Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009598.1 Corchorus capsularis cultivar CVL-1 contig09619, 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: 54037
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:23189 original size:27 final size:27
Alignment explanation
Indices: 23133--23215 Score: 121
Period size: 27 Copynumber: 3.0 Consensus size: 27
23123 TGGAACATCT
*
23133 TTTGGAACTTCAGTTTCAACAGCAGCAGCA
1 TTTGGAACTTCAG---CGACAGCAGCAGCA
23163 TTTGGAACTTCAGCGACAGCAGCAGCA
1 TTTGGAACTTCAGCGACAGCAGCAGCA
*
23190 GTTGGAACTTCAGCGACAGCAGCAGC
1 TTTGGAACTTCAGCGACAGCAGCAGC
23216 TTCGTCACCA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
27 38 0.75
30 13 0.25
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.20
Consensus pattern (27 bp):
TTTGGAACTTCAGCGACAGCAGCAGCA
Found at i:27171 original size:2 final size:2
Alignment explanation
Indices: 27164--27191 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27154 CTAGCAATTC
27164 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
27192 GCAAATCAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29576 original size:5 final size:5
Alignment explanation
Indices: 29566--29606 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
29556 GTTGTTGTTT
*
29566 TTTTA TTTTA TTTTA TTTTTA TTTTTT TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA -TTTTA -TTTTA TTTTA TTTTA TTTT
29607 TTCCTCTCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 23 0.70
6 10 0.30
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTA
Found at i:29585 original size:11 final size:11
Alignment explanation
Indices: 29566--29607 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
29556 GTTGTTGTTT
29566 TTTTA-TTTTA
1 TTTTATTTTTA
29576 TTTTATTTTTA
1 TTTTATTTTTA
*
29587 TTTTTTTTTTA
1 TTTTATTTTTA
29598 TTTTATTTTT
1 TTTTATTTTT
29608 TCCTCTCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 5 0.17
11 24 0.83
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:29590 original size:22 final size:22
Alignment explanation
Indices: 29565--29607 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
29555 CGTTGTTGTT
29565 TTTTTATTTTATTTTATTTTTA
1 TTTTTATTTTATTTTATTTTTA
*
29587 TTTTTTTTTTATTTTATTTTT
1 TTTTTATTTTATTTTATTTTT
29608 TCCTCTCTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (22 bp):
TTTTTATTTTATTTTATTTTTA
Found at i:31405 original size:30 final size:30
Alignment explanation
Indices: 31369--31519 Score: 203
Period size: 33 Copynumber: 4.8 Consensus size: 30
31359 GGAACATCTT
*** *
31369 TTGGAACTTCAGTTTCAACAGCAGCGGCAG
1 TTGGAACTTCAGCGACAACAGCAGCAGCAG
31399 TTGGAACTTCAGCGACAGCAGCAGCAGCAGCAG
1 TTGGAACTTCAGCGACA--A-CAGCAGCAGCAG
31432 TTGGAACTTCAGCGACAACAGCAGCAGCAGCAG
1 TTGGAACTTCAGCGAC-A-A-CAGCAGCAGCAG
31465 TTGGAACTTCAGCGACAACAGCAGCAGCAG
1 TTGGAACTTCAGCGACAACAGCAGCAGCAG
*
31495 TTGGAACTTCAGCGACAGCAGCAGC
1 TTGGAACTTCAGCGACAACAGCAGC
31520 TTCGTCACCA
Statistics
Matches: 112, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
30 50 0.45
31 1 0.01
32 2 0.02
33 58 0.52
34 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.15
Consensus pattern (30 bp):
TTGGAACTTCAGCGACAACAGCAGCAGCAG
Found at i:31432 original size:33 final size:33
Alignment explanation
Indices: 31387--31519 Score: 227
Period size: 33 Copynumber: 4.1 Consensus size: 33
31377 TCAGTTTCAA
*
31387 CAGCAGCGGCAGTTGGAACTTCAGCGACAGCAG
1 CAGCAGCAGCAGTTGGAACTTCAGCGACAGCAG
*
31420 CAGCAGCAGCAGTTGGAACTTCAGCGACAACAG
1 CAGCAGCAGCAGTTGGAACTTCAGCGACAGCAG
31453 CAGCAGCAGCAGTTGGAACTTCAGCGACA--A-
1 CAGCAGCAGCAGTTGGAACTTCAGCGACAGCAG
31483 CAGCAGCAGCAGTTGGAACTTCAGCGACAGCAG
1 CAGCAGCAGCAGTTGGAACTTCAGCGACAGCAG
31516 CAGC
1 CAGC
31520 TTCGTCACCA
Statistics
Matches: 95, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
30 29 0.31
31 1 0.01
32 1 0.01
33 64 0.67
ACGTcount: A:0.31, C:0.28, G:0.29, T:0.12
Consensus pattern (33 bp):
CAGCAGCAGCAGTTGGAACTTCAGCGACAGCAG
Found at i:31451 original size:63 final size:62
Alignment explanation
Indices: 31369--31519 Score: 216
Period size: 63 Copynumber: 2.4 Consensus size: 62
31359 GGAACATCTT
***
31369 TTGGAACTTCAGTTTCAACAGCAGC-G-GCAGTTGGAACTTCAGCGACAGCAGCAGCAGCAGCAG
1 TTGGAACTTCAGCGACAACAGCAGCAGAGCAGTTGGAACTTCAGCGACA--A-CAGCAGCAGCAG
31432 TTGGAACTTCAGCGACAACAGCAGCAGCAGCAGTTGGAACTTCAGCGACAACAGCAGCAGCAG
1 TTGGAACTTCAGCGACAACAGCAGCAG-AGCAGTTGGAACTTCAGCGACAACAGCAGCAGCAG
*
31495 TTGGAACTTCAGCGACAGCAGCAGC
1 TTGGAACTTCAGCGACAACAGCAGC
31520 TTCGTCACCA
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
63 58 0.72
64 2 0.02
66 21 0.26
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.15
Consensus pattern (62 bp):
TTGGAACTTCAGCGACAACAGCAGCAGAGCAGTTGGAACTTCAGCGACAACAGCAGCAGCAG
Found at i:31579 original size:30 final size:30
Alignment explanation
Indices: 31545--31610 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
31535 TGAAATTGTT
*
31545 GCAGCTGCAACAACAACAACAACTACAGCA
1 GCAGCAGCAACAACAACAACAACTACAGCA
* * *
31575 GCAGCAGCAGCAACAACAACAGCTACAGCG
1 GCAGCAGCAACAACAACAACAACTACAGCA
31605 GCAGCA
1 GCAGCA
31611 TTCTCATGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.33, G:0.20, T:0.05
Consensus pattern (30 bp):
GCAGCAGCAACAACAACAACAACTACAGCA
Found at i:33145 original size:3 final size:3
Alignment explanation
Indices: 33137--33161 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
33127 AAACCTTTCT
33137 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
33162 ATATATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:34694 original size:102 final size:106
Alignment explanation
Indices: 34513--34797 Score: 388
Period size: 109 Copynumber: 2.7 Consensus size: 106
34503 ACTATTATAG
*
34513 TTTTATTCTACTAGAAACTCTATTTTTATTCAATCAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTATTTTTATT---T--AATTAAATCTAATATCTTTATAATTACTT
34578 TATTTTTACCAAAAAATTTGG-ATA-T-A-TTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGAATATTAATTTTTTCTAATATACAA
34620 TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
34685 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGA-ATATT--AATTTTTTCTAATATACAA
* * *
34729 TTTTATTCTATTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATT--TTT-T
1 TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATCT-AATATCTT-TATAATTACTTTAT
34790 TTTTACCA
64 TTTTACCA
34798 TTTTAATTTA
Statistics
Matches: 165, Mismatches: 4, Indels: 18
0.88 0.02 0.10
Matches are distributed among these distances:
102 50 0.30
104 4 0.02
105 1 0.01
107 38 0.23
108 5 0.03
109 60 0.36
110 7 0.04
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.51
Consensus pattern (106 bp):
TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGAATATTAATTTTTTCTAATATACAA
Found at i:36413 original size:14 final size:14
Alignment explanation
Indices: 36394--36424 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
36384 TCTCTCTCTC
36394 TTTCTTTCTGCATT
1 TTTCTTTCTGCATT
*
36408 TTTCTTTCTTCATT
1 TTTCTTTCTGCATT
36422 TTT
1 TTT
36425 TGTCAATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTCTTTCTGCATT
Found at i:36848 original size:40 final size:40
Alignment explanation
Indices: 36791--36869 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
36781 AAGTTTCTTC
*
36791 ATTTCTTGCAACCCAAGAAACCCACCAAAAAA-AGAGGAAG
1 ATTTCTTGCAACACAAGAAACCC-CCAAAAAAGAGAGGAAG
36831 ATTTCTTGCAACACAAGAAACCCCCAAAAAAGAGAGGAA
1 ATTTCTTGCAACACAAGAAACCCCCAAAAAAGAGAGGAA
36870 AATGAAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
39 8 0.22
40 29 0.78
ACGTcount: A:0.48, C:0.24, G:0.15, T:0.13
Consensus pattern (40 bp):
ATTTCTTGCAACACAAGAAACCCCCAAAAAAGAGAGGAAG
Found at i:45258 original size:3 final size:3
Alignment explanation
Indices: 45250--45278 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
45240 TAAAAAATTA
45250 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
45279 CCCATCAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:46360 original size:21 final size:20
Alignment explanation
Indices: 46315--46372 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
46305 TTGTTTAGTA
46315 ACTGTACAGATGAGATT-AC
1 ACTGTACAGATGAGATTAAC
* *
46334 ACTGTACAGATTAGATTAAAT
1 ACTGTACAGATGAGATT-AAC
*
46355 ACTGTATAGATGAGATTA
1 ACTGTACAGATGAGATTA
46373 TTAGAACAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 16 0.48
20 1 0.03
21 16 0.48
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAAC
Found at i:47002 original size:39 final size:39
Alignment explanation
Indices: 46958--47036 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
46948 AATGTCCACA
*
46958 GGTGAAAGTCCAATGAATCCATAAATTCCAAATTGGGTC
1 GGTGAAAGTCCAATGAATCCATAAATCCCAAATTGGGTC
* *
46997 GGTGAAAGTTCAATGAATCCGTAAATCCCAAATTGGGTC
1 GGTGAAAGTCCAATGAATCCATAAATCCCAAATTGGGTC
47036 G
1 G
47037 ACGGTTTACC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (39 bp):
GGTGAAAGTCCAATGAATCCATAAATCCCAAATTGGGTC
Found at i:49909 original size:78 final size:77
Alignment explanation
Indices: 49827--49988 Score: 184
Period size: 78 Copynumber: 2.1 Consensus size: 77
49817 CATTCAAGAA
* *
49827 ATTTAAAAAAAACTAATATATCAAGTTTT-TTAACTAAAATAGTAAAATTGTAAAATATAATAGT
1 ATTTAAAAAAAA-TAA-AAATCAAGTTTTATTAACTAAAATAGTAAAATCGTAAAATATAATAGT
*
49891 TATAAGGGTATTAG
64 TATAAGGATATTAG
** * ** * *
49905 ATTT-AATTATATAAAAATTGAGTTTTAAGTTGAGTAAAATAGTAAAATCGTAAAATATAATAGT
1 ATTTAAAAAAAATAAAAATCAAGTTTT-A-TTAACTAAAATAGTAAAATCGTAAAATATAATAGT
49969 TATAAGGATATTAG
64 TATAAGGATATTAG
49983 ATTTAA
1 ATTTAA
49989 TTATATAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
75 9 0.13
76 3 0.04
77 4 0.06
78 53 0.76
79 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (77 bp):
ATTTAAAAAAAATAAAAATCAAGTTTTATTAACTAAAATAGTAAAATCGTAAAATATAATAGTTA
TAAGGATATTAG
Found at i:49920 original size:39 final size:39
Alignment explanation
Indices: 49877--49998 Score: 94
Period size: 39 Copynumber: 3.1 Consensus size: 39
49867 AGTAAAATTG
49877 TAAAATATAATAGTTATAAGGGTATTAGATTTAATTATA
1 TAAAATATAATAGTTATAAGGGTATTAGATTTAATTATA
* * * * *
49916 TAAAA-AT--TGAGTTTTAAGTTGAGTA--AAATAGTAA-AATCG
1 TAAAATATAAT-AGTTATAAG--G-GTATTAGAT-TTAATTAT-A
*
49955 TAAAATATAATAGTTATAAGGATATTAGATTTAATTATA
1 TAAAATATAATAGTTATAAGGGTATTAGATTTAATTATA
49994 TAAAA
1 TAAAA
49999 ATAGAGTTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 24
0.63 0.12 0.25
Matches are distributed among these distances:
36 1 0.02
37 8 0.13
38 9 0.15
39 23 0.38
40 10 0.17
41 8 0.13
42 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.13, T:0.38
Consensus pattern (39 bp):
TAAAATATAATAGTTATAAGGGTATTAGATTTAATTATA
Found at i:49941 original size:70 final size:70
Alignment explanation
Indices: 49867--50091 Score: 297
Period size: 70 Copynumber: 3.1 Consensus size: 70
49857 TAACTAAAAT
* * *
49867 AGTAAAATTGTAAAATATAATAGTTATAAGGGTATTAGATTTAATTATATAAAAATTGAGTTTTA
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
49932 AGTTG
66 AGTTG
49937 AGTAAAATAGTAAAATCGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGT-AAA-A-T----T-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
50002 GAGTTTTTAGTTG
58 GAGTTTTTAGTTG
* * * * * *
50015 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
50080 AGTTG
66 AGTTG
50085 AGTAAAA
1 AGTAAAA
50092 CTATAAAAAC
Statistics
Matches: 138, Mismatches: 9, Indels: 16
0.85 0.06 0.10
Matches are distributed among these distances:
70 66 0.48
71 3 0.02
72 1 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 4 0.03
78 61 0.44
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (70 bp):
AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTG
Found at i:49990 original size:78 final size:77
Alignment explanation
Indices: 49861--50099 Score: 341
Period size: 78 Copynumber: 3.2 Consensus size: 77
49851 GTTTTTTAAC
* *
49861 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGGTATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
*
49926 GTTTTAAGTTGAG
65 GTTTTTAGTTGAG
49939 TAAAATAGTAAAATCGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
50004 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
50017 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
50075 TTTTTAGTTGAG
66 TTTTTAGTTGAG
50087 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
50100 ACCTAAACAA
Statistics
Matches: 153, Mismatches: 6, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
70 56 0.37
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 86 0.56
ACGTcount: A:0.50, C:0.01, G:0.13, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:50199 original size:6 final size:6
Alignment explanation
Indices: 50183--50223 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
50173 GAACGTACTT
50183 TATAG- TATAGA TATAGA TATAG- -ATAGA TATAGA TATAGA TA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TA
50224 GATTATATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.12
5 5 0.15
6 24 0.73
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (6 bp):
TATAGA
Found at i:50210 original size:16 final size:16
Alignment explanation
Indices: 50183--50226 Score: 79
Period size: 16 Copynumber: 2.7 Consensus size: 16
50173 GAACGTACTT
50183 TATAGTATAGATATAGA
1 TATAG-ATAGATATAGA
50200 TATAGATAGATATAGA
1 TATAGATAGATATAGA
50216 TATAGATAGAT
1 TATAGATAGAT
50227 TATATGCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 22 0.81
17 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (16 bp):
TATAGATAGATATAGA
Found at i:51386 original size:4 final size:4
Alignment explanation
Indices: 51377--51415 Score: 60
Period size: 4 Copynumber: 9.5 Consensus size: 4
51367 AATAAAATAC
*
51377 ATTT ATTT ATTT ATTT ATTT ATTC AGTTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT AT
51416 GAGTAGGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:51519 original size:22 final size:22
Alignment explanation
Indices: 51491--51535 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
51481 ATGTGGATTA
*
51491 TTAAATACCGTCTCAGTTTTTG
1 TTAAATACCGTCCCAGTTTTTG
* *
51513 TTAAATATCGTCCCATTTTTTG
1 TTAAATACCGTCCCAGTTTTTG
51535 T
1 T
51536 ACTTTTGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (22 bp):
TTAAATACCGTCCCAGTTTTTG
Found at i:51769 original size:32 final size:33
Alignment explanation
Indices: 51733--51794 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
51723 GAGGGCGGCA
51733 GGGGCGGCCTT-GCAACGGC-AGGCCGCCCCGGT
1 GGGGCGG-CTTAGCAACGGCTAGGCCGCCCCGGT
* *
51765 GGGGCGGCTTAGCCACGGCTATGCCGCCCC
1 GGGGCGGCTTAGCAACGGCTAGGCCGCCCC
51795 ACTAGGGCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 3 0.12
32 14 0.54
33 9 0.35
ACGTcount: A:0.10, C:0.39, G:0.40, T:0.11
Consensus pattern (33 bp):
GGGGCGGCTTAGCAACGGCTAGGCCGCCCCGGT
Found at i:51859 original size:23 final size:22
Alignment explanation
Indices: 51825--51879 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
51815 TTTTTTTCAA
51825 AAAAATAATAATTAGCTA-TTTT
1 AAAAATAATAATTA-CTATTTTT
* *
51847 AAAAATAGCTAATTATTATTTTT
1 AAAAATA-ATAATTACTATTTTT
*
51870 AAAAAAAATA
1 AAAAATAATA
51880 GCTTTGCCGC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (22 bp):
AAAAATAATAATTACTATTTTT
Found at i:51982 original size:11 final size:11
Alignment explanation
Indices: 51966--52017 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
51956 CCCCTGGGGT
*
51966 GGCATTGCAAC
1 GGCATTGCGAC
*
51977 GGCATTGCTAC
1 GGCATTGCGAC
** *
51988 CCCATTGGGAC
1 GGCATTGCGAC
*
51999 GGCATTGGGAC
1 GGCATTGCGAC
52010 GGCATTGC
1 GGCATTGC
52018 CGCCCCACTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.19, C:0.27, G:0.33, T:0.21
Consensus pattern (11 bp):
GGCATTGCGAC
Found at i:52004 original size:33 final size:33
Alignment explanation
Indices: 51966--52044 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
51956 CCCCTGGGGT
* *
51966 GGCATTGCAACGGCATTGCTACCCCATTGGGAC
1 GGCATTGCAACGGCATTGCCACCCCACTGGGAC
** * *
51999 GGCATTGGGACGGCATTGCCGCCCCACTGGGGC
1 GGCATTGCAACGGCATTGCCACCCCACTGGGAC
* *
52032 GGCCTTGCCACGG
1 GGCATTGCAACGG
52045 TACAGCCAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.15, C:0.33, G:0.34, T:0.18
Consensus pattern (33 bp):
GGCATTGCAACGGCATTGCCACCCCACTGGGAC
Found at i:52653 original size:30 final size:30
Alignment explanation
Indices: 52617--52685 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
52607 ATCATGTACT
*
52617 TACTATTC-CTT-CAAAAAAGAAATTATCATA
1 TACTATTCACTTCCAAAAAA-AAAAT-TCATA
*
52647 TACTATTCATTTCCAAAAAAAAAATTCATA
1 TACTATTCACTTCCAAAAAAAAAATTCATA
52677 TACTATTCA
1 TACTATTCA
52686 TTGTGATCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 22 0.63
31 6 0.17
32 7 0.20
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.35
Consensus pattern (30 bp):
TACTATTCACTTCCAAAAAAAAAATTCATA
Found at i:52686 original size:30 final size:32
Alignment explanation
Indices: 52628--52687 Score: 97
Period size: 30 Copynumber: 1.9 Consensus size: 32
52618 ACTATTCCTT
*
52628 CAAAAAAGAAATTATCATATACTATTCATTTC
1 CAAAAAAGAAAATATCATATACTATTCATTTC
52660 CAAAAAA-AAAAT-TCATATACTATTCATT
1 CAAAAAAGAAAATATCATATACTATTCATT
52688 GTGATCAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 16 0.59
31 4 0.15
32 7 0.26
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (32 bp):
CAAAAAAGAAAATATCATATACTATTCATTTC
Found at i:53735 original size:109 final size:109
Alignment explanation
Indices: 53517--53812 Score: 450
Period size: 109 Copynumber: 2.7 Consensus size: 109
53507 TAAATTAAAA
** *
53517 TGGTAAAAATAAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGTAAAAAT-AAAGTAATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGT
*
53581 AGAATAAAGTTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
63 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
53628 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
*
53693 ATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* *
53737 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
53802 GTAGAATAAAA
61 GTAGAATAAAA
53813 CTATAATAGT
Statistics
Matches: 172, Mismatches: 7, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
109 120 0.70
110 13 0.08
111 11 0.06
114 28 0.16
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Done.