Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold588
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: 72490
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:10384 original size:15 final size:14
Alignment explanation
Indices: 10348--10402 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
10338 TCTATTGATC
10348 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
10362 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
10376 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
10391 GAAAGAAAAGAA
1 GAGA-AAAAGAA
10403 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:17262 original size:16 final size:16
Alignment explanation
Indices: 17228--17266 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
17218 TTTAACTTGA
17228 TTTTTTTTGCTCACCTT
1 TTTTTTTTGCTCA-CTT
17245 TTTTTTTTGCTCGA-TT
1 TTTTTTTTGCTC-ACTT
17261 TTTTTT
1 TTTTTT
17267 CACTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 12 0.57
18 1 0.05
ACGTcount: A:0.05, C:0.15, G:0.08, T:0.72
Consensus pattern (16 bp):
TTTTTTTTGCTCACTT
Found at i:17274 original size:12 final size:12
Alignment explanation
Indices: 17259--17327 Score: 59
Period size: 12 Copynumber: 5.5 Consensus size: 12
17249 TTTTGCTCGA
*
17259 TTTTTTTTCACT
1 TTTTTTTTCAAT
*
17271 TTTTTTTTGAATT
1 TTTTTTTTCAA-T
17284 TTTTTTTCAATCAAT
1 TTTTTTT---TCAAT
*
17299 TTTTTTTTGAAT
1 TTTTTTTTCAAT
*
17311 TTTTTTTT-GAT
1 TTTTTTTTCAAT
17322 TTTTTT
1 TTTTTT
17328 GTTACTCCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
11 8 0.17
12 21 0.44
13 8 0.17
15 8 0.17
16 3 0.06
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.75
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:21826 original size:6 final size:6
Alignment explanation
Indices: 21813--21849 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
21803 CAATTTTTTT
* *
21813 TCTCAA TATCAA TATCAA TCTCAA TCTCAA TCTCAA T
1 TCTCAA TCTCAA TCTCAA TCTCAA TCTCAA TCTCAA T
21850 TTTTTTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (6 bp):
TCTCAA
Found at i:21871 original size:25 final size:24
Alignment explanation
Indices: 21837--21897 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
21827 TCAATCTCAA
* *
21837 TCTCAATCTCAATTTTTTTTCTTTT
1 TCTCACTCTCAATTTTTCTT-TTTT
21862 TCTCACTCTC-A-TTTTCTTTTTT
1 TCTCACTCTCAATTTTTCTTTTTT
*
21884 TCT-TCTCTCAATTT
1 TCTCACTCTCAATTT
21898 CATTCAAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 5 0.16
22 8 0.26
23 8 0.26
24 1 0.03
25 9 0.29
ACGTcount: A:0.13, C:0.25, G:0.00, T:0.62
Consensus pattern (24 bp):
TCTCACTCTCAATTTTTCTTTTTT
Found at i:21898 original size:21 final size:20
Alignment explanation
Indices: 21854--21898 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
21844 CTCAATTTTT
*
21854 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
* *
21874 TTTCTTTTTTTCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
21895 TTTC
1 TTTC
21899 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:22748 original size:29 final size:31
Alignment explanation
Indices: 22706--22775 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 31
22696 CAATCACTCT
**
22706 TTTTTTTTTCAATTTTG-ATTTTTTTTCTTC
1 TTTTTTTTTCAATTCCGAATTTTTTTTCTTC
22736 TTTTTTTTT-AATTCCGAATTTTTTTTCTTC
1 TTTTTTTTTCAATTCCGAATTTTTTTTCTTC
*
22766 TTCTTTTTTC
1 TTTTTTTTTC
22776 TTCAATACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 5 0.14
30 30 0.86
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (31 bp):
TTTTTTTTTCAATTCCGAATTTTTTTTCTTC
Found at i:22837 original size:13 final size:13
Alignment explanation
Indices: 22814--22863 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
22804 AAATTGAATA
22814 CAAACTTTTTTTTT
1 CAAA-TTTTTTTTT
*
22828 -GAATTTTTTTTT
1 CAAATTTTTTTTT
*
22840 CAAAATTTTTTTT
1 CAAATTTTTTTTT
22853 CAAATTTTTTT
1 CAAATTTTTTT
22864 ATATTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 9 0.29
13 22 0.71
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.66
Consensus pattern (13 bp):
CAAATTTTTTTTT
Found at i:22873 original size:12 final size:12
Alignment explanation
Indices: 22819--22863 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
22809 GAATACAAAC
*
22819 TTTTTTTTTGAA
1 TTTTTTTTTAAA
22831 TTTTTTTTTCAAAA
1 TTTTTTTTT--AAA
*
22845 TTTTTTTTCAAA
1 TTTTTTTTTAAA
22857 TTTTTTT
1 TTTTTTT
22864 ATATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 19 0.66
14 10 0.34
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (12 bp):
TTTTTTTTTAAA
Found at i:23050 original size:30 final size:30
Alignment explanation
Indices: 23016--23112 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
23006 TAAACTAAAA
*
23016 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
23046 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
23076 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
23105 ATGAGCTA
1 -TGAGCTA
23113 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:28228 original size:13 final size:13
Alignment explanation
Indices: 28210--28234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28200 AACCGTATGC
28210 AATTTTTTTTTCA
1 AATTTTTTTTTCA
28223 AATTTTTTTTTC
1 AATTTTTTTTTC
28235 TTTTTTTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
AATTTTTTTTTCA
Found at i:28588 original size:21 final size:21
Alignment explanation
Indices: 28558--28620 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
28548 TTGGTATTTG
28558 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
28579 GGAATAGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
28600 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
28621 ACGGTTCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 21 0.60
22 14 0.40
ACGTcount: A:0.32, C:0.03, G:0.33, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:33307 original size:23 final size:22
Alignment explanation
Indices: 33255--33307 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33245 TCCACGTCTT
*
33255 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
33277 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
33300 TTTCTTTT
1 TTTCTTTT
33308 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:37636 original size:11 final size:11
Alignment explanation
Indices: 37604--37637 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
37594 AGATCGTATG
37604 CAATTTTTTTCT
1 CAATTTTTTT-T
37616 CAATTTTTTTT
1 CAATTTTTTTT
*
37627 CGATTTTTTTT
1 CAATTTTTTTT
37638 GAATCTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.15, C:0.12, G:0.03, T:0.71
Consensus pattern (11 bp):
CAATTTTTTTT
Found at i:43814 original size:20 final size:20
Alignment explanation
Indices: 43777--43814 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43767 AGTTCATAAG
*
43777 AAAAAATTCAAAAAAAAACA
1 AAAAAATTAAAAAAAAAACA
43797 AAAAAATTAAAAAAAAAA
1 AAAAAATTAAAAAAAAAA
43815 GCTTGGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAAAATTAAAAAAAAAACA
Found at i:44726 original size:22 final size:20
Alignment explanation
Indices: 44694--44744 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
44684 ATCTTCTTGT
*
44694 AAAAAAGAAAACGAGAAAAGC
1 AAAAAAGAAAAAGA-AAAAGC
*
44715 AAAAGAAGAAAAAGAAAAAGA
1 AAAA-AAGAAAAAGAAAAAGC
44736 AATAAAAGA
1 AA-AAAAGA
44745 GAGGCAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (20 bp):
AAAAAAGAAAAAGAAAAAGC
Found at i:44744 original size:15 final size:15
Alignment explanation
Indices: 44695--44736 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
44685 TCTTCTTGTA
*
44695 AAAAAGAAAACG-AG
1 AAAAAGAAAAAGAAG
*
44709 -AAAAGCAAAAGAAG
1 AAAAAGAAAAAGAAG
44723 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
44737 ATAAAAGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 9 0.39
14 2 0.09
15 12 0.52
ACGTcount: A:0.76, C:0.05, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAGAAG
Found at i:44853 original size:12 final size:12
Alignment explanation
Indices: 44833--44876 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
44823 GAAAAAGAAC
*
44833 AAAAAGAGAGTG
1 AAAAAGAGAATG
* *
44845 AAAATGAGATTG
1 AAAAAGAGAATG
44857 AAAAAGAGAATG
1 AAAAAGAGAATG
44869 AAAAAGAG
1 AAAAAGAG
44877 TTTGAGAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.11
Consensus pattern (12 bp):
AAAAAGAGAATG
Found at i:44864 original size:24 final size:24
Alignment explanation
Indices: 44833--44881 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
44823 GAAAAAGAAC
* *
44833 AAAAAGAGAGTGAAAATGAGATTG
1 AAAAAGAGAATGAAAAAGAGATTG
*
44857 AAAAAGAGAATGAAAAAGAGTTTG
1 AAAAAGAGAATGAAAAAGAGATTG
44881 A
1 A
44882 GAGAGAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (24 bp):
AAAAAGAGAATGAAAAAGAGATTG
Found at i:49194 original size:23 final size:22
Alignment explanation
Indices: 49142--49194 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
49132 TTCACGTCTT
*
49142 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
49164 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
49187 TTTCTTTT
1 TTTCTTTT
49195 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:52351 original size:13 final size:13
Alignment explanation
Indices: 52333--52357 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52323 GTATTGATCA
52333 TGTGTTCACACCT
1 TGTGTTCACACCT
52346 TGTGTTCACACC
1 TGTGTTCACACC
52358 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:52958 original size:30 final size:30
Alignment explanation
Indices: 52931--53018 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
52921 CTTGCTCATA
52931 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * *
52961 TTCAGCTTAGGAGTTTAATCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* *
52991 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAACCTTAGCTCA
53019 TTTTAGTTTA
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:54025 original size:20 final size:20
Alignment explanation
Indices: 54002--54055 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
53992 AGTTTTTCCC
*
54002 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
54022 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
54042 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
54056 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:54037 original size:30 final size:30
Alignment explanation
Indices: 54002--54075 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
53992 AGTTTTTCCC
54002 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
54032 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
54062 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
54076 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:54065 original size:20 final size:20
Alignment explanation
Indices: 54002--54066 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
53992 AGTTTTTCCC
* * * *
54002 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
54022 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
54041 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
54062 AGCTC
1 AGCTC
54067 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:59980 original size:1 final size:1
Alignment explanation
Indices: 59974--60029 Score: 103
Period size: 1 Copynumber: 56.0 Consensus size: 1
59964 CTTCTTAGCC
*
59974 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
60030 TTTTGTAAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.98, C:0.00, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:60361 original size:12 final size:11
Alignment explanation
Indices: 60340--60400 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 11
60330 GGCTGCACCG
60340 TTTTTCTTCTT
1 TTTTTCTTCTT
60351 TTTTATCTTCTT
1 TTTT-TCTTCTT
*
60363 TCGTTTCTTCTCT
1 T-TTTTCTTCT-T
*
60376 TTTTTCATTTCTC
1 TTTTTC--TTCTT
60389 TTTTTCTT-TT
1 TTTTTCTTCTT
60399 TT
1 TT
60401 CACCCGGAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
10 3 0.07
11 6 0.15
12 18 0.44
13 10 0.24
14 4 0.10
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTTCTTCTT
Done.