Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013239.1 Corchorus capsularis cultivar CVL-1 contig13260, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 118797
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6692 original size:7 final size:7
Alignment explanation
Indices: 6680--6710 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
6670 TTTTTTTTTC
6680 CTTTGTT
1 CTTTGTT
6687 CTTTGTT
1 CTTTGTT
6694 CTTTGTT
1 CTTTGTT
6701 CTTT-TT
1 CTTTGTT
6707 CTTT
1 CTTT
6711 CTTAAGGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.00, C:0.16, G:0.10, T:0.74
Consensus pattern (7 bp):
CTTTGTT
Found at i:6699 original size:14 final size:13
Alignment explanation
Indices: 6674--6710 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
6664 ACTCCATTTT
6674 TTTTTCCTTTGTTC
1 TTTTT-CTTTGTTC
6688 TTTGTTCTTTGTTC
1 TTT-TTCTTTGTTC
6702 TTTTTCTTT
1 TTTTTCTTT
6711 CTTAAGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 14 0.64
15 2 0.09
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTTCTTTGTTC
Found at i:8360 original size:14 final size:14
Alignment explanation
Indices: 8341--8374 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
8331 GCATATTAAC
8341 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
8355 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
*
8369 ATTAGT
1 TTTAGT
8375 ATGATAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:10689 original size:31 final size:30
Alignment explanation
Indices: 10592--10690 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 30
10582 TATTTTACTG
* *
10592 CAATTTGAGGCATGTTCATGTTGATTTGTTT
1 CAATTTGAGGCTTGTTCATGTTAATTTG-TT
* * * * *
10623 CAACTTAATGCTTGATT-ATGGTAGATCTT-TG
1 CAATTTGAGGCTTG-TTCATGTTA-AT-TTGTT
10654 CAATTTGAGGCTTGTTCATGTTAATTTGCTT
1 CAATTTGAGGCTTGTTCATGTTAATTTG-TT
10685 CAATTT
1 CAATTT
10691 AAGACTGGTT
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
29 2 0.04
30 4 0.08
31 38 0.76
32 4 0.08
33 2 0.04
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (30 bp):
CAATTTGAGGCTTGTTCATGTTAATTTGTT
Found at i:12107 original size:74 final size:74
Alignment explanation
Indices: 12021--12165 Score: 256
Period size: 74 Copynumber: 2.0 Consensus size: 74
12011 TTAAGGAAGG
* *
12021 GAAATGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAAT-GGTTGAAACTCATAGAGGGGCTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGG-GGAAACTCATAGAGGGGCTTT
12085 TTAGTCATTT
65 TTAGTCATTT
12095 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTT
12160 TAGTCA
66 TAGTCA
12166 CCCGAAAAGT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
74 66 0.97
75 2 0.03
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (74 bp):
GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTT
TAGTCATTT
Found at i:15607 original size:2 final size:2
Alignment explanation
Indices: 15600--15629 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15590 ATCACACCAA
15600 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
15630 GCAAGTGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15878 original size:14 final size:13
Alignment explanation
Indices: 15843--15883 Score: 73
Period size: 13 Copynumber: 3.1 Consensus size: 13
15833 GGTTTGGAAG
15843 AAGTGTTTTTGAA
1 AAGTGTTTTTGAA
15856 AAGTGTTTTTGAA
1 AAGTGTTTTTGAA
15869 AAGTGCTTTTTGAA
1 AAGTG-TTTTTGAA
15883 A
1 A
15884 TTGCAGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 18 0.67
14 9 0.33
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.44
Consensus pattern (13 bp):
AAGTGTTTTTGAA
Found at i:19663 original size:22 final size:23
Alignment explanation
Indices: 19633--19696 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
19623 TGTTAGTAAT
* *
19633 CACTCTGAAATTTTGATAA-TCA
1 CACTATGAAATTTTGATAACCCA
* *
19655 CACTATGAAATTGTGATAACCCT
1 CACTATGAAATTTTGATAACCCA
* *
19678 CGCTATGAAATTTTTATAA
1 CACTATGAAATTTTGATAA
19697 ATCTTCCTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 17 0.50
23 17 0.50
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (23 bp):
CACTATGAAATTTTGATAACCCA
Found at i:19706 original size:23 final size:23
Alignment explanation
Indices: 19680--19742 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
19670 ATAACCCTCG
* *
19680 CTATGAAATTTTTATAAATCTTC
1 CTATAAAATTTTAATAAATCTTC
*
19703 CTATAAAATTTTAATAAATC-CC
1 CTATAAAATTTTAATAAATCTTC
*
19725 CATATAAAATTTTGATAA
1 C-TATAAAATTTTAATAA
19743 CTTTCTTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 2 0.06
23 33 0.94
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTAATAAATCTTC
Found at i:19818 original size:22 final size:22
Alignment explanation
Indices: 19658--19886 Score: 116
Period size: 22 Copynumber: 10.6 Consensus size: 22
19648 ATAATCACAC
* * *
19658 TATGAAATTGTGATAACCCTCGC
1 TATGAAATTTTGATAACCTTC-T
* * *
19681 TATGAAATTTTTATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCT
* * * *
19704 TATAAAATTTTAATAAATCC-CCA
1 TATGAAATTTTGAT-AA-CCTTCT
* *
19727 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCT
*
19749 TATGAAATCTTGATAA----C-
1 TATGAAATTTTGATAACCTTCT
* *
19766 TA-CAAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCT
** *
19786 TATGATTTTTTGATAACCTTAT
1 TATGAAATTTTGATAACCTTCT
* * * *
19808 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCT
* * *
19830 TATGAAATTTTGATCTA-CATAT
1 TATGAAATTTTGAT-AACCTTCT
*
19852 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCT
19874 TATGAAATTTTGA
1 TATGAAATTTTGA
19887 AAACTAAACT
Statistics
Matches: 157, Mismatches: 38, Indels: 23
0.72 0.17 0.11
Matches are distributed among these distances:
16 11 0.07
17 2 0.01
18 1 0.01
19 1 0.01
20 2 0.01
21 14 0.09
22 77 0.49
23 43 0.27
24 6 0.04
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCT
Found at i:19929 original size:20 final size:20
Alignment explanation
Indices: 19901--19949 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
19891 TAAACTATGG
* *
19901 AATTGTGATATCCTCCCTGA
1 AATTTTGATATCCTCACTGA
*
19921 AATTTTGATATCCTCATTGA
1 AATTTTGATATCCTCACTGA
19941 AATTTTGAT
1 AATTTTGAT
19950 TACTCCATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (20 bp):
AATTTTGATATCCTCACTGA
Found at i:20167 original size:22 final size:23
Alignment explanation
Indices: 20142--20243 Score: 106
Period size: 22 Copynumber: 4.6 Consensus size: 23
20132 AACCTCGTTT
*
20142 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAATCAACTCTA
**
20164 TGAAATTTTGATAATCTTC-CTA
1 TGAAATTTTGATAATCAACTCTA
20186 T-AAATTTTGATAATCAATCTCTA
1 TGAAATTTTGATAATCAA-CTCTA
* *
20209 CGAAATTTCGATAATC-ACTCTA
1 TGAAATTTTGATAATCAACTCTA
*
20231 TGAGA-TTTGATAA
1 TGAAATTTTGATAA
20244 CCTTCTATCA
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
21 21 0.31
22 27 0.40
23 6 0.09
24 13 0.19
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (23 bp):
TGAAATTTTGATAATCAACTCTA
Found at i:20260 original size:21 final size:22
Alignment explanation
Indices: 20144--20260 Score: 68
Period size: 21 Copynumber: 5.4 Consensus size: 22
20134 CCTCGTTTTG
* *
20144 AAATTTTGATAACAAC-ACTATG
1 AAATTTTGATAAC-ACTTCTATC
*
20166 AAATTTTGATAA-TCTTCCTAT-
1 AAATTTTGATAACACTT-CTATC
*
20187 AAATTTTGATAATCAATCTCTA-C
1 AAATTTTGATAA-CACT-TCTATC
* *
20210 GAAATTTCGATAATCAC-TCTATG
1 -AAATTTTGATAA-CACTTCTATC
*
20233 AGA-TTTGATAAC-CTTCTATC
1 AAATTTTGATAACACTTCTATC
20253 AAATTTTG
1 AAATTTTG
20261 GTACTCCTTA
Statistics
Matches: 74, Mismatches: 11, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
19 1 0.01
20 9 0.12
21 23 0.31
22 22 0.30
23 4 0.05
24 15 0.20
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACACTTCTATC
Found at i:20312 original size:22 final size:22
Alignment explanation
Indices: 20142--20422 Score: 79
Period size: 22 Copynumber: 12.6 Consensus size: 22
20132 AACCTCGTTT
**
20142 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAACCTTCA-TA
* *
20164 TGAAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAACCTTCATA
*
20186 T-AAATTTTGATAATCAATCTC-TA
1 TGAAATTTTGATAA-C-CT-TCATA
* *
20209 CGAAATTTCGATAATCAC-TC-TA
1 TGAAATTTTGATAA-C-CTTCATA
*
20231 TGAGA-TTTGATAACCTTC-TA
1 TGAAATTTTGATAACCTTCATA
* * *
20251 TCAAATTTTGGTACTCCTT-ATGAAA
1 TGAAATTTTGATA-ACCTTCAT---A
*
20276 TTGAGACTTTT-ATAACCTTCATA
1 -TGA-AATTTTGATAACCTTCATA
*
20299 TGAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
* * * **
20321 TAAAATCTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTTCATA
* *
20343 TGAAATATT-AGTAACC-TCCTAA
1 TGAAATTTTGA-TAACCTTCAT-A
* *
20365 TGAAATTTTGTTAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
*
20387 TGAAATTCTT-ATAACC-TCGCTA
1 TGAAATT-TTGATAACCTTC-ATA
*
20409 TGACATTTTGATAA
1 TGAAATTTTGATAA
20423 TCTCTTTGAT
Statistics
Matches: 196, Mismatches: 38, Indels: 50
0.69 0.13 0.18
Matches are distributed among these distances:
19 1 0.01
20 8 0.04
21 37 0.19
22 108 0.55
23 10 0.05
24 16 0.08
25 5 0.03
26 6 0.03
27 5 0.03
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:20519 original size:24 final size:22
Alignment explanation
Indices: 20458--20633 Score: 99
Period size: 22 Copynumber: 7.9 Consensus size: 22
20448 TTGTGATAAT
* *
20458 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
20480 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
20502 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
*
20526 TAACC-ACACTATGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
** * **
20548 TAA-CTTCCATATGAAACTTTGG
1 TAACCAACC-TATGAAATTTTAA
* *
20570 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* *
20592 TAACC-TCCTCATGAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
20614 TAGCCATCTTATGAAATTTT
1 TAACCAACCTATGAAATTTT
20634 GATAGCCATA
Statistics
Matches: 122, Mismatches: 23, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
21 5 0.04
22 94 0.77
23 5 0.04
24 18 0.15
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.34
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:20530 original size:46 final size:44
Alignment explanation
Indices: 20465--20609 Score: 161
Period size: 44 Copynumber: 3.2 Consensus size: 44
20455 AATTAACCAC
*** * *
20465 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTGGTAACCACA-CTATGAAATTTTGATAACCT--T
20511 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAA-CTT
1 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTT
* *
20554 CCATATGAAACTTTGGTAACCACACTATGGAATTTTGATAACC-T
1 CC-TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTT
20598 CCTCATGAAATT
1 CCT-ATGAAATT
20610 ATAATAGCCA
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
43 4 0.05
44 46 0.53
45 3 0.03
46 33 0.38
47 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.33
Consensus pattern (44 bp):
CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTT
Found at i:20838 original size:19 final size:20
Alignment explanation
Indices: 20807--20844 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
20797 TATTGACAGT
20807 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
20826 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
20845 AATAATAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:21573 original size:29 final size:29
Alignment explanation
Indices: 21531--21590 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
21521 CTACTTGTAT
* *
21531 AATAGGAATTATGGCGATATACAATGAAG
1 AATAGGAATCATGGCAATATACAATGAAG
* *
21560 AATAGGAATCATGGCAATATGCCATGAAG
1 AATAGGAATCATGGCAATATACAATGAAG
21589 AA
1 AA
21591 CAACCACCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22
Consensus pattern (29 bp):
AATAGGAATCATGGCAATATACAATGAAG
Found at i:21892 original size:22 final size:22
Alignment explanation
Indices: 21865--21909 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
21855 ATTATTGTGA
21865 TTTTTCTCTATTGGGTTATAAT
1 TTTTTCTCTATTGGGTTATAAT
21887 TTTTTCTCTATTGGGTTATAAT
1 TTTTTCTCTATTGGGTTATAAT
21909 T
1 T
21910 ATATACTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.09, G:0.13, T:0.60
Consensus pattern (22 bp):
TTTTTCTCTATTGGGTTATAAT
Found at i:23131 original size:18 final size:18
Alignment explanation
Indices: 23098--23132 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23088 GCACACCATT
**
23098 TTTTTGCTTTTTTTTTTC
1 TTTTTGCTTTAATTTTTC
23116 TTTTTGCTTTAATTTTT
1 TTTTTGCTTTAATTTTT
23133 TTTCCTCTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.80
Consensus pattern (18 bp):
TTTTTGCTTTAATTTTTC
Found at i:25878 original size:43 final size:43
Alignment explanation
Indices: 25808--25894 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
25798 AAAATATAGT
* * * *
25808 ATAGAGTTAGACTTGACAGGAATATATCTGACTATATGTTATG
1 ATAGAGTTAGACTTGAAAGCAACATATCTGACTATATATTATG
*
25851 ATAGAGTTAGACTTGAAAGCAACATATCTGATTATATATTATG
1 ATAGAGTTAGACTTGAAAGCAACATATCTGACTATATATTATG
25894 A
1 A
25895 CAGAAAAGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.34
Consensus pattern (43 bp):
ATAGAGTTAGACTTGAAAGCAACATATCTGACTATATATTATG
Found at i:30138 original size:2 final size:2
Alignment explanation
Indices: 30131--30160 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
30121 TGCTTTGGTT
30131 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30161 GAAGAACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:33655 original size:23 final size:23
Alignment explanation
Indices: 33625--33702 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
33615 TTTTTTTCCG
*
33625 CTTCTTCTTCATCCCATCTTTTT
1 CTTCTTCTTCATCTCATCTTTTT
** *
33648 CTTCTTCTTC-T-TTTTTTTTTT
1 CTTCTTCTTCATCTCATCTTTTT
33669 CGCTTCTTCTTCATCTCATCTTTTT
1 --CTTCTTCTTCATCTCATCTTTTT
33694 CTTCTTCTT
1 CTTCTTCTT
33703 TTTTTATAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
21 6 0.14
22 1 0.02
23 29 0.66
24 1 0.02
25 7 0.16
ACGTcount: A:0.05, C:0.29, G:0.01, T:0.64
Consensus pattern (23 bp):
CTTCTTCTTCATCTCATCTTTTT
Found at i:33676 original size:46 final size:47
Alignment explanation
Indices: 33605--33707 Score: 183
Period size: 46 Copynumber: 2.2 Consensus size: 47
33595 CCTCATGTTT
33605 TTCTTCTTTTTTTTTTTCCGCTTCTTCTTCATCCCATCTTTTTCTTC
1 TTCTTCTTTTTTTTTTTCCGCTTCTTCTTCATCCCATCTTTTTCTTC
*
33652 TTCTTCTTTTTTTTTTT-CGCTTCTTCTTCATCTCATCTTTTTCTTC
1 TTCTTCTTTTTTTTTTTCCGCTTCTTCTTCATCCCATCTTTTTCTTC
33698 TTCTT-TTTTT
1 TTCTTCTTTTT
33708 ATAATAATAA
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
45 5 0.09
46 33 0.60
47 17 0.31
ACGTcount: A:0.04, C:0.26, G:0.02, T:0.68
Consensus pattern (47 bp):
TTCTTCTTTTTTTTTTTCCGCTTCTTCTTCATCCCATCTTTTTCTTC
Found at i:35069 original size:31 final size:31
Alignment explanation
Indices: 35033--35102 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
35023 TTTTGTGCAC
35033 GTGGCATGCCACATACCACTTTTTGAAACAT
1 GTGGCATGCCACATACCACTTTTTGAAACAT
* ** **
35064 GTGGCATGCCACGTGTCACTTTTTGGTACAT
1 GTGGCATGCCACATACCACTTTTTGAAACAT
35095 GTGGCATG
1 GTGGCATG
35103 ACATTTGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.31
Consensus pattern (31 bp):
GTGGCATGCCACATACCACTTTTTGAAACAT
Found at i:35112 original size:31 final size:31
Alignment explanation
Indices: 35049--35131 Score: 121
Period size: 31 Copynumber: 2.7 Consensus size: 31
35039 TGCCACATAC
** *
35049 CACTTTTTGAAACATGTGGCATGCCACGTGT
1 CACTTTTTGGTACATGTGGCATGACACGTGT
**
35080 CACTTTTTGGTACATGTGGCATGACATTTGT
1 CACTTTTTGGTACATGTGGCATGACACGTGT
35111 CACTTTTTGGTACATGTGGCA
1 CACTTTTTGGTACATGTGGCA
35132 CGACTTTTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (31 bp):
CACTTTTTGGTACATGTGGCATGACACGTGT
Found at i:35165 original size:53 final size:53
Alignment explanation
Indices: 35081--35183 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
35071 GCCACGTGTC
** * *
35081 ACTTTTTGGTACATGTGGCATGACATTTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACATGTGGCATGACACATGTCACTTATTGGTACACGTGGCACG
** *
35134 ACTTTTTGGTACATGTGGTGTGCCACATGTCACTTATTGGTACACGTGGC
1 ACTTTTTGGTACATGTGGCATGACACATGTCACTTATTGGTACACGTGGC
35184 GTGCCACGTC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (53 bp):
ACTTTTTGGTACATGTGGCATGACACATGTCACTTATTGGTACACGTGGCACG
Found at i:36014 original size:2 final size:2
Alignment explanation
Indices: 36009--36048 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
35999 TCTGTGTGTG
*
36009 TA TA TA TA TA TA TA -A TA TA TG TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36049 TTCAGGAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36084 original size:39 final size:39
Alignment explanation
Indices: 36030--36104 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
36020 ATAATATATG
36030 TATATATATATATATA-TATTTCAGGAATTGTTTTTTTGT
1 TATATATATATATATATTA-TTCAGGAATTGTTTTTTTGT
36069 TATATATATATATATATTATTCAGGAATTGTTTTTT
1 TATATATATATATATATTATTCAGGAATTGTTTTTT
36105 GTTTGGTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 33 0.94
40 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (39 bp):
TATATATATATATATATTATTCAGGAATTGTTTTTTTGT
Found at i:52853 original size:22 final size:22
Alignment explanation
Indices: 52828--53388 Score: 185
Period size: 22 Copynumber: 25.7 Consensus size: 22
52818 ATGATCCCAT
52828 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCA
* * *
52850 TATGAAATTTTAATAACGATACA
1 TATGAAATTTTGATAAC-CTTCA
* * * **
52873 -ATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCA
* ** *
52894 TAT-AATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCA
** * * * *
52915 TATGACGTTTGGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCA
* *
52937 TAAGTAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-A
*
52959 TATGAAATTTTGATAA-CTTCC
1 TATGAAATTTTGATAACCTTCA
**
52980 TAATGAAATTTTGATAACCAACA
1 T-ATGAAATTTTGATAACCTTCA
* *
53003 CTATGAGATGTTGATAACC-TCAA
1 -TATGAAATTTTGATAACCTTC-A
* * * *
53026 TATGATATATTGATAACC-ACGT
1 TATGAAATTTTGATAACCTTC-A
* * *
53048 TATGAAAATTT-AAACACCTCCA
1 TATGAAATTTTGATA-ACCTTCA
* *
53070 TATG-AATTGTT-AGTAATC-ACA
1 TATGAAATT-TTGA-TAACCTTCA
* * * *
53091 CTCTAAAATTTTGATAATC-ACA
1 -TATGAAATTTTGATAACCTTCA
* *
53113 CTATGAAATTGTGATAACC-TCGC
1 -TATGAAATTTTGATAACCTTC-A
* *
53136 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCA
* * *
53159 TATAAAATTTTGATAAACCTCCT
1 TATGAAATTTTGAT-AACCTTCA
* * *
53182 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCA
*
53204 TATGAAATCTTGATAA----C-
1 TATGAAATTTTGATAACCTTCA
* *
53221 TA-CAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAACCTTCA
** *
53242 TATGATTTTTTGATAATC-TCA
1 TATGAAATTTTGATAACCTTCA
* * * *
53263 TTATGAAATTTTGTTAATCTCCC
1 -TATGAAATTTTGATAACCTTCA
* * *
53286 TATGAAATTTTGATCTACATAC-
1 TATGAAATTTTGAT-AACCTTCA
* *
53308 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCA
* * **
53330 TGTGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTTCA
* *
53351 CTATGAAATTTTAATAAGCTTCA
1 -TATGAAATTTTGATAACCTTCA
53374 TATGAAATTTTGATA
1 TATGAAATTTTGATA
53389 TCCTCCCTGA
Statistics
Matches: 399, Mismatches: 107, Indels: 66
0.70 0.19 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 1 0.00
21 36 0.09
22 270 0.68
23 75 0.19
24 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:53166 original size:23 final size:23
Alignment explanation
Indices: 53094--53197 Score: 101
Period size: 23 Copynumber: 4.6 Consensus size: 23
53084 AATCACACTC
*
53094 TAAAATTTTGAT-AATCAC-ACTA
1 TAAAATTTTGATAAATC-CTCCTA
* *
53116 TGAAATTGTGAT-AA-CCTCGCTA
1 TAAAATTTTGATAAATCCTC-CTA
* *
53138 TGAAATTTTGATAAATCTTCCTA
1 TAAAATTTTGATAAATCCTCCTA
53161 TAAAATTTTGATAAA-CCTCCTTA
1 TAAAATTTTGATAAATCCTCC-TA
53184 TAAAATTTTGATAA
1 TAAAATTTTGATAA
53198 CTTTCTTATG
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 30 0.43
23 35 0.50
24 3 0.04
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
TAAAATTTTGATAAATCCTCCTA
Found at i:53218 original size:45 final size:45
Alignment explanation
Indices: 53094--53219 Score: 127
Period size: 45 Copynumber: 2.8 Consensus size: 45
53084 AATCACACTC
*
53094 TAAAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGCTA
1 TAAAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCGCTA
* *
53138 TGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTC-CTTA
1 TAAAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCGC-TA
* *
53184 TAAAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 TAAAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
53220 CTACAAATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
44 12 0.17
45 32 0.46
46 25 0.36
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (45 bp):
TAAAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCGCTA
Found at i:53421 original size:20 final size:20
Alignment explanation
Indices: 53376--53422 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
53366 AAGCTTCATA
53376 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
* * *
53396 TG-AATTTTTATATCTTCCT
1 TGAAATTTTGATATCCTCCC
53415 TGAAATTT
1 TGAAATTT
53423 AAATTACTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:53548 original size:44 final size:44
Alignment explanation
Indices: 53498--53690 Score: 148
Period size: 44 Copynumber: 4.4 Consensus size: 44
53488 GAAATACCAC
53498 TATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAA-TTTTGATAATCACATTTTGAAAATTTGATAACCTCTT
* * * * *
53542 TATGAAATTTTGATAATCTC-TTTAT-AAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCACATTT-TGAAAA-TTTGATAACCTCTT
* * * * *
53586 TATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAATCACATTTTGAAAATTTGATAACCTC-TT
* * * *
53631 T-TGAAATTTTGATAA-CAACACTATGAAATTTTGATAATCT-TT
1 TATGAAATTTTGATAATC-ACATTTTGAAAATTTGATAACCTCTT
*
53673 CTAT-AAATTCTGATAATC
1 -TATGAAATTTTGATAATC
53691 CGATCTCTAT
Statistics
Matches: 118, Mismatches: 21, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
42 1 0.01
43 25 0.21
44 87 0.74
45 5 0.04
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTTTGAAAATTTGATAACCTCTT
Found at i:53638 original size:66 final size:66
Alignment explanation
Indices: 53541--53669 Score: 152
Period size: 66 Copynumber: 2.0 Consensus size: 66
53531 GATAACCTCT
* * * * ** *
53541 TTATGAAATTTTGATAATCTCTTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCAC
1 TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
53606 A
66 A
* * *
53607 TTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACACTATGAAATTTTGATAATC
1 TTATGAAATTTTGATAACCTC-CTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATC
53670 TTTCTATAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 50 0.96
67 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
A
Found at i:53657 original size:22 final size:21
Alignment explanation
Indices: 53495--53667 Score: 89
Period size: 22 Copynumber: 7.9 Consensus size: 21
53485 CCAGAAATAC
53495 CACTATGAAATTTTTG-TAATCA
1 CACTATGAAA-TTTTGATAA-CA
* * *
53517 CATTTTGAAAATTTGATAAC-
1 CACTATGAAATTTTGATAACA
* *
53537 CTCTTTATGAAATTTTGATAATCT
1 CAC--TATGAAATTTTGATAA-CA
** * * * *
53561 CTTTATAAAATTTTGTTGACCC
1 CACTATGAAATTTTGAT-AACA
* *
53583 CTCTATGAAATTCTGATAATCA
1 CACTATGAAATTTTGATAA-CA
* * *
53605 CATTATGTAATTTTGATAACCT
1 CACTATGAAATTTTGATAA-CA
* *
53627 CGCTTTGAAATTTTGATAACAA
1 CACTATGAAATTTTGATAAC-A
53649 CACTATGAAATTTTGATAA
1 CACTATGAAATTTTGATAA
53668 TCTTTCTATA
Statistics
Matches: 112, Mismatches: 31, Indels: 16
0.70 0.19 0.10
Matches are distributed among these distances:
20 1 0.01
21 7 0.06
22 100 0.89
23 2 0.02
24 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (21 bp):
CACTATGAAATTTTGATAACA
Found at i:53660 original size:88 final size:88
Alignment explanation
Indices: 53497--53690 Score: 207
Period size: 88 Copynumber: 2.2 Consensus size: 88
53487 AGAAATACCA
* * * *
53497 CTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAATCT
1 CTATGAAA-TTCTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAATCA
** * *
53561 CTTTATAAAATTTTGTTGACCCCT
65 CACTATAAAATTTTGATAACCCCT
* *
53585 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAA-CA
1 CTATGAAATTCTGATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAATC-
* * **
53648 ACACTATGAAATTTTGATAATCTTT
64 ACACTATAAAATTTTGATAACCCCT
53673 CTAT-AAATTCTGATAATC
1 CTATGAAATTCTGATAATC
53691 CGATCTCTAT
Statistics
Matches: 89, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
87 19 0.21
88 68 0.76
89 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (88 bp):
CTATGAAATTCTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAATCAC
ACTATAAAATTTTGATAACCCCT
Found at i:53676 original size:22 final size:21
Alignment explanation
Indices: 53652--53769 Score: 62
Period size: 21 Copynumber: 5.4 Consensus size: 21
53642 ATAACAACAC
53652 TATGAAATTTTGATAATCTTT
1 TATGAAATTTTGATAATCTTT
* *
53673 CTAT-AAATTCTGATAATCCGATCTC
1 -TATGAAATTTTGATAAT-C--T-TT
* *
53698 TATGAAATTTAGATAAATCACTT
1 TATGAAATTTTGAT-AATC-TTT
* *
53721 TATGAGA-TTTGATAACCTTT
1 TATGAAATTTTGATAATCTTT
* * * *
53741 TATCAAATTTTGGTACTC-CT
1 TATGAAATTTTGATAATCTTT
53761 TATGAAATT
1 TATGAAATT
53770 GAGACTTTTA
Statistics
Matches: 72, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
20 16 0.22
21 22 0.31
22 9 0.12
23 7 0.10
24 5 0.07
25 10 0.14
26 3 0.04
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (21 bp):
TATGAAATTTTGATAATCTTT
Found at i:53804 original size:22 final size:21
Alignment explanation
Indices: 53775--53829 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
53765 AAATTGAGAC
53775 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTTC-TATGAAA
** *
53796 TTTTGATAACCACACTATAAAA
1 TTTTGATAACC-TTCTATGAAA
53818 TTTTGATAACCT
1 TTTTGATAACCT
53830 CCCCATGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.14
22 23 0.82
23 1 0.04
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (21 bp):
TTTTGATAACCTTCTATGAAA
Found at i:53840 original size:22 final size:22
Alignment explanation
Indices: 53790--53840 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
53780 TAACCTTCAT
*
53790 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* * *
53812 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACC
53834 ATGAAAT
1 ATGAAAT
53841 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:53904 original size:22 final size:22
Alignment explanation
Indices: 53846--53904 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
53836 GAAATATTTA
*
53846 ATGAAATTTTGTTAACCACACT
1 ATGAAATTTTGATAACCACACT
***
53868 ATGAAATTCTT-ATAACCTTGCT
1 ATGAAATT-TTGATAACCACACT
53890 ATGAAATTTTGATAA
1 ATGAAATTTTGATAA
53905 TCTCTTTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACT
Found at i:54004 original size:24 final size:22
Alignment explanation
Indices: 53940--54104 Score: 100
Period size: 22 Copynumber: 7.3 Consensus size: 22
53930 TTATGATAAT
* *
53940 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
* *
53962 TAACCAACCTAAGAGATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
53984 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
**
54008 TAACC-ACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
54030 TAACCAGTACACTATGGAATTTTGA
1 TAACCA--AC-CTATGAAATTTTAA
* **
54055 TAACC-TCCTCATGAAATCGTAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
54077 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
54099 TAACCA
1 TAACCA
54105 CATAGAGACA
Statistics
Matches: 114, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
21 3 0.03
22 71 0.62
23 3 0.03
24 17 0.15
25 20 0.18
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:54050 original size:25 final size:22
Alignment explanation
Indices: 53994--54059 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 22
53984 TAACCTGATC
53994 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
54016 CTATGAAATTTTGGTAACCAGTACA
1 CTATGAAATTTTGGTAACC---ACA
* *
54041 CTATGGAATTTTGATAACC
1 CTATGAAATTTTGGTAACC
54060 TCCTCATGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
22 19 0.49
25 20 0.51
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:54301 original size:19 final size:20
Alignment explanation
Indices: 54270--54307 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
54260 TATTGACATT
54270 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
54289 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
54308 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:55351 original size:17 final size:17
Alignment explanation
Indices: 55325--55359 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
55315 AAATACATAG
55325 AACTACCTAGTGTAACA
1 AACTACCTAGTGTAACA
*
55342 AACTATCTAGTGTAACA
1 AACTACCTAGTGTAACA
55359 A
1 A
55360 CTTTATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (17 bp):
AACTACCTAGTGTAACA
Found at i:56712 original size:3 final size:3
Alignment explanation
Indices: 56635--56699 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
56625 TTTAAAATCC
*
56635 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
56683 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
56700 GGGTTATTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:57973 original size:37 final size:37
Alignment explanation
Indices: 57892--57973 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
57882 ATTTCATCAT
* * *
57892 CATCACCCTAACTTGGGGTGATCAAAATTTCCAACAG
1 CATCACCCTAACATGGGGTGACCAAAATTTCCAAAAG
* *
57929 CACCACCCTAACATGGGGTGGCCAAAA-TTCCAAAACG
1 CATCACCCTAACATGGGGTGACCAAAATTTCCAAAA-G
*
57966 CTTCACCC
1 CATCACCC
57974 CAGGGGTGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
36 7 0.19
37 30 0.81
ACGTcount: A:0.32, C:0.33, G:0.16, T:0.20
Consensus pattern (37 bp):
CATCACCCTAACATGGGGTGACCAAAATTTCCAAAAG
Found at i:58231 original size:24 final size:24
Alignment explanation
Indices: 58199--58244 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
58189 TTTGAACCCT
58199 TAGATCTTTGTAATTCAACGATCA
1 TAGATCTTTGTAATTCAACGATCA
58223 TAGATCTTTGTAATTCAACGAT
1 TAGATCTTTGTAATTCAACGAT
58245 TATATTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (24 bp):
TAGATCTTTGTAATTCAACGATCA
Found at i:60639 original size:13 final size:13
Alignment explanation
Indices: 60621--60645 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60611 CACTGATCCC
60621 TCAAGAGAGTCTA
1 TCAAGAGAGTCTA
60634 TCAAGAGAGTCT
1 TCAAGAGAGTCT
60646 TCTTGTTGTC
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:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (13 bp):
TCAAGAGAGTCTA
Found at i:61045 original size:29 final size:29
Alignment explanation
Indices: 60971--61056 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 29
60961 TGCGGCTAAA
60971 TGCTCGATTTGGTCCTAAACCTTTCACGGTC
1 TGCTCGATTTGGTCCTAAACCTTTCAC-G-C
* *
61002 CGCTCGATTTGGTCCTAAACCTTCTGAC-C
1 TGCTCGATTTGGTCCTAAACCTT-TCACGC
*
61031 TGCTCAATTTGGTCCTAAACCTTTCA
1 TGCTCGATTTGGTCCTAAACCTTTCA
61057 ATTTCTTAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
28 2 0.04
29 22 0.45
31 22 0.45
32 3 0.06
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (29 bp):
TGCTCGATTTGGTCCTAAACCTTTCACGC
Found at i:62418 original size:17 final size:17
Alignment explanation
Indices: 62392--62428 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
62382 AAAAAAATAT
*
62392 CATAACATACAGTCTTC
1 CATAAAATACAGTCTTC
62409 CATAAAATACAGTCTTC
1 CATAAAATACAGTCTTC
62426 CAT
1 CAT
62429 TAGTAGTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (17 bp):
CATAAAATACAGTCTTC
Found at i:67076 original size:31 final size:28
Alignment explanation
Indices: 67006--67090 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 28
66996 GTTAAGAAAT
*
67006 TGAAAGGTTTAGGACCAAATTGAGCGGG
1 TGAAAGGTTTAGGACCAAATCGAGCGGG
*
67034 TCAGAAGGTTTAGGACCAAATCGAGCGGACCG
1 TGA-AAGGTTTAGGACCAAATCGAGCGG---G
67066 TGAAAGGTTTAGGACCAAATCGAGC
1 TGAAAGGTTTAGGACCAAATCGAGC
67091 ATTTAGCCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 2 0.04
29 23 0.46
31 22 0.44
32 3 0.06
ACGTcount: A:0.33, C:0.16, G:0.32, T:0.19
Consensus pattern (28 bp):
TGAAAGGTTTAGGACCAAATCGAGCGGG
Found at i:79088 original size:15 final size:15
Alignment explanation
Indices: 79068--79100 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
79058 CCAAACTATT
79068 TAACATCAATCCTCC
1 TAACATCAATCCTCC
79083 TAACATCAATCCTCC
1 TAACATCAATCCTCC
79098 TAA
1 TAA
79101 TGGAGTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.27
Consensus pattern (15 bp):
TAACATCAATCCTCC
Found at i:80793 original size:13 final size:13
Alignment explanation
Indices: 80775--80799 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
80765 TTTAAGCATA
80775 AAGAAGCAGAGTC
1 AAGAAGCAGAGTC
80788 AAGAAGCAGAGT
1 AAGAAGCAGAGT
80800 TTTCAAAGTT
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:0.48, C:0.12, G:0.32, T:0.08
Consensus pattern (13 bp):
AAGAAGCAGAGTC
Found at i:86181 original size:13 final size:13
Alignment explanation
Indices: 86163--86188 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
86153 TTAAATTCTT
86163 AATCCTTACTATA
1 AATCCTTACTATA
86176 AATCCTTACTATA
1 AATCCTTACTATA
86189 CCTGAAGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (13 bp):
AATCCTTACTATA
Found at i:93533 original size:1 final size:1
Alignment explanation
Indices: 93527--93551 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
93517 AGATTTATTT
93527 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
93552 CTTTGACAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:105315 original size:46 final size:45
Alignment explanation
Indices: 105215--105373 Score: 255
Period size: 45 Copynumber: 3.5 Consensus size: 45
105205 CTTGGAGCAC
* *
105215 TCGGCAATCATGCAGCCAAAGCTCTCTTTGATCTCCTTCAAGTTT
1 TCGGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTCAAGTAT
* * *
105260 TCAGAAATCATGGAGCCAAAGCTCTCTTTTGTTCTCCTTCAAGTAT
1 TCGGCAATCATGGAGCCAAAGCTCTC-TTTGATCTCCTTCAAGTAT
105306 TCGGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTCAAGTAT
1 TCGGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTCAAGTAT
*
105351 TCGGCAATCATGGAGCCTAAGCT
1 TCGGCAATCATGGAGCCAAAGCT
105374 TTCACTGTGC
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 63 0.61
46 41 0.39
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (45 bp):
TCGGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTCAAGTAT
Found at i:107084 original size:40 final size:40
Alignment explanation
Indices: 107028--107397 Score: 526
Period size: 40 Copynumber: 9.2 Consensus size: 40
107018 TGAGGGCCAT
* *
107028 TGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAA
1 TGTGAA-TAAGGCAAGTTCAATGTGATTTGGGAAAGTTGGA
* *
107069 TGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAA
1 TGTGAATAAGGCAAGTTCAATGTGATTTGGGAAAGTTGGA
* *
107109 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAATTTGGA
1 TGTGAATAAGGCAAGTTCAATGTGATTTGGGAAAGTTGGA
* *
107149 TGTGAATAAGGCAAGTTCAATGTTATTTGGGAAATTTTGGA
1 TGTGAATAAGGCAAGTTCAATGTGATTTGGGAAA-GTTGGA
* * *
107190 TGTGAATAAGGCAAGTTCAATGTTATTTGGGAAATTTGTA
1 TGTGAATAAGGCAAGTTCAATGTGATTTGGGAAAGTTGGA
* * * *
107230 TGTGAGTAAGGCAAGTTCAATGTTATTTGGAAAATTTGGA
1 TGTGAATAAGGCAAGTTCAATGTGATTTGGGAAAGTTGGA
*
107270 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGA
1 TGTGAATAAGGCAAGTTCAATGTGATTTGGGAAAGTTGGA
*
107310 TGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTGGA
1 TGTGAATAAGGCAAGTTCAATGTGATTTGGGAAAGTTGGA
**
107350 TGTGAATTAAGGCAAGTTCAATGTCGA-TTGGGAAAGTTAAA
1 TGTGAA-TAAGGCAAGTTCAATGT-GATTTGGGAAAGTTGGA
107391 TGTGAAT
1 TGTGAAT
107398 GTGCCGCGTA
Statistics
Matches: 309, Mismatches: 17, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
40 226 0.73
41 81 0.26
42 2 0.01
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (40 bp):
TGTGAATAAGGCAAGTTCAATGTGATTTGGGAAAGTTGGA
Found at i:107300 original size:161 final size:161
Alignment explanation
Indices: 107028--107397 Score: 573
Period size: 161 Copynumber: 2.3 Consensus size: 161
107018 TGAGGGCCAT
107028 TGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATGTG
1 TGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATGTG
* *
107093 AATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAATTTGGATGTGAATAA
66 AATTGGAAAAGTTGAATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATAA
* * *
107158 GGCAAGTTCAATGTTATTTGGGAAATTTTGGA
131 GGCAAGTTCAATGTGAATTGGGAAA-GTTGGA
* * * * * *
107190 TGTGAA-TAAGGCAAGTTCAATGTTATTTGGGAAATTTGTATGTGAGTAAGGCAAGTTCAATGTT
1 TGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATGTG
* * *
107254 ATTTGGAAAATTTGGATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATAA
66 AATTGGAAAAGTTGAATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATAA
107319 GGCAAGTTCAATGTGAATTGGGAAAGTTGGA
131 GGCAAGTTCAATGTGAATTGGGAAAGTTGGA
*
107350 TGTGAATTAAGGCAAGTTCAATGTCG-ATTGGGAAAGTTAAATGTGAAT
1 TGTGAATTAAGGCAAGTTCAATGT-GAATTGGGAAAGTTGAATGTGAAT
107398 GTGCCGCGTA
Statistics
Matches: 186, Mismatches: 20, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
160 11 0.06
161 169 0.91
162 6 0.03
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (161 bp):
TGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATGTG
AATTGGAAAAGTTGAATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATAA
GGCAAGTTCAATGTGAATTGGGAAAGTTGGA
Found at i:107397 original size:121 final size:120
Alignment explanation
Indices: 107028--107384 Score: 554
Period size: 121 Copynumber: 3.0 Consensus size: 120
107018 TGAGGGCCAT
* * *
107028 TGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATGTG
1 TGTGAA-TAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATAAGGCAAGTTCAATGTG
107093 AATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAATTTGGA
65 AATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAATTTGGA
* * *
107149 TGTGAATAAGGCAAGTTCAATGTTATTTGGGAAATTTTGGATGTGAATAAGGCAAGTTCAATGTT
1 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAA-GTTGGATGTGAATAAGGCAAGTTCAATGTG
* * * * * *
107214 ATTTGGGAAATTTGTATGTGAGTAAGGCAAGTTCAATGTTATTTGGAAAATTTGGA
65 AATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAATTTGGA
107270 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATAAGGCAAGTTCAATGTGA
1 TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATAAGGCAAGTTCAATGTGA
*
107335 ATTGGGAAAGTTGGATGTGAATTAAGGCAAGTTCAATGTCGA-TTGGGAAA
66 ATTGGGAAAGTTGAATGTGAA-TAAGGCAAGTTCAATGTC-ATTTGGGAAA
107385 GTTAAATGTG
Statistics
Matches: 213, Mismatches: 20, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
120 72 0.34
121 140 0.66
122 1 0.00
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.32
Consensus pattern (120 bp):
TGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATAAGGCAAGTTCAATGTGA
ATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAATTTGGA
Found at i:108387 original size:19 final size:20
Alignment explanation
Indices: 108363--108408 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
108353 CTAGTATTCT
*
108363 CATTTTAC-GTAGTCCGAGA
1 CATTTTACAGGAGTCCGAGA
*
108382 CATTTTACAGGATTCCGAGA
1 CATTTTACAGGAGTCCGAGA
108402 CATTTTA
1 CATTTTA
108409 TATCATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (20 bp):
CATTTTACAGGAGTCCGAGA
Found at i:111160 original size:20 final size:20
Alignment explanation
Indices: 111137--111210 Score: 55
Period size: 20 Copynumber: 3.6 Consensus size: 20
111127 AGGCGAGGCT
111137 AGAAGACACGAGGGTACACG
1 AGAAGACACGAGGGTACACG
* **
111157 AGAAGAAAGCAGAGGCG-AGGTC-
1 AGAAGACA-C-GAGG-GTA-CACG
*
111179 AGAAGACATGAGGGTACACG
1 AGAAGACACGAGGGTACACG
111199 AGAAGACA-GAGG
1 AGAAGACACGAGG
111211 CCTCCGCAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 13
0.67 0.11 0.21
Matches are distributed among these distances:
19 6 0.15
20 20 0.49
21 1 0.02
22 12 0.29
23 2 0.05
ACGTcount: A:0.42, C:0.15, G:0.38, T:0.05
Consensus pattern (20 bp):
AGAAGACACGAGGGTACACG
Found at i:111185 original size:42 final size:43
Alignment explanation
Indices: 111079--111206 Score: 152
Period size: 42 Copynumber: 2.9 Consensus size: 43
111069 AGGCCTCCGC
* * * *
111079 AGGAGGCGAGGCCAGCAGACACGAAGGTACATGAGAAGACATGA
1 AGGAGGCGAGG-CAGAAGACACGAGGGTACACGAGAAGACAAGA
*
111123 AGTGAGGCGAGGCTAGAAGACACGAGGGTACACGAGAAGA-AAGC
1 AG-GAGGCGAGGC-AGAAGACACGAGGGTACACGAGAAGACAAGA
*
111167 A-GAGGCGAGGTCAGAAGACATGAGGGTACACGAGAAGACA
1 AGGAGGCGAGG-CAGAAGACACGAGGGTACACGAGAAGACA
111207 GAGGCCTCCG
Statistics
Matches: 74, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
42 34 0.46
43 2 0.03
44 6 0.08
45 32 0.43
ACGTcount: A:0.39, C:0.16, G:0.38, T:0.07
Consensus pattern (43 bp):
AGGAGGCGAGGCAGAAGACACGAGGGTACACGAGAAGACAAGA
Found at i:111225 original size:52 final size:52
Alignment explanation
Indices: 111168--111619 Score: 676
Period size: 52 Copynumber: 8.8 Consensus size: 52
111158 GAAGAAAGCA
* * * * * *
111168 GAGGCGAGGTCAGAAGACATGAGGGTACACGAGAAGACAGAGGCCTCCGCAG
1 GAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGCCTCCGCAG
* * * * * *
111220 AAGGCGAGGCCAGCAGACACGAAGGTCCACGAGAAGACAGAGACCACCGCGG
1 GAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGCCTCCGCAG
* * *
111272 GAGGCGAGGCCAGCAGAAACGAAGGTCCACGAGAAGACAGAGGCCTCCGCAG
1 GAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGCCTCCGCAG
111324 GAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGCCTCCGCAG
1 GAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGCCTCCGCAG
*
111376 GAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGCCTTCGCAG
1 GAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGCCTCCGCAG
*
111428 GAGGCGAGGCCAGCACACACGAAGGTGC-CAAGAAGACAGAGGCCTCCGCAG
1 GAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGCCTCCGCAG
* * *
111479 GAGGCGAGGCCAGCACACACGAAGGTGCACAAGAAGACAGAGGCCTCCTCCG
1 GAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGCCTCCGCAG
*
111531 GAGGCGAGGCCAGCACACTCGAAGGTGCACGAGAAGAC--AGGCCTCCGCAG
1 GAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGCCTCCGCAG
* *
111581 GAGGCGAGGCCAGCAGACACGAAGGTACACGAGAAGACA
1 GAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACA
111620 CACACGAAGG
Statistics
Matches: 369, Mismatches: 29, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
50 45 0.12
51 49 0.13
52 275 0.75
ACGTcount: A:0.32, C:0.27, G:0.36, T:0.05
Consensus pattern (52 bp):
GAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGCCTCCGCAG
Found at i:111534 original size:155 final size:155
Alignment explanation
Indices: 111199--111619 Score: 668
Period size: 155 Copynumber: 2.7 Consensus size: 155
111189 AGGGTACACG
* * * *
111199 AGAAGACAGAGGCCTCCGCAGAAGGCGAGGCCAGCAGACACGAAGGTCCACGAGAAGACAGAGAC
1 AGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGC
* * *
111264 CACCGCGGGAGGCGAGGCCAGCAGAAACGAAGGTCCACGAGAAGACAGAGGCCTCCGCAGGAGGC
66 CTCCGCAGGAGGCGAGGCCAGCAGACACGAAGGTCCAC-AGAAGACAGAGGCCTCCGCAGGAGGC
*
111329 GAGGCCAGCACACACGAAGGTGCACG
130 GAGGCCAGCACACACGAAGGTGCACA
111355 AGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGC
1 AGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGC
* *
111420 CTTCGCAGGAGGCGAGGCCAGCACACACGAAGGTGCCA-AGAAGACAGAGGCCTCCGCAGGAGGC
66 CTCCGCAGGAGGCGAGGCCAGCAGACACGAAGGT-CCACAGAAGACAGAGGCCTCCGCAGGAGGC
111484 GAGGCCAGCACACACGAAGGTGCACA
130 GAGGCCAGCACACACGAAGGTGCACA
* * *
111510 AGAAGACAGAGGCCTCCTCCGGAGGCGAGGCCAGCACACTCGAAGGTGCACGAGAAGAC--AGGC
1 AGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGC
*
111573 CTCCGCAGGAGGCGAGGCCAGCAGACACGAAGGTACACGAGAAGACA
66 CTCCGCAGGAGGCGAGGCCAGCAGACACGAAGGTCCAC-AGAAGACA
111620 CACACGAAGG
Statistics
Matches: 246, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
152 2 0.01
153 36 0.15
154 8 0.03
155 107 0.43
156 90 0.37
157 3 0.01
ACGTcount: A:0.32, C:0.28, G:0.35, T:0.04
Consensus pattern (155 bp):
AGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCACACACGAAGGTGCACGAGAAGACAGAGGC
CTCCGCAGGAGGCGAGGCCAGCAGACACGAAGGTCCACAGAAGACAGAGGCCTCCGCAGGAGGCG
AGGCCAGCACACACGAAGGTGCACA
Found at i:111767 original size:6 final size:6
Alignment explanation
Indices: 111756--111787 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
111746 GAGCAAGCGA
*
111756 GAGAGC GAGAGC GAGAGC GAGAGC AAGAGC GA
1 GAGAGC GAGAGC GAGAGC GAGAGC GAGAGC GA
111788 AGAGAGAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.38, C:0.16, G:0.47, T:0.00
Consensus pattern (6 bp):
GAGAGC
Found at i:111883 original size:4 final size:4
Alignment explanation
Indices: 111863--111954 Score: 94
Period size: 4 Copynumber: 23.0 Consensus size: 4
111853 AAGGAAATCT
* * * * *
111863 AGAG CGAG AGCG AGAG AGAG AGGG AGAG AGAG CGAG CGAG AGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
* * * * *
111911 AGAG CGAG CGAG AGAG AGAG AGAG CGAG CGAG CGAG AGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
111955 GAAAGGGGAG
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 76 1.00
ACGTcount: A:0.39, C:0.10, G:0.51, T:0.00
Consensus pattern (4 bp):
AGAG
Found at i:111903 original size:20 final size:20
Alignment explanation
Indices: 111863--111954 Score: 139
Period size: 20 Copynumber: 4.5 Consensus size: 20
111853 AAGGAAATCT
* *
111863 AGAGCGAGAGCGAGAGAGAG
1 AGAGAGAGAGCGAGCGAGAG
111883 AGGGAGAGAGAGCGAGCGAGAG
1 A--GAGAGAGAGCGAGCGAGAG
111905 AGAGAGAGAGCGAGCGAGAG
1 AGAGAGAGAGCGAGCGAGAG
*
111925 AGAGAGAGAGCGAGCGAGCG
1 AGAGAGAGAGCGAGCGAGAG
111945 AGAGAGAGAG
1 AGAGAGAGAG
111955 GAAAGGGGAG
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 49 0.73
22 18 0.27
ACGTcount: A:0.39, C:0.10, G:0.51, T:0.00
Consensus pattern (20 bp):
AGAGAGAGAGCGAGCGAGAG
Found at i:111953 original size:24 final size:24
Alignment explanation
Indices: 111863--111954 Score: 130
Period size: 24 Copynumber: 3.8 Consensus size: 24
111853 AAGGAAATCT
* * *
111863 AGAGCGAGAGCGAGAGAGAGAGGG
1 AGAGCGAGCGAGAGAGAGAGAGAG
* *
111887 AGAGAGAGCGAGCGAGAGAGAGAG
1 AGAGCGAGCGAGAGAGAGAGAGAG
111911 AGAGCGAGCGAGAGAGAGAGAGAG
1 AGAGCGAGCGAGAGAGAGAGAGAG
*
111935 CGAGCGAGCGAGAGAGAGAG
1 AGAGCGAGCGAGAGAGAGAG
111955 GAAAGGGGAG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.39, C:0.10, G:0.51, T:0.00
Consensus pattern (24 bp):
AGAGCGAGCGAGAGAGAGAGAGAG
Found at i:112998 original size:13 final size:14
Alignment explanation
Indices: 112970--113002 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
112960 AGAAAATAGA
*
112970 AAAAAAAATTTATT
1 AAAAATAATTTATT
112984 AAAAATAATTT-TT
1 AAAAATAATTTATT
112997 AAAAAT
1 AAAAAT
113003 TATTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAAATAATTTATT
Found at i:115667 original size:27 final size:28
Alignment explanation
Indices: 115617--115669 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
115607 AAACAAATAT
115617 TTGCTTTTAAATTTTGAAAAAAAAAAAA
1 TTGCTTTTAAATTTTGAAAAAAAAAAAA
* *
115645 TTGCTTTTGAA-TTTGAGAAAAAAAA
1 TTGCTTTTAAATTTTGAAAAAAAAAA
115670 GATGAGTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (28 bp):
TTGCTTTTAAATTTTGAAAAAAAAAAAA
Done.