Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 25 of 93
Found at i:10742633 original size:22 final size:19
Alignment explanation
Indices: 10742607--10742651 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
10742597 ACGTGAAAAA
10742607 TTTTACATGTAAATATTATCAT
1 TTTTACAT-TAAA-ATTAT-AT
*
10742629 TTTTATATTAAAATTATAT
1 TTTTACATTAAAATTATAT
10742648 TTTT
1 TTTT
10742652 TAACAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 5 0.23
21 4 0.18
22 7 0.32
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTACATTAAAATTATAT
Found at i:10743700 original size:28 final size:28
Alignment explanation
Indices: 10743656--10743709 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
10743646 TGTTACAAAT
*
10743656 AAATAAATTACACCAAATATAAATAAGC
1 AAATAAATTACACCAAACATAAATAAGC
*
10743684 AAATAAATTACATCAAACATAAATAA
1 AAATAAATTACACCAAACATAAATAA
10743710 AGTTTCAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.63, C:0.13, G:0.02, T:0.22
Consensus pattern (28 bp):
AAATAAATTACACCAAACATAAATAAGC
Found at i:10747813 original size:2 final size:2
Alignment explanation
Indices: 10747806--10747833 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10747796 GCCTACTGGA
10747806 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
10747834 GATTAGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:10760272 original size:51 final size:53
Alignment explanation
Indices: 10760164--10760272 Score: 159
Period size: 51 Copynumber: 2.1 Consensus size: 53
10760154 GGTGATCAGC
* * *
10760164 TTTATTTTTAATAAAATATTTTATTAAATAGTTTATAATGTTACACAAAATAT
1 TTTATTTTCAATAAAATATTTTATTAAATAGTTTAAAACGTTACACAAAATAT
* *
10760217 TTTATTTTCAATAGAATATTTTA-TAAATA-TTTAAAACGTTACACAGAATAT
1 TTTATTTTCAATAAAATATTTTATTAAATAGTTTAAAACGTTACACAAAATAT
10760268 TTTAT
1 TTTAT
10760273 CTTGATTTGG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 24 0.47
52 6 0.12
53 21 0.41
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.48
Consensus pattern (53 bp):
TTTATTTTCAATAAAATATTTTATTAAATAGTTTAAAACGTTACACAAAATAT
Found at i:10760484 original size:32 final size:33
Alignment explanation
Indices: 10760434--10760633 Score: 208
Period size: 32 Copynumber: 6.1 Consensus size: 33
10760424 ATTCTGTCGC
* * *
10760434 TATAAATATTTTATAATGTGATACAGAATATTT
1 TATAAATATTTTATAATATTATACAAAATATTT
* *
10760467 TATAAATA-TTTATAATGTTACACAAAATATTT
1 TATAAATATTTTATAATATTATACAAAATATTT
* * *
10760499 TATTAAATATTTTATAACATTATATAGAATATTT
1 TA-TAAATATTTTATAATATTATACAAAATATTT
* * * *
10760533 TATAAATA-TTTATAATGTTACATAAAACATTT
1 TATAAATATTTTATAATATTATACAAAATATTT
* *
10760565 TATTAAATATTTTATAACATTTTACAAAATATTT
1 TA-TAAATATTTTATAATATTATACAAAATATTT
** *
10760599 TATGGATA-TTGATAATATTATACAAAATATTT
1 TATAAATATTTTATAATATTATACAAAATATTT
10760631 TAT
1 TAT
10760634 CTTAATTTCC
Statistics
Matches: 139, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
32 68 0.49
33 30 0.22
34 41 0.29
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (33 bp):
TATAAATATTTTATAATATTATACAAAATATTT
Found at i:10760508 original size:12 final size:11
Alignment explanation
Indices: 10760491--10760601 Score: 77
Period size: 12 Copynumber: 10.0 Consensus size: 11
10760481 ATGTTACACA
10760491 AAATATTTTATT
1 AAATATTTTA-T
10760503 AAATATTTTAT
1 AAATATTTTAT
* *
10760514 -AACATTATAT
1 AAATATTTTAT
10760524 AGAATATTTTAT
1 A-AATATTTTAT
10760536 AAATA-TTTAT
1 AAATATTTTAT
* **
10760546 -AATGTTACAT
1 AAATATTTTAT
*
10760556 AAAACATTTTATT
1 -AAATATTTTA-T
10760569 AAATATTTTAT
1 AAATATTTTAT
* *
10760580 -AACATTTTACA
1 AAATATTTTA-T
10760591 AAATATTTTAT
1 AAATATTTTAT
10760602 GGATATTGAT
Statistics
Matches: 75, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
9 3 0.04
10 24 0.32
11 6 0.08
12 41 0.55
13 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.49
Consensus pattern (11 bp):
AAATATTTTAT
Found at i:10760514 original size:66 final size:66
Alignment explanation
Indices: 10760436--10760633 Score: 279
Period size: 66 Copynumber: 3.0 Consensus size: 66
10760426 TCTGTCGCTA
** *
10760436 TAAATATTTTATAATGTGATACAGAATATTTTATAAATATTTATAATGTTACACAAAATATTTTA
1 TAAATATTTTATAACATTATACAGAATATTTTATAAATATTTATAATGTTACACAAAATATTTTA
10760501 T
66 T
* * *
10760502 TAAATATTTTATAACATTATATAGAATATTTTATAAATATTTATAATGTTACATAAAACATTTTA
1 TAAATATTTTATAACATTATACAGAATATTTTATAAATATTTATAATGTTACACAAAATATTTTA
10760567 T
66 T
* * ** * * *
10760568 TAAATATTTTATAACATTTTACAAAATATTTTATGGATATTGATAATATTATACAAAATATTTTA
1 TAAATATTTTATAACATTATACAGAATATTTTATAAATATTTATAATGTTACACAAAATATTTTA
10760633 T
66 T
10760634 CTTAATTTCC
Statistics
Matches: 116, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 116 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (66 bp):
TAAATATTTTATAACATTATACAGAATATTTTATAAATATTTATAATGTTACACAAAATATTTTA
T
Found at i:10760583 original size:22 final size:21
Alignment explanation
Indices: 10760495--10760601 Score: 92
Period size: 22 Copynumber: 4.9 Consensus size: 21
10760485 TACACAAAAT
10760495 ATTTTATTAAATATTTTATAAC
1 ATTTTA-TAAATATTTTATAAC
*
10760517 ATTATATAGAATATTTTATAA-
1 ATTTTATA-AATATTTTATAAC
* * *
10760538 ATATTTAT-AATGTTACATAAAAC
1 AT-TTTATAAATATT--TTATAAC
10760561 ATTTTATTAAATATTTTATAAC
1 ATTTTA-TAAATATTTTATAAC
*
10760583 ATTTTACAAAATATTTTAT
1 ATTTTA-TAAATATTTTAT
10760602 GGATATTGAT
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
20 5 0.07
21 4 0.06
22 51 0.75
23 3 0.04
24 5 0.07
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTTTATAAATATTTTATAAC
Found at i:10764841 original size:24 final size:25
Alignment explanation
Indices: 10764777--10764841 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
10764767 CGATCTATCC
*
10764777 ATTTAAAATATATTTATTAATATAT
1 ATTTTAAATATATTTATTAATATAT
*
10764802 ATTTTAAAT-TATTT-TATATTA-ATT
1 ATTTTAAATATATTTAT-TAATATA-T
10764826 ATTTTAAATATATTTA
1 ATTTTAAATATATTTA
10764842 AAATTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 2 0.06
24 19 0.56
25 13 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTTAAATATATTTATTAATATAT
Found at i:10765280 original size:30 final size:30
Alignment explanation
Indices: 10765244--10765300 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
10765234 TTGTAAGAAC
10765244 TTATTTGACTT-AAAATAAAAATATAAAAAT
1 TTATTTG-CTTCAAAATAAAAATATAAAAAT
*
10765274 TTATTTGGTTCAAAATAAAAATATAAA
1 TTATTTGCTTCAAAATAAAAATATAAA
10765301 GACATCATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.37
Consensus pattern (30 bp):
TTATTTGCTTCAAAATAAAAATATAAAAAT
Found at i:10769819 original size:15 final size:15
Alignment explanation
Indices: 10769799--10769838 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
10769789 TAATTCAGAT
10769799 TTTTTTCCTATGAGG
1 TTTTTTCCTATGAGG
10769814 TTTTTTCCTATGAGG
1 TTTTTTCCTATGAGG
10769829 TTTTTTCCTA
1 TTTTTTCCTA
10769839 AGGTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.57
Consensus pattern (15 bp):
TTTTTTCCTATGAGG
Found at i:10769842 original size:13 final size:14
Alignment explanation
Indices: 10769799--10769845 Score: 69
Period size: 15 Copynumber: 3.3 Consensus size: 14
10769789 TAATTCAGAT
10769799 TTTTTTCCTATGAGG
1 TTTTTTCCTA-GAGG
10769814 TTTTTTCCTATGAGG
1 TTTTTTCCTA-GAGG
10769829 TTTTTTCCTA-AGG
1 TTTTTTCCTAGAGG
10769842 TTTT
1 TTTT
10769846 AATGAGGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.22
15 25 0.78
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (14 bp):
TTTTTTCCTAGAGG
Found at i:10772424 original size:20 final size:20
Alignment explanation
Indices: 10772423--10772518 Score: 68
Period size: 20 Copynumber: 5.2 Consensus size: 20
10772413 AAATTAAAAT
*
10772423 ATTAAAAAAATTAATATTTAA
1 ATTAAAATA-TTAATATTTAA
*
10772444 CTTAAAATATTAA-A---AA
1 ATTAAAATATTAATATTTAA
*
10772460 TTTAAAAATATTAATATTT-A
1 ATT-AAAATATTAATATTTAA
10772480 ATT-AAA-A--AA-ATTTAA
1 ATTAAAATATTAATATTTAA
*
10772495 CTTAAAATATTAATATTTAA
1 ATTAAAATATTAATATTTAA
10772515 ATTA
1 ATTA
10772519 TTCAATACTA
Statistics
Matches: 58, Mismatches: 6, Indels: 23
0.67 0.07 0.26
Matches are distributed among these distances:
14 4 0.07
15 5 0.09
16 7 0.12
17 12 0.21
18 4 0.07
19 3 0.05
20 16 0.28
21 7 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTAAAATATTAATATTTAA
Found at i:10772438 original size:29 final size:29
Alignment explanation
Indices: 10772403--10772459 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
10772393 TTTGATAAAT
10772403 ATTAATATTTAAATTAAAATATTAAAAAA
1 ATTAATATTTAAATTAAAATATTAAAAAA
*
10772432 ATTAATATTTAACTTAAAATATTAAAAA
1 ATTAATATTTAAATTAAAATATTAAAAA
10772460 TTTAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
ATTAATATTTAAATTAAAATATTAAAAAA
Found at i:10772704 original size:26 final size:26
Alignment explanation
Indices: 10772658--10772707 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
10772648 ATATACATTT
* *
10772658 ATAATTATAAATTTTGAATATTTTAC
1 ATAATTATAAATATCGAATATTTTAC
10772684 ATAATTGATAAATATCG-ATATTTT
1 ATAATT-ATAAATATCGAATATTTT
10772708 TATTATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (26 bp):
ATAATTATAAATATCGAATATTTTAC
Found at i:10783887 original size:2 final size:2
Alignment explanation
Indices: 10783880--10783907 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10783870 TATGAAATTT
10783880 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
10783908 ATTTTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10793474 original size:55 final size:55
Alignment explanation
Indices: 10793415--10793524 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
10793405 TAAGCACCCG
10793415 TAATATTCTTCTATTAAAAATGTTAGCTTATAAATAAAGGAACAAGAACATCCAA
1 TAATATTCTTCTATTAAAAATGTTAGCTTATAAATAAAGGAACAAGAACATCCAA
* *
10793470 TAATATTCTTCTATTAAAAATGTTAGCTTATGAATAGAGGAACAAGAACATCCAA
1 TAATATTCTTCTATTAAAAATGTTAGCTTATAAATAAAGGAACAAGAACATCCAA
10793525 GAGGGTGAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (55 bp):
TAATATTCTTCTATTAAAAATGTTAGCTTATAAATAAAGGAACAAGAACATCCAA
Found at i:10793704 original size:59 final size:59
Alignment explanation
Indices: 10793635--10793762 Score: 256
Period size: 59 Copynumber: 2.2 Consensus size: 59
10793625 TAAAACTTTT
10793635 TCAAAAACTCTTTAAACAAATGTGTAGTCGATTATGAAGACTTGATAATCTATCTTAGA
1 TCAAAAACTCTTTAAACAAATGTGTAGTCGATTATGAAGACTTGATAATCTATCTTAGA
10793694 TCAAAAACTCTTTAAACAAATGTGTAGTCGATTATGAAGACTTGATAATCTATCTTAGA
1 TCAAAAACTCTTTAAACAAATGTGTAGTCGATTATGAAGACTTGATAATCTATCTTAGA
10793753 TCAAAAACTC
1 TCAAAAACTC
10793763 GTTTTGGAAG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 69 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (59 bp):
TCAAAAACTCTTTAAACAAATGTGTAGTCGATTATGAAGACTTGATAATCTATCTTAGA
Found at i:10794287 original size:64 final size:64
Alignment explanation
Indices: 10794169--10794324 Score: 163
Period size: 64 Copynumber: 2.5 Consensus size: 64
10794159 CTTAAGGAAA
* * * * ** * *
10794169 CATGCTTTTTAACGGAATCAATCACAACCCTTACAAATGCCTTTTAACTGGAGCAAATATAA-C
1 CATGGTTTTTAACGGGATCAACCACAAACCTTACAAATGCCTTTTAACAAGAGCAAACACAATC
* * *
10794232 TCATGGTTTTTAACGGGTTCAACCACAAACCTTACAAATGCTTTTTACCAAGAGCAAACACAATC
1 -CATGGTTTTTAACGGGATCAACCACAAACCTTACAAATGCCTTTTAACAAGAGCAAACACAATC
* * *
10794297 CATAGTTTTTAATGGGCTCAACCA-AAAC
1 CATGGTTTTTAACGGGATCAACCACAAAC
10794325 AGCACACGAA
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
63 4 0.05
64 72 0.94
65 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (64 bp):
CATGGTTTTTAACGGGATCAACCACAAACCTTACAAATGCCTTTTAACAAGAGCAAACACAATC
Found at i:10794779 original size:21 final size:21
Alignment explanation
Indices: 10794753--10794792 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10794743 CATAGCTTAG
10794753 AAGGTTAACTATAGCTTTGTC
1 AAGGTTAACTATAGCTTTGTC
* *
10794774 AAGGTTGACTATGGCTTTG
1 AAGGTTAACTATAGCTTTG
10794793 AAAAGTTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (21 bp):
AAGGTTAACTATAGCTTTGTC
Found at i:10795758 original size:62 final size:62
Alignment explanation
Indices: 10795647--10795769 Score: 178
Period size: 62 Copynumber: 2.0 Consensus size: 62
10795637 TATTTACTAC
* *
10795647 TTCAATTGCTAATTAGCAATATTGGGTTATTGGGCTGGACAGCTGAGATATAACATGTTATA
1 TTCAATAGCTAATTAGCAATATTGGGTTATTGGGCTGGACAGCTAAGATATAACATGTTATA
* *
10795709 TTCAATAGCTAATTAGCAATATTGGGTTATTGGG-TTGATCTA-CTAAGATATAATATGTTAT
1 TTCAATAGCTAATTAGCAATATTGGGTTATTGGGCTGGA-C-AGCTAAGATATAACATGTTAT
10795770 GATAGGCTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
61 3 0.05
62 51 0.93
63 1 0.02
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (62 bp):
TTCAATAGCTAATTAGCAATATTGGGTTATTGGGCTGGACAGCTAAGATATAACATGTTATA
Found at i:10798862 original size:2 final size:2
Alignment explanation
Indices: 10798855--10798927 Score: 130
Period size: 2 Copynumber: 36.5 Consensus size: 2
10798845 AATCTAAATG
10798855 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T NAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
10798897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10798928 GATTAATCCT
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.01
2 67 0.97
3 1 0.01
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10804127 original size:2 final size:2
Alignment explanation
Indices: 10804117--10804151 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
10804107 GAGGGAAAAA
10804117 AG AG TAG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10804152 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (2 bp):
AG
Found at i:10806014 original size:4 final size:4
Alignment explanation
Indices: 10805998--10806035 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
10805988 AGGTACACAT
*
10805998 ATAC ATAC CTAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
10806036 GGAAATGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:10813482 original size:2 final size:2
Alignment explanation
Indices: 10813475--10813506 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10813465 ATTGTCATTC
10813475 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
10813507 GAGAGAGTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10813546 original size:2 final size:2
Alignment explanation
Indices: 10813534--10813571 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
10813524 NNNNNNNNNN
10813534 TA TA CTA 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 T
10813572 GAGAGAGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10815754 original size:21 final size:21
Alignment explanation
Indices: 10815707--10815754 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
10815697 ATTGGTAATA
*
10815707 GTTAAAAAAAAAGAGTAAATG
1 GTTAAAAAAAAAGAATAAATG
* *
10815728 GGTAAAAGAAAAGAATATAA-G
1 GTTAAAAAAAAAGAATA-AATG
10815749 GTTAAA
1 GTTAAA
10815755 TGACAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.21, T:0.19
Consensus pattern (21 bp):
GTTAAAAAAAAAGAATAAATG
Found at i:10816474 original size:2 final size:2
Alignment explanation
Indices: 10816467--10816491 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10816457 CGTTGTTAAA
10816467 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
10816492 CAGTACACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10822127 original size:2 final size:2
Alignment explanation
Indices: 10822120--10822151 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10822110 ATTAATCCAA
10822120 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
10822152 TCTGTTGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10828511 original size:35 final size:35
Alignment explanation
Indices: 10828394--10828501 Score: 198
Period size: 35 Copynumber: 3.1 Consensus size: 35
10828384 CTTACTCAGC
10828394 TCATGTGCACTCCCTACACGCACATTTCAATATCA
1 TCATGTGCACTCCCTACACGCACATTTCAATATCA
*
10828429 TCATGTTCACTCCCTACACGCACATTTCAATATCA
1 TCATGTGCACTCCCTACACGCACATTTCAATATCA
*
10828464 TCATGTGCACTCCCTACACGCATATTTCAATATCA
1 TCATGTGCACTCCCTACACGCACATTTCAATATCA
10828499 TCA
1 TCA
10828502 CACGCACTCC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.29, C:0.33, G:0.07, T:0.31
Consensus pattern (35 bp):
TCATGTGCACTCCCTACACGCACATTTCAATATCA
Found at i:10829793 original size:19 final size:19
Alignment explanation
Indices: 10829769--10829810 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
10829759 GGTGGTAAGG
10829769 TGAAAATAGTATGGGAGCA
1 TGAAAATAGTATGGGAGCA
* *
10829788 TGAAAATGGTGTGGGAGCA
1 TGAAAATAGTATGGGAGCA
10829807 TGAA
1 TGAA
10829811 GGACAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.36, T:0.21
Consensus pattern (19 bp):
TGAAAATAGTATGGGAGCA
Found at i:10835279 original size:45 final size:45
Alignment explanation
Indices: 10835219--10835312 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 45
10835209 AATATTTAAA
* * * *
10835219 TATTATTTCACTATAATAAATATTATAAAGCATATTACTTAATAT
1 TATTATTTCAATATAATAAATATAACAAAGAATATTACTTAATAT
* * * *
10835264 TATTATTTGAATATAATAAATGTAACAAAGAATATTATTTAGTAT
1 TATTATTTCAATATAATAAATATAACAAAGAATATTACTTAATAT
10835309 TATT
1 TATT
10835313 TAAATTTAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (45 bp):
TATTATTTCAATATAATAAATATAACAAAGAATATTACTTAATAT
Found at i:10835416 original size:23 final size:22
Alignment explanation
Indices: 10835350--10835425 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 22
10835340 TTTTAATATT
*
10835350 AAATATTATTTAATTATAATAA
1 AAATATTATTAAATTATAATAA
** *
10835372 AAAGGT-TTAATTATCTTCTAATACA
1 AAA--TATT-ATTAAATTATAATA-A
10835397 AAATATTATTAAATTATAATAA
1 AAATATTATTAAATTATAATAA
10835419 AAATATT
1 AAATATT
10835426 TTTATATTTN
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
22 11 0.26
23 14 0.33
24 13 0.31
25 4 0.10
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (22 bp):
AAATATTATTAAATTATAATAA
Found at i:10839420 original size:1 final size:1
Alignment explanation
Indices: 10839416--10839501 Score: 145
Period size: 1 Copynumber: 86.0 Consensus size: 1
10839406 TCCTTTTTCC
* **
10839416 TTTTTCTTTTTTTTTTTTTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10839481 TTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTT
10839502 CAGGGGATTT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 81 1.00
ACGTcount: A:0.00, C:0.01, G:0.02, T:0.97
Consensus pattern (1 bp):
T
Found at i:10839749 original size:21 final size:21
Alignment explanation
Indices: 10839719--10839766 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
10839709 TTTGAAAGAG
*
10839719 AAGATAGAGGTGCTACAGTCT
1 AAGATAGAGGTGCAACAGTCT
*
10839740 AAGATGGAGGTGCAACAGTCT
1 AAGATAGAGGTGCAACAGTCT
*
10839761 GAGATA
1 AAGATA
10839767 AACTCTTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.31, T:0.21
Consensus pattern (21 bp):
AAGATAGAGGTGCAACAGTCT
Found at i:10842890 original size:28 final size:26
Alignment explanation
Indices: 10842843--10842896 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
10842833 TTTTATGAAC
*
10842843 GAAAATAAACAATAAATAAAAAAAAT
1 GAAAATAAAAAATAAATAAAAAAAAT
10842869 GAAAATGAAAAAATGAAATAAAAAAAAT
1 GAAAAT-AAAAAAT-AAATAAAAAAAAT
10842897 AGAAGAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 6 0.24
27 6 0.24
28 13 0.52
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (26 bp):
GAAAATAAAAAATAAATAAAAAAAAT
Found at i:10842893 original size:14 final size:14
Alignment explanation
Indices: 10842856--10842896 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
10842846 AATAAACAAT
10842856 AAATAAAAAAAATG
1 AAATAAAAAAAATG
*
10842870 AAA-ATGAAAAAATG
1 AAATA-AAAAAAATG
10842884 AAATAAAAAAAAT
1 AAATAAAAAAAAT
10842897 AGAAGAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (14 bp):
AAATAAAAAAAATG
Found at i:10843573 original size:2 final size:2
Alignment explanation
Indices: 10843566--10843595 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10843556 CAGCGCGTAT
10843566 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10843596 CTGATCGCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10844823 original size:10 final size:10
Alignment explanation
Indices: 10844808--10844832 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10844798 CATGTTATGT
10844808 AAAAAATAAA
1 AAAAAATAAA
10844818 AAAAAATAAA
1 AAAAAATAAA
10844828 AAAAA
1 AAAAA
10844833 GATAGAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:10844960 original size:8 final size:8
Alignment explanation
Indices: 10844949--10844986 Score: 58
Period size: 8 Copynumber: 4.5 Consensus size: 8
10844939 TATAATAATC
10844949 AAAATATA
1 AAAATATA
10844957 AAAATAATA
1 AAAAT-ATA
10844966 AATAATATA
1 AA-AATATA
10844975 AAAATATA
1 AAAATATA
10844983 AAAA
1 AAAA
10844987 AATGTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 15 0.54
9 10 0.36
10 3 0.11
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATATA
Found at i:10844963 original size:20 final size:18
Alignment explanation
Indices: 10844949--10845005 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
10844939 TATAATAATC
10844949 AAAATATAAAAATAATAA
1 AAAATATAAAAATAATAA
*
10844967 ATAATATAAAAAT-ATAAA
1 AAAATATAAAAATAAT-AA
*
10844985 AAAATGTAAAAAATAATAA
1 AAAATAT-AAAAATAATAA
10845004 AA
1 AA
10845006 TTTTTGTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
17 2 0.06
18 19 0.58
19 10 0.30
20 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
AAAATATAAAAATAATAA
Found at i:10844989 original size:28 final size:28
Alignment explanation
Indices: 10844920--10844986 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
10844910 GATTGCTTAC
* * *
10844920 AAAAAAATAATAATAGTAATATAATAAT
1 AAAAATATAAAAATAATAATATAATAAT
*
10844948 CAAAATATAAAAATAATAA-ATAAT-AT
1 AAAAATATAAAAATAATAATATAATAAT
10844974 AAAAATATAAAAA
1 AAAAATATAAAAA
10844987 AATGTAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 14 0.41
27 5 0.15
28 15 0.44
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (28 bp):
AAAAATATAAAAATAATAATATAATAAT
Found at i:10845140 original size:24 final size:25
Alignment explanation
Indices: 10845105--10845157 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
10845095 AAAATGTAAA
*
10845105 AAAATAATAATAATAATTAAA-AAT
1 AAAATAAAAATAATAATTAAATAAT
10845129 AAAATAAAAATAATAATTAAATAAT
1 AAAATAAAAATAATAATTAAATAAT
10845154 AAAA
1 AAAA
10845158 AAATGACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (25 bp):
AAAATAAAAATAATAATTAAATAAT
Found at i:10848425 original size:165 final size:163
Alignment explanation
Indices: 10848153--10848484 Score: 619
Period size: 165 Copynumber: 2.0 Consensus size: 163
10848143 TTTATGTTAG
10848153 TGAACAATTATTAGAAAATGAATTTGTTCCTTGAATGATGCAAGAAAATTATCACAATTTGGATC
1 TGAACAATTATTAGAAAATGAATTTGTTCCTTGAATGATGCAAGAAAATTATCACAATTTGGATC
10848218 AAATGTGTCAATGATTGACTTTTCAGATTCCATTTAAGCATACTCTGAATTTTGTTTCATAACAA
66 AAATGTGTCAATGATTGACTTTTCAGATTCCATTTAAGCATACTCTGAATTTTGTTTCATAACAA
10848283 CAAGGAGGATTTCAACCAAAAAAATAATATAATA
131 CAAGGAGGATTTC-ACCAAAAAAATAATATAATA
10848317 NTGAACAATTATTAGAAAATGAATTTGTTCCTTGAATGATGCAAGAAAATTATCACAATTTGGAT
1 -TGAACAATTATTAGAAAATGAATTTGTTCCTTGAATGATGCAAGAAAATTATCACAATTTGGAT
10848382 CAAATGTGTCAATGATTGACTTTTCAGATTCCATTTAAGCATACTCTGAATTTTGTTTCATAACA
65 CAAATGTGTCAATGATTGACTTTTCAGATTCCATTTAAGCATACTCTGAATTTTGTTTCATAACA
10848447 ACAAGGAGGATTTCACCAAAAAAAATAAAATATAATA
130 ACAAGGAGGATTTCACC-AAAAAAAT--AATATAATA
10848484 T
1 T
10848485 AATAATAAAA
Statistics
Matches: 164, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
164 3 0.02
165 151 0.92
166 1 0.01
167 9 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (163 bp):
TGAACAATTATTAGAAAATGAATTTGTTCCTTGAATGATGCAAGAAAATTATCACAATTTGGATC
AAATGTGTCAATGATTGACTTTTCAGATTCCATTTAAGCATACTCTGAATTTTGTTTCATAACAA
CAAGGAGGATTTCACCAAAAAAATAATATAATA
Found at i:10848493 original size:18 final size:18
Alignment explanation
Indices: 10848470--10848504 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10848460 CACCAAAAAA
*
10848470 AATAAAATATAATATAAT
1 AATAAAATAAAATATAAT
10848488 AATAAAATAAAATATAA
1 AATAAAATAAAATATAA
10848505 AAAAAAAAAA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAAAATAAAATATAAT
Found at i:10848512 original size:18 final size:18
Alignment explanation
Indices: 10848466--10848512 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
10848456 ATTTCACCAA
*
10848466 AAAAAATAAAATATAATAT
1 AAAAAA-AAAATAAAATAT
* *
10848485 AATAATAAAATAAAATAT
1 AAAAAAAAAATAAAATAT
10848503 AAAAAAAAAA
1 AAAAAAAAAA
10848513 AACCAAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAAAAAAATAAAATAT
Found at i:10852293 original size:80 final size:80
Alignment explanation
Indices: 10852163--10852320 Score: 264
Period size: 80 Copynumber: 2.0 Consensus size: 80
10852153 ACAATCAATC
**
10852163 AAAAAAAAAAAAGCAAAAAGCAAGTGTGAAAGATGAAGCTCTAGGGTGAAAACCCGAAAGGGCAG
1 AAAAAAAAAAAAGCAAAAAGCAAGTGAAAAAGATGAAGCTCTAGGGTGAAAACCCGAAAGGGCAG
10852228 TCTAGAGCGAAGAAA
66 TCTAGAGCGAAGAAA
**
10852243 AAAAAAAAAGAAAG-AAAAAGTGAGTGAAAAAGATGAAGCTCTAGGGTGAAAACCCGAAAGGGCA
1 AAAAAAAAA-AAAGCAAAAAGCAAGTGAAAAAGATGAAGCTCTAGGGTGAAAACCCGAAAGGGCA
10852307 GTCTAGAGCGAAGA
65 GTCTAGAGCGAAGA
10852321 TGAGAATTTA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
80 69 0.95
81 4 0.05
ACGTcount: A:0.51, C:0.11, G:0.27, T:0.10
Consensus pattern (80 bp):
AAAAAAAAAAAAGCAAAAAGCAAGTGAAAAAGATGAAGCTCTAGGGTGAAAACCCGAAAGGGCAG
TCTAGAGCGAAGAAA
Found at i:10853873 original size:140 final size:141
Alignment explanation
Indices: 10853468--10853936 Score: 674
Period size: 141 Copynumber: 3.3 Consensus size: 141
10853458 AGATAATGAA
* *
10853468 TGTCAAGATTTTTTAAGTTACGTTGTCTCAGTTTTCGAGGAGCCACATTTTCTAAATCCTCCGGG
1 TGTCAAGATTTTTTAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCCTAAATCCTCCGGG
* ** *
10853533 TACATTTTGAAGACCTTTGGGCACATTATTCTCTTAAAGCCTCCGGGTGCATCTTCTAAAACCTC
66 TACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAACCCTCCGGGTGCATCTTCTAAAACCTC
10853598 CGGGTAATTAG
131 CGGGTAATTAG
* * * * **
10853609 TGTCAAAATTTTTTAAGTTACGTTGCCTCAGTTTTCGAGGAGCCATATTTCCAAAACCCTCTAGG
1 TGTCAAGATTTTTTAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCCTAAATCCTCCGGG
* *
10853674 TACATTCTGAAGACCTCCGGGCACATTATTCT-TTTAACCCTCCAGGTGCATCTTCTAAAACCTC
66 TACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAACCCTCCGGGTGCATCTTCTAAAACCTC
10853738 CGGGTAATTAG
131 CGGGTAATTAG
* *
10853749 TGTCAAGA-TTTTTGAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCCTAAATTCTCCGGG
1 TGTCAAGATTTTTTAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCCTAAATCCTCCGGG
* * * *
10853813 TACATTCTGAAGACCTCCAGGCACATTATTCTCTTAAATCTTTCGGGTGCATCTTCTAAAACCTC
66 TACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAACCCTCCGGGTGCATCTTCTAAAACCTC
*
10853878 CAGGTAATTAG
131 CGGGTAATTAG
* * * ** *
10853889 TTTCAAGGTTTTTAAAGTTACGTTGCCTCAACTTT-GAGGAGCCTCATT
1 TGTCAAGATTTTTTAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATT
10853937 CAAAAAAAAA
Statistics
Matches: 290, Mismatches: 36, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
139 80 0.28
140 102 0.35
141 108 0.37
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (141 bp):
TGTCAAGATTTTTTAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCCTAAATCCTCCGGG
TACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAACCCTCCGGGTGCATCTTCTAAAACCTC
CGGGTAATTAG
Found at i:10853956 original size:14 final size:14
Alignment explanation
Indices: 10853938--10854006 Score: 56
Period size: 13 Copynumber: 5.2 Consensus size: 14
10853928 AGCCTCATTC
10853938 AAAAAAAA-AAC-A
1 AAAAAAAACAACAA
*
10853950 ACAAAAAACAACAA
1 AAAAAAAACAACAA
* **
10853964 GAAAGCAACAACAA
1 AAAAAAAACAACAA
*
10853978 AATAAAAACAA-AA
1 AAAAAAAACAACAA
*
10853991 AACAAAAACAA-AA
1 AAAAAAAACAACAA
10854004 AAA
1 AAA
10854007 CAACAAAGAG
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
12 7 0.16
13 19 0.43
14 18 0.41
ACGTcount: A:0.81, C:0.14, G:0.03, T:0.01
Consensus pattern (14 bp):
AAAAAAAACAACAA
Found at i:10853957 original size:11 final size:11
Alignment explanation
Indices: 10853941--10854013 Score: 69
Period size: 12 Copynumber: 6.3 Consensus size: 11
10853931 CTCATTCAAA
10853941 AAAAAAACAAC
1 AAAAAAACAAC
10853952 -AAAAAACAAC
1 AAAAAAACAAC
10853962 AAGAAAGCAACAAC
1 AA-AAA--AACAAC
10853976 AAAATAAA-AAC
1 AAAA-AAACAAC
*
10853987 AAAAAACAAAAAC
1 -AAAAA-AACAAC
10854000 AAAAAAACAAC
1 AAAAAAACAAC
10854011 AAA
1 AAA
10854014 GAGGAAAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
10 10 0.19
11 13 0.25
12 16 0.30
13 5 0.09
14 9 0.17
ACGTcount: A:0.79, C:0.16, G:0.03, T:0.01
Consensus pattern (11 bp):
AAAAAAACAAC
Found at i:10853977 original size:24 final size:23
Alignment explanation
Indices: 10853939--10854013 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 23
10853929 GCCTCATTCA
*
10853939 AAAAAAAAACAACAAAAAACAAC
1 AAAAAACAACAACAAAAAACAAC
* *
10853962 AAGAAAGCAACAACAAAATAAAAAC
1 AA-AAAACAACAACAAAA-AACAAC
*
10853987 AAAAAACAAAAACAAAAAAACAAC
1 AAAAAACAACAAC-AAAAAACAAC
10854011 AAA
1 AAA
10854014 GAGGAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.05
24 30 0.70
25 11 0.26
ACGTcount: A:0.80, C:0.16, G:0.03, T:0.01
Consensus pattern (23 bp):
AAAAAACAACAACAAAAAACAAC
Found at i:10853988 original size:38 final size:38
Alignment explanation
Indices: 10853937--10854012 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
10853927 GAGCCTCATT
* * *
10853937 CAAAAAAAAAACAACAAAA-AACAACAAGAAAGCAACAA
1 CAAAAAAAAAACAA-AAAACAAAAACAAAAAAACAACAA
*
10853975 CAAAATAAAAACAAAAAACAAAAACAAAAAAACAACAA
1 CAAAAAAAAAACAAAAAACAAAAACAAAAAAACAACAA
10854013 AGAGGAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 4 0.12
38 29 0.88
ACGTcount: A:0.79, C:0.17, G:0.03, T:0.01
Consensus pattern (38 bp):
CAAAAAAAAAACAAAAAACAAAAACAAAAAAACAACAA
Found at i:10853995 original size:35 final size:36
Alignment explanation
Indices: 10853940--10854013 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 36
10853930 CCTCATTCAA
* * **
10853940 AAAAAAAACAACAAAAAACAACAAGAAAGCAACAAC
1 AAAAAAAACAACAAAAAACAAAAACAAAAAAACAAC
*
10853976 AAAATAAA-AACAAAAAACAAAAACAAAAAAACAAC
1 AAAAAAAACAACAAAAAACAAAAACAAAAAAACAAC
10854011 AAA
1 AAA
10854014 GAGGAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
35 26 0.79
36 7 0.21
ACGTcount: A:0.80, C:0.16, G:0.03, T:0.01
Consensus pattern (36 bp):
AAAAAAAACAACAAAAAACAAAAACAAAAAAACAAC
Found at i:10854007 original size:14 final size:14
Alignment explanation
Indices: 10853970--10854009 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
10853960 ACAAGAAAGC
* *
10853970 AACAACAAAATAAA
1 AACAAAAAAACAAA
10853984 AAC-AAAAAACAAA
1 AACAAAAAAACAAA
10853997 AACAAAAAAACAA
1 AACAAAAAAACAA
10854010 CAAAGAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.82, C:0.15, G:0.00, T:0.03
Consensus pattern (14 bp):
AACAAAAAAACAAA
Found at i:10854021 original size:24 final size:24
Alignment explanation
Indices: 10853943--10854022 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 24
10853933 CATTCAAAAA
10853943 AAAAACAACAAAAAACAACAAGAAAGC
1 AAAAAC-A-AAAAAACAACAA-AAAGC
* *
10853970 AACAACAAAATAAA-AACAAAAAAC
1 AAAAACAAAA-AAACAACAAAAAGC
* *
10853994 AAAAACAAAAAAACAACAAAGAGG
1 AAAAACAAAAAAACAACAAAAAGC
10854018 AAAAA
1 AAAAA
10854023 AACTTTGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
23 3 0.07
24 25 0.56
25 8 0.18
26 4 0.09
27 5 0.11
ACGTcount: A:0.78, C:0.15, G:0.06, T:0.01
Consensus pattern (24 bp):
AAAAACAAAAAAACAACAAAAAGC
Found at i:10854191 original size:8 final size:8
Alignment explanation
Indices: 10854180--10854204 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
10854170 TAAAAATATG
10854180 AAAATGAA
1 AAAATGAA
10854188 AAAATGAA
1 AAAATGAA
10854196 AAAATGAA
1 AAAATGAA
10854204 A
1 A
10854205 TAAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAATGAA
Found at i:10854213 original size:22 final size:22
Alignment explanation
Indices: 10854156--10854215 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 22
10854146 TTATAAACGA
10854156 AAATAAACAATAAATAAAAATATG
1 AAATAAA-AA-AAATAAAAATATG
*
10854180 AAA-ATGAAAAAATGAAAAA-ATG
1 AAATA-AAAAAAAT-AAAAATATG
10854202 AAATAAAAAAAATA
1 AAATAAAAAAAATA
10854216 GAAGAGAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
21 1 0.03
22 17 0.55
23 9 0.29
24 4 0.13
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.17
Consensus pattern (22 bp):
AAATAAAAAAAATAAAAATATG
Found at i:10856008 original size:21 final size:19
Alignment explanation
Indices: 10855984--10856043 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
10855974 TAGTAATAAT
10855984 AATAAAAATAAAAAATAGACA
1 AATAAAAATAAAAAAT--ACA
*
10856005 AATAATAA-AAAAAAT-CA
1 AATAAAAATAAAAAATACA
*
10856022 AAGAATAAATAAAAAATA-A
1 AATAA-AAATAAAAAATACA
10856041 AAT
1 AAT
10856044 GATAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 6 0.19
18 2 0.06
19 10 0.31
20 7 0.22
21 7 0.22
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (19 bp):
AATAAAAATAAAAAATACA
Found at i:10856017 original size:27 final size:28
Alignment explanation
Indices: 10855978--10856042 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
10855968 TAATAATAGT
* *
10855978 AATAATAATAAAAAT-AAAAAATAGACA
1 AATAATAAAAAAAATCAAAAAATAAACA
* *
10856005 AATAATAAAAAAAATCAAAGAATAAATA
1 AATAATAAAAAAAATCAAAAAATAAACA
*
10856033 AAAAATAAAA
1 AATAATAAAA
10856043 TGATAATAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 14 0.44
28 18 0.56
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (28 bp):
AATAATAAAAAAAATCAAAAAATAAACA
Found at i:10856240 original size:10 final size:10
Alignment explanation
Indices: 10856225--10856249 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10856215 CATGTTATGT
10856225 AAAAAATAAA
1 AAAAAATAAA
10856235 AAAAAATAAA
1 AAAAAATAAA
10856245 AAAAA
1 AAAAA
10856250 GATAGAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:10856377 original size:8 final size:8
Alignment explanation
Indices: 10856366--10856403 Score: 58
Period size: 8 Copynumber: 4.5 Consensus size: 8
10856356 TATAATAATC
10856366 AAAATATA
1 AAAATATA
10856374 AAAATAATA
1 AAAAT-ATA
10856383 AATAATATA
1 AA-AATATA
10856392 AAAATATA
1 AAAATATA
10856400 AAAA
1 AAAA
10856404 AATGTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 15 0.54
9 10 0.36
10 3 0.11
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATATA
Found at i:10856380 original size:20 final size:18
Alignment explanation
Indices: 10856366--10856422 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
10856356 TATAATAATC
10856366 AAAATATAAAAATAATAA
1 AAAATATAAAAATAATAA
*
10856384 ATAATATAAAAAT-ATAAA
1 AAAATATAAAAATAAT-AA
*
10856402 AAAATGTAAAAAATAATAA
1 AAAATAT-AAAAATAATAA
10856421 AA
1 AA
10856423 TTTTTGTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
17 2 0.06
18 19 0.58
19 10 0.30
20 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
AAAATATAAAAATAATAA
Found at i:10856406 original size:28 final size:28
Alignment explanation
Indices: 10856337--10856403 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
10856327 GATTGCTTAC
* * *
10856337 AAAAAAATAATAATAGTAATATAATAAT
1 AAAAATATAAAAATAATAATATAATAAT
*
10856365 CAAAATATAAAAATAATAA-ATAAT-AT
1 AAAAATATAAAAATAATAATATAATAAT
10856391 AAAAATATAAAAA
1 AAAAATATAAAAA
10856404 AATGTAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 14 0.41
27 5 0.15
28 15 0.44
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (28 bp):
AAAAATATAAAAATAATAATATAATAAT
Found at i:10858533 original size:22 final size:22
Alignment explanation
Indices: 10858486--10858533 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
10858476 TGTGTGTTCA
* **
10858486 ATTATAATAATATGTACATTTT
1 ATTAGAATAATATGTACATTGC
*
10858508 ATTAGAATAATATGTATATTGC
1 ATTAGAATAATATGTACATTGC
10858530 ATTA
1 ATTA
10858534 TAATGATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (22 bp):
ATTAGAATAATATGTACATTGC
Found at i:10858849 original size:21 final size:20
Alignment explanation
Indices: 10858807--10858849 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
10858797 TAATAGTTAA
*
10858807 AAAAGAAAGAATAAATGGTT
1 AAAAGAAAGAATAAATGATT
10858827 AAAAGAAAAGAATATAA-GATT
1 AAAAG-AAAGAATA-AATGATT
10858848 AA
1 AA
10858850 TGTAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 13 0.65
22 2 0.10
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (20 bp):
AAAAGAAAGAATAAATGATT
Found at i:10863632 original size:21 final size:22
Alignment explanation
Indices: 10863606--10863652 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
10863596 AGCTTTCCAT
*
10863606 TTTTTTTTTC-TTTTTTAAACN
1 TTTTTTTTTCTTTTTTTAAACA
10863627 TTTTTTTTTCTTTTTTTAAACA
1 TTTTTTTTTCTTTTTTTAAACA
10863649 TTTT
1 TTTT
10863653 GGAAACATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTTTTTCTTTTTTTAAACA
Found at i:10867743 original size:2 final size:2
Alignment explanation
Indices: 10867736--10867784 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
10867726 ACCTTGATTC
10867736 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
10867778 AT AT AT A
1 AT AT AT A
10867785 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10871118 original size:16 final size:16
Alignment explanation
Indices: 10871093--10871125 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
10871083 TAGGTGTCCC
10871093 CCTCGCCCAGCCTCCA
1 CCTCGCCCAGCCTCCA
*
10871109 CCTCGTCCAGCCTCCA
1 CCTCGCCCAGCCTCCA
10871125 C
1 C
10871126 GCGGTGAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.61, G:0.12, T:0.15
Consensus pattern (16 bp):
CCTCGCCCAGCCTCCA
Found at i:10872179 original size:20 final size:20
Alignment explanation
Indices: 10872151--10872194 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
10872141 TAGATACGTA
*
10872151 TATAATTTTTAAATTATATT
1 TATAATTTTTAAATAATATT
* *
10872171 TATACTTTTTAAATAATTTT
1 TATAATTTTTAAATAATATT
10872191 TATA
1 TATA
10872195 TTAATATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TATAATTTTTAAATAATATT
Found at i:10873819 original size:13 final size:13
Alignment explanation
Indices: 10873803--10873927 Score: 81
Period size: 13 Copynumber: 9.2 Consensus size: 13
10873793 ATGTCATATA
10873803 TTTTATTTTTATT
1 TTTTATTTTTATT
*
10873816 TTTTATAATATTATAT
1 TTTTAT--TTTTAT-T
10873832 TTTTA-TTTTATT
1 TTTTATTTTTATT
*** *
10873844 TTTTAAAATAATT
1 TTTTATTTTTATT
* *
10873857 TTTTATATTATATA
1 TTTTAT-TTTTATT
10873871 TTTTATTTTTATT
1 TTTTATTTTTATT
* *
10873884 TTTAATTCTTATT
1 TTTTATTTTTATT
*
10873897 TTGTATATTTTATT
1 TTTTAT-TTTTATT
*
10873911 TTAATATTTTTTATT
1 TT-TTA-TTTTTATT
10873926 TT
1 TT
10873928 AATTATAATA
Statistics
Matches: 85, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
12 6 0.07
13 40 0.47
14 16 0.19
15 16 0.19
16 7 0.08
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:10873819 original size:28 final size:27
Alignment explanation
Indices: 10873788--10873847 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
10873778 CTTAAAAATA
*
10873788 TTTTAATGTCATATATTTTATTTTTATTT
1 TTTTAATATCATAT-TTTTA-TTTTATTT
*
10873817 TTTATAATATTATATTTTTATTTTATTT
1 TTT-TAATATCATATTTTTATTTTATTT
10873845 TTT
1 TTT
10873848 AAAATAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 11 0.39
29 8 0.29
30 9 0.32
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (27 bp):
TTTTAATATCATATTTTTATTTTATTT
Found at i:10873820 original size:7 final size:7
Alignment explanation
Indices: 10873803--10873927 Score: 55
Period size: 7 Copynumber: 18.3 Consensus size: 7
10873793 ATGTCATATA
10873803 TTTTA-T
1 TTTTATT
10873809 TTTTATT
1 TTTTATT
*
10873816 TTTTATAA
1 TTTTAT-T
*
10873824 TATTATAT
1 TTTTAT-T
10873832 TTTTA--
1 TTTTATT
10873837 TTTTATT
1 TTTTATT
*
10873844 TTTTA-A
1 TTTTATT
** *
10873850 AATAATT
1 TTTTATT
*
10873857 TTTTATA
1 TTTTATT
* *
10873864 TTATATA
1 TTTTATT
10873871 TTTTA-T
1 TTTTATT
10873877 TTTTA-T
1 TTTTATT
*
10873883 TTTTAAT
1 TTTTATT
*
10873890 TCTTATT
1 TTTTATT
* *
10873897 TTGTATA
1 TTTTATT
10873904 TTTTATT
1 TTTTATT
*
10873911 TTAATATT
1 TT-TTATT
10873919 TTTTATT
1 TTTTATT
10873926 TT
1 TT
10873928 AATTATAATA
Statistics
Matches: 87, Mismatches: 25, Indels: 13
0.70 0.20 0.10
Matches are distributed among these distances:
5 5 0.06
6 18 0.21
7 48 0.55
8 16 0.18
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (7 bp):
TTTTATT
Found at i:10873858 original size:23 final size:28
Alignment explanation
Indices: 10873799--10873942 Score: 88
Period size: 27 Copynumber: 5.1 Consensus size: 28
10873789 TTTAATGTCA
10873799 TATATTTTATTTTTATTTTTTATAATAT
1 TATATTTTATTTTTATTTTTTATAATAT
10873827 TATATTTT-TATTTTATTTTTTA-AA-AT
1 TATATTTTAT-TTTTATTTTTTATAATAT
* * * * *
10873853 AATTTTTTATATTATATATTTTAT--TTT
1 TATATTTTAT-TTTTATTTTTTATAATAT
* * *
10873880 TAT-TTTTAATTCTTATTTTGTAT-ATTT
1 TATATTTT-ATTTTTATTTTTTATAATAT
10873907 TAT-TTTAATATTTTTTATTTTAATTATAATAT
1 TATATTT--TA-TTTTTATTTT--TTATAATAT
10873939 TATA
1 TATA
10873943 AAATATTTTT
Statistics
Matches: 90, Mismatches: 13, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
26 21 0.23
27 29 0.32
28 21 0.23
29 10 0.11
31 3 0.03
32 6 0.07
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.69
Consensus pattern (28 bp):
TATATTTTATTTTTATTTTTTATAATAT
Found at i:10873898 original size:40 final size:41
Alignment explanation
Indices: 10873803--10873933 Score: 121
Period size: 40 Copynumber: 3.2 Consensus size: 41
10873793 ATGTCATATA
* *
10873803 TTTT-ATTTTTATTTTTTATAATATTATATTTT-TATTTTATT
1 TTTTAATTATTATTTTTTATATTA-TATATTTTATATTTTA-T
* *
10873844 TTTTAA-AATAATTTTTTATATTATATATTTTAT-TTTTAT
1 TTTTAATTATTATTTTTTATATTATATATTTTATATTTTAT
* * *
10873883 TTTTAATTCTTATTTTGTATATT-T-TATTTTAATATTTTTT
1 TTTTAATTATTATTTTTTATATTATATATTTT-ATATTTTAT
10873923 ATTTTAATTAT
1 -TTTTAATTAT
10873934 AATATTATAA
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
38 6 0.08
39 10 0.14
40 30 0.41
41 27 0.36
42 1 0.01
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.71
Consensus pattern (41 bp):
TTTTAATTATTATTTTTTATATTATATATTTTATATTTTAT
Found at i:10879499 original size:36 final size:36
Alignment explanation
Indices: 10879452--10879524 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
10879442 CTAAGTAAGT
* *
10879452 ATATTTACGAATTACTATACTCTAAATGACATACCC
1 ATATTTACGAATTACCATACGCTAAATGACATACCC
*
10879488 ATATTTACGAATTACCATACGCTAAATGATATACCC
1 ATATTTACGAATTACCATACGCTAAATGACATACCC
10879524 A
1 A
10879525 CAACCCTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.32
Consensus pattern (36 bp):
ATATTTACGAATTACCATACGCTAAATGACATACCC
Found at i:10883316 original size:40 final size:40
Alignment explanation
Indices: 10883261--10883336 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
10883251 TATTTTTTAA
* * * *
10883261 TTTTTTTATACTAATGTCGATAAATATTAAATATAATGAT
1 TTTTTTTATAATAATGCCGAAAAATATTAAAAATAATGAT
* *
10883301 TTTTTTTGTAATAATGCCTAAAAATATTAAAAATAA
1 TTTTTTTATAATAATGCCGAAAAATATTAAAAATAA
10883337 AAAAAATTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (40 bp):
TTTTTTTATAATAATGCCGAAAAATATTAAAAATAATGAT
Found at i:10898215 original size:39 final size:39
Alignment explanation
Indices: 10898132--10898208 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
10898122 TCTAATCTCT
*
10898132 CAAGTTTTAGTATCATTTAGTTGTCATCATCTCCAAGTC
1 CAAGTTTTAGTATCATTTAGTTGTCATCATCTCAAAGTC
* * *
10898171 CAAGTTTT-GATATTATTTAGTTTTGATCATCTCAAAGT
1 CAAGTTTTAG-TATCATTTAGTTGTCATCATCTCAAAGT
10898209 TGAAGTTCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (39 bp):
CAAGTTTTAGTATCATTTAGTTGTCATCATCTCAAAGTC
Found at i:10898431 original size:27 final size:26
Alignment explanation
Indices: 10898374--10898440 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
10898364 AAAATCAAGT
*
10898374 AAGTGGATGGATAATTTTACTCGTTAA
1 AAGT-GATGGATAATTTTACTCGCTAA
*
10898401 AAGTGAATGGATAATTTTA-TCAGCTAG
1 AAGTG-ATGGATAATTTTACTC-GCTAA
10898428 AAGTCGATGGATA
1 AAGT-GATGGATA
10898441 GCTTTATCCG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 3 0.09
27 31 0.89
28 1 0.03
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (26 bp):
AAGTGATGGATAATTTTACTCGCTAA
Found at i:10898468 original size:54 final size:54
Alignment explanation
Indices: 10898426--10898572 Score: 140
Period size: 54 Copynumber: 2.8 Consensus size: 54
10898416 TTTATCAGCT
* * * * *
10898426 AGAAGTCGATGGATAGCTTTATCCGTTAGGAGTGGATAGATAAATTTACTTACA
1 AGAAGTCGATGGATACCTTTATCCATGAGAAGTGGATAGATAAATTTACTCACA
* * ** *
10898480 AGAAGTGGATGGATACCTTTATCCATGAGAAGTGGATGGATACCTTTA-T-TCA
1 AGAAGTCGATGGATACCTTTATCCATGAGAAGTGGATAGATAAATTTACTCACA
* * *
10898532 AGAAGTAGATGAATACC-TTACCCACTG-GAAGTGGATAGATA
1 AGAAGTCGATGGATACCTTTATCCA-TGAGAAGTGGATAGATA
10898573 TCTTTACCCG
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
51 19 0.24
52 19 0.24
53 1 0.01
54 40 0.51
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (54 bp):
AGAAGTCGATGGATACCTTTATCCATGAGAAGTGGATAGATAAATTTACTCACA
Found at i:10898542 original size:25 final size:25
Alignment explanation
Indices: 10898478--10898550 Score: 101
Period size: 27 Copynumber: 2.8 Consensus size: 25
10898468 AATTTACTTA
10898478 CAAGAAGTGGATGGATACCTTTATC
1 CAAGAAGTGGATGGATACCTTTATC
*
10898503 CATGAGAAGTGGATGGATACCTTTATT
1 CA--AGAAGTGGATGGATACCTTTATC
* *
10898530 CAAGAAGTAGATGAATACCTT
1 CAAGAAGTGGATGGATACCTT
10898551 ACCCACTGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 19 0.44
27 24 0.56
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (25 bp):
CAAGAAGTGGATGGATACCTTTATC
Found at i:10904411 original size:20 final size:20
Alignment explanation
Indices: 10904386--10904431 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
10904376 CTTCTAAACC
10904386 TCAAATCATACTCCAAT-AA
1 TCAAATCATACTCCAATGAA
*
10904405 GTCAAATTATACTCCAATGAA
1 -TCAAATCATACTCCAATGAA
10904426 TCAAAT
1 TCAAAT
10904432 GGGGCCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATGAA
Found at i:10905249 original size:27 final size:27
Alignment explanation
Indices: 10905183--10905276 Score: 107
Period size: 27 Copynumber: 3.5 Consensus size: 27
10905173 TTCCCGTTAA
10905183 AAGTGGATAGATAATTTTACCCATTAG
1 AAGTGGATAGATAATTTTACCCATTAG
** *
10905210 AAGTAAATGGATAATTTTACCCATTAG
1 AAGTGGATAGATAATTTTACCCATTAG
* ** * **
10905237 AAGTGGACAGATACCTTTACTCACAAG
1 AAGTGGATAGATAATTTTACCCATTAG
10905264 AAGTGGATAGATA
1 AAGTGGATAGATA
10905277 CCTTTACTCA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (27 bp):
AAGTGGATAGATAATTTTACCCATTAG
Found at i:10905277 original size:27 final size:28
Alignment explanation
Indices: 10905235--10905325 Score: 100
Period size: 27 Copynumber: 3.4 Consensus size: 28
10905225 TTTACCCATT
*
10905235 AGAAGTGGACAGATACCTTTACTCAC-A
1 AGAAGTGGATAGATACCTTTACTCACGA
10905262 AGAAGTGGATAGATACCTTTACTCACGA
1 AGAAGTGGATAGATACCTTTACTCACGA
** * *
10905290 A-AAGTATATGGATACCTTTA-TCCTCG-
1 AGAAGTGGATAGATACCTTTACT-CACGA
10905316 AGAAGTGGAT
1 AGAAGTGGAT
10905326 GTATATTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
26 2 0.04
27 50 0.93
28 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (28 bp):
AGAAGTGGATAGATACCTTTACTCACGA
Found at i:10905385 original size:27 final size:27
Alignment explanation
Indices: 10905180--10905409 Score: 79
Period size: 27 Copynumber: 8.5 Consensus size: 27
10905170 GCTTTCCCGT
* *
10905180 TAAAAGTGGATAGATA-ATTTTACCCAT
1 TAAAAGTGGATGGATACA-TTTACCCAC
* ** *
10905207 TAGAAGTAAATGGATA-ATTTTACCCAT
1 TAAAAGTGGATGGATACA-TTTACCCAC
* ** * *
10905234 TAGAAGTGGACAGATACCTTTACTCAC
1 TAAAAGTGGATGGATACATTTACCCAC
* * *
10905261 -AAGAAGTGGATAGATACCTTTACTCAC
1 TAA-AAGTGGATGGATACATTTACCCAC
* ** * * *
10905288 GAAAAGTATATGGATACCTTTATCCTC
1 TAAAAGTGGATGGATACATTTACCCAC
* * * ** ** *
10905315 GAGAAGTGGATGTATATTTTTACTTAA
1 TAAAAGTGGATGGATACATTTACCCAC
* * * **
10905342 GAAAAATAGATAAATACATTTACCCAC
1 TAAAAGTGGATGGATACATTTACCCAC
* * **
10905369 TAACAGTGGATGGATACCTTTACCTGC
1 TAAAAGTGGATGGATACATTTACCCAC
10905396 TAAAAGTGGATGGA
1 TAAAAGTGGATGGA
10905410 AGTGAATAGA
Statistics
Matches: 150, Mismatches: 50, Indels: 6
0.73 0.24 0.03
Matches are distributed among these distances:
26 1 0.01
27 147 0.98
28 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (27 bp):
TAAAAGTGGATGGATACATTTACCCAC
Found at i:10905448 original size:27 final size:27
Alignment explanation
Indices: 10905408--10905525 Score: 112
Period size: 27 Copynumber: 4.4 Consensus size: 27
10905398 AAAGTGGATG
* * *
10905408 GAAGTGAATAGATACATTTATCC-AACA
1 GAAGTGGATGGATACCTTTA-CCTAACA
* *
10905435 GTAGTGGATGGATACCTTTACCTAATA
1 GAAGTGGATGGATACCTTTACCTAACA
** *
10905462 GAAGTTTATGGATACCTTTACCTATCA
1 GAAGTGGATGGATACCTTTACCTAACA
* * *
10905489 GAAGTGGATGGATAGCTTTACCCATCA
1 GAAGTGGATGGATACCTTTACCTAACA
*
10905516 GAAATGGATG
1 GAAGTGGATG
10905526 AGTAGTGAAG
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
26 2 0.03
27 73 0.97
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (27 bp):
GAAGTGGATGGATACCTTTACCTAACA
Found at i:10908839 original size:29 final size:28
Alignment explanation
Indices: 10908780--10908846 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
10908770 TCAATTTTTA
**
10908780 ATTATAATTTATTTATTTTTAGTTGTTTT
1 ATTATAA-TTATTTATTTTTAGTTGAGTT
10908809 ATTATAATTAGTTTATTTTTAAG-TGAGTT
1 ATTATAATTA-TTTATTTTT-AGTTGAGTT
*
10908838 ATTTTAATT
1 ATTATAATT
10908847 TTATATTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 3 0.09
29 28 0.85
30 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (28 bp):
ATTATAATTATTTATTTTTAGTTGAGTT
Found at i:10918731 original size:17 final size:17
Alignment explanation
Indices: 10918709--10918744 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
10918699 TAATTGTGTA
10918709 TTAATTGTTGAATCATG
1 TTAATTGTTGAATCATG
*
10918726 TTAATTGTTTAATCATG
1 TTAATTGTTGAATCATG
10918743 TT
1 TT
10918745 TTTAACTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.53
Consensus pattern (17 bp):
TTAATTGTTGAATCATG
Found at i:10918830 original size:2 final size:2
Alignment explanation
Indices: 10918818--10918848 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
10918808 ATTATTCAAC
*
10918818 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10918849 GTTTTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10927202 original size:137 final size:137
Alignment explanation
Indices: 10926956--10927226 Score: 506
Period size: 137 Copynumber: 2.0 Consensus size: 137
10926946 TCTTTCAATA
10926956 ATGGTAGCCACACCTTACATCTAAATTTGATATCCCAATTTCAAATTCCAGTCTCCCCAAAGTTT
1 ATGGTAGCCACACCTTACATCTAAATTTGATATCCCAATTTCAAATTCCAGTCTCCCCAAAGTTT
* *
10927021 AATAATGAATTTTTATCTTTTCCTAGTACAGATATCAGTAACCAAATGACAAATTTCAAAAACAT
66 AATAATGAATTTTTATCTTCTCCCAGTACAGATATCAGTAACCAAATGACAAATTTCAAAAACAT
10927086 CCAAATG
131 CCAAATG
*
10927093 ATGGTAGCCACACCTTACATCTAAATTTGATATCCCAATTTCAAATTCCCGTCTCCCCAAAGTTT
1 ATGGTAGCCACACCTTACATCTAAATTTGATATCCCAATTTCAAATTCCAGTCTCCCCAAAGTTT
*
10927158 AATAATGAATTTTTATCTTCTCCCAGTATAGATATCAGTAACCAAATGACAAATTTCAAAAACAT
66 AATAATGAATTTTTATCTTCTCCCAGTACAGATATCAGTAACCAAATGACAAATTTCAAAAACAT
10927223 CCAA
131 CCAA
10927227 CTCATCAGAA
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 130 1.00
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.32
Consensus pattern (137 bp):
ATGGTAGCCACACCTTACATCTAAATTTGATATCCCAATTTCAAATTCCAGTCTCCCCAAAGTTT
AATAATGAATTTTTATCTTCTCCCAGTACAGATATCAGTAACCAAATGACAAATTTCAAAAACAT
CCAAATG
Found at i:10948550 original size:12 final size:12
Alignment explanation
Indices: 10948535--10948560 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10948525 TTTGATAAAA
10948535 TTTTTTTATAAG
1 TTTTTTTATAAG
10948547 TTTTTTTATAAG
1 TTTTTTTATAAG
10948559 TT
1 TT
10948561 ATAATTTTTG
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:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTTTTTTATAAG
Found at i:10948580 original size:18 final size:19
Alignment explanation
Indices: 10948540--10948580 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
10948530 TAAAATTTTT
*
10948540 TTATAAGTTTTTTTATAAG
1 TTATAAGTTTTTTTATAAA
10948559 TTATAA-TTTTTGTTA-AAA
1 TTATAAGTTTTT-TTATAAA
10948577 TTAT
1 TTAT
10948581 CATAAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (19 bp):
TTATAAGTTTTTTTATAAA
Found at i:10949257 original size:27 final size:27
Alignment explanation
Indices: 10949217--10949269 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
10949207 TTAATTTAAA
10949217 AAATAATAAGAAAAAA-AATAAAAAGTC
1 AAATAATAAGAAAAAATAA-AAAAAGTC
10949244 AAATAATATA-AAAAAATAAAAAAAGT
1 AAATAATA-AGAAAAAATAAAAAAAGT
10949270 AGTTAGCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (27 bp):
AAATAATAAGAAAAAATAAAAAAAGTC
Found at i:10949557 original size:47 final size:46
Alignment explanation
Indices: 10949479--10949573 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 46
10949469 GAATAACCTT
10949479 TTTTATATTTTGTGACAAGTTATCTTTATATATATATATATATATA
1 TTTTATATTTTGTGACAAGTTATCTTTATATATATATATATATATA
10949525 NTTTTATTATTTTGTGACAAGTTATCTTATATATATATATATATATATA
1 -TTTTA-TATTTTGTGACAAGTTATCTT-TATATATATATATATATATA
10949574 AAATGGTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 5 0.11
48 21 0.46
49 20 0.43
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.54
Consensus pattern (46 bp):
TTTTATATTTTGTGACAAGTTATCTTTATATATATATATATATATA
Found at i:10955511 original size:15 final size:15
Alignment explanation
Indices: 10955491--10955532 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
10955481 TAATATTATA
10955491 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
10955506 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
*
10955521 A-TAATATAAAAA
1 ATTAAAATAAAAA
10955533 TTAAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:10955518 original size:20 final size:20
Alignment explanation
Indices: 10955482--10955538 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
10955472 AATATTTTAT
*
10955482 AATATTATAATTAAAATAAAA
1 AATATTA-AAATAAAATAAAA
* *
10955503 AATATTAAAATAAAATATAT
1 AATATTAAAATAAAATAAAA
*
10955523 AATATAAAAATTAAAA
1 AATATTAAAA-TAAAA
10955539 ATTAAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATATTAAAATAAAATAAAA
Found at i:10955552 original size:26 final size:25
Alignment explanation
Indices: 10955493--10955561 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 25
10955483 ATATTATAAT
*
10955493 TAAAATA-AAAAATATTAAAATAAAA
1 TAAAATATAAAAAT-TAAAAATAAAA
10955518 TATATAATATAAAAATTAAAAATTAAAA
1 TA-A-AATATAAAAATTAAAAA-TAAAA
10955546 TAAAATATAAAAATTA
1 TAAAATATAAAAATTA
10955562 TAGTAAAGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 2 0.05
26 14 0.36
27 10 0.26
28 13 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAAATATAAAAATTAAAAATAAAA
Found at i:10968024 original size:2 final size:2
Alignment explanation
Indices: 10968017--10968121 Score: 74
Period size: 2 Copynumber: 53.0 Consensus size: 2
10968007 AAATAAATAA
* *
10968017 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT CT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
10968058 AA AGG AT AA AT -T TT GA- ACC AN AT A- AT AA AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT -AT A-T AT AT AT AT AT AT AT AT AT AT AT
10968098 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
10968122 CTCTTAAAGG
Statistics
Matches: 85, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
1 4 0.05
2 79 0.93
3 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:10968123 original size:69 final size:68
Alignment explanation
Indices: 10968012--10968148 Score: 265
Period size: 69 Copynumber: 2.0 Consensus size: 68
10968002 TTCCAAAATA
10968012 AATAAATATATATATATATATATATATATATATATATATATCTCTTAAAGGATAAATTTTGAACC
1 AATAAATATATATATATATATATATATATATATATATATATCTCTTAAAGGATAAATTTTGAACC
10968077 ANAT
66 A-AT
10968081 AATAAATATATATATATATATATATATATATATATATATATCTCTTAAAGGATAAATTTTGAACC
1 AATAAATATATATATATATATATATATATATATATATATATCTCTTAAAGGATAAATTTTGAACC
10968146 AAT
66 AAT
10968149 CAAATTTATA
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 2 0.03
69 66 0.97
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.41
Consensus pattern (68 bp):
AATAAATATATATATATATATATATATATATATATATATATCTCTTAAAGGATAAATTTTGAACC
AAT
Found at i:10979125 original size:12 final size:11
Alignment explanation
Indices: 10979106--10979135 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
10979096 TATACTTGTA
10979106 TAAATTACAAT
1 TAAATTACAAT
10979117 TATAATTACAAT
1 TA-AATTACAAT
10979129 TAAATTA
1 TAAATTA
10979136 TTTTCAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATTACAAT
Found at i:10982511 original size:2 final size:2
Alignment explanation
Indices: 10982506--10982531 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10982496 GAAAAAAAAA
10982506 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
10982532 TTAACATCAT
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:10982960 original size:125 final size:120
Alignment explanation
Indices: 10982814--10983052 Score: 408
Period size: 126 Copynumber: 1.9 Consensus size: 120
10982804 TAAAATACCT
10982814 TTTATTAAATTTAATTTAAAATATTTAATTTTTTGATAATTTATT-AAAATATTAAAAAATTGTA
1 TTTATTAAATTTAATTTAAAATATTTAATTTTTTGATAATTTATTAAAAATATTAAAAAATTGTA
10982878 ATTAAACCTTTAATATGATTATTTATTTTATTTTTTCTCTATTTTAATNNNTAAATAC
66 ATTAAACCTTTAATATGATTATTTATTTTATTTTTTCTCTATTTTAAT---TAAATAC
*
10982936 TTTATTAAATTATGATTTATAAAATATTTAATTTTTTGATAATTTATTAAAAATATTAAAAAATT
1 TTTATTAAATT-T-AATT-TAAAATATTTAATTTTTTGATAATTTATTAAAAATATTAAAAAATT
10983001 GTAATTAAACCTTTAATATGATTATTTATTTTATTTTTTCTCTATTTTAATT
63 GTAATTAAACCTTTAATATGATTATTTATTTTATTTTTTCTCTATTTTAATT
10983053 TTTTTAAATA
Statistics
Matches: 112, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
122 11 0.10
123 2 0.02
124 3 0.03
125 29 0.26
126 67 0.60
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (120 bp):
TTTATTAAATTTAATTTAAAATATTTAATTTTTTGATAATTTATTAAAAATATTAAAAAATTGTA
ATTAAACCTTTAATATGATTATTTATTTTATTTTTTCTCTATTTTAATTAAATAC
Found at i:10983097 original size:81 final size:81
Alignment explanation
Indices: 10982962--10983115 Score: 186
Period size: 81 Copynumber: 1.9 Consensus size: 81
10982952 TTATAAAATA
* * * *
10982962 TTTAATTTTTTGATAATTTATTAAAAATATTAAAAAATTGTAATTAAACCTTTAATATGATTATT
1 TTTAATTTTTT-ATAATATATTAAAAATATTAAAAAATTATAATGAAAACTTT-A-ATGATTATT
10983027 TATTTTATTTTTTCTCTAT
63 TATTTTATTTTTTCTCTAT
* * * * *
10983046 TTTAATTTTTT-TAA-ATATTGAAAATATTAATAATTTATAATGAAAATTTTAATGATTCTTTAT
1 TTTAATTTTTTATAATATATTAAAAATATTAAAAAATTATAATGAAAACTTTAATGATTATTTAT
10983109 TTTATTT
66 TTTATTT
10983116 CCTTATCTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
79 18 0.30
80 1 0.02
81 28 0.46
82 3 0.05
84 11 0.18
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (81 bp):
TTTAATTTTTTATAATATATTAAAAATATTAAAAAATTATAATGAAAACTTTAATGATTATTTAT
TTTATTTTTTCTCTAT
Found at i:10983109 original size:126 final size:123
Alignment explanation
Indices: 10982820--10983101 Score: 342
Period size: 126 Copynumber: 2.3 Consensus size: 123
10982810 ACCTTTTATT
* *
10982820 AAATT-TAATTTA-AAATATTTAATTTTTTGATAATTTATTAAAATATTAAAAAATTGTAATTAA
1 AAATTATAATTTATAAATA-TAAATTTTATGATAATTTATTAAAATATTAAAAAATTGTAATTAA
*** * *
10982883 ACCTTTAATATGATTATTTATTTTATTTTTTCTCTATTTTAATNNNTAAATACTTTATT
65 ACCTTTAATATGATTATTTATTTTATTTTTTCTCTATTTTAATTTTTAAATACTTGATA
* * *
10982942 AAATTATGATTTATAAAATATTTAATTTTTTGATAATTTATTAAAAATATTAAAAAATTGTAATT
1 AAATTATAATTTAT-AAATA-TAAATTTTATGATAATTTATT-AAAATATTAAAAAATTGTAATT
10983007 AAACCTTTAATATGATTATTTATTTTATTTTTTCTCTATTTTAATTTTTTTAAATA-TTGA-A
63 AAACCTTTAATATGATTATTTATTTTATTTTTTCTCTATTTTAA--TTTTTAAATACTTGATA
10983068 AATATTAATAATTTAT-AATGA-AAATTTTAATGAT
1 AA-ATT-ATAATTTATAAAT-ATAAATTTT-ATGAT
10983102 TCTTTATTTT
Statistics
Matches: 141, Mismatches: 9, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
122 5 0.04
123 6 0.04
125 33 0.23
126 75 0.53
127 7 0.05
128 15 0.11
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.52
Consensus pattern (123 bp):
AAATTATAATTTATAAATATAAATTTTATGATAATTTATTAAAATATTAAAAAATTGTAATTAAA
CCTTTAATATGATTATTTATTTTATTTTTTCTCTATTTTAATTTTTAAATACTTGATA
Found at i:10983177 original size:25 final size:27
Alignment explanation
Indices: 10983144--10983217 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 27
10983134 ATATTAAAAA
10983144 TTTATAATTTATAATTAAAA-AT-ATCT
1 TTTA-AATTTATAATTAAAATATCATCT
* *
10983170 TTTAAATTTTTAATTAGAAATATCATTT
1 TTTAAATTTATAATTA-AAATATCATCT
*
10983198 TTTGTAATTTATAATTAAAA
1 TTT-AAATTTATAATTAAAA
10983218 CTTAATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 11 0.28
26 7 0.17
27 2 0.05
28 9 0.22
29 11 0.28
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (27 bp):
TTTAAATTTATAATTAAAATATCATCT
Found at i:10991233 original size:18 final size:18
Alignment explanation
Indices: 10991212--10991255 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
10991202 GATTACGATG
*
10991212 ATGATGAGGAGGAATATT
1 ATGATGAGGAAGAATATT
* *
10991230 ATGATGATGAAGATTATT
1 ATGATGAGGAAGAATATT
10991248 ATGATGAG
1 ATGATGAG
10991256 AAACATGAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.32
Consensus pattern (18 bp):
ATGATGAGGAAGAATATT
Found at i:10991245 original size:15 final size:15
Alignment explanation
Indices: 10991159--10991254 Score: 59
Period size: 15 Copynumber: 6.4 Consensus size: 15
10991149 ATGGCAAGGG
10991159 TGATGAAGATGATGA
1 TGATGAAGATGATGA
* *
10991174 AGATGAAGAAT-ATTA
1 TGATGAAG-ATGATGA
* *
10991189 TTATGACGATGATGA
1 TGATGAAGATGATGA
* * *
10991204 TTACGATGATGATGA
1 TGATGAAGATGATGA
* * * *
10991219 GGAGGAATATTATGA
1 TGATGAAGATGATGA
* *
10991234 TGATGAAGATTATTA
1 TGATGAAGATGATGA
10991249 TGATGA
1 TGATGA
10991255 GAAACATGAG
Statistics
Matches: 61, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
14 2 0.03
15 57 0.93
16 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.27, T:0.31
Consensus pattern (15 bp):
TGATGAAGATGATGA
Found at i:10991284 original size:18 final size:18
Alignment explanation
Indices: 10991263--10991303 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
10991253 GAGAAACATG
10991263 AGAAAAATGAGAAAGAAA
1 AGAAAAATGAGAAAGAAA
**
10991281 AGAAAGCTGAGAAAGAAA
1 AGAAAAATGAGAAAGAAA
10991299 AGAAA
1 AGAAA
10991304 TAAACTTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.68, C:0.02, G:0.24, T:0.05
Consensus pattern (18 bp):
AGAAAAATGAGAAAGAAA
Found at i:10994991 original size:21 final size:21
Alignment explanation
Indices: 10994967--10995037 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
10994957 AGTGGATATG
10994967 AGTTGGGAGGTTTAGAGATAA
1 AGTTGGGAGGTTTAGAGATAA
* ** * * *
10994988 AGTTGGAAGGCTGAAAATGTTAG
1 AGTTGGGAGG-TTTAGA-GATAA
10995011 AGTTTGGG-GGTTTAGAGATAA
1 AG-TTGGGAGGTTTAGAGATAA
10995032 AGTTGG
1 AGTTGG
10995038 AAGGCTGAAA
Statistics
Matches: 35, Mismatches: 12, Indels: 7
0.65 0.22 0.13
Matches are distributed among these distances:
20 4 0.11
21 14 0.40
22 6 0.17
23 7 0.20
24 4 0.11
ACGTcount: A:0.31, C:0.01, G:0.38, T:0.30
Consensus pattern (21 bp):
AGTTGGGAGGTTTAGAGATAA
Found at i:10995029 original size:44 final size:45
Alignment explanation
Indices: 10994969--10995060 Score: 168
Period size: 44 Copynumber: 2.1 Consensus size: 45
10994959 TGGATATGAG
*
10994969 TTGGGAGGTTTAGAGATAAAGTTGGAAGGCTGAAAATGTTAGAGT
1 TTGGGAGGTTTAGAGATAAAGTTGGAAGGCTGAAAATGTTAGAAT
10995014 TTGGG-GGTTTAGAGATAAAGTTGGAAGGCTGAAAATGTTAGAAT
1 TTGGGAGGTTTAGAGATAAAGTTGGAAGGCTGAAAATGTTAGAAT
10995058 TTG
1 TTG
10995061 AGGTTCTGGA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 41 0.89
45 5 0.11
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (45 bp):
TTGGGAGGTTTAGAGATAAAGTTGGAAGGCTGAAAATGTTAGAAT
Found at i:10998238 original size:23 final size:23
Alignment explanation
Indices: 10998212--10998258 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
10998202 GGGAAGAGAT
* *
10998212 GAAAAGAAAATGAAGGTTGAAGG
1 GAAAAGAAAATGAAAGTTAAAGG
10998235 GAAAAGAAAATGAAAGTTAAAGG
1 GAAAAGAAAATGAAAGTTAAAGG
10998258 G
1 G
10998259 CTTTTCGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.32, T:0.13
Consensus pattern (23 bp):
GAAAAGAAAATGAAAGTTAAAGG
Found at i:10998393 original size:34 final size:34
Alignment explanation
Indices: 10998354--10998420 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
10998344 TTTGTTTGAT
10998354 AAAAGTTGTTGGAAGTTATTGAAATATTGAATGC
1 AAAAGTTGTTGGAAGTTATTGAAATATTGAATGC
* *
10998388 AAAAGTTGTTGTAAGTTGTTGAAATATTGAATG
1 AAAAGTTGTTGGAAGTTATTGAAATATTGAATG
10998421 GATATAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.37, C:0.01, G:0.24, T:0.37
Consensus pattern (34 bp):
AAAAGTTGTTGGAAGTTATTGAAATATTGAATGC
Found at i:11004461 original size:3 final size:3
Alignment explanation
Indices: 11004453--11004517 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
11004443 TAAATATAAT
*
11004453 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAT TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
11004501 TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TA
11004518 GAGATAAAGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
TAC
Found at i:11006003 original size:8 final size:8
Alignment explanation
Indices: 11005985--11006037 Score: 63
Period size: 8 Copynumber: 6.8 Consensus size: 8
11005975 GAGTTTTTGT
11005985 TGGGT-AA
1 TGGGTAAA
11005992 TGGGTAAA
1 TGGGTAAA
*
11006000 TGGGTATA
1 TGGGTAAA
* *
11006008 TGGGTTAG
1 TGGGTAAA
*
11006016 TGGGTAAG
1 TGGGTAAA
11006024 TGGGTAAA
1 TGGGTAAA
11006032 TGGGTA
1 TGGGTA
11006038 GTCCAAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
7 5 0.13
8 34 0.87
ACGTcount: A:0.26, C:0.00, G:0.43, T:0.30
Consensus pattern (8 bp):
TGGGTAAA
Found at i:11006012 original size:16 final size:15
Alignment explanation
Indices: 11005985--11006037 Score: 70
Period size: 16 Copynumber: 3.4 Consensus size: 15
11005975 GAGTTTTTGT
11005985 TGGGTAATGGGTAAA
1 TGGGTAATGGGTAAA
* *
11006000 TGGGTATATGGGTTAG
1 TGGGTA-ATGGGTAAA
11006016 TGGGTAAGTGGGTAAA
1 TGGGTAA-TGGGTAAA
11006032 TGGGTA
1 TGGGTA
11006038 GTCCAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 7 0.22
16 25 0.78
ACGTcount: A:0.26, C:0.00, G:0.43, T:0.30
Consensus pattern (15 bp):
TGGGTAATGGGTAAA
Found at i:11006344 original size:12 final size:12
Alignment explanation
Indices: 11006309--11006354 Score: 65
Period size: 12 Copynumber: 3.6 Consensus size: 12
11006299 CTTGCCACTT
11006309 TTTTTTTTTGAAA
1 TTTTTTTTTG-AA
11006322 TTTGGTTTTTTGAA
1 TTT--TTTTTTGAA
11006336 TTTTTTTTTGAA
1 TTTTTTTTTGAA
11006348 TTTTTTT
1 TTTTTTT
11006355 GAATTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 16 0.52
13 3 0.10
14 5 0.16
15 7 0.23
ACGTcount: A:0.15, C:0.00, G:0.11, T:0.74
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:11006371 original size:10 final size:10
Alignment explanation
Indices: 11006327--11006360 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
11006317 TGAAATTTGG
11006327 TTTTTTGAATTT
1 TTTTTTGAA--T
11006339 TTTTTTGAAT
1 TTTTTTGAAT
11006349 TTTTTTGAAT
1 TTTTTTGAAT
11006359 TT
1 TT
11006361 AAATTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.59
12 9 0.41
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (10 bp):
TTTTTTGAAT
Found at i:11008128 original size:57 final size:57
Alignment explanation
Indices: 11008031--11008145 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
11008021 TTCGATTATA
11008031 CGCTATTTTATTCAAGGTCTACCTAAATCTCTTTTGTAAAGGTTTAACTTAAGTTTT
1 CGCTATTTTATTCAAGGTCTACCTAAATCTCTTTTGTAAAGGTTTAACTTAAGTTTT
11008088 CGCTATTTTATTCAAGGTCTACCTAAATCTCCTTTT-TAAAGGTTTAACTTAAGTTTT
1 CGCTATTTTATTCAAGGTCTACCTAAATCT-CTTTTGTAAAGGTTTAACTTAAGTTTT
11008145 C
1 C
11008146 AATTTAATCT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
57 52 0.91
58 5 0.09
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.45
Consensus pattern (57 bp):
CGCTATTTTATTCAAGGTCTACCTAAATCTCTTTTGTAAAGGTTTAACTTAAGTTTT
Found at i:11011108 original size:145 final size:145
Alignment explanation
Indices: 11010930--11011228 Score: 433
Period size: 145 Copynumber: 2.1 Consensus size: 145
11010920 TATGTGGATA
* * *
11010930 TGTTGAACATAAACCGTTAGAACCGATCTTACCGACTGGTCGTTAGCACCGTGTGTTTGAGGAGG
1 TGTTGAACATAAACCATTAGAACCGATCTTACCGACTGGTCGTTAGCACCGTGAGTCTGAGGAGG
* *
11010995 ACCTCTC-AGTGGTCGATG-AGCTGTCGTCGCATGGTCCAATTGCAAATACAGATATGTTATTCG
66 ACCTCTCGA-TGGT-GATGAAGCTGTCGTCGCATGGTCCAACTGCAAACACAGATATGTTATTCG
*
11011058 ATAATCACATATGGAAT
129 ATAATCACATATGAAAT
* * * *
11011075 TGTTGAACATAAACCATTATAACCG-TCCTTACCGGCTTGTCGTTAGCACTGTGAGTCTGAGGAG
1 TGTTGAACATAAACCATTAGAACCGAT-CTTACCGACTGGTCGTTAGCACCGTGAGTCTGAGGAG
* * *
11011139 GACTTCTCGATGGTTATGAAGCTGTCGTCGCATGGTCCAACTGCAAACATAGATATGTTATTCGA
65 GACCTCTCGATGGTGATGAAGCTGTCGTCGCATGGTCCAACTGCAAACACAGATATGTTATTCGA
11011204 TAATCACATATGAAAT
130 TAATCACATATGAAAT
11011220 TGTTGAACA
1 TGTTGAACA
11011229 CAATATGTTA
Statistics
Matches: 138, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
144 4 0.03
145 133 0.96
146 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (145 bp):
TGTTGAACATAAACCATTAGAACCGATCTTACCGACTGGTCGTTAGCACCGTGAGTCTGAGGAGG
ACCTCTCGATGGTGATGAAGCTGTCGTCGCATGGTCCAACTGCAAACACAGATATGTTATTCGAT
AATCACATATGAAAT
Found at i:11012687 original size:31 final size:31
Alignment explanation
Indices: 11012649--11012820 Score: 256
Period size: 31 Copynumber: 5.5 Consensus size: 31
11012639 GTTAACCCAT
11012649 AATGTTGTAACACGCCATGCATATAACGTAA
1 AATGTTGTAACACGCCATGCATATAACGTAA
*
11012680 AATGTTGTAACACGCCATGCATATAATGTAA
1 AATGTTGTAACACGCCATGCATATAACGTAA
*
11012711 AATGTTGTAACACGCCATGCATATAACATAA
1 AATGTTGTAACACGCCATGCATATAACGTAA
* * *
11012742 AATGTTGTAACATGCCATGTATATAATGTAA
1 AATGTTGTAACACGCCATGCATATAACGTAA
* * *
11012773 AATGTTGTAACACACCATGCGTATCAA-GTCA
1 AATGTTGTAACACGCCATGCATAT-AACGTAA
11012804 AATGTTGTAACACGCCA
1 AATGTTGTAACACGCCA
11012821 AAGCTGACAT
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
31 125 0.98
32 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (31 bp):
AATGTTGTAACACGCCATGCATATAACGTAA
Found at i:11013457 original size:23 final size:23
Alignment explanation
Indices: 11013425--11013468 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
11013415 TTTTCCCTTT
*
11013425 TTCAAACCATGTCGTGTCACATG
1 TTCAAACCATGCCGTGTCACATG
*
11013448 TTCAAGCCATGCCGTGTCACA
1 TTCAAACCATGCCGTGTCACA
11013469 CACTCTAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (23 bp):
TTCAAACCATGCCGTGTCACATG
Done.