Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005225.1 Hibiscus syriacus cultivar Beakdansim tig00011831_pilon, 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: 75367
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5177 original size:33 final size:33
Alignment explanation
Indices: 5132--5221 Score: 98
Period size: 29 Copynumber: 2.8 Consensus size: 33
5122 GATAGTTCAA
* *
5132 GTATTATTTTAGATATTTTATCAAAGTATACAT
1 GTATTATATTAGACATTTTATCAAAGTATACAT
* * *
5165 GTATTGTATTAGACATCTTA--AAAG--TGCAT
1 GTATTATATTAGACATTTTATCAAAGTATACAT
*
5194 GTATTATATTAAACATTTTATCAAAGTA
1 GTATTATATTAGACATTTTATCAAAGTA
5222 CATGCATCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
29 21 0.47
31 8 0.18
33 16 0.36
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (33 bp):
GTATTATATTAGACATTTTATCAAAGTATACAT
Found at i:5234 original size:31 final size:31
Alignment explanation
Indices: 5132--5234 Score: 93
Period size: 29 Copynumber: 3.3 Consensus size: 31
5122 GATAGTTCAA
* * *
5132 GTATTATTTTAGATATTTTATCAAAGTATACAT
1 GTATTATATTAAACATTTTATCAAAG--TACAT
* * * *
5165 GTATTGTATTAGACATCTTA--AAAGTGCAT
1 GTATTATATTAAACATTTTATCAAAGTACAT
5194 GTATTATATTAAACATTTTATCAAAGTACAT
1 GTATTATATTAAACATTTTATCAAAGTACAT
* *
5225 GCATCATATT
1 GTATTATATT
5235 GAATATTCTG
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 21 0.37
31 20 0.35
33 16 0.28
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.43
Consensus pattern (31 bp):
GTATTATATTAAACATTTTATCAAAGTACAT
Found at i:9643 original size:34 final size:35
Alignment explanation
Indices: 9598--9665 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
9588 AATAGGAATT
* *
9598 ACAACTTCTCTC-GATCTAACAAGGAGAAAACAATA
1 ACAACTTCTCTCTGAT-AAAAAAGGAGAAAACAATA
9633 ACAA-TTCTCTCTTGATAAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAAGGAGAAAACAA
9666 CTCTCAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 7 0.24
35 19 0.66
36 3 0.10
ACGTcount: A:0.49, C:0.19, G:0.12, T:0.21
Consensus pattern (35 bp):
ACAACTTCTCTCTGATAAAAAAGGAGAAAACAATA
Found at i:15962 original size:23 final size:25
Alignment explanation
Indices: 15915--15963 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
15905 ATTTCGTTTG
*
15915 TTTCTTAATGTTTTAATTATTTAAT
1 TTTCTTAATGTTTTAAGTATTTAAT
15940 TTTCTTAATG-TTT-AGTATTTAAT
1 TTTCTTAATGTTTTAAGTATTTAAT
15963 T
1 T
15964 GTTTTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.43
24 3 0.13
25 10 0.43
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (25 bp):
TTTCTTAATGTTTTAAGTATTTAAT
Found at i:19667 original size:9 final size:9
Alignment explanation
Indices: 19645--19743 Score: 67
Period size: 9 Copynumber: 10.6 Consensus size: 9
19635 ATAAAAAAGT
*
19645 GAAAATGAA
1 GAAAATAAA
*
19654 TAAAATAAA
1 GAAAATAAA
19663 GAAAATAAA
1 GAAAATAAA
* **
19672 AATAAAGCAA
1 GA-AAATAAA
19682 -AAAATAAAA
1 GAAAAT-AAA
19691 GTAAAATAAA
1 G-AAAATAAA
19701 GAAAATAAATA
1 GAAAAT-AA-A
*
19712 AATAAATAAA
1 GA-AAATAAA
*
19722 -TAAATAAA
1 GAAAATAAA
19730 GAAAATAAA
1 GAAAATAAA
19739 GAAAA
1 GAAAA
19744 CATATATATA
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
8 10 0.14
9 36 0.51
10 12 0.17
11 9 0.13
12 4 0.06
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.15
Consensus pattern (9 bp):
GAAAATAAA
Found at i:19695 original size:24 final size:23
Alignment explanation
Indices: 19623--19738 Score: 89
Period size: 23 Copynumber: 5.1 Consensus size: 23
19613 ATACCCTTAA
** *
19623 AAAATAAAGACGATAAA-AAAGT
1 AAAATAAAGAAAATAAATAAAAT
* * *
19645 GAAAATGAATAAAATAAAGAAAAT
1 -AAAATAAAGAAAATAAATAAAAT
*
19669 AAAAATAAAGCAAA-AAATAAAAGT
1 -AAAATAAAGAAAATAAATAAAA-T
19693 AAAATAAAGAAAATAAAT-AAAT
1 AAAATAAAGAAAATAAATAAAAT
* *
19715 -AAATAAA-TAAATAAAGAAAAT
1 AAAATAAAGAAAATAAATAAAAT
19736 AAA
1 AAA
19739 GAAAACATAT
Statistics
Matches: 75, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
20 7 0.09
21 11 0.15
22 3 0.04
23 35 0.47
24 19 0.25
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.16
Consensus pattern (23 bp):
AAAATAAAGAAAATAAATAAAAT
Found at i:19696 original size:38 final size:39
Alignment explanation
Indices: 19654--19743 Score: 125
Period size: 38 Copynumber: 2.4 Consensus size: 39
19644 TGAAAATGAA
19654 TAAAATAAAGAAAAT-AA-AAATAAAGCAAA-AAATAAAAG
1 TAAAATAAAGAAAATAAATAAATAAA-CAAATAAAT-AAAG
*
19692 TAAAATAAAGAAAATAAATAAATAAATAAATAAATAAAG
1 TAAAATAAAGAAAATAAATAAATAAACAAATAAATAAAG
19731 -AAAATAAAGAAAA
1 TAAAATAAAGAAAA
19744 CATATATATA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
38 28 0.58
39 9 0.19
40 11 0.23
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.16
Consensus pattern (39 bp):
TAAAATAAAGAAAATAAATAAATAAACAAATAAATAAAG
Found at i:19712 original size:4 final size:4
Alignment explanation
Indices: 19703--19729 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
19693 AAAATAAAGA
19703 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
19730 GAAAATAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:19937 original size:2 final size:2
Alignment explanation
Indices: 19930--19955 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19920 ACGAAAACAA
19930 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
19956 TAATCAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20016 original size:14 final size:13
Alignment explanation
Indices: 19978--20017 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 13
19968 GTACTTAAAT
19978 AAAAATAAATTAAG
1 AAAAATAAA-TAAG
19992 AAAAATAAATAAGG
1 AAAAATAAATAA-G
20006 AAAAATAAATAA
1 AAAAATAAATAA
20018 TGGATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 3 0.12
14 22 0.88
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (13 bp):
AAAAATAAATAAG
Found at i:22051 original size:118 final size:120
Alignment explanation
Indices: 21842--22118 Score: 353
Period size: 118 Copynumber: 2.3 Consensus size: 120
21832 TTGAACTTTG
* * * * **
21842 AATTGGATATCATTTGTCGTGAAGTTGAAATCCAATCTAGAGTTTTATGATGCCTGTGGGCACGA
1 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATAAATGATGCCTGTGGGCACGA
* *** *
21907 TATCCTTCGTCGTGAAGTTGATATCGTGGATGGCCCCTTTGTT-T-TGAGCCTTA
66 TATCCTTCGTCGTGAAGTTGAAATCGTGGACAACCCCTTCGTTGTATGAGCCTTA
* *
21960 AATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATAAATGTTG-CTGGTGGGCACG
1 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATAAATGATGCCT-GTGGGCACG
*
22024 ATATCCTTCGTCGTGAAGTTGAAATCGTGGACAACCCCTTCGTTGTGAAGCTGAGCCTTG
65 ATATCCTTCGTCGTGAAGTTGAAATCGTGGACAACCCCTTCGTTGT--A--TGAGCCTTA
*
22084 AATTGGATATCCTTCGTTGTGAAGTTGAAATCCAA
1 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
22119 GTATTGTTTG
Statistics
Matches: 136, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
117 2 0.01
118 92 0.68
119 1 0.01
124 41 0.30
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (120 bp):
AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATAAATGATGCCTGTGGGCACGA
TATCCTTCGTCGTGAAGTTGAAATCGTGGACAACCCCTTCGTTGTATGAGCCTTA
Found at i:22997 original size:7 final size:6
Alignment explanation
Indices: 22974--23014 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
22964 TGAACCCACA
*
22974 TTCTTT TTCTTT TTCTTT TCTCTTT TTTTTT GTTCTTT TTC
1 TTCTTT TTCTTT TTCTTT T-TCTTT TTCTTT -TTCTTT TTC
23015 AATTTAGGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (6 bp):
TTCTTT
Found at i:22999 original size:13 final size:12
Alignment explanation
Indices: 22974--23014 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
22964 TGAACCCACA
22974 TTCTTTTTCTTT
1 TTCTTTTTCTTT
22986 TTCTTTTCTCTTT
1 TTCTTTT-TCTTT
*
22999 TTTTTTGTTCTTT
1 TTCTTT-TTCTTT
23012 TTC
1 TTC
23015 AATTTAGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.28
13 17 0.68
14 1 0.04
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (12 bp):
TTCTTTTTCTTT
Found at i:26149 original size:23 final size:23
Alignment explanation
Indices: 26112--26180 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
26102 CACCACAGCT
* *
26112 CGTATAAATGAACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
26135 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
26158 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
26181 TATAAAGTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:35829 original size:9 final size:9
Alignment explanation
Indices: 35807--35941 Score: 57
Period size: 9 Copynumber: 14.8 Consensus size: 9
35797 TTAAAAAAGT
*
35807 GAAAATCAA
1 GAAAATAAA
*
35816 TAAAATAAA
1 GAAAATAAA
35825 GAAAATAAA
1 GAAAATAAA
*
35834 CTAAAGA-AAA
1 -GAAA-ATAAA
*
35844 TAAAAATAAA
1 -GAAAATAAA
*
35854 GCAAA-AAA
1 GAAAATAAA
*
35862 -TAAA-AAA
1 GAAAATAAA
*
35869 GTAAAT-AA
1 GAAAATAAA
35877 GATAAATAAA
1 GA-AAATAAA
35887 GAAAATAAA
1 GAAAATAAA
*
35896 -AAAGTAAAAA
1 GAAA--ATAAA
*
35906 GAAAAAAGAA
1 GAAAATA-AA
*
35916 AATAAATAAA
1 GA-AAATAAA
35926 GAAAATAAA
1 GAAAATAAA
*
35935 GATAATA
1 GAAAATA
35942 TATATATGAT
Statistics
Matches: 99, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
7 6 0.06
8 13 0.13
9 46 0.46
10 26 0.26
11 8 0.08
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (9 bp):
GAAAATAAA
Found at i:35911 original size:44 final size:44
Alignment explanation
Indices: 35798--35925 Score: 116
Period size: 48 Copynumber: 2.8 Consensus size: 44
35788 ATAAAGACGT
* *
35798 TAAAAAAGTGAAAATCAATAAAA-TAAAGAAAATAAACTAAAGAAAA
1 TAAAAAAGT-AAAAACAA-AAAAGTAAA-TAAATAAACTAAAGAAAA
* *
35844 TAAAAATAAAGCAAAAAATAAAAAAGTAAATAAGATAAA-TAAAGAAAA
1 T--AAA-AAAG-TAAAAACAAAAAAGTAAATAA-ATAAACTAAAGAAAA
* *
35892 TAAAAAAGTAAAAAGAAAAAAGAAAATAAATAAA
1 TAAAAAAGTAAAAACAAAAAAGTAAATAAATAAA
35926 GAAAATAAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
43 5 0.07
44 18 0.26
45 4 0.06
46 4 0.06
48 19 0.28
49 19 0.28
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (44 bp):
TAAAAAAGTAAAAACAAAAAAGTAAATAAATAAACTAAAGAAAA
Found at i:35922 original size:48 final size:47
Alignment explanation
Indices: 35839--35941 Score: 115
Period size: 48 Copynumber: 2.1 Consensus size: 47
35829 ATAAACTAAA
35839 GAAAAT-AAAAATAAAGCAAAAAATAAAAAAGTAAATAAGATAAATAAA
1 GAAAATAAAAAATAAA-CAAAAAATAAAAAA-TAAATAAGATAAATAAA
35887 GAAAATAAAAAAGTAAA-AAGAAAA-AAGAAAATAAATAAAGA-AAATAAA
1 GAAAATAAAAAA-TAAACAA-AAAATAA-AAAATAAAT-AAGATAAATAAA
*
35935 GATAATA
1 GAAAATA
35942 TATATATGAT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
48 28 0.57
49 17 0.35
50 4 0.08
ACGTcount: A:0.76, C:0.01, G:0.10, T:0.14
Consensus pattern (47 bp):
GAAAATAAAAAATAAACAAAAAATAAAAAATAAATAAGATAAATAAA
Found at i:36161 original size:14 final size:14
Alignment explanation
Indices: 36139--36183 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
36129 ATATAGTACT
*
36139 TAAATAAAAATAAA
1 TAAAGAAAAATAAA
36153 TAAAGAAAAATAAA
1 TAAAGAAAAATAAA
*
36167 TAAGGAAAAATAAA
1 TAAAGAAAAATAAA
36181 TAA
1 TAA
36184 TGGTCATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.18
Consensus pattern (14 bp):
TAAAGAAAAATAAA
Found at i:36594 original size:21 final size:21
Alignment explanation
Indices: 36568--36613 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
36558 GAGTGATGAA
36568 GAACACGGTTGGGTTCTTGAT
1 GAACACGGTTGGGTTCTTGAT
36589 GAACACGGTTGGGTTCTTGAT
1 GAACACGGTTGGGTTCTTGAT
36610 GAAC
1 GAAC
36614 CCAGAAACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.15, G:0.33, T:0.30
Consensus pattern (21 bp):
GAACACGGTTGGGTTCTTGAT
Found at i:41886 original size:21 final size:21
Alignment explanation
Indices: 41858--41899 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
41848 ATAATTTCCC
41858 CTTTA-TTTTAAATAATTTAT
1 CTTTATTTTTAAATAATTTAT
*
41878 CTTTAATTTTTAACTAATTTAT
1 CTTT-ATTTTTAAATAATTTAT
41900 AATTATACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 1 0.05
22 14 0.74
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
CTTTATTTTTAAATAATTTAT
Found at i:43453 original size:21 final size:24
Alignment explanation
Indices: 43417--43476 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
43407 ATATATATAT
* *
43417 ATAATAAATATAATAACG-AAAA-A
1 ATAAT-AATGTAATAAAGTAAAATA
*
43440 A-AATAATTTAATAAAGTAAAATA
1 ATAATAATGTAATAAAGTAAAATA
43463 ATAATAATGTAATA
1 ATAATAATGTAATA
43477 TAATATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 10 0.32
22 7 0.23
23 3 0.10
24 11 0.35
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (24 bp):
ATAATAATGTAATAAAGTAAAATA
Found at i:43469 original size:16 final size:16
Alignment explanation
Indices: 43448--43485 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
43438 AAAAATAATT
43448 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
43464 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
43480 T-ATAAA
1 TAATAAA
43486 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:43683 original size:21 final size:23
Alignment explanation
Indices: 43657--43702 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
43647 TTATATACGT
43657 TAATAG-TAAAAATA-ATAAATA
1 TAATAGTTAAAAATATATAAATA
* *
43678 TAATAGTTATAAATATATATATA
1 TAATAGTTAAAAATATATAAATA
43701 TA
1 TA
43703 TATATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 7 0.33
23 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (23 bp):
TAATAGTTAAAAATATATAAATA
Found at i:43697 original size:2 final size:2
Alignment explanation
Indices: 43685--43714 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
43675 ATATAATAGT
*
43685 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43715 ATAACTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:44217 original size:36 final size:36
Alignment explanation
Indices: 44167--44257 Score: 103
Period size: 35 Copynumber: 2.5 Consensus size: 36
44157 GTACTTGTGG
44167 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTAAAACATAGCAAAATTCT
* * * * *
44204 ATCCTATTTTAGGAG-TTGAATCCTTGCAGAATTCT
1 ATCCTATTTTAGGAGTTTAAAACATAGCAAAATTCT
*
44239 ATCCTATTTTTGAGAGTTT
1 ATCCTATTTTAG-GAGTTT
44258 GAATCCTAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 26 0.57
36 11 0.24
37 9 0.20
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTAAAACATAGCAAAATTCT
Found at i:45118 original size:109 final size:102
Alignment explanation
Indices: 44727--45696 Score: 751
Period size: 98 Copynumber: 9.3 Consensus size: 102
44717 AATATTGTTC
* * * * *
44727 CGAGTCCAATATCCTCCG-CTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTATTTGTTGAC
1 CGAGTCCAATATCCTTCGTC-GTGGAGTTGAAATTGG--CTGAAACT-GAAAATT-GTTGTTGAC
** * ** * *
44791 AGTCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCT
61 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * * * * *
44833 CGAGTTTAATATTCTTCG-CTGTGAAGATGAAATTGACTCTG-AAC-G-AAA-TCTTGTTGACAA
1 CGAGTCCAATATCCTTCGTC-GTGGAGTTGAAATTG--GCTGAAACTGAAAATTGTTGTTGACAA
* *
44893 TCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
63 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
44933 CGAGTCCAATATCCTTCG-C-TGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGA
1 CGAGTCCAATATCCTTCGTCGTG-G-AGTTGAAATTGG--CTGAAA-CTGAAAATTG-TTGTTGA
*
44996 CAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
60 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
45039 CGAGTGGCATGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGAAACTGAAAAGTTGTTCGTTG
1 CGAGT-CCA--ATATCCTTCGTCGTGGAGTTGAAAT--TGGCTGAAACTGAAAA-TTGTT-GTTG
* * *
45104 ACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACATGTGTTATCT
59 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * * *
45148 CGGGTAGCACGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTATTTGTTG
1 CGAGT--C-CAATATCCTTCGTCGTGGAGTTGAAATTGG--CTGAAACT-GAAAATT-GTTGTTG
*
45213 ACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
59 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * **
45257 TGAGTCCAATATCCTTCG-CTGTGAAGTTGAGATTGGCT----CCG-AAATTGCTTGTCGACAGT
1 CGAGTCCAATATCCTTCGTC-GTGGAGTTGAAATTGGCTGAAACTGAAAATTG-TTGTTGACAAC
* * * *
45316 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
64 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
45355 TGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCTGAAACTGGGAAATTATTGTTGACAAC
1 CGAGTCCAATATCCTTCGTCGTGGAGTTGAAATTGG-CTGAAACT-GAAAATTGTTGTTGACAAC
45420 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * **
45459 CGAGTTCAATATCCTTCG-CTGTGAAGTTGAGATTGGCT----CCG-AAATTGTTTGTCGACAGT
1 CGAGTCCAATATCCTTCGTC-GTGGAGTTGAAATTGGCTGAAACTGAAAATTG-TTGTTGACAAC
* * * * *
45518 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTATCT
64 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
45557 TGGGTCCAATATCCTTCG-CTGTGAAGTTAAAATTGGCCCTGAAACTGGGAAATTATTGTTGACA
1 CGAGTCCAATATCCTTCGTC-GTGGAGTTGAAATTGG--CTGAAACT-GAAAATTGTTGTTGACA
45621 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
62 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
45662 CGAGTCCAATATCCTTCG-CTGTGAAGTCGAAATTG
1 CGAGTCCAATATCCTTCGTC-GTGGAGTTGAAATTG
45697 ACTCTAGCTA
Statistics
Matches: 710, Mismatches: 107, Indels: 95
0.78 0.12 0.10
Matches are distributed among these distances:
97 5 0.01
98 157 0.22
99 4 0.01
100 76 0.11
101 3 0.00
102 3 0.00
103 5 0.01
104 80 0.11
105 84 0.12
106 113 0.16
107 5 0.01
108 8 0.01
109 152 0.21
110 9 0.01
111 6 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (102 bp):
CGAGTCCAATATCCTTCGTCGTGGAGTTGAAATTGGCTGAAACTGAAAATTGTTGTTGACAACCA
GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:45560 original size:202 final size:202
Alignment explanation
Indices: 44730--45696 Score: 1082
Period size: 202 Copynumber: 4.7 Consensus size: 202
44720 ATTGTTCCGA
* * * **
44730 GTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTATTTGTTGACAGTC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGG-CCTGAAACTGGGAAATTA-TTGTTGACAACC
* ** * * ** * *
44795 AGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTCGAGTTTAATATTCTTCGCTGTGAAGA
64 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGT
* * * **
44860 TGAAATTGACTCTGAACGAAA-T-CTTGTTGACAATCAGCCGTCCCTTCATTGTGAAGTTGAACT
129 TGAAATTGGCTC----CGAAATTGCTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAACT
* * *
44923 TGTGTTGTCTCGA
190 TGTGCTATCTCGG
* * **
44936 GTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGT-TTGTTGACAAC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC-CTGAAA-CTGGGAAAT-TATTGTTGACAAC
* * *
45000 CAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCATGATATCCTCCG-TCGT
63 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-CCA--ATATCCTTCGCT-GT
* * * * * * * *
45064 GGAGTTGAAATCGTGGATGAAACTGAAAAGTTG-TTCGTTGACAACCAGTCGTCCCTTCGTTGTG
124 GAAGTTGAAAT--TGGCT----CCG-AAA-TTGCTT-GTCGACAATCAGCCGCCCCTTCGCTGTG
* *
45128 AAGTTGAACATGTGTTATCTCGG
180 AAGTTGAACTTGTGCTATCTCGG
* * * * * *
45151 GTAGCACGATATCCTCCG-TCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTATTTGTTGAC
1 GT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGC-CTGAAACTGGGAAATTA-TTGTTGAC
* *
45215 AACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTG
60 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTG
* * *
45280 AAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCT
125 AAGTTGAAATTGGCTCCGAAATTGCTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAACT
* *
45345 TGTGCTGTCTTGG
190 TGTGCTATCTCGG
*
45358 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCTGAAACTGGGAAATTATTGTTGACAACCAG
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCTGAAACTGGGAAATTATTGTTGACAACCAG
*
45423 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTGAAGTTG
66 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTG
* * * *
45488 AGATTGGCTCCGAAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCT
131 AAATTGGCTCCGAAATTGCTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCT
*
45553 ATCTTGG
196 ATCTCGG
*
45560 GTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCCCTGAAACTGGGAAATTATTGTTGACAACCA
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGG-CCTGAAACTGGGAAATTATTGTTGACAACCA
*
45625 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTC
65 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTT
45690 GAAATTG
130 GAAATTG
45697 ACTCTAGCTA
Statistics
Matches: 659, Mismatches: 74, Indels: 59
0.83 0.09 0.07
Matches are distributed among these distances:
202 177 0.27
203 115 0.17
204 25 0.04
205 2 0.00
206 83 0.13
207 52 0.08
208 7 0.01
209 21 0.03
211 4 0.01
212 3 0.00
213 4 0.01
214 3 0.00
215 68 0.10
216 2 0.00
217 11 0.02
218 82 0.12
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (202 bp):
GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCTGAAACTGGGAAATTATTGTTGACAACCAG
CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTG
AAATTGGCTCCGAAATTGCTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCT
ATCTCGG
Found at i:46020 original size:37 final size:37
Alignment explanation
Indices: 45971--46344 Score: 213
Period size: 37 Copynumber: 10.9 Consensus size: 37
45961 AAGATATTTG
* *
45971 TTGTTTCAAGGGAAACGGTCTTAAGGGAGACAAAATT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* *
46008 TTGTTTCAAGGGAAA-TGTTTTCAA---TG------TT
1 TTGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAATT
*
46036 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 T-TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* *
46074 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-T
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
** * **
46110 TCATTTCAAGGGAAA-TGTTTC--------CAATGTT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* * **
46138 TATGTTTCAAGAGAAACTGTCTCAATGGAGACGGAATT
1 T-TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* * * *
46176 TTATTTCAAGGGAAACTATCTCAAGAGAGACAAAA-C
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
** * *
46212 TCATTTCAAGGGAAA-TGTTTTCAA---TG------TT
1 TTGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAATT
*
46240 TATGTTTCAAGAGAAACTGTCTCAAGGGAGA-AAAA-T
1 T-TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* *
46276 TTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
*
46312 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAA
46345 TGGTGAGCAT
Statistics
Matches: 255, Mismatches: 44, Indels: 76
0.68 0.12 0.20
Matches are distributed among these distances:
27 3 0.01
28 6 0.02
29 45 0.18
30 9 0.04
32 2 0.01
33 1 0.00
34 1 0.00
35 35 0.14
36 68 0.27
37 78 0.31
38 7 0.03
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (37 bp):
TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
Found at i:46124 original size:36 final size:36
Alignment explanation
Indices: 46038--46344 Score: 220
Period size: 36 Copynumber: 8.9 Consensus size: 36
46028 TCAATGTTTA
* *
46038 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
*
46075 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
46111 CATTTCAAGGGAAA-TGTTTCCA-A-TG-----TTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
46139 ATGTTTCAAGAGAAACTGTCTCAATG-GAGACGGAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GAGAGAC-AAAATT
* * *
46177 TATTTCAAGGGAAACTATCTCAAGAGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * *
46213 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
* *
46241 ATGTTTCAAGAGAAACTGTCTCAAGGGAGA-AAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
46277 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
46313 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
46345 TGGTGAGCAT
Statistics
Matches: 209, Mismatches: 38, Indels: 47
0.71 0.13 0.16
Matches are distributed among these distances:
28 3 0.01
29 25 0.12
30 9 0.04
32 2 0.01
33 2 0.01
34 2 0.01
35 34 0.16
36 73 0.35
37 56 0.27
38 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:46140 original size:102 final size:102
Alignment explanation
Indices: 45971--46326 Score: 545
Period size: 102 Copynumber: 3.5 Consensus size: 102
45961 AAGATATTTG
** * * **
45971 TTGTTTCAAGGGAAACGGTCTTAAGGGAGACAAAATTTTGTTTCAAGGGAAATGTTTTCAATGTT
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTCATTTCAAGGGAAATGTTTTCAATGTT
46036 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
65 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
*
46074 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTT
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTT
* **
46139 ATGTTTCAAGAGAAACTGTCTCAATGGAGACGGAATT
66 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
* *
46176 TTATTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTT
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTT
46241 ATGTTTCAAGAGAAACTGTCTCAAGGGAGA-AAAA-T
66 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
* * **
46276 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
46327 CTGTCTCAAG
Statistics
Matches: 231, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
100 46 0.20
101 2 0.01
102 152 0.66
103 31 0.13
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (102 bp):
TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTT
ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
Found at i:46253 original size:50 final size:50
Alignment explanation
Indices: 46094--46253 Score: 124
Period size: 50 Copynumber: 3.2 Consensus size: 50
46084 GGAAACTATC
* *
46094 TCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTATGTT
1 TCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
* *** * ** * * * * *** * *
46144 TCAAGAGAAAC-TGTCTCAATGGAGACGGAATTTTATTTCAAGGGAAACTATC
1 TCAAGAGAGACAAAACTCATTTCA-AGGGAAATGT-TTTCAATGTTTA-TGTT
46196 TCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
1 TCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
46246 TCAAGAGA
1 TCAAGAGA
46254 AACTGTCTCA
Statistics
Matches: 72, Mismatches: 34, Indels: 8
0.63 0.30 0.07
Matches are distributed among these distances:
49 5 0.07
50 27 0.38
51 15 0.21
52 19 0.26
53 6 0.08
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (50 bp):
TCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
Found at i:47225 original size:22 final size:22
Alignment explanation
Indices: 47200--47250 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
47190 TTGTGTTTGG
47200 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
47222 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
47244 TCAAAGG
1 TCAAAGG
47251 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:47883 original size:20 final size:21
Alignment explanation
Indices: 47860--47905 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
47850 TTTGTCCCCT
*
47860 TTTTTTATTTTTGTTCTTT-C
1 TTTTTTATTCTTGTTCTTTCC
* *
47880 TTTTTTGTTCTTGTTTTTTCC
1 TTTTTTATTCTTGTTCTTTCC
47901 TTTTT
1 TTTTT
47906 GCTTCTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.02, C:0.11, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTTTATTCTTGTTCTTTCC
Found at i:47911 original size:21 final size:20
Alignment explanation
Indices: 47870--47925 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
47860 TTTTTTATTT
* *
47870 TTGTTCTTTCTTTTTTGTTC
1 TTGTTTTTTCCTTTTTGTTC
47890 TTGTTTTTTCCTTTTTGCTTC
1 TTGTTTTTTCCTTTTTG-TTC
*
47911 TT-TCTTTTTTCTTTT
1 TTGT-TTTTTCCTTTT
47926 GCCCTTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (20 bp):
TTGTTTTTTCCTTTTTGTTC
Found at i:52281 original size:16 final size:16
Alignment explanation
Indices: 52260--52293 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
52250 AAAAATAATT
52260 TAATAATGTAAAATAA
1 TAATAATGTAAAATAA
*
52276 TAATAATGTAATATAA
1 TAATAATGTAAAATAA
52292 TA
1 TA
52294 TAAATACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TAATAATGTAAAATAA
Found at i:52538 original size:11 final size:11
Alignment explanation
Indices: 52462--52545 Score: 62
Period size: 11 Copynumber: 7.3 Consensus size: 11
52452 TTATATACGT
*
52462 TAATAGTAAAA
1 TAATATTAAAA
*
52473 TAATAATAAATA
1 TAATATTAAA-A
*
52485 TAATAGTTATAA
1 TAATA-TTAAAA
*
52497 TATATATATATAA
1 TA-ATAT-TAAAA
*
52510 TAACTTTTAAAA
1 TAA-TATTAAAA
52522 -AATATTAAAA
1 TAATATTAAAA
*
52532 TAATATTAGAA
1 TAATATTAAAA
52543 TAA
1 TAA
52546 AAATATATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
10 7 0.12
11 23 0.38
12 15 0.25
13 15 0.25
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (11 bp):
TAATATTAAAA
Found at i:53016 original size:35 final size:36
Alignment explanation
Indices: 52971--53044 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 36
52961 GTTTAAAACA
52971 TAGCAAAATTCTATCCTA-TTTTAGGAG-TTGAATCC
1 TAGCAAAATTCTATCCTATTTTTA-GAGTTTGAATCC
*
53006 TAGCAGAATTCTATCCTATTTTTTAGAGTTTGAATCC
1 TAGCAAAATTCTATCCTA-TTTTTAGAGTTTGAATCC
53043 TA
1 TA
53045 ATAGGACGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
35 17 0.49
36 3 0.09
37 15 0.43
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (36 bp):
TAGCAAAATTCTATCCTATTTTTAGAGTTTGAATCC
Found at i:60743 original size:21 final size:20
Alignment explanation
Indices: 60717--60759 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
60707 TTAAATTCCC
* *
60717 TAATTATATTTATAATTTAAT
1 TAATTATAGTT-TAAGTTAAT
60738 TAATTATAGTTTAAGTTAAT
1 TAATTATAGTTTAAGTTAAT
60758 TA
1 TA
60760 CATATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
TAATTATAGTTTAAGTTAAT
Found at i:60758 original size:16 final size:15
Alignment explanation
Indices: 60726--60770 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
60716 CTAATTATAT
60726 TTATAATTTAATTAA
1 TTATAATTTAATTAA
*
60741 TTATAGTTTAAGTTAA
1 TTATAATTTAA-TTAA
*
60757 TTACATATTTAATT
1 TTATA-ATTTAATT
60771 CCCTTTAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 10 0.40
16 10 0.40
17 5 0.20
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (15 bp):
TTATAATTTAATTAA
Found at i:60887 original size:15 final size:15
Alignment explanation
Indices: 60869--60901 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
60859 ATTCATAATC
60869 ATTTTAT-TATTTATT
1 ATTTTATGTA-TTATT
60884 ATTTTATGTATTATT
1 ATTTTATGTATTATT
60899 ATT
1 ATT
60902 ACATTACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
ATTTTATGTATTATT
Done.