Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009720.1 Corchorus capsularis cultivar CVL-1 contig09741, 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: 68789
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:42 original size:32 final size:32
Alignment explanation
Indices: 1--109 Score: 130
Period size: 32 Copynumber: 3.3 Consensus size: 32
1 CCTGCCGTGGCGAAACCGCCCCA-TGAGGGCGG
1 CCTGCCGTGGCGAAACCGCCCCAGTG-GGGCGG
33 CCTGCCGTGGCGAAACCGCCCCAGTGGGGCGG
1 CCTGCCGTGGCGAAACCGCCCCAGTGGGGCGG
* * * * *
65 CCTGCCCATGGTGAAGCCGCCCTAGTGGGGAGG
1 CCTG-CCGTGGCGAAACCGCCCCAGTGGGGCGG
*
98 CTCCGCCGTGGC
1 C-CTGCCGTGGC
110 TGAGCCGTCC
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
32 33 0.50
33 31 0.47
34 2 0.03
ACGTcount: A:0.13, C:0.37, G:0.39, T:0.12
Consensus pattern (32 bp):
CCTGCCGTGGCGAAACCGCCCCAGTGGGGCGG
Found at i:4979 original size:102 final size:101
Alignment explanation
Indices: 4786--4992 Score: 301
Period size: 102 Copynumber: 2.0 Consensus size: 101
4776 ATATAATATC
* *
4786 TATATAACTATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTTAAATATATTAGAATTT
1 TATATAACTATTTTATTTTTACCATTATACTATTTTAATTAAAAAACTTAAATAAATTAGAA--T
* *
4851 TTTTTAATATATTTCTTAAATGACATTGTATAAACTTT
64 TTTTAAATATATTTCTTAAATAACATTGTATAAACTTT
* *
4889 TATAGTAACTATTTTATTTTTACCATTAT-CTATTTTAATTAAAAAAAACTTAGATAAATTATAA
1 TATA-TAACTATTTTATTTTTACCATTATACTATTTTAATT--AAAAAACTTAAATAAATTAGAA
4953 -TTTTAAATATATTTCTTAAATAACATTGTATAAACTTT
63 TTTTTAAATATATTTCTTAAATAACATTGTATAAACTTT
4991 TA
1 TA
4993 CAGTTTTATT
Statistics
Matches: 95, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
102 38 0.40
103 15 0.16
104 23 0.24
105 19 0.20
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (101 bp):
TATATAACTATTTTATTTTTACCATTATACTATTTTAATTAAAAAACTTAAATAAATTAGAATTT
TTAAATATATTTCTTAAATAACATTGTATAAACTTT
Found at i:8672 original size:22 final size:21
Alignment explanation
Indices: 8633--8684 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
8623 ATAGATTAAT
*
8633 TAATTATT-AAAAACTGATAGTA
1 TAATTATTGTAAAACTGAT-G-A
8655 TAATTATTGTAAAA-TGATGA
1 TAATTATTGTAAAACTGATGA
*
8675 TAATCATTGT
1 TAATTATTGT
8685 TAGAAAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.37
21 1 0.04
22 12 0.44
23 4 0.15
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (21 bp):
TAATTATTGTAAAACTGATGA
Found at i:23948 original size:18 final size:19
Alignment explanation
Indices: 23907--23953 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
23897 GGCCGAAATA
23907 TTTA-TATTTATATTTATT
1 TTTATTATTTATATTTATT
**
23925 AGTATTATTT-TATTTATT
1 TTTATTATTTATATTTATT
23943 TTTATT-TTTAT
1 TTTATTATTTAT
23954 GACACCAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
17 3 0.13
18 15 0.65
19 5 0.22
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTATTATTTATATTTATT
Found at i:39599 original size:6 final size:6
Alignment explanation
Indices: 39588--39613 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39578 CAAGTCACTT
39588 ACAAGC ACAAGC ACAAGC ACAAGC AC
1 ACAAGC ACAAGC ACAAGC ACAAGC AC
39614 CAGTACATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.15, T:0.00
Consensus pattern (6 bp):
ACAAGC
Found at i:44967 original size:19 final size:20
Alignment explanation
Indices: 44938--44978 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
44928 GGGAGAATTT
44938 TTTTTTCAGTCTTTATTTAG
1 TTTTTTCAGTCTTTATTTAG
44958 TTTTTT-AGTCTTTATTTAG
1 TTTTTTCAGTCTTTATTTAG
44977 TT
1 TT
44979 GCTCCTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (20 bp):
TTTTTTCAGTCTTTATTTAG
Found at i:51173 original size:35 final size:33
Alignment explanation
Indices: 51115--51916 Score: 544
Period size: 35 Copynumber: 23.4 Consensus size: 33
51105 TCTCTACTTC
* *
51115 TTACTAA--ACTTAATTATCTTGAATTAAGTTGA
1 TTACTAACTACTTAATTACCCTGAATTAAGTT-A
* *
51147 TTACTAAACTACTTAATTGCCCTGAATTAAATTAA
1 TTACT-AACTACTTAATTACCCTGAATTAAGTT-A
* * * *
51182 TAACTGAATTACTTAATTACCCTAAATTAAGTTT
1 TTACT-AACTACTTAATTACCCTGAATTAAGTTA
** *
51216 TTTTTAAAGAGTTACTTAATTACCCTGAATTAAGTTA
1 TTACT--A-A-CTACTTAATTACCCTGAATTAAGTTA
* * * *
51253 CTAAATGACCTGCTTAATTACCCTGAATTAAG---
1 -TTACT-AACTACTTAATTACCCTGAATTAAGTTA
* **
51285 CTACGT-ACTGACTTAATCGCCCTGAATTAAGCTTA
1 TTAC-TAACT-ACTTAATTACCCTGAATTAAG-TTA
* * *
51320 TTACTGAATTACTTAATTACCCTGAAATAAGTTTC
1 TTACT-AACTACTTAATTACCCTGAATTAAG-TTA
* **
51355 TTAATGAGTTACTTAATTACCCTGAATTAAGTTA
1 TTACT-AACTACTTAATTACCCTGAATTAAGTTA
* ** * *
51389 CTAACTGGCCTGCTTAATTACCCTGAATTAAGCTA
1 -TTACT-AACTACTTAATTACCCTGAATTAAGTTA
* ***
51424 CTTACT---GACTTAATCGTCCTGAATTAAGCTTA
1 -TTACTAACTACTTAATTACCCTGAATTAAG-TTA
51456 TTACTGAA-TCACTTAATTACCCTGAATTAAAGTTGA
1 TTACT-AACT-ACTTAATTACCCTGAATT-AAGTT-A
* *
51492 CTACTGACTCACTTAATTACCCTGAATTAAGTTGA
1 TTACTAACT-ACTTAATTACCCTGAATTAAGTT-A
**
51527 TTACCGACTCACTTAATTACCCTGAATTAAAGTTGA
1 TTACTAACT-ACTTAATTACCCTGAATT-AAGTT-A
*
51563 TTACTGACTCACTTAATTACCCTGAATTAAAGTTGA
1 TTACTAACT-ACTTAATTACCCTGAATT-AAGTT-A
* *
51599 TTACTGACTCACTTAATTACCCTGAACTAAGTTGA
1 TTACTAACT-ACTTAATTACCCTGAATTAAGTT-A
*
51634 TTACTGAATTACTTAATTACCCTGAATTAAGTTA
1 TTACT-AACTACTTAATTACCCTGAATTAAGTTA
* * *
51668 TTGC---CTTACTTAATTTCCCTGAACTAAGTTA
1 TTACTAAC-TACTTAATTACCCTGAATTAAGTTA
* * *
51699 CTAACTGACTTTACTTAATTACCCTGAATTAAGCTA
1 -TTACTAAC--TACTTAATTACCCTGAATTAAGTTA
* *
51735 CTTACT---GACTTAATTACCCTGAATTAAGCTA
1 -TTACTAACTACTTAATTACCCTGAATTAAGTTA
*
51766 CTTACTGACTCACTTAATTACCCTGAATTAAGTTGA
1 -TTACTAACT-ACTTAATTACCCTGAATTAAGTT-A
*
51802 TTACTTAATTACTTAATTACCCTGAATTAAGTTA
1 TTAC-TAACTACTTAATTACCCTGAATTAAGTTA
*
51836 TTGC---CTTACTTAATTACCCTGAATTAAGTTGA
1 TTACTAAC-TACTTAATTACCCTGAATTAAGTT-A
*
51868 TTACTGACTTACTTAATTACCCTGAATTAAGTTA
1 TTACTAAC-TACTTAATTACCCTGAATTAAGTTA
*
51902 CTTATTAACTCACTT
1 -TTACTAACT-ACTT
51917 TTCCTTACTT
Statistics
Matches: 635, Mismatches: 90, Indels: 87
0.78 0.11 0.11
Matches are distributed among these distances:
30 2 0.00
31 118 0.19
32 14 0.02
33 2 0.00
34 15 0.02
35 323 0.51
36 134 0.21
37 25 0.04
38 2 0.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (33 bp):
TTACTAACTACTTAATTACCCTGAATTAAGTTA
Found at i:51747 original size:17 final size:17
Alignment explanation
Indices: 51722--51773 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
51712 CTTAATTACC
51722 CTGAATTAAGCTACTTA
1 CTGAATTAAGCTACTTA
* * *
51739 CTGACTTAA-TTAC--C
1 CTGAATTAAGCTACTTA
51753 CTGAATTAAGCTACTTA
1 CTGAATTAAGCTACTTA
51770 CTGA
1 CTGA
51774 CTCACTTAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
14 8 0.31
15 3 0.12
16 3 0.12
17 12 0.46
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (17 bp):
CTGAATTAAGCTACTTA
Found at i:51806 original size:66 final size:66
Alignment explanation
Indices: 51122--51916 Score: 593
Period size: 66 Copynumber: 11.6 Consensus size: 66
51112 TTCTTACTAA
* * * * * *
51122 ACTTAATTATCTTGAATTAAGTTGA-TTACTAAACT-ACTTAATTGCCCTGAATTAAATTAATAA
1 ACTTAATTACCCTGAATTAAGTT-ACTTACT-GACTCACTTAATTACCCTGAATTAAGTT-ATTA
51185 CTGAATT
63 CTG---T
* ** ** * * *
51192 ACTTAATTACCCTAAATTAAGTTTTTTTTAAAGAGTTACTTAATTACCCTGAATTAAGTTACTAA
1 ACTTAATTACCCTGAATTAAG--TTACTTACTGACTCACTTAATTACCCTGAATTAAGTTA-TTA
*
51257 ATGACCT
63 CTG---T
* * * **
51264 GCTTAATTACCCTGAATTAAGCTACGTACTG----ACTTAATCGCCCTGAATTAAGCTTATTACT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTCACTTAATTACCCTGAATTAAG-TTATTACT
51325 GAATT
65 G---T
* * * * * *
51330 ACTTAATTACCCTGAAATAAGTTTCTTAATGAGTTACTTAATTACCCTGAATTAAGTTACTAACT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTCACTTAATTACCCTGAATTAAGTTA-TTACT
51395 GGCCT
65 -G--T
* * ***
51400 GCTTAATTACCCTGAATTAAGCTACTTACTG----ACTTAATCGTCCTGAATTAAGCTTATTACT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTCACTTAATTACCCTGAATTAAG-TTATTACT
51461 GAAT
65 G--T
51465 CACTTAATTACCCTGAATTAAAGTTGAC-TACTGACTCACTTAATTACCCTGAATTAAGTTGATT
1 -ACTTAATTACCCTGAATT-AAGTT-ACTTACTGACTCACTTAATTACCCTGAATTAAGTT-ATT
*
51529 ACCGACT
62 ACTG--T
51536 CACTTAATTACCCTGAATTAAAGTTGA-TTACTGACTCACTTAATTACCCTGAATTAAAGTTGAT
1 -ACTTAATTACCCTGAATT-AAGTT-ACTTACTGACTCACTTAATTACCCTGAATT-AAGTT-AT
51600 TACTGACT
61 TACTG--T
* * * *
51608 CACTTAATTACCCTGAACTAAGTTGA-TTACTGAATTACTTAATTACCCTGAATTAAGTTATTGC
1 -ACTTAATTACCCTGAATTAAGTT-ACTTACTGACTCACTTAATTACCCTGAATTAAGTTATT-A
51672 CT-T
63 CTGT
* * * * *
51675 ACTTAATTTCCCTGAACTAAGTTACTAACTGACTTTACTTAATTACCCTGAATTAAGCTACTTAC
1 ACTTAATTACCCTGAATTAAGTTACTTACTGAC-TCACTTAATTACCCTGAATTAAGTTA-TTAC
51740 TG-
64 TGT
*
51742 ACTTAATTACCCTGAATTAAGCTACTTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTCACTTAATTACCCTGAATTAAGTT-ATTAC-
*
51807 TAATT
64 T--GT
* *
51812 ACTTAATTACCCTGAATTAAGTTA--T--TGCCTTACTTAATTACCCTGAATTAAGTTGATTACT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTCACTTAATTACCCTGAATTAAGTT-ATTACT
51873 GACTT
65 G---T
* *
51878 ACTTAATTACCCTGAATTAAGTTACTTATTAACTCACTT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTCACTT
51917 TTCCTTACTT
Statistics
Matches: 605, Mismatches: 80, Indels: 80
0.79 0.10 0.10
Matches are distributed among these distances:
65 4 0.01
66 202 0.33
67 74 0.12
68 6 0.01
69 6 0.01
70 111 0.18
71 117 0.19
72 85 0.14
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (66 bp):
ACTTAATTACCCTGAATTAAGTTACTTACTGACTCACTTAATTACCCTGAATTAAGTTATTACTG
T
Found at i:54401 original size:22 final size:22
Alignment explanation
Indices: 54357--54401 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
54347 TACCAAATGT
* *
54357 AAAATGCTTGCTTAAAAGTTTA
1 AAAATGCTAGCTTAAAAATTTA
54379 AAAATGCTAGC-TAAAAATATTA
1 AAAATGCTAGCTTAAAAAT-TTA
54401 A
1 A
54402 CATGTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (22 bp):
AAAATGCTAGCTTAAAAATTTA
Found at i:55787 original size:106 final size:106
Alignment explanation
Indices: 55656--55898 Score: 353
Period size: 106 Copynumber: 2.3 Consensus size: 106
55646 TAAAATAAGT
* * *
55656 AACTGAAGAAAAACCACCCTGGATCATTCCAAACTGAATTGAAGAACGACCACCCTCGATCATTC
1 AACTGAAG-AAGACCACCCTGGATCATTCCAAACTGAACTGAAGAACAACCACCCTCGATCATTC
*
55721 CGACGCAAACTGAAGAAAGACCACCCT-GGTCAACTGAAATA
65 CGACGAAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATA
* **
55762 AACTGAAGAACGACCACCCTCGATCATTCCGGACTGAACTGAAGAACAACCACCCTCGATCATTC
1 AACTGAAGAA-GACCACCCTGGATCATTCCAAACTGAACTGAAGAACAACCACCCTCGATCATTC
* *
55827 CGACTAAAACTGAAGAAAGACCACCTTGGGTCAACTGAAATA
65 CGACGAAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATA
* *
55869 AACTAAAGGAAGATCACCCTGGATCATTCC
1 AACTGAA-GAAGACCACCCTGGATCATTCC
55899 GACACAAACT
Statistics
Matches: 122, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
105 2 0.02
106 80 0.66
107 37 0.30
108 3 0.02
ACGTcount: A:0.38, C:0.28, G:0.16, T:0.17
Consensus pattern (106 bp):
AACTGAAGAAGACCACCCTGGATCATTCCAAACTGAACTGAAGAACAACCACCCTCGATCATTCC
GACGAAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATA
Found at i:55901 original size:71 final size:70
Alignment explanation
Indices: 55798--56038 Score: 308
Period size: 71 Copynumber: 3.4 Consensus size: 70
55788 TTCCGGACTG
* *
55798 AACTGAAGAACAACCACCCTCGATCATTCCGACTA-AAACTGAAGAAAGACCACCTTGGGTCAAC
1 AACTGAAGAACGACCACCCTCGATCATTCCGAC-ACAAACTGATGAAAGACCACC-TGGGTCAAC
55862 TGAAATA
64 TGAAATA
* * *
55869 AACTAAAGGAA-GATCACCCTGGATCATTCCGACACAAACTGATGAAAGACCACCCTGGGTCAAC
1 AACTGAA-GAACGACCACCCTCGATCATTCCGACACAAACTGATGAAAGACCA-CCTGGGTCAAC
55933 TGAAATA
64 TGAAATA
* * * * * *
55940 TACTGAAGAATGACCACCCTCGATCA-TCCTGAAATAAATTGATGGAAGACCATCCTGGGTCAAC
1 AACTGAAGAACGACCACCCTCGATCATTCC-GACACAAACTGATGAAAGACCA-CCTGGGTCAAC
56004 TGAAATA
64 TGAAATA
56011 AACTGAAGAACGACCACCCTCGATCATT
1 AACTGAAGAACGACCACCCTCGATCATT
56039 TTGAAATAAA
Statistics
Matches: 148, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
70 7 0.05
71 135 0.91
72 6 0.04
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.19
Consensus pattern (70 bp):
AACTGAAGAACGACCACCCTCGATCATTCCGACACAAACTGATGAAAGACCACCTGGGTCAACTG
AAATA
Found at i:55921 original size:107 final size:106
Alignment explanation
Indices: 55668--55924 Score: 333
Period size: 106 Copynumber: 2.4 Consensus size: 106
55658 CTGAAGAAAA
* * * *
55668 ACCACCCTGGATCATTCC-AAACTGAATTGAAGAACGACCACCCTCGATCATTCCGACGCAAACT
1 ACCACCCTGGATCATTCCGACAC-GAACTGAAGAAAGACCACCCTCGATCATTCCGACGAAAACT
*
55732 GAAGAAAGACCACCCTGGTCAACTGAAATAAACTGAAGAACG
65 GAAGAAAGACCACCCTGGTCAACTGAAATAAACTAAAGAACG
* * *
55774 ACCACCCTCGATCATTCCGGAC-TGAACTGAAGAACA-ACCACCCTCGATCATTCCGACTAAAAC
1 ACCACCCTGGATCATTCC-GACACGAACTGAAGAA-AGACCACCCTCGATCATTCCGACGAAAAC
*
55837 TGAAGAAAGACCACCTTGGGTCAACTGAAATAAACTAAAGGAA-G
64 TGAAGAAAGACCACCCT-GGTCAACTGAAATAAACTAAA-GAACG
* * *
55881 ATCACCCTGGATCATTCCGACACAAACTGATGAAAGACCACCCT
1 ACCACCCTGGATCATTCCGACACGAACTGAAGAAAGACCACCCT
55925 GGGTCAACTG
Statistics
Matches: 130, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
106 72 0.55
107 54 0.42
108 4 0.03
ACGTcount: A:0.37, C:0.30, G:0.16, T:0.17
Consensus pattern (106 bp):
ACCACCCTGGATCATTCCGACACGAACTGAAGAAAGACCACCCTCGATCATTCCGACGAAAACTG
AAGAAAGACCACCCTGGTCAACTGAAATAAACTAAAGAACG
Found at i:56054 original size:36 final size:36
Alignment explanation
Indices: 55656--56054 Score: 276
Period size: 36 Copynumber: 11.2 Consensus size: 36
55646 TAAAATAAGT
** * * *
55656 AACTGAAGAAAAACCACCCTGGATCATTC-CAAACTG
1 AACTGAAGAACGACCACCCTCGATCATTCTGAAA-TA
* * ***
55692 AATTGAAGAACGACCACCCTCGATCATTCCGACGCA
1 AACTGAAGAACGACCACCCTCGATCATTCTGAAATA
* * *
55728 AACTGAAGAAAGACCACCCT-GGTCA-ACTGAAATA
1 AACTGAAGAACGACCACCCTCGATCATTCTGAAATA
* * * *
55762 AACTGAAGAACGACCACCCTCGATCATTCCGGACTG
1 AACTGAAGAACGACCACCCTCGATCATTCTGAAATA
* * *
55798 AACTGAAGAACAACCACCCTCGATCATTCCG-ACTAA
1 AACTGAAGAACGACCACCCTCGATCATTCTGAAAT-A
* * * * *
55834 AACTGAAGAAAGACCACCTTGGGTCA-ACTGAAATA
1 AACTGAAGAACGACCACCCTCGATCATTCTGAAATA
* * * * * *
55869 AACTAAAGGAA-GATCACCCTGGATCATTCCGACACA
1 AACTGAA-GAACGACCACCCTCGATCATTCTGAAATA
* * * * *
55905 AACTGATGAAAGACCACCCTGGGTCA-ACTGAAATA
1 AACTGAAGAACGACCACCCTCGATCATTCTGAAATA
* * *
55940 TACTGAAGAATGACCACCCTCGATCATCCTGAAATA
1 AACTGAAGAACGACCACCCTCGATCATTCTGAAATA
* * * * * *
55976 AATTGATGGAA-GACCATCCTGGGTCA-ACTGAAATA
1 AACTGA-AGAACGACCACCCTCGATCATTCTGAAATA
*
56011 AACTGAAGAACGACCACCCTCGATCATTTTGAAATA
1 AACTGAAGAACGACCACCCTCGATCATTCTGAAATA
*
56047 AATTGAAG
1 AACTGAAG
56055 TACTAAATGA
Statistics
Matches: 280, Mismatches: 71, Indels: 24
0.75 0.19 0.06
Matches are distributed among these distances:
34 26 0.09
35 86 0.31
36 164 0.59
37 4 0.01
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (36 bp):
AACTGAAGAACGACCACCCTCGATCATTCTGAAATA
Found at i:56121 original size:34 final size:35
Alignment explanation
Indices: 56067--56161 Score: 95
Period size: 34 Copynumber: 2.7 Consensus size: 35
56057 CTAAATGAAG
* *
56067 AATTGAAGAAAGACCACCCTGGATCATTG-AAGTA
1 AATTGAAGAAAGATCGCCCTGGATCATTGAAAGTA
* * * *
56101 AATTGAAGAATGATCGCCCTGAACCAATTGAAATTA
1 AATTGAAGAAAGATCGCCCTGGATC-ATTGAAAGTA
* *
56137 ACTT-AAGAAAAATCGCCCTGGATCA
1 AATTGAAGAAAGATCGCCCTGGATCA
56162 GTTCACTTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
34 21 0.44
35 20 0.42
36 7 0.15
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (35 bp):
AATTGAAGAAAGATCGCCCTGGATCATTGAAAGTA
Found at i:57585 original size:16 final size:16
Alignment explanation
Indices: 57565--57610 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
57555 TAGAGCTTTA
57565 TCTCTTTTCTTCTTTTC
1 TCTCTTTTCTT-TTTTC
*
57582 -CTCTTTCCTTTTTTC
1 TCTCTTTTCTTTTTTC
*
57597 TTTCTTTTCTTTTT
1 TCTCTTTTCTTTTT
57611 CGATCGCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TCTCTTTTCTTTTTTC
Found at i:57743 original size:13 final size:13
Alignment explanation
Indices: 57715--57762 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
57705 ATAAATCAAT
*
57715 TTTTATTTTTAT-
1 TTTTATTTTTTTG
57727 TTTTATTTTTTTG
1 TTTTATTTTTTTG
* *
57740 TTTTGTTTTGTTG
1 TTTTATTTTTTTG
57753 TTTT-TTTTTT
1 TTTTATTTTTT
57763 GGACAATCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 16 0.52
13 15 0.48
ACGTcount: A:0.06, C:0.00, G:0.08, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTTTG
Found at i:58348 original size:26 final size:27
Alignment explanation
Indices: 58319--58369 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
58309 GCGACTCTTA
58319 AAAACC-TTT-TTGAAAACTCATTTTGG
1 AAAACCTTTTCTTGAAAAC-CATTTTGG
58345 AAAACCTTTTCTTGAAAACCATTTT
1 AAAACCTTTTCTTGAAAACCATTTT
58370 TTTGAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 6 0.26
27 9 0.39
28 8 0.35
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (27 bp):
AAAACCTTTTCTTGAAAACCATTTTGG
Found at i:58361 original size:14 final size:13
Alignment explanation
Indices: 58319--58377 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 13
58309 GCGACTCTTA
58319 AAAACC-TTTTTG
1 AAAACCTTTTTTG
* *
58331 AAAACTCATTTTGG
1 AAAAC-CTTTTTTG
58345 AAAACCTTTTCTTG
1 AAAACCTTTT-TTG
58359 AAAACCATTTTTTTG
1 AAAACC--TTTTTTG
58374 AAAA
1 AAAA
58378 ACGTCTCTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 5 0.13
13 5 0.13
14 18 0.46
15 7 0.18
16 4 0.10
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.39
Consensus pattern (13 bp):
AAAACCTTTTTTG
Found at i:58374 original size:15 final size:15
Alignment explanation
Indices: 58325--58377 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 15
58315 CTTAAAAACC
58325 TTTTTGAAAACTCA--
1 TTTTTGAAAAC-CATT
*
58339 TTTTGGAAAACC-TT
1 TTTTTGAAAACCATT
*
58353 TTCTTGAAAACCATT
1 TTTTTGAAAACCATT
58368 TTTTTGAAAA
1 TTTTTGAAAA
58378 ACGTCTCTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 1 0.03
14 20 0.62
15 11 0.34
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (15 bp):
TTTTTGAAAACCATT
Found at i:58515 original size:18 final size:18
Alignment explanation
Indices: 58450--58516 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 18
58440 ATTCTTTTTA
58450 TTCTCTTTTTGCGACCTCT
1 TTCT-TTTTTGCGACCTCT
* *
58469 TTCTTTTTTAG-GCCCAGTTTT
1 TTCTTTTTT-GCGACC---TCT
*
58490 TTCCTTTTTGCGACCTCT
1 TTCTTTTTTGCGACCTCT
58508 TTCTTTTTT
1 TTCTTTTTT
58517 AGGCCCAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
18 18 0.49
19 5 0.14
20 1 0.03
21 13 0.35
ACGTcount: A:0.06, C:0.25, G:0.10, T:0.58
Consensus pattern (18 bp):
TTCTTTTTTGCGACCTCT
Found at i:65938 original size:130 final size:130
Alignment explanation
Indices: 65705--65967 Score: 472
Period size: 130 Copynumber: 2.0 Consensus size: 130
65695 ATAGCAAGGC
65705 TTTCTACCTGCTTCCTTGTCCCTATTTGTTGCATGGCTGACACAGAAGACATGTGTGATGAATAA
1 TTTCTACCTGCTTCCTTGTCCCTATTTGTTGCATGGCTGACACAGAAGACATGTGTGATGAATAA
*
65770 GCGTTAAAGGTAGTAAGCGTTACACTAACGCGGGATTGGATGGAGTGGTAAGCAACTCATTCCAG
66 GCGTTAAAGGTAGTAAGCGTTACACTAACGCGGGATTGGATGAAGTGGTAAGCAACTCATTCCAG
* * *
65835 TTTCTACCTGCTTCCTTGTTCCTATTTGTTGCATGGTTGACATAGAAGACATGTGTGATGAATAA
1 TTTCTACCTGCTTCCTTGTCCCTATTTGTTGCATGGCTGACACAGAAGACATGTGTGATGAATAA
* *
65900 GCGTTAAAGGTCGTAAGCGTTATACTAACGCGGGATTGGATGAAGTGGTAAGCAACTCATTCCAG
66 GCGTTAAAGGTAGTAAGCGTTACACTAACGCGGGATTGGATGAAGTGGTAAGCAACTCATTCCAG
65965 TTT
1 TTT
65968 AAGTAGGTCT
Statistics
Matches: 127, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 127 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (130 bp):
TTTCTACCTGCTTCCTTGTCCCTATTTGTTGCATGGCTGACACAGAAGACATGTGTGATGAATAA
GCGTTAAAGGTAGTAAGCGTTACACTAACGCGGGATTGGATGAAGTGGTAAGCAACTCATTCCAG
Done.