Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, whole genome shotgun sequence
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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 20 of 91
Found at i:3494238 original size:24 final size:24
Alignment explanation
Indices: 3494211--3494280 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
3494201 TTTATTAAAA
3494211 TTTTAAATCGA-ATTATTTTTATAT
1 TTTTAAATC-ATATTATTTTTATAT
* *
3494235 TTTTTATTCATATTATTTTTATA-
1 TTTTAAATCATATTATTTTTATAT
*
3494258 TTATAACATCATATTATATTTTA
1 TTTTAA-ATCATATTAT-TTTTA
3494281 AATTATCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 5 0.13
24 28 0.74
25 5 0.13
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (24 bp):
TTTTAAATCATATTATTTTTATAT
Found at i:3494260 original size:11 final size:11
Alignment explanation
Indices: 3494222--3494261 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
3494212 TTTAAATCGA
3494222 ATTATTTTTAT
1 ATTATTTTTAT
*
3494233 ATTTTTTATTCAT
1 ATTATTT-TT-AT
3494246 ATTATTTTTAT
1 ATTATTTTTAT
3494257 ATTAT
1 ATTAT
3494262 AACATCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 13 0.52
12 4 0.16
13 8 0.32
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTATTTTTAT
Found at i:3494642 original size:2 final size:2
Alignment explanation
Indices: 3494635--3494660 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3494625 TCCTGAAATC
3494635 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
3494661 GCCTTTGATA
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):
AT
Found at i:3501121 original size:22 final size:21
Alignment explanation
Indices: 3501096--3501155 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 21
3501086 AAAATTACAA
* *
3501096 AAAAATTAATATTTTTTGTTAT
1 AAAAATTATTATTTTTT-TAAT
3501118 -AAAATTATTTAATTTTTTTAAT
1 AAAAATTA-TT-ATTTTTTTAAT
3501140 AAAAATTATTATTTTT
1 AAAAATTATTATTTTT
3501156 AATTCATAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 13 0.39
22 6 0.18
23 14 0.42
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
AAAAATTATTATTTTTTTAAT
Found at i:3501239 original size:21 final size:21
Alignment explanation
Indices: 3501215--3501271 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
3501205 TCATAAATTT
3501215 AAATTATATAAATTTAA-AAAA
1 AAATTAT-TAAATTTAATAAAA
* *
3501236 AAATTAATTTTAA-TTAATAAAT
1 AAATT-A-TTAAATTTAATAAAA
3501258 AAATTATTAAATTT
1 AAATTATTAAATTT
3501272 TAATTTTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
20 4 0.14
21 12 0.41
22 12 0.41
23 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTATTAAATTTAATAAAA
Found at i:3501469 original size:21 final size:21
Alignment explanation
Indices: 3501444--3501488 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3501434 GTTTTAGTTG
3501444 ATTAATAAATTTAAT-TTTAAA
1 ATTAA-AAATTTAATATTTAAA
* *
3501465 ATTAAAATTTTAATATTTATA
1 ATTAAAAATTTAATATTTAAA
3501486 ATT
1 ATT
3501489 TTTTTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTAAAAATTTAATATTTAAA
Found at i:3509521 original size:32 final size:32
Alignment explanation
Indices: 3509485--3509545 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
3509475 TTTTATTTAG
* * *
3509485 AATTAATAATTCGTATATTTATATTATATAAA
1 AATTAAAAATTCGTATATTCATATCATATAAA
*
3509517 AATTAAAAATTTGTATATTCATATCATAT
1 AATTAAAAATTCGTATATTCATATCATAT
3509546 TTTATATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (32 bp):
AATTAAAAATTCGTATATTCATATCATATAAA
Found at i:3510236 original size:2 final size:2
Alignment explanation
Indices: 3510178--3510217 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3510168 CCTCCAACCA
3510178 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
3510218 GGGAGAGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3510695 original size:12 final size:12
Alignment explanation
Indices: 3510675--3510716 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
3510665 TATATTATTT
3510675 TTTAATTTTATA
1 TTTAATTTTATA
*
3510687 TTTATTTTTATATA
1 TTTA-ATTT-TATA
3510701 TTTAATTTTATA
1 TTTAATTTTATA
3510713 TTTA
1 TTTA
3510717 TATAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 12 0.46
13 6 0.23
14 8 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTAATTTTATA
Found at i:3510702 original size:14 final size:14
Alignment explanation
Indices: 3510675--3510713 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3510665 TATATTATTT
3510675 TTTAA-TTT-TATA
1 TTTAATTTTATATA
*
3510687 TTTATTTTTATATA
1 TTTAATTTTATATA
3510701 TTTAATTTTATAT
1 TTTAATTTTATAT
3510714 TTATATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 4 0.17
13 3 0.13
14 16 0.70
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTAATTTTATATA
Found at i:3510745 original size:19 final size:19
Alignment explanation
Indices: 3510710--3510758 Score: 75
Period size: 18 Copynumber: 2.7 Consensus size: 19
3510700 ATTTAATTTT
3510710 ATATTTATA-TAAAAAATA
1 ATATTTATATTAAAAAATA
*
3510728 ATATTTATATTTAAAAATA
1 ATATTTATATTAAAAAATA
3510747 ATATTT-TATTAA
1 ATATTTATATTAA
3510759 TTTCGGGTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATTTATATTAAAAAATA
Found at i:3510761 original size:22 final size:19
Alignment explanation
Indices: 3510710--3510756 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
3510700 ATTTAATTTT
*
3510710 ATATTTATA-TAAAAAATA
1 ATATTTATATTTAAAAATA
3510728 ATATTTATATTTAAAAATA
1 ATATTTATATTTAAAAATA
3510747 ATATTT-TATT
1 ATATTTATATT
3510757 AATTTCGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATATTTAAAAATA
Found at i:3511727 original size:60 final size:60
Alignment explanation
Indices: 3511662--3511824 Score: 150
Period size: 60 Copynumber: 2.7 Consensus size: 60
3511652 CATAAATAGA
* * * * *
3511662 CAAAATTATTATACTGTCACTCTATCAAAATTATGAAAATAACCC-TCATACTATAATGGT
1 CAAAATTACTATAATATCACTCTATCAAAATTATAAAAAT-ACCCTTAATACTATAATGGT
*** * **
3511722 CAAAATTACTATAATATTTTTCTATCATAATTATAAAAATACCCTTAATACTATAATTTAT
1 CAAAATTACTATAATATCACTCTATCAAAATTATAAAAATACCCTTAATACTATAA-TGGT
* * * *
3511783 CAAAATTACAATAATATC-CTTTGATCATAATTACAAAAATAC
1 CAAAATTACTATAATATCACTCT-ATCAAAATTATAAAAATAC
3511825 TCTTTTAATT
Statistics
Matches: 84, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
59 4 0.05
60 44 0.52
61 36 0.43
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36
Consensus pattern (60 bp):
CAAAATTACTATAATATCACTCTATCAAAATTATAAAAATACCCTTAATACTATAATGGT
Found at i:3511810 original size:61 final size:59
Alignment explanation
Indices: 3511685--3511824 Score: 156
Period size: 61 Copynumber: 2.3 Consensus size: 59
3511675 CTGTCACTCT
* * * * * * *
3511685 ATCAAAATTATGAAAATAACCCTCATACTATAATGGTCAAAATTACTATAATATTTTTCT
1 ATCATAATTATAAAAAT-ACCCTAATACTATAATGATCAAAATTACAATAATATCTTTCG
*
3511745 ATCATAATTATAAAAATACCCTTAATACTATAATTTATCAAAATTACAATAATATCCTTT-G
1 ATCATAATTATAAAAATACCC-TAATACTATAA-TGATCAAAATTACAATAATAT-CTTTCG
*
3511806 ATCATAATTACAAAAATAC
1 ATCATAATTATAAAAATAC
3511825 TCTTTTAATT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
59 4 0.06
60 25 0.37
61 36 0.53
62 3 0.04
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (59 bp):
ATCATAATTATAAAAATACCCTAATACTATAATGATCAAAATTACAATAATATCTTTCG
Found at i:3512279 original size:16 final size:15
Alignment explanation
Indices: 3512258--3512300 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
3512248 GCCCAATTCG
3512258 ATTTTTATTTTGTATT
1 ATTTTTATTTT-TATT
*
3512274 ATTTTTATTTTTTTT
1 ATTTTTATTTTTATT
3512289 ATTTTGTATTTT
1 ATTTT-TATTTT
3512301 AGGTATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (15 bp):
ATTTTTATTTTTATT
Found at i:3512307 original size:25 final size:25
Alignment explanation
Indices: 3512259--3512326 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
3512249 CCCAATTCGA
**
3512259 TTTTTATTTTGTATTATTTTTATTT
1 TTTTTATTTTGTATTATTGGTATTT
3512284 TTTTTATTTTGTATT-TTAGGTA-TT
1 TTTTTATTTTGTATTATT-GGTATTT
* *
3512308 TTATTATTTATTTATTATT
1 TTTTTATTT-TGTATTATT
3512327 ACTATATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 12 0.33
25 22 0.61
26 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (25 bp):
TTTTTATTTTGTATTATTGGTATTT
Found at i:3512320 original size:4 final size:4
Alignment explanation
Indices: 3512307--3512447 Score: 83
Period size: 4 Copynumber: 34.2 Consensus size: 4
3512297 TTTTAGGTAT
* * * * * *
3512307 TTTA -TTA TTTA TTTA -TTA TTACTA TATA TTAA TATA TGTA TATC TTTA
1 TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
3512355 TTTA TTTA TTTA TTTA TTTA TATGTA TTTTA TTTA TATA GTTA TATA TTTA
1 TTTA TTTA TTTA TTTA TTTA T-T-TA -TTTA TTTA TTTA TTTA TTTA TTTA
* *
3512406 -TTA TTATA TTATAA TTTA TTTA TTTA -TTA TTTC TTTT TTTA T
1 TTTA TT-TA TT-T-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
3512448 CTTGTAATAT
Statistics
Matches: 107, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
3 12 0.11
4 75 0.70
5 10 0.09
6 9 0.08
7 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:3512374 original size:57 final size:59
Alignment explanation
Indices: 3512307--3512442 Score: 142
Period size: 59 Copynumber: 2.3 Consensus size: 59
3512297 TTTTAGGTAT
*
3512307 TTTA-TTATTTATTTATTATTA-CTATATA-TTAATATATGTA-TATCTTTATT-T-ATTTA
1 TTTATTTATTTATTTATT-TTATCTATATAGTT-ATATATGTATTAT-TATATTATAATTTA
* *
3512363 TTTATTTATTTATATGTATTTTATTTATATAGTTATATATTTATTATTATATTATAATTTA
1 TTTATTTATTTAT-T-TATTTTATCTATATAGTTATATATGTATTATTATATTATAATTTA
*
3512424 TTTATTTA-TTATTTCTTTT
1 TTTATTTATTTATTTATTTT
3512443 TTTATCTTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
56 4 0.06
57 8 0.12
58 9 0.13
59 24 0.35
60 10 0.15
61 13 0.19
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (59 bp):
TTTATTTATTTATTTATTTTATCTATATAGTTATATATGTATTATTATATTATAATTTA
Found at i:3512481 original size:57 final size:54
Alignment explanation
Indices: 3512307--3512491 Score: 150
Period size: 57 Copynumber: 3.4 Consensus size: 54
3512297 TTTTAGGTAT
* * * *
3512307 TTTA-TTATTTATTTATTAT-TACTATATATTA-ATA-TATGTATATCTTTATTTA
1 TTTATTTATTTATTTATTATGTATTTTAT-TTATATAGT-TATATATTTTTATTTA
3512359 TTTATTTATTTATTTA-TATGTATTTTATTTATATAGTTATATATTTATTATTATA
1 TTTATTTATTTATTTATTATGTATTTTATTTATATAGTTATATATTT-TTATT-TA
* * * *
3512414 TTATAATTTATTTATTTATTATTTCTTTT-TTTATCTTGTAATATATATTTTTATTTA
1 TT-T-ATTTATTTATTTATTATGTATTTTATTTATATAGT--TATATATTTTTATTTA
*
3512471 TCTTATTTTATTT-TTAATTAT
1 T-TTA-TTTATTTATTTATTAT
3512492 CTGTTAATTT
Statistics
Matches: 111, Mismatches: 9, Indels: 22
0.78 0.06 0.15
Matches are distributed among these distances:
52 10 0.09
53 27 0.24
54 6 0.05
55 4 0.04
56 9 0.08
57 32 0.29
58 14 0.13
59 9 0.08
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (54 bp):
TTTATTTATTTATTTATTATGTATTTTATTTATATAGTTATATATTTTTATTTA
Found at i:3513439 original size:5 final size:5
Alignment explanation
Indices: 3513429--3513521 Score: 70
Period size: 5 Copynumber: 18.6 Consensus size: 5
3513419 TCTTTTTACC
* * *
3513429 TTTAT TTTA- TTT-T TTTATT TTTGT TTTAC TTT-C TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
*
3513477 TATTAT TATTTT TTTCACT TTTAT TTTAT TTTA- -TTAT TTTAT TTT
1 T-TTAT T-TTAT TTT-A-T TTTAT TTTAT TTTAT TTTAT TTTAT TTT
3513522 CTTTAAATAA
Statistics
Matches: 73, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
3 3 0.04
4 10 0.14
5 41 0.56
6 15 0.21
7 4 0.05
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:3513445 original size:19 final size:18
Alignment explanation
Indices: 3513429--3513521 Score: 84
Period size: 19 Copynumber: 5.2 Consensus size: 18
3513419 TCTTTTTACC
3513429 TTTATTTTATTTTTTTATT
1 TTTATTTTATTTTTTTA-T
* *
3513448 TTTGTTTTACTTTCTTTAT
1 TTTATTTTA-TTTTTTTAT
*
3513467 TTTATTTTATTATTATTAT
1 TTTATTTTATT-TTTTTAT
* *
3513486 TTT-TTTCA--CTTTTAT
1 TTTATTTTATTTTTTTAT
*
3513501 TTTATTTTATTATTTTAT
1 TTTATTTTATTTTTTTAT
3513519 TTT
1 TTT
3513522 CTTTAAATAA
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
15 8 0.14
16 4 0.07
18 15 0.25
19 25 0.42
20 7 0.12
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.77
Consensus pattern (18 bp):
TTTATTTTATTTTTTTAT
Found at i:3513467 original size:33 final size:32
Alignment explanation
Indices: 3513416--3513526 Score: 118
Period size: 33 Copynumber: 3.3 Consensus size: 32
3513406 GTTTATTTAG
*
3513416 TATTCTTTTTACCTTTATTTTATTTTTTTATTTT
1 TATT-TTTTTA-CTTTATTTTATTTTATTATTTT
* *
3513450 TGTTTTACTTT-CTTTATTTTATTTTATTATTAT
1 TATTTT--TTTACTTTATTTTATTTTATTATTTT
3513483 TATTTTTTTCACTTTTATTTTATTTTATTA-TTT
1 TATTTTTTT-AC-TTTATTTTATTTTATTATTTT
3513516 TATTTTCTTTA
1 TATTTT-TTTA
3513527 AATAAAAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
31 3 0.05
33 37 0.56
34 23 0.35
35 3 0.05
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.75
Consensus pattern (32 bp):
TATTTTTTTACTTTATTTTATTTTATTATTTT
Found at i:3513682 original size:58 final size:57
Alignment explanation
Indices: 3513539--3514465 Score: 1016
Period size: 59 Copynumber: 15.7 Consensus size: 57
3513529 TAAAAATAAA
* * *
3513539 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC
** * *
3513596 AAAAAAGGTTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAATTTTC
* * *
3513654 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTTT
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAA--TTTTC
* * *
3513713 AAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATAAATTTTCCTTGAAAATCAAAGTTTTC
1 AAAAAATA---TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAA-TTTTC
* * * **
3513775 AAAGAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTAAAA
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTT--TC
* * * *
3513834 AAAAAAGGATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAATTTTTC
1 AAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAA-TTTTC
* * * *
3513893 AAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAA-TTTCCTTAAAAATAAAATTTC
1 -AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC
* * * * * *
3513950 AAAAAAAAGGTTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTC
1 AAAAAATA--TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAATTTTC
**
3514010 AAAAAATATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC
* * *
3514067 AAAAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTC
1 --AAAAAATA--TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC
* * *
3514128 AAAAAAAAAGGATTTTTGGGGAAAAGTTGAAAGTATCCATTTTCCTTAAAAATAAATTTTCC
1 ---AAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTT-C
** * *
3514190 AAAAAAAATATTTTTGGAAAAAAGTTAAAAGTATTAATTTTCCTT-AAAAGTAAATTTTC
1 --AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAA-TAAATTTTC
** *
3514249 AAAAAA-ACGGTTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTTC
1 AAAAAATA---TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAA-TTTTC
*
3514310 AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTT-AAGAATAAATTTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAA-AATAAATTTTC
* * *
3514367 AAAAAAAAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAATA-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAATTTTC
* *
3514426 AAAAGAGTATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
1 AAAA-AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
3514466 TTCTACACAA
Statistics
Matches: 747, Mismatches: 87, Indels: 70
0.83 0.10 0.08
Matches are distributed among these distances:
56 8 0.01
57 79 0.11
58 173 0.23
59 207 0.28
60 108 0.14
61 111 0.15
62 57 0.08
63 4 0.01
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (57 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC
Found at i:3514247 original size:17 final size:18
Alignment explanation
Indices: 3514214--3514248 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3514204 TGGAAAAAAG
3514214 TTAAAAGTATTAATTTTCC
1 TTAAAAGTA-TAATTTTCC
3514233 TTAAAAGTA-AATTTTC
1 TTAAAAGTATAATTTTC
3514249 AAAAAAACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.46
Consensus pattern (18 bp):
TTAAAAGTATAATTTTCC
Found at i:3517711 original size:8 final size:8
Alignment explanation
Indices: 3517693--3517808 Score: 152
Period size: 8 Copynumber: 14.6 Consensus size: 8
3517683 ATGAGAAAAA
3517693 AAAAGAATG
1 AAAA-AATG
3517702 AAAAAATG
1 AAAAAATG
3517710 AAAAAATG
1 AAAAAATG
3517718 AAAAAATG
1 AAAAAATG
3517726 AAAAAATG
1 AAAAAATG
3517734 AAAAAATG
1 AAAAAATG
*
3517742 AAAAAATA
1 AAAAAATG
3517750 AAAAAAT-
1 AAAAAATG
3517757 AAAAAAT-
1 AAAAAATG
3517764 AAAAAAT-
1 AAAAAATG
3517771 AAAAAATG
1 AAAAAATG
3517779 AAAAAA-G
1 AAAAAATG
3517786 ATAAAAATGG
1 A-AAAAAT-G
3517796 AAGAAAA-G
1 AA-AAAATG
3517804 AAAAA
1 AAAAA
3517809 TTCAAATTGA
Statistics
Matches: 101, Mismatches: 1, Indels: 12
0.89 0.01 0.11
Matches are distributed among these distances:
7 26 0.26
8 64 0.63
9 5 0.05
10 6 0.06
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:3518895 original size:36 final size:36
Alignment explanation
Indices: 3518850--3518929 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
3518840 TTTGAGTTTT
*
3518850 TTTTAAATAAAAAATCTTCAAATGAGAATCTTTGAG
1 TTTTAAATAAAAAATCTTCAAATAAGAATCTTTGAG
* *
3518886 TTTTAAATAAGAAATTTTCAAATAAGAATCTTTGAG
1 TTTTAAATAAAAAATCTTCAAATAAGAATCTTTGAG
*
3518922 TCTTAAAT
1 TTTTAAAT
3518930 GAGAATCTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (36 bp):
TTTTAAATAAAAAATCTTCAAATAAGAATCTTTGAG
Found at i:3518898 original size:21 final size:21
Alignment explanation
Indices: 3518869--3519120 Score: 130
Period size: 21 Copynumber: 11.8 Consensus size: 21
3518859 AAAAATCTTC
*
3518869 AAATGAGAATCTTTGAGTTTT
1 AAATAAGAATCTTTGAGTTTT
3518890 AAATAAGAA------A-TTTT
1 AAATAAGAATCTTTGAGTTTT
*
3518904 CAAATAAGAATCTTTGAGTCTT
1 -AAATAAGAATCTTTGAGTTTT
* *
3518926 AAATGAGAATCTTTAAGACATTTT
1 AAATAAGAATCTTT--GA-GTTTT
* *
3518950 CAAATGAGAATCTTTGAGTCTT
1 -AAATAAGAATCTTTGAGTTTT
* *
3518972 AAATAAGAATTTTTTGAGTCTT
1 AAATAAGAA-TCTTTGAGTTTT
* * * *
3518994 AAATGATAATCTTTAAGACATTTCC
1 AAATAAGAATCTTT--GA-GTTT-T
* * *
3519019 AAATGAGAATCTTTGAATCTT
1 AAATAAGAATCTTTGAGTTTT
*
3519040 --ATGAA-AATCTTTAAGATGTTTC
1 AAAT-AAGAATCTTT--GA-GTTTT
*
3519062 AAATAAGAATCTTTGAATTTT
1 AAATAAGAATCTTTGAGTTTT
*
3519083 AAATAAGAATCTTTGAATTTT
1 AAATAAGAATCTTTGAGTTTT
3519104 AAATGAA-AATCTTTGAG
1 AAAT-AAGAATCTTTGAG
3519121 ATGTGAAACC
Statistics
Matches: 181, Mismatches: 25, Indels: 50
0.71 0.10 0.20
Matches are distributed among these distances:
14 4 0.02
15 10 0.06
19 9 0.05
20 1 0.01
21 73 0.40
22 33 0.18
23 10 0.06
24 14 0.08
25 27 0.15
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (21 bp):
AAATAAGAATCTTTGAGTTTT
Found at i:3518950 original size:46 final size:46
Alignment explanation
Indices: 3518893--3518981 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
3518883 GAGTTTTAAA
*
3518893 TAAGAAATTTTCAAATAAGAATCTTTGAGTCTTAAATGAGAATCTT
1 TAAGAAATTTTCAAATAAGAATCTTTGAGTCTTAAATAAGAATCTT
* *
3518939 TAAGACATTTTCAAATGAGAATCTTTGAGTCTTAAATAAGAAT
1 TAAGAAATTTTCAAATAAGAATCTTTGAGTCTTAAATAAGAAT
3518982 TTTTTGAGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (46 bp):
TAAGAAATTTTCAAATAAGAATCTTTGAGTCTTAAATAAGAATCTT
Found at i:3518993 original size:68 final size:67
Alignment explanation
Indices: 3518905--3519120 Score: 234
Period size: 68 Copynumber: 3.3 Consensus size: 67
3518895 AGAAATTTTC
* *
3518905 AAATAAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTC
1 AAATAAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTCCAAATGAGAATCTTTGAATC
3518970 TT
66 TT
* *
3518972 AAATAAGAATTTTTTGAGTCTTAAATGATAATCTTTAAGACATTTCCAAATGAGAATCTTTGAAT
1 AAATAAGAA-TCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTCCAAATGAGAATCTTTGAAT
3519037 CTT
65 CTT
* * *
3519040 --ATGAA-AATCTTTAAGATGT-TTCAAATAAGAATCTTT--GA-ATTT-TAAATAAGAATCTTT
1 AAAT-AAGAATCTTT--GA-GTCTT-AAATGAGAATCTTTAAGACATTTCCAAATGAGAATCTTT
*
3519097 GAATTTT
61 GAATCTT
3519104 AAATGAA-AATCTTTGAG
1 AAAT-AAGAATCTTTGAG
3519121 ATGTGAAACC
Statistics
Matches: 131, Mismatches: 10, Indels: 20
0.81 0.06 0.12
Matches are distributed among these distances:
63 1 0.01
64 21 0.16
65 8 0.06
66 18 0.14
67 15 0.11
68 68 0.52
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (67 bp):
AAATAAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACATTTCCAAATGAGAATCTTTGAATC
TT
Found at i:3519072 original size:43 final size:45
Alignment explanation
Indices: 3518972--3519084 Score: 131
Period size: 43 Copynumber: 2.5 Consensus size: 45
3518962 TTTGAGTCTT
* * *
3518972 AAATAAGAATTTTTTGAGTCTTAAATGATAATCTTTAAGACATTTCC
1 AAATAAGAA-TCTTTGAATCTT-AATGAAAATCTTTAAGACATTTCC
* **
3519019 AAATGAGAATCTTTGAATCTT-ATGAAAATCTTTAAGATGTTT-C
1 AAATAAGAATCTTTGAATCTTAATGAAAATCTTTAAGACATTTCC
*
3519062 AAATAAGAATCTTTGAATTTTAA
1 AAATAAGAATCTTTGAATCTTAA
3519085 ATAAGAATCT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
43 20 0.35
44 19 0.33
46 10 0.18
47 8 0.14
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (45 bp):
AAATAAGAATCTTTGAATCTTAATGAAAATCTTTAAGACATTTCC
Found at i:3519212 original size:59 final size:58
Alignment explanation
Indices: 3519101--3519214 Score: 147
Period size: 58 Copynumber: 1.9 Consensus size: 58
3519091 ATCTTTGAAT
* **
3519101 TTTAAATGAAAATCTTTGAGATGTGAAACCCAAAATTTGTTGAATGTGAATCTTCGAC
1 TTTAAATGAAAATCTTTGAGATATGAAACCCAAAATTTGTTGAATGCAAATCTTCGAC
* * * **
3519159 TTTAAATGAAAATTTTTTAGATATGAAACCCTAAAGTTTGTTGGGTGCAAATCTTC
1 TTTAAATGAAAATCTTTGAGATATGAAACCC-AAAATTTGTTGAATGCAAATCTTC
3519215 AAACTAATGA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
58 28 0.60
59 19 0.40
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (58 bp):
TTTAAATGAAAATCTTTGAGATATGAAACCCAAAATTTGTTGAATGCAAATCTTCGAC
Found at i:3519730 original size:42 final size:41
Alignment explanation
Indices: 3519643--3519746 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 41
3519633 TCCTTGTCAT
* * * *
3519643 GAGCATTTTATTTTTTAAAGTTGTGTTGTCTCTGTTTAGAG
1 GAGCAATTTATTTTTTAAAGTTGTGTTGCCTCTGTATAGAA
* *
3519684 GAGCAATTTATTTTTTGAAGTCATG-GTTGCCTTTGTATAGAA
1 GAGCAATTTATTTTTTAAAGT--TGTGTTGCCTCTGTATAGAA
* *
3519726 GAGCAATTTAGTTTTCAAAGT
1 GAGCAATTTATTTTTTAAAGT
3519747 CGTTGAGCCT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 19 0.37
42 31 0.60
43 2 0.04
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.45
Consensus pattern (41 bp):
GAGCAATTTATTTTTTAAAGTTGTGTTGCCTCTGTATAGAA
Found at i:3519845 original size:45 final size:45
Alignment explanation
Indices: 3519737--3519869 Score: 153
Period size: 44 Copynumber: 3.0 Consensus size: 45
3519727 AGCAATTTAG
* ** *
3519737 TTTTCAAAGTCGTTGAGCCTCTGATAAGATTAGC-TTTATTTATT
1 TTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTTGTTTATT
** * * *
3519781 TTTAAAAAATCATTAAGCCTCTGATTAGAGGAGCTTTTGTTTATT
1 TTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTTGTTTATT
* *
3519826 TTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGA-ATTTTGTTTATT
1 TTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTTGTTTATT
3519870 CTCTAAAAGT
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
44 37 0.51
45 35 0.49
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (45 bp):
TTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTTGTTTATT
Found at i:3519879 original size:44 final size:44
Alignment explanation
Indices: 3519796--3519896 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 44
3519786 AAAATCATTA
* * * *
3519796 AGCCTCTGATTAGAGGAGCTTTTGTTTATTTTTTCAAAGTCGTTG
1 AGCCTCTGATTAGAGGAGATTTTGTTTATTCTCTAAAAGTCG-TG
* *
3519841 AGCCTCTGTTTAGAGGA-ATTTTGTTTATTCTCTAAAAGTTGTG
1 AGCCTCTGATTAGAGGAGATTTTGTTTATTCTCTAAAAGTCGTG
* *
3519884 AACCTCTGCTTAG
1 AGCCTCTGATTAG
3519897 GGTGTTTCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 13 0.27
44 19 0.40
45 16 0.33
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.43
Consensus pattern (44 bp):
AGCCTCTGATTAGAGGAGATTTTGTTTATTCTCTAAAAGTCGTG
Found at i:3520974 original size:6 final size:6
Alignment explanation
Indices: 3520963--3521006 Score: 58
Period size: 5 Copynumber: 7.7 Consensus size: 6
3520953 TCCTTAATTT
3520963 TTTTAA TTTTAA TTTTAA TTTTTAA -TTTAA -TTTAA -TTTAA TTTT
1 TTTTAA TTTTAA TTTTAA -TTTTAA TTTTAA TTTTAA TTTTAA TTTT
3521007 TCTTTTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 15 0.42
6 15 0.42
7 6 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:3520980 original size:12 final size:11
Alignment explanation
Indices: 3520956--3521006 Score: 63
Period size: 10 Copynumber: 4.7 Consensus size: 11
3520946 TTGATATTCC
3520956 TTAATTTT--T
1 TTAATTTTAAT
3520965 TTAATTTTAATT
1 TTAATTTTAA-T
3520977 TTAATTTTTAAT
1 TTAA-TTTTAAT
3520989 TTAA-TTTAAT
1 TTAATTTTAAT
3520999 TTAATTTT
1 TTAATTTT
3521007 TCTTTTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
9 8 0.22
10 10 0.27
11 3 0.08
12 10 0.27
13 6 0.16
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTAATTTTAAT
Found at i:3521043 original size:14 final size:15
Alignment explanation
Indices: 3521024--3521058 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
3521014 AATGATTTTC
3521024 CTAAAATAAA-ATTT
1 CTAAAATAAATATTT
3521038 CTAAAATAAATATTT
1 CTAAAATAAATATTT
3521053 CTAAAA
1 CTAAAA
3521059 GTATTTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (15 bp):
CTAAAATAAATATTT
Found at i:3521235 original size:74 final size:74
Alignment explanation
Indices: 3521116--3521255 Score: 192
Period size: 74 Copynumber: 1.9 Consensus size: 74
3521106 AGGTTTTTAA
* *
3521116 AAAAATATTTTTAGGAAAAAATTGAAAATATCAATTTTCCTTGAAAATAAAATTTCTAAAATAAA
1 AAAAATATTTTGAGGAAAAAATTGAAAATATCAATTTTCCTTGAAAATAAAATTTC-AAAAAAAA
3521181 AATTATCAAG
65 AATTATCAAG
* * * ** *
3521191 AAAAATATTTTGAGG-AAAAGTTGAAAGTATTAATTTTTTTTGAAATTAAAATTTCAAAAAAAAA
1 AAAAATATTTTGAGGAAAAAATTGAAAATATCAATTTTCCTTGAAAATAAAATTTCAAAAAAAAA
3521255 A
66 A
3521256 CATTTTAAGG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 9 0.16
74 34 0.60
75 14 0.25
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (74 bp):
AAAAATATTTTGAGGAAAAAATTGAAAATATCAATTTTCCTTGAAAATAAAATTTCAAAAAAAAA
ATTATCAAG
Found at i:3521254 original size:59 final size:60
Alignment explanation
Indices: 3521174--3521288 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
3521164 AAAATTTCTA
* * * ** * *
3521174 AAATAAAAATTATC-AAGAAAAATATTTTGAGGAAAAGTTGAAAGTATTAATTTTTTTTG
1 AAATAAAAATTATCAAAAAAAAACATTTTAAGGAAAAACTAAAAGTATCAATTTTTTTTG
*
3521233 AAATTAAAATT-TCAAAAAAAAAACATTTTAAGGAAAAACTAAAAGTATCAATTTTT
1 AAATAAAAATTATC-AAAAAAAAACATTTTAAGGAAAAACTAAAAGTATCAATTTTT
3521289 CTTATACAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
58 2 0.04
59 10 0.22
60 34 0.74
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (60 bp):
AAATAAAAATTATCAAAAAAAAACATTTTAAGGAAAAACTAAAAGTATCAATTTTTTTTG
Found at i:3522454 original size:16 final size:18
Alignment explanation
Indices: 3522410--3522447 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3522400 ATATAGATAG
**
3522410 ATAATATATTAAATATAA
1 ATAATATAAAAAATATAA
3522428 ATAATATAAAAAATA-AA
1 ATAATATAAAAAATATAA
3522445 ATA
1 ATA
3522448 TTTAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAATATAAAAAATATAA
Found at i:3537248 original size:32 final size:32
Alignment explanation
Indices: 3537182--3537244 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
3537172 AAAAATGAAA
*
3537182 CAATAAATAATAATAATTAAAAAAATAATTTT
1 CAATAAATAATAAAAATTAAAAAAATAATTTT
* *
3537214 CAATAAATAA-AAAAATTAAGAAAATTATTTT
1 CAATAAATAATAAAAATTAAAAAAATAATTTT
3537245 TCAAACACCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (32 bp):
CAATAAATAATAAAAATTAAAAAAATAATTTT
Found at i:3540164 original size:29 final size:29
Alignment explanation
Indices: 3540127--3540185 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3540117 GCTGAATTAA
*
3540127 TTTATAATTGAAATATAAAATTAAAAATT
1 TTTAAAATTGAAATATAAAATTAAAAATT
* * * *
3540156 TTTAAAATTTAAATATCATATTAAATATT
1 TTTAAAATTGAAATATAAAATTAAAAATT
3540185 T
1 T
3540186 AATTATAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (29 bp):
TTTAAAATTGAAATATAAAATTAAAAATT
Found at i:3540200 original size:18 final size:19
Alignment explanation
Indices: 3540156--3540211 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
3540146 ATTAAAAATT
* *
3540156 TTTAAAATTTAAATATCATA
1 TTTAATATTTAATTAT-ATA
*
3540176 TTAAATATTTAATTATA-A
1 TTTAATATTTAATTATATA
* *
3540194 TTTAATAATTATTTATAT
1 TTTAATATTTAATTATAT
3540212 CGTTAATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 15 0.52
19 1 0.03
20 13 0.45
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAATATTTAATTATATA
Found at i:3541571 original size:2 final size:2
Alignment explanation
Indices: 3541564--3541598 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3541554 TTAACCATGT
3541564 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3541599 AACTCATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3544674 original size:72 final size:72
Alignment explanation
Indices: 3544502--3544674 Score: 202
Period size: 72 Copynumber: 2.4 Consensus size: 72
3544492 TTTAAAAAAG
** * ** *
3544502 TCATATTTTCAACAAAAGTTACGATTTTATCTTTAAAGTATCATTTTTATTAAATTCTAAAAAAT
1 TCATATTTTCAACAAAAACTACGATTTTATCTTAAAAACATCATTTTTATTAAATTCTAAAAAAC
*
3544567 ATATTTT
66 ATAATTT
* * * ** ** *
3544574 TTATGTTTTTAACAAAAACTATAATTTTATCTTAAAAACATCATTTTTATTGTATTCTGAAAAAC
1 TCATATTTTCAACAAAAACTACGATTTTATCTTAAAAACATCATTTTTATTAAATTCTAAAAAAC
3544639 ATAATTT
66 ATAATTT
*
3544646 TCATATTTTCAACAAAAACTACGTTTTTA
1 TCATATTTTCAACAAAAACTACGATTTTA
3544675 ATTTAGAAAT
Statistics
Matches: 80, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
72 80 1.00
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (72 bp):
TCATATTTTCAACAAAAACTACGATTTTATCTTAAAAACATCATTTTTATTAAATTCTAAAAAAC
ATAATTT
Found at i:3544724 original size:39 final size:39
Alignment explanation
Indices: 3544649--3544724 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
3544639 ATAATTTTCA
*
3544649 TATTTTCAACAAAAACTACGTTTTTAATTTAGAAATGTCG
1 TATTTTCAACAAAAAATAC-TTTTTAATTTAGAAATGTCG
*
3544689 TATTTTCAACAAAAAATA-TATTTTATTTTAGAAATG
1 TATTTTCAACAAAAAATACT-TTTTAATTTAGAAATG
3544725 ATGTCTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 1 0.03
39 15 0.45
40 17 0.52
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (39 bp):
TATTTTCAACAAAAAATACTTTTTAATTTAGAAATGTCG
Found at i:3544811 original size:41 final size:41
Alignment explanation
Indices: 3544761--3544850 Score: 99
Period size: 41 Copynumber: 2.2 Consensus size: 41
3544751 CATTTTTTTT
* * *
3544761 TCATATTTTCAACAAAGATTGTATTTTCTATATTAGAAACA
1 TCATTTTTTCAACAAAAATTATATTTTCTATATTAGAAACA
* * * * *
3544802 TCATTTTTTCAATAAAAATTATTTTTTTTATTTTAGAAACG
1 TCATTTTTTCAACAAAAATTATATTTTCTATATTAGAAACA
*
3544843 TCGTTTTT
1 TCATTTTT
3544851 GTTAAATTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (41 bp):
TCATTTTTTCAACAAAAATTATATTTTCTATATTAGAAACA
Found at i:3544858 original size:118 final size:115
Alignment explanation
Indices: 3544709--3544975 Score: 285
Period size: 118 Copynumber: 2.3 Consensus size: 115
3544699 AAAAAATATA
* *
3544709 TTTTATTTTAGAAATGAT-GTCTTTGTTAAATTTTGAAA-ACTACATTTTTTTTTCATATTT-TC
1 TTTTATTTTAGAAACG-TCGTCTTTGTTAAATTTTGAAATA-TA-A--CTTTTTTCATATTTAT-
* * *
3544771 AACAAAGATTGTATTTTCTATATTAGAAA--CATCATTTTTTCAATAAAAATT-ATTTT
60 AACAAAAATTGCATTTT-TATATTAGAAATGCA--ATCTTTTCAATAAAAATTAATTTT
* *
3544827 TTTTATTTTAGAAACGTCGTTTTTGTTAAATTTTGAAATATAACTTTTTTCATGTTTATAACAAA
1 TTTTATTTTAGAAACGTCGTCTTTGTTAAATTTTGAAATATAACTTTTTTCATATTTATAACAAA
* *
3544892 AATTGCATTTTTATCTTAGAAATGCAATCTTTTCAATAACAATTACATTTT
66 AATTGCATTTTTATATTAGAAATGCAATCTTTTCAATAAAAATTA-ATTTT
* * *
3544943 TTTTAATTTTAAAAACATCATCTTTGTTAAATT
1 TTTT-ATTTTAGAAACGTCGTCTTTGTTAAATT
3544976 CTAAAAAAAA
Statistics
Matches: 128, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
114 26 0.20
115 27 0.21
116 12 0.09
117 26 0.20
118 36 0.28
119 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (115 bp):
TTTTATTTTAGAAACGTCGTCTTTGTTAAATTTTGAAATATAACTTTTTTCATATTTATAACAAA
AATTGCATTTTTATATTAGAAATGCAATCTTTTCAATAAAAATTAATTTT
Found at i:3546997 original size:27 final size:25
Alignment explanation
Indices: 3546966--3547019 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
3546956 AAATTTAGAG
3546966 AAATTT-CTCACTTAAAGATTTCTTAAA
1 AAATTTAC-CACTTAAA-ATTT-TTAAA
*
3546993 AAATTTACCATTTAAAATTTTTAAA
1 AAATTTACCACTTAAAATTTTTAAA
3547018 AA
1 AA
3547020 TCTCATCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 7 0.28
26 4 0.16
27 13 0.52
28 1 0.04
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (25 bp):
AAATTTACCACTTAAAATTTTTAAA
Found at i:3547369 original size:30 final size:32
Alignment explanation
Indices: 3547310--3547369 Score: 97
Period size: 30 Copynumber: 1.9 Consensus size: 32
3547300 TAATGAAAAT
3547310 TATAAAACAAAGTGAATAAATAAACAATTATG
1 TATAAAACAAAGTGAATAAATAAACAATTATG
*
3547342 TATAAAAC-AA-TGAATAAATAAATAATTA
1 TATAAAACAAAGTGAATAAATAAACAATTA
3547370 AAGAATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 17 0.63
31 2 0.07
32 8 0.30
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.27
Consensus pattern (32 bp):
TATAAAACAAAGTGAATAAATAAACAATTATG
Found at i:3550505 original size:3 final size:3
Alignment explanation
Indices: 3550497--3550526 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3550487 AACACTTTTC
3550497 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3550527 CAGTCGGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3551293 original size:2 final size:2
Alignment explanation
Indices: 3551286--3551313 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3551276 TGCGGGATTG
3551286 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
3551314 TTGATACTTC
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):
AT
Found at i:3551486 original size:29 final size:28
Alignment explanation
Indices: 3551452--3551513 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
3551442 ACTTTTGTCC
*
3551452 CAAAA-TCATCAAGGTTGAAAGTATAATGA
1 CAAAATTCATCAA-ATT-AAAGTATAATGA
* *
3551481 TAAAATTCATGAAATTAAAGTATAATGA
1 CAAAATTCATCAAATTAAAGTATAATGA
3551509 CAAAA
1 CAAAA
3551514 AAATTGAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
28 16 0.57
29 6 0.21
30 6 0.21
ACGTcount: A:0.53, C:0.08, G:0.13, T:0.26
Consensus pattern (28 bp):
CAAAATTCATCAAATTAAAGTATAATGA
Found at i:3557093 original size:11 final size:10
Alignment explanation
Indices: 3557079--3557116 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
3557069 AAATTTTAAA
3557079 TTATATTACTT
1 TTATATTA-TT
3557090 TTATATT-TT
1 TTATATTATT
3557099 TTATATTATTT
1 TTATATTA-TT
3557110 TTATATT
1 TTATATT
3557117 GTGTCATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.36
11 16 0.64
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (10 bp):
TTATATTATT
Found at i:3557104 original size:20 final size:20
Alignment explanation
Indices: 3557079--3557116 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3557069 AAATTTTAAA
3557079 TTATATTACTTTTATATTTT
1 TTATATTACTTTTATATTTT
*
3557099 TTATATTATTTTTATATT
1 TTATATTACTTTTATATT
3557117 GTGTCATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATATTACTTTTATATTTT
Found at i:3559553 original size:10 final size:10
Alignment explanation
Indices: 3559509--3559564 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
3559499 TATAAAAATA
*
3559509 ATTTTTTTA-
1 ATTTTTATAT
*
3559518 ATTATTTATTT
1 ATT-TTTATAT
*
3559529 AATTTTATAATT
1 ATTTTTAT-A-T
3559541 ATTTTTATAT
1 ATTTTTATAT
3559551 ATTTTTATAT
1 ATTTTTATAT
3559561 ATTT
1 ATTT
3559565 AATTTTATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 3 0.08
10 24 0.63
11 3 0.08
12 8 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:3559563 original size:20 final size:20
Alignment explanation
Indices: 3559509--3559564 Score: 51
Period size: 22 Copynumber: 2.7 Consensus size: 20
3559499 TATAAAAATA
* *
3559509 ATTTTTTTA-ATTATTTATTT
1 ATTTTTATATATT-TTTATAT
*
3559529 AATTTTATAATTATTTTTATAT
1 ATTTTTAT-A-TATTTTTATAT
3559551 ATTTTTATATATTT
1 ATTTTTATATATTT
3559565 AATTTTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 13 0.45
23 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTTTATATATTTTTATAT
Found at i:3559577 original size:20 final size:20
Alignment explanation
Indices: 3559519--3559580 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
3559509 ATTTTTTTAA
* *
3559519 TTATTTATTTAATTTTATAA
1 TTATATATTTAATTTTATAT
* *
3559539 TTAT-T-TTT-A-TATATTT
1 TTATATATTTAATTTTATAT
3559555 TTATATATTTAATTTTATAT
1 TTATATATTTAATTTTATAT
3559575 TTATAT
1 TTATAT
3559581 TAAAAATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 8 0.24
17 2 0.06
18 6 0.18
19 2 0.06
20 15 0.45
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATATATTTAATTTTATAT
Found at i:3563141 original size:159 final size:158
Alignment explanation
Indices: 3562781--3563436 Score: 502
Period size: 161 Copynumber: 4.1 Consensus size: 158
3562771 TTTAGGCAAA
* * * * *
3562781 TTTAATATCATGTATTTAAGCTATCTAAACTATTAAAATAAAAATATAACTATAAAATTACATTT
1 TTTAATATCATGTATTTAAGCTATCCAAACTGTTAAAATAGAAATATAA-TGTAAAATTATA-TT
* * * * ** * * * * *
3562846 TTACC-CTTAAC-GACACAACAAGTGTTAAATAGACATAAA-AGACAATCATTTCACACATGTTA
64 TTGCCTTTTAACAG-CATAA-AAATCCTAAACAGACATAAACA-ATAACCTTTTCACACATATTA
* * * * * *
3562908 A-TTATGGAAACCAAGTTCAATCATTTGGACAAA
126 ACAT-TGAAAACTAAGTTCAATCATTCGAACAAG
* * **
3562941 TTTAAATATCTTATATTTAAGCTATTTAAACTGTTAAAATAGAAATATAACTGTAAAATTATATT
1 TTT-AATATCATGTATTTAAGCTATCCAAACTGTTAAAATAGAAATATAA-TGTAAAATTATATT
* ** * *
3563006 TGTGCTTTTTAACAGCATAAAATATCCTAAACAGACATAAACGGTAACTTTTTCTCACATATT-A
64 T-TGCCTTTTAACAGCATAAAA-ATCCTAAACAGACATAAACAATAACCTTTTCACACATATTAA
** *
3563070 -ATTGTCAACTAAGTTCAATGATTCGAACAAG
127 CATTGAAAACTAAGTTCAATCATTCGAACAAG
* * * *
3563101 TTTAATATCATGTATTGAAGCTATCCAAACTGTTACAATAGAGCAATA-ATTGCAAATATGTAT-
1 TTTAATATCATGTATTTAAGCTATCCAAACTGTTAAAATAGA--AATATAATGTAAA-AT-TATA
* * * *
3563164 TTTTGCCTTTTAATAGTATAAAAGTCCTAAACAGACATAAACAATAACCTTTTCACATATATTAA
62 TTTTGCCTTTTAACAGCATAAAAATCCTAAACAGACATAAACAATAACCTTTTCACACATATTAA
* *
3563229 TCATTGAAAACTAAATTCAATCATTCGAATAAG
127 -CATTGAAAACTAAGTTCAATCATTCGAACAAG
* * *
3563262 TTTAATATCATGTATTTAAGCTATCCAAACTATTAAAACATAAATATAATCGTAAAATTATATTT
1 TTTAATATCATGTATTTAAGCTATCCAAACTGTTAAAATAGAAATATAAT-GTAAAATTATATTT
* * ** * * * * * * * * * *
3563327 TTCCCTTTAATGGCACAAAAAGTCTTAAATAGGCACAAATATTAA-TTTTTCACACATATCAACC
65 TGCCTTTTAACAGCATAAAAA-TCCTAAACAGACATAAACAATAACCTTTTCACACATATTAACA
* * * *
3563391 GTGAAAACCAAATTCAATCATTCGGACAAG
129 TTGAAAACTAAGTTCAATCATTCGAACAAG
*
3563421 TTTAATATCATATATT
1 TTTAATATCATGTATT
3563437 GAAACAATTA
Statistics
Matches: 398, Mismatches: 81, Indels: 35
0.77 0.16 0.07
Matches are distributed among these distances:
158 34 0.09
159 105 0.26
160 73 0.18
161 149 0.37
162 36 0.09
163 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (158 bp):
TTTAATATCATGTATTTAAGCTATCCAAACTGTTAAAATAGAAATATAATGTAAAATTATATTTT
GCCTTTTAACAGCATAAAAATCCTAAACAGACATAAACAATAACCTTTTCACACATATTAACATT
GAAAACTAAGTTCAATCATTCGAACAAG
Found at i:3566872 original size:24 final size:22
Alignment explanation
Indices: 3566828--3566874 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
3566818 TTTTTTTTAA
* *
3566828 ATTTTTTTAATTTTTATATATT
1 ATTTTATTAATTTTTACATATT
3566850 ATTTTATTAATATTTATACATATT
1 ATTTTATTAAT-TTT-TACATATT
3566874 A
1 A
3566875 AAATATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 3 0.14
24 8 0.38
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTTTATTAATTTTTACATATT
Found at i:3574363 original size:141 final size:144
Alignment explanation
Indices: 3574209--3574816 Score: 571
Period size: 141 Copynumber: 4.2 Consensus size: 144
3574199 ATTTAAAAAC
* *
3574209 AGATGAAAATTTTAAAGTTGTTGAACCTCTGCTGAGAGGAGCTTTTTCAAGAGATTTTTAAAGTT
1 AGATGAAAATTTTAAAGTTGTTGAACCTCTGCTGAAAGGAGCCTTTTCAAGAGATTTTTAAAGTT
* * * * *
3574274 GTTAAGCTTCTGCTGAGATG-AGCTTTTTCA-A-GAGATTTTTAAAGTTGTTGAGCCTCTGTTGA
66 ATTGAGCCTCTGCTGAGAGGAAGCTTTTTCAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGA
3574336 GAGGAGCTTTTTCA
131 GAGGAGCTTTTTCA
* * * * * ** *
3574350 AGATGAAATTTTTAAAGTTGTT-AAGCCTCTACTGAGATGAGCCTTTT-AA-A-CTTTCAAAAAT
1 AGATGAAAATTTTAAAGTTGTTGAA-CCTCTGCTGAAAGGAGCCTTTTCAAGAGATTTTTAAAGT
* * * *
3574411 ATCAATTGAGCCTCTGTTGAGA-GAAGCTTTTTCA-A-GAGATTTTTAAAGTTGCTGAGCTTTTG
65 -T--ATTGAGCCTCTGCTGAGAGGAAGCTTTTTCAGATGAGATTTTTAAAGTTGTTGAGCCTCTG
* *
3574473 CTGAAAGGAGCTTTTCCA
127 CTGAGAGGAGCTTTTTCA
* * *
3574491 AGATGAAAATTTTTAAGTTGTTGAGCCTCTGCTGAAAGGAGCTTTTTCAAGAGATTTTTAAAGTT
1 AGATGAAAATTTTAAAGTTGTTGAACCTCTGCTGAAAGGAGCCTTTTCAAGAGATTTTTAAAGTT
* * * * *
3574556 GTTGAGCCTCTGTTGAGAGG-AGCTTTTCCAAGATGAGAATTCTAAAGTTGTTGAGCCTCTGCTG
66 ATTGAGCCTCTGCTGAGAGGAAGCTTTTTC-AGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTG
*
3574620 AGAAGAG-TTTTTCCA
130 AGAGGAGCTTTTT-CA
* * * * *
3574635 AGAAGAGAATTTTAAAGTTATT-AAGCCTCTGCTCAAAGGAGCCCTTTTCAAGATAAGAATTTTA
1 AGATGAAAATTTTAAAGTTGTTGAA-CCTCTGCTGAAAGGAG-CCTTTTCAAG---AGATTTTTA
* * * * *
3574699 AAGTTATTGAGCCTCTGCTGAGAGGAACCCTTTTCATGATATGAGA-TTTAAAAGTTTTTAAGCC
61 AAGTTATTGAGCCTCTGCTGAGAGGAAGCTTTTTCA-G--ATGAGATTTTTAAAGTTGTTGAGCC
* *
3574763 TCTGTTGAGATGAGCTTTTTCA
123 TCTGCTGAGAGGAGCTTTTTCA
** **
3574785 A-AAAAAAAAATTAAAGTTGTTGAACCTCTGCT
1 AGATGAAAATTTTAAAGTTGTTGAACCTCTGCT
3574817 AAGAAAAGCC
Statistics
Matches: 379, Mismatches: 63, Indels: 42
0.78 0.13 0.09
Matches are distributed among these distances:
138 7 0.02
139 2 0.01
140 5 0.01
141 167 0.44
142 5 0.01
143 8 0.02
144 72 0.19
145 9 0.02
148 32 0.08
149 30 0.08
150 31 0.08
151 11 0.03
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (144 bp):
AGATGAAAATTTTAAAGTTGTTGAACCTCTGCTGAAAGGAGCCTTTTCAAGAGATTTTTAAAGTT
ATTGAGCCTCTGCTGAGAGGAAGCTTTTTCAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGA
GAGGAGCTTTTTCA
Found at i:3574377 original size:49 final size:49
Alignment explanation
Indices: 3574209--3574816 Score: 488
Period size: 46 Copynumber: 12.7 Consensus size: 49
3574199 ATTTAAAAAC
* *
3574209 AGATGAAAATTTTAAAGTTGTTGAACCTCTGCTGAGAGGAGCTTTTTCA
1 AGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCA
* * *
3574258 AGA-G--ATTTTTAAAGTTGTTAAGCTTCTGCTGAGATGAGCTTTTTCA
1 AGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCA
*
3574304 AGA-G--ATTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTCA
1 AGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCA
* * * * *
3574350 AGATGAAATTTTTAAAGTTGTTAAGCCTCTACTGAGATGAGCCTTTTAA
1 AGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCA
** * ** * * * *
3574399 ACTTTCAAAAATATCAA----TTGAGCCTCTGTTGAGAGAAGCTTTTTCA
1 A-GATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCA
* * * * *
3574445 AGA-G--ATTTTTAAAGTTGCTGAGCTTTTGCTGAAAGGAGCTTTTCCA
1 AGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCA
*
3574491 AGATGAAAATTTTT-AAGTTGTTGAGCCTCTGCTGAAAGGAGCTTTTTCA
1 AGATG-AAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCA
* *
3574540 AGA-G--ATTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTCCA
1 AGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCA
* *
3574586 AGATGAGAA-TTCTAAAGTTGTTGAGCCTCTGCTGAGAAGAG-TTTTTCCA
1 AGATGA-AATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT-CA
* * * * * *
3574635 AGAAGAGAA-TTTTAAAGTTATTAAGCCTCTGCTCAAAGGAGCCCTTTTCA
1 AGATGA-AATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCA
* * * *
3574685 AGAT-AAGAATTTTAAAGTTATTGAGCCTCTGCTGAGAGGAACCCTTTTCA
1 AGATGAA-ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGG-AGCTTTTTCA
* * * * * * *
3574735 TGATATGAGA-TTTAAAAGTTTTTAAGCCTCTGTTGAGATGAGCTTTTTCA
1 --AGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCA
** *** *
3574785 A-AAAAAAAAATTAAAGTTGTTGAACCTCTGCT
1 AGATGAAATTTTTAAAGTTGTTGAGCCTCTGCT
3574817 AAGAAAAGCC
Statistics
Matches: 446, Mismatches: 86, Indels: 55
0.76 0.15 0.09
Matches are distributed among these distances:
42 5 0.01
45 6 0.01
46 165 0.37
47 6 0.01
48 25 0.06
49 141 0.32
50 63 0.14
51 30 0.07
52 4 0.01
53 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (49 bp):
AGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCA
Found at i:3574772 original size:51 final size:50
Alignment explanation
Indices: 3574483--3574772 Score: 213
Period size: 49 Copynumber: 5.9 Consensus size: 50
3574473 CTGAAAGGAG
* * * * *
3574483 CTTTTCCAAGATGAA-AATTTTTAAGTTGTTGAGCCTCTGCTGAAAGG-AGC
1 CTTTT-CAAGAT-AAGAATTTTAAAGTTATTAAGCCTCTGCTGAGAGGAACC
* * * * * *
3574533 TTTTTCAAG---AGATTTTTAAAGTTGTTGAGCCTCTGTTGAGAGG-A-G
1 CTTTTCAAGATAAGAATTTTAAAGTTATTAAGCCTCTGCTGAGAGGAACC
* * * * * *
3574578 CTTTTCCAAGATGAGAATTCTAAAGTTGTTGAGCCTCTGCTGAGAAG-A-G
1 CTTTT-CAAGATAAGAATTTTAAAGTTATTAAGCCTCTGCTGAGAGGAACC
* * * *
3574627 TTTTTCCAAGA-AGAGAATTTTAAAGTTATTAAGCCTCTGCTCAAAGGAGCC
1 CTTTT-CAAGATA-AGAATTTTAAAGTTATTAAGCCTCTGCTGAGAGGAACC
*
3574678 CTTTTCAAGATAAGAATTTTAAAGTTATTGAGCCTCTGCTGAGAGGAACC
1 CTTTTCAAGATAAGAATTTTAAAGTTATTAAGCCTCTGCTGAGAGGAACC
* * * * *
3574728 CTTTTCATGATATGAGATTTAAAAGTTTTTAAGCCTCTGTTGAGA
1 CTTTTCAAGATAAGA-ATTTTAAAGTTATTAAGCCTCTGCTGAGA
3574773 TGAGCTTTTT
Statistics
Matches: 198, Mismatches: 32, Indels: 19
0.80 0.13 0.08
Matches are distributed among these distances:
45 5 0.03
46 33 0.17
49 74 0.37
50 56 0.28
51 30 0.15
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.35
Consensus pattern (50 bp):
CTTTTCAAGATAAGAATTTTAAAGTTATTAAGCCTCTGCTGAGAGGAACC
Found at i:3574781 original size:99 final size:96
Alignment explanation
Indices: 3574216--3574816 Score: 419
Period size: 95 Copynumber: 6.3 Consensus size: 96
3574206 AACAGATGAA
* * *
3574216 AATTTTAAAGTTGTTGAACCTCTGCTGAGAGGAGCTTTT--TCAAGAGATTTTTAAAGTTGTTAA
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCATGAAGAGA-TTTTAAAGTTATTAA
* * * *
3574279 GCTTCTGCTGAGATGAGCTTTTTCAAG---AG
65 GCCTCTGTTGAGAGGAGCTTTTCCAAGATAAG
* * * * * *
3574308 ATTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTCAAGATGAAATTTTTAAAGTTGTTA
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTCATGAAGAGA-TTTTAAAGTTATTA
** * * **
3574373 AGCCTCTACTGAGATGAGCCTTTT-AAACTTTCAA-
64 AGCCTCTGTTGAGAGGAG-CTTTTCCAA-GAT-AAG
* * * * * * ** *
3574407 AAATATCAA----TTGAGCCTCTGTTGAGAGAAGCTTTT--TCAAGAGATTTTTAAAGTTGCTGA
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCATGAAGAGA-TTTTAAAGTTATTAA
* * * *
3574466 GCTTTTGCTGAAAGGAGCTTTTCCAAGATGAA-
65 GCCTCTGTTGAGAGGAGCTTTTCCAAGAT-AAG
* * * * *
3574498 AATTTTTAAGTTGTTGAGCCTCTGCTGAAAGGAGCTTTT--TCAAGAGATTTTTAAAGTTGTTGA
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCATGAAGAGA-TTTTAAAGTTATTAA
*
3574561 GCCTCTGTTGAGAGGAGCTTTTCCAAGATGAG
65 GCCTCTGTTGAGAGGAGCTTTTCCAAGATAAG
* * * *
3574593 AATTCTAAAGTTGTTGAGCCTCTGCTGAGAAGAGTTTTTCCAAGAAGAGAATTTTAAAGTTATTA
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT-CATGAAGAG-ATTTTAAAGTTATTA
* * *
3574658 AGCCTCTGCTCAAAGGAGCCCTTTT-CAAGATAAG
64 AGCCTCTGTTGAGAGGAG--CTTTTCCAAGATAAG
* * * *
3574692 AATTTTAAAGTTATTGAGCCTCTGCTGAGAGGAACCCTTTTCATGATATGAGATTTAAAAGTTTT
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG-A-GCTTTTCATGA-A-GAGATTTTAAAGTTAT
* * * *
3574757 TAAGCCTCTGTTGAGATGAGCTTTTTCAA-AAAAA
62 TAAGCCTCTGTTGAGAGGAGCTTTTCCAAGATAAG
** *
3574791 AAAATTAAAGTTGTTGAACCTCTGCT
1 AATTTTAAAGTTGTTGAGCCTCTGCT
3574817 AAGAAAAGCC
Statistics
Matches: 409, Mismatches: 74, Indels: 45
0.77 0.14 0.09
Matches are distributed among these distances:
91 14 0.03
92 64 0.16
93 4 0.01
94 5 0.01
95 163 0.40
96 5 0.01
98 32 0.08
99 73 0.18
100 14 0.03
101 32 0.08
102 3 0.01
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (96 bp):
AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCATGAAGAGATTTTAAAGTTATTAAG
CCTCTGTTGAGAGGAGCTTTTCCAAGATAAG
Found at i:3575108 original size:14 final size:14
Alignment explanation
Indices: 3575076--3575114 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3575066 TCTTCTTTTC
*
3575076 TTTT-CTTCTTCTT
1 TTTTCCTTCTTCCT
3575089 TCTTTCCTTCTTCCT
1 T-TTTCCTTCTTCCT
3575104 TTTTCCTTCTT
1 TTTTCCTTCTT
3575115 TTTCATCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 13 0.57
15 9 0.39
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCCTTCTTCCT
Found at i:3578861 original size:11 final size:11
Alignment explanation
Indices: 3578843--3578884 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
3578833 AATCCCATAA
3578843 GAGATTTGTTT
1 GAGATTTGTTT
* *
3578854 GGGATTTGTTA
1 GAGATTTGTTT
3578865 GAGATTTGTTT
1 GAGATTTGTTT
3578876 GAGATTTGT
1 GAGATTTGT
3578885 CAGATATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:3578867 original size:22 final size:22
Alignment explanation
Indices: 3578842--3578898 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
3578832 AAATCCCATA
* *
3578842 AGAGATTTGTTTGGGATTTGTT
1 AGAGATTTGTTTGAGATTTGTC
3578864 AGAGATTTGTTTGAGATTTGTC
1 AGAGATTTGTTTGAGATTTGTC
*
3578886 AGATA-TTGTTTGA
1 AGAGATTTGTTTGA
3578899 TGGACAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (22 bp):
AGAGATTTGTTTGAGATTTGTC
Found at i:3578988 original size:52 final size:53
Alignment explanation
Indices: 3578920--3579061 Score: 202
Period size: 52 Copynumber: 2.7 Consensus size: 53
3578910 ACTTGCAAAA
*
3578920 AAGAATTCTAAGAGAAAGA-AGATTCTTAATAGGTAAGTTTGACTTACAAGAG
1 AAGAATTCTAAGAGAAAGAGAGATTCTTAATAGGCAAGTTTGACTTACAAGAG
* *
3578972 AAGAATTCTAAAAGAAA-ATG-GATTCTTAATAGGCAAGTTTGACTTACAGGAG
1 AAGAATTCTAAGAGAAAGA-GAGATTCTTAATAGGCAAGTTTGACTTACAAGAG
* *
3579024 AAGAATTCTAAGAG-GAGAGAGATTCTTAATGGGCAAGT
1 AAGAATTCTAAGAGAAAGAGAGATTCTTAATAGGCAAGT
3579062 CTGTATGGTT
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
51 3 0.04
52 77 0.96
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.26
Consensus pattern (53 bp):
AAGAATTCTAAGAGAAAGAGAGATTCTTAATAGGCAAGTTTGACTTACAAGAG
Found at i:3579930 original size:11 final size:11
Alignment explanation
Indices: 3579914--3579944 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
3579904 AATCTCATAA
3579914 GAGATTTGTTT
1 GAGATTTGTTT
3579925 GAGATTTGTTT
1 GAGATTTGTTT
3579936 GAGATTTGT
1 GAGATTTGT
3579945 CAGATATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:3580123 original size:52 final size:52
Alignment explanation
Indices: 3579982--3580093 Score: 152
Period size: 52 Copynumber: 2.2 Consensus size: 52
3579972 TTGCAAAAAA
* * * *
3579982 AATTCTAAGAGAAAGAAAATTCTTAATAGGCAAGTTTAACTTGCAAGAGAAG
1 AATTCTAAAAGAAAAAAAATTCTTAATAGGCAAGTTTGACTTACAAGAGAAG
* * * *
3580034 AATTTTAAAAGAAAAAAAATTTTTAATTGGCAAGTTTGACTTATAAGAGAAG
1 AATTCTAAAAGAAAAAAAATTCTTAATAGGCAAGTTTGACTTACAAGAGAAG
3580086 AATTCTAA
1 AATTCTAA
3580094 GGGGAGAGAG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.29
Consensus pattern (52 bp):
AATTCTAAAAGAAAAAAAATTCTTAATAGGCAAGTTTGACTTACAAGAGAAG
Found at i:3580731 original size:25 final size:24
Alignment explanation
Indices: 3580674--3580755 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 24
3580664 TTTTGAAACA
*
3580674 TGAGAAGAGTTAAAGATTCAAGATG
1 TGAGAAGAGTTAAAG-TTTAAGATG
* *
3580699 TTAAAAGAGTTGAAAGTTTAAGATG
1 TGAGAAGAGTT-AAAGTTTAAGATG
* * * *
3580724 TGAGAAGAGCTAAAAATTTGATATG
1 TGAGAAGAG-TTAAAGTTTAAGATG
3580749 TGAGAAG
1 TGAGAAG
3580756 TGCATGGTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
25 41 0.89
26 5 0.11
ACGTcount: A:0.44, C:0.02, G:0.27, T:0.27
Consensus pattern (24 bp):
TGAGAAGAGTTAAAGTTTAAGATG
Found at i:3581153 original size:52 final size:51
Alignment explanation
Indices: 3581075--3581208 Score: 155
Period size: 52 Copynumber: 2.6 Consensus size: 51
3581065 ACTTACAAAA
* * *
3581075 AAGAATTATAAGAGAAAGATGATTCTTAATAGGTAAGTTTAACTTGTA-AGAG
1 AAGAATTCTAAAAGAAAGA-GATTCTTAATAGGTAAGTTTAACTTATAGA-AG
*
3581127 AAGAATTCTAAAAGAAAAGAGATTCTTAATAGGTAAGTTTGACTTATAGAAG
1 AAGAATTCTAAAAG-AAAGAGATTCTTAATAGGTAAGTTTAACTTATAGAAG
* *
3581179 AAGAATTC-AAAGAGGAGAGAGATTTTTAAT
1 AAGAATTCTAAA-A-GAAAGAGATTCTTAAT
3581209 GAGCAAGTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
51 3 0.04
52 62 0.86
53 7 0.10
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (51 bp):
AAGAATTCTAAAAGAAAGAGATTCTTAATAGGTAAGTTTAACTTATAGAAG
Found at i:3582086 original size:11 final size:11
Alignment explanation
Indices: 3582069--3582100 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3582059 AAATCTTATA
3582069 AGAGATTTGTT
1 AGAGATTTGTT
*
3582080 TGAGATTTGTT
1 AGAGATTTGTT
3582091 AGAGATTTGT
1 AGAGATTTGT
3582101 CAAATATTAT
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:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (11 bp):
AGAGATTTGTT
Found at i:3582202 original size:51 final size:51
Alignment explanation
Indices: 3582136--3582250 Score: 178
Period size: 51 Copynumber: 2.2 Consensus size: 51
3582126 ACTTGCAAAA
* *
3582136 AAGAATTCTAAAAGAAAAA-AGATTCTTAATAGGTAAGTTTGACTTGTAAGAG
1 AAGAATTCT-AAAGAAAAAGA-ATTCTTAATAGGTAAGTTTGAATTATAAGAG
*
3582188 AAGAATTCTAAAGAAAAAGAATTCTTAATAGGTAAGTTTGAATTATAGGAG
1 AAGAATTCTAAAGAAAAAGAATTCTTAATAGGTAAGTTTGAATTATAAGAG
3582239 AAGAATTCTAAA
1 AAGAATTCTAAA
3582251 AGGAGAGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
51 49 0.83
52 10 0.17
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (51 bp):
AAGAATTCTAAAGAAAAAGAATTCTTAATAGGTAAGTTTGAATTATAAGAG
Found at i:3583139 original size:11 final size:11
Alignment explanation
Indices: 3583122--3583160 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3583112 ATCTCATAGA
3583122 AGATTTGTTTG
1 AGATTTGTTTG
* *
3583133 GGATTTGTTAG
1 AGATTTGTTTG
*
3583144 AGATTTATTTG
1 AGATTTGTTTG
3583155 AGATTT
1 AGATTT
3583161 ATCAGATATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (11 bp):
AGATTTGTTTG
Found at i:3583327 original size:52 final size:51
Alignment explanation
Indices: 3583199--3583343 Score: 150
Period size: 52 Copynumber: 2.8 Consensus size: 51
3583189 CTTGCAAAAA
* * * *
3583199 AAAAATTTTAAGAGAAAAAAGATTCTTAATAAGTAAGTTTGACTTGCAAGAG
1 AAAAATTTTAAGAG-AAAGAGATTCTTAATAGGCAAGTTTGACTTACAAGAG
* * * *
3583251 AAGAATTATAAAAAGAAAGGGATTCTTAATAGGCAAGTTTGACTTAC-AGAAG
1 AAAAATT-TTAAGAGAAAGAGATTCTTAATAGGCAAGTTTGACTTACAAG-AG
*
3583303 AAAAATTTTATGAGAAGAGAGATTCTTAAT-GGACAAGTTTG
1 AAAAATTTTAAGAGAA-AGAGATTCTTAATAGG-CAAGTTTG
3583344 TATGGTTATC
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
51 10 0.13
52 61 0.80
53 5 0.07
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (51 bp):
AAAAATTTTAAGAGAAAGAGATTCTTAATAGGCAAGTTTGACTTACAAGAG
Found at i:3583953 original size:25 final size:25
Alignment explanation
Indices: 3583925--3583978 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
3583915 TGAGGATTCA
*
3583925 AGATATGAAAAGAGTTGAAA-GTTTG
1 AGATATGAAAAGAGCT-AAAGGTTTG
* *
3583950 AGATGTGGAAAGAGCTAAAGGTTTG
1 AGATATGAAAAGAGCTAAAGGTTTG
3583975 AGAT
1 AGAT
3583979 GTGGAAAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.41, C:0.02, G:0.31, T:0.26
Consensus pattern (25 bp):
AGATATGAAAAGAGCTAAAGGTTTG
Found at i:3585449 original size:52 final size:52
Alignment explanation
Indices: 3585362--3585506 Score: 179
Period size: 52 Copynumber: 2.8 Consensus size: 52
3585352 TGGACAAGAA
*
3585362 GACTTGCAA-AAAAAAATTTTAAAAGAAAGAAGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAAAAGAATTTTAAAAGAAAGAAGATTCTTAATAGGTAAGTTT
*
3585413 GACTTGCAAGAAAAGAATTTTAAAAAGAAA-AGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAAAAGAATTTT-AAAAGAAAGAAGATTCTTAATAGGTAAGTTT
* * * * * *
3585465 AACTTACAGGAAAAGAATTCTAAGAG-GAGAGAGATTCTTAAT
1 GACTTGCAAGAAAAGAATTTTAAAAGAAAGA-AGATTCTTAAT
3585507 GAGCAAGTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
50 1 0.01
51 14 0.17
52 58 0.72
53 8 0.10
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.28
Consensus pattern (52 bp):
GACTTGCAAGAAAAGAATTTTAAAAGAAAGAAGATTCTTAATAGGTAAGTTT
Found at i:3586127 original size:25 final size:25
Alignment explanation
Indices: 3586099--3586156 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
3586089 GATTCAAGAT
*
3586099 GTGAAAAGAGCTGAAAGTTTGAGAC
1 GTGAAAAGAGCTAAAAGTTTGAGAC
* *
3586124 GTGAGAAGAGCTAAAAGTTTGAGAT
1 GTGAAAAGAGCTAAAAGTTTGAGAC
3586149 GTGAAAAG
1 GTGAAAAG
3586157 TGCATGGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.41, C:0.05, G:0.33, T:0.21
Consensus pattern (25 bp):
GTGAAAAGAGCTAAAAGTTTGAGAC
Found at i:3586131 original size:50 final size:50
Alignment explanation
Indices: 3586055--3586156 Score: 118
Period size: 50 Copynumber: 2.0 Consensus size: 50
3586045 AAGTAATATT
*
3586055 AGAGCTGAAGTTTCAAAACGTAAGAAGAG-TTAAAGATTCAAGATGTGAAA
1 AGAGCTGAAGTTTCAAAACGTAAGAAGAGCTAAAAG-TTCAAGATGTGAAA
* * * **
3586105 AGAGCTGAAAGTTT-GAGACGTGAGAAGAGCTAAAAGTTTGAGATGTGAAA
1 AGAGCTG-AAGTTTCAAAACGTAAGAAGAGCTAAAAGTTCAAGATGTGAAA
3586155 AG
1 AG
3586157 TGCATGGTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
50 33 0.75
51 11 0.25
ACGTcount: A:0.43, C:0.07, G:0.28, T:0.22
Consensus pattern (50 bp):
AGAGCTGAAGTTTCAAAACGTAAGAAGAGCTAAAAGTTCAAGATGTGAAA
Found at i:3586414 original size:11 final size:11
Alignment explanation
Indices: 3586396--3586437 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
3586386 AATCTCATAA
3586396 GAGATTTGTTT
1 GAGATTTGTTT
* *
3586407 GGGATTTGTTA
1 GAGATTTGTTT
3586418 GAGATTTGTTT
1 GAGATTTGTTT
3586429 GAGATTTGT
1 GAGATTTGT
3586438 CAGATATTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:3586423 original size:22 final size:22
Alignment explanation
Indices: 3586395--3586437 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3586385 AAATCTCATA
*
3586395 AGAGATTTGTTTGGGATTTGTT
1 AGAGATTTGTTTGAGATTTGTT
3586417 AGAGATTTGTTTGAGATTTGT
1 AGAGATTTGTTTGAGATTTGT
3586438 CAGATATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTGAGATTTGTT
Found at i:3586581 original size:52 final size:53
Alignment explanation
Indices: 3586470--3586616 Score: 167
Period size: 52 Copynumber: 2.8 Consensus size: 53
3586460 AAGACTTGCA
* *
3586470 AAAAAAAATTCTAAGA-GAAAGAGGATTCTTAATAGGTAAGTTTAACTTGTAAG
1 AAAAAGAATTCTAAGAGGAAA-AAGATTCTTAATAGGTAAGTTTAACTTGTAAG
* * *
3586523 -AGAAGAATTCTAAAAGGAAAAAGATTTTTAATAGGTAAGTTTAAC-T-TACAG
1 AAAAAGAATTCTAAGAGGAAAAAGATTCTTAATAGGTAAGTTTAACTTGTA-AG
* * * *
3586574 AAAAAGAATTTTAAGAGGAGAAAGATTCTTAATGGGCAAGTTT
1 AAAAAGAATTCTAAGAGGAAAAAGATTCTTAATAGGTAAGTTT
3586617 GTATGGTTAT
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
50 2 0.03
51 3 0.04
52 70 0.89
53 4 0.05
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (53 bp):
AAAAAGAATTCTAAGAGGAAAAAGATTCTTAATAGGTAAGTTTAACTTGTAAG
Found at i:3587181 original size:25 final size:25
Alignment explanation
Indices: 3587147--3587211 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
3587137 CAAGTGGTAT
* * *
3587147 AAGAGCTGAAGTTTCGAAACATGAG
1 AAGAGTTGAAGTTTCAAAACATGAA
* **
3587172 AAGAGTTGAAGATTCAAAATGTGAA
1 AAGAGTTGAAGTTTCAAAACATGAA
3587197 AAGAGTTGAAAGTTT
1 AAGAGTTG-AAGTTT
3587212 GAGATGTGGG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 27 0.84
26 5 0.16
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.25
Consensus pattern (25 bp):
AAGAGTTGAAGTTTCAAAACATGAA
Found at i:3587620 original size:52 final size:52
Alignment explanation
Indices: 3587542--3587688 Score: 208
Period size: 52 Copynumber: 2.8 Consensus size: 52
3587532 AGACTTGTAA
*
3587542 AAAAGAATTCT-AAAAGAAAGAAGATTCTTAATAGGTAAGTTTGACTTACAAG
1 AAAAGAATTCTAAAAAGAAAG-AGATTCTTAATAGGCAAGTTTGACTTACAAG
*
3587594 AGAAGAATTCTAAAAAGAAATG-GATTCTTAATAGGCAAGTTTGACTTACAAG
1 AAAAGAATTCTAAAAAGAAA-GAGATTCTTAATAGGCAAGTTTGACTTACAAG
* * * *
3587646 AAAAAAATTCTAAGAGGAAAGAGATTCTTAATGGGCAAGTTTG
1 AAAAGAATTCTAAAAAGAAAGAGATTCTTAATAGGCAAGTTTG
3587689 TATAGTTATA
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
51 1 0.01
52 75 0.88
53 8 0.09
54 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.27
Consensus pattern (52 bp):
AAAAGAATTCTAAAAAGAAAGAGATTCTTAATAGGCAAGTTTGACTTACAAG
Found at i:3588288 original size:25 final size:24
Alignment explanation
Indices: 3588260--3588321 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
3588250 TGAAGATTCA
3588260 AGATGTGGAAAATGCTGAAA-GTTTG
1 AGATGTGGAAAA-GCT-AAAGGTTTG
*
3588285 AGATGTGGGAAGAGCTAAAGGTTTG
1 AGATGT-GGAAAAGCTAAAGGTTTG
3588310 AGATGT-GAAAAG
1 AGATGTGGAAAAG
3588322 TGCATGATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 5 0.15
24 3 0.09
25 20 0.61
26 5 0.15
ACGTcount: A:0.37, C:0.03, G:0.35, T:0.24
Consensus pattern (24 bp):
AGATGTGGAAAAGCTAAAGGTTTG
Found at i:3588583 original size:11 final size:12
Alignment explanation
Indices: 3588564--3588605 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
3588554 AATCCTATAA
3588564 GAGATTTGTTTG
1 GAGATTTGTTTG
*
3588576 GA-ATTTG-TTA
1 GAGATTTGTTTG
3588586 GAGATTTGTTT-
1 GAGATTTGTTTG
3588597 GAGATTTGT
1 GAGATTTGT
3588606 CAGATATTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.15
11 19 0.70
12 4 0.15
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (12 bp):
GAGATTTGTTTG
Found at i:3588591 original size:22 final size:23
Alignment explanation
Indices: 3588563--3588618 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
3588553 AAATCCTATA
*
3588563 AGAGATTTGTTTGGA-ATTTGTT
1 AGAGATTTGTTTGGAGATTTGTC
3588585 AGAGATTTGTTT-GAGATTTGTC
1 AGAGATTTGTTTGGAGATTTGTC
*
3588607 AGATA-TTGTTTG
1 AGAGATTTGTTTG
3588619 ATGAACAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 8 0.27
22 22 0.73
ACGTcount: A:0.23, C:0.02, G:0.27, T:0.48
Consensus pattern (23 bp):
AGAGATTTGTTTGGAGATTTGTC
Found at i:3588717 original size:52 final size:53
Alignment explanation
Indices: 3588645--3588784 Score: 171
Period size: 52 Copynumber: 2.7 Consensus size: 53
3588635 GCAAAAAAAT
* **
3588645 ATTCTAAG-AGAAAA-AGGATTCTTAATAGGTAAGTTTAACTTGTAAGAGAAGA
1 ATTCTAAGAAGAAAAGA-GATTCTTAATAGGCAAGTTTAACTTACAAGAGAAGA
* * *
3588697 ATTTTAA-AAGAAAAGAGATTCTTAATAGGCAAGTTTGACTTACAGGAGAAGA
1 ATTCTAAGAAGAAAAGAGATTCTTAATAGGCAAGTTTAACTTACAAGAGAAGA
* *
3588749 ATTCTAAGAAG-AGAGAGATTCTTAATGGGCAAGTTT
1 ATTCTAAGAAGAAAAGAGATTCTTAATAGGCAAGTTT
3588785 GTATGGTTAT
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
52 72 0.95
53 4 0.05
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.29
Consensus pattern (53 bp):
ATTCTAAGAAGAAAAGAGATTCTTAATAGGCAAGTTTAACTTACAAGAGAAGA
Found at i:3592627 original size:2 final size:2
Alignment explanation
Indices: 3592622--3592646 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3592612 CACGAGTGTG
3592622 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
3592647 GTAATTATAC
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:3597158 original size:12 final size:13
Alignment explanation
Indices: 3597132--3597160 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3597122 GTTAAGTTTG
3597132 AAAATTAAAAGAA
1 AAAATTAAAAGAA
3597145 AAAATTAAAA-AA
1 AAAATTAAAAGAA
3597157 AAAA
1 AAAA
3597161 GCTTTTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAATTAAAAGAA
Found at i:3597364 original size:31 final size:31
Alignment explanation
Indices: 3597302--3597365 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
3597292 AAGATCATCT
* * **
3597302 AAAATCAAATTTTAGTGATAAAATTTGATAA
1 AAAATAAAAGTTTAGTGATAAAATTCAATAA
*
3597333 AAAATAAAAGTTTAGTGGTAAAATTCAATAA
1 AAAATAAAAGTTTAGTGATAAAATTCAATAA
3597364 AA
1 AA
3597366 TTAAAATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.31
Consensus pattern (31 bp):
AAAATAAAAGTTTAGTGATAAAATTCAATAA
Found at i:3599897 original size:14 final size:14
Alignment explanation
Indices: 3599858--3599899 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
3599848 TTTATTAAAG
3599858 TTATTTTAAA-TAT
1 TTATTTTAAATTAT
* *
3599871 TAAATTTATAATTAT
1 TTATTTTA-AATTAT
3599886 TTATTTTAAATTAT
1 TTATTTTAAATTAT
3599900 AAAATATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 6 0.26
14 8 0.35
15 9 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTTTAAATTAT
Found at i:3602579 original size:200 final size:196
Alignment explanation
Indices: 3602209--3602579 Score: 435
Period size: 200 Copynumber: 1.9 Consensus size: 196
3602199 TTTGAGTGCC
* * *
3602209 CTAAAAGTACAAATTAATCTATCTTGGAAATACTTATTAAGAAGTTTTCTCAACCAGTCCTTTTT
1 CTAAAAGTACAAATTAAGCTAGCTTGGAAATACTTATTAAGAAGTTTTCTCAACCAGTAC--TTT
* * * *
3602274 TTTTTATATTGTTTTAAGTATGAACTGTTTGGAATCTGTTTTTGTTGTTGTTGTTTTTTTATTTT
64 CTTTTATATTGTTTTAAGTATGAACTGTTTGGAATATGTTTTTGTTATTCTTGTTTTTTTATTTT
* * * *
3602339 ATTTTTATAATTGAAACTTCTTAAACTGAGTTTATTTCTTTATAAGGTGAATTGGCTTGCTTGGT
129 ATATTGATAA-TGAAACTTATTAAACTGAATTTATTTCTTTATAAGGTGAATTGGCTTGCTTGGT
3602404 TGTA
193 TGTA
* * * * * *
3602408 CTAAAAGTACAAATTAAGCTGGGTTAGGGAATGCTTGTTAAGAAGTTTTTTCAACCAGTAC-TTC
1 CTAAAAGTACAAATTAAGCTAGCTT-GGAAATACTTATTAAGAAGTTTTCTCAACCAGTACTTTC
* * *
3602472 TTTTATATTGCCATTTTAAGTATGAAGTGTTTGGAATATGTTTTTGTTATTCTTCCTTTTTTTTC
65 TTTTATATTG---TTTTAAGTATGAACTGTTTGGAATATGTTTTTGTTATTCTT--GTTTTTTTA
3602537 TTTTA-ATTGATAA-G-AACTTATTAAAACTGAATTTATTTTCTTT
125 TTTTATATTGATAATGAAACTTATT-AAACTGAATTTA-TTTCTTT
3602580 GTAGGGCCAA
Statistics
Matches: 144, Mismatches: 20, Indels: 15
0.80 0.11 0.08
Matches are distributed among these distances:
197 12 0.08
198 7 0.05
199 33 0.23
200 74 0.51
201 6 0.04
202 12 0.08
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.49
Consensus pattern (196 bp):
CTAAAAGTACAAATTAAGCTAGCTTGGAAATACTTATTAAGAAGTTTTCTCAACCAGTACTTTCT
TTTATATTGTTTTAAGTATGAACTGTTTGGAATATGTTTTTGTTATTCTTGTTTTTTTATTTTAT
ATTGATAATGAAACTTATTAAACTGAATTTATTTCTTTATAAGGTGAATTGGCTTGCTTGGTTGT
A
Found at i:3603862 original size:11 final size:9
Alignment explanation
Indices: 3603831--3603855 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3603821 TGATTTAGTG
3603831 TTTTTTTAT
1 TTTTTTTAT
3603840 TTTTTTTAT
1 TTTTTTTAT
3603849 TTTTTTT
1 TTTTTTT
3603856 CCATTTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:3614846 original size:21 final size:21
Alignment explanation
Indices: 3614822--3614862 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3614812 TCTCTCAATT
*
3614822 TTTCGTCTTTTTTCATGATTG
1 TTTCGTCTTTTTCCATGATTG
*
3614843 TTTCTTCTTTTTCCATGATT
1 TTTCGTCTTTTTCCATGATT
3614863 TACATTCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.17, G:0.10, T:0.63
Consensus pattern (21 bp):
TTTCGTCTTTTTCCATGATTG
Found at i:3618158 original size:3 final size:3
Alignment explanation
Indices: 3618150--3618189 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
3618140 AAATTAAACC
*
3618150 AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT -AC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3618190 TGGGCCAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 3 0.09
3 30 0.91
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3618170 original size:14 final size:14
Alignment explanation
Indices: 3618151--3618189 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
3618141 AATTAAACCA
3618151 ATAATAATAATAAT
1 ATAATAATAATAAT
3618165 ATAATAATAATAAT
1 ATAATAATAATAAT
*
3618179 ACAATAATAAT
1 ATAATAATAAT
3618190 TGGGCCAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:3618172 original size:17 final size:17
Alignment explanation
Indices: 3618150--3618189 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
3618140 AAATTAAACC
3618150 AATAATAATAATA-ATAT
1 AATAATAATAATACA-AT
3618167 AATAATAATAATACAAT
1 AATAATAATAATACAAT
3618184 AATAAT
1 AATAAT
3618190 TGGGCCAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAATAATACAAT
Found at i:3619560 original size:24 final size:24
Alignment explanation
Indices: 3619516--3619561 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3619506 ATTTTAATTT
* *
3619516 AAAATATAAGGATAAATAAAAATA
1 AAAATATAAAGATAAAGAAAAATA
3619540 AAAATATTAAAGA-AAAGAAAAA
1 AAAATA-TAAAGATAAAGAAAAA
3619562 GAAACTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (24 bp):
AAAATATAAAGATAAAGAAAAATA
Found at i:3619854 original size:18 final size:18
Alignment explanation
Indices: 3619828--3619863 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3619818 AAAATTTATT
*
3619828 TAAACAATATAAAAATAA
1 TAAACAATAAAAAAATAA
*
3619846 TAAATAATAAAAAAATAA
1 TAAACAATAAAAAAATAA
3619864 ATCAAAAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAACAATAAAAAAATAA
Found at i:3632671 original size:63 final size:62
Alignment explanation
Indices: 3632591--3632834 Score: 271
Period size: 63 Copynumber: 3.9 Consensus size: 62
3632581 TACCCTTAAT
* *
3632591 AAATTTTTATCAA-GGATTATTGAAGGTATTTTTGGCCAAAAACGCCTTCAATAATCCTTTCC
1 AAATTTTT-TGAATGGATTATTGAAGGCATTTTTGGCCAAAAACGCCTTCAATAATCCTTTCC
* * * * **
3632653 AAATTTTGTTAAAGGGATTATTGAAAGTGC--TTTTGGACAAAAACGCCTTTAATAATCCCCTCC
1 AAATTTT-TTGAATGGATTATTG-AAG-GCATTTTTGGCCAAAAACGCCTTCAATAATCCTTTCC
* * **
3632716 AAAATTTTTTGTATGGATTATTGAAGCCATTTTTGGCCAAAAACGTATTCAATAATCCATTTCC
1 -AAATTTTTTGAATGGATTATTGAAGGCATTTTTGGCCAAAAACGCCTTCAATAATCC-TTTCC
* * *
3632780 AAAATTTTTGAATAGATTATTGAAGGCATTTTTGGCC-AAAACACCTTCAATAATC
1 AAATTTTTTGAATGGATTATTGAAGGCATTTTTGGCCAAAAACGCCTTCAATAATC
3632835 TCATTCAATT
Statistics
Matches: 151, Mismatches: 23, Indels: 16
0.79 0.12 0.08
Matches are distributed among these distances:
61 1 0.01
62 28 0.19
63 108 0.72
64 13 0.09
65 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (62 bp):
AAATTTTTTGAATGGATTATTGAAGGCATTTTTGGCCAAAAACGCCTTCAATAATCCTTTCC
Found at i:3632674 original size:126 final size:128
Alignment explanation
Indices: 3632544--3632787 Score: 300
Period size: 126 Copynumber: 1.9 Consensus size: 128
3632534 TTCAATATGG
* *
3632544 TTATTCAAGGT-ATTTATGGA-AAAAAAGCCTTGAATAATACCCTTAATAAATTTTTAT-CAAGG
1 TTATTCAAAGTGATTT-TGGACAAAAAAGCCTTGAATAATACCCTCAA-AAATTTTT-TGCAAGG
** *
3632606 ATTATTGAAGGTATTTTTGGCCAAAAACGCCTTCAATAATCC-TTTCC-AAATTTTGTTAAAGGG
63 ATTATTGAAGCCATTTTTGGCCAAAAACGCATTCAATAATCCATTTCCAAAATTTTGTTAAAGGG
3632669 A
128 A
* * * * * * * *
3632670 TTATTGAAAGTGCTTTTGGACAAAAACGCCTTTAATAATCCCCTCCAAAATTTTTTGTATGGATT
1 TTATTCAAAGTGATTTTGGACAAAAAAGCCTTGAATAATACCCTCAAAAATTTTTTGCAAGGATT
*
3632735 ATTGAAGCCATTTTTGGCCAAAAACGTATTCAATAATCCATTTCCAAAATTTT
66 ATTGAAGCCATTTTTGGCCAAAAACGCATTCAATAATCCATTTCCAAAATTTT
3632788 TGAATAGATT
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
125 1 0.01
126 62 0.63
127 29 0.29
128 7 0.07
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (128 bp):
TTATTCAAAGTGATTTTGGACAAAAAAGCCTTGAATAATACCCTCAAAAATTTTTTGCAAGGATT
ATTGAAGCCATTTTTGGCCAAAAACGCATTCAATAATCCATTTCCAAAATTTTGTTAAAGGGA
Found at i:3632813 original size:126 final size:125
Alignment explanation
Indices: 3632604--3632834 Score: 306
Period size: 126 Copynumber: 1.8 Consensus size: 125
3632594 TTTTTATCAA
** * * *
3632604 GGATTATTGAAGGTATTTTTGGCCAAAAACGCCTTCAATAATCCTTTCCAAATTTTGTTAAAGGG
1 GGATTATTGAAGCCATTTTTGGCCAAAAACGCATTCAATAATCCTTTCCAAAATTTGTTAAAGAG
* *
3632669 ATTATTGAAAGTGCTTTTGGACAAAAACGCCTTTAATAATCCCCTCCAAAATTTTTTGTAT
66 ATTATTGAAAGTGCTTTTGG-CAAAAACACCTTCAATAATCCCCTCCAAAATTTTTTGTAT
* * *
3632730 GGATTATTGAAGCCATTTTTGGCCAAAAACGTATTCAATAATCCATTTCCAAAATTT-TTGAATA
1 GGATTATTGAAGCCATTTTTGGCCAAAAACGCATTCAATAATCC-TTTCCAAAATTTGTTAAAGA
*
3632794 GATTATTG-AAG-GCATTTTTGGCCAAAACACCTTCAATAATC
65 GATTATTGAAAGTGC--TTTTGGCAAAAACACCTTCAATAATC
3632835 TCATTCAATT
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
124 2 0.02
125 20 0.22
126 58 0.64
127 11 0.12
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (125 bp):
GGATTATTGAAGCCATTTTTGGCCAAAAACGCATTCAATAATCCTTTCCAAAATTTGTTAAAGAG
ATTATTGAAAGTGCTTTTGGCAAAAACACCTTCAATAATCCCCTCCAAAATTTTTTGTAT
Found at i:3636806 original size:3 final size:3
Alignment explanation
Indices: 3636798--3636830 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3636788 TTTTAAATAT
3636798 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3636831 AACTAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3637473 original size:17 final size:17
Alignment explanation
Indices: 3637443--3637478 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
3637433 GAATTCTAAA
3637443 AAAAGGAAGAGAGAAAT
1 AAAAGGAAGAGAGAAAT
3637460 AAAAGAGAAG-GAGAAAT
1 AAAAG-GAAGAGAGAAAT
3637477 AA
1 AA
3637479 GATAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.06
Consensus pattern (17 bp):
AAAAGGAAGAGAGAAAT
Found at i:3639316 original size:2 final size:2
Alignment explanation
Indices: 3639309--3639335 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3639299 TATACGTGTT
3639309 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 T
3639336 TGTTGTTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3640269 original size:17 final size:17
Alignment explanation
Indices: 3640235--3640267 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3640225 CATTTGTATT
*
3640235 TTAAATATTTTATTAAA
1 TTAAATATTTTATAAAA
3640252 TTAAAT-TTTTATAAAA
1 TTAAATATTTTATAAAA
3640268 ATATATTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAATATTTTATAAAA
Found at i:3640467 original size:7 final size:7
Alignment explanation
Indices: 3640455--3640486 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
3640445 TCTAAAGAGA
3640455 TTTAAAT
1 TTTAAAT
3640462 TTTAAAT
1 TTTAAAT
3640469 TTTAAAT
1 TTTAAAT
3640476 TTTAAAT
1 TTTAAAT
3640483 TTTA
1 TTTA
3640487 GTATGAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTAAAT
Found at i:3642006 original size:2 final size:2
Alignment explanation
Indices: 3641999--3642031 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3641989 CTTAGCAATA
3641999 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3642032 GCTATTGACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3643415 original size:6 final size:6
Alignment explanation
Indices: 3643404--3643431 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3643394 ATTTATGATT
3643404 TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATT
3643432 ATAAGTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:3643532 original size:17 final size:18
Alignment explanation
Indices: 3643495--3643533 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3643485 TAATTTAATT
* *
3643495 TTTATGAAATTATTTTTA
1 TTTATAAAATTATTATTA
3643513 TTTATAAAATTA-TATTA
1 TTTATAAAATTATTATTA
3643530 TTTA
1 TTTA
3643534 AATAAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTATAAAATTATTATTA
Found at i:3644657 original size:15 final size:16
Alignment explanation
Indices: 3644637--3644666 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3644627 ATAAAAAAAT
3644637 TTTATA-TTTAATTAG
1 TTTATATTTTAATTAG
3644652 TTTATATTTTAATTA
1 TTTATATTTTAATTA
3644667 AAGCTTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTATATTTTAATTAG
Found at i:3646909 original size:17 final size:17
Alignment explanation
Indices: 3646881--3646913 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
3646871 TGAAATATAA
3646881 TAAAACATATATTAAAAC
1 TAAAACATATA-TAAAAC
3646899 TAAAA-ATATATAAAA
1 TAAAACATATATAAAA
3646914 TTGCCCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAACATATATAAAAC
Found at i:3647764 original size:60 final size:61
Alignment explanation
Indices: 3647687--3647835 Score: 173
Period size: 60 Copynumber: 2.5 Consensus size: 61
3647677 TGATATGAGA
* * * *
3647687 GGTATTGTAGTAATTTTGGCTAATTATGGTAG-GAGGGACATTT-TCATAATTATG-TGAA-AT
1 GGTATTATAATAATTTTGGCTAATTATGGCAGAAAGGG-CATTTCT-ATAATTATGAT-AAGAT
* *
3647747 GGTATTATAATAATTTTGACTAATTATAGCAGAAAGGGCATTTCTATAATTATGATAAGAT
1 GGTATTATAATAATTTTGGCTAATTATGGCAGAAAGGGCATTTCTATAATTATGATAAGAT
3647808 GGTATTATAATAA-TTTGGACTAATTATG
1 GGTATTATAATAATTTTGG-CTAATTATG
3647836 TAAAAAGTAA
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
60 47 0.62
61 29 0.38
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (61 bp):
GGTATTATAATAATTTTGGCTAATTATGGCAGAAAGGGCATTTCTATAATTATGATAAGAT
Found at i:3647859 original size:17 final size:15
Alignment explanation
Indices: 3647828--3647871 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 15
3647818 TAATTTGGAC
3647828 TAATTATGTAAAAAG
1 TAATTATGTAAAAAG
3647843 TAATTATGATAAAAAAG
1 TAATTATG-T-AAAAAG
3647860 T-ATTATAGTAAA
1 TAATTAT-GTAAA
3647872 TTTGGATACG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 11 0.42
16 7 0.27
17 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (15 bp):
TAATTATGTAAAAAG
Found at i:3648117 original size:129 final size:128
Alignment explanation
Indices: 3647954--3648236 Score: 322
Period size: 129 Copynumber: 2.2 Consensus size: 128
3647944 TATATGTCAT
* * *
3647954 TTAACATTTAATA-ATTAATTTAATAAGGGTATTATAGTAAATTTTAAACAAAAT-TCCAAATGT
1 TTAAAATTTAATATA-TAATTTAAT-AGGGAATTATAATAAATTTTAAACAAAATAT-CAAATGT
* * * *
3648017 CAAATATTTATAAAGTAATA-GAAATGG-TATTTTAGTAATTTAAAATGTTGTTAATTTTATATT
63 CAAATATTTATAAAGCAA-AGGAAA-GGATATATTAATAATTTAAAATGTAGTTAATTTTATATT
3648080 ATA
126 ATA
* * * * * *
3648083 TTAAAATTTCATATGTAATTTAATAGGAGAATTATAATCATTTTTAAATAAAATATCACATGTCA
1 TTAAAATTTAATATATAATTTAATAGG-GAATTATAATAAATTTTAAACAAAATATCAAATGTCA
* * ** *
3648148 AATTTTTATAAAGCAAAGGCAAGGATATATTAATAATTTAATGTGTAGTTAATTTTATATTATG
65 AATATTTATAAAGCAAAGGAAAGGATATATTAATAATTTAAAATGTAGTTAATTTTATATTATA
3648212 TTAAAATTTAATATATAATTTAATA
1 TTAAAATTTAATATATAATTTAATA
3648237 AATGTATTGC
Statistics
Matches: 129, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
128 6 0.05
129 122 0.95
130 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42
Consensus pattern (128 bp):
TTAAAATTTAATATATAATTTAATAGGGAATTATAATAAATTTTAAACAAAATATCAAATGTCAA
ATATTTATAAAGCAAAGGAAAGGATATATTAATAATTTAAAATGTAGTTAATTTTATATTATA
Found at i:3648480 original size:61 final size:61
Alignment explanation
Indices: 3648364--3648480 Score: 166
Period size: 61 Copynumber: 1.9 Consensus size: 61
3648354 CTAAGGGTAT
* * * *
3648364 TTTCATAATTTTAGTAAGAAGGGTATTATAGTAATTTTAGCTAATTATGATAAGAGGGATA
1 TTTCATAATTTTAGTAAGAAGAGTATTATAATAATTTTAGCTAATTATAAAAAGAGGGATA
3648425 TTTCTATAATTATT-GTAAG-AGAGTATTATAATAATTTTAGCTAATTATAAAAAGAG
1 TTTC-ATAATT-TTAGTAAGAAGAGTATTATAATAATTTTAGCTAATTATAAAAAGAG
3648481 AAATGCTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
61 37 0.74
62 11 0.22
63 2 0.04
ACGTcount: A:0.40, C:0.03, G:0.16, T:0.40
Consensus pattern (61 bp):
TTTCATAATTTTAGTAAGAAGAGTATTATAATAATTTTAGCTAATTATAAAAAGAGGGATA
Found at i:3648512 original size:61 final size:61
Alignment explanation
Indices: 3648380--3648515 Score: 150
Period size: 61 Copynumber: 2.2 Consensus size: 61
3648370 AATTTTAGTA
* * * * ** *
3648380 AGAAGGGTATTATAGTAATTTTAGCTAATTATGATAAGAGGGATATTTCTATAATTATTGT
1 AGAAAGGTATTATAATAATTTTAGCTAATTATAAAAAGAGAAATATTTCTATAATTATGGT
* * *
3648441 A-AGAGAGTATTATAATAATTTTAGCTAATTATAAAAAGAGAAATGCTTT-TGTAATTATGGT
1 AGAAAG-GTATTATAATAATTTTAGCTAATTATAAAAAGAGAAAT-ATTTCTATAATTATGGT
3648502 AGAAAGGTATTATA
1 AGAAAGGTATTATA
3648516 GTAAGTTTGG
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
60 2 0.03
61 53 0.87
62 6 0.10
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.38
Consensus pattern (61 bp):
AGAAAGGTATTATAATAATTTTAGCTAATTATAAAAAGAGAAATATTTCTATAATTATGGT
Found at i:3649007 original size:26 final size:28
Alignment explanation
Indices: 3648928--3649010 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 28
3648918 ATTTTTAAGG
*
3648928 TATTTTCGTAATTATGACATGA-AGGTAT
1 TATTTTCATAATTATGACATGAGA-GTAT
* * *
3648956 TATTTTATATAATTAT-AAAAGAAGAG-A-
1 TATTTT-CATAATTATGACATG-AGAGTAT
3648983 TATTTTCATAATTATGACATGAGAGTAT
1 TATTTTCATAATTATGACATGAGAGTAT
3649011 AATAGTCAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
26 12 0.29
27 10 0.24
28 10 0.24
29 9 0.21
30 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (28 bp):
TATTTTCATAATTATGACATGAGAGTAT
Done.