Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014064.1 Corchorus capsularis cultivar CVL-1 contig14085, 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: 47382
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:5024 original size:21 final size:21
Alignment explanation
Indices: 5000--5045 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4990 TTGGGCGCCT
* * *
5000 ATGTGGTATGCTTGGCGCCCC
1 ATGTGGTATGCCTCGCGACCC
*
5021 ATGTGGTTTGCCTCGCGACCC
1 ATGTGGTATGCCTCGCGACCC
5042 ATGT
1 ATGT
5046 ACTTCAGTGC
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:0.11, C:0.28, G:0.30, T:0.30
Consensus pattern (21 bp):
ATGTGGTATGCCTCGCGACCC
Found at i:6121 original size:6 final size:6
Alignment explanation
Indices: 6112--6139 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6102 TAAAGCAAAG
6112 TAAATC TAAATC TAAATC TAAATC TAAA
1 TAAATC TAAATC TAAATC TAAATC TAAA
6140 GCAAATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (6 bp):
TAAATC
Found at i:6151 original size:12 final size:13
Alignment explanation
Indices: 6136--6169 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
6126 AATCTAAATC
6136 TAAAGCAAATT-A
1 TAAAGCAAATTAA
6148 TAAAGCAAATTAA
1 TAAAGCAAATTAA
6161 TAAAGCAAA
1 TAAAGCAAA
6170 CAATAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.21
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:6174 original size:12 final size:12
Alignment explanation
Indices: 6136--6175 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
6126 AATCTAAATC
*
6136 TAAAGCAAATTA
1 TAAAGCAAATAA
6148 TAAAGCAAATTAA
1 TAAAGCAAA-TAA
*
6161 TAAAGCAAACAA
1 TAAAGCAAATAA
6173 TAA
1 TAA
6176 TTATAAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.20
Consensus pattern (12 bp):
TAAAGCAAATAA
Found at i:11587 original size:17 final size:17
Alignment explanation
Indices: 11565--11598 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11555 AAAGTGGTAA
11565 TCAGTAATTAAATTTAG
1 TCAGTAATTAAATTTAG
11582 TCAGTAATTAAATTTAG
1 TCAGTAATTAAATTTAG
11599 CTAGTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
TCAGTAATTAAATTTAG
Found at i:11633 original size:7 final size:7
Alignment explanation
Indices: 11621--11696 Score: 62
Period size: 7 Copynumber: 10.7 Consensus size: 7
11611 AATAATAATC
11621 AGTAAAA
1 AGTAAAA
11628 AGTAAAA
1 AGTAAAA
* **
11635 TGATAATT
1 AG-TAAAA
11643 AGTAAAA
1 AGTAAAA
*
11650 AGTAAAG
1 AGTAAAA
**
11657 AGTAATC
1 AGTAAAA
*
11664 AGTAAAG
1 AGTAAAA
**
11671 AGTAAGG
1 AGTAAAA
11678 AGTAAAA
1 AGTAAAA
11685 AGTAAAA
1 AGTAAAA
11692 AGTAA
1 AGTAA
11697 TCAGTAAAGA
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
7 50 0.93
8 4 0.07
ACGTcount: A:0.59, C:0.01, G:0.20, T:0.20
Consensus pattern (7 bp):
AGTAAAA
Found at i:11662 original size:21 final size:20
Alignment explanation
Indices: 11605--11696 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 20
11595 TTAGCTAGTG
11605 AAAAGTAATAA-TAATCAGTA
1 AAAAGTAA-AAGTAATCAGTA
*
11625 AAAAGTAAAATGATAATTAGTA
1 AAAAGTAAAA-G-TAATCAGTA
11647 AAAAGTAAAGAGTAATCAGTA
1 AAAAGTAAA-AGTAATCAGTA
* * **
11668 AAGAGTAAGGAGTAAAAAGTA
1 AAAAGTAA-AAGTAATCAGTA
11689 AAAAGTAA
1 AAAAGTAA
11697 TCAGTAAAGA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.03
20 8 0.13
21 31 0.52
22 18 0.30
23 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAAGTAAAAGTAATCAGTA
Found at i:11689 original size:42 final size:41
Alignment explanation
Indices: 11616--12000 Score: 148
Period size: 42 Copynumber: 9.1 Consensus size: 41
11606 AAAGTAATAA
* * *
11616 TAATCAGTAAAAAGTAAAATGATAATTAGTAAAAAGTAAAGAG
1 TAATCAGTAAAGAGTAAGA-G-TAATAAGTAAAAAGTAAAGAG
* **
11659 TAATCAGTAAAGAGTAAGGAGTAAAAAGTAAAAAGTAATCAG
1 TAATCAGTAAAGAGTAA-GAGTAATAAGTAAAAAGTAAAGAG
* * * * *
11701 TAA--AGAAAAATAGTAAGGAGTGAGAAG-AAATCAGTAAA-ATGG
1 TAATCAG-TAAAGAGTAA-GAGTAATAAGTAAA-AAGTAAAGA--G
** * * * * * *
11743 TAAAGAATGAAGAGTAATTAGTAA-AATGGTAGAGAGT-AATAG
1 TAATCAGTAAAGAGTAA-GAGTAATAA--GTAAAAAGTAAAGAG
*
11785 TAATCAGT-AAGAAGTAATG-GTAATCAGTAAAAAGTACAA-AGG
1 TAATCAGTAAAG-AGTAA-GAGTAATAAGTAAAAAGTA-AAGA-G
* * * * *
11827 CAATCAGGAAAAAGTAAAATGGTAATCAGTAAAAAGTAAAG-G
1 TAATCAGTAAAGAGTAAGA--GTAATAAGTAAAAAGTAAAGAG
* * *
11869 TAATCAGTGAAA-AGTAAAATGGTAATTAG-AAAAGAGTAAAAGGG
1 TAATCAGT-AAAGAGTAAGA--GTAATAAGTAAAA-AGT-AAAGAG
* * *
11913 TAATCAGTAAAAAGTAAAATGGTAATTAGTAAAAAGTAAAGAG
1 TAATCAGTAAAGAGTAAGA--GTAATAAGTAAAAAGTAAAGAG
* *
11956 TAATCAGTAAAGAGTAAAGAGTAA-AGAGTAAAGAGTAAAAAG
1 TAATCAGTAAAGAGT-AAGAGTAATA-AGTAAAAAGTAAAGAG
11998 TAA
1 TAA
12001 AAAGTAATCA
Statistics
Matches: 272, Mismatches: 41, Indels: 59
0.73 0.11 0.16
Matches are distributed among these distances:
40 13 0.05
41 34 0.12
42 100 0.37
43 63 0.23
44 56 0.21
45 6 0.02
ACGTcount: A:0.54, C:0.03, G:0.22, T:0.20
Consensus pattern (41 bp):
TAATCAGTAAAGAGTAAGAGTAATAAGTAAAAAGTAAAGAG
Found at i:11838 original size:22 final size:22
Alignment explanation
Indices: 11784--11973 Score: 225
Period size: 22 Copynumber: 8.9 Consensus size: 22
11774 GAGAGTAATA
*
11784 GTAATCAGTAAGAAGT--AATG
1 GTAATCAGTAAAAAGTAAAATG
11804 GTAATCAGTAAAAAGTACAAA-G
1 GTAATCAGTAAAAAGTA-AAATG
* *
11826 GCAATCAGGAAAAAGTAAAATG
1 GTAATCAGTAAAAAGTAAAATG
11848 GTAATCAGTAAAAAGT-AAA-G
1 GTAATCAGTAAAAAGTAAAATG
*
11868 GTAATCAGTGAAAAGTAAAATG
1 GTAATCAGTAAAAAGTAAAATG
* *
11890 GTAATTAG-AAAAGAGTAAAAGG
1 GTAATCAGTAAAA-AGTAAAATG
11912 GTAATCAGTAAAAAGTAAAATG
1 GTAATCAGTAAAAAGTAAAATG
*
11934 GTAATTAGTAAAAAGT-AAA-G
1 GTAATCAGTAAAAAGTAAAATG
*
11954 AGTAATCAGTAAAGAGTAAA
1 -GTAATCAGTAAAAAGTAAA
11974 GAGTAAAGAG
Statistics
Matches: 146, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
20 32 0.22
21 29 0.20
22 79 0.54
23 6 0.04
ACGTcount: A:0.53, C:0.05, G:0.22, T:0.21
Consensus pattern (22 bp):
GTAATCAGTAAAAAGTAAAATG
Found at i:11855 original size:64 final size:64
Alignment explanation
Indices: 11784--11973 Score: 226
Period size: 64 Copynumber: 3.0 Consensus size: 64
11774 GAGAGTAATA
* *
11784 GTAATCAGTAAGAAGTAATGGTAATCAGTAAAAAGTACAAA-GGCAATCAGGAAAA-AGTAAAAT
1 GTAATCAGTAAAAAGTAATGGTAATCAGTAAAAAGTA-AAATGGCAATCA-GAAAAGAGTAAAAG
11847 G
64 G
* * * *
11848 GTAATCAGTAAAAAGTAAAGGTAATCAGTGAAAAGTAAAATGGTAATTAGAAAAGAGTAAAAGG
1 GTAATCAGTAAAAAGTAATGGTAATCAGTAAAAAGTAAAATGGCAATCAGAAAAGAGTAAAAGG
* * *
11912 GTAATCAGTAAAAAGTAAAATGGTAATTAGTAAAAAGT-AAA-GAGTAATCAGTAAAGAGTAAA
1 GTAATCAGTAAAAAGT--AATGGTAATCAGTAAAAAGTAAAATG-GCAATCAGAAAAGAGTAAA
11974 GAGTAAAGAG
Statistics
Matches: 110, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
63 8 0.07
64 65 0.59
65 20 0.18
66 17 0.15
ACGTcount: A:0.53, C:0.05, G:0.22, T:0.21
Consensus pattern (64 bp):
GTAATCAGTAAAAAGTAATGGTAATCAGTAAAAAGTAAAATGGCAATCAGAAAAGAGTAAAAGG
Found at i:11928 original size:7 final size:7
Alignment explanation
Indices: 11918--12007 Score: 81
Period size: 7 Copynumber: 12.7 Consensus size: 7
11908 AAGGGTAATC
11918 AGTAAAA
1 AGTAAAA
11925 AGTAAAA
1 AGTAAAA
* **
11932 TGGTAATT
1 -AGTAAAA
11940 AGTAAAA
1 AGTAAAA
*
11947 AGTAAAG
1 AGTAAAA
**
11954 AGTAATC
1 AGTAAAA
*
11961 AGTAAAG
1 AGTAAAA
*
11968 AGTAAAG
1 AGTAAAA
*
11975 AGTAAAG
1 AGTAAAA
*
11982 AGTAAAG
1 AGTAAAA
11989 AGTAAAA
1 AGTAAAA
11996 AGTAAAA
1 AGTAAAA
12003 AGTAA
1 AGTAA
12008 TCAGTAAAGA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
7 66 0.94
8 4 0.06
ACGTcount: A:0.59, C:0.01, G:0.21, T:0.19
Consensus pattern (7 bp):
AGTAAAA
Found at i:12001 original size:21 final size:21
Alignment explanation
Indices: 11940--12017 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
11930 AATGGTAATT
* **
11940 AGTAAAAAGTAAAGAGTAATC
1 AGTAAAGAGTAAAGAGTAAAA
*
11961 AGTAAAGAGTAAAGAGTAAAG
1 AGTAAAGAGTAAAGAGTAAAA
*
11982 AGTAAAGAGTAAAAAGTAAAA
1 AGTAAAGAGTAAAGAGTAAAA
**
12003 AGTAATCAGTAAAGA
1 AGTAAAGAGTAAAGA
12018 CAAAATAGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.59, C:0.03, G:0.22, T:0.17
Consensus pattern (21 bp):
AGTAAAGAGTAAAGAGTAAAA
Found at i:12015 original size:14 final size:14
Alignment explanation
Indices: 11940--12007 Score: 91
Period size: 14 Copynumber: 4.9 Consensus size: 14
11930 AATGGTAATT
11940 AGTAAAAAGTAAAG
1 AGTAAAAAGTAAAG
**
11954 AGTAATCAGTAAAG
1 AGTAAAAAGTAAAG
*
11968 AGTAAAGAGTAAAG
1 AGTAAAAAGTAAAG
* *
11982 AGTAAAGAGTAAAA
1 AGTAAAAAGTAAAG
11996 AGTAAAAAGTAA
1 AGTAAAAAGTAA
12008 TCAGTAAAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 48 1.00
ACGTcount: A:0.60, C:0.01, G:0.22, T:0.16
Consensus pattern (14 bp):
AGTAAAAAGTAAAG
Found at i:12085 original size:27 final size:29
Alignment explanation
Indices: 12041--12098 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 29
12031 GGTGAGAAGA
*
12041 AATCAGTAAAATGGAAAA-GGATAAAGAGT
1 AATCAGTAAAATGAAAAATGG-TAAAGAGT
12070 AATCAGT-AAA-GAAAAATGGTAAAGAGT
1 AATCAGTAAAATGAAAAATGGTAAAGAGT
12097 AA
1 AA
12099 AATATTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 15 0.56
28 5 0.19
29 7 0.26
ACGTcount: A:0.57, C:0.03, G:0.22, T:0.17
Consensus pattern (29 bp):
AATCAGTAAAATGAAAAATGGTAAAGAGT
Found at i:12113 original size:42 final size:43
Alignment explanation
Indices: 12067--12177 Score: 111
Period size: 42 Copynumber: 2.6 Consensus size: 43
12057 AAGGATAAAG
*
12067 AGTAATCAGTAAAGAAAAAT-GGTAAAGAGTAAAATATTAA-T
1 AGTAATCAGTAAAGAAAAATCAGTAAAGAGTAAAATATTAACT
** * **
12108 CAGTAAAAAGTAATG-GCAATCAGTAAAGAGTAAAATATTAACT
1 -AGTAATCAGTAAAGAAAAATCAGTAAAGAGTAAAATATTAACT
* **
12151 TGTAATCAGTAAAGAGTAATCAGTAAA
1 AGTAATCAGTAAAGAAAAATCAGTAAA
12178 AAATGAATAA
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
41 3 0.05
42 40 0.73
43 12 0.22
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.24
Consensus pattern (43 bp):
AGTAATCAGTAAAGAAAAATCAGTAAAGAGTAAAATATTAACT
Found at i:14622 original size:12 final size:12
Alignment explanation
Indices: 14605--14629 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14595 GATTAGCTAA
14605 CTCTCAATTTAG
1 CTCTCAATTTAG
14617 CTCTCAATTTAG
1 CTCTCAATTTAG
14629 C
1 C
14630 AATAAGTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (12 bp):
CTCTCAATTTAG
Found at i:17307 original size:32 final size:32
Alignment explanation
Indices: 17265--17342 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
17255 AATAAAAGAG
* *
17265 GAAGTGATCAGTAGAATGGACTGAAAGTAAAA
1 GAAGTAATCAGTAAAATGGACTGAAAGTAAAA
*
17297 GAAGTAATCAGTAAAATGGAGTGAAAGTAAAA
1 GAAGTAATCAGTAAAATGGACTGAAAGTAAAA
17329 GAAGTAATCAGTAA
1 GAAGTAATCAGTAA
17343 GTTGGTAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.50, C:0.05, G:0.26, T:0.19
Consensus pattern (32 bp):
GAAGTAATCAGTAAAATGGACTGAAAGTAAAA
Found at i:17309 original size:16 final size:16
Alignment explanation
Indices: 17290--17342 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
17280 ATGGACTGAA
17290 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
*
17306 AGTAAAATGGAGTGAA--
1 AGTAAAA-GAAGT-AATC
17322 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
17338 AGTAA
1 AGTAA
17343 GTTGGTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 2 0.06
15 4 0.13
16 19 0.61
17 4 0.13
18 2 0.06
ACGTcount: A:0.55, C:0.04, G:0.23, T:0.19
Consensus pattern (16 bp):
AGTAAAAGAAGTAATC
Found at i:17365 original size:40 final size:40
Alignment explanation
Indices: 17315--17423 Score: 182
Period size: 40 Copynumber: 2.7 Consensus size: 40
17305 CAGTAAAATG
* **
17315 GAGTGAAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
17355 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
*
17395 GAGTAAAAGTAAAAGAAATAATCAGTAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAA
17424 TCGGTAAAGA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.54, C:0.03, G:0.21, T:0.22
Consensus pattern (40 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
Found at i:17447 original size:16 final size:17
Alignment explanation
Indices: 17421--17454 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17411 AATAATCAGT
*
17421 AAATCGGTAAAGAGTAA
1 AAATCGGTAAAAAGTAA
17438 AAAT-GGTAAAAAGTAA
1 AAATCGGTAAAAAGTAA
17454 A
1 A
17455 GAGTAATCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.59, C:0.03, G:0.21, T:0.18
Consensus pattern (17 bp):
AAATCGGTAAAAAGTAA
Found at i:17448 original size:40 final size:39
Alignment explanation
Indices: 17315--17439 Score: 166
Period size: 40 Copynumber: 3.2 Consensus size: 39
17305 CAGTAAAATG
* * *
17315 GAGTGAAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAATCGGTAA-TAA
17355 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAT-GGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGT-AAATCGGTAA-TAA
*
17395 GAGTAAAAGTAAAAGAAATAATCAGTAAATCGGT-A-AA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAATCGGTAATAA
17432 GAGTAAAA
1 GAGTAAAA
17440 ATGGTAAAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
37 10 0.12
39 5 0.06
40 62 0.77
41 3 0.04
ACGTcount: A:0.54, C:0.03, G:0.22, T:0.22
Consensus pattern (39 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAATCGGTAATAA
Found at i:17510 original size:32 final size:31
Alignment explanation
Indices: 17473--17561 Score: 98
Period size: 32 Copynumber: 3.0 Consensus size: 31
17463 AGTAAAGAGT
17473 AAAATGGTAATTAAATTCAAAGAGTAAAATG
1 AAAATGGTAATTAAATTCAAAGAGTAAAATG
**
17504 ACAAATGGCGATTAAATTCAAAGAG-----TG
1 A-AAATGGTAATTAAATTCAAAGAGTAAAATG
*
17531 AAAATAGTAATTAAATTCAAGAGAGTAAAAT
1 AAAATGGTAATTAAATTCAA-AGAGTAAAAT
17562 AGTAATCAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
26 16 0.35
27 7 0.15
31 1 0.02
32 22 0.48
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.25
Consensus pattern (31 bp):
AAAATGGTAATTAAATTCAAAGAGTAAAATG
Found at i:17543 original size:26 final size:26
Alignment explanation
Indices: 17514--17567 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
17504 ACAAATGGCG
17514 ATTAAATTCAA-AGAGTGAAAATAGTA
1 ATTAAATTCAAGAGAGT-AAAATAGTA
17540 ATTAAATTCAAGAGAGTAAAATAGTA
1 ATTAAATTCAAGAGAGTAAAATAGTA
17566 AT
1 AT
17568 CAGTAAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.28
Consensus pattern (26 bp):
ATTAAATTCAAGAGAGTAAAATAGTA
Found at i:17592 original size:7 final size:7
Alignment explanation
Indices: 17569--17679 Score: 64
Period size: 7 Copynumber: 15.7 Consensus size: 7
17559 AATAGTAATC
17569 AGTAAAG
1 AGTAAAG
*
17576 AGAAAAG
1 AGTAAAG
17583 AGTAAAG
1 AGTAAAG
**
17590 AGTAATC
1 AGTAAAG
17597 AGTAAAG
1 AGTAAAG
*
17604 AGTAAAAA
1 AGT-AAAG
**
17612 AGTAATC
1 AGTAAAG
17619 AGTAAAG
1 AGTAAAG
**
17626 AGTAATC
1 AGTAAAG
*
17633 AGTAAAA
1 AGTAAAG
**
17640 AGTAATC
1 AGTAAAG
17647 AGTAAAGGG
1 AGTAAA--G
*
17656 AG-AATG
1 AGTAAAG
17662 -GTAAAG
1 AGTAAAG
17668 AGTAAAG
1 AGTAAAG
*
17675 GGTAA
1 AGTAA
17680 TCAGTAAGAG
Statistics
Matches: 77, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
5 1 0.01
6 4 0.05
7 62 0.81
8 8 0.10
9 2 0.03
ACGTcount: A:0.54, C:0.04, G:0.25, T:0.17
Consensus pattern (7 bp):
AGTAAAG
Found at i:17616 original size:50 final size:50
Alignment explanation
Indices: 17552--17653 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
17542 TAAATTCAAG
* * *
17552 AGAGTAAAATAGTAATCAGTAAAGAGAAAAGAGTAAAGAGTAATCAGTAA
1 AGAGTAAAAAAGTAATCAGTAAAGAGAAAACAGTAAAAAGTAATCAGTAA
* *
17602 AGAGTAAAAAAGTAATCAGTAAAGAGTAATCAGTAAAAAGTAATCAGTAA
1 AGAGTAAAAAAGTAATCAGTAAAGAGAAAACAGTAAAAAGTAATCAGTAA
17652 AG
1 AG
17654 GGAGAATGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.19
Consensus pattern (50 bp):
AGAGTAAAAAAGTAATCAGTAAAGAGAAAACAGTAAAAAGTAATCAGTAA
Found at i:17631 original size:14 final size:14
Alignment explanation
Indices: 17562--17653 Score: 106
Period size: 14 Copynumber: 7.0 Consensus size: 14
17552 AGAGTAAAAT
17562 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
* **
17576 AGAAAAGAGTAAAG
1 AGTAATCAGTAAAG
17590 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
17604 AGT-A--A--AAA-
1 AGTAATCAGTAAAG
17612 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
*
17626 AGTAATCAGTAAAA
1 AGTAATCAGTAAAG
17640 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
17654 GGAGAATGGT
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
8 3 0.05
9 4 0.06
11 2 0.03
13 4 0.06
14 51 0.80
ACGTcount: A:0.55, C:0.05, G:0.21, T:0.18
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:17665 original size:28 final size:26
Alignment explanation
Indices: 17555--17672 Score: 100
Period size: 28 Copynumber: 4.4 Consensus size: 26
17545 ATTCAAGAGA
*
17555 GTAAAATAGTAATCAGTAAAGAGAAAAG
1 GTAAAA-AGTAATCAGTAAAGAG-AATG
*
17583 AGTAAAGAGTAATCAGTAAAGAG--T-
1 -GTAAAAAGTAATCAGTAAAGAGAATG
* *
17607 -AAAAAAGTAATCAGTAAAGAGTAATCA
1 GTAAAAAGTAATCAGTAAAGAG-AAT-G
17634 GTAAAAAGTAATCAGTAAAGGGAGAATG
1 GTAAAAAGTAATCAGTAAA--GAGAATG
*
17662 GTAAAGAGTAA
1 GTAAAAAGTAA
17673 AGGGTAATCA
Statistics
Matches: 74, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
22 19 0.26
25 1 0.01
28 43 0.58
29 8 0.11
30 3 0.04
ACGTcount: A:0.54, C:0.04, G:0.23, T:0.19
Consensus pattern (26 bp):
GTAAAAAGTAATCAGTAAAGAGAATG
Found at i:17697 original size:35 final size:35
Alignment explanation
Indices: 17633--17714 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
17623 AAGAGTAATC
* * *
17633 AGTAAAAAGTAATCAGTAAAGGGAGAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAGGCAAAATGGTAAAG
* **
17668 AGTAAAGGGTAATCAGT-AAGAGCAAAATGGTAATT
1 AGTAAAGAGTAATCAGTAAAG-GCAAAATGGTAAAG
17703 AGTAAAGAGTAA
1 AGTAAAGAGTAA
17715 AATAGTAATC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 3 0.08
35 36 0.92
ACGTcount: A:0.50, C:0.04, G:0.27, T:0.20
Consensus pattern (35 bp):
AGTAAAGAGTAATCAGTAAAGGCAAAATGGTAAAG
Found at i:17722 original size:15 final size:15
Alignment explanation
Indices: 17702--17766 Score: 57
Period size: 15 Copynumber: 4.4 Consensus size: 15
17692 AAATGGTAAT
17702 TAGTAAAGAGTAAAA
1 TAGTAAAGAGTAAAA
**
17717 TAGTAATCAGTAAAA
1 TAGTAAAGAGTAAAA
17732 -AGT-AAGAAGGT--AA
1 TAGTAAAG-A-GTAAAA
17745 TCAGTAAAGAGTAAAA
1 T-AGTAAAGAGTAAAA
17761 TAGTAA
1 TAGTAA
17767 TCAGTAAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
13 3 0.08
14 6 0.15
15 24 0.62
16 6 0.15
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.22
Consensus pattern (15 bp):
TAGTAAAGAGTAAAA
Found at i:17778 original size:36 final size:36
Alignment explanation
Indices: 17732--17909 Score: 115
Period size: 35 Copynumber: 5.2 Consensus size: 36
17722 ATCAGTAAAA
17732 AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
1 AGTAA-AAGGTAATCAGTAAAGAGTAAAATAGTAATC
* *
17769 AGTAAAAGGTAATCAGT-AATAGTAAAATTGTAATC
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
* * * ** **
17804 GGCAAAAAGTAAAGAGTAATTAGTAAAAT-G---T-
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
* * **
17835 -G-AAAAGGCAATCAGTAAAGAGTAAAATGGTAAAA
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
* * * * *
17869 AGT-AATGGTGATTAGTAAAGAGT-AAAGAGCAATC
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
17903 AGTAAAA
1 AGTAAAA
17910 AAGGGAATAG
Statistics
Matches: 107, Mismatches: 25, Indels: 20
0.70 0.16 0.13
Matches are distributed among these distances:
29 20 0.19
30 2 0.02
32 1 0.01
34 9 0.08
35 48 0.45
36 22 0.21
37 5 0.05
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (36 bp):
AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
Found at i:17780 original size:22 final size:22
Alignment explanation
Indices: 17676--17795 Score: 101
Period size: 22 Copynumber: 5.6 Consensus size: 22
17666 AGAGTAAAGG
* * *
17676 GTAATCAGTAAGA-GCAAAATG
1 GTAATCAGTAAAAGGTAAAATA
*
17697 GTAATTAGT-AAAGAGTAAAATA
1 GTAATCAGTAAAAG-GTAAAATA
* *
17719 GTAATCAGTAAAAAGTAAGAA-G
1 GTAATCAGTAAAAGGTAA-AATA
17741 GTAATCAGT-AAAGAGTAAAATA
1 GTAATCAGTAAAAG-GTAAAATA
17763 GTAATCAGTAAAAGGT--AATCA
1 GTAATCAGTAAAAGGTAAAAT-A
17784 GTAAT-AGTAAAA
1 GTAATCAGTAAAA
17796 TTGTAATCGG
Statistics
Matches: 82, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
20 12 0.15
21 19 0.23
22 42 0.51
23 9 0.11
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.23
Consensus pattern (22 bp):
GTAATCAGTAAAAGGTAAAATA
Found at i:17839 original size:29 final size:29
Alignment explanation
Indices: 17807--17887 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
17797 TGTAATCGGC
*
17807 AAAAAGTAAAGAGTAATTAGTAAAAT-GT
1 AAAAAGTAATGAGTAATTAGTAAAATGGT
* * * **
17835 GAAAAGGCAATCAGTAAAGAGTAAAATGGT
1 -AAAAAGTAATGAGTAATTAGTAAAATGGT
*
17865 AAAAAGTAATG-GTGATTAGTAAA
1 AAAAAGTAATGAGTAATTAGTAAA
17888 GAGTAAAGAG
Statistics
Matches: 39, Mismatches: 12, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
28 9 0.23
29 28 0.72
30 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.22, T:0.22
Consensus pattern (29 bp):
AAAAAGTAATGAGTAATTAGTAAAATGGT
Found at i:20984 original size:36 final size:36
Alignment explanation
Indices: 20937--21014 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
20927 TCTCGATGGA
20937 TGTGTTAAATTTATGGGTGTTCATTGTTATGGTTTC
1 TGTGTTAAATTTATGGGTGTTCATTGTTATGGTTTC
* *
20973 TGTGTTAAATTTGTGGGTGTTCATTGTTATGGTTTT
1 TGTGTTAAATTTATGGGTGTTCATTGTTATGGTTTC
21009 TGTGTT
1 TGTGTT
21015 TACTTTGGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.14, C:0.04, G:0.27, T:0.55
Consensus pattern (36 bp):
TGTGTTAAATTTATGGGTGTTCATTGTTATGGTTTC
Found at i:21183 original size:38 final size:39
Alignment explanation
Indices: 21111--21191 Score: 128
Period size: 38 Copynumber: 2.1 Consensus size: 39
21101 CTCTATTTGC
*
21111 AATGTGTTTATGGTTTGGTGGGATGATTTTGAATGGTTAT
1 AATGTGTTTATGGTTTGGT-GGATGATTTTGAATGGTGAT
*
21151 AATGTGTTTTTGGTTTGGT-GATGATTTTGAATGGTGAT
1 AATGTGTTTATGGTTTGGTGGATGATTTTGAATGGTGAT
21189 AAT
1 AAT
21192 TGTGGATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
38 21 0.54
40 18 0.46
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (39 bp):
AATGTGTTTATGGTTTGGTGGATGATTTTGAATGGTGAT
Found at i:22824 original size:13 final size:13
Alignment explanation
Indices: 22806--22832 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22796 AAGACCTAGT
22806 TATTGGGAAATTA
1 TATTGGGAAATTA
22819 TATTGGGAAATTA
1 TATTGGGAAATTA
22832 T
1 T
22833 TGAAAGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (13 bp):
TATTGGGAAATTA
Found at i:27036 original size:17 final size:18
Alignment explanation
Indices: 26983--27037 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
26973 GAGCCCTTCA
*
26983 AACCCACCTAATCCCCCC
1 AACCCACCTAATCTCCCC
*
27001 AACCCACC-AGATTTCCCC
1 AACCCACCTA-ATCTCCCC
27019 AACCCACCTAA-CTCCCC
1 AACCCACCTAATCTCCCC
27036 AA
1 AA
27038 GAATCATCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 8 0.25
18 23 0.72
19 1 0.03
ACGTcount: A:0.31, C:0.55, G:0.02, T:0.13
Consensus pattern (18 bp):
AACCCACCTAATCTCCCC
Found at i:37534 original size:15 final size:15
Alignment explanation
Indices: 37510--37540 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
37500 AGAAATAGAC
*
37510 TTTCTTAAAGCAGTT
1 TTTCTAAAAGCAGTT
37525 TTTCTAAAAGCAGTT
1 TTTCTAAAAGCAGTT
37540 T
1 T
37541 CTGCACAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (15 bp):
TTTCTAAAAGCAGTT
Found at i:42767 original size:13 final size:13
Alignment explanation
Indices: 42749--42783 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
42739 TTAATTATTG
42749 TTTGCTTTATTAA
1 TTTGCTTTATTAA
42762 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
42775 TCTGCTTTA
1 TTTGCTTTA
42784 GATTTAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:44194 original size:41 final size:41
Alignment explanation
Indices: 44095--44201 Score: 141
Period size: 41 Copynumber: 2.7 Consensus size: 41
44085 TAATTCAAGG
* * ** *
44095 TGACAACTTCTGATGTC--A-GTAATTATAATTTACCGGAG
1 TGACAACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAA
44133 TGAC-ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAA
1 TGACAACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAA
44173 TGACAACTTCTGGTGTCAAAGGTAATTTT
1 TGACAACTTCTGGTGTCAAAGGTAATTTT
44202 CAATATTATT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
37 11 0.18
38 4 0.07
39 1 0.02
40 20 0.33
41 24 0.40
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.36
Consensus pattern (41 bp):
TGACAACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAA
Found at i:44774 original size:21 final size:21
Alignment explanation
Indices: 44750--44796 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
44740 AAATATTGTA
* *
44750 TTTATTCTACAATGGGCAGTT
1 TTTATTCTAAAATGAGCAGTT
*
44771 TTTA-TCTAAAATGAGTAGTT
1 TTTATTCTAAAATGAGCAGTT
44791 TTTATT
1 TTTATT
44797 TTATTTTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.49
Consensus pattern (21 bp):
TTTATTCTAAAATGAGCAGTT
Found at i:45204 original size:31 final size:31
Alignment explanation
Indices: 45166--45228 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
45156 GTGAGATTAA
*
45166 AATTGTAACTTTGTGAACTTAACCAGCGATG
1 AATTGTAACTTTGAGAACTTAACCAGCGATG
45197 AATTGTAACTTTGAGAACTTAACCAGCGATG
1 AATTGTAACTTTGAGAACTTAACCAGCGATG
45228 A
1 A
45229 GAAAATACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (31 bp):
AATTGTAACTTTGAGAACTTAACCAGCGATG
Found at i:46014 original size:62 final size:63
Alignment explanation
Indices: 45922--46056 Score: 254
Period size: 62 Copynumber: 2.1 Consensus size: 63
45912 TATTTTCCTT
45922 TATAAACTACTTAATTTTTTTTTTATTTTCCTTAAGAAAATTCGGTTATACCTATTTGAATAGG
1 TATAAACTACTTAA-TTTTTTTTTATTTTCCTTAAGAAAATTCGGTTATACCTATTTGAATAGG
45986 TATAAACTACTTAA-TTTTTTTTATTTTCCTTAAGAAAATTCGGTTATACCTATTTGAATAGG
1 TATAAACTACTTAATTTTTTTTTATTTTCCTTAAGAAAATTCGGTTATACCTATTTGAATAGG
46048 TATAAACTA
1 TATAAACTA
46057 TCAAAGACGG
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 57 0.80
64 14 0.20
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (63 bp):
TATAAACTACTTAATTTTTTTTTATTTTCCTTAAGAAAATTCGGTTATACCTATTTGAATAGG
Found at i:46823 original size:22 final size:22
Alignment explanation
Indices: 46795--46838 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
46785 CAAAACTAAA
*
46795 TTGCATTGTGTCTTCTTTACTT
1 TTGCATTGTGTCTTCTCTACTT
46817 TTGCATTGTGTCTTCTCTACTT
1 TTGCATTGTGTCTTCTCTACTT
46839 GGTCTCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.20, G:0.14, T:0.57
Consensus pattern (22 bp):
TTGCATTGTGTCTTCTCTACTT
Done.