Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1059
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: 187435
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 2 of 2
Found at i:101293 original size:28 final size:28
Alignment explanation
Indices: 101262--101331 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
101252 TAAATTAATT
*
101262 AAATTTAAAATTTTAATGATGTTATTAA
1 AAATTTAAAATTTTAATAATGTTATTAA
101290 AAATTTAAAATTTTAATAATGTTATTAA
1 AAATTTAAAATTTTAATAATGTTATTAA
*
101318 AAATTTAAATTTTT
1 AAATTTAAAATTTT
101332 TTTAAAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
AAATTTAAAATTTTAATAATGTTATTAA
Found at i:107074 original size:2 final size:2
Alignment explanation
Indices: 107067--107101 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
107057 CGAAAGGGGC
107067 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
107102 AGATCGAGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:107305 original size:20 final size:21
Alignment explanation
Indices: 107282--107320 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
107272 TTATTTTTAT
107282 TTAAT-AAATTTTAATTATTA
1 TTAATAAAATTTTAATTATTA
107302 TTAATAAAATTTTAATTAT
1 TTAATAAAATTTTAATTAT
107321 AAAATAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAATAAAATTTTAATTATTA
Found at i:107687 original size:19 final size:19
Alignment explanation
Indices: 107656--107714 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 19
107646 ATATTACTTT
107656 AAAT-ATATAAAAAATAAAA
1 AAATAATAT-AAAAATAAAA
107675 AAATAATATAAAAATAATTAA
1 AAATAATATAAAAATAA--AA
*
107696 AATATATTATAAAAATAAA
1 AA-ATAATATAAAAATAAA
107715 TATAACATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
19 12 0.34
20 5 0.14
21 4 0.11
22 14 0.40
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAATAATATAAAAATAAAA
Found at i:107712 original size:13 final size:12
Alignment explanation
Indices: 107658--107719 Score: 57
Period size: 11 Copynumber: 5.7 Consensus size: 12
107648 ATTACTTTAA
107658 ATATATAAAAA-
1 ATATATAAAAAT
107669 ATA-A-AAAAAT
1 ATATATAAAAAT
107679 A-ATATAAAAAT
1 ATATATAAAAAT
107690 A-AT-T-AAAAT
1 ATATATAAAAAT
107699 ATATTATAAAAAT
1 ATA-TATAAAAAT
*
107712 AAATATAA
1 ATATATAA
107720 CATGAATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
9 12 0.28
10 5 0.12
11 13 0.30
12 6 0.14
13 7 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
ATATATAAAAAT
Found at i:107728 original size:45 final size:41
Alignment explanation
Indices: 107656--107755 Score: 100
Period size: 45 Copynumber: 2.4 Consensus size: 41
107646 ATATTACTTT
107656 AAATATA-TA-AAAAATAAAAAAATAATATAA-AA-ATAATTA
1 AAATATATTATAAAAATAAAAAAATAATATAAGAACAT-A-TA
107695 AAATATATTATAAAAATAAATATAACATGAATATAAGAACATATA
1 AAATATATTATAAAAATAAA-A-AA-AT-AATATAAGAACATATA
*
107740 ATATATATGTATAAAA
1 AAATATAT-TATAAAA
107756 TATTATACAA
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
39 7 0.14
40 2 0.04
41 9 0.18
42 1 0.02
43 2 0.04
44 2 0.04
45 16 0.31
46 10 0.20
47 2 0.04
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (41 bp):
AAATATATTATAAAAATAAAAAAATAATATAAGAACATATA
Found at i:107994 original size:18 final size:20
Alignment explanation
Indices: 107951--107995 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
107941 TTATGTAGTT
107951 AATTTTATATTATTAATAAA
1 AATTTTATATTATTAATAAA
107971 AA-TTTA-ATTA-TAA-AATA
1 AATTTTATATTATTAATAA-A
107988 AATTTTAT
1 AATTTTAT
107996 TAAATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.09
17 6 0.27
18 8 0.36
19 4 0.18
20 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTTATATTATTAATAAA
Found at i:108004 original size:17 final size:17
Alignment explanation
Indices: 107960--108005 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
107950 TAATTTTATA
107960 TTATT-AATAA-AAATT
1 TTATTAAATAATAAATT
*
107975 TAATTATAA-AATAAATT
1 TTATTA-AATAATAAATT
107992 TTATTAAATAATAA
1 TTATTAAATAATAA
108006 TTATGTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.16
16 4 0.16
17 17 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTATTAAATAATAAATT
Found at i:108379 original size:22 final size:19
Alignment explanation
Indices: 108342--108392 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
108332 TAAATATACA
108342 AAAAATAAAAAAATAAAAT
1 AAAAATAAAAAAATAAAAT
*
108361 AAAAATAATTAAAATATAATAT
1 AAAAATAA--AAAA-ATAAAAT
108383 AAAAAATAAA
1 -AAAAATAAA
108393 TATGATACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 8 0.30
21 5 0.19
22 6 0.22
23 8 0.30
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAATAAAAAAATAAAAT
Found at i:108415 original size:8 final size:8
Alignment explanation
Indices: 108333--108423 Score: 52
Period size: 8 Copynumber: 11.9 Consensus size: 8
108323 ATATTATTTT
108333 AAATATACA
1 AAATATA-A
*
108342 AAAAATAA
1 AAATATAA
*
108350 AAA-A-AT
1 AAATATAA
108356 AAA-ATAA
1 AAATATAA
*
108363 AAATAATTA
1 AAAT-ATAA
108372 AAATAT--
1 AAATATAA
108378 -AATATAA
1 AAATATAA
108385 AAA-ATAA
1 AAATATAA
* *
108392 ATATGATAC
1 AAAT-ATAA
*
108401 GAATATAA
1 AAATATAA
108409 AAATATAA
1 AAATATAA
108417 AAATATA
1 AAATATA
108424 TGTGTACAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
5 5 0.08
6 5 0.08
7 11 0.17
8 25 0.39
9 18 0.28
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (8 bp):
AAATATAA
Found at i:108511 original size:677 final size:652
Alignment explanation
Indices: 107288--108628 Score: 1716
Period size: 677 Copynumber: 2.0 Consensus size: 652
107278 TTATTTAATA
* * **
107288 AATTTTAATTATTATTAATAAAATTTTAATTATAAAATAAGTTTTATTAAATAATGTTTATGTAT
1 AATTTT-A-TATTATTAATAAAAATTTAATTATAAAATAAATTTTATTAAATAATAATTATGTAT
*** * * *
107353 TTAAATTTTATATTTAAAATTAAAAATAAATTTTAATTATAATGTAAAAATTTATTTTTTAAATA
64 TTAAATTTTATATTTAAAATTAAAAATAAATTTTAATTATAAAACAAAAATTCATTCTTTAAACA
* *
107418 TATTATTTAAAAATAAAATAATTAATGTTATTTATAATTATTTTTAATAAAAATTAAATTTTATT
129 CATTATTTAAAAATAAAATAAATAATGTTATTTATAATTATTTTTAATAAAAATTAAATTTTATT
** * *
107483 AAATAATATATATTTATTTAAATCTGTATTTAGCATAGGATATAAATTTTAAATCGATCATACAT
194 AAATAATATATATTTATTTAAATCTACATTTAGAATAGAATATAAATTTTAAATCGATCATACAT
* * * *
107548 CAATATATAGATCTAATATTTTAAATATATTATTTAATTACACTAACGTATCAATATACATAAAC
259 CAATATAAAAATCTAACATTTTAAATATATTATTTAATTACACTAACGTATAAATATACATAAAC
* *
107613 AAATAATTAATATGTAAAAATTTATATAAATTTATATTACTTTAAATATATAAAAAATAAAAAAA
324 AAATAATTAATATGCAAAAATTTATATAAATTTATATTACTTTAAATATACAAAAAATAAAAAAA
* * * *
107678 TAATATAAAAATAATTAAAATATATTATAAAAATAAATATAACATGAATATAAGAACATATAATA
389 TAAAATAAAAATAATTAAAATATAATATAAAAATAAATATAACACGAATATAAGAACATATAAAA
*
107743 TATATGTATAAAATATTATACAAATTTATAATACTTTAAACAATAAAAAATAAATAAATATAAAT
454 TATATGTATAAAATATTATACAAATTTATAATACTTTAAACAATAAAAAATAAACAAATATAAAT
* *
107808 ATAAACATATTAAATTTTCTTTTTATTTC-TCTCTCTC-TTTTCCTTTATTTTATT-TTTT-ATT
519 ATAAACATATTAAATTTTCTTTTTATTTCAT-TCTCTCAATTT-CTTT-TTTT-TTCTTTTCATC
* * * * * *
107869 TTCTTTGCACCTTTCTC-TTTCCCTGCTTAAAAAAAAATTTAAAAGTAGAACATGTGTTAACATC
580 TT-TTT----CTCTCCCATTT---TGC-T-AAAAAAAACTCAAAAGCAGAACATGTATTAACATC
*
107933 AAATTTATTTATGTAGTT
635 AAATTTATTTATATAGTT
107951 AATTTTATATTATTAATAAAAATTTAATTATAAAATAAATTTTATTAAATAATAATTATGTATTT
1 AATTTTATATTATTAATAAAAATTTAATTATAAAATAAATTTTATTAAATAATAATTATGTATTT
*
108016 AAATTTTGTATTTAAAATTAAAAATAAA-TTTAATTGTTTTGTGAGTTAAAACAAAAATTCATTA
66 AAATTTTATATTTAAAATTAAAAATAAATTTTAA------T-T-A--TAAAACAAAAATTCATT-
**
108080 CTTTAAACACATTATTTAAAAATAAAATAAATAATGCATT-TTTAATTTTTTATATTTTTAATAA
120 CTTTAAACACATTATTTAAAAATAAAATAAATAATG--TTATTT-A--TAAT-TATTTTTAATAA
* * *
108144 AAATTAAATTTTATTAAATAATATTTATTTATTTAAATTTACATTTAGAATAGAATATGAA-TTT
179 AAATTAAATTTTATTAAATAATATATATTTATTTAAATCTACATTTAGAATAGAATATAAATTTT
** * * *
108208 AAATCGATGGTATATCAACT-TAAAAATTTAACATTTTAAATATATTATTTAATTACATTAACGT
244 AAATCGATCATACATCAA-TATAAAAATCTAACATTTTAAATATATTATTTAATTACACTAACGT
* * * * *
108272 GTTAAAATATATATATATAAATAATTAATATGCAAAAATTTATATAAATTTATATTATTTTAAAT
308 -AT-AAATATACATAAACAAATAATTAATATGCAAAAATTTATATAAATTTATATTACTTTAAAT
* *
108337 ATACAAAAAATAAAAAAATAAAATAAAAATAATTAAAATATAATATAAAAAATAAATATGATACG
371 ATACAAAAAATAAAAAAATAAAATAAAAATAATTAAAATATAATAT-AAAAATAAATATAACACG
* * * *
108402 AATATAA-AA-ATATAAAAATATATGTGTACAATATTATATAAATTTATAATACTTTAAATAATA
435 AATATAAGAACATAT-AAAATATATGTATAAAATATTATACAAATTTATAATACTTTAAACAATA
*
108465 AAAAATAATACAAATATAAATATAAATATATTAAATTTTC-TTTTATTTCATTCTCTCAATTTCT
499 AAAAATAA-ACAAATATAAATATAAACATATTAAATTTTCTTTTTATTTCATTCTCTCAATTTCT
108529 TTTTTTTTCTTTTCATCTTTTTCTCTCCCATTTTGCTAAAAAAAACTCAAAAGCAGAACATGTAT
563 TTTTTTTTCTTTTCATCTTTTTCTCTCCCATTTTGCTAAAAAAAACTCAAAAGCAGAACATGTAT
108594 TAACATCAAATTTATTTATATAGTT
628 TAACATCAAATTTATTTATATAGTT
108619 AATTTTATAT
1 AATTTTATAT
108629 GTATGTATAG
Statistics
Matches: 591, Mismatches: 59, Indels: 51
0.84 0.08 0.07
Matches are distributed among these distances:
660 5 0.01
661 81 0.14
662 1 0.00
663 6 0.01
666 1 0.00
667 1 0.00
668 59 0.10
669 1 0.00
670 16 0.03
671 32 0.05
672 8 0.01
673 6 0.01
675 61 0.10
676 83 0.14
677 175 0.30
678 55 0.09
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (652 bp):
AATTTTATATTATTAATAAAAATTTAATTATAAAATAAATTTTATTAAATAATAATTATGTATTT
AAATTTTATATTTAAAATTAAAAATAAATTTTAATTATAAAACAAAAATTCATTCTTTAAACACA
TTATTTAAAAATAAAATAAATAATGTTATTTATAATTATTTTTAATAAAAATTAAATTTTATTAA
ATAATATATATTTATTTAAATCTACATTTAGAATAGAATATAAATTTTAAATCGATCATACATCA
ATATAAAAATCTAACATTTTAAATATATTATTTAATTACACTAACGTATAAATATACATAAACAA
ATAATTAATATGCAAAAATTTATATAAATTTATATTACTTTAAATATACAAAAAATAAAAAAATA
AAATAAAAATAATTAAAATATAATATAAAAATAAATATAACACGAATATAAGAACATATAAAATA
TATGTATAAAATATTATACAAATTTATAATACTTTAAACAATAAAAAATAAACAAATATAAATAT
AAACATATTAAATTTTCTTTTTATTTCATTCTCTCAATTTCTTTTTTTTTCTTTTCATCTTTTTC
TCTCCCATTTTGCTAAAAAAAACTCAAAAGCAGAACATGTATTAACATCAAATTTATTTATATAG
TT
Found at i:108961 original size:9 final size:9
Alignment explanation
Indices: 108946--108982 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
108936 ATACGTAAAT
108946 TTTTTTTTC
1 TTTTTTTTC
*
108955 CTTTTTTTC
1 TTTTTTTTC
108964 TTTCTTTTTC
1 TTT-TTTTTC
108974 TTTTTTTTC
1 TTTTTTTTC
108983 ATTCAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:109276 original size:21 final size:21
Alignment explanation
Indices: 109237--109278 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
109227 CATTTTAATT
*
109237 AATAAAATTTTAAAAATTTAA
1 AATAAAATTTAAAAAATTTAA
109258 AATAAAA-TTAAAAATATTTAA
1 AATAAAATTTAAAAA-ATTTAA
109279 GACCTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AATAAAATTTAAAAAATTTAA
Found at i:109462 original size:22 final size:22
Alignment explanation
Indices: 109437--109484 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
109427 GTCGAATATT
109437 AATCAAA-AATAAATATTTTAAA
1 AATCAAATAAT-AATATTTTAAA
*
109459 AATCAAATAATAATATTTTATA
1 AATCAAATAATAATATTTTAAA
109481 AATC
1 AATC
109485 TTTATATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (22 bp):
AATCAAATAATAATATTTTAAA
Found at i:110812 original size:32 final size:31
Alignment explanation
Indices: 110771--110863 Score: 73
Period size: 32 Copynumber: 2.9 Consensus size: 31
110761 TTTATTGAAA
*
110771 ATATCATATTTAAATATATTAAATTAAATTT
1 ATATTATATTTAAATATATTAAATTAAATTT
*** * *
110802 ATTATTATATTATTTTTACATT-TATTAAATTT
1 A-TATTATATT-TAAATATATTAAATTAAATTT
*
110834 ATATTTTATTTAAA-ATTATTAAATTTAAAT
1 ATATTATATTTAAATA-TATTAAA-TTAAAT
110864 AACATAAAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 9
0.68 0.18 0.14
Matches are distributed among these distances:
29 1 0.02
30 4 0.09
31 10 0.22
32 24 0.53
33 6 0.13
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (31 bp):
ATATTATATTTAAATATATTAAATTAAATTT
Found at i:110813 original size:17 final size:16
Alignment explanation
Indices: 110785--110843 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 16
110775 CATATTTAAA
*
110785 TATATTAAATTAAATT
1 TATATTATATTAAATT
**
110801 TATTATTATATTATTTT
1 TA-TATTATATTAAATT
*
110818 TACATT-TATTAAATT
1 TATATTATATTAAATT
*
110833 TATATTTTATT
1 TATATTATATT
110844 TAAAATTATT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
15 12 0.35
16 9 0.26
17 13 0.38
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATTATATTAAATT
Found at i:110845 original size:26 final size:26
Alignment explanation
Indices: 110806--110860 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
110796 AAATTTATTA
* *
110806 TTATATTATTTTTACATTTATTAAAT
1 TTATATTATTTTTAAAATTATTAAAT
110832 TTATATT-TTATTTAAAATTATTAAAT
1 TTATATTATT-TTTAAAATTATTAAAT
110858 TTA
1 TTA
110861 AATAACATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATATTATTTTTAAAATTATTAAAT
Found at i:111838 original size:15 final size:13
Alignment explanation
Indices: 111797--111838 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
111787 ACATTAACAA
111797 AAAAAAATATAAT
1 AAAAAAATATAAT
*
111810 TAAAAAATATAAT
1 AAAAAAATATAAT
111823 AAAACAATATATAAT
1 AAAA-AA-ATATAAT
111838 A
1 A
111839 TTTTAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 15 0.60
14 2 0.08
15 8 0.32
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAAAATATAAT
Found at i:114028 original size:5 final size:5
Alignment explanation
Indices: 114020--114052 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
114010 TTTTTTTTAA
114020 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAA
114053 TCCCCTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TAAAT
Found at i:114212 original size:3 final size:3
Alignment explanation
Indices: 114204--114232 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
114194 CATTACTTAC
114204 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
114233 CCATTTGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:114265 original size:2 final size:2
Alignment explanation
Indices: 114258--114285 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
114248 TCATGGAATT
114258 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
114286 CACACGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:116140 original size:17 final size:19
Alignment explanation
Indices: 116103--116142 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
116093 CAAGGAATAT
*
116103 TTTTAAATTTAAAATTGAG
1 TTTTAAATTTAAAATTAAG
116122 TTTTAAA-TT-AAATTAAG
1 TTTTAAATTTAAAATTAAG
116139 TTTT
1 TTTT
116143 TTCATCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 11 0.55
18 2 0.10
19 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (19 bp):
TTTTAAATTTAAAATTAAG
Found at i:116870 original size:18 final size:19
Alignment explanation
Indices: 116835--116873 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
116825 TTGTTTACGT
116835 ATAAATTTATATATTATTA
1 ATAAATTTATATATTATTA
116854 ATAAATTATATGATATTATT
1 ATAAATT-TAT-ATATTATT
116874 TCATAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
ATAAATTTATATATTATTA
Found at i:117659 original size:16 final size:16
Alignment explanation
Indices: 117609--117659 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
117599 TCAAAATATT
117609 TTATATAAATTTT-AA
1 TTATATAAATTTTAAA
* *
117624 -TATATTAATAATTTATA
1 TTATA-TAA-ATTTTAAA
117641 TTATATAAATTTTAAA
1 TTATATAAATTTTAAA
117657 TTA
1 TTA
117660 ATTATTTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
14 4 0.14
15 3 0.11
16 13 0.46
17 4 0.14
18 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATATAAATTTTAAA
Found at i:117875 original size:9 final size:9
Alignment explanation
Indices: 117861--117906 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
117851 TAAAAAAAGA
117861 ATATTTTAT
1 ATATTTTAT
117870 ATATTTT-T
1 ATATTTTAT
117878 ATTATATTTAT
1 A-TAT-TTTAT
*
117889 ATTTTTTAT
1 ATATTTTAT
117898 -TATTTTAT
1 ATATTTTAT
117906 A
1 A
117907 ATTAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
8 9 0.29
9 15 0.48
10 5 0.16
11 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
ATATTTTAT
Found at i:117891 original size:17 final size:17
Alignment explanation
Indices: 117862--117906 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 17
117852 AAAAAAAGAA
117862 TATTTTATATATTTTTAT
1 TATTTTATAT-TTTTTAT
117880 TATATTTATATTTTTTAT
1 TAT-TTTATATTTTTTAT
117898 TATTTTATA
1 TATTTTATA
117907 ATTAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.23
18 13 0.50
19 7 0.27
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTATATTTTTTAT
Found at i:118625 original size:6 final size:6
Alignment explanation
Indices: 118614--118638 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
118604 TCTCCGCCGT
118614 TGCCAC TGCCAC TGCCAC TGCCAC T
1 TGCCAC TGCCAC TGCCAC TGCCAC T
118639 TTTAATGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (6 bp):
TGCCAC
Found at i:119572 original size:32 final size:32
Alignment explanation
Indices: 119533--119716 Score: 145
Period size: 32 Copynumber: 5.7 Consensus size: 32
119523 TTAAAATATT
119533 TTATATAAATTTTAATATATTAATAATTTATA
1 TTATATAAATTTTAATATATTAATAATTTATA
*
119565 TTATATAAATTTT-A-A-ATTAATTATTT-TA
1 TTATATAAATTTTAATATATTAATAATTTATA
* *
119593 TT-TATATAATATTAATATAATTAAAAAATTTCGTTTCATA
1 TTATATA-AATTTTAATAT-ATT-AATAA-----TTT-ATA
*
119633 TTTTATAAATTTTAATATATTAATAATTTATA
1 TTATATAAATTTTAATATATTAATAATTTATA
*
119665 TTATATAAATTTT-A-A-ATTAATTATTT-TA
1 TTATATAAATTTTAATATATTAATAATTTATA
*
119693 TTCATAT-AATATTAATATAATTAA
1 TT-ATATAAATTTTAATAT-ATTAA
119717 AAGATTCCAG
Statistics
Matches: 124, Mismatches: 9, Indels: 38
0.73 0.05 0.22
Matches are distributed among these distances:
27 4 0.03
28 18 0.15
29 26 0.21
30 4 0.03
31 2 0.02
32 36 0.29
33 6 0.05
38 7 0.06
39 3 0.02
40 14 0.11
41 4 0.03
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.53
Consensus pattern (32 bp):
TTATATAAATTTTAATATATTAATAATTTATA
Found at i:119642 original size:100 final size:100
Alignment explanation
Indices: 119536--119718 Score: 357
Period size: 100 Copynumber: 1.8 Consensus size: 100
119526 AAATATTTTA
*
119536 TATAAATTTTAATATATTAATAATTTATATTATATAAATTTTAAATTAATTATTTTATTTATATA
1 TATAAATTTTAATATATTAATAATTTATATTATATAAATTTTAAATTAATTATTTTATTCATATA
119601 ATATTAATATAATTAAAAAATTTCGTTTCATATTT
66 ATATTAATATAATTAAAAAATTTCGTTTCATATTT
119636 TATAAATTTTAATATATTAATAATTTATATTATATAAATTTTAAATTAATTATTTTATTCATATA
1 TATAAATTTTAATATATTAATAATTTATATTATATAAATTTTAAATTAATTATTTTATTCATATA
119701 ATATTAATATAATTAAAA
66 ATATTAATATAATTAAAA
119719 GATTCCAGCA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 82 1.00
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.52
Consensus pattern (100 bp):
TATAAATTTTAATATATTAATAATTTATATTATATAAATTTTAAATTAATTATTTTATTCATATA
ATATTAATATAATTAAAAAATTTCGTTTCATATTT
Found at i:119691 original size:46 final size:46
Alignment explanation
Indices: 119541--119692 Score: 139
Period size: 46 Copynumber: 3.1 Consensus size: 46
119531 TTTTATATAA
119541 ATTTTAATATATTAATAATTTATATTATATAAATTTTAAATTAATT
1 ATTTTAATATATTAATAATTTATATTATATAAATTTTAAATTAATT
* * * * *
119587 ATTTT-ATTTATATAAT-ATTAATATAATTA-AAAAATTTCGTTTCATATTTTATAA
1 ATTTTAATATAT-TAATAATT--TAT-ATTATATAAA--T--TTT-A-AATTAAT-T
119641 ATTTTAATATATTAATAATTTATATTATATAAATTTTAAATTAATT
1 ATTTTAATATATTAATAATTTATATTATATAAATTTTAAATTAATT
119687 ATTTTA
1 ATTTTA
119693 TTCATATAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 28
0.68 0.08 0.23
Matches are distributed among these distances:
45 8 0.10
46 15 0.18
47 12 0.15
48 5 0.06
49 4 0.05
51 4 0.05
52 5 0.06
53 12 0.15
54 9 0.11
55 8 0.10
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (46 bp):
ATTTTAATATATTAATAATTTATATTATATAAATTTTAAATTAATT
Found at i:126715 original size:30 final size:29
Alignment explanation
Indices: 126634--126717 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 29
126624 TCAACATTTA
*
126634 AAAATTTATTTTT-TCATTTAAAATATATT
1 AAAATTTATTTTTATTATTT-AAATATATT
* * * *
126663 AAAATATTAATTCTA-TAATTAAATTTATCT
1 AAAAT-TTATTTTTATTATTTAAATATAT-T
126693 AAAATTTATTTTTATTATTTAAATA
1 AAAATTTATTTTTATTATTTAAATA
126718 ATAATTTATA
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
29 19 0.45
30 23 0.55
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (29 bp):
AAAATTTATTTTTATTATTTAAATATATT
Found at i:127654 original size:26 final size:26
Alignment explanation
Indices: 127584--127654 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
127574 TTTATTTAAA
* *
127584 TTAAATTAATTTGATTTAAAT-TATTAT
1 TTAAATTAA-TT-ATATAAATATTTTAT
127611 TT-AATTAA-TA-A-AAATATTTTAT
1 TTAAATTAATTATATAAATATTTTAT
127633 TTAAATTAATTATATAAATATT
1 TTAAATTAATTATATAAATATT
127655 AATATAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
21 4 0.11
22 7 0.19
23 7 0.19
24 3 0.08
25 1 0.03
26 13 0.35
27 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (26 bp):
TTAAATTAATTATATAAATATTTTAT
Found at i:127786 original size:10 final size:9
Alignment explanation
Indices: 127771--127809 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
127761 ACCCATGCTA
127771 TTTTTAGTTT
1 TTTTTA-TTT
127781 TTTTTATTT
1 TTTTTATTT
*
127790 TTTAT-TTT
1 TTTTTATTT
127798 TTTTTATTT
1 TTTTTATTT
127807 TTT
1 TTT
127810 AATTATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 7 0.27
9 13 0.50
10 6 0.23
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (9 bp):
TTTTTATTT
Found at i:127793 original size:17 final size:17
Alignment explanation
Indices: 127771--127810 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
127761 ACCCATGCTA
127771 TTTTTAGTTTTTTTTAT
1 TTTTTAGTTTTTTTTAT
*
127788 TTTTTATTTTTTTTTAT
1 TTTTTAGTTTTTTTTAT
127805 TTTTTA
1 TTTTTA
127811 ATTATTTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTAGTTTTTTTTAT
Found at i:127818 original size:17 final size:17
Alignment explanation
Indices: 127771--127818 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
127761 ACCCATGCTA
*
127771 TTTTTAGTTTTTTTTAT
1 TTTTTAATTTTTTTTAT
*
127788 TTTTTATTTTTTTTTAT
1 TTTTTAATTTTTTTTAT
127805 TTTTTAATTATTTT
1 TTTTTAATT-TTTT
127819 ACATTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 24 0.86
18 4 0.14
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (17 bp):
TTTTTAATTTTTTTTAT
Found at i:128620 original size:16 final size:16
Alignment explanation
Indices: 128595--128625 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
128585 TTAAAAAAAT
*
128595 AAAAATATTAAATTTG
1 AAAAAAATTAAATTTG
128611 AAAAAAATTAAATTT
1 AAAAAAATTAAATTT
128626 ATTAAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
AAAAAAATTAAATTTG
Found at i:128632 original size:17 final size:17
Alignment explanation
Indices: 128593--128634 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
128583 TCTTAAAAAA
128593 ATAAAAATATTAAATTTG
1 ATAAAAA-ATTAAATTTG
128611 A-AAAAAATTAAATTT-
1 ATAAAAAATTAAATTTG
128626 ATTAAAAAA
1 A-TAAAAAA
128635 ATAAGTCGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.05
16 9 0.41
17 11 0.50
18 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
ATAAAAAATTAAATTTG
Found at i:128632 original size:18 final size:16
Alignment explanation
Indices: 128594--128636 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
128584 CTTAAAAAAA
*
128594 TAAAAATATTAAATTT
1 TAAAAAAATTAAATTT
*
128610 GAAAAAAATTAAATTTAT
1 TAAAAAAATTAAA-TT-T
128628 TAAAAAAAT
1 TAAAAAAAT
128637 AAGTCGAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 11 0.50
17 2 0.09
18 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
TAAAAAAATTAAATTT
Found at i:128734 original size:25 final size:24
Alignment explanation
Indices: 128687--128735 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
128677 CAATTATAAA
128687 ATATATTATATTTATTTATATATAT
1 ATATATTATATTTA-TTATATATAT
128712 ATATATTATAATTTA-TATCATATA
1 ATATATTAT-ATTTATTAT-ATATA
128736 CTATTAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.14
25 14 0.64
26 5 0.23
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATATTATATTTATTATATATAT
Found at i:129025 original size:2 final size:2
Alignment explanation
Indices: 128973--129008 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
128963 ACTTGAACAA
128973 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
129009 TGTTAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:130731 original size:11 final size:11
Alignment explanation
Indices: 130717--130745 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
130707 AAATATGATT
130717 ATAATATAAAA
1 ATAATATAAAA
130728 ATAATATAAAA
1 ATAATATAAAA
130739 ATAATAT
1 ATAATAT
130746 GAATACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:130916 original size:12 final size:12
Alignment explanation
Indices: 130899--130929 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
130889 CAAAGTAACC
130899 CCAATTGGAAAA
1 CCAATTGGAAAA
130911 CCAATTGGAAAA
1 CCAATTGGAAAA
130923 CCAATTG
1 CCAATTG
130930 AGGATTACTT
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:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (12 bp):
CCAATTGGAAAA
Found at i:131709 original size:2 final size:2
Alignment explanation
Indices: 131702--131727 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
131692 CCATCTATCT
131702 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
131728 AATATCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:131934 original size:2 final size:2
Alignment explanation
Indices: 131922--131951 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
131912 AAATCATCAA
*
131922 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
131952 TATTGTAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:133417 original size:13 final size:13
Alignment explanation
Indices: 133399--133425 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
133389 GGCCCCCTTC
133399 AATATTTATATAT
1 AATATTTATATAT
133412 AATATTTATATAT
1 AATATTTATATAT
133425 A
1 A
133426 GAGGAGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATATTTATATAT
Found at i:134603 original size:2 final size:2
Alignment explanation
Indices: 134596--134632 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
134586 CTTATGGTAC
134596 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
134633 GAGATTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:136039 original size:2 final size:2
Alignment explanation
Indices: 136034--136059 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
136024 TGTAAATTTT
136034 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
136060 CACGTATCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:139509 original size:2 final size:2
Alignment explanation
Indices: 139502--139544 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
139492 TTTTCATCTT
* *
139502 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
139544 T
1 T
139545 TACGCTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:140219 original size:3 final size:3
Alignment explanation
Indices: 140209--140248 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
140199 AAAATTTTGA
140209 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
140249 ATAAAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:140721 original size:15 final size:16
Alignment explanation
Indices: 140696--140728 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
140686 AATATTATTT
*
140696 TTATATTTATATTTAA
1 TTATATTTATAATTAA
140712 TTAT-TTTATAATTAA
1 TTATATTTATAATTAA
140727 TT
1 TT
140729 TTAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATATTTATAATTAA
Found at i:140731 original size:21 final size:22
Alignment explanation
Indices: 140689--140732 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
140679 AACCCAAAAT
*
140689 ATTATTTTTATATTTATATTTA
1 ATTATTTTTATATTAATATTTA
140711 ATTA-TTTTATAATTAAT-TTTA
1 ATTATTTTTAT-ATTAATATTTA
140732 A
1 A
140733 ATAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTATTTTTATATTAATATTTA
Found at i:142770 original size:19 final size:19
Alignment explanation
Indices: 142735--142813 Score: 56
Period size: 19 Copynumber: 4.1 Consensus size: 19
142725 ATTATATTTA
142735 AAATATTTTATATTTATAT
1 AAATATTTTATATTTATAT
* *
142754 AAAT-TTTTATGTATTATAAC
1 AAATATTTTATAT-TTAT-AT
*
142774 AGTAATAATTTATA-TTATAT
1 A--AATATTTTATATTTATAT
*
142794 AAAT-TTTAAATATTTATAT
1 AAATATTT-TATATTTATAT
142813 A
1 A
142814 TTTAATTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
17 2 0.04
18 13 0.28
19 15 0.33
20 4 0.09
21 4 0.09
22 3 0.07
23 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (19 bp):
AAATATTTTATATTTATAT
Found at i:142835 original size:14 final size:14
Alignment explanation
Indices: 142803--142850 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
142793 TAAATTTTAA
*
142803 ATATTTATATATTT
1 ATATTTATATAATT
* * *
142817 A-ATTTTTTTTATT
1 ATATTTATATAATT
142830 ATATTTATATAATT
1 ATATTTATATAATT
142844 ATATTTA
1 ATATTTA
142851 ATGTGATTAG
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATATTTATATAATT
Found at i:143394 original size:27 final size:26
Alignment explanation
Indices: 143343--143394 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
143333 TGATATGTAA
* * *
143343 ATATAATTTTTAAAAAATTTTAATAC
1 ATATAAATATTAAAAAATTTAAATAC
143369 ATATAAATATTAAAAAATATTAAATA
1 ATATAAATATTAAAAAAT-TTAAATA
143395 TATTTATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
ATATAAATATTAAAAAATTTAAATAC
Found at i:150273 original size:18 final size:17
Alignment explanation
Indices: 150226--150275 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
150216 ATATATGTTT
*
150226 TAAAATTTAAAT-AATA
1 TAAAATTTATATAAATA
*
150242 TAAAATAT-TA-AAATA
1 TAAAATTTATATAAATA
150257 TCAAAATTTATATAAATA
1 T-AAAATTTATATAAATA
150275 T
1 T
150276 TTATATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
15 6 0.22
16 13 0.48
17 2 0.07
18 6 0.22
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:150319 original size:18 final size:19
Alignment explanation
Indices: 150296--150336 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
150286 ATATGATTAT
150296 AATATAATA-AAATATATA
1 AATATAATACAAATATATA
*
150314 AATATAATACAAATATATG
1 AATATAATACAAATATATA
150333 AATA
1 AATA
150337 AACTCTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
AATATAATACAAATATATA
Found at i:152383 original size:2 final size:2
Alignment explanation
Indices: 152378--152403 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
152368 GTGAGCAAGC
152378 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
152404 ACCGTCTTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:153898 original size:23 final size:22
Alignment explanation
Indices: 153853--153898 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
153843 TGGTTATGGA
153853 AAATTGAAAATTGTTTTGGCTAT
1 AAATTGAAAATTGTTTT-GCTAT
153876 AAATGTGAAAATTGTGTTT-CTAT
1 AAAT-TGAAAATTGT-TTTGCTAT
153899 GAACAGCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 8 0.38
24 10 0.48
25 3 0.14
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.43
Consensus pattern (22 bp):
AAATTGAAAATTGTTTTGCTAT
Found at i:154322 original size:3 final size:3
Alignment explanation
Indices: 154314--154354 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
154304 TGATCGGGAA
154314 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
154355 AAATTAGCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:154819 original size:15 final size:14
Alignment explanation
Indices: 154789--154827 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
154779 TAGAAAAAAT
*
154789 AAAATAAAAGTTTA
1 AAAATAAAAATTTA
154803 AAAATAATAAATTTA
1 AAAATAA-AAATTTA
154818 AAAA-AAAAAT
1 AAAATAAAAAT
154828 ATTTTTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 9 0.39
15 10 0.43
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAATAAAAATTTA
Found at i:155874 original size:17 final size:17
Alignment explanation
Indices: 155823--155874 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
155813 CATGAATATG
* **
155823 ATATACATATAATACGA
1 ATATACATAAAATAAAA
* *
155840 ATATACGTACATATAAAA
1 ATATACATA-AAATAAAA
155858 ATATACATAAAATAAAA
1 ATATACATAAAATAAAA
155875 TAAATTATTA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.60, C:0.10, G:0.04, T:0.27
Consensus pattern (17 bp):
ATATACATAAAATAAAA
Found at i:156579 original size:27 final size:25
Alignment explanation
Indices: 156549--156605 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
156539 CATATATAAA
*
156549 AATATACATAAAATA-AAATAAATTATT
1 AATATACAAAAAATATAAA-AAA-TA-T
*
156576 AATATATAAAAAATATAAAAAATAT
1 AATATACAAAAAATATAAAAAATAT
156601 AATAT
1 AATAT
156606 TTTACATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.22
26 2 0.07
27 16 0.59
28 3 0.11
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (25 bp):
AATATACAAAAAATATAAAAAATAT
Found at i:156673 original size:8 final size:8
Alignment explanation
Indices: 156653--156712 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
156643 AAAAAATTTC
156653 CTTTTTCTT
1 CTTTTT-TT
156662 -TTTTTTT
1 CTTTTTTT
*
156669 ATTTTTCTT
1 CTTTTT-TT
*
156678 CTTTCTTT
1 CTTTTTTT
156686 CTTTTTTT
1 CTTTTTTT
**
156694 -TTCCTTT
1 CTTTTTTT
156701 CTTTTTTT
1 CTTTTTTT
156709 CTTT
1 CTTT
156713 CTCAGCTGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
7 7 0.17
8 28 0.68
9 6 0.15
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (8 bp):
CTTTTTTT
Found at i:156681 original size:19 final size:21
Alignment explanation
Indices: 156656--156708 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
156646 AAATTTCCTT
156656 TTTCTTTTTTTTTATTTTT-C
1 TTTCTTTTTTTTTATTTTTCC
*
156676 -TTCTTTCTTTCTTTTTTTTTCC
1 TTTCTTT-TTT-TTTATTTTTCC
156698 TTTCTTTTTTT
1 TTTCTTTTTTT
156709 CTTTCTCAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 6 0.21
20 3 0.11
21 9 0.32
22 4 0.14
23 6 0.21
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTCTTTTTTTTTATTTTTCC
Found at i:156682 original size:23 final size:20
Alignment explanation
Indices: 156656--156708 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
156646 AAATTTCCTT
156656 TTTCTTTTTTTTTATTTTTCTTC
1 TTTCTTTTTTTTT-TTTTTC--C
*
156679 TTTC-TTTCTTTTTTTTTCC
1 TTTCTTTTTTTTTTTTTTCC
156698 TTTCTTTTTTT
1 TTTCTTTTTTT
156709 CTTTCTCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 5 0.19
21 6 0.22
22 7 0.26
23 4 0.15
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTCTTTTTTTTTTTTTTCC
Found at i:156707 original size:13 final size:12
Alignment explanation
Indices: 156670--156714 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 12
156660 TTTTTTTTTA
156670 TTTTTC-TTCTT
1 TTTTTCTTTCTT
*
156681 TCTTTCTTT-TT
1 TTTTTCTTTCTT
*
156692 TTTTCCTTTCTT
1 TTTTTCTTTCTT
156704 TTTTTCTTTCT
1 TTTTTCTTTCT
156715 CAGCTGCCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 14 0.50
12 14 0.50
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:156709 original size:23 final size:24
Alignment explanation
Indices: 156649--156712 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
156639 ATAAAAAAAA
156649 TTTCCTTT-TTCTTTTT-TTTTATT
1 TTTCCTTTCTT-TTTTTCTTTTATT
*
156672 TTT-C-TTCTTTCTTTCTTTT-TT
1 TTTCCTTTCTTTTTTTCTTTTATT
156693 TTTCCTTTCTTTTTTTCTTT
1 TTTCCTTTCTTTTTTTCTTT
156713 CTCAGCTGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
21 11 0.31
22 8 0.23
23 16 0.46
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTCCTTTCTTTTTTTCTTTTATT
Found at i:156911 original size:21 final size:19
Alignment explanation
Indices: 156887--156942 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
156877 GACGTTATAA
156887 ATATTATTTAATAATTTTT
1 ATATTATTTAATAATTTTT
*
156906 ACATATTTTTTAATATATTTTT
1 --ATATTATTTAATA-ATTTTT
156928 -TATTATTTATATAAT
1 ATATTATTTA-ATAAT
156943 AATTGATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 10 0.32
20 3 0.10
21 12 0.39
22 6 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTATTTAATAATTTTT
Found at i:156974 original size:30 final size:28
Alignment explanation
Indices: 156920--156975 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
156910 ATTTTTTAAT
* *
156920 ATATTTTTTATTATTTATATAATAATTG
1 ATATTTTTTATAATTAATATAATAATTG
156948 ATATTTTATTATAATTAATCATAATAAT
1 ATATTTT-TTATAATTAAT-ATAATAAT
156976 ATGGTCGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 9 0.38
30 8 0.33
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (28 bp):
ATATTTTTTATAATTAATATAATAATTG
Found at i:157191 original size:21 final size:20
Alignment explanation
Indices: 157153--157195 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
157143 TAATTAATAA
157153 AAAAATATTTAAAAATTTTAT
1 AAAAATATTTAAAAA-TTTAT
* * *
157174 AAAAATTTTTATATATTTAT
1 AAAAATATTTAAAAATTTAT
157194 AA
1 AA
157196 TTAAATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAAATATTTAAAAATTTAT
Found at i:157414 original size:29 final size:30
Alignment explanation
Indices: 157381--157459 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
157371 AAAAAAAATT
*
157381 AATATAATATAATATTAACAA-ATAAT-TAA
1 AATATAATATAATAATAA-AATATAATATAA
*
157410 AATATAATATAA-AATAAAATATTATATAA
1 AATATAATATAATAATAAAATATAATATAA
*
157439 AA-ATAATATAATTATATAAAT
1 AATATAATATAATAATA-AAAT
157460 TTACGAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 2 0.05
28 17 0.40
29 20 0.47
30 4 0.09
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (30 bp):
AATATAATATAATAATAAAATATAATATAA
Found at i:157454 original size:17 final size:17
Alignment explanation
Indices: 157410--157459 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
157400 AAATAATTAA
157410 AATATAA-TAT-AAAAT
1 AATATAATTATAAAAAT
* *
157425 AAAATATTATATAAAAAT
1 AATATAAT-TATAAAAAT
*
157443 AATATAATTATATAAAT
1 AATATAATTATAAAAAT
157460 TTACGAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 5 0.19
17 11 0.41
18 11 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATATAATTATAAAAAT
Found at i:157634 original size:13 final size:14
Alignment explanation
Indices: 157607--157640 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
157597 AATTATTATA
157607 TTAATAATAATAAT
1 TTAATAATAATAAT
157621 TTAATAAT-ATAAT
1 TTAATAATAATAAT
157634 TTAATAA
1 TTAATAA
157641 AATTATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATAATAATAAT
Found at i:157654 original size:20 final size:22
Alignment explanation
Indices: 157624--157663 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
157614 TAATAATTTA
157624 ATAATATAATTT-AATAAAATT
1 ATAATATAATTTAAATAAAATT
157645 ATAA-ATAATTTAAATAAAA
1 ATAATATAATTTAAATAAAA
157664 ATTAATGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAATATAATTTAAATAAAATT
Found at i:160320 original size:11 final size:11
Alignment explanation
Indices: 160304--160335 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
160294 TTAATATATA
160304 TTTTTTTAATT
1 TTTTTTTAATT
*
160315 TTTTTTCAATT
1 TTTTTTTAATT
160326 TTTTTTTAAT
1 TTTTTTTAAT
160336 GATAAGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTAATT
Found at i:163099 original size:84 final size:84
Alignment explanation
Indices: 162958--163130 Score: 310
Period size: 84 Copynumber: 2.1 Consensus size: 84
162948 ACGGCACTGA
*
162958 TTTCAAGTAAAGAATGTTTTCACACAACAGCAGAAGTTTGTAGCCAATAGGCTGCAAAGTTTCTT
1 TTTCAAGTAAAGAATGTTTTCACACAACAGCAGAAGTTTGTAGCCAATAGGCTGCAAAATTTCTT
163023 TAAACGCATGAGGTAAATG
66 TAAACGCATGAGGTAAATG
*
163042 TTTCAAGTAAAGAATGTTTTCGCACAACAGCAGAAGTTTGTAGCCAATAGGCTGCAAAATTTCTT
1 TTTCAAGTAAAGAATGTTTTCACACAACAGCAGAAGTTTGTAGCCAATAGGCTGCAAAATTTCTT
* *
163107 TAAACTCATGAGGTATATG
66 TAAACGCATGAGGTAAATG
163126 TTTCA
1 TTTCA
163131 TGATATTGCA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (84 bp):
TTTCAAGTAAAGAATGTTTTCACACAACAGCAGAAGTTTGTAGCCAATAGGCTGCAAAATTTCTT
TAAACGCATGAGGTAAATG
Found at i:163872 original size:40 final size:40
Alignment explanation
Indices: 163801--163879 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
163791 TCTGAGTCTG
* *
163801 CATTACTTTTACGGATAATAAATTCGGATATCCAAATCCC
1 CATTACTTATACGGATAATAAATTCGCATATCCAAATCCC
** * *
163841 CATTACTTATACGGATAATGGATTTGCATATCCGAATCC
1 CATTACTTATACGGATAATAAATTCGCATATCCAAATCC
163880 ATTATCCATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.33
Consensus pattern (40 bp):
CATTACTTATACGGATAATAAATTCGCATATCCAAATCCC
Found at i:165077 original size:14 final size:14
Alignment explanation
Indices: 165047--165079 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
165037 AATACTATAG
*
165047 AAAAATATTCTTTA
1 AAAAAAATTCTTTA
165061 AAAAAAATT-TTTA
1 AAAAAAATTCTTTA
165074 AAAAAA
1 AAAAAA
165080 TCCAAACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAAAATTCTTTA
Found at i:170017 original size:8 final size:8
Alignment explanation
Indices: 170004--170097 Score: 54
Period size: 8 Copynumber: 11.2 Consensus size: 8
169994 TTGTAATAAG
170004 TTATATAT
1 TTATATAT
170012 TTATATAAATT
1 TTATAT--A-T
170023 TTAGTATAT
1 TTA-TATAT
*
170032 TAATA-AT
1 TTATATAT
170039 TTATATAAATT
1 TTATAT--A-T
170050 TTAATATAT
1 TT-ATATAT
170059 TTATATAT
1 TTATATAT
170067 TTATATTAT
1 TTATA-TAT
170076 TT-TAT-T
1 TTATATAT
170082 TT-TAT-T
1 TTATATAT
*
170088 TTATCTAT
1 TTATATAT
170096 TT
1 TT
170098 TTATTGTAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 24
0.72 0.03 0.24
Matches are distributed among these distances:
6 9 0.13
7 9 0.13
8 24 0.34
9 11 0.15
10 4 0.06
11 7 0.10
12 7 0.10
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (8 bp):
TTATATAT
Found at i:170066 original size:10 final size:10
Alignment explanation
Indices: 170005--170077 Score: 54
Period size: 10 Copynumber: 7.9 Consensus size: 10
169995 TGTAATAAGT
170005 TATATATTTA
1 TATATATTTA
*
170015 TATAAATTT-
1 TATATATTTA
170024 TAGTATA-TTA
1 TA-TATATTTA
170034 -ATA-ATTTA
1 TATATATTTA
*
170042 TATAAATTT-
1 TATATATTTA
170051 TA-ATATATT-
1 TATATAT-TTA
170060 TATATATTTA
1 TATATATTTA
170070 TAT-TATTT
1 TATATATTT
170078 TATTTTTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
7 1 0.02
8 8 0.15
9 21 0.40
10 22 0.42
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (10 bp):
TATATATTTA
Found at i:170079 original size:27 final size:28
Alignment explanation
Indices: 170004--170072 Score: 113
Period size: 27 Copynumber: 2.5 Consensus size: 28
169994 TTGTAATAAG
*
170004 TTATATATTTATATAAATTTTAGTATAT
1 TTATATATTTATATAAATTTTAATATAT
*
170032 TAATA-ATTTATATAAATTTTAATATAT
1 TTATATATTTATATAAATTTTAATATAT
170059 TTATATATTTATAT
1 TTATATATTTATAT
170073 TATTTTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 25 0.68
28 12 0.32
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
TTATATATTTATATAAATTTTAATATAT
Found at i:172380 original size:2 final size:2
Alignment explanation
Indices: 172363--172415 Score: 54
Period size: 2 Copynumber: 26.5 Consensus size: 2
172353 ACGGTATCAA
* * *
172363 AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT A- AT AT CAT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
*
172405 TT AT AT AT AT A
1 AT AT AT AT AT A
172416 AATGCCAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:172409 original size:26 final size:26
Alignment explanation
Indices: 172363--172415 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
172353 ACGGTATCAA
172363 ATATATACATACATATATATATATAT
1 ATATATACATACATATATATATATAT
* *
172389 ATATATA-ATATCATTTTTATATATAT
1 ATATATACATA-CATATATATATATAT
172415 A
1 A
172416 AATGCCAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 3 0.12
26 21 0.88
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (26 bp):
ATATATACATACATATATATATATAT
Found at i:174140 original size:17 final size:18
Alignment explanation
Indices: 174120--174164 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
174110 TAATTCTAAT
*
174120 ATATATTTTATCA-TTTA
1 ATATATTTTATAACTTTA
*
174137 ATATA-TATATAACTTTA
1 ATATATTTTATAACTTTA
174154 AT-TATTTTATA
1 ATATATTTTATA
174165 TATATACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATATTTTATAACTTTA
Found at i:174146 original size:25 final size:25
Alignment explanation
Indices: 174129--174177 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
174119 TATATATTTT
174129 ATCATTTAATATATATATAACTTTA
1 ATCATTTAATATATATATAACTTTA
*
174154 ATTATTT--TATATATAT-ACTTTA
1 ATCATTTAATATATATATAACTTTA
174176 AT
1 AT
174178 ATGATATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 9 0.39
25 6 0.26
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (25 bp):
ATCATTTAATATATATATAACTTTA
Found at i:174188 original size:14 final size:14
Alignment explanation
Indices: 174162--174201 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
174152 TAATTATTTT
174162 ATATATATACTTTA
1 ATATATATACTTTA
174176 ATATGATAT-CTTTA
1 ATAT-ATATACTTTA
174190 ATA-AT-TACTTTA
1 ATATATATACTTTA
174202 TTTTCTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 1 0.04
12 7 0.29
14 12 0.50
15 4 0.17
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (14 bp):
ATATATATACTTTA
Found at i:175905 original size:29 final size:27
Alignment explanation
Indices: 175853--175906 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
175843 AAAAATTTAA
175853 ATTTAATAATTTATATTATATTTAAAT
1 ATTTAATAATTTATATTATATTTAAAT
* *
175880 ATTTTATAATATTATAATTATGTTTAA
1 ATTTAATAAT-TTAT-ATTATATTTAA
175907 GATAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 4 0.17
29 10 0.43
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
ATTTAATAATTTATATTATATTTAAAT
Found at i:175954 original size:25 final size:25
Alignment explanation
Indices: 175926--175975 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
175916 TAATACATTT
*
175926 ATAATTTATATTATA-TAAATTTTAA
1 ATAATATAT-TTATATTAAATTTTAA
*
175951 ATAATATATTTATATTATATTTTAA
1 ATAATATATTTATATTAAATTTTAA
175976 GTACTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
ATAATATATTTATATTAAATTTTAA
Found at i:177919 original size:13 final size:13
Alignment explanation
Indices: 177892--177924 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
177882 ATTTTTTTAA
*
177892 AATTT-AAATATT
1 AATTTAAAAAATT
177904 AATTTAAAAAATT
1 AATTTAAAAAATT
177917 AATTTAAA
1 AATTTAAA
177925 TTAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATTTAAAAAATT
Found at i:177948 original size:12 final size:11
Alignment explanation
Indices: 177892--177948 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 11
177882 ATTTTTTTAA
177892 AATTTAAATATT
1 AATTTAAA-ATT
177904 AATTTAAAAAATT
1 AATTT--AAAATT
177917 AATTT-AAATT
1 AATTTAAAATT
*
177927 AA-TAAAAATT
1 AATTTAAAATT
177937 ATATTTAAAATT
1 A-ATTTAAAATT
177949 TGGTGAACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 1 0.03
10 13 0.34
11 1 0.03
12 12 0.32
13 8 0.21
14 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:178470 original size:21 final size:21
Alignment explanation
Indices: 178407--178482 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
178397 TATTAACACG
*
178407 ATATAAATATA-TAAATATGTCAA
1 ATATAAATATATTAAA-AT-T-AT
*
178430 ATATAAATA-ACTAAAATTAT
1 ATATAAATATATTAAAATTAT
*
178450 ATACT-AATATATTAAATTTAT
1 ATA-TAAATATATTAAAATTAT
178471 ATATAAATATAT
1 ATATAAATATAT
178483 AATATTTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 9 0.20
21 21 0.46
22 3 0.07
23 13 0.28
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (21 bp):
ATATAAATATATTAAAATTAT
Found at i:178536 original size:17 final size:15
Alignment explanation
Indices: 178506--178543 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
178496 CGATTGTAAT
178506 ATATAAAAAATATAA
1 ATATAAAAAATATAA
178521 ATATAATAAAATTATAA
1 ATATAA-AAAA-TATAA
178538 AT-TAAA
1 ATATAAA
178544 TATTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 7 0.33
17 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATATAAAAAATATAA
Found at i:178949 original size:40 final size:41
Alignment explanation
Indices: 178829--178957 Score: 174
Period size: 41 Copynumber: 3.1 Consensus size: 41
178819 TTATTAAAAT
* *
178829 ATTAAAATATTTTAGATTATATATTTTTAAAATTAAATTTAA
1 ATTAAAAAATTATA-ATTATATATTTTTAAAATTAAATTTAA
178871 A-TAAAAAATTATAATTTATATATTTTTAAAATTAAATTTAA
1 ATTAAAAAATTATAA-TTATATATTTTTAAAATTAAATTTAA
* *
178912 ATTAAAAAATTATAATT-TATATTATT-AAATAATAATTTAA
1 ATTAAAAAATTATAATTATATATTTTTAAAATTA-AATTTAA
178952 ATTAAA
1 ATTAAA
178958 CTAAACCATT
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
39 5 0.06
40 22 0.28
41 39 0.49
42 14 0.17
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.47
Consensus pattern (41 bp):
ATTAAAAAATTATAATTATATATTTTTAAAATTAAATTTAA
Found at i:179109 original size:2 final size:2
Alignment explanation
Indices: 179092--179125 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
179082 CGTCATAATC
*
179092 TA TA -A TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
179126 GAGTGTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:179480 original size:22 final size:22
Alignment explanation
Indices: 179455--179504 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
179445 TAAATAATAC
179455 ATATAAATATATTTATGAAAAT
1 ATATAAATATATTTATGAAAAT
** * *
179477 ATATATTTATATTTTTTAAAAT
1 ATATAAATATATTTATGAAAAT
*
179499 AAATAA
1 ATATAA
179505 GGTGACAACA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATATAAATATATTTATGAAAAT
Done.