Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009061.1 Corchorus capsularis cultivar CVL-1 contig09082, 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: 41808
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:673 original size:16 final size:16
Alignment explanation
Indices: 652--683 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
642 TGCCCTTGAA
652 GCCATTAATTGGACAT
1 GCCATTAATTGGACAT
668 GCCATTAATTGGACAT
1 GCCATTAATTGGACAT
684 AGGATATGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (16 bp):
GCCATTAATTGGACAT
Found at i:6400 original size:2 final size:2
Alignment explanation
Indices: 6395--6419 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6385 AATGTGTGTG
6395 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6420 GTTGAACTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10325 original size:31 final size:31
Alignment explanation
Indices: 10290--10402 Score: 105
Period size: 31 Copynumber: 3.9 Consensus size: 31
10280 TCATGTGGAT
*
10290 CAAAAAGTGACATGTGGCACGCCACGTGTGC
1 CAAAAAGTGACATGTGGCACGCCACGTGTAC
** *
10321 C--AAA---A-A-GTGGCACATCACATGTAC
1 CAAAAAGTGACATGTGGCACGCCACGTGTAC
* * *
10345 CAAAAAGTGATACGTGGCACGACACGTGTAC
1 CAAAAAGTGACATGTGGCACGCCACGTGTAC
*
10376 CAAAAAGTGACATGTGGCATGCCACGT
1 CAAAAAGTGACATGTGGCACGCCACGT
10403 TCACAAAAGG
Statistics
Matches: 64, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
24 15 0.23
25 1 0.02
26 4 0.06
29 4 0.06
30 1 0.02
31 39 0.61
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.17
Consensus pattern (31 bp):
CAAAAAGTGACATGTGGCACGCCACGTGTAC
Found at i:11226 original size:2 final size:2
Alignment explanation
Indices: 11219--11252 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
11209 AAGTATTTTA
*
11219 AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11253 TCAAAACAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13136 original size:2 final size:2
Alignment explanation
Indices: 13129--13158 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13119 GTGATCACTC
13129 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13159 GAATGGGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20521 original size:29 final size:29
Alignment explanation
Indices: 20458--20528 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
20448 ACACCGAACC
****
20458 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
20487 GCCAAATAAGCCCCTGAACTCTTAAAAAA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
20516 GTCAAATAAGCCC
1 GTCAAATAAGCCC
20529 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Found at i:21140 original size:31 final size:32
Alignment explanation
Indices: 21095--21160 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
21085 AAACTTTATG
* *
21095 TTTTCCGATAGTACCCTTTTTTTTAAAATATA
1 TTTTCCGATAGTACCCTTTTCTTTAAAACATA
*
21127 TTTT-CGATTGTACCCTTTTCTTTAAAACATA
1 TTTTCCGATAGTACCCTTTTCTTTAAAACATA
21158 TTT
1 TTT
21161 CTAAATTGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.52
Consensus pattern (32 bp):
TTTTCCGATAGTACCCTTTTCTTTAAAACATA
Found at i:21466 original size:19 final size:20
Alignment explanation
Indices: 21439--21477 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
21429 TACTATTATT
21439 TTTTGAATTT-AATATTTTAA
1 TTTTGAATTTCAAT-TTTTAA
21459 TTTT-AATTTCAATTTTTAA
1 TTTTGAATTTCAATTTTTAA
21478 ATGCCAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAA
Found at i:21698 original size:22 final size:22
Alignment explanation
Indices: 21670--21809 Score: 113
Period size: 22 Copynumber: 6.3 Consensus size: 22
21660 TGTCTCTATG
*
21670 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
21692 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
21715 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
21736 CGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
21758 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
21782 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
21804 TGGTTA
1 TGGTTA
21810 ATTATCACAA
Statistics
Matches: 94, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
21 3 0.03
22 71 0.76
23 3 0.03
24 17 0.18
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:21870 original size:22 final size:22
Alignment explanation
Indices: 21845--21903 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
21835 ATCAAAGAGA
*
21845 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
21867 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
*
21889 TTAACAAAATTTCAT
1 TTATCAAAATTTCAT
21904 TAAATATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:22022 original size:20 final size:22
Alignment explanation
Indices: 21999--22076 Score: 79
Period size: 25 Copynumber: 3.5 Consensus size: 22
21989 ATGAGTACCA
* *
21999 AAATTTGATAGAA-GGTTATC-
1 AAATTTCATAGAATGATTATCG
*
22019 AAATCTCATAGAATGATTATCG
1 AAATTTCATAGAATGATTATCG
*
22041 AAATTTCATAGAGATCGGATTATCA
1 AAATTTCATAGA-AT--GATTATCG
22066 AAATTTCATAG
1 AAATTTCATAG
22077 TGTTGTTATC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.23
21 6 0.12
22 11 0.23
23 2 0.04
25 18 0.38
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
AAATTTCATAGAATGATTATCG
Found at i:22131 original size:44 final size:44
Alignment explanation
Indices: 21922--22509 Score: 179
Period size: 44 Copynumber: 13.2 Consensus size: 44
21912 TCATGGGGAT
* * *
21922 GTTATCAAAATTTTATAATGTGGTTATCAAAATTTCATATGA-AG
1 GTTATCAAAATTTCATAATGTGATTATCAAAATTTCA-AAGAGAG
* * * * *
21966 GTTATAAAAGTCTCAATTTCATAA--TGAGTACCAAAATTTGATAGA-AG
1 GTTAT-CAA-----AATTTCATAATGTGATTATCAAAATTTCAAAGAGAG
* * * *
22013 GTTATC-AAATCTCATAGA-ATGATTATCGAAATTTCATAGAGATCG
1 GTTATCAAAATTTCATA-ATGTGATTATCAAAATTTCAAAGAGA--G
* *
22058 GATTATCAAAATTTCATAGTGTTG-TTATCAAAATTTCAAAGCGAG
1 G-TTATCAAAATTTCATAATG-TGATTATCAAAATTTCAAAGAGAG
* * * * *
22103 GTTATTAAAATTACATAATGTGATTATCAGAATTTCATAGAGGG
1 GTTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGAGAG
* * * * * *
22147 GTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAA-AGAG
1 GTTATCAAAATTTCATAATGTGATTATCAAAATTTCA-AAGAGAG
*
22191 GTTATC-AAATTTCCAAAATGTGATTA-CAAAAATTTCATAGTGGTATTTCTGTAGAG
1 GTTATCAAAATTT-CATAATGTGATTATC-AAAATTTCA-A-----A-----G-AGAG
* * * * *
22247 GTTATCAAAATTTCATAGTATGGTTA-CCAAA-TT--AGGA-AG
1 GTTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGAGAG
* * ** * *
22286 GTTATTAAACTTTTGTTATG-GAGTAATCAAAATTTC-AAG-GAG
1 GTTATCAAAATTTCATAATGTGA-TTATCAAAATTTCAAAGAGAG
* * *
22328 GATATCAAAA-TTC--AATGAGGA-TATCAAAATTTCATATGA-AG
1 GTTATCAAAATTTCATAATG-TGATTATCAAAATTTCA-AAGAGAG
* *
22369 GTTATCAAAATTTCATAAT-TTAGTTTTCAAAATTTCACAAGAG-G
1 GTTATCAAAATTTCATAATGTGA-TTATCAAAATTTCA-AAGAGAG
* * * * *
22413 GTTATCAAAATTTCATAGCATGT-A-GATCGAAATTTCACAGTGAC
1 GTTATCAAAATTTCATA--ATGTGATTATCAAAATTTCAAAGAGAG
* * * * * **
22457 ATTAACAAATTTTCATAATGAGGTTATCAAAAAATCATAA-AGAG
1 GTTATCAAAATTTCATAATGTGATTATCAAAATTTCA-AAGAGAG
22501 GTTATCAAA
1 GTTATCAAA
22510 TTTGTAGTTA
Statistics
Matches: 394, Mismatches: 95, Indels: 110
0.66 0.16 0.18
Matches are distributed among these distances:
38 1 0.00
39 31 0.08
40 13 0.03
41 21 0.05
42 35 0.09
43 13 0.03
44 170 0.43
45 9 0.02
46 8 0.02
47 36 0.09
48 15 0.04
49 1 0.00
50 9 0.02
51 1 0.00
54 2 0.01
55 3 0.01
56 20 0.05
57 6 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (44 bp):
GTTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGAGAG
Found at i:22156 original size:66 final size:65
Alignment explanation
Indices: 22058--22203 Score: 150
Period size: 66 Copynumber: 2.2 Consensus size: 65
22048 ATAGAGATCG
* ** * * * * *
22058 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATTAAAATTACATAAT
1 GATTATC-AAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAAA
*
22122 GT
64 GA
* *
22124 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAG
1 GATTATCA-AATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAAAG
22189 A
65 A
*
22190 GGTTATCAAATTTC
1 GATTATCAAATTTC
22204 CAAAATGTGA
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
65 7 0.11
66 57 0.86
67 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (65 bp):
GATTATCAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAAAGA
Found at i:22193 original size:22 final size:22
Alignment explanation
Indices: 21980--22203 Score: 131
Period size: 22 Copynumber: 10.3 Consensus size: 22
21970 TAAAAGTCTC
* *
21980 AATTTCATAATGA-G-TACCAA
1 AATTTCATAAAGAGGTTATCAA
* *
22000 AATTTGATAGA-AGGTTATC-A
1 AATTTCATAAAGAGGTTATCAA
* *
22020 AATCTCATAGAATGA--TTATCGA
1 AATTTCATA-AA-GAGGTTATCAA
*
22042 AATTTCATAGAGATCGGATTATCAA
1 AATTTCATAAAGA--GG-TTATCAA
** **
22067 AATTTCATAGTGTTGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
* *
22089 AATTTCA-AAGCGAGGTTATTAA
1 AATTTCATAA-AGAGGTTATCAA
* * * * *
22111 AATTACATAATGTGATTATCAG
1 AATTTCATAAAGAGGTTATCAA
* * * *
22133 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAAAGAGGTTATCAA
*
22155 AATTTTATAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
22177 AATTTCATAAAGAGGTTATC-A
1 AATTTCATAAAGAGGTTATCAA
22198 AATTTC
1 AATTTC
22204 CAAAATGTGA
Statistics
Matches: 153, Mismatches: 38, Indels: 25
0.71 0.18 0.12
Matches are distributed among these distances:
19 1 0.01
20 19 0.12
21 18 0.12
22 94 0.61
23 4 0.03
25 17 0.11
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
AATTTCATAAAGAGGTTATCAA
Found at i:22341 original size:19 final size:19
Alignment explanation
Indices: 22311--22358 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
22301 TTATGGAGTA
22311 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
*
22331 ATCAAAATTCAATGAGGAT
1 ATCAAAATTCAAGGAGGAT
22350 ATCAAAATT
1 ATCAAAATT
22359 TCATATGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:22487 original size:22 final size:22
Alignment explanation
Indices: 22311--22772 Score: 134
Period size: 22 Copynumber: 21.4 Consensus size: 22
22301 TTATGGAGTA
* *
22311 ATCAAAATTTC--AAGGAGGAT
1 ATCAAAATTTCATAATGAGGTT
*
22331 ATCAAAA-TTC--AATGAGGAT
1 ATCAAAATTTCATAATGAGGTT
22350 ATCAAAATTTCAT-ATGAAGGTT
1 ATCAAAATTTCATAATG-AGGTT
*
22372 ATCAAAATTTCATAATTTA-GTT
1 ATCAAAATTTCATAA-TGAGGTT
* *
22394 TTCAAAATTTCACAA-GAGGGTT
1 ATCAAAATTTCATAATGA-GGTT
22416 ATCAAAATTTCATAGCATGTA-G--
1 ATCAAAATTTCATA--ATG-AGGTT
* * * **
22438 ATCGAAATTTCACAGTGACATT
1 ATCAAAATTTCATAATGAGGTT
* *
22460 AACAAATTTTCATAATGAGGTT
1 ATCAAAATTTCATAATGAGGTT
** *
22482 ATCAAAAAATCATAAAGAGGTT
1 ATCAAAATTTCATAATGAGGTT
*
22504 ATC-AAA-TT--T-GT-A-GTT
1 ATCAAAATTTCATAATGAGGTT
* * ** **
22519 ATCAAGATTTTATAAGAAACTT
1 ATCAAAATTTCATAATGAGGTT
* ** *
22541 ATCAAAATTTTATAGGGAGATTT
1 ATCAAAATTTCATAATGAG-GTT
* * *
22564 ATCAAAATTTTAT-AGGAAGATTT
1 ATCAAAATTTCATAATG-AG-GTT
***
22587 ATCAAAATTTCATGGCGAGGTT
1 ATCAAAATTTCATAATGAGGTT
* *
22609 ATCACAATTTCATAAT-ATGATT
1 ATCAAAATTTCATAATGA-GGTT
*
22631 ATCAAAATTTCAGAGTATGA--TT
1 ATCAAAATTTCATA--ATGAGGTT
*
22653 A-CTAACAA-TTCAT-ATGGTGGTT
1 ATC-AA-AATTTCATAAT-GAGGTT
* * *
22675 -TTAAAATTTTCATAACGTGGTT
1 ATCAAAA-TTTCATAATGAGGTT
* *
22697 ATCAATATATCAT-ATGGAGGTT
1 ATCAAAATTTCATAAT-GAGGTT
* * * *
22719 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAATG-AGGTT
*
22742 ATCAAAATTTCATATTGAGGTCT
1 ATCAAAATTTCATAATGAGGT-T
22765 -TCAAAATT
1 ATCAAAATT
22773 CCTTAGGGAG
Statistics
Matches: 334, Mismatches: 65, Indels: 84
0.69 0.13 0.17
Matches are distributed among these distances:
15 6 0.02
16 3 0.01
17 2 0.01
18 1 0.00
19 22 0.07
20 17 0.05
21 12 0.04
22 198 0.59
23 64 0.19
24 6 0.02
25 2 0.01
26 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAATGAGGTT
Found at i:22569 original size:23 final size:23
Alignment explanation
Indices: 22517--22596 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
22507 AAATTTGTAG
* * * *
22517 TTATCAAGATTTTATA-AGAAAC
1 TTATCAAAATTTTATAGGGAGAT
22539 TTATCAAAATTTTATAGGGAGAT
1 TTATCAAAATTTTATAGGGAGAT
*
22562 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGAT
22585 TTATCAAAATTT
1 TTATCAAAATTT
22597 CATGGCGAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
22 15 0.29
23 37 0.71
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGAT
Found at i:22611 original size:45 final size:45
Alignment explanation
Indices: 22515--22642 Score: 136
Period size: 45 Copynumber: 2.8 Consensus size: 45
22505 TCAAATTTGT
* *
22515 AGTTATCAAGATTTTATAAGAA-ACTTATCAAAATTTTATAGGGAG
1 AGTTATCAAAATTTTATAAGAAGA-TTATCAAAATTTCATAGGGAG
* *
22560 ATTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCAT-GGCGAG
1 AGTTATCAAAATTTTATAAGAAGA-TTATCAAAATTTCATAGG-GAG
* * * *
22606 -GTTATCACAATTTCATAATATGATTATCAAAATTTCA
1 AGTTATCAAAATTTTATAAGAAGATTATCAAAATTTCA
22643 GAGTATGATT
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
44 14 0.20
45 38 0.54
46 18 0.26
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (45 bp):
AGTTATCAAAATTTTATAAGAAGATTATCAAAATTTCATAGGGAG
Found at i:23002 original size:2 final size:2
Alignment explanation
Indices: 22997--23023 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22987 AACTAGTGTG
22997 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
23024 TGGTACCTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27012 original size:2 final size:2
Alignment explanation
Indices: 27005--27040 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
26995 AAGAATTTGA
27005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27041 CAATCAAACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29435 original size:6 final size:6
Alignment explanation
Indices: 29424--29456 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
29414 TGAATGATAA
29424 AATTCC AATTCC AATTCC AATTCC AATTCC AAT
1 AATTCC AATTCC AATTCC AATTCC AATTCC AAT
29457 CTAGGAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (6 bp):
AATTCC
Found at i:35829 original size:29 final size:29
Alignment explanation
Indices: 35758--35815 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
35748 ATTAAAATTT
*
35758 CATACCTACATAAATTATTGAGTCGATTG
1 CATACCTACATGAATTATTGAGTCGATTG
35787 CATACCTACATGAATTATTGAGTCGATTG
1 CATACCTACATGAATTATTGAGTCGATTG
35816 GCGATTGCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (29 bp):
CATACCTACATGAATTATTGAGTCGATTG
Found at i:36200 original size:31 final size:32
Alignment explanation
Indices: 36155--36222 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 32
36145 AAAATGGAAA
* * *
36155 AATTACATAGTAATCCATTA-GATTTATATGT
1 AATTGCATAATAATCCACTAGGATTTATATGT
36186 AATTGCATAATAATCCACTAGGATTTATATGT
1 AATTGCATAATAATCCACTAGGATTTATATGT
36218 AATTG
1 AATTG
36223 TAGTTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 17 0.52
32 16 0.48
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (32 bp):
AATTGCATAATAATCCACTAGGATTTATATGT
Found at i:37716 original size:36 final size:36
Alignment explanation
Indices: 37669--37738 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
37659 GACCTTTGAG
*
37669 ATTACCCTAATTATTTTTTTATTATATAATTTTGCA
1 ATTACCCTAATTATATTTTTATTATATAATTTTGCA
*
37705 ATTACCTTAATTATATTTTTATTATATAATTTTG
1 ATTACCCTAATTATATTTTTATTATATAATTTTG
37739 TATGGTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (36 bp):
ATTACCCTAATTATATTTTTATTATATAATTTTGCA
Found at i:40060 original size:3 final size:3
Alignment explanation
Indices: 40052--40087 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
40042 TTACAAGTAT
40052 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40088 CTTGAATGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Done.