Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167826.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_1, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 36299135
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 357000 characters in sequence are not A, C, G, or T
File 14 of 402
Found at i:3145066 original size:397 final size:397
Alignment explanation
Indices: 3144333--3145128 Score: 1405
Period size: 397 Copynumber: 2.0 Consensus size: 397
3144323 TAGGTTGAAT
3144333 TAACACATCACCTACTTGGATGTTTCGTTTCTATCATATACTTGTTGCATCCAAGTTGAACCTTT
1 TAACACATCACCTACTTGGATGTTTCGTTTCTATCATATACTTGTTGCATCCAAGTTGAACCTTT
3144398 AATACCGACATTAGAGAACATGGATGAACTGTCCTATTAACACTTCTTTTGGGTCAAGCAACCTC
66 AATACCGACATTAGAGAACATGGATGAACTGTCCTATTAACACTTCTTTTGGGTCAAGCAACCTC
** * * *
3144463 ACATCTCTAGTGGGCTTTCGGGGCAGGCCATAACACTTAATCTTGCCACTTAGGTTATCTCAGTG
131 ACATCTCTAGTAAGCTTTCGGGGCAGGCCATAACACTTAATCTTGCCACCTAGATTATCTCAATG
*
3144528 TTCCTTCAAGCTTACACTCTAGATTGACTTAACACATCACCTACTTGGATGTTTCATTTCTATCA
196 CTCCTTCAAGCTTACACTCTAGATTGACTTAACACATCACCTACTTGGATGTTTCATTTCTATCA
3144593 TATACTTGTTGCATCCAAGTTGAACATTTAATACCGACATTAGAAAACATGGATGAACCTTTAAT
261 TATACTTGTTGCATCCAAGTTGAACATTTAATACCGACATTAGAAAACATGGATGAACCTTTAAT
* * * * *
3144658 GCTGATGTTTGAATACATGGAGTTGATGGATGTGGTTAATCTTCAATCTGCCAATAATCTTCCTT
326 GATGATGTTTGAATACATGAAATTGATGGATGTGGTTAACCTTCAATCTGCCAACAATC-TCCTT
3144723 -CCAACAA
390 CCCAACAA
3144730 TAACACATCACCTACTTGGATGTTTCGTTTCTATCATATACTTGTTGCATCCAAGTTGAACCTTT
1 TAACACATCACCTACTTGGATGTTTCGTTTCTATCATATACTTGTTGCATCCAAGTTGAACCTTT
*
3144795 AATACCGACATTAGAGAACATGGATGAACTGTCCTATTAACACTTCTTTTGGGTCAAGTAACCTC
66 AATACCGACATTAGAGAACATGGATGAACTGTCCTATTAACACTTCTTTTGGGTCAAGCAACCTC
* * *
3144860 ACATCTCTAGTAAGCTTTCGGGGCAGGCCATAGCACTTAATCTTGCCACCTAGATTGTTTCAATG
131 ACATCTCTAGTAAGCTTTCGGGGCAGGCCATAACACTTAATCTTGCCACCTAGATTATCTCAATG
* *
3144925 CTCCTTCAATCTTACACTCTAGGTTGACTTAACACATCACCTACTTGGATGTTTCATTTCTATCA
196 CTCCTTCAAGCTTACACTCTAGATTGACTTAACACATCACCTACTTGGATGTTTCATTTCTATCA
* *
3144990 TATACTTGTTGCATCCAAGTTGAACATTTAATATCGACATTAGAGAACATGGATGAACCTTTAAT
261 TATACTTGTTGCATCCAAGTTGAACATTTAATACCGACATTAGAAAACATGGATGAACCTTTAAT
3145055 GATGATGTTTGAATACATGAAATTGATGGATGTGGTTAACCTTCAATCTGCCAACAATCTCCTTC
326 GATGATGTTTGAATACATGAAATTGATGGATGTGGTTAACCTTCAATCTGCCAACAATCTCCTTC
3145120 CCAACAA
391 CCAACAA
3145127 TA
1 TA
3145129 TTATTGGGAC
Statistics
Matches: 379, Mismatches: 19, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
396 5 0.01
397 374 0.99
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (397 bp):
TAACACATCACCTACTTGGATGTTTCGTTTCTATCATATACTTGTTGCATCCAAGTTGAACCTTT
AATACCGACATTAGAGAACATGGATGAACTGTCCTATTAACACTTCTTTTGGGTCAAGCAACCTC
ACATCTCTAGTAAGCTTTCGGGGCAGGCCATAACACTTAATCTTGCCACCTAGATTATCTCAATG
CTCCTTCAAGCTTACACTCTAGATTGACTTAACACATCACCTACTTGGATGTTTCATTTCTATCA
TATACTTGTTGCATCCAAGTTGAACATTTAATACCGACATTAGAAAACATGGATGAACCTTTAAT
GATGATGTTTGAATACATGAAATTGATGGATGTGGTTAACCTTCAATCTGCCAACAATCTCCTTC
CCAACAA
Found at i:3146118 original size:41 final size:41
Alignment explanation
Indices: 3146039--3146118 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
3146029 TCTGATCTGC
*
3146039 CAACAATCTCTCCCTAGCAACACTACTGAGACTTGAACCAG
1 CAACAATCTCTCCCTAGCAACACTACTGAGACTCGAACCAG
*
3146080 CAACAATCTC-CCCTCAGCAACACTATTG-GAACTCGAACC
1 CAACAATCTCTCCCT-AGCAACACTACTGAG-ACTCGAACC
3146119 GGTGACTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 5 0.14
41 30 0.86
ACGTcount: A:0.34, C:0.36, G:0.11, T:0.19
Consensus pattern (41 bp):
CAACAATCTCTCCCTAGCAACACTACTGAGACTCGAACCAG
Found at i:3147257 original size:2 final size:2
Alignment explanation
Indices: 3147250--3147282 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3147240 TTGCTGTACA
*
3147250 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3147283 CGAATACCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3148288 original size:3 final size:3
Alignment explanation
Indices: 3148282--3148328 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
3148272 TTTTAATATC
3148282 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ACTT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
3148326 ATT
1 ATT
3148329 TTTCTTTCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 35 0.85
4 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:3150581 original size:20 final size:21
Alignment explanation
Indices: 3150551--3150590 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3150541 CTTTCAACAA
3150551 AAAAGTAAAAAAAAAAAATTG
1 AAAAGTAAAAAAAAAAAATTG
*
3150572 AAAA-TAAAAAGAAAAAATT
1 AAAAGTAAAAAAAAAAAATT
3150591 CACACATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (21 bp):
AAAAGTAAAAAAAAAAAATTG
Found at i:3161603 original size:48 final size:48
Alignment explanation
Indices: 3161547--3161672 Score: 182
Period size: 48 Copynumber: 2.6 Consensus size: 48
3161537 TTTCGAGAAC
3161547 AGATGAGATTTTAAAGTTATTAAGCCTCTACTGAGAGGAGCTTTTTCA
1 AGATGAGATTTTAAAGTTATTAAGCCTCTACTGAGAGGAGCTTTTTCA
* *
3161595 AGATGAGATTTTAAAGTTGTTGAA-CCTCTGCTGAGAGGAGCTTTTTCA
1 AGATGAGATTTTAAAGTTATT-AAGCCTCTACTGAGAGGAGCTTTTTCA
* * *
3161643 AAATAAGATTTTTAAAGTTATTGAGCCTCT
1 AGATGAGA-TTTTAAAGTTATTAAGCCTCT
3161673 GCCCAGATGA
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
48 50 0.72
49 19 0.28
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.37
Consensus pattern (48 bp):
AGATGAGATTTTAAAGTTATTAAGCCTCTACTGAGAGGAGCTTTTTCA
Found at i:3162908 original size:23 final size:24
Alignment explanation
Indices: 3162877--3162923 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3162867 AGGTAAATTT
* * *
3162877 TTTTTTTAAT-TTTTTATATATTA
1 TTTTATTAATATTTATACATATTA
3162900 TTTTATTAATATTTATACATATTA
1 TTTTATTAATATTTATACATATTA
3162924 AAATATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTTATTAATATTTATACATATTA
Found at i:3164623 original size:3 final size:3
Alignment explanation
Indices: 3164615--3164646 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3164605 TCTCTTAAGT
3164615 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3164647 TCTAATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3170459 original size:16 final size:16
Alignment explanation
Indices: 3170416--3170462 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
3170406 ATTTAATCAT
3170416 TATTTCTATTTATTGT-A
1 TATTT-TATTT-TTGTAA
*
3170433 TTTTTTA-TTTTGTAA
1 TATTTTATTTTTGTAA
3170448 TATTTTATTTTTGTA
1 TATTTTATTTTTGTA
3170463 TAAATAGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 4 0.15
15 9 0.35
16 9 0.35
17 4 0.15
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.70
Consensus pattern (16 bp):
TATTTTATTTTTGTAA
Found at i:3175671 original size:21 final size:23
Alignment explanation
Indices: 3175631--3175674 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3175621 TTAAGTTTTA
*
3175631 TTTTGTATGAATTTGTTTTAATT
1 TTTTGTATGAATTTGATTTAATT
3175654 TTTTG-ATGAATTT-ATTTAATT
1 TTTTGTATGAATTTGATTTAATT
3175675 ATATTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 8 0.40
23 5 0.25
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (23 bp):
TTTTGTATGAATTTGATTTAATT
Found at i:3175703 original size:31 final size:32
Alignment explanation
Indices: 3175646--3175709 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 32
3175636 TATGAATTTG
*
3175646 TTTTAATTTTTTGATGAATTTATTTAATTATA
1 TTTTAATTTATTGATGAATTTATTTAATTATA
3175678 TTTTAATTTATTGATTG-A-TTATTTAATTATA
1 TTTTAATTTATTGA-TGAATTTATTTAATTATA
3175709 T
1 T
3175710 AATACTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 14 0.47
32 14 0.47
33 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (32 bp):
TTTTAATTTATTGATGAATTTATTTAATTATA
Found at i:3177967 original size:52 final size:52
Alignment explanation
Indices: 3177861--3178003 Score: 181
Period size: 52 Copynumber: 2.8 Consensus size: 52
3177851 AAACTTGCTC
* *
3177861 ATTAAGAATCTCTCTCCTCTTAGAATTCTTCTC-T--AAGTCAAACTTGCCT
1 ATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
*
3177910 ATTAAGAATACT-TTTCCTTTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
1 ATTAAGAAT-CTCTTTCCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
*
3177962 ATTAAGAATCCTCTTT-CTCTT-GAAATTCTTCTTTTGCAAGTC
1 ATTAAGAAT-CTCTTTCCTCTTAG-AATTCTTCTCTTGCAAGTC
3178004 TTCTTGTCCA
Statistics
Matches: 82, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
49 28 0.34
50 3 0.04
51 1 0.01
52 47 0.57
53 3 0.04
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (52 bp):
ATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
Found at i:3178068 original size:11 final size:11
Alignment explanation
Indices: 3178028--3178069 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
3178018 GCAATATCTG
*
3178028 ACAAATCCCAA
1 ACAAATCTCAA
3178039 ACAAATCT-ATA
1 ACAAATCTCA-A
3178050 ACAAATCTCAA
1 ACAAATCTCAA
3178061 ACAAATCTC
1 ACAAATCTC
3178070 TTATGGGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 1 0.04
11 26 0.93
12 1 0.04
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:3178361 original size:24 final size:25
Alignment explanation
Indices: 3178321--3178429 Score: 91
Period size: 25 Copynumber: 4.4 Consensus size: 25
3178311 CTTCCCAAAC
*
3178321 CTTT-AGCTCTTCCCACATCTCGAA
1 CTTTCAGCTCTTCTCACATCTCGAA
3178345 CTTTCAGCTCTT-TCACATCTCGAA
1 CTTTCAGCTCTTCTCACATCTCGAA
* * *
3178369 CCTTCGGCTCTT-TCCACATCTTGAA
1 CTTTCAGCTCTTCT-CACATCTCGAA
* * * *
3178394 -TCTTCAACTCTTCTCATATTTCAAA
1 CT-TTCAGCTCTTCTCACATCTCGAA
*
3178419 CCTTCAGCTCT
1 CTTTCAGCTCT
3178430 GATACCACTT
Statistics
Matches: 67, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
24 26 0.39
25 40 0.60
26 1 0.01
ACGTcount: A:0.20, C:0.35, G:0.07, T:0.38
Consensus pattern (25 bp):
CTTTCAGCTCTTCTCACATCTCGAA
Found at i:3178405 original size:49 final size:50
Alignment explanation
Indices: 3178316--3178429 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 50
3178306 ATGCACTTCC
* *
3178316 CAAACCTTTAGCTCTTCCCACATCTCGAACTTTCAGCTCTT-TCACATCT
1 CAAACCTTCAGCTCTTCCCACATCTCGAACTTTCAACTCTTCTCACATCT
* * * * * *
3178365 CGAACCTTCGGCTCTTTCCACATCTTGAA-TCTTCAACTCTTCTCATATTT
1 CAAACCTTCAGCTCTTCCCACATCTCGAACT-TTCAACTCTTCTCACATCT
3178415 CAAACCTTCAGCTCT
1 CAAACCTTCAGCTCT
3178430 GATACCACTT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
48 1 0.02
49 33 0.62
50 19 0.36
ACGTcount: A:0.22, C:0.35, G:0.07, T:0.36
Consensus pattern (50 bp):
CAAACCTTCAGCTCTTCCCACATCTCGAACTTTCAACTCTTCTCACATCT
Found at i:3178465 original size:31 final size:31
Alignment explanation
Indices: 3178423--3178597 Score: 278
Period size: 31 Copynumber: 5.6 Consensus size: 31
3178413 TTCAAACCTT
* *
3178423 CAGCTCTGATACCACTTGTTGGGGAACACCA
1 CAGCTCTGATACCATTTGTTGAGGAACACCA
* * *
3178454 CAGTTCTGATACCATTTGTTGGGGATCACCA
1 CAGCTCTGATACCATTTGTTGAGGAACACCA
*
3178485 CAGCTCTGATACCATTTGTTGAGGAATACCA
1 CAGCTCTGATACCATTTGTTGAGGAACACCA
* *
3178516 CAGCTCTGATACCATTTATTGAGGAATACCA
1 CAGCTCTGATACCATTTGTTGAGGAACACCA
3178547 CAGCTCTGATACCATTTGTTGAGGAACACCA
1 CAGCTCTGATACCATTTGTTGAGGAACACCA
3178578 CAGCTCTGATACCATTTGTT
1 CAGCTCTGATACCATTTGTT
3178598 AGGCTAAAAG
Statistics
Matches: 134, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 134 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (31 bp):
CAGCTCTGATACCATTTGTTGAGGAACACCA
Found at i:3179203 original size:52 final size:51
Alignment explanation
Indices: 3179097--3179239 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 51
3179087 AAACTTGCTC
* *
3179097 ATTAAGAATCTCTCTCCTCTTAGAATTCTTCTC-T--AAGTCAAACTTGCCT
1 ATTAAGAATCT-TTTCCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
*
3179146 ATTAAGAATACTTTTCCTTTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
1 ATTAAGAAT-CTTTTCCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
* *
3179198 ATTAAGAATCCTTTTTCTCTT-GAAATTCTTCTTTTGCAAGTC
1 ATTAAGAAT-CTTTTCCTCTTAG-AATTCTTCTCTTGCAAGTC
3179240 TTCTTGTCCA
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
49 28 0.34
50 3 0.04
51 1 0.01
52 50 0.61
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (51 bp):
ATTAAGAATCTTTTCCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
Found at i:3180497 original size:15 final size:15
Alignment explanation
Indices: 3180477--3180506 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3180467 AAATAAAAAA
*
3180477 TTTATTATATATTTT
1 TTTATTAAATATTTT
3180492 TTTATTAAATATTTT
1 TTTATTAAATATTTT
3180507 ATACAGAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTAAATATTTT
Found at i:3181398 original size:12 final size:12
Alignment explanation
Indices: 3181381--3181421 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
3181371 GTTTTAAAGA
3181381 AAAATTTTCTTT
1 AAAATTTTCTTT
3181393 AAAATTTTCTTTT
1 AAAATTTTC-TTT
3181406 AAAACTTTT-TTT
1 AAAA-TTTTCTTT
3181418 AAAA
1 AAAA
3181422 CAAAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 16 0.59
13 7 0.26
14 4 0.15
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (12 bp):
AAAATTTTCTTT
Found at i:3181422 original size:12 final size:12
Alignment explanation
Indices: 3181380--3181422 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
3181370 TGTTTTAAAG
*
3181380 AAAAATTTTCTTT
1 AAAACTTTT-TTT
*
3181393 AAAATTTTCTTTT
1 AAAACTTT-TTTT
3181406 AAAACTTTTTTT
1 AAAACTTTTTTT
3181418 AAAAC
1 AAAAC
3181423 AAAATTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 9 0.33
13 17 0.63
14 1 0.04
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (12 bp):
AAAACTTTTTTT
Found at i:3185822 original size:9 final size:10
Alignment explanation
Indices: 3185795--3185822 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3185785 TAAATATATC
3185795 AAAATTTTTT
1 AAAATTTTTT
3185805 AAAATTTTTT
1 AAAATTTTTT
3185815 AAAATTTT
1 AAAATTTT
3185823 ATACGTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
AAAATTTTTT
Found at i:3188457 original size:2 final size:2
Alignment explanation
Indices: 3188450--3188498 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
3188440 TAGTTGGAGA
3188450 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
3188492 AT GAT AT
1 AT -AT AT
3188499 TCTCTGCTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3189050 original size:15 final size:16
Alignment explanation
Indices: 3189021--3189054 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
3189011 CTAGACATTA
3189021 ATTGTAAATTTTTTAT
1 ATTGTAAATTTTTTAT
3189037 ATTGTAAA-TTTTTAT
1 ATTGTAAATTTTTTAT
3189052 ATT
1 ATT
3189055 TTCAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
ATTGTAAATTTTTTAT
Found at i:3191137 original size:43 final size:41
Alignment explanation
Indices: 3191058--3191138 Score: 94
Period size: 41 Copynumber: 1.9 Consensus size: 41
3191048 TATATCTTTT
*
3191058 TTTTAATTATTTTTTAAATATGTAAAGAATATATATCACTA
1 TTTTAATTATTTTTTAAATATGTAAAAAATATATATCACTA
*
3191099 TTTTAATT-TTATTTATAAA-ATTTAAAAAATTATAATATCA
1 TTTTAATTATT-TTT-TAAATATGTAAAAAA-TAT-ATATCA
3191139 ATATATTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
40 2 0.06
41 19 0.56
42 7 0.21
43 6 0.18
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (41 bp):
TTTTAATTATTTTTTAAATATGTAAAAAATATATATCACTA
Found at i:3191889 original size:17 final size:17
Alignment explanation
Indices: 3191869--3191902 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3191859 TATTCTCATA
3191869 TTTT-AAATTTTTATTAT
1 TTTTAAAATTTTT-TTAT
3191886 TTTTAAAATTTTTTTAT
1 TTTTAAAATTTTTTTAT
3191903 ATTTCGAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTAAAATTTTTTTAT
Found at i:3199773 original size:14 final size:14
Alignment explanation
Indices: 3199756--3199792 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3199746 AATTAAAGAT
3199756 TATAAATATTAAAA
1 TATAAATATTAAAA
*
3199770 TATAAAT-TTTAAA
1 TATAAATATTAAAA
3199783 T-TAAATATTA
1 TATAAATATTA
3199793 TCTTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
12 5 0.25
13 8 0.40
14 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TATAAATATTAAAA
Found at i:3201243 original size:29 final size:31
Alignment explanation
Indices: 3201180--3201245 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 31
3201170 AATAAAAATA
*
3201180 TATTTGGATATATATATCAAAATATATAAGTT
1 TATTTGGATATATATA-CAAAATATATAAGGT
*
3201212 TATTTGGGTATA-ATA-AAAATATA-AAGAGT
1 TATTTGGATATATATACAAAATATATAAG-GT
3201241 TATTT
1 TATTT
3201246 AATTTGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 3 0.10
29 14 0.45
31 3 0.10
32 11 0.35
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (31 bp):
TATTTGGATATATATACAAAATATATAAGGT
Found at i:3201579 original size:55 final size:55
Alignment explanation
Indices: 3201494--3201598 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 55
3201484 AATATTTTAA
*
3201494 TTTTTCAATCCATTAAGGGTGTCTAATACCGTCCTACTTCAACGTATGCATCCTT
1 TTTTTCAATCCATTAAGGGTGTCTAATACCGTCCTACTTCAACCTATGCATCCTT
* *
3201549 TTTTTCAATCTC-TTAAGGGTGTCTATTACCGTCCTACTTCAGCCTATGCA
1 TTTTTCAATC-CATTAAGGGTGTCTAATACCGTCCTACTTCAACCTATGCA
3201599 GCCAACTGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
55 45 0.98
56 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (55 bp):
TTTTTCAATCCATTAAGGGTGTCTAATACCGTCCTACTTCAACCTATGCATCCTT
Found at i:3202338 original size:2 final size:2
Alignment explanation
Indices: 3202331--3202355 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3202321 ACAAATATTG
3202331 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 A
3202356 ATCATGCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3204184 original size:26 final size:26
Alignment explanation
Indices: 3204154--3204207 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3204144 TATAACATAT
3204154 CGTCTTTGTTCTTTATACATGTGTCA
1 CGTCTTTGTTCTTTATACATGTGTCA
3204180 CGTCTTTGTTCTTTATACATGTGTCA
1 CGTCTTTGTTCTTTATACATGTGTCA
3204206 CG
1 CG
3204208 GGTCGAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (26 bp):
CGTCTTTGTTCTTTATACATGTGTCA
Found at i:3205270 original size:3 final size:3
Alignment explanation
Indices: 3205262--3205289 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3205252 ATCTGGAGTT
3205262 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3205290 GACATACCTC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3210101 original size:31 final size:31
Alignment explanation
Indices: 3210054--3210135 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
3210044 TAATATTTTA
* *
3210054 ATTTAAA-AAATATATATTTTAATATCAATT
1 ATTTAAATATATATATATTTTAACATCAATT
*
3210084 ATTTAGATATATATATATGTTT-ACATCAATT
1 ATTTAAATATATATATAT-TTTAACATCAATT
*
3210115 ATTTAAATAT-TTTATATTTTA
1 ATTTAAATATATATATATTTTA
3210136 TATTTATTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 3 0.07
30 12 0.27
31 26 0.59
32 3 0.07
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (31 bp):
ATTTAAATATATATATATTTTAACATCAATT
Found at i:3215665 original size:2 final size:2
Alignment explanation
Indices: 3215658--3215685 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3215648 TTAACGTTAA
3215658 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
3215686 TAATGTTAGG
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:3229759 original size:19 final size:20
Alignment explanation
Indices: 3229716--3229759 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3229706 AATTAATCTA
** *
3229716 AAATAAAATTTTATATTATT
1 AAATAAAAAATTATATTACT
3229736 AAATAAAAAATTAT-TTACT
1 AAATAAAAAATTATATTACT
3229755 AAATA
1 AAATA
3229760 TATATAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATAAAAAATTATATTACT
Found at i:3240190 original size:41 final size:41
Alignment explanation
Indices: 3240145--3240223 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
3240135 TTCCTACGAG
3240145 TTCGTAAATAACCAAAATATCAACACTCAAAAACCATCGAT
1 TTCGTAAATAACCAAAATATCAACACTCAAAAACCATCGAT
3240186 TTCGTAAATAACCAAAATATCAACACTCAAAAACCATC
1 TTCGTAAATAACCAAAATATCAACACTCAAAAACCATC
3240224 CATTAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.49, C:0.25, G:0.04, T:0.22
Consensus pattern (41 bp):
TTCGTAAATAACCAAAATATCAACACTCAAAAACCATCGAT
Found at i:3240719 original size:13 final size:13
Alignment explanation
Indices: 3240701--3240784 Score: 53
Period size: 13 Copynumber: 6.2 Consensus size: 13
3240691 CTATAGATTA
*
3240701 TAATTTGATATTT
1 TAATTTGAAATTT
*
3240714 TAATTTCAAAGTTT
1 TAATTTGAAA-TTT
* *
3240728 TCAATAT-AAATTA
1 T-AATTTGAAATTT
* *
3240741 TAATTTTATATTT
1 TAATTTGAAATTT
3240754 TAATTTGAAAGTTTT
1 TAATTTGAAA--TTT
* *
3240769 TTATTTAAAATTT
1 TAATTTGAAATTT
3240782 TAA
1 TAA
3240785 AATATGAGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
12 4 0.07
13 28 0.52
14 7 0.13
15 15 0.28
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (13 bp):
TAATTTGAAATTT
Found at i:3240741 original size:40 final size:40
Alignment explanation
Indices: 3240692--3240768 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
3240682 TCCTTGGTCC
*
3240692 TATAGATTATAATTTGATATTTTAATTTCAAAGTTTTCAA
1 TATAAATTATAATTTGATATTTTAATTTCAAAGTTTTCAA
* *
3240732 TATAAATTATAATTTTATATTTTAATTTGAAAGTTTT
1 TATAAATTATAATTTGATATTTTAATTTCAAAGTTTT
3240769 TTATTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (40 bp):
TATAAATTATAATTTGATATTTTAATTTCAAAGTTTTCAA
Found at i:3242451 original size:23 final size:23
Alignment explanation
Indices: 3242416--3242459 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3242406 CTCAATCCAA
*
3242416 TTTAAAATTAATA-AAATATTATT
1 TTTAAAATAAATATAAA-ATTATT
*
3242439 TTTAATATAAATATAAAATTA
1 TTTAAAATAAATATAAAATTA
3242460 AATATATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAATAAATATAAAATTATT
Found at i:3242468 original size:14 final size:14
Alignment explanation
Indices: 3242449--3242495 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
3242439 TTTAATATAA
3242449 ATATAAAATTAAAT
1 ATATAAAATTAAAT
*
3242463 ATATAAAAAT-AAT
1 ATATAAAATTAAAT
*
3242476 -TATAAAATAAAAT
1 ATATAAAATTAAAT
*
3242489 AAATAAA
1 ATATAAA
3242496 TAAATTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 7 0.26
13 6 0.22
14 14 0.52
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATATAAAATTAAAT
Found at i:3242479 original size:26 final size:26
Alignment explanation
Indices: 3242445--3242503 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
3242435 TATTTTTAAT
* * *
3242445 ATAAATATAAAATTAAATATATAAAA
1 ATAATTATAAAATAAAATAAATAAAA
*
3242471 ATAATTATAAAATAAAATAAATAAAT
1 ATAATTATAAAATAAAATAAATAAAA
3242497 A-AATTAT
1 ATAATTAT
3242504 TTTTATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (26 bp):
ATAATTATAAAATAAAATAAATAAAA
Found at i:3243936 original size:25 final size:25
Alignment explanation
Indices: 3243902--3243976 Score: 86
Period size: 25 Copynumber: 3.1 Consensus size: 25
3243892 TATTAAAATT
*
3243902 ATATCTTATTTTTATGAATATTTAAA
1 ATATTTTATTTTTATG-ATATTTAAA
3243928 AT-TTTTATTTTTAT-AT-TTTAAA
1 ATATTTTATTTTTATGATATTTAAA
*
3243950 ATTATTTTATTTTT-TGATATTAAAA
1 A-TATTTTATTTTTATGATATTTAAA
3243975 AT
1 AT
3243977 CATGAAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
22 7 0.16
23 4 0.09
24 13 0.30
25 17 0.40
26 2 0.05
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (25 bp):
ATATTTTATTTTTATGATATTTAAA
Found at i:3243972 original size:24 final size:25
Alignment explanation
Indices: 3243891--3243974 Score: 95
Period size: 24 Copynumber: 3.4 Consensus size: 25
3243881 TTTAAGATAT
3243891 ATATTAAAATTATATCTTATTTTTATG
1 ATATTAAAATTAT-T-TTATTTTTATG
3243918 AATATTTAAAA-T-TTTTATTTTTAT-
1 -ATA-TTAAAATTATTTTATTTTTATG
*
3243942 ATTTTAAAATTATTTTATTTTT-TG
1 ATATTAAAATTATTTTATTTTTATG
3243966 ATATTAAAA
1 ATATTAAAA
3243975 ATCATGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
22 6 0.12
23 4 0.08
24 18 0.36
25 10 0.20
26 1 0.02
27 1 0.02
28 4 0.08
29 6 0.12
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (25 bp):
ATATTAAAATTATTTTATTTTTATG
Found at i:3245096 original size:91 final size:91
Alignment explanation
Indices: 3244984--3245161 Score: 313
Period size: 91 Copynumber: 2.0 Consensus size: 91
3244974 AGAGTTTTAG
*
3244984 ATTCAAAGCAAATTAGGTTTTGGC-TCGCAGGTAATTTTTATTATTGTTCTTCCTAAAAGTTTCA
1 ATTCAAAGCAAATTAGGTTTTGGCTTC-CAGGTAATTTTTATGATTGTTCTTCCTAAAAGTTTCA
3245048 TGTATGCTATTTCTTTTAATTATTATT
65 TGTATGCTATTTCTTTTAATTATTATT
*
3245075 ATTCAAAGCAAATTAGGTTTTGTCTTCCAGGTAATTTTTATGATTGTTCTTCCTAAAAGTTTCAT
1 ATTCAAAGCAAATTAGGTTTTGGCTTCCAGGTAATTTTTATGATTGTTCTTCCTAAAAGTTTCAT
*
3245140 GTGTGCTATTTCTTTTAATTAT
66 GTATGCTATTTCTTTTAATTAT
3245162 GTTCTTCCTA
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
91 81 0.98
92 2 0.02
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.48
Consensus pattern (91 bp):
ATTCAAAGCAAATTAGGTTTTGGCTTCCAGGTAATTTTTATGATTGTTCTTCCTAAAAGTTTCAT
GTATGCTATTTCTTTTAATTATTATT
Found at i:3245169 original size:42 final size:42
Alignment explanation
Indices: 3245119--3245203 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
3245109 TTTTTATGAT
* *
3245119 TGTTCTTCCTAAAAGTTTCATGTGTGCTATTTCTTTTAATTA
1 TGTTCTTCCTAAAAGTTTCATGTATGCTATTTCCTTTAATTA
3245161 TGTTCTTCCTAAAAGTTTCATGTATGCTATTTCCTTTAATTA
1 TGTTCTTCCTAAAAGTTTCATGTATGCTATTTCCTTTAATTA
3245203 T
1 T
3245204 TATCATCTCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (42 bp):
TGTTCTTCCTAAAAGTTTCATGTATGCTATTTCCTTTAATTA
Found at i:3245227 original size:24 final size:24
Alignment explanation
Indices: 3245195--3245245 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
3245185 TGCTATTTCC
3245195 TTTAATTATTATCATCTCCTACCG
1 TTTAATTATTATCATCTCCTACCG
*
3245219 TTTAATTATTATCATCTCCTGCCG
1 TTTAATTATTATCATCTCCTACCG
3245243 TTT
1 TTT
3245246 TTTGAACAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.06, T:0.49
Consensus pattern (24 bp):
TTTAATTATTATCATCTCCTACCG
Found at i:3250384 original size:42 final size:42
Alignment explanation
Indices: 3250301--3250384 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
3250291 TTCAAATTTA
* * **
3250301 TACCTTCTTATATAATTCCATGTTTTCTTGACGAATTAGGTT
1 TACCTTCTTATAGAATTCCATGTTTTCTTGACAAACGAGGTT
* *
3250343 TACCTTCTTATAGAGTTCCA-GATTTTCTTGATAAACGAGGTT
1 TACCTTCTTATAGAATTCCATG-TTTTCTTGACAAACGAGGTT
3250385 CCCCTGCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (42 bp):
TACCTTCTTATAGAATTCCATGTTTTCTTGACAAACGAGGTT
Found at i:3253288 original size:392 final size:397
Alignment explanation
Indices: 3252554--3253310 Score: 1037
Period size: 392 Copynumber: 1.9 Consensus size: 397
3252544 TATGATTTCT
** * *
3252554 TGGAGGAAGCTTTTGCCTATTTTAAGGCATTAAAAAGATGAAGAGATGGTTTGTCAAGAAAGTCA
1 TGGAGGAAGCTTTTGCCTATTTTAAGGCACGAAAAAGATGAAGAGATGGCTTCTCAAGAAAGTCA
* * * ** * *
3252619 ATTAAGTCTTTATGGAAAGGGGTAAATGTAAGGATTTTTCTATTTTTTAAGGTAACTGCTTGTTG
66 ATGAAGTCTTTATGGAAAGGGGTAAATGTAAGGATTTTCCTATTTTCTAAGAAAAATGCTTCTTG
** * *
3252684 AAATTTTAATAGGAAAAGAGATGAAAATGGCCCTGATTTTTGGATTGCCTGATCAAGCAACTTTA
131 AAACGTTAATAGGAAAAGAGATGAAAACGGCCCTGATTTTTGGA-TGACTGATCAAGCAACTTTA
* * *
3252749 GCAAGTAAAATTAGGCTGCTAGAGATAGCAACTTTTCAAAATCCAATGTGAAACTTATATGCACC
195 GCAAGTAAAATTAGGCTACTAGAGATA-CAACTTCTCAAAATCCAATATGAAACTTATATGCACC
* *
3252814 AATAGATGCTTTGCTTCTGGATATTGCAAAGTACAAACTTTCTTCTTAGAGTAATATGATTTCTA
259 AATAGATGCTTTGCTTCTGGATATTGCAAAGCACAAACTTTCTTCTTAGAGTAACATGATTTCTA
*
3252879 TTTGGACATTAGAGAATGCTTCTGGCTTCTATT-TATATCAGCAGGGGTGGAGATATGTAATCCA
324 TTTGGACATTAGAGAATGCTTCTAGCTTCT-TTATATATCAGCAGGGGTGGAGATATGTAATCCA
3252943 AAGTAGTTGA
388 AAGTAGTTGA
* * *
3252953 TGGAGGAAGCTTTTTCCTATTTTGAGGCACGAAAGAGATGAAGAGATGGCTTCTCAAGGAAAGT-
1 TGGAGGAAGCTTTTGCCTATTTTAAGGCACGAAAAAGATGAAGAGATGGCTTCTCAA-GAAAGTC
* **
3253017 AATGAAGTCTTTATGGAAAGGGGTAATTGTATTGATTTTCCTA-TTTCTAAGAAAAATGCTTCTT
65 AATGAAGTCTTTATGGAAAGGGGTAAATGTAAGGATTTTCCTATTTTCTAAGAAAAATGCTTCTT
* *
3253081 GAAACGTTAGTAGGAAAGGAGATGAAAACGGCCCTGATTTTTGG-TGACTGATCAAGCAAC-TTA
130 GAAACGTTAATAGGAAAAGAGATGAAAACGGCCCTGATTTTTGGATGACTGATCAAGCAACTTTA
* * *
3253144 GCAAGTAAAATTAGGCTATTAGAG-T-TAACTTCTCAAAATCCCATATG-AACTTTATATGCACC
195 GCAAGTAAAATTAGGCTACTAGAGATACAACTTCTCAAAATCCAATATGAAAC-TTATATGCACC
* * * * *
3253206 TATTGATGCTTTTTCTTCTGGCTATTGC-AAGCACAAACTTTCTTCTTGGAGTAACATGATTTCT
259 AATAGATGC-TTTGCTTCTGGATATTGCAAAGCACAAACTTTCTTCTTAGAGTAACATGATTTCT
* * *
3253270 ATTTGGAGATTGGAGAATGTTTCTAGCTTCTTTATATATCA
323 ATTTGGACATTAGAGAATGCTTCTAGCTTCTTTATATATCA
3253311 CTGGTAAAAA
Statistics
Matches: 314, Mismatches: 40, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
391 5 0.02
392 103 0.33
393 16 0.05
394 1 0.00
395 25 0.08
396 15 0.05
398 55 0.18
399 88 0.28
400 6 0.02
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (397 bp):
TGGAGGAAGCTTTTGCCTATTTTAAGGCACGAAAAAGATGAAGAGATGGCTTCTCAAGAAAGTCA
ATGAAGTCTTTATGGAAAGGGGTAAATGTAAGGATTTTCCTATTTTCTAAGAAAAATGCTTCTTG
AAACGTTAATAGGAAAAGAGATGAAAACGGCCCTGATTTTTGGATGACTGATCAAGCAACTTTAG
CAAGTAAAATTAGGCTACTAGAGATACAACTTCTCAAAATCCAATATGAAACTTATATGCACCAA
TAGATGCTTTGCTTCTGGATATTGCAAAGCACAAACTTTCTTCTTAGAGTAACATGATTTCTATT
TGGACATTAGAGAATGCTTCTAGCTTCTTTATATATCAGCAGGGGTGGAGATATGTAATCCAAAG
TAGTTGA
Found at i:3257309 original size:4 final size:4
Alignment explanation
Indices: 3257300--3257328 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3257290 CTCTGTTATG
3257300 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
3257329 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:3261171 original size:2 final size:2
Alignment explanation
Indices: 3261164--3261197 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3261154 TTACAATTAA
3261164 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
3261198 GTTTGAAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3261414 original size:29 final size:33
Alignment explanation
Indices: 3261357--3261420 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
3261347 AAATTCATTT
3261357 AATATAATTTTATTTTATAAATTACTAAAAAATA
1 AATATAATTTTA-TTTATAAATTACTAAAAAATA
3261391 AATATAATTTTA-TTA-AAA-TA-TAAAAAATA
1 AATATAATTTTATTTATAAATTACTAAAAAATA
3261420 A
1 A
3261421 TAAGAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 10 0.33
30 2 0.07
31 3 0.10
32 3 0.10
34 12 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (33 bp):
AATATAATTTTATTTATAAATTACTAAAAAATA
Found at i:3266060 original size:2 final size:2
Alignment explanation
Indices: 3266053--3266099 Score: 78
Period size: 2 Copynumber: 23.5 Consensus size: 2
3266043 GCTTGTTCAA
3266053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AGT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
3266095 AT AT A
1 AT AT A
3266100 AGGCAAACAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 41 0.95
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3266211 original size:24 final size:26
Alignment explanation
Indices: 3266169--3266220 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
3266159 GTCTTCAAGT
3266169 ATATATATTCATTATATACTTAG-CAA
1 ATATATATTCATTATATAC-TAGACAA
3266195 ATATATATTCA-T-TATACTAGACAA
1 ATATATATTCATTATATACTAGACAA
3266219 AT
1 AT
3266221 TTTAAAAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 3 0.12
24 10 0.40
25 1 0.04
26 11 0.44
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (26 bp):
ATATATATTCATTATATACTAGACAA
Found at i:3268079 original size:27 final size:27
Alignment explanation
Indices: 3268041--3268093 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
3268031 CCTCATTATC
3268041 TTATGTTCTTATTAATGACCAAATGCA
1 TTATGTTCTTATTAATGACCAAATGCA
3268068 TTATGTTCTTATTAATGACCAAATGC
1 TTATGTTCTTATTAATGACCAAATGC
3268094 GTATTAACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (27 bp):
TTATGTTCTTATTAATGACCAAATGCA
Found at i:3268400 original size:17 final size:17
Alignment explanation
Indices: 3268378--3268417 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3268368 AGTCGATATT
3268378 TATTTAAATCATTTTTA
1 TATTTAAATCATTTTTA
* *
3268395 T-TTTTAATTATTTTTA
1 TATTTAAATCATTTTTA
3268411 TATTTAA
1 TATTTAA
3268418 CTTAAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTAAATCATTTTTA
Found at i:3269230 original size:23 final size:22
Alignment explanation
Indices: 3269200--3269263 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
3269190 AAAGAATAAT
3269200 AAAAATTATATATATATAATTAA
1 AAAAATTATA-ATATATAATTAA
*
3269223 AAAAATTATAAT-TATGATTAA
1 AAAAATTATAATATATAATTAA
* * *
3269244 AAGAATTTTAATATAAAATT
1 AAAAATTATAATATATAATT
3269264 TATATTAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 18 0.51
22 7 0.20
23 10 0.29
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (22 bp):
AAAAATTATAATATATAATTAA
Found at i:3269278 original size:28 final size:26
Alignment explanation
Indices: 3269226--3269295 Score: 63
Period size: 26 Copynumber: 2.6 Consensus size: 26
3269216 TAATTAAAAA
*
3269226 AATTATAA-TTATGATTAAAAGAATTTT
1 AATTAAAATTTAT-ATTAAAAGAA-TTT
3269253 AATATAAAATTTATATTAAATA-AATTT
1 AAT-TAAAATTTATATTAAA-AGAATTT
* *
3269280 CATTAAAATTAATATT
1 AATTAAAATTTATATT
3269296 TGAACCAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
26 12 0.32
27 8 0.22
28 12 0.32
29 5 0.14
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (26 bp):
AATTAAAATTTATATTAAAAGAATTT
Found at i:3270404 original size:20 final size:21
Alignment explanation
Indices: 3270379--3270417 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3270369 TTATCAGTAT
*
3270379 ATAAATTTTAT-ATATTATCA
1 ATAAATTTAATAATATTATCA
3270399 ATAAATTTAATAATATTAT
1 ATAAATTTAATAATATTAT
3270418 ATCGATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAATTTAATAATATTATCA
Found at i:3271096 original size:14 final size:13
Alignment explanation
Indices: 3271075--3271111 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
3271065 ATTAAAAAAA
3271075 TTTTAATAAATTT
1 TTTTAATAAATTT
*
3271088 TTTTAAATAGATTT
1 TTTT-AATAAATTT
3271102 TTTTAATAAA
1 TTTTAATAAA
3271112 AATATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
TTTTAATAAATTT
Found at i:3272646 original size:2 final size:2
Alignment explanation
Indices: 3272639--3272670 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3272629 TGAACCCTTA
3272639 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
3272671 GTGTGATAAT
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:3276071 original size:2 final size:2
Alignment explanation
Indices: 3276066--3276098 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3276056 TTTATGTGTG
3276066 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
3276099 GAGATAATGC
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:3279469 original size:3 final size:3
Alignment explanation
Indices: 3279461--3279494 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3279451 CCATCACTAA
3279461 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C
3279495 CCCCTTGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:3280879 original size:41 final size:41
Alignment explanation
Indices: 3280834--3280923 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
3280824 GTAAGTTTAA
* * *
3280834 CAAAATTATATCAAATGCTA-TCAAAAGTATATCAATGTTAT
1 CAAAATTACATCAAATACTACT-AAAAGTATATCAAAGTTAT
* * *
3280875 CAAAATTACATCAAATATTACTAAAATTATATTAAAGTTAT
1 CAAAATTACATCAAATACTACTAAAAGTATATCAAAGTTAT
3280916 CAAAATTA
1 CAAAATTA
3280924 AATTAACCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 41 0.98
42 1 0.02
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.34
Consensus pattern (41 bp):
CAAAATTACATCAAATACTACTAAAAGTATATCAAAGTTAT
Found at i:3280974 original size:11 final size:10
Alignment explanation
Indices: 3280935--3281006 Score: 53
Period size: 11 Copynumber: 7.3 Consensus size: 10
3280925 ATTAACCAAA
3280935 AAAAT-TATC
1 AAAATCTATC
*
3280944 AAAATCAAGTC
1 AAAATCTA-TC
*
3280955 AAAGT-TATC
1 AAAATCTATC
3280964 AAAATCATATC
1 AAAATC-TATC
*
3280975 AAAGTCTATC
1 AAAATCTATC
*
3280985 AAAATTTTATC
1 AAAA-TCTATC
3280996 -AAA-CTATC
1 AAAATCTATC
3281004 AAA
1 AAA
3281007 GTTATATCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
8 4 0.08
9 13 0.27
10 12 0.24
11 20 0.41
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.29
Consensus pattern (10 bp):
AAAATCTATC
Found at i:3281004 original size:19 final size:20
Alignment explanation
Indices: 3280834--3281122 Score: 122
Period size: 21 Copynumber: 13.8 Consensus size: 20
3280824 GTAAGTTTAA
3280834 CAAAATTATATCAAATGCTAT
1 CAAAATTATATCAAA-GCTAT
* * *
3280855 CAAAAGTATATCAATGTTAT
1 CAAAATTATATCAAAGCTAT
*
3280875 CAAAATTACATCAAA--TATT
1 CAAAATTATATCAAAGCTA-T
* *
3280894 ACTAAAATTATATTAAAGTTAT
1 -C-AAAATTATATCAAAGCTAT
* **
3280916 CAAAATTAAATTAACCAAAAAAATTAT
1 CAAAATT--A-T-ATC---AAAGCTAT
* *
3280943 CAAAATCA-AGTCAAAGTTAT
1 CAAAATTATA-TCAAAGCTAT
*
3280963 CAAAATCATATCAAAGTCTAT
1 CAAAATTATATCAAAG-CTAT
*
3280984 CAAAATTTTATCAAA-CTAT
1 CAAAATTATATCAAAGCTAT
* *
3281003 CAAAGTTATATCAAAGAT-T
1 CAAAATTATATCAAAGCTAT
* *
3281022 CTAAAATTACATCAAAAGTTAT
1 C-AAAATTATATC-AAAGCTAT
* * * **
3281044 CAAAATTACATCCAATGTTGC
1 CAAAATTATAT-CAAAGCTAT
* *
3281065 CAAAATTTATATTAAAGATTAT
1 CAAAA-TTATATCAAAG-CTAT
* * *
3281087 -TACATTATATTAAAGGCTAT
1 CAAAATTATATCAAA-GCTAT
3281107 CAAAATTATATCAAAG
1 CAAAATTATATCAAAG
3281123 ATTAGTAACA
Statistics
Matches: 207, Mismatches: 37, Indels: 49
0.71 0.13 0.17
Matches are distributed among these distances:
18 2 0.01
19 20 0.10
20 68 0.33
21 85 0.41
22 13 0.06
23 4 0.02
24 1 0.00
25 1 0.00
27 13 0.06
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.33
Consensus pattern (20 bp):
CAAAATTATATCAAAGCTAT
Found at i:3281295 original size:21 final size:22
Alignment explanation
Indices: 3281165--3281327 Score: 92
Period size: 21 Copynumber: 7.7 Consensus size: 22
3281155 CAAATTTATT
* *
3281165 AAATATATATAAAAAAATTATCA
1 AAAT-TATATTAAAAGATTATCA
*
3281188 AAATCT-TA-TAAAAAATTAAT-A
1 AAAT-TATATTAAAAGATT-ATCA
* *
3281209 AAATTATATCAATA-ATTATCA
1 AAATTATATTAAAAGATTATCA
* * * *
3281230 AAATCAAATT-AAAGATCAACA
1 AAATTATATTAAAAGATTATCA
* * *
3281251 ATATTATATTAAATG-TTA-CT
1 AAATTATATTAAAAGATTATCA
*
3281271 AAATTATATTAAAAGA-TGTCA
1 AAATTATATTAAAAGATTATCA
*
3281292 AAATCATATT-AAAGATTATCA
1 AAATTATATTAAAAGATTATCA
* *
3281313 ACATTATATGAAAAG
1 AAATTATATTAAAAG
3281328 TACACAAAAT
Statistics
Matches: 105, Mismatches: 25, Indels: 21
0.70 0.17 0.14
Matches are distributed among these distances:
20 25 0.24
21 61 0.58
22 14 0.13
23 5 0.05
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.33
Consensus pattern (22 bp):
AAATTATATTAAAAGATTATCA
Found at i:3282031 original size:14 final size:14
Alignment explanation
Indices: 3281996--3282033 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
3281986 TATTATTTTT
*
3281996 TAAATATAAATATA
1 TAAATATATATATA
3282010 -AAAT-TATATATA
1 TAAATATATATATA
3282022 TAAATATATATA
1 TAAATATATATA
3282034 ATTAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 7 0.33
13 8 0.38
14 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAATATATATATA
Found at i:3282039 original size:14 final size:13
Alignment explanation
Indices: 3281995--3282041 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
3281985 ATATTATTTT
*
3281995 TTAAATATAAATA
1 TTAAATATATATA
*
3282008 TAAAAT-TATATA
1 TTAAATATATATA
3282020 TATAAATATATATAA
1 T-TAAATATATAT-A
3282035 TTAAATA
1 TTAAATA
3282042 AATAATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 6 0.21
13 9 0.32
14 11 0.39
15 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAAATATATATA
Found at i:3282061 original size:12 final size:13
Alignment explanation
Indices: 3282031--3282062 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3282021 ATAAATATAT
3282031 ATAA-TTAAATAA
1 ATAATTTAAATAA
3282043 ATAATTTAAA-AA
1 ATAATTTAAATAA
3282055 ATAATTTA
1 ATAATTTA
3282063 TATTTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATTTAAATAA
Found at i:3288915 original size:88 final size:88
Alignment explanation
Indices: 3288766--3288941 Score: 343
Period size: 88 Copynumber: 2.0 Consensus size: 88
3288756 TTTGGACTGT
3288766 CTCATGTCGGGCTGGATAATGTAGGTAGCACAGATAACATTTACCTAATTATTATATCTTCTATT
1 CTCATGTCGGGCTGGATAATGTAGGTAGCACAGATAACATTTACCTAATTATTATATCTTCTATT
3288831 TAAAAGTAAAATCGTATTTTATG
66 TAAAAGTAAAATCGTATTTTATG
3288854 CTCATGTCGGGCTGGATAATGTAGGTAGCACAGATAACATTTACCTAATTATTATATCTTCTATT
1 CTCATGTCGGGCTGGATAATGTAGGTAGCACAGATAACATTTACCTAATTATTATATCTTCTATT
*
3288919 TAAAAGTAAAATGGTATTTTATG
66 TAAAAGTAAAATCGTATTTTATG
3288942 AAGTAGCCAT
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (88 bp):
CTCATGTCGGGCTGGATAATGTAGGTAGCACAGATAACATTTACCTAATTATTATATCTTCTATT
TAAAAGTAAAATCGTATTTTATG
Found at i:3292898 original size:2 final size:2
Alignment explanation
Indices: 3292891--3292925 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3292881 CAATGGTAAT
3292891 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3292926 AGTTAACATC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3302438 original size:7 final size:7
Alignment explanation
Indices: 3302426--3302455 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
3302416 CAATAACCTC
3302426 TACAGGT
1 TACAGGT
3302433 TACAGGT
1 TACAGGT
3302440 TACAGGT
1 TACAGGT
3302447 TACAGGT
1 TACAGGT
3302454 TA
1 TA
3302456 TGCAAGCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (7 bp):
TACAGGT
Found at i:3305130 original size:32 final size:30
Alignment explanation
Indices: 3305078--3305138 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 30
3305068 TTTAATTCAG
*
3305078 TTCGATTATTATCGAGTTGAACTCGAATAA
1 TTCGATTATTATCGAATTGAACTCGAATAA
*
3305108 TTCGACTTATTAATCGAATTGAATTCGAATA
1 TTCGA-TTATT-ATCGAATTGAACTCGAATA
3305139 TTCTTATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 5 0.19
31 5 0.19
32 17 0.63
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (30 bp):
TTCGATTATTATCGAATTGAACTCGAATAA
Found at i:3306987 original size:5 final size:5
Alignment explanation
Indices: 3306977--3307008 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
3306967 AATTTTTTAA
3306977 TTATT TTATT TTATT TTATT TTATT TTGATT T
1 TTATT TTATT TTATT TTATT TTATT TT-ATT T
3307009 AATATCGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:3308024 original size:18 final size:19
Alignment explanation
Indices: 3308003--3308038 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3307993 ATTTTAGTCG
*
3308003 AATTAATTGA-TTTAATTT
1 AATTAATTAATTTTAATTT
3308021 AATTAATTAATTTTAATT
1 AATTAATTAATTTTAATT
3308039 GATTAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
AATTAATTAATTTTAATTT
Found at i:3308043 original size:14 final size:14
Alignment explanation
Indices: 3308005--3308045 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
3307995 TTTAGTCGAA
3308005 TTAATTGATTTAA-T
1 TTAATTGA-TTAATT
*
3308019 TTAATTAATTAATT
1 TTAATTGATTAATT
3308033 TTAATTGATTAAT
1 TTAATTGATTAAT
3308046 ACAAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (14 bp):
TTAATTGATTAATT
Found at i:3308412 original size:15 final size:15
Alignment explanation
Indices: 3308392--3308421 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3308382 AAAATAAAAT
*
3308392 AATTTAATTAATTCA
1 AATTTAAATAATTCA
3308407 AATTTAAATAATTCA
1 AATTTAAATAATTCA
3308422 TATTCAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTAAATAATTCA
Found at i:3309444 original size:9 final size:9
Alignment explanation
Indices: 3309403--3309461 Score: 55
Period size: 10 Copynumber: 6.1 Consensus size: 9
3309393 ATTAAAAATA
3309403 TAATTTAACT
1 TAATTTAA-T
*
3309413 TAATTTATT
1 TAATTTAAT
*
3309422 TATTTTTCAAT
1 TA-ATTT-AAT
*
3309433 TAATTGAAT
1 TAATTTAAT
3309442 TAATTTAAT
1 TAATTTAAT
3309451 TCAATTTAAT
1 T-AATTTAAT
3309461 T
1 T
3309462 TTGAAATAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
9 15 0.38
10 21 0.52
11 4 0.10
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (9 bp):
TAATTTAAT
Found at i:3309926 original size:16 final size:15
Alignment explanation
Indices: 3309889--3309927 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3309879 GAGCAGAAAG
3309889 AAAGAAAGAGAAGAA
1 AAAGAAAGAGAAGAA
*
3309904 ACTAGAAAGAAGAAGAA
1 A-AAGAAAG-AGAAGAA
3309921 AAAGAAA
1 AAAGAAA
3309928 AAAAAGGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 11 0.55
17 8 0.40
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.03
Consensus pattern (15 bp):
AAAGAAAGAGAAGAA
Found at i:3319104 original size:24 final size:24
Alignment explanation
Indices: 3319050--3319108 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
3319040 AGAAAACCTT
*
3319050 GATGATGATGAGGATGAGATGTCGG
1 GATGATGATGAGGATGAGATGAC-G
*
3319075 GA-GATGATGGGGATGAAGATGAC-
1 GATGATGATGAGGATG-AGATGACG
3319098 GATGATGATGA
1 GATGATGATGA
3319109 TGACCATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 2 0.07
24 19 0.66
25 8 0.28
ACGTcount: A:0.32, C:0.03, G:0.42, T:0.22
Consensus pattern (24 bp):
GATGATGATGAGGATGAGATGACG
Found at i:3319206 original size:15 final size:15
Alignment explanation
Indices: 3319170--3319207 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3319160 CGCAGATCAA
*
3319170 GATGATCATGAGATT
1 GATGATGATGAGATT
*
3319185 GATGATGATGAGTTT
1 GATGATGATGAGATT
3319200 GATGATGA
1 GATGATGA
3319208 AGTATTGGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.34
Consensus pattern (15 bp):
GATGATGATGAGATT
Found at i:3333684 original size:19 final size:19
Alignment explanation
Indices: 3333660--3333696 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3333650 TTTCTTACAT
3333660 TTTTTA-TTAATTTATACTA
1 TTTTTATTTAA-TTATACTA
3333679 TTTTTATTTAATTATACT
1 TTTTTATTTAATTATACT
3333697 TATCAAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTATTTAATTATACTA
Found at i:3334802 original size:10 final size:10
Alignment explanation
Indices: 3334789--3334821 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3334779 AAAAGTTATC
3334789 AAAAAGAAAA
1 AAAAAGAAAA
*
3334799 AAAAAG-AAG
1 AAAAAGAAAA
3334808 AAAAAGAAAA
1 AAAAAGAAAA
3334818 AAAA
1 AAAA
3334822 TATAAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:3335292 original size:47 final size:48
Alignment explanation
Indices: 3335223--3335594 Score: 376
Period size: 45 Copynumber: 8.0 Consensus size: 48
3335213 CAACAATTTT
* * * *
3335223 AAAAATCTCATCTTAGCAGAGGCTTAACAACTTTAAAAA-TCATCTTG
1 AAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTG
* *
3335270 AAAAAGCTCATCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCTTG
1 AAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAAT-TCATCTTG
* * *
3335319 AAAAAGCTTCTCTCAGTAGAGGCTCAACAACTTTAAAAATT--T-TTG
1 AAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTG
* * *
3335364 AAAATGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTCGTCTTG
1 AAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTG
* *
3335412 AAAAAACTCCTCTAAGCAGAGGCTCTACAACTTTAAAAA-T--TCTTG
1 AAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTG
* * * *
3335457 AAAATGCTCCTCTCAGCAGAAGCTCAACAA-TTTAAAAATTTATCTTG
1 AAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTG
* * * *
3335504 AAAAGGCTCCTCTAGGCAGAGACTCCACAACTTT-AAAATT--T-TT-
1 AAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTG
* * * * *
3335547 AAAAATACTCATCTCAA-TAGAGGCTCAATAACTTTAAAATTTCATCTT
1 AAAAA-GCTCCTCT-AAGCAGAGGCTCAACAACTTTAAAAATTCATCTT
3335595 TTCTTAAAAC
Statistics
Matches: 276, Mismatches: 34, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
43 4 0.01
44 30 0.11
45 79 0.29
46 1 0.00
47 73 0.26
48 44 0.16
49 45 0.16
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (48 bp):
AAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTG
Found at i:3335458 original size:93 final size:93
Alignment explanation
Indices: 3335223--3335594 Score: 435
Period size: 93 Copynumber: 4.0 Consensus size: 93
3335213 CAACAATTTT
* * * * * *
3335223 AAAAATCTCATCTTAGCAGAGGCT-TAACAACTTTAAAAATCATCTTGAAAAAGCTCATCTAAGT
1 AAAAAGCTCCTCTAAGCAGAGGCTCT-ACAACTTTAAAAAT--TCTTGAAAATGCTCATCTCAGC
3335287 AGAGGCTCAACAACTTTAAAAATCTCATCTTG
63 AGAGGCTCAACAACTTTAAAAAT-TCATCTTG
* * * * * *
3335319 AAAAAGCTTCTCTCAGTAGAGGCTCAACAACTTTAAAAATTTTTGAAAATGCTCCTCTCAGCAGA
1 AAAAAGCTCCTCTAAGCAGAGGCTCTACAACTTTAAAAATTCTTGAAAATGCTCATCTCAGCAGA
*
3335384 GGCTCAACAACTTTAAAAATTCGTCTTG
66 GGCTCAACAACTTTAAAAATTCATCTTG
* *
3335412 AAAAAACTCCTCTAAGCAGAGGCTCTACAACTTTAAAAATTCTTGAAAATGCTCCTCTCAGCAGA
1 AAAAAGCTCCTCTAAGCAGAGGCTCTACAACTTTAAAAATTCTTGAAAATGCTCATCTCAGCAGA
* *
3335477 AGCTCAACAA-TTTAAAAATTTATCTTG
66 GGCTCAACAACTTTAAAAATTCATCTTG
* * * * * * * **
3335504 AAAAGGCTCCTCTAGGCAGAGACTCCACAACTTT-AAAATTTTTAAAAATACTCATCTCAATAGA
1 AAAAAGCTCCTCTAAGCAGAGGCTCTACAACTTTAAAAATTCTTGAAAATGCTCATCTCAGCAGA
* *
3335568 GGCTCAATAACTTTAAAATTTCATCTT
66 GGCTCAACAACTTTAAAAATTCATCTT
3335595 TTCTTAAAAC
Statistics
Matches: 238, Mismatches: 36, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
91 32 0.13
92 58 0.24
93 75 0.32
94 40 0.17
96 33 0.14
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (93 bp):
AAAAAGCTCCTCTAAGCAGAGGCTCTACAACTTTAAAAATTCTTGAAAATGCTCATCTCAGCAGA
GGCTCAACAACTTTAAAAATTCATCTTG
Found at i:3341378 original size:21 final size:21
Alignment explanation
Indices: 3341339--3341379 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3341329 CTTTGACTTT
*
3341339 CTTTTTCTTTTCATTCTTTTA
1 CTTTTTCTTTTCATACTTTTA
3341360 CTTTTTCTTTTC-TAACTTTT
1 CTTTTTCTTTTCAT-ACTTTT
3341380 TTTATAGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.71
Consensus pattern (21 bp):
CTTTTTCTTTTCATACTTTTA
Found at i:3347787 original size:202 final size:202
Alignment explanation
Indices: 3347424--3347793 Score: 451
Period size: 202 Copynumber: 1.8 Consensus size: 202
3347414 TAAAACTTTG
* * * * * *
3347424 AAGAAAATGAAATTTTTATTATATTGAAGATTTTTTATAAATATTCTAATATACTGGTAATATTT
1 AAGAAAATAAAAATTTTATTATATTGAAAACTTTTTATAAATACTCTAATACACTGGTAATATTT
** * * * *
3347489 AAAAAATCTTTATCACCTAGGGATTTCTTAAAGTATCTCTATTCAGAATACTTTTAGAATCTCAT
66 AAAAAATCTTTATCACCTAAAGATTTCGTAAAGTATCACTACTCAGAATACCTTTAGAATCTCAT
** * *
3347554 AATCGGATAAAATTTCTTTTTTTCTCA-TTTTTTATTACTTATTCTTAATTTATTAATTAATTAT
131 AATCGGATAAAATACCTTTTCTTCACATTTTTTTATTACTTATTCTTAATTTATTAATTAATTAT
3347618 TTTATTA
196 TTTATTA
* *
3347625 AAGAAAATAAAAAATTTTATTGTATTGAAAACTTTTTATAAATACTCTAATACACTGGTAGTATT
1 AAGAAAAT-AAAAATTTTATTATATTGAAAACTTTTTATAAATACTCTAATACACTGGTAATATT
* * * * *
3347690 TAAAAAAATTTTTTTCACCTAAAGATTTCGT-AGGTATCACTACTCGGAGTACCTTT-GAATCTC
65 T-AAAAAATCTTTATCACCTAAAGATTTCGTAAAGTATCACTACTCAGAATACCTTTAGAATCTC
**
3347753 ATCGTCGGATAAAAATACCATTTTCTT-ACATTTTTTTATTA
129 ATAATCGGAT-AAAATACC-TTTTCTTCACATTTTTTTATTA
3347794 ATTTATACTA
Statistics
Matches: 139, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
201 23 0.17
202 76 0.55
203 40 0.29
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (202 bp):
AAGAAAATAAAAATTTTATTATATTGAAAACTTTTTATAAATACTCTAATACACTGGTAATATTT
AAAAAATCTTTATCACCTAAAGATTTCGTAAAGTATCACTACTCAGAATACCTTTAGAATCTCAT
AATCGGATAAAATACCTTTTCTTCACATTTTTTTATTACTTATTCTTAATTTATTAATTAATTAT
TTTATTA
Found at i:3347825 original size:20 final size:19
Alignment explanation
Indices: 3347785--3347821 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3347775 TTCTTACATT
3347785 TTTTTATTAATTTATACTA
1 TTTTTATTAATTTATACTA
3347804 TTTTTATTTAA-TTATACT
1 TTTTTA-TTAATTTATACT
3347822 TATTAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTATTAATTTATACTA
Found at i:3358935 original size:4 final size:4
Alignment explanation
Indices: 3358928--3358961 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
3358918 TATATATGTA
* *
3358928 TATG TATG TATG TATG TAAG TATG TATG CATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TA
3358962 AGTGGGTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.44
Consensus pattern (4 bp):
TATG
Found at i:3358952 original size:16 final size:16
Alignment explanation
Indices: 3358931--3358964 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3358921 ATATGTATAT
*
3358931 GTATGTATGTATGTAA
1 GTATGTATGCATGTAA
3358947 GTATGTATGCATGTAA
1 GTATGTATGCATGTAA
3358963 GT
1 GT
3358965 GGGTATAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.41
Consensus pattern (16 bp):
GTATGTATGCATGTAA
Found at i:3373315 original size:20 final size:20
Alignment explanation
Indices: 3373290--3373329 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3373280 ATCATTTGGG
3373290 TGCCAAAAATCACAATTCAA
1 TGCCAAAAATCACAATTCAA
3373310 TGCCAAAAATCACAATTCAA
1 TGCCAAAAATCACAATTCAA
3373330 ACTATCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.25, G:0.05, T:0.20
Consensus pattern (20 bp):
TGCCAAAAATCACAATTCAA
Found at i:3383081 original size:2 final size:2
Alignment explanation
Indices: 3383074--3383104 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3383064 TGAATGCAAT
3383074 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 T
3383105 TCTAAATTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3390301 original size:42 final size:43
Alignment explanation
Indices: 3390224--3390322 Score: 105
Period size: 42 Copynumber: 2.3 Consensus size: 43
3390214 TTTTTTAATT
* * *
3390224 AATAAAATAATAAATATTTTTAAATTAAATTTTTAAAT-TTTA
1 AATAAAATAATAAATATTTTTAAATAAAATATTTAAATATTGA
*
3390266 AATAAATTAAATAAA-ATTATTT-AATAAAATATTTAAATATTGA
1 AATAAAAT-AATAAATATT-TTTAAATAAAATATTTAAATATTGA
* *
3390309 AATAACATATTAAA
1 AATAAAATAATAAA
3390323 AACTCTCATA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
42 29 0.62
43 18 0.38
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (43 bp):
AATAAAATAATAAATATTTTTAAATAAAATATTTAAATATTGA
Found at i:3390304 original size:13 final size:14
Alignment explanation
Indices: 3390232--3390304 Score: 55
Period size: 13 Copynumber: 5.3 Consensus size: 14
3390222 TTAATAAAAT
3390232 AATAAATATT-TTTA
1 AATAAA-ATTATTTA
*
3390246 AATTAAATT-TTTA
1 AATAAAATTATTTA
* * *
3390259 AATTTTAAATAAATTA
1 AA--TAAAATTATTTA
3390275 AATAAAATTATTT-
1 AATAAAATTATTTA
3390288 AATAAAA-TATTTA
1 AATAAAATTATTTA
3390301 AATA
1 AATA
3390305 TTGAAATAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
12 5 0.10
13 20 0.41
14 13 0.27
15 6 0.12
16 5 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATAAAATTATTTA
Found at i:3390409 original size:29 final size:29
Alignment explanation
Indices: 3390354--3390409 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
3390344 AAATTGATTC
* * *
3390354 ATTTTATATATTTTTTGTTTTATATTTAT
1 ATTTTATATATTTTTTGATTAAAATTTAT
3390383 ATTTTACTATATTTTTT-ATTAAAATTT
1 ATTTTA-TATATTTTTTGATTAAAATTT
3390410 TAATTAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 13 0.57
30 10 0.43
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (29 bp):
ATTTTATATATTTTTTGATTAAAATTTAT
Found at i:3390992 original size:38 final size:38
Alignment explanation
Indices: 3390928--3391000 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
3390918 AAGTTGAATT
* *
3390928 AAAATATTAAATATTAAATTTATATATAATTTTTATCA
1 AAAATATTAAATAATAAATTTATATATAATATTTATCA
* *
3390966 AAAAT-TTAAATAATATTATTTTTATATAATATTTA
1 AAAATATTAAATAATA-AATTTATATATAATATTTA
3391001 AAATGATCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 9 0.30
38 21 0.70
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (38 bp):
AAAATATTAAATAATAAATTTATATATAATATTTATCA
Found at i:3391635 original size:13 final size:12
Alignment explanation
Indices: 3391611--3391640 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
3391601 GAAATTTTGA
3391611 AATTTAAAATTT
1 AATTTAAAATTT
3391623 AATTTATAAATTT
1 AATTTA-AAATTT
3391636 AATTT
1 AATTT
3391641 TTTATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAAAATTT
Found at i:3391677 original size:31 final size:31
Alignment explanation
Indices: 3391614--3391677 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
3391604 ATTTTGAAAT
* **
3391614 TTAAAATTTAATTTATAAATTTAATTTTTTA
1 TTAAAATTTAATTCATAAATTTAATTAATTA
*
3391645 TTAAAATTTGATTCAT-AATTTAATTAAATTA
1 TTAAAATTTAATTCATAAATTTAATT-AATTA
3391676 TT
1 TT
3391678 TGAACTGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (31 bp):
TTAAAATTTAATTCATAAATTTAATTAATTA
Found at i:3392466 original size:18 final size:19
Alignment explanation
Indices: 3392416--3392467 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
3392406 AATAATATTT
3392416 TAAAAATTATTAAT-TAAA
1 TAAAAATTATTAATATAAA
*
3392434 TAAAAATTATAAATAT-AA
1 TAAAAATTATTAATATAAA
* *
3392452 TCAAATTTATTAATAT
1 TAAAAATTATTAATAT
3392468 TTTATTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 28 0.97
19 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAAATTATTAATATAAA
Found at i:3392660 original size:16 final size:16
Alignment explanation
Indices: 3392629--3392664 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
3392619 TAAGAGGGAA
3392629 AAAATATAAATTAAAT
1 AAAATATAAATTAAAT
3392645 AAAAT-TAAATTAAAAT
1 AAAATATAAATT-AAAT
3392661 AAAA
1 AAAA
3392665 GGAAGAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATATAAATTAAAT
Found at i:3397906 original size:14 final size:14
Alignment explanation
Indices: 3397887--3397917 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3397877 TTGATTATCG
3397887 TCTTTCTATTTTCT
1 TCTTTCTATTTTCT
3397901 TCTTTCTATTTTCT
1 TCTTTCTATTTTCT
3397915 TCT
1 TCT
3397918 CTACTCTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (14 bp):
TCTTTCTATTTTCT
Found at i:3398702 original size:31 final size:31
Alignment explanation
Indices: 3398667--3398725 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3398657 AATTCTCGTT
*
3398667 TCGC-TCCAAAATAGAGCTTTAAACTAGAAAC
1 TCGCTTCC-AAATAGAGCCTTAAACTAGAAAC
*
3398698 TCGCTTCCAAATGGAGCCTTAAACTAGA
1 TCGCTTCCAAATAGAGCCTTAAACTAGA
3398726 CAAATTAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (31 bp):
TCGCTTCCAAATAGAGCCTTAAACTAGAAAC
Found at i:3404759 original size:3 final size:3
Alignment explanation
Indices: 3404751--3404775 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3404741 CTTTTGATAC
3404751 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
3404776 CTTAGTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3406928 original size:36 final size:36
Alignment explanation
Indices: 3406881--3406958 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
3406871 CTAATTCGCC
3406881 TAGGTCATATGGAGTGTTACTTGTAGAAAATAGTTT
1 TAGGTCATATGGAGTGTTACTTGTAGAAAATAGTTT
*
3406917 TAGGTCATATGGAGTGTTACTTGTAGAAAATTGTTT
1 TAGGTCATATGGAGTGTTACTTGTAGAAAATAGTTT
*
3406953 TTGGTC
1 TAGGTC
3406959 TAATCTGGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.27, C:0.06, G:0.26, T:0.41
Consensus pattern (36 bp):
TAGGTCATATGGAGTGTTACTTGTAGAAAATAGTTT
Found at i:3408949 original size:42 final size:42
Alignment explanation
Indices: 3408886--3409048 Score: 177
Period size: 42 Copynumber: 3.9 Consensus size: 42
3408876 AGTGGTGAAG
*
3408886 CTTCTGTCCAAGCCCAAAATCAGTCTCAACAAGGTCCTATCA
1 CTTCTGTCCAAGCCCAAAATCAGTCTCAACAAGGTCCTATTA
* * * *
3408928 CTTCTGTCTCAA-CCCACAATCAGCCTCAAAAAGGTCCAATTA
1 CTTCTGTC-CAAGCCCAAAATCAGTCTCAACAAGGTCCTATTA
* ** * * * *
3408970 CTTATGTCCCCGCCCAAAATCTGTCTCAGCAAGGTCCTGTTG
1 CTTCTGTCCAAGCCCAAAATCAGTCTCAACAAGGTCCTATTA
*
3409012 CTTCAGTCCAAGTCCC-AAATCAGTCTCAACAAGGTCC
1 CTTCTGTCCAAG-CCCAAAATCAGTCTCAACAAGGTCC
3409049 CATGACTACA
Statistics
Matches: 96, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
41 1 0.01
42 89 0.93
43 6 0.06
ACGTcount: A:0.28, C:0.34, G:0.13, T:0.25
Consensus pattern (42 bp):
CTTCTGTCCAAGCCCAAAATCAGTCTCAACAAGGTCCTATTA
Found at i:3421997 original size:3 final size:3
Alignment explanation
Indices: 3421989--3422028 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3421979 ACTCTAAATC
3421989 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3422029 CTTGGAAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3428031 original size:125 final size:123
Alignment explanation
Indices: 3427902--3428142 Score: 272
Period size: 124 Copynumber: 1.9 Consensus size: 123
3427892 ATATCATCAA
* * * * * * *
3427902 TAAAAAAAAT-TAGAAATTATTTAAGACATTTTCAATTG-AAAAATGCCTTAAATTATTTTTTTA
1 TAAAAAAAATGAAGAAATTATTTAAGACATTTT---TGGAAAAAATACCTTAAA-AAATCTTTAA
* * * *
3427965 TTTTTTAAAAATAGATTATTTAAAATATTTTTTATT-CAAAAGTACCTTAAATAAATATCATT
62 TTTTTAAAAAAAAGATTATTTAAAATATTTTTGATTAAAAAAG-ACCTTAAATAAATATCATT
* * **
3428027 TAAAAAATATGAAGAGATTATTTAAGGTATTTTTGGAAAAAAATACCTTAAAAAATCTTTAATTT
1 TAAAAAAAATGAAGAAATTATTTAAGACATTTTTGG-AAAAAATACCTTAAAAAATCTTTAATTT
3428092 TTAAAAAAAAGATTATTTAAAATATTTTTGATTAAAAAAGACCTTAAATAA
65 TTAAAAAAAAGATTATTTAAAATATTTTTGATTAAAAAAGACCTTAAATAA
3428143 TTTCTTCATA
Statistics
Matches: 97, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
123 2 0.02
124 50 0.52
125 27 0.28
126 18 0.19
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (123 bp):
TAAAAAAAATGAAGAAATTATTTAAGACATTTTTGGAAAAAATACCTTAAAAAATCTTTAATTTT
TAAAAAAAAGATTATTTAAAATATTTTTGATTAAAAAAGACCTTAAATAAATATCATT
Found at i:3430706 original size:4 final size:4
Alignment explanation
Indices: 3430663--3430687 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3430653 AGGTAGCAAG
3430663 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
3430688 CAGTTTCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:3453843 original size:13 final size:13
Alignment explanation
Indices: 3453825--3453850 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3453815 TTAGTTAAAG
3453825 AAAAATCAAAATA
1 AAAAATCAAAATA
3453838 AAAAATCAAAATA
1 AAAAATCAAAATA
3453851 GAAAGGAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATCAAAATA
Found at i:3453962 original size:62 final size:61
Alignment explanation
Indices: 3453890--3454129 Score: 321
Period size: 60 Copynumber: 4.0 Consensus size: 61
3453880 TTGCGTAGGA
*
3453890 AAAATTGATACTTTCAACTTTT-CTCCAAAAAT-ATTTTTTTTTGGAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAATCATTTTTTTTT-GAAATTTT-ATTTTTAAGG
* *
3453952 AAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTTTAAA-TTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCATTTTTTTTTGAAATTTTATTTTTAAGG
* *
3454012 AAAATTGATACTTTCAACTTTTCCTCAAAAATCATTTTTTTTTGAAAATTTATTTTTTAA-A
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCATTTTTTTTTGAAATTTTA-TTTTTAAGG
* * *
3454073 AAAATTGATACTTTCAACTTTTCC-CTAAAA-GATTTTTTTTGGAAATTTTGATTTTTA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCATTTTTTTTTGAAATTTT-ATTTTTA
3454130 TTTAAAGAAA
Statistics
Matches: 163, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
59 22 0.13
60 60 0.37
61 31 0.19
62 39 0.24
63 11 0.07
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (61 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATCATTTTTTTTTGAAATTTTATTTTTAAGG
Found at i:3454180 original size:29 final size:30
Alignment explanation
Indices: 3454147--3454233 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 30
3454137 AAAATAGAAT
* *
3454147 AATAAAATAAAAAAATGAAAGTGAAAAT-A
1 AATAAAATAAAAAAATGAAAATAAAAATAA
* **
3454176 AATAAAAAAAAAAAAACAAAATAAAAATAA
1 AATAAAATAAAAAAATGAAAATAAAAATAA
*
3454206 AATAAAGATAAAAAGAATGTTAAATAAA
1 AATAAA-ATAAAAA-AATG-AAAATAAA
3454234 CCTAATCTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
29 23 0.51
30 7 0.16
31 6 0.13
32 2 0.04
33 7 0.16
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.16
Consensus pattern (30 bp):
AATAAAATAAAAAAATGAAAATAAAAATAA
Found at i:3454216 original size:6 final size:5
Alignment explanation
Indices: 3454147--3454218 Score: 53
Period size: 5 Copynumber: 14.4 Consensus size: 5
3454137 AAAATAGAAT
* * *
3454147 AATAA AAT-A AA-AA AATGAA AGTGAA AAT-A AATAA AA-AA AAAAA AACAA
1 AATAA AATAA AATAA AAT-AA AAT-AA AATAA AATAA AATAA AATAA AATAA
3454195 AATAAA AATAA AATAA AGATAA AA
1 AAT-AA AATAA AATAA A-ATAA AA
3454219 AGAATGTTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
4 14 0.25
5 23 0.41
6 19 0.34
ACGTcount: A:0.79, C:0.01, G:0.06, T:0.14
Consensus pattern (5 bp):
AATAA
Found at i:3454271 original size:21 final size:22
Alignment explanation
Indices: 3454245--3454287 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3454235 CTAATCTAAT
* *
3454245 AAATAAAT-AAAATAAATAAAC
1 AAATAAATGAAAAAAAAAAAAC
3454266 AAATAAATGAAAAAAAAAAAAC
1 AAATAAATGAAAAAAAAAAAAC
3454288 CTGGAGCGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (22 bp):
AAATAAATGAAAAAAAAAAAAC
Found at i:3455174 original size:17 final size:17
Alignment explanation
Indices: 3455154--3455191 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3455144 AAAAATAATA
* *
3455154 ATAATAATAATAATCAG
1 ATAATAAAAAAAATCAG
3455171 ATAATAAAAAAAATCAG
1 ATAATAAAAAAAATCAG
3455188 ATAA
1 ATAA
3455192 AATTAACAGA
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:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (17 bp):
ATAATAAAAAAAATCAG
Found at i:3455250 original size:3 final size:3
Alignment explanation
Indices: 3455242--3455289 Score: 71
Period size: 3 Copynumber: 15.7 Consensus size: 3
3455232 TATATTTAAA
3455242 AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT -AT AAT AAT ATAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
3455288 AA
1 AA
3455290 CTATATACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.81
4 6 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3455262 original size:16 final size:16
Alignment explanation
Indices: 3455241--3455289 Score: 80
Period size: 16 Copynumber: 2.9 Consensus size: 16
3455231 ATATATTTAA
3455241 AAATAATAATAATAAT
1 AAATAATAATAATAAT
3455257 AAATAATAATAATAAT
1 AAATAATAATAATAAT
3455273 AATATAATAATATATAA
1 AA-ATAATAATA-ATAA
3455290 CTATATACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 18 0.58
17 9 0.29
18 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATAATAATAATAAT
Found at i:3455309 original size:24 final size:22
Alignment explanation
Indices: 3455242--3455309 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 22
3455232 TATATTTAAA
3455242 AATAATAATAATAATAAATA-AT
1 AATAATAATAAT-ATAAATATAT
3455264 AATAATAATAATAT-AATA-AT
1 AATAATAATAATATAAATATAT
3455284 ATATAACTATATACATATAAATATAT
1 A-ATAA-TA-ATA-ATATAAATATAT
3455310 TCTAAATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.17
21 6 0.15
22 14 0.35
23 3 0.08
24 4 0.10
25 4 0.10
26 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAATAATAATATAAATATAT
Found at i:3455371 original size:11 final size:11
Alignment explanation
Indices: 3455340--3455370 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3455330 TATACAAACA
3455340 AGAAAAAAAAG
1 AGAAAAAAAAG
3455351 AGAAAAAAAAG
1 AGAAAAAAAAG
3455362 -GAAAAAAAA
1 AGAAAAAAAA
3455371 ACATACAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:3457740 original size:4 final size:4
Alignment explanation
Indices: 3457728--3457764 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
3457718 ACACACACAG
* *
3457728 ACAT TCAT ACAT ACAT ACAT ACAT AAAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
3457765 TATATATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:3464737 original size:24 final size:25
Alignment explanation
Indices: 3464694--3464758 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
3464684 ATAAAAGAAA
3464694 ACATAAAAAAATAAA-AAATTT-AA-
1 ACATAAAAAAA-AAACAAATTTCAAG
**
3464717 ATGTAAAAAAAAAACATAATTTCAAG
1 ACATAAAAAAAAAACA-AATTTCAAG
3464743 ACATAAAAAAAAAACA
1 ACATAAAAAAAAAACA
3464759 GAAAGAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
22 3 0.09
23 10 0.29
24 5 0.15
25 2 0.06
26 14 0.41
ACGTcount: A:0.71, C:0.08, G:0.03, T:0.18
Consensus pattern (25 bp):
ACATAAAAAAAAAACAAATTTCAAG
Found at i:3465456 original size:27 final size:27
Alignment explanation
Indices: 3465424--3465476 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3465414 ATCGAATTTA
*
3465424 ATTTGATTTGATATT-ATATAAAATTAT
1 ATTTGATATGAT-TTAATATAAAATTAT
*
3465451 ATTTGATATGATTTAATTTAAAATTA
1 ATTTGATATGATTTAATATAAAATTA
3465477 ATAAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (27 bp):
ATTTGATATGATTTAATATAAAATTAT
Done.