Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 180 of 190
Found at i:52677861 original size:2 final size:2
Alignment explanation
Indices: 52677856--52677887 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52677846 AATCACACGC
52677856 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
52677888 TATTACAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52678462 original size:18 final size:19
Alignment explanation
Indices: 52678441--52678476 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
52678431 AAATAGTATA
*
52678441 TATAAAGTAAAT-TTTTTT
1 TATAAAATAAATGTTTTTT
52678459 TATAAAATAAATGTTTTT
1 TATAAAATAAATGTTTTT
52678477 ATTAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
TATAAAATAAATGTTTTTT
Found at i:52678673 original size:31 final size:30
Alignment explanation
Indices: 52678635--52678732 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 30
52678625 AGTATCAAAA
* *
52678635 TAGTCACTTTTGTTTACCTCATGTTACATTT
1 TAGTCACTTATGTTTA-CTAATGTTACATTT
52678666 TAGTCACTTATGTTTGA--AATGTTACATTT
1 TAGTCACTTATGTTT-ACTAATGTTACATTT
* ** *
52678695 TAGTCACTTATGTTAACGTGTTGTAACATTT
1 TAGTCACTTATGTTTAC-TAATGTTACATTT
52678726 TAGTCAC
1 TAGTCAC
52678733 AGAGCCGTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
28 1 0.02
29 25 0.44
31 30 0.53
32 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.47
Consensus pattern (30 bp):
TAGTCACTTATGTTTACTAATGTTACATTT
Found at i:52697093 original size:16 final size:16
Alignment explanation
Indices: 52697072--52697104 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
52697062 CACCATCCCA
52697072 TCCTTAAATTTAGAGG
1 TCCTTAAATTTAGAGG
52697088 TCCTTAAATTTAGAGG
1 TCCTTAAATTTAGAGG
52697104 T
1 T
52697105 ATATGACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (16 bp):
TCCTTAAATTTAGAGG
Found at i:52703478 original size:31 final size:31
Alignment explanation
Indices: 52703420--52703491 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
52703410 TTTTTGGTCC
* **
52703420 AATTTGTTACCCAAACTTGACTTTTTTTCCT
1 AATTTGATACCCAAACTTGACACTTTTTCCT
* *
52703451 AATTTGATACCTAAACTTGACACTTTTTCTT
1 AATTTGATACCCAAACTTGACACTTTTTCCT
*
52703482 AAGTTGATAC
1 AATTTGATAC
52703492 TTAATCTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.44
Consensus pattern (31 bp):
AATTTGATACCCAAACTTGACACTTTTTCCT
Found at i:52704050 original size:59 final size:58
Alignment explanation
Indices: 52703925--52704074 Score: 149
Period size: 59 Copynumber: 2.5 Consensus size: 58
52703915 AATTGAACTA
* * * * *
52703925 AAAAAAAGCTTAGGTACCAAATTAGGAAAAAATTATCAAGTTCAGGCATCAAATTGGGGC
1 AAAAAAAGTTTAGGTACCAAATTA-GAAAAAAGTATAAAGCTCA-GCATCAAATTGGGAC
** * *
52703985 CCAAAAAGTTTAGGTACTAAATTAGAAAAAAGTGTAAAGCTCA-CATACCAAATTGGGAC
1 AAAAAAAGTTTAGGTACCAAATTAGAAAAAAGTATAAAGCTCAGCAT--CAAATTGGGAC
* * *
52704044 AAAAAAATTTTAAGTACCAAATTAAAAAAAA
1 AAAAAAAGTTTAGGTACCAAATTAGAAAAAA
52704075 AATCAAATTT
Statistics
Matches: 73, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
57 3 0.04
59 50 0.68
60 20 0.27
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.22
Consensus pattern (58 bp):
AAAAAAAGTTTAGGTACCAAATTAGAAAAAAGTATAAAGCTCAGCATCAAATTGGGAC
Found at i:52706257 original size:4 final size:4
Alignment explanation
Indices: 52706248--52706275 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
52706238 GATCCGATGC
52706248 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
52706276 TATCACTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:52710441 original size:31 final size:29
Alignment explanation
Indices: 52710392--52710461 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 29
52710382 TCGTTAGAAA
*
52710392 TTAATTGATTTTTCTATTATTTTATAAGCGT
1 TTAATTGATTTTTCTATTATTTT-TAA-AGT
*
52710423 TTAATT-ATTATTTTTATTATTTTTAAAGT
1 TTAATTGATT-TTTCTATTATTTTTAAAGT
52710452 TTAATTGATT
1 TTAATTGATT
52710462 GTTTAAGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 8 0.23
30 9 0.26
31 18 0.51
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.61
Consensus pattern (29 bp):
TTAATTGATTTTTCTATTATTTTTAAAGT
Found at i:52711818 original size:19 final size:19
Alignment explanation
Indices: 52711783--52711824 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
52711773 ATTTTTATGA
* *
52711783 ATTTTTTATTTTTTAAA-T
1 ATTTTTTAATTTATAAATT
52711801 ATTTTTATAATTTATAAATT
1 ATTTTT-TAATTTATAAATT
52711821 ATTT
1 ATTT
52711825 GTTGATGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 9 0.45
20 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTTAATTTATAAATT
Found at i:52713552 original size:24 final size:25
Alignment explanation
Indices: 52713493--52713556 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
52713483 TATATATATC
*
52713493 TAAATACATATTTC-TTTAATTTTCA
1 TAAATACATA-TACATTTAATTTTCA
*
52713518 TAAATATATATACATTTACATTTT-A
1 TAAATACATATACATTTA-ATTTTCA
52713543 T-AATACATATACAT
1 TAAATACATATACAT
52713557 CTTCCATATC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 14 0.41
25 15 0.44
26 5 0.15
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (25 bp):
TAAATACATATACATTTAATTTTCA
Found at i:52713671 original size:32 final size:32
Alignment explanation
Indices: 52713635--52713696 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
52713625 ATTATTATAA
* *
52713635 ATATATATTTCATTTT-TTATATATATATACTT
1 ATATATATGT-ATTTTAATATATATATATACTT
*
52713667 ATATATATGTATTTTAATATATGTATATAC
1 ATATATATGTATTTTAATATATATATATAC
52713697 ATATTTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 5 0.19
32 21 0.81
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (32 bp):
ATATATATGTATTTTAATATATATATATACTT
Found at i:52713737 original size:19 final size:17
Alignment explanation
Indices: 52713714--52713761 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
52713704 CAAAATTTAC
52713714 TTATATATAT-CATACTT
1 TTATATATATACATA-TT
52713731 TTATATATATACATATT
1 TTATATATATACATATT
*
52713748 TTGTA-A-ATACATAT
1 TTATATATATACATAT
52713762 ACATATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 8 0.28
16 1 0.03
17 16 0.55
18 4 0.14
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (17 bp):
TTATATATATACATATT
Found at i:52721140 original size:3 final size:3
Alignment explanation
Indices: 52721127--52721166 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
52721117 TTTTAACTAT
*
52721127 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
52721167 AATACATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:52728172 original size:45 final size:45
Alignment explanation
Indices: 52728107--52728680 Score: 407
Period size: 45 Copynumber: 12.9 Consensus size: 45
52728097 AACAGATCGG
* * * **
52728107 TGAAGATAACAAATCATATCTCCATGAAGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * * * * **
52728152 TGAAGATAACAAGTCTTATCTCCTTGAAGATGCAGCAGAGCAGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * * **
52728197 TGAAGATAGCAAATCCTATCTACCTAAAGTTGTAGTGGAGTGGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * * * * * *
52728242 TGAAGATAGCAAGTCTTATCTCCCTGAGGTTGCAGCGGAGTAAAC
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * * **
52728287 TAAAGATAGCAAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * * * * * * *
52728332 TGAAAATAACAAGTCTTATCTCCCTAAAATTGCAGCGGAGCAGAC
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * *
52728377 TGAAGATAGCAAATCCTATCTCCCTAAAGTTGCAGTTGAACAGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * *
52728422 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * *
52728467 TGAAGA-A-AATAATCCTATCTCCCTGAAGTTGCAGTAGAGCTGAT
1 TGAAGATAGCA-AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * * * * * *
52728511 T-AAAACT-GTAGATCTTATCTCTCTAAAGTTGCAGAGG-GCAGA-
1 TGAAGA-TAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * * * * * *
52728553 T-CACAT--CTAGTCTTATCTCCCTAAAGTTGCAGAT-GAGCAGAC
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAG-TGGAGCAGAT
* * * * *
52728595 TGAATA-AACCAAT-CTGATTTCCCTGAAATTGCAGTGGAGCAGAT
1 TGAAGATAGCAAATCCT-ATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * * *
52728639 TAAAGATAACAAATCATATCTCCATGAAGTTGCAGTGGAGCA
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCA
52728681 TATAAAAATC
Statistics
Matches: 410, Mismatches: 105, Indels: 28
0.76 0.19 0.05
Matches are distributed among these distances:
40 22 0.05
41 6 0.01
42 4 0.01
43 12 0.03
44 81 0.20
45 284 0.69
46 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (45 bp):
TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
Found at i:52728260 original size:90 final size:90
Alignment explanation
Indices: 52728107--52728501 Score: 490
Period size: 90 Copynumber: 4.4 Consensus size: 90
52728097 AACAGATCGG
* * * *
52728107 TGAAGATAACAAATCATATCTCCATGAAGTTGCAGTGGAGTGGATTGAAGATAACAAGTCTTATC
1 TGAAGATAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTGAAGATAACAAGTCTTATC
* * *
52728172 TCCTTGAAGATGCAGCAGAGCAGAT
66 TCCCTGAAGATGCAGCGGAGCAGAC
* * *
52728197 TGAAGATAGCAAATCCTATCTACCTAAAGTTGTAGTGGAGTGGATTGAAGATAGCAAGTCTTATC
1 TGAAGATAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTGAAGATAACAAGTCTTATC
* * * *
52728262 TCCCTGAGGTTGCAGCGGAGTAAAC
66 TCCCTGAAGATGCAGCGGAGCAGAC
* * *
52728287 TAAAGATAGCAAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTGAAAATAACAAGTCTTATC
1 TGAAGATAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTGAAGATAACAAGTCTTATC
*
52728352 TCCCT-AAAATTGCAGCGGAGCAGAC
66 TCCCTGAAGA-TGCAGCGGAGCAGAC
* *** *
52728377 TGAAGATAGCAAATCCTATCTCCCTAAAGTTGCAGTTGAACAGATTGAAGATAGCAAGTCTTATC
1 TGAAGATAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTGAAGATAACAAGTCTTATC
* * * *
52728442 TCCCTGAAGTTACAGTGGAGCAGAT
66 TCCCTGAAGATGCAGCGGAGCAGAC
* *
52728467 TGAAGA-A-AATAATCCTATCTCCCTGAAGTTGCAGT
1 TGAAGATAGCA-AATCCTATCTCCCTAAAGTTGCAGT
52728502 AGAGCTGATT
Statistics
Matches: 264, Mismatches: 38, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
88 1 0.00
89 26 0.10
90 235 0.89
91 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (90 bp):
TGAAGATAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTGAAGATAACAAGTCTTATC
TCCCTGAAGATGCAGCGGAGCAGAC
Found at i:52728661 original size:173 final size:171
Alignment explanation
Indices: 52728393--52728717 Score: 422
Period size: 173 Copynumber: 1.9 Consensus size: 171
52728383 TAGCAAATCC
* * * * * *
52728393 TATCTCCCTAAAGTTGCAGTTGAACAGATTGAAGATAGCAAGTCTTATCTCCCTGAAGTTACAGT
1 TATCTCCCTAAAGTTGCAGATGAACAGACTGAAGAAACCAAGTCTGATCTCCCTGAAATTACAGT
* * * * *
52728458 GGAGCAGATTGAAGAAAATAATCCTATCTCCCTGAAGTTGCAGTAGAGC-TGATTAAAACTGTAG
66 GGAGCAGATTAAAGAAAATAATCATATCTCCATGAAGTTGCAGTAGAGCAT-A-TAAAAAT-CAG
52728522 ATCTTATCTCTCTAAAGTTGCAGAGGGCAGATCACATCTAGTCT
128 ATCTTATCTCTCTAAAGTTGCAGAGGGCAGATCACATCTAGTCT
* * * *
52728566 TATCTCCCTAAAGTTGCAGATGAGCAGACTGAATAAACCAA-TCTGATTTCCCTGAAATTGCAGT
1 TATCTCCCTAAAGTTGCAGATGAACAGACTGAAGAAACCAAGTCTGATCTCCCTGAAATTACAGT
*
52728630 GGAGCAGATTAAAGATAACA-AATCATATCTCCATGAAGTTGCAGTGGAGCATATAAAAATCAGA
66 GGAGCAGATTAAAGA-AA-ATAATCATATCTCCATGAAGTTGCAGTAGAGCATATAAAAATCAGA
* *
52728694 TCTTATCTCTCTGATGTTGCAGAG
129 TCTTATCTCTCTAAAGTTGCAGAG
52728718 AGTAGATTGC
Statistics
Matches: 131, Mismatches: 18, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
171 25 0.19
172 39 0.30
173 65 0.50
174 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (171 bp):
TATCTCCCTAAAGTTGCAGATGAACAGACTGAAGAAACCAAGTCTGATCTCCCTGAAATTACAGT
GGAGCAGATTAAAGAAAATAATCATATCTCCATGAAGTTGCAGTAGAGCATATAAAAATCAGATC
TTATCTCTCTAAAGTTGCAGAGGGCAGATCACATCTAGTCT
Found at i:52730451 original size:17 final size:19
Alignment explanation
Indices: 52730427--52730467 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
52730417 AATTTTACTT
52730427 ATATATATCATACTTT-TAA
1 ATATATA-CATACTTTGTAA
*
52730446 ATATATACATATTTTGTAA
1 ATATATACATACTTTGTAA
52730465 ATA
1 ATA
52730468 CATGTACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATATACATACTTTGTAA
Found at i:52731810 original size:40 final size:40
Alignment explanation
Indices: 52731766--52731859 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 40
52731756 AAAAATTATA
* *
52731766 TTTAATAAAATAAAACATTTCTTATATTTAT-TTGTGTTTT
1 TTTAATAAAATAAAACATTTATTATATTTATATAGTG-TTT
* *
52731806 TTTAATATAACAAAACATTTATTATATTTATGATAGTGTTT
1 TTTAATAAAATAAAACATTTATTATATTTAT-ATAGTGTTT
52731847 TTTAATATAAATA
1 TTTAATA-AAATA
52731860 CTTTTTAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 28 0.62
41 10 0.22
42 7 0.16
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.51
Consensus pattern (40 bp):
TTTAATAAAATAAAACATTTATTATATTTATATAGTGTTT
Found at i:52733568 original size:10 final size:9
Alignment explanation
Indices: 52733548--52733606 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
52733538 CATTGTTAAG
52733548 TTAA-ATTT
1 TTAATATTT
52733556 TTAATATTTT
1 TTAATA-TTT
52733566 TTAATATTT
1 TTAATATTT
*
52733575 AT-ATATTT
1 TTAATATTT
52733583 TTAATACTTT
1 TTAATA-TTT
*
52733593 TTGA-ATTT
1 TTAATATTT
52733601 TTAATA
1 TTAATA
52733607 AATTTAATTC
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
8 17 0.40
9 10 0.24
10 15 0.36
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTAATATTT
Found at i:52733612 original size:27 final size:27
Alignment explanation
Indices: 52733555--52733614 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
52733545 AAGTTAAATT
* **
52733555 TTTAATATTTTTTAATATTTATATATT
1 TTTAATATTTTTGAATATTTATATAAA
*
52733582 TTTAATACTTTTTGAATTTTTA-ATAAA
1 TTTAATA-TTTTTGAATATTTATATAAA
52733609 TTTAAT
1 TTTAAT
52733615 TCCATTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 16 0.57
28 12 0.43
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTAATATTTTTGAATATTTATATAAA
Found at i:52741538 original size:5 final size:5
Alignment explanation
Indices: 52741523--52741552 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
52741513 TATAGTGGAA
52741523 CTTTT -TTTT CTTTT CTTTT CTTTT CTTTT C
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT C
52741553 ATTGTACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:52743287 original size:17 final size:18
Alignment explanation
Indices: 52743255--52743288 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52743245 AATTTTTTTT
*
52743255 CTCTCTATATATGATTAA
1 CTCTCTATATAAGATTAA
52743273 CTCTC-ATATAAGATTA
1 CTCTCTATATAAGATTA
52743289 CAAGAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (18 bp):
CTCTCTATATAAGATTAA
Found at i:52757555 original size:22 final size:23
Alignment explanation
Indices: 52757527--52757595 Score: 90
Period size: 22 Copynumber: 3.1 Consensus size: 23
52757517 TATGCACTAT
*
52757527 TAAACAGAGAGCACTAAA-GTTC
1 TAAACAGAGAGCACTAAATGTGC
*
52757549 TATACAGAGAGCA-TAAATGTGC
1 TAAACAGAGAGCACTAAATGTGC
*
52757571 TAAACGGAGAGCACT-AATGTGC
1 TAAACAGAGAGCACTAAATGTGC
52757593 TAA
1 TAA
52757596 CAATTAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.10
22 36 0.88
23 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (23 bp):
TAAACAGAGAGCACTAAATGTGC
Found at i:52761554 original size:33 final size:32
Alignment explanation
Indices: 52761471--52761547 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
52761461 AATTAGAGGC
52761471 ATTGATAAATTTGACTTTCATTTTCATTTTCA
1 ATTGATAAATTTGACTTTCATTTTCATTTTCA
**
52761503 ATTTTTAAAATTTGACTTT-ATTATT-ATTATTCA
1 ATTGAT-AAATTTGACTTTCATT-TTCATT-TTCA
52761536 ATTGATAAATTT
1 ATTGATAAATTT
52761548 TTACTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
32 16 0.42
33 22 0.58
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (32 bp):
ATTGATAAATTTGACTTTCATTTTCATTTTCA
Found at i:52767463 original size:18 final size:18
Alignment explanation
Indices: 52767422--52767463 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
52767412 GATAATTCTC
52767422 ATATTTTATTTTTAAAGTA
1 ATATTTTATTTTTAAAG-A
52767441 A-ATTTTATTTTTAACA-A
1 ATATTTTATTTTTAA-AGA
52767458 ATATTT
1 ATATTT
52767464 GGATTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.10
18 17 0.81
19 2 0.10
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
ATATTTTATTTTTAAAGA
Found at i:52770848 original size:14 final size:14
Alignment explanation
Indices: 52770825--52770854 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52770815 AAAATGTTGG
*
52770825 TTAAATTTCTTATA
1 TTAAACTTCTTATA
52770839 TTAAACTTCTTATA
1 TTAAACTTCTTATA
52770853 TT
1 TT
52770855 GATTGCAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAACTTCTTATA
Found at i:52775619 original size:19 final size:20
Alignment explanation
Indices: 52775588--52775652 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 20
52775578 TTTCGTATTA
*
52775588 AAATTATAA-TTTCTTTTTC
1 AAATTAGAATTTTCTTTTTC
* * *
52775607 AAATTA-AATTTTCATATTA
1 AAATTAGAATTTTCTTTTTC
52775626 AAATTAGAATTTT-TTTCATTC
1 AAATTAGAATTTTCTTT--TTC
52775647 AAATTA
1 AAATTA
52775653 ATCCTTGATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 2 0.06
19 20 0.56
20 6 0.17
21 8 0.22
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATTAGAATTTTCTTTTTC
Found at i:52775625 original size:38 final size:39
Alignment explanation
Indices: 52775576--52775653 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 39
52775566 TTTAGAAATT
* *
52775576 ATTTTCGTATTAAAATTATAATTTCTTT-TTCAAATTAA
1 ATTTTCATATTAAAATTAGAATTTCTTTATTCAAATTAA
*
52775614 ATTTTCATATTAAAATTAGAATTTTTTTCATTCAAATTAA
1 ATTTTCATATTAAAATTAGAATTTCTTT-ATTCAAATTAA
52775654 TCCTTGATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 25 0.71
40 10 0.29
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (39 bp):
ATTTTCATATTAAAATTAGAATTTCTTTATTCAAATTAA
Found at i:52790526 original size:18 final size:18
Alignment explanation
Indices: 52790505--52790544 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52790495 CTTTCTTCAA
* * *
52790505 TTTCTTTTTCACTTTTCT
1 TTTCTGTTTCACATTCCT
52790523 TTTCTGTTTCACATTCCT
1 TTTCTGTTTCACATTCCT
52790541 TTTC
1 TTTC
52790545 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.07, C:0.25, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTCTGTTTCACATTCCT
Found at i:52795196 original size:21 final size:21
Alignment explanation
Indices: 52795154--52795196 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
52795144 TATCTAATTC
*
52795154 ATTGATAATATATAAAACTAT
1 ATTGATAATACATAAAACTAT
*
52795175 ATTGATTAATACATCAAA-TAT
1 ATTGA-TAATACATAAAACTAT
52795196 A
1 A
52795197 AATTTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (21 bp):
ATTGATAATACATAAAACTAT
Found at i:52799069 original size:33 final size:33
Alignment explanation
Indices: 52799002--52799069 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
52798992 GCATGATCAA
* * *
52799002 GAATTTGATATTCCTTAACAAAGTCTCCTGTTT
1 GAATTCGATATTCCTTAACAAAATCTCCTATTT
*
52799035 GAATTCGATATTCCTTGAA-AAAATCTCTTATTT
1 GAATTCGATATTCCTT-AACAAAATCTCCTATTT
52799068 GA
1 GA
52799070 GTTCAATAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (33 bp):
GAATTCGATATTCCTTAACAAAATCTCCTATTT
Found at i:52800439 original size:38 final size:39
Alignment explanation
Indices: 52800367--52800444 Score: 90
Period size: 38 Copynumber: 2.0 Consensus size: 39
52800357 ACATTAAATT
* *
52800367 TGAATTATAATTTATATTTTTTATTTTAATTTAAT-TAA
1 TGAAATATAATTTATATTTTTTATATTAATTTAATATAA
*
52800405 TGAAATAT-ATTTATTTATTTTTATATTAGA-TTAATATAA
1 TGAAATATAATTTATAT-TTTTTATATTA-ATTTAATATAA
52800444 T
1 T
52800445 TTTTTGTGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
37 7 0.21
38 22 0.65
39 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (39 bp):
TGAAATATAATTTATATTTTTTATATTAATTTAATATAA
Found at i:52803779 original size:39 final size:40
Alignment explanation
Indices: 52803697--52803771 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 40
52803687 AAATTAAAAC
*
52803697 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAAAAAGTATTTTAAAAATATATTAAAATTAA
52803737 AAAAATT-AAAAAAGTATTTTAAAAA-A-ATTAAAATT
1 AAAAATTAAAAAAAGTATTTTAAAAATATATTAAAATT
52803772 TTAAAAAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 8 0.24
38 1 0.03
39 18 0.53
40 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (40 bp):
AAAAATTAAAAAAAGTATTTTAAAAATATATTAAAATTAA
Found at i:52803800 original size:30 final size:30
Alignment explanation
Indices: 52803713--52803802 Score: 102
Period size: 30 Copynumber: 3.1 Consensus size: 30
52803703 TAAAAAAAGT
*
52803713 ATTTT-AAAAA-TATTTTAAAATTAA-AAAA
1 ATTTTAAAAAAGTATTTTAAAA-AAATAAAA
*
52803741 A--TTAAAAAAGTATTTTAAAAAAATTAAA
1 ATTTTAAAAAAGTATTTTAAAAAAATAAAA
52803769 ATTTTAAAAAAGTATTTTAAAAATAA-AAAA
1 ATTTTAAAAAAGTATTTTAAAAA-AATAAAA
52803799 ATTT
1 ATTT
52803803 ATTATATTCG
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.04
27 7 0.13
28 15 0.28
30 27 0.51
31 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (30 bp):
ATTTTAAAAAAGTATTTTAAAAAAATAAAA
Found at i:52811676 original size:2 final size:2
Alignment explanation
Indices: 52811669--52811699 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52811659 TATTAAATAC
52811669 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 A
52811700 AGCAAAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52816680 original size:31 final size:31
Alignment explanation
Indices: 52816645--52816705 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
52816635 CTAAATCCAA
52816645 CTTATTAGCATAATAATATAGATAGGTGGGG
1 CTTATTAGCATAATAATATAGATAGGTGGGG
*
52816676 CTTATTAGCATAGTAATATAGATAGGTGGG
1 CTTATTAGCATAATAATATAGATAGGTGGG
52816706 AAGGCAGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.26, T:0.33
Consensus pattern (31 bp):
CTTATTAGCATAATAATATAGATAGGTGGGG
Found at i:52818462 original size:17 final size:16
Alignment explanation
Indices: 52818415--52818469 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
52818405 GGCCTATAAT
*
52818415 ATTTGGATAGATTATTG
1 ATTT-GATAGATTATTA
*
52818432 ATTTGATAAAATTAGTTA
1 ATTTGAT-AGATTA-TTA
52818450 ATTTGATAGATTAATTA
1 ATTTGATAGATT-ATTA
52818467 ATT
1 ATT
52818470 ATGGGATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 3 0.09
17 19 0.59
18 10 0.31
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (16 bp):
ATTTGATAGATTATTA
Found at i:52819050 original size:21 final size:21
Alignment explanation
Indices: 52818968--52819055 Score: 88
Period size: 21 Copynumber: 4.1 Consensus size: 21
52818958 TTCGGGTGGA
*
52818968 TCAGCTCTTACGAGCTTC-AGT
1 TCAGCTCTTATGAGCTTCTA-T
*
52818989 TCAGCTTTTTATGAGCTTCTAT
1 TCAGC-TCTTATGAGCTTCTAT
* * *
52819011 TCAGCTCTCACGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTAT
**
52819032 TCTTCTCTTATGAGCTTCTAT
1 TCAGCTCTTATGAGCTTCTAT
52819053 TCA
1 TCA
52819056 ACTTTCGAGC
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
21 35 0.66
22 17 0.32
23 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.15, T:0.42
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTAT
Found at i:52823938 original size:17 final size:18
Alignment explanation
Indices: 52823896--52823938 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
52823886 TCTCTCTTCG
* *
52823896 TTTTATTTTATTTTATCT
1 TTTTAATTTATCTTATCT
52823914 TTTT-ATTTATCTT-TCT
1 TTTTAATTTATCTTATCT
52823930 TTTTAATTT
1 TTTTAATTT
52823939 TGTTTTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 11 0.50
18 4 0.18
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTAATTTATCTTATCT
Found at i:52825980 original size:23 final size:23
Alignment explanation
Indices: 52825944--52825994 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
52825934 TACCAATTAG
* **
52825944 AAGAAGACCTAAGAGGGCACTCA
1 AAGAAGACCGAAGAAAGCACTCA
* *
52825967 AAGAAGATCGAAGAAAGCACTCG
1 AAGAAGACCGAAGAAAGCACTCA
52825990 AAGAA
1 AAGAA
52825995 CGTCATCGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.18, G:0.25, T:0.08
Consensus pattern (23 bp):
AAGAAGACCGAAGAAAGCACTCA
Found at i:52826924 original size:98 final size:98
Alignment explanation
Indices: 52826755--52826951 Score: 369
Period size: 98 Copynumber: 2.0 Consensus size: 98
52826745 CTAGTACTTT
52826755 TAGTCCTCGTGGATACGATATTCTCTACTCACCATAACTATACTATTGTTCGATAGGTGTGCTTG
1 TAGTCCTCGTGGATACGATATTCTCTACTCACCATAACTATACTATTGTTCGATAGGTGTGCTTG
52826820 CCTTAGTCGTATTTATAGTTAGTTTAGTGACCA
66 CCTTAGTCGTATTTATAGTTAGTTTAGTGACCA
*
52826853 TAGTCCTCGTGGATACGATATT-TCCTACTCACCATAACTATGCTATTGTTCGATAGGTGTGCTT
1 TAGTCCTCGTGGATACGATATTCT-CTACTCACCATAACTATACTATTGTTCGATAGGTGTGCTT
52826917 GCCTTAGTCGTATTTATAGTTAGTTTAGTGACCA
65 GCCTTAGTCGTATTTATAGTTAGTTTAGTGACCA
52826951 T
1 T
52826952 CAAGTGAATA
Statistics
Matches: 97, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
97 1 0.01
98 96 0.99
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (98 bp):
TAGTCCTCGTGGATACGATATTCTCTACTCACCATAACTATACTATTGTTCGATAGGTGTGCTTG
CCTTAGTCGTATTTATAGTTAGTTTAGTGACCA
Found at i:52833461 original size:13 final size:13
Alignment explanation
Indices: 52833443--52833469 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52833433 CATAAGTCTC
52833443 CTTACACATCATG
1 CTTACACATCATG
52833456 CTTACACATCATG
1 CTTACACATCATG
52833469 C
1 C
52833470 AATTGTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (13 bp):
CTTACACATCATG
Found at i:52841463 original size:7 final size:7
Alignment explanation
Indices: 52841451--52841480 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
52841441 TTTCAATTTT
52841451 AATTCTG
1 AATTCTG
52841458 AATTCTG
1 AATTCTG
52841465 AATTCTG
1 AATTCTG
*
52841472 AATTTTG
1 AATTCTG
52841479 AA
1 AA
52841481 ATTTAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (7 bp):
AATTCTG
Found at i:52862257 original size:18 final size:19
Alignment explanation
Indices: 52862224--52862259 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
52862214 AAATTCAAGG
52862224 TTCAAGATTTAAGTTTGGA
1 TTCAAGATTTAAGTTTGGA
*
52862243 TTCAAG-TTTAGGTTTGG
1 TTCAAGATTTAAGTTTGG
52862260 GGTTTAGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (19 bp):
TTCAAGATTTAAGTTTGGA
Found at i:52864837 original size:4 final size:4
Alignment explanation
Indices: 52864828--52864855 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
52864818 AAGTCAAGAA
52864828 CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC
52864856 ATGTCTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.50, G:0.00, T:0.25
Consensus pattern (4 bp):
CATC
Found at i:52878116 original size:5 final size:5
Alignment explanation
Indices: 52878106--52878180 Score: 127
Period size: 5 Copynumber: 15.4 Consensus size: 5
52878096 AAATATATAT
*
52878106 TATTA TA-T- TATTA TATTA TATTG TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
52878154 TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TA
52878181 GTGATAAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
3 2 0.03
4 2 0.03
5 62 0.94
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:52878214 original size:4 final size:4
Alignment explanation
Indices: 52878205--52878243 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
52878195 AATAAATGAG
*
52878205 AAGA AAGA AAGA AAGA AAGAA AAGA AA-A AGGA AAGA AAG
1 AAGA AAGA AAGA AAGA AAG-A AAGA AAGA AAGA AAGA AAG
52878244 GATGGAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 2 0.06
4 25 0.81
5 4 0.13
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:52878226 original size:16 final size:15
Alignment explanation
Indices: 52878191--52878243 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 15
52878181 GTGATAAAAT
*
52878191 AAAGAATAAATGAGAAG
1 AAAGAA-AAAAGA-AAG
52878208 AAAGAAAGAAAGAAAG
1 AAAGAAA-AAAGAAAG
*
52878224 AAAAGAAAAAGGAAAG
1 -AAAGAAAAAAGAAAG
52878240 AAAG
1 AAAG
52878244 GATGGAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 4 0.12
16 11 0.34
17 17 0.53
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.04
Consensus pattern (15 bp):
AAAGAAAAAAGAAAG
Found at i:52879185 original size:41 final size:39
Alignment explanation
Indices: 52879140--52879247 Score: 121
Period size: 37 Copynumber: 2.7 Consensus size: 39
52879130 ACTTCGAGTT
*
52879140 GATGAGACACTGGGTGTCAATTTACTACTTCGGACTAATTC
1 GATGAGACACTGGGTGTCAATTTA-TACTTCGGACTAA-CC
* * * **
52879181 GATGAGGCACTAGGTGCCAA-TT-TACTTCGGTTTAACC
1 GATGAGACACTGGGTGTCAATTTATACTTCGGACTAACC
52879218 GATGAGACACTGGGTGTCAATTTATTACTT
1 GATGAGACACTGGGTGTCAATTTA-TACTT
52879248 TGAATTATCT
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
37 18 0.33
38 13 0.24
40 7 0.13
41 17 0.31
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (39 bp):
GATGAGACACTGGGTGTCAATTTATACTTCGGACTAACC
Found at i:52879262 original size:40 final size:40
Alignment explanation
Indices: 52879139--52879273 Score: 116
Period size: 40 Copynumber: 3.4 Consensus size: 40
52879129 GACTTCGAGT
* * *
52879139 TGATGAGACACTGGGTGTCAATTTACTACTTCGGACTAAT-
1 TGATGAGACACTGGGTGTCAATTTATTACTTC-GAATTATC
* * * ** *
52879179 TCGATGAGGCACTAGGTGCCAA--T-TTACTTCGGTTTAAC
1 T-GATGAGACACTGGGTGTCAATTTATTACTTCGAATTATC
* *
52879217 CGATGAGACACTGGGTGTCAATTTATTACTTTGAATTATC
1 TGATGAGACACTGGGTGTCAATTTATTACTTCGAATTATC
*
52879257 TGATGAGGCACTGGGTG
1 TGATGAGACACTGGGTG
52879274 CCAAAATGGT
Statistics
Matches: 72, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
37 20 0.28
38 6 0.08
39 2 0.03
40 27 0.38
41 17 0.24
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TGATGAGACACTGGGTGTCAATTTATTACTTCGAATTATC
Found at i:52881367 original size:14 final size:14
Alignment explanation
Indices: 52881346--52881379 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
52881336 TGGTATGGGT
52881346 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
52881359 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
52881373 TTATAGG
1 TTATAGG
52881380 AAAATAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:52893408 original size:11 final size:10
Alignment explanation
Indices: 52893365--52893407 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
52893355 ATCATATATT
52893365 ACAAAAAAAA
1 ACAAAAAAAA
52893375 ACAAAAAAAA
1 ACAAAAAAAA
52893385 A-AAAAAAAA
1 ACAAAAAAAA
*
52893394 ACACAAAACAA
1 ACA-AAAAAAA
52893405 ACA
1 ACA
52893408 CTTGCAGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 9 0.30
10 12 0.40
11 9 0.30
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (10 bp):
ACAAAAAAAA
Found at i:52894317 original size:6 final size:6
Alignment explanation
Indices: 52894306--52894332 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52894296 AGTTGAATCT
52894306 TTTGGA TTTGGA TTTGGA TTTGGA TTT
1 TTTGGA TTTGGA TTTGGA TTTGGA TTT
52894333 TTCAAGCAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.56
Consensus pattern (6 bp):
TTTGGA
Found at i:52895790 original size:19 final size:18
Alignment explanation
Indices: 52895738--52895781 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
52895728 TAAAAATTAA
*
52895738 AAAATATT--TTTATTTT
1 AAAATATTAATTTAATTT
52895754 AAAATATTAATTTAATTT
1 AAAATATTAATTTAATTT
52895772 AATAATATTA
1 AA-AATATTA
52895782 TTATCATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 8 0.33
18 9 0.38
19 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AAAATATTAATTTAATTT
Found at i:52906879 original size:15 final size:16
Alignment explanation
Indices: 52906854--52906883 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52906844 TTTTGTATTG
52906854 TTTTAATATTAAATAT
1 TTTTAATATTAAATAT
52906870 TTTTAA-ATTAAATA
1 TTTTAATATTAAATA
52906884 ACATTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAATATTAAATAT
Found at i:52913569 original size:6 final size:6
Alignment explanation
Indices: 52913558--52913586 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
52913548 TTATAGTATT
52913558 AATTAG AATTAG AATTAG AATTAG AATTA
1 AATTAG AATTAG AATTAG AATTAG AATTA
52913587 AACTCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
AATTAG
Found at i:52914363 original size:15 final size:15
Alignment explanation
Indices: 52914338--52914374 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
52914328 AACAGTAAAA
52914338 TTTCAGTACTTAA-T
1 TTTCAGTACTTAACT
52914352 TTTCATGTACTTAACT
1 TTTCA-GTACTTAACT
52914368 TTTCAGT
1 TTTCAGT
52914375 TTATCAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.24
15 10 0.48
16 6 0.29
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.51
Consensus pattern (15 bp):
TTTCAGTACTTAACT
Found at i:52917255 original size:22 final size:20
Alignment explanation
Indices: 52917208--52917270 Score: 80
Period size: 19 Copynumber: 3.2 Consensus size: 20
52917198 GAATTAATGA
52917208 ATTTTT-ATTTTTTATAATT
1 ATTTTTGATTTTTTATAATT
52917227 -TTTTTGATTTTTTATATATAT
1 ATTTTTGATTTTTTATA-AT-T
52917248 ATTTTTGA-TTTTTATAATT
1 ATTTTTGATTTTTTATAATT
52917267 -TTTT
1 ATTTT
52917271 AAAATTGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.22
19 11 0.28
20 4 0.10
21 9 0.22
22 7 0.17
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (20 bp):
ATTTTTGATTTTTTATAATT
Found at i:52917283 original size:40 final size:40
Alignment explanation
Indices: 52917208--52917284 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
52917198 GAATTAATGA
** * **
52917208 ATTTTTATTTTTTATAATTTTTTTGATTTTTTATATATAT
1 ATTTTTATTTTTTATAATTTTTTAAAATTGATATATATAT
52917248 ATTTTTGA-TTTTTATAATTTTTTAAAATTGATATATA
1 ATTTTT-ATTTTTTATAATTTTTTAAAATTGATATATA
52917285 AATACATGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 30 0.97
41 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (40 bp):
ATTTTTATTTTTTATAATTTTTTAAAATTGATATATATAT
Found at i:52918154 original size:27 final size:28
Alignment explanation
Indices: 52918110--52918168 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
52918100 AATAAACATT
*
52918110 AAAAAATTATTTTAAAAATAAAAAAATA
1 AAAAAAGTATTTTAAAAATAAAAAAATA
*
52918138 AAAAAAGTATTTT-AAAATTAAAAAATA
1 AAAAAAGTATTTTAAAAATAAAAAAATA
52918165 AAAA
1 AAAA
52918169 TAAAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (28 bp):
AAAAAAGTATTTTAAAAATAAAAAAATA
Found at i:52923423 original size:3 final size:3
Alignment explanation
Indices: 52923415--52923442 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
52923405 TTGTGGTTTG
52923415 CAA CAA CAA CAA CAA CAA CAA CAA CAA C
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA C
52923443 TCCATGCTAA
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:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:52925300 original size:20 final size:21
Alignment explanation
Indices: 52925261--52925364 Score: 65
Period size: 20 Copynumber: 4.9 Consensus size: 21
52925251 TTGAGTTTTT
*
52925261 TTTTATATTT-GAGTATTTAA
1 TTTTATATTTGGAGTAATTAA
52925281 TTTTATATTTGGA-TAATTAA
1 TTTTATATTTGGAGTAATTAA
* * *
52925301 TTAAATAATTTAATTGGATTAAGTT-A
1 TT---T--TATATTTGGAGTAA-TTAA
*
52925327 TTTTATATTT-GAGTATTTAA
1 TTTTATATTTGGAGTAATTAA
*
52925347 TTTTACATTTGGA-TAATT
1 TTTTATATTTGGAGTAATT
52925365 TATTGAGTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
19 2 0.03
20 36 0.55
21 9 0.14
23 2 0.03
25 8 0.12
26 6 0.09
27 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.11, T:0.55
Consensus pattern (21 bp):
TTTTATATTTGGAGTAATTAA
Found at i:52925396 original size:66 final size:66
Alignment explanation
Indices: 52925261--52925409 Score: 201
Period size: 66 Copynumber: 2.3 Consensus size: 66
52925251 TTGAGTTTTT
* *
52925261 TTTTATATTTGAGTATTTAATTTTATATTTGGATAATTAATTAAATAATTTAATTGGATTAAGTT
1 TTTTATATTTGAGTATTTAATTTTACATTTGGATAATTAATTAAATAATTTAATTGGATTAAGTA
52925326 A
66 A
* * * **
52925327 TTTTATATTTGAGTATTTAATTTTACATTTGGATAATTTATTGAGTAATTTAATTAGG-TTGTGT
1 TTTTATATTTGAGTATTTAATTTTACATTTGGATAATTAATTAAATAATTTAATT-GGATTAAGT
52925391 AA
65 AA
* *
52925393 TTTTGTATTTGAATATT
1 TTTTATATTTGAGTATT
52925410 AAGTAGGAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
66 71 0.97
67 2 0.03
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (66 bp):
TTTTATATTTGAGTATTTAATTTTACATTTGGATAATTAATTAAATAATTTAATTGGATTAAGTA
A
Found at i:52926216 original size:11 final size:10
Alignment explanation
Indices: 52926177--52926226 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
52926167 ATGAATCCTA
*
52926177 TTTTATTAAT
1 TTTTAATAAT
*
52926187 TCTT-ATAAT
1 TTTTAATAAT
*
52926196 TCTTAATAAT
1 TTTTAATAAT
52926206 TTTTAAATAAT
1 TTTT-AATAAT
52926217 TTTTAATAAT
1 TTTTAATAAT
52926227 CATATATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.23
10 17 0.49
11 10 0.29
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:52926485 original size:18 final size:17
Alignment explanation
Indices: 52926454--52926487 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52926444 TAAAAAAATA
*
52926454 TTTATTTTTGATATTTT
1 TTTATTTTTAATATTTT
52926471 TTTATTTTTAAATATTT
1 TTTATTTTT-AATATTT
52926488 ATTGATATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTATTTTTAATATTTT
Found at i:52944469 original size:16 final size:16
Alignment explanation
Indices: 52944448--52944479 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
52944438 AAGAAACATC
52944448 CTGAATAAATAAATTG
1 CTGAATAAATAAATTG
52944464 CTGAATAAATAAATTG
1 CTGAATAAATAAATTG
52944480 AAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (16 bp):
CTGAATAAATAAATTG
Found at i:52945806 original size:16 final size:15
Alignment explanation
Indices: 52945762--52945804 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
52945752 TTTAGAAAAA
*
52945762 TTTTAGTTTTTGGAT
1 TTTTAGTTTTTAGAT
52945777 TTTCTAGCTTTTTAGAT
1 TTT-TAG-TTTTTAGAT
52945794 TTTTAGTTTTT
1 TTTTAGTTTTT
52945805 TATATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 8 0.32
16 6 0.24
17 11 0.44
ACGTcount: A:0.14, C:0.05, G:0.14, T:0.67
Consensus pattern (15 bp):
TTTTAGTTTTTAGAT
Found at i:52945818 original size:16 final size:16
Alignment explanation
Indices: 52945762--52945806 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
52945752 TTTAGAAAAA
*
52945762 TTTTAG-TTTTTGGAT
1 TTTTAGTTTTTTAGAT
*
52945777 TTTCTAGCTTTTTAGAT
1 TTT-TAGTTTTTTAGAT
52945794 TTTTAGTTTTTTA
1 TTTTAGTTTTTTA
52945807 TATATTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 3 0.12
16 12 0.46
17 11 0.42
ACGTcount: A:0.16, C:0.04, G:0.13, T:0.67
Consensus pattern (16 bp):
TTTTAGTTTTTTAGAT
Found at i:52945926 original size:23 final size:25
Alignment explanation
Indices: 52945882--52945929 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
52945872 ATTGATGAGA
52945882 AATATATATAGAGTATAGTAAAAAT
1 AATATATATAGAGTATAGTAAAAAT
*
52945907 AATATATATATA-TATA-TAAAAAT
1 AATATATATAGAGTATAGTAAAAAT
52945930 GGACACGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 4 0.18
25 11 0.50
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (25 bp):
AATATATATAGAGTATAGTAAAAAT
Found at i:52947351 original size:22 final size:21
Alignment explanation
Indices: 52947322--52947377 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
52947312 TGCACTAATG
*
52947322 AACAGAGAGCACTGAAGTGCT
1 AACAGAGAGCACAGAAGTGCT
*
52947343 ATACAGAGAGCACAGATGTGCT
1 A-ACAGAGAGCACAGAAGTGCT
52947365 AATCAGAGAGCAC
1 AA-CAGAGAGCAC
52947378 CAACGTGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 2 0.06
22 29 0.94
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (21 bp):
AACAGAGAGCACAGAAGTGCT
Found at i:52947385 original size:22 final size:22
Alignment explanation
Indices: 52947323--52947390 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 22
52947313 GCACTAATGA
*
52947323 ACAGAGAGCACTGAAGTGCT-AT
1 ACAGAGAGCAC-CAAGTGCTAAT
52947345 ACAGAGAGCA-CAGATGTGCTAAT
1 ACAGAGAGCACCA-A-GTGCTAAT
52947368 -CAGAGAGCACCAACGTGCTAAT
1 ACAGAGAGCACCAA-GTGCTAAT
52947390 A
1 A
52947391 ATTAGAGAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 1 0.03
21 1 0.03
22 33 0.85
23 4 0.10
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (22 bp):
ACAGAGAGCACCAAGTGCTAAT
Found at i:52948288 original size:13 final size:13
Alignment explanation
Indices: 52948270--52948294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52948260 CAAAATTCCC
52948270 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
52948283 TTTTCTTTCTTT
1 TTTTCTTTCTTT
52948295 CCTTTCTCCT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTCTTTCTTTT
Found at i:52951255 original size:17 final size:17
Alignment explanation
Indices: 52951221--52951267 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
52951211 AATTTAGAAG
* *
52951221 AATTTTTGAATTAGTGA
1 AATTTGTGATTTAGTGA
*
52951238 AATTTGTGATTTATTGA
1 AATTTGTGATTTAGTGA
*
52951255 ATTTTGTGATTTA
1 AATTTGTGATTTA
52951268 AAAAGAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (17 bp):
AATTTGTGATTTAGTGA
Found at i:52954732 original size:17 final size:17
Alignment explanation
Indices: 52954698--52954744 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
52954688 AATTTAGAAG
* *
52954698 AATTTTTGAATTAGTGA
1 AATTTGTGATTTAGTGA
*
52954715 AATTTGTGATTTATTGA
1 AATTTGTGATTTAGTGA
*
52954732 ATTTTGTGATTTA
1 AATTTGTGATTTA
52954745 AAAAGAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (17 bp):
AATTTGTGATTTAGTGA
Found at i:52956044 original size:46 final size:46
Alignment explanation
Indices: 52955970--52956107 Score: 231
Period size: 46 Copynumber: 3.0 Consensus size: 46
52955960 CATGGCAAAG
*
52955970 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAATCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
52956016 TGTGAAAAGTAGGTATGGTGTTTTAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
52956062 TGTGAAAAGAAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
52956108 AATAGCAATG
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.36, C:0.08, G:0.27, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:52960085 original size:2 final size:2
Alignment explanation
Indices: 52960078--52960112 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
52960068 TGCCCACTTT
52960078 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52960113 TCTACTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52964406 original size:2 final size:2
Alignment explanation
Indices: 52964399--52964431 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
52964389 TGTTCTGAGA
52964399 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
52964432 AGCTTTTAGT
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:52965473 original size:31 final size:30
Alignment explanation
Indices: 52965365--52965479 Score: 80
Period size: 31 Copynumber: 3.8 Consensus size: 30
52965355 AAGAAATCAA
* *
52965365 AAATCAAAGTTTCATGCATACATTTA-A-ATG
1 AAATCAAAGTTT-ATGTATA-ATTTACACATC
52965395 ACAATCAAAGTTTCATGTGTATAA-TT--ACATC
1 A-AATCAAAGTTT-A--TGTATAATTTACACATC
* *
52965426 AAATTAAAGTTTATGTATCAATTTACACATT
1 AAATCAAAGTTTATGTAT-AATTTACACATC
52965457 AAATCAAA-TTTAATGTATAATTT
1 AAATCAAAGTTT-ATGTATAATTT
52965480 TAAGATTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
27 5 0.07
28 2 0.03
29 3 0.04
30 20 0.28
31 35 0.49
32 1 0.01
33 5 0.07
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (30 bp):
AAATCAAAGTTTATGTATAATTTACACATC
Found at i:52971511 original size:16 final size:16
Alignment explanation
Indices: 52971490--52971523 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52971480 TTGGTCTAAA
*
52971490 TATTAAATTTAAAATT
1 TATTAAACTTAAAATT
*
52971506 TATTAAACTTAATATT
1 TATTAAACTTAAAATT
52971522 TA
1 TA
52971524 GAATTCAGTA
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:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTAAACTTAAAATT
Found at i:52976303 original size:12 final size:12
Alignment explanation
Indices: 52976266--52976308 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
52976256 TTTTATATAA
*
52976266 ATATAATAAAAT
1 ATATAAAAAAAT
*
52976278 ATCAATAAACAAAT
1 AT--ATAAAAAAAT
52976292 ATATAAAAAAAT
1 ATATAAAAAAAT
52976304 ATATA
1 ATATA
52976309 TGATAATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 16 0.62
14 10 0.38
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (12 bp):
ATATAAAAAAAT
Found at i:53001927 original size:30 final size:30
Alignment explanation
Indices: 53001893--53001955 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
53001883 ACTTAACAAG
53001893 CAAATGCCTATAAAATAATAACAAAATTAA
1 CAAATGCCTATAAAATAATAACAAAATTAA
*
53001923 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTATAAAATAATAACAAAATTAA
53001953 CAA
1 CAA
53001956 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTATAAAATAATAACAAAATTAA
Found at i:53002041 original size:22 final size:22
Alignment explanation
Indices: 53001999--53002041 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
53001989 CAACAAAATA
* *
53001999 GTAGCAACATAATAGTAAAAAG
1 GTAGCAAAATAATAGGAAAAAG
53002021 GTAGCAAAATAA-AGGAGAAAA
1 GTAGCAAAATAATAGGA-AAAA
53002042 TAACATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.58, C:0.07, G:0.21, T:0.14
Consensus pattern (22 bp):
GTAGCAAAATAATAGGAAAAAG
Found at i:53003391 original size:26 final size:26
Alignment explanation
Indices: 53003343--53003392 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
53003333 AGTTTAGTTT
* *
53003343 TTTAAAATATATTTTTTTATTTTTTA
1 TTTAAAAAATATTTTATTATTTTTTA
53003369 TTTAAAAAATATTTATATT-TTTTT
1 TTTAAAAAATATTT-TATTATTTTT
53003393 AAAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTAAAAAATATTTTATTATTTTTTA
Found at i:53008457 original size:12 final size:12
Alignment explanation
Indices: 53008434--53008468 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
53008424 AACTCTGTGT
53008434 TAATTGTTTTATA
1 TAATT-TTTTATA
*
53008447 TTATTTTTTATA
1 TAATTTTTTATA
53008459 TAATTTTTTA
1 TAATTTTTTA
53008469 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (12 bp):
TAATTTTTTATA
Found at i:53021846 original size:21 final size:22
Alignment explanation
Indices: 53021804--53021847 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53021794 CCAATTAAAG
**
53021804 TAATGTATTAATATTTTTTTAA
1 TAATGTATTAATATTTCATTAA
53021826 TAATGTATTAA-ATTTCATTAA
1 TAATGTATTAATATTTCATTAA
53021847 T
1 T
53021848 GGGTGTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
TAATGTATTAATATTTCATTAA
Found at i:53026536 original size:18 final size:19
Alignment explanation
Indices: 53026502--53026539 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
53026492 CGTTGAAGAA
53026502 ATGAGACAAGAGCTGAATT
1 ATGAGACAAGAGCTGAATT
53026521 ATGAGA-AAGA-CATGAATT
1 ATGAGACAAGAGC-TGAATT
53026539 A
1 A
53026540 CAATCTTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 11 0.61
19 6 0.33
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.21
Consensus pattern (19 bp):
ATGAGACAAGAGCTGAATT
Found at i:53029106 original size:2 final size:2
Alignment explanation
Indices: 53029099--53029126 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53029089 ATTTCCACAA
53029099 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
53029127 TGACAAAGCA
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:53035407 original size:26 final size:27
Alignment explanation
Indices: 53035371--53035433 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
53035361 AGCCCGGCCC
* * * *
53035371 ATTTTTAAAAT-AAACATTAAAAATTT
1 ATTTTAAAAATAAAAAATAAAAAAATT
53035397 ATTTTAAAAATAAAAAAATAAAAAAATT
1 ATTTTAAAAAT-AAAAAATAAAAAAATT
53035425 ATTTTAAAA
1 ATTTTAAAA
53035434 GTATTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 10 0.32
28 21 0.68
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
ATTTTAAAAATAAAAAATAAAAAAATT
Found at i:53038265 original size:2 final size:2
Alignment explanation
Indices: 53038258--53038290 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
53038248 GTTAATTTGT
53038258 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53038291 TTAGGATTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53039064 original size:21 final size:21
Alignment explanation
Indices: 53039020--53039071 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
53039010 ATTATTTTTA
* *
53039020 ATAATTTTTAAATAATTTCTT
1 ATAAATTTTAAATAAATTCTT
53039041 ATAAATTTTAAATAAAATTC-T
1 ATAAATTTTAAAT-AAATTCTT
*
53039062 ATAACTTTTA
1 ATAAATTTTA
53039072 GAATTATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAATTTTAAATAAATTCTT
Found at i:53041923 original size:12 final size:12
Alignment explanation
Indices: 53041907--53041972 Score: 80
Period size: 12 Copynumber: 5.5 Consensus size: 12
53041897 TTGATAATCA
53041907 TTTCTTTTCATC
1 TTTCTTTTCATC
* *
53041919 CTTCTTTTCGTC
1 TTTCTTTTCATC
53041931 TTTCTTTTCATC
1 TTTCTTTTCATC
* *
53041943 TTTCTTGTCGTC
1 TTTCTTTTCATC
53041955 TTT-TTTGTCATC
1 TTTCTTT-TCATC
53041967 TTTCTT
1 TTTCTT
53041973 CTCTTCTTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.05, C:0.24, G:0.06, T:0.65
Consensus pattern (12 bp):
TTTCTTTTCATC
Found at i:53041934 original size:24 final size:24
Alignment explanation
Indices: 53041907--53041981 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
53041897 TTGATAATCA
* *
53041907 TTTCTTTTCATCCTTCTTTTCGTC
1 TTTCTTTTCATCTTTCTTCTCGTC
*
53041931 TTTCTTTTCATCTTTCTTGTCGTC
1 TTTCTTTTCATCTTTCTTCTCGTC
*
53041955 TTT-TTTGTCATCTTTCTTCTCTTC
1 TTTCTTT-TCATCTTTCTTCTCGTC
53041979 TTT
1 TTT
53041982 AGCAGGTCCC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 43 0.93
ACGTcount: A:0.04, C:0.25, G:0.05, T:0.65
Consensus pattern (24 bp):
TTTCTTTTCATCTTTCTTCTCGTC
Found at i:53044155 original size:13 final size:13
Alignment explanation
Indices: 53044139--53044204 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
53044129 TTTAAACCAA
*
53044139 ACTTTTTAAAAAT
1 ACTTTTTAAAAAC
* * *
53044152 ACTTCTCAAAATC
1 ACTTTTTAAAAAC
*
53044165 ACTTTTTCAAAAC
1 ACTTTTTAAAAAC
*
53044178 ACTTTTTAAAAGC
1 ACTTTTTAAAAAC
*
53044191 AATTTTTAAAAAC
1 ACTTTTTAAAAAC
53044204 A
1 A
53044205 ATGCTAAACT
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.38
Consensus pattern (13 bp):
ACTTTTTAAAAAC
Found at i:53044169 original size:26 final size:26
Alignment explanation
Indices: 53044139--53044204 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
53044129 TTTAAACCAA
* *
53044139 ACTTTTTAAAAATACTTCTCAAAATC
1 ACTTTTTAAAAACACTTCTCAAAAGC
* * *
53044165 ACTTTTTCAAAACACTTTTTAAAAGC
1 ACTTTTTAAAAACACTTCTCAAAAGC
*
53044191 AATTTTTAAAAACA
1 ACTTTTTAAAAACA
53044205 ATGCTAAACT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.38
Consensus pattern (26 bp):
ACTTTTTAAAAACACTTCTCAAAAGC
Found at i:53056289 original size:21 final size:21
Alignment explanation
Indices: 53056263--53056330 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
53056253 ATTATTTTCG
53056263 TATTTTATTTTGAAGGTGAGA
1 TATTTTATTTTGAAGGTGAGA
* * *
53056284 TATTTT-TTAT-AA-ATAATG-
1 TATTTTATTTTGAAGGTGA-GA
53056302 TATTTTATTTTGAAGGTGAGA
1 TATTTTATTTTGAAGGTGAGA
*
53056323 CATTTTAT
1 TATTTTAT
53056331 AAATAATGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
18 8 0.23
19 6 0.17
20 6 0.17
21 15 0.43
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.51
Consensus pattern (21 bp):
TATTTTATTTTGAAGGTGAGA
Found at i:53056338 original size:37 final size:38
Alignment explanation
Indices: 53056262--53056338 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 38
53056252 AATTATTTTC
*
53056262 GTATTTTATTTTGAAGGTGAGATATTTTTTATAAATAAT
1 GTATTTTATTTTGAAGGTGAGACA-TTTTTATAAATAAT
53056301 GTATTTTATTTTGAAGGTGAGACA-TTTTATAAATAAT
1 GTATTTTATTTTGAAGGTGAGACATTTTTATAAATAAT
53056338 G
1 G
53056339 AAACTTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
37 14 0.38
39 23 0.62
ACGTcount: A:0.34, C:0.01, G:0.17, T:0.48
Consensus pattern (38 bp):
GTATTTTATTTTGAAGGTGAGACATTTTTATAAATAAT
Found at i:53056454 original size:23 final size:23
Alignment explanation
Indices: 53056404--53056454 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
53056394 TGATAATCAT
* *
53056404 TTCTTTTTTTCACCCTTCTTTTC
1 TTCTTCTTTTCACCCTTCTTCTC
* * *
53056427 GTCTTCTTTTCATCTTTCTTCTC
1 TTCTTCTTTTCACCCTTCTTCTC
53056450 TTCTT
1 TTCTT
53056455 TAGCAGGTCC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.04, C:0.29, G:0.02, T:0.65
Consensus pattern (23 bp):
TTCTTCTTTTCACCCTTCTTCTC
Found at i:53058952 original size:26 final size:27
Alignment explanation
Indices: 53058901--53058954 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
53058891 TTTAAAATAC
* *
53058901 TTTTAAAATATTTTTTTATTTTTTTAT
1 TTTTAAAATATTTTTTTATGTGTTTAT
53058928 TTTTAAAATATTTTTTT-TGTGTTTAT
1 TTTTAAAATATTTTTTTATGTGTTTAT
53058954 T
1 T
53058955 AAAAATCGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (27 bp):
TTTTAAAATATTTTTTTATGTGTTTAT
Found at i:53060264 original size:36 final size:35
Alignment explanation
Indices: 53060197--53060264 Score: 100
Period size: 36 Copynumber: 1.9 Consensus size: 35
53060187 ATTTAACCCA
*
53060197 AAGGCTATACTCCATATTTGAGCATATTAAAATAC
1 AAGGCTATACTCCATATTTGAGCATAGTAAAATAC
* *
53060232 AAGGACTATATTCCATATTTGAGCATGGTAAAA
1 AAGG-CTATACTCCATATTTGAGCATAGTAAAA
53060265 AGACCAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 4 0.14
36 25 0.86
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (35 bp):
AAGGCTATACTCCATATTTGAGCATAGTAAAATAC
Found at i:53070275 original size:3 final size:3
Alignment explanation
Indices: 53070267--53070314 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
53070257 TTAAAAGATA
53070267 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53070315 GTTGTTGTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:53070319 original size:3 final size:3
Alignment explanation
Indices: 53070313--53070351 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
53070303 ATTATTATTA
53070313 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
53070352 AAACAAGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:53071261 original size:21 final size:20
Alignment explanation
Indices: 53071235--53071288 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
53071225 AATAGCGATG
*
53071235 GCGGTGAGATTAATTACTGTA
1 GCGGTGAGATTAA-TAATGTA
*
53071256 GCGGTGAGATTGGATAATGTA
1 GCGGTGAGATT-AATAATGTA
53071277 GCGGTGAGATTA
1 GCGGTGAGATTA
53071289 GAAACAATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.35, T:0.30
Consensus pattern (20 bp):
GCGGTGAGATTAATAATGTA
Found at i:53079323 original size:17 final size:16
Alignment explanation
Indices: 53079287--53079325 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
53079277 AGGTTTAAGA
*
53079287 AATAAAACAATTATGT
1 AATAAAAAAATTATGT
53079303 -ATAAAAAAATTATGT
1 AATAAAAAAATTATGT
53079318 GAATAAAA
1 -AATAAAA
53079326 GGTTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 14 0.70
17 6 0.30
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.28
Consensus pattern (16 bp):
AATAAAAAAATTATGT
Found at i:53079443 original size:20 final size:19
Alignment explanation
Indices: 53079399--53079448 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
53079389 ATATGTATTT
* *
53079399 TTAAATAATATTGATACAT
1 TTAAAAAATATTGATACAA
*
53079418 TTAAAACATATTGATAACAA
1 TTAAAAAATATTGAT-ACAA
53079438 TTAAAAAATAT
1 TTAAAAAATAT
53079449 ATTATTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (19 bp):
TTAAAAAATATTGATACAA
Found at i:53080408 original size:12 final size:12
Alignment explanation
Indices: 53080393--53080420 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
53080383 CCATTTACAG
53080393 AAAATAAAATAA
1 AAAATAAAATAA
53080405 AAAATAAAATAA
1 AAAATAAAATAA
53080417 AAAA
1 AAAA
53080421 ATGCTGTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:53080743 original size:15 final size:15
Alignment explanation
Indices: 53080723--53080771 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
53080713 GTCATGGGCA
53080723 TTTGGGCTAGTTGGG
1 TTTGGGCTAGTTGGG
*
53080738 TTTGGG-TAG-TGGA
1 TTTGGGCTAGTTGGG
* *
53080751 TTTGGGCTAATTAGG
1 TTTGGGCTAGTTGGG
53080766 TTTGGG
1 TTTGGG
53080772 TAATGGATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 9 0.32
14 5 0.18
15 14 0.50
ACGTcount: A:0.12, C:0.04, G:0.43, T:0.41
Consensus pattern (15 bp):
TTTGGGCTAGTTGGG
Found at i:53080754 original size:28 final size:28
Alignment explanation
Indices: 53080722--53080785 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
53080712 GGTCATGGGC
* * *
53080722 ATTTGGGCTAGTTGGGTTTGGGTAGTGG
1 ATTTGGGCTAATTAGGTTTGGGTAATGG
53080750 ATTTGGGCTAATTAGGTTTGGGTAATGG
1 ATTTGGGCTAATTAGGTTTGGGTAATGG
53080778 ATTTGGGC
1 ATTTGGGC
53080786 CATTAGGCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.16, C:0.05, G:0.41, T:0.39
Consensus pattern (28 bp):
ATTTGGGCTAATTAGGTTTGGGTAATGG
Found at i:53081860 original size:2 final size:2
Alignment explanation
Indices: 53081853--53081881 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53081843 TAGTAAAGTA
53081853 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 A
53081882 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53081886 original size:2 final size:2
Alignment explanation
Indices: 53081881--53081917 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
53081871 ATATATATAT
53081881 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
53081918 ATAGAACGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53101234 original size:32 final size:32
Alignment explanation
Indices: 53101192--53101254 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
53101182 ACTTTTTTAT
*
53101192 TTTTTAAGAGATTTAAAAGCAATTTTGCAATA
1 TTTTAAAGAGATTTAAAAGCAATTTTGCAATA
53101224 TTTTAAAGAGATTTAAAAGCAATTTTGCAAT
1 TTTTAAAGAGATTTAAAAGCAATTTTGCAAT
53101255 TTGAGGGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (32 bp):
TTTTAAAGAGATTTAAAAGCAATTTTGCAATA
Found at i:53104395 original size:19 final size:22
Alignment explanation
Indices: 53104352--53104395 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
53104342 GCTTCAAATT
*
53104352 TTTGCATTTTTTATATTTAATA
1 TTTGCATTTTCTATATTTAATA
53104374 TTTG-ATTTTCTAT-TTTAA-A
1 TTTGCATTTTCTATATTTAATA
53104393 TTT
1 TTT
53104396 CAAATAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 5 0.24
21 8 0.38
22 4 0.19
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTGCATTTTCTATATTTAATA
Found at i:53122011 original size:18 final size:19
Alignment explanation
Indices: 53121988--53122036 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
53121978 AAGTTTTATT
*
53121988 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
53122006 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
53122025 TTTAATTTTTAT
1 TTT-ATTTTTAT
53122037 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:53122016 original size:22 final size:22
Alignment explanation
Indices: 53121979--53122036 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
53121969 CAAGTTGTAA
* *
53121979 AGTTTTATTTTTATTTTTATTT
1 AGTTTAATTTTTATTTTTACTT
*
53122001 A-TTTATTTATTTATTTTTACTT
1 AGTTTAATT-TTTATTTTTACTT
53122023 AGTTTAATTTTTAT
1 AGTTTAATTTTTAT
53122037 GTAAATATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 5 0.17
22 19 0.63
23 6 0.20
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.72
Consensus pattern (22 bp):
AGTTTAATTTTTATTTTTACTT
Found at i:53139522 original size:19 final size:19
Alignment explanation
Indices: 53139494--53139530 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53139484 TTAGACCAAC
* *
53139494 AAAAATTAAAAATTTATAA
1 AAAAAATAAAAATATATAA
53139513 AAAAAATAAAAATATATA
1 AAAAAATAAAAATATATA
53139531 TTAAATTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAAATAAAAATATATAA
Found at i:53140951 original size:19 final size:20
Alignment explanation
Indices: 53140913--53140952 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
53140903 CATTTATATC
* *
53140913 TTAATAAATTATATATTATT
1 TTAATAAATAATAAATTATT
53140933 TTAATAAA-AATAAATTATT
1 TTAATAAATAATAAATTATT
53140952 T
1 T
53140953 ATTATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATAAATAATAAATTATT
Found at i:53141512 original size:19 final size:18
Alignment explanation
Indices: 53141488--53141544 Score: 51
Period size: 21 Copynumber: 2.9 Consensus size: 18
53141478 TTTATGAAGT
53141488 TTATAAAATTTTGAAAATG
1 TTATAAAATTTT-AAAATG
*
53141507 TTATAATTAGTTTTAAACATG
1 TTATAA--AATTTTAAA-ATG
*
53141528 TTATATAATTTTTAAAA
1 TTATA-AAATTTTAAAA
53141545 ATTTGAAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 7 0.22
20 11 0.34
21 13 0.41
22 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (18 bp):
TTATAAAATTTTAAAATG
Found at i:53141566 original size:27 final size:27
Alignment explanation
Indices: 53141527--53141580 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
53141517 TTTTAAACAT
53141527 GTTATATAATTTTTAA-AAATTTGAAAC
1 GTTATATAA-TTTTAATAAATTTGAAAC
*
53141554 GTTATA-AAGTTTTAATAAATTTTAAAC
1 GTTATATAA-TTTTAATAAATTTGAAAC
53141581 AAATTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (27 bp):
GTTATATAATTTTAATAAATTTGAAAC
Found at i:53141588 original size:29 final size:28
Alignment explanation
Indices: 53141517--53141598 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
53141507 TTATAATTAG
*
53141517 TTTTAAACATGTTATATAATTTTTAA-AAA
1 TTTTAAACA-GTTATA-AAGTTTTAATAAA
*
53141546 TTTGAAAC-GTTATAAAGTTTTAATAAA
1 TTTTAAACAGTTATAAAGTTTTAATAAA
* *
53141573 TTTTAAACAAATTATAAAGTTCTAAT
1 TTTTAAAC-AGTTATAAAGTTTTAAT
53141599 TTTTTTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 8 0.18
27 16 0.36
29 21 0.47
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (28 bp):
TTTTAAACAGTTATAAAGTTTTAATAAA
Found at i:53147964 original size:2 final size:2
Alignment explanation
Indices: 53147957--53147989 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
53147947 CTGAAACATG
53147957 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53147990 TGTGTTCTGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53155517 original size:37 final size:35
Alignment explanation
Indices: 53155475--53155551 Score: 120
Period size: 34 Copynumber: 2.2 Consensus size: 35
53155465 GAATCAATGG
53155475 CTAAGAAAAGACCAGTTAGTAACATATTGAGCATTAA
1 CTAAG-AAA-ACCAGTTAGTAACATATTGAGCATTAA
*
53155512 CTAAG-AAACCAGTTAGTAATATATTGAGCATTAA
1 CTAAGAAAACCAGTTAGTAACATATTGAGCATTAA
53155546 CTAAGA
1 CTAAGA
53155552 GACAAGATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
34 31 0.82
35 2 0.05
37 5 0.13
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (35 bp):
CTAAGAAAACCAGTTAGTAACATATTGAGCATTAA
Done.