Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2281
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: 210577
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
File 2 of 2
Found at i:155704 original size:29 final size:29
Alignment explanation
Indices: 155613--155708 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 29
155603 ATCATTTTTT
155613 TTAAATAAATTTTTATACTTTT-A-TTATAC
1 TTAAATAAA-TTTT-TACTTTTAATTTATAC
* * ** * *
155642 TCAAATTAATCCTTA-TTATAATTTTTAC
1 TTAAATAAATTTTTACTTTTAATTTATAC
* *
155670 TAAAATAAATTTTTACTTTTAATTTATAT
1 TTAAATAAATTTTTACTTTTAATTTATAC
155699 TTAAATAAAT
1 TTAAATAAAT
155709 CAATATTTTT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
26 3 0.06
27 3 0.06
28 18 0.36
29 26 0.52
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (29 bp):
TTAAATAAATTTTTACTTTTAATTTATAC
Found at i:155887 original size:4 final size:4
Alignment explanation
Indices: 155880--155910 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
155870 AATGGAGGTG
155880 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
155911 CCAGTGAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:156233 original size:18 final size:18
Alignment explanation
Indices: 156198--156232 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
156188 CAAGACTTGA
156198 AAATTATAATAATATTTT
1 AAATTATAATAATATTTT
*
156216 AAATTGTAA-AATATTTT
1 AAATTATAATAATATTTT
156233 TTTTTACTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AAATTATAATAATATTTT
Found at i:156576 original size:20 final size:21
Alignment explanation
Indices: 156547--156587 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
156537 ATATTTAAAA
156547 TTTTAATATATTTA-ATAATT
1 TTTTAATATATTTATATAATT
*
156567 TTTTATTATATTTATATAATT
1 TTTTAATATATTTATATAATT
156588 ATATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAATATATTTATATAATT
Found at i:157496 original size:28 final size:27
Alignment explanation
Indices: 157442--157496 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
157432 CCTTAAAAGG
*
157442 TATTATTTAAGTTTAGAATTAATATTA
1 TATTATTTAAGTTTAGAATGAATATTA
*
157469 TATTA-TTAAGATTTAAGAATGAGTATTA
1 TATTATTTAAG-TTT-AGAATGAATATTA
157497 GATATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 8 0.33
28 11 0.46
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (27 bp):
TATTATTTAAGTTTAGAATGAATATTA
Found at i:157577 original size:25 final size:26
Alignment explanation
Indices: 157524--157577 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
157514 AATTGTATTT
* *
157524 AAAATTATTTTTAATTTTTTTATCAA
1 AAAATTATTTTTAATTTATATATCAA
157550 AAAATTATTTTTATATTTATAT-TCAA
1 AAAATTATTTTTA-ATTTATATATCAA
157576 AA
1 AA
157578 TATATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (26 bp):
AAAATTATTTTTAATTTATATATCAA
Found at i:157583 original size:25 final size:24
Alignment explanation
Indices: 157519--157583 Score: 60
Period size: 26 Copynumber: 2.6 Consensus size: 24
157509 TATTCAATTG
* *
157519 TATTTAAAAT-TATTTTTAATTTT
1 TATTCAAAATATATTTTTAATTTA
* *
157542 TTTATCAAAAAATTATTTTTATATTTA
1 TAT-TCAAAATA-TATTTTTA-ATTTA
157569 TATTCAAAATATATT
1 TATTCAAAATATATT
157584 AAATATAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
23 2 0.06
24 5 0.16
25 4 0.12
26 15 0.47
27 6 0.19
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTCAAAATATATTTTTAATTTA
Found at i:158368 original size:2 final size:2
Alignment explanation
Indices: 158361--158399 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
158351 TTATAATGCC
158361 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
158400 CAAACACAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:161143 original size:17 final size:17
Alignment explanation
Indices: 161117--161149 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
161107 AATAAAATGC
*
161117 TATTATTATAAATAATA
1 TATTAATATAAATAATA
161134 TATTAATATAAATAAT
1 TATTAATATAAATAAT
161150 TTTAAATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATTAATATAAATAATA
Found at i:163148 original size:27 final size:27
Alignment explanation
Indices: 163112--163165 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
163102 CATAAGAGAA
163112 AAAAATCGAATATTTAGGTTATATTGT
1 AAAAATCGAATATTTAGGTTATATTGT
163139 AAAAATCGAATATTTAGGTTATATTGT
1 AAAAATCGAATATTTAGGTTATATTGT
163166 GTGTGGGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.41
Consensus pattern (27 bp):
AAAAATCGAATATTTAGGTTATATTGT
Found at i:169584 original size:18 final size:18
Alignment explanation
Indices: 169563--169599 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
169553 AAAAGATAAA
169563 TTATATTATTTTTAATTT
1 TTATATTATTTTTAATTT
169581 TTATATTATTTTTAATTT
1 TTATATTATTTTTAATTT
169599 T
1 T
169600 AAAACATCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTATATTATTTTTAATTT
Found at i:170379 original size:14 final size:13
Alignment explanation
Indices: 170335--170381 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
170325 CGATTACAAC
170335 TTAAATTAAAATT
1 TTAAATTAAAATT
**
170348 TTAAATTAAATAAA
1 TTAAATTAAA-ATT
170362 TTAAATTAACAATT
1 TTAAATTAA-AATT
170376 TTAAAT
1 TTAAAT
170382 AATTACATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 10 0.36
14 17 0.61
15 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
TTAAATTAAAATT
Found at i:171596 original size:28 final size:28
Alignment explanation
Indices: 171564--171618 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
171554 TAAATGACAC
*
171564 CCTTTGTATTTGTGAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
171592 CCTTTGTATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
171619 ATTTTTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.18, C:0.09, G:0.24, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:174643 original size:21 final size:21
Alignment explanation
Indices: 174617--174662 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
174607 AAAGTAAAAT
*
174617 TACTAAAAT-ACGCTTAAGGTA
1 TACTAAAATAAC-CTTAAAGTA
174638 TACTAAAATAACCTTAAAGTA
1 TACTAAAATAACCTTAAAGTA
174659 TACT
1 TACT
174663 TTTGACATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (21 bp):
TACTAAAATAACCTTAAAGTA
Found at i:174815 original size:29 final size:29
Alignment explanation
Indices: 174783--174838 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
174773 CTATTAAGTC
174783 ACTAAACTTTTCAAAACTACATTTTGACA
1 ACTAAACTTTTCAAAACTACATTTTGACA
* ** *
174812 ACTAACCTTTTTGAAATTACATTTTGA
1 ACTAAACTTTTCAAAACTACATTTTGA
174839 TCCCAAAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (29 bp):
ACTAAACTTTTCAAAACTACATTTTGACA
Found at i:177782 original size:21 final size:20
Alignment explanation
Indices: 177744--177782 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
177734 TCTAGTAGTC
**
177744 TAAAAATAATTATGATATAA
1 TAAAAATAATTAAAATATAA
177764 TAAAAATAATTTAAAATAT
1 TAAAAATAA-TTAAAATAT
177783 TTTATTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAAAATAATTAAAATATAA
Found at i:178495 original size:21 final size:21
Alignment explanation
Indices: 178445--178513 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
178435 AGTGATACGA
*
178445 ATATAAAAATATATCAA-AATT
1 ATATAAAAATAAAT-AATAATT
*
178466 -TATATAAAATAAATTATTAA-T
1 ATATA-AAAATAAA-TAATAATT
*
178487 ATATAAAAATTAATAATAATT
1 ATATAAAAATAAATAATAATT
178508 ATATAA
1 ATATAA
178514 TACATGATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
20 9 0.23
21 23 0.59
22 7 0.18
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAAAAATAAATAATAATT
Found at i:179517 original size:19 final size:20
Alignment explanation
Indices: 179494--179547 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
179484 AGGTTTTTTT
179494 TACATAATATTATTACAATTACA
1 TACAT-ATATTA-TA-AATTACA
179517 TACATATATTATAAATTACA
1 TACATATATTATAAATTACA
*
179537 TATA-ATATTAT
1 TACATATATTAT
179548 CTTGATATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 7 0.23
20 10 0.33
21 2 0.07
22 6 0.20
23 5 0.17
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (20 bp):
TACATATATTATAAATTACA
Found at i:179595 original size:67 final size:65
Alignment explanation
Indices: 179493--179739 Score: 188
Period size: 67 Copynumber: 3.8 Consensus size: 65
179483 TAGGTTTTTT
* * * *
179493 TTACATAATATTATTAC-AATTACATACATATATTATAAATTACATATAATATTATCTTGATATG
1 TTACATAA-AATATTACAAATTACATATAAATATTATAAGTTACATATAATATTATCTT-ATATG
179557 TAA
64 -AA
* * * * *
179560 TTACATAAAATATTACAAATTATATATAAACATTATTAGTTACAAATAATATT-GC--A-A-G--
1 TTACATAAAATATTACAAATTACATATAAATATTATAAGTTACATATAATATTATCTTATATGAA
* * *
179618 TTACATAAAAATATTACTAATTACAAATAATTATTATAAGTTACATA-AATCATTATCTTTATAT
1 TTACAT-AAAATATTACAAATTACATATAAATATTATAAGTTACATATAAT-ATTATC-TTATAT
179682 GCAA
63 G-AA
* * * * ** * *
179686 TTATATAAAACATTAAAAATTAAATATAAATATTACCAGTTACAAAAAATATTA
1 TTACATAAAATATTACAAATTACATATAAATATTATAAGTTACATATAATATTA
179740 CTTTTACATG
Statistics
Matches: 140, Mismatches: 27, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
58 9 0.06
59 36 0.26
60 1 0.01
61 1 0.01
62 1 0.01
63 2 0.01
64 1 0.01
65 1 0.01
66 8 0.06
67 72 0.51
68 8 0.06
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.38
Consensus pattern (65 bp):
TTACATAAAATATTACAAATTACATATAAATATTATAAGTTACATATAATATTATCTTATATGAA
Found at i:179611 original size:39 final size:39
Alignment explanation
Indices: 179557--179666 Score: 114
Period size: 39 Copynumber: 2.8 Consensus size: 39
179547 TCTTGATATG
* * *
179557 TAATTACATAA-AATATTACAAATTATATATAAACATTAT
1 TAATTACA-AATAATATTACAAATTACATAAAAACATTAC
* * * *
179596 TAGTTACAAATAATATTGCAAGTTACATAAAAATATTAC
1 TAATTACAAATAATATTACAAATTACATAAAAACATTAC
* *
179635 TAATTACAAATAATTATTATAAGTTACATAAA
1 TAATTACAAATAA-TATTACAAATTACATAAA
179667 TCATTATCTT
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
38 2 0.03
39 41 0.69
40 16 0.27
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (39 bp):
TAATTACAAATAATATTACAAATTACATAAAAACATTAC
Found at i:179641 original size:20 final size:20
Alignment explanation
Indices: 179557--179666 Score: 77
Period size: 20 Copynumber: 5.6 Consensus size: 20
179547 TCTTGATATG
179557 TAATTACAT-AAAATATTAC
1 TAATTACATAAAAATATTAC
* * * * *
179576 AAATTATATATAAACATTAT
1 TAATTACATAAAAATATTAC
* * *
179596 TAGTTACA-AATAATATTGC
1 TAATTACATAAAAATATTAC
179615 -AAGTTACATAAAAATATTAC
1 TAA-TTACATAAAAATATTAC
*
179635 TAATTACA-AATAATTATTA-
1 TAATTACATAA-AAATATTAC
179654 TAAGTTACATAAA
1 TAA-TTACATAAA
179667 TCATTATCTT
Statistics
Matches: 67, Mismatches: 17, Indels: 13
0.69 0.18 0.13
Matches are distributed among these distances:
18 1 0.01
19 23 0.34
20 39 0.58
21 4 0.06
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (20 bp):
TAATTACATAAAAATATTAC
Found at i:179655 original size:126 final size:125
Alignment explanation
Indices: 179493--179738 Score: 318
Period size: 126 Copynumber: 2.0 Consensus size: 125
179483 TAGGTTTTTT
* *
179493 TTACATAATATTATTACAATTACATACATATATTATAAATTACATATAAT-ATTATCTTGATATG
1 TTACATAAAAATATTACAATTACATACATATATTATAAATTACATA-AATCATTATCTTGATATG
* * * * ** *
179557 TAATTACATAAAATATTACAAATTATATATAAACATTATTAGTTACAAATAATATTGCAAG
65 CAATTACATAAAACATTAAAAATTAAATATAAACATTACCAGTTACAAAAAATATTGCAAG
* *
179618 TTACATAAAAATATTACTAATTACA-A-ATAATTATTATAAGTTACATAAATCATTATCTTTATA
1 TTACATAAAAATATTAC-AATTACATACAT-A-TATTATAAATTACATAAATCATTATCTTGATA
* *
179681 TGCAATTATATAAAACATTAAAAATTAAATATAAATATTACCAGTTACAAAAAATATT
63 TGCAATTACATAAAACATTAAAAATTAAATATAAACATTACCAGTTACAAAAAATATT
179739 ACTTTTACAT
Statistics
Matches: 104, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
124 2 0.02
125 20 0.19
126 82 0.79
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (125 bp):
TTACATAAAAATATTACAATTACATACATATATTATAAATTACATAAATCATTATCTTGATATGC
AATTACATAAAACATTAAAAATTAAATATAAACATTACCAGTTACAAAAAATATTGCAAG
Found at i:180561 original size:18 final size:17
Alignment explanation
Indices: 180516--180565 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
180506 GTGTTTGCAT
* *
180516 TTATATATTTTTATAAA
1 TTATATATATTTAAAAA
180533 TTATAATTATATTTAAAATA
1 TTAT-A-TATATTTAAAA-A
180553 TTATATATATTTA
1 TTATATATATTTA
180566 TTTAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 4 0.14
18 9 0.32
19 10 0.36
20 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATATATTTAAAAA
Found at i:180580 original size:15 final size:15
Alignment explanation
Indices: 180560--180607 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
180550 ATATTATATA
180560 TATTTATTTAAATTT
1 TATTTATTTAAATTT
*
180575 TATTTA-TCAAATATT
1 TATTTATTTAAAT-TT
*
180590 TATATTATATAAATTT
1 TAT-TTATTTAAATTT
180606 TA
1 TA
180608 ACATATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 5 0.19
15 11 0.41
16 7 0.26
17 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTTATTTAAATTT
Found at i:180599 original size:11 final size:11
Alignment explanation
Indices: 180533--180643 Score: 50
Period size: 11 Copynumber: 10.1 Consensus size: 11
180523 TTTTTATAAA
180533 TTATAATTATAT
1 TTAT-ATTATAT
* *
180545 TTAAAATATTAT
1 TTATATTA-TAT
*
180557 ATATATT-TAT
1 TTATATTATAT
* *
180567 TTAAATTTTAT
1 TTATATTATAT
*
180578 TTATCA-AATAT
1 TTAT-ATTATAT
180589 TTATATTATAT
1 TTATATTATAT
** * *
180600 AAATTTTA-AC
1 TTATATTATAT
*
180610 ATAT-TTATATT
1 TTATATTATA-T
*
180621 TTACATTATAT
1 TTATATTATAT
180632 TTATATTATAT
1 TTATATTATAT
180643 T
1 T
180644 ACATTTTAAT
Statistics
Matches: 72, Mismatches: 20, Indels: 15
0.67 0.19 0.14
Matches are distributed among these distances:
9 3 0.04
10 14 0.19
11 39 0.54
12 16 0.22
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TTATATTATAT
Found at i:180737 original size:37 final size:37
Alignment explanation
Indices: 180695--180772 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
180685 TAAAACCAAG
*
180695 CACAAGACTTAATTTTTCTACGCACTAAAACTTTGGA
1 CACAAGACTTAATTTTTCCACGCACTAAAACTTTGGA
180732 CACAAGACTTAATTTTTCCACGCACTAAAACTTTGGA
1 CACAAGACTTAATTTTTCCACGCACTAAAACTTTGGA
180769 CACA
1 CACA
180773 TATGTTAGCC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.29
Consensus pattern (37 bp):
CACAAGACTTAATTTTTCCACGCACTAAAACTTTGGA
Found at i:182839 original size:23 final size:25
Alignment explanation
Indices: 182808--182854 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
182798 CGGTTTATTC
182808 ATTTATTAT-TAATATATTAAAAAT
1 ATTTATTATCTAATATATTAAAAAT
*
182832 ATTT-TTATGCTAATATTTTAAAA
1 ATTTATTAT-CTAATATATTAAAA
182855 TTAAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 4 0.20
25 12 0.60
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (25 bp):
ATTTATTATCTAATATATTAAAAAT
Found at i:182915 original size:22 final size:20
Alignment explanation
Indices: 182876--182920 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
182866 ATAAAAGTGT
182876 AATTTTTATTAATATAATTAA
1 AATTTTTATTAATATAA-TAA
* *
182897 AATTTTTATTTATTTTAATAA
1 AATTTTTA-TTAATATAATAA
182918 AAT
1 AAT
182921 ATTTGACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTTTTATTAATATAATAA
Found at i:191458 original size:3 final size:3
Alignment explanation
Indices: 191450--191487 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
191440 CGCGTCTAAC
191450 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
191488 GATGATGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:191829 original size:30 final size:30
Alignment explanation
Indices: 191795--191852 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
191785 TTTAAGATAA
*
191795 AAAAT-TTTATTAAATATTATTAAAAATATT
1 AAAATATTTAATAAA-ATTATTAAAAATATT
* *
191825 AAAATATTTAATAAAATTTTTGAAAATA
1 AAAATATTTAATAAAATTATTAAAAATA
191853 AAAAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
AAAATATTTAATAAAATTATTAAAAATATT
Found at i:195908 original size:79 final size:79
Alignment explanation
Indices: 195803--195949 Score: 186
Period size: 79 Copynumber: 1.9 Consensus size: 79
195793 AAAAAAAAAA
* ** * * * **
195803 AGTCTTTAGGAGTATATTGGTATTTTCATATTAAGATATGTGTATTAAAGTCATTTTTGTGAGTT
1 AGTCCTTAGGAGTATATTAATATTTTCATATCAAGACATGTGCATTAAAGTCATTTTAATGAGTT
195868 TCATATAAAATCCG
66 TCATATAAAATCCG
* * * *
195882 AGTCCTTAGGAGTATGTTAATATTTTCGTATCGAGACATGTGCATTAAGGTCATTTTAATGAGTT
1 AGTCCTTAGGAGTATATTAATATTTTCATATCAAGACATGTGCATTAAAGTCATTTTAATGAGTT
195947 TCA
66 TCA
195950 CGGAAAATCG
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
79 56 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (79 bp):
AGTCCTTAGGAGTATATTAATATTTTCATATCAAGACATGTGCATTAAAGTCATTTTAATGAGTT
TCATATAAAATCCG
Found at i:198245 original size:47 final size:47
Alignment explanation
Indices: 198176--198270 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
198166 AGAACCTCTC
198176 ATCCCAATTTACTTTTCACAGCTTTCCTTGCTTCCTACTTTGCAAAG
1 ATCCCAATTTACTTTTCACAGCTTTCCTTGCTTCCTACTTTGCAAAG
198223 ATCCCAATTTACTTTTCACAGCTTTCCTTGCTTCCTACTTTGCAAAG
1 ATCCCAATTTACTTTTCACAGCTTTCCTTGCTTCCTACTTTGCAAAG
198270 A
1 A
198271 AAGAGCTCAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.22, C:0.29, G:0.08, T:0.40
Consensus pattern (47 bp):
ATCCCAATTTACTTTTCACAGCTTTCCTTGCTTCCTACTTTGCAAAG
Found at i:200954 original size:52 final size:52
Alignment explanation
Indices: 200849--201015 Score: 217
Period size: 52 Copynumber: 3.2 Consensus size: 52
200839 TGTTATAAAA
* * * * *
200849 TAATTATAAAATTTACTATCAATAATTGACCACTATCTTATCTACTAATTGC
1 TAATTATAAAATTTACTATCAATAATTTACTATTATATTATCTATTAATTGC
* * * * *
200901 TACTTATAAAATTTGCTGTCAATAATTTACTATTATATTAACTATTAAATGC
1 TAATTATAAAATTTACTATCAATAATTTACTATTATATTATCTATTAATTGC
* *
200953 TAATTATAAAATTTATTATCAATAATTTACTATAATATTATCTATTAATTGC
1 TAATTATAAAATTTACTATCAATAATTTACTATTATATTATCTATTAATTGC
*
201005 TAATTAGAAAA
1 TAATTATAAAA
201016 AATTAAATTA
Statistics
Matches: 97, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 97 1.00
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.43
Consensus pattern (52 bp):
TAATTATAAAATTTACTATCAATAATTTACTATTATATTATCTATTAATTGC
Found at i:201029 original size:52 final size:52
Alignment explanation
Indices: 200919--201032 Score: 149
Period size: 52 Copynumber: 2.2 Consensus size: 52
200909 AAATTTGCTG
* * * *
200919 TCAATAATTTACTATTATATTAACTATTAAATGCTAATTATAAAATTTATTA
1 TCAATAATTTACTATAATATTAACTATTAAATGCTAATTAAAAAAATTATAA
* *
200971 TCAATAATTTACTATAATATTATCTATTAATTGCTAATTAGAAAAAATTA-AA
1 TCAATAATTTACTATAATATTAACTATTAAATGCTAATTA-AAAAAATTATAA
*
201023 TTAATAATTT
1 TCAATAATTT
201033 TATTATAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 47 0.87
53 7 0.13
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (52 bp):
TCAATAATTTACTATAATATTAACTATTAAATGCTAATTAAAAAAATTATAA
Found at i:201029 original size:104 final size:102
Alignment explanation
Indices: 200849--201039 Score: 226
Period size: 104 Copynumber: 1.9 Consensus size: 102
200839 TGTTATAAAA
* * *
200849 TAATTATAAAATTTACTATCAATAATTGACCACTATCTTATCTACTAATTGCTACTTATAAAATT
1 TAATTATAAAATTTACTATCAATAATTGACCACTATATTATCTACTAATTGCTAATTAAAAAATT
***
200914 TGCTGTCAATAATTTACTATTATATTAACTATTAAATGC
66 AAATGTCAATAATTT--TATTATATTAACTATTAAATGC
* * * *
200953 TAATTATAAAATTTATTATCAATAATTTACTA-TAATATTATCTATTAATTGCTAATTAGAAAAA
1 TAATTATAAAATTTACTATCAATAATTGACCACT-ATATTATCTACTAATTGCTAATT--AAAAA
201017 ATTAAAT-T-AATAATTTTATTATA
63 ATTAAATGTCAATAATTTTATTATA
201040 AAAACGTTTA
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
102 7 0.09
103 1 0.01
104 57 0.77
105 1 0.01
106 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (102 bp):
TAATTATAAAATTTACTATCAATAATTGACCACTATATTATCTACTAATTGCTAATTAAAAAATT
AAATGTCAATAATTTTATTATATTAACTATTAAATGC
Found at i:202701 original size:21 final size:21
Alignment explanation
Indices: 202677--202719 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
202667 GTAAAATTAA
202677 TAAAAT-ACGCTTAAAGTATAC
1 TAAAATAAC-CTTAAAGTATAC
202698 TAAAATAACCTTAAAGTATAC
1 TAAAATAACCTTAAAGTATAC
202719 T
1 T
202720 TTTGACATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (21 bp):
TAAAATAACCTTAAAGTATAC
Found at i:207570 original size:34 final size:34
Alignment explanation
Indices: 207524--207708 Score: 266
Period size: 34 Copynumber: 5.5 Consensus size: 34
207514 GTAAAAACCA
*
207524 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
207558 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
*
207592 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
207626 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
207660 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
207693 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
207709 TCTCCCACTT
Statistics
Matches: 137, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
33 18 0.13
34 115 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:207666 original size:102 final size:101
Alignment explanation
Indices: 207524--207708 Score: 325
Period size: 102 Copynumber: 1.8 Consensus size: 101
207514 GTAAAAACCA
207524 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
207589 CACCCATTTAATCAACAATGGTAAGCTACCAAATCTC
66 CA-CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * *
207626 CCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
207691 CACCATTTAATCAACAAT
66 CACCATTTAATCAACAAT
207709 TCTCCCACTT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 16 0.20
102 63 0.80
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (101 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
CACCATTTAATCAACAATGGTAAGCTACCAAATCTC
Done.