Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015006.1 Corchorus olitorius cultivar O-4 contig15039, 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: 57440
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:5840 original size:3 final size:3
Alignment explanation
Indices: 5832--5881 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
5822 AAATTGGCAC
*
5832 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5880 AA
1 AA
5882 ACCAATTCCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:15561 original size:32 final size:33
Alignment explanation
Indices: 15494--15561 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
15484 TTGATCCATT
* * *
15494 AAACAGCAACAAAATCAGCATTAAAACAGCGACA
1 AAACAACAACAAAA-CAGCAGTAAAACAGCAACA
15528 AAACAACAACAAAA-AGCAGTAAAACAGCAACA
1 AAACAACAACAAAACAGCAGTAAAACAGCAACA
15560 AA
1 AA
15562 CAATATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 18 0.58
34 13 0.42
ACGTcount: A:0.62, C:0.22, G:0.10, T:0.06
Consensus pattern (33 bp):
AAACAACAACAAAACAGCAGTAAAACAGCAACA
Found at i:15573 original size:11 final size:11
Alignment explanation
Indices: 15559--15594 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
15549 AAACAGCAAC
15559 AAACAATATAA
1 AAACAATATAA
15570 AAACAATATAA
1 AAACAATATAA
*
15581 AAACAGTATAA
1 AAACAATATAA
15592 AAA
1 AAA
15595 AAGCAAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.17
Consensus pattern (11 bp):
AAACAATATAA
Found at i:20630 original size:29 final size:30
Alignment explanation
Indices: 20566--20630 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
20556 ACTGAGATAT
*
20566 AAAAAAAACCATTATATACATAGTGCATCC
1 AAAAAAAACCATTATATACATAATGCATCC
* *
20596 AAAAAAAGACCATTCTATACATAATGTATCC
1 AAAAAAA-ACCATTATATACATAATGCATCC
20627 AAAA
1 AAAA
20631 TCCCATGTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.52, C:0.18, G:0.06, T:0.23
Consensus pattern (30 bp):
AAAAAAAACCATTATATACATAATGCATCC
Found at i:20675 original size:2 final size:2
Alignment explanation
Indices: 20668--20748 Score: 73
Period size: 2 Copynumber: 40.0 Consensus size: 2
20658 AAATAGACCA
20668 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT ACT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
20709 AT ACT A- AT AT ACT AT ACT A- AT ACT A- AT AT AT AT ACT AT AT
1 AT A-T AT AT AT A-T AT A-T AT AT A-T AT AT AT AT AT A-T AT AT
20749 GTTATTTGAA
Statistics
Matches: 68, Mismatches: 0, Indels: 22
0.76 0.00 0.24
Matches are distributed among these distances:
1 5 0.07
2 52 0.76
3 11 0.16
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:27153 original size:15 final size:15
Alignment explanation
Indices: 27133--27163 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
27123 ACTTCTTTTT
27133 TTATACATAAAACAA
1 TTATACATAAAACAA
27148 TTATACATAAAACAA
1 TTATACATAAAACAA
27163 T
1 T
27164 CAAAGCAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (15 bp):
TTATACATAAAACAA
Found at i:27607 original size:6 final size:6
Alignment explanation
Indices: 27596--27632 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
27586 GGCAGAAGCT
* *
27596 ACATTA ACATTA ACACTA ACATTA ACATTA ACTTTA A
1 ACATTA ACATTA ACATTA ACATTA ACATTA ACATTA A
27633 AAAAGCACCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (6 bp):
ACATTA
Found at i:31148 original size:178 final size:179
Alignment explanation
Indices: 30843--31280 Score: 501
Period size: 178 Copynumber: 2.5 Consensus size: 179
30833 CACTCTGGAT
* * * *
30843 ATCTGATTAAGGTGATTCAAGTGTCTATTAAAATGTTATTCAATGATCTACAACTTTTAT-GAAG
1 ATCTGATTGAGGTGATTCAAGTGTCTATTAAAAGGTTATTCCATGATCTACAACTTTCATGGAAG
** * * * *
30907 GGCTCGAAAACTAAATTTAATGTTTCAAATATCAAAAATACTTCCGAAAAATTAGTTGTTTTGGT
66 AACTCGAAAACTAAATTTAATATTTCAAATATCAAAAATACTTCCAAAAAAATAGTAGTTTTGGT
* *
30972 TAGCGAGAAT-GAGCGGTCCACTTAATATTACATAACTTTTCCTCCAAAC
131 TAGAGAGAATGGA-CGATCCACTTAATATTACATAACTTTTCCTCCAAAC
* * * *
31021 GTCTGATTGAGGTGATTCAAGTGTCTCTTAAAAGGTTGTTCCATGATCTACGACTTTCATGGAA-
1 ATCTGATTGAGGTGATTCAAGTGTCTATTAAAAGGTTATTCCATGATCTACAACTTTCATGGAAG
* * *
31085 AACTCTAAAGCTAAATTTAATATTTCAAATAT-AAGAAATGCTT-CAAAAAACATAGTAGTTTTG
66 AACTCGAAAACTAAATTTAATATTTCAAATATCAA-AAATACTTCCAAAAAA-ATAGTAGTTTTG
* * * * ** * ***
31148 GTTAGAGGGAATGGATGATCTACTTAATATTACATAATTTTTGTTCTAGGT
129 GTTAGAGAGAATGGACGATCCACTTAATATTACATAACTTTTCCTCCAAAC
* * *
31199 ATCTGATTGAGATGATTCAAGTGTCTGTTAAAAGGTTATTTCATGATCTACAACTTTCAT-GAAG
1 ATCTGATTGAGGTGATTCAAGTGTCTATTAAAAGGTTATTCCATGATCTACAACTTTCATGGAAG
* *
31263 AATTCAAAAACTAAATTT
66 AACTCGAAAACTAAATTT
31281 TATTGTGACC
Statistics
Matches: 217, Mismatches: 38, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
177 11 0.05
178 201 0.93
179 5 0.02
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (179 bp):
ATCTGATTGAGGTGATTCAAGTGTCTATTAAAAGGTTATTCCATGATCTACAACTTTCATGGAAG
AACTCGAAAACTAAATTTAATATTTCAAATATCAAAAATACTTCCAAAAAAATAGTAGTTTTGGT
TAGAGAGAATGGACGATCCACTTAATATTACATAACTTTTCCTCCAAAC
Found at i:32353 original size:164 final size:166
Alignment explanation
Indices: 32068--32370 Score: 463
Period size: 164 Copynumber: 1.8 Consensus size: 166
32058 TCGAACATTC
*
32068 TAATAAATTGTTTTAAATTTCTTCTCGTGTAATACTACTATAACTAAATTAGTGTCCACTATCAC
1 TAATAAATTGTTTTAAATTTCGTCTCGTGTAATACTACTATAACTAAATTAGTGTCCACTATCAC
32133 CTCATGTAAATCCCCCTTAAAAATAAATAAATAAGAATTCTGTCCATTTTGGG-AAAA-GAAAAA
66 CTCATGTAAATCCCCCTTAAAAATAAATAAATAAGAATTCTGTCCATTTTGGGAAAAATGAAAAA
*
32196 GAAAAAAAAGGAAAGTGTTTCTTCAAAAAAAAGTTA
131 AAAAAAAAAGGAAAGTGTTTCTTCAAAAAAAAGTTA
* *
32232 TAATAGATTGTTTTAAATTTCGTCTCGTGTAATACTACTATAACTAAATTAGTGTCCACTATTAC
1 TAATAAATTGTTTTAAATTTCGTCTCGTGTAATACTACTATAACTAAATTAGTGTCCACTATCAC
** * * *
32297 CTTGTGTAACTTCCCCTTGAATAAATAAATAAA-AAG-CTTC-GTCCATTTTGGGGAAAAATGAA
66 CTCATGTAAATCCCCCTT-AA-AAATAAATAAATAAGAATTCTGTCCATTTT-GGGAAAAATGAA
32359 AAAAAAAAAAAA
128 AAAAAAAAAAAA
32371 AACTCGATCA
Statistics
Matches: 125, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
163 9 0.07
164 82 0.66
165 9 0.07
166 25 0.20
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (166 bp):
TAATAAATTGTTTTAAATTTCGTCTCGTGTAATACTACTATAACTAAATTAGTGTCCACTATCAC
CTCATGTAAATCCCCCTTAAAAATAAATAAATAAGAATTCTGTCCATTTTGGGAAAAATGAAAAA
AAAAAAAAAGGAAAGTGTTTCTTCAAAAAAAAGTTA
Found at i:33271 original size:15 final size:15
Alignment explanation
Indices: 33247--33276 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33237 ACAAAAAGTT
*
33247 TCCGAGTTGTCAAAA
1 TCCGAATTGTCAAAA
33262 TCCGAATTGTCAAAA
1 TCCGAATTGTCAAAA
33277 GTTCCGGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (15 bp):
TCCGAATTGTCAAAA
Found at i:33549 original size:195 final size:196
Alignment explanation
Indices: 33286--35148 Score: 1085
Period size: 213 Copynumber: 9.0 Consensus size: 196
33276 AGTTCCGGAG
* * * * * * *
33286 TTGTCGAACCCTAAAGTTCCAAAAGTTTCTGAGCTAGAACAGTCAAAAACTCCGGATGAACTCTC
1 TTGTCGAAGCCTGAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGATGAACTCTC
* * * * *
33351 AAAATCAGAGAGC-CCAATTGCTCCAAAGCCAAATATATCCAACCAGGCTGAATTGCCTAAGCCG
66 AAAA-CAGAGAGCTCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCG
* *
33415 GAGTTCCCAAAGTCTGAGTTACCAAAACCTGAACAACAAAAAGCTTCAGAGTTGCCAAAACC-TG
130 GAGTTCCCAAAGCCTGAGTTACCAAAACCTGAACAACAAAAAGCTTCAGAGTTGTCAAAACCATG
33479 AA
195 AA
33481 TTGTCGAAGCCTGAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGATGAACTCTC
1 TTGTCGAAGCCTGAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGATGAACTCTC
* * * * *
33546 AAAACCGAAAACTCCAATTGTTCCAAAGCCAAACATAGCCAACCAACCTGAGTTGCCTAAGCCGG
66 AAAACAGAGAGCTCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCGG
** * *
33611 AAATACCAAAGCCTGAGTT-CTCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTGA
131 AGTTCCCAAAGCCTGAGTTAC-CAAAACCTGAACAACAAAAAGCTTCAGAGTTGTCAAAACC---
33675 AATGTCAAAAGA
192 -ATG-----A-A
* * * *
33687 TCCAAAAGTGTCGAAGCCTGAAGTTCCTA-AAATTTCTGAA-CTAGAAAAGTCGAAAGTTCCAGA
1 T-------TGTCGAAGCCTGAAGTTCC-ACAAGTTTCT-AACCTAGAAAAGTCAAAAATTCCGGA
* * * * *
33750 TGAACTTTCAAAACA-AGAGCACCCAAATGTTCCAAAGCCAAATATACCCAACCAGCATGAGTTG
57 TGAACTCTCAAAACAGAGAGC-TCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTG
* * * * *
33814 CCTAACCCGGAGTTCCCAAAGTCTGAGTTGCCAAAACGTGAACAACAAAAAGCTTCTGAGTTGTC
121 CCTAAGCCGGAGTTCCCAAAGCCTGAGTTACCAAAACCTGAACAACAAAAAGCTTCAGAGTTGTC
33879 AAAACCTGAATTGTCGAAAGTTCCGAA
186 AAAA-C--------C---A--T--GAA
33906 GTTGTCGAAGCCTGAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGATGAACTCT
1 -TTGTCGAAGCCTGAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGATGAACTCT
* * * * *
33971 CAAAAACAAAGA-CTTCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTCGCATATGCC
65 C-AAAACAGAGAGCTCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCC
* *
34035 GGAGTTGCCAAAGCCTGAGTTATCAAAACCTGAACAACAAAAA-CTTTCAGAGTTGTCAAAACCT
129 GGAGTTCCCAAAGCCTGAGTTACCAAAACCTGAACAACAAAAAGC-TTCAGAGTTGTCAAAACC-
34099 GAATTGTCTAAA
192 --A-TG----AA
* * * * * *
34111 GTTTCAGAGTTTTCTAAGCCTGAAGTTCCTA-AAGTTTCTGAGCTACAACAA-TCGAAAGTTCCG
1 --TT----G---TCGAAGCCTGAAGTTCC-ACAAGTTTCTAACCTAGAA-AAGTCAAAAATTCCG
* * * * *
34174 GATGAGCTTTCAAAACCAGAGCA-C-CCAAATGTTCCAAAGCCAAACACACCCAACCAACCTGAG
55 GATGAACTCTCAAAA-CAGAG-AGCTCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAG
* * * * * * * * *
34237 ATGTCTAAGCCGGAGTTACCAAAGTCTGAGTTACCAAAACATGAACAGCCAAAAGTTTTC-GAAT
118 TTGCCTAAGCCGGAGTTCCCAAAGCCTGAGTTACCAAAACCTGAACAACAAAAAG-CTTCAGAGT
*
34301 TGTCAAAAATTGAATCGTCAAAAGTTCTAGAG
182 TGTC---AA---AA-C--C---A----T-GAA
* * * *
34333 TTGTCGAAGCCTGAAGTTCCAAAAGTTTCTGAGCTAGAAAAGTCAAAAGTTCCGGATGAACTCTC
1 TTGTCGAAGCCTGAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGATGAACTCTC
* * ** * *
34398 AAAACCAGAAAGC-CCAATTGTTCCAAAGCCAAACATACCCAACCAGCCGGAGTTAACAAAGCCT
66 AAAA-CAGAGAGCTCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCG
* ** * *** * * * * **
34462 AAGTTGTCAAAACCTGAACAACAACAACAAGTTTCTGAGTTC-TC-AAAA-C--CTGAAATGTCG
130 GAGTTCCCAAAGCCTGAGTTAC--CAA-AA---CCTGA--ACAACAAAAAGCTTCAGAGTTGTC-
*
34522 AAAATTCCA-GAG
186 AAAA--CCATGAA
* ** * ** * * *
34534 TTGTCGAAGCCTGAAGTTTCTA-AAGTTTCCGAGCTAGAAAAGTTGAAAGTTCCGGATGAATTTT
1 TTGTCGAAGCCTGAAG-TTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGATGAACTCT
* * * * *
34598 CAAAACA-AGAGCACCCAAATGTTCCAAAGCCAAACTTACCCAACCAGTCTGAGTTGCCTAACCC
65 CAAAACAGAGAGC-TCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCC
* * * * * * *
34662 AGAGTTACCAAAGCCTGATTTGCCAAAACCTGAACAACAAAAAG-TTTATGAGCTATCAAAACCT
129 GGAGTTCCCAAAGCCTGAGTTACCAAAACCTGAACAACAAAAAGCTTCA-GAGTTGTCAAAACC-
34726 GAATTGTCGAAAGTTTCGGA
192 --A---T-G--A-------A
* * * * * ** * *
34746 GTTGTCAAAGCCTAAAGTTCCACAAGTTTCTGAGCTAGAAAAGTCGAAAATTCTAGATGAAGTGT
1 -TTGTCGAAGCCTGAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGATGAACTCT
*
34811 CAAAACCAGAGAGC-CCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAACCC
65 CAAAA-CAGAGAGCTCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCC
* * * * * *
34875 GGAGTTACCAAAGTCTGAGTTGCCAAATCCTGAACAACAAAAAGTTTCGGAGTTGTCAAAACCTG
129 GGAGTTCCCAAAGCCTGAGTTACCAAAACCTGAACAACAAAAAGCTTCAGAGTTGTCAAAACC--
34940 AATTGCCTAAA
192 -A-TG----AA
* * * * *
34951 GTTCTGAAGTTAACGAATCCTAAAGTTCCAAAAGTTTCTGACCTAGAAAAGTCAAAAATTCCGAA
1 --T-T---G-T--CGAAGCCTGAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGA
* * * * * *
35016 TGAAGTCTTAAAACCAAAGAGC-CCCATTGTTCCAAATCCAAACATACCCAACCAGCCTAAGTTG
57 TGAACTCTCAAAA-CAGAGAGCTCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTG
* * ** * *
35080 CCTAAGCCGGAGTTACCAAAGCATGAGTCCCCAAAACCTGAACAACAAAAAGTTTCAGAGTTCTC
121 CCTAAGCCGGAGTTCCCAAAGCCTGAGTTACCAAAACCTGAACAACAAAAAGCTTCAGAGTTGTC
35145 AAAA
186 AAAA
35149 TCTGATTTGT
Statistics
Matches: 1334, Mismatches: 206, Indels: 238
0.75 0.12 0.13
Matches are distributed among these distances:
193 1 0.00
194 7 0.01
195 171 0.13
197 4 0.00
198 8 0.01
199 7 0.01
200 4 0.00
201 118 0.09
202 4 0.00
203 3 0.00
204 3 0.00
205 5 0.00
206 5 0.00
207 2 0.00
210 4 0.00
211 4 0.00
212 24 0.02
213 880 0.66
214 26 0.02
215 12 0.01
216 12 0.01
219 10 0.01
220 6 0.00
221 5 0.00
222 5 0.00
223 1 0.00
225 2 0.00
226 1 0.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.22
Consensus pattern (196 bp):
TTGTCGAAGCCTGAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGATGAACTCTC
AAAACAGAGAGCTCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCGG
AGTTCCCAAAGCCTGAGTTACCAAAACCTGAACAACAAAAAGCTTCAGAGTTGTCAAAACCATGA
A
Found at i:33858 original size:213 final size:212
Alignment explanation
Indices: 33481--35229 Score: 1834
Period size: 213 Copynumber: 8.3 Consensus size: 212
33471 AAAACCTGAA
* * *
33481 TTGTCGAAGCCTGAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGATGAACTCTC
1 TTGTCGAAGCCTGAAGTTCCA-AAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGAACTTTC
* ** * *
33546 AAAAC-CGAAAACTCCAATTGTTCCAAAGCCAAACATAGCCAACCAACCTGAGTTGCCTAAGCCG
65 AAAACAAGAGCAC-CCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCG
**
33610 GAAATACCAAAGCCTGAGTT-CTCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTG
129 GAGTTACCAAAGCCTGAGTTGC-CAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTG
* * *
33674 AAATGTCAAAAGATCCAAAAG
193 AATTGTCAAAAGTTTC-AAAG
* * * * *
33695 -TGTCGAAGCCTGAAGTTCCTAAAATTTCTGAACTAGAAAAGTCGAAAGTTCCAGATGAACTTTC
1 TTGTCGAAGCCTGAAGTTCC-AAAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGAACTTTC
* * * *
33759 AAAACAAGAGCACCCAAATGTTCCAAAGCCAAATATACCCAACCAGCATGAGTTGCCTAACCCGG
65 AAAACAAGAGCACCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCGG
* * * * *
33824 AGTTCCCAAAGTCTGAGTTGCCAAAACGTGAACAACAAAAAGCTTCTGAGTTGTCAAAACCTGAA
130 AGTTACCAAAGCCTGAGTTGCCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTGAA
* * *
33889 TTGTCGAAAGTTCCGAAG
195 TTGTCAAAAGTTTCAAAG
* * *
33907 TTGTCGAAGCCTGAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGATGAACTCTC
1 TTGTCGAAGCCTGAAGTTCCA-AAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGAACTTTC
* * * *
33972 AAAAACAA-AG-ACTTCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTCGCATATGCC
65 -AAAACAAGAGCAC-CCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCC
* ** *
34035 GGAGTTGCCAAAGCCTGAGTTATCAAAACCTGAACAACAAAAACTTTCAGAGTTGTCAAAACCTG
128 GGAGTTACCAAAGCCTGAGTTGCCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTG
* *
34100 AATTGTCTAAAGTTTCAGAG
193 AATTGTCAAAAGTTTCAAAG
* * * * * *
34120 TTTTCTAAGCCTGAAGTTCCTAAAGTTTCTGAGCTACAACAA-TCGAAAGTTCCGGATGAGCTTT
1 TTGTCGAAGCCTGAAGTTCC-AAAGTTTCTGAGCTAGAA-AAGTCAAAAATTCCGGATGAACTTT
* * * * * *
34184 CAAAACCAGAGCACCCAAATGTTCCAAAGCCAAACACACCCAACCAACCTGAGATGTCTAAGCCG
64 CAAAACAAGAGCACCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCG
* * * * * * **
34249 GAGTTACCAAAGTCTGAGTTACCAAAACATGAACAGCCAAAAGTTTTC-GAATTGTCAAAAATTG
129 GAGTTACCAAAGCCTGAGTTGCCAAAACCTGAACAACAAAAAG-TTTCAGAGTTGTCAAAACCTG
* *
34313 AATCGTCAAAAG-TTCTAGAG
193 AATTGTCAAAAGTTTC-AAAG
* *
34333 TTGTCGAAGCCTGAAGTTCCAAAAGTTTCTGAGCTAGAAAAGTCAAAAGTTCCGGATGAACTCTC
1 TTGTCGAAGCCTGAAGTTCC-AAAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGAACTTTC
* *
34398 AAAACCAGA-AAGCCCAATTGTTCCAAAGCCAAACATA--C--CCA-----A----CC--AGCCG
65 AAAACAAGAGCA-CCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCG
* * * * *
34447 GAGTTAACAAAGCCTAAGTTGTCAAAACCTGAACAACAACAACAAGTTTCTGAGTTCTCAAAACC
129 GAGTTACCAAAGCCTGAGTTGCCAAAACCTGAACAAC-A-AA-AAGTTTCAGAGTTGTCAAAACC
* * *
34512 TGAAATGTCGAAAA-TTCCAGAG
191 TGAATTGTC-AAAAGTTTCAAAG
* * ** * *
34534 TTGTCGAAGCCTGAAGTTTCTAAAGTTTCCGAGCTAGAAAAGTTGAAAGTTCCGGATGAATTTTC
1 TTGTCGAAGCCTGAAG-TTCCAAAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGAACTTTC
* * * * *
34599 AAAACAAGAGCACCCAAATGTTCCAAAGCCAAACTTACCCAACCAGTCTGAGTTGCCTAACCCAG
65 AAAACAAGAGCACCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCGG
* * *
34664 AGTTACCAAAGCCTGATTTGCCAAAACCTGAACAACAAAAAGTTT-ATGAGCTATCAAAACCTGA
130 AGTTACCAAAGCCTGAGTTGCCAAAACCTGAACAACAAAAAGTTTCA-GAGTTGTCAAAACCTGA
* **
34728 ATTGTCGAAAGTTTCGGAG
194 ATTGTCAAAAGTTTCAAAG
* * * ** * *
34747 TTGTCAAAGCCTAAAGTTCCACAAGTTTCTGAGCTAGAAAAGTCGAAAATTCTAGATGAAGTGTC
1 TTGTCGAAGCCTGAAGTTCCA-AAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGAACTTTC
* *
34812 AAAACCAGAG-AGCCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAACCCG
65 AAAACAAGAGCA-CCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCG
* * *
34876 GAGTTACCAAAGTCTGAGTTGCCAAATCCTGAACAACAAAAAGTTTCGGAGTTGTCAAAACCTGA
129 GAGTTACCAAAGCCTGAGTTGCCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTGA
* * *
34941 ATTGCCTAAAG-TTCTGAAG
194 ATTGTCAAAAGTTTC-AAAG
** * * * * *
34960 TTAACGAATCCTAAAGTTCCAAAAGTTTCTGACCTAGAAAAGTCAAAAATTCCGAATGAAGTCTT
1 TTGTCGAAGCCTGAAGTTCC-AAAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGAACT-TT
* *
35025 -AAAACCAAAGAGC-CCC-ATTGTTCCAAATCCAAACATACCCAACCAGCCTAAGTTGCCTAAGC
64 CAAAA-C-AAGAGCACCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGC
* ** * *
35087 CGGAGTTACCAAAGCATGAGTCCCCAAAACCTGAACAACAAAAAGTTTCAGAGTTCTCAAAATCT
127 CGGAGTTACCAAAGCCTGAGTTGCCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCT
* * *
35152 GATTTGTCAAAAGCTTCGGAA-
192 GAATTGTCAAAAGTTTC-AAAG
* * * **
35173 TTGTCAAAGCCTGAAGTTCCTAAAGTTTCTGAGCTACAAAAATCGGAAATTCCGGAT
1 TTGTCGAAGCCTGAAGTTCC-AAAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGAT
35230 ATATTCTCAA
Statistics
Matches: 1289, Mismatches: 196, Indels: 101
0.81 0.12 0.06
Matches are distributed among these distances:
198 35 0.03
200 7 0.01
201 110 0.09
202 10 0.01
203 1 0.00
204 1 0.00
205 3 0.00
209 3 0.00
210 1 0.00
211 1 0.00
212 29 0.02
213 1009 0.78
214 38 0.03
215 5 0.00
216 36 0.03
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.22
Consensus pattern (212 bp):
TTGTCGAAGCCTGAAGTTCCAAAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGAACTTTCA
AAACAAGAGCACCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCGGA
GTTACCAAAGCCTGAGTTGCCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTGAAT
TGTCAAAAGTTTCAAAG
Found at i:34048 original size:426 final size:425
Alignment explanation
Indices: 33481--35242 Score: 2056
Period size: 426 Copynumber: 4.2 Consensus size: 425
33471 AAAACCTGAA
* *
33481 TTGTCGAAGCCTGAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGATGAACTCTC
1 TTGTCGAAGCCTGAAGTTCCACAAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGAACTCTC
* *
33546 AAAACCGAAAA-CTCCAATTGTTCCAAAGCCAAACATAGCCAACCAACCTGAGTTGCCTAAGCCG
66 AAAACC-AAAAGC-CCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCG
**
33610 GAAATACCAAAGCCTGAGTTCTCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTGA
129 GAGTTACCAAAGCCTGAGTTCTCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTGA
* *
33675 AATGTCAAAAGATCCAAAAG-TGTCGAAGCCTGAAGTTCCTAAAATTTCTGAACTAGAAAAGTCG
194 AATGTCAAAAGTTCC-AAAGTTGTCGAAGCCTGAAGTTCCTAAAATTTCTGAGCTAGAAAAGTCG
* *
33739 AAAGTTCCAGATGAACTTTCAAAACAAGAGCACCCAAATGTTCCAAAGCCAAATATACCCAACCA
258 AAAGTTCCGGATGAACTTTCAAAACAAGAGCACCCAAATGTTCCAAAGCCAAACATACCCAACCA
* * * *
33804 GCATGAGTTGCCTAACCCGGAGTTCCCAAAGTCTGAGTTGCCAAAACGTGAACAACAAAAAGCTT
323 GCCTGAGTTGCCTAACCCGGAGTTACCAAAGTCTGAGTTGCCAAAACCTGAACAACAAAAAGTTT
*
33869 CTGAGTTGTCAAAACCTGAATTGTCGAAAGTTCCGAAG
388 CTGAGTTGTCAAAACCTGAATTGTCAAAAGTTCCGAAG
* *
33907 TTGTCGAAGCCTGAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGATGAACTCTC
1 TTGTCGAAGCCTGAAGTTCCACAAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGAACTCTC
* * * * *
33972 AAAAAC-AAAGACTTCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTCGCATATGCCG
66 AAAACCAAAAG-C-CCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCG
* * *
34036 GAGTTGCCAAAGCCTGAGTTATCAAAACCTGAACAACAAAAACTTTCAGAGTTGTCAAAACCTGA
129 GAGTTACCAAAGCCTGAGTTCTCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTGA
* * * * * * * *
34101 ATTGTCTAAAGTTTCAGAGTTTTCTAAGCCTGAAGTTCCTAAAGTTTCTGAGCTACAACAA-TCG
194 AATGTCAAAAGTTCCAAAGTTGTCGAAGCCTGAAGTTCCTAAAATTTCTGAGCTAGAA-AAGTCG
* * *
34165 AAAGTTCCGGATGAGCTTTCAAAACCAGAGCACCCAAATGTTCCAAAGCCAAACACACCCAACCA
258 AAAGTTCCGGATGAACTTTCAAAACAAGAGCACCCAAATGTTCCAAAGCCAAACATACCCAACCA
* * * * * * * *
34230 ACCTGAGATGTCTAAGCCGGAGTTACCAAAGTCTGAGTTACCAAAACATGAACAGCCAAAAGTTT
323 GCCTGAGTTGCCTAACCCGGAGTTACCAAAGTCTGAGTTGCCAAAACCTGAACAACAAAAAGTTT
* ** * *
34295 -TCGAATTGTCAAAAATTGAATCGTCAAAAGTT-CTAGAG
388 CT-GAGTTGTCAAAACCTGAATTGTCAAAAGTTCCGA-AG
* *
34333 TTGTCGAAGCCTGAAGTTCCAAAAGTTTCTGAGCTAGAAAAGTCAAAAGTTCCGGATGAACTCTC
1 TTGTCGAAGCCTGAAGTTCCACAAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGAACTCTC
34398 AAAACCAGAAAGCCCAATTGTTCCAAAGCCAAACATA--C--CCA-----A----CC--AGCCGG
66 AAAACCA-AAAGCCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCGG
* * * * *
34448 AGTTAACAAAGCCTAAGTTGTCAAAACCTGAACAACAACAACAAGTTTCTGAGTTCTCAAAACCT
130 AGTTACCAAAGCCTGAGTTCTCAAAACCTGAACAAC-A-AA-AAGTTTCAGAGTTGTCAAAACCT
* * * *
34513 GAAATGTCGAAAA-TTCCAGAGTTGTCGAAGCCTGAAGTTTCTAAAGTTTCCGAGCTAGAAAAGT
192 GAAATGTC-AAAAGTTCCAAAGTTGTCGAAGCCTGAAGTTCCTAAAATTTCTGAGCTAGAAAAGT
* * *
34577 TGAAAGTTCCGGATGAATTTTCAAAACAAGAGCACCCAAATGTTCCAAAGCCAAACTTACCCAAC
256 CGAAAGTTCCGGATGAACTTTCAAAACAAGAGCACCCAAATGTTCCAAAGCCAAACATACCCAAC
* * * *
34642 CAGTCTGAGTTGCCTAACCCAGAGTTACCAAAGCCTGATTTGCCAAAACCTGAACAACAAAAAGT
321 CAGCCTGAGTTGCCTAACCCGGAGTTACCAAAGTCTGAGTTGCCAAAACCTGAACAACAAAAAGT
* * * * * *
34707 TTATGAGCTATCAAAACCTGAATTGTCGAAAGTTTCGGAG
386 TTCTGAGTTGTCAAAACCTGAATTGTCAAAAGTTCCGAAG
* * * ** * *
34747 TTGTCAAAGCCTAAAGTTCCACAAGTTTCTGAGCTAGAAAAGTCGAAAATTCTAGATGAAGTGTC
1 TTGTCGAAGCCTGAAGTTCCACAAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGAACTCTC
* *
34812 AAAACCAGAGAGCCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAACCCGG
66 AAAACCA-AAAGCCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCGG
* * *
34877 AGTTACCAAAGTCTGAGTTGC-CAAATCCTGAACAACAAAAAGTTTCGGAGTTGTCAAAACCTGA
130 AGTTACCAAAGCCTGAGTT-CTCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTGA
* * * ** ** * * * *
34941 ATTGCCTAAAGTTCTGAAGTTAACGAATCCTAAAGTTCC-AAAAGTTTCTGACCTAGAAAAGTCA
194 AATGTCAAAAGTTCCAAAGTTGTCGAAGCCTGAAGTTCCTAAAA-TTTCTGAGCTAGAAAAGTCG
* * * * *
35005 AAAATTCCGAATGAAGTCTT-AAAACCAAAGAGC-CCC-ATTGTTCCAAATCCAAACATACCCAA
258 AAAGTTCCGGATGAACT-TTCAAAA-C-AAGAGCACCCAAATGTTCCAAAGCCAAACATACCCAA
* * **
35067 CCAGCCTAAGTTGCCTAAGCCGGAGTTACCAAAG-CATGAGTCCCCAAAACCTGAACAACAAAAA
320 CCAGCCTGAGTTGCCTAACCCGGAGTTACCAAAGTC-TGAGTTGCCAAAACCTGAACAACAAAAA
* * * * *
35131 GTTTCAGAGTTCTCAAAATCTGATTTGTCAAAAGCTTCGGAA-
384 GTTTCTGAGTTGTCAAAACCTGAATTGTCAAAAG-TTCCGAAG
* * * ** *
35173 TTGTCAAAGCCTGAAGTTCCTA-AAGTTTCTGAGCTACAAAAATCGGAAATTCCGGAT-ATATTC
1 TTGTCGAAGCCTGAAGTTCC-ACAAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGA-ACTC
35236 TCAAAAC
64 TCAAAAC
35243 ATGAACCAAA
Statistics
Matches: 1137, Mismatches: 159, Indels: 80
0.83 0.12 0.06
Matches are distributed among these distances:
411 37 0.03
412 1 0.00
413 5 0.00
414 300 0.26
415 5 0.00
416 1 0.00
417 1 0.00
418 3 0.00
422 3 0.00
423 1 0.00
424 4 0.00
425 14 0.01
426 698 0.61
427 18 0.02
428 11 0.01
429 35 0.03
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.22
Consensus pattern (425 bp):
TTGTCGAAGCCTGAAGTTCCACAAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGAACTCTC
AAAACCAAAAGCCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCCTAAGCCGGA
GTTACCAAAGCCTGAGTTCTCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTGAAA
TGTCAAAAGTTCCAAAGTTGTCGAAGCCTGAAGTTCCTAAAATTTCTGAGCTAGAAAAGTCGAAA
GTTCCGGATGAACTTTCAAAACAAGAGCACCCAAATGTTCCAAAGCCAAACATACCCAACCAGCC
TGAGTTGCCTAACCCGGAGTTACCAAAGTCTGAGTTGCCAAAACCTGAACAACAAAAAGTTTCTG
AGTTGTCAAAACCTGAATTGTCAAAAGTTCCGAAG
Found at i:34116 original size:33 final size:33
Alignment explanation
Indices: 34079--34148 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
34069 CAACAAAAAC
*
34079 TTTCAGAGTTGTCAAAACCTGAA-TTGTCTAAAG
1 TTTCAGAGTTGTCAAAACCTGAAGTT-CCTAAAG
* * *
34112 TTTCAGAGTTTTCTAAGCCTGAAGTTCCTAAAG
1 TTTCAGAGTTGTCAAAACCTGAAGTTCCTAAAG
34145 TTTC
1 TTTC
34149 TGAGCTACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (33 bp):
TTTCAGAGTTGTCAAAACCTGAAGTTCCTAAAG
Found at i:34832 original size:840 final size:836
Alignment explanation
Indices: 33202--35242 Score: 2433
Period size: 840 Copynumber: 2.4 Consensus size: 836
33192 CAACCAGTCT
* * * * *
33202 GAGTTGCCTAAGGCAGAGTTTCCAAAACTTGAACAACAAAAAGTTTCCGAGTTGTCAAAATCC-G
1 GAGTTGCCAAAGCCTGAGTTT-CAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAA-CCTG
* * * * *
33266 AATTGTCAAAAGTTCCGGAGTTGTCGAACCCTAAAGTTCCAAAAGTTTCTGAGCTAGAACAGTCA
64 AATTGTCTAAAGTTTCAGAGTTATCGAACCCTAAAGTTCCAAAAGTTTCTGAGCTAGAACAATCA
* * * * * * *
33331 AAAACTCCGGATGAACTCTCAAAATCAGAG-AGCCCAATTGCTCCAAAGCCAAATATATCCAACC
129 AAAATTCCGGATGAGCTTTCAAAACCAGAGCA-CCCAATTGTTCCAAAGCCAAACATACCCAACC
* *
33395 AGGCTGA-ATTGCCTAAGCCGGAGTTCCCAAAGTCTGAGTTACCAAAACCTGAACAACAAAAAG-
193 AGCCTGAGA-TGCCTAAGCCGGAGTTACCAAAGTCTGAGTTACCAAAACCTGAACAACAAAAAGT
* * * * *
33458 --C---TTCAGAGTTG--C--CAAAA--CCTGAATTGTCGAAGCCTGAAGTTCCACAAGTTTCTA
257 TTCGATTTCAAAATTGATCGTCAAAAGTTCTGAATTGTCGAAGCCTGAAGTTCCAAAAGTTTCTG
*
33512 ACCTAGAAAAGTCAAAAATTCCGGATGAACTCTCAAAACCGAAAACTCCAATTGTTCCAAAGCCA
322 AGCTAGAAAAGTCAAAAATTCCGGATGAACTCTCAAAACCGAAAACTCCAATTGTTCCAAAGCCA
* *
33577 AACATAGCCAACCAACCTGAGTTGCCTAAGCCGGAAATACCAAAGCCTGAGTTCTCAAAACCTGA
387 AACATA-CC-ACCAA-C--A---GCC-AAGCCGGAAATAACAAAGCCTAAGTTCTCAAAACCTGA
*
33642 ACAACAAAAAGTTTCAGAGTTGTCAAAACCTGAAATGTCAAAAGATCCAAAAGTGTCGAAGCCTG
443 ACAACAAAAAGTTTCAGAGTTCTCAAAACCTGAAATGTCAAAAGATCCAAAAGTGTCGAAGCCTG
*
33707 AAGTTCCTAAAATTTCTGAACTAGAAAAGTCGAAAGTTCCAGATGAACTTTCAAAACAAGAGCAC
508 AAGTTCCTAAAATTTCCGAACTAGAAAAGTCGAAAGTTCCAGATGAACTTTCAAAACAAGAGCAC
* * *
33772 CCAAATGTTCCAAAGCCAAATATACCCAACCAGCATGAGTTGCCTAACCCGGAGTTCCCAAAGTC
573 CCAAATGTTCCAAAGCCAAATATACCCAACCAGCATGAGTTGCCTAACCCAGAGTTACCAAAGCC
* * * *
33837 TGAGTTGCCAAAACGTGAACAACAAAAAGCTTCTGAGTTGTCAAAACCTGAATTGTCGAAAGTTC
638 TGAGTTGCCAAAACCTGAACAACAAAAAGCTTATGAGCTATCAAAACCTGAATTGTCGAAAGTTC
* * *
33902 CGAAGTTGTCGAAGCCTGAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCGGATGAA
703 CGAAGTTGTCAAAGCCTAAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCAGATGAA
* *
33967 CTCTCAAAAACAAAGACTTCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTCGCATAT
768 CTCTCAAAAACAAAGACTCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTCGCATAA
*
34032 GCCG
833 CCCG
*
34036 GAGTTGCCAAAGCCTGAGTTATCAAAACCTGAACAACAAAAACTTTCAGAGTTGTCAAAACCTGA
1 GAGTTGCCAAAGCCTGAGTT-TCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTGA
* * * * * * *
34101 ATTGTCTAAAGTTTCAGAGTTTTCTAAGCCTGAAGTTCCTAAAGTTTCTGAGCTACAACAATCGA
65 ATTGTCTAAAGTTTCAGAGTTATCGAACCCTAAAGTTCCAAAAGTTTCTGAGCTAGAACAATCAA
* * * *
34166 AAGTTCCGGATGAGCTTTCAAAACCAGAGCACCCAAATGTTCCAAAGCCAAACACACCCAACCAA
130 AAATTCCGGATGAGCTTTCAAAACCAGAGCACCCAATTGTTCCAAAGCCAAACATACCCAACCAG
* * * *
34231 CCTGAGATGTCTAAGCCGGAGTTACCAAAGTCTGAGTTACCAAAACATGAACAGCCAAAAGTTTT
195 CCTGAGATGCCTAAGCCGGAGTTACCAAAGTCTGAGTTACCAAAACCTGAACAACAAAAAG-TTT
*
34296 CGAATTGTCAAAAATTGAATCGTCAAAAGTTCTAGAGTTGTCGAAGCCTGAAGTTCCAAAAGTTT
259 CG-ATT-TC-AAAATTG-ATCGTCAAAAGTTCT-GAATTGTCGAAGCCTGAAGTTCCAAAAGTTT
* *
34361 CTGAGCTAGAAAAGTCAAAAGTTCCGGATGAACTCTCAAAACCAGAAAGC-CCAATTGTTCCAAA
319 CTGAGCTAGAAAAGTCAAAAATTCCGGATGAACTCTCAAAACC-GAAAACTCCAATTGTTCCAAA
** *
34425 GCCAAACATA-C-CC-A-A-CC-AGCCGGAGTTAACAAAGCCTAAGTTGTCAAAACCTGAACAAC
383 GCCAAACATACCACCAACAGCCAAGCCGGAAATAACAAAGCCTAAGTTCTCAAAACCTGAACAAC
* * *
34484 AACAACAAGTTTCTGAGTTCTCAAAACCTGAAATGTCGAAAA-TTCC-AGAGTTGTCGAAGCCTG
448 -A-AA-AAGTTTCAGAGTTCTCAAAACCTGAAATGTC-AAAAGATCCAAAAG-TGTCGAAGCCTG
* * * * * *
34547 AAGTTTCTAAAGTTTCCGAGCTAGAAAAGTTGAAAGTTCCGGATGAATTTTCAAAACAAGAGCAC
508 AAGTTCCTAAAATTTCCGAACTAGAAAAGTCGAAAGTTCCAGATGAACTTTCAAAACAAGAGCAC
34612 CCAAATGTTCCAAAGCCAAACT-TACCCAACCAGTC-TGAGTTGCCTAACCCAGAGTTACCAAAG
573 CCAAATGTTCCAAAGCCAAA-TATACCCAACCAG-CATGAGTTGCCTAACCCAGAGTTACCAAAG
* *
34675 CCTGATTTGCCAAAACCTGAACAACAAAAAGTTTATGAGCTATCAAAACCTGAATTGTCGAAAGT
636 CCTGAGTTGCCAAAACCTGAACAACAAAAAGCTTATGAGCTATCAAAACCTGAATTGTCGAAAGT
* * * * * *
34740 TTCGGAGTTGTCAAAGCCTAAAGTTCCACAAGTTTCTGAGCTAGAAAAGTCGAAAATTCTAGATG
701 TCCGAAGTTGTCAAAGCCTAAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCAGATG
* * * * * *
34805 AAGTGTCAAAACCAGAGAGC-CCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTTGCC
766 AACTCTCAAAAACAAAGA-CTCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTCGCA
34869 TAACCCG
830 TAACCCG
* * * * *
34876 GAGTTACCAAAGTCTGAGTTGCCAAATCCTGAACAACAAAAAGTTTCGGAGTTGTCAAAACCTGA
1 GAGTTGCCAAAGCCTGAGTT-TCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTGA
* * * * *
34941 ATTGCCTAAAG-TTCTGAAGTTAACGAATCCTAAAGTTCCAAAAGTTTCTGACCTAGAA-AAGTC
65 ATTGTCTAAAGTTTCAG-AGTTATCGAACCCTAAAGTTCCAAAAGTTTCTGAGCTAGAACAA-TC
* *
35004 AAAAATTCCGAATGAAG-TCTT-AAAACCAAAGAGC-CCC-ATTGTTCCAAATCCAAACATACCC
128 AAAAATTCCGGATG-AGCT-TTCAAAACC--AGAGCACCCAATTGTTCCAAAGCCAAACATACCC
* * **
35065 AACCAGCCTAAGTTGCCTAAGCCGGAGTTACCAAAG-CATGAGTCCCCAAAACCTGAACAACAAA
189 AACCAGCCTGAGATGCCTAAGCCGGAGTTACCAAAGTC-TGAGTTACCAAAACCTGAACAACAAA
* * * *
35129 AAGTTTCAGAGTTCTCAAAATCTGATTTGTCAAAAGCTTCGGAATTGTCAAAGCCTGAAGTTCCT
253 AAGTTTC-GA-TT-TCAAAAT-TGA-TCGTCAAAAG-TTCTGAATTGTCGAAGCCTGAAGTTCCA
* * ** *
35194 AAAGTTTCTGAGCTACAAAAATCGGAAATTCCGGAT-ATATTCTCAAAAC
312 AAAGTTTCTGAGCTAGAAAAGTCAAAAATTCCGGATGA-ACTCTCAAAAC
35243 ATGAACCAAA
Statistics
Matches: 1033, Mismatches: 130, Indels: 82
0.83 0.10 0.07
Matches are distributed among these distances:
833 2 0.00
834 213 0.21
835 3 0.00
837 37 0.04
838 2 0.00
839 26 0.03
840 609 0.59
841 17 0.02
842 6 0.01
843 3 0.00
844 5 0.00
847 2 0.00
848 2 0.00
849 5 0.00
850 1 0.00
851 2 0.00
852 93 0.09
853 5 0.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.22
Consensus pattern (836 bp):
GAGTTGCCAAAGCCTGAGTTTCAAAACCTGAACAACAAAAAGTTTCAGAGTTGTCAAAACCTGAA
TTGTCTAAAGTTTCAGAGTTATCGAACCCTAAAGTTCCAAAAGTTTCTGAGCTAGAACAATCAAA
AATTCCGGATGAGCTTTCAAAACCAGAGCACCCAATTGTTCCAAAGCCAAACATACCCAACCAGC
CTGAGATGCCTAAGCCGGAGTTACCAAAGTCTGAGTTACCAAAACCTGAACAACAAAAAGTTTCG
ATTTCAAAATTGATCGTCAAAAGTTCTGAATTGTCGAAGCCTGAAGTTCCAAAAGTTTCTGAGCT
AGAAAAGTCAAAAATTCCGGATGAACTCTCAAAACCGAAAACTCCAATTGTTCCAAAGCCAAACA
TACCACCAACAGCCAAGCCGGAAATAACAAAGCCTAAGTTCTCAAAACCTGAACAACAAAAAGTT
TCAGAGTTCTCAAAACCTGAAATGTCAAAAGATCCAAAAGTGTCGAAGCCTGAAGTTCCTAAAAT
TTCCGAACTAGAAAAGTCGAAAGTTCCAGATGAACTTTCAAAACAAGAGCACCCAAATGTTCCAA
AGCCAAATATACCCAACCAGCATGAGTTGCCTAACCCAGAGTTACCAAAGCCTGAGTTGCCAAAA
CCTGAACAACAAAAAGCTTATGAGCTATCAAAACCTGAATTGTCGAAAGTTCCGAAGTTGTCAAA
GCCTAAAGTTCCACAAGTTTCTAACCTAGAAAAGTCAAAAATTCCAGATGAACTCTCAAAAACAA
AGACTCCAATTGTTCCAAAGCCAAACATACCCAACCAGCCTGAGTCGCATAACCCG
Found at i:35711 original size:35 final size:31
Alignment explanation
Indices: 35672--35742 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
35662 TTATGAGTCT
*
35672 TTTGTAAACCTAAATGCATCTTATTATATGTGTTG
1 TTTGTAAACCT-AATGCATC---GTATATGTGTTG
* *
35707 TTTGTAGACCTAATGTATCGTATATGTGTTG
1 TTTGTAAACCTAATGCATCGTATATGTGTTG
35738 TTTGT
1 TTTGT
35743 GTTTGTGGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 16 0.48
34 7 0.21
35 10 0.30
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.48
Consensus pattern (31 bp):
TTTGTAAACCTAATGCATCGTATATGTGTTG
Found at i:35784 original size:28 final size:28
Alignment explanation
Indices: 35738--35791 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
35728 ATATGTGTTG
*
35738 TTTGTGTTTGTGGTGTCAGAGTGATTCT
1 TTTGTGTTTATGGTGTCAGAGTGATTCT
* *
35766 TTTGTGTTTATTGTTTCAGAGTGATT
1 TTTGTGTTTATGGTGTCAGAGTGATT
35792 ATAGCGTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.13, C:0.06, G:0.28, T:0.54
Consensus pattern (28 bp):
TTTGTGTTTATGGTGTCAGAGTGATTCT
Found at i:44073 original size:270 final size:269
Alignment explanation
Indices: 43537--44350 Score: 1495
Period size: 270 Copynumber: 3.0 Consensus size: 269
43527 TTTTTTGTTC
*
43537 TTTTAAGCATATTAGTCAGTCAGCAAATACTTTGGCTCATAATCTAGCCCAACTTGAATGTGATG
1 TTTTAAGCATATTAGTCGGTCAGCAAATACTTTGGCTCATAATCTAGCCCAACTTGAATGTGATG
43602 TAGGGGCTAATTATGTTTGGTGCGGATTACCTCTGCACGTTTGTAATTCTGATTTTTGATATCAA
66 TAGGGGCTAATTATGTTTGGTGCGGATTACCTCTGCACGTTTGTAATTCTGATTTTTGATATCAA
* *
43667 TGAAAATTGATCGTTTTTACTAAAATAACATGATAGGGACAAATTTGTGAAATTATTCCTTAGGT
131 TGAAAATTGATCGTTTTAATTAAAA-AACATGATAGGGACAAATTTGTGAAATTATTCCTTAGGT
* *
43732 GTATTTCATGTAAGCCAATGTTTTTCAATACGTGTCCAACCTTTAAGAAAAAGAAAAACAAATCT
195 GTATTTCATGTAAGCCAATGTTTTTCAATACGTGTCCAAGCTTTAAGAAAAAGAAAAACAAATCC
43797 TTTTGCAGAA
260 TTTTGCAGAA
*
43807 TTTTAAGCATATTAGTCGGTCAGCAAATACTTTGACTCATAATCTAGCCCAACTTGAATGTGATG
1 TTTTAAGCATATTAGTCGGTCAGCAAATACTTTGGCTCATAATCTAGCCCAACTTGAATGTGATG
*
43872 TAGGGGCTAATCATGTTTGGTGCGGATTACCTCTGCACGTTTGTAATTCTGATTTTTGATATCAA
66 TAGGGGCTAATTATGTTTGGTGCGGATTACCTCTGCACGTTTGTAATTCTGATTTTTGATATCAA
43937 TGAAAATTGATCGTTTTAATTAAAAAACATGATAGGGACAAATTTGTGAAATTATTCCTTAGGTG
131 TGAAAATTGATCGTTTTAATTAAAAAACATGATAGGGACAAATTTGTGAAATTATTCCTTAGGTG
44002 TATTTCATGTAAGCCAATGTTTTTCAATACGTGTCCAAGCTTTAAGAAAAAGAAAAACAAATCGC
196 TATTTCATGTAAGCCAATGTTTTTCAATACGTGTCCAAGCTTTAAGAAAAAGAAAAACAAATC-C
44067 TTTTGCAGAA
260 TTTTGCAGAA
44077 TTTTAAGCATATTAGTCGGTCAGCAAATACTTTGGCTCATAATCTAGCCCAACTTGAATGTGATG
1 TTTTAAGCATATTAGTCGGTCAGCAAATACTTTGGCTCATAATCTAGCCCAACTTGAATGTGATG
* *
44142 TAGGGACTAATTATGTTTGGTGCGGATTACTTCTGCACGTTTGTAATTCTGATTTTTGATATCAA
66 TAGGGGCTAATTATGTTTGGTGCGGATTACCTCTGCACGTTTGTAATTCTGATTTTTGATATCAA
*
44207 TGAAAATTGATCGTTTTAACTAAAAAAACATGATAGGGACAAATTTGTGAAATTATTCCTTAGGT
131 TGAAAATTGATCGTTTTAA-TTAAAAAACATGATAGGGACAAATTTGTGAAATTATTCCTTAGGT
44272 GTATTTCATGTAAGCCAATGTTTTTCAATACGTGTCCAAGCTTTAAGAAAAAGAAAAACAAAT-C
195 GTATTTCATGTAAGCCAATGTTTTTCAATACGTGTCCAAGCTTTAAGAAAAAGAAAAACAAATCC
44336 TCTTTGCAGAA
260 T-TTTGCAGAA
44347 TTTT
1 TTTT
44351 GATGAAATAT
Statistics
Matches: 529, Mismatches: 12, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
269 104 0.20
270 318 0.60
271 107 0.20
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (269 bp):
TTTTAAGCATATTAGTCGGTCAGCAAATACTTTGGCTCATAATCTAGCCCAACTTGAATGTGATG
TAGGGGCTAATTATGTTTGGTGCGGATTACCTCTGCACGTTTGTAATTCTGATTTTTGATATCAA
TGAAAATTGATCGTTTTAATTAAAAAACATGATAGGGACAAATTTGTGAAATTATTCCTTAGGTG
TATTTCATGTAAGCCAATGTTTTTCAATACGTGTCCAAGCTTTAAGAAAAAGAAAAACAAATCCT
TTTGCAGAA
Found at i:45025 original size:15 final size:15
Alignment explanation
Indices: 45007--45055 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
44997 TTAATCTCGA
45007 CCTTTCTCTTCTCTC
1 CCTTTCTCTTCTCTC
* **
45022 CC-TTCTGCGTCTCAA
1 CCTTTCT-CTTCTCTC
45037 CCTTTCTCTTCTCTC
1 CCTTTCTCTTCTCTC
45052 CCTT
1 CCTT
45056 CTGCGTCTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 4 0.15
15 18 0.69
16 4 0.15
ACGTcount: A:0.04, C:0.45, G:0.04, T:0.47
Consensus pattern (15 bp):
CCTTTCTCTTCTCTC
Found at i:45042 original size:30 final size:30
Alignment explanation
Indices: 45001--45069 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
44991 TCAAAATTAA
*
45001 TCTCGACCTTTCTCTTCTCTCCCTTCTGCG
1 TCTCAACCTTTCTCTTCTCTCCCTTCTGCG
45031 TCTCAACCTTTCTCTTCTCTCCCTTCTGCG
1 TCTCAACCTTTCTCTTCTCTCCCTTCTGCG
45061 TCTCAACCT
1 TCTCAACCT
45070 CTCATTGGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.07, C:0.43, G:0.07, T:0.42
Consensus pattern (30 bp):
TCTCAACCTTTCTCTTCTCTCCCTTCTGCG
Found at i:45064 original size:15 final size:15
Alignment explanation
Indices: 45016--45064 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
45006 ACCTTTCTCT
45016 TCTCTCCCTTCTGCG
1 TCTCTCCCTTCTGCG
* * *
45031 TCTCAACCTTTCT-CT
1 TCTC-TCCCTTCTGCG
45046 TCTCTCCCTTCTGCG
1 TCTCTCCCTTCTGCG
45061 TCTC
1 TCTC
45065 AACCTCTCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 6 0.23
15 14 0.54
16 6 0.23
ACGTcount: A:0.04, C:0.45, G:0.08, T:0.43
Consensus pattern (15 bp):
TCTCTCCCTTCTGCG
Found at i:45695 original size:21 final size:21
Alignment explanation
Indices: 45648--45697 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
45638 TTTGGCATCG
*
45648 TTTTCGTTTTTTTGTTTTTTGT
1 TTTT-GTTTTTTTGTTTTTTGC
45670 TTTTGTTTTGTTT-TTTTTTGC
1 TTTTGTTTT-TTTGTTTTTTGC
45691 TTTTGTT
1 TTTTGTT
45698 ACGTTGTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.00, C:0.04, G:0.14, T:0.82
Consensus pattern (21 bp):
TTTTGTTTTTTTGTTTTTTGC
Found at i:55426 original size:6 final size:6
Alignment explanation
Indices: 55415--55447 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
55405 ACCAATGGGC
55415 CAATGG CAATGG CAATGG CAATGG CAATGG CAA
1 CAATGG CAATGG CAATGG CAATGG CAATGG CAA
55448 AGCCTCTCTC
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:0.18, G:0.30, T:0.15
Consensus pattern (6 bp):
CAATGG
Done.