Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015049.1 Corchorus capsularis cultivar CVL-1 contig15070, 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: 17852
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1327 original size:51 final size:51
Alignment explanation
Indices: 1248--1348 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
1238 CCCGGCCCAA
*
1248 CCTGCGAGGTATTGTCCGCTTTGGCCCAAAGGCCTCATGGATTTGTCCTTT
1 CCTGCGAGGTATTGTCCGCTTTGACCCAAAGGCCTCATGGATTTGTCCTTT
1299 CCTGCGAGGTATTGTCCGCTTTGACCCAAAGGCCTCATGGATTTGTCCTT
1 CCTGCGAGGTATTGTCCGCTTTGACCCAAAGGCCTCATGGATTTGTCCTT
1349 CCCAAAAGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (51 bp):
CCTGCGAGGTATTGTCCGCTTTGACCCAAAGGCCTCATGGATTTGTCCTTT
Found at i:1577 original size:168 final size:168
Alignment explanation
Indices: 1299--1613 Score: 576
Period size: 168 Copynumber: 1.9 Consensus size: 168
1289 TTTGTCCTTT
* *
1299 CCTGCGAGGTATTGTCCGCTTTGACCCAAAGGCCTCATGGATTTGTCCTTCCCAAAAGGTGCCTC
1 CCTGCGAGGTATTGTCCGCTTTGACCCAAAGGCCTCACGGATTTGTCCTTCCCAAAAGGCGCCTC
*
1364 ACAAGTTTGGGTTGGATCTCTATTATATAAACCACAATAGATCACCACATCCTCCTGATGTGGGA
66 ACAAGTTTGGGTTGGATCTCTATTATATAAACCACAATAGATCACCACATCCACCTGATGTGGGA
*
1429 TCTTGGGGTGTCACAATAACTATAGAGATCCGGTCCAA
131 TCTTGGGGCGTCACAATAACTATAGAGATCCGGTCCAA
*
1467 CCTGCGAGGTATTGTCCGCTTTGGCCCAAAGGCCTCACGGATTTGTCCTTCCCAAAAGGCGCCTC
1 CCTGCGAGGTATTGTCCGCTTTGACCCAAAGGCCTCACGGATTTGTCCTTCCCAAAAGGCGCCTC
*
1532 ACAAGTTTGGGTTGGATTTCTATTATATAAACCACAATAGATCACCACATCCACCTGATGTGGGA
66 ACAAGTTTGGGTTGGATCTCTATTATATAAACCACAATAGATCACCACATCCACCTGATGTGGGA
1597 TCTTGGGGCGTCACAAT
131 TCTTGGGGCGTCACAAT
1614 CTACCCCGAC
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
168 141 1.00
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (168 bp):
CCTGCGAGGTATTGTCCGCTTTGACCCAAAGGCCTCACGGATTTGTCCTTCCCAAAAGGCGCCTC
ACAAGTTTGGGTTGGATCTCTATTATATAAACCACAATAGATCACCACATCCACCTGATGTGGGA
TCTTGGGGCGTCACAATAACTATAGAGATCCGGTCCAA
Found at i:3304 original size:2 final size:2
Alignment explanation
Indices: 3297--3332 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3287 ATTAGAATGG
3297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3333 CACACAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5800 original size:7 final size:7
Alignment explanation
Indices: 5784--5813 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
5774 GTATATTAAT
5784 CAAGAAG
1 CAAGAAG
*
5791 CAAGAGG
1 CAAGAAG
5798 CAAGAAG
1 CAAGAAG
5805 CAAGAAG
1 CAAGAAG
5812 CA
1 CA
5814 GTATGGAGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.53, C:0.17, G:0.30, T:0.00
Consensus pattern (7 bp):
CAAGAAG
Found at i:5940 original size:30 final size:30
Alignment explanation
Indices: 5900--5959 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
5890 GAGGTAACCC
*
5900 ATATTCAATATGCTGATGATACATTGATTT
1 ATATTAAATATGCTGATGATACATTGATTT
5930 ATATTAAATATGCTGATGATACATTGATTT
1 ATATTAAATATGCTGATGATACATTGATTT
5960 TTTGTGATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.43
Consensus pattern (30 bp):
ATATTAAATATGCTGATGATACATTGATTT
Found at i:6406 original size:121 final size:121
Alignment explanation
Indices: 6192--6421 Score: 399
Period size: 121 Copynumber: 1.9 Consensus size: 121
6182 TTAATATGGT
*
6192 GACCGGTGATTGATAATTTTAGAACTAAATTGGAGAATTGGAAAGGTTCTTATCTCTCACTTGGT
1 GACCGGTGATTGATAATTTTAGAACTAAATTGAAGAATTGGAAAGGTTCTTATCTCTCACTTGGT
*
6257 GGGGAATCACTCTTTTATAAATATGTGCTTGCCAAATATTTTTTTTGTCCTTGTGA
66 GGGGAATCACTCTTATATAAATATGTGCTTGCCAAATATTTTTTTTGTCCTTGTGA
* *
6313 GACCGGTGATTGATAATTTTAGAACTAAATTGAAGAATTGGAAAGGTTCTTATCTTTCGCTTGGT
1 GACCGGTGATTGATAATTTTAGAACTAAATTGAAGAATTGGAAAGGTTCTTATCTCTCACTTGGT
*
6378 GGGAGAATCACTCTTATA-AAATCTGTGCTTGCCAAATATTTTTT
66 GGG-GAATCACTCTTATATAAATATGTGCTTGCCAAATATTTTTT
6422 GTCCCTGTTC
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
121 90 0.87
122 13 0.13
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (121 bp):
GACCGGTGATTGATAATTTTAGAACTAAATTGAAGAATTGGAAAGGTTCTTATCTCTCACTTGGT
GGGGAATCACTCTTATATAAATATGTGCTTGCCAAATATTTTTTTTGTCCTTGTGA
Found at i:8179 original size:2 final size:2
Alignment explanation
Indices: 8174--8199 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8164 TACCATTACA
8174 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
8200 GAAAAAGGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10121 original size:2 final size:2
Alignment explanation
Indices: 10114--10143 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10104 AAATAATATA
10114 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
10144 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:10512 original size:27 final size:27
Alignment explanation
Indices: 10473--10546 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
10463 GCCCTTCTCC
*
10473 AGTGATCTTGAGATCATTCAAT-GCTCT
1 AGTGATCTAGAGATCATTCAATAG-TCT
*
10500 AGTGATATAGAGATCATTCAATAGTCT
1 AGTGATCTAGAGATCATTCAATAGTCT
* *
10527 AGGGATCCAGAGATCATTCA
1 AGTGATCTAGAGATCATTCA
10547 CTTGCCTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
27 40 0.98
28 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (27 bp):
AGTGATCTAGAGATCATTCAATAGTCT
Found at i:10917 original size:27 final size:27
Alignment explanation
Indices: 10872--10936 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
10862 CATATCTTTT
* * *
10872 GAGATCATTTAATGCTCTAGTGATATA
1 GAGATCATTCAATGCTCTAGGGATACA
* *
10899 GAGATCATTCAATAG-TCTAGGGATCCG
1 GAGATCATTCAAT-GCTCTAGGGATACA
10926 GAGATCATTCA
1 GAGATCATTCA
10937 CTTGCCTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (27 bp):
GAGATCATTCAATGCTCTAGGGATACA
Found at i:11064 original size:195 final size:195
Alignment explanation
Indices: 10480--11065 Score: 1082
Period size: 195 Copynumber: 3.0 Consensus size: 195
10470 TCCAGTGATC
*
10480 TTGAGATCATTCAATGCTCTAGTGATATAGAGATCATTCAATAGTCTAGGGATCCAGAGATCATT
1 TTGAGATCATTCAATGCTCTAGTGATATAGAGATCATTCAATAGTCTAGGGATCCGGAGATCATT
*
10545 CACTTGCCTATTATTCTGCTGACGTGATATTGCTCTAATTGCTTATTGTTTGGCTCTAACAGGGA
66 CACTTGCCTATTATTCTGCTGACGTGATATTGCTCTAATTGCTCATTGTTTGGCTCTAACAGGGA
*
10610 CTCAAAGCTCCTCCTCCTTCAAACAGAGAGCTTCTAGTAGTTTAGGGCGCCTTACAACATATCTC
131 CTCAAAGCTCCTCCTCCTTCAAACAGAGAGCTTCTAGTAGTTTAGGGCGCCTTACAACATATCTT
* *
10675 TTGAGATCATTCAATGCTTTAGTGATATAGAGATCATTCAATAGTCTAGGGACCCGGAGATCATT
1 TTGAGATCATTCAATGCTCTAGTGATATAGAGATCATTCAATAGTCTAGGGATCCGGAGATCATT
*
10740 CACTTGCCTATTATACTGCTGACGTGATATTGCTCTAATTGCTCATTGTTTGGCTCTAACAGGGA
66 CACTTGCCTATTATTCTGCTGACGTGATATTGCTCTAATTGCTCATTGTTTGGCTCTAACAGGGA
10805 CTCAAAGCTCCTCCTCCTTCAAACAGAGAGCTTCTAGTAGTTTAGGGCGCCTTACAACATATCTT
131 CTCAAAGCTCCTCCTCCTTCAAACAGAGAGCTTCTAGTAGTTTAGGGCGCCTTACAACATATCTT
*
10870 TTGAGATCATTTAATGCTCTAGTGATATAGAGATCATTCAATAGTCTAGGGATCCGGAGATCATT
1 TTGAGATCATTCAATGCTCTAGTGATATAGAGATCATTCAATAGTCTAGGGATCCGGAGATCATT
* *
10935 CACTTGCCTATTATTCTACTGACGTCATATTGCTCTAATTGCTCATTGTTTGGCTCTAACAGGGA
66 CACTTGCCTATTATTCTGCTGACGTGATATTGCTCTAATTGCTCATTGTTTGGCTCTAACAGGGA
*
11000 CTAAAAGCTCCTCCTCCTTCAAACAGAGAGCTTCTAGTAGTTTAGGGCGCCTTACAACATATCTT
131 CTCAAAGCTCCTCCTCCTTCAAACAGAGAGCTTCTAGTAGTTTAGGGCGCCTTACAACATATCTT
11065 T
1 T
11066 CAGCATCGAG
Statistics
Matches: 378, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
195 378 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.33
Consensus pattern (195 bp):
TTGAGATCATTCAATGCTCTAGTGATATAGAGATCATTCAATAGTCTAGGGATCCGGAGATCATT
CACTTGCCTATTATTCTGCTGACGTGATATTGCTCTAATTGCTCATTGTTTGGCTCTAACAGGGA
CTCAAAGCTCCTCCTCCTTCAAACAGAGAGCTTCTAGTAGTTTAGGGCGCCTTACAACATATCTT
Found at i:11296 original size:30 final size:30
Alignment explanation
Indices: 11260--11319 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
11250 GAGGTAACCC
11260 ATATTCAATATGCTGATGATACATTGATTT
1 ATATTCAATATGCTGATGATACATTGATTT
11290 ATATTCAATATGCTGATGATACATTGATTT
1 ATATTCAATATGCTGATGATACATTGATTT
11320 TTCGTGATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (30 bp):
ATATTCAATATGCTGATGATACATTGATTT
Found at i:11768 original size:119 final size:118
Alignment explanation
Indices: 11555--11791 Score: 429
Period size: 119 Copynumber: 2.0 Consensus size: 118
11545 TTTCAATATG
11555 GAGACCGGTGATTGATAATTTTAAAACTAAATTGGAGAATTGGAAAGGTTCTTATCTCTCACTTG
1 GAGACCGGTGATTGATAATTTTAAAACTAAATTGGAGAATTGGAAAGGTTCTTATCTCTCACTTG
*
11620 GTAGGAGAATCACTCTTATAAAATCTGTGCTTGCCAAATATTTTTTGTCCTTGT
66 GTAGGAGAATCACTCTTATAAAATATGTGCTTG-CAAATATTTTTTGTCCTTGT
* *
11674 GAGACCGGTGATTGATAATTTTAGAACTAAATTGGAGGATTGGAAAGGTTCTTATCTCTCACTTG
1 GAGACCGGTGATTGATAATTTTAAAACTAAATTGGAGAATTGGAAAGGTTCTTATCTCTCACTTG
*
11739 GTGGGAGAATCACTCTTATAAAATATGTGCTTGCAAATATTTTTTGTCCTTGT
66 GTAGGAGAATCACTCTTATAAAATATGTGCTTGCAAATATTTTTTGTCCTTGT
11792 TCCCTTGCCT
Statistics
Matches: 114, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
118 20 0.18
119 94 0.82
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.37
Consensus pattern (118 bp):
GAGACCGGTGATTGATAATTTTAAAACTAAATTGGAGAATTGGAAAGGTTCTTATCTCTCACTTG
GTAGGAGAATCACTCTTATAAAATATGTGCTTGCAAATATTTTTTGTCCTTGT
Found at i:12675 original size:2 final size:2
Alignment explanation
Indices: 12668--12693 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12658 AGAAAACAGG
12668 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
12694 TAGTATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12919 original size:13 final size:13
Alignment explanation
Indices: 12901--12925 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12891 GTTATCAAAT
12901 TTACAGTAATTAA
1 TTACAGTAATTAA
12914 TTACAGTAATTA
1 TTACAGTAATTA
12926 TCAAATTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
TTACAGTAATTAA
Found at i:14171 original size:22 final size:21
Alignment explanation
Indices: 14140--14263 Score: 108
Period size: 22 Copynumber: 5.7 Consensus size: 21
14130 GATAATGATG
* *
14140 TGAAAATTTGATAACATCATTA
1 TGAAATTTTGATAAC-TCACTA
*
14162 TGAAATTTTGATAACTACACTG
1 TGAAATTTTGATAACT-CACTA
*
14184 TGAAATTTTGATAATCTCCCTA
1 TGAAATTTTGATAA-CTCACTA
*
14206 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAA-CTCACTA
* * *
14228 T-AAA-ATTGGTAACCACACTA
1 TGAAATTTTGATAA-CTCACTA
14248 TGAAAATTTTGATAAC
1 TG-AAATTTTGATAAC
14264 CACACCATTA
Statistics
Matches: 85, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
20 14 0.16
21 4 0.05
22 59 0.69
23 8 0.09
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.35
Consensus pattern (21 bp):
TGAAATTTTGATAACTCACTA
Found at i:14188 original size:44 final size:45
Alignment explanation
Indices: 14138--14268 Score: 139
Period size: 44 Copynumber: 3.0 Consensus size: 45
14128 TTGATAATGA
*
14138 TGTGAAAATTTGATAA-CATCATTATGAAATTTTGATAACTACAC
1 TGTGAAAATTTGATAACCATCACTATGAAATTTTGATAACTACAC
* * *
14182 TGTGAAATTTTGATAATC-TCCCTATGAAATTTTGATAA-TCACAC
1 TGTGAAAATTTGATAACCATCACTATGAAATTTTGATAACT-ACAC
* * *
14226 TAT-AAAA-TTGGTAACCA-CACTATGAAAATTTTGATAACCACAC
1 TGTGAAAATTTGATAACCATCACTATG-AAATTTTGATAACTACAC
14269 CATTAAGTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
42 13 0.18
43 20 0.27
44 39 0.53
45 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (45 bp):
TGTGAAAATTTGATAACCATCACTATGAAATTTTGATAACTACAC
Found at i:14216 original size:66 final size:65
Alignment explanation
Indices: 14140--14262 Score: 151
Period size: 66 Copynumber: 1.9 Consensus size: 65
14130 GATAATGATG
* * * *
14140 TGAAAATTTGATAA-CATCATTATGAAATTTTGATAACTACACTGTG-AAATTTTGATAATCTCC
1 TGAAAATTTGATAATCA-CACTAT-AAA-ATTGATAACCACACTATGAAAATTTTGATAATCTCC
14203 CTA
63 CTA
* *
14206 TGAAATTTTGATAATCACACTATAAAATTGGTAACCACACTATGAAAATTTTGATAA
1 TGAAAATTTGATAATCACACTATAAAATTGATAACCACACTATGAAAATTTTGATAA
14263 CCACACCATT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
64 14 0.29
65 15 0.31
66 18 0.37
67 2 0.04
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.36
Consensus pattern (65 bp):
TGAAAATTTGATAATCACACTATAAAATTGATAACCACACTATGAAAATTTTGATAATCTCCCTA
Found at i:14420 original size:26 final size:26
Alignment explanation
Indices: 14373--14422 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
14363 ATTTTGTTAA
*
14373 CCTCCCTAGGAAACTTTCATAACCTC
1 CCTCCCTAGAAAACTTTCATAACCTC
* * *
14399 CCTCCCTATAAAATTTTGATAACC
1 CCTCCCTAGAAAACTTTCATAACC
14423 ACACTGTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.30, C:0.34, G:0.06, T:0.30
Consensus pattern (26 bp):
CCTCCCTAGAAAACTTTCATAACCTC
Found at i:14569 original size:22 final size:20
Alignment explanation
Indices: 14494--14552 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 20
14484 ATGACTATTT
*
14494 TATGAAATTTTGGTAACGT-C
1 TATGAAATTTTGATAAC-TAC
*
14514 TGTATGGAATTTTGATAACTAC
1 --TATGAAATTTTGATAACTAC
*
14536 TATGAAAATTTGATAAC
1 TATGAAATTTTGATAAC
14553 CTTCCTATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 15 0.47
21 1 0.03
22 16 0.50
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (20 bp):
TATGAAATTTTGATAACTAC
Found at i:16016 original size:118 final size:118
Alignment explanation
Indices: 15808--16023 Score: 387
Period size: 118 Copynumber: 1.8 Consensus size: 118
15798 GTTAACGCGT
* *
15808 TTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGAAAATTTAAGGACTTG
1 TTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAATTGAAGGACTTG
* * *
15873 AAATTCCTCAAAACAATATTTATGGTTGTGGTGAAGCGCTTGGGATCTAAGAA
66 AAATTACTCAAAACAATATTAATGGTTGGGGTGAAGCGCTTGGGATCTAAGAA
15926 TTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAATTGAAGGACTTG
1 TTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAATTGAAGGACTTG
15991 AAATTACTCAAAACAATATTAATGGTTGGGGTG
66 AAATTACTCAAAACAATATTAATGGTTGGGGTG
16024 GATGTTCTTC
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 93 1.00
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.36
Consensus pattern (118 bp):
TTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAATTGAAGGACTTG
AAATTACTCAAAACAATATTAATGGTTGGGGTGAAGCGCTTGGGATCTAAGAA
Found at i:16541 original size:31 final size:32
Alignment explanation
Indices: 16503--16575 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
16493 ACCCAATACC
* *
16503 ATACTCACTTGGTAA-ATACTGACATGGTGAA
1 ATACTCACTTGGTAAGATACTCACATAGTGAA
* * *
16534 ATACTCACCTGGTAAGATACTCACCTAGTGAG
1 ATACTCACTTGGTAAGATACTCACATAGTGAA
16566 ATACTCACTT
1 ATACTCACTT
16576 ACAAAAGCCC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
31 14 0.40
32 21 0.60
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (32 bp):
ATACTCACTTGGTAAGATACTCACATAGTGAA
Found at i:16546 original size:16 final size:15
Alignment explanation
Indices: 16503--16573 Score: 70
Period size: 16 Copynumber: 4.5 Consensus size: 15
16493 ACCCAATACC
*
16503 ATACTCACTTGGTAA
1 ATACTCACCTGGTAA
* *
16518 ATACTGACATGGTGAA
1 ATACTCACCTGGT-AA
16534 ATACTCACCTGGTAA
1 ATACTCACCTGGTAA
* *
16549 GATACTCACCTAGTGAG
1 -ATACTCACCTGGT-AA
16566 ATACTCAC
1 ATACTCAC
16574 TTACAAAAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
15 13 0.28
16 33 0.70
17 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (15 bp):
ATACTCACCTGGTAA
Found at i:17508 original size:2 final size:2
Alignment explanation
Indices: 17501--17537 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
17491 CCAATTTGGG
*
17501 TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17538 AGTTTAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.