Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3101
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: 34169
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:2101 original size:41 final size:41
Alignment explanation
Indices: 2039--2124 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
2029 TTTAATTAGG
* *
2039 TGTTTTAAATATGCCTGGACGAATTTAATGCCGCCACTACA
1 TGTTATAAATATGCCTGGACGAATTTAATGCCACCACTACA
* *
2080 TGTTATAAATATGCCTGGACGAATTTAATGCTACTACTACA
1 TGTTATAAATATGCCTGGACGAATTTAATGCCACCACTACA
2121 TGTT
1 TGTT
2125 TGGCCGAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (41 bp):
TGTTATAAATATGCCTGGACGAATTTAATGCCACCACTACA
Found at i:6957 original size:13 final size:13
Alignment explanation
Indices: 6939--6973 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
6929 TAGTTTCTTC
6939 AAAAAAATTCAAA
1 AAAAAAATTCAAA
6952 AAAAAAATTCAAA
1 AAAAAAATTCAAA
6965 AAAAAAATT
1 AAAAAAATT
6974 GGTTTCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:7030 original size:15 final size:15
Alignment explanation
Indices: 7010--7064 Score: 92
Period size: 15 Copynumber: 3.5 Consensus size: 15
7000 GATATCAAGT
7010 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
7025 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
7040 TGAAAAAAAAATTTTCG
1 TGAAAAAAAAA--TTCG
7057 TGAAAAAA
1 TGAAAAAA
7065 GAAGAAGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 26 0.68
17 12 0.32
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.22
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:7034 original size:17 final size:17
Alignment explanation
Indices: 7012--7064 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
7002 TATCAAGTTG
7012 AAAAAAAAATTCGTG--
1 AAAAAAAAATTCGTGAA
7027 AAAAAAAAATTCGTGAA
1 AAAAAAAAATTCGTGAA
**
7044 AAAAAAATTTTCGTGAA
1 AAAAAAAAATTCGTGAA
7061 AAAA
1 AAAA
7065 GAAGAAGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
15 15 0.44
17 19 0.56
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (17 bp):
AAAAAAAAATTCGTGAA
Found at i:15019 original size:23 final size:22
Alignment explanation
Indices: 14968--15019 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
14958 CCTCGTCTTT
*
14968 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
14990 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
15013 TTCTTTT
1 TTCTTTT
15020 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
Found at i:18107 original size:12 final size:12
Alignment explanation
Indices: 18092--18154 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
18082 TCAAGCTCGC
18092 TTTCAATTTCTT
1 TTTCAATTTCTT
*
18104 TTTCTAGTCTTTCTT
1 TTTC-A--ATTTCTT
18119 TTTC---TTCTT
1 TTTCAATTTCTT
18128 TTTCAATTTCTT
1 TTTCAATTTCTT
*
18140 TTTCAATCTCTT
1 TTTCAATTTCTT
18152 TTT
1 TTT
18155 GCTTTTCACT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 9 0.21
12 23 0.53
13 1 0.02
15 10 0.23
ACGTcount: A:0.11, C:0.19, G:0.02, T:0.68
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:18213 original size:15 final size:14
Alignment explanation
Indices: 18193--18240 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
18183 CTCATTTTCA
18193 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
18208 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
*
18222 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTT
18237 TCTT
1 TCTT
18241 CTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:18245 original size:22 final size:21
Alignment explanation
Indices: 18193--18251 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
18183 CTCATTTTCA
* *
18193 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
18214 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
18235 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
18252 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:19143 original size:13 final size:11
Alignment explanation
Indices: 19122--19166 Score: 56
Period size: 10 Copynumber: 4.0 Consensus size: 11
19112 ATTGAATACC
19122 AATTTTTTTTA
1 AATTTTTTTTA
*
19133 AATAATTTTTTTC
1 AAT--TTTTTTTA
19146 AATTTTTTTT-
1 AATTTTTTTTA
19156 AATTTTTTTTA
1 AATTTTTTTTA
19167 CAATATCGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 10 0.33
11 10 0.33
13 10 0.33
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
AATTTTTTTTA
Found at i:20518 original size:55 final size:55
Alignment explanation
Indices: 20403--20519 Score: 148
Period size: 55 Copynumber: 2.1 Consensus size: 55
20393 TGCATGTTTT
* * *
20403 CATT-AATGCCGTCCATGCATGGGAACATCTCATTAAATCCATGTCTTTGCTTCC
1 CATTAAATGCCGTCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCTGCA
* * * *
20457 CTTTAAATGCCGTTCCATGCATGGGAACATCTCCTT-AATTCGTGGCTTTGCTGCA
1 CATTAAATGCCG-TCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCTGCA
20512 CATTAAAT
1 CATTAAAT
20520 CAGCAAGCAG
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
54 3 0.06
55 28 0.53
56 22 0.42
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (55 bp):
CATTAAATGCCGTCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCTGCA
Found at i:20740 original size:23 final size:22
Alignment explanation
Indices: 20706--20769 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 22
20696 GACACCATTT
*
20706 AAAACATGCATTAAATTCGGCC
1 AAAACATACATTAAATTCGGCC
20728 AGAAACATACATTAAATTCGGCC
1 A-AAACATACATTAAATTCGGCC
20751 AAAGACATACATTAAATTC
1 AAA-ACATACATTAAATTC
20770 ATCTGGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 3 0.08
23 36 0.92
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.23
Consensus pattern (22 bp):
AAAACATACATTAAATTCGGCC
Found at i:21007 original size:13 final size:13
Alignment explanation
Indices: 20991--21025 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
20981 TTTAAGCAAA
*
20991 TTAATTAACTTAT
1 TTAATTAACTAAT
21004 TTAATTAACTAAT
1 TTAATTAACTAAT
*
21017 TTAACTAAC
1 TTAATTAAC
21026 AGCAACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAACTAAT
Found at i:23748 original size:40 final size:39
Alignment explanation
Indices: 23657--23919 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
23647 TCCTCGTTCA
* * * *
23657 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
23696 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
23735 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
23775 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * * *
23815 AAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
23855 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
23896 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
23920 CAGCATTCAA
Statistics
Matches: 195, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
39 38 0.19
40 146 0.75
41 11 0.06
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:23865 original size:120 final size:119
Alignment explanation
Indices: 23657--23919 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
23647 TCCTCGTTCA
* * * *
23657 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGACT
* * *
23722 TAATAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTC-GGATCTTAACCCGGATATAATAACTTAGCAC
* * * *
23775 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACTTAACCCGG-
* * ** * *
23840 ACTT-GTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTAGCAC
63 ACTTAATAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAATAACTTAGCAC
*
23896 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
23920 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 76 0.63
121 8 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGACT
TAATAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAATAACTTAGCAC
Found at i:23928 original size:41 final size:41
Alignment explanation
Indices: 23851--23928 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
23841 CTTGTATCTC
* * *
23851 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
23892 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
23929 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:31349 original size:40 final size:39
Alignment explanation
Indices: 31258--31518 Score: 285
Period size: 40 Copynumber: 6.6 Consensus size: 39
31248 TCCTCGTTCA
* * * *
31258 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
31297 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
31336 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
31376 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
31416 AAAGGCCTTCGGG-CTTAACCCGGAATT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
** * * * *
31454 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
31495 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
31519 CAGCATTCAA
Statistics
Matches: 195, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
37 2 0.01
38 20 0.10
39 57 0.29
40 108 0.55
41 8 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:31359 original size:79 final size:79
Alignment explanation
Indices: 31258--31518 Score: 287
Period size: 79 Copynumber: 3.3 Consensus size: 79
31248 TCCTCGTTCA
* * * *
31258 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
31322 TTAATAACTCGCAC
66 TTAATAACTCGCAC
* *
31336 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
* *
31401 TTTAGTATCTCGCAC
65 TTTAATAACTCGCAC
* * * **
31416 AAAGGCCTTCGGG-CTTAACCCGGAATT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * * *
31478 ATATATTCACTTAGCAC
64 ATTTAATAAC-TCGCAC
* *
31495 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
31519 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
77 3 0.02
78 43 0.28
79 62 0.40
80 48 0.31
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
TTAATAACTCGCAC
Found at i:31527 original size:41 final size:41
Alignment explanation
Indices: 31450--31527 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
31440 ATTGTATCTC
* * *
31450 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
31491 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
31528 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.