Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2156
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: 47204
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:8618 original size:27 final size:28
Alignment explanation
Indices: 8534--8631 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
8524 CATGAGATTG
* * * *
8534 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
8563 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
8591 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
8618 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
8632 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:8642 original size:27 final size:27
Alignment explanation
Indices: 8562--8644 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
8552 TAAATTGTAC
* *
8562 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
8590 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
8617 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
8644 A
1 A
8645 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:8645 original size:29 final size:27
Alignment explanation
Indices: 8534--8645 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
8524 CATGAGATTG
** * *
8534 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
8563 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
8591 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
8618 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
8646 TTTGAATCAC
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:23134 original size:21 final size:22
Alignment explanation
Indices: 23110--23152 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
23100 GACAATTTTA
23110 AGATAGTTAAGAGA-AAGTGAT
1 AGATAGTTAAGAGAGAAGTGAT
23131 AGATAGTTAAGAGAGAAGTGAT
1 AGATAGTTAAGAGAGAAGTGAT
23153 GGCTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (22 bp):
AGATAGTTAAGAGAGAAGTGAT
Found at i:27641 original size:27 final size:26
Alignment explanation
Indices: 27585--27641 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
27575 CAACCTTAAC
* * *
27585 CCTAGGGGTATATCAATAATTTTGCT
1 CCTAGGGGTAAATCAATAATTTTCCA
**
27611 CCTAGGGGTAAATCTGTAAATTTTCCA
1 CCTAGGGGTAAATCAAT-AATTTTCCA
27638 CCTA
1 CCTA
27642 TAAAGGTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (26 bp):
CCTAGGGGTAAATCAATAATTTTCCA
Found at i:33368 original size:42 final size:42
Alignment explanation
Indices: 33221--33368 Score: 124
Period size: 42 Copynumber: 3.5 Consensus size: 42
33211 CCTGATTTCA
*
33221 TCACCGGCAATAAGCCTGCTAGACCTTTAAGTCCGATATCATT
1 TCACCGGCATTAAGCCTGCTAGACCTTTAAGT-CGATATCATT
* * * *** *
33264 TCACTGGCATTACGCCTGCTAG-GCTCGGAGCCCGATA--ATAT
1 TCACCGGCATTAAGCCTGCTAGACCTTTAAG-TCGATATCAT-T
* * *
33305 TCATCAGC-TTAAAGCTTGCTAGACCTTTAAGTCGATATCATT
1 TCACCGGCATT-AAGCCTGCTAGACCTTTAAGTCGATATCATT
*
33347 TCACCGGCATTACGCCTGCTAG
1 TCACCGGCATTAAGCCTGCTAG
33369 GCTCAAAGCC
Statistics
Matches: 76, Mismatches: 22, Indels: 15
0.67 0.19 0.13
Matches are distributed among these distances:
40 4 0.05
41 20 0.26
42 29 0.38
43 23 0.30
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (42 bp):
TCACCGGCATTAAGCCTGCTAGACCTTTAAGTCGATATCATT
Found at i:33408 original size:83 final size:85
Alignment explanation
Indices: 33217--33409 Score: 254
Period size: 83 Copynumber: 2.3 Consensus size: 85
33207 ATAACCTGAT
*
33217 TTCATCACCGGCAATAAGCCTGCTAGACCTTTAAGTCCGATATCATTTCACTGGCATTACGCCTG
1 TTCATCACCGGCAA-AAGCCTGCTAGACCTTTAAGTCCGATATCATTTCACCGGCATTACGCCTG
**
33282 CTAGGCTCGGAGCCCGATAATA
65 CTAGGCTCAAAGCCCGA-AATA
* *
33304 TTCATCA---GCTTAAAGCTTGCTAGACCTTTAAGT-CGATATCATTTCACCGGCATTACGCCTG
1 TTCATCACCGGC-AAAAGCCTGCTAGACCTTTAAGTCCGATATCATTTCACCGGCATTACGCCTG
33365 CTAGGCTCAAAGCCCG-AA-A
65 CTAGGCTCAAAGCCCGAAATA
*
33384 TTCATCACCGGCACAAGGCCTGCTAG
1 TTCATCACCGGCA-AAAGCCTGCTAG
33410 GTTTGAAACC
Statistics
Matches: 93, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
80 8 0.09
81 2 0.02
83 53 0.57
84 22 0.24
85 1 0.01
87 7 0.08
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (85 bp):
TTCATCACCGGCAAAAGCCTGCTAGACCTTTAAGTCCGATATCATTTCACCGGCATTACGCCTGC
TAGGCTCAAAGCCCGAAATA
Found at i:35718 original size:40 final size:40
Alignment explanation
Indices: 35673--35938 Score: 324
Period size: 40 Copynumber: 6.7 Consensus size: 40
35663 GCTCCTCGTT
* * *
35673 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAAT-TAGTAACTCGCA
* *
35713 GAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
*
35753 CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
* *
35793 CAAATGCCTTCAGGACTTAACCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
*
35833 CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
* ** * * *
35873 CAAAGGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAAT-TAGTAAC-TCGCA
*
35914 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
35939 CATCATTCAA
Statistics
Matches: 204, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
39 5 0.02
40 186 0.91
41 13 0.06
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
Found at i:43736 original size:39 final size:40
Alignment explanation
Indices: 43615--43814 Score: 220
Period size: 39 Copynumber: 5.1 Consensus size: 40
43605 GCTCCTCATT
* * * *
43615 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCGCA
* *
43654 C--ATGCCTTCGGGAC-TAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCA
*
43691 CAAAATGCC-TCGGGACTTAACCCGGGATTAGTATCTCGCA
1 C-AAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCA
*
43731 CAAATGCCTTC-GGCCTTAACCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCA
43770 CAAA-GCC-TCGGGACTTAACGCCGGAATTAAGTATCTTCGCA
1 CAAATGCCTTCGGGACTTAAC-CCGGAATT-AGTATC-TCGCA
43811 CAAA
1 CAAA
43815 GGCTTCGATC
Statistics
Matches: 143, Mismatches: 7, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
37 30 0.21
38 17 0.12
39 53 0.37
40 34 0.24
41 9 0.06
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCA
Found at i:43821 original size:79 final size:79
Alignment explanation
Indices: 43642--43814 Score: 230
Period size: 79 Copynumber: 2.2 Consensus size: 79
43632 AGCCCGGTTA
* * *
43642 TAGTAACTCGCAC--ATGCCTTCGGGAC-TAACCCGGATTTAGTAACTCGCACAAAATGCCTCGG
1 TAGTATCTCGCACAAATGCCTTC-GGCCTTAACCCGGAATTAGTAACTCGCACAAAATGCCTCGG
*
43704 GACTTAACCCGGGAT
65 GACTTAACCCGGAAT
*
43719 TAGTATCTCGCACAAATGCCTTCGGCCTTAACCCGGAATTAGTATCTCGCAC-AAA-GCCTCGGG
1 TAGTATCTCGCACAAATGCCTTCGGCCTTAACCCGGAATTAGTAACTCGCACAAAATGCCTCGGG
43782 ACTTAACGCCGGAAT
66 ACTTAAC-CCGGAAT
43797 TAAGTATCTTCGCACAAA
1 T-AGTATC-TCGCACAAA
43815 GGCTTCGATC
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
77 27 0.32
78 13 0.15
79 36 0.42
80 9 0.11
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (79 bp):
TAGTATCTCGCACAAATGCCTTCGGCCTTAACCCGGAATTAGTAACTCGCACAAAATGCCTCGGG
ACTTAACCCGGAAT
Found at i:43854 original size:78 final size:77
Alignment explanation
Indices: 43668--43873 Score: 204
Period size: 79 Copynumber: 2.6 Consensus size: 77
43658 CCTTCGGGAC
* * * *
43668 TAACCCGGATTTAGTAACTCGCACAAAATGCCTCGGGACTTAACCCGGGATTAGTATCTCGCACA
1 TAACCCGGAATTAGTATCTAGCAC-AAA-GCCTCGGGACTTAACCCGGAATTAGTATCTCGCACA
*
43733 AATGCCTTCGGCCT
64 AATGCCTTCGACCT
*
43747 TAACCCGGAATTAGTATCTCGCACAAAGCCTCGGGACTTAACGCCGGAATTAAGTATCTTCGCAC
1 TAACCCGGAATTAGTATCTAGCACAAAGCCTCGGGACTTAAC-CCGGAATT-AGTATC-TCGCAC
* *
43812 AAA-GGCTTCGATCT
63 AAATGCCTTCGACCT
* * *
43826 T-ATCCGG-ATATGGTCA-CTAGCACAAAGCCCTTCGGGACTTAGCCCGGA
1 TAACCCGGAAT-TAGT-ATCTAGCACAAAG-CC-TCGGGACTTAACCCGGA
43874 CATCCTTCAA
Statistics
Matches: 110, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
77 17 0.15
78 28 0.25
79 45 0.41
80 20 0.18
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (77 bp):
TAACCCGGAATTAGTATCTAGCACAAAGCCTCGGGACTTAACCCGGAATTAGTATCTCGCACAAA
TGCCTTCGACCT
Done.