Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007748.1 Hibiscus syriacus cultivar Beakdansim tig00110013_pilon, 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: 4568288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 24
Found at i:520738 original size:173 final size:175
Alignment explanation
Indices: 520448--520791 Score: 665
Period size: 173 Copynumber: 2.0 Consensus size: 175
520438 GATAGTAACC
520448 ACTGAATGACTCCCACCAGGTATAACTTGTCGATTTTGTGTGACTTGAGGGATCACACCTTCCTC
1 ACTGAATGACTCCCACCAGGTATAACTTGTCGATTTTGTGTGACTTGAGGGATCACACCTTCCTC
520513 CATTGCTATCATACTTATCTGTTTAAGAACCCGACTATCCATAACATCATCTTTTTTACTTGTAT
66 CATTGCTATCATACTTATCTGTTTAAGAACCCGACTATCCATAACATCATCTTTTTTACTTGTAT
520578 TTGTCCGCCTACCAGAACCAGCCTCCTTTGGAACA-TATCCGTAA
131 TTGTCCGCCTACCAGAACCAGCCTCCTTTGGAACACTATCCGTAA
520622 ACTGAATGACTCCCACCAGGTATAACTTGTCGA-TTTGTGTGACTTGAGGGATCACACCTTCCTC
1 ACTGAATGACTCCCACCAGGTATAACTTGTCGATTTTGTGTGACTTGAGGGATCACACCTTCCTC
520686 CATTGCTATCATACTTATCTGTTTAAGAACCCGACTATCCATAACATCATCTTTTTTACTTGTAT
66 CATTGCTATCATACTTATCTGTTTAAGAACCCGACTATCCATAACATCATCTTTTTTACTTGTAT
*
520751 TTGTCCGCCTGCCAGAACCAGCCTCCTTTGGAACACTATCC
131 TTGTCCGCCTACCAGAACCAGCCTCCTTTGGAACACTATCC
520792 ATTACATCTT
Statistics
Matches: 168, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
173 130 0.77
174 38 0.23
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.33
Consensus pattern (175 bp):
ACTGAATGACTCCCACCAGGTATAACTTGTCGATTTTGTGTGACTTGAGGGATCACACCTTCCTC
CATTGCTATCATACTTATCTGTTTAAGAACCCGACTATCCATAACATCATCTTTTTTACTTGTAT
TTGTCCGCCTACCAGAACCAGCCTCCTTTGGAACACTATCCGTAA
Found at i:522511 original size:238 final size:235
Alignment explanation
Indices: 522089--522560 Score: 917
Period size: 238 Copynumber: 2.0 Consensus size: 235
522079 TATCTTAGTA
522089 CATAAATTAATCGACCAAATTCGACTCGATCTATGGTTAGAAATATTATTGAAAGTTTATTAATT
1 CATAAATTAATCGACCAAATTCGACTCGATCTATGGTTAGAAATATTATTGAAAGTTTATTAATT
522154 CACTTATTTTATTAACATCGACTGTTAAATTTAACATTTTTTTTGAATTATTGGTGTTATAAGTT
66 CACTTATTTTATTAACATCGACTGTTAAATTTAACATTTTTTTTGAATTATTGGTGTTATAAGTT
522219 AAGTTTAAATTATATTATTGAGTTAGGTCGGATAAAATGGGTGGAAACTTTTTTTTTTGTAAATG
131 AAGTTTAAATTATATTATTGAGTTAGGTCGGATAAAATGGGTGGAAACTTTTTTTTTTGTAAATG
522284 GGTGAGAGAGAAGGTGTTGTGTCCATACCTAATTGCATTG
196 GGTGAGAGAGAAGGTGTTGTGTCCATACCTAATTGCATTG
522324 CATAAATTAATCGACCAAAATTCGACTCGATCTATGGTTAGAAATATTTATTGAAAGTTTATTAA
1 CATAAATTAATCGACC-AAATTCGACTCGATCTATGGTTAGAAATA-TTATTGAAAGTTTATTAA
522389 TTCACTTATTTTATTAACATCGACTGTTAAATTTAACATTTTTTTTTGAATTATTGGTGTTATAA
64 TTCACTTATTTTATTAACATCGACTGTTAAATTTAACA-TTTTTTTTGAATTATTGGTGTTATAA
522454 GTTAAGTTTAAATTATATTATTGAGTTAGGTCGGATAAAATGGGTGGAAACTTTTTTTTTTGTAA
128 GTTAAGTTTAAATTATATTATTGAGTTAGGTCGGATAAAATGGGTGGAAACTTTTTTTTTTGTAA
522519 ATGGGTGAGAGAGAAGGTGTTGTGTCCATACCTAATTGCATT
193 ATGGGTGAGAGAGAAGGTGTTGTGTCCATACCTAATTGCATT
522561 TGCACATGCA
Statistics
Matches: 234, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
235 16 0.07
236 29 0.12
237 56 0.24
238 133 0.57
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.42
Consensus pattern (235 bp):
CATAAATTAATCGACCAAATTCGACTCGATCTATGGTTAGAAATATTATTGAAAGTTTATTAATT
CACTTATTTTATTAACATCGACTGTTAAATTTAACATTTTTTTTGAATTATTGGTGTTATAAGTT
AAGTTTAAATTATATTATTGAGTTAGGTCGGATAAAATGGGTGGAAACTTTTTTTTTTGTAAATG
GGTGAGAGAGAAGGTGTTGTGTCCATACCTAATTGCATTG
Found at i:522760 original size:22 final size:23
Alignment explanation
Indices: 522715--522760 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
522705 TTTAATTGAT
**
522715 TAAAAAACTTTTATAAAACTAATC
1 TAAAAAAC-TTTATAAAAAAAATC
522739 TAAAAAA-TTTATAAAAAAAATC
1 TAAAAAACTTTATAAAAAAAATC
522761 AGTAAAGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAAAACTTTATAAAAAAAATC
Found at i:524732 original size:2 final size:2
Alignment explanation
Indices: 524727--524761 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
524717 TAAAAGATAA
*
524727 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
524762 ATAATTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:526159 original size:15 final size:16
Alignment explanation
Indices: 526128--526160 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
526118 ATAAGAAACA
526128 TATAAATTTGAATATTT
1 TATAAATTT-AATATTT
526145 TATAAATTT-ATATTT
1 TATAAATTTAATATTT
526160 T
1 T
526161 TCTATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TATAAATTTAATATTT
Found at i:526476 original size:2 final size:2
Alignment explanation
Indices: 526469--526496 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
526459 CGTGAAAATA
526469 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
526497 CTCTTTTATA
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:527053 original size:3 final size:3
Alignment explanation
Indices: 527045--527069 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
527035 TGGGAAGGGT
527045 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
527070 ACTTTGCATG
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:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:530517 original size:22 final size:22
Alignment explanation
Indices: 530436--530517 Score: 53
Period size: 22 Copynumber: 3.8 Consensus size: 22
530426 TCCTATCCAC
* *
530436 TAATGTTCTTTTGTAATATCTG
1 TAATGTTCTTCTGTGATATCTG
*
530458 TAATGTT-TTGTGTGATA--TG
1 TAATGTTCTTCTGTGATATCTG
* ** **
530477 TATTAGTGATATCACTGATATCTG
1 TAAT-GTTCT-TCTGTGATATCTG
530501 TAATGTTCTTCTGTGAT
1 TAATGTTCTTCTGTGAT
530518 GACTGATGAG
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
19 5 0.12
20 2 0.05
21 9 0.21
22 19 0.44
23 3 0.07
24 5 0.12
ACGTcount: A:0.23, C:0.09, G:0.18, T:0.50
Consensus pattern (22 bp):
TAATGTTCTTCTGTGATATCTG
Found at i:535502 original size:32 final size:30
Alignment explanation
Indices: 535456--535541 Score: 104
Period size: 32 Copynumber: 2.9 Consensus size: 30
535446 GAGTCGAGGG
*
535456 TACCTATGTACTTCGGGACATATGGACAGGAT
1 TACCTATGTACTTCGGGACATATGGACA-G-C
*
535488 TACCTATGTCCTTCGGGACATAT--ACAGC
1 TACCTATGTACTTCGGGACATATGGACAGC
* *
535516 TACCTATGTTCTTCGGAACATATGGA
1 TACCTATGTACTTCGGGACATATGGA
535542 TAGTGGTCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 21 0.44
29 1 0.02
30 4 0.08
32 22 0.46
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (30 bp):
TACCTATGTACTTCGGGACATATGGACAGC
Found at i:535574 original size:22 final size:23
Alignment explanation
Indices: 535527--535578 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
535517 ACCTATGTTC
* *
535527 TTCGGAACATATGGATAGTGGTCA
1 TTCGGGACATATGCATAG-GGTCA
535551 TTCGGGACATATGCATA-GGTCA
1 TTCGGGACATATGCATAGGGTCA
535573 TT-GGGA
1 TTCGGGA
535579 TATTTTTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 7 0.27
24 15 0.58
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (23 bp):
TTCGGGACATATGCATAGGGTCA
Found at i:537201 original size:22 final size:22
Alignment explanation
Indices: 537176--537217 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
537166 TGCACTGAAG
*
537176 TGCCACGTAGAATTACACCGTA
1 TGCCACGTAGAAATACACCGTA
*
537198 TGCCGCGTAGAAATACACCG
1 TGCCACGTAGAAATACACCG
537218 AAGTGCCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (22 bp):
TGCCACGTAGAAATACACCGTA
Found at i:538085 original size:2 final size:2
Alignment explanation
Indices: 538078--538102 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
538068 TAATTTACCC
538078 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
538103 GTTACACTAC
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:541884 original size:23 final size:23
Alignment explanation
Indices: 541858--541915 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
541848 TCGTATAAAT
* *
541858 ACCGAAGTGCTACGTAGAATTGC
1 ACCGAAGTGCCACGTAGAAATGC
*
541881 ACCGTAA-TGCCGCGTAGAAATGC
1 ACCG-AAGTGCCACGTAGAAATGC
541904 ACCGAAGTGCCA
1 ACCGAAGTGCCA
541916 TATAAGTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 25 0.86
24 2 0.07
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
ACCGAAGTGCCACGTAGAAATGC
Found at i:542165 original size:22 final size:24
Alignment explanation
Indices: 542139--542189 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
542129 TCATAGTTCT
*
542139 TCACATAGCTCAT-T-CATATAAA
1 TCACATAGCACATATACATATAAA
*
542161 TCACATATCACATATACATATAAA
1 TCACATAGCACATATACATATAAA
542185 -CACAT
1 TCACAT
542190 GGTTCACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.44
23 6 0.24
24 8 0.32
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (24 bp):
TCACATAGCACATATACATATAAA
Found at i:542795 original size:28 final size:26
Alignment explanation
Indices: 542742--542795 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
542732 TACTTAAATC
* *
542742 ATATAATATCTAATTTACCTATATAT
1 ATATAATATATAATTTACCTACATAT
*
542768 ATATATATATATAGTTTACGCTACATAT
1 ATATA-ATATATAATTTAC-CTACATAT
542796 TCAAATAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 5 0.22
27 11 0.48
28 7 0.30
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (26 bp):
ATATAATATATAATTTACCTACATAT
Found at i:547583 original size:160 final size:162
Alignment explanation
Indices: 547362--547685 Score: 577
Period size: 160 Copynumber: 2.0 Consensus size: 162
547352 CTGTATAAAG
547362 ATGTGCCATTTGCTTACTTTATCAACATTCATCTCTAAAATTTCAATCTTGGTTATCCTTGTTTG
1 ATGTGCCATTTGCTTACTTTATCAACATTCATCTCTAAAATTTCAATCTTGGTTATCCTTGTTTG
547427 CTTGTTTTGTGGAAGC-TTTT-TGTTGTTAAAGGA-TTTTTTCTTTTAAGGTCAATC-TGATTTG
66 CTTGTTTTGTGGAAGCTTTTTATGTTGTTAAAGGATTTTTTTCTTTTAAGGTCAATCTTGATTTG
547488 GTTTTTTATTTAACTA-TTTATTTCATGCTAA
131 GTTTTTTATTTAACTATTTTATTTCATGCTAA
547519 ATGTGCCATTTGCTTACTTTTATCAACATTTCATCTCTAAAATTTTCAATCTTGGTTATCCTTGT
1 ATGTGCCATTTGCTTAC-TTTATCAACA-TTCATCTCTAAAA-TTTCAATCTTGGTTATCCTTGT
547584 TTGCTTGTTTTGTGGAAGCTTTTTATGTTGTTAAAGGATTTTTTTTCTTTTAAGGTCAATCTTGA
63 TTGCTTGTTTTGTGGAAGCTTTTTATGTTGTTAAAGGA-TTTTTTTCTTTTAAGGTCAATCTTGA
547649 TTTGGTTTTTTATTTAACTATTTTATTTCATGCTAA
127 TTTGGTTTTTTATTTAACTATTTTATTTCATGCTAA
547685 A
1 A
547686 GACCCGATTT
Statistics
Matches: 158, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
157 17 0.11
158 10 0.06
159 13 0.08
160 41 0.26
161 4 0.03
162 13 0.08
164 21 0.13
165 23 0.15
166 16 0.10
ACGTcount: A:0.22, C:0.13, G:0.14, T:0.52
Consensus pattern (162 bp):
ATGTGCCATTTGCTTACTTTATCAACATTCATCTCTAAAATTTCAATCTTGGTTATCCTTGTTTG
CTTGTTTTGTGGAAGCTTTTTATGTTGTTAAAGGATTTTTTTCTTTTAAGGTCAATCTTGATTTG
GTTTTTTATTTAACTATTTTATTTCATGCTAA
Found at i:553436 original size:39 final size:38
Alignment explanation
Indices: 553356--553431 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
553346 CATTAAACCT
*
553356 TTTTATATTTTAAATTTTGTAAAAAAAAATTATATAAA
1 TTTTATAATTTAAATTTTGTAAAAAAAAATTATATAAA
*
553394 TTTTATGAATTTAAATTTT-TAAAAAAATA-TATATAAA
1 TTTTAT-AATTTAAATTTTGTAAAAAAAAATTATATAAA
553431 T
1 T
553432 ATTTTGTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
37 9 0.26
38 15 0.43
39 11 0.31
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (38 bp):
TTTTATAATTTAAATTTTGTAAAAAAAAATTATATAAA
Found at i:563374 original size:18 final size:19
Alignment explanation
Indices: 563336--563374 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
563326 AAAATTTTTT
*
563336 AAAAATAAAAAATATTATA
1 AAAAATAAAAAATAATATA
563355 AAAAATAAAAAATAAT-TA
1 AAAAATAAAAAATAATATA
563373 AA
1 AA
563375 TTTATGAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAATAAAAAATAATATA
Found at i:571437 original size:21 final size:21
Alignment explanation
Indices: 571413--571479 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
571403 AAATTTACGT
* * *
571413 TGCGATTTTCCTAATTCGCAA
1 TGCGATTTACGTAAATCGCAA
*
571434 TGCGA-ATACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
571454 TGCGATTTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
571475 TGCGA
1 TGCGA
571480 ATCTGTAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (21 bp):
TGCGATTTACGTAAATCGCAA
Found at i:571453 original size:20 final size:20
Alignment explanation
Indices: 571428--571494 Score: 100
Period size: 20 Copynumber: 3.3 Consensus size: 20
571418 TTTTCCTAAT
571428 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
571448 TCGCAATGCGATTTACGTAAA
1 TCGCAATGCGA-ATACGTAAA
571469 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
571489 TCGCAA
1 TCGCAA
571495 CGAGATTCTG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.02
20 23 0.53
21 19 0.44
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:571458 original size:41 final size:41
Alignment explanation
Indices: 571413--571494 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
571403 AAATTTACGT
* *
571413 TGCGATTTTCCTAATTCGCAATGCGAATAC-GTAAATCGCAA
1 TGCGATTTACCTAAATCGCAATGCGAAT-CTGTAAATCGCAA
*
571454 TGCGATTTACGTAAATCGCAATGCGAATCTGTAAATCGCAA
1 TGCGATTTACCTAAATCGCAATGCGAATCTGTAAATCGCAA
571495 CGAGATTCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (41 bp):
TGCGATTTACCTAAATCGCAATGCGAATCTGTAAATCGCAA
Found at i:571504 original size:20 final size:20
Alignment explanation
Indices: 571464--571504 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
571454 TGCGATTTAC
* *
571464 GTAAATCGCAATGCGAATCT
1 GTAAATCGCAACGAGAATCT
*
571484 GTAAATCGCAACGAGATTCT
1 GTAAATCGCAACGAGAATCT
571504 G
1 G
571505 ACTATCGCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
GTAAATCGCAACGAGAATCT
Found at i:572385 original size:24 final size:24
Alignment explanation
Indices: 572358--572411 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
572348 GTATTCAAAA
572358 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
572382 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
572406 TTTGAT
1 TTTGAT
572412 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:574871 original size:20 final size:20
Alignment explanation
Indices: 574846--574934 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
574836 CAATGCGGAA
574846 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
574866 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* * *
574886 ATCGCAATGCAGAATTGACT
1 ATCGCAACGCGGAAATGACT
574906 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
574926 ATCGCAACG
1 ATCGCAACG
574935 AGAGAATCGC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 57 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:574905 original size:40 final size:40
Alignment explanation
Indices: 574846--574934 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
574836 CAATGCGGAA
574846 ATCGCAACGCGAATATGACTATCGCAACACGGAAATGACT
1 ATCGCAACGCGAATATGACTATCGCAACACGGAAATGACT
* *
574886 ATCGCAATGCAGAAT-TGACTATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAATATGACTATCGCAACACGGAAATGACT
574926 ATCGCAACG
1 ATCGCAACG
574935 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 41 0.91
41 4 0.09
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (40 bp):
ATCGCAACGCGAATATGACTATCGCAACACGGAAATGACT
Found at i:574994 original size:34 final size:33
Alignment explanation
Indices: 574906--575001 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
574896 AGAATTGACT
* **
574906 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
574940 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
574973 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
575002 CGAAATTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:574997 original size:20 final size:19
Alignment explanation
Indices: 574939--575007 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
574929 GCAACGAGAG
574939 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
574958 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
574972 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
574992 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
575008 TAGTTTCGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.07
19 12 0.29
20 11 0.27
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:575081 original size:19 final size:19
Alignment explanation
Indices: 575011--575135 Score: 170
Period size: 19 Copynumber: 6.8 Consensus size: 19
575001 GCGAAATTAG
575011 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
575030 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
575048 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
**
575064 TTTCGCATTGTTATTTTCA
1 TTTCGCATTGCGATTTTCA
575083 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
575102 TTTCGCATTGCGGTTTTCA
1 TTTCGCATTGCGATTTTCA
575121 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
575136 CTCTCGTTGC
Statistics
Matches: 92, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.07
16 7 0.08
17 3 0.03
18 4 0.04
19 59 0.64
20 13 0.14
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:575289 original size:14 final size:14
Alignment explanation
Indices: 575270--575306 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
575260 CATCAATTAA
575270 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
575284 ACAAATCATCTTTT
1 ACAAATCAACATTT
575298 ACAAATCAA
1 ACAAATCAA
575307 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:576322 original size:9 final size:9
Alignment explanation
Indices: 576308--576336 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
576298 TAATCAAACT
576308 GAAATATAA
1 GAAATATAA
576317 GAAATATAA
1 GAAATATAA
576326 GAAATATAA
1 GAAATATAA
576335 GA
1 GA
576337 CTTACCCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.21
Consensus pattern (9 bp):
GAAATATAA
Found at i:576777 original size:42 final size:42
Alignment explanation
Indices: 576679--576777 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 42
576669 TTGAGAGGGA
* * * *
576679 CCTCTTCAACGATGAAAGTGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAAAGGGGCCTCTTGAACGATGGGAGAGG
* ** * *
576721 ACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAGGG-GATG
1 CCTCTTGAACGATGAAAGGGGCCTCTTGAACGAT-GGGAGAGG
576763 CCTCTTGAACGATGA
1 CCTCTTGAACGATGA
576778 CAGGTGAGTC
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
42 41 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.23
Consensus pattern (42 bp):
CCTCTTGAACGATGAAAGGGGCCTCTTGAACGATGGGAGAGG
Found at i:577292 original size:20 final size:20
Alignment explanation
Indices: 577269--577327 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
577259 AAATCACAAC
577269 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
577289 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
* **
577309 ACGAATTTGACTATCGCAA
1 GCGAAAATGACTATCGCAA
577328 CGAGAGAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (20 bp):
GCGAAAATGACTATCGCAAT
Found at i:577397 original size:34 final size:34
Alignment explanation
Indices: 577353--577474 Score: 145
Period size: 34 Copynumber: 3.4 Consensus size: 34
577343 GCGATTTTCA
577353 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
1 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
*
577387 TTTCGTATTGCGATAGTCATTTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGAT--TC--TTTCG--TTGCGATAGTCAT
* *
577427 TTTCACATTGCGATTCTCTCGTTGCGATAGTCAT
1 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
* *
577461 TTTCACGTTGCGAT
1 TTTCGCATTGCGAT
577475 AGTCATTTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
34 39 0.51
36 6 0.08
38 7 0.09
40 25 0.32
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (34 bp):
TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
Found at i:577399 original size:20 final size:20
Alignment explanation
Indices: 577374--577497 Score: 143
Period size: 20 Copynumber: 6.5 Consensus size: 20
577364 GATTCTTTCG
*
577374 TTGCGATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
577394 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
577414 TTGCGATAGTCATTTTCACA
1 TTGCGATAGTCATTTTCGCA
*
577434 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
* *
577448 TTGCGATAGTCATTTTCACG
1 TTGCGATAGTCATTTTCGCA
*
577468 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
*
577488 TTACGATAGT
1 TTGCGATAGT
577498 AAACTATTCT
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
14 7 0.08
16 5 0.06
18 5 0.06
20 71 0.81
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:577456 original size:74 final size:73
Alignment explanation
Indices: 577336--577497 Score: 225
Period size: 74 Copynumber: 2.2 Consensus size: 73
577326 AACGAGAGAA
* ** * * **
577336 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCATTTTCGTATTGCGAT
1 TCGCATTGCGATAGTCATTTCACATTGCGATTCTCTCGTTGCGATAGTCATTTTCACATTGCGAT
577401 AGTCATTT
66 AGTCATTT
*
577409 TCGCATTGCGATAGTCATTTTCACATTGCGATTCTCTCGTTGCGATAGTCATTTTCACGTTGCGA
1 TCGCATTGCGATAGTCA-TTTCACATTGCGATTCTCTCGTTGCGATAGTCATTTTCACATTGCGA
577474 TAGTCATTT
65 TAGTCATTT
* *
577483 TTGCATTACGATAGT
1 TCGCATTGCGATAGT
577498 AAACTATTCT
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
73 14 0.18
74 64 0.82
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (73 bp):
TCGCATTGCGATAGTCATTTCACATTGCGATTCTCTCGTTGCGATAGTCATTTTCACATTGCGAT
AGTCATTT
Found at i:579424 original size:20 final size:20
Alignment explanation
Indices: 579376--579425 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
579366 CTGAAACTTT
*
579376 AAATCGCAAAACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
579396 AAATTGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
**
579416 CTATCGCAAC
1 AAATCGCAAC
579426 GCAAGAATCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.52, C:0.20, G:0.14, T:0.14
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:579496 original size:20 final size:20
Alignment explanation
Indices: 579471--579517 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
579461 GATTCTCTCG
579471 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
579491 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
579511 TTGCGAT
1 TTGCGAT
579518 TCACTCGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:580157 original size:21 final size:21
Alignment explanation
Indices: 580127--580200 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
580117 ATTTACGTAT
* * *
580127 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTTGGGAAA
580148 TCGCAATGCGAATTTGGGAAA
1 TCGCAATGCGAATTTGGGAAA
580169 TCGCAATGCGAATTTGGGAAA
1 TCGCAATGCGAATTTGGGAAA
580190 TCGCAATGCGA
1 TCGCAATGCGA
580201 TAGTCAGAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGGAAA
Found at i:581346 original size:29 final size:30
Alignment explanation
Indices: 581295--581352 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
581285 TTTGAGTAAT
* * *
581295 GAAATAAAACGTTAGACACTAAATTGAAAC
1 GAAATAAAACATTAAACAATAAATTGAAAC
581325 GAAAT-AAACATTAAACAATAAATTGAAA
1 GAAATAAAACATTAAACAATAAATTGAAA
581353 AAACGAGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.21
Consensus pattern (30 bp):
GAAATAAAACATTAAACAATAAATTGAAAC
Found at i:594655 original size:12 final size:12
Alignment explanation
Indices: 594638--594662 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
594628 TTCTTACGAT
594638 AATTAGTATCAA
1 AATTAGTATCAA
594650 AATTAGTATCAA
1 AATTAGTATCAA
594662 A
1 A
594663 GTATCAGGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
AATTAGTATCAA
Found at i:609425 original size:11 final size:11
Alignment explanation
Indices: 609375--609428 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
609365 TTCCCCCTTG
609375 AATATATA-AT
1 AATATATATAT
609385 AATAGT-TATAT
1 AATA-TATATAT
* *
609396 AATA-AAATAG
1 AATATATATAT
609406 AACTATATATAT
1 AA-TATATATAT
609418 AATATATATAT
1 AATATATATAT
609429 GGTTTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
10 11 0.31
11 18 0.51
12 6 0.17
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (11 bp):
AATATATATAT
Found at i:617500 original size:59 final size:59
Alignment explanation
Indices: 617405--617518 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 59
617395 AATAGATGGA
* * * *
617405 TAAGTGTCCTATCGAACTCTCCTAGTCGCGATGAAAA-GACAAACTCGATAATATGACTC
1 TAAGTGTCCTATCAAACCCTCCTAGTCGCAACGAAAAGGA-AAACTCGATAATATGACTC
617464 TAAGTGTCCTATCAAACCCTCCTAGTCGCAACGAAAAGGAAAACTCGATAATATG
1 TAAGTGTCCTATCAAACCCTCCTAGTCGCAACGAAAAGGAAAACTCGATAATATG
617519 TAGGGATGGC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 48 0.96
60 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (59 bp):
TAAGTGTCCTATCAAACCCTCCTAGTCGCAACGAAAAGGAAAACTCGATAATATGACTC
Found at i:620712 original size:18 final size:19
Alignment explanation
Indices: 620677--620713 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
620667 CACGGAATGT
620677 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
620697 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
620714 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:622227 original size:59 final size:59
Alignment explanation
Indices: 622129--622245 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 59
622119 GATGGATAAT
*
622129 TGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGACAAACTCGATAATATGACTCTAAG
1 TGTCCTATCAAACCATCCTAGTCGCAATGAAAAGACAAACTCGATAATATGACTCTAAG
* *
622188 TGTCCTATCGAACCATCCTAGTCGCAATGAAAATG-CAAACTCGATAATATGGCTCTAA
1 TGTCCTATCAAACCATCCTAGTCGCAATGAAAA-GACAAACTCGATAATATGACTCTAA
622246 CCAGCCCTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 53 0.98
60 1 0.02
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.25
Consensus pattern (59 bp):
TGTCCTATCAAACCATCCTAGTCGCAATGAAAAGACAAACTCGATAATATGACTCTAAG
Found at i:624695 original size:6 final size:6
Alignment explanation
Indices: 624660--624693 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
624650 AGACACGTAT
*
624660 GACCAC GACCAC GACCAC GACCAC GACCCC GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACC
624694 CCAACCCGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:625221 original size:6 final size:6
Alignment explanation
Indices: 625205--625296 Score: 177
Period size: 6 Copynumber: 15.5 Consensus size: 6
625195 GTCCGTCTCG
625205 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
625252 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
625297 AATACGTGTC
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.06
6 81 0.94
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:627137 original size:14 final size:14
Alignment explanation
Indices: 627118--627218 Score: 89
Period size: 14 Copynumber: 7.0 Consensus size: 14
627108 TAACAGACTT
627118 GTTTGTTTTCTACA
1 GTTTGTTTTCTACA
627132 GTTTGTTTTCTACA
1 GTTTGTTTTCTACA
*
627146 -TTCTGTTTTATACA
1 GTT-TGTTTTCTACA
* *
627160 ATCTGTTTTCTACATCA
1 GTTTGTTTTCT--A-CA
*
627177 GTCTGTTTTCTACA
1 GTTTGTTTTCTACA
*
627191 -TTCTGTTTTATACA
1 GTT-TGTTTTCTACA
*
627205 GTCTGTTTTCTACA
1 GTTTGTTTTCTACA
627219 TGGTATCAGG
Statistics
Matches: 72, Mismatches: 8, Indels: 14
0.77 0.09 0.15
Matches are distributed among these distances:
13 3 0.04
14 53 0.74
15 3 0.04
16 1 0.01
17 12 0.17
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.53
Consensus pattern (14 bp):
GTTTGTTTTCTACA
Found at i:627185 original size:31 final size:28
Alignment explanation
Indices: 627121--627218 Score: 115
Period size: 28 Copynumber: 3.4 Consensus size: 28
627111 CAGACTTGTT
* *
627121 TGTTTTCTACAGTTTGTTTTCTACATTC
1 TGTTTTCTACAATCTGTTTTCTACATTC
*
627149 TGTTTTATACAATCTGTTTTCTACATCAGTC
1 TGTTTTCTACAATCTGTTTTCTACAT---TC
* * *
627180 TGTTTTCTACATTCTGTTTTATACAGTC
1 TGTTTTCTACAATCTGTTTTCTACATTC
627208 TGTTTTCTACA
1 TGTTTTCTACA
627219 TGGTATCAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 36 0.60
31 24 0.40
ACGTcount: A:0.18, C:0.18, G:0.10, T:0.53
Consensus pattern (28 bp):
TGTTTTCTACAATCTGTTTTCTACATTC
Found at i:627190 original size:45 final size:45
Alignment explanation
Indices: 627130--627219 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
627120 TTGTTTTCTA
*
627130 CAGTTTGTTTTCTACATTCTGTTTTATACAATCTGTTTTCTACAT
1 CAGTCTGTTTTCTACATTCTGTTTTATACAATCTGTTTTCTACAT
*
627175 CAGTCTGTTTTCTACATTCTGTTTTATACAGTCTGTTTTCTACAT
1 CAGTCTGTTTTCTACATTCTGTTTTATACAATCTGTTTTCTACAT
627220 GGTATCAGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (45 bp):
CAGTCTGTTTTCTACATTCTGTTTTATACAATCTGTTTTCTACAT
Found at i:628009 original size:34 final size:34
Alignment explanation
Indices: 627966--628042 Score: 136
Period size: 34 Copynumber: 2.3 Consensus size: 34
627956 CTGATGGTGC
*
627966 CACCAGTTCAGCGAACAGATGCTTCTGCACTTGT
1 CACCAGTTCAACGAACAGATGCTTCTGCACTTGT
*
628000 CACCAGTTCAACGAACAGATGCTTCTGTACTTGT
1 CACCAGTTCAACGAACAGATGCTTCTGCACTTGT
628034 CACCAGTTC
1 CACCAGTTC
628043 CACCTCTAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (34 bp):
CACCAGTTCAACGAACAGATGCTTCTGCACTTGT
Found at i:631950 original size:14 final size:14
Alignment explanation
Indices: 631928--632027 Score: 101
Period size: 14 Copynumber: 6.9 Consensus size: 14
631918 TAATAGACTT
*
631928 GTCTATTTTCTACA
1 GTCTGTTTTCTACA
*
631942 GTCTGTTTTCTATA
1 GTCTGTTTTCTACA
* *
631956 TTCTGTTTTATACA
1 GTCTGTTTTCTACA
631970 GTCTGTTTTCTACATCA
1 GTCTGTTTTCT--A-CA
*
631987 GTTTGTTTTCTACA
1 GTCTGTTTTCTACA
* * *
632001 TTTTGTTTTATACA
1 GTCTGTTTTCTACA
632015 GTCTGTTTTCTAC
1 GTCTGTTTTCTAC
632028 CTCTTTCCAC
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
14 56 0.80
15 1 0.01
16 1 0.01
17 12 0.17
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:631993 original size:17 final size:17
Alignment explanation
Indices: 631968--632001 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
631958 CTGTTTTATA
631968 CAGTCTGTTTTCTACAT
1 CAGTCTGTTTTCTACAT
*
631985 CAGTTTGTTTTCTACAT
1 CAGTCTGTTTTCTACAT
632002 TTTGTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.50
Consensus pattern (17 bp):
CAGTCTGTTTTCTACAT
Found at i:631998 original size:45 final size:45
Alignment explanation
Indices: 631940--632027 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
631930 CTATTTTCTA
*
631940 CAGTCTGTTTTCTATATTCTGTTTTATACAGTCTGTTTTCTACAT
1 CAGTCTGTTTTCTACATTCTGTTTTATACAGTCTGTTTTCTACAT
* *
631985 CAGTTTGTTTTCTACATTTTGTTTTATACAGTCTGTTTTCTAC
1 CAGTCTGTTTTCTACATTCTGTTTTATACAGTCTGTTTTCTAC
632028 CTCTTTCCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (45 bp):
CAGTCTGTTTTCTACATTCTGTTTTATACAGTCTGTTTTCTACAT
Found at i:633411 original size:81 final size:81
Alignment explanation
Indices: 633276--633433 Score: 280
Period size: 81 Copynumber: 2.0 Consensus size: 81
633266 AGGCAACCGG
* * *
633276 TTACTAATCGGTGTGGCTGGAAGGTTAAGAAGTGGTTGGATAAGGAATAGATCTTTGTCCTTATC
1 TTACTAATCGGTGTGGCTAGAAGGTCAAGAAGTGGCTGGATAAGGAATAGATCTTTGTCCTTATC
633341 TTCTTTGAATGAAATC
66 TTCTTTGAATGAAATC
*
633357 TTACTAATTGGTGTGGCTAGAAGGTCAAGAAGTGGCTGGATAAGGAATAGATCTTTGTCCTTATC
1 TTACTAATCGGTGTGGCTAGAAGGTCAAGAAGTGGCTGGATAAGGAATAGATCTTTGTCCTTATC
633422 TTCTTTGAATGA
66 TTCTTTGAATGA
633434 GATTTCCCCC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.35
Consensus pattern (81 bp):
TTACTAATCGGTGTGGCTAGAAGGTCAAGAAGTGGCTGGATAAGGAATAGATCTTTGTCCTTATC
TTCTTTGAATGAAATC
Found at i:633998 original size:12 final size:12
Alignment explanation
Indices: 633963--634000 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
633953 CTAAAGCCAA
633963 ATAATATAT-AT
1 ATAATATATAAT
633974 ATATATATATAAT
1 ATA-ATATATAAT
*
633987 ATAATATTTAAT
1 ATAATATATAAT
633999 AT
1 AT
634001 TTTCGATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 3 0.12
12 16 0.67
13 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:636648 original size:3 final size:3
Alignment explanation
Indices: 636640--636703 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
636630 AAATTTAAAT
*
636640 TTA TTA TTA TTA TTA -AA TTA 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
*
636687 TTAA ATA TTA TTTA TTA
1 TT-A TTA TTA -TTA TTA
636704 AATATTACAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 1 0.02
3 48 0.89
4 5 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:637972 original size:12 final size:12
Alignment explanation
Indices: 637955--638042 Score: 72
Period size: 12 Copynumber: 7.2 Consensus size: 12
637945 TTAATTCCGT
*
637955 TTATTTTAATCA
1 TTATTTTAATTA
*
637967 TTATTTGCAA-TA
1 TTATTT-TAATTA
637979 TTATTTT-ATTA
1 TTATTTTAATTA
*
637990 TTATTATTATTTA
1 TTATT-TTAATTA
*
638003 TTAATTTAATTA
1 TTATTTTAATTA
*
638015 TTATTTCATTATTA
1 TTATTT--TAATTA
*
638029 TTATTTTTATTA
1 TTATTTTAATTA
638041 TT
1 TT
638043 TATATAAATA
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
10 1 0.02
11 7 0.11
12 34 0.55
13 9 0.15
14 11 0.18
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (12 bp):
TTATTTTAATTA
Found at i:637990 original size:3 final size:3
Alignment explanation
Indices: 637977--638042 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
637967 TTATTTGCAA
*
637977 TAT TAT T-T TAT TAT TAT TAT TATT TAT TAAT T-T AAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT T-AT TAT TAT TAT TAT TAT
* *
638021 CAT TAT TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
638043 TATATAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 4 0.08
3 42 0.81
4 6 0.12
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:638016 original size:19 final size:18
Alignment explanation
Indices: 637977--638044 Score: 74
Period size: 17 Copynumber: 3.9 Consensus size: 18
637967 TTATTTGCAA
637977 TATTATTTTATTA-TT-AT
1 TATTA-TTTATTATTTAAT
637994 TATTATTTATTAATTTAAT
1 TATTATTTATT-ATTTAAT
638013 TATTATTTCATTA-TT-AT
1 TATTATTT-ATTATTTAAT
638030 TATT-TTTATTATTTA
1 TATTATTTATTATTTA
638045 TATAAATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.09
16 11 0.24
17 12 0.27
18 4 0.09
19 11 0.24
20 3 0.07
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTATTTATTATTTAAT
Found at i:638026 original size:36 final size:34
Alignment explanation
Indices: 637977--638044 Score: 109
Period size: 36 Copynumber: 1.9 Consensus size: 34
637967 TTATTTGCAA
*
637977 TATTATTTTATTATTATTATTATTTATTAATTTAAT
1 TATTATTTCATTATTATTATT-TTTATT-ATTTAAT
638013 TATTATTTCATTATTATTATTTTTATTATTTA
1 TATTATTTCATTATTATTATTTTTATTATTTA
638045 TATAAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 5 0.16
35 6 0.19
36 20 0.65
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (34 bp):
TATTATTTCATTATTATTATTTTTATTATTTAAT
Found at i:638055 original size:2 final size:2
Alignment explanation
Indices: 638043--638093 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
638033 TTTTATTATT
* *
638043 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA -A TA AA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
638083 TT TA TT TA TA T
1 TA TA TA TA TA T
638094 GTTAAAATCC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:638230 original size:114 final size:116
Alignment explanation
Indices: 638096--638321 Score: 279
Period size: 116 Copynumber: 2.0 Consensus size: 116
638086 ATTTATATGT
*
638096 TAAAATCCTATATTTCATAAATTACTA-A-TCA-TATTTTAA-TATATATTTATTTTTTTCAATA
1 TAAAATCCTATATTTCATAAATTA-TATATTAATTATTTTAATTATATATTTATTTTTTT-AATA
*
638157 T-TAAGAAA-AGGACTGTCTTAAAGCACCTAGAAGTCCGTTTTCTGATATTTTTAC
64 TCGAAGAAAGA-G-CTGTCTTAAAGCACCTAGAAGTCC-TTTTCTGATATTTTTAC
* *
638211 TAAATATCCTAT-TTT-ATAAATTATATATTAATTGTTTTAATTATTTATTTATTTTTTTAATAT
1 TAAA-ATCCTATATTTCATAAATTATATATTAATTATTTTAATTATATATTTATTTTTTTAATAT
* **
638274 CGAAGAAAGAGTTGTCTTACGGCACCTAGAAGTCCTTTTCTGATATTT
65 CGAAGAAAGAGCTGTCTTAAAGCACCTAGAAGTCCTTTTCTGATATTT
638322 CTAAATAAAT
Statistics
Matches: 97, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
113 2 0.02
114 9 0.09
115 22 0.23
116 40 0.41
117 23 0.24
118 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.46
Consensus pattern (116 bp):
TAAAATCCTATATTTCATAAATTATATATTAATTATTTTAATTATATATTTATTTTTTTAATATC
GAAGAAAGAGCTGTCTTAAAGCACCTAGAAGTCCTTTTCTGATATTTTTAC
Found at i:638254 original size:20 final size:20
Alignment explanation
Indices: 638229--638271 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
638219 CTATTTTATA
638229 AATTATATATTAATTGTTTT
1 AATTATATATTAATTGTTTT
* * *
638249 AATTATTTATTTATTTTTTT
1 AATTATATATTAATTGTTTT
638269 AAT
1 AAT
638272 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTATATATTAATTGTTTT
Found at i:638353 original size:116 final size:116
Alignment explanation
Indices: 638129--638359 Score: 265
Period size: 116 Copynumber: 2.0 Consensus size: 116
638119 ACTAATCATA
*
638129 TTTTAATATATATTTATTTTTTTCAATATTAAGAAAAGGACTGTCTTAAAGCACCTAGAAGTCCG
1 TTTTAATATATATTTATTTTTTTCAATATGAAGAAAAGGACTGTCTTAAAGCACCTAGAAGTCCG
* * ** * *
638194 TTTTCTGATATTTTTACTAAATATCCTATTTTATAAATTATATATTAATTG
66 TTTTCTGATATTTTAAATAAATATAATATTTTATAAATAATATATAAATTG
* * **
638245 TTTTAATTATTTATTTATTTTTTT-AATATCGAAG-AAA-GAGTTGTCTTACGGCACCTAGAAGT
1 TTTTAA-TATATATTTATTTTTTTCAATAT-GAAGAAAAGGA-CTGTCTTAAAGCACCTAGAAGT
**
638307 CC-TTTTCTGATATTTCTAAATAAATA-AATATTTTATTTATAAATATATAAATT
63 CCGTTTTCTGATATTT-TAAATAAATATAATATTTTATAAAT-AATATATAAATT
638360 AATATTTTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
115 25 0.26
116 53 0.55
117 19 0.20
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.47
Consensus pattern (116 bp):
TTTTAATATATATTTATTTTTTTCAATATGAAGAAAAGGACTGTCTTAAAGCACCTAGAAGTCCG
TTTTCTGATATTTTAAATAAATATAATATTTTATAAATAATATATAAATTG
Found at i:638865 original size:2 final size:2
Alignment explanation
Indices: 638858--638884 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
638848 TTTTCAAAAT
638858 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
638885 TTTTTCCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:643456 original size:6 final size:6
Alignment explanation
Indices: 643435--643503 Score: 70
Period size: 6 Copynumber: 11.5 Consensus size: 6
643425 TCCAGTAAAG
* * * *
643435 AAAGAA GAAGGAA AAAGAA AAA-AG AAAG-A AAACAA AAAGGA AAAGAA
1 AAAGAA -AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
643482 AAAGAA AAAGAA AAATGAA AAA
1 AAAGAA AAAGAA AAA-GAA AAA
643504 AATGAGAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
5 7 0.14
6 33 0.65
7 11 0.22
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (6 bp):
AAAGAA
Found at i:643462 original size:11 final size:11
Alignment explanation
Indices: 643446--643489 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
643436 AAGAAGAAGG
643446 AAAAAGAAAA-
1 AAAAAGAAAAC
643456 AAGAAAGAAAAC
1 AA-AAAGAAAAC
*
643468 AAAAAGGAAAAG
1 AAAAA-GAAAAC
643480 AAAAAGAAAA
1 AAAAAGAAAA
643490 AGAAAAATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 2 0.07
11 16 0.53
12 12 0.40
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAC
Found at i:643494 original size:17 final size:17
Alignment explanation
Indices: 643431--643495 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
643421 CTCATCCAGT
*
643431 AAAGAAAGAAG-AAGGAA
1 AAAGAAA-AAGAAAAGAA
643448 AAAGAAAAA-AGAAAGAA
1 AAAGAAAAAGA-AAAGAA
*
643465 AACA-AAAAGGAAAAGAA
1 AA-AGAAAAAGAAAAGAA
643482 AAAGAAAAAGAAAA
1 AAAGAAAAAGAAAA
643496 ATGAAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
16 3 0.08
17 35 0.88
18 2 0.05
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAAAGAA
Found at i:645897 original size:114 final size:114
Alignment explanation
Indices: 645697--645916 Score: 352
Period size: 114 Copynumber: 1.9 Consensus size: 114
645687 CACGTTCTCG
* * * * *
645697 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGAACCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTC
*
645762 GGTATGAACCCCAAAACCAATCATT-AAATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTGAAA-TTGAAAGATGAATTTGCTCA
645811 TAGTAGAAATAAGAAGACCCAATAGAACCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTC
1 TAGTAGAAATAAGAAGACCCAATAGAACCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTC
* *
645876 GGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAA
645917 CTGCATGATC
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
114 95 0.98
115 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (114 bp):
TAGTAGAAATAAGAAGACCCAATAGAACCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTC
GGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTGCTCA
Found at i:648416 original size:22 final size:22
Alignment explanation
Indices: 648390--648444 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
648380 ATATACACTC
648390 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
648412 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
648434 TTCAAAGATGA
1 TTCAAAGATGA
648445 AAGTTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:649245 original size:76 final size:76
Alignment explanation
Indices: 649119--649770 Score: 1173
Period size: 76 Copynumber: 8.6 Consensus size: 76
649109 CTATTTCCCA
* * *
649119 CATCTATAAGTCTTACAGTACATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
649184 AGCCTTAGGGT
66 AGCCTTAGGGT
649195 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
649260 AGCCTTAGGGT
66 AGCCTTAGGGT
*
649271 CATCTGTAAGTCCTACAGTGCATGATGTTACCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
649336 AGCCTTAGGGT
66 AGCCTTAGGGT
*
649347 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
649412 AGCCTTAGTGT
66 AGCCTTAGGGT
*
649423 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
649488 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
649499 CATCTGTAAGTCCTACAGTGCATGATGTTACCAAAAAGCCTTCTGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
649564 AGCCTTAGGGT
66 AGCCTTAGGGT
649575 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
649640 AGCCTTAGGGT
66 AGCCTTAGGGT
*
649651 CATCTGTAAGTCCTACGGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
649716 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
649727 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
649771 TCATCTGTAA
Statistics
Matches: 555, Mismatches: 21, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
74 8 0.01
75 4 0.01
76 543 0.98
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:649757 original size:45 final size:45
Alignment explanation
Indices: 649704--649805 Score: 186
Period size: 45 Copynumber: 2.3 Consensus size: 45
649694 GGGAGCTTTT
*
649704 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
*
649749 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
649794 TGATGTTTTCAA
1 TGATGTTTTCAA
649806 CATTTCCATC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:649948 original size:3 final size:3
Alignment explanation
Indices: 649940--649984 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
649930 AAATTTAAAT
**
649940 TTA TTA TTA TTA TTA AAA 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
649985 AATATTACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:651258 original size:12 final size:11
Alignment explanation
Indices: 651241--651283 Score: 59
Period size: 12 Copynumber: 3.7 Consensus size: 11
651231 TTAATTCCTT
651241 TTATTTTAATCA
1 TTATTTTAAT-A
651253 TTATTTGTAATA
1 TTATTT-TAATA
*
651265 TTATTTTATTA
1 TTATTTTAATA
651276 TTATTTTA
1 TTATTTTA
651284 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 12 0.41
12 13 0.45
13 4 0.14
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:651276 original size:3 final size:3
Alignment explanation
Indices: 651263--651330 Score: 58
Period size: 3 Copynumber: 24.3 Consensus size: 3
651253 TTATTTGTAA
*
651263 TAT TAT T-T TAT TAT TAT T-T TAT T-T T-T TAT TACT T-T AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* *
651304 TAT T-T CAT TAT TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
651331 TATATAAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
2 10 0.19
3 41 0.77
4 2 0.04
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:651292 original size:35 final size:36
Alignment explanation
Indices: 651252--651331 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 36
651242 TATTTTAATC
*
651252 ATTATTTGTAA-TATTATTTTATTATTATTTTATTTTTT
1 ATTATTTGTAATTATTATTTCATTATTA--TTA-TTTTT
*
651290 ATTACTT-TAATTATTATTTCATTATTATTATTTTT
1 ATTATTTGTAATTATTATTTCATTATTATTATTTTT
651325 ATTATTT
1 ATTATTT
651332 ATATAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
35 11 0.29
36 3 0.08
37 3 0.08
38 21 0.55
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.69
Consensus pattern (36 bp):
ATTATTTGTAATTATTATTTCATTATTATTATTTTT
Found at i:651293 original size:15 final size:16
Alignment explanation
Indices: 651263--651330 Score: 68
Period size: 15 Copynumber: 4.1 Consensus size: 16
651253 TTATTTGTAA
651263 TATTATTTTATTATTAT
1 TATTATTTT-TTATTAT
651280 T-TTATTTTTTATTACTT
1 TATTATTTTTTATTA--T
*
651297 TAATTATTATTTCATTAT
1 T-ATTATT-TTTTATTAT
651315 TATTA-TTTTTATTAT
1 TATTATTTTTTATTAT
651330 T
1 T
651331 TATATAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
15 15 0.34
16 8 0.18
17 7 0.16
18 2 0.05
19 5 0.11
20 7 0.16
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTATTTTTTATTAT
Found at i:651317 original size:26 final size:26
Alignment explanation
Indices: 651263--651330 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
651253 TTATTTGTAA
* *
651263 TATTATTTTATTATTATTTTATTTTT
1 TATTATTTTATTATTATTTCATTTAT
*
651289 TATTACTTTAATTATTATTTCA-TTAT
1 TATTA-TTTTATTATTATTTCATTTAT
651315 TATTATTTTTATTATT
1 TATTA-TTTTATTATT
651331 TATATAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
26 22 0.61
27 14 0.39
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (26 bp):
TATTATTTTATTATTATTTCATTTAT
Found at i:651511 original size:113 final size:117
Alignment explanation
Indices: 651378--651603 Score: 277
Period size: 116 Copynumber: 2.0 Consensus size: 117
651368 GTTTATTTGT
*
651378 TAAAATCCTATATTTCATAAATTACTA-A-TCA-TATTTTAA-TATATATTTATTTTTTCAATAT
1 TAAAATCCTATATTTCATAAATTA-TATATTAATTATTTTAATTATATATTTATTTTTTCAATAT
* * * *
651439 -TAAAAAAAGGACTGTCTTAAAGCACCTAGAAGTCTGTTTTCTGATATTTTTAC
65 CGAAAAAAAGAACTATCTTAAAGCACCTAGAAGTC-ATTTTCTGATATTTTTAC
* * *
651492 TAAATATCCTAT-TTT-ATAAATTATATATTAATTGTTTTAATTATTTATTTATTTTTTTAATAT
1 TAAA-ATCCTATATTTCATAAATTATATATTAATTATTTTAATTATATATTTATTTTTTCAATAT
* **
651555 CGAAGAAAAGAACTATCTTATGGCACCTAGAAGTCATTTTCTGATATTT
65 CGAAAAAAAGAACTATCTTAAAGCACCTAGAAGTCATTTTCTGATATTT
651604 CTAAATAAAT
Statistics
Matches: 95, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
112 2 0.02
113 9 0.09
114 9 0.09
115 14 0.15
116 33 0.35
117 28 0.29
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.46
Consensus pattern (117 bp):
TAAAATCCTATATTTCATAAATTATATATTAATTATTTTAATTATATATTTATTTTTTCAATATC
GAAAAAAAGAACTATCTTAAAGCACCTAGAAGTCATTTTCTGATATTTTTAC
Found at i:651535 original size:20 final size:20
Alignment explanation
Indices: 651510--651552 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
651500 CTATTTTATA
651510 AATTATATATTAATTGTTTT
1 AATTATATATTAATTGTTTT
* * *
651530 AATTATTTATTTATTTTTTT
1 AATTATATATTAATTGTTTT
651550 AAT
1 AAT
651553 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTATATATTAATTGTTTT
Found at i:651641 original size:29 final size:29
Alignment explanation
Indices: 651608--651664 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
651598 ATATTTCTAA
651608 ATAAATAAATATTTTATTT-ATAAATATAT
1 ATAAATAAATATTTT-TTTCATAAATATAT
* *
651637 ATAAATTAATATTTTTTTCATAATTATA
1 ATAAATAAATATTTTTTTCATAAATATA
651665 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAAATAAATATTTTTTTCATAAATATAT
Found at i:657096 original size:17 final size:18
Alignment explanation
Indices: 657074--657110 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
657064 TTTTAACTCA
657074 AAATTATTT-AAAAATTT
1 AAATTATTTGAAAAATTT
*
657091 AAATTATTTGATAAATTT
1 AAATTATTTGAAAAATTT
657109 AA
1 AA
657111 CAATAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
AAATTATTTGAAAAATTT
Found at i:661610 original size:3 final size:3
Alignment explanation
Indices: 661602--661628 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
661592 ATGGTTTTCA
661602 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
661629 GTGTATACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:670846 original size:36 final size:36
Alignment explanation
Indices: 670799--670871 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
670789 CTAAATCCCC
670799 TAGGCAAGTCAACCAATTTCCAAGTATGATTAGACA
1 TAGGCAAGTCAACCAATTTCCAAGTATGATTAGACA
* *
670835 TAGGCAAGTCAATCAATTTCCAAGTGTGATTAGACA
1 TAGGCAAGTCAACCAATTTCCAAGTATGATTAGACA
670871 T
1 T
670872 TATCGATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (36 bp):
TAGGCAAGTCAACCAATTTCCAAGTATGATTAGACA
Found at i:671698 original size:17 final size:17
Alignment explanation
Indices: 671676--671719 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
671666 TCTAAGTCAT
671676 TTGATTCTCATATCTAA
1 TTGATTCTCATATCTAA
*
671693 TTGATTCTCCTATCTAA
1 TTGATTCTCATATCTAA
671710 TTGATTCTCA
1 TTGATTCTCA
671720 ACTTCTGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48
Consensus pattern (17 bp):
TTGATTCTCATATCTAA
Found at i:677098 original size:2 final size:2
Alignment explanation
Indices: 677091--677121 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
677081 CAACTCATAC
677091 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
677122 CAATCAATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:677365 original size:13 final size:13
Alignment explanation
Indices: 677343--677403 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
677333 GTAAATTAAC
*
677343 ATAAAAGAACACA
1 ATAAATGAACACA
677356 ATAAATGAAC-C-
1 ATAAATGAACACA
677367 -TAAATGAACACA
1 ATAAATGAACACA
* *
677379 CGTAAACGAACACA
1 -ATAAATGAACACA
677393 ATAAATGAACA
1 ATAAATGAACA
677404 TAAACGAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
10 9 0.22
11 1 0.03
12 1 0.03
13 18 0.45
14 11 0.28
ACGTcount: A:0.59, C:0.18, G:0.10, T:0.13
Consensus pattern (13 bp):
ATAAATGAACACA
Found at i:677370 original size:23 final size:23
Alignment explanation
Indices: 677334--677378 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
677324 TAAACTGATG
*
677334 TAAATTAACATAAAAGAACACAA
1 TAAATGAACATAAAAGAACACAA
* *
677357 TAAATGAACCTAAATGAACACA
1 TAAATGAACATAAAAGAACACA
677379 CGTAAACGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.60, C:0.16, G:0.07, T:0.18
Consensus pattern (23 bp):
TAAATGAACATAAAAGAACACAA
Found at i:677412 original size:10 final size:10
Alignment explanation
Indices: 677393--677427 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
677383 AACGAACACA
*
677393 ATAAATGAAC
1 ATAAACGAAC
677403 ATAAACGAAC
1 ATAAACGAAC
*
677413 AAAAACGAAC
1 ATAAACGAAC
677423 ATAAA
1 ATAAA
677428 TCAACTTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.66, C:0.14, G:0.09, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:681027 original size:23 final size:23
Alignment explanation
Indices: 681001--681061 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
680991 CACCACAGCT
*
681001 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
681024 CGTAGAATTGCACCGGAGTGTCG
1 CGTAGAATTGCACCGAAGTGCCA
*
681047 CGTAGAATTACACCG
1 CGTAGAATTGCACCG
681062 TATTTGCCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:689567 original size:80 final size:80
Alignment explanation
Indices: 689470--689630 Score: 313
Period size: 80 Copynumber: 2.0 Consensus size: 80
689460 ATAAATAAAT
*
689470 GTATAGACGACATAAGAGGTTCTTCGTGGTTGGTTTTGCTTAGGGATGTTCAACGTAGGGGAGAT
1 GTATAGACGACATAAGAGGTTCTTCGTGGTTGGTTTTGCTTAGGGATATTCAACGTAGGGGAGAT
689535 TTCCAAGAGAACAGA
66 TTCCAAGAGAACAGA
689550 GTATAGACGACATAAGAGGTTCTTCGTGGTTGGTTTTGCTTAGGGATATTCAACGTAGGGGAGAT
1 GTATAGACGACATAAGAGGTTCTTCGTGGTTGGTTTTGCTTAGGGATATTCAACGTAGGGGAGAT
689615 TTCCAAGAGAACAGA
66 TTCCAAGAGAACAGA
689630 G
1 G
689631 CAAGAATAAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.28, C:0.12, G:0.31, T:0.29
Consensus pattern (80 bp):
GTATAGACGACATAAGAGGTTCTTCGTGGTTGGTTTTGCTTAGGGATATTCAACGTAGGGGAGAT
TTCCAAGAGAACAGA
Found at i:690552 original size:49 final size:50
Alignment explanation
Indices: 690468--690566 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 50
690458 CGGGCGTCTT
*
690468 CGAGGCATGGAGGAACTTGTCGTGTAACCCCGTGGAGGTAAATCATTTTC
1 CGAGGCATGGAGGAACTTATCGTGTAACCCCGTGGAGGTAAATCATTTTC
* * *
690518 CGAGGCGTGGAGG-ACTTATCTTGTAACTCCGTGGAGGTAAATCATTTTC
1 CGAGGCATGGAGGAACTTATCGTGTAACCCCGTGGAGGTAAATCATTTTC
690567 TCTGATAGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 33 0.73
50 12 0.27
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.28
Consensus pattern (50 bp):
CGAGGCATGGAGGAACTTATCGTGTAACCCCGTGGAGGTAAATCATTTTC
Found at i:693844 original size:17 final size:18
Alignment explanation
Indices: 693822--693856 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
693812 TATAATAATT
*
693822 TTAAAAT-ATATTTAAAA
1 TTAAAATCATACTTAAAA
693839 TTAAAATCATACTTAAAA
1 TTAAAATCATACTTAAAA
693857 AAATGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAAAATCATACTTAAAA
Found at i:696129 original size:37 final size:37
Alignment explanation
Indices: 696043--696143 Score: 112
Period size: 37 Copynumber: 2.7 Consensus size: 37
696033 TTCGTCCTAT
* * **
696043 TAGGATTTAAACTCCTAAAAATATGATAAAATTTTGT
1 TAGGATTTAAACTCCTAAAAATAGGATAAAATTCTAC
* * *
696080 TAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTAC
1 TAGGATTTAAACTCCTAAAAATAGGATAAAATTCTAC
** *
696117 TATTATTTAAACTCCTAAAGATAGGAT
1 TAGGATTTAAACTCCTAAAAATAGGAT
696144 CCACAAACAT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.34
Consensus pattern (37 bp):
TAGGATTTAAACTCCTAAAAATAGGATAAAATTCTAC
Found at i:696586 original size:23 final size:24
Alignment explanation
Indices: 696558--696605 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
696548 TATATATATA
696558 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTTATTTCATT
*
696581 TATTTATTATAATTTTTTTTCATT
1 TATTTATTATAATTTTATTTCATT
696605 T
1 T
696606 TTCTTTGCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TATTTATTATAATTTTATTTCATT
Found at i:696688 original size:21 final size:21
Alignment explanation
Indices: 696662--696711 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
696652 TATTATATTA
*
696662 TTATTTTTTATCTATGTTTAC
1 TTATTTTTTATATATGTTTAC
* * *
696683 TTATTTATTATATTTTTTTAC
1 TTATTTTTTATATATGTTTAC
696704 TATATTTT
1 T-TATTTT
696712 CCTAACGTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (21 bp):
TTATTTTTTATATATGTTTAC
Found at i:696755 original size:103 final size:105
Alignment explanation
Indices: 696575--696775 Score: 227
Period size: 103 Copynumber: 1.9 Consensus size: 105
696565 TTATATTTTA
* * * ** *
696575 TTTATTTATTTATTATAATTTTTTTTCATTTTTCTTTGCGTTATATTATATTATTTTTTTTATTA
1 TTTACTTATTTATTATAATTTTTTTACATTTTTCCTAACGTTATATTATATTATTTTCTTTATTA
*
696640 TATATATATATATAT-TAT-ATTATTATTTTTTATCTATG
66 TATATATATATATATCTATGATTACTATTTTTTATCTATG
696678 TTTACTTATTTATTAT-ATTTTTTTACTATATTTTCCTAACGTTATA-TATATATATTCTTACTT
1 TTTACTTATTTATTATAATTTTTTTAC-AT-TTTTCCTAACGTTATATTATAT-TATT-TT-CTT
* *
696741 TATT-T-TAT-TTTATATTTCTATGATTACTATTTTTT
61 TATTATATATATATATATATCTATGATTACTATTTTTT
696776 TAGTTAATAT
Statistics
Matches: 82, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
102 9 0.11
103 29 0.35
104 23 0.28
105 15 0.18
106 6 0.07
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.65
Consensus pattern (105 bp):
TTTACTTATTTATTATAATTTTTTTACATTTTTCCTAACGTTATATTATATTATTTTCTTTATTA
TATATATATATATATCTATGATTACTATTTTTTATCTATG
Found at i:697024 original size:23 final size:22
Alignment explanation
Indices: 696958--697025 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
696948 TCGTACTTTG
*
696958 TTATTATCATTTTTTATTTG-TT
1 TTATTAT-ATTTTATATTTGTTT
* *
696980 TTATT-TATTTTCT-TTTCTTTT
1 TTATTATATTTTATATTT-GTTT
697001 TTATATATATTTTATATTTGTTT
1 TTAT-TATATTTTATATTTGTTT
697024 TT
1 TT
697026 TTTTACTTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
19 3 0.08
20 6 0.16
21 7 0.19
22 6 0.16
23 12 0.32
24 3 0.08
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.75
Consensus pattern (22 bp):
TTATTATATTTTATATTTGTTT
Found at i:699190 original size:19 final size:19
Alignment explanation
Indices: 699166--699208 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
699156 CACTACGTAT
699166 TCACCTTTGAGAGAGTTCA
1 TCACCTTTGAGAGAGTTCA
699185 TCACCTTTGAGAGAGTTCA
1 TCACCTTTGAGAGAGTTCA
699204 TCACC
1 TCACC
699209 ATGAAATGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (19 bp):
TCACCTTTGAGAGAGTTCA
Found at i:701645 original size:23 final size:23
Alignment explanation
Indices: 701619--701701 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
701609 TCCAATCAAG
*
701619 AACAAAAAAGCAAAGAAGCAAAA
1 AACAAAAAAGAAAAGAAGCAAAA
* *
701642 AACAAATAAA-AAAGAGAATC-AAG
1 AACAAA-AAAGAAA-AGAAGCAAAA
701665 AACAAAAAAGAAAAGAAGCAAAA
1 AACAAAAAAGAAAAGAAGCAAAA
*
701688 ATC-AAAAAGAAAAG
1 AACAAAAAAGAAAAG
701702 GGACAAAAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
22 19 0.38
23 23 0.46
24 8 0.16
ACGTcount: A:0.73, C:0.10, G:0.13, T:0.04
Consensus pattern (23 bp):
AACAAAAAAGAAAAGAAGCAAAA
Found at i:701662 original size:46 final size:46
Alignment explanation
Indices: 701612--701701 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
701602 GCGAAGATCC
*
701612 AATCAAGAACAAAAAAGCAAAGAAGCAAAAAACAAATAA-AAAAGAG
1 AATCAAGAACAAAAAAGAAAAGAAGCAAAAAACAAA-AAGAAAAGAG
*
701658 AATCAAGAACAAAAAAGAAAAGAAGCAAAAATCAAAAAGAAAAG
1 AATCAAGAACAAAAAAGAAAAGAAGCAAAAAACAAAAAGAAAAG
701702 GGACAAAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 2 0.05
46 39 0.95
ACGTcount: A:0.72, C:0.10, G:0.13, T:0.04
Consensus pattern (46 bp):
AATCAAGAACAAAAAAGAAAAGAAGCAAAAAACAAAAAGAAAAGAG
Found at i:701710 original size:22 final size:22
Alignment explanation
Indices: 701623--701701 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
701613 ATCAAGAACA
* *
701623 AAAAAGCAAAGAAGCAAAAAAC
1 AAAAAGAAAAGAAGCAAAAATC
* * *
701645 AAATAAAAAAGAGAATCAAGAA-C
1 AAA-AAGAAA-AGAAGCAAAAATC
701668 AAAAAAGAAAAGAAGCAAAAATC
1 -AAAAAGAAAAGAAGCAAAAATC
701691 AAAAAGAAAAG
1 AAAAAGAAAAG
701702 GGACAAAAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
22 23 0.50
23 11 0.24
24 12 0.26
ACGTcount: A:0.73, C:0.09, G:0.14, T:0.04
Consensus pattern (22 bp):
AAAAAGAAAAGAAGCAAAAATC
Found at i:703420 original size:106 final size:106
Alignment explanation
Indices: 703292--704383 Score: 1769
Period size: 106 Copynumber: 10.3 Consensus size: 106
703282 ATATCGTACC
* * * *
703292 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
703357 AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
703398 ACTCCAGACAACACAAGTTCAACTTCAAGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
703463 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
703504 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
703569 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
703610 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTAGTTGTCAATAAACAAC-TCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
703674 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT-G
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
703714 -CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
703778 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
703819 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTAGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
703884 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
703925 TCTCCAGACAATGCAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
**
703990 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
704031 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAATACCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
704096 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * * * * *
704137 ACTTGAGACAACGCAAGTTCAAATTCACGACAAAGGGACCGCTGGTTTTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
704202 AATTTC-GAAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAG-AGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
704243 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
704308 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
704349 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
704384 AGAATTTCAG
Statistics
Matches: 916, Mismatches: 65, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
103 55 0.06
104 44 0.05
105 45 0.05
106 771 0.84
107 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:704437 original size:78 final size:78
Alignment explanation
Indices: 704308--704461 Score: 290
Period size: 78 Copynumber: 2.0 Consensus size: 78
704298 ACAATTTCCC
*
704308 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
704373 TCACGACGAAGAG
66 TCACGACGAAGAG
*
704386 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
704451 TCACGACGAAG
66 TCACGACGAAG
704462 GGACCGCTGG
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (78 bp):
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGAG
Found at i:704528 original size:184 final size:184
Alignment explanation
Indices: 704202--704567 Score: 617
Period size: 184 Copynumber: 2.0 Consensus size: 184
704192 ATAATTTCCC
704202 AATTTCGAAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACT
1 AATTTCGAAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACT
704267 TCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTC
66 TCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTC
* * * *
704332 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGAG
131 ACAACAAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGAG
* *
704386 AATTTC-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAAC
1 AATTTCGA-AGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAAC
* * **
704450 TTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTTTCAATTTCGGAGCCAATTTCAACTT
65 TTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTT
*
704515 CACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
130 CACAACAAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAG
704568 GGACGACTGG
Statistics
Matches: 170, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
183 1 0.01
184 169 0.99
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (184 bp):
AATTTCGAAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTC
ACAACAAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGAG
Found at i:704571 original size:106 final size:106
Alignment explanation
Indices: 704386--704622 Score: 368
Period size: 106 Copynumber: 2.2 Consensus size: 106
704376 CGACGAAGAG
* * *
704386 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACT
* * **
704451 TCACGACGAAGGGACCG-CTGGTTGTCAACAAATAATTTTTC
66 TCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCC
*
704492 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACT
704557 TCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
66 TCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
* *
704598 GATTCCAGAGCCAATTTCAACTTCA
1 AATTTCAGAGCCAATTTCAACTTCA
704623 TGACGGATGA
Statistics
Matches: 119, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
105 2 0.02
106 117 0.98
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
AATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACT
TCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
Found at i:704642 original size:290 final size:290
Alignment explanation
Indices: 704096--704622 Score: 896
Period size: 290 Copynumber: 1.8 Consensus size: 290
704086 ACAAATACCC
*
704096 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTTGAGACAACGCAAGTTCAAAT
1 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCGAGACAACGCAAGTTCAAAT
*
704161 TCACGACAAAGGGACCGCTGGTTTTCAACAAATAATTTCCCAATTTCGAAGCCAATTTCAACTTC
66 TCACGACAAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCGAAGCCAATTTCAACTTC
* *
704226 ACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTG
131 ACAACGAAAGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTG
* *
704291 TCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
196 TCAACAAACAATTTCCCAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
704356 ACAACGCAAGTTCAACTTCACGACGAAGAG
261 ACAACGCAAGTTCAACTTCACGACGAAGAG
* *
704386 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCGAGACAACGCAAGTTCAAAT
* ** *
704451 TCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTTTCAATTTCGGAGCCAATTTCAACTTC
66 TCACGACAAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCGAAGCCAATTTCAACTTC
*
704516 ACAAC-AAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGT
131 ACAACGAAA-GATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCG-CTGGT
*
704579 TGTCAACAAACAATTTCCCGATTCCAGAGCCAATTTCAACTTCA
194 TGTCAACAAACAATTTCCCAATTCCAGAGCCAATTTCAACTTCA
704623 TGACGGATGA
Statistics
Matches: 221, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
289 5 0.02
290 216 0.98
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (290 bp):
AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCGAGACAACGCAAGTTCAAAT
TCACGACAAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCGAAGCCAATTTCAACTTC
ACAACGAAAGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTG
TCAACAAACAATTTCCCAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
ACAACGCAAGTTCAACTTCACGACGAAGAG
Found at i:705913 original size:20 final size:20
Alignment explanation
Indices: 705888--705928 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
705878 TGTATATATA
705888 TATATATTATTTATTT-ATTT
1 TATATATT-TTTATTTCATTT
*
705908 TATATATTTTTTTTTCATTT
1 TATATATTTTTATTTCATTT
705928 T
1 T
705929 CTTTGCGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TATATATTTTTATTTCATTT
Found at i:706076 original size:29 final size:30
Alignment explanation
Indices: 706043--706128 Score: 87
Period size: 29 Copynumber: 3.0 Consensus size: 30
706033 ATATACTTAC
706043 TTTTTTATTTATAT-TTATATGATTACTAT
1 TTTTTTATTTATATATTATATGATTACTAT
*
706072 TTTTTTAGTTA-ATATTATATGTATT--TAT
1 TTTTTTATTTATATATTATATG-ATTACTAT
706100 TTTCATTTATTTAT-TATTAT-TG-TTACTAT
1 TTT--TTTATTTATATATTATATGATTACTAT
706129 ATATATATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
27 2 0.04
28 8 0.17
29 22 0.46
30 16 0.33
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (30 bp):
TTTTTTATTTATATATTATATGATTACTAT
Found at i:706210 original size:21 final size:20
Alignment explanation
Indices: 706186--706226 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
706176 TCTTTTCGTC
706186 ATTTAATTATTAATTTATATA
1 ATTTAATT-TTAATTTATATA
*
706207 ATTTAATTTTTATTTATATA
1 ATTTAATTTTAATTTATATA
706227 TATATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTAATTTTAATTTATATA
Found at i:706293 original size:17 final size:18
Alignment explanation
Indices: 706268--706304 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
706258 TGTTTATTTG
706268 TTTTATTTATT-TTTTTT
1 TTTTATTTATTATTTTTT
*
706285 TTTTTTTTATTATTTTTT
1 TTTTATTTATTATTTTTT
706303 TT
1 TT
706305 ATTGTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (18 bp):
TTTTATTTATTATTTTTT
Found at i:706304 original size:12 final size:12
Alignment explanation
Indices: 706247--706326 Score: 69
Period size: 12 Copynumber: 6.8 Consensus size: 12
706237 TCGTACTTTG
*
706247 TTATTATTGTTT
1 TTATTATTTTTT
* *
706259 GT-TTATTTGTT
1 TTATTATTTTTT
*
706270 TTATT-TATTTT
1 TTATTATTTTTT
706281 TT-TT-TTTTTT
1 TTATTATTTTTT
706291 TTATTATTTTTT
1 TTATTATTTTTT
*
706303 TTATTGTTTTTT
1 TTATTATTTTTT
706315 ACTTATTATTTT
1 --TTATTATTTT
706327 ATATTTGCTT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
10 9 0.17
11 16 0.30
12 20 0.37
14 9 0.17
ACGTcount: A:0.14, C:0.01, G:0.05, T:0.80
Consensus pattern (12 bp):
TTATTATTTTTT
Found at i:706312 original size:20 final size:20
Alignment explanation
Indices: 706247--706312 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 20
706237 TCGTACTTTG
706247 TTATTATTGTTTGTTTATTTGTT
1 TTATTATT-TTT-TTTA-TTGTT
* *
706270 TTATTTATTTTTTTTTTTTTT
1 TTA-TTATTTTTTTTATTGTT
706291 TTATTATTTTTTTTATTGTT
1 TTATTATTTTTTTTATTGTT
706311 TT
1 TT
706313 TTACTTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 17 0.45
21 7 0.18
22 3 0.08
23 6 0.16
24 5 0.13
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (20 bp):
TTATTATTTTTTTTATTGTT
Found at i:706320 original size:26 final size:23
Alignment explanation
Indices: 706270--706326 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 23
706260 TTTATTTGTT
*
706270 TTATTTATTTTTTTTTTTTTTTTA
1 TTATTT-TTTTTTTTTTTTTCTTA
706294 TTATTTTTTTTATTGTTTTTTACTTA
1 TTATTTTTTTT-TT-TTTTTT-CTTA
706320 TTATTTT
1 TTATTTT
706327 ATATTTGCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 5 0.17
24 8 0.28
25 6 0.21
26 10 0.34
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82
Consensus pattern (23 bp):
TTATTTTTTTTTTTTTTTTCTTA
Found at i:706323 original size:29 final size:29
Alignment explanation
Indices: 706268--706332 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 29
706258 TGTTTATTTG
* ** *
706268 TTTTATTTATTTTTTTTTTTTTTTTATTA
1 TTTTATTTATTGTTTTTTACTTATTATTA
*
706297 TTTTTTTTATTGTTTTTTACTTATTATT-
1 TTTTATTTATTGTTTTTTACTTATTATTA
*
706325 TTATATTT
1 TTTTATTT
706333 GCTTTCTTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.82
Consensus pattern (29 bp):
TTTTATTTATTGTTTTTTACTTATTATTA
Found at i:706326 original size:24 final size:21
Alignment explanation
Indices: 706247--706332 Score: 93
Period size: 24 Copynumber: 3.9 Consensus size: 21
706237 TCGTACTTTG
*
706247 TTATTATTGTTTGTTTATTTGTT
1 TTATTATT-TTT-TTTATTTTTT
706270 TTATTTATTTTTTTT-TTTTTT
1 TTA-TTATTTTTTTTATTTTTT
706291 TTATTATTTTTTTTATTGTTTT
1 TTATTATTTTTTTTATT-TTTT
*
706313 TTACTTATTATTTTATATTT
1 TTA-TTATT-TTTTTTATTT
706333 GCTTTCTTCA
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.20
21 10 0.18
22 10 0.18
23 12 0.21
24 13 0.23
ACGTcount: A:0.15, C:0.01, G:0.05, T:0.79
Consensus pattern (21 bp):
TTATTATTTTTTTTATTTTTT
Found at i:723113 original size:2 final size:2
Alignment explanation
Indices: 723106--723136 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
723096 GTTTTGCTTA
723106 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
723137 AGCCAAACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:738487 original size:10 final size:10
Alignment explanation
Indices: 738472--738496 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
738462 TGTTACATGA
738472 TATATGTTAG
1 TATATGTTAG
738482 TATATGTTAG
1 TATATGTTAG
738492 TATAT
1 TATAT
738497 ATGTGAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (10 bp):
TATATGTTAG
Found at i:738958 original size:21 final size:21
Alignment explanation
Indices: 738920--738959 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
738910 ATATATGTGA
* *
738920 TATGTAGTCCTTCGGGACATC
1 TATGTAGTCATTCAGGACATC
*
738941 TATGTGGTCATTCAGGACA
1 TATGTAGTCATTCAGGACA
738960 AATTTCATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (21 bp):
TATGTAGTCATTCAGGACATC
Found at i:745527 original size:16 final size:16
Alignment explanation
Indices: 745508--745542 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
745498 ATAAATTTTC
*
745508 ATTAAAATGTATAAAA
1 ATTAAAATATATAAAA
*
745524 ATTAAAATATATAATA
1 ATTAAAATATATAAAA
745540 ATT
1 ATT
745543 TTAAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTAAAATATATAAAA
Done.