Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1240
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: 18795
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Found at i:7174 original size:27 final size:27
Alignment explanation
Indices: 7143--7196 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
7133 TGACGTCAGG
7143 TGCAT-CACCCACCTCTCGGC-GACGAGC
1 TGCATACA-CCACCTCT-GGCTGACGAGC
*
7170 TGCATACACCAGCTCTGGCTGACGAGC
1 TGCATACACCACCTCTGGCTGACGAGC
7197 CTCAGTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 3 0.12
27 19 0.79
28 2 0.08
ACGTcount: A:0.20, C:0.39, G:0.24, T:0.17
Consensus pattern (27 bp):
TGCATACACCACCTCTGGCTGACGAGC
Found at i:9589 original size:27 final size:26
Alignment explanation
Indices: 9541--9600 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
9531 GCGAAGCTGC
*
9541 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
9568 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
9594 CAGATAT
1 CAGATAT
9601 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:16935 original size:27 final size:26
Alignment explanation
Indices: 16887--16946 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
16877 AGCAGGCTGC
*
16887 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
16914 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
16940 CATATAT
1 CAGATAT
16947 ATATGTGGCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:17004 original size:68 final size:66
Alignment explanation
Indices: 16914--17049 Score: 193
Period size: 66 Copynumber: 2.0 Consensus size: 66
16904 TCACCAGATA
* * * *
16914 CAGATATTGTGGCTAGGCCACCAGAACATATATATATGTGGCGAAG-CACCAGATTGCAGCGAGG
1 CAGATATTGTGACGAAGCCACCAGAAC--AGATATATGTGGCG-AGCCACCAGATTGCAGCGAGG
16978 CTGC
63 CTGC
*
16982 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGCCACCAGATTGCAGCGAGGCTG
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAGCCACCAGATTGCAGCGAGGCTG
17047 C
66 C
17048 CA
1 CA
17050 AACGCTTCCT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
65 2 0.03
66 37 0.60
68 23 0.37
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (66 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAGCCACCAGATTGCAGCGAGGCTG
C
Found at i:17029 original size:26 final size:26
Alignment explanation
Indices: 16982--17032 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
16972 GCGAGGCTGC
*
16982 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
17008 CAGATATATGTGGCG-AGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
17033 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:18115 original size:29 final size:26
Alignment explanation
Indices: 18054--18121 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 26
18044 TTAGGTTACC
* *
18054 AAATTACTAAAAAACCCCCAGTTGTA
1 AAATTACCAAAAAACCCCCAGTTATA
*
18080 AAGATTACCAAAAAGTACCCCCGATTTATA
1 AA-ATTACCAAAAA--ACCCCC-AGTTATA
18110 AAATTACCAAAA
1 AAATTACCAAAA
18122 TCCTCATTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 2 0.06
27 10 0.29
29 16 0.46
30 7 0.20
ACGTcount: A:0.49, C:0.22, G:0.07, T:0.22
Consensus pattern (26 bp):
AAATTACCAAAAAACCCCCAGTTATA
Found at i:18284 original size:25 final size:26
Alignment explanation
Indices: 18211--18308 Score: 144
Period size: 25 Copynumber: 3.7 Consensus size: 26
18201 TGTAAGATAG
18211 GAATTACCATTCTTACCCTCGATTTACA
1 GAATTACCATT-TTACCCTC-ATTTACA
* * *
18239 GAATTATCATTTTACCTTCATTTATA
1 GAATTACCATTTTACCCTCATTTACA
18265 GAATTACCA-TTTACCCTCATTTACA
1 GAATTACCATTTTACCCTCATTTACA
18290 GAATTACCATTTTACCCTC
1 GAATTACCATTTTACCCTC
18309 GGTTTTTTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
25 23 0.37
26 23 0.37
27 7 0.11
28 10 0.16
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.40
Consensus pattern (26 bp):
GAATTACCATTTTACCCTCATTTACA
Found at i:18469 original size:28 final size:29
Alignment explanation
Indices: 18425--18493 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
18415 CCTATTTTGT
18425 GAATTACCAAAATTACCATTTGTA-GGTA
1 GAATTACCAAAATTACCATTTGTAGGGTA
* *
18453 GAATTACTGAAAA-TACCCTTTGTAGGGTA
1 GAATTAC-CAAAATTACCATTTGTAGGGTA
18482 GAA-TACCAAAAT
1 GAATTACCAAAAT
18494 ACCCCTATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 4 0.11
28 20 0.57
29 11 0.31
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (29 bp):
GAATTACCAAAATTACCATTTGTAGGGTA
Found at i:18499 original size:28 final size:27
Alignment explanation
Indices: 18372--18563 Score: 103
Period size: 27 Copynumber: 7.1 Consensus size: 27
18362 CGATCAATAA
* * ** *
18372 AATTACCAAAAATACCCCTGGTTTGTAA
1 AATTACC-AAAATACCCTTTGTAGGTAG
*
18400 AATTACCAAAATACCCCTATT-T-TGT-G
1 AATTACCAAAATA-CCCT-TTGTAGGTAG
*
18426 AATTACCAAAATTACCATTTGTAGGTAG
1 AATTACCAAAA-TACCCTTTGTAGGTAG
*
18454 AATTACTGAAAATACCCTTTGTAGGGTAG
1 AATTAC-CAAAATACCCTTTGTA-GGTAG
* *
18483 AA-TACCAAAATACCC-CTATAGGGTTAG
1 AATTACCAAAATACCCTTTGTA-GG-TAG
** *
18510 AATTACC-GGATACCCTGTGT-GGTAGG
1 AATTACCAAAATACCCTTTGTAGGTA-G
** *
18536 AATTACCGGAATACCC-CTGTAGGTAG
1 AATTACCAAAATACCCTTTGTAGGTAG
18562 AA
1 AA
18564 CTTATCGGAA
Statistics
Matches: 134, Mismatches: 16, Indels: 30
0.74 0.09 0.17
Matches are distributed among these distances:
25 4 0.03
26 37 0.28
27 44 0.33
28 37 0.28
29 12 0.09
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCTTTGTAGGTAG
Found at i:18525 original size:26 final size:27
Alignment explanation
Indices: 18445--18722 Score: 241
Period size: 26 Copynumber: 10.6 Consensus size: 27
18435 AATTACCATT
* * *
18445 TGTA-GGTAGAATTACTGAAAATACCCTT
1 TGTAGGGTAGAATTACCG-GAATACCC-C
**
18473 TGTAGGGTAGAA-TACCAAAATACCCC
1 TGTAGGGTAGAATTACCGGAATACCCC
*
18499 TATAGGGTTAGAATTACCGG-ATA-CCC
1 TGTAGGG-TAGAATTACCGGAATACCCC
18525 TGT-GTGGTAGGAATTACCGGAATACCCC
1 TGTAG-GGTA-GAATTACCGGAATACCCC
*
18553 TGTA-GGTAGAACTTATCGGAATA-CCC
1 TGTAGGGTAGAA-TTACCGGAATACCCC
*
18579 TGTAGGGTTAGAA-TCCCGGAATACCCC
1 TGTAGGG-TAGAATTACCGGAATACCCC
18606 TGT-GGGATAGAATTA-CGGAATACCCC
1 TGTAGGG-TAGAATTACCGGAATACCCC
18632 TGT-GGGTAGAATTACC-GAATACCCC
1 TGTAGGGTAGAATTACCGGAATACCCC
* *
18657 TGTAGGGTA-AA-TACTGAAATACCCC
1 TGTAGGGTAGAATTACCGGAATACCCC
*
18682 TGTAGGTTAGAATTACC-GAGATA-CCC
1 TGTAGGGTAGAATTACCGGA-ATACCCC
*
18708 T-T-GGGTAAAATTACC
1 TGTAGGGTAGAATTACC
18723 ATTTTACCAT
Statistics
Matches: 212, Mismatches: 19, Indels: 42
0.78 0.07 0.15
Matches are distributed among these distances:
24 14 0.07
25 42 0.20
26 79 0.37
27 48 0.23
28 22 0.10
29 7 0.03
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (27 bp):
TGTAGGGTAGAATTACCGGAATACCCC
Found at i:18693 original size:51 final size:54
Alignment explanation
Indices: 18445--18707 Score: 225
Period size: 53 Copynumber: 5.0 Consensus size: 54
18435 AATTACCATT
* * * **
18445 TGTA-GGTAGAATTACTGAAAATACCCTTTGTAGGGTAGAA-TACCAAAATACCCC
1 TGTAGGGTAGAATTACTG-GAATACCC-CTGTAGGTTAGAATTACCGGAATACCCC
* * *
18499 TATAGGGTTAGAATTACCGG-ATA-CCCTGT-GTGGTAGGAATTACCGGAATACCCC
1 TGTAGGG-TAGAATTACTGGAATACCCCTGTAG-GTTA-GAATTACCGGAATACCCC
*
18553 TGTA-GGTAGAACTTA-TCGGAATA-CCCTGTAGGGTTAGAA-TCCCGGAATACCCC
1 TGTAGGGTAGAA-TTACT-GGAATACCCCTGTA-GGTTAGAATTACCGGAATACCCC
*
18606 TGT-GGGATAGAATTAC-GGAATACCCCTGT-GGGTAGAATTACC-GAATACCCC
1 TGTAGGG-TAGAATTACTGGAATACCCCTGTAGGTTAGAATTACCGGAATACCCC
*
18657 TGTAGGGTA-AA-TACTGAAATACCCCTGTAGGTTAGAATTACC-GAGATACCC
1 TGTAGGGTAGAATTACTGGAATACCCCTGTAGGTTAGAATTACCGGA-ATACCC
18708 TTGGGTAAAA
Statistics
Matches: 176, Mismatches: 14, Indels: 40
0.77 0.06 0.17
Matches are distributed among these distances:
49 3 0.02
50 14 0.08
51 36 0.20
52 30 0.17
53 39 0.22
54 38 0.22
55 5 0.03
56 11 0.06
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (54 bp):
TGTAGGGTAGAATTACTGGAATACCCCTGTAGGTTAGAATTACCGGAATACCCC
Done.