Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014373.1 Kokia drynarioides strain JFW-HI SEQ_129411, 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: 813680
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 179 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:413067 original size:199 final size:200
Alignment explanation
Indices: 412560--413069 Score: 487
Period size: 200 Copynumber: 2.6 Consensus size: 200
412550 TGGAATGGAG
* * * * * *
412560 TGAAGTTACCACATCAAATCCTATATCCTTGAAATTTG-AGG-GATCAGATTAAAACTACAGTAG
1 TGAAGTTACGAAATCAAATCCTATATCCCTG-AAGTTGCAGGAAAT-AGATTAAAACTACAATAG
*** * * * * * * *
412623 CAAAT-CTTTATCTCTGTGAAGTTGTAGCACAGCAAGATGAAGCTACAACATCAAATTATATACC
64 CAAATGC-TTATCTCTCCAAAGATGCAGTAGAGTAAGATAAAGCTACAACATCAAATCATATACC
* *
412687 CCTAAAGTTGCAATGGATCGGATTGAAGCTATAACAACAAATCTTATCTCCCTAAAGATGTAATG
128 CCTAAAGTTGCAATGGATCAGATTGAAGCTATAACAACAAATCTTATCTCCCTAAAGATGCAATG
*
412752 GAGTAAGA
193 GAGCAAGA
* * * * *
412760 TGAAGTTACTACATCAAATCCTATATCCTTGAAGTTGCAGGGATTAGATTAAAACTACAATAGCA
1 TGAAGTTACGAAATCAAATCCTATATCCCTGAAGTTGCAGGAAATAGATTAAAACTACAATAGCA
* * * * * * * *
412825 AATGTTTATCTCTCTAAAGTTGCAGTAGAGTAAGATGAAGCTACCACATCAAATCCTATATCTCT
66 AATGCTTATCTCTCCAAAGATGCAGTAGAGTAAGATAAAGCTACAACATCAAATCATATACCCCT
* * * * * * * *
412890 GAAGTTGTAGTGGATCAGATTGAAGCTCA-AA-AGCAAATTTTATCTCCTTGAAGATGCAGTGGA
131 AAAGTTGCAATGGATCAGATTGAAGCT-ATAACAACAAATCTTATCTCCCTAAAGATGCAATGGA
412953 GCAAGA
195 GCAAGA
* * *
412959 TGAAGTTACGAAATCAAATCCTATATCCCTGAAGTTGCAGTAAATCGAATTAAATA-TACATTAG
1 TGAAGTTACGAAATCAAATCCTATATCCCTGAAGTTGCAGGAAATAG-ATTAAA-ACTACAATAG
* * *
413023 C-AA-GCCTTATGTCTCCAAAGATGCAGTGGAGTATGATAAAGCTACAA
64 CAAATG-CTTATCTCTCCAAAGATGCAGTAGAGTAAGATAAAGCTACAA
413070 TATTGAATTC
Statistics
Matches: 259, Mismatches: 44, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
198 1 0.00
199 112 0.43
200 143 0.55
201 3 0.01
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (200 bp):
TGAAGTTACGAAATCAAATCCTATATCCCTGAAGTTGCAGGAAATAGATTAAAACTACAATAGCA
AATGCTTATCTCTCCAAAGATGCAGTAGAGTAAGATAAAGCTACAACATCAAATCATATACCCCT
AAAGTTGCAATGGATCAGATTGAAGCTATAACAACAAATCTTATCTCCCTAAAGATGCAATGGAG
CAAGA
Found at i:414826 original size:8 final size:8
Alignment explanation
Indices: 414808--414847 Score: 62
Period size: 8 Copynumber: 4.8 Consensus size: 8
414798 AGCATTTTTA
414808 TTTTATGTT
1 TTTTAT-TT
414817 TTTTATTTT
1 TTTTA-TTT
414826 TTTTATTT
1 TTTTATTT
414834 TTTTATTT
1 TTTTATTT
414842 TTTTAT
1 TTTTAT
414848 CCTTGATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 17 0.57
9 12 0.40
10 1 0.03
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (8 bp):
TTTTATTT
Found at i:414835 original size:17 final size:18
Alignment explanation
Indices: 414803--414845 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
414793 TTTCCAGCAT
414803 TTTTATTTTATGTTTTTTA
1 TTTT-TTTTATGTTTTTTA
414822 TTTTTTTTAT-TTTTTTA
1 TTTTTTTTATGTTTTTTA
414839 TTTTTTT
1 TTTTTTT
414846 ATCCTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 14 0.58
18 6 0.25
19 4 0.17
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.86
Consensus pattern (18 bp):
TTTTTTTTATGTTTTTTA
Found at i:415015 original size:25 final size:25
Alignment explanation
Indices: 414979--415039 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
414969 ATGTTATATC
414979 TTTATTTATGTTATTAATTATATTA
1 TTTATTTATGTTATTAATTATATTA
* *
415004 TTTA-TTAGTGTTATTTATTTTATTA
1 TTTATTTA-TGTTATTAATTATATTA
* *
415029 TTCATGTATGT
1 TTTATTTATGT
415040 ATTTTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 3 0.10
25 25 0.83
26 2 0.07
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.64
Consensus pattern (25 bp):
TTTATTTATGTTATTAATTATATTA
Found at i:415019 original size:13 final size:12
Alignment explanation
Indices: 414979--415022 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
414969 ATGTTATATC
414979 TTTATTTATGTTA
1 TTTA-TTATGTTA
* *
414992 TTAATTATATTA
1 TTTATTATGTTA
415004 TTTATTAGTGTTA
1 TTTATTA-TGTTA
415017 TTTATT
1 TTTATT
415023 TTATTATTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 13 0.50
13 13 0.50
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (12 bp):
TTTATTATGTTA
Found at i:418341 original size:9 final size:8
Alignment explanation
Indices: 418318--418370 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 8
418308 TAAAAATATT
418318 TATTTTTAA
1 TATTTTT-A
*
418327 TGTTTTTA
1 TATTTTTA
418335 GTATTTTT-
1 -TATTTTTA
418343 TATTTATTA
1 TATTT-TTA
418352 TATTTTTA
1 TATTTTTA
*
418360 AATTTTTA
1 TATTTTTA
418368 TAT
1 TAT
418371 AAAAATCATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
7 5 0.14
8 15 0.41
9 17 0.46
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (8 bp):
TATTTTTA
Found at i:418368 original size:16 final size:16
Alignment explanation
Indices: 418318--418370 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
418308 TAAAAATATT
*
418318 TATTTTTAATGTTTTTA
1 TATTTTTAA-ATTTTTA
*
418335 GTATTTTT-TATTTATTA
1 -TATTTTTAAATTT-TTA
418352 TATTTTTAAATTTTTA
1 TATTTTTAAATTTTTA
418368 TAT
1 TAT
418371 AAAAATCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 16 0.53
17 7 0.23
18 7 0.23
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (16 bp):
TATTTTTAAATTTTTA
Found at i:421440 original size:18 final size:19
Alignment explanation
Indices: 421417--421452 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
421407 CTTCTCCAAT
421417 AGCTCTT-TGAATCAAATC
1 AGCTCTTGTGAATCAAATC
*
421435 AGCTCTTGTGATTCAAAT
1 AGCTCTTGTGAATCAAAT
421453 GAGCCCCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (19 bp):
AGCTCTTGTGAATCAAATC
Found at i:429028 original size:13 final size:13
Alignment explanation
Indices: 429010--429035 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
429000 GGTTTTCTCC
429010 AAAATGAAAATGA
1 AAAATGAAAATGA
429023 AAAATGAAAATGA
1 AAAATGAAAATGA
429036 TCTGAAAATG
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:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAATGAAAATGA
Found at i:429028 original size:58 final size:58
Alignment explanation
Indices: 428905--429025 Score: 172
Period size: 57 Copynumber: 2.1 Consensus size: 58
428895 ATAGAAATGG
*
428905 TGAAAATGGAGAAATGAGAAACATCTGGAAATGATTATGATTTTCTCCAAAATAAAAA
1 TGAAAATGGAGAAATGAGAAACATCTGGAAATGAATATGATTTTCTCCAAAATAAAAA
* * * * * *
428963 TGAAAATGGAGAAAT-TGAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATGAGAAACATCTGGAAATGAATATGATTTTCTCCAAAATAAAAA
429020 TGAAAA
1 TGAAAA
429026 ATGAAAATGA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 41 0.73
58 15 0.27
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.27
Consensus pattern (58 bp):
TGAAAATGGAGAAATGAGAAACATCTGGAAATGAATATGATTTTCTCCAAAATAAAAA
Found at i:432977 original size:26 final size:26
Alignment explanation
Indices: 432941--433013 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
432931 CTAGGAGTTT
432941 GGCCTAGTGAACTGGGGTCGCCATAA
1 GGCCTAGTGAACTGGGGTCGCCATAA
* *
432967 GGCCTAGTGAACTGAGGTCGCCATTA
1 GGCCTAGTGAACTGGGGTCGCCATAA
* * *
432993 GGTCTAGTGAGCTGGAGTCGC
1 GGCCTAGTGAACTGGGGTCGC
433014 TAATTTGGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.21, C:0.22, G:0.36, T:0.22
Consensus pattern (26 bp):
GGCCTAGTGAACTGGGGTCGCCATAA
Found at i:434189 original size:16 final size:17
Alignment explanation
Indices: 434170--434211 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
434160 TTAATCTTTT
434170 AAAAATTATAAAAATA-
1 AAAAATTATAAAAATAG
*
434186 AAAAATAAT-AAAATAG
1 AAAAATTATAAAAATAG
*
434202 TAAAATTATA
1 AAAAATTATA
434212 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAAATTATAAAAATAG
Found at i:448672 original size:52 final size:52
Alignment explanation
Indices: 448588--448961 Score: 473
Period size: 52 Copynumber: 7.2 Consensus size: 52
448578 AATGTAAAAG
* * *
448588 GGTCCGATGACTATGTGTTATCGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGA
* * * **
448640 GGTCTGATGACTACATGTCATCGTGAGCATATGAATCCTTTATGGATTATGA
1 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGA
* **
448692 GG-CTCGATGACTACGTGTCATCATGAGTATATGAATTTTTTACAGATTATGA
1 GGTC-CGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGA
* * * *
448744 GGTTCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACAGATTTTGA
1 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGA
* * ** *
448796 GGTCCGATAACTACGTGTCATCGTGAGCA-AGTGAATCCTTTATGGATTGTGA
1 GGTCCGATGACTACGTGTCATCGTGAGTATA-TGAATCCTTTACAGATTATGA
*
448848 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAA
1 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGA
* * * * *
448900 GGTCCGATAACTACGTGTCATCGTGAGCATGTGAATCCTTTACAGATTGTAA
1 GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGA
*
448952 GGTTCGATGA
1 GGTCCGATGA
448962 TTTTGTTTCA
Statistics
Matches: 279, Mismatches: 39, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
51 2 0.01
52 276 0.99
53 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.34
Consensus pattern (52 bp):
GGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGA
Found at i:448876 original size:156 final size:156
Alignment explanation
Indices: 448588--448947 Score: 535
Period size: 156 Copynumber: 2.3 Consensus size: 156
448578 AATGTAAAAG
* * * *
448588 GGTCCGATGACTATGTGTTATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCTGATGACTA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATAACTA
448653 CATGTCATCGTGAGCATATGAATCCTTTATGGATTATGAGGCTCGATGACTACGTGTCATCATGA
66 CATGTCATCGTGAGCATATGAATCCTTTATGGATTATGAGGCTCGATGACTACGTGTCATCATGA
** *
448718 GTATATGAATTTTTTACAGATTATGA
131 GTATATGAATCCTTTACAGATTATAA
* * *
448744 GGTTCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACAGATTTTGAGGTCCGATAACTA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATAACTA
* * *
448809 CGTGTCATCGTGAGCA-AGTGAATCCTTTATGGATTGTGAGG-TCCGATGACTACGTGTCATCGT
66 CATGTCATCGTGAGCATA-TGAATCCTTTATGGATTATGAGGCT-CGATGACTACGTGTCATCAT
448872 GAGTATATGAATCCTTTACAGATTATAA
129 GAGTATATGAATCCTTTACAGATTATAA
* * * *
448900 GGTCCGATAACTACGTGTCATCGTGAGCATGTGAATCCTTTACAGATT
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATT
448948 GTAAGGTTCG
Statistics
Matches: 183, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
155 2 0.01
156 181 0.99
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (156 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATAACTA
CATGTCATCGTGAGCATATGAATCCTTTATGGATTATGAGGCTCGATGACTACGTGTCATCATGA
GTATATGAATCCTTTACAGATTATAA
Found at i:450886 original size:19 final size:19
Alignment explanation
Indices: 450862--450898 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
450852 CACATTAAAC
450862 ACACAATTAGATCATTTTA
1 ACACAATTAGATCATTTTA
* *
450881 ACACAATTTGATCCTTTT
1 ACACAATTAGATCATTTT
450899 TTGAAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (19 bp):
ACACAATTAGATCATTTTA
Found at i:451427 original size:2 final size:2
Alignment explanation
Indices: 451420--451454 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
451410 CTTTAATTTA
451420 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
451455 CTAATGGTAA
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:454357 original size:5 final size:5
Alignment explanation
Indices: 454349--454376 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
454339 TTCCTTCTAT
454349 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
454377 TATGATTTTT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:457256 original size:18 final size:18
Alignment explanation
Indices: 457217--457257 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
457207 ATTTTAGAAG
*
457217 AAATTAAAATAAAAGATT
1 AAATTAAAATAAAAGATA
457235 AAATTAAAATAAAA-ATGA
1 AAATTAAAATAAAAGAT-A
457253 AAATT
1 AAATT
457258 TTTGGGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
AAATTAAAATAAAAGATA
Found at i:457395 original size:60 final size:60
Alignment explanation
Indices: 457305--457477 Score: 154
Period size: 60 Copynumber: 2.9 Consensus size: 60
457295 AATTAAAAAC
* **
457305 TTTGGAAAGTTCGAGGG-TCAAATTTGAATTTTTAGAAAGTTTAAGGGTCAAAACATAATT
1 TTTGGAAAGTTCGAGGGCTAAAACAT-AATTTTTAGAAAGTTTAAGGGTCAAAACATAATT
* * ** * *
457365 TTTGGAAAGTTCGGGGGCTAAAACATAATTTTTGGAAAGTTCGAGGG-CTAACACATGATT
1 TTTGGAAAGTTCGAGGGCTAAAACATAATTTTTAGAAAGTTTAAGGGTC-AAAACATAATT
*** * * * *
457425 TTCAAAAAATT-TATGGGCCAAAACATAATTTTTAGAAAGTTTAAGGGTAAAAA
1 TTTGGAAAGTTCGA-GGGCTAAAACATAATTTTTAGAAAGTTTAAGGGTCAAAA
457478 ATGGAATTTT
Statistics
Matches: 88, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
59 1 0.01
60 82 0.93
61 5 0.06
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (60 bp):
TTTGGAAAGTTCGAGGGCTAAAACATAATTTTTAGAAAGTTTAAGGGTCAAAACATAATT
Found at i:457413 original size:30 final size:29
Alignment explanation
Indices: 457305--457426 Score: 127
Period size: 30 Copynumber: 4.1 Consensus size: 29
457295 AATTAAAAAC
* **
457305 TTTGGAAAGTTCGAGGGTCAAATTTGAATT
1 TTTGGAAAGTTCGAGGGTAAAACAT-AATT
* **
457335 TTTAGAAAGTTTAAGGGTCAAAACATAATT
1 TTTGGAAAGTTCGAGGGT-AAAACATAATT
*
457365 TTTGGAAAGTTCGGGGGCTAAAACATAATT
1 TTTGGAAAGTTCGAGGG-TAAAACATAATT
* *
457395 TTTGGAAAGTTCGAGGGCTAACACATGATT
1 TTTGGAAAGTTCGAGGG-TAAAACATAATT
457425 TT
1 TT
457427 CAAAAAATTT
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
30 72 0.94
31 5 0.06
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.34
Consensus pattern (29 bp):
TTTGGAAAGTTCGAGGGTAAAACATAATT
Found at i:457488 original size:90 final size:90
Alignment explanation
Indices: 457305--457479 Score: 203
Period size: 90 Copynumber: 2.0 Consensus size: 90
457295 AATTAAAAAC
** * * * * *
457305 TTTGGAAAGTTCGAGGGTCAAATTTGAATTTTTAGAAAGTTTAAGGGTCAAAACATAATTTTTGG
1 TTTGGAAAGTTCGAGGGTCAAACATGAATTTTCAAAAAATTTAAGGGCCAAAACATAATTTTTAG
** *
457370 AAAGTTCGGGGGCTAAAACATAATT
66 AAAGTTCAAGGGCTAAAAAATAATT
*
457395 TTTGGAAAGTTCGAGGG-CTAACACATG-ATTTTCAAAAAATTTATGGGCCAAAACATAATTTTT
1 TTTGGAAAGTTCGAGGGTC-AA-ACATGAATTTTCAAAAAATTTAAGGGCCAAAACATAATTTTT
*
457458 AGAAAGTTTAAGGG-TAAAAAAT
64 AGAAAGTTCAAGGGCTAAAAAAT
457480 GGAATTTTGA
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
89 8 0.11
90 60 0.85
91 3 0.04
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (90 bp):
TTTGGAAAGTTCGAGGGTCAAACATGAATTTTCAAAAAATTTAAGGGCCAAAACATAATTTTTAG
AAAGTTCAAGGGCTAAAAAATAATT
Found at i:461697 original size:26 final size:26
Alignment explanation
Indices: 461635--461715 Score: 101
Period size: 26 Copynumber: 3.2 Consensus size: 26
461625 CGAATCCAAA
* * * * *
461635 CAGAGTATCACTCTTACAAGCCTGAT
1 CAGAATATCGCTCTTACGAGCCAGTT
461661 -AGAATATCGCTCTTACGAGCCAGTT
1 CAGAATATCGCTCTTACGAGCCAGTT
*
461686 CAGAATATCGCTCTTATGAGCCAGTT
1 CAGAATATCGCTCTTACGAGCCAGTT
461712 CAGA
1 CAGA
461716 GTTTAACCAG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
25 20 0.42
26 28 0.58
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (26 bp):
CAGAATATCGCTCTTACGAGCCAGTT
Found at i:463386 original size:22 final size:22
Alignment explanation
Indices: 463361--463412 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
463351 CAATCAAACA
463361 AACTAATTTATAATTTAGCCTT
1 AACTAATTTATAATTTAGCCTT
463383 AACTAATTTATAATTTAGCCTT
1 AACTAATTTATAATTTAGCCTT
463405 AACTAATT
1 AACTAATT
463413 AGGACTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.44
Consensus pattern (22 bp):
AACTAATTTATAATTTAGCCTT
Found at i:468064 original size:26 final size:26
Alignment explanation
Indices: 468007--468064 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
467997 ATCTTAGTGC
* * *
468007 GCTCTCCGTTATTTAGCACGTTATGT
1 GCTCTCCGTTACTCAGCACGTTATAT
*
468033 GATCTCCGTTACTCAGCACGTGTA-AT
1 GCTCTCCGTTACTCAGCACGT-TATAT
468059 GCTCTC
1 GCTCTC
468065 TGATTAGCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (26 bp):
GCTCTCCGTTACTCAGCACGTTATAT
Found at i:468104 original size:22 final size:22
Alignment explanation
Indices: 468058--468108 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
468048 GCACGTGTAA
* **
468058 TGCTCTCTGATTAGCACGTTTG
1 TGCTCTCTGATTAGCACCTCGG
468080 TGCTCTCTGATTAGCACCTCGG
1 TGCTCTCTGATTAGCACCTCGG
468102 TGCTCTC
1 TGCTCTC
468109 CGTTCATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.12, C:0.29, G:0.22, T:0.37
Consensus pattern (22 bp):
TGCTCTCTGATTAGCACCTCGG
Found at i:474378 original size:31 final size:31
Alignment explanation
Indices: 474335--474422 Score: 140
Period size: 31 Copynumber: 2.8 Consensus size: 31
474325 ACTCAACTTT
*
474335 GAAAATGTGACAAAACAGTCACTAAGGTTATC
1 GAAAA-GTGACAAAACAGTCACTAACGTTATC
474367 GAAAAGTGACAAAACAGTCACTAACGTTATC
1 GAAAAGTGACAAAACAGTCACTAACGTTATC
* *
474398 AAAAAGTGACAAAACAGTCTCTAAC
1 GAAAAGTGACAAAACAGTCACTAAC
474423 TCAACACTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 48 0.91
32 5 0.09
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (31 bp):
GAAAAGTGACAAAACAGTCACTAACGTTATC
Found at i:474464 original size:3 final size:3
Alignment explanation
Indices: 474456--474582 Score: 114
Period size: 3 Copynumber: 42.7 Consensus size: 3
474446 AGGGTTTAAA
* *
474456 AAG AAG AAG AAA AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * * * * * * * *
474504 -TG GAG GAG GAG GAG GAG AAG AA- AGAG ACG GAG ACG GAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG A-AG AAG AAG AAG AAG AAG AAG
*
474548 AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
474583 TGAGGAGGAG
Statistics
Matches: 104, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
2 2 0.02
3 101 0.97
4 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.36, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:474646 original size:12 final size:12
Alignment explanation
Indices: 474629--474655 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
474619 TATAAGAAGG
474629 AGAAGAAAAAGA
1 AGAAGAAAAAGA
474641 AGAAGAAAAAGA
1 AGAAGAAAAAGA
474653 AGA
1 AGA
474656 GGAGGAGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAGAAAAAGA
Found at i:474660 original size:3 final size:3
Alignment explanation
Indices: 474654--474692 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
474644 AGAAAAAGAA
* *
474654 GAG GAG GAG GAG GAG GAA GAG AAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
474693 AAAGAGACTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:474672 original size:18 final size:18
Alignment explanation
Indices: 474651--474694 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
474641 AGAAGAAAAA
*
474651 GAAGAGGAGGAGGAGGAG
1 GAAGAGAAGGAGGAGGAG
474669 GAAGAGAAGGAGGAGGAG
1 GAAGAGAAGGAGGAGGAG
*
474687 GAGGAGAA
1 GAAGAGAA
474695 AGAGACTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (18 bp):
GAAGAGAAGGAGGAGGAG
Found at i:474673 original size:21 final size:21
Alignment explanation
Indices: 474655--474819 Score: 77
Period size: 21 Copynumber: 7.7 Consensus size: 21
474645 GAAAAAGAAG
474655 AGGAGGAGGAGGAGGAAGAGA
1 AGGAGGAGGAGGAGGAAGAGA
474676 AGGAGGAGGAGGAGG-AGA-A
1 AGGAGGAGGAGGAGGAAGAGA
*
474695 AGAGACTGAGACGGA-GAAGAAGAAGA
1 AG-GA--G-GA-GGAGGAGGAAG-AGA
* * * * *
474721 AGAAGAAGAAAGAGGAAGAGG
1 AGGAGGAGGAGGAGGAAGAGA
* **
474742 AGGAGGAGAATAAGG-AGAAGA
1 AGGAGGAGGAGGAGGAAG-AGA
* * * *
474763 AGGAGAAGGAGAAGGAGGATA
1 AGGAGGAGGAGGAGGAAGAGA
* * * * *
474784 AAGAGAAGAAGGAGGAAAAGG
1 AGGAGGAGGAGGAGGAAGAGA
474805 AGGAGGAGGAGGAGG
1 AGGAGGAGGAGGAGG
474820 TTGTTCGAGT
Statistics
Matches: 107, Mismatches: 26, Indels: 22
0.69 0.17 0.14
Matches are distributed among these distances:
19 3 0.03
20 7 0.07
21 72 0.67
22 9 0.08
23 6 0.06
24 5 0.05
25 2 0.02
26 3 0.03
ACGTcount: A:0.48, C:0.01, G:0.48, T:0.02
Consensus pattern (21 bp):
AGGAGGAGGAGGAGGAAGAGA
Found at i:474777 original size:6 final size:6
Alignment explanation
Indices: 474658--474779 Score: 57
Period size: 6 Copynumber: 19.8 Consensus size: 6
474648 AAAGAAGAGG
* * * * **
474658 AGGAGG AGGAGGA A-GAGA AGGAGG AGGAGG AGGAGA AAGAGA CTGAGA
1 AGGAGA AGGA-GA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
* * * * * * ** *
474706 CGGAGA AGAAGA AGAAGA AGAAGA AAGAGGAA GAGGAGG AGGAGA ATAAGG
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGA-G-A -AGGAGA AGGAGA AGGAGA
*
474757 AGAAGA AGGAGA AGGAGA AGGAG
1 AGGAGA AGGAGA AGGAGA AGGAG
474780 GATAAAGAGA
Statistics
Matches: 91, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
5 3 0.03
6 80 0.88
7 3 0.03
8 2 0.02
9 3 0.03
ACGTcount: A:0.49, C:0.02, G:0.48, T:0.02
Consensus pattern (6 bp):
AGGAGA
Found at i:474781 original size:9 final size:9
Alignment explanation
Indices: 474658--474818 Score: 78
Period size: 9 Copynumber: 17.9 Consensus size: 9
474648 AAAGAAGAGG
*
474658 AGGAGGAGG
1 AGGAGGAGA
*
474667 AGGAAGAGA
1 AGGAGGAGA
*
474676 AGGAGGAGG
1 AGGAGGAGA
474685 AGGAGGAGAA
1 AGGAGGAG-A
*
474695 AGAGACTGAGA
1 AG-GA-GGAGA
* *
474706 CGGAGAAGA
1 AGGAGGAGA
* *
474715 AGAAGAAGA
1 AGGAGGAGA
* *
474724 A-GAAGAAA
1 AGGAGGAGA
* *
474732 GAGGAAGAGG
1 -AGGAGGAGA
474742 AGGAGGAGA
1 AGGAGGAGA
**
474751 ATAAGGAGA
1 AGGAGGAGA
*
474760 AGAAGGAG-
1 AGGAGGAGA
474768 A--AGGAGA
1 AGGAGGAGA
*
474775 AGGAGGATA
1 AGGAGGAGA
* *
474784 AAGAGAAGA
1 AGGAGGAGA
*
474793 AGGAGGAAA
1 AGGAGGAGA
*
474802 AGGAGGAGG
1 AGGAGGAGA
474811 AGGAGGAG
1 AGGAGGAG
474819 GTTGTTCGAG
Statistics
Matches: 113, Mismatches: 31, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
6 5 0.04
7 1 0.01
8 4 0.04
9 87 0.77
10 9 0.08
11 4 0.04
12 3 0.03
ACGTcount: A:0.49, C:0.01, G:0.48, T:0.02
Consensus pattern (9 bp):
AGGAGGAGA
Found at i:474809 original size:30 final size:31
Alignment explanation
Indices: 474724--474811 Score: 99
Period size: 30 Copynumber: 2.8 Consensus size: 31
474714 AAGAAGAAGA
* * *
474724 AGAAGAAAGAGGAAGAGGAGGAGGAGAATAAGG
1 AGAAGAAGGAGGAAGA--AGGAGGAGGATAAAG
* *
474757 AGAAGAAGGA-GAAGGAGAAGGAGGATAAAG
1 AGAAGAAGGAGGAAGAAGGAGGAGGATAAAG
474787 AGAAGAAGGAGGAA-AAGGAGGAGGA
1 AGAAGAAGGAGGAAGAAGGAGGAGGA
474812 GGAGGAGGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
30 31 0.66
31 3 0.06
32 4 0.09
33 9 0.19
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.02
Consensus pattern (31 bp):
AGAAGAAGGAGGAAGAAGGAGGAGGATAAAG
Found at i:474844 original size:3 final size:3
Alignment explanation
Indices: 474836--474888 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
474826 GAGTCTTTAT
474836 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
474884 GAG AA
1 AAG AA
474889 AGAGGAGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:488920 original size:2 final size:2
Alignment explanation
Indices: 488913--488940 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
488903 TATGTCTAGA
488913 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
488941 GTTCAAATTG
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:489896 original size:23 final size:23
Alignment explanation
Indices: 489853--489896 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
489843 CAAAAGCATC
* *
489853 ATAATTAATCAAGAATTAAAATG
1 ATAATTAATCAAAAATGAAAATG
489876 ATAA-TAATCTAAAAATGAAAA
1 ATAATTAATC-AAAAATGAAAA
489897 ATTAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (23 bp):
ATAATTAATCAAAAATGAAAATG
Found at i:498796 original size:31 final size:31
Alignment explanation
Indices: 498758--498819 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
498748 AAGTCTACAA
498758 GACCATCGCAAGGCAGAAATGGGAAACCTTT
1 GACCATCGCAAGGCAGAAATGGGAAACCTTT
*
498789 GACCATCGCAAGGTAGAAATGGGAAACCTTT
1 GACCATCGCAAGGCAGAAATGGGAAACCTTT
498820 TGCACTCACC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.18
Consensus pattern (31 bp):
GACCATCGCAAGGCAGAAATGGGAAACCTTT
Found at i:501500 original size:26 final size:26
Alignment explanation
Indices: 501470--501523 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
501460 AAATGCTCAC
501470 TAAGAAAGAGGAAAAGGGAGTGCTTT
1 TAAGAAAGAGGAAAAGGGAGTGCTTT
501496 TAAGAAAGAGGAAAAGGGAGTGCTTT
1 TAAGAAAGAGGAAAAGGGAGTGCTTT
501522 TA
1 TA
501524 GTGCATATTC
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:0.43, C:0.04, G:0.33, T:0.20
Consensus pattern (26 bp):
TAAGAAAGAGGAAAAGGGAGTGCTTT
Found at i:506433 original size:23 final size:23
Alignment explanation
Indices: 506407--506820 Score: 578
Period size: 23 Copynumber: 18.0 Consensus size: 23
506397 CTATGCTGAG
506407 ATATTAATGTGATTTGTGCTTAA
1 ATATTAATGTGATTTGTGCTTAA
* *
506430 ATATTATTATGATTTGTGCTTAA
1 ATATTAATGTGATTTGTGCTTAA
* *
506453 ATATTAATGTAATTTATGCTTAA
1 ATATTAATGTGATTTGTGCTTAA
*
506476 ATATTAATGTAATTTGTGCTTAA
1 ATATTAATGTGATTTGTGCTTAA
* * *
506499 ATATTAATATGATTTATGATTAA
1 ATATTAATGTGATTTGTGCTTAA
506522 ATATTAATGTGATTTGTGCTTAA
1 ATATTAATGTGATTTGTGCTTAA
* * **
506545 GTATGAATGTGATTCATGCTTAA
1 ATATTAATGTGATTTGTGCTTAA
* *
506568 ATATTAATATGATTTGTGCTCAA
1 ATATTAATGTGATTTGTGCTTAA
* *
506591 ATATTAATGTGATTTATACTTAA
1 ATATTAATGTGATTTGTGCTTAA
*
506614 ATATTAATGTGATTTATGCTTAA
1 ATATTAATGTGATTTGTGCTTAA
*
506637 ATATTAATGTGATTTGTGCTTTA
1 ATATTAATGTGATTTGTGCTTAA
* *
506660 ATATTAATATGATTTGTGCTCAA
1 ATATTAATGTGATTTGTGCTTAA
*
506683 ATATTAATGTTATTTGTGCTTAA
1 ATATTAATGTGATTTGTGCTTAA
* *
506706 ATATTAATATGATTTGTGCTCAA
1 ATATTAATGTGATTTGTGCTTAA
*
506729 ATATTAATGTGATTTATGCTTAA
1 ATATTAATGTGATTTGTGCTTAA
506752 ATATTAATGTGA-TTGTGCTTAA
1 ATATTAATGTGATTTGTGCTTAA
* * *
506774 ATATTAATATGATTTATGATTAA
1 ATATTAATGTGATTTGTGCTTAA
506797 ATATTAATGTGATTTGTGCTTAA
1 ATATTAATGTGATTTGTGCTTAA
506820 A
1 A
506821 GAATTAAGAT
Statistics
Matches: 340, Mismatches: 50, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
22 20 0.06
23 320 0.94
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (23 bp):
ATATTAATGTGATTTGTGCTTAA
Found at i:506949 original size:36 final size:36
Alignment explanation
Indices: 506900--506990 Score: 114
Period size: 36 Copynumber: 2.5 Consensus size: 36
506890 TGTGAAAGTG
506900 AATATGCTA-GTATGTTCTTCATG-TCATGTGACAAAA
1 AATATG-TAGGTATGTTCTTCATGCT-ATGTGACAAAA
* * *
506936 AATTTGTAGGTATGTTTTTCATGCTATGTGACAGAA
1 AATATGTAGGTATGTTCTTCATGCTATGTGACAAAA
*
506972 AATATGTGGGTATGTTCTT
1 AATATGTAGGTATGTTCTT
506991 TGAAAGGGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 2 0.04
36 44 0.94
37 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.41
Consensus pattern (36 bp):
AATATGTAGGTATGTTCTTCATGCTATGTGACAAAA
Found at i:508510 original size:18 final size:19
Alignment explanation
Indices: 508479--508522 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
508469 AGACCTTTCC
* *
508479 TTATTTTTTATTTATGTGT
1 TTATTTTGTATTTATGTAT
*
508498 TTATTTTGT-TTTATTTAT
1 TTATTTTGTATTTATGTAT
508516 TTATTTT
1 TTATTTT
508523 ATTTATTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (19 bp):
TTATTTTGTATTTATGTAT
Found at i:508524 original size:13 final size:14
Alignment explanation
Indices: 508506--508537 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
508496 GTTTATTTTG
508506 TTTTATTTATTTA-
1 TTTTATTTATTTAC
508519 TTTTATTTATTTAC
1 TTTTATTTATTTAC
508533 TTTTA
1 TTTTA
508538 GCACTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTATTTAC
Found at i:508574 original size:28 final size:28
Alignment explanation
Indices: 508515--508574 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
508505 GTTTTATTTA
* *
508515 TTTATTTTATTTATTTACTTTTAGCACT
1 TTTATTTTATTTATCTACTTTTAGCACC
508543 TTTATTTTATTTTATCTACATTTT-GC-CC
1 TTTATTTTA-TTTATCTAC-TTTTAGCACC
508571 TTTA
1 TTTA
508575 AATAATGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 14 0.50
29 10 0.36
30 4 0.14
ACGTcount: A:0.20, C:0.13, G:0.03, T:0.63
Consensus pattern (28 bp):
TTTATTTTATTTATCTACTTTTAGCACC
Found at i:508796 original size:19 final size:20
Alignment explanation
Indices: 508754--508803 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
508744 CTACTATCCC
**
508754 TATTATTATTTCAATTGTTT
1 TATTATTATTTCAATTGTAG
*
508774 TATTATTATTT-GATTGTAG
1 TATTATTATTTCAATTGTAG
*
508793 TATTTTTATTT
1 TATTATTATTT
508804 TATCTTATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.66
Consensus pattern (20 bp):
TATTATTATTTCAATTGTAG
Found at i:510702 original size:28 final size:28
Alignment explanation
Indices: 510660--510742 Score: 130
Period size: 28 Copynumber: 3.0 Consensus size: 28
510650 AAATGAGCAT
510660 CATGACCTTTGGGTCAATAGGGAGTAAG
1 CATGACCTTTGGGTCAATAGGGAGTAAG
* * *
510688 TATGACCTTTAGGTCAACAGGGAGTAAG
1 CATGACCTTTGGGTCAATAGGGAGTAAG
*
510716 CATGACCTTTGGGTTAATAGGGAGTAA
1 CATGACCTTTGGGTCAATAGGGAGTAA
510743 ATCAGATATT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (28 bp):
CATGACCTTTGGGTCAATAGGGAGTAAG
Found at i:515835 original size:23 final size:23
Alignment explanation
Indices: 515808--516352 Score: 714
Period size: 23 Copynumber: 23.7 Consensus size: 23
515798 TTCTTATATC
*
515808 TATGCTTAAATATTAATGTGATA
1 TATGCTTAAATATTAATGTGATT
*
515831 TATGCTTAAATATTAATGTGATA
1 TATGCTTAAATATTAATGTGATT
*
515854 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* * * *
515877 TAGGATTAAATATTGATGTAATT
1 TATGCTTAAATATTAATGTGATT
* *
515900 TGTGCTTAAGTATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
515923 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* *
515946 TGTGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* * *
515969 TGTGTTTAAATATTAATGTTATT
1 TATGCTTAAATATTAATGTGATT
515992 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
516015 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* * * *
516038 TGTACTTAAAAATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
516061 TATGTTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
516084 TGTGCTTAAGTATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
516107 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* *
516130 TTTGCTTAAAAATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
516153 TATGCTTAAATAATAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
516176 TGTGCTTAAGTATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
516199 TGTGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
516222 TGTGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* *
516245 TGTGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
516268 TATGCTTAAATATTAATGTGA-T
1 TATGCTTAAATATTAATGTGATT
* * *
516290 TGTCCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* *
516313 GATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
516336 TGTGCTTAAATAATTAA
1 TATGCTTAAAT-ATTAA
516353 GATGTGATAT
Statistics
Matches: 452, Mismatches: 68, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
22 19 0.04
23 428 0.95
24 5 0.01
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.46
Consensus pattern (23 bp):
TATGCTTAAATATTAATGTGATT
Found at i:522729 original size:27 final size:28
Alignment explanation
Indices: 522697--522757 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
522687 ACCTGATGAC
*
522697 TTTGACTCGTTGATCATTGA-CTTTGAA
1 TTTGACTCGTTGATCATTGACCATTGAA
* *
522724 TTTGAC-CGTTGATCGTTGACCATTGAC
1 TTTGACTCGTTGATCATTGACCATTGAA
522751 TTTGACT
1 TTTGACT
522758 ATTGACTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.43
Consensus pattern (28 bp):
TTTGACTCGTTGATCATTGACCATTGAA
Found at i:522762 original size:27 final size:26
Alignment explanation
Indices: 522693--522762 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 26
522683 ATTGACCTGA
*
522693 TGACTTTGACTCGTTGATCATTGACTT
1 TGACTTTGACT-GTTGATCATTGACAT
* * *
522720 TGAATTTGACCGTTGATCGTTGACCAT
1 TGACTTTGACTGTTGATCATTGA-CAT
*
522747 TGACTTTGACTATTGA
1 TGACTTTGACTGTTGA
522763 CTTTTTTGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
26 11 0.31
27 24 0.69
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.41
Consensus pattern (26 bp):
TGACTTTGACTGTTGATCATTGACAT
Found at i:524819 original size:23 final size:23
Alignment explanation
Indices: 524789--524832 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
524779 TACGAAACAA
524789 ATCACGAAACA-TGTAAGTACTGT
1 ATCACGAAACATTG-AAGTACTGT
*
524812 ATCACGAAGCATTGAAGTACT
1 ATCACGAAACATTGAAGTACT
524833 ATTACAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (23 bp):
ATCACGAAACATTGAAGTACTGT
Found at i:526641 original size:25 final size:25
Alignment explanation
Indices: 526535--526730 Score: 241
Period size: 25 Copynumber: 7.7 Consensus size: 25
526525 ACAAAGTTTA
*
526535 GCTCTTACGAGCTTATACAGAATATC
1 GCTCTTACGAGC-TAGACAGAATATC
*
526561 GCTCTTACGAGCTTATACAGAATATC
1 GCTCTTACGAGC-TAGACAGAATATC
*
526587 GCTCTTACGAGCTTATACAGAATATC
1 GCTCTTACGAGC-TAGACAGAATATC
* *
526613 GCTCTTACGAGCCAGACAAAATATC
1 GCTCTTACGAGCTAGACAGAATATC
* *
526638 GCTCTTACGAGCCAAACAGAATATC
1 GCTCTTACGAGCTAGACAGAATATC
* * *
526663 GCTCTTACGAG-TCAGATAGAAAATA
1 GCTCTTACGAGCT-AGACAGAATATC
* *
526688 ACTCTTACGAGCTAGATAGAATATC
1 GCTCTTACGAGCTAGACAGAATATC
526713 GCTCTTACGAGCTAGACA
1 GCTCTTACGAGCTAGACA
526731 AAGTTTAACC
Statistics
Matches: 153, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
25 88 0.58
26 65 0.42
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (25 bp):
GCTCTTACGAGCTAGACAGAATATC
Found at i:529720 original size:10 final size:10
Alignment explanation
Indices: 529695--529734 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
529685 TATATATATA
529695 TAAATC-TTT
1 TAAATCATTT
529704 TACAATCATTT
1 TA-AATCATTT
529715 TAAATCATTT
1 TAAATCATTT
*
529725 TAGATCATTT
1 TAAATCATTT
529735 CCTGTACAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 2 0.07
10 21 0.75
11 5 0.18
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (10 bp):
TAAATCATTT
Found at i:531184 original size:30 final size:30
Alignment explanation
Indices: 531148--531208 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
531138 TACAAAATCT
*
531148 GAGGGACTTCTATCGGTTCTTGTTGGACAA
1 GAGGGACTTCTACCGGTTCTTGTTGGACAA
531178 GAGGGACTTCTACCGGTTCTTGTTGGACAA
1 GAGGGACTTCTACCGGTTCTTGTTGGACAA
531208 G
1 G
531209 TATCAGTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (30 bp):
GAGGGACTTCTACCGGTTCTTGTTGGACAA
Found at i:532044 original size:26 final size:26
Alignment explanation
Indices: 531997--532113 Score: 103
Period size: 25 Copynumber: 4.6 Consensus size: 26
531987 TCTAGAAATT
* * * *
531997 TAGCTCATACGAGCCTAGACAGAATT
1 TAGCTCTTACGAGCCCAAACAGAATA
* *
532023 TAGCTCTTACAAGCCCAAACAGAGTA
1 TAGCTCTTACGAGCCCAAACAGAATA
* *
532049 TCGCTCTTACGAG-CCAAATAGAATA
1 TAGCTCTTACGAGCCCAAACAGAATA
* * *
532074 TCGCTCTTACGAG-CTAAACAGATTA
1 TAGCTCTTACGAGCCCAAACAGAATA
* *
532099 TCGCTCTTATGAGCC
1 TAGCTCTTACGAGCC
532114 AGACATAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
25 44 0.58
26 32 0.42
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (26 bp):
TAGCTCTTACGAGCCCAAACAGAATA
Found at i:532075 original size:25 final size:25
Alignment explanation
Indices: 532025--532145 Score: 111
Period size: 25 Copynumber: 4.8 Consensus size: 25
532015 ACAGAATTTA
* * *
532025 GCTCTTACAAGCCCAAACAGAGTATC
1 GCTCTTACGAG-CCAAATAGAATATC
532051 GCTCTTACGAGCCAAATAGAATATC
1 GCTCTTACGAGCCAAATAGAATATC
* * *
532076 GCTCTTACGAGCTAAACAGATTATC
1 GCTCTTACGAGCCAAATAGAATATC
* *
532101 GCTCTTATGAGCCAGACATA-AA-ATT
1 GCTCTTACGAGCCA-A-ATAGAATATC
* *
532126 GCTCTTATGAGCCAGATAGA
1 GCTCTTACGAGCCAAATAGA
532146 GTTTAACCAG
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
23 3 0.04
24 1 0.01
25 62 0.77
26 12 0.15
27 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (25 bp):
GCTCTTACGAGCCAAATAGAATATC
Found at i:532130 original size:50 final size:50
Alignment explanation
Indices: 532025--532139 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 50
532015 ACAGAATTTA
*
532025 GCTCTTACAAGCCCAAACAGAGTATCGCTCTTACGAGCCAAATAGAATATC
1 GCTCTTACGAG-CCAAACAGAGTATCGCTCTTACGAGCCAAATAGAATATC
* * * *
532076 GCTCTTACGAGCTAAACAGATTATCGCTCTTATGAGCCAGACATA-AA-ATT
1 GCTCTTACGAGCCAAACAGAGTATCGCTCTTACGAGCCA-A-ATAGAATATC
*
532126 GCTCTTATGAGCCA
1 GCTCTTACGAGCCA
532140 GATAGAGTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
50 39 0.71
51 13 0.24
52 3 0.05
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (50 bp):
GCTCTTACGAGCCAAACAGAGTATCGCTCTTACGAGCCAAATAGAATATC
Found at i:532422 original size:110 final size:110
Alignment explanation
Indices: 532229--532509 Score: 393
Period size: 110 Copynumber: 2.6 Consensus size: 110
532219 CATGTTACCC
* *
532229 ACTCACGATGCTGCTCACAAAAGCTCTCAGGAAACTGCAATATATGCAGGGTCCAAACCATTGTA
1 ACTCACGATGCTGCTCAAAAAAGCTCTCAGGAAACTGCAACATATGCAGGGTCCAAACCATTGTA
*
532294 GGGGTCCATACAGTCAGTATCTAGTATTCATTCAGAATTCTATTG
66 GGGGTCCATACAGTCAGTATCTAGTATTCATTCAGAATTCTATCG
* * * *
532339 ACTCACGATGCTTCTCAAAAAAGCTCTCAGGAAACTGCAACATATGCATGGTCCCAGCCATTGTA
1 ACTCACGATGCTGCTCAAAAAAGCTCTCAGGAAACTGCAACATATGCAGGGTCCAAACCATTGTA
*
532404 GGGGTCCATACAGTCAGTATCTAGTATTCATTTAGAATTCTATCG
66 GGGGTCCATACAGTCAGTATCTAGTATTCATTCAGAATTCTATCG
* * ** * * * * *
532449 CCTCACGATGCTGCTGACACTAA-CTGTAAGGAAACTACAACATATGCAGGATCCGAACCAT
1 ACTCACGATGCTGCTCA-AAAAAGCTCTCAGGAAACTGCAACATATGCAGGGTCCAAACCAT
532510 CGCGTCGATA
Statistics
Matches: 150, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
110 147 0.98
111 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (110 bp):
ACTCACGATGCTGCTCAAAAAAGCTCTCAGGAAACTGCAACATATGCAGGGTCCAAACCATTGTA
GGGGTCCATACAGTCAGTATCTAGTATTCATTCAGAATTCTATCG
Found at i:534483 original size:20 final size:20
Alignment explanation
Indices: 534458--534495 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
534448 TAACATAAAA
534458 TTTTCCCATATTCATGTTAT
1 TTTTCCCATATTCATGTTAT
534478 TTTTCCCATATTCATGTT
1 TTTTCCCATATTCATGTT
534496 TTATCCCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTTCCCATATTCATGTTAT
Found at i:536659 original size:199 final size:201
Alignment explanation
Indices: 536319--536720 Score: 603
Period size: 199 Copynumber: 2.0 Consensus size: 201
536309 TGAAAAATCT
*
536319 TATTCTAATCAATACGAAATCAATGAAGTGTAGTTCTATACCCCACACAGACCCCTTAATTTCGC
1 TATTCTAATCAATACGAAATCAATGAAGTGTAGTTCTATACCCCACACAAACCCCTTAATTTCGC
* * * *
536384 CACTGTACTTCTTTTTAATAAAGATTTGAGTCACACAATTCTAACAATTTTTGCACTTAATAGTA
66 CACTATACTTCTTTTTAATAAAAAATAGAGTCACACAATTCTAACAATTTTTGCACTTAATAGTA
* *
536449 TAGATAAGGTGAGGCATTGCATCCTTGTGGTTAATCTTAAGACCGTTGGA-G-TGTCCTTAATTG
131 TAGATAAGGTGAGGCATTACATCCATGTGGTTAATCTTAAGACCGTTGGAGGATGTCCTTAATTG
536512 TTGGAA
196 TTGGAA
** *
536518 TATTCTAATCAATGTGAAATCAATGAAGTGTAGTTCTATACCCCACACAAACCCCTTAATTTTGC
1 TATTCTAATCAATACGAAATCAATGAAGTGTAGTTCTATACCCCACACAAACCCCTTAATTTCGC
* * * * * * *
536583 CATTATA-TTTTTCTTTGATAAAAAATAGGGTCACACAATTCTAATAGTTTTTGTACTTAATAGT
66 CACTATACTTCTT-TTTAATAAAAAATAGAGTCACACAATTCTAACAATTTTTGCACTTAATAGT
*
536647 ATAGCTAAGGTGAGGCATTACATCCATGTGGTTAATCTTAAGACCGTTGGAGGATTGTCCTTAAT
130 ATAGATAAGGTGAGGCATTACATCCATGTGGTTAATCTTAAGACCGTTGGAGGA-TGTCCTTAAT
536712 TGTTGGAA
194 TGTTGGAA
536720 T
1 T
536721 TATTACTCCA
Statistics
Matches: 181, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
198 4 0.02
199 157 0.87
200 1 0.01
202 19 0.10
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (201 bp):
TATTCTAATCAATACGAAATCAATGAAGTGTAGTTCTATACCCCACACAAACCCCTTAATTTCGC
CACTATACTTCTTTTTAATAAAAAATAGAGTCACACAATTCTAACAATTTTTGCACTTAATAGTA
TAGATAAGGTGAGGCATTACATCCATGTGGTTAATCTTAAGACCGTTGGAGGATGTCCTTAATTG
TTGGAA
Found at i:536903 original size:18 final size:19
Alignment explanation
Indices: 536864--536912 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
536854 ACCAGTAAAG
* *
536864 AAAACTAGCAAAGATAGGA
1 AAAACCAGCAAAGATAGAA
536883 AAAACCAGCAAAGA-AGAA
1 AAAACCAGCAAAGATAGAA
536901 AAAACCAGCAAA
1 AAAACCAGCAAA
536913 AAAACAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.63, C:0.16, G:0.16, T:0.04
Consensus pattern (19 bp):
AAAACCAGCAAAGATAGAA
Found at i:536921 original size:18 final size:18
Alignment explanation
Indices: 536882--536922 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
536872 CAAAGATAGG
*
536882 AAAAACCAGCAAAGAAGA
1 AAAAACCAGCAAAGAAAA
536900 AAAAACCAGCAAA-AAAA
1 AAAAACCAGCAAAGAAAA
536917 CAAAAA
1 -AAAAA
536923 GGAAACTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.73, C:0.17, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAACCAGCAAAGAAAA
Found at i:544258 original size:9 final size:9
Alignment explanation
Indices: 544236--544287 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
544226 GACATGTGGA
*
544236 AAAAACTAT
1 AAAAATTAT
544245 AAAAATTAGT
1 AAAAATTA-T
544255 AAAAATTAT
1 AAAAATTAT
*
544264 AAAAAAATAT
1 -AAAAATTAT
*
544274 TAAAATTAT
1 AAAAATTAT
544283 AAAAA
1 AAAAA
544288 AATATAGATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 19 0.53
10 17 0.47
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (9 bp):
AAAAATTAT
Found at i:544264 original size:19 final size:18
Alignment explanation
Indices: 544236--544293 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
544226 GACATGTGGA
* *
544236 AAAAACTATAAAAATTAGT
1 AAAAATTATAAAAAATA-T
544255 AAAAATTATAAAAAAATAT
1 AAAAATTAT-AAAAAATAT
*
544274 TAAAATTATAAAAAAATAT
1 AAAAATTAT-AAAAAATAT
544293 A
1 A
544294 GATTTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 27 0.79
20 7 0.21
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAAATTATAAAAAATAT
Found at i:544288 original size:10 final size:10
Alignment explanation
Indices: 544235--544293 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
544225 TGACATGTGG
*
544235 AAAAAACTAT
1 AAAAAATTAT
544245 -AAAAATTAGT
1 AAAAAATTA-T
544255 -AAAAATTAT
1 AAAAAATTAT
*
544264 AAAAAAATAT
1 AAAAAATTAT
*
544274 -TAAAATTAT
1 AAAAAATTAT
*
544283 AAAAAAATAT
1 AAAAAATTAT
544293 A
1 A
544294 GATTTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
9 15 0.38
10 25 0.62
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:544288 original size:29 final size:29
Alignment explanation
Indices: 544235--544293 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
544225 TGACATGTGG
* * *
544235 AAAAAACTATAAAAATTAGTAAAAATTAT
1 AAAAAAATATAAAAATTAGAAAAAAATAT
* *
544264 AAAAAAATATTAAAATTATAAAAAAATAT
1 AAAAAAATATAAAAATTAGAAAAAAATAT
544293 A
1 A
544294 GATTTTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (29 bp):
AAAAAAATATAAAAATTAGAAAAAAATAT
Found at i:544368 original size:19 final size:19
Alignment explanation
Indices: 544304--544368 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
544294 GATTTTTTTT
*
544304 TTATAAAAATTGTAAAAAA
1 TTATAAAAATTATAAAAAA
* ***
544323 -TATCAAAAATTTTAAACTT
1 TTAT-AAAAATTATAAAAAA
*
544342 TTACAAAAATTATAAAAAA
1 TTATAAAAATTATAAAAAA
544361 TTATAAAA
1 TTATAAAA
544369 TGCATTAGAA
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
18 3 0.09
19 29 0.85
20 2 0.06
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
TTATAAAAATTATAAAAAA
Found at i:544580 original size:19 final size:19
Alignment explanation
Indices: 544556--544611 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
544546 GTACGATACT
544556 TTTTATAATTTTTTACGA-A
1 TTTTATAATTTTTTAC-ATA
*
544575 TTTTAT-ATTTCTTTACATT
1 TTTTATAATTT-TTTACATA
544594 TTTTATAATTTTCTTACA
1 TTTTATAATTTT-TTACA
544612 ACTTAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 5 0.16
19 18 0.56
20 9 0.28
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTATAATTTTTTACATA
Found at i:545082 original size:85 final size:85
Alignment explanation
Indices: 544791--545083 Score: 300
Period size: 85 Copynumber: 3.3 Consensus size: 85
544781 AATTAGAGGC
* * * * *
544791 AGTTCAAGTACCCAATTGAGTGCAATAAAATCAGGAGTTTAATTGCTTTTTTGAAAAAGTTTGAG
1 AGTTCAAATACCCAATTGAGTGCAA-AAAAGCAGGGGCTTAATTGTTTTTTTGAAAAAGTTTGAG
* *
544856 GCCCTTTTTTAATACATTTTGAT
65 G-GCTTTTTT-ATATATTTTGAT
* * * * * *
544879 AATTCAAGTACCCGATTGAGTGCAAAAAAAAAAGCAGAGGCTTAATTATTGTTTTCGAAAAAGTT
1 AGTTCAAATACCCAATTGAGTGC----AAAAAAGCAGGGGCTTAATTGTT-TTTTTGAAAAAGTT
* * *
544944 TGAGGGTCTTTTTTATGTACTTTGAC
61 TGAGGG-CTTTTTTATATATTTTGAT
* * * *
544970 AGTTCAAATACTCAATTGAAT-AAAAAAAACAGGGGCTTAATTGTTTTTTTGAAAAAGTTTGAGG
1 AGTTCAAATACCCAATTGAGTGCAAAAAAGCAGGGGCTTAATTGTTTTTTTGAAAAAGTTTGAGG
545034 GCTTTTTTATTATATTTTGAT
66 GCTTTTTTA-TATATTTTGAT
*
545055 AGTTCAAATACCCGATTGAGTGCAAAAAA
1 AGTTCAAATACCCAATTGAGTGCAAAAAA
545084 AAAGAAGACT
Statistics
Matches: 166, Mismatches: 31, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
84 8 0.05
85 45 0.27
86 26 0.16
88 21 0.13
91 39 0.23
92 27 0.16
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (85 bp):
AGTTCAAATACCCAATTGAGTGCAAAAAAGCAGGGGCTTAATTGTTTTTTTGAAAAAGTTTGAGG
GCTTTTTTATATATTTTGAT
Found at i:546073 original size:9 final size:9
Alignment explanation
Indices: 546059--546086 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
546049 AATTTACATT
546059 TTTTTAATA
1 TTTTTAATA
546068 TTTTTAATA
1 TTTTTAATA
546077 TTTTTAATA
1 TTTTTAATA
546086 T
1 T
546087 GAAGAATACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTAATA
Found at i:550251 original size:132 final size:132
Alignment explanation
Indices: 550011--550392 Score: 514
Period size: 132 Copynumber: 2.9 Consensus size: 132
550001 AAATGGGCCT
*
550011 GCTCACACGAGCTGTGGGTTGAGATGTTAGGCTACACGATGCTACTCACACGAGCTATGGAGAAT
1 GCTCACACGAGCTGTGGGTTGAGATGTTAGGCTACACGATGCTACTCACACGAGCTGTGGAGAAT
* * * * * * *
550076 CCGTAACAAATGCATGACCTCAACTATCGATAGGACATCTAAGACCAGTACCCATATAACCTGTA
66 TCGCAACAAATGCAAGACCTCAGCCATCGATAGGACATCTAAGACCAGCACCCATATAACCTATA
550141 AC
131 AC
* ** * * * * *
550143 GTTCACACGAGCTGTGGGTCAAAATGTTAGGCTACACAATGCTGCTCATACCAGCTGTGGAGAAT
1 GCTCACACGAGCTGTGGGTTGAGATGTTAGGCTACACGATGCTACTCACACGAGCTGTGGAGAAT
* * *
550208 TCGCAACAAATGCAGGACCTCAGCCATCGATAGGACATTTAAGAACAGCACCCATATAACCTATA
66 TCGCAACAAATGCAAGACCTCAGCCATCGATAGGACATCTAAGACCAGCACCCATATAACCTATA
550273 AC
131 AC
* * * *
550275 GCTCACATGAGCTGTTGGTTGGGATGTTAGGCTACACGTTGCTACTCACACGAGCTGTGGAGAA-
1 GCTCACACGAGCTGTGGGTTGAGATGTTAGGCTACACGATGCTACTCACACGAGCTGTGGAGAAT
* * * *
550339 TCGCAACAAAAGCAAGACCTCAGCCATAGGTAGGACATCCAAGACCAGCACCCA
66 TCGCAACAAATGCAAGACCTCAGCCATCGATAGGACATCTAAGACCAGCACCCA
550393 AAACTGTAAA
Statistics
Matches: 213, Mismatches: 37, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
131 47 0.22
132 166 0.78
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (132 bp):
GCTCACACGAGCTGTGGGTTGAGATGTTAGGCTACACGATGCTACTCACACGAGCTGTGGAGAAT
TCGCAACAAATGCAAGACCTCAGCCATCGATAGGACATCTAAGACCAGCACCCATATAACCTATA
AC
Found at i:550543 original size:2 final size:2
Alignment explanation
Indices: 550536--550564 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
550526 CATATTTTTC
550536 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
550565 CTTGATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:553682 original size:27 final size:27
Alignment explanation
Indices: 553642--553740 Score: 137
Period size: 27 Copynumber: 3.6 Consensus size: 27
553632 CATTCGCCAC
553642 AAAGGCTTCCTTTAACAGAATTAGTCAT
1 AAAGGC-TCCTTTAACAGAATTAGTCAT
*
553670 GAAA-GCTCCTTTAACAGAATTAGTCAC
1 -AAAGGCTCCTTTAACAGAATTAGTCAT
* *
553697 AAAGGCTTCTTTAACAGAATTAGCCAT
1 AAAGGCTCCTTTAACAGAATTAGTCAT
553724 AAAGGCTTCCTTTAACA
1 AAAGGC-TCCTTTAACA
553741 AAATCGGCCA
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.05
27 46 0.73
28 11 0.17
29 3 0.05
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.29
Consensus pattern (27 bp):
AAAGGCTCCTTTAACAGAATTAGTCAT
Found at i:553703 original size:55 final size:56
Alignment explanation
Indices: 553637--553785 Score: 178
Period size: 55 Copynumber: 2.7 Consensus size: 56
553627 CTCCACATTC
* * *
553637 GCCACAAAGGCTTCCTTTAACAGAATTAGTCATGAAA-GC-TCCTTTAACAGAATTA
1 GCCACAAAGGCTTCCTTTAACAGAATTAGCCAT-AAAGGCTTCCTTTAACAAAATCA
* *
553692 GTCACAAAGGCTT-CTTTAACAGAATTAGCCATAAAGGCTTCCTTTAACAAAATCG
1 GCCACAAAGGCTTCCTTTAACAGAATTAGCCATAAAGGCTTCCTTTAACAAAATCA
** * * *
553747 GCCACAAAAACTTCCTTTAACATAATCAGCCACAAAGGC
1 GCCACAAAGGCTTCCTTTAACAGAATTAGCCATAAAGGC
553786 CTTCATACAA
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
53 3 0.04
54 20 0.25
55 35 0.44
56 22 0.28
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (56 bp):
GCCACAAAGGCTTCCTTTAACAGAATTAGCCATAAAGGCTTCCTTTAACAAAATCA
Found at i:553750 original size:28 final size:28
Alignment explanation
Indices: 553637--553785 Score: 169
Period size: 28 Copynumber: 5.4 Consensus size: 28
553627 CTCCACATTC
553637 GCCACAAAGGCTTCCTTTAACAGAATTA
1 GCCACAAAGGCTTCCTTTAACAGAATTA
* *
553665 GTCATGAAA-GC-TCCTTTAACAGAATTA
1 GCCA-CAAAGGCTTCCTTTAACAGAATTA
*
553692 GTCACAAAGGCTT-CTTTAACAGAATTA
1 GCCACAAAGGCTTCCTTTAACAGAATTA
* * **
553719 GCCATAAAGGCTTCCTTTAACAAAATCG
1 GCCACAAAGGCTTCCTTTAACAGAATTA
** * *
553747 GCCACAAAAACTTCCTTTAACATAATCA
1 GCCACAAAGGCTTCCTTTAACAGAATTA
553775 GCCACAAAGGC
1 GCCACAAAGGC
553786 CTTCATACAA
Statistics
Matches: 102, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
26 3 0.03
27 47 0.46
28 49 0.48
29 3 0.03
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (28 bp):
GCCACAAAGGCTTCCTTTAACAGAATTA
Found at i:564715 original size:14 final size:14
Alignment explanation
Indices: 564692--564721 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
564682 GAAGATCTAT
*
564692 AACAATCACTATAA
1 AACAAACACTATAA
564706 AACAAACACTATAA
1 AACAAACACTATAA
564720 AA
1 AA
564722 GTTGAATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.20, G:0.00, T:0.17
Consensus pattern (14 bp):
AACAAACACTATAA
Found at i:570202 original size:20 final size:20
Alignment explanation
Indices: 570179--570216 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
570169 AAATAAATAA
570179 TTAAAAATTAAAAATTAATT
1 TTAAAAATTAAAAATTAATT
* *
570199 TTAAAATTTAAAATTTAA
1 TTAAAAATTAAAAATTAA
570217 ATATTATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAAAATTAAAAATTAATT
Found at i:570218 original size:13 final size:14
Alignment explanation
Indices: 570172--570222 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
570162 TAACTCAAAA
*
570172 TAAATAATTAAAAAT
1 TAAA-AATTAAAATT
*
570187 TAAAAATT-AATTT
1 TAAAAATTAAAATT
*
570200 TAAAATTTAAAATT
1 TAAAAATTAAAATT
*
570214 TAAATATTA
1 TAAAAATTA
570223 TTTAAATTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
13 10 0.34
14 15 0.52
15 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAAATTAAAATT
Found at i:572600 original size:58 final size:60
Alignment explanation
Indices: 572512--572623 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 60
572502 TTAAATTTTT
* * *
572512 AAAAAAAGTTTAGGTATCAAATTAG-GAAAAAGTGTCAAATTCAGGTACCAAATTGGGTC
1 AAAAAAAGTTTAAGTACCAAATTAGAAAAAAAGTGTCAAATTCAGGTACCAAATTGGGTC
* *
572571 AAAAAAA-TTTAAGTACCAAATTAGAAAAAAAGTGTCAAGTTCATGTACCAAAT
1 AAAAAAAGTTTAAGTACCAAATTAGAAAAAAAGTGTCAAATTCAGGTACCAAAT
572624 ATTATATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 15 0.32
59 32 0.68
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (60 bp):
AAAAAAAGTTTAAGTACCAAATTAGAAAAAAAGTGTCAAATTCAGGTACCAAATTGGGTC
Found at i:572666 original size:21 final size:21
Alignment explanation
Indices: 572637--572680 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
572627 ATATTAAACC
*
572637 TTTTTTGTTTAATAAT-TTTAG
1 TTTTATGTTTAA-AATCTTTAG
*
572658 TTTTATGTTTGAAATCTTTAG
1 TTTTATGTTTAAAATCTTTAG
572679 TT
1 TT
572681 CTTTTTGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.23, C:0.02, G:0.11, T:0.64
Consensus pattern (21 bp):
TTTTATGTTTAAAATCTTTAG
Found at i:573365 original size:17 final size:17
Alignment explanation
Indices: 573340--573377 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
573330 AACCCATTTT
* *
573340 TTTAGATTTATTTTAAG
1 TTTAAATTTATTTTAAA
573357 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
573374 TTTA
1 TTTA
573378 TTCTAAATTT
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:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:573371 original size:11 final size:11
Alignment explanation
Indices: 573357--573388 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
573347 TTATTTTAAG
573357 TTTAAATTTAT
1 TTTAAATTTAT
573368 TTTAAATTTAT
1 TTTAAATTTAT
*
573379 TCTAAATTTA
1 TTTAAATTTA
573389 AATTAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:573377 original size:28 final size:27
Alignment explanation
Indices: 573335--573392 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
573325 AATTAAACCC
* * *
573335 ATTTTTTTAGATTTATTTTAAGTTTAA
1 ATTTTTTTAAATTTATTCTAAATTTAA
573362 ATTTATTTTAAATTTATTCTAAATTTAA
1 ATTT-TTTTAAATTTATTCTAAATTTAA
573390 ATT
1 ATT
573393 AATAATGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (27 bp):
ATTTTTTTAAATTTATTCTAAATTTAA
Found at i:574082 original size:3 final size:3
Alignment explanation
Indices: 574074--574105 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
574064 GAATTAAATA
574074 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
574106 ATAAATAAAT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:575254 original size:29 final size:28
Alignment explanation
Indices: 575157--575638 Score: 236
Period size: 30 Copynumber: 16.5 Consensus size: 28
575147 AAGGACTCTG
*
575157 AACTATCCAAAAATTATATTTTAACCGCCA
1 AACT-TCCAAAAATTATATTTTAACC-TCA
* *
575187 AACTCTCTAAAAATTATATTTTAACCCCTA
1 AACT-TCCAAAAATTATATTTTAACCTC-A
*
575217 AACTTTCCAAAAATTATATTTTAACACTCG
1 AAC-TTCCAAAAATTATATTTTAAC-CTCA
* *
575247 AACTTCCAAAAATTACATTTTGACC-CTA
1 AACTTCCAAAAATTATATTTTAACCTC-A
* * *
575275 AACTTCTAAAAAATTATATTTTATCCT-G
1 AACTTC-CAAAAATTATATTTTAACCTCA
* ** *
575303 AACTTCTCAAAAATTACATTTCGACCCCTA
1 AACTTC-CAAAAATTATATTTTAACCTC-A
* * * * * *
575333 AACTTTTCATAAACTACATTTT-TCCCCTA
1 AAC-TTCCAAAAATTATATTTTAACCTC-A
* ** *
575362 AACTTCTCAAAAATTACATTTTTTCCTGTA
1 AACTTC-CAAAAATTATATTTTAACCT-CA
* * *
575392 AACTTCCAAAAATTACATTTTGATCCCCA
1 AACTTCCAAAAATTATATTTT-AACCTCA
* *
575421 AACTTTCCAAAAATTATCTTGTT-GCCTCCA
1 AAC-TTCCAAAAATTATATT-TTAACCT-CA
* * **
575451 AACTTCCAAAAATCACATTTTTGCCTCA
1 AACTTCCAAAAATTATATTTTAACCTCA
* *
575479 AACTTCTCAAATATTATATTTTTACCCTCA
1 AACTTC-CAAAAATTATA-TTTTAACCTCA
* * *
575509 AACTTCCAGAAAATTAAATTTTGATCCCCA
1 AACTTCCA-AAAATTATATTTT-AACCTCA
* ** *
575539 AACTTTCCAAAAATTACATTTTTGCTCTCG
1 AAC-TTCCAAAAATTATATTTTAAC-CTCA
* * * * *
575569 AACTTTCAAAAATCACATTTTTACCCCTA
1 AACTTCCAAAAATTATATTTTAACCTC-A
* * * * *
575598 TACTT-CAAAAATCACATTTTTACCCCTA
1 AACTTCCAAAAATTATATTTTAACCTC-A
575626 AACTTCCAAAAAT
1 AACTTCCAAAAAT
575639 CACCATTTTA
Statistics
Matches: 366, Mismatches: 61, Indels: 51
0.77 0.13 0.11
Matches are distributed among these distances:
27 1 0.00
28 69 0.19
29 140 0.38
30 144 0.39
31 12 0.03
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (28 bp):
AACTTCCAAAAATTATATTTTAACCTCA
Found at i:575292 original size:58 final size:58
Alignment explanation
Indices: 575165--575637 Score: 229
Period size: 59 Copynumber: 8.1 Consensus size: 58
575155 TGAACTATCC
* * * * * *
575165 AAAAATTATATTTTAACCGCCAAACTCTCTAAAAATTATATTTTAACCCCTAAACTTTCC
1 AAAAATTATATTTTAACC-TCGAACT-TCCAAAAATTACATTTTGACCCCTAAACTTTCA
575225 AAAAATTATATTTTAACACTCGAACTTCCAAAAATTACATTTTGA-CCCTAAAC-TTCTA
1 AAAAATTATATTTTAAC-CTCGAACTTCCAAAAATTACATTTTGACCCCTAAACTTTC-A
* *
575283 AAAAATTATATTTTATCCT-GAACTTCTCAAAAATTACATTTCGACCCCTAAACTTTTC-
1 AAAAATTATATTTTAACCTCGAACTTC-CAAAAATTACATTTTGACCCCTAAAC-TTTCA
* * * * * * ** ** *
575341 ATAAACTACATTTT-TCCCCTAAACTTCTCAAAAATTACATTTTTTCCTGTAAAC-TTCC
1 AAAAATTATATTTTAACCTC-GAACTTC-CAAAAATTACATTTTGACCCCTAAACTTTCA
* * * * *
575399 AAAAATTACATTTTGATCCCCAAACTTTCCAAAAATTATC-TTGTTG-CCTCC-AAAC-TTCC
1 AAAAATTATATTTT-AACCTCGAAC-TTCCAAAAATTA-CATT-TTGACC-CCTAAACTTTCA
* * ** * * * * *
575458 AAAAATCACATTTTTGCCTCAAACTTCTCAAATATTATATTTTTA-CCCTCAAACTTCCA
1 AAAAATTATATTTTAACCTCGAACTTC-CAAAAATTACATTTTGACCCCT-AAACTTTCA
* * * * * * *
575517 GAAAATTAAATTTTGATCCCCAAACTTTCCAAAAATTACATTTTTG--CTCTCGAACTTTC-
1 AAAAATTATATTTT-AACCTCGAAC-TTCCAAAAATTACA-TTTTGACCCCT-AAACTTTCA
* * * * * * * *
575576 AAAAATCACATTTTTACCCCTATACTT-CAAAAATCACATTTTTACCCCTAAACTTCCA
1 AAAAATTATATTTTAACCTCGA-ACTTCCAAAAATTACATTTTGACCCCTAAACTTTCA
575634 AAAA
1 AAAA
575638 TCACCATTTT
Statistics
Matches: 330, Mismatches: 55, Indels: 58
0.74 0.12 0.13
Matches are distributed among these distances:
56 13 0.04
57 49 0.15
58 90 0.27
59 108 0.33
60 62 0.19
61 8 0.02
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (58 bp):
AAAAATTATATTTTAACCTCGAACTTCCAAAAATTACATTTTGACCCCTAAACTTTCA
Found at i:575394 original size:59 final size:58
Alignment explanation
Indices: 575157--575559 Score: 247
Period size: 59 Copynumber: 6.8 Consensus size: 58
575147 AAGGACTCTG
* * * * **
575157 AACTATCCAAAAATTATATTTTAACCGCCAAAC-TCTCTAAAAATTATATTTTAACCCCTA
1 AACT-TCCAAAAACTACATTTTATCC-CCAAACTTCTC-AAAAATTACATTTCGACCCCTA
* * * * * *
575217 AACTTTCCAAAAATTATATTTTAACACTCGAACTTC-CAAAAATTACATTTTGA-CCCTA
1 AAC-TTCCAAAAACTACATTTTATC-CCCAAACTTCTCAAAAATTACATTTCGACCCCTA
* * * **
575275 AACTTCTAAAAAATTATATTTTAT-CCTGAACTTCTCAAAAATTACATTTCGACCCCTA
1 AACTTC-CAAAAACTACATTTTATCCCCAAACTTCTCAAAAATTACATTTCGACCCCTA
* * *** **
575333 AACTTTTCATAAACTACATTTT-TCCCCTAAACTTCTCAAAAATTACATTTTTTCCTGTA
1 AAC-TTCCAAAAACTACATTTTATCCCC-AAACTTCTCAAAAATTACATTTCGACCCCTA
* *
575392 AACTTCCAAAAATTACATTTTGATCCCCAAACTT-TCCAAAAATTATC-TTGTTG-CCTCC-A
1 AACTTCCAAAAACTACATTTT-ATCCCCAAACTTCT-CAAAAATTA-CATT-TCGACC-CCTA
* * * **
575451 AACTTCCAAAAA-TCACATTTT-TGCCTCAAACTTCTCAAATATTATATTTTTA-CCCTCA
1 AACTTCCAAAAACT-ACATTTTAT-CCCCAAACTTCTCAAAAATTACATTTCGACCCCT-A
* *
575509 AACTTCCAGAAAATTAAATTTTGATCCCCAAACTT-TCCAAAAATTACATTT
1 AACTTCCA-AAAACTACATTTT-ATCCCCAAACTTCT-CAAAAATTACATTT
575560 TTGCTCTCGA
Statistics
Matches: 281, Mismatches: 35, Indels: 54
0.76 0.09 0.15
Matches are distributed among these distances:
56 10 0.04
57 24 0.09
58 89 0.32
59 95 0.34
60 58 0.21
61 5 0.02
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (58 bp):
AACTTCCAAAAACTACATTTTATCCCCAAACTTCTCAAAAATTACATTTCGACCCCTA
Found at i:575461 original size:88 final size:85
Alignment explanation
Indices: 575215--575647 Score: 305
Period size: 88 Copynumber: 4.9 Consensus size: 85
575205 TTTTAACCCC
* * * * *
575215 TAAACTT-TCCAAAAATTATATTTTAACACTCGAAC-TTCCAAAAATTACATTTTGACCCTAAAC
1 TAAACTTCT-CAAAAATTACATTTTGAC-CCCAAACTTTCCAAAAATTAC-TTTTG-CCCCAAAC
* * *
575278 TTCTAAAAAATTATATTTTATCCTG
62 TTC-CAAAAATTACATTTTTTCCTG
* * * * *
575303 --AACTTCTCAAAAATTACATTTCGACCCCTAAACTTTTCATAAACTACATTTTTCCCCTAAACT
1 TAAACTTCTCAAAAATTACATTTTGACCCC-AAACTTTCCAAAAATTAC-TTTTGCCCC-AAACT
575366 TCTCAAAAATTACATTTTTTCCTG
63 TC-CAAAAATTACATTTTTTCCTG
575390 TAAACTTC-CAAAAATTACATTTTGATCCCCAAACTTTCCAAAAATTATCTTGTTGCCTCCAAAC
1 TAAACTTCTCAAAAATTACATTTTGA-CCCCAAACTTTCCAAAAATTA-CTT-TTGCC-CCAAAC
* *
575454 TTCCAAAAATCACATTTTTGCCT-
62 TTCCAAAAATTACATTTTTTCCTG
* * * * *
575477 CAAACTTCTCAAATATTATATTTTTACCCTCAAAC-TTCCAGAAAATTAAATTTTGATCCCCAAA
1 TAAACTTCTCAAAAATTACATTTTGACCC-CAAACTTTCCA-AAAATT-ACTTTTG--CCCCAAA
*
575541 CTTTCCAAAAATTACATTTTTGCTCTCG
61 C-TTCCAAAAATTACATTTTTTC-CT-G
* * * * *
575569 --AACTT-TCAAAAATCACATTTTTACCCCTATAC-TT-CAAAAATCACATTTTTACCCCTAAAC
1 TAAACTTCTCAAAAATTACATTTTGACCCC-AAACTTTCCAAAAATTAC--TTTTGCCCC-AAAC
*
575629 TTCCAAAAATCACCATTTT
62 TTCCAAAAATTA-CATTTT
575648 ACCCCCTAGC
Statistics
Matches: 286, Mismatches: 34, Indels: 51
0.77 0.09 0.14
Matches are distributed among these distances:
85 2 0.01
86 42 0.15
87 75 0.26
88 90 0.31
89 68 0.24
90 9 0.03
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (85 bp):
TAAACTTCTCAAAAATTACATTTTGACCCCAAACTTTCCAAAAATTACTTTTGCCCCAAACTTCC
AAAAATTACATTTTTTCCTG
Found at i:575484 original size:117 final size:116
Alignment explanation
Indices: 575247--575647 Score: 376
Period size: 118 Copynumber: 3.4 Consensus size: 116
575237 TTAACACTCG
* * * * **
575247 AACTTC-CAAAAATTACATTTTGACCCTAAACTTCTAAAAAATTATATTTT-AT-CCTGAAC-TT
1 AACTTCTCAAAAATTACATTTTTACCTTAAACTTC-CAAAAATTACATTTTGATCCCCAAACTTT
* * * *
575308 CTCAAAAATTACATT-TCGAC-CCCTAAACTTTTCATAAA-CTACATTTTTCCCCTA
65 C-CAAAAATTACATTGTTG-CTCTC-AAAC-TTCCAAAAATC-ACATTTTTCCCCTA
*
575362 AACTTCTCAAAAATTACATTTTTTCCTGTAAACTTCCAAAAATTACATTTTGATCCCCAAACTTT
1 AACTTCTCAAAAATTACATTTTTACCT-TAAACTTCCAAAAATTACATTTTGATCCCCAAACTTT
*
575427 CCAAAAATTATC-TTGTTGC-CTCCAAACTTCCAAAAATCACATTTTT-GCCTCA
65 CCAAAAATTA-CATTGTTGCTCT-CAAACTTCCAAAAATCACATTTTTCCCCT-A
* * * *
575479 AACTTCTCAAATATTATATTTTTACCCTCAAACTTCCAGAAAATTAAATTTTGATCCCCAAACTT
1 AACTTCTCAAAAATTACATTTTTA-CCTTAAACTTCCA-AAAATTACATTTTGATCCCCAAACTT
* * *
575544 TCCAAAAATTACATTTTTGCTCTCGAACTTTCAAAAATCACATTTTTACCCCTA
64 TCCAAAAATTACATTGTTGCTCTCAAACTTCCAAAAATCACATTTTT-CCCCTA
* * * *
575598 TAC-T-TCAAAAATCACATTTTTACCCCTAAACTTCCAAAAATCACCATTTT
1 AACTTCTCAAAAATTACATTTTTA-CCTTAAACTTCCAAAAATTA-CATTTT
575648 ACCCCCTAGC
Statistics
Matches: 240, Mismatches: 29, Indels: 32
0.80 0.10 0.11
Matches are distributed among these distances:
115 6 0.03
116 39 0.16
117 89 0.37
118 91 0.38
119 12 0.05
120 3 0.01
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (116 bp):
AACTTCTCAAAAATTACATTTTTACCTTAAACTTCCAAAAATTACATTTTGATCCCCAAACTTTC
CAAAAATTACATTGTTGCTCTCAAACTTCCAAAAATCACATTTTTCCCCTA
Found at i:575639 original size:29 final size:29
Alignment explanation
Indices: 575157--575694 Score: 347
Period size: 29 Copynumber: 18.4 Consensus size: 29
575147 AAGGACTCTG
* *
575157 AACTATCCAAAAATTATATTTTAACCGCC-A
1 AACT-TCCAAAAATTACATTTTTACC-CCTA
* * *
575187 AACTCTCTAAAAATTATATTTTAACCCCTA
1 AACT-TCCAAAAATTACATTTTTACCCCTA
* * * *
575217 AACTTTCCAAAAATTATA-TTTTAACACTCG
1 AAC-TTCCAAAAATTACATTTTTACCCCT-A
*
575247 AACTTCCAAAAATTACATTTTGA-CCCTA
1 AACTTCCAAAAATTACATTTTTACCCCTA
* * * *
575275 AACTTCTAAAAAATTATA-TTTTA-TCCTG
1 AACTTC-CAAAAATTACATTTTTACCCCTA
**
575303 AACTTCTCAAAAATTACATTTCGACCCCTA
1 AACTTC-CAAAAATTACATTTTTACCCCTA
* * *
575333 AACTTTTCATAAACTACATTTTT-CCCCTA
1 AAC-TTCCAAAAATTACATTTTTACCCCTA
* **
575362 AACTTCTCAAAAATTACATTTTTTCCTGTA
1 AACTTC-CAAAAATTACATTTTTACCCCTA
*
575392 AACTTCCAAAAATTACATTTTGATCCCC-A
1 AACTTCCAAAAATTACATTTTTA-CCCCTA
* *
575421 AACTTTCCAAAAATTATC-TTGTTGCCTCC-A
1 AAC-TTCCAAAAATTA-CATTTTTACC-CCTA
* * *
575451 AACTTCCAAAAATCACATTTTTGCCTC-A
1 AACTTCCAAAAATTACATTTTTACCCCTA
* *
575479 AACTTCTCAAATATTATATTTTTA-CCCTCA
1 AACTTC-CAAAAATTACATTTTTACCCCT-A
* *
575509 AACTTCCAGAAAATTAAATTTTGATCCCC-A
1 AACTTCCA-AAAATTACATTTTTA-CCCCTA
* * *
575539 AACTTTCCAAAAATTACATTTTT-GCTCTCG
1 AAC-TTCCAAAAATTACATTTTTACCCCT-A
* *
575569 AACTTTCAAAAATCACATTTTTACCCCTA
1 AACTTCCAAAAATTACATTTTTACCCCTA
* *
575598 TACTT-CAAAAATCACATTTTTACCCCTA
1 AACTTCCAAAAATTACATTTTTACCCCTA
*
575626 AACTTCCAAAAATCACCA-TTTTACCCCCT-
1 AACTTCCAAAAATTA-CATTTTTA-CCCCTA
* *
575655 AGCATT-CAAAAATTACCA-TTTTACCCTTA
1 AAC-TTCCAAAAATTA-CATTTTTACCCCTA
**
575684 ATTTTCCAAAA
1 AACTTCCAAAA
575695 GTTCGACTTC
Statistics
Matches: 410, Mismatches: 67, Indels: 63
0.76 0.12 0.12
Matches are distributed among these distances:
28 77 0.19
29 173 0.42
30 148 0.36
31 9 0.02
32 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.36
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACCCCTA
Found at i:580586 original size:12 final size:12
Alignment explanation
Indices: 580569--580603 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
580559 TCAAAATTGA
580569 AAGTGAAAGTGG
1 AAGTGAAAGTGG
*
580581 AAGTGAAATTGG
1 AAGTGAAAGTGG
*
580593 AATTGAAAGTG
1 AAGTGAAAGTG
580604 ATATGAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (12 bp):
AAGTGAAAGTGG
Found at i:584022 original size:75 final size:75
Alignment explanation
Indices: 583899--584048 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
583889 GTGAAAACCT
583899 CACGAAGGAGTAGCTTCTCACTTCCACTTAAGCGGTGTAATAACAAATGTATGTATGCAAAAACT
1 CACGAAGGAGTAGCTTCTCACTTCCACTTAAGCGGTGTAATAACAAATGTATGTATGCAAAAACT
583964 TAAGCATATA
66 TAAGCATATA
583974 CACGAAGGAGTAGCTTCTCACTTCCACTTAAGCGGTGTAATAACAAATGTATGTATGCAAAAACT
1 CACGAAGGAGTAGCTTCTCACTTCCACTTAAGCGGTGTAATAACAAATGTATGTATGCAAAAACT
*
584039 TAGGCATATA
66 TAAGCATATA
584049 ATATTAGCAT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (75 bp):
CACGAAGGAGTAGCTTCTCACTTCCACTTAAGCGGTGTAATAACAAATGTATGTATGCAAAAACT
TAAGCATATA
Found at i:585469 original size:62 final size:63
Alignment explanation
Indices: 585371--585540 Score: 270
Period size: 62 Copynumber: 2.7 Consensus size: 63
585361 TTTGTTTTTT
* *
585371 ATTTATTTATCTATATTCATAAAATAATAAATAAATAATAAAATAAAATAAATATTATTTTAC
1 ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATAAATATTATTTTAC
* * *
585434 ATTTATTT-TTTATATTCATACAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAT
1 ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATAAATATTATTTTAC
585496 ATTTATTTATTTATATTCATAAAAATAATAAATAAATAAATAAAA
1 ATTTATTTATTTATATTCAT-AAAATAATAAATAAAT-AATAAAA
585541 ATAATAAGAA
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
62 57 0.58
63 19 0.19
64 15 0.15
65 7 0.07
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (63 bp):
ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATAAATATTATTTTAC
Found at i:585890 original size:28 final size:27
Alignment explanation
Indices: 585846--585898 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
585836 TTAAATTAAA
*
585846 ATTTAATTTGAATAAAATTTTAATTTTT
1 ATTTAATTTGAATAAAA-ATTAATTTTT
*
585874 ATTTAATTTCTAA-AAAAATTAATTT
1 ATTTAATTT-GAATAAAAATTAATTT
585899 AAATAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 7 0.32
28 13 0.59
29 2 0.09
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTTAATTTGAATAAAAATTAATTTTT
Found at i:586140 original size:23 final size:21
Alignment explanation
Indices: 586114--586163 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
586104 CCATATTAGT
*
586114 TTTTTTTTTAAATATTTATATTA
1 TTTTTTTTT-AATATTTA-ATAA
*
586137 TTTTATTTTAATATTTAATAA
1 TTTTTTTTTAATATTTAATAA
586158 TTTTTT
1 TTTTTT
586164 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.33
22 8 0.33
23 8 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTTTTTAATATTTAATAA
Found at i:586149 original size:22 final size:22
Alignment explanation
Indices: 586114--586161 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
586104 CCATATTAGT
* *
586114 TTTTTTTTTAAATATTTATATTA
1 TTTTATTTTAAATATTTA-ATAA
586137 TTTTATTTT-AATATTTAATAA
1 TTTTATTTTAAATATTTAATAA
586158 TTTT
1 TTTT
586162 TTAATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 8 0.35
23 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTATTTTAAATATTTAATAA
Found at i:586164 original size:23 final size:23
Alignment explanation
Indices: 586113--586213 Score: 68
Period size: 23 Copynumber: 4.3 Consensus size: 23
586103 CCCATATTAG
586113 TTTTTT-TTTTAAATATTT-AT-A
1 TTTTTTATTTT-AATATTTAATAA
586134 TTATTTTATTTTAATATTTAATAA
1 TT-TTTTATTTTAATATTTAATAA
* *
586158 TTTTTTAATTTT-TTATTTATTGAAA
1 TTTTTT-ATTTTAATATTTAAT--AA
* *
586183 TTTTTTA-TATAGTCATCTTAATAA
1 TTTTTTATTTTAAT-AT-TTAATAA
586207 TTTTTTA
1 TTTTTTA
586214 ATGTAGAATC
Statistics
Matches: 65, Mismatches: 5, Indels: 17
0.75 0.06 0.20
Matches are distributed among these distances:
21 2 0.03
22 11 0.17
23 19 0.29
24 19 0.29
25 10 0.15
26 4 0.06
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTTTATTTTAATATTTAATAA
Found at i:606953 original size:3 final size:3
Alignment explanation
Indices: 606945--606994 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
606935 TATCTATTGC
*
606945 TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
606993 TT
1 TT
606995 TGTGAGCGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:620943 original size:20 final size:20
Alignment explanation
Indices: 620900--620945 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
620890 CAAGGGGAAA
*
620900 GTATCGATACTAAATTATAAG
1 GTATCGATACTAAA-TACAAG
620921 GTATCGATACCTAAA-ACAAG
1 GTATCGATA-CTAAATACAAG
620941 GTATC
1 GTATC
620946 TGTACCCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 9 0.39
22 5 0.22
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
GTATCGATACTAAATACAAG
Found at i:621312 original size:12 final size:12
Alignment explanation
Indices: 621295--621324 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
621285 GTCACACGGT
621295 CGTGTAACAACC
1 CGTGTAACAACC
*
621307 CGTGTAACCACC
1 CGTGTAACAACC
621319 CGTGTA
1 CGTGTA
621325 TACATGCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (12 bp):
CGTGTAACAACC
Found at i:627941 original size:23 final size:23
Alignment explanation
Indices: 627911--628009 Score: 157
Period size: 23 Copynumber: 4.3 Consensus size: 23
627901 ACAATAGCGC
*
627911 GCTTACTG-TTCAGCACTGTGTGT
1 GCTTACTGATTC-GCATTGTGTGT
627934 GCTTACTGATTCGCATTGTGTGT
1 GCTTACTGATTCGCATTGTGTGT
627957 GCTTACTGATTCGCATTGTGTGT
1 GCTTACTGATTCGCATTGTGTGT
627980 GCTTACTGA-TCAGCATTGTGTGT
1 GCTTACTGATTC-GCATTGTGTGT
628003 GCTTACT
1 GCTTACT
628010 ATTGCCCAGC
Statistics
Matches: 73, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
22 2 0.03
23 68 0.93
24 3 0.04
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.41
Consensus pattern (23 bp):
GCTTACTGATTCGCATTGTGTGT
Found at i:628285 original size:24 final size:24
Alignment explanation
Indices: 628240--628286 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
628230 TATATGTGTA
*
628240 TAAGTAATTAAATGATGATAAAAC
1 TAAGTAATTAAATGAGGATAAAAC
*
628264 TAAGTAAGTTAAA-GAGGCTAAAA
1 TAAGTAA-TTAAATGAGGATAAAA
628287 TAGCTAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.26
Consensus pattern (24 bp):
TAAGTAATTAAATGAGGATAAAAC
Found at i:629267 original size:37 final size:37
Alignment explanation
Indices: 629214--629467 Score: 303
Period size: 37 Copynumber: 6.9 Consensus size: 37
629204 TAGGGGTGTT
* *
629214 ACACAAAGACTTCTAGGCACATAGCCTGAATACACCG
1 ACACAAAGCCTACTAGGCACATAGCCTGAATACACCG
* * **
629251 ACACAAAGCCTACTAGGCACAAAGCTTGAATACACTT
1 ACACAAAGCCTACTAGGCACATAGCCTGAATACACCG
* * *
629288 ACACAAAGCATACTAGGCCCATAGCCTAAATACACCG
1 ACACAAAGCCTACTAGGCACATAGCCTGAATACACCG
* * *
629325 GCACAAAGCCTACTAGGCACATAGCTTGAATACACCT
1 ACACAAAGCCTACTAGGCACATAGCCTGAATACACCG
* *
629362 ACACAAAGCATACTAGGCACATAGCCTGAAGACACCG
1 ACACAAAGCCTACTAGGCACATAGCCTGAATACACCG
* * **
629399 GCACAAAGCCTACTAGGCACATAGCTTGAATATTCC-
1 ACACAAAGCCTACTAGGCACATAGCCTGAATACACCG
* * *
629435 AGCACAAAGTCTGCTATGCACATAGCCTGAATA
1 A-CACAAAGCCTACTAGGCACATAGCCTGAATA
629468 TTTAGATGCA
Statistics
Matches: 181, Mismatches: 35, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
37 181 1.00
ACGTcount: A:0.38, C:0.29, G:0.16, T:0.17
Consensus pattern (37 bp):
ACACAAAGCCTACTAGGCACATAGCCTGAATACACCG
Found at i:629333 original size:74 final size:74
Alignment explanation
Indices: 629212--629430 Score: 359
Period size: 74 Copynumber: 3.0 Consensus size: 74
629202 TGTAGGGGTG
* * *
629212 TTACACAAAG-ACTTCTAGGCACATAGCCTGAATACACCGACACAAAGCCTACTAGGCACAAAGC
1 TTACACAAAGCA-TACTAGGCACATAGCCTGAATACACCGGCACAAAGCCTACTAGGCACATAGC
629276 TTGAATACAC
65 TTGAATACAC
* *
629286 TTACACAAAGCATACTAGGCCCATAGCCTAAATACACCGGCACAAAGCCTACTAGGCACATAGCT
1 TTACACAAAGCATACTAGGCACATAGCCTGAATACACCGGCACAAAGCCTACTAGGCACATAGCT
629351 TGAATACAC
66 TGAATACAC
* *
629360 CTACACAAAGCATACTAGGCACATAGCCTGAAGACACCGGCACAAAGCCTACTAGGCACATAGCT
1 TTACACAAAGCATACTAGGCACATAGCCTGAATACACCGGCACAAAGCCTACTAGGCACATAGCT
629425 TGAATA
66 TGAATA
629431 TTCCAGCACA
Statistics
Matches: 135, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
74 134 0.99
75 1 0.01
ACGTcount: A:0.38, C:0.29, G:0.16, T:0.17
Consensus pattern (74 bp):
TTACACAAAGCATACTAGGCACATAGCCTGAATACACCGGCACAAAGCCTACTAGGCACATAGCT
TGAATACAC
Found at i:629441 original size:74 final size:73
Alignment explanation
Indices: 629226--629467 Score: 351
Period size: 74 Copynumber: 3.3 Consensus size: 73
629216 ACAAAGACTT
* * *
629226 CTAGGCACATAGCCTGAATACACCGACACAAAGCCTACTAGGCACAAAGCTTGAATACACTTACA
1 CTAGGCACATAGCCTGAATACACCGGCACAAAGCCTACTAGGCACATAGCTTGAATACAC-CACA
629291 CAAAGCATA
65 CAAAGCATA
* *
629300 CTAGGCCCATAGCCTAAATACACCGGCACAAAGCCTACTAGGCACATAGCTTGAATACACCTACA
1 CTAGGCACATAGCCTGAATACACCGGCACAAAGCCTACTAGGCACATAGCTTGAATACACC-ACA
629365 CAAAGCATA
65 CAAAGCATA
* **
629374 CTAGGCACATAGCCTGAAGACACCGGCACAAAGCCTACTAGGCACATAGCTTGAATATTCCAGCA
1 CTAGGCACATAGCCTGAATACACCGGCACAAAGCCTACTAGGCACATAGCTTGAATACACCA-CA
*
629439 CAAAGTC-TG
65 CAAAG-CATA
*
629448 CTATGCACATAGCCTGAATA
1 CTAGGCACATAGCCTGAATA
629468 TTTAGATGCA
Statistics
Matches: 152, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
73 1 0.01
74 150 0.99
75 1 0.01
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (73 bp):
CTAGGCACATAGCCTGAATACACCGGCACAAAGCCTACTAGGCACATAGCTTGAATACACCACAC
AAAGCATA
Found at i:632883 original size:52 final size:52
Alignment explanation
Indices: 632821--632980 Score: 257
Period size: 52 Copynumber: 3.1 Consensus size: 52
632811 CCTTCACTCG
* *
632821 AAATCACATGACCGAGAAATCCCACTTTCGAAAGCCAAAACTCGCATTTTCT
1 AAATCACATGACCGAGAAATCTCACTTTCGAAAGCCAAAACTCGCATTTGCT
** *
632873 AAATCACATGATTGAGAAATCTCACTTTCGAAAGCCAAAACTCGTATTTGCT
1 AAATCACATGACCGAGAAATCTCACTTTCGAAAGCCAAAACTCGCATTTGCT
*
632925 AAACTTACATGACCGAGAAATCTCACTTTCGAAAGCCAAAACTCGCATTTGCT
1 AAA-TCACATGACCGAGAAATCTCACTTTCGAAAGCCAAAACTCGCATTTGCT
632978 AAA
1 AAA
632981 CTTATCATAT
Statistics
Matches: 98, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
52 50 0.51
53 48 0.49
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (52 bp):
AAATCACATGACCGAGAAATCTCACTTTCGAAAGCCAAAACTCGCATTTGCT
Found at i:632958 original size:53 final size:53
Alignment explanation
Indices: 632826--632984 Score: 257
Period size: 53 Copynumber: 3.0 Consensus size: 53
632816 ACTCGAAATC
* * *
632826 ACATGACCGAGAAATCCCACTTTCGAAAGCCAAAACTCGCATTTTCTAAA-TC
1 ACATGACCGAGAAATCTCACTTTCGAAAGCCAAAACTCGCATTTGCTAAACTT
** *
632878 ACATGATTGAGAAATCTCACTTTCGAAAGCCAAAACTCGTATTTGCTAAACTT
1 ACATGACCGAGAAATCTCACTTTCGAAAGCCAAAACTCGCATTTGCTAAACTT
632931 ACATGACCGAGAAATCTCACTTTCGAAAGCCAAAACTCGCATTTGCTAAACTT
1 ACATGACCGAGAAATCTCACTTTCGAAAGCCAAAACTCGCATTTGCTAAACTT
632984 A
1 A
632985 TCATATAATT
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
52 45 0.46
53 52 0.54
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (53 bp):
ACATGACCGAGAAATCTCACTTTCGAAAGCCAAAACTCGCATTTGCTAAACTT
Found at i:636741 original size:37 final size:37
Alignment explanation
Indices: 636691--636987 Score: 346
Period size: 37 Copynumber: 8.0 Consensus size: 37
636681 CTTCTTGATT
*
636691 CACCGGCACAAAGCCTAC-ATGGCATATAG-CTCGAATA
1 CACCGGCACAAAGCCTACTA-GGCACATAGCCT-GAATA
* *
636728 CACCGGCACAAAGCCTACTAAGCACATAGCCTAAATA
1 CACCGGCACAAAGCCTACTAGGCACATAGCCTGAATA
* * * *
636765 CACCGGCACAAAGACTTCTAGGCACATAGCCTAAATG
1 CACCGGCACAAAGCCTACTAGGCACATAGCCTGAATA
* * *
636802 CACTGGCACAAAGCCTACTAGGCACATAGCTTGAATG
1 CACCGGCACAAAGCCTACTAGGCACATAGCCTGAATA
* * * *
636839 CACCGGCAGAAAACTTGCTAGGCACATTAGCCTGAATA
1 CACCGGCACAAAGCCTACTAGGCACA-TAGCCTGAATA
* *
636877 CACCGGCACAAAGCCTGCTAGGCACATAGCCTGGATA
1 CACCGGCACAAAGCCTACTAGGCACATAGCCTGAATA
* * * *
636914 TACTGGCACAAAGCCTGCTAGGCACATAGCCTGGATA
1 CACCGGCACAAAGCCTACTAGGCACATAGCCTGAATA
* * *
636951 TACTGGCACAAAGCCTGCTAGGCACATAGCCTGAATA
1 CACCGGCACAAAGCCTACTAGGCACATAGCCTGAATA
636988 TTTAAATGCA
Statistics
Matches: 231, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
37 196 0.85
38 35 0.15
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.17
Consensus pattern (37 bp):
CACCGGCACAAAGCCTACTAGGCACATAGCCTGAATA
Found at i:636902 original size:16 final size:16
Alignment explanation
Indices: 636881--636983 Score: 71
Period size: 16 Copynumber: 5.8 Consensus size: 16
636871 TGAATACACC
636881 GGCACAAAGCCTGCTA
1 GGCACAAAGCCTGCTA
* *
636897 GGCACATAGCCTGGATATA
1 GGCACAAAGCCT-G--CTA
636916 CTGGCACAAAGCCTGCTA
1 --GGCACAAAGCCTGCTA
* *
636934 GGCACATAGCCTGGATATA
1 GGCACAAAGCCT-G--CTA
636953 CTGGCACAAAGCCTGCTA
1 --GGCACAAAGCCTGCTA
*
636971 GGCACATAGCCTG
1 GGCACAAAGCCTG
636984 AATATTTAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
16 34 0.50
17 2 0.03
18 4 0.06
19 4 0.06
20 2 0.03
21 22 0.32
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.17
Consensus pattern (16 bp):
GGCACAAAGCCTGCTA
Found at i:636923 original size:21 final size:21
Alignment explanation
Indices: 636897--636967 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
636887 AAGCCTGCTA
*
636897 GGCACATAGCCTGGATATACT
1 GGCACAAAGCCTGGATATACT
*
636918 GGCACAAAGCCT-G--CTA--
1 GGCACAAAGCCTGGATATACT
*
636934 GGCACATAGCCTGGATATACT
1 GGCACAAAGCCTGGATATACT
636955 GGCACAAAGCCTG
1 GGCACAAAGCCTG
636968 CTAGGCACAT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
16 11 0.28
17 1 0.03
18 2 0.05
19 2 0.05
20 1 0.03
21 23 0.57
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (21 bp):
GGCACAAAGCCTGGATATACT
Found at i:641828 original size:63 final size:63
Alignment explanation
Indices: 641758--641883 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
641748 ATGATGATTG
* *
641758 GATGATGATTTATATTTAAGTAAATAAGAATTGATGTCATGATGGATTGATATTGAATTGTAT
1 GATGATGATATATATTTAAGTAAATAAGAATGGATGTCATGATGGATTGATATTGAATTGTAT
641821 GATGATGATATATATTTAAGTAAATAAGAATGGATGTCATGATGGATTGATATTGAATTGTAT
1 GATGATGATATATATTTAAGTAAATAAGAATGGATGTCATGATGGATTGATATTGAATTGTAT
641884 AGTATACAGT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (63 bp):
GATGATGATATATATTTAAGTAAATAAGAATGGATGTCATGATGGATTGATATTGAATTGTAT
Found at i:647356 original size:16 final size:17
Alignment explanation
Indices: 647317--647372 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 17
647307 ATTTGGAAGC
*
647317 ACTTTTTCTCTAAAAA-
1 ACTTTTTGTCTAAAAAT
** *
647333 ACAGTTTGTTTAAAAAT
1 ACTTTTTGTCTAAAAAT
647350 A-TTTTTGTCTAAAAAT
1 ACTTTTTGTCTAAAAAT
647366 ACTTTTT
1 ACTTTTT
647373 ATGTGAAAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
16 25 0.81
17 6 0.19
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (17 bp):
ACTTTTTGTCTAAAAAT
Found at i:663562 original size:18 final size:18
Alignment explanation
Indices: 663527--663572 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
663517 CATTTGAAGT
* **
663527 TGTGAGCTCGTTGGAAAC
1 TGTGAGCTCATTCAAAAC
663545 TGTGAGCTCATTCAAAAC
1 TGTGAGCTCATTCAAAAC
*
663563 TGCGAGCTCA
1 TGTGAGCTCA
663573 CCCAAAGACG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (18 bp):
TGTGAGCTCATTCAAAAC
Found at i:679655 original size:12 final size:12
Alignment explanation
Indices: 679638--679684 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
679628 TATCTTCTTG
679638 TTTTTCATTTTC
1 TTTTTCATTTTC
* *
679650 TTTTTC-TACTTG
1 TTTTTCAT-TTTC
679662 TTTTTCATTTTC
1 TTTTTCATTTTC
*
679674 TTTTTCCTTTT
1 TTTTTCATTTT
679685 AAGAACTCTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
11 1 0.04
12 26 0.93
13 1 0.04
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTTCATTTTC
Found at i:679662 original size:24 final size:24
Alignment explanation
Indices: 679634--679679 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
679624 TGGGTATCTT
679634 CTTGTTTTTCATTTTCTTTTTCTA
1 CTTGTTTTTCATTTTCTTTTTCTA
679658 CTTGTTTTTCATTTTCTTTTTC
1 CTTGTTTTTCATTTTCTTTTTC
679680 CTTTTAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.72
Consensus pattern (24 bp):
CTTGTTTTTCATTTTCTTTTTCTA
Found at i:691896 original size:24 final size:24
Alignment explanation
Indices: 691861--691909 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
691851 TAAGCAATAA
*
691861 GGATAAACCAAGAAGAGATGGAAT
1 GGATAAAACAAGAAGAGATGGAAT
691885 GGATAAAACAAGAAGAGATGGAAT
1 GGATAAAACAAGAAGAGATGGAAT
691909 G
1 G
691910 AAGAAATGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.06, G:0.31, T:0.12
Consensus pattern (24 bp):
GGATAAAACAAGAAGAGATGGAAT
Found at i:696419 original size:11 final size:10
Alignment explanation
Indices: 696403--696438 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
696393 TTATTTTTTC
696403 TTTTTCTATTA
1 TTTTTCT-TTA
*
696414 TTTTTCTTTT
1 TTTTTCTTTA
696424 TTTTTCTTTA
1 TTTTTCTTTA
696434 TTTTT
1 TTTTT
696439 TTATCATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTCTTTA
Found at i:696424 original size:31 final size:31
Alignment explanation
Indices: 696388--696449 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
696378 CCACGGAATA
* * *
696388 TTTTTTTATTTTTTCTTTTTCTATTATTTTTC
1 TTTTTTT-TTCTTTATTTTTCTATCATTTTTC
*
696420 TTTTTTTTTCTTTATTTTTTTATCATTTTT
1 TTTTTTTTTCTTTATTTTTCTATCATTTTT
696450 TTTGTGAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (31 bp):
TTTTTTTTTCTTTATTTTTCTATCATTTTTC
Found at i:696439 original size:11 final size:11
Alignment explanation
Indices: 696403--696439 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
696393 TTATTTTTTC
696403 TTTTTCTATTA-
1 TTTTTCT-TTAT
696414 TTTTTCTTT-T
1 TTTTTCTTTAT
696424 TTTTTCTTTAT
1 TTTTTCTTTAT
696435 TTTTT
1 TTTTT
696440 TATCATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 11 0.46
11 13 0.54
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTAT
Found at i:696439 original size:21 final size:22
Alignment explanation
Indices: 696398--696438 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
696388 TTTTTTTATT
696398 TTTTCTTTTTCTATTATTTTTC
1 TTTTCTTTTTCTATTATTTTTC
696420 TTTT-TTTTTCT-TTATTTTT
1 TTTTCTTTTTCTATTATTTTT
696439 TTATCATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 7 0.37
22 4 0.21
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTCTTTTTCTATTATTTTTC
Found at i:718437 original size:19 final size:18
Alignment explanation
Indices: 718415--718450 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
718405 TCAAAAAGTC
718415 GAGAAAAAAAGAAAAATAT
1 GAGAAAAAAA-AAAAATAT
*
718434 GAGAAAAATAAAAAATA
1 GAGAAAAAAAAAAAATA
718451 AAAAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (18 bp):
GAGAAAAAAAAAAAATAT
Done.