Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009471.1 Corchorus capsularis cultivar CVL-1 contig09492, 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: 33775
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:383 original size:199 final size:199
Alignment explanation
Indices: 28--1006 Score: 1237
Period size: 199 Copynumber: 4.9 Consensus size: 199
18 ATACTATGCG
* * * * * * *
28 TAAGTGGAGTTTAGCAGACTGCATGTACAGGGCTTAAGGGTTAATATGTGTCTCCTTAAGGAATA
1 TAAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATA
*
93 TGTATTAATATTAAATA-TT--TTAATTATGAAAATAGG---TA-GTCAACTTCTTAACCCACTT
66 TGTATTAATATTAAATATTTAATTAATTATG-AAATGGGATATATGTCAACTTCTTAACCCACTT
* * *
151 ATGGAGTCCAAAATTTATACTGACAGTTTATTGTATAATAATCCTATAAGAAAAATTATACTATA
130 TTGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACTATA
216 CACCA
195 CACCA
*
221 TAAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTGAGGGTTGACATGTGTCCCCTTAGGGAATA
1 TAAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATA
* **
286 TGTATTAATATTAACTATTTAATTAATTATGAAATGGGATATGCGTCAACTTCTTAACCCACTTT
66 TGTATTAATATTAAATATTTAATTAATTATGAAATGGGATATATGTCAACTTCTTAACCCACTTT
* * *
351 TGGAGTCCAAAATTTACAGTGACAGTTTATTGTATAATAATCCTATGAGAAAAATT-TACTATA-
131 TGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACTATAC
*
414 ACCG
196 ACCA
* *
418 TAAGTGGAGTTTAGCAGACTGCACGTGTAGGGTTTAAGGGTTGACATGTGTCCCCTAAGGGAATA
1 TAAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATA
** * * * *
483 TGTATTAATATTGTATATTTAATTGATGATGAAATGAGATATATGTCAACTTCTTAACCC-GTTT
66 TGTATTAATATTAAATATTTAATTAATTATGAAATGGGATATATGTCAACTTCTTAACCCACTTT
* * * * * *
547 ATAGAGTCTAAAATTTACACTGACAGCGTGTTGTATGATAATCCTACAAGAAAAATTATA-TAAT
131 -TGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACT-AT
611 ACACCA
194 ACACCA
* * * * *
617 TAAGTCGAGTTTAGCAGACTGCAGGTGCGGGGTTTAAGGGTTGACATGTGTCCCATTGGGGAATA
1 TAAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATA
* * * *
682 TGTATTAATATAAAATATTTAATTAATTATGAAATGGGGTATATGTCAACTTCTTAACCCGCTTA
66 TGTATTAATATTAAATATTTAATTAATTATGAAATGGGATATATGTCAACTTCTTAACCCACTTT
* * * *
747 TGGAGTTCAAAATTTACATTGACAGTGGATTGTATAATAATCTTATAAGAAAAATTATACTATAC
131 TGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACTATAC
*
812 ACCG
196 ACCA
* * * * *
816 TCAA-TCGAATTTAGCAGACTGCACGTGCAGGGTTTAAAGGTTGACATGTGTCCCCTCAAGGAAT
1 T-AAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAAT
* * * * *
880 ATGTATTAATATTAAATATTTAATTGATTATGAAATGAGATATGTGTTATAACTTCTTAACCCGC
65 ATGTATTAATATTAAATATTTAATTAATTATGAAATGGGATATATG-T-CAACTTCTTAACCCAC
* * ** *
945 -TTAGGAAATGTAAAATTTACACTGAAAAGTGTATTGTATAATAATCCTATAAGAAAAATTAT
128 TTTTGG-AGTCCAAAATTTACACTG-ACAGTGTATTGTATAATAATCCTATAAGAAAAATTAT
1007 GTAATGTGAT
Statistics
Matches: 680, Mismatches: 88, Indels: 27
0.86 0.11 0.03
Matches are distributed among these distances:
193 73 0.11
194 2 0.00
195 6 0.01
196 12 0.02
197 165 0.24
198 13 0.02
199 337 0.50
200 9 0.01
201 29 0.04
202 34 0.05
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (199 bp):
TAAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATA
TGTATTAATATTAAATATTTAATTAATTATGAAATGGGATATATGTCAACTTCTTAACCCACTTT
TGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACTATAC
ACCA
Found at i:760 original size:396 final size:394
Alignment explanation
Indices: 1--1011 Score: 1353
Period size: 396 Copynumber: 2.6 Consensus size: 394
* * * * *
1 AATCCTATAGAAAAAGTATACTAT--GCGTAAGTGGAGTTTAGCAGACTGCATGTACAGGGCTTA
1 AATCCTATAGAAAAA-TTTACTATAACCGTAAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTA
* * *
64 AGGGTTAATATGTGTCTCCTTAAGGAATATGTATTAATATTAAATATTTTAATT-ATGA--AAAT
65 AGGGTTGACATGTGTC-CCCTAAGGAATATGTATTAATATTAAATA-TTTAATTGATGATGAAAT
* * * * *
126 -AG--GTA-GTCAACTTCTTAACCCACTTATGGAGTCCAAAATTTATACTGACAGTTTATTGTAT
128 GAGATATATGTCAACTTCTTAACCCGCTTATGGAGTCTAAAATTTACACTGACAGTGTATTGTAT
*
187 AATAATCCTATAAGAAAAATTATACT-ATACACCATAAGTGGAGTTTAGCAGACTGCACGTGCAG
193 AATAATCCTATAAGAAAAATTATA-TAATACACCATAAGTCGAGTTTAGCAGACTGCACGTGCAG
* * * *
251 GGTTTGAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAACTATTTAATTAATTAT
257 GGTTTAAGGGTTGACATGTGTCCCATTAGGGAATATGTATTAATATAAAATATTTAATTAATTAT
* * **
316 GAAATGGGATATGCGTCAACTTCTTAACCCACTTTTGGAGTCCAAAATTTACAGTGACAGTTTAT
322 GAAATGGGATATACGTCAACTTCTTAACCCACTTATGGAGTCCAAAATTTACAGTGACAGTGGAT
381 TGTATAAT
387 TGTATAAT
*
389 AATCCTATGAGAAAAATTTACTATAACCGTAAGTGGAGTTTAGCAGACTGCACGTGTAGGGTTTA
1 AATCCTAT-AGAAAAATTTACTATAACCGTAAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTA
**
454 AGGGTTGACATGTGTCCCCTAAGGGAATATGTATTAATATTGTATATTTAATTGATGATGAAATG
65 AGGGTTGACATGTGTCCCCTAA-GGAATATGTATTAATATTAAATATTTAATTGATGATGAAATG
* * * * *
519 AGATATATGTCAACTTCTTAACCCGTTTATAGAGTCTAAAATTTACACTGACAGCGTGTTGTATG
129 AGATATATGTCAACTTCTTAACCCGCTTATGGAGTCTAAAATTTACACTGACAGTGTATTGTATA
* * *
584 ATAATCCTACAAGAAAAATTATATAATACACCATAAGTCGAGTTTAGCAGACTGCAGGTGCGGGG
194 ATAATCCTATAAGAAAAATTATATAATACACCATAAGTCGAGTTTAGCAGACTGCACGTGCAGGG
*
649 TTTAAGGGTTGACATGTGTCCCATTGGGGAATATGTATTAATATAAAATATTTAATTAATTATGA
259 TTTAAGGGTTGACATGTGTCCCATTAGGGAATATGTATTAATATAAAATATTTAATTAATTATGA
* * * * *
714 AATGGGGTATATGTCAACTTCTTAACCCGCTTATGGAGTTCAAAATTTACATTGACAGTGGATTG
324 AATGGGATATACGTCAACTTCTTAACCCACTTATGGAGTCCAAAATTTACAGTGACAGTGGATTG
779 TATAAT
389 TATAAT
* * *
785 AATCTTATAAGAAAAATTATACTATACACCGTCAA-TCGAATTTAGCAGACTGCACGTGCAGGGT
1 AATCCTAT-AGAAAAATT-TACTATA-ACCGT-AAGTGGAGTTTAGCAGACTGCACGTGCAGGGT
* *
849 TTAAAGGTTGACATGTGTCCCCTCAAGGAATATGTATTAATATTAAATATTTAATTGATTATGAA
62 TTAAGGGTTGACATGTGTCCCCT-AAGGAATATGTATTAATATTAAATATTTAATTGATGATGAA
* * * * *
914 ATGAGATATGTGTTATAACTTCTTAACCCGCTTA-GGAAATGTAAAATTTACACTGAAAAGTGTA
126 ATGAGATATATG-T-CAACTTCTTAACCCGCTTATGG-AGTCTAAAATTTACACTG-ACAGTGTA
*
978 TTGTATAATAATCCTATAAGAAAAATTATGTAAT
187 TTGTATAATAATCCTATAAGAAAAATTATATAAT
1012 GTGATTTTGA
Statistics
Matches: 543, Mismatches: 60, Indels: 27
0.86 0.10 0.04
Matches are distributed among these distances:
388 15 0.03
389 19 0.03
390 73 0.13
392 4 0.01
393 2 0.00
395 3 0.01
396 245 0.45
397 7 0.01
398 100 0.18
399 6 0.01
400 33 0.06
401 36 0.07
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (394 bp):
AATCCTATAGAAAAATTTACTATAACCGTAAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTAA
GGGTTGACATGTGTCCCCTAAGGAATATGTATTAATATTAAATATTTAATTGATGATGAAATGAG
ATATATGTCAACTTCTTAACCCGCTTATGGAGTCTAAAATTTACACTGACAGTGTATTGTATAAT
AATCCTATAAGAAAAATTATATAATACACCATAAGTCGAGTTTAGCAGACTGCACGTGCAGGGTT
TAAGGGTTGACATGTGTCCCATTAGGGAATATGTATTAATATAAAATATTTAATTAATTATGAAA
TGGGATATACGTCAACTTCTTAACCCACTTATGGAGTCCAAAATTTACAGTGACAGTGGATTGTA
TAAT
Found at i:2638 original size:28 final size:28
Alignment explanation
Indices: 2570--2665 Score: 120
Period size: 28 Copynumber: 3.3 Consensus size: 28
2560 TTTCTCTGCT
* * *
2570 AAAATCTCAATTCGGTACCAAACCTTAGTAA
1 AAAATTTCAATTTGGTA-CAAAACTT--TAA
*
2601 AAAATTTCAATTTGGTACAAAACTTTTA
1 AAAATTTCAATTTGGTACAAAACTTTAA
2629 AAAATTTCAATTTGGTACAAAACTTTAA
1 AAAATTTCAATTTGGTACAAAACTTTAA
2657 AACAATTTC
1 AA-AATTTC
2666 CCATAACGCA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
28 31 0.53
29 6 0.10
30 7 0.12
31 15 0.25
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (28 bp):
AAAATTTCAATTTGGTACAAAACTTTAA
Found at i:2745 original size:38 final size:40
Alignment explanation
Indices: 2678--2759 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 40
2668 ATAACGCACA
*
2678 TTTTTTTCTACTAATTTTTCCAAATATATTTCT-TCCATT
1 TTTTTTTCTACTAATTATTCCAAATATATTTCTCTCCATT
* *
2717 TTTTTTTGCTGCTAATTATTCC-AA-ATATTTCTCTCTATT
1 TTTTTTT-CTACTAATTATTCCAAATATATTTCTCTCCATT
2756 TTTT
1 TTTT
2760 CATAGAATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 8 0.21
39 18 0.47
40 12 0.32
ACGTcount: A:0.21, C:0.17, G:0.02, T:0.60
Consensus pattern (40 bp):
TTTTTTTCTACTAATTATTCCAAATATATTTCTCTCCATT
Found at i:4387 original size:14 final size:14
Alignment explanation
Indices: 4368--4410 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
4358 CAAACCCCAA
4368 ACAAACAAACAAAC
1 ACAAACAAACAAAC
*
4382 ACAAACAAA-AAGC
1 ACAAACAAACAAAC
*
4395 ATCAAACAAACGAAC
1 A-CAAACAAACAAAC
4410 A
1 A
4411 AAAGCACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 4 0.17
14 17 0.71
15 3 0.12
ACGTcount: A:0.67, C:0.26, G:0.05, T:0.02
Consensus pattern (14 bp):
ACAAACAAACAAAC
Found at i:4388 original size:18 final size:19
Alignment explanation
Indices: 4355--4390 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4345 CTACATTTTT
*
4355 AAACAAACCCCAAACAAAC
1 AAACAAACCACAAACAAAC
4374 AAACAAA-CACAAACAAA
1 AAACAAACCACAAACAAA
4391 AAGCATCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (19 bp):
AAACAAACCACAAACAAAC
Found at i:6473 original size:1 final size:1
Alignment explanation
Indices: 6469--6497 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
6459 ATTTATCTTG
6469 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6498 CTCCCTGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12122 original size:105 final size:105
Alignment explanation
Indices: 12006--12218 Score: 417
Period size: 105 Copynumber: 2.0 Consensus size: 105
11996 TGCTCAGAAG
*
12006 GAAGCAACTGAATGGAAAGACAAGTATGATGTTGCTGTTAAAGAAGCTGAAGCTGCTATGCAGAA
1 GAAGCAACTGAATGGAAAGACAAGTATGATGGTGCTGTTAAAGAAGCTGAAGCTGCTATGCAGAA
12071 GGCAGCTATAGCTGAGGAGAGCTTAAATGCTCTTAGGATA
66 GGCAGCTATAGCTGAGGAGAGCTTAAATGCTCTTAGGATA
12111 GAAGCAACTGAATGGAAAGACAAGTATGATGGTGCTGTTAAAGAAGCTGAAGCTGCTATGCAGAA
1 GAAGCAACTGAATGGAAAGACAAGTATGATGGTGCTGTTAAAGAAGCTGAAGCTGCTATGCAGAA
12176 GGCAGCTATAGCTGAGGAGAGCTTAAATGCTCTTAGGATA
66 GGCAGCTATAGCTGAGGAGAGCTTAAATGCTCTTAGGATA
12216 GAA
1 GAA
12219 TTCTCCAGCA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 107 1.00
ACGTcount: A:0.36, C:0.13, G:0.29, T:0.22
Consensus pattern (105 bp):
GAAGCAACTGAATGGAAAGACAAGTATGATGGTGCTGTTAAAGAAGCTGAAGCTGCTATGCAGAA
GGCAGCTATAGCTGAGGAGAGCTTAAATGCTCTTAGGATA
Found at i:21215 original size:151 final size:151
Alignment explanation
Indices: 21004--21309 Score: 567
Period size: 151 Copynumber: 2.0 Consensus size: 151
20994 TTTCTACAGA
* * *
21004 TTTAGGCAATACACCATGTCTAACTAAGAAAATTACAACCTAACCTACCCCTTAATGGACAACTT
1 TTTAGGCAATAAACCATGCCTAACTAAGAAAATTACAACCCAACCTACCCCTTAATGGACAACTT
*
21069 AGATCAGCTTTAGAGCAGCTTAAAATCCGGCAAAAAATCCAAGAAATTAGGAAAAGCTGGATTCA
66 AGATCAGCTTTAGAGCAGCTTAAAATCCGGCAAAAAATCCAAAAAATTAGGAAAAGCTGGATTCA
21134 AGGGTCATTACATGTTGACAT
131 AGGGTCATTACATGTTGACAT
*
21155 TTTAGGCAATAAACCATGCCTAACTAAGAAAATTATAACCCAACCTACCCCTTAATGGACAACTT
1 TTTAGGCAATAAACCATGCCTAACTAAGAAAATTACAACCCAACCTACCCCTTAATGGACAACTT
21220 AGATCAGCTTTAGAGCAGCTTAAAATCCGGCAAAAAATCCAAAAAATTAGGAAAAGCTGGATTCA
66 AGATCAGCTTTAGAGCAGCTTAAAATCCGGCAAAAAATCCAAAAAATTAGGAAAAGCTGGATTCA
21285 AGGGTCATTACATGTTGACAT
131 AGGGTCATTACATGTTGACAT
21306 TTTA
1 TTTA
21310 AGCATTTTAT
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
151 150 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (151 bp):
TTTAGGCAATAAACCATGCCTAACTAAGAAAATTACAACCCAACCTACCCCTTAATGGACAACTT
AGATCAGCTTTAGAGCAGCTTAAAATCCGGCAAAAAATCCAAAAAATTAGGAAAAGCTGGATTCA
AGGGTCATTACATGTTGACAT
Found at i:21623 original size:21 final size:21
Alignment explanation
Indices: 21597--21673 Score: 97
Period size: 21 Copynumber: 3.7 Consensus size: 21
21587 AACCCTAAAG
21597 TTTGAT-GATCAAACTCCAAAA
1 TTTGATAG-TCAAACTCCAAAA
*
21618 TTTGATAGTCAAAC-CCTAAAG
1 TTTGATAGTCAAACTCC-AAAA
21639 TTTGAT-GATCAAACTCCAAAA
1 TTTGATAG-TCAAACTCCAAAA
21660 TTTGATAGTCAAAC
1 TTTGATAGTCAAAC
21674 CATGTTAAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
20 3 0.06
21 42 0.86
22 4 0.08
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (21 bp):
TTTGATAGTCAAACTCCAAAA
Found at i:21634 original size:42 final size:42
Alignment explanation
Indices: 21587--21674 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
21577 AATTGTTATT
21587 AACCCTAAAGTTTGATGATCAAACTCCAAAATTTGATAGTCA
1 AACCCTAAAGTTTGATGATCAAACTCCAAAATTTGATAGTCA
21629 AACCCTAAAGTTTGATGATCAAACTCCAAAATTTGATAGTCA
1 AACCCTAAAGTTTGATGATCAAACTCCAAAATTTGATAGTCA
21671 AACC
1 AACC
21675 ATGTTAAACC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (42 bp):
AACCCTAAAGTTTGATGATCAAACTCCAAAATTTGATAGTCA
Found at i:21758 original size:21 final size:21
Alignment explanation
Indices: 21735--21837 Score: 127
Period size: 21 Copynumber: 4.9 Consensus size: 21
21725 TGTTTTGCCC
21735 AAATTTTGATGGTCAAATCCC-
1 AAATTTTGATGGTCAAA-CCCT
*
21756 AAATTTTAATGGTCAAACCCT
1 AAATTTTGATGGTCAAACCCT
* *
21777 AAATTTTGATGATCGAACCCT
1 AAATTTTGATGGTCAAACCCT
* *
21798 AAAGTTTGATAGTCAAACCCT
1 AAATTTTGATGGTCAAACCCT
* *
21819 AAAGTTTGATGATCAAACC
1 AAATTTTGATGGTCAAACC
21838 ATGTTAAACC
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 3 0.04
21 68 0.96
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (21 bp):
AAATTTTGATGGTCAAACCCT
Found at i:21899 original size:163 final size:163
Alignment explanation
Indices: 21587--21949 Score: 502
Period size: 163 Copynumber: 2.2 Consensus size: 163
21577 AATTGTTATT
* * * * * *
21587 AACCCTAAAGTTTGATGATCAAACTCCAAAATTTGAT-AGTCAAACCCTAAAGTTTGATGATCAA
1 AACCCCAAAGTTTAATGGTCAAACCCCAAAGTTTGATGA-TCGAACCCTAAAGTTTGATGATCAA
21651 ACTCCAAAATTTGATAGTCAAACCATGTTAAACCTTATAAATTGAAGCACCCACCACATTTTTGC
65 ACTCCAAAATTTGATAGTCAAACCATGTTAAACCTTATAAATTGAAGCACCCACCACATTTTTGC
*
21716 CAAAAATTGTGTTTTGCCCAAATTTTGATGGTCA
130 CAAAAACTGTGTTTTGCCCAAATTTTGATGGTCA
* * * *
21750 AATCCCAAATTTTAATGGTCAAACCCTAAATTTTGATGATCGAACCCTAAAGTTTGAT-AGTCAA
1 AACCCCAAAGTTTAATGGTCAAACCCCAAAGTTTGATGATCGAACCCTAAAGTTTGATGA-TCAA
* * *
21814 AC-CCTAAAGTTTGAT-GATCAAACCATGTTAAACCTTATCAATTGAAGCA-CCACCACGTTTTT
65 ACTCC-AAAATTTGATAG-TCAAACCATGTTAAACCTTATAAATTGAAGCACCCACCACATTTTT
*
21876 GCCCAAAACTGTGTTTTTGCCCAAATTTTGATGGTCA
128 GCCAAAAACTGTG-TTTTGCCCAAATTTTGATGGTCA
*
21913 AACCCCAAAGTTTGATGGTCAAACCCCAAAGTTTGAT
1 AACCCCAAAGTTTAATGGTCAAACCCCAAAGTTTGAT
21950 AGCTAAATCA
Statistics
Matches: 176, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
162 27 0.15
163 148 0.84
164 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (163 bp):
AACCCCAAAGTTTAATGGTCAAACCCCAAAGTTTGATGATCGAACCCTAAAGTTTGATGATCAAA
CTCCAAAATTTGATAGTCAAACCATGTTAAACCTTATAAATTGAAGCACCCACCACATTTTTGCC
AAAAACTGTGTTTTGCCCAAATTTTGATGGTCA
Found at i:21921 original size:21 final size:21
Alignment explanation
Indices: 21895--21949 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
21885 TGTGTTTTTG
*
21895 CCCAAATTTTGATGGTCAAAC
1 CCCAAAGTTTGATGGTCAAAC
21916 CCCAAAGTTTGATGGTCAAAC
1 CCCAAAGTTTGATGGTCAAAC
21937 CCCAAAGTTTGAT
1 CCCAAAGTTTGAT
21950 AGCTAAATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (21 bp):
CCCAAAGTTTGATGGTCAAAC
Found at i:22023 original size:121 final size:121
Alignment explanation
Indices: 21777--22016 Score: 338
Period size: 121 Copynumber: 2.0 Consensus size: 121
21767 GTCAAACCCT
* * *
21777 AAATTTTGATGATCGAACCCTAAAGTTTGATAGTCAAACCCTAAAGTTTGATGATCAAACCATGT
1 AAATTTTGATGATCAAACCCCAAAGTTTGATAGTCAAACCCCAAAGTTTGATGATCAAACCATGT
* * **
21842 TAAACCTTATCAATTGAAGCACCACCACGTTTTTGCCCAAAACTGTGTTTTTGCCC
66 TAAACCTTATCAATTGAAGCACCAACACATTTTTGCCCAAAACTGTGTTTAAGCCC
* * * *
21898 AAATTTTGATGGTCAAACCCCAAAGTTTGATGGTCAAACCCCAAAGTTTGAT-AGCTAAATCATG
1 AAATTTTGATGATCAAACCCCAAAGTTTGATAGTCAAACCCCAAAGTTTGATGATC-AAACCATG
* *
21962 TTAAACCTTATCAATTGACGCACCCAACACATTTTTGCCTAAAACTGTGTTTAAG
65 TTAAACCTTATCAATTGAAGCA-CCAACACATTTTTGCCCAAAACTGTGTTTAAG
22017 GCAAATTATA
Statistics
Matches: 104, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
120 2 0.02
121 75 0.72
122 27 0.26
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (121 bp):
AAATTTTGATGATCAAACCCCAAAGTTTGATAGTCAAACCCCAAAGTTTGATGATCAAACCATGT
TAAACCTTATCAATTGAAGCACCAACACATTTTTGCCCAAAACTGTGTTTAAGCCC
Found at i:26596 original size:2 final size:2
Alignment explanation
Indices: 26584--26618 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
26574 TTGGCATGAT
*
26584 TA TA TA CA TA TA TA -A 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
26619 CTGAATGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:29880 original size:12 final size:12
Alignment explanation
Indices: 29863--29890 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
29853 CGCAACACCT
29863 GCCACATGACCG
1 GCCACATGACCG
29875 GCCACATGACCG
1 GCCACATGACCG
29887 GCCA
1 GCCA
29891 TCGCATGCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.43, G:0.25, T:0.07
Consensus pattern (12 bp):
GCCACATGACCG
Found at i:30913 original size:8 final size:8
Alignment explanation
Indices: 30900--30933 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
30890 CTTCTTGAAA
30900 AAAAATTC
1 AAAAATTC
30908 AAAAATTC
1 AAAAATTC
*
30916 AGAAACTTC
1 A-AAAATTC
30925 AAAAATTC
1 AAAAATTC
30933 A
1 A
30934 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:31024 original size:5 final size:5
Alignment explanation
Indices: 31007--31036 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
30997 GTTATATCGA
31007 AAAAT ATAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAA
31037 AAATTTTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Done.