Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007489.1 Corchorus capsularis cultivar CVL-1 contig07510, 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: 55926
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:5025 original size:33 final size:32
Alignment explanation
Indices: 4983--5048 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 32
4973 TGTCGTGCCT
*
4983 CATGCCCGGCCTTGTTCGCGCCATCCTGTGCGC
1 CATGCCCGGCCTTGTCCGCGCCATCC-GTGCGC
*
5016 CATGCCCGGCCTTGTCCGCTCCATCCGTGCGC
1 CATGCCCGGCCTTGTCCGCGCCATCCGTGCGC
5048 C
1 C
5049 CTGCTAAGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.06, C:0.45, G:0.26, T:0.23
Consensus pattern (32 bp):
CATGCCCGGCCTTGTCCGCGCCATCCGTGCGC
Found at i:6930 original size:21 final size:21
Alignment explanation
Indices: 6890--6931 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6880 TATTTTTATA
* *
6890 GCTATTTTTCTATGTTTTTTT
1 GCTATTTTTATATGTATTTTT
*
6911 GCTATTTTTATGTGTATTTTT
1 GCTATTTTTATATGTATTTTT
6932 ACCCTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.07, G:0.12, T:0.69
Consensus pattern (21 bp):
GCTATTTTTATATGTATTTTT
Found at i:14415 original size:12 final size:12
Alignment explanation
Indices: 14398--14425 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
14388 ACGTATGGGA
14398 CATCGCACGGGC
1 CATCGCACGGGC
14410 CATCGCACGGGC
1 CATCGCACGGGC
14422 CATC
1 CATC
14426 CGGCCACAAC
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:0.18, C:0.43, G:0.29, T:0.11
Consensus pattern (12 bp):
CATCGCACGGGC
Found at i:15971 original size:14 final size:14
Alignment explanation
Indices: 15954--15980 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
15944 TCTTTAAAAT
15954 TTTTTATTTTTTGC
1 TTTTTATTTTTTGC
15968 TTTTTATTTTTTG
1 TTTTTATTTTTTG
15981 TTTAAGAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTTTATTTTTTGC
Found at i:19322 original size:21 final size:20
Alignment explanation
Indices: 19289--19337 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
19279 AAGAATTGTA
**
19289 GCTTCTTGGAAATGGCTCTT
1 GCTTCTTGGAAATCCCTCTT
*
19309 GCTTCCTTTGAAATCCCTCTT
1 GCTT-CTTGGAAATCCCTCTT
19330 GCATTCTT
1 GC-TTCTT
19338 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 18 0.75
22 2 0.08
ACGTcount: A:0.14, C:0.27, G:0.16, T:0.43
Consensus pattern (20 bp):
GCTTCTTGGAAATCCCTCTT
Found at i:20485 original size:22 final size:22
Alignment explanation
Indices: 20460--20513 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
20450 TAAAAGTACC
*
20460 AAATAAAAA-TAAACAAAACGAA
1 AAATAAAAAGGAAA-AAAACGAA
*
20482 AAATAAAAAGGAAAATAACGAA
1 AAATAAAAAGGAAAAAAACGAA
*
20504 AAAGAAAAAG
1 AAATAAAAAG
20514 ATAAAGGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.76, C:0.06, G:0.11, T:0.07
Consensus pattern (22 bp):
AAATAAAAAGGAAAAAAACGAA
Found at i:20519 original size:28 final size:28
Alignment explanation
Indices: 20465--20520 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
20455 GTACCAAATA
* *
20465 AAAATAAACAAAACGAAAAATAAAAAGG
1 AAAATAAACAAAAAGAAAAAGAAAAAGG
*
20493 AAAAT-AACGAAAAAGAAAAAGATAAAGG
1 AAAATAAAC-AAAAAGAAAAAGAAAAAGG
20521 GTAAGAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.07
Consensus pattern (28 bp):
AAAATAAACAAAAAGAAAAAGAAAAAGG
Found at i:23652 original size:33 final size:32
Alignment explanation
Indices: 23615--23719 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 32
23605 ATAAGCATCC
* * *
23615 AAAACAAATTTAGTGTCATCACAAACAACACCT
1 AAAACAGATTTAGTATCATCGCAAACAACA-CT
*
23648 AAAACAGATTTAGTTTCATCGCAAACAACACT
1 AAAACAGATTTAGTATCATCGCAAACAACACT
** *
23680 CAAATTAGGTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGTATCATCGCAAACAACA-CT
23714 AAAACA
1 AAAACA
23720 CTCTTTGCAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
32 2 0.03
33 57 0.93
34 2 0.03
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.24
Consensus pattern (32 bp):
AAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:31855 original size:21 final size:22
Alignment explanation
Indices: 31826--31887 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
31816 AAAAACGGAA
31826 AAAACTTTTTTTTTATAGACGC
1 AAAACTTTTTTTTTATAGACGC
* *
31848 AAAATTTTTTTTTTATGGACG-
1 AAAACTTTTTTTTTATAGACGC
*
31869 TAAACTTTTTTTTTATAGA
1 AAAACTTTTTTTTTATAGA
31888 ATAAACGGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
21 16 0.46
22 19 0.54
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.52
Consensus pattern (22 bp):
AAAACTTTTTTTTTATAGACGC
Found at i:33170 original size:10 final size:10
Alignment explanation
Indices: 33155--33180 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
33145 GAGCACTCTA
33155 GAATTTTCTG
1 GAATTTTCTG
33165 GAATTTTCTG
1 GAATTTTCTG
33175 GAATTT
1 GAATTT
33181 GGCAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:35546 original size:6 final size:6
Alignment explanation
Indices: 35537--35600 Score: 62
Period size: 6 Copynumber: 10.7 Consensus size: 6
35527 AGAAGAGTAA
*
35537 AAAAAG AAAAAGG AAAACG -AAAAG AAAAAG AAAAAG AAGAAA- AAAAAGG
1 AAAAAG AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG AAAAA-G
*
35586 AAAACG -AAAAG AAAA
1 AAAAAG AAAAAG AAAA
35601 GCCACGTCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
5 11 0.23
6 25 0.52
7 12 0.25
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:37682 original size:10 final size:10
Alignment explanation
Indices: 37667--37698 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
37657 AGTTAGTATC
37667 TAAAAAAATA
1 TAAAAAAATA
37677 TAAAAAAATA
1 TAAAAAAATA
*
37687 TAAAAATATA
1 TAAAAAAATA
37697 TA
1 TA
37699 TATATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:45671 original size:37 final size:37
Alignment explanation
Indices: 45539--45694 Score: 183
Period size: 36 Copynumber: 4.3 Consensus size: 37
45529 CTCTTTTTAG
* * * *
45539 ATTAAGT-TCTTTATTGACTCGACTCAATTACCCTGA
1 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
* ** * *
45575 ATTAAGT-TCTTTATTGATTCCACTTAATTACCCTAA
1 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
* *
45611 ATTAAG-CCCCTTATTGACGCTACTTAATTACCTTGA
1 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
45647 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
*
45684 ACTAAGTCCCT
1 ATTAAGTCCCT
45695 GACTTGACTT
Statistics
Matches: 104, Mismatches: 14, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
36 66 0.63
37 38 0.37
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (37 bp):
ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
Found at i:45710 original size:32 final size:34
Alignment explanation
Indices: 45669--45743 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 34
45659 TATTGACGCT
45669 ACTTAATTACCCTGAACT-A-AGTCCCTGACTTG
1 ACTTAATTACCCTGAACTAATAGTCCCTGACTTG
*
45701 ACTTAATTACCCTGAATTAATTAGTCCCTGACTTG
1 ACTTAATTACCCTGAACTAA-TAGTCCCTGACTTG
45736 ACTTAATT
1 ACTTAATT
45744 TCCTTCCTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
32 17 0.44
33 1 0.03
35 21 0.54
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (34 bp):
ACTTAATTACCCTGAACTAATAGTCCCTGACTTG
Found at i:45777 original size:37 final size:37
Alignment explanation
Indices: 45719--46643 Score: 407
Period size: 37 Copynumber: 24.1 Consensus size: 37
45709 ACCCTGAATT
* *
45719 AATT-AGTCCCTGACTTGACTTAATTTCCTTCCTTGA
1 AATTAAGTCCTTGACTTTACTTAATTTCCTTCCTTGA
* *
45755 AATTAAGTCCTTGACTCTACTTAATTTCCTTTCTTGA
1 AATTAAGTCCTTGACTTTACTTAATTTCCTTCCTTGA
* * **
45792 AATTAAGTCCTTAACTCTACTTAATTTCCTTTTTTGA
1 AATTAAGTCCTTGACTTTACTTAATTTCCTTCCTTGA
* * * *
45829 AATTAAGT-CATGAACTCTACTTAATTCCCTTCCTTGG
1 AATTAAGTCCTTG-ACTTTACTTAATTTCCTTCCTTGA
* * * *
45866 AATT-AGTCCTTAACTCTACTTAATTTCCCTCCTTGG
1 AATTAAGTCCTTGACTTTACTTAATTTCCTTCCTTGA
* * * * *
45902 AATCAAGTCCTTTACTCTACTTAATTCCCTTCCTTGG
1 AATTAAGTCCTTGACTTTACTTAATTTCCTTCCTTGA
* * * * * *
45939 AATCAAGTCTTTTACTCTACTTAATTCCCTTCCTTGG
1 AATTAAGTCCTTGACTTTACTTAATTTCCTTCCTTGA
* * **
45976 AACTAAGTCATTTTCTTTACTTAA--TCC--CCTTG-
1 AATTAAGTCCTTGACTTTACTTAATTTCCTTCCTTGA
** * * *
46008 GGTTAAGTCTTTGACCGATCTTACTTAA--T-CATCTTTG-
1 AATTAAGTCCTTGA-C--T-TTACTTAATTTCCTTCCTTGA
* * *
46045 GATTAAGTCTTTGTTGA-TTTACTTAA-TT-CTT--GTGA
1 AATTAAGTC---CTTGACTTTACTTAATTTCCTTCCTTGA
* ***
46080 AATTAAGTCTTTGTTGA-TTTACTTAATTATCCTGAATT--
1 AATTAAGTC---CTTGACTTTACTTAATT-TCCTTCCTTGA
* * * * *
46118 AAGTATGTGCTTGCCTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCCTTGACTTTACTTAATTTCCTTCCTTGA
* *
46155 AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTC----CTTGACTTTACTTAATTTCCTTCCTTGA
* *
46196 AATTAAGT-CTGTGCTTACTTTACCTAATTTCCTTCCTAGA
1 AATTAAGTCCT-TG---ACTTTACTTAATTTCCTTCCTTGA
* * *
46236 AATTAAGT-TTGTGATTACTTTACCTAATTTCC-TCCCTGA
1 AATTAAGTCCT-TG---ACTTTACTTAATTTCCTTCCTTGA
* *
46275 AATTAAGT-CTATGCTTACTTTACCTAATTTCC-TCCCTGA
1 AATTAAGTCCT-TG---ACTTTACTTAATTTCCTTCCTTGA
* * *
46314 AATTAAGTCTGTGCTTTACTCTACCTAATTTCCTTCCTTGA
1 AATTAAGTC----CTTGACTTTACTTAATTTCCTTCCTTGA
*
46355 AATTAAGTCTGTGCTTTACTTTACTTAATTTCCTTCCTTGA
1 AATTAAGTC----CTTGACTTTACTTAATTTCCTTCCTTGA
* *
46396 AATTAAGTCTGTGCTTTACTTTACGTAATTTCCTTCCTTGA
1 AATTAAGTC----CTTGACTTTACTTAATTTCCTTCCTTGA
* *
46437 AATTAAGTCTGTGCTTTAACTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTC----C-TTGACTTTACTTAATTTCCTTCCTTGA
* * * *
46479 AATTAAGT-CTGTGCTTACATTACCTAATTTCTTTCCTTCA
1 AATTAAGTCCT-TG---ACTTTACTTAATTTCCTTCCTTGA
*
46519 AATTAAGTCTGTGCTTTACTTTACTTAATTTCCTTCCTT-A
1 AATTAAGTC----CTTGACTTTACTTAATTTCCTTCCTTGA
*
46559 AAGTTAAGT-CTGTG-CTTATATTAACCTAATTTCCTTCCTTGA
1 AA-TTAAGTCCT-TGAC---T-TT-ACTTAATTTCCTTCCTTGA
* *
46601 AATTAAGT-TTGTGCTTACTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCCT-TG---ACTTTACTTAATTTCCTTCCTTGA
46641 AAT
1 AAT
46644 GTCTTTACTT
Statistics
Matches: 748, Mismatches: 82, Indels: 114
0.79 0.09 0.12
Matches are distributed among these distances:
32 8 0.01
33 6 0.01
34 2 0.00
35 46 0.06
36 64 0.09
37 205 0.27
38 8 0.01
39 50 0.07
40 128 0.17
41 187 0.25
42 37 0.05
43 1 0.00
44 3 0.00
45 3 0.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.45
Consensus pattern (37 bp):
AATTAAGTCCTTGACTTTACTTAATTTCCTTCCTTGA
Found at i:45887 original size:110 final size:111
Alignment explanation
Indices: 45736--45984 Score: 338
Period size: 110 Copynumber: 2.3 Consensus size: 111
45726 CCCTGACTTG
* * * * * *
45736 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTGACTCTACTTAATTTCCTTTCTTGAAATTAAGTC
1 ACTTAATTCCCTTCCTTGGAATTAAGTCCTTAACTCTACTTAATTTCCCTCCTTGAAATCAAGTC
* ** *
45801 CTTAACTCTACTTAATTTCCTTTTTTGAAATTAAGTCATGAACTCT
66 CTTAACTCTACTTAATTCCCTTCCTTGAAATCAAGTCATGAACTCT
*
45847 ACTTAATTCCCTTCCTTGGAATT-AGTCCTTAACTCTACTTAATTTCCCTCCTTGGAATCAAGTC
1 ACTTAATTCCCTTCCTTGGAATTAAGTCCTTAACTCTACTTAATTTCCCTCCTTGAAATCAAGTC
* * * **
45911 CTTTACTCTACTTAATTCCCTTCCTTGGAATCAAGTCTTTTACTCT
66 CTTAACTCTACTTAATTCCCTTCCTTGAAATCAAGTCATGAACTCT
*
45957 ACTTAATTCCCTTCCTTGGAACTAAGTC
1 ACTTAATTCCCTTCCTTGGAATTAAGTC
45985 ATTTTCTTTA
Statistics
Matches: 120, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
110 95 0.79
111 25 0.21
ACGTcount: A:0.24, C:0.25, G:0.08, T:0.43
Consensus pattern (111 bp):
ACTTAATTCCCTTCCTTGGAATTAAGTCCTTAACTCTACTTAATTTCCCTCCTTGAAATCAAGTC
CTTAACTCTACTTAATTCCCTTCCTTGAAATCAAGTCATGAACTCT
Found at i:45985 original size:147 final size:147
Alignment explanation
Indices: 45719--45986 Score: 367
Period size: 147 Copynumber: 1.8 Consensus size: 147
45709 ACCCTGAATT
* * * *
45719 AATTAGTCCCTGACTTGACTTAATTTCCTTCCTTGAAATTAAGTCCTTGACTCTACTTAATTTCC
1 AATTAGTCCCTAACTTGACTTAATTTCCCTCCTTGAAATCAAGTCCTTGACTCTACTTAATTCCC
* * * ** *
45784 TTTCTTGAAATTAAGTCCTTAACTCTACTTAATTTCCTTTTTTGAAATTAAGTCATGAACTCTAC
66 TTCCTTGAAATCAAGTCCTTAACTCTACTTAATTCCCTTCCTTGAAACTAAGTCATGAACTCTAC
45849 TTAATTCCCTTCCTTGG
131 TTAATTCCCTTCCTTGG
* * *
45866 AATTAGTCCTTAACTCT-ACTTAATTTCCCTCCTTGGAATCAAGTCCTTTACTCTACTTAATTCC
1 AATTAGTCCCTAACT-TGACTTAATTTCCCTCCTTGAAATCAAGTCCTTGACTCTACTTAATTCC
* * * *
45930 CTTCCTTGGAATCAAGTCTTTTACTCTACTTAATTCCCTTCCTTGGAACTAAGTCAT
65 CTTCCTTGAAATCAAGTCCTTAACTCTACTTAATTCCCTTCCTTGAAACTAAGTCAT
45987 TTTCTTTACT
Statistics
Matches: 103, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
147 102 0.99
148 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.42
Consensus pattern (147 bp):
AATTAGTCCCTAACTTGACTTAATTTCCCTCCTTGAAATCAAGTCCTTGACTCTACTTAATTCCC
TTCCTTGAAATCAAGTCCTTAACTCTACTTAATTCCCTTCCTTGAAACTAAGTCATGAACTCTAC
TTAATTCCCTTCCTTGG
Found at i:46075 original size:20 final size:20
Alignment explanation
Indices: 46047--46105 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
46037 CATCTTTGGA
46047 TTAAGTCTTTGTTGATTTAC
1 TTAAGTCTTTGTTGATTTAC
* *
46067 TTAATTC-TTG-TGA---AA
1 TTAAGTCTTTGTTGATTTAC
46082 TTAAGTCTTTGTTGATTTAC
1 TTAAGTCTTTGTTGATTTAC
46102 TTAA
1 TTAA
46106 TTATCCTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
15 7 0.23
16 3 0.10
17 3 0.10
18 3 0.10
19 3 0.10
20 11 0.37
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.53
Consensus pattern (20 bp):
TTAAGTCTTTGTTGATTTAC
Found at i:46228 original size:40 final size:40
Alignment explanation
Indices: 46114--46643 Score: 780
Period size: 41 Copynumber: 13.1 Consensus size: 40
46104 AATTATCCTG
* *
46114 AATTAAGTATGTGCTTGCCTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTT-ACTTTACCTAATTTCCTTCCTTGA
*
46155 AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTT-ACTTTACCTAATTTCCTTCCTTGA
*
46196 AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTAGA
1 AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTTGA
* * *
46236 AATTAAGTTTGTGATTACTTTACCTAATTTCC-TCCCTGA
1 AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTTGA
* *
46275 AATTAAGTCTATGCTTACTTTACCTAATTTCC-TCCCTGA
1 AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTTGA
*
46314 AATTAAGTCTGTGCTTTACTCTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGC-TTACTTTACCTAATTTCCTTCCTTGA
*
46355 AATTAAGTCTGTGCTTTACTTTACTTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGC-TTACTTTACCTAATTTCCTTCCTTGA
*
46396 AATTAAGTCTGTGCTTTACTTTACGTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGC-TTACTTTACCTAATTTCCTTCCTTGA
46437 AATTAAGTCTGTGCTTTAACTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGC-TT-ACTTTACCTAATTTCCTTCCTTGA
* * *
46479 AATTAAGTCTGTGCTTACATTACCTAATTTCTTTCCTTCA
1 AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTTGA
*
46519 AATTAAGTCTGTGCTTTACTTTACTTAATTTCCTTCCTT-A
1 AATTAAGTCTGTGC-TTACTTTACCTAATTTCCTTCCTTGA
46559 AAGTTAAGTCTGTGCTTA-TATTAACCTAATTTCCTTCCTTGA
1 AA-TTAAGTCTGTGCTTACT-TT-ACCTAATTTCCTTCCTTGA
*
46601 AATTAAGTTTGTGCTTACTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTTGA
46641 AAT
1 AAT
46644 GTCTTTACTT
Statistics
Matches: 454, Mismatches: 26, Indels: 19
0.91 0.05 0.04
Matches are distributed among these distances:
39 55 0.12
40 134 0.30
41 224 0.49
42 41 0.09
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (40 bp):
AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTTGA
Found at i:46688 original size:37 final size:37
Alignment explanation
Indices: 46647--47052 Score: 507
Period size: 37 Copynumber: 10.9 Consensus size: 37
46637 TTGAAATGTC
* * *
46647 TTTACTTAATTACCATGAATTAAGTCCTTTTACAGTT
1 TTTACTTAATTACCCTGAATTAAGTCCTTTTACTGCT
* * *
46684 TTTACTTAATTTCCCTAAATTAAGTAC-TTTACCTGCT
1 TTTACTTAATTACCCTGAATTAAGTCCTTTTA-CTGCT
* * *
46721 TTTACTTAATTTCCATGAATTAAGTCCTTTAACTGCT
1 TTTACTTAATTACCCTGAATTAAGTCCTTTTACTGCT
* *
46758 TTTACTTAATTTCCCTGAATTGAGTCC-TTTACTGCTT
1 TTTACTTAATTACCCTGAATTAAGTCCTTTTACTGC-T
* *
46795 ACTTTCCTTAATTACCCTGAATTAAGT-CTTTTGCTTGCT
1 --TTTACTTAATTACCCTGAATTAAGTCCTTTTAC-TGCT
* *
46834 TTTACTTAATTATCCTGAATTAAGTCTTTTTACTGCT
1 TTTACTTAATTACCCTGAATTAAGTCCTTTTACTGCT
*
46871 TTTACTTAATTTCCCTGAATTAAGTCC-TTTACCTGCT
1 TTTACTTAATTACCCTGAATTAAGTCCTTTTA-CTGCT
*
46908 TTTACTTAATTACCCTGAATTAAGTCCTTTAACTGCT
1 TTTACTTAATTACCCTGAATTAAGTCCTTTTACTGCT
* *
46945 TTTACTTAATTACCCTGAATTAAGTTCTTTAACTGCT
1 TTTACTTAATTACCCTGAATTAAGTCCTTTTACTGCT
* *
46982 TTTACTTAATTACCCCGAATTAAGTCCTTTAACTGCT
1 TTTACTTAATTACCCTGAATTAAGTCCTTTTACTGCT
* * *
47019 TTTACTTAATTACCCCGAAATAAGT-CTTTGACTG
1 TTTACTTAATTACCCTGAATTAAGTCCTTTTACTG
47053 TGTTTATTTT
Statistics
Matches: 328, Mismatches: 31, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
36 23 0.07
37 263 0.80
38 12 0.04
39 27 0.08
40 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.09, T:0.45
Consensus pattern (37 bp):
TTTACTTAATTACCCTGAATTAAGTCCTTTTACTGCT
Found at i:47114 original size:43 final size:43
Alignment explanation
Indices: 47017--47268 Score: 280
Period size: 43 Copynumber: 5.8 Consensus size: 43
47007 CCTTTAACTG
* * * *
47017 CTTTTACTTAATTACCCCGAAATAAGTCTTTGACTGTG-TTTAT
1 CTTTT-CTTAATTACCCTGAATTAAGACTTTGACTGTGTTTTCT
* *
47060 -TTTTCTTAATTACCAC-GAATTAAGACTTTCACTTTGTTTTCT
1 CTTTTCTTAATTACC-CTGAATTAAGACTTTGACTGTGTTTTCT
* * * **
47102 CTTTTGTTAATTACCCTGAATTAAGACTTTCACTTTAAATGTGCTCT
1 CTTTTCTTAATTACCCTGAATTAAGACTTTGAC--T--GTGTTTTCT
*
47149 CTTTTCTTAATTACCCTAAATTAAGACTTTGACTGTGTTTTCT
1 CTTTTCTTAATTACCCTGAATTAAGACTTTGACTGTGTTTTCT
*
47192 CTTTTCTTAATTACCCTGAATTAAGACTTTGACTGTG-TTT-A
1 CTTTTCTTAATTACCCTGAATTAAGACTTTGACTGTGTTTTCT
* *
47233 CTTTTCTTAATTACCATGAATTAAGACTTCGACTGT
1 CTTTTCTTAATTACCCTGAATTAAGACTTTGACTGT
47269 ATTCTTCTGA
Statistics
Matches: 182, Mismatches: 19, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
41 60 0.33
42 13 0.07
43 71 0.39
45 2 0.01
47 36 0.20
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (43 bp):
CTTTTCTTAATTACCCTGAATTAAGACTTTGACTGTGTTTTCT
Found at i:50457 original size:33 final size:33
Alignment explanation
Indices: 50420--50526 Score: 135
Period size: 33 Copynumber: 3.2 Consensus size: 33
50410 AGCACTAGTG
* *
50420 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* * *
50453 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* *
50486 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
50518 AACCGGCCA
1 -ACCGGCCA
50527 TCGCTAGGCG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 2 0.03
33 61 0.97
ACGTcount: A:0.23, C:0.38, G:0.29, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
Found at i:51506 original size:8 final size:8
Alignment explanation
Indices: 51493--51526 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
51483 CACCTTCTTG
51493 AAAAATTC
1 AAAAATTC
51501 AAAAATTC
1 AAAAATTC
*
51509 AGAAACTTC
1 A-AAAATTC
51518 AAAAATTC
1 AAAAATTC
51526 A
1 A
51527 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:51615 original size:5 final size:5
Alignment explanation
Indices: 51605--51631 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
51595 ATCGAAAAAT
51605 ATAAA ATAAA ATAAA ATAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA AT
51632 TTCGACCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
ATAAA
Done.