Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011273.1 Corchorus capsularis cultivar CVL-1 contig11294, 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: 82932
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:6871 original size:13 final size:14
Alignment explanation
Indices: 6855--6883 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6845 TTAAATTTCC
6855 AATTGTAA-TTTGA
1 AATTGTAATTTTGA
6868 AATTGTAATTTTGA
1 AATTGTAATTTTGA
6882 AA
1 AA
6884 CTATACTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (14 bp):
AATTGTAATTTTGA
Found at i:11336 original size:13 final size:14
Alignment explanation
Indices: 11320--11348 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
11310 TTAAATTTCC
11320 AATTGTAA-TTTGA
1 AATTGTAATTTTGA
11333 AATTGTAATTTTGA
1 AATTGTAATTTTGA
11347 AA
1 AA
11349 CTATACTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (14 bp):
AATTGTAATTTTGA
Found at i:16230 original size:2 final size:2
Alignment explanation
Indices: 16223--16259 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
16213 AGTTGCTCTT
16223 TA TA TA TA TGA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
16260 TTATTTTACG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18075 original size:29 final size:30
Alignment explanation
Indices: 17997--18075 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 30
17987 AAACTTACAT
17997 AAAACGGCCAAATAAACTCCTGAACTCTAATTG
1 AAAA-GGCCAAATAAAC-CCTGAACTCT-ATTG
* *
18030 --CA-GCCAAATAAGCCCCTGAACTCT-TTG
1 AAAAGGCCAAATAA-ACCCTGAACTCTATTG
18057 AAAAGGCCAAATAAACCCT
1 AAAAGGCCAAATAAACCCT
18076 TTTTGGATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
27 3 0.08
29 24 0.63
30 10 0.26
31 1 0.03
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.19
Consensus pattern (30 bp):
AAAAGGCCAAATAAACCCTGAACTCTATTG
Found at i:21388 original size:21 final size:21
Alignment explanation
Indices: 21359--21400 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
21349 GTCATATTGG
*
21359 ACAATTTAATTAATCTTCCAA
1 ACAAATTAATTAATCTTCCAA
21380 ACAAATTAATTAATCTTCCAA
1 ACAAATTAATTAATCTTCCAA
21401 GTGATTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (21 bp):
ACAAATTAATTAATCTTCCAA
Found at i:23095 original size:31 final size:31
Alignment explanation
Indices: 23026--23174 Score: 149
Period size: 31 Copynumber: 4.9 Consensus size: 31
23016 TCCTTTTGTG
* * **
23026 CACGTGGCATGCCACATGTCACTTTTTGAAA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* * *
23057 CATGTGGCATGCCATGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* * * *
23088 CACGTGGCGTGACATGTGTCATTTTTTTGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
*
23119 CACGTGTCGTG--ACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* * *
23148 TACGTGGCGTGCCACATGTCAATTTTT
1 CACGTGGCGTGCCACGTGTCACTTTTT
23175 TGTAGATAGA
Statistics
Matches: 98, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
29 24 0.24
31 74 0.76
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (31 bp):
CACGTGGCGTGCCACGTGTCACTTTTTGGTA
Found at i:23103 original size:60 final size:58
Alignment explanation
Indices: 23026--23174 Score: 138
Period size: 60 Copynumber: 2.4 Consensus size: 58
23016 TCCTTTTGTG
* * * *
23026 CACGTGGCATGCCACATGTCACTTTTTGAAACATGTGGCATGCCATGTGTCACTTTTTGGTA
1 CACGTGGCGTG-CACATGTCAATTTTTG-AACACGTGGCATG--ACGTGTCACTTTTTGGTA
* * * *
23088 CACGTGGCGTG-ACATGTGTCATTTTTTTGTACACGTGTCGTGACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCACA--TGTCA-ATTTTTGAACACGTGGCATGACGTGTCACTTTTTGGTA
*
23148 TACGTGGCGTGCCACATGTCAATTTTT
1 CACGTGGCGTG-CACATGTCAATTTTT
23175 TGTAGATAGA
Statistics
Matches: 73, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
59 5 0.07
60 35 0.48
62 27 0.37
63 6 0.08
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (58 bp):
CACGTGGCGTGCACATGTCAATTTTTGAACACGTGGCATGACGTGTCACTTTTTGGTA
Found at i:28712 original size:12 final size:12
Alignment explanation
Indices: 28695--28720 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28685 ATATTAATTT
28695 TAATAATACTAA
1 TAATAATACTAA
28707 TAATAATACTAA
1 TAATAATACTAA
28719 TA
1 TA
28721 TGATTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (12 bp):
TAATAATACTAA
Found at i:34763 original size:27 final size:27
Alignment explanation
Indices: 34725--34777 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
34715 GGTACCTAAG
34725 TTTCATACTACCTCAAAGTTAAAATCC
1 TTTCATACTACCTCAAAGTTAAAATCC
34752 TTTCATACTACCTCAAAGTTAAAATC
1 TTTCATACTACCTCAAAGTTAAAATC
34778 TGGGGAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.34
Consensus pattern (27 bp):
TTTCATACTACCTCAAAGTTAAAATCC
Found at i:37764 original size:17 final size:17
Alignment explanation
Indices: 37738--37770 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
37728 GTTTTTCATA
37738 ATTTTATCTGTTTTACG
1 ATTTTATCTGTTTTACG
*
37755 ATTTTCTCTGTTTTAC
1 ATTTTATCTGTTTTAC
37771 AAAAAGTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.09, T:0.61
Consensus pattern (17 bp):
ATTTTATCTGTTTTACG
Found at i:38161 original size:72 final size:72
Alignment explanation
Indices: 38071--38209 Score: 269
Period size: 72 Copynumber: 1.9 Consensus size: 72
38061 ATGGCCAATC
38071 TTCCCCATTCCAACAACTCTAAGCAAAACCCAAGTCTCCGACATACAAAAACCAAAAAAACCCAT
1 TTCCCCATTCCAACAACTCTAAGCAAAACCCAAGTCTCCGACATACAAAAACCAAAAAAACCCAT
38136 CATCAGA
66 CATCAGA
*
38143 TTCCCCATTCCAACAACTCTAAGCAAAACCCAAGTCTCCGACGTACAAAAACCAAAAAAACCCAT
1 TTCCCCATTCCAACAACTCTAAGCAAAACCCAAGTCTCCGACATACAAAAACCAAAAAAACCCAT
38208 CA
66 CA
38210 GATTCAGACC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.44, C:0.35, G:0.06, T:0.15
Consensus pattern (72 bp):
TTCCCCATTCCAACAACTCTAAGCAAAACCCAAGTCTCCGACATACAAAAACCAAAAAAACCCAT
CATCAGA
Found at i:38386 original size:63 final size:63
Alignment explanation
Indices: 38319--38446 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
38309 AACACTACTC
38319 TCTGCCAATCCCAAAACCAAAACTCTTGGCCAAACCCCAAAACTCTCTCTTTGTGAAGCCTTG
1 TCTGCCAATCCCAAAACCAAAACTCTTGGCCAAACCCCAAAACTCTCTCTTTGTGAAGCCTTG
*
38382 TCTGCCAATCCCAAAACCAAAACTCTTGGCCAAACCCCAAAACTCTCTGTTTGTGAAGCCTTG
1 TCTGCCAATCCCAAAACCAAAACTCTTGGCCAAACCCCAAAACTCTCTCTTTGTGAAGCCTTG
38445 TC
1 TC
38447 GATTTGGCGG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.30, C:0.34, G:0.12, T:0.24
Consensus pattern (63 bp):
TCTGCCAATCCCAAAACCAAAACTCTTGGCCAAACCCCAAAACTCTCTCTTTGTGAAGCCTTG
Found at i:39074 original size:89 final size:92
Alignment explanation
Indices: 38922--39092 Score: 233
Period size: 89 Copynumber: 1.9 Consensus size: 92
38912 ATCAATAGTT
* * * * *
38922 TAGTTCATGCCCAAATTTAAACCCAAACATGAAAGAATATCTTTAGCAGGCTGAAATATTTTTTC
1 TAGTTCATGCCCAAATCTAAACCAAAACATAAAAGAAAATCTTTAGCAGGCTGAAAGATTTTTTC
38987 TCTTTT-TT-CTTCTTATCAATATCAA
66 TCTTTTGTTCCTTCTTATCAATATCAA
*
39012 TAGTTCATGCCCAAATCT-AAGCAAAACATAAAAGAAAATCTTTAGCAGGCT-AAAGATCTTTTT
1 TAGTTCATGCCCAAATCTAAACCAAAACATAAAAGAAAATCTTTAGCAGGCTGAAAGAT-TTTTT
* *
39075 TTTTTTTGTTCCTTCTTA
65 CTCTTTTGTTCCTTCTTA
39093 CTGTGCCAGT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
88 5 0.07
89 39 0.56
90 19 0.27
91 7 0.10
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (92 bp):
TAGTTCATGCCCAAATCTAAACCAAAACATAAAAGAAAATCTTTAGCAGGCTGAAAGATTTTTTC
TCTTTTGTTCCTTCTTATCAATATCAA
Found at i:42562 original size:26 final size:26
Alignment explanation
Indices: 42533--42591 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
42523 CTGTTTCTGT
42533 TTATGATTGGCTTGTTTTTTGTTGAA
1 TTATGATTGGCTTGTTTTTTGTTGAA
42559 TTATGATTGGCTTGTTTTTTGTTGAA
1 TTATGATTGGCTTGTTTTTTGTTGAA
42585 TTATGAT
1 TTATGAT
42592 ATTGATGACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.17, C:0.03, G:0.22, T:0.58
Consensus pattern (26 bp):
TTATGATTGGCTTGTTTTTTGTTGAA
Found at i:42798 original size:14 final size:15
Alignment explanation
Indices: 42778--42815 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
42768 TGTTTTGATT
42778 AACCCGACTACACCG
1 AACCCGACTACACCG
*
42793 -ACCCGACTGCACCG
1 AACCCGACTACACCG
42807 AACCCGACT
1 AACCCGACT
42816 TTGTCGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.29, C:0.47, G:0.16, T:0.08
Consensus pattern (15 bp):
AACCCGACTACACCG
Found at i:44054 original size:20 final size:21
Alignment explanation
Indices: 44017--44057 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
44007 AACCCGTTAA
*
44017 TTAAAGCGTGTCAGTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
44038 TTAAA-CGTGTTAATCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
44058 CTGACACGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:44127 original size:42 final size:43
Alignment explanation
Indices: 44047--44129 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 43
44037 CTTAAACGTG
*
44047 TTAATCGTGTCCTGACACGATTAAAATACGAAACACGATAATC
1 TTAATCGTGTCCTGACACGATTAAAACACGAAACACGATAATC
* * * *
44090 TTAATCGTGTCC-GACACGATTCAGACACGAGATACGATAA
1 TTAATCGTGTCCTGACACGATTAAAACACGAAACACGATAA
44130 GTCAAACACG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 23 0.66
43 12 0.34
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (43 bp):
TTAATCGTGTCCTGACACGATTAAAACACGAAACACGATAATC
Found at i:45628 original size:25 final size:27
Alignment explanation
Indices: 45576--45628 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
45566 TTACTCAACT
* **
45576 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTATATTTTTATTTTAATGTAA
45603 AAAAACTATATTTTTA-TTTAAT-TAA
1 AAAAACTATATTTTTATTTTAATGTAA
45628 A
1 A
45629 TCTAATATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 15 0.65
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTATATTTTTATTTTAATGTAA
Found at i:52335 original size:12 final size:12
Alignment explanation
Indices: 52318--52349 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
52308 GGACGATGAG
*
52318 GAAGAAGAATCT
1 GAAGAAGAATCA
52330 GAAGAAGAATCA
1 GAAGAAGAATCA
52342 GAAGAAGA
1 GAAGAAGA
52350 GAAGGGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.28, T:0.09
Consensus pattern (12 bp):
GAAGAAGAATCA
Found at i:58696 original size:6 final size:6
Alignment explanation
Indices: 58682--58712 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
58672 AATTATTAAA
*
58682 TGCAAC TGCACC TGCACC TGCACC TGCACC T
1 TGCACC TGCACC TGCACC TGCACC TGCACC T
58713 CATTATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.45, G:0.16, T:0.19
Consensus pattern (6 bp):
TGCACC
Found at i:61764 original size:9 final size:8
Alignment explanation
Indices: 61750--61788 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 8
61740 TTTTTAGATC
61750 ATTATTAT
1 ATTATTAT
61758 GATTATTAT
1 -ATTATTAT
61767 ATATATTAT
1 AT-TATTAT
61776 ATTA-TAT
1 ATTATTAT
61783 ATTATT
1 ATTATT
61789 TTTGTCCCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.25
8 5 0.18
9 16 0.57
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (8 bp):
ATTATTAT
Found at i:63266 original size:18 final size:18
Alignment explanation
Indices: 63245--63286 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
63235 GAAAGGAACC
63245 GGGCCCTGTCAAGGTTCA
1 GGGCCCTGTCAAGGTTCA
63263 GGGCCCTGTCAAGGTTCA
1 GGGCCCTGTCAAGGTTCA
*
63281 AGGCCC
1 GGGCCC
63287 ACCGAGCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.33, T:0.19
Consensus pattern (18 bp):
GGGCCCTGTCAAGGTTCA
Found at i:63563 original size:18 final size:18
Alignment explanation
Indices: 63540--63591 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
63530 CCTGTGCGGT
63540 CCAACTCGTCAAGTCTGC
1 CCAACTCGTCAAGTCTGC
*
63558 CCAACTCGTCAAGTTTGC
1 CCAACTCGTCAAGTCTGC
63576 CCAACTCGTCAAGTCT
1 CCAACTCGTCAAGTCT
63592 TAAGTCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.23, C:0.37, G:0.15, T:0.25
Consensus pattern (18 bp):
CCAACTCGTCAAGTCTGC
Found at i:67192 original size:79 final size:78
Alignment explanation
Indices: 67080--67319 Score: 381
Period size: 78 Copynumber: 3.1 Consensus size: 78
67070 AGTTTTTAAT
67080 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
67145 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* ** *
67158 TAAAATGGTAAAATGGTTAAAATATTTTAGTTATAAGGATATTAGCTTTAATTATATAAAAATAG
1 TAAAATAGTAAAATGG-TAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAG
67223 AGTTTTTAGTTGAG
65 AGTTTTTAGTTGAG
* * * * *
67237 TAAAATAGTAAAATGATAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
*
67302 GTTTTTAGTTGAC
66 GTTTTTAGTTGAG
67315 TAAAA
1 TAAAA
67320 CTAAAAAAAC
Statistics
Matches: 147, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
78 74 0.50
79 73 0.50
ACGTcount: A:0.48, C:0.01, G:0.14, T:0.38
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:67436 original size:10 final size:10
Alignment explanation
Indices: 67417--67459 Score: 61
Period size: 10 Copynumber: 4.2 Consensus size: 10
67407 ACTTTTTAAT
67417 ATAG-TATAG
1 ATAGATATAG
67426 ATAGATATAG
1 ATAGATATAG
67436 ATATAGATATAG
1 --ATAGATATAG
67448 ATAGATATAG
1 ATAGATATAG
67458 AT
1 AT
67460 GTACGTACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 4 0.13
10 17 0.55
12 10 0.32
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.33
Consensus pattern (10 bp):
ATAGATATAG
Found at i:67437 original size:6 final size:6
Alignment explanation
Indices: 67415--67459 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
67405 GTACTTTTTA
67415 ATATAG -TATAG --ATAG ATATAG ATATAG ATATAG --ATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
67458 AT
1 AT
67460 GTACGTACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 8 0.23
5 5 0.14
6 22 0.63
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:67442 original size:16 final size:16
Alignment explanation
Indices: 67415--67459 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
67405 GTACTTTTTA
67415 ATATAG-TATAGATAG
1 ATATAGATATAGATAG
*
67430 ATATAGATATAGATAT
1 ATATAGATATAGATAG
*
67446 AGATAGATATAGAT
1 ATATAGATATAGAT
67460 GTACGTACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (16 bp):
ATATAGATATAGATAG
Found at i:78939 original size:23 final size:24
Alignment explanation
Indices: 78913--78963 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
78903 GCCAGAATTC
* * *
78913 AGAACCCAGAGACGAAAAC-AAAG
1 AGAACCCAGAAAAGAAAACGAAAA
78936 AGAACCCAGAAAAGAAAACGAAAA
1 AGAACCCAGAAAAGAAAACGAAAA
78960 AGAA
1 AGAA
78964 AAGCAACCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.63, C:0.18, G:0.20, T:0.00
Consensus pattern (24 bp):
AGAACCCAGAAAAGAAAACGAAAA
Found at i:80919 original size:20 final size:21
Alignment explanation
Indices: 80894--80940 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
80884 ATAATCTGGA
80894 TTACTAAAT-ACCG-TCCCCTT
1 TTACTAAATCACCGCT-CCCTT
*
80914 TTACT-AGTCACCGCTCCCTT
1 TTACTAAATCACCGCTCCCTT
80934 TTACTAA
1 TTACTAA
80941 CCACCGCCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.09
20 19 0.83
21 2 0.09
ACGTcount: A:0.23, C:0.34, G:0.06, T:0.36
Consensus pattern (21 bp):
TTACTAAATCACCGCTCCCTT
Found at i:80953 original size:20 final size:20
Alignment explanation
Indices: 80909--80947 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
80899 AAATACCGTC
**
80909 CCCTTTTACTAGTCACCGCT
1 CCCTTTTACTAACCACCGCT
80929 CCCTTTTACTAACCACCGC
1 CCCTTTTACTAACCACCGC
80948 CTCCTTGGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.44, G:0.08, T:0.31
Consensus pattern (20 bp):
CCCTTTTACTAACCACCGCT
Found at i:81241 original size:20 final size:20
Alignment explanation
Indices: 81216--81254 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
81206 CATATAAAAT
*
81216 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
81236 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
81255 CTTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:81508 original size:24 final size:24
Alignment explanation
Indices: 81475--81527 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
81465 TTGAATGATT
*
81475 AAGGTTTG-AAAGTTTGAAGGTTG
1 AAGGATTGAAAAGTTTGAAGGTTG
* *
81498 AGAGGATTGAAAATTTTGAAGTTTG
1 A-AGGATTGAAAAGTTTGAAGGTTG
81523 AAGGA
1 AAGGA
81528 AAATAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.04
24 10 0.40
25 14 0.56
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (24 bp):
AAGGATTGAAAAGTTTGAAGGTTG
Done.