Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold47
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: 2157611
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 149227 characters in sequence are not A, C, G, or T
File 8 of 15
Found at i:1000452 original size:21 final size:22
Alignment explanation
Indices: 1000426--1000476 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1000416 TTTTTTTAAA
1000426 AAAAGAATTC-AAAGAAAACTT
1 AAAAGAATTCGAAAGAAAACTT
* * *
1000447 AAAAGAA-ACGACAGCAAACTT
1 AAAAGAATTCGAAAGAAAACTT
1000468 AAAAGAATT
1 AAAAGAATT
1000477 ATTAAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.61, C:0.12, G:0.12, T:0.16
Consensus pattern (22 bp):
AAAAGAATTCGAAAGAAAACTT
Found at i:1000845 original size:28 final size:28
Alignment explanation
Indices: 1000812--1000865 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1000802 TTATATTATT
*
1000812 AAATTAAATAT-ATATTTTTATTAATTAC
1 AAATTAAATATAATATTTAT-TTAATTAC
*
1000840 AAATTACATATAATATTTATTTAATT
1 AAATTAAATATAATATTTATTTAATT
1000866 TTAAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (28 bp):
AAATTAAATATAATATTTATTTAATTAC
Found at i:1000871 original size:28 final size:28
Alignment explanation
Indices: 1000801--1000875 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 28
1000791 TAAATTAAAA
*
1000801 ATTATATTATTAAATTAAATATATATTTTT
1 ATTA-ATT-TTAAATTAAATATATATTTAT
** *
1000831 ATTAATTACAAATTACATATAATATTTAT
1 ATTAATTTTAAATTAAATAT-ATATTTAT
1000860 -TTAATTTTAAA-TAAAT
1 ATTAATTTTAAATTAAAT
1000876 TTTTAATTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 4 0.11
28 19 0.51
29 10 0.27
30 4 0.11
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTAATTTTAAATTAAATATATATTTAT
Found at i:1000910 original size:18 final size:18
Alignment explanation
Indices: 1000866--1000911 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
1000856 TTATTTAATT
1000866 TTAAATAAATT--TTTAA
1 TTAAATAAATTAGTTTAA
*
1000882 TTAAATCAATTAGTTTAA
1 TTAAATAAATTAGTTTAA
*
1000900 TTAATTAAATTA
1 TTAAATAAATTA
1000912 ATTAAATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.40
18 15 0.60
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
TTAAATAAATTAGTTTAA
Found at i:1001705 original size:20 final size:20
Alignment explanation
Indices: 1001682--1001741 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 20
1001672 AAAATAAAAA
1001682 ATAATTAAAATATATATAAT
1 ATAATTAAAATATATATAAT
* *
1001702 ATAAAT-ATA-ATATA-AAT
1 ATAATTAAAATATATATAAT
* *
1001719 AT-ATTAAAATTTATATAGT
1 ATAATTAAAATATATATAAT
1001738 ATAA
1 ATAA
1001742 ATTATTAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
16 2 0.07
17 7 0.23
18 9 0.30
19 6 0.20
20 6 0.20
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
ATAATTAAAATATATATAAT
Found at i:1001709 original size:11 final size:11
Alignment explanation
Indices: 1001695--1001781 Score: 58
Period size: 11 Copynumber: 8.2 Consensus size: 11
1001685 ATTAAAATAT
1001695 ATATAATATAA
1 ATATAATATAA
1001706 ATATAATATAA
1 ATATAATATAA
*
1001717 ATATATTA-AA
1 ATATAATATAA
*
1001727 AT-TTATAT-A
1 ATATAATATAA
* *
1001736 GTATAAATTATTA
1 ATAT-AA-TATAA
*
1001749 ATATATTA-AA
1 ATATAATATAA
*
1001759 AT-TTATATAA
1 ATATAATATAA
*
1001769 ATATAAAATAA
1 ATATAATATAA
1001780 AT
1 AT
1001782 TAAATATGAT
Statistics
Matches: 57, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
9 8 0.14
10 12 0.21
11 29 0.51
12 4 0.07
13 4 0.07
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1001733 original size:18 final size:17
Alignment explanation
Indices: 1001712--1001777 Score: 52
Period size: 17 Copynumber: 3.9 Consensus size: 17
1001702 ATAAATATAA
1001712 TATAAATATATTAAAATT
1 TATAAATATA-TAAAATT
1001730 TAT--ATAGTAT-AAA-T
1 TATAAATA-TATAAAATT
*
1001744 TATTAATATATTAAAATT
1 TATAAATATA-TAAAATT
1001762 TATATAA-ATATAAAAT
1 TATA-AATATATAAAAT
1001778 AAATTAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 15
0.71 0.02 0.27
Matches are distributed among these distances:
14 4 0.10
15 5 0.12
16 8 0.20
17 11 0.28
18 10 0.25
19 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TATAAATATATAAAATT
Found at i:1002073 original size:22 final size:22
Alignment explanation
Indices: 1002054--1002095 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1002044 AAAAATAATT
*
1002054 TTATTTAAAT-TTAATTATAAA
1 TTATATAAATATTAATTATAAA
1002075 TTATATAAATATTAATT-TAAA
1 TTATATAAATATTAATTATAAA
1002096 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTATATAAATATTAATTATAAA
Found at i:1002307 original size:25 final size:24
Alignment explanation
Indices: 1002248--1002310 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
1002238 TTAAATTATA
*
1002248 ATAATAAATA-TATTTTTAATTAT
1 ATAATAAATATTATTTTTAATAAT
* ** *
1002271 ATCATATTTATTATTTTTTATAAAT
1 ATAATAAATATTATTTTTAAT-AAT
1002296 ATAATAAATATTATT
1 ATAATAAATATTATT
1002311 ATAATTAATA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
23 7 0.23
24 9 0.30
25 14 0.47
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
ATAATAAATATTATTTTTAATAAT
Found at i:1002560 original size:31 final size:35
Alignment explanation
Indices: 1002518--1002591 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 35
1002508 TACGAATTTT
1002518 TTAAAAATTTA-TTTTATTATT-T-ATTATA-TT-A
1 TTAAAAATTTATTTTTA-TATTCTAATTATATTTAA
*
1002549 TTAAAATTTTATTTTTATATTCTAATTATATTTAA
1 TTAAAAATTTATTTTTATATTCTAATTATATTTAA
1002584 TTAAAAAT
1 TTAAAAAT
1002592 ATAGGCTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
31 14 0.39
32 6 0.17
33 6 0.17
34 2 0.06
35 8 0.22
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (35 bp):
TTAAAAATTTATTTTTATATTCTAATTATATTTAA
Found at i:1003333 original size:15 final size:16
Alignment explanation
Indices: 1003310--1003343 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1003300 TATTTAGCTA
1003310 TTTA-CTTTTATTTTT
1 TTTATCTTTTATTTTT
*
1003325 TTTATTTTTTATTTTT
1 TTTATCTTTTATTTTT
1003341 TTT
1 TTT
1003344 GGCCAGAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTATCTTTTATTTTT
Found at i:1003850 original size:18 final size:18
Alignment explanation
Indices: 1003829--1003864 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1003819 ATTTAGTTTG
1003829 TAAATTCTTTTTATTATT
1 TAAATTCTTTTTATTATT
* *
1003847 TAAATTTTTTTTGTTATT
1 TAAATTCTTTTTATTATT
1003865 AATAGTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (18 bp):
TAAATTCTTTTTATTATT
Found at i:1003908 original size:22 final size:21
Alignment explanation
Indices: 1003882--1003939 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
1003872 ATATATTTTT
1003882 ATAATTATATTTAAATAAAAA
1 ATAATTATATTTAAATAAAAA
* *
1003903 ATTAATT-TTTATTAAATAAATA
1 A-TAATTATAT-TTAAATAAAAA
*
1003925 ATAATTTAAATTTAA
1 ATAA-TTATATTTAA
1003940 TTTAATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
21 6 0.21
22 22 0.76
23 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAATTATATTTAAATAAAAA
Found at i:1004679 original size:3 final size:3
Alignment explanation
Indices: 1004671--1004712 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1004661 TTATCAGCAG
1004671 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1004713 GAAAACATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1005506 original size:33 final size:32
Alignment explanation
Indices: 1005432--1005508 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
1005422 AATATATGAT
*
1005432 ACAATATAAA-TA-TATATTTTAAAATTTATA
1 ACAATATAAATTATTATATATTAAAATTTATA
*
1005462 A-AATATGAATTATTAATATATTAAAATTTA-A
1 ACAATATAAATTATT-ATATATTAAAATTTATA
1005493 ATCAATATAAATTATT
1 A-CAATATAAATTATT
1005509 TTAAATATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 7 0.18
30 3 0.08
31 3 0.08
32 14 0.36
33 12 0.31
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (32 bp):
ACAATATAAATTATTATATATTAAAATTTATA
Found at i:1006234 original size:19 final size:19
Alignment explanation
Indices: 1006191--1006237 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1006181 ACAATTCAAA
* *
1006191 TTAAATCAAATTTTATTTT
1 TTAAATTAATTTTTATTTT
*
1006210 AT-AATTAATTTTTATTTT
1 TTAAATTAATTTTTATTTT
1006228 TTAAATTAAT
1 TTAAATTAAT
1006238 AAAAAATCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAAATTAATTTTTATTTT
Found at i:1006634 original size:34 final size:35
Alignment explanation
Indices: 1006566--1006658 Score: 104
Period size: 34 Copynumber: 2.7 Consensus size: 35
1006556 ATTTTATTTT
* *
1006566 TTTAATTTATTTATTAAAAATTTAATATTTAATAA
1 TTTAATTTATTTATTAAAAATTTAAAATTAAATAA
*
1006601 TTTAATTT-TTTATT-AAAGTTTAAAATATAAATAA
1 TTTAATTTATTTATTAAAAATTTAAAAT-TAAATAA
* *
1006635 TTTAATATATTT-TT-AATATTTAAA
1 TTTAATTTATTTATTAAAAATTTAAA
1006659 CTATAATATT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
33 10 0.20
34 29 0.58
35 11 0.22
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (35 bp):
TTTAATTTATTTATTAAAAATTTAAAATTAAATAA
Found at i:1006664 original size:34 final size:34
Alignment explanation
Indices: 1006566--1006677 Score: 99
Period size: 34 Copynumber: 3.3 Consensus size: 34
1006556 ATTTTATTTT
* * *
1006566 TTTAATTTATTTATTAAAAATTTAATAT-TTAATAA
1 TTTAA-TTATTTATT-AAAGTTTAAAATATAAATAA
*
1006601 TTTAATTTTTTATTAAAGTTTAAAATATAAATAA
1 TTTAATTATTTATTAAAGTTTAAAATATAAATAA
*
1006635 TTTAATATATTT-TTAATA-TTTAAACTAT-AAT-A
1 TTTAAT-TATTTATTAA-AGTTTAAAATATAAATAA
1006667 TTATAATTATT
1 TT-TAATTATT
1006678 AAATCTTTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
32 7 0.10
33 17 0.25
34 33 0.49
35 10 0.15
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (34 bp):
TTTAATTATTTATTAAAGTTTAAAATATAAATAA
Found at i:1007161 original size:14 final size:14
Alignment explanation
Indices: 1007117--1007161 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
1007107 AACATATGAT
* *
1007117 TATATATATATATA
1 TATATGTATATGTA
*
1007131 TACATGTATATGTA
1 TATATGTATATGTA
1007145 TATATGTATATGTA
1 TATATGTATATGTA
1007159 TAT
1 TAT
1007162 GCTGTTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (14 bp):
TATATGTATATGTA
Found at i:1008752 original size:2 final size:2
Alignment explanation
Indices: 1008745--1008779 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1008735 GGATCAAATT
1008745 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 T
1008780 GTGCAGATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1012957 original size:18 final size:19
Alignment explanation
Indices: 1012914--1012958 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1012904 ATATATTAGA
* *
1012914 ATATTAAAATCTTATTTTT
1 ATATTAAAATCTTATATAT
1012933 ATATTAAAAT-TTATATAT
1 ATATTAAAATCTTATATAT
*
1012951 ATTTTAAA
1 ATATTAAA
1012959 TAAATTTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTAAAATCTTATATAT
Found at i:1013004 original size:23 final size:23
Alignment explanation
Indices: 1012970--1013022 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
1012960 AAATTTAAGT
**
1012970 AAATAA-ATATTTTTATTAATTTA
1 AAATAATATATTTAAATTAA-TTA
1012993 AAATAATA-ATTTAAATTAATTA
1 AAATAATATATTTAAATTAATTA
*
1013015 AGATAATA
1 AAATAATA
1013023 CAAAATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 10 0.38
23 15 0.58
24 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AAATAATATATTTAAATTAATTA
Found at i:1013598 original size:36 final size:36
Alignment explanation
Indices: 1013558--1013638 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
1013548 ATCTAATTCG
1013558 AACTTTAAAAATAAAATTTAATCGAACTAAACTTCA
1 AACTTTAAAAATAAAATTTAATCGAACTAAACTTCA
** * * * *
1013594 AACTTTAAATTTTAATTTTTATCGAACTAAACTTTA
1 AACTTTAAAAATAAAATTTAATCGAACTAAACTTCA
*
1013630 AATTTTAAA
1 AACTTTAAA
1013639 TTTCAATTCG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (36 bp):
AACTTTAAAAATAAAATTTAATCGAACTAAACTTCA
Found at i:1013639 original size:36 final size:36
Alignment explanation
Indices: 1013578--1013646 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
1013568 ATAAAATTTA
*
1013578 ATCGAACTAAACTTCAAACTTTAAATTTTAATTTTT
1 ATCGAACTAAACTTCAAACTTTAAATTTCAATTTTT
* *
1013614 ATCGAACTAAACTTTAAATTTTAAATTTCAATT
1 ATCGAACTAAACTTCAAACTTTAAATTTCAATT
1013647 CGTGCATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.43
Consensus pattern (36 bp):
ATCGAACTAAACTTCAAACTTTAAATTTCAATTTTT
Found at i:1017201 original size:32 final size:33
Alignment explanation
Indices: 1017099--1017205 Score: 89
Period size: 32 Copynumber: 3.3 Consensus size: 33
1017089 TTTATAAGAT
* * *
1017099 ATTTTAAAGTTT-AAGTTATTTT-ATTTTAAAGTC
1 ATTTTAAATTTTGAA-TTATTTTAAATTTGAA-TC
* *
1017132 A-TTTCAATTTTGAATTATTTTAAATTTGTATC
1 ATTTTAAATTTTGAATTATTTTAAATTTGAATC
*
1017164 ATTTTAAATTTT-AATTA-TTTAGATTTTGAATC
1 ATTTTAAATTTTGAATTATTTTA-AATTTGAATC
*
1017196 TTTTTAAATT
1 ATTTTAAATT
1017206 CAAGTTGATC
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
31 4 0.07
32 40 0.66
33 17 0.28
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (33 bp):
ATTTTAAATTTTGAATTATTTTAAATTTGAATC
Found at i:1017394 original size:17 final size:16
Alignment explanation
Indices: 1017359--1017393 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1017349 TTTGATTCAA
*
1017359 TTTAGATTCAATTTAT
1 TTTAGATTCAAATTAT
*
1017375 TTTAGATTTAAATTAT
1 TTTAGATTCAAATTAT
1017391 TTT
1 TTT
1017394 TTAATTGAGT
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:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (16 bp):
TTTAGATTCAAATTAT
Found at i:1018277 original size:2 final size:2
Alignment explanation
Indices: 1018270--1018296 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1018260 ATAATGTATG
1018270 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1018297 TTCACTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1022383 original size:2 final size:2
Alignment explanation
Indices: 1022378--1022412 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1022368 ATATTGACGG
1022378 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 T
1022413 GTCATACAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1022919 original size:30 final size:28
Alignment explanation
Indices: 1022885--1022944 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 28
1022875 ACTCGTTCGG
* *
1022885 TTCAAATTAAATTAGTTATAATATTTTTTA
1 TTCAAATTAAATTAATT-TAA-ATTTATTA
*
1022915 TTCAAGTTAAATTAATTTAAATTTATTA
1 TTCAAATTAAATTAATTTAAATTTATTA
1022943 TT
1 TT
1022945 AGATATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 9 0.33
29 3 0.11
30 15 0.56
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (28 bp):
TTCAAATTAAATTAATTTAAATTTATTA
Found at i:1034599 original size:2 final size:2
Alignment explanation
Indices: 1034592--1034629 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1034582 TCTTGCTGTA
1034592 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
1034630 CAAAGAGGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1035134 original size:14 final size:14
Alignment explanation
Indices: 1035115--1035148 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1035105 TGTCCATTTT
*
1035115 ATAAAATATTGATA
1 ATAAAATATTAATA
*
1035129 ATAAAATATTAATT
1 ATAAAATATTAATA
1035143 ATAAAA
1 ATAAAA
1035149 AAATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (14 bp):
ATAAAATATTAATA
Found at i:1037940 original size:3 final size:3
Alignment explanation
Indices: 1037934--1037965 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1037924 AGGTGTTGTT
1037934 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1037966 TTTCTATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1039526 original size:2 final size:2
Alignment explanation
Indices: 1039519--1039556 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1039509 TTAAAGGCTA
1039519 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
1039557 TTTGATAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1043375 original size:36 final size:36
Alignment explanation
Indices: 1043301--1043377 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 36
1043291 TAAATTAAGT
*
1043301 TATT-TATATATAAATAAAATAATAAAAATAGATAA
1 TATTATATATATAAATAAAAAAATAAAAATAGATAA
* *
1043336 TATTATATATTATAAA-AAATAAAATATAAATA-ATGA
1 TATTATATA-TATAAATAAA-AAAATAAAAATAGATAA
1043372 TATTAT
1 TATTAT
1043378 TAAATATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 4 0.11
36 16 0.44
37 16 0.44
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (36 bp):
TATTATATATATAAATAAAAAAATAAAAATAGATAA
Found at i:1043379 original size:39 final size:41
Alignment explanation
Indices: 1043312--1043390 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 41
1043302 ATTTATATAT
1043312 AAATAAAATAATAAAAATAGATAATATT-ATATATTATAAA
1 AAATAAAATAATAAAAATAGATAATATTAATATATTATAAA
*
1043352 AAATAAAAT-ATAAATAAT-GATATTATTAAATATATTATA
1 AAATAAAATAATAAA-AATAGATAATATT-AATATATTATA
1043391 TTTAAACTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
39 13 0.37
40 12 0.34
41 10 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (41 bp):
AAATAAAATAATAAAAATAGATAATATTAATATATTATAAA
Found at i:1043486 original size:15 final size:15
Alignment explanation
Indices: 1043468--1043502 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1043458 TATTAATTAA
1043468 TTAAATTT-ATTTTAT
1 TTAAATTTGA-TTTAT
1043483 TTAAATTTGATTTAT
1 TTAAATTTGATTTAT
1043498 TTAAA
1 TTAAA
1043503 AATAAACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 18 0.95
16 1 0.05
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TTAAATTTGATTTAT
Found at i:1043779 original size:14 final size:14
Alignment explanation
Indices: 1043738--1043785 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1043728 AAAATATTTT
*
1043738 TATAAAACTTAATA
1 TATAAAACTAAATA
*
1043752 TATATAAATTAAATA
1 TATA-AAACTAAATA
*
1043767 TATAAAACCAAATA
1 TATAAAACTAAATA
*
1043781 AATAA
1 TATAA
1043786 TTCGAGTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (14 bp):
TATAAAACTAAATA
Found at i:1047333 original size:17 final size:17
Alignment explanation
Indices: 1047313--1047352 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1047303 ATAAAAAGGG
1047313 AAAAAAAAAAAAAGAAC
1 AAAAAAAAAAAAAGAAC
** *
1047330 AAAAAAATCAAAAGAAG
1 AAAAAAAAAAAAAGAAC
1047347 AAAAAA
1 AAAAAA
1047353 GGCAAAACTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.85, C:0.05, G:0.07, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAAAAAGAAC
Found at i:1048370 original size:2 final size:2
Alignment explanation
Indices: 1048363--1048412 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1048353 TCTGAAACAC
1048363 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1048405 GA GA GA GA
1 GA GA GA GA
1048413 TCTTAGAGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1051193 original size:16 final size:17
Alignment explanation
Indices: 1051169--1051214 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1051159 AATGAACATA
*
1051169 AACTCAAATTTAAAATT
1 AACTTAAATTTAAAATT
* *
1051186 -ACTTAAA-TTCAATTT
1 AACTTAAATTTAAAATT
1051201 AACTTAAATTTAAA
1 AACTTAAATTTAAA
1051215 TAATTTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
15 6 0.26
16 13 0.57
17 4 0.17
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (17 bp):
AACTTAAATTTAAAATT
Found at i:1058781 original size:12 final size:12
Alignment explanation
Indices: 1058764--1058789 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1058754 TCATTTGCTT
1058764 CATGAAAGCATG
1 CATGAAAGCATG
1058776 CATGAAAGCATG
1 CATGAAAGCATG
1058788 CA
1 CA
1058790 ATGTTTCTTC
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:0.42, C:0.19, G:0.23, T:0.15
Consensus pattern (12 bp):
CATGAAAGCATG
Found at i:1058982 original size:23 final size:23
Alignment explanation
Indices: 1058956--1058999 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1058946 TTTTGTTTTC
*
1058956 TTTCTTT-TTTTTTGAATTTTTGA
1 TTTCTTTAATTTTT-AATTTTTGA
1058979 TTTCTTTAATTTTTAATTTTT
1 TTTCTTTAATTTTTAATTTTT
1059000 TTGGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.75
Consensus pattern (23 bp):
TTTCTTTAATTTTTAATTTTTGA
Found at i:1059653 original size:85 final size:85
Alignment explanation
Indices: 1059553--1059745 Score: 217
Period size: 85 Copynumber: 2.3 Consensus size: 85
1059543 AATATGGAAA
* * * * * *
1059553 AGTCTCCAGGATCAAAGCTAACAGACTGACTAAAGGGTAAAAAAAGTCTCCAAGGTTAAAGTCGA
1 AGTCTCTAGGGTCAAAGCCAACAGACAGACTAAAGGGT-AAAAAAGTCTCCAAGGTCAAAGCCGA
* **
1059618 CAAGCAGA-TTTATATGAGGC
65 CAAGCAGACTTTAGACAAGGC
* ** * *
1059638 AGTCTCTAGGGTCAAAGCCAACAGGCAGACTGGAGGGTAAAAAAGTCTCTAGGGTCAAAGCCGAC
1 AGTCTCTAGGGTCAAAGCCAACAGACAGACTAAAGGGTAAAAAAGTCTCCAAGGTCAAAGCCGAC
* *
1059703 AGGTAGACTTTAGACAAGGC
66 AAGCAGACTTTAGACAAGGC
*
1059723 AGTCTTTAGGGTCAAAGCCAACA
1 AGTCTCTAGGGTCAAAGCCAACA
1059746 ACCAGATTGA
Statistics
Matches: 90, Mismatches: 17, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
84 28 0.31
85 62 0.69
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (85 bp):
AGTCTCTAGGGTCAAAGCCAACAGACAGACTAAAGGGTAAAAAAGTCTCCAAGGTCAAAGCCGAC
AAGCAGACTTTAGACAAGGC
Found at i:1059740 original size:42 final size:43
Alignment explanation
Indices: 1059638--1060467 Score: 245
Period size: 42 Copynumber: 19.0 Consensus size: 43
1059628 TATATGAGGC
* * * * *
1059638 AGTCTCTAGGGTCAAAGCCAACAGGCAGACTGGAGGGTAA-AAA
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTGA-GATAAGGAA
* * *
1059681 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTTAGACAAGG-C
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTGAGATAAGGAA
* * *** * *
1059723 AGTCTTTAGGGTCAAAGCCAACAACCAGA-TTGAGGTTAGGAA
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTGAGATAAGGAA
* * ** *
1059765 AGTCTCTAGGGTCAAAGTCGATAGACAGAC-TGAGGGT-AGGAA
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTGA-GATAAGGAA
* * * * *
1059807 AGTCTCCAGGGTCAAAGCTGACAGGTGGACTTTAGATAAGG-C
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTGAGATAAGGAA
* * * * ** *
1059849 AGTCTTTAGGGTCAAAGCCGATAGGTAGACTAAGGGGCAAGAAA
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACT-TGAGATAAGGAA
** *
1059893 AGTCTCTAGGGTCAAAGCCGACAGACAGAC-TGAAGGGT-AGGAA
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTG-A-GATAAGGAA
* * ** **
1059936 AGTCTCCAAGGTC-AAGCCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGGTAAGAAA
1 AGTCTCTAGGGTCAAAGCCGAC-AGGT---A---GACTTG-AGA-TAA---G---G-AA
* * ** * *
1059994 AGTCTCTAAGGTCAAAGCCAACAAATAGACTTTAGATAAGG-T
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTGAGATAAGGAA
* * * ** *
1060036 AGTCTCTAGGGTCAAAGTCGACAAGCAGAC-TGAGGGGCAAGAAA
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTGA--GATAAGGAA
* * * *
1060080 AGTCTCCAGGGTCAAAGCCGACATGTAGACTTTAGATAAGGCA
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTGAGATAAGGAA
* * * * ** * *
1060123 A-TCTCCAAGGTCAAAGCCTATAGACAGA-TTAAAGGGT-AGGAAA
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTT-GA-GATAAGG-AA
* * * *
1060166 AGTCT-TCAGAGTCAAAGCCGACAGGCATAC-TGAAGGGT-AGGAA
1 AGTCTCT-AGGGTCAAAGCCGACAGGTAGACTTG-A-GATAAGGAA
* * * * ** * * *
1060209 AGTTTCCAGGGTCAAAACTGACAGACAAACTTTAGATAAGG-C
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTGAGATAAGGAA
* * ** *
1060251 AGT-TTTCAGGATCAAAGCCGACAGACAGAC-TGAAGGGT-AGGAA
1 AGTCTCT-AGGGTCAAAGCCGACAGGTAGACTTG-A-GATAAGGAA
* * * * * *
1060294 AGTCTCTAAGGTCAAAGCTGACAAGCAGACTTTAGATAAGG-T
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTGAGATAAGGAA
* * * * *
1060336 AGTCTCCAAGGTCAAAGCCAACAGGCAGAC-TGAAAGGT-AGGAA
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTG--AGATAAGGAA
* *
1060379 AGTCTCCAGGGTCAAAGTCGACAGGTAGAC-TGAAGGAT-AGGAA
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTG-A-GATAAGGAA
* * * *
1060422 AGTCTCTAAGGTCAAAGTCGACAGGCAGACTTTAGATAAGGCAA
1 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTGAGATAAGG-AA
1060466 AG
1 AG
1060468 CCGACATGCA
Statistics
Matches: 579, Mismatches: 152, Indels: 111
0.69 0.18 0.13
Matches are distributed among these distances:
41 14 0.02
42 230 0.40
43 197 0.34
44 92 0.16
45 2 0.00
46 1 0.00
47 1 0.00
49 4 0.01
50 6 0.01
51 4 0.01
52 3 0.01
54 1 0.00
55 1 0.00
57 1 0.00
58 16 0.03
59 6 0.01
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (43 bp):
AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTGAGATAAGGAA
Found at i:1059810 original size:126 final size:128
Alignment explanation
Indices: 1059638--1059950 Score: 405
Period size: 126 Copynumber: 2.4 Consensus size: 128
1059628 TATATGAGGC
* * ** *
1059638 AGTCTCTAGGGTCAAAGCCAACAGGCAGACTGGAGGGTAAAAAAGTCTCTAGGGTCAAAGCCGAC
1 AGTCTCTAGGGTCAAAGCCGACAGACAGACT-GAGGGTAGGAAAGTCTCCAGGGTCAAAGCCGAC
* ** *
1059703 AGGTAGACTTTAGACAAGGCAGTCTTTAGGGTCAAAGCCAACAACCAGA-T-TGAGGTTAGGAA
65 AGGTAGACTTTAGACAAGGCAGTCTTTAGGGTCAAAGCCAACAACCAGACTAAGAGGCAAGAAA
* * *
1059765 AGTCTCTAGGGTCAAAGTCGATAGACAGACTGAGGGTAGGAAAGTCTCCAGGGTCAAAGCTGACA
1 AGTCTCTAGGGTCAAAGCCGACAGACAGACTGAGGGTAGGAAAGTCTCCAGGGTCAAAGCCGACA
* * * * *** *
1059830 GGTGGACTTTAGATAAGGCAGTCTTTAGGGTCAAAGCCGATAGGTAGACTAAGGGGCAAGAAA
66 GGTAGACTTTAGACAAGGCAGTCTTTAGGGTCAAAGCCAACAACCAGACTAAGAGGCAAGAAA
*
1059893 AGTCTCTAGGGTCAAAGCCGACAGACAGACTGAAGGGTAGGAAAGTCTCCAAGGTCAA
1 AGTCTCTAGGGTCAAAGCCGACAGACAGACTG-AGGGTAGGAAAGTCTCCAGGGTCAA
1059951 GCCTCCAAGG
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
126 71 0.44
127 28 0.17
128 37 0.23
129 24 0.15
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.18
Consensus pattern (128 bp):
AGTCTCTAGGGTCAAAGCCGACAGACAGACTGAGGGTAGGAAAGTCTCCAGGGTCAAAGCCGACA
GGTAGACTTTAGACAAGGCAGTCTTTAGGGTCAAAGCCAACAACCAGACTAAGAGGCAAGAAA
Found at i:1060232 original size:43 final size:43
Alignment explanation
Indices: 1059953--1060452 Score: 298
Period size: 43 Copynumber: 11.7 Consensus size: 43
1059943 AAGGTCAAGC
* *
1059953 CTCCAAGGTCAAAGCCGACAGGCAGACT-AAGGGGTAAGAAAAGT
1 CTCCAGGGTCAAAGCCGACAGGCAGACTGAA-GGGT-AGGAAAGT
* * * *** ** * *
1059997 CTCTAAGGTCAAAGCCAACAAATAGACTTTA-GATAAGG-TAGT
1 CTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGGT-AGGAAAGT
* * * * * *
1060039 CTCTAGGGTCAAAGTCGACAAGCAGACTGAGGGGCAAGAAAAGT
1 CTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGG-TAGGAAAGT
* * ** * *
1060083 CTCCAGGGTCAAAGCCGACATGTAGACTTTA-GATAAGGCAA-T
1 CTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGGT-AGGAAAGT
* * * * * *
1060125 CTCCAAGGTCAAAGCCTATAGACAGATTAAAGGGTAGGAAAAGT
1 CTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGGTAGG-AAAGT
* * *
1060169 CTTCAGAGTCAAAGCCGACAGGCATACTGAAGGGTAGGAAAGT
1 CTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGGTAGGAAAGT
* * * * * ** * *
1060212 TTCCAGGGTCAAAACTGACAGACAAACTTTA-GATAAGG-CAGT
1 CTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGGT-AGGAAAGT
* * * *
1060254 TTTCAGGATCAAAGCCGACAGACAGACTGAAGGGTAGGAAAGT
1 CTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGGTAGGAAAGT
* * * * ** * *
1060297 CTCTAAGGTCAAAGCTGACAAGCAGACTTTA-GATAAGG-TAGT
1 CTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGGT-AGGAAAGT
* * *
1060339 CTCCAAGGTCAAAGCCAACAGGCAGACTGAAAGGTAGGAAAGT
1 CTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGGTAGGAAAGT
* * *
1060382 CTCCAGGGTCAAAGTCGACAGGTAGACTGAAGGATAGGAAAGT
1 CTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGGTAGGAAAGT
* * *
1060425 CTCTAAGGTCAAAGTCGACAGGCAGACT
1 CTCCAGGGTCAAAGCCGACAGGCAGACT
1060453 TTAGATAAGG
Statistics
Matches: 341, Mismatches: 101, Indels: 29
0.72 0.21 0.06
Matches are distributed among these distances:
42 117 0.34
43 143 0.42
44 80 0.23
45 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.18
Consensus pattern (43 bp):
CTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGGTAGGAAAGT
Found at i:1060241 original size:129 final size:129
Alignment explanation
Indices: 1060036--1060452 Score: 335
Period size: 128 Copynumber: 3.2 Consensus size: 129
1060026 TAGATAAGGT
* * * *
1060036 AGTCTCTAGGGTCAAAGTCGACAAGCAGACTGAGGGGCAAGAAAAGTCTCCAGGGTCAAAGCCGA
1 AGTCTCTAAGGTCAAAGCCGACAAGCAGACTGAAGGGCAAGAAAAGTCTCCAGGGTCAAAACCGA
* * * * *
1060101 CATGTAGACTTTAGATAAGGCAATCTCCAAGG-TCAAAGCCTATAGACAGATTAAAGGGTAGGAA
66 CATGCAAACTTTAGATAAGGCAATCTCC-AGGATCAAAGCCGACAGACAGACTAAAGGGTAGG-A
1060165 A
129 A
* * * * * * *
1060166 AGTCT-TCAGAGTCAAAGCCGACAGGCATACTGAAGGG-TAGGAAAGTTTCCAGGGTCAAAACTG
1 AGTCTCTAAG-GTCAAAGCCGACAAGCAGACTGAAGGGCAAGAAAAGTCTCCAGGGTCAAAACCG
* * * *
1060229 ACA-GACAAACTTTAGATAAGGCAGTTTTCAGGATCAAAGCCGACAGACAGACTGAAGGGTAGGA
65 ACATG-CAAACTTTAGATAAGGCAATCTCCAGGATCAAAGCCGACAGACAGACTAAAGGGTAGGA
1060293 A
129 A
* ** ** ** * * *
1060294 AGTCTCTAAGGTCAAAGCTGACAAGCAGACTTTA-GATAAG-GTAGTCTCCAAGGTCAAAGCCAA
1 AGTCTCTAAGGTCAAAGCCGACAAGCAGACTGAAGGGCAAGAAAAGTCTCCAGGGTCAAAACCGA
* * ** * * * * ** * *
1060357 CAGGCAGACTGAAAGGT-AGGAAAGTCTCCAGGGTCAAAGTCGACAGGTAGACTGAAGGATAGGA
66 CATGCAAACT-TTAGATAAGGCAA-TCTCCAGGATCAAAGCCGACAGACAGACTAAAGGGTAGGA
1060421 A
129 A
* *
1060422 AGTCTCTAAGGTCAAAGTCGACAGGCAGACT
1 AGTCTCTAAGGTCAAAGCCGACAAGCAGACT
1060453 TTAGATAAGG
Statistics
Matches: 228, Mismatches: 51, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
127 28 0.12
128 98 0.43
129 74 0.32
130 28 0.12
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (129 bp):
AGTCTCTAAGGTCAAAGCCGACAAGCAGACTGAAGGGCAAGAAAAGTCTCCAGGGTCAAAACCGA
CATGCAAACTTTAGATAAGGCAATCTCCAGGATCAAAGCCGACAGACAGACTAAAGGGTAGGAA
Found at i:1060395 original size:85 final size:85
Alignment explanation
Indices: 1060176--1060452 Score: 310
Period size: 85 Copynumber: 3.2 Consensus size: 85
1060166 AGTCTTCAGA
* * * *
1060176 GTCAAAGCCGACAGGCATACTGAAGGGTAGGAAAGTTTCCAGGGTCAAAACTGAC-AGACAAACT
1 GTCAAAGCCGACAGGCAGACTGAAGGGTAGGAAAGTCTCCAGGGTCAAAGCTGACAAG-CAGACT
* * *
1060240 TTAGATAAGGCAGTTTTC-AG
65 TTAGATAAGGAAGTCTCCAAG
* * *
1060260 GATCAAAGCCGACAGACAGACTGAAGGGTAGGAAAGTCTCTAAGGTCAAAGCTGACAAGCAGACT
1 G-TCAAAGCCGACAGGCAGACTGAAGGGTAGGAAAGTCTCCAGGGTCAAAGCTGACAAGCAGACT
*
1060325 TTAGATAAGGTAGTCTCCAAG
65 TTAGATAAGGAAGTCTCCAAG
* * * *
1060346 GTCAAAGCCAACAGGCAGACTGAAAGGTAGGAAAGTCTCCAGGGTCAAAG-TCGACAGGTAGACT
1 GTCAAAGCCGACAGGCAGACTGAAGGGTAGGAAAGTCTCCAGGGTCAAAGCT-GACAAGCAGACT
** *
1060410 GAAGGAT-AGGAAAGTCTCTAAG
65 TTA-GATAAGG-AAGTCTCCAAG
*
1060432 GTCAAAGTCGACAGGCAGACT
1 GTCAAAGCCGACAGGCAGACT
1060453 TTAGATAAGG
Statistics
Matches: 164, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
84 2 0.01
85 126 0.77
86 36 0.22
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.17
Consensus pattern (85 bp):
GTCAAAGCCGACAGGCAGACTGAAGGGTAGGAAAGTCTCCAGGGTCAAAGCTGACAAGCAGACTT
TAGATAAGGAAGTCTCCAAG
Found at i:1060518 original size:73 final size:72
Alignment explanation
Indices: 1060391--1060526 Score: 182
Period size: 73 Copynumber: 1.9 Consensus size: 72
1060381 TCTCCAGGGT
* * * * *
1060391 CAAAGTCGACAGGTAGACTGAAGGATAGGAAAGTCTCTAAGGTCAAAGTCGACAGGCAGACTTTA
1 CAAAGCCGACAGGCAGACTGAAGGATAGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTA
1060456 GATAAGG
66 GATAAGG
* * * *
1060463 CAAAGCCGACATGCAGACTGAAGGGTAAGAAAAGTCTCCAGGGTCAAGGCCGACAGGCAGACTT
1 CAAAGCCGACAGGCAGACTGAAGGAT-AGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTT
1060527 GAGGGAAGGA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
72 22 0.41
73 32 0.59
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.15
Consensus pattern (72 bp):
CAAAGCCGACAGGCAGACTGAAGGATAGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTA
GATAAGG
Found at i:1060676 original size:44 final size:44
Alignment explanation
Indices: 1060628--1061430 Score: 755
Period size: 44 Copynumber: 18.0 Consensus size: 44
1060618 AACAAATGAT
* * * * *
1060628 AAGAGTTTAACTAGGACTAATGCCTATGCAGTCAAATGAGGGAA
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
* *
1060672 AAGAGTTTGACCAGGGCTAATGGCAATACAGTCAAATGAGAGAA
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
* ** * * *
1060716 AAGAGTTTGACTAGGTCTTACCGACAATACAGTCAAATAAAAGAA
1 AAGAGTTTGACTAGGGC-TAATGCCAATACAGTCAAATGAGAGAA
* * * * **
1060761 AAGAGTTTAATTAGGTCCTAACGCCAATACAGTCAAACAAGAGAA
1 AAGAGTTTGACTAGG-GCTAATGCCAATACAGTCAAATGAGAGAA
* * * *
1060806 AAGAGTTTGATTAGGGCTAATGCTAATATAGTCAAACGAGAGAA
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
* * * * * * *
1060850 AAGAGTTTGACCATGACTAATGCCAATACAATCAAACAAGGGTGAA
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTC-AA-ATGAGAGAA
* * ** *
1060896 AAGAGTTTGA-TCAGGTCCTAACGTTAATACAGTCAAATGAGAAAA
1 AAGAGTTTGACT-AGG-GCTAATGCCAATACAGTCAAATGAGAGAA
*
1060941 AAGAGTTTGACTAGGGCTAATGGCAATACAGTCAAATGAGAGAA
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
* * * * *
1060985 AATAGTTTGACCAGGGCTAATGCAAATACAATCAAACGAGAGAA
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
* * * * *
1061029 AAGAGTTTGACTAGGTCCTAACGCCAATATAGTTAAATGAAAGAA
1 AAGAGTTTGACTAGG-GCTAATGCCAATACAGTCAAATGAGAGAA
* * * * * **
1061074 AAGAGTTTGACCAGGTCTTAACGTCAATATAGTCAAACAAGAGAA
1 AAGAGTTTGACTAGGGC-TAATGCCAATACAGTCAAATGAGAGAA
*
1061119 AAGAGTTTGACTAGGGTTAATGCCAATACAGTCAAATGAGAGAA
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
* * * * * * *
1061163 AATAGTTTGACCAGGACTAATGCCAATACAATCAAACAAGGGTGAA
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTC-AA-ATGAGAGAA
* ** * * *
1061209 AAGAGTTTGACCAAGTCCTAACGCCAATACTGTCAAATGA-AAAA
1 AAGAGTTTGA-CTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
* * * *
1061253 AAAAGTTTGACTAGGGCTAAAGCCAATACAATCAAATAAGAGAA
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
* * * *
1061297 AAGAGTTTGACCATGGCTAATGCCAATATAGTCAAATGAGATAA
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
* * * *
1061341 AAGAGTTTGACCAGGGCTAATGCTAATACAGTCAAACGAAAGAA
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
* * *
1061385 AAGAGTTTAACTAGGGCTAATGCCAATACAGTCAAACGAGAAAA
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
1061429 AA
1 AA
1061431 TATTTGTTTG
Statistics
Matches: 615, Mismatches: 131, Indels: 26
0.80 0.17 0.03
Matches are distributed among these distances:
43 22 0.04
44 357 0.58
45 167 0.27
46 39 0.06
47 30 0.05
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (44 bp):
AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
Found at i:1060853 original size:178 final size:177
Alignment explanation
Indices: 1060628--1061430 Score: 869
Period size: 178 Copynumber: 4.5 Consensus size: 177
1060618 AACAAATGAT
* * * * * * *
1060628 AAGAGTTTAACTAGGACTAATGCCT-ATGCAGTCAAATGAGGGAAAAGAGTTTGACCAGGGCTAA
1 AAGAGTTTGACCAGGGCTAATG-CTAATACAGTCAAACGAGAGAAAAGAGTTTGACCAGGCCTAA
* * *
1060692 TGGCAATACAGTCAAATGAGAGAAAAGAGTTTGACTAGGTCTTACCGACAATACAGTCAAATAAA
65 TGCCAATACAGTCAAATGAGAGAAAAGAGTTTGACTAGGTCTTAACGTCAATACAGTCAAATAAA
* * * * **
1060757 AGAAAAGAGTTTAATTAGGTCCTAACGCCAATACAGTCAAACAAGAGAA
130 AGAAAAGAGTTTGACTAGG-GCTAATGCCAATACAGTCAAATGAGAGAA
** * * *
1060806 AAGAGTTTGATTAGGGCTAATGCTAATATAGTCAAACGAGAGAAAAGAGTTTGACCATGACTAAT
1 AAGAGTTTGACCAGGGCTAATGCTAATACAGTCAAACGAGAGAAAAGAGTTTGACCAGGCCTAAT
* * * * * *
1060871 GCCAATACAATCAAACAAGGGTGAAAAGAGTTTGA-TCAGGTCCTAACGTTAATACAGTCAAATG
66 GCCAATACAGTC-AA-ATGAGAGAAAAGAGTTTGACT-AGGTCTTAACGTCAATACAGTCAAAT-
* *
1060935 AGAA-AAAAGAGTTTGACTAGGGCTAATGGCAATACAGTCAAATGAGAGAA
127 AAAAGAAAAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
* * * *
1060985 AATAGTTTGACCAGGGCTAATGCAAATACAATCAAACGAGAGAAAAGAGTTTGACTAGGTCCTAA
1 AAGAGTTTGACCAGGGCTAATGCTAATACAGTCAAACGAGAGAAAAGAGTTTGACCAGG-CCTAA
* * * * * * * *
1061050 CGCCAATATAGTTAAATGAAAGAAAAGAGTTTGACCAGGTCTTAACGTCAATATAGTCAAACAAG
65 TGCCAATACAGTCAAATGAGAGAAAAGAGTTTGACTAGGTCTTAACGTCAATACAGTCAAATAAA
*
1061115 AGAAAAGAGTTTGACTAGGGTTAATGCCAATACAGTCAAATGAGAGAA
130 AGAAAAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
* * * * * * *
1061163 AATAGTTTGACCAGGACTAATGCCAATACAATCAAACAAGGGTGAAAAGAGTTTGACCAAGTCCT
1 AAGAGTTTGACCAGGGCTAATGCTAATACAGTCAAAC--GAGAGAAAAGAGTTTGACC-AGGCCT
* * * * * * * *
1061228 AACGCCAATACTGTCAAATGA-AAAAAAAAGTTTGACTAGGGC-TAAAGCCAATACAATCAAATA
63 AATGCCAATACAGTCAAATGAGAGAAAAGAGTTTGACTAGGTCTTAACGTCAATACAGTCAAATA
* * * * *
1061291 AGAGAAAAGAGTTTGACCATGGCTAATGCCAATATAGTCAAATGAGATAA
128 AAAGAAAAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
* * * *
1061341 AAGAGTTTGACCAGGGCTAATGCTAATACAGTCAAACGAAAGAAAAGAGTTTAACTAGGGCTAAT
1 AAGAGTTTGACCAGGGCTAATGCTAATACAGTCAAACGAGAGAAAAGAGTTTGACCAGGCCTAAT
* *
1061406 GCCAATACAGTCAAACGAGAAAAAA
66 GCCAATACAGTCAAATGAGAGAAAA
1061431 TATTTGTTTG
Statistics
Matches: 524, Mismatches: 89, Indels: 26
0.82 0.14 0.04
Matches are distributed among these distances:
175 22 0.04
176 20 0.04
177 4 0.01
178 273 0.52
179 97 0.19
180 103 0.20
181 5 0.01
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (177 bp):
AAGAGTTTGACCAGGGCTAATGCTAATACAGTCAAACGAGAGAAAAGAGTTTGACCAGGCCTAAT
GCCAATACAGTCAAATGAGAGAAAAGAGTTTGACTAGGTCTTAACGTCAATACAGTCAAATAAAA
GAAAAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAA
Found at i:1061126 original size:313 final size:311
Alignment explanation
Indices: 1060628--1061430 Score: 1106
Period size: 313 Copynumber: 2.6 Consensus size: 311
1060618 AACAAATGAT
* * * * *
1060628 AAGAGTTTAACTAGGACTAATGCCTATGCAGTCAAATGAGGGAAAAGAGTTTGACCAGGGCTAAT
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAAAAGAGTTTGACCAGGGCTAAT
* * * *
1060693 GGCAATACAGTCAAATGAGAGAAAAGAGTTTGACTAGGTCTTACCGACAATACAGTCAAATAAAA
66 -GCAATACAGTCAAATGAGAGAAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAATGAAA
** *
1060758 GAAAAGAGTTTAATTAGGTCCTAACGCCAATACAGTCAAACAAGAGAAAAGAGTTTGATTAGGGC
130 GAAAAGAGTTTAACCAGGTCCTAACGCCAATACAGTCAAACAAGAGAAAAGAGTTTGACTAGGGC
* * *
1060823 TAATGCTAATATAGTCAAACGAGAGAAAAGAGTTTGACCATGACTAATGCCAATACAATCAAACA
195 TAATGCCAATACAGTCAAACGAGAGAAAAGAGTTTGACCAGGACTAATGCCAATACAATCAAACA
* * **
1060888 AGGGTGAAAAGAGTTTGATCAGGTCCTAACGTTAATACAGTCAAATGAGAAAA
260 AGGGTGAAAAGAGTTTGACCAAGTCCTAACGCCAATACAGTCAAATGA-AAAA
* *
1060941 AAGAGTTTGACTAGGGCTAATGGCAATACAGTCAAATGAGAGAAAATAGTTTGACCAGGGCTAAT
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAAAAGAGTTTGACCAGGGCTAAT
* * * *
1061006 GCAAATACAATCAAACGAGAGAAAAGAGTTTGACTAGGTCCTAACGCCAATATAGTTAAATGAAA
66 GC-AATACAGTCAAATGAGAGAAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAATGAAA
* * * * *
1061071 GAAAAGAGTTTGACCAGGTCTTAACGTCAATATAGTCAAACAAGAGAAAAGAGTTTGACTAGGGT
130 GAAAAGAGTTTAACCAGGTCCTAACGCCAATACAGTCAAACAAGAGAAAAGAGTTTGACTAGGGC
* *
1061136 TAATGCCAATACAGTCAAATGAGAGAAAATAGTTTGACCAGGACTAATGCCAATACAATCAAACA
195 TAATGCCAATACAGTCAAACGAGAGAAAAGAGTTTGACCAGGACTAATGCCAATACAATCAAACA
*
1061201 AGGGTGAAAAGAGTTTGACCAAGTCCTAACGCCAATACTGTCAAATGAAAAA
260 AGGGTGAAAAGAGTTTGACCAAGTCCTAACGCCAATACAGTCAAATGAAAAA
* * * * *
1061253 AAAAGTTTGACTAGGGCTAAAGCCAATACAATCAAATAAGAGAAAAGAGTTTGACCATGGCTAAT
1 AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAAAAGAGTTTGACCAGGGCTAAT
* * * * * * *
1061318 GCCAATATAGTCAAATGAGATAAAAGAGTTTGACCAGG-GCTAATGCTAATACAGTCAAACGAAA
66 G-CAATACAGTCAAATGAGAGAAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAATGAAA
* * * * *
1061382 GAAAAGAGTTTAACTAGG-GCTAATGCCAATACAGTCAAACGAGAAAAAA
130 GAAAAGAGTTTAACCAGGTCCTAACGCCAATACAGTCAAACAAGAGAAAA
1061431 TATTTGTTTG
Statistics
Matches: 428, Mismatches: 60, Indels: 7
0.86 0.12 0.01
Matches are distributed among these distances:
310 24 0.06
311 36 0.08
312 95 0.22
313 273 0.64
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (311 bp):
AAGAGTTTGACTAGGGCTAATGCCAATACAGTCAAATGAGAGAAAAGAGTTTGACCAGGGCTAAT
GCAATACAGTCAAATGAGAGAAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAATGAAAG
AAAAGAGTTTAACCAGGTCCTAACGCCAATACAGTCAAACAAGAGAAAAGAGTTTGACTAGGGCT
AATGCCAATACAGTCAAACGAGAGAAAAGAGTTTGACCAGGACTAATGCCAATACAATCAAACAA
GGGTGAAAAGAGTTTGACCAAGTCCTAACGCCAATACAGTCAAATGAAAAA
Found at i:1080889 original size:12 final size:12
Alignment explanation
Indices: 1080872--1080912 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
1080862 TCATGTGATG
1080872 GTTTTCTTTTTT
1 GTTTTCTTTTTT
1080884 GTTTTCTTTCTTT
1 GTTTTCTTT-TTT
*
1080897 TTTTTCTTTTTT
1 GTTTTCTTTTTT
1080909 -TTTT
1 GTTTT
1080913 GAATTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 4 0.15
12 12 0.44
13 11 0.41
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (12 bp):
GTTTTCTTTTTT
Found at i:1080919 original size:9 final size:8
Alignment explanation
Indices: 1080907--1080953 Score: 53
Period size: 9 Copynumber: 5.8 Consensus size: 8
1080897 TTTTTCTTTT
1080907 TTTTTTGAA
1 TTTTTTG-A
1080916 TTTTTT-A
1 TTTTTTGA
1080923 TTTCTTTGA
1 TTT-TTTGA
1080932 -TTTTTGA
1 TTTTTTGA
1080939 TTTTTTGGA
1 TTTTTT-GA
1080948 TTTTTT
1 TTTTTT
1080954 AAAAAAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 9 0.26
8 10 0.29
9 15 0.44
ACGTcount: A:0.13, C:0.02, G:0.11, T:0.74
Consensus pattern (8 bp):
TTTTTTGA
Found at i:1080921 original size:24 final size:23
Alignment explanation
Indices: 1080894--1080944 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
1080884 GTTTTCTTTC
**
1080894 TTTTT-TTTCTTTTTTTTTTGAAT
1 TTTTTATTTCTTTGATTTTTG-AT
1080917 TTTTTATTTCTTTGATTTTTGAT
1 TTTTTATTTCTTTGATTTTTGAT
1080940 TTTTT
1 TTTTT
1080945 GGATTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.80
Consensus pattern (23 bp):
TTTTTATTTCTTTGATTTTTGAT
Found at i:1080936 original size:16 final size:15
Alignment explanation
Indices: 1080873--1080954 Score: 62
Period size: 16 Copynumber: 5.3 Consensus size: 15
1080863 CATGTGATGG
* *
1080873 TTTTCTTTTTTGTTT
1 TTTTATTTTTTGATT
*
1080888 TCTTTCTTTTTT--TT
1 T-TTTATTTTTTGATT
1080902 CTTTT-TTTTTTGAATT
1 -TTTTATTTTTTG-ATT
1080918 TTTTATTTCTTTGATT
1 TTTTATTT-TTTGATT
*
1080934 TTTGATTTTTTGGATT
1 TTTTATTTTTT-GATT
1080950 TTTTA
1 TTTTA
1080955 AAAAAATATT
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
13 6 0.11
14 5 0.09
15 9 0.16
16 33 0.58
17 4 0.07
ACGTcount: A:0.09, C:0.06, G:0.07, T:0.78
Consensus pattern (15 bp):
TTTTATTTTTTGATT
Found at i:1085702 original size:15 final size:17
Alignment explanation
Indices: 1085671--1085704 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1085661 ATGAAACGAG
1085671 TTTAGATATATTTTTAA
1 TTTAGATATATTTTTAA
1085688 TTTAGAT-TA-TTTTAA
1 TTTAGATATATTTTTAA
1085703 TT
1 TT
1085705 GAATTACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 2 0.12
17 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTAGATATATTTTTAA
Found at i:1086682 original size:18 final size:18
Alignment explanation
Indices: 1086661--1086708 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1086651 AATATAAATA
1086661 TTAATATAAAAATAATTT
1 TTAATATAAAAATAATTT
*** *
1086679 TTAATATTTTAATATTTT
1 TTAATATAAAAATAATTT
1086697 TTAATAATAAAA
1 TTAAT-ATAAAA
1086709 TGAACTTTAA
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATATAAAAATAATTT
Found at i:1087206 original size:19 final size:19
Alignment explanation
Indices: 1087182--1087223 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1087172 GTAAAATTAA
1087182 AAATTATTATATATCTTTT
1 AAATTATTATATATCTTTT
* * *
1087201 AAATTATTTTTTATTTTTT
1 AAATTATTATATATCTTTT
1087220 AAAT
1 AAAT
1087224 ATACATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
AAATTATTATATATCTTTT
Found at i:1089270 original size:2 final size:2
Alignment explanation
Indices: 1089263--1089302 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1089253 ATTACATGGA
1089263 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
1089303 CAAGTTAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1090308 original size:20 final size:21
Alignment explanation
Indices: 1090273--1090341 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 21
1090263 GAATAAGGTT
* *
1090273 TTTTTATTATAAAATT-TCTA
1 TTTTTATAATAAAATTATATA
*
1090293 TTTTTATAATATAATTATATA
1 TTTTTATAATAAAATTATATA
* *
1090314 TGTTTTATAAGAATATT-TATA
1 T-TTTTATAATAAAATTATATA
*
1090335 ATTTTAT
1 TTTTTAT
1090342 TTTACTAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 20 0.50
21 8 0.20
22 12 0.30
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (21 bp):
TTTTTATAATAAAATTATATA
Found at i:1090705 original size:21 final size:22
Alignment explanation
Indices: 1090675--1090716 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1090665 GACTCGAACT
* *
1090675 TAAATTAATTTTATTTTAAAAC
1 TAAATTAATTTAAATTTAAAAC
1090697 TAAA-TAATTTAAATTTAAAA
1 TAAATTAATTTAAATTTAAAA
1090717 TGATCTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATTAATTTAAATTTAAAAC
Found at i:1091903 original size:2 final size:2
Alignment explanation
Indices: 1091896--1091946 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1091886 ACAATCTGAG
1091896 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
1091938 AT AT AT AT A
1 AT AT AT AT A
1091947 ACACGTGCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1092142 original size:22 final size:23
Alignment explanation
Indices: 1092106--1092148 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1092096 AATTCAGAGG
*
1092106 AATCATAATGGCATAAGTGAATC
1 AATCATAATGACATAAGTGAATC
1092129 AATCA-AATGACATAAGTGAA
1 AATCATAATGACATAAGTGAA
1092149 AACCCCCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (23 bp):
AATCATAATGACATAAGTGAATC
Found at i:1092411 original size:2 final size:2
Alignment explanation
Indices: 1092404--1092444 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1092394 CTAAATTCAA
* * *
1092404 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1092445 CTTAAGTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1093856 original size:2 final size:2
Alignment explanation
Indices: 1093845--1093891 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
1093835 CATAGCATGT
* *
1093845 TA TA TA -A TA TA TA TA TA TA TA TT TA TA TA TA TA CA 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
1093886 T- TA TA T
1 TA TA TA T
1093892 CATTAGGAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1094611 original size:24 final size:25
Alignment explanation
Indices: 1094571--1094624 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
1094561 AAAATTTTAA
* *
1094571 AAATA-ATATTTTTATAT-TATATTT
1 AAATATATATTTTGATATAAATA-TT
1094595 AAATATATA-TTTGATATAAATATT
1 AAATATATATTTTGATATAAATATT
1094619 AAATAT
1 AAATAT
1094625 TTTTAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
AAATATATATTTTGATATAAATATT
Found at i:1095251 original size:12 final size:12
Alignment explanation
Indices: 1095234--1095271 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1095224 TTTATAAATT
1095234 TATATTATATTA
1 TATATTATATTA
*
1095246 TATATTTTATTA
1 TATATTATATTA
*
1095258 TATAATA-ATTA
1 TATATTATATTA
1095269 TAT
1 TAT
1095272 TTAAAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 7 0.30
12 16 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATATTATATTA
Found at i:1095328 original size:32 final size:33
Alignment explanation
Indices: 1095276--1095338 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
1095266 TTATATTTAA
* *
1095276 AATATTTTATATTTATATAAATTTTAATATATT
1 AATAATTTATATTTATATAAAATTTAATATATT
* *
1095309 AATAATTTAT-TTTTTATAAAATTTGATATA
1 AATAATTTATATTTATATAAAATTTAATATA
1095339 CATATTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (33 bp):
AATAATTTATATTTATATAAAATTTAATATATT
Found at i:1095365 original size:17 final size:17
Alignment explanation
Indices: 1095343--1095376 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1095333 GATATACATA
1095343 TTTATA-TTATTTTATAT
1 TTTATATTTA-TTTATAT
1095360 TTTATATTTATTTATAT
1 TTTATATTTATTTATAT
1095377 GAATATAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATATTTATTTATAT
Found at i:1095874 original size:13 final size:13
Alignment explanation
Indices: 1095858--1095903 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
1095848 TTAATTATAT
1095858 TAAATATTAATAA
1 TAAATATTAATAA
*
1095871 TAAATAATAATAA
1 TAAATATTAATAA
1095884 TAAA-ATT-ATAA
1 TAAATATTAATAA
*
1095895 AAAATATTA
1 TAAATATTA
1095904 CGATCTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 7 0.25
12 5 0.18
13 16 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAATATTAATAA
Found at i:1098013 original size:2 final size:2
Alignment explanation
Indices: 1098006--1098045 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1097996 AGTGCAAACT
*
1098006 TA TA TA TA TA TA AA 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
1098046 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1099001 original size:2 final size:2
Alignment explanation
Indices: 1098994--1099018 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1098984 TTTGTTTGAA
1098994 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1099019 TCAGAGAAAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1099204 original size:20 final size:18
Alignment explanation
Indices: 1099162--1099207 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
1099152 GGTATAATAG
*
1099162 GATATAAATTATAATATT
1 GATATAAATGATAATATT
*
1099180 AATATAATATGATATATATT
1 GATATAA-ATGATA-ATATT
1099200 GATATAAA
1 GATATAAA
1099208 AATTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 11 0.48
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (18 bp):
GATATAAATGATAATATT
Found at i:1099329 original size:29 final size:30
Alignment explanation
Indices: 1099262--1099336 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 30
1099252 GAAATTTTTT
*
1099262 TATATATAATAAATTATAATAAAATTATTAA
1 TATATA-AATAAATTTTAATAAAATTATTAA
*
1099293 -A-AT-AATAAATTTTAATTAAA-TATTAA
1 TATATAAATAAATTTTAATAAAATTATTAA
*
1099319 TATATAAATAATTTTTAA
1 TATATAAATAAATTTTAA
1099337 AATTTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
26 6 0.16
27 16 0.42
28 2 0.05
29 13 0.34
30 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
TATATAAATAAATTTTAATAAAATTATTAA
Found at i:1099364 original size:19 final size:22
Alignment explanation
Indices: 1099324--1099380 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 22
1099314 ATTAATATAT
1099324 AAATAATTTTTAAAATTTTTAA
1 AAATAATTTTTAAAATTTTTAA
1099346 AAATAA-TTTT-AAA-TTTTAA
1 AAATAATTTTTAAAATTTTTAA
1099365 AAAT--TTTATTAAAATT
1 AAATAATTT-TTAAAATT
1099381 AAATTATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
18 2 0.06
19 12 0.39
20 6 0.19
21 5 0.16
22 6 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATAATTTTTAAAATTTTTAA
Found at i:1099416 original size:22 final size:20
Alignment explanation
Indices: 1099365--1099417 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
1099355 TAAATTTTAA
1099365 AAATTTTATTAAAATTAAAT
1 AAATTTTATTAAAATTAAAT
* *
1099385 TATTTGTTATTAAAATATAAAT
1 AAATT-TTATTAAAAT-TAAAT
1099407 AAATTATTATT
1 AAATT-TTATT
1099418 CATATGTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 3 0.12
21 10 0.38
22 13 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
AAATTTTATTAAAATTAAAT
Found at i:1099437 original size:20 final size:20
Alignment explanation
Indices: 1099406--1099456 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1099396 AAAATATAAA
* *
1099406 TAAATTATTATTCATATGTGT
1 TAAATTA-TATTCAAATATGT
*
1099427 TAAATTATATTTAAATATGT
1 TAAATTATATTCAAATATGT
*
1099447 TTAATTATAT
1 TAAATTATAT
1099457 GATATTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (20 bp):
TAAATTATATTCAAATATGT
Found at i:1099486 original size:19 final size:19
Alignment explanation
Indices: 1099429--1099497 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
1099419 ATATGTGTTA
* *
1099429 AATTATATTTAAATATGTTT
1 AATTATATTTTATTAT-TTT
**
1099449 AATTATATGATATTATTTT
1 AATTATATTTTATTATTTT
1099468 AATTATATCTTTATT-TTTT
1 AATTATAT-TTTATTATTTT
*
1099487 AAATATATTTT
1 AATTATATTTT
1099498 TATATATTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
18 3 0.07
19 22 0.54
20 16 0.39
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (19 bp):
AATTATATTTTATTATTTT
Found at i:1099499 original size:19 final size:20
Alignment explanation
Indices: 1099459--1099505 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1099449 AATTATATGA
*
1099459 TATTATTTTAATTATATCTT
1 TATTATTTTAAATATATCTT
*
1099479 TATT-TTTTAAATATATTTT
1 TATTATTTTAAATATATCTT
1099498 TATATATT
1 TAT-TATT
1099506 CAATACGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 16 0.70
20 5 0.22
21 2 0.09
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTATTTTAAATATATCTT
Found at i:1100356 original size:24 final size:24
Alignment explanation
Indices: 1100329--1100387 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
1100319 ATTTTAAATT
1100329 TAAATTATAATTTTTT-TATTAAAC
1 TAAATTATAATTTTTTAT-TTAAAC
* *
1100353 TAAAATAATAATTTTTTATTTAAAT
1 T-AAATTATAATTTTTTATTTAAAC
*
1100378 TTAATTATAA
1 TAAATTATAA
1100388 ATATTAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 8 0.28
25 20 0.69
26 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TAAATTATAATTTTTTATTTAAAC
Found at i:1100375 original size:25 final size:24
Alignment explanation
Indices: 1100320--1100376 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
1100310 TTAAATTAAA
* * *
1100320 TTTTAAATTTAAATTATAATTTTT
1 TTTTAAACTAAAATAATAATTTTT
1100344 TTATTAAACTAAAATAATAATTTTT
1 TT-TTAAACTAAAATAATAATTTTT
1100369 TATTTAAA
1 T-TTTAAA
1100377 TTTAATTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.07
25 25 0.89
26 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTAAACTAAAATAATAATTTTT
Found at i:1100822 original size:19 final size:19
Alignment explanation
Indices: 1100786--1100825 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1100776 GTAAGATATA
* **
1100786 TTTATTTATTTATTAATTT
1 TTTATATATTTAAAAATTT
1100805 TTTATATATTTAAAAATTT
1 TTTATATATTTAAAAATTT
1100824 TT
1 TT
1100826 AAAGAATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTTAAAAATTT
Found at i:1100956 original size:30 final size:32
Alignment explanation
Indices: 1100886--1100990 Score: 85
Period size: 30 Copynumber: 3.3 Consensus size: 32
1100876 TTTTAAAAAA
*
1100886 TAAA-AATA-AAATAATTAATAAATTTATTCATAAAT
1 TAAATAATATAAATAA-TATTAAA-TTATTCAT---T
** *
1100921 TAAATAATATATTTAAT-TTAAATTATT-TTT
1 TAAATAATATAAATAATATTAAATTATTCATT
*
1100951 TAAATAAT-TAAATAATATTTAATTATTCATT
1 TAAATAATATAAATAATATTAAATTATTCATT
1100982 TAAATAATA
1 TAAATAATA
1100991 ATCTAAATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
29 6 0.11
30 18 0.32
31 10 0.18
33 1 0.02
34 5 0.09
35 8 0.14
36 5 0.09
37 4 0.07
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (32 bp):
TAAATAATATAAATAATATTAAATTATTCATT
Found at i:1101208 original size:22 final size:22
Alignment explanation
Indices: 1101166--1101209 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
1101156 TTTCAATCCT
* *
1101166 AATTGCAAAAGAAAGATAAAAG
1 AATTGCAAAAGAAAAAAAAAAG
*
1101188 AATTGTCAAAAAAAAAAAAAAA
1 AATTG-CAAAAGAAAAAAAAAA
1101210 AAAAGGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (22 bp):
AATTGCAAAAGAAAAAAAAAAG
Found at i:1101229 original size:15 final size:15
Alignment explanation
Indices: 1101201--1101230 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1101191 TGTCAAAAAA
1101201 AAAAAAAAAAAAAGG
1 AAAAAAAAAAAAAGG
*
1101216 AAAAAAGAAAAAAGG
1 AAAAAAAAAAAAAGG
1101231 TCTCCAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGG
Found at i:1101347 original size:20 final size:20
Alignment explanation
Indices: 1101324--1101363 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1101314 GATATAATAA
1101324 TTTT-TAAATTTATATTATAT
1 TTTTATAAATTT-TATTATAT
*
1101344 TTTTATATATTTTATTATAT
1 TTTTATAAATTTTATTATAT
1101364 AATAATTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATAAATTTTATTATAT
Found at i:1101452 original size:6 final size:6
Alignment explanation
Indices: 1101441--1101504 Score: 62
Period size: 6 Copynumber: 10.3 Consensus size: 6
1101431 TTTTGATACC
1101441 TATATT TATA-T TATATT ATATATTT TATATT T-TATAT T-TATT TATATT
1 TATATT TATATT TATATT -TATA-TT TATATT TATAT-T TATATT TATATT
1101489 TATATAAT TATATT TA
1 TATAT--T TATATT TA
1101505 AAATTATTCT
Statistics
Matches: 51, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
5 10 0.20
6 25 0.49
7 8 0.16
8 8 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:1101463 original size:40 final size:38
Alignment explanation
Indices: 1101419--1101509 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 38
1101409 ATTAATAATT
*
1101419 TATATTTTAAAATTTTGATACCTATATTTATA-TTATATTA
1 TATATTTTAAAATTTT-ATA--TATATTTATATTTATATAA
* *
1101459 TATATTTT-ATATTTTATATTTATTTATATTTATATAA
1 TATATTTTAAAATTTTATATATATTTATATTTATATAA
1101496 T-TATATTTAAAATT
1 TATAT-TTTAAAATT
1101510 ATTCTATGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
36 12 0.27
37 11 0.25
38 7 0.16
39 6 0.14
40 8 0.18
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.59
Consensus pattern (38 bp):
TATATTTTAAAATTTTATATATATTTATATTTATATAA
Found at i:1101470 original size:14 final size:14
Alignment explanation
Indices: 1101451--1101501 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
1101441 TATATTTATA
1101451 TTATATTATATATT
1 TTATATTATATATT
*
1101465 TTATATTTTATA-T
1 TTATATTATATATT
1101478 TTAT-TTATAT-TT
1 TTATATTATATATT
*
1101490 ATATAATTATAT
1 TTAT-ATTATAT
1101502 TTAAAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 9 0.29
13 5 0.16
14 17 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATATTATATATT
Found at i:1101477 original size:32 final size:31
Alignment explanation
Indices: 1101441--1101503 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
1101431 TTTTGATACC
*
1101441 TATATTTATATTATA-TTATATATTTTATATTT
1 TATATTTAT-TTATATTTATATA-ATTATATTT
1101473 TATATTTATTTATATTTATATAATTATATTT
1 TATATTTATTTATATTTATATAATTATATTT
1101504 AAAATTATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (31 bp):
TATATTTATTTATATTTATATAATTATATTT
Found at i:1102269 original size:2 final size:2
Alignment explanation
Indices: 1102262--1102298 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1102252 TTGCAGAAGA
1102262 AT AT AT 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 AT AT AT A
1102299 AAAGAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1102663 original size:13 final size:12
Alignment explanation
Indices: 1102645--1102702 Score: 62
Period size: 13 Copynumber: 4.6 Consensus size: 12
1102635 TTTTAATTTT
1102645 TTTATTATCAATA
1 TTTATTAT-AATA
*
1102658 TTTATTATTGATA
1 TTTATTA-TAATA
1102671 TTTATTATAATTA
1 TTTATTATAA-TA
* *
1102684 ATTATAATAATA
1 TTTATTATAATA
1102696 TTTATTA
1 TTTATTA
1102703 ATTAAATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
12 9 0.24
13 27 0.73
14 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (12 bp):
TTTATTATAATA
Found at i:1102734 original size:24 final size:23
Alignment explanation
Indices: 1102668--1102734 Score: 55
Period size: 23 Copynumber: 2.8 Consensus size: 23
1102658 TTTATTATTG
* *
1102668 ATATTTATTATAATTAATTATAATA
1 ATATTTA--ATAAATAAATATAATA
* *
1102693 ATATTTATTAATTAAATATATATA
1 ATATTTAATAAATAAATATA-ATA
1102717 AT-TTTAATAAATATAATA
1 ATATTTAATAAATA-AATA
1102735 CCAACGAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 20 0.56
24 9 0.25
25 7 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATTTAATAAATAAATATAATA
Found at i:1103162 original size:2 final size:2
Alignment explanation
Indices: 1103155--1103182 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1103145 TAGAAATGGG
1103155 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1103183 ATACAATTCT
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:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:1104251 original size:2 final size:2
Alignment explanation
Indices: 1104244--1104283 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1104234 GAAAATCTGA
* *
1104244 AT AT AT AT AT AT AC AT AT AT AT AT AC 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
1104284 GCTGGCATCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1104263 original size:12 final size:12
Alignment explanation
Indices: 1104246--1104280 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
1104236 AAATCTGAAT
1104246 ATATATATATAC
1 ATATATATATAC
1104258 ATATATATATAC
1 ATATATATATAC
1104270 ATATATATATA
1 ATATATATATA
1104281 TATGCTGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATATATAC
Found at i:1107680 original size:13 final size:13
Alignment explanation
Indices: 1107662--1107688 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1107652 GAGTTCCAGC
1107662 CGGTAGCTAATCT
1 CGGTAGCTAATCT
1107675 CGGTAGCTAATCT
1 CGGTAGCTAATCT
1107688 C
1 C
1107689 CAATTTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (13 bp):
CGGTAGCTAATCT
Found at i:1109622 original size:19 final size:19
Alignment explanation
Indices: 1109598--1109637 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1109588 CCTGCCCATA
1109598 ATCTTATATCTATCATCCT
1 ATCTTATATCTATCATCCT
1109617 ATCTTATATCTATCATCCT
1 ATCTTATATCTATCATCCT
1109636 AT
1 AT
1109638 ATTCAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (19 bp):
ATCTTATATCTATCATCCT
Found at i:1110537 original size:2 final size:2
Alignment explanation
Indices: 1110530--1110577 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1110520 CGCAATCATG
1110530 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
1110572 TA TA TA
1 TA TA TA
1110578 GAGAGAGAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1110582 original size:2 final size:2
Alignment explanation
Indices: 1110577--1110625 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
1110567 ATATATATAT
*
1110577 AG AG AG AG AG AG AG AG AG AA 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 AG AG AG AG
*
1110619 AG GG AG A
1 AG AG AG A
1110626 TCATCATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1110717 original size:14 final size:14
Alignment explanation
Indices: 1110698--1110725 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1110688 AACAAATCAA
1110698 ATTATATAATCTAT
1 ATTATATAATCTAT
1110712 ATTATATAATCTAT
1 ATTATATAATCTAT
1110726 TAGTAAGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTATATAATCTAT
Found at i:1112494 original size:41 final size:42
Alignment explanation
Indices: 1112443--1112527 Score: 154
Period size: 41 Copynumber: 2.0 Consensus size: 42
1112433 TTTTTCAATG
1112443 TTCAATTAAATGGTCGGCTAATAA-TGGGAAATTTGATGTTT
1 TTCAATTAAATGGTCGGCTAATAAGTGGGAAATTTGATGTTT
1112484 TTCAATTAAATGGTCGGCTAATAATGTGGGAAATTTGATGTTT
1 TTCAATTAAATGGTCGGCTAATAA-GTGGGAAATTTGATGTTT
1112527 T
1 T
1112528 CGATCAGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 24 0.57
43 18 0.43
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (42 bp):
TTCAATTAAATGGTCGGCTAATAAGTGGGAAATTTGATGTTT
Found at i:1114059 original size:16 final size:17
Alignment explanation
Indices: 1114035--1114084 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
1114025 TTTATTCGAT
*
1114035 ATAAAATAAAAAAT-AA
1 ATAATATAAAAAATAAA
*
1114051 ATAATAT-AATAATAAA
1 ATAATATAAAAAATAAA
1114067 ATAAT-TAAAAAATTAAA
1 ATAATATAAAAAA-TAAA
1114084 A
1 A
1114085 AAAATCAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 17 0.61
17 5 0.18
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAATATAAAAAATAAA
Found at i:1114079 original size:38 final size:39
Alignment explanation
Indices: 1114037--1114127 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
1114027 TATTCGATAT
1114037 AAAATAAAAAATAAAT-AATATAAT-AA-TAAAA-T-AATTAA
1 AAAATAAAAAA-AAATCAATA-AATCAATTAAAATTCAA--AA
*
1114075 AAAATTAAAAAAAATCAATAAATCAATTAAAATTCAAAA
1 AAAATAAAAAAAAATCAATAAATCAATTAAAATTCAAAA
1114114 AAAATAAAAAAAAA
1 AAAATAAAAAAAAA
1114128 AAAAATTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
37 7 0.15
38 16 0.35
39 20 0.43
40 1 0.02
41 2 0.04
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (39 bp):
AAAATAAAAAAAAATCAATAAATCAATTAAAATTCAAAA
Found at i:1114085 original size:9 final size:9
Alignment explanation
Indices: 1114063--1114170 Score: 61
Period size: 9 Copynumber: 12.6 Consensus size: 9
1114053 AATATAATAA
*
1114063 TAAAATAAT
1 TAAAAAAAT
1114072 T-AAAAAAT
1 TAAAAAAAT
*
1114080 TAAAAAAAA
1 TAAAAAAAT
* *
1114089 TCAATAAAT
1 TAAAAAAAT
* *
1114098 CAATTAAAAT
1 TAA-AAAAAT
*
1114108 TCAAAAAAAA
1 T-AAAAAAAT
1114118 TAAAAAAA-
1 TAAAAAAAT
1114126 -AAAAAAAT
1 TAAAAAAAT
1114134 T--AAAAAT
1 TAAAAAAAT
*
1114141 TAAAGAAA-
1 TAAAAAAAT
1114149 TAAAAGAAA-
1 TAAAA-AAAT
1114158 TAAAAAAA-
1 TAAAAAAAT
1114166 TAAAA
1 TAAAA
1114171 TCATCAAAAA
Statistics
Matches: 77, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
7 14 0.18
8 19 0.25
9 33 0.43
10 9 0.12
11 2 0.03
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:1114122 original size:8 final size:8
Alignment explanation
Indices: 1114111--1114170 Score: 77
Period size: 8 Copynumber: 7.5 Consensus size: 8
1114101 TTAAAATTCA
1114111 AAAAAAAT
1 AAAAAAAT
1114119 AAAAAAA-
1 AAAAAAAT
1114126 AAAAAAAT
1 AAAAAAAT
* *
1114134 TAAAAATT
1 AAAAAAAT
*
1114142 AAAGAAAT
1 AAAAAAAT
1114150 AAAAGAAAT
1 AAAA-AAAT
1114159 AAAAAAAT
1 AAAAAAAT
1114167 AAAA
1 AAAA
1114171 TCATCAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
7 7 0.16
8 29 0.66
9 8 0.18
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1114135 original size:32 final size:33
Alignment explanation
Indices: 1114099--1114186 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 33
1114089 TCAATAAATC
1114099 AATTAAAATTCAAAAAAAATAAAAAAA-AAAAA
1 AATTAAAATTCAAAAAAAATAAAAAAATAAAAA
*
1114131 AATTAAAAATT--AAAGAAATAAAAGAAATAAAAA
1 AATT-AAAATTCAAAAAAAATAAAA-AAATAAAAA
**
1114164 AA-TAAAA-TCATCAAAAATAAAAA
1 AATTAAAATTCAAAAAAAATAAAAA
1114187 TTAGAAATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
30 1 0.02
31 16 0.34
32 17 0.36
33 13 0.28
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.17
Consensus pattern (33 bp):
AATTAAAATTCAAAAAAAATAAAAAAATAAAAA
Found at i:1114181 original size:23 final size:23
Alignment explanation
Indices: 1114155--1114217 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
1114145 GAAATAAAAG
1114155 AAATAAAAAAATAAAATCATCAA
1 AAATAAAAAAATAAAATCATCAA
* *
1114178 AAAT-AAAAATTAGAAATCATTAA
1 AAATAAAAAAATA-AAATCATCAA
* *
1114201 AAGTAATAAAATCAAAA
1 AAATAAAAAAAT-AAAA
1114218 AGAAATGGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 7 0.22
23 16 0.50
24 8 0.25
25 1 0.03
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (23 bp):
AAATAAAAAAATAAAATCATCAA
Found at i:1114976 original size:62 final size:63
Alignment explanation
Indices: 1114895--1115012 Score: 193
Period size: 62 Copynumber: 1.9 Consensus size: 63
1114885 ACAGCTCTAG
* *
1114895 CAGCTTCCAGCAGCGACAGCACCCGAAACCAACAGCTCTAGTAGCTTCCACGAACATCGACAA
1 CAGCTTCCAACAGCGACAGCACCCGAAACCAACAGCTCTAGCAGCTTCCACGAACATCGACAA
* *
1114958 CAGC-TCCAACAGCGACAGCACCCGAAACCAGCAGCTTTAGCAGCTTCCACGAACA
1 CAGCTTCCAACAGCGACAGCACCCGAAACCAACAGCTCTAGCAGCTTCCACGAACA
1115013 CCGGCAGCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
62 47 0.92
63 4 0.08
ACGTcount: A:0.33, C:0.37, G:0.18, T:0.12
Consensus pattern (63 bp):
CAGCTTCCAACAGCGACAGCACCCGAAACCAACAGCTCTAGCAGCTTCCACGAACATCGACAA
Found at i:1123507 original size:13 final size:13
Alignment explanation
Indices: 1123489--1123513 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1123479 ATTACTCAAA
1123489 TGTATCGATACAT
1 TGTATCGATACAT
1123502 TGTATCGATACA
1 TGTATCGATACA
1123514 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1123565 original size:52 final size:52
Alignment explanation
Indices: 1123522--1123650 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
1123512 CACTGATCTT
*
1123522 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATAAAG
1 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
1123574 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
1123626 TGTATTGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGAAAATTT
1123651 TCATATTTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1132036 original size:43 final size:43
Alignment explanation
Indices: 1131934--1132168 Score: 191
Period size: 41 Copynumber: 5.6 Consensus size: 43
1131924 TTCTTATCCC
* * * *
1131934 TCAGTCTGCCTGTTGACTTTGACCCTGGAGACTGTCCTATC--
1 TCAGTCTGCTTGTTGGCTTTGACCTTGGAGACTTTCCTATCAT
*
1131975 TCAGTTTGCTTGTTGGCTTTGACCTTGGAGACTTTCCTATCAT
1 TCAGTCTGCTTGTTGGCTTTGACCTTGGAGACTTTCCTATCAT
* * *
1132018 TCAGTCTGCTTATCGGCTTTGACCTTGGAGAC-TACCT-T-AT
1 TCAGTCTGCTTGTTGGCTTTGACCTTGGAGACTTTCCTATCAT
* * * **
1132058 CTCAGTCTACCTGTTGGCTTTGACCTTGGAGACTTTCATA-CCC
1 -TCAGTCTGCTTGTTGGCTTTGACCTTGGAGACTTTCCTATCAT
* ** * **
1132101 TCAGTCTGCCTGTCAGCTTTGATCC-TAGAGACTACCCTAT--T
1 TCAGTCTGCTTGTTGGCTTTGA-CCTTGGAGACTTTCCTATCAT
* * *
1132142 TAAGTCTACCTGTTGGCTTTGACCTTG
1 TCAGTCTGCTTGTTGGCTTTGACCTTG
1132169 AAGATTGCCT
Statistics
Matches: 155, Mismatches: 30, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
40 4 0.03
41 84 0.54
42 36 0.23
43 31 0.20
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.37
Consensus pattern (43 bp):
TCAGTCTGCTTGTTGGCTTTGACCTTGGAGACTTTCCTATCAT
Found at i:1132120 original size:42 final size:42
Alignment explanation
Indices: 1131931--1132467 Score: 274
Period size: 42 Copynumber: 12.8 Consensus size: 42
1131921 TTTTTCTTAT
* * * *
1131931 CCCTCAGTCTGCCTGTTGACTTTGACCCTGGAGACTGTCCTA
1 CCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTA
* * * *
1131973 -TCTCAGTTTGCTTGTTGGCTTTGACCTTGGAGACTTTCCTA
1 CCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTA
** * * *
1132014 TCATTCAGTCTGCTTATCGGCTTTGACCTTGGAGAC-TACCTTA
1 -CCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCC-TA
* * * *
1132057 -TCTCAGTCTACCTGTTGGCTTTGACCTTGGAGACTTTCATA
1 CCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTA
* * **
1132098 CCCTCAGTCTGCCTGTCAGCTTTGATCC-TAGAGACTACCCTA
1 CCCTCAGTCTGCCTGTCGGCTTTGA-CCTTGGAGACTTTCCTA
** * * * * *
1132140 -TTTAAGTCTACCTGTTGGCTTTGACCTTGAAGA-TTGCCT-
1 CCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTA
* * * * * *
1132179 CATCTAAAGTTTGCCTGTCAGCTTTGACCCTGAAGACTTTCCTA
1 C-CCT-CAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTA
* * * * *
1132223 CCCTTAGTCTGCCTGTCGACTTTGACCCTGGAAAC-TGCCTTA
1 CCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCC-TA
* * ** * ** *
1132265 -TCTAAAGTCTAACTGTCGGCTTTGACCTTGAAGACTTTTTTCC
1 CCCT-CAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCT-A
* * * *
1132308 CCCTTAGTCTGCTTGTCGGCTTTGATCTTGGAGAC-TGCCT-
1 CCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTA
* * * * *
1132348 CATCTAAAGTTTACCTGTCGGCTTTGACCTTGGAGACTTTCTTA
1 C-CCT-CAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTA
* * * * * *
1132392 CCCTCAAT-TTCCTGTTGGCTTTGACCCTGGACAC-TACTCTA
1 CCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTC-CTA
** * *
1132433 -TTTAAAGTCTGTCTGTCGGCTTTGACCTTGGAGAC
1 CCCT-CAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
1132468 CGCCTTATTT
Statistics
Matches: 370, Mismatches: 101, Indels: 48
0.71 0.19 0.09
Matches are distributed among these distances:
40 10 0.03
41 122 0.33
42 163 0.44
43 71 0.19
44 4 0.01
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.36
Consensus pattern (42 bp):
CCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTA
Found at i:1132194 original size:83 final size:83
Alignment explanation
Indices: 1131931--1132205 Score: 216
Period size: 83 Copynumber: 3.3 Consensus size: 83
1131921 TTTTTCTTAT
* * * * ** * * * *
1131931 CCCTCAGTCTGCCTGT-TGACTTTGACCCTGGAGACTGTCCTATCTCAGTTTGCTTGTTGGCTTT
1 CCCTAAGTCTGCCTGTCAG-CTTTGATCCTAGAGACTACCCTATCTAAGTCTACCTGTTGGCTTT
* * *
1131995 GACCTTGGAGACTTTCCTA
65 GACCTTGAAGACTTGCATA
** * * * * * * *
1132014 TCATTCAGTCTGCTTATCGGCTTTGA-CCTTGGAGACTACCTTATCTCAGTCTACCTGTTGGCTT
1 -CCCTAAGTCTGCCTGTCAGCTTTGATCC-TAGAGACTACCCTATCTAAGTCTACCTGTTGGCTT
* *
1132078 TGACCTTGGAGACTTTCATA
64 TGACCTTGAAGACTTGCATA
* *
1132098 CCCTCAGTCTGCCTGTCAGCTTTGATCCTAGAGACTACCCTATTTAAGTCTACCTGTTGGCTTTG
1 CCCTAAGTCTGCCTGTCAGCTTTGATCCTAGAGACTACCCTATCTAAGTCTACCTGTTGGCTTTG
*
1132163 ACCTTGAAGA-TTGCCT-
66 ACCTTGAAGACTTGCATA
* *
1132179 CATCTAAAGTTTGCCTGTCAGCTTTGA
1 C-CCT-AAGTCTGCCTGTCAGCTTTGA
1132206 CCCTGAAGAC
Statistics
Matches: 159, Mismatches: 27, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
81 1 0.01
82 6 0.04
83 83 0.52
84 68 0.43
85 1 0.01
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.37
Consensus pattern (83 bp):
CCCTAAGTCTGCCTGTCAGCTTTGATCCTAGAGACTACCCTATCTAAGTCTACCTGTTGGCTTTG
ACCTTGAAGACTTGCATA
Found at i:1132196 original size:125 final size:125
Alignment explanation
Indices: 1132030--1132300 Score: 321
Period size: 125 Copynumber: 2.2 Consensus size: 125
1132020 AGTCTGCTTA
* * * ** * *
1132030 TCGGCTTTGACCTTGGAGACTACCTTATCTCAGTCTACCTGTTGGCTTTGACCTTGGAGACTTTC
1 TCGGCTTTGACCTTGAAGACTACCTCATCTAAGTCTACCTGTCAGCTTTGACCCTGAAGACTTTC
* * * *
1132095 ATACCCTCAGTCTGCCTGTC-AGCTTTGATCCTAGAGACTACCCTAT-TTAAGTCTACCTG
66 ATACCCTCAGTCTGCCTGTCGA-CTTTGACCCTAGAAACTACCCTATCTAAAGTCTAACTG
* * * * *
1132154 TTGGCTTTGACCTTGAAGATTGCCTCATCTAAAGTTTGCCTGTCAGCTTTGACCCTGAAGACTTT
1 TCGGCTTTGACCTTGAAGACTACCTCATCT-AAGTCTACCTGTCAGCTTTGACCCTGAAGACTTT
* * * * *
1132219 CCTACCCTTAGTCTGCCTGTCGACTTTGACCCTGGAAACTGCCTTATCTAAAGTCTAACTG
65 CATACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAAACTACCCTATCTAAAGTCTAACTG
1132280 TCGGCTTTGACCTTGAAGACT
1 TCGGCTTTGACCTTGAAGACT
1132301 TTTTTCCCCC
Statistics
Matches: 121, Mismatches: 23, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
124 25 0.21
125 65 0.54
126 31 0.26
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (125 bp):
TCGGCTTTGACCTTGAAGACTACCTCATCTAAGTCTACCTGTCAGCTTTGACCCTGAAGACTTTC
ATACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAAACTACCCTATCTAAAGTCTAACTG
Found at i:1132216 original size:83 final size:82
Alignment explanation
Indices: 1132033--1132385 Score: 259
Period size: 83 Copynumber: 4.2 Consensus size: 82
1132023 CTGCTTATCG
* * * * * *
1132033 GCTTTGACCTTGGAGACTACCTTATCTCAGTCTACCTGTTGGCTTTGACCTTGGAGACT--TTCA
1 GCTTTGACCTTGAAGACTACCCTA-CTTAGTCTACCTGTCGGCTTTGACCTTGAAGACTGCCTCA
* *
1132096 TACCCT-CAGTCTGCCTGTCA
65 T---CTAAAGTCTACCTGTCA
* * * *
1132116 GCTTTGATCCTAG-AGACTACCCTATTTAAGTCTACCTGTTGGCTTTGACCTTGAAGATTGCCTC
1 GCTTTGA-CCTTGAAGACTACCCTACTT-AGTCTACCTGTCGGCTTTGACCTTGAAGACTGCCTC
* *
1132180 ATCTAAAGTTTGCCTGTCA
64 ATCTAAAGTCTACCTGTCA
* ** * * *
1132199 GCTTTGACCCTGAAGACTTTCCTACCCTTAGTCTGCCTGTCGACTTTGACCCTGGAA-ACTGCCT
1 GCTTTGACCTTGAAGACTACCCTA--CTTAGTCTACCTGTCGGCTTTGA-CCTTGAAGACTGCCT
* * *
1132263 TATCTAAAGTCTAACTGTCG
63 CATCTAAAGTCTACCTGTCA
* * * * * *
1132283 GCTTTGACCTTGAAGACTTTTTTCCC-CCTTAGTCTGCTTGTCGGCTTTGATCTTGGAGACTGCC
1 GCTTTGACCTTGAAGAC----TACCCTACTTAGTCTACCTGTCGGCTTTGACCTTGAAGACTGCC
* *
1132347 TCATCTAAAGTTTACCTGTCG
62 TCATCTAAAGTCTACCTGTCA
*
1132368 GCTTTGACCTTGGAGACT
1 GCTTTGACCTTGAAGACT
1132386 TTCTTACCCT
Statistics
Matches: 220, Mismatches: 36, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
81 1 0.00
82 6 0.03
83 74 0.34
84 62 0.28
85 73 0.33
88 4 0.02
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.35
Consensus pattern (82 bp):
GCTTTGACCTTGAAGACTACCCTACTTAGTCTACCTGTCGGCTTTGACCTTGAAGACTGCCTCAT
CTAAAGTCTACCTGTCA
Found at i:1132353 original size:85 final size:84
Alignment explanation
Indices: 1132144--1132467 Score: 328
Period size: 85 Copynumber: 3.9 Consensus size: 84
1132134 ACCCTATTTA
* * * * * * *
1132144 AGTCTACCTGTTGGCTTTGACCTTGAAGATTGCCTCATCTAAAGTTTGCCTGTCAGCTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTTTACCTGTCGGCTTTGACCT
1132209 TGAAGACTTTCCTACCCTT
66 TGAAGACTTTCCTACCCTT
* * * * * *
1132228 AGTCTGCCTGTCGACTTTGACCCTGGAAACTGCCTTATCTAAAGTCTAACTGTCGGCTTTGACCT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTTTACCTGTCGGCTTTGACCT
** *
1132293 TGAAGACTTTTTTCCCCCTT
66 TGAAGACTTTCCT-ACCCTT
* *
1132313 AGTCTGCTTGTCGGCTTTGATCTTGGAGACTGCCTCATCTAAAGTTTACCTGTCGGCTTTGACCT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTTTACCTGTCGGCTTTGACCT
* * *
1132378 TGGAGACTTTCTTACCCTC
66 TGAAGACTTTCCTACCCTT
* * * * * * * * **
1132397 AAT-TTCCTGTTGGCTTTGACCCTGGACACT-ACTCTATTTAAAGTCTGTCTGTCGGCTTTGACC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTC-ATCTAAAGTTTACCTGTCGGCTTTGACC
*
1132460 TTGGAGAC
65 TTGAAGAC
1132468 CGCCTTATTT
Statistics
Matches: 198, Mismatches: 40, Indels: 5
0.81 0.16 0.02
Matches are distributed among these distances:
82 3 0.02
83 53 0.27
84 69 0.35
85 73 0.37
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.36
Consensus pattern (84 bp):
AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTTTACCTGTCGGCTTTGACCT
TGAAGACTTTCCTACCCTT
Found at i:1132356 original size:169 final size:168
Alignment explanation
Indices: 1132156--1132467 Score: 428
Period size: 169 Copynumber: 1.9 Consensus size: 168
1132146 TCTACCTGTT
* *
1132156 GGCTTTGACCTTGAAGATTGCCTCATCTAAAGTTTGCCTGTCAGCTTTGACCCTGAAGACTTTCC
1 GGCTTTGACCTTGAAGACTGCCTCATCTAAAGTTTACCTGTCAGCTTTGACCCTGAAGACTTTCC
* * *
1132221 TACCCTTAGTCTGCCTGTCGACTTTGACCCTGGAAACTGC-CTTATCTAAAGTCTAACTGTCGGC
66 TACCCTCAAT-TGCCTGTCGACTTTGACCCTGGAAACTACTC-TATCTAAAGTCTAACTGTCGGC
1132285 TTTGACCTTGAAGACTTTTTTCCCCCTTAGTCTGCTTGTC
129 TTTGACCTTGAAGACTTTTTTCCCCCTTAGTCTGCTTGTC
* * * * * *
1132325 GGCTTTGATCTTGGAGACTGCCTCATCTAAAGTTTACCTGTCGGCTTTGACCTTGGAGACTTTCT
1 GGCTTTGACCTTGAAGACTGCCTCATCTAAAGTTTACCTGTCAGCTTTGACCCTGAAGACTTTCC
* * * * * **
1132390 TACCCTCAATTTCCTGTTGGCTTTGACCCTGGACACTACTCTATTTAAAGTCTGTCTGTCGGCTT
66 TACCCTCAATTGCCTGTCGACTTTGACCCTGGAAACTACTCTATCTAAAGTCTAACTGTCGGCTT
*
1132455 TGACCTTGGAGAC
131 TGACCTTGAAGAC
1132468 CGCCTTATTT
Statistics
Matches: 123, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
168 57 0.46
169 66 0.54
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.36
Consensus pattern (168 bp):
GGCTTTGACCTTGAAGACTGCCTCATCTAAAGTTTACCTGTCAGCTTTGACCCTGAAGACTTTCC
TACCCTCAATTGCCTGTCGACTTTGACCCTGGAAACTACTCTATCTAAAGTCTAACTGTCGGCTT
TGACCTTGAAGACTTTTTTCCCCCTTAGTCTGCTTGTC
Found at i:1133021 original size:46 final size:47
Alignment explanation
Indices: 1132961--1133049 Score: 112
Period size: 46 Copynumber: 1.9 Consensus size: 47
1132951 GATATAAAAT
*
1132961 AAAAAATAAATAATATAAT-AATAAAAAAATT-AAAAAATTAAAATCAC
1 AAAAAATAAATAATA-AATCAAT-AAAAAATTCAAAAAAATAAAATCAC
* *
1133008 AAAAAA-AATTAATAAATCAATTAAAAATTCAAAAAAATAAAA
1 AAAAAATAAATAATAAATCAATAAAAAATTCAAAAAAATAAAA
1133050 AAATCAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
45 10 0.27
46 21 0.57
47 6 0.16
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (47 bp):
AAAAAATAAATAATAAATCAATAAAAAATTCAAAAAAATAAAATCAC
Done.