Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015088.1 Corchorus capsularis cultivar CVL-1 contig15109, 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: 90822
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:642 original size:68 final size:69
Alignment explanation
Indices: 533--684 Score: 252
Period size: 68 Copynumber: 2.2 Consensus size: 69
523 AATGTGACCA
* *
533 GAAATGCAGTAAGAACTATAAGCAATGTGACCAACCTAAAACTAACGATTCAGAAATGG-AATCA
1 GAAATACAGTAAGAACTATAAGCAATGTGACCAACCTAAAACTAACAATTCAGAAATGGAAATCA
*
597 CTAG
66 ATAG
601 GAAATACAGTAAGAACTATAAGCAATGTGACCAACCTAAAACTAACAATTCAGAAATGGAAATCA
1 GAAATACAGTAAGAACTATAAGCAATGTGACCAACCTAAAACTAACAATTCAGAAATGGAAATCA
*
666 ATAT
66 ATAG
*
670 GAAAAACAGTAAGAA
1 GAAATACAGTAAGAA
685 TCCTCACCTT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 57 0.73
69 21 0.27
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (69 bp):
GAAATACAGTAAGAACTATAAGCAATGTGACCAACCTAAAACTAACAATTCAGAAATGGAAATCA
ATAG
Found at i:11941 original size:21 final size:20
Alignment explanation
Indices: 11902--12091 Score: 221
Period size: 21 Copynumber: 9.4 Consensus size: 20
11892 GGCAATTAAC
* *
11902 AAGAGT-AATAGTGATCAGT
1 AAGAGTAAAAAGTAATCAGT
11921 AAGAGTAAAAAGATAATCAGT
1 AAGAGTAAAAAG-TAATCAGT
*
11942 ---A--AAATAGTAATCAGT
1 AAGAGTAAAAAGTAATCAGT
*
11957 AAGAGTAAAATAGTGATCAGT
1 AAGAGTAAAA-AGTAATCAGT
11978 AAGAGTAAAAAGATAATCAGT
1 AAGAGTAAAAAG-TAATCAGT
11999 AAGAGTAAAATAGTAATCAGT
1 AAGAGTAAAA-AGTAATCAGT
12020 AAGAGTAAAAAGATAATCAGT
1 AAGAGTAAAAAG-TAATCAGT
12041 AAGAGTAAAATAGTAATCAGT
1 AAGAGTAAAA-AGTAATCAGT
*
12062 AAGAGTAAAATGGTAATCAGT
1 AAGAGTAAAA-AGTAATCAGT
12083 AAGGAGTAA
1 AA-GAGTAA
12092 GATGGTAATT
Statistics
Matches: 151, Mismatches: 7, Indels: 23
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.05
16 5 0.03
18 2 0.01
19 6 0.04
20 11 0.07
21 109 0.72
22 10 0.07
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.22
Consensus pattern (20 bp):
AAGAGTAAAAAGTAATCAGT
Found at i:11944 original size:15 final size:15
Alignment explanation
Indices: 11924--11958 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
11914 GATCAGTAAG
11924 AGTAAAA-AGATAATC
1 AGTAAAATAG-TAATC
11939 AGTAAAATAGTAATC
1 AGTAAAATAGTAATC
11954 AGTAA
1 AGTAA
11959 GAGTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.57, C:0.06, G:0.14, T:0.23
Consensus pattern (15 bp):
AGTAAAATAGTAATC
Found at i:11985 original size:42 final size:42
Alignment explanation
Indices: 11939--12100 Score: 254
Period size: 42 Copynumber: 3.8 Consensus size: 42
11929 AAAGATAATC
*
11939 AGTAAAATAG-TAATCAGTAAGAGTAAAATAGTGATCAGTAAG
1 AGTAAAA-AGATAATCAGTAAGAGTAAAATAGTAATCAGTAAG
11981 AGTAAAAAGATAATCAGTAAGAGTAAAATAGTAATCAGTAAG
1 AGTAAAAAGATAATCAGTAAGAGTAAAATAGTAATCAGTAAG
12023 AGTAAAAAGATAATCAGTAAGAGTAAAATAGTAATCAGTAAG
1 AGTAAAAAGATAATCAGTAAGAGTAAAATAGTAATCAGTAAG
* * * *
12065 AGTAAAATGGTAATCAGTAAGGAGTAAGATGGTAAT
1 AGTAAAAAGATAATCAGTAA-GAGTAAAATAGTAAT
12101 TAGAAAAGAG
Statistics
Matches: 113, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
41 2 0.02
42 98 0.87
43 13 0.12
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.23
Consensus pattern (42 bp):
AGTAAAAAGATAATCAGTAAGAGTAAAATAGTAATCAGTAAG
Found at i:12012 original size:63 final size:63
Alignment explanation
Indices: 11908--12091 Score: 267
Period size: 63 Copynumber: 3.0 Consensus size: 63
11898 TAACAAGAGT
11908 AATAGTGATCAGTAAGAGTAAAAAGATAATC------AGTAAAATAGTAATCAGTAAGAGTAA
1 AATAGTGATCAGTAAGAGTAAAAAGATAATCAGTAAGAGTAAAATAGTAATCAGTAAGAGTAA
11965 AATAGTGATCAGTAAGAGTAAAAAGATAATCAGTAAGAGTAAAATAGTAATCAGTAAGAGTAA
1 AATAGTGATCAGTAAGAGTAAAAAGATAATCAGTAAGAGTAAAATAGTAATCAGTAAGAGTAA
* *
12028 AA-AGATAATCAGTAAGAGTAAAATAG-TAATCAGTAAGAGTAAAATGGTAATCAGTAAGGAGTA
1 AATAG-TGATCAGTAAGAGTAAAA-AGATAATCAGTAAGAGTAAAATAGTAATCAGTAA-GAGTA
12091 A
63 A
12092 GATGGTAATT
Statistics
Matches: 116, Mismatches: 2, Indels: 11
0.90 0.02 0.09
Matches are distributed among these distances:
57 31 0.27
62 2 0.02
63 75 0.65
64 8 0.07
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.22
Consensus pattern (63 bp):
AATAGTGATCAGTAAGAGTAAAAAGATAATCAGTAAGAGTAAAATAGTAATCAGTAAGAGTAA
Found at i:12200 original size:34 final size:34
Alignment explanation
Indices: 12162--12334 Score: 242
Period size: 34 Copynumber: 5.1 Consensus size: 34
12152 GGTAAAAAAA
*
12162 TAAAGAGTAATCAGTAAAGAAAAGTGGTAAAAAG
1 TAAAGAGTAATCAGTAAAGAAAAGTGGTAAAGAG
*
12196 TAAAGAGTAATCAATAAAG-AAAGATGGTAAAGAG
1 TAAAGAGTAATCAGTAAAGAAAAG-TGGTAAAGAG
* *
12230 TGAAGAGTAATTAGTAAAGAAAAGTGGTAAAGAG
1 TAAAGAGTAATCAGTAAAGAAAAGTGGTAAAGAG
12264 TAAAGAGTAATCAGTAAAGAAGAA-TGGTAAAGAG
1 TAAAGAGTAATCAGTAAAGAA-AAGTGGTAAAGAG
* * *
12298 TAAAGAATAATCAGTAAAGAAAAAATGGTAAGGAG
1 TAAAGAGTAATCAGTAAAG-AAAAGTGGTAAAGAG
12333 TA
1 TA
12335 GTTAATCAGT
Statistics
Matches: 125, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
33 4 0.03
34 102 0.82
35 19 0.15
ACGTcount: A:0.54, C:0.02, G:0.25, T:0.18
Consensus pattern (34 bp):
TAAAGAGTAATCAGTAAAGAAAAGTGGTAAAGAG
Found at i:12268 original size:7 final size:7
Alignment explanation
Indices: 12222--12317 Score: 56
Period size: 7 Copynumber: 14.0 Consensus size: 7
12212 AAGAAAGATG
12222 GTAAAGA
1 GTAAAGA
*
12229 GTGAAGA
1 GTAAAGA
**
12236 GTAATTA
1 GTAAAGA
12243 GTAAAGA
1 GTAAAGA
*
12250 --AAAGTG
1 GTAAAG-A
12256 GTAAAGA
1 GTAAAGA
12263 GTAAAGA
1 GTAAAGA
**
12270 GTAATCA
1 GTAAAGA
12277 GTAAAGAA
1 GTAAAG-A
*
12285 G-AATG-
1 GTAAAGA
12290 GTAAAGA
1 GTAAAGA
12297 GTAAAGA
1 GTAAAGA
* **
12304 ATAATCA
1 GTAAAGA
12311 GTAAAGA
1 GTAAAGA
12318 AAAAATGGTA
Statistics
Matches: 63, Mismatches: 20, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
5 5 0.08
6 3 0.05
7 49 0.78
8 6 0.10
ACGTcount: A:0.53, C:0.02, G:0.26, T:0.19
Consensus pattern (7 bp):
GTAAAGA
Found at i:16073 original size:144 final size:146
Alignment explanation
Indices: 15817--16087 Score: 420
Period size: 144 Copynumber: 1.9 Consensus size: 146
15807 AGAGAGTGAC
* * *
15817 GTATCAAACATTCAGCCCATTCTGATACCGAATAAGACTGCACCTTTCAGTCAATGTTTTAAATT
1 GTATCAAAAATTCAGCCCATTCTGACACCGAATAAGAC-GCACCTTCCAGTCAATGTTTTAAATT
* * *
15882 TGACTCGACCATCCGATTCTTCTTGTCAAGATCTTTCAAACGTCGCCAGAATCACCTTAATCGAC
65 TGACTAGACCATCCGATTCTTCTTGTCAAGATCTTTCAAACGCCGCCAAAATCACCTTAATCGAC
15947 AACCCTCAAAGAGTAAG
130 AACCCTCAAAGAGTAAG
** * *
15964 GTATCAAAAATTCAGCCTGTTTTGACACCGAATAAGAC-C-GCTTCCAGTCAATGTTTTAAATTT
1 GTATCAAAAATTCAGCCCATTCTGACACCGAATAAGACGCACCTTCCAGTCAATGTTTTAAATTT
*
16027 GACTAGACCATCCGATTCTTCTTGTCAAGATCTTTCAAACGCCGCCAAAATCGCCTTAATC
66 GACTAGACCATCCGATTCTTCTTGTCAAGATCTTTCAAACGCCGCCAAAATCACCTTAATC
16088 AGAAGTCGTA
Statistics
Matches: 113, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
144 79 0.70
145 1 0.01
147 33 0.29
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.30
Consensus pattern (146 bp):
GTATCAAAAATTCAGCCCATTCTGACACCGAATAAGACGCACCTTCCAGTCAATGTTTTAAATTT
GACTAGACCATCCGATTCTTCTTGTCAAGATCTTTCAAACGCCGCCAAAATCACCTTAATCGACA
ACCCTCAAAGAGTAAG
Found at i:16729 original size:31 final size:31
Alignment explanation
Indices: 16692--16756 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
16682 TAGGGTTATC
16692 AGTCTCCAGATCTTTAAATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAAATCTTGGATGTTTG
*
16723 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAAATCTTGGATGTTTG
16754 AGT
1 AGT
16757 TAGTTCAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.42
Consensus pattern (31 bp):
AGTCTCCAGATCTTTAAATCTTGGATGTTTG
Found at i:19046 original size:1 final size:1
Alignment explanation
Indices: 19040--19074 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
19030 TACACTACAT
*
19040 AAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19075 CAACACACAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19079 original size:13 final size:13
Alignment explanation
Indices: 19040--19079 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
19030 TACACTACAT
*
19040 AAAAAAAAAAAAA
1 AAAAAAAAAAAAC
19053 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
*
19066 AAAAAAAAACAAC
1 AAAAAAAAAAAAC
19079 A
1 A
19080 CACACACACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:32120 original size:115 final size:115
Alignment explanation
Indices: 31918--32148 Score: 417
Period size: 115 Copynumber: 2.0 Consensus size: 115
31908 GGGCGTAACA
* *
31918 TTTTTTCTCAAATACAGGATACGTACTGGTACCGTTATATTTTGGTGTCCCGTTTCAGGATTTTC
1 TTTTTTCTCAAATACAGGATACGTACTAGTACCGTTATATTTTGGTGTCCCGTTTCAAGATTTTC
31983 GGTATATATAATATTTTTTAAATAAATATATATATATTAAAATAAGATTT
66 GGTATATATAATATTTTTTAAATAAATATATATATATTAAAATAAGATTT
**
32033 TTTTTTCTCAGGTACAGGATACGTACTAGTACCGTTATATTTTGGTGTCCCGTTTCAAGATTTTC
1 TTTTTTCTCAAATACAGGATACGTACTAGTACCGTTATATTTTGGTGTCCCGTTTCAAGATTTTC
*
32098 GGTATATATAATATTTTTTAAATATATATATATATATTAAAATAAGATTT
66 GGTATATATAATATTTTTTAAATAAATATATATATATTAAAATAAGATTT
32148 T
1 T
32149 ATGATTATAA
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
115 111 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (115 bp):
TTTTTTCTCAAATACAGGATACGTACTAGTACCGTTATATTTTGGTGTCCCGTTTCAAGATTTTC
GGTATATATAATATTTTTTAAATAAATATATATATATTAAAATAAGATTT
Found at i:33232 original size:53 final size:51
Alignment explanation
Indices: 33170--33273 Score: 172
Period size: 53 Copynumber: 2.0 Consensus size: 51
33160 TTCTATATTT
33170 CCGATGTCCATAGCAAATACAACAACTATAAGCTACGAAAAAAATCAACTATC
1 CCGATGTCCATAGCAAATACAACAACTATAAGCTACG--AAAAATCAACTATC
* *
33223 CCGATGTCCATAGCAAATACAACAGCTATAAGCTACGCAAAATCAACTATC
1 CCGATGTCCATAGCAAATACAACAACTATAAGCTACGAAAAATCAACTATC
33274 ATTATAGCTA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 13 0.27
53 36 0.73
ACGTcount: A:0.44, C:0.26, G:0.11, T:0.19
Consensus pattern (51 bp):
CCGATGTCCATAGCAAATACAACAACTATAAGCTACGAAAAATCAACTATC
Found at i:36385 original size:35 final size:35
Alignment explanation
Indices: 36345--36417 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
36335 CCCGGAAATT
36345 ACCATGACCTTTGAACTTGCCTTCACACGACACAC
1 ACCATGACCTTTGAACTTGCCTTCACACGACACAC
36380 ACCATGACCTTTGAACTTGCCTTCACACGACACAC
1 ACCATGACCTTTGAACTTGCCTTCACACGACACAC
36415 ACC
1 ACC
36418 TTTGGAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.29, C:0.38, G:0.11, T:0.22
Consensus pattern (35 bp):
ACCATGACCTTTGAACTTGCCTTCACACGACACAC
Found at i:44663 original size:17 final size:17
Alignment explanation
Indices: 44641--44673 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
44631 TATCCTTCTA
44641 TTCATCTCATC-AAGTTT
1 TTCATC-CATCTAAGTTT
44658 TTCATCCATCTAAGTT
1 TTCATCCATCTAAGTT
44674 CATCTAGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TTCATCCATCTAAGTTT
Found at i:53501 original size:33 final size:33
Alignment explanation
Indices: 53464--53553 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
53454 GTCTCCTATA
53464 CATTGATCTTCATTTAAATCAAAATCTTCCACC
1 CATTGATCTTCATTTAAATCAAAATCTTCCACC
*
53497 CATTGATCTTCATTTCAATCAAAATCTTCCACC
1 CATTGATCTTCATTTAAATCAAAATCTTCCACC
* * *
53530 CATTGATCTTTATCTAAATAAAAA
1 CATTGATCTTCATTTAAATCAAAA
53554 AGAGTCTCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (33 bp):
CATTGATCTTCATTTAAATCAAAATCTTCCACC
Found at i:63990 original size:12 final size:13
Alignment explanation
Indices: 63972--64005 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
63962 AAACCGAAAA
63972 AAAATATAATAAT
1 AAAATATAATAAT
63985 -AAATATAAATAAT
1 AAAATAT-AATAAT
63998 AAAATATA
1 AAAATATA
64006 TATTCGCGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 6 0.32
13 7 0.37
14 6 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATATAATAAT
Found at i:65457 original size:44 final size:44
Alignment explanation
Indices: 65408--65494 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
65398 TGGCATTATA
65408 ATTCTCTACATATATAATGTCACGAGTGACATCAGTCACTACCC
1 ATTCTCTACATATATAATGTCACGAGTGACATCAGTCACTACCC
65452 ATTCTCTACATATATAATGTCACGAGTGACATCAGTCACTACC
1 ATTCTCTACATATATAATGTCACGAGTGACATCAGTCACTACC
65495 ACAACATCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.30
Consensus pattern (44 bp):
ATTCTCTACATATATAATGTCACGAGTGACATCAGTCACTACCC
Found at i:66233 original size:22 final size:22
Alignment explanation
Indices: 66208--66280 Score: 94
Period size: 22 Copynumber: 3.3 Consensus size: 22
66198 AGCACTTGAT
*
66208 CGGCCACACCGGCTACATGACC
1 CGGCCACACCGGCCACATGACC
**
66230 CGGCCATGCCGGTCGCACATG-CC
1 CGGCCACACCGG-C-CACATGACC
66253 CGGCCACACCGGCCACATGACC
1 CGGCCACACCGGCCACATGACC
66275 CGGCCA
1 CGGCCA
66281 TGCCCATGCA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 6 0.14
22 19 0.44
23 13 0.30
24 5 0.12
ACGTcount: A:0.19, C:0.47, G:0.26, T:0.08
Consensus pattern (22 bp):
CGGCCACACCGGCCACATGACC
Found at i:78667 original size:30 final size:30
Alignment explanation
Indices: 78633--78724 Score: 91
Period size: 33 Copynumber: 3.0 Consensus size: 30
78623 CATGCGACAT
78633 CGCATGGAGCAACCGGCCACAACCGGCCAA
1 CGCATGGAGCAACCGGCCACAACCGGCCAA
*
78663 CGCAT-GAGGCAACAATCGGCCACAACCGGCCAT
1 CGCATGGA-GCAAC---CGGCCACAACCGGCCAA
*
78696 CGCATGG-GCCATCCAGG-CACAACCGGCCA
1 CGCATGGAG-CAACC-GGCCACAACCGGCCA
78725 TTTGATCCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
29 2 0.04
30 23 0.43
31 2 0.04
32 1 0.02
33 24 0.45
34 1 0.02
ACGTcount: A:0.28, C:0.39, G:0.26, T:0.07
Consensus pattern (30 bp):
CGCATGGAGCAACCGGCCACAACCGGCCAA
Found at i:83927 original size:21 final size:21
Alignment explanation
Indices: 83901--83940 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
83891 GTTCTAACCC
* *
83901 TACTCACCCAGTACAATACAA
1 TACTCACACAATACAATACAA
83922 TACTCACACAATACAATAC
1 TACTCACACAATACAATAC
83941 TCACTTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.33, G:0.03, T:0.20
Consensus pattern (21 bp):
TACTCACACAATACAATACAA
Found at i:83934 original size:16 final size:16
Alignment explanation
Indices: 83913--83944 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
83903 CTCACCCAGT
83913 ACAATACAATACTCAC
1 ACAATACAATACTCAC
83929 ACAATACAATACTCAC
1 ACAATACAATACTCAC
83945 TTACAAAGGC
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:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (16 bp):
ACAATACAATACTCAC
Found at i:84404 original size:12 final size:12
Alignment explanation
Indices: 84387--84411 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
84377 AACCCAATAG
84387 GTTACTACGAAT
1 GTTACTACGAAT
84399 GTTACTACGAAT
1 GTTACTACGAAT
84411 G
1 G
84412 CTATACTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (12 bp):
GTTACTACGAAT
Found at i:89344 original size:19 final size:18
Alignment explanation
Indices: 89304--89343 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
89294 ACACCTTATG
** *
89304 AAAATCCAAAAGTTTTTC
1 AAAATCCAAAAAATCTTC
89322 AAAATCCAAAAAATCTTC
1 AAAATCCAAAAAATCTTC
89340 AAAA
1 AAAA
89344 AACATTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.25
Consensus pattern (18 bp):
AAAATCCAAAAAATCTTC
Done.