Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009608.1 Corchorus capsularis cultivar CVL-1 contig09629, 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: 71981
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:4388 original size:60 final size:60
Alignment explanation
Indices: 4295--4478 Score: 314
Period size: 60 Copynumber: 3.0 Consensus size: 60
4285 TCATCGTTCA
* * *
4295 TATCCTTGTCCCACAAGGGTTAGGAAAATATTCAAAGAATAAAAAATCAGATAATTGCCC
1 TATCCTTTTCCAATAAGGGTTAGGAAAATATTCAAAGAATAAAAAATCAGATAATTGCCC
4355 TATCCTTTTCCAATAAGGGTTAGGAAAATATTCAAAGAATAAAAAATCAGATAATTGCCC
1 TATCCTTTTCCAATAAGGGTTAGGAAAATATTCAAAGAATAAAAAATCAGATAATTGCCC
*
4415 TATCTTTTTCCAATAAGGGTTAGGAAAATATTCAAAGAATAAAAATAATCAGATAATTGCCC
1 TATCCTTTTCCAATAAGGGTTAGGAAAATATTCAAAGAAT-AAAA-AATCAGATAATTGCCC
4477 TA
1 TA
4479 ATATATTAAA
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
60 96 0.81
61 4 0.03
62 18 0.15
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (60 bp):
TATCCTTTTCCAATAAGGGTTAGGAAAATATTCAAAGAATAAAAAATCAGATAATTGCCC
Found at i:7460 original size:13 final size:13
Alignment explanation
Indices: 7442--7469 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
7432 AGTTGGGAAA
7442 ACTTTGTCACATT
1 ACTTTGTCACATT
7455 ACTTTGTCACATT
1 ACTTTGTCACATT
7468 AC
1 AC
7470 ATTCTGTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.43
Consensus pattern (13 bp):
ACTTTGTCACATT
Found at i:8827 original size:69 final size:69
Alignment explanation
Indices: 8711--8843 Score: 221
Period size: 69 Copynumber: 1.9 Consensus size: 69
8701 AAATTAGTAC
8711 TAATTGTCAAAAATGATTTTATTATTAATTTAAAAATAAATGCGGTTTAATTATATCAACACCCA
1 TAATTGTCAAAAATGATTTTATTATTAATTTAAAAATAAATGCGGTTTAATTATATCAACACCCA
8776 ATTT
66 ATTT
* * * * *
8780 TAATTGTCAATAATGGTTTTATTGTTAATTTAAAAATAATTGGGGTTTAATTATATCAACACCC
1 TAATTGTCAAAAATGATTTTATTATTAATTTAAAAATAAATGCGGTTTAATTATATCAACACCC
8844 TCAAATTGAG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (69 bp):
TAATTGTCAAAAATGATTTTATTATTAATTTAAAAATAAATGCGGTTTAATTATATCAACACCCA
ATTT
Found at i:11932 original size:36 final size:36
Alignment explanation
Indices: 11885--11965 Score: 153
Period size: 36 Copynumber: 2.2 Consensus size: 36
11875 TACTTTCTTT
11885 ATCATACTCGTCAGAGTCATACCCATACGGTGGAGA
1 ATCATACTCGTCAGAGTCATACCCATACGGTGGAGA
*
11921 ATCATACTCGTCAGAGTCATACTCATACGGTGGAGA
1 ATCATACTCGTCAGAGTCATACCCATACGGTGGAGA
11957 ATCATACTC
1 ATCATACTC
11966 TGTAGCCATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (36 bp):
ATCATACTCGTCAGAGTCATACCCATACGGTGGAGA
Found at i:11964 original size:21 final size:21
Alignment explanation
Indices: 11901--11965 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
11891 CTCGTCAGAG
*
11901 TCATACCCATACGGTGGAGAA
1 TCATACTCATACGGTGGAGAA
* *
11922 TCATA--C-T-C-GT-CAGAG
1 TCATACTCATACGGTGGAGAA
11937 TCATACTCATACGGTGGAGAA
1 TCATACTCATACGGTGGAGAA
11958 TCATACTC
1 TCATACTC
11966 TGTAGCCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 8 0.24
16 2 0.06
17 2 0.06
18 2 0.06
19 2 0.06
20 2 0.06
21 16 0.47
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
TCATACTCATACGGTGGAGAA
Found at i:13522 original size:157 final size:157
Alignment explanation
Indices: 13255--13693 Score: 851
Period size: 157 Copynumber: 2.8 Consensus size: 157
13245 AAGCGGGTTC
13255 GGGTTTTTCGAGTATAGGACTCAGATTCAATTGGGATTTTATTAAATAAAACATAATTTTAATTT
1 GGGTTTTTCGAGTATAGGACTCAGATTCAATTGGGATTTTATTAAATAAAACATAATTTTAATTT
13320 TATAATATCCTTGAATCATTCGAGTTAACTTCTTGAATTATTCACGTTATGGATTTGTTAATGTC
66 TATAATATCCTTGAATCATTCGAGTTAACTTCTTGAATTATTCACGTTATGGATTTGTTAATGTC
* *
13385 ACCCGGGTTCTAGGTCATTCGGGTTTT
131 ACCCAGGTTCTAGGTCATTCAGGTTTT
13412 GGGTTTTTCGAGTATAGGACTCAGATTCAATTGGGATTTTATTAAATAAAACATAATTTTAATTT
1 GGGTTTTTCGAGTATAGGACTCAGATTCAATTGGGATTTTATTAAATAAAACATAATTTTAATTT
*
13477 TATAATATCATTGAATCATTCGAGTTAACTTCTTGAATTATTCACGTTATGGATTTGTTAATGTC
66 TATAATATCCTTGAATCATTCGAGTTAACTTCTTGAATTATTCACGTTATGGATTTGTTAATGTC
13542 ACCCAGGTTCTAGGTCATTCAGGTTTT
131 ACCCAGGTTCTAGGTCATTCAGGTTTT
13569 GGGTTTTTCGAGTATAGGACTCAGATTCAATTGGGATTTTATTAAATAAAACATAATTTTAATTT
1 GGGTTTTTCGAGTATAGGACTCAGATTCAATTGGGATTTTATTAAATAAAACATAATTTTAATTT
13634 TATAATATCCTTGAATCATTCGAGTTAACTTCTTGAATTATTCACGTTATGGATTTGTTA
66 TATAATATCCTTGAATCATTCGAGTTAACTTCTTGAATTATTCACGTTATGGATTTGTTA
13694 GGAATCCATA
Statistics
Matches: 278, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 278 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (157 bp):
GGGTTTTTCGAGTATAGGACTCAGATTCAATTGGGATTTTATTAAATAAAACATAATTTTAATTT
TATAATATCCTTGAATCATTCGAGTTAACTTCTTGAATTATTCACGTTATGGATTTGTTAATGTC
ACCCAGGTTCTAGGTCATTCAGGTTTT
Found at i:17117 original size:2 final size:2
Alignment explanation
Indices: 17110--17138 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17100 AATTCCCAAC
17110 AT 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 AT A
17139 ATTCAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18943 original size:16 final size:16
Alignment explanation
Indices: 18909--18957 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
18899 AGTATGGAAA
*
18909 AGACAAGAGAATA-GAG
1 AGACAATAGAATATG-G
18925 AGACAATAGAATATGG
1 AGACAATAGAATATGG
*
18941 AG--AATAGAATATTG
1 AGACAATAGAATATGG
18955 AGA
1 AGA
18958 AGAAGAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 13 0.45
16 15 0.52
17 1 0.03
ACGTcount: A:0.53, C:0.04, G:0.27, T:0.16
Consensus pattern (16 bp):
AGACAATAGAATATGG
Found at i:18948 original size:14 final size:14
Alignment explanation
Indices: 18929--18958 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18919 ATAGAGAGAC
18929 AATAGAATATGGAG
1 AATAGAATATGGAG
*
18943 AATAGAATATTGAG
1 AATAGAATATGGAG
18957 AA
1 AA
18959 GAAGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (14 bp):
AATAGAATATGGAG
Found at i:19188 original size:11 final size:11
Alignment explanation
Indices: 19174--19211 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19164 ATTCATAACA
19174 AATTTATAATT
1 AATTTATAATT
19185 AATTTATAATT
1 AATTTATAATT
19196 -ATTTGATAATT
1 AATTT-ATAATT
*
19207 TATTT
1 AATTT
19212 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:19433 original size:15 final size:15
Alignment explanation
Indices: 19415--19443 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19405 TGCAATTATA
19415 TTTATAATAATTACG
1 TTTATAATAATTACG
19430 TTTATAATAATTAC
1 TTTATAATAATTAC
19444 ATTCACATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (15 bp):
TTTATAATAATTACG
Found at i:27256 original size:57 final size:57
Alignment explanation
Indices: 27182--27295 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
27172 CACGCCACAC
*
27182 GCAAATATTTAAGAACCTACTTGGATGTTAAAGTTTAAAGTTTAAACCTTTTAACTT
1 GCAAATATTTAAGAACCTACTTGGATGTTAAAGTTTAAAGTTTAAACCTTATAACTT
*
27239 GCAAATATTTAGGAACCTACTTGGATGTTAAAGTTTAAAGTTTAAACCTTATAACTT
1 GCAAATATTTAAGAACCTACTTGGATGTTAAAGTTTAAAGTTTAAACCTTATAACTT
27296 CCAAGTCAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (57 bp):
GCAAATATTTAAGAACCTACTTGGATGTTAAAGTTTAAAGTTTAAACCTTATAACTT
Found at i:28946 original size:6 final size:6
Alignment explanation
Indices: 28935--29004 Score: 86
Period size: 6 Copynumber: 11.2 Consensus size: 6
28925 GATATCAAGT
* **
28935 TCATGG TCATGG TCATAGAGG TCATGG TCATGG TCATGG GCATTT TCATGG
1 TCATGG TCATGG TCAT---GG TCATGG TCATGG TCATGG TCATGG TCATGG
28986 TCATGG TCATGG TCATGG T
1 TCATGG TCATGG TCATGG T
29005 TCTATCTTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
6 49 0.89
9 6 0.11
ACGTcount: A:0.19, C:0.16, G:0.31, T:0.34
Consensus pattern (6 bp):
TCATGG
Found at i:31782 original size:2 final size:2
Alignment explanation
Indices: 31775--31799 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31765 ATTAATTCAA
31775 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 A
31800 CTAGTAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32507 original size:99 final size:100
Alignment explanation
Indices: 32396--32595 Score: 366
Period size: 101 Copynumber: 2.0 Consensus size: 100
32386 TACATTTTTA
* *
32396 GAAATTTTAGTAACAATTCAATAAT-AAGTTACCCAATATATTTTTATTTTAGGTTACTAAAAAT
1 GAAATTTTAGTAACAATTCAATAATAAAGTTACCCAATATATTTTTATATAAGGTTACTAAAAAT
32460 GCTACACAAATTGTCAAAGATGTTATATTTCTATC
66 GCTACACAAATTGTCAAAGATGTTATATTTCTATC
32495 GAAATTTTAGTAACAATTCAATAATGAAAGTTACCCAATATATTTTTATATAAGGTTACTAAAAA
1 GAAATTTTAGTAACAATTCAATAAT-AAAGTTACCCAATATATTTTTATATAAGGTTACTAAAAA
32560 TGCTACACAAATTGTCAAAGATGTTATATTTCTATC
65 TGCTACACAAATTGTCAAAGATGTTATATTTCTATC
32596 AATAATTTCA
Statistics
Matches: 97, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
99 25 0.26
101 72 0.74
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.38
Consensus pattern (100 bp):
GAAATTTTAGTAACAATTCAATAATAAAGTTACCCAATATATTTTTATATAAGGTTACTAAAAAT
GCTACACAAATTGTCAAAGATGTTATATTTCTATC
Found at i:36896 original size:159 final size:161
Alignment explanation
Indices: 36597--36906 Score: 518
Period size: 159 Copynumber: 1.9 Consensus size: 161
36587 TATCAACAAA
36597 TTAATAACTAACCTTAAATCCTTAATAACTTAATAACCTTTCATCAAAAGTCATTAAAAAAAGCT
1 TTAATAACTAACCTTAAATCCTTAATAACTTAATAACCTTTCATCAAAAGTCATTAAAAAAAGCT
36662 ATAAAATTGAGTAGTATTAAAAATGTTGTATTGCTATAAAAGAAAATTTTGATGTTCTCACAACA
66 AT-AAA-T-AGTAGTATTAAAAATGTTGTATTGCTATAAAAGAAAATTTTGATGTTCTCACAACA
36727 ATTATGATGCTAGCAATTCAATTATCTTGCATCT
128 ATTATGATGCTAGCAATTCAATTATCTTGCATCT
*
36761 TTAATAAGTAACCTTAAATCCTTAATAACTTAATAACCTTTCATCAAAAGTCA-TAAAACAAAGC
1 TTAATAACTAACCTTAAATCCTTAATAACTTAATAACCTTTCATCAAAAGTCATTAAAA-AAAGC
* * *
36825 TAT-AA-AGTAGTATTATAAATGTTGTATTGCTATAAAAGAAGATTTTGATGTTCTGACAACAAT
65 TATAAATAGTAGTATTAAAAATGTTGTATTGCTATAAAAGAAAATTTTGATGTTCTCACAACAAT
*
36888 TATGATGCTATCAATTCAA
130 TATGATGCTAGCAATTCAA
36907 CTTTCTCACA
Statistics
Matches: 140, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
159 73 0.52
162 2 0.01
163 5 0.04
164 60 0.43
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.35
Consensus pattern (161 bp):
TTAATAACTAACCTTAAATCCTTAATAACTTAATAACCTTTCATCAAAAGTCATTAAAAAAAGCT
ATAAATAGTAGTATTAAAAATGTTGTATTGCTATAAAAGAAAATTTTGATGTTCTCACAACAATT
ATGATGCTAGCAATTCAATTATCTTGCATCT
Found at i:39774 original size:18 final size:17
Alignment explanation
Indices: 39747--39782 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
39737 TTTCTCTTCA
39747 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
39764 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
39782 T
1 T
39783 TTAGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:40548 original size:20 final size:21
Alignment explanation
Indices: 40512--40559 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
40502 TAGATTTAGA
*
40512 TTTAATTTAATTTGCTTTGTT
1 TTTAATTTAATTTGCTTTCTT
*
40533 TTTAGTTTAA-TTGCTTTCTT
1 TTTAATTTAATTTGCTTTCTT
40553 TTTAATT
1 TTTAATT
40560 GATAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.19, C:0.06, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTAATTTAATTTGCTTTCTT
Found at i:40916 original size:26 final size:27
Alignment explanation
Indices: 40863--40922 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
40853 TAATGCACCC
* * *
40863 AAAACATTTTAATAAAAATCATTTATA
1 AAAACAATTTAATAAAAATCAGTAATA
*
40890 AAAACAATTTATTAAAAAT-AGTAATA
1 AAAACAATTTAATAAAAATCAGTAATA
40916 AAAACAA
1 AAAACAA
40923 GTCCCTCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAACAATTTAATAAAAATCAGTAATA
Found at i:41523 original size:16 final size:15
Alignment explanation
Indices: 41498--41558 Score: 56
Period size: 16 Copynumber: 4.0 Consensus size: 15
41488 TAATTCTCCC
41498 TTTT-TTTATTATTA
1 TTTTATTTATTATTA
41512 TTATTATTTATTTAATT-
1 TT-TTATTTA-TT-ATTA
41529 TTTTATTT-TTATTA
1 TTTTATTTATTATTA
*
41543 TTTTTATTTTTTATTA
1 -TTTTATTTATTATTA
41559 ACATAATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.08
14 4 0.10
15 10 0.25
16 16 0.40
17 4 0.10
18 3 0.08
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTTATTATTA
Found at i:41534 original size:22 final size:22
Alignment explanation
Indices: 41509--41558 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
41499 TTTTTTATTA
41509 TTATTATTATT-TATTTAATTTT
1 TTATTATTATTAT-TTTAATTTT
* *
41531 TTATTTTTATTATTTTTATTTT
1 TTATTATTATTATTTTAATTTT
41553 TTATTA
1 TTATTA
41559 ACATAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (22 bp):
TTATTATTATTATTTTAATTTT
Found at i:41572 original size:34 final size:33
Alignment explanation
Indices: 41498--41573 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 33
41488 TAATTCTCCC
* **
41498 TTTTTTTATTATTATTATTATTTATTTAATTTT
1 TTTTTTTATTATTATTATTATTTATTAAATAAT
* *
41531 TTATTTTTATTATTTTTATTTTTTATTAACATAAT
1 TT-TTTTTATTATTATTATTATTTATTAA-ATAAT
41566 TTTTTTTA
1 TTTTTTTA
41574 AAGAACCGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 2 0.06
34 29 0.81
35 5 0.14
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (33 bp):
TTTTTTTATTATTATTATTATTTATTAAATAAT
Found at i:55620 original size:25 final size:27
Alignment explanation
Indices: 55568--55620 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
55558 TTACTCAACT
**
55568 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
55595 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
55620 A
1 A
55621 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:65267 original size:36 final size:36
Alignment explanation
Indices: 65220--65291 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
65210 CAATTGGTTG
65220 TGCTTTGTTTCATTGTAGTTTTCTCATAAGTGATTA
1 TGCTTTGTTTCATTGTAGTTTTCTCATAAGTGATTA
65256 TGCTTTGTTTCATTGTAGTTTTCTCATAAGTGATTA
1 TGCTTTGTTTCATTGTAGTTTTCTCATAAGTGATTA
65292 AGCAATTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.11, G:0.17, T:0.53
Consensus pattern (36 bp):
TGCTTTGTTTCATTGTAGTTTTCTCATAAGTGATTA
Found at i:65607 original size:29 final size:30
Alignment explanation
Indices: 65524--65611 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 30
65514 TTTAGTTTCT
65524 ACTATAATCTTAGTGAATCCTTTGTTTGGAG
1 ACTATAATCTTAGTGAATCCTTTGTTT-GAG
** * ** * * *
65555 AGGAGAAAATAAGAGAATCGTTTGTTTGA-
1 ACTATAATCTTAGTGAATCCTTTGTTTGAG
65584 ACTATAATCTTAGTGAATCCTTTGTTTG
1 ACTATAATCTTAGTGAATCCTTTGTTTG
65612 GAGAGGAGAA
Statistics
Matches: 41, Mismatches: 16, Indels: 2
0.69 0.27 0.03
Matches are distributed among these distances:
29 20 0.49
30 2 0.05
31 19 0.46
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (30 bp):
ACTATAATCTTAGTGAATCCTTTGTTTGAG
Found at i:65617 original size:60 final size:61
Alignment explanation
Indices: 65524--65645 Score: 237
Period size: 60 Copynumber: 2.0 Consensus size: 61
65514 TTTAGTTTCT
65524 ACTATAATCTTAGTGAATCCTTTGTTTGGAGAGGAGAAAATAAGAGAATC-GTTTGTTTGA
1 ACTATAATCTTAGTGAATCCTTTGTTTGGAGAGGAGAAAATAAGAGAATCGGTTTGTTTGA
65584 ACTATAATCTTAGTGAATCCTTTGTTTGGAGAGGAGAAAATAAGAGAATCGGTTTGTTTGA
1 ACTATAATCTTAGTGAATCCTTTGTTTGGAGAGGAGAAAATAAGAGAATCGGTTTGTTTGA
65645 A
1 A
65646 GGAGAGAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 50 0.82
61 11 0.18
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (61 bp):
ACTATAATCTTAGTGAATCCTTTGTTTGGAGAGGAGAAAATAAGAGAATCGGTTTGTTTGA
Found at i:65640 original size:32 final size:31
Alignment explanation
Indices: 65538--65663 Score: 114
Period size: 31 Copynumber: 4.1 Consensus size: 31
65528 TAATCTTAGT
*
65538 GAATCCTTTGTTTGGAGAGGAGAAAATAAGA
1 GAATCGTTTGTTTGGAGAGGAGAAAATAAGA
** * ** * *
65569 GAATCGTTTGTTT-GA-ACTATAATCTTAGT
1 GAATCGTTTGTTTGGAGAGGAGAAAATAAGA
*
65598 GAATCCTTTGTTTGGAGAGGAGAAAATAAGA
1 GAATCGTTTGTTTGGAGAGGAGAAAATAAGA
* *
65629 GAATCGGTTTGTTTGAAG-GAGAGAAAAGAAGA
1 GAATC-GTTTGTTTGGAGAG-GAGAAAATAAGA
65661 GAA
1 GAA
65664 AATTAGTTGA
Statistics
Matches: 72, Mismatches: 19, Indels: 7
0.73 0.19 0.07
Matches are distributed among these distances:
29 19 0.26
30 4 0.06
31 25 0.35
32 24 0.33
ACGTcount: A:0.37, C:0.06, G:0.28, T:0.29
Consensus pattern (31 bp):
GAATCGTTTGTTTGGAGAGGAGAAAATAAGA
Found at i:65693 original size:43 final size:42
Alignment explanation
Indices: 65629--65724 Score: 156
Period size: 43 Copynumber: 2.2 Consensus size: 42
65619 GAAAATAAGA
65629 GAATCGGTTTGTTTGAAGGAGAGAAAAGAAGAGAAAATTAGTT
1 GAATC-GTTTGTTTGAAGGAGAGAAAAGAAGAGAAAATTAGTT
*
65672 GAATCGTTTGTTTGGATGGAGAGAAAAGAAGAGAAAATTAGTT
1 GAATCGTTTGTTT-GAAGGAGAGAAAAGAAGAGAAAATTAGTT
*
65715 GAATTGTTTG
1 GAATCGTTTG
65725 AGAAAAGAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
42 8 0.16
43 42 0.84
ACGTcount: A:0.39, C:0.02, G:0.30, T:0.29
Consensus pattern (42 bp):
GAATCGTTTGTTTGAAGGAGAGAAAAGAAGAGAAAATTAGTT
Found at i:65893 original size:18 final size:17
Alignment explanation
Indices: 65863--65900 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
65853 GATGGAAAAT
*
65863 GAGAAAACTAGAGACGA
1 GAGAAAAATAGAGACGA
65880 GAGAAAAATGAGAGACGA
1 GAGAAAAAT-AGAGACGA
65898 GAG
1 GAG
65901 TGTCAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.53, C:0.08, G:0.34, T:0.05
Consensus pattern (17 bp):
GAGAAAAATAGAGACGA
Found at i:68191 original size:12 final size:12
Alignment explanation
Indices: 68145--68197 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
68135 GATATCAACA
68145 AAATTTTTTCTT
1 AAATTTTTTCTT
*
68157 AATTTTTTATACGTT
1 AAATTTTT-T-C-TT
**
68172 GTATTTTTTCTT
1 AAATTTTTTCTT
68184 AAATTTTTTCTT
1 AAATTTTTTCTT
68196 AA
1 AA
68198 TTGGTTCTGG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
12 21 0.66
13 2 0.06
14 2 0.06
15 7 0.22
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.64
Consensus pattern (12 bp):
AAATTTTTTCTT
Done.