Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1671
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: 46755
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:17530 original size:14 final size:14
Alignment explanation
Indices: 17484--17536 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
17474 TCATATCAAC
*
17484 AAATTTAACAATACT
1 AAATTTAA-AATATT
*
17499 AATAATTAAAAT-TT
1 AA-ATTTAAAATATT
17513 AAATTTAAAATATT
1 AAATTTAAAATATT
*
17527 AAATATAAAA
1 AAATTTAAAA
17537 ACTAAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 8 0.25
14 14 0.44
15 5 0.16
16 5 0.16
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATTTAAAATATT
Found at i:17565 original size:22 final size:22
Alignment explanation
Indices: 17519--17564 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
17509 ATTTAAATTT
17519 AAAATATTAAATATAAAAACTA
1 AAAATATTAAATATAAAAACTA
*
17541 AAAATTTTAAA-ATAAAAA-TA
1 AAAATATTAAATATAAAAACTA
17561 AAAA
1 AAAA
17565 AGGGGGAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.26
21 7 0.30
22 10 0.43
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAATATTAAATATAAAAACTA
Found at i:21177 original size:5 final size:5
Alignment explanation
Indices: 21167--21195 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
21157 AATTAGCCTA
21167 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
21196 ATCAAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:21764 original size:4 final size:4
Alignment explanation
Indices: 21755--21793 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
21745 TTGAACTATT
*
21755 TTTA TTTA TTTA TTTG TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
21794 TTGTTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:22150 original size:20 final size:22
Alignment explanation
Indices: 22125--22173 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
22115 TAATTTTTTT
22125 TATACATACATATT-CTA-AA-A
1 TATACATACAT-TTCCTATAATA
*
22145 TATACATTCATTTCCTATAATA
1 TATACATACATTTCCTATAATA
22167 TATACAT
1 TATACAT
22174 TTTTCAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 13 0.52
21 2 0.08
22 8 0.32
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (22 bp):
TATACATACATTTCCTATAATA
Found at i:27390 original size:19 final size:19
Alignment explanation
Indices: 27366--27408 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
27356 TTTGGGTTAA
27366 AAGTGTTTTTACACTGCAG
1 AAGTGTTTTTACACTGCAG
*
27385 AAGTGTTTTTCCACTGCAG
1 AAGTGTTTTTACACTGCAG
27404 AAGTG
1 AAGTG
27409 ACGAAGAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (19 bp):
AAGTGTTTTTACACTGCAG
Found at i:27525 original size:27 final size:27
Alignment explanation
Indices: 27494--27559 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 27
27484 ATACTCTTAG
* *
27494 ATTAATTTATATTTTATATATTATTAT
1 ATTAATTTAAATCTTATATATTATTAT
*
27521 ATTAATTGTTTAAATCTTATTTATTATTAT
1 ATTAA---TTTAAATCTTATATATTATTAT
27551 ATTTAATTT
1 A-TTAATTT
27560 TTTTCAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
27 5 0.16
28 3 0.09
30 20 0.62
31 4 0.12
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
ATTAATTTAAATCTTATATATTATTAT
Found at i:36894 original size:44 final size:45
Alignment explanation
Indices: 36689--36947 Score: 195
Period size: 44 Copynumber: 5.8 Consensus size: 45
36679 GAAAATAGAC
* * * * *
36689 CTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAACAGAT
1 CTTGTCTTCACATACTGGTCGTGAAGTAGATCGAAGAAAGCAGAT
* ** * * *
36734 CTTATCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAGCAGGT
1 CTTGTCTTCACATACTGGTCGTGAAGTAGATCGAAGAAAGCAGAT
* * * * * * *
36778 CCTGTCTTC-CTATATTGGTAGCGAAGTGGATCGAATATA-CAGAT
1 CTTGTCTTCAC-ATACTGGTCGTGAAGTAGATCGAAGAAAGCAGAT
* * * * * * *
36822 -TTCATCTCCCCATACTGGTGGCGGAGTAGATTGAAGAAAGCAGAT
1 CTT-GTCTTCACATACTGGTCGTGAAGTAGATCGAAGAAAGCAGAT
* * *
36867 CTTGTCTTCACGTGCTGG-CGTGAAGTAGATCAAAGAAAGCAGAT
1 CTTGTCTTCACATACTGGTCGTGAAGTAGATCGAAGAAAGCAGAT
* *
36911 CTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGA
1 CTTGTCTTCACATACTGGTCGTGAAGTAGATCGAAGA
36948 TACAAGTCTT
Statistics
Matches: 160, Mismatches: 47, Indels: 14
0.72 0.21 0.06
Matches are distributed among these distances:
43 1 0.01
44 97 0.61
45 60 0.38
46 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (45 bp):
CTTGTCTTCACATACTGGTCGTGAAGTAGATCGAAGAAAGCAGAT
Found at i:36964 original size:133 final size:133
Alignment explanation
Indices: 36693--36951 Score: 383
Period size: 133 Copynumber: 1.9 Consensus size: 133
36683 ATAGACCTTG
* *
36693 TCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAACAGATCTTATCTTCATGTACTGGCGTGAA
1 TCTCCCCATACTGGTGGCGGAGTAGATCGAAGAAAACAGATCTTATCTTCACGTACTGGCGTGAA
* * * * * *
36758 GTAGATCAAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAATATACAGATT
66 GTAGATCAAAGAAAGCAGATCCTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGATACAGATT
36823 TCA
131 TCA
* * * *
36826 TCTCCCCATACTGGTGGCGGAGTAGATTGAAGAAAGCAGATCTTGTCTTCACGTGCTGGCGTGAA
1 TCTCCCCATACTGGTGGCGGAGTAGATCGAAGAAAACAGATCTTATCTTCACGTACTGGCGTGAA
* * *
36891 GTAGATCAAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATACA
66 GTAGATCAAAGAAAGCAGATCCTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGATACA
36952 AGTCTTATCT
Statistics
Matches: 111, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
133 111 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (133 bp):
TCTCCCCATACTGGTGGCGGAGTAGATCGAAGAAAACAGATCTTATCTTCACGTACTGGCGTGAA
GTAGATCAAAGAAAGCAGATCCTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGATACAGATT
TCA
Found at i:38512 original size:3 final size:3
Alignment explanation
Indices: 38504--38536 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
38494 ATTTATTTAT
*
38504 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38537 CTATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:40086 original size:12 final size:12
Alignment explanation
Indices: 40069--40116 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
40059 AATTAAAATT
40069 TATTATTAATAA
1 TATTATTAATAA
40081 TATTA-T--TAA
1 TATTATTAATAA
*
40090 TATTATTAATAT
1 TATTATTAATAA
40102 TATTATTAAATAA
1 TATTATT-AATAA
40115 TA
1 TA
40117 AGAAGTGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
9 8 0.27
10 1 0.03
11 1 0.03
12 14 0.47
13 6 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATTATTAATAA
Found at i:40090 original size:9 final size:9
Alignment explanation
Indices: 40072--40106 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
40062 TAAAATTTAT
*
40072 TATTAATAA
1 TATTATTAA
40081 TATTATTAA
1 TATTATTAA
40090 TATTATTAA
1 TATTATTAA
40099 TATTATTA
1 TATTATTA
40107 TTAAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TATTATTAA
Found at i:40542 original size:19 final size:17
Alignment explanation
Indices: 40514--40559 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
40504 ACTTATAAAC
*
40514 ATAAATATTTAAAAAAGTT
1 ATAAAAATTT-AAAAA-TT
*
40533 ATAAAAATTTTAAAATT
1 ATAAAAATTTAAAAATT
40550 ATAAAAATTT
1 ATAAAAATTT
40560 TAATTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.48
18 4 0.16
19 9 0.36
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
ATAAAAATTTAAAAATT
Found at i:40553 original size:17 final size:18
Alignment explanation
Indices: 40526--40562 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
40516 AAATATTTAA
40526 AAAAGTTATAAAAATTTT
1 AAAAGTTATAAAAATTTT
40544 AAAA-TTATAAAAATTTT
1 AAAAGTTATAAAAATTTT
40561 AA
1 AA
40563 TTAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AAAAGTTATAAAAATTTT
Found at i:43216 original size:14 final size:14
Alignment explanation
Indices: 43197--43224 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43187 CCCCGTCATT
43197 CGTGTTCACACTAG
1 CGTGTTCACACTAG
43211 CGTGTTCACACTAG
1 CGTGTTCACACTAG
43225 ATCTAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (14 bp):
CGTGTTCACACTAG
Found at i:44424 original size:33 final size:33
Alignment explanation
Indices: 44386--44531 Score: 143
Period size: 34 Copynumber: 4.3 Consensus size: 33
44376 TGGTTTACAT
* *
44386 ATAAAACCAAAACCAAGACCTAAAATTT-CAAGA
1 ATAAAA-CAAAATCAAGACCTAAAATTTCCATGA
* * * *
44419 ATAAAAAAAAATCAAGACTTAAATTTTCCATTA
1 ATAAAACAAAATCAAGACCTAAAATTTCCATGA
*
44452 ATAAAACCAAAATCAAGA-CTAAAAATTTTCATGA
1 ATAAAA-CAAAATCAAGACCT-AAAATTTCCATGA
* * *
44486 ATAGAAACGAAATCAAGGCCTAAATTTTCCATGA
1 ATA-AAACAAAATCAAGACCTAAAATTTCCATGA
44520 ATGAAAACAAAA
1 AT-AAAACAAAA
44532 CCATGAATTA
Statistics
Matches: 91, Mismatches: 16, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
32 17 0.19
33 16 0.18
34 52 0.57
35 6 0.07
ACGTcount: A:0.55, C:0.16, G:0.08, T:0.22
Consensus pattern (33 bp):
ATAAAACAAAATCAAGACCTAAAATTTCCATGA
Found at i:44531 original size:68 final size:66
Alignment explanation
Indices: 44386--44534 Score: 185
Period size: 68 Copynumber: 2.2 Consensus size: 66
44376 TGGTTTACAT
* *
44386 ATAAAACCAAAACCAAGACCTAAAATTTCAAGAATAAAAAAAAATCAAGACTTAAATTTTCCATT
1 ATAAAACCAAAACCAAGACCTAAAATTTCAAGAATAAAAAAAAATCAAGACCTAAATTTTCCATG
44451 A
66 A
* * ** *
44452 ATAAAACCAAAATCAAGA-CTAAAAATTTTCATGAATAGAAACGAAATCAAGGCCTAAATTTTCC
1 ATAAAACCAAAACCAAGACCT-AAAA-TTTCAAGAATA-AAAAAAAATCAAGACCTAAATTTTCC
44516 ATGA
63 ATGA
44520 ATGAAAA-CAAAACCA
1 AT-AAAACCAAAACCA
44535 TGAATTAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
65 2 0.03
66 21 0.30
67 10 0.14
68 34 0.48
69 4 0.06
ACGTcount: A:0.54, C:0.17, G:0.07, T:0.21
Consensus pattern (66 bp):
ATAAAACCAAAACCAAGACCTAAAATTTCAAGAATAAAAAAAAATCAAGACCTAAATTTTCCATG
A
Found at i:44537 original size:18 final size:18
Alignment explanation
Indices: 44514--44549 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
44504 CCTAAATTTT
44514 CCATGAATGAAAACAAAA
1 CCATGAATGAAAACAAAA
*
44532 CCATGAATTAAAACAAAA
1 CCATGAATGAAAACAAAA
44550 TCAAGGCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.61, C:0.17, G:0.08, T:0.14
Consensus pattern (18 bp):
CCATGAATGAAAACAAAA
Done.