Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013678.1 Corchorus capsularis cultivar CVL-1 contig13699, 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: 42883
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:11911 original size:27 final size:29
Alignment explanation
Indices: 11855--11913 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
11845 TATTTAATAC
* *
11855 TACTACTATATGAGATTATTGGGGGAAAAA
1 TACTACTATACGAAATTATT-GGGGAAAAA
*
11885 TACTACTATACGAAATTATTGGGAAAAAA
1 TACTACTATACGAAATTATTGGGGAAAAA
11914 CCGAATTGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (29 bp):
TACTACTATACGAAATTATTGGGGAAAAA
Found at i:15283 original size:6 final size:6
Alignment explanation
Indices: 15266--15308 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
15256 CAAGCTGCAC
*
15266 CACAAT CGCAAT CACAAT CACAAT CACAAT CACAAT CACAAT C
1 CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT C
15309 TTGCCAACAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.35, G:0.02, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:15370 original size:39 final size:39
Alignment explanation
Indices: 15307--15576 Score: 449
Period size: 39 Copynumber: 7.0 Consensus size: 39
15297 ACAATCACAA
* *
15307 TCTTGCCAA-CAGTTTAACCCCCTGAGGCACGGGTCCAT
1 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCAC
*
15345 TCTTACCAATCAGTTTAACCCCCTGAGGCACAGGTCCAC
1 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCAC
*
15384 TCTTACC-ATCAGTTTAACCCCCTGAGGCGCGGGTCCAC
1 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCAC
*
15422 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGATCCAC
1 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCAC
15461 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCAC
15500 TCTTACCAA-CAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCAC
**
15538 TCTTACC-ATCAGTTTAACCCCCTGAGGTGCGGGTCCAC
1 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCAC
15576 T
1 T
15577 ATGCACAGTC
Statistics
Matches: 219, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
37 1 0.00
38 108 0.49
39 110 0.50
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.24
Consensus pattern (39 bp):
TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCAC
Found at i:15407 original size:77 final size:76
Alignment explanation
Indices: 15307--15576 Score: 443
Period size: 77 Copynumber: 3.5 Consensus size: 76
15297 ACAATCACAA
* * *
15307 TCTTGCCAACAGTTTAACCCCCTGAGGCACGGGTCCATTCTTACCAATCAGTTTAACCCCCTGAG
1 TCTTACCATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAATCAGTTTAACCCCCTGAG
15372 GCACAGGTCCAC
66 GCAC-GGTCCAC
*
15384 TCTTACCATCAGTTTAACCCCCTGAGGCGCGGGTCCACTCTTACCAATCAGTTTAACCCCCTGAG
1 TCTTACCATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAATCAGTTTAACCCCCTGAG
15449 GCACGGATCCAC
66 GCACGG-TCCAC
15461 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAA-CAGTTTAACCCCCTGA
1 TCTTACC-ATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAATCAGTTTAACCCCCTGA
15525 GGCACGGGTCCAC
65 GGCAC-GGTCCAC
**
15538 TCTTACCATCAGTTTAACCCCCTGAGGTGCGGGTCCACT
1 TCTTACCATCAGTTTAACCCCCTGAGGCACGGGTCCACT
15577 ATGCACAGTC
Statistics
Matches: 183, Mismatches: 7, Indels: 7
0.93 0.04 0.04
Matches are distributed among these distances:
76 32 0.17
77 110 0.60
78 41 0.22
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.24
Consensus pattern (76 bp):
TCTTACCATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAATCAGTTTAACCCCCTGAG
GCACGGTCCAC
Found at i:15520 original size:116 final size:116
Alignment explanation
Indices: 15307--15564 Score: 448
Period size: 116 Copynumber: 2.2 Consensus size: 116
15297 ACAATCACAA
* * *
15307 TCTTGCCAA-CAGTTTAACCCCCTGAGGCACGGGTCCATTCTTACCAATCAGTTTAACCCCCTGA
1 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGATCCACTCTTACCAATCAGTTTAACCCCCTGA
* *
15371 GGCACAGGTCCACTCTTACCATCAGTTTAACCCCCTGAGGCGCGGGTCCAC
66 GGCACAGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
15422 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGATCCACTCTTACCAATCAGTTTAACCCCCTGA
1 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGATCCACTCTTACCAATCAGTTTAACCCCCTGA
*
15487 GGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
66 GGCACAGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
15538 TCTTACC-ATCAGTTTAACCCCCTGAGG
1 TCTTACCAATCAGTTTAACCCCCTGAGG
15565 TGCGGGTCCA
Statistics
Matches: 136, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
115 28 0.21
116 108 0.79
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (116 bp):
TCTTACCAATCAGTTTAACCCCCTGAGGCACGGATCCACTCTTACCAATCAGTTTAACCCCCTGA
GGCACAGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
Found at i:17759 original size:6 final size:6
Alignment explanation
Indices: 17742--17778 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
17732 CAAGATGCAC
* *
17742 CACAAT CGCAAT CACAAT CACAAT CGCAAT CACAAT C
1 CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT C
17779 TTGCCAACAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.43, C:0.35, G:0.05, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:17765 original size:18 final size:18
Alignment explanation
Indices: 17742--17778 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
17732 CAAGATGCAC
17742 CACAATCGCAATCACAAT
1 CACAATCGCAATCACAAT
17760 CACAATCGCAATCACAAT
1 CACAATCGCAATCACAAT
17778 C
1 C
17779 TTGCCAACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.35, G:0.05, T:0.16
Consensus pattern (18 bp):
CACAATCGCAATCACAAT
Found at i:17833 original size:38 final size:38
Alignment explanation
Indices: 17777--17969 Score: 323
Period size: 38 Copynumber: 5.0 Consensus size: 38
17767 GCAATCACAA
*
17777 TCTTGCCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
17815 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
* * *
17853 TCTTACCATCAATTTAACCCCCTGAGGCGCGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
17891 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAA-CAGTTTAACCCCCTGAGGCACGGGTCCAC
*
17930 TCTTTACCATCAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TC-TTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
17969 T
1 T
17970 ATGCACAGCC
Statistics
Matches: 145, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
38 80 0.55
39 59 0.41
40 6 0.04
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (38 bp):
TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
Found at i:20644 original size:33 final size:33
Alignment explanation
Indices: 20602--20667 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
20592 AACTTCATTC
20602 ACGATGTATTGTATAATTTGTCTTTCTTTATTA
1 ACGATGTATTGTATAATTTGTCTTTCTTTATTA
20635 ACGATGTATTGTATAATTTGTCTTTCTTTATTA
1 ACGATGTATTGTATAATTTGTCTTTCTTTATTA
20668 GTTTCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (33 bp):
ACGATGTATTGTATAATTTGTCTTTCTTTATTA
Found at i:24943 original size:9 final size:9
Alignment explanation
Indices: 24911--24949 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
24901 TTACTATTAC
24911 TATTACTAT
1 TATTACTAT
* * *
24920 TACTATTAC
1 TATTACTAT
24929 TATTACTAT
1 TATTACTAT
24938 TATTACTAT
1 TATTACTAT
24947 TAT
1 TAT
24950 GTAAAATCAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (9 bp):
TATTACTAT
Found at i:24948 original size:6 final size:6
Alignment explanation
Indices: 24901--24939 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
24891 ATATCTTATC
24901 TTACTA TTACTA TTACTA TTACTA TTACTA TTACTA TTA
1 TTACTA TTACTA TTACTA TTACTA TTACTA TTACTA TTA
24940 TTACTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.51
Consensus pattern (6 bp):
TTACTA
Found at i:25073 original size:20 final size:18
Alignment explanation
Indices: 25036--25077 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
25026 ATAAGTATTC
25036 TTTTTAGTCATTAACTTT
1 TTTTTAGTCATTAACTTT
*
25054 TTTTTAGATGATTCAACTTT
1 TTTTTAG-TCATT-AACTTT
25074 TTTT
1 TTTT
25078 ATTAATTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 4 0.19
20 10 0.48
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (18 bp):
TTTTTAGTCATTAACTTT
Found at i:25279 original size:159 final size:159
Alignment explanation
Indices: 24988--25306 Score: 545
Period size: 159 Copynumber: 2.0 Consensus size: 159
24978 TGGGAAATTT
* *
24988 CATAAATATCCATAGTATTATAGTATAATAATTATTTAATAAGTATTCTTTTTAGTCATTAACTT
1 CATAAATACCCATAGTATTATAGTATAATAATTATTTAATAAGTATTCTTTTAAGTCATTAACTT
*
25053 TTTTTTAGATGATTCAACTTTTTTTATTAATTATGGAAAGATAATGTAAATCCAATATTTAAATT
66 TTTTTTAGATGATTCAACTTTTTTTATTAATTATGCAAAGATAATGTAAATCCAATATTTAAATT
25118 TTTTAAATTAT-GAAAAGATATTAATAATC
131 TTTTAAATTATGGAAAA-ATATTAATAATC
* * *
25147 CATAAATACCCTTAGTATTGTAGTATAATAATTTTTTAATAAGTATTCTTTTAAGTCATTTAAC-
1 CATAAATACCCATAGTATTATAGTATAATAATTATTTAATAAGTATTCTTTTAAGTCA-TTAACT
25211 TTTTTTTAGATGATTCAAC-TTTTTTATTAATTATGCAAAGATAATGTAAATCCAATATTTAAAT
65 TTTTTTTAGATGATTCAACTTTTTTTATTAATTATGCAAAGATAATGTAAATCCAATATTTAAAT
25275 TTTTTAAATTATGGAAAAATATTAATAATC
130 TTTTTAAATTATGGAAAAATATTAATAATC
25305 CA
1 CA
25307 CTATAATTGT
Statistics
Matches: 152, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
158 70 0.46
159 77 0.51
160 5 0.03
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (159 bp):
CATAAATACCCATAGTATTATAGTATAATAATTATTTAATAAGTATTCTTTTAAGTCATTAACTT
TTTTTTAGATGATTCAACTTTTTTTATTAATTATGCAAAGATAATGTAAATCCAATATTTAAATT
TTTTAAATTATGGAAAAATATTAATAATC
Found at i:25372 original size:34 final size:33
Alignment explanation
Indices: 25325--25388 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
25315 GTAATTGATA
* *
25325 ATTTACTTCTAATAATTATT-TTTAGATTATATAT
1 ATTTAATTATAAT-ATTATTATTTA-ATTATATAT
25359 ATTTAATTATAATATTATTATTTAATTATA
1 ATTTAATTATAATATTATTATTTAATTATA
25389 CTCATGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 12 0.44
34 15 0.56
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (33 bp):
ATTTAATTATAATATTATTATTTAATTATATAT
Found at i:27629 original size:296 final size:295
Alignment explanation
Indices: 27116--28220 Score: 1062
Period size: 296 Copynumber: 3.8 Consensus size: 295
27106 TTTTTATTTA
* * * * * * *
27116 CTAAAAACGCGTTCCATGGCCCCGAGGCAGTTTTGCATGATTTTTGATGCCAAGACTCCTTGA-A
1 CTAAAAA-GCGTTTCAGGGCCTCGAGTCAATTTTGCATGATTTCTGACGCCAAGACTCCTTGAGA
* * **
27180 -ATAT-T-TATATTCATCTAATCAAATGTCAGCCACATTGGATTGAAGAATCTATTTTTACGAGC
65 TATATATCCATATTCATCTAATCAAATCTCAGCCACATTACATTGAAGAATCTATTTTTACGAGC
* * * * * *
27242 ATCTAAACCTTGTTTCGATTTAATTATAAATTAATTCAGAAAAAGTAGGAAAACCGATATTAGAA
130 ATCTAAACCTTGTTTCAATTTAATTAGAAAATAATTCAGAAAAAGTAGGAAAAACGATATGAAAA
*
27307 GCGTAAAAAATCCTTCAATATTTTTGGCGTTGAGTTCAATATTTCGGATCAATTTGTGCAGAATT
195 GCGTAAAAAATCCTCCAATATTTTTGGCGTTGA-TTCAATATTTCGGATCAATTTGTGCAGAATT
27372 TTAGCCGAAATCGTGTAATAATCATCACGATTTTTGG
259 TTAGCCGAAATCGTGTAATAATCATCACGATTTTTGG
27409 CTAAAAAGCGTTTCAGGGCCTCGAGTCAATTTTGCATGATTTCTGACGCCAAGACTCCTTGAGAT
1 CTAAAAAGCGTTTCAGGGCCTCGAGTCAATTTTGCATGATTTCTGACGCCAAGACTCCTTGAGAT
* * * *
27474 ATATATCCATATTCATCTAATCAAATCTCAGCCATATTACACTT-AAGGATTTGTTTTTACGAGC
66 ATATATCCATATTCATCTAATCAAATCTCAGCCACATTACA-TTGAAGAATCTATTTTTACGAGC
* * *
27538 ATCTGAATCTTGTTTCAATTTAATTAGAAAATAATTCAGAAGAAA-TATGAAAAACGATATGAAA
130 ATCTAAACCTTGTTTCAATTTAATTAGAAAATAATTCAGAA-AAAGTAGGAAAAACGATATGAAA
* * * * ** *
27602 AGCGTGAAAAGTCCTCCAATCTTTTTGGC--T--TT-AA-ATTAT-GTAT--ATTAAATG-AGTA
194 AGCGTAAAAAATCCTCCAATATTTTTGGCGTTGATTCAATATT-TCGGATCAATT-TGTGCAGAA
* * * * * ** *** *
27657 TTTTAGCCAAAAATTGAGGAAAAATTTTTTGGGTCATTTTTTG
257 TTTTAGCC-GAAATCGTGTAATAA-TCATCACG--ATTTTTGG
* * * *** * * *
27700 C--AAAA--GTTT-A--G-C-CGA---AATTATGTACATCATGGTTTTTTTTTTGCAAAAACGTG
1 CTAAAAAGCGTTTCAGGGCCTCGAGTCAATT-T-T---GCAT-G-ATTTCTGACGCCAAGAC-TC
* * * * * * **
27753 TTTCGGGGTTCCTAGAAATATCTATATTCATCTAATCAAATGTCAGCCACATTGGATTGAAGAAT
58 CTT--GAG-----ATATATATCCATATTCATCTAATCAAATCTCAGCCACATTACATTGAAGAAT
* *
27818 CTATTTTTACGAGCATCTAAACCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAGTAGGAA
116 CTATTTTTACGAGCATCTAAACCTTGTTTCAATTTAATTAGAAAATAATTCAGAAAAAGTAGGAA
* * * *
27883 AACCGATATTAGAAGCGTAAAAAATCCTTCAATATTTTTGGCGTTGAATTCAATATTTCGGATCA
181 AAACGATATGAAAAGCGTAAAAAATCCTCCAATATTTTTGGCGTTG-ATTCAATATTTCGGATCA
27948 ATTTGTGCAGAATTTTAGCCGAAATCGTGTAATAATCATCACGATTTTTGG
245 ATTTGTGCAGAATTTTAGCCGAAATCGTGTAATAATCATCACGATTTTTGG
* *
27999 CTAAAAAGCGTTTCAGGGCCTCAAGTCAGTTTTGCATGATTTCTGACGCCAAGACTCCTTGAGAT
1 CTAAAAAGCGTTTCAGGGCCTCGAGTCAATTTTGCATGATTTCTGACGCCAAGACTCCTTGAGAT
* * * *
28064 ATATATCCATATTCATCTAATCAAATCTCAGCCACATTACATTTAAGGATTTGTTTTTACGAGCA
66 ATATATCCATATTCATCTAATCAAATCTCAGCCACATTACATTGAAGAATCTATTTTTACGAGCA
* * *
28129 TCTGAATCTTGTTTCAATTTAATTAGAAAATAATTCAGAATAAA-TATGAAAAACGATATGAAAA
131 TCTAAACCTTGTTTCAATTTAATTAGAAAATAATTCAGAA-AAAGTAGGAAAAACGATATGAAAA
* * *
28193 GCGTGAAAAGTCCTCCAATCTTTTTGGC
195 GCGTAAAAAATCCTCCAATATTTTTGGC
28221 TTTAAATTAT
Statistics
Matches: 633, Mismatches: 126, Indels: 103
0.73 0.15 0.12
Matches are distributed among these distances:
279 4 0.01
280 1 0.00
281 1 0.00
282 3 0.00
283 1 0.00
284 4 0.01
285 1 0.00
286 11 0.02
287 21 0.03
288 12 0.02
289 15 0.02
290 3 0.00
291 10 0.02
292 48 0.08
293 13 0.02
294 135 0.21
295 1 0.00
296 256 0.40
297 8 0.01
299 10 0.02
300 3 0.00
301 15 0.02
302 12 0.02
303 21 0.03
304 11 0.02
305 1 0.00
306 4 0.01
307 1 0.00
308 2 0.00
309 1 0.00
310 1 0.00
311 3 0.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (295 bp):
CTAAAAAGCGTTTCAGGGCCTCGAGTCAATTTTGCATGATTTCTGACGCCAAGACTCCTTGAGAT
ATATATCCATATTCATCTAATCAAATCTCAGCCACATTACATTGAAGAATCTATTTTTACGAGCA
TCTAAACCTTGTTTCAATTTAATTAGAAAATAATTCAGAAAAAGTAGGAAAAACGATATGAAAAG
CGTAAAAAATCCTCCAATATTTTTGGCGTTGATTCAATATTTCGGATCAATTTGTGCAGAATTTT
AGCCGAAATCGTGTAATAATCATCACGATTTTTGG
Found at i:27858 original size:294 final size:291
Alignment explanation
Indices: 27476--28534 Score: 1093
Period size: 296 Copynumber: 3.6 Consensus size: 291
27466 CTTGAGATAT
* *
27476 ATATCCATATTCATCTAATCAAATCTCAGCCATATTACACTTAAGGATTTGTTTTTACGAGCATC
1 ATATCCATATTCATCTAATCAAATCTCAGCCACATTACATTTAAGGATTTGTTTTTACGAGCATC
27541 TGAATCTTGTTTCAATTTAATTAGAAAATAATTCAGAAGAAATATGAAAAACGATATGAAAAGCG
66 TGAATCTTGTTTCAATTTAATTAGAAAATAATTCAGAA-AAATATGAAAAACGATATGAAAAGCG
* * *
27606 TGAAAAGTCCTCCAATCTTTTTGGCTTTAAATTATGTATATTAAATGAGTATTTTAGCCAAAAAT
130 TAAAAAGTCCTCCAATCTTTTTGGCGTTAAATTATATATATTAAATGAGTATTTTAGCCAAAAAT
27671 TGAGGAAAAATTTTTTGGGTCATTTTTTGCAAAAGTTTAGCCGAAATTATGTACATCATGGTTTT
195 TGAGGAAAAATTTTTTGGGTCATTTTTTGCAAAAGTTTAGCCGAAATTATGTACATCATGG--TT
27736 TTTTTTGCAAAAACGTGTTTCGGGGTTCCTAGAA
258 TTTTTTGCAAAAACGTGTTTCGGGGTTCCTAGAA
* * ** * * * *
27770 ATATCTATATTCATCTAATCAAATGTCAGCCACATTGGATTGAAGAATCTATTTTTACGAGCATC
1 ATATCCATATTCATCTAATCAAATCTCAGCCACATTACATTTAAGGATTTGTTTTTACGAGCATC
* * * * * * * *
27835 TAAACCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAGTAGGAAAACCGATATTAGAAGCG
66 TGAATCTTGTTTCAATTTAATTAGAAAATAATTCAGAAAAA-TATGAAAAACGATATGAAAAGCG
* * * * * * * *
27900 TAAAAAATCCTTCAATATTTTTGGCGTTGAATTCAATATTTCGGATCAATTTGTGCAGAATTTTA
130 TAAAAAGTCCTCCAATCTTTTTGGCGTTAAATT--ATATAT---ATTAA---ATG-AGTATTTTA
* * * * * ** *** * * * *
27965 GCC-GAAATCGTGTAATAA-TCATCACG--ATTTTTGGCTAAAAAGCGTTTCAGGGCCTCAAGTC
186 GCCAAAAATTGAGGAAAAATTTTTTGGGTCATTTTTTGC--AAAA--GTTT-A--GCC-GAAATT
** * * *** * * ** * * *
28026 A-GT-TTTGCATGATTTCTGACGCCAAGAC-TCCTT--GAG-----ATAT
243 ATGTACAT-CATGGTTTTTTTTGCAAAAACGTGTTTCGGGGTTCCTAGAA
28066 ATATCCATATTCATCTAATCAAATCTCAGCCACATTACATTTAAGGATTTGTTTTTACGAGCATC
1 ATATCCATATTCATCTAATCAAATCTCAGCCACATTACATTTAAGGATTTGTTTTTACGAGCATC
28131 TGAATCTTGTTTCAATTTAATTAGAAAATAATTCAGAATAAATATGAAAAACGATATGAAAAGCG
66 TGAATCTTGTTTCAATTTAATTAGAAAATAATTCAGAA-AAATATGAAAAACGATATGAAAAGCG
* * *
28196 TGAAAAGTCCTCCAATCTTTTTGGCTTTAAATTATGTATATTAAATGAGTATTTTAGCCAAAAAT
130 TAAAAAGTCCTCCAATCTTTTTGGCGTTAAATTATATATATTAAATGAGTATTTTAGCCAAAAAT
28261 TGAGGAAAAATTTTTTGGGTCATTTTTTGCAAAAGTTTAGCCGAAATTATGTACATCATGGTTTT
195 TGAGGAAAAATTTTTTGGGTCATTTTTTGCAAAAGTTTAGCCGAAATTATGTACATCATGGTTTT
28326 TTTTGCAAAAACGTGTTTCGGGGTTCCTAGAA
260 TTTTGCAAAAACGTGTTTCGGGGTTCCTAGAA
* * *
28358 ATATCTATATTCATCTAATCAAATCTCAGCCTCATTGAAATATATTTAAGGATTTGTTTTTACGA
1 ATATCCATATTCATCTAATCAAATCTCAGCCACA-T----TACATTTAAGGATTTGTTTTTACGA
* * * * ** *
28423 GTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATAATATTAA
61 GCATCTGAATCTTGTTTCAATTTAATTAGAAAATAATTCAG-AAAAATATGAAAAACGATATGAA
* * *
28488 AAACGTAAAAAGTACCTCCAATCATTTTGGCGTTGAATTATATATAT
125 AAGCGTAAAAAGT-CCTCCAATCTTTTTGGCGTTAAATTATATATAT
28535 ATATATATAT
Statistics
Matches: 596, Mismatches: 128, Indels: 78
0.74 0.16 0.10
Matches are distributed among these distances:
283 4 0.01
284 19 0.03
285 4 0.01
286 1 0.00
287 17 0.03
288 12 0.02
289 7 0.01
291 12 0.02
292 34 0.06
293 4 0.01
294 139 0.23
296 143 0.24
297 93 0.16
298 31 0.05
299 12 0.02
301 9 0.02
302 12 0.02
303 18 0.03
304 11 0.02
305 1 0.00
306 9 0.02
307 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (291 bp):
ATATCCATATTCATCTAATCAAATCTCAGCCACATTACATTTAAGGATTTGTTTTTACGAGCATC
TGAATCTTGTTTCAATTTAATTAGAAAATAATTCAGAAAAATATGAAAAACGATATGAAAAGCGT
AAAAAGTCCTCCAATCTTTTTGGCGTTAAATTATATATATTAAATGAGTATTTTAGCCAAAAATT
GAGGAAAAATTTTTTGGGTCATTTTTTGCAAAAGTTTAGCCGAAATTATGTACATCATGGTTTTT
TTTGCAAAAACGTGTTTCGGGGTTCCTAGAA
Found at i:28295 original size:590 final size:588
Alignment explanation
Indices: 27172--28526 Score: 2361
Period size: 590 Copynumber: 2.3 Consensus size: 588
27162 ATGCCAAGAC
* *
27172 TCCTTGAAATATTTATATTCATCTAATCAAATGTCAGCCACATTGGATTGAAGAATCTATTTTTA
1 TCCTAGAAATATCTATATTCATCTAATCAAATGTCAGCCACATTGGATTGAAGAATCTATTTTTA
*
27237 CGAGCATCTAAACCTTGTTTCGATTTAATTATAAATTAATTCAGAAAAAGTAGGAAAACCGATAT
66 CGAGCATCTAAACCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAGTAGGAAAACCGATAT
*
27302 TAGAAGCGTAAAAAATCCTTCAATATTTTTGGCGTTGAGTTCAATATTTCGGATCAATTTGTGCA
131 TAGAAGCGTAAAAAATCCTTCAATATTTTTGGCGTTGAATTCAATATTTCGGATCAATTTGTGCA
*
27367 GAATTTTAGCCGAAATCGTGTAATAATCATCACGATTTTTGGCTAAAAAGCGTTTCAGGGCCTCG
196 GAATTTTAGCCGAAATCGTGTAATAATCATCACGATTTTTGGCTAAAAAGCGTTTCAGGGCCTCA
27432 AGTCAATTTTGCATGATTTCTGACGCCAAGACTCCTTGAGATATATATCCATATTCATCTAATCA
261 AGTCAATTTTGCATGATTTCTGACGCCAAGACTCCTTGAGATATATATCCATATTCATCTAATCA
*
27497 AATCTCAGCCATATTACACTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAAT
326 AATCTCAGCCACATTACACTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAAT
27562 TAGAAAATAATTCAGAAGAAATATGAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAATCTTTT
391 TAGAAAATAATTCAGAAGAAATATGAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAATCTTTT
27627 TGGCTTTAAATTATGTATATTAAATGAGTATTTTAGCCAAAAATTGAGGAAAAATTTTTTGGGTC
456 TGGCTTTAAATTATGTATATTAAATGAGTATTTTAGCCAAAAATTGAGGAAAAATTTTTTGGGTC
27692 ATTTTTTGCAAAAGTTTAGCCGAAATTATGTACATCATGGTTTTTTTTTTGCAAAAACGTGTTTC
521 ATTTTTTGCAAAAGTTTAGCCGAAATTATGTACATCATGG--TTTTTTTTGCAAAAACGTGTTTC
27757 GGGGT
584 GGGGT
27762 TCCTAGAAATATCTATATTCATCTAATCAAATGTCAGCCACATTGGATTGAAGAATCTATTTTTA
1 TCCTAGAAATATCTATATTCATCTAATCAAATGTCAGCCACATTGGATTGAAGAATCTATTTTTA
27827 CGAGCATCTAAACCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAGTAGGAAAACCGATAT
66 CGAGCATCTAAACCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAGTAGGAAAACCGATAT
27892 TAGAAGCGTAAAAAATCCTTCAATATTTTTGGCGTTGAATTCAATATTTCGGATCAATTTGTGCA
131 TAGAAGCGTAAAAAATCCTTCAATATTTTTGGCGTTGAATTCAATATTTCGGATCAATTTGTGCA
27957 GAATTTTAGCCGAAATCGTGTAATAATCATCACGATTTTTGGCTAAAAAGCGTTTCAGGGCCTCA
196 GAATTTTAGCCGAAATCGTGTAATAATCATCACGATTTTTGGCTAAAAAGCGTTTCAGGGCCTCA
*
28022 AGTCAGTTTTGCATGATTTCTGACGCCAAGACTCCTTGAGATATATATCCATATTCATCTAATCA
261 AGTCAATTTTGCATGATTTCTGACGCCAAGACTCCTTGAGATATATATCCATATTCATCTAATCA
*
28087 AATCTCAGCCACATTACATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAAT
326 AATCTCAGCCACATTACACTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAAT
*
28152 TAGAAAATAATTCAGAATAAATATGAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAATCTTTT
391 TAGAAAATAATTCAGAAGAAATATGAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAATCTTTT
28217 TGGCTTTAAATTATGTATATTAAATGAGTATTTTAGCCAAAAATTGAGGAAAAATTTTTTGGGTC
456 TGGCTTTAAATTATGTATATTAAATGAGTATTTTAGCCAAAAATTGAGGAAAAATTTTTTGGGTC
28282 ATTTTTTGCAAAAGTTTAGCCGAAATTATGTACATCATGGTTTTTTTTGCAAAAACGTGTTTCGG
521 ATTTTTTGCAAAAGTTTAGCCGAAATTATGTACATCATGGTTTTTTTTGCAAAAACGTGTTTCGG
28347 GGT
586 GGT
* * * * * * *
28350 TCCTAGAAATATCTATATTCATCTAATCAAATCTCAGCCTCATTGAAATATATTTAAGGATTTGT
1 TCCTAGAAATATCTATATTCATCTAATCAAATGTCAGCCACATTG-----GATTGAAGAATCTAT
* * * * * * **
28415 TTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAAT
61 TTTTACGAGCATCTAAACCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAGTAGGAAAACC
* * * * *
28480 AATATTAAAAACGTAAAAAGTACCTCCAATCA-TTTTGGCGTTGAATT
126 GATATTAGAAGCGTAAAAAAT-CCTTCAAT-ATTTTTGGCGTTGAATT
28527 ATATATATAT
Statistics
Matches: 729, Mismatches: 29, Indels: 10
0.95 0.04 0.01
Matches are distributed among these distances:
588 71 0.10
590 551 0.76
593 84 0.12
594 22 0.03
595 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (588 bp):
TCCTAGAAATATCTATATTCATCTAATCAAATGTCAGCCACATTGGATTGAAGAATCTATTTTTA
CGAGCATCTAAACCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAGTAGGAAAACCGATAT
TAGAAGCGTAAAAAATCCTTCAATATTTTTGGCGTTGAATTCAATATTTCGGATCAATTTGTGCA
GAATTTTAGCCGAAATCGTGTAATAATCATCACGATTTTTGGCTAAAAAGCGTTTCAGGGCCTCA
AGTCAATTTTGCATGATTTCTGACGCCAAGACTCCTTGAGATATATATCCATATTCATCTAATCA
AATCTCAGCCACATTACACTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAAT
TAGAAAATAATTCAGAAGAAATATGAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAATCTTTT
TGGCTTTAAATTATGTATATTAAATGAGTATTTTAGCCAAAAATTGAGGAAAAATTTTTTGGGTC
ATTTTTTGCAAAAGTTTAGCCGAAATTATGTACATCATGGTTTTTTTTGCAAAAACGTGTTTCGG
GGT
Found at i:30029 original size:332 final size:331
Alignment explanation
Indices: 28685--30053 Score: 1253
Period size: 331 Copynumber: 4.1 Consensus size: 331
28675 TGATGTCGAA
* *
28685 TTATATATTTTGATGAGTATTTTAGTCAAAAATTGAGGAAATATCTT-TAGGATCAATTTTTACA
1 TTATATATTTT-ATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTCT-GGGTCAATTTTTACA
* * * * * * **
28749 AAA-TTTAGCCAAAATCGTGTACTAATCATCTCAGTTTTTGGCTAAAAATTGCGATCCG-GGGTC
64 AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA-CGCGTTCCGAGGACC
* * * * ** *
28812 ACGACT-ATATTTTGCATCATTTTTTGCGCTGAGACTCCTTGAAATATTTATATTCATCTAACCA
128 ACGGCTCA-GTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCA
* * * * * *
28876 AATCTTAGCCACATTGAATTTAACGG-TTTGTTTTTACGAGCATTTGAATCATGTTTCGATTTAA
192 AATCTCAG-CACATTGGATTTAA-GGATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAA
* * * * *
28940 TTAGAAATTAATTT-TAAAAAATTGGGAAAATGATATTA-AAGCAT-AAGAAGCCCTTCAATCTT
255 TTAGAAATTAATTTCAAAAAAATAGGAAAAACGATATTAGAAGCATGAA-AAGCCC-TCAATTTT
29002 TTTGGTGTTGAA--
318 TTTGGTGTTGAATT
* * * * * * *
29014 TTATATATTTTTTGAGTATTGTGGCTAAAAAAATTGAGTAAAATAT-TTC-AGGTCAATTTTTGC
1 TTATATATTTTATGAGTATTTTAGC--CAAAAATTGAG-GAAATATCTTCTGGGTCAATTTTTAC
* * * **** ** *
29077 AAAATTTTAACCGAAATCGTGTACCATTACGAT-TTTTTTTTTGGCTAAAAACATGTT-CTAGGA
63 AAAATTTTAGCCGAAATCGTGTA-C-TAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAGGA
* * * * **
29140 CC-TGGGTCAGTTTTGCATTATTTTTGGCGCCAAGACTTCTCAAAATATATCTATATTCATCTAA
126 CCACGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCT-TGAA-ATATCTATATTCATCTAA
* * *
29204 CCAAATATCAGGCACATTGTATTTAAGGATTTGTTTTTACAAGTATCTAAATCTTGTATT-GATT
189 CCAAATCTCA-GCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGT-TTCGATT
* * * **
29268 TAATCAGAAATTAATTTGGAAATAAAATAGGAAAAACGATATTAGAAGCGTGAAAAAGACTTTCA
252 TAATTAGAAATTAATTT-CAAA-AAAATAGGAAAAACGATATTAGAAGCATG-AAAAG-CCCTCA
* *
29333 ACTTTTTTGGCGTTGAATT
313 ATTTTTTTGGTGTTGAATT
* * * * *
29352 ATATAT-TTTTATGAGTATTTTCGCTAGAAATTGAGGGAAA-ATCTTTTGGGTCAATTTTTACAA
1 TTATATATTTTATGAGTATTTTAGCCAAAAATTGA-GGAAATATCTTCTGGGTCAATTTTTACAA
* ** * *
29415 AATTTTAGCCGAAATCGTGTA-TCAACCATCACGGTTTTCGATTAAAAACGTGTTTCG-GGACC-
65 AATTTTAGCCGAAATCGTGTACT-AACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAGGACCA
* * * * * *
29477 CGGTTCAGTTTTCCATGACTTTTGGTGCCAAGACTCCTTGAAATATCTATATTTATCTAACTAAA
129 CGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAA
* * * *
29542 TCTCAGCGACATTGGATTTAAGAATTTGTTTTTACAAGAATCTAAATATTGTTTCAATTTAATTA
194 TCTCAGC-ACATTGGATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAATTA
* * *
29607 GAAATTAA-TTCAAAAAAAATAGGAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATTTTTTT
258 GAAATTAATTTC-AAAAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCCC-TCAATTTTTTT
* *
29671 GATGTCGAATT
321 GGTGTTGAATT
* *
29682 ATATAT-TTCTTATGAGTATTTTAGCCAAAAATTAAGGAAATATCTTCTGGGTCAATTTTTACAA
1 TTATATATT-TTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTCTGGGTCAATTTTTACAA
* * *
29746 AATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGTCTAAAAACGCGTTCCGATG-CCAG
65 AATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAGGACCAC
** * *** * * * *
29810 GGCTGTGTTTTGCATGATTTTTGACGCTGGGACTCCTTG-AATGATCTTTATTTATTTAATCAAA
130 GGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT-ATCTATATTCATCTAACCAAA
** *
29874 TCTCAGTCACATTGGATTTAAGGATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTTAATTA
194 TCTCAG-CACATTGGATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAATTA
* * * * * *
29939 GAAATT-AGTTCAGAAAAATATGAAAATCGATATTTAGAAGCATGAAAAGTCCTCTATTCTTTTT
258 GAAATTAATTTCAAAAAAATAGGAAAAACGATA-TTAGAAGCATGAAAAGCCCTCAATT-TTTTT
*
30003 GGTATTGAATT
321 GGTGTTGAATT
*
30014 TTATATATATTATGAGTATTTTTA-CCAAAAATTGAGGAAA
1 TTATATATTTTATGAGTA-TTTTAGCCAAAAATTGAGGAAA
30054 AATTCCGGTC
Statistics
Matches: 844, Mismatches: 151, Indels: 87
0.78 0.14 0.08
Matches are distributed among these distances:
328 10 0.01
329 55 0.07
330 74 0.09
331 252 0.30
332 187 0.22
333 91 0.11
334 26 0.03
335 70 0.08
336 56 0.07
337 18 0.02
338 5 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (331 bp):
TTATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTCTGGGTCAATTTTTACAAA
ATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAGGACCACG
GCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATC
TCAGCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAATTAGAA
ATTAATTTCAAAAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCCCTCAATTTTTTTGGTGT
TGAATT
Found at i:34054 original size:28 final size:28
Alignment explanation
Indices: 34014--34069 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
34004 AACAAGACGC
34014 TAATGGTTACTATTCGATGAGCTTAGTT
1 TAATGGTTACTATTCGATGAGCTTAGTT
34042 TAATGGTTACTATTCGATGAGCTTAGTT
1 TAATGGTTACTATTCGATGAGCTTAGTT
34070 GATACTAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (28 bp):
TAATGGTTACTATTCGATGAGCTTAGTT
Found at i:35388 original size:25 final size:25
Alignment explanation
Indices: 35359--35410 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
35349 TCTTAGCCTC
35359 TACTTTACCCCTCCGTTCTTTTCAA
1 TACTTTACCCCTCCGTTCTTTTCAA
35384 TACTTTACCCCTCCGTTCTTTTCAA
1 TACTTTACCCCTCCGTTCTTTTCAA
35409 TA
1 TA
35411 AATCAGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.17, C:0.35, G:0.04, T:0.44
Consensus pattern (25 bp):
TACTTTACCCCTCCGTTCTTTTCAA
Found at i:37007 original size:31 final size:30
Alignment explanation
Indices: 36969--37132 Score: 99
Period size: 31 Copynumber: 5.4 Consensus size: 30
36959 TTAGGCTAAT
36969 TGCTCAAATAAGGATCTAACGTTTATCAAAA
1 TGCTCAAATAAGGATCTAAC-TTTATCAAAA
* **
37000 TGCTCAAATAACGG-TCTGATCTTT-T-AATT
1 TGCTCAAATAA-GGATCT-AACTTTATCAAAA
* * *
37029 TGCCCAAATAAGGACCTAACATTATCGAAAA
1 TGCTCAAATAAGGATCTAACTTTATC-AAAA
* * * * **
37060 TGTTCAAATAAGGGTCCGATCTTT-T-AATT
1 TGCTCAAATAAGGAT-CTAACTTTATCAAAA
37089 TGGC-CAAATAAGGATCTAA-TGTTATCGAAAA
1 T-GCTCAAATAAGGATCTAACT-TTATC-AAAA
37120 TGCTCAAATAAGG
1 TGCTCAAATAAGG
37133 GTCCGATGTC
Statistics
Matches: 96, Mismatches: 24, Indels: 26
0.66 0.16 0.18
Matches are distributed among these distances:
27 1 0.01
28 10 0.10
29 29 0.30
30 4 0.04
31 43 0.45
32 9 0.09
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (30 bp):
TGCTCAAATAAGGATCTAACTTTATCAAAA
Found at i:37040 original size:60 final size:60
Alignment explanation
Indices: 36968--37139 Score: 256
Period size: 60 Copynumber: 2.9 Consensus size: 60
36958 TTTAGGCTAA
* * *
36968 TTGCTCAAATAAGGATCTAACGTTTATC-AAAATGCTCAAATAACGGTCTGATCTTTTAAT
1 TTGCCCAAATAAGGATCTAACG-TTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAAT
* * *
37028 TTGCCCAAATAAGGACCTAACATTATCGAAAATGTTCAAATAAGGGTCCGATCTTTTAAT
1 TTGCCCAAATAAGGATCTAACGTTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAAT
* *
37088 TTGGCCAAATAAGGATCTAATGTTATCGAAAATGCTCAAATAAGGGTCCGAT
1 TTGCCCAAATAAGGATCTAACGTTATCGAAAATGCTCAAATAAGGGTCCGAT
37140 GTCAATTTGG
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 5 0.05
60 95 0.95
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (60 bp):
TTGCCCAAATAAGGATCTAACGTTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAAT
Found at i:37336 original size:60 final size:59
Alignment explanation
Indices: 37182--37338 Score: 163
Period size: 60 Copynumber: 2.6 Consensus size: 59
37172 ACCAGGCCCT
* * * * * *
37182 TATTTGAGCATTTTGGCAAACTTTAGACCCTTATTTGGCCAAAGTAAAAGATCGGGCTCT
1 TATTTGAGCATTTTGGCAAA-TTTAGGCCTTTATTTGGCCAAAGTAAAAGATCAGACCCC
* *** * *
37242 TATTTGAGTATTTTGGCAAACGGCAGG-TTCTTATTTGGCCAAATTAAAAGATCAGACCCC
1 TATTTGAGCATTTTGGCAAA-TTTAGGCCT-TTATTTGGCCAAAGTAAAAGATCAGACCCC
37302 TATTTGAGCATTTTGGCAAATATTAGGCCTTTATTTG
1 TATTTGAGCATTTTGGCAAAT-TTAGGCCTTTATTTG
37339 AGTAATTAAC
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
60 76 0.99
61 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (59 bp):
TATTTGAGCATTTTGGCAAATTTAGGCCTTTATTTGGCCAAAGTAAAAGATCAGACCCC
Found at i:38335 original size:37 final size:37
Alignment explanation
Indices: 38294--38368 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
38284 AAAAATAGTT
38294 TAGGAGATTATATAATTTGTTTATAAAACATAATAAA
1 TAGGAGATTATATAATTTGTTTATAAAACATAATAAA
38331 TAGGAGATTATATAATTTGTTTATAAAACATAATAAA
1 TAGGAGATTATATAATTTGTTTATAAAACATAATAAA
38368 T
1 T
38369 GCTCATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.39
Consensus pattern (37 bp):
TAGGAGATTATATAATTTGTTTATAAAACATAATAAA
Found at i:41776 original size:12 final size:13
Alignment explanation
Indices: 41759--41787 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
41749 TTTGCAGAAG
41759 ATATCTATAT-CT
1 ATATCTATATACT
41771 ATATCTATATACT
1 ATATCTATATACT
41784 ATAT
1 ATAT
41788 AAGTCTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATCTATATACT
Done.