Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011912.1 Corchorus capsularis cultivar CVL-1 contig11933, 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: 27422
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2098 original size:27 final size:27
Alignment explanation
Indices: 2040--2119 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 27
2030 AGGTGAACTT
* * * * *
2040 AAAAATGACTAAAATGCCCCCGAGTGT
1 AAAAATGACCAAAATGCCCCTGGGCGC
2067 AAAAATGACCAAAATGCCCCTGGGCGC
1 AAAAATGACCAAAATGCCCCTGGGCGC
* * *
2094 GAAAATGACCAAAATACCCTTGGGCG
1 AAAAATGACCAAAATGCCCCTGGGCG
2120 ACCCCAATGC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.15
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCTGGGCGC
Found at i:12866 original size:17 final size:18
Alignment explanation
Indices: 12834--12868 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
12824 CTTCAAAATC
*
12834 AATTTTCATTTTTCTTGA
1 AATTTTCATGTTTCTTGA
12852 AATTTT-ATGTTTCTTGA
1 AATTTTCATGTTTCTTGA
12869 CAGGTACGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.60
Consensus pattern (18 bp):
AATTTTCATGTTTCTTGA
Found at i:17504 original size:13 final size:13
Alignment explanation
Indices: 17486--17511 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17476 TCACTAACAA
17486 CAGGTTGAGACAG
1 CAGGTTGAGACAG
17499 CAGGTTGAGACAG
1 CAGGTTGAGACAG
17512 GAAAATTTCT
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:0.31, C:0.15, G:0.38, T:0.15
Consensus pattern (13 bp):
CAGGTTGAGACAG
Found at i:21399 original size:25 final size:26
Alignment explanation
Indices: 21379--21435 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
21369 AAAAAACGTT
21379 TAAACATCAT-CAAATCGAAAACCCA
1 TAAACATCATCCAAATCGAAAACCCA
*
21404 TAAACATCATCCAAATTGAAAACCCA
1 TAAACATCATCCAAATCGAAAACCCA
21430 TAAACA
1 TAAACA
21436 AATTAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.53, C:0.26, G:0.04, T:0.18
Consensus pattern (26 bp):
TAAACATCATCCAAATCGAAAACCCA
Found at i:22190 original size:21 final size:21
Alignment explanation
Indices: 22166--22207 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
22156 CCACACCCGC
22166 TTGTTAGATCAACTAGTAGTG
1 TTGTTAGATCAACTAGTAGTG
* *
22187 TTGTTCGATCAGCTAGTAGTG
1 TTGTTAGATCAACTAGTAGTG
22208 GCGGATATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (21 bp):
TTGTTAGATCAACTAGTAGTG
Found at i:23132 original size:31 final size:31
Alignment explanation
Indices: 23097--23162 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
23087 AATTTTATGT
*
23097 TTTCCGATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTACCCTT-TTCTTTAAAACATA
23128 TTTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTTCCAATTGTACCCTTTTCTTTAAAACATA
23159 TTTC
1 TTTC
23163 TAAATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTCTTTAAAACATA
Found at i:23333 original size:38 final size:35
Alignment explanation
Indices: 23269--23345 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 35
23259 AATTTGCCTT
23269 TTTGTTTCCAACGTCCTATTTAATTTTGCTTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTGC--TTTGTC
**
23306 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATTTTGCTTTGTC
23342 TTTG
1 TTTG
23346 ATCTTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 10 0.27
37 11 0.30
38 16 0.43
ACGTcount: A:0.13, C:0.16, G:0.13, T:0.58
Consensus pattern (35 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCTTTGTC
Found at i:23714 original size:22 final size:22
Alignment explanation
Indices: 23686--23768 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
23676 TGTCTCTATG
23686 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
23708 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
23731 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
23752 TGGTTACCAAAATTTCA
1 TGGTTATCAAAATTTCA
23769 CAGGATCAGG
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.02
22 44 0.92
23 3 0.06
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:23805 original size:22 final size:22
Alignment explanation
Indices: 23685--23825 Score: 70
Period size: 22 Copynumber: 6.3 Consensus size: 22
23675 TTGTCTCTAT
* * *
23685 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATTAAAATCTCATAGG
* * *
23707 ATGGTTATTATAATTTCAT-GAG
1 GTGGTTATTAAAATCTCATAG-G
* * *
23729 GAGGTTATCAAAAT-TCCATAGT
1 GTGGTTATTAAAATCT-CATAGG
** * *
23751 GTGGTTACCAAAATTTCACAGG
1 GTGGTTATTAAAATCTCATAGG
* *
23773 ATCAGGTTATTAAAATCTCTTAGG
1 GT--GGTTATTAAAATCTCATAGG
* * *
23797 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATCTCATAGG
23819 GTGGTTA
1 GTGGTTA
23826 ATTATCACAA
Statistics
Matches: 89, Mismatches: 24, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
21 1 0.01
22 70 0.79
23 2 0.02
24 16 0.18
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.38
Consensus pattern (22 bp):
GTGGTTATTAAAATCTCATAGG
Found at i:23886 original size:22 final size:22
Alignment explanation
Indices: 23861--23913 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
23851 ATCAAAGAGA
23861 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATGTCATAGCGAGG
* * *
23883 TTAT-AATAATTTCATAGTGTGG
1 TTATCAA-AATGTCATAGCGAGG
*
23905 TTAACAAAA
1 TTATCAAAA
23914 CTTCATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 21 0.84
23 2 0.08
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (22 bp):
TTATCAAAATGTCATAGCGAGG
Found at i:23984 original size:22 final size:22
Alignment explanation
Indices: 23925--24132 Score: 67
Period size: 22 Copynumber: 9.3 Consensus size: 22
23915 TTCATTAAAT
**
23925 ATTTCATGGGAAGGTTATCAAA
1 ATTTCATATGAAGGTTATCAAA
* * *
23947 ATTTTATAGTG-TGGTTATCGAA
1 ATTTCATA-TGAAGGTTATCAAA
23969 ATTTCATATGAAGGTTAT-AAA
1 ATTTCATATGAAGGTTATCAAA
* * * * *
23990 AGTCTCAATTTCATAGGGAGTACCAAA
1 A-TTTC-ATATGA-A-GG-TTATCAAA
*
24017 ATTTGATA-GAAGGTTATC-AA
1 ATTTCATATGAAGGTTATCAAA
* * *
24037 ATCTCATA-G-AGTGATTAACGAA
1 ATTTCATATGAAG-G-TTATCAAA
24059 ATTTCATA-GAGATCGGATTATCAAA
1 ATTTCATATGA-A--GG-TTATCAAA
*
24084 ATTT-ATA-GAAAGATTATCAAA
1 ATTTCATATG-AAGGTTATCAAA
**
24105 ATTTCATAGTG-TTGTTATCAAA
1 ATTTCATA-TGAAGGTTATCAAA
24127 ATTTCA
1 ATTTCA
24133 AAGCGAGATT
Statistics
Matches: 138, Mismatches: 29, Indels: 38
0.67 0.14 0.19
Matches are distributed among these distances:
19 2 0.01
20 10 0.07
21 24 0.17
22 61 0.44
23 6 0.04
24 9 0.07
25 17 0.12
26 5 0.04
27 4 0.03
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
ATTTCATATGAAGGTTATCAAA
Found at i:24144 original size:22 final size:22
Alignment explanation
Indices: 24013--24263 Score: 106
Period size: 22 Copynumber: 11.5 Consensus size: 22
24003 TAGGGAGTAC
* * *
24013 CAAAATTTGATAGA-AGGTTAT
1 CAAAATTTCAAAGAGAGATTAT
* * * *
24034 C-AAATCTCATAGAGTGATTAA
1 CAAAATTTCAAAGAGAGATTAT
* *
24055 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCAAAGAGA---GATTAT
* *
24080 CAAAATTT-ATAGAAAGATTAT
1 CAAAATTTCAAAGAGAGATTAT
* * *
24101 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCAAAGAG-AGATTAT
*
24123 CAAAATTTCAAAGCGAGATTAT
1 CAAAATTTCAAAGAGAGATTAT
* * * *
24145 TAAAATTACATAA-TGTGATTAT
1 CAAAATTTCA-AAGAGAGATTAT
* * * * * *
24167 CAGAATTTCATAGAGGGGTCAA
1 CAAAATTTCAAAGAGAGATTAT
*
24189 CAAAATTTTATAA-AGAGATTAT
1 CAAAATTTCA-AAGAGAGATTAT
*
24211 CAAAATTTCATAA-AGAGGTTAT
1 CAAAATTTCA-AAGAGAGATTAT
* *
24233 CAAATTTTCAAA-ATGTGATTA-
1 CAAAATTTCAAAGA-GAGATTAT
24254 CAAAATTTCA
1 CAAAATTTCA
24264 TAGTGGTATT
Statistics
Matches: 176, Mismatches: 42, Indels: 24
0.73 0.17 0.10
Matches are distributed among these distances:
20 10 0.06
21 34 0.19
22 110 0.62
23 4 0.02
24 6 0.03
25 12 0.07
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
CAAAATTTCAAAGAGAGATTAT
Found at i:24150 original size:44 final size:44
Alignment explanation
Indices: 24074--24263 Score: 136
Period size: 44 Copynumber: 4.4 Consensus size: 44
24064 ATAGAGATCG
* * *
24074 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAAAGATTATCAAAATTACATAATG-T
** *
24118 G-TTATCAAAATTTCAAAGCGAGATTATTAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAAAGATTATCAAAATTACATAATGT
* * ** * * * ** * *
24161 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCAAAGAAAGATTATCAAAATTACATAATGT
* * * * *
24205 GATTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAAAGATTATCAAAATTACATAATGT
24249 GATTA-CAAAATTTCA
1 GATTATCAAAATTTCA
24264 TAGTGGTATT
Statistics
Matches: 115, Mismatches: 28, Indels: 7
0.77 0.19 0.05
Matches are distributed among these distances:
43 24 0.21
44 90 0.78
45 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.35
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAAAGATTATCAAAATTACATAATGT
Found at i:24193 original size:66 final size:66
Alignment explanation
Indices: 24095--24242 Score: 154
Period size: 66 Copynumber: 2.2 Consensus size: 66
24085 TTTATAGAAA
* ** * * * *
24095 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGATTATTAAAATTACATAAT
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGATTATCAAAATTACATAAT
24159 GT
65 GT
* * * *
24161 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGATTATCAAAATTTCATAAAG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGATTATCAAAATTACATAATG
*
24226 A
66 T
* *
24227 GGTTATCAAATTTTCA
1 GATTATCAAAATTTCA
24243 AAATGTGATT
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
66 64 0.97
67 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGATTATCAAAATTACATAATG
T
Found at i:24388 original size:19 final size:19
Alignment explanation
Indices: 24353--24400 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
24343 TTATGAAGTA
24353 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
*
24373 ATCAAAATTCAGGGAGGAT
1 ATCAAAATTCAAGGAGGAT
24392 ATCAAAATT
1 ATCAAAATT
24401 TCATATGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:24419 original size:22 final size:22
Alignment explanation
Indices: 24391--24951 Score: 221
Period size: 22 Copynumber: 25.7 Consensus size: 22
24381 TCAGGGAGGA
24391 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
24413 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
24435 TTTCAAAATTTCACAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* * *
24457 TATTAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
24478 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
24501 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** *
24523 TATCAAAAAATCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
*
24545 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
24561 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
24583 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
24606 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
24629 TATCAAAATTTCAT-TGCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
24651 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
24673 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
24695 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
24717 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
24739 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * *
24761 TATCAACATCTCATA-GTATTGGT
1 TATCAAAATTTCATATG-A-AGGT
24784 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
* *
24806 TATTAAAATTTCATATTG-CGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
24828 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* * *
24850 TACCCAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** * **
24872 TAAAAAAAATT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
24893 TCTCGAAATTTCATAAT-ATTGT
1 TATCAAAATTTCAT-ATGAAGGT
*
24915 TATTAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
24937 TATCAAAATTTCATA
1 TATCAAAATTTCATA
24952 ATGGGATCAT
Statistics
Matches: 399, Mismatches: 102, Indels: 76
0.69 0.18 0.13
Matches are distributed among these distances:
16 9 0.02
17 2 0.01
18 2 0.01
20 2 0.01
21 33 0.08
22 282 0.71
23 64 0.16
24 4 0.01
25 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:24820 original size:45 final size:45
Alignment explanation
Indices: 24735--24820 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
24725 TTTCATAACG
* * *
24735 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTAT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTAT
* * *
24780 TGGTTATCAAAATTTCAT-TGGGAAGTTATTAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
24821 TTGCGGTCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 1 0.03
45 33 0.97
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTAT
Found at i:24952 original size:44 final size:43
Alignment explanation
Indices: 24391--24953 Score: 247
Period size: 44 Copynumber: 12.9 Consensus size: 43
24381 TCAGGGAGGA
*
24391 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATA--ATAGGT
* * * * * * *
24435 TTTCAAAATTTCACAAGAGGGTTATTAAAATTTCATAGTATGT
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAATAGGT
* * * * *
24478 AGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGT
1 -TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAAT-AGGT
** * *
24523 TATCAAAAAATCATAGGAAGGTTATCAAAA-TT--T-GTA-GT
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAATAGGT
* * * * **
24561 TATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATA-ATAGG-T
* * * ***
24606 TATCAAAATTTTATAGGAAGATTTATCAAAATTTCATTGCGAGGT
1 TATCAAAATTTCATATGAAG-GTTATCAAAATTTCA-TAATAGGT
* * * * *
24651 TATCACAATTTCATAGTG-TGATTATCAAAATTTCAGAGT-GTGAT
1 TATCAAAATTTCATA-TGAAGGTTATCAAAATTTCATAATAG-G-T
* * * *
24695 TA-CTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAACGT-GGT
1 TATC-AA-AATTTCATATGAAGGTTATCAAAATTTCATAA--TAGGT
* * * * * *
24739 TATCAATATATCATATGGAGGTTATCAACATCTCATAGTATTGGT
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATA--ATAGGT
* * *
24784 TATCAAAATTTCAT-TGGGAA-GTTATTAAAATTTCATATTGCGGT
1 TATCAAAATTTCATAT--GAAGGTTATCAAAATTTCATAAT-AGGT
* * * * * * *
24828 CT-TCAAAATTCCTTAGGGAGGTTACCCAAATTTCATAAGAAGGT
1 -TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAA-TAGGT
** * ** * * *
24872 TAAAAAAAATT-ATAAAAAGGTTCTCGAAATTTCATAATATTGT
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAATA-GGT
*
24915 TATTAAAATTTCATATGAAGGTTATCAAAATTTCATAAT
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAAT
24954 GGGATCATAA
Statistics
Matches: 384, Mismatches: 100, Indels: 70
0.69 0.18 0.13
Matches are distributed among these distances:
38 27 0.07
39 3 0.01
40 1 0.00
41 2 0.01
42 4 0.01
43 44 0.11
44 210 0.55
45 69 0.18
46 23 0.06
47 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (43 bp):
TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAATAGGT
Found at i:24994 original size:22 final size:22
Alignment explanation
Indices: 24966--25009 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
24956 GATCATAAAA
*
24966 AATAGTGTAATTATCATAATTT
1 AATAGTGGAATTATCATAATTT
**
24988 AATAGTGGGGTTATCATAATTT
1 AATAGTGGAATTATCATAATTT
25010 CATATGAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (22 bp):
AATAGTGGAATTATCATAATTT
Found at i:25882 original size:21 final size:21
Alignment explanation
Indices: 25858--25898 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25848 ACATCATGAG
25858 AATTTTT-TTCAAAGAAAATGT
1 AATTTTTATTC-AAGAAAATGT
*
25879 AATTTTTATTCATGAAAATG
1 AATTTTTATTCAAGAAAATG
25899 ATATTACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (21 bp):
AATTTTTATTCAAGAAAATGT
Found at i:26258 original size:31 final size:31
Alignment explanation
Indices: 26220--26284 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
26210 AACTGAACTA
* * * *
26220 ACTCAAACATCCAAGTTTTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAAATCCGGAG
26251 ACTCAAACATCCAAGATCTAAAAATCCGGAG
1 ACTCAAACATCCAAGATCTAAAAATCCGGAG
26282 ACT
1 ACT
26285 GATAACCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.22
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAAATCCGGAG
Done.