Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008509.1 Corchorus capsularis cultivar CVL-1 contig08530, 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: 64781
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:9126 original size:16 final size:16
Alignment explanation
Indices: 9105--9136 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9095 TTTGTGACTT
9105 CACATTATAATTAGTA
1 CACATTATAATTAGTA
9121 CACATTATAATTAGTA
1 CACATTATAATTAGTA
9137 TAGATGAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
CACATTATAATTAGTA
Found at i:17542 original size:15 final size:14
Alignment explanation
Indices: 17514--17573 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
17504 AATTAGTAAT
17514 TTATTAATTA-TTAA
1 TTATT-ATTATTTAA
17528 TTACTTATTATTTAA
1 TTA-TTATTATTTAA
* *
17543 TTAGGTATTATTGTTA
1 TTA-TTATTATT-TAA
*
17559 TTATTATTAATTAA
1 TTATTATTATTTAA
17573 T
1 T
17574 ATGATAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 10 0.27
15 22 0.59
16 5 0.14
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (14 bp):
TTATTATTATTTAA
Found at i:30433 original size:42 final size:42
Alignment explanation
Indices: 30380--30459 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
30370 CATACTTAAA
*
30380 GTTTCAAACTAAACCTATTAGATATTTCCTTCCCTAACTTAT
1 GTTTCAAACTAAACCTATTAGATATTTCATTCCCTAACTTAT
30422 GTTTCAAACTAAACCTATTAGATATTTCATTCCCTAAC
1 GTTTCAAACTAAACCTATTAGATATTTCATTCCCTAAC
30460 ATATCTTTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.39
Consensus pattern (42 bp):
GTTTCAAACTAAACCTATTAGATATTTCATTCCCTAACTTAT
Found at i:35432 original size:26 final size:27
Alignment explanation
Indices: 35399--35471 Score: 121
Period size: 26 Copynumber: 2.7 Consensus size: 27
35389 GGTCACATAG
35399 GGGCATTTTGGTCATTTTTACATT-AA
1 GGGCATTTTGGTCATTTTTACATTCAA
**
35425 GGGCATTTTGGTCATTTGCACATTCAA
1 GGGCATTTTGGTCATTTTTACATTCAA
35452 GGGCATTTTGGTCATTTTTA
1 GGGCATTTTGGTCATTTTTA
35472 GTCGACTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 22 0.52
27 20 0.48
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.44
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTTTACATTCAA
Found at i:39104 original size:26 final size:26
Alignment explanation
Indices: 39057--39267 Score: 205
Period size: 26 Copynumber: 8.0 Consensus size: 26
39047 ATAGTCAATT
* *
39057 AGTAATCAGTAAAAAAGAGTAAGAAAT
1 AGTATTCAGT-AAAAAGAGTAAGAAAC
*
39084 AGTATTCAGTAAAAAGAGTAA-AAAA
1 AGTATTCAGTAAAAAGAGTAAGAAAC
* *
39109 AGAATCATCAGTAAAAAAAAGTAAGAAAC
1 AGTAT--TCAGT-AAAAAGAGTAAGAAAC
* *
39138 AATATTCAGTAAAAAGAGTAAGAAAAG
1 AGTATTCAGTAAAAAGAGTAAG-AAAC
*
39165 AGCCA-TCAGTAAAAAGAGTAAGAAAC
1 AG-TATTCAGTAAAAAGAGTAAGAAAC
* *
39191 AGTATTCAGTAAGAAGAGTAAGAAAAG
1 AGTATTCAGTAAAAAGAGTAAG-AAAC
* *
39218 AGTCA-TCAGT-AAAATAGTAGGAAAC
1 AGT-ATTCAGTAAAAAGAGTAAGAAAC
*
39243 AATATTCAGTAAAAAGAGTAAGAAA
1 AGTATTCAGTAAAAAGAGTAAGAAA
39268 AGCACAATAG
Statistics
Matches: 151, Mismatches: 22, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
24 1 0.01
25 18 0.12
26 63 0.42
27 51 0.34
28 12 0.08
29 6 0.04
ACGTcount: A:0.57, C:0.07, G:0.18, T:0.18
Consensus pattern (26 bp):
AGTATTCAGTAAAAAGAGTAAGAAAC
Found at i:39119 original size:54 final size:53
Alignment explanation
Indices: 39061--39269 Score: 303
Period size: 54 Copynumber: 3.9 Consensus size: 53
39051 TCAATTAGTA
* * * *
39061 ATCAGTAAAAAAGAGTAAGAAATAGTATTCAGTAAAAAGAGTAAAAAAAGAATC
1 ATCAGT-AAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
* *
39115 ATCAGTAAAAAAAAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGCC
1 ATCAGT-AAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
* *
39169 ATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAGAAGAGTAAGAAAAGAGTC
1 ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
* *
39222 ATCAGT-AAAATAGTAGGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
1 ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
39270 CACAATAGTA
Statistics
Matches: 141, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
52 38 0.27
53 49 0.35
54 54 0.38
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (53 bp):
ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
Found at i:39311 original size:105 final size:105
Alignment explanation
Indices: 39060--39269 Score: 296
Period size: 107 Copynumber: 2.0 Consensus size: 105
39050 GTCAATTAGT
* * *
39060 AATCAGTAAAAAAGAGTAAGAAATAGTATTCAGTAAAAAGAGTAAAAAAAGAATCATCAGTAAAA
1 AATCAGT-AAAAAGAG-AAGAAACAGTAATCAGTAAGAAGAGTAAAAAAAGAATCATCAGT-AAA
39125 AAAAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGC
63 AAAAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGC
* * * *
39168 CATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAGAAGAGTAAGAAAAGAGTCATCAGT-AAAA
1 AATCAGTAAAAAGAG-AAGAAACAGTAATCAGTAAGAAGAGTAAAAAAAGAATCATCAGTAAAAA
* *
39232 TAGTAGGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
65 AAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
39270 CACAATAGTA
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
105 40 0.42
107 49 0.52
108 6 0.06
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (105 bp):
AATCAGTAAAAAGAGAAGAAACAGTAATCAGTAAGAAGAGTAAAAAAAGAATCATCAGTAAAAAA
AGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGC
Found at i:39454 original size:22 final size:22
Alignment explanation
Indices: 39454--39713 Score: 276
Period size: 22 Copynumber: 12.4 Consensus size: 22
39444 AGTAAAGAGT
* *
39454 AAAGTAAAGTGG-GATCAGTAA
1 AAAGTAAAATGGTAATCAGTAA
**
39475 AAAG-AAAATGGTAAAGAGT--
1 AAAGTAAAATGGTAATCAGTAA
*
39494 AAAGTAAAA-AGTAATCAGTAA
1 AAAGTAAAATGGTAATCAGTAA
**
39515 AAAAAAAAATGGTAATCAGTAA
1 AAAGTAAAATGGTAATCAGTAA
* *
39537 AGAGT--AATAGTAATCAGTAA
1 AAAGTAAAATGGTAATCAGTAA
*
39557 GAAGT--AATGGTAATCAGTAA
1 AAAGTAAAATGGTAATCAGTAA
*
39577 AAAGTAAAA-GGTAATCAATAA
1 AAAGTAAAATGGTAATCAGTAA
39598 AAAGTAAAATGGTAATCAGTAA
1 AAAGTAAAATGGTAATCAGTAA
* *
39620 AAAGT-AAA-GGTAATTAGTGA
1 AAAGTAAAATGGTAATCAGTAA
*
39640 AAAGTAAAATGGTAATTAG-AA
1 AAAGTAAAATGGTAATCAGTAA
*
39661 AAGAGTAAAAGGGTAATCAGTAA
1 AA-AGTAAAATGGTAATCAGTAA
*
39684 AAAGTAAAATGGTAATTAGTAA
1 AAAGTAAAATGGTAATCAGTAA
39706 AAAGTAAA
1 AAAGTAAA
39714 GAGTAATCCG
Statistics
Matches: 200, Mismatches: 27, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
19 11 0.05
20 60 0.30
21 44 0.22
22 81 0.41
23 4 0.02
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.21
Consensus pattern (22 bp):
AAAGTAAAATGGTAATCAGTAA
Found at i:39460 original size:34 final size:34
Alignment explanation
Indices: 39347--39497 Score: 140
Period size: 34 Copynumber: 4.2 Consensus size: 34
39337 AAAGGCAATC
* *
39347 AGTAAAGAGTAATCAGTGAAGAAAAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAGGAAAATGGTAAAG
*
39381 AGTAAAGAGTAATCAGTAGAGGAAAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAGGAAAATGGTAAAG
* * * * *
39415 AATGAAGAGTAATTAGTAAAATGGTAAATAGTAAAG
1 AGTAAAGAGTAATCAGT-AAA-GGAAAATGGTAAAG
* *
39451 AGTAAAGTAAAGTGGGATCAGTAAAAAGAAAATGGTAAAG
1 AGTAAAG---AGT--AATCAGT-AAAGGAAAATGGTAAAG
39491 AGTAAAG
1 AGTAAAG
39498 TAAAAAGTAA
Statistics
Matches: 94, Mismatches: 16, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
34 45 0.48
35 2 0.02
36 17 0.18
39 3 0.03
40 18 0.19
41 9 0.10
ACGTcount: A:0.52, C:0.02, G:0.26, T:0.19
Consensus pattern (34 bp):
AGTAAAGAGTAATCAGTAAAGGAAAATGGTAAAG
Found at i:39489 original size:47 final size:46
Alignment explanation
Indices: 39432--39769 Score: 144
Period size: 42 Copynumber: 7.9 Consensus size: 46
39422 AGTAATTAGT
* *
39432 AAAATGGTAAATAGTAAAGAGTAAAGTAAAGTGGGATCAGT-AAAAAG
1 AAAATGGTAAATAGTAAAGAGTAAAGTAAAGT--AATCAGTAAAAAAA
*
39479 AAAATGGTAAAGAGT-AA-AGT-AA--AAAGTAATCAGTAAAAAAA
1 AAAATGGTAAATAGTAAAGAGTAAAGTAAAGTAATCAGTAAAAAAA
*
39520 AAAATGGT-AATCAGTAAAGAGT-AA-T--AGTAATCAGT--AAGAA
1 AAAATGGTAAAT-AGTAAAGAGTAAAGTAAAGTAATCAGTAAAAAAA
** * * * **
39560 GTAATGGT-AATCAGTAAAAAGT-AA--AAGGTAATCAATAAAAAGT
1 AAAATGGTAAAT-AGTAAAGAGTAAAGTAAAGTAATCAGTAAAAAAA
* * * **
39603 AAAATGGT-AATCAGTAAAAAGTAAAG----GTAATTAGTGAAAAGT
1 AAAATGGTAAAT-AGTAAAGAGTAAAGTAAAGTAATCAGTAAAAAAA
* * ** **
39645 AAAATGGTAATTAGAAAAGAGTAAA--AGGGTAATCAGTAAAAAGT
1 AAAATGGTAAATAGTAAAGAGTAAAGTAAAGTAATCAGTAAAAAAA
* * * *
39689 AAAATGGTAATTAGTAAAAAGTAAAG---AGTAATCCGT-AAAGAA
1 AAAATGGTAAATAGTAAAGAGTAAAGTAAAGTAATCAGTAAAAAAA
* * **
39731 AAAATAGTAAAGAGTAATCAGTAAAG---AGTAATCAGTAAA
1 AAAATGGTAAATAGTAAAGAGTAAAGTAAAGTAATCAGTAAA
39770 GAGTAAAGAG
Statistics
Matches: 238, Mismatches: 36, Indels: 38
0.76 0.12 0.12
Matches are distributed among these distances:
40 33 0.14
41 24 0.10
42 82 0.34
43 39 0.16
44 41 0.17
45 3 0.01
46 2 0.01
47 14 0.06
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.21
Consensus pattern (46 bp):
AAAATGGTAAATAGTAAAGAGTAAAGTAAAGTAATCAGTAAAAAAA
Found at i:39582 original size:7 final size:7
Alignment explanation
Indices: 39572--39789 Score: 59
Period size: 7 Copynumber: 30.7 Consensus size: 7
39562 AATGGTAATC
39572 AGTAAAA
1 AGTAAAA
39579 AGTAAAA
1 AGTAAAA
* *
39586 GGTAATCA
1 AGTAA-AA
39594 A-TAAAA
1 AGTAAAA
39600 AGTAAAA
1 AGTAAAA
* **
39607 TGGTAATC
1 -AGTAAAA
39615 AGTAAAA
1 AGTAAAA
39622 AGT-AAA
1 AGTAAAA
* **
39628 GGTAATT
1 AGTAAAA
*
39635 AGTGAAA
1 AGTAAAA
39642 AGTAAAA
1 AGTAAAA
* **
39649 TGGTAATT
1 -AGTAAAA
39657 AG-AAAA
1 AGTAAAA
39663 GAGTAAAA
1 -AGTAAAA
* **
39671 GGGTAATC
1 -AGTAAAA
39679 AGTAAAA
1 AGTAAAA
39686 AGTAAAA
1 AGTAAAA
* **
39693 TGGTAATT
1 -AGTAAAA
39701 AGTAAAA
1 AGTAAAA
*
39708 AGTAAAG
1 AGTAAAA
**
39715 AGTAATC
1 AGTAAAA
*
39722 CGTAAAGA
1 AGTAAA-A
39730 A--AAAA
1 AGTAAAA
*
39735 TAGTAAAG
1 -AGTAAAA
**
39743 AGTAATC
1 AGTAAAA
*
39750 AGTAAAG
1 AGTAAAA
**
39757 AGTAATC
1 AGTAAAA
*
39764 AGTAAAG
1 AGTAAAA
*
39771 AGTAAAG
1 AGTAAAA
39778 AGTAAAA
1 AGTAAAA
39785 AGTAA
1 AGTAA
39790 TCAGTAAAGA
Statistics
Matches: 146, Mismatches: 53, Indels: 24
0.65 0.24 0.11
Matches are distributed among these distances:
5 1 0.01
6 13 0.09
7 107 0.73
8 25 0.17
ACGTcount: A:0.56, C:0.03, G:0.20, T:0.21
Consensus pattern (7 bp):
AGTAAAA
Found at i:39718 original size:14 final size:14
Alignment explanation
Indices: 39708--39799 Score: 114
Period size: 14 Copynumber: 6.6 Consensus size: 14
39698 ATTAGTAAAA
39708 AGTAAAGAGTAATC
1 AGTAAAGAGTAATC
* **
39722 CGTAAAGAAAAAAT-
1 AGTAAAG-AGTAATC
39736 AGTAAAGAGTAATC
1 AGTAAAGAGTAATC
39750 AGTAAAGAGTAATC
1 AGTAAAGAGTAATC
**
39764 AGTAAAGAGTAAAG
1 AGTAAAGAGTAATC
*
39778 AGTAAAAAGTAATC
1 AGTAAAGAGTAATC
39792 AGTAAAGA
1 AGTAAAGA
39800 AAAAATAGTA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
13 4 0.06
14 56 0.88
15 4 0.06
ACGTcount: A:0.55, C:0.05, G:0.21, T:0.18
Consensus pattern (14 bp):
AGTAAAGAGTAATC
Found at i:39771 original size:42 final size:41
Alignment explanation
Indices: 39467--39769 Score: 267
Period size: 42 Copynumber: 7.2 Consensus size: 41
39457 GTAAAGTGGG
** *
39467 ATCAGTAAAAAGAAAATGGTAAAGAGT--AAAGTAAAAAGTA
1 ATCAGTAAAAA-AAAATGGTAATCAGTAAAAAGTAAAGAGTA
* *
39507 ATCAGTAAAAAAAAAAATGGTAATCAGTAAAGAGT-AATAGTA
1 ATCAGT--AAAAAAAAATGGTAATCAGTAAAAAGTAAAGAGTA
* **
39549 ATCAGTAAGAAGTAATGGTAATCAGTAAAAAGTAAA-AGGTA
1 ATCAGTAAAAAAAAATGGTAATCAGTAAAAAGTAAAGA-GTA
*
39590 ATCAATAAAAAGTAAAATGGTAATCAGTAAAAAGTAAAG-GTA
1 ATCAGTAAAAA--AAAATGGTAATCAGTAAAAAGTAAAGAGTA
* * * *
39632 ATTAGTGAAAAGTAAAATGGTAATTAG-AAAAGAGTAAAAGGGTA
1 ATCAGT-AAAA-AAAAATGGTAATCAGTAAAA-AGT-AAAGAGTA
*
39676 ATCAGTAAAAAGTAAAATGGTAATTAGTAAAAAGTAAAGAGTA
1 ATCAGTAAAAA--AAAATGGTAATCAGTAAAAAGTAAAGAGTA
* * ** **
39719 ATCCGTAAAGAAAAAATAGTAAAGAGTAATCAGTAAAGAGTA
1 ATCAGTAAA-AAAAAATGGTAATCAGTAAAAAGTAAAGAGTA
39761 ATCAGTAAA
1 ATCAGTAAA
39770 GAGTAAAGAG
Statistics
Matches: 219, Mismatches: 26, Indels: 34
0.78 0.09 0.12
Matches are distributed among these distances:
40 30 0.14
41 31 0.14
42 73 0.33
43 54 0.25
44 27 0.12
45 4 0.02
ACGTcount: A:0.55, C:0.04, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCAGTAAAAAAAAATGGTAATCAGTAAAAAGTAAAGAGTA
Found at i:39809 original size:14 final size:15
Alignment explanation
Indices: 39708--39810 Score: 69
Period size: 14 Copynumber: 7.3 Consensus size: 15
39698 ATTAGTAAAA
*
39708 AGTAAAG-AGTAATC
1 AGTAAAGAAGAAATC
* *
39722 CGTAAAGAAAAAAT-
1 AGTAAAGAAGAAATC
*
39736 AGTAAAG-AGTAATC
1 AGTAAAGAAGAAATC
*
39750 AGTAAAG-AGTAATC
1 AGTAAAGAAGAAATC
*
39764 AGTAAAG-AGTAAA-G
1 AGTAAAGAAG-AAATC
*
39778 AGTAAA-AAGTAATC
1 AGTAAAGAAGAAATC
*
39792 AGTAAAGAAAAAAT-
1 AGTAAAGAAGAAATC
39806 AGTAA
1 AGTAA
39811 GGAGTGAGAA
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
13 6 0.08
14 54 0.76
15 11 0.15
ACGTcount: A:0.57, C:0.05, G:0.19, T:0.18
Consensus pattern (15 bp):
AGTAAAGAAGAAATC
Found at i:39809 original size:21 final size:21
Alignment explanation
Indices: 39743--39867 Score: 58
Period size: 21 Copynumber: 5.9 Consensus size: 21
39733 AATAGTAAAG
**
39743 AGTAATCAGTAAAG-AGTAAT
1 AGTAATCAGTAAAGAAAAAAT
** ** *
39763 CAGTAAAGAGTAAAGAGTAAAA
1 -AGTAATCAGTAAAGAAAAAAT
39785 AGTAATCAGTAAAGAAAAAAT
1 AGTAATCAGTAAAGAAAAAAT
** * *
39806 AGTAAGGAGT-GAGAAGAAAT
1 AGTAATCAGTAAAGAAAAAAT
* * * *
39826 CAGTAAAAT-GGTAAAGGATAAAG
1 -AGT--AATCAGTAAAGAAAAAAT
39849 AGTAATCAGTAAAGAAAAA
1 AGTAATCAGTAAAGAAAAA
39868 TGGTAAAGAG
Statistics
Matches: 74, Mismatches: 24, Indels: 12
0.67 0.22 0.11
Matches are distributed among these distances:
20 11 0.15
21 48 0.65
22 7 0.09
23 8 0.11
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.18
Consensus pattern (21 bp):
AGTAATCAGTAAAGAAAAAAT
Found at i:39891 original size:64 final size:64
Alignment explanation
Indices: 39757--39897 Score: 157
Period size: 64 Copynumber: 2.2 Consensus size: 64
39747 ATCAGTAAAG
* *
39757 AGTAATCAGT-AAAGAGTAAAGAGTAAAAAGTAATCAGTAAAGAAAAAATAGTAAGGAGTGAGA
1 AGTAATCAGTAAAAGAGTAAAGAGTAAAAAGTAATCAGTAAAGAAAAAATAGTAAAGAGTGAAA
* * *
39820 AGAAATCAGTAAAATG-GTAAAG-GATAAAGAGTAATCAGTAAAG-AAAAATGGTAAAGAGT-AA
1 AGTAATCAGTAAAA-GAGTAAAGAG-TAAAAAGTAATCAGTAAAGAAAAAATAGTAAAGAGTGAA
39881 A
64 A
*
39882 ATCTTAATCAGTAAAA
1 A--GTAATCAGTAAAA
39898 ACTAATGGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
62 3 0.05
63 24 0.36
64 38 0.58
65 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.19
Consensus pattern (64 bp):
AGTAATCAGTAAAAGAGTAAAGAGTAAAAAGTAATCAGTAAAGAAAAAATAGTAAAGAGTGAAA
Found at i:49916 original size:30 final size:32
Alignment explanation
Indices: 49880--49943 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 32
49870 AGGTCAAATC
49880 CCCTAATTTTCG-AAAAACCCAAATCCC-TAA
1 CCCTAATTTTCGAAAAAACCCAAATCCCATAA
49910 CCCTAATTTTCGAAAAAACCCAAATCCCATAA
1 CCCTAATTTTCGAAAAAACCCAAATCCCATAA
49942 CC
1 CC
49944 ACATGATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 12 0.38
31 15 0.47
32 5 0.16
ACGTcount: A:0.41, C:0.34, G:0.03, T:0.22
Consensus pattern (32 bp):
CCCTAATTTTCGAAAAAACCCAAATCCCATAA
Found at i:50702 original size:13 final size:13
Alignment explanation
Indices: 50684--50708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50674 ACTTTTATAT
50684 ATAGTATAGATAG
1 ATAGTATAGATAG
50697 ATAGTATAGATA
1 ATAGTATAGATA
50709 TATTAATTAA
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:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (13 bp):
ATAGTATAGATAG
Found at i:54596 original size:1 final size:1
Alignment explanation
Indices: 54590--54617 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
54580 GTGTAAGTAG
54590 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
54618 GCCACGATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:59357 original size:31 final size:31
Alignment explanation
Indices: 59317--59395 Score: 124
Period size: 31 Copynumber: 2.5 Consensus size: 31
59307 AATTTTAGCA
*
59317 ACCAATTTGAGTTTAAACCTTTCAAAAGTT-
1 ACCAATTTGAGTCTAAACCTTTCAAAAGTTG
59347 ACTCAATTTGAGTCTAAACCTTTCAAAAGTTG
1 AC-CAATTTGAGTCTAAACCTTTCAAAAGTTG
*
59379 ACCAATTTGAGCCTAAA
1 ACCAATTTGAGTCTAAA
59396 TACATAAACG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
30 2 0.04
31 41 0.91
32 2 0.04
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (31 bp):
ACCAATTTGAGTCTAAACCTTTCAAAAGTTG
Found at i:64568 original size:142 final size:146
Alignment explanation
Indices: 64362--64655 Score: 445
Period size: 142 Copynumber: 2.0 Consensus size: 146
64352 TATGTTATAT
64362 TATATATGTTCTTGATAATTTTTAGCAACACATAGATAGTTTACAAATCTAATAATTAGTTGCTT
1 TATATATGTTCTTGATAATTTTTAGCAACAC--A-ATAGTTTACAAATCTAATAATTAGTTGCTT
* *
64427 ATGCTGGTTTTGAACTTACAAAAACAAATGATCGGA-ATTAT-A-AATACAAATGCTAATATATA
63 ATGATGGTTTTGAACTTACAAAAACAAATGATC-AATATTATAATAATACAAATGCTAATATATA
64489 -TTGTGACTTGGCTAAAAAA
127 TTTGTGACTTGGCTAAAAAA
64508 TATATATGTTCTTGATAATTTTTAGCAACAC-ATAGTTTACAAATCTAATAATTAGTTGCTTATG
1 TATATATGTTCTTGATAATTTTTAGCAACACAATAGTTTACAAATCTAATAATTAGTTGCTTATG
* *
64572 ATGGTTTTGAACTTACAAAAACAAATGATCAATATTATAATTAATATAGATGCTAATATATATTT
66 ATGGTTTTGAACTTACAAAAACAAATGATCAATATTATAA-TAATACAAATGCTAATATATA--T
*
64637 TTTTGACTTGGCTAAAAAA
128 TTGTGACTTGGCTAAAAAA
64656 ATACATGAAG
Statistics
Matches: 136, Mismatches: 5, Indels: 12
0.89 0.03 0.08
Matches are distributed among these distances:
141 1 0.01
142 67 0.49
143 1 0.01
145 18 0.13
146 31 0.23
148 18 0.13
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (146 bp):
TATATATGTTCTTGATAATTTTTAGCAACACAATAGTTTACAAATCTAATAATTAGTTGCTTATG
ATGGTTTTGAACTTACAAAAACAAATGATCAATATTATAATAATACAAATGCTAATATATATTTG
TGACTTGGCTAAAAAA
Done.