Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015956.1 Corchorus capsularis cultivar CVL-1 contig15977, 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: 52933
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Found at i:4866 original size:18 final size:18
Alignment explanation
Indices: 4843--4880 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4833 AATCACAGTA
4843 GTTGTTATCACCAAATAT
1 GTTGTTATCACCAAATAT
4861 GTTGTTATCACCAAATAT
1 GTTGTTATCACCAAATAT
4879 GT
1 GT
4881 AATGAATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (18 bp):
GTTGTTATCACCAAATAT
Found at i:6433 original size:214 final size:214
Alignment explanation
Indices: 6006--6499 Score: 600
Period size: 214 Copynumber: 2.3 Consensus size: 214
5996 TGAAAAATGT
* * * *
6006 TATAAATGTCGGAGAAGTCTGTCCTAAAGCGACGTTTGTTAAAAAAAAGTCGCATGATTGTGAAC
1 TATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTT-AAAAAATGTCGCATGA-T-TGAAC
** * * ***
6071 GGGGTTTGAGAAAACGTCTCTATAAACGTCGCAAAAACATAAACTAGAGCGACGTTATTAAAAAA
63 GACGTTTGAGAAAACATCTCTATAAACGTCGCAAAAACATAAACAAGAGCGACACAATTAAAAAA
* * * * *
6136 CGTTACTCAATTTAAAAAAGTGTCGCAAGGTGATGCGACGTTTATTAAAATGTCATATATTAAAA
128 CGTCACTCAATTTAAAAAAGAGTCGCAAGATGATACGACGTTTATTAAAATGTAATATATTAAAA
* *
6201 CGACGTTTCTAAAAAACGTCGC
193 CGACGTTTCCAAAAAACGTCAC
* * *
6223 TATAATTGTTGGAAAAGTCTATCTTAAAGCGACGTTTGTTAAAAAATGTCACATGATTGAACGAC
1 TATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTAAAAAATGTCGCATGATTGAACGAC
**
6288 GTTTGAGAAAACATCTCT-TCAAACGTCGCAAAAGTATAAACAAGAGCGACACAATTAAAAAACG
66 GTTTGAGAAAACATCTCTAT-AAACGTCGCAAAAACATAAACAAGAGCGACACAATTAAAAAACG
** *
6352 TCACTCAAATTTAAAAAAGAGTCGCAAGATTTTAC-AGCGTTTATTAAAATGTAATTTATT-AAA
130 TCACTC-AATTTAAAAAAGAGTCGCAAGATGATACGA-CGTTTATTAAAATGTAATATATTAAAA
* ** ** * *
6415 TGTTGTTTCCCTAAAACGTTAT
193 CGACGTTTCCAAAAAACGTCAC
*
6437 TATAAATGTCGGAAAAGTCTATCTTAAAGCGAGGTTTGTT-AAAAATGTCGCATGATTGAACGA
1 TATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTAAAAAATGTCGCATGATTGAACGA
6500 TGTTAGGAAA
Statistics
Matches: 237, Mismatches: 37, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
213 23 0.10
214 120 0.51
215 45 0.19
216 14 0.06
217 35 0.15
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (214 bp):
TATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTAAAAAATGTCGCATGATTGAACGAC
GTTTGAGAAAACATCTCTATAAACGTCGCAAAAACATAAACAAGAGCGACACAATTAAAAAACGT
CACTCAATTTAAAAAAGAGTCGCAAGATGATACGACGTTTATTAAAATGTAATATATTAAAACGA
CGTTTCCAAAAAACGTCAC
Found at i:7703 original size:11 final size:11
Alignment explanation
Indices: 7687--7711 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
7677 TTTGGGACTG
7687 AATGAAGAGGT
1 AATGAAGAGGT
7698 AATGAAGAGGT
1 AATGAAGAGGT
7709 AAT
1 AAT
7712 TGATAACTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (11 bp):
AATGAAGAGGT
Found at i:7845 original size:24 final size:25
Alignment explanation
Indices: 7818--7865 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
7808 TGACATCCTA
*
7818 AAAATAAATAAACAAGA-AAATAAT
1 AAAATAAAGAAACAAGATAAATAAT
* *
7842 AAAATTAAGCAACAAGATAAATAA
1 AAAATAAAGAAACAAGATAAATAA
7866 ATACTCCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (25 bp):
AAAATAAAGAAACAAGATAAATAAT
Found at i:9188 original size:13 final size:13
Alignment explanation
Indices: 9170--9194 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9160 CAGCTTTGAA
9170 CATGTGGATTATT
1 CATGTGGATTATT
9183 CATGTGGATTAT
1 CATGTGGATTAT
9195 CAAACATAAA
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:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (13 bp):
CATGTGGATTATT
Found at i:11487 original size:38 final size:38
Alignment explanation
Indices: 11374--11601 Score: 272
Period size: 38 Copynumber: 6.1 Consensus size: 38
11364 AAAATGCCTT
*
11374 TTGATGGGATCTTTCCCTAAATTGAAAACTTTAAAAAAAAC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTT---GAAAAC
* *
11415 TAGATGGGATCTTTCCCTAAATT-CAAA-----AAAAC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAC
* * * *
11447 TTGGTGGGATCTTTCCCTAAACTAAAAACTTTGAAGAC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAC
* *
11485 TTGATGGGATCTTTCCTTAAATTGAAAACTTTGGAAAC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAC
*
11523 TAGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAC
* *
11561 TGGATGGGAT-TTTTCCTAAATTGAAAACTTTGAAAAC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAC
11598 TTGA
1 TTGA
11602 CTCCTGATTT
Statistics
Matches: 162, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
32 25 0.15
33 3 0.02
37 29 0.18
38 80 0.49
40 3 0.02
41 22 0.14
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (38 bp):
TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAC
Found at i:13123 original size:17 final size:17
Alignment explanation
Indices: 13101--13133 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
13091 TTTTTTTGAG
13101 ATCACCAAGATTACTTT
1 ATCACCAAGATTACTTT
13118 ATCACCAAGATTACTT
1 ATCACCAAGATTACTT
13134 ATTTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (17 bp):
ATCACCAAGATTACTTT
Found at i:15559 original size:62 final size:60
Alignment explanation
Indices: 15400--15656 Score: 285
Period size: 58 Copynumber: 4.3 Consensus size: 60
15390 CATCCTTTGA
* * * *
15400 CTTTCAGGAATTGTCTTCAGATCCAT-GT-ATGAACTGTCTTCAGTCTCACTCTTAAAAT
1 CTTTTAGGAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTCAGTCTCACTCTTAAAAT
* * * * *
15458 CATTCAGGAACTGTCTTCAGATCCATCATCGTGAACTGTCTTTAGAT-TCACTCTTAAATAC
1 CTTTTAGGAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTCAG-TCTCACTCTTAAA-AT
* *
15519 CTTTTGGGAACTGTCTTCAGAACCCATCTTCGTGAACTGTCTTCAGAT-TCACTCTTAAAAT
1 CTTTTAGGAACTGTCTTCAG-ATCCATCTTCGTGAACTGTCTTCAG-TCTCACTCTTAAAAT
* * * * *
15580 CTTTT-GGAACTATCTTCAGATCCAT-TT-GTGAGCTGTCTTCAGTCTCAATTTTCAAAT
1 CTTTTAGGAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTCAGTCTCACTCTTAAAAT
15637 CTTTTAGGAACTGTCTTCAG
1 CTTTTAGGAACTGTCTTCAG
15657 CCTCACTCTT
Statistics
Matches: 172, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
56 1 0.01
57 29 0.17
58 39 0.23
59 6 0.03
60 37 0.22
61 25 0.15
62 35 0.20
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (60 bp):
CTTTTAGGAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTCAGTCTCACTCTTAAAAT
Found at i:15672 original size:35 final size:35
Alignment explanation
Indices: 15612--15691 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
15602 CATTTGTGAG
* * * * *
15612 CTGTCTTCAGTCTCAATTTTCAAATCTTTTAGGAA
1 CTGTCTTCAGCCTCAATCTTAAAATCTTTCAAGAA
*
15647 CTGTCTTCAGCCTCACTCTTAAAATCTTTCAAGAA
1 CTGTCTTCAGCCTCAATCTTAAAATCTTTCAAGAA
15682 CTGTCTTCAG
1 CTGTCTTCAG
15692 ATCCATCTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (35 bp):
CTGTCTTCAGCCTCAATCTTAAAATCTTTCAAGAA
Found at i:15710 original size:93 final size:92
Alignment explanation
Indices: 15552--15750 Score: 335
Period size: 93 Copynumber: 2.2 Consensus size: 92
15542 CCATCTTCGT
* ** *
15552 GAACTGTCTTCAGATTCACTCTTAAAATCTTTTGGAACTATCTTCAGATCCATTTGTGAGCTGTC
1 GAACTGTCTTCAGACTCACTCTTAAAATCTTTAAGAACTATCTTCAGATCCATCTGTGAGCTGTC
15617 TTCAGTCTCAATTTTCAAATCTTTTAG
66 TTCAGTCTCAATTTTCAAATCTTTTAG
* *
15644 GAACTGTCTTCAGCCTCACTCTTAAAATCTTTCAAGAACTGTCTTCAGATCCATCTGTGAGCTGT
1 GAACTGTCTTCAGACTCACTCTTAAAATCTTT-AAGAACTATCTTCAGATCCATCTGTGAGCTGT
15709 CTTCAGTCTCAATTTTCAAATCTTTTAG
65 CTTCAGTCTCAATTTTCAAATCTTTTAG
15737 GAACTGTCTTCAGA
1 GAACTGTCTTCAGA
15751 TCCATCTGTG
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
92 30 0.30
93 69 0.70
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.39
Consensus pattern (92 bp):
GAACTGTCTTCAGACTCACTCTTAAAATCTTTAAGAACTATCTTCAGATCCATCTGTGAGCTGTC
TTCAGTCTCAATTTTCAAATCTTTTAG
Found at i:15741 original size:58 final size:58
Alignment explanation
Indices: 15647--15841 Score: 318
Period size: 58 Copynumber: 3.4 Consensus size: 58
15637 CTTTTAGGAA
* *
15647 CTGTCTTCAGCCTCACTCTTAAAATCTTTCAAGAACTGTCTTCAGATCCATCTGTGAG
1 CTGTCTTCAGCCTCAATCTTAAAATCTTTCAGGAACTGTCTTCAGATCCATCTGTGAG
* * * *
15705 CTGTCTTCAGTCTCAATTTTCAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAG
1 CTGTCTTCAGCCTCAATCTTAAAATCTTTCAGGAACTGTCTTCAGATCCATCTGTGAG
*
15763 CTGTCTTCAGCCTCAATCTTAAAATCTTTCAGGAACTGTCTTCAGATCTATCTGTGAG
1 CTGTCTTCAGCCTCAATCTTAAAATCTTTCAGGAACTGTCTTCAGATCCATCTGTGAG
*
15821 CTGTCTTCAGTCTCAATCTTA
1 CTGTCTTCAGCCTCAATCTTA
15842 GAAGGATCGT
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 125 1.00
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.37
Consensus pattern (58 bp):
CTGTCTTCAGCCTCAATCTTAAAATCTTTCAGGAACTGTCTTCAGATCCATCTGTGAG
Found at i:15767 original size:151 final size:154
Alignment explanation
Indices: 15490--15808 Score: 423
Period size: 151 Copynumber: 2.1 Consensus size: 154
15480 CCATCATCGT
* * ***
15490 GAACTGTCTTTAGATTCACTCTTAAATACCTTTTGGGAACTGTCTTCAGAACCCATCTTCGTGAA
1 GAACTGTCTTCAGACTCACTCTTAAATACCTTTCAAGAACTGTCTTCAGAACCCATCTTCGTGAA
* *
15555 CTGTCTTCAGATTCACTCTTAAAATCTTTTGGAACTATCTTCAGATCCATTTGTGAGCTGTCTTC
66 CTGTCTTCAGATTCAATCTTAAAATCTTTTGGAACTATCTTCAGATCCATCTGTGAGCTGTCTTC
* * * *
15620 AGTCTCAATTTTCAAATCTTTTAG
131 AGCCTCAATCTTAAAATCTTTCAG
* * * *
15644 GAACTGTCTTCAGCCTCACTCTTAAA-ATCTTTCAAGAACTGTCTTCAG-ATCCATC-T-GTGAG
1 GAACTGTCTTCAGACTCACTCTTAAATACCTTTCAAGAACTGTCTTCAGAACCCATCTTCGTGAA
* * *
15705 CTGTCTTCAG-TCTCAATTTTCAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCT
66 CTGTCTTCAGAT-TCAATCTTAAAATCTTTT-GGAACTATCTTCAGATCCATCTGTGAGCTGTCT
15769 TCAGCCTCAATCTTAAAATCTTTCAG
129 TCAGCCTCAATCTTAAAATCTTTCAG
15795 GAACTGTCTTCAGA
1 GAACTGTCTTCAGA
15809 TCTATCTGTG
Statistics
Matches: 144, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
149 1 0.01
150 29 0.20
151 67 0.47
152 6 0.04
153 18 0.12
154 23 0.16
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.38
Consensus pattern (154 bp):
GAACTGTCTTCAGACTCACTCTTAAATACCTTTCAAGAACTGTCTTCAGAACCCATCTTCGTGAA
CTGTCTTCAGATTCAATCTTAAAATCTTTTGGAACTATCTTCAGATCCATCTGTGAGCTGTCTTC
AGCCTCAATCTTAAAATCTTTCAG
Found at i:15887 original size:85 final size:86
Alignment explanation
Indices: 15781--16013 Score: 332
Period size: 85 Copynumber: 2.7 Consensus size: 86
15771 AGCCTCAATC
* * ** * *
15781 TTAAAATCTTTCAGGAACTGTCTTCAGA-TCTATCTGTGAGCTGTCTTCAGTCTCAAT-CTTAGA
1 TTAAAATCTTTCATGATCTGTCTTCAGATTC-ATCCATGAGCTGTCTTCAGACTCAATACTTAAA
*
15844 AGGATCGTCTTCGATCCATCAT
65 AGGATCGTCTACGATCCATCAT
15866 TTAAAATCTTTCATGATCTGTCTTCAGATTCATCCATGAGCTGTCTTCAGACTC-ATACTTAAAA
1 TTAAAATCTTTCATGATCTGTCTTCAGATTCATCCATGAGCTGTCTTCAGACTCAATACTTAAAA
15930 GGATCGTCTACGATCCATCAT
66 GGATCGTCTACGATCCATCAT
* *
15951 TCAAAATCTTTTC-TGATCTGTCTTCATATTCATCCATGAGCTGTCTTCAGACTC-ATACTTAAA
1 TTAAAATC-TTTCATGATCTGTCTTCAGATTCATCCATGAGCTGTCTTCAGACTCAATACTTAAA
16014 TTTCTTTCAG
Statistics
Matches: 136, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
84 2 0.01
85 128 0.94
86 6 0.04
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (86 bp):
TTAAAATCTTTCATGATCTGTCTTCAGATTCATCCATGAGCTGTCTTCAGACTCAATACTTAAAA
GGATCGTCTACGATCCATCAT
Found at i:15903 original size:23 final size:23
Alignment explanation
Indices: 15877--15921 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
15867 TAAAATCTTT
* *
15877 CATGATCTGTCTTCAGATTCATC
1 CATGAGCTGTCTTCAGACTCATC
15900 CATGAGCTGTCTTCAGACTCAT
1 CATGAGCTGTCTTCAGACTCAT
15922 ACTTAAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.36
Consensus pattern (23 bp):
CATGAGCTGTCTTCAGACTCATC
Found at i:16458 original size:64 final size:65
Alignment explanation
Indices: 16336--16458 Score: 171
Period size: 65 Copynumber: 1.9 Consensus size: 65
16326 CTGGTGCTTC
* *
16336 TTTTAACAAGATCGTCTTCCAGTCAACTTCTCAAACATTTTCGAGAAACTATCTTCTGGTATACT
1 TTTTAAAAAGATCGTCTTCCAGTCAACTTCTCAAACATTTTCGAGAAACCATCTTCTGGTATACT
* *
16401 TTTTAAAAAGATCGTCTTCC-GATCAACTTCTGACA-ATTATT-GAGAAACCATCTTCTGG
1 TTTTAAAAAGATCGTCTTCCAG-TCAACTTCTCAAACATT-TTCGAGAAACCATCTTCTGG
16459 ATTATCTTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
64 20 0.38
65 32 0.62
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (65 bp):
TTTTAAAAAGATCGTCTTCCAGTCAACTTCTCAAACATTTTCGAGAAACCATCTTCTGGTATACT
Found at i:18276 original size:14 final size:14
Alignment explanation
Indices: 18259--18325 Score: 75
Period size: 14 Copynumber: 4.8 Consensus size: 14
18249 TTAGGTCCAG
18259 TTTTTTTCTTTCTC
1 TTTTTTTCTTTCTC
*
18273 TTTTTTTTTTTCTC
1 TTTTTTTCTTTCTC
* *
18287 TTTTTCT-TTTCTT
1 TTTTTTTCTTTCTC
18300 TTTCTTTTCTTTCT-
1 TTT-TTTTCTTTCTC
18314 TCTTTTTTCTTT
1 T-TTTTTTCTTT
18326 GAATTGAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
13 8 0.17
14 31 0.67
15 7 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTTCTTTCTC
Found at i:18290 original size:11 final size:11
Alignment explanation
Indices: 18262--18319 Score: 75
Period size: 11 Copynumber: 5.4 Consensus size: 11
18252 GGTCCAGTTT
*
18262 TTTTCTTTCTC
1 TTTTCTTTTTC
18273 TTTT-TTTTT-
1 TTTTCTTTTTC
*
18282 TTCTCTTTTTC
1 TTTTCTTTTTC
18293 TTTTCTTTTTC
1 TTTTCTTTTTC
18304 TTTTCTTTCTTC
1 TTTTCTTT-TTC
18316 TTTT
1 TTTT
18320 TTCTTTGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
9 3 0.07
10 9 0.22
11 22 0.54
12 7 0.17
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:18297 original size:31 final size:30
Alignment explanation
Indices: 18262--18325 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
18252 GGTCCAGTTT
* *
18262 TTTTCTTTCTCTTTTTTTTTTTCTCTTTTTC
1 TTTTCTTTCTCTTTTCTTTCTTCT-TTTTTC
*
18293 TTTTCTTTTTCTTTTCTTTCTTCTTTTTTC
1 TTTTCTTTCTCTTTTCTTTCTTCTTTTTTC
18323 TTT
1 TTT
18326 GAATTGAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (30 bp):
TTTTCTTTCTCTTTTCTTTCTTCTTTTTTC
Found at i:21846 original size:38 final size:38
Alignment explanation
Indices: 21795--21954 Score: 275
Period size: 38 Copynumber: 4.2 Consensus size: 38
21785 TAAATTGAAA
* *
21795 AAAACTTGGTGGGATCTTTCCCTAAACTGAAAACTTTG
1 AAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
21833 AAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
1 AAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
* *
21871 GAAACTGGATGGGATCTTTCCCTAAATTGAAAACTTTG
1 AAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
*
21909 AAAACTGGATGGGATCTTTCCCTAAATTGAAAACTTTG
1 AAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
21947 AAAACTTG
1 AAAACTTG
21955 GCTCCTGATA
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 116 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (38 bp):
AAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
Found at i:21893 original size:76 final size:74
Alignment explanation
Indices: 21768--21949 Score: 275
Period size: 76 Copynumber: 2.5 Consensus size: 74
21758 AAAATGCCTT
*
21768 TTGATGGGATCATTCCCTAAATTGAAAA-----AAACTTGGTGGGATCTTTCCCTAAACTGAAAA
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAC-TGGTGGGATCTTTCCCTAAACTGAAAA
21828 CTTTGAAAAC
65 CTTTGAAAAC
*
21838 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGGAAACTGGATGGGATCTTTCCCTAAATTGAAA
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTT-GAAACTGG-TGGGATCTTTCCCTAAACTGAAA
21903 ACTTTGAAAAC
64 ACTTTGAAAAC
*
21914 TGGATGGGATCTTTCCCTAAATTGAAAACTTTGAAA
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAA
21950 ACTTGGCTCC
Statistics
Matches: 102, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
70 27 0.26
75 7 0.07
76 68 0.67
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (74 bp):
TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAACTGGTGGGATCTTTCCCTAAACTGAAAAC
TTTGAAAAC
Found at i:23609 original size:34 final size:34
Alignment explanation
Indices: 23564--23629 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
23554 AAATAAAAAC
*
23564 AAATCAAGCCCA-TATAACAGTAAATAAACAGAAA
1 AAATCAAGCCCACTAAAACA-TAAATAAACAGAAA
* *
23598 AAATGAAGCCCACTAAAACATAAATAATCAGA
1 AAATCAAGCCCACTAAAACATAAATAAACAGA
23630 GAAGTCCGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 22 0.79
35 6 0.21
ACGTcount: A:0.58, C:0.18, G:0.09, T:0.15
Consensus pattern (34 bp):
AAATCAAGCCCACTAAAACATAAATAAACAGAAA
Found at i:32332 original size:68 final size:68
Alignment explanation
Indices: 32223--32358 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 68
32213 AGGAGATTAA
* * * *
32223 GAAAGTTGATCCGTGCTTTTGGGAGGGTAGTACTGTAGTAGCTCAGATTAAGGAATTTGCGGCTT
1 GAAAGTTGATCCATGCTTTTGGGAGGATAGTACTCTAGTAGCTAAGATTAAGGAATTTGCGGCTT
32288 TTT
66 TTT
*
32291 GAAAGTTGATCCATGCTTTTGGGAGGATAGTACTCTAGTAGCTAAGATTAAGGAATTTGTGGCTT
1 GAAAGTTGATCCATGCTTTTGGGAGGATAGTACTCTAGTAGCTAAGATTAAGGAATTTGCGGCTT
32356 TTT
66 TTT
32359 CCGTTTTATT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.24, C:0.11, G:0.29, T:0.36
Consensus pattern (68 bp):
GAAAGTTGATCCATGCTTTTGGGAGGATAGTACTCTAGTAGCTAAGATTAAGGAATTTGCGGCTT
TTT
Found at i:52256 original size:30 final size:29
Alignment explanation
Indices: 52193--52270 Score: 111
Period size: 30 Copynumber: 2.7 Consensus size: 29
52183 CTTTGTAACC
* *
52193 TTTGGACGTTTTACCCCCTGAACTTCAAT
1 TTTGGACATTTTACCCCCTAAACTTCAAT
* *
52222 TTTGGACATTTTGCCCCCTAAACTCTCGAT
1 TTTGGACATTTTACCCCCTAAACT-TCAAT
52252 TTTGGACATTTTACCCCCT
1 TTTGGACATTTTACCCCCT
52271 CTCAAACGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 21 0.49
30 22 0.51
ACGTcount: A:0.19, C:0.29, G:0.13, T:0.38
Consensus pattern (29 bp):
TTTGGACATTTTACCCCCTAAACTTCAAT
Found at i:52398 original size:30 final size:29
Alignment explanation
Indices: 52351--52408 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
52341 ATCGTTTAAG
52351 AGGGGGCAAAACTTCCAAAATTGAGAGTTC
1 AGGGGGCAAAACTTCCAAAATTGA-AGTTC
* *
52381 AGGGGGTAAAA-TATCCAACATTGAAGTT
1 AGGGGGCAAAACT-TCCAAAATTGAAGTT
52409 TAGAGGCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (29 bp):
AGGGGGCAAAACTTCCAAAATTGAAGTTC
Done.