Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 62
Found at i:325834 original size:2 final size:2
Alignment explanation
Indices: 325787--325823 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
325777 ACTTTCGGAC
325787 AT AT -T 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
325824 GACATTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:326148 original size:15 final size:15
Alignment explanation
Indices: 326128--326158 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
326118 ATGTGGACCC
326128 TAAAAATATTTCATT
1 TAAAAATATTTCATT
*
326143 TAAAAATATTTTATT
1 TAAAAATATTTCATT
326158 T
1 T
326159 GTACCTCGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAAAATATTTCATT
Found at i:332552 original size:2 final size:2
Alignment explanation
Indices: 332545--332571 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
332535 ACTCCAATAC
332545 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
332572 GATAGATCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:340631 original size:60 final size:60
Alignment explanation
Indices: 340553--340705 Score: 175
Period size: 60 Copynumber: 2.5 Consensus size: 60
340543 TTCAAATTGG
* * * *
340553 TCCCTAAACTTTTAAACATTTCAATTTCATCCTTAAACTATGA-CTATTATTCTAAA-TCAT
1 TCCC-AAACTTTTGAACATTTCAATTTCATCCTCAAACTATGATCT-TCATCCTAAATTCAT
* * **
340613 TCCTCAAACTTTTGAACATTTCATTTTCATCCTCAAGCTATGATCTTCATCCTAAATTGGT
1 TCC-CAAACTTTTGAACATTTCAATTTCATCCTCAAACTATGATCTTCATCCTAAATTCAT
* *
340674 TCCCAAACTTTTGAATATTTCAATTTTATCCT
1 TCCCAAACTTTTGAACATTTCAATTTCATCCT
340706 AAATTATTCA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
60 71 0.90
61 8 0.10
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (60 bp):
TCCCAAACTTTTGAACATTTCAATTTCATCCTCAAACTATGATCTTCATCCTAAATTCAT
Found at i:340937 original size:60 final size:60
Alignment explanation
Indices: 340837--341021 Score: 228
Period size: 60 Copynumber: 3.1 Consensus size: 60
340827 GATGAATTTG
* * * * * * *
340837 GGGATGAAATT-GAAAGATCTAAAAGTTTAAGGATTGATTTAAAATGATATTCATATTTTA
1 GGGATGAAATTAG-AATATTTAAAAGTTTAAGGACTAATTTAAAATAAGATTCATAGTTTA
*
340897 GGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAGAATAAGATTCATAGTTTA
1 GGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAAAATAAGATTCATAGTTTA
* * * * *
340957 AGAATGAAATTAGAATATTTAAAAATGTAAGGACTAATTTAAAATAAGAGTCATAGTTTA
1 GGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAAAATAAGATTCATAGTTTA
*
341017 AGGAT
1 GGGAT
341022 ATAAGATGCA
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
60 108 0.99
61 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (60 bp):
GGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAAAATAAGATTCATAGTTTA
Found at i:340958 original size:31 final size:31
Alignment explanation
Indices: 340920--341020 Score: 91
Period size: 31 Copynumber: 3.3 Consensus size: 31
340910 AATATTTAAA
340920 AGTTTAAGGACTAATTTAGAATAAGATTCAT
1 AGTTTAAGGACTAATTTAGAATAAGATTCAT
* * * * *
340951 AGTTTAA-GAATGAAATTAGAAT-A-TTTAAA
1 AGTTTAAGGACT-AATTTAGAATAAGATTCAT
* * * *
340980 AATGTAAGGACTAATTTAAAATAAGAGTCAT
1 AGTTTAAGGACTAATTTAGAATAAGATTCAT
341011 AGTTTAAGGA
1 AGTTTAAGGA
341021 TATAAGATGC
Statistics
Matches: 50, Mismatches: 16, Indels: 8
0.68 0.22 0.11
Matches are distributed among these distances:
29 16 0.32
30 8 0.16
31 26 0.52
ACGTcount: A:0.47, C:0.04, G:0.17, T:0.33
Consensus pattern (31 bp):
AGTTTAAGGACTAATTTAGAATAAGATTCAT
Found at i:343677 original size:21 final size:21
Alignment explanation
Indices: 343653--343694 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
343643 TTGATAAAAA
*
343653 ATTATTGAAAATATTATTATT
1 ATTATTGAAAATATTAATATT
**
343674 ATTATTTTAAATATTAATATT
1 ATTATTGAAAATATTAATATT
343695 TTTTAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTATTGAAAATATTAATATT
Found at i:343702 original size:16 final size:18
Alignment explanation
Indices: 343667--343704 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
343657 TTGAAAATAT
*
343667 TATTATTATTATTTTAAA
1 TATTAATATTATTTTAAA
343685 TATTAATATT-TTTT-AA
1 TATTAATATTATTTTAAA
343701 TATT
1 TATT
343705 TCTAATAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 4 0.21
18 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTAATATTATTTTAAA
Found at i:343808 original size:18 final size:18
Alignment explanation
Indices: 343779--343826 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
343769 AGATATGTTA
*
343779 AAAAATTAATAAAAC-GCT
1 AAAAA-TAATAAAACTGAT
343797 AAATAATAATAAAACTGAT
1 AAA-AATAATAAAACTGAT
343816 AAAAATAATAA
1 AAAAATAATAA
343827 TTTTTTTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.23
Consensus pattern (18 bp):
AAAAATAATAAAACTGAT
Found at i:348929 original size:31 final size:31
Alignment explanation
Indices: 348853--348939 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
348843 TTCGATAATA
* * *
348853 TAATAATAATTTTATAGT-ATTTAGATAAATT
1 TAATAATAAATTTATAATCTTTTA-ATAAATT
*
348884 TATTAATAAATTTATAATCTTTTAATAAATT
1 TAATAATAAATTTATAATCTTTTAATAAATT
* *
348915 TAATAAGT-ATTTTATAATTTTTTAA
1 TAATAA-TAAATTTATAATCTTTTAA
348940 AATTTATTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 42 0.89
32 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (31 bp):
TAATAATAAATTTATAATCTTTTAATAAATT
Found at i:348931 original size:20 final size:19
Alignment explanation
Indices: 348886--348928 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
348876 GATAAATTTA
*
348886 TTAATAAATTTATAATCTT
1 TTAATAAATTTATAATATT
348905 TTAATAAATTTAATAAGTATT
1 TTAATAAATTT-ATAA-TATT
348926 TTA
1 TTA
348929 TAATTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 4 0.19
21 6 0.29
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TTAATAAATTTATAATATT
Found at i:349699 original size:31 final size:30
Alignment explanation
Indices: 349664--349750 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
349654 TCAATAAAGT
349664 TTAAAATATTATAAAATACTTATTAAATTTA
1 TTAAAATATTATAAAATA-TTATTAAATTTA
* * *
349695 TTAAAAGATTATAAAATTATTAATACATTTA
1 TTAAAATATTATAAAA-TATTATTAAATTTA
*
349726 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAATATTATAAAAT-ATTATTA
349751 TATTATCGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 43 0.91
32 3 0.06
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.43
Consensus pattern (30 bp):
TTAAAATATTATAAAATATTATTAAATTTA
Found at i:349716 original size:11 final size:10
Alignment explanation
Indices: 349665--349716 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
349655 CAATAAAGTT
349665 TAAAATATTA
1 TAAAATATTA
349675 TAAAATACTTA
1 TAAAATA-TTA
*
349686 TTAAAT-TTA
1 TAAAATATTA
*
349695 TTAAAAGATTA
1 -TAAAATATTA
349706 TAAAATTATTA
1 TAAAA-TATTA
349717 ATACATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
9 3 0.09
10 16 0.47
11 15 0.44
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (10 bp):
TAAAATATTA
Found at i:359841 original size:127 final size:127
Alignment explanation
Indices: 359615--359866 Score: 486
Period size: 127 Copynumber: 2.0 Consensus size: 127
359605 GTAGATTAGA
*
359615 GAAGGTTAGCTGGCATCGTCTTCTGTGGTTTCCAGGCCACATTCCTAAATTCTCATTAATCTCAT
1 GAAGGTTAACTGGCATCGTCTTCTGTGGTTTCCAGGCCACATTCCTAAATTCTCATTAATCTCAT
359680 GGATGACAATTTTAGACAAATTGCCTACAAAAGACAAGCTTGCAAGATTTGGTTTGACTGTT
66 GGATGACAATTTTAGACAAATTGCCTACAAAAGACAAGCTTGCAAGATTTGGTTTGACTGTT
359742 GAAGGTTAACTGGCATCGTCTTCTGTGGTTTCCAGGCCACATTCCTAAATTCTCATTAATCTCAT
1 GAAGGTTAACTGGCATCGTCTTCTGTGGTTTCCAGGCCACATTCCTAAATTCTCATTAATCTCAT
*
359807 GGATGACAATTTTAGACAAATTGCCTACAAAAGACAGGCTTGCAAGATTTGGTTTGACTG
66 GGATGACAATTTTAGACAAATTGCCTACAAAAGACAAGCTTGCAAGATTTGGTTTGACTG
359867 CTGACAATGG
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 123 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (127 bp):
GAAGGTTAACTGGCATCGTCTTCTGTGGTTTCCAGGCCACATTCCTAAATTCTCATTAATCTCAT
GGATGACAATTTTAGACAAATTGCCTACAAAAGACAAGCTTGCAAGATTTGGTTTGACTGTT
Found at i:363837 original size:29 final size:30
Alignment explanation
Indices: 363793--363884 Score: 105
Period size: 35 Copynumber: 2.9 Consensus size: 30
363783 ATATACATTT
**
363793 CAATAATCTTTTATTCCTTT-AACCAAACA
1 CAATAATCTTACATTCCTTTAAACCAAACA
363822 CAATAATCTTACATTCCTGTTAAATCAACCAAACA
1 CAATAATCTTACATTCCT-TT--A--AACCAAACA
363857 CAATAATCTTACATTCCTGTTAAACCAA
1 CAATAATCTTACATTCCT-TTAAACCAA
363885 CCAAACACAA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
29 16 0.29
30 2 0.04
31 6 0.11
33 1 0.02
35 30 0.55
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.33
Consensus pattern (30 bp):
CAATAATCTTACATTCCTTTAAACCAAACA
Found at i:363859 original size:35 final size:35
Alignment explanation
Indices: 363813--363894 Score: 155
Period size: 35 Copynumber: 2.3 Consensus size: 35
363803 TTATTCCTTT
*
363813 AACCAAACACAATAATCTTACATTCCTGTTAAATC
1 AACCAAACACAATAATCTTACATTCCTGTTAAACC
363848 AACCAAACACAATAATCTTACATTCCTGTTAAACC
1 AACCAAACACAATAATCTTACATTCCTGTTAAACC
363883 AACCAAACACAA
1 AACCAAACACAA
363895 AATACAGCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.46, C:0.28, G:0.02, T:0.23
Consensus pattern (35 bp):
AACCAAACACAATAATCTTACATTCCTGTTAAACC
Found at i:366719 original size:42 final size:42
Alignment explanation
Indices: 366645--366727 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
366635 GTCACAATGA
* * * *
366645 TATATGCCCAGTCCTCCACTTCAGATGCCATCTCCTCAGGGG
1 TATATGCCAAGCCCACCACTTCAGATGCCATCTCCGCAGGGG
* * *
366687 TATATGCCAAGCCCACCAGTTCATATGTCATCTCCGCAGGG
1 TATATGCCAAGCCCACCACTTCAGATGCCATCTCCGCAGGG
366728 TTACATTCCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.25
Consensus pattern (42 bp):
TATATGCCAAGCCCACCACTTCAGATGCCATCTCCGCAGGGG
Found at i:366747 original size:21 final size:21
Alignment explanation
Indices: 366721--366771 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
366711 ATGTCATCTC
*
366721 CGCAGGGTTACATTCCTAGCT
1 CGCAGGGTTACATGCCTAGCT
366742 CGCAGGGTTACATGCCTAGCT
1 CGCAGGGTTACATGCCTAGCT
*
366763 CGTAGGGTT
1 CGCAGGGTT
366772 TTATACCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.25, G:0.29, T:0.27
Consensus pattern (21 bp):
CGCAGGGTTACATGCCTAGCT
Found at i:367381 original size:33 final size:34
Alignment explanation
Indices: 367292--367397 Score: 126
Period size: 34 Copynumber: 3.1 Consensus size: 34
367282 ATAAATATTT
367292 TTAAAATACAAATTATAGTATT-AGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCA-AAATTTAAAA
* * *
367326 TTAAAATACAAATAATATTATTCAAAATTTAAAT
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
** * *
367360 TTAAAAT-TTAATTATAGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
367393 TTAAA
1 TTAAA
367398 TTCAAGATTC
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
33 24 0.39
34 36 0.59
35 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.39
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCAAAATTTAAAA
Found at i:367447 original size:70 final size:67
Alignment explanation
Indices: 367302--367447 Score: 163
Period size: 70 Copynumber: 2.1 Consensus size: 67
367292 TTAAAATACA
* *
367302 AATTATAGTATTAGAAATTTAAAATTAAAATACAAATAATATTATTCAAAATTTAAATTTAAAAT
1 AATTATAGTATTAGAAATTTAAAATTAAAATACAAATAATATTATTCAAAATTAAAAGTTAAAAT
367367 TT
66 TT
* * *
367369 AATTATAGTATTCGAAATTTAACATT-AAATTCAAGATTCCAAT-TGTATTCAAAATTAAAAGTT
1 AATTATAGTATTAGAAATTTAAAATTAAAATACAA-A-T--AATAT-TATTCAAAATTAAAAGTT
*
367432 -ATATTT
61 AAAATTT
367438 CAATTATAGT
1 -AATTATAGT
367448 TCACAGTACT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
66 7 0.10
67 25 0.37
68 1 0.01
69 6 0.09
70 28 0.42
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.40
Consensus pattern (67 bp):
AATTATAGTATTAGAAATTTAAAATTAAAATACAAATAATATTATTCAAAATTAAAAGTTAAAAT
TT
Found at i:370794 original size:18 final size:19
Alignment explanation
Indices: 370757--370794 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
370747 TCTTAAACTT
* *
370757 TCTATTATTTTATTATAAA
1 TCTAATATTTTATAATAAA
370776 TCTAATATTTT-TAATAAA
1 TCTAATATTTTATAATAAA
370794 T
1 T
370795 TATCAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTAATATTTTATAATAAA
Found at i:371417 original size:14 final size:14
Alignment explanation
Indices: 371369--371409 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
371359 GGTGTTAGAT
371369 ATTAGGATTTTAAGG
1 ATTAGGA-TTTAAGG
371384 ATTAGGATTTAAGG
1 ATTAGGATTTAAGG
371398 ATTAGGATTTAA
1 ATTAGGATTTAA
371410 AGTTTAGGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (14 bp):
ATTAGGATTTAAGG
Found at i:372315 original size:10 final size:10
Alignment explanation
Indices: 372300--372329 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
372290 GGACCGGCTG
372300 AAAACCGGGA
1 AAAACCGGGA
372310 AAAACCGGGA
1 AAAACCGGGA
*
372320 AAAATCGGGA
1 AAAACCGGGA
372330 TTTTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.30, T:0.03
Consensus pattern (10 bp):
AAAACCGGGA
Found at i:372603 original size:14 final size:14
Alignment explanation
Indices: 372584--372611 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
372574 AAGTGAAAGA
372584 ATAGTTATATAATT
1 ATAGTTATATAATT
372598 ATAGTTATATAATT
1 ATAGTTATATAATT
372612 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:377754 original size:9 final size:10
Alignment explanation
Indices: 377730--377755 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
377720 TTTTATATAA
377730 ATTTTTTATT
1 ATTTTTTATT
377740 ATTTTTTATT
1 ATTTTTTATT
377750 ATTTTT
1 ATTTTT
377756 GATCATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
ATTTTTTATT
Found at i:382879 original size:185 final size:186
Alignment explanation
Indices: 382538--383298 Score: 1026
Period size: 185 Copynumber: 4.2 Consensus size: 186
382528 ATCTTTCCCT
* * * *
382538 ATTCTGAATTCAGAGAGCTTTATTTGTAGAATTCTCTGCTGAAGTGCCTGTTTTAGTGTGAAAAA
1 ATTCTGAATTCAGAGAGCTTTATTTATAGAATTCTCTGCTGAATTGCATGTTTTAATGTG--AAA
* * * * **
382603 AAAAGGATGGAAGACATCTGTTTTGGTACTTTGTGGTGAATTTAGTGATGGGTTTGTTGAAAATT
64 AAAAGGATGAAAGACATCTGTTTTAGTACTTTATGGTGAATTTAGTGGTGAATTTGTTGAAAATT
* *
382668 TGAAGTTAATGAAGTGAAAAAG-GAATCTCTTCCCTCTTGTTTTTGTTATTATTTTCTTC
129 TGAAGTTAATGAAGTG-AAAAGTGAATCT-TTCCCCCTTGTTTTTGTTATTATTTCCTTC
382727 ATTCTGAATTCAGAGAGCTTTATTTATAGAATTCTCTGCTGAATTGCATGTTTTAATGTGAAAAA
1 ATTCTGAATTCAGAGAGCTTTATTTATAGAATTCTCTGCTGAATTGCATGTTTTAATGTGAAAAA
* *
382792 AAGGATG-AA-ACATGTGTTTTAGTACTTTATGGTGAATTTAGTGGTGAATTTGTTGAAAATTTT
66 AAGGATGAAAGACATCTGTTTTAGTACTTTATGGTGAATTTAGTGGTGAATTTGTTGAAAATTTG
* *
382855 AAGTTAATGAAGTGAAAAAG-GAATCTCTTCCCTCTTGTTTTTGTTATTATTTTCTTC
131 AAGTTAATGAAGTG-AAAAGTGAATCT-TTCCCCCTTGTTTTTGTTATTATTTCCTTC
382912 ATTCTGAATTCAGAGAGCTTTATTTATAGAATTCTCTGCTGAATTGCATGTTTTAATGTGAAAAA
1 ATTCTGAATTCAGAGAGCTTTATTTATAGAATTCTCTGCTGAATTGCATGTTTTAATGTGAAAAA
* *
382977 AAGGGTGAAAGACATGTCTGTTTTAGTATTTTATGGTGAATTTAGTGGTGAATTTGTTGAAAATT
66 AAGGATGAAAGACA--TCTGTTTTAGTACTTTATGGTGAATTTAGTGGTGAATTTGTTGAAAATT
*
383042 TTAAGTTAATGAAGTGAAAAGTGAATCTTTCCTCCCTTGTTTTTGTTATTATTTCCTTC
129 TGAAGTTAATGAAGTGAAAAGTGAATCTTTCC-CCCTTGTTTTTGTTATTATTTCCTTC
* * * * *
383101 GTTCTGAATT---TGAGCTTTATTTATAGAATTCTCTGCCGAATT-CAACGTTTTAGTGTG--AA
1 ATTCTGAATTCAGAGAGCTTTATTTATAGAATTCTCTGCTGAATTGC-ATGTTTTAATGTGAAAA
383160 AAAGGATGAAAGACATCTGTTTTAGTACTTTATGGTGAATTT-GT--TG-A-------AAAA-TT
65 AAAGGATGAAAGACATCTGTTTTAGTACTTTATGGTGAATTTAGTGGTGAATTTGTTGAAAATTT
*
383213 GAAGTTAATGAAGTGAAAAGTGAATCTTTCCCCCCTTATTTTTGTTATTATTTCCTTC
130 GAAGTTAATGAAGTGAAAAGTGAATCTTT-CCCCCTTGTTTTTGTTATTATTTCCTTC
* *
383271 ATTCTGAATTGAGAGAGCTTTATATATA
1 ATTCTGAATTCAGAGAGCTTTATTTATA
383299 TATATATATA
Statistics
Matches: 533, Mismatches: 28, Indels: 38
0.89 0.05 0.06
Matches are distributed among these distances:
170 64 0.12
171 6 0.01
173 13 0.02
178 1 0.00
179 2 0.00
181 2 0.00
182 26 0.05
184 16 0.03
185 176 0.33
186 45 0.08
187 15 0.03
188 9 0.02
189 158 0.30
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (186 bp):
ATTCTGAATTCAGAGAGCTTTATTTATAGAATTCTCTGCTGAATTGCATGTTTTAATGTGAAAAA
AAGGATGAAAGACATCTGTTTTAGTACTTTATGGTGAATTTAGTGGTGAATTTGTTGAAAATTTG
AAGTTAATGAAGTGAAAAGTGAATCTTTCCCCCTTGTTTTTGTTATTATTTCCTTC
Found at i:386335 original size:4 final size:4
Alignment explanation
Indices: 386326--386355 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
386316 TCATAAGATA
386326 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
386356 GCATCATGGT
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:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:387117 original size:4 final size:4
Alignment explanation
Indices: 387110--387148 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
387100 TATATATATA
*
387110 GTAT GTAT GTAT GTTT GTAT GTAT GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
387149 GAGAGGGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (4 bp):
GTAT
Found at i:389431 original size:38 final size:36
Alignment explanation
Indices: 389389--389473 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 36
389379 AAATCATACC
389389 TAAAATTTAGTTTTTGTTTCATTTTAGTACCCTACTGT-
1 TAAAATTTAGTTTTTGTTTCATTTTAGTA--CT-CTGTA
*
389427 TAAAATCTTTAGTTTTTGTTTTATTTTAGTACTCTGTA
1 TAAAA--TTTAGTTTTTGTTTCATTTTAGTACTCTGTA
389465 TAAAATTTA
1 TAAAATTTA
389474 ACGTTAAGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
36 4 0.09
37 4 0.09
38 12 0.28
40 23 0.53
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.54
Consensus pattern (36 bp):
TAAAATTTAGTTTTTGTTTCATTTTAGTACTCTGTA
Found at i:392285 original size:17 final size:17
Alignment explanation
Indices: 392265--392298 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
392255 ACTATATATT
*
392265 TTAAATATATTTTTATA
1 TTAAAAATATTTTTATA
392282 TTAAAAATATTTTTATA
1 TTAAAAATATTTTTATA
392299 CTTCCTAAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAAAATATTTTTATA
Found at i:395207 original size:31 final size:31
Alignment explanation
Indices: 395163--395284 Score: 138
Period size: 31 Copynumber: 4.0 Consensus size: 31
395153 AGCAATAAAC
* *
395163 TTAATGAGCACGAGTTGAGCAACAAGTTTTT
1 TTAACGAGCACGAGTCGAGCAACAAGTTTTT
* * *
395194 TTAACGAACACGAGTTGAGCAACAATTTTTT
1 TTAACGAGCACGAGTCGAGCAACAAGTTTTT
* * * *
395225 TTAACCAGCACGAGTCGAGAAACAAATTGTT
1 TTAACGAGCACGAGTCGAGCAACAAGTTTTT
* *
395256 TTAATGAGCACAAGTCGAGCAA-AAGTTTT
1 TTAACGAGCACGAGTCGAGCAACAAGTTTT
395285 AACGAGTAAC
Statistics
Matches: 76, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
30 5 0.07
31 71 0.93
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (31 bp):
TTAACGAGCACGAGTCGAGCAACAAGTTTTT
Found at i:410801 original size:11 final size:11
Alignment explanation
Indices: 410785--410809 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
410775 TTCTTATTAT
410785 AACAATAATTG
1 AACAATAATTG
410796 AACAATAATTG
1 AACAATAATTG
410807 AAC
1 AAC
410810 CCTTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (11 bp):
AACAATAATTG
Found at i:411786 original size:24 final size:24
Alignment explanation
Indices: 411754--411799 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
411744 CAATTGTTCC
411754 TGCTTCCTCGTCTCTCTTCTTCGA
1 TGCTTCCTCGTCTCTCTTCTTCGA
*
411778 TGCTTCCTCTTCTCTCTTCTTC
1 TGCTTCCTCGTCTCTCTTCTTC
411800 TCCAACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.02, C:0.39, G:0.09, T:0.50
Consensus pattern (24 bp):
TGCTTCCTCGTCTCTCTTCTTCGA
Found at i:414705 original size:3 final size:3
Alignment explanation
Indices: 414697--414723 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
414687 ATAATTTTGA
414697 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
414724 CGAGTGATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:414853 original size:37 final size:37
Alignment explanation
Indices: 414812--414985 Score: 135
Period size: 37 Copynumber: 5.0 Consensus size: 37
414802 GTTATATTAG
414812 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
1 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
* ***
414849 ATAATA-ATCAAGTGACCAAA-A--CA---TAAATTAA
1 ATAATATAT-AAGTGACCAAATAGGTAGTTTACCCTAA
* *
414880 ATAATATATATGTTACCAAATAGGTAGTTTACCCTAA
1 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
* * *
414917 ATAATA-ATCGAGTGACCAAAATA--TAG---A--TTAG
1 ATAATATAT-AAGTGACC-AAATAGGTAGTTTACCCTAA
414948 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
1 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
414985 A
1 A
414986 AAAATTCCTA
Statistics
Matches: 101, Mismatches: 18, Indels: 36
0.65 0.12 0.23
Matches are distributed among these distances:
30 5 0.05
31 35 0.35
32 8 0.08
33 1 0.01
34 2 0.02
35 1 0.01
36 8 0.08
37 36 0.36
38 5 0.05
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.29
Consensus pattern (37 bp):
ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
Found at i:414898 original size:68 final size:68
Alignment explanation
Indices: 414715--414985 Score: 352
Period size: 68 Copynumber: 4.0 Consensus size: 68
414705 TAATAATAAT
* * * *
414715 AATAATAATCGAGTGATCAAAACATAAATTAGATAATATATAAGTGACCAAATAAGTAGTTTACA
1 AATAATAATCAAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACC
414780 CTA
66 CTA
* * ** ** *
414783 AATAAAAAT-ATA-T-A-TATGAGTTATATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
1 AATAATAATCA-AGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
414844 CCTA
65 CCTA
* * *
414848 AATAATAATCAAGTGACCAAAACATAAATTAAATAATATATATGTTACCAAATAGGTAGTTTACC
1 AATAATAATCAAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACC
414913 CTA
66 CTA
* * *
414916 AATAATAATCGAGTGACCAAAATATAGATTAGATAATATATAAGTGACCAAATAGGTAGTTTACC
1 AATAATAATCAAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACC
414981 CTA
66 CTA
414984 AA
1 AA
414986 AAAATTCCTA
Statistics
Matches: 172, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
65 52 0.30
66 3 0.02
67 2 0.01
68 115 0.67
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.30
Consensus pattern (68 bp):
AATAATAATCAAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACC
CTA
Found at i:423000 original size:23 final size:24
Alignment explanation
Indices: 422973--423019 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
422963 TTTAATTTCC
422973 AACTATT-T-ATAACTCTTGTAATT
1 AACTATTGTAATAACT-TTGTAATT
*
422996 AACTATTGTAATTACTTTGTAATT
1 AACTATTGTAATAACTTTGTAATT
423020 GGCACAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 9 0.43
25 5 0.24
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (24 bp):
AACTATTGTAATAACTTTGTAATT
Found at i:423017 original size:11 final size:13
Alignment explanation
Indices: 422982--423019 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
422972 CAACTATTTA
*
422982 TAACTCTTGTAAT
1 TAACTATTGTAAT
422995 TAACTATTGTAAT
1 TAACTATTGTAAT
423008 T-ACT-TTGTAAT
1 TAACTATTGTAAT
423019 T
1 T
423020 GGCACAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.33
12 3 0.12
13 13 0.54
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (13 bp):
TAACTATTGTAAT
Found at i:426585 original size:77 final size:77
Alignment explanation
Indices: 426498--426647 Score: 273
Period size: 77 Copynumber: 1.9 Consensus size: 77
426488 AAATATTATT
* *
426498 ATTAATGAATTGTTTAGGAGATTGTGATTTAAAATATATTTGAATACATTTTCCTTCTATTTAAA
1 ATTAATGAATTATTTAGGAGATTGTGATTCAAAATATATTTGAATACATTTTCCTTCTATTTAAA
426563 GGTAGTTCTATA
66 GGTAGTTCTATA
*
426575 ATTAATGAATTATTTAGGAGATTGTGATTCAAAATATATTTGAATACATTTTTCTTCTATTTAAA
1 ATTAATGAATTATTTAGGAGATTGTGATTCAAAATATATTTGAATACATTTTCCTTCTATTTAAA
426640 GGTAGTTC
66 GGTAGTTC
426648 ACCAAATAAG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (77 bp):
ATTAATGAATTATTTAGGAGATTGTGATTCAAAATATATTTGAATACATTTTCCTTCTATTTAAA
GGTAGTTCTATA
Found at i:441250 original size:20 final size:21
Alignment explanation
Indices: 441225--441263 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
441215 CTATCTTGGA
441225 AAGTTTCAAAAC-TCTGGTAG
1 AAGTTTCAAAACATCTGGTAG
*
441245 AAGTTTCGAAACATCTGGT
1 AAGTTTCAAAACATCTGGT
441264 CAATGCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (21 bp):
AAGTTTCAAAACATCTGGTAG
Found at i:445640 original size:24 final size:24
Alignment explanation
Indices: 445608--445664 Score: 96
Period size: 24 Copynumber: 2.3 Consensus size: 24
445598 ATAAATGATT
*
445608 TTTACTAAAATAGTGTATGTAATTA
1 TTTA-TAAAATAGTGTATATAATTA
445633 TTTATAAAATAGTGTATATAATTA
1 TTTATAAAATAGTGTATATAATTA
445657 TTTATAAA
1 TTTATAAA
445665 TGATTTTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.46
Consensus pattern (24 bp):
TTTATAAAATAGTGTATATAATTA
Found at i:448062 original size:15 final size:16
Alignment explanation
Indices: 448042--448071 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
448032 TTTGATAAAC
448042 AATTAAATTT-TAATA
1 AATTAAATTTATAATA
448057 AATTAAATTTATAAT
1 AATTAAATTTATAAT
448072 TATATTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAAATTTATAATA
Found at i:448349 original size:50 final size:49
Alignment explanation
Indices: 448289--448470 Score: 235
Period size: 50 Copynumber: 3.7 Consensus size: 49
448279 ATTTACACTA
* ** *
448289 GTGTAAAGTATGTGTTAAGTGTTACATTTTTTATTTTATTTGCTTATACTC
1 GTGT-AAGTATGTGTTAAGTGCTACATTTTTTATTTTATTCACTTACAC-C
*
448340 GTGTAAGTATGTGTTAAGTGCTACA-CTTTT-TTTTATTCACTTACACC
1 GTGTAAGTATGTGTTAAGTGCTACATTTTTTATTTTATTCACTTACACC
* *
448387 GATGT-AGTATGTGTTAAGTGTTACACTTGTTTATTTTATTCACTTACACC
1 G-TGTAAGTATGTGTTAAGTGCTACA-TTTTTTATTTTATTCACTTACACC
448437 GGTGTAAGTATGTGTTAAGTGCTACATTTTTTAT
1 -GTGTAAGTATGTGTTAAGTGCTACATTTTTTAT
448471 AGTATGAATT
Statistics
Matches: 115, Mismatches: 10, Indels: 13
0.83 0.07 0.09
Matches are distributed among these distances:
47 21 0.18
48 16 0.14
49 7 0.06
50 47 0.41
51 24 0.21
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.48
Consensus pattern (49 bp):
GTGTAAGTATGTGTTAAGTGCTACATTTTTTATTTTATTCACTTACACC
Found at i:474118 original size:17 final size:17
Alignment explanation
Indices: 474096--474140 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
474086 TAAAGTCTAA
474096 ATTTTAAATTAATTTAG
1 ATTTTAAATTAATTTAG
474113 ATTTTAAATTAATTTAG
1 ATTTTAAATTAATTTAG
474130 ATTTTAAATTA
1 ATTTTAAATTA
474141 TACTAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
ATTTTAAATTAATTTAG
Found at i:474799 original size:20 final size:20
Alignment explanation
Indices: 474774--474825 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
474764 TAGTTGAAAA
474774 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTTCATT
474794 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTTCATT
474814 TCGCGTTGCGAT
1 TCGCGTTGCGAT
474826 AGTCTACAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (20 bp):
TCGCGTTGCGATTTTTCATT
Found at i:475040 original size:41 final size:41
Alignment explanation
Indices: 474983--475065 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
474973 GCACCTTAAA
*
474983 ACAACTGTAGACTATCGCAA-CGAATTTGGAAAATCGCAACG
1 ACAACTGTAGACTATCGCAACCGAA-ATGGAAAATCGCAACG
*
475024 ACAACTGTAGACTATCGTAACGCGAAATGGAAAATCGCAACG
1 ACAACTGTAGACTATCGCAAC-CGAAATGGAAAATCGCAACG
475066 CGATTTTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 19 0.50
42 15 0.39
43 4 0.11
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (41 bp):
ACAACTGTAGACTATCGCAACCGAAATGGAAAATCGCAACG
Found at i:495585 original size:22 final size:22
Alignment explanation
Indices: 495557--495600 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
495547 ATGATTAATG
* *
495557 ACGAAAAACGTTGGTCAAAGGA
1 ACGAAAAAAGTTGGTAAAAGGA
495579 ACGAAAAAAGTTGGTAAAAGGA
1 ACGAAAAAAGTTGGTAAAAGGA
495601 CCACATTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.27, T:0.14
Consensus pattern (22 bp):
ACGAAAAAAGTTGGTAAAAGGA
Found at i:498725 original size:128 final size:128
Alignment explanation
Indices: 498497--498754 Score: 489
Period size: 128 Copynumber: 2.0 Consensus size: 128
498487 CCCATTAGAT
498497 TAAATATAGCCATTCTAGACCAATTATAAAGGGTATTGGGCCTAAGGTAGGCCCAAGAGTTAAGT
1 TAAATATAGCCATTCTAGACCAATTATAAAGGGTATTGGGCCTAAGGTAGGCCCAAGAGTTAAGT
498562 TTAGTGATAGTTTTAAATTAAATAAGAAAGGAGAGGGACCTAGATAACAATTTACCCATAGCC
66 TTAGTGATAGTTTTAAATTAAATAAGAAAGGAGAGGGACCTAGATAACAATTTACCCATAGCC
498625 TAAATATAGCCATTCTAGACCAATTATAAAGGGTATTGGGCCTAAGGTAGGCCCAAGAGTTAAGT
1 TAAATATAGCCATTCTAGACCAATTATAAAGGGTATTGGGCCTAAGGTAGGCCCAAGAGTTAAGT
* * *
498690 TTAGTGATAGTTTTAAATTAAATAAGAAATGAGAGGGGCCTAGATAACAATTTACCCCTAGCC
66 TTAGTGATAGTTTTAAATTAAATAAGAAAGGAGAGGGACCTAGATAACAATTTACCCATAGCC
498753 TA
1 TA
498755 TTTTAAGGTT
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 127 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (128 bp):
TAAATATAGCCATTCTAGACCAATTATAAAGGGTATTGGGCCTAAGGTAGGCCCAAGAGTTAAGT
TTAGTGATAGTTTTAAATTAAATAAGAAAGGAGAGGGACCTAGATAACAATTTACCCATAGCC
Found at i:504400 original size:2 final size:2
Alignment explanation
Indices: 504393--504431 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
504383 TATTATAAAG
504393 TA TA TA TA TA 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 TA TA TA TA TA T
504432 GTATGGATCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:508976 original size:2 final size:2
Alignment explanation
Indices: 508969--509006 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
508959 CGAGGTGACC
508969 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
509007 GAAGATGTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:509358 original size:31 final size:32
Alignment explanation
Indices: 509314--509373 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
509304 TACCCCACTT
509314 CATACCATAAATTTATGTTATTGATATATCTC
1 CATACCATAAATTTATGTTATTGATATATCTC
*
509346 CATACTAT-AATTTATGTTATTGATATAT
1 CATACCATAAATTTATGTTATTGATATAT
509374 ATGTGTTTAC
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:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (32 bp):
CATACCATAAATTTATGTTATTGATATATCTC
Found at i:512005 original size:7 final size:7
Alignment explanation
Indices: 511962--512018 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 7
511952 TATAAACATG
511962 AACCCTA
1 AACCCTA
* *
511969 AATCAT-
1 AACCCTA
511975 AACCCTA
1 AACCCTA
*
511982 TAACCTCTC
1 -AACC-CTA
*
511991 AACTCTA
1 AACCCTA
511998 AACCCTA
1 AACCCTA
512005 AACCCTA
1 AACCCTA
512012 AACCCTA
1 AACCCTA
512019 GCATAGGGCT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
6 4 0.10
7 26 0.67
8 7 0.18
9 2 0.05
ACGTcount: A:0.40, C:0.39, G:0.00, T:0.21
Consensus pattern (7 bp):
AACCCTA
Found at i:514798 original size:30 final size:29
Alignment explanation
Indices: 514749--514819 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 29
514739 TAAACCTTAT
* *
514749 GTTATTATTTTAGTGTTTAGAGG-TTATAGG
1 GTTATGATTTTAGTGTTTAG-GGTTTATA-A
514779 GTTATGATTTTAG-GATTTAGGGTTTATAA
1 GTTATGATTTTAGTG-TTTAGGGTTTATAA
*
514808 TTTATGATTTTA
1 GTTATGATTTTA
514820 AGTTAGGAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 14 0.39
30 22 0.61
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (29 bp):
GTTATGATTTTAGTGTTTAGGGTTTATAA
Found at i:519261 original size:31 final size:32
Alignment explanation
Indices: 519189--519314 Score: 121
Period size: 31 Copynumber: 3.8 Consensus size: 32
519179 TGGTATATAG
*
519189 TTTTTAAAGTTATGATAAAATTAAAGTTCAAAAATAT
1 TTTTTAAAGTTATGATAAAATT-AA----AAAAATAC
*
519226 TTTTTAAAGTCATGATAAAATTAAAAAAATA-
1 TTTTTAAAGTTATGATAAAATTAAAAAAATAC
* *
519257 TTTTTAAAGTTAAGATAAAGTT-AAAAAATAC
1 TTTTTAAAGTTATGATAAAATTAAAAAAATAC
* * * *
519288 TTTTTAAAATTAAGGTAAAGTTAAAAA
1 TTTTTAAAGTTATGATAAAATTAAAAA
519315 TATTTTTGGT
Statistics
Matches: 81, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
30 8 0.10
31 39 0.48
32 11 0.14
36 2 0.02
37 21 0.26
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (32 bp):
TTTTTAAAGTTATGATAAAATTAAAAAAATAC
Found at i:519285 original size:30 final size:31
Alignment explanation
Indices: 519210--519321 Score: 131
Period size: 31 Copynumber: 3.7 Consensus size: 31
519200 ATGATAAAAT
* * * *
519210 TAAAGTTCAAAAATATTTTTTAAAGTCATGA
1 TAAAGTTAAAAAATACTTTTTAAAGTTAAGA
*
519241 TAAAATTAAAAAAATA-TTTTTAAAGTTAAGA
1 TAAAGTT-AAAAAATACTTTTTAAAGTTAAGA
* *
519272 TAAAGTTAAAAAATACTTTTTAAAATTAAGG
1 TAAAGTTAAAAAATACTTTTTAAAGTTAAGA
519303 TAAAGTT-AAAAATA-TTTTT
1 TAAAGTTAAAAAATACTTTTT
519322 GGTTTATTCA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
29 5 0.07
30 15 0.21
31 45 0.62
32 7 0.10
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (31 bp):
TAAAGTTAAAAAATACTTTTTAAAGTTAAGA
Found at i:519565 original size:19 final size:20
Alignment explanation
Indices: 519524--519567 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
519514 AATTGGAGGA
519524 TTTAATTTTAATAGATTTAT
1 TTTAATTTTAATAGATTTAT
519544 TTTAA-TTTAATAGATTTAT
1 TTTAATTTTAATAGATTTAT
519563 TTTAA
1 TTTAA
519568 CATGTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTAATTTTAATAGATTTAT
Found at i:525455 original size:20 final size:20
Alignment explanation
Indices: 525361--525729 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
525351 GATTTTCCAT
* ** *
525361 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
525381 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
525401 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
525421 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
525441 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
525461 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
525481 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
525501 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
525521 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
525541 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
525561 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
525581 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
525601 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
525621 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
525641 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
525661 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
525681 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
525701 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
525721 AATCACAAC
1 AATCGCAAC
525730 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:526434 original size:24 final size:23
Alignment explanation
Indices: 526395--526440 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
526385 AAATTTGGTC
526395 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGA-TTTGATA
526419 TTGGTCAATA-CACGGATTTGAT
1 TTGGTCAATATC-CGGATTTGAT
526441 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (23 bp):
TTGGTCAATATCCGGATTTGATA
Found at i:528980 original size:32 final size:33
Alignment explanation
Indices: 528930--529230 Score: 218
Period size: 33 Copynumber: 8.7 Consensus size: 33
528920 CGGAAAATAC
*
528930 AATCGCAACGCGAAATGAAAATCCCAAC-A-AA
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAA
* *
528961 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCCCAACGAGAA
**
528995 AATCGCAATGCGAAATGAAAATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
* * * * *
529033 AATCGCAACGAGAGAATCG-CAATGCGAA--ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACGA-GAA
* *
529066 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAA
* * *
529099 AATCGCAATGCAAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
* *
529137 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
*
529175 AATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAA
529207 GAATCGCAATGCGAAATGAAAATC
1 -AATCGCAATGCGAAATGAAAATC
529231 GCAATGCGAA
Statistics
Matches: 226, Mismatches: 25, Indels: 36
0.79 0.09 0.13
Matches are distributed among these distances:
31 11 0.05
32 26 0.12
33 83 0.37
34 14 0.06
35 4 0.02
36 2 0.01
37 2 0.01
38 75 0.33
39 8 0.04
40 1 0.00
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAA
Found at i:529023 original size:19 final size:19
Alignment explanation
Indices: 528959--529253 Score: 378
Period size: 19 Copynumber: 16.5 Consensus size: 19
528949 AATCCCAACA
528959 AAAATCGCAATGCGGAAATG
1 AAAATCGCAATGC-GAAATG
528979 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATG
*
528993 AGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
529012 AAAATCGTAATGCGAAATG
1 AAAATCGCAATGCGAAATG
529031 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATG
*
529045 AGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
529064 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
529083 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATG
* *
529097 AGAATCGCAATGCAAAATG
1 AAAATCGCAATGCGAAATG
*
529116 AAAATCGCAATGCGAAATT
1 AAAATCGCAATGCGAAATG
*
529135 AAAATCGCAATACGAAATG
1 AAAATCGCAATGCGAAATG
529154 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
529173 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
529192 AAAATCGCAA--CGAAA-G
1 AAAATCGCAATGCGAAATG
529208 --AATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
529225 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
529244 AAAATCGCAA
1 AAAATCGCAA
529254 CGAGATAATC
Statistics
Matches: 241, Mismatches: 14, Indels: 41
0.81 0.05 0.14
Matches are distributed among these distances:
14 38 0.16
15 3 0.01
16 11 0.05
17 11 0.05
18 4 0.02
19 164 0.68
20 10 0.04
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:529291 original size:52 final size:52
Alignment explanation
Indices: 528959--529275 Score: 526
Period size: 52 Copynumber: 6.0 Consensus size: 52
528949 AATCCCAACA
528959 AAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
1 AAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
*
529012 AAAATCGTAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
*
529064 AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATG
1 AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
* *
529116 AAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAAATG
*
529173 AAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
*
529225 AAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
529276 TATAAACGCA
Statistics
Matches: 248, Mismatches: 11, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
52 182 0.73
53 14 0.06
54 3 0.01
55 3 0.01
56 2 0.01
57 44 0.18
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
Found at i:529326 original size:19 final size:19
Alignment explanation
Indices: 529282--529382 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
529272 AAATTATAAA
529282 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
529301 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
529321 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
529337 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
529354 CGCATTGCGATTTTCA-TT
1 CGCATTGCGATTTTCATTT
529372 CGCATTGCGAT
1 CGCATTGCGAT
529383 AGTCATTTTG
Statistics
Matches: 74, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
18 13 0.18
19 22 0.30
20 19 0.26
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:529503 original size:13 final size:14
Alignment explanation
Indices: 529487--529522 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
529477 CATCAATTAC
529487 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
529500 ACAAATCATCTTTT
1 ACAAATCAACTTTT
529514 ACAAATCAA
1 ACAAATCAA
529523 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:529534 original size:12 final size:12
Alignment explanation
Indices: 529517--529589 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
529507 ATCTTTTACA
529517 AATCAATTAAAC
1 AATCAATTAAAC
*
529529 AATCAA--AAATTG
1 AATCAATTAAA--C
**
529541 AATCAACTTTTAC
1 AATCAA-TTAAAC
529554 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
529567 AATCAA-AAAAC
1 AATCAATTAAAC
529578 AATCAATTAAAC
1 AATCAATTAAAC
529590 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:529551 original size:38 final size:38
Alignment explanation
Indices: 529503--529575 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
529493 CAACTTTACA
*
529503 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
529541 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
529576 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:531407 original size:19 final size:19
Alignment explanation
Indices: 531367--531465 Score: 91
Period size: 19 Copynumber: 5.4 Consensus size: 19
531357 TAGTTTACTT
* *
531367 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
531387 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
531406 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
531425 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
**
531439 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
531458 TCGCAACG
1 TCGCAACG
531466 AAAGAATCGC
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 38 0.58
20 13 0.20
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:531442 original size:14 final size:14
Alignment explanation
Indices: 531423--531479 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
531413 GCGAAATGAA
*
531423 AATCGCAACGACAG
1 AATCGCAACGAAAG
531437 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
531454 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
531470 AATCGCAACG
1 AATCGCAACG
531480 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:531446 original size:33 final size:33
Alignment explanation
Indices: 531404--531495 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
531394 GCGAAACCAA
*
531404 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
531437 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
531470 AATCGCAACGCGAAATG-AAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
531496 TGCGATTTTG
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 9 0.16
33 49 0.84
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:531518 original size:19 final size:19
Alignment explanation
Indices: 531496--531624 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
531486 GAAATCGCAA
531496 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
531515 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
531529 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
531548 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
531562 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
531581 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
531600 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
531620 TGCGA
1 TGCGA
531625 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:531538 original size:33 final size:33
Alignment explanation
Indices: 531496--531587 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
531486 GAAATCGCAA
531496 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
531529 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
531562 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
531588 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:531968 original size:91 final size:93
Alignment explanation
Indices: 531668--532044 Score: 717
Period size: 92 Copynumber: 4.1 Consensus size: 93
531658 TTGAATGGAT
531668 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
531733 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
531761 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
531825 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
531853 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTG-TAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
531916 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
531944 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
532008 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
532036 AAATTTACT
1 AAATTTACT
532045 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 1, Indels: 7
0.97 0.00 0.02
Matches are distributed among these distances:
91 88 0.31
92 154 0.55
93 38 0.14
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:531978 original size:183 final size:185
Alignment explanation
Indices: 531668--532044 Score: 715
Period size: 183 Copynumber: 2.0 Consensus size: 185
531658 TTGAATGGAT
531668 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
531733 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
531797 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTA-TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
531853 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTG-TAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
531916 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
531981 TACTATTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
532036 AAATTTACT
1 AAATTTACT
532045 AAGCAATCTA
Statistics
Matches: 190, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
183 132 0.69
184 19 0.10
185 39 0.21
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:533748 original size:14 final size:14
Alignment explanation
Indices: 533729--533818 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
533719 TTGAAATGAA
533729 AATCGCAACGAGAG
1 AATCGCAACGAGAG
533743 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
533760 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
533776 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
533795 AATCGCAACGAGAG
1 AATCGCAACGAGAG
533809 AATCGCAACG
1 AATCGCAACG
533819 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:533766 original size:33 final size:33
Alignment explanation
Indices: 533721--533835 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
533711 TCTTTTGGTT
533721 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
533754 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
533787 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
533820 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
533836 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:533767 original size:19 final size:18
Alignment explanation
Indices: 533728--533840 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
533718 GTTGAAATGA
533728 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
533743 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
533760 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
533776 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
533793 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
533809 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
533826 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
533841 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:533871 original size:14 final size:14
Alignment explanation
Indices: 533852--533906 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
533842 TTTGGTTTCG
533852 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
533866 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
533885 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
533899 CGTTGCGA
1 CGTTGCGA
533907 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:534064 original size:33 final size:33
Alignment explanation
Indices: 534022--534092 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
534012 AAATACTAAC
*
534022 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
534055 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
534088 TGAAA
1 TGAAA
534093 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:534488 original size:20 final size:20
Alignment explanation
Indices: 534463--534654 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
534453 CTTTAAATAT
534463 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
534483 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
534505 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
534524 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
534544 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
534564 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
534584 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
534604 CGCGTTGCGA-TTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
** *
534623 CGCGTTGCGATTT-CATATT
1 CGCGTTGCGATTTACGGATA
534642 CGCGTTGCGATTT
1 CGCGTTGCGATTT
534655 TGGAAATCGC
Statistics
Matches: 145, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
19 32 0.22
20 97 0.67
21 14 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:534733 original size:20 final size:20
Alignment explanation
Indices: 534708--534759 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
534698 AAGAATCGCG
*
534708 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
534728 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
534748 TTGCGATTCTGG
1 TTGCGATTCTGG
534760 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:539511 original size:3 final size:3
Alignment explanation
Indices: 539503--539528 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
539493 ATAAAATATA
539503 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
539529 AACATGGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:546109 original size:16 final size:16
Alignment explanation
Indices: 546050--546116 Score: 55
Period size: 16 Copynumber: 4.2 Consensus size: 16
546040 TAATTTTGGA
** *
546050 TCGGGTTAAACTCGGT
1 TCGGGTTAATTTCAGT
*
546066 TCGGGTT-GTTTCAGT
1 TCGGGTTAATTTCAGT
** **
546081 TCAAGTTGTTTTCAGT
1 TCGGGTTAATTTCAGT
546097 TCGGGTTAATTTCAGT
1 TCGGGTTAATTTCAGT
546113 TCGG
1 TCGG
546117 ATTGTTTCTG
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
15 9 0.23
16 30 0.77
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.42
Consensus pattern (16 bp):
TCGGGTTAATTTCAGT
Found at i:548135 original size:41 final size:41
Alignment explanation
Indices: 548054--548136 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
548044 TTTCATTCAT
* * * ***
548054 TCAACTAATTTAAATTTGTATAAAACTAAAATAGTTTTATA
1 TCAACTAACTTAAATTTATATAAAACTAAAAAAAAATTATA
*
548095 TCAACTAACTTAAATTTATGTAAAACTAAAAAAAAATTATA
1 TCAACTAACTTAAATTTATATAAAACTAAAAAAAAATTATA
548136 T
1 T
548137 TGTGTGAGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (41 bp):
TCAACTAACTTAAATTTATATAAAACTAAAAAAAAATTATA
Found at i:548349 original size:2 final size:2
Alignment explanation
Indices: 548342--548400 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
548332 ATCCATCCTC
*
548342 AT AT AT AT AT A- AT AT AT AT AT 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
548383 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
548401 TTTGAGAGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:556283 original size:2 final size:2
Alignment explanation
Indices: 556276--556304 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
556266 GATCTTACCC
556276 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
556305 GCAGTAATCA
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:556743 original size:21 final size:20
Alignment explanation
Indices: 556657--556814 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
556647 AAATGACCAA
**
556657 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
556676 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
556696 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
556716 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
556737 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
556758 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
556778 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
556799 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
556815 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:556807 original size:20 final size:20
Alignment explanation
Indices: 556782--557171 Score: 448
Period size: 20 Copynumber: 19.4 Consensus size: 20
556772 GATTTTCAAT
* ** *
556782 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
556802 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
556822 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
556842 AATCGCAACGTGTATCCGTAA
1 AATCGCAACGCGTATCCGT-A
**
556863 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
556883 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
556903 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * **
556923 AATCGCAACG-ATAATACAAA
1 AATCGCAACGCGT-ATCCGTA
556943 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
556963 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
556983 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
557003 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
557023 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
557043 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
557063 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
557083 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
557103 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
557123 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
557143 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
557163 AATCACAAC
1 AATCGCAAC
557172 ACTGAAATTT
Statistics
Matches: 317, Mismatches: 42, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
19 4 0.01
20 292 0.92
21 21 0.07
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:557882 original size:24 final size:24
Alignment explanation
Indices: 557843--557889 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
557833 AAATTTGGTC
557843 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
557867 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
557890 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:560380 original size:19 final size:19
Alignment explanation
Indices: 560358--560731 Score: 397
Period size: 19 Copynumber: 21.4 Consensus size: 19
560348 CGGAAAATAC
*
560358 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
560377 AATCCCAA--C---ATG-A
1 AATCGCAATGCGAAATGAA
560390 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
560410 AATCGCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
560424 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
560444 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
560458 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
560477 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
560491 AATCGCAATGCAGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
560511 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
560525 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
560544 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
560563 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
560577 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
560596 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
560615 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
560634 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
560653 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
560672 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
560686 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
560705 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
560724 AATCGCAA
1 AATCGCAA
560732 CGAGATAATC
Statistics
Matches: 303, Mismatches: 13, Indels: 78
0.77 0.03 0.20
Matches are distributed among these distances:
13 8 0.03
14 66 0.22
15 4 0.01
16 14 0.05
17 12 0.04
18 6 0.02
19 158 0.52
20 35 0.12
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:560409 original size:33 final size:32
Alignment explanation
Indices: 560358--560753 Score: 301
Period size: 33 Copynumber: 11.5 Consensus size: 32
560348 CGGAAAATAC
* *
560358 AATCGCAACGCGAAATGAAAATCCCAACATGA
1 AATCGCAATGCGAAATGAAAATCGCAACATGA
560390 AATCGCAATGCGGAAATGAAAATCGCAACATGAA
1 AATCGCAATGC-GAAATGAAAATCGCAACATG-A
560424 AATCGCAATGCGGAAATGAAAATCGCAACGA-GA
1 AATCGCAATGC-GAAATGAAAATCGCAAC-ATGA
*
560457 GAATCGCAATGCGAAATGAAAATCCCAACATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAACATG-A
560491 AATCGCAATGCAGAAATGAAAATCGCAACGA-GA
1 AATCGCAATGC-GAAATGAAAATCGCAAC-ATGA
*
560524 GAATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--C---ATG-A
* * *
560563 AATCGCAACGAGAGAATCG-CAAT-GCGAA-ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCGC-AACATG-A
560596 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAAAATCGCAA--C---AT-GA
560634 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C---ATG-A
560672 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C---ATG-A
560705 AATCGCAATGCGAAATGAAAATCGCAACGA-GA
1 AATCGCAATGCGAAATGAAAATCGCAAC-ATGA
560737 TAATCGCAATGCGAAAT
1 -AATCGCAATGCGAAAT
560754 TATAAACGCA
Statistics
Matches: 318, Mismatches: 12, Indels: 67
0.80 0.03 0.17
Matches are distributed among these distances:
31 1 0.00
32 20 0.06
33 127 0.40
34 71 0.22
35 9 0.03
36 7 0.02
37 2 0.01
38 70 0.22
39 10 0.03
40 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (32 bp):
AATCGCAATGCGAAATGAAAATCGCAACATGA
Found at i:560630 original size:13 final size:13
Alignment explanation
Indices: 560577--560672 Score: 51
Period size: 13 Copynumber: 7.6 Consensus size: 13
560567 GCAACGAGAG
*
560577 AATCGCAATGCGA
1 AATCGAAATGCGA
*
560590 AAT-GAAAAT-CGC
1 AATCG-AAATGCGA
*
560602 AATGCGAAATG-AA
1 AAT-CGAAATGCGA
*
560615 AATCGCAATGCGA
1 AATCGAAATGCGA
* *
560628 AATGGAAAT-CGC
1 AATCGAAATGCGA
*
560640 AATGCGAAATG-AA
1 AAT-CGAAATGCGA
*
560653 AATCGCAATGCGA
1 AATCGAAATGCGA
560666 AAT-GAAA
1 AATCGAAA
560673 ATCGCAACGA
Statistics
Matches: 60, Mismatches: 15, Indels: 17
0.65 0.16 0.18
Matches are distributed among these distances:
12 26 0.43
13 33 0.55
14 1 0.02
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.16
Consensus pattern (13 bp):
AATCGAAATGCGA
Found at i:560769 original size:52 final size:52
Alignment explanation
Indices: 560389--560753 Score: 476
Period size: 52 Copynumber: 7.0 Consensus size: 52
560379 TCCCAACATG
*
560389 AAATCGCAATGCGGAAATGAAAATCGCAAC-ATGAAAATCGCAATGCGGAAATGA
1 AAATCGCAATGC-GAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGA
* * * * * *
560443 AAATCGCAA--CG--A-GAGAATCGCAATGCGA-AAT-GAAAATCCCAACATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA-ATGA
*
560490 AAATCGCAATGCAGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGA
1 AAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
560543 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
*
560595 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G-AATCGCAATGCGAAATGA
*
560652 AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
*
560704 AAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
560754 TATAAACGCA
Statistics
Matches: 278, Mismatches: 17, Indels: 34
0.84 0.05 0.10
Matches are distributed among these distances:
46 3 0.01
47 20 0.07
48 12 0.04
49 2 0.01
50 1 0.00
51 1 0.00
52 135 0.49
53 30 0.11
54 21 0.08
55 6 0.02
56 1 0.00
57 46 0.17
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
Found at i:560783 original size:33 final size:33
Alignment explanation
Indices: 560746--560836 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 33
560736 ATAATCGCAA
560746 TGCGAAATT-ATAAACGCATTGCGATTCTCTCGT
1 TGCGAAATTCAT-AACGCATTGCGATTCTCTCGT
** **
560779 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATTCATAACGCATTGCGATTCTCTCGT
** **
560812 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGAAATTCATAACGCATTGCGAT
560837 AGTCATTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 51 0.96
34 2 0.04
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (33 bp):
TGCGAAATTCATAACGCATTGCGATTCTCTCGT
Found at i:560802 original size:19 final size:19
Alignment explanation
Indices: 560778--560836 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
560768 GATTCTCTCG
560778 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
560797 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
560811 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
560830 TTGCGAT
1 TTGCGAT
560837 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:560844 original size:19 final size:17
Alignment explanation
Indices: 560760--560836 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 17
560750 AAATTATAAA
*
560760 CGCATTGCGATTC-TCT
1 CGCATTGCGATTCATTT
560776 CG--TTGCGATTTTCATTT
1 CGCATTGCGA--TTCATTT
*
560793 CGCATTGCGATTC-TCT
1 CGCATTGCGATTCATTT
560809 CG--TTGCGATTTTCATTT
1 CGCATTGCGA--TTCATTT
560826 CGCATTGCGAT
1 CGCATTGCGAT
560837 AGTCATTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 19
0.69 0.04 0.27
Matches are distributed among these distances:
14 12 0.25
16 12 0.25
17 12 0.25
19 12 0.25
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.43
Consensus pattern (17 bp):
CGCATTGCGATTCATTT
Found at i:560979 original size:14 final size:14
Alignment explanation
Indices: 560943--560979 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
560933 CATCAATTAC
*
560943 ACAAATCAACTTTT
1 ACAAATCATCTTTT
560957 ACAAATCATCTTTT
1 ACAAATCATCTTTT
560971 ACAAATCAT
1 ACAAATCAT
560980 TAAACAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCATCTTTT
Found at i:562908 original size:19 final size:19
Alignment explanation
Indices: 562868--563002 Score: 101
Period size: 19 Copynumber: 7.6 Consensus size: 19
562858 TAGTTTACTT
* *
562868 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
562888 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
562907 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
562926 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
*
562940 TCGCAATGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
562959 TCGCAA--CG-AA--AGAA
1 TCGCAACGCGAAACCAAAA
**
562973 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
562992 TCGCAATGCGA
1 TCGCAACGCGA
563003 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 18 0.19
15 1 0.01
16 6 0.06
17 6 0.06
18 1 0.01
19 50 0.53
20 13 0.14
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:562943 original size:14 final size:14
Alignment explanation
Indices: 562924--562980 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
562914 GCGAAATGAA
562924 AATCGCAACGACAG
1 AATCGCAACGACAG
*
562938 AATCGCAATGCGAAACCAA
1 AATCGCAA--CG--A-CAG
*
562957 AATCGCAACGAAAG
1 AATCGCAACGACAG
562971 AATCGCAACG
1 AATCGCAACG
562981 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.26, G:0.19, T:0.09
Consensus pattern (14 bp):
AATCGCAACGACAG
Found at i:562951 original size:33 final size:33
Alignment explanation
Indices: 562905--562997 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
562895 GCGAAACCAA
*
562905 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* **
562938 AATCGCAATGCGAAACCAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
562971 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
562998 TGCGATTTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:562994 original size:52 final size:54
Alignment explanation
Indices: 562868--563002 Score: 149
Period size: 52 Copynumber: 2.5 Consensus size: 54
562858 TAGTTTACTT
* *
562868 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAATGCGAAACCAAAATCGCAAC-CGAAATG-AAA
*
562926 TCGCAA-CGACA-G--AATCGCAATGCGAAACCAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACCGAAATGAAA
562973 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAATGCGA
563003 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.07
50 6 0.09
52 39 0.57
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:563020 original size:19 final size:19
Alignment explanation
Indices: 562998--563125 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
562988 AAAATCGCAA
562998 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
563017 TGCGA-TCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
563030 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
563049 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
563063 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
563082 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
563101 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
563121 TGCGA
1 TGCGA
563126 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
13 8 0.09
14 13 0.15
15 2 0.02
16 1 0.01
17 3 0.03
18 3 0.03
19 45 0.51
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:563064 original size:33 final size:33
Alignment explanation
Indices: 562998--563088 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
562988 AAAATCGCAA
562998 TGCGATTTTGGTTTCGCGTTGCGA-TCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
563030 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
563063 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
563089 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 24 0.43
33 32 0.57
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:563065 original size:14 final size:14
Alignment explanation
Indices: 563014--563069 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
563004 TTTGGTTTCG
563014 CGTTGCGA-TCTGT
1 CGTTGCGATTCTGT
*
563027 CGTTGCGATTTTGGTTT
1 CGTTGCGATTCT-G--T
563044 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTGT
563060 CGTTGCGATT
1 CGTTGCGATT
563070 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
13 8 0.23
14 12 0.34
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.07, C:0.20, G:0.30, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTGT
Found at i:563341 original size:91 final size:93
Alignment explanation
Indices: 563169--563545 Score: 717
Period size: 91 Copynumber: 4.1 Consensus size: 93
563159 TTGAATGGAT
563169 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
563234 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
563262 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
563325 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
563353 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
563416 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
563444 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
563509 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
563537 AAATTTACT
1 AAATTTACT
563546 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 1, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
90 6 0.02
91 168 0.60
92 6 0.02
93 100 0.36
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:565266 original size:14 final size:14
Alignment explanation
Indices: 565247--565336 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
565237 TTGAAATGAA
565247 AATCGCAACGAGAG
1 AATCGCAACGAGAG
565261 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
565278 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
565294 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
565313 AATCGCAACGAGAG
1 AATCGCAACGAGAG
565327 AATCGCAACG
1 AATCGCAACG
565337 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:565284 original size:33 final size:33
Alignment explanation
Indices: 565239--565355 Score: 216
Period size: 33 Copynumber: 3.5 Consensus size: 33
565229 TCTTTTGGTT
565239 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
565272 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
565305 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
565338 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
565356 CGAAATGAAA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:565285 original size:19 final size:19
Alignment explanation
Indices: 565261--565377 Score: 119
Period size: 19 Copynumber: 6.7 Consensus size: 19
565251 GCAACGAGAG
* *
565261 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAA
*
565280 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
565294 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
565313 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
565327 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
565346 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
565365 AATCGCAATGCGA
1 AATCGCAACGCGA
565378 TTTTGGTTTC
Statistics
Matches: 83, Mismatches: 5, Indels: 20
0.77 0.05 0.19
Matches are distributed among these distances:
14 20 0.24
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 51 0.61
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:565408 original size:14 final size:14
Alignment explanation
Indices: 565389--565443 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
565379 TTTGGTTTCG
565389 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
565403 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
565422 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
565436 CGTTGCGA
1 CGTTGCGA
565444 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:565421 original size:33 final size:33
Alignment explanation
Indices: 565373--565443 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
565363 AAAATCGCAA
**
565373 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
565406 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
565439 TGCGA
1 TGCGA
565444 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:565451 original size:33 final size:33
Alignment explanation
Indices: 565384--565465 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
565374 GCGATTTTGG
***
565384 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
565417 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
565450 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
565466 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:565470 original size:20 final size:20
Alignment explanation
Indices: 565396--565484 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
565386 TCGCGTTGCG
565396 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
565416 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
565429 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
565449 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
565469 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
565485 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:565606 original size:33 final size:33
Alignment explanation
Indices: 565564--565634 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
565554 AATACTAACT
565564 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
***
565597 TGAAAATCGCAACGAGAGAATCTTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
565630 TGAAA
1 TGAAA
565635 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:565867 original size:22 final size:22
Alignment explanation
Indices: 565815--565869 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
565805 TGGTTGCGAG
**
565815 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
565837 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
565859 GGATTTCTTCG
1 GGATTTCTTCG
565870 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:566040 original size:20 final size:20
Alignment explanation
Indices: 566015--566208 Score: 212
Period size: 20 Copynumber: 9.6 Consensus size: 20
566005 CTTTAAATAT
566015 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
566035 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
566057 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
566076 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
566096 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
566116 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
566137 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
566157 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
566177 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
566197 CGCGTTGCGATT
1 CGCGTTGCGATT
566209 ATTGAAAAAT
Statistics
Matches: 146, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.01
20 110 0.75
21 32 0.22
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:566092 original size:61 final size:60
Alignment explanation
Indices: 566015--566208 Score: 237
Period size: 61 Copynumber: 3.2 Consensus size: 60
566005 CTTTAAATAT
*
566015 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTAGCGTTGCGATTTACGGATA
* * ***
566076 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCA-TACGCGTTGCGATTTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTA-GCGTTGCGA-TTTACGGATA
* * * * ** *
566137 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
566197 CGCGTTGCGATT
1 CGCGTTGCGATT
566209 ATTGAAAAAT
Statistics
Matches: 111, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
59 2 0.02
60 30 0.27
61 78 0.70
62 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
Found at i:566185 original size:81 final size:81
Alignment explanation
Indices: 566014--566208 Score: 241
Period size: 81 Copynumber: 2.4 Consensus size: 81
566004 GCTTTAAATA
** * * *
566014 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACGC
1 TCGCGTTGCGATTTACACATACGCGTTGCGATTTTACGGATTAACGTTGCGATTTACGGATACGC
566079 GTTGCGATATACGGAT
66 GTTGCGATATACGGAT
* * *
566095 ACGCATTGCGATTTACCCATACGCGTTGCGATTTTACGGA-TACACGTTGCGATTTACGGATACG
1 TCGCGTTGCGATTTACACATACGCGTTGCGATTTTACGGATTA-ACGTTGCGATTTACGGATACG
* *
566159 CGTTGCGATTTATGTG-T
65 CGTTGCGATATACG-GAT
* * *
566176 TCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACACATACGCGTTGCGATT
566209 ATTGAAAAAT
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
80 2 0.02
81 94 0.97
82 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (81 bp):
TCGCGTTGCGATTTACACATACGCGTTGCGATTTTACGGATTAACGTTGCGATTTACGGATACGC
GTTGCGATATACGGAT
Found at i:576046 original size:2 final size:2
Alignment explanation
Indices: 576035--576067 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
576025 CCATATGCTG
576035 AT AT -T 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
576068 GGTGGTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:577457 original size:60 final size:59
Alignment explanation
Indices: 577345--577480 Score: 139
Period size: 60 Copynumber: 2.3 Consensus size: 59
577335 ATAGTCGGGT
* *
577345 GACCATTTTGTAACTTTTAATAATAGAGGAACTCAACAAAGCAACACTCTATAGTCAGAG
1 GACCATTTTGTAACTTTTAATAATAGAGGAACTCAACAAAACAACACCCTATAGT-AGAG
* * * * * * ** * *
577405 GACCATTTTGTAACTTTTAATAGTTGAGGGACTTAATAAAATAGTACCCTATAGTTGAT
1 GACCATTTTGTAACTTTTAATAATAGAGGAACTCAACAAAACAACACCCTATAGTAGAG
577464 GACCATTTGTGT-ACTTT
1 GACCATTT-TGTAACTTT
577481 ACCCTATTAT
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 15 0.24
60 48 0.76
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (59 bp):
GACCATTTTGTAACTTTTAATAATAGAGGAACTCAACAAAACAACACCCTATAGTAGAG
Found at i:578537 original size:18 final size:18
Alignment explanation
Indices: 578514--578557 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
578504 CCGGTTCTTC
*
578514 CGACCGGTCGGACCGATT
1 CGACCGGTCGAACCGATT
* *
578532 CGACCGGTTGAACCGGTT
1 CGACCGGTCGAACCGATT
578550 CGACCGGT
1 CGACCGGT
578558 AGCATGACCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (18 bp):
CGACCGGTCGAACCGATT
Found at i:578943 original size:35 final size:35
Alignment explanation
Indices: 578896--578981 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
578886 AAAACAGTCA
* * *
578896 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
578931 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
578966 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
578982 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:578975 original size:21 final size:21
Alignment explanation
Indices: 578950--578992 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
578940 TTCTAAACCC
578950 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
578971 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
578992 T
1 T
578993 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Done.