Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 69 of 91
Found at i:24797035 original size:9 final size:9
Alignment explanation
Indices: 24797018--24797065 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
24797008 TTATTATATC
24797018 TTTTATTTTA
1 TTTT-TTTTA
24797028 TTTTTTTTA
1 TTTTTTTTA
* *
24797037 TGTTTTATA
1 TTTTTTTTA
*
24797046 TTTTTTATTC
1 TTTTTT-TTA
24797056 TTTTTTTTA
1 TTTTTTTTA
24797065 T
1 T
24797066 ATTAACTATC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
9 20 0.65
10 11 0.35
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:24797052 original size:30 final size:28
Alignment explanation
Indices: 24797003--24797069 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
24796993 TCCTTTATTA
*
24797003 TTTTATTATTATATCTTTTATTTTATTTT
1 TTTTATTATTATATCTTTTATTCT-TTTT
* *
24797032 TTTTATGTTTTATATTTTTTATTCTTTTT
1 TTTTAT-TATTATATCTTTTATTCTTTTT
24797061 TTTATATTA
1 TTT-TATTA
24797070 ACTATCTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (28 bp):
TTTTATTATTATATCTTTTATTCTTTTT
Found at i:24797059 original size:8 final size:7
Alignment explanation
Indices: 24796996--24797068 Score: 51
Period size: 8 Copynumber: 9.9 Consensus size: 7
24796986 TTTCATATCC
24796996 TTTATTAT
1 TTTATT-T
24797004 TTTATTAT
1 TTTATT-T
* *
24797012 TATATCT
1 TTTATTT
24797019 TTTATTT
1 TTTATTT
24797026 TATT-TTT
1 T-TTATTT
24797033 TTTATGTT
1 TTTAT-TT
24797041 TTATATTT
1 TT-TATTT
24797049 TTTATTCT
1 TTTATT-T
24797057 TTT-TTT
1 TTTATTT
*
24797063 TATATT
1 TTTATT
24797069 AACTATCTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
6 5 0.09
7 20 0.37
8 26 0.48
9 3 0.06
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.77
Consensus pattern (7 bp):
TTTATTT
Found at i:24797235 original size:3 final size:3
Alignment explanation
Indices: 24797227--24797254 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
24797217 TCACAAATTT
24797227 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
24797255 CTTTTGGACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:24802820 original size:47 final size:47
Alignment explanation
Indices: 24802720--24802812 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 47
24802710 ATTTTTTTTT
*
24802720 AAGACTTAACATGAGTTATTTCGTGCATAACACAAATTTCAAACTAA
1 AAGAATTAACATGAGTTATTTCGTGCATAACACAAATTTCAAACTAA
* ** *
24802767 AAGAATTAACTTGAGTTATCTT-GTGCATAACAGGAGTTTCAAACTA
1 AAGAATTAACATGAGTTAT-TTCGTGCATAACACAAATTTCAAACTA
24802813 GTAGAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 38 0.95
48 2 0.05
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (47 bp):
AAGAATTAACATGAGTTATTTCGTGCATAACACAAATTTCAAACTAA
Found at i:24822013 original size:33 final size:33
Alignment explanation
Indices: 24821971--24822037 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
24821961 TGCTACATAG
24821971 CCTGGTGGTTTGCTTCCCTTAAAAATTTGTGGT
1 CCTGGTGGTTTGCTTCCCTTAAAAATTTGTGGT
24822004 CCTGGTGGTTTGCTTCCCTTAAAAATTTGTGGT
1 CCTGGTGGTTTGCTTCCCTTAAAAATTTGTGGT
24822037 C
1 C
24822038 TTTGGTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (33 bp):
CCTGGTGGTTTGCTTCCCTTAAAAATTTGTGGT
Found at i:24832154 original size:42 final size:42
Alignment explanation
Indices: 24832107--24832190 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
24832097 GGATTAGGCT
* *
24832107 GGATTGCCTACCATTTTTGAAGTTCACTGATATTTACATCAA
1 GGATTGCCTACCATTTTCGAAGCTCACTGATATTTACATCAA
*
24832149 GGATTGCCTACTATTTTCGAAGCTCACTGATATTTACATCAA
1 GGATTGCCTACCATTTTCGAAGCTCACTGATATTTACATCAA
24832191 AGGAATATCC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (42 bp):
GGATTGCCTACCATTTTCGAAGCTCACTGATATTTACATCAA
Found at i:24834327 original size:37 final size:38
Alignment explanation
Indices: 24834254--24834329 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
24834244 ATTTTGTTGC
*
24834254 AATTATCACTTTGATGATTATCAATGGTAAATATTTAA
1 AATTATCACTTTGACGATTATCAATGGTAAATATTTAA
*
24834292 AATTATCA-TTCTGACGATTATC-ATGGTGAATATTTAA
1 AATTATCACTT-TGACGATTATCAATGGTAAATATTTAA
24834329 A
1 A
24834330 CTCTATCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
37 17 0.49
38 18 0.51
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (38 bp):
AATTATCACTTTGACGATTATCAATGGTAAATATTTAA
Found at i:24836450 original size:12 final size:12
Alignment explanation
Indices: 24836433--24836457 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24836423 TTATCCCATG
24836433 TGAGGTAAAAGT
1 TGAGGTAAAAGT
24836445 TGAGGTAAAAGT
1 TGAGGTAAAAGT
24836457 T
1 T
24836458 TTAAATAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (12 bp):
TGAGGTAAAAGT
Found at i:24837762 original size:14 final size:15
Alignment explanation
Indices: 24837745--24837777 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
24837735 AATTTAAAAA
24837745 TTTATTTTTTTA-TT
1 TTTATTTTTTTACTT
24837759 TTTA-TTTTTTACTT
1 TTTATTTTTTTACTT
24837773 TTTAT
1 TTTAT
24837778 ATAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTATTTTTTTACTT
Found at i:24839293 original size:17 final size:17
Alignment explanation
Indices: 24839273--24839318 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 17
24839263 TTTATTTAAG
24839273 TATATATATTATAA-GA
1 TATATATATTATAATGA
*
24839289 T-TATATA-AATAATGA
1 TATATATATTATAATGA
24839304 TATATATATTATAAT
1 TATATATATTATAAT
24839319 TAATAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 4 0.16
15 9 0.36
16 7 0.28
17 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (17 bp):
TATATATATTATAATGA
Found at i:24839390 original size:20 final size:20
Alignment explanation
Indices: 24839365--24839403 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24839355 AACAAAATAA
*
24839365 AAAGTAAATATATTTATATT
1 AAAGTAAATATATATATATT
*
24839385 AAAGTATATATATATATAT
1 AAAGTAAATATATATATAT
24839404 ATATATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AAAGTAAATATATATATATT
Found at i:24839398 original size:16 final size:15
Alignment explanation
Indices: 24839369--24839420 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
24839359 AAATAAAAAG
*
24839369 TAAATATATTTATAT
1 TAAATATATATATAT
24839384 TAAAGTATATATATA-
1 TAAA-TATATATATAT
*
24839399 TATATATATATAATAT
1 TAAATATATAT-ATAT
*
24839415 AAAATA
1 TAAATA
24839421 GTAATTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 7 0.23
15 10 0.33
16 13 0.43
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TAAATATATATATAT
Found at i:24846787 original size:2 final size:2
Alignment explanation
Indices: 24846726--24846771 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
24846716 ACACCTAGAC
24846726 AT AT AT 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 AT AT AT
24846768 AT AT
1 AT AT
24846772 TGTGCATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24864702 original size:9 final size:9
Alignment explanation
Indices: 24864688--24864731 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
24864678 GGAGGGCATA
24864688 AGAAAAAAG
1 AGAAAAAAG
24864697 AGAAAAAAG
1 AGAAAAAAG
* *
24864706 AAAAAAAAA
1 AGAAAAAAG
* *
24864715 AGTAGAAAG
1 AGAAAAAAG
24864724 AGAAAAAA
1 AGAAAAAA
24864732 AAATAAATAG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (9 bp):
AGAAAAAAG
Found at i:24864715 original size:20 final size:20
Alignment explanation
Indices: 24864690--24864734 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
24864680 AGGGCATAAG
24864690 AAAAAAG-AGAAAAAAGAAAA
1 AAAAAAGTAG-AAAAAGAAAA
*
24864710 AAAAAAGTAGAAAGAGAAAA
1 AAAAAAGTAGAAAAAGAAAA
24864730 AAAAA
1 AAAAA
24864735 TAAATAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAAAAGTAGAAAAAGAAAA
Found at i:24864731 original size:22 final size:23
Alignment explanation
Indices: 24864690--24864747 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
24864680 AGGGCATAAG
24864690 AAAAAAG-AGAAA-A-AAGAAAA
1 AAAAAAGTAGAAAGAGAAGAAAA
24864710 AAAAAAGTAGAAAGAGAA-AAAA
1 AAAAAAGTAGAAAGAGAAGAAAA
24864732 AAATAAA-TAGAAAGAG
1 AAA-AAAGTAGAAAGAG
24864748 GCCGGTGTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.21
21 5 0.15
22 17 0.50
23 5 0.15
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (23 bp):
AAAAAAGTAGAAAGAGAAGAAAA
Found at i:24868037 original size:18 final size:19
Alignment explanation
Indices: 24868011--24868058 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
24868001 GTGACTGGTG
*
24868011 AAAAAAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
*
24868029 AAAATAATATTTTATGAAT
1 AAAATAATATTTTATAAAT
24868048 AAAATAATATT
1 AAAATAATATT
24868059 AAAATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:24868062 original size:35 final size:32
Alignment explanation
Indices: 24868009--24868076 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 32
24867999 CGGTGACTGG
*
24868009 TGAAAAAAATATTTTAAAATAAAATAATATTTTA
1 TGAAAAAAATATATTAAAAT--AATAATATTTTA
* *
24868043 TGAATAAAATAATATTAAAATATTAATATTTTA
1 TGAAAAAAAT-ATATTAAAATAATAATATTTTA
24868076 T
1 T
24868077 TTATTATTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 12 0.40
34 9 0.30
35 9 0.30
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (32 bp):
TGAAAAAAATATATTAAAATAATAATATTTTA
Found at i:24869294 original size:4 final size:4
Alignment explanation
Indices: 24869285--24869349 Score: 57
Period size: 4 Copynumber: 17.2 Consensus size: 4
24869275 CTTCTTACTC
* * * *
24869285 CTTT CTTT CTTT CTTC CTTT C-TT CTTC CTTT C-TC CTTT C-TT CTTC
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
*
24869330 CTTT C-TC CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT C
24869350 CTCCCTTTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
3 10 0.21
4 37 0.79
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (4 bp):
CTTT
Found at i:24869309 original size:11 final size:11
Alignment explanation
Indices: 24869289--24869368 Score: 64
Period size: 11 Copynumber: 7.7 Consensus size: 11
24869279 TTACTCCTTT
24869289 CTTTCTTTCTTC
1 CTTTC-TTCTTC
24869301 CTTTCTTCTTC
1 CTTTCTTCTTC
24869312 C--T-TTC-TC
1 CTTTCTTCTTC
24869319 CTTTCTTCTTC
1 CTTTCTTCTTC
* *
24869330 CTTTCTCCTTT
1 CTTTCTTCTTC
24869341 CTTTC-T-TTC
1 CTTTCTTCTTC
** *
24869350 CTCCCTTTTTC
1 CTTTCTTCTTC
24869361 CTTTCTTC
1 CTTTCTTC
24869369 CTTTCTCCTT
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
7 3 0.06
8 3 0.06
9 7 0.13
10 4 0.08
11 31 0.58
12 5 0.09
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (11 bp):
CTTTCTTCTTC
Found at i:24869371 original size:8 final size:8
Alignment explanation
Indices: 24869283--24869384 Score: 81
Period size: 7 Copynumber: 13.4 Consensus size: 8
24869273 TTCTTCTTAC
24869283 TCCTTTCT
1 TCCTTTCT
*
24869291 TTCTTTCT
1 TCCTTTCT
24869299 TCCTTTCT
1 TCCTTTCT
*
24869307 T-CTTCCT
1 TCCTTTCT
* *
24869314 TTC-TCCT
1 TCCTTTCT
*
24869321 TTC-TTCT
1 TCCTTTCT
24869328 TCCTTTC-
1 TCCTTTCT
24869335 TCCTTTCT
1 TCCTTTCT
*
24869343 TTCTTTCCT
1 TCCTTT-CT
*
24869352 CCCTTT-T
1 TCCTTTCT
24869359 TCCTTTCT
1 TCCTTTCT
24869367 TCCTTTC-
1 TCCTTTCT
*
24869374 TCCTTGCT
1 TCCTTTCT
24869382 TCC
1 TCC
24869385 ACGTCGATTT
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
7 37 0.47
8 35 0.45
9 6 0.08
ACGTcount: A:0.00, C:0.38, G:0.01, T:0.61
Consensus pattern (8 bp):
TCCTTTCT
Found at i:24869377 original size:15 final size:15
Alignment explanation
Indices: 24869273--24869378 Score: 74
Period size: 15 Copynumber: 6.6 Consensus size: 15
24869263 CCTTAACTTA
*
24869273 TTCTT-CTTACTCCT
1 TTCTTCCTTTCTCCT
*
24869287 TTCTTTCTTTCTTCCTTT
1 TTCTTCCTTTC-TCC--T
24869305 CTTCTTCCTTTCTCCTTT
1 -TTCTTCCTTTCTCC--T
24869323 CTTCTTCCTTTCTCCT
1 -TTCTTCCTTTCTCCT
*
24869339 TTCTTTCTTTCCTCCCT
1 TTCTTCCTTT-CT-CCT
24869356 TT-TTCCTTTCTTCCT
1 TTCTTCCTTTC-TCCT
24869371 TTC-TCCTT
1 TTCTTCCTT
24869379 GCTTCCACGT
Statistics
Matches: 79, Mismatches: 4, Indels: 17
0.79 0.04 0.17
Matches are distributed among these distances:
14 5 0.06
15 24 0.30
16 13 0.16
17 5 0.06
18 22 0.28
19 10 0.13
ACGTcount: A:0.01, C:0.37, G:0.00, T:0.62
Consensus pattern (15 bp):
TTCTTCCTTTCTCCT
Found at i:24870492 original size:18 final size:19
Alignment explanation
Indices: 24870453--24870500 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
24870443 TTAATATTTT
24870453 AATATTATTTTATTTATAA
1 AATATTATTTTATTTATAA
*
24870472 AATATTATTTTA-TTCTAA
1 AATATTATTTTATTTATAA
*
24870490 AATATTCTTTT
1 AATATTATTTT
24870501 CACCCGTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
AATATTATTTTATTTATAA
Found at i:24871186 original size:43 final size:43
Alignment explanation
Indices: 24871125--24871213 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
24871115 ATATTGATAG
24871125 AAAGAGGCCACATATTGATCTCATATAATTGATACAAATAGGA
1 AAAGAGGCCACATATTGATCTCATATAATTGATACAAATAGGA
24871168 AAAGAGGCCACATATTGATCTCATATAATTGATACAAATAGGA
1 AAAGAGGCCACATATTGATCTCATATAATTGATACAAATAGGA
24871211 AAA
1 AAA
24871214 ACATTGATGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (43 bp):
AAAGAGGCCACATATTGATCTCATATAATTGATACAAATAGGA
Found at i:24876692 original size:2 final size:2
Alignment explanation
Indices: 24876687--24876711 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24876677 GTTATATAGC
24876687 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 T
24876712 GATGTAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24886548 original size:18 final size:18
Alignment explanation
Indices: 24886527--24886567 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
24886517 AAATATTTTG
24886527 AAAAAAAATTAAAAAAAA
1 AAAAAAAATTAAAAAAAA
* *
24886545 AAAAAAATTTAAAAAATA
1 AAAAAAAATTAAAAAAAA
24886563 AAAAA
1 AAAAA
24886568 GAAGAGATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAAAAATTAAAAAAAA
Found at i:24886549 original size:17 final size:17
Alignment explanation
Indices: 24886527--24886567 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
24886517 AAATATTTTG
24886527 AAAAAAAATTAAAAAAA
1 AAAAAAAATTAAAAAAA
*
24886544 AAAAAAAATTTAAAAAA
1 AAAAAAAATTAAAAAAA
*
24886561 TAAAAAA
1 AAAAAAA
24886568 GAAGAGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAAAAATTAAAAAAA
Found at i:24886861 original size:48 final size:49
Alignment explanation
Indices: 24886803--24886921 Score: 136
Period size: 48 Copynumber: 2.4 Consensus size: 49
24886793 TCTAAAATAG
* *
24886803 AAATTATTTTTAGGTTTTTTAAATTTTTTAGA-ATTTTT-AAAAATTAAA
1 AAATTATTTTTA-GTTTTTTAAAATTTATAGATATTTTTCAAAAATTAAA
* * * *
24886851 AAATTATTTTTATGTTGTTCAAAATTTATAGATTTTTTTCAAAAATTTAA
1 AAATTATTTTTA-GTTTTTTAAAATTTATAGATATTTTTCAAAAATTAAA
*
24886901 AAA-TATTTTTAATTTTTTAAA
1 AAATTATTTTTAGTTTTTTAAA
24886922 GTGATAAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
48 34 0.58
49 13 0.22
50 12 0.20
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (49 bp):
AAATTATTTTTAGTTTTTTAAAATTTATAGATATTTTTCAAAAATTAAA
Found at i:24886909 original size:21 final size:21
Alignment explanation
Indices: 24886871--24886910 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
24886861 TATGTTGTTC
* * *
24886871 AAAATTTATAGATTTTTTTCA
1 AAAATTTAAAAATATTTTTCA
24886892 AAAATTTAAAAATATTTTT
1 AAAATTTAAAAATATTTTT
24886911 AATTTTTTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (21 bp):
AAAATTTAAAAATATTTTTCA
Found at i:24899720 original size:5 final size:5
Alignment explanation
Indices: 24899710--24899745 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
24899700 ACGCTTGAGA
24899710 GTTTT GTTTT GTTTT GTTTT -TTTT -TTTT -TTTT GTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTT
24899746 GCTAAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 12 0.40
5 18 0.60
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (5 bp):
GTTTT
Found at i:24903742 original size:15 final size:15
Alignment explanation
Indices: 24903705--24903734 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24903695 AGATAAACCT
*
24903705 TTATTCTTCATTTTA
1 TTATTTTTCATTTTA
24903720 TTATTTTTCATTTTA
1 TTATTTTTCATTTTA
24903735 ATTTTTTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATTTTTCATTTTA
Found at i:24924600 original size:5 final size:5
Alignment explanation
Indices: 24924590--24924617 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
24924580 TCTGTATATT
24924590 AATCA AATCA AATCA AATCA AATCA AAT
1 AATCA AATCA AATCA AATCA AATCA AAT
24924618 GTTTGTGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (5 bp):
AATCA
Found at i:24925190 original size:5 final size:5
Alignment explanation
Indices: 24925173--24925211 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
24925163 TTCCCTTAGA
*
24925173 TTCTT TTCCT TTCTT TTCTT TTCTT TTCTT TTCTT TTCT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCT
24925212 AGTTTTTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTCTT
Found at i:24930283 original size:2 final size:2
Alignment explanation
Indices: 24930276--24930309 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
24930266 TGATAAAGTA
*
24930276 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24930310 GATTTTAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24938858 original size:3 final size:3
Alignment explanation
Indices: 24938850--24938880 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
24938840 TGTAAATAAT
*
24938850 GAA GAA GAA GAA GAA GAA GAG GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
24938881 GAGAGAAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:24957691 original size:27 final size:27
Alignment explanation
Indices: 24957630--24957692 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
24957620 CCAACTACCC
* *
24957630 ATTTAATTATTATTTTATTTTCAAAAT
1 ATTTAAATATTATTTTATTTTAAAAAT
* *
24957657 AATAAAATATTATTTTTATTTTAAAAAT
1 ATTTAAATATTA-TTTTATTTTAAAAAT
24957685 -TTTAAATA
1 ATTTAAATA
24957693 AATATTATAG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTTAAATATTATTTTATTTTAAAAAT
Found at i:24964308 original size:505 final size:499
Alignment explanation
Indices: 24963520--24965114 Score: 1793
Period size: 505 Copynumber: 3.2 Consensus size: 499
24963510 TATTATTATG
* * * * * * * *
24963520 ACTTATTATGTTAAATCTCATACGTCTACGTCAATATTTTGATACTATTTATTTCATCTTTATAA
1 ACTTATTATATTAAATCTTACACATTTACGTCAATATTTTGATAATATTTATTACATCTGTATAA
* * * * *
24963585 TATTTTACGTTAATTTTTATAATTTTACATCAAGACTTTTAAACTATTAATTTTCATCATAATTC
66 T-TTTTACGTTAA-TTTTACAGTTTTACGTCAAGACTTTTCAACTATTAATTTTCATTATAATTC
* * * **
24963650 TTTATATCCTTACTATTATTTACGCATAAATTAAAATTTGTAAGCCGTAAAATACTTTAAACTTG
129 TTTTTATCCTTACTATTA-TTACACATAAATTAAAATTTGTAAGCCGTAAAACACTTTAAACTCA
* * * *
24963715 AGAATAACAATTCAAATGTTTAATTTCCCCCAAAATTATGTTTATTTGATATATGATTAACTTGT
193 AGAATAACAATTCAAATGTTTAATTTCCTCAAAAATTATGTTTATTTGACATATGATTAACTTAT
** * * *
24963780 TACGTTAAATCTCACACATTTACATTAATATTTTGACAATACTAGTTCCACCTTTATAAAGTATT
258 TACGTTAAAT-T-TTACATTTACATTAATATTTTGACAATGCTTGTTCCACCTTTATAAAGTTTT
* *
24963845 ACGTTAATTCTTATCATTTTACGTCAAGGTTTTCAACTATTAATTTTCA-CTATAATTCTTTTTA
321 ACATTAATTCTTA-CATTTTACGTCAAGGTTTTCAACTACTAATTTTCATC-ATAATTCTTTTTA
* *** * * * * *
24963909 TCTTTCCTATTATTCACGTATAAATTAAAATTTGTAAACCACAAAACACTTTGAACTCAAAAATA
384 TCTTTACTATTATTCATACATAGATTAAAATTTGTAAGCCACAAAACACTTTAAACTCGAGAATA
* * * *
24963974 AAAATTTAAATGCTTAATTTCTTTAAAAATTATGTTTATTTGACATAATTG
449 AAAATTTAAATGTTTAATTTCTTTAAAAATTATATTTATTTAACATAATTA
* ** * * * *
24964025 ACTTGTTACGTTAAAT-TTCACACATTTACGTTAATATTTTGATAATTTTTGTTACATCCGTATA
1 ACTTATTATATTAAATCTT-ACACATTTACGTCAATATTTTGATAATATTTATTACATCTGTATA
* * ** *
24964089 ATCTTTTACGTTAATTTTCACAGTTTTATGTTAAGGTTTTTCAACTACTAATTTTCATTATAATT
65 AT-TTTTACGTTAATTTT-ACAGTTTTACGTCAAGACTTTTCAACTATTAATTTTCATTATAATT
* * * * *
24964154 CTTTTTATCCTCACTATTAGTTATACATAGATTAAAATATGTAAGCCATAAAACACTTTAAACTC
128 CTTTTTATCCTTACTATTA-TTACACATAAATTAAAATTTGTAAGCCGTAAAACACTTTAAACTC
** * * *
24964219 AAGAATAACAATTCAAATGTTTAATTTCCTTGAGAATTATGTTTATTTAACATATAATTAACTTA
192 AAGAATAACAATTCAAATGTTTAATTTCCTCAAAAATTATGTTTATTTGACATATGATTAACTTA
* * * **
24964284 TTACGTTAAATTTTACGTATTTACATTAATATTTGGATAATGTTTGTTCCACCTTTATATTGTTT
257 TTACGTTAAATTTTAC--ATTTACATTAATATTTTGACAATGCTTGTTCCACCTTTATAAAGTTT
* * *
24964349 TACATTAATT-TTCACGGTTTTACATCAAGGCTTTTCATCTACTAATTTTCATCATAATT-TTCT
320 TACATTAATTCTT-AC-ATTTTACGTCAAGG-TTTTCAACTACTAATTTTCATCATAATTCTT-T
* * * * * **
24964412 ATAT-TCTTGCTATTATTTATACATAGATTAAAATTAGTAAGTCGTAAAACACTTTAAACTCGAG
381 TTATCT-TTACTATTATTCATACATAGATTAAAATTTGTAAGCCACAAAACACTTTAAACTCGAG
* * * *
24964476 AATAACAATTTAAATGTTTAATTACTTCAAAAATTATATTTATTTAATATAATTA
445 AATAAAAATTTAAATGTTTAATTTCTTTAAAAATTATATTTATTTAACATAATTA
* * * * * *
24964531 ACTTATTATATTAAATCTTATACATTTATGTCAATATTTTAAAAATATTTGTCCTAC-T-TTTAT
1 ACTTATTATATTAAATCTTACACATTTACGTCAATATTTTGATAATATTTAT--TACATCTGTAT
* *
24964594 AATGTTTTACATTAATTGTTACAGCTTTACGTCAAGACTTTTCAACTATTAATTTTCATTATAAT
64 AAT-TTTTACGTTAATT-TTACAGTTTTACGTCAAGACTTTTCAACTATTAATTTTCATTATAAT
* * * *
24964659 TTTTTTTATCCTTACTATTATTCACACATAAATTAAAATTTGTAAGCTGTAAAGCACTTTAAATT
127 TCTTTTTATCCTTACTATTATT-ACACATAAATTAAAATTTGTAAGCCGTAAAACACTTTAAACT
* * *
24964724 CTAGAATAACAATTTAAATGTTTAATTTCCTCAAAAATTATGTTTATTTGACTTATGATTAACTT
191 CAAGAATAACAATTCAAATGTTTAATTTCCTCAAAAATTATGTTTATTTGACATATGATTAACTT
* * * * ** **
24964789 ATTACGTTAAATCTCATACATTTACGTCAATATTTTAACAATGCTTGTTTTACAATTATAAAGTT
256 ATTACGTTAAAT-T-TTACATTTACATTAATATTTTGACAATGCTTGTTCCACCTTTATAAAGTT
* * * *
24964854 TTATATTAATTCTTACCACTTTACGTCAAGATTTTCAACTACCAATTTTCATCATAATTCTTTTT
319 TTACATTAATTCTTA-CATTTTACGTCAAGGTTTTCAACTACTAATTTTCATCATAATTCTTTTT
* * * * * *
24964919 ATCCTTACTATTATTCATACATAGGTTAAAATTTATAAGCTACAAAACACTTTAAATTTGAGAAT
383 ATCTTTACTATTATTCATACATAGATTAAAATTTGTAAGCCACAAAACACTTTAAACTCGAGAAT
*
24964984 AAAAATTTAAATATTTAATTT-TTTAAAAAATTATATTTATTTAACATAATTA
448 AAAAATTTAAATGTTTAATTTCTTT-AAAAATTATATTTATTTAACATAATTA
* * * *
24965036 AGTTGTTATATTAAATCTTACACATTTACGTCAATATTTTGATAATCTTTATTGCATCTGTATAA
1 ACTTATTATATTAAATCTTACACATTTACGTCAATATTTTGATAATATTTATTACATCTGTATAA
*
24965101 TTTTTATGTTAATT
66 TTTTTACGTTAATT
24965115 CTTATCACTT
Statistics
Matches: 899, Mismatches: 167, Indels: 49
0.81 0.15 0.04
Matches are distributed among these distances:
503 4 0.00
504 23 0.03
505 461 0.51
506 395 0.44
507 10 0.01
508 6 0.01
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (499 bp):
ACTTATTATATTAAATCTTACACATTTACGTCAATATTTTGATAATATTTATTACATCTGTATAA
TTTTTACGTTAATTTTACAGTTTTACGTCAAGACTTTTCAACTATTAATTTTCATTATAATTCTT
TTTATCCTTACTATTATTACACATAAATTAAAATTTGTAAGCCGTAAAACACTTTAAACTCAAGA
ATAACAATTCAAATGTTTAATTTCCTCAAAAATTATGTTTATTTGACATATGATTAACTTATTAC
GTTAAATTTTACATTTACATTAATATTTTGACAATGCTTGTTCCACCTTTATAAAGTTTTACATT
AATTCTTACATTTTACGTCAAGGTTTTCAACTACTAATTTTCATCATAATTCTTTTTATCTTTAC
TATTATTCATACATAGATTAAAATTTGTAAGCCACAAAACACTTTAAACTCGAGAATAAAAATTT
AAATGTTTAATTTCTTTAAAAATTATATTTATTTAACATAATTA
Found at i:24966139 original size:254 final size:252
Alignment explanation
Indices: 24965390--24966808 Score: 1545
Period size: 254 Copynumber: 5.6 Consensus size: 252
24965380 AGTAAGGATA
* * * * * *
24965390 GAATAATAGTAAGTATATAAATAATTATGGTGAAAATTAATAGTTGAAAAACCTTGATGTAAAGT
1 GAATAATAGTAAGGATAAAAAGAATTATAGTGAAAATTAATAGTTGAAAAACCTTGACGTAAAGC
* * * * * *
24965455 CATAAAAATTAATGTAAAACATTAT-AAAGTTAGAACAAACATTGTCAAAATATTTATGTAAATG
66 CGTAAGAATTAACGTAAAACATTATAAAAGTGA-AACAAGCATTGTCAAAATATTGATGTAAATG
24965519 TGTGAGATTTAACGTAACAAGTCAATCATATGTCAAATAAATATAATTTTTGGAGAAATTAAACA
130 TGTGAGATTTAACGTAACAAGTCAATCATATGTCAAATAAATATAATTTTTGGA-AAATTAAACA
* * * * *
24965584 TTTGAATTGTTATTCTTGAGTTTAAAGTATTTTACGGTTTATAAATTTTAATCTATGCAT
194 TTTAAATTGTTATT-TCGAGTTTAAAGTGTTTTACGGCTTACAAATTTTAATCTATGCAT
* * * * * * * *
24965644 AAATAACAGTAAGGATAAAAAGAATTATTGTGAAAATTAGTAGTTGAAATATCTTGATGTAAAAC
1 GAATAATAGTAAGGATAAAAAGAATTATAGTGAAAATTAATAGTTGAAAAACCTTGACGTAAAGC
* *
24965709 CGTGAGAATTAACGTAAAACATTATAAAGACG-GAATA-AA-CATTATCAAAATATTGATGTAAA
66 CGTAAGAATTAACGTAAAACATTATAAA-A-GTGAA-ACAAGCATTGTCAAAATATTGATGTAAA
* * * *
24965771 TGTATGAGATTTAACGTAACAAGTCAAT--TGTGTCAAATAAATATAATTTTCAGAAAAATTAAA
128 TGTGTGAGATTTAACGTAACAAGTCAATCATATGTCAAATAAATATAATTTT-TGGAAAATTAAA
* * *
24965834 CATTTAAATTGTTATTTTCGAGTTTAAAGTGTTTTACGGCTTACAAATTTTAATTTATACGT
192 CATTTAAATTGTTA-TTTCGAGTTTAAAGTGTTTTACGGCTTACAAATTTTAATCTATGCAT
* * * *
24965896 GAATAATAATAAGGATAGAAAGAATTATAGTAAAAATTAATAGTT-AAAAAGTCTTGACGTAAAG
1 GAATAATAGTAAGGATAAAAAGAATTATAGTGAAAATTAATAGTTGAAAAA-CCTTGACGTAAAG
* * * *
24965960 TCGTAAGAATTAACGTAAAACATTATAAAAGTGAAACAAGCATTGTCAAAATATTAACGTAAATA
65 CCGTAAGAATTAACGTAAAACATTATAAAAGTGAAACAAGCATTGTCAAAATATTGATGTAAATG
** * * * *
24966025 TGTGAGATTTAATATAACTAGTTAATCATATGTCAAATAAACATAATTTTCGGGAAAATTAAACA
130 TGTGAGATTTAACGTAACAAGTCAATCATATGTCAAATAAATATAATTTT-TGGAAAATTAAACA
* * ** * ***
24966090 TTTGAATTGTTATTTACCAGTTTAAAGTGTTTTACAACTTACAAATTTTAATATATATGT
194 TTTAAATTGTTATTT-CGAGTTTAAAGTGTTTTACGGCTTACAAATTTTAATCTATGCAT
* * * * *
24966150 GAATAATAGTAAGGATAAAAAGAATTATGGTGAAAATTAGTAATT-CAAAGCCTTGACGTAAAGC
1 GAATAATAGTAAGGATAAAAAGAATTATAGTGAAAATTAATAGTTGAAAAACCTTGACGTAAAGC
* * * * * * * *
24966214 CTTTAAGAATTGACGTAAAATATTATAAAGGTGGAATAAACATTGTCAAAATATTGACGTAAATG
66 C-GTAAGAATTAACGTAAAACATTATAAAAGTGAAACAAGCATTGTCAAAATATTGATGTAAATG
* * * *
24966279 TGTGAGATTTAACGTAACAAG-CTAAACATATGTCAAATAAACATAATTTTTAGAAAATTAAATA
130 TGTGAGATTTAACGTAACAAGTC-AATCATATGTCAAATAAATATAATTTTTGGAAAATTAAACA
* * *
24966343 TTTAAATTGTTATTTACGAATTTAAAGTGTTTTACGGTTTAGAAATTTTAATCTATGCAT
194 TTTAAATTGTTATTT-CGAGTTTAAAGTGTTTTACGGCTTACAAATTTTAATCTATGCAT
* * * * * *
24966403 AAATAGTAGTAAGAATAAAAAGAATTAT-GATGAAAATTAGTAATTGAAAAACCTTAACGTAAAG
1 GAATAATAGTAAGGATAAAAAGAATTATAG-TGAAAATTAATAGTTGAAAAACCTTGACGTAAAG
* * *
24966467 CCGTAAGAATTAACGTAAAACTTTA-AAAAGGTGGAACAAGCATTGTCAAAATATTGAGGTAAAT
65 CCGTAAGAATTAACGTAAAACATTATAAAA-GTGAAACAAGCATTGTCAAAATATTGATGTAAAT
* * ** *
24966531 GTGTGAGATTTAATGTAATAAGTCAAT--TATGTCAAATAAATATAATTTTTTTTAAAATTAAAT
129 GTGTGAGATTTAACGTAACAAGTCAATCATATGTCAAATAAATATAA-TTTTTGGAAAATTAAAC
* ** * *
24966594 ATTTATATTGTTATTCTTTAATTTAAAGTGTTTTACGGCTTACAAATTTTAATCTTTGCAT
193 ATTTAAATTGTTATT-TCGAGTTTAAAGTGTTTTACGGCTTACAAATTTTAATCTATGCAT
* * * * * * * **
24966655 GAATAATAGTAAGAATAAAAACAATTATAGTGAAAATTAA-ATTTTAAAAACTTTAATGTAAAAT
1 GAATAATAGTAAGGATAAAAAGAATTATAGTGAAAATTAATAGTTGAAAAACCTTGACGTAAAGC
* * * * * *
24966719 CGTAAAAATTAACGTAAAAAATTAT-AAAGCTGAAATAAGCATTGTAAAAATATTGATGTCAATA
66 CGTAAGAATTAACGTAAAACATTATAAAAG-TGAAACAAGCATTGTCAAAATATTGATGTAAATG
* * *
24966783 CGTGAGATTTAACATAATAAGTCAAT
130 TGTGAGATTTAACGTAACAAGTCAAT
24966809 TGTGTCCAAA
Statistics
Matches: 994, Mismatches: 147, Indels: 51
0.83 0.12 0.04
Matches are distributed among these distances:
250 3 0.00
251 120 0.12
252 304 0.31
253 194 0.20
254 364 0.37
255 5 0.01
256 3 0.00
257 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (252 bp):
GAATAATAGTAAGGATAAAAAGAATTATAGTGAAAATTAATAGTTGAAAAACCTTGACGTAAAGC
CGTAAGAATTAACGTAAAACATTATAAAAGTGAAACAAGCATTGTCAAAATATTGATGTAAATGT
GTGAGATTTAACGTAACAAGTCAATCATATGTCAAATAAATATAATTTTTGGAAAATTAAACATT
TAAATTGTTATTTCGAGTTTAAAGTGTTTTACGGCTTACAAATTTTAATCTATGCAT
Found at i:24966627 original size:759 final size:768
Alignment explanation
Indices: 24965188--24966808 Score: 2011
Period size: 759 Copynumber: 2.1 Consensus size: 768
24965178 TAAAGCTGTG
* ** * * * * * * *
24965188 AGAATTAACATAAAATTTTATAAAAGTGGAACAAGTATTATTAAAATATTCACATAAATGTGTGA
1 AGAATTAACGTAAAAAATTATAAAAGTGAAACAAGCATTGTAAAAATATTAACGTAAATATGTGA
* * **
24965253 GATTTAATGTAACAAGTCAATTATATGTCAAATAAACATAATTTTTTAAAAAATTAAACATTTAA
66 GATTTAATATAACAAGTCAATCATATGTCAAATAAACATAATTTTCGAAAAAATTAAACATTTAA
** **
24965318 ATTATTATTCTTTCGTTTAAAGTGTTTTACTGCTTACAAATTTTAATCTATGTGAGAATAATAGT
131 ATTATTATTCTACCGTTTAAAGTGTTTTACAACTTACAAATTTTAA--TA-GT---AATAATAGT
* * * * *
24965383 AAGGATAGAATAATAGTAAGTATATAAATAATTATGGTGAAAATTAATAGTTGAAAAACCTTGAT
190 -A-GATAGAATAATAGTAAGGATAAAAAGAATTATGGTGAAAATTAATAATTGAAAAACCTTGAC
* * * * *
24965448 GTAAAGTCATAAAAATTAATGTAAAACATTATAAAGTTAGAACAAACATTGTCAAAATATTTATG
253 GTAAAGCCATAAAAATTAACGTAAAACATTATAAAGGTAGAACAAACATTGTCAAAATATTGACG
* * *
24965513 TAAATGTGTGAGATTTAACGTAACAAGTCAATCATATGTCAAATAAATATAATTTTTGGAGAAAT
318 TAAATGTGTGAGATTTAACGTAACAAGTCAAACATATGTCAAATAAACATAATTTTTAGAGAAAT
* * * *
24965578 TAAACATTTGAATTGTTATTCTTGAGTTTAAAGTATTTTACGGTTTATAAATTTTAATCTATGCA
383 TAAACATTTAAATTGTTATTCTCGAATTTAAAGTATTTTACGGTTTAGAAATTTTAATCTATGCA
* * * * * *
24965643 TAAATAACAGTAAGGATAAAAAGAATTATTGTGAAAATTAGTAGTTGAAATATCTTGATGTAAAA
448 TAAATAACAGTAAGAATAAAAAGAATTATTGTGAAAATTAGTAATTGAAAAACCTTAACGTAAAA
* * * *
24965708 CCGTGAGAATTAACGTAAAACATTATAAAGACGGAATAAACATTATCAAAATATTGATGTAAATG
513 CCGTAAGAATTAACGTAAAACATTAAAAAGACGGAACAAACATTATCAAAATATTGAGGTAAATG
*
24965773 TATGAGATTTAACGTAACAAGTCAATTGTGTCAAATAAATATAATTTTCAGAAAAATTAAACATT
578 TATGAGATTTAACGTAACAAGTCAATTATGTCAAATAAATATAATTTTCAGAAAAATTAAACATT
* *
24965838 TAAATTGTTATTTTCGAGTTTAAAGTGTTTTACGGCTTACAAATTTTAAT-TTATACGTGAATAA
643 TAAATTGTTATTTTCGAATTTAAAGTGTTTTACGGCTTACAAATTTTAATCTT-TACATGAATAA
* * * * * *
24965902 TAATAAGGATAGAAAGAATTATAGTAAAAATT-AATAGTTAAAAAGTCTTGACGTAAAGTCGTA
707 TAATAAGAATAAAAACAATTATAGTAAAAATTAAAT-GTTAAAAACT-TTAACGTAAAATCGTA
* *
24965965 AGAATTAACGTAAAACATTATAAAAGTGAAACAAGCATTGTCAAAATATTAACGTAAATATGTGA
1 AGAATTAACGTAAAAAATTATAAAAGTGAAACAAGCATTGTAAAAATATTAACGTAAATATGTGA
* * ** *
24966030 GATTTAATATAACTAGTTAATCATATGTCAAATAAACATAATTTTCGGGAAAATTAAACATTTGA
66 GATTTAATATAACAAGTCAATCATATGTCAAATAAACATAATTTTCGAAAAAATTAAACATTTAA
*
24966095 ATTGTTATT-TACCAGTTTAAAGTGTTTTACAACTTACAAATTTT-A-A-T-AT-ATA-T-G-T-
131 ATTATTATTCTACC-GTTTAAAGTGTTTTACAACTTACAAATTTTAATAGTAATAATAGTAGATA
* * *
24966150 GAATAATAGTAAGGATAAAAAGAATTATGGTGAAAATTAGTAATT-CAAAGCCTTGACGTAAAGC
195 GAATAATAGTAAGGATAAAAAGAATTATGGTGAAAATTAATAATTGAAAAACCTTGACGTAAAGC
* * * * * *
24966214 CTTTAAGAATTGACGTAAAATATTATAAAGGTGGAATAAACATTGTCAAAATATTGACGTAAATG
260 C-ATAAAAATTAACGTAAAACATTATAAAGGTAGAACAAACATTGTCAAAATATTGACGTAAATG
*
24966279 TGTGAGATTTAACGTAACAAG-CTAAACATATGTCAAATAAACATAATTTTTAGA-AAATTAAAT
324 TGTGAGATTTAACGTAACAAGTC-AAACATATGTCAAATAAACATAATTTTTAGAGAAATTAAAC
*
24966342 ATTTAAATTGTTATT-TACGAATTTAAAGTGTTTTACGGTTTAGAAATTTTAATCTATGCATAAA
388 ATTTAAATTGTTATTCT-CGAATTTAAAGTATTTTACGGTTTAGAAATTTTAATCTATGCATAAA
** *
24966406 TAGTAGTAAGAATAAAAAGAATTA-TGATGAAAATTAGTAATTGAAAAACCTTAACGTAAAGCCG
452 TAACAGTAAGAATAAAAAGAATTATTG-TGAAAATTAGTAATTGAAAAACCTTAACGTAAAACCG
* ** * * *
24966470 TAAGAATTAACGTAAAACTTTAAAAAGGTGGAACAAGCATTGTCAAAATATTGAGGTAAATGTGT
516 TAAGAATTAACGTAAAACATTAAAAAGACGGAACAAACATTATCAAAATATTGAGGTAAATGTAT
* * **** * *
24966535 GAGATTTAATGTAATAAGTCAATTATGTCAAATAAATATAATTTTTTTTAAAATTAAATATTTAT
581 GAGATTTAACGTAACAAGTCAATTATGTCAAATAAATATAATTTTCAGAAAAATTAAACATTTAA
* * *
24966600 ATTGTTATTCTT-TAATTTAAAGTGTTTTACGGCTTACAAATTTTAATCTTTGCATGAATAATAG
646 ATTGTTATT-TTCGAATTTAAAGTGTTTTACGGCTTACAAATTTTAATCTTTACATGAATAATAA
* * *
24966664 TAAGAATAAAAACAATTATAGTGAAAATTAAATTTTAAAAACTTTAATGTAAAATCGTA
710 TAAGAATAAAAACAATTATAGTAAAAATTAAATGTTAAAAACTTTAACGTAAAATCGTA
* * * * * *
24966723 AAAATTAACGTAAAAAATTAT-AAAGCTGAAATAAGCATTGTAAAAATATTGATGTCAATACGTG
1 AGAATTAACGTAAAAAATTATAAAAG-TGAAACAAGCATTGTAAAAATATTAACGTAAATATGTG
* *
24966787 AGATTTAACATAATAAGTCAAT
65 AGATTTAATATAACAAGTCAAT
24966809 TGTGTCCAAA
Statistics
Matches: 729, Mismatches: 106, Indels: 37
0.84 0.12 0.04
Matches are distributed among these distances:
757 4 0.01
758 85 0.12
759 331 0.45
760 149 0.20
761 1 0.00
762 1 0.00
765 1 0.00
766 3 0.00
767 2 0.00
771 1 0.00
773 1 0.00
776 3 0.00
777 147 0.20
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.35
Consensus pattern (768 bp):
AGAATTAACGTAAAAAATTATAAAAGTGAAACAAGCATTGTAAAAATATTAACGTAAATATGTGA
GATTTAATATAACAAGTCAATCATATGTCAAATAAACATAATTTTCGAAAAAATTAAACATTTAA
ATTATTATTCTACCGTTTAAAGTGTTTTACAACTTACAAATTTTAATAGTAATAATAGTAGATAG
AATAATAGTAAGGATAAAAAGAATTATGGTGAAAATTAATAATTGAAAAACCTTGACGTAAAGCC
ATAAAAATTAACGTAAAACATTATAAAGGTAGAACAAACATTGTCAAAATATTGACGTAAATGTG
TGAGATTTAACGTAACAAGTCAAACATATGTCAAATAAACATAATTTTTAGAGAAATTAAACATT
TAAATTGTTATTCTCGAATTTAAAGTATTTTACGGTTTAGAAATTTTAATCTATGCATAAATAAC
AGTAAGAATAAAAAGAATTATTGTGAAAATTAGTAATTGAAAAACCTTAACGTAAAACCGTAAGA
ATTAACGTAAAACATTAAAAAGACGGAACAAACATTATCAAAATATTGAGGTAAATGTATGAGAT
TTAACGTAACAAGTCAATTATGTCAAATAAATATAATTTTCAGAAAAATTAAACATTTAAATTGT
TATTTTCGAATTTAAAGTGTTTTACGGCTTACAAATTTTAATCTTTACATGAATAATAATAAGAA
TAAAAACAATTATAGTAAAAATTAAATGTTAAAAACTTTAACGTAAAATCGTA
Found at i:24976774 original size:2 final size:2
Alignment explanation
Indices: 24976757--24976793 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
24976747 TTATTTTTTT
24976757 TA TA -A TA T- TA TA -A 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 TA TA TA TA TA TA
24976794 GTATTATAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:24987651 original size:9 final size:9
Alignment explanation
Indices: 24987637--24987670 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
24987627 TTTACTGCTA
24987637 TTATTATTG
1 TTATTATTG
*
24987646 TTATTATTA
1 TTATTATTG
24987655 TTATTATTG
1 TTATTATTG
*
24987664 TTGTTAT
1 TTATTAT
24987671 AAAAGTATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (9 bp):
TTATTATTG
Found at i:24988311 original size:26 final size:26
Alignment explanation
Indices: 24988282--24988335 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
24988272 AAGACAACGT
*
24988282 ATTCAGATTGAAAACTATTCATATTC
1 ATTCAAATTGAAAACTATTCATATTC
24988308 ATTCAAATTGAAAACTATTCATATTC
1 ATTCAAATTGAAAACTATTCATATTC
24988334 AT
1 AT
24988336 CTCCTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (26 bp):
ATTCAAATTGAAAACTATTCATATTC
Found at i:24990203 original size:22 final size:24
Alignment explanation
Indices: 24990178--24990221 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
24990168 GAACAAATAG
24990178 AATAGAAA-TG-AAAAAATAAACA
1 AATAGAAATTGAAAAAAATAAACA
*
24990200 AATATAAATTGAAAAAAATAAA
1 AATAGAAATTGAAAAAAATAAA
24990222 AAAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 2 0.11
24 10 0.53
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (24 bp):
AATAGAAATTGAAAAAAATAAACA
Found at i:24994951 original size:2 final size:2
Alignment explanation
Indices: 24994944--24994982 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
24994934 AGTAATTGAC
*
24994944 TA TA TA TA GA 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 TA T
24994983 TAGTATCAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:24995185 original size:3 final size:3
Alignment explanation
Indices: 24995177--24995205 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
24995167 TCTATAAAAG
24995177 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
24995206 AAGGTCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:25006384 original size:24 final size:23
Alignment explanation
Indices: 25006356--25006400 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
25006346 AATTATTATT
25006356 TATTT-TTTCTGCTTTTTCTTTCAA
1 TATTTCTTT-TGCTTTTT-TTTCAA
*
25006380 TATTTCTTTTTCTTTTTTTTC
1 TATTTCTTTTGCTTTTTTTTC
25006401 CATTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 12 0.63
25 3 0.16
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.73
Consensus pattern (23 bp):
TATTTCTTTTGCTTTTTTTTCAA
Found at i:25007791 original size:28 final size:25
Alignment explanation
Indices: 25007759--25007820 Score: 61
Period size: 28 Copynumber: 2.4 Consensus size: 25
25007749 TCTCATGAAT
* *
25007759 AAAAATTTTCAACGATAAGATTTTCTCA
1 AAAAATTTTCAAAGACAA-ATTTT-T-A
* *
25007787 AAAAAATTACAAAGACAAATTTTTA
1 AAAAATTTTCAAAGACAAATTTTTA
25007812 AAAAATTTT
1 AAAAATTTT
25007821 GTAAGTGAGG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 8 0.29
26 1 0.04
27 5 0.18
28 14 0.50
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.34
Consensus pattern (25 bp):
AAAAATTTTCAAAGACAAATTTTTA
Found at i:25028166 original size:22 final size:22
Alignment explanation
Indices: 25028140--25028197 Score: 91
Period size: 21 Copynumber: 2.7 Consensus size: 22
25028130 TTAATTACTG
25028140 CGTGATTGATTTTTAGGCATTA
1 CGTGATTGATTTTTAGGCATTA
* *
25028162 CGTGATT-AGTTTTAGGCATTG
1 CGTGATTGATTTTTAGGCATTA
25028183 CGTGATTGATTTTTA
1 CGTGATTGATTTTTA
25028198 AGTAATACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 19 0.59
22 13 0.41
ACGTcount: A:0.21, C:0.09, G:0.24, T:0.47
Consensus pattern (22 bp):
CGTGATTGATTTTTAGGCATTA
Found at i:25028275 original size:21 final size:21
Alignment explanation
Indices: 25028249--25028290 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25028239 ACGCAAATCT
* * *
25028249 CAAAGTTAATCATGCATTGCC
1 CAAAGTCAATCACGCAATGCC
25028270 CAAAGTCAATCACGCAATGCC
1 CAAAGTCAATCACGCAATGCC
25028291 TAAAAACTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (21 bp):
CAAAGTCAATCACGCAATGCC
Found at i:25028709 original size:12 final size:12
Alignment explanation
Indices: 25028679--25028718 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
25028669 TTAATGATAA
25028679 AAATATTAATAATT
1 AAATA-TAA-AATT
25028693 AAAATATAAAATT
1 -AAATATAAAATT
25028706 AAATATAAAATT
1 AAATATAAAATT
25028718 A
1 A
25028719 TAATTTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 13 0.52
13 4 0.16
14 3 0.12
15 5 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAATATAAAATT
Found at i:25029191 original size:24 final size:23
Alignment explanation
Indices: 25029153--25029217 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
25029143 ACATATGAAC
* *
25029153 AAATAGAATAGAAATGAAAACAAAT
1 AAATA-AATATAAATAAAAAC-AAT
25029178 AAATAAATATAAATAAAAACAAT
1 AAATAAATATAAATAAAAACAAT
25029201 AATATAAAT-TAAA-AAAA
1 AA-ATAAATATAAATAAAA
25029218 TTTAAAATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
22 4 0.11
23 9 0.24
24 19 0.51
25 5 0.14
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (23 bp):
AAATAAATATAAATAAAAACAAT
Found at i:25033062 original size:23 final size:23
Alignment explanation
Indices: 25033035--25033091 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
25033025 CCTTATTACA
25033035 AGTCACGCAATGTCATATCAACC
1 AGTCACGCAATGTCATATCAACC
*
25033058 AGTCACGCAATGTTATATCAACC
1 AGTCACGCAATGTCATATCAACC
25033081 AGTCACGCAAT
1 AGTCACGCAAT
25033092 ATTTAAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (23 bp):
AGTCACGCAATGTCATATCAACC
Found at i:25033163 original size:65 final size:65
Alignment explanation
Indices: 25033081--25033231 Score: 164
Period size: 65 Copynumber: 2.3 Consensus size: 65
25033071 TATATCAACC
*
25033081 AGTCACGCAAT-ATTTAAAAACTAATCACGCAATA-CTCAAAGTCAGTCACATAATA-TCTAAAA
1 AGTCACGCAATGA-TTAAAAACTAATCACGCAATACCT-AAAATCAGTCACATAATACT-TAAAA
25033143 ATT
63 ATT
* * * * * * *
25033146 AGTCACACAATGATTAAAAACTAGTCATGTAATGCCTAAAATTAGTCACGTAATACTTAAAAATT
1 AGTCACGCAATGATTAAAAACTAATCACGCAATACCTAAAATCAGTCACATAATACTTAAAAATT
* *
25033211 AGTCACGCAATGCTCAAAAAC
1 AGTCACGCAATGATTAAAAAC
25033232 CACTAAAATT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
65 68 0.94
66 4 0.06
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (65 bp):
AGTCACGCAATGATTAAAAACTAATCACGCAATACCTAAAATCAGTCACATAATACTTAAAAATT
Found at i:25033217 original size:22 final size:22
Alignment explanation
Indices: 25033081--25033230 Score: 101
Period size: 22 Copynumber: 6.9 Consensus size: 22
25033071 TATATCAACC
* *
25033081 AGTCACGCAATATTTAAAAACT
1 AGTCACGCAATACTTAAAAATT
* * * *
25033103 AATCACGCAATAC-TCAAAGTC
1 AGTCACGCAATACTTAAAAATT
**
25033124 AGTCACATAATA-TCTAAAAATT
1 AGTCACGCAATACT-TAAAAATT
* *
25033146 AGTCACACAATGA-TTAAAAACT
1 AGTCACGCAAT-ACTTAAAAATT
* * * *
25033168 AGTCATGTAATGCCT-AAAATT
1 AGTCACGCAATACTTAAAAATT
*
25033189 AGTCACGTAATACTTAAAAATT
1 AGTCACGCAATACTTAAAAATT
* *
25033211 AGTCACGCAATGCTCAAAAA
1 AGTCACGCAATACTTAAAAA
25033231 CCACTAAAAT
Statistics
Matches: 97, Mismatches: 26, Indels: 10
0.73 0.20 0.08
Matches are distributed among these distances:
21 30 0.31
22 65 0.67
23 2 0.02
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (22 bp):
AGTCACGCAATACTTAAAAATT
Found at i:25033223 original size:43 final size:43
Alignment explanation
Indices: 25033140--25033223 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
25033130 ATAATATCTA
* *
25033140 AAAATTAGTCACACAATGATTAAAAACTAGTCATGTAATGCCT
1 AAAATTAGTCACACAATGATTAAAAACTAGTCACGCAATGCCT
** *
25033183 AAAATTAGTCACGTAAT-ACTTAAAAATTAGTCACGCAATGC
1 AAAATTAGTCACACAATGA-TTAAAAACTAGTCACGCAATGC
25033224 TCAAAAACCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.03
43 34 0.97
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (43 bp):
AAAATTAGTCACACAATGATTAAAAACTAGTCACGCAATGCCT
Found at i:25036324 original size:18 final size:18
Alignment explanation
Indices: 25036301--25036346 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
25036291 AGACCGGTGG
25036301 GGAAGTTGCCTAGTTGGT
1 GGAAGTTGCCTAGTTGGT
25036319 GGAAGTTGCCTAGTTGGT
1 GGAAGTTGCCTAGTTGGT
*
25036337 GGATGTTGCC
1 GGAAGTTGCC
25036347 AATGATCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.13, G:0.39, T:0.33
Consensus pattern (18 bp):
GGAAGTTGCCTAGTTGGT
Found at i:25038959 original size:29 final size:29
Alignment explanation
Indices: 25038927--25039021 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
25038917 GTACAGTTTC
* * *
25038927 TTCTATTGTACCTGTTTATATACAACTTT
1 TTCTATTCTACCTATTCATATACAACTTT
* * *
25038956 TTCTCTTCTACCTATTCATGTACAACTTC
1 TTCTATTCTACCTATTCATATACAACTTT
* ** * * *
25038985 ATCCCTTGTACCTATTCATGTACAGCTCTT
1 TTCTATTCTACCTATTCATATACAACT-TT
25039015 TTCTATT
1 TTCTATT
25039022 AGCTCCTACT
Statistics
Matches: 51, Mismatches: 14, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
29 46 0.90
30 5 0.10
ACGTcount: A:0.21, C:0.25, G:0.06, T:0.47
Consensus pattern (29 bp):
TTCTATTCTACCTATTCATATACAACTTT
Found at i:25043211 original size:20 final size:18
Alignment explanation
Indices: 25043173--25043208 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
25043163 TATATCATTC
25043173 TATTTTTTATTTAAAAAT
1 TATTTTTTATTTAAAAAT
25043191 TATTATTTTATTTAAAAA
1 TATT-TTTTATTTAAAAA
25043209 ATTTCCTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTTTTATTTAAAAAT
Found at i:25043377 original size:15 final size:14
Alignment explanation
Indices: 25043344--25043403 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
25043334 TATTTAAATT
25043344 TATAAAAT-TAA-A
1 TATAAAATATAATA
*
25043356 CATAAAATTATAATA
1 TATAAAA-TATAATA
25043371 TATAAAATATAA-A
1 TATAAAATATAATA
* *
25043384 TAGTTAAATATGATA
1 TA-TAAAATATAATA
25043399 TATAA
1 TATAA
25043404 TATTAATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
12 6 0.16
13 4 0.11
14 18 0.47
15 10 0.26
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (14 bp):
TATAAAATATAATA
Found at i:25050073 original size:22 final size:21
Alignment explanation
Indices: 25050043--25050127 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 21
25050033 GTGACTTAAT
*
25050043 CATTGCGTGACTGATTTTTAGG
1 CATTACGTGA-TGATTTTTAGG
* * *
25050065 CATTACGTGATTAGTTTTAGC
1 CATTACGTGATGATTTTTAGG
* *
25050086 CATTAAGTGATTAGTTTTTAGG
1 CATTACGTGATGA-TTTTTAGG
**
25050108 CATTGTGTGACTGATTTTTA
1 CATTACGTGA-TGATTTTTA
25050128 AGCAATGCCT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
21 20 0.39
22 29 0.57
23 2 0.04
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.45
Consensus pattern (21 bp):
CATTACGTGATGATTTTTAGG
Found at i:25050084 original size:21 final size:22
Alignment explanation
Indices: 25050057--25050111 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
25050047 GCGTGACTGA
*
25050057 TTTTTAGGCATTACGTGATTAG
1 TTTTTAGGCATTAAGTGATTAG
*
25050079 -TTTTAGCCATTAAGTGATTAG
1 TTTTTAGGCATTAAGTGATTAG
25050100 TTTTTAGGCATT
1 TTTTTAGGCATT
25050112 GTGTGACTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.47
Consensus pattern (22 bp):
TTTTTAGGCATTAAGTGATTAG
Found at i:25050291 original size:43 final size:43
Alignment explanation
Indices: 25050244--25050348 Score: 102
Period size: 43 Copynumber: 2.4 Consensus size: 43
25050234 ACGTAATATT
* * * *
25050244 TAAAAACTAGTTAAGCAATACTCAAAGTCAGTCATGCAATACC
1 TAAAAACTAGTCAAGCAATACTCAAAATCAATCACGCAATACC
* * * * * *
25050287 TAAAAACCAGTCACGTAATGCTCAAAATTAATCACGCAATGCC
1 TAAAAACTAGTCAAGCAATACTCAAAATCAATCACGCAATACC
* *
25050330 TAAAAACTAATCACGCAAT
1 TAAAAACTAGTCAAGCAAT
25050349 GCACAAAAAC
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.22
Consensus pattern (43 bp):
TAAAAACTAGTCAAGCAATACTCAAAATCAATCACGCAATACC
Found at i:25050340 original size:22 final size:22
Alignment explanation
Indices: 25050279--25050358 Score: 83
Period size: 22 Copynumber: 3.7 Consensus size: 22
25050269 AGTCAGTCAT
* * *
25050279 GCAATACCTAAAAACCAGTCAC
1 GCAATGCCTAAAAACTAATCAC
* * *
25050301 GTAATG-CTCAAAATTAATCAC
1 GCAATGCCTAAAAACTAATCAC
25050322 GCAATGCCTAAAAACTAATCAC
1 GCAATGCCTAAAAACTAATCAC
25050344 GCAATGCAC-AAAAAC
1 GCAATGC-CTAAAAAC
25050359 CACCAAAACC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 16 0.34
22 30 0.64
23 1 0.02
ACGTcount: A:0.46, C:0.26, G:0.10, T:0.17
Consensus pattern (22 bp):
GCAATGCCTAAAAACTAATCAC
Found at i:25057692 original size:22 final size:22
Alignment explanation
Indices: 25057667--25057716 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
25057657 TCTTAATTTT
25057667 AATTTCAT-TAAATAT-ATATTCA
1 AATTT-ATATAAATATAATATT-A
*
25057689 AATTTATATATATATAATATTA
1 AATTTATATAAATATAATATTA
25057711 AATTTA
1 AATTTA
25057717 AGAGTTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 18 0.72
23 5 0.20
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTTATATAAATATAATATTA
Found at i:25058980 original size:17 final size:17
Alignment explanation
Indices: 25058933--25058981 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
25058923 TTTGTAAGTG
*
25058933 TTTAATGAAAGAAAAAT
1 TTTAATGAAAGAAGAAT
*
25058950 TTTAATTAAAGAAGAAT
1 TTTAATGAAAGAAGAAT
25058967 TTTAATGAAAGAAGA
1 TTTAATGAAAGAAGA
25058982 GAGCAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (17 bp):
TTTAATGAAAGAAGAAT
Found at i:25067522 original size:2 final size:2
Alignment explanation
Indices: 25067511--25067553 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
25067501 TGATCCCAAT
25067511 TA TA -A TA TA TA TA 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 TA TA TA TA TA TA TA
25067552 TA
1 TA
25067554 CATTTACTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:25068029 original size:26 final size:27
Alignment explanation
Indices: 25068000--25068062 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
25067990 AATCTCTACC
*
25068000 TCTTTTCTCTTTTTTCTT-TTTCTTTT
1 TCTTTTCTCTTTTTTCTTCTTTCTTCT
*
25068026 TCTTTTCT-TTTTTTTTTCTTTCTTCT
1 TCTTTTCTCTTTTTTCTTCTTTCTTCT
25068052 TCTCTTTCTCT
1 TCT-TTTCTCT
25068063 CCTTTCCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 8 0.25
26 18 0.56
27 5 0.16
28 1 0.03
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (27 bp):
TCTTTTCTCTTTTTTCTTCTTTCTTCT
Found at i:25068031 original size:11 final size:11
Alignment explanation
Indices: 25068010--25068058 Score: 62
Period size: 11 Copynumber: 4.3 Consensus size: 11
25068000 TCTTTTCTCT
25068010 TTTTTCTTTTTC
1 TTTTTC-TTTTC
25068022 TTTTTCTTTTC
1 TTTTTCTTTTC
*
25068033 TTTTTTTTTTC
1 TTTTTCTTTTC
*
25068044 TTTCTTCTTCTC
1 TTT-TTCTTTTC
25068056 TTT
1 TTT
25068059 CTCTCCTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
11 18 0.55
12 15 0.45
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:25068054 original size:6 final size:6
Alignment explanation
Indices: 25068000--25068052 Score: 65
Period size: 6 Copynumber: 8.7 Consensus size: 6
25067990 AATCTCTACC
25068000 TCTTTT CTCTTTTT TCTTTT TCTTTT TC-TTT TCTTTT T-TTTT TCTTTCT
1 TCTTTT -TC-TTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTT-T
25068049 TCTT
1 TCTT
25068053 CTCTTTCTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 10 0.24
6 19 0.45
7 9 0.21
8 4 0.10
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:25068776 original size:16 final size:16
Alignment explanation
Indices: 25068757--25068818 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
25068747 TTTTTTACTT
25068757 TTATTTTTTATTTTTA
1 TTATTTTTTATTTTTA
* * **
25068773 TTATATTATATCATTA
1 TTATTTTTTATTTTTA
*
25068789 TT-TATTTTTATTTTTG
1 TTAT-TTTTTATTTTTA
25068805 TTA-TTTTTATTTTT
1 TTATTTTTTATTTTT
25068819 TATTTATTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
15 12 0.34
16 23 0.66
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (16 bp):
TTATTTTTTATTTTTA
Found at i:25068808 original size:15 final size:15
Alignment explanation
Indices: 25068790--25068818 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25068780 ATATCATTAT
25068790 TTATTTTTATTTTTG
1 TTATTTTTATTTTTG
25068805 TTATTTTTATTTTT
1 TTATTTTTATTTTT
25068819 TATTTATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TTATTTTTATTTTTG
Found at i:25068822 original size:32 final size:32
Alignment explanation
Indices: 25068740--25068826 Score: 86
Period size: 32 Copynumber: 2.6 Consensus size: 32
25068730 TTTCAGCCTC
25068740 TTTTTATTTTTTTACTTTTATTTTTTATTTTTATTA
1 TTTTTA-TTTTTTA--TTTA-TTTTTATTTTTATTA
* ** *
25068776 -TATTATATCATTATTTATTTTTATTTTTGTTA
1 TTTTTAT-TTTTTATTTATTTTTATTTTTATTA
25068808 TTTTTATTTTTTATTTATT
1 TTTTTATTTTTTATTTATT
25068827 GAATGAATGG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
32 24 0.57
33 9 0.21
34 1 0.02
35 8 0.19
ACGTcount: A:0.20, C:0.02, G:0.01, T:0.77
Consensus pattern (32 bp):
TTTTTATTTTTTATTTATTTTTATTTTTATTA
Found at i:25072859 original size:17 final size:17
Alignment explanation
Indices: 25072834--25072877 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
25072824 TTATCATTCC
* * *
25072834 TATACATTTTATTACTA
1 TATATATTTTATAAATA
*
25072851 TGTATATTTTATAAATA
1 TATATATTTTATAAATA
25072868 TATATATTTT
1 TATATATTTT
25072878 TTCGTTGGCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (17 bp):
TATATATTTTATAAATA
Found at i:25074202 original size:10 final size:10
Alignment explanation
Indices: 25074187--25074220 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
25074177 TAAATTCATT
25074187 TTTTTTATTA
1 TTTTTTATTA
25074197 TTTTTTATTA
1 TTTTTTATTA
25074207 --TTTTATTA
1 TTTTTTATTA
25074215 TTTTTT
1 TTTTTT
25074221 TAAATGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
10 14 0.64
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:25075174 original size:29 final size:29
Alignment explanation
Indices: 25075132--25075211 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
25075122 CTCATTTGTT
25075132 AACCTTGTTGTCTTTGTTAAAAACTATTG
1 AACCTTGTTGTCTTTGTTAAAAACTATTG
25075161 AACCTTGTTGTCTTTGTTAAAAACTATTG
1 AACCTTGTTGTCTTTGTTAAAAACTATTG
*
25075190 AACCTTG-TCTCTTTTGTTAAAA
1 AACCTTGTTGTC-TTTGTTAAAA
25075212 TTTTGGAATC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 3 0.06
29 46 0.94
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (29 bp):
AACCTTGTTGTCTTTGTTAAAAACTATTG
Found at i:25078862 original size:29 final size:29
Alignment explanation
Indices: 25078805--25078864 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
25078795 CTAATGACCA
* * *
25078805 ACGTCTTTCCTAATTACCCTGGTGTAGTT
1 ACGTCTTTCCTAATTACCATGATGGAGTT
25078834 ACGTCTTTCCTAATTACCATGATGGAGTT
1 ACGTCTTTCCTAATTACCATGATGGAGTT
25078863 AC
1 AC
25078865 ACTATTGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (29 bp):
ACGTCTTTCCTAATTACCATGATGGAGTT
Found at i:25085618 original size:30 final size:31
Alignment explanation
Indices: 25085584--25085662 Score: 101
Period size: 30 Copynumber: 2.5 Consensus size: 31
25085574 AACTATTAAT
25085584 TATAAAAACTTATTTAATTCAAA-ATAA-AAA
1 TATAAAAACTTATTTAATT-AAATATAATAAA
*
25085614 TATAAAAACTTAATTAATTAAATATAATAAA
1 TATAAAAACTTATTTAATTAAATATAATAAA
25085645 -ATTAAAAACTTTATTTAA
1 TA-TAAAAAC-TTATTTAA
25085663 ATTTTTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 3 0.07
30 23 0.53
31 10 0.23
32 7 0.16
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (31 bp):
TATAAAAACTTATTTAATTAAATATAATAAA
Found at i:25085705 original size:16 final size:16
Alignment explanation
Indices: 25085684--25085715 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25085674 AATGTTGTGA
25085684 AAATTTTTTGAGTATT
1 AAATTTTTTGAGTATT
25085700 AAATTTTTTGAGTATT
1 AAATTTTTTGAGTATT
25085716 TTGTTTGACT
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:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (16 bp):
AAATTTTTTGAGTATT
Found at i:25097280 original size:13 final size:13
Alignment explanation
Indices: 25097262--25097286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25097252 ACATAAAATA
25097262 AATATAATATAAT
1 AATATAATATAAT
25097275 AATATAATATAA
1 AATATAATATAA
25097287 ACTCTAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATAATATAAT
Found at i:25097716 original size:25 final size:25
Alignment explanation
Indices: 25097688--25097735 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
25097678 GAATGGTTAA
25097688 ATAT-TTTATTAAT-TATCTTAATTTT
1 ATATATTT-TTAATATA-CTTAATTTT
25097713 ATATATTTTTAATATACTTAATT
1 ATATATTTTTAATATACTTAATT
25097736 ATATTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (25 bp):
ATATATTTTTAATATACTTAATTTT
Found at i:25099690 original size:21 final size:22
Alignment explanation
Indices: 25099659--25099699 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
25099649 ATCAGCATGA
25099659 TTTATGTTAAAATT-TAAAATTT
1 TTTATGTT-AAATTCTAAAATTT
25099681 TTTAT-TTAAATTCTAAAAT
1 TTTATGTTAAATTCTAAAAT
25099700 AGATTGAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTATGTTAAATTCTAAAATTT
Found at i:25111596 original size:31 final size:31
Alignment explanation
Indices: 25111561--25111654 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 31
25111551 TTCATGGGAT
25111561 CATCAAAGATATGCACAGCCTTCATATGCTC
1 CATCAAAGATATGCACAGCCTTCATATGCTC
** ** *
25111592 CATC-AAGCCGA-G-ACTA---TTCATGGGAT-
1 CATCAAAG-ATATGCAC-AGCCTTCATATGCTC
25111618 CATCAAAGATATGCACAGCCTTCATATGCTC
1 CATCAAAGATATGCACAGCCTTCATATGCTC
25111649 CATCAA
1 CATCAA
25111655 GCCGAGACTA
Statistics
Matches: 44, Mismatches: 10, Indels: 18
0.61 0.14 0.25
Matches are distributed among these distances:
26 5 0.11
27 12 0.27
28 2 0.05
29 2 0.05
30 12 0.27
31 11 0.25
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (31 bp):
CATCAAAGATATGCACAGCCTTCATATGCTC
Found at i:25111617 original size:57 final size:57
Alignment explanation
Indices: 25111550--25111665 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
25111540 TCTAATTCAC
25111550 ATTCATGGGATCATCAAAGATATGCACAGCCTTCATATGCTCCATCAAGCCGAGACT
1 ATTCATGGGATCATCAAAGATATGCACAGCCTTCATATGCTCCATCAAGCCGAGACT
25111607 ATTCATGGGATCATCAAAGATATGCACAGCCTTCATATGCTCCATCAAGCCGAGACT
1 ATTCATGGGATCATCAAAGATATGCACAGCCTTCATATGCTCCATCAAGCCGAGACT
25111664 AT
1 AT
25111666 GTTCCTCAGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (57 bp):
ATTCATGGGATCATCAAAGATATGCACAGCCTTCATATGCTCCATCAAGCCGAGACT
Found at i:25120698 original size:2 final size:2
Alignment explanation
Indices: 25120691--25120722 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
25120681 CAACAAAGGC
*
25120691 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25120723 TCTAGCAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25130537 original size:13 final size:13
Alignment explanation
Indices: 25130519--25130543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25130509 TTTCAGAAAA
25130519 TTTATAAAATCAT
1 TTTATAAAATCAT
25130532 TTTATAAAATCA
1 TTTATAAAATCA
25130544 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:25131805 original size:19 final size:19
Alignment explanation
Indices: 25131781--25131817 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
25131771 CTTCTAAACT
25131781 TCAAATCATACTCCAATAC
1 TCAAATCATACTCCAATAC
25131800 TCAAATCATACTCCAATA
1 TCAAATCATACTCCAATA
25131818 AATCAAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (19 bp):
TCAAATCATACTCCAATAC
Found at i:25145352 original size:11 final size:12
Alignment explanation
Indices: 25145331--25145357 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
25145321 GGTTTTCTGG
25145331 TTTTTCTTTTTT
1 TTTTTCTTTTTT
25145343 TTTTTCTTTTTT
1 TTTTTCTTTTTT
25145355 TTT
1 TTT
25145358 GGTGTGTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:25159751 original size:24 final size:23
Alignment explanation
Indices: 25159694--25159739 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
25159684 ATACAATAAC
**
25159694 CTTATCCTAATTTAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
25159717 CTTATCCTAATAGAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
25159740 TGTTATTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:25177574 original size:22 final size:20
Alignment explanation
Indices: 25177538--25177587 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
25177528 TTATTTAATT
*
25177538 TTTTTAAAAATATAATAATAA
1 TTTTTAAAAATATAA-AAAAA
*
25177559 TTTTTAAAATTAATAAAAAAA
1 TTTTTAAAAAT-ATAAAAAAA
25177580 TATTTTAA
1 T-TTTTAA
25177588 TATTTTCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTTAAAAATATAAAAAAA
Found at i:25178312 original size:156 final size:155
Alignment explanation
Indices: 25178026--25178764 Score: 1049
Period size: 155 Copynumber: 4.7 Consensus size: 155
25178016 GAGTAAGCAT
* * *
25178026 GATGGATTTAGAACCCTTTTTCTTGTTTTCTTGTATTTT-TTTCAACTATTTTAATGATTTAGAA
1 GATGGATTTAGAACTCTTTTTCTTGTTTTCTTGTATTTTCTTTCAATTTTTTTAATGATTTAGAA
* * * *
25178090 TATATATTTACGTTGCTAATGAAGTTTTTTGGTATGAATTTAGAACTTTCTTTCTTGGTTTT-TT
66 TATATATTTACGTTGCTAATGAAGCTTTTAGG-ATGGATTTAGAATTTTCTTTCTT-GTTTTCTT
* *
25178154 GTATTTCTTTGGTTATGAATCTTTTAG
129 GTATTTCTTTAGTTATGAAGCTTTTAG
* * *
25178181 GATGGATTTAGAAATCTTTATCTT-TTTTCCTTGTATTTTCTTTCAATTTTTTTAATGGTTTAGA
1 GATGGATTTAGAACTCTTTTTCTTGTTTT-CTTGTATTTTCTTTCAATTTTTTTAATGATTTAGA
*
25178245 ATATATATTTGCGTTGCTAATGAAGCTTTTAGGATGGATTTAGAATTTTTCTTTCTTGTTTTCTT
65 ATATATATTTACGTTGCTAATGAAGCTTTTAGGATGGATTTAGAA-TTTTCTTTCTTGTTTTCTT
25178310 GTATTTCTTTAGTTATGAAGCTTTTAG
129 GTATTTCTTTAGTTATGAAGCTTTTAG
* *
25178337 GATAGATTTAGAACTCTTTTGCTTGTTTTCTTGTATTTTCTTTCAA-TTTTTTAATGATTTAGAA
1 GATGGATTTAGAACTCTTTTTCTTGTTTTCTTGTATTTTCTTTCAATTTTTTTAATGATTTAG--
* * * *
25178401 TATATATATATATATACGTTGTTAATGAAGCTTTTAGAATAGATTTAGAACTTTCTTTCTTGTTT
64 -A-ATATATAT-T-TACGTTGCTAATGAAGCTTTTAGGATGGATTTAGAATTTTCTTTCTTGTTT
*
25178466 TCTTGTATTTCTTTAGTTATGAAGGTTTTAG
125 TCTTGTATTTCTTTAGTTATGAAGCTTTTAG
*
25178497 GATGGATTTAGAACTCTTTTTCTTGTTTTCTTCTATTTTCTTTCAATTTTTTTAATGATTTAGAA
1 GATGGATTTAGAACTCTTTTTCTTGTTTTCTTGTATTTTCTTTCAATTTTTTTAATGATTTAGAA
* * *
25178562 TATGTATTTACATTGCTAATGAAGCTTTTAGGATGGATGTAGAATTTTCTTTCTTGTTTTCTTGT
66 TATATATTTACGTTGCTAATGAAGCTTTTAGGATGGATTTAGAATTTTCTTTCTTGTTTTCTTGT
*
25178627 ATTTCTTTAATTATGAAGCTTTTAG
131 ATTTCTTTAGTTATGAAGCTTTTAG
*
25178652 GATGGATTTA-AATCTCTTTTTTTTTTGTTTTCTTGTATTTTCTTTCAATTTTTTTAATGATTTA
1 GATGGATTTAGAA-CTC--TTTTTCTTGTTTTCTTGTATTTTCTTTCAATTTTTTTAATGATTTA
* * *
25178716 GAATATATATTTGA-GTTGCTAATGAAGTTTTTAGGATGTATTTAAAATT
63 GAATATATATTT-ACGTTGCTAATGAAGCTTTTAGGATGGATTTAGAATT
25178765 AACAAAACTT
Statistics
Matches: 524, Mismatches: 44, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
154 6 0.01
155 149 0.28
156 126 0.24
157 96 0.18
158 3 0.01
159 8 0.02
160 88 0.17
161 48 0.09
ACGTcount: A:0.23, C:0.08, G:0.14, T:0.54
Consensus pattern (155 bp):
GATGGATTTAGAACTCTTTTTCTTGTTTTCTTGTATTTTCTTTCAATTTTTTTAATGATTTAGAA
TATATATTTACGTTGCTAATGAAGCTTTTAGGATGGATTTAGAATTTTCTTTCTTGTTTTCTTGT
ATTTCTTTAGTTATGAAGCTTTTAG
Found at i:25178333 original size:60 final size:60
Alignment explanation
Indices: 25178264--25178379 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 60
25178254 TGCGTTGCTA
* * * *
25178264 ATGAAGCTTTTAGGATGGATTTAGAATTTTTCTTTCTTGTTTTCTTGTA-TTTCTTTAGTT
1 ATGAAGCTTTTAGGATAGATTTAGAACTCTT-TTGCTTGTTTTCTTGTATTTTCTTTAGTT
25178324 ATGAAGCTTTTAGGATAGATTTAGAACTCTTTTGCTTGTTTTCTTGTATTTTCTTT
1 ATGAAGCTTTTAGGATAGATTTAGAACTCTTTTGCTTGTTTTCTTGTATTTTCTTT
25178380 CAATTTTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 16 0.31
60 35 0.69
ACGTcount: A:0.19, C:0.09, G:0.16, T:0.55
Consensus pattern (60 bp):
ATGAAGCTTTTAGGATAGATTTAGAACTCTTTTGCTTGTTTTCTTGTATTTTCTTTAGTT
Found at i:25178519 original size:59 final size:60
Alignment explanation
Indices: 25178425--25178539 Score: 171
Period size: 59 Copynumber: 1.9 Consensus size: 60
25178415 TACGTTGTTA
*
25178425 ATGAAGCTTTTAGAATAGATTTAGAACTTTCTTTCTTGTTTTCTTGTA-TTTCTTTAGTT
1 ATGAAGCTTTTAGAATAGATTTAGAACTTTCTTTCTTGTTTTCTTCTATTTTCTTTAGTT
* * *
25178484 ATGAAGGTTTTAGGATGGATTTAGAACTCTT-TTTCTTGTTTTCTTCTATTTTCTTT
1 ATGAAGCTTTTAGAATAGATTTAGAACT-TTCTTTCTTGTTTTCTTCTATTTTCTTT
25178540 CAATTTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 41 0.82
60 9 0.18
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.55
Consensus pattern (60 bp):
ATGAAGCTTTTAGAATAGATTTAGAACTTTCTTTCTTGTTTTCTTCTATTTTCTTTAGTT
Found at i:25178598 original size:316 final size:315
Alignment explanation
Indices: 25178030--25178749 Score: 1038
Period size: 316 Copynumber: 2.3 Consensus size: 315
25178020 AAGCATGATG
* *
25178030 GATTTAGAACCCTTTTTCTTGTTTTCTTGTATTTT-TTTCAACTATTTTAATGATTTAG---A-A
1 GATTTAGAACTCTTTTTCTTGTTTTCTTGTATTTTCTTTCAACTTTTTTAATGATTTAGAATATA
* * *
25178090 TATATATTTACGTTGCTAATGAAGTTTTTTGGTATGAATTTAGAACTTTCTTTCTTGGTTTTTTG
66 TATATATTTACGTTGCTAATGAAGCTTTTAGATATGAATTTAGAACTTTCTTTCTTGGTTTTTTG
* * *
25178155 TATTTCTTTGGTTATGAATCTTTTAGGATGGATTTAGAAATCTTTATCTTTTTTCCTTGTATTTT
131 TATTTCTTTAGTTATGAAGCTTTTAGGATGGATTTAGAAATCTTTATCTTTTTTCCTTCTATTTT
* * * *
25178220 CTTTCAATTTTTTTAATGGTTTAGAATATATATTTGCGTTGCTAATGAAGCTTTTAGGATGGATT
196 CTTTCAATTTTTTTAATGATTTAGAATATATATTTACATTGCTAATGAAGCTTTTAGGATGGATG
*
25178285 TAGAATTTTTCTTTCTTGTTTTCTTGTATTTCTTTAGTTATGAAGCTTTTAGGATA
261 TAGAA-TTTTCTTTCTTGTTTTCTTGTATTTCTTTAATTATGAAGCTTTTAGGATA
*
25178341 GATTTAGAACTCTTTTGCTTGTTTTCTTGTATTTTCTTTCAA-TTTTTTAATGATTTAGAATATA
1 GATTTAGAACTCTTTTTCTTGTTTTCTTGTATTTTCTTTCAACTTTTTTAATGATTTAGAATATA
*
25178405 TATATATATATACGTTGTTAATGAAGCTTTTAGA-AT-AGATTTAGAACTTTCTTTCTT-GTTTT
66 TATATAT-T-TACGTTGCTAATGAAGCTTTTAGATATGA-ATTTAGAACTTTCTTTCTTGGTTTT
* * *
25178467 CTTGTATTTCTTTAGTTATGAAGGTTTTAGGATGGATTTAGAACTCTTTTTCTTGTTTT-CTTCT
128 -TTGTATTTCTTTAGTTATGAAGCTTTTAGGATGGATTTAGAAATCTTTATCTT-TTTTCCTTCT
*
25178531 ATTTTCTTTCAATTTTTTTAATGATTTAGAATATGTATTTACATTGCTAATGAAGCTTTTAGGAT
191 ATTTTCTTTCAATTTTTTTAATGATTTAGAATATATATTTACATTGCTAATGAAGCTTTTAGGAT
*
25178596 GGATGTAGAATTTTCTTTCTTGTTTTCTTGTATTTCTTTAATTATGAAGCTTTTAGGATG
256 GGATGTAGAATTTTCTTTCTTGTTTTCTTGTATTTCTTTAATTATGAAGCTTTTAGGATA
* *
25178656 GATTTA-AATCTCTTTTTTTTTTGTTTTCTTGTATTTTCTTTCAATTTTTTTAATGATTTAG-A-
1 GATTTAGAA-CTC--TTTTTCTTGTTTTCTTGTATTTTCTTTCAACTTTTTTAATGATTTAGAAT
* *
25178718 ATATATAT-TTGA-GTTGCTAATGAAGTTTTTAG
63 ATATATATATTTACGTTGCTAATGAAGCTTTTAG
25178750 GATGTATTTA
Statistics
Matches: 370, Mismatches: 25, Indels: 27
0.88 0.06 0.06
Matches are distributed among these distances:
311 48 0.13
312 24 0.06
313 1 0.00
314 4 0.01
315 72 0.19
316 152 0.41
317 53 0.14
318 16 0.04
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.54
Consensus pattern (315 bp):
GATTTAGAACTCTTTTTCTTGTTTTCTTGTATTTTCTTTCAACTTTTTTAATGATTTAGAATATA
TATATATTTACGTTGCTAATGAAGCTTTTAGATATGAATTTAGAACTTTCTTTCTTGGTTTTTTG
TATTTCTTTAGTTATGAAGCTTTTAGGATGGATTTAGAAATCTTTATCTTTTTTCCTTCTATTTT
CTTTCAATTTTTTTAATGATTTAGAATATATATTTACATTGCTAATGAAGCTTTTAGGATGGATG
TAGAATTTTCTTTCTTGTTTTCTTGTATTTCTTTAATTATGAAGCTTTTAGGATA
Found at i:25178645 original size:59 final size:62
Alignment explanation
Indices: 25178580--25178701 Score: 171
Period size: 59 Copynumber: 2.0 Consensus size: 62
25178570 TACATTGCTA
25178580 ATGAAGCTTTTAGGATGGATGTAGAA-T-TTTCTTTCTTGTTTTCTTGTA-TTTCTTT-AATT
1 ATGAAGCTTTTAGGATGGATGTA-AACTCTTTCTTTCTTGTTTTCTTGTATTTTCTTTCAATT
* * *
25178639 ATGAAGCTTTTAGGATGGATTTAAATCTCTTTTTTTTTTGTTTTCTTGTATTTTCTTTCAATT
1 ATGAAGCTTTTAGGATGGATGTAAA-CTCTTTCTTTCTTGTTTTCTTGTATTTTCTTTCAATT
25178702 TTTTTAATGA
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
58 2 0.04
59 22 0.40
60 1 0.02
61 19 0.35
62 7 0.13
63 4 0.07
ACGTcount: A:0.20, C:0.09, G:0.15, T:0.57
Consensus pattern (62 bp):
ATGAAGCTTTTAGGATGGATGTAAACTCTTTCTTTCTTGTTTTCTTGTATTTTCTTTCAATT
Found at i:25179468 original size:27 final size:27
Alignment explanation
Indices: 25179422--25179481 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
25179412 GCCTTACCTC
* *
25179422 ATAAATCATGCGATAGATGTGCA-TCTA
1 ATAAATCATGCAATAAATGTGCATTC-A
*
25179449 ATAAATCGTGCAATAAATGTGCATTCA
1 ATAAATCATGCAATAAATGTGCATTCA
25179476 ATAAAT
1 ATAAAT
25179482 TGTGTCACAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (27 bp):
ATAAATCATGCAATAAATGTGCATTCA
Found at i:25182455 original size:21 final size:22
Alignment explanation
Indices: 25182430--25182470 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
25182420 CCTAGGTGGA
*
25182430 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
25182451 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
25182471 AAAAAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:25182471 original size:20 final size:21
Alignment explanation
Indices: 25182430--25182474 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
25182420 CCTAGGTGGA
*
25182430 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
25182451 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
25182471 AAAA
1 AAAA
25182475 AAAAGGTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:25182475 original size:21 final size:20
Alignment explanation
Indices: 25182428--25182475 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
25182418 ACCCTAGGTG
*
25182428 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
25182448 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
25182470 GAAAAA
1 GAAAAA
25182476 AAAGGTAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:25204604 original size:16 final size:16
Alignment explanation
Indices: 25204572--25204605 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25204562 TGTGTGGTAG
* *
25204572 ATAAAATTTTAATTTA
1 ATAAAATTTCAAATTA
25204588 ATAAAATTTCAAATTA
1 ATAAAATTTCAAATTA
25204604 AT
1 AT
25204606 CTATACACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAAATTTCAAATTA
Found at i:25207462 original size:50 final size:49
Alignment explanation
Indices: 25207383--25207481 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 49
25207373 ATTTTGTCAT
* * *
25207383 TTACTTTACTTGCACATCAAATAGATTTAGGTTCAGTTTGATTATTATAA
1 TTACTTTACTTACACACCAAATAGATTTAGGTTCAG-TTGACTATTATAA
* *
25207433 TTACTTTACTTACACACCAAGTA-AGTTTAGGTTTAGTTGACTATTATAA
1 TTACTTTACTTACACACCAAATAGA-TTTAGGTTCAGTTGACTATTATAA
25207482 ATAACCTCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 13 0.30
50 30 0.70
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.42
Consensus pattern (49 bp):
TTACTTTACTTACACACCAAATAGATTTAGGTTCAGTTGACTATTATAA
Found at i:25211358 original size:21 final size:20
Alignment explanation
Indices: 25211333--25211371 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25211323 CGGCCATAAG
25211333 GAGAGAACAAGAAAGAAAATA
1 GAGAGAA-AAGAAAGAAAATA
* *
25211354 GAGAGGAAAGGAAGAAAA
1 GAGAGAAAAGAAAGAAAA
25211372 GAGAAAAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.64, C:0.03, G:0.31, T:0.03
Consensus pattern (20 bp):
GAGAGAAAAGAAAGAAAATA
Found at i:25217932 original size:15 final size:15
Alignment explanation
Indices: 25217903--25217942 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
25217893 TTGATTTACA
*
25217903 TTTTA-TATAAATTT
1 TTTTATTATTAATTT
25217917 TTTTATTATTAATTT
1 TTTTATTATTAATTT
*
25217932 TTTGATTATTA
1 TTTTATTATTA
25217943 GTTGAGTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTTATTATTAATTT
Found at i:25218855 original size:31 final size:31
Alignment explanation
Indices: 25218817--25218879 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
25218807 GATTTGGTTG
*
25218817 ATTGATTTATTGTGTGATTAATATCCATCTT
1 ATTGATTTATCGTGTGATTAATATCCATCTT
*
25218848 ATTGATTTGTCGTGTGATTAATATCCATCTT
1 ATTGATTTATCGTGTGATTAATATCCATCTT
25218879 A
1 A
25218880 GAATCGGACC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.49
Consensus pattern (31 bp):
ATTGATTTATCGTGTGATTAATATCCATCTT
Found at i:25220198 original size:2 final size:2
Alignment explanation
Indices: 25220191--25220244 Score: 56
Period size: 2 Copynumber: 26.5 Consensus size: 2
25220181 TGTCCAAATT
** *
25220191 TA TA TA TA TA TA TA TA TA TA TA GTA TA GCG TA TA TC T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA
25220234 TA TA TA TA TA T
1 TA TA TA TA TA T
25220245 TGTATTTTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
1 1 0.02
2 41 0.93
3 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:25221555 original size:2 final size:2
Alignment explanation
Indices: 25221543--25221592 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
25221533 CTAATTAAAT
25221543 TA TA T- TA TA TA TA 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 TA TA TA TA TA TA TA
25221584 TA TA TA TA T
1 TA TA TA TA T
25221593 GTATTTTGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25224743 original size:30 final size:30
Alignment explanation
Indices: 25224709--25224798 Score: 153
Period size: 30 Copynumber: 3.0 Consensus size: 30
25224699 GTATAGATCA
*
25224709 CAGGGAAAAACCAAGGAAAAGCACTGATAG
1 CAGGGACAAACCAAGGAAAAGCACTGATAG
*
25224739 CAGGGACAAGCCAAGGAAAAGCACTGATAG
1 CAGGGACAAACCAAGGAAAAGCACTGATAG
*
25224769 CAGGGACAAATCAAGGAAAAGCACTGATAG
1 CAGGGACAAACCAAGGAAAAGCACTGATAG
25224799 GCCAGAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.47, C:0.18, G:0.28, T:0.08
Consensus pattern (30 bp):
CAGGGACAAACCAAGGAAAAGCACTGATAG
Found at i:25225154 original size:12 final size:12
Alignment explanation
Indices: 25225137--25225161 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25225127 TTGTATGTTG
25225137 GTCTTCAAAGTT
1 GTCTTCAAAGTT
25225149 GTCTTCAAAGTT
1 GTCTTCAAAGTT
25225161 G
1 G
25225162 CATGAAAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (12 bp):
GTCTTCAAAGTT
Found at i:25226614 original size:27 final size:27
Alignment explanation
Indices: 25226584--25226639 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
25226574 AAACACTTGG
*
25226584 GGGTGTTCCGAATGC-GAAGACACCTAA
1 GGGTGTTCCAAATGCAGAAG-CACCTAA
* *
25226611 GGGTGTTTCAAATGCAGAAGCGCCTAA
1 GGGTGTTCCAAATGCAGAAGCACCTAA
25226638 GG
1 GG
25226640 ACATTCCAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.20
Consensus pattern (27 bp):
GGGTGTTCCAAATGCAGAAGCACCTAA
Found at i:25226716 original size:54 final size:54
Alignment explanation
Indices: 25226612--25226716 Score: 120
Period size: 54 Copynumber: 1.9 Consensus size: 54
25226602 GACACCTAAG
* * * * * *
25226612 GGTGTTTCAAATGCAGAAGCGCCTAAGGACATTCCAAGCACATAAGTACCTGAA
1 GGTGTTCCAAATGCAGAAGCGCCCAAAGACATTCCAAACACAGAAATACCTGAA
* * **
25226666 GGTGTTCCAAATGCGGAAGCGCCCAAAGATATTCCAAACGTAGAAATACCT
1 GGTGTTCCAAATGCAGAAGCGCCCAAAGACATTCCAAACACAGAAATACCT
25226717 AAGAACAAGC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
54 41 1.00
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (54 bp):
GGTGTTCCAAATGCAGAAGCGCCCAAAGACATTCCAAACACAGAAATACCTGAA
Found at i:25236098 original size:22 final size:22
Alignment explanation
Indices: 25236073--25236139 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
25236063 TCCTAAATTA
25236073 TTTAGAAAAATTCAAATGAGTC
1 TTTAGAAAAATTCAAATGAGTC
* * *
25236095 TTTA-AAAATTTGTAAAT---TA
1 TTTAGAAAAATT-CAAATGAGTC
25236114 TTTAGAAAAATTCAAATGAGTC
1 TTTAGAAAAATTCAAATGAGTC
25236136 TTTA
1 TTTA
25236140 AACTTTTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
19 9 0.26
20 6 0.18
21 6 0.18
22 13 0.38
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (22 bp):
TTTAGAAAAATTCAAATGAGTC
Found at i:25236103 original size:20 final size:20
Alignment explanation
Indices: 25236078--25236141 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
25236068 AATTATTTAG
25236078 AAAAATTCAAATGAGTCTTT
1 AAAAATTCAAATGAGTCTTT
* * *
25236098 AAAAATTTGTAAATTA-T-TTAG
1 AAAAA-TT-CAAATGAGTCTT-T
25236119 AAAAATTCAAATGAGTCTTT
1 AAAAATTCAAATGAGTCTTT
25236139 AAA
1 AAA
25236142 CTTTTATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
19 5 0.15
20 13 0.39
21 10 0.30
22 5 0.15
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (20 bp):
AAAAATTCAAATGAGTCTTT
Found at i:25236112 original size:41 final size:41
Alignment explanation
Indices: 25236057--25236141 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
25236047 TCATATTTAA
25236057 AAAAATTCCTAAATTATTTAGAAAAATTCAAATGAGTCTTT
1 AAAAATTCCTAAATTATTTAGAAAAATTCAAATGAGTCTTT
**
25236098 AAAAATTTGTAAATTATTTAGAAAAATTCAAATGAGTCTTT
1 AAAAATTCCTAAATTATTTAGAAAAATTCAAATGAGTCTTT
25236139 AAA
1 AAA
25236142 CTTTTATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.36
Consensus pattern (41 bp):
AAAAATTCCTAAATTATTTAGAAAAATTCAAATGAGTCTTT
Found at i:25236200 original size:30 final size:30
Alignment explanation
Indices: 25236125--25236221 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 30
25236115 TTAGAAAAAT
* * *
25236125 TCAAATGAGTCTTTA-AACTTTTATTAT-AT
1 TCAAATAAGTCTTTATAA-TTTTATTTTGAA
* *
25236154 TC-AATCAAGTCCTTATAATTTTATTTTGAG
1 TCAAAT-AAGTCTTTATAATTTTATTTTGAA
*
25236184 TCAAATAAGTCTTTATATTTTTATTTTGAA
1 TCAAATAAGTCTTTATAATTTTATTTTGAA
*
25236214 TTAAATAA
1 TCAAATAA
25236222 ATTCTTATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
28 3 0.05
29 17 0.30
30 33 0.59
31 3 0.05
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.48
Consensus pattern (30 bp):
TCAAATAAGTCTTTATAATTTTATTTTGAA
Found at i:25236230 original size:30 final size:29
Alignment explanation
Indices: 25236160--25236231 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
25236150 ATATTCAATC
*
25236160 AAGTCCTTATAATTTTATTTTGAGTCAAAT
1 AAGT-CTTATAATTTTATTTTGAATCAAAT
* *
25236190 AAGTCTTTATATTTTTATTTTGAATTAAAT
1 AAGTC-TTATAATTTTATTTTGAATCAAAT
*
25236220 AAATTCTTATAA
1 -AAGTCTTATAA
25236232 CTAATTATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 1 0.03
30 30 0.86
31 4 0.11
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (29 bp):
AAGTCTTATAATTTTATTTTGAATCAAAT
Found at i:25241025 original size:16 final size:16
Alignment explanation
Indices: 25240954--25241028 Score: 50
Period size: 16 Copynumber: 4.8 Consensus size: 16
25240944 AATTATTTTA
25240954 AAAT-ATTTT-AATTC
1 AAATCATTTTAAATTC
* * * *
25240968 TAGTCATTATAAATTT
1 AAATCATTTTAAATTC
*
25240984 AAATCAATTTAAGTATTC
1 AAATCATTTTAA--ATTC
*
25241002 --ATCGTTTTAAATTC
1 AAATCATTTTAAATTC
25241016 AAATCATTTTAAA
1 AAATCATTTTAAA
25241029 ATTGGAGTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
14 6 0.14
15 4 0.09
16 30 0.70
18 3 0.07
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.45
Consensus pattern (16 bp):
AAATCATTTTAAATTC
Found at i:25241951 original size:30 final size:30
Alignment explanation
Indices: 25241915--25241974 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
25241905 ACGTTTAAGC
* *
25241915 ATTTTTATTTTTAGTTAAATAAATTTTTAT
1 ATTTTTATTTTTAGTCAAATAAATCTTTAT
25241945 ATTTTTATTTTTAGTCAAATAAATCTTTAT
1 ATTTTTATTTTTAGTCAAATAAATCTTTAT
25241975 TATTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (30 bp):
ATTTTTATTTTTAGTCAAATAAATCTTTAT
Found at i:25247528 original size:19 final size:19
Alignment explanation
Indices: 25247501--25247547 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
25247491 AACCAAAGAG
*
25247501 ATAAGATAAAATTTT-TAAA
1 ATAAAATAAAATTTTAT-AA
* *
25247520 ATAAAATAATATTTTATTA
1 ATAAAATAAAATTTTATAA
25247539 ATAAAATAA
1 ATAAAATAA
25247548 TATTAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAAAATAAAATTTTATAA
Found at i:25251337 original size:17 final size:17
Alignment explanation
Indices: 25251317--25251353 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
25251307 TATAACTTTT
25251317 TAAAAAATAAATAAAAA
1 TAAAAAATAAATAAAAA
25251334 TAAAAAATAAATAAAAA
1 TAAAAAATAAATAAAAA
25251351 TAA
1 TAA
25251354 GTATTTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
TAAAAAATAAATAAAAA
Found at i:25255381 original size:24 final size:24
Alignment explanation
Indices: 25255348--25255401 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
25255338 ACTGAATTTT
*
25255348 ATATT-AAATAGCCTCATTCTAGA
1 ATATTCAAATAGACTCATTCTAGA
* *
25255371 ATATTCAAATAGACTTATTTTAGA
1 ATATTCAAATAGACTCATTCTAGA
*
25255395 ACATTCA
1 ATATTCA
25255402 GTGTGACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (24 bp):
ATATTCAAATAGACTCATTCTAGA
Done.