Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014384.1 Corchorus capsularis cultivar CVL-1 contig14405, 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: 77288
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:7569 original size:2 final size:2
Alignment explanation
Indices: 7562--7593 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7552 GAAATAAAAG
7562 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7594 GTTTGTTGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13369 original size:3 final size:3
Alignment explanation
Indices: 13361--13394 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
13351 GAACCATATA
13361 AAG AAG AAG AAG AAG -AG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
13395 TGCTCAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:13381 original size:14 final size:14
Alignment explanation
Indices: 13362--13390 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13352 AACCATATAA
13362 AGAAGAAGAAGAAG
1 AGAAGAAGAAGAAG
13376 AGAAGAAGAAGAAG
1 AGAAGAAGAAGAAG
13390 A
1 A
13391 AGAATGCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAAGAAG
Found at i:13383 original size:17 final size:17
Alignment explanation
Indices: 13361--13393 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
13351 GAACCATATA
13361 AAGAAGAAGAAGAAGAG
1 AAGAAGAAGAAGAAGAG
13378 AAGAAGAAGAAGAAGA
1 AAGAAGAAGAAGAAGA
13394 ATGCTCAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
AAGAAGAAGAAGAAGAG
Found at i:14477 original size:30 final size:30
Alignment explanation
Indices: 14395--14477 Score: 114
Period size: 31 Copynumber: 2.8 Consensus size: 30
14385 CCATTTTGCC
* *
14395 AAATTA-TCAATTTGAGTCTAAACCTTTTA
1 AAATTACTCAATTTGAGTCTAAACATTTCA
*
14424 AAAGTTACTCAATTTGAATCTAAACATTTCA
1 AAA-TTACTCAATTTGAGTCTAAACATTTCA
*
14455 AAATTACTCAATTTGAGCCTAAA
1 AAATTACTCAATTTGAGTCTAAA
14478 AACAAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
29 3 0.06
30 21 0.45
31 23 0.49
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (30 bp):
AAATTACTCAATTTGAGTCTAAACATTTCA
Found at i:16777 original size:20 final size:18
Alignment explanation
Indices: 16752--16795 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
16742 CCCCATCTCG
16752 TCCCCGACTTCACAACCTCA
1 TCCCCGAC-TC-CAACCTCA
* *
16772 TCCCCGTCTCCATCCTCA
1 TCCCCGACTCCAACCTCA
16790 TCCCCG
1 TCCCCG
16796 GCGGGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 13 0.59
19 2 0.09
20 7 0.32
ACGTcount: A:0.16, C:0.55, G:0.07, T:0.23
Consensus pattern (18 bp):
TCCCCGACTCCAACCTCA
Found at i:16919 original size:16 final size:16
Alignment explanation
Indices: 16898--16931 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
16888 AAGGAAAATA
16898 TAATTCATAAAAAGTT
1 TAATTCATAAAAAGTT
16914 TAATTCATAAAAAGTT
1 TAATTCATAAAAAGTT
16930 TA
1 TA
16932 CTACAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (16 bp):
TAATTCATAAAAAGTT
Found at i:17067 original size:20 final size:20
Alignment explanation
Indices: 17016--17074 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
17006 AATATATATT
* *
17016 TATATTATTAGTAAGTTAGTA
1 TATATTATTATTTA-TTAGTA
*
17037 AATA-T-TTATTTATTAGTA
1 TATATTATTATTTATTAGTA
17055 TATATTATTATTTATTAGTA
1 TATATTATTATTTATTAGTA
17075 AAACATATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 9 0.28
19 6 0.19
20 14 0.44
21 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
TATATTATTATTTATTAGTA
Found at i:20205 original size:34 final size:34
Alignment explanation
Indices: 20156--20220 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
20146 ATTTCTGTAT
20156 TTTCCAAAAATATTACAAGGACAAGATTAAATCG
1 TTTCCAAAAATATTACAAGGACAAGATTAAATCG
*
20190 TTTCCAAGAAA-ATTACAAGGATAAGATTAAA
1 TTTCCAA-AAATATTACAAGGACAAGATTAAA
20221 CTGTTATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.26
Consensus pattern (34 bp):
TTTCCAAAAATATTACAAGGACAAGATTAAATCG
Found at i:20823 original size:16 final size:16
Alignment explanation
Indices: 20802--20835 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
20792 ACAATTCAGA
20802 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
20818 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
20834 AA
1 AA
20836 ATATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:21123 original size:41 final size:40
Alignment explanation
Indices: 21078--21201 Score: 124
Period size: 47 Copynumber: 2.9 Consensus size: 40
21068 ATTTTGTTTG
* *
21078 TTCAAGATCAAGTC-GTCAAGACCCTTGAATTAAATCATCAA
1 TTCAAGACCAAGTCAGTC--GACCCTTGAATCAAATCATCAA
*
21119 TTCAAGACCAAGTCATTCGACCCTTGAATCAAATCAAATCAAATCAA
1 TTCAAGACCAAGTCAGTCGACCCTTG-----AATCAAATC--ATCAA
*
21166 TTCAAGACCAAGTCATTCGACCCTTGAATCAAATCA
1 TTCAAGACCAAGTCAGTCGACCCTTGAATCAAATCA
21202 AATCAAATCA
Statistics
Matches: 72, Mismatches: 3, Indels: 17
0.78 0.03 0.18
Matches are distributed among these distances:
40 9 0.12
41 13 0.18
42 11 0.15
45 8 0.11
47 31 0.43
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (40 bp):
TTCAAGACCAAGTCAGTCGACCCTTGAATCAAATCATCAA
Found at i:21176 original size:47 final size:47
Alignment explanation
Indices: 21114--21212 Score: 198
Period size: 47 Copynumber: 2.1 Consensus size: 47
21104 GAATTAAATC
21114 ATCAATTCAAGACCAAGTCATTCGACCCTTGAATCAAATCAAATCAA
1 ATCAATTCAAGACCAAGTCATTCGACCCTTGAATCAAATCAAATCAA
21161 ATCAATTCAAGACCAAGTCATTCGACCCTTGAATCAAATCAAATCAA
1 ATCAATTCAAGACCAAGTCATTCGACCCTTGAATCAAATCAAATCAA
21208 ATCAA
1 ATCAA
21213 ACTCTCAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.23
Consensus pattern (47 bp):
ATCAATTCAAGACCAAGTCATTCGACCCTTGAATCAAATCAAATCAA
Found at i:21196 original size:42 final size:42
Alignment explanation
Indices: 21097--21212 Score: 155
Period size: 47 Copynumber: 2.7 Consensus size: 42
21087 AAGTCGTCAA
*
21097 GACCCTTGAATTAAATC--ATCAATTCAAGACCAAGTCATTC
1 GACCCTTGAATCAAATCAAATCAATTCAAGACCAAGTCATTC
21137 GACCCTTGAATCAAATCAAATCAAATCAATTCAAGACCAAGTCATTC
1 GACCCTTG-----AATCAAATCAAATCAATTCAAGACCAAGTCATTC
*
21184 GACCCTTGAATCAAATCAAATCAAATCAA
1 GACCCTTGAATCAAATCAAATCAATTCAA
21213 ACTCTCAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
40 8 0.12
42 20 0.30
45 8 0.12
47 31 0.46
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.24
Consensus pattern (42 bp):
GACCCTTGAATCAAATCAAATCAATTCAAGACCAAGTCATTC
Found at i:23117 original size:64 final size:65
Alignment explanation
Indices: 23015--23152 Score: 233
Period size: 64 Copynumber: 2.1 Consensus size: 65
23005 CAAACCAAAC
* *
23015 CAAAAAAAAAAAGAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAG
1 CAAAAAAAAAAAGAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACAGCTTAGGCAAAACTTAGAG
*
23080 CAAAAAAAAAAA-AGGCTCGCTAAGTTGAAAATCCTGCAAAGGACAGCTTAGGCAAAACTTAGAG
1 CAAAAAAAAAAAGAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACAGCTTAGGCAAAACTTAGAG
*
23144 CACAAAAAA
1 CAAAAAAAA
23153 CAAATGAAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
64 57 0.83
65 12 0.17
ACGTcount: A:0.49, C:0.17, G:0.20, T:0.14
Consensus pattern (65 bp):
CAAAAAAAAAAAGAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACAGCTTAGGCAAAACTTAGAG
Found at i:23926 original size:16 final size:16
Alignment explanation
Indices: 23905--23938 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
23895 ACAATTCAGA
*
23905 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAACTCTG
23921 AAGCAGAAAAACTCTG
1 AAGCAGAAAAACTCTG
23937 AA
1 AA
23939 ATATTTCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.21, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAACTCTG
Found at i:24263 original size:41 final size:40
Alignment explanation
Indices: 24218--24388 Score: 137
Period size: 47 Copynumber: 3.9 Consensus size: 40
24208 ATTTTGTTTG
* *
24218 TTCAAGATCAAGTC-GTCAAGACCCTTGAATTAAATCATCAA
1 TTCAAGACCAAGTCAGTC--GACCCTTGAATCAAATCATCAA
*
24259 TTCAAGACCAAGTCATTCGACCCTTGAATCAAATCAAATCAAATCAA
1 TTCAAGACCAAGTCAGTCGACCCTTG-----AATCAAATC--ATCAA
* *
24306 TTCAAGACCAAGTCATTCGACCCTTAAATCAAATCAAATCAAATCAA
1 TTCAAGACCAAGTCAGTCGACCC-T---T-GAATCAAATC--ATCAA
*
24353 TTCAAGACCAAGTCATTCGACCCTTGAATCAAATCA
1 TTCAAGACCAAGTCAGTCGACCCTTGAATCAAATCA
24389 AATCAAATCA
Statistics
Matches: 112, Mismatches: 5, Indels: 27
0.78 0.03 0.19
Matches are distributed among these distances:
40 9 0.08
41 13 0.12
42 11 0.10
43 1 0.01
45 8 0.07
46 1 0.01
47 67 0.60
48 1 0.01
51 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (40 bp):
TTCAAGACCAAGTCAGTCGACCCTTGAATCAAATCATCAA
Found at i:24316 original size:47 final size:47
Alignment explanation
Indices: 24254--24399 Score: 283
Period size: 47 Copynumber: 3.1 Consensus size: 47
24244 GAATTAAATC
24254 ATCAATTCAAGACCAAGTCATTCGACCCTTGAATCAAATCAAATCAA
1 ATCAATTCAAGACCAAGTCATTCGACCCTTGAATCAAATCAAATCAA
*
24301 ATCAATTCAAGACCAAGTCATTCGACCCTTAAATCAAATCAAATCAA
1 ATCAATTCAAGACCAAGTCATTCGACCCTTGAATCAAATCAAATCAA
24348 ATCAATTCAAGACCAAGTCATTCGACCCTTGAATCAAATCAAATCAA
1 ATCAATTCAAGACCAAGTCATTCGACCCTTGAATCAAATCAAATCAA
24395 ATCAA
1 ATCAA
24400 ACTCTCAAAT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 97 1.00
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.23
Consensus pattern (47 bp):
ATCAATTCAAGACCAAGTCATTCGACCCTTGAATCAAATCAAATCAA
Found at i:24688 original size:20 final size:20
Alignment explanation
Indices: 24663--24706 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
24653 AATCTCCATT
24663 AAAAAAAAGATTAGAAATAG
1 AAAAAAAAGATTAGAAATAG
24683 AAAAAAAAGATTAGAAATAG
1 AAAAAAAAGATTAGAAATAG
24703 AAAA
1 AAAA
24707 GAAACTTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAAAAAAGATTAGAAATAG
Found at i:28407 original size:69 final size:72
Alignment explanation
Indices: 28326--28505 Score: 276
Period size: 73 Copynumber: 2.5 Consensus size: 72
28316 ATGAAGGGAA
* * *
28326 TAATTAGGTATTAATTAGCTATTATTCCCT-T-T-TAATCATATTGAATTTATTCATTATTAATT
1 TAATTAGATATTAATTAGCTATTATTACATATATATAATCATATTGAATTTATTCATTATTAATT
28388 TAACTAT
66 TAACTAT
*
28395 TAATTAGATATTAATTAGCTATTAATTAGATATATATAATCATATTGAATTTATTCATTATTAAT
1 TAATTAGATATTAATTAGCTATT-ATTACATATATATAATCATATTGAATTTATTCATTATTAAT
28460 TTAACTAT
65 TTAACTAT
*
28468 TAATTAGATATTAATTAGCTATTAATTAGATATATATA
1 TAATTAGATATTAATTAGCTATT-ATTACATATATATA
28506 GTATAATGGA
Statistics
Matches: 103, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
69 22 0.21
70 4 0.04
71 1 0.01
72 1 0.01
73 75 0.73
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (72 bp):
TAATTAGATATTAATTAGCTATTATTACATATATATAATCATATTGAATTTATTCATTATTAATT
TAACTAT
Found at i:28408 original size:11 final size:11
Alignment explanation
Indices: 28392--28500 Score: 78
Period size: 11 Copynumber: 9.3 Consensus size: 11
28382 TTAATTTAAC
28392 TATTAATTAGA
1 TATTAATTAGA
*
28403 TATTAATTAGC
1 TATTAATTAGA
28414 TATTAATTAGA
1 TATTAATTAGA
* *
28425 TA-TATATAATCA
1 TATTA-ATTA-GA
*
28437 TATTGAATTTATTCA
1 TATT-AA-TTA--GA
28452 TTATTAATTTA-A
1 -TATTAA-TTAGA
28464 CTATTAATTAGA
1 -TATTAATTAGA
*
28476 TATTAATTAGC
1 TATTAATTAGA
28487 TATTAATTAGA
1 TATTAATTAGA
28498 TAT
1 TAT
28501 ATATAGTATA
Statistics
Matches: 82, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
10 2 0.02
11 51 0.62
12 11 0.13
13 2 0.02
14 3 0.04
15 9 0.11
16 4 0.05
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (11 bp):
TATTAATTAGA
Found at i:28419 original size:22 final size:22
Alignment explanation
Indices: 28380--28500 Score: 111
Period size: 22 Copynumber: 5.1 Consensus size: 22
28370 ATTTATTCAT
28380 TATTAATTTAACTATTAATTAGA
1 TATTAA-TTAACTATTAATTAGA
*
28403 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
28425 TA-T-ATATAATCATATTGAATTTATTCA
1 TATTAAT-TAA-C-TATT-AA-TTA--GA
28452 TTATTAATTTAACTATTAATTAGA
1 -TATTAA-TTAACTATTAATTAGA
*
28476 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
28498 TAT
1 TAT
28501 ATATAGTATA
Statistics
Matches: 82, Mismatches: 5, Indels: 23
0.75 0.05 0.21
Matches are distributed among these distances:
20 2 0.02
21 3 0.04
22 36 0.44
23 16 0.20
24 3 0.04
25 3 0.04
26 3 0.04
27 3 0.04
28 6 0.07
29 2 0.02
30 4 0.05
31 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:33925 original size:31 final size:31
Alignment explanation
Indices: 33879--33938 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
33869 TTTTTAGCCA
33879 TCAATTTAAGCCTAAACCTTTCAAAAGTTGC
1 TCAATTTAAGCCTAAACCTTTCAAAAGTTGC
* *
33910 TCAATTTGAGGCTAAACCTTTCAAAAGTT
1 TCAATTTAAGCCTAAACCTTTCAAAAGTT
33939 AACTAATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (31 bp):
TCAATTTAAGCCTAAACCTTTCAAAAGTTGC
Found at i:33947 original size:31 final size:31
Alignment explanation
Indices: 33879--33950 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
33869 TTTTTAGCCA
* *
33879 TCAATTTAAGCCTAAACCTTTCAAAAGTTGC
1 TCAATTTGAGCCTAAACCTTTCAAAAGTTAC
*
33910 TCAATTTGAGGCTAAACCTTTCAAAAGTTAAC
1 TCAATTTGAGCCTAAACCTTTCAAAAGTT-AC
33942 T-AATTTGAG
1 TCAATTTGAG
33951 TATAAAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 35 0.95
32 2 0.05
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (31 bp):
TCAATTTGAGCCTAAACCTTTCAAAAGTTAC
Found at i:35714 original size:16 final size:16
Alignment explanation
Indices: 35693--35729 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
35683 CGATCGGCTC
* *
35693 TTTCTTTTTCTTTTTG
1 TTTCTTTTTCCTTATG
35709 TTTCTTTTTCCTTATG
1 TTTCTTTTTCCTTATG
35725 TTTCT
1 TTTCT
35730 GTTTATTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (16 bp):
TTTCTTTTTCCTTATG
Found at i:43208 original size:2 final size:2
Alignment explanation
Indices: 43203--43229 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43193 ACATATATAG
43203 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
43230 AGTACCTGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:44550 original size:25 final size:26
Alignment explanation
Indices: 44522--44592 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 26
44512 TAATAATTTT
44522 AGTTTTAATTTATAATTTATAT-ATA
1 AGTTTTAATTTATAATTTATATAATA
*
44547 AGTTTTAAATTT-TAATGTTTTATAATA
1 AGTTTT-AATTTATAAT-TTATATAATA
44574 A-TTTATATATTTAT-ATTTA
1 AGTTT-TA-ATTTATAATTTA
44593 ACATTTAGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
25 10 0.26
26 16 0.42
27 11 0.29
28 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (26 bp):
AGTTTTAATTTATAATTTATATAATA
Found at i:44558 original size:38 final size:37
Alignment explanation
Indices: 44475--44583 Score: 100
Period size: 38 Copynumber: 2.9 Consensus size: 37
44465 TATATAATAT
* *
44475 TTTTATATTTTA-TTTTATATATAATTTATCA-A-AAG
1 TTTTAAATTTTAGTTTTATTTATAATTTAT-ATATAAG
* *
44510 ATTAATAATTTTAGTTTTAATTTATAATTTATATATAAG
1 TTTTA-AATTTTAGTTTT-ATTTATAATTTATATATAAG
*
44549 TTTTAAATTTTAATGTTTTA-TAATAATTTATATAT
1 TTTTAAATTTT-A-GTTTTATTTATAATTTATATAT
44584 TTATATTTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
35 3 0.05
36 6 0.10
37 5 0.08
38 33 0.55
39 8 0.13
40 5 0.08
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.57
Consensus pattern (37 bp):
TTTTAAATTTTAGTTTTATTTATAATTTATATATAAG
Found at i:45314 original size:11 final size:11
Alignment explanation
Indices: 45298--45322 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
45288 AATCAAAGAC
45298 TTGTTGCTTTG
1 TTGTTGCTTTG
45309 TTGTTGCTTTG
1 TTGTTGCTTTG
45320 TTG
1 TTG
45323 ATGGAGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.28, T:0.64
Consensus pattern (11 bp):
TTGTTGCTTTG
Found at i:45347 original size:35 final size:35
Alignment explanation
Indices: 45301--45410 Score: 150
Period size: 35 Copynumber: 3.1 Consensus size: 35
45291 CAAAGACTTG
45301 TTGCTTTGTTGTTGCTTTGTTGATGGAGAAGAACT
1 TTGCTTTGTTGTTGCTTTGTTGATGGAGAAGAACT
*
45336 TTGCTTTGTTGTTGCTTTGTTGATGGAGAAGATCT
1 TTGCTTTGTTGTTGCTTTGTTGATGGAGAAGAACT
* * * *
45371 TTGCTTCAGAT-TTGCTTTGCTTGATGCAGAATAACT
1 TTGCTT-TGTTGTTGCTTTG-TTGATGGAGAAGAACT
45407 TTGC
1 TTGC
45411 CTTGCCTTGA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
35 48 0.72
36 19 0.28
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.45
Consensus pattern (35 bp):
TTGCTTTGTTGTTGCTTTGTTGATGGAGAAGAACT
Found at i:54854 original size:16 final size:16
Alignment explanation
Indices: 54833--54881 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
54823 GCTCCATCTT
54833 TTATGGCTTTCATGAC
1 TTATGGCTTTCATGAC
54849 TTATGGCTTTCATCG-C
1 TTATGGCTTTCAT-GAC
54865 TTATGGCTTTCATGAC
1 TTATGGCTTTCATGAC
54881 T
1 T
54882 AGCCGTCCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.03
16 29 0.94
17 1 0.03
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (16 bp):
TTATGGCTTTCATGAC
Found at i:56375 original size:46 final size:46
Alignment explanation
Indices: 56200--56374 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
56190 TCTTTCGACA
*
56200 TTGGTGGGGTTGATTATTTTATCGCCCTCTACCTCTGCATCGGCCTT-
1 TTGGCGGGGTTGATT-TTTTATCGCCCTCTACCTCTGCATCGG-CTTC
**
56247 TTGGCGGGGTTGATTTTTTTTTATCGCCCTCTACCTCTGTGTCGGCTTC
1 TTGGCGGGGTTGA---TTTTTTATCGCCCTCTACCTCTGCATCGGCTTC
* * * * *
56296 TCGGCGGGGTTGATTATTTATCGCCCTCCACCTTTGCATCAGCTTC
1 TTGGCGGGGTTGATTTTTTATCGCCCTCTACCTCTGCATCGGCTTC
* *
56342 TTGGCGGGGTTGATTGTTCATCGCCCTCTACCT
1 TTGGCGGGGTTGATTTTTTATCGCCCTCTACCT
56375 TGTTTATTTG
Statistics
Matches: 110, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
46 56 0.51
47 12 0.11
48 3 0.03
49 37 0.34
50 2 0.02
ACGTcount: A:0.10, C:0.27, G:0.24, T:0.39
Consensus pattern (46 bp):
TTGGCGGGGTTGATTTTTTATCGCCCTCTACCTCTGCATCGGCTTC
Found at i:57377 original size:90 final size:90
Alignment explanation
Indices: 57224--57407 Score: 332
Period size: 90 Copynumber: 2.0 Consensus size: 90
57214 GATAACTCCT
* * *
57224 TTTTGCCTTGAAGATCGAGCACTCAACCTATCGAACACAGATTTACTAGTTTGAGGCATTCCAAG
1 TTTTGCCTTGAAGATCGAGCACTCAACCTATCGAACACAGATTTACGAGTTTGAGCCATTCCAAA
57289 ACAATCAAAGGCTGACACACGAGGC
66 ACAATCAAAGGCTGACACACGAGGC
*
57314 TTTTGCCTTGAAGATCGAGCACTCAACCTATCGAACATAGATTTACGAGTTTGAGCCATTCCAAA
1 TTTTGCCTTGAAGATCGAGCACTCAACCTATCGAACACAGATTTACGAGTTTGAGCCATTCCAAA
57379 ACAATCAAAGGCTGACACACGAGGC
66 ACAATCAAAGGCTGACACACGAGGC
57404 TTTT
1 TTTT
57408 CATCTTCTGA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (90 bp):
TTTTGCCTTGAAGATCGAGCACTCAACCTATCGAACACAGATTTACGAGTTTGAGCCATTCCAAA
ACAATCAAAGGCTGACACACGAGGC
Found at i:59950 original size:35 final size:35
Alignment explanation
Indices: 59904--60000 Score: 124
Period size: 35 Copynumber: 2.7 Consensus size: 35
59894 ACTTTCGTAG
* *
59904 GCTTTGTTGATGGAGAAGAACTTTGCTT-TGTTGTT
1 GCTTTGTTGATGGAGAAGAACTTTGCTTCAGAT-TT
*
59939 GCTTTGTTGATGGAGAAGATCTTTGCTTCAGATTT
1 GCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTT
**
59974 GCTTTGTTTGATACAGAAGAACTTTGC
1 GCTTTG-TTGATGGAGAAGAACTTTGC
60001 CTTGCCTTGA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
35 35 0.65
36 19 0.35
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (35 bp):
GCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTT
Found at i:63934 original size:20 final size:20
Alignment explanation
Indices: 63898--63937 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
63888 CAAAATTAAC
63898 CCTATTTTTATGATTATTTT
1 CCTATTTTTATGATTATTTT
*
63918 CCTATGTTTT-TGGTTATTTT
1 CCTAT-TTTTATGATTATTTT
63938 TATGTGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65
Consensus pattern (20 bp):
CCTATTTTTATGATTATTTT
Done.