Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014968.1 Corchorus olitorius cultivar O-4 contig15001, 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: 34798
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:3830 original size:33 final size:33
Alignment explanation
Indices: 3785--3891 Score: 169
Period size: 33 Copynumber: 3.2 Consensus size: 33
3775 ACTTGTAGAA
*
3785 CTCAAATTTGATGTAGGTATTGTCGAATTCAAG
1 CTCAATTTTGATGTAGGTATTGTCGAATTCAAG
*
3818 CCCAATTTTGATGTAGGTATTGTCGAATTCAAG
1 CTCAATTTTGATGTAGGTATTGTCGAATTCAAG
* * *
3851 CTCAATTTTGATGTAGATAGTGTTGAATTCAAG
1 CTCAATTTTGATGTAGGTATTGTCGAATTCAAG
3884 CTCAATTT
1 CTCAATTT
3892 CCGCAGCAAC
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (33 bp):
CTCAATTTTGATGTAGGTATTGTCGAATTCAAG
Found at i:5165 original size:35 final size:35
Alignment explanation
Indices: 5072--5360 Score: 374
Period size: 34 Copynumber: 8.3 Consensus size: 35
5062 TTTTTGTAAA
5072 TTGAAAAC-TAAAACCTGATGGGAACTTTCCCAAT
1 TTGAAAACTTAAAACCTGATGGGAACTTTCCCAAT
*
5106 TTAAAAACTTTGAAAA-CTGAATGGGAA-TTTCCCAAT
1 TTGAAAAC-TT-AAAACCTG-ATGGGAACTTTCCCAAT
* *
5142 TTGAAAACTTAAAAACTTTATGGGAACTTTCCCAAT
1 TTGAAAACTT-AAAACCTGATGGGAACTTTCCCAAT
* * *
5178 TTGAAAATTTAAAAACTTGTTGGGAACTTTCCCAAT
1 TTGAAAACTT-AAAACCTGATGGGAACTTTCCCAAT
*
5214 TTGAAAAC-TAAAACCTGGTGGGAACTTTCCCAAT
1 TTGAAAACTTAAAACCTGATGGGAACTTTCCCAAT
* *
5248 TTGAAAAC-TAAAACCTGGTGGGAACTTTCCCAAC
1 TTGAAAACTTAAAACCTGATGGGAACTTTCCCAAT
*
5282 TTGAAAACTT-AAACCGGATGGGAACTTTCCCAAT
1 TTGAAAACTTAAAACCTGATGGGAACTTTCCCAAT
* * *
5316 TTGAAAATTTAAAAACTGATGGGAACTTTTCCAAT
1 TTGAAAACTTAAAACCTGATGGGAACTTTCCCAAT
5351 TTGAAAACTT
1 TTGAAAACTT
5361 CGAAAACTGA
Statistics
Matches: 227, Mismatches: 20, Indels: 15
0.87 0.08 0.06
Matches are distributed among these distances:
34 101 0.44
35 45 0.20
36 70 0.31
37 11 0.05
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (35 bp):
TTGAAAACTTAAAACCTGATGGGAACTTTCCCAAT
Found at i:7217 original size:21 final size:22
Alignment explanation
Indices: 7193--7234 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
7183 TTTGCCTCAT
7193 GCATTCATTCAT-CATGCCATG
1 GCATTCATTCATGCATGCCATG
*
7214 GCATTCATTCATGCATTCCAT
1 GCATTCATTCATGCATGCCAT
7235 TAAACCTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (22 bp):
GCATTCATTCATGCATGCCATG
Found at i:9334 original size:17 final size:17
Alignment explanation
Indices: 9290--9327 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
9280 TCCCAATTAT
9290 AAAAAAGAAAAAAAATG
1 AAAAAAGAAAAAAAATG
9307 AAAAAAGAAAAAAAATG
1 AAAAAAGAAAAAAAATG
9324 AAAA
1 AAAA
9328 TGAAAAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (17 bp):
AAAAAAGAAAAAAAATG
Found at i:10546 original size:50 final size:51
Alignment explanation
Indices: 10402--10551 Score: 164
Period size: 51 Copynumber: 3.0 Consensus size: 51
10392 GAAGTTTTAC
* *
10402 AATAAAATTGC-TTCC-TTTT-CGAGCCCAAGATCAAAATTTGCTTTTCAA
1 AATAAAATTGCATTCCATTTTGTGAGACCAAGATCAAAATTTGCTTTTCAA
* * * *
10450 AATAAAATTGCTTTCCATTTTGTGAGACCAAGTTCAAAATTCGCTTTTCAG
1 AATAAAATTGCATTCCATTTTGTGAGACCAAGATCAAAATTTGCTTTTCAA
** ** * *
10501 GGTAAGGTTGCATTCCA-TTTGTGAGTCCAAGATCAAACTTTGCTTTTCAA
1 AATAAAATTGCATTCCATTTTGTGAGACCAAGATCAAAATTTGCTTTTCAA
10551 A
1 A
10552 GGTCATTTAA
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
48 11 0.13
49 4 0.05
50 32 0.39
51 36 0.43
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (51 bp):
AATAAAATTGCATTCCATTTTGTGAGACCAAGATCAAAATTTGCTTTTCAA
Found at i:11529 original size:69 final size:69
Alignment explanation
Indices: 11445--11628 Score: 296
Period size: 69 Copynumber: 2.7 Consensus size: 69
11435 CCATCCGAAT
*
11445 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAATTCAAGCCTTGGTTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTCAAGCCTTGGTTCCATCCA
11510 AGCA
66 AGCA
* * * *
11514 GCATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTCAAGCCTTGGTTCCATCCA
11579 AGCA
66 AGCA
* * *
11583 ACATAGGCTTATCCATAAGTCAAACTCGTTTCCATACGAGTCAATT
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATT
11629 AGCAACGGGG
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 104 1.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (69 bp):
ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTCAAGCCTTGGTTCCATCCA
AGCA
Found at i:11667 original size:118 final size:113
Alignment explanation
Indices: 11518--11853 Score: 357
Period size: 118 Copynumber: 3.0 Consensus size: 113
11508 CAAGCAGCAT
* *
11518 GGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCA
1 GGGCTTTTTCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA
* *
11583 ACATAGGCTTATCCATAAGTCAAACTCGTTTCCATACGAGTCAATTAGCAA
66 ACATAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATT--C-A
* *
11634 CGGGGCTTTTTCACAAGCCAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCACCCAAG
1 --GGGCTTTTTCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
* ** ** * * *
11699 CGACAGGGGCTTTTCCATAAGCCAAGTTCATCTCCAT---A-TAAATTCA
64 CAACATAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTCA
* * *
11745 --G--TCTTC-CAAGACTAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGC
1 GGGCTTTTTCACAAG-CCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC
* * * * *
11805 AACGTAGGCTTTTCAACAAGCCAAACTCGTTCCCATACGAGTCAGTTCA
65 AACATAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTCA
11854 AGCCTTGGTT
Statistics
Matches: 182, Mismatches: 31, Indels: 19
0.78 0.13 0.08
Matches are distributed among these distances:
104 4 0.02
105 74 0.41
107 1 0.01
108 1 0.01
109 6 0.03
111 1 0.01
112 1 0.01
114 5 0.03
115 1 0.01
118 88 0.48
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (113 bp):
GGGCTTTTTCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA
ACATAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTCA
Found at i:11869 original size:69 final size:68
Alignment explanation
Indices: 11758--11981 Score: 322
Period size: 69 Copynumber: 3.2 Consensus size: 68
11748 TTCCAAGACT
* *
11758 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCAACGTAGGCTTTTCAACA
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC-ACATAGGCTTTTCAACA
11823 AGCC
65 AGCC
* *
11827 AAACTCGTTCCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCACATAGGCTTTTCCACA
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG-CACATAGGCTTTTCAACA
11892 AGCC
65 AGCC
* * * * *
11896 AAACTCGTTTCCATACGGGTCAGTTTAAGCCTTGGTTCCATCCAGGGCACATGGGCTTTTCTACA
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA-AGCACATAGGCTTTTCAACA
11961 AGCC
65 AGCC
* *
11965 ACATTCGTTTCCATACG
1 AAACTCGTTTCCATACG
11982 GTGCATTACC
Statistics
Matches: 141, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
69 139 0.99
70 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.27
Consensus pattern (68 bp):
AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCACATAGGCTTTTCAACAA
GCC
Found at i:18486 original size:46 final size:45
Alignment explanation
Indices: 18415--18623 Score: 194
Period size: 46 Copynumber: 4.6 Consensus size: 45
18405 CATCGAATCA
*
18415 ATCTGATTCACCGAATC-AACATTTGAAGAGATACTGCACTG-AGT
1 ATCTGATTCACCGAATCAAAC-TTTGAAGAAATACTGCACTGCAGT
*
18459 CCATCTGATTCACTC-AATCAAACTTTGAAGAAATACTGCACCGCAGT
1 --ATCTGATTCAC-CGAATCAAACTTTGAAGAAATACTGCACTGCAGT
* * *
18506 AACTTGATCCACCGAATCAAACTTTAAAGAAATACTGCACTGCAGT
1 ATC-TGATTCACCGAATCAAACTTTGAAGAAATACTGCACTGCAGT
* * * *
18552 AACTTGATTCACCGAATTAAACTTTTGAA-AAATAATGCA-TCGCATT
1 ATC-TGATTCACCGAATCAAAC-TTTGAAGAAATACTGCACT-GCAGT
* * *
18598 AACTTGATTCACCGTATCCAACTTTG
1 ATC-TGATTCACCGAATCAAACTTTG
18624 GACTGTTTGA
Statistics
Matches: 142, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
45 8 0.06
46 122 0.86
47 12 0.08
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.28
Consensus pattern (45 bp):
ATCTGATTCACCGAATCAAACTTTGAAGAAATACTGCACTGCAGT
Found at i:18560 original size:92 final size:91
Alignment explanation
Indices: 18418--18717 Score: 243
Period size: 92 Copynumber: 3.2 Consensus size: 91
18408 CGAATCAATC
* * *
18418 TGATTCACCGAATCAACATTTGAAGAGATACTGCACTGAGTCCATCTGATTCACTC-AATCAAAC
1 TGATTCACCGAATCAAC-TTTAAAGAAATACTGCACTGAGTACATCTGATTCAC-CGAATCAAAC
*
18482 -TTTGAAGAAATACTGCACCGCAGTAACT
64 TTTTGAA-AAATAATGCACCGCAGTAACT
* *
18510 TGATCCACCGAATCAAACTTTAAAGAAATACTGCACTGCAGTA-A-CTTGATTCACCGAATTAAA
1 TGATTCACCGAATC-AACTTTAAAGAAATACTGCACTG-AGTACATC-TGATTCACCGAATCAAA
* *
18573 CTTTTGAAAAATAATGCATCGCATTAACT
63 CTTTTGAAAAATAATGCACCGCAGTAACT
* ** * * *
18602 TGATTCACCGTATCCAACTTTGGACTGTTTGAAAAGGTACTGCACCGAGTTAC-CCTGATTCACT
1 TGATTCACCGAAT-CAACTTT--A----AAG-AAA--TACTGCACTGAG-TACATCTGATTCACC
** *
18666 GAATCTGACTTTT-AGAAAATAATGCACCGCATTAACT
55 GAATCAAACTTTTGA-AAAATAATGCACCGCAGTAACT
18703 TGATTCACCGAATCA
1 TGATTCACCGAATCA
18718 CCCTGATCTG
Statistics
Matches: 170, Mismatches: 19, Indels: 30
0.78 0.09 0.14
Matches are distributed among these distances:
91 2 0.01
92 82 0.48
93 13 0.08
94 1 0.01
98 1 0.01
99 3 0.02
100 5 0.03
101 62 0.36
102 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (91 bp):
TGATTCACCGAATCAACTTTAAAGAAATACTGCACTGAGTACATCTGATTCACCGAATCAAACTT
TTGAAAAATAATGCACCGCAGTAACT
Found at i:18823 original size:90 final size:90
Alignment explanation
Indices: 18682--18938 Score: 397
Period size: 90 Copynumber: 2.8 Consensus size: 90
18672 GACTTTTAGA
* * *
18682 AAATAATGCACCGCATTAACTTGATTCACCGAATCACCCTGATCTGCTTGAAAATGTGCTGCATC
1 AAATAATGCACCGCATTAACTTGATTCACCGAATCACCCTGAACTGTTTGAAAATGTGCTGCAAC
*
18747 GAGCTCACTGAATTCAATCATGAAG
66 GAGCTCACTGAATCCAATCATGAAG
* * * * *
18772 AAATAATGCACCGCATTATCTTGATTCACCGAATTACCCTAAACTGTTTGAAAATGTGTTGCACC
1 AAATAATGCACCGCATTAACTTGATTCACCGAATCACCCTGAACTGTTTGAAAATGTGCTGCAAC
*
18837 GAGCTCACTGAATCCAATCTTGAAG
66 GAGCTCACTGAATCCAATCATGAAG
* *
18862 AAATTATGCACCGCATTAACTTGATTCACCGAATCACCCTGAACTATTTGAAAATGTGCTGCAAC
1 AAATAATGCACCGCATTAACTTGATTCACCGAATCACCCTGAACTGTTTGAAAATGTGCTGCAAC
18927 GAGCTCATCTGA
66 GAGCTCA-CTGA
18939 TTTACCGAAT
Statistics
Matches: 150, Mismatches: 16, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
90 146 0.97
91 4 0.03
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (90 bp):
AAATAATGCACCGCATTAACTTGATTCACCGAATCACCCTGAACTGTTTGAAAATGTGCTGCAAC
GAGCTCACTGAATCCAATCATGAAG
Found at i:19110 original size:54 final size:54
Alignment explanation
Indices: 18947--19185 Score: 186
Period size: 54 Copynumber: 4.5 Consensus size: 54
18937 GATTTACCGA
* ** * * * *
18947 ATCACTAGAAGATAAACCCAAATCACTGA-AAACTTCCTTGACTAACCGCACTGG
1 ATCACTTGAAGATAAACTTAAACCACT-ATAAACTTTCTTGATTGACCGCACTGG
* *** * * ** *
19001 ATCACTTGAAGATAAATTTAAAACCACTGGCAACCTTC-TGAATGATTGCATTGG
1 ATCACTTGAAGATAAACTT-AAACCACTATAAACTTTCTTGATTGACCGCACTGG
* * *
19055 ATCACTTAAACATAAACCTAAACCACTATAAACTTTCTTGATTGACCGCACTGG
1 ATCACTTGAAGATAAACTTAAACCACTATAAACTTTCTTGATTGACCGCACTGG
* * * *
19109 ATCTCTTGAAGATAAACTTAAACAAC-AGTAAA----CTTGATTGATCGCACTAG
1 ATCACTTGAAGATAAACTTAAACCACTA-TAAACTTTCTTGATTGACCGCACTGG
*
19159 ATCCCTTGAAGATAAACTTAAACCACT
1 ATCACTTGAAGATAAACTTAAACCACT
19186 TGAAAGTTTT
Statistics
Matches: 145, Mismatches: 35, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
50 40 0.28
53 15 0.10
54 78 0.54
55 12 0.08
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (54 bp):
ATCACTTGAAGATAAACTTAAACCACTATAAACTTTCTTGATTGACCGCACTGG
Found at i:19246 original size:16 final size:16
Alignment explanation
Indices: 19208--19238 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19198 ACTGACCGTA
19208 AATTGAAGCATTGGAG
1 AATTGAAGCATTGGAG
*
19224 AATTGAAGCTTTGGA
1 AATTGAAGCATTGGA
19239 TACTTGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (16 bp):
AATTGAAGCATTGGAG
Found at i:19260 original size:24 final size:24
Alignment explanation
Indices: 19224--19278 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
19214 AGCATTGGAG
* *
19224 AATTGAAGCTTTGGATACTTGAAA
1 AATTGAAGATTTGAATACTTGAAA
19248 AATTGAAGATTTGAATACTTGAAA
1 AATTGAAGATTTGAATACTTGAAA
*
19272 ATTTGAA
1 AATTGAA
19279 AAACTGAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (24 bp):
AATTGAAGATTTGAATACTTGAAA
Found at i:19261 original size:16 final size:16
Alignment explanation
Indices: 19242--19287 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
19232 CTTTGGATAC
19242 TTGAAAAATTGAAGAT
1 TTGAAAAATTGAAGAT
* * *
19258 TTGAATACTTGAAAAT
1 TTGAAAAATTGAAGAT
*
19274 TTGAAAAACTGAAG
1 TTGAAAAATTGAAG
19288 CGTAGAAGAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.30
Consensus pattern (16 bp):
TTGAAAAATTGAAGAT
Found at i:19286 original size:24 final size:24
Alignment explanation
Indices: 19238--19286 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
19228 GAAGCTTTGG
* **
19238 ATACTTGAAAAATTGAAGATTTGA
1 ATACTTGAAAAATTGAAAAACTGA
*
19262 ATACTTGAAAATTTGAAAAACTGA
1 ATACTTGAAAAATTGAAAAACTGA
19286 A
1 A
19287 GCGTAGAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (24 bp):
ATACTTGAAAAATTGAAAAACTGA
Found at i:19310 original size:22 final size:22
Alignment explanation
Indices: 19283--19331 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
19273 TTTGAAAAAC
* *
19283 TGAAGCGTAGAAGAATTGAAAT
1 TGAAGCATAGAAAAATTGAAAT
*
19305 TGAAGCATTGAAAAATTGAAAT
1 TGAAGCATAGAAAAATTGAAAT
19327 TGAAG
1 TGAAG
19332 AAAGGCCACC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.04, G:0.24, T:0.24
Consensus pattern (22 bp):
TGAAGCATAGAAAAATTGAAAT
Found at i:19462 original size:35 final size:35
Alignment explanation
Indices: 19391--19826 Score: 388
Period size: 35 Copynumber: 12.8 Consensus size: 35
19381 GGTCAACTTA
* * * *
19391 AAGAAAGATCGCTCTAGATTAATTG-AAGTAAACTG
1 AAGAAAGATCGCCCTGGATCAATTGAAACT-AACTG
* * *
19426 AAGAATGATCGCCCTAGATCAATTGAAACTAGCTG
1 AAGAAAGATCGCCCTGGATCAATTGAAACTAACTG
* * *
19461 AAGAAAGA-CTGCCTTGG-GC-----CAACT---TG
1 AAGAAAGATC-GCCCTGGATCAATTGAAACTAACTG
* *
19487 AAGAAAGATCGCTCTGGATCAATT-AAAGTAAACTG
1 AAGAAAGATCGCCCTGGATCAATTGAAACT-AACTG
*
19522 AAGAATGATCGCCCTGGATCAATTGAAACTAACTG
1 AAGAAAGATCGCCCTGGATCAATTGAAACTAACTG
* * *
19557 AAGAAAGACCGCCCTGGGTCAATTGAAACTAACCG
1 AAGAAAGATCGCCCTGGATCAATTGAAACTAACTG
* *
19592 AAGAAAGATCGCCCTAGATCAATT-AAAGTAAACTG
1 AAGAAAGATCGCCCTGGATCAATTGAAACT-AACTG
* *
19627 AAGAAAGATCGTCCTGGATCAATTGAAACAAACTG
1 AAGAAAGATCGCCCTGGATCAATTGAAACTAACTG
*
19662 AAGAAAGATCGCCCTGGATCAATTG-AAGTAACTG
1 AAGAAAGATCGCCCTGGATCAATTGAAACTAACTG
* * *
19696 AA-AAATGAACGCCCTGGATCAATTG-AAGTAAATTG
1 AAGAAA-GATCGCCCTGGATCAATTGAAACT-AACTG
* * * *
19731 AAGAATGATCGCACTAGATCAATTG-AAGTAAACTG
1 AAGAAAGATCGCCCTGGATCAATTGAAACT-AACTG
*
19766 AA-AAATGATCGTCCTGGATCAATTGAAACTAACTG
1 AAGAAA-GATCGCCCTGGATCAATTGAAACTAACTG
**
19801 AAGAAAG-TCGCCCTAAATCAATTGAA
1 AAGAAAGATCGCCCTGGATCAATTGAA
19827 GTAAACTAAA
Statistics
Matches: 331, Mismatches: 49, Indels: 43
0.78 0.12 0.10
Matches are distributed among these distances:
26 15 0.05
27 2 0.01
29 4 0.01
31 3 0.01
33 3 0.01
34 55 0.17
35 231 0.70
36 18 0.05
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (35 bp):
AAGAAAGATCGCCCTGGATCAATTGAAACTAACTG
Found at i:19476 original size:96 final size:97
Alignment explanation
Indices: 19363--19757 Score: 391
Period size: 96 Copynumber: 3.9 Consensus size: 97
19353 TGAAGTAAAT
* * * * *
19363 TGAAGAAAGACCACCTTGGGTCAACTTA-AAGAAAGATCGCTCTAGATTAATTGAAGTAAACTGA
1 TGAAGAAAGACCGCCCTGGGTCAACTTACAAGAAAGATCGCCCTAGATCAATTAAAGTAAACTGA
*
19427 AGAATGATCGCCCTAGATCAATTGAAACTAGC
66 AGAATGATCGCCCTAGATCAATTGAAACTAAC
* * * * * *
19459 TGAAGAAAGACTGCCTTGGGCCAACTT-GAAGAAAGATCGCTCTGGATCAATTAAAGTAAACTGA
1 TGAAGAAAGACCGCCCTGGGTCAACTTACAAGAAAGATCGCCCTAGATCAATTAAAGTAAACTGA
*
19523 AGAATGATCGCCCTGGATCAATTGAAACTAAC
66 AGAATGATCGCCCTAGATCAATTGAAACTAAC
*
19555 TGAAGAAAGACCGCCCTGGGTCAATTGAAACTAACCGAAGAAAGATCGCCCTAGATCAATTAAAG
1 TGAAGAAAGACCGCCCTGGGTC------AACTTA-C-AAGAAAGATCGCCCTAGATCAATTAAAG
* * * *
19620 TAAACTGAAGAAAGATCGTCCTGGATCAATTGAAACAAAC
58 TAAACTGAAGAATGATCGCCCTAGATCAATTGAAACTAAC
* * * * * *
19660 TGAAGAAAGATCGCCCTGGATCAA-TTGAAGTAACTGAAAAATGAACGCCCTGGATCAATTGAAG
1 TGAAGAAAGACCGCCCTGGGTCAACTT--A-CAA--G--AAA-GATCGCCCTAGATCAATTAAAG
* *
19724 TAAATTGAAGAATGATCGCACTAGATCAATTGAA
58 TAAACTGAAGAATGATCGCCCTAGATCAATTGAA
19758 GTAAACTGAA
Statistics
Matches: 251, Mismatches: 31, Indels: 26
0.81 0.10 0.08
Matches are distributed among these distances:
96 106 0.42
98 1 0.00
99 4 0.02
100 1 0.00
101 1 0.00
102 4 0.02
103 3 0.01
104 48 0.19
105 83 0.33
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (97 bp):
TGAAGAAAGACCGCCCTGGGTCAACTTACAAGAAAGATCGCCCTAGATCAATTAAAGTAAACTGA
AGAATGATCGCCCTAGATCAATTGAAACTAAC
Found at i:19602 original size:70 final size:70
Alignment explanation
Indices: 19485--19842 Score: 442
Period size: 70 Copynumber: 5.1 Consensus size: 70
19475 TGGGCCAACT
* * * *
19485 TGAAGAAAGATCGCTCTGGATCAATT-AAAGTAAACTGAAGAATGATCGCCCTGGATCAATTGAA
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACT-AACTGAAGAAAGATCGCCCTAGATCAATTG-A
*
19549 ACT-AAC
64 AGTAAAC
* * * *
19555 TGAAGAAAGACCGCCCTGGGTCAATTGAAACTAACCGAAGAAAGATCGCCCTAGATCAATTAAAG
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAACTGAAGAAAGATCGCCCTAGATCAATTGAAG
19620 TAAAC
66 TAAAC
* * *
19625 TGAAGAAAGATCGTCCTGGATCAATTGAAACAAACTGAAGAAAGATCGCCCTGGATCAATTGAAG
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAACTGAAGAAAGATCGCCCTAGATCAATTGAAG
19690 T-AAC
66 TAAAC
* * * * *
19694 TGAA-AAATGAACGCCCTGGATCAATTG-AAGTAAATTGAAGAATGATCGCACTAGATCAATTGA
1 TGAAGAAA-GATCGCCCTGGATCAATTGAAACT-AACTGAAGAAAGATCGCCCTAGATCAATTGA
19757 AGTAAAC
64 AGTAAAC
* *
19764 TGAA-AAATGATCGTCCTGGATCAATTGAAACTAACTGAAGAAAG-TCGCCCTAAATCAATTGAA
1 TGAAGAAA-GATCGCCCTGGATCAATTGAAACTAACTGAAGAAAGATCGCCCTAGATCAATTGAA
19827 GTAAAC
65 GTAAAC
*
19833 TAAAGAAAGA
1 TGAAGAAAGA
19843 CCACCTTGGG
Statistics
Matches: 249, Mismatches: 32, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
68 5 0.02
69 85 0.34
70 152 0.61
71 7 0.03
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.21
Consensus pattern (70 bp):
TGAAGAAAGATCGCCCTGGATCAATTGAAACTAACTGAAGAAAGATCGCCCTAGATCAATTGAAG
TAAAC
Found at i:19764 original size:104 final size:104
Alignment explanation
Indices: 19485--19839 Score: 459
Period size: 104 Copynumber: 3.4 Consensus size: 104
19475 TGGGCCAACT
* *
19485 TGAAGAAAGATCGCTCTGGATCAATTAAAGTAAACTGAAGAATGATCGCCCTGGATCAATTGAAA
1 TGAAGAAAGATCGCCCTAGATCAATTAAAGTAAACTGAAGAATGATCG-CCTGGATCAATTGAAA
* *
19550 CT-AACTGAAGAAAGACCGCCCTGGGTCAATTGAAACTAAC
65 -TAAACTGAAGAAAGATCGCCCTGGATCAATTGAAACTAAC
* *
19590 CGAAGAAAGATCGCCCTAGATCAATTAAAGTAAACTGAAGAAAGATCGTCCTGGATCAATTGAAA
1 TGAAGAAAGATCGCCCTAGATCAATTAAAGTAAACTGAAGAATGATCG-CCTGGATCAATTGAAA
* *
19655 CAAACTGAAGAAAGATCGCCCTGGATCAATTG-AAGTAAC
65 TAAACTGAAGAAAGATCGCCCTGGATCAATTGAAACTAAC
* * * * *
19694 TGAA-AAATGAACGCCCTGGATCAATTGAAGTAAATTGAAGAATGATCGCACTAGATCAATTGAA
1 TGAAGAAA-GATCGCCCTAGATCAATTAAAGTAAACTGAAGAATGATCGC-CTGGATCAATTGAA
* *
19758 GTAAACTGAA-AAATGATCGTCCTGGATCAATTGAAACTAAC
64 ATAAACTGAAGAAA-GATCGCCCTGGATCAATTGAAACTAAC
* * *
19799 TGAAGAAAG-TCGCCCTAAATCAATTGAAGTAAACTAAAGAA
1 TGAAGAAAGATCGCCCTAGATCAATTAAAGTAAACTGAAGAA
19840 AGACCACCTT
Statistics
Matches: 219, Mismatches: 25, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
103 7 0.03
104 110 0.50
105 99 0.45
106 3 0.01
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.21
Consensus pattern (104 bp):
TGAAGAAAGATCGCCCTAGATCAATTAAAGTAAACTGAAGAATGATCGCCTGGATCAATTGAAAT
AAACTGAAGAAAGATCGCCCTGGATCAATTGAAACTAAC
Found at i:20520 original size:43 final size:43
Alignment explanation
Indices: 20192--20520 Score: 429
Period size: 43 Copynumber: 7.8 Consensus size: 43
20182 CCAATAACCA
* * *
20192 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
20235 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * * *
20277 -AAGTCCCCAAACACATATATAACACAGGGGCACCACTATTAG
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
20319 AAAGTCCTCAAAAACATATATAACACAGAGGCATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
20360 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
20403 AAAGTCCTCAAACACATATATAACACAGAGGCAT-T-TA-TATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
* *
20444 AAAGTCCCCAAACACATATATAACACCGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
20487 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
20521 TTCTCCTTAT
Statistics
Matches: 249, Mismatches: 29, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.01
41 104 0.42
42 5 0.02
43 136 0.55
44 2 0.01
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.20
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
Found at i:20522 original size:84 final size:84
Alignment explanation
Indices: 20192--20520 Score: 561
Period size: 84 Copynumber: 3.9 Consensus size: 84
20182 CCAATAACCA
*
20192 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTCCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
*
20257 ACACAGAGGCACCTATATTC
66 ACACAGAGGCATCTATA-TC
* * *
20277 -AAGTCCCCAAACACATATATAACACAGGGGCACCACTATTAGAAAGTCCTCAAAAACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
20341 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
*
20360 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
*
20425 ACACAGAGGCATTTATATC
66 ACACAGAGGCATCTATATC
* *
20444 AAAGTCCCCAAACACATATATAACACCGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
20509 ACACAGAGGCAT
66 ACACAGAGGCAT
20521 TTCTCCTTAT
Statistics
Matches: 231, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
83 2 0.01
84 229 0.99
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.20
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:27904 original size:23 final size:23
Alignment explanation
Indices: 27873--27949 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 23
27863 AAAGACTTAA
*
27873 AAAGTAAATGGGCCAAAATGATT
1 AAAGGAAATGGGCCAAAATGATT
27896 AAAGGAAAT--G---AAA-GACTT
1 AAAGGAAATGGGCCAAAATGA-TT
*
27914 AAAAAGCAAATGGGCCAAAATGATT
1 --AAAGGAAATGGGCCAAAATGATT
27939 AAAGGAAATGG
1 AAAGGAAATGG
27950 AAAATGAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
17 2 0.05
18 5 0.12
20 8 0.19
21 1 0.02
22 1 0.02
23 18 0.43
25 5 0.12
26 2 0.05
ACGTcount: A:0.52, C:0.08, G:0.23, T:0.17
Consensus pattern (23 bp):
AAAGGAAATGGGCCAAAATGATT
Found at i:27925 original size:43 final size:43
Alignment explanation
Indices: 27863--27948 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
27853 ATGATCAAAC
*
27863 AAAGACTTAAAAAGTAAATGGGCCAAAATGATTAAAGGAAATG
1 AAAGACTTAAAAAGCAAATGGGCCAAAATGATTAAAGGAAATG
27906 AAAGACTTAAAAAGCAAATGGGCCAAAATGATTAAAGGAAATG
1 AAAGACTTAAAAAGCAAATGGGCCAAAATGATTAAAGGAAATG
27949 GAAAATGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.53, C:0.08, G:0.21, T:0.17
Consensus pattern (43 bp):
AAAGACTTAAAAAGCAAATGGGCCAAAATGATTAAAGGAAATG
Found at i:27955 original size:20 final size:20
Alignment explanation
Indices: 27887--27956 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 20
27877 TAAATGGGCC
27887 AAAATGATTAAAGGAAAT-G
1 AAAATGATTAAAGGAAATGG
*
27906 -AAA-GACTTAAAAAGCAAATGGG
1 AAAATGA-TT--AAAGGAAAT-GG
27928 CCAAAATGATTAAAGGAAATGG
1 --AAAATGATTAAAGGAAATGG
27950 AAAATGA
1 AAAATGA
27957 AAGGAGAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 17
0.68 0.03 0.29
Matches are distributed among these distances:
17 2 0.05
18 5 0.12
20 15 0.38
22 3 0.08
23 8 0.20
25 5 0.12
26 2 0.05
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAATGATTAAAGGAAATGG
Found at i:28337 original size:27 final size:26
Alignment explanation
Indices: 28267--28335 Score: 138
Period size: 26 Copynumber: 2.7 Consensus size: 26
28257 CTGAGTATGC
28267 AAATGACCAAAATGCCCTTAGTGTAA
1 AAATGACCAAAATGCCCTTAGTGTAA
28293 AAATGACCAAAATGCCCTTAGTGTAA
1 AAATGACCAAAATGCCCTTAGTGTAA
28319 AAATGACCAAAATGCCC
1 AAATGACCAAAATGCCC
28336 CTGGGAGACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.20
Consensus pattern (26 bp):
AAATGACCAAAATGCCCTTAGTGTAA
Found at i:29704 original size:15 final size:16
Alignment explanation
Indices: 29679--29717 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
29669 GAGGTTGAAA
29679 AAAAGCAATTAAAC-AG
1 AAAA-CAATTAAACTAG
*
29695 AAAACAATTATACTAG
1 AAAACAATTAAACTAG
29711 AAAACAA
1 AAAACAA
29718 AGCAAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.64, C:0.13, G:0.08, T:0.15
Consensus pattern (16 bp):
AAAACAATTAAACTAG
Done.