Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009581.1 Hibiscus syriacus cultivar Beakdansim tig00116958_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: 2551150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 13
Found at i:640707 original size:23 final size:21
Alignment explanation
Indices: 640681--640730 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
640671 TTTATTCGGC
640681 TTAATCAACATTTGGGTTTAGTT
1 TTAATCAACATTTGGG-TTA-TT
* **
640704 TTAATCGATGTTTGGGTTATT
1 TTAATCAACATTTGGGTTATT
640725 TTAATC
1 TTAATC
640731 GGCATTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.33
22 3 0.12
23 13 0.54
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.50
Consensus pattern (21 bp):
TTAATCAACATTTGGGTTATT
Found at i:641664 original size:17 final size:15
Alignment explanation
Indices: 641625--641657 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
641615 GTACATTGAC
641625 ATTTAGAAA-AAAAAT
1 ATTTA-AAATAAAAAT
641640 ATTTAAAATAAAAAT
1 ATTTAAAATAAAAAT
641655 ATT
1 ATT
641658 GTTAAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
ATTTAAAATAAAAAT
Found at i:641929 original size:15 final size:16
Alignment explanation
Indices: 641899--641932 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
641889 GTACATTGAC
641899 ATTTAGAAAAAAAAAT
1 ATTTAGAAAAAAAAAT
*
641915 ATTTA-AAATAAAAAT
1 ATTTAGAAAAAAAAAT
641930 ATT
1 ATT
641933 GTTAAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
ATTTAGAAAAAAAAAT
Found at i:642093 original size:23 final size:22
Alignment explanation
Indices: 642067--642116 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
642057 AGTTTTCTGA
642067 ATTTTCATAT-TTTTATACTTTTT
1 ATTTT-ATATATTTTA-ACTTTTT
*
642090 ATTTTATATAATTTTAATTTTTT
1 ATTTTATAT-ATTTTAACTTTTT
642113 ATTT
1 ATTT
642117 AAAGGATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 4 0.17
23 15 0.62
24 5 0.21
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTTTATATATTTTAACTTTTT
Found at i:642852 original size:13 final size:14
Alignment explanation
Indices: 642834--642867 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
642824 ATTGATTTAA
642834 TTTTTTAT-CTAAT
1 TTTTTTATCCTAAT
642847 TTTTTTATCCTAAT
1 TTTTTTATCCTAAT
*
642861 ATTTTTA
1 TTTTTTA
642868 CTTAAATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTTTATCCTAAT
Found at i:643243 original size:2 final size:2
Alignment explanation
Indices: 643236--643262 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
643226 ATCCTACCTT
643236 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
643263 TCCTTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:645471 original size:17 final size:17
Alignment explanation
Indices: 645449--645488 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
645439 TATGAACATC
*
645449 AAATAAATTAACAACAA
1 AAATAAAATAACAACAA
*
645466 AAATAAAATAACAATAA
1 AAATAAAATAACAACAA
645483 AAATAA
1 AAATAA
645489 TTTCTATAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (17 bp):
AAATAAAATAACAACAA
Found at i:646932 original size:25 final size:25
Alignment explanation
Indices: 646894--647017 Score: 214
Period size: 25 Copynumber: 5.0 Consensus size: 25
646884 TGGAAGGGGA
*
646894 TTAGGG-TTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
646918 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
646943 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
646968 TTAGGGTTTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
646993 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
647018 GGGTTGTTGG
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
24 6 0.06
25 89 0.94
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:647155 original size:3 final size:3
Alignment explanation
Indices: 647147--647210 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
647137 GCAAAAATTG
*
647147 TAA TAA TAAA TAA TAA TAA -AA TAA TAA T-A TAA TGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
647191 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
647211 CGGAAAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:648162 original size:18 final size:18
Alignment explanation
Indices: 648141--648175 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
648131 GAATGAGCTG
648141 ATTTTTTTAATAAAAAAC
1 ATTTTTTTAATAAAAAAC
*
648159 ATTTTTTTATTAAAAAA
1 ATTTTTTTAATAAAAAA
648176 AATTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTTTTTAATAAAAAAC
Found at i:659920 original size:18 final size:18
Alignment explanation
Indices: 659888--659932 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
659878 AAATATTAAA
*
659888 ATATAATA-GTAAAATA-
1 ATATAATATTTAAAATAT
659904 ATATGAATATTTAAAATAT
1 ATAT-AATATTTAAAATAT
659923 ATATAATATT
1 ATATAATATT
659933 AACACTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 4 0.16
17 4 0.16
18 13 0.52
19 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
ATATAATATTTAAAATAT
Found at i:662058 original size:14 final size:14
Alignment explanation
Indices: 662039--662068 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
662029 AGTGACCCGC
*
662039 ACACCTAATTTTCA
1 ACACCTAATTTACA
662053 ACACCTAATTTACA
1 ACACCTAATTTACA
662067 AC
1 AC
662069 TCTTAAGTAA
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:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (14 bp):
ACACCTAATTTACA
Found at i:663492 original size:18 final size:18
Alignment explanation
Indices: 663471--663505 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
663461 GTTTATAGTA
*
663471 ATATATAATAAAAATAAC
1 ATATATAAAAAAAATAAC
*
663489 ATATTTAAAAAAAATAA
1 ATATATAAAAAAAATAA
663506 AGAATAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
ATATATAAAAAAAATAAC
Found at i:664997 original size:21 final size:20
Alignment explanation
Indices: 664972--665036 Score: 57
Period size: 21 Copynumber: 3.4 Consensus size: 20
664962 ATTTTGTTAG
664972 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAATTATT-TAT
*
664993 TA-TTTAATT--TT-TTTAT
1 TATTTTATTTAATTATTTAT
*
665009 TTTTTTATTTAATTATTTTAT
1 TATTTTATTTAATTA-TTTAT
*
665030 TTTTTTA
1 TATTTTA
665037 CAGTTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 4 0.11
17 8 0.22
18 2 0.06
19 2 0.06
20 6 0.17
21 14 0.39
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (20 bp):
TATTTTATTTAATTATTTAT
Found at i:665007 original size:29 final size:29
Alignment explanation
Indices: 664974--665036 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
664964 TTTGTTAGTA
664974 TTTTATTTAATTATTGT-ATTATTTAATTT
1 TTTTATTTAATTATT-TAATTATTTAATTT
** *
665003 TTTTATTTTTTTATTTAATTATTTTATTT
1 TTTTATTTAATTATTTAATTATTTAATTT
665032 TTTTA
1 TTTTA
665037 CAGTTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (29 bp):
TTTTATTTAATTATTTAATTATTTAATTT
Found at i:665306 original size:13 final size:13
Alignment explanation
Indices: 665288--665348 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
665278 AACTGTAAAA
665288 AAATAAAATAATT
1 AAATAAAATAATT
665301 AAATAAAATAA-T
1 AAATAAAATAATT
* *
665313 AAAAAAAATTAAAT
1 AAATAAAA-TAATT
*
665327 -AATACAATAATT
1 AAATAAAATAATT
665339 AAATAAAATA
1 AAATAAAATA
665349 CTAACAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 12 0.30
13 27 0.68
14 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:665335 original size:22 final size:22
Alignment explanation
Indices: 665283--665336 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
665273 TTTATAACTG
* *
665283 TAAAAAAAT-AAAATAATTAAA
1 TAAAACAATAAAAAAAATTAAA
*
665304 TAAAATAATAAAAAAAATTAAA
1 TAAAACAATAAAAAAAATTAAA
*
665326 TAATACAATAA
1 TAAAACAATAA
665337 TTAAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAAACAATAAAAAAAATTAAA
Found at i:665355 original size:22 final size:21
Alignment explanation
Indices: 665283--665348 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
665273 TTTATAACTG
* *
665283 TAAAAAAATAAAATAATTAAA
1 TAAAATAATACAATAATTAAA
665304 TAAAATAATA-AA-AA--AAA
1 TAAAATAATACAATAATTAAA
*
665321 TTAAATAATACAATAATTAAA
1 TAAAATAATACAATAATTAAA
665342 TAAAATA
1 TAAAATA
665349 CTAACAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 12 0.32
18 2 0.05
19 4 0.11
20 2 0.05
21 18 0.47
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAAATAATACAATAATTAAA
Found at i:668652 original size:23 final size:23
Alignment explanation
Indices: 668626--668684 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
668616 ATAAGAATAA
* * *
668626 TTCTATGTTTATAGCATGTTTAT
1 TTCTATCTTTATAACACGTTTAT
*
668649 TTCTGTCTTTATAACACGTTTAT
1 TTCTATCTTTATAACACGTTTAT
668672 TTCT-TCCTTTATA
1 TTCTAT-CTTTATA
668685 GTACGTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.20, C:0.15, G:0.08, T:0.56
Consensus pattern (23 bp):
TTCTATCTTTATAACACGTTTAT
Found at i:668690 original size:23 final size:23
Alignment explanation
Indices: 668633--668692 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
668623 TAATTCTATG
*
668633 TTTATAGCATGTTTATTTCTGTC
1 TTTATAGCACGTTTATTTCTGTC
*
668656 TTTATAACACGTTTATTTCT-TCC
1 TTTATAGCACGTTTATTTCTGT-C
*
668679 TTTATAGTACGTTT
1 TTTATAGCACGTTT
668693 TTTATTCGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.55
Consensus pattern (23 bp):
TTTATAGCACGTTTATTTCTGTC
Found at i:673544 original size:63 final size:63
Alignment explanation
Indices: 673422--673544 Score: 158
Period size: 63 Copynumber: 2.0 Consensus size: 63
673412 CAACGGAATA
* * *
673422 AAAACATCAAATGCAATTAGTGCATCGATGTATAGGGAGTGCATCGATACACCCCTTAAGATG
1 AAAACATCAAATGCAATTAGTGCATCGATGCATAGGGAGTGCATCGATACACACATTAAGATG
* * * * *
673485 AAAACATCGAATGCGATTTGTGCA-CTGATGCATAGGTAGTGCATCGATGCACACATTAAG
1 AAAACATCAAATGCAATTAGTGCATC-GATGCATAGGGAGTGCATCGATACACACATTAAG
673545 GGATGCATCG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 1 0.02
63 50 0.98
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (63 bp):
AAAACATCAAATGCAATTAGTGCATCGATGCATAGGGAGTGCATCGATACACACATTAAGATG
Found at i:674141 original size:18 final size:18
Alignment explanation
Indices: 674118--674152 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
674108 AGGGATTATC
674118 AGTGGTCATTCGAGACAT
1 AGTGGTCATTCGAGACAT
*
674136 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGAGACA
674153 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGAGACAT
Found at i:680115 original size:21 final size:22
Alignment explanation
Indices: 680068--680115 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
680058 TTGAATACCA
680068 TATAAAGAATAGGATTTTGAGG
1 TATAAAGAATAGGATTTTGAGG
*
680090 T-TAAAGAA-ATGATTATTGA-G
1 TATAAAGAATAGGATT-TTGAGG
680110 TATAAA
1 TATAAA
680116 TGACTGTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 7 0.30
21 15 0.65
22 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (22 bp):
TATAAAGAATAGGATTTTGAGG
Found at i:680637 original size:32 final size:30
Alignment explanation
Indices: 680596--680665 Score: 104
Period size: 32 Copynumber: 2.3 Consensus size: 30
680586 CCGAGATAGT
*
680596 ATATTTTAAATATTTTAGTAAACACTTATTAA
1 ATATTTTAAATATTTTAGTAAACAATTA--AA
*
680628 ATATTTTAAATATTTTAGTAAATAATTAAA
1 ATATTTTAAATATTTTAGTAAACAATTAAA
680658 ATATTTTA
1 ATATTTTA
680666 TTATTCATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 10 0.28
32 26 0.72
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (30 bp):
ATATTTTAAATATTTTAGTAAACAATTAAA
Found at i:680651 original size:21 final size:21
Alignment explanation
Indices: 680625--680665 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
680615 AAACACTTAT
* *
680625 TAAATATTTTAAATATTTTAG
1 TAAATAATTAAAATATTTTAG
680646 TAAATAATTAAAATATTTTA
1 TAAATAATTAAAATATTTTA
680666 TTATTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TAAATAATTAAAATATTTTAG
Found at i:681575 original size:59 final size:59
Alignment explanation
Indices: 681511--681681 Score: 200
Period size: 59 Copynumber: 2.9 Consensus size: 59
681501 AGATTAAAAC
** *
681511 CAAATTTATTAACTAATTTCAAATTATATACCAAATTAAAGTAATTAAGAAACTTCAGT
1 CAAATTTATTAACTAATTTCAAATTATGGACCAAATTAAATTAATTAAGAAACTTCAGT
* * * * * *
681570 CAAATTTATTAACTAATTTCGAGTTATGGACTAAATTGAATTAATTAAGAAATTTGAGT
1 CAAATTTATTAACTAATTTCAAATTATGGACCAAATTAAATTAATTAAGAAACTTCAGT
* * * *
681629 CAATTTTATTAA-TCAATTTCATATTAGGGATCAAATTAAAATTAATTAAGAAA
1 CAAATTTATTAACT-AATTTCAAATTATGGACCAAATT-AAATTAATTAAGAAA
681682 TTAGCGTCGA
Statistics
Matches: 93, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
58 1 0.01
59 78 0.84
60 14 0.15
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (59 bp):
CAAATTTATTAACTAATTTCAAATTATGGACCAAATTAAATTAATTAAGAAACTTCAGT
Found at i:681716 original size:60 final size:59
Alignment explanation
Indices: 681543--681717 Score: 155
Period size: 59 Copynumber: 2.9 Consensus size: 59
681533 ATTATATACC
* * * *
681543 AAATTAAAGTAATTAAGAAACTT-CAGTCAAAT-TTATTAACTAATTTCGAG-TTATGGACT
1 AAATTAAATTAATTAAGAAA-TTAGAGTC-AATGTTATTAACTAATTT-AAGTTTAGGGACT
* * * *
681602 AAATTGAATTAATTAAGAAATTTGAGTCAATTTTATTAA-TCAATTTCA-TATTAGGGA-T
1 AAATTAAATTAATTAAGAAATTAGAGTCAATGTTATTAACT-AATTTAAGT-TTAGGGACT
* *
681660 CAAATTAAAATTAATTAAGAAATTAGCGTCGATGTTATTAACTAATTTAAGTTTAGGG
1 -AAATT-AAATTAATTAAGAAATTAGAGTCAATGTTATTAACTAATTTAAGTTTAGGG
681718 GAAAAAAACT
Statistics
Matches: 96, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
58 8 0.08
59 45 0.47
60 41 0.43
61 2 0.02
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (59 bp):
AAATTAAATTAATTAAGAAATTAGAGTCAATGTTATTAACTAATTTAAGTTTAGGGACT
Found at i:682554 original size:18 final size:19
Alignment explanation
Indices: 682517--682554 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
682507 TGGGCCACAA
682517 AGTTTAGTATTCAATGCAATT
1 AGTTTAGTATT--ATGCAATT
682538 AGTTTAGTATT-TGCAAT
1 AGTTTAGTATTATGCAAT
682555 CATAGGCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
21 11 0.65
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (19 bp):
AGTTTAGTATTATGCAATT
Found at i:682787 original size:20 final size:20
Alignment explanation
Indices: 682763--682843 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 20
682753 CATAGTTTCC
682763 AAATTCGCAACACGAATTTG
1 AAATTCGCAACACGAATTTG
* * *
682783 GAATTCGCAACACAGAA-GTA
1 AAATTCGCAACAC-GAATTTG
* *
682803 AAATTCGCAACTCGAATCTG
1 AAATTCGCAACACGAATTTG
682823 ACAATTTCGCAACACGAATTT
1 A-AA-TTCGCAACACGAATTT
682844 CTTTTTCGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.06
20 26 0.54
21 5 0.10
22 14 0.29
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (20 bp):
AAATTCGCAACACGAATTTG
Found at i:683424 original size:20 final size:20
Alignment explanation
Indices: 683401--683451 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
683391 AATTCGCAAT
*
683401 ATGAAAATCGCAACTCGAAA
1 ATGAAAATCGCAACGCGAAA
*
683421 ATGAAATTCGCAACGCGAAA
1 ATGAAAATCGCAACGCGAAA
683441 ACT-AAAATCGC
1 A-TGAAAATCGC
683452 GTTGCGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.16
Consensus pattern (20 bp):
ATGAAAATCGCAACGCGAAA
Found at i:685050 original size:42 final size:42
Alignment explanation
Indices: 684984--685149 Score: 178
Period size: 42 Copynumber: 4.0 Consensus size: 42
684974 CGCCACTTTT
* * **
684984 TCATCAAGTCGATTCTTCAGTTCGACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTACACCTCGACACCGAGATCCATCACC
* *
685026 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTACACCTCGACACCGAGATCCATCACC
* * * *
685068 TGATCGAG-CTTATTCTACACCTCGACATCGAGAGCCATCACC
1 TCATCGAGTC-GATTCTACACCTCGACACCGAGATCCATCACC
* * *
685110 T-AT--AGCCAACTCTACACCTCGACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTACACCTCGACACCGAGATCCATCACC
685149 T
1 T
685150 ATTCCATCAC
Statistics
Matches: 109, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
39 31 0.28
40 1 0.01
41 3 0.03
42 74 0.68
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (42 bp):
TCATCGAGTCGATTCTACACCTCGACACCGAGATCCATCACC
Found at i:685285 original size:21 final size:21
Alignment explanation
Indices: 685261--685309 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
685251 TGAGTTAGGG
685261 GCTTTACGTAATGAGGTCAGT
1 GCTTTACGTAATGAGGTCAGT
*
685282 GCTTTACGTGATGAGGTCAGT
1 GCTTTACGTAATGAGGTCAGT
*
685303 GTTTTAC
1 GCTTTAC
685310 ATGATGTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.29, T:0.37
Consensus pattern (21 bp):
GCTTTACGTAATGAGGTCAGT
Found at i:685314 original size:21 final size:21
Alignment explanation
Indices: 685261--685315 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
685251 TGAGTTAGGG
* *
685261 GCTTTACGTAATGAGGTCAGT
1 GCTTTACATGATGAGGTCAGT
*
685282 GCTTTACGTGATGAGGTCAGT
1 GCTTTACATGATGAGGTCAGT
*
685303 GTTTTACATGATG
1 GCTTTACATGATG
685316 TCAATGGTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (21 bp):
GCTTTACATGATGAGGTCAGT
Found at i:685353 original size:21 final size:21
Alignment explanation
Indices: 685245--685363 Score: 66
Period size: 21 Copynumber: 5.7 Consensus size: 21
685235 CTCCACCTCC
* *
685245 ACGTGATGAGTTAGGGGCTTT
1 ACGTGATGAGGTAGGGTCTTT
* *
685266 ACGTAATGAGGTCAGTG-CTTT
1 ACGTGATGAGGT-AGGGTCTTT
*
685287 ACGTGATGAGGTCAGTGT-TTT
1 ACGTGATGAGGT-AGGGTCTTT
* *** * * *
685308 ACATGATG-TCAATGGTGCATG
1 ACGTGATGAGGTAGGGT-CTTT
685329 ACGTGATGAGGTAGGGTCTTT
1 ACGTGATGAGGTAGGGTCTTT
685350 ACGT-AGTGAGGTAG
1 ACGTGA-TGAGGTAG
685364 CTATTTTACG
Statistics
Matches: 73, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
19 3 0.04
20 1 0.01
21 62 0.85
22 7 0.10
ACGTcount: A:0.23, C:0.11, G:0.34, T:0.32
Consensus pattern (21 bp):
ACGTGATGAGGTAGGGTCTTT
Found at i:685375 original size:42 final size:43
Alignment explanation
Indices: 685329--685424 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 43
685319 ATGGTGCATG
685329 ACGTGATGAGGTA-GG-GTCTTTACGTAGTGAGGTAGCTATTTT
1 ACGTGATGAGGTATGGTGT-TTTACGTAGTGAGGTAGCTATTTT
** * * *
685371 ACGTGATGA-CAATGGTGTTTTACGTGGTTAGGTAGCTGTTTT
1 ACGTGATGAGGTATGGTGTTTTACGTAGTGAGGTAGCTATTTT
685413 ACGTGATGAGGT
1 ACGTGATGAGGT
685425 CGGTGCTCTA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
41 1 0.02
42 41 0.93
43 2 0.05
ACGTcount: A:0.21, C:0.09, G:0.33, T:0.36
Consensus pattern (43 bp):
ACGTGATGAGGTATGGTGTTTTACGTAGTGAGGTAGCTATTTT
Found at i:685396 original size:63 final size:62
Alignment explanation
Indices: 685261--685425 Score: 163
Period size: 63 Copynumber: 2.6 Consensus size: 62
685251 TGAGTTAGGG
* * * *
685261 GCTTTACGTAATGAGGTCAGTGCTTTACGTGATGAGGTCAGTGTTTTACATGATGTCAATGGT
1 GCTTTACGTGATGAGGT-AGGGCTTTACGTGATGAGGTCAGTATTTTACATGATGACAATGGT
* * *
685324 GCATGACGTGATGAGGTAGGGTCTTTACGT-AGTGAGGT-AGCTATTTTACGTGATGACAATGGT
1 GCTTTACGTGATGAGGTAGGG-CTTTACGTGA-TGAGGTCAG-TATTTTACATGATGACAATGGT
* * * * *
685387 GTTTTACGTGGTTAGGTAGCTGTTTTACGTGATGAGGTC
1 GCTTTACGTGATGAGGTAG-GGCTTTACGTGATGAGGTC
685426 GGTGCTCTAC
Statistics
Matches: 82, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
62 6 0.07
63 74 0.90
64 2 0.02
ACGTcount: A:0.21, C:0.12, G:0.32, T:0.36
Consensus pattern (62 bp):
GCTTTACGTGATGAGGTAGGGCTTTACGTGATGAGGTCAGTATTTTACATGATGACAATGGT
Found at i:685424 original size:21 final size:21
Alignment explanation
Indices: 685329--685424 Score: 81
Period size: 21 Copynumber: 4.6 Consensus size: 21
685319 ATGGTGCATG
*
685329 ACGTGATGAGGTAG-GGTCTTT
1 ACGTGATGAGGTAGCTGT-TTT
*
685350 ACGT-AGTGAGGTAGCTATTTT
1 ACGTGA-TGAGGTAGCTGTTTT
** *
685371 ACGTGATGA-CAATGGTGTTTT
1 ACGTGATGAGGTA-GCTGTTTT
* *
685392 ACGTGGTTAGGTAGCTGTTTT
1 ACGTGATGAGGTAGCTGTTTT
685413 ACGTGATGAGGT
1 ACGTGATGAGGT
685425 CGGTGCTCTA
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
20 2 0.04
21 52 0.91
22 3 0.05
ACGTcount: A:0.21, C:0.09, G:0.33, T:0.36
Consensus pattern (21 bp):
ACGTGATGAGGTAGCTGTTTT
Found at i:685437 original size:42 final size:41
Alignment explanation
Indices: 685329--685438 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 41
685319 ATGGTGCATG
*
685329 ACGTGATGAGGTAGG-GTCTTTACGTAGTGAGGTAGCTATTTT
1 ACGTGATGAGGT-GGTG-CTTTACGTGGTGAGGTAGCTATTTT
** * * *
685371 ACGTGATGACAATGGTGTTTTACGTGGTTAGGTAGCTGTTTT
1 ACGTGATGA-GGTGGTGCTTTACGTGGTGAGGTAGCTATTTT
*
685413 ACGTGATGAGGTCGGTGCTCTACGTG
1 ACGTGATGAGGT-GGTGCTTTACGTG
685439 AGATTGTTTC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
41 1 0.02
42 52 0.95
43 2 0.04
ACGTcount: A:0.19, C:0.12, G:0.34, T:0.35
Consensus pattern (41 bp):
ACGTGATGAGGTGGTGCTTTACGTGGTGAGGTAGCTATTTT
Found at i:685766 original size:21 final size:21
Alignment explanation
Indices: 685715--685776 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
685705 GAAGAAGCCT
* *
685715 GATCCACCTACCATTATTCAG
1 GATCCACCTCCCATTGTTCAG
685736 GATCCACCTCCCATTGTTCAG
1 GATCCACCTCCCATTGTTCAG
* * *
685757 GATTCACCTCTCATCGTTCA
1 GATCCACCTCCCATTGTTCA
685777 AGAGGTCCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.23, C:0.35, G:0.11, T:0.31
Consensus pattern (21 bp):
GATCCACCTCCCATTGTTCAG
Found at i:685787 original size:21 final size:20
Alignment explanation
Indices: 685763--685818 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
685753 TCAGGATTCA
*
685763 CCTCTCATCGTTCAAGAGGTC
1 CCTC-CATCGTTCAAGAGGCC
*
685784 CCTCCAATCGTTCAAGCGGCC
1 CCTCC-ATCGTTCAAGAGGCC
685805 CCTCCCATCGTTCA
1 CCT-CCATCGTTCA
685819 GGATCCACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 1 0.03
21 28 0.90
22 2 0.06
ACGTcount: A:0.18, C:0.41, G:0.16, T:0.25
Consensus pattern (20 bp):
CCTCCATCGTTCAAGAGGCC
Found at i:687406 original size:34 final size:34
Alignment explanation
Indices: 687363--687451 Score: 115
Period size: 34 Copynumber: 2.6 Consensus size: 34
687353 TTTAAGAAAA
* ***
687363 TCAAATTCGCAATGCGAAAATTGTAACTCGATAT
1 TCAAATTCGCAACGCGAAAATCACAACTCGATAT
*
687397 TCAAATTCGCAACACGAAAATCACAACTCGATAT
1 TCAAATTCGCAACGCGAAAATCACAACTCGATAT
* *
687431 TTAAATTCACAACGCGAAAAT
1 TCAAATTCGCAACGCGAAAAT
687452 GAAAATGAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (34 bp):
TCAAATTCGCAACGCGAAAATCACAACTCGATAT
Found at i:687580 original size:94 final size:94
Alignment explanation
Indices: 687472--687644 Score: 251
Period size: 94 Copynumber: 1.8 Consensus size: 94
687462 ATCGATTTTC
* * *
687472 ATTTTCGCGTTGCGAATTATATTTTCGAGTTGTGAATTAT-ATTTTCGAGTTACGAATTAT-ATT
1 ATTTTCGCATTGCGAATTAGATTTTCGAGTTGCGAATT-TGATTTTCGAGTTACGAATT-TGATT
687535 TTCGAGTTGCGAATTTTAATATCGAGTTGCG
64 TTCGAGTTGCGAATTTTAATATCGAGTTGCG
* * * *
687566 ATTTTCGTATTGCGAATTCGATTTTCGCGTTGCGAATTTGATTTTCGAGTTGCGAATTTGATTTT
1 ATTTTCGCATTGCGAATTAGATTTTCGAGTTGCGAATTTGATTTTCGAGTTACGAATTTGATTTT
687631 CGAGTTGCGAATTT
66 CGAGTTGCGAATTT
687645 GGAATTCGAG
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
93 2 0.03
94 68 0.97
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.45
Consensus pattern (94 bp):
ATTTTCGCATTGCGAATTAGATTTTCGAGTTGCGAATTTGATTTTCGAGTTACGAATTTGATTTT
CGAGTTGCGAATTTTAATATCGAGTTGCG
Found at i:687645 original size:20 final size:20
Alignment explanation
Indices: 687472--687666 Score: 178
Period size: 20 Copynumber: 10.1 Consensus size: 20
687462 ATCGATTTTC
*
687472 ATTTTCGCGTTGCGAATTAT-
1 ATTTTCGAGTTGCGAATT-TG
*
687492 ATTTTCGAGTTGTGAATTAT-
1 ATTTTCGAGTTGCGAATT-TG
*
687512 ATTTTCGAGTTACGAATTAT-
1 ATTTTCGAGTTGCGAATT-TG
*
687532 ATTTTCGAGTTGCGAATTTT
1 ATTTTCGAGTTGCGAATTTG
* *
687552 AATATCGAGTTGC------G
1 ATTTTCGAGTTGCGAATTTG
*
687566 ATTTTCGTA-TTGCGAATTCG
1 ATTTTCG-AGTTGCGAATTTG
*
687586 ATTTTCGCGTTGCGAATTTG
1 ATTTTCGAGTTGCGAATTTG
687606 ATTTTCGAGTTGCGAATTTG
1 ATTTTCGAGTTGCGAATTTG
687626 ATTTTCGAGTTGCGAATTTGG
1 ATTTTCGAGTTGCGAATTT-G
* *
687647 A-ATTCGAGCTGCGAATTTG
1 ATTTTCGAGTTGCGAATTTG
687666 A
1 A
687667 GTTGTGAATC
Statistics
Matches: 150, Mismatches: 15, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
14 9 0.06
15 1 0.01
19 3 0.02
20 135 0.90
21 2 0.01
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.43
Consensus pattern (20 bp):
ATTTTCGAGTTGCGAATTTG
Found at i:690317 original size:24 final size:24
Alignment explanation
Indices: 690250--690309 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
690240 TTGAAACATA
690250 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* * *
690274 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
690298 ATCAAATTTCGA
1 ATCAAAATTCGA
690310 ATACTGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:691257 original size:20 final size:20
Alignment explanation
Indices: 691230--691420 Score: 156
Period size: 20 Copynumber: 9.6 Consensus size: 20
691220 CAAAAAATTT
691230 GTGTTGCGAAAAAGAAAATC
1 GTGTTGCGAAAAAGAAAATC
* *
691250 GAGTTGCGAAAAAGAAATTC
1 GTGTTGCGAAAAAGAAAATC
* *
691270 GTGTTGCGAAAAATAAATTC
1 GTGTTGCGAAAAAGAAAATC
* *
691290 GTGTTGCGAAAAATAAATTC
1 GTGTTGCGAAAAAGAAAATC
*
691310 GTGTTGTGAAAAAGAAAATC
1 GTGTTGCGAAAAAGAAAATC
* * * * *
691330 -TAGTTGTGGAGAATAAATTC
1 GT-GTTGCGAAAAAGAAAATC
**
691350 GTGTTGCGAATTCA-AAAATC
1 GTGTTGCGAA-AAAGAAAATC
* * *
691370 GAGTTGCGAAATTA-AAAATA
1 GTGTTGCGAAA-AAGAAAATC
**
691390 GTGTTGCGAAAAAGAACTTC
1 GTGTTGCGAAAAAGAAAATC
691410 GTGTTGC-AAAA
1 GTGTTGCGAAAA
691421 TTGTCAAAAT
Statistics
Matches: 141, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
19 6 0.04
20 133 0.94
21 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (20 bp):
GTGTTGCGAAAAAGAAAATC
Found at i:691274 original size:40 final size:40
Alignment explanation
Indices: 691224--691405 Score: 199
Period size: 40 Copynumber: 4.5 Consensus size: 40
691214 TATACCCAAA
* *
691224 AAATTTGTGTTGCGAAAAAGAAAATCGAGTTGCGAAAAAG
1 AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAAAAT
* * *
691264 AAATTCGTGTTGCGAAAAATAAATTCGTGTTGCGAAAAAT
1 AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAAAAT
* * * * *
691304 AAATTCGTGTTGTGAAAAAGAAAATCTAGTTGTGGAGAAT
1 AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAAAAT
**
691344 AAATTCGTGTTGCGAATTCA-AAAATCGAGTTGCGAAATTAA-
1 AAATTCGTGTTGCGAA-AAAGAAAATCGAGTTGCGAAA--AAT
*
691385 AAA-TAGTGTTGCGAAAAAGAA
1 AAATTCGTGTTGCGAAAAAGAA
691406 CTTCGTGTTG
Statistics
Matches: 115, Mismatches: 23, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 108 0.94
41 4 0.03
42 2 0.02
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (40 bp):
AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAAAAT
Found at i:691288 original size:60 final size:59
Alignment explanation
Indices: 691224--691438 Score: 195
Period size: 60 Copynumber: 3.6 Consensus size: 59
691214 TATACCCAAA
*
691224 AAATTTGTGTTGCGAAAAAGAAAATCGAGTTGCGAAAAAGAAATTCGTGTTGCGAAAAAT
1 AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAAAAGAAA-TCGTGTTGCGAAAAAT
* * * * * * *
691284 AAATTCGTGTTGCGAAAAATAAATTCGTGTTGTGAAAAAGAAAATC-TAGTTGTGGAGAAT
1 AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAAAAG-AAATCGT-GTTGCGAAAAAT
** * *
691344 AAATTCGTGTTGCGAATTCA-AAAATCGAGTTGCGAAATTAA-AAATAGTGTTGCGAAAAAG
1 AAATTCGTGTTGCGAA-AAAGAAAATCGAGTTGCGAAA--AAGAAATCGTGTTGCGAAAAAT
* *
691404 AACTTCGTGTTGC-AAAATTGTCAAAATCGAGTTGC
1 AAATTCGTGTTGCGAAAA-AG--AAAATCGAGTTGC
691439 AAATTTGACT
Statistics
Matches: 123, Mismatches: 22, Indels: 18
0.75 0.13 0.11
Matches are distributed among these distances:
59 3 0.02
60 100 0.81
61 5 0.04
62 15 0.12
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (59 bp):
AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAAAAGAAATCGTGTTGCGAAAAAT
Found at i:691501 original size:22 final size:23
Alignment explanation
Indices: 691474--691528 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
691464 TGGAAACTGT
*
691474 GTTGCGAAATTGTCAAAATC-GA
1 GTTGCGAAATTGCCAAAATCTGA
* *
691496 GTTGCG-AATT-CCAAATTCTGT
1 GTTGCGAAATTGCCAAAATCTGA
691517 GTTGCGAAATTG
1 GTTGCGAAATTG
691529 GAGTTCGCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 6 0.22
21 11 0.41
22 10 0.37
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (23 bp):
GTTGCGAAATTGCCAAAATCTGA
Found at i:691541 original size:63 final size:60
Alignment explanation
Indices: 691346--691549 Score: 171
Period size: 62 Copynumber: 3.3 Consensus size: 60
691336 TGGAGAATAA
* * ** *
691346 ATTCGTGTTGCG-AA-T-TCAAAAATCGAGTTGCGAAATTAAAAATAGTGTTGCGAAAAAGA
1 ATTCGTGTTGCGAAATTGTC-AAAATCGAGTTGCG-AATTAAAATTTGTGTTGCGAAATTGG
* * ** * *
691405 ACTTCGTGTTGCAAAATTGTCAAAATCGAGTTGCAAATTTGACTTATGTGTTGCGAATTTGG
1 A-TTCGTGTTGCGAAATTGTCAAAATCGAGTTGCGAATTAAAATT-TGTGTTGCGAAATTGG
** *
691467 AAACTGTGTTGCGAAATTGTCAAAATCGAGTTGCGAATTCCAAATTCTGTGTTGCGAAATTGG
1 ATTC-GTGTTGCGAAATTGTCAAAATCGAGTTGCGAATT-AAAATT-TGTGTTGCGAAATTGG
* *
691530 AGTTCGCGTTGCGAATTTGT
1 A-TTCGTGTTGCGAAATTGT
691550 TGGTTATTTT
Statistics
Matches: 113, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
59 1 0.01
60 10 0.09
61 9 0.08
62 58 0.51
63 34 0.30
64 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.33
Consensus pattern (60 bp):
ATTCGTGTTGCGAAATTGTCAAAATCGAGTTGCGAATTAAAATTTGTGTTGCGAAATTGG
Found at i:700642 original size:114 final size:114
Alignment explanation
Indices: 700442--700669 Score: 456
Period size: 114 Copynumber: 2.0 Consensus size: 114
700432 AACACTAACA
700442 AACATTAAATTGTTTTTATTCATAAAATGTATATTTTTATCATTACGTCTTTTTTATGTATAAAT
1 AACATTAAATTGTTTTTATTCATAAAATGTATATTTTTATCATTACGTCTTTTTTATGTATAAAT
700507 GCTGTAAGGAGTCTTTTATGAACAAAAGAATAAATAACCGGTAAAATAC
66 GCTGTAAGGAGTCTTTTATGAACAAAAGAATAAATAACCGGTAAAATAC
700556 AACATTAAATTGTTTTTATTCATAAAATGTATATTTTTATCATTACGTCTTTTTTATGTATAAAT
1 AACATTAAATTGTTTTTATTCATAAAATGTATATTTTTATCATTACGTCTTTTTTATGTATAAAT
700621 GCTGTAAGGAGTCTTTTATGAACAAAAGAATAAATAACCGGTAAAATAC
66 GCTGTAAGGAGTCTTTTATGAACAAAAGAATAAATAACCGGTAAAATAC
700670 GTAATAATAT
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (114 bp):
AACATTAAATTGTTTTTATTCATAAAATGTATATTTTTATCATTACGTCTTTTTTATGTATAAAT
GCTGTAAGGAGTCTTTTATGAACAAAAGAATAAATAACCGGTAAAATAC
Found at i:704669 original size:15 final size:16
Alignment explanation
Indices: 704639--704670 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
704629 GTATTATGAA
704639 TTAATTAAATATTATT
1 TTAATTAAATATTATT
704655 TTAATTAAA-ATTATT
1 TTAATTAAATATTATT
704670 T
1 T
704671 ACCTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATTAAATATTATT
Found at i:706548 original size:21 final size:21
Alignment explanation
Indices: 706524--706565 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
706514 TATGTGTCTA
*
706524 AAGTATTGATGTGATGTATAT
1 AAGTATTGATGTGATATATAT
*
706545 AAGTGTTGATGTGATATATAT
1 AAGTATTGATGTGATATATAT
706566 TATGTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (21 bp):
AAGTATTGATGTGATATATAT
Found at i:706635 original size:32 final size:32
Alignment explanation
Indices: 706538--706636 Score: 126
Period size: 32 Copynumber: 3.1 Consensus size: 32
706528 ATTGATGTGA
*
706538 TGTATATAAGTGTTGATGTGATATATATTATG
1 TGTATATAAGTGATGATGTGATATATATTATG
* * * * *
706570 TATTTAAAAGTGATGATATGATATATACTATG
1 TGTATATAAGTGATGATGTGATATATATTATG
* *
706602 TGTACATAAGTGATGATGTGATATATGTTATG
1 TGTATATAAGTGATGATGTGATATATATTATG
706634 TGT
1 TGT
706637 TCAAAATGAT
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.43
Consensus pattern (32 bp):
TGTATATAAGTGATGATGTGATATATATTATG
Found at i:707130 original size:27 final size:26
Alignment explanation
Indices: 707085--707193 Score: 77
Period size: 27 Copynumber: 4.2 Consensus size: 26
707075 CTTATACAAG
*
707085 AATAT-ATTATTTATGTTATAAAATATT
1 AATATAATAATTTAT-TTATAAAATA-T
707112 AATATAATAATTTATTTATTTAAAATAT
1 AATATAATAATTTATTTA--TAAAATAT
* * *
707140 -AT-TAATATTTTA-TAATATAA-AT
1 AATATAATAATTTATTTATAAAATAT
*
707162 AATATAATAA-TTATTTATGAAAAAATT
1 AATATAATAATTTATTTAT-AAAATA-T
707189 AATAT
1 AATAT
707194 CAATCTAGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
22 2 0.03
23 9 0.14
24 8 0.12
25 5 0.08
26 10 0.15
27 16 0.24
28 9 0.14
29 7 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
AATATAATAATTTATTTATAAAATAT
Found at i:707139 original size:50 final size:49
Alignment explanation
Indices: 707085--707179 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 49
707075 CTTATACAAG
* *
707085 AATATATTATTTATGTTATAAAAT-ATTAATATAATAATTTATTTATTTAA
1 AATATATTA-ATATGTTATAAAATAAATAATATAATAA-TTATTTATTTAA
* *
707135 AATATATTAATATTTTATAATATAAATAATATAATAATTATTTAT
1 AATATATTAATATGTTATAAAATAAATAATATAATAATTATTTAT
707180 GAAAAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
49 19 0.47
50 21 0.52
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (49 bp):
AATATATTAATATGTTATAAAATAAATAATATAATAATTATTTATTTAA
Found at i:707187 original size:50 final size:50
Alignment explanation
Indices: 707076--707187 Score: 120
Period size: 50 Copynumber: 2.2 Consensus size: 50
707066 TAATATATGC
* * *
707076 TTATACAAGAATATATTATTTATGTTATAAAATATTAATATAATAATTTAT
1 TTATA-AAAAATATATTATATATGTTATAAAATAATAATATAATAATTTAT
** * *
707127 TTATTTAAAATATATTA-ATATTTTATAATATAAATAATATAATAA-TTAT
1 TTATAAAAAATATATTATATATGTTATAAAAT-AATAATATAATAATTTAT
707176 TTATGAAAAAAT
1 TTAT-AAAAAAT
707188 TAATATCAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
49 19 0.38
50 27 0.54
51 4 0.08
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (50 bp):
TTATAAAAAATATATTATATATGTTATAAAATAATAATATAATAATTTAT
Found at i:710342 original size:31 final size:30
Alignment explanation
Indices: 710296--710375 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 30
710286 TTCGATAATA
*
710296 TAATAATTATTTTATAGTATTTAGATAAATT
1 TAATAA-TATTTTATAATATTTAGATAAATT
* *
710327 TATTAATAATTTTATAATATTTTGATAAATT
1 TAATAAT-ATTTTATAATATTTAGATAAATT
710358 TAATAAGTATTTTATAAT
1 TAATAA-TATTTTATAAT
710376 TTTTTAAACT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.02
31 41 0.95
32 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTATAATATTTAGATAAATT
Found at i:710357 original size:20 final size:19
Alignment explanation
Indices: 710332--710378 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
710322 AAATTTATTA
710332 ATAATTTTATAA-TATTTT
1 ATAATTTTATAAGTATTTT
*
710350 GATAAATTTAATAAGTATTTT
1 -AT-AATTTTATAAGTATTTT
710371 ATAATTTT
1 ATAATTTT
710379 TTAAACTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 7 0.29
20 11 0.46
21 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (19 bp):
ATAATTTTATAAGTATTTT
Found at i:711123 original size:31 final size:31
Alignment explanation
Indices: 711065--711132 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
711055 TCAATAAAGT
**
711065 TTAAAAAATTATAAAATACTTCTTAAATTTA
1 TTAAAAAATTATAAAATACTTAATAAATTTA
*
711096 TTAAAAGATTATAAAATTA-TTAATAAATTTA
1 TTAAAAAATTATAAAA-TACTTAATAAATTTA
711127 TCTAAA
1 T-TAAA
711133 TACTATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (31 bp):
TTAAAAAATTATAAAATACTTAATAAATTTA
Found at i:711140 original size:31 final size:31
Alignment explanation
Indices: 711065--711148 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 31
711055 TCAATAAAGT
* * * **
711065 TTAAAAAATTATAAAATACTTCTTAAATTTA
1 TTAAAAGACTATAAAATAATTAATAAATTTA
* *
711096 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAGACTATAAAATAATTAATAAATTTA
*
711127 TCT-AAATACTATAAAATAATTA
1 T-TAAAAGACTATAAAATAATTA
711149 TTATATTATC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 43 0.98
32 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (31 bp):
TTAAAAGACTATAAAATAATTAATAAATTTA
Found at i:716711 original size:7 final size:7
Alignment explanation
Indices: 716699--716728 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
716689 AAAAGGGGAT
716699 GAATTAA
1 GAATTAA
716706 GAATTAA
1 GAATTAA
716713 GAATTAA
1 GAATTAA
*
716720 GAATGAA
1 GAATTAA
716727 GA
1 GA
716729 GATGGGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (7 bp):
GAATTAA
Found at i:720125 original size:21 final size:20
Alignment explanation
Indices: 720092--720131 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
720082 AAATTGTTTA
720092 AAATAAATTTATATATAATT
1 AAATAAATTTATATATAATT
720112 AAATAAATTATATATATAAT
1 AAATAAATT-TATATATAAT
720132 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATAAATTTATATATAATT
Found at i:720136 original size:13 final size:12
Alignment explanation
Indices: 720097--720142 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 12
720087 GTTTAAAATA
720097 AATT-TATATAT
1 AATTATATATAT
720108 AATTA-A-ATA-
1 AATTATATATAT
720117 AATTATATATAT
1 AATTATATATAT
720129 AATATATATATAT
1 AAT-TATATATAT
720142 A
1 A
720143 TAACAATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 5 0.17
10 4 0.13
11 8 0.27
12 3 0.10
13 10 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AATTATATATAT
Found at i:720140 original size:17 final size:16
Alignment explanation
Indices: 720094--720145 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
720084 ATTGTTTAAA
*
720094 ATAAATTTATATATA-
1 ATAAATATATATATAT
*
720109 ATTAAATAAAT-TATAT
1 A-TAAATATATATATAT
720125 ATATAATATATATATAT
1 ATA-AATATATATATAT
720142 ATAA
1 ATAA
720146 CAATGTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
15 7 0.23
16 15 0.50
17 8 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAATATATATATAT
Found at i:720857 original size:60 final size:60
Alignment explanation
Indices: 720721--720857 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 60
720711 TAAATTGGTT
* * * *
720721 CCTAAATTTTTAAATATTTTAATTTCATCCCTAAACCATAGCTATCATTCTAAGTCAGTC
1 CCTAAACTTTTAAATATTTTAATTTCATCCCTAAACCATACCTATCATTCTAAATCAATC
* * * * ** *
720781 CCCAAACATTTAAATATTTTATTTTCATCCCTAAACTATATCCT-TTGTTCTAAATTAATC
1 CCTAAACTTTTAAATATTTTAATTTCATCCCTAAACCATA-CCTATCATTCTAAATCAATC
*
720841 CCTAAACTTTTGAATAT
1 CCTAAACTTTTAAATAT
720858 AATTGCATCT
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
60 60 0.97
61 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.42
Consensus pattern (60 bp):
CCTAAACTTTTAAATATTTTAATTTCATCCCTAAACCATACCTATCATTCTAAATCAATC
Found at i:721407 original size:17 final size:18
Alignment explanation
Indices: 721385--721420 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
721375 AAAAATTATA
721385 AAATAATTATTATT-TTT
1 AAATAATTATTATTATTT
721402 AAATAATTATTATTATTT
1 AAATAATTATTATTATTT
721420 A
1 A
721421 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATAATTATTATTATTT
Found at i:721728 original size:29 final size:29
Alignment explanation
Indices: 721691--721783 Score: 125
Period size: 29 Copynumber: 3.1 Consensus size: 29
721681 TTTTTTGAAT
721691 AATTATGAAATAGTAATTAAATTTATCAA
1 AATTATGAAATAGTAATTAAATTTATCAA
721720 AATTATGAAATAGTAATTAAATTTATCAAA
1 AATTATGAAATAGTAATTAAATTTATC-AA
* * *
721750 ATATTATAAAATAAT-CTCTAAATTTATCAA
1 A-ATTATGAAATAGTAAT-TAAATTTATCAA
721780 AATT
1 AATT
721784 TATCTTTATT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
29 30 0.52
30 7 0.12
31 21 0.36
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (29 bp):
AATTATGAAATAGTAATTAAATTTATCAA
Found at i:726563 original size:28 final size:28
Alignment explanation
Indices: 726532--726587 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
726522 GTATATACAA
* *
726532 CCATACGTAAATATATACATACATGCAT
1 CCATACATAAATACATACATACATGCAT
* *
726560 CCATACATAAATACCTCCATACATGCAT
1 CCATACATAAATACATACATACATGCAT
726588 GGATACTATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.41, C:0.27, G:0.05, T:0.27
Consensus pattern (28 bp):
CCATACATAAATACATACATACATGCAT
Found at i:726565 original size:16 final size:16
Alignment explanation
Indices: 726546--726588 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
726536 ACGTAAATAT
726546 ATACATACATGCATCC
1 ATACATACATGCATCC
* * *
726562 ATACATAAATACCTCC
1 ATACATACATGCATCC
*
726578 ATACATGCATG
1 ATACATACATG
726589 GATACTATCC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.26
Consensus pattern (16 bp):
ATACATACATGCATCC
Found at i:731706 original size:20 final size:21
Alignment explanation
Indices: 731681--731773 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
731671 TTTTCCCAAT
*
731681 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
731701 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
731722 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
731742 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
731763 TCGCAATGCGA
1 TCGCAATGCGA
731774 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:731726 original size:41 final size:41
Alignment explanation
Indices: 731681--731773 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
731671 TTTTCCCAAT
731681 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
731722 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
731763 TCGCAATGCGA
1 TCGCAATGCGA
731774 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:731786 original size:41 final size:41
Alignment explanation
Indices: 731700--731834 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
731690 GAATAAGTAA
* *
731700 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
731741 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
731782 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
731823 TTCGCAACGCGA
1 ATCGCAACGCGA
731835 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:731787 original size:20 final size:20
Alignment explanation
Indices: 731762--731876 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
731752 AATTGGGAAA
*
731762 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
731782 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
731803 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
731823 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
731843 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
731863 TTCGCAACGCGATA
1 ATCGCAACGCGATA
731877 ATACATAATC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 65 0.82
21 14 0.18
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:731835 original size:41 final size:41
Alignment explanation
Indices: 731759--731896 Score: 143
Period size: 41 Copynumber: 3.4 Consensus size: 41
731749 GCGAATTGGG
* * *
731759 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
* * * *
731800 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACT-G
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
*** * *
731840 ACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
* *
731881 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
731897 TTTCAAAGCG
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 32 0.42
41 45 0.58
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
Found at i:732092 original size:22 final size:22
Alignment explanation
Indices: 732064--732107 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
732054 CACTCTCTCA
732064 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
732086 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
732108 TATTTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:732409 original size:20 final size:20
Alignment explanation
Indices: 732386--732428 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
732376 GATAGTCGAA
732386 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
732406 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
732426 TTC
1 TTC
732429 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:735088 original size:19 final size:19
Alignment explanation
Indices: 735066--735196 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
735056 GGAAATTACT
735066 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
735085 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
735099 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
735118 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
735132 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
735151 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
735165 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
735184 ATCGCAACGCGAA
1 ATCGCAATGCGAA
735197 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:735108 original size:33 final size:33
Alignment explanation
Indices: 735066--735192 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
735056 GGAAATTACT
735066 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
735099 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
735131 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
735165 ATCACAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
735193 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:735173 original size:66 final size:66
Alignment explanation
Indices: 735067--735199 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
735057 GAAATTACTA
* *
735067 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
735132 T
66 T
*
735133 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
735198 T
66 T
735199 T
1 T
735200 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:735214 original size:19 final size:20
Alignment explanation
Indices: 735192--735234 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
735182 AAATCGCAAC
735192 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
735211 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
735231 GCGA
1 GCGA
735235 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:735246 original size:14 final size:14
Alignment explanation
Indices: 735227--735264 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
735217 TTCATTTTCG
735227 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
735241 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
735255 CGTTGCGATT
1 CGTTGCGATT
735265 TTCATTTCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.08, C:0.26, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:735408 original size:14 final size:14
Alignment explanation
Indices: 735389--735425 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
735379 CATCAATTAA
735389 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
735403 ACAAATCACCTTTT
1 ACAAATCAACTTTT
735417 ACAAATCAA
1 ACAAATCAA
735426 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:736848 original size:21 final size:21
Alignment explanation
Indices: 736782--736848 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
736772 GTGAATCGGG
*
736782 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
736802 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
736824 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
736845 CTCT
1 CTCT
736849 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:736867 original size:42 final size:41
Alignment explanation
Indices: 736782--736904 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
736772 GTGAATCGGG
* * * * *
736782 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
736824 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * ** *
736866 CTCTTCAACGATAGGAGTAGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
736905 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:738937 original size:20 final size:19
Alignment explanation
Indices: 738906--739085 Score: 101
Period size: 19 Copynumber: 9.8 Consensus size: 19
738896 TCTTTTGGTT
738906 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
738925 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
738946 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
738965 G--A-G--AATTGCAACGC
1 GAAATGAAAATCGCAACGA
**
738979 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
738995 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
739012 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* *
739032 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
739051 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
* *
739070 GAAATAAAAATAGCAA
1 GAAATGAAAATCGCAA
739086 TGCGATTTTT
Statistics
Matches: 126, Mismatches: 22, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
14 16 0.13
15 1 0.01
16 4 0.03
17 4 0.03
18 1 0.01
19 51 0.40
20 47 0.37
21 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:738988 original size:33 final size:33
Alignment explanation
Indices: 738931--739029 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
738921 ACGAGATAAT
*
738931 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
* *
738965 GAGAATTGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
738998 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
739030 GCGAAATAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 44 0.77
34 13 0.23
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:739023 original size:19 final size:19
Alignment explanation
Indices: 739001--739090 Score: 135
Period size: 19 Copynumber: 4.7 Consensus size: 19
738991 GCGACCAGAC
*
739001 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
739020 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATAAA
*
739040 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
739059 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
* *
739078 AATAGCAATGCGA
1 AATCGCAACGCGA
739091 TTTTTGTTTC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 47 0.72
20 18 0.28
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:739044 original size:39 final size:38
Alignment explanation
Indices: 739001--739090 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
738991 GCGACCAGAC
739001 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
739040 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
* *
739078 AATAGCAATGCGA
1 AATCGCAACGCGA
739091 TTTTTGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:739108 original size:19 final size:19
Alignment explanation
Indices: 739086--739152 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
739076 AAAATAGCAA
*
739086 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
739105 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
739124 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
739144 TGCGATTTT
1 TGCGATTTT
739153 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:739730 original size:20 final size:20
Alignment explanation
Indices: 739705--739778 Score: 139
Period size: 20 Copynumber: 3.7 Consensus size: 20
739695 GATTTTGTAT
*
739705 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTCAG
739725 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
739745 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
739765 TATCGCATTGCGAT
1 TATCGCATTGCGAT
739779 TTTCCCAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTCAG
Found at i:741759 original size:23 final size:23
Alignment explanation
Indices: 741733--741776 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
741723 TAAATATCCT
741733 ATTTAGATTAAATGATATTAACG
1 ATTTAGATTAAATGATATTAACG
*
741756 ATTTAGATTAAATGATTTTAA
1 ATTTAGATTAAATGATATTAA
741777 TGTAATCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (23 bp):
ATTTAGATTAAATGATATTAACG
Found at i:741886 original size:34 final size:34
Alignment explanation
Indices: 741848--741922 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
741838 ATATAATTAC
741848 AGTTAAATATAAATGTTAGTATTAAAATTGACAA
1 AGTTAAATATAAATGTTAGTATTAAAATTGACAA
741882 AGTTAAATATAAATGTTAGTATTAAAATTGACAA
1 AGTTAAATATAAATGTTAGTATTAAAATTGACAA
*
741916 AATTAAA
1 AGTTAAA
741923 AGAGTAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.52, C:0.03, G:0.11, T:0.35
Consensus pattern (34 bp):
AGTTAAATATAAATGTTAGTATTAAAATTGACAA
Found at i:748472 original size:32 final size:30
Alignment explanation
Indices: 748403--748523 Score: 170
Period size: 30 Copynumber: 3.9 Consensus size: 30
748393 GAAGGACCTA
* *
748403 TCCATATGTTCCGAAGAACATAGGTAACTG
1 TCCATATGTCCCGAAGGACATAGGTAACTG
748433 TCCATATGTCCCGAAGGACATAGGTAATCTTG
1 TCCATATGTCCCGAAGGACATAGGTAA-C-TG
*
748465 TCCATATGTCCCGAAGGACATAGGTAAACTA
1 TCCATATGTCCCGAAGGACATAGGT-AACTG
* *
748496 TCCATATGTCTCGAAAGACATAGGTAAC
1 TCCATATGTCCCGAAGGACATAGGTAAC
748524 CCTCGACTCT
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
30 28 0.34
31 25 0.30
32 28 0.34
33 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (30 bp):
TCCATATGTCCCGAAGGACATAGGTAACTG
Found at i:749423 original size:20 final size:20
Alignment explanation
Indices: 749395--749434 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
749385 AAATAGACTC
749395 ATCGCGAGTCTTATTTCCAT
1 ATCGCGAGTCTTATTTCCAT
*
749415 ATCGTGAGTCTTATTTCCAT
1 ATCGCGAGTCTTATTTCCAT
749435 TCATCATACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (20 bp):
ATCGCGAGTCTTATTTCCAT
Found at i:751124 original size:20 final size:20
Alignment explanation
Indices: 751098--751164 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
751088 CATAACTAAT
*
751098 AACATAATCATTTGATATAT
1 AACATAATCATTTGATATAG
* * *
751118 CACATAAGTAATTTGACATAG
1 AACATAA-TCATTTGATATAG
751139 AACATAA-CGATTTGATATAG
1 AACATAATC-ATTTGATATAG
751159 AACATA
1 AACATA
751165 GAAAAGGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AACATAATCATTTGATATAG
Found at i:769949 original size:19 final size:18
Alignment explanation
Indices: 769906--769941 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
769896 ACTTAAAATT
769906 ATATAAAATTTTTTCATG
1 ATATAAAATTTTTTCATG
*
769924 ACATAAAATTTTGTTCAT
1 ATATAAAATTTT-TTCAT
769942 ATTATAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (18 bp):
ATATAAAATTTTTTCATG
Found at i:777321 original size:13 final size:13
Alignment explanation
Indices: 777303--777327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
777293 AAAAAAACTA
777303 TAAAAATATACCT
1 TAAAAATATACCT
777316 TAAAAATATACC
1 TAAAAATATACC
777328 ATGTCAGCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAAAATATACCT
Found at i:780947 original size:60 final size:60
Alignment explanation
Indices: 780827--780958 Score: 174
Period size: 60 Copynumber: 2.2 Consensus size: 60
780817 TAGTAAGGTT
* * * **
780827 ACCATTTTGTAACTTTTAATAGTCAAAGGACTCAACAGAGCAACATCATATAGTTTGGGG
1 ACCATTTTATAACTATTAATAGTCAAAGGACTCAACAAAGCAACATCATATAGTCGGGGG
* * * *
780887 ACTATTTTATAACTATTAATAGTCAGAGGCCTCAACAAAGCAACATCCTATAGTCGGGGG
1 ACCATTTTATAACTATTAATAGTCAAAGGACTCAACAAAGCAACATCATATAGTCGGGGG
780947 ACCATTTATATA
1 ACCATTT-TATA
780959 CTTTACCCTA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 57 0.93
61 4 0.07
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (60 bp):
ACCATTTTATAACTATTAATAGTCAAAGGACTCAACAAAGCAACATCATATAGTCGGGGG
Found at i:781241 original size:25 final size:25
Alignment explanation
Indices: 781213--781260 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
781203 TAACTTGATA
781213 TTAAGCATGATCTATTACAATTGTT
1 TTAAGCATGATCTATTACAATTGTT
781238 TTAAGCATGATCTATTACAATTG
1 TTAAGCATGATCTATTACAATTG
781261 AATCGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (25 bp):
TTAAGCATGATCTATTACAATTGTT
Found at i:781995 original size:95 final size:95
Alignment explanation
Indices: 781827--782022 Score: 383
Period size: 95 Copynumber: 2.1 Consensus size: 95
781817 TGTTTCATCA
*
781827 ATGCCACATTGTTACAAAGAAAATGGGTTATTTCAAAACTATATATCTGTCATATATACGCACAT
1 ATGCAACATTGTTACAAAGAAAATGGGTTATTTCAAAACTATATATCTGTCATATATACGCACAT
781892 AGATATAAAAAATCATGCGTTCGTCCCTAT
66 AGATATAAAAAATCATGCGTTCGTCCCTAT
781922 ATGCAACATTGTTACAAAGAAAATGGGTTATTTCAAAACTATATATCTGTCATATATACGCACAT
1 ATGCAACATTGTTACAAAGAAAATGGGTTATTTCAAAACTATATATCTGTCATATATACGCACAT
781987 AGATATAAAAAATCATGCGTTCGTCCCTAT
66 AGATATAAAAAATCATGCGTTCGTCCCTAT
782017 ATGCAA
1 ATGCAA
782023 GCGGTAGAGT
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 100 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (95 bp):
ATGCAACATTGTTACAAAGAAAATGGGTTATTTCAAAACTATATATCTGTCATATATACGCACAT
AGATATAAAAAATCATGCGTTCGTCCCTAT
Found at i:782550 original size:80 final size:80
Alignment explanation
Indices: 782417--782578 Score: 324
Period size: 80 Copynumber: 2.0 Consensus size: 80
782407 GTCGAAACCG
782417 CTCAAAGATTGGTTCGGAATCGCTTCTTTCTCGGCCCTCGAATTGTTAACCTTGTCCAACAGCAC
1 CTCAAAGATTGGTTCGGAATCGCTTCTTTCTCGGCCCTCGAATTGTTAACCTTGTCCAACAGCAC
782482 CGATGCATCACATCC
66 CGATGCATCACATCC
782497 CTCAAAGATTGGTTCGGAATCGCTTCTTTCTCGGCCCTCGAATTGTTAACCTTGTCCAACAGCAC
1 CTCAAAGATTGGTTCGGAATCGCTTCTTTCTCGGCCCTCGAATTGTTAACCTTGTCCAACAGCAC
782562 CGATGCATCACATCC
66 CGATGCATCACATCC
782577 CT
1 CT
782579 AACATGGTAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.29
Consensus pattern (80 bp):
CTCAAAGATTGGTTCGGAATCGCTTCTTTCTCGGCCCTCGAATTGTTAACCTTGTCCAACAGCAC
CGATGCATCACATCC
Found at i:783387 original size:16 final size:15
Alignment explanation
Indices: 783366--783403 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
783356 ATACTCGATC
*
783366 TAAATTAAATGATTAA
1 TAAATTAAAT-ATAAA
783382 TAAATTAAATATAAA
1 TAAATTAAATATAAA
783397 T-AATTAA
1 TAAATTAA
783404 GCTTAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 5 0.24
16 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
TAAATTAAATATAAA
Found at i:787246 original size:59 final size:58
Alignment explanation
Indices: 787155--787266 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 58
787145 AATGGGTGAT
* * * *
787155 GGTCTCCGACTATAAGAAGTTGTTTTGTTGAGTCATCCGATTATTAAAAGTTAAAAAC
1 GGTCTCCGACTATAAGAAGTTGCTTTATTGAGTCATCCAACTATTAAAAGTTAAAAAC
* *
787213 GGTCTCTCGACTATAAGACA-TTGCTTTATTGAGTCCTCTAACTATTAAAAGTTA
1 GGTCTC-CGACTATAAGA-AGTTGCTTTATTGAGTCATCCAACTATTAAAAGTTA
787267 TAATATAATC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 6 0.13
59 39 0.85
60 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (58 bp):
GGTCTCCGACTATAAGAAGTTGCTTTATTGAGTCATCCAACTATTAAAAGTTAAAAAC
Found at i:791388 original size:2 final size:2
Alignment explanation
Indices: 791381--791420 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
791371 GCAAAATGCT
*
791381 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
791421 GATAAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:793472 original size:57 final size:56
Alignment explanation
Indices: 793384--793622 Score: 192
Period size: 57 Copynumber: 4.2 Consensus size: 56
793374 ATGGGTGTAT
* * * * * *
793384 GCTTCTTTGTGCAAATTTCTCGATGTTTTATGTAGAGGTATTTGTTATAAGGAAAAG
1 GCTTCTTCGCGCAAAGTTCTCGACGCTTTATGCAGAGGTATTTGTT-TAAGGAAAAG
* * * *
793441 GCTTCTTCGCGTAAATTTCTCGACGCTTTATGCAGAGGTATTTGTTTTAGAGAGAAG
1 GCTTCTTCGCGCAAAGTTCTCGACGCTTTATGCAGAGGTATTTGTTTAAG-GAAAAG
* ** * * * * * * *
793498 GTTTCTTCATGCCAAGTTCTCAATGCTTTGTACAGAGGTATTTGTTATAGGGCAAAG
1 GCTTCTTCGCGCAAAGTTCTCGACGCTTTATGCAGAGGTATTTGTT-TAAGGAAAAG
* * * * *
793555 ACTCCTTC-CTGCAAAGTTCTCGACGTTTTATGCAGAGGTATTTGTTTTAGGATGAAG
1 GCTTCTTCGC-GCAAAGTTCTCGACGCTTTATGCAGAGGTATTTGTTTAAGGA-AAAG
*
793612 GCTTTTTCGCG
1 GCTTCTTCGCG
793623 TCAGGTTCTT
Statistics
Matches: 138, Mismatches: 39, Indels: 10
0.74 0.21 0.05
Matches are distributed among these distances:
56 6 0.04
57 129 0.93
58 3 0.02
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (56 bp):
GCTTCTTCGCGCAAAGTTCTCGACGCTTTATGCAGAGGTATTTGTTTAAGGAAAAG
Found at i:793631 original size:114 final size:114
Alignment explanation
Indices: 793417--793640 Score: 292
Period size: 114 Copynumber: 2.0 Consensus size: 114
793407 TGTTTTATGT
* * * *
793417 AGAGGTATTTGTTATAAGGAAAAGGCTTCTTCGCGTAAATTTCTCGACGCTTTATGCAGAGGTAT
1 AGAGGTATTTGTTATAAGGAAAAGACTCCTTCGCGCAAAGTTCTCGACGCTTTATGCAGAGGTAT
*
793482 TTGTTTTAGAGAGAAGGTTTCTTCATGCCAAGTTCTCAATGCTTTGTAC
66 TTGTTTTAGAGAGAAGGTTTCTTCACGCCAAGTTCTCAATGCTTTGTAC
* * *
793531 AGAGGTATTTGTTATAGGGCAAAGACTCCTTC-CTGCAAAGTTCTCGACGTTTTATGCAGAGGTA
1 AGAGGTATTTGTTATAAGGAAAAGACTCCTTCGC-GCAAAGTTCTCGACGCTTTATGCAGAGGTA
* * * *
793595 TTTGTTTTAG-GATGAAGGCTTT-TTCGCGTCAGGTTCTTAATGCTTT
65 TTTGTTTTAGAGA-GAAGG-TTTCTTCACGCCAAGTTCTCAATGCTTT
793641 ATGTGGAGGA
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
113 3 0.03
114 89 0.94
115 3 0.03
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.38
Consensus pattern (114 bp):
AGAGGTATTTGTTATAAGGAAAAGACTCCTTCGCGCAAAGTTCTCGACGCTTTATGCAGAGGTAT
TTGTTTTAGAGAGAAGGTTTCTTCACGCCAAGTTCTCAATGCTTTGTAC
Found at i:794678 original size:198 final size:199
Alignment explanation
Indices: 794340--794736 Score: 778
Period size: 198 Copynumber: 2.0 Consensus size: 199
794330 TCCATACTCT
794340 TTTAGCCAGCAAATGATGACATCTCAACACTTAGAGAGGAGGTGGCTCAACGCTTCTTAGCCAAA
1 TTTAGCCAGCAAATGATGACATCTCAACACTTAGAGAGGAGGTGGCTCAACGCTTCTTAGCCAAA
794405 GGGAGAGACATCTTCACTATGGCAATACAGTGGAAGCATCTCAAACTGGGGTAATACACTAGAGG
66 GGGAGAGACATCTTCACTATGGCAATACAGTGGAAGCATCTCAAACTGGGGTAATACACTAGAGG
*
794470 ATAGTAGTAAAAA-ATACCTATAGACTCAAATTTTCAGTGGAGGTATAAAAGTTCCTAACTTCAT
131 ATAGTAGTAAAAATATACCTATAGACTCAAATTTTCAGTGGAGGTATAAAAGTTCATAACTTCAT
794534 ATAC
196 ATAC
794538 TTTAGCCAGCAAATGATGACATCTCAACACTTAGAGAGGAGGTGGCTCAACGCTTCTTAGCCAAA
1 TTTAGCCAGCAAATGATGACATCTCAACACTTAGAGAGGAGGTGGCTCAACGCTTCTTAGCCAAA
794603 GGGAGAGACATCTTCACTATGGCAATACAGTGGAAGCATCTCAAACTGGGGTAATACACTAGAGG
66 GGGAGAGACATCTTCACTATGGCAATACAGTGGAAGCATCTCAAACTGGGGTAATACACTAGAGG
794668 ATAGTAGTAAAAATATACCTATAGACTCAAATTTTCAGTGGAGGTATAAAAGTTCATAACTTCAT
131 ATAGTAGTAAAAATATACCTATAGACTCAAATTTTCAGTGGAGGTATAAAAGTTCATAACTTCAT
794733 ATAC
196 ATAC
794737 CTACATGTAT
Statistics
Matches: 197, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
198 143 0.73
199 54 0.27
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (199 bp):
TTTAGCCAGCAAATGATGACATCTCAACACTTAGAGAGGAGGTGGCTCAACGCTTCTTAGCCAAA
GGGAGAGACATCTTCACTATGGCAATACAGTGGAAGCATCTCAAACTGGGGTAATACACTAGAGG
ATAGTAGTAAAAATATACCTATAGACTCAAATTTTCAGTGGAGGTATAAAAGTTCATAACTTCAT
ATAC
Found at i:810253 original size:101 final size:101
Alignment explanation
Indices: 810078--810280 Score: 406
Period size: 101 Copynumber: 2.0 Consensus size: 101
810068 TGCCTGCATG
810078 TTCGTATATATAGAAAAATGGCATCACAACAGAAATAAATCACCAAGATGAGCATGTTTATGTTG
1 TTCGTATATATAGAAAAATGGCATCACAACAGAAATAAATCACCAAGATGAGCATGTTTATGTTG
810143 CACATGAGACAAAAAAGCCTGTCTAAGAGATTTGGA
66 CACATGAGACAAAAAAGCCTGTCTAAGAGATTTGGA
810179 TTCGTATATATAGAAAAATGGCATCACAACAGAAATAAATCACCAAGATGAGCATGTTTATGTTG
1 TTCGTATATATAGAAAAATGGCATCACAACAGAAATAAATCACCAAGATGAGCATGTTTATGTTG
810244 CACATGAGACAAAAAAGCCTGTCTAAGAGATTTGGA
66 CACATGAGACAAAAAAGCCTGTCTAAGAGATTTGGA
810280 T
1 T
810281 GCATACCGTC
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (101 bp):
TTCGTATATATAGAAAAATGGCATCACAACAGAAATAAATCACCAAGATGAGCATGTTTATGTTG
CACATGAGACAAAAAAGCCTGTCTAAGAGATTTGGA
Found at i:828469 original size:65 final size:65
Alignment explanation
Indices: 828365--828492 Score: 256
Period size: 65 Copynumber: 2.0 Consensus size: 65
828355 CGCTCCTTTC
828365 TCTTATGGAATTCCTTCACATATCTATTGAAACCTTTCCAACGTTCTCTCCTAACTTTGAACATT
1 TCTTATGGAATTCCTTCACATATCTATTGAAACCTTTCCAACGTTCTCTCCTAACTTTGAACATT
828430 TCTTATGGAATTCCTTCACATATCTATTGAAACCTTTCCAACGTTCTCTCCTAACTTTGAACA
1 TCTTATGGAATTCCTTCACATATCTATTGAAACCTTTCCAACGTTCTCTCCTAACTTTGAACA
828493 CGTCATCCAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.39
Consensus pattern (65 bp):
TCTTATGGAATTCCTTCACATATCTATTGAAACCTTTCCAACGTTCTCTCCTAACTTTGAACATT
Found at i:833221 original size:49 final size:49
Alignment explanation
Indices: 833149--833247 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
833139 TTTCCCTCCT
833149 TCCAATGTCCTTCATGTTATGTTTGTAACATGGAGGATAAGAAGGGGGG
1 TCCAATGTCCTTCATGTTATGTTTGTAACATGGAGGATAAGAAGGGGGG
833198 TCCAATGTCCTTCATGTTATGTTTGTAACATGGAGGATAAGAAGGGGGG
1 TCCAATGTCCTTCATGTTATGTTTGTAACATGGAGGATAAGAAGGGGGG
833247 T
1 T
833248 TTTAATGAGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.31
Consensus pattern (49 bp):
TCCAATGTCCTTCATGTTATGTTTGTAACATGGAGGATAAGAAGGGGGG
Found at i:837322 original size:27 final size:27
Alignment explanation
Indices: 837274--837325 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
837264 TTTTAATAGG
* *
837274 AATATAATTAAATTATATTTTTTTAAA
1 AATATAATTAAATTAGAATTTTTTAAA
**
837301 AATATAATTATTTTAGAATTTTTTA
1 AATATAATTAAATTAGAATTTTTTA
837326 TCGTTTAGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
AATATAATTAAATTAGAATTTTTTAAA
Found at i:840253 original size:33 final size:33
Alignment explanation
Indices: 840211--840278 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
840201 ATGTGTGTGA
840211 TATGGTATGATGAAATTGAGAGATGAAATTACT
1 TATGGTATGATGAAATTGAGAGATGAAATTACT
840244 TATGGTATGATGAAATTGAGAGATGAAATTACT
1 TATGGTATGATGAAATTGAGAGATGAAATTACT
840277 TA
1 TA
840279 GTGACGGACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.34
Consensus pattern (33 bp):
TATGGTATGATGAAATTGAGAGATGAAATTACT
Found at i:840621 original size:24 final size:24
Alignment explanation
Indices: 840588--840643 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
840578 CATTTAATCA
* *
840588 TATAATTTCGCAC-CCCTGAAATTT
1 TATAACTTCG-ACTCCCTAAAATTT
*
840612 TATAACTTCGACTCCTTAAAATTT
1 TATAACTTCGACTCCCTAAAATTT
*
840636 TTTAACTT
1 TATAACTT
840644 TTCTAATTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.43
Consensus pattern (24 bp):
TATAACTTCGACTCCCTAAAATTT
Found at i:841114 original size:216 final size:218
Alignment explanation
Indices: 840742--841176 Score: 824
Period size: 216 Copynumber: 2.0 Consensus size: 218
840732 TGTGAGACAC
840742 ACCAGATGACCAAGATCTTGGTGCCTTTTGTTTAATATGAAGAATGAATCACATCATGTGGTTGA
1 ACCAGATGACCAAGATCTTGGTGCCTTTTGTTTAATATGAAGAATGAATCACATCATGTGGTTGA
840807 TGATGCTTAATATAATACCGGTATTTAGGTGAACCTGTTTTGTCTGTTTTTAGACTGCCCTTTAA
66 TGATGCTTAATATAATACCGGTATTTAGGTGAACCTGTTTTGTCTGTTTTTAGACTGCCCTTTAA
840872 TCTCATCCCTAAATTTGATCCTTCTTTTTCTTTCTTTTTCGCC-TTTTATAC-TTTAGAGTCCCA
131 TCTCATCCCTAAATTTGATCCTTCTTTTTCTTTCTTTTTCGCCTTTTTATACTTTTAGAGTCCCA
840935 TGCT-C-CTTGGGAGACCACCTT
196 TGCTCCACTTGGGAGACCACCTT
840956 ACCAGATGACCAAGATCTTGGTGCCTTTTGTTTAATATGAAGAATGAATCACATCATGTGGTTGA
1 ACCAGATGACCAAGATCTTGGTGCCTTTTGTTTAATATGAAGAATGAATCACATCATGTGGTTGA
841021 TGATGCTTAATATATAATACCGGTATTTAGGTGAACCTGTTTTGTCTGTTTTTAGACTGCCCTTT
66 TGATGCTT-A-ATATAATACCGGTATTTAGGTGAACCTGTTTTGTCTGTTTTTAGACTGCCCTTT
841086 AATCTCATCCCTAAATTTGATCCTTCTTTTTCTTTCTTTTTCGCCTTTTTATACTTTTAGAGTCC
129 AATCTCATCCCTAAATTTGATCCTTCTTTTTCTTTCTTTTTCGCCTTTTTATACTTTTAGAGTCC
841151 CATGCTCCACTTGGGAGACCACCTT
194 CATGCTCCACTTGGGAGACCACCTT
841176 A
1 A
841177 TTTATTTTGT
Statistics
Matches: 215, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
214 73 0.34
215 1 0.00
216 99 0.46
217 8 0.04
218 16 0.07
219 1 0.00
220 17 0.08
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (218 bp):
ACCAGATGACCAAGATCTTGGTGCCTTTTGTTTAATATGAAGAATGAATCACATCATGTGGTTGA
TGATGCTTAATATAATACCGGTATTTAGGTGAACCTGTTTTGTCTGTTTTTAGACTGCCCTTTAA
TCTCATCCCTAAATTTGATCCTTCTTTTTCTTTCTTTTTCGCCTTTTTATACTTTTAGAGTCCCA
TGCTCCACTTGGGAGACCACCTT
Found at i:842447 original size:41 final size:41
Alignment explanation
Indices: 842366--842477 Score: 170
Period size: 41 Copynumber: 2.7 Consensus size: 41
842356 TCCGAATTCT
*
842366 CGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATATTTTCC
1 CGTGTTTGTTTCACGTAATTCG-TTTTCCGAAAATATTTTCC
* * *
842408 CGTGTTTGTTTAACATAATTCGTTTTCCGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGAAAATATTTTCC
*
842449 CGTGTTTGTTTCACGTAATTCATTTTCCG
1 CGTGTTTGTTTCACGTAATTCGTTTTCCG
842478 GAATGTAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 43 0.68
42 20 0.32
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.47
Consensus pattern (41 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGAAAATATTTTCC
Found at i:842731 original size:29 final size:30
Alignment explanation
Indices: 842660--842732 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
842650 TATTTTTATT
842660 TATT-TATTATTAATATTTATAATAATATAA
1 TATTATATTA-TAATATTTATAATAATATAA
*
842690 TATTAT-TTTTAATA-TTAT-ATAA-ATAA
1 TATTATATTATAATATTTATAATAATATAA
842716 TCAATTATATTATAATA
1 T--ATTATATTATAATA
842733 ATAAGATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
26 5 0.14
27 4 0.11
28 9 0.24
29 12 0.32
30 6 0.16
31 1 0.03
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (30 bp):
TATTATATTATAATATTTATAATAATATAA
Found at i:842734 original size:52 final size:49
Alignment explanation
Indices: 842672--842803 Score: 129
Period size: 55 Copynumber: 2.5 Consensus size: 49
842662 TTTATTATTA
* * **
842672 ATATTTATAATAATATAATATTATTTTTAATATTATATAAATAATCAATT
1 ATATATATAATAATATAATATTATTTTTAATAATATAT-AATAAAAAATT
* *
842722 ATATTATAATAATAAGATATTATATTTTTATTTTAATAATATATAATAAAAAATT
1 ATA-TAT-ATAAT-A-ATATAATA-TTAT-TTTTAATAATATATAATAAAAAATT
*
842777 ATATATTTAATAATGATAATATTATTT
1 ATATATATAATAAT-ATAATATTATTT
842804 ATATATTTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
50 5 0.08
51 7 0.11
52 11 0.17
53 5 0.08
54 10 0.15
55 15 0.23
56 13 0.20
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (49 bp):
ATATATATAATAATATAATATTATTTTTAATAATATATAATAAAAAATT
Found at i:842756 original size:56 final size:55
Alignment explanation
Indices: 842681--842828 Score: 149
Period size: 56 Copynumber: 2.6 Consensus size: 55
842671 AATATTTATA
* * **
842681 ATAATATAATATTAT-TTTTAATATTATATAAATAATCAATTATAT-TATAATAATAAG
1 ATAATATTAT-TTATATTTTAATAATATAT-AATAAAAAATTATATATATAATAAT--G
* * *
842738 ATATTA-TATTTTTATTTTAATAATATATAATAAAAAATTATATATTTAATAATG
1 ATAATATTATTTATATTTTAATAATATATAATAAAAAATTATATATATAATAATG
*
842792 ATAATATTATTTATATATTTAATAATATTTTAATAAA
1 ATAATATTATTTATAT-TTTAATAATA-TATAATAAA
842829 GATATTTAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
54 6 0.08
55 24 0.32
56 33 0.43
57 13 0.17
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (55 bp):
ATAATATTATTTATATTTTAATAATATATAATAAAAAATTATATATATAATAATG
Found at i:843186 original size:14 final size:14
Alignment explanation
Indices: 843164--843202 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
843154 ATGTAATTCA
*
843164 TTTTACGGAAAACG
1 TTTTCCGGAAAACG
843178 TTTTCCGGAAAACG
1 TTTTCCGGAAAACG
*
843192 TTTTCCAGAAA
1 TTTTCCGGAAA
843203 TGTAATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (14 bp):
TTTTCCGGAAAACG
Found at i:843229 original size:20 final size:20
Alignment explanation
Indices: 843192--843230 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
843182 CCGGAAAACG
**
843192 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
843212 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
843231 CAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Done.