Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004487.1 Hibiscus syriacus cultivar Beakdansim tig00009886_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: 95216
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:6976 original size:20 final size:20
Alignment explanation
Indices: 6951--6991 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
6941 ATTAGTCATG
6951 AATAATTTATTTAATTTTTT
1 AATAATTTATTTAATTTTTT
*
6971 AATAATTTGTTTAATTTTTT
1 AATAATTTATTTAATTTTTT
6991 A
1 A
6992 TCCTTAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
AATAATTTATTTAATTTTTT
Found at i:7792 original size:9 final size:9
Alignment explanation
Indices: 7778--7808 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
7768 TTAATTTTAC
7778 AAATATAAA
1 AAATATAAA
7787 AAATATAAA
1 AAATATAAA
7796 AAATATAAA
1 AAATATAAA
7805 AAAT
1 AAAT
7809 CCAAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATATAAA
Found at i:7814 original size:18 final size:18
Alignment explanation
Indices: 7778--7814 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7768 TTAATTTTAC
*
7778 AAATATAAAAAATATAAA
1 AAATATAAAAAATACAAA
*
7796 AAATATAAAAAATCCAAA
1 AAATATAAAAAATACAAA
7814 A
1 A
7815 TAAAAATCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (18 bp):
AAATATAAAAAATACAAA
Found at i:7833 original size:12 final size:13
Alignment explanation
Indices: 7803--7832 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
7793 AAAAAATATA
7803 AAAAATCCAAAAT
1 AAAAATCCAAAAT
7816 AAAAATCCAAAAT
1 AAAAATCCAAAAT
7829 AAAA
1 AAAA
7833 TTAATATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.13, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAATCCAAAAT
Found at i:7855 original size:21 final size:20
Alignment explanation
Indices: 7833--7873 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
7823 CAAAATAAAA
7833 TTAATATGATTATTTATCTAATT
1 TTAATAT-ATT-TTTATCTAA-T
7856 TTAATATATTTTTATCTA
1 TTAATATATTTTTATCTA
7874 TCTTATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.44
22 3 0.17
23 7 0.39
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (20 bp):
TTAATATATTTTTATCTAAT
Found at i:11588 original size:216 final size:216
Alignment explanation
Indices: 11338--12360 Score: 1628
Period size: 216 Copynumber: 4.8 Consensus size: 216
11328 ATTTAAGAAT
*
11338 TAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
11403 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTATTACAAAAAAGTACTAAAGTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
*
11468 CCATTTAAAAATTTATGGGCCAATTAAAAAATAGAATTAAGTAAAAAGTATGGATCAATTTCAGA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAAAAAGTATGGATCAATTTCAGA
11533 TGCAAATAAAATTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
11554 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
*
11619 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAATAAAA-TACTAAAGTATA
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAA-AAAAGTACTAAATTATA
* *
11683 CCCATTTAAAAATTTATGGGCCAATTAAAAAATAGAATTAAGGAAAAAGTATGGATCAATTTCAG
130 CCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAAAAAGTATGGATCAATTTCAG
11748 ATGCAAATAAAATTTGGAGGAC
195 ATGCAAATAAAATTTGGAGGAC
* *
11770 TAAATTGAGCAAATATGAAATTATAAATAAAAATTTAAATAAATTAAACAACACA-A---A--AG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * *
11829 GGATGAAATCAAAATAATTTTAAATTGTGATGTTGAAATTAATAC-AAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* *
11893 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAAAAAGTATGTATCAATTTCATA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAAAAAGTATGGATCAATTTCAGA
11958 TGCAAATAAAATTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
* *
11979 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATTAATTAAACAACACACGTTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
12044 GGATCAAATCGAAATAAATTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATA-
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * * * * *
12108 -CATTTAAAAAGTTATGAGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCACA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAAAAAGTATGGATCAATTTCAGA
*
12172 TGCAAATAAAATTTAGAGGAC
196 TGCAAATAAAATTTGGAGGAC
* *
12193 TAAATTGAACAAATATAAAATTACAAATAAAAATTTAAATAAACTAAACAACACA-A---A--AG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * *
12252 GGATCAAATCTAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAATGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * *
12317 TCATTTAAAAAGTTATGGGCCAATTAATAAATAGAAATAAGTAA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAA
12361 TGCAAATAAA
Statistics
Matches: 756, Mismatches: 40, Indels: 28
0.92 0.05 0.03
Matches are distributed among these distances:
208 65 0.09
209 147 0.19
210 85 0.11
212 1 0.00
213 1 0.00
214 129 0.17
215 45 0.06
216 279 0.37
217 4 0.01
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (216 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAAAAAGTATGGATCAATTTCAGA
TGCAAATAAAATTTGGAGGAC
Found at i:11935 original size:425 final size:423
Alignment explanation
Indices: 11320--12360 Score: 1654
Period size: 425 Copynumber: 2.4 Consensus size: 423
11310 TTTTATGAAA
* *
11320 AAATACAAATTTA-AGAATTAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTA
1 AAATA-AAATTTAGAGGACTAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTA
* *
11384 AACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTATTACA
65 AACAACACA-A---A--AGGGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATAC-
* *
11449 AAAAAGTACTAAAGTATACCCATTTAAAAATTTATGGGCCAATTAAAAAATAGAATTAAGTAAAA
123 AAAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAAAA
11514 AGTATGGATCAATTTCAGATGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACA
188 AGTATGGATCAATTTCAGATGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACA
*
11579 AATAAAAATTTAAATAAATTAAACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAAT
253 AATAAAAATTTAAATAAATTAAACAACACACATTGATGAGGGATCAAATCGAAATAAATTTAAAT
* *
11644 TGTGAGGTTGAAATTAATACAATAAAA-TACTAAAGTATACCCATTTAAAAATTTATGGGCCAAT
318 TGTGAGGTTGAAATTAATACAA-AAAAGTACTAAAGTATA--CATTTAAAAAGTTATGAGCCAAT
* *
11708 TAAAAAATAGAATTAAGGAAAAAGTATGGATCAATTTCAGATGC
380 TAAAAAATAGAAATAAGGAAAAAGTATGGATCAATTTCACATGC
* * *
11752 AAATAAAATTTGGAGGACTAAATTGAGCAAATATGAAATTATAAATAAAAATTTAAATAAATTAA
1 AAATAAAATTTAGAGGACTAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAA
* *
11817 ACAACACAAAAGGGATGAAATCAAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAGTA
66 ACAACACAAAAGGGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAGTA
*
11882 CTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAAAAAGTATGTA
131 CTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAAAAAGTATGGA
*
11947 TCAATTTCATATGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAA
196 TCAATTTCAGATGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAA
* * *
12012 TTTAAATTAATTAAACAACACACGTTGATGAGGGATCAAATCGAAATAAATTTAAATTGTGATGT
261 TTTAAATAAATTAAACAACACACATTGATGAGGGATCAAATCGAAATAAATTTAAATTGTGAGGT
* *
12077 TGAAATTAATACAAAAAAGTACTAAATTATACATTTAAAAAGTTATGAGCCAATTTAAAAATAGA
326 TGAAATTAATACAAAAAAGTACTAAAGTATACATTTAAAAAGTTATGAGCCAATTAAAAAATAGA
* * *
12142 AATAAGTAATAAGTATGGGTCAATTTCACATGC
391 AATAAGGAAAAAGTATGGATCAATTTCACATGC
* * *
12175 AAATAAAATTTAGAGGACTAAATTGAACAAATATAAAATTACAAATAAAAATTTAAATAAACTAA
1 AAATAAAATTTAGAGGACTAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAA
* *
12240 ACAACACAAAAGGGATCAAATCTAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAATGT
66 ACAACACAAAAGGGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAA-GT
* * *
12305 ACTAAATTATACTCATTTAAAAAGTTATGGGCCAATTAATAAATAGAAATAAGTAA
130 ACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAA
12361 TGCAAATAAA
Statistics
Matches: 568, Mismatches: 38, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
423 177 0.31
424 59 0.10
425 220 0.39
426 43 0.08
428 1 0.00
431 7 0.01
432 61 0.11
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (423 bp):
AAATAAAATTTAGAGGACTAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAA
ACAACACAAAAGGGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAGTA
CTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAAAAAGTATGGA
TCAATTTCAGATGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAA
TTTAAATAAATTAAACAACACACATTGATGAGGGATCAAATCGAAATAAATTTAAATTGTGAGGT
TGAAATTAATACAAAAAAGTACTAAAGTATACATTTAAAAAGTTATGAGCCAATTAAAAAATAGA
AATAAGGAAAAAGTATGGATCAATTTCACATGC
Found at i:12545 original size:20 final size:20
Alignment explanation
Indices: 12520--12584 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
12510 AAACAACTAA
12520 TATATATATATAATATAAAC
1 TATATATATATAATATAAAC
* *
12540 TATATAGTTTAT-ATATAAAG
1 TATATA-TATATAATATAAAC
*
12560 TATATGTATTATATATATAAAC
1 TATATATA-TATA-ATATAAAC
12582 TAT
1 TAT
12585 GTAGTTTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 1 0.03
20 21 0.58
21 4 0.11
22 10 0.28
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
TATATATATATAATATAAAC
Found at i:12577 original size:22 final size:22
Alignment explanation
Indices: 12526--12600 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
12516 CTAATATATA
12526 TATATAATATAAACTATATAG-T
1 TATAT-ATATAAACTATATAGTT
*
12548 T-TATATATAAAGTATAT-GTAT
1 TATATATATAAACTATATAGT-T
*
12569 TATATATATAAACTATGTAGTT
1 TATATATATAAACTATATAGTT
12591 TATATATATA
1 TATATATATA
12601 TATTATGTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
19 1 0.02
20 12 0.26
21 5 0.11
22 26 0.57
23 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (22 bp):
TATATATATAAACTATATAGTT
Found at i:12607 original size:22 final size:22
Alignment explanation
Indices: 12526--12609 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 22
12516 CTAATATATA
*
12526 TATATAATATAAACTATATAGTT
1 TATAT-ATATAAACTATGTAGTT
12549 TATATATA-AAGTA-TATGTA--T
1 TATATATATAA--ACTATGTAGTT
12569 TATATATATAAACTATGTAGTT
1 TATATATATAAACTATGTAGTT
* *
12591 TATATATATATATTATGTA
1 TATATATATAAACTATGTA
12610 TAAACTCTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
19 1 0.02
20 15 0.29
21 4 0.08
22 26 0.50
23 6 0.12
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (22 bp):
TATATATATAAACTATGTAGTT
Found at i:12629 original size:42 final size:42
Alignment explanation
Indices: 12532--12629 Score: 101
Period size: 42 Copynumber: 2.3 Consensus size: 42
12522 TATATATATA
* * *
12532 ATATAAACTATATAGTTTATATATAAAGTATATGTATTATAT
1 ATATAAACCATGTAGTTTATATATAAAGTATATGTATTAAAT
* *
12574 ATATAAACTATGTAGTTTATATATATA-TATTATGTA-TAAACT
1 ATATAAACCATGTAGTTTATATATAAAGTA-TATGTATTAAA-T
* *
12616 CTATATACCATGTA
1 ATATAAACCATGTA
12630 TAAACTATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
41 5 0.10
42 43 0.90
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (42 bp):
ATATAAACCATGTAGTTTATATATAAAGTATATGTATTAAAT
Found at i:12777 original size:23 final size:21
Alignment explanation
Indices: 12739--12780 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 21
12729 AATTTATATT
12739 TATATTATGTATAATTATAAA
1 TATATTATGTATAATTATAAA
12760 TATATATATGTATAAATTATA
1 TATAT-TATGTAT-AATTATA
12781 TAGTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
TATATTATGTATAATTATAAA
Found at i:12814 original size:20 final size:20
Alignment explanation
Indices: 12532--12815 Score: 114
Period size: 20 Copynumber: 14.2 Consensus size: 20
12522 TATATATATA
12532 ATATAAACTATATAGTTTAT
1 ATATAAACTATATAGTTTAT
*
12552 ATATAAAGTATAT-GTATTATAT
1 ATATAAACTATATAG--TT-TAT
*
12574 ATATAAACTATGTAGTTTAT
1 ATATAAACTATATAGTTTAT
* *
12594 ATATATA-TAT-TA-TGTAT
1 ATATAAACTATATAGTTTAT
** * *
12611 A-A-ACTCTATATACCATGTATAA
1 ATATAAACTATAT---A-GTTTAT
12633 ACTATAATACTATATAGTTTAT
1 A-TATAA-ACTATATAGTTTAT
* **
12655 ATATGAACTAT-T-GAACTAT
1 ATATAAACTATATAG-TTTAT
* * *
12674 ATAGAACCTACATAGTTTAT
1 ATATAAACTATATAGTTTAT
* *
12694 ATATAAATTATATATGAATTAT
1 ATATAAACTATATA-G-TTTAT
* *
12716 ATATAAACTATACAATTTAT
1 ATATAAACTATATAGTTTAT
* * *
12736 ATTTATA-T-TAT-GTATA-
1 ATATAAACTATATAGTTTAT
12752 ATTATAAA-TATATA---TAT
1 A-TATAAACTATATAGTTTAT
* *
12769 GTATAAATTATATAGTTTATT
1 ATATAAACTATATAGTTTA-T
12790 AATATAAACTATATAGTTTAT
1 -ATATAAACTATATAGTTTAT
12811 ATATA
1 ATATA
12816 TAGTATATAT
Statistics
Matches: 193, Mismatches: 41, Indels: 60
0.66 0.14 0.20
Matches are distributed among these distances:
15 1 0.01
16 13 0.07
17 20 0.10
18 8 0.04
19 16 0.08
20 57 0.30
21 12 0.06
22 56 0.29
23 2 0.01
24 1 0.01
25 1 0.01
26 6 0.03
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (20 bp):
ATATAAACTATATAGTTTAT
Found at i:12816 original size:22 final size:22
Alignment explanation
Indices: 12764--12817 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
12754 TATAAATATA
* *
12764 TATATGTATAAATTATATAGTT
1 TATATATATAAACTATATAGTT
12786 TAT-TAATATAAACTATATAGTT
1 TATAT-ATATAAACTATATAGTT
12808 TATATATATA
1 TATATATATA
12818 GTATATATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (22 bp):
TATATATATAAACTATATAGTT
Found at i:12852 original size:21 final size:21
Alignment explanation
Indices: 12826--12873 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
12816 TAGTATATAT
*
12826 GGTTTAGGCTTTA-TGTATTAG
1 GGTTTAGGCTTTAGGGT-TTAG
*
12847 GGTTTAGGGTTTAGGGTTTAG
1 GGTTTAGGCTTTAGGGTTTAG
12868 GGTTTA
1 GGTTTA
12874 TGGTGTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.17, C:0.02, G:0.35, T:0.46
Consensus pattern (21 bp):
GGTTTAGGCTTTAGGGTTTAG
Found at i:12853 original size:7 final size:7
Alignment explanation
Indices: 12843--12873 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
12833 GCTTTATGTA
12843 TTAGGGT
1 TTAGGGT
12850 TTAGGGT
1 TTAGGGT
12857 TTAGGGT
1 TTAGGGT
12864 TTAGGGT
1 TTAGGGT
12871 TTA
1 TTA
12874 TGGTGTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (7 bp):
TTAGGGT
Found at i:12890 original size:6 final size:6
Alignment explanation
Indices: 12879--12907 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12869 GTTTATGGTG
12879 TATATT TATATT TATATT TATATT TATAT
1 TATATT TATATT TATATT TATATT TATAT
12908 AAACTACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:12952 original size:40 final size:39
Alignment explanation
Indices: 12879--12969 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 39
12869 GTTTATGGTG
12879 TATATTTATATTTATATTTATATTTATATAAACTACA-TAT
1 TATATTTATATTTATA-TTATATTTATATAAACTACAGT-T
*
12919 TATAATTTATATTTATA-TACTATTTATATAAACTATAGTT
1 TAT-ATTTATATTTATATTA-TATTTATATAAACTACAGTT
12959 TATATTTATAT
1 TATATTTATAT
12970 ACTATATATA
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
39 10 0.21
40 23 0.49
41 14 0.30
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (39 bp):
TATATTTATATTTATATTATATTTATATAAACTACAGTT
Found at i:12966 original size:33 final size:33
Alignment explanation
Indices: 12885--13019 Score: 127
Period size: 33 Copynumber: 4.1 Consensus size: 33
12875 GGTGTATATT
* * *
12885 TATA-TTTATATTTATAT-TTATATAAACTACATAT
1 TATAGTTTATATTTATATACTATATATA-TA-A-AC
* *
12919 TATAATTTATATTTATATACTATTTATATAAAC
1 TATAGTTTATATTTATATACTATATATATAAAC
*
12952 TATAGTTTATATTTATATACTATATATATGAAC
1 TATAGTTTATATTTATATACTATATATATAAAC
* *
12985 AATAGTTTACA--TATGA-ACTATATATATAAAC
1 TATAGTTTATATTTAT-ATACTATATATATAAAC
13016 TATA
1 TATA
13020 TAGTTGACAT
Statistics
Matches: 87, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
31 20 0.23
32 1 0.01
33 40 0.46
34 5 0.06
35 15 0.17
36 6 0.07
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (33 bp):
TATAGTTTATATTTATATACTATATATATAAAC
Found at i:13023 original size:33 final size:32
Alignment explanation
Indices: 12937--13045 Score: 116
Period size: 33 Copynumber: 3.4 Consensus size: 32
12927 ATATTTATAT
* *
12937 ACTATTTATATAAAC-TATAGTTTATATTTAT-A
1 ACTATATATATAAACATATAGTTTACA--TATGA
*
12969 TACTATATATATGAACA-ATAGTTTACATATGA
1 -ACTATATATATAAACATATAGTTTACATATGA
*
13001 ACTATATATATAAACTATATAGTTGACATATGA
1 ACTATATATATAAAC-ATATAGTTTACATATGA
*
13034 ATTATATATATA
1 ACTATATATATA
13046 CTAAAGTTGA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
31 17 0.26
32 2 0.03
33 47 0.71
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.42
Consensus pattern (32 bp):
ACTATATATATAAACATATAGTTTACATATGA
Found at i:13082 original size:18 final size:18
Alignment explanation
Indices: 13061--13128 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
13051 GTTGATATTT
13061 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
13079 ATATAAACTATATAGTTTAT
1 ATATGAAC--TATAGTTTAC
13099 ATACT-AACTATAGTTTAC
1 ATA-TGAACTATAGTTTAC
*
13117 ATATGACCTATA
1 ATATGAACTATA
13129 TATATACTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.02
18 25 0.60
20 15 0.36
21 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (18 bp):
ATATGAACTATAGTTTAC
Found at i:13083 original size:20 final size:19
Alignment explanation
Indices: 13060--13120 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
13050 AGTTGATATT
13060 TATATGAACTATAGTTTACA
1 TATAT-AACTATAGTTTACA
13080 TATA-AACTATATAGTTT--A
1 TATATAAC--TATAGTTTACA
13098 TATACTAACTATAGTTTACA
1 TATA-TAACTATAGTTTACA
13118 TAT
1 TAT
13121 GACCTATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
18 16 0.46
20 19 0.54
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.43
Consensus pattern (19 bp):
TATATAACTATAGTTTACA
Found at i:13128 original size:29 final size:29
Alignment explanation
Indices: 13096--13195 Score: 117
Period size: 29 Copynumber: 3.7 Consensus size: 29
13086 CTATATAGTT
13096 TATATACTA-ACTATAGTTTACATATGACC
1 TATATA-TATACTATAGTTTACATATGACC
* *
13125 TATATATATACTATAG-TT-GATAT---T
1 TATATATATACTATAGTTTACATATGACC
13149 TATATAT-TA-TATAGTTTACATATGACC
1 TATATATATACTATAGTTTACATATGACC
13176 TATATATATACTATAGTTTA
1 TATATATATACTATAGTTTA
13196 TATTTATATA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
22 5 0.08
23 4 0.07
24 11 0.19
27 11 0.19
28 6 0.10
29 22 0.37
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (29 bp):
TATATATATACTATAGTTTACATATGACC
Found at i:13130 original size:20 final size:18
Alignment explanation
Indices: 13069--13181 Score: 62
Period size: 20 Copynumber: 6.2 Consensus size: 18
13059 TTATATGAAC
13069 TATAGTTTACATATAAACTA
1 TATAGTTTACATAT--ACTA
13089 TATAGTTT--ATATACTAA
1 TATAGTTTACATATACT-A
13106 CTATAGTTTACATATGACCTA
1 -TATAGTTTACATAT-A-CTA
* *
13127 TATA-TATAC-TATAGT-
1 TATAGTTTACATATACTA
*
13142 TGATA-TTT--ATATATTA
1 T-ATAGTTTACATATACTA
13158 TATAGTTTACATATGACCTA
1 TATAGTTTACATAT-A-CTA
13178 TATA
1 TATA
13182 TATACTATAG
Statistics
Matches: 74, Mismatches: 5, Indels: 28
0.69 0.05 0.26
Matches are distributed among these distances:
15 9 0.12
16 13 0.18
17 2 0.03
18 19 0.26
19 5 0.07
20 22 0.30
21 2 0.03
22 2 0.03
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (18 bp):
TATAGTTTACATATACTA
Found at i:13134 original size:89 final size:84
Alignment explanation
Indices: 12976--13185 Score: 271
Period size: 89 Copynumber: 2.4 Consensus size: 84
12966 ATATACTATA
* *
12976 TATATGAACAATAGTTTACATATGAACTATATATATAAACTATATAGTTGACATATGAATTATAT
1 TATATGAACTATAGTTTACATATGAACTATATATATAAACTATATAGTTGACATATGAACTATAT
13041 ATATACTAAAGTTGATATT
66 ATATACTAAAGTTGATATT
* * * *
13060 TATATGAACTATAGTTTACATATAAACTATATAGTTTATATACTAACTATAGTTTACATATGACC
1 TATATGAACTATAGTTTACATATGAACTATATA---TATAAACT-A-TATAGTTGACATATGAAC
*
13125 TATATATATACTATAGTTGATATT
61 TATATATATACTAAAGTTGATATT
*
13149 TATAT-ATTA-TATAGTTTACATATGACCTATATATATA
1 TATATGA--ACTATAGTTTACATATGAACTATATATATA
13186 CTATAGTTTA
Statistics
Matches: 110, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
84 31 0.28
86 4 0.04
87 7 0.06
88 2 0.02
89 65 0.59
90 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (84 bp):
TATATGAACTATAGTTTACATATGAACTATATATATAAACTATATAGTTGACATATGAACTATAT
ATATACTAAAGTTGATATT
Found at i:13164 original size:51 final size:51
Alignment explanation
Indices: 13094--13243 Score: 205
Period size: 51 Copynumber: 2.9 Consensus size: 51
13084 AACTATATAG
13094 TTTATATACTAACTATAGTTTACATATGACCTATATATATACTATAGTTGATA
1 TTTATATACT-A-TATAGTTTACATATGACCTATATATATACTATAGTTGATA
* *
13147 TTTATATATTATATAGTTTACATATGACCTATATATATACTATAGTTTATA
1 TTTATATACTATATAGTTTACATATGACCTATATATATACTATAGTTGATA
* * *
13198 TTTATATACTATATA-TTATATATATAAACTATATATACTA-TATAGT
1 TTTATATACTATATAGTT-TACATATGACCTATATATA-TACTATAGT
13244 ATAATTTACA
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
50 2 0.02
51 75 0.84
52 3 0.03
53 9 0.10
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (51 bp):
TTTATATACTATATAGTTTACATATGACCTATATATATACTATAGTTGATA
Found at i:13183 original size:2 final size:2
Alignment explanation
Indices: 13176--13246 Score: 54
Period size: 2 Copynumber: 33.0 Consensus size: 2
13166 ACATATGACC
* *
13176 TA TA TA TA TA CTA TA GTT TA TA TT TA TA TA CTA TA TA T- TA TA
1 TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
13218 TA TA TA AA CTA TA TA TA CTA TA TA GTA TA
1 TA TA TA TA -TA TA TA TA -TA TA TA -TA TA
13247 ATTTACATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
1 1 0.02
2 45 0.80
3 10 0.18
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13190 original size:9 final size:9
Alignment explanation
Indices: 13178--13241 Score: 51
Period size: 9 Copynumber: 6.7 Consensus size: 9
13168 ATATGACCTA
13178 TATATATAC
1 TATATATAC
13187 TATAGTTTATA-
1 TATA---TATAC
*
13198 TTTATATAC
1 TATATATAC
13207 TATATATTA-
1 TATATA-TAC
13216 TATATATAAAC
1 TATATAT--AC
13227 TATATATAC
1 TATATATAC
13236 TATATA
1 TATATA
13242 GTATAATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
8 5 0.11
9 23 0.51
10 3 0.07
11 10 0.22
12 4 0.09
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (9 bp):
TATATATAC
Found at i:13205 original size:20 final size:20
Alignment explanation
Indices: 13176--13246 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
13166 ACATATGACC
13176 TATATATATACTATAGT-TTA
1 TATATATATACTATA-TATTA
*
13196 TATTTATATACTATATATTA
1 TATATATATACTATATATTA
*
13216 TATATATAAACTATATA-TA
1 TATATATATACTATATATTA
13235 CTATATAGTATA
1 -TATATA-TATA
13247 ATTTACATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
19 3 0.07
20 38 0.86
21 3 0.07
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (20 bp):
TATATATATACTATATATTA
Found at i:13263 original size:34 final size:36
Alignment explanation
Indices: 13200--13268 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 36
13190 AGTTTATATT
*
13200 TATATACTATATATTATATATATAAACTATATATAC
1 TATATACTATATATTATACATATAAACTATATATAC
* *
13236 TATATAGTATA-ATT-TACATATGAACTATATATA
1 TATATACTATATATTATACATATAAACTATATATA
13269 AAACCATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 17 0.57
35 3 0.10
36 10 0.33
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (36 bp):
TATATACTATATATTATACATATAAACTATATATAC
Found at i:13268 original size:29 final size:28
Alignment explanation
Indices: 13149--13268 Score: 65
Period size: 29 Copynumber: 4.3 Consensus size: 28
13139 AGTTGATATT
* *
13149 TATATAT-TATATAGTTTACA-TATGACC
1 TATATATATATATAATTTACATTAT-AAC
* *
13176 TATATATATACTATAGTTTATATTTATATAC
1 TATATATATA-TATAATTTACA-TTATA-AC
* * *
13207 TATATAT-TATAT-ATATAAACTAT-A-
1 TATATATATATATAATTTACATTATAAC
13231 TATACTATATAGTATAATTTACA-TATGAAC
1 TATA-TATATA-TATAATTTACATTAT-AAC
13261 TATATATA
1 TATATATA
13269 AAACCATATA
Statistics
Matches: 73, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
24 4 0.05
25 4 0.05
26 2 0.03
27 16 0.22
28 11 0.15
29 18 0.25
30 7 0.10
31 11 0.15
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.46
Consensus pattern (28 bp):
TATATATATATATAATTTACATTATAAC
Found at i:14022 original size:17 final size:19
Alignment explanation
Indices: 13994--14042 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
13984 TATTTTGAAA
13994 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
14012 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
14031 CACCGATGCACT
1 CATCGATGCACT
14043 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:22252 original size:14 final size:13
Alignment explanation
Indices: 22221--22253 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
22211 GGGAGTAATT
22221 TTTC-AAACTTGA
1 TTTCAAAACTTGA
22233 TTTCAAAACTTGA
1 TTTCAAAACTTGA
22246 TTGTCAAA
1 TT-TCAAA
22254 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 10 0.53
14 5 0.26
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (13 bp):
TTTCAAAACTTGA
Found at i:25753 original size:23 final size:21
Alignment explanation
Indices: 25721--25779 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
25711 AGAACCCCAG
*
25721 GGGGGTATCGATTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-TC-AA
* *
25744 GGGGGAATCGGTT-CCCTCAT
1 GGGGGAATCGATTCCCCTCAA
*
25764 GGGGGGATCGATTCCC
1 GGGGGAATCGATTCCC
25780 TTTGCACAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 12 0.40
21 4 0.13
22 3 0.10
23 11 0.37
ACGTcount: A:0.17, C:0.25, G:0.34, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTCAA
Found at i:31540 original size:20 final size:22
Alignment explanation
Indices: 31502--31545 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
31492 CCGTTATACA
31502 AGGGGGAATCGGTACCCCT-TG
1 AGGGGGAATCGGTACCCCTCTG
*
31523 AGGGGGAATCGGT-TCCCTCTG
1 AGGGGGAATCGGTACCCCTCTG
31544 AG
1 AG
31546 CAATCTGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.18, C:0.23, G:0.39, T:0.20
Consensus pattern (22 bp):
AGGGGGAATCGGTACCCCTCTG
Found at i:32162 original size:67 final size:64
Alignment explanation
Indices: 32024--32234 Score: 200
Period size: 65 Copynumber: 3.3 Consensus size: 64
32014 TTTTTCATAG
* * * * **
32024 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCA-CTAGCCATGCATCGATGCACTCA-GG-TTATTTTGAAACATCGAATGCA
32087 TT
63 TT
* * * *
32089 TCATGCATCGATGCACATA-TCATGCATCGATGCACTGAGAGTT-TTTAATGAAAACTTCGAATG
1 TGATGCATCGATGCAC-TAGCCATGCATCGATGCACTCAG-GTTATTT--TG-AAACATCGAATG
32152 CATT
61 CATT
* *
32156 TGATGCATCGATG--CTAGCCATGCATCGATGCACTCTGGTTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACTAGCCATGCATCGATGCACTCAGGTTATTTTGAAACATCGAATGCATT
32218 TGATGCATCGATGCACT
1 TGATGCATCGATGCACT
32235 CTCACTAAGG
Statistics
Matches: 120, Mismatches: 15, Indels: 23
0.76 0.09 0.15
Matches are distributed among these distances:
62 27 0.22
63 3 0.03
64 25 0.21
65 39 0.32
67 26 0.22
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (64 bp):
TGATGCATCGATGCACTAGCCATGCATCGATGCACTCAGGTTATTTTGAAACATCGAATGCATT
Found at i:34231 original size:51 final size:49
Alignment explanation
Indices: 34176--34306 Score: 142
Period size: 51 Copynumber: 2.6 Consensus size: 49
34166 TAATATAAAA
34176 ATAAATTTCAAAAAAGTAATTATATTAATTTGAA-TATCATAATAATTTATG
1 ATAAATTTCAAAAAAGTAATTATATTAATTT-AATTATCAT-A-AATTTATG
* * * *
34227 ATAAAATTTC-AAATAGTAATCATATTAATTTAATTATCATAAGTTTATT
1 AT-AAATTTCAAAAAAGTAATTATATTAATTTAATTATCATAAATTTATG
*
34276 ATAAATTT-AAAATAACATAATTATATTAATT
1 ATAAATTTCAAAA-AA-GTAATTATATTAATT
34307 GTAACTTTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
48 9 0.13
49 9 0.13
50 16 0.24
51 27 0.40
52 7 0.10
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.43
Consensus pattern (49 bp):
ATAAATTTCAAAAAAGTAATTATATTAATTTAATTATCATAAATTTATG
Found at i:34402 original size:16 final size:16
Alignment explanation
Indices: 34383--34421 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
34373 TGAGTAAATT
*
34383 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTTCAAA
*
34399 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
34415 ACAGGTC
1 ACAGGTC
34422 GGGTAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:37222 original size:20 final size:19
Alignment explanation
Indices: 37194--37234 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
37184 GCTATTTAAT
*
37194 TTATTAAATAATATTTAAAA
1 TTATAAAAT-ATATTTAAAA
*
37214 TTATAAAATATATTTATAA
1 TTATAAAATATATTTAAAA
37233 TT
1 TT
37235 TTTTAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATAAAATATATTTAAAA
Found at i:37242 original size:20 final size:20
Alignment explanation
Indices: 37190--37243 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
37180 TAGTGCTATT
37190 TAATTTATTAAATAATATTTA
1 TAATTTATTAAAT-ATATTTA
* *
37211 -AAATTATAAAATATATTTA
1 TAATTTATTAAATATATTTA
*
37230 TAATTTTTTAAATA
1 TAATTTATTAAATA
37244 AAAGATTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATTTATTAAATATATTTA
Found at i:38569 original size:41 final size:40
Alignment explanation
Indices: 38512--38662 Score: 200
Period size: 39 Copynumber: 3.8 Consensus size: 40
38502 ATACACATGA
*
38512 AAGACACATTGCACTCCATGCGTCTCTCTCCCTTTCCCCCG
1 AAGACGCATTGCACTCCATGCGTCTCTC-CCCTTTCCCCCG
* * *
38553 AAGACGTATTGCACTCCATGCG--TCTCCACTTTCCCTCTG
1 AAGACGCATTGCACTCCATGCGTCTCTCCCCTTTCCC-CCG
*
38592 AAGACGCATTGCACTCCATGCGTCTC-CCCCTTTCCCCCT
1 AAGACGCATTGCACTCCATGCGTCTCTCCCCTTTCCCCCG
* *
38631 AAGACGCATTGCACTCCATGCATCGCTCCCCT
1 AAGACGCATTGCACTCCATGCGTCTCTCCCCT
38663 GCTTGATACC
Statistics
Matches: 96, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
38 8 0.08
39 52 0.54
40 14 0.15
41 22 0.23
ACGTcount: A:0.18, C:0.42, G:0.14, T:0.26
Consensus pattern (40 bp):
AAGACGCATTGCACTCCATGCGTCTCTCCCCTTTCCCCCG
Found at i:38844 original size:3 final size:3
Alignment explanation
Indices: 38836--38961 Score: 77
Period size: 3 Copynumber: 41.7 Consensus size: 3
38826 GAGAATGAAT
38836 GAA GAA GAA GAAA GAA -AA GAA GAA GGAA GCAA TGAA GAA G-A GAA -AA
1 GAA GAA GAA G-AA GAA GAA GAA GAA -GAA G-AA -GAA GAA GAA GAA GAA
* * * *
38882 GAG GAAA GAA TAA GAA -AA -AA GAG GAA GAGA GAA GAA GAA GAG GAAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA G-AA
* *
38928 GAA GAA GAA -AA -AA GAG GGA GAAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA GA
38962 GAAAATAAGA
Statistics
Matches: 98, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
2 14 0.14
3 64 0.65
4 19 0.19
5 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.33, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:38902 original size:13 final size:13
Alignment explanation
Indices: 38836--38972 Score: 80
Period size: 13 Copynumber: 10.5 Consensus size: 13
38826 GAGAATGAAT
*
38836 GAAGAAGAAGAAA
1 GAAGAAGAAAAAA
* *
38849 GAA-AAGAAGAAG
1 GAAGAAGAAAAAA
*
38861 GAAGCAATGAAGAAGA
1 GAAG-AA-GAA-AAAA
**
38877 GAA-AAGAGGAAA
1 GAAGAAGAAAAAA
*
38889 GAATAAGAAAAAA
1 GAAGAAGAAAAAA
* * *
38902 GAGGAAGAGAGAA
1 GAAGAAGAAAAAA
**
38915 GAAGAAGAGGAAA
1 GAAGAAGAAAAAA
38928 GAAGAAGAAAAAA
1 GAAGAAGAAAAAA
* * *
38941 GAGGGAGAAAGAA
1 GAAGAAGAAAAAA
*
38954 GAAGAAGAGAAAA
1 GAAGAAGAAAAAA
*
38967 TAAGAA
1 GAAGAA
38973 AGTTAGAGTC
Statistics
Matches: 93, Mismatches: 26, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
12 16 0.17
13 66 0.71
14 4 0.04
15 3 0.03
16 4 0.04
ACGTcount: A:0.65, C:0.01, G:0.32, T:0.02
Consensus pattern (13 bp):
GAAGAAGAAAAAA
Found at i:38914 original size:23 final size:22
Alignment explanation
Indices: 38836--38959 Score: 109
Period size: 20 Copynumber: 5.7 Consensus size: 22
38826 GAGAATGAAT
38836 GAAGAAGAAGAAAGAAAAGAAGAAG
1 GAAGAAGAAG-AAGAAAA-AAG-AG
*
38861 GAAGCAATGAAGAAGAGAAAAGAG
1 GAAG-AA-GAAGAAGAAAAAAGAG
*
38885 G-A-AAGAATAAGAAAAAAGAG
1 GAAGAAGAAGAAGAAAAAAGAG
*
38905 GAAG-AG-AGAAG-AAGAAGAG
1 GAAGAAGAAGAAGAAAAAAGAG
38924 G-A-AAGAAGAAGAAAAAAGAG
1 GAAGAAGAAGAAGAAAAAAGAG
*
38944 GGAGAAAGAAGAAGAA
1 GAAG-AAGAAGAAGAA
38960 GAGAAAATAA
Statistics
Matches: 83, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
18 3 0.04
19 13 0.16
20 27 0.33
21 6 0.07
23 12 0.14
24 3 0.04
25 7 0.08
26 8 0.10
27 4 0.05
ACGTcount: A:0.65, C:0.01, G:0.33, T:0.02
Consensus pattern (22 bp):
GAAGAAGAAGAAGAAAAAAGAG
Found at i:40622 original size:56 final size:56
Alignment explanation
Indices: 40531--40642 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
40521 CGTATGGTCC
*
40531 AAGTAGATGGTACGTGGTTGTATGGTCAATATAAACATATATTGTTGATGGCATTT
1 AAGTAGATGGTACATGGTTGTATGGTCAATATAAACATATATTGTTGATGGCATTT
* * *
40587 AAGTTGATGGTACATGGTTGTATGGTCAATATAAACATGTATTGTTGATGGTATTT
1 AAGTAGATGGTACATGGTTGTATGGTCAATATAAACATATATTGTTGATGGCATTT
40643 GCGCAAGATG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.29, C:0.06, G:0.25, T:0.39
Consensus pattern (56 bp):
AAGTAGATGGTACATGGTTGTATGGTCAATATAAACATATATTGTTGATGGCATTT
Found at i:41500 original size:21 final size:21
Alignment explanation
Indices: 41474--41513 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
41464 TAAAAAACCC
41474 AACCCGATCGGG-TCGGGTCAG
1 AACCCG-TCGGGTTCGGGTCAG
41495 AACCCGTCGGGTTCGGGTC
1 AACCCGTCGGGTTCGGGTC
41514 CCATGCCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.15, C:0.30, G:0.38, T:0.17
Consensus pattern (21 bp):
AACCCGTCGGGTTCGGGTCAG
Found at i:42963 original size:40 final size:40
Alignment explanation
Indices: 42911--42996 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
42901 CGTTTTTTGA
* *
42911 ACAAATGCCGCAAAAAACCTAACTTTAGAGGCGTTTGTAT
1 ACAAACGCCGCAAAAAACCTAACTTTAGAGGCATTTGTAT
* * * *
42951 ACAAACGCCGCAAAAGATCTTACTTTAGTGGCATTTGTAT
1 ACAAACGCCGCAAAAAACCTAACTTTAGAGGCATTTGTAT
42991 ACAAAC
1 ACAAAC
42997 ACTGCTAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (40 bp):
ACAAACGCCGCAAAAAACCTAACTTTAGAGGCATTTGTAT
Found at i:43007 original size:40 final size:40
Alignment explanation
Indices: 42932--43355 Score: 343
Period size: 41 Copynumber: 10.4 Consensus size: 40
42922 AAAAAACCTA
* * * *
42932 ACTTTAGAGGCGTTTGTATACAAACGCCGCAAAAGATCTT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGATCAT
* * * * *
42972 ACTTTAGTGGCATTTGTATACAAACACTGCTAAAGATTAGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGATCA-T
* * * * *
43013 ATTTTAGTGGCGTTTTTACACAAACGCCGGTATAGAATCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAG-ATCAT
* *
43054 TCTTTAGGGGCGTTTTTATACAAACGCCGCTAAAGACTCAT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGA-TCAT
** *
43095 ACTTTAGTGGCGTTTTTATA-AAAGCGTTGCTATAA-CTCAT
1 ACTTTAGTGGCGTTTTTATACAAA-CGCCGCTA-AAGATCAT
* * * * *
43135 ACTTTATTGGCATTTTTATAAAAACGCTGCTATAA-CTCAT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTA-AAGATCAT
* * *
43175 ACTTTAGTGGCGTTTTTGTTTACAAACGCCGCTATAGACTCGT
1 ACTTTAGTGGCG-TTTT-TATACAAACGCCGCTAAAGA-TCAT
* * * * **
43218 ACTTTAGTGGCGTTTTTTTACAAACGTCACTATAGACTTGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGA-TCAT
* * * *
43259 ACTTTAGTGGCGTTTTTATAAAAATGCCGCAAAAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGA-TCAT
** *
43300 ACGCTAGTGGCGTTTTTATACAAACGCCG-TAAAAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCT-AAAGA-TCAT
43341 ACTTTAGTGGCGTTT
1 ACTTTAGTGGCGTTT
43356 GTATCGCAAA
Statistics
Matches: 315, Mismatches: 58, Indels: 21
0.80 0.15 0.05
Matches are distributed among these distances:
40 83 0.26
41 196 0.62
42 21 0.07
43 15 0.05
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (40 bp):
ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGATCAT
Found at i:43088 original size:82 final size:82
Alignment explanation
Indices: 42932--43355 Score: 387
Period size: 82 Copynumber: 5.2 Consensus size: 82
42922 AAAAAACCTA
* * * * * * *
42932 ACTTTAGAGGCGTTTGTATACAAACGCCGCAAAAGA-TCTTACTTTAGTGGCATTTGTATACAAA
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAA
* *
42996 CACTGCTAAAGATTAGT
66 CGCCGCTAAAGATTAGT
* * * * * *
43013 ATTTTAGTGGCGTTTTTACACAAACGCCGGTATAGAATCGTTCTTTAGGGGCGTTTTTATACAAA
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAA
*
43078 CGCCGCTAAAGACTCA-T
66 CGCCGCTAAAGA-TTAGT
** * * * *
43095 ACTTTAGTGGCGTTTTTATA-AAAGCGTTGCTATA-ACTCATACTTTATTGGCATTTTTATAAAA
1 ACTTTAGTGGCGTTTTTATACAAA-CGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAA
* * *
43158 ACGCTGCTATAA-CTCA-T
65 ACGCCGCTA-AAGATTAGT
* *
43175 ACTTTAGTGGCGTTTTTGTTTACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTTTACA
1 ACTTTAGTGGCG-TTTT-TATACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACA
* * *
43240 AACGTCACTATAGACTT-GT
64 AACGCCGCTAAAGA-TTAGT
* * * * **
43259 ACTTTAGTGGCGTTTTTATAAAAATGCCGCAAAAGACTCGTACGCTAGTGGCGTTTTTATACAAA
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAA
* *
43324 CGCCG-TAAAAGACTCGT
66 CGCCGCT-AAAGATTAGT
43341 ACTTTAGTGGCGTTT
1 ACTTTAGTGGCGTTT
43356 GTATCGCAAA
Statistics
Matches: 275, Mismatches: 55, Indels: 25
0.77 0.15 0.07
Matches are distributed among these distances:
80 16 0.06
81 68 0.25
82 138 0.50
83 39 0.14
84 14 0.05
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (82 bp):
ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAA
CGCCGCTAAAGATTAGT
Found at i:43205 original size:123 final size:123
Alignment explanation
Indices: 42932--43355 Score: 403
Period size: 123 Copynumber: 3.5 Consensus size: 123
42922 AAAAAACCTA
* * * * * *
42932 ACTTTAGAGGCGTTTGTATACAAACGCCGCAAAAGA-TCTTACTTTAGTGGCATTTGTATACAAA
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAA
* * * * * * * * ** * * *
42996 C-ACTGCTAAAGA-TTAGTATTTTAGTGGCGTTTTTACACAAACGCCGGTATAGAATCGT
66 CGTC-ACTATAGACTCA-TACTTTAGTGGCATTTTTATAAAAACGCCGCAAAAGACTCAT
* * *
43054 TCTTTAGGGGCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATA-AAA
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAA
** * * * *
43118 GCGTTGCTATA-ACTCATACTTTATTGGCATTTTTATAAAAACGCTGCTATA-ACTCAT
66 -CGTCACTATAGACTCATACTTTAGTGGCATTTTTATAAAAACGCCGCAAAAGACTCAT
* * *
43175 ACTTTAGTGGCGTTTTTGTTTACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTTTACA
1 ACTTTAGTGGCG-TTTT-TATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACA
** * * *
43240 AACGTCACTATAGACTTGTACTTTAGTGGCGTTTTTATAAAAATGCCGCAAAAGACTCGT
64 AACGTCACTATAGACTCATACTTTAGTGGCATTTTTATAAAAACGCCGCAAAAGACTCAT
**
43300 ACGCTAGTGGCGTTTTTATACAAACGCCG-TAAAAGACTCGTACTTTAGTGGCGTTT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCT-AAAGACTCGTACTTTAGTGGCGTTT
43356 GTATCGCAAA
Statistics
Matches: 251, Mismatches: 41, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
121 14 0.06
122 69 0.27
123 114 0.45
124 39 0.16
125 15 0.06
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (123 bp):
ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAA
CGTCACTATAGACTCATACTTTAGTGGCATTTTTATAAAAACGCCGCAAAAGACTCAT
Found at i:46030 original size:43 final size:43
Alignment explanation
Indices: 45965--46319 Score: 392
Period size: 43 Copynumber: 8.3 Consensus size: 43
45955 ATGGTAATTA
* * *
45965 GCGGCGTTTGTATCCAAAAACGCCGCTATATATATGACCTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGATCTGACCTTTT
*
46008 GCGACGTTTGTGTCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * *
46051 GCGGCGTTTGTGTCCAAAAAAGCCGCTATAGGTCTGACATTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * *
46094 GCGGCATTTGTGTCAAAAAACGCCACTATAGGTCTGACCTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * * * *
46137 ACGGCGTTTGT-TCTAAAAATGCCAG-TATAGGTCTTATCTTTT
1 GCGGCGTTTGTGTCCAAAAACGCC-GCTATAGATCTGACCTTTT
* * *
46179 GCGACGTTTGTATCCAAAAACGCCGCTATAGATCTGACATTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * * * * *
46222 GCGGCGTTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGATC-TGACCTTTT
* * *
46266 GCGTCGTTTAT-TCCAAAAACGCCGCTATAGATATCGACCTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGATCT-GACCTTTT
46309 GCGGCGTTTGT
1 GCGGCGTTTGT
46320 TTAAAAACCG
Statistics
Matches: 261, Mismatches: 46, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
42 36 0.14
43 209 0.80
44 16 0.06
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (43 bp):
GCGGCGTTTGTGTCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:46204 original size:128 final size:129
Alignment explanation
Indices: 45965--46319 Score: 374
Period size: 128 Copynumber: 2.8 Consensus size: 129
45955 ATGGTAATTA
* * * * *
45965 GCGGCGTTTGTATCCAAAAACGCCGCTATATATATGACCTTTTGCGACGTTTGTGTCCAAAAACG
1 GCGGCATTTGTATCAAAAAACGCCACTATAGATATGACCTTTTACGACGTTTGTGTCCAAAAACG
* * *
46030 CCGCTATAGATCTGACCTTTTGCGGCGTTTGTGTCCAAAAAAGCCGCTATAGGTCTGACATTTT
66 CCGCTATAGATCTGACCTTTTGCGACGTTTGTATCCAAAAAAGCCGCTATAGATCTGACATTTT
* * * * * *
46094 GCGGCATTTGTGTCAAAAAACGCCACTATAGGTCTGACCTTTTACGGCGTTTGT-TCTAAAAATG
1 GCGGCATTTGTATCAAAAAACGCCACTATAGATATGACCTTTTACGACGTTTGTGTCCAAAAACG
* * * *
46158 CCAG-TATAGGTCTTATCTTTTGCGACGTTTGTATCCAAAAACGCCGCTATAGATCTGACATTTT
66 CC-GCTATAGATCTGACCTTTTGCGACGTTTGTATCCAAAAAAGCCGCTATAGATCTGACATTTT
* * * * * * * * * * * *
46222 GCGGCGTTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTTGCGTCGTTTAT-TCCAAAAAC
1 GCGGCATTTGTATCAAAAAACGCCACTATAGAT-ATGACCTTTTACGACGTTTGTGTCCAAAAAC
* *
46286 GCCGCTATAGATATCGACCTTTTGCGGCGTTTGT
65 GCCGCTATAGATCT-GACCTTTTGCGACGTTTGT
46320 TTAAAAACCG
Statistics
Matches: 183, Mismatches: 39, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
128 89 0.49
129 78 0.43
130 16 0.09
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (129 bp):
GCGGCATTTGTATCAAAAAACGCCACTATAGATATGACCTTTTACGACGTTTGTGTCCAAAAACG
CCGCTATAGATCTGACCTTTTGCGACGTTTGTATCCAAAAAAGCCGCTATAGATCTGACATTTT
Found at i:46286 original size:171 final size:171
Alignment explanation
Indices: 46003--46326 Score: 445
Period size: 171 Copynumber: 1.9 Consensus size: 171
45993 TATATATGAC
* *
46003 CTTTTGCGACGTTTGTGTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTGTCCAA
1 CTTTTGCGACGTTTGTATCCAAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTGTGTCCAA
* * * * *
46068 AAAAGCCGCTATAGGTCTGACATTTTGCGGCATTTGTGTCAAAAAACGCCACTATAGGTCT-GAC
66 AAAAGCCGCTATAGATCTAACATTTTGCGGCATTTATGTCAAAAAACGCCACTATAGATATCGAC
46132 CTTTTACGGCGTTTGTTCTAAAAATGCCAGTATAGGTCTTAT
131 CTTTTACGGCGTTTGTT-TAAAAATGCCAGTATAGGTCTTAT
* * * *
46174 CTTTTGCGACGTTTGTATCCAAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTTTTTCTAG
1 CTTTTGCGACGTTTGTATCCAAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTGTGTCCAA
* * * * * * *
46239 AAACGCCGCTATATATCATAACTTTTTGCGTCGTTTAT-TCCAAAAACGCCGCTATAGATATCGA
66 AAAAGCCGCTATAGATC-TAACATTTTGCGGCATTTATGTCAAAAAACGCCACTATAGATATCGA
*
46303 CCTTTTGCGGCGTTTGTTTAAAAA
130 CCTTTTACGGCGTTTGTTTAAAAA
46327 CCGTCGTAAT
Statistics
Matches: 132, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
171 98 0.74
172 34 0.26
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (171 bp):
CTTTTGCGACGTTTGTATCCAAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTGTGTCCAA
AAAAGCCGCTATAGATCTAACATTTTGCGGCATTTATGTCAAAAAACGCCACTATAGATATCGAC
CTTTTACGGCGTTTGTTTAAAAATGCCAGTATAGGTCTTAT
Found at i:46354 original size:86 final size:85
Alignment explanation
Indices: 45965--46360 Score: 381
Period size: 86 Copynumber: 4.6 Consensus size: 85
45955 ATGGTAATTA
* *
45965 GCGGCGTTTGTATCCAAAAACGCCGCTATATATA-TGACCTTTTGCGACGTTTGTGTCCAAAAAC
1 GCGGCGTTTGT-TCTAAAAACGCCG-TATAGATATTGACCTTTTGCGACGTTTGTGTCCAAAAAC
46029 GCCGCTATAGATCTGACCTTTT
64 GCCGCTATAGATCTGACCTTTT
* * * * * * * *
46051 GCGGCGTTTGTGTCCAAAAAAGCCGCTATAGGT-CTGACATTTTGCGGCATTTGTGTCAAAAAAC
1 GCGGCGTTTGT-TCTAAAAACGCCG-TATAGATATTGACCTTTTGCGACGTTTGTGTCCAAAAAC
* *
46115 GCCACTATAGGTCTGACCTTTT
64 GCCGCTATAGATCTGACCTTTT
* * * * * *
46137 ACGGCGTTTGTTCTAAAAATGCCAGTATAGGTCTT-ATCTTTTGCGACGTTTGTATCCAAAAACG
1 GCGGCGTTTGTTCTAAAAACGCC-GTATAGATATTGACCTTTTGCGACGTTTGTGTCCAAAAACG
*
46201 CCGCTATAGATCTGACATTTT
65 CCGCTATAGATCTGACCTTTT
* * * * * * *
46222 GCGGCGTTTTTTTCTAGAAACGCCGCTATATATCA-TAACTTTTTGCGTCGTTTAT-TCCAAAAA
1 GCGGCG-TTTGTTCTAAAAACGCCG-TATAGAT-ATTGACCTTTTGCGACGTTTGTGTCCAAAAA
*
46285 CGCCGCTATAGATATCGACCTTTT
63 CGCCGCTATAGATCT-GACCTTTT
* * *
46309 GCGGCGTTTGTT-TAAAAACCGTCGTAATAGATATTGACCTATTGCGGCGTTT
1 GCGGCGTTTGTTCTAAAAA-CGCCGT-ATAGATATTGACCTTTTGCGACGTTT
46361 TTTGTTCTCA
Statistics
Matches: 255, Mismatches: 44, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
85 71 0.28
86 157 0.62
87 27 0.11
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (85 bp):
GCGGCGTTTGTTCTAAAAACGCCGTATAGATATTGACCTTTTGCGACGTTTGTGTCCAAAAACGC
CGCTATAGATCTGACCTTTT
Found at i:47536 original size:8 final size:8
Alignment explanation
Indices: 47523--47548 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
47513 ATTAGACGCG
47523 AAATTATA
1 AAATTATA
47531 AAATTATA
1 AAATTATA
47539 AAATTATA
1 AAATTATA
47547 AA
1 AA
47549 TAAATCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAATTATA
Found at i:48949 original size:18 final size:18
Alignment explanation
Indices: 48918--49008 Score: 77
Period size: 18 Copynumber: 5.2 Consensus size: 18
48908 TTATTATTTT
48918 TTCTT-TTTCCTTTCTTCA
1 TTCTTCTTT-CTTTCTTCA
48936 TTCTTC-TT-TTT-TTC-
1 TTCTTCTTTCTTTCTTCA
* *
48950 TTCTTCTTCCTTTGTTCA
1 TTCTTCTTTCTTTCTTCA
*
48968 TTTTTCTTTTCTTTCTTC-
1 TTCTTC-TTTCTTTCTTCA
*
48986 TTCTCCCTTTCTTTCTTCA
1 TTCT-TCTTTCTTTCTTCA
49005 TTCT
1 TTCT
49009 CATATTTTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
14 6 0.10
15 4 0.07
16 6 0.10
17 3 0.05
18 26 0.44
19 14 0.24
ACGTcount: A:0.03, C:0.27, G:0.01, T:0.68
Consensus pattern (18 bp):
TTCTTCTTTCTTTCTTCA
Found at i:48960 original size:32 final size:32
Alignment explanation
Indices: 48914--48998 Score: 118
Period size: 32 Copynumber: 2.7 Consensus size: 32
48904 TACTTTATTA
*
48914 TTTT-TTCTTTTTCCTTTCTTCATTCTTCTTT
1 TTTTCTTCTTCTTCCTTTCTTCATTCTTCTTT
* *
48945 TTTTCTTCTTCTTCCTTTGTTCATTTTTCTTT
1 TTTTCTTCTTCTTCCTTTCTTCATTCTTCTTT
*
48977 TCTTTCTTCTTCTCCCTTTCTT
1 T-TTTCTTCTTCTTCCTTTCTT
48999 TCTTCATTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 4 0.09
32 25 0.53
33 18 0.38
ACGTcount: A:0.02, C:0.26, G:0.01, T:0.71
Consensus pattern (32 bp):
TTTTCTTCTTCTTCCTTTCTTCATTCTTCTTT
Found at i:59063 original size:3 final size:3
Alignment explanation
Indices: 59055--59101 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
59045 TATTACACTT
* *
59055 GAA GAA GAA GAA GAA GAA AAA G-A GAA GAA GAA GAA GAA GAA AAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
59102 ATGAGGGTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:59082 original size:17 final size:17
Alignment explanation
Indices: 59060--59094 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
59050 CACTTGAAGA
59060 AGAAGAAGAAGAAAAAG
1 AGAAGAAGAAGAAAAAG
*
59077 AGAAGAAGAAGAAGAAG
1 AGAAGAAGAAGAAAAAG
59094 A
1 A
59095 AAAAGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AGAAGAAGAAGAAAAAG
Found at i:59085 original size:23 final size:23
Alignment explanation
Indices: 59055--59100 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
59045 TATTACACTT
59055 GAAGAAGAAGAAGAAGAAAAAGA
1 GAAGAAGAAGAAGAAGAAAAAGA
59078 GAAGAAGAAGAAGAAGAAAAAGA
1 GAAGAAGAAGAAGAAGAAAAAGA
59101 AATGAGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (23 bp):
GAAGAAGAAGAAGAAGAAAAAGA
Found at i:60569 original size:126 final size:127
Alignment explanation
Indices: 60117--60616 Score: 718
Period size: 127 Copynumber: 4.0 Consensus size: 127
60107 TATAAGCATT
* * * **
60117 GATAACTAGCGGTCCTCATCACATAGAAAATGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
1 GATAACCAGCCGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
*
60182 CAAATGAGCAGTGTTATCACATGACCAGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCA
66 CAAATGAGCAGTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCA
* *
60244 GATAACCGGCCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
1 GATAACCAGCCGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
* *
60309 CAAATGAGCAGTGTCATCACATGACCAGATATCCTCATTATGTAAGGAGTTGTGTCAACTCA
66 CAAATGAGCAGTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCA
* * *
60371 GATAACCAACAGTCCTCATCACATATGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
1 GATAACCAGCCGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
* * * * *
60436 CATATGAGCAGTGTCATCACCT-TCCTAGATCTCTTCATTATGT-ATGAGCTGTGTCAACTCA
66 CAAATGAGCAGTGTCATCACATGACC-AGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCA
* *
60497 GATAACCAGCCGTCCTCATCATATAGGAACTGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
1 GATAACCAGCCGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
* * * * * * * *
60562 CAGATGAGCAGTGTCATCACTTTACTAGATCTCTTCATCACGT-ACGAGCTGTGTC
66 CAAATGAGCAGTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGCTGTGTC
60617 GTCTCCCAAA
Statistics
Matches: 337, Mismatches: 34, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
126 124 0.37
127 213 0.63
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (127 bp):
GATAACCAGCCGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
CAAATGAGCAGTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCA
Found at i:62278 original size:19 final size:19
Alignment explanation
Indices: 62239--62279 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
62229 GGATTATTTT
*
62239 AATTAATTAATTTGAAGTA
1 AATTAATTAATTTCAAGTA
62258 AATTAATTAAATTTCAA-TA
1 AATTAATT-AATTTCAAGTA
62277 AAT
1 AAT
62280 AGATCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (19 bp):
AATTAATTAATTTCAAGTA
Found at i:65440 original size:5 final size:5
Alignment explanation
Indices: 65430--65456 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
65420 AAAAAATAAA
65430 TCGGG TCGGG TCGGG TCGGG TCGGG TC
1 TCGGG TCGGG TCGGG TCGGG TCGGG TC
65457 AAATTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.56, T:0.22
Consensus pattern (5 bp):
TCGGG
Found at i:66789 original size:31 final size:31
Alignment explanation
Indices: 66751--66873 Score: 194
Period size: 31 Copynumber: 4.0 Consensus size: 31
66741 CCCGAAGGAC
* *
66751 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
66782 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
66813 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
66844 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
66874 CCCTCGACCC
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:70716 original size:31 final size:31
Alignment explanation
Indices: 70678--70800 Score: 194
Period size: 31 Copynumber: 4.0 Consensus size: 31
70668 CCCGAAGGAC
* *
70678 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
70709 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
70740 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
70771 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
70801 CCCTCGACCC
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:80377 original size:55 final size:55
Alignment explanation
Indices: 80293--80402 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
80283 ATATTTTCTT
80293 TAATAGATTTGCGTGTGCAACGGTTGCCACTTGCTAGTTGGTGAGGTTCACCGGC
1 TAATAGATTTGCGTGTGCAACGGTTGCCACTTGCTAGTTGGTGAGGTTCACCGGC
80348 TAATAGATTTGCGTGTGCAACGGTTGCCACTTGCTAGTTGGTGAGGTTCACCGGC
1 TAATAGATTTGCGTGTGCAACGGTTGCCACTTGCTAGTTGGTGAGGTTCACCGGC
80403 GCCAAAGCGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (55 bp):
TAATAGATTTGCGTGTGCAACGGTTGCCACTTGCTAGTTGGTGAGGTTCACCGGC
Found at i:82588 original size:2 final size:2
Alignment explanation
Indices: 82583--82625 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
82573 ATTAATCCTT
82583 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
82625 T
1 T
82626 GTCTTTTCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:82711 original size:20 final size:19
Alignment explanation
Indices: 82683--82722 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
82673 TGTTCACCCA
*
82683 TTTATTATTTAATTTATTAT
1 TTTAGTATTTAA-TTATTAT
82703 TTTAGTATTTAATTATTAT
1 TTTAGTATTTAATTATTAT
82722 T
1 T
82723 GAACAATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTAGTATTTAATTATTAT
Found at i:85828 original size:23 final size:23
Alignment explanation
Indices: 85781--85830 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
85771 AATAACATAT
* **
85781 TAGGTAGCACTTATATAATGTAA
1 TAGGTAACACTTATATAATAAAA
*
85804 TAGGTAACGCTTATATAATAAAA
1 TAGGTAACACTTATATAATAAAA
85827 TAGG
1 TAGG
85831 CATTTAATCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (23 bp):
TAGGTAACACTTATATAATAAAA
Found at i:85890 original size:87 final size:87
Alignment explanation
Indices: 85744--85906 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
85734 TATGTTATAT
* * *
85744 CATTTAACCGGAAATATTATTAAGTACAATAACATATTAGGTAGCACTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGAT
85809 AACGCTTATATAATAAAATAGG
66 AACGCTTATATAATAAAATAGG
* *
85831 CATTTAATCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGAT
*
85896 AGCGCTTATAT
66 AACGCTTATAT
85907 TGACCTATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGAT
AACGCTTATATAATAAAATAGG
Found at i:86335 original size:200 final size:197
Alignment explanation
Indices: 85907--86431 Score: 621
Period size: 200 Copynumber: 2.6 Consensus size: 197
85897 GCGCTTATAT
* * *
85907 TGACCTATTTTCTAAGT-AAACTGGTATATTTATACCGGTAACATTGCAAATTTACCTATTACAT
1 TGACCTATTTTCTAA-TAAAACCGGTATATTTATACAGGT-ACATTGTAAATTTACCTATTACAT
* * *
85971 TATAATTATCGGTTTCGATGTTTTTTGGATTGATACAATTT--TAAATGTATCGACACTTTATGC
64 TATAATTATCGGTTTCGATG-TTTTGGGATCGATACATTTTAATAAATGTATCGACACTTTATGC
*
86034 ATGCACCTCGTTGGGCATTCACTATGGAAAAAGGTATCAACACAAACTTAAAAAGTGTCGATACA
128 ATGCACCTCGTTGGGCATTCACTATGGAAAAAAGTATCAACACAAACTTAAAAAGTGTCGATACA
*
86099 TTATT
193 TTATC
* * * * * **
86104 TAGACTTATTTTCTCATAAAACCGGTATATTTCTATCGGGTACATTGTAATTTTACCTATCGCAT
1 T-GACCTATTTTCTAATAAAACCGGTATATTTATA-CAGGTACATTGTAAATTTACCTATTACAT
*
86169 TGTAATTATCGGTTTCGATGTTTGTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGC
64 TATAATTATCGGTTTCGATGTTT-TGGGATCGATACATTTTAATAAATGTATCGACACTTTATGC
* * * * * * **
86233 GTGCACCAT-GTTTGGCATTCATTATGGACAAAAAGTATCGATACAAATTTAAATGGTGTCGATA
128 ATGCACC-TCGTTGGGCATTCACTATGGA-AAAAAGTATCAACACAAACTTAAAAAGTGTCGATA
*
86297 CTTTATGC
191 CATTAT-C
* * * * *
86305 TGACCTATTTTCTTATAAAACCGATATATTTATACCAGTTACATTGTAAATTTATCTATTACGTT
1 TGACCTATTTTCTAATAAAACCGGTATATTTATA-CAGGTACATTGTAAATTTACCTATTACATT
*
86370 ATAATTATCGGTTTCGATGTTATTGGGATCGATACTTTTTAATAAATGTATC-AGCACTTTAT
65 ATAATTATCGGTTTCGATGTT-TTGGGATCGATACATTTTAATAAATGTATCGA-CACTTTAT
86432 ATTATGGACA
Statistics
Matches: 279, Mismatches: 37, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
197 8 0.03
198 76 0.27
199 49 0.18
200 120 0.43
201 26 0.09
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (197 bp):
TGACCTATTTTCTAATAAAACCGGTATATTTATACAGGTACATTGTAAATTTACCTATTACATTA
TAATTATCGGTTTCGATGTTTTGGGATCGATACATTTTAATAAATGTATCGACACTTTATGCATG
CACCTCGTTGGGCATTCACTATGGAAAAAAGTATCAACACAAACTTAAAAAGTGTCGATACATTA
TC
Found at i:86566 original size:178 final size:179
Alignment explanation
Indices: 86253--86586 Score: 445
Period size: 178 Copynumber: 1.9 Consensus size: 179
86243 TTTGGCATTC
* * * ** * *
86253 ATTATGGACAAAAAGTATCGATACAAATTTAAATGGTGTCGATACTTTATGCTGACCTATTTTCT
1 ATTATGGACAAAAAGTATAGACACAAATTCAAAAAGTGTCGATACATTATGCTGACATATTTTCT
* * * *
86318 TATAAAACCGATATATTTATACCAGTTACATTGTAAATTTATCTATTACGTTATAATTATCGGTT
66 AATAAAACCGATATATTTATACCAGTTACATTGTAAATTTACCTATTACATTAAAATTATCGGTT
86383 TCGATGTTATTGGGATCGATACTTTTTAATAAATGTATCAGCACTTTAT
131 TCGATGTTATTGGGATCGATACTTTTTAATAAATGTATCAGCACTTTAT
* * * *
86432 ATTATGGACAATAAGTATAGACACAAATTCAAAAATTGTCGATACATTATGTTGACATGTTTTCT
1 ATTATGGACAAAAAGTATAGACACAAATTCAAAAAGTGTCGATACATTATGCTGACATATTTTCT
* ** * * * *
86497 AAT-TAACCGATATATTTATACTGGTTATATTGTTAATTTACCTATTATATTAAAATTATTGGTT
66 AATAAAACCGATATATTTATACCAGTTACATTGTAAATTTACCTATTACATTAAAATTATCGGTT
* *
86561 TCGATGTTTTTGGGGTCGATACTTTT
131 TCGATGTTATTGGGATCGATACTTTT
86587 AGAAAATGTA
Statistics
Matches: 131, Mismatches: 24, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
178 75 0.57
179 56 0.43
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (179 bp):
ATTATGGACAAAAAGTATAGACACAAATTCAAAAAGTGTCGATACATTATGCTGACATATTTTCT
AATAAAACCGATATATTTATACCAGTTACATTGTAAATTTACCTATTACATTAAAATTATCGGTT
TCGATGTTATTGGGATCGATACTTTTTAATAAATGTATCAGCACTTTAT
Found at i:89108 original size:19 final size:19
Alignment explanation
Indices: 89084--89132 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
89074 TTACATTCAC
89084 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
* *
89103 ATACAACATTATAAATCTT
1 ATACAAAATTATAAATCGT
89122 ATACAAAATTA
1 ATACAAAATTA
89133 ACCCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:90815 original size:200 final size:196
Alignment explanation
Indices: 90451--91023 Score: 799
Period size: 200 Copynumber: 2.9 Consensus size: 196
90441 GCGTAATTTA
* * *
90451 AAAACGTATCGACACAAATTTAAAAGTGTCGATACATTATGTTAACATATTTTCTCATAAAACCG
1 AAAATGTATCGACACAAATTAAAAAGTGTCGATACATTATGTT-ACCTATTTTCTCATAAAACCG
* ** * *
90516 ATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTTTGTTTCAATATTTT
65 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCAGTTTCGAT-GTTT
* *
90581 TTGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCATTTTGCATTCATTCT
129 TTGGATCGATACTTTTTA-AAATGTATCGACACTTTATGCGTGCACCCCATTTGGCATTCATTAT
*
90646 GGAC
193 GAAC
* *
90650 AAAATGTATCGACACAAATCTAAAAAGTGTCGATATATTATGTTCACCTATTTTCTCATAAAACT
1 AAAATGTATCGACACAAAT-TAAAAAGTGTCGATACATTATGTT-ACCTATTTTCTCATAAAACC
* * * * *
90715 GGTATACTTATATCGGTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGTTT
64 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCAGTTTCGATGTTT
* * *
90780 TTGAGATTGATACTTTTTAAAAATATATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTA
129 TTG-GATCGATACTTTTT-AAAATGTATCGACACTTTATGCGTGCACCCCATTTGGCATTCATTA
*
90845 TGAAT
192 TGAAC
90850 AAAATGTATCGACACAAATTTAAACAA-TGTCGATACATTATGTATACCTATTTTCTCATAAAAC
1 AAAATGTATCGACACAAA-TTAAA-AAGTGTCGATACATTATGT-TACCTATTTTCTCATAAAAC
90914 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCAGTTTCGATGTT
63 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCAGTTTCGATG-T
* *
90979 TTTTGGATCGATTCAATTTT-AAATGTATCGACACTTTTATGCGTG
127 TTTTGGATCGATAC-TTTTTAAAATGTATCGACAC-TTTATGCGTG
91024 AAGCTCGTTG
Statistics
Matches: 332, Mismatches: 33, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
199 37 0.11
200 280 0.84
201 15 0.05
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (196 bp):
AAAATGTATCGACACAAATTAAAAAGTGTCGATACATTATGTTACCTATTTTCTCATAAAACCGG
TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCAGTTTCGATGTTTTT
GGATCGATACTTTTTAAAATGTATCGACACTTTATGCGTGCACCCCATTTGGCATTCATTATGAA
C
Found at i:93347 original size:199 final size:199
Alignment explanation
Indices: 92997--94153 Score: 1094
Period size: 200 Copynumber: 5.8 Consensus size: 199
92987 CGCGATATTG
* * * * * *
92997 AAAATAGTATCGACACAAATTTAACAATTGTTGATACTTTATGCT-GACCTATTTTCTCATAAAA
1 AAAA-AGTATCGACACAAATTCAACAAGTATCGATACATTATG-TAGACCTATTCTCTCATAAAA
* * * * * * *
93061 CTGATATATTTATACTGGTTACATTGGAAATTTGCCTATTACATTATAATTATCGGTTTTGATGT
64 CCGGTATATTTATACTGGTTACATTAGAAAATTACCTATTACATTATAATTATGGGTTTCGATGT
* *
93126 TTTTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTGGGCATTCAT
129 TTTTGGGATCGACA-TTTTTAAAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCAT
*
93191 TCTAGAC
193 TCTGGAC
* * * *
93198 AAAAAGTATCGACACAAATTCAACAAGTATCAATACATTTTATAGATCTATTCTCTCATAAAACC
1 AAAAAGTATCGACACAAATTCAACAAGTATCGATACATTATGTAGACCTATTCTCTCATAAAACC
* **
93263 GGTATATTTATACTGGTTACATT-GAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTT
66 GGTATATTTATACTGGTTACATTAGAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * * *
93327 TTAGGATCGACATATTTTAAAAATGTGTCGACACTTTATGAGTGCACCCCTTTTGGGCATTCCTT
131 TTGGGATCGACAT-TTTTAAAAATGTATCGACACTTTATGCGTGCA-CCCTTTTGGGCATTCATT
*
93392 CGGGAC
194 CTGGAC
* * *** ** * * * **
93398 AAAAAGTATTGACACAAATT-AACAAGTATCGACACAAATTCAACAAGTGTCGATACATTTTGTA
1 AAAAAGTATCGACACAAATTCAACAAGTATCGATAC--ATT-ATGTAG-ACCTATTC-TCTCATA
* * * *
93462 GAGCC--TAT-TCTCTCATAAAATCGGTATATTTATACCGATTATATGAAATTA-CTATTACATT
61 AAACCGGTATAT-T-T-AT--ACT-GG------T-TA-C-ATTAGA--AAATTACCTATTACATT
93523 ATAATTAT--GTTTCGATGTTTTTGGGATCGACATTTTTAAAAATGTATCGACACTTTATGCGTG
109 ATAATTATGGGTTTCGATGTTTTTGGGATCGACATTTTTAAAAATGTATCGACACTTTATGCGTG
*
93586 CACCTTTTTGGGCATTCATTCTGGAC
174 CACCCTTTTGGGCATTCATTCTGGAC
* * * * *
93612 AAAATGTATCGACACAAAATT-AAAAAGTGTCGATACATTATGTTGACCTATTCTCACATAAAAC
1 AAAAAGTATCGACAC-AAATTCAACAAGTATCGATACATTATGTAGACCTATTCTCTCATAAAAC
* * * * * *
93676 CGATATATTTATACCGGTTACCTTACAAAATTACTTATTACATTATAATTATGGGTTTCGATGTC
65 CGGTATATTTATACTGGTTACATTAGAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
* *
93741 TCTGGGATCGACACTTTTTAAAAATGTATCGACACTTTATG-GTGCA-CCTTTTGGGCATTCCTT
130 TTTGGGATCGACA-TTTTTAAAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATT
*
93804 GTGGAC
194 CTGGAC
* * * * *
93810 AAACAGTATCGACAC-AATTCCAGAAGTATCGATATATTATGTAGACAT-TTCTCTCATAAAACC
1 AAAAAGTATCGACACAAATTCAACAAGTATCGATACATTATGTAGACCTATTCTCTCATAAAACC
* * *
93873 GGTATAGTTATA-TCGATTACATT-GTAAATTTACCTATTACATTAT-ATTATGGGTTTCGATGT
66 GGTATATTTATACT-GGTTACATTAG-AAAATTACCTATTACATTATAATTATGGGTTTCGATGT
* * * * ** * * *
93935 TTCTGGGATCAATACTTTTGTAAATGTATCGACACTTTATGCGTTCACCATTTTGTGCATTCATT
129 TTTTGGGATCGACATTTTTAAAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATT
*
94000 ATGGAC
194 CTGGAC
* * * *
94006 AAAAAGTATCGACACCAATTTCAA-AAGTGTCGATATATTATGTAGACCTATTCTCACATAAAAC
1 AAAAAGTATCGACA-CAAATTCAACAAGTATCGATACATTATGTAGACCTATTCTCTCATAAAAC
* * * * *
94070 TGGTATATTTATACCGGTTATATTACAAAATTACATATTACATTATAA-T-TGGGTTTCGATGTT
65 CGGTATATTTATACTGGTTACATTAGAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
* *
94133 TTTGGGATCGATACTTTTAAA
130 TTTGGGATCGACATTTTTAAA
94154 TGATCGACAC
Statistics
Matches: 790, Mismatches: 121, Indels: 94
0.79 0.12 0.09
Matches are distributed among these distances:
194 24 0.03
195 32 0.04
196 91 0.12
197 94 0.12
198 93 0.12
199 121 0.15
200 139 0.18
201 9 0.01
202 6 0.01
203 6 0.01
204 9 0.01
206 2 0.00
207 4 0.01
208 1 0.00
210 8 0.01
211 5 0.01
212 6 0.01
213 5 0.01
214 36 0.05
215 48 0.06
216 27 0.03
217 1 0.00
218 18 0.02
219 5 0.01
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (199 bp):
AAAAAGTATCGACACAAATTCAACAAGTATCGATACATTATGTAGACCTATTCTCTCATAAAACC
GGTATATTTATACTGGTTACATTAGAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
TTGGGATCGACATTTTTAAAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATTCT
GGAC
Found at i:93426 original size:20 final size:21
Alignment explanation
Indices: 93401--93450 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
93391 TCGGGACAAA
*
93401 AAGTATTGACACAAATT-AAC
1 AAGTATCGACACAAATTCAAC
93421 AAGTATCGACACAAATTCAAC
1 AAGTATCGACACAAATTCAAC
*
93442 AAGTGTCGA
1 AAGTATCGA
93451 TACATTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.22
Consensus pattern (21 bp):
AAGTATCGACACAAATTCAAC
Found at i:93919 original size:414 final size:401
Alignment explanation
Indices: 93096--94150 Score: 1115
Period size: 394 Copynumber: 2.6 Consensus size: 401
93086 GGAAATTTGC
*
93096 CTATTACATTATAATTATCGGTTTTGATGTTTTTGGGATCGATACTTTTTAAAAATGTATCGACA
1 CTATTACATTATAATTAT--GTTTCGATGTTTTTGGGATCGATA-TTTTTAAAAATGTATCGACA
* * * *
93161 CTTTATGGGTGCACCCTTTTGGGCATTCATTCTAGACAAAAAGTATCGACACAAATTCAACAAGT
63 CTTTATGCGTGCACCATTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATT-AAAAAGT
* * * * * * * *
93226 ATCAATACATTTTATAGATCTATTCTCTCATAAAACCGGTATATTTATACTGGTTACATT-GAAA
127 GTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACATTACAAA
* * ** * *
93290 TTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTAGGATCGACA-TATTTTAAAAATGTG
192 ATTACATATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACT-TTTTAAAAATGTA
*
93354 TCGACACTTTATGAGTGCACCCCTTTTGGGCATTCCTTCGGGACAAAAAGTATTGACACAAATTA
256 TCGACACTTTATGAGTGCA-CCCTTTTGGGCATTCCTTCGGGACAAAAAGTATCGACACAAATTA
* * * **** *
93419 ACAAGTATCGACACAAATTCAACAAGTGTCGATACATTTTGTAGAGCCTATTCTCTCATAAAATC
320 ACAAGTATCGACACAAATTCAACAAGTCTCCATAAAACCGGTAGAGCCTATTATCTCATAAAATC
* *
93484 GGTATATTTATACCGATTATATGAAATT
385 GGTA-AATT-T----A-TA-ACG--A-T
*
93512 ACTATTACATTATAATTATGTTTCGATGTTTTTGGGATCGACATTTTTAAAAATGTATCGACACT
1 -CTATTACATTATAATTATGTTTCGATGTTTTTGGGATCGATATTTTTAAAAATGTATCGACACT
* *
93577 TTATGCGTGCACCTTTTTGGGCATTCATTCTGGACAAAATGTATCGACACAAAATTAAAAAGTGT
65 TTATGCGTGCACCATTTTGGGCATTCATTCTGGACAAAAAGTATCGACAC-AAATTAAAAAGTGT
* * *
93642 CGATACATTATGTTGACCTATTCTCACATAAAACCGATATATTTATACCGGTTACCTTACAAAAT
129 CGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACATTACAAAAT
* * *
93707 TACTTATTACATTATAATTATGGGTTTCGATGTCTCTGGGATCGACACTTTTTAAAAATGTATCG
194 TACATATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTTAAAAATGTATCG
* * *
93772 ACACTTTATG-GTGCA-CCTTTTGGGCATTCCTT-GTGGACAAACAGTATCGACAC-AATTCCAG
259 ACACTTTATGAGTGCACCCTTTTGGGCATTCCTTCG-GGACAAAAAGTATCGACACAAATT-AAC
* * * ** * * * * *
93833 AAGTATCGATATATTATGT-AGACATTTCTCTCATAAAACCGGTATAG-TTA-TATC-GATTACA
322 AAGTATCGACACA-AAT-TCA-ACAAGTCTC-CATAAAACCGGTAGAGCCTATTATCTCATAAAA
*
93894 T-TGTAAA-TT-T-AC---
383 TCGGTAAATTTATAACGAT
* * * **
93906 CTATTACATTAT-ATTATGGGTTTCGATGTTTCTGGGATCAATACTTTTGTAAATGTATCGACAC
1 CTATTACATTATAATTAT--GTTTCGATGTTTTTGGGATCGATATTTTTAAAAATGTATCGACAC
* * * * *
93970 TTTATGCGTTCACCATTTTGTGCATTCATTATGGACAAAAAGTATCGACACCAATTTCAAAAGTG
64 TTTATGCGTGCACCATTTTGGGCATTCATTCTGGACAAAAAGTATCGACA-CAAATTAAAAAGTG
* * *
94035 TCGATATATTATGTAGACCTATTCTCACATAAAACTGGTATATTTATACCGGTTATATTACAAAA
128 TCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACATTACAAAA
*
94100 TTACATATTACATTATAA-T-TGGGTTTCGATGTTTTTGGGATCGATACTTTT
193 TTACATATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTT
94151 AAATGATCGA
Statistics
Matches: 552, Mismatches: 74, Indels: 49
0.82 0.11 0.07
Matches are distributed among these distances:
392 34 0.06
393 13 0.02
394 171 0.31
395 1 0.00
400 1 0.00
402 1 0.00
408 1 0.00
409 1 0.00
410 1 0.00
411 8 0.01
412 51 0.09
413 6 0.01
414 138 0.25
415 106 0.19
416 1 0.00
417 18 0.03
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (401 bp):
CTATTACATTATAATTATGTTTCGATGTTTTTGGGATCGATATTTTTAAAAATGTATCGACACTT
TATGCGTGCACCATTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTAAAAAGTGTCG
ATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACATTACAAAATTA
CATATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTTAAAAATGTATCGAC
ACTTTATGAGTGCACCCTTTTGGGCATTCCTTCGGGACAAAAAGTATCGACACAAATTAACAAGT
ATCGACACAAATTCAACAAGTCTCCATAAAACCGGTAGAGCCTATTATCTCATAAAATCGGTAAA
TTTATAACGAT
Found at i:94007 original size:196 final size:196
Alignment explanation
Indices: 93421--94163 Score: 899
Period size: 196 Copynumber: 3.8 Consensus size: 196
93411 ACAAATTAAC
* * * *
93421 AAGTATCGACACAAATTCAACAAGTGTCGATACATTTTGTAGAGCCTATTCTCTCATAAAATCGG
1 AAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTAGA-CCTATTCTCACATAAAACCGG
** *
93486 TATATTTATACCGATT--A-TATGAAATTA-CTATTACATTATAATTAT--GTTTCGATGTTTTT
65 TATATTTATACCGATTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCT
*
93545 GGGATCGACA-TTTTTAAAAATGTATCGACACTTTATGCGTGCACCTTTTTGGGCATTCATTCTG
130 GGGATCGACACTTTTT--AAATGTATCGACACTTTATGCGTGCACC-TTTTGGGCATTCATTATG
93609 GACAA
192 GACAA
*
93614 AATGTATCGACACAAAATT-AAAAAGTGTCGATACATTATGTTGACCTATTCTCACATAAAACCG
1 AA-GTATCGACAC-AAATTCAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCG
* * * * *
93678 ATATATTTATACCGGTTACCTTACAAAATTACTTATTACATTATAATTATGGGTTTCGATGTCTC
64 GTATATTTATACCGATTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTC
* *
93743 TGGGATCGACACTTTTTAAAAATGTATCGACACTTTATG-GTGCACCTTTTGGGCATTCCTTGTG
129 TGGGATCGACACTTTTT--AAATGTATCGACACTTTATGCGTGCACCTTTTGGGCATTCATTATG
93807 GACAA
192 GACAA
* * * * * *
93812 ACAGTATCGACAC-AATTCCAGAAGTATCGATATATTATGTAGACAT-TTCTCTCATAAAACCGG
1 A-AGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGG
* * ** *
93875 TATAGTTATATCGATTACATTGTAAATTTACCTATTACATTAT-ATTATGGGTTTCGATGTTTCT
65 TATATTTATACCGATTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCT
* * * *
93939 GGGATCAATACTTTTGTAAATGTATCGACACTTTATGCGTTCACCATTTTGTGCATTCATTATGG
130 GGGATCGACACTTTT-TAAATGTATCGACACTTTATGCGTGCACC-TTTTGGGCATTCATTATGG
94004 ACAAA
193 AC-AA
* * *
94009 AAGTATCGACACCAATTTC-AAAAGTGTCGATATATTATGTAGACCTATTCTCACATAAAACTGG
1 AAGTATCGACA-CAAATTCAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGG
* * * *
94073 TATATTTATACCGGTTATATTACAAAATTACATATTACATTATAA-T-TGGGTTTCGATGTTTTT
65 TATATTTATACCGATTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCT
*
94136 GGGATCGATAC-TTTTAAATG-ATCGACAC
130 GGGATCGACACTTTTTAAATGTATCGACAC
94164 ATCTGCTTAC
Statistics
Matches: 477, Mismatches: 54, Indels: 37
0.84 0.10 0.07
Matches are distributed among these distances:
193 35 0.07
194 60 0.13
195 50 0.10
196 94 0.20
197 93 0.19
198 87 0.18
199 31 0.06
200 27 0.06
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (196 bp):
AAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGT
ATATTTATACCGATTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTG
GGATCGACACTTTTTAAATGTATCGACACTTTATGCGTGCACCTTTTGGGCATTCATTATGGACA
A
Found at i:94537 original size:18 final size:19
Alignment explanation
Indices: 94510--94556 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
94500 TTACATTCAC
*
94510 ATAC-AAATTATAAATCGT
1 ATACAAAATTATAAATAGT
*
94528 ATA-AAAATTATAAATATT
1 ATACAAAATTATAAATAGT
94546 ATACAAAATTA
1 ATACAAAATTA
94557 ACCCTACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.34
Consensus pattern (19 bp):
ATACAAAATTATAAATAGT
Done.