Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5565.1
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: 21132
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Found at i:3485 original size:4 final size:4
Alignment explanation
Indices: 3478--3505 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3468 GACATTTATG
3478 CATT CATT CATT CATT CATT CATT CATT
1 CATT CATT CATT CATT CATT CATT CATT
3506 GCATATCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
CATT
Found at i:12392 original size:28 final size:28
Alignment explanation
Indices: 12342--12452 Score: 84
Period size: 28 Copynumber: 3.9 Consensus size: 28
12332 CCATTCAGAA
* *
12342 ATCAGTGTTAA-CTAGGCCTTAGCCCAT
1 ATCAGTATTAATCTAGGCCATAGCCCAT
*
12369 ATCAGTATTAATCTAGGCCATAGCCCCT
1 ATCAGTATTAATCTAGGCCATAGCCCAT
* *
12397 -TACAGTAATAGAGTATACTGGGCC-TAGCCCAT
1 AT-CAGT-AT-TA--AT-CTAGGCCATAGCCCAT
* *
12429 ATCAGTATCAATCTGGGCCATAGC
1 ATCAGTATTAATCTAGGCCATAGC
12453 TCTATACAAG
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
27 18 0.26
28 24 0.35
29 2 0.03
30 2 0.03
31 2 0.03
32 13 0.19
33 7 0.10
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (28 bp):
ATCAGTATTAATCTAGGCCATAGCCCAT
Found at i:19813 original size:14 final size:14
Alignment explanation
Indices: 19794--19827 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
19784 GCTGAGGTAA
*
19794 TTTCAATTTCTGTT
1 TTTCAATTTCTGCT
19808 TTTCAATTTCTGCT
1 TTTCAATTTCTGCT
19822 TTTCAA
1 TTTCAA
19828 AAAAATCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (14 bp):
TTTCAATTTCTGCT
Found at i:19847 original size:89 final size:84
Alignment explanation
Indices: 19734--19948 Score: 276
Period size: 89 Copynumber: 2.5 Consensus size: 84
19724 GTATTTTGAT
19734 TTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGG-GCATGCTGAGGTAATTT-
1 TTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCT-AGGTGCATGCTGAGGT-ATTTC
19797 CAATTTCTGTTTTTCAATTTC-TG
64 CAATTTCTG-TTTT-AA-TTCATG
* * **
19820 CTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGTTTATGCTGAGGTATTT
1 -TTTTC--AAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTAGGTGCATGCTGAGGTATTT
19885 CCAATTTCTGTTTTAATTCATG
63 CCAATTTCTGTTTTAATTCATG
*
19907 TTTTCAAAAATCAACTCATATTACGAGAA-GTGAGTTGAGCCT
1 TTTTCAAAAATCAACTCATATTGCGA-AAGGTGAGTTGAGCCT
19949 TTTAATTTCG
Statistics
Matches: 116, Mismatches: 6, Indels: 15
0.85 0.04 0.11
Matches are distributed among these distances:
84 33 0.28
85 1 0.01
86 8 0.07
87 9 0.08
88 10 0.09
89 55 0.47
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (84 bp):
TTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTAGGTGCATGCTGAGGTATTTCCA
ATTTCTGTTTTAATTCATG
Found at i:19976 original size:54 final size:54
Alignment explanation
Indices: 19895--20077 Score: 282
Period size: 54 Copynumber: 3.4 Consensus size: 54
19885 CCAATTTCTG
* *
19895 TTTTAAT-TC-ATGTTTTCAAAAATCAACTCATATTACGAGAAGTGAGTTGAGCC
1 TTTTAATGTCTAT-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* **
19948 TTTTAATTTCGGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTAATGTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
20002 TTTTAATGTCTATTTTTCAAAAAT-ATACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTAATGTCTATTTTTCAAAAATCA-ACTCATATTGCGAGAGGTGAGTTGAGCC
20056 TTTTAATGTCTATTTTTCAAAA
1 TTTTAATGTCTATTTTTCAAAA
20078 TCTACTTTTC
Statistics
Matches: 121, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
53 8 0.07
54 112 0.93
55 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (54 bp):
TTTTAATGTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
Found at i:20250 original size:89 final size:90
Alignment explanation
Indices: 20069--20254 Score: 227
Period size: 89 Copynumber: 2.1 Consensus size: 90
20059 TAATGTCTAT
* * *
20069 TTTTCAAAATCTACTTTTCAATTTATACTTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTT
1 TTTTCAAAATCTACTTTTCAAATTATACGTTTCAAAAAATCAACTCATATAGCGAGAAGTGAGTT
* * *
20134 GAGCCTCGGGTCACATAACGAGGTA
66 GAGCCTCGGCTCACAGAACGAGCTA
*
20159 TTTTCAAAA-CTTACTTTTCAAATTA-A-GTTTCAAAAAAATCAACTCATATAGCGAGAGGTGAG
1 TTTTCAAAATC-TACTTTTCAAATTATACGTTTC-AAAAAATCAACTCATATAGCGAGAAGTGAG
* **
20221 TTGAGCCTTGGCTCAC-GCGCTGAGCTA
64 TTGAGCCTCGGCTCACAGAAC-GAGCTA
20248 TTTTCAA
1 TTTTCAA
20255 TTTCTATTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
88 5 0.06
89 56 0.67
90 22 0.27
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (90 bp):
TTTTCAAAATCTACTTTTCAAATTATACGTTTCAAAAAATCAACTCATATAGCGAGAAGTGAGTT
GAGCCTCGGCTCACAGAACGAGCTA
Found at i:20569 original size:37 final size:37
Alignment explanation
Indices: 20518--20776 Score: 408
Period size: 37 Copynumber: 7.2 Consensus size: 37
20508 ACATTAGAGA
*
20518 AGATTGAAGCTACAAGGCGTATATCAGAAGATGCAGT
1 AGATTGAAGTTACAAGGCGTATATCAGAAGATGCAGT
20555 AGATTGAAGTTACAAGGCGTATATCAGAAGATGCAGT
1 AGATTGAAGTTACAAGGCGTATATCAGAAGATGCAGT
*
20592 AGATTGAAGTTACAAGGCGTATATCAGAAGATACAGT
1 AGATTGAAGTTACAAGGCGTATATCAGAAGATGCAGT
20629 AGATTGAAGTTACAAGGCG----T-AG-AGA--CAGT
1 AGATTGAAGTTACAAGGCGTATATCAGAAGATGCAGT
*
20658 AGATTGAAGTTACAAGGCGTATATCAGAAAATGCAGT
1 AGATTGAAGTTACAAGGCGTATATCAGAAGATGCAGT
20695 AGATTGAAGTTACAAGGCGTATATCAGAAGATGCAGT
1 AGATTGAAGTTACAAGGCGTATATCAGAAGATGCAGT
* *
20732 AGATTGAAGCTACAAGGCGTATATCAGAATATGCAGT
1 AGATTGAAGTTACAAGGCGTATATCAGAAGATGCAGT
*
20769 GGATTGAA
1 AGATTGAA
20777 CCAAAGCTAC
Statistics
Matches: 207, Mismatches: 7, Indels: 16
0.90 0.03 0.07
Matches are distributed among these distances:
29 23 0.11
31 3 0.01
32 2 0.01
33 2 0.01
34 2 0.01
35 2 0.01
37 173 0.84
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.24
Consensus pattern (37 bp):
AGATTGAAGTTACAAGGCGTATATCAGAAGATGCAGT
Found at i:20626 original size:21 final size:21
Alignment explanation
Indices: 20523--20626 Score: 57
Period size: 21 Copynumber: 5.4 Consensus size: 21
20513 AGAGAAGATT
*
20523 GAAGCTACAAGGCGTATATCA
1 GAAGATACAAGGCGTATATCA
* * *
20544 GAAGATGC-A---GTAGAT-T
1 GAAGATACAAGGCGTATATCA
*
20560 GAAGTTACAAGGCGTATATCA
1 GAAGATACAAGGCGTATATCA
* * *
20581 GAAGATGC-A---GTAGAT-T
1 GAAGATACAAGGCGTATATCA
*
20597 GAAGTTACAAGGCGTATATCA
1 GAAGATACAAGGCGTATATCA
20618 GAAGATACA
1 GAAGATACA
20627 GTAGATTGAA
Statistics
Matches: 56, Mismatches: 17, Indels: 20
0.60 0.18 0.22
Matches are distributed among these distances:
16 12 0.21
17 12 0.21
20 12 0.21
21 20 0.36
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.22
Consensus pattern (21 bp):
GAAGATACAAGGCGTATATCA
Found at i:20694 original size:140 final size:140
Alignment explanation
Indices: 20518--20776 Score: 464
Period size: 140 Copynumber: 1.9 Consensus size: 140
20508 ACATTAGAGA
*
20518 AGATTGAAGCTACAAGGCGTATATCAGAAGATGCAGTAGATTGAAGTTACAAGGCGTATATCAGA
1 AGATTGAAGCTACAAGGCGTATATCAGAAAATGCAGTAGATTGAAGTTACAAGGCGTATATCAGA
*
20583 AGATGCAGTAGATTGAAGTTACAAGGCGTATATCAGAAGATACAGTAGATTGAAGTTACAAGGCG
66 AGATGCAGTAGATTGAAGCTACAAGGCGTATATCAGAAGATACAGTAGATTGAAGTTACAAGGCG
20648 TAGAGACAGT
131 TAGAGACAGT
*
20658 AGATTGAAGTTACAAGGCGTATATCAGAAAATGCAGTAGATTGAAGTTACAAGGCGTATATCAGA
1 AGATTGAAGCTACAAGGCGTATATCAGAAAATGCAGTAGATTGAAGTTACAAGGCGTATATCAGA
* * *
20723 AGATGCAGTAGATTGAAGCTACAAGGCGTATATCAGAATATGCAGTGGATTGAA
66 AGATGCAGTAGATTGAAGCTACAAGGCGTATATCAGAAGATACAGTAGATTGAA
20777 CCAAAGCTAC
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 113 1.00
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.24
Consensus pattern (140 bp):
AGATTGAAGCTACAAGGCGTATATCAGAAAATGCAGTAGATTGAAGTTACAAGGCGTATATCAGA
AGATGCAGTAGATTGAAGCTACAAGGCGTATATCAGAAGATACAGTAGATTGAAGTTACAAGGCG
TAGAGACAGT
Found at i:20732 original size:103 final size:103
Alignment explanation
Indices: 20551--20752 Score: 377
Period size: 103 Copynumber: 2.0 Consensus size: 103
20541 TCAGAAGATG
*
20551 CAGTAGATTGAAGTTACAAGGCGTATATCAGAAGATGCAGTAGATTGAAGTTACAAGGCGTATAT
1 CAGTAGATTGAAGTTACAAGGCGTATATCAGAAAATGCAGTAGATTGAAGTTACAAGGCGTATAT
*
20616 CAGAAGATACAGTAGATTGAAGTTACAAGGCGTAGAGA
66 CAGAAGATACAGTAGATTGAAGCTACAAGGCGTAGAGA
20654 CAGTAGATTGAAGTTACAAGGCGTATATCAGAAAATGCAGTAGATTGAAGTTACAAGGCGTATAT
1 CAGTAGATTGAAGTTACAAGGCGTATATCAGAAAATGCAGTAGATTGAAGTTACAAGGCGTATAT
*
20719 CAGAAGATGCAGTAGATTGAAGCTACAAGGCGTA
66 CAGAAGATACAGTAGATTGAAGCTACAAGGCGTA
20753 TATCAGAATA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 96 1.00
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (103 bp):
CAGTAGATTGAAGTTACAAGGCGTATATCAGAAAATGCAGTAGATTGAAGTTACAAGGCGTATAT
CAGAAGATACAGTAGATTGAAGCTACAAGGCGTAGAGA
Done.