Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014235.1 Corchorus capsularis cultivar CVL-1 contig14256, 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: 110830
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1963 original size:78 final size:80
Alignment explanation
Indices: 1875--2042 Score: 232
Period size: 84 Copynumber: 2.1 Consensus size: 80
1865 GTTTTTTAAT
** * *
1875 TAAAATAGTAAAATTTTAAAATATAATAGTTATAAGG-GT-ATTAAATTTAATTATATAAAAATA
1 TAAAATAGTAAAATGGTAAAATATAATAGTCATAAGGACTCATTAAATTTAATTATATAAAAATA
*
1938 GATTTTTTAGTTGAG
66 GAGTTTTTAGTTGAG
*
1953 TAAAATAGTAAAATGGTAAAATATAATAGTCATAAGGATTCACTCATTATATTTAATTATATAAA
1 TAAAATAGTAAAATGGTAAAATATAATAGTCATAAGG----ACTCATTAAATTTAATTATATAAA
2018 AATAGAGTTTTTAGTTGAG
62 AATAGAGTTTTTAGTTGAG
2037 TAAAAT
1 TAAAAT
2043 TATAAAAACC
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
78 34 0.44
83 1 0.01
84 43 0.55
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39
Consensus pattern (80 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTCATAAGGACTCATTAAATTTAATTATATAAAAATA
GAGTTTTTAGTTGAG
Found at i:2963 original size:88 final size:88
Alignment explanation
Indices: 2814--2986 Score: 328
Period size: 88 Copynumber: 2.0 Consensus size: 88
2804 CGAACCCATT
*
2814 CCACCTAATAATTTCTCCCAAATTCGTCTCGGGTCCTACACCTCTAATTAATTTTCTTTTTCTCA
1 CCACCTAATAATTTCTCCCAAATTCGTCTCGGATCCTACACCTCTAATTAATTTTCTTTTTCTCA
2879 CCAAGATTTGAAACTCCGACATC
66 CCAAGATTTGAAACTCCGACATC
*
2902 CCACCTAATAATTTCTCCCAAATTCGTCTCGGATCTTACACCTCTAATTAATTTTCTTTTTCTCA
1 CCACCTAATAATTTCTCCCAAATTCGTCTCGGATCCTACACCTCTAATTAATTTTCTTTTTCTCA
2967 CCAAGATTTGAAACTCCGAC
66 CCAAGATTTGAAACTCCGAC
2987 TCCGACTCCG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 83 1.00
ACGTcount: A:0.27, C:0.30, G:0.08, T:0.36
Consensus pattern (88 bp):
CCACCTAATAATTTCTCCCAAATTCGTCTCGGATCCTACACCTCTAATTAATTTTCTTTTTCTCA
CCAAGATTTGAAACTCCGACATC
Found at i:7869 original size:2 final size:2
Alignment explanation
Indices: 7862--7903 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
7852 AGAGTCCTAC
7862 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7904 GATAGATAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12392 original size:22 final size:22
Alignment explanation
Indices: 12366--12412 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
12356 ATTTATTCAT
12366 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
12388 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
12410 TAT
1 TAT
12413 ATTATAATGG
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:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:12408 original size:11 final size:11
Alignment explanation
Indices: 12366--12408 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
12356 ATTTATTCAT
*
12366 TATTAATTAAC
1 TATTAATTAGC
*
12377 TATTAATTAGA
1 TATTAATTAGC
12388 TATTAATTAGC
1 TATTAATTAGC
12399 TATTAATTAG
1 TATTAATTAG
12409 ATATATTATA
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:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:12955 original size:21 final size:21
Alignment explanation
Indices: 12931--12997 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
12921 GTAGCTATAC
12931 AAATTCATATAAATATATTGT
1 AAATTCATATAAATATATTGT
* ** *
12952 AAATTC-TA-AGCAGCTA-TAT
1 AAATTCATATA-AATATATTGT
12971 AAATTCATATAAATATATTGT
1 AAATTCATATAAATATATTGT
12992 AAATTC
1 AAATTC
12998 TCTAGTCTCA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 9 0.26
20 10 0.29
21 15 0.44
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (21 bp):
AAATTCATATAAATATATTGT
Found at i:12967 original size:40 final size:40
Alignment explanation
Indices: 12917--12998 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
12907 TATTGACATG
*
12917 CTAAGTAGCTATACAAATTCATATAAATATATTGTAAATT
1 CTAAGCAGCTATACAAATTCATATAAATATATTGTAAATT
*
12957 CTAAGCAGCTATATAAATTCATATAAATATATTGTAAATT
1 CTAAGCAGCTATACAAATTCATATAAATATATTGTAAATT
12997 CT
1 CT
12999 CTAGTCTCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (40 bp):
CTAAGCAGCTATACAAATTCATATAAATATATTGTAAATT
Found at i:17372 original size:13 final size:13
Alignment explanation
Indices: 17354--17381 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17344 TTTAGTAGAA
17354 TAAAATTGTATAT
1 TAAAATTGTATAT
17367 TAAAATTGTATAT
1 TAAAATTGTATAT
17380 TA
1 TA
17382 GAAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (13 bp):
TAAAATTGTATAT
Found at i:17401 original size:123 final size:125
Alignment explanation
Indices: 17244--17485 Score: 373
Period size: 123 Copynumber: 1.9 Consensus size: 125
17234 TTTAGTAGAA
*
17244 TAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTTGGTAAAAAAAAAAGAAATTTT
1 TAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTTGGT-AAAAAAAAAGAAATTAT
* *
17309 AAAGATATT-A-T-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATAT
65 AAAGATATTAATTAATTTAATTAAATAAAAATAGAGTTTCTAGTAGAATAAAATTGTATAT
* * *
17367 TAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAATTATA
1 TAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTTGGTAAAAAAAAAGAAATTATA
*
17432 AAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAA
66 AAGATATTA-A-TTAATTTAATTAAATAAAAATAGAGTTTCTAGTAGAATAAAA
17486 CTATAATAGT
Statistics
Matches: 107, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
122 23 0.21
123 46 0.43
124 1 0.01
126 1 0.01
127 36 0.34
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.38
Consensus pattern (125 bp):
TAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTTGGTAAAAAAAAAGAAATTATA
AAGATATTAATTAATTTAATTAAATAAAAATAGAGTTTCTAGTAGAATAAAATTGTATAT
Found at i:19959 original size:28 final size:27
Alignment explanation
Indices: 19918--19981 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
19908 AACCCACTAA
* * *
19918 ATTTCAATTCTTTTAAATATATATAGATT
1 ATTT-AATGCTTTTAAATA-AAAAAGATT
**
19947 ATTTAATGCTTTTGGATAAAAAAGATT
1 ATTTAATGCTTTTAAATAAAAAAGATT
19974 ATTTAATG
1 ATTTAATG
19982 TAAAATCAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 15 0.50
28 11 0.37
29 4 0.13
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (27 bp):
ATTTAATGCTTTTAAATAAAAAAGATT
Found at i:28176 original size:11 final size:11
Alignment explanation
Indices: 28160--28184 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28150 ATGTTGATGC
28160 TGAAACCCAGG
1 TGAAACCCAGG
28171 TGAAACCCAGG
1 TGAAACCCAGG
28182 TGA
1 TGA
28185 TGCTGGAAGT
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:0.36, C:0.24, G:0.28, T:0.12
Consensus pattern (11 bp):
TGAAACCCAGG
Found at i:28995 original size:32 final size:32
Alignment explanation
Indices: 28945--29008 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
28935 AAAACCAAAA
*
28945 TAGCGGCGTTTGAGTACGGAAATGCCACTATT
1 TAGCGGCGTTTGAGTACGGAAACGCCACTATT
*** *
28977 TAGCGGCGTTTTTTTACGGAAACGCCGCTATT
1 TAGCGGCGTTTGAGTACGGAAACGCCACTATT
29009 CCTAAGGCTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (32 bp):
TAGCGGCGTTTGAGTACGGAAACGCCACTATT
Found at i:36272 original size:6 final size:6
Alignment explanation
Indices: 36261--36293 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
36251 ATTGCATCAA
36261 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
36294 TGGAAAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:39979 original size:53 final size:54
Alignment explanation
Indices: 39898--40003 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 54
39888 GTTAGATATG
*
39898 AGAAAGGGGAAAAACTCTAACCCTAGAAAAACAATTTGAACCAGATTAAACCTA
1 AGAAAGGGGAAAAACTCTAACCCTAGAAAAACAATTTGAACCAGACTAAACCTA
39952 AGAAAGGGG-AAAACTCTAACCCTAGAAAAACAATTTGAACCAGACTAAACCT
1 AGAAAGGGGAAAAACTCTAACCCTAGAAAAACAATTTGAACCAGACTAAACCT
40004 GCAAATAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 42 0.82
54 9 0.18
ACGTcount: A:0.49, C:0.20, G:0.15, T:0.16
Consensus pattern (54 bp):
AGAAAGGGGAAAAACTCTAACCCTAGAAAAACAATTTGAACCAGACTAAACCTA
Found at i:40809 original size:7 final size:7
Alignment explanation
Indices: 40797--40828 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
40787 CATCGTCCCC
40797 CTCTGGA
1 CTCTGGA
40804 CTCTGGA
1 CTCTGGA
40811 CTCTGGA
1 CTCTGGA
40818 CTCTGGA
1 CTCTGGA
40825 CTCT
1 CTCT
40829 AGTGCATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.31, G:0.25, T:0.31
Consensus pattern (7 bp):
CTCTGGA
Found at i:41562 original size:2 final size:2
Alignment explanation
Indices: 41555--41583 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41545 TGCCTCCCTT
41555 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
41584 TTGATCTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:48934 original size:31 final size:31
Alignment explanation
Indices: 48898--48968 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
48888 TCCTTTTGTG
* * *
48898 CACGTGGCATGCCACGTGTTATTTTTTGATA
1 CACGTGGCATGACACGTGTCACTTTTTGATA
* * *
48929 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCATGACACGTGTCACTTTTTGATA
*
48960 CATGTGGCA
1 CACGTGGCA
48969 CGACTTTTTG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (31 bp):
CACGTGGCATGACACGTGTCACTTTTTGATA
Found at i:49001 original size:53 final size:53
Alignment explanation
Indices: 48920--49020 Score: 157
Period size: 53 Copynumber: 1.9 Consensus size: 53
48910 CACGTGTTAT
*
48920 TTTTTGATACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACGAC
1 TTTTTGATACACGTGGCGTGACACGTGTCACTTTTTGGTACATGTGGCACGAC
* * * *
48973 TTTTTGGTACATGTGGCGTGTCACGTGTCATTTTTTGGTACATGTGGC
1 TTTTTGATACACGTGGCGTGACACGTGTCACTTTTTGGTACATGTGGC
49021 GTGCCACGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.16, C:0.17, G:0.28, T:0.40
Consensus pattern (53 bp):
TTTTTGATACACGTGGCGTGACACGTGTCACTTTTTGGTACATGTGGCACGAC
Found at i:50343 original size:31 final size:31
Alignment explanation
Indices: 50266--50343 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
50256 TCTTATAGAG
*
50266 TTTGGACG-TTTG-ACCCCTAAAACTTCAAT
1 TTTGGACGTTTTGCCCCCCTAAAACTTCAAT
* **
50295 TTTGGACATTTAACCCCCCT-AAACTCTCAAT
1 TTTGGACGTTTTGCCCCCCTAAAACT-TCAAT
50326 TTTGGACGTTTTGCCCCC
1 TTTGGACGTTTTGCCCCC
50344 TCTCAAACGA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 7 0.18
30 7 0.18
31 25 0.64
ACGTcount: A:0.23, C:0.29, G:0.13, T:0.35
Consensus pattern (31 bp):
TTTGGACGTTTTGCCCCCCTAAAACTTCAAT
Found at i:50428 original size:38 final size:38
Alignment explanation
Indices: 50377--50451 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
50367 ACCGTGATAT
50377 CGCTGATGTGGCAATGCCACGCAGCACAAAAAATGTCA
1 CGCTGATGTGGCAATGCCACGCAGCACAAAAAATGTCA
50415 CGCTGATGTGGCAATGCCACGCAGCACAAAAAATGTC
1 CGCTGATGTGGCAATGCCACGCAGCACAAAAAATGTC
50452 GGGCATGACG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (38 bp):
CGCTGATGTGGCAATGCCACGCAGCACAAAAAATGTCA
Found at i:52116 original size:24 final size:24
Alignment explanation
Indices: 52084--52133 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
52074 TCAATCCCGA
52084 TGTGCCGAGTTCGAAAAGGGTTCT
1 TGTGCCGAGTTCGAAAAGGGTTCT
52108 TGTGCCGAGTTCGAAAAGGGTTCT
1 TGTGCCGAGTTCGAAAAGGGTTCT
52132 TG
1 TG
52134 AGCTCGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.16, G:0.34, T:0.30
Consensus pattern (24 bp):
TGTGCCGAGTTCGAAAAGGGTTCT
Found at i:58572 original size:59 final size:61
Alignment explanation
Indices: 58507--58623 Score: 193
Period size: 59 Copynumber: 2.0 Consensus size: 61
58497 AGTTATACTT
* * *
58507 TAACAGAATTTGATTTTATTTTTCGAATGTATATCTTGT-AAA-AGTAAAATCAAATTTTG
1 TAACAGAATTTGATTTTAATTTTCAAATGTATATCTTGTGAAATACTAAAATCAAATTTTG
58566 TAACAGAATTTGATTTTAATTTTCAAATGTATATCTTGTGAAATACTAAAATCAAATT
1 TAACAGAATTTGATTTTAATTTTCAAATGTATATCTTGTGAAATACTAAAATCAAATT
58624 CTGTTAGAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
59 37 0.70
60 3 0.06
61 13 0.25
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (61 bp):
TAACAGAATTTGATTTTAATTTTCAAATGTATATCTTGTGAAATACTAAAATCAAATTTTG
Found at i:60222 original size:14 final size:14
Alignment explanation
Indices: 60203--60230 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
60193 GAACTCTGTA
60203 TTAGTATTTAGTTT
1 TTAGTATTTAGTTT
60217 TTAGTATTTAGTTT
1 TTAGTATTTAGTTT
60231 CCCGTGTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.64
Consensus pattern (14 bp):
TTAGTATTTAGTTT
Found at i:62967 original size:26 final size:27
Alignment explanation
Indices: 62938--62990 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
62928 AGTTCAGGTA
62938 AGTTGTATATTACCCTAAAA-TAGTTT
1 AGTTGTATATTACCCTAAAACTAGTTT
62964 AGTTGTATATTACCCTAAAACTAGTTT
1 AGTTGTATATTACCCTAAAACTAGTTT
62991 TTCTATGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (27 bp):
AGTTGTATATTACCCTAAAACTAGTTT
Found at i:75582 original size:18 final size:18
Alignment explanation
Indices: 75559--75593 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
75549 CAGGGGCTTG
75559 GCCCTAACTAATCCGGAA
1 GCCCTAACTAATCCGGAA
*
75577 GCCCTAATTAATCCGGA
1 GCCCTAACTAATCCGGA
75594 TCCGACCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.20
Consensus pattern (18 bp):
GCCCTAACTAATCCGGAA
Found at i:77972 original size:25 final size:25
Alignment explanation
Indices: 77944--78069 Score: 252
Period size: 25 Copynumber: 5.0 Consensus size: 25
77934 AAAGAAATGG
77944 AGAAGGAATTTGAATATATGCATTT
1 AGAAGGAATTTGAATATATGCATTT
77969 AGAAGGAATTTGAATATATGCATTT
1 AGAAGGAATTTGAATATATGCATTT
77994 AGAAGGAATTTGAATATATGCATTT
1 AGAAGGAATTTGAATATATGCATTT
78019 AGAAGGAATTTGAATATATGCATTT
1 AGAAGGAATTTGAATATATGCATTT
78044 AGAAGGAATTTGAATATATGCATTT
1 AGAAGGAATTTGAATATATGCATTT
78069 A
1 A
78070 TCATTTCCTC
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 101 1.00
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (25 bp):
AGAAGGAATTTGAATATATGCATTT
Found at i:80118 original size:6 final size:6
Alignment explanation
Indices: 80107--80171 Score: 103
Period size: 6 Copynumber: 10.8 Consensus size: 6
80097 TTAAAAGATA
*
80107 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATT
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
* *
80155 TATGTC TAAATC TATAT
1 TATATC TATATC TATAT
80172 ATTTTTATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.51
Consensus pattern (6 bp):
TATATC
Found at i:82584 original size:2 final size:2
Alignment explanation
Indices: 82528--82570 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
82518 TTAGTAATTC
* *
82528 TA TA T- TA TA TA TA TA TA TA TA TA TA CA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
82569 TA
1 TA
82571 ACCTACAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:82671 original size:21 final size:23
Alignment explanation
Indices: 82627--82677 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
82617 ACAAAGCTCA
*
82627 AACTCGACTCAATGACCTACTCG
1 AACTCGACTCAATGACCGACTCG
*
82650 AACTCGAC-C-ATGACCGAGTCG
1 AACTCGACTCAATGACCGACTCG
*
82671 AATTCGA
1 AACTCGA
82678 GTTTTCTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 16 0.64
22 1 0.04
23 8 0.32
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (23 bp):
AACTCGACTCAATGACCGACTCG
Found at i:82945 original size:13 final size:13
Alignment explanation
Indices: 82927--82952 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
82917 TCAACCGTCT
82927 CTAATAAATGATG
1 CTAATAAATGATG
82940 CTAATAAATGATG
1 CTAATAAATGATG
82953 AAGCGTTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
CTAATAAATGATG
Found at i:84002 original size:15 final size:16
Alignment explanation
Indices: 83982--84020 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
83972 GGACAGGGAC
83982 ATATAATAAT-ATAAT
1 ATATAATAATAATAAT
83997 ATATAAT-ATAATAAT
1 ATATAATAATAATAAT
*
84012 AAATAATAA
1 ATATAATAA
84021 GGCAATCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.86
16 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATAATAATAATAAT
Found at i:84007 original size:20 final size:18
Alignment explanation
Indices: 83982--84020 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
83972 GGACAGGGAC
83982 ATATAATAATATAATATATA
1 ATATAATAATA-AATA-ATA
84002 ATATAATAATAAATAATA
1 ATATAATAATAAATAATA
84020 A
1 A
84021 GGCAATCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
20 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATAATAATAAATAATA
Found at i:84339 original size:6 final size:6
Alignment explanation
Indices: 84328--84382 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
84318 GTTCAGTGTA
84328 AAAGTT AAAGTT AAAGTT AAAGTT AAAGTT AAAGTT AAAGTT AAAGTT
1 AAAGTT AAAGTT AAAGTT AAAGTT AAAGTT AAAGTT AAAGTT AAAGTT
84376 AAAGTT A
1 AAAGTT A
84383 GTCTTGGTGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (6 bp):
AAAGTT
Found at i:85666 original size:7 final size:7
Alignment explanation
Indices: 85654--85678 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
85644 CAATCTCTGA
85654 ATCTCTC
1 ATCTCTC
85661 ATCTCTC
1 ATCTCTC
85668 ATCTCTC
1 ATCTCTC
85675 ATCT
1 ATCT
85679 TCCATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.40, G:0.00, T:0.44
Consensus pattern (7 bp):
ATCTCTC
Found at i:86442 original size:24 final size:24
Alignment explanation
Indices: 86415--86464 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
86405 TTTAGTCCTG
*
86415 TTCTTCTCTGTTTTTATCTGCATT
1 TTCTTCTCTGTTCTTATCTGCATT
*
86439 TTCTTCTCTGTTCTTCTCTGCATT
1 TTCTTCTCTGTTCTTATCTGCATT
86463 TT
1 TT
86465 TTTTGTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.06, C:0.24, G:0.08, T:0.62
Consensus pattern (24 bp):
TTCTTCTCTGTTCTTATCTGCATT
Found at i:86601 original size:195 final size:195
Alignment explanation
Indices: 86262--86635 Score: 565
Period size: 195 Copynumber: 1.9 Consensus size: 195
86252 CTTGTTAATC
* * *
86262 TTTTGTTTTTTTTTTCCCATATTCTACCTCTGTTTTTGTTTAACATTTTTGTGCGTTGAAGGCTT
1 TTTTGTTTTTTTTTTCCCATATTCTACCTCTGTTTTTGTCTAACATTATTATGCGTTGAAGGC--
*
86327 TAGTATCTCCTCTATAGATTGTTGTTAAGGGTAGTATAAGGAAGATTTTAACCGTTGAAGTATTT
64 ---T-TCTCCTCTATAGATTGTTGTTAAGGGTAGTATAAGGAAGATTTTAACCGTTAAAGTATTT
86392 CAACTTTATTTTGTTTAGTCCTGTTCTTCTCTGTTTTTATCTGCATTTTCTTCTCTGTTCTTCTC
125 CAACTTTATTTTGTTTAGT-CT-TTCTTCTCTGTTTTTATCTGCATTTTCTTCTCTGTTCTTCTC
86457 TGCATTTT
188 TGCATTTT
* *
86465 TTTTGTTCTTTTTTTT-TCATATTCTACCTCTGTTTTTGTCTAACATTATTATGCGTTGGAGGC-
1 TTTTGTT-TTTTTTTTCCCATATTCTACCTCTGTTTTTGTCTAACATTATTATGCGTTGAAGGCT
86528 TCTCCTCTATAGATTGTTGTTAA-GGTAGTATAAGGAAGATTTTAACCGTTAAAGTATTTCAACT
65 TCTCCTCTATAGATTGTTGTTAAGGGTAGTATAAGGAAGATTTTAACCGTTAAAGTATTTCAACT
* * *
86592 TTTTTTTGTTTAGTCTTTCTTCTCTGTTTTTATCTTCGTTTTCT
130 TTATTTTGTTTAGTCTTTCTTCTCTGTTTTTATCTGCATTTTCT
86636 CTTCTTTTAA
Statistics
Matches: 161, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
193 26 0.16
194 2 0.01
195 53 0.33
196 23 0.14
203 49 0.30
204 8 0.05
ACGTcount: A:0.17, C:0.15, G:0.14, T:0.53
Consensus pattern (195 bp):
TTTTGTTTTTTTTTTCCCATATTCTACCTCTGTTTTTGTCTAACATTATTATGCGTTGAAGGCTT
CTCCTCTATAGATTGTTGTTAAGGGTAGTATAAGGAAGATTTTAACCGTTAAAGTATTTCAACTT
TATTTTGTTTAGTCTTTCTTCTCTGTTTTTATCTGCATTTTCTTCTCTGTTCTTCTCTGCATTTT
Found at i:93285 original size:27 final size:25
Alignment explanation
Indices: 93236--93283 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
93226 TGGATAAAAC
*
93236 TATAAAAGAAAGTATACAATATAAT
1 TATAAAAAAAAGTATACAATATAAT
93261 TATAAAAAAAAGTATACAATATA
1 TATAAAAAAAAGTATACAATATA
93284 TAGTACTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (25 bp):
TATAAAAAAAAGTATACAATATAAT
Found at i:110776 original size:2 final size:2
Alignment explanation
Indices: 110769--110797 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
110759 TAAATTTGAG
110769 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
110798 GCATATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.