Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1425
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: 32825
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3260 original size:56 final size:56
Alignment explanation
Indices: 3174--3349 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
3164 ACAAGGGATG
3174 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
3230 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
3286 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
3342 ATGGGCAA
1 ATGGGCAA
3350 TAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:4708 original size:40 final size:40
Alignment explanation
Indices: 4477--4701 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
4467 TCGAATGATG
* * * *
4477 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * **
4517 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGATACTAGT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
4557 TCCGGGCTAAG-CCCGAAGGCA-TTGATGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTG-TGCGAGTTACTAAA
*
4596 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
4636 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
4677 -CCGGGCTATGTCCCAAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
4702 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
38 3 0.02
39 29 0.18
40 117 0.73
41 12 0.07
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:4723 original size:119 final size:119
Alignment explanation
Indices: 4477--4724 Score: 274
Period size: 119 Copynumber: 2.1 Consensus size: 119
4467 TCGAATGATG
* *
4477 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* * *
4542 GTACGAGATACTAGTTCCGGGCTAAGCCCGAAGGCATTGATGCGAGTTACTAAA
66 GTACGAGATACTAGTACCGGGCTAAGCCCAAAGGCATTGATACGAGTTACTAAA
* * * **
4596 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
4659 TTGTGCGAGTTACTA-TAACCGGGCTATGTCCCAAAGGCATTTGA-ACGAG-TAGCTATA
64 TTGTACGAGATACTAGT-ACCGGGCTAAG-CCCAAAGGCA-TTGATACGAGTTA-CTAAA
4716 TCC-GGTTAA
1 TCCGGGTTAA
4725 ATTCTGAAGG
Statistics
Matches: 109, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
118 2 0.02
119 76 0.70
120 27 0.25
121 4 0.04
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTACGAGATACTAGTACCGGGCTAAGCCCAAAGGCATTGATACGAGTTACTAAA
Found at i:6111 original size:40 final size:40
Alignment explanation
Indices: 6067--6219 Score: 195
Period size: 40 Copynumber: 3.9 Consensus size: 40
6057 GGGGTGTTAC
*
6067 AGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTT
1 AGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTT
* * *
6107 AGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGAAATT
1 AGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTT
* *
6146 AGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATAT
1 AGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATTT
* *
6186 AGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 AGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
6220 TGACATCATT
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.33
40 52 0.54
41 11 0.11
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
AGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTT
Found at i:6206 original size:79 final size:80
Alignment explanation
Indices: 6067--6219 Score: 213
Period size: 79 Copynumber: 1.9 Consensus size: 80
6057 GGGGTGTTAC
* * *
6067 AGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG
1 AGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCGGG
6132 -CTTAGCCCGAAATT
66 ACTTAGCCCGAAATT
** *
6146 AGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA-CAAAGCCTTCG
1 AGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACCAAAGCCTTCG
6209 GGACTTAGCCC
64 GGACTTAGCCC
6220 TGACATCATT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
78 3 0.05
79 50 0.77
80 12 0.18
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (80 bp):
AGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCGGG
ACTTAGCCCGAAATT
Found at i:10385 original size:19 final size:18
Alignment explanation
Indices: 10363--10434 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 18
10353 TTTTCCAACT
10363 ATTTTGAAATAAAATTTTG
1 ATTTTGAAA-AAAATTTTG
* **
10382 ATTTTTAAGAAAAATAGTG
1 ATTTTGAA-AAAAATTTTG
* *
10401 ATTTTTTAAAGAAAACTTTG
1 A-TTTTGAAA-AAAATTTTG
10421 ATTTTGCAAAAAAA
1 ATTTTG-AAAAAAA
10435 ATAAAATAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 24 0.57
20 18 0.43
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (18 bp):
ATTTTGAAAAAAATTTTG
Found at i:10422 original size:20 final size:19
Alignment explanation
Indices: 10373--10425 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
10363 ATTTTGAAAT
*
10373 AAAATTTTGA-TTTTTAAG
1 AAAAATTTGATTTTTTAAG
*
10391 AAAAATAGTGATTTTTTAAAG
1 AAAAAT-TTGATTTTTT-AAG
*
10412 AAAACTTTGATTTT
1 AAAAATTTGATTTT
10426 GCAAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 5 0.18
19 3 0.11
20 12 0.43
21 8 0.29
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (19 bp):
AAAAATTTGATTTTTTAAG
Found at i:12498 original size:18 final size:18
Alignment explanation
Indices: 12468--12519 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
12458 ATTATTATGG
* *
12468 CGAACTGTGTTAATTTGG
1 CGAACTGTATTAATTTGA
* * *
12486 TGATCTGTATTAATATGA
1 CGAACTGTATTAATTTGA
12504 CGAACTGTATTAATTT
1 CGAACTGTATTAATTT
12520 TTCAAAATGT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (18 bp):
CGAACTGTATTAATTTGA
Found at i:13213 original size:17 final size:17
Alignment explanation
Indices: 13193--13247 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
13183 GAATGGATTA
13193 TTATATTGAATGAACTG
1 TTATATTGAATGAACTG
* * *
13210 TTATAATGTATAAACTG
1 TTATATTGAATGAACTG
*
13227 TTATATTGAGTGAACTG
1 TTATATTGAATGAACTG
13244 TTAT
1 TTAT
13248 TTTATGCGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (17 bp):
TTATATTGAATGAACTG
Found at i:13921 original size:75 final size:75
Alignment explanation
Indices: 13798--14010 Score: 363
Period size: 75 Copynumber: 2.8 Consensus size: 75
13788 TTAATCATGA
* *
13798 GTTTAGTTTGCATGAAATGTAAAATTGGATAAATTATGTAAATAGCAGGTGGCTTATGAACTAAT
1 GTTTAGTTTGCATGAAATGTAAAATTGGACAAATTATGTAAATAGCAGGTGGCCTATGAACTAAT
*
13863 TAGATAATTT
66 TAAATAATTT
13873 GTTTAGTTTGCATGAAATGTAAAATTGGACAAATTATGTAAATAGCAGGTGGCCTATGAACTAAT
1 GTTTAGTTTGCATGAAATGTAAAATTGGACAAATTATGTAAATAGCAGGTGGCCTATGAACTAAT
13938 TAAATAATTT
66 TAAATAATTT
* * **
13948 GTTTAGTTTGTATGAAATGTAAAATTGGACAAATTGTGTAAATAATAGGTGGCCTATGAACTA
1 GTTTAGTTTGCATGAAATGTAAAATTGGACAAATTATGTAAATAGCAGGTGGCCTATGAACTA
14011 TACTATTTTC
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 131 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.36
Consensus pattern (75 bp):
GTTTAGTTTGCATGAAATGTAAAATTGGACAAATTATGTAAATAGCAGGTGGCCTATGAACTAAT
TAAATAATTT
Found at i:16452 original size:38 final size:40
Alignment explanation
Indices: 16412--16491 Score: 115
Period size: 44 Copynumber: 1.9 Consensus size: 40
16402 TTCTACATTC
*
16412 ACCATGACTTATCAATATCAAACGTTTTCTCAACCATCACCA
1 ACCATGACTTATCAATATCAAACGTTTACTCAACCAT--CCA
16454 TGACCATGACTTATCAATATCAAACGTTTACTCAACCA
1 --ACCATGACTTATCAATATCAAACGTTTACTCAACCA
16492 AACATGGCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.36, C:0.29, G:0.06, T:0.29
Consensus pattern (40 bp):
ACCATGACTTATCAATATCAAACGTTTACTCAACCATCCA
Found at i:16748 original size:41 final size:41
Alignment explanation
Indices: 16698--16780 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
16688 TAGAAAGTTC
16698 ATATCTAAATAACAAGTAACATAACAATACAAATATACCAA
1 ATATCTAAATAACAAGTAACATAACAATACAAATATACCAA
*
16739 ATATGTAAATAACAAGTAACATAACAATACAAATATACCAA
1 ATATCTAAATAACAAGTAACATAACAATACAAATATACCAA
16780 A
1 A
16781 CAACTTTAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.59, C:0.16, G:0.04, T:0.22
Consensus pattern (41 bp):
ATATCTAAATAACAAGTAACATAACAATACAAATATACCAA
Found at i:17132 original size:46 final size:46
Alignment explanation
Indices: 17064--17234 Score: 288
Period size: 46 Copynumber: 3.7 Consensus size: 46
17054 AACCAGCCCC
17064 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
*
17110 TAAGTGAACTCGGACTCGACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
* * *
17156 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
* *
17202 TAAGTGAACTTGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGG
17235 ATGCTCAACC
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 119 1.00
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
Found at i:21960 original size:21 final size:21
Alignment explanation
Indices: 21936--21983 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
21926 GGGCACACAT
21936 CCGTATGGAAGCGCAACACGC
1 CCGTATGGAAGCGCAACACGC
** * *
21957 CCGTGCGGAAGGGCAATACGC
1 CCGTATGGAAGCGCAACACGC
21978 CC-TATG
1 CCGTATG
21984 TCCTTCACCC
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.25, C:0.31, G:0.31, T:0.12
Consensus pattern (21 bp):
CCGTATGGAAGCGCAACACGC
Found at i:23712 original size:27 final size:27
Alignment explanation
Indices: 23682--23859 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
23672 ATATTGAGCC
* *
23682 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
23709 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
23736 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
23764 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
23791 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
23818 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
23845 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
23860 GTACAATTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 104 0.81
28 25 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:23821 original size:82 final size:81
Alignment explanation
Indices: 23703--23858 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
23693 TGCTATATAA
* * *
23703 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTC-GAATCGCA
23768 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
23785 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCA
23849 CACTTAGTGC
65 CACTTAGTGC
23859 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:31712 original size:27 final size:27
Alignment explanation
Indices: 31682--31859 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
31672 ATATTGAGCC
* *
31682 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
31709 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
31736 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
31764 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
31791 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
31818 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
31845 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31860 GTACAATTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 104 0.81
28 25 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:31821 original size:82 final size:81
Alignment explanation
Indices: 31703--31858 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
31693 TGCTATATAA
* *
31703 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
31768 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
31785 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31849 CACTTAGTGC
65 CACTTAGTGC
31859 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.