Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold675
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: 17704
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:59 original size:1 final size:1
Alignment explanation
Indices: 55--134 Score: 160
Period size: 1 Copynumber: 80.0 Consensus size: 1
45 CCCCCTTCCT
55 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
120 CCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCC
135 ACTTCTTCTG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 79 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1144 original size:13 final size:13
Alignment explanation
Indices: 1126--1155 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1116 CCAAGCTTTT
1126 TTTATTATTATTA
1 TTTATTATTATTA
*
1139 TTTATTATTATTT
1 TTTATTATTATTA
1152 TTTA
1 TTTA
1156 ATTTGATCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:6608 original size:20 final size:20
Alignment explanation
Indices: 6583--6622 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
6573 CGATTAAATT
6583 TAATATAAATTATTATTTAA
1 TAATATAAATTATTATTTAA
*
6603 TAATATAAATTTTTATTTAA
1 TAATATAAATTATTATTTAA
6623 ATTTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATATAAATTATTATTTAA
Found at i:7108 original size:25 final size:26
Alignment explanation
Indices: 7054--7109 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
7044 TAACTTTAAA
*
7054 AAATTATATTAATAAATTAAAATATT
1 AAATTATATTAATAAATTAAAAAATT
*
7080 -AATTATTTTTAA-AAA-TAAAAAATT
1 AAATTA-TATTAATAAATTAAAAAATT
7104 AAATTA
1 AAATTA
7110 AAAAGGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 8 0.31
25 13 0.50
26 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATTATATTAATAAATTAAAAAATT
Found at i:7237 original size:115 final size:106
Alignment explanation
Indices: 7028--7299 Score: 264
Period size: 109 Copynumber: 2.5 Consensus size: 106
7018 TTATTTTTAA
* * * *
7028 TAAAATAATATTTAATTAACTTTAAAAAATTATATTAATAAATTAAAATATTAATTATTTTTAAA
1 TAAAATAATATTTAATTAAATTAAAAAAATTACATTAACAAATTAAAATATTAATTATTTTTAAA
*
7093 AATAAAAAATTAAATTAAAAAGGATTTATTATTATATTTTTAATAAAAT
66 AAT---AAA--AAAGT-AAAAGGATTTATTATTAT-TTTTTAAT-AAAT
7142 TAAAATAATATTTAATTAAATTCAAAAAAATTACATTAACAAATTAAAATATTAATTAATGTTTT
1 TAAAATAATATTTAATTAAATT-AAAAAAATTACATTAACAAATTAAAATATTAATT-A--TTTT
* ***
7207 TACAAAA-ATAAAAGT--ACTTA-TTATTATTATTTTTTAATAAAT
62 TA-AAAATAAAAAAGTAAAAGGATTTATTATTATTTTTTAATAAAT
* * *
7249 AAAAAGTGATATTTAATTAAATTTTAAAAAATTTACATTAACAAATTAAAA
1 TAAAA-TAATATTTAATTAAA--TTAAAAAAATTACATTAACAAATTAAAA
7300 AATAATATTT
Statistics
Matches: 138, Mismatches: 12, Indels: 21
0.81 0.07 0.12
Matches are distributed among these distances:
107 8 0.06
108 22 0.16
109 35 0.25
110 4 0.03
113 4 0.03
114 21 0.15
115 33 0.24
116 1 0.01
118 6 0.04
119 4 0.03
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (106 bp):
TAAAATAATATTTAATTAAATTAAAAAAATTACATTAACAAATTAAAATATTAATTATTTTTAAA
AATAAAAAAGTAAAAGGATTTATTATTATTTTTTAATAAAT
Found at i:7300 original size:22 final size:22
Alignment explanation
Indices: 7272--7348 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
7262 TAATTAAATT
7272 TTAAAAAATTTACATTAACAAA
1 TTAAAAAATTTACATTAACAAA
* * *
7294 TTAAAAAATAATA-TTTAAGAAA
1 TTAAAAAAT-TTACATTAACAAA
*
7316 TTAAAAAAATTTATCATTATTCAAA
1 TT-AAAAAATTTA-CATTA-ACAAA
7341 -TAAAAAAT
1 TTAAAAAAT
7349 CCTCTATTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
22 20 0.47
23 16 0.37
24 4 0.09
25 3 0.07
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (22 bp):
TTAAAAAATTTACATTAACAAA
Found at i:7336 original size:108 final size:109
Alignment explanation
Indices: 7118--7325 Score: 269
Period size: 109 Copynumber: 1.9 Consensus size: 109
7108 TAAAAAGGAT
*
7118 TTATTATTATATTTTTAATAAAATTAAAATAATATTTAATTAAATTCAAAAAAATTACATTAACA
1 TTATTATTATATTTTTAATAAAATAAAAATAATATTTAATTAAATTCAAAAAAATTACATTAACA
* *** *
7183 AATTAAAATATTAATTAATGTTTTTACAAAAATAAAAGTACTTA
66 AATTAAAATAATAATTAATGAAATTAAAAAAATAAAAGTACTTA
* * *
7227 TTATTATTAT-TTTTTAAT-AAATAAAAAGTGATATTTAATTAAATTTTAAAAAATTTACATTAA
1 TTATTATTATATTTTTAATAAAATAAAAA-TAATATTTAATTAAA-TTCAAAAAAATTACATTAA
*
7290 CAAATTAAAAAATAATATTTAA-GAAATTAAAAAAAT
64 CAAATT--AAAATAATAATTAATGAAATTAAAAAAAT
7326 TTATCATTAT
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
107 8 0.09
108 22 0.26
109 33 0.39
110 10 0.12
111 12 0.14
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (109 bp):
TTATTATTATATTTTTAATAAAATAAAAATAATATTTAATTAAATTCAAAAAAATTACATTAACA
AATTAAAATAATAATTAATGAAATTAAAAAAATAAAAGTACTTA
Found at i:7598 original size:20 final size:20
Alignment explanation
Indices: 7561--7599 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
7551 TTAGATGGTG
*
7561 ATTTTCTCAACGAAAAAAAT
1 ATTTTCTCAACAAAAAAAAT
*
7581 ATTTTCTCAA-AAATAAAAT
1 ATTTTCTCAACAAAAAAAAT
7600 TAAATAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (20 bp):
ATTTTCTCAACAAAAAAAAT
Found at i:7802 original size:122 final size:123
Alignment explanation
Indices: 7632--7904 Score: 365
Period size: 122 Copynumber: 2.2 Consensus size: 123
7622 CAATAAATTG
* * *
7632 TTTTTAATTTAAATTTTTTTATTTTTAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAA
1 TTTTTATTTTAAAATTTTTTATTTTTAAAAACATAATAATTAATATTTTAATTTGTTAATATAAA
** * *
7697 TTTTTAAACTTAATTAAATATTATGTTTTTTTTAT-TAAAAATTATAATAA-AAAACC-T
66 TTTTTAAACTTAATTAAATATT-T-TTAATTTTATAAAAAAATAATAATAATAAAACCTT
* *
7754 TTTTTATTTTAAAATTTTTAATTTTATAAAAATATAATAATTAA-ATTTTAATTTGTTAATATAA
1 TTTTTATTTTAAAATTTTTTATTTT-TAAAAACATAATAATTAATATTTTAATTTGTTAATATAA
* *
7818 TTTTTTAAACTTAATTAAATATTTTTAATTTTATAAAAAAATAATAATAATAAACCCTT
65 ATTTTTAAACTTAATTAAATATTTTTAATTTTATAAAAAAATAATAATAATAAAACCTT
*
7877 TTATTTTTATTTAAAATTTTTTATTTTT
1 TT-TTTAT-TTTAAAATTTTTTATTTTT
7905 TTAAATTAAT
Statistics
Matches: 132, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
120 8 0.06
121 14 0.11
122 68 0.52
123 20 0.15
124 5 0.04
125 17 0.13
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (123 bp):
TTTTTATTTTAAAATTTTTTATTTTTAAAAACATAATAATTAATATTTTAATTTGTTAATATAAA
TTTTTAAACTTAATTAAATATTTTTAATTTTATAAAAAAATAATAATAATAAAACCTT
Found at i:7962 original size:20 final size:20
Alignment explanation
Indices: 7899--7963 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 20
7889 AAAATTTTTT
*
7899 ATTT-TTTTAAATTAATAT-
1 ATTTATTTTAAGTTAATATA
*
7917 -TTTAATTT-A-TTAATATA
1 ATTTATTTTAAGTTAATATA
*
7934 ATTTTTTTTAAGTTAAT-TA
1 ATTTATTTTAAGTTAATATA
7953 ATATTATTTTA
1 AT-TTATTTTA
7964 TTAAAAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
16 7 0.19
17 4 0.11
18 9 0.24
19 5 0.14
20 12 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTATTTTAAGTTAATATA
Found at i:7962 original size:23 final size:23
Alignment explanation
Indices: 7916--7962 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
7906 TAAATTAATA
*
7916 TTTTAATTTATTAATATAATTTT
1 TTTTAATTAATTAATATAATTTT
*
7939 TTTTAAGTTAATTAATATTATTTT
1 TTTTAA-TTAATTAATATAATTTT
7963 ATTAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTTAATTAATTAATATAATTTT
Found at i:8010 original size:32 final size:29
Alignment explanation
Indices: 7940--8010 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
7930 TATAATTTTT
7940 TTTAAGTTAATTAATATTATTTTATTAAAA
1 TTTAA-TTAATTAATATTATTTTATTAAAA
* *
7970 -ATAA-TAATTAATACATTATTATTTTTAAAA
1 TTTAATTAATTAAT--ATTATT-TTATTAAAA
8000 TTTAATTAATT
1 TTTAATTAATT
8011 TATAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
27 8 0.24
29 9 0.27
30 8 0.24
31 3 0.09
32 5 0.15
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (29 bp):
TTTAATTAATTAATATTATTTTATTAAAA
Found at i:8574 original size:112 final size:113
Alignment explanation
Indices: 8441--8722 Score: 314
Period size: 112 Copynumber: 2.5 Consensus size: 113
8431 TTGATAGGAC
* * * *
8441 TAATA-TTTATTTTTTAATGTATATTTTTAAAATTTAATTAAATATCATTTTTTTATT-GTATTA
1 TAATATTTTATTTATTAATGTAT-TTTTTTAAATTTAATTAAATATTATTTTTTAATTGGTATTA
8504 AAAAATAATAATAA-AAAATACTTTTT-A-TT-TTTATA-AAAACATATAAT
65 AAAAATAATAATAATAAAAT-CTTTTTAAGTTATTTATAGAAAA-A-ATAAT
*
8551 TAATATTTTAGTTTATTAATGTATTTTTTTTAAATTTAATGAAATATTA-TTTTTAATTGGTATT
1 TAATATTTTA-TTTATTAATGTA-TTTTTTTAAATTTAATTAAATATTATTTTTTAATTGGTATT
* * * **
8615 AAAAAATAGTAATAATAAAATTTTTTTAAGTTAATTTTTAGTTTAAAATAAT
64 AAAAAATAATAATAATAAAATCTTTTTAAGTT-ATTTATAG-AAAAAATAAT
*
8667 TAATATTTTAATTTATTAATATATTTTTTTAAA-TTAATTAAATATTA-TTTTTAATT
1 TAATATTTT-ATTTATTAATGTATTTTTTTAAATTTAATTAAATATTATTTTTTAATT
8723 AAAATAATAA
Statistics
Matches: 148, Mismatches: 12, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
110 5 0.03
111 12 0.08
112 56 0.38
113 7 0.05
114 24 0.16
115 10 0.07
116 30 0.20
117 2 0.01
118 2 0.01
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (113 bp):
TAATATTTTATTTATTAATGTATTTTTTTAAATTTAATTAAATATTATTTTTTAATTGGTATTAA
AAAATAATAATAATAAAATCTTTTTAAGTTATTTATAGAAAAAATAAT
Found at i:8698 original size:21 final size:21
Alignment explanation
Indices: 8672--8724 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
8662 ATAATTAATA
*
8672 TTTTAATTTATTAATATATT-T
1 TTTTAATTAATTAA-ATATTAT
8693 TTTTAAATTAATTAAATATTAT
1 TTTT-AATTAATTAAATATTAT
8715 TTTTAATTAA
1 TTTTAATTAA
8725 AATAATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTAATTAATTAAATATTAT
Found at i:8730 original size:26 final size:23
Alignment explanation
Indices: 8684--8730 Score: 58
Period size: 26 Copynumber: 1.9 Consensus size: 23
8674 TTAATTTATT
*
8684 AATATATTTTTTTAAATTAATTA
1 AATATATTTTTTTAAAATAATTA
8707 AATATTATTTTTAATTAAAATAAT
1 AATA-TATTTTT--TTAAAATAAT
8731 AATTAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 7 0.35
26 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATATATTTTTTTAAAATAATTA
Found at i:8731 original size:21 final size:21
Alignment explanation
Indices: 8648--8731 Score: 50
Period size: 21 Copynumber: 3.9 Consensus size: 21
8638 TTTTAAGTTA
* *
8648 ATTTTTAGTTTAAAATAAT-TA
1 ATTTTTA-ATTAAAATAATATT
*
8669 ATATTTTAATTTATTAAT-ATATT
1 AT-TTTTAA-TTA-AAATAATATT
*
8692 -TTTTTAAATT-AATTAAATATT
1 ATTTTT-AATTAAAAT-AATATT
8713 ATTTTTAATTAAAATAATA
1 ATTTTTAATTAAAATAATA
8732 ATTAATATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
19 2 0.04
21 21 0.44
22 21 0.44
23 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (21 bp):
ATTTTTAATTAAAATAATATT
Found at i:8735 original size:22 final size:22
Alignment explanation
Indices: 8660--8735 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
8650 TTTTAGTTTA
*
8660 AAATAAT-TAATA-TTTTAATT
1 AAATAATATATTATTTTTAATT
* *
8680 TATTAATATATT-TTTTTAAATT
1 AAATAATATATTATTTTT-AATT
*
8702 AATTAA-ATATTATTTTTAATT
1 AAATAATATATTATTTTTAATT
8723 AAAATAATA-ATTA
1 -AAATAATATATTA
8736 ATATTTTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
20 5 0.11
21 16 0.36
22 23 0.51
23 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AAATAATATATTATTTTTAATT
Done.