Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 22 of 106
Found at i:9416944 original size:29 final size:28
Alignment explanation
Indices: 9416903--9417064 Score: 144
Period size: 30 Copynumber: 5.5 Consensus size: 28
9416893 CAGCTTTAAC
*
9416903 ATGTTTGTCTTAATTTAGACAAAGAAAT
1 ATGTTTGTCTTAATTTAGACAAAAAAAT
*
9416931 ATGTTTAGTCTTAATTTAGATAAAAAAAAT
1 ATGTTT-GTCTTAATTTAGA-CAAAAAAAT
9416961 ATGTTTGTCTTAATTTAAGACAAGAAAAAT
1 ATGTTTGTCTTAATTT-AGACAA-AAAAAT
* * * *
9416991 ATTTTTTATCTTAATTTAGACAAGAAAAC
1 A-TGTTTGTCTTAATTTAGACAAAAAAAT
* * * * * *
9417020 ATATTTATCTCAATTTTGATAATATCAAAT
1 ATGTTTGTCTTAATTTAGACAA-A-AAAAT
*
9417050 ATTTTTGTCTTAATT
1 ATGTTTGTCTTAATT
9417065 AAAGACAAGA
Statistics
Matches: 110, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
28 23 0.21
29 30 0.27
30 44 0.40
31 13 0.12
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.43
Consensus pattern (28 bp):
ATGTTTGTCTTAATTTAGACAAAAAAAT
Found at i:9417061 original size:89 final size:89
Alignment explanation
Indices: 9416910--9417074 Score: 226
Period size: 89 Copynumber: 1.9 Consensus size: 89
9416900 AACATGTTTG
* * *
9416910 TCTTAATTTAGACAAAGAAATATGTTTAGTCTTAATTTAGATAAAAAAAATATGTTTGTCTTAAT
1 TCTTAATTTAGACAAAGAAACATATTTAGTCTCAATTTAGATAAAAAAAATATGTTTGTCTTAAT
*
9416975 TTAAGACAAGAAAAATATTTTTTA
66 TAAAGACAAGAAAAATATTTTTTA
* ** *
9416999 TCTTAATTTAGAC-AAGAAAACATATTTA-TCTCAATTTTGATAATATCAAATATTTTTGTCTTA
1 TCTTAATTTAGACAAAG-AAACATATTTAGTCTCAATTTAGATAA-AAAAAATATGTTTGTCTTA
9417062 ATTAAAGACAAGA
64 ATTAAAGACAAGA
9417075 GTTGTCTTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
88 16 0.24
89 50 0.76
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (89 bp):
TCTTAATTTAGACAAAGAAACATATTTAGTCTCAATTTAGATAAAAAAAATATGTTTGTCTTAAT
TAAAGACAAGAAAAATATTTTTTA
Found at i:9419390 original size:15 final size:15
Alignment explanation
Indices: 9419370--9419403 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
9419360 GATTAATGTA
*
9419370 AAAATATAAATAAAT
1 AAAATAAAAATAAAT
*
9419385 AAAATAAAAATAACT
1 AAAATAAAAATAAAT
9419400 AAAA
1 AAAA
9419404 AGAGAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATAAAAATAAAT
Found at i:9420234 original size:123 final size:121
Alignment explanation
Indices: 9420015--9420259 Score: 472
Period size: 123 Copynumber: 2.0 Consensus size: 121
9420005 GAGGTACCTA
9420015 ATTGATCTGTCTACTAATTGCAAGGTAACTGTAGTAGGTTGTATCATTTTAAATCCAAGTTTCCT
1 ATTGATCTGTCTACTAATTGCAAGGTAACTGTAGTAGGTTGTATCATTTTAAATCCAAGTTTCCT
9420080 ATAAATAAAAAAAGGCATTTTTGAAACATTGGCACCCAAATCACACAAAGACTTTAG
66 ATAAATAAAAAAAGGCATTTTTGAAACATTGGCACCCAAATCACACAAAG-CTTTAG
9420137 NATTGATCTGTCTACTAATTGCAAGGTAACTGTAGTAGGTTGTATCATTTTAAATCCAAGTTTCC
1 -ATTGATCTGTCTACTAATTGCAAGGTAACTGTAGTAGGTTGTATCATTTTAAATCCAAGTTTCC
9420202 TATAAATAAAAAAAGGCATTTTTGAAACATTGGCACCCAAATCACACAAAGCTTTAG
65 TATAAATAAAAAAAGGCATTTTTGAAACATTGGCACCCAAATCACACAAAGCTTTAG
9420259 A
1 A
9420260 AATTTTAAAA
Statistics
Matches: 122, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
121 1 0.01
122 6 0.05
123 115 0.94
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (121 bp):
ATTGATCTGTCTACTAATTGCAAGGTAACTGTAGTAGGTTGTATCATTTTAAATCCAAGTTTCCT
ATAAATAAAAAAAGGCATTTTTGAAACATTGGCACCCAAATCACACAAAGCTTTAG
Found at i:9424441 original size:15 final size:15
Alignment explanation
Indices: 9424421--9424451 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9424411 TTCTCGTTGC
*
9424421 TTTCTCTTTTCTACT
1 TTTCTCTTCTCTACT
9424436 TTTCTCTTCTCTACT
1 TTTCTCTTCTCTACT
9424451 T
1 T
9424452 AGCCTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTCTCTTCTCTACT
Found at i:9435039 original size:22 final size:23
Alignment explanation
Indices: 9435008--9435052 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
9434998 TGCGAATTTC
*
9435008 CCCCCGTGCATGAGT-TACATGT
1 CCCCCATGCATGAGTATACATGT
9435030 CCCCCATGCATGAGTATACATGT
1 CCCCCATGCATGAGTATACATGT
9435053 GAGCTAGGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (23 bp):
CCCCCATGCATGAGTATACATGT
Found at i:9435134 original size:24 final size:24
Alignment explanation
Indices: 9435107--9435159 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
9435097 TTTTTATTTT
9435107 TTTGACCAAGCCTTTTTACTAGAA
1 TTTGACCAAGCCTTTTTACTAGAA
* *
9435131 TTTGACCAAGCTTTTTTATTAGAA
1 TTTGACCAAGCCTTTTTACTAGAA
9435155 TTTGA
1 TTTGA
9435160 TTTGGTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (24 bp):
TTTGACCAAGCCTTTTTACTAGAA
Found at i:9435643 original size:21 final size:21
Alignment explanation
Indices: 9435609--9435648 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
9435599 CTACTAAAAA
9435609 TATTTTTAATAACACTTTTTTT
1 TATTTTTAATAACA-TTTTTTT
9435631 TATTTTTAA-AACATTTTT
1 TATTTTTAATAACATTTTT
9435649 GTATATCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTTAATAACATTTTTTT
Found at i:9436298 original size:2 final size:2
Alignment explanation
Indices: 9436293--9436333 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
9436283 TGTGTGTGTG
9436293 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9436334 GAAAGTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9436593 original size:3 final size:3
Alignment explanation
Indices: 9436585--9436619 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
9436575 ATTTGTCCTT
*
9436585 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9436620 GTTGTTGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:9439424 original size:21 final size:21
Alignment explanation
Indices: 9439390--9439473 Score: 69
Period size: 22 Copynumber: 3.9 Consensus size: 21
9439380 TATCAACCAA
9439390 TCACGCAATACTTAAAAATTG
1 TCACGCAATACTTAAAAATTG
* * *
9439411 TCACGTAATGCTTAAAAATTAA
1 TCACGCAATACTTAAAAATT-G
* * **
9439433 TAACACAATACTTAAAAACTAA
1 TCACGCAATACTTAAAAA-TTG
* *
9439455 TCACGCAATGCTCAAAAAT
1 TCACGCAATACTTAAAAAT
9439474 CAGTTATGTA
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
21 19 0.39
22 29 0.59
23 1 0.02
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.26
Consensus pattern (21 bp):
TCACGCAATACTTAAAAATTG
Found at i:9439673 original size:60 final size:60
Alignment explanation
Indices: 9439594--9439721 Score: 184
Period size: 60 Copynumber: 2.1 Consensus size: 60
9439584 TACTTGGTGA
**
9439594 AAAATACTCAAAATGCTCAAAAATTTTTCTTCATGTATCAAAAATCACTTCAAAATGGTT
1 AAAATACTCAAAACACTCAAAAATTTTTCTTCATGTATCAAAAATCACTTCAAAATGGTT
* * * * * *
9439654 AAAATGCTCAAAACACTCAAAAGTTTTTCTTCGTGTATCAAAAATCATTTCAAAATGCTC
1 AAAATACTCAAAACACTCAAAAATTTTTCTTCATGTATCAAAAATCACTTCAAAATGGTT
9439714 AAAATACT
1 AAAATACT
9439722 TAAAGATTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (60 bp):
AAAATACTCAAAACACTCAAAAATTTTTCTTCATGTATCAAAAATCACTTCAAAATGGTT
Found at i:9442465 original size:22 final size:22
Alignment explanation
Indices: 9442430--9442471 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
9442420 TTTTTGTTTC
9442430 TCTTATTTCATTTTTATGTATT
1 TCTTATTTCATTTTTATGTATT
*
9442452 TCTTACTTTC-TTTTTGTGTA
1 TCTTA-TTTCATTTTTATGTA
9442472 AAAGTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.14, C:0.12, G:0.07, T:0.67
Consensus pattern (22 bp):
TCTTATTTCATTTTTATGTATT
Found at i:9446645 original size:2 final size:2
Alignment explanation
Indices: 9446638--9446673 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
9446628 CAATTTCCCT
*
9446638 TC TC TC TC TC TC TC TC TC GTC TC TC TC TT TC TC TC T
1 TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC T
9446674 GTTTTTCTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.00, C:0.44, G:0.03, T:0.53
Consensus pattern (2 bp):
TC
Found at i:9446662 original size:17 final size:17
Alignment explanation
Indices: 9446640--9446672 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9446630 ATTTCCCTTC
9446640 TCTCTCTCTCTCTCTCG
1 TCTCTCTCTCTCTCTCG
*
9446657 TCTCTCTCTTTCTCTC
1 TCTCTCTCTCTCTCTC
9446673 TGTTTTTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.52
Consensus pattern (17 bp):
TCTCTCTCTCTCTCTCG
Found at i:9447614 original size:2 final size:2
Alignment explanation
Indices: 9447555--9447594 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9447545 TAACTTAATA
9447555 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
9447595 NNNNNNNNNN
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:9447615 original size:2 final size:2
Alignment explanation
Indices: 9447607--9447641 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9447597 NNNNNNNNNN
9447607 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9447642 ACAATTTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9450478 original size:363 final size:363
Alignment explanation
Indices: 9449812--9450490 Score: 1333
Period size: 363 Copynumber: 1.9 Consensus size: 363
9449802 AATAATGTCA
9449812 TGTGATACTAATATGATGACGTCACAATATTGACGTGATATTGGCATGCTGACGTGTTAATGTCA
1 TGTGATACTAATATGATGACGTCACAATATTGACGTGATATTGGCATGCTGACGTGTTAATGTCA
9449877 TGTGACAATGCTGACGTGGCAAATCAAGAAAAAAAATTTTTTAAAAAAATATGTGCTATGTCATA
66 TGTGACAATGCTGACGTGGCAAATCAAGAAAAAAAATTTTTTAAAAAAATATGTGCTATGTCATA
9449942 AGGACTAAATTAAATAAAAATATATAATACATGGATTAAATTAAAAAAATTAAAGTGTTGAGGGA
131 AGGACTAAATTAAATAAAAATATATAATACATGGATTAAATTAAAAAAATTAAAGTGTTGAGGGA
9450007 CCAAATTGAAAAAAATATTTGAAAAATAAAAATCTTTAAGTAGATGATATATATACTTATTAATA
196 CCAAATTGAAAAAAATATTTGAAAAATAAAAATCTTTAAGTAGATGATATATATACTTATTAATA
*
9450072 AGTCAAATATTTAAATATAAAAGATTAATGGTGTTTAAATATATATATAT-TATATTTTTTTATA
261 AGTCAAATATTTAAATATAAAAGATTAATGGTGTTAAAATATATATATATATATATTTTTTTATA
9450136 CTTATATTATTATTTCACTATTTATTTATTTTATTTCT
326 CTTATATTATTATTTCACTATTTATTTATTTTATTTCT
9450174 TNGTGATACTAATATGATGACGTCACAATATTGACGTGATATTGGCATGCTGACGTGTTAATGTC
1 T-GTGATACTAATATGATGACGTCACAATATTGACGTGATATTGGCATGCTGACGTGTTAATGTC
9450239 ATGTGACAATGCTGACGTGGCAAATCAAGAAAAAAAATTTTTTAAAAAAATATGTGCTATGTCAT
65 ATGTGACAATGCTGACGTGGCAAATCAAGAAAAAAAATTTTTTAAAAAAATATGTGCTATGTCAT
9450304 AAGGACTAAATTAAATAAAAATATATAATACATGGATTAAATTAAAAAAATTAAAGTGTTGAGGG
130 AAGGACTAAATTAAATAAAAATATATAATACATGGATTAAATTAAAAAAATTAAAGTGTTGAGGG
9450369 ACCAAATTGAAAAAAATATTTGAAAAATAAAAATCTTTAAGTAGATGATATATATACTTATTAAT
195 ACCAAATTGAAAAAAATATTTGAAAAATAAAAATCTTTAAGTAGATGATATATATACTTATTAAT
9450434 AAGTCAAATATTTAAATATAAAAGATTAATGGTGTTAAAATATATATATATATATAT
260 AAGTCAAATATTTAAATATAAAAGATTAATGGTGTTAAAATATATATATATATATAT
9450491 ATATATTTTT
Statistics
Matches: 314, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
362 1 0.00
363 308 0.98
364 5 0.02
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (363 bp):
TGTGATACTAATATGATGACGTCACAATATTGACGTGATATTGGCATGCTGACGTGTTAATGTCA
TGTGACAATGCTGACGTGGCAAATCAAGAAAAAAAATTTTTTAAAAAAATATGTGCTATGTCATA
AGGACTAAATTAAATAAAAATATATAATACATGGATTAAATTAAAAAAATTAAAGTGTTGAGGGA
CCAAATTGAAAAAAATATTTGAAAAATAAAAATCTTTAAGTAGATGATATATATACTTATTAATA
AGTCAAATATTTAAATATAAAAGATTAATGGTGTTAAAATATATATATATATATATTTTTTTATA
CTTATATTATTATTTCACTATTTATTTATTTTATTTCT
Found at i:9450546 original size:17 final size:17
Alignment explanation
Indices: 9450524--9450557 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9450514 ATTTGATTTC
* *
9450524 AAAATATGTATATTAAT
1 AAAATACGTACATTAAT
9450541 AAAATACGTACATTAAT
1 AAAATACGTACATTAAT
9450558 TTATATGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (17 bp):
AAAATACGTACATTAAT
Found at i:9450907 original size:17 final size:17
Alignment explanation
Indices: 9450874--9450907 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9450864 TTAAATTATT
*
9450874 AATTTGTATATACAAAA
1 AATTTGTAAATACAAAA
*
9450891 AATTTGTAAATATAAAA
1 AATTTGTAAATACAAAA
9450908 TAAAATTGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (17 bp):
AATTTGTAAATACAAAA
Found at i:9451023 original size:16 final size:17
Alignment explanation
Indices: 9451002--9451045 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
9450992 ATATAACATG
*
9451002 AAATATTAAACAAA-AA
1 AAATATTAAAAAAACAA
*
9451018 AAATATAAAAAAAACAA
1 AAATATTAAAAAAACAA
*
9451035 AAAAATTAAAA
1 AAATATTAAAA
9451046 GGGTGGAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (17 bp):
AAATATTAAAAAAACAA
Found at i:9453044 original size:1 final size:1
Alignment explanation
Indices: 9453038--9453066 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
9453028 TNGTTATGGT
9453038 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9453067 TTTGATGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9453839 original size:2 final size:2
Alignment explanation
Indices: 9453832--9453857 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9453822 ACTATCTCAT
9453832 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
9453858 ATAATTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:9455200 original size:50 final size:52
Alignment explanation
Indices: 9455136--9455237 Score: 127
Period size: 53 Copynumber: 2.0 Consensus size: 52
9455126 TCCACTATTA
** *
9455136 AGATTCTTACTTTTTAAC-AGA-AAATTATAACCCTTACACAATCTATAAAG
1 AGATTCTTACTTTTTAACAAGACAAACGATAACCCTTACACAATCCATAAAG
* * *
9455186 AGATTCTTATTTTTTCACAAGATCAAGCGATAACCCTTACACAATCCATAAA
1 AGATTCTTACTTTTTAACAAGA-CAAACGATAACCCTTACACAATCCATAAA
9455238 TGGATCTTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
50 16 0.37
51 3 0.07
53 24 0.56
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.32
Consensus pattern (52 bp):
AGATTCTTACTTTTTAACAAGACAAACGATAACCCTTACACAATCCATAAAG
Found at i:9455228 original size:53 final size:51
Alignment explanation
Indices: 9455162--9455262 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 51
9455152 ACAGAAAATT
* *
9455162 ATAACCCTTACACAATCTATAAA-GAGATTCTTATTTTTTCACAAGATCAAGCG
1 ATAACCCTTACACAATCCATAAATG-GA-TCTT-TGTTTTCACAAGATCAAGCG
*
9455215 ATAACCCTTACACAATCCATAAATGGATCTTTGTTTTCACGAGATCAA
1 ATAACCCTTACACAATCCATAAATGGATCTTTGTTTTCACAAGATCAA
9455263 AGAATAACCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
51 15 0.34
52 4 0.09
53 24 0.55
54 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.32
Consensus pattern (51 bp):
ATAACCCTTACACAATCCATAAATGGATCTTTGTTTTCACAAGATCAAGCG
Found at i:9457020 original size:79 final size:79
Alignment explanation
Indices: 9456885--9457047 Score: 274
Period size: 79 Copynumber: 2.1 Consensus size: 79
9456875 CTAGTAAATA
* * *
9456885 AGGGGGTATTTGGTCTTGGGAAGCTGACCAACGGAGGCTGTTGAAGCTAGTGGGTAAGGTTAGAT
1 AGGGGGTATTTGGTCTTGGGAAGCCGACCAACGGAGGCTGTTGAAGCTAGTAGGTAAGGTCAGAT
9456950 C-GACGCCGGTAGAG
66 CAG-CGCCGGTAGAG
*
9456964 AGGGGGTATTTGGTCTTGGGAAGCCGACCGACGGAGGCTGTTGAAGCTAGTAGGTAAGGTCAGAT
1 AGGGGGTATTTGGTCTTGGGAAGCCGACCAACGGAGGCTGTTGAAGCTAGTAGGTAAGGTCAGAT
9457029 CAGCGCCGGTAGAG
66 CAGCGCCGGTAGAG
9457043 AGGGG
1 AGGGG
9457048 AGCAACACTT
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
79 78 0.99
80 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.42, T:0.21
Consensus pattern (79 bp):
AGGGGGTATTTGGTCTTGGGAAGCCGACCAACGGAGGCTGTTGAAGCTAGTAGGTAAGGTCAGAT
CAGCGCCGGTAGAG
Found at i:9457495 original size:2 final size:2
Alignment explanation
Indices: 9457488--9457529 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
9457478 AAAAGTTATT
* *
9457488 TA TA TA TA GTA TA TA TA TA TA TA TA CA TA TA CA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9457530 TAAATATGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:9457800 original size:2 final size:2
Alignment explanation
Indices: 9457788--9457822 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
9457778 ATACTTGTAA
9457788 AT AT A- AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9457823 AACAAAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9458450 original size:20 final size:19
Alignment explanation
Indices: 9458425--9458464 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
9458415 CGAGGAGCTN
*
9458425 TAATAAAATATATAAAATAA
1 TAATAAAATAAAT-AAATAA
9458445 TAATAAAATAAATAAATAA
1 TAATAAAATAAATAAATAA
9458464 T
1 T
9458465 CCATGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TAATAAAATAAATAAATAA
Found at i:9458637 original size:233 final size:233
Alignment explanation
Indices: 9458192--9458658 Score: 769
Period size: 233 Copynumber: 2.0 Consensus size: 233
9458182 CTAAATAGAA
*
9458192 AATAATAAATATATAATAATAATAAAATAAATAATAAATCCATGAAAAAAAATGACAAAATAAAT
1 AATAATAAATATAAAATAATAATAAAATAAATAATAAATCCATGAAAAAAAATGACAAAATAAAT
9458257 ATATAAATAAGGTGATAAATTATTAAACACATAATTGGATGAATTATGAACCATCTAAGTCAATA
66 ATATAAATAAGGTGATAAATTATTAAACACATAATTGGATGAATTATGAACCATCTAAGTCAATA
* * **
9458322 AACGCCTGCATGTAGACATCATTATTTAATCCTGTCATAGCATGTCACATTTATCTTATTAATGG
131 AACGCCTGCATGTAGACATCATTATTTAATCCTATCATAGCATGCCACATTTATCTTACAAATGG
9458387 GGCGAAAATTCCGATGATGGGATTTCCCCGAGGAGCTNT
196 GGCGAAAATTCCGATGATGGGATTTCCCCGAGGAGCT-T
9458426 AATAA-AATATATAAAATAATAATAAAATAAATAA-ATAATCCATG-AAAAAAATGACAAAATAA
1 AATAATAA-ATATAAAATAATAATAAAATAAATAATA-AATCCATGAAAAAAAATGACAAAATAA
*
9458488 ATATATAAATAAGGTGATAAATTATTAAACACATAATTGGATGAATTATGAACCATTTAAGTCAA
64 ATATATAAATAAGGTGATAAATTATTAAACACATAATTGGATGAATTATGAACCATCTAAGTCAA
* * *
9458553 TAAACGCCTGCATGTAGACATCATTATTTTATCCTATCATAGCATGCCGCATTTATCTTGCAAAT
129 TAAACGCCTGCATGTAGACATCATTATTTAATCCTATCATAGCATGCCACATTTATCTTACAAAT
* * * *
9458618 GGTGTGAGAATTTCGATGATGGGATTTCCCCGAGGAGCTT
194 GGGGCGAAAATTCCGATGATGGGATTTCCCCGAGGAGCTT
9458658 A
1 A
9458659 TAAAGACGAG
Statistics
Matches: 218, Mismatches: 13, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
232 2 0.01
233 178 0.82
234 38 0.17
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (233 bp):
AATAATAAATATAAAATAATAATAAAATAAATAATAAATCCATGAAAAAAAATGACAAAATAAAT
ATATAAATAAGGTGATAAATTATTAAACACATAATTGGATGAATTATGAACCATCTAAGTCAATA
AACGCCTGCATGTAGACATCATTATTTAATCCTATCATAGCATGCCACATTTATCTTACAAATGG
GGCGAAAATTCCGATGATGGGATTTCCCCGAGGAGCTT
Found at i:9470379 original size:60 final size:59
Alignment explanation
Indices: 9470308--9470784 Score: 456
Period size: 60 Copynumber: 7.9 Consensus size: 59
9470298 CATTAAAGAA
* *
9470308 TTAAATCGAACCTGTTTTGAGATAGGTAGAGCCTAGATTAAGTCTAGGAATTTTATTTGT
1 TTAAATCGAACCTGTTTTGAGATAGGTAGAGCCTAGATCAAGTCTAGGAATTTTAATT-T
* * * * *
9470368 TTAAATCGAACCTGTTTTGAGATAGGTAGAGCTTAGATTAAGTCTAGAAATTTCATTTGT
1 TTAAATCGAACCTGTTTTGAGATAGGTAGAGCCTAGATCAAGTCTAGGAATTTTAATT-T
* * * * * **
9470428 TTAAATCAAACCTGTTGTGAGATAGGTTGAGCTTAGATTAAGTCTAAAAATTTTAACTTT
1 TTAAATCGAACCTGTTTTGAGATAGGTAGAGCCTAGATCAAGTCTAGGAATTTTAA-TTT
* * *
9470488 TTAAAATCGAACCTGATTTGAAATAGGTAGAGCCTAGATTAAGTCTAGGAATTTTAATTT
1 TT-AAATCGAACCTGTTTTGAGATAGGTAGAGCCTAGATCAAGTCTAGGAATTTTAATTT
* * * * * *
9470548 TTAAATCGAACCTATCTTCGGATATAGATCA-AGCAC-AGGTCAAGTCTAGGAATTCTAATTCT
1 TTAAATCGAACCTGT-TT-TGAGATAGGT-AGAGC-CTAGATCAAGTCTAGGAATTTTAATT-T
* ** * * *
9470610 TTAAATCGAACCTGTCTTGTGAGATGGGTCTAGCCTAGGTCAAGTTTAGGAATTTCAATTCT
1 TTAAATCGAACCTGT-TT-TGAGATAGGTAGAGCCTAGATCAAGTCTAGGAATTTTAATT-T
* * * * * *
9470672 TTAAGTCGAACCTGTTGTGAGATAGGTCGAGCTTAGATCAAGTCTAGGAATTTCAGTTT
1 TTAAATCGAACCTGTTTTGAGATAGGTAGAGCCTAGATCAAGTCTAGGAATTTTAATTT
* * * * *
9470731 TTAAGTCAAACCTGTTGTGAGATAGGTCA-AGTCTAGATCAAGTCTAGAAATTTT
1 TTAAATCGAACCTGTTTTGAGATAGGT-AGAGCCTAGATCAAGTCTAGGAATTTT
9470785 CGTTTTTTCT
Statistics
Matches: 358, Mismatches: 49, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
59 59 0.16
60 152 0.42
61 81 0.23
62 66 0.18
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (59 bp):
TTAAATCGAACCTGTTTTGAGATAGGTAGAGCCTAGATCAAGTCTAGGAATTTTAATTT
Found at i:9470616 original size:121 final size:120
Alignment explanation
Indices: 9470308--9470783 Score: 378
Period size: 121 Copynumber: 3.9 Consensus size: 120
9470298 CATTAAAGAA
* * *
9470308 TTAAATCGAACCTGT-TT-TGAGATAGGT-AGAGC-CTAGATTAAGTCTAGGAATTTTATTTGTT
1 TTAAATCGAACCT-TCTTGTGAGATAGATCA-AGCAC-AGATCAAGTCTAGGAATTTTAATT-TT
* * * * *
9470369 TAAATCGAACCTGTTTTGAGATAGGTAGAGCTTAGATTAAGTCTAGAAATTTCATTTGT
62 TAAATCGAACCTGATTTGAGATAGGTAGAGCCTAGATTAAGTCTAGGAATTTCAATTCT
* * * ** ** * **
9470428 TTAAATCAAACC-TGTTGTGAGATAGGTTGAGCTTAGATTAAGTCTAAAAATTTTAACTTTTTAA
1 TTAAATCGAACCTTCTTGTGAGATAGATCAAGCACAGATCAAGTCTAGGAATTTTAA-TTTTT-A
* *
9470492 AATCGAACCTGATTTGAAATAGGTAGAGCCTAGATTAAGTCTAGGAATTTTAATT-T
64 AATCGAACCTGATTTGAGATAGGTAGAGCCTAGATTAAGTCTAGGAATTTCAATTCT
* * *
9470548 TTAAATCGAACCTATCTTCG-GATATAGATCAAGCACAGGTCAAGTCTAGGAATTCTAATTCTTT
1 TTAAATCGAACCT-TCTT-GTGAGATAGATCAAGCACAGATCAAGTCTAGGAATTTTAATT-TTT
* * ** * * *
9470612 AAATCGAACCTGTCTTGTGAGATGGGTCTAGCCTAGGTCAAGTTTAGGAATTTCAATTCT
63 AAATCGAACCTG-ATT-TGAGATAGGTAGAGCCTAGATTAAGTCTAGGAATTTCAATTCT
* * * * ** * * *
9470672 TTAAGTCGAACC-TGTTGTGAGATAGGTCGAGCTTAGATCAAGTCTAGGAATTTCAGTTTTTAAG
1 TTAAATCGAACCTTCTTGTGAGATAGATCAAGCACAGATCAAGTCTAGGAATTTTAATTTTTAAA
* * * *
9470736 TCAAACCTG-TTGTGAGATAGGTCA-AGTCTAGATCAAGTCTAGAAATTT
66 TCGAACCTGATT-TGAGATAGGT-AGAGCCTAGATTAAGTCTAGGAATTT
9470784 TCGTTTTTTC
Statistics
Matches: 288, Mismatches: 53, Indels: 31
0.77 0.14 0.08
Matches are distributed among these distances:
118 1 0.00
119 34 0.12
120 58 0.20
121 80 0.28
122 69 0.24
123 34 0.12
124 12 0.04
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (120 bp):
TTAAATCGAACCTTCTTGTGAGATAGATCAAGCACAGATCAAGTCTAGGAATTTTAATTTTTAAA
TCGAACCTGATTTGAGATAGGTAGAGCCTAGATTAAGTCTAGGAATTTCAATTCT
Found at i:9471076 original size:16 final size:16
Alignment explanation
Indices: 9471042--9471090 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 16
9471032 ACCTACTTCA
9471042 AAAAAAAT-AAAA--T
1 AAAAAAATAAAAAGTT
*
9471055 AAAAAATAAAAAAAGGTT
1 AAAAAA-ATAAAAA-GTT
9471073 AAAAAAATAAAAAGTT
1 AAAAAAATAAAAAGTT
9471089 AA
1 AA
9471091 TAAAGAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 6 0.21
14 1 0.03
15 4 0.14
16 5 0.17
17 6 0.21
18 7 0.24
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (16 bp):
AAAAAAATAAAAAGTT
Found at i:9472267 original size:14 final size:13
Alignment explanation
Indices: 9472248--9472285 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
9472238 TAGGAAAAGT
9472248 TATATATATACATA
1 TATATATATAC-TA
9472262 TATATATATACTA
1 TATATATATACTA
9472275 TATACTATATA
1 TATA-TATATA
9472286 AAGTAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (13 bp):
TATATATATACTA
Found at i:9475522 original size:13 final size:14
Alignment explanation
Indices: 9475493--9475523 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
9475483 ATATTAAAAT
9475493 ATTAAAAATTTATA
1 ATTAAAAATTTATA
9475507 ATTAAAAATTTA-A
1 ATTAAAAATTTATA
9475520 ATTA
1 ATTA
9475524 TTTTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTAAAAATTTATA
Found at i:9484017 original size:11 final size:12
Alignment explanation
Indices: 9483997--9484030 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
9483987 CCTATACCCA
9483997 TTTATATAATAT
1 TTTATATAATAT
9484009 TTTAT-TAATA-
1 TTTATATAATAT
9484019 TTTATATAATAT
1 TTTATATAATAT
9484031 ACAATAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.25
11 10 0.50
12 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTATATAATAT
Found at i:9484674 original size:2 final size:2
Alignment explanation
Indices: 9484663--9484694 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9484653 TACATAAACT
9484663 TA TA -A 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
9484695 GCACACACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9487456 original size:66 final size:65
Alignment explanation
Indices: 9487378--9487535 Score: 158
Period size: 65 Copynumber: 2.4 Consensus size: 65
9487368 GTGATCGTCT
* * * *
9487378 ATGACTAGCACGTTCTCCCATGATTGAGCTTAATACCCAATAAGTCATCCCTTAACGTGCTCTTT
1 ATGACAAGCACGTTCTCCCATGATTGAGATTAACACCCAATAA-CCATCCCTTAACGTGCT-TTT
9487443 -C
64 CC
* * ** * ***
9487444 ATGGCAATCACGTTCTGCCC-TGATCAAGATTAACATCCAATAACCATTTTTTAACGTGCTTTTC
1 ATGACAAGCACGTTCT-CCCATGATTGAGATTAACACCCAATAACCATCCCTTAACGTGCTTTTC
9487508 C
65 C
*
9487509 ATGACAAGCACGTTCTCTCATGATTGA
1 ATGACAAGCACGTTCTCCCATGATTGA
9487536 ACGTGTTCTC
Statistics
Matches: 72, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
64 5 0.07
65 33 0.46
66 31 0.43
67 3 0.04
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (65 bp):
ATGACAAGCACGTTCTCCCATGATTGAGATTAACACCCAATAACCATCCCTTAACGTGCTTTTCC
Found at i:9499792 original size:25 final size:25
Alignment explanation
Indices: 9499764--9499811 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
9499754 AAAGAAAAAT
*
9499764 AAAAAATCACAACAA-AAAAAAAACC
1 AAAAAAT-ACAAAAAGAAAAAAAACC
9499789 AAAAAATACAAAAAGAAAAAAAA
1 AAAAAATACAAAAAGAAAAAAAA
9499812 ATGGGAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.81, C:0.12, G:0.02, T:0.04
Consensus pattern (25 bp):
AAAAAATACAAAAAGAAAAAAAACC
Found at i:9500008 original size:4 final size:4
Alignment explanation
Indices: 9499999--9500050 Score: 50
Period size: 4 Copynumber: 12.2 Consensus size: 4
9499989 GAAAAAGGAG
* * *
9499999 AGAA AGAA AGAA AGAGA GAGAA GGAA AGAA AGAG AGAGA AGGA AGAA AGAA
1 AGAA AGAA AGAA AGA-A -AGAA AGAA AGAA AGAA AGA-A AGAA AGAA AGAA
9500050 A
1 A
9500051 AAGGAGAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 32 0.82
5 4 0.10
6 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:9500027 original size:22 final size:22
Alignment explanation
Indices: 9499994--9500059 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
9499984 GCGAAGAAAA
9499994 AGGAGAGAAAGAAAGAAAGAGAG
1 AGGA-AGAAAGAAAGAAAGAGAG
*
9500017 A-GAAGGAAAGAAAGAGAGAGA-
1 AGGAA-GAAAGAAAGAAAGAGAG
*
9500038 AGGAAGAAAGAAA-AAGGAGAG
1 AGGAAGAAAGAAAGAAAGAGAG
9500059 A
1 A
9500060 AGAGATCTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 5 0.14
21 11 0.30
22 20 0.54
23 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (22 bp):
AGGAAGAAAGAAAGAAAGAGAG
Found at i:9500061 original size:18 final size:18
Alignment explanation
Indices: 9499987--9500062 Score: 82
Period size: 18 Copynumber: 4.0 Consensus size: 18
9499977 GTGAATGGCG
9499987 AAGAAAAAGGAGAGAAAGA
1 AAGAAAAAGGAGAG-AAGA
*
9500006 AAGAAAGA-GAGAGAAGGA
1 AAGAAAAAGGAGAGAA-GA
*
9500024 AAGAAAGAGAGAGAAGGAAGA
1 AAGAAAAAG-GAG-A-GAAGA
9500045 AAGAAAAAGGAGAGAAGA
1 AAGAAAAAGGAGAGAAGA
9500063 GATCTGCGAC
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
17 2 0.04
18 20 0.40
19 8 0.16
20 6 0.12
21 11 0.22
22 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (18 bp):
AAGAAAAAGGAGAGAAGA
Found at i:9500213 original size:43 final size:44
Alignment explanation
Indices: 9500128--9500217 Score: 157
Period size: 43 Copynumber: 2.1 Consensus size: 44
9500118 AGAGAGAACA
9500128 AAAGGAGAGAAAAAGAAAAAGAAAAAAAATGGGAGAAAGAACCC
1 AAAGGAGAGAAAAAGAAAAAGAAAAAAAATGGGAGAAAGAACCC
9500172 NAAAGGAGAG-AAAA-AAAAAGAAAAAAAATGGGAGAAAGAACCC
1 -AAAGGAGAGAAAAAGAAAAAGAAAAAAAATGGGAGAAAGAACCC
9500215 AAA
1 AAA
9500218 ACGACGCGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
42 3 0.07
43 29 0.64
44 4 0.09
45 9 0.20
ACGTcount: A:0.67, C:0.07, G:0.23, T:0.02
Consensus pattern (44 bp):
AAAGGAGAGAAAAAGAAAAAGAAAAAAAATGGGAGAAAGAACCC
Found at i:9502573 original size:4 final size:4
Alignment explanation
Indices: 9502564--9502608 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
9502554 ATTCATTTTG
**
9502564 AAAT AAAT AAAT AAAT AAAT AAAT -GTT AAAT AAA- AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
9502609 AAGGAAGCAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 4 0.11
4 31 0.89
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:9502604 original size:11 final size:11
Alignment explanation
Indices: 9502564--9502610 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
9502554 ATTCATTTTG
9502564 AAATAAATAAA
1 AAATAAATAAA
9502575 TAAATAAATAAA
1 -AAATAAATAAA
***
9502587 TGTTAAATAAA
1 AAATAAATAAA
9502598 AAATAAATAAA
1 AAATAAATAAA
9502609 AA
1 AA
9502611 GGAAGCAGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:9503609 original size:15 final size:16
Alignment explanation
Indices: 9503578--9503611 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
9503568 TAGTTTTTTT
*
9503578 AAATAATATATATAAA
1 AAATAATATAAATAAA
9503594 AAATAATA-AAATAAA
1 AAATAATATAAATAAA
9503609 AAA
1 AAA
9503612 ATATATTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAATATAAATAAA
Found at i:9503614 original size:16 final size:16
Alignment explanation
Indices: 9503578--9503611 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9503568 TAGTTTTTTT
*
9503578 AAATAATATATATAAA
1 AAATAATAAATATAAA
9503594 AAATAATAAA-ATAAA
1 AAATAATAAATATAAA
9503609 AAA
1 AAA
9503612 ATATATTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAATAAATATAAA
Found at i:9504927 original size:15 final size:15
Alignment explanation
Indices: 9504903--9504936 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
9504893 ACTTTAGGTT
9504903 TAAAAATAATAATAA
1 TAAAAATAATAATAA
*
9504918 TAAAATTAATAATAA
1 TAAAAATAATAATAA
9504933 TAAA
1 TAAA
9504937 TTAGAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAATAATAATAA
Found at i:9506589 original size:18 final size:18
Alignment explanation
Indices: 9506566--9506611 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
9506556 ACACGTTTAC
9506566 TTAATCGTGTTATCATGT
1 TTAATCGTGTTATCATGT
*
9506584 TTAATCGTGTTATCGTGT
1 TTAATCGTGTTATCATGT
*
9506602 TTAAACGTGT
1 TTAATCGTGT
9506612 ATACGTGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.11, G:0.20, T:0.48
Consensus pattern (18 bp):
TTAATCGTGTTATCATGT
Found at i:9506876 original size:19 final size:19
Alignment explanation
Indices: 9506800--9506876 Score: 61
Period size: 19 Copynumber: 4.1 Consensus size: 19
9506790 TTTTTGTTTT
* *
9506800 ATTATAATTATTTT-TATA
1 ATTATAAATATTTTATTTA
* *
9506818 ATTATAGAT-TTTAAATTTAA
1 ATTATAAATATTT-TATTT-A
* *
9506838 ATAATAAA-ATTATATTTA
1 ATTATAAATATTTTATTTA
9506856 ATTATAAATATTTTATTTA
1 ATTATAAATATTTTATTTA
9506875 AT
1 AT
9506877 CGTGTTAAAC
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
17 3 0.07
18 15 0.34
19 17 0.39
20 9 0.20
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (19 bp):
ATTATAAATATTTTATTTA
Found at i:9508945 original size:3 final size:3
Alignment explanation
Indices: 9508937--9509025 Score: 61
Period size: 3 Copynumber: 31.7 Consensus size: 3
9508927 TATTTTTTAT
* *
9508937 TTA TTA TTA TT- TAA TTA TTA TT- TTCA TT- TTA TCA -TA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA -TTA TTA
*
9508980 TTA TTA -TA TT- TT- TTA TT- TTA TTCC TTA TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
9509021 TTA TT
1 TTA TT
9509026 TATATCTTAT
Statistics
Matches: 69, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
2 16 0.23
3 47 0.68
4 6 0.09
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:9508949 original size:14 final size:14
Alignment explanation
Indices: 9508927--9509028 Score: 67
Period size: 14 Copynumber: 7.7 Consensus size: 14
9508917 TGCAATTGTC
*
9508927 TATTTTTTATTTAT
1 TATTATTTATTTAT
*
9508941 TATTATTTAATTAT
1 TATTATTTATTTAT
*
9508955 TATT-TTCA-TT-T
1 TATTATTTATTTAT
*
9508966 TATCA--TATTTAT
1 TATTATTTATTTAT
*
9508978 TATTATTATATTTTT
1 TATTATT-TATTTAT
**
9508993 TA-T-TTTATTCCT
1 TATTATTTATTTAT
9509005 TATTATTT-TATTAT
1 TATTATTTAT-TTAT
9509019 TATTATTTAT
1 TATTATTTAT
9509029 ATCTTATATT
Statistics
Matches: 67, Mismatches: 11, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
10 1 0.01
11 6 0.09
12 14 0.21
13 7 0.10
14 30 0.45
15 9 0.13
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTATTTATTTAT
Found at i:9508953 original size:11 final size:10
Alignment explanation
Indices: 9508933--9509022 Score: 68
Period size: 9 Copynumber: 9.5 Consensus size: 10
9508923 TGTCTATTTT
9508933 TTATTTATTA
1 TTATTTATTA
9508943 TTATTTAATTA
1 TTATTT-ATTA
*
9508954 TTATTT-TCA
1 TTATTTATTA
*
9508963 -T-TTTATCA
1 TTATTTATTA
9508971 -TATTTATTA
1 TTATTTATTA
9508980 TTA-TTA-TA
1 TTATTTATTA
*
9508988 TTTTTTATT-
1 TTATTTATTA
**
9508997 TTATTCCTTA
1 TTATTTATTA
9509007 TTATTTTATTA
1 TTA-TTTATTA
9509018 TTATT
1 TTATT
9509023 ATTTATATCT
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
7 3 0.05
8 9 0.14
9 20 0.31
10 14 0.22
11 18 0.28
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (10 bp):
TTATTTATTA
Found at i:9509070 original size:24 final size:25
Alignment explanation
Indices: 9509030--9509076 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
9509020 ATTATTTATA
*
9509030 TCTTATATTTTTATTTTA-AATTCC
1 TCTTATATTTTCATTTTATAATTCC
*
9509054 TCTTATATTTTCCTTTTATAATT
1 TCTTATATTTTCATTTTATAATT
9509077 AGATAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (25 bp):
TCTTATATTTTCATTTTATAATTCC
Found at i:9509299 original size:24 final size:26
Alignment explanation
Indices: 9509258--9509305 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
9509248 ATTATTTATA
*
9509258 TCTTAATATTTTTATTTTA-AATTCC
1 TCTTAATATTTTCATTTTATAATTCC
*
9509283 TCTT-ATATTTTCCTTTTATAATT
1 TCTTAATATTTTCATTTTATAATT
9509306 AGATAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (26 bp):
TCTTAATATTTTCATTTTATAATTCC
Found at i:9509414 original size:228 final size:227
Alignment explanation
Indices: 9509006--9509459 Score: 865
Period size: 229 Copynumber: 2.0 Consensus size: 227
9508996 TTTATTCCTT
9509006 ATTATTTTATTATTATTATTTATATCTTATATTTTTATTTTAAATTCCTCTTATATTTTCCTTTT
1 ATTATTTTATTATTATTATTTATATCTTATATTTTTATTTTAAATTCCTCTTATATTTTCCTTTT
9509071 ATAATTAGATAAATTATTTATGATTCCATTTAATGCTTAATTTTAAATTAATTATTGTCTTAGAT
66 ATAATTAGATAAATTATTTATGATTCCATTTAATGCTTAATTTTAAATTAATTATTGTCTTAGAT
9509136 TTTTATTATTATTTATTTTTTTTATTGAGTAATATCATGTATATTGCATTTTTACAAATTAATTA
131 TTTTATTATTATTTATTTTTTTTATTGAGTAATATCATGTATATTGCATTTTTACAAATTAATTA
*
9509201 CTTACTATATATTTGAATCATTATTATTANTTA
196 CTTACTATATATTCGAATCATTATTATTA-TTA
9509234 ATTATTTTATTATTATTATTTATATCTTAATATTTTTATTTTAAATTCCTCTTATATTTTCCTTT
1 ATTATTTTATTATTATTATTTATATCTT-ATATTTTTATTTTAAATTCCTCTTATATTTTCCTTT
9509299 TATAATTAGATAAATTATTTATGATTCCATTTAATGCTTAATTTTAAATTAATTATTGTCTTAGA
65 TATAATTAGATAAATTATTTATGATTCCATTTAATGCTTAATTTTAAATTAATTATTGTCTTAGA
9509364 TTTTTATTATTA-TTATTTTTTTTATTGAGTAATATCATGTATATTGCATTTTTACAAATTAATT
130 TTTTTATTATTATTTATTTTTTTTATTGAGTAATATCATGTATATTGCATTTTTACAAATTAATT
*
9509428 ACTTACTATATATTCGAATTATTATTATTATT
195 ACTTACTATATATTCGAATCATTATTATTATT
9509460 TTTATCATCA
Statistics
Matches: 223, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
227 2 0.01
228 108 0.48
229 113 0.51
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.57
Consensus pattern (227 bp):
ATTATTTTATTATTATTATTTATATCTTATATTTTTATTTTAAATTCCTCTTATATTTTCCTTTT
ATAATTAGATAAATTATTTATGATTCCATTTAATGCTTAATTTTAAATTAATTATTGTCTTAGAT
TTTTATTATTATTTATTTTTTTTATTGAGTAATATCATGTATATTGCATTTTTACAAATTAATTA
CTTACTATATATTCGAATCATTATTATTATTA
Found at i:9509494 original size:10 final size:10
Alignment explanation
Indices: 9509445--9509506 Score: 51
Period size: 9 Copynumber: 6.6 Consensus size: 10
9509435 ATATATTCGA
9509445 ATTATTA-TT
1 ATTATTATTT
9509454 ATTATT-TTT
1 ATTATTATTT
* *
9509463 ATCATCATTT
1 ATTATTATTT
* *
9509473 -TTTTTATCT
1 ATTATTATTT
*
9509482 ATTGTTATTT
1 ATTATTATTT
9509492 ATTATTATTT
1 ATTATTATTT
9509502 -TTATT
1 ATTATT
9509507 GAATAATTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
9 22 0.54
10 19 0.46
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (10 bp):
ATTATTATTT
Found at i:9511251 original size:74 final size:74
Alignment explanation
Indices: 9511166--9511428 Score: 312
Period size: 74 Copynumber: 3.5 Consensus size: 74
9511156 TTTTTAGATG
* * * *
9511166 AAACTCTTCAAAGCTGAGGCAACGAAACTTCTAAAAATGAACTTCTCAAAGCTGAGGCAACG-AA
1 AAACTCCTCAAAACTGAGGCAACGAAACTT-TAAAAATGAACTCCTCAAAACTGAGGCAACGAAA
*
9511230 CTTTTAAAAT
65 CTTCTAAAAT
* * ** *
9511240 AAACTCCTCAAAACTGAGGTAATGGGACTTTAAAAAATGAACTCCTCAAAACTAAGGCAACGAAA
1 AAACTCCTCAAAACTGAGGCAACGAAACTTT-AAAAATGAACTCCTCAAAACTGAGGCAACGAAA
9511305 CTTCTAAAAT
65 CTTCTAAAAT
* * * * * *
9511315 GAACTCCTCAAAACTAAGGCAACAAAACTTTAACAATGAACTCCTCAAAATTGAGGCAATGAAAC
1 AAACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
**
9511380 TTGAAAAAT
66 TTCTAAAAT
* * *
9511389 AAACTCCTCAAAGCTGAGGTACCGAAACTTTAAAAATGAA
1 AAACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAA
9511429 TTTCCCTCTT
Statistics
Matches: 157, Mismatches: 30, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
73 1 0.01
74 121 0.77
75 35 0.22
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (74 bp):
AAACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
TTCTAAAAT
Found at i:9511270 original size:37 final size:37
Alignment explanation
Indices: 9511167--9511428 Score: 267
Period size: 37 Copynumber: 7.1 Consensus size: 37
9511157 TTTTAGATGA
* * *
9511167 AACTCTTCAAAGCTGAGGCAACGAAACTTCTAAAAATG
1 AACTCCTCAAAACTGAGGCAACGAAACTT-TTAAAATG
* * *
9511205 AACTTCTCAAAGCTGAGGCAACG-AACTTTTAAAATA
1 AACTCCTCAAAACTGAGGCAACGAAACTTTTAAAATG
* * ** *
9511241 AACTCCTCAAAACTGAGGTAATGGGACTTTAAAAAATG
1 AACTCCTCAAAACTGAGGCAACGAAACTTT-TAAAATG
* *
9511279 AACTCCTCAAAACTAAGGCAACGAAACTTCTAAAATG
1 AACTCCTCAAAACTGAGGCAACGAAACTTTTAAAATG
* *
9511316 AACTCCTCAAAACTAAGGCAACAAAAC-TTTAACAATG
1 AACTCCTCAAAACTGAGGCAACGAAACTTTTAA-AATG
* * ** *
9511353 AACTCCTCAAAATTGAGGCAATGAAACTTGAAAAATA
1 AACTCCTCAAAACTGAGGCAACGAAACTTTTAAAATG
* * * *
9511390 AACTCCTCAAAGCTGAGGTACCGAAACTTTAAAAATG
1 AACTCCTCAAAACTGAGGCAACGAAACTTTTAAAATG
9511427 AA
1 AA
9511429 TTTCCCTCTT
Statistics
Matches: 186, Mismatches: 34, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
36 29 0.16
37 104 0.56
38 53 0.28
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (37 bp):
AACTCCTCAAAACTGAGGCAACGAAACTTTTAAAATG
Found at i:9511313 original size:112 final size:112
Alignment explanation
Indices: 9511166--9511428 Score: 336
Period size: 111 Copynumber: 2.4 Consensus size: 112
9511156 TTTTTAGATG
* * * * *
9511166 AAACTCTTCAAAGCTGAGGCAACGAAACTTCTAAAAATGAACTTCTCAAAGCTGAGGCAAC-GAA
1 AAACTCCTCAAAGCTGAGGCAACGAAACTTCTAAAAATGAACTCCTCAAAACTAAGGCAACAAAA
* **
9511230 CTTTTAA-AATAAACTCCTCAAAACTGAGGTAATGGGACTTTAAAAAAT
66 C-TTTAACAATAAACTCCTCAAAACTGAGGCAATGAAAC-TTAAAAAAT
* * *
9511278 GAACTCCTCAAAACTAAGGCAACGAAACTTCT-AAAATGAACTCCTCAAAACTAAGGCAACAAAA
1 AAACTCCTCAAAGCTGAGGCAACGAAACTTCTAAAAATGAACTCCTCAAAACTAAGGCAACAAAA
* * *
9511342 CTTTAACAATGAACTCCTCAAAATTGAGGCAATGAAACTTGAAAAAT
66 CTTTAACAATAAACTCCTCAAAACTGAGGCAATGAAACTTAAAAAAT
* *
9511389 AAACTCCTCAAAGCTGAGGTACCGAAACTT-TAAAAATGAA
1 AAACTCCTCAAAGCTGAGGCAACGAAACTTCTAAAAATGAA
9511429 TTTCCCTCTT
Statistics
Matches: 129, Mismatches: 19, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
110 1 0.01
111 71 0.55
112 57 0.44
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (112 bp):
AAACTCCTCAAAGCTGAGGCAACGAAACTTCTAAAAATGAACTCCTCAAAACTAAGGCAACAAAA
CTTTAACAATAAACTCCTCAAAACTGAGGCAATGAAACTTAAAAAAT
Found at i:9523298 original size:3 final size:3
Alignment explanation
Indices: 9523278--9523386 Score: 69
Period size: 3 Copynumber: 38.3 Consensus size: 3
9523268 TGCAATTGTC
*
9523278 TAT TATT TATT TATT TAT TAT TAT T-T AAT TAT TAT T-T TCAT T-T TAT
1 TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
* *
9523324 CA- TAT T-T T-T TAT TAT TA- TAT T-T T-T TAT T-T TAT TCCT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
9523363 TAT T-T TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
9523387 TATATCTTAT
Statistics
Matches: 88, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
2 20 0.23
3 53 0.60
4 15 0.17
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:9523298 original size:15 final size:15
Alignment explanation
Indices: 9523278--9523389 Score: 62
Period size: 14 Copynumber: 7.7 Consensus size: 15
9523268 TGCAATTGTC
9523278 TATTATTTATTTATT
1 TATTATTTATTTATT
*
9523293 TATTA-TTATTTAAT
1 TATTATTTATTTATT
*
9523307 TATTA-TT-TTCATTT
1 TATTATTTATTTA-TT
9523321 TATCATATTT-TTTA-T
1 TAT--TATTTATTTATT
*
9523336 TATTATATTTTTTATTT
1 TATTAT-TTATTTA-TT
**
9523353 TATTCCTTA-TTATTT
1 TATTATTTATTTA-TT
9523368 TATTA-TTA-TTA-T
1 TATTATTTATTTATT
9523380 TATTATTTAT
1 TATTATTTAT
9523390 ATCTTATATT
Statistics
Matches: 79, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
12 6 0.08
13 9 0.11
14 27 0.34
15 23 0.29
16 4 0.05
17 10 0.13
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTATTTATT
Found at i:9523355 original size:20 final size:21
Alignment explanation
Indices: 9523326--9523385 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 21
9523316 CATTTTATCA
9523326 TATT-TTTTATTATTATATTT
1 TATTATTTTATTATTATATTT
*
9523346 T-TTATTTTATTCCTTATTATTT
1 TATTATTTTATT-ATTA-TATTT
9523368 TATTATTATTATTATTAT
1 TATTATT-TTATTATTAT
9523386 TTATATCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 2 0.06
20 8 0.24
21 3 0.09
22 7 0.21
23 8 0.24
24 5 0.15
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (21 bp):
TATTATTTTATTATTATATTT
Found at i:9523379 original size:24 final size:24
Alignment explanation
Indices: 9523335--9523401 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
9523325 ATATTTTTTA
*
9523335 TTATTATATTTTTTATTTTATTCC
1 TTATTATATTTATTATTTTATTCC
*
9523359 TTATTAT-TTTATTATTATTATT-A
1 TTATTATATTTATTATT-TTATTCC
9523382 TTATTTATATCTTA-TATTTT
1 TTA-TTATAT-TTATTATTTT
9523402 TATCCTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
23 11 0.30
24 18 0.49
25 5 0.14
26 3 0.08
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.70
Consensus pattern (24 bp):
TTATTATATTTATTATTTTATTCC
Found at i:9523396 original size:20 final size:19
Alignment explanation
Indices: 9523278--9523391 Score: 71
Period size: 17 Copynumber: 6.0 Consensus size: 19
9523268 TGCAATTGTC
9523278 TATTATTTATT-TATTTATTAT
1 TATTA-TTATTAT-TTTA-TAT
*
9523299 TATTTAATTATTATTTT-CAT
1 TA-TT-ATTATTATTTTATAT
* *
9523319 T-TTATCA-TATTTTTTAT
1 TATTATTATTATTTTATAT
*
9523336 TATTA-TATT-TTTTATTT
1 TATTATTATTATTTTATAT
*
9523353 TATTCCTTATTATTTTATTAT
1 TATT-ATTATTATTTTA-TAT
9523374 TATTATTATTA-TTTATAT
1 TATTATTATTATTTTATAT
9523392 CTTATATTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
16 6 0.08
17 17 0.23
18 9 0.12
19 8 0.11
20 14 0.19
21 8 0.11
22 10 0.14
23 2 0.03
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTATTATTATTTTATAT
Found at i:9524304 original size:24 final size:25
Alignment explanation
Indices: 9524277--9524329 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
9524267 TATTTTCATT
*
9524277 TTTTTC-TTTATTATTTT-TTTATCA
1 TTTTTCATTCATT-TTTTCTTTATCA
*
9524301 -TTTTCATTCATTTTTTCTTTATGA
1 TTTTTCATTCATTTTTTCTTTATCA
9524325 TTTTT
1 TTTTT
9524330 AATTAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 9 0.38
24 11 0.46
25 4 0.17
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (25 bp):
TTTTTCATTCATTTTTTCTTTATCA
Found at i:9536447 original size:28 final size:28
Alignment explanation
Indices: 9536416--9536474 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
9536406 TTAATATTTT
* *
9536416 TTATTTTTTTATTACTTTAAGTTAAATA
1 TTATTTTTTTATTACTTTAAATCAAATA
*
9536444 TTATTTTTTTATTATTTTAAATCAAATA
1 TTATTTTTTTATTACTTTAAATCAAATA
9536472 TTA
1 TTA
9536475 ATATTCATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (28 bp):
TTATTTTTTTATTACTTTAAATCAAATA
Found at i:9537254 original size:113 final size:106
Alignment explanation
Indices: 9537105--9537479 Score: 346
Period size: 109 Copynumber: 3.4 Consensus size: 106
9537095 TCCAACTTTT
* *
9537105 AATAAA-ATATTAATATTAAAATATAAATAAAATATTAATATTTAAATTATCAATTATTAATA-A
1 AATAAACATAATAATATTTAAAT-TAAATAAAATATTAATATTTAAATTATCAATTATTAATATA
* ** *
9537168 AATAAATTATAAATTATTCCTATTTAAAAACAAAATAAATTAAAAATA
65 AATAAATTACAAATTATTAATATTT---AA-AAAATAAAAT-AAAA-A
* * *
9537216 AATAAACATAAT-ATCATTTAAATTAGATAAACAATATTAATAATTAAATCATCAATTATTAATA
1 AATAAACATAATAAT-ATTTAAATTAAAT-AA-AATATTAATATTTAAATTATCAATTATTAATA
*
9537280 TTTTAAATAAATTACCAATTATTAATATTTAAAAAATAAAATAAAAA
63 ---TAAATAAATTACAAATTATTAATATTTAAAAAATAAAATAAAAA
* ** *
9537327 ATTAGTCATAATAATATTTAAATTAAATAAAATATTAATATTTAAATTATCTATTATTAATATTT
1 AATAAACATAATAATATTTAAATTAAATAAAATATTAATATTTAAATTATCAATTATTAATA---
* * *
9537392 TAACTAAATAATC-AATTATTAAT-TTTCAAAAATAAAATAAAATAA
63 TAAATAAATTA-CAAATTATTAATATTTAAAAAATAAAAT-AAA-AA
*
9537437 AATAATTGATCATCATAATATTTAAATTAAATAAAATATTAAT
1 AATAA---A-CATAATAATATTTAAATTAAATAAAATATTAAT
9537480 NNNNNNNNNN
Statistics
Matches: 224, Mismatches: 24, Indels: 29
0.81 0.09 0.10
Matches are distributed among these distances:
108 14 0.06
109 54 0.24
110 8 0.04
111 34 0.15
112 19 0.08
113 39 0.17
114 34 0.15
117 22 0.10
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (106 bp):
AATAAACATAATAATATTTAAATTAAATAAAATATTAATATTTAAATTATCAATTATTAATATAA
ATAAATTACAAATTATTAATATTTAAAAAATAAAATAAAAA
Found at i:9537392 original size:109 final size:112
Alignment explanation
Indices: 9537115--9537479 Score: 408
Period size: 113 Copynumber: 3.2 Consensus size: 112
9537105 AATAAAATAT
*
9537115 TAATATTAAAATATAAATAAAATATTAATATTTAAATTATCAATTATTAATA----AAATAAATT
1 TAATATTTAAAT-TAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATT
* ** * * **
9537176 ATAAATTATTCCTATTTAAAAACAAAATAAATTAAAAATAAATAAACATAA
65 ATCAATTATTAATATTT--AAACAAAATAAAAT-AAAATAATTAGTCATAA
* * *
9537227 T-ATCATTTAAATTAGATAAACAATATTAATAATTAAATCATCAATTATTAATATTTTAAATAAA
1 TAAT-ATTTAAATTAAAT-AA-AATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAA
*
9537291 TTACCAATTATTAATATTT-AA-AAAATAAAATAAAA-AATTAGTCATAA
63 TTATCAATTATTAATATTTAAACAAAATAAAATAAAATAATTAGTCATAA
* * *
9537338 TAATATTTAAATTAAATAAAATATTAATATTTAAATTATCTATTATTAATATTTTAACTAAATAA
1 TAATATTTAAATTAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATTA
* *
9537403 TCAATTATTAAT-TTTCAAAAATAAAATAAAATAAAATAATT-GATCATCA
66 TCAATTATTAATATTT---AAACAAAATAAAATAAAATAATTAG-TCATAA
9537452 TAATATTTAAATTAAATAAAATATTAAT
1 TAATATTTAAATTAAATAAAATATTAAT
9537480 NNNNNNNNNN
Statistics
Matches: 218, Mismatches: 20, Indels: 28
0.82 0.08 0.11
Matches are distributed among these distances:
108 3 0.01
109 52 0.24
110 2 0.01
111 28 0.13
112 18 0.08
113 54 0.25
114 39 0.18
117 22 0.10
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.39
Consensus pattern (112 bp):
TAATATTTAAATTAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATTA
TCAATTATTAATATTTAAACAAAATAAAATAAAATAATTAGTCATAA
Found at i:9537424 original size:24 final size:26
Alignment explanation
Indices: 9537370--9537426 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
9537360 ATTAATATTT
* * *
9537370 AAATTATCTATTATTAATATTTTAAC
1 AAATAATCAATTATTAATATTTCAAC
9537396 TAAATAATCAATTATTAAT-TTTCAA-
1 -AAATAATCAATTATTAATATTTCAAC
9537421 AAATAA
1 AAATAA
9537427 AATAAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 6 0.22
26 5 0.19
27 16 0.59
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATAATCAATTATTAATATTTCAAC
Found at i:9537700 original size:25 final size:27
Alignment explanation
Indices: 9537654--9537705 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
9537644 AATATATTAT
*
9537654 ATTATTAATATTTTAATTAAAATTCTAG
1 ATTATTAATATTTTAA-TAAAAATCTAG
9537682 ATTATTAATATTTT-A-AAAAATCTA
1 ATTATTAATATTTTAATAAAAATCTA
9537706 ATAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
27 1 0.04
28 14 0.61
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (27 bp):
ATTATTAATATTTTAATAAAAATCTAG
Found at i:9538639 original size:28 final size:27
Alignment explanation
Indices: 9538600--9538673 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
9538590 GTCTTCCAAA
* *
9538600 ATTTTATAATTTTATAATTT-TTTTATT
1 ATTTTAAAATTTTATAATTTCGTTT-TT
* *
9538627 TTTTTAAAAATTTTATAGTTTCGTTTTT
1 ATTTT-AAAATTTTATAATTTCGTTTTT
*
9538655 ATTTTAAAATTTTAAAATT
1 ATTTTAAAATTTTATAATT
9538674 ACAAAAACTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 16 0.42
28 19 0.50
29 3 0.08
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (27 bp):
ATTTTAAAATTTTATAATTTCGTTTTT
Found at i:9538868 original size:18 final size:18
Alignment explanation
Indices: 9538834--9538876 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
9538824 ATTTGTAGCG
*
9538834 ATAAAATTAAAAAAAATT
1 ATAAAATAAAAAAAAATT
9538852 A-AAAATAAAAAAGAAATT
1 ATAAAATAAAAAA-AAATT
9538870 ATAAAAT
1 ATAAAAT
9538877 TTTGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 7 0.32
19 5 0.23
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
ATAAAATAAAAAAAAATT
Found at i:9539419 original size:28 final size:28
Alignment explanation
Indices: 9539388--9539520 Score: 130
Period size: 28 Copynumber: 4.8 Consensus size: 28
9539378 TGATATGATG
* *
9539388 TGTAATAAGTATAATTTTTAATATAACA
1 TGTAATAATTATAATTTTTAATATAATA
*
9539416 TGTAATAATT-TAATTTTTAAGATTTTTAATA
1 TGTAATAATTATAATTTTT-A-A--TATAATA
* * *
9539447 TATAATAATTATATTTTTTAATATGATA
1 TGTAATAATTATAATTTTTAATATAATA
* *
9539475 TATAATAATTA-AAATTTTAATATAATA
1 TGTAATAATTATAATTTTTAATATAATA
9539502 TGTAA-AATTAT-ATTTTTAA
1 TGTAATAATTATAATTTTTAA
9539521 CGTAATTTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
26 12 0.14
27 25 0.29
28 26 0.30
29 1 0.01
30 1 0.01
31 15 0.17
32 7 0.08
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.50
Consensus pattern (28 bp):
TGTAATAATTATAATTTTTAATATAATA
Found at i:9540407 original size:22 final size:24
Alignment explanation
Indices: 9540369--9540464 Score: 69
Period size: 20 Copynumber: 4.1 Consensus size: 24
9540359 TATCAAAAGA
9540369 TTAATATTTATAAAAATAAAAATT
1 TTAATATTTATAAAAATAAAAATT
*
9540393 TTAA-ATTT-TAAAAATTAAAA--
1 TTAATATTTATAAAAATAAAAATT
* *
9540413 TT-ATA-TTATAAAATTTAAAATT
1 TTAATATTTATAAAAATAAAAATT
**
9540435 AAACATATATTATAAAAATTTAAAAATT
1 TTA-ATAT-TTATAAAAA--TAAAAATT
9540463 TT
1 TT
9540465 GAAGTAGGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
19 3 0.06
20 14 0.26
22 11 0.20
23 4 0.07
24 7 0.13
26 8 0.15
28 7 0.13
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAATATTTATAAAAATAAAAATT
Found at i:9540432 original size:27 final size:27
Alignment explanation
Indices: 9540394--9540462 Score: 97
Period size: 26 Copynumber: 2.6 Consensus size: 27
9540384 ATAAAAATTT
*
9540394 TAAATTTTAAAAATTAAA-ATTATATTA
1 TAAAATTTAAAAATTAAACA-TATATTA
9540421 TAAAATTT-AAAATTAAACATATATTA
1 TAAAATTTAAAAATTAAACATATATTA
9540447 TAAAAATTTAAAAATT
1 T-AAAATTTAAAAATT
9540463 TTGAAGTAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
26 17 0.45
27 15 0.39
28 6 0.16
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAAATTTAAAAATTAAACATATATTA
Found at i:9540443 original size:26 final size:26
Alignment explanation
Indices: 9540394--9540459 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
9540384 ATAAAAATTT
*
9540394 TAAATTTTAAAAATTAAAATTATATTA
1 TAAAATTT-AAAATTAAAATTATATTA
9540421 TAAAATTTAAAATTAAACA-TATATTA
1 TAAAATTTAAAATTAAA-ATTATATTA
9540447 TAAAAATTTAAAA
1 T-AAAATTTAAAA
9540460 ATTTTGAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 17 0.47
27 19 0.53
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
TAAAATTTAAAATTAAAATTATATTA
Found at i:9542937 original size:43 final size:43
Alignment explanation
Indices: 9542848--9542973 Score: 180
Period size: 43 Copynumber: 2.9 Consensus size: 43
9542838 AAAAAGCTCA
* *
9542848 TCATCTGGAATGAGGCTATATCACTTTAAAAATGAATAAATTCC
1 TCATCTAGAATGAGGCTATATCACTTT-AAAATGAATAAACTCC
* *
9542892 TCATCTAGAATGAGGTTATGTCACTTTAAAATGAATAAACTCC
1 TCATCTAGAATGAGGCTATATCACTTTAAAATGAATAAACTCC
* * *
9542935 TCATCTAGAATAAGGCTATATAACTTTAAGATGAATAAA
1 TCATCTAGAATGAGGCTATATCACTTTAAAATGAATAAA
9542974 GGCTCTTCAT
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
43 49 0.67
44 24 0.33
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.32
Consensus pattern (43 bp):
TCATCTAGAATGAGGCTATATCACTTTAAAATGAATAAACTCC
Found at i:9543119 original size:23 final size:23
Alignment explanation
Indices: 9543086--9543397 Score: 108
Period size: 23 Copynumber: 13.5 Consensus size: 23
9543076 ATAGAATTTG
*
9543086 AAAATGATTACTCAGAGGTTTTA
1 AAAATGGTTACTCAGAGGTTTTA
*
9543109 AAAATGGTTACTCGGAGGTTTTGA
1 AAAATGGTTACTCAGAGGTTTT-A
* * * * *
9543133 TAAATAGTTACCCAGAAGATGTTGA
1 AAAATGGTTACTCAG-AGGT-TTTA
* * *
9543158 AATAT-G-TACTC-GAAGGATTTG
1 AAAATGGTTACTCAG-AGGTTTTA
* *
9543179 AAAATGATTACTCAGAGGTCTTA
1 AAAATGGTTACTCAGAGGTTTTA
* * * *
9543202 AAAATGATTAC-CTAAAGGTTCTG
1 AAAATGGTTACTC-AGAGGTTTTA
* *
9543225 AAAATGGTTAC-CCGAAGGTTTTT
1 AAAATGGTTACTCAG-AGGTTTTA
*
9543248 AAAATGGTTGCTC-GAAGGTTTTGA
1 AAAATGGTTACTCAG-AGGTTTT-A
* * **
9543272 AATATGGTTAAC-CTGAGCATTTA
1 AAAATGGTT-ACTCAGAGGTTTTA
* * * *
9543295 AAAGAT-G-TGCTCGGAGGATTTG
1 AAA-ATGGTTACTCAGAGGTTTTA
* * *
9543317 AAAATGATTACTC-GAACGTTTTG
1 AAAATGGTTACTCAG-AGGTTTTA
* * *
9543340 AAAATGGTTAC-CTAAAGATTTTG
1 AAAATGGTTACTC-AGAGGTTTTA
*
9543363 AAAATGGTTACTC-GACTGTTTTGA
1 AAAATGGTTACTCAGA-GGTTTT-A
9543387 AAAATGGTTAC
1 AAAATGGTTAC
9543398 CTGAAGGATT
Statistics
Matches: 215, Mismatches: 52, Indels: 43
0.69 0.17 0.14
Matches are distributed among these distances:
21 9 0.04
22 20 0.09
23 132 0.61
24 43 0.20
25 9 0.04
26 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (23 bp):
AAAATGGTTACTCAGAGGTTTTA
Found at i:9543352 original size:138 final size:139
Alignment explanation
Indices: 9543084--9543397 Score: 352
Period size: 138 Copynumber: 2.3 Consensus size: 139
9543074 CCATAGAATT
* * * *
9543084 TGAAAATGATTACTCAGAGGTTTTAAAAATGGTTACTCGGAGGTTTTGATAAATAGTTACCCAGA
1 TGAAAATGGTTACCCAGAGGTTTTAAAAATGGTTACTCGAAGGTTTTGATAAATAGTTAACCAGA
* * *
9543149 AGATGTTGAAATATGTACTCGAAGGATTTGAAAATGATTACTCAGAGGTCTTAAAAATGATTACC
66 AGATGTTAAAAGATGTACTCGAAGGATTTGAAAATGATTACTCAGACGTCTTAAAAATGATTACC
*
9543214 TAAAGGTTC
131 TAAAGATTC
* * * *
9543223 TGAAAATGGTTACCC-GAAGGTTTTTAAAATGGTTGCTCGAAGGTTTTGA-AATATGGTTAACCT
1 TGAAAATGGTTACCCAG-AGGTTTTAAAAATGGTTACTCGAAGGTTTTGATAA-ATAGTTAACCA
* * * * *
9543286 G-AGCAT-TTAAAAGATGTGCTCGGAGGATTTGAAAATGATTACTC-GAACGTTTTGAAAATGGT
64 GAAG-ATGTTAAAAGATGTACTCGAAGGATTTGAAAATGATTACTCAG-ACGTCTTAAAAATGAT
*
9543348 TACCTAAAGATTT
127 TACCTAAAGATTC
* *
9543361 TGAAAATGGTTACTC-GACTGTTTTGAAAAATGGTTAC
1 TGAAAATGGTTACCCAGA-GGTTTT-AAAAATGGTTAC
9543398 CTGAAGGATT
Statistics
Matches: 147, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
137 2 0.01
138 82 0.56
139 63 0.43
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (139 bp):
TGAAAATGGTTACCCAGAGGTTTTAAAAATGGTTACTCGAAGGTTTTGATAAATAGTTAACCAGA
AGATGTTAAAAGATGTACTCGAAGGATTTGAAAATGATTACTCAGACGTCTTAAAAATGATTACC
TAAAGATTC
Found at i:9543363 original size:46 final size:48
Alignment explanation
Indices: 9543313--9543408 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 48
9543303 GCTCGGAGGA
9543313 TTTGAAAATGATTACTCGAAC-GTTTTG-AAAATGGTTACCT-AAAGAT
1 TTTGAAAATGATTACTCG-ACTGTTTTGAAAAATGGTTACCTGAAAGAT
* *
9543359 TTTGAAAATGGTTACTCGACTGTTTTGAAAAATGGTTACCTGAAGGAT
1 TTTGAAAATGATTACTCGACTGTTTTGAAAAATGGTTACCTGAAAGAT
9543407 TT
1 TT
9543409 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
45 2 0.04
46 23 0.51
47 13 0.29
48 7 0.16
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.36
Consensus pattern (48 bp):
TTTGAAAATGATTACTCGACTGTTTTGAAAAATGGTTACCTGAAAGAT
Found at i:9543413 original size:24 final size:24
Alignment explanation
Indices: 9543340--9543436 Score: 76
Period size: 23 Copynumber: 4.1 Consensus size: 24
9543330 GAACGTTTTG
**
9543340 AAAATGGTTACCT-AAAGATTTTG
1 AAAATGGTTACCTGAAAGATTTAA
** * *
9543363 AAAATGGTTA-CTCGACTGTTTTGA
1 AAAATGGTTACCT-GAAAGATTTAA
*
9543387 AAAATGGTTACCTGAAGGATTTAA
1 AAAATGGTTACCTGAAAGATTTAA
*
9543411 AAAGAT-G-TACCTGAAAGATATAA
1 AAA-ATGGTTACCTGAAAGATTTAA
9543434 AAA
1 AAA
9543437 TGATTACTAT
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
22 2 0.03
23 27 0.46
24 26 0.44
25 4 0.07
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (24 bp):
AAAATGGTTACCTGAAAGATTTAA
Found at i:9565108 original size:24 final size:23
Alignment explanation
Indices: 9565081--9565126 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
9565071 TACTTAACAA
*
9565081 GATTGCCTAAAGGATTTGAAAGAG
1 GATTACCTAAAGGATTT-AAAGAG
* *
9565105 GATTACTTGAAGGATTTAAAGA
1 GATTACCTAAAGGATTTAAAGA
9565127 TGTATCTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.28
Consensus pattern (23 bp):
GATTACCTAAAGGATTTAAAGAG
Found at i:9568225 original size:67 final size:67
Alignment explanation
Indices: 9568154--9568325 Score: 222
Period size: 66 Copynumber: 2.6 Consensus size: 67
9568144 TAATCGTGGT
* * * *
9568154 AAAAACCATTGTTATAGGTTGTGGTTGAGCCTTGGAAAAACCACTTTGGGTTTTAGTTTAGGTCG
1 AAAAACCATTGTTAAAGGTTGTGGTTGAGCCTTGGAAAAACAACTTTGGGTTTTAGTTGAGCTCG
9568219 TG
66 TG
* * * * *
9568221 AAAAACTAGTGTAAAAGGTTGTGGTTGAGCCTT-GAAAAACAACTTTGGGTTTTGGTTGATCTCG
1 AAAAACCATTGTTAAAGGTTGTGGTTGAGCCTTGGAAAAACAACTTTGGGTTTTAGTTGAGCTCG
9568285 TG
66 TG
**
9568287 AAAAACCATTACTAAAGGTTGTGGTTGAG-CTTGCGAAAA
1 AAAAACCATTGTTAAAGGTTGTGGTTGAGCCTTG-GAAAA
9568326 GCCATTGTAA
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
65 3 0.03
66 52 0.58
67 34 0.38
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.33
Consensus pattern (67 bp):
AAAAACCATTGTTAAAGGTTGTGGTTGAGCCTTGGAAAAACAACTTTGGGTTTTAGTTGAGCTCG
TG
Found at i:9568287 original size:66 final size:66
Alignment explanation
Indices: 9568132--9568325 Score: 216
Period size: 66 Copynumber: 2.9 Consensus size: 66
9568122 AAGTTGGTTG
* * * *
9568132 TTGGGTTTTGGTTAATCGTGGT-AAAAACCATTGTTATAGGTTGTGGTTGAGCCTTGGAAAAACC
1 TTGGGTTTTGGTTAATC-TCGTGAAAAACCA-TGTAAAAGGTTGTGGTTGAGCCTTGGAAAAACA
9568196 ACT
64 ACT
* * ** *
9568199 TTGGGTTTTAGTTTAGGTCGTGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCTT-GAAAAACAA
1 TTGGGTTTTGGTTAATCTCGTGAAAAACCA-TGTAAAAGGTTGTGGTTGAGCCTTGGAAAAACAA
9568263 CT
65 CT
*
9568265 TTGGGTTTTGGTTGATCTCGTGAAAAACCAT-TACTAAAGGTTGTGGTTGAG-CTTGCGAAAA
1 TTGGGTTTTGGTTAATCTCGTGAAAAACCATGTA--AAAGGTTGTGGTTGAGCCTTG-GAAAA
9568326 GCCATTGTAA
Statistics
Matches: 107, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
64 2 0.02
65 4 0.04
66 54 0.50
67 47 0.44
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (66 bp):
TTGGGTTTTGGTTAATCTCGTGAAAAACCATGTAAAAGGTTGTGGTTGAGCCTTGGAAAAACAAC
T
Found at i:9569972 original size:2 final size:2
Alignment explanation
Indices: 9569965--9570011 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
9569955 ACAAAAATGC
9569965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9570007 AT AT A
1 AT AT A
9570012 ATAAGTNATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9570114 original size:2 final size:2
Alignment explanation
Indices: 9570107--9570148 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
9570097 ACAAAAATGC
9570107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9570149 GTAGAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9570128 original size:142 final size:141
Alignment explanation
Indices: 9569877--9570148 Score: 535
Period size: 142 Copynumber: 1.9 Consensus size: 141
9569867 CCTATAAAAC
9569877 ATATTTTTTTTGTGTCAAATTTTATCTTGTTCGTAATAAAATCATTATATGATGTTATTGATAAA
1 ATATTTTTTTTGTGTCAAATTTTATCTTGTTCGTAATAAAATCATTATATGATGTTATTGATAAA
9569942 GTTAACATATAGCACAAAAATGCATATATATATATATATATATATATATATATATATATATATAT
66 GTTAACATATAGCACAAAAATGCATATATATATATATATATATATATATATATATATATATATAT
9570007 ATATAATAAGT
131 ATATAATAAGT
9570018 NATATTTTTTTTGTGTCAAATTTTATCTTGTTCGTAATAAAATCATTATATGATGTTATTGATAA
1 -ATATTTTTTTTGTGTCAAATTTTATCTTGTTCGTAATAAAATCATTATATGATGTTATTGATAA
9570083 AGTTAACATATAGCACAAAAATGCATATATATATATATATATATATATATATATATATATATATA
65 AGTTAACATATAGCACAAAAATGCATATATATATATATATATATATATATATATATATATATATA
9570148 T
130 T
9570149 GTAGAAAAAA
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 130 1.00
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (141 bp):
ATATTTTTTTTGTGTCAAATTTTATCTTGTTCGTAATAAAATCATTATATGATGTTATTGATAAA
GTTAACATATAGCACAAAAATGCATATATATATATATATATATATATATATATATATATATATAT
ATATAATAAGT
Found at i:9578861 original size:17 final size:17
Alignment explanation
Indices: 9578836--9578873 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
9578826 AATTGTATTT
*
9578836 AAAATATATAAAAATTA
1 AAAAAATATAAAAATTA
*
9578853 AAAAAATATAAAAGTTA
1 AAAAAATATAAAAATTA
9578870 AAAA
1 AAAA
9578874 TAATTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAAAATATAAAAATTA
Found at i:9579722 original size:30 final size:30
Alignment explanation
Indices: 9579688--9579745 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
9579678 GTTAACGAAA
9579688 AGATTCAAAATGATCATAGAAATCATGAAG
1 AGATTCAAAATGATCATAGAAATCATGAAG
9579718 AGATTCAAAATGATCATAGAAATCATGA
1 AGATTCAAAATGATCATAGAAATCATGA
9579746 TGAAGAGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.24
Consensus pattern (30 bp):
AGATTCAAAATGATCATAGAAATCATGAAG
Found at i:9587064 original size:6 final size:5
Alignment explanation
Indices: 9587026--9587063 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
9587016 TTAATATTAA
9587026 AAAAT AAAAT AAAAT AAAAT -AAAT AATAAT AATAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AA-AAT AA
9587064 TTCAATATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.13
5 16 0.52
6 11 0.35
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:9587194 original size:12 final size:12
Alignment explanation
Indices: 9587114--9587203 Score: 73
Period size: 12 Copynumber: 7.7 Consensus size: 12
9587104 AAAATGAAAA
*
9587114 AATAAAAAATAT
1 AATAAATAATAT
*
9587126 -ATATAATAAAAT
1 AATA-AATAATAT
*
9587138 AAAAAATAATGAT
1 AATAAATAAT-AT
* *
9587151 GAT-AATAAAAT
1 AATAAATAATAT
9587162 AA-AAA-AATA-
1 AATAAATAATAT
9587171 AATAAATAAATAT
1 AATAAAT-AATAT
9587184 AATAAATAATAT
1 AATAAATAATAT
9587196 AATAAATA
1 AATAAATA
9587204 TTTGAGTATT
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
9 2 0.03
10 6 0.10
11 8 0.13
12 33 0.54
13 12 0.20
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (12 bp):
AATAAATAATAT
Found at i:9587204 original size:21 final size:21
Alignment explanation
Indices: 9587112--9587201 Score: 103
Period size: 21 Copynumber: 4.1 Consensus size: 21
9587102 AAAAAATGAA
9587112 AAAATAAAAAATATATATAAT
1 AAAATAAAAAATATATATAAT
9587133 AAAATAAAAAATAATGATGATAAT
1 AAAATAAAAAAT-AT-AT-ATAAT
*
9587157 AAAATAAAAAA-ATAAATAAAT
1 AAAATAAAAAATATATAT-AAT
*
9587178 AAATATAATAAATA-ATATAAT
1 AAA-ATAAAAAATATATATAAT
9587199 AAA
1 AAA
9587202 TATTTGAGTA
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
20 2 0.03
21 25 0.42
22 14 0.23
23 3 0.05
24 16 0.27
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAATAAAAAATATATATAAT
Found at i:9592070 original size:5 final size:5
Alignment explanation
Indices: 9592060--9592087 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
9592050 TATGCTTCAG
9592060 TTTTC TTTTC TTTTC TTTTC TTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTT
9592088 CTGTCTCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:9593909 original size:19 final size:20
Alignment explanation
Indices: 9593882--9593927 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
9593872 AGGAGACAAG
*
9593882 ATAAAATTTTTA-AAATAAA
1 ATAATATTTTTATAAATAAA
*
9593901 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATAAATAAA
9593920 ATAATATT
1 ATAATATT
9593928 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATAAATAAA
Found at i:9609692 original size:116 final size:116
Alignment explanation
Indices: 9609488--9609717 Score: 370
Period size: 116 Copynumber: 2.0 Consensus size: 116
9609478 GTTCTTTAAG
* * * * *
9609488 TATACAAGACAAAATCTTAATTTGGTCTTGTGTAAAATTAATGAAATGGGAACATTTCCCATAGC
1 TATACAAGACAAAATCTTAATTTCGTCTTGTGCAAAATTAATGAAATAGAAACATTTCCCATAGA
* * * *
9609553 ATTTTATGTTTAATGGTTCATATACGTCTATATGTATGAGACCTTTAAACA
66 ATTTTATGTTTAATGGTTCATATACATCTAGATGTATAAGACATTTAAACA
*
9609604 TATACAAGACAAAATCTTAATTTCGTCTTGTGCAAAATTAATGAAATAGAAACATTTCCGATAGA
1 TATACAAGACAAAATCTTAATTTCGTCTTGTGCAAAATTAATGAAATAGAAACATTTCCCATAGA
9609669 ATTTTATGTTTAATGGTTCATATACATCTAGATGTATAAGACATTTAAA
66 ATTTTATGTTTAATGGTTCATATACATCTAGATGTATAAGACATTTAAA
9609718 ACGTACCAAA
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
116 104 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (116 bp):
TATACAAGACAAAATCTTAATTTCGTCTTGTGCAAAATTAATGAAATAGAAACATTTCCCATAGA
ATTTTATGTTTAATGGTTCATATACATCTAGATGTATAAGACATTTAAACA
Found at i:9613909 original size:13 final size:13
Alignment explanation
Indices: 9613891--9613920 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
9613881 ATTCAATAAG
9613891 TGTTAACATTAAA
1 TGTTAACATTAAA
*
9613904 TGTTAACATTAGA
1 TGTTAACATTAAA
9613917 TGTT
1 TGTT
9613921 GCTATTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (13 bp):
TGTTAACATTAAA
Found at i:9619132 original size:101 final size:101
Alignment explanation
Indices: 9618932--9619125 Score: 334
Period size: 101 Copynumber: 1.9 Consensus size: 101
9618922 ACTTTTAAAA
* *
9618932 AAATACTCTTTTAAATTATTGTTTGTTGTAGTGTATCAAAATGTTTATTGTTGTGGAGTTACGGA
1 AAATACTCTTTTAAATTATTGTTTGTTGTAGTGTATCAAAATGTTTATTGTTATGGAGTTACAGA
9618997 AGCGATGACGACATATGTTTAGTACATAAATTTTTT
66 AGCGATGACGACATATGTTTAGTACATAAATTTTTT
* *
9619033 AAATACTTTTTTAAATTATTGTTTGTTGTAGTGTATCAAAATGTTTATTGTTATGTAGTTACAGA
1 AAATACTCTTTTAAATTATTGTTTGTTGTAGTGTATCAAAATGTTTATTGTTATGGAGTTACAGA
* *
9619098 AGTGATGATGACATATGTTTAGTACATA
66 AGCGATGACGACATATGTTTAGTACATA
9619126 CTTTTTTGAA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 87 1.00
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (101 bp):
AAATACTCTTTTAAATTATTGTTTGTTGTAGTGTATCAAAATGTTTATTGTTATGGAGTTACAGA
AGCGATGACGACATATGTTTAGTACATAAATTTTTT
Found at i:9620161 original size:35 final size:35
Alignment explanation
Indices: 9620105--9620175 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
9620095 ATTTAGTACA
* *
9620105 TAAATTTTTAAAATACTCTTTTATATTATTATTTG
1 TAAATTTTTAAAATACCCTTTTAAATTATTATTTG
* * *
9620140 TAAATTTTTTACATACCCTTTTAAATTATTGTTTG
1 TAAATTTTTAAAATACCCTTTTAAATTATTATTTG
9620175 T
1 T
9620176 TGTAGTGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.56
Consensus pattern (35 bp):
TAAATTTTTAAAATACCCTTTTAAATTATTATTTG
Found at i:9620814 original size:38 final size:40
Alignment explanation
Indices: 9620772--9620874 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 40
9620762 ATAGTGCCCG
*
9620772 TGTGCACGATGTGGGGGGATGTACACGATAG-CACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATAGTCACGGATA
* * * * ** *
9620810 TGTGCACGATGTGGGTGGATGCACATGATGGTGTCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATAGTCACGGATA
9620850 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
9620875 TGAGCCGGGA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 27 0.51
39 3 0.06
40 23 0.43
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATAGTCACGGATA
Found at i:9624523 original size:2 final size:2
Alignment explanation
Indices: 9624516--9624541 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9624506 NNNNTGCAAC
9624516 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
9624542 GTGTGTGTGT
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:9647257 original size:19 final size:19
Alignment explanation
Indices: 9647233--9647276 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
9647223 GCATTTTTTG
* * *
9647233 TTTTTGTTTTTGTTCTTCT
1 TTTTTGTGTTTGTCCTCCT
9647252 TTTTTGTGTTTGTCCTCCT
1 TTTTTGTGTTTGTCCTCCT
9647271 TTTTTG
1 TTTTTG
9647277 CAGGTGCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.73
Consensus pattern (19 bp):
TTTTTGTGTTTGTCCTCCT
Found at i:9647409 original size:11 final size:11
Alignment explanation
Indices: 9647390--9647437 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
9647380 TTGGGAACTT
9647390 GATGG-GAAGG
1 GATGGTGAAGG
9647400 GATGGTGAAGG
1 GATGGTGAAGG
* *
9647411 AATGGTGAGGG
1 GATGGTGAAGG
*
9647422 GATGGGGAAGG
1 GATGGTGAAGG
9647433 GATGG
1 GATGG
9647438 CTGGGCGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 5 0.16
11 27 0.84
ACGTcount: A:0.27, C:0.00, G:0.58, T:0.15
Consensus pattern (11 bp):
GATGGTGAAGG
Found at i:9650779 original size:33 final size:33
Alignment explanation
Indices: 9650740--9650807 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
9650730 GTAAAATGAT
9650740 ATCATGGTATTAGTACAATTAATTGCATTTCCC
1 ATCATGGTATTAGTACAATTAATTGCATTTCCC
9650773 ATCATGGTATTAGTACAATTAATTGCATTTCCC
1 ATCATGGTATTAGTACAATTAATTGCATTTCCC
9650806 AT
1 AT
9650808 TGCATGAGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.40
Consensus pattern (33 bp):
ATCATGGTATTAGTACAATTAATTGCATTTCCC
Found at i:9651260 original size:18 final size:18
Alignment explanation
Indices: 9651237--9651278 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
9651227 GGTTCTTTCC
9651237 CATTAACATTGCACTGTT
1 CATTAACATTGCACTGTT
* *
9651255 CATTAACTTTTCACTGTT
1 CATTAACATTGCACTGTT
*
9651273 TATTAA
1 CATTAA
9651279 TGTCTCTAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (18 bp):
CATTAACATTGCACTGTT
Found at i:9652426 original size:20 final size:20
Alignment explanation
Indices: 9652389--9652427 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9652379 CAAAAAAAGA
*
9652389 TATATAGTAAATAGTTCTTG
1 TATATAGTAAATAATTCTTG
* *
9652409 TATATATTAATTAATTCTT
1 TATATAGTAAATAATTCTT
9652428 CATTATTAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (20 bp):
TATATAGTAAATAATTCTTG
Found at i:9655009 original size:23 final size:24
Alignment explanation
Indices: 9654981--9655036 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
9654971 AGTATTCATT
9654981 TTATTTATT-ATAATTTTT-TAATA
1 TTATTTATTAAT-ATTTTTGTAATA
9655004 TTATTT-TTAATATTTTTGTAATA
1 TTATTTATTAATATTTTTGTAATA
9655027 TTGATTTATT
1 TT-ATTTATT
9655037 TTAAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.28
23 15 0.52
24 4 0.14
25 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (24 bp):
TTATTTATTAATATTTTTGTAATA
Found at i:9655012 original size:12 final size:12
Alignment explanation
Indices: 9654995--9655033 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
9654985 TTATTATAAT
9654995 TTTTTAATATTA
1 TTTTTAATATTA
9655007 TTTTTAATATT-
1 TTTTTAATATTA
*
9655018 TTTGTAATATTGA
1 TTTTTAATATT-A
9655031 TTT
1 TTT
9655034 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 10 0.42
12 11 0.46
13 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (12 bp):
TTTTTAATATTA
Found at i:9665359 original size:25 final size:24
Alignment explanation
Indices: 9665322--9665375 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
9665312 TGTTTAAAAA
*
9665322 TTTTTTTGATTATTTATTA-TTTAT
1 TTTTTTTGATTATATA-TACTTTAT
9665346 TATTTTTT-ACTTATATATACTTTAT
1 T-TTTTTTGA-TTATATATACTTTAT
9665371 TTTTT
1 TTTTT
9665376 GGTTTTCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (24 bp):
TTTTTTTGATTATATATACTTTAT
Found at i:9665723 original size:11 final size:11
Alignment explanation
Indices: 9665709--9665741 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
9665699 ATTCAAATTA
9665709 TATTATTTATT
1 TATTATTTATT
9665720 TATTATTTATT
1 TATTATTTATT
9665731 TATTA-TTATT
1 TATTATTTATT
9665741 T
1 T
9665742 TTTGATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTATTTATT
Found at i:9681358 original size:3 final size:3
Alignment explanation
Indices: 9681339--9681372 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
9681329 ATAATTTAAA
9681339 ATT ATTT ATT AATT ATT ATT ATT ATT ATT ATT AT
1 ATT A-TT ATT -ATT ATT ATT ATT ATT ATT ATT AT
9681373 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:9681690 original size:63 final size:65
Alignment explanation
Indices: 9681570--9681702 Score: 166
Period size: 63 Copynumber: 2.1 Consensus size: 65
9681560 CAAAAAACAA
* * * *
9681570 TTTTAAATTTTTTATAACTTATTTTTATACTTTTAAAATTTTATAATTCCGTCTTTACAA-AATT
1 TTTTAAATTTTTTACAACATATTTTTATACTTTTAAAATTTTAAAATTACGTCTTTACAATAATT
**
9681634 TTTTAAATTTTTT-CAACATATTTTTATTTTTTTAAAATTTTAAAATTTTAC-T-TTTACAATAA
1 TTTTAAATTTTTTACAACATATTTTTATACTTTTAAAATTTTAAAA--TTACGTCTTTACAATAA
9681696 TT
64 TT
9681698 TTTTA
1 TTTTA
9681703 TTTGATGAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
63 34 0.57
64 23 0.38
65 3 0.05
ACGTcount: A:0.33, C:0.08, G:0.01, T:0.59
Consensus pattern (65 bp):
TTTTAAATTTTTTACAACATATTTTTATACTTTTAAAATTTTAAAATTACGTCTTTACAATAATT
Found at i:9683491 original size:21 final size:20
Alignment explanation
Indices: 9683453--9683492 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
9683443 TTGGCTGAAA
*
9683453 AAAAATTGCAGTCATAGGTG
1 AAAAATTGCAGCCATAGGTG
*
9683473 AAAAATATGCAGCCTTAGGT
1 AAAAAT-TGCAGCCATAGGT
9683493 TAAGGCTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (20 bp):
AAAAATTGCAGCCATAGGTG
Found at i:9686416 original size:2 final size:2
Alignment explanation
Indices: 9686409--9686436 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9686399 TTTAAAATTC
9686409 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
9686437 GAGTATATCT
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:9689360 original size:8 final size:8
Alignment explanation
Indices: 9689347--9689389 Score: 52
Period size: 9 Copynumber: 5.1 Consensus size: 8
9689337 CTTAGCTTAA
9689347 ATAAAAAT
1 ATAAAAAT
9689355 ATAAAAAT
1 ATAAAAAT
9689363 AATAAAAAT
1 -ATAAAAAT
9689372 A-AAAATAT
1 ATAAAA-AT
9689380 ATAAATAAT
1 ATAAA-AAT
9689389 A
1 A
9689390 ACAATAACGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 4 0.13
8 12 0.39
9 14 0.45
10 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
ATAAAAAT
Found at i:9689372 original size:23 final size:23
Alignment explanation
Indices: 9689345--9689396 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
9689335 TGCTTAGCTT
9689345 AAATAAAAATATAAAAATAATAA
1 AAATAAAAATATAAAAATAATAA
*
9689368 AAATAAAAATATATAAATAATAA
1 AAATAAAAATATAAAAATAATAA
*
9689391 CAATAA
1 AAATAA
9689397 CGATAATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (23 bp):
AAATAAAAATATAAAAATAATAA
Found at i:9689390 original size:17 final size:16
Alignment explanation
Indices: 9689345--9689396 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 16
9689335 TGCTTAGCTT
9689345 AAATAA-AAAT-ATAA
1 AAATAATAAATAATAA
9689359 AAATAATAAA-AATAA
1 AAATAATAAATAATAA
9689374 AAATATATAAATAATAA
1 AAATA-ATAAATAATAA
*
9689391 CAATAA
1 AAATAA
9689397 CGATAATAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.18
15 12 0.36
16 6 0.18
17 9 0.27
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAATAAATAATAA
Found at i:9689498 original size:7 final size:7
Alignment explanation
Indices: 9689496--9689544 Score: 55
Period size: 7 Copynumber: 6.6 Consensus size: 7
9689486 ATAAATAATA
9689496 AATAAAT
1 AATAAAT
9689503 AATAAAT
1 AATAAAT
9689510 AAATAAAT
1 -AATAAAT
9689518 AATGAAA-
1 AAT-AAAT
9689525 AATAATAAT
1 AAT-A-AAT
9689534 AATAAAT
1 AATAAAT
9689541 AATA
1 AATA
9689545 TAATTGGAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
7 21 0.57
8 13 0.35
9 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (7 bp):
AATAAAT
Found at i:9689499 original size:4 final size:4
Alignment explanation
Indices: 9689481--9689547 Score: 58
Period size: 4 Copynumber: 18.2 Consensus size: 4
9689471 TCATGATGCG
* *
9689481 AATA TATA AAT- AATA AATA AAT- AATA AATA AATA AAT- AATG AA-A
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
9689525 AAT- AAT- AAT- AATA AATA ATATA A
1 AATA AATA AATA AATA AATA A-ATA A
9689548 TTGGAACAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
3 20 0.37
4 30 0.56
5 4 0.07
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:9689504 original size:15 final size:14
Alignment explanation
Indices: 9689489--9689548 Score: 79
Period size: 15 Copynumber: 4.2 Consensus size: 14
9689479 CGAATATATA
9689489 AATAATAAATAAAT
1 AATAATAAATAAAT
9689503 AATAAATAAATAAAT
1 AAT-AATAAATAAAT
9689518 AATGAA-AAAT-AAT
1 AAT-AATAAATAAAT
9689531 AATAATAAATAATAT
1 AATAATAAATAA-AT
9689546 AAT
1 AAT
9689549 TGGAACAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
12 2 0.05
13 10 0.24
14 8 0.20
15 21 0.51
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (14 bp):
AATAATAAATAAAT
Done.