Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016214.1 Corchorus capsularis cultivar CVL-1 contig16235, 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: 11728
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:2970 original size:90 final size:90
Alignment explanation
Indices: 2650--3155 Score: 730
Period size: 90 Copynumber: 5.6 Consensus size: 90
2640 CCCAGAATCT
* * * *
2650 CAACTTGATTCATCGAATCATCCTGAACTGTTTGAAAATCTGCTGCACCGAGCTCACCGAATC-C
1 CAACTTGATTCACCGAATGATCTTGAACTGTTTGAAAATCTGCTGCACCGAGCTCACCGAATCTG
* * *
2714 AATCTTGAAGAAATAAGGCACCGCCT
66 ACT-TTGAAGAAGTAAGGCACCGCCC
* * * * * *
2740 TAACTTGATTCACCGAATCATCCT-AACTATTTGAAAATCTGCTGCACCAAGCTCACTGAATCTG
1 CAACTTGATTCACCGAATGATCTTGAACTGTTTGAAAATCTGCTGCACCGAGCTCACCGAATCTG
2804 ACTTTGAAGAAGTAAGGCACCG-CC
66 ACTTTGAAGAAGTAAGGCACCGCCC
* *
2828 CAACTTGATTCACCGAATGTTCTTGAACTGTTTGAAAATCTGCTGCATCGAGCTCACCGAATCTG
1 CAACTTGATTCACCGAATGATCTTGAACTGTTTGAAAATCTGCTGCACCGAGCTCACCGAATCTG
2893 ACTTTGAAGAAGTAAGGCACCGCCC
66 ACTTTGAAGAAGTAAGGCACCGCCC
*
2918 CAACTTGATTCACCGAATGATCTTGAACTGTTTGAAAATCTGCTACACCGAGCTCACCGAATCTG
1 CAACTTGATTCACCGAATGATCTTGAACTGTTTGAAAATCTGCTGCACCGAGCTCACCGAATCTG
2983 ACTTTGAAGAAGTAAGGCACCGCCC
66 ACTTTGAAGAAGTAAGGCACCGCCC
* *
3008 CAACTTGATTCATCGAATGTTCTTGAACTGTTTGAAAATCTGCTGCACCGAGCTCACCGAATCTG
1 CAACTTGATTCACCGAATGATCTTGAACTGTTTGAAAATCTGCTGCACCGAGCTCACCGAATCTG
3073 ACTTTGAAGAAGTAAGGCACCGCCC
66 ACTTTGAAGAAGTAAGGCACCGCCC
* * * * * * * * **
3098 CAGCTTGATTCACCTAATTACCATGATCTGTGTGAAAATTTATTGCACCGAGCTCACC
1 CAACTTGATTCACCGAATGATCTTGAACTGTTTGAAAATCTGCTGCACCGAGCTCACC
3156 ATATTCCAAT
Statistics
Matches: 378, Mismatches: 35, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
88 21 0.06
89 111 0.29
90 246 0.65
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (90 bp):
CAACTTGATTCACCGAATGATCTTGAACTGTTTGAAAATCTGCTGCACCGAGCTCACCGAATCTG
ACTTTGAAGAAGTAAGGCACCGCCC
Found at i:3467 original size:35 final size:35
Alignment explanation
Indices: 3295--3469 Score: 233
Period size: 35 Copynumber: 5.0 Consensus size: 35
3285 GTTCACCTAA
* * * * *
3295 TCCAACTTTGGAGATGCTTCACCGACTCATCTTAA
1 TCCAACTTTGAAGATGCTGCACCGAGTCATCTGAT
*
3330 TCCAACTTTGAAGATGCTGCACCGAGTCATCTGAA
1 TCCAACTTTGAAGATGCTGCACCGAGTCATCTGAT
* * * *
3365 ACCAACTTTGAAAATGCTCCACCGAGTCATCTAAT
1 TCCAACTTTGAAGATGCTGCACCGAGTCATCTGAT
3400 TCCAACTTTGAAGATGCTGCACCGAGTCATCTGAT
1 TCCAACTTTGAAGATGCTGCACCGAGTCATCTGAT
* **
3435 TCCAACTTTGAAGATGCTACACTAAGTCATCTGAT
1 TCCAACTTTGAAGATGCTGCACCGAGTCATCTGAT
3470 GCACTGAATC
Statistics
Matches: 124, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 124 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (35 bp):
TCCAACTTTGAAGATGCTGCACCGAGTCATCTGAT
Found at i:3589 original size:46 final size:46
Alignment explanation
Indices: 3500--3590 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
3490 ATACATAAAT
*
3500 CACTGGAAACTTCCTTGACTGACCGCACTGGTTCACTTAAAGATAC
1 CACTGGAAACTTCCTTGACTGACCGCACTGGATCACTTAAAGATAC
* * ** * *
3546 CACTGGAAACTTTCTTGATTGACCGTGCTGGATCATTTGAAGATA
1 CACTGGAAACTTCCTTGACTGACCGCACTGGATCACTTAAAGATA
3591 AACTCAATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (46 bp):
CACTGGAAACTTCCTTGACTGACCGCACTGGATCACTTAAAGATAC
Found at i:3629 original size:101 final size:104
Alignment explanation
Indices: 3471--3747 Score: 305
Period size: 110 Copynumber: 2.7 Consensus size: 104
3461 TCATCTGATG
* * * ** * * *
3471 CACTGAATCACTTGAAGACATACAT-AA-ATCACTGGAAACTTCCTTGACTGACCGCACTGGTTC
1 CACTGGATCACTTGAAGATAAAC-TCAATATCACTATAAACTTTCTTGATTGACCGCACTGGATC
*
3534 ACTTAAAGAT-A-C-CACTGGAAACTTTCTTGATTGACCG
65 ACTTAAAGATAACCACACTGGAAACTTTCTTGATTGACCA
** * *
3571 TGCTGGATCATTTGAAGATAAACTCAATATCACTATAAACTTTCTTGATTGACTGCACTGGATCA
1 CACTGGATCACTTGAAGATAAACTCAATATCACTATAAACTTTCTTGATTGACCGCACTGGATCA
* *
3636 CTTGAAGATAAACTCAATATCACTGTAAACTTTCTTGATTGACCA
66 CTTAAAGAT-AAC-C---A-CACTGGAAACTTTCTTGATTGACCA
*
3681 CACTGGATCACTTGAAGATAAACTCAATATCACTGTAAACTTTC-TGATTGACCGCACTGGATCA
1 CACTGGATCACTTGAAGATAAACTCAATATCACTATAAACTTTCTTGATTGACCGCACTGGATCA
3745 CTT
66 CTT
3748 GAAATTCGGC
Statistics
Matches: 146, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
99 1 0.01
100 19 0.13
101 39 0.27
103 1 0.01
105 1 0.01
109 22 0.15
110 63 0.43
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (104 bp):
CACTGGATCACTTGAAGATAAACTCAATATCACTATAAACTTTCTTGATTGACCGCACTGGATCA
CTTAAAGATAACCACACTGGAAACTTTCTTGATTGACCA
Found at i:3641 original size:55 final size:55
Alignment explanation
Indices: 3546--3750 Score: 340
Period size: 55 Copynumber: 3.7 Consensus size: 55
3536 TTAAAGATAC
* ** *
3546 CACTGGAAACTTTCTTGATTGACCGTGCTGGATCATTTGAAGATAAACTCAATAT
1 CACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTCAATAT
* *
3601 CACTATAAACTTTCTTGATTGACTGCACTGGATCACTTGAAGATAAACTCAATAT
1 CACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTCAATAT
*
3656 CACTGTAAACTTTCTTGATTGACCACACTGGATCACTTGAAGATAAACTCAATAT
1 CACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTCAATAT
3711 CACTGTAAACTTTC-TGATTGACCGCACTGGATCACTTGAA
1 CACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAA
3751 ATTCGGCTAA
Statistics
Matches: 140, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
54 25 0.18
55 115 0.82
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (55 bp):
CACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTCAATAT
Found at i:5201 original size:16 final size:17
Alignment explanation
Indices: 5162--5203 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5152 CTATTCTTTA
* *
5162 TTCCATCTTTTATCTCT
1 TTCCTTCTTTTATCACT
*
5179 TTTCTTCTTTT-TCACT
1 TTCCTTCTTTTATCACT
5195 TTCCTTCTT
1 TTCCTTCTT
5204 ACTTCTTTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (17 bp):
TTCCTTCTTTTATCACT
Found at i:6170 original size:14 final size:15
Alignment explanation
Indices: 6153--6188 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
6143 AAAACTCATT
*
6153 TTGAAAAC-CTTTTC
1 TTGAAAACAATTTTC
6167 TTGAAAACAATTTTC
1 TTGAAAACAATTTTC
6182 TTGAAAA
1 TTGAAAA
6189 ATATCTCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (15 bp):
TTGAAAACAATTTTC
Found at i:7478 original size:27 final size:27
Alignment explanation
Indices: 7443--7497 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
7433 CGCAAGTCTC
7443 GTATGCATGAAATTGACGCATGACATG
1 GTATGCATGAAATTGACGCATGACATG
* *
7470 GTATTCATGAAATTGACGCATGAGATG
1 GTATGCATGAAATTGACGCATGACATG
7497 G
1 G
7498 CAAAATGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (27 bp):
GTATGCATGAAATTGACGCATGACATG
Found at i:8269 original size:16 final size:16
Alignment explanation
Indices: 8232--8268 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
8222 AAAGAAGAAT
*
8232 TAAAATTAAATCTAAC
1 TAAAAATAAATCTAAC
8248 TAAAAATAAAT-TAAC
1 TAAAAATAAATCTAAC
8263 TAAAAA
1 TAAAAA
8269 AGCAATCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAATAAATCTAAC
Found at i:9360 original size:19 final size:18
Alignment explanation
Indices: 9327--9362 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9317 TTGAAATAAT
9327 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
9345 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
9363 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:10453 original size:43 final size:43
Alignment explanation
Indices: 10419--10935 Score: 315
Period size: 43 Copynumber: 11.8 Consensus size: 43
10409 TATCAAATTG
* * * *
10419 CTTAGTTACACTGAATTAACTTGATTACCAAATTACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
* *
10462 CTTAATTACACCAAATTAAGTTGTTTACTAAATTACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
10505 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATCACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACC-----A---AA--T--T-ACCAATTTA
*
10561 CTTAATTACACCGAATTAAGTTGCTTACCAAATTACC-----A
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
* *
10599 ---AATTACACCGAATCAAGTTG---A-----TTACCAATATA
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
*
10631 CTTAATTACACCGAATTAAGTTGCTTACCAAATTACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
*
10674 CTTAGTTACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATCACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACC-----A---AA--T--T-ACCAATTTA
10730 CTTAATTACACCGAATTAAGTTGTTTACC-----A--AA-TTA
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
* *
10765 CTTAATTGCACCGAATCAAGTTG---A-----TTACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
*
10800 CTTAATTACACCCGAATTAAGTTATTTACCAAATTACTTAATTTAATCACCAATTTA
1 CTTAATTACA-CCGAATTAAGTTGTTTACC-----A---AA--T--T-ACCAATTTA
*
10857 CTTAATTACACCGAATTAAGTTGCTTACCAAATTACCAATTTA
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
10900 CTTAATTACACCGAATTAAGTTGTTTACCAAATTAC
1 CTTAATTACACCGAATTAAGTTGTTTACCAAATTAC
10936 TTAATTACAC
Statistics
Matches: 382, Mismatches: 23, Indels: 138
0.70 0.04 0.25
Matches are distributed among these distances:
27 5 0.01
32 4 0.01
34 2 0.01
35 74 0.19
36 13 0.03
38 3 0.01
39 1 0.00
43 148 0.39
44 2 0.01
46 2 0.01
48 6 0.02
51 6 0.02
53 2 0.01
54 1 0.00
55 2 0.01
56 92 0.24
57 19 0.05
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (43 bp):
CTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTA
Found at i:10464 original size:24 final size:25
Alignment explanation
Indices: 10432--10479 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
10422 AGTTACACTG
*
10432 AATTAACTTGATT-ACCAAATTACC
1 AATTAACTTAATTAACCAAATTACC
*
10456 AATTTACTTAATTACACCAAATTA
1 AATTAACTTAATTA-ACCAAATTA
10480 AGTTGTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
26 9 0.45
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (25 bp):
AATTAACTTAATTAACCAAATTACC
Found at i:10560 original size:56 final size:56
Alignment explanation
Indices: 10496--10771 Score: 278
Period size: 56 Copynumber: 4.9 Consensus size: 56
10486 TTACTAAATT
10496 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATC
* * *
10552 ACCAATTTACTTAATTACACCGAATTAAGTTGCTTACCAAATTAC-CAAATT-A-C
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATC
** * * * * * * * ** * *
10605 ACCGAATCAAGTTGATT--ACC-AA-TATACTTAATTACACCGAATTAAGTTGCTTACCAAATT
1 ACC-AATTTACTTAATTACACCGAATTA-AGTT-GTT-TACCAAATT-ACTTAATT---TAATC
*
10665 ACCAATTTACTTAGTTACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATC
10721 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAATT
10772 GCACCGAATC
Statistics
Matches: 171, Mismatches: 34, Indels: 30
0.73 0.14 0.13
Matches are distributed among these distances:
50 2 0.01
51 5 0.03
52 4 0.02
53 11 0.06
54 11 0.06
55 5 0.03
56 97 0.57
59 14 0.08
60 10 0.06
61 5 0.03
62 5 0.03
63 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (56 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATC
Found at i:10591 original size:35 final size:35
Alignment explanation
Indices: 10552--10715 Score: 175
Period size: 35 Copynumber: 4.5 Consensus size: 35
10542 TAATTTAATC
10552 ACCAATTTACTTAATTACACCGAATTAAGTTGCTT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGCTT
* ** * *
10587 ACCAAATTACCAAATTACACCGAATCAAGTTGATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGCTT
*
10622 ACCAATATACTTAATTACACCGAATTAAGTTGCTTACCAAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTG-----C---TT
* *
10665 ACCAATTTACTTAGTTACACCGAATTAAGTTGTTT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGCTT
*
10700 ACCAAATTACTTAATT
1 ACCAATTTACTTAATT
10716 TAATCACCAA
Statistics
Matches: 105, Mismatches: 16, Indels: 16
0.77 0.12 0.12
Matches are distributed among these distances:
35 73 0.70
43 32 0.30
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (35 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGCTT
Found at i:10670 original size:169 final size:169
Alignment explanation
Indices: 10450--10836 Score: 675
Period size: 169 Copynumber: 2.3 Consensus size: 169
10440 TGATTACCAA
* *
10450 ATTACCAATTTACTTAATTACACCAAATTAAGTTGTTTACTAAATTACCAATTTACTTAATTACA
1 ATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACA
10515 CCGAATTAAGTTGTTTACCAAATTACTTAATTTAATCACCAATTTACTTAATTACACCGAATTAA
66 CCGAATTAAGTTGTTTACCAAATTACTTAATTTAATCACCAATTTACTTAATTACACCGAATTAA
10580 GTTGCTTACCAAATTACCAAATTACACCGAATCAAGTTG
131 GTTGCTTACCAAATTACCAAATTACACCGAATCAAGTTG
* * *
10619 ATTACCAATATACTTAATTACACCGAATTAAGTTGCTTACCAAATTACCAATTTACTTAGTTACA
1 ATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACA
10684 CCGAATTAAGTTGTTTACCAAATTACTTAATTTAATCACCAATTTACTTAATTACACCGAATTAA
66 CCGAATTAAGTTGTTTACCAAATTACTTAATTTAATCACCAATTTACTTAATTACACCGAATTAA
* ** *
10749 GTTGTTTACCAAATTACTTAATTGCACCGAATCAAGTTG
131 GTTGCTTACCAAATTACCAAATTACACCGAATCAAGTTG
*
10788 ATTACCAATTTACTTAATTACACCCGAATTAAGTTATTTACCAAATTAC
1 ATTACCAATTTACTTAATTACA-CCGAATTAAGTTGTTTACCAAATTAC
10837 TTAATTTAAT
Statistics
Matches: 205, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
169 181 0.88
170 24 0.12
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (169 bp):
ATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACA
CCGAATTAAGTTGTTTACCAAATTACTTAATTTAATCACCAATTTACTTAATTACACCGAATTAA
GTTGCTTACCAAATTACCAAATTACACCGAATCAAGTTG
Found at i:10822 original size:36 final size:35
Alignment explanation
Indices: 10721--10963 Score: 197
Period size: 35 Copynumber: 7.1 Consensus size: 35
10711 TAATTTAATC
* *
10721 ACCAATTTACTTAATTACACCGAATTAAGTTGTTT
1 ACCAAATTACTTAATTACACCGAATTAAGTTGATT
* *
10756 ACCAAATTACTTAATTGCACCGAATCAAGTTGATT
1 ACCAAATTACTTAATTACACCGAATTAAGTTGATT
*
10791 ACCAATTTACTTAATTACACCCGAATTAAGTT-ATTT
1 ACCAAATTACTTAATTACA-CCGAATTAAGTTGA-TT
* * *
10827 ACCAAATTACTTAATTTAATCACC-AATTTACTTAATT
1 ACCAAATTACTTAA-TT-A-CACCGAATTAAGTTGATT
* * **
10864 ACACCGAATTAAGTTGCTT--ACC-----AA----ATT
1 --ACCAAATT-ACTTAATTACACCGAATTAAGTTGATT
* *
10891 ACCAATTTACTTAATTACACCGAATTAAGTTGTTT
1 ACCAAATTACTTAATTACACCGAATTAAGTTGATT
10926 ACCAAATTACTTAATTACACCGAATTAAGTTGATT
1 ACCAAATTACTTAATTACACCGAATTAAGTTGATT
10961 ACC
1 ACC
10964 CACTGATTTA
Statistics
Matches: 165, Mismatches: 23, Indels: 40
0.72 0.10 0.18
Matches are distributed among these distances:
24 5 0.03
25 6 0.04
26 3 0.02
27 3 0.02
31 3 0.02
35 90 0.55
36 26 0.16
37 11 0.07
38 4 0.02
39 11 0.07
40 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.36
Consensus pattern (35 bp):
ACCAAATTACTTAATTACACCGAATTAAGTTGATT
Found at i:10840 original size:21 final size:21
Alignment explanation
Indices: 10816--10861 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
10806 TACACCCGAA
* *
10816 TTAAGTTATTTACCAAATTAC
1 TTAAGTTAATCACCAAATTAC
* *
10837 TTAATTTAATCACCAATTTAC
1 TTAAGTTAATCACCAAATTAC
10858 TTAA
1 TTAA
10862 TTACACCGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.15, G:0.02, T:0.43
Consensus pattern (21 bp):
TTAAGTTAATCACCAAATTAC
Found at i:10927 original size:19 final size:19
Alignment explanation
Indices: 10904--10962 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 19
10894 AATTTACTTA
10904 ATTACACCGAATTAAGTTG
1 ATTACACCGAATTAAGTTG
* * * *
10923 -TT-TACCAAATT-ACTTA
1 ATTACACCGAATTAAGTTG
10939 ATTACACCGAATTAAGTTG
1 ATTACACCGAATTAAGTTG
10958 ATTAC
1 ATTAC
10963 CCACTGATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
16 3 0.10
17 9 0.31
18 9 0.31
19 8 0.28
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (19 bp):
ATTACACCGAATTAAGTTG
Found at i:11033 original size:55 final size:54
Alignment explanation
Indices: 10974--11157 Score: 274
Period size: 55 Copynumber: 3.5 Consensus size: 54
10964 CACTGATTTA
* * *
10974 ACTTAATTGCTAATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTT
1 ACTTAATTACTGATTTACTGATTACTATTA-CTTGACTCTGATTAATCTCTTTTT
11029 ACTTAATTACTGATTTACTGATTACTATTACATTGACTCTGATTAATCTC-TTTT
1 ACTTAATTACTGATTTACTGATTACTATTAC-TTGACTCTGATTAATCTCTTTTT
11083 ACTTAATTACTGATTTACT-ATTAC----A-TTGACTCTGATTAATCTCTTTTT
1 ACTTAATTACTGATTTACTGATTACTATTACTTGACTCTGATTAATCTCTTTTT
11131 ACTTAATTACTGATTTACTGATTACTA
1 ACTTAATTACTGATTTACTGATTACTA
11158 ATGAACTTAA
Statistics
Matches: 121, Mismatches: 3, Indels: 14
0.88 0.02 0.10
Matches are distributed among these distances:
47 18 0.15
48 23 0.19
49 6 0.05
53 5 0.04
54 24 0.20
55 45 0.37
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (54 bp):
ACTTAATTACTGATTTACTGATTACTATTACTTGACTCTGATTAATCTCTTTTT
Found at i:11040 original size:47 final size:49
Alignment explanation
Indices: 10988--11155 Score: 236
Period size: 48 Copynumber: 3.4 Consensus size: 49
10978 AATTGCTAAT
*
10988 TTACTGA-TTACT-ATTACCTTAACTCTGATTAATCTCTTTTTACTTAA
1 TTACTGATTTACTGATTACCTTGACTCTGATTAATCTCTTTTTACTTAA
11035 TTACTGATTTACTGATTACTATTACATTGACTCTGATTAATCTC-TTTTACTTAA
1 TTACTGATTTACTGATTAC-----C-TTGACTCTGATTAATCTCTTTTTACTTAA
*
11089 TTACTGATTTACT-ATTACATTGACTCTGATTAATCTCTTTTTACTTAA
1 TTACTGATTTACTGATTACCTTGACTCTGATTAATCTCTTTTTACTTAA
11137 TTACTGATTTACTGATTAC
1 TTACTGATTTACTGATTAC
11156 TAATGAACTT
Statistics
Matches: 109, Mismatches: 2, Indels: 18
0.84 0.02 0.14
Matches are distributed among these distances:
47 25 0.23
48 28 0.26
49 10 0.09
53 5 0.05
54 24 0.22
55 17 0.16
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (49 bp):
TTACTGATTTACTGATTACCTTGACTCTGATTAATCTCTTTTTACTTAA
Done.