Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 2 of 193
Found at i:514218 original size:41 final size:41
Alignment explanation
Indices: 514161--514243 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
514151 TTGTTAGTAG
514161 AGAATTCTTGTCAAGGTAGAGATTGTTAAAATTGGGTTACT
1 AGAATTCTTGTCAAGGTAGAGATTGTTAAAATTGGGTTACT
514202 AGAATTCTTGTCAAGGTAGAGATTGTTAAAATTGGGTTACT
1 AGAATTCTTGTCAAGGTAGAGATTGTTAAAATTGGGTTACT
514243 A
1 A
514244 TAAAATTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (41 bp):
AGAATTCTTGTCAAGGTAGAGATTGTTAAAATTGGGTTACT
Found at i:523345 original size:23 final size:24
Alignment explanation
Indices: 523314--523370 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
523304 AAGATAATGC
*
523314 AAATTATCA-AGTTAAATTGCTCA
1 AAATCATCATAGTTAAATTGCTCA
*
523337 AAATCATCATCGTTAAATTGCTCA
1 AAATCATCATAGTTAAATTGCTCA
523361 AAATCATCAT
1 AAATCATCAT
523371 CATGCATGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 8 0.26
24 23 0.74
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (24 bp):
AAATCATCATAGTTAAATTGCTCA
Found at i:523355 original size:24 final size:24
Alignment explanation
Indices: 523324--523371 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
523314 AAATTATCAA
523324 GTTAAATTGCTCAAAATCATCATC
1 GTTAAATTGCTCAAAATCATCATC
523348 GTTAAATTGCTCAAAATCATCATC
1 GTTAAATTGCTCAAAATCATCATC
523372 ATGCATGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (24 bp):
GTTAAATTGCTCAAAATCATCATC
Found at i:525623 original size:23 final size:25
Alignment explanation
Indices: 525597--525642 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
525587 CCAATTAAGG
525597 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
525620 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
525643 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:535299 original size:75 final size:75
Alignment explanation
Indices: 535176--535326 Score: 241
Period size: 75 Copynumber: 2.0 Consensus size: 75
535166 CCAAAGTATT
* *
535176 CGATCGAGTATTCAAGACTGTTACCTTTGCATGCTCTAAATTTAAGCATTATTGAACTACAGAAC
1 CGATCGAGTATTCAAAACTGTTACCTTTGCATGCTCTAAATTTAAGCATTATCGAACTACAGAAC
535241 AATCTAGTTG
66 AATCTAGTTG
* * *
535251 CGATCGAGTGTTCAAAATTGTTACCTTTGCATGCT-TCAAGTTTAAGCATTATCGAACTACAGAA
1 CGATCGAGTATTCAAAACTGTTACCTTTGCATGCTCT-AAATTTAAGCATTATCGAACTACAGAA
535315 CAATCTAGTTG
65 CAATCTAGTTG
535326 C
1 C
535327 CAAATTCATG
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
74 1 0.01
75 69 0.99
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (75 bp):
CGATCGAGTATTCAAAACTGTTACCTTTGCATGCTCTAAATTTAAGCATTATCGAACTACAGAAC
AATCTAGTTG
Found at i:539472 original size:23 final size:23
Alignment explanation
Indices: 539442--539485 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
539432 CCCTCATTTT
539442 ACATTTTAATAA-AAATTTAAAAC
1 ACATTTT-ATAATAAATTTAAAAC
*
539465 ACATTTTATAATTAATTTAAA
1 ACATTTTATAATAAATTTAAA
539486 TTTAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (23 bp):
ACATTTTATAATAAATTTAAAAC
Found at i:539486 original size:29 final size:26
Alignment explanation
Indices: 539454--539513 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 26
539444 ATTTTAATAA
539454 AAATTTAAAACACATTTTATAATTAATTT
1 AAATTTAAAA-ACATTTT-TAATT-ATTT
*
539483 AAATTTAAAAATATTTTTAATTATTT
1 AAATTTAAAAACATTTTTAATTATTT
539509 AAATT
1 AAATT
539514 AAATTTGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 9 0.30
27 5 0.17
28 6 0.20
29 10 0.33
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
AAATTTAAAAACATTTTTAATTATTT
Found at i:545794 original size:3 final size:3
Alignment explanation
Indices: 545786--545823 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
545776 ATATTTGATA
545786 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
545824 GAGTTTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:545879 original size:15 final size:15
Alignment explanation
Indices: 545859--545892 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
545849 TTAAAATGAT
*
545859 AATAAATATTTAAAA
1 AATAAATATATAAAA
545874 AATAAATATATAAAA
1 AATAAATATATAAAA
545889 AATA
1 AATA
545893 TATAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAAATATATAAAA
Found at i:555799 original size:25 final size:25
Alignment explanation
Indices: 555765--555813 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
555755 CCAAGCCCAT
*
555765 CAATATTTATAAATGGTTAATTCAC
1 CAATATTTATAAATGATTAATTCAC
555790 CAATATTTATAAATGATTAATTCA
1 CAATATTTATAAATGATTAATTCA
555814 AACTCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (25 bp):
CAATATTTATAAATGATTAATTCAC
Found at i:564130 original size:41 final size:41
Alignment explanation
Indices: 564073--564166 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
564063 CCCATTGTCA
564073 GGATGAATTTTCTTGGTGTTTGACTTCATATGTCAAGTATG
1 GGATGAATTTTCTTGGTGTTTGACTTCATATGTCAAGTATG
564114 GGATGAATTTTCTTGGTGTTTGACTTCATATGTCAAGTATG
1 GGATGAATTTTCTTGGTGTTTGACTTCATATGTCAAGTATG
* *
564155 GTATGAAATTTC
1 GGATGAATTTTC
564167 AAATTCGGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.44
Consensus pattern (41 bp):
GGATGAATTTTCTTGGTGTTTGACTTCATATGTCAAGTATG
Found at i:564625 original size:16 final size:18
Alignment explanation
Indices: 564588--564635 Score: 66
Period size: 16 Copynumber: 2.8 Consensus size: 18
564578 CCGATTAATC
*
564588 AAAATAACTCTAAATTTT
1 AAAATAACTCTAAATATT
564606 AAAATAACT-TAAA-ATT
1 AAAATAACTCTAAATATT
564622 AAAATAACTC-AAAT
1 AAAATAACTCTAAAT
564636 CCAAAATATC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 14 0.52
17 4 0.15
18 9 0.33
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATAACTCTAAATATT
Found at i:568323 original size:22 final size:22
Alignment explanation
Indices: 568295--568346 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
568285 ACGGTGGTTT
568295 CCTCCTCC-CTCTCTCACACGTG
1 CCTCCTCCTCTC-CTCACACGTG
*
568317 CCTCCTCCTCTCCTCGCACGTG
1 CCTCCTCCTCTCCTCACACGTG
*
568339 ACT-CTCCT
1 CCTCCTCCT
568347 ACCCCCCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 5 0.19
22 19 0.70
23 3 0.11
ACGTcount: A:0.08, C:0.54, G:0.10, T:0.29
Consensus pattern (22 bp):
CCTCCTCCTCTCCTCACACGTG
Found at i:595949 original size:15 final size:15
Alignment explanation
Indices: 595929--595959 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
595919 TAACGTTTCC
595929 GTTATTGACGATTTT
1 GTTATTGACGATTTT
595944 GTTATTGACGATTTT
1 GTTATTGACGATTTT
595959 G
1 G
595960 CTTTCAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.23, T:0.52
Consensus pattern (15 bp):
GTTATTGACGATTTT
Found at i:600834 original size:29 final size:30
Alignment explanation
Indices: 600745--600892 Score: 201
Period size: 30 Copynumber: 4.9 Consensus size: 30
600735 ACCCGGGAGT
* *
600745 AAATGTAATTTTT-GAAAAGTTTGGGAGGTCA
1 AAATGTAATTTTTAG-AAAGTTTTGG-GGTTA
* *
600776 AAATGTAATTTTCAGAAAGTATTGGGGTTA
1 AAATGTAATTTTTAGAAAGTTTTGGGGTTA
* * *
600806 AAATATAA-TTTTAGGAAGTTTTAGGGTTA
1 AAATGTAATTTTTAGAAAGTTTTGGGGTTA
600835 AAATGTAATTTTTAGAAAGTTTTGGGGTTA
1 AAATGTAATTTTTAGAAAGTTTTGGGGTTA
600865 AAATGTAATTTTTAGAAAGTTTTGGGGT
1 AAATGTAATTTTTAGAAAGTTTTGGGGT
600893 CAATTTTGTA
Statistics
Matches: 103, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
29 24 0.23
30 58 0.56
31 20 0.19
32 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.24, T:0.40
Consensus pattern (30 bp):
AAATGTAATTTTTAGAAAGTTTTGGGGTTA
Found at i:600844 original size:59 final size:60
Alignment explanation
Indices: 600775--600892 Score: 184
Period size: 59 Copynumber: 2.0 Consensus size: 60
600765 TTGGGAGGTC
*
600775 AAAATGTAATTTTCAGAAAGTATTGGGGTTAAAATATAA-TTTTAGGAAGTTTTAGGGTT
1 AAAATGTAATTTTCAGAAAGTATTGGGGTTAAAATATAATTTTTAGAAAGTTTTAGGGTT
* * * *
600834 AAAATGTAATTTTTAGAAAGTTTTGGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGT
1 AAAATGTAATTTTCAGAAAGTATTGGGGTTAAAATATAATTTTTAGAAAGTTTTAGGGT
600893 CAATTTTGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
59 36 0.68
60 17 0.32
ACGTcount: A:0.36, C:0.01, G:0.23, T:0.41
Consensus pattern (60 bp):
AAAATGTAATTTTCAGAAAGTATTGGGGTTAAAATATAATTTTTAGAAAGTTTTAGGGTT
Found at i:601855 original size:3 final size:3
Alignment explanation
Indices: 601833--601907 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
601823 TGCTATTACC
* * * *
601833 ATT ATT CTT ATT ATT CTT ATT ATT AAT ATTT ATT ACT ATT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT A-TT ATT
* * **
601880 ATT ATA ATT ATT AAT GGT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
601908 ACAACATTTA
Statistics
Matches: 55, Mismatches: 15, Indels: 4
0.74 0.20 0.05
Matches are distributed among these distances:
3 50 0.91
4 5 0.09
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:601867 original size:13 final size:13
Alignment explanation
Indices: 601849--601892 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
601839 CTTATTATTC
601849 TTATTATTAATAT
1 TTATTATTAATAT
* *
601862 TTATTACTATTAT
1 TTATTATTAATAT
*
601875 TTATTATT-ATAA
1 TTATTATTAATAT
601887 TTATTA
1 TTATTA
601893 ATGGTATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTATTAATAT
Found at i:602665 original size:19 final size:18
Alignment explanation
Indices: 602621--602671 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
602611 AATTCAAATC
**
602621 AAATTTAAACTT-AATTA
1 AAATTTAAACTTAAAAGA
602638 AAATTTAAACTTAAAAGA
1 AAATTTAAACTTAAAAGA
602656 AAAGTTTAAACTTAAA
1 AAA-TTTAAACTTAAA
602672 CTAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 12 0.40
18 6 0.20
19 12 0.40
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (18 bp):
AAATTTAAACTTAAAAGA
Found at i:602801 original size:31 final size:34
Alignment explanation
Indices: 602763--602826 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
602753 ATTGGGCTTC
*
602763 AACAAAAT-ACATT-AATTTT-TAATTTGAGTTT
1 AACAAAATCACATTGAATTTTATAATTTAAGTTT
*
602794 AACAAAATCACTTTGAATTTTATAATTTAAGTT
1 AACAAAATCACATTGAATTTTATAATTTAAGTT
602827 ACTCCAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 8 0.29
32 4 0.14
33 6 0.21
34 10 0.36
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (34 bp):
AACAAAATCACATTGAATTTTATAATTTAAGTTT
Found at i:605660 original size:2 final size:2
Alignment explanation
Indices: 605653--605685 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
605643 ATAACTACTT
605653 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 T
605686 GGTGAAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:608755 original size:31 final size:29
Alignment explanation
Indices: 608686--608759 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
608676 TTATCTCCCT
*
608686 AACATAAGTGACTAAAACGTAACATGTCA
1 AACATAAGTGACTAAAACGTAACATGGCA
* *
608715 AACATAAGTGACTAAAATGTAACCTGAGGCA
1 AACATAAGTGACTAAAACGTAACAT--GGCA
*
608746 AACAAAAGTGACTA
1 AACATAAGTGACTA
608760 TTTTTATACT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 23 0.59
31 16 0.41
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATGGCA
Found at i:627552 original size:2 final size:2
Alignment explanation
Indices: 627545--627585 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
627535 TGTAGTTAGT
627545 TA 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 TA T
627586 TTGTATTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:628092 original size:21 final size:22
Alignment explanation
Indices: 628049--628093 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
628039 ATTGTACGAG
* *
628049 TATTGAATTTATATTAGAAAAT
1 TATTGAATTTATAGTAAAAAAT
628071 TATTGAATTTA-AGTAAAAAAT
1 TATTGAATTTATAGTAAAAAAT
628092 TA
1 TA
628094 AAACGGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (22 bp):
TATTGAATTTATAGTAAAAAAT
Found at i:637031 original size:16 final size:16
Alignment explanation
Indices: 636997--637031 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
636987 AAATTTCTCA
**
636997 AACTCAAAATAATTTG
1 AACTCAAAATAATCCG
637013 AACTCAAAATAATCCG
1 AACTCAAAATAATCCG
637029 AAC
1 AAC
637032 CTAAAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.20, G:0.06, T:0.23
Consensus pattern (16 bp):
AACTCAAAATAATCCG
Found at i:646381 original size:2 final size:2
Alignment explanation
Indices: 646374--646399 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
646364 CACTTGCTTC
646374 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
646400 CGAGAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:649011 original size:70 final size:70
Alignment explanation
Indices: 648931--649128 Score: 387
Period size: 70 Copynumber: 2.8 Consensus size: 70
648921 ATTGTCGCAT
*
648931 TCGAATTCGATATAGACTCGGGTTTTATATGTAGAGAATTGTTGATATGTTGTTGTTGCTGCGGT
1 TCGAATTCGATATAGACTCAGGTTTTATATGTAGAGAATTGTTGATATGTTGTTGTTGCTGCGGT
648996 TGTCA
66 TGTCA
649001 TCGAATTCGATATAGACTCAGGTTTTATATGTAGAGAATTGTTGATATGTTGTTGTTGCTGCGGT
1 TCGAATTCGATATAGACTCAGGTTTTATATGTAGAGAATTGTTGATATGTTGTTGTTGCTGCGGT
649066 TGTCA
66 TGTCA
649071 TCGAATTCGATATAGACTCAGGTTTTATATGTAGAGAATTGTTGATATGTTGTTGTTG
1 TCGAATTCGATATAGACTCAGGTTTTATATGTAGAGAATTGTTGATATGTTGTTGTTG
649129 TTGCTGTATT
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 127 1.00
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.42
Consensus pattern (70 bp):
TCGAATTCGATATAGACTCAGGTTTTATATGTAGAGAATTGTTGATATGTTGTTGTTGCTGCGGT
TGTCA
Found at i:649218 original size:58 final size:58
Alignment explanation
Indices: 649091--649235 Score: 163
Period size: 58 Copynumber: 2.5 Consensus size: 58
649081 TATAGACTCA
* * *
649091 GGTTTTATATGTAGAGAATTGTTGATATGTTGTTGTTGTTGCTGTATTTGTAGAATCG
1 GGTTTTATATGTAGAGAATTGTTGATATGTTGTTCTTGTTGCAGTATATGTAGAATCG
649149 GGTTTTATATGTAGAGAATTGTTGATATGTTGTTCTATGAATT-CAG-ATAT-T-GAATCG
1 GGTTTTATATGTAGAGAATTGTTGATATGTTGTTCT-TG--TTGCAGTATATGTAGAATCG
* * * *
649206 GTTTTTTGTATGTGGATAATTGTTGATATG
1 G-GTTTTATATGTAGAGAATTGTTGATATG
649236 ATATGTATGT
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
57 7 0.09
58 60 0.79
59 5 0.07
60 2 0.03
61 2 0.03
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.48
Consensus pattern (58 bp):
GGTTTTATATGTAGAGAATTGTTGATATGTTGTTCTTGTTGCAGTATATGTAGAATCG
Found at i:651682 original size:15 final size:15
Alignment explanation
Indices: 651653--651699 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
651643 CAAATTTTAA
*
651653 TTAAAATGATATAAAT
1 TTAAAATGAT-TAAAC
651669 TTAAAATGATTAAAC
1 TTAAAATGATTAAAC
*
651684 TTGAAATGATTTAAAC
1 TTAAAATGA-TTAAAC
651700 CCGCAATCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (15 bp):
TTAAAATGATTAAAC
Found at i:652547 original size:210 final size:210
Alignment explanation
Indices: 652178--652582 Score: 487
Period size: 210 Copynumber: 1.9 Consensus size: 210
652168 CTCGAGCCTT
* * * **
652178 TTTTTTTCTCATTATTACAAGTACAGTACGGGTTGTATAAATATATATCCGACCAACTATAATGT
1 TTTTTTTCTCACTATTACAAATACAATACAAGTTGTATAAATATATATCCGACCAACTATAATGT
** * *
652243 AGAATCAAATCAATACAAAGTGTAGCAGACAAAAAGCTGGACTAAACCCTCACATGGCATACACA
66 AGAATCAAATCAATACAAAGCATAGCAGACAAAAAGCCGGACTAAACCCACACATGGCATACACA
* * * * * * *
652308 CCTGGTGGGACAAAGATACACATATCGCAATTGTGCATGGTGGAACTCGAACCTGGGTACTCAAG
131 CATGGTGGGACAAAGACACAAACATCGCAATTGCGCATGATGGAACTCAAACCTGGGTACTCAAG
652373 GACTCAGGGTCTCCA
196 GACTCAGGGTCTCCA
*
652388 TTTTTTT-TCACTATTACAAATACAATACAAGTTGTATAGATATA-ATGCCCGACCAACTATTAA
1 TTTTTTTCTCACTATTACAAATACAATACAAGTTGTATAAATATATAT--CCGACCAACTA-TAA
* * *
652451 TGTAGAATCAAACTC-GTACAAAGCATAGCAGATAAAGAA-CCGGAC-AAACCCACTCATGGCAT
63 TGTAGAATCAAA-TCAATACAAAGCATAGCAGACAAA-AAGCCGGACTAAACCCACACATGGCAT
** * * * * *
652513 ATGCACATGGTGGGACGAAGACCCAAACATCGCAATTGCGCTTGATGGGACTTAAACCTGGGTAC
126 ACACACATGGTGGGACAAAGACACAAACATCGCAATTGCGCATGATGGAACTCAAACCTGGGTAC
652578 TCAAG
191 TCAAG
652583 AACTTGTGTC
Statistics
Matches: 163, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
208 2 0.01
209 31 0.19
210 89 0.55
211 37 0.23
212 4 0.02
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (210 bp):
TTTTTTTCTCACTATTACAAATACAATACAAGTTGTATAAATATATATCCGACCAACTATAATGT
AGAATCAAATCAATACAAAGCATAGCAGACAAAAAGCCGGACTAAACCCACACATGGCATACACA
CATGGTGGGACAAAGACACAAACATCGCAATTGCGCATGATGGAACTCAAACCTGGGTACTCAAG
GACTCAGGGTCTCCA
Found at i:659048 original size:183 final size:183
Alignment explanation
Indices: 658740--659106 Score: 716
Period size: 183 Copynumber: 2.0 Consensus size: 183
658730 AGTGTATTAA
658740 ATATGATTCACGTTAGATCTAAATTGACAAGTAAGGCTAACGAAAGGATTTAATTAATAAATATT
1 ATATGATTCACGTTAGATCTAAATTGACAAGTAAGGCTAACGAAAGGATTTAATTAATAAATATT
658805 GATACTTCGAAAACTCAATCATAACCTTTTGAAGTTCAGGGATCGATTCAAAATTTAAATGATAG
66 GATACTTCGAAAACTCAATCATAACCTTTTGAAGTTCAGGGATCGATTCAAAATTTAAATGATAG
658870 TTTAGATGTGTTTGTTGAAAATTACCCTTTAGGTATATAAGTAATATATTTTG
131 TTTAGATGTGTTTGTTGAAAATTACCCTTTAGGTATATAAGTAATATATTTTG
*
658923 ATATGATTCACGTTAGATCTAAATTGACAAGTAAGGCTAACGAAAGGATTTGATTAATAAATATT
1 ATATGATTCACGTTAGATCTAAATTGACAAGTAAGGCTAACGAAAGGATTTAATTAATAAATATT
658988 GATACTTCGAAAACTCAATCATAACCTTTTGAAGTTCAGGGATCGATTCAAAATTTAAATGATAG
66 GATACTTCGAAAACTCAATCATAACCTTTTGAAGTTCAGGGATCGATTCAAAATTTAAATGATAG
*
659053 TTTAGATGTGTTTGTTGAAAATTACCCTTTAGTTATATAAGTAATATATTTTG
131 TTTAGATGTGTTTGTTGAAAATTACCCTTTAGGTATATAAGTAATATATTTTG
659106 A
1 A
659107 AGGTTTAATT
Statistics
Matches: 182, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 182 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (183 bp):
ATATGATTCACGTTAGATCTAAATTGACAAGTAAGGCTAACGAAAGGATTTAATTAATAAATATT
GATACTTCGAAAACTCAATCATAACCTTTTGAAGTTCAGGGATCGATTCAAAATTTAAATGATAG
TTTAGATGTGTTTGTTGAAAATTACCCTTTAGGTATATAAGTAATATATTTTG
Found at i:665658 original size:2 final size:2
Alignment explanation
Indices: 665651--665696 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
665641 TAGATTTAGC
665651 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
665693 -A TA T
1 TA TA T
665697 CAATTTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:670771 original size:31 final size:31
Alignment explanation
Indices: 670736--670833 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 31
670726 ATAATATATT
* * *
670736 ATTTGGTAATTGAGTTTGTCTTTAATATTCA
1 ATTTGGTAATTGAATTTGGCTTCAATATTCA
* * *
670767 ATTTGATACTTGAATTTGGCTTCAATGTTCA
1 ATTTGGTAATTGAATTTGGCTTCAATATTCA
* *
670798 ATTTGGT-ATCTGAATTTGACTTCAATGTTCA
1 ATTTGGTAAT-TGAATTTGGCTTCAATATTCA
*
670829 GTTTG
1 ATTTG
670834 AAACCCAGGT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 1 0.02
31 55 0.98
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.48
Consensus pattern (31 bp):
ATTTGGTAATTGAATTTGGCTTCAATATTCA
Found at i:676544 original size:18 final size:18
Alignment explanation
Indices: 676493--676544 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 18
676483 TTTAAGAACA
*
676493 TTTATATTATTTTCA-TT
1 TTTATATTTTTTTCATTT
* * *
676510 TTAATA-TTTATTGATTT
1 TTTATATTTTTTTCATTT
676527 TTTATATTTTTTTCATTT
1 TTTATATTTTTTTCATTT
676545 ATTGAAAGGT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
16 5 0.19
17 12 0.46
18 9 0.35
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTATATTTTTTTCATTT
Found at i:679328 original size:2 final size:2
Alignment explanation
Indices: 679321--679375 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
679311 ACTTGATAGT
679321 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
679363 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
679376 GGGGTGTGCC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:680714 original size:15 final size:15
Alignment explanation
Indices: 680696--680726 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
680686 AACCGTACCC
680696 TTGTAAACCAATGGA
1 TTGTAAACCAATGGA
680711 TTGTAAACCAATGGA
1 TTGTAAACCAATGGA
680726 T
1 T
680727 GAAAGGGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (15 bp):
TTGTAAACCAATGGA
Found at i:681492 original size:6 final size:6
Alignment explanation
Indices: 681481--681513 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
681471 AGAAAAATAG
*
681481 TTTTCT TTTTCT TTTTCT TTTT-T TTTCCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
681514 AGTATCTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:685908 original size:29 final size:30
Alignment explanation
Indices: 685822--685910 Score: 99
Period size: 31 Copynumber: 3.0 Consensus size: 30
685812 GATTAAATCA
* * * *
685822 AAATTAAAGTTTCAAGTATACATTTGAATC
1 AAATTAAAGTTTCATGTATACAATTGCACC
* * *
685852 ATAATTAGAGTTTCATGTGTATAATTGCACC
1 A-AATTAAAGTTTCATGTATACAATTGCACC
685883 AAATTAAAGTTT-ATGTATACAATTGCAC
1 AAATTAAAGTTTCATGTATACAATTGCAC
685911 ATTAAATCAA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 14 0.29
30 11 0.23
31 23 0.48
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.37
Consensus pattern (30 bp):
AAATTAAAGTTTCATGTATACAATTGCACC
Found at i:689158 original size:21 final size:21
Alignment explanation
Indices: 689134--689186 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
689124 CTATGACAGT
*
689134 TCTACCGATACAAGTGA-GACA
1 TCTACCGATACAAGTCATG-CA
*
689155 TCTACCGATACAAGTCATGCT
1 TCTACCGATACAAGTCATGCA
689176 TCTACCGATAC
1 TCTACCGATAC
689187 CAAAAACTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (21 bp):
TCTACCGATACAAGTCATGCA
Found at i:700555 original size:29 final size:29
Alignment explanation
Indices: 700516--700676 Score: 90
Period size: 29 Copynumber: 5.5 Consensus size: 29
700506 TTTAGGGGCG
700516 AAATGGTAATTTTGGTGAAATCGGGGTCAA
1 AAATGG-AATTTTGGTGAAATCGGGGTCAA
* *
700546 AAATAGAATTTT-G-GAAGGTTCGGGGGT--A
1 AAATGGAATTTTGGTGAA--ATC-GGGGTCAA
*
700574 AAATGGTAATTTTTGGTTGAAAT-TGGGTC-A
1 AAATGG-AA-TTTTGG-TGAAATCGGGGTCAA
* *
700604 AAACGAGAATTTT-G-GAAAGTTCGAGGGT--G
1 AAATG-GAATTTTGGTGAAA--TCG-GGGTCAA
*
700633 AAATGGTAATTTTGGTGAAATTGGGGTCAA
1 AAATGG-AATTTTGGTGAAATCGGGGTCAA
700663 AAATGGAATTTTGG
1 AAATGGAATTTTGG
700677 AAGGTTCGGG
Statistics
Matches: 101, Mismatches: 11, Indels: 39
0.67 0.07 0.26
Matches are distributed among these distances:
26 4 0.04
27 3 0.03
28 14 0.14
29 38 0.38
30 32 0.32
31 7 0.07
33 3 0.03
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (29 bp):
AAATGGAATTTTGGTGAAATCGGGGTCAA
Found at i:700591 original size:117 final size:117
Alignment explanation
Indices: 700457--700702 Score: 399
Period size: 117 Copynumber: 2.1 Consensus size: 117
700447 ACTTGAGGGC
*
700457 AAAATGGTAA-ATTTGGTTAAAATTGGGTCAAAACGAGAATTTTGGAAAGTTTAG-GGGCGAAAT
1 AAAATGGTAATTTTTGGTTAAAATTGGGTCAAAACGAGAATTTTGGAAAG-TTAGAGGGCGAAAT
700520 GGTAATTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAGGTTCGGGGGT
65 GGTAATTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAGGTTCGGGGGT
* * *
700573 AAAATGGTAATTTTTGGTTGAAATTGGGTCAAAACGAGAATTTTGGAAAGTTCGAGGGTGAAATG
1 AAAATGGTAATTTTTGGTTAAAATTGGGTCAAAACGAGAATTTTGGAAAGTTAGAGGGCGAAATG
* *
700638 GTAATTTTGGTGAAATTGGGGTCAAAAATGGAATTTTGGAAGGTTCGGGGGT
66 GTAATTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAGGTTCGGGGGT
*
700690 AAAAT-ATAATTTT
1 AAAATGGTAATTTT
700703 AGAAAAGTTT
Statistics
Matches: 121, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
116 20 0.17
117 101 0.83
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.31
Consensus pattern (117 bp):
AAAATGGTAATTTTTGGTTAAAATTGGGTCAAAACGAGAATTTTGGAAAGTTAGAGGGCGAAATG
GTAATTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAGGTTCGGGGGT
Found at i:700684 original size:58 final size:58
Alignment explanation
Indices: 700451--700702 Score: 280
Period size: 58 Copynumber: 4.3 Consensus size: 58
700441 TTGGATACTT
* * *
700451 GAGGGCAAAATGGTAAATTTGGTTAAAATTGGGTCAAAACGAGAATTTTGGAAAGTT-
1 GAGGGTAAAATGGTAATTTTGGTTGAAATTGGGTCAAAACGAGAATTTTGGAAAGTTC
* ** * ** *
700508 TAGGGGCGAAATGGTAATTTTGG-TGAAATCGGGGTCAAAAATAGAATTTTGGAAGGTTC
1 GA-GGGTAAAATGGTAATTTTGGTTGAAAT-TGGGTCAAAACGAGAATTTTGGAAAGTTC
*
700567 GGGGGTAAAATGGTAATTTTTGGTTGAAATTGGGTCAAAACGAGAATTTTGGAAAGTTC
1 GAGGGTAAAATGGTAA-TTTTGGTTGAAATTGGGTCAAAACGAGAATTTTGGAAAGTTC
* * *
700626 GAGGGTGAAATGGTAATTTTGG-TGAAATTGGGGTCAAAAATG-GAATTTTGGAAGGTTC
1 GAGGGTAAAATGGTAATTTTGGTTGAAATT-GGGTC-AAAACGAGAATTTTGGAAAGTTC
* *
700684 GGGGGTAAAAT-ATAATTTT
1 GAGGGTAAAATGGTAATTTT
700703 AGAAAAGTTT
Statistics
Matches: 165, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
57 20 0.12
58 89 0.54
59 50 0.30
60 6 0.04
ACGTcount: A:0.34, C:0.05, G:0.31, T:0.31
Consensus pattern (58 bp):
GAGGGTAAAATGGTAATTTTGGTTGAAATTGGGTCAAAACGAGAATTTTGGAAAGTTC
Found at i:700687 original size:29 final size:27
Alignment explanation
Indices: 700481--700687 Score: 86
Period size: 29 Copynumber: 7.1 Consensus size: 27
700471 GGTTAAAATT
* *
700481 GGGTCAAAACGAGAATTTTGGAAAGTTTAG
1 GGGTCAAAATG-GAATTTTGG-AAG-TTCG
* *
700511 GGG-CGAAATGGTAATTTTGGTGAA-ATCG
1 GGGTCAAAATGG-AATTTT-G-GAAGTTCG
*
700539 GGGTCAAAAATAGAATTTTGGAAGGTTCGG
1 GGGTC-AAAATGGAATTTTGGAA-GTTC-G
*
700569 GGGT-AAAATGGTAATTTTTGGTTGAAATT--
1 GGGTCAAAATGG-AA-TTTT-G--GAAGTTCG
*
700598 GGGTCAAAACGAGAATTTTGGAAAGTTCG
1 GGGTCAAAATG-GAATTTTGG-AAGTTCG
* *
700627 AGGGT-GAAATGGTAATTTTGGTGAAATT-G
1 -GGGTCAAAATGG-AATTTT-G-GAAGTTCG
700656 GGGTCAAAAATGGAATTTTGGAAGGTTCG
1 GGGTC-AAAATGGAATTTTGGAA-GTTCG
700685 GGG
1 GGG
700688 GTAAAATATA
Statistics
Matches: 135, Mismatches: 16, Indels: 53
0.66 0.08 0.26
Matches are distributed among these distances:
26 1 0.01
27 10 0.07
28 22 0.16
29 51 0.38
30 42 0.31
31 4 0.03
32 2 0.01
33 3 0.02
ACGTcount: A:0.32, C:0.05, G:0.33, T:0.29
Consensus pattern (27 bp):
GGGTCAAAATGGAATTTTGGAAGTTCG
Found at i:700693 original size:29 final size:28
Alignment explanation
Indices: 700538--700693 Score: 74
Period size: 30 Copynumber: 5.3 Consensus size: 28
700528 TGGTGAAATC
*
700538 GGGGTCAAAAATAGAATTTTGGAAGGTTCG
1 GGGGT-AAAAATGGAATTTTGGAA-GTTCG
*
700568 GGGGT-AAAATGGTAATTTTTGGTTGAAATT--
1 GGGGTAAAAATGG-AA-TTTT-G--GAAGTTCG
* *
700598 -GGGTCAAAACGAGAATTTTGGAAAGTTCG
1 GGGGTAAAAATG-GAATTTTGG-AAGTTCG
* * *
700627 AGGGT-GAAATGGTAATTTTGGTGAAATT--
1 GGGGTAAAAATGG-AATTTT-G-GAAGTTCG
700655 GGGGTCAAAAATGGAATTTTGGAAGGTTCG
1 GGGGT-AAAAATGGAATTTTGGAA-GTTCG
700685 GGGGTAAAA
1 GGGGTAAAA
700694 TATAATTTTA
Statistics
Matches: 97, Mismatches: 10, Indels: 39
0.66 0.07 0.27
Matches are distributed among these distances:
26 1 0.01
27 7 0.07
28 15 0.15
29 30 0.31
30 36 0.37
31 3 0.03
32 2 0.02
33 3 0.03
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.29
Consensus pattern (28 bp):
GGGGTAAAAATGGAATTTTGGAAGTTCG
Found at i:701906 original size:21 final size:21
Alignment explanation
Indices: 701859--701908 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
701849 TTAATGCTTT
701859 TATTT-AAAATTAATTAATAC
1 TATTTAAAAATTAATTAATAC
*
701879 TATTTAAAACATTAATTAATGC
1 TATTTAAAA-ATTAATTAATAC
701901 -ATTTAAAA
1 TATTTAAAA
701909 TATTCAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 5 0.19
21 11 0.41
22 11 0.41
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (21 bp):
TATTTAAAAATTAATTAATAC
Found at i:702613 original size:17 final size:16
Alignment explanation
Indices: 702574--702649 Score: 66
Period size: 18 Copynumber: 4.6 Consensus size: 16
702564 GACACCCTAT
* *
702574 TAAATTTATAATAATTT
1 TAAATTTA-ATTAATTC
702591 TAAAATTTACATTAATTC
1 T-AAATTTA-ATTAATTC
702609 TAAATTTAAATTAAATT-
1 TAAATTT-AATT-AATTC
*
702626 TAAATTTAA-TAAATC
1 TAAATTTAATTAATTC
702641 TAAATTTAA
1 TAAATTTAA
702650 AATAAATTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
14 3 0.06
15 10 0.20
16 2 0.04
17 17 0.33
18 19 0.37
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATTTAATTAATTC
Found at i:702620 original size:6 final size:6
Alignment explanation
Indices: 702604--702667 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
702594 AATTTACATT
*
702604 AATTCTA AATTTA AA-TTA AATTTA AATTT- AA--TA AATCTA AATTTA
1 AATT-TA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* *
702649 AA-ATA AATTTA ATTTTA AA
1 AATTTA AATTTA AATTTA AA
702668 ATGAATTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 11 0.23
6 29 0.62
7 4 0.09
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:702625 original size:11 final size:11
Alignment explanation
Indices: 702609--702660 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
702599 ACATTAATTC
702609 TAAATTTAAAT
1 TAAATTTAAAT
702620 TAAATTTAAAT
1 TAAATTTAAAT
*
702631 TTAA--TAAAT
1 TAAATTTAAAT
*
702640 CTAAATTTAAAA
1 -TAAATTTAAAT
702652 TAAATTTAA
1 TAAATTTAA
702661 TTTTAAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 5 0.14
10 3 0.09
11 23 0.66
12 4 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:702645 original size:26 final size:26
Alignment explanation
Indices: 702609--702661 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
702599 ACATTAATTC
* *
702609 TAAATTTAAA-TTAAATTTAAATTTAA
1 TAAATCTAAATTTAAA-ATAAATTTAA
702635 TAAATCTAAATTTAAAATAAATTTAA
1 TAAATCTAAATTTAAAATAAATTTAA
702661 T
1 T
702662 TTTAAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAATCTAAATTTAAAATAAATTTAA
Found at i:702653 original size:17 final size:17
Alignment explanation
Indices: 702573--702675 Score: 95
Period size: 17 Copynumber: 6.1 Consensus size: 17
702563 GGACACCCTA
* *
702573 TTAAATTTATAATAATT
1 TTAAATTTAAAATAAAT
* *
702590 TTAAAATTT-ACATTAAT
1 TT-AAATTTAAAATAAAT
*
702607 TCTAAATTTAAATTAAAT
1 T-TAAATTTAAAATAAAT
702625 TTAAATTT--AATAAAT
1 TTAAATTTAAAATAAAT
*
702640 CTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
* *
702657 TTAATTTTAAAATGAAT
1 TTAAATTTAAAATAAAT
702674 TT
1 TT
702676 TAAAATGATT
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
15 13 0.19
17 43 0.62
18 13 0.19
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.47
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:702674 original size:12 final size:12
Alignment explanation
Indices: 702659--702683 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
702649 AAATAAATTT
702659 AATTTTAAAATG
1 AATTTTAAAATG
702671 AATTTTAAAATG
1 AATTTTAAAATG
702683 A
1 A
702684 TTTGGCTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AATTTTAAAATG
Found at i:713404 original size:39 final size:40
Alignment explanation
Indices: 713317--713404 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 40
713307 GTGCTTTATA
* *
713317 CTTTAGCGATGCTTTCCCATAAACGTCGCTATTGCTCTGAC
1 CTTTAGCGATGCTTTCCCATAAACATCGC-ATTACTCTGAC
* *
713358 ATTTAGCGATGCTTTTCCA-AAAGCATCG-ATTACTCTGAC
1 CTTTAGCGATGCTTTCCCATAAA-CATCGCATTACTCTGAC
713397 CTTTAGCG
1 CTTTAGCG
713405 GCGCTTGCCT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 17 0.41
40 3 0.07
41 21 0.51
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (40 bp):
CTTTAGCGATGCTTTCCCATAAACATCGCATTACTCTGAC
Found at i:713441 original size:41 final size:41
Alignment explanation
Indices: 713394--713502 Score: 182
Period size: 41 Copynumber: 2.7 Consensus size: 41
713384 CGATTACTCT
713394 GACCTTTAGCGGCGCTTGCCTATAAGCGACGCTATTGCTCA
1 GACCTTTAGCGGCGCTTGCCTATAAGCGACGCTATTGCTCA
* * *
713435 GACCTTTAGCGACGCTTGCCTATAAGTGCCGCTATTGCTCA
1 GACCTTTAGCGGCGCTTGCCTATAAGCGACGCTATTGCTCA
*
713476 GACCTTTAGCGGCGCTTGCCCATAAGC
1 GACCTTTAGCGGCGCTTGCCTATAAGC
713503 ACCGCAAATC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.19, C:0.30, G:0.24, T:0.27
Consensus pattern (41 bp):
GACCTTTAGCGGCGCTTGCCTATAAGCGACGCTATTGCTCA
Found at i:714065 original size:80 final size:80
Alignment explanation
Indices: 713933--714136 Score: 281
Period size: 80 Copynumber: 2.6 Consensus size: 80
713923 TATTTTATCC
* * * * * *
713933 TAATTTAAAAGAAAGAAAAGGATATAAT-GAATAAGTTTGATGGAAATTGTATTTTAGTATGTTG
1 TAATTTAAAAGAATGGAAAGCATACAATCGAATAAGTTTGGTGGAAATAGTATTTTAGTATGTTG
* *
713997 ATGTTAGGATCCCAA
66 ATCTTAGAATCCCAA
714012 TAATTTAAAAGAATGGAAAGCATA-AGCA-CGAATAAGTTTGGTGGAAATAGTATTTTAGTATGT
1 TAATTTAAAAGAATGGAAAGCATACA--ATCGAATAAGTTTGGTGGAAATAGTATTTTAGTATGT
*
714075 TGCTCTTAGAATCCCAA
64 TGATCTTAGAATCCCAA
714092 TAATTTAAAAGAATGGAAAGCATACAATC-AATAAGTTTGGTGGAA
1 TAATTTAAAAGAATGGAAAGCATACAATCGAATAAGTTTGGTGGAA
714137 GTTGTGTTGA
Statistics
Matches: 112, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
78 1 0.01
79 38 0.34
80 72 0.64
81 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (80 bp):
TAATTTAAAAGAATGGAAAGCATACAATCGAATAAGTTTGGTGGAAATAGTATTTTAGTATGTTG
ATCTTAGAATCCCAA
Found at i:714169 original size:38 final size:38
Alignment explanation
Indices: 714118--714196 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
714108 AAAGCATACA
*
714118 ATCAATAAGTTTGGTGGAAGTTGTGTTGAAGTGTGTTG
1 ATCAATAAGTTTGGTGGAAGTTGTATTGAAGTGTGTTG
714156 ATCAATAAGTTTGGTGGAAGTTGTATTGAAGTGTGTTG
1 ATCAATAAGTTTGGTGGAAGTTGTATTGAAGTGTGTTG
714194 ATC
1 ATC
714197 GTACGATTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.25, C:0.04, G:0.32, T:0.39
Consensus pattern (38 bp):
ATCAATAAGTTTGGTGGAAGTTGTATTGAAGTGTGTTG
Found at i:714759 original size:7 final size:7
Alignment explanation
Indices: 714747--714790 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
714737 GTCTACCCTA
714747 ATTCTCC
1 ATTCTCC
714754 ATTCTCC
1 ATTCTCC
714761 ATTCTCC
1 ATTCTCC
714768 ATTCTCC
1 ATTCTCC
714775 ATTCTCC
1 ATTCTCC
714782 ATTCTCC
1 ATTCTCC
714789 AT
1 AT
714791 AACCTCCGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.16, C:0.41, G:0.00, T:0.43
Consensus pattern (7 bp):
ATTCTCC
Found at i:715370 original size:101 final size:104
Alignment explanation
Indices: 715198--715382 Score: 270
Period size: 101 Copynumber: 1.8 Consensus size: 104
715188 GATTTTCAGT
* *
715198 CTTTGTTGAAAATATATAGTAACAAAATCAAACGGTATTTAATTAAGGGGTTACTATAGTTTCCA
1 CTTTGTTGAAAATATATAGTAAAAAAATCAAAAGGTATTTAATTAAGGGGTTACTATAGTTTCCA
715263 CCCTTCAAATTATAATTAAATAAAAAATTAAAATTCTAG
66 CCCTTCAAATTATAATTAAATAAAAAATTAAAATTCTAG
* * *
715302 CTTTTTTGAAAA-ATA-A-TAAAAAAATTAAAAGGTATTTGATTAAGGGGTTTACTATAGTTTCC
1 CTTTGTTGAAAATATATAGTAAAAAAATCAAAAGGTATTTAATTAAGGGG-TTACTATAGTTTCC
* *
715364 A-TCTTCAAATTATAGTTAA
65 ACCCTTCAAATTATAATTAA
715383 TTAGTATAAC
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
101 43 0.59
102 16 0.22
103 3 0.04
104 11 0.15
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (104 bp):
CTTTGTTGAAAATATATAGTAAAAAAATCAAAAGGTATTTAATTAAGGGGTTACTATAGTTTCCA
CCCTTCAAATTATAATTAAATAAAAAATTAAAATTCTAG
Found at i:719664 original size:2 final size:2
Alignment explanation
Indices: 719657--719700 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
719647 AGTTCCAGCG
719657 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
719699 AT
1 AT
719701 TAATTTTTGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:720189 original size:26 final size:28
Alignment explanation
Indices: 720151--720210 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
720141 AATTTTAAAA
* *
720151 AAAAAATTAGGGTTT-ATTAAATTTTTT
1 AAAAAATTAGGGTTTAATGAAATTTTTC
* *
720178 AAAAAA-TGGGGTTTAATGATATTTTTC
1 AAAAAATTAGGGTTTAATGAAATTTTTC
720205 AAAAAA
1 AAAAAA
720211 CTAAGGGATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.45, C:0.02, G:0.13, T:0.40
Consensus pattern (28 bp):
AAAAAATTAGGGTTTAATGAAATTTTTC
Found at i:720247 original size:20 final size:20
Alignment explanation
Indices: 720224--720266 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
720214 AGGGATCTAG
720224 TTTAAAAAAATTTGAGAAAA
1 TTTAAAAAAATTTGAGAAAA
* **
720244 TTTAAAAGAATTTTTGAAAA
1 TTTAAAAAAATTTGAGAAAA
720264 TTT
1 TTT
720267 TAGAGATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (20 bp):
TTTAAAAAAATTTGAGAAAA
Found at i:729792 original size:17 final size:18
Alignment explanation
Indices: 729761--729798 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
729751 ACCTCTTTTA
*
729761 AAAGTAAAAATTAAAAAT
1 AAAGTAAAAACTAAAAAT
*
729779 AAAGT-AAAACTAAAACT
1 AAAGTAAAAACTAAAAAT
729796 AAA
1 AAA
729799 ACTAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAGTAAAAACTAAAAAT
Found at i:729895 original size:16 final size:15
Alignment explanation
Indices: 729859--729895 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
729849 TTAAAATTAA
729859 TATTTTTAAAATATT
1 TATTTTTAAAATATT
*
729874 TATTTTTATAATATT
1 TATTTTTAAAATATT
729889 TATTTTT
1 TATTTTT
729896 CTTAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTAAAATATT
Found at i:729905 original size:16 final size:15
Alignment explanation
Indices: 729849--729905 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
729839 TTTTAAAATC
*
729849 TTAAAATTAATATTTT
1 TTAAAATTTAT-TTTT
*
729865 TAAAATATTTATTTTT
1 TTAAA-ATTTATTTTT
* *
729881 ATAATATTTATTTTT
1 TTAAAATTTATTTTT
729896 CTTAAAATTT
1 -TTAAAATTT
729906 CATTCTAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 10 0.31
16 17 0.53
17 5 0.16
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAAAATTTATTTTT
Found at i:731485 original size:5 final size:5
Alignment explanation
Indices: 731475--731502 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
731465 TTTTAAAATA
731475 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
731503 TAATAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:744763 original size:17 final size:17
Alignment explanation
Indices: 744732--744765 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
744722 TATTTTGGCC
**
744732 GTTTAAATTTTTAAAAA
1 GTTTAAATTAATAAAAA
744749 GTTTAAATTAATAAAAA
1 GTTTAAATTAATAAAAA
744766 AAATTACACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
GTTTAAATTAATAAAAA
Found at i:749076 original size:29 final size:31
Alignment explanation
Indices: 749024--749086 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 31
749014 AATAGATTTG
* *
749024 AATTTTGAAATTTGAAAAGTAAAAGTATTAA
1 AATTTTGAAATATGAAAAGTAAAAGGATTAA
749055 AATTTTGAAA-AT-AAAAGTAAAAGGATTAA
1 AATTTTGAAATATGAAAAGTAAAAGGATTAA
749084 AAT
1 AAT
749087 CCAAGTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 19 0.63
30 1 0.03
31 10 0.33
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.32
Consensus pattern (31 bp):
AATTTTGAAATATGAAAAGTAAAAGGATTAA
Found at i:762786 original size:2 final size:2
Alignment explanation
Indices: 762779--762809 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
762769 ACATACATAC
762779 AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
762810 CACCATCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:773525 original size:12 final size:13
Alignment explanation
Indices: 773508--773536 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
773498 AAATAACTAT
773508 AACTA-TTTTTTG
1 AACTATTTTTTTG
773520 AACTATTTTTTTG
1 AACTATTTTTTTG
773533 AACT
1 AACT
773537 CATGTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (13 bp):
AACTATTTTTTTG
Found at i:773785 original size:17 final size:16
Alignment explanation
Indices: 773747--773787 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
773737 GGTTATATTT
*
773747 TATTTTTGTAATTTCA
1 TATTTTTGTAATTTAA
773763 TGATTTTTGTAATTTTAA
1 T-ATTTTTGTAA-TTTAA
773781 TATTTTT
1 TATTTTT
773788 TTGAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 16 0.73
18 5 0.23
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.66
Consensus pattern (16 bp):
TATTTTTGTAATTTAA
Found at i:777167 original size:13 final size:13
Alignment explanation
Indices: 777149--777173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
777139 TTTTCAAAAA
777149 ATAATTTTTTTAT
1 ATAATTTTTTTAT
777162 ATAATTTTTTTA
1 ATAATTTTTTTA
777174 CGTTTTTCAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATAATTTTTTTAT
Found at i:789129 original size:29 final size:30
Alignment explanation
Indices: 789086--789143 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
789076 GCATTGGATC
789086 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
*
789116 AAATCAAAA-TTCATGTATAAATTTACAC
1 AAATCAAAATTTCATGTATAAAATTACAC
789144 GTTAAACCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:789158 original size:31 final size:29
Alignment explanation
Indices: 789090--789165 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
789080 TGGATCAAAT
*
789090 CAAAATTTCATGTATAAAATTACACAAAAT
1 CAAAA-TTCATGTATAAAATTACACAAAAC
* *
789120 CAAAATTCATGTATAAATTTACACGTTAAAC
1 CAAAATTCATGTATAAAATTACAC--AAAAC
*
789151 CAAAATTCATATATA
1 CAAAATTCATGTATA
789166 GTTTTGAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 18 0.45
30 5 0.12
31 17 0.43
ACGTcount: A:0.50, C:0.14, G:0.04, T:0.32
Consensus pattern (29 bp):
CAAAATTCATGTATAAAATTACACAAAAC
Found at i:791044 original size:27 final size:27
Alignment explanation
Indices: 790986--791046 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
790976 AGTAAAAATC
*
790986 AATTAATTTGATCGATTCGATTATAAA
1 AATTCATTTGATCGATTCGATTATAAA
791013 AATTCATTTGATCGATTCGATTATAAA
1 AATTCATTTGATCGATTCGATTATAAA
791040 AATTCAT
1 AATTCAT
791047 GAACTATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (27 bp):
AATTCATTTGATCGATTCGATTATAAA
Found at i:793737 original size:58 final size:58
Alignment explanation
Indices: 793667--793780 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
793657 ATATTTGGGA
*
793667 CCTGAACTTGACAAATGTTCTCACATT-GAGGCTTAAAG-TTTTTTTGTTCAAGTTAGTC
1 CCTGAACTTGACAAATGTTCTCACATTAG-GGCTT-AAGCTTTTTTTGTCCAAGTTAGTC
*
793725 CCTGAACTTGACAATTGTTCTCACATTAGGGCTTAAGCTTTTTTTGTCCAAGTTAG
1 CCTGAACTTGACAAATGTTCTCACATTAGGGCTTAAGCTTTTTTTGTCCAAGTTAG
793781 GCCTTGATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
57 3 0.06
58 48 0.92
59 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (58 bp):
CCTGAACTTGACAAATGTTCTCACATTAGGGCTTAAGCTTTTTTTGTCCAAGTTAGTC
Found at i:796161 original size:294 final size:294
Alignment explanation
Indices: 795632--796229 Score: 1124
Period size: 294 Copynumber: 2.0 Consensus size: 294
795622 CAATTCTAAG
*
795632 AAAACATCAAATTAGAGAATTCTATTTATAGTCAACAAAAATTTTCGAAAATTTTCTTTCAAAAA
1 AAAACATCAAATTAGAGAATTCTATTGATAGTCAACAAAAATTTTCGAAAATTTTCTTTCAAAAA
795697 GTCCATCGCATAACTTGAGGGATTGTCAAGAATAATCAGTTGGTCTATCACATCATCATCTGCCT
66 GTCCATCGCATAACTTGAGGGATTGTCAAGAATAATCAGTTGGTCTATCACATCATCATCTGCCT
795762 TAGCAACATGAATGCATCTTATTTCATCAACATTATTCACTGATATTTAACCATTCCGAATGAAT
131 TAGCAACATGAATGCATCTTATTTCATCAACATTATTCACTGATATTTAACCATTCCGAATGAAT
795827 TTAATCAACATTACATTATCACTTTTTAACTCAACTTGCCTCAATACTCGGTTCCAAACCAATTT
196 TTAATCAACATTACATTATCACTTTTTAACTCAACTTGCCTCAATACTCGGTTCCAAACCAATTT
*
795892 CAAACCTTCTAAAACTGTTCAGGCTTCTACTTGT
261 CAAACCTTCTAAAACTGCTCAGGCTTCTACTTGT
795926 AAAACATCAAATTAGAGAATTCTATTGATAGTCAACAAAAATTTTCGAAAATTTTCTTTCAAAAA
1 AAAACATCAAATTAGAGAATTCTATTGATAGTCAACAAAAATTTTCGAAAATTTTCTTTCAAAAA
*
795991 GTCCATCGCATAACTTGAGGGATTGTCAAGAATAATTAGTTGGTCTATCACATCATCATCTGCCT
66 GTCCATCGCATAACTTGAGGGATTGTCAAGAATAATCAGTTGGTCTATCACATCATCATCTGCCT
*
796056 TAGCAACATGAATGCATCTTATTTCATCAACATTATTCACTGATGTTTAACCATTCCGAATGAAT
131 TAGCAACATGAATGCATCTTATTTCATCAACATTATTCACTGATATTTAACCATTCCGAATGAAT
* * * *
796121 TTAATCAACATTGCATTATCACTTTTTAATTCAACTTGCCTCAATCCTCGGTTTCAAACCAATTT
196 TTAATCAACATTACATTATCACTTTTTAACTCAACTTGCCTCAATACTCGGTTCCAAACCAATTT
796186 CAAACCTTCTAAAACTGCTCAGGCTTCTACTTGT
261 CAAACCTTCTAAAACTGCTCAGGCTTCTACTTGT
796220 AAAACATCAA
1 AAAACATCAA
796230 TCAAACCAAC
Statistics
Matches: 296, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
294 296 1.00
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (294 bp):
AAAACATCAAATTAGAGAATTCTATTGATAGTCAACAAAAATTTTCGAAAATTTTCTTTCAAAAA
GTCCATCGCATAACTTGAGGGATTGTCAAGAATAATCAGTTGGTCTATCACATCATCATCTGCCT
TAGCAACATGAATGCATCTTATTTCATCAACATTATTCACTGATATTTAACCATTCCGAATGAAT
TTAATCAACATTACATTATCACTTTTTAACTCAACTTGCCTCAATACTCGGTTCCAAACCAATTT
CAAACCTTCTAAAACTGCTCAGGCTTCTACTTGT
Found at i:800624 original size:7 final size:7
Alignment explanation
Indices: 800603--800661 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
800593 AAAAATATTT
800603 TTTAATA
1 TTTAATA
800610 TTTAAATA
1 TTT-AATA
800618 TTTAATA
1 TTTAATA
*
800625 TTATAATT
1 TT-TAATA
*
800633 TTTTAT-
1 TTTAATA
800639 TTTCAA-A
1 TTT-AATA
800646 TTTAA-A
1 TTTAATA
800652 TTTAATA
1 TTTAATA
800659 TTT
1 TTT
800662 TTTATTTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
6 11 0.25
7 20 0.45
8 13 0.30
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTAATA
Found at i:800639 original size:28 final size:29
Alignment explanation
Indices: 800596--800674 Score: 92
Period size: 28 Copynumber: 2.7 Consensus size: 29
800586 CAAAGTTAAA
800596 AATATTTTTTAATATTTAAATATTT-AATATT
1 AATATTTTTT-AT-TTTAAATATTTAAAT-TT
*
800627 -ATAATTTTTTATTTTCAA-ATTTAAATTT
1 AAT-ATTTTTTATTTTAAATATTTAAATTT
800655 AATATTTTTTATTTTAAATA
1 AATATTTTTTATTTTAAATA
800675 AATAATTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
28 20 0.48
29 11 0.26
30 4 0.10
31 7 0.17
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (29 bp):
AATATTTTTTATTTTAAATATTTAAATTT
Found at i:800681 original size:28 final size:28
Alignment explanation
Indices: 800596--800686 Score: 87
Period size: 28 Copynumber: 3.1 Consensus size: 28
800586 CAAAGTTAAA
*
800596 AATATTTTTTAATATTTAAATATTTAATATT
1 AATATTTTTT-AT-TTTAAATATATAAT-TT
*
800627 -ATAATTTTTTATTTTCAAATTTA-AATTT
1 AAT-ATTTTTTATTTT-AAATATATAATTT
*
800655 AATATTTTTTATTTTAAATAAATAATTAT
1 AATATTTTTTATTTTAAATATATAATT-T
800684 AAT
1 AAT
800687 GTGACATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
27 5 0.10
28 18 0.35
29 12 0.24
30 9 0.18
31 7 0.14
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (28 bp):
AATATTTTTTATTTTAAATATATAATTT
Found at i:816238 original size:58 final size:57
Alignment explanation
Indices: 816127--816236 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 57
816117 TTTTTTGAAC
* * * *
816127 ACTCAATTATGAAAAGTTGTAAAATGATCACCCAACTATTAATAAATTTTTTTTGGTG
1 ACTCAACTATAAAAAATTATAAAATGATCACCCAACTATTAAT-AATTTTTTTTGGTG
* *
816185 ACTCAACTATAAAAAATTATAAAATGATCACTCAATTATT--TAATTTTATTTT
1 ACTCAACTATAAAAAATTATAAAATGATCACCCAACTATTAATAATTTT-TTTT
816237 TTTCATCTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 6 0.13
56 5 0.11
58 34 0.76
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (57 bp):
ACTCAACTATAAAAAATTATAAAATGATCACCCAACTATTAATAATTTTTTTTGGTG
Found at i:816676 original size:18 final size:19
Alignment explanation
Indices: 816635--816677 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
816625 GTATTGTTTG
* *
816635 ATAATTCATTGAAATATTT
1 ATAATTTATTGAAATATTA
816654 A-AATTTATTGAAA-ATTA
1 ATAATTTATTGAAATATTA
816671 ATAATTT
1 ATAATTT
816678 TAGTGTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 16 0.76
19 1 0.05
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (19 bp):
ATAATTTATTGAAATATTA
Found at i:819370 original size:15 final size:16
Alignment explanation
Indices: 819350--819380 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
819340 TATTTAATAA
819350 ATTTA-TAAATTTTTT
1 ATTTATTAAATTTTTT
819365 ATTTATTAAATTTTTT
1 ATTTATTAAATTTTTT
819381 TATATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTATTAAATTTTTT
Found at i:819444 original size:19 final size:16
Alignment explanation
Indices: 819428--819461 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
819418 TATATTTAGT
819428 ATAAGTTTATTTTTTTA
1 ATAAGTTT-TTTTTTTA
*
819445 ATATGTTTTTTTTTTA
1 ATAAGTTTTTTTTTTA
819461 A
1 A
819462 CCCAGTCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
ATAAGTTTTTTTTTTA
Found at i:823824 original size:6 final size:6
Alignment explanation
Indices: 823813--823838 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
823803 TGGTTCGAGA
823813 AACTAG AACTAG AACTAG AACTAG AA
1 AACTAG AACTAG AACTAG AACTAG AA
823839 TGCAATTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (6 bp):
AACTAG
Found at i:832461 original size:211 final size:212
Alignment explanation
Indices: 831963--832498 Score: 661
Period size: 212 Copynumber: 2.5 Consensus size: 212
831953 TCAATACGGA
* ** * * * *
831963 TATGATTAGACTTTCCCAAGTTTTCCCATATATTGGGGGTTCTTTGGAGTTCATGTCTCGATATC
1 TATGATTAGACTTTCCCAAGTTTTTCCATATATTAAGGGATCTTTGAAGGTCATGTCTCCATATC
* * * *
832028 CGTGTATCGAACACTAATGTTGGACTGGGGTACTTAAAAAAGAATGAAGCCAACAATGGGGGTAG
66 CGTGTATCAAACACTAATGTCGGACAGGGGTACTTCAAAAAGAATGAAGCCAACAATGGGGGTAG
* * ** * * *
832093 ATAGTTTTTCTTTTAAGTTCTTGGTTACATCGTTATTGTCATAGGTTTACCTAGACTCGGGTTTG
131 ATAGTTTTTCTTTTAAGTTCTTCGTTACACCGGCATTGTCACAGGTTTACCTAGACTCAGGTGTG
* * *
832158 AGAGTCCCCGGCACGAG
196 AGAATCCCCGACAAGAG
* * *
832175 TATGATTAGATTTTCCCAAGGTTTTCCATATATTAAGGGATCTTTGAGGGTCATGTCTCCATATC
1 TATGATTAGACTTTCCCAAGTTTTTCCATATATTAAGGGATCTTTGAAGGTCATGTCTCCATATC
* * *
832240 TGTGTATCAAACACTAATGTCGGACAGGGGTACTTCAAGAAGAATGAAGCCAACAATTGGGGTAG
66 CGTGTATCAAACACTAATGTCGGACAGGGGTACTTCAAAAAGAATGAAGCCAACAATGGGGGTAG
* * * *
832305 ATGGTTTTTCATTTT-AGTTCTTCGTTGCACCGGCATTGTTCACATG-TTA-CTCGACTCAGGTG
131 ATAGTTTTTC-TTTTAAGTTCTTCGTTACACCGGCATTG-TCACAGGTTTACCTAGACTCAGGTG
832367 TGA-ATATCCCCGACATAG-G
194 TGAGA-ATCCCCGACA-AGAG
*
832386 TATGATTAGACTTTCTCAAGTTTTTCCATATATTAAGGGATCTTTGAAGGTCATGTCTCCATATC
1 TATGATTAGACTTTCCCAAGTTTTTCCATATATTAAGGGATCTTTGAAGGTCATGTCTCCATATC
*** * *
832451 CACATATCAAACACTAAAGTCAGACA-GGGTACTTCAAAAAGAATGAAG
66 CGTGTATCAAACACTAATGTCGGACAGGGGTACTTCAAAAAGAATGAAG
832499 AATCCGAGCA
Statistics
Matches: 278, Mismatches: 42, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
210 22 0.08
211 103 0.37
212 144 0.52
213 9 0.03
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (212 bp):
TATGATTAGACTTTCCCAAGTTTTTCCATATATTAAGGGATCTTTGAAGGTCATGTCTCCATATC
CGTGTATCAAACACTAATGTCGGACAGGGGTACTTCAAAAAGAATGAAGCCAACAATGGGGGTAG
ATAGTTTTTCTTTTAAGTTCTTCGTTACACCGGCATTGTCACAGGTTTACCTAGACTCAGGTGTG
AGAATCCCCGACAAGAG
Found at i:833942 original size:12 final size:12
Alignment explanation
Indices: 833925--833949 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
833915 GGTAAAATGA
833925 TTTTGGTTTCCT
1 TTTTGGTTTCCT
833937 TTTTGGTTTCCT
1 TTTTGGTTTCCT
833949 T
1 T
833950 GTTGCTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (12 bp):
TTTTGGTTTCCT
Found at i:834530 original size:7 final size:7
Alignment explanation
Indices: 834518--834548 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
834508 ACTAAATCAT
834518 TTGAAAG
1 TTGAAAG
834525 TTGAAAG
1 TTGAAAG
834532 TTGAAAG
1 TTGAAAG
834539 TTGAAAG
1 TTGAAAG
834546 TTG
1 TTG
834549 TCATTTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (7 bp):
TTGAAAG
Found at i:836201 original size:212 final size:210
Alignment explanation
Indices: 835725--836268 Score: 648
Period size: 211 Copynumber: 2.6 Consensus size: 210
835715 TGCTTGGATT
* *** **
835725 CTTCATTCTTTTTGAAGTACCCCCCTGTCTGACATTAGTGTTTGATATGTGGATATGGAGACACA
1 CTTCATTCTTTTTGAAGTA--CCCCTGTCCGACATTAGTGTTTGATACACGGATATGGAGACATG
* * * * * *
835790 ACCTTCAAAGATCCCTTAATATATGGAAAAACTTGAGAAAGTCTAATCACACCCATGTCGGGGAT
64 ACCTCCAAAGATCCCTTAATATATGG-AAAACTTGGGAAAATCTAATCATACCCGTGCCGGGGAT
* * * * * * *
835855 ATTCACACCTGAGTCGCGTAACATGTGAACAATGCGGGTGCAACGAAGAACTAAAATGAAAAACC
128 ACTCAAACCCGAGTCGCGTAACATATGAACAATGCCGATGCAACCAAGAACTAAAATGAAAAACC
835920 ATCTGCCCCAATTGTTGG
193 ATCTGCCCCAATTGTTGG
* * *
835938 CTTCATTCTTCTTGAAGTACCCCTGTCCGTCATTAGTGTTTGATTCACGGATATGGAGACATGAC
1 CTTCATTCTTTTTGAAGTACCCCTGTCCGACATTAGTGTTTGATACACGGATATGGAGACATGAC
* *
836003 CCCCAAAGATCCCTTAATATATGGAAAACCTTGGGAAAATCTAATCATACTCGTGCCGGGGACT-
66 CTCCAAAGATCCCTTAATATATGGAAAA-CTTGGGAAAATCTAATCATACCCGTGCCGGGGA-TA
* * *
836067 CTCAAACCCGAGTCTAG-GTAAACCTATG-ATAATGCCGATGTAACCAAGAACTTAAAA-GAAAA
129 CTCAAACCCGAGTC--GCGT-AACATATGAACAATGCCGATGCAACCAAGAAC-TAAAATGAAAA
* *
836129 ACTATCTGCCCCCATTGTTGG
190 ACCATCTGCCCCAATTGTTGG
* * * *
836150 CTTCATTCTTTTTTAAGTACCCCAGTCCGACATTAGTGTCTGATACACGGATATCGAGACATGAC
1 CTTCATTCTTTTTGAAGTACCCCTGTCCGACATTAGTGTTTGATACACGGATATGGAGACATGAC
* *
836215 CTCCAAAGAACCC-CAATATATGGGAAAACTTGGGAAAATCTAATCATACCCGTG
66 CTCCAAAGATCCCTTAATATAT-GGAAAACTTGGGAAAATCTAATCATACCCGTG
836269 TTGAGGTTGA
Statistics
Matches: 284, Mismatches: 40, Indels: 16
0.84 0.12 0.05
Matches are distributed among these distances:
210 4 0.01
211 130 0.46
212 120 0.42
213 30 0.11
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (210 bp):
CTTCATTCTTTTTGAAGTACCCCTGTCCGACATTAGTGTTTGATACACGGATATGGAGACATGAC
CTCCAAAGATCCCTTAATATATGGAAAACTTGGGAAAATCTAATCATACCCGTGCCGGGGATACT
CAAACCCGAGTCGCGTAACATATGAACAATGCCGATGCAACCAAGAACTAAAATGAAAAACCATC
TGCCCCAATTGTTGG
Found at i:841814 original size:179 final size:172
Alignment explanation
Indices: 841505--841991 Score: 682
Period size: 179 Copynumber: 2.8 Consensus size: 172
841495 TAAAACTAGA
*
841505 GTAAACCATAAAATACCAGGAAAAAGCTTCTGCATTCATAAAAAATCTCTAGAACTAGGCTTTAA
1 GTAAACCATAAAATACCAGGAAAAAGCTTCTGCATTCATAAAAAATCTCTAGAACTAGGCTGTAA
*
841570 AAATTCAGT-AAAAGTCATTCAACATGTAAATATGAT--AAAAAA-AAAAGGGGTATTCAAAGAA
66 AAATTCAGTAAAAAGTCATTCAACATGTAAATATGATAAAAAAAACAAAAAGGGTATTCAAAGAA
* * *
841631 TTAAGCTTT-ATTTTTGTCGAAAACAAATAGAATTAAGCTCGG
131 TTAAGCTTTAATTTTTAT-GAAAACAAAGAGAATTAAGCTCCG
* * *
841673 GTAAACCATACAAGACCAGGAAAAAGCTTCTGCATTCATAAAAAAAATCTATAGAACTTAGGCTG
1 GTAAACCATAAAATACCAGGAAAAAGCTTCTGCATTCAT--AAAAAATCTCTAGAAC-TAGGCTG
* *
841738 TAAAAATTCAGTAAAAAGCCATTCGACATGTAAATATGATAAAACAAACTACAGAAAAGGGTATT
63 TAAAAATTCAGTAAAAAGTCATTCAACATGTAAATATGATAAAA-AAA--ACA-AAAAGGGTATT
* *
841803 CAAAGAATTAAGCTTTAATTTTTATGAAAATACAGAGAATTAAGCTCCG
124 CAAAGAATTAAGCTTTAATTTTTATGAAAACAAAGAGAATTAAGCTCCG
841852 GTAAACCATAAAAATACCAGG-AAAAGCTTCTGCATTCATGAAAAAATCTCTAGAACTAGGCTGT
1 GTAAACCAT-AAAATACCAGGAAAAAGCTTCTGCATTCAT-AAAAAATCTCTAGAACTAGGCTGT
* *
841916 AAAAAATTGAGTAAAAA-TCATACAACATGTAAATATGATAAAAAAAAAACAAAAAGGGTATTCA
64 -AAAAATTCAGTAAAAAGTCATTCAACATGTAAATATGAT--AAAAAAAACAAAAAGGGTATTCA
841980 AAGAATTAAGCT
126 AAGAATTAAGCT
841992 CGGGTAAACC
Statistics
Matches: 283, Mismatches: 20, Indels: 25
0.86 0.06 0.08
Matches are distributed among these distances:
168 37 0.13
170 15 0.05
171 18 0.06
172 25 0.09
174 2 0.01
175 28 0.10
176 3 0.01
177 28 0.10
178 34 0.12
179 77 0.27
180 16 0.06
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.25
Consensus pattern (172 bp):
GTAAACCATAAAATACCAGGAAAAAGCTTCTGCATTCATAAAAAATCTCTAGAACTAGGCTGTAA
AAATTCAGTAAAAAGTCATTCAACATGTAAATATGATAAAAAAAACAAAAAGGGTATTCAAAGAA
TTAAGCTTTAATTTTTATGAAAACAAAGAGAATTAAGCTCCG
Found at i:842026 original size:142 final size:143
Alignment explanation
Indices: 841838--842126 Score: 449
Period size: 143 Copynumber: 2.0 Consensus size: 143
841828 GAAAATACAG
*
841838 AGAATTAAGCTCCGGTAAACCATAAAAATACCAGGAAAAGCTTCTGCATTCAT-GAAAAAATCTC
1 AGAATTAAGCTCCGGTAAACCATAAAAATACCAGGAAAAGCTTCTGCATTCATAAAAAAAATCTC
* * *
841902 TAGAACTAGGCTGTAAAAAATTGAGTAAAAATCATACAACATGTAAATATGATAAAAAAAAAACA
66 TAGAACTAGGCTGTAAAAAATTAAATAAAAACCATACAACATGTAAATATGAT-AAAAAAAAACA
*
841967 AAAAGGGTATTCAA
130 AAAAGGGAATTCAA
*
841981 AGAATTAAGCTCGGGTAAACCAT-AAAATACCAGGAAAAG-TCTCTGCATTCATAAAAAAAATCT
1 AGAATTAAGCTCCGGTAAACCATAAAAATACCAGGAAAAGCT-TCTGCATTCATAAAAAAAATCT
* * * *
842044 CTAGAACTAGGCTGTAAATAATTAAATAAAAACCATTCAACATTTAAATATGATAAAAAGAAACA
65 CTAGAACTAGGCTGTAAAAAATTAAATAAAAACCATACAACATGTAAATATGATAAAAAAAAACA
842109 AAAAGGGAATTCAA
130 AAAAGGGAATTCAA
842123 AGAA
1 AGAA
842127 GTGGAGATGA
Statistics
Matches: 134, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
141 1 0.01
142 54 0.40
143 79 0.59
ACGTcount: A:0.51, C:0.14, G:0.13, T:0.22
Consensus pattern (143 bp):
AGAATTAAGCTCCGGTAAACCATAAAAATACCAGGAAAAGCTTCTGCATTCATAAAAAAAATCTC
TAGAACTAGGCTGTAAAAAATTAAATAAAAACCATACAACATGTAAATATGATAAAAAAAAACAA
AAAGGGAATTCAA
Found at i:846123 original size:20 final size:20
Alignment explanation
Indices: 846078--846124 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
846068 GAAGATAAAC
*
846078 ATTAAAGTTAGTTGTAAAAT
1 ATTAAAGGTAGTTGTAAAAT
*
846098 ACTAAAGGTAGTTGTAAAAT
1 ATTAAAGGTAGTTGTAAAAT
*
846118 TTTAAAG
1 ATTAAAG
846125 AAGAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.36
Consensus pattern (20 bp):
ATTAAAGGTAGTTGTAAAAT
Found at i:846405 original size:17 final size:18
Alignment explanation
Indices: 846375--846408 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
846365 CTTATTTTGA
*
846375 ATTTTTATTCATTGATAG
1 ATTTTTATTAATTGATAG
846393 ATTTTTA-TAATTGATA
1 ATTTTTATTAATTGATA
846409 AATATTTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (18 bp):
ATTTTTATTAATTGATAG
Found at i:846443 original size:14 final size:15
Alignment explanation
Indices: 846426--846456 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
846416 TGTATTTAAA
846426 ATTTATTTAAT-TTT
1 ATTTATTTAATATTT
846440 ATTTATTTAATATTT
1 ATTTATTTAATATTT
846455 AT
1 AT
846457 ATATATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTATTTAATATTT
Found at i:847293 original size:22 final size:21
Alignment explanation
Indices: 847253--847294 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
847243 TTTTCATTTT
* *
847253 TTTTGAATTTTTTATATATTA
1 TTTTGAATTTTTGAAATATTA
847274 TTTTGAATTTTTAGAAATATT
1 TTTTGAATTTTT-GAAATATT
847295 TATATGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (21 bp):
TTTTGAATTTTTGAAATATTA
Found at i:847536 original size:21 final size:22
Alignment explanation
Indices: 847490--847536 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
847480 TTCTAAAATT
847490 TTATTTTTTTAAAAAACTTCAA
1 TTATTTTTTTAAAAAACTTCAA
* *
847512 --ATTTTTTTGAAAAA-TTGAA
1 TTATTTTTTTAAAAAACTTCAA
847531 TTATTT
1 TTATTT
847537 ATATGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (22 bp):
TTATTTTTTTAAAAAACTTCAA
Found at i:847687 original size:22 final size:22
Alignment explanation
Indices: 847662--847704 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
847652 CAAAATGAGA
* *
847662 AAACGAGTATAATTCAAGGGCC
1 AAACAAGTATAAGTCAAGGGCC
*
847684 AAACAAGTATAAGTCATGGGC
1 AAACAAGTATAAGTCAAGGGC
847705 TAAATTTTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (22 bp):
AAACAAGTATAAGTCAAGGGCC
Found at i:847913 original size:18 final size:17
Alignment explanation
Indices: 847881--847914 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
847871 GGTTTACTAA
*
847881 TAGTACATGAATACAAT
1 TAGTACATAAATACAAT
847898 TAGTACATCAAATACAA
1 TAGTACAT-AAATACAA
847915 CTCCTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (17 bp):
TAGTACATAAATACAAT
Found at i:857990 original size:23 final size:21
Alignment explanation
Indices: 857959--858027 Score: 59
Period size: 24 Copynumber: 3.0 Consensus size: 21
857949 TTTTTATAGA
857959 AAAAT-AAATTTAAAAAATAT
1 AAAATAAAATTTAAAAAATAT
*
857979 AATACATAAAATATACTAAAAATATT
1 AA-A-ATAAAATTTA--AAAAATA-T
858005 AAAATAAATATTTTAAAAAATAT
1 AAAATAAA-A-TTTAAAAAATAT
858028 TTTTTTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
20 2 0.05
21 1 0.03
22 2 0.05
23 7 0.18
24 12 0.31
25 9 0.23
26 6 0.15
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATAAAATTTAAAAAATAT
Found at i:858207 original size:21 final size:21
Alignment explanation
Indices: 858142--858207 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
858132 ATATTCATAC
*
858142 AATAACAATAAAATAGTAACAA
1 AATAATAATAAAATAGTAA-AA
* *
858164 TATAATAATAAAAT-GATAGAA
1 AATAATAATAAAATAG-TAAAA
858185 AATAATGAA-AAAATAGTAAAA
1 AATAAT-AATAAAATAGTAAAA
858206 AA
1 AA
858208 ACAACAACAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
21 19 0.53
22 17 0.47
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (21 bp):
AATAATAATAAAATAGTAAAA
Found at i:858324 original size:23 final size:23
Alignment explanation
Indices: 858297--858345 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
858287 TTTTCATTTT
*
858297 AAAAATGAAATT-TATTTTTATTC
1 AAAAAT-AAATTATATTTTTACTC
*
858320 AAAAATAATTTATATTTTTACTC
1 AAAAATAAATTATATTTTTACTC
858343 AAA
1 AAA
858346 CTCTTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (23 bp):
AAAAATAAATTATATTTTTACTC
Found at i:862010 original size:14 final size:14
Alignment explanation
Indices: 861991--862017 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
861981 TACCAATCAA
861991 TTAAATTGAAAATT
1 TTAAATTGAAAATT
862005 TTAAATTGAAAAT
1 TTAAATTGAAAAT
862018 ATAAAATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
TTAAATTGAAAATT
Found at i:864024 original size:13 final size:13
Alignment explanation
Indices: 864001--864033 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
863991 CGAATTAGGG
864001 TTTTA-TTGGGCT
1 TTTTATTTGGGCT
864013 TTTTATTTGGGCT
1 TTTTATTTGGGCT
864026 TTTTATTT
1 TTTTATTT
864034 AGACGTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.67
Consensus pattern (13 bp):
TTTTATTTGGGCT
Found at i:864133 original size:56 final size:56
Alignment explanation
Indices: 864050--864159 Score: 127
Period size: 56 Copynumber: 2.0 Consensus size: 56
864040 AATAACTATG
* ** *
864050 AAAATTTATAAAATATTCATTTGATTAT-TAGTAATTTTTTTGGTCA-TTAATTATAA
1 AAAAGTTATAAAATATTCATTCAATTATGT-G-AATTTTTTTGATCACTTAATTATAA
*
864106 AAAAGTTATAAAATGA-TCATTCAATTATGTGAATTTTTTTTATCACTTAATTAT
1 AAAAGTTATAAAAT-ATTCATTCAATTATGTGAATTTTTTTGATCACTTAATTAT
864160 TTTAAAATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
55 12 0.26
56 32 0.70
57 2 0.04
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.48
Consensus pattern (56 bp):
AAAAGTTATAAAATATTCATTCAATTATGTGAATTTTTTTGATCACTTAATTATAA
Found at i:866252 original size:30 final size:30
Alignment explanation
Indices: 866228--866282 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 30
866218 ATTTTAAATT
*
866228 TTTAAGAT-ATAAAAATAAA-TATTTTATA
1 TTTAAAATAATAAAAATAAATTATTTTATA
866256 TTTAAAATAATAAAAATAAATTATTTT
1 TTTAAAATAATAAAAATAAATTATTTT
866283 TAAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 7 0.29
29 11 0.46
30 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
TTTAAAATAATAAAAATAAATTATTTTATA
Found at i:866291 original size:29 final size:29
Alignment explanation
Indices: 866236--866293 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
866226 TTTTTAAGAT
***
866236 ATAAAAATAAATATTTTATATTTAAAATA
1 ATAAAAATAAATATTTTATAAAAAAAATA
866265 ATAAAAATAAATTATTTT-TAAAAAAAATA
1 ATAAAAATAAA-TATTTTATAAAAAAAATA
866294 TTTATGAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
ATAAAAATAAATATTTTATAAAAAAAATA
Found at i:876330 original size:19 final size:20
Alignment explanation
Indices: 876287--876333 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
876277 TTGCTATTTG
* *
876287 AAAATTTTTATTAAGCTCCT
1 AAAATTTTAATTAAGCTCCC
876307 AAAATTTTAATTAAGC-CCC
1 AAAATTTTAATTAAGCTCCC
*
876326 CAAATTTT
1 AAAATTTT
876334 TTTGGAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.40
Consensus pattern (20 bp):
AAAATTTTAATTAAGCTCCC
Found at i:876366 original size:31 final size:30
Alignment explanation
Indices: 876307--876380 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
876297 TTAAGCTCCT
876307 AAAATTTTAATTAAGCCCCCAAATTTTTTTG
1 AAAATTTTAATTAAGCCCCCAAA-TTTTTTG
* * * *
876338 GAAATTTTCATTAAGCCTCTAGAA-TTTTTG
1 AAAATTTTAATTAAGCCCCCA-AATTTTTTG
876368 AAAATTTTAATTA
1 AAAATTTTAATTA
876381 CCCCCTACCC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 17 0.47
31 17 0.47
32 2 0.06
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.43
Consensus pattern (30 bp):
AAAATTTTAATTAAGCCCCCAAATTTTTTG
Found at i:877718 original size:21 final size:21
Alignment explanation
Indices: 877694--877736 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
877684 ATAGTTTTTA
877694 AAGTTAAAA-GTCAAAACCATT
1 AAGTTAAAAGGT-AAAACCATT
877715 AAGTTAAAAGGTAAAACCATT
1 AAGTTAAAAGGTAAAACCATT
877736 A
1 A
877737 TATTGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACCATT
Found at i:878106 original size:26 final size:27
Alignment explanation
Indices: 878063--878124 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 27
878053 TTAAATCAAA
*
878063 TTTTTCAAAAATATTTTTTAAAATCAC
1 TTTTTCAAAAATACTTTTTAAAATCAC
*
878090 TTTTTCAAATA-ACTTTTTAAAATCAC
1 TTTTTCAAAAATACTTTTTAAAATCAC
878116 -TTTTCAAAA
1 TTTTTCAAAA
878125 GCAATATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 8 0.25
26 14 0.44
27 10 0.31
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (27 bp):
TTTTTCAAAAATACTTTTTAAAATCAC
Found at i:885763 original size:3 final size:3
Alignment explanation
Indices: 885757--885785 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
885747 ATGATGATGA
885757 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
885786 TTTGTTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:892970 original size:22 final size:22
Alignment explanation
Indices: 892942--892983 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
892932 AATAAAAATT
*
892942 AAATAAATCCCCA-AAAAATAAA
1 AAATAAA-ACCCAGAAAAATAAA
892964 AAATAAAACCCAGAAAAATA
1 AAATAAAACCCAGAAAAATA
892984 GTAGCTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.69, C:0.17, G:0.02, T:0.12
Consensus pattern (22 bp):
AAATAAAACCCAGAAAAATAAA
Found at i:893825 original size:199 final size:200
Alignment explanation
Indices: 893485--894392 Score: 1047
Period size: 199 Copynumber: 4.5 Consensus size: 200
893475 TTTGAATTAA
* * * *
893485 CTTGATCTGTTAGTAGGAATTTTACTTAGCATCTATGTTACTCGGACTGGGGCATAGGTGTCCAA
1 CTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCGGACTGGGGTATAGGTGTCCAA
* * * * *
893550 TACAGTAGGGTCGGACACGAGTTTAGAGGTCATATCTGTAT-CCCTTTGTCGGACATAGGTACTT
66 TACAGTAGTGTCAGACACGAGTTTAGAGGTCATATCTCTATATCCTATGTCGGACATAGGTACTT
* * * * *
893614 CAAGAAAAATGAAGAGTTCGAGCATCATAGCTTAGTACAAACTAAGACTAGGTAATGGCAATGAT
131 CAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACAAACCAAAACTAGGTAATGGCAGTGAT
893679 AAAAT
196 AAAAT
893684 CTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCGGACTGGGGTATAGGTGTCCAA
1 CTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCGGACTGGGGTATAGGTGTCCAA
* *
893749 TACGGTAGTGTCAGACACGAGTTTAAAGGTCATATCTCTATATCCTATGTCGGACATAGGTACTT
66 TACAGTAGTGTCAGACACGAGTTTAGAGGTCATATCTCTATATCCTATGTCGGACATAGGTACTT
* * ** *
893814 CAAG-AAAATGAAGAGTCTGAGCGTCATAGCTTAGCACGGACTAAAACTAGGTAATGGCAGTGAT
131 CAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACAAACCAAAACTAGGTAATGGCAGTGAT
893878 AAAAT
196 AAAAT
* *
893883 CTTGATCTCTTAGTAGGAATTTTACTTAGAACCTATGTTACTCGGAC-GTGGGTATAGGTGTCCA
1 CTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCGGACTG-GGGTATAGGTGTCCA
* * * * *
893947 TTACAGTAGTGT-ACGACATGAGTTTAGAGGCCATATCGCTATAT-CTGGATGTTGGACACATAG
65 ATACAGTAGTGTCA-GACACGAGTTTAGAGGTCATATCTCTATATCCT--ATGTCGG--ACATAG
**
894010 GTACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCATGAACCAAAACTAGGTAATGGC
125 GTACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACAAACCAAAACTAGGTAATGGC
894075 AGTGATAAAAT
190 AGTGATAAAAT
* * * * * * * *
894086 CTTGATCTCTTTGTTGGAATTTTACATAGCACCTATGTTACTCAGATTTGGGTGTAGTTGTCCGA
1 CTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCGGACTGGGGTATAGGTGTCCAA
* * * ** * ** * ** * *
894151 TACTGGT-GATGTCTGACATGAGTTTAGAGGTTGTATCTCTGTATTTGTGTGTCAAACACAGATA
66 TAC-AGTAG-TGTCAGACACGAGTTTAGAGGTCATATCTCTATA-TCCTATGTCGGACATAGGTA
* *
894215 CTTCAAGAAAAATGAAGAATCCGAGCATCATAGCTTAGCACAAACCAAAACTAGGTAATGGTAGT
128 CTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACAAACCAAAACTAGGTAATGGCAGT
894280 GATAAAAT
193 GATAAAAT
* * ** * ** * * * * * *
894288 CTTG-TCCACTTATTTATAAATTTACTTAGCACCCGTGTTACTCAGATTTGGGTGTAGTTGTCCG
1 CTTGAT-CTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCGGACTGGGGTATAGGTGTCCA
* **
894352 ATACTAGTAGTGTCTGACACGAGTTTAGAGGTTGTATCTCT
65 ATAC-AGTAGTGTCAGACACGAGTTTAGAGGTCATATCTCT
894393 GTATTTCAGT
Statistics
Matches: 620, Mismatches: 73, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
198 4 0.01
199 250 0.40
200 31 0.05
201 1 0.00
202 182 0.29
203 118 0.19
204 32 0.05
205 1 0.00
206 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (200 bp):
CTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCGGACTGGGGTATAGGTGTCCAA
TACAGTAGTGTCAGACACGAGTTTAGAGGTCATATCTCTATATCCTATGTCGGACATAGGTACTT
CAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACAAACCAAAACTAGGTAATGGCAGTGAT
AAAAT
Found at i:894283 original size:202 final size:201
Alignment explanation
Indices: 893485--894506 Score: 1000
Period size: 199 Copynumber: 5.0 Consensus size: 201
893475 TTTGAATTAA
* * * * * * *
893485 CTTGATCTGTTAGTAGGAATTTTACTTAGCATCTATGTTACTCGGACTGGGGCATAGGTGTCCAA
1 CTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCAGACTTGGGTATAGGTGTCCGA
* * * *** ** * *
893550 TACAGTAGGGTCGGACACGAGTTTAGAGGTCATATCTGTATCCCT-T-TGTCGGACATAGGTACT
66 TACAGTAGTGTCTGACACGAGTTTAGAGGTCATATCTCTATATTTGTGTGTCAAACACAGATACT
* * * *
893613 TCAAGAAAAATGAAGAGTTCGAGCATCATAGCTTAGTACAAACTAAGACTAGGTAATGGCAATGA
131 TCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACAAACTAAAACTAGGTAATGGCAGTGA
893678 TAAAAT
196 TAAAAT
* * *
893684 CTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCGGACTGGGGTATAGGTGTCCAA
1 CTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCAGACTTGGGTATAGGTGTCCGA
* * * ** * ** * *
893749 TACGGTAGTGTCAGACACGAGTTTAAAGGTCATATCTCTATA-TCCTATGTCGGACATAGGTACT
66 TACAGTAGTGTCTGACACGAGTTTAGAGGTCATATCTCTATATTTGTGTGTCAAACACAGATACT
* * **
893813 TCAAG-AAAATGAAGAGTCTGAGCGTCATAGCTTAGCACGGACTAAAACTAGGTAATGGCAGTGA
131 TCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACAAACTAAAACTAGGTAATGGCAGTGA
893877 TAAAAT
196 TAAAAT
* * * *
893883 CTTGATCTCTTAGTAGGAATTTTACTTAGAACCTATGTTACTCGGACGTGGGTATAGGTGTCC-A
1 CTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCAGACTTGGGTATAGGTGTCCGA
* * * * * * *
893947 TTACAGTAGTGTAC-GACATGAGTTTAGAGGCCATATCGCTATATCTG-GATGTTGGACACATAG
66 -TACAGTAGTGT-CTGACACGAGTTTAGAGGTCATATCTCTATATTTGTG-TG-T-CAAACACAG
* ** *
894010 GTACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCATGAACCAAAACTAGGTAATGGC
126 ATACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACAAACTAAAACTAGGTAATGGC
894075 AGTGATAAAAT
191 AGTGATAAAAT
* * * * *
894086 CTTGATCTCTTTGTTGGAATTTTACATAGCACCTATGTTACTCAGATTTGGGTGTAGTTGTCCGA
1 CTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCAGACTTGGGTATAGGTGTCCGA
* * ** *
894151 TACTGGT-GATGTCTGACATGAGTTTAGAGGTTGTATCTCTGTATTTGTGTGTCAAACACAGATA
66 TAC-AGTAG-TGTCTGACACGAGTTTAGAGGTCATATCTCTATATTTGTGTGTCAAACACAGATA
* * *
894215 CTTCAAGAAAAATGAAGAATCCGAGCATCATAGCTTAGCACAAACCAAAACTAGGTAATGGTAGT
129 CTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACAAACTAAAACTAGGTAATGGCAGT
894280 GATAAAAT
194 GATAAAAT
* * ** * ** * * *
894288 CTTG-TCCACTTATTTATAAATTTACTTAGCACCCGTGTTACTCAGATTTGGGTGTAGTTGTCCG
1 CTTGAT-CTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCAGACTTGGGTATAGGTGTCCG
** * *
894352 ATACTAGTAGTGTCTGACACGAGTTTAGAGGTTGTATCTCTGTATTTCAGTGTCGGACATGAGTG
65 ATAC-AGTAGTGTCTGACACGAGTTTAGAGGTCATATCTCTATATTT--GTGT--GTCA--A---
* * * *
894417 TCAGGCACAGATACTTCAAGAAAAATGAAGAGTTCGAGCATCATAGCGTAGGACAAACTAAAATT
120 --A--CACAGATACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACAAACTAAAACT
* * *
894482 ATGTAATTGTAGTGATAAAAT
181 AGGTAATGGCAGTGATAAAAT
894503 CTTG
1 CTTG
894507 GAACATAGTT
Statistics
Matches: 709, Mismatches: 85, Indels: 42
0.85 0.10 0.05
Matches are distributed among these distances:
198 1 0.00
199 249 0.35
200 25 0.04
201 2 0.00
202 189 0.27
203 121 0.17
204 39 0.06
205 1 0.00
206 3 0.00
208 1 0.00
213 1 0.00
215 77 0.11
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (201 bp):
CTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCAGACTTGGGTATAGGTGTCCGA
TACAGTAGTGTCTGACACGAGTTTAGAGGTCATATCTCTATATTTGTGTGTCAAACACAGATACT
TCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACAAACTAAAACTAGGTAATGGCAGTGA
TAAAAT
Found at i:901082 original size:17 final size:17
Alignment explanation
Indices: 901060--901109 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
901050 AATAAATTTT
901060 TTTAAATAATTTAGTGA
1 TTTAAATAATTTAGTGA
*
901077 TTTAAATGAA--TA-T-T
1 TTTAAAT-AATTTAGTGA
901091 TTTAAATAATTTAGTGA
1 TTTAAATAATTTAGTGA
901108 TT
1 TT
901110 ATTTTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 2 0.08
14 7 0.27
15 3 0.12
16 3 0.12
17 9 0.35
18 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (17 bp):
TTTAAATAATTTAGTGA
Found at i:901093 original size:31 final size:31
Alignment explanation
Indices: 901047--901109 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
901037 TCTCAATGAA
*
901047 TTAAATAAATTTTTTTAAATAATTTAGTGAT
1 TTAAATAAATATTTTTAAATAATTTAGTGAT
*
901078 TTAAATGAATATTTTTAAATAATTTAGTGAT
1 TTAAATAAATATTTTTAAATAATTTAGTGAT
901109 T
1 T
901110 ATTTTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (31 bp):
TTAAATAAATATTTTTAAATAATTTAGTGAT
Found at i:903246 original size:21 final size:22
Alignment explanation
Indices: 903222--903265 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
903212 TCAACAAAGT
903222 TGACATCTACTATTTAA-AAAA
1 TGACATCTACTATTTAATAAAA
* *
903243 TGACATTTATTATTTAATAAAA
1 TGACATCTACTATTTAATAAAA
903265 T
1 T
903266 TATATTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (22 bp):
TGACATCTACTATTTAATAAAA
Found at i:905320 original size:16 final size:17
Alignment explanation
Indices: 905298--905338 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
905288 AATTTTTGGG
905298 TTATTTTG-AGTTCGAGT
1 TTATTTTGTA-TTCGAGT
*
905315 TTTTTTTGTATTCGAG-
1 TTATTTTGTATTCGAGT
905331 TTATTTTG
1 TTATTTTG
905339 GGGTTAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 7 0.33
17 13 0.62
18 1 0.05
ACGTcount: A:0.15, C:0.05, G:0.20, T:0.61
Consensus pattern (17 bp):
TTATTTTGTATTCGAGT
Found at i:910239 original size:24 final size:24
Alignment explanation
Indices: 910199--910244 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
910189 TCCCTCCAAA
* *
910199 ATAATTTCAATGAATTACAAATAT
1 ATAATTTCAATAAATTAAAAATAT
910223 ATAATTTC-ATAATATTAAAAAT
1 ATAATTTCAATAA-ATTAAAAAT
910245 TGAAAAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (24 bp):
ATAATTTCAATAAATTAAAAATAT
Found at i:934396 original size:12 final size:12
Alignment explanation
Indices: 934379--934404 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
934369 ATATAAATAT
934379 AATGACATCATC
1 AATGACATCATC
934391 AATGACATCATC
1 AATGACATCATC
934403 AA
1 AA
934405 ACTAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (12 bp):
AATGACATCATC
Found at i:936332 original size:13 final size:13
Alignment explanation
Indices: 936302--936338 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
936292 AGAATAAAAT
936302 TGATAAAA-ATAAA
1 TGATAAAATAT-AA
936315 T-ATAAAATATAA
1 TGATAAAATATAA
936327 TGATAAAATATA
1 TGATAAAATATA
936339 TTATATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (13 bp):
TGATAAAATATAA
Found at i:939106 original size:16 final size:16
Alignment explanation
Indices: 939085--939116 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
939075 CAGTTTACAT
939085 AAGTCTTTCAAGTTGA
1 AAGTCTTTCAAGTTGA
939101 AAGTCTTTCAAGTTGA
1 AAGTCTTTCAAGTTGA
939117 TGGTTTGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (16 bp):
AAGTCTTTCAAGTTGA
Done.