Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009439.1 Corchorus capsularis cultivar CVL-1 contig09460, 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: 11639
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:3711 original size:25 final size:25
Alignment explanation
Indices: 3677--3740 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
3667 CTTCAAGCAG
3677 TGTACTTCCAGCTCATAGAGGCTGA
1 TGTACTTCCAGCTCATAGAGGCTGA
3702 TGTACTTCCAGCTCATAGAGGCTGA
1 TGTACTTCCAGCTCATAGAGGCTGA
3727 TGTACTTCCAGCTC
1 TGTACTTCCAGCTC
3741 TGTTCTTGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.30
Consensus pattern (25 bp):
TGTACTTCCAGCTCATAGAGGCTGA
Found at i:4923 original size:20 final size:20
Alignment explanation
Indices: 4864--4930 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
4854 TACATTGGGC
4864 CAATGTGAATTAAGGCAAGTT
1 CAATGTG-ATTAAGGCAAGTT
* ** *
4885 CAATGTCATTTGGGAAAGTT
1 CAATGTGATTAAGGCAAGTT
**
4905 GGATGTGATTAAGGCAAGTT
1 CAATGTGATTAAGGCAAGTT
4925 CAATGT
1 CAATGT
4931 CATTTGGATG
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
20 28 0.82
21 6 0.18
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (20 bp):
CAATGTGATTAAGGCAAGTT
Found at i:4953 original size:32 final size:32
Alignment explanation
Indices: 4903--5033 Score: 246
Period size: 32 Copynumber: 4.1 Consensus size: 32
4893 TTTGGGAAAG
4903 TTGGATGTG-ATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
4934 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
4966 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
*
4998 TTGGATGTGAATTAAGGCAAGTTCAATGTCTT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
5030 TTGG
1 TTGG
5034 GAAAGTTGGA
Statistics
Matches: 98, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
31 9 0.09
32 89 0.91
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.36
Consensus pattern (32 bp):
TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
Found at i:5067 original size:21 final size:21
Alignment explanation
Indices: 5002--5067 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
4992 TGTCATTTGG
5002 ATGTGAATTAAGGCAAGTTCA
1 ATGTGAATTAAGGCAAGTTCA
** ** * **
5023 ATGT-CTTTTGGGAAAGTTGG
1 ATGTGAATTAAGGCAAGTTCA
5043 ATGTGAATTAAGGCAAGTTCA
1 ATGTGAATTAAGGCAAGTTCA
5064 ATGT
1 ATGT
5068 CTTTTGGGAA
Statistics
Matches: 30, Mismatches: 14, Indels: 2
0.65 0.30 0.04
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.32, C:0.08, G:0.27, T:0.33
Consensus pattern (21 bp):
ATGTGAATTAAGGCAAGTTCA
Found at i:5120 original size:20 final size:20
Alignment explanation
Indices: 5016--5127 Score: 62
Period size: 20 Copynumber: 5.5 Consensus size: 20
5006 GAATTAAGGC
**
5016 AAGTTCAATGTCTTTTGGGA
1 AAGTTCAATGTCAATTGGGA
** * * *
5036 AAGTTGGATGTGAATTAAGGC
1 AAGTTCAATGTCAATT-GGGA
**
5057 AAGTTCAATGTCTTTTGGGA
1 AAGTTCAATGTCAATTGGGA
** * * ** *
5077 AAGTTGGATATGAATAAGGC
1 AAGTTCAATGTCAATTGGGA
5097 AAGTTCAATGTCAATTGGGA
1 AAGTTCAATGTCAATTGGGA
*
5117 AAGTTAAATGT
1 AAGTTCAATGT
5128 GAATGTGCCG
Statistics
Matches: 60, Mismatches: 31, Indels: 2
0.65 0.33 0.02
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (20 bp):
AAGTTCAATGTCAATTGGGA
Found at i:5131 original size:40 final size:41
Alignment explanation
Indices: 4998--5131 Score: 216
Period size: 41 Copynumber: 3.3 Consensus size: 41
4988 TCAATGTCAT
4998 TTGGATGTGAATTAAGGCAAGTTCAATGTCTTTTGGGAAAG
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCTTTTGGGAAAG
5039 TTGGATGTGAATTAAGGCAAGTTCAATGTCTTTTGGGAAAG
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCTTTTGGGAAAG
* **
5080 TTGGATATGAA-TAAGGCAAGTTCAATGTCAATTGGGAAAG
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCTTTTGGGAAAG
**
5120 TTAAATGTGAAT
1 TTGGATGTGAAT
5132 GTGCCGCGTG
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
40 35 0.41
41 51 0.59
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.33
Consensus pattern (41 bp):
TTGGATGTGAATTAAGGCAAGTTCAATGTCTTTTGGGAAAG
Found at i:8883 original size:329 final size:328
Alignment explanation
Indices: 7385--9411 Score: 1850
Period size: 329 Copynumber: 6.1 Consensus size: 328
7375 CAAATTACTC
* * * * * *
7385 CAAGGAGTCTCGGTGCAAAAAAAATCAAGCAAAACTGAGTTGAGGCCTCGGAACACGTTTTTAGC
1 CAAGGAGTCTGGGTGC--CAAAAATCAAGCAAAACTGAGCTGGGGCC-CAGAACGCGTTTTTAGC
* ** * * * ***
7450 CGAAACCCATGATAGTTAGTACATGATTTCAGCTAAAATTTTGCAAAAAATGAAAAATGATCCAA
63 CAAAAATCGTGAT-GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATG--ACCCGA---AA
* **
7515 ATTTTTTTTTTTCAATTTTT-AGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
122 A--GTTTTTCCTCAATTTTTGA-CCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
* *
7579 TTGAAGGGCTTTTCAAGCATCTAATATCGCTTTTCC-TATTTTTTCTGAATTAATTTCTGATTAA
184 TTGAAGGGCTTTTCAAGCATCTAATATCGTTTTTCCAT-TTTTTTCTGAATTAATTTCTAATTAA
* * *
7643 ATCGAAACATGATTTAGATGCTCATAAAAACAAATCCTTAAATTCAATATG-GTTGAGATTTGGT
248 ATCGAAACAAGATTTAGATGCTCAT-AAAAGAAATCCTTAAA-TCAA-ACGTGTTGAGATTTGGT
*
7707 TAGATGAATATAGATATTT
310 TAGATGAATATATATATTT
* * * *
7726 CAAGGAGTCTGGATGCTAAAAATCAAGTC-AAACTGAGCTGGGGCCCTAGAATGTGTTTTTAGCC
1 CAAGGAGTCTGGGTGCCAAAAATCAAG-CAAAACTGAGCTGGGGCCC-AGAACGCGTTTTTAGCC
* * * * * *
7790 AAAAA-CAGTGATGGTTAGTACATGATTTCGGCTAAATTTTTGCAAAAAATAATCTGAATAGTTT
64 AAAAATC-GTGAT-GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAGTTT
* * * * **
7854 TACCTTAATTTTTTACCACAACACTC-GTAAAAAAATATATAATTCAACGCCAAAGTTGATTGAA
127 TTCCTCAATTTTTGACCACAATACTCAG--AAAAAATATATAATTCAACGCCAAA-AAGATTGAA
* * * * *
7918 GGGCTTTACGCA-CATCTAGTATCATTTTTCCATTTCTTTTAC-GAATTAATTTCTAATTAAATA
189 GGGCTTTTC-AAGCATCTAATATCGTTTTTCCATTT-TTTT-CTGAATTAATTTCTAATTAAATC
* * * * *
7981 GAAACAATATTTAGATGCTCGTAAAA-ACAAGACCTTAAATGC-AATGTGGTTGAAATTTGGTTA
251 GAAACAAGATTTAGATGCTCATAAAAGA-AA-TCCTTAAAT-CAAACGT-GTTGAGATTTGGTTA
* * *
8044 GATGCATATGTATGTTT
312 GATGAATATATATATTT
* * * * *
8061 CAATGAGTCTGGGCGCCAAAAATCAAACAAAACTGAGTTGGGGCGCC-GAAACGTGTTTTTAGCC
1 CAAGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAGCTGGGGC-CCAG-AACGCGTTTTTAGCC
* * * **
8125 ----ACCGTGATGGTTAGTACACGATTTCAGCAAAAATTTTGCAAAAAATGATTCG-AAAGTTTT
64 AAAAATCGTGAT-GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAG-TTT
* * * * * * * ***
8185 TTCCTTAATTTTTGACAACAATACTCAGAAAAAATAAATCATTCAATGCCTAAAAGATAGAATTT
127 TTCCTCAATTTTTGACCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGG
* * * * * *
8250 CTTTTCAAGCATCTAATGTCGCTTTTCCTATTTTTTTTTTAATTAATTTCTGATTAAGTCGAAAC
192 CTTTTCAAGCATCTAATATCGTTTTTCC-ATTTTTTTCTGAATTAATTTCTAATTAAATCGAAAC
* * * * ** *
8315 ---A--T--ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCCGAGATTTGG-TAAATGAAT
256 AAGATTTAGATGCTCAT-AAAAGAAATCCTTAAATCAAACGT-GTTGAGATTTGGTTAGATGAAT
8372 ATATATATTT
319 ATATATATTT
* * * * * *
8382 CAAGGAATCTGGGCGCCAAAAATCAAGCAAAACCGAG-TCGGGGCCCCGGAATGCGTTTTTAGCA
1 CAAGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAGCT-GGGG-CCCAGAACGCGTTTTTAGCC
* **
8446 AAAAATTGTGATGGTTAGTACACGATTTCACCTAAAATTTTGCAAAAAATGACCCGAAAA-TGTT
64 AAAAATCGTGAT-GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAGT-TT
* * * *
8510 TTCCTCAA-TTTTCACCACAATTA-T-AAAAAAAAGGTATATAATTCAACTCCAAAAATATTGAA
127 TTCCTCAATTTTTGACCACAA-TACTCAGAAAAAA--TATATAATTCAACGCCAAAAAGATTGAA
** * *
8572 GGGCTTTTCAATTATATAATATCGTTTTTCCATTTTATTCTGAATTAATTTCTAATTAAATCGAA
189 GGGCTTTTCAAGCATCTAATATCGTTTTTCCATTTTTTTCTGAATTAATTTCTAATTAAATCGAA
* * * * * * *
8637 ACAAGACTCAAATGCTCGTAAAAGGAATCCTTATATCAAACGTGTCTGAGATTTGGTTAGATAAA
254 ACAAGATTTAGATGCTCATAAAAGAAATCCTTAAATCAAACGTGT-TGAGATTTGGTTAGATGAA
* *
8702 TATAAATGTTT
318 TATATATATTT
* * * *
8713 CAAGAAGACTGGGTGCCAAAAATCAAGTAAAATTGAGCTGGGGTCCCAGAACGCGTTTTTAGCCA
1 CAAGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAGCTGGGG-CCCAGAACGCGTTTTTAGCCA
* * * *
8778 AAAATCGTAAT-AT-GTACATGATTTTGGCTAAAATTTTTGCAAAAAATGACCCGAAAAGTTTTT
65 AAAATCGTGATGTTAGTACACGATTTCGGCTAAAA-TTTTGCAAAAAATGACCCGAAAAGTTTTT
*** * * * *
8841 CCTCAATTTTTGACCACAATACTTTTAAAAAATTTATAATTCAACGACAAAAAGATTGGAGGTCT
129 CCTCAATTTTTGACCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCT
* *
8906 TTTCAAGCATCTAATGTCGTTTTTCCATTTTTTTCTGAATTAATTTCTAATTAAATAGAAACAAG
194 TTTCAAGCATCTAATATCGTTTTTCCATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAG
* * * *
8971 ATTTAGATGCTCATAATAAGAAATCCTTAAATCTAACATGGTTGAGATTTGATTAGATGTATATA
259 ATTTAGATGCTCATAA-AAGAAATCCTTAAATCAAACGT-GTTGAGATTTGGTTAGATGAATATA
* *
9036 TATGTAT
322 TATATTT
* * * * * *
9043 CAAGGAGTCTGGATGCCAAAAATCAAGCATAATTGAGATGGGGCCTCGGAACACGTTTTTAGCCA
1 CAAGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAGCTGGGGCC-CAGAACGCGTTTTTAGCCA
* * * *
9108 AAAAACTGTGATGGTTAGTATACGATTTCGGCTAAAATTTTACAAAAAATTGACCCAAAAAGTTT
65 AAAATC-GTGAT-GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAA-TGACCCGAAAAGTTT
* * * * * * *
9173 TTCCTTATTTTTTGGCCATAATACTCAGAAAAAATATATAATTCAACTCCAAAAGGATTGAATGG
127 TTCCTCAATTTTTGACCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGG
* * *
9238 ATTTTCAAGCATCTAATATTGTTTTTCC-TATTTTTCTGAATTAATTTCTAATTAAATCGAAACA
192 CTTTTCAAGCATCTAATATCGTTTTTCCATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
* * ** * ** *
9302 TGATTCAGATGCTCATAAAAGAAATTATTAAATCCAACGTGACCGAGATTTGGTTAGGTGAATAT
257 AGATTTAGATGCTCATAAAAGAAATCCTTAAATCAAACGTG-TTGAGATTTGGTTAGATGAATAT
*
9367 AGATATTT
321 ATATATTT
**
9375 CAAGGAGTCCCGGTGCCAAAAATCAAGCAAAACTGAG
1 CAAGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAG
9412 TTGGAACCCC
Statistics
Matches: 1382, Mismatches: 240, Indels: 137
0.79 0.14 0.08
Matches are distributed among these distances:
320 1 0.00
321 67 0.05
322 33 0.02
323 13 0.01
324 45 0.03
325 101 0.07
326 4 0.00
327 1 0.00
328 17 0.01
329 189 0.14
330 171 0.12
331 166 0.12
332 98 0.07
333 92 0.07
334 152 0.11
335 129 0.09
336 3 0.00
337 4 0.00
338 2 0.00
339 79 0.06
340 1 0.00
341 14 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (328 bp):
CAAGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAGCTGGGGCCCAGAACGCGTTTTTAGCCAA
AAATCGTGATGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAGTTTTTCC
TCAATTTTTGACCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTT
TCAAGCATCTAATATCGTTTTTCCATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGAT
TTAGATGCTCATAAAAGAAATCCTTAAATCAAACGTGTTGAGATTTGGTTAGATGAATATATATA
TTT
Found at i:9765 original size:41 final size:40
Alignment explanation
Indices: 9700--9793 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 40
9690 AGTGCTATCA
* *
9700 TGGGCCTTCAAGCTTATTGTTAAAAATCATAG-GCTTATAT
1 TGGGCCTTCAAGCATATTGTTAAAAATCA-AGAGATTATAT
*
9740 TGGGCCTTCAAAGCATATTGTTAAAAATCACGAGATTATAT
1 TGGGCCTTC-AAGCATATTGTTAAAAATCAAGAGATTATAT
9781 TGGGCCTTTCAAG
1 TGGGCC-TTCAAG
9794 TAATGAATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
40 10 0.21
41 35 0.73
42 3 0.06
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (40 bp):
TGGGCCTTCAAGCATATTGTTAAAAATCAAGAGATTATAT
Found at i:10659 original size:17 final size:17
Alignment explanation
Indices: 10633--10671 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
10623 AAACTTACTT
*
10633 CATTTTCAGCTGTCC-AC
1 CATTTCCAGCTG-CCGAC
10650 CATTTCCAGCTGCCGAC
1 CATTTCCAGCTGCCGAC
10667 CATTT
1 CATTT
10672 ACAACCTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.18, C:0.36, G:0.13, T:0.33
Consensus pattern (17 bp):
CATTTCCAGCTGCCGAC
Found at i:10906 original size:85 final size:85
Alignment explanation
Indices: 10695--11195 Score: 783
Period size: 85 Copynumber: 5.9 Consensus size: 85
10685 GACATGGAGA
*
10695 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGGCTCG
1 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCG
*
10760 CAGACACGACACACGCGAAGG
66 C-GACACGACACACACGAAGG
* *
10781 TACACGAGAAGGACATCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGGCTCG
1 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCG
* * *
10846 CGACGCAACACACACGAAGC
66 CGACACGACACACACGAAGG
* * *
10866 TACACGAGAAGGACAGCGGCTCTCGGCAGTGAGGCTCTCAAAACAGCCGCCAACTACGAGGCTCG
1 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCG
*
10931 CGACGCGACACACACGAAGG
66 CGACACGACACACACGAAGG
*
10951 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTATGAGGCTCG
1 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCG
* *
11016 CAACACGACACACACGAAGC
66 CGACACGACACACACGAAGG
* * *
11036 TACAC---AAGGACAGCGGCTCTCAGCAATGAGGCTCTCAAAACTGCCGCCAACTACGAGGCTCG
1 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCG
* **
11098 GGACGTGACACACACGAAGG
66 CGACACGACACACACGAAGG
*
11118 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGGCTCG
1 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCG
11183 CGACACGACACAC
66 CGACACGACACAC
11196 GAAGACACGG
Statistics
Matches: 377, Mismatches: 35, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
82 73 0.19
85 239 0.63
86 65 0.17
ACGTcount: A:0.29, C:0.32, G:0.29, T:0.10
Consensus pattern (85 bp):
TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCG
CGACACGACACACACGAAGG
Found at i:11135 original size:167 final size:168
Alignment explanation
Indices: 10702--11195 Score: 801
Period size: 167 Copynumber: 2.9 Consensus size: 168
10692 AGATACACGA
* * * *
10702 GAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGGCTCGCAGACAC
1 GAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACAGCCGCCAACTACGAGGCTCG-AGACGC
* *
10767 GACACACGCGAAGGTACACGAGAAGGACATCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCC
65 GACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCC
* *
10832 GACTGCGAGGCTCGCGACGCAACACACACGAAGCTACAC
130 GACTGCGAGGCTCGCGACACGACACACACGAAGCTACAC
* *
10871 GAGAAGGACAGCGGCTCTCGGCAGTGAGGCTCTCAAAACAGCCGCCAACTACGAGGCTCGCGACG
1 --GAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACAGCCGCCAACTACGAGGCTCGAGACG
10936 CGACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGC
64 CGACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGC
** *
11001 CGACTATGAGGCTCGCAACACGACACACACGAAGCTACAC
129 CGACTGCGAGGCTCGCGACACGACACACACGAAGCTACAC
* * * *
11041 -AAGGACAGCGGCTCTCAGCAATGAGGCTCTCAAAACTGCCGCCAACTACGAGGCTCGGGACGTG
1 GAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACAGCCGCCAACTACGAGGCTCGAGACGCG
11105 ACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCG
66 ACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCG
11170 ACTGCGAGGCTCGCGACACGACACAC
131 ACTGCGAGGCTCGCGACACGACACAC
11196 GAAGACACGG
Statistics
Matches: 302, Mismatches: 21, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
167 147 0.49
170 101 0.33
171 54 0.18
ACGTcount: A:0.29, C:0.32, G:0.29, T:0.10
Consensus pattern (168 bp):
GAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACAGCCGCCAACTACGAGGCTCGAGACGCG
ACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCG
ACTGCGAGGCTCGCGACACGACACACACGAAGCTACAC
Found at i:11149 original size:252 final size:254
Alignment explanation
Indices: 10695--11195 Score: 808
Period size: 252 Copynumber: 2.0 Consensus size: 254
10685 GACATGGAGA
*
10695 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGGCTCG
1 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCG
* * * *
10760 CAGACACGACACACGCGAAGGTACACGAGAAGGACATCGGCTCTCAGCAGTGAGGCTCTCAAAAC
66 CAGACACGACACACACGAAGCTACAC--GAAGGACAGCGGCTCTCAGCAATGAGGCTCTCAAAAC
* *
10825 GGCCGCCGACTGCGAGGCTCGCGACGCAACACACACGAAGCTACACGAGAAGGACAGCGGCTCTC
129 GGCCGCCAACTACGAGGCTCGCGACGCAACACACACGAAGCTACACGAGAAGGACAGCGGCTCTC
* *
10890 GGCAGTGAGGCTCTCAAAACAGCCGCCAACTACGAGGCTCGCGACGCGACACACACGAAGG
194 AGCAGTGAGGCTCTCAAAACAGCCGCCAACTACGAGGCTCGCGACACGACACACACGAAGG
*
10951 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTATGAGGCTCG
1 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCG
*
11016 CA-ACACGACACACACGAAGCTACAC-AAGGACAGCGGCTCTCAGCAATGAGGCTCTCAAAACTG
66 CAGACACGACACACACGAAGCTACACGAAGGACAGCGGCTCTCAGCAATGAGGCTCTCAAAACGG
* ** *
11079 CCGCCAACTACGAGGCTCGGGACGTGACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAG
131 CCGCCAACTACGAGGCTCGCGACGCAACACACACGAAGCTACACGAGAAGGACAGCGGCTCTCAG
* * *
11144 CAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGGCTCGCGACACGACACAC
196 CAGTGAGGCTCTCAAAACAGCCGCCAACTACGAGGCTCGCGACACGACACAC
11196 GAAGACACGG
Statistics
Matches: 227, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
252 141 0.62
255 21 0.09
256 65 0.29
ACGTcount: A:0.29, C:0.32, G:0.29, T:0.10
Consensus pattern (254 bp):
TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCG
CAGACACGACACACACGAAGCTACACGAAGGACAGCGGCTCTCAGCAATGAGGCTCTCAAAACGG
CCGCCAACTACGAGGCTCGCGACGCAACACACACGAAGCTACACGAGAAGGACAGCGGCTCTCAG
CAGTGAGGCTCTCAAAACAGCCGCCAACTACGAGGCTCGCGACACGACACACACGAAGG
Found at i:11583 original size:53 final size:53
Alignment explanation
Indices: 11512--11630 Score: 184
Period size: 53 Copynumber: 2.2 Consensus size: 53
11502 CAACAGCAAC
* *
11512 AGAGAGAGAGAGAGAACGAGCGCAAGAATCTCCTGGTAAAAAGAGAGAGAGCG
1 AGAGAGAGAGAGACAACGAGCGCAAGAATCTCCTGGTAAAAAGAGAGAGAGAG
* * * *
11565 AGCGAGCGAGAGACAACGAGCGCAAGAATCTCCTGGTAGAGAGAGAGAGAGAG
1 AGAGAGAGAGAGACAACGAGCGCAAGAATCTCCTGGTAAAAAGAGAGAGAGAG
11618 AGAGAGAGAGAGA
1 AGAGAGAGAGAGA
11631 GAGAGAGAG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.42, C:0.13, G:0.38, T:0.07
Consensus pattern (53 bp):
AGAGAGAGAGAGACAACGAGCGCAAGAATCTCCTGGTAAAAAGAGAGAGAGAG
Found at i:11609 original size:2 final size:2
Alignment explanation
Indices: 11602--11639 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11592 ATCTCCTGGT
11602 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.