Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007988.1 Hibiscus syriacus cultivar Beakdansim tig00110435_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: 847207
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:511068 original size:2 final size:2
Alignment explanation
Indices: 511061--511099 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
511051 TCATTGGAAA
511061 AT AT 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 AT AT A
511100 AAATAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:514444 original size:20 final size:21
Alignment explanation
Indices: 514415--514454 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
514405 AGTATGTTCA
*
514415 GGGGGTATCGA-TTCCCCCTG
1 GGGGGAATCGATTTCCCCCTG
514435 GGGGGAATCGATTTCCCCCT
1 GGGGGAATCGATTTCCCCCT
514455 AAAGGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.12, C:0.30, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGATTTCCCCCTG
Found at i:515093 original size:15 final size:15
Alignment explanation
Indices: 515073--515104 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
515063 GGGTATTGTT
515073 GTCCTTCGGGACGTA
1 GTCCTTCGGGACGTA
515088 GTCCTTCGGGACGTA
1 GTCCTTCGGGACGTA
515103 GT
1 GT
515105 GGTCCTACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.25, G:0.34, T:0.28
Consensus pattern (15 bp):
GTCCTTCGGGACGTA
Found at i:521173 original size:15 final size:15
Alignment explanation
Indices: 521155--521204 Score: 100
Period size: 15 Copynumber: 3.3 Consensus size: 15
521145 CGAGGGTATT
521155 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
521170 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
521185 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
521200 GTAGT
1 GTAGT
521205 GGTCCTATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.14, C:0.24, G:0.34, T:0.28
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:521216 original size:18 final size:18
Alignment explanation
Indices: 521188--521235 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
521178 TCGGGACGTA
*
521188 GTCCTTCGGGACGTAGTG
1 GTCCTACGGGACGTAGTG
*
521206 GTCCTATGGGACGTAGTG
1 GTCCTACGGGACGTAGTG
521224 GTCCTACGGGAC
1 GTCCTACGGGAC
521236 ATATATAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (18 bp):
GTCCTACGGGACGTAGTG
Found at i:528464 original size:12 final size:12
Alignment explanation
Indices: 528427--528476 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
528417 ATTATTTAAA
528427 ATAA-TAAAATT
1 ATAATTAAAATT
*
528438 ATAATTACAATT
1 ATAATTAAAATT
*
528450 ATAATTAAAAAT
1 ATAATTAAAATT
* *
528462 ATAAATAACATT
1 ATAATTAAAATT
528474 ATA
1 ATA
528477 TCTAAATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 4 0.12
12 28 0.88
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (12 bp):
ATAATTAAAATT
Found at i:534775 original size:86 final size:86
Alignment explanation
Indices: 534624--534800 Score: 255
Period size: 86 Copynumber: 2.1 Consensus size: 86
534614 TCCTGTTTGG
* *
534624 TGTCGATAAGTGGAGGTCACTCTCATTGGTTTTAGGCTAATCGGTTATATTAATGGATTATAACC
1 TGTCGACAAGTGGAGGTCACTCTCATTGGTTTTAGGCTAATCGGTTATATTAATGGATTACAACC
* *
534689 TTCCATATTTCAGTTTACCGA
66 TTCCACATCTCAGTTTACCGA
* * * * *
534710 TGTCGACAAGTGGAGGTCACTCTCATTGGTTTTGGGCTATTCGGTTATATTGATTGATTGCAACC
1 TGTCGACAAGTGGAGGTCACTCTCATTGGTTTTAGGCTAATCGGTTATATTAATGGATTACAACC
* *
534775 TTCCACATCTCGGTTTACTGA
66 TTCCACATCTCAGTTTACCGA
534796 TGTCG
1 TGTCG
534801 CAACAAAAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (86 bp):
TGTCGACAAGTGGAGGTCACTCTCATTGGTTTTAGGCTAATCGGTTATATTAATGGATTACAACC
TTCCACATCTCAGTTTACCGA
Found at i:537256 original size:7 final size:7
Alignment explanation
Indices: 537244--537269 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
537234 AAGAAAGCAT
537244 GTATTCA
1 GTATTCA
537251 GTATTCA
1 GTATTCA
537258 GTATTCA
1 GTATTCA
537265 GTATT
1 GTATT
537270 TCATCTGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (7 bp):
GTATTCA
Found at i:538309 original size:23 final size:24
Alignment explanation
Indices: 538283--538334 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
538273 TTATTTTTTA
*
538283 TTCATGAACATATTCGTTTA-ATG
1 TTCATAAACATATTCGTTTATATG
* *
538306 TTCATAAACGTATTCGTTTATTTG
1 TTCATAAACATATTCGTTTATATG
538330 TTCAT
1 TTCAT
538335 TTAGCGTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (24 bp):
TTCATAAACATATTCGTTTATATG
Found at i:538589 original size:38 final size:38
Alignment explanation
Indices: 538545--538617 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
538535 GAGTAAACGA
538545 GCTTGTTCATGAACATAAATGAATGAGTCGATAAACAT
1 GCTTGTTCATGAACATAAATGAATGAGTCGATAAACAT
*
538583 GCTTGTTCGTGAACATAAATGAATGAGTCGATAAA
1 GCTTGTTCATGAACATAAATGAATGAGTCGATAAA
538618 TGAATCAGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (38 bp):
GCTTGTTCATGAACATAAATGAATGAGTCGATAAACAT
Found at i:539315 original size:20 final size:21
Alignment explanation
Indices: 539290--539343 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
539280 GACCAACAAA
539290 TTCGCAACGCGAATTT-CAAT
1 TTCGCAACGCGAATTTCCAAT
* *
539310 TTCGCAACAC-AGTTTCCAAT
1 TTCGCAACGCGAATTTCCAAT
539330 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
539344 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 22 0.79
21 2 0.07
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (21 bp):
TTCGCAACGCGAATTTCCAAT
Found at i:539389 original size:20 final size:20
Alignment explanation
Indices: 539366--539474 Score: 128
Period size: 20 Copynumber: 5.5 Consensus size: 20
539356 TTGCGATTTT
**
539366 TCAAATTCGCGTTGCGATAG
1 TCAAATTCGCAATGCGATAG
*
539386 TCAAATTCGCAATGCGAAAG
1 TCAAATTCGCAATGCGATAG
*
539406 TCAAATTCGCAACGCGATAG
1 TCAAATTCGCAATGCGATAG
** * *
539426 TCAAATTCGCAACACAAAAG
1 TCAAATTCGCAATGCGATAG
* *
539446 TCAAATTCGCAACGCGAAAG
1 TCAAATTCGCAATGCGATAG
539466 TCAAATTCG
1 TCAAATTCG
539475 TGTTGCGAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
TCAAATTCGCAATGCGATAG
Found at i:539455 original size:60 final size:60
Alignment explanation
Indices: 539384--539531 Score: 192
Period size: 60 Copynumber: 2.5 Consensus size: 60
539374 GCGTTGCGAT
*
539384 AGTCAAATTCGCAATGCGAAAGTCAAATTCGCAACGCG-A-TAGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAATTAGT-AAA-TCGCAACACAAA
**** * *
539444 AGTCAAATTCGCAACGCGAAAGTCAAATTCGTGTTGCGAATTTGTAAATCGCAACACAGA
1 AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAATTAGTAAATCGCAACACAAA
*
539504 AGTTAAATTCGCAACGCGAAAGTCAAAT
1 AGTCAAATTCGCAACGCGAAAGTCAAAT
539532 GTTTTTACGC
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
60 71 0.91
61 4 0.05
62 3 0.04
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (60 bp):
AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAATTAGTAAATCGCAACACAAA
Found at i:539482 original size:20 final size:20
Alignment explanation
Indices: 539379--539531 Score: 150
Period size: 20 Copynumber: 7.7 Consensus size: 20
539369 AATTCGCGTT
* *
539379 GCGATAGTCAAATTCGCAAT
1 GCGAAAGTCAAATTCGCAAC
539399 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
*
539419 GCGATAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
* *
539439 ACAAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
****
539459 GCGAAAGTCAAATTCGTGTT
1 GCGAAAGTCAAATTCGCAAC
*
539479 GCGAATTTGT-AAA-TCGCAAC
1 GCGAA--AGTCAAATTCGCAAC
* *
539499 AC-AGAAGTTAAATTCGCAAC
1 GCGA-AAGTCAAATTCGCAAC
539519 GCGAAAGTCAAAT
1 GCGAAAGTCAAAT
539532 GTTTTTACGC
Statistics
Matches: 106, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
18 2 0.02
19 4 0.04
20 94 0.89
21 4 0.04
22 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:539684 original size:22 final size:22
Alignment explanation
Indices: 539659--539709 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
539649 CTACGGCGAC
539659 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* * *
539681 ATCCATTCCCATTTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
539703 AACCGTC
1 ATCCGTC
539710 TATCTCCATC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.25, C:0.41, G:0.12, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:540037 original size:20 final size:20
Alignment explanation
Indices: 539967--540030 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
539957 CACAACGCGC
*
539967 TTTTCATTTTCGCGTTGCGC
1 TTTTCATTTTCGCGTTGCGA
*
539987 TTTTCATTTTCGCGTTGCAA
1 TTTTCATTTTCGCGTTGCGA
540007 TTTTCATTTTCGCGTTGCGA
1 TTTTCATTTTCGCGTTGCGA
540027 TTTT
1 TTTT
540031 AAGTTTCAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.09, C:0.20, G:0.17, T:0.53
Consensus pattern (20 bp):
TTTTCATTTTCGCGTTGCGA
Found at i:543755 original size:61 final size:62
Alignment explanation
Indices: 543655--543794 Score: 176
Period size: 66 Copynumber: 2.2 Consensus size: 62
543645 TTTTACATTG
*
543655 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
* ** * *
543715 AAAGTTGATTTGTTTACTTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTA-ATTGATGAGGAAATAAGAATTA--TTTTT-CTTGATTAATTGATTTGT
543780 A
62 A
543781 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
543795 GTTTCTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
60 16 0.24
61 17 0.25
64 4 0.06
66 31 0.46
ACGTcount: A:0.30, C:0.01, G:0.17, T:0.51
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
Found at i:543902 original size:20 final size:20
Alignment explanation
Indices: 543879--543922 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
543869 AATAAGCGTT
* *
543879 GCGACAGTCAAATTTGCAAC
1 GCGAAAGTCAAATTCGCAAC
543899 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
543919 GCGA
1 GCGA
543923 TTTTTGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:544216 original size:39 final size:39
Alignment explanation
Indices: 544161--544243 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
544151 TCAAGTTGTA
* *
544161 GATTTTGATTTCCTTTTGCTTGGCAACATATGAGATTTG
1 GATTTGGATTTCCTTTTGCTTGGCAACAAATGAGATTTG
* * * *
544200 GATTTGGATTTTCTTTTTCTTGGCACCAAATGAGCTTTG
1 GATTTGGATTTCCTTTTGCTTGGCAACAAATGAGATTTG
544239 GATTT
1 GATTT
544244 TGATGAGCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.19, C:0.13, G:0.20, T:0.47
Consensus pattern (39 bp):
GATTTGGATTTCCTTTTGCTTGGCAACAAATGAGATTTG
Found at i:544657 original size:25 final size:25
Alignment explanation
Indices: 544623--544672 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
544613 ATTATTTTTC
*
544623 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
544648 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
544673 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:544819 original size:20 final size:20
Alignment explanation
Indices: 544794--544851 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
544784 CGATTTTGCG
544794 TTGCGAATTTGACTATCGCA
1 TTGCGAATTTGACTATCGCA
* * *
544814 TTGCGAATTTGTCTTTCGCG
1 TTGCGAATTTGACTATCGCA
544834 TTGCGAATTTGACTATCG
1 TTGCGAATTTGACTATCG
544852 TAACGCTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCA
Found at i:545199 original size:18 final size:18
Alignment explanation
Indices: 545176--545211 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
545166 AAGCCTGTTG
545176 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
545194 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
545212 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:547496 original size:24 final size:24
Alignment explanation
Indices: 547469--547522 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
547459 TCATCACATC
*
547469 ATCAAAATCTGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
547493 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
547517 ATCAAA
1 ATCAAA
547523 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:548465 original size:20 final size:20
Alignment explanation
Indices: 548429--548539 Score: 95
Period size: 19 Copynumber: 5.6 Consensus size: 20
548419 ACTAAAACCT
*
548429 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
548448 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
** *
548467 GTTGCGAATTTGACTTTTGC
1 GTTGCGAATTTGAAATTCGC
548487 GTTGCGAATTT-ACATATTCGC
1 GTTGCGAATTTGA-A-ATTCGC
* * *
548508 GTTGCGAAATTGGAAACT-GT
1 GTTGCG-AATTTGAAATTCGC
548528 GTTGCGAATTTG
1 GTTGCGAATTTG
548540 TTGGTCATTT
Statistics
Matches: 73, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
19 31 0.42
20 24 0.33
21 12 0.16
22 5 0.07
23 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:555039 original size:18 final size:18
Alignment explanation
Indices: 555016--555050 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
555006 ACTGAATATT
555016 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
555034 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
555051 GTAATCCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:557930 original size:19 final size:18
Alignment explanation
Indices: 557886--557930 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
557876 TAATATCTTG
*
557886 AATTTATACATATCATAT
1 AATTTATACATAACATAT
**
557904 AACCTATACCATAACATAT
1 AATTTATA-CATAACATAT
557923 AATTTATA
1 AATTTATA
557931 TCGCTTATCT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTTATACATAACATAT
Found at i:559410 original size:23 final size:23
Alignment explanation
Indices: 559340--559436 Score: 67
Period size: 23 Copynumber: 4.1 Consensus size: 23
559330 TTACTATTAA
* *
559340 TAAAATAT-TTTAATAACATTTT
1 TAAAATATATTTATTAATATTTT
*
559362 AATCAAAATATTAATTT-TTAAAATTTT
1 --T-AAAATA-T-ATTTATTAATATTTT
*
559389 TAAAATATATTTATTAATATTTC
1 TAAAATATATTTATTAATATTTT
*
559412 TAATAATATA-ATATT-ATATTTT
1 TAA-AATATATTTATTAATATTTT
559434 TAA
1 TAA
559437 TATTATAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
22 13 0.21
23 16 0.26
24 13 0.21
25 7 0.11
26 1 0.02
27 8 0.13
28 3 0.05
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (23 bp):
TAAAATATATTTATTAATATTTT
Found at i:559420 original size:22 final size:22
Alignment explanation
Indices: 559400--559446 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
559390 AAAATATATT
559400 TATTAATATTTCTAATAATATAA
1 TATT-ATATTTCTAATAATATAA
* *
559423 TATTATATTTTTAATATTATAA
1 TATTATATTTCTAATAATATAA
559445 TA
1 TA
559447 AACAATCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATATTTCTAATAATATAA
Found at i:559459 original size:31 final size:32
Alignment explanation
Indices: 559394--559471 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 32
559384 ATTTTTAAAA
* *
559394 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAATACAATAT
559426 TATATTT-TTAATA-TTATAATAA-ACAATCAAT
1 TATATTTATTAATATTTATAATAATACAAT--AT
*
559457 TATATTATAATAATA
1 TATATT-TATTAATA
559472 AAGATTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 4 0.10
30 8 0.21
31 14 0.36
32 8 0.21
33 5 0.13
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAATACAATAT
Found at i:559494 original size:26 final size:28
Alignment explanation
Indices: 559456--559508 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 28
559446 AAACAATCAA
* *
559456 TTATATTATAATA-ATAA-AGATTATTT
1 TTATATTAAAATATATAATAAATTATTT
*
559482 TTATTTTAAAATATATAATAAATTATT
1 TTATATTAAAATATATAATAAATTATT
559509 AATAAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 11 0.50
27 4 0.18
28 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
TTATATTAAAATATATAATAAATTATTT
Found at i:559580 original size:19 final size:18
Alignment explanation
Indices: 559556--559624 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
559546 ATATTATTAA
559556 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
559575 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
559593 ATTAATCTAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
559615 ATT-TTAATAA
1 ATTATTAATAA
559625 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:559639 original size:23 final size:23
Alignment explanation
Indices: 559619--559663 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
559609 AATAATATTT
559619 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
559642 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
559664 ATATAACACT
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:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:559797 original size:89 final size:89
Alignment explanation
Indices: 559632--559803 Score: 208
Period size: 89 Copynumber: 1.9 Consensus size: 89
559622 TAAAGATATT
* * * * * *
559632 TAAAATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAATA
1 TAAAATATACTAATTAATATTTGTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAATA
559697 TAATTTATAATATTTTTATTTCAA
66 TAATTTATAATATTTTTATTTCAA
*
559721 TAAAATATACTAATATTAATATTTGTATTAATAAAATTATAAAAATAATA-TTTAATAAA-AAAT
1 TAAAATATACT-A-ATTAATATTTGTA-AAATAAAA-TATAAAAATAATACTTTAATAAATAAAT
*
559784 AA-ATTATTT-TAATATTTTTA
62 AATATAATTTATAATATTTTTA
559804 AAATAATAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
89 22 0.31
90 7 0.10
91 17 0.24
92 15 0.21
93 10 0.14
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (89 bp):
TAAAATATACTAATTAATATTTGTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAATA
TAATTTATAATATTTTTATTTCAA
Found at i:560633 original size:43 final size:43
Alignment explanation
Indices: 560585--560670 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
560575 AATTGGGCAC
560585 ATAGTTTTTAAAATTTGCAATTTAGTAACTGGCCCTGATTTAG
1 ATAGTTTTTAAAATTTGCAATTTAGTAACTGGCCCTGATTTAG
560628 ATAGTTTTTAAAATTTGCAATTTAGTAACTGGCCCTGATTTAG
1 ATAGTTTTTAAAATTTGCAATTTAGTAACTGGCCCTGATTTAG
560671 GATGTTACAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (43 bp):
ATAGTTTTTAAAATTTGCAATTTAGTAACTGGCCCTGATTTAG
Found at i:576957 original size:18 final size:17
Alignment explanation
Indices: 576936--576977 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
576926 ATATATATAT
*
576936 ATATATATAATATTTAAA
1 ATATATATAATA-ATAAA
*
576954 ATATTTATAATAATAAA
1 ATATATATAATAATAAA
576971 AT-TATAT
1 ATATATAT
576978 TTTGACTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 4 0.19
17 6 0.29
18 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATATATAATAATAAA
Found at i:577358 original size:15 final size:15
Alignment explanation
Indices: 577319--577391 Score: 76
Period size: 15 Copynumber: 4.9 Consensus size: 15
577309 TTGGTTTTTC
577319 GGAAAATGAATTACT
1 GGAAAATGAATTACT
* **
577334 GCAATTTGAATTACT
1 GGAAAATGAATTACT
*
577349 GGAAAATGAATTAGT
1 GGAAAATGAATTACT
** *
577364 GGAATTTAAATT-CT
1 GGAAAATGAATTACT
577378 GGAAAATGAATTAC
1 GGAAAATGAATTAC
577392 ATTTCTGGAA
Statistics
Matches: 43, Mismatches: 14, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
14 10 0.23
15 33 0.77
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:577389 original size:29 final size:30
Alignment explanation
Indices: 577319--577391 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
577309 TTGGTTTTTC
*
577319 GGAAAATGAATTACTGCAATTTGAATTACT
1 GGAAAATGAATTACTGCAATTTAAATTACT
* *
577349 GGAAAATGAATTAGTGGAATTTAAATT-CT
1 GGAAAATGAATTACTGCAATTTAAATTACT
577378 GGAAAATGAATTAC
1 GGAAAATGAATTAC
577392 ATTTCTGGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 15 0.38
30 24 0.62
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (30 bp):
GGAAAATGAATTACTGCAATTTAAATTACT
Found at i:577774 original size:28 final size:26
Alignment explanation
Indices: 577720--577783 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
577710 TTTACTAAAA
* *
577720 TATTATTTAAATATATAATAATATTAT
1 TATTA-TTAAATATATAAAAAAATTAT
577747 TCATTATTAAATATATAAAAAAATTTAT
1 T-ATTATTAAATATATAAAAAAA-TTAT
577775 TATATATTA
1 TAT-TATTA
577784 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 18 0.56
28 14 0.44
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTATTAAATATATAAAAAAATTAT
Found at i:577809 original size:31 final size:33
Alignment explanation
Indices: 577727--577828 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 33
577717 AAATATTATT
*
577727 TAAATATATAATAATATTAT-TCATTATTAAATA
1 TAAAAATATAAT-ATATTATATCATTATTAAATA
*
577760 TATAAAA-A-AATTTATTATAT-ATTATTAAA-A
1 TA-AAAATATAATATATTATATCATTATTAAATA
* *
577790 TAAAAATATAATATCTTATATTATATTATTATAATA
1 TAAAAATATAATATATTATA-T-CATTATTA-AATA
577826 TAA
1 TAA
577829 TTGATTATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
29 4 0.07
30 4 0.07
31 24 0.43
32 5 0.09
33 3 0.05
34 10 0.18
35 2 0.04
36 4 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (33 bp):
TAAAAATATAATATATTATATCATTATTAAATA
Found at i:577860 original size:31 final size:30
Alignment explanation
Indices: 577777--577890 Score: 96
Period size: 28 Copynumber: 3.8 Consensus size: 30
577767 AAATTTATTA
* *
577777 TATATTAT-TAA-AATAAAAATATAATATCT
1 TATATTATATAATATTAAAAATATAAT-TGT
*
577806 TATATTATAT--TATT-ATAATATAATTGAT
1 TATATTATATAATATTAAAAATATAATTG-T
*
577834 TATTTTATATAATATTAAAAATATAA-TGT
1 TATATTATATAATATTAAAAATATAATTGT
*
577863 TATGTTATTATAAATATTAATAAATATA
1 TATATTA-TAT-AATATTAA-AAATATA
577891 TTTTAAATAT
Statistics
Matches: 70, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
27 1 0.01
28 19 0.27
29 17 0.24
30 10 0.14
31 16 0.23
32 7 0.10
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (30 bp):
TATATTATATAATATTAAAAATATAATTGT
Found at i:577897 original size:21 final size:23
Alignment explanation
Indices: 577868--577918 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
577858 AATGTTATGT
*
577868 TATTATAAATA-TTAATAAAT-A
1 TATTTTAAATATTTAATAAATAA
577889 TATTTTAAATATTTTAATAAATAA
1 TATTTTAAATA-TTTAATAAATAA
577913 TATTTT
1 TATTTT
577919 GATGGAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 10 0.38
23 9 0.35
24 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTTAAATATTTAATAAATAA
Found at i:578205 original size:42 final size:42
Alignment explanation
Indices: 578090--578205 Score: 180
Period size: 42 Copynumber: 2.8 Consensus size: 42
578080 ATGAATTACA
* *
578090 TTCCGGAAAACGAATTACGTGAAACAAACACAGGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
578132 TTTC-AGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGA-AAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
578174 TTCCGAAAAACGAATTACATGAAACAAACACG
1 TTCCGAAAAACGAATTACGTGAAACAAACACG
578206 AAATTTCAGG
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
42 66 0.99
43 1 0.01
ACGTcount: A:0.48, C:0.19, G:0.16, T:0.17
Consensus pattern (42 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:603070 original size:7 final size:7
Alignment explanation
Indices: 603058--603139 Score: 101
Period size: 7 Copynumber: 11.7 Consensus size: 7
603048 GATTACACCT
603058 TAAACCC
1 TAAACCC
603065 TAAACCC
1 TAAACCC
* *
603072 TAAATCT
1 TAAACCC
*
603079 TAAATCC
1 TAAACCC
603086 TAAACCC
1 TAAACCC
603093 TAAACCC
1 TAAACCC
*
603100 TAAACCT
1 TAAACCC
603107 TAAACCC
1 TAAACCC
***
603114 TAAATTT
1 TAAACCC
603121 TAAACCC
1 TAAACCC
603128 TAAACCC
1 TAAACCC
603135 TAAAC
1 TAAAC
603140 ACTTAATTCG
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 63 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:603080 original size:21 final size:21
Alignment explanation
Indices: 603056--603138 Score: 121
Period size: 21 Copynumber: 4.0 Consensus size: 21
603046 TAGATTACAC
603056 CTTAAACCCTAAACCCTAAAT
1 CTTAAACCCTAAACCCTAAAT
* *
603077 CTTAAATCCTAAACCCTAAAC
1 CTTAAACCCTAAACCCTAAAT
* *
603098 CCTAAACCTTAAACCCTAAAT
1 CTTAAACCCTAAACCCTAAAT
*
603119 TTTAAACCCTAAACCCTAAA
1 CTTAAACCCTAAACCCTAAA
603139 CACTTAATTC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (21 bp):
CTTAAACCCTAAACCCTAAAT
Found at i:603147 original size:28 final size:28
Alignment explanation
Indices: 603093--603147 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
603083 TCCTAAACCC
* *
603093 TAAACCCTAAACCTTAAACCCTAAATTT
1 TAAACCCTAAACCCTAAACACTAAATTT
*
603121 TAAACCCTAAACCCTAAACACTTAATT
1 TAAACCCTAAACCCTAAACACTAAATT
603148 CGATTATGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (28 bp):
TAAACCCTAAACCCTAAACACTAAATTT
Found at i:603234 original size:7 final size:7
Alignment explanation
Indices: 603224--603248 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
603214 CCCTAAACTC
603224 TAAACCA
1 TAAACCA
603231 TAAACCA
1 TAAACCA
603238 TAAACCA
1 TAAACCA
603245 TAAA
1 TAAA
603249 TCTCAAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCA
Found at i:603281 original size:14 final size:14
Alignment explanation
Indices: 603257--603291 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
603247 AATCTCAAAT
*
603257 CCTAA-CCATAAGC
1 CCTAAGCCATAAAC
603270 CCTAAGCCATAAAC
1 CCTAAGCCATAAAC
603284 CCTAAGCC
1 CCTAAGCC
603292 CTTAACTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.37, C:0.40, G:0.09, T:0.14
Consensus pattern (14 bp):
CCTAAGCCATAAAC
Found at i:609138 original size:30 final size:29
Alignment explanation
Indices: 609099--609157 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
609089 AAGAATTTAC
* *
609099 ATGAACTACGTGATTAAATGTATATGTGA
1 ATGAACTACGCGATTAAATGAATATGTGA
* *
609128 ATGAAGCTACGCGTTTATATGAATATGTGA
1 ATGAA-CTACGCGATTAAATGAATATGTGA
609158 TATGTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGCGATTAAATGAATATGTGA
Found at i:609419 original size:46 final size:46
Alignment explanation
Indices: 609356--609455 Score: 107
Period size: 46 Copynumber: 2.2 Consensus size: 46
609346 TTTAAGGAAT
* *
609356 TTTCTACGTGGTCCTTAGG-GACAA-TCTTATATGGCAATTCGGTGCA
1 TTTCTACGCGGTCCTTAGGTG-CAATTC-TACATGGCAATTCGGTGCA
* *
609402 TTTCTACGCGG-CACTTAGGTGCAATTCTACGTGGCACTTCGGTGCA
1 TTTCTACGCGGTC-CTTAGGTGCAATTCTACATGGCAATTCGGTGCA
*
609448 TTTATACG
1 TTTCTACG
609456 AGCTGTGGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
45 1 0.02
46 42 0.91
47 3 0.07
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (46 bp):
TTTCTACGCGGTCCTTAGGTGCAATTCTACATGGCAATTCGGTGCA
Found at i:609422 original size:23 final size:23
Alignment explanation
Indices: 609396--609455 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
609386 ATGGCAATTC
609396 GGTGCATTTCTACGCGGCACTTA
1 GGTGCATTTCTACGCGGCACTTA
* * *
609419 GGTGCAATTCTACGTGGCACTTC
1 GGTGCATTTCTACGCGGCACTTA
*
609442 GGTGCATTTATACG
1 GGTGCATTTCTACG
609456 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (23 bp):
GGTGCATTTCTACGCGGCACTTA
Found at i:612615 original size:20 final size:20
Alignment explanation
Indices: 612590--612663 Score: 139
Period size: 20 Copynumber: 3.7 Consensus size: 20
612580 AAATTTTGAA
612590 GGTGCATCGATGCAGTAAGG
1 GGTGCATCGATGCAGTAAGG
612610 GGTGCATCGATGCAGTAAGG
1 GGTGCATCGATGCAGTAAGG
612630 GGTGCATCGATGCAGTAAGG
1 GGTGCATCGATGCAGTAAGG
*
612650 GGTGCATTGATGCA
1 GGTGCATCGATGCA
612664 TCAATATTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.24, C:0.15, G:0.39, T:0.22
Consensus pattern (20 bp):
GGTGCATCGATGCAGTAAGG
Found at i:613892 original size:30 final size:29
Alignment explanation
Indices: 613853--613911 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
613843 AAGAATTTAC
* *
613853 ATGAACTACGTGATTAAATGTATATGTGA
1 ATGAACTACGAGATTAAATGAATATGTGA
* *
613882 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGATTAAATGAATATGTGA
613912 TATGTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTAAATGAATATGTGA
Found at i:614173 original size:23 final size:23
Alignment explanation
Indices: 614143--614233 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
614133 AATCTTATAT
*
614143 GGCACTTCGGTGCATTTTTACGC
1 GGCACTTCGGTGCATTTCTACGC
614166 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
614189 GACACTTAGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
614212 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
614234 AGCTGTGGTG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:614677 original size:2 final size:2
Alignment explanation
Indices: 614670--614698 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
614660 AAGGAAATGG
614670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
614699 GTTTGGATGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:620229 original size:34 final size:34
Alignment explanation
Indices: 620164--620235 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 34
620154 CTATTATCAT
*
620164 TTTTCAACAAACATCTACCAAACTTGAAAAACTA
1 TTTTCAACAAACATCTACCAAACTTGAAAAACCA
* *
620198 TTTTCAAAGAAACATTTACCAAACTTG-AAAACCA
1 TTTTC-AACAAACATCTACCAAACTTGAAAAACCA
620232 TTTT
1 TTTT
620236 AATACTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 15 0.44
35 19 0.56
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (34 bp):
TTTTCAACAAACATCTACCAAACTTGAAAAACCA
Found at i:624244 original size:16 final size:16
Alignment explanation
Indices: 624220--624267 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
624210 TATCGCCGAC
* *
624220 CAAATTTCACTATTTA
1 CAAAATTCACTATTCA
624236 CAAAATTCACTATTCA
1 CAAAATTCACTATTCA
*
624252 CAAAATTCAATATTCA
1 CAAAATTCACTATTCA
624268 TATGAATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (16 bp):
CAAAATTCACTATTCA
Found at i:642384 original size:3 final size:3
Alignment explanation
Indices: 642369--642408 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
642359 AGGAGAATTG
*
642369 ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
642409 GCAAACTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:651793 original size:30 final size:30
Alignment explanation
Indices: 651759--651817 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
651749 AAGAGTTATA
* *
651759 CTTACTTTTACTGTTTTTTATCACATTCTT
1 CTTACATTTACTGTTTTTAATCACATTCTT
651789 CTTACATTTACTGTTTTTAATCACATTCT
1 CTTACATTTACTGTTTTTAATCACATTCT
651818 AACCCGTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.56
Consensus pattern (30 bp):
CTTACATTTACTGTTTTTAATCACATTCTT
Found at i:654418 original size:10 final size:10
Alignment explanation
Indices: 654403--654432 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
654393 TTTCGTTCTA
*
654403 ATTTCATTGT
1 ATTTCATGGT
654413 ATTTCATGGT
1 ATTTCATGGT
654423 ATTTCATGGT
1 ATTTCATGGT
654433 TTTACCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.20, C:0.10, G:0.17, T:0.53
Consensus pattern (10 bp):
ATTTCATGGT
Found at i:656020 original size:10 final size:11
Alignment explanation
Indices: 656005--656067 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 11
655995 ACACGGTGGG
656005 CATCCGAG-GC
1 CATCCGAGAGC
656015 CATCCGAGAAGC
1 CATCCGAG-AGC
* *
656027 TATGCGAGAG-
1 CATCCGAGAGC
656037 CATCCGAG-GC
1 CATCCGAGAGC
656047 CATCCGACCGAGGC
1 CATCCGA--GA-GC
656061 CATCCGA
1 CATCCGA
656068 CCGAGGGCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 1 0.02
10 21 0.50
11 2 0.05
12 9 0.21
14 9 0.21
ACGTcount: A:0.25, C:0.35, G:0.29, T:0.11
Consensus pattern (11 bp):
CATCCGAGAGC
Found at i:656059 original size:14 final size:14
Alignment explanation
Indices: 656040--656096 Score: 105
Period size: 14 Copynumber: 4.1 Consensus size: 14
656030 GCGAGAGCAT
656040 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
656054 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
656068 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
656082 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
656096 C
1 C
656097 TGAATTATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.21, C:0.42, G:0.30, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:656143 original size:23 final size:23
Alignment explanation
Indices: 656113--656159 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
656103 ATGTGAGGGC
*
656113 ATGCGAGGATAGCCGAGCGAGCT
1 ATGCGAGGACAGCCGAGCGAGCT
* *
656136 ATGCGAGGGCATCCGAGCGAGCT
1 ATGCGAGGACAGCCGAGCGAGCT
656159 A
1 A
656160 GCAAGGGTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.23, G:0.38, T:0.13
Consensus pattern (23 bp):
ATGCGAGGACAGCCGAGCGAGCT
Found at i:656210 original size:29 final size:29
Alignment explanation
Indices: 656168--656281 Score: 192
Period size: 29 Copynumber: 3.9 Consensus size: 29
656158 TAGCAAGGGT
*
656168 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
656197 AGGTCGCCAGGAGTGCATGGCGACCTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
*
656226 AGGTCGCCAGGATTGCATGGCGACCTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
* *
656255 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCAGGAGTGCATGGCGACCTA
656282 TGCTTGGGGA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 80 1.00
ACGTcount: A:0.22, C:0.29, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCAGGAGTGCATGGCGACCTACA
Found at i:657171 original size:29 final size:30
Alignment explanation
Indices: 657110--657184 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
657100 CTGCATGGAT
*
657110 TGCATGGCGACCTACCTAGGTCGTTGGGAG
1 TGCATGGCGACCTACCTAGGTCGCTGGGAG
** *
657140 TGCATGGCGACCT-GGTAGGTCGCTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGAG
657169 TGCATGGCGACCTACC
1 TGCATGGCGACCTACC
657185 CCATCTAACA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 25 0.66
30 13 0.34
ACGTcount: A:0.15, C:0.27, G:0.37, T:0.21
Consensus pattern (30 bp):
TGCATGGCGACCTACCTAGGTCGCTGGGAG
Found at i:657434 original size:30 final size:30
Alignment explanation
Indices: 657366--657440 Score: 125
Period size: 29 Copynumber: 2.5 Consensus size: 30
657356 TGTTAGATGG
657366 GGTAGGTCGCCATGCACGCCCAGCGACCTA
1 GGTAGGTCGCCATGCACGCCCAGCGACCTA
**
657396 -CCAGGTCGCCATGCACGCCCAGCGACCTA
1 GGTAGGTCGCCATGCACGCCCAGCGACCTA
657425 GGTAGGTCGCCATGCA
1 GGTAGGTCGCCATGCA
657441 ATCCATGCTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 27 0.68
30 13 0.32
ACGTcount: A:0.20, C:0.37, G:0.29, T:0.13
Consensus pattern (30 bp):
GGTAGGTCGCCATGCACGCCCAGCGACCTA
Found at i:658263 original size:30 final size:30
Alignment explanation
Indices: 658227--658301 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
658217 GGGGCTGGAT
*
658227 TGCATGGCGACCTACCTAGGTTGTTGGGCG
1 TGCATGGCGACCTACCTAGGTCGTTGGGCG
658257 TGCATGGCGACCTGA--TAGGTCGTTGGGCG
1 TGCATGGCGACCT-ACCTAGGTCGTTGGGCG
658286 TGCATGGCGACCTACC
1 TGCATGGCGACCTACC
658302 CTATCTAACA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
28 1 0.02
29 26 0.63
30 13 0.32
31 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.36, T:0.24
Consensus pattern (30 bp):
TGCATGGCGACCTACCTAGGTCGTTGGGCG
Found at i:659683 original size:23 final size:23
Alignment explanation
Indices: 659657--659702 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
659647 GCCATCTGAC
** *
659657 CGAGGCCATTCGAGCGAGCTATG
1 CGAGGCCAGCCGAACGAGCTATG
*
659680 CGAGGGCAGCCGAACGAGCTATG
1 CGAGGCCAGCCGAACGAGCTATG
659703 TAAGGAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.37, T:0.13
Consensus pattern (23 bp):
CGAGGCCAGCCGAACGAGCTATG
Found at i:670401 original size:21 final size:21
Alignment explanation
Indices: 670368--670415 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
670358 GCGAATATGT
670368 AAATT-GCATTGCGATTTTCC
1 AAATTCGCATTGCGATTTTCC
*
670388 AAATTCGCGTTGCGATTTTCC
1 AAATTCGCATTGCGATTTTCC
670409 AAATTCG
1 AAATTCG
670416 TAACGCGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (21 bp):
AAATTCGCATTGCGATTTTCC
Found at i:670423 original size:21 final size:21
Alignment explanation
Indices: 670306--670478 Score: 81
Period size: 20 Copynumber: 8.6 Consensus size: 21
670296 AAATGAACAA
*
670306 CAAATTCGCAACGCGA-ATTC
1 CAAATTCGCAACGCGATTTTC
* * * *
670326 TAATTTCGCAAC-CAAGTTTC
1 CAAATTCGCAACGCGATTTTC
* * * *
670346 CAATTTCGCAACGCGAATATG
1 CAAATTCGCAACGCGATTTTC
* **
670367 TAAATT-GCATTGCGATTTTC
1 CAAATTCGCAACGCGATTTTC
***
670387 CAAATTCGCGTTGCGATTTTC
1 CAAATTCGCAACGCGATTTTC
* **
670408 CAAATTCGTAACGCGATAAT-
1 CAAATTCGCAACGCGATTTTC
* ***
670428 CAAATTCGCAACACGAAAGT-
1 CAAATTCGCAACGCGATTTTC
* *
670448 CAAATTCGCAAC-TGAATTT-
1 CAAATTCGCAACGCGATTTTC
670467 CAAATTCGCAAC
1 CAAATTCGCAAC
670479 AGGTTTTAGT
Statistics
Matches: 119, Mismatches: 31, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
19 18 0.15
20 66 0.55
21 35 0.29
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (21 bp):
CAAATTCGCAACGCGATTTTC
Found at i:670666 original size:16 final size:15
Alignment explanation
Indices: 670636--670672 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
670626 CCCCATCTCT
670636 ATTTTTTTATATATA
1 ATTTTTTTATATATA
*
670651 ATTTTATTTTTATATA
1 ATTTT-TTTATATATA
670667 ATTTTT
1 ATTTTT
670673 CAATGATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTTTTATATATA
Found at i:671247 original size:12 final size:12
Alignment explanation
Indices: 671226--671259 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
671216 ACCACATTTC
*
671226 CAATACCAAACA
1 CAATATCAAACA
671238 CAATATCAAACA
1 CAATATCAAACA
*
671250 CAATCTCAAA
1 CAATATCAAA
671260 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:671412 original size:24 final size:24
Alignment explanation
Indices: 671385--671438 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
671375 GTATTCGAAA
671385 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
671409 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
671433 TTTGAT
1 TTTGAT
671439 GATGTGATGG
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:671624 original size:6 final size:6
Alignment explanation
Indices: 671614--671654 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
671604 TATAACCCTG
* * *
671614 AAGAAG AAGAAA AAGAAA AAGAAC AAGAAC AAGAAC AAGAA
1 AAGAAC AAGAAC AAGAAC AAGAAC AAGAAC AAGAAC AAGAA
671655 GTCCCCGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (6 bp):
AAGAAC
Found at i:673723 original size:18 final size:18
Alignment explanation
Indices: 673697--673732 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
673687 AAGCAAAAGG
*
673697 AAATTAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
673715 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
673733 CAACCAGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.19, G:0.03, T:0.22
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:674230 original size:25 final size:25
Alignment explanation
Indices: 674196--674247 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
674186 AACAAATCAA
*
674196 TTAAACATTGTTGTGGATACATTAT
1 TTAAACATTGTTATGGATACATTAT
*
674221 TTAAACATTGTTATGGGTACATTAT
1 TTAAACATTGTTATGGATACATTAT
674246 TT
1 TT
674248 GGAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (25 bp):
TTAAACATTGTTATGGATACATTAT
Found at i:674643 original size:24 final size:25
Alignment explanation
Indices: 674616--674678 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
674606 TTTCAAATTC
*
674616 ATTTCATATGT-AATTGGAGTTTGA
1 ATTTCAAATGTAAATTGGAGTTTGA
* *
674640 ATTT-AAATTTAAATTTGAGTTTGA
1 ATTTCAAATGTAAATTGGAGTTTGA
*
674664 ATTTC-AATATAAATT
1 ATTTCAAATGTAAATT
674679 TCGACTCCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 4 0.12
24 29 0.88
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.48
Consensus pattern (25 bp):
ATTTCAAATGTAAATTGGAGTTTGA
Found at i:674679 original size:24 final size:24
Alignment explanation
Indices: 674627--674679 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
674617 TTTCATATGT
* *
674627 AATTGGAGTTTGAATTTAAATTTA
1 AATTTGAGTTTGAATTTAAATATA
*
674651 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
674675 AATTT
1 AATTT
674680 CGACTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:675024 original size:39 final size:39
Alignment explanation
Indices: 674981--675067 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
674971 TCCGATGCTC
674981 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGAAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGAAA
* *
675020 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGAAA
675059 ATCAAAATC
1 ATCAAAATC
675068 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGAAA
Found at i:675455 original size:14 final size:14
Alignment explanation
Indices: 675421--675474 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
675411 AAAATTCTTA
*
675421 TTTACAAATCAAAT
1 TTTACAAATCAACT
**
675435 TAAACAAATCAACT
1 TTTACAAATCAACT
*
675449 TTTACAAATCATCT
1 TTTACAAATCAACT
675463 TTTACAAATCAA
1 TTTACAAATCAA
675475 TTAATCAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (14 bp):
TTTACAAATCAACT
Found at i:677154 original size:17 final size:17
Alignment explanation
Indices: 677124--677167 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
677114 CGGGCCGCTG
* *
677124 AAAATAAATTAATATAT
1 AAAATAAATAAATAAAT
*
677141 AAAATCAATAAATAAAT
1 AAAATAAATAAATAAAT
677158 -AAATAAATAA
1 AAAATAAATAA
677168 TGCCGAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATAAATAAATAAAT
Found at i:677156 original size:4 final size:4
Alignment explanation
Indices: 677125--677167 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
677115 GGGCCGCTGA
* * *
677125 AAAT AAAT TAAT ATAT AAAAT CAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AA
677168 TGCCGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:677436 original size:42 final size:41
Alignment explanation
Indices: 677340--677439 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
677330 AGTAAAAAAT
* * *
677340 CCACCTCACCACGTAAAGATCGAACCTCATCACGCCATGCA
1 CCACCTCATCACGTAAAGATCGAACCTCATCACGCAAAGCA
** * *
677381 CCATTATCTTCACGTAAAGTATCG-ACCTCATGACGCAAAGCA
1 CCA-CCTCATCACGTAAAG-ATCGAACCTCATCACGCAAAGCA
677423 CCGACCTCATCACGTAA
1 CC-ACCTCATCACGTAA
677440 TTCCCCTAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
41 3 0.07
42 38 0.83
43 5 0.11
ACGTcount: A:0.32, C:0.36, G:0.13, T:0.19
Consensus pattern (41 bp):
CCACCTCATCACGTAAAGATCGAACCTCATCACGCAAAGCA
Found at i:677581 original size:33 final size:33
Alignment explanation
Indices: 677516--677583 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
677506 CCTATCATGA
* * *
677516 GGTGAAGGTGGAGAAGAGGCTCGGTGATGTGAT
1 GGTGAAGGTGGAGAAGAGGCTCGATCAGGTGAT
* *
677549 GGTGGAGGTGGAGAATAGGCTCGATCAGGTGAT
1 GGTGAAGGTGGAGAAGAGGCTCGATCAGGTGAT
677582 GG
1 GG
677584 CTCCGGGTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.24, C:0.07, G:0.49, T:0.21
Consensus pattern (33 bp):
GGTGAAGGTGGAGAAGAGGCTCGATCAGGTGAT
Found at i:679127 original size:20 final size:21
Alignment explanation
Indices: 679115--679152 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
679105 AAACTTAAAT
679115 TCGCAACGC-AAAAATGAAAA
1 TCGCAACGCGAAAAATGAAAA
679135 TCGCAACGCG-AAAATGAA
1 TCGCAACGCGAAAAATGAA
679153 CATTGAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.11
Consensus pattern (21 bp):
TCGCAACGCGAAAAATGAAAA
Found at i:679465 original size:22 final size:22
Alignment explanation
Indices: 679433--679479 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
679423 GATGGAGATA
*
679433 GACGGATTTCGTCAGAAATGGG
1 GACGGAATTCGTCAGAAATGGG
* *
679455 GACGGAATTCGTCGGAGATGGG
1 GACGGAATTCGTCAGAAATGGG
679477 GAC
1 GAC
679480 AGATGTCGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.15, G:0.40, T:0.19
Consensus pattern (22 bp):
GACGGAATTCGTCAGAAATGGG
Found at i:679667 original size:20 final size:20
Alignment explanation
Indices: 679611--679755 Score: 93
Period size: 20 Copynumber: 7.2 Consensus size: 20
679601 GCGTAAAAAC
*
679611 ATTTGACTTTCGCGTTACGA
1 ATTTGACTTTCGCGTTGCGA
*
679631 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
679651 ATTTGACTTTTGTGTTGCG-
1 ATTTGACTTTCGCGTTGCGA
* *
679670 ATTT-ACAAATTCACGTTGCGAA
1 ATTTGAC--TTTCGCGTTGCG-A
* * *
679692 ATTGGA-ATTCACGTTGCGAA
1 ATTTGACTTTCGCGTTGCG-A
* *
679712 ATTGGA-ATTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
679731 TATTGGA-ATTCGCGTTGCGA
1 -ATTTGACTTTCGCGTTGCGA
679751 ATTTG
1 ATTTG
679756 TTGGTCATTT
Statistics
Matches: 107, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
18 2 0.02
19 9 0.08
20 92 0.86
22 3 0.03
23 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:679708 original size:40 final size:39
Alignment explanation
Indices: 679664--679753 Score: 108
Period size: 40 Copynumber: 2.3 Consensus size: 39
679654 TGACTTTTGT
*
679664 GTTGCGATTTACAAATTCACGTTGCGAAATTGGAATTCAC
1 GTTGCGAATT-CAAATTCACGTTGCGAAATTGGAATTCAC
** * * *
679704 GTTGCGAAATTGGAATTCGCGTTGCGATATTGGAATTCGC
1 GTTGCG-AATTCAAATTCACGTTGCGAAATTGGAATTCAC
679744 GTTGCGAATT
1 GTTGCGAATT
679754 TGTTGGTCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
39 4 0.09
40 36 0.84
41 3 0.07
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (39 bp):
GTTGCGAATTCAAATTCACGTTGCGAAATTGGAATTCAC
Found at i:680274 original size:31 final size:33
Alignment explanation
Indices: 680207--680274 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
680197 TTAAGTAACG
680207 TTTAATATTAACATTTTTAATAGAAAAATAATAT
1 TTTAATATTAACATTTTTAATA-AAAAATAATAT
680241 TTTAATATTAACA-TTTTAAGT-AAAAA-AATAT
1 TTTAATATTAACATTTTTAA-TAAAAAATAATAT
680272 TTT
1 TTT
680275 CTGTCACCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
31 8 0.24
32 5 0.15
33 6 0.18
34 14 0.42
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (33 bp):
TTTAATATTAACATTTTTAATAAAAAATAATAT
Found at i:680455 original size:29 final size:29
Alignment explanation
Indices: 680410--680467 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
680400 GTGTTGGCCG
* *
680410 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGAACTAC
* *
680439 TAGGTCGTCATGTCTTCCCGGCGAACTAC
1 TAGGTCGCCATGCCTTCCCGGCGAACTAC
680468 AAGAGATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.34, G:0.26, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGAACTAC
Found at i:680543 original size:23 final size:23
Alignment explanation
Indices: 680511--680559 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
680501 GCTGGGCATC
680511 CGAGGCCATCCGAACGAGCTATG
1 CGAGGCCATCCGAACGAGCTATG
* *
680534 CGAGGGCATCCGAGCGAGCTATG
1 CGAGGCCATCCGAACGAGCTATG
680557 CGA
1 CGA
680560 AGGAATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.29, G:0.35, T:0.12
Consensus pattern (23 bp):
CGAGGCCATCCGAACGAGCTATG
Found at i:683640 original size:12 final size:12
Alignment explanation
Indices: 683623--683647 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
683613 TATTAAATAA
683623 TAATAATATTTT
1 TAATAATATTTT
683635 TAATAATATTTT
1 TAATAATATTTT
683647 T
1 T
683648 TTATCGTATA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAATAATATTTT
Found at i:687130 original size:15 final size:15
Alignment explanation
Indices: 687110--687215 Score: 57
Period size: 15 Copynumber: 7.5 Consensus size: 15
687100 TATCGATGAT
687110 TTTTTATAGAAATAA
1 TTTTTATAGAAATAA
**
687125 TTTTTATTTAAAT-A
1 TTTTTATAGAAATAA
* *
687139 -TATTATCG--ATGAA
1 TTTTTATAGAAAT-AA
687152 TTTTTATAGAAATAA
1 TTTTTATAGAAATAA
**
687167 TTTTTATTTAAAT-A
1 TTTTTATAGAAATAA
* *
687181 -TATTATCG--ATGAA
1 TTTTTATAGAAAT-AA
*
687194 TTTTTATATAAATAA
1 TTTTTATAGAAATAA
687209 TTTTTAT
1 TTTTTAT
687216 TTAAATATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 20
0.65 0.15 0.20
Matches are distributed among these distances:
11 4 0.06
13 12 0.18
14 13 0.20
15 33 0.50
16 4 0.06
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTTTATAGAAATAA
Found at i:687141 original size:42 final size:42
Alignment explanation
Indices: 687093--687223 Score: 244
Period size: 42 Copynumber: 3.1 Consensus size: 42
687083 ATAATAAAGT
*
687093 AATATATTATCGATGATTTTTTATAGAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
687135 AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
*
687177 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
687219 AATAT
1 AATAT
687224 TTAGAATTCA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (42 bp):
AATATATTATCGATGAATTTTTATAGAAATAATTTTTATTTA
Found at i:687602 original size:2 final size:2
Alignment explanation
Indices: 687588--687627 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
687578 ATTCATACAC
*
687588 AT AT AT A- AT -T AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
687628 TTAGGATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:691017 original size:3 final size:3
Alignment explanation
Indices: 691009--691040 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
690999 TACAATTGCA
*
691009 ATT ATT ATT ATT ATA ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
691041 CTAGTAGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:700690 original size:21 final size:21
Alignment explanation
Indices: 700610--700691 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 21
700600 CGCAAATCAG
*
700610 TTTCCATATTCGCAACGCGAT
1 TTTCCATATTCGCAATGCGAT
* *
700631 TAT-GACTA-TCGCAATGCGAT
1 TTTCCA-TATTCGCAATGCGAT
* **
700651 TTTCCATTTTCGCGTTGCGAT
1 TTTCCATATTCGCAATGCGAT
700672 TTTCCCA-ATTCGCAATGCGA
1 TTT-CCATATTCGCAATGCGA
700692 ATAAGTAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
20 15 0.33
21 28 0.61
22 3 0.07
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (21 bp):
TTTCCATATTCGCAATGCGAT
Found at i:700706 original size:20 final size:21
Alignment explanation
Indices: 700681--700732 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
700671 TTTTCCCAAT
*
700681 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
700701 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
700722 TCGCAATGCGA
1 TCGCAATGCGA
700733 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:700711 original size:41 final size:41
Alignment explanation
Indices: 700666--700958 Score: 195
Period size: 41 Copynumber: 7.2 Consensus size: 41
700656 ATTTTCGCGT
* *
700666 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
* *** * *
700707 TGCGAATTTGGAAAATCGCAATGCG-ATAC-TGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGT-A-AATCGCAA
* * * * **
700748 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATACGTAAATCGCAA
*
700789 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
* *** *
700830 CGCGA-TTAAGTAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
* *** * * *
700870 CGCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TACGTAAATCGCAA
* * * * * *
700911 TGCGA-ATACGTAAATCGCAATGCGAAT-CTTACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTA-AATCGCAA
700951 TGCGATTT
1 TGCGATTT
700959 ACATAGCGCC
Statistics
Matches: 202, Mismatches: 41, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
39 2 0.01
40 79 0.39
41 117 0.58
43 3 0.01
44 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
Found at i:700776 original size:21 final size:21
Alignment explanation
Indices: 700742--700814 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
700732 ATACTGACTA
* *
700742 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
700763 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
700783 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
700804 TCGCAATGCGA
1 TCGCAATGCGA
700815 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:700829 original size:20 final size:20
Alignment explanation
Indices: 700804--700955 Score: 189
Period size: 20 Copynumber: 7.5 Consensus size: 20
700794 TTTTCATAAT
700804 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
700824 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
700844 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
700864 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
700884 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
700905 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
700925 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
700945 TCGCAATGCGA
1 TCGCAATGCGA
700956 TTTACATAGC
Statistics
Matches: 113, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
19 3 0.03
20 92 0.81
21 18 0.16
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:700848 original size:40 final size:40
Alignment explanation
Indices: 700804--700937 Score: 214
Period size: 40 Copynumber: 3.3 Consensus size: 40
700794 TTTTCATAAT
700804 TCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAA
700844 TCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAA
* * * * *
700884 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAA-TACGTAAATCGCAACGCGATTAAGTAAA
700925 TCGCAATGCGAAT
1 TCGCAATGCGAAT
700938 CTTACTATCG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 53 0.60
41 35 0.40
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAA
Found at i:700854 original size:61 final size:62
Alignment explanation
Indices: 700681--700937 Score: 204
Period size: 61 Copynumber: 4.2 Consensus size: 62
700671 TTTTCCCAAT
* * *
700681 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACT--A
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATATTCA-TAAA
*** * * * * * * ** * *
700742 TCGCAATGC-AATTTTCCTAATTCGCATTGCGATTTACG-TATTCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGAA--TAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATATTCATAAA
* * * * * *
700804 TCGCAATGCGAATACGTAAATCGCAACGCG-ATTAAGTAAATCGCAATGCGA-ATACGTAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATATTCATAAA
* * * *
700864 TCGCAACGCGATTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGA-ATACGTAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATATTCATAAA
700925 TCGCAATGCGAAT
1 TCGCAATGCGAAT
700938 CTTACTATCG
Statistics
Matches: 150, Mismatches: 39, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
60 38 0.25
61 84 0.56
62 26 0.17
63 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (62 bp):
TCGCAATGCGAATAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATATTCATAAA
Found at i:701258 original size:12 final size:11
Alignment explanation
Indices: 701240--701272 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
701230 CCGAGGGTTA
701240 GTTTTTTTTTT
1 GTTTTTTTTTT
701251 GTTTTTTTTTT
1 GTTTTTTTTTT
701262 GTTTTTTTTTT
1 GTTTTTTTTTT
701273 AAAATTTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:701562 original size:33 final size:33
Alignment explanation
Indices: 701523--701610 Score: 149
Period size: 33 Copynumber: 2.6 Consensus size: 33
701513 AACGCGATTT
701523 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAA
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAA
* *
701556 TTATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAA
701589 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
701611 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTTGCGATAA
Found at i:701612 original size:20 final size:20
Alignment explanation
Indices: 701578--701635 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
701568 GCGATTCTCT
**
701578 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
701598 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
701618 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
701636 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:705220 original size:14 final size:14
Alignment explanation
Indices: 705201--705234 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
705191 TGTTTAATTT
705201 ATTTGTAAAAGGTG
1 ATTTGTAAAAGGTG
*
705215 ATTTGTAAAAGTTG
1 ATTTGTAAAAGGTG
705229 ATTTGT
1 ATTTGT
705235 TTAATTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
ATTTGTAAAAGGTG
Found at i:705365 original size:19 final size:19
Alignment explanation
Indices: 705341--705387 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
705331 AAAAAGTACT
*
705341 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
705360 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
705379 ATCGCAACG
1 ATCGCAACG
705388 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:705434 original size:19 final size:19
Alignment explanation
Indices: 705412--705562 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
705402 CGAAATTAAA
705412 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
705431 TTCGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* * *
705446 -CCTCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
* *
705464 TTCGCATTGCGA----AAT
1 TTCGCGTTGCGATTTTCAT
705479 -TCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
705497 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
705512 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
705530 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
705549 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
705563 AGACATTAAG
Statistics
Matches: 94, Mismatches: 22, Indels: 31
0.64 0.15 0.21
Matches are distributed among these distances:
14 26 0.28
15 2 0.02
16 5 0.05
17 6 0.06
18 2 0.02
19 43 0.46
20 10 0.11
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:705458 original size:33 final size:32
Alignment explanation
Indices: 705416--705542 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
705406 ATTAAATTCG
*
705416 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* *
705449 CGTTGCGATTTTTATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
705482 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
705515 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
705543 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:705494 original size:66 final size:66
Alignment explanation
Indices: 705409--705541 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
705399 ATGCGAAATT
* *
705409 AAATTCGCGTTGCGATTTTCATTTCGCATTGTGATTCCCTCGTTGCGATTTTTATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
705474 G
66 G
*
705475 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
705540 G
66 G
705541 A
1 A
705542 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:707376 original size:21 final size:21
Alignment explanation
Indices: 707352--707412 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
707342 AACGGTGGGT
*
707352 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
707373 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
*
707394 GGGGACTCTTGAGGAATGA
1 GGGGACTCTTGAGGGATGA
707413 CAGGTGAGTC
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.23, C:0.13, G:0.41, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:707379 original size:42 final size:42
Alignment explanation
Indices: 707324--707412 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
707314 CCTCTTCAAC
* * * *
707324 AATGACAGTGGCCTCTTGAACGGTGGGTGGGGACTCTTGAGG
1 AATGATAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
* *
707366 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 AATGATAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
707408 AATGA
1 AATGA
707413 CAGGTGAGTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.22, C:0.15, G:0.39, T:0.24
Consensus pattern (42 bp):
AATGATAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:707802 original size:19 final size:19
Alignment explanation
Indices: 707775--707825 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
707765 ACACGAAACT
*
707775 TACTTTCGCAACGCCAAAA
1 TACTATCGCAACGCCAAAA
**
707794 TACTATCGCAACGCGGAAA
1 TACTATCGCAACGCCAAAA
707813 TGACTATCGCAAC
1 T-ACTATCGCAAC
707826 ACGGAAATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.20
Consensus pattern (19 bp):
TACTATCGCAACGCCAAAA
Found at i:707820 original size:20 final size:20
Alignment explanation
Indices: 707780--707865 Score: 95
Period size: 20 Copynumber: 4.4 Consensus size: 20
707770 AAACTTACTT
**
707780 TCGCAACGCCAAAAT-ACTA
1 TCGCAACGCGGAAATGACTA
707799 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
* *
707819 TCGCAACACGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
707839 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
707858 TCGCAACG
1 TCGCAACG
707866 ACAAAATCGC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 27 0.48
20 29 0.52
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:707823 original size:39 final size:39
Alignment explanation
Indices: 707780--707872 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 39
707770 AAACTTACTT
**
707780 TCGCAACGCCAAAAT-ACTATCGCAACGCGGAAATGACTA
1 TCGCAACGCCAAAATGACTATCGCAACGC-GAAATGAAAA
* ** * *
707819 TCGCAACACGGAAATGGCTATCGCAATGCGAAATGAAAA
1 TCGCAACGCCAAAATGACTATCGCAACGCGAAATGAAAA
*
707858 TCGCAACGACAAAAT
1 TCGCAACGCCAAAAT
707873 CGCAACGCGA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
39 31 0.74
40 11 0.26
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (39 bp):
TCGCAACGCCAAAATGACTATCGCAACGCGAAATGAAAA
Found at i:707913 original size:19 final size:18
Alignment explanation
Indices: 707891--707954 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
707881 GAAACACAAA
707891 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
* *
707910 TCGCGTTGCGA-TTT-TG
1 TCGCATTGCGATTTTATT
707926 TCG--TTGCGATTTTTATT
1 TCGCATTGCGA-TTTTATT
707943 TCGCATTGCGAT
1 TCGCATTGCGAT
707955 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
14 6 0.16
16 7 0.19
17 4 0.11
18 4 0.11
19 16 0.43
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:707962 original size:19 final size:20
Alignment explanation
Indices: 707940--707982 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
707930 TGCGATTTTT
707940 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
707959 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
707979 ATTT
1 ATTT
707983 TCGTGTTACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:708551 original size:18 final size:18
Alignment explanation
Indices: 708528--708575 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
708518 CGGGTCGATC
708528 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
708546 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
708564 AGGTGATGGCTC
1 AGGTGATGGCTC
708576 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:709875 original size:20 final size:20
Alignment explanation
Indices: 709850--709892 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
709840 AATAGTTTCT
709850 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
709870 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
709890 GAA
1 GAA
709893 TTTGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:710431 original size:20 final size:20
Alignment explanation
Indices: 710406--710472 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
710396 GTATTATCTC
*
710406 GTTGCGAAAGTCAGTATTGA
1 GTTGCGAAAGTCAGTATCGA
* *
710426 GTTGCGAAATTAAGTATCGA
1 GTTGCGAAAGTCAGTATCGA
*
710446 GTTGCGAAAGTCAGTATCGC
1 GTTGCGAAAGTCAGTATCGA
710466 GTTGCGA
1 GTTGCGA
710473 TTTTGTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.28
Consensus pattern (20 bp):
GTTGCGAAAGTCAGTATCGA
Done.