Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012071.1 Corchorus capsularis cultivar CVL-1 contig12092, 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: 17478
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Found at i:122 original size:32 final size:32
Alignment explanation
Indices: 81--188 Score: 137
Period size: 32 Copynumber: 3.4 Consensus size: 32
71 TAGGTCATAC
*
81 GGGTCTCGGGTCA-CTCGGGTTACGGGTTATTT
1 GGGTCTCGGGTCATCT-GGGTTACGGGTCATTT
* *
113 GGGTTTCGGGTCATCTGGGTTACGGGTCATTC
1 GGGTCTCGGGTCATCTGGGTTACGGGTCATTT
* * *
145 GAGTCTCGGGTCATCTGGGTTTCAGGTCATTT
1 GGGTCTCGGGTCATCTGGGTTACGGGTCATTT
*
177 GGGTCTCAGGTC
1 GGGTCTCGGGTC
189 GGGCGGGTTC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 63 0.97
33 2 0.03
ACGTcount: A:0.10, C:0.19, G:0.36, T:0.34
Consensus pattern (32 bp):
GGGTCTCGGGTCATCTGGGTTACGGGTCATTT
Found at i:125 original size:48 final size:47
Alignment explanation
Indices: 52--188 Score: 134
Period size: 48 Copynumber: 2.9 Consensus size: 47
42 CGGGTTAACT
* * *
52 TCTCGGGTTATTCGGGTTTTAGGTCATACGGGTCTCGGGTCACTCGGG
1 TCTCGGGTTATTTGGGTTTCAGGTCAT-CGGGTCTCGGGTCACTCGAG
* *
100 T-TACGGGTTATTTGGGTTTCGGGTCATCTGGGT-TACGGGTCATTCGAG
1 TCT-CGGGTTATTTGGGTTTCAGGTCATC-GGGTCT-CGGGTCACTCGAG
* * * *
148 TCTCGGGTCATCTGGGTTTCAGGTCATTTGGGTCTCAGGTC
1 TCTCGGGTTATTTGGGTTTCAGGTCA-TCGGGTCTCGGGTC
189 GGGCGGGTTC
Statistics
Matches: 73, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
47 3 0.04
48 67 0.92
49 3 0.04
ACGTcount: A:0.11, C:0.19, G:0.34, T:0.36
Consensus pattern (47 bp):
TCTCGGGTTATTTGGGTTTCAGGTCATCGGGTCTCGGGTCACTCGAG
Found at i:172 original size:16 final size:16
Alignment explanation
Indices: 81--180 Score: 87
Period size: 16 Copynumber: 6.2 Consensus size: 16
71 TAGGTCATAC
*
81 GGGTCTCGGGTCA-CT
1 GGGTTTCGGGTCATCT
* * *
96 CGGGTTACGGGTTATTT
1 -GGGTTTCGGGTCATCT
113 GGGTTTCGGGTCATCT
1 GGGTTTCGGGTCATCT
*
129 GGGTTACGGGTCAT-T
1 GGGTTTCGGGTCATCT
* *
144 CGAGTCTCGGGTCATCT
1 -GGGTTTCGGGTCATCT
* *
161 GGGTTTCAGGTCATTT
1 GGGTTTCGGGTCATCT
177 GGGT
1 GGGT
181 CTCAGGTCGG
Statistics
Matches: 66, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
15 1 0.02
16 63 0.95
17 2 0.03
ACGTcount: A:0.10, C:0.18, G:0.37, T:0.35
Consensus pattern (16 bp):
GGGTTTCGGGTCATCT
Found at i:414 original size:15 final size:16
Alignment explanation
Indices: 387--416 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
377 TGACAAAGTG
387 AACCCGACCCGAAAAA
1 AACCCGACCCGAAAAA
403 AACCCG-CCCGAAAA
1 AACCCGACCCGAAAA
417 CTCGATCCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.40, G:0.13, T:0.00
Consensus pattern (16 bp):
AACCCGACCCGAAAAA
Found at i:512 original size:16 final size:16
Alignment explanation
Indices: 484--573 Score: 92
Period size: 16 Copynumber: 5.7 Consensus size: 16
474 GTCTGAACCT
*
484 GAACCCG-AAAAGCCC
1 GAACCCGAAAAAGCTC
*
499 GAATCCGAAAAAGCTC
1 GAACCCGAAAAAGCTC
* * *
515 AAACCCGAAAAAACCC
1 GAACCCGAAAAAGCTC
531 GAACCCGAAAAAGCTC
1 GAACCCGAAAAAGCTC
* * *
547 AAACTCGAAAAAACTC
1 GAACCCGAAAAAGCTC
*
563 GAATCCGAAAA
1 GAACCCGAAAA
574 CTTATGAAAA
Statistics
Matches: 59, Mismatches: 15, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
15 6 0.10
16 53 0.90
ACGTcount: A:0.49, C:0.30, G:0.14, T:0.07
Consensus pattern (16 bp):
GAACCCGAAAAAGCTC
Found at i:539 original size:32 final size:32
Alignment explanation
Indices: 485--573 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
475 TCTGAACCTG
*
485 AACCCG-AAAAGCCCGAATCCGAAAAAGCTCA
1 AACCCGAAAAAACCCGAATCCGAAAAAGCTCA
*
516 AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
1 AACCCGAAAAAACCCGAATCCGAAAAAGCTCA
* *
548 AACTCGAAAAAACTCGAATCCGAAAA
1 AACCCGAAAAAACCCGAATCCGAAAA
574 CTTATGAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
31 6 0.12
32 46 0.88
ACGTcount: A:0.49, C:0.30, G:0.13, T:0.07
Consensus pattern (32 bp):
AACCCGAAAAAACCCGAATCCGAAAAAGCTCA
Found at i:571 original size:48 final size:47
Alignment explanation
Indices: 479--573 Score: 111
Period size: 48 Copynumber: 2.0 Consensus size: 47
469 GACCCGTCTG
* * *
479 AACCTGAACCCGAAAAGCCCGAATCCGAAAAAGCTCAAACCCGAAAA
1 AACCCGAACCCGAAAAGCCCAAATCCGAAAAAACTCAAACCCGAAAA
* * *
526 AACCCGAACCCGAAAAAGCTCAAA-CTCGAAAAAACTCGAATCCGAAAA
1 AACCCGAACCCG-AAAAGCCCAAATC-CGAAAAAACTCAAACCCGAAAA
574 CTTATGAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
47 12 0.30
48 28 0.70
ACGTcount: A:0.48, C:0.31, G:0.14, T:0.07
Consensus pattern (47 bp):
AACCCGAACCCGAAAAGCCCAAATCCGAAAAAACTCAAACCCGAAAA
Found at i:6960 original size:40 final size:40
Alignment explanation
Indices: 6905--6995 Score: 173
Period size: 40 Copynumber: 2.3 Consensus size: 40
6895 AAGTTAATTG
6905 AGTGTTCAAAAGTTAATTGGGGTCTCTAGTAAATTTGCTA
1 AGTGTTCAAAAGTTAATTGGGGTCTCTAGTAAATTTGCTA
6945 AGTGTTCAAAAGTTAATTGGGGTCTCTAGTAAATTTGCTA
1 AGTGTTCAAAAGTTAATTGGGGTCTCTAGTAAATTTGCTA
*
6985 AGTGTTGAAAA
1 AGTGTTCAAAA
6996 TTATACACAG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (40 bp):
AGTGTTCAAAAGTTAATTGGGGTCTCTAGTAAATTTGCTA
Found at i:7450 original size:11 final size:11
Alignment explanation
Indices: 7434--7476 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
7424 TATACTATAT
7434 CTAATTAATAG
1 CTAATTAATAG
*
7445 CTAATTAATAT
1 CTAATTAATAG
7456 CTAATTAATAG
1 CTAATTAATAG
*
7467 TTAATTAATA
1 CTAATTAATA
7477 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:7458 original size:22 final size:22
Alignment explanation
Indices: 7430--7476 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
7420 CCATTATACT
7430 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
7452 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
7474 ATA
1 ATA
7477 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:10272 original size:36 final size:36
Alignment explanation
Indices: 10223--10447 Score: 307
Period size: 36 Copynumber: 6.4 Consensus size: 36
10213 CTCTTTTTTA
* *
10223 AATTAAATCCTTTATTGACTCCACTTAATTGTCCC-G
1 AATTAAGTCCTTTATTGACTCCACTTAATT-ACCCTG
*
10259 AATTAAGTTCTTTATTGACTCCACTTAATTACCCTG
1 AATTAAGTCCTTTATTGACTCCACTTAATTACCCTG
* * * *
10295 AATTAAGTTCATTATTGACTCTACTTAATTATCCTG
1 AATTAAGTCCTTTATTGACTCCACTTAATTACCCTG
* *
10331 AATTAAGCCCTTTATTGACTCTACTTAATTACCCTG
1 AATTAAGTCCTTTATTGACTCCACTTAATTACCCTG
*
10367 AATTAAGCCCTTTATTGACTCCACTTAATTACCCTG
1 AATTAAGTCCTTTATTGACTCCACTTAATTACCCTG
*
10403 AATTAAGTCC----TTGACTCTACTTAATTACCCTG
1 AATTAAGTCCTTTATTGACTCCACTTAATTACCCTG
10435 AATTAAGTCCTTT
1 AATTAAGTCCTTT
10448 TCTTTACTTA
Statistics
Matches: 172, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
32 31 0.18
35 3 0.02
36 138 0.80
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.40
Consensus pattern (36 bp):
AATTAAGTCCTTTATTGACTCCACTTAATTACCCTG
Found at i:10516 original size:37 final size:35
Alignment explanation
Indices: 10450--10568 Score: 103
Period size: 36 Copynumber: 3.3 Consensus size: 35
10440 AGTCCTTTTC
* * *
10450 TTTACTTAATCCCCTTGGGTTAAGTCTTTGATTGGT
1 TTTACTTAATCCCCTTGGATTAAGTCTTTG-CTGAT
* *
10486 TTTACTTAATCATCTTTGGATTAAGTCTTTGCTGAT
1 TTTACTTAATC-CCCTTGGATTAAGTCTTTGCTGAT
** * * *
10522 TTTACTTAATTTCCTTGAAATTAAGTCTGTGCTTAT
1 TTTACTTAATCCCCTTG-GATTAAGTCTTTGCTGAT
*
10558 CTTTACCTAAT
1 -TTTACTTAAT
10569 TTCCTTCCTT
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
35 5 0.07
36 39 0.57
37 25 0.36
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (35 bp):
TTTACTTAATCCCCTTGGATTAAGTCTTTGCTGAT
Found at i:10587 original size:41 final size:40
Alignment explanation
Indices: 10532--10940 Score: 412
Period size: 38 Copynumber: 10.5 Consensus size: 40
10522 TTTACTTAAT
*
10532 TTCCTTGAAATTAAGTCTGTGCTTATCTTTACCTAATTTCC
1 TTCCTTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTT-C
*
10573 TTCCTTGAAATTAAGTTTGTGCTTGTCTTTACCTAATTTCC
1 TTCCTTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTT-C
* * *
10614 ATCCTTGAAATTAAGTTTGTGCTTGTCTTTACTTAA--T-
1 TTCCTTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTC
*
10651 TTCCTTGAAATTAAGTCTGTTCTTGTCTTTTACCTAA--T-
1 TTCCTTGAAATTAAGTCTGTGCTTGTC-TTTACCTAATTTC
*
10689 TTCCTTGAAATTAAGTCTGTGTTTTGTCTTTACCTAATTTCC
1 TTCCTTGAAATTAAGTCTGTG-CTTGTCTTTACCTAATTT-C
* * *
10731 TTCTTTGAAATTAAGTATGTGCTTATCTTTTACCTAATTTC
1 TTCCTTGAAATTAAGTCTGTGCTTGTC-TTTACCTAATTTC
*
10772 --CC-TGAAATTAAGTCTGTGCTTATCTTTTACCTAA--T-
1 TTCCTTGAAATTAAGTCTGTGCTTGTC-TTTACCTAATTTC
*
10807 TTCCTTGAAATTAAGTCTGTGCCTGT-TTTACCTAA--T-
1 TTCCTTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTC
* *
10843 TTCCTTGAAATTAAATCTGTACTTTGTCTTTTACCTAA--T-
1 TTCCTTGAAATTAAGTCTGTGC-TTGTC-TTTACCTAATTTC
* *
10882 TTCCTTGAAATTAAATCTGTACTTTGTCTTTTACCTAA--T-
1 TTCCTTGAAATTAAGTCTGTGC-TTGTC-TTTACCTAATTTC
*
10921 TTCCTTGAAATTAAATCTGT
1 TTCCTTGAAATTAAGTCTGT
10941 ATTAAGTCTG
Statistics
Matches: 334, Mismatches: 21, Indels: 28
0.87 0.05 0.07
Matches are distributed among these distances:
36 31 0.09
37 29 0.09
38 88 0.26
39 76 0.23
40 1 0.00
41 78 0.23
42 31 0.09
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.48
Consensus pattern (40 bp):
TTCCTTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTC
Found at i:10613 original size:78 final size:79
Alignment explanation
Indices: 10505--11153 Score: 740
Period size: 78 Copynumber: 8.2 Consensus size: 79
10495 TCATCTTTGG
* * * *
10505 ATTAAGTCTTTGC-TG-ATTTTACTTAATTTCCTTGAAATTAAGTCTGTGCTTATCTTTACCTAA
1 ATTAAGTCTGTGCTTGTCTTTTACCTAATTTCCTTGAAATTAAGTCTGTGCTTGTCTTTACCTAA
10568 TTTCCTTCCTTGAA
66 TTTCCTTCCTTGAA
* *
10582 ATTAAGTTTGTGCTTGTC-TTTACCTAATTTCCATCCTTGAAATTAAGTTTGTGCTTGTCTTTAC
1 ATTAAGTCTGTGCTTGTCTTTTACCTAA-TT---TCCTTGAAATTAAGTCTGTGCTTGTCTTTAC
*
10646 TTAA--T--TTCCTTGAA
62 CTAATTTCCTTCCTTGAA
* *
10660 ATTAAGTCTGTTCTTGTCTTTTACCTAATTTCCTTGAAATTAAGTCTGTGTTTTGTCTTTACCTA
1 ATTAAGTCTGTGCTTGTCTTTTACCTAATTTCCTTGAAATTAAGTCTGTG-CTTGTCTTTACCTA
*
10725 ATTTCCTTCTTTGAA
65 ATTTCCTTCCTTGAA
* * * *
10740 ATTAAGTATGTGCTTATCTTTTACCTAATTTCCCTGAAATTAAGTCTGTGCTTATCTTTTACCTA
1 ATTAAGTCTGTGCTTGTCTTTTACCTAATTTCCTTGAAATTAAGTCTGTGCTTGTC-TTTACCTA
10805 A--T--TTCCTTGAA
65 ATTTCCTTCCTTGAA
* * *
10816 ATTAAGTCTGTGCCTG--TTTTACCTAATTTCCTTGAAATTAAATCTGTACTTTGTCTTTTACCT
1 ATTAAGTCTGTGCTTGTCTTTTACCTAATTTCCTTGAAATTAAGTCTGTGC-TTGTC-TTTACCT
10879 AA--T--TTCCTTGAA
64 AATTTCCTTCCTTGAA
* * *
10891 ATTAAATCTGTACTTTGTCTTTTACCTAATTTCCTTGAAATTAAATCTGTATTAAGTCTGTGCAT
1 ATTAAGTCTGTGC-TTGTCTTTTACCTAATTTCCTTGAAATTAAGTCTG---T--G-CT-TG---
10956 TTCTTTACCTAATTTCCTTCCTTGAA
55 -TCTTTACCTAATTTCCTTCCTTGAA
* * *
10982 ATTAAATCTGTGCTTTGTCTTTTACCTAATTTCCTTGAAATTAAGTCTGTGCTTTTCTTTACCCA
1 ATTAAGTCTGTGC-TTGTCTTTTACCTAATTTCCTTGAAATTAAGTCTGTGCTTGTCTTTACCTA
11047 ATTTCCTTCCTTGAA
65 ATTTCCTTCCTTGAA
* * *
11062 AATAAGTCTGTGCTT-TTTTTTACCTAATTTCCTTGAAATTAAGTCTGTGCTTGCCTTTACCTAA
1 ATTAAGTCTGTGCTTGTCTTTTACCTAATTTCCTTGAAATTAAGTCTGTGCTTGTCTTTACCTAA
11126 TTTCCTTCCTTGAA
66 TTTCCTTCCTTGAA
*
11140 ATTAAGTATGTGCT
1 ATTAAGTCTGTGCT
11154 AAATAAATGA
Statistics
Matches: 497, Mismatches: 43, Indels: 63
0.82 0.07 0.10
Matches are distributed among these distances:
74 30 0.06
75 54 0.11
76 36 0.07
77 11 0.02
78 140 0.28
79 17 0.03
80 99 0.20
81 1 0.00
82 32 0.06
83 1 0.00
84 4 0.01
85 2 0.00
86 1 0.00
87 9 0.02
88 3 0.01
89 1 0.00
91 56 0.11
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.48
Consensus pattern (79 bp):
ATTAAGTCTGTGCTTGTCTTTTACCTAATTTCCTTGAAATTAAGTCTGTGCTTGTCTTTACCTAA
TTTCCTTCCTTGAA
Found at i:11069 original size:41 final size:40
Alignment explanation
Indices: 10532--11153 Score: 574
Period size: 41 Copynumber: 15.6 Consensus size: 40
10522 TTTACTTAAT
*
10532 TTCCTTGAAATTAAGTCTGTGCTTATCTTTACCTAATTTCC
1 TTCCTTGAAATTAAGTCTGTGCTTTTCTTTACCTAATTT-C
* *
10573 TTCCTTGAAATTAAGTTTGTGCTTGTCTTTACCTAATTTCC
1 TTCCTTGAAATTAAGTCTGTGCTTTTCTTTACCTAATTT-C
* * * *
10614 ATCCTTGAAATTAAGTTTGTGCTTGTCTTTACTTAA--T-
1 TTCCTTGAAATTAAGTCTGTGCTTTTCTTTACCTAATTTC
* *
10651 TTCCTTGAAATTAAGTCTGTTCTTGTCTTTTACCTAA--T-
1 TTCCTTGAAATTAAGTCTGTGCTTTTC-TTTACCTAATTTC
*
10689 TTCCTTGAAATTAAGTCTGTGTTTTGTCTTTACCTAATTTCC
1 TTCCTTGAAATTAAGTCTGTGCTTT-TCTTTACCTAATTT-C
* * *
10731 TTCTTTGAAATTAAGTATGTGCTTATCTTTTACCTAATTTC
1 TTCCTTGAAATTAAGTCTGTGCTTTTC-TTTACCTAATTTC
*
10772 --CC-TGAAATTAAGTCTGTGCTTATCTTTTACCTAA--T-
1 TTCCTTGAAATTAAGTCTGTGCTTTTC-TTTACCTAATTTC
* *
10807 TTCCTTGAAATTAAGTCTGTGCCTGT-TTTACCTAA--T-
1 TTCCTTGAAATTAAGTCTGTGCTTTTCTTTACCTAATTTC
* *
10843 TTCCTTGAAATTAAATCTGTACTTTGTCTTTTACCTAA--T-
1 TTCCTTGAAATTAAGTCTGTGCTTT-TC-TTTACCTAATTTC
* *
10882 TTCCTTGAAATTAAATCTGTACTTTGTCTTTTACCTAATTTCC
1 TTCCTTGAAATTAAGTCTGTGCTTT-TC-TTTACCTAATTT-C
** * *
10925 TTGAAATTAAATCTGTATTAAGTCTGTGCATTTCTTTACCTAATTTCC
1 TT--CCTTGAA-----ATTAAGTCTGTGCTTTTCTTTACCTAATTT-C
*
10973 TTCCTTGAAATTAAATCTGTGCTTTGTCTTTTACCTAA--T-
1 TTCCTTGAAATTAAGTCTGTGCTTT-TC-TTTACCTAATTTC
*
11012 TTCCTTGAAATTAAGTCTGTGCTTTTCTTTACCCAATTTCC
1 TTCCTTGAAATTAAGTCTGTGCTTTTCTTTACCTAATTT-C
* *
11053 TTCCTTGAAAATAAGTCTGTGCTTTTTTTTACCTAA--T-
1 TTCCTTGAAATTAAGTCTGTGCTTTTCTTTACCTAATTTC
**
11090 TTCCTTGAAATTAAGTCTGTGCTTGCCTTTACCTAATTTCC
1 TTCCTTGAAATTAAGTCTGTGCTTTTCTTTACCTAATTT-C
*
11131 TTCCTTGAAATTAAGTATGTGCT
1 TTCCTTGAAATTAAGTCTGTGCT
11154 AAATAAATGA
Statistics
Matches: 503, Mismatches: 44, Indels: 68
0.82 0.07 0.11
Matches are distributed among these distances:
36 32 0.06
37 67 0.13
38 92 0.18
39 79 0.16
40 1 0.00
41 147 0.29
42 35 0.07
43 11 0.02
45 4 0.01
46 4 0.01
48 16 0.03
49 2 0.00
50 13 0.03
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (40 bp):
TTCCTTGAAATTAAGTCTGTGCTTTTCTTTACCTAATTTC
Found at i:11085 original size:169 final size:163
Alignment explanation
Indices: 10778--11109 Score: 433
Period size: 169 Copynumber: 2.0 Consensus size: 163
10768 TTTCCCTGAA
*
10778 ATTAAGTCTGTGCTTATCTTTTACCTAATTTCCTTGAAATTAAGTCTGTGCCTGTTTTACCTAAT
1 ATTAAGTCTGTGCTTATCTTTTACCTAATTTCCTTGAAATTAAATCTGTGCCTGTTTTACCTAAT
* *
10843 TTCCTTGAAATTAAATCTGTACTTTGTCTTTTACCTAATTTCCTTGAAATTAAATCTGTACTTTG
66 TTCCTTGAAATTAAATCTGTACTTTGTCTTTTACCCAATTTCCTTGAAAATAAATCTGTACTTTG
10908 TCTTTTACCTAATTTCCTTGAAATTAAATCTGT
131 TCTTTTACCTAATTTCCTTGAAATTAAATCTGT
*
10941 ATTAAGTCTGTGCATT-TC-TTTACCTAATTTCCTTCCTTGAAATTAAATCTGTGCTTTGTCTTT
1 ATTAAGTCTGTGC-TTATCTTTTACCTAA--T--TTCCTTGAAATTAAATCTGTGC-CTG--TTT
* *
11004 TACCTAATTTCCTTGAAATTAAGTCTGTGCTTT-TC-TTTACCCAATTTCCTTCCTTGAAAATAA
58 TACCTAATTTCCTTGAAATTAAATCTGTACTTTGTCTTTTACCCAA--T--TTCCTTGAAAATAA
* * *
11067 GTCTGTGCTTT-T-TTTTACCTAATTTCCTTGAAATTAAGTCTGT
119 ATCTGTACTTTGTCTTTTACCTAATTTCCTTGAAATTAAATCTGT
11110 GCTTGCCTTT
Statistics
Matches: 148, Mismatches: 9, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
162 9 0.06
163 15 0.10
164 3 0.02
166 21 0.14
167 10 0.07
168 2 0.01
169 65 0.44
170 1 0.01
171 22 0.15
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.47
Consensus pattern (163 bp):
ATTAAGTCTGTGCTTATCTTTTACCTAATTTCCTTGAAATTAAATCTGTGCCTGTTTTACCTAAT
TTCCTTGAAATTAAATCTGTACTTTGTCTTTTACCCAATTTCCTTGAAAATAAATCTGTACTTTG
TCTTTTACCTAATTTCCTTGAAATTAAATCTGT
Found at i:12964 original size:11 final size:10
Alignment explanation
Indices: 12946--12979 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
12936 AATTGTCTTC
12946 AAATCTTCAA
1 AAATCTTCAA
12956 AATATCTTCAA
1 AA-ATCTTCAA
12967 GAAATCTTCAA
1 -AAATCTTCAA
12978 AA
1 AA
12980 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:14962 original size:19 final size:19
Alignment explanation
Indices: 14927--14966 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
14917 AATGTGTGCG
14927 TAAAATGCAGTGTATGTGAA
1 TAAAATGCAGTGTATGT-AA
*
14947 TAAATTGCAGTG-ATGTAA
1 TAAAATGCAGTGTATGTAA
14965 TA
1 TA
14967 TATGCTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
20 11 0.58
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.33
Consensus pattern (19 bp):
TAAAATGCAGTGTATGTAA
Found at i:15935 original size:67 final size:66
Alignment explanation
Indices: 15730--16229 Score: 453
Period size: 67 Copynumber: 7.5 Consensus size: 66
15720 ATGACAAGCT
* * ***** * * *
15730 TGACCCTTTGACCGAAAGGGCATTTTTGGAAATTTGCA-AGTAAACTTAGATGCGAAAAATGAAG
1 TGACCCTTCGACCGAAAGGGTATTTTTGGAAAAGAAAATACTAAACTTAAATGC--AAAA-GACG
*
15794 AAAC
63 AAAA
* * * *
15798 TGACCCTTTC-ACCGAAGGGGCATTTTTGG--AAGACAAA-ACTAGACTCAAATGCAAAAAGACG
1 TGACCC-TTCGACCGAAAGGGTATTTTTGGAAAAGA-AAATACTAAACTTAAATGC-AAAAGACG
15859 AAAA
63 AAAA
* * * * *
15863 TGACCCTTCGACCGGAAGGGTATTTTTTGGAAAGGAAGATACTAAACTTGAATACAAAAGAC-AA
1 TGACCCTTCGACCGAAAGGGTA-TTTTTGGAAAAGAAAATACTAAACTTAAATGCAAAAGACGAA
15927 CAA
65 -AA
* * * **
15930 TGACCCTTTGACCGAAAGGGTACTCTTGGGAAAAGAAAATACTAAACTTAAATGCAACGGACGAA
1 TGACCCTTCGACCGAAAGGGTA-TTTTTGGAAAAGAAAATACTAAACTTAAATGCAAAAGACGAA
15995 AA
65 AA
* * * * *
15997 TTACCCTTTC-ACCGAAAGGGTATTTTTGGGAATGAGAATACTAAACTTGAATGCAAAAGAC-AA
1 TGACCC-TTCGACCGAAAGGGTATTTTTGGAAAAGAAAATACTAAACTTAAATGCAAAAGACGAA
*
16060 TAC
65 -AA
* * * *
16063 TGACCCTTTGACCGAAAGGGTATTTTTGGGAAAAGAAAATA-TCATACCTAAATGCAAAAGACAA
1 TGACCCTTCGACCGAAAGGGTATTTTT-GGAAAAGAAAATACT-AAACTTAAATGCAAAAGACGA
16127 AAA
64 AAA
* *
16130 TGACCCTTCCACCGAAAGGGTA-TTTTGGAGAAAGAAAATACTAAACTTAAATACGAAAAGACGA
1 TGACCCTTCGACCGAAAGGGTATTTTTGGA-AAAGAAAATACTAAACTTAAATGC-AAAAGACGA
16194 AAA
64 AAA
*
16197 TAACCCTTCGACCGAAAGGGTATTTTTGGAAAA
1 TGACCCTTCGACCGAAAGGGTATTTTTGGAAAA
16230 ACAAAATAAA
Statistics
Matches: 352, Mismatches: 61, Indels: 39
0.78 0.13 0.09
Matches are distributed among these distances:
64 3 0.01
65 28 0.08
66 93 0.26
67 175 0.50
68 51 0.14
69 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (66 bp):
TGACCCTTCGACCGAAAGGGTATTTTTGGAAAAGAAAATACTAAACTTAAATGCAAAAGACGAAA
A
Found at i:16048 original size:133 final size:132
Alignment explanation
Indices: 15844--16237 Score: 490
Period size: 133 Copynumber: 2.9 Consensus size: 132
15834 AACTAGACTC
* *
15844 AAATGCAAAAAGACGAAAATGACCC-TTCGACCGGAAGGGTATTTTTTGGAAAG-GAAGATACTA
1 AAATGC-AAAAGACGAAAATGACCCTTTC-ACCGAAAGGGTATTTTTGGGAAAGAG-A-ATACTA
* *
15907 AACTTGAATACAAAAGACAACAATGACCCTTTGACCGAAAGGGTACTCTTGGGAAAAGAAAATA-
62 AACTTGAATACAAAAGACAA-AATGACCCTTTGACCGAAAGGGTATTTTTGGGAAAAGAAAATAT
*
15971 CTAAACTT
126 C-AAACCT
** * *
15979 AAATGCAACGGACGAAAATTACCCTTTCACCGAAAGGGTATTTTTGGGAATGAGAATACTAAACT
1 AAATGCAAAAGACGAAAATGACCCTTTCACCGAAAGGGTATTTTTGGGAAAGAGAATACTAAACT
* * *
16044 TGAATGCAAAAGACAATACTGACCCTTTGACCGAAAGGGTATTTTTGGGAAAAGAAAATATCATA
66 TGAATACAAAAGACAA-AATGACCCTTTGACCGAAAGGGTATTTTTGGGAAAAGAAAATATCAAA
16109 CCT
130 CCT
* * *
16112 AAATGCAAAAGACAAAAATGACCCTTCCACCGAAAGGGTA-TTTTGGAGAAAGAAAATACTAAAC
1 AAATGCAAAAGACGAAAATGACCCTTTCACCGAAAGGGTATTTTTGG-GAAAGAGAATACTAAAC
* * * * *
16176 TTAAATACGAAAAGACGAAAATAACCCTTCGACCGAAAGGGTATTTTTGGAAAAACAAAATA
65 TTGAATAC-AAAAGAC-AAAATGACCCTTTGACCGAAAGGGTATTTTTGGGAAAAGAAAATA
16238 AAAATTTACT
Statistics
Matches: 226, Mismatches: 27, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
132 6 0.03
133 125 0.55
134 83 0.37
135 12 0.05
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (132 bp):
AAATGCAAAAGACGAAAATGACCCTTTCACCGAAAGGGTATTTTTGGGAAAGAGAATACTAAACT
TGAATACAAAAGACAAAATGACCCTTTGACCGAAAGGGTATTTTTGGGAAAAGAAAATATCAAAC
CT
Found at i:16084 original size:200 final size:200
Alignment explanation
Indices: 15800--16239 Score: 527
Period size: 200 Copynumber: 2.2 Consensus size: 200
15790 GAAGAAACTG
* * *
15800 ACCCTTTCACCGAAGGGGCATTTTT-GGAAGACAAAACTAGACTCAAATGCAAAAAGACGAAAAT
1 ACCCTTTCACCGAAAGGGTATTTTTGGGAAGACAAAACTAAACTCAAATGCAAAAAGACGAAAAT
* * * * * * *
15864 GACCCTTCGACCGGAAGGGTATTTTTTGGAAAGGAAGATA-CTAAACTTGAATACAAAAGACAAC
66 GACCCTTCGACCGAAAGGGTATTTTTGGGAAAAGAAAATATC-AAACCTAAATACAAAAGACAAA
** * **
15928 AATGACCCTTTGACCGAAAGGGTACTCTTGGGA-AAAGAAAATACTAAACTTAAATGC-AACGGA
130 AATGACCCTTCCACCGAAAGGGTA-T-TTGGGAGAAAGAAAATACTAAACTTAAATACGAAAAGA
*
15991 CGAAAATT
193 CGAAAATA
* * **
15999 ACCCTTTCACCGAAAGGGTATTTTTGGGAATGAGAATACTAAACTTGAATGC-AAAAGAC-AATA
1 ACCCTTTCACCGAAAGGGTATTTTTGGGAA-GACAAAACTAAACTCAAATGCAAAAAGACGAA-A
* * * *
16062 CTGACCCTTTGACCGAAAGGGTATTTTTGGGAAAAGAAAATATCATACCTAAATGCAAAAGACAA
64 ATGACCCTTCGACCGAAAGGGTATTTTTGGGAAAAGAAAATATCAAACCTAAATACAAAAGACAA
*
16127 AAATGACCCTTCCACCGAAAGGGTATTTTGGAGAAAGAAAATACTAAACTTAAATACGAAAAGAC
129 AAATGACCCTTCCACCGAAAGGGTATTTGGGAGAAAGAAAATACTAAACTTAAATACGAAAAGAC
16192 GAAAATA
194 GAAAATA
* *
16199 ACCC-TTCGACCGAAAGGGTATTTTTGGAAAAACAAAA-TAAA
1 ACCCTTTC-ACCGAAAGGGTATTTTTGGGAAGACAAAACTAAA
16240 AATTTACTTT
Statistics
Matches: 205, Mismatches: 29, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
198 9 0.04
199 56 0.27
200 123 0.60
201 17 0.08
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (200 bp):
ACCCTTTCACCGAAAGGGTATTTTTGGGAAGACAAAACTAAACTCAAATGCAAAAAGACGAAAAT
GACCCTTCGACCGAAAGGGTATTTTTGGGAAAAGAAAATATCAAACCTAAATACAAAAGACAAAA
ATGACCCTTCCACCGAAAGGGTATTTGGGAGAAAGAAAATACTAAACTTAAATACGAAAAGACGA
AAATA
Found at i:16256 original size:6 final size:6
Alignment explanation
Indices: 16242--16283 Score: 75
Period size: 6 Copynumber: 6.8 Consensus size: 6
16232 AAAATAAAAA
16242 TTTACTT TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT
1 TTTA-TT TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT
16284 CAACTCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 31 0.89
7 4 0.11
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Done.