Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011923.1 Corchorus capsularis cultivar CVL-1 contig11944, 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: 39119
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Found at i:6092 original size:18 final size:19
Alignment explanation
Indices: 6071--6106 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6061 CTTTAATTAC
6071 TTGTC-TTTTTACTTTCTT
1 TTGTCATTTTTACTTTCTT
*
6089 TTGTCATTTTTATTTTCT
1 TTGTCATTTTTACTTTCT
6107 ACTTTTTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.72
Consensus pattern (19 bp):
TTGTCATTTTTACTTTCTT
Found at i:7215 original size:3 final size:3
Alignment explanation
Indices: 7207--7236 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
7197 TAATTTAGTT
*
7207 TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7237 AACAATACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:8363 original size:60 final size:60
Alignment explanation
Indices: 8296--8458 Score: 175
Period size: 60 Copynumber: 2.7 Consensus size: 60
8286 GCTAATTGCT
* * * *** *
8296 CAAATAAGAGTCTAACATT-TGCCAAAATGCTCAAATAAAGGTTTGATCTTTTAATTTGGC
1 CAAATAAGGGTCTAACGTTAT-CAAAAATGCTCAAATAAAGGTCCAATCTTTAAATTTGGC
* * * *
8356 CAAATAAGGGCCTAACGTTATAAAAAATGCTCAAACAAGGGTCCAATCTTTAAATTTGGC
1 CAAATAAGGGTCTAACGTTATCAAAAATGCTCAAATAAAGGTCCAATCTTTAAATTTGGC
* * * *
8416 TATATAAGGGTCTAACGTTATCGAAAATGCTCAAATAAGGGTC
1 CAAATAAGGGTCTAACGTTATCAAAAATGCTCAAATAAAGGTC
8459 TGGCGTAAGT
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
60 84 0.99
61 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (60 bp):
CAAATAAGGGTCTAACGTTATCAAAAATGCTCAAATAAAGGTCCAATCTTTAAATTTGGC
Found at i:8457 original size:31 final size:29
Alignment explanation
Indices: 8356--8459 Score: 79
Period size: 31 Copynumber: 3.4 Consensus size: 29
8346 TTAATTTGGC
*
8356 CAAATAAGGGCCTAACGTTATAAAAAATGCT
1 CAAATAAGGGTCTAACGTTAT--AAAATGCT
* * *
8387 CAAACAAGGGTCCAATC-TT-TAAATTTGGCT
1 CAAATAAGGGTCTAA-CGTTATAAA-AT-GCT
*
8417 -ATATAAGGGTCTAACGTTATCGAAAATGCT
1 CAAATAAGGGTCTAACGTTAT--AAAATGCT
8447 CAAATAAGGGTCT
1 CAAATAAGGGTCT
8460 GGCGTAAGTT
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
28 4 0.07
29 14 0.25
30 8 0.14
31 26 0.46
32 4 0.07
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (29 bp):
CAAATAAGGGTCTAACGTTATAAAATGCT
Found at i:8536 original size:31 final size:31
Alignment explanation
Indices: 8498--8665 Score: 102
Period size: 31 Copynumber: 5.5 Consensus size: 31
8488 TTTCGATGTC
8498 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
** **
8529 AGGCCCTTATTTG-GCCAAATT-AAAAGACCG--
1 AGGCCCTTATTTGAG-CATTTTGGCAA-A-CGTT
* * *
8559 -GGTCCTTATTTGAGTATTTTGGCAAATGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
** * *
8589 AGGCCCTTATTTG-GCCAAATT---AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGGCAAACG-TT
* *
8618 ATGCCCTTATCTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
*
8649 AGACCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
8666 ATTATCCATT
Statistics
Matches: 97, Mismatches: 26, Indels: 28
0.64 0.17 0.19
Matches are distributed among these distances:
28 5 0.05
29 31 0.32
30 8 0.08
31 47 0.48
32 6 0.06
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACGTT
Found at i:8595 original size:60 final size:60
Alignment explanation
Indices: 8497--8661 Score: 258
Period size: 60 Copynumber: 2.8 Consensus size: 60
8487 TTTTCGATGT
8497 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAC
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAC
* * * * *
8557 CGGGTCCTTATTTGAGTATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAC
* * *
8617 CATGCCCTTATCTGAGCATTTTGGCAAACGTTAGACCCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
8662 AGCAATTATC
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 93 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAC
Found at i:18869 original size:3 final size:3
Alignment explanation
Indices: 18861--18914 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
18851 CACCACAGTT
18861 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
18909 TGC TTC
1 TTC TTC
18915 CTGGTTGGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:20441 original size:50 final size:50
Alignment explanation
Indices: 20366--20475 Score: 211
Period size: 50 Copynumber: 2.2 Consensus size: 50
20356 TGAGGATGTT
*
20366 ACATTACAGCCACCCGTTTGATAGATGGAACTTTAGTACATGACCTAACA
1 ACATTTCAGCCACCCGTTTGATAGATGGAACTTTAGTACATGACCTAACA
20416 ACATTTCAGCCACCCGTTTGATAGATGGAACTTTAGTACATGACCTAACA
1 ACATTTCAGCCACCCGTTTGATAGATGGAACTTTAGTACATGACCTAACA
20466 ACATTTCAGC
1 ACATTTCAGC
20476 TAATGTATCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (50 bp):
ACATTTCAGCCACCCGTTTGATAGATGGAACTTTAGTACATGACCTAACA
Found at i:24713 original size:35 final size:36
Alignment explanation
Indices: 24662--24955 Score: 146
Period size: 35 Copynumber: 7.9 Consensus size: 36
24652 CCTTTTACTC
24662 TTTACTGATTACTATTTTACTC-TTACTGATTACCT
1 TTTACTGATTACTATTTTACTCTTTACTGATTACCT
*
24697 TTTACTGATTATTATTTTACTCTTTACTGATTACCTTCTTACTT
1 TTTACTGATTACTATTTTACTCTTTACTGATTA----C---C-T
*
24741 TTTACTGATTAATATTTTACTCTTTACTGATTACCAT
1 TTTACTGATTACTATTTTACTCTTTACTGATTACC-T
* *
24778 TTTGCT-CTTACTGATTACCTT-CTACTAATTACT-ATTTTA-CT
1 TTTACTGATTACT-ATT---TTACT-CT--TTACTGA--TTACCT
*
24819 CTTTACTGATTACCT-TCTTACT-TTTACTGATTACC-
1 -TTTACTGATTA-CTATTTTACTCTTTACTGATTACCT
* ** *
24854 ATTACTTTTTACCATTTTACTCTTTACTGA-T-CTCT
1 TTTACTGATTACTATTTTACTCTTTACTGATTAC-CT
** *
24889 CTTTACTTTTTACCATTCTT-CT-TTTACTGATTA-CT
1 -TTTACTGATTACTATT-TTACTCTTTACTGATTACCT
** *
24924 CTTTACTTTTTACCATTTTACTCTTTACTGAT
1 -TTTACTGATTACTATTTTACTCTTTACTGAT
24956 CTCTCTTTAC
Statistics
Matches: 210, Mismatches: 15, Indels: 67
0.72 0.05 0.23
Matches are distributed among these distances:
33 2 0.01
34 18 0.09
35 61 0.29
36 47 0.22
37 13 0.06
38 1 0.00
39 4 0.02
40 8 0.04
41 2 0.01
42 12 0.06
43 7 0.03
44 35 0.17
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.53
Consensus pattern (36 bp):
TTTACTGATTACTATTTTACTCTTTACTGATTACCT
Found at i:24722 original size:22 final size:22
Alignment explanation
Indices: 24697--24795 Score: 121
Period size: 22 Copynumber: 4.5 Consensus size: 22
24687 CTGATTACCT
*
24697 TTTACTGATTATTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
24719 TTTACTGATTACCT-TCTTACTT
1 TTTACTGATTA-CTATTTTACTC
*
24741 TTTACTGATTAATATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
24763 TTTACTGATTACCATTTTGCTC
1 TTTACTGATTACTATTTTACTC
24785 -TTACTGATTAC
1 TTTACTGATTAC
24796 CTTCTACTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
21 12 0.18
22 53 0.80
23 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.54
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:24749 original size:44 final size:44
Alignment explanation
Indices: 24691--24775 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
24681 CTCTTACTGA
*
24691 TTACCTTTTACTGATTATTATTTTACTCTTTACTGATTACCTTC
1 TTACCTTTTACTGATTAATATTTTACTCTTTACTGATTACCTTC
*
24735 TTACTTTTTACTGATTAATATTTTACTCTTTACTGATTACC
1 TTACCTTTTACTGATTAATATTTTACTCTTTACTGATTACC
24776 ATTTTGCTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.54
Consensus pattern (44 bp):
TTACCTTTTACTGATTAATATTTTACTCTTTACTGATTACCTTC
Found at i:24768 original size:101 final size:100
Alignment explanation
Indices: 24654--24851 Score: 342
Period size: 101 Copynumber: 2.0 Consensus size: 100
24644 ACTGATCACC
* * * *
24654 TTTTACTCTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACTGATTATTATTTTACTC
1 TTTTACTCTTTACTGATTACCATTTTACTCTTACTGATTACCTTCTACTAATTACTATTTTACTC
24719 TTTACTGATTACCTTCTTACTTTTTACTGATTAATA
66 TTTACTGATTACCTTCTTAC-TTTTACTGATTAATA
*
24755 TTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCTTCTACTAATTACTATTTTACTC
1 TTTTACTCTTTACTGATTACCATTTTACTCTTACTGATTACCTTCTACTAATTACTATTTTACTC
24820 TTTACTGATTACCTTCTTACTTTTACTGATTA
66 TTTACTGATTACCTTCTTACTTTTACTGATTA
24852 CCATTACTTT
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 12 0.13
101 80 0.87
ACGTcount: A:0.22, C:0.20, G:0.05, T:0.53
Consensus pattern (100 bp):
TTTTACTCTTTACTGATTACCATTTTACTCTTACTGATTACCTTCTACTAATTACTATTTTACTC
TTTACTGATTACCTTCTTACTTTTACTGATTAATA
Found at i:24825 original size:22 final size:21
Alignment explanation
Indices: 24792--24852 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
24782 CTCTTACTGA
* *
24792 TTAC-CTTCTACTAATTACTATT
1 TTACTCTT-TACTGATTACT-TC
24814 TTACTCTTTACTGATTACCTTC
1 TTACTCTTTACTGATTA-CTTC
24836 TTACT-TTTACTGATTAC
1 TTACTCTTTACTGATTAC
24853 CATTACTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.31
22 18 0.51
23 5 0.14
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.51
Consensus pattern (21 bp):
TTACTCTTTACTGATTACTTC
Found at i:24846 original size:36 final size:37
Alignment explanation
Indices: 24813--25202 Score: 256
Period size: 37 Copynumber: 10.8 Consensus size: 37
24803 TAATTACTAT
**
24813 TTTACTCTTTACTGATTACC-TTCTTACT-TTTACTGA
1 TTTACTCTTTACTTTTTACCATT-TTACTCTTTACTGA
*
24849 -TTAC-CATTACTTTTTACCATTTTACTCTTTACTGA
1 TTTACTCTTTACTTTTTACCATTTTACTCTTTACTGA
*
24884 TCT-CTCTTTACTTTTTACCATTCTT-CT-TTTACTGA
1 TTTACTCTTTACTTTTTACCATT-TTACTCTTTACTGA
24919 -TTACTCTTTACTTTTTACCATTTTACTCTTTACTGA
1 TTTACTCTTTACTTTTTACCATTTTACTCTTTACTGA
* **
24955 TCT-CTCTTTACTTTTTACCATTTTACTGATTACT-A
1 TTTACTCTTTACTTTTTACCATTTTACTCTTTACTGA
* *
24990 TTTTACTCTCTTGAATTTAATTACTATTTT-CTCTCTT--TGAA
1 -TTTACTCT-TT-ACTTT--TTACCATTTTACTCT-TTACTG-A
* ** **
25031 TTTAATC---ACCATTTGTCATTTTACTC-TT--TGAA
1 TTTACTCTTTACTTTTTACCATTTTACTCTTTACTG-A
* * *
25063 TTTA---ATTACCATTTTACCATTTTACTCTTTACCGA
1 TTTACTCTTTA-CTTTTTACCATTTTACTCTTTACTGA
* *
25098 -TTACTCTTTACTTTTTACCATTTTTATTCTTTACCGA
1 TTTACTCTTTACTTTTTACCA-TTTTACTCTTTACTGA
* *
25135 -TTACTCTTTACTTTTTACCATTTTTATTCTTTACCGA
1 TTTACTCTTTACTTTTTACCA-TTTTACTCTTTACTGA
**
25172 TTTACTGATTACTTCTTTTA-C-TTTTACTCTT
1 TTTACTCTTTAC-T-TTTTACCATTTTACTCTT
25203 AATTACCATT
Statistics
Matches: 289, Mismatches: 32, Indels: 65
0.75 0.08 0.17
Matches are distributed among these distances:
32 11 0.04
33 21 0.07
34 27 0.09
35 48 0.17
36 68 0.24
37 71 0.25
38 11 0.04
39 7 0.02
40 13 0.04
41 12 0.04
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.55
Consensus pattern (37 bp):
TTTACTCTTTACTTTTTACCATTTTACTCTTTACTGA
Found at i:24846 original size:57 final size:56
Alignment explanation
Indices: 24742--24884 Score: 189
Period size: 57 Copynumber: 2.5 Consensus size: 56
24732 TTCTTACTTT
* * * *
24742 TTACTGATTAATATTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCT
1 TTACTAATTACTATTTTACTCTTTACTGATTACCATTTTACTCTTACTGATTACCA
*
24798 TCTACTAATTACTATTTTACTCTTTACTGATTACC-TTCTTACTTTTACTGATTACCA
1 T-TACTAATTACTATTTTACTCTTTACTGATTACCATT-TTACTCTTACTGATTACCA
** *
24855 TTACTTTTTACCATTTTACTCTTTACTGAT
1 TTACTAATTACTATTTTACTCTTTACTGAT
24885 CTCTCTTTAC
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
56 29 0.38
57 48 0.62
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (56 bp):
TTACTAATTACTATTTTACTCTTTACTGATTACCATTTTACTCTTACTGATTACCA
Found at i:24880 original size:28 final size:30
Alignment explanation
Indices: 24806--24881 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 30
24796 CTTCTACTAA
* *
24806 TTACTATTTTACTCTTTACTGATTACCTTC
1 TTACCATTTTACTCTTTACTCATTACCTTC
** *
24836 TTA-C-TTTTACTGATTAC-CATTA-CTTT
1 TTACCATTTTACTCTTTACTCATTACCTTC
24862 TTACCATTTTACTCTTTACT
1 TTACCATTTTACTCTTTACT
24882 GATCTCTCTT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
26 6 0.17
27 5 0.14
28 22 0.61
30 3 0.08
ACGTcount: A:0.21, C:0.22, G:0.03, T:0.54
Consensus pattern (30 bp):
TTACCATTTTACTCTTTACTCATTACCTTC
Found at i:24939 original size:71 final size:71
Alignment explanation
Indices: 24817--24981 Score: 273
Period size: 71 Copynumber: 2.4 Consensus size: 71
24807 TACTATTTTA
**
24817 CTCTTTACTGATTACC-TTCTTACTTTTACTGATTACCATTACTTTTTACCATTTTACTCTTTAC
1 CTCTTTACTTTTTACCATTCTTACTTTTACTGATTACCATTACTTTTTACCATTTTACTCTTTAC
24881 TGATCT
66 TGATCT
*
24887 CTCTTTACTTTTTACCATTCTT-CTTTTACTGATTACTCTTTACTTTTTACCATTTTACTCTTTA
1 CTCTTTACTTTTTACCATTCTTACTTTTACTGATTAC-CATTACTTTTTACCATTTTACTCTTTA
24951 CTGATCT
65 CTGATCT
24958 CTCTTTACTTTTTACCATT-TTACT
1 CTCTTTACTTTTTACCATTCTTACT
24982 GATTACTATT
Statistics
Matches: 89, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
70 30 0.34
71 59 0.66
ACGTcount: A:0.18, C:0.24, G:0.03, T:0.55
Consensus pattern (71 bp):
CTCTTTACTTTTTACCATTCTTACTTTTACTGATTACCATTACTTTTTACCATTTTACTCTTTAC
TGATCT
Found at i:25014 original size:26 final size:26
Alignment explanation
Indices: 24983--25077 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 26
24973 CATTTTACTG
24983 ATTACTATTTTACTCTC-TTGAATTTA
1 ATTACTATTTT-CTCTCTTTGAATTTA
25009 ATTACTATTTTCTCTCTTTGAATTTA
1 ATTACTATTTTCTCTCTTTGAATTTA
* *
25035 ATCACCATTTGTCATTTTACTCTTTGAATTTA
1 ATTACTATTT-TC----T-CTCTTTGAATTTA
*
25067 ATTACCATTTT
1 ATTACTATTTT
25078 ACCATTTTAC
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
25 5 0.08
26 28 0.47
27 2 0.03
31 2 0.03
32 22 0.37
ACGTcount: A:0.25, C:0.17, G:0.04, T:0.54
Consensus pattern (26 bp):
ATTACTATTTTCTCTCTTTGAATTTA
Found at i:25084 original size:33 final size:32
Alignment explanation
Indices: 25022--25092 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
25012 ACTATTTTCT
25022 CTCTTTGAATTTAATCACCATTTGTCATTTTA
1 CTCTTTGAATTTAATCACCATTTGTCATTTTA
*
25054 CTCTTTGAATTTAATTACCATTT-TACCATTTTA
1 CTCTTTGAATTTAATCACCATTTGT--CATTTTA
25087 CTCTTT
1 CTCTTT
25093 ACCGATTACT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
31 1 0.03
32 22 0.61
33 13 0.36
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.52
Consensus pattern (32 bp):
CTCTTTGAATTTAATCACCATTTGTCATTTTA
Found at i:25197 original size:37 final size:37
Alignment explanation
Indices: 25119--25235 Score: 116
Period size: 40 Copynumber: 3.1 Consensus size: 37
25109 TTTTTACCAT
**
25119 TTTTATTCTTTACCGA-TTACTCTTTAC-T-TTTTACC
1 TTTTATTCTTTACCGATTTACTGATTACTTCTTTTA-C
25154 ATTTTTATTCTTTACCGATTTACTGATTACTTCTTTTAC
1 --TTTTATTCTTTACCGATTTACTGATTACTTCTTTTAC
*
25193 TTTTACTCTTAATTACC-ATTTTACTGATTACTTCTTTTAC
1 TTTTATTC-T--TTACCGA-TTTACTGATTACTTCTTTTAC
25233 TTT
1 TTT
25236 GACTCTTTTA
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
37 23 0.33
38 10 0.14
39 3 0.04
40 34 0.49
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (37 bp):
TTTTATTCTTTACCGATTTACTGATTACTTCTTTTAC
Found at i:25209 original size:40 final size:41
Alignment explanation
Indices: 25165--25283 Score: 145
Period size: 40 Copynumber: 2.9 Consensus size: 41
25155 TTTTTATTCT
*
25165 TTACCGATTTACTGATTACTTCTTTTACTTTTACTC-TTAA
1 TTACCGATTTACTGATTACTTCTTTTACTTTGACTCTTTAA
25205 TTACC-ATTTTACTGATTACTTCTTTTACTTTGACTCTTTTAA
1 TTACCGA-TTTACTGATTACTTCTTTTACTTTGACTC-TTTAA
* * * *
25247 TTACTGATTTCACTGATTA-ATCTCTTACCTTGACTCT
1 TTACCGATTT-ACTGATTACTTCTTTTACTTTGACTCT
25284 GGATTATCAA
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
39 1 0.01
40 33 0.48
41 1 0.01
42 25 0.36
43 9 0.13
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.51
Consensus pattern (41 bp):
TTACCGATTTACTGATTACTTCTTTTACTTTGACTCTTTAA
Found at i:29125 original size:28 final size:27
Alignment explanation
Indices: 29094--29185 Score: 87
Period size: 27 Copynumber: 3.4 Consensus size: 27
29084 ACTAAAAGTT
*
29094 ACCAAAATGTCCCTGAATGTGCAA-AATG
1 ACCAAAATGCCCCT-AA-GTGCAAGAATG
* *
29122 ACCAAAATGCCCCTTAGTGTAAGAATG
1 ACCAAAATGCCCCTAAGTGCAAGAATG
* * * * *
29149 ACCAAAATACCCTTAAATGCAAAAAAG
1 ACCAAAATGCCCCTAAGTGCAAGAATG
29176 ACCAAAATGC
1 ACCAAAATGC
29186 TAATTCGACC
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
26 5 0.10
27 34 0.65
28 13 0.25
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (27 bp):
ACCAAAATGCCCCTAAGTGCAAGAATG
Found at i:30563 original size:24 final size:24
Alignment explanation
Indices: 30516--30563 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
30506 CTCTTATTAC
30516 TTTGTTTCTTTCTTCTCTCGACAG
1 TTTGTTTCTTTCTTCTCTCGACAG
30540 TTTGTTTCTTTCTTCTCTCGACAG
1 TTTGTTTCTTTCTTCTCTCGACAG
30564 AGCGCCGCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.25, G:0.12, T:0.54
Consensus pattern (24 bp):
TTTGTTTCTTTCTTCTCTCGACAG
Found at i:38775 original size:26 final size:26
Alignment explanation
Indices: 38739--38788 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
38729 TGCCTACAAA
*
38739 TGCCCAATGCTCCCACACTCATATAC
1 TGCCAAATGCTCCCACACTCATATAC
38765 TGCCAAATGCTCCCACACTCATAT
1 TGCCAAATGCTCCCACACTCATAT
38789 CGGTTTGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.40, G:0.08, T:0.24
Consensus pattern (26 bp):
TGCCAAATGCTCCCACACTCATATAC
Done.