Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold742
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: 30497
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:2528 original size:47 final size:47
Alignment explanation
Indices: 2466--2995 Score: 876
Period size: 47 Copynumber: 11.4 Consensus size: 47
2456 TTCAGCCAAG
2466 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
* *
2513 AAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
2560 AAGTG--TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
2605 AAGTG--TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
* *
2649 AAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
2696 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
2743 AAGTG--TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
*
2788 AAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
*
2835 AAGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
2882 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
* * * * * * *
2929 AAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
* *
2976 AAGTGCATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
2996 TCCCGAAGGG
Statistics
Matches: 455, Mismatches: 23, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
44 5 0.01
45 127 0.28
46 37 0.08
47 286 0.63
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
Found at i:2596 original size:22 final size:22
Alignment explanation
Indices: 2568--2641 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
2558 GAAAGTGTAT
2568 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
* * ***
2590 ATGTGATGAATG--TGAAAGTGTAT
1 ATGTGAT-AAGGCCT-AATG-GCCG
2613 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
2635 ATGTGAT
1 ATGTGAT
2642 GAATGTGAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
21 1 0.03
22 21 0.57
23 14 0.38
24 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.31, T:0.28
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCG
Found at i:2734 original size:22 final size:22
Alignment explanation
Indices: 2706--2779 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
2696 AAGTGTATAT
2706 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
* * ***
2728 ATGTGATGAATG--TGAAAGTGTAT
1 ATGTGAT-AAGGCCT-AATG-GCCG
2751 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
2773 ATGTGAT
1 ATGTGAT
2780 GAATGTGAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
21 1 0.03
22 21 0.57
23 14 0.38
24 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.31, T:0.28
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCG
Found at i:3169 original size:37 final size:37
Alignment explanation
Indices: 3113--3191 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
3103 CCGAGCTCTA
* *
3113 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
3150 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
3187 AAGAC
1 AAGAC
3192 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:5100 original size:43 final size:43
Alignment explanation
Indices: 5052--5154 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
5042 TTGGTTTTCA
5052 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
5095 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
5138 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
5155 TTGAAATGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:5171 original size:29 final size:29
Alignment explanation
Indices: 5136--5209 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
5126 GTTGTGAGAT
* *
5136 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
5165 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
5194 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
5210 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:5643 original size:40 final size:40
Alignment explanation
Indices: 5599--5808 Score: 267
Period size: 40 Copynumber: 5.2 Consensus size: 40
5589 GAGTTACTAA
*
5599 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
5639 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * *
5679 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* ** * * * *
5719 ATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * * *
5759 GTCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGACGTGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA--TGT
5801 ATCCGGGC
1 ATCCGGGC
5809 CTTCGTGCCT
Statistics
Matches: 148, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
40 139 0.94
42 9 0.06
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
Found at i:5657 original size:80 final size:80
Alignment explanation
Indices: 5558--5808 Score: 258
Period size: 80 Copynumber: 3.1 Consensus size: 80
5548 TAAGTGACCA
* * *
5558 TATCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGAG
1 TATCCGGGCTAAG-TCCCGAAGAGCATTCGTGCGAGTTA-TATATCCGGGCTAAGTCCCGAAGAG
*
5621 CATTCATGCTAGCGATG
64 CATTCATGCTAGTGATG
* * * * *
5638 TATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCGAGTTATATATCCGGGCTAAGTCCCGAAGAGCA
* *
5703 TTCGTGCTAGTGATA
66 TTCATGCTAGTGATG
* ** * *
5718 TATCCGTGCTAAACCCCGAAGAGCATTCGTGCTG-GTGT-TATGTCCGGGCTAGGTCCCGAAGAG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGC-GAGT-TATATATCCGGGCTAAGTCCCGAAGAG
* *
5781 CAATCATGCTGGTGACGTG
64 CATTCATGCTAGTGA--TG
5800 TATCCGGGC
1 TATCCGGGC
5809 CTTCGTGCCT
Statistics
Matches: 139, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
79 1 0.01
80 117 0.84
81 12 0.09
82 9 0.06
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (80 bp):
TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCGAGTTATATATCCGGGCTAAGTCCCGAAGAGCA
TTCATGCTAGTGATG
Found at i:5736 original size:120 final size:121
Alignment explanation
Indices: 5558--5808 Score: 308
Period size: 120 Copynumber: 2.1 Consensus size: 121
5548 TAAGTGACCA
* * * **
5558 TATCCGGACTAAGATCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGAGCA
1 TATCCGGGCTAAGATCCGAAGGCATTCGTGCGAGTGACTAAATCCGGGCTAAACCCCGAAGAGCA
* *
5623 TTCATGCTAGCGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TG
66 TTCATGCTAGCGATATATCCGGGCTAAGTCCCGAAGAGCAATCATGCTAGTGACTG
* * * *
5678 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGA-TATATCCGTGCTAAACCCCGAAGAGC
1 TATCCGGGCTAAGATCCGAAG-GCATTCGTGCGAGTGACTAAATCCGGGCTAAACCCCGAAGAGC
* * * * * * *
5742 ATTCGTGCTGGTGTTATGTCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGACGTG
65 ATTCATGCTAGCGATATATCCGGGCTAAGTCCCGAAGAGCAATCATGCTAGTGAC-TG
5800 TATCCGGGC
1 TATCCGGGC
5809 CTTCGTGCCT
Statistics
Matches: 110, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
120 86 0.78
121 13 0.12
122 11 0.10
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (121 bp):
TATCCGGGCTAAGATCCGAAGGCATTCGTGCGAGTGACTAAATCCGGGCTAAACCCCGAAGAGCA
TTCATGCTAGCGATATATCCGGGCTAAGTCCCGAAGAGCAATCATGCTAGTGACTG
Found at i:8522 original size:47 final size:47
Alignment explanation
Indices: 8464--9047 Score: 974
Period size: 47 Copynumber: 12.5 Consensus size: 47
8454 ATTCAGCCAA
8464 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* *
8511 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
8558 GAAAGTG--TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* *
8603 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* *
8650 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
8697 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
8744 GAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* *
8791 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
8838 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
8885 GAAAGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
8932 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* * * * * * *
8979 GAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* *
9026 GAAAGTGCATAAATGTGATAAG
1 GAAAGTGTATATATGTGATAAG
9048 TCCCGAAGGG
Statistics
Matches: 508, Mismatches: 27, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
45 43 0.08
47 465 0.92
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
Found at i:9222 original size:37 final size:37
Alignment explanation
Indices: 9166--9244 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
9156 CCGAGCTCTA
* *
9166 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
9203 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
9240 AAGAC
1 AAGAC
9245 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:12974 original size:26 final size:26
Alignment explanation
Indices: 12938--12990 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
12928 TTTCTTCGAA
* *
12938 CCACCTTAGTACCTTAGTTAGATTGG
1 CCACCTTAGTACCATAGCTAGATTGG
12964 CCACCTTAGTACCATAGCTAGATTGG
1 CCACCTTAGTACCATAGCTAGATTGG
12990 C
1 C
12991 TAAGCAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (26 bp):
CCACCTTAGTACCATAGCTAGATTGG
Found at i:22830 original size:39 final size:40
Alignment explanation
Indices: 22753--22899 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
22743 TAGCTCCTCG
* * *
22753 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
22793 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
22832 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
22872 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
22900 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:22910 original size:80 final size:80
Alignment explanation
Indices: 22799--22979 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
22789 CTCATTCAAT
* * *
22799 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
22862 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
22878 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
22942 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
22959 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
22980 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:22939 original size:40 final size:40
Alignment explanation
Indices: 22796--22979 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
22786 TAACTCATTC
* *
22796 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
22836 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
22876 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
22916 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
22957 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
22980 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Done.