Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014547.1 Corchorus capsularis cultivar CVL-1 contig14568, 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: 115108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:162 original size:31 final size:31
Alignment explanation
Indices: 124--583 Score: 520
Period size: 31 Copynumber: 15.5 Consensus size: 31
114 GATTTTAGCC
124 AATATGCAACTATATGATTATGGCCCTACTG
1 AATATGCAACTATATGATTATGGCCCTACTG
* *
155 AATATGCAACTATATTATTATTGCCCTACTG
1 AATATGCAACTATATGATTATGGCCCTACTG
*
186 AATATGCAACTATATG-----GCCCCTACTG
1 AATATGCAACTATATGATTATGGCCCTACTG
*
212 AATATGCAACTATATGA--A--G-CGTACTG
1 AATATGCAACTATATGATTATGGCCCTACTG
238 AATATGCAACTATATG---A--GCCCTACTG
1 AATATGCAACTATATGATTATGGCCCTACTG
*
264 AATATGCAACTATATG-----GCCCCTACTG
1 AATATGCAACTATATGATTATGGCCCTACTG
*
290 AATATGCAACTATATGATTATGGTCCTACTG
1 AATATGCAACTATATGATTATGGCCCTACTG
* *
321 AATATGCAGCTATATGATTATAGCCCTACTTG
1 AATATGCAACTATATGATTATGGCCCTAC-TG
* *
353 -ATATG---CTAT-GGAACTATATGGTCCTACTG
1 AATATGCAACTATATG-A-T-TATGGCCCTACTG
* *
382 AACATGCAACTAAATGATTATGGCCCTACTG
1 AATATGCAACTATATGATTATGGCCCTACTG
413 AATATGCAACTATATGATTATGGCCCTACTG
1 AATATGCAACTATATGATTATGGCCCTACTG
* * *
444 AATATGCAACTATGTGATTCTGACCCTACTG
1 AATATGCAACTATATGATTATGGCCCTACTG
* *
475 AATATGCAACTATATGATTCTGACCCTACTG
1 AATATGCAACTATATGATTATGGCCCTACTG
* *
506 AATATGCAACTATATGATTATGACCCTACTT
1 AATATGCAACTATATGATTATGGCCCTACTG
*
537 AATATGCAACTATATGATTATGACCCTACTG
1 AATATGCAACTATATGATTATGGCCCTACTG
*
568 AATATGTAACTATATG
1 AATATGCAACTATATG
584 GCCTTACTGA
Statistics
Matches: 380, Mismatches: 31, Indels: 36
0.85 0.07 0.08
Matches are distributed among these distances:
25 2 0.01
26 92 0.24
27 1 0.00
28 5 0.01
29 3 0.01
30 13 0.03
31 256 0.67
32 3 0.01
33 4 0.01
34 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (31 bp):
AATATGCAACTATATGATTATGGCCCTACTG
Found at i:253 original size:62 final size:59
Alignment explanation
Indices: 124--635 Score: 461
Period size: 62 Copynumber: 8.8 Consensus size: 59
114 GATTTTAGCC
*
124 AATATGCAACTATATGATTATGGCCCTACTGAATATGCAACTATATTATTATTGCCCTACTG
1 AATATGCAACTATATGATTATGGCCCTACTGAATATGCAACTATATGA-TA--GCCCTACTG
* *
186 AATATGCAACTATATG-----GCCCCTACTGAATATGCAACTATATGA-AG-CGTACTG
1 AATATGCAACTATATGATTATGGCCCTACTGAATATGCAACTATATGATAGCCCTACTG
238 AATATGCAACTATATG---A--GCCCTACTGAATATGCAACTATATG---GCCCCTACTG
1 AATATGCAACTATATGATTATGGCCCTACTGAATATGCAACTATATGATAG-CCCTACTG
* *
290 AATATGCAACTATATGATTATGGTCCTACTGAATATGCAGCTATATGATTATAGCCCTACTTG
1 AATATGCAACTATATGATTATGGCCCTACTGAATATGCAACTATATG---ATAGCCCTAC-TG
* * * *
353 -ATATG---CTAT-GGAACTATATGGTCCTACTGAACATGCAACTAAATGATTATGGCCCTACTG
1 AATATGCAACTATATG-A-T-TATGGCCCTACTGAATATGCAACTATATGA-TA--GCCCTACTG
* *
413 AATATGCAACTATATGATTATGGCCCTACTGAATATGCAACTATGTGATTCTGACCCTACTG
1 AATATGCAACTATATGATTATGGCCCTACTGAATATGCAACTATATGA-T-AG-CCCTACTG
* * *
475 AATATGCAACTATATGATTCTGACCCTACTGAATATGCAACTATATGATTATGACCCTACTT
1 AATATGCAACTATATGATTATGGCCCTACTGAATATGCAACTATATGA-TA-G-CCCTACTG
* * *
537 AATATGCAACTATATGATTATGACCCTACTGAATATGTAACTATATG---GCCTTACTG
1 AATATGCAACTATATGATTATGGCCCTACTGAATATGCAACTATATGATAGCCCTACTG
* * *
593 AATATGTAAC----CG--TATGGCTCTACTGAATATGCAACTATATGAT
1 AATATGCAACTATATGATTATGGCCCTACTGAATATGCAACTATATGAT
636 CGTACTAAAT
Statistics
Matches: 388, Mismatches: 31, Indels: 72
0.79 0.06 0.15
Matches are distributed among these distances:
50 27 0.07
52 69 0.18
53 1 0.00
55 2 0.01
56 15 0.04
57 49 0.13
58 2 0.01
59 7 0.02
60 3 0.01
61 39 0.10
62 164 0.42
63 4 0.01
64 5 0.01
65 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (59 bp):
AATATGCAACTATATGATTATGGCCCTACTGAATATGCAACTATATGATAGCCCTACTG
Found at i:591 original size:25 final size:25
Alignment explanation
Indices: 562--633 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
552 GATTATGACC
562 CTACTGAATATGTAACTATATGGC-
1 CTACTGAATATGTAACTATATGGCT
**
586 CTTACTGAATATGTAACCGTATGGCT
1 C-TACTGAATATGTAACTATATGGCT
*
612 CTACTGAATATGCAACTATATG
1 CTACTGAATATGTAACTATATG
634 ATCGTACTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
24 1 0.02
25 39 0.95
26 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (25 bp):
CTACTGAATATGTAACTATATGGCT
Found at i:641 original size:25 final size:24
Alignment explanation
Indices: 562--647 Score: 82
Period size: 25 Copynumber: 3.5 Consensus size: 24
552 GATTATGACC
**
562 CTACTGAATATGTAACTATATGGC
1 CTACTGAATATGTAACTATATGAT
** *
586 CTTACTGAATATGTAACCGTATGGCT
1 C-TACTGAATATGTAACTATAT-GAT
*
612 CTACTGAATATGCAACTATATGAT
1 CTACTGAATATGTAACTATATGAT
*
636 CGTACTAAATAT
1 C-TACTGAATAT
648 AAGGTATATG
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
24 4 0.08
25 44 0.88
26 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (24 bp):
CTACTGAATATGTAACTATATGAT
Found at i:6943 original size:26 final size:27
Alignment explanation
Indices: 6891--6944 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
6881 TATATACTAT
6891 AAGAAAAATGTAACTTTTACCCAAAAAAA
1 AAGAAAAATGTAA--TTTACCCAAAAAAA
*
6920 AAGAAAAATGTAA-TTACTCAAAAAA
1 AAGAAAAATGTAATTTACCCAAAAAA
6945 TATATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 11 0.46
29 13 0.54
ACGTcount: A:0.61, C:0.11, G:0.07, T:0.20
Consensus pattern (27 bp):
AAGAAAAATGTAATTTACCCAAAAAAA
Found at i:9019 original size:2 final size:2
Alignment explanation
Indices: 9014--9040 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9004 TATACATGAC
9014 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9041 ATCGAGTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24585 original size:31 final size:29
Alignment explanation
Indices: 24512--24569 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
24502 TCTCATTTTT
*
24512 AAAAGTTAAGGGGCCAATTTATCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
24541 AAAAGTTAAGGGGCCAATTTGT-CCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
24569 A
1 A
24570 TGGATTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.21
Consensus pattern (29 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAAA
Found at i:24986 original size:243 final size:243
Alignment explanation
Indices: 24558--25045 Score: 967
Period size: 243 Copynumber: 2.0 Consensus size: 243
24548 AAGGGGCCAA
*
24558 TTTGTCCAAAAATGGATTGTTAAGGGGCTAATTTGGGTATTAAGCCCTTTAAAGGTTGGAGAGGG
1 TTTGTCCAAAAATGGATAGTTAAGGGGCTAATTTGGGTATTAAGCCCTTTAAAGGTTGGAGAGGG
24623 ACAAAAATCAAACTCTTTAAATTGATTACTTCATATTGAATAATTGAATATTCTTGCTGGTCCCA
66 ACAAAAATCAAACTCTTTAAATTGATTACTTCATATTGAATAATTGAATATTCTTGCTGGTCCCA
24688 ACGACAAAACCCATGTTGGTTACCTTATAAAAATTTTAATGAATCTAACTTTTTGTGAATATGAC
131 ACGACAAAACCCATGTTGGTTACCTTATAAAAATTTTAATGAATCTAACTTTTTGTGAATATGAC
24753 ATTTAGCAGAGTCATAAACGTCAGAATTTCATAATGCAATAGTAAAAT
196 ATTTAGCAGAGTCATAAACGTCAGAATTTCATAATGCAATAGTAAAAT
24801 TTTGTCCAAAAATGGATAGTTAAGGGGCTAATTTGGGTATTAAGCCCTTTAAAGGTTGGAGAGGG
1 TTTGTCCAAAAATGGATAGTTAAGGGGCTAATTTGGGTATTAAGCCCTTTAAAGGTTGGAGAGGG
24866 ACAAAAATCAAACTCTTTAAATTGATTACTTCATATTGAATAATTGAATATTCTTGCTGGTCCCA
66 ACAAAAATCAAACTCTTTAAATTGATTACTTCATATTGAATAATTGAATATTCTTGCTGGTCCCA
24931 ACGACAAAACCCATGTTGGTTACCTTATAAAAATTTTAATGAATCTAACTTTTTGTGAATATGAC
131 ACGACAAAACCCATGTTGGTTACCTTATAAAAATTTTAATGAATCTAACTTTTTGTGAATATGAC
24996 ATTTAGCAGAGTCATAAACGTCAGAATTTCATAATGCAATAGTAAAAT
196 ATTTAGCAGAGTCATAAACGTCAGAATTTCATAATGCAATAGTAAAAT
25044 TT
1 TT
25046 GAGCTTAATC
Statistics
Matches: 244, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
243 244 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (243 bp):
TTTGTCCAAAAATGGATAGTTAAGGGGCTAATTTGGGTATTAAGCCCTTTAAAGGTTGGAGAGGG
ACAAAAATCAAACTCTTTAAATTGATTACTTCATATTGAATAATTGAATATTCTTGCTGGTCCCA
ACGACAAAACCCATGTTGGTTACCTTATAAAAATTTTAATGAATCTAACTTTTTGTGAATATGAC
ATTTAGCAGAGTCATAAACGTCAGAATTTCATAATGCAATAGTAAAAT
Found at i:42667 original size:4 final size:4
Alignment explanation
Indices: 42658--42703 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
42648 GCTCCCTTAC
42658 ATGT ATGT ATGT A--T ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
42702 AT
1 AT
42704 ATGTTATAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.11
4 34 0.89
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:42676 original size:10 final size:10
Alignment explanation
Indices: 42661--42707 Score: 76
Period size: 10 Copynumber: 4.5 Consensus size: 10
42651 CCCTTACATG
42661 TATGTATGTA
1 TATGTATGTA
42671 TATGTATGTA
1 TATGTATGTA
42681 TATGTATGTA
1 TATGTATGTA
42691 TGTATGTATGTA
1 --TATGTATGTA
42703 TATGT
1 TATGT
42708 TATAGATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
10 25 0.71
12 10 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (10 bp):
TATGTATGTA
Found at i:42707 original size:14 final size:14
Alignment explanation
Indices: 42658--42699 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
42648 GCTCCCTTAC
42658 ATGTATGTATGTAT
1 ATGTATGTATGTAT
* *
42672 ATGTATGTATATGT
1 ATGTATGTATGTAT
42686 ATGTATGTATGTAT
1 ATGTATGTATGTAT
42700 GTATATGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
ATGTATGTATGTAT
Found at i:44324 original size:50 final size:50
Alignment explanation
Indices: 44264--44413 Score: 255
Period size: 50 Copynumber: 3.0 Consensus size: 50
44254 AGGAGTTGAA
* * *
44264 GGTGAATCCTTAAGTACTCTCCATTGGCACTTGCTCTACATGGAAGACTT
1 GGTGAGTCCTTAAGTAATCTCCATTGGCACTTGCTCTACATAGAAGACTT
* *
44314 GGTGAGTCCTTAAGTAATCTCCATTGGCACTTGCTATACATAAAAGACTT
1 GGTGAGTCCTTAAGTAATCTCCATTGGCACTTGCTCTACATAGAAGACTT
44364 GGTGAGTCCTTAAGTAATCTCCATTGGCACTTGCTCTACATAGAAGACTT
1 GGTGAGTCCTTAAGTAATCTCCATTGGCACTTGCTCTACATAGAAGACTT
44414 TCCTTGTAGG
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 93 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (50 bp):
GGTGAGTCCTTAAGTAATCTCCATTGGCACTTGCTCTACATAGAAGACTT
Found at i:48931 original size:50 final size:50
Alignment explanation
Indices: 48863--48960 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
48853 AAGATGAAGG
48863 TGGTGAGTCCTTAAGTAATCTCCATTGGCACTTGCTCTACATAGAAGAGT
1 TGGTGAGTCCTTAAGTAATCTCCATTGGCACTTGCTCTACATAGAAGAGT
*
48913 TGGTGAGTCCTTGAGTAATCTCCATTGGCACTTGCTCTACATAGAAGA
1 TGGTGAGTCCTTAAGTAATCTCCATTGGCACTTGCTCTACATAGAAGA
48961 CTTTCCTTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (50 bp):
TGGTGAGTCCTTAAGTAATCTCCATTGGCACTTGCTCTACATAGAAGAGT
Found at i:49064 original size:50 final size:49
Alignment explanation
Indices: 48987--49082 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 49
48977 TTAGACAACC
*
48987 AATTAAATACAAGATATTTTAGCCTATTAGT-GCTCTTTATCCTAATCCT
1 AATTAAATACAAGATATTTTAGCCTATTA-TCGCTCCTTATCCTAATCCT
* *
49036 AATTAAATACAATA-AGGTTTTAGCCTATTATCGCTCCTTATTCTAAT
1 AATTAAATACAAGATA--TTTTAGCCTATTATCGCTCCTTATCCTAAT
49083 TGTATTTTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
48 1 0.02
49 14 0.34
50 26 0.63
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (49 bp):
AATTAAATACAAGATATTTTAGCCTATTATCGCTCCTTATCCTAATCCT
Found at i:49432 original size:31 final size:30
Alignment explanation
Indices: 49396--49507 Score: 105
Period size: 31 Copynumber: 3.9 Consensus size: 30
49386 GGCATGTCAC
49396 GTGTCACTTTTTGGTACACGTGGTGTGACAT
1 GTGTCACTTTTTGGTACACGTGGTGTG-CAT
49427 GTGTCACTTTTTGGTACA--T-GTG-GCA-
1 GTGTCACTTTTTGGTACACGTGGTGTGCAT
* * *
49452 -CG--ACTTTTTGGTACATGTGGCGTGCCAT
1 GTGTCACTTTTTGGTACACGTGGTGTG-CAT
* *
49480 ATGTCACTTTTTGGTACACGTGGCGTGC
1 GTGTCACTTTTTGGTACACGTGGTGTGC
49508 CACGTCGAAC
Statistics
Matches: 68, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
22 13 0.19
24 2 0.03
25 2 0.03
26 3 0.04
27 3 0.04
28 3 0.04
29 2 0.03
30 1 0.01
31 39 0.57
ACGTcount: A:0.15, C:0.19, G:0.29, T:0.38
Consensus pattern (30 bp):
GTGTCACTTTTTGGTACACGTGGTGTGCAT
Found at i:49458 original size:53 final size:53
Alignment explanation
Indices: 49401--49503 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
49391 GTCACGTGTC
* * *
49401 ACTTTTTGGTACACGTGGTGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACATATGTCACTTTTTGGTACACGTGGCACG
* *
49454 ACTTTTTGGTACATGTGGCGTGCCATATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACATATGTCACTTTTTGGTACACGTGGC
49504 GTGCCACGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.38
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACATATGTCACTTTTTGGTACACGTGGCACG
Found at i:68392 original size:9 final size:9
Alignment explanation
Indices: 68380--68426 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
68370 AATAATAGTT
*
68380 ATTATTATT
1 ATTATTATA
68389 ATTATTATA
1 ATTATTATA
*
68398 ATTAATAATA
1 ATT-ATTATA
*
68408 ATTATTAAA
1 ATTATTATA
68417 ATTATTATA
1 ATTATTATA
68426 A
1 A
68427 ATAATAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 24 0.75
10 8 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATTATTATA
Found at i:68409 original size:34 final size:32
Alignment explanation
Indices: 68365--68478 Score: 102
Period size: 34 Copynumber: 3.4 Consensus size: 32
68355 AATAACTATT
*
68365 ATAATAATAATAGTTATTATTATTATTATTATA
1 ATAATAATAATA-TTATTATTATTATTATAATA
** *
68398 ATTAATAATAATTATTAAAATTATTATAAATAATA
1 A-TAATAATAA-TATTATTATTATTAT-TATAATA
* * * *
68433 ATAATAATAATTTTTTTAATAATTAATAATAATA
1 ATAATAATAATATTATT-ATTATT-ATTATAATA
68467 ATAATAATAATA
1 ATAATAATAATA
68479 ATAATAATAA
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
33 4 0.06
34 52 0.79
35 10 0.15
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.46
Consensus pattern (32 bp):
ATAATAATAATATTATTATTATTATTATAATA
Found at i:68432 original size:3 final size:3
Alignment explanation
Indices: 68426--68489 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
68416 AATTATTATA
** **
68426 AAT AAT AAT AAT AAT AAT TTT TTT AAT AATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
68472 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
68490 TAGATAGCTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:68435 original size:6 final size:6
Alignment explanation
Indices: 68395--68489 Score: 84
Period size: 6 Copynumber: 15.3 Consensus size: 6
68385 TATTATTATT
* * * *
68395 ATAATTA ATAATA ATTATTA A-AATT ATTATAA ATAATA ATAATA ATAATT
1 ATAA-TA ATAATA A-TAATA ATAATA ATAAT-A ATAATA ATAATA ATAATA
* **
68445 TTTTTA ATAATTA ATAATA ATAATA ATAATA ATAATA ATAATA AT
1 ATAATA ATAA-TA ATAATA ATAATA ATAATA ATAATA ATAATA AT
68490 TAGATAGCTT
Statistics
Matches: 70, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
5 3 0.04
6 48 0.69
7 19 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
ATAATA
Found at i:68438 original size:9 final size:9
Alignment explanation
Indices: 68395--68489 Score: 84
Period size: 9 Copynumber: 10.2 Consensus size: 9
68385 TATTATTATT
68395 ATAATTAATA
1 ATAA-TAATA
*
68405 ATAATTATTA
1 ATAA-TAATA
* *
68415 A-AATTATT
1 ATAATAATA
68423 ATAAATAATA
1 AT-AATAATA
68433 ATAATAATA
1 ATAATAATA
** **
68442 ATTTTTTTA
1 ATAATAATA
68451 ATAATTAATA
1 ATAA-TAATA
68461 ATAATAATA
1 ATAATAATA
68470 ATAATAATA
1 ATAATAATA
68479 ATAATAATA
1 ATAATAATA
68488 AT
1 AT
68490 TAGATAGCTT
Statistics
Matches: 68, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
8 3 0.04
9 41 0.60
10 24 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
ATAATAATA
Found at i:68466 original size:28 final size:27
Alignment explanation
Indices: 68352--68489 Score: 113
Period size: 28 Copynumber: 5.1 Consensus size: 27
68342 GTTTTGGCGA
* *
68352 AATAATAACTATTATAATAA-TAATAGTT
1 AATAATAA-TATTATTATAATTAATA-AT
* * *
68380 ATTATTATTATTATTATAATTAATAAT
1 AATAATAATATTATTATAATTAATAAT
* * *
68407 AATTATTAAAATTATTATAAATAATAAT
1 AA-TAATAATATTATTATAATTAATAAT
* *
68435 AATAATAATTTTTTTAATAATTAATAAT
1 AATAATAATATTATT-ATAATTAATAAT
*
68463 AATAATAATA--ATAATAA-TAATAAT
1 AATAATAATATTATTATAATTAATAAT
68487 AAT
1 AAT
68490 TAGATAGCTT
Statistics
Matches: 90, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
24 10 0.11
25 4 0.04
26 1 0.01
27 21 0.23
28 54 0.60
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (27 bp):
AATAATAATATTATTATAATTAATAAT
Found at i:68487 original size:34 final size:35
Alignment explanation
Indices: 68400--68491 Score: 98
Period size: 34 Copynumber: 2.6 Consensus size: 35
68390 TTATTATAAT
*
68400 TAATAATAATTATTAA-AATTATTATAAATAATAATAA
1 TAATAAT-ATTAATAATAATTA--ATAAATAATAATAA
* **
68437 TAATAATTTTTTTAATAATTAAT-AATAATAATAA
1 TAATAATATTAATAATAATTAATAAATAATAATAA
*
68471 TAATAATAATAATAATAATTA
1 TAATAATATTAATAATAATTA
68492 GATAGCTTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
34 28 0.58
35 2 0.04
36 6 0.12
37 12 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (35 bp):
TAATAATATTAATAATAATTAATAAATAATAATAA
Found at i:71965 original size:27 final size:27
Alignment explanation
Indices: 71935--71989 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
71925 AGAATTATAT
*
71935 AGCCATGAAACAGTGTTCTTATTGAAG
1 AGCCATGAAACAGCGTTCTTATTGAAG
71962 AGCCATGAAACAGCGTTCTTATTGAAG
1 AGCCATGAAACAGCGTTCTTATTGAAG
71989 A
1 A
71990 TGATCGAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (27 bp):
AGCCATGAAACAGCGTTCTTATTGAAG
Found at i:75743 original size:52 final size:52
Alignment explanation
Indices: 75681--75783 Score: 206
Period size: 52 Copynumber: 2.0 Consensus size: 52
75671 AAGACCCAAG
75681 TCTCAGACTTTTTTGTTCTGCCTTTCAACAGTTTTTTTCCATTTGAATTCAT
1 TCTCAGACTTTTTTGTTCTGCCTTTCAACAGTTTTTTTCCATTTGAATTCAT
75733 TCTCAGACTTTTTTGTTCTGCCTTTCAACAGTTTTTTTCCATTTGAATTCA
1 TCTCAGACTTTTTTGTTCTGCCTTTCAACAGTTTTTTTCCATTTGAATTCA
75784 AATTCCTACC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.17, C:0.21, G:0.10, T:0.51
Consensus pattern (52 bp):
TCTCAGACTTTTTTGTTCTGCCTTTCAACAGTTTTTTTCCATTTGAATTCAT
Found at i:77362 original size:29 final size:29
Alignment explanation
Indices: 77311--77388 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
77301 AGGTGTCTCC
* *
77311 AAATTACAAATTCAGGGGGCAAAACGTCTA
1 AAATTACAAATTCAGGAGCCAAAACGTC-A
*
77341 AAATTA-AAATTTAGGAGCCAAAACGTCA
1 AAATTACAAATTCAGGAGCCAAAACGTCA
77369 AAATCGTACAAAATTCAGGA
1 AAAT--TAC-AAATTCAGGA
77389 AGTAAAAGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 5 0.12
29 18 0.45
30 8 0.20
32 9 0.22
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (29 bp):
AAATTACAAATTCAGGAGCCAAAACGTCA
Found at i:86931 original size:18 final size:17
Alignment explanation
Indices: 86903--86942 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
86893 GGAATGGGAA
*
86903 TGGTGCGGCGGCAGCGG
1 TGGTGCGGCGGCAGAGG
*
86920 TGGTGACGGCGGCGGAGG
1 TGGTG-CGGCGGCAGAGG
86938 TGGTG
1 TGGTG
86943 GCTGTGGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.07, C:0.17, G:0.60, T:0.15
Consensus pattern (17 bp):
TGGTGCGGCGGCAGAGG
Found at i:97348 original size:74 final size:74
Alignment explanation
Indices: 97259--97407 Score: 264
Period size: 74 Copynumber: 2.0 Consensus size: 74
97249 ATTAAGGAAT
* *
97259 GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATGGGGGAAACTCATAGAGGGGCTTTTTAGTC
1 GTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
97324 ATCC-GAAAA
66 A-CCTGAAAA
97333 GTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
1 GTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
97398 ACCTGAAAA
66 ACCTGAAAA
97407 G
1 G
97408 ACCAAAAATG
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
73 2 0.03
74 70 0.97
ACGTcount: A:0.40, C:0.09, G:0.30, T:0.20
Consensus pattern (74 bp):
GTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
ACCTGAAAA
Found at i:98553 original size:4 final size:4
Alignment explanation
Indices: 98544--98570 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
98534 ATATTGTTGC
98544 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
98571 CCTGATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:101371 original size:20 final size:20
Alignment explanation
Indices: 101348--101386 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
101338 AATTGTCTTA
101348 AACA-AAAATAACAAAATTTC
1 AACACAAAA-AACAAAATTTC
*
101368 AACACATAAAACAAAATTT
1 AACACAAAAAACAAAATTT
101387 TATTATTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (20 bp):
AACACAAAAAACAAAATTTC
Found at i:115058 original size:14 final size:13
Alignment explanation
Indices: 115023--115061 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
115013 GGTAGTAGTA
*
115023 TTTTCTTTTTTCT
1 TTTTCTTTTTCCT
*
115036 TTTTTTTTTTCCT
1 TTTTCTTTTTCCT
115049 TTTTGCTTTTTCC
1 TTTT-CTTTTTCC
115062 AACGAGAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTCTTTTTCCT
Done.