**Composition Alignment Tool**

**Function 1**: The simplest function, a constant times the length of the match.

**Function 2**: Square root of length of extended match times a constant.

**Function 3**: Log base 2 of length+1 of extended match times a constant.

**Function 4**: Relative entropy of substring composition with respect to background composition times length of extended match times a constant.

**Function 5**: Relative entropy of substring composition with respect to background composition times length of extended match times a constant. For length =1, normal match value prevents two identical sequences composed of only one letter from scoring zero if the background is the same letter.

**Function 6**: Shannon-Jensen entropy of substring composition versus the background composition times length of extended match times a constant.