Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012696.1 Corchorus capsularis cultivar CVL-1 contig12717, 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: 43714
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1427 original size:10 final size:10
Alignment explanation
Indices: 1412--1436 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1402 ATTTAATATA
1412 GATATTTACG
1 GATATTTACG
1422 GATATTTACG
1 GATATTTACG
1432 GATAT
1 GATAT
1437 ATCAAGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (10 bp):
GATATTTACG
Found at i:10656 original size:40 final size:40
Alignment explanation
Indices: 10607--10682 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
10597 GCACAATTAA
*
10607 AGTCTTAATTCAGTGTAATTAAGAAAAGTTAAGAAAAGTG
1 AGTCTTAATTCAGTGTAATTAAGAAAAATTAAGAAAAGTG
*
10647 AGTCTTAATTCAGTGTAATTAAGAAAAATTAGGAAA
1 AGTCTTAATTCAGTGTAATTAAGAAAAATTAAGAAA
10683 GTCAAACACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.30
Consensus pattern (40 bp):
AGTCTTAATTCAGTGTAATTAAGAAAAATTAAGAAAAGTG
Found at i:10739 original size:39 final size:39
Alignment explanation
Indices: 10687--10838 Score: 189
Period size: 39 Copynumber: 3.8 Consensus size: 39
10677 AGGAAAGTCA
*
10687 AACACAGTTAAAATCTTAATTCAAGGTAATTAAGGAATG
1 AACACAGTTAAAATCTTAATTCAAGGTAATTAAGAAATG
* *
10726 AACACAGTAAAAATCTTAATTCATA-GTAATTAAGAAAAG
1 AACACAGTTAAAATCTTAATTCA-AGGTAATTAAGAAATG
* * * *
10765 AACACAGTCAAAGTCTTAATTCATGGTAATTAAGAAAGTCA
1 AACACAGTTAAAATCTTAATTCAAGGTAATTAAGAAA-T-G
* *
10806 AACACAGTTAAAATCTTAATTCATGGTGATTAA
1 AACACAGTTAAAATCTTAATTCAAGGTAATTAA
10839 AAAAGGTAAA
Statistics
Matches: 98, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
39 67 0.68
40 1 0.01
41 30 0.31
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (39 bp):
AACACAGTTAAAATCTTAATTCAAGGTAATTAAGAAATG
Found at i:10782 original size:78 final size:79
Alignment explanation
Indices: 10687--10843 Score: 219
Period size: 78 Copynumber: 2.0 Consensus size: 79
10677 AGGAAAGTCA
* * *
10687 AACACAGTTAAAATCTTAATTCAAGGTAATTAAGGAA-T-GAACACAGTAAAAATCTTAATTCAT
1 AACACAGTCAAAATCTTAATTCAAGGTAATTAAGAAAGTCAAACACAGTAAAAATCTTAATTCAT
10750 AGTAATTAAGAAAAG
66 AGTAATTAA-AAAAG
* * *
10765 AACACAGTCAAAGTCTTAATTCATGGTAATTAAGAAAGTCAAACACAGTTAAAATCTTAATTCAT
1 AACACAGTCAAAATCTTAATTCAAGGTAATTAAGAAAGTCAAACACAGTAAAAATCTTAATTCAT
* *
10830 GGTGATTAAAAAAG
66 AGTAATTAAAAAAG
10844 GTAAATGCAG
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
78 33 0.48
79 6 0.09
80 30 0.43
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.27
Consensus pattern (79 bp):
AACACAGTCAAAATCTTAATTCAAGGTAATTAAGAAAGTCAAACACAGTAAAAATCTTAATTCAT
AGTAATTAAAAAAG
Found at i:10873 original size:42 final size:42
Alignment explanation
Indices: 10680--10880 Score: 188
Period size: 39 Copynumber: 5.0 Consensus size: 42
10670 AAAAATTAGG
* * *
10680 AAAGTCAAACACAGTTAAAA-TCTTAATTCAAGGTAATTAAG
1 AAAGTCAAACACAGTCAAAAGTCTTAATTCATGGTAATTAAA
* * * *
10721 GAA-T-GAACACAGT-AAAAATCTTAATTCATAGTAATTAAGA
1 AAAGTCAAACACAGTCAAAAGTCTTAATTCATGGTAATTAA-A
*
10761 AAAG---AACACAGTC-AAAGTCTTAATTCATGGTAATTAAG
1 AAAGTCAAACACAGTCAAAAGTCTTAATTCATGGTAATTAAA
* *
10799 AAAGTCAAACACAGTTAAAA-TCTTAATTCATGGTGATTAAA
1 AAAGTCAAACACAGTCAAAAGTCTTAATTCATGGTAATTAAA
** * *
10840 AAAGGT-AAATGCAGTCAAAAGACTTAATTCATGGAAATTAA
1 AAA-GTCAAACACAGTCAAAAGTCTTAATTCATGGTAATTAA
10881 GTAAAAACAT
Statistics
Matches: 132, Mismatches: 18, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
38 8 0.06
39 56 0.42
40 3 0.02
41 43 0.33
42 22 0.17
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (42 bp):
AAAGTCAAACACAGTCAAAAGTCTTAATTCATGGTAATTAAA
Found at i:10889 original size:80 final size:78
Alignment explanation
Indices: 10687--10889 Score: 216
Period size: 80 Copynumber: 2.6 Consensus size: 78
10677 AGGAAAGTCA
* * * *
10687 AACACAGTTAAA-ATCTTAATTCAAGGTAATTAAGGAATGAACACAGTAAAAATCTTAATTCATA
1 AACACAGTCAAAGA-CTTAATTCATGGTAATTAAGAAATAAACACAGTAAAAATCTTAATTCATA
10751 GTAATTAAGAAAAG
65 GTAATTAAGAAAAG
* *
10765 AACACAGTCAAAGTCTTAATTCATGGTAATTAAGAAAGTCAAACACAGTTAAAATCTTAATTCAT
1 AACACAGTCAAAGACTTAATTCATGGTAATTAAGAAA-T-AAACACAGTAAAAATCTTAATTCAT
* *
10830 GGTGATTAA-AAAAGG
64 AGTAATTAAGAAAA-G
* *
10845 TAA-ATGCAGTCAAAAGACTTAATTCATGGAAATTAAGTAA-AAACA
1 -AACA--CAGTC-AAAGACTTAATTCATGGTAATTAAGAAATAAACA
10890 TTAGAGAAGA
Statistics
Matches: 106, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
78 32 0.30
79 5 0.05
80 37 0.35
81 2 0.02
82 5 0.05
83 25 0.24
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (78 bp):
AACACAGTCAAAGACTTAATTCATGGTAATTAAGAAATAAACACAGTAAAAATCTTAATTCATAG
TAATTAAGAAAAG
Found at i:11002 original size:39 final size:39
Alignment explanation
Indices: 10894--11537 Score: 876
Period size: 39 Copynumber: 17.3 Consensus size: 39
10884 AAAACATTAG
10894 AGAAGACTGACTTAATTTC----AAGGAAATTAGGT-AA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
*
10928 AGAAAGACTAACTTAATTTC----AAGGAAATTAGGTAAA
1 AG-AAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
10964 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
* *
11003 AAAAGACTAACTTAATTTC----AAGGAAATTAGGTAAA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
11038 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT-AA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
11076 AGATAGACTGACTTAATTTC----AAGGAAATTAGGT-AA
1 AGA-AGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
11111 AGAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
1 AG-AAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
* *
11151 AAAAGACTGACTTAATTTCAAGAAAGCAAATTAGGTAAA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
11190 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT-AA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
*
11228 AGATAGACCGACTTAATTTC----AAGGAAATTAGGTAAA
1 AGA-AGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
11264 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
*
11303 AGAATACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
*
11342 AGAAGACTGACTTAATTTCGAGAAAGGAAATTAGGTAAA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
11381 AGAAGACTGA-TTAATTTCAAGAAAGGAAATTAGGT-AA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
*
11418 AGATGGACTGACTTAATTTC----AAGGAAATTAGGT-AA
1 AGA-AGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
11453 AGATAGACTGACTTAATTTC----AAGGAAATTAGGTAAA
1 AGA-AGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
11489 AGAAGACTGACTTAATTTCAA-AGAAGGAAATTAGGT-AA
1 AGAAGACTGACTTAATTTCAAGA-AAGGAAATTAGGTAAA
11527 AGAAAGACTGA
1 AG-AAGACTGA
11538 GGCACCGGCT
Statistics
Matches: 561, Mismatches: 18, Indels: 57
0.88 0.03 0.09
Matches are distributed among these distances:
34 2 0.00
35 202 0.36
36 15 0.03
37 5 0.01
38 44 0.08
39 290 0.52
40 3 0.01
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.25
Consensus pattern (39 bp):
AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA
Found at i:11009 original size:74 final size:74
Alignment explanation
Indices: 10894--11537 Score: 938
Period size: 74 Copynumber: 8.7 Consensus size: 74
10884 AAAACATTAG
*
10894 AGAAGACTGACTTAATTTC----AAGGAAATTAGGTAAAGAAAGACTAACTTAATTTCAAGGAAA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAA
10955 TTAGGTAAA
66 TTAGGTAAA
* *
10964 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAAAAAGACTAACTTAATTTCAAGGAAA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAA
11029 TTAGGTAAA
66 TTAGGTAAA
*
11038 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAGATAGACTGACTTAATTTCAAGGAAA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAA
11103 TTAGGT-AA
66 TTAGGTAAA
*
11111 AGAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAAAAAGACTGACTTAATTTCAAGAAA
1 AG-AAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAAG---
11176 GCAAATTAGGTAAA
62 G-AAATTAGGTAAA
* *
11190 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAGATAGACCGACTTAATTTCAAGGAAA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAA
11255 TTAGGTAAA
66 TTAGGTAAA
*
11264 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAA-AGAATACTGACTTAATTTCAAGAAA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAGA-AAGACTGACTTAATTTC----AA
11328 GGAAATTAGGTAAA
61 GGAAATTAGGTAAA
*
11342 AGAAGACTGACTTAATTTCGAGAAAGGAAATTAGGTAAA-AGAAGACTGA-TTAATTTCAAGAAA
1 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAGA-AAGACTGACTTAATTTC----AA
11405 GGAAATTAGGT-AA
61 GGAAATTAGGTAAA
* *
11418 AGATGGACTGACTTAATTTC----AAGGAAATTAGGTAAAGATAGACTGACTTAATTTCAAGGAA
1 AGA-AGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAA
11479 ATTAGGTAAA
65 ATTAGGTAAA
11489 AGAAGACTGACTTAATTTCAA-AGAAGGAAATTAGGTAAAGAAAGACTGA
1 AGAAGACTGACTTAATTTCAAGA-AAGGAAATTAGGTAAAGAAAGACTGA
11538 GGCACCGGCT
Statistics
Matches: 533, Mismatches: 18, Indels: 42
0.90 0.03 0.07
Matches are distributed among these distances:
70 47 0.09
71 5 0.01
73 28 0.05
74 274 0.51
75 1 0.00
76 5 0.01
77 41 0.08
78 128 0.24
79 4 0.01
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.25
Consensus pattern (74 bp):
AGAAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAA
TTAGGTAAA
Found at i:11601 original size:33 final size:33
Alignment explanation
Indices: 11564--11724 Score: 151
Period size: 36 Copynumber: 4.7 Consensus size: 33
11554 CAGGGAAGGA
*
11564 AATTAAGTAAAATAAAAGAATTTAATTCAGGGT
1 AATTAAGTAAAATAAAAGAACTTAATTCAGGGT
** *
11597 AATTAAGTAGAGTTAATAAGTGACTTAATTCAGGGT
1 AATTAAGTA-AAATAA-AAG-AACTTAATTCAGGGT
*
11633 AATTAAGTAGAATAAAAGAACTTAATTCAGGGT
1 AATTAAGTAAAATAAAAGAACTTAATTCAGGGT
**** **
11666 AATTAAGTGGGGTTAAAAAGTGGCTTAATTCAGGGT
1 AATTAAGT-AAAAT-AAAAG-AACTTAATTCAGGGT
**
11702 AATTAAGTGGAATAAAAGAACTT
1 AATTAAGTAAAATAAAAGAACTT
11725 GATCTAAAAA
Statistics
Matches: 105, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
33 34 0.32
34 14 0.13
35 14 0.13
36 43 0.41
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (33 bp):
AATTAAGTAAAATAAAAGAACTTAATTCAGGGT
Found at i:11632 original size:36 final size:35
Alignment explanation
Indices: 11585--11709 Score: 173
Period size: 36 Copynumber: 3.6 Consensus size: 35
11575 ATAAAAGAAT
11585 TTAATTCAGGGTAATTAAGTAGAGTTAATAAGTGAC
1 TTAATTCAGGGTAATTAAGTAGAGTTAA-AAGTGAC
* *
11621 TTAATTCAGGGTAATTAAGTAGA-ATAAAAG-AAC
1 TTAATTCAGGGTAATTAAGTAGAGTTAAAAGTGAC
* * *
11654 TTAATTCAGGGTAATTAAGTGGGGTTAAAAAGTGGC
1 TTAATTCAGGGTAATTAAGTAGAGTT-AAAAGTGAC
11690 TTAATTCAGGGTAATTAAGT
1 TTAATTCAGGGTAATTAAGT
11710 GGAATAAAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
33 23 0.29
34 4 0.05
35 8 0.10
36 44 0.56
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (35 bp):
TTAATTCAGGGTAATTAAGTAGAGTTAAAAGTGAC
Found at i:11639 original size:69 final size:69
Alignment explanation
Indices: 11564--11724 Score: 259
Period size: 69 Copynumber: 2.3 Consensus size: 69
11554 CAGGGAAGGA
* * *
11564 AATTAAGTAAAATAAAAGAATTTAATTCAGGGTAATTAAGTAGAGTTAATAAGTGACTTAATTCA
1 AATTAAGTAGAATAAAAGAACTTAATTCAGGGTAATTAAGTAGAGTTAAAAAGTGACTTAATTCA
11629 GGGT
66 GGGT
* * *
11633 AATTAAGTAGAATAAAAGAACTTAATTCAGGGTAATTAAGTGGGGTTAAAAAGTGGCTTAATTCA
1 AATTAAGTAGAATAAAAGAACTTAATTCAGGGTAATTAAGTAGAGTTAAAAAGTGACTTAATTCA
11698 GGGT
66 GGGT
*
11702 AATTAAGTGGAATAAAAGAACTT
1 AATTAAGTAGAATAAAAGAACTT
11725 GATCTAAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 85 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (69 bp):
AATTAAGTAGAATAAAAGAACTTAATTCAGGGTAATTAAGTAGAGTTAAAAAGTGACTTAATTCA
GGGT
Found at i:16450 original size:21 final size:22
Alignment explanation
Indices: 16409--16451 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
16399 AAGATTTCAA
*
16409 CTGAAGATTATATGGAGATTAT
1 CTGAAGATTATAAGGAGATTAT
*
16431 CTGAAGATT-TAAGTAGATTAT
1 CTGAAGATTATAAGGAGATTAT
16452 ATTTAGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (22 bp):
CTGAAGATTATAAGGAGATTAT
Found at i:19280 original size:129 final size:129
Alignment explanation
Indices: 19050--19295 Score: 379
Period size: 129 Copynumber: 1.9 Consensus size: 129
19040 GAACTATCTC
*
19050 CTGCTTTGCAGCAGCAGTCACTTGAACTCCCTACTTCACCTGGAAATCTTGCACCTCAGCCTGCC
1 CTGCTTTGCAGCAGCAGCCACTTGAACTCCCTACTTCACCTGGAAATCTTGCACCTCAGCCTGCC
* * *
19115 TCTCCTGTTTCACCCCATCATGATGGTCTGAATAAGGGCAAGGAACTTGTAGCAGTTGGTCCCT
66 TCTCCTGTTTCACCCCATCAAGATGGTCGGAATAAGGGCAAGCAACTTGTAGCAGTTGGTCCCT
* * ** *
19179 CTGCTTTGCAGCGGCAGCCACTTGAACTGCCTACTTCACCTGGTCA-CATTGCACCTCAGCCTGT
1 CTGCTTTGCAGCAGCAGCCACTTGAACTCCCTACTTCACCTGGAAATC-TTGCACCTCAGCCTGC
19243 CTCTCCTGTTTCACCCCATCAAGATGG-CAGGAATAAGGGCAAGCAACTTGTAG
65 CTCTCCTGTTTCACCCCATCAAGATGGTC-GGAATAAGGGCAAGCAACTTGTAG
19296 TAGCTGAGCC
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
128 2 0.02
129 104 0.98
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (129 bp):
CTGCTTTGCAGCAGCAGCCACTTGAACTCCCTACTTCACCTGGAAATCTTGCACCTCAGCCTGCC
TCTCCTGTTTCACCCCATCAAGATGGTCGGAATAAGGGCAAGCAACTTGTAGCAGTTGGTCCCT
Found at i:19616 original size:45 final size:45
Alignment explanation
Indices: 19552--19643 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
19542 TACTGTGAAA
19552 TGCATAGGCTTTGTCTGTATTGTTTATATTGTTTATAGGTTTCTT
1 TGCATAGGCTTTGTCTGTATTGTTTATATTGTTTATAGGTTTCTT
19597 TGCATAGGCTTTGTCTGTATTGTTTATATTGTTTATAGGTTTCTT
1 TGCATAGGCTTTGTCTGTATTGTTTATATTGTTTATAGGTTTCTT
19642 TG
1 TG
19644 GATACATCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.15, C:0.09, G:0.21, T:0.55
Consensus pattern (45 bp):
TGCATAGGCTTTGTCTGTATTGTTTATATTGTTTATAGGTTTCTT
Found at i:22487 original size:16 final size:17
Alignment explanation
Indices: 22461--22494 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
22451 TGAGTTTCAT
22461 AAGGTTGAAAAAAGATG
1 AAGGTTGAAAAAAGATG
*
22478 AAGG-TGAAAAATGATG
1 AAGGTTGAAAAAAGATG
22494 A
1 A
22495 CCAGATTCTT
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:0.53, C:0.00, G:0.29, T:0.18
Consensus pattern (17 bp):
AAGGTTGAAAAAAGATG
Found at i:31193 original size:3 final size:3
Alignment explanation
Indices: 31185--31222 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
31175 ACCCTCTTTG
31185 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
31223 GTTTTTTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:38974 original size:1 final size:1
Alignment explanation
Indices: 38970--39008 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
38960 GTCTATATTT
38970 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
39009 CTCAATTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:40070 original size:16 final size:15
Alignment explanation
Indices: 40032--40086 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
40022 TCTTAACCAT
*
40032 ATGACCCGAAACTGAAA
1 ATGACCC-AAAC-CAAA
*
40049 AAGACCCAAACCAAA
1 ATGACCCAAACCAAA
*
40064 ATTGACCCAAACCCAA
1 A-TGACCCAAACCAAA
40080 ATGACCC
1 ATGACCC
40087 GATACTTGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 10 0.30
16 17 0.52
17 6 0.18
ACGTcount: A:0.47, C:0.33, G:0.11, T:0.09
Consensus pattern (15 bp):
ATGACCCAAACCAAA
Done.