Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, 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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 67 of 117
Found at i:12421486 original size:33 final size:33
Alignment explanation
Indices: 12421437--12421501 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
12421427 CAAGATACCT
* * * *
12421437 ATATCTTGAATTTATCTGTTGGTTCGAGTGACG
1 ATATCTTAAATGTATCTGTTAGTCCGAGTGACG
12421470 ATATCTTAAATGTATCTGTTAGTCCGAGTGAC
1 ATATCTTAAATGTATCTGTTAGTCCGAGTGAC
12421502 AAAAAACTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.40
Consensus pattern (33 bp):
ATATCTTAAATGTATCTGTTAGTCCGAGTGACG
Found at i:12422561 original size:33 final size:33
Alignment explanation
Indices: 12422512--12422576 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
12422502 CAAGATACCT
* * * *
12422512 ATATCTTGAATTTATCTGTTGGTTCGAGTGACG
1 ATATCTTAAATGTATCTGTTAGTCCGAGTGACG
12422545 ATATCTTAAATGTATCTGTTAGTCCGAGTGAC
1 ATATCTTAAATGTATCTGTTAGTCCGAGTGAC
12422577 AAAAAACTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.40
Consensus pattern (33 bp):
ATATCTTAAATGTATCTGTTAGTCCGAGTGACG
Found at i:12429961 original size:94 final size:94
Alignment explanation
Indices: 12429835--12430022 Score: 340
Period size: 94 Copynumber: 2.0 Consensus size: 94
12429825 TGAAAGAGTT
* * *
12429835 TTTATTTCAACACTAACAGCGTAAACGATTTCCAAATGTGATTCTGTAGACTGAAATTCACAAAT
1 TTTATGTCAACACTAACACCGTAAACAATTTCCAAATGTGATTCTGTAGACTGAAATTCACAAAT
12429900 TGAAGAATAGAAATCTAATGCAGCATAAG
66 TGAAGAATAGAAATCTAATGCAGCATAAG
12429929 TTTATGTCAACACTAACACCGTAAACAATTTCCAAATGTGATTCTGTAGACTGAAATTCACAAAT
1 TTTATGTCAACACTAACACCGTAAACAATTTCCAAATGTGATTCTGTAGACTGAAATTCACAAAT
*
12429994 TGAAGCATAGAAATCTAATGCAGCATAAG
66 TGAAGAATAGAAATCTAATGCAGCATAAG
12430023 GCTCACTCCT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.28
Consensus pattern (94 bp):
TTTATGTCAACACTAACACCGTAAACAATTTCCAAATGTGATTCTGTAGACTGAAATTCACAAAT
TGAAGAATAGAAATCTAATGCAGCATAAG
Found at i:12432672 original size:11 final size:12
Alignment explanation
Indices: 12432650--12432674 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12432640 ATTTAAAACC
12432650 AAAAAGTAAAAA
1 AAAAAGTAAAAA
12432662 AAAAAGTAAAAA
1 AAAAAGTAAAAA
12432674 A
1 A
12432675 GAAACAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAGTAAAAA
Found at i:12441014 original size:20 final size:21
Alignment explanation
Indices: 12440977--12441016 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12440967 TTAAATAGAT
*
12440977 AAAATTTACACAAATAAAATA
1 AAAAATTACACAAATAAAATA
*
12440998 AAAAATTAC-CAATTAAAAT
1 AAAAATTACACAAATAAAAT
12441017 CAATTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAAATTACACAAATAAAATA
Found at i:12442970 original size:67 final size:66
Alignment explanation
Indices: 12442833--12442994 Score: 173
Period size: 67 Copynumber: 2.4 Consensus size: 66
12442823 TGCTTGGAGA
* * * * * *
12442833 ACTTAAAAGATTAATGCCTAAAGTTTTATAGATCATGCTTAGAGGATTTGGTGATTATACTCGAG
1 ACTTAAAAGA-TCATGCTTAAAGTTTTATAGATCATGCTTAGAGAACTTGGTGATTATACTCAAA
*
12442898 GG
65 AG
* * * *
12442900 ACTTAAAAGATCATGCTTGAAGGTTTTATAGATCATG-TTCGAAGAACTTGGTGATTATGCTTAA
1 ACTTAAAAGATCATGCTT-AAAGTTTTATAGATCATGCTTAG-AGAACTTGGTGATTATACTCAA
12442964 AAG
64 AAG
*
12442967 ACTTAAAAGATCATGCTTAGAGATTTTA
1 ACTTAAAAGATCATGCTTAAAG-TTTTA
12442995 CAAATCATAC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
66 11 0.14
67 68 0.86
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (66 bp):
ACTTAAAAGATCATGCTTAAAGTTTTATAGATCATGCTTAGAGAACTTGGTGATTATACTCAAAA
G
Found at i:12450942 original size:33 final size:32
Alignment explanation
Indices: 12450824--12450949 Score: 89
Period size: 33 Copynumber: 3.8 Consensus size: 32
12450814 TAAACTACAA
* *
12450824 TAAAAATA-AAAATTTAAAGTAAATAAAGAAAAG
1 TAAAAATATAAAA--TAAAATAAATAAATAAAAG
* *
12450857 AATAAAAATAAAAAAT-AAGTAAGATAAATAAAA-
1 --TAAAAATATAAAATAAAATAA-ATAAATAAAAG
* * *
12450890 CAAATATATATAAA-CAAATAAATACAATAAAAG
1 TAAAAATATA-AAATAAAATAAATA-AATAAAAG
12450923 TAAAAATATAAAATAAAATAAAATAAA
1 TAAAAATATAAAATAAAAT-AAATAAA
12450950 ATAGAAAATT
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
31 10 0.13
32 18 0.24
33 20 0.27
34 15 0.20
35 8 0.11
36 4 0.05
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (32 bp):
TAAAAATATAAAATAAAATAAATAAATAAAAG
Found at i:12450950 original size:23 final size:24
Alignment explanation
Indices: 12450899--12450949 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
12450889 ACAAATATAT
*
12450899 ATAAACAA-AT-AAATACAATAAA
1 ATAAACAATATAAAATAAAATAAA
12450921 AGTAAA-AATATAAAATAAAATAAA
1 A-TAAACAATATAAAATAAAATAAA
12450945 ATAAA
1 ATAAA
12450950 ATAGAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 3 0.12
23 10 0.40
24 12 0.48
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.20
Consensus pattern (24 bp):
ATAAACAATATAAAATAAAATAAA
Found at i:12453257 original size:3 final size:3
Alignment explanation
Indices: 12453244--12453283 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
12453234 CAAAAAACTA
12453244 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12453284 GTTAAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:12453635 original size:20 final size:19
Alignment explanation
Indices: 12453599--12453641 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
12453589 TCAACGACAA
*
12453599 AAAAAAAAGGAAACAAAAT
1 AAAAAAAAGGAAACAAAAG
12453618 AAAAAAAA-GAATACCAAAAG
1 AAAAAAAAGGAA-A-CAAAAG
12453638 AAAA
1 AAAA
12453642 GTGATGGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 9 0.43
20 9 0.43
ACGTcount: A:0.79, C:0.07, G:0.09, T:0.05
Consensus pattern (19 bp):
AAAAAAAAGGAAACAAAAG
Found at i:12455817 original size:18 final size:18
Alignment explanation
Indices: 12455794--12455874 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 18
12455784 AAAAATAATC
12455794 AAATTAAATAAAGAATAA
1 AAATTAAATAAAGAATAA
*
12455812 AAATTAAAATGAGAGTTAAATATA
1 AAATT-AAAT-AAAG---AATA-A
*
12455836 AAATCTAAA-AAATAAT-A
1 AAAT-TAAATAAAGAATAA
*
12455853 AAATTAAATAAAGAAAAA
1 AAATTAAATAAAGAATAA
12455871 AAAT
1 AAAT
12455875 GAGATTTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
16 4 0.08
17 10 0.20
18 10 0.20
19 7 0.14
20 3 0.06
22 2 0.04
23 4 0.08
24 8 0.16
25 1 0.02
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.23
Consensus pattern (18 bp):
AAATTAAATAAAGAATAA
Found at i:12456647 original size:26 final size:26
Alignment explanation
Indices: 12456611--12456700 Score: 92
Period size: 26 Copynumber: 3.5 Consensus size: 26
12456601 ACTGTAGACA
* *
12456611 CCCATTTGTGTCGAGGCCCAATTAGG
1 CCCATTGGTGTCGAGGTCCAATTAGG
*
12456637 CCCATTGGTGTTCG-GGTTCAATTAGG
1 CCCATTGGTG-TCGAGGTCCAATTAGG
* * *
12456663 CCCATTGATGTCCAGGTCCAACTAGG
1 CCCATTGGTGTCGAGGTCCAATTAGG
* *
12456689 CCTATTTGTGTC
1 CCCATTGGTGTC
12456701 ACTGTTATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
25 2 0.04
26 47 0.90
27 3 0.06
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (26 bp):
CCCATTGGTGTCGAGGTCCAATTAGG
Found at i:12456727 original size:6 final size:6
Alignment explanation
Indices: 12456716--12456741 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12456706 TATTTGATTA
12456716 TTATAT TTATAT TTATAT TTATAT TT
1 TTATAT TTATAT TTATAT TTATAT TT
12456742 TTCTTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTATAT
Found at i:12456776 original size:3 final size:3
Alignment explanation
Indices: 12456768--12456810 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
12456758 TCTGTGTTTA
* * *
12456768 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAG TAT TTT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12456811 TTCTTCTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:12457806 original size:3 final size:3
Alignment explanation
Indices: 12457798--12457840 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
12457788 ATATTTACAA
12457798 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12457841 AAAATATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:12457846 original size:15 final size:15
Alignment explanation
Indices: 12457796--12457843 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
12457786 AAATATTTAC
12457796 AAAATAATAATAATA
1 AAAATAATAATAATA
*
12457811 ATAATAATAATAATA
1 AAAATAATAATAATA
*
12457826 ATAATAATAA-AATA
1 AAAATAATAATAATA
12457840 AAAA
1 AAAA
12457844 ATATTAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 7 0.23
15 24 0.77
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAATAATAATA
Found at i:12457852 original size:9 final size:9
Alignment explanation
Indices: 12457796--12457843 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
12457786 AAATATTTAC
12457796 AAAATAATA
1 AAAATAATA
*
12457805 ATAATAATA
1 AAAATAATA
*
12457814 ATAATAATA
1 AAAATAATA
*
12457823 ATAATAATA
1 AAAATAATA
*
12457832 ATAA-AATA
1 AAAATAATA
12457840 AAAA
1 AAAA
12457844 ATATTAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
8 7 0.19
9 30 0.81
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAATAATA
Found at i:12458474 original size:12 final size:12
Alignment explanation
Indices: 12458457--12458482 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12458447 AACTTGAAAT
12458457 TTATTTTCTTTC
1 TTATTTTCTTTC
12458469 TTATTTTCTTTC
1 TTATTTTCTTTC
12458481 TT
1 TT
12458483 TTCATTGCTT
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:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (12 bp):
TTATTTTCTTTC
Found at i:12461880 original size:8 final size:8
Alignment explanation
Indices: 12461867--12461962 Score: 72
Period size: 8 Copynumber: 11.5 Consensus size: 8
12461857 AAAGTGTGCA
12461867 AAAAAAAG
1 AAAAAAAG
12461875 AAAAAAA-
1 AAAAAAAG
12461882 AAGTAAAAAG
1 AA--AAAAAG
*
12461892 CAAAAAA-
1 AAAAAAAG
*
12461899 AAAAAAAC
1 AAAAAAAG
12461907 AAACAAAAG
1 AAA-AAAAG
*
12461916 AAAAGAAG
1 AAAAAAAG
12461924 AAAAGAAAG
1 AAAA-AAAG
12461933 AAAAAAA-
1 AAAAAAAG
12461940 AAACAAAGGAG
1 AAA-AAA--AG
*
12461951 GAAAAAAG
1 AAAAAAAG
12461959 AAAA
1 AAAA
12461963 CTTAAATTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 20
0.72 0.07 0.20
Matches are distributed among these distances:
7 11 0.15
8 34 0.48
9 19 0.27
10 5 0.07
11 2 0.03
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:12461891 original size:17 final size:17
Alignment explanation
Indices: 12461868--12461962 Score: 73
Period size: 18 Copynumber: 5.2 Consensus size: 17
12461858 AAGTGTGCAA
12461868 AAAAAAGAAAAAAAAAG
1 AAAAAAGAAAAAAAAAG
* *
12461885 TAAAAAGCAAAAAAAAAA
1 AAAAAAG-AAAAAAAAAG
* *
12461903 AAACAAACAAAAGAAAAG
1 AAA-AAAGAAAAAAAAAG
*
12461921 AAGAAAAGAAAGAAAAAAA
1 AA-AAAAGAAA-AAAAAAG
**
12461940 AAACAAAGGAGGAAAAAAG
1 AAA-AAA-GAAAAAAAAAG
12461959 AAAA
1 AAAA
12461963 CTTAAATTAA
Statistics
Matches: 60, Mismatches: 12, Indels: 11
0.72 0.14 0.13
Matches are distributed among these distances:
17 6 0.10
18 29 0.48
19 23 0.38
20 2 0.03
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.01
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAAG
Found at i:12461937 original size:37 final size:36
Alignment explanation
Indices: 12461866--12461946 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 36
12461856 AAAAGTGTGC
* *
12461866 AAAAA-AAAGAAAAAAAAAGTAAAAAGCAAAAAAAA
1 AAAAACAAACAAAAAAAAAGAAAAAAGCAAAAAAAA
*
12461901 AAAAACAAACAAAAGAAAAGAAGAAAAG-AAAGAAAAA
1 AAAAACAAACAAAAAAAAAGAA-AAAAGCAAA-AAAAA
12461938 AAAAACAAA
1 AAAAACAAA
12461947 GGAGGAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
35 5 0.12
36 16 0.40
37 19 0.47
ACGTcount: A:0.84, C:0.05, G:0.10, T:0.01
Consensus pattern (36 bp):
AAAAACAAACAAAAAAAAAGAAAAAAGCAAAAAAAA
Found at i:12462989 original size:86 final size:86
Alignment explanation
Indices: 12462874--12463043 Score: 214
Period size: 86 Copynumber: 2.0 Consensus size: 86
12462864 TTGTTATGAA
* * ** * * * * *
12462874 ATCTTTGTGAATGTAGAGTCTTTGTGAAACTTGAAGTCTTGCGAATCTTTTTTTTTTATGAACCA
1 ATCTTTATGAATCTAGAACCTTTGCGAAACTTGAAGTCTTACAAATCTTTCTTTCTTATGAACCA
12462939 AAAAATCCTTACGAATCTTGC
66 AAAAATCCTTACGAATCTTGC
** *
12462960 ATCTTTATGAATCTAGAACCTTTGCGAAACTTGGGGTCTTACAAATCTTTCTTTCTTATGAACCT
1 ATCTTTATGAATCTAGAACCTTTGCGAAACTTGAAGTCTTACAAATCTTTCTTTCTTATGAACCA
* *
12463025 AAAAATCTTTGCGAATCTT
66 AAAAATCCTTACGAATCTT
12463044 TCTATCTTGC
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
86 70 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (86 bp):
ATCTTTATGAATCTAGAACCTTTGCGAAACTTGAAGTCTTACAAATCTTTCTTTCTTATGAACCA
AAAAATCCTTACGAATCTTGC
Found at i:12463252 original size:86 final size:86
Alignment explanation
Indices: 12463038--12463253 Score: 227
Period size: 86 Copynumber: 2.5 Consensus size: 86
12463028 AATCTTTGCG
* * * * *
12463038 AATCTTTCTATCTTGCAAATATGAAAATCCTTGTAAATCTTGCATCATTGTGAATCTAGAACCTT
1 AATCTTTCTTTCTTGCGAACATGAAAACCCTTGTGAATCTTGCATCATTGTGAATCTAGAACCTT
**
12463103 TGTAAAACTTGGAGTTTTACA
66 TACAAAACTTGGAGTTTTACA
* ** * **
12463124 AATCTTTCTTTCTTGCGAACATTAAAATTCTTGCGAATCTTGCATTTTTGTGAATCTAGAACCTT
1 AATCTTTCTTTCTTGCGAACATGAAAACCCTTGTGAATCTTGCATCATTGTGAATCTAGAACCTT
* * *
12463189 TACGAAACTT-GAGGTTTTGCT
66 TACAAAACTTGGA-GTTTTACA
* * ** *
12463210 AATCTTTTTTTCTTGCGAACCTGAATGCCCTTGTGAACCTTGCA
1 AATCTTTCTTTCTTGCGAACATGAAAACCCTTGTGAATCTTGCA
12463254 CATGTGCAAA
Statistics
Matches: 106, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
85 2 0.02
86 104 0.98
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (86 bp):
AATCTTTCTTTCTTGCGAACATGAAAACCCTTGTGAATCTTGCATCATTGTGAATCTAGAACCTT
TACAAAACTTGGAGTTTTACA
Found at i:12463314 original size:17 final size:18
Alignment explanation
Indices: 12463272--12463314 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
12463262 AAACTTGAAA
12463272 TCTTGTGAATCTTTCCTT
1 TCTTGTGAATCTTTCCTT
*
12463290 T-TTCTGAATCTTT-CTT
1 TCTTGTGAATCTTTCCTT
12463306 TCTTGTGAA
1 TCTTGTGAA
12463315 CCTAAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 4 0.18
17 17 0.77
18 1 0.05
ACGTcount: A:0.14, C:0.19, G:0.12, T:0.56
Consensus pattern (18 bp):
TCTTGTGAATCTTTCCTT
Found at i:12464257 original size:3 final size:3
Alignment explanation
Indices: 12464251--12464276 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12464241 TATTATTATT
12464251 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
12464277 TAGTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:12465103 original size:13 final size:13
Alignment explanation
Indices: 12465087--12465116 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12465077 TCTATTTCTA
12465087 TTTTCATTTTATT
1 TTTTCATTTTATT
*
12465100 TTTTGATTTTATT
1 TTTTCATTTTATT
12465113 TTTT
1 TTTT
12465117 TAAATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.80
Consensus pattern (13 bp):
TTTTCATTTTATT
Found at i:12465124 original size:21 final size:21
Alignment explanation
Indices: 12465100--12465140 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12465090 TCATTTTATT
*
12465100 TTTTGATTTTATTTTTTTAAA
1 TTTTGATTTTATTTATTTAAA
*
12465121 TTTTTATTTTATTTATTTAA
1 TTTTGATTTTATTTATTTAA
12465141 CTTCACTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTGATTTTATTTATTTAAA
Found at i:12465267 original size:3 final size:3
Alignment explanation
Indices: 12465259--12465320 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
12465249 ATATTTACAA
12465259 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12465307 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
12465321 AAAAAAAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12466525 original size:21 final size:22
Alignment explanation
Indices: 12466482--12466526 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
12466472 AATTAAGACA
12466482 TTGTATATATTATGTTATTTTG
1 TTGTATATATTATGTTATTTTG
*
12466504 TTGTAT-TA-TATGGTTGTTTTG
1 TTGTATATATTAT-GTTATTTTG
12466525 TT
1 TT
12466527 ATTTCTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 12 0.57
22 6 0.29
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (22 bp):
TTGTATATATTATGTTATTTTG
Found at i:12470642 original size:20 final size:19
Alignment explanation
Indices: 12470602--12470653 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
12470592 TGTAAAAAAC
12470602 AAAAAAGA-AAAATA-GTAAA
1 AAAAAAGAGAAAA-AGGT-AA
*
12470621 AAAAAAGAGAAAAAGGTGA
1 AAAAAAGAGAAAAAGGTAA
12470640 AAAAAAG-GAAAAAG
1 AAAAAAGAGAAAAAG
12470654 ACAAATGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 7 0.23
19 17 0.57
20 6 0.20
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (19 bp):
AAAAAAGAGAAAAAGGTAA
Found at i:12470642 original size:21 final size:19
Alignment explanation
Indices: 12470602--12470652 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
12470592 TGTAAAAAAC
12470602 AAAAAAGAAAAATAGTAAA
1 AAAAAAGAAAAATAGTAAA
*
12470621 AAAAAAGAGAAAA-AGGTGAA
1 AAAAAAGA-AAAATA-GTAAA
*
12470641 AAAAAGGAAAAA
1 AAAAAAGAAAAA
12470653 GACAAATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (19 bp):
AAAAAAGAAAAATAGTAAA
Found at i:12471207 original size:26 final size:26
Alignment explanation
Indices: 12471149--12471220 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 26
12471139 AAGAAAAAGT
* *
12471149 GAAAGAATGAAAAGGAAAAAGGTGAG
1 GAAAGAATGAAAAGGAAAAAAGTGAA
12471175 GAGAAGAA-GAAAAGGAAAAAAGTGAAA
1 GA-AAGAATGAAAAGGAAAAAAGTG-AA
*
12471202 GAAAGAATAACAAAGGAAA
1 GAAAGAATGA-AAAGGAAA
12471221 TGAAAGAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 22 0.56
27 9 0.23
28 8 0.21
ACGTcount: A:0.64, C:0.01, G:0.29, T:0.06
Consensus pattern (26 bp):
GAAAGAATGAAAAGGAAAAAAGTGAA
Found at i:12471236 original size:20 final size:19
Alignment explanation
Indices: 12471191--12471229 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
12471181 AAGAAAAGGA
12471191 AAAAAGTGAAAGAAAGAAT
1 AAAAAGTGAAAGAAAGAAT
12471210 AACAAAG-GAAATGAAAGAAT
1 AA-AAAGTGAAA-GAAAGAAT
12471230 TCAAAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (19 bp):
AAAAAGTGAAAGAAAGAAT
Found at i:12472170 original size:30 final size:30
Alignment explanation
Indices: 12472136--12472195 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
12472126 GGTAAGACCG
*
12472136 GTTTATTTAGCA-TCCAGGATTTAAGCCCAA
1 GTTTAATTAGCACT-CAGGATTTAAGCCCAA
* *
12472166 GTTTAATTGGCACTCAGGTTTTAAGCCCAA
1 GTTTAATTAGCACTCAGGATTTAAGCCCAA
12472196 CTTAATTGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (30 bp):
GTTTAATTAGCACTCAGGATTTAAGCCCAA
Found at i:12472338 original size:22 final size:22
Alignment explanation
Indices: 12472313--12472412 Score: 112
Period size: 22 Copynumber: 4.5 Consensus size: 22
12472303 CAAACCTAGA
* *
12472313 TTAGCTGGCATATAAACTCAGT
1 TTAGCTGGCACACAAACTCAGT
* * *
12472335 TTAGTTGGCACACAAGCCCTA-T
1 TTAGCTGGCACACAAACTC-AGT
*
12472357 TTAGCTGGCACACAAGCTCAGT
1 TTAGCTGGCACACAAACTCAGT
* *
12472379 TTAGTTAGCACACAAACTCAGT
1 TTAGCTGGCACACAAACTCAGT
12472401 TTAGCTGGCACA
1 TTAGCTGGCACA
12472413 TATGCTTAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
21 1 0.02
22 62 0.97
23 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (22 bp):
TTAGCTGGCACACAAACTCAGT
Found at i:12472361 original size:44 final size:44
Alignment explanation
Indices: 12472303--12472412 Score: 132
Period size: 44 Copynumber: 2.5 Consensus size: 44
12472293 AGTTGGCATG
* * * * *
12472303 CAAACCTAGATTAGCTGGCATATAAACTCAGTTTAGTTGGCACA
1 CAAACCCAGTTTAGCTGGCACACAAACTCAGTTTAGTTAGCACA
* *
12472347 CAAGCCCTA-TTTAGCTGGCACACAAGCTCAGTTTAGTTAGCACA
1 CAAACCC-AGTTTAGCTGGCACACAAACTCAGTTTAGTTAGCACA
*
12472391 CAAACTCAGTTTAGCTGGCACA
1 CAAACCCAGTTTAGCTGGCACA
12472413 TATGCTTAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
43 1 0.02
44 53 0.96
45 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (44 bp):
CAAACCCAGTTTAGCTGGCACACAAACTCAGTTTAGTTAGCACA
Found at i:12472763 original size:18 final size:18
Alignment explanation
Indices: 12472740--12472774 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12472730 AAAAAATCAA
12472740 ATATAAAATA-TAAAAAAT
1 ATATAAAA-AGTAAAAAAT
12472758 ATATAAAAAGTAAAAAA
1 ATATAAAAAGTAAAAAA
12472775 AAAAGCCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 15 0.94
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
ATATAAAAAGTAAAAAAT
Found at i:12475360 original size:17 final size:16
Alignment explanation
Indices: 12475317--12475363 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
12475307 GAAGTTATTA
12475317 AATAATAA-AAAAAAT
1 AATAATAATAAAAAAT
12475332 AATAA-AAGTAAATAAAT
1 AATAATAA-TAAA-AAAT
12475349 AATAATAATAAAAAA
1 AATAATAATAAAAAA
12475364 CTTTAATGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 2 0.07
15 5 0.18
16 6 0.21
17 13 0.46
18 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (16 bp):
AATAATAATAAAAAAT
Found at i:12475643 original size:26 final size:26
Alignment explanation
Indices: 12475614--12475679 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
12475604 GTTTGGACCC
* *
12475614 AATTAGGCCCATTTACATCTAGGCCT
1 AATTAGGCCCATTTACATCCAAGCCT
* **
12475640 AATTAGGCCCATTGATGTCCAAGCCT
1 AATTAGGCCCATTTACATCCAAGCCT
12475666 AATTAGGCCCATTT
1 AATTAGGCCCATTT
12475680 GTGTCACTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (26 bp):
AATTAGGCCCATTTACATCCAAGCCT
Found at i:12475752 original size:35 final size:36
Alignment explanation
Indices: 12475703--12475771 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
12475693 TTCATTATTA
* *
12475703 TGTTTTTAT-TTT-TATTTTTACTTTTCTTTCTTTGG
1 TGTTTCTATGTTTATATTATTA-TTTTCTTTCTTTGG
*
12475738 TGTTTCTATGTTTATATTATTATTTTTTTTCTTT
1 TGTTTCTATGTTTATATTATTATTTTCTTTCTTT
12475772 TTTTTCTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 8 0.28
36 14 0.48
37 7 0.24
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.74
Consensus pattern (36 bp):
TGTTTCTATGTTTATATTATTATTTTCTTTCTTTGG
Found at i:12476674 original size:3 final size:3
Alignment explanation
Indices: 12476666--12476703 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
12476656 ATATTTACAA
*
12476666 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12476704 ATATAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:12480653 original size:17 final size:17
Alignment explanation
Indices: 12480633--12480717 Score: 50
Period size: 18 Copynumber: 4.8 Consensus size: 17
12480623 AAATGTGTGC
12480633 AAAAAAAAAGAGAAGAA
1 AAAAAAAAAGAGAAGAA
12480650 AAAAAAAGCAA-A-AAGCAA
1 AAAAAAA--AAGAGAAG-AA
* * *
12480668 AAAAAAAAAAAAAACAA
1 AAAAAAAAAGAGAAGAA
12480685 ACAAAAGAAAAGAAGAA-AA
1 A-AAAA-AAAAG-AGAAGAA
*
12480704 GAAAGAAAAAGAGA
1 -AAAAAAAAAGAGA
12480718 CAAAAGAGGA
Statistics
Matches: 55, Mismatches: 4, Indels: 18
0.71 0.05 0.23
Matches are distributed among these distances:
16 2 0.04
17 17 0.31
18 21 0.38
19 11 0.20
20 4 0.07
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAGAAGAA
Found at i:12480677 original size:15 final size:15
Alignment explanation
Indices: 12480631--12480678 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
12480621 AAAAATGTGT
*
12480631 GCAAAAAAAAAGAGAA
1 GCAAAAAAAAA-AAAA
*
12480647 GAAAAAAAAAGCAAAAA
1 GCAAAAAAAA--AAAAA
12480664 GCAAAAAAAAAAAAA
1 GCAAAAAAAAAAAAA
12480679 AAACAAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 5 0.19
16 9 0.33
17 12 0.44
18 1 0.04
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.00
Consensus pattern (15 bp):
GCAAAAAAAAAAAAA
Found at i:12480696 original size:32 final size:32
Alignment explanation
Indices: 12480660--12480724 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
12480650 AAAAAAAGCA
12480660 AAAAGCAA-AAAAAAAAAAAAAACAAACAAAAG
1 AAAAG-AAGAAAAAAAAAAAAAACAAACAAAAG
* * * *
12480692 AAAAGAAGAAAAGAAAGAAAAAGAGACAAAAG
1 AAAAGAAGAAAAAAAAAAAAAACAAACAAAAG
12480724 A
1 A
12480725 GGAAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 2 0.07
32 26 0.93
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (32 bp):
AAAAGAAGAAAAAAAAAAAAAACAAACAAAAG
Found at i:12481911 original size:136 final size:137
Alignment explanation
Indices: 12481654--12481940 Score: 355
Period size: 136 Copynumber: 2.1 Consensus size: 137
12481644 AAAACTTAGA
* * * *
12481654 ATCTTATGAATCTTTCTTTCTTACGAACCTAAAAATCCTTGAGAATCTTGCATCTTTGCGAATCT
1 ATCTTGTGAATCTTTCTTTCTTACGAACCTAAAAATCCTTGAAAATCTTGCATCTTTACAAATCT
* * * *
12481719 TGAACCTTTGTAAAACTTGAGGTCTTACAAATCTTTCTTTCTTGAGAACCTAAAAATCTTTGTGA
66 AGAACCTTTGTAAAACTTGAGGTCTTACAAATCTTTCTTTATTGAGAACCTAAAAATCCTTGCGA
12481784 ATCGTGC
131 ATCGTGC
* * *
12481791 ATCTTGTGAATCTTTCTTTCTTGCGAACTTGAAAATCCTT-ACAAAT-TTGCATCTTTACAAATC
1 ATCTTGTGAATCTTTCTTTCTTACGAACCTAAAAATCCTTGA-AAATCTTGCATCTTTACAAATC
* ** * ** *
12481854 TAGAACCTTTGTGAAACTT-AGGGTCTTATGAATCTTTCTTTATTGCGAATTTGAAAATCCTTGC
65 TAGAACCTTTGTAAAACTTGA-GGTCTTACAAATCTTTCTTTATTGAGAACCTAAAAATCCTTGC
*
12481918 GAATCTTGC
129 GAATCGTGC
12481927 ATCTTTGTGAATCT
1 ATC-TTGTGAATCT
12481941 AGAACCTTTA
Statistics
Matches: 128, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
135 1 0.01
136 78 0.61
137 49 0.38
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (137 bp):
ATCTTGTGAATCTTTCTTTCTTACGAACCTAAAAATCCTTGAAAATCTTGCATCTTTACAAATCT
AGAACCTTTGTAAAACTTGAGGTCTTACAAATCTTTCTTTATTGAGAACCTAAAAATCCTTGCGA
ATCGTGC
Found at i:12481995 original size:86 final size:86
Alignment explanation
Indices: 12481792--12482023 Score: 288
Period size: 86 Copynumber: 2.7 Consensus size: 86
12481782 GAATCGTGCA
* ***
12481792 TCTTGTGAATCTTTCTTTCTTGCGAACTTGAAAATCCTTACAAAT-TTGCATCTTTACAAATCTA
1 TCTTGTGAATCTTTCTTTCTTGCGAACTTGAAAATCCTTACGAATCTTGCATCTTTGTGAATCTA
**
12481856 GAACCTTTGTGAAACTTAGGG
66 GAACCTTTACGAAACTTAGGG
* * * *
12481877 TCTTATGAATCTTTCTTTATTGCGAATTTGAAAATCCTTGCGAATCTTGCATCTTTGTGAATCTA
1 TCTTGTGAATCTTTCTTTCTTGCGAACTTGAAAATCCTTACGAATCTTGCATCTTTGTGAATCTA
*
12481942 GAACCTTTACGAAACTTGGGG
66 GAACCTTTACGAAACTTAGGG
* *** * * *
12481963 TCTTGCGAATCTTTCTTTCTTATAAACCTGAAAATCTTTATGAATCTTGCATC-TTGTGAAT
1 TCTTGTGAATCTTTCTTTCTTGCGAACTTGAAAATCCTTACGAATCTTGCATCTTTGTGAAT
12482024 ATTTTTTTCT
Statistics
Matches: 124, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
85 48 0.39
86 76 0.61
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (86 bp):
TCTTGTGAATCTTTCTTTCTTGCGAACTTGAAAATCCTTACGAATCTTGCATCTTTGTGAATCTA
GAACCTTTACGAAACTTAGGG
Found at i:12482018 original size:51 final size:51
Alignment explanation
Indices: 12481963--12482061 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
12481953 AAACTTGGGG
* *
12481963 TCTTGCGAATCTTTCTTTCTTATAAACCTGAAAATCTTTATGAATCTTGCA
1 TCTTGCGAATATTTCTTTCTTATAAACCTGAAAATCCTTATGAATCTTGCA
* * * *
12482014 TCTTGTGAATATTTTTTTCTTATGAACCTGAAAATCCTTGTGAATCTT
1 TCTTGCGAATATTTCTTTCTTATAAACCTGAAAATCCTTATGAATCTT
12482062 ACATTTTTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.45
Consensus pattern (51 bp):
TCTTGCGAATATTTCTTTCTTATAAACCTGAAAATCCTTATGAATCTTGCA
Found at i:12482048 original size:222 final size:222
Alignment explanation
Indices: 12481645--12482052 Score: 575
Period size: 222 Copynumber: 1.8 Consensus size: 222
12481635 AGTCTTTGCA
*
12481645 AAACTTAGAATCTTATGAATCTTTCTTTCTTACGAACCTAAAAATCCTTGAGAATCTTGCATCTT
1 AAACTTAGAATCTTATGAATCTTTCTTTATTACGAACCTAAAAATCCTTGAGAATCTTGCATCTT
* ** *
12481710 TGCGAATCTTGAACCTTTGTAAAACTTGAGGTCTTACAAATCTTTCTTTCTTGAGAACCTAAAAA
66 TGCGAATCTAGAACCTTTACAAAACTTGAGGTCTTACAAATCTTTCTTTCTTGAAAACCTAAAAA
* * * *
12481775 TCTTTGTGAATCGTGCATCTTGTGAATCTTTCTTTCTTGCGAACTTGAAAATCCTTACAAATTTG
131 TCTTTATGAATCGTGCATCTTGTGAATATTTCTTTCTTACGAACCTGAAAATCCTTACAAATTTG
12481840 CATCTTTACAAATCTAGAACCTTTGTG
196 CATCTTTACAAATCTAGAACCTTTGTG
** * ** * *
12481867 AAACTTAGGGTCTTATGAATCTTTCTTTATTGCGAATTTGAAAATCCTTGCGAATCTTGCATCTT
1 AAACTTAGAATCTTATGAATCTTTCTTTATTACGAACCTAAAAATCCTTGAGAATCTTGCATCTT
* * * * * *
12481932 TGTGAATCTAGAACCTTTACGAAACTTGGGGTCTTGCGAATCTTTCTTTCTT-ATAAACCTGAAA
66 TGCGAATCTAGAACCTTTACAAAACTTGAGGTCTTACAAATCTTTCTTTCTTGA-AAACCTAAAA
* * *
12481996 ATCTTTATGAATCTTGCATCTTGTGAATATTTTTTTCTTATGAACCTGAAAATCCTT
130 ATCTTTATGAATCGTGCATCTTGTGAATATTTCTTTCTTACGAACCTGAAAATCCTT
12482053 GTGAATCTTA
Statistics
Matches: 160, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
221 1 0.01
222 159 0.99
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (222 bp):
AAACTTAGAATCTTATGAATCTTTCTTTATTACGAACCTAAAAATCCTTGAGAATCTTGCATCTT
TGCGAATCTAGAACCTTTACAAAACTTGAGGTCTTACAAATCTTTCTTTCTTGAAAACCTAAAAA
TCTTTATGAATCGTGCATCTTGTGAATATTTCTTTCTTACGAACCTGAAAATCCTTACAAATTTG
CATCTTTACAAATCTAGAACCTTTGTG
Found at i:12482884 original size:120 final size:120
Alignment explanation
Indices: 12482548--12482886 Score: 378
Period size: 120 Copynumber: 2.8 Consensus size: 120
12482538 TATGGTTCAA
* * * *
12482548 TCCTGGTCACTTGATCTT-GATTCAGTCCAGATCATTTTTTATGATTCGTGGTTTCATCCTGATT
1 TCCTGATCACTTGATCTTGGCTT-AGTCCAGATCATTTCTTATGATTCGTGGTTTCATCCTGATC
* * * ** * * *
12482612 ATTTATTTTTGACCTCAACTCAGTCTTGATCACTTTATTTTTGACTCGTGGTTTTG
65 ATTTATTTTTGACTTCGACTCAGTCTTGGTTGCTTTACTTTTGACTCATGGTTTCG
* ** * * *
12482668 T-CTCAATCACTCAATCTTGGCTCAGTCTAGATCATTTCTTATGATTCATGGTTTCATCCTGATC
1 TCCT-GATCACTTGATCTTGGCTTAGTCCAGATCATTTCTTATGATTCGTGGTTTCATCCTGATC
* * * *
12482732 ATTTATTTTTAACCTT-GACTCGGTCCTAGTTGCTTTACTTTTGACTCATGGTTTCG
65 ATTTATTTTTGA-CTTCGACTCAGTCTTGGTTGCTTTACTTTTGACTCATGGTTTCG
* * * *
12482788 TCCTGATCACTTGATCTTGGCTTAGTCCAAATCATTTCTTATGACTCGTGGTTTCATCCCGGTCA
1 TCCTGATCACTTGATCTTGGCTTAGTCCAGATCATTTCTTATGATTCGTGGTTTCATCCTGATCA
* *
12482853 TTTATGTTTGACTTCGACTCAATCTTGGTTGCTT
66 TTTATTTTTGACTTCGACTCAGTCTTGGTTGCTT
12482887 CATTTTCAGA
Statistics
Matches: 176, Mismatches: 38, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
119 5 0.03
120 165 0.94
121 6 0.03
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.45
Consensus pattern (120 bp):
TCCTGATCACTTGATCTTGGCTTAGTCCAGATCATTTCTTATGATTCGTGGTTTCATCCTGATCA
TTTATTTTTGACTTCGACTCAGTCTTGGTTGCTTTACTTTTGACTCATGGTTTCG
Found at i:12483052 original size:26 final size:26
Alignment explanation
Indices: 12483023--12483157 Score: 112
Period size: 26 Copynumber: 5.2 Consensus size: 26
12483013 CTGTAGACAA
*
12483023 CCATTTATGTTCAGGCCCAATTAGGC
1 CCATTGATGTTCAGGCCCAATTAGGC
*
12483049 CCATTGGTGTTCAGGCCCAATTAGGC
1 CCATTGATGTTCAGGCCCAATTAGGC
* ** * * *
12483075 CCATTTACATT-ATGGCTCAATCAAGC
1 CCATTGATGTTCA-GGCCCAATTAGGC
** * *
12483101 CCATTGATGTTTGGGTCTAATTAGGC
1 CCATTGATGTTCAGGCCCAATTAGGC
* * *
12483127 CCATTGATG-TCTGACCCAACTAGGC
1 CCATTGATGTTCAGGCCCAATTAGGC
12483152 CCATTG
1 CCATTG
12483158 TGTCACTGTT
Statistics
Matches: 83, Mismatches: 24, Indels: 5
0.74 0.21 0.04
Matches are distributed among these distances:
25 17 0.20
26 66 0.80
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (26 bp):
CCATTGATGTTCAGGCCCAATTAGGC
Found at i:12483231 original size:3 final size:3
Alignment explanation
Indices: 12483223--12483286 Score: 101
Period size: 3 Copynumber: 21.3 Consensus size: 3
12483213 TTTGTGTTTA
12483223 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
12483271 CAT TAG TAT TTT TAT T
1 TAT TAT TAT TAT TAT T
12483287 TTCTTCTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:12485009 original size:66 final size:61
Alignment explanation
Indices: 12484961--12485080 Score: 176
Period size: 61 Copynumber: 2.0 Consensus size: 61
12484951 ATAATTCCTT
*
12484961 AATTTAAAAAATAAT-AAATTAAATAATGAATAAAAAATAAAAGTAAGATCTTAAATATAA
1 AATTTAAAAAATAATAAAATTAAATAAAGAATAAAAAATAAAAGTAAGATCTTAAATATAA
* * *
12485021 AATTTTAAAAATAATAAAATTAAATAAAGAATGAAAAATAAAA--AAAAT-TTAAATATAA
1 AATTTAAAAAATAATAAAATTAAATAAAGAATAAAAAATAAAAGTAAGATCTTAAATATAA
12485079 AA
1 AA
12485081 AAGTTGTACC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
58 12 0.22
59 4 0.07
60 14 0.25
61 25 0.45
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.28
Consensus pattern (61 bp):
AATTTAAAAAATAATAAAATTAAATAAAGAATAAAAAATAAAAGTAAGATCTTAAATATAA
Found at i:12485043 original size:29 final size:29
Alignment explanation
Indices: 12484993--12485080 Score: 74
Period size: 29 Copynumber: 2.9 Consensus size: 29
12484983 ATAATGAATA
* *
12484993 AAAAATAAAAGTAAGATCTTAAATATAAAATTTT
1 AAAAATAAAA--AAAAT-TTAAATATAAAA--TG
*
12485027 AAAAAT-AATAAAA-TTAAATA-AAGAATG
1 AAAAATAAAAAAAATTTAAATATAA-AATG
12485054 AAAAATAAAAAAAATTTAAATATAAAA
1 AAAAATAAAAAAAATTTAAATATAAAA
12485081 AAGTTGTACC
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
27 7 0.15
28 8 0.17
29 18 0.39
30 2 0.04
31 3 0.07
33 2 0.04
34 6 0.13
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (29 bp):
AAAAATAAAAAAAATTTAAATATAAAATG
Found at i:12488457 original size:25 final size:25
Alignment explanation
Indices: 12488407--12488453 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
12488397 ATATGCGTTA
*
12488407 AATGCATGAATATAATAGCATGATG
1 AATGCATGAATATAATAACATGATG
12488432 AATGCATGACA-AT-ATAACATGA
1 AATGCATGA-ATATAATAACATGA
12488454 ATGACAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 11 0.55
26 1 0.05
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.26
Consensus pattern (25 bp):
AATGCATGAATATAATAACATGATG
Found at i:12488593 original size:7 final size:7
Alignment explanation
Indices: 12488581--12488779 Score: 103
Period size: 7 Copynumber: 29.6 Consensus size: 7
12488571 TGGGGGTCTA
12488581 GTTTAGG
1 GTTTAGG
12488588 GTTTAGG
1 GTTTAGG
*
12488595 ATTTA--
1 GTTTAGG
12488600 GTTT-GG
1 GTTTAGG
12488606 GATTTAGG
1 G-TTTAGG
12488614 GTTT--G
1 GTTTAGG
*
12488619 GATTAGG
1 GTTTAGG
12488626 GTTT--G
1 GTTTAGG
12488631 GTTTA-G
1 GTTTAGG
*
12488637 ATTTAGG
1 GTTTAGG
* **
12488644 ATTTAAA
1 GTTTAGG
*
12488651 GTTTAAG
1 GTTTAGG
*
12488658 GCTTA-G
1 GTTTAGG
12488664 GTTTAGG
1 GTTTAGG
*
12488671 GTTTAAG
1 GTTTAGG
*
12488678 GTTTAGT
1 GTTTAGG
* *
12488685 GCTTAAG
1 GTTTAGG
*
12488692 GTTT-GAA
1 GTTTAG-G
12488699 GTTTAGG
1 GTTTAGG
*
12488706 GTTTAAG
1 GTTTAGG
*
12488713 GTTTATG
1 GTTTAGG
*
12488720 GTTTAAG
1 GTTTAGG
*
12488727 GTTTGGG
1 GTTTAGG
*
12488734 GTTTAAG
1 GTTTAGG
*
12488741 GTTTAGA
1 GTTTAGG
*
12488748 GTTTAAG
1 GTTTAGG
*
12488755 GTTTGGG
1 GTTTAGG
*
12488762 GTTTAGT
1 GTTTAGG
*
12488769 GTTTAGT
1 GTTTAGG
12488776 GTTT
1 GTTT
12488780 CATGGGATTT
Statistics
Matches: 145, Mismatches: 36, Indels: 22
0.71 0.18 0.11
Matches are distributed among these distances:
5 12 0.08
6 11 0.08
7 118 0.81
8 4 0.03
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:12488668 original size:20 final size:21
Alignment explanation
Indices: 12488639--12488683 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
12488629 TGGTTTAGAT
12488639 TTAGGATTTAAAGTTTAAGGC
1 TTAGGATTTAAAGTTTAAGGC
** *
12488660 TTAGG-TTTAGGGTTTAAGGT
1 TTAGGATTTAAAGTTTAAGGC
12488680 TTAG
1 TTAG
12488684 TGCTTAAGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.42
Consensus pattern (21 bp):
TTAGGATTTAAAGTTTAAGGC
Found at i:12488668 original size:27 final size:27
Alignment explanation
Indices: 12488633--12488695 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
12488623 AGGGTTTGGT
*
12488633 TTAGATTTAGGATTTAAAGTTTAAG-GC
1 TTAGGTTTAGGATTTAAAGTTT-AGTGC
* *
12488660 TTAGGTTTAGGGTTTAAGGTTTAGTGC
1 TTAGGTTTAGGATTTAAAGTTTAGTGC
12488687 TTAAGGTTT
1 TT-AGGTTT
12488696 GAAGTTTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 2 0.06
27 23 0.74
28 6 0.19
ACGTcount: A:0.25, C:0.03, G:0.27, T:0.44
Consensus pattern (27 bp):
TTAGGTTTAGGATTTAAAGTTTAGTGC
Found at i:12488722 original size:28 final size:27
Alignment explanation
Indices: 12488651--12488779 Score: 120
Period size: 28 Copynumber: 4.6 Consensus size: 27
12488641 AGGATTTAAA
* * **
12488651 GTTTAAGGCTTAGGTTTAGGGTTTAAG
1 GTTTAAGGTTTAGGTTTAAGGTTTGGG
* *
12488678 GTTT-AGTGCTTAAGGTTTGAA-GTTTAGG
1 GTTTAAG-G-TTTAGGTTT-AAGGTTTGGG
12488706 GTTTAAGGTTTATGGTTTAAGGTTTGGG
1 GTTTAAGGTTTA-GGTTTAAGGTTTGGG
12488734 GTTTAAGGTTTAGAGTTTAAGGTTTGGG
1 GTTTAAGGTTTAG-GTTTAAGGTTTGGG
12488762 GTTT-AGTGTTTAGTGTTT
1 GTTTAAG-GTTTAG-GTTT
12488780 CATGGGATTT
Statistics
Matches: 87, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
26 2 0.02
27 13 0.15
28 69 0.79
29 3 0.03
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.46
Consensus pattern (27 bp):
GTTTAAGGTTTAGGTTTAAGGTTTGGG
Found at i:12491516 original size:32 final size:31
Alignment explanation
Indices: 12491367--12491516 Score: 122
Period size: 32 Copynumber: 4.7 Consensus size: 31
12491357 GTCAGTTAGG
* *
12491367 CTGGGCTTAATTCTCCTTGGCGCCAGCTAAT
1 CTGGGTTTAATTCTCCTTGGTGCCAGCTAAT
* * * * * *
12491398 TTGGGCTTAATTCCTCCTTGGTACTAGTTATT
1 CTGGGTTTAATT-CTCCTTGGTGCCAGCTAAT
** *
12491430 CTGGGTTTAATTCTCCTTAATACCAGCTAGAT
1 CTGGGTTTAATTCTCCTTGGTGCCAGCTA-AT
* * * *
12491462 -TGGGTTTAAATTTTCATAGGTGCCAACTAAT
1 CTGGGTTT-AATTCTCCTTGGTGCCAGCTAAT
12491493 CTGGGTTTAATTCTCCTTTGGTGC
1 CTGGGTTTAATTCTCC-TTGGTGC
12491517 ATGGCAAACT
Statistics
Matches: 91, Mismatches: 23, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
31 39 0.43
32 52 0.57
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.40
Consensus pattern (31 bp):
CTGGGTTTAATTCTCCTTGGTGCCAGCTAAT
Found at i:12491821 original size:8 final size:8
Alignment explanation
Indices: 12491808--12491855 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
12491798 GGCATTCTCC
12491808 TTTTTTCT
1 TTTTTTCT
12491816 TTTTTTCT
1 TTTTTTCT
12491824 TCTTTCTTCT
1 T-TTT-TTCT
** *
12491834 TTCATACT
1 TTTTTTCT
12491842 TTTTTTCT
1 TTTTTTCT
12491850 TTTTTT
1 TTTTTT
12491856 TCTTCTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
8 23 0.72
9 4 0.12
10 5 0.16
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCT
Found at i:12491855 original size:43 final size:43
Alignment explanation
Indices: 12491808--12491905 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
12491798 GGCATTCTCC
* *
12491808 TTTTTTCTTTTTTTCTTCT-TTCTTCTT-TCATACTTTTTTTCTT
1 TTTTTTCTTTTTTTATT-TATTATTCTTCTCA-ACTTTTTTTCTT
* *
12491851 TTTTTTCTTCTTTTATTTATTATTCTTCTCAATTTTTTTTCTT
1 TTTTTTCTTTTTTTATTTATTATTCTTCTCAACTTTTTTTCTT
*
12491894 TTCTATTCTTTT
1 TT-TTTTCTTTT
12491906 CATTTTTTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
42 1 0.02
43 35 0.76
44 10 0.22
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (43 bp):
TTTTTTCTTTTTTTATTTATTATTCTTCTCAACTTTTTTTCTT
Found at i:12493817 original size:30 final size:29
Alignment explanation
Indices: 12493772--12493846 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
12493762 CAAGCATTAA
* *
12493772 TTTC-TTTTCTTTTTTTCCTTT-TTTTAT
1 TTTCTTTTTATTTTTTTCCTTTCTTTCAT
12493799 TATTCTTTATTATTTTTTTCCTTTCTTTCAT
1 T-TTCTTT-TTATTTTTTTCCTTTCTTTCAT
*
12493830 TTTCTTTTTTTTTTTTT
1 TTTCTTTTTATTTTTTT
12493847 ATTTTCTTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.02
28 3 0.07
29 11 0.27
30 20 0.49
31 6 0.15
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (29 bp):
TTTCTTTTTATTTTTTTCCTTTCTTTCAT
Found at i:12495094 original size:13 final size:14
Alignment explanation
Indices: 12495071--12495099 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12495061 CGAAAGAAAA
12495071 TTTTCTCCTTTTTT
1 TTTTCTCCTTTTTT
12495085 TTTTCT-CTTTTTT
1 TTTTCTCCTTTTTT
12495098 TT
1 TT
12495100 CTTTTGAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTCCTTTTTT
Found at i:12495133 original size:29 final size:28
Alignment explanation
Indices: 12495083--12495138 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
12495073 TTCTCCTTTT
* * **
12495083 TTTTTTCTCTTTTTTTTCTTTTGAGGAAC
1 TTTTTGCTCTTTTCTTGATTTTG-GGAAC
12495112 TTTTTGCTCTTTTCTTGATTTTGGGAA
1 TTTTTGCTCTTTTCTTGATTTTGGGAA
12495139 TTAATTATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.11, C:0.12, G:0.14, T:0.62
Consensus pattern (28 bp):
TTTTTGCTCTTTTCTTGATTTTGGGAAC
Found at i:12498131 original size:35 final size:34
Alignment explanation
Indices: 12498075--12498190 Score: 142
Period size: 35 Copynumber: 3.3 Consensus size: 34
12498065 CATTAAGAGG
*
12498075 TGCATGAGATAGAATGCATGTACTATCTACTAAGA
1 TGCATGAGATAG-ATGAATGTACTATCTACTAAGA
* *
12498110 TGCATGAAATGAGATGAATGTACTATCTACTGAGA
1 TGCATGAGAT-AGATGAATGTACTATCTACTAAGA
* *
12498145 TGCATGAGATAGGAGTGTATGTACTATCTATTAAGA
1 TGCATGAGATA-GA-TGAATGTACTATCTACTAAGA
*
12498181 TGTATGAGAT
1 TGCATGAGAT
12498191 GTGGTGTATG
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
34 1 0.01
35 40 0.57
36 29 0.41
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.31
Consensus pattern (34 bp):
TGCATGAGATAGATGAATGTACTATCTACTAAGA
Found at i:12498212 original size:36 final size:36
Alignment explanation
Indices: 12497980--12498213 Score: 144
Period size: 36 Copynumber: 6.4 Consensus size: 36
12497970 AATGGAATAC
* * *
12497980 ATGTACTATCTATTGAGATATGCATGAGA-AAGAGTGC
1 ATGTACTATCTATT-A-AGATGCATGAGATAGGAGTGT
* * * *
12498017 ATGTACTTATCTTTTTACGATGTGCTTGAGATAGG-G-GC
1 ATGTAC-TATC-TATTAAGA--TGCATGAGATAGGAGTGT
* * *
12498055 ATGTACCA-CTCATTAAGAGGTGCATGAGATA-GAATGC
1 ATGTACTATCT-ATTAAGA--TGCATGAGATAGGAGTGT
* * *
12498092 ATGTACTATCTACTAAGATGCATGA-A-ATGAGATGA
1 ATGTACTATCTATTAAGATGCATGAGATAGGAG-TGT
* *
12498127 ATGTACTATCTACTGAGATGCATGAGATAGGAGTGT
1 ATGTACTATCTATTAAGATGCATGAGATAGGAGTGT
*
12498163 ATGTACTATCTATTAAGATGTATGAGAT-GTG-GTGT
1 ATGTACTATCTATTAAGATGCATGAGATAG-GAGTGT
*
12498198 ATGTATTATCCTATTA
1 ATGTACTAT-CTATTA
12498214 TTTCTAATTT
Statistics
Matches: 160, Mismatches: 22, Indels: 31
0.75 0.10 0.15
Matches are distributed among these distances:
33 1 0.01
34 3 0.02
35 48 0.30
36 52 0.32
37 27 0.17
38 15 0.09
39 12 0.08
40 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (36 bp):
ATGTACTATCTATTAAGATGCATGAGATAGGAGTGT
Found at i:12499176 original size:25 final size:25
Alignment explanation
Indices: 12499147--12499200 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
12499137 AATATATAAT
*
12499147 AATGACATAATTAAAATATGCATGA
1 AATGACATAATTAAAATATACATGA
*
12499172 AATGACATAATTAAAATGTACATGA
1 AATGACATAATTAAAATATACATGA
12499197 AATG
1 AATG
12499201 TAAAACACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.52, C:0.07, G:0.13, T:0.28
Consensus pattern (25 bp):
AATGACATAATTAAAATATACATGA
Found at i:12500167 original size:25 final size:24
Alignment explanation
Indices: 12500135--12500181 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
12500125 TCATGCATGA
12500135 AATGCATGA-ACATAATAACATGACG
1 AATGCATGACA-AT-ATAACATGACG
12500160 AATGCATGACAATATAACATGA
1 AATGCATGACAATATAACATGA
12500182 ATGACAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.43
25 11 0.52
26 1 0.05
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (24 bp):
AATGCATGACAATATAACATGACG
Found at i:12500181 original size:24 final size:25
Alignment explanation
Indices: 12500135--12500181 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
12500125 TCATGCATGA
12500135 AATGCATGAACATAATAACATGACG
1 AATGCATGAACATAATAACATGACG
12500160 AATGCATG-ACA-ATATAACATGA
1 AATGCATGAACATA-ATAACATGA
12500182 ATGACAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 1 0.05
24 12 0.57
25 8 0.38
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (25 bp):
AATGCATGAACATAATAACATGACG
Found at i:12500187 original size:17 final size:16
Alignment explanation
Indices: 12500160--12500211 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
12500150 TAACATGACG
*
12500160 AATGCATGACAATATA
1 AATGAATGACAATATA
*
12500176 ACATGAATGACAAAGTATG
1 A-ATGAATGAC-AA-TATA
*
12500195 AATGCATGACAATATA
1 AATGAATGACAATATA
12500211 A
1 A
12500212 TAATGAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
16 5 0.17
17 10 0.34
18 10 0.34
19 4 0.14
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (16 bp):
AATGAATGACAATATA
Found at i:12500216 original size:18 final size:18
Alignment explanation
Indices: 12500160--12500216 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
12500150 TAACATGACG
12500160 AATGCATGACAATATAA-
1 AATGCATGACAATATAAT
* *
12500177 CATGAATGACAA-AGT-AT
1 AATGCATGACAATA-TAAT
12500194 GAATGCATGACAATATAAT
1 -AATGCATGACAATATAAT
12500213 AATG
1 AATG
12500217 AATGTAATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
16 2 0.06
17 11 0.35
18 15 0.48
19 3 0.10
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.25
Consensus pattern (18 bp):
AATGCATGACAATATAAT
Found at i:12500412 original size:17 final size:17
Alignment explanation
Indices: 12500391--12500445 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
12500381 AGTTTCAAGG
12500391 GATTTGAGGTTTCAT-A
1 GATTTGAGGTTTCATGA
12500407 GAATTT-AGAGTTTCATGA
1 G-ATTTGAG-GTTTCATGA
*
12500425 GATTTGGGGTTTCATGA
1 GATTTGAGGTTTCATGA
12500442 GATT
1 GATT
12500446 ATACATGTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
16 3 0.09
17 28 0.82
18 3 0.09
ACGTcount: A:0.25, C:0.05, G:0.27, T:0.42
Consensus pattern (17 bp):
GATTTGAGGTTTCATGA
Found at i:12501755 original size:36 final size:35
Alignment explanation
Indices: 12501695--12501799 Score: 88
Period size: 36 Copynumber: 2.9 Consensus size: 35
12501685 TAATGATAAT
* *
12501695 AAATGAAATTAAAAATCTAA-AAGAATAAAACAAATA
1 AAATGAAATAAAAAAT-AAATAAGAATAAAA-AAATA
*
12501731 AAATGAAATAAAAAATAAATAAGAAATTTAGAAAAATA
1 AAATGAAATAAAAAATAAATAAG-AA--TAAAAAAATA
* *
12501769 AAAT-AAATAAAAATGTAAATAGAAAATAAAA
1 AAATGAAATAAAAA-ATAAATA-AGAATAAAA
12501800 TGAAAAAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
35 2 0.04
36 22 0.39
37 11 0.19
38 17 0.30
39 5 0.09
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (35 bp):
AAATGAAATAAAAAATAAATAAGAATAAAAAAATA
Found at i:12501764 original size:26 final size:24
Alignment explanation
Indices: 12501734--12501798 Score: 71
Period size: 26 Copynumber: 2.7 Consensus size: 24
12501724 ACAAATAAAA
*
12501734 TGAAATAAAAAATAAATAAGAAATT
1 TGAAATAAAAAATAAATAA-AAATG
12501759 TAGAAA-AATAAAATAAATAAAAATG
1 T-GAAATAA-AAAATAAATAAAAATG
*
12501784 T-AAATAGAAAATAAA
1 TGAAATAAAAAATAAA
12501799 ATGAAAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
23 11 0.31
24 1 0.03
25 8 0.23
26 15 0.43
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (24 bp):
TGAAATAAAAAATAAATAAAAATG
Found at i:12501801 original size:18 final size:19
Alignment explanation
Indices: 12501773--12501812 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
12501763 AAAATAAAAT
* *
12501773 AAATAAAAATGTAAATAGA
1 AAATAAAAATGAAAAAAGA
12501792 AAAT-AAAATGAAAAAAGA
1 AAATAAAAATGAAAAAAGA
12501810 AAA
1 AAA
12501813 CCTACGACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (19 bp):
AAATAAAAATGAAAAAAGA
Found at i:12511067 original size:9 final size:9
Alignment explanation
Indices: 12511053--12511116 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 9
12511043 AATCTAAAAG
12511053 AATAAAATA
1 AATAAAATA
12511062 AATAAAATGA
1 AATAAAAT-A
12511072 AATAGAAAATA
1 AAT--AAAATA
12511083 AATAAGAA-A
1 AATAA-AATA
* *
12511092 ATCTAGAA-A
1 A-ATAAAATA
12511101 AATAAAATA
1 AATAAAATA
12511110 AATAAAA
1 AATAAAA
12511117 ATGTAAATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
8 4 0.09
9 24 0.53
10 8 0.18
11 4 0.09
12 5 0.11
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (9 bp):
AATAAAATA
Found at i:12511093 original size:48 final size:50
Alignment explanation
Indices: 12511041--12511134 Score: 158
Period size: 48 Copynumber: 1.9 Consensus size: 50
12511031 AATGAAATTA
12511041 AAAATCTA-AAAGAATAAAATAAAT-AAAATG-AAATAGAAAATAAATAAG
1 AAAATCTAGAAA-AATAAAATAAATAAAAATGTAAATAGAAAATAAATAAG
12511089 AAAATCTAGAAAAATAAAATAAATAAAAATGTAAATAGAAAATAAA
1 AAAATCTAGAAAAATAAAATAAATAAAAATGTAAATAGAAAATAAA
12511135 ATGAAAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
48 20 0.47
49 9 0.21
50 14 0.33
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.19
Consensus pattern (50 bp):
AAAATCTAGAAAAATAAAATAAATAAAAATGTAAATAGAAAATAAATAAG
Found at i:12511320 original size:17 final size:17
Alignment explanation
Indices: 12511295--12511328 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12511285 CTGTCTCAAC
12511295 CCTTCTCTCTCTAGCTT
1 CCTTCTCTCTCTAGCTT
* *
12511312 CCTTTTCTCTCTCGCTT
1 CCTTCTCTCTCTAGCTT
12511329 TTCTCTAGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.41, G:0.06, T:0.50
Consensus pattern (17 bp):
CCTTCTCTCTCTAGCTT
Found at i:12511442 original size:13 final size:13
Alignment explanation
Indices: 12511424--12511448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12511414 TCAAACCTTC
12511424 TCAAAAAATTCAA
1 TCAAAAAATTCAA
12511437 TCAAAAAATTCA
1 TCAAAAAATTCA
12511449 TGTGTTCTTC
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:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (13 bp):
TCAAAAAATTCAA
Found at i:12514555 original size:18 final size:17
Alignment explanation
Indices: 12514500--12514555 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
12514490 ACATTTTTAA
*
12514500 TTTTAATTTGATTTAATT
1 TTTTTATTTG-TTTAATT
* *
12514518 TGTTTTATTTATTTATTT
1 T-TTTTATTTGTTTAATT
12514536 TTCTTTATTTGTTTAATT
1 TT-TTTATTTGTTTAATT
12514554 TT
1 TT
12514556 ACTTATTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 1 0.03
18 23 0.74
19 7 0.23
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (17 bp):
TTTTTATTTGTTTAATT
Found at i:12514561 original size:18 final size:18
Alignment explanation
Indices: 12514521--12514564 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
12514511 TTTAATTTGT
*
12514521 TTTATTTATTTATTTTTC
1 TTTATTTATTTATTTTAC
*
12514539 TTTATTTGTTTAATTTTAC
1 TTTATTTATTT-ATTTTAC
12514558 -TTATTTA
1 TTTATTTA
12514565 AAAAAAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTATTTATTTATTTTAC
Found at i:12515555 original size:11 final size:11
Alignment explanation
Indices: 12515541--12515597 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
12515531 TTTTTTTTCC
12515541 ATTTTATTTTT
1 ATTTTATTTTT
*
12515552 ATTTTTTATTTTG
1 A--TTTTATTTTT
12515565 ATTTTATTTTTCCT
1 ATTTTA-TTTT--T
*
12515579 ATTTTATTTTC
1 ATTTTATTTTT
12515590 ATTTTATT
1 ATTTTATT
12515598 ATATATATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
11 14 0.37
12 4 0.11
13 14 0.37
14 6 0.16
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:12515563 original size:25 final size:25
Alignment explanation
Indices: 12515529--12515597 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
12515519 TGATCGCAGG
12515529 TTTTTT-TTTTCCATTTTATTTTT-A
1 TTTTTTATTTT-CATTTTATTTTTCA
* *
12515553 TTTTTTATTTTGATTTTATTTTTCC
1 TTTTTTATTTTCATTTTATTTTTCA
*
12515578 TATTTTATTTTCATTTTATT
1 TTTTTTATTTTCATTTTATT
12515598 ATATATATCT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
24 17 0.44
25 22 0.56
ACGTcount: A:0.14, C:0.07, G:0.01, T:0.77
Consensus pattern (25 bp):
TTTTTTATTTTCATTTTATTTTTCA
Found at i:12521668 original size:17 final size:19
Alignment explanation
Indices: 12521648--12521686 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
12521638 TTATAAAAAT
*
12521648 AAATTTTAAATA-AT-TAA
1 AAATATTAAATATATATAA
12521665 AAATATTAAATATATATAA
1 AAATATTAAATATATATAA
12521684 AAA
1 AAA
12521687 AGTAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 2 0.11
19 6 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATATTAAATATATATAA
Found at i:12521693 original size:24 final size:22
Alignment explanation
Indices: 12521666--12521710 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
12521656 AATAATTAAA
*
12521666 AATATTAAATATATATAAAAAAGT
1 AATAATAAA-ATAT-TAAAAAAGT
*
12521690 AATAATAAAATATTAGAAAAG
1 AATAATAAAATATTAAAAAAG
12521711 ACTAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 4 0.21
24 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (22 bp):
AATAATAAAATATTAAAAAAGT
Found at i:12521725 original size:25 final size:26
Alignment explanation
Indices: 12521662--12521728 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
12521652 TTTAAATAAT
* *
12521662 TAAAAATATTAAATATATATAAAAAAG
1 TAAAAA-ATTAAATATATAGAAAAAAC
* * *
12521689 T-AATAATAAAATAT-TAGAAAAGAC
1 TAAAAAATTAAATATATAGAAAAAAC
12521713 TAAAAAATTAAATATA
1 TAAAAAATTAAATATA
12521729 AATACAAATA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
24 8 0.26
25 19 0.61
26 3 0.10
27 1 0.03
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (26 bp):
TAAAAAATTAAATATATAGAAAAAAC
Found at i:12523360 original size:20 final size:20
Alignment explanation
Indices: 12523322--12523361 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12523312 TTAAGTAGCC
*
12523322 TTTTTTATTATTACCATTAT
1 TTTTTTATTATTACAATTAT
*
12523342 TTTTTTATTATTATAATTAT
1 TTTTTTATTATTACAATTAT
12523362 GCTTATTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTTATTATTACAATTAT
Found at i:12523664 original size:21 final size:21
Alignment explanation
Indices: 12523638--12523680 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
12523628 AGAATTATTA
12523638 AATAATAAAATTTAAATAAAT
1 AATAATAAAATTTAAATAAAT
*
12523659 AATAATAAAATTTTAATAAAT
1 AATAATAAAATTTAAATAAAT
12523680 A
1 A
12523681 GAAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAATAAAATTTAAATAAAT
Found at i:12523800 original size:13 final size:12
Alignment explanation
Indices: 12523782--12523884 Score: 80
Period size: 13 Copynumber: 8.0 Consensus size: 12
12523772 AAATCCAAGG
12523782 TGAAACCCTAAGA
1 TGAAACCCTAA-A
12523795 TGAAACCCTAAA
1 TGAAACCCTAAA
*
12523807 GTAAAACCCTAAA
1 -TGAAACCCTAAA
** *
12523820 ACAAACCTTAAAA
1 TGAAACCCT-AAA
*
12523833 TAAAACCCTATAA
1 TGAAACCCTA-AA
*
12523846 TGAAATCCTTAAA
1 TGAAA-CCCTAAA
*
12523859 CTAAAACCCTAGAA
1 -TGAAACCCTA-AA
12523873 TGAAACCCTAAA
1 TGAAACCCTAAA
12523885 CCTAAGTGAA
Statistics
Matches: 72, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
12 10 0.14
13 52 0.72
14 10 0.14
ACGTcount: A:0.51, C:0.23, G:0.07, T:0.18
Consensus pattern (12 bp):
TGAAACCCTAAA
Found at i:12523831 original size:25 final size:26
Alignment explanation
Indices: 12523797--12523869 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 26
12523787 CCCTAAGATG
* *
12523797 AAACCCTAAAGTAAAACCCTA-AAAC
1 AAACCTTAAAATAAAACCCTATAAAC
**
12523822 AAACCTTAAAATAAAACCCTATAATG
1 AAACCTTAAAATAAAACCCTATAAAC
*
12523848 AAATCCTTAAACTAAAACCCTA
1 AAA-CCTTAAAATAAAACCCTA
12523870 GAATGAAACC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
25 19 0.46
26 5 0.12
27 17 0.41
ACGTcount: A:0.53, C:0.25, G:0.03, T:0.19
Consensus pattern (26 bp):
AAACCTTAAAATAAAACCCTATAAAC
Found at i:12523888 original size:19 final size:19
Alignment explanation
Indices: 12523862--12523954 Score: 109
Period size: 19 Copynumber: 4.9 Consensus size: 19
12523852 CCTTAAACTA
*
12523862 AAACCCTAGAATGAAACCCT
1 AAACCCTA-AGTGAAACCCT
*
12523882 AAA-CCTAAGTG-AACCCA
1 AAACCCTAAGTGAAACCCT
* *
12523899 AAACCATAAGTAAAACCCT
1 AAACCCTAAGTGAAACCCT
* *
12523918 AAACCCTAGGTGAAATCCT
1 AAACCCTAAGTGAAACCCT
12523937 AAACCCTAAGTGAAACCC
1 AAACCCTAAGTGAAACCC
12523955 CGAAGCCTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.13
18 9 0.15
19 40 0.67
20 3 0.05
ACGTcount: A:0.45, C:0.29, G:0.11, T:0.15
Consensus pattern (19 bp):
AAACCCTAAGTGAAACCCT
Found at i:12523889 original size:27 final size:25
Alignment explanation
Indices: 12523784--12523885 Score: 114
Period size: 27 Copynumber: 3.9 Consensus size: 25
12523774 ATCCAAGGTG
*
12523784 AAACCCTAAGATGAAACCCTAAAGTA
1 AAACCCTAA-ATGAAACCCTAAACTA
** * *
12523810 AAACCCTAAAACAAACCTTAAAATA
1 AAACCCTAAATGAAACCCTAAACTA
*
12523835 AAACCCTATAATGAAATCCTTAAACTA
1 AAACCCTA-AATGAAA-CCCTAAACTA
12523862 AAACCCTAGAATGAAACCCTAAAC
1 AAACCCTA-AATGAAACCCTAAAC
12523886 CTAAGTGAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
25 20 0.31
26 21 0.32
27 24 0.37
ACGTcount: A:0.52, C:0.25, G:0.06, T:0.18
Consensus pattern (25 bp):
AAACCCTAAATGAAACCCTAAACTA
Found at i:12523980 original size:39 final size:38
Alignment explanation
Indices: 12523875--12523980 Score: 99
Period size: 39 Copynumber: 2.8 Consensus size: 38
12523865 CCCTAGAATG
* * *
12523875 AAACCCTAAA-CCTAAGTG-AACCCAAAACCATAAGTA
1 AAACCCGAAACCCTAGGTGAAATCCAAAACCATAAGTA
* * *
12523911 AAACCCTAAACCCTAGGTGAAATCCTAAACCCTAAGTGA
1 AAACCCGAAACCCTAGGTGAAATCCAAAACCATAAGT-A
* * * *
12523950 AACCCCGAAGCCTTAGGTGAAGTCCAAAACC
1 AAACCCGAAACCCTAGGTGAAATCCAAAACC
12523981 TTAATCCACT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
36 10 0.18
37 7 0.12
38 14 0.25
39 26 0.46
ACGTcount: A:0.42, C:0.29, G:0.13, T:0.15
Consensus pattern (38 bp):
AAACCCGAAACCCTAGGTGAAATCCAAAACCATAAGTA
Found at i:12525955 original size:17 final size:17
Alignment explanation
Indices: 12525935--12525969 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12525925 AAAAAGTATT
12525935 AGGTGATTAAAAATGTA
1 AGGTGATTAAAAATGTA
12525952 AGGTGATTAAAAATGTA
1 AGGTGATTAAAAATGTA
12525969 A
1 A
12525970 AAATATTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.29
Consensus pattern (17 bp):
AGGTGATTAAAAATGTA
Found at i:12527298 original size:24 final size:24
Alignment explanation
Indices: 12527253--12527298 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
12527243 TTTTTAAATT
*
12527253 AATAAATTCAATTTAATTAATTAA
1 AATAAATTCAATTTAATGAATTAA
*
12527277 AATAAATAT-AATTTGATGAATT
1 AATAAAT-TCAATTTAATGAATT
12527299 CTATTCTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
AATAAATTCAATTTAATGAATTAA
Found at i:12530126 original size:3 final size:3
Alignment explanation
Indices: 12530118--12530167 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
12530108 AGTTGAGACT
12530118 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12530166 TT
1 TT
12530168 GAGGTTTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12540145 original size:17 final size:18
Alignment explanation
Indices: 12540123--12540170 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
12540113 TAAAAATAGC
12540123 AAAATATAAAATAAATA-
1 AAAATATAAAATAAATAT
* *
12540140 AAAATATTACATAAATATT
1 AAAATATAAAATAAATA-T
12540159 AAAAT-TAAAATA
1 AAAATATAAAATA
12540171 TAAATAGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 15 0.60
18 5 0.20
19 5 0.20
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATATAAAATAAATAT
Found at i:12540411 original size:14 final size:13
Alignment explanation
Indices: 12540390--12540423 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
12540380 ATATTTATCA
12540390 TTATTATTATATT
1 TTATTATTATATT
*
12540403 TTCATTATTTTATT
1 TT-ATTATTATATT
12540417 TTATTAT
1 TTATTAT
12540424 AGATAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTATTATATT
Found at i:12540693 original size:6 final size:6
Alignment explanation
Indices: 12540622--12540736 Score: 67
Period size: 6 Copynumber: 19.3 Consensus size: 6
12540612 AGTATTTTTT
* * * * * *
12540622 ATAAAA ACATAA AT-AAA ATAAAA CTAAAA CTAAAA CTAAAA AGAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
* * * *
12540669 A-CAAA AT-GAA ATAAGAA ATGAAA ATAAAA ATAACA ATAAAA ATACCAAA
1 ATAAAA ATAAAA ATAA-AA ATAAAA ATAAAA ATAAAA ATAAAA ATA--AAA
* *
12540718 AAAAAA ACAAAA A-AAAA AT
1 ATAAAA ATAAAA ATAAAA AT
12540737 TAATTATCAA
Statistics
Matches: 86, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
5 17 0.20
6 59 0.69
7 5 0.06
8 5 0.06
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.13
Consensus pattern (6 bp):
ATAAAA
Found at i:12541741 original size:22 final size:22
Alignment explanation
Indices: 12541713--12541761 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
12541703 CCATTTTATT
12541713 AATAAACAAAACAAAA-AAACAA
1 AATAAAC-AAACAAAAGAAACAA
*
12541735 AATAAACAAACAAAAGAAACAG
1 AATAAACAAACAAAAGAAACAA
12541757 AATAA
1 AATAA
12541762 GATAGAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.78, C:0.12, G:0.04, T:0.06
Consensus pattern (22 bp):
AATAAACAAACAAAAGAAACAA
Found at i:12541754 original size:13 final size:13
Alignment explanation
Indices: 12541716--12541755 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
12541706 TTTTATTAAT
*
12541716 AAACAAAACAAAA
1 AAACAAAACAAAC
*
12541729 AAACAAAATAAAC
1 AAACAAAACAAAC
*
12541742 AAACAAAAGAAAC
1 AAACAAAACAAAC
12541755 A
1 A
12541756 GAATAAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.80, C:0.15, G:0.03, T:0.03
Consensus pattern (13 bp):
AAACAAAACAAAC
Found at i:12541835 original size:12 final size:12
Alignment explanation
Indices: 12541798--12541848 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
12541788 GCCGCTGTCG
12541798 CCAG-CCCCCGA
1 CCAGCCCCCCGA
* ** *
12541809 CCAACTACCCTA
1 CCAGCCCCCCGA
12541821 CCAGCCCCCCGA
1 CCAGCCCCCCGA
*
12541833 CCAGCCTCCCGA
1 CCAGCCCCCCGA
12541845 CCAG
1 CCAG
12541849 TCACCCTACA
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
11 3 0.10
12 27 0.90
ACGTcount: A:0.22, C:0.59, G:0.14, T:0.06
Consensus pattern (12 bp):
CCAGCCCCCCGA
Found at i:12541847 original size:24 final size:23
Alignment explanation
Indices: 12541798--12541848 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
12541788 GCCGCTGTCG
*
12541798 CCAGCCCCCGACCAACTACCCTA
1 CCAGCCCCCGACCAACTACCCGA
*
12541821 CCAGCCCCCCGACCAGCCT-CCCGA
1 CCAG-CCCCCGACCA-ACTACCCGA
12541845 CCAG
1 CCAG
12541849 TCACCCTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 18 0.75
25 2 0.08
ACGTcount: A:0.22, C:0.59, G:0.14, T:0.06
Consensus pattern (23 bp):
CCAGCCCCCGACCAACTACCCGA
Found at i:12542678 original size:14 final size:15
Alignment explanation
Indices: 12542654--12542710 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 15
12542644 TCTGACTGAA
12542654 CCAGAACCGAACCGC
1 CCAGAACCGAACCGC
*
12542669 CCAG-ACCGAACCGAA
1 CCAGAACCGAACCG-C
* *
12542684 ACGGAACCGAACCGC
1 CCAGAACCGAACCGC
12542699 CCAG-ACCGAACC
1 CCAGAACCGAACC
12542711 AAACCGGTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 17 0.50
15 8 0.24
16 9 0.26
ACGTcount: A:0.35, C:0.44, G:0.21, T:0.00
Consensus pattern (15 bp):
CCAGAACCGAACCGC
Found at i:12542693 original size:30 final size:30
Alignment explanation
Indices: 12542652--12542739 Score: 115
Period size: 30 Copynumber: 2.9 Consensus size: 30
12542642 GGTCTGACTG
*
12542652 AACCAGAACCGAACCGCCCAGACCGAACCGA
1 AACCGGAACCGAACCGCCCAGACCGAACC-A
12542683 AA-CGGAACCGAACCGCCCAGACCGAACCA
1 AACCGGAACCGAACCGCCCAGACCGAACCA
* * * *
12542712 AACCGGTACTGGACCGTCCAGACCGAAC
1 AACCGGAACCGAACCGCCCAGACCGAAC
12542740 GAACCGTCGA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
29 3 0.06
30 46 0.90
31 2 0.04
ACGTcount: A:0.35, C:0.40, G:0.22, T:0.03
Consensus pattern (30 bp):
AACCGGAACCGAACCGCCCAGACCGAACCA
Found at i:12543672 original size:193 final size:192
Alignment explanation
Indices: 12543426--12543807 Score: 669
Period size: 193 Copynumber: 2.0 Consensus size: 192
12543416 GCATGGCATG
* * *
12543426 CATGACATAATTTCTTACGAAAAGTAAGTTTAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
1 CATGACAT-ATTTCTTACGAAAAATAAATTGAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
12543491 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAATTCTTTTAATGTTACCAACGTACTGGA
65 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAATTCTTTTAATGTTACCAACGTACTGGA
12543556 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTTAA
130 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTA-TTTTCTCGAGAAT-AATTTTTTTAA
12543621 CATGACAT-TTTCTTACGAAAAATAAATTCGAG-CCTCCAAAGATGAGATTCTAAAAGTATTCCG
1 CATGACATATTTCTTACGAAAAATAAATT-GAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
*
12543684 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGGA
65 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAATTCTTTTAATGTTACCAACGTACTGGA
*
12543749 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTGATTTATTTTCTCGAGAATAATTTTT
130 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTCTCGAGAATAATTTTT
12543808 AATAAATAAA
Statistics
Matches: 181, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
191 7 0.04
192 13 0.07
193 151 0.83
194 2 0.01
195 8 0.04
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (192 bp):
CATGACATATTTCTTACGAAAAATAAATTGAGACCTCCAAAGATGAGATTCTAAAAGTATTCCGA
GTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAATTCTTTTAATGTTACCAACGTACTGGAA
CATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTCTCGAGAATAATTTTTTTAA
Found at i:12553213 original size:26 final size:26
Alignment explanation
Indices: 12553183--12553235 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
12553173 GTTGACTTAG
*
12553183 GCATACGGAGTTCATTCCCAGTCTAA
1 GCATACGGAGTTCATTCCCAGTATAA
12553209 GCATACGGAGTTCATTCCCAGTATAA
1 GCATACGGAGTTCATTCCCAGTATAA
12553235 G
1 G
12553236 ACCAGATCGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (26 bp):
GCATACGGAGTTCATTCCCAGTATAA
Found at i:12558263 original size:48 final size:49
Alignment explanation
Indices: 12558199--12558575 Score: 577
Period size: 48 Copynumber: 7.8 Consensus size: 49
12558189 AAATTTGAAA
*
12558199 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTC
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTC
* * *
12558248 AAGAAGA-AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCC
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTC
* *
12558296 AAGATGAG-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCC
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTC
12558344 AAGATGAGAATTTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGC-TTTTC
1 AAGATGAGAA-TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTC
*
12558393 AAGATGAGATTTTTAAAGTTGTGGA-CCTCTGCTGAGAGGAGC-TTTTC
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTC
*
12558440 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTG-TGAGAGGAGCTTTTCC
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTC
* * *
12558488 AAGATGAGAATTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTTTC
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTC
* * *
12558537 AAGATGAGAATTTTAAAGTTGTTGAGCTTTTGCTGAGAG
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGCTGAGAG
12558576 CAGAGGAGCT
Statistics
Matches: 304, Mismatches: 18, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
47 56 0.18
48 147 0.48
49 69 0.23
50 32 0.11
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (49 bp):
AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTC
Found at i:12558529 original size:193 final size:193
Alignment explanation
Indices: 12558199--12558575 Score: 616
Period size: 193 Copynumber: 2.0 Consensus size: 193
12558189 AAATTTGAAA
*
12558199 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAGAAATTTTAAA
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAAGAAATTTTAAA
* *
12558264 GTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGATTTTAAAGTTGTTGAGCCTCTGCT
66 GTTGTGGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGATTTTAAAGTTGTTGAGCCTCTACT
12558329 GAGAGGAGCTTTTCCAAGATGAGAATTTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTC
131 GAGAGGAGCTTTTCCAAGATGAGAA-TTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTC
* *
12558393 AAGATGAGATTTTTAAAGTTGTGGA-CCTCTGCTGAGAGGAGC-TTTTCAAGATGAGAATTTTAA
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAAGA-AATTTTAA
12558456 AGTTGTGGAGCCTCTG-TGAGAGGAGCTTTTCCAAGATGAGAATTTTAAAGTTGTTGAGCCTCTA
65 AGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAG-ATTTTAAAGTTGTTGAGCCTCTA
* * * * *
12558520 CTTAGAGGAGCTTTTTCAAGATGAGAATTTTAAAGTTGTTGAGCTTTTGCTGAGAG
129 CTGAGAGGAGCTTTTCCAAGATGAGAATTTTAAAGTTGTGGAGCCTCTGCTGAGAG
12558576 CAGAGGAGCT
Statistics
Matches: 171, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
192 61 0.36
193 86 0.50
194 24 0.14
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (193 bp):
AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAAGAAATTTTAAA
GTTGTGGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGATTTTAAAGTTGTTGAGCCTCTACT
GAGAGGAGCTTTTCCAAGATGAGAATTTTAAAGTTGTGGAGCCTCTGCTGAGAGGAGCTTTTC
Found at i:12558768 original size:22 final size:22
Alignment explanation
Indices: 12558740--12558788 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
12558730 CCATTTTATT
12558740 AATAAACAAAACAAAA-AAACAA
1 AATAAAC-AAACAAAAGAAACAA
*
12558762 AATAAACAAACAAAAGAAACAG
1 AATAAACAAACAAAAGAAACAA
12558784 AATAA
1 AATAA
12558789 GATAGAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.78, C:0.12, G:0.04, T:0.06
Consensus pattern (22 bp):
AATAAACAAACAAAAGAAACAA
Found at i:12558781 original size:13 final size:13
Alignment explanation
Indices: 12558743--12558782 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
12558733 TTTTATTAAT
*
12558743 AAACAAAACAAAA
1 AAACAAAACAAAC
*
12558756 AAACAAAATAAAC
1 AAACAAAACAAAC
*
12558769 AAACAAAAGAAAC
1 AAACAAAACAAAC
12558782 A
1 A
12558783 GAATAAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.80, C:0.15, G:0.03, T:0.03
Consensus pattern (13 bp):
AAACAAAACAAAC
Found at i:12558862 original size:12 final size:12
Alignment explanation
Indices: 12558825--12558875 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
12558815 GCCGCTGTCG
12558825 CCAG-CCCCCGA
1 CCAGCCCCCCGA
* ** *
12558836 CCAACTACCCTA
1 CCAGCCCCCCGA
12558848 CCAGCCCCCCGA
1 CCAGCCCCCCGA
*
12558860 CCAGCCTCCCGA
1 CCAGCCCCCCGA
12558872 CCAG
1 CCAG
12558876 TCACCCTACA
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
11 3 0.10
12 27 0.90
ACGTcount: A:0.22, C:0.59, G:0.14, T:0.06
Consensus pattern (12 bp):
CCAGCCCCCCGA
Found at i:12558874 original size:24 final size:23
Alignment explanation
Indices: 12558825--12558875 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
12558815 GCCGCTGTCG
*
12558825 CCAGCCCCCGACCAACTACCCTA
1 CCAGCCCCCGACCAACTACCCGA
*
12558848 CCAGCCCCCCGACCAGCCT-CCCGA
1 CCAG-CCCCCGACCA-ACTACCCGA
12558872 CCAG
1 CCAG
12558876 TCACCCTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 18 0.75
25 2 0.08
ACGTcount: A:0.22, C:0.59, G:0.14, T:0.06
Consensus pattern (23 bp):
CCAGCCCCCGACCAACTACCCGA
Found at i:12559690 original size:5 final size:5
Alignment explanation
Indices: 12559674--12559739 Score: 50
Period size: 5 Copynumber: 13.2 Consensus size: 5
12559664 CGGTCTGACT
*
12559674 GAACC AGAACC GAACC G-CCC AGAA-C GAACC GAACC GGAACC GAACC
1 GAACC -GAACC GAACC GAACC -GAACC GAACC GAACC -GAACC GAACC
*
12559720 G--CC CAGACC GAACC GAACC G
1 GAACC GA-ACC GAACC GAACC G
12559740 GTACTGGACC
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
3 2 0.04
4 5 0.10
5 29 0.59
6 13 0.27
ACGTcount: A:0.36, C:0.41, G:0.23, T:0.00
Consensus pattern (5 bp):
GAACC
Found at i:12559714 original size:30 final size:30
Alignment explanation
Indices: 12559674--12559768 Score: 129
Period size: 30 Copynumber: 3.2 Consensus size: 30
12559664 CGGTCTGACT
* *
12559674 GAACCAGAACCGAACCGCCCAGAACGAACC
1 GAACCGGAACCGAACCGCCCAGACCGAACC
12559704 GAACCGGAACCGAACCGCCCAGACCGAACC
1 GAACCGGAACCGAACCGCCCAGACCGAACC
* * * *
12559734 GAACCGGTACTGGACCGTCCAGACCGAA-C
1 GAACCGGAACCGAACCGCCCAGACCGAACC
12559763 GAACCG
1 GAACCG
12559769 TCGAACCAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 7 0.12
30 52 0.88
ACGTcount: A:0.34, C:0.39, G:0.24, T:0.03
Consensus pattern (30 bp):
GAACCGGAACCGAACCGCCCAGACCGAACC
Found at i:12559878 original size:18 final size:18
Alignment explanation
Indices: 12559855--12559891 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12559845 TTATTTTATT
*
12559855 AATATTTATGTATGTTAA
1 AATATTTATATATGTTAA
*
12559873 AATATTTATATTTGTTAA
1 AATATTTATATATGTTAA
12559891 A
1 A
12559892 CTAATTGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (18 bp):
AATATTTATATATGTTAA
Found at i:12560696 original size:193 final size:192
Alignment explanation
Indices: 12560450--12560831 Score: 669
Period size: 193 Copynumber: 2.0 Consensus size: 192
12560440 GCATGGCATG
* * *
12560450 CATGACATAATTTCTTACGAAAAGTAAGTTTAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
1 CATGACAT-ATTTCTTACGAAAAATAAATTGAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
12560515 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAATTCTTTTAATGTTACCAACGTACTGGA
65 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAATTCTTTTAATGTTACCAACGTACTGGA
12560580 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTTAA
130 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTA-TTTTCTCGAGAAT-AATTTTTTTAA
12560645 CATGACAT-TTTCTTACGAAAAATAAATTCGAG-CCTCCAAAGATGAGATTCTAAAAGTATTCCG
1 CATGACATATTTCTTACGAAAAATAAATT-GAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
*
12560708 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGGA
65 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAATTCTTTTAATGTTACCAACGTACTGGA
*
12560773 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTGATTTATTTTCTCGAGAATAATTTTT
130 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTCTCGAGAATAATTTTT
12560832 AATAAATAAA
Statistics
Matches: 181, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
191 7 0.04
192 13 0.07
193 151 0.83
194 2 0.01
195 8 0.04
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (192 bp):
CATGACATATTTCTTACGAAAAATAAATTGAGACCTCCAAAGATGAGATTCTAAAAGTATTCCGA
GTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAATTCTTTTAATGTTACCAACGTACTGGAA
CATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTCTCGAGAATAATTTTTTTAA
Found at i:12565116 original size:34 final size:34
Alignment explanation
Indices: 12565078--12565154 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
12565068 CGTCTCAAAT
* *
12565078 ATACAAACGCCTTTAAAATAGT-AGCATTTTCTAA
1 ATACAAACGCCGTTAAAATAATGA-CATTTTCTAA
* *
12565112 ATACAAACGCCGTTAATATAATGACATTTTCTAG
1 ATACAAACGCCGTTAAAATAATGACATTTTCTAA
*
12565146 ATATAAACG
1 ATACAAACG
12565155 TCGCTAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 36 0.97
35 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (34 bp):
ATACAAACGCCGTTAAAATAATGACATTTTCTAA
Found at i:12565211 original size:34 final size:34
Alignment explanation
Indices: 12565102--12565210 Score: 103
Period size: 34 Copynumber: 3.2 Consensus size: 34
12565092 AAAATAGTAG
* * * *
12565102 CATTTTCTAAATACAAACGCCGTTAATATAATGA
1 CATTTTCTAAATTCAAACGTCGCTAATATAACGA
* *
12565136 CATTTTCTAGATAT-AAACGTCGCTAATATTAACGG
1 CATTTTCTAAAT-TCAAACGTCGCTAATA-TAACGA
** * *
12565171 TGTTTTTTAAATTCAAATGTCGCTAATATAACGA
1 CATTTTCTAAATTCAAACGTCGCTAATATAACGA
12565205 CATTTT
1 CATTTT
12565211 TCACATACAA
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
34 33 0.57
35 25 0.43
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (34 bp):
CATTTTCTAAATTCAAACGTCGCTAATATAACGA
Found at i:12575802 original size:20 final size:21
Alignment explanation
Indices: 12575764--12575816 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
12575754 TTTAAAACAT
* *
12575764 ATAAAATAGTA-TTACTATTT
1 ATAAAATATTATTTACTATTA
*
12575784 TTAAAATATTATTTA-TATTA
1 ATAAAATATTATTTACTATTA
*
12575804 ATATAATATTATT
1 ATAAAATATTATT
12575817 AAAAATATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
ATAAAATATTATTTACTATTA
Done.