Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006104.1 Corchorus capsularis cultivar CVL-1 contig06122, 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: 26960
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:103 original size:2 final size:2
Alignment explanation
Indices: 96--129 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
86 AGTCCTACAA
*
96 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
130 CAATGTTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:621 original size:27 final size:27
Alignment explanation
Indices: 583--635 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
573 ACTCTCTCTG
583 TTCCTTTTTAATTGTCCA-TTTCCCTTA
1 TTCCTTTTTAATTGT-CATTTTCCCTTA
610 TTCCTTTTTAATTGTCATTTTCCCTT
1 TTCCTTTTTAATTGTCATTTTCCCTT
636 GTTTTCCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.13, C:0.25, G:0.04, T:0.58
Consensus pattern (27 bp):
TTCCTTTTTAATTGTCATTTTCCCTTA
Found at i:5787 original size:13 final size:14
Alignment explanation
Indices: 5764--5792 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5754 ACTTCTATTT
5764 AATGCATGGATGCA
1 AATGCATGGATGCA
5778 AATG-ATGGATGCA
1 AATGCATGGATGCA
5791 AA
1 AA
5793 GTCCGATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (14 bp):
AATGCATGGATGCA
Found at i:8915 original size:16 final size:16
Alignment explanation
Indices: 8867--8916 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
8857 TGGGAGGGAG
8867 TAACTAATATGATTAA
1 TAACTAATATGATTAA
*
8883 CAACTAATATGATTAA
1 TAACTAATATGATTAA
*
8899 TGACTAATATGATTAA
1 TAACTAATATGATTAA
8915 TA
1 TA
8917 GAAAAGTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (16 bp):
TAACTAATATGATTAA
Found at i:11786 original size:30 final size:30
Alignment explanation
Indices: 11727--11790 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
11717 GAATACCATT
* *
11727 TTACTTTTTGATTTTAATTACTAACTACCA
1 TTACTTTTTGATCTTAATTACCAACTACCA
* * *
11757 TTACTTTTTGATCTTAGTTACCGATTACCA
1 TTACTTTTTGATCTTAATTACCAACTACCA
11787 TTAC
1 TTAC
11791 CATTTTACTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (30 bp):
TTACTTTTTGATCTTAATTACCAACTACCA
Found at i:11847 original size:22 final size:22
Alignment explanation
Indices: 11821--12279 Score: 346
Period size: 22 Copynumber: 21.5 Consensus size: 22
11811 TTTTTCCTTA
11821 CTTTACTGATTACCATTTTACT
1 CTTTACTGATTACCATTTTACT
* *
11843 CTTTACTAATTACCATTTTATT
1 CTTTACTGATTACCATTTTACT
* ** * *
11865 CTTTTCCAATTACCATATTACC
1 CTTTACTGATTACCATTTTACT
* *
11887 CTTTACTGATTGCCTTTTTACT
1 CTTTACTGATTACCATTTTACT
*
11909 TTTTACTGATTACCATTTTACT
1 CTTTACTGATTACCATTTTACT
* * *
11931 CTTTAATAATTACCATTTTAAT
1 CTTTACTGATTACCATTTTACT
* * * *
11953 CTTTGCTAATTACCATATTACC
1 CTTTACTGATTACCATTTTACT
* *
11975 CTTTACTGATGACCTTTTTACT
1 CTTTACTGATTACCATTTTACT
11997 -TTTCACTGATTACC-TTTTAACT
1 CTTT-ACTGATTACCATTTT-ACT
* * *
12019 TTTTACTAATTACCTTTTTACT
1 CTTTACTGATTACCATTTTACT
**
12041 -TTTACTGATTAGTATTTTACT
1 CTTTACTGATTACCATTTTACT
* *
12062 C-TTACTAATTACC--TTCACT
1 CTTTACTGATTACCATTTTACT
* * *
12081 TTTTACTAATTACCTTTTTACT
1 CTTTACTGATTACCATTTTACT
* *
12103 -TTTACAGATTACTATTTTACT
1 CTTTACTGATTACCATTTTACT
12124 C-TTACTGATTACC--TTTACT
1 CTTTACTGATTACCATTTTACT
* * * *
12143 TTTTACTGATTA-C-TATTGCC
1 CTTTACTGATTACCATTTTACT
12163 CTTTACTGATTACC-TTTTCACT
1 CTTTACTGATTACCATTTT-ACT
*
12185 -TCTT-CTGATTACCTTTTTACT
1 CT-TTACTGATTACCATTTTACT
*
12206 C-TTAGC-GATTA-C-TATTACT
1 CTTTA-CTGATTACCATTTTACT
* * * *
12225 CCTTACTCATTGCCATTTTACC
1 CTTTACTGATTACCATTTTACT
*
12247 CTTTACTGATTACCTTTTTACT
1 CTTTACTGATTACCATTTTACT
*
12269 C-TAACTGATTA
1 CTTTACTGATTA
12280 TCTCTTACTA
Statistics
Matches: 346, Mismatches: 69, Indels: 45
0.75 0.15 0.10
Matches are distributed among these distances:
19 20 0.06
20 45 0.13
21 92 0.27
22 182 0.53
23 7 0.02
ACGTcount: A:0.23, C:0.22, G:0.05, T:0.50
Consensus pattern (22 bp):
CTTTACTGATTACCATTTTACT
Found at i:12155 original size:27 final size:27
Alignment explanation
Indices: 12111--12169 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
12101 CTTTTACAGA
*
12111 TTACTATTTTACTCTTACTGATT-ACCT
1 TTACTATTTTACTATTACT-ATTGACCT
*
12138 TTACT-TTTTACTGATTACTATTGCCCT
1 TTACTATTTTACT-ATTACTATTGACCT
12165 TTACT
1 TTACT
12170 GATTACCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.20, C:0.22, G:0.05, T:0.53
Consensus pattern (27 bp):
TTACTATTTTACTATTACTATTGACCT
Found at i:12195 original size:82 final size:84
Alignment explanation
Indices: 12001--12264 Score: 217
Period size: 82 Copynumber: 3.2 Consensus size: 84
11991 TTTACTTTTC
* * *
12001 ACTGATTACCTTTTAACTTTTTACTA-ATTACCTTTTTACTTTTA-CTGATTAGTATTTTACT-C
1 ACTGATTACCTTTTCAC-TTTTAC-AGATTACCTTTTTACTCTTAGC-GATTACTA--TTACTCC
* * * **
12063 TTACTAATT-ACCT-TCACTTTTT
61 TTACTCATTGACATATTACCCTTT
* * **
12085 ACTAATTACCTTTTTACTTTTACAGATTA-CTATTTTACTCTTA-CTGATTACCT-TTACTTTTT
1 ACTGATTACCTTTTCACTTTTACAGATTACCT-TTTTACTCTTAGC-GATTA-CTATTACTCCTT
* *
12147 ACTGATT-AC-TATTGCCCTTT
63 ACTCATTGACATATTACCCTTT
*
12167 ACTGATTACCTTTTCACTTCTT-CTGATTACCTTTTTACTCTTAGCGATTACTATTACTCCTTAC
1 ACTGATTACCTTTTCACTT-TTACAGATTACCTTTTTACTCTTAGCGATTACTATTACTCCTTAC
* *
12231 TCATTGCCATTTTACCCTTT
65 TCATTGACATATTACCCTTT
12251 ACTGATTACCTTTT
1 ACTGATTACCTTTT
12265 TACTCTAACT
Statistics
Matches: 150, Mismatches: 19, Indels: 22
0.79 0.10 0.12
Matches are distributed among these distances:
81 8 0.05
82 70 0.47
83 33 0.22
84 39 0.26
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.51
Consensus pattern (84 bp):
ACTGATTACCTTTTCACTTTTACAGATTACCTTTTTACTCTTAGCGATTACTATTACTCCTTACT
CATTGACATATTACCCTTT
Found at i:12217 original size:21 final size:21
Alignment explanation
Indices: 11980--12201 Score: 83
Period size: 21 Copynumber: 10.6 Consensus size: 21
11970 TTACCCTTTA
* *
11980 CTGATGACCTTTTTACTT-TT
1 CTGATTACCTTTTCACTTCTT
* *
12000 CACTGATTACCTTTTAACTTTTT
1 --CTGATTACCTTTTCACTTCTT
* *
12023 ACTAATTACCTTTTTACTT-TT
1 -CTGATTACCTTTTCACTTCTT
* *
12044 ACTGATTA-GTATTTTAC-TCTT
1 -CTGATTACCT-TTTCACTTCTT
* *
12065 ACTAATTACC--TTCACTTTTT
1 -CTGATTACCTTTTCACTTCTT
* *
12085 ACTAATTACCTTTTTACTT-TT
1 -CTGATTACCTTTTCACTTCTT
* *
12106 ACAGATTA-CTATTTTAC-TCTT
1 -CTGATTACCT-TTTCACTTCTT
*
12127 ACTGATTACC-TTT-ACTTTTT
1 -CTGATTACCTTTTCACTTCTT
* * *
12147 ACTGATTA-CTATTGCCCTT-TA
1 -CTGATTACCT-TTTCACTTCTT
12168 CTGATTACCTTTTCACTTCTT
1 CTGATTACCTTTTCACTTCTT
12189 CTGATTACCTTTT
1 CTGATTACCTTTT
12202 TACTCTTAGC
Statistics
Matches: 163, Mismatches: 21, Indels: 33
0.75 0.10 0.15
Matches are distributed among these distances:
19 7 0.04
20 45 0.28
21 66 0.40
22 43 0.26
23 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.52
Consensus pattern (21 bp):
CTGATTACCTTTTCACTTCTT
Found at i:12275 original size:21 final size:21
Alignment explanation
Indices: 11818--12351 Score: 257
Period size: 22 Copynumber: 25.5 Consensus size: 21
11808 TCTTTTTTCC
*
11818 TTACT-TTACTGATTACCATT
1 TTACTCTTACTGATTACCTTT
* *
11838 TTACTCTTTACTAATTACCATT
1 TTACTC-TTACTGATTACCTTT
* * ** * *
11860 TTATTCTTTTCCAATTACCATA
1 TTACTC-TTACTGATTACCTTT
* *
11882 TTACCCTTTACTGATTGCCTTT
1 TTACTC-TTACTGATTACCTTT
* *
11904 TTACTTTTTACTGATTACCATT
1 TTAC-TCTTACTGATTACCTTT
* * *
11926 TTACTCTTTAATAATTACCATT
1 TTACTC-TTACTGATTACCTTT
* * * * *
11948 TTAATCTTTGCTAATTACCATA
1 TTACTC-TTACTGATTACCTTT
* *
11970 TTACCCTTTACTGATGACCTTT
1 TTACTC-TTACTGATTACCTTT
*
11992 TTACTTTTCACTGATTACCTTT
1 TTACTCTT-ACTGATTACCTTT
* * *
12014 TAACTTTTTACTAATTACCTTT
1 TTAC-TCTTACTGATTACCTTT
* *
12036 TTACTTTTACTGATTA-GTATT
1 TTACTCTTACTGATTACCT-TT
*
12057 TTACTCTTACTAATTACC--T
1 TTACTCTTACTGATTACCTTT
* * *
12076 TCACTTTTTACTAATTACCTTT
1 TTAC-TCTTACTGATTACCTTT
* *
12098 TTACTTTTACAGATTA-CTATT
1 TTACTCTTACTGATTACCT-TT
12119 TTACTCTTACTGATTACC--T
1 TTACTCTTACTGATTACCTTT
* *
12138 TTACTTTTTACTGATTA-C-TA
1 TTAC-TCTTACTGATTACCTTT
* *
12158 TTGCCCTTTACTGATTACCTTT
1 TTACTC-TTACTGATTACCTTT
*
12180 TCACTTCTT-CTGATTACCTTT
1 TTAC-TCTTACTGATTACCTTT
*
12201 TTACTCTTAGC-GATTA-C-TA
1 TTACTCTTA-CTGATTACCTTT
* * *
12220 TTACTCCTTACTCATTGCCATT
1 TTACT-CTTACTGATTACCTTT
*
12242 TTACCCTTTACTGATTACCTTT
1 TTACTC-TTACTGATTACCTTT
*
12264 TTACTCTAACTGATTA-----
1 TTACTCTTACTGATTACCTTT
* *** *
12280 -T-CTCTTACTAATTATTATC
1 TTACTCTTACTGATTACCTTT
12299 TTACTCTTACTGATTACC-TT
1 TTACTCTTACTGATTACCTTT
* *
12319 TTACTTTTTACTAATTA-CTATT
1 TTAC-TCTTACTGATTACCT-TT
12341 TTACTCTTACT
1 TTACTCTTACT
12352 TTTTTAGTGT
Statistics
Matches: 400, Mismatches: 78, Indels: 71
0.73 0.14 0.13
Matches are distributed among these distances:
14 11 0.03
15 1 0.00
19 17 0.04
20 64 0.16
21 116 0.29
22 186 0.47
23 5 0.01
ACGTcount: A:0.23, C:0.22, G:0.04, T:0.51
Consensus pattern (21 bp):
TTACTCTTACTGATTACCTTT
Found at i:16770 original size:6 final size:6
Alignment explanation
Indices: 16759--16788 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
16749 GACTTTATCA
16759 TTCTTT TTCTTT TTCTTT TTCTTT TT-TTT T
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT T
16789 GAAAAATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTCTTT
Found at i:21610 original size:26 final size:26
Alignment explanation
Indices: 21559--21687 Score: 104
Period size: 26 Copynumber: 4.9 Consensus size: 26
21549 TCTTACTATC
*
21559 AATTACCATTTTATT--TCTTGATTACT
1 AATTACCATTTT-TTACTCTT-TTTACT
*
21585 AATTACCATTTTTTACTCTTTGTACT
1 AATTACCATTTTTTACTCTTTTTACT
* *
21611 GATTACCA-TATTTACTCTTTTTTACT
1 AATTACCATTTTTTACTC-TTTTTACT
* * *
21637 GATTACCCCTTTTCTTACTGTTTTTACT
1 AATTA-CCATTTT-TTACTCTTTTTACT
*
21665 GAA-TACCACTTTTTACTCTTTTT
1 -AATTACCATTTTTTACTCTTTTT
21688 TACCATTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
25 10 0.12
26 45 0.54
27 11 0.13
28 12 0.14
29 6 0.07
ACGTcount: A:0.22, C:0.20, G:0.05, T:0.53
Consensus pattern (26 bp):
AATTACCATTTTTTACTCTTTTTACT
Found at i:21618 original size:52 final size:53
Alignment explanation
Indices: 21560--21684 Score: 128
Period size: 52 Copynumber: 2.3 Consensus size: 53
21550 CTTACTATCA
*
21560 ATTACCATTTTATTTCTTGATTACTAATTA-CCATTTT-TTACTCTTTGTACTG
1 ATTACCATTTTA-CTCTTGATTACTAATTACCCATTTTCTTACTCTTTGTACTG
** * * * *
21612 ATTACCATATTTACTCTTTTTTACTGATTACCCCTTTTCTTACTGTTTTTACTG
1 ATTACCAT-TTTACTCTTGATTACTAATTACCCATTTTCTTACTCTTTGTACTG
*
21666 AATACCACTTTTTACTCTT
1 ATTACCA--TTTTACTCTT
21685 TTTTACCATT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
52 21 0.35
53 10 0.17
54 19 0.32
55 9 0.15
56 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.53
Consensus pattern (53 bp):
ATTACCATTTTACTCTTGATTACTAATTACCCATTTTCTTACTCTTTGTACTG
Found at i:21672 original size:54 final size:53
Alignment explanation
Indices: 21580--21690 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 53
21570 TATTTCTTGA
*
21580 TTACTAATTACCATTTTTTACTCTTTGTACTGATTACCA-TATTTACTCTTTT
1 TTACTAATTACCATTTTTTACTCTTTGTACTGAATACCACTATTTACTCTTTT
* * * * *
21632 TTACTGATTACCCCTTTTCTTACTGTTTTTACTGAATACCACTTTTTACTCTTTT
1 TTACTAATTA-CCATTTT-TTACTCTTTGTACTGAATACCACTATTTACTCTTTT
21687 TTAC
1 TTAC
21691 CATTTTTACT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
52 9 0.18
53 6 0.12
54 19 0.38
55 16 0.32
ACGTcount: A:0.21, C:0.22, G:0.05, T:0.53
Consensus pattern (53 bp):
TTACTAATTACCATTTTTTACTCTTTGTACTGAATACCACTATTTACTCTTTT
Found at i:21679 original size:17 final size:17
Alignment explanation
Indices: 21657--21717 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
21647 TTTCTTACTG
21657 TTTTTACTGAATACCAC
1 TTTTTACTGAATACCAC
***
21674 TTTTTACTCTTTTTTACCA-
1 TTTTTA--C-TGAATACCAC
21693 TTTTTACTGAATACCAC
1 TTTTTACTGAATACCAC
21710 TTTTTACT
1 TTTTTACT
21718 CTTTTTTACT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
16 6 0.18
17 15 0.44
19 7 0.21
20 6 0.18
ACGTcount: A:0.23, C:0.21, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTTTACTGAATACCAC
Found at i:21698 original size:36 final size:36
Alignment explanation
Indices: 21657--21726 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
21647 TTTCTTACTG
21657 TTTTTACTGAATACCACTTTTTACTCTTTTTTACCA
1 TTTTTACTGAATACCACTTTTTACTCTTTTTTACCA
21693 TTTTTACTGAATACCACTTTTTACTCTTTTTTAC
1 TTTTTACTGAATACCACTTTTTACTCTTTTTTAC
21727 TGATCACCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.54
Consensus pattern (36 bp):
TTTTTACTGAATACCACTTTTTACTCTTTTTTACCA
Found at i:21723 original size:90 final size:89
Alignment explanation
Indices: 21593--21783 Score: 230
Period size: 90 Copynumber: 2.1 Consensus size: 89
21583 CTAATTACCA
* * * *
21593 TTTTTTACTCTTTGTACTGATTACCATATTTACTCTTTTTTACTGATTACCCCTTTTCTTACTGT
1 TTTTTTACTCTTTGTACTGAATACCATATTTACTCTTTTTTACTGA-T-CACCATTTCTTACTCT
21658 TT-TTACTGAA-TACCACT-TTTTACTC
64 TTATTACT-AATTA-CACTCTTTTACTC
* *
21683 TTTTTTAC-CATTTTTACTGAATACCACTTTTTACTCTTTTTTACTGATCACCATTTCTTACTCT
1 TTTTTTACTC-TTTGTACTGAATACCA-TATTTACTCTTTTTTACTGATCACCATTTCTTACTCT
*
21747 TTATTACTAATTACTCTCTTTTACTC
64 TTATTACTAATTACACTCTTTTACTC
21773 TTTTTTA-TCTT
1 TTTTTTACTCTT
21784 ACTTGCCATT
Statistics
Matches: 88, Mismatches: 7, Indels: 13
0.81 0.06 0.12
Matches are distributed among these distances:
89 23 0.26
90 46 0.52
91 19 0.22
ACGTcount: A:0.19, C:0.22, G:0.04, T:0.55
Consensus pattern (89 bp):
TTTTTTACTCTTTGTACTGAATACCATATTTACTCTTTTTTACTGATCACCATTTCTTACTCTTT
ATTACTAATTACACTCTTTTACTC
Found at i:21726 original size:63 final size:64
Alignment explanation
Indices: 21629--21753 Score: 159
Period size: 63 Copynumber: 2.0 Consensus size: 64
21619 TATTTACTCT
* * *
21629 TTTTTACTGATTACCCCTTTTCTTACTGTTTTTACTGAAT-ACCACTTT-TTACTCTTTTTTACC
1 TTTTTACTGAATACCACTTTTCTTACTGTTTTTACTG-ATCACCA-TTTCTTACTCTTTATTACC
21692 A
64 A
*
21693 TTTTTACTGAATACCAC-TTT-TTACTCTTTTTTACTGATCACCATTTCTTACTCTTTATTAC
1 TTTTTACTGAATACCACTTTTCTTACT-GTTTTTACTGATCACCATTTCTTACTCTTTATTAC
21754 TAATTACTCT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
62 10 0.19
63 29 0.54
64 15 0.28
ACGTcount: A:0.20, C:0.23, G:0.04, T:0.53
Consensus pattern (64 bp):
TTTTTACTGAATACCACTTTTCTTACTGTTTTTACTGATCACCATTTCTTACTCTTTATTACCA
Found at i:21735 original size:27 final size:26
Alignment explanation
Indices: 21684--21779 Score: 90
Period size: 27 Copynumber: 3.6 Consensus size: 26
21674 TTTTTACTCT
*
21684 TTTTTAC-CATTTTTACTGAATACCAC
1 TTTTTACTCTTTTTTACTG-ATACCAC
21710 TTTTTACTCTTTTTTACTGATCACCA-
1 TTTTTACTCTTTTTTACTGAT-ACCAC
* * *
21736 TTTCTTACTCTTTATTACTAATTA-CTC
1 TTT-TTACTCTTTTTTACTGA-TACCAC
21763 TCTTTTACTCTTTTTTA
1 T-TTTTACTCTTTTTTA
21780 TCTTACTTGC
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
26 13 0.22
27 43 0.73
28 3 0.05
ACGTcount: A:0.21, C:0.22, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTTTACTCTTTTTTACTGATACCAC
Found at i:22290 original size:71 final size:71
Alignment explanation
Indices: 22088--22307 Score: 268
Period size: 72 Copynumber: 3.1 Consensus size: 71
22078 GATCACTTTA
* * *
22088 ACTCTTAATCATCGATTTACTGATTACTA--TTTTTACCTAGA-CACTTTAA-TTACTGATTAAT
1 ACTCTTAATTATCAATTTACTGATTACTATCTTTTTACCT-GATTAC--TAATTTACTGATT-A-
*
22149 CTCTTACCTTG
61 CTATTACCTTG
* *
22160 ACTCTTAATTATCAATTTACTGATTACTTATCTTTTTACTTAATTACTAATTTACTGATTACTAT
1 ACTCTTAATTATCAATTTACTGATTAC-TATCTTTTTACCTGATTACTAATTTACTGATTACTAT
* *
22225 TATCTGG
65 TACCTTG
* *
22232 ACTCTTAATTATCAATTTATTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATT
1 ACTCTTAATTATCAATTTACTGATTACTATCTTTTTACCTGATTACTAATTTACTGATTACTATT
22297 ACCTTG
66 ACCTTG
22303 ACTCT
1 ACTCT
22308 GATTAATCTC
Statistics
Matches: 129, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
71 44 0.34
72 59 0.46
73 6 0.05
74 10 0.08
75 10 0.08
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (71 bp):
ACTCTTAATTATCAATTTACTGATTACTATCTTTTTACCTGATTACTAATTTACTGATTACTATT
ACCTTG
Found at i:22311 original size:55 final size:55
Alignment explanation
Indices: 22252--22406 Score: 247
Period size: 55 Copynumber: 2.8 Consensus size: 55
22242 ATCAATTTAT
* * * * *
22252 TGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATTACCTTGACTC
1 TGATTAATCTCTTTTTACTTAATTACTGATTTACTAATTACTATTACCTTGACTC
*
22307 TGATTAATCTCTTTTCACTTAATTACTGATTTACTAATTACTATTACCTTGACTC
1 TGATTAATCTCTTTTTACTTAATTACTGATTTACTAATTACTATTACCTTGACTC
*
22362 TGATTAATCTCTTTTTACTTAATTACTGATTTACTTATTACTATT
1 TGATTAATCTCTTTTTACTTAATTACTGATTTACTAATTACTATT
22407 GAACTTAATT
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (55 bp):
TGATTAATCTCTTTTTACTTAATTACTGATTTACTAATTACTATTACCTTGACTC
Done.