Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1354
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: 27391
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2737 original size:20 final size:20
Alignment explanation
Indices: 2691--2737 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2681 AGCTCGTTTC
*
2691 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
2711 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
2731 CAGCTCA
1 CAGCTCA
2738 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:5072 original size:29 final size:29
Alignment explanation
Indices: 5039--5107 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
5029 ATGTATTAGT
*
5039 TTAGGACATATTTAAAACACTTGAA-TAAA
1 TTAGGACATATTTAAAACACTTAAACT-AA
5068 TTAGGACATATTTAAAACACTTAAACTAA
1 TTAGGACATATTTAAAACACTTAAACTAA
5097 TTAGGACATAT
1 TTAGGACATAT
5108 CTAATTATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 37 0.97
30 1 0.03
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACTTAAACTAA
Found at i:12759 original size:30 final size:30
Alignment explanation
Indices: 12725--12821 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
12715 TAAACTAAAA
12725 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
12755 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
12785 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
12814 ATGAGCTA
1 -TGAGCTA
12822 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:15014 original size:12 final size:12
Alignment explanation
Indices: 14999--15029 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
14989 TTCTTTTTGC
14999 TTTTCAAAGGCT
1 TTTTCAAAGGCT
15011 TTTTCAAAGGCT
1 TTTTCAAAGGCT
15023 TTTTCAA
1 TTTTCAA
15030 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:15087 original size:5 final size:5
Alignment explanation
Indices: 15077--15118 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
15067 CTCTTGCCTC
15077 TCTTT TCTTT T-TATT TCTTTT TCTTTT TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTTT TCTTT TCTTT
15119 GTTTTCTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 1 0.03
5 22 0.65
6 10 0.29
7 1 0.03
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:15100 original size:16 final size:16
Alignment explanation
Indices: 15077--15118 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
15067 CTCTTGCCTC
15077 TCTTTTCTTTTTA-TT
1 TCTTTTCTTTTTATTT
*
15092 TCTTTTTCTTTTTCTTT
1 TC-TTTTCTTTTTATTT
15109 TCTTTTCTTT
1 TCTTTTCTTT
15119 GTTTTCTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 2 0.08
16 18 0.75
17 4 0.17
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (16 bp):
TCTTTTCTTTTTATTT
Found at i:15128 original size:16 final size:15
Alignment explanation
Indices: 15075--15129 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
15065 GCCTCTTGCC
15075 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTT-T
15091 T-TCTTTTTCTTTTTCT
1 TCTC-TTTTCTTTTT-T
*
15107 TTTCTTTTCTTTGTTT
1 TCTCTTTTCTTT-TTT
15123 TCTCTTT
1 TCTCTTT
15130 ACAAGAATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.06
16 28 0.82
17 4 0.12
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (15 bp):
TCTCTTTTCTTTTTT
Found at i:16057 original size:12 final size:12
Alignment explanation
Indices: 16041--16111 Score: 58
Period size: 12 Copynumber: 5.8 Consensus size: 12
16031 TTTCAACTCG
16041 ATTTTTTTTTC-
1 ATTTTTTTTTCA
*
16052 ACTTTTTTTTCA
1 ATTTTTTTTTCA
16064 ATTTTTTTTCAATCAA
1 ATTTTTTTT---TC-A
16080 ATTTTTTTTTTCA
1 A-TTTTTTTTTCA
*
16093 AATTTTTTTT--
1 ATTTTTTTTTCA
16103 ATTTTTTTT
1 ATTTTTTTT
16112 GTTACTCCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
10 8 0.16
11 10 0.20
12 16 0.32
13 2 0.04
14 2 0.04
15 2 0.04
16 2 0.04
17 8 0.16
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.73
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:16059 original size:11 final size:11
Alignment explanation
Indices: 16043--16076 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
16033 TCAACTCGAT
*
16043 TTTTTTTTCAC
1 TTTTTTTTCAA
16054 TTTTTTTTCAA
1 TTTTTTTTCAA
16065 TTTTTTTTCAA
1 TTTTTTTTCAA
16076 T
1 T
16077 CAAATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:16071 original size:14 final size:14
Alignment explanation
Indices: 16054--16102 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
16044 TTTTTTTCAC
16054 TTTTTTTTCAATTT
1 TTTTTTTTCAATTT
** *
16068 TTTTTCAATCAAATT
1 TTTTT-TTTCAATTT
16083 TTTTTTTTCAAATTT
1 TTTTTTTTC-AATTT
16098 TTTTT
1 TTTTT
16103 ATTTTTTTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 7 0.26
15 20 0.74
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTTTCAATTT
Found at i:16071 original size:40 final size:39
Alignment explanation
Indices: 16016--16111 Score: 108
Period size: 39 Copynumber: 2.4 Consensus size: 39
16006 TTCACTTTTG
* * *
16016 TTTTTTCTTCTTTTTTTTCAACTC-GA-TTTTTTTTTC-AC
1 TTTTTT-TTATTTTTTTTCAA-TCAAATTTTTTTTTTCAAA
16054 TTTTTTTTCAATTTTTTTTCAATCAAATTTTTTTTTTCAAA
1 TTTTTTTT--ATTTTTTTTCAATCAAATTTTTTTTTTCAAA
16095 TTTTTTTTATTTTTTTT
1 TTTTTTTTATTTTTTTT
16112 GTTACTCCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
37 2 0.04
38 8 0.16
39 21 0.42
40 10 0.20
41 9 0.18
ACGTcount: A:0.16, C:0.11, G:0.01, T:0.72
Consensus pattern (39 bp):
TTTTTTTTATTTTTTTTCAATCAAATTTTTTTTTTCAAA
Found at i:16084 original size:16 final size:14
Alignment explanation
Indices: 16054--16104 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
16044 TTTTTTTCAC
16054 TTTTTTT-TC-AAT
1 TTTTTTTATCAAAT
16066 TTTTTTTCAATCAAAT
1 TTTTTTT--ATCAAAT
*
16082 TTTTTTTTTCAAAT
1 TTTTTTTATCAAAT
16096 TTTTTTTAT
1 TTTTTTTAT
16105 TTTTTTTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 7 0.21
14 14 0.42
15 2 0.06
16 10 0.30
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTTATCAAAT
Found at i:16458 original size:12 final size:13
Alignment explanation
Indices: 16441--16477 Score: 56
Period size: 13 Copynumber: 2.7 Consensus size: 13
16431 CAACTCAAAA
16441 TTTTTTTTTGATT
1 TTTTTTTTTGATT
16454 TTTTTTTTTGATT
1 TTTTTTTTTGATT
16467 TCCTTTTTTTT
1 T--TTTTTTTT
16478 TTCGTTACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 14 0.64
15 8 0.36
ACGTcount: A:0.05, C:0.05, G:0.05, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTGATT
Found at i:16631 original size:30 final size:30
Alignment explanation
Indices: 16597--16693 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
16587 TAAACTAAAA
16597 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
16627 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
16657 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
16686 ATGAGCTA
1 -TGAGCTA
16694 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:20465 original size:21 final size:23
Alignment explanation
Indices: 20420--20466 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
20410 TCACCTGCAA
* *
20420 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
20443 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
20464 TAA
1 TAA
20467 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:25209 original size:8 final size:9
Alignment explanation
Indices: 25199--25231 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
25189 TAAACTAAGT
25199 AAATAAAT-
1 AAATAAATA
25207 AAATAAATA
1 AAATAAATA
*
25216 AAAAAAATA
1 AAATAAATA
25225 AAATAAA
1 AAATAAA
25232 ACTTTACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (9 bp):
AAATAAATA
Found at i:26629 original size:23 final size:22
Alignment explanation
Indices: 26578--26629 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
26568 CCTCGTCTTT
*
26578 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
26600 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
26623 TTCTTTT
1 TTCTTTT
26630 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Done.