Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 56
Found at i:641621 original size:59 final size:59
Alignment explanation
Indices: 641502--641622 Score: 174
Period size: 59 Copynumber: 2.0 Consensus size: 59
641492 CTATATATAT
* *
641502 AAAAATTAATATTTAATTTATTTAAAAAATTAATATAAAAATATCTATAATATAATATTA
1 AAAAATTAATATTTAATTTATTTAAAAAATTAATATAAAAATA-CAATAATATAAAATTA
*
641562 AAAAATTAATATTTAATTTA-TTAAAAAATTAATATTAAAAT-CAAATAATATAAAAATTA
1 AAAAATTAATATTTAATTTATTTAAAAAATTAATATAAAAATAC-AATAATAT-AAAATTA
641621 AA
1 AA
641623 TATAAAACTT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
57 1 0.02
58 7 0.12
59 28 0.50
60 20 0.36
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (59 bp):
AAAAATTAATATTTAATTTATTTAAAAAATTAATATAAAAATACAATAATATAAAATTA
Found at i:641698 original size:20 final size:20
Alignment explanation
Indices: 641651--641698 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
641641 AGGTTAGAAG
* *
641651 ACGTCTGCATACATAAAACC
1 ACGTCTGTAGACATAAAACC
* *
641671 ACGTCTGTAGACATAAGACT
1 ACGTCTGTAGACATAAAACC
641691 ACGTCTGT
1 ACGTCTGT
641699 GCCGTGCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (20 bp):
ACGTCTGTAGACATAAAACC
Found at i:644938 original size:20 final size:20
Alignment explanation
Indices: 644913--644951 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
644903 ATTTGTGAAG
644913 TGATGCA-CAGATGCACTCAT
1 TGATGCATC-GATGCACTCAT
644933 TGATGCATCGATGCACTCA
1 TGATGCATCGATGCACTCA
644952 CCATTTCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
TGATGCATCGATGCACTCAT
Found at i:644991 original size:18 final size:18
Alignment explanation
Indices: 644970--645038 Score: 129
Period size: 18 Copynumber: 3.8 Consensus size: 18
644960 AATGCATTTT
*
644970 ATGCATCGATGTACTTCC
1 ATGCATCGATGCACTTCC
644988 ATGCATCGATGCACTTCC
1 ATGCATCGATGCACTTCC
645006 ATGCATCGATGCACTTCC
1 ATGCATCGATGCACTTCC
645024 ATGCATCGATGCACT
1 ATGCATCGATGCACT
645039 CAGGTTTTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.29
Consensus pattern (18 bp):
ATGCATCGATGCACTTCC
Found at i:645829 original size:21 final size:21
Alignment explanation
Indices: 645803--645847 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
645793 GATTTCTGGG
* *
645803 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
645824 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
645845 CAA
1 CAA
645848 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:646438 original size:18 final size:18
Alignment explanation
Indices: 646415--646449 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
646405 CTAGGAGATT
646415 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
646433 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
646450 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:647501 original size:145 final size:148
Alignment explanation
Indices: 647278--647719 Score: 769
Period size: 145 Copynumber: 3.0 Consensus size: 148
647268 GAGTCGAGGG
647278 TCTACGCGG-TCTTCGGGACATATGTAT-TTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACA-GTGTGAAGTCTGGAAAGACACAT
647341 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
647406 TATGGCACTACGGTGCACT
130 TATGGCACTACGGTGCACT
647425 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACA-TGTGAAGTCTGG-AAGAC-CATA
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACAGTGTGAAGTCTGGAAAGACACATA
647487 CTTGATCCCTAGCATATGTATATGATTC-TAAAGAATTCTATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTAT
*
647551 ATGGCA-TACGATGCACT
131 ATGGCACTACGGTGCACT
647568 TCTACGCGGTTCTTCGGGAC--ATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACA-GTGTGAAGTCTGGAAAGACACAT
*
647631 ACTTGATCCCTAGCATATGTATA-GATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
65 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
*
647695 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCACT
647714 TCTACG
1 TCTACG
647720 GGGCACTTCG
Statistics
Matches: 283, Mismatches: 4, Indels: 17
0.93 0.01 0.06
Matches are distributed among these distances:
141 19 0.07
143 42 0.15
144 52 0.18
145 99 0.35
146 20 0.07
147 21 0.07
148 18 0.06
149 12 0.04
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (148 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACAGTGTGAAGTCTGGAAAGACACATA
CTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTGCACT
Found at i:647742 original size:23 final size:23
Alignment explanation
Indices: 647698--647742 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
647688 ATCATTATAT
*
647698 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
647721 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
647743 AGCTGTGGTG
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:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:653838 original size:21 final size:21
Alignment explanation
Indices: 653814--653911 Score: 74
Period size: 21 Copynumber: 4.4 Consensus size: 21
653804 TTGTGCATAA
653814 TGCATCGATACACTATGAATG
1 TGCATCGATACACTATGAATG
* *
653835 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGAT--A-CACTATGAATG
653859 TGCATCGATACATCT-TGAA-G
1 TGCATCGATACA-CTATGAATG
* *
653879 ATGCACCGATGCACTACTTGAATG
1 -TGCATCGATACACTA--TGAATG
*
653903 TTCATCGAT
1 TGCATCGAT
653912 GCACAATGCC
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
20 3 0.05
21 24 0.39
22 3 0.05
23 12 0.20
24 19 0.31
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (21 bp):
TGCATCGATACACTATGAATG
Found at i:658658 original size:24 final size:24
Alignment explanation
Indices: 658626--658682 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
658616 GGATTGTGGG
*
658626 ATTCCCATGGGATGGGAATCTCAC
1 ATTCCCATGGGATGGGAATCCCAC
658650 ATTCCCATGGGATGGGAATCCCAC
1 ATTCCCATGGGATGGGAATCCCAC
658674 ATTCCCATG
1 ATTCCCATG
658683 TTTAGTTGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (24 bp):
ATTCCCATGGGATGGGAATCCCAC
Found at i:659072 original size:37 final size:36
Alignment explanation
Indices: 658997--659072 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
658987 TTTTTTATAT
*
658997 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
659033 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
659070 TTT
1 TTT
659073 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:659254 original size:20 final size:20
Alignment explanation
Indices: 659218--659255 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
659208 ATCCTATTCC
**
659218 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
659238 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
659256 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:660218 original size:22 final size:22
Alignment explanation
Indices: 660193--660253 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
660183 CAGTGTTATG
* *
660193 GCACTTTAGTATCAGTGCAGAT
1 GCACTTTAGTATTAGTGCAAAT
*
660215 GCACTTTTG-ATTTAGTGCAAAT
1 GCACTTTAGTA-TTAGTGCAAAT
*
660237 GCAATTTAGTATTAGTG
1 GCACTTTAGTATTAGTG
660254 ATACGACACT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (22 bp):
GCACTTTAGTATTAGTGCAAAT
Found at i:661238 original size:2 final size:2
Alignment explanation
Indices: 661231--661258 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
661221 GTGAGGCATA
661231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
661259 CAATGCATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:661560 original size:20 final size:20
Alignment explanation
Indices: 661510--661583 Score: 93
Period size: 18 Copynumber: 3.9 Consensus size: 20
661500 TGAATATTTA
661510 TCCCGAAGGACCACT-A-TG
1 TCCCGAAGGACCACTGATTG
*
661528 TCTCGAAGGACCACTGATTG
1 TCCCGAAGGACCACTGATTG
* *
661548 TTCCGAAGAACCACT-A-TG
1 TCCCGAAGGACCACTGATTG
661566 TCCCGAAGGACCACTGAT
1 TCCCGAAGGACCACTGAT
661584 AATCCCTCGA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
18 29 0.63
19 3 0.07
20 14 0.30
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (20 bp):
TCCCGAAGGACCACTGATTG
Found at i:668416 original size:18 final size:18
Alignment explanation
Indices: 668393--668465 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
668383 ACTGAATATT
*
668393 TGTCCCGAAGGACAACTA
1 TGTCCCGAAGGACCACTA
668411 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
668430 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
668449 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
668466 GATAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 2 0.04
20 15 0.32
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:668440 original size:38 final size:38
Alignment explanation
Indices: 668392--668468 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
668382 CACTGAATAT
*
668392 TTGTCCCGAAGGACAACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACAACTATGTCCCGAAGGACCACTGA
* * *
668430 TTGTTCCGAAGAACCACTATGTCCTGAAGGACCACTGA
1 TTGTCCCGAAGAACAACTATGTCCCGAAGGACCACTGA
668468 T
1 T
668469 AATCCCTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (38 bp):
TTGTCCCGAAGAACAACTATGTCCCGAAGGACCACTGA
Found at i:669125 original size:19 final size:19
Alignment explanation
Indices: 669101--669152 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
669091 TTTAAGCGGG
669101 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
*
669120 TGCATCGATGCACTCTTTA
1 TGCATCGATGCACTCCTTA
*
669139 TGCATCAATGCACT
1 TGCATCGATGCACT
669153 AATGTCATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:672210 original size:21 final size:23
Alignment explanation
Indices: 672177--672219 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
672167 ATAAATTTGA
*
672177 ATATTTTGAATTT-AG-GGATTT
1 ATATTTAGAATTTCAGAGGATTT
*
672198 ATATTTAGGATTTCAGAGGATT
1 ATATTTAGAATTTCAGAGGATT
672220 AGGATGATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (23 bp):
ATATTTAGAATTTCAGAGGATTT
Found at i:674995 original size:148 final size:143
Alignment explanation
Indices: 674709--674998 Score: 445
Period size: 143 Copynumber: 2.0 Consensus size: 143
674699 AAATACTCAA
* *
674709 TTCAGTTTATTAAATAGTTGACTCAAAAAATTTTCGATTTGAATTTATAAAATTTAAATCAAGTC
1 TTCAGCTTATAAAATAGTTGACTCAAAAAATTTTCGATTTGAATTTATAAAATTTAAATCAAGTC
* * *
674774 GAATTGAATTTTTGAGTTTCTGTTTAAATTTAATTATAACTATTTATCATATTATAATATTATTT
66 GAATTGAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTT
674839 GATTCTAATTTAG
131 GATTCTAATTTAG
*** *
674852 TTCAGCTTATAAAATAGTTGACTCAAATTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAGCTTATAAAATAGTTGACTCAAAAAATTTTCGATTTGAATTTATAAAATTTAAATCAAGTC
*
674917 GAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATTTTTATAATACTATAATAT
66 GAATTGAA-T---TTTT-GAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
674982 TATTTGATTCTAATTTA
126 TATTTGATTCTAATTTA
674999 AATAGTTTTT
Statistics
Matches: 132, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
143 67 0.51
144 1 0.01
147 4 0.03
148 60 0.45
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (143 bp):
TTCAGCTTATAAAATAGTTGACTCAAAAAATTTTCGATTTGAATTTATAAAATTTAAATCAAGTC
GAATTGAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTT
GATTCTAATTTAG
Found at i:675047 original size:13 final size:13
Alignment explanation
Indices: 675023--675054 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
675013 CTATATACAA
675023 TACATATTTTTTT
1 TACATATTTTTTT
675036 T-CATATTTTTTT
1 TACATATTTTTTT
675048 TACATAT
1 TACATAT
675055 GTGATATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (13 bp):
TACATATTTTTTT
Found at i:675522 original size:35 final size:34
Alignment explanation
Indices: 675483--675578 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 34
675473 AATAAATTAT
* *
675483 GAATTTGGGGTT-GGATATGTAATTGAAGTATTTTG
1 GAATTTGGGGTTAGAATATG--ATTAAAGTATTTTG
* *
675518 GAATTCGAGGTTTAGAATATGATTAAAGTATTTTG
1 GAATTTG-GGGTTAGAATATGATTAAAGTATTTTG
* *
675553 GAATTTAGGGTTTAGAATATAATTAA
1 GAATTT-GGGGTTAGAATATGATTAA
675579 TGACTGTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
35 41 0.79
36 5 0.10
37 6 0.12
ACGTcount: A:0.33, C:0.01, G:0.25, T:0.41
Consensus pattern (34 bp):
GAATTTGGGGTTAGAATATGATTAAAGTATTTTG
Found at i:680112 original size:4 final size:4
Alignment explanation
Indices: 680103--680127 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
680093 TACTGATACG
680103 TGCA TGCA TGCA TGCA TGCA TGCA T
1 TGCA TGCA TGCA TGCA TGCA TGCA T
680128 AGGATACGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (4 bp):
TGCA
Found at i:680299 original size:9 final size:9
Alignment explanation
Indices: 680279--680314 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
680269 TAATCTTAAT
680279 GGTAGA-AA
1 GGTAGAGAA
680287 GGTAGAGAA
1 GGTAGAGAA
*
680296 GGTAGATAA
1 GGTAGAGAA
680305 GGTAGAGAA
1 GGTAGAGAA
680314 G
1 G
680315 TAGGAAGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 6 0.24
9 19 0.76
ACGTcount: A:0.44, C:0.00, G:0.42, T:0.14
Consensus pattern (9 bp):
GGTAGAGAA
Found at i:680308 original size:18 final size:17
Alignment explanation
Indices: 680279--680314 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
680269 TAATCTTAAT
680279 GGTAGAAAGGTAGAGAA
1 GGTAGAAAGGTAGAGAA
680296 GGTAGATAAGGTAGAGAA
1 GGTAGA-AAGGTAGAGAA
680314 G
1 G
680315 TAGGAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.42, T:0.14
Consensus pattern (17 bp):
GGTAGAAAGGTAGAGAA
Found at i:681011 original size:29 final size:28
Alignment explanation
Indices: 680978--681035 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
680968 TGTTCGAAAA
*
680978 GTGAACTTAAAC-TTTTAAAATTTTAAGAG
1 GTGAACTTAAACGTATT-AAATTTT-AGAG
681007 GTGAACTTAAACGTATTAAATTTTAGAG
1 GTGAACTTAAACGTATTAAATTTTAGAG
681035 G
1 G
681036 AGACAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.19
29 19 0.70
30 3 0.11
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (28 bp):
GTGAACTTAAACGTATTAAATTTTAGAG
Found at i:685254 original size:2 final size:2
Alignment explanation
Indices: 685247--685272 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
685237 CGTTAGTTTT
685247 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
685273 CATTATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:688053 original size:16 final size:16
Alignment explanation
Indices: 688034--688072 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
688024 TTAACGAAAT
688034 TGAAATCAACCAGAAC
1 TGAAATCAACCAGAAC
* **
688050 TGAAATTAACCCTAAC
1 TGAAATCAACCAGAAC
688066 TGAAATC
1 TGAAATC
688073 GACATTAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (16 bp):
TGAAATCAACCAGAAC
Found at i:688115 original size:16 final size:16
Alignment explanation
Indices: 688062--688123 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 16
688052 AAATTAACCC
* * *
688062 TAACTGAAATCGACAT
1 TAACTCAAACCGAAAT
* *
688078 TAACTCAAACCAAAAG
1 TAACTCAAACCGAAAT
**
688094 CGACTCAAACCGAAAT
1 TAACTCAAACCGAAAT
*
688110 TAACTCGAACCGAA
1 TAACTCAAACCGAA
688124 TTTTAACCTC
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (16 bp):
TAACTCAAACCGAAAT
Found at i:688179 original size:16 final size:16
Alignment explanation
Indices: 688137--688183 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
688127 TAACCTCATT
688137 CGAAAGCAACCCGAAC
1 CGAAAGCAACCCGAAC
** *
688153 C-AAATTTAACCCGACC
1 CGAAA-GCAACCCGAAC
688169 CGAAAGCAACCCGAA
1 CGAAAGCAACCCGAA
688184 TAGATTGAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 4
0.70 0.18 0.12
Matches are distributed among these distances:
15 3 0.13
16 17 0.74
17 3 0.13
ACGTcount: A:0.43, C:0.36, G:0.15, T:0.06
Consensus pattern (16 bp):
CGAAAGCAACCCGAAC
Found at i:688259 original size:18 final size:18
Alignment explanation
Indices: 688238--688290 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
688228 CAATAATAAA
688238 TTAATTTAAATAAAATTG
1 TTAATTTAAATAAAATTG
* *
688256 TTAATTT-ATTAAAAATG
1 TTAATTTAAATAAAATTG
688273 TTAGATTTATAATAAAAT
1 TTA-ATTTA-AATAAAAT
688291 AATAGAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 11 0.39
18 11 0.39
20 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (18 bp):
TTAATTTAAATAAAATTG
Found at i:688268 original size:17 final size:17
Alignment explanation
Indices: 688238--688282 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
688228 CAATAATAAA
* *
688238 TTAATTTAAATAAAATTG
1 TTAATTT-ATTAAAAATG
688256 TTAATTTATTAAAAATG
1 TTAATTTATTAAAAATG
688273 TTAGATTTAT
1 TTA-ATTTAT
688283 AATAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (17 bp):
TTAATTTATTAAAAATG
Found at i:692422 original size:18 final size:18
Alignment explanation
Indices: 692378--692422 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
692368 GAATAAGGGG
*
692378 AAAAAAGAAAATCACAAA
1 AAAAAAGAAAATCAAAAA
** *
692396 AAATGAGAAACTCAAAAA
1 AAAAAAGAAAATCAAAAA
692414 AAAAAAGAA
1 AAAAAAGAA
692423 GGAAAAATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.76, C:0.09, G:0.09, T:0.07
Consensus pattern (18 bp):
AAAAAAGAAAATCAAAAA
Found at i:692649 original size:2 final size:2
Alignment explanation
Indices: 692644--692679 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
692634 TCACACACAC
692644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
692680 GTCTAGTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:694403 original size:16 final size:17
Alignment explanation
Indices: 694377--694425 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
694367 TTTCTATTAT
694377 TTTTATTATAAATTAATA
1 TTTTA-TATAAATTAATA
*
694395 TTTTA-ATAAATT-ATC
1 TTTTATATAAATTAATA
*
694410 TTTTATTTAAATTAAT
1 TTTTATATAAATTAAT
694426 TTATTATTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 7 0.26
16 13 0.48
17 2 0.07
18 5 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTATATAAATTAATA
Found at i:694815 original size:3 final size:3
Alignment explanation
Indices: 694803--694843 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
694793 TCCTACTATC
* *
694803 ATT A-T ATT ATT ATT ATT ATC ATT ATT ATT A-T GTT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
694844 ATACAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 3 0.09
3 29 0.91
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:698586 original size:26 final size:25
Alignment explanation
Indices: 698550--698600 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
698540 CAATTTAATT
*
698550 TATTTTTAAATGATAAAATTTATTAA
1 TATTTTCAAATGATAAAA-TTATTAA
*
698576 TATTTTCAAATTATAAAATTATTAA
1 TATTTTCAAATGATAAAATTATTAA
698601 AAAATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
TATTTTCAAATGATAAAATTATTAA
Found at i:698618 original size:31 final size:32
Alignment explanation
Indices: 698583--698642 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
698573 TAATATTTTC
*
698583 AAATTATAAAATTATTAAAAA-ATAATAATCT
1 AAATTATAAAATGATTAAAAATATAATAATCT
698614 AAATTATAAAATGATTAAAAATATAATAA
1 AAATTATAAAATGATTAAAAATATAATAA
698643 GAGTTTGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (32 bp):
AAATTATAAAATGATTAAAAATATAATAATCT
Found at i:698996 original size:22 final size:21
Alignment explanation
Indices: 698937--698996 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
698927 AAAAATTTCT
698937 TAAAACATTATTATTTTTACA
1 TAAAACATTATTATTTTTACA
698958 TAAAACATTATTATTTTTACA
1 TAAAACATTATTATTTTTACA
*
698979 TAAAACATTAATATTTTT
1 TAAAACATTATTATTTTT
698997 TAACATTTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAAACATTATTATTTTTACA
Found at i:702387 original size:42 final size:42
Alignment explanation
Indices: 702339--702672 Score: 420
Period size: 42 Copynumber: 8.0 Consensus size: 42
702329 TCTGCTTTTT
*
702339 CCGTCGAAGGCTTCTCCACCGATTGTTTGGATTCTGCAGTTT
1 CCGTCGAAGGCTTCTCCACCGATTGTTTGGATTCTGCAGTTC
* * *
702381 CCGTCGAAGGCTTCTCCACCGATTGTTTGGAATCTGCATTTT
1 CCGTCGAAGGCTTCTCCACCGATTGTTTGGATTCTGCAGTTC
* * *
702423 CCGTCAAAGGCTTCTCCACCGATTGTTCGGATGCTGCAGTTC
1 CCGTCGAAGGCTTCTCCACCGATTGTTTGGATTCTGCAGTTC
* * *
702465 CCGTCAAAGGCTTCTCCACCGATTGTTTGGATTCTGCGGCTC
1 CCGTCGAAGGCTTCTCCACCGATTGTTTGGATTCTGCAGTTC
* * *
702507 CCGTCGAAGTCTTCTCCACCGATTGTTTGGATTCCGCGGTTC
1 CCGTCGAAGGCTTCTCCACCGATTGTTTGGATTCTGCAGTTC
* * * *
702549 CCGTCGAAGGCTTCTCTACCGATTGTTTGGAATCGGCGGTTC
1 CCGTCGAAGGCTTCTCCACCGATTGTTTGGATTCTGCAGTTC
* *
702591 CCG-CCAATGGCTTCTCCACCGATTGTTTGGATTCTG-AGGTTT
1 CCGTCGAA-GGCTTCTCCACCGATTGTTTGGATTCTGCA-GTTC
* * * * *
702633 CCGTCAAAGGCTTCGCTACCGATTGTTTGGGTTGTGCAGT
1 CCGTCGAAGGCTTCTCCACCGATTGTTTGGATTCTGCAGT
702673 ATCTGTTGAG
Statistics
Matches: 257, Mismatches: 31, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
41 3 0.01
42 250 0.97
43 4 0.02
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (42 bp):
CCGTCGAAGGCTTCTCCACCGATTGTTTGGATTCTGCAGTTC
Found at i:709395 original size:32 final size:32
Alignment explanation
Indices: 709359--709424 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
709349 AGTACTGATT
709359 GAAATATGATTACTAAATATATTTAGATATGG
1 GAAATATGATTACTAAATATATTTAGATATGG
709391 GAAATATGATTACTAAATATATTTAGATATGG
1 GAAATATGATTACTAAATATATTTAGATATGG
709423 GA
1 GA
709425 CGTGGTTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.36
Consensus pattern (32 bp):
GAAATATGATTACTAAATATATTTAGATATGG
Found at i:715270 original size:20 final size:22
Alignment explanation
Indices: 715247--715286 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
715237 AGTCGTATCT
715247 AGCTG-TTGGGGATG-TTTTAG
1 AGCTGTTTGGGGATGATTTTAG
715267 AGCTGTTTGGGGATGATTTT
1 AGCTGTTTGGGGATGATTTT
715287 TCTGCAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.15, C:0.05, G:0.38, T:0.42
Consensus pattern (22 bp):
AGCTGTTTGGGGATGATTTTAG
Found at i:715440 original size:15 final size:15
Alignment explanation
Indices: 715420--715483 Score: 60
Period size: 15 Copynumber: 4.0 Consensus size: 15
715410 CCCCTGCAGG
715420 GGGTATCGG-TACCCA
1 GGGTAT-GGATACCCA
715435 GGGTATGGATACCCATA
1 GGGTATGGATACCC--A
715452 GGGGGTATCGG-TACCCA
1 --GGGTAT-GGATACCCA
715469 GGGTATGGATACCCA
1 GGGTATGGATACCCA
715484 TAGGGGGTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
14 4 0.10
15 23 0.55
17 2 0.05
19 11 0.26
20 2 0.05
ACGTcount: A:0.23, C:0.22, G:0.34, T:0.20
Consensus pattern (15 bp):
GGGTATGGATACCCA
Found at i:715501 original size:34 final size:34
Alignment explanation
Indices: 715399--715493 Score: 163
Period size: 34 Copynumber: 2.7 Consensus size: 34
715389 TAGAGCCAGG
*
715399 GGGTATGGATACCCCTGCAGGGGGTATCGGTACCCA
1 GGGTATGGATACCCAT--AGGGGGTATCGGTACCCA
715435 GGGTATGGATACCCATAGGGGGTATCGGTACCCA
1 GGGTATGGATACCCATAGGGGGTATCGGTACCCA
715469 GGGTATGGATACCCATAGGGGGTAT
1 GGGTATGGATACCCATAGGGGGTAT
715494 TTTTACCCTT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
34 43 0.74
36 15 0.26
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.21
Consensus pattern (34 bp):
GGGTATGGATACCCATAGGGGGTATCGGTACCCA
Found at i:726662 original size:22 final size:22
Alignment explanation
Indices: 726634--726689 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
726624 AGTCGAGGGT
* *
726634 TTCATAGGTCATTCGGGACATA
1 TTCATAGGTCATTAGGGACAAA
* *
726656 TTCATAGTTCCTTAGGGACAAA
1 TTCATAGGTCATTAGGGACAAA
*
726678 TCTCATATGTCA
1 T-TCATAGGTCA
726690 CTCAGTGGAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (22 bp):
TTCATAGGTCATTAGGGACAAA
Found at i:728254 original size:3 final size:3
Alignment explanation
Indices: 728246--728311 Score: 80
Period size: 3 Copynumber: 21.7 Consensus size: 3
728236 CTACAAAAAA
*
728246 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAAG TA- TAT TACT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA-T TAT TAT
* *
728292 TAT TAT TAG TAT TGT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
728312 AATTATATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
2 2 0.04
3 48 0.87
4 5 0.09
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:730854 original size:81 final size:81
Alignment explanation
Indices: 730707--731448 Score: 1002
Period size: 81 Copynumber: 9.2 Consensus size: 81
730697 TTTAATTCCT
* * ** * * * *
730707 TTAGTCTTTTACCCAACA-GCATTTGGCCTTTCATCTAACTTGCATGACTGACACATTTCTGCCA
1 TTAGTCTTTTACTCAA-AGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCA
* *
730771 AATGCACAACTAGACTA
65 AATGCACAACTAGGCCA
* * * * * * *
730788 TTAATCTTTTACACAAAGGTATTTAACCTTTAATCTAACTGGCATAATTGATACCTTTTTTTCAA
1 TTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
* *
730853 ATGCAAAACTAGGTCA
66 ATGCACAACTAGGCCA
* * * *
730869 TTAGTCTTTTACTCAAAGGTATTTAACATTTCATCTATCTGACATAATTGACATATTTCTGTCAA
1 TTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
* * *
730934 ATGCACATCGAAGCCA
66 ATGCACAACTAGGCCA
* * **
730950 TTAGTATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCGTAATTGACATTTTTCTGTCAA
1 TTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
731015 ATGCACAACTAGGCCA
66 ATGCACAACTAGGCCA
* *
731031 TTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCCAACTGACATAATTGACACATTTCTGTCAA
1 TTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
* *
731096 ATGCATAGCTAGGCCA
66 ATGCACAACTAGGCCA
* *
731112 TTAGTCTTTTACTCAAAGGTATTTAATCTTACATCTAACTGGCATAATTGACACATTTCTGTCAA
1 TTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
*
731177 ATGCACAGCTAGGCCA
66 ATGCACAACTAGGCCA
* * * * *
731193 TTAGTATTTTACTCAAAAGTATTTAACCTTTTATCTAACTGGCATAATTAACATC-TTTATGTCA
1 TTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA-CATTTCTGTCA
*
731257 AATGCACAGCTAGGCCA
65 AATGCACAACTAGGCCA
* * *
731274 TTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACATATTTCTGTCAA
1 TTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
*
731339 ATGCACAGCTAGGCCA
66 ATGCACAACTAGGCCA
* * *
731355 TTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGTATAATTGACACCTTTCTGTCAA
1 TTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
731420 ATGCACAACTAGGCCA
66 ATGCACAACTAGGCCA
731436 TTAGTCTTTTACT
1 TTAGTCTTTTACT
731449 TTTGTAATAG
Statistics
Matches: 582, Mismatches: 76, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
80 1 0.00
81 580 1.00
82 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (81 bp):
TTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
ATGCACAACTAGGCCA
Found at i:738204 original size:19 final size:19
Alignment explanation
Indices: 738180--738216 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
738170 GCAACAACTT
738180 CACAACTACCTGCTAACAA
1 CACAACTACCTGCTAACAA
738199 CACAACTACCTGCTAACA
1 CACAACTACCTGCTAACA
738217 GCTAGCCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.38, G:0.05, T:0.16
Consensus pattern (19 bp):
CACAACTACCTGCTAACAA
Found at i:741413 original size:17 final size:17
Alignment explanation
Indices: 741393--741426 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
741383 GACCCGACCT
*
741393 GTTGACCAGCGTTAACC
1 GTTGACCACCGTTAACC
741410 GTTGACCACCGTTAACC
1 GTTGACCACCGTTAACC
741427 AGAACTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (17 bp):
GTTGACCACCGTTAACC
Found at i:742453 original size:10 final size:11
Alignment explanation
Indices: 742414--742455 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
742404 GAATCCATTG
742414 ATCAACA-AGA
1 ATCAACAGAGA
742424 ATCAACA-AGA
1 ATCAACAGAGA
*
742434 ATCAAGAGAGA
1 ATCAACAGAGA
742445 ATCAA-AGAGA
1 ATCAACAGAGA
742455 A
1 A
742456 AGCATCAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.60, C:0.14, G:0.17, T:0.10
Consensus pattern (11 bp):
ATCAACAGAGA
Found at i:753104 original size:24 final size:24
Alignment explanation
Indices: 753012--753093 Score: 137
Period size: 24 Copynumber: 3.4 Consensus size: 24
753002 CAATTTGAAC
*
753012 TCTGTTATGATACCTGACATGGAT
1 TCTGTTATGATACCTGACCTGGAT
753036 TCTGTTATGATACCTGACCTGGAT
1 TCTGTTATGATACCTGACCTGGAT
* *
753060 TCTGATATGATACTTGACCTGGAT
1 TCTGTTATGATACCTGACCTGGAT
753084 TCTGTTATGA
1 TCTGTTATGA
753094 AATCTAACCT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (24 bp):
TCTGTTATGATACCTGACCTGGAT
Found at i:753104 original size:48 final size:48
Alignment explanation
Indices: 753012--753104 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
753002 CAATTTGAAC
* * *
753012 TCTGTTATGATACCTGACATGGATTCTGTTATGATACCTGACCTGGAT
1 TCTGATATGATACCTGACATGGATTCTGTTATGAAACCTAACCTGGAT
* * *
753060 TCTGATATGATACTTGACCTGGATTCTGTTATGAAATCTAACCTG
1 TCTGATATGATACCTGACATGGATTCTGTTATGAAACCTAACCTG
753105 AATTATGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (48 bp):
TCTGATATGATACCTGACATGGATTCTGTTATGAAACCTAACCTGGAT
Found at i:758995 original size:14 final size:14
Alignment explanation
Indices: 758976--759005 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
758966 ATCTTTGTAT
758976 AGAGAAATATGCCG
1 AGAGAAATATGCCG
*
758990 AGAGAAATATGTCG
1 AGAGAAATATGCCG
759004 AG
1 AG
759006 CAACTGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.10, G:0.30, T:0.17
Consensus pattern (14 bp):
AGAGAAATATGCCG
Found at i:760565 original size:47 final size:45
Alignment explanation
Indices: 760395--760558 Score: 240
Period size: 45 Copynumber: 3.6 Consensus size: 45
760385 AATTATTGAC
760395 TTTATTTTGTTTCTTAATATTTTTATTTAATTATGGATTTTTTTA
1 TTTATTTTGTTTCTTAATATTTTTATTTAATTATGGATTTTTTTA
*
760440 TTTATTTTGTTTCTTAATATTTTTATTTAATTTTGGATTTTTTTA
1 TTTATTTTGTTTCTTAATATTTTTATTTAATTATGGATTTTTTTA
* * *
760485 TTTATTTTGTTTCTTAATGTTTTTATTATTTAATAATGGA-CTTTTTA
1 TTTATTTTGTTTCTTAA--TATTT-TTATTTAATTATGGATTTTTTTA
* *
760532 TTTATTTTATTTCTTAATGTTTTTATT
1 TTTATTTTGTTTCTTAATATTTTTATT
760559 ATTTAATTGT
Statistics
Matches: 109, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
44 5 0.05
45 65 0.60
47 26 0.24
48 13 0.12
ACGTcount: A:0.21, C:0.03, G:0.07, T:0.69
Consensus pattern (45 bp):
TTTATTTTGTTTCTTAATATTTTTATTTAATTATGGATTTTTTTA
Found at i:760586 original size:92 final size:85
Alignment explanation
Indices: 760350--760575 Score: 258
Period size: 92 Copynumber: 2.6 Consensus size: 85
760340 GATAAACTTG
* * *
760350 TTTTTATTTATCTTGTTTCTTAATTTTTT-TTATTTAATTATTGACTTTATTTTGTTTCTTAATA
1 TTTTTATTTATTTTGTTTCTTAATTTTTTATTATTTAATTTTTGAATTTATTTTGTTTCTTAATA
* *
760414 TTTTTATTTAATTATGGATT
66 TTTTTATTTAATAATGGATC
* **
760434 TTTTTATTTATTTTGTTTCTTAATATTTTTATTTAATTTTGGATTTTTTTATTTATTTTGTTTCT
1 TTTTTATTTATTTTGTTTCTTAAT-TTTTTA-TT-A-TTT-AATTTTTGAATTTATTTTGTTTCT
*
760499 TAATGTTTTTATTATTTAATAATGGA-C
61 TAA--TATTT-TTATTTAATAATGGATC
*
760526 TTTTTATTTATTTTATTTCTTAATGTTTTTATTATTTAATTGTTTGAATT
1 TTTTTATTTATTTTGTTTCTTAAT-TTTTTATTATTTAATT-TTTGAATT
760576 GTAATGTTTG
Statistics
Matches: 118, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
84 23 0.19
85 5 0.04
87 2 0.02
88 4 0.03
89 12 0.10
90 23 0.19
91 2 0.02
92 33 0.28
93 14 0.12
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.68
Consensus pattern (85 bp):
TTTTTATTTATTTTGTTTCTTAATTTTTTATTATTTAATTTTTGAATTTATTTTGTTTCTTAATA
TTTTTATTTAATAATGGATC
Found at i:760590 original size:47 final size:47
Alignment explanation
Indices: 760494--760590 Score: 106
Period size: 47 Copynumber: 2.1 Consensus size: 47
760484 ATTTATTTTG
* * * * *
760494 TTTCTTAATGTTTTTATTATTTAATAATGGACTTTTTATTTATTTTA
1 TTTCTTAATGTTTTTATTATTTAATAATGGAATTGTAATGTATTGTA
** *
760541 TTTCTTAATGTTTTTATTATTTAATTGTTTGAATTGTAATGT-TTGTA
1 TTTCTTAATGTTTTTATTATTTAA-TAATGGAATTGTAATGTATTGTA
760588 TTT
1 TTT
760591 AATTTTGTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
47 31 0.76
48 10 0.24
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.64
Consensus pattern (47 bp):
TTTCTTAATGTTTTTATTATTTAATAATGGAATTGTAATGTATTGTA
Found at i:762534 original size:29 final size:29
Alignment explanation
Indices: 762501--762556 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
762491 GCGCTTTGTC
762501 AGAAAGGGTGC-TAGATCA-GTAATATTTGG
1 AGAAAGGGTGCAT-GAT-AGGTAATATTTGG
762530 AGAAAGGGTGCATGATAGGTAATATTT
1 AGAAAGGGTGCATGATAGGTAATATTT
762557 CGTTGTTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 1 0.04
29 23 0.92
30 1 0.04
ACGTcount: A:0.36, C:0.05, G:0.30, T:0.29
Consensus pattern (29 bp):
AGAAAGGGTGCATGATAGGTAATATTTGG
Found at i:763593 original size:2 final size:2
Alignment explanation
Indices: 763586--763614 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
763576 TAACAGTTTC
763586 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
763615 TATTGTTACA
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:764065 original size:36 final size:37
Alignment explanation
Indices: 764032--764100 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 37
764022 TACAAATTGT
*
764032 AAAATATTTATAT-ATTTTCTTTA-AAATTTAAATTC
1 AAAATATTTATATAATTTTCTTTACAAAATTAAATTC
* *
764067 ATAATATTTATATAATTTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTCTTTACAAAATTAAA
764101 AATATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 12 0.41
36 9 0.31
37 8 0.28
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (37 bp):
AAAATATTTATATAATTTTCTTTACAAAATTAAATTC
Found at i:766159 original size:22 final size:21
Alignment explanation
Indices: 766117--766159 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
766107 TGAAATGGTG
*
766117 AAATTGTTATATAATCCTTTT
1 AAATTGTTATATAATCATTTT
*
766138 AAATATGTTATATATTCATTTT
1 AAAT-TGTTATATAATCATTTT
766160 GTACAAGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (21 bp):
AAATTGTTATATAATCATTTT
Found at i:769653 original size:14 final size:14
Alignment explanation
Indices: 769634--769660 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
769624 GATATTACTA
769634 TTATATATATATAG
1 TTATATATATATAG
769648 TTATATATATATA
1 TTATATATATATA
769661 TATATAAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
TTATATATATATAG
Found at i:772368 original size:23 final size:21
Alignment explanation
Indices: 772309--772423 Score: 103
Period size: 21 Copynumber: 5.6 Consensus size: 21
772299 TATACGGTTA
* *
772309 TTAGGGACATATATTTGGTCC
1 TTAGGGACATTTATGTGGTCC
* *
772330 TT-TGGA-A-ATATGTGGTCC
1 TTAGGGACATTTATGTGGTCC
772348 TTAGGGACAATTTTATGTGGTCC
1 TTAGGGAC-A-TTTATGTGGTCC
*
772371 TTCGGGACATTTATGTGGTCC
1 TTAGGGACATTTATGTGGTCC
* * *
772392 TT-CGGACATATATGTGGTCA
1 TTAGGGACATTTATGTGGTCC
*
772412 TTCGGGACATTT
1 TTAGGGACATTT
772424 TCTACGCGGT
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
18 12 0.15
19 4 0.05
20 20 0.26
21 24 0.31
22 1 0.01
23 17 0.22
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (21 bp):
TTAGGGACATTTATGTGGTCC
Found at i:772385 original size:21 final size:21
Alignment explanation
Indices: 772338--772423 Score: 120
Period size: 21 Copynumber: 4.0 Consensus size: 21
772328 CCTTTGGAAA
*
772338 TATGTGGTCCTTAGGGACAATTT
1 TATGTGGTCCTTCGGGAC-A-TT
772361 TATGTGGTCCTTCGGGACATT
1 TATGTGGTCCTTCGGGACATT
*
772382 TATGTGGTCCTTC-GGACATA
1 TATGTGGTCCTTCGGGACATT
*
772402 TATGTGGTCATTCGGGACATT
1 TATGTGGTCCTTCGGGACATT
772423 T
1 T
772424 TCTACGCGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.31
21 22 0.38
22 1 0.02
23 17 0.29
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.38
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACATT
Found at i:772406 original size:41 final size:42
Alignment explanation
Indices: 772313--772423 Score: 122
Period size: 41 Copynumber: 2.7 Consensus size: 42
772303 CGGTTATTAG
* * * *
772313 GGACATATATTTGGTCCTT-TGGA-A-ATATGTGGTCCTTAG
1 GGACATATATGTGGTCCTTCGGGACATTTATGTGGTCCTTAC
*
772352 GGACAATTTTATGTGGTCCTTCGGGACATTTATGTGGTCCTT-C
1 GGAC-A-TATATGTGGTCCTTCGGGACATTTATGTGGTCCTTAC
*
772395 GGACATATATGTGGTCATTCGGGACATTT
1 GGACATATATGTGGTCCTTCGGGACATTT
772424 TCTACGCGGT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
39 4 0.07
40 1 0.02
41 34 0.57
42 4 0.07
43 5 0.08
44 12 0.20
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (42 bp):
GGACATATATGTGGTCCTTCGGGACATTTATGTGGTCCTTAC
Found at i:773251 original size:20 final size:20
Alignment explanation
Indices: 773147--773263 Score: 66
Period size: 20 Copynumber: 5.8 Consensus size: 20
773137 AAAATGTTAT
* *
773147 ATAAAA-AATAATAATAATA
1 ATAAAATAAAAATAAAAATA
**
773166 AT-AAATAAAAA-AGGAA-A
1 ATAAAATAAAAATAAAAATA
*
773183 ATAAAAT-AAAATAAAGATA
1 ATAAAATAAAAATAAAAATA
*
773202 TATTAAATAAATCAAAGTAAAAA-A
1 -ATAAAAT-AA--AAA-TAAAAATA
*
773226 TGTAAAATAAAAATAAAAATA
1 -ATAAAATAAAAATAAAAATA
*
773247 ATAAAATAATAATAAAA
1 ATAAAATAAAAATAAAA
773264 TAACGAATCA
Statistics
Matches: 75, Mismatches: 12, Indels: 21
0.69 0.11 0.19
Matches are distributed among these distances:
17 7 0.09
18 12 0.16
19 7 0.09
20 27 0.36
21 4 0.05
22 1 0.01
23 2 0.03
24 10 0.13
25 5 0.07
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (20 bp):
ATAAAATAAAAATAAAAATA
Found at i:773254 original size:44 final size:42
Alignment explanation
Indices: 773101--773255 Score: 113
Period size: 44 Copynumber: 3.6 Consensus size: 42
773091 TAAATCAAGG
* * * *
773101 AAATAACA-AAAAATAAAAAAAATAAATCAAAAGGGAAAAATGTT
1 AAATAAAATAAAAAT-AATAAAATAAATC-AAA-GAAAAAATGTA
* * *
773145 ATATAAAA-AATAATAATAATAATAAAT-AAA-AAAGGAAA-ATA
1 AAATAAAATAAAAATAATAA-AATAAATCAAAGAAA--AAATGTA
* *
773186 AAATAAAATAAAGATATATTAAATAAATCAAAGTAAAAAATGTA
1 AAATAAAATAAAAATA-ATAAAATAAATCAAAG-AAAAAATGTA
773230 AAATAAAAATAAAAATAATAAAATAA
1 AAAT-AAAATAAAAATAATAAAATAA
773256 TAATAAAATA
Statistics
Matches: 87, Mismatches: 14, Indels: 20
0.72 0.12 0.17
Matches are distributed among these distances:
40 2 0.02
41 8 0.09
42 18 0.21
43 13 0.15
44 32 0.37
45 14 0.16
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.21
Consensus pattern (42 bp):
AAATAAAATAAAAATAATAAAATAAATCAAAGAAAAAATGTA
Found at i:773266 original size:55 final size:54
Alignment explanation
Indices: 773211--773318 Score: 139
Period size: 55 Copynumber: 1.9 Consensus size: 54
773201 ATATTAAATA
773211 AATCAAAGTAAA-AAATGTAAAATAAAAATAAAAATAATAAAATAATAATAAAATAAC
1 AATCAAAG-AAAGAAA-G-AAAAT-AAAATAAAAATAATAAAATAATAATAAAATAAC
*
773268 GAATCAAAGAAAGAAAGAAAATAAGAT-AAAATAGATAAAATAATAATAAAA
1 -AATCAAAGAAAGAAAGAAAATAAAATAAAAATA-ATAAAATAATAATAAAA
773319 AATAAATAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
54 6 0.13
55 21 0.45
56 5 0.11
57 4 0.09
58 11 0.23
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (54 bp):
AATCAAAGAAAGAAAGAAAATAAAATAAAAATAATAAAATAATAATAAAATAAC
Found at i:773318 original size:11 final size:10
Alignment explanation
Indices: 773147--773335 Score: 64
Period size: 11 Copynumber: 17.1 Consensus size: 10
773137 AAAATGTTAT
773147 ATAAAAAATA
1 ATAAAAAATA
773157 ATAATAATAATAA
1 ATAA-AA-AAT-A
*
773170 ATAAAAAAGGA
1 ATAAAAAA-TA
773181 A-AATAAAATA
1 ATAA-AAAATA
773191 A-AATAAAGATA
1 ATAA-AAA-ATA
773202 TATTAAATAAATCAA
1 -A-TAAA-AAAT--A
773217 AGTAAAAAAT-
1 A-TAAAAAATA
* *
773227 GTAAAATAAAA
1 ATAAAA-AATA
773238 AT-AAAAATA
1 ATAAAAAATA
773247 ATAAAATAATA
1 ATAAAA-AATA
*
773258 ATAAAATAACGA
1 ATAAAA-AA-TA
*
773270 ATCAAAGAAAGA
1 AT-AAA-AAATA
*
773282 A-AGAAAATA
1 ATAAAAAATA
* *
773291 AGATAAAATA
1 ATAAAAAATA
773301 GATAAAATAATA
1 -ATAAAA-AATA
773313 ATAAAAAATAA
1 ATAAAAAAT-A
773324 ATAAATAAATA
1 ATAAA-AAATA
773335 A
1 A
773336 CATATTTAAA
Statistics
Matches: 142, Mismatches: 13, Indels: 47
0.70 0.06 0.23
Matches are distributed among these distances:
9 15 0.11
10 34 0.24
11 45 0.32
12 20 0.14
13 17 0.12
14 10 0.07
15 1 0.01
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.21
Consensus pattern (10 bp):
ATAAAAAATA
Found at i:773387 original size:7 final size:6
Alignment explanation
Indices: 773377--773478 Score: 59
Period size: 6 Copynumber: 17.5 Consensus size: 6
773367 TATGTTTAGA
* * *
773377 ACATAGT ACATAT ACATAT --ATAT A-ATAT ATATAT ATATAT ATATAT
1 ACATA-T ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
* * * * * * * *
773423 A-ATAA ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
*
773470 ATATAT ACA
1 ACATAT ACA
773479 AGAGATATAA
Statistics
Matches: 89, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.04
5 9 0.10
6 71 0.80
7 5 0.06
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (6 bp):
ACATAT
Found at i:773399 original size:2 final size:2
Alignment explanation
Indices: 773386--773476 Score: 150
Period size: 2 Copynumber: 46.5 Consensus size: 2
773376 AACATAGTAC
*
773386 AT AT AC AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
773426 AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
773468 AT AT AT AT A
1 AT AT AT AT A
773477 CAAGAGATAT
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
1 2 0.02
2 81 0.98
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:775676 original size:15 final size:15
Alignment explanation
Indices: 775638--775676 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
775628 TATACTTTTG
*
775638 AACTTGTGGGATATA
1 AACTTGTGTGATATA
* *
775653 AACTTGTGTGATGTC
1 AACTTGTGTGATATA
775668 AACTTGTGT
1 AACTTGTGT
775677 TTAACCTAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (15 bp):
AACTTGTGTGATATA
Found at i:775827 original size:38 final size:37
Alignment explanation
Indices: 775748--775917 Score: 200
Period size: 37 Copynumber: 4.5 Consensus size: 37
775738 TATAACATTG
* * *
775748 TATTTCAATCTAATATAAATTTGTAATAATATATTCA
1 TATTTTAATCGAATATAAATTTGTAATAATATATTCT
* *
775785 TATTTTAATTGAATATAAATTCATG-AATAATATATTCG
1 TATTTTAATCGAATATAAATT--TGTAATAATATATTCT
* *
775823 TA-TTTAATCAAATATAAATTTATAAATAATATATTCT
1 TATTTTAATCGAATATAAATTTGT-AATAATATATTCT
* *
775860 TATTTCAATCGAATATAAATTTGTAATAATAAATTCTT
1 TATTTTAATCGAATATAAATTTGTAATAATATATTC-T
*
775898 TATTTTAATTGAATATAAAT
1 TATTTTAATCGAATATAAAT
775918 ATTTAAATAA
Statistics
Matches: 113, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
35 1 0.01
37 59 0.52
38 51 0.45
39 2 0.02
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (37 bp):
TATTTTAATCGAATATAAATTTGTAATAATATATTCT
Found at i:775939 original size:38 final size:38
Alignment explanation
Indices: 775748--775939 Score: 169
Period size: 37 Copynumber: 5.1 Consensus size: 38
775738 TATAACATTG
* * * * *
775748 TATTTCAATCTAATATAAATTTGT-AATAATATATTCA
1 TATTTTAATCGAATATAAATTTATAAATAATATAATCT
* * * * *
775785 TATTTTAATTGAATATAAATTCATGAATAATATATTCG
1 TATTTTAATCGAATATAAATTTATAAATAATATAATCT
* *
775823 TA-TTTAATCAAATATAAATTTATAAATAATATATTCT
1 TATTTTAATCGAATATAAATTTATAAATAATATAATCT
* *
775860 TATTTCAATCGAATATAAATTTGT-AATAATA-AATTCTT
1 TATTTTAATCGAATATAAATTTATAAATAATATAA-TC-T
* * *
775898 TATTTTAATTGAATATAAATATT-TAAATAATAGAATAT
1 TATTTTAATCGAATATAAAT-TTATAAATAATATAATCT
775936 TATT
1 TATT
775940 AATATTCGAA
Statistics
Matches: 130, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
36 1 0.01
37 60 0.46
38 57 0.44
39 10 0.08
40 2 0.02
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (38 bp):
TATTTTAATCGAATATAAATTTATAAATAATATAATCT
Found at i:778358 original size:12 final size:12
Alignment explanation
Indices: 778341--778365 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
778331 CCACCGTCAC
778341 CCTCATTATCTT
1 CCTCATTATCTT
778353 CCTCATTATCTT
1 CCTCATTATCTT
778365 C
1 C
778366 TCTTAAGTAC
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:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (12 bp):
CCTCATTATCTT
Found at i:779246 original size:12 final size:12
Alignment explanation
Indices: 779224--779261 Score: 67
Period size: 12 Copynumber: 3.1 Consensus size: 12
779214 GTGAAGTTCT
779224 TAAGAGAAGATAA
1 TAAG-GAAGATAA
779237 TAAGGAAGATAA
1 TAAGGAAGATAA
779249 TAAGGAAGATAA
1 TAAGGAAGATAA
779261 T
1 T
779262 GAGGGTGACG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (12 bp):
TAAGGAAGATAA
Found at i:781048 original size:17 final size:17
Alignment explanation
Indices: 781026--781058 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
781016 TTCAAATATA
781026 TATTTATAAA-ATTTAAT
1 TATTTA-AAATATTTAAT
781043 TATTTAAAATATTTAA
1 TATTTAAAATATTTAA
781059 AATAATCGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTTAAAATATTTAAT
Found at i:788322 original size:7 final size:7
Alignment explanation
Indices: 788313--788371 Score: 93
Period size: 7 Copynumber: 8.6 Consensus size: 7
788303 TTCATCTTCT
*
788313 CTTCTCT
1 CTTCTCC
*
788320 CTTCTCT
1 CTTCTCC
788327 CTTCTCC
1 CTTCTCC
788334 CTTCTCC
1 CTTCTCC
788341 CTTCTCC
1 CTTCTCC
788348 CTTCTCC
1 CTTCTCC
788355 CTTCTCC
1 CTTCTCC
788362 C-TCTCC
1 CTTCTCC
788368 CTTC
1 CTTC
788372 ACATTCATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
6 6 0.12
7 44 0.88
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (7 bp):
CTTCTCC
Found at i:789162 original size:19 final size:20
Alignment explanation
Indices: 789135--789179 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
789125 GGTTATACTA
*
789135 TTGATACTAGA-GCTCGGTG
1 TTGAGACTAGATGCTCGGTG
* *
789154 TTGAGACTAGATGCTTGGTT
1 TTGAGACTAGATGCTCGGTG
789174 TTGAGA
1 TTGAGA
789180 TTCCTGGTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.22, C:0.11, G:0.31, T:0.36
Consensus pattern (20 bp):
TTGAGACTAGATGCTCGGTG
Found at i:795361 original size:19 final size:18
Alignment explanation
Indices: 795337--795399 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
795327 TTTTGATATT
795337 GATACTCAGGGTGAGTATC
1 GATACTCAGGGT-AGTATC
* *
795356 GATACTCAGGGTCTGTATA
1 GATACTCAGGGT-AGTATC
*
795375 GATACTGCAGGCATAGTATC
1 GATACT-CAGG-GTAGTATC
795395 GATAC
1 GATAC
795400 CACAATCATG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 22 0.61
20 13 0.36
21 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (18 bp):
GATACTCAGGGTAGTATC
Found at i:796696 original size:21 final size:22
Alignment explanation
Indices: 796672--796712 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
796662 ATGTGAACAT
796672 ATGTGTTTG-AGATTA-ATGAAA
1 ATGT-TTTGAAGATTATATGAAA
796693 ATGTTTTGAAGATTATATGA
1 ATGTTTTGAAGATTATATGA
796713 GTAAAATGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (22 bp):
ATGTTTTGAAGATTATATGAAA
Found at i:796787 original size:18 final size:19
Alignment explanation
Indices: 796752--796788 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
796742 CACGGAATGG
796752 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
796772 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
796789 GGATTACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:798047 original size:4 final size:4
Alignment explanation
Indices: 798038--798067 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
798028 GATACAATAC
798038 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
798068 CAATGCTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:799061 original size:19 final size:20
Alignment explanation
Indices: 799034--799078 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
799024 TAAATTTAAT
799034 CATAATTG-TTTTTTTAAAA
1 CATAATTGTTTTTTTTAAAA
*
799053 CATAGTTGTTTTTTTTAAAA
1 CATAATTGTTTTTTTTAAAA
*
799073 AATAAT
1 CATAAT
799079 GGTTAGAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (20 bp):
CATAATTGTTTTTTTTAAAA
Found at i:799663 original size:9 final size:9
Alignment explanation
Indices: 799649--799694 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
799639 TTTTTATTAC
799649 TATTTTATT
1 TATTTTATT
799658 TATTTTATT
1 TATTTTATT
**
799667 TATTTTACG
1 TATTTTATT
799676 TA-TTTATTT
1 TATTTTA-TT
799685 TATTTTATT
1 TATTTTATT
799694 T
1 T
799695 TAATGATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 4 0.13
9 23 0.74
10 4 0.13
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (9 bp):
TATTTTATT
Found at i:799664 original size:5 final size:5
Alignment explanation
Indices: 799649--799696 Score: 55
Period size: 5 Copynumber: 9.4 Consensus size: 5
799639 TTTTTATTAC
799649 TATTT TA-TT TATTT TA-TT TATTT TACGTATT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TA--T-TT TATTT TATTT TATTT
799695 TA
1 TA
799697 ATGATTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
4 8 0.21
5 24 0.63
6 1 0.03
7 1 0.03
8 4 0.11
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (5 bp):
TATTT
Found at i:799703 original size:23 final size:23
Alignment explanation
Indices: 799654--799696 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
799644 ATTACTATTT
799654 TATTTATTTTA-TTTATTTTACG
1 TATTTATTTTATTTTATTTTACG
799676 TATTTATTTTATTTTATTTTA
1 TATTTATTTTATTTTATTTTA
799697 ATGATTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
TATTTATTTTATTTTATTTTACG
Found at i:803151 original size:36 final size:36
Alignment explanation
Indices: 803100--803324 Score: 290
Period size: 36 Copynumber: 6.3 Consensus size: 36
803090 AAGTTTGCAT
* *
803100 CGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGACACTTC
* * *
803136 CGATTCAAGTAGAACGGAGGGAAACATCGACACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGACACTTC
* * * *
803172 CGATTCAAATCGAATGGAAGGAAGCATCGATACTTT
1 CGATTCAAGTCGAACGGAAGGAAGCATCGACACTTC
*
803208 CGATTCAAGT-GAACGGAATGAAGCATCGACACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGACACTTC
* * *
803243 CGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTT
1 CGATTCAAGTCGAACGGAAGGAAGCATCGACACTTC
* * * *
803279 CGATTCAAATCAAACGGAATGAAGCATCGGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGACACTTC
803315 CGATTCAAGT
1 CGATTCAAGT
803325 GTTCATTTTT
Statistics
Matches: 163, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
35 31 0.19
36 132 0.81
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (36 bp):
CGATTCAAGTCGAACGGAAGGAAGCATCGACACTTC
Found at i:803241 original size:107 final size:107
Alignment explanation
Indices: 803099--803325 Score: 328
Period size: 107 Copynumber: 2.1 Consensus size: 107
803089 AAAGTTTGCA
* *
803099 TCGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCCGATTCAAGTAGAACGGAGGGAAACATC
1 TCGATTCAAGT-GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTAGAACGGAGGGAAACATC
* * *
803164 GACACTTCCGATTCAAATCGAATGGAAGGAAGCATCGATACTT
65 GACACTTCCGATTCAAATCAAACGGAAGGAAGCATCGACACTT
* * *
803207 TCGATTCAAGTGAACGGAATGAAGCATCGACACTTCCGATTCAAGTCGAACGGAGGGAAGCATCG
1 TCGATTCAAGTGAACGGAAGGAAGCATCGACACTTCCGATTCAAGTAGAACGGAGGGAAACATCG
* * * *
803272 GCACTTTCGATTCAAATCAAACGGAATGAAGCATCGGCACTT
66 ACACTTCCGATTCAAATCAAACGGAAGGAAGCATCGACACTT
*
803314 CCGATTCAAGTG
1 TCGATTCAAGTG
803326 TTCATTTTTT
Statistics
Matches: 106, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
107 95 0.90
108 11 0.10
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (107 bp):
TCGATTCAAGTGAACGGAAGGAAGCATCGACACTTCCGATTCAAGTAGAACGGAGGGAAACATCG
ACACTTCCGATTCAAATCAAACGGAAGGAAGCATCGACACTT
Found at i:805334 original size:15 final size:16
Alignment explanation
Indices: 805316--805367 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 16
805306 ATGATGTGAA
805316 GAAAAATGTTCTA-GT
1 GAAAAATGTTCTACGT
805331 GAAAAATGTGATCTACGT
1 GAAAAATGT--TCTACGT
*
805349 G-AAACTGTTCTACGT
1 GAAAAATGTTCTACGT
805364 GAAA
1 GAAA
805368 GTAAACTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 17 0.53
16 2 0.06
17 10 0.31
18 3 0.09
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (16 bp):
GAAAAATGTTCTACGT
Found at i:805554 original size:23 final size:24
Alignment explanation
Indices: 805528--805585 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
805518 ACAATCTATG
*
805528 TGGTCCTTCGGGAC-ATTTCTACA
1 TGGTCCTTCGGGACAAATTCTACA
** *
805551 TGGTTATTCGGGACAAATTCTACG
1 TGGTCCTTCGGGACAAATTCTACA
*
805575 CGGTCCTTCGG
1 TGGTCCTTCGG
805586 AAAAAACCTA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (24 bp):
TGGTCCTTCGGGACAAATTCTACA
Found at i:805607 original size:23 final size:23
Alignment explanation
Indices: 805580--805631 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
805570 CTACGCGGTC
805580 CTTCGGAAAAAACCTATGTGGCA
1 CTTCGGAAAAAACCTATGTGGCA
*** **
805603 CTTCGGTGCAATTCTATGTGGCA
1 CTTCGGAAAAAACCTATGTGGCA
805626 CTTCGG
1 CTTCGG
805632 TGTAAATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (23 bp):
CTTCGGAAAAAACCTATGTGGCA
Found at i:809167 original size:5 final size:5
Alignment explanation
Indices: 809157--809191 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
809147 ATTCTGGATA
809157 CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT
1 CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT
809192 ATTCTCTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CTCTT
Found at i:810466 original size:18 final size:18
Alignment explanation
Indices: 810445--810482 Score: 55
Period size: 15 Copynumber: 2.3 Consensus size: 18
810435 CATAAATGAT
810445 GTGAAGAAAAATGTTCTA
1 GTGAAGAAAAATGTTCTA
810463 GT---GAAAAATGTTCTA
1 GTGAAGAAAAATGTTCTA
810478 GTGAA
1 GTGAA
810483 AAATGTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 6
0.74 0.00 0.26
Matches are distributed among these distances:
15 15 0.88
18 2 0.12
ACGTcount: A:0.42, C:0.05, G:0.24, T:0.29
Consensus pattern (18 bp):
GTGAAGAAAAATGTTCTA
Found at i:810485 original size:16 final size:15
Alignment explanation
Indices: 810450--810488 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
810440 ATGATGTGAA
810450 GAAAAATGTTCTAGT
1 GAAAAATGTTCTAGT
810465 GAAAAATGTTCTAGT
1 GAAAAATGTTCTAGT
810480 GAAAAATGT
1 GAAAAATGT
810489 GATATATGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (15 bp):
GAAAAATGTTCTAGT
Found at i:810702 original size:23 final size:23
Alignment explanation
Indices: 810661--810739 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
810651 TACGCAGTCT
* *
810661 TTCGTGACAA-TCTATGTGGTCC
1 TTCGGGACAATTCTACGTGGTCC
*
810683 TTCGGGACATTTCTACGTGGTCC
1 TTCGGGACAATTCTACGTGGTCC
* **
810706 TTCAGGGAAAATTCTACACGGTCC
1 TTC-GGGACAATTCTACGTGGTCC
810730 TTCGGGACAA
1 TTCGGGACAA
810740 ACCTATGTGG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 8 0.17
23 20 0.43
24 19 0.40
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (23 bp):
TTCGGGACAATTCTACGTGGTCC
Found at i:810720 original size:24 final size:23
Alignment explanation
Indices: 810671--810736 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
810661 TTCGTGACAA
* * *
810671 TCTATGTGGTCCTTCGGGACATT
1 TCTACGTGGTCCTTCGGGAAAAT
810694 TCTACGTGGTCCTTCAGGGAAAAT
1 TCTACGTGGTCCTTC-GGGAAAAT
**
810718 TCTACACGGTCCTTCGGGA
1 TCTACGTGGTCCTTCGGGA
810737 CAAACCTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGAAAAT
Found at i:810755 original size:23 final size:23
Alignment explanation
Indices: 810729--810786 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
810719 CTACACGGTC
810729 CTTCGG-GACAAACCTATGTGGCA
1 CTTCGGTG-CAAACCTATGTGGCA
**
810752 CTTCGGTGCAATTCTATGTGGCA
1 CTTCGGTGCAAACCTATGTGGCA
810775 CTTCGGTGCAAA
1 CTTCGGTGCAAA
810787 TTATGTGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
CTTCGGTGCAAACCTATGTGGCA
Found at i:811698 original size:17 final size:17
Alignment explanation
Indices: 811663--811718 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
811653 AAAGTATTAA
*
811663 AAAAAAATAATAATGAAT
1 AAAAAAATAAAAAT-AAT
*
811681 AAAAAAACAAAAATAAT
1 AAAAAAATAAAAATAAT
*
811698 AAAAAAATATAAATATAT
1 AAAAAAATAAAAATA-AT
811716 AAA
1 AAA
811719 GTTATAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 16 0.48
18 17 0.52
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAAAAATAAAAATAAT
Found at i:811995 original size:18 final size:17
Alignment explanation
Indices: 811974--812016 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
811964 ATATATACAT
811974 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
811992 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
812009 ATAA-AATA
1 ATAATAATA
812017 TTCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:811995 original size:56 final size:55
Alignment explanation
Indices: 811897--812004 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 55
811887 ATATTAAAGA
*
811897 AATATATATATATATATAATAATAAAATATAGTAAAAAAATAAATGAAAATAATTT
1 AATATATATATATATATAATAATAAAATATAGTAAAAAAAT-AATAAAAATAATTT
**
811953 AATATATATATATATATACAT-ATAATAATA-A-TAACATGAATAATAAAAATAA
1 AATATATATATATATATA-ATAATAA-AATATAGTAA-AAAAATAATAAAAATAA
812005 ATGAATAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
55 13 0.28
56 27 0.59
57 6 0.13
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (55 bp):
AATATATATATATATATAATAATAAAATATAGTAAAAAAATAATAAAAATAATTT
Found at i:812024 original size:60 final size:59
Alignment explanation
Indices: 811898--812017 Score: 145
Period size: 62 Copynumber: 2.0 Consensus size: 59
811888 TATTAAAGAA
* * *
811898 ATATATATATATATATAATAATAAAATATAGTAAAAAAATAAATGAAAATAATTTAATATAT
1 ATATATATATACATATAATAATAAAACATAATAAAAAAATAAATG-AAATAA--TAATATAT
811960 ATATATATATACATATAATAATAATAACATGAATAATAAAAATAAATG-AATAA-AATAT
1 ATATATATATACATATAATAATAA-AACAT-AATAA-AAAAATAAATGAAATAATAATAT
812018 TCATATAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
60 5 0.10
62 23 0.44
63 9 0.17
64 4 0.08
65 11 0.21
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (59 bp):
ATATATATATACATATAATAATAAAACATAATAAAAAAATAAATGAAATAATAATATAT
Found at i:813237 original size:105 final size:106
Alignment explanation
Indices: 813018--813473 Score: 648
Period size: 105 Copynumber: 4.3 Consensus size: 106
813008 CATTGTTCCA
* * * ** *
813018 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* *
813083 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * * *
813124 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGATAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* * *
813188 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
*
813229 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
813293 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-G
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
813333 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTGGACAA
1 -AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
813398 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
813440 AGTGCCACGATATCCTCCGTTGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
813474 CGCGGATGGC
Statistics
Matches: 319, Mismatches: 25, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
104 1 0.00
105 196 0.61
106 95 0.30
107 4 0.01
109 23 0.07
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
Found at i:814250 original size:65 final size:65
Alignment explanation
Indices: 814077--814530 Score: 284
Period size: 65 Copynumber: 6.7 Consensus size: 65
814067 AAGATATATG
* * * **
814077 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
814142 TT
64 TT
* * * *
814144 TGTGTTTCAATAGTAATTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
814209 T
65 T
* ** * * *
814210 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
* *
814275 ACAAA-ACT
57 TCAAAGATT
* * * * * * * * * * *
814283 TAGTTCCAAAAGCAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * * * *
814348 TTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
*
814413 ACAAA-ATT
57 TCAAAGATT
* * * * * * *** *
814421 TTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
814485 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAA
814531 AAAAGCAATC
Statistics
Matches: 298, Mismatches: 67, Indels: 46
0.73 0.16 0.11
Matches are distributed among these distances:
64 11 0.04
65 121 0.41
66 4 0.01
67 24 0.08
68 31 0.10
70 1 0.00
72 2 0.01
73 94 0.32
74 10 0.03
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:814261 original size:36 final size:36
Alignment explanation
Indices: 814209--814471 Score: 254
Period size: 36 Copynumber: 7.4 Consensus size: 36
814199 ATTCAAAGAT
* *
814209 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
814245 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * * *
814281 CTTAGTTCCAAAAGCAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * * *
814318 TTTGTTTCAAAGAAAACATAT-TC-----A-A-ATAT
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
*
814347 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
814383 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
814419 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
814456 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
814472 TGTTTTCAAT
Statistics
Matches: 184, Mismatches: 32, Indels: 22
0.77 0.13 0.09
Matches are distributed among these distances:
28 2 0.01
29 17 0.09
30 1 0.01
31 1 0.01
34 1 0.01
35 1 0.01
36 97 0.53
37 64 0.35
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:814341 original size:138 final size:138
Alignment explanation
Indices: 814161--814530 Score: 472
Period size: 138 Copynumber: 2.7 Consensus size: 138
814151 CAATAGTAAT
* * * *
814161 TGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGAAAC
* *
814226 TGTCTCAAGATAGACGAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA
66 TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA
*
814291 AAAGCAAC
131 AAAGAAAC
* * * * *
814299 TGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGAAAT
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGAAAC
* * * * * *
814364 TGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCA
66 TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA
**
814429 AGGGAAAC
131 AAAGAAAC
* * * * * * *
814437 TATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAGAAA
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTT-TGTTTCAAGGGAAA
*
814501 CTGTCTCAAGGGAGACAAAATTTGTTTTAA
65 CTGTCTCAAGAGAGACAAAATTTGTTTTAA
814531 AAAAGCAATC
Statistics
Matches: 196, Mismatches: 35, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
137 3 0.02
138 193 0.98
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (138 bp):
TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGAAAC
TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA
AAAGAAAC
Found at i:814378 original size:102 final size:102
Alignment explanation
Indices: 814245--814429 Score: 264
Period size: 102 Copynumber: 1.8 Consensus size: 102
814235 ATAGACGAAA
* * *
814245 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGCAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAG
*
814310 AGACGAAA-TTTGTTTCAAAGAAAACATATTCAAATAT
65 AGACAAAATTTTGTTTCAAAGAAAACATATTCAAATAT
* * * * **
814347 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
814412 GACAAAATTTTGTTTCAA
66 GACAAAATTTTGTTTCAA
814430 GGGAAACTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
101 26 0.36
102 46 0.64
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (102 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
GACAAAATTTTGTTTCAAAGAAAACATATTCAAATAT
Found at i:814920 original size:18 final size:18
Alignment explanation
Indices: 814893--814928 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
814883 TGTTGAATCC
* *
814893 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
814911 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
814929 TTGATGTTGA
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:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:815354 original size:22 final size:22
Alignment explanation
Indices: 815328--815382 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
815318 TTGTGTTTGG
*
815328 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
815350 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
815372 TCAAATGTTTG
1 TCAAAGGTTTG
815383 ATGGGATAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:816047 original size:23 final size:23
Alignment explanation
Indices: 816012--816069 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
816002 CTTTTTGTCC
*
816012 CTTTTTCTTTTTGATTTTTG-CTCT
1 CTTTTTC-TTTTG-TTCTTGTCTCT
* *
816036 TTTTTTCTTTTGTTCTTGTTTCT
1 CTTTTTCTTTTGTTCTTGTCTCT
816059 CTTTTTCTTTT
1 CTTTTTCTTTT
816070 TTTTTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 5 0.17
23 18 0.62
24 6 0.21
ACGTcount: A:0.02, C:0.16, G:0.07, T:0.76
Consensus pattern (23 bp):
CTTTTTCTTTTGTTCTTGTCTCT
Found at i:816064 original size:34 final size:29
Alignment explanation
Indices: 816026--816112 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 29
816016 TTCTTTTTGA
816026 TTTTTGCTCTTTTTTTCTTTTGTTCTTG-T
1 TTTTTGCTCTTTTTTT-TTTTGTTCTTGCT
** *
816055 TTCTCTTTTTCTTTTTTTTTTT-TTTTTGCT
1 TT-T-TTGCTCTTTTTTTTTTTGTTCTTGCT
*
816085 TTTTTGCTTCTTTTCTTTTTTGTTCTTG
1 TTTTTGC-TCTTTTTTTTTTTGTTCTTG
816113 ATTGGATCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
28 2 0.04
29 20 0.43
30 13 0.28
31 11 0.24
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (29 bp):
TTTTTGCTCTTTTTTTTTTTGTTCTTGCT
Found at i:816072 original size:8 final size:8
Alignment explanation
Indices: 816033--816105 Score: 69
Period size: 8 Copynumber: 9.0 Consensus size: 8
816023 TGATTTTTGC
816033 TCTTTTTT
1 TCTTTTTT
*
816041 TCTTTTGT
1 TCTTTTTT
*
816049 TCTTGTTTC
1 TCTT-TTTT
816058 TCTTTTTCT
1 TCTTTTT-T
816067 T-TTTTTT
1 TCTTTTTT
816074 T-TTTTTT
1 TCTTTTTT
816081 TGCTTTTTT
1 T-CTTTTTT
* *
816090 GCTTCTTT
1 TCTTTTTT
816098 TCTTTTTT
1 TCTTTTTT
816106 GTTCTTGATT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
7 9 0.17
8 31 0.58
9 13 0.25
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (8 bp):
TCTTTTTT
Found at i:819952 original size:17 final size:18
Alignment explanation
Indices: 819930--819968 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
819920 ATAATAATGA
819930 ATAAAAAAAAACA-AAAT
1 ATAAAAAAAAACATAAAT
* *
819947 ATAAAAAATAATATAAAT
1 ATAAAAAAAAACATAAAT
819965 ATAA
1 ATAA
819969 GTTATAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (18 bp):
ATAAAAAAAAACATAAAT
Found at i:820157 original size:21 final size:21
Alignment explanation
Indices: 820133--820173 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
820123 CTATAAGTAA
*
820133 ATATTAAAGAAATATATATAT
1 ATATTAAAGAAATAAATATAT
* *
820154 ATATTATATAAATAAATATA
1 ATATTAAAGAAATAAATATA
820174 GTAAAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
ATATTAAAGAAATAAATATAT
Found at i:820245 original size:18 final size:17
Alignment explanation
Indices: 820222--820264 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
820212 ATATATATAC
820222 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
820240 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
820257 ATAA-AATA
1 ATAATAATA
820265 TTCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:821890 original size:13 final size:12
Alignment explanation
Indices: 821861--821894 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
821851 CCTTCCTACA
*
821861 AATTTTATTTTT
1 AATTTTATTTCT
821873 AATTTTATGTTCT
1 AATTTTAT-TTCT
821886 AATTTTATT
1 AATTTTATT
821895 AGCAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (12 bp):
AATTTTATTTCT
Found at i:824487 original size:22 final size:24
Alignment explanation
Indices: 824451--824500 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
824441 TTAGTGGATT
* *
824451 TTGAAGGATGGTATCGGTACTG-G
1 TTGAAGGAGGGTATCGATACTGAG
824474 TTGAA-GAGGGTATCGATACTGAG
1 TTGAAGGAGGGTATCGATACTGAG
824497 TTGA
1 TTGA
824501 GAGAATCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.26, C:0.08, G:0.36, T:0.30
Consensus pattern (24 bp):
TTGAAGGAGGGTATCGATACTGAG
Found at i:825205 original size:23 final size:23
Alignment explanation
Indices: 825177--825252 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
825167 TCGGGACAAT
*
825177 TATGTGGCATTTCGGTGCAAACA
1 TATGTGGCACTTCGGTGCAAACA
*
825200 TATGTGGCACTTCGGTGCAAACT
1 TATGTGGCACTTCGGTGCAAACA
*
825223 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACA
825246 TATGTGG
1 TATGTGG
825253 TCCTTTGGGA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAAACA
Found at i:831437 original size:2 final size:2
Alignment explanation
Indices: 831430--831517 Score: 151
Period size: 2 Copynumber: 44.5 Consensus size: 2
831420 AATGAAAACA
* *
831430 AT AT AT AT AT AT AT AT AT CT -T AT AT AT AT AT AG 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
831471 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
831513 AT AT A
1 AT AT A
831518 AACACTGTAA
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
1 1 0.01
2 81 0.99
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:833481 original size:102 final size:102
Alignment explanation
Indices: 833334--833547 Score: 392
Period size: 102 Copynumber: 2.1 Consensus size: 102
833324 TTGAATCAAA
*
833334 AGAAAATTAAAAAAAAAAGGAAATGAAAACTCGAGAGACGACAATACTTAGATCGTCGTTTCAAG
1 AGAAAATT-AAAAAAAAAGGAAATGAAAACCCGAGAGACGACAATACTTAGATCGTCGTTTCAAG
*
833399 TGATACTTCGAAAGAAAAACTCGATAATCACTCTAAAG
65 TGATACTTAGAAAGAAAAACTCGATAATCACTCTAAAG
*
833437 AGAAAATTAAAAAAGAAGGAAATGAAAACCCGAGAGACGACAATACTTAGATCGTCGTTTCAAGT
1 AGAAAATTAAAAAAAAAGGAAATGAAAACCCGAGAGACGACAATACTTAGATCGTCGTTTCAAGT
833502 GATACTTAGAAAGAAAAACTCGATAATCACTCTAAAG
66 GATACTTAGAAAGAAAAACTCGATAATCACTCTAAAG
833539 AGAAAATTA
1 AGAAAATTA
833548 TACATGATAA
Statistics
Matches: 108, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
102 100 0.93
103 8 0.07
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (102 bp):
AGAAAATTAAAAAAAAAGGAAATGAAAACCCGAGAGACGACAATACTTAGATCGTCGTTTCAAGT
GATACTTAGAAAGAAAAACTCGATAATCACTCTAAAG
Found at i:833694 original size:15 final size:16
Alignment explanation
Indices: 833668--833697 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
833658 CAGTCCGTGG
833668 GCCTTAATTCATTTTA
1 GCCTTAATTCATTTTA
833684 GCCTT-ATTCATTTT
1 GCCTTAATTCATTTT
833698 GTCAACATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (16 bp):
GCCTTAATTCATTTTA
Done.