Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 167 of 279
Found at i:55470349 original size:24 final size:22
Alignment explanation
Indices: 55470289--55470350 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
55470279 AACAATAGTA
55470289 ATAAAGATAAAAA-ATATATATAC
1 ATAAA-ATAAAAATA-ATATATAC
** *
55470312 ATAAAATAGTAATAATATATAT
1 ATAAAATAAAAATAATATATAC
55470334 ATAACTAATAAAAATAA
1 ATAA--AATAAAAATAA
55470351 AAATAAAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 16 0.52
23 6 0.19
24 9 0.29
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (22 bp):
ATAAAATAAAAATAATATATAC
Found at i:55470576 original size:27 final size:28
Alignment explanation
Indices: 55470542--55470598 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
55470532 TAGATAGCTA
55470542 ATAATATT-AAAACATATACATAATAAT
1 ATAATATTAAAAACATATACATAATAAT
* *
55470569 ATAATATTAAAAACATATATATATTAAT
1 ATAATATTAAAAACATATACATAATAAT
55470597 AT
1 AT
55470599 GAAAAATGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (28 bp):
ATAATATTAAAAACATATACATAATAAT
Found at i:55470749 original size:23 final size:22
Alignment explanation
Indices: 55470723--55470795 Score: 71
Period size: 23 Copynumber: 3.4 Consensus size: 22
55470713 AATATATACG
55470723 TAATATATATATAGTAGTAACTA
1 TAATATATATATAGTAGTAA-TA
* *
55470746 TAATAAATATATATTAGTAATA
1 TAATATATATATAGTAGTAATA
* * *
55470768 -AATATAAAAATAATAGT-A-A
1 TAATATATATATAGTAGTAATA
55470787 TAATATATA
1 TAATATATA
55470796 AAAAGAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 1 0.02
20 8 0.19
21 13 0.31
22 2 0.05
23 18 0.43
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.37
Consensus pattern (22 bp):
TAATATATATATAGTAGTAATA
Found at i:55470798 original size:21 final size:22
Alignment explanation
Indices: 55470729--55470798 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 22
55470719 TACGTAATAT
*
55470729 ATATATAGTAGTAACTATAATAAA
1 ATATATAGTAATAA-TAT-ATAAA
55470753 TATATATTAGTAATAA-ATATAAA
1 -ATATA-TAGTAATAATATATAAA
55470776 A-ATAATAGTAATAATATATAAA
1 ATAT-ATAGTAATAATATATAAA
55470798 A
1 A
55470799 AGAAAATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
21 11 0.27
22 10 0.24
23 5 0.12
24 2 0.05
25 5 0.12
26 8 0.20
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.34
Consensus pattern (22 bp):
ATATATAGTAATAATATATAAA
Found at i:55471422 original size:11 final size:11
Alignment explanation
Indices: 55471406--55471448 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
55471396 AAAACTCTAA
*
55471406 TTTTTTTTCTT
1 TTTTTTTTATT
*
55471417 TTTTTTTTGTT
1 TTTTTTTTATT
*
55471428 TTCTTTTTATT
1 TTTTTTTTATT
*
55471439 TTCTTTTTAT
1 TTTTTTTTAT
55471449 ATTCTCGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.05, C:0.07, G:0.02, T:0.86
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:55471431 original size:16 final size:15
Alignment explanation
Indices: 55471405--55471445 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
55471395 TAAAACTCTA
55471405 ATTTTTTTTCTTTTT
1 ATTTTTTTTCTTTTT
*
55471420 TTTTTGTTTTCTTTTT
1 ATTTT-TTTTCTTTTT
55471436 ATTTTCTTTT
1 ATTTT-TTTT
55471446 TATATTCTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.05, C:0.07, G:0.02, T:0.85
Consensus pattern (15 bp):
ATTTTTTTTCTTTTT
Found at i:55472996 original size:87 final size:87
Alignment explanation
Indices: 55472876--55473179 Score: 463
Period size: 87 Copynumber: 3.4 Consensus size: 87
55472866 ATGTGGCCCA
55472876 AGGCTCAACTCA-CTTCTCGCAATATGAGTTGATTTGGAAAAGTAGAAATTAAAGACAGAAATTG
1 AGGCTCAACTCATC-TCTCGCAATATGAGTTGATTTGGAAAAGTAGAAATTAAAGACAGAAATTG
55472940 AAATTACCTCAGCGTGTGAACCG
65 AAATTACCTCAGCGTGTGAACCG
55472963 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTTGGAAAAGTAGAAATTAAAGACAGAAATTGA
1 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTTGGAAAAGTAGAAATTAAAGACAGAAATTGA
55473028 AATTACCTCAGCGTGTGAACCG
66 AATTACCTCAGCGTGTGAACCG
55473050 AGGCTCAAGTCACCTCAACTCACCTCTCGCAATATGAGTTGATTTGGAAAAGTAGAAATTAAAGA
1 AGGCTC-A---A-CTC-A-T---CTCTCGCAATATGAGTTGATTTGGAAAAGTAGAAATTAAAGA
55473115 CAGAAATTGAAATTACCTCAGCGTGT---CCTG
56 CAGAAATTGAAATTACCTCAGCGTGTGAACC-G
*
55473145 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTT
55473180 CTGAGAACAG
Statistics
Matches: 204, Mismatches: 1, Indels: 26
0.88 0.00 0.11
Matches are distributed among these distances:
85 22 0.11
87 91 0.45
88 2 0.01
89 1 0.00
90 3 0.01
91 2 0.01
92 3 0.01
93 1 0.00
94 4 0.02
95 7 0.03
97 68 0.33
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (87 bp):
AGGCTCAACTCATCTCTCGCAATATGAGTTGATTTGGAAAAGTAGAAATTAAAGACAGAAATTGA
AATTACCTCAGCGTGTGAACCG
Found at i:55473132 original size:97 final size:95
Alignment explanation
Indices: 55472966--55473160 Score: 338
Period size: 97 Copynumber: 2.0 Consensus size: 95
55472956 TGAACCGAGG
*
55472966 CTCAACTCATCTCTCGCAATATGAGTTGATTTGGAAAAGTAGAAATTAAAGACAGAAATTGAAAT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTGGAAAAGTAGAAATTAAAGACAGAAATTGAAAT
*
55473031 TACCTCAGCGTGTGAACC-GAGGCTCAAGTCAC
66 TACCTCAGCGTGT---CCTGAGGCTCAACTCAC
55473063 CTCAACTCACCTCTCGCAATATGAGTTGATTTGGAAAAGTAGAAATTAAAGACAGAAATTGAAAT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTGGAAAAGTAGAAATTAAAGACAGAAATTGAAAT
55473128 TACCTCAGCGTGTCCTGAGGCTCAACTCAC
66 TACCTCAGCGTGTCCTGAGGCTCAACTCAC
55473158 CTC
1 CTC
55473161 TCGCAATATG
Statistics
Matches: 95, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
94 2 0.02
95 16 0.17
97 77 0.81
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (95 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTGGAAAAGTAGAAATTAAAGACAGAAATTGAAAT
TACCTCAGCGTGTCCTGAGGCTCAACTCAC
Found at i:55479396 original size:23 final size:25
Alignment explanation
Indices: 55479351--55479397 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
55479341 AATAAATATA
*
55479351 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
55479376 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
55479398 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:55488557 original size:20 final size:21
Alignment explanation
Indices: 55488532--55488577 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
55488522 AGAAATATAC
*
55488532 TATACAT-AATATTCAAAATA
1 TATACATAAATAGTCAAAATA
55488552 TATACATGAAATAGTCAAAATA
1 TATACAT-AAATAGTCAAAATA
55488574 TATA
1 TATA
55488578 TATACTACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
22 16 0.70
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (21 bp):
TATACATAAATAGTCAAAATA
Found at i:55489330 original size:24 final size:22
Alignment explanation
Indices: 55489270--55489331 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
55489260 AACAATAGTA
*
55489270 ATAAAGATAAAAAAAATATATAC
1 ATAAA-ATAAAAATAATATATAC
** *
55489293 ATAAAATAGTAATAATATATAT
1 ATAAAATAAAAATAATATATAC
55489315 ATAACTAATAAAAATAA
1 ATAA--AATAAAAATAA
55489332 AAATAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 17 0.55
23 5 0.16
24 9 0.29
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (22 bp):
ATAAAATAAAAATAATATATAC
Found at i:55489556 original size:27 final size:28
Alignment explanation
Indices: 55489522--55489578 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
55489512 TAGATAGCTA
55489522 ATAATATT-AAAACATATACATAATAAT
1 ATAATATTAAAAACATATACATAATAAT
* *
55489549 ATAATATTAAAAACATATATATATTAAT
1 ATAATATTAAAAACATATACATAATAAT
55489577 AT
1 AT
55489579 GAAAAATGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (28 bp):
ATAATATTAAAAACATATACATAATAAT
Found at i:55489729 original size:23 final size:22
Alignment explanation
Indices: 55489703--55489775 Score: 71
Period size: 23 Copynumber: 3.4 Consensus size: 22
55489693 AATATATACG
55489703 TAATATATATATAGTAGTAACTA
1 TAATATATATATAGTAGTAA-TA
* *
55489726 TAATAAATATATATTAGTAATA
1 TAATATATATATAGTAGTAATA
* * *
55489748 -AATATAAAAATAATAGT-A-A
1 TAATATATATATAGTAGTAATA
55489767 TAATATATA
1 TAATATATA
55489776 AAAAGAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 1 0.02
20 8 0.19
21 13 0.31
22 2 0.05
23 18 0.43
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.37
Consensus pattern (22 bp):
TAATATATATATAGTAGTAATA
Found at i:55489778 original size:21 final size:22
Alignment explanation
Indices: 55489709--55489778 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 22
55489699 TACGTAATAT
*
55489709 ATATATAGTAGTAACTATAATAAA
1 ATATATAGTAATAA-TAT-ATAAA
55489733 TATATATTAGTAATAA-ATATAAA
1 -ATATA-TAGTAATAATATATAAA
55489756 A-ATAATAGTAATAATATATAAA
1 ATAT-ATAGTAATAATATATAAA
55489778 A
1 A
55489779 AGAAAATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
21 11 0.27
22 10 0.24
23 5 0.12
24 2 0.05
25 5 0.12
26 8 0.20
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.34
Consensus pattern (22 bp):
ATATATAGTAATAATATATAAA
Found at i:55492902 original size:26 final size:26
Alignment explanation
Indices: 55492871--55493004 Score: 232
Period size: 26 Copynumber: 5.2 Consensus size: 26
55492861 TGAAATGCCC
*
55492871 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
55492897 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55492923 ATCATGGAACATTTACCCAACCTATT
1 ATCATGGAACATTTACCTAACCCATT
55492949 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
55492975 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
55493001 ATCA
1 ATCA
55493005 ATTTTTATCA
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 102 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:55496559 original size:21 final size:20
Alignment explanation
Indices: 55496531--55496570 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
55496521 CCCTTCCAAG
*
55496531 TGCCCCACGTCCATGGCCAT
1 TGCCCCACGACCATGGCCAT
*
55496551 TGCCACCACGACCTTGGCCA
1 TGCC-CCACGACCATGGCCA
55496571 CGACCTCTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.17, C:0.45, G:0.20, T:0.17
Consensus pattern (20 bp):
TGCCCCACGACCATGGCCAT
Found at i:55497620 original size:12 final size:12
Alignment explanation
Indices: 55497603--55497633 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
55497593 AGTACTACCT
*
55497603 CGGCCTCGACCA
1 CGGCCTCGACAA
55497615 CGGCCTCGACAA
1 CGGCCTCGACAA
55497627 CGGCCTC
1 CGGCCTC
55497634 TTCCCCGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.48, G:0.26, T:0.10
Consensus pattern (12 bp):
CGGCCTCGACAA
Found at i:55500893 original size:15 final size:14
Alignment explanation
Indices: 55500869--55500915 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 14
55500859 TAAAACTCTA
55500869 ATTTTTTTCTTTTT
1 ATTTTTTTCTTTTT
55500883 ATTTGTTTTCTTTTT
1 ATTT-TTTTCTTTTT
* *
55500898 ATTTTCTT-TTTAT
1 ATTTTTTTCTTTTT
55500911 ATTTT
1 ATTTT
55500916 CGTATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 9 0.30
14 7 0.23
15 14 0.47
ACGTcount: A:0.11, C:0.06, G:0.02, T:0.81
Consensus pattern (14 bp):
ATTTTTTTCTTTTT
Found at i:55507736 original size:18 final size:16
Alignment explanation
Indices: 55507691--55507741 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 16
55507681 TTATGTATTT
55507691 TTAAAATT-TTAAAAA
1 TTAAAATTATTAAAAA
*
55507706 TTAAAAATCATTAAAATCA
1 TT-AAAATTATTAAAA--A
55507725 TTAAAATTATTAAAAA
1 TTAAAATTATTAAAAA
55507741 T
1 T
55507742 ATATTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 2 0.07
16 7 0.23
17 6 0.20
18 12 0.40
19 3 0.10
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAAATTATTAAAAA
Found at i:55507740 original size:10 final size:9
Alignment explanation
Indices: 55507709--55507739 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
55507699 TTAAAAATTA
55507709 AAAATCATT
1 AAAATCATT
55507718 AAAATCATT
1 AAAATCATT
*
55507727 AAAATTATT
1 AAAATCATT
55507736 AAAA
1 AAAA
55507740 ATATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATCATT
Found at i:55512303 original size:22 final size:23
Alignment explanation
Indices: 55512278--55512337 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
55512268 TGGACTGAAT
55512278 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
55512300 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
55512322 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
55512338 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:55512305 original size:4 final size:4
Alignment explanation
Indices: 55512287--55512320 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
55512277 TATAAAAATT
55512287 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
55512321 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:55513726 original size:23 final size:22
Alignment explanation
Indices: 55513674--55513726 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
55513664 TCCACGTCTT
*
55513674 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
55513696 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
55513719 TTTCTTTT
1 TTTCTTTT
55513727 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:55516101 original size:22 final size:23
Alignment explanation
Indices: 55516076--55516135 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
55516066 TGGACTGAAT
55516076 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
55516098 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
55516120 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
55516136 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:55516103 original size:4 final size:4
Alignment explanation
Indices: 55516085--55516118 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
55516075 TATAAAAATT
55516085 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
55516119 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:55517267 original size:13 final size:13
Alignment explanation
Indices: 55517248--55517280 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
55517238 TTTTGCATTT
55517248 TATGTGTGAGAAAA
1 TATGTGTGA-AAAA
55517262 -ATGTGTGAAAAA
1 TATGTGTGAAAAA
55517274 TATGTGT
1 TATGTGT
55517281 TTACTTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.33
Consensus pattern (13 bp):
TATGTGTGAAAAA
Found at i:55524543 original size:15 final size:15
Alignment explanation
Indices: 55524518--55524555 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
55524508 AGACCATGGA
*
55524518 AGAAGAGGTGGA-GT
1 AGAAGAAGTGGAGGT
55524532 ATGAAGAAGTGGAGGT
1 A-GAAGAAGTGGAGGT
55524548 AGAAGAAG
1 AGAAGAAG
55524556 AAGGAGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 17 0.81
16 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.13
Consensus pattern (15 bp):
AGAAGAAGTGGAGGT
Found at i:55524554 original size:3 final size:3
Alignment explanation
Indices: 55524548--55524628 Score: 92
Period size: 3 Copynumber: 27.0 Consensus size: 3
55524538 AAGTGGAGGT
* * * * *
55524548 AGA AGA AGA AGG AGA GGA AGA A-A TAGA AGA GGA AGT GGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA
*
55524593 AGA AGA AGA AGA AGA AGA AGA GGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
55524629 CCTGGATGTT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
2 1 0.02
3 62 0.97
4 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:55528985 original size:21 final size:21
Alignment explanation
Indices: 55528959--55529007 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
55528949 TTCTTCATTA
55528959 TCTTCTTCTTCG-TCTTGTTCT
1 TCTTCTTCTTCGAT-TTGTTCT
*
55528980 TGTTCTTCTTCGATTTGTTCT
1 TCTTCTTCTTCGATTTGTTCT
55529001 TCTTCTT
1 TCTTCTT
55529008 TATGATTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.02, C:0.24, G:0.10, T:0.63
Consensus pattern (21 bp):
TCTTCTTCTTCGATTTGTTCT
Found at i:55552088 original size:63 final size:63
Alignment explanation
Indices: 55551979--55552105 Score: 184
Period size: 63 Copynumber: 2.0 Consensus size: 63
55551969 AAGTATGGTG
* *
55551979 CTTTAGTGCCATATGGTATATCTATCTCAACCATTATAAACATGCCATACTTGGCACAATAGA
1 CTTTAGTGCCATATGGTATAGCTATCTCAACCATTATAAACATGCCATACTTGGCACAAAAGA
* * * *
55552042 CTTTGGTGCCATATGGTATAGCTATCTTC-ACCATTATCAGCCTGCCATACTTGGCACAAAAGA
1 CTTTAGTGCCATATGGTATAGCTATC-TCAACCATTATAAACATGCCATACTTGGCACAAAAGA
55552105 C
1 C
55552106 AGATACACAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 55 0.96
64 2 0.04
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (63 bp):
CTTTAGTGCCATATGGTATAGCTATCTCAACCATTATAAACATGCCATACTTGGCACAAAAGA
Found at i:55555303 original size:22 final size:22
Alignment explanation
Indices: 55555278--55555320 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
55555268 TATCCAAACA
55555278 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
55555300 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
55555321 AATAGAGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:55555324 original size:11 final size:11
Alignment explanation
Indices: 55555285--55555325 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
55555275 ACAATAACAA
55555285 CAAAATAGTAG
1 CAAAATAGTAG
* *
55555296 CAACATAATAG
1 CAAAATAGTAG
*
55555307 TAAAATAGTAG
1 CAAAATAGTAG
55555318 CAAAATAG
1 CAAAATAG
55555326 AGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:55555333 original size:22 final size:22
Alignment explanation
Indices: 55555286--55555335 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
55555276 CAATAACAAC
* *
55555286 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
55555308 AAAATAGTAGCAAAATAGAGAG-
1 AAAATAGTAGCAAAATA-AGAGT
55555330 AAAATA
1 AAAATA
55555336 ATAAGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.60, C:0.06, G:0.16, T:0.18
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:55560511 original size:52 final size:48
Alignment explanation
Indices: 55560492--55560694 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
55560482 TGACAAGTGG
* *
55560492 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
55560538 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
55560590 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
55560636 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
55560682 AAAGTGATAAGTG
1 AAAGTGATAAGTG
55560695 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:55560546 original size:98 final size:98
Alignment explanation
Indices: 55560426--55560694 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
55560416 TTTGAGTACT
*
55560426 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
55560491 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
55560524 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
55560589 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
55560622 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
55560687 GATAAGTG
65 GAAAAGTG
55560695 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:55560702 original size:37 final size:37
Alignment explanation
Indices: 55560658--55560766 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
55560648 GATAGCTTTA
55560658 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
55560695 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
55560732 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
55560767 ATCATACGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:55563290 original size:18 final size:18
Alignment explanation
Indices: 55563267--55563549 Score: 169
Period size: 18 Copynumber: 15.3 Consensus size: 18
55563257 GAATAATTAT
55563267 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
55563285 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
55563303 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
*
55563321 TTATTCAGTATCGATCAATTGATCGG
1 TTATTCAGTA---A-C-A--G-TCAG
* *
55563347 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
*
55563365 TTATTCAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * *
55563382 ATATTCAGTAACTATTAAG
1 TTATTCAGTAAC-AGTCAG
*
55563401 TTATTCAGTAGCAGTCA-
1 TTATTCAGTAACAGTCAG
* *
55563418 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAG
* *
55563437 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* *
55563455 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
55563473 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAGTC-AG
* * *
55563491 ATATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* * *
55563509 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
55563527 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
55563545 TTATT
1 TTATT
55563550 TTATACCTTT
Statistics
Matches: 202, Mismatches: 47, Indels: 32
0.72 0.17 0.11
Matches are distributed among these distances:
17 17 0.08
18 151 0.75
19 18 0.09
21 2 0.01
22 1 0.00
23 2 0.01
26 11 0.05
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:55563309 original size:36 final size:36
Alignment explanation
Indices: 55563267--55563549 Score: 196
Period size: 36 Copynumber: 7.6 Consensus size: 36
55563257 GAATAATTAT
* *
55563267 TTATTCAGTAACAGTCAGTTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * * * *
55563303 TTATTCAATAATAACCAGTTATTCAGTATCGATCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* *
55563339 TTGATCGGTTATCCAGTAACAGTCAATTATTCAGTAA-AATCAGA
1 TT-A-----T-T-CAGTAACAATCAGTTATTCAGTAACAATCA-A
* * * *
55563383 -TATTCAGTAACTATTAAGTTATTCAGTAGCAGTC-A
1 TTATTCAGTAAC-AATCAGTTATTCAGTAACAATCAA
* **
55563418 TTCATTCAGTGACAATCAGTTATTCAGTAATGATCAA
1 TT-ATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * *
55563455 TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATC-AA
* * * * * *
55563492 -TATCCAGTAACAGTCAATTATCCGGTAACAGTCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
*
55563527 TTATTCAGTAATAATCAGTTATT
1 TTATTCAGTAACAATCAGTTATT
55563550 TTATACCTTT
Statistics
Matches: 188, Mismatches: 43, Indels: 32
0.71 0.16 0.12
Matches are distributed among these distances:
35 10 0.05
36 132 0.70
37 19 0.10
42 2 0.01
43 6 0.03
44 19 0.10
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (36 bp):
TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
Found at i:55563482 original size:72 final size:71
Alignment explanation
Indices: 55563348--55563549 Score: 228
Period size: 72 Copynumber: 2.8 Consensus size: 71
55563338 ATTGATCGGT
* * *
55563348 TATCCAGTAACAGTCAATTATTCAGTAAAATCAGA-TATTCAGTAACTATTAAGTTATTCAGTAG
1 TATCCAGTAACAATCAATTATTCAGTAAAATCA-ATTATTCAGTAA-TATTCAGTTATTCAGTAA
*
55563412 CAGTC-AT
64 CAGTCTAA
* * * *
55563419 TCATTCAGTGACAATCAGTTATTCAGTAATGATCAATTATTCAGTAATATTCAGTTATTCAGTAA
1 T-ATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATTCAGTAA
55563484 CAGTCTAA
64 CAGTCTAA
* * * * *
55563492 TATCCAGTAACAGTCAATTATCCGGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 TATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATT
55563550 TTATACCTTT
Statistics
Matches: 109, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
71 1 0.01
72 92 0.84
73 16 0.15
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (71 bp):
TATCCAGTAACAATCAATTATTCAGTAAAATCAATTATTCAGTAATATTCAGTTATTCAGTAACA
GTCTAA
Found at i:55563724 original size:6 final size:6
Alignment explanation
Indices: 55563713--55563737 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55563703 ACAAATTCGG
55563713 AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT A
55563738 TTCAACACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:55563766 original size:45 final size:45
Alignment explanation
Indices: 55563717--55563821 Score: 156
Period size: 45 Copynumber: 2.3 Consensus size: 45
55563707 ATTCGGAACA
* * * *
55563717 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCG
1 GTAACAGTAGCAGTAACAATATTCAACACACAAAATGCCGAATCG
* *
55563762 GTAACGGTAGCAGTAACAATATTCGACACACAAAATGCCGAATCG
1 GTAACAGTAGCAGTAACAATATTCAACACACAAAATGCCGAATCG
55563807 GTAACAGTAGCAGTA
1 GTAACAGTAGCAGTA
55563822 GCGGTAACAG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (45 bp):
GTAACAGTAGCAGTAACAATATTCAACACACAAAATGCCGAATCG
Found at i:55564087 original size:5 final size:5
Alignment explanation
Indices: 55564079--55564119 Score: 64
Period size: 5 Copynumber: 8.0 Consensus size: 5
55564069 ATTCCTTTCC
*
55564079 ATTCA ATTCA ATTCA ATTCA ATTCA ATTTA ATTCAA ATTCA
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA ATTC-A ATTCA
55564120 TTTTTCCACT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTCA
Found at i:55564498 original size:21 final size:21
Alignment explanation
Indices: 55564473--55564533 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
55564463 TTCAATTTCA
55564473 ATTCAATAA-CAATTCACATAT
1 ATTCAATAATCAATTCA-ATAT
55564494 ATTC-ATAAATCAATTCAATAT
1 ATTCAAT-AATCAATTCAATAT
* * *
55564515 AATCAATATTCAATCCAAT
1 ATTCAATAATCAATTCAAT
55564534 TCATATAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.06
21 23 0.68
22 9 0.26
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (21 bp):
ATTCAATAATCAATTCAATAT
Found at i:55579338 original size:27 final size:27
Alignment explanation
Indices: 55579307--55579359 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
55579297 AGTGTACAAA
*
55579307 ATATTGAGAATGGCACTTAGTGTGCAG
1 ATATTGAGAATGACACTTAGTGTGCAG
*
55579334 ATATTGAGAGTGACACTTAGTGTGCA
1 ATATTGAGAATGACACTTAGTGTGCA
55579360 AAATATCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.30
Consensus pattern (27 bp):
ATATTGAGAATGACACTTAGTGTGCAG
Found at i:55586292 original size:24 final size:23
Alignment explanation
Indices: 55586238--55586303 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 23
55586228 ACCCATTAAA
55586238 AATTAATAATCTTAAAAGCTCAAACC
1 AATTAA-AAT-TTAAAA-CTCAAACC
55586264 AATTAAAATTTAAAACTCAATACTC
1 AATTAAAATTTAAAACTCAA-AC-C
*
55586289 -ATTAATATTTAAAAC
1 AATTAAAATTTAAAAC
55586304 CTAAACTGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 5 0.14
24 22 0.59
25 4 0.11
26 6 0.16
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.32
Consensus pattern (23 bp):
AATTAAAATTTAAAACTCAAACC
Found at i:55590050 original size:9 final size:9
Alignment explanation
Indices: 55590036--55590065 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
55590026 AGATATAATT
55590036 AAAATTTAA
1 AAAATTTAA
55590045 AAAATTTAA
1 AAAATTTAA
55590054 AATAATTTAA
1 AA-AATTTAA
55590064 AA
1 AA
55590066 TAAGAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAATTTAA
Found at i:55590062 original size:10 final size:10
Alignment explanation
Indices: 55590038--55590068 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
55590028 ATATAATTAA
55590038 AATTTAAAA-
1 AATTTAAAAT
55590047 AATTTAAAAT
1 AATTTAAAAT
55590057 AATTTAAAAT
1 AATTTAAAAT
55590067 AA
1 AA
55590069 GAATTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AATTTAAAAT
Found at i:55591056 original size:12 final size:12
Alignment explanation
Indices: 55591039--55591064 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55591029 TTAATTAATT
55591039 TAAAAAATTAAA
1 TAAAAAATTAAA
55591051 TAAAAAATTAAA
1 TAAAAAATTAAA
55591063 TA
1 TA
55591065 TTTTTTTATA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAAAAATTAAA
Found at i:55602415 original size:20 final size:19
Alignment explanation
Indices: 55602379--55602420 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
55602369 CACTTTTATC
*
55602379 TTTTTCATGTCTTTTCTTTG
1 TTTTTCATGTCTGTTC-TTG
55602399 TTTTTC-TGTTCTGTTCTTG
1 TTTTTCATG-TCTGTTCTTG
55602418 TTT
1 TTT
55602421 AATTGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.02, C:0.14, G:0.12, T:0.71
Consensus pattern (19 bp):
TTTTTCATGTCTGTTCTTG
Found at i:55606297 original size:16 final size:15
Alignment explanation
Indices: 55606256--55606307 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
55606246 TGGTTCATTG
*
55606256 TAATAGAATAGAACTA
1 TAAT-GAATAGAGCTA
55606272 TAATTGAATAGAGCTA
1 TAA-TGAATAGAGCTA
*
55606288 TAATGAAATAGAGCTG
1 TAATG-AATAGAGCTA
55606304 TAAT
1 TAAT
55606308 TAGTAATTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 2 0.06
16 29 0.91
17 1 0.03
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (15 bp):
TAATGAATAGAGCTA
Found at i:55609410 original size:168 final size:168
Alignment explanation
Indices: 55609132--55609470 Score: 678
Period size: 168 Copynumber: 2.0 Consensus size: 168
55609122 GAAATATACA
55609132 TATATTATATGAAACTTTTTAATTTACCTTTTAAAAATTCGATCTTTAATTTACCTTCAATTCAA
1 TATATTATATGAAACTTTTTAATTTACCTTTTAAAAATTCGATCTTTAATTTACCTTCAATTCAA
55609197 TCTTTAAAAGTTGATTGATGACCAATTTCTATATCTACCGAGATTATATTATTTTTGTCTAAATT
66 TCTTTAAAAGTTGATTGATGACCAATTTCTATATCTACCGAGATTATATTATTTTTGTCTAAATT
55609262 TTATAATAACATTATATTTATAAAAATATAATTATTAT
131 TTATAATAACATTATATTTATAAAAATATAATTATTAT
55609300 TATATTATATGAAACTTTTTAATTTACCTTTTAAAAATTCGATCTTTAATTTACCTTCAATTCAA
1 TATATTATATGAAACTTTTTAATTTACCTTTTAAAAATTCGATCTTTAATTTACCTTCAATTCAA
55609365 TCTTTAAAAGTTGATTGATGACCAATTTCTATATCTACCGAGATTATATTATTTTTGTCTAAATT
66 TCTTTAAAAGTTGATTGATGACCAATTTCTATATCTACCGAGATTATATTATTTTTGTCTAAATT
55609430 TTATAATAACATTATATTTATAAAAATATAATTATTAT
131 TTATAATAACATTATATTTATAAAAATATAATTATTAT
55609468 TAT
1 TAT
55609471 TTTTTATTGT
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
168 171 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (168 bp):
TATATTATATGAAACTTTTTAATTTACCTTTTAAAAATTCGATCTTTAATTTACCTTCAATTCAA
TCTTTAAAAGTTGATTGATGACCAATTTCTATATCTACCGAGATTATATTATTTTTGTCTAAATT
TTATAATAACATTATATTTATAAAAATATAATTATTAT
Found at i:55615892 original size:29 final size:29
Alignment explanation
Indices: 55615859--55615916 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
55615849 TCAAAGGTTC
55615859 TAACAAACCCAATTTACAAAAGCTGCAAA
1 TAACAAACCCAATTTACAAAAGCTGCAAA
*
55615888 TAACAAACCCAATTTACAGAAGCTGCAAA
1 TAACAAACCCAATTTACAAAAGCTGCAAA
55615917 ACATGATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.50, C:0.24, G:0.09, T:0.17
Consensus pattern (29 bp):
TAACAAACCCAATTTACAAAAGCTGCAAA
Found at i:55618832 original size:46 final size:46
Alignment explanation
Indices: 55618765--55618893 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
55618755 TGTAACCCGC
* * * *
55618765 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
55618811 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
55618857 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
55618894 TGCTCAACCA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:55618912 original size:46 final size:45
Alignment explanation
Indices: 55618773--55618912 Score: 140
Period size: 46 Copynumber: 3.0 Consensus size: 45
55618763 GCCCATAAGC
* ** * *
55618773 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T-AGT
*** *
55618819 GAACTCGGACTCAACTCAACGAGTTCGGACATTC-GCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T-AGT
55618865 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-ACCATCCTAGT
55618911 GA
1 GA
55618913 CATGTCACTT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
46 79 0.93
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCCTAGT
Found at i:55625062 original size:132 final size:131
Alignment explanation
Indices: 55624798--55625063 Score: 343
Period size: 131 Copynumber: 2.0 Consensus size: 131
55624788 TTGCCTCGCC
* * * * * * * * *
55624798 TTAGAAAACGCGAGTGAAGTTCCAAAGGGATATTCGATTATTTTGAACAAACGGGAGATTGCGAC
1 TTAGAAAACACGAATGAAATTCCAAAGGGACATTCAATTATGTTGAACAAACGAGAAATTGCAAC
* ** *
55624863 CCAGCACGATAGGCACTATTCCCCGAATTGCCAAACATCGAACATTTCCTTCGTTTTAAAGAGTT
66 CCAGCACGATAGGCACTATTCCCCAAATTGCCAAACATCGAACATCGCCTTCGTTTTAAAGAATT
55624928 T
131 T
* * *
55624929 TTAGAAAACATGAATGAAATTCTAAAGGGACATTCAATTATGTTGAGCAAACGAGAAATTGCAAC
1 TTAGAAAACACGAATGAAATTCCAAAGGGACATTCAATTATGTTGAACAAACGAGAAATTGCAAC
* * * *
55624994 CCAGCACGTTAGGGCACTATTCCGCAAATTGCCAAATATCTAACATCGCCTTCGTTTTAAAGAAT
66 CCAGCACGATA-GGCACTATTCCCCAAATTGCCAAACATCGAACATCGCCTTCGTTTTAAAGAAT
55625059 TT
130 TT
55625061 TTA
1 TTA
55625064 AATGAATAAT
Statistics
Matches: 114, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
131 63 0.55
132 51 0.45
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (131 bp):
TTAGAAAACACGAATGAAATTCCAAAGGGACATTCAATTATGTTGAACAAACGAGAAATTGCAAC
CCAGCACGATAGGCACTATTCCCCAAATTGCCAAACATCGAACATCGCCTTCGTTTTAAAGAATT
T
Found at i:55626069 original size:10 final size:10
Alignment explanation
Indices: 55626056--55626098 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
55626046 AAATAAATAA
55626056 ATAGATATAT
1 ATAGATATAT
* *
55626066 ATAGTTACAT
1 ATAGATATAT
55626076 ATAGATATAT
1 ATAGATATAT
* *
55626086 ATACATGTAT
1 ATAGATATAT
55626096 ATA
1 ATA
55626099 AATGAAAGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (10 bp):
ATAGATATAT
Found at i:55628400 original size:46 final size:46
Alignment explanation
Indices: 55628333--55628507 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
55628323 TGTAACCCAC
*
55628333 CCATAAGTGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
55628379 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * ** * ** *
55628429 -C-TCA-CGAACTCGTTCTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
55628472 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
55628508 ATGCCTAGTT
Statistics
Matches: 103, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 59 0.57
47 24 0.23
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:55628449 original size:93 final size:93
Alignment explanation
Indices: 55628341--55628534 Score: 325
Period size: 93 Copynumber: 2.1 Consensus size: 93
55628331 ACCCATAAGT
** *
55628341 GAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
55628406 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
** *
55628434 GAACTCGTTCTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
55628499 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
55628527 GAACTCGA
1 GAACTCGA
55628535 CTTGTATCCT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:55628455 original size:47 final size:47
Alignment explanation
Indices: 55628387--55628533 Score: 151
Period size: 47 Copynumber: 3.1 Consensus size: 47
55628377 ATCCATAAGT
55628387 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
** * * * * *
55628434 GAACTCGTTCTCAACTCAACGAGTTC-GA--AC-A-TTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT-C-TCA-C
*
55628480 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
55628527 GAACTCG
1 GAACTCG
55628534 ACTTGTATCC
Statistics
Matches: 76, Mismatches: 15, Indels: 18
0.70 0.14 0.17
Matches are distributed among these distances:
42 2 0.03
43 4 0.05
44 2 0.03
45 2 0.03
46 25 0.33
47 32 0.42
48 1 0.01
49 2 0.03
50 4 0.05
51 2 0.03
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:55631812 original size:20 final size:20
Alignment explanation
Indices: 55631775--55631812 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55631765 TGATGGGGAG
*
55631775 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
55631795 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
55631813 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:55633764 original size:46 final size:46
Alignment explanation
Indices: 55633712--55633893 Score: 283
Period size: 46 Copynumber: 4.0 Consensus size: 46
55633702 AGTGTGCTCT
*
55633712 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
55633758 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
55633804 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
55633850 ATGACAGGAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
55633894 TCATGTCAAA
Statistics
Matches: 127, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 127 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:55643939 original size:21 final size:21
Alignment explanation
Indices: 55643896--55643940 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
55643886 ATAACCTGTA
* *
55643896 AAATTATTAATAATTTCATTT
1 AAATTATTAATAAATTAATTT
55643917 AAATTA-TAATAAATTAATATT
1 AAATTATTAATAAATTAAT-TT
55643938 AAA
1 AAA
55643941 ACTATAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTATTAATAAATTAATTT
Found at i:55661454 original size:26 final size:27
Alignment explanation
Indices: 55661404--55661455 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
55661394 CATATTCAGG
55661404 CGAAATCAGAGATAAGATTACCACAGC
1 CGAAATCAGAGATAAGATTACCACAGC
*
55661431 CGAAATCATAGAT-AGATTACCACAG
1 CGAAATCAGAGATAAGATTACCACAG
55661456 GTGGGAACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.17
Consensus pattern (27 bp):
CGAAATCAGAGATAAGATTACCACAGC
Found at i:55663768 original size:15 final size:16
Alignment explanation
Indices: 55663750--55663779 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55663740 TGACATTAAT
55663750 ATTTAA-CAAAATAAC
1 ATTTAATCAAAATAAC
55663765 ATTTAATCAAAATAA
1 ATTTAATCAAAATAA
55663780 TTACGGACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTTAATCAAAATAAC
Found at i:55666501 original size:18 final size:19
Alignment explanation
Indices: 55666466--55666503 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
55666456 ACATGTATAC
*
55666466 TTTATTTTTTTTACGAACTT
1 TTTATATTTTTTA-GAACTT
55666486 TTTATATTTTTT-GAACTT
1 TTTATATTTTTTAGAACTT
55666504 GTAAGGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTATATTTTTTAGAACTT
Found at i:55667615 original size:14 final size:16
Alignment explanation
Indices: 55667586--55667619 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
55667576 TGTTTTTATC
55667586 AAAATAAAATATTTAA
1 AAAATAAAATATTTAA
55667602 AAAAT-AAATA-TTAA
1 AAAATAAAATATTTAA
55667616 AAAA
1 AAAA
55667620 CACATTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 5 0.28
16 5 0.28
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAAAATATTTAA
Found at i:55672565 original size:21 final size:21
Alignment explanation
Indices: 55672539--55672578 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55672529 TTGGGTCATC
55672539 TTCTTCTTCCTCTTGTTCTGG
1 TTCTTCTTCCTCTTGTTCTGG
* *
55672560 TTCTTCTTCTTGTTGTTCT
1 TTCTTCTTCCTCTTGTTCT
55672579 TCTTCAGAAT
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:0.00, C:0.25, G:0.12, T:0.62
Consensus pattern (21 bp):
TTCTTCTTCCTCTTGTTCTGG
Found at i:55674445 original size:14 final size:14
Alignment explanation
Indices: 55674426--55674453 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55674416 TTTGCTCTAC
55674426 TACTTATTCCGCTT
1 TACTTATTCCGCTT
55674440 TACTTATTCCGCTT
1 TACTTATTCCGCTT
55674454 CACAGTAGAT
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:0.14, C:0.29, G:0.07, T:0.50
Consensus pattern (14 bp):
TACTTATTCCGCTT
Found at i:55690468 original size:21 final size:21
Alignment explanation
Indices: 55690429--55690468 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
55690419 TATTTAAGTA
*
55690429 TAATTTTTTAAAATTTATTCT
1 TAATTTTTTAAAATATATTCT
55690450 TAATTTTTTGAAAA-ATATT
1 TAATTTTTT-AAAATATATT
55690469 TATTTTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
TAATTTTTTAAAATATATTCT
Found at i:55696821 original size:9 final size:9
Alignment explanation
Indices: 55696800--55696869 Score: 52
Period size: 10 Copynumber: 7.4 Consensus size: 9
55696790 TTATCTATAG
55696800 TTTTTAATA
1 TTTTTAATA
*
55696809 -TTTTATTA
1 TTTTTAATA
*
55696817 TTTTTAAAA
1 TTTTTAATA
**
55696826 TTGTGAAATGA
1 TT-TTTAAT-A
*
55696837 TTTTAAATA
1 TTTTTAATA
55696846 TATTTTAATAA
1 T-TTTTAAT-A
55696857 TTTTTAATA
1 TTTTTAATA
55696866 TTTT
1 TTTT
55696870 GTTGTTCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 7 0.15
9 15 0.31
10 21 0.44
11 5 0.10
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTTAATA
Found at i:55697399 original size:19 final size:19
Alignment explanation
Indices: 55697375--55697431 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 19
55697365 TTCTACGTAA
55697375 AATTAAATATTTTTTAAAT
1 AATTAAATATTTTTTAAAT
*
55697394 AATTAAATCA-TTTTTACAT
1 AATTAAAT-ATTTTTTAAAT
55697413 AAGTTTAAAATATTTTTTA
1 AA--TT-AAATATTTTTTA
55697432 TTGATATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 18 0.56
20 1 0.03
21 3 0.09
22 10 0.31
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (19 bp):
AATTAAATATTTTTTAAAT
Found at i:55699039 original size:21 final size:21
Alignment explanation
Indices: 55699015--55699068 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
55699005 TTGTATTGTA
*
55699015 TAAAAATAAATATTTTAAA-AT
1 TAAAAATAAATA-TATAAATAT
* * *
55699036 TAAATATACATATATAAATTT
1 TAAAAATAAATATATAAATAT
55699057 TAAAAATAAATA
1 TAAAAATAAATA
55699069 AATTAAAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAAATAAATATATAAATAT
Found at i:55699043 original size:27 final size:27
Alignment explanation
Indices: 55699013--55699068 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
55699003 ATTTGTATTG
*
55699013 TATAAAAATA-AATATTTTAAAATTAAA
1 TATAAAAATATAA-ATTTTAAAAATAAA
* *
55699040 TATACATATATAAATTTTAAAAATAAA
1 TATAAAAATATAAATTTTAAAAATAAA
55699067 TA
1 TA
55699069 AATTAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
TATAAAAATATAAATTTTAAAAATAAA
Found at i:55701086 original size:31 final size:31
Alignment explanation
Indices: 55701049--55701109 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
55701039 TTGGTTACTA
55701049 AACTATTTAAAAATT-TTCATTTAAGTCATTG
1 AACTATTTAAAAATTCTT-ATTTAAGTCATTG
*
55701080 AACTATTTAAAAGTTCTTATTTAAGTCATT
1 AACTATTTAAAAATTCTTATTTAAGTCATT
55701110 AGGTTGTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (31 bp):
AACTATTTAAAAATTCTTATTTAAGTCATTG
Found at i:55702913 original size:21 final size:20
Alignment explanation
Indices: 55702871--55702913 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
55702861 TATTGTGTAA
**
55702871 TTTGATTTTTTTTTTGCAAT
1 TTTGATTTTTTTTTAACAAT
*
55702891 TTTGATTTTTTTTATAACCAT
1 TTTGATTTTTTTT-TAACAAT
55702912 TT
1 TT
55702914 CACCTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTGATTTTTTTTTAACAAT
Found at i:55703548 original size:12 final size:12
Alignment explanation
Indices: 55703531--55703556 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55703521 ATCAGATTAA
55703531 ATTATAATTTTT
1 ATTATAATTTTT
55703543 ATTATAATTTTT
1 ATTATAATTTTT
55703555 AT
1 AT
55703557 GATAGTAAAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTATAATTTTT
Found at i:55710500 original size:19 final size:19
Alignment explanation
Indices: 55710458--55710558 Score: 75
Period size: 19 Copynumber: 5.3 Consensus size: 19
55710448 ATGGAAGTAA
*
55710458 TAAAATATGTATAATAAA-AT
1 TAAAATGTGTA-AA-AAATAT
55710478 TAAAATGTGTAAAAAATAT
1 TAAAATGTGTAAAAAATAT
* *
55710497 TAAAATAATG-AAAGTAATA-
1 TAAAAT-GTGTAAA-AAATAT
* * * *
55710516 GAATATGTATAATAAA-AT
1 TAAAATGTGTAAAAAATAT
55710534 TAAAATGTGTAAAAAATAT
1 TAAAATGTGTAAAAAATAT
55710553 TAAAAT
1 TAAAAT
55710559 AAAGTCAGCT
Statistics
Matches: 62, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
17 1 0.02
18 18 0.29
19 27 0.44
20 16 0.26
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (19 bp):
TAAAATGTGTAAAAAATAT
Found at i:55710521 original size:56 final size:56
Alignment explanation
Indices: 55710452--55710560 Score: 209
Period size: 56 Copynumber: 1.9 Consensus size: 56
55710442 TAATCGATGG
55710452 AAGTAATAAAATATGTATAATAAAATTAAAATGTGTAAAAAATATTAAAATAATGA
1 AAGTAATAAAATATGTATAATAAAATTAAAATGTGTAAAAAATATTAAAATAATGA
*
55710508 AAGTAATAGAATATGTATAATAAAATTAAAATGTGTAAAAAATATTAAAATAA
1 AAGTAATAAAATATGTATAATAAAATTAAAATGTGTAAAAAATATTAAAATAA
55710561 AGTCAGCTGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (56 bp):
AAGTAATAAAATATGTATAATAAAATTAAAATGTGTAAAAAATATTAAAATAATGA
Found at i:55755339 original size:16 final size:15
Alignment explanation
Indices: 55755298--55755491 Score: 72
Period size: 16 Copynumber: 12.2 Consensus size: 15
55755288 CCTTTTTCCG
55755298 TTTT-TTTTCATTTCAA
1 TTTTATTTT-ATTTC-A
55755314 TTTATATTTTAATTTCA
1 TTT-TATTTT-ATTTCA
55755331 TTTTATTTTATATTCA
1 TTTTATTTTAT-TTCA
* *
55755347 TTTCACATTTCATTTCA
1 TTT--TATTTTATTTCA
** * *
55755364 TTACATTTCATTTAA
1 TTTTATTTTATTTCA
*
55755379 ATTTATTTT-TTTCA
1 TTTTATTTTATTTCA
* * *
55755393 TTTAAATTTATTTAA
1 TTTTATTTTATTTCA
* *
55755408 ATTTATTTTTTTTCA
1 TTTTATTTTATTTCA
*
55755423 TATTCATTTT-TTTC-
1 T-TTTATTTTATTTCA
*
55755437 TGTTTCCATTTTTTTTCA
1 T-TTT--ATTTTATTTCA
* *
55755455 TTTCAATTTATATTTTAA
1 TTT-TATTT-TA-TTTCA
*
55755473 TTTTATTTCATATTCA
1 TTTTATTTTAT-TTCA
55755489 TTT
1 TTT
55755492 CAATGTTAAT
Statistics
Matches: 134, Mismatches: 29, Indels: 30
0.69 0.15 0.16
Matches are distributed among these distances:
14 13 0.10
15 37 0.28
16 39 0.29
17 22 0.16
18 23 0.17
ACGTcount: A:0.24, C:0.10, G:0.01, T:0.65
Consensus pattern (15 bp):
TTTTATTTTATTTCA
Found at i:55755351 original size:5 final size:5
Alignment explanation
Indices: 55755325--55755666 Score: 74
Period size: 5 Copynumber: 63.6 Consensus size: 5
55755315 TTATATTTTA
* * *
55755325 ATTTC ATTTT ATTTT ATATTC ATTTCAC ATTTC ATTTC ATTAC ATTTC
1 ATTTC ATTTC ATTTC AT-TTC ATTT--C ATTTC ATTTC ATTTC ATTTC
* * * * *
55755373 ATTTAA ATTT- ATTT- TTTTC ATTTAA ATTT- ATTTAA ATTT- ATTTT
1 ATTT-C ATTTC ATTTC ATTTC ATTT-C ATTTC ATTT-C ATTTC ATTTC
* * * * * *
55755417 TTTTC ATATTC ATTT- TTTTC TGTTTCC ATTTT TTTTC ATTTC AATTTAT
1 ATTTC AT-TTC ATTTC ATTTC -ATTT-C ATTTC ATTTC ATTTC -ATTT-C
* * * *
55755466 ATTTTA ATTTT ATTTC ATATTC ATTTC AATGTTA ATTTC ATTTC ACATTC
1 A-TTTC ATTTC ATTTC AT-TTC ATTTC -AT-TTC ATTTC ATTTC A-TTTC
* * *
55755516 ATTAC AACTTTC ATTTCAC ATTTC ATTT- -TTTGT TTTTC ATTTTC ATTT-
1 ATTTC -A-TTTC ATTT--C ATTTC ATTTC ATTT-C ATTTC A-TTTC ATTTC
* * * *
55755564 TTTTCC ATTTC AATTT- -TTTCC ATATTC ATTTT TTTCTC ATTTC AATTTAT
1 ATTT-C ATTTC -ATTTC ATTT-C AT-TTC ATTTC ATT-TC ATTTC -ATTT-C
*
55755614 ATTTTA ATTTC ATTTC AAATTTC ATTTC ATTTC ATATTC ATTTC ATATTC
1 A-TTTC ATTTC ATTTC --ATTTC ATTTC ATTTC AT-TTC ATTTC AT-TTC
55755664 ATT
1 ATT
55755667 CCAATTTTTT
Statistics
Matches: 255, Mismatches: 39, Indels: 86
0.67 0.10 0.23
Matches are distributed among these distances:
3 6 0.02
4 21 0.08
5 113 0.44
6 86 0.34
7 29 0.11
ACGTcount: A:0.24, C:0.14, G:0.01, T:0.61
Consensus pattern (5 bp):
ATTTC
Found at i:55755393 original size:19 final size:19
Alignment explanation
Indices: 55755369--55755405 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
55755359 TTTCATTACA
55755369 TTTCATTTAAATTTATTTT
1 TTTCATTTAAATTTATTTT
55755388 TTTCATTTAAATTTATTT
1 TTTCATTTAAATTTATTT
55755406 AAATTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTCATTTAAATTTATTTT
Found at i:55755394 original size:29 final size:29
Alignment explanation
Indices: 55755359--55755419 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
55755349 TCACATTTCA
*
55755359 TTTCA-TTACATTTCATTTAAATTTATTTT
1 TTTCATTTAAATTT-ATTTAAATTTATTTT
55755388 TTTCATTTAAATTTATTTAAATTTATTTT
1 TTTCATTTAAATTTATTTAAATTTATTTT
55755417 TTT
1 TTT
55755420 TCATATTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTCATTTAAATTTATTTAAATTTATTTT
Found at i:55755420 original size:30 final size:31
Alignment explanation
Indices: 55755359--55755423 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
55755349 TCACATTTCA
*
55755359 TTTCA-TTACATTTCATTTAAATTTA-TTTT
1 TTTCATTTAAATTTCATTTAAATTTATTTTT
55755388 TTTCATTTAAATTT-ATTTAAATTTATTTTT
1 TTTCATTTAAATTTCATTTAAATTTATTTTT
55755418 TTTCAT
1 TTTCAT
55755424 ATTCATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.65
Consensus pattern (31 bp):
TTTCATTTAAATTTCATTTAAATTTATTTTT
Found at i:55755491 original size:28 final size:28
Alignment explanation
Indices: 55755444--55755518 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
55755434 TTCTGTTTCC
* *
55755444 ATTTTTTTTCAT-TTCAATTT-ATATTTTA
1 ATTTTATTTCATATTC-ATTTCA-ATGTTA
55755472 ATTTTATTTCATATTCATTTCAATGTTA
1 ATTTTATTTCATATTCATTTCAATGTTA
* *
55755500 ATTTCATTTCACATTCATT
1 ATTTTATTTCATATTCATT
55755519 ACAACTTTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 37 0.90
29 4 0.10
ACGTcount: A:0.27, C:0.12, G:0.01, T:0.60
Consensus pattern (28 bp):
ATTTTATTTCATATTCATTTCAATGTTA
Found at i:55755516 original size:23 final size:22
Alignment explanation
Indices: 55755499--55755542 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 22
55755489 TTTCAATGTT
55755499 AATTTCATTTCACATTCATTAC
1 AATTTCATTTCACATTCATTAC
55755521 AACTTTCATTTCACATTTCATT
1 AA-TTTCATTTCACA-TTCATT
55755543 TTTTGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 12 0.60
24 6 0.30
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTTCATTTCACATTCATTAC
Found at i:55755539 original size:12 final size:12
Alignment explanation
Indices: 55755500--55755543 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
55755490 TTCAATGTTA
55755500 ATTTCATTTCAC
1 ATTTCATTTCAC
*
55755512 A-TTCATTACA-
1 ATTTCATTTCAC
55755522 ACTTTCATTTCAC
1 A-TTTCATTTCAC
55755535 ATTTCATTT
1 ATTTCATTT
55755544 TTTGTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 1 0.04
11 8 0.30
12 17 0.63
13 1 0.04
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTCATTTCAC
Found at i:55755595 original size:31 final size:31
Alignment explanation
Indices: 55755548--55755611 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
55755538 TCATTTTTTG
*
55755548 TTTTTCATTTTCATTTTTTTC-CATTTCAAT
1 TTTTTCATATTCATTTTTTTCTCATTTCAAT
55755578 TTTTTCCATATTCATTTTTTTCTCATTTCAAT
1 TTTTT-CATATTCATTTTTTTCTCATTTCAAT
55755610 TT
1 TT
55755612 ATATTTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 5 0.16
31 15 0.48
32 11 0.35
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (31 bp):
TTTTTCATATTCATTTTTTTCTCATTTCAAT
Found at i:55755655 original size:11 final size:11
Alignment explanation
Indices: 55755632--55755666 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
55755622 TTCATTTCAA
55755632 ATTTCAT-TTC
1 ATTTCATATTC
55755642 ATTTCATATTC
1 ATTTCATATTC
55755653 ATTTCATATTC
1 ATTTCATATTC
55755664 ATT
1 ATT
55755667 CCAATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 7 0.29
11 17 0.71
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTCATATTC
Found at i:55755664 original size:17 final size:17
Alignment explanation
Indices: 55755600--55755665 Score: 73
Period size: 17 Copynumber: 3.8 Consensus size: 17
55755590 CATTTTTTTC
55755600 TCATTTCAATTT-ATATTT
1 TCATTTC-ATTTCATA-TT
* *
55755618 TAATTTCATTTCAAATT
1 TCATTTCATTTCATATT
55755635 TCATTTCATTTCATA-T
1 TCATTTCATTTCATATT
55755651 TCATTTCATATTCAT
1 TCATTTCAT-TTCAT
55755666 TCCAATTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 10 0.24
17 24 0.57
18 8 0.19
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (17 bp):
TCATTTCATTTCATATT
Found at i:55755712 original size:148 final size:148
Alignment explanation
Indices: 55755292--55755715 Score: 401
Period size: 147 Copynumber: 2.9 Consensus size: 148
55755282 TTGTCACCTT
* * *
55755292 TTTCCGTTTTTTTTCATTTCAATTTATATTTTAATTTCATTT--TATTTTATATTCATTTCACAT
1 TTTCCATTTTTTTTCATTTCAATTTATATTTTAATTTCATTTCATATTTCAT-TTCATTTCATA-
* * * * *
55755355 TTCATTTCAT-TACATTTC-ATTTAAATTTATTTTTTTCATTTAAA-TTTATTTAAATTTATTTT
64 TTCATTTCATATTCATTACAATTTAATTTTATTTTTTT-AATTAAATTTTATTT-TATTTATTTT
* * **
55755417 TTTTCATATTCATTTTTTTCTG
127 TTTCCATATTCAATTTTTTCCA
* *
55755439 TTTCCATTTTTTTTCATTTCAATTTATATTTTAATTTTATTTCATA-TTCATTTCAATGTTAAT-
1 TTTCCATTTTTTTTCATTTCAATTTATATTTTAATTTCATTTCATATTTCATTTC-AT-TTCATA
* * * ** * *
55755502 TTCATTTCACATTCATTACAACTTTCATTTCA--CATTTCATT---TTTTGTTTTTCATTTTCAT
64 TTCATTTCATATTCATTACAA-TTTAATTTTATTTTTTTAATTAAATTTT-ATTTT-A-TTT-AT
55755562 TTTTTTCCAT-TTCAATTTTTTCCA
124 TTTTTTCCATATTCAATTTTTTCCA
*
55755586 TATT-CATTTTTTTCTCATTTCAATTTATATTTTAATTTCATTTCAAATTTCATTTCATTTCATA
1 T-TTCCATTTTTTT-TCATTTCAATTTATATTTTAATTTCATTTCATATTTCATTTCATTTCATA
* * *
55755650 TTCATTTCATATTCATTCCAATTT-TTTTTATTTTTTTAATTAAATTTTATTTTATTTAATTTTT
64 TTCATTTCATATTCATTACAATTTAATTTTATTTTTTTAATTAAATTTTATTTTATTTATTTTTT
55755714 TC
129 TC
55755716 TCATTTTAAA
Statistics
Matches: 223, Mismatches: 33, Indels: 42
0.75 0.11 0.14
Matches are distributed among these distances:
145 3 0.01
146 8 0.04
147 93 0.42
148 89 0.40
149 15 0.07
150 11 0.05
151 4 0.02
ACGTcount: A:0.24, C:0.13, G:0.01, T:0.62
Consensus pattern (148 bp):
TTTCCATTTTTTTTCATTTCAATTTATATTTTAATTTCATTTCATATTTCATTTCATTTCATATT
CATTTCATATTCATTACAATTTAATTTTATTTTTTTAATTAAATTTTATTTTATTTATTTTTTTC
CATATTCAATTTTTTCCA
Found at i:55755721 original size:148 final size:146
Alignment explanation
Indices: 55755292--55755721 Score: 393
Period size: 148 Copynumber: 2.9 Consensus size: 146
55755282 TTGTCACCTT
* * *
55755292 TTTCCGTTTTTTTTCATTTCAATTTATATTTTAATTTCATTT--TATTTTATATTCATTTCACAT
1 TTTCCATTTTTTTTCATTTCAATTTATATTTTAATTTCATTTCATATTTCAT-TTCATTTCATA-
* * * * *
55755355 TTCATTTCAT-TACATTTC-ATTTAAATTTATTTTTTTCATTTAAA-TTTATTTAAATTTATTTT
64 TTCATTTCATATTCATTACAATTTAATTTTATTTTTTT-AATTAAATTTTATTT-TATTTA-TTT
* **
55755417 TTTTCATATTCATTTTTTTCTG
126 TTTTCAT-TTCAATTTTTTCCA
* *
55755439 TTTCCATTTTTTTTCATTTCAATTTATATTTTAATTTTATTTCATA-TTCATTTCAATGTTAAT-
1 TTTCCATTTTTTTTCATTTCAATTTATATTTTAATTTCATTTCATATTTCATTTC-AT-TTCATA
* * * ** * *
55755502 TTCATTTCACATTCATTACAACTTTCATTTCA--CATTTCATT---TTTTGTTTTTCATTTTCAT
64 TTCATTTCATATTCATTACAA-TTTAATTTTATTTTTTTAATTAAATTTT-ATTTT-A-TTT-AT
55755562 TTTTTTCCATTTCAATTTTTTCCA
124 TTTTTT-CATTTCAATTTTTTCCA
*
55755586 TATT-CATTTTTTTCTCATTTCAATTTATATTTTAATTTCATTTCAAATTTCATTTCATTTCATA
1 T-TTCCATTTTTTT-TCATTTCAATTTATATTTTAATTTCATTTCATATTTCATTTCATTTCATA
* *
55755650 TTCATTTCATATTCATTCCAATTT-TTTTTATTTTTTTAATTAAATTTTATTTTATTTAATTTTT
64 TTCATTTCATATTCATTACAATTTAATTTTATTTTTTTAATTAAATTTTATTTTATTT-ATTTTT
55755714 TCTCATTT
128 T-TCATTT
55755722 TAAATTTCAT
Statistics
Matches: 228, Mismatches: 32, Indels: 45
0.75 0.10 0.15
Matches are distributed among these distances:
145 3 0.01
146 8 0.04
147 92 0.40
148 94 0.41
149 16 0.07
150 11 0.05
151 4 0.02
ACGTcount: A:0.24, C:0.13, G:0.01, T:0.62
Consensus pattern (146 bp):
TTTCCATTTTTTTTCATTTCAATTTATATTTTAATTTCATTTCATATTTCATTTCATTTCATATT
CATTTCATATTCATTACAATTTAATTTTATTTTTTTAATTAAATTTTATTTTATTTATTTTTTTC
ATTTCAATTTTTTCCA
Found at i:55755738 original size:10 final size:10
Alignment explanation
Indices: 55755632--55755740 Score: 53
Period size: 10 Copynumber: 10.6 Consensus size: 10
55755622 TTCATTTCAA
*
55755632 ATTTCATTTC
1 ATTTCATTTT
*
55755642 ATTTCATATTC
1 ATTTCAT-TTT
*
55755653 ATTTCATATTC
1 ATTTCAT-TTT
*
55755664 ATTCCAATTTT
1 ATTTC-ATTTT
*
55755675 -TTTTATTTT
1 ATTTCATTTT
* **
55755684 -TTTAATTAA
1 ATTTCATTTT
*
55755693 ATTTTATTTT
1 ATTTCATTTT
*
55755703 ATTTAATTTT
1 ATTTCATTTT
55755713 -TTCTCATTTT
1 ATT-TCATTTT
55755723 AAATTTCATTTT
1 --ATTTCATTTT
55755735 ATTTCA
1 ATTTCA
55755741 AAATTTTAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
9 13 0.16
10 36 0.45
11 20 0.25
12 9 0.11
13 2 0.03
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (10 bp):
ATTTCATTTT
Found at i:55755773 original size:26 final size:25
Alignment explanation
Indices: 55755718--55755772 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
55755708 ATTTTTTCTC
* * *
55755718 ATTTTAAATTTCATTTTATTTCAAA
1 ATTTTAAAATTCATTTAAATTCAAA
55755743 ATTTTAAAATTCATTTAAATTCAAA
1 ATTTTAAAATTCATTTAAATTCAAA
*
55755768 TTTTT
1 ATTTT
55755773 TCTCATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTTTAAAATTCATTTAAATTCAAA
Found at i:55756938 original size:18 final size:17
Alignment explanation
Indices: 55756907--55756940 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
55756897 AGTTGATAAA
*
55756907 TTGAATTAATTTGTATT
1 TTGAATTAAATTGTATT
55756924 TTGAGATTAAATTGTAT
1 TTGA-ATTAAATTGTAT
55756941 ATAATTGTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (17 bp):
TTGAATTAAATTGTATT
Found at i:55757688 original size:28 final size:28
Alignment explanation
Indices: 55757631--55757693 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
55757621 ATTATATATC
* ** *
55757631 CATTTCAATTTCTATTCAATTTAAATTT
1 CATTTCAACTTCTATTCAATAAAAAATT
55757659 CATTTCAACTTC-ATTTCAATAAAAAATT
1 CATTTCAACTTCTA-TTCAATAAAAAATT
55757687 CAATTTC
1 C-ATTTC
55757694 TTTTTTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 1 0.03
28 23 0.79
29 5 0.17
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (28 bp):
CATTTCAACTTCTATTCAATAAAAAATT
Found at i:55757791 original size:111 final size:111
Alignment explanation
Indices: 55757648--55757962 Score: 494
Period size: 112 Copynumber: 2.8 Consensus size: 111
55757638 ATTTCTATTC
* *
55757648 AATTTAAATTTCATTTCAACTTCATTTCAATAAAAAATTCAATTTCTTTTTTAAATTTTACCCAT
1 AATTT-AATTTCATTCCAACTTCATTTCAATAAAAAATTCAATTTCTTTTTTAAATTTTACTCAT
55757713 ATATCTTTTTTAAATATAATTTCATTTCACATTCCC-A-AATTTAATTT
65 ATATCTTTTTTAAATATAATTTCATTT--CATTCCCAATAATTTAATTT
*
55757760 AATTTAATTTCATTCCAACTTCATTTAAATAAAAAATTCAATTTCTTTTTTAAATTTTACTC--A
1 AATTTAATTTCATTCCAACTTCATTTCAATAAAAAATTCAATTTCTTTTTTAAATTTTACTCATA
55757823 TATCTTTTTTAAATATAATTTCATTTCATTCCCAAATTTAATTTAATTT
66 TATCTTTTTTAAATATAATTTCATTTCATTCCC-AA--TAATTTAATTT
*
55757872 AATTTAATTTCATTCCAACTTCATTTCAATAAAAAATTTAATTTCTTTTTTAAATTTTACTCATA
1 AATTTAATTTCATTCCAACTTCATTTCAATAAAAAATTCAATTTCTTTTTTAAATTTTACTCATA
* *
55757937 TATCTTTCTTAAATATAATTCCATTT
66 TATCTTTTTTAAATATAATTTCATTT
55757963 TAATTTCACT
Statistics
Matches: 189, Mismatches: 7, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
107 7 0.04
109 28 0.15
111 54 0.29
112 75 0.40
114 25 0.13
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (111 bp):
AATTTAATTTCATTCCAACTTCATTTCAATAAAAAATTCAATTTCTTTTTTAAATTTTACTCATA
TATCTTTTTTAAATATAATTTCATTTCATTCCCAATAATTTAATTT
Found at i:55757899 original size:5 final size:5
Alignment explanation
Indices: 55757857--55757881 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
55757847 TTCATTCCCA
55757857 AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT
55757882 CATTCCAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:55761150 original size:58 final size:58
Alignment explanation
Indices: 55761075--55761188 Score: 201
Period size: 58 Copynumber: 2.0 Consensus size: 58
55761065 ATCACATTTA
*
55761075 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTG
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTG
* *
55761133 TCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCACTTGTCACT
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACT
55761189 GATCAGAAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (58 bp):
TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTG
Found at i:55763830 original size:46 final size:46
Alignment explanation
Indices: 55763760--55763851 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
55763750 CTTATTTATC
* * *
55763760 TTTGACATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTT
1 TTTGACATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTT
* * *
55763806 TTTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTT
1 TTTGACATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTT
55763852 CATATCTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (46 bp):
TTTGACATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTT
Found at i:55765782 original size:3 final size:3
Alignment explanation
Indices: 55765768--55765816 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
55765758 TTTTATACTA
*
55765768 AAT AATT AAT AAT AA- AAT AAT AAT GA- AAT AAT AAT AA- AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55765811 AA- AAT A
1 AAT AAT A
55765817 TCTCATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:55765790 original size:11 final size:11
Alignment explanation
Indices: 55765774--55765812 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
55765764 ACTAAATAAT
55765774 TAATAATAAAA
1 TAATAATAAAA
*
55765785 TAATAATGAAA
1 TAATAATAAAA
55765796 TAATAATAAAA
1 TAATAATAAAA
55765807 TAATAA
1 TAATAA
55765813 AATATCTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:55765799 original size:19 final size:19
Alignment explanation
Indices: 55765775--55765816 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
55765765 CTAAATAATT
*
55765775 AATAATAAAATAATAATGA
1 AATAATAAAATAATAATAA
55765794 AATAATAATAA-AATAATAA
1 AATAATAA-AATAATAATAA
55765813 AATA
1 AATA
55765817 TCTCATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAATAAAATAATAATAA
Found at i:55765839 original size:20 final size:21
Alignment explanation
Indices: 55765786--55765861 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 21
55765776 ATAATAAAAT
* *
55765786 AATAATGAAATA-ATAA-TAA
1 AATAATAAAATATCTAATTAA
*
55765805 AATAATAAAATATCTCATTAA
1 AATAATAAAATATCTAATTAA
*
55765826 AATAAT-ATATATCTAATTAAA
1 AATAATAAAATATCTAATT-AA
*
55765847 TAATCATAAAATATC
1 -AATAATAAAATATC
55765862 ATCAACATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 11 0.24
20 12 0.27
21 11 0.24
22 5 0.11
23 6 0.13
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:55766127 original size:30 final size:31
Alignment explanation
Indices: 55766059--55766117 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
55766049 CACAGTTAAA
** *
55766059 ATATTTACACTATTAGTCCTTCAAATTTTTC
1 ATATTTACACTATTAACCCCTCAAATTTTTC
55766090 ATATTTACACT-TTAACCCCTCAAATTTT
1 ATATTTACACTATTAACCCCTCAAATTTT
55766118 GAGTATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.31, C:0.22, G:0.02, T:0.46
Consensus pattern (31 bp):
ATATTTACACTATTAACCCCTCAAATTTTTC
Found at i:55768021 original size:27 final size:28
Alignment explanation
Indices: 55767991--55768066 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 28
55767981 TATATACTAA
55767991 TAAAATAATAATAATAAAATATTTTAT-
1 TAAAATAATAATAATAAAATATTTTATC
*
55768018 TAAAATATTAATAA-AATAAT-TTTTATC
1 TAAAATAATAATAATAA-AATATTTTATC
* *
55768045 T-AATTAAATAATTATAAAATAT
1 TAAAAT-AATAATAATAAAATAT
55768067 CAAAATATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
26 11 0.28
27 26 0.65
28 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAAATAATAATAATAAAATATTTTATC
Found at i:55770991 original size:14 final size:14
Alignment explanation
Indices: 55770974--55771005 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
55770964 CTGAAATATG
55770974 AAATCTTAAAAAAA
1 AAATCTTAAAAAAA
*
55770988 AAATCTTAAAAATA
1 AAATCTTAAAAAAA
55771002 AAAT
1 AAAT
55771006 TATGATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (14 bp):
AAATCTTAAAAAAA
Found at i:55773720 original size:29 final size:27
Alignment explanation
Indices: 55773638--55773721 Score: 64
Period size: 29 Copynumber: 3.0 Consensus size: 27
55773628 AAATGTCACA
55773638 AGAAAATTAAGTATTTAAA-ATAAAAAT
1 AGAAAATTAA-TATTTAAATATAAAAAT
* * * *
55773665 ATTAAATTTTAAT-TTTAATTTTAAAAAAT
1 A-GAAA-ATTAATATTTAAATAT-AAAAAT
55773694 AGAAAATATAATATTTAAATATCAAAAA
1 AGAAAAT-TAATATTTAAATAT-AAAAA
55773722 ATACTTTTGA
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
27 7 0.17
28 12 0.29
29 23 0.55
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (27 bp):
AGAAAATTAATATTTAAATATAAAAAT
Found at i:55774055 original size:22 final size:21
Alignment explanation
Indices: 55773998--55774056 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
55773988 TTAAATACTT
**
55773998 TTTTTAAAATTTATAATTATA
1 TTTTTAAAATTTATAAAAATA
*
55774019 TGTTTTAGAATTTTATAAAAAATA
1 T-TTTTA-AAATTTAT-AAAAATA
*
55774043 TTTTTAAACTTTAT
1 TTTTTAAAATTTAT
55774057 TTTTTTTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 12 0.39
23 12 0.39
24 6 0.19
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TTTTTAAAATTTATAAAAATA
Found at i:55775648 original size:23 final size:23
Alignment explanation
Indices: 55775622--55775665 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
55775612 TATATAATTT
*
55775622 TTAAAAAATTATAAAATTATAAA
1 TTAAAAAATAATAAAATTATAAA
* *
55775645 TTAATACATAATAAAATTATA
1 TTAAAAAATAATAAAATTATA
55775666 TTTTAACCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
TTAAAAAATAATAAAATTATAAA
Found at i:55776148 original size:9 final size:9
Alignment explanation
Indices: 55776136--55776176 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
55776126 CAGTTAAGTT
*
55776136 ATTAATATA
1 ATTAATTTA
*
55776145 ATTAGTTTA
1 ATTAATTTA
*
55776154 ATTAGTTTA
1 ATTAATTTA
55776163 ATTAATTTA
1 ATTAATTTA
55776172 ATTAA
1 ATTAA
55776177 AAATTATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (9 bp):
ATTAATTTA
Found at i:55779534 original size:21 final size:21
Alignment explanation
Indices: 55779510--55779573 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
55779500 CTCATTTTCT
55779510 AACATGACATTTATTTATTAA
1 AACATGACATTTATTTATTAA
*
55779531 AACA--ATA-TT-TTTA-TAA
1 AACATGACATTTATTTATTAA
55779547 GCAACATGACATTTATTTATTAA
1 --AACATGACATTTATTTATTAA
55779570 AACA
1 AACA
55779574 ATATTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
16 3 0.09
17 4 0.12
18 6 0.18
19 2 0.06
20 2 0.06
21 10 0.29
22 4 0.12
23 3 0.09
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (21 bp):
AACATGACATTTATTTATTAA
Found at i:55779556 original size:39 final size:39
Alignment explanation
Indices: 55779510--55779591 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
55779500 CTCATTTTCT
55779510 AACATGACATTTATTTATTAAAACAATATTTTTATAAGC
1 AACATGACATTTATTTATTAAAACAATATTTTTATAAGC
55779549 AACATGACATTTATTTATTAAAACAATATTTTTATAAGC
1 AACATGACATTTATTTATTAAAACAATATTTTTATAAGC
55779588 AACA
1 AACA
55779592 AAAGTTAAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (39 bp):
AACATGACATTTATTTATTAAAACAATATTTTTATAAGC
Found at i:55783319 original size:16 final size:17
Alignment explanation
Indices: 55783288--55783320 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55783278 TTCATAAGTA
55783288 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
55783305 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
55783321 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:55783667 original size:46 final size:46
Alignment explanation
Indices: 55783607--55783788 Score: 249
Period size: 46 Copynumber: 4.0 Consensus size: 46
55783597 TTTGACATGA
* * * *
55783607 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATAGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGT
* * * *
55783653 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATTAGGC
1 TGCCATAGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* *
55783699 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATAGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
55783745 TGCCATAGTATCTTTCAACCATGGTCTTACGCATTTCATATCAG
1 TGCCATAGTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
55783789 AGAGCACACT
Statistics
Matches: 121, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
45 4 0.03
46 117 0.97
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATAGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
Found at i:55786141 original size:52 final size:53
Alignment explanation
Indices: 55786085--55786193 Score: 123
Period size: 53 Copynumber: 2.1 Consensus size: 53
55786075 ATTACAATGT
* *
55786085 CATTGGTGCAATGT-AATATGTG-CTCCTGTATAAGACCATAGCTGGACTATGG
1 CATTGGTGCAATGTGAATATGTGTCTCC-GTATAAGACCATAGCTGGAATATGA
** * * * *
55786137 CATTGGTGTGATGTGATTATTTGTTTCCGTATAAGACCATATCTGGAATATGA
1 CATTGGTGCAATGTGAATATGTGTCTCCGTATAAGACCATAGCTGGAATATGA
55786190 CATT
1 CATT
55786194 TGTATGATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
52 12 0.26
53 32 0.68
54 3 0.06
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.36
Consensus pattern (53 bp):
CATTGGTGCAATGTGAATATGTGTCTCCGTATAAGACCATAGCTGGAATATGA
Found at i:55792207 original size:49 final size:50
Alignment explanation
Indices: 55792140--55792272 Score: 164
Period size: 49 Copynumber: 2.7 Consensus size: 50
55792130 TCCATCAAGT
* *
55792140 CGATGCCATGTCCCAGACATGGTCTTACACTAACTATCGA-A-AT-TGAAAC
1 CGATGCCATGTCCTAGACATGGTCTTACACTAACTATC-ACATATCCG-AAC
* * * **
55792189 CGATGCTATGTCCTAGACATGGTCTTACACTAGCTCTCACATATCCGTGC
1 CGATGCCATGTCCTAGACATGGTCTTACACTAACTATCACATATCCGAAC
55792239 CGATGCCATGTCCTAGACATGGTCTTACACTAAC
1 CGATGCCATGTCCTAGACATGGTCTTACACTAAC
55792273 ACATCTCGTA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
48 1 0.01
49 35 0.49
50 35 0.49
51 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (50 bp):
CGATGCCATGTCCTAGACATGGTCTTACACTAACTATCACATATCCGAAC
Found at i:55792256 original size:50 final size:47
Alignment explanation
Indices: 55792140--55792410 Score: 213
Period size: 46 Copynumber: 5.7 Consensus size: 47
55792130 TCCATCAAGT
* * * **
55792140 CGATGCCATGTCCCAGACATGGTCTTACACTAACTATCGAAAT-T-GAAAC
1 CGATGCCATGTCCTAGACAT-GTCTTACACTAGCT-TC-ACATCTCG-TGC
* *
55792189 CGATGCTATGTCCTAGACATGGTCTTACACTAGCTCTCACATATCCGTGC
1 CGATGCCATGTCCTAGACAT-GTCTTACACTAGCT-TCACATCT-CGTGC
* *
55792239 CGATGCCATGTCCTAGACATGGTCTTACACTA---ACACATCTCGTAAC
1 CGATGCCATGTCCTAGACAT-GTCTTACACTAGCTTCACATCTCGT-GC
* * * *
55792285 CGAT-ACATGTCCCAAACATGTCTTACACTGGCTT-ACATCTCGTAGC
1 CGATGCCATGTCCTAGACATGTCTTACACTAGCTTCACATCTCGT-GC
* *
55792331 CGATG-CATGTTCC-AGACATGTCTTACACTGGCTT-ACATCTCGAGGC
1 CGATGCCATG-TCCTAGACATGTCTTACACTAGCTTCACATCTCG-TGC
*
55792377 CGATG-CATGTCCTAAACATGTCTTACACTAGCTT
1 CGATGCCATGTCCTAGACATGTCTTACACTAGCTT
55792411 TCGTGTAATA
Statistics
Matches: 190, Mismatches: 21, Indels: 25
0.81 0.09 0.11
Matches are distributed among these distances:
44 10 0.05
45 18 0.09
46 88 0.46
47 3 0.02
48 3 0.02
49 35 0.18
50 32 0.17
51 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (47 bp):
CGATGCCATGTCCTAGACATGTCTTACACTAGCTTCACATCTCGTGC
Found at i:55792325 original size:46 final size:46
Alignment explanation
Indices: 55792188--55792410 Score: 220
Period size: 46 Copynumber: 4.8 Consensus size: 46
55792178 GAAATTGAAA
* * * *
55792188 CCGATGCTATGTCCTAGACATGGTCTTACACTAGCTCTCACATATCCGT-G
1 CCGATGC-ATGTCCCAAACAT-GTCTTACACTGGCT-T-ACATCT-CGTAG
* * ** *
55792238 CCGATGCCATGTCCTAGACATGGTCTTACACTAAC--ACATCTCGTAA
1 CCGATG-CATGTCCCAAACAT-GTCTTACACTGGCTTACATCTCGTAG
*
55792284 CCGATACATGTCCCAAACATGTCTTACACTGGCTTACATCTCGTAG
1 CCGATGCATGTCCCAAACATGTCTTACACTGGCTTACATCTCGTAG
* *
55792330 CCGATGCATGTTCCAGACATGTCTTACACTGGCTTACATCTCG-AGG
1 CCGATGCATGTCCCAAACATGTCTTACACTGGCTTACATCTCGTA-G
* *
55792376 CCGATGCATGTCCTAAACATGTCTTACACTAGCTT
1 CCGATGCATGTCCCAAACATGTCTTACACTGGCTT
55792411 TCGTGTAATA
Statistics
Matches: 152, Mismatches: 16, Indels: 14
0.84 0.09 0.08
Matches are distributed among these distances:
44 11 0.07
45 16 0.11
46 92 0.61
50 32 0.21
51 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.29
Consensus pattern (46 bp):
CCGATGCATGTCCCAAACATGTCTTACACTGGCTTACATCTCGTAG
Found at i:55792369 original size:92 final size:92
Alignment explanation
Indices: 55792140--55792410 Score: 282
Period size: 92 Copynumber: 2.9 Consensus size: 92
55792130 TCCATCAAGT
* ** * *
55792140 CGATGCCATGTCCCAGACATGGTCTTACACTAACTATCGAAATTGAAACCGATGCTATGTCCTAG
1 CGATGCCATGTCCTAGACATGGTCTTACACTAAC-A-C-ATCTCG-AACCGATGC-ATGTCCTAA
55792205 ACATGGTCTTACACTAGCTCTCACATATCCGTGC
61 ACAT-GTCTTACACTAGCT-TCACATATCCGTGC
* *
55792239 CGATGCCATGTCCTAGACATGGTCTTACACTAACACATCTCGTAACCGATACATGTCCCAAACAT
1 CGATGCCATGTCCTAGACATGGTCTTACACTAACACATCTCG-AACCGATGCATGTCCTAAACAT
* *
55792304 GTCTTACACTGGCTT-ACATCT-CGTAGC
65 GTCTTACACTAGCTTCACATATCCGT-GC
** *
55792331 CGATG-CATGTTCC-AGACAT-GTCTTACACTGGCTTACATCTCGAGGCCGATGCATGTCCTAAA
1 CGATGCCATG-TCCTAGACATGGTCTTACACTAAC--ACATCTCGA-ACCGATGCATGTCCTAAA
55792393 CATGTCTTACACTAGCTT
62 CATGTCTTACACTAGCTT
55792411 TCGTGTAATA
Statistics
Matches: 151, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
90 11 0.07
91 14 0.09
92 55 0.36
93 1 0.01
94 13 0.09
95 11 0.07
96 11 0.07
97 1 0.01
98 1 0.01
99 33 0.22
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (92 bp):
CGATGCCATGTCCTAGACATGGTCTTACACTAACACATCTCGAACCGATGCATGTCCTAAACATG
TCTTACACTAGCTTCACATATCCGTGC
Found at i:55792908 original size:11 final size:11
Alignment explanation
Indices: 55792894--55792946 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
55792884 AGATAAATAT
55792894 TATTTTATTAA
1 TATTTTATTAA
*
55792905 TATTTTAATAA
1 TATTTTATTAA
* * *
55792916 GATATT-TTAT
1 TATTTTATTAA
*
55792926 TATTTTATTAT
1 TATTTTATTAA
55792937 TATTTTATTA
1 TATTTTATTA
55792947 GTATATAAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
10 6 0.18
11 28 0.82
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Done.