Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011942.1 Corchorus capsularis cultivar CVL-1 contig11963, 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: 18517
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Found at i:4938 original size:32 final size:32
Alignment explanation
Indices: 4902--4962 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
4892 TAAAAGTAGC
* *
4902 AATCAGTAATTAAGGGTCAAAGTAAAAGGGTA
1 AATCAATAATTAAGAGTCAAAGTAAAAGGGTA
* *
4934 AATCAATAATTAAGATTCAAGGTAAAAGG
1 AATCAATAATTAAGAGTCAAAGTAAAAGG
4963 ATTAATTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.23
Consensus pattern (32 bp):
AATCAATAATTAAGAGTCAAAGTAAAAGGGTA
Found at i:5065 original size:104 final size:103
Alignment explanation
Indices: 4851--5057 Score: 229
Period size: 104 Copynumber: 2.0 Consensus size: 103
4841 TTAAGAGGAA
* *
4851 GTAAAAGGATTAATTAGTAAATTGATAACTAAGAGAGGAAGTAAAAGTAGCAATCAGTAATTAAG
1 GTAAAAGGATTAATTAGTAAATTGATAACTAAGAGAAGAAGTAAAAGAAGCAATCAGTAATTAA-
* * * * ** *
4916 GGTCAAAGTAAAAGGGTAAATCAATAATTAAGATTCAAG
65 GGTAAAAGTAAAAGGATAAATAAAAAAAGAAGAATCAAG
* * ** *
4955 GTAAAAGGATTAATTAGTAAATTGATAATTAAGAGAAGAAGTAAAAGAAGTAATTGGTCAA-TCA
1 GTAAAAGGATTAATTAGTAAATTGATAACTAAGAGAAGAAGTAAAAGAAGCAATCAGT-AATTAA
5019 -GTAAAAGTAAAAGGATAAAATAAAAAAGAGAAGTAATCA
65 GGTAAAAGTAAAAGGAT-AAATAAAAAA-AGAAG-AATCA
5058 GTAAAAAGAA
Statistics
Matches: 85, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
102 14 0.16
103 8 0.09
104 57 0.67
105 6 0.07
ACGTcount: A:0.52, C:0.04, G:0.20, T:0.23
Consensus pattern (103 bp):
GTAAAAGGATTAATTAGTAAATTGATAACTAAGAGAAGAAGTAAAAGAAGCAATCAGTAATTAAG
GTAAAAGTAAAAGGATAAATAAAAAAAGAAGAATCAAG
Found at i:5127 original size:32 final size:32
Alignment explanation
Indices: 5091--5152 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
5081 TTATTAGTAG
*
5091 AATGGAGTGAAAGTAAAAGAAGTAATCAGTGA
1 AATGGAGTAAAAGTAAAAGAAGTAATCAGTGA
*
5123 AATGGAGTAAAAGTAAAAGAAGTAGTCAGT
1 AATGGAGTAAAAGTAAAAGAAGTAATCAGT
5153 AAGTTGGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.27, T:0.19
Consensus pattern (32 bp):
AATGGAGTAAAAGTAAAAGAAGTAATCAGTGA
Found at i:5171 original size:40 final size:40
Alignment explanation
Indices: 5127--5248 Score: 150
Period size: 40 Copynumber: 3.2 Consensus size: 40
5117 CAGTGAAATG
* **
5127 GAGTAAAAGTAAAAGAAGTAGTCAGTAAGTTGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
5167 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
*
5207 GAGTAAAA--AAATG--GTAAT---TAAAATGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
*
5240 AAGTAAAAG
1 GAGTAAAAG
5249 AAGTAATCAG
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
33 22 0.29
36 5 0.07
38 4 0.05
40 45 0.59
ACGTcount: A:0.53, C:0.02, G:0.21, T:0.24
Consensus pattern (40 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
Found at i:5231 original size:12 final size:12
Alignment explanation
Indices: 5192--5241 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
5182 AAGTAATCAG
5192 TAAAATGGTAAT
1 TAAAATGGTAAT
*
5204 TAAGA--GTAA-
1 TAAAATGGTAAT
*
5213 AAAAATGGTAAT
1 TAAAATGGTAAT
5225 TAAAATGGTAAT
1 TAAAATGGTAAT
5237 TAAAA
1 TAAAA
5242 GTAAAAGAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
9 3 0.10
10 4 0.13
11 4 0.13
12 20 0.65
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (12 bp):
TAAAATGGTAAT
Found at i:5342 original size:32 final size:33
Alignment explanation
Indices: 5270--5360 Score: 111
Period size: 32 Copynumber: 2.9 Consensus size: 33
5260 AAAGAGTAAA
*
5270 AAAATGGTAA--AAAGT-AAAGAGTAAAATGGT
1 AAAATGGTAATCAAATTCAAAGAGTAAAATGGT
5300 AAAATGGTAATCAAATTCAAAGAGTAAAAT-G-
1 AAAATGGTAATCAAATTCAAAGAGTAAAATGGT
* *
5331 ACAAATGGTAATTAAATTCAAATAGTAAAA
1 A-AAATGGTAATCAAATTCAAAGAGTAAAA
5361 ATATTAGTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
30 10 0.19
31 1 0.02
32 31 0.57
33 12 0.22
ACGTcount: A:0.56, C:0.04, G:0.16, T:0.23
Consensus pattern (33 bp):
AAAATGGTAATCAAATTCAAAGAGTAAAATGGT
Found at i:5362 original size:26 final size:27
Alignment explanation
Indices: 5333--5395 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 27
5323 GTAAAATGAC
* *
5333 AAATGGTAATTAAATTCAA-ATAGTAA
1 AAATAGTAATTAAATTCAAGAGAGTAA
* *
5359 AAATATTAGTTAAATTCAAGAGAGTAA
1 AAATAGTAATTAAATTCAAGAGAGTAA
5386 AAATAGTAAT
1 AAATAGTAAT
5396 CAGTAAAGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 16 0.53
27 14 0.47
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.30
Consensus pattern (27 bp):
AAATAGTAATTAAATTCAAGAGAGTAA
Found at i:5410 original size:7 final size:7
Alignment explanation
Indices: 5397--5544 Score: 117
Period size: 7 Copynumber: 20.7 Consensus size: 7
5387 AATAGTAATC
5397 AGTAAAG
1 AGTAAAG
*
5404 AGAAAAG
1 AGTAAAG
5411 AGTAAAG
1 AGTAAAG
5418 AGTAAA-
1 AGTAAAG
5424 ATGGTAAAG
1 A--GTAAAG
5433 AGTAAAG
1 AGTAAAG
5440 AGTAAAAG
1 AGT-AAAG
*
5448 AGAAAAG
1 AGTAAAG
5455 AGTAAAG
1 AGTAAAG
5462 AGTAAAG
1 AGTAAAG
**
5469 AGTAATC
1 AGTAAAG
5476 AGTAAAG
1 AGTAAAG
5483 AGTAAA-
1 AGTAAAG
5489 ATGGTCAAA-
1 A--GT-AAAG
5498 AGTAAAG
1 AGTAAAG
**
5505 AGTAATC
1 AGTAAAG
5512 AGTAAAAG
1 AGT-AAAG
*
5520 AAG-AATG
1 -AGTAAAG
*
5527 -GTAAAA
1 AGTAAAG
5533 AGTAAAG
1 AGTAAAG
5540 AGTAA
1 AGTAA
5545 TCAGTAAAGG
Statistics
Matches: 113, Mismatches: 16, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
5 1 0.01
6 7 0.06
7 83 0.73
8 15 0.13
9 7 0.06
ACGTcount: A:0.57, C:0.02, G:0.25, T:0.16
Consensus pattern (7 bp):
AGTAAAG
Found at i:5434 original size:29 final size:28
Alignment explanation
Indices: 5401--5544 Score: 100
Period size: 29 Copynumber: 5.0 Consensus size: 28
5391 GTAATCAGTA
5401 AAGAGAAAAGAGTAAAGAGTAAA-ATGGTA
1 AAGAGAAAAGAGTAAAGAGTAAAGA--GTA
* *
5430 AAGAGTAAAGAGTAAAAGAGAAAAGAGTA
1 AAGAGAAAAGAGT-AAAGAGTAAAGAGTA
* **
5459 AAGAGTAAAGAGTAATCAGTAAAGAGTA
1 AAGAGAAAAGAGTAAAGAGTAAAGAGTA
* **
5487 AA-ATGGTCAAA-AGTAAAGAGTAATCAGTA
1 AAGA--G-AAAAGAGTAAAGAGTAAAGAGTA
*
5516 AA-AGAAGAATG-GTAAAAAGTAAAGAGTA
1 AAGAGAA-AA-GAGTAAAGAGTAAAGAGTA
5544 A
1 A
5545 TCAGTAAAGG
Statistics
Matches: 93, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.01
27 4 0.04
28 29 0.31
29 46 0.49
30 12 0.13
31 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (28 bp):
AAGAGAAAAGAGTAAAGAGTAAAGAGTA
Found at i:5435 original size:22 final size:22
Alignment explanation
Indices: 5400--5509 Score: 129
Period size: 22 Copynumber: 5.0 Consensus size: 22
5390 AGTAATCAGT
*
5400 AAAGAGAAAAGAGTAAAGAGTA
1 AAAGAGTAAAGAGTAAAGAGTA
5422 AAATG-GTAAAGAGTAAAGAGTA
1 AAA-GAGTAAAGAGTAAAGAGTA
*
5444 AAAGAGAAAAGAGTAAAGAGT-
1 AAAGAGTAAAGAGTAAAGAGTA
**
5465 AAAGAGTAATCAGTAAAGAGTA
1 AAAGAGTAAAGAGTAAAGAGTA
5487 AAATG-GTCAAA-AGTAAAGAGTA
1 AAA-GAGT-AAAGAGTAAAGAGTA
5509 A
1 A
5510 TCAGTAAAAG
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
21 19 0.25
22 54 0.70
23 4 0.05
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (22 bp):
AAAGAGTAAAGAGTAAAGAGTA
Found at i:5516 original size:43 final size:43
Alignment explanation
Indices: 5400--5516 Score: 132
Period size: 43 Copynumber: 2.7 Consensus size: 43
5390 AGTAATCAGT
**
5400 AAAGAGAAAAGAGTAAAGAGTAAA-ATGGTAAAGAGTAAAGAGTA
1 AAAGAGAAAAGAGTAAAGAGTAAACA--GTAATCAGTAAAGAGTA
*
5444 AAAGAGAAAAGAGTAAAGAGTAAAGAGTAATCAGTAAAGAGTA
1 AAAGAGAAAAGAGTAAAGAGTAAACAGTAATCAGTAAAGAGTA
* *
5487 AAATG-GTCAAA-AGTAAAGAGTAATCAGTAA
1 AAA-GAG-AAAAGAGTAAAGAGTAAACAGTAA
5517 AAGAAGAATG
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
43 36 0.55
44 28 0.43
45 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.25, T:0.15
Consensus pattern (43 bp):
AAAGAGAAAAGAGTAAAGAGTAAACAGTAATCAGTAAAGAGTA
Found at i:5596 original size:15 final size:15
Alignment explanation
Indices: 5576--5638 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 15
5566 GAGTAAAGGG
5576 TAATCAGTAAAATGA
1 TAATCAGTAAAATGA
5591 TAATCAGTAAAGAGTGAAATA
1 TAATCAGTAAA-A-TG----A
*
5612 GTAATCAGTAAAAAGA
1 -TAATCAGTAAAATGA
5628 TAATCAGTAAA
1 TAATCAGTAAA
5639 GAGTAAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
15 22 0.55
16 2 0.05
17 2 0.05
20 1 0.03
21 2 0.05
22 11 0.28
ACGTcount: A:0.54, C:0.06, G:0.16, T:0.24
Consensus pattern (15 bp):
TAATCAGTAAAATGA
Found at i:5600 original size:22 final size:22
Alignment explanation
Indices: 5575--5659 Score: 69
Period size: 22 Copynumber: 4.2 Consensus size: 22
5565 AGAGTAAAGG
5575 GTAATCAGTAAAATGATAATCA
1 GTAATCAGTAAAATGATAATCA
*
5597 GTAA--AG---AGTGA-AAT-A
1 GTAATCAGTAAAATGATAATCA
*
5612 GTAATCAGTAAAAAGATAATCA
1 GTAATCAGTAAAATGATAATCA
**
5634 GTAAAGAGTAAAAT-AGTAATCA
1 GTAATCAGTAAAATGA-TAATCA
5656 GTAA
1 GTAA
5660 AAGGTAATCA
Statistics
Matches: 49, Mismatches: 6, Indels: 16
0.69 0.08 0.23
Matches are distributed among these distances:
15 5 0.10
16 3 0.06
17 6 0.12
20 5 0.10
21 4 0.08
22 26 0.53
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (22 bp):
GTAATCAGTAAAATGATAATCA
Found at i:5658 original size:15 final size:14
Alignment explanation
Indices: 5640--5676 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5630 ATCAGTAAAG
5640 AGTAAAATAGTAATC
1 AGTAAAA-AGTAATC
*
5655 AGTAAAAGGTAATC
1 AGTAAAAAGTAATC
5669 AGTAAAAA
1 AGTAAAAA
5677 AAGGTAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.57, C:0.05, G:0.16, T:0.22
Consensus pattern (14 bp):
AGTAAAAAGTAATC
Found at i:5660 original size:22 final size:22
Alignment explanation
Indices: 5618--5805 Score: 179
Period size: 22 Copynumber: 9.0 Consensus size: 22
5608 AATAGTAATC
5618 AGTAAAA-AGATAATCAGTAAAG
1 AGTAAAATAG-TAATCAGTAAAG
5640 AGTAAAATAGTAATCAGTAAA-
1 AGTAAAATAGTAATCAGTAAAG
*
5661 AGGT--AATCAGTAA--A-AAAAG
1 A-GTAAAAT-AGTAATCAGTAAAG
5680 -GT--AAT-GATAATCAGTAAA-
1 AGTAAAATAG-TAATCAGTAAAG
5698 AGGTAAAATAGTAATCAGT-AAG
1 A-GTAAAATAGTAATCAGTAAAG
* * *
5720 AGCAAAATGGAAATCAGTAAAG
1 AGTAAAATAGTAATCAGTAAAG
*
5742 AGTAAAATAGTAATCAGTAAAA
1 AGTAAAATAGTAATCAGTAAAG
*
5764 AGTAAAA-GGTAATCAGTAAAG
1 AGTAAAATAGTAATCAGTAAAG
5785 AGTAAAATAGTAATCAGTAAA
1 AGTAAAATAGTAATCAGTAAA
5806 AGGTAATCAG
Statistics
Matches: 138, Mismatches: 12, Indels: 32
0.76 0.07 0.18
Matches are distributed among these distances:
15 1 0.01
16 3 0.02
17 5 0.04
18 4 0.03
19 4 0.03
20 5 0.04
21 41 0.30
22 72 0.52
23 3 0.02
ACGTcount: A:0.55, C:0.05, G:0.19, T:0.21
Consensus pattern (22 bp):
AGTAAAATAGTAATCAGTAAAG
Found at i:5747 original size:43 final size:42
Alignment explanation
Indices: 5688--5919 Score: 196
Period size: 43 Copynumber: 5.6 Consensus size: 42
5678 AGGTAATGAT
*
5688 AATCAGTAAA-AGGTAAAATAGTAATCAGTAAGAGCAAAATGGA
1 AATCAGTAAAGA-GTAAAATAGTAATCAGTAAAAGCAAAA-GGA
* *
5731 AATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGT
1 AATCAGTAAAGAGTAAAATAGTAATCAGT-AAAAGCAAAAGGA
*
5774 AATCAGTAAAGAGTAAAATAGTAATCAGT------AAAAGGT
1 AATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAAGGA
* * * *
5810 AATCAGT-AAGAGTAAAATAGTAATCGGCAAAAAG-TAAAGAGT
1 AATCAGTAAAGAGTAAAATAGTAATCAG-TAAAAGCAAAAG-GA
* * * * *
5852 AATTAGT-AAGAAGTCAAATTGTAATCAGTAAAATGTGAAAAGGC
1 AATCAGTAAAG-AGTAAAATAGTAATCAGTAAAA-G-CAAAAGGA
*
5896 AATCAGTAAAGAGTAAAATGGTAA
1 AATCAGTAAAGAGTAAAATAGTAA
5920 AAAGTAATGG
Statistics
Matches: 159, Mismatches: 16, Indels: 27
0.79 0.08 0.13
Matches are distributed among these distances:
35 19 0.12
36 14 0.09
41 4 0.03
42 15 0.09
43 73 0.46
44 27 0.17
45 7 0.04
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.21
Consensus pattern (42 bp):
AATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAAGGA
Found at i:5830 original size:78 final size:79
Alignment explanation
Indices: 5731--5884 Score: 224
Period size: 78 Copynumber: 2.0 Consensus size: 79
5721 GCAAAATGGA
*
5731 AATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAA-AGGTAATCAGTAA-AGAGTAAAATA
1 AATCAGTAAAGAGTAAAATAGTAATCAGCAAAAAGTAAAGA-GTAATCAGTAAGA-AGTAAAATA
5794 GTAATCAGTAAAAGGT
64 GTAATCAGTAAAAGGT
* * * *
5810 AATCAGT-AAGAGTAAAATAGTAATCGGCAAAAAGTAAAGAGTAATTAGTAAGAAGTCAAATTGT
1 AATCAGTAAAGAGTAAAATAGTAATCAGCAAAAAGTAAAGAGTAATCAGTAAGAAGTAAAATAGT
5874 AATCAGTAAAA
66 AATCAGTAAAA
5885 TGTGAAAAGG
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
78 59 0.87
79 9 0.13
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.22
Consensus pattern (79 bp):
AATCAGTAAAGAGTAAAATAGTAATCAGCAAAAAGTAAAGAGTAATCAGTAAGAAGTAAAATAGT
AATCAGTAAAAGGT
Found at i:5843 original size:36 final size:36
Alignment explanation
Indices: 5575--5674 Score: 137
Period size: 37 Copynumber: 2.7 Consensus size: 36
5565 AGAGTAAAGG
* * *
5575 GTAATCAGTAAAATGATAATCAGTAAAGAGTGAAATA
1 GTAATCAG-AAAAAGGTAATCAGTAAAGAGTAAAATA
*
5612 GTAATCAGTAAAAAGATAATCAGTAAAGAGTAAAATA
1 GTAATCAG-AAAAAGGTAATCAGTAAAGAGTAAAATA
*
5649 GTAATCAGTAAAAGGTAATCAGTAAA
1 GTAATCAGAAAAAGGTAATCAGTAAA
5675 AAAAGGTAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
36 16 0.27
37 43 0.73
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.23
Consensus pattern (36 bp):
GTAATCAGAAAAAGGTAATCAGTAAAGAGTAAAATA
Found at i:5853 original size:35 final size:35
Alignment explanation
Indices: 5767--5853 Score: 102
Period size: 35 Copynumber: 2.5 Consensus size: 35
5757 AGTAAAAAGT
* * *
5767 AAAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGT
1 AAAAAGTAAACAGT-AAGAGTAAAATAGTAATCAGC
* * *
5803 AAAAGGTAATCAGTAAGAGTAAAATAGTAATCGGC
1 AAAAAGTAAACAGTAAGAGTAAAATAGTAATCAGC
*
5838 AAAAAGTAAAGAGTAA
1 AAAAAGTAAACAGTAA
5854 TTAGTAAGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 32 0.70
36 14 0.30
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.20
Consensus pattern (35 bp):
AAAAAGTAAACAGTAAGAGTAAAATAGTAATCAGC
Found at i:5921 original size:29 final size:29
Alignment explanation
Indices: 5800--5921 Score: 90
Period size: 29 Copynumber: 4.2 Consensus size: 29
5790 AATAGTAATC
*
5800 AGTAAAAGGTAATCAGT-AAGAGTAAAAT
1 AGTAAAAGGCAATCAGTAAAGAGTAAAAT
** ** *
5828 AGTAATCGGCAAAAAGTAAAGAGT-AATT
1 AGTAAAAGGCAATCAGTAAAGAGTAAAAT
* * **
5856 AGTAAGAAGTCAAAT-TGTAATCAGTAAAAT
1 AGTAA-AAGGC-AATCAGTAAAGAGTAAAAT
5886 -GTGAAAAGGCAATCAGTAAAGAGTAAAAT
1 AGT-AAAAGGCAATCAGTAAAGAGTAAAAT
*
5915 GGTAAAA
1 AGTAAAA
5922 AGTAATGGTG
Statistics
Matches: 69, Mismatches: 18, Indels: 13
0.69 0.18 0.13
Matches are distributed among these distances:
28 23 0.33
29 37 0.54
30 9 0.13
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (29 bp):
AGTAAAAGGCAATCAGTAAAGAGTAAAAT
Found at i:7889 original size:21 final size:21
Alignment explanation
Indices: 7865--7913 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
7855 TTTTCCTATA
*
7865 TGCTACGAGCTTATTTGCATT
1 TGCTACGAGCTTATTTACATT
7886 TGCTACGAGCTTATTTACATT
1 TGCTACGAGCTTATTTACATT
*
7907 TGTTACG
1 TGCTACG
7914 GACATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43
Consensus pattern (21 bp):
TGCTACGAGCTTATTTACATT
Found at i:10387 original size:30 final size:30
Alignment explanation
Indices: 10353--10412 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
10343 GCGCGGGCTA
10353 AAATCTAGTAGTGGATAATTAAAGAGATCT
1 AAATCTAGTAGTGGATAATTAAAGAGATCT
*
10383 AAATCTAGTAGTGGATACTTAAAGAGATCT
1 AAATCTAGTAGTGGATAATTAAAGAGATCT
10413 TATAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (30 bp):
AAATCTAGTAGTGGATAATTAAAGAGATCT
Found at i:11948 original size:179 final size:178
Alignment explanation
Indices: 11725--12086 Score: 600
Period size: 179 Copynumber: 2.0 Consensus size: 178
11715 TTATAAACAT
* * *
11725 TTAGTAACCTCTCATCCTTAAAGTTTATGCAACTTTTTTAATTACCACTCCTTACTTTTAAAACT
1 TTAGTAACCTCTCATCCTTAAAATTTATGCAACTTTTTTAATTACCACCCCTTACTTTCAAAACT
11790 TAATAAAGATAATAGATTGACCATAAGTATTAATTTGAAGTATTAATAATTGAAAAATATATTGT
66 TAATAAAGATAATAGATTGACCATAAGTATTAATTTGAAGTATTAATAATTGAAAAATATATTGT
*
11855 TATTTGCTATACTAATTTCTCC-TATTATCGTTTCATATATCCTTTTAA
131 TA-TTGCTATACTAATTTCTCCATATTATCGTTTCACATATCCTTTTAA
* * *
11903 TTAGTAATCTCTCATCCTTAAAAATTTATGCAATTTTTTTAATTACTACCCCTTACTTTCAAAAC
1 TTAGTAACCTCTCATCCTT-AAAATTTATGCAACTTTTTTAATTACCACCCCTTACTTTCAAAAC
*
11968 TTAATAAAGATAATAGATTGACCATAAGTATTAATTTGAAGTATTAATAATTGAAATATATATTG
65 TTAATAAAGATAATAGATTGACCATAAGTATTAATTTGAAGTATTAATAATTGAAAAATATATTG
12033 TTATTGCTATACTAATTTCTCCTATATATTATCGTTTCACATATCCTTTTAA
130 TTATTGCTATACTAATTTCTCC---ATATTATCGTTTCACATATCCTTTTAA
12085 TT
1 TT
12087 TATTCATAAT
Statistics
Matches: 171, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
178 37 0.22
179 107 0.63
182 27 0.16
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (178 bp):
TTAGTAACCTCTCATCCTTAAAATTTATGCAACTTTTTTAATTACCACCCCTTACTTTCAAAACT
TAATAAAGATAATAGATTGACCATAAGTATTAATTTGAAGTATTAATAATTGAAAAATATATTGT
TATTGCTATACTAATTTCTCCATATTATCGTTTCACATATCCTTTTAA
Found at i:13695 original size:199 final size:198
Alignment explanation
Indices: 13085--13993 Score: 1112
Period size: 199 Copynumber: 4.6 Consensus size: 198
13075 TTTATATTTC
* *
13085 TTTTCTTATAGGATTATTATACAATACACTTTTCAGTGTAAATTTTACACTCCATAAGCGGGTTA
1 TTTTCTTATAGGATTATTATACAATACAC-TGTCAGTGTAAATTTT-GACTCCATAAGCGGGTTA
* * * * *
13150 AGAAGTTGACACATAACACATTTCATAATCAATTAAATATTTAATATTTACACATATTCCTTAAG
64 AGAAGTTGACACATACCTCATTTCATAATCAATTAAATATTTAATATTAATACATATTCCCTAAG
* * * * * * *
13215 GGGACACATGTCAA-CCATTAAACCCTGC-CTGTGCAGTCTACTAAATTCGAATGACGGTGCATA
129 GGGACACATGTCAATCC-TTAAACCCCGCAC-ATGCAGTCTGCTAAACTCCACTGACGGTGTATA
13278 GTATAAT
192 GTATAAT
* *
13285 TTTTCTTATAAGATTATTATACAATCCACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAA
1 TTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTT-GACTCCATAAGCGGGTTAA
* * *
13350 GAAGTTGACATATACC-CAATTTCATAA-CAAATTAAATATTTGATATTTAGTACATATTCCCTA
65 GAAGTTGACACATACCTC-ATTTCATAATC-AATTAAATATTTAATA-TTAATACATATTCCCTA
* * * * * * *
13413 AGGCGACACATATCAACCCTTAAACCCCGCATATGCAGTATGCTAAAATCCACTGGCGGTGTATT
127 AGGGGACACATGTCAATCCTTAAACCCCGCACATGCAGTCTGCTAAACTCCACTGACGGTGTA-T
13478 A-TATAAT
191 AGTATAAT
* * * **
13485 TTTTCTTATAGGCTTATTATACAACACGCTGTCAGTGTAAATTTTAGACTATATAAGCGGGTTAA
1 TTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTT-GACTCCATAAGCGGGTTAA
* * * * *
13550 GAAGTTGACACATACCTTATTTCATCATCAATAAAATATATAATATTAATGCATATTCCCTAAGG
65 GAAGTTGACACATACCTCATTTCATAATCAATTAAATATTTAATATTAATACATATTCCCTAAGG
* * * *
13615 GGACACATGTCAATCCTTAAACCCTGCACATGCAGTCTGCTAAACTCCATTGACGGTATATTGTA
130 GGACACATGTCAATCCTTAAACCCCGCACATGCAGTCTGCTAAACTCCACTGACGGTGTATAGTA
13680 TAAT
195 TAAT
* * * *
13684 TGTTT-TTATAGGGTTATCATACAATACACTGTCAATGTAAATTTTGAACTCCATAAGCAGGTTA
1 T-TTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTG-ACTCCATAAGCGGGTTA
* * * *
13748 AGAAGTTGACGCATATGCT-ATTTCATAATTAATTAAATATTTAATATTAATACATATTCCTTAA
64 AGAAGTTGACACATA-CCTCATTTCATAATCAATTAAATATTTAATATTAATACATATTCCCTAA
* * * * **
13812 AGGGACATATGTCAATCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCGACTGATTGTGTATAG
128 GGGGACACATGTCAATCCTTAAACCCCGCACATGCAGTCTGCTAAACTCCACTGACGGTGTATAG
13877 TATAAT
193 TATAAT
*
13883 TTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGAACTCCATAAGCGGGTTAA
1 TTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTG-ACTCCATAAGCGGGTTAA
* * * *
13948 GAAGTTGACATATACCTCATTTCATCATGAATTAAATATATAATAT
65 GAAGTTGACACATACCTCATTTCATAATCAATTAAATATTTAATAT
13994 CATGTCAACC
Statistics
Matches: 609, Mismatches: 86, Indels: 29
0.84 0.12 0.04
Matches are distributed among these distances:
198 9 0.01
199 404 0.66
200 191 0.31
201 5 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (198 bp):
TTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGACTCCATAAGCGGGTTAAG
AAGTTGACACATACCTCATTTCATAATCAATTAAATATTTAATATTAATACATATTCCCTAAGGG
GACACATGTCAATCCTTAAACCCCGCACATGCAGTCTGCTAAACTCCACTGACGGTGTATAGTAT
AAT
Found at i:14115 original size:175 final size:175
Alignment explanation
Indices: 13820--14168 Score: 527
Period size: 175 Copynumber: 2.0 Consensus size: 175
13810 AAAGGGACAT
* * * * * ** * *
13820 ATGTCAATCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCGACTGATTGTGTATAGTATAATTT
1 ATGTCAACCCTTAAACCACACACGTGCAATCTGCTAAACTCCACTGACGGTGCATAGTATAATTG
*
13885 TTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGAACTCCATAAGCGGGTTAAGA
66 TTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTATGAACTCCATAAGCGGGTTAAGA
* *
13950 AGTTGACATATACCTCATTTCATCATGAATTAAATATATAATATC
131 AGTTGACACATACCTCATTTCATAATGAATTAAATATATAATATC
* *
13995 ATGTCAACCCTTAAACCATACACGTGCAATCTGCTAAACTCCACTGACGGTGCATTGTATAATTG
1 ATGTCAACCCTTAAACCACACACGTGCAATCTGCTAAACTCCACTGACGGTGCATAGTATAATTG
*
14060 TTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTATGAACTTCATAAGCGGGTTAAGA
66 TTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTATGAACTCCATAAGCGGGTTAAGA
* * * *
14125 AGTTGGCACATACTTCATTTCATAATTAATTAAATATTTAATAT
131 AGTTGACACATACCTCATTTCATAATGAATTAAATATATAATAT
14169 TAATTCATAT
Statistics
Matches: 155, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
175 155 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (175 bp):
ATGTCAACCCTTAAACCACACACGTGCAATCTGCTAAACTCCACTGACGGTGCATAGTATAATTG
TTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTATGAACTCCATAAGCGGGTTAAGA
AGTTGACACATACCTCATTTCATAATGAATTAAATATATAATATC
Found at i:16289 original size:12 final size:12
Alignment explanation
Indices: 16272--16320 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
16262 ATTTCTGATT
16272 TTTTAATTTTTA
1 TTTTAATTTTTA
**
16284 TTTTAATAATTA
1 TTTTAATTTTTA
*
16296 TTTTAAATTTTA
1 TTTTAATTTTTA
16308 --TTAATTTTTA
1 TTTTAATTTTTA
16318 TTT
1 TTT
16321 ATTTAAATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
10 9 0.31
12 20 0.69
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTAATTTTTA
Found at i:16324 original size:19 final size:19
Alignment explanation
Indices: 16278--16330 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
16268 GATTTTTTAA
16278 TTTTTATTTTAATAATTAT
1 TTTTTATTTTAATAATTAT
** *
16297 TTTAAATTTTATTAATT-T
1 TTTTTATTTTAATAATTAT
*
16315 TTATTTATTTAAATAA
1 TT-TTTATTTTAATAA
16331 AATAAAAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 3 0.12
19 23 0.88
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTATTTTAATAATTAT
Done.