Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold684
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10179
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.26
Warning! 1375 characters in sequence are not A, C, G, or T
Found at i:237 original size:21 final size:20
Alignment explanation
Indices: 209--250 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
199 GAAAAATCTG
* *
209 TGATGAAATTCAAATAGTTT
1 TGATGAAACTCAAATACTTT
229 TGATAGAAACTCAAATACTTT
1 TGAT-GAAACTCAAATACTTT
250 T
1 T
251 CCTTTTCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (20 bp):
TGATGAAACTCAAATACTTT
Found at i:4992 original size:138 final size:138
Alignment explanation
Indices: 4744--5020 Score: 545
Period size: 138 Copynumber: 2.0 Consensus size: 138
4734 CGCTCCACGA
4744 TGGCCGCCTTGATTTTCGTAAACACCGAGTAGAGATGGATATTGTGCTTTTTCATGAGAGCCATG
1 TGGCCGCCTTGATTTTCGTAAACACCGAGTAGAGATGGATATTGTGCTTTTTCATGAGAGCCATG
4809 AAATTCTTGTTGTAAAATTCCGAGCCGTTGTCAACTTGGAACAGTCTCGGTGGACTCGTCGTCTT
66 AAATTCTTGTTGTAAAATTCCGAGCCGTTGTCAACTTGGAACAGTCTCGGTGGACTCGTCGTCTT
4874 CAGGACGG
131 CAGGACGG
4882 TGGCCGCCTTGATTTTCGTAAACACCGAGTAGAGATGGATATTGTGCTTTTTCATGAGAGCCATG
1 TGGCCGCCTTGATTTTCGTAAACACCGAGTAGAGATGGATATTGTGCTTTTTCATGAGAGCCATG
4947 AAATTCTTGTTGTAAAATTCCGAGCCGTTGTCAACTTGGAACAGTCTCGGTGGACTCGTCGTCTT
66 AAATTCTTGTTGTAAAATTCCGAGCCGTTGTCAACTTGGAACAGTCTCGGTGGACTCGTCGTCTT
*
5012 CAGTACGG
131 CAGGACGG
5020 T
1 T
5021 TTCCATCGCT
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 138 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (138 bp):
TGGCCGCCTTGATTTTCGTAAACACCGAGTAGAGATGGATATTGTGCTTTTTCATGAGAGCCATG
AAATTCTTGTTGTAAAATTCCGAGCCGTTGTCAACTTGGAACAGTCTCGGTGGACTCGTCGTCTT
CAGGACGG
Found at i:10055 original size:192 final size:192
Alignment explanation
Indices: 9728--10179 Score: 895
Period size: 192 Copynumber: 2.4 Consensus size: 192
9718 TAACCCCGAT
9728 TTTTACAACACTGGTAACGATAGGTAGGCAACAGTCGCTAGTGACGACACATCATGGTTGTAAAA
1 TTTTACAACACTGGTAACGATAGGTAGGCAACAGTCGCTAGTGACGACACATCATGGTTGTAAAA
9793 TCATGCACCATACCCCAGCCCTCATCCTAAAAAAAATTCAGATTTTTCCGCACAATTTTACAACA
66 TCATGCACCATACCCCAGCCCTCATCCTAAAAAAAATTCAGATTTTTCCGCACAATTTTACAACA
9858 CCTCGTAACATGATAACATTGTTGCCAGATTATCGCGGAATAATTCGGATTTTCCTGCACAA
131 CCTCGTAACATGATAACATTGTTGCCAGATTATCGCGGAATAATTCGGATTTTCCTGCACAA
*
9920 TTTTACACCACTGGTAACGATAGGTAGGCAACAGTCGCTAGTGACGACACATCATGGTTGTAAAA
1 TTTTACAACACTGGTAACGATAGGTAGGCAACAGTCGCTAGTGACGACACATCATGGTTGTAAAA
9985 TCATGCACCATACCCCAGCCCTCATCCTAAAAAAAATTCAGATTTTTCCGCACAATTTTACAACA
66 TCATGCACCATACCCCAGCCCTCATCCTAAAAAAAATTCAGATTTTTCCGCACAATTTTACAACA
10050 CCTCGTAACATGATAACATTGTTGCCAGATTATCGCGGAATAATTCGGATTTTCCTGCACAA
131 CCTCGTAACATGATAACATTGTTGCCAGATTATCGCGGAATAATTCGGATTTTCCTGCACAA
10112 TTTTACAACACTGGTAACGATAGGTAGGCAACAGTCGCTAGTGACGACACATCATGGTTGTAAAA
1 TTTTACAACACTGGTAACGATAGGTAGGCAACAGTCGCTAGTGACGACACATCATGGTTGTAAAA
10177 TCA
66 TCA
Statistics
Matches: 258, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
192 258 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (192 bp):
TTTTACAACACTGGTAACGATAGGTAGGCAACAGTCGCTAGTGACGACACATCATGGTTGTAAAA
TCATGCACCATACCCCAGCCCTCATCCTAAAAAAAATTCAGATTTTTCCGCACAATTTTACAACA
CCTCGTAACATGATAACATTGTTGCCAGATTATCGCGGAATAATTCGGATTTTCCTGCACAA
Done.