Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1137
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: 2624
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Found at i:817 original size:105 final size:107
Alignment explanation
Indices: 673--933 Score: 357
Period size: 105 Copynumber: 2.4 Consensus size: 107
663 AAAATATTAT
*
673 TTCATTTTGAACAAAATGACGTCGTTTTGCTATGCACAAAATTTTTTATTTTGTTTTTTA-AAAT
1 TTCATTTTGAACAAAATGACGCCGTTTTGCTATGCACAAAATTTTTTATTTTGTTTTTTATAAAT
* ***
737 TGATTTA-TTTTTTGCAGCGTTTTTAGGGAAAACGCCGCAAC
66 TGATTTACTTTTTTGCAGCGTTTTAAACAAAAACGCCGCAAC
*
778 TTCAATTTGAACAAAATGACGCCGTTTTGCTATGCACAAAATTTTTTATTTTGTTTTTTATAAAT
1 TTCATTTTGAACAAAATGACGCCGTTTTGCTATGCACAAAATTTTTTATTTTGTTTTTTATAAAT
* * *
843 TGATTTACTTTTTTGCGGCGTTTTAAACAAAAACGCCGCTAT
66 TGATTTACTTTTTTGCAGCGTTTTAAACAAAAACGCCGCAAC
* * * * *
885 TTCATTTTGAAGAAAAACGGCGCCGTTTTTCTATACA-AATAATTTTTTA
1 TTCATTTTGAA-CAAAATGACGCCGTTTTGCTATGCACAA-AATTTTTTA
934 AATTTATTTA
Statistics
Matches: 137, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
105 58 0.42
106 11 0.08
107 39 0.28
108 29 0.21
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (107 bp):
TTCATTTTGAACAAAATGACGCCGTTTTGCTATGCACAAAATTTTTTATTTTGTTTTTTATAAAT
TGATTTACTTTTTTGCAGCGTTTTAAACAAAAACGCCGCAAC
Found at i:1134 original size:137 final size:137
Alignment explanation
Indices: 932--1191 Score: 366
Period size: 137 Copynumber: 1.9 Consensus size: 137
922 AATAATTTTT
*
932 TAAATTTATTTATTTTCTCTGCGACGTATTATAAAAAAAGCCGCTATTGCTTATATTTTGCGGCG
1 TAAATTGATTTATTTTCTCTGCGACGTATTATAAAAAAAGCCGCTATTGCTTATATTTTGCGGCG
*
997 TTTTTG-TGAAAAATGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATTT
66 -TTTTGAT-AAAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATTT
1061 TGTTTTCTA
129 TGTTTTCTA
* * * * * *
1070 TAAATTGATTTATTTT-T-TGCGGCGTTTTTATAGAAAACGTCGCTATTTG-TTATCTTTTGCGG
1 TAAATTGATTTATTTTCTCTGCGACG-TATTATAAAAAAAGCCGCTA-TTGCTTATATTTTGCGG
*
1132 CGTTTTGCATAAAAACGCTGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTG
64 CGTTTTG-ATAAAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTG
1192 TTATGCTAAT
Statistics
Matches: 109, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
136 11 0.10
137 79 0.72
138 19 0.17
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (137 bp):
TAAATTGATTTATTTTCTCTGCGACGTATTATAAAAAAAGCCGCTATTGCTTATATTTTGCGGCG
TTTTGATAAAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATTTTG
TTTTCTA
Found at i:1687 original size:14 final size:14
Alignment explanation
Indices: 1670--1696 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1660 AACCCTTAAA
1670 CCATAATCCCTAAT
1 CCATAATCCCTAAT
1684 CCATAATCCCTAA
1 CCATAATCCCTAA
1697 ACCCATACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:2085 original size:115 final size:116
Alignment explanation
Indices: 1793--2237 Score: 562
Period size: 114 Copynumber: 3.9 Consensus size: 116
1783 TGTTTTTTTA
** * *
1793 CGGCGCTTTCCTAAAAAACG-CCGCTAAATCCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTT
1 CGGCGCTTTCCTAAAAAACGACTACTAAAT-CCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTT
* * *
1857 ATGTCT-TTTTGCGGCGCTTTCTCACAAACGCCGCTAAAGCACTGAGCATTAG
65 A-GTTTATTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
* * * * * *
1909 CGGC-ATATCCTAAAAAACGAC-ACTAAATTCACAAAAGCTAAGAAAACGGCGTCGTTGGGCTTA
1 CGGCGCTTTCCTAAAAAACGACTACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* * *
1972 GTTTATTTTGCGGCGCTTCCTCAAAAACGGCGCTAAAGCCCTCAGCATTAG
66 GTTTATTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
** * *
2023 CGGCGCTTTATTAAGAAACG-CTACTAAATCCGCGAAAGCTCAGAAAGCGGCGTCGTTGGGCTTA
1 CGGCGCTTTCCTAAAAAACGACTACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* * *
2087 GTTTATTTTGCGGCGCTTTATCAAAAATGCCGCAAAAGCCCTGAGCATTAG
66 GTTTATTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
* *
2138 CAGCGC-TTCCTAAAAAACGCCT-CTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
1 CGGCGCTTTCCTAAAAAACGACTACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* * * *
2201 GATTATTTTGCGGCGCTTTATCAAAAGCACCGCTAAA
66 GTTTATTTTGCGGCGCTTTCTCAAAAACGCCGCTAAA
2238 TCCCCGAAAG
Statistics
Matches: 286, Mismatches: 38, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
113 3 0.01
114 160 0.56
115 118 0.41
116 5 0.02
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.24
Consensus pattern (116 bp):
CGGCGCTTTCCTAAAAAACGACTACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
GTTTATTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
Found at i:2259 original size:73 final size:73
Alignment explanation
Indices: 2150--2310 Score: 225
Period size: 73 Copynumber: 2.2 Consensus size: 73
2140 GCGCTTCCTA
* * * * *
2150 AAAAACGCCTCTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA-GATTATTTTGCGG
1 AAAAACACCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGGCTTATG-TCATTTTGCGG
2214 CGCTTTATC
65 CGCTTTATC
* *
2223 AAAAGCACCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGGCTTATGTCCTTTTGCGGC
1 AAAAACACCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGGCTTATGTCATTTTGCGGC
*
2288 GCTTTCTC
66 GCTTTATC
*
2296 AAAAACGCCGCTAAA
1 AAAAACACCGCTAAA
2311 AGCCCTGAGC
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
73 76 0.99
74 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (73 bp):
AAAAACACCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGGCTTATGTCATTTTGCGGC
GCTTTATC
Found at i:2362 original size:188 final size:185
Alignment explanation
Indices: 2046--2405 Score: 551
Period size: 188 Copynumber: 1.9 Consensus size: 185
2036 AGAAACGCTA
* * * *
2046 CTAAATCCGCGAAAGCTCAGAAAGCGGCGTCGTTGGGCTTAGTTTATTTTGCGGCGCTTTATCAA
1 CTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGGCTTAGTTCATTTTGCGGCGCTTTATCAA
* * *
2111 AAATGCCGCAAAAGCCCTGAGCATTAGCAGCGCTTCCTAAAAAACGCCTCTAAATCCGCGAAAGC
66 AAACGCCGCAAAAGCCCTGAGCATTAGCAGCGCTTACTAAAAAACGCCACTAAATCCGCGAAAGC
* *
2176 TCAGAAAACGGCGTCGTTGGGCTTAGATTATTTTGCGGCGCTTTATCAAAAGCACCG
131 GCAGAAAACGACGTCGTTGGGCTTAG-TT-TTTTGCGGCGCTTTATCAAAAGCACCG
* *
2233 CTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGGCTTA-TGTCCTTTTGCGGCGCTTTCTCA
1 CTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGGCTTAGT-TCATTTTGCGGCGCTTTATCA
* *
2297 AAAACGCCGCTAAAAGCCCTGAGCATTAGCGGCGCTTACTAAAAAACGCCACTAAATCTGCGAAA
65 AAAACGCCGC-AAAAGCCCTGAGCATTAGCAGCGCTTACTAAAAAACGCCACTAAATCCGCGAAA
*
2362 GCGCAGAAAACGACGTCGTTTGGCTTAGTTTTTTGCGGCGCTTT
129 GCGCAGAAAACGACGTCGTTGGGCTTAGTTTTTTGCGGCGCTTT
2406 TTAAAAAACG
Statistics
Matches: 157, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
186 15 0.10
187 67 0.43
188 75 0.48
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (185 bp):
CTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGGCTTAGTTCATTTTGCGGCGCTTTATCAA
AAACGCCGCAAAAGCCCTGAGCATTAGCAGCGCTTACTAAAAAACGCCACTAAATCCGCGAAAGC
GCAGAAAACGACGTCGTTGGGCTTAGTTTTTTGCGGCGCTTTATCAAAAGCACCG
Done.