Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016474.1 Corchorus capsularis cultivar CVL-1 contig16495, 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: 8490
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Found at i:338 original size:40 final size:42
Alignment explanation
Indices: 235--338 Score: 142
Period size: 40 Copynumber: 2.5 Consensus size: 42
225 ATGGATTAAC
* * *
235 GAAGTAATCAGTGAAATCAGTAATTAAAGAGTCAAAGTAAAA
1 GAAGTAATCAGTAAAATCGGTAATTAAAGAGTAAAAGTAAAA
*
277 AAAGTAATCAGTAAAAT-GGTAATT-AAGAGTAAAAGTAAAA
1 GAAGTAATCAGTAAAATCGGTAATTAAAGAGTAAAAGTAAAA
*
317 GAAGTGATCAGT-AAATCGGTAA
1 GAAGTAATCAGTAAAATCGGTAA
339 AGAATAAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
39 4 0.07
40 30 0.55
41 6 0.11
42 15 0.27
ACGTcount: A:0.52, C:0.06, G:0.20, T:0.22
Consensus pattern (42 bp):
GAAGTAATCAGTAAAATCGGTAATTAAAGAGTAAAAGTAAAA
Found at i:451 original size:26 final size:26
Alignment explanation
Indices: 422--475 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
412 GCAAATGGTG
*
422 ATTAAGTTCAA-AGAGTGAAAATAGTA
1 ATTAAATTCAAGAGAGT-AAAATAGTA
448 ATTAAATTCAAGAGAGTAAAATAGTA
1 ATTAAATTCAAGAGAGTAAAATAGTA
474 AT
1 AT
476 CAGTAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.28
Consensus pattern (26 bp):
ATTAAATTCAAGAGAGTAAAATAGTA
Found at i:520 original size:37 final size:37
Alignment explanation
Indices: 479--565 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
469 TAGTAATCAG
* *
479 TAAAATGGTAAAAAAATAAAGAGA-GATCAGTAAAGAA
1 TAAAATGGTAAAAAAATAAAGA-ATAACCAGTAAAGAA
* **
516 TAAAAATGGT-AAAAAGTAAAGAATAACCAGTAAAGGG
1 T-AAAATGGTAAAAAAATAAAGAATAACCAGTAAAGAA
553 TAAAATGGTAAAA
1 TAAAATGGTAAAA
566 TGGTAATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
36 9 0.21
37 25 0.60
38 8 0.19
ACGTcount: A:0.60, C:0.03, G:0.20, T:0.17
Consensus pattern (37 bp):
TAAAATGGTAAAAAAATAAAGAATAACCAGTAAAGAA
Found at i:645 original size:56 final size:56
Alignment explanation
Indices: 580--722 Score: 162
Period size: 56 Copynumber: 2.5 Consensus size: 56
570 AATTAAATTC
* ** *
580 AAAGAGTAAAATGGTAAAAAGTAATGGTAATCAGAAAAAATAAGAA-GGTAATCAGT
1 AAAGAGTAAAATAGTAAAAAGTAAAAGTAATCAGAAAAAACAA-AATGGTAATCAGT
** * *
636 AAAGAGTAAAATAGTAATTAGTAAAAGTAATCAGTAAGAACAAAATGGTAATCAGT
1 AAAGAGTAAAATAGTAAAAAGTAAAAGTAATCAGAAAAAACAAAATGGTAATCAGT
* **
692 AAAGAGTAAAATATTAATCAGTAAAAAGTAA
1 AAAGAGTAAAATAGTAAAAAGT-AAAAGTAA
723 GAAGGTAATC
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
55 2 0.03
56 65 0.87
57 8 0.11
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (56 bp):
AAAGAGTAAAATAGTAAAAAGTAAAAGTAATCAGAAAAAACAAAATGGTAATCAGT
Found at i:702 original size:22 final size:22
Alignment explanation
Indices: 655--766 Score: 117
Period size: 22 Copynumber: 5.2 Consensus size: 22
645 AATAGTAATT
655 AGTAAAA--GTAATCAGT-AAG
1 AGTAAAATGGTAATCAGTAAAG
**
674 AACAAAATGGTAATCAGTAAAG
1 AGTAAAATGGTAATCAGTAAAG
** *
696 AGTAAAATATTAATCAGTAAAA
1 AGTAAAATGGTAATCAGTAAAG
718 AGTAAGAA-GGTAATCAGTAAAG
1 AGTAA-AATGGTAATCAGTAAAG
*
740 AGTAAAATGATAATCAGTAGAAG
1 AGTAAAATGGTAATCAGTA-AAG
763 -GTAA
1 AGTAA
767 TTAGTAAGAG
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
19 5 0.07
21 11 0.14
22 55 0.72
23 5 0.07
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (22 bp):
AGTAAAATGGTAATCAGTAAAG
Found at i:731 original size:100 final size:100
Alignment explanation
Indices: 607--803 Score: 299
Period size: 100 Copynumber: 2.0 Consensus size: 100
597 AAAGTAATGG
*
607 TAATCAGAAAAAATAAGAAGGTAATCAGTAAAGAGTAAAAT-AGTAATTAGTA-AAAGTAATCAG
1 TAATCAGAAAAAATAAGAAGGTAATCAGTAAAGAGTAAAATGA-TAATCAGTAGAAAGTAATCAG
*
670 TAAGAACAAAATGGTAATCAGTAAAGAGTAAAATAT
65 TAAGAACAAAATAGTAATCAGTAAAGAGTAAAATAT
* * *
706 TAATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATGATAATCAGTAGAAGGTAATTAG
1 TAATCAG-AAAAAATAAGAAGGTAATCAGTAAAGAGTAAAATGATAATCAGTAGAAAGTAATCAG
**
771 TAAGAGTAAAATAGTAATCAGTAAAGAGTAAAA
65 TAAGAACAAAATAGTAATCAGTAAAGAGTAAAA
804 GGTGGTCAGT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
99 7 0.08
100 41 0.47
101 40 0.45
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.22
Consensus pattern (100 bp):
TAATCAGAAAAAATAAGAAGGTAATCAGTAAAGAGTAAAATGATAATCAGTAGAAAGTAATCAGT
AAGAACAAAATAGTAATCAGTAAAGAGTAAAATAT
Found at i:787 original size:21 final size:22
Alignment explanation
Indices: 763--803 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
753 TCAGTAGAAG
*
763 GTAATTAGT-AAGAGTAAAATA
1 GTAATCAGTAAAGAGTAAAATA
784 GTAATCAGTAAAGAGTAAAA
1 GTAATCAGTAAAGAGTAAAA
804 GGTGGTCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.54, C:0.02, G:0.20, T:0.24
Consensus pattern (22 bp):
GTAATCAGTAAAGAGTAAAATA
Found at i:934 original size:29 final size:29
Alignment explanation
Indices: 873--936 Score: 96
Period size: 27 Copynumber: 2.2 Consensus size: 29
863 GTGGTAATCA
*
873 ATAAAAGAGAGTGAGAAAAGAGTAAATAT
1 ATAAAAGAGAGTGAGAAAAGAGTAAAAAT
902 -TAAAA-AGAGTGAGAAAAGAGTAAAAAT
1 ATAAAAGAGAGTGAGAAAAGAGTAAAAAT
929 GATAAAAG
1 -ATAAAAG
937 TAGCATGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 21 0.68
28 5 0.16
29 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (29 bp):
ATAAAAGAGAGTGAGAAAAGAGTAAAAAT
Found at i:1751 original size:28 final size:28
Alignment explanation
Indices: 1711--1767 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1701 GAGAATGAAA
* *
1711 AAGTAAGCTCCAAAACAAACTAAAAGAT
1 AAGTAACCCCCAAAACAAACTAAAAGAT
* *
1739 AAGTAACCCCCAAATCAAACTAAAGGAT
1 AAGTAACCCCCAAAACAAACTAAAAGAT
1767 A
1 A
1768 TTCCTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.54, C:0.21, G:0.11, T:0.14
Consensus pattern (28 bp):
AAGTAACCCCCAAAACAAACTAAAAGAT
Found at i:3793 original size:21 final size:21
Alignment explanation
Indices: 3716--3996 Score: 115
Period size: 21 Copynumber: 13.5 Consensus size: 21
3706 CTGATCCCCC
*
3716 TTTACTCTTTACTGATTACCAT
1 TTTACTC-TTACTGATTACTAT
* * *
3738 TTGACTCTTACTAATTA-TCAC
1 TTTACTCTTACTGATTACT-AT
* * *
3759 TTTGCTCTTGCTGGTTACTAT
1 TTTACTCTTACTGATTACTAT
* *
3780 TTTACTCTTACTGGTTA-TCT
1 TTTACTCTTACTGATTACTAT
*
3800 TTTA----T--TGATTATTAT
1 TTTACTCTTACTGATTACTAT
*
3815 TTTACT----CT--TTACGGAT
1 TTTACTCTTACTGATTAC-TAT
3831 TTTACTCTTTACTGATTACCT-T
1 TTTACTC-TTACTGATTA-CTAT
* * *
3853 CTTACTTTTTACTGATTACCAT
1 TTTAC-TCTTACTGATTACTAT
*
3875 TTTACTCTTTTACTGATTACCAT
1 TTTACTC--TTACTGATTACTAT
*
3898 TTTACTCTTTTTTACTGATTACTCT
1 TTTACTC----TTACTGATTACTAT
3923 TTTACTTCTTACTGATTACTAT
1 TTTAC-TCTTACTGATTACTAT
* * * *
3945 TTGACTCTTACTAATTACCAC
1 TTTACTCTTACTGATTACTAT
* * * * *
3966 TTTGCTCTCACCGGTTACTGT
1 TTTACTCTTACTGATTACTAT
3987 TTTACTCTTA
1 TTTACTCTTA
3997 ATGACTACCT
Statistics
Matches: 196, Mismatches: 41, Indels: 45
0.70 0.15 0.16
Matches are distributed among these distances:
14 5 0.03
15 9 0.05
16 9 0.05
17 1 0.01
20 6 0.03
21 75 0.38
22 44 0.22
23 25 0.13
24 1 0.01
25 19 0.10
26 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.07, T:0.52
Consensus pattern (21 bp):
TTTACTCTTACTGATTACTAT
Found at i:3834 original size:16 final size:16
Alignment explanation
Indices: 3813--3847 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3803 ATTGATTATT
3813 ATTTTACTCTTTACGG
1 ATTTTACTCTTTACGG
*
3829 ATTTTACTCTTTACTG
1 ATTTTACTCTTTACGG
3845 ATT
1 ATT
3848 ACCTTCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (16 bp):
ATTTTACTCTTTACGG
Found at i:3863 original size:22 final size:22
Alignment explanation
Indices: 3829--3964 Score: 143
Period size: 22 Copynumber: 6.0 Consensus size: 22
3819 CTCTTTACGG
*
3829 ATTTTACTCTTTACTGATTACC
1 ATTTTACTTTTTACTGATTACC
3851 -TTCTTACTTTTTACTGATTACC
1 ATT-TTACTTTTTACTGATTACC
3873 ATTTTACTCTTTTACTGATTACC
1 ATTTTACT-TTTTACTGATTACC
3896 ATTTTACTCTTTTTTACTGATTACTC
1 ATTTTA--C-TTTTTACTGATTAC-C
* *
3922 -TTTTACTTCTTACTGATTACT
1 ATTTTACTTTTTACTGATTACC
* * *
3943 ATTTGAC-TCTTACTAATTACC
1 ATTTTACTTTTTACTGATTACC
3964 A
1 A
3965 CTTTGCTCTC
Statistics
Matches: 100, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
21 15 0.15
22 41 0.41
23 23 0.23
25 19 0.19
26 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.52
Consensus pattern (22 bp):
ATTTTACTTTTTACTGATTACC
Found at i:3863 original size:45 final size:46
Alignment explanation
Indices: 3814--3953 Score: 137
Period size: 45 Copynumber: 3.0 Consensus size: 46
3804 TTGATTATTA
* *
3814 TTTTACTCTTTACGGATTTTACTC-TTTACTGATTACC-TTCTTACT-
1 TTTTACTCATTAC-CATTTTACTCTTTTACTGATTACCATT-TTACTC
*
3859 TTTTACTGATTACCATTTTACTCTTTTACTGATTACCATTTTACTC
1 TTTTACTCATTACCATTTTACTCTTTTACTGATTACCATTTTACTC
* * * *
3905 TTTTTTACTGATTACTC-TTTTACT-TCTTACTGATTACTATTTGACTC
1 --TTTTACTCATTAC-CATTTTACTCTTTTACTGATTACCATTTTACTC
3952 TT
1 TT
3954 ACTAATTACC
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
44 9 0.11
45 31 0.37
46 2 0.02
47 20 0.24
48 20 0.24
49 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.54
Consensus pattern (46 bp):
TTTTACTCATTACCATTTTACTCTTTTACTGATTACCATTTTACTC
Found at i:4068 original size:22 final size:21
Alignment explanation
Indices: 4042--4089 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
4032 ATGGTTGTCT
4042 TTTACTGATTACTAATTTACTC
1 TTTACTGATTA-TAATTTACTC
**
4064 TTTACTGATTATTCTTTACTC
1 TTTACTGATTATAATTTACTC
4085 TTTAC
1 TTTAC
4090 CATTTTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.23, C:0.19, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTACTGATTATAATTTACTC
Found at i:4104 original size:21 final size:21
Alignment explanation
Indices: 4057--4100 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4047 TGATTACTAA
*
4057 TTTACTCTTTACTGATTATTC
1 TTTACTCTTTACTCATTATTC
*
4078 TTTACTCTTTAC-CATTTTTC
1 TTTACTCTTTACTCATTATTC
4098 TTT
1 TTT
4101 TACTAATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTACTCTTTACTCATTATTC
Found at i:4276 original size:31 final size:31
Alignment explanation
Indices: 4222--4287 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
4212 AATTACTGAT
4222 TTACTGATTACTATTTTTACCTTGACTCTTAA
1 TTACTGATTAC-ATTTTTACCTTGACTCTTAA
4254 TTACTGATTA-ATTTCTTACCTTGACTCTTAA
1 TTACTGATTACATTT-TTACCTTGACTCTTAA
4285 TTA
1 TTA
4288 TCAATTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 4 0.12
31 19 0.58
32 10 0.30
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (31 bp):
TTACTGATTACATTTTTACCTTGACTCTTAA
Found at i:4357 original size:55 final size:53
Alignment explanation
Indices: 4297--4429 Score: 136
Period size: 47 Copynumber: 2.5 Consensus size: 53
4287 ATCAATTTAC
*
4297 TGATTACTATGTTTTTACTTGATTACTGATTTACTGATTACCATCACTTTGACTT
1 TGATTA-TAT-TTTTTACTTGATTACTGATTTACTGATCACCATCACTTTGACTT
* *
4352 TGATTA-A---TCT-CTT-TTTACTGATTTACTGATCACCATCACTTTGACTT
1 TGATTATATTTTTTACTTGATTACTGATTTACTGATCACCATCACTTTGACTT
*
4399 TGATTAATCTCTTTTTAC-TGATTTACTGATT
1 TGATT-ATAT-TTTTTACTTGA-TTACTGATT
4430 ACCATCACCT
Statistics
Matches: 63, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
47 37 0.59
48 4 0.06
49 2 0.03
53 4 0.06
54 1 0.02
55 15 0.24
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (53 bp):
TGATTATATTTTTTACTTGATTACTGATTTACTGATCACCATCACTTTGACTT
Found at i:4388 original size:47 final size:47
Alignment explanation
Indices: 4319--4478 Score: 268
Period size: 47 Copynumber: 3.4 Consensus size: 47
4309 TTTTACTTGA
4319 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
*
4366 TTACTGATTTACTGATCACCATCACTTTGACTTTGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
* * * *
4413 TTACTGATTTACTGATTACCATCACCTTGACTCTGTTTAAGCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
4460 TTACTGA-TTACTGATTACC
1 TTACTGATTTACTGATTACC
4479 CCTTTTTACT
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
46 12 0.11
47 95 0.89
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.46
Consensus pattern (47 bp):
TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
Found at i:5471 original size:99 final size:99
Alignment explanation
Indices: 5320--5599 Score: 284
Period size: 99 Copynumber: 2.8 Consensus size: 99
5310 GTTATATCTC
* * * * *
5320 TATTTACTAATTACTCTAAAAA-TCAATCATTT-GCTCAAAGGTGACATCTTTACTTACTAATCA
1 TATTCACTAATTACT-TAAAAATTCAATCTTTTACCT-AGAGATGACATCTTTACTTACTAATCA
* * *
5383 TTAAAAGTTTCCATCTTTTACCCAAAGATGACATTTT
64 CTAAAA-ATTCAATCTTTTACCCAAAGATGACATTTT
* * *
5420 TACTT-ACTAATTAC-TAAAAGTTCAATCTTTTACCTAGAGATGACATTTTTACTTACTAATTAC
1 TA-TTCACTAATTACTTAAAAATTCAATCTTTTACCTAGAGATGACATCTTTACTTACTAATCAC
* **
5483 TAAAAATTCAATCTTTTACCCAAAGGTTTCATTTT
65 TAAAAATTCAATCTTTTACCCAAAGATGACATTTT
* * * * *
5518 TATTCACTAATTACTTAAAAATTCAATCTTTTA-TTTGAAGGTTG-CATCTTTATTTACTAATTA
1 TATTCACTAATTACTTAAAAATTCAATCTTTTACCTAG-A-GATGACATCTTTACTTACTAATCA
5581 CTTAAAAATTCAATCTTTT
64 C-TAAAAATTCAATCTTTT
5600 GTTCAAAGGT
Statistics
Matches: 153, Mismatches: 19, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
97 2 0.01
98 43 0.28
99 73 0.48
100 33 0.22
101 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (99 bp):
TATTCACTAATTACTTAAAAATTCAATCTTTTACCTAGAGATGACATCTTTACTTACTAATCACT
AAAAATTCAATCTTTTACCCAAAGATGACATTTT
Found at i:5620 original size:50 final size:50
Alignment explanation
Indices: 5266--5620 Score: 306
Period size: 50 Copynumber: 7.1 Consensus size: 50
5256 GGATGTCATC
* * * * * * *
5266 TTTATTCACTAATTATTTGTAAAAATCCAATCTTTTATTCAAAAGTTATATC
1 TTTATTTACTAATTA-CT-TAAAAATTCAATCTTTTACTCAAAGGTTACATT
* * * * *
5318 TCTATTTACTAATTACTCTAAAAA-TCAATCATTTGCTCAAAGGTGACATC
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTACTCAAAGGTTACATT
* * * * * * *
5368 TTTACTTACTAATCA-TTAAAAGTTTCCATCTTTTACCCAAAGATGACATT
1 TTTATTTACTAATTACTTAAAA-ATTCAATCTTTTACTCAAAGGTTACATT
* * * * *
5418 TTTACTTACTAATTAC-TAAAAGTTCAATCTTTTAC-CTAGAGATGACATT
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTACTC-AAAGGTTACATT
* * *
5467 TTTACTTACTAATTAC-TAAAAATTCAATCTTTTACCCAAAGGTTTCATT
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTACTCAAAGGTTACATT
* * ** * *
5516 TTTATTCACTAATTACTTAAAAATTCAATCTTTTATTTGAAGGTTGCATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTACTCAAAGGTTACATT
** *
5566 TTTATTTACTAATTACTTAAAAATTCAATCTTTTGTTCAAAGGTTAAATT
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTACTCAAAGGTTACATT
5616 TTTAT
1 TTTAT
5621 GCTAAAAAAA
Statistics
Matches: 252, Mismatches: 45, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
48 6 0.02
49 80 0.32
50 146 0.58
51 7 0.03
52 13 0.05
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (50 bp):
TTTATTTACTAATTACTTAAAAATTCAATCTTTTACTCAAAGGTTACATT
Found at i:7867 original size:55 final size:54
Alignment explanation
Indices: 7792--7917 Score: 198
Period size: 55 Copynumber: 2.3 Consensus size: 54
7782 TTTTCTTCCC
* * *
7792 TTTTATTATTGGTATTTTTGTAAACCCAAATGCATTAGTGTACTTATGAAGGAT
1 TTTTACTATTGGTATTTTTGTAAACACAAATGCAATAGTGTACTTATGAAGGAT
* *
7846 TTTTACTATTGAGTATTTTTGTATACACAAATGCAATAGTGTACTTATTAAGGAT
1 TTTTACTATTG-GTATTTTTGTAAACACAAATGCAATAGTGTACTTATGAAGGAT
7901 TTTTACTATTGGTATTT
1 TTTTACTATTGGTATTT
7918 AATCTTTTTG
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 16 0.24
55 50 0.76
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (54 bp):
TTTTACTATTGGTATTTTTGTAAACACAAATGCAATAGTGTACTTATGAAGGAT
Found at i:8393 original size:27 final size:27
Alignment explanation
Indices: 8333--8439 Score: 133
Period size: 27 Copynumber: 3.9 Consensus size: 27
8323 TGATCTTTAA
* * *
8333 AAAAATGACTAAAATGCCCTCCTGAGTGC
1 AAAAATGACCAAAAT-ACC-CCTGGGTGC
*
8362 AAAAATGACCGAAATACCCCTGGGTGC
1 AAAAATGACCAAAATACCCCTGGGTGC
* *
8389 GAAAATGACCAAAATGCCCCTGGGTGC
1 AAAAATGACCAAAATACCCCTGGGTGC
*
8416 AAAAATGACCAAAATACCCTTGGG
1 AAAAATGACCAAAATACCCCTGGG
8440 CGACTCTAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 53 0.78
28 2 0.03
29 13 0.19
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (27 bp):
AAAAATGACCAAAATACCCCTGGGTGC
Found at i:8431 original size:54 final size:56
Alignment explanation
Indices: 8334--8439 Score: 162
Period size: 54 Copynumber: 1.9 Consensus size: 56
8324 GATCTTTAAA
* *
8334 AAAATGACTAAAATGCCCTCCTGAGTGCAAAAATGACCGAAATACCCCTGGGTGCG
1 AAAATGACCAAAATGCCCTCCTGAGTGCAAAAATGACCAAAATACCCCTGGGTGCG
* *
8390 AAAATGACCAAAATG-CC-CCTGGGTGCAAAAATGACCAAAATACCCTTGGG
1 AAAATGACCAAAATGCCCTCCTGAGTGCAAAAATGACCAAAATACCCCTGGG
8440 CGACTCTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 30 0.65
55 2 0.04
56 14 0.30
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (56 bp):
AAAATGACCAAAATGCCCTCCTGAGTGCAAAAATGACCAAAATACCCCTGGGTGCG
Done.