Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011620.1 Corchorus capsularis cultivar CVL-1 contig11641, 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: 53308
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:4827 original size:27 final size:27
Alignment explanation
Indices: 4766--4827 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
4756 GTGTTCAAGA
* *
4766 TTTAGGGGTTACTAACTCCCTTTTTTC
1 TTTAGAGGTTACTAACACCCTTTTTTC
* *
4793 TTTTGAGGTTACTAACACTCTTTTTT-
1 TTTAGAGGTTACTAACACCCTTTTTTC
4819 TTTCAGAGG
1 TTT-AGAGG
4828 GACAATACTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (27 bp):
TTTAGAGGTTACTAACACCCTTTTTTC
Found at i:8604 original size:11 final size:11
Alignment explanation
Indices: 8588--8612 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8578 GCAAATAATT
8588 GAAGCATTTTA
1 GAAGCATTTTA
8599 GAAGCATTTTA
1 GAAGCATTTTA
8610 GAA
1 GAA
8613 TTAAGGCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (11 bp):
GAAGCATTTTA
Found at i:11241 original size:31 final size:31
Alignment explanation
Indices: 11203--11390 Score: 101
Period size: 31 Copynumber: 5.5 Consensus size: 31
11193 GTCCTAAGTT
11203 GGGTAATTAAGAAAAGTAAAGTCTTAATTCA
1 GGGTAATTAAGAAAAGTAAAGTCTTAATTCA
* * *
11234 GGGTAATTAAG-AAAGGAAAGTACAATCAAGGTCCTAA
1 GGGTAATTAAGAAAAGTAAAGT-C--TTAA--T--TCA
*
11271 GTTGGGCAATTAAGAAAAGTAAAGTCTTAATTCA
1 ---GGGTAATTAAGAAAAGTAAAGTCTTAATTCA
* * *
11305 GGGTAATTAAG-AAAGGAAAGTACAGTCAAGGTCCTAA
1 GGGTAATTAAGAAAAGTAAAGT-C--TTAA--T--TCA
* *
11342 GTTGGGCAATTAAGAAAAGTAAAGCCTTAATTCA
1 ---GGGTAATTAAGAAAAGTAAAGTCTTAATTCA
11376 GGGTAATTAAGAAAA
1 GGGTAATTAAGAAAA
11391 AAAAGTGCAG
Statistics
Matches: 118, Mismatches: 17, Indels: 44
0.66 0.09 0.25
Matches are distributed among these distances:
30 18 0.15
31 37 0.31
33 6 0.05
34 4 0.03
35 2 0.02
36 2 0.02
37 4 0.03
38 6 0.05
40 22 0.19
41 17 0.14
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.24
Consensus pattern (31 bp):
GGGTAATTAAGAAAAGTAAAGTCTTAATTCA
Found at i:11508 original size:71 final size:71
Alignment explanation
Indices: 11068--11479 Score: 639
Period size: 71 Copynumber: 5.8 Consensus size: 71
11058 TAAAGGAAGC
* *
11068 TAAGGAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAGAGTACAGTCAAGGTCCTAAGTTG
1 TAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTTG
*
11133 GGCACT
66 GGCAAT
*
11139 TAAGAAGAA-CAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTT
1 TAAGAA-AAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTT
*
11203 GGGTAAT
65 GGGCAAT
*
11210 TAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAATCAAGGTCCTAAGTTG
1 TAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTTG
11275 GGCAAT
66 GGCAAT
11281 TAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTTG
1 TAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTTG
11346 GGCAAT
66 GGCAAT
* ** * *
11352 TAAGAAAAGTAAAGCCTTAATTCAGGGTAATTAAGAAAAAAAAGTGCAGTCAAGGTCATAAGTTG
1 TAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTTG
*
11417 GGC-AG
66 GGCAAT
* * * * *
11422 CAAGGAAGAGTAAAGTCTTAATTTAGGGTAATTAAGAAAAGAAAGTATAGTCAAGGTC
1 TAA-GAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAGTCAAGGTC
11480 ATAATTTAGA
Statistics
Matches: 316, Mismatches: 22, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
70 5 0.02
71 309 0.98
72 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (71 bp):
TAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTTG
GGCAAT
Found at i:11529 original size:213 final size:213
Alignment explanation
Indices: 11073--11532 Score: 593
Period size: 213 Copynumber: 2.2 Consensus size: 213
11063 GAAGCTAAGG
* ** * *
11073 AAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAGAGTACAGTCAAGGTCCTAAGTTGGGCAC
1 AAAGTAAAGTCTTAATCCAGGACAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTTGGGCAA
* ** *
11138 TTAAGAAGAACAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTT
66 TTAAGAAGAACAAAGCCTTAATTCAGGGTAATTAAGAAAAAAAAGTACAGTCAAGGTCATAAGTT
** * *
11203 GGGTAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAATCAAGGTCC
131 GGGTAAGCAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAATCAAGGTCA
* * *
11268 TAAGTTGGGCAATTAAGA
196 TAAGTTAGACAATCAAGA
* **
11286 AAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTTGGGCAA
1 AAAGTAAAGTCTTAATCCAGGACAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTTGGGCAA
* *
11351 TTAAGAA-AAGTAAAGCCTTAATTCAGGGTAATTAAGAAAAAAAAGTGCAGTCAAGGTCATAAGT
66 TTAAGAAGAA-CAAAGCCTTAATTCAGGGTAATTAAGAAAAAAAAGTACAGTCAAGGTCATAAGT
* * * * *
11415 TGGG-CAGCAAGGAAGAGTAAAGTCTTAATTTAGGGTAATTAAGAAAAGAAAGTATAGTCAAGGT
130 TGGGTAAGCAA-GAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAATCAAGGT
* *
11479 CATAATTTAGATAATCAAGA
194 CATAAGTTAGACAATCAAGA
** *
11499 TGAGTAAAGT-TCTAATCCAGGACGATTAAGAAAG
1 AAAGTAAAGTCT-TAATCCAGGACAATTAAGAAAG
11533 TCAAAACATA
Statistics
Matches: 216, Mismatches: 28, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
212 6 0.03
213 210 0.97
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.24
Consensus pattern (213 bp):
AAAGTAAAGTCTTAATCCAGGACAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTTGGGCAA
TTAAGAAGAACAAAGCCTTAATTCAGGGTAATTAAGAAAAAAAAGTACAGTCAAGGTCATAAGTT
GGGTAAGCAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAATCAAGGTCA
TAAGTTAGACAATCAAGA
Found at i:11606 original size:41 final size:41
Alignment explanation
Indices: 11503--11748 Score: 266
Period size: 41 Copynumber: 6.0 Consensus size: 41
11493 TCAAGATGAG
* * *
11503 TAAAGTTCTAATCCAGGACGATTAAGAAAGTCAAAACATAGA
1 TAAAGTTTTAATCCAGGGCGATTAAGAAAGTC-AAACATAGT
*
11545 TAAAGTTTTAATCCAGGGCGATTAAGAAAGTCAAAGATAGT
1 TAAAGTTTTAATCCAGGGCGATTAAGAAAGTCAAACATAGT
* * *
11586 CAAGGTTTTAATCCAGGGCGATTAAGAAAGTCCAACATAGT
1 TAAAGTTTTAATCCAGGGCGATTAAGAAAGTCAAACATAGT
*
11627 TAAAGTTTTAATCCAGGGCAATTAAGAAAGTCAAACATAGT
1 TAAAGTTTTAATCCAGGGCGATTAAGAAAGTCAAACATAGT
* * * * **
11668 T-AAGGTTTAAT-CTGGAGTGATTAAGAATGTCAGGCATAGT
1 TAAAGTTTTAATCCAGG-GCGATTAAGAAAGTCAAACATAGT
* * **
11708 T-AGGTTTTTAATACAGGGTAATTAAGAAAAGT-AAACATAGT
1 TAAAG-TTTTAATCCAGGGCGATTAAG-AAAGTCAAACATAGT
11749 CAGTCAAAAT
Statistics
Matches: 174, Mismatches: 26, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
39 3 0.02
40 31 0.18
41 103 0.59
42 37 0.21
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (41 bp):
TAAAGTTTTAATCCAGGGCGATTAAGAAAGTCAAACATAGT
Found at i:11789 original size:36 final size:35
Alignment explanation
Indices: 11749--12051 Score: 222
Period size: 37 Copynumber: 8.3 Consensus size: 35
11739 TAAACATAGT
11749 CAGTCAAAATCTTAATTCAAGGA-AA-TAAGGTAAAAG
1 CAGTCAAAA-CTTAATTC-AGGACAATTAA-GTAAAAG
11785 CAGTCAAAGGAGCTTAATTCAGGGA-AATTAAGT-AAA-
1 CAGTCAAA--A-CTTAATTCA-GGACAATTAAGTAAAAG
*
11821 CATGGTCAAAGAACTTAATTCAGGATAATTAAGTAAAAAG
1 CA--GTC-AA-AACTTAATTCAGGACAATTAAGT-AAAAG
* *
11861 CAGTTAAGAACTTAGTTCAGGACAATTAAGTAAAAG
1 CAGTCAA-AACTTAATTCAGGACAATTAAGTAAAAG
* *
11897 CAGTTAAGAACTTAATTCTGG-CTAATTAAGTAAAAAG
1 CAGTCAA-AACTTAATTCAGGAC-AATTAAGT-AAAAG
* * *
11934 CTGTTAAGAACTTAGTTCAGGACAATTAAGTAAAAG
1 CAGTCAA-AACTTAATTCAGGACAATTAAGTAAAAG
* * **
11970 CAGTTAAGAACTTAATTTAGGGTAATTAAGTAAAAG
1 CAGTCAA-AACTTAATTCAGGACAATTAAGTAAAAG
* * ** *
12006 CAGTTGAAGGACTTAATTCAGGGTAATTAAGTAAAAA
1 CAG-TCAA-AACTTAATTCAGGACAATTAAGTAAAAG
*
12043 CAGTTAAAA
1 CAGTCAAAA
12052 AGTAAAGTAA
Statistics
Matches: 231, Mismatches: 20, Indels: 33
0.81 0.07 0.12
Matches are distributed among these distances:
35 2 0.01
36 87 0.38
37 108 0.47
38 23 0.10
39 8 0.03
40 3 0.01
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (35 bp):
CAGTCAAAACTTAATTCAGGACAATTAAGTAAAAG
Found at i:11923 original size:73 final size:73
Alignment explanation
Indices: 11829--12049 Score: 329
Period size: 73 Copynumber: 3.0 Consensus size: 73
11819 AACATGGTCA
*
11829 AAGAACTTAATTCAGGATAATTAAGTAAAAAGCAGTTAAGAACTTAGTTCAGGACAATTAAGTAA
1 AAGAACTTAATTCTGGATAATTAAGTAAAAAGCAGTTAAGAACTTAGTTCAGGACAATTAAGTAA
11894 AAGCAGTT
66 AAGCAGTT
* *
11902 AAGAACTTAATTCTGGCTAATTAAGTAAAAAGCTGTTAAGAACTTAGTTCAGGACAATTAAGTAA
1 AAGAACTTAATTCTGGATAATTAAGTAAAAAGCAGTTAAGAACTTAGTTCAGGACAATTAAGTAA
11967 AAGCAGTT
66 AAGCAGTT
* * * **
11975 AAGAACTTAATT-TAGGGTAATTAAGT-AAAAGCAGTTGAAGGACTTAATTCAGGGTAATTAAGT
1 AAGAACTTAATTCT-GGATAATTAAGTAAAAAGCAGTT-AAGAACTTAGTTCAGGACAATTAAGT
*
12038 AAAAACAGTT
64 AAAAGCAGTT
12048 AA
1 AA
12050 AAAGTAAAGT
Statistics
Matches: 136, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
72 10 0.07
73 126 0.93
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (73 bp):
AAGAACTTAATTCTGGATAATTAAGTAAAAAGCAGTTAAGAACTTAGTTCAGGACAATTAAGTAA
AAGCAGTT
Found at i:12047 original size:37 final size:36
Alignment explanation
Indices: 11797--12049 Score: 290
Period size: 37 Copynumber: 6.9 Consensus size: 36
11787 GTCAAAGGAG
* * ** *
11797 CTTAATTCAGGGAAATTAAGTAAACATGGTCAAAGAA
1 CTTAATTCAGGGTAATTAAGTAAAAACAGT-TAAGAA
*
11834 CTTAATTCAGGATAATTAAGTAAAAAGCAGTTAAGAA
1 CTTAATTCAGGGTAATTAAGTAAAAA-CAGTTAAGAA
* ** *
11871 CTTAGTTCAGGACAATTAAGTAAAAGCAGTTAAGAA
1 CTTAATTCAGGGTAATTAAGTAAAAACAGTTAAGAA
* * *
11907 CTTAATTCTGGCTAATTAAGTAAAAAGCTGTTAAGAA
1 CTTAATTCAGGGTAATTAAGTAAAAA-CAGTTAAGAA
* ** *
11944 CTTAGTTCAGGACAATTAAGTAAAAGCAGTTAAGAA
1 CTTAATTCAGGGTAATTAAGTAAAAACAGTTAAGAA
* * *
11980 CTTAATTTAGGGTAATTAAGTAAAAGCAGTTGAAGGA
1 CTTAATTCAGGGTAATTAAGTAAAAACAGTT-AAGAA
12017 CTTAATTCAGGGTAATTAAGTAAAAACAGTTAA
1 CTTAATTCAGGGTAATTAAGTAAAAACAGTTAA
12050 AAAGTAAAGT
Statistics
Matches: 185, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
36 69 0.37
37 114 0.62
38 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (36 bp):
CTTAATTCAGGGTAATTAAGTAAAAACAGTTAAGAA
Found at i:12111 original size:41 final size:40
Alignment explanation
Indices: 12060--12313 Score: 271
Period size: 41 Copynumber: 6.5 Consensus size: 40
12050 AAAGTAAAGT
12060 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
1 AAGCACAGACTTAATTTC-AGGAAGGAAATTAGGTAAAGAC
* * *
12101 AAGCATAGACTTAA-TTC-GG--GGTAATTAAGTAAAGTA-
1 AAGCACAGACTTAATTTCAGGAAGGAAATTAGGTAAAG-AC
12137 AA-CACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
1 AAGCACAGACTTAATTTC-AGGAAGGAAATTAGGTAAAGAC
* * * *
12177 AAGCATAGACTTAA-TTCA-G--GGTAATTAAGTAAAG-T
1 AAGCACAGACTTAATTTCAGGAAGGAAATTAGGTAAAGAC
* * *
12212 AAGCACAGACTTAATTTCAGTAAAGGAAGTCAGGTAAAGAC
1 AAGCACAGACTTAATTTCAG-GAAGGAAATTAGGTAAAGAC
*
12253 AAGCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
1 AAGCACAGACTTAATTTC-AGGAAGGAAATTAGGTAAAGAC
*
12294 AAGCACATACTTAA-TTCAGG
1 AAGCACAGACTTAATTTCAGG
12314 GTAATTAAGT
Statistics
Matches: 175, Mismatches: 23, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
35 23 0.13
36 35 0.20
37 1 0.01
38 5 0.03
39 5 0.03
40 35 0.20
41 69 0.39
42 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (40 bp):
AAGCACAGACTTAATTTCAGGAAGGAAATTAGGTAAAGAC
Found at i:12143 original size:76 final size:76
Alignment explanation
Indices: 12051--12268 Score: 375
Period size: 76 Copynumber: 2.9 Consensus size: 76
12041 AACAGTTAAA
12051 AAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAAT
1 AAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAAT
*
12116 TCGGGGTAATT
66 TCAGGGTAATT
*
12127 AAGTAAAGTAAACACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAAT
1 AAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAAT
12192 TCAGGGTAATT
66 TCAGGGTAATT
* * *
12203 AAGTAAAGTAAGCACAGACTTAATTTC-AGTAAAGGAAGTCAGGTAAAGACAAGCATAGACTTAA
1 AAGTAAAGTAAGCACAGACTTAATTTCAAG-GAAGGAAATTAGGTAAAGACAAGCATAGACTTAA
12267 TT
65 TT
12269 TCAAGGAAGG
Statistics
Matches: 135, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
75 2 0.01
76 133 0.99
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (76 bp):
AAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAAT
TCAGGGTAATT
Found at i:12392 original size:36 final size:36
Alignment explanation
Indices: 12316--12414 Score: 105
Period size: 36 Copynumber: 2.8 Consensus size: 36
12306 AATTCAGGGT
* *
12316 AATTAAGT-AAATTAACAAAGACTTAATTTCATAAG
1 AATTAAGTAAAATCAACAAAGACTTAATTCCATAAG
*
12351 AATTAAGTAAAATCATCAAAGACTTAA-TCCA-AAG
1 AATTAAGTAAAATCAACAAAGACTTAATTCCATAAG
* *
12385 ATGATTAAGTAAGATCAGACAAAAACTTAA
1 A--ATTAAGTAAAATCA-ACAAAGACTTAA
12415 CCTCCGAGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
34 4 0.07
35 11 0.20
36 29 0.54
37 10 0.19
ACGTcount: A:0.53, C:0.11, G:0.10, T:0.26
Consensus pattern (36 bp):
AATTAAGTAAAATCAACAAAGACTTAATTCCATAAG
Found at i:12477 original size:37 final size:37
Alignment explanation
Indices: 12424--12615 Score: 285
Period size: 37 Copynumber: 5.2 Consensus size: 37
12414 ACCTCCGAGG
* * *
12424 ATTAAGTAAAGAAAAGGACTTGGTTCCAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
*
12461 ATTAAGTAGAGCAAAGGACTTGATTCCAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
*
12498 ATTAAGTAGAGTAAGGGACTTGATTCCAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
* *
12535 ATCAAGTAGAGTAGAGGACTTGATTCCAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
* * * *
12572 ATTAAGTAGAGTAGAGGACTTAATTTCAAGGAAGGAA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
12609 ATTAAGT
1 ATTAAGT
12616 CAAGTTAGGG
Statistics
Matches: 143, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 143 1.00
ACGTcount: A:0.41, C:0.08, G:0.30, T:0.21
Consensus pattern (37 bp):
ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
Found at i:12534 original size:19 final size:19
Alignment explanation
Indices: 12476--12534 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
12466 GTAGAGCAAA
12476 GGACTTGATTCCAAGGAAG
1 GGACTTGATTCCAAGGAAG
* * * *
12495 GGAATTAAGT--AGAGTAAG
1 GGACTTGATTCCA-AGGAAG
12513 GGACTTGATTCCAAGGAAG
1 GGACTTGATTCCAAGGAAG
12532 GGA
1 GGA
12535 ATCAAGTAGA
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
17 1 0.03
18 12 0.41
19 15 0.52
20 1 0.03
ACGTcount: A:0.36, C:0.10, G:0.34, T:0.20
Consensus pattern (19 bp):
GGACTTGATTCCAAGGAAG
Found at i:12716 original size:36 final size:36
Alignment explanation
Indices: 12627--12778 Score: 216
Period size: 36 Copynumber: 4.2 Consensus size: 36
12617 AAGTTAGGGA
* *
12627 CTTAATTCGGGGTAATTAAGTAGCGTCAATAAAGGG
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
* *
12663 ACTTAATTTAGGATAATTAAGTAGCGTCAATAAAAGG
1 -CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
*
12700 CTTAATTCAGGGTAATTAAGTAGTGTCAATAAAAGG
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
* *
12736 CTTAATTCAGGGTAATTAAGTGGAGTCAAT-AAAGAG
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAG-G
12772 CTTAATT
1 CTTAATT
12779 TAAGAAGAGA
Statistics
Matches: 105, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
35 4 0.04
36 69 0.66
37 32 0.30
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.30
Consensus pattern (36 bp):
CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
Found at i:15030 original size:22 final size:22
Alignment explanation
Indices: 15005--15046 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
14995 TAAATAAGAG
*
15005 TAAAGTAAAA-ACTAAATTAAAC
1 TAAACTAAAATAC-AAATTAAAC
15027 TAAACTAAAATACAAATTAA
1 TAAACTAAAATACAAATTAA
15047 GAAATCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.64, C:0.10, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAACTAAAATACAAATTAAAC
Found at i:15035 original size:27 final size:26
Alignment explanation
Indices: 14984--15035 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
14974 AAATCACAAT
* *
14984 TAAAAAGTAATTAAATAAGAGTAAAG
1 TAAAAACTAATTAAATAAGACTAAAG
15010 TAAAAACTAAATTAAACTAA-ACTAAA
1 TAAAAACT-AATTAAA-TAAGACTAAA
15036 ATACAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 7 0.32
27 12 0.55
28 3 0.14
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.23
Consensus pattern (26 bp):
TAAAAACTAATTAAATAAGACTAAAG
Found at i:18359 original size:33 final size:33
Alignment explanation
Indices: 18289--18426 Score: 120
Period size: 33 Copynumber: 4.2 Consensus size: 33
18279 ATGATCAACC
** *
18289 AAAACAGATTT-GTTTACATCACAATTAGCATCC-
1 AAAACAGATTTAGTTT-CATCACAAACAACA-CCT
*
18322 AAAACAGATTTTGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
* *
18355 AAAACAGATTTAGTGTCATCGCAAACAACA-CT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
** * * * *
18387 CAAATTAGGTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGTTTCATCACAAACAACACCT
18421 AAAACA
1 AAAACA
18427 CTCCTTGCAA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
32 4 0.04
33 79 0.89
34 6 0.07
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTTTCATCACAAACAACACCT
Found at i:25911 original size:21 final size:21
Alignment explanation
Indices: 25885--25938 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
25875 AGCACTGGAG
* *
25885 CACATGGGGCGCCAGGCAAAC
1 CACATGGGGCACCAAGCAAAC
*
25906 CACATGGGGCACCAAGCATAC
1 CACATGGGGCACCAAGCAAAC
*
25927 CGCAT-GGGCACC
1 CACATGGGGCACC
25939 CAGGGGGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.28, C:0.35, G:0.30, T:0.07
Consensus pattern (21 bp):
CACATGGGGCACCAAGCAAAC
Found at i:29537 original size:42 final size:42
Alignment explanation
Indices: 29464--29565 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
29454 CATGGAGCAA
** * * *
29464 CCGGCCATGACCGGCCAACGCATGGGACATCGCACGGGCCAT
1 CCGGCCACAACCGGCCATCGCACGGGACATCGCACGGACCAT
* * *
29506 CCGGCCACAACTGGCCATCGCACGGGCCATCGCATGGACCAT
1 CCGGCCACAACCGGCCATCGCACGGGACATCGCACGGACCAT
* *
29548 CTGGCGACAACCGGCCAT
1 CCGGCCACAACCGGCCAT
29566 TTGATCCTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.22, C:0.39, G:0.28, T:0.11
Consensus pattern (42 bp):
CCGGCCACAACCGGCCATCGCACGGGACATCGCACGGACCAT
Found at i:34189 original size:12 final size:12
Alignment explanation
Indices: 34150--34189 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
34140 CATGACCGGC
*
34150 CATCGCATGGGA
1 CATCGCACGGGA
*
34162 CATCGCACGGAA
1 CATCGCACGGGA
*
34174 CATCGCACGGGC
1 CATCGCACGGGA
34186 CATC
1 CATC
34190 TGGCCACCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.25, C:0.35, G:0.28, T:0.12
Consensus pattern (12 bp):
CATCGCACGGGA
Found at i:34209 original size:42 final size:42
Alignment explanation
Indices: 34162--34248 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
34152 TCGCATGGGA
* * *
34162 CATCGCACGGAAC-ATCGCACGGGCCATCTGGCCACCACCGGC
1 CATCGCACGG-ACTATCGCACGGACCATCCGGCCACAACCGGC
* * *
34204 CATCGCACGGGCTATCGCATGGACCATCCGGCCACAACTGGC
1 CATCGCACGGACTATCGCACGGACCATCCGGCCACAACCGGC
34246 CAT
1 CAT
34249 TTGATCCTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.03
42 37 0.97
ACGTcount: A:0.22, C:0.40, G:0.25, T:0.13
Consensus pattern (42 bp):
CATCGCACGGACTATCGCACGGACCATCCGGCCACAACCGGC
Found at i:38164 original size:30 final size:30
Alignment explanation
Indices: 38120--38176 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
38110 CAAGTCGATA
38120 ATAAGTCCTTGGCGCATCATTCCCTCCATG
1 ATAAGTCCTTGGCGCATCATTCCCTCCATG
38150 ATAAG-CCTTGGGCGCATCATTCCCTCC
1 ATAAGTCCTT-GGCGCATCATTCCCTCC
38177 CCCTTGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.19, C:0.35, G:0.18, T:0.28
Consensus pattern (30 bp):
ATAAGTCCTTGGCGCATCATTCCCTCCATG
Found at i:38586 original size:33 final size:33
Alignment explanation
Indices: 38549--38613 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
38539 GTCCTATTTT
38549 CAATGATATGATCAACCAAAACAGATTTGTTTG
1 CAATGATATGATCAACCAAAACAGATTTGTTTG
38582 CAATGATATGATCAACCAAAACAGATTTGTTT
1 CAATGATATGATCAACCAAAACAGATTTGTTT
38614 TCATCACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (33 bp):
CAATGATATGATCAACCAAAACAGATTTGTTTG
Found at i:38694 original size:33 final size:32
Alignment explanation
Indices: 38632--38736 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 32
38622 ATTAGCATCC
* * * *
38632 AAAACAGATATAGTTTCATCACAACCAACACCT
1 AAAACAGATTTAGTATCATCGCAAACAACA-CT
* *
38665 AAAACAGATTTAGTGTCATTGCAAACAACACT
1 AAAACAGATTTAGTATCATCGCAAACAACACT
** *
38697 CAAATTAGGTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGTATCATCGCAAACAACA-CT
38731 AAAACA
1 AAAACA
38737 CTCTTTGCAA
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
32 2 0.03
33 54 0.93
34 2 0.03
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.24
Consensus pattern (32 bp):
AAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:41010 original size:16 final size:16
Alignment explanation
Indices: 40989--41020 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40979 TAAAGGCTAC
40989 ACAAAAGAACCTTCTA
1 ACAAAAGAACCTTCTA
41005 ACAAAAGAACCTTCTA
1 ACAAAAGAACCTTCTA
41021 GAAACTATCC
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:0.25, G:0.06, T:0.19
Consensus pattern (16 bp):
ACAAAAGAACCTTCTA
Found at i:43002 original size:21 final size:21
Alignment explanation
Indices: 42976--43021 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
42966 ACGAGATTAT
42976 GCCTTTTACTAGCTTCAATAG
1 GCCTTTTACTAGCTTCAATAG
42997 GCCTTTTACTAGCTTCAATAG
1 GCCTTTTACTAGCTTCAATAG
43018 GCCT
1 GCCT
43022 AATAAAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (21 bp):
GCCTTTTACTAGCTTCAATAG
Found at i:47791 original size:42 final size:42
Alignment explanation
Indices: 47745--47845 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
47735 CATGGAGCAA
** * *
47745 CCGGCCATGACCGGCCAACGCATGGGACATCGCACGAGCCAT
1 CCGGCCACAACCGGCCAACGCACGGGACATCGCAAGAGCCAT
* * *
47787 CCGGCCACAACCGGCCATCGCACGGGCCATCGCAAGGGCCAT
1 CCGGCCACAACCGGCCAACGCACGGGACATCGCAAGAGCCAT
47829 CCGGCCACAACCGGCCA
1 CCGGCCACAACCGGCCA
47846 CTTGACCCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.23, C:0.43, G:0.28, T:0.07
Consensus pattern (42 bp):
CCGGCCACAACCGGCCAACGCACGGGACATCGCAAGAGCCAT
Found at i:47816 original size:12 final size:12
Alignment explanation
Indices: 47799--47829 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
47789 GGCCACAACC
*
47799 GGCCATCGCACG
1 GGCCATCGCAAG
47811 GGCCATCGCAAG
1 GGCCATCGCAAG
47823 GGCCATC
1 GGCCATC
47830 CGGCCACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.39, G:0.32, T:0.10
Consensus pattern (12 bp):
GGCCATCGCAAG
Found at i:47975 original size:3 final size:3
Alignment explanation
Indices: 47967--47997 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
47957 AAAAATTAAA
*
47967 ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
47998 AAATATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Done.