Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold518
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: 97151
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 7441 characters in sequence are not A, C, G, or T
Found at i:251 original size:40 final size:40
Alignment explanation
Indices: 196--274 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
186 GTAATATAGC
196 AAATAAGAAATGAAAAACAAAGAAATTGAAGGAAAATAAG
1 AAATAAGAAATGAAAAACAAAGAAATTGAAGGAAAATAAG
236 AAATAAGAAATGAAAAACAAAGAAATTGAAGGAAAATAA
1 AAATAAGAAATGAAAAACAAAGAAATTGAAGGAAAATAA
275 TAAACTAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.68, C:0.03, G:0.16, T:0.13
Consensus pattern (40 bp):
AAATAAGAAATGAAAAACAAAGAAATTGAAGGAAAATAAG
Found at i:5053 original size:3 final size:3
Alignment explanation
Indices: 5047--5078 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5037 TGATGACAAT
*
5047 GAA GAA GAA GAA GAA GAA GAA GAG GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
5079 GGAGAATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:6833 original size:3 final size:3
Alignment explanation
Indices: 6827--6856 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6817 TTATTATTAT
6827 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
6857 AATTGTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TAG
Found at i:22658 original size:5 final size:5
Alignment explanation
Indices: 22613--22642 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
22603 TTATTATCTC
*
22613 ATTTT ATTTT ATTTT ACTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
22643 TTTGTGGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:23825 original size:31 final size:32
Alignment explanation
Indices: 23787--23848 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
23777 NNNNNNNNNN
23787 AAAGAG-TTTTATTAGGATTCAATTACTCTTT
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTT
23818 AAAGAGTTTTTATTAGGATTCAATTACTCTT
1 AAAGAGTTTTTATTAGGATTCAATTACTCTT
23849 GTAATTTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 6 0.20
32 24 0.80
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (32 bp):
AAAGAGTTTTTATTAGGATTCAATTACTCTTT
Found at i:34565 original size:7 final size:7
Alignment explanation
Indices: 34555--34586 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
34545 TTATATACAT
34555 AATACTA
1 AATACTA
34562 AATACTA
1 AATACTA
34569 AATACTA
1 AATACTA
*
34576 AATACAA
1 AATACTA
34583 AATA
1 AATA
34587 TCTATTTGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (7 bp):
AATACTA
Found at i:34572 original size:14 final size:14
Alignment explanation
Indices: 34549--34586 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
34539 TATTAGTTAT
*
34549 ATACATAATACTAA
1 ATACAAAATACTAA
*
34563 ATACTAAATACTAA
1 ATACAAAATACTAA
34577 ATACAAAATA
1 ATACAAAATA
34587 TCTATTTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (14 bp):
ATACAAAATACTAA
Found at i:35727 original size:51 final size:51
Alignment explanation
Indices: 35670--35790 Score: 181
Period size: 51 Copynumber: 2.4 Consensus size: 51
35660 TTTTAAAAAG
* * * *
35670 GAAATTGAGAGCAAATTGAAATTAAATATGGGTTTGA-GAGATTTTTGGAAT
1 GAAATTGAGAGAAAATTGAAATTAAATATGGATTT-ATGAGAATTTTGGAAA
*
35721 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTATGAGAATTTTGGAAA
1 GAAATTGAGAGAAAATTGAAATTAAATATGGATTTATGAGAATTTTGGAAA
35772 GAAATTGAGAGAAAATTGA
1 GAAATTGAGAGAAAATTGA
35791 GAGGAAATTG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 1 0.02
51 63 0.98
ACGTcount: A:0.44, C:0.01, G:0.25, T:0.31
Consensus pattern (51 bp):
GAAATTGAGAGAAAATTGAAATTAAATATGGATTTATGAGAATTTTGGAAA
Found at i:35789 original size:11 final size:11
Alignment explanation
Indices: 35773--35817 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
35763 TTTTGGAAAG
35773 AAATTGAGAGA
1 AAATTGAGAGA
*
35784 AAATTGAGAGG
1 AAATTGAGAGA
*
35795 AAATTGAGAGG
1 AAATTGAGAGA
35806 AAATATGAGAGA
1 AAAT-TGAGAGA
35818 GGATTTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 25 0.81
12 6 0.19
ACGTcount: A:0.51, C:0.00, G:0.31, T:0.18
Consensus pattern (11 bp):
AAATTGAGAGA
Found at i:35797 original size:22 final size:23
Alignment explanation
Indices: 35772--35816 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
35762 ATTTTGGAAA
35772 GAAATTGAGAGAAAAT-TGAGAG
1 GAAATTGAGAGAAAATATGAGAG
*
35794 GAAATTGAGAGGAAATATGAGAG
1 GAAATTGAGAGAAAATATGAGAG
35817 AGGATTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.49, C:0.00, G:0.33, T:0.18
Consensus pattern (23 bp):
GAAATTGAGAGAAAATATGAGAG
Found at i:37227 original size:25 final size:27
Alignment explanation
Indices: 37199--37249 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
37189 GTTATATATT
*
37199 AAATATA-TATT-TTTTATTTTTAATC
1 AAATATACTATTGTTTTATTATTAATC
*
37224 AAATATACTTTTGTTTTATTATTAAT
1 AAATATACTATTGTTTTATTATTAAT
37250 TTGGCTATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 3 0.14
27 12 0.55
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (27 bp):
AAATATACTATTGTTTTATTATTAATC
Found at i:44234 original size:11 final size:11
Alignment explanation
Indices: 44218--44275 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 11
44208 AAATTATATA
44218 TTAAAATAAAT
1 TTAAAATAAAT
44229 TTAAAATAAAT
1 TTAAAATAAAT
44240 AATATATAAATGAAAAT
1 --T-TA-AAAT--AAAT
*
44257 TTGAAATAAAT
1 TTAAAATAAAT
44268 TTAAAATA
1 TTAAAATA
44276 CGGTTAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
11 22 0.56
13 5 0.13
14 3 0.08
15 5 0.13
17 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
TTAAAATAAAT
Found at i:44239 original size:28 final size:27
Alignment explanation
Indices: 44203--44268 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
44193 AATACGAAAG
*
44203 AAAAGAAATTATATATTAAA-ATAAATTT
1 AAAATAAATTATATA-TAAATA-AAATTT
*
44231 AAAATAAATAATATATAAATGAAAATTT
1 AAAATAAATTATATATAAAT-AAAATTT
*
44259 GAAATAAATT
1 AAAATAAATT
44269 TAAAATACGG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 4 0.12
28 27 0.84
29 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (27 bp):
AAAATAAATTATATATAAATAAAATTT
Found at i:44650 original size:15 final size:15
Alignment explanation
Indices: 44632--44662 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44622 CTAATAGTTC
*
44632 TAATAACATTAATAA
1 TAATAACAATAATAA
44647 TAATAACAATAATAA
1 TAATAACAATAATAA
44662 T
1 T
44663 GAAAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (15 bp):
TAATAACAATAATAA
Found at i:51127 original size:43 final size:42
Alignment explanation
Indices: 51091--51172 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 42
51081 CTTACATGTT
*
51091 ATCAAATATCGATGCC-ACTGTCCCAGACAGGGTCTTAGACGAA
1 ATCAAATA-CGATGCCGA-TGTCCCAGACAGGGTCTTACACGAA
* *
51134 ATCATATACGATGCCGATGTCCCAGACATGGTCTTACAC
1 ATCAAATACGATGCCGATGTCCCAGACAGGGTCTTACAC
51173 AATATCACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 27 0.77
43 8 0.23
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (42 bp):
ATCAAATACGATGCCGATGTCCCAGACAGGGTCTTACACGAA
Found at i:54314 original size:33 final size:33
Alignment explanation
Indices: 54272--54373 Score: 102
Period size: 32 Copynumber: 3.1 Consensus size: 33
54262 CTCTGTTTGT
*
54272 TGTGATGGTTGT-TTTAACTTTTATGAGCATTAG
1 TGTGATGGTTGTGTTTAAC-TCTATGAGCATTAG
* *
54305 TGTGATGGTT-TGTTTAGCTCTATGAGCATTGG
1 TGTGATGGTTGTGTTTAACTCTATGAGCATTAG
* * * *
54337 TGTGATGGTTG-GATTAGCTCTTATGAACATTGG
1 TGTGATGGTTGTGTTTAACTC-TATGAGCATTAG
54370 TGTG
1 TGTG
54374 TTGGAGGGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
32 31 0.51
33 30 0.49
ACGTcount: A:0.19, C:0.08, G:0.29, T:0.44
Consensus pattern (33 bp):
TGTGATGGTTGTGTTTAACTCTATGAGCATTAG
Found at i:54334 original size:32 final size:33
Alignment explanation
Indices: 54272--54373 Score: 125
Period size: 33 Copynumber: 3.1 Consensus size: 33
54262 CTCTGTTTGT
** * * *
54272 TGTGATGGTTGTTTTAACTTTTATGAGCATTAG
1 TGTGATGGTTGGATTAGCTCTTATGAGCATTGG
* *
54305 TGTGATGGTTTGTTTAGCTC-TATGAGCATTGG
1 TGTGATGGTTGGATTAGCTCTTATGAGCATTGG
*
54337 TGTGATGGTTGGATTAGCTCTTATGAACATTGG
1 TGTGATGGTTGGATTAGCTCTTATGAGCATTGG
54370 TGTG
1 TGTG
54374 TTGGAGGGAT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 29 0.48
33 31 0.52
ACGTcount: A:0.19, C:0.08, G:0.29, T:0.44
Consensus pattern (33 bp):
TGTGATGGTTGGATTAGCTCTTATGAGCATTGG
Found at i:54384 original size:33 final size:32
Alignment explanation
Indices: 54318--54384 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 32
54308 GATGGTTTGT
* **
54318 TTAGCTCTATGAGCATTGGTGTGATGGTTGGA
1 TTAGCTCTATGAACATTGGTGTGATGGAGGGA
*
54350 TTAGCTCTTATGAACATTGGTGTGTTGGAGGGA
1 TTAGCTC-TATGAACATTGGTGTGATGGAGGGA
54383 TT
1 TT
54385 GACTTGGGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 7 0.23
33 23 0.77
ACGTcount: A:0.19, C:0.09, G:0.33, T:0.39
Consensus pattern (32 bp):
TTAGCTCTATGAACATTGGTGTGATGGAGGGA
Found at i:56768 original size:41 final size:41
Alignment explanation
Indices: 56711--56792 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
56701 CCTGAGTCCA
*
56711 AATCATGCAAATTAACCATTTTTAATACAAACCCATGCTAG
1 AATCATGCAAATTAACCATTTCTAATACAAACCCATGCTAG
56752 AATCATGCAAATTAACCATTTCTAATACAAACCCATGCTAG
1 AATCATGCAAATTAACCATTTCTAATACAAACCCATGCTAG
56793 CAAAATATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.28
Consensus pattern (41 bp):
AATCATGCAAATTAACCATTTCTAATACAAACCCATGCTAG
Found at i:62963 original size:11 final size:11
Alignment explanation
Indices: 62947--62980 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
62937 GAATGAATAG
62947 TTGGACATGTT
1 TTGGACATGTT
62958 TTGGACATGTT
1 TTGGACATGTT
62969 TTGTG-CATGTT
1 TTG-GACATGTT
62980 T
1 T
62981 GAATGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 21 0.95
12 1 0.05
ACGTcount: A:0.15, C:0.09, G:0.26, T:0.50
Consensus pattern (11 bp):
TTGGACATGTT
Found at i:69685 original size:31 final size:31
Alignment explanation
Indices: 69650--69711 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
69640 AAACACAAAT
69650 TTAACAAAACAA-TACATACTAACAGTTAAAC
1 TTAACAAAACAATTA-ATACTAACAGTTAAAC
*
69681 TTAACAAAACAATTAATGCTAACAGTTAAAC
1 TTAACAAAACAATTAATACTAACAGTTAAAC
69712 CTAAATGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.53, C:0.18, G:0.05, T:0.24
Consensus pattern (31 bp):
TTAACAAAACAATTAATACTAACAGTTAAAC
Found at i:80082 original size:1 final size:1
Alignment explanation
Indices: 80078--80106 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
80068 GAGGGAAAAA
80078 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
80107 TTGATCCTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:88872 original size:26 final size:26
Alignment explanation
Indices: 88843--88908 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
88833 CTTAAACCAA
*
88843 ACTTTTCAAAAGTACT-TATCAAAATC
1 ACTTTTCAAAAGTA-TATATCAAAAAC
* * *
88869 ACTTTTCGAAAGTATATTTTAAAAAC
1 ACTTTTCAAAAGTATATATCAAAAAC
*
88895 ACTTCTCAAAAGTA
1 ACTTTTCAAAAGTA
88909 ATGCTAAACT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 1 0.03
26 32 0.97
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (26 bp):
ACTTTTCAAAAGTATATATCAAAAAC
Found at i:94934 original size:16 final size:15
Alignment explanation
Indices: 94913--94965 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 15
94903 AGAATTACCT
94913 ATTACGTCTCTATTCC
1 ATTACG-CTCTATTCC
94929 ATTACGCATCTATTCC
1 ATTACGC-TCTATTCC
*
94945 ATTACACCTCTATTCC
1 ATTAC-GCTCTATTCC
94961 ATTAC
1 ATTAC
94966 AACGAACCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
15 1 0.03
16 32 0.94
17 1 0.03
ACGTcount: A:0.25, C:0.32, G:0.04, T:0.40
Consensus pattern (15 bp):
ATTACGCTCTATTCC
Found at i:94966 original size:16 final size:16
Alignment explanation
Indices: 94920--94966 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
94910 CCTATTACGT
*
94920 CTCTATTCCATTACGC
1 CTCTATTCCATTACAC
*
94936 ATCTATTCCATTACAC
1 CTCTATTCCATTACAC
94952 CTCTATTCCATTACA
1 CTCTATTCCATTACA
94967 ACGAACCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.26, C:0.34, G:0.02, T:0.38
Consensus pattern (16 bp):
CTCTATTCCATTACAC
Found at i:96450 original size:16 final size:16
Alignment explanation
Indices: 96429--96460 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
96419 ATATACAAGG
96429 TATTAAAATCACATGA
1 TATTAAAATCACATGA
96445 TATTAAAATCACATGA
1 TATTAAAATCACATGA
96461 CAAGCAGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (16 bp):
TATTAAAATCACATGA
Done.