Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020050.1 Corchorus olitorius cultivar O-4 contig20083, 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: 53541
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6902 original size:42 final size:44
Alignment explanation
Indices: 6851--6945 Score: 115
Period size: 46 Copynumber: 2.2 Consensus size: 44
6841 AGTGCATTAC
* *
6851 CTAA-ATTCTA-CTCCATCTCTAGGT-AATTCATCAAAATAAAT
1 CTAATATTCTACCTCCATCTCTAGATAAATTCATCAAAATAAAG
*
6892 CTAATATTCTACTCCTCCATCTCTAGATAAATTTATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAAATTCATCAAAATAAAG
*
6938 CTCATATT
1 CTAATATT
6946 ATTTGTTGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 13 0.29
46 22 0.49
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACCTCCATCTCTAGATAAATTCATCAAAATAAAG
Found at i:7281 original size:13 final size:13
Alignment explanation
Indices: 7238--7292 Score: 69
Period size: 13 Copynumber: 4.3 Consensus size: 13
7228 AAATATATTA
7238 AATATAAGCAACT
1 AATATAAGCAACT
* *
7251 AATAGAA--ACCT
1 AATATAAGCAACT
7262 CAATATAAGCAACT
1 -AATATAAGCAACT
7276 AATATAAGCAACT
1 AATATAAGCAACT
7289 AATA
1 AATA
7293 GAAATCTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 3 0.09
12 6 0.17
13 23 0.66
14 3 0.09
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.22
Consensus pattern (13 bp):
AATATAAGCAACT
Found at i:8506 original size:32 final size:32
Alignment explanation
Indices: 8470--8568 Score: 135
Period size: 32 Copynumber: 3.1 Consensus size: 32
8460 ATTCAAAGTG
*
8470 ATTAAGTTCAAAAAGTAAAATGGTAATCAGTA
1 ATTAAATTCAAAAAGTAAAATGGTAATCAGTA
** *
8502 ATTAAATTCAATCAGTAAAATGGCAATCAGTA
1 ATTAAATTCAAAAAGTAAAATGGTAATCAGTA
* * *
8534 ATTAAATTTAAAAAGTAAAAGGGTAATCAATA
1 ATTAAATTCAAAAAGTAAAATGGTAATCAGTA
8566 ATT
1 ATT
8569 CACTTAATTC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.29
Consensus pattern (32 bp):
ATTAAATTCAAAAAGTAAAATGGTAATCAGTA
Found at i:8516 original size:17 final size:17
Alignment explanation
Indices: 8494--8541 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 17
8484 GTAAAATGGT
8494 AATCAGTAATTAAATTC
1 AATCAGTAATTAAATTC
*
8511 AATCAGT-A--AAATGGC
1 AATCAGTAATTAAAT-TC
8526 AATCAGTAATTAAATT
1 AATCAGTAATTAAATT
8542 TAAAAAGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
14 4 0.16
15 8 0.32
16 2 0.08
17 7 0.28
18 4 0.16
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.31
Consensus pattern (17 bp):
AATCAGTAATTAAATTC
Found at i:8530 original size:15 final size:15
Alignment explanation
Indices: 8483--8534 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
8473 AAGTTCAAAA
*
8483 AGTAAAATGGTAATC
1 AGTAAAATGGCAATC
*
8498 AGTAATTAAAT-TCAATC
1 AGT-A--AAATGGCAATC
8515 AGTAAAATGGCAATC
1 AGTAAAATGGCAATC
8530 AGTAA
1 AGTAA
8535 TTAAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
14 4 0.13
15 13 0.43
16 2 0.07
17 7 0.23
18 4 0.13
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (15 bp):
AGTAAAATGGCAATC
Found at i:8587 original size:83 final size:84
Alignment explanation
Indices: 8498--8706 Score: 296
Period size: 83 Copynumber: 2.5 Consensus size: 84
8488 AATGGTAATC
* ** * *
8498 AGTAATTAAATTCAATCAGTAAAATGGCAATCAGTAATTAAATTTAAAAAG-TAAAAGGGTAATC
1 AGTAATTAAGTTCAAAAAGTAAAATGGAAATCAGTAATTAAATTTAAAAAGAAAAAAGGGTAATC
8562 AATAATTCACTTAATTCAG
66 AATAATTCACTTAATTCAG
*
8581 AGTAATTAAGTT-AAAAAGTAAAATGGAAATCAGTAATTAAGTTTAAAAAGAAAAAAGGGTAATC
1 AGTAATTAAGTTCAAAAAGTAAAATGGAAATCAGTAATTAAATTTAAAAAGAAAAAAGGGTAATC
** *
8645 AATAATTGGCTTAATTTAG
66 AATAATTCACTTAATTCAG
* *
8664 AGTAATTAAGTTCCAAAAAGTAAAATGGTAACCAGTAATTAAA
1 AGTAATTAAGTT-CAAAAAGTAAAATGGAAATCAGTAATTAAA
8707 ATGGTAATCA
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
82 34 0.31
83 51 0.46
85 26 0.23
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (84 bp):
AGTAATTAAGTTCAAAAAGTAAAATGGAAATCAGTAATTAAATTTAAAAAGAAAAAAGGGTAATC
AATAATTCACTTAATTCAG
Found at i:8645 original size:115 final size:116
Alignment explanation
Indices: 8409--8651 Score: 310
Period size: 115 Copynumber: 2.1 Consensus size: 116
8399 TCAAAGGTAA
* * * * ** *
8409 TAATCAGTAATTAATTTTAAAAAAGTATAAGGGTAATTAGTAATTGGCTTAATTCAAAGTGATTA
1 TAATCAGTAATTAAATTTAAAAAAGTAAAAGGGTAATCAATAATTCACTTAATTCAAAGTAATTA
* ** * *
8474 AGTTCAAAAAGTAAAATGGTAATCAGTAATTAAATTCAATCAGTAAAATGG
66 AGTTCAAAAAGTAAAATGGAAATCAGTAATTAAATTCAAAAAGAAAAAGGG
* *
8525 CAATCAGTAATTAAATTT-AAAAAGTAAAAGGGTAATCAATAATTCACTTAATTCAGAGTAATTA
1 TAATCAGTAATTAAATTTAAAAAAGTAAAAGGGTAATCAATAATTCACTTAATTCAAAGTAATTA
* *
8589 AGTT-AAAAAGTAAAATGGAAATCAGTAATTAAGTTTAAAAAGAAAAAAGGG
66 AGTTCAAAAAGTAAAATGGAAATCAGTAATTAAATTCAAAAAG-AAAAAGGG
*
8640 TAATCAATAATT
1 TAATCAGTAATT
8652 GGCTTAATTT
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
114 33 0.31
115 59 0.55
116 16 0.15
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.30
Consensus pattern (116 bp):
TAATCAGTAATTAAATTTAAAAAAGTAAAAGGGTAATCAATAATTCACTTAATTCAAAGTAATTA
AGTTCAAAAAGTAAAATGGAAATCAGTAATTAAATTCAAAAAGAAAAAGGG
Found at i:8651 original size:33 final size:31
Alignment explanation
Indices: 8583--8651 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 31
8573 TAATTCAGAG
* * *
8583 TAATTAAGTTAAAAAGTAAAATGGAAATCAG
1 TAATTAAGTTAAAAAGAAAAAGGGAAATCAA
*
8614 TAATTAAGTTTAAAAAGAAAAAAGGGTAATCAA
1 TAATTAAG-TTAAAAAG-AAAAAGGGAAATCAA
8647 TAATT
1 TAATT
8652 GGCTTAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 8 0.25
32 8 0.25
33 16 0.50
ACGTcount: A:0.55, C:0.03, G:0.14, T:0.28
Consensus pattern (31 bp):
TAATTAAGTTAAAAAGAAAAAGGGAAATCAA
Found at i:8708 original size:19 final size:19
Alignment explanation
Indices: 8684--8720 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
8674 TTCCAAAAAG
8684 TAAAATGGTAACCAGTAAT
1 TAAAATGGTAACCAGTAAT
*
8703 TAAAATGGTAATCAGTAA
1 TAAAATGGTAACCAGTAA
8721 AATGGTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (19 bp):
TAAAATGGTAACCAGTAAT
Found at i:8757 original size:86 final size:83
Alignment explanation
Indices: 8515--8763 Score: 277
Period size: 83 Copynumber: 3.0 Consensus size: 83
8505 AAATTCAATC
* * * * **
8515 AGTAAAATGGCAATCAGTAATTAAATTTAAAAAG-TAAAAGGGTAATCAATAATTCACTTAATTC
1 AGTAAAATGGAAACCAGTAATTAAATGTAAAAAGAAAAAAGGGTAATCAATAATTGGCTTAATTC
8579 AGAGTAATTAAGTTAAAA
66 AGAGTAATTAAGTTAAAA
* * * *
8597 AGTAAAATGGAAATCAGTAATTAAGTTTAAAAAGAAAAAAGGGTAATCAATAATTGGCTTAATTT
1 AGTAAAATGGAAACCAGTAATTAAATGTAAAAAGAAAAAAGGGTAATCAATAATTGGCTTAATTC
8662 AGAGTAATTAAGTTCCAAAA
66 AGAGTAATTAAGTT--AAAA
* ** * * ** * *
8682 AGTAAAATGGTAACCAGTAATTAAAATGGTAATCAG-TAAAATGGTAATCCGTAGTTGGCTTGAT
1 AGTAAAATGGAAACCAGTAATT-AAAT-GTAAAAAGAAAAAAGGGTAATCAATAATTGGCTTAAT
8746 TCAGAGTAATTAAGTTAA
64 TCAGAGTAATTAAGTTAA
8764 TTAAGAAACT
Statistics
Matches: 143, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
82 32 0.22
83 40 0.28
84 2 0.01
85 24 0.17
86 40 0.28
87 5 0.03
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (83 bp):
AGTAAAATGGAAACCAGTAATTAAATGTAAAAAGAAAAAAGGGTAATCAATAATTGGCTTAATTC
AGAGTAATTAAGTTAAAA
Found at i:10088 original size:49 final size:49
Alignment explanation
Indices: 10031--10128 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
10021 AGCGAAACAA
*
10031 CACAGCACAAGAGATAACTCAAGTATGTAATAAATGAATGTGACAGAAT
1 CACAGCACAAGAGATAACTCAAGTATGTAATAAATGAATATGACAGAAT
10080 CACAGCACAAGAGATAACTCAAGTATGTAATAAATGAATATGACAGAAT
1 CACAGCACAAGAGATAACTCAAGTATGTAATAAATGAATATGACAGAAT
10129 GAATAAATGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.20
Consensus pattern (49 bp):
CACAGCACAAGAGATAACTCAAGTATGTAATAAATGAATATGACAGAAT
Found at i:11719 original size:78 final size:77
Alignment explanation
Indices: 11627--11794 Score: 275
Period size: 78 Copynumber: 2.2 Consensus size: 77
11617 TTGTTTAAAC
* *
11627 TTTTA-TAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAAAT
11691 ATTTTATTTTACCA
65 ATTTTATTTTA-CA
*
11705 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAATA
1 TTTTACTATTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAAATA
11770 TTTTATTTTACA
66 TTTTATTTTACA
*
11782 ATTTACTATTTTA
1 TTTTACTATTTTA
11795 ATAAAAAAAC
Statistics
Matches: 85, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
77 14 0.16
78 69 0.81
79 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.01, T:0.52
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAAATA
TTTTATTTTACA
Found at i:12358 original size:17 final size:17
Alignment explanation
Indices: 12336--12368 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12326 TCATTACATC
12336 AATTAA-AATTATAAATT
1 AATTAATAA-TATAAATT
12353 AATTAATAATATAAAT
1 AATTAATAATATAAAT
12369 ATCCAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTAATAATATAAATT
Found at i:12535 original size:15 final size:15
Alignment explanation
Indices: 12515--12543 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12505 CTAATTATAA
12515 ATTATTCATATAATT
1 ATTATTCATATAATT
12530 ATTATTCATATAAT
1 ATTATTCATATAAT
12544 GAAGTTCAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTATTCATATAATT
Found at i:31526 original size:16 final size:16
Alignment explanation
Indices: 31505--31551 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
31495 ATATATATAG
31505 TAATTTGTATAGTATT
1 TAATTTGTATAGTATT
* *
31521 TCATTTTTATAG-A-T
1 TAATTTGTATAGTATT
*
31535 AAATTTGTATAGTATT
1 TAATTTGTATAGTATT
31551 T
1 T
31552 TGAATATCCC
Statistics
Matches: 23, Mismatches: 6, Indels: 4
0.70 0.18 0.12
Matches are distributed among these distances:
14 10 0.43
15 2 0.09
16 11 0.48
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (16 bp):
TAATTTGTATAGTATT
Found at i:39712 original size:25 final size:25
Alignment explanation
Indices: 39678--39726 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
39668 TGACACACAT
39678 CCATTTTATGAATTAATTTTGTTTC
1 CCATTTTATGAATTAATTTTGTTTC
39703 CCATTTTATGAATTAATTTTGTTT
1 CCATTTTATGAATTAATTTTGTTT
39727 TTAAAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.08, T:0.57
Consensus pattern (25 bp):
CCATTTTATGAATTAATTTTGTTTC
Found at i:44429 original size:5 final size:5
Alignment explanation
Indices: 44419--44495 Score: 79
Period size: 5 Copynumber: 15.4 Consensus size: 5
44409 TCAAAATTAG
* *
44419 TTGTT TTGTT TTGTT TTTTT TTGTT TT-TT GTT-TT TTGTT TT-TT TTTTGT
1 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT -TTGTT TTGTT TTGTT TTGT-T
*
44468 TTGTT TTTTT TTGTTT TTGTT TTGTT TT
1 TTGTT TTGTT TTG-TT TTGTT TTGTT TT
44496 TTTCAGAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
4 8 0.13
5 45 0.73
6 9 0.15
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (5 bp):
TTGTT
Found at i:44438 original size:1 final size:1
Alignment explanation
Indices: 44422--44498 Score: 64
Period size: 1 Copynumber: 77.0 Consensus size: 1
44412 AAATTAGTTG
* * * * * * * * *
44422 TTTTGTTTTGTTTTTTTTTGTTTTTTGTTTTTTGTTTTTTTTTTGTTTGTTTTTTTTTGTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
44487 TTTTGTTTTTTT
1 TTTTTTTTTTTT
44499 CAGAAAAAGA
Statistics
Matches: 56, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (1 bp):
T
Found at i:44466 original size:25 final size:24
Alignment explanation
Indices: 44422--44498 Score: 111
Period size: 25 Copynumber: 3.2 Consensus size: 24
44412 AAATTAGTTG
*
44422 TTTTGTTTTGTTTT-TTTTTGTTT
1 TTTTTTTTTGTTTTTTTTTTGTTT
44445 TTTGTTTTTTGTTTTTTTTTTGTTT
1 TTT-TTTTTTGTTTTTTTTTTGTTT
*
44470 GTTTTTTTTTGTTTTTGTTTTGTTT
1 -TTTTTTTTTGTTTTTTTTTTGTTT
44495 TTTT
1 TTTT
44499 CAGAAAAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
23 3 0.06
24 14 0.29
25 29 0.59
26 3 0.06
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (24 bp):
TTTTTTTTTGTTTTTTTTTTGTTT
Found at i:44482 original size:39 final size:37
Alignment explanation
Indices: 44422--44498 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 37
44412 AAATTAGTTG
44422 TTTTGTTTTGTTTTTTTTTGTTTTTTGTTTTTTGTTTTTT
1 TTTTGTTTTGTTTTTTTTTG-TTTTTG--TTTTGTTTTTT
44462 TTTTG-TTTGTTTTTTTTTGTTTTTGTTTTGTTTTTT
1 TTTTGTTTTGTTTTTTTTTGTTTTTGTTTTGTTTTTT
44498 T
1 T
44499 CAGAAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
36 12 0.32
38 6 0.16
39 14 0.38
40 5 0.14
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (37 bp):
TTTTGTTTTGTTTTTTTTTGTTTTTGTTTTGTTTTTT
Found at i:45260 original size:31 final size:29
Alignment explanation
Indices: 45214--45288 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
45204 GCTAAATGCC
* *
45214 CAAAAAAATCCCTTATATTTTGCTTTTGGGA
1 CAAAATAATCCCTTATATTTT--TTTCGGGA
* *
45245 CAAAATAATCTCTTATGTTTTTTTCGGGA
1 CAAAATAATCCCTTATATTTTTTTCGGGA
*
45274 CAAATTAATCCCTTA
1 CAAAATAATCCCTTA
45289 CGTTTCAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 20 0.53
31 18 0.47
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (29 bp):
CAAAATAATCCCTTATATTTTTTTCGGGA
Found at i:45428 original size:31 final size:31
Alignment explanation
Indices: 45390--45455 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
45380 GAGGGACTAA
45390 TTTGTCCCATAAA-AAAAACATAAAGGATTAT
1 TTTGTCCCA-AAAGAAAAACATAAAGGATTAT
* *
45421 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAAGGATTAT
45452 TTTG
1 TTTG
45456 ATATTTAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAAGGATTAT
Found at i:46076 original size:177 final size:179
Alignment explanation
Indices: 45857--46214 Score: 553
Period size: 177 Copynumber: 2.0 Consensus size: 179
45847 TTGACGACTG
* * * *
45857 TACCCTTATTTTTTGATTATATTTCTTAAATGCCATTGTTTAAATTTTTATAGTTTTACTCAACT
1 TACCCTTATTTTTTCATTATATTTCTTAAATGCCATTGTTTAAACTTTTACAATTTTACTCAACT
* * *
45922 AAAATCTCTATTTTTATTTAATTTAA-TCTAATATATTTATAAATATTTTATTTTTACCATTTTA
66 AAAAACTCTATTTTTATTTAA-TCAATTCTAATATATTTATAAATATTTTATTTTTACAATTTTA
45986 ATATTTTAATT-AAGAACTTAGATATATCAGAATTTTTTAAATATATTTCT
130 ATATTTTAATTAAAGAA-TTAGATATATCAGAATTTTTTAAATATATTTCT
*
46036 TACCCTTA-TTTTTCA-TATATTTCTTAAATGCCATTGTTTAAACTTTTACAATTTTACTCAATT
1 TACCCTTATTTTTTCATTATATTTCTTAAATGCCATTGTTTAAACTTTTACAATTTTACTCAACT
* * *
46099 AAAAACTCTATTTTTATTTAATCAATTCTAATATATTTATAACTATTTTATTTTTATAATTTTAC
66 AAAAACTCTATTTTTATTTAATCAATTCTAATATATTTATAAATATTTTATTTTTACAATTTTAA
* *
46164 TATTTTAATTAAAGAATTAGATATATTATAATTTTTTAAATATATTTCT
131 TATTTTAATTAAAGAATTAGATATATCAGAATTTTTTAAATATATTTCT
46213 TA
1 TA
46215 AATGACATTA
Statistics
Matches: 164, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
176 3 0.02
177 142 0.87
178 11 0.07
179 8 0.05
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.53
Consensus pattern (179 bp):
TACCCTTATTTTTTCATTATATTTCTTAAATGCCATTGTTTAAACTTTTACAATTTTACTCAACT
AAAAACTCTATTTTTATTTAATCAATTCTAATATATTTATAAATATTTTATTTTTACAATTTTAA
TATTTTAATTAAAGAATTAGATATATCAGAATTTTTTAAATATATTTCT
Found at i:46533 original size:30 final size:29
Alignment explanation
Indices: 46466--46557 Score: 132
Period size: 31 Copynumber: 3.1 Consensus size: 29
46456 TAAATACTAA
* *
46466 AAAAAATCTCTTATGTTTTTCTTTTGAAAC
1 AAAAAATCCCTTATGTTTTTCTTTTG-GAC
46496 AAAAAAATCCCTTATGTTTTTCTTTTAGGAC
1 -AAAAAATCCCTTATGTTTTTCTTTT-GGAC
46527 AAAAAATCCCTTATGTTTTT-TTTTGGAC
1 AAAAAATCCCTTATGTTTTTCTTTTGGAC
46555 AAA
1 AAA
46558 TTAGTCCCTT
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
28 7 0.12
29 4 0.07
30 20 0.34
31 26 0.45
32 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (29 bp):
AAAAAATCCCTTATGTTTTTCTTTTGGAC
Found at i:51246 original size:19 final size:18
Alignment explanation
Indices: 51213--51248 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
51203 TTGAAATTAT
51213 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
51231 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
51249 TAAATCTTCA
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:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:52900 original size:100 final size:99
Alignment explanation
Indices: 52763--52962 Score: 285
Period size: 102 Copynumber: 2.0 Consensus size: 99
52753 ATTTTAATTT
* * *
52763 TAATTTGGGATAAACTTGGTGGATTAGTTATATATTTTCTTTCTAAAACCCTATAACAAT-ATTA
1 TAATTTGGGATAAACTTAGTGAATTAGTTATATATTTTATTTCTAAAACCCTATAACAATAATTA
*
52827 TTAATTATGGAATTTACCCTTAAAATAAAAAAAA
66 TTAATTATGAAATTTACCCTTAAAATAAAAAAAA
* * * *
52861 TAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAATCCCTATAACAATAAA
1 TAATTT-GGGATAAACTTAGTG-AATTAGTTATATATTTTATTTCTAAAACCCTATAACAAT-AA
*
52926 TTATTAATTTTGAAATTTACCCTTAAAATAAAAAAAA
63 TTATTAATTATGAAATTTACCCTTAAAATAAAAAAAA
52963 ACATATTTGA
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
98 6 0.07
99 13 0.15
100 34 0.38
102 36 0.40
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40
Consensus pattern (99 bp):
TAATTTGGGATAAACTTAGTGAATTAGTTATATATTTTATTTCTAAAACCCTATAACAATAATTA
TTAATTATGAAATTTACCCTTAAAATAAAAAAAA
Done.