Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018743.1 Corchorus olitorius cultivar O-4 contig18776, 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: 147660
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:891 original size:19 final size:19
Alignment explanation
Indices: 869--914 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
859 TGGATCGGGT
*
869 CAAACCGGTTCGGTCCGAC
1 CAAACCGGTTCGGACCGAC
*
888 CAAACCGGTTCGGACCGGC
1 CAAACCGGTTCGGACCGAC
*
907 CAAGCCGG
1 CAAACCGG
915 CTCATGAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.22, C:0.37, G:0.30, T:0.11
Consensus pattern (19 bp):
CAAACCGGTTCGGACCGAC
Found at i:8463 original size:19 final size:19
Alignment explanation
Indices: 8410--8463 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
8400 TTTTTTTTTG
*
8410 GGTT-GGATCGGATCAAACC
1 GGTTCGGATCGG-CCAAACC
*
8429 GGTTCGG-TCCGACCAAACC
1 GGTTCGGAT-CGGCCAAACC
8448 GGTTCGGATCGGCCAA
1 GGTTCGGATCGGCCAA
8464 GCCGCGGCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 24 0.83
20 5 0.17
ACGTcount: A:0.22, C:0.28, G:0.31, T:0.19
Consensus pattern (19 bp):
GGTTCGGATCGGCCAAACC
Found at i:11435 original size:33 final size:33
Alignment explanation
Indices: 11382--11445 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
11372 AAAAGGTTGT
* *
11382 CAATGCAAATTTCCACCCCGGC-AGGAGTGAGTA
1 CAATACAAATTTCCAACCCGGCAAGG-GTGAGTA
*
11415 CAATACAATTTTCCAACCCGGCAAGGGTGAG
1 CAATACAAATTTCCAACCCGGCAAGGGTGAG
11446 CACACATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 24 0.89
34 3 0.11
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (33 bp):
CAATACAAATTTCCAACCCGGCAAGGGTGAGTA
Found at i:13823 original size:75 final size:76
Alignment explanation
Indices: 13745--13885 Score: 182
Period size: 74 Copynumber: 1.9 Consensus size: 76
13735 TTAGATTAAA
* * *
13745 AAAAACTTT-AAATTCTTGTTATAAA-TAAAGAATTA-ATTTTA-ATCACAATAAATTAAACTAC
1 AAAAA-TTTCAAATTCTTATTAAAAAGGAAAGAA-TACATTTTACATCACAATAAATTAAACTAC
13806 CAGTATGCACTCC
64 CAGTATGCACTCC
*
13819 AAAAATTTCAAATTCTTATTAAAAAGGAAAGAATACATTTTAGTCATCACAATAATTTAAACTAC
1 AAAAATTTCAAATTCTTATTAAAAAGGAAAGAATACATTTTA--CATCACAATAAATTAAACTAC
13884 CA
64 CA
13886 ACACACTCCA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
73 3 0.05
74 21 0.37
75 12 0.21
78 21 0.37
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.33
Consensus pattern (76 bp):
AAAAATTTCAAATTCTTATTAAAAAGGAAAGAATACATTTTACATCACAATAAATTAAACTACCA
GTATGCACTCC
Found at i:34669 original size:37 final size:37
Alignment explanation
Indices: 34626--34698 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
34616 CCGAATACAA
* *
34626 AGTGGCTAACCCAAACTTTTGAGTAGTTTCTGGGTTG
1 AGTGGCTAACCCAAACGTTTCAGTAGTTTCTGGGTTG
34663 AGTGGCTAACCCAAACGTTTCAGTAGTTTCTGGGTT
1 AGTGGCTAACCCAAACGTTTCAGTAGTTTCTGGGTT
34699 TTAAAGAACG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (37 bp):
AGTGGCTAACCCAAACGTTTCAGTAGTTTCTGGGTTG
Found at i:35567 original size:14 final size:13
Alignment explanation
Indices: 35531--35569 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
35521 TATATATTAG
35531 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
35544 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
35558 AATTTTTTAAAT
1 AATTTTTTAAAT
35570 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:51220 original size:15 final size:15
Alignment explanation
Indices: 51200--51232 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
51190 TGGTTGCGTA
51200 TTTTTGTTTTTGTTT
1 TTTTTGTTTTTGTTT
51215 TTTTTGTTTTTGTTT
1 TTTTTGTTTTTGTTT
51230 TTT
1 TTT
51233 GTTCGCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (15 bp):
TTTTTGTTTTTGTTT
Found at i:59135 original size:26 final size:24
Alignment explanation
Indices: 59077--59150 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 24
59067 TTAGGGTCAC
59077 CTAAGGGCATTTTGGTCATTTTTGCA
1 CTAAGGGCATTTTGGTCA--TTTGCA
*
59103 CTAAGGGCATTTTGTTCATTTGCA
1 CTAAGGGCATTTTGGTCATTTGCA
* *
59127 CATTCAGGGGTATTTTGGTCATTT
1 C--T-AAGGGCATTTTGGTCATTT
59151 TAAGTCCACT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 7 0.17
26 18 0.44
27 16 0.39
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (24 bp):
CTAAGGGCATTTTGGTCATTTGCA
Found at i:69112 original size:22 final size:22
Alignment explanation
Indices: 69069--69112 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
69059 TCATTTCGAC
* * *
69069 TGTATTTTTCATCGATGGAATT
1 TGTATTATTCATCAATGAAATT
*
69091 TGTATTATTCATCAATTAAATT
1 TGTATTATTCATCAATGAAATT
69113 GTCAAAAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (22 bp):
TGTATTATTCATCAATGAAATT
Found at i:70896 original size:17 final size:18
Alignment explanation
Indices: 70855--70896 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
70845 TTTAGAAGAT
*
70855 ATTAAAAAAGATATAATA
1 ATTAAAAAAGAAATAATA
70873 A-TAAAAAAGGAAATAA-A
1 ATTAAAAAA-GAAATAATA
70890 ATTAAAA
1 ATTAAAA
70897 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
ATTAAAAAAGAAATAATA
Found at i:70968 original size:9 final size:10
Alignment explanation
Indices: 70945--70978 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
70935 ATTAAATTAC
70945 AAAAAATAAT
1 AAAAAATAAT
*
70955 AAAAAATGAT
1 AAAAAATAAT
70965 AAAATAATAAT
1 AAAA-AATAAT
70976 AAA
1 AAA
70979 TTTAAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 13 0.62
11 8 0.38
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:77262 original size:17 final size:16
Alignment explanation
Indices: 77219--77265 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
77209 ATTTCCCTTG
77219 TTCCTTC-TCTTTTCCT
1 TTCCTTCTTC-TTTCCT
* *
77235 TTCCTTTTTCTTTCTT
1 TTCCTTCTTCTTTCCT
77251 TTCTCTTCTTCTTTC
1 TTC-CTTCTTCTTTC
77266 AAATTGGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (16 bp):
TTCCTTCTTCTTTCCT
Found at i:90714 original size:6 final size:6
Alignment explanation
Indices: 90694--90731 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
90684 ATTTTTTTAA
90694 AAAAAG AAGAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AA-AAAG AAAAAG AAAAAG AAAAAG AAAAAG A
90732 GAGGTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:94498 original size:9 final size:9
Alignment explanation
Indices: 94468--94509 Score: 57
Period size: 9 Copynumber: 4.4 Consensus size: 9
94458 AATTCCCATA
94468 AAAAAAATG
1 AAAAAAATG
*
94477 AAGAATGAATG
1 AA-AA-AAATG
94488 AAAAAAATG
1 AAAAAAATG
94497 AAAAAAATG
1 AAAAAAATG
94506 AAAA
1 AAAA
94510 TAAAGGCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 19 0.66
10 4 0.14
11 6 0.21
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (9 bp):
AAAAAAATG
Found at i:94598 original size:14 final size:13
Alignment explanation
Indices: 94569--94613 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
94559 AGAGTCATGG
94569 TTTTCAAAAATGT
1 TTTTCAAAAATGT
94582 TTTTCAAAAATGT
1 TTTTCAAAAATGT
*
94595 TTTTCGAAAAATGG
1 TTTTC-AAAAATGT
94609 TTTTC
1 TTTTC
94614 GGAAACTCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 18 0.60
14 12 0.40
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (13 bp):
TTTTCAAAAATGT
Found at i:95593 original size:50 final size:50
Alignment explanation
Indices: 95518--95625 Score: 171
Period size: 50 Copynumber: 2.2 Consensus size: 50
95508 AGAACAAGAA
* *
95518 TTTTCAAAATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGC
1 TTTTCAAAATAAGATTGCATTCCATTTGTGAGACCAAGACCAAAATTCGC
* * *
95568 TTTTCAAAATAAGATTGCATTCCATTTGTGAGACCAAGACCGAAGTTTGC
1 TTTTCAAAATAAGATTGCATTCCATTTGTGAGACCAAGACCAAAATTCGC
95618 TTTTCAAA
1 TTTTCAAA
95626 GGGCATTTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (50 bp):
TTTTCAAAATAAGATTGCATTCCATTTGTGAGACCAAGACCAAAATTCGC
Found at i:96739 original size:69 final size:69
Alignment explanation
Indices: 96620--96917 Score: 377
Period size: 69 Copynumber: 4.3 Consensus size: 69
96610 TCTGGTCTTC
* * *
96620 CAAGACCAAACTCGTTTCCATACGAGTCAATTTAAGCCTTGGTTCTATCCAAGCAGTA-AGGGCT
1 CAAG-CCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAGCATA-GGCT
96684 TTTCCA
64 TTTCCA
* ** * *
96690 CAAGCCAAACTAGTTTCCATACGAGTCAGTACAAACCTTGGTTCCATCCAAGTAGCATAGGCTTT
1 CAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAGCATAGGCTTT
96755 TCCA
66 TCCA
*
96759 CAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTTCATCCAAGCCA-CATAGGCTT
1 CAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAG-CAGCATAGGCTT
96823 TTCCA
65 TTCCA
* * ** * *
96828 CAAGCCAAACCCGTTTCCATACGAGTCAATTTAAGTATTAGTTCCATCCAAGCAACAT-GGCTTT
1 CAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAGCATAGGCTTT
96892 TCCA
66 TCCA
* ** *
96896 TAAGCCAAGTTCATTTCCATAC
1 CAAGCCAAACTCGTTTCCATAC
96918 AAATTCAGTC
Statistics
Matches: 200, Mismatches: 25, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
68 29 0.14
69 165 0.82
70 6 0.03
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (69 bp):
CAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAGCATAGGCTTT
TCCA
Found at i:97453 original size:22 final size:22
Alignment explanation
Indices: 97428--97492 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
97418 TTCGATCCTG
97428 GTTTAGGATCATTGATTCTTGA
1 GTTTAGGATCATTGATTCTTGA
97450 GTTT---AT--TTCGA-TCTTG-
1 GTTTAGGATCATT-GATTCTTGA
* *
97466 GTTTAGGATCATTGCTTCATGA
1 GTTTAGGATCATTGATTCTTGA
97488 GTTTA
1 GTTTA
97493 TTCCAATCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
16 4 0.12
17 7 0.21
18 2 0.06
19 4 0.12
20 1 0.03
21 6 0.18
22 9 0.27
ACGTcount: A:0.20, C:0.11, G:0.22, T:0.48
Consensus pattern (22 bp):
GTTTAGGATCATTGATTCTTGA
Found at i:97458 original size:38 final size:37
Alignment explanation
Indices: 97375--97557 Score: 199
Period size: 38 Copynumber: 4.8 Consensus size: 37
97365 CATAGGTTAA
* * *
97375 TTTATTTTGATCATGTTTTAGGATCATTGCTT-TGTTAG
1 TTTATTTCGATCCTGGTTTAGGATCATTGCTTATG--AG
* * *
97413 TTAATTTCGATCCTGGTTTAGGATCATTGATTCTTGAG
1 TTTATTTCGATCCTGGTTTAGGATCATTGCTT-ATGAG
*
97451 TTTATTTCGATCTTGGTTTAGGATCATTGCTTCATGAG
1 TTTATTTCGATCCTGGTTTAGGATCATTGCTT-ATGAG
* * *
97489 TTTATTCCAATCCTGGTTTAGGATCATTGCTTATCAG
1 TTTATTTCGATCCTGGTTTAGGATCATTGCTTATGAG
*
97526 TTTATTTCAGAATCCT-GTTCAGGATCATTGCT
1 TTTATTTC-G-ATCCTGGTTTAGGATCATTGCT
97558 CTATTAATTT
Statistics
Matches: 125, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
37 11 0.09
38 107 0.86
39 5 0.04
40 2 0.02
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.47
Consensus pattern (37 bp):
TTTATTTCGATCCTGGTTTAGGATCATTGCTTATGAG
Found at i:99990 original size:42 final size:44
Alignment explanation
Indices: 99939--100032 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 44
99929 AGTGCATTAT
*
99939 CTAA-ATTCTA-C-TCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTTCCATCTCTAGATAATTCATCAAAATAAAG
99980 CTAATATTCTACTCTTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTAC-CTTCCATCTCTAGATAATTCATCAAAATAAAG
100025 CTAATATT
1 CTAATATT
100033 AATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
44 1 0.02
45 37 0.77
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACCTTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:102006 original size:17 final size:19
Alignment explanation
Indices: 101963--102004 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
101953 TCTTATGGTC
101963 TTGTGTACTTGGTGAATAT
1 TTGTGTACTTGGTGAATAT
*
101982 TTGTGTACTTGGTGAATTT
1 TTGTGTACTTGGTGAATAT
102001 TTGT
1 TTGT
102005 ACCTGTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.17, C:0.05, G:0.26, T:0.52
Consensus pattern (19 bp):
TTGTGTACTTGGTGAATAT
Found at i:117105 original size:47 final size:47
Alignment explanation
Indices: 117047--117312 Score: 433
Period size: 47 Copynumber: 5.6 Consensus size: 47
117037 TACCAAGGTA
* * *
117047 ACAACTTCTGGTGTCAATTAAATTTACTAAAATAAAAATTTAATTTG
1 ACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTG
*
117094 ACAACTTCTGGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTG
1 ACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTG
* * *
117141 ACAACTTCTAGTGTCAAGTATATTTACTAAAGTAGAATTTTAATTTG
1 ACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTG
*
117188 ACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAGATTTTAATTTG
1 ACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTG
117235 ACAACTTCTAGTGTCAATTAAATTTACTAAAAGTAAAATTTTAATTTG
1 ACAACTTCTAGTGTCAATTAAATTTACT-AAAGTAAAATTTTAATTTG
*
117283 ACAACTTCTGGTGTCAATTAAAATTTACTA
1 ACAACTTCTAGTGTCAATT-AAATTTACTA
117313 GATCTCTCGT
Statistics
Matches: 205, Mismatches: 12, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
47 159 0.78
48 37 0.18
49 9 0.04
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (47 bp):
ACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTG
Found at i:118967 original size:21 final size:22
Alignment explanation
Indices: 118938--118978 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
118928 TATCGTAAAG
118938 TCTCCAGTCTTCATC-TTGTGT
1 TCTCCAGTCTTCATCATTGTGT
*
118959 TCTCTAGTCTTCATCATTGT
1 TCTCCAGTCTTCATCATTGT
118979 TCTTGTTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.27, G:0.12, T:0.49
Consensus pattern (22 bp):
TCTCCAGTCTTCATCATTGTGT
Found at i:121016 original size:16 final size:17
Alignment explanation
Indices: 120997--121038 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
120987 TTAAGAGATT
120997 AATAATAAA-TTTTAAA
1 AATAATAAAGTTTTAAA
121013 AATAA-AAAGTTTTAAA
1 AATAATAAAGTTTTAAA
121029 AATAAATAAA
1 AAT-AATAAA
121039 AAAATTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.13
16 15 0.65
17 2 0.09
18 3 0.13
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
AATAATAAAGTTTTAAA
Found at i:121049 original size:20 final size:20
Alignment explanation
Indices: 121012--121050 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
121002 TAAATTTTAA
** *
121012 AAATAAAAAGTTTTAAAAAT
1 AAATAAAAAAATTGAAAAAT
121032 AAATAAAAAAATTGAAAAA
1 AAATAAAAAAATTGAAAAA
121051 ATTCATATGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (20 bp):
AAATAAAAAAATTGAAAAAT
Found at i:140261 original size:176 final size:176
Alignment explanation
Indices: 139964--140313 Score: 628
Period size: 176 Copynumber: 2.0 Consensus size: 176
139954 GGACTCCAAG
*
139964 GCTTTCTCCTCCAAATCTTCAACTTCTACAATATTTTCTAAAGGGAATAGAATACAATACATGAA
1 GCTTTCTCCTCCAAACCTTCAACTTCTACAATATTTTCTAAAGGGAATAGAATACAATACATGAA
* *
140029 AACCTAGATCTAAAGTGGCTATTTATAGTAGAAATAATCCTAAAGACTCTAATTACACTTAGGAT
66 AACCTAGATCTAAAGTGGCTATTTATAGTAGAAATAACCCTAAAGACTCCAATTACACTTAGGAT
*
140094 AGGACTCTAGGACGGTTTAAGGGCTGATTTGGTCTCCAAGTTGCGA
131 AGGACTCTAGGACGGTTTAAGGGCTGACTTGGTCTCCAAGTTGCGA
* *
140140 GCTTTCTCCTCTAAACCTTCAACTTCTAGAATATTTTCTAAAGGGAATAGAATACAATACATGAA
1 GCTTTCTCCTCCAAACCTTCAACTTCTACAATATTTTCTAAAGGGAATAGAATACAATACATGAA
* *
140205 AACCTAGATCTAAGGTGGCTATTTATAGTGGAAATAACCCTAAAGACTCCAATTACACTTAGGAT
66 AACCTAGATCTAAAGTGGCTATTTATAGTAGAAATAACCCTAAAGACTCCAATTACACTTAGGAT
140270 AGGACTCTAGGACGGTTTAAGGGCTGACTTGGTCTCCAAGTTGC
131 AGGACTCTAGGACGGTTTAAGGGCTGACTTGGTCTCCAAGTTGC
140314 CTTAAAAGTC
Statistics
Matches: 166, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
176 166 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (176 bp):
GCTTTCTCCTCCAAACCTTCAACTTCTACAATATTTTCTAAAGGGAATAGAATACAATACATGAA
AACCTAGATCTAAAGTGGCTATTTATAGTAGAAATAACCCTAAAGACTCCAATTACACTTAGGAT
AGGACTCTAGGACGGTTTAAGGGCTGACTTGGTCTCCAAGTTGCGA
Found at i:140800 original size:19 final size:18
Alignment explanation
Indices: 140767--140802 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
140757 TTGAAATAAT
140767 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
140785 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
140803 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:141939 original size:21 final size:21
Alignment explanation
Indices: 141915--142045 Score: 194
Period size: 21 Copynumber: 6.2 Consensus size: 21
141905 CTTAGACAAT
*
141915 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
141936 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
141957 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
141978 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
141999 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
142020 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
142041 TCCAA
1 TCCAA
142046 GGAACTTCTA
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
20 3 0.03
21 102 0.97
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Done.