Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold729
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: 181220
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:117217 original size:5 final size:5
Alignment explanation
Indices: 117198--117231 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
117188 AGAAAGGAGG
*
117198 AAAAT TAAA- AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
117232 TGCACTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 23 0.88
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:117431 original size:19 final size:20
Alignment explanation
Indices: 117409--117455 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
117399 TAAAAAATAT
117409 TTATTTATT-TTTTAAATTA
1 TTATTTATTATTTTAAATTA
*
117428 TTATTTTTATTATTTTCAATTA
1 TTA--TTTATTATTTTAAATTA
117450 TT-TTTA
1 TTATTTA
117456 CTTAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTATTATTTTAAATTA
Found at i:117502 original size:38 final size:38
Alignment explanation
Indices: 117426--117499 Score: 134
Period size: 36 Copynumber: 2.0 Consensus size: 38
117416 TTTTTTAAAT
117426 TATTATTTTTATTATTTTCAATTATTTTTACTTAAAAA
1 TATTATTTTTATTATTTTCAATTATTTTTACTTAAAAA
117464 TATTATTTTTATT-TTTTC-ATTATTTTTACTTAAAAA
1 TATTATTTTTATTATTTTCAATTATTTTTACTTAAAAA
117500 AATTTGTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 18 0.50
37 5 0.14
38 13 0.36
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (38 bp):
TATTATTTTTATTATTTTCAATTATTTTTACTTAAAAA
Found at i:118785 original size:1 final size:1
Alignment explanation
Indices: 118779--118803 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
118769 CAAGAGCTAG
118779 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
118804 CCGTAATGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:122662 original size:20 final size:20
Alignment explanation
Indices: 122630--122704 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
122620 TTTTACCCAG
*
122630 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
122650 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
122670 ATGTATCGAAATATTCTTCA
1 ATGTATCGATACATTTTTCA
122690 ATGTATCGATACATT
1 ATGTATCGATACATT
122705 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:122740 original size:15 final size:15
Alignment explanation
Indices: 122720--122749 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
122710 TTTTTACCTA
122720 GATGCATCGATACAT
1 GATGCATCGATACAT
122735 GATGCATCGATACAT
1 GATGCATCGATACAT
122750 TGAATAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (15 bp):
GATGCATCGATACAT
Found at i:130798 original size:22 final size:23
Alignment explanation
Indices: 130752--130807 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
130742 TGGACATGTT
130752 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
130775 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
130797 AAAAATGCATG
1 AAAAATGCATG
130808 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:131769 original size:20 final size:20
Alignment explanation
Indices: 131722--131796 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
131712 AAAAAGACAT
*
131722 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
131741 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
131762 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
131782 AATGTATCGATACAT
1 AATGTATCGATACAT
131797 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:131790 original size:40 final size:39
Alignment explanation
Indices: 131719--131796 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
131709 GGTAAAAAGA
* *
131719 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
131758 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
131797 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:132505 original size:28 final size:28
Alignment explanation
Indices: 132404--133773 Score: 1151
Period size: 28 Copynumber: 47.5 Consensus size: 28
132394 CACTGACACA
* **
132404 TGTGGGCTTTGAAAAGAGTGTTACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
132433 TGCGTGGGCTTTAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTGAAAGGATGCCACTGACT
132463 TGCGTGGGCTTTGAAAGGATGCCACTGACT
1 T--GTGGGCTTTGAAAGGATGCCACTGACT
*
132493 CGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
132521 TGTGGGCTTTGAAAGG-TGCCACTTACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
132548 CGTGGGCTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
132576 TGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
132603 TGTGGGCTTT-AAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
132631 CGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
132659 TGCGTAGGCTTTGAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGGA-TGCCACTGAC-T
* *
132691 GTGTGGGCTTTGAAAGGGTGCCACTAACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
*
132720 CGTGGGCTTTGAAAGGATGCCACTGACTT
1 TGTGGGCTTTGAAAGGATGCCACTGAC-T
* *
132749 GTGTGGGCTTTGAAAGGGTGCCACTAACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
* *
132778 CGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
132806 TGTGGGCTTTGAAA-GAGTGTCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
132834 CGTGGGCTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
132862 TGCGTGAGCTTTAAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGGA-TGCCACTGAC-T
* *
132894 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
*
132923 TGTGGGCTTTGAAA-GAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
132951 TGTGGGCTTCGCAATGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
132979 TGTGGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
133007 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
133035 TGTGGGCTTTGAAAAGAGTGCCA-TCGATT
1 TGTGGGCTTTGAAAGGA-TGCCACT-GACT
* *
133064 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
133093 TGTGGGCTTTGAAAGGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
133122 TGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 TGTGGGCTTTGAAAGGA-TGCCACTGAC-T
*
133152 GTGTGGGCTTT-AAAAGAGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
133181 TGTGGGCTTTGAAA-GAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
133209 TGTGGGCTTCGCAATGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * *
133237 TGTGGGCTTCGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
133265 TGCGTGGGCTTTGAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTG-AAAGGATGCCACTGACT
*
133296 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
133324 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
133353 TGTGGGCTTTAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
133381 TGCGTGGGCTTTGAAAGGGGTGCCACTGACT
1 T--GTGGGCTTTGAAA-GGATGCCACTGACT
* *
133412 TGTGGGCTTTGAAAGGGTGCCACCGACTT
1 TGTGGGCTTTGAAAGGATGCCACTGAC-T
* *
133441 GTGTGGGCTTTGAAAAGTGTTGCCACCGACTT
1 -TGTGGGCTTTG-AAAG-GATGCCACTGAC-T
* *
133473 GTGTGGGCTTTGAAATGGGTTGCCACCGACTT
1 -TGTGGGCTTTGAAA--GGATGCCACTGAC-T
* * *
133505 ATGTGGGCTTTGAAATGGGTTGCCACCGAATT
1 -TGTGGGCTTTGAAA--GGATGCCACTG-ACT
* * *
133537 GTGTGGGCTTTGAAATGGGTGCCACAGAGT
1 -TGTGGGCTTTGAAA-GGATGCCACTGACT
* * * * *
133567 TGT-GGATTTTAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
** * * * *
133595 TGTGGATTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
** * * * *
133623 TGTGGATTTTTAAAGGGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
133651 TGTGGACTCT-AAAGAGATGCCACGGAGT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
* * * * * *
133679 TATGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
133706 TGTGGTC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * *
133733 TGTGGAC-TTAAAAGGGTGCTACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
133760 TGTGGGCTTT-AAAG
1 TGTGGGCTTTGAAAG
133774 AGGTCACACT
Statistics
Matches: 1171, Mismatches: 111, Indels: 120
0.84 0.08 0.09
Matches are distributed among these distances:
26 5 0.00
27 133 0.11
28 499 0.43
29 174 0.15
30 156 0.13
31 117 0.10
32 83 0.07
33 4 0.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:132832 original size:203 final size:200
Alignment explanation
Indices: 132404--133645 Score: 1450
Period size: 203 Copynumber: 6.1 Consensus size: 200
132394 CACTGACACA
**
132404 TGTGGGCTTTGAAAAGAGTGTTACTGACTTGCGTGGGCTTT-AAAAGGGTGCCACTGACTTGCGT
1 TGTGGGCTTTG-AAAGAGTGCCACTGAC-T-CGTGGGCTTTGAAAA-GGTGCCACTGACTTGCGT
* *
132468 GGGCTTTGAAAGGA-TGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTG
62 GGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* * * *
132532 AAA-G-GTGCCACTTACTCGTGGGCTTTGAAAAGGTACCACTGACTTGTGGGC-TTGAAAGGGTG
127 AAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTG
132594 CCACTGACT
192 CCACTGACT
* *
132603 TGTGGGCTTTAAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTAGGC
1 TGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGC
* *
132668 TTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTAACTCGTGGGCTTTGAA
66 TTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
* * *
132733 AGGA-TGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTAACTCGTGGGCTTTGAAAGGATG
129 AGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTG
*
132797 CCACTAACT
192 CCACTGACT
* * *
132806 TGTGGGCTTTGAAAGAGTGTCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGC
1 TGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGC
* *
132871 TTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAA
66 TTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
* * * * *
132936 A-GAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCC
129 AGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCC
133000 ACTGACT
194 ACTGACT
* * *
133007 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCA-TCGA-TT-TGTGG
1 TGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAG-GTGCCACT-GACTTGCGTGG
* * *
133069 GCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTAACTTGTGGGCTTTGA
64 GCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGA
* * *
133134 AAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGT
128 AAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGT
*
133199 GCCACTGAAT
191 GCCACTGACT
* * * * * *
133209 TGTGGGCTTCGCAATG-GTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTAACTTGCGTGGG
1 TGTGGGCTTTG-AAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGG
133273 CTTTGAAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
65 CTTTG-AAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
* * * *
133337 AAGAGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTTGAAAGGGGT
129 AGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAA-GGGT
133402 GCCACTGACT
191 GCCACTGACT
* * * * *
133412 TGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGCTTTGAAAAGTGTTGCCACCGACTTGTGT
1 TGTGGGCTTTGAAAGAGTGCCACTGAC-T-CGTGGGCTTTGAAAAG-G-TGCCACTGACTTGCGT
* * *
133477 GGGCTTTGAAATGG-GTTGCCACCGACTTATGTGGGCTTTGAAATGGGTTGCCACCGAATTGTGT
62 GGGCTTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGCTTTGAAA-GGG-TGCCACTG-ACT-TGT
* * ** * * * * **
133541 GGGCTTTGAAATGG-GTGCCACAGAGTTGTGGATTTTAAAAGAGTGCCACGGAGTTGTGGATTTT
119 GGGCTTTGAAA-GGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
* * *
133605 AAAAGGGTGCCACGGAGT
183 GAAAGGGTGCCACTGACT
** * *
133623 TGTGGATTTTTAAAGGGTGCCAC
1 TGTGGGCTTTGAAAGAGTGCCAC
133646 AGAGTTGTGG
Statistics
Matches: 907, Mismatches: 98, Indels: 64
0.85 0.09 0.06
Matches are distributed among these distances:
196 41 0.05
197 15 0.02
198 30 0.03
199 74 0.08
200 72 0.08
201 102 0.11
202 180 0.20
203 221 0.24
204 5 0.01
205 14 0.02
206 4 0.00
207 24 0.03
208 9 0.01
209 1 0.00
210 14 0.02
211 35 0.04
212 17 0.02
213 2 0.00
214 46 0.05
215 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.28
Consensus pattern (200 bp):
TGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGC
TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
GAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
TGACT
Found at i:133180 original size:258 final size:258
Alignment explanation
Indices: 132358--133645 Score: 1435
Period size: 258 Copynumber: 4.9 Consensus size: 258
132348 TAAAAAAAAT
* * *
132358 GTGCCACT-AGCTTGTGTAGGCTTTGAAAAAAGTTGCCACTGACACATGTGGGCTTTGAAAAGAG
1 GTGCCACTGA-CTTGTGTGGGCTTT-AAAAGAG-TGCCACTG--ACTTGTGGGCTTTG-AAAGAG
** * * * *
132422 TGTTACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGATGCCA
60 TGCCACTGAATT--GTGGGCTTTGAAATGGTGCCACTGACTT--GTGGGCTTTGAAAGGGTGCCA
* * * *
132487 CTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAG-GTGCCACTTACTCG
121 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
* * *
132550 TGGGCTTTGAAAAG-GTACCACTGACTTGTGGGC-TTGAAAGGGTGCCACTGACTT-GTGGGCTT
186 TGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTCGTGGGCTT
*
132612 T-AAAAGA
251 TGAAAGGA
* *
132619 GTGCCACTGAC-T-CGTGGGCTTTGAAAAG-GTGCCACTGACTTGCGTAGGCTTTGAAAGGAGTG
1 GTGCCACTGACTTGTGTGGGCTTT-AAAAGAGTGCCACTGACTT--GTGGGCTTTGAAA-GAGTG
* * * * *
132681 CCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTAACTCGTGGGCTTTGAAAGGATGCCACTGA
62 CCACTGA-AT-TGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
* * * *
132746 CTTGTGTGGGCTTTGAAAGGGTGCCACTAACTCGTGGGCTTTGAAAGGA-TGCCACTAACTTGTG
125 C-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
* * * * * * *
132810 GGCTTTG-AAAGAGTGTCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGCTTT
188 GGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTT-CGTGGGCTTT
*
132874 AAAAGGA
252 GAAAGGA
*
132881 GTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCAC
1 GTGCCACTGACTTGTGTGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCAC
* * *
132946 TGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTG
66 TGAATTGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTG
*
133011 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCA-TCGATTTGTGGGCTTTG
131 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACT-GACTTGTGGGCTTTG
133075 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTAACTT-GTGGGCTTTGAAAGGA
195 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGG-GTGCCACTAACTTCGTGGGCTTTGAAAGGA
133139 GTGCCACTGACTTGTGTGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCAC
1 GTGCCACTGACTTGTGTGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCAC
* * * *
133204 TGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTAACTTGCG
66 TGAATTGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--G
*
133269 TGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTT
129 TGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT
*
133333 TGAAAAGAGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTTGAAAG
193 TGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTT-CGTGGGCTTTGAAAG
*
133398 GG
257 GA
* * * *
133400 GTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGCTTTGAAAAGTGTTG
1 GTGCCACTGACTTGTGTGGGCTTTAAAAGAGTGCCACTGAC-T-TGTGGGCTTTG-AAAGAG-TG
* * *
133463 CCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATGGGTTGC
62 CCACTGA-AT-TGTGGGCTTTGAAAT-GG-TGCCACTGAC-T-TGTGGGCTTTGAAA-GGG-TGC
* * * * * * *
133528 CACCGAATTGTGTGGGCTTTGAAATGGGTGCCACAGAGTTGT-GGATTTTAAAAGAGTGCCACGG
119 CACTG-ACT-TGTGGGCTTTGAAA-GGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTG
* * * * ** * ** *
133592 AGTTGT-GGATTTTAAAAGGGTGCCACGGAGTTGTGGATTTTTAAAGGGTGCCAC
181 ACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCAC
133646 AGAGTTGTGG
Statistics
Matches: 900, Mismatches: 83, Indels: 79
0.85 0.08 0.07
Matches are distributed among these distances:
255 29 0.03
256 4 0.00
257 134 0.15
258 199 0.22
259 147 0.16
260 82 0.09
261 95 0.11
262 34 0.04
263 14 0.02
264 23 0.03
265 13 0.01
266 2 0.00
267 9 0.01
268 1 0.00
269 13 0.01
270 50 0.06
271 48 0.05
272 2 0.00
273 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (258 bp):
GTGCCACTGACTTGTGTGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCAC
TGAATTGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTG
GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGA
AAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTCGTGGGCTTTGAAAGGA
Found at i:141278 original size:22 final size:22
Alignment explanation
Indices: 141250--141304 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
141240 TGGACATGTT
141250 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
141272 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
141294 AAAAATGCATG
1 AAAAATGCATG
141305 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:142266 original size:20 final size:20
Alignment explanation
Indices: 142219--142293 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
142209 AAAAAGACAT
*
142219 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
142238 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
142259 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
142279 AATGTATCGATACAT
1 AATGTATCGATACAT
142294 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:142287 original size:40 final size:39
Alignment explanation
Indices: 142216--142293 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
142206 GGTAAAAAGA
* *
142216 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
142255 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
142294 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:143002 original size:28 final size:28
Alignment explanation
Indices: 142901--144270 Score: 1151
Period size: 28 Copynumber: 47.5 Consensus size: 28
142891 CACTGACACA
* **
142901 TGTGGGCTTTGAAAAGAGTGTTACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
142930 TGCGTGGGCTTTAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTGAAAGGATGCCACTGACT
142960 TGCGTGGGCTTTGAAAGGATGCCACTGACT
1 T--GTGGGCTTTGAAAGGATGCCACTGACT
*
142990 CGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
143018 TGTGGGCTTTGAAAGG-TGCCACTTACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
143045 CGTGGGCTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
143073 TGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
143100 TGTGGGCTTT-AAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
143128 CGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
143156 TGCGTAGGCTTTGAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGGA-TGCCACTGAC-T
* *
143188 GTGTGGGCTTTGAAAGGGTGCCACTAACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
*
143217 CGTGGGCTTTGAAAGGATGCCACTGACTT
1 TGTGGGCTTTGAAAGGATGCCACTGAC-T
* *
143246 GTGTGGGCTTTGAAAGGGTGCCACTAACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
* *
143275 CGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
143303 TGTGGGCTTTGAAA-GAGTGTCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
143331 CGTGGGCTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
143359 TGCGTGAGCTTTAAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGGA-TGCCACTGAC-T
* *
143391 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
*
143420 TGTGGGCTTTGAAA-GAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
143448 TGTGGGCTTCGCAATGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
143476 TGTGGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
143504 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
143532 TGTGGGCTTTGAAAAGAGTGCCA-TCGATT
1 TGTGGGCTTTGAAAGGA-TGCCACT-GACT
* *
143561 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
143590 TGTGGGCTTTGAAAGGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
143619 TGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 TGTGGGCTTTGAAAGGA-TGCCACTGAC-T
*
143649 GTGTGGGCTTT-AAAAGAGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
143678 TGTGGGCTTTGAAA-GAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
143706 TGTGGGCTTCGCAATGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * *
143734 TGTGGGCTTCGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
143762 TGCGTGGGCTTTGAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTG-AAAGGATGCCACTGACT
*
143793 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
143821 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
143850 TGTGGGCTTTAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
143878 TGCGTGGGCTTTGAAAGGGGTGCCACTGACT
1 T--GTGGGCTTTGAAA-GGATGCCACTGACT
* *
143909 TGTGGGCTTTGAAAGGGTGCCACCGACTT
1 TGTGGGCTTTGAAAGGATGCCACTGAC-T
* *
143938 GTGTGGGCTTTGAAAAGTGTTGCCACCGACTT
1 -TGTGGGCTTTG-AAAG-GATGCCACTGAC-T
* *
143970 GTGTGGGCTTTGAAATGGGTTGCCACCGACTT
1 -TGTGGGCTTTGAAA--GGATGCCACTGAC-T
* * *
144002 ATGTGGGCTTTGAAATGGGTTGCCACCGAATT
1 -TGTGGGCTTTGAAA--GGATGCCACTG-ACT
* * *
144034 GTGTGGGCTTTGAAATGGGTGCCACAGAGT
1 -TGTGGGCTTTGAAA-GGATGCCACTGACT
* * * * *
144064 TGT-GGATTTTAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
** * * * *
144092 TGTGGATTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
** * * * *
144120 TGTGGATTTTTAAAGGGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
144148 TGTGGACTCT-AAAGAGATGCCACGGAGT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
* * * * * *
144176 TATGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
144203 TGTGGTC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * *
144230 TGTGGAC-TTAAAAGGGTGCTACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
144257 TGTGGGCTTT-AAAG
1 TGTGGGCTTTGAAAG
144271 AGGTCACACT
Statistics
Matches: 1171, Mismatches: 111, Indels: 120
0.84 0.08 0.09
Matches are distributed among these distances:
26 5 0.00
27 133 0.11
28 499 0.43
29 174 0.15
30 156 0.13
31 117 0.10
32 83 0.07
33 4 0.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:143329 original size:203 final size:200
Alignment explanation
Indices: 142901--144142 Score: 1450
Period size: 203 Copynumber: 6.1 Consensus size: 200
142891 CACTGACACA
**
142901 TGTGGGCTTTGAAAAGAGTGTTACTGACTTGCGTGGGCTTT-AAAAGGGTGCCACTGACTTGCGT
1 TGTGGGCTTTG-AAAGAGTGCCACTGAC-T-CGTGGGCTTTGAAAA-GGTGCCACTGACTTGCGT
* *
142965 GGGCTTTGAAAGGA-TGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTG
62 GGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* * * *
143029 AAA-G-GTGCCACTTACTCGTGGGCTTTGAAAAGGTACCACTGACTTGTGGGC-TTGAAAGGGTG
127 AAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTG
143091 CCACTGACT
192 CCACTGACT
* *
143100 TGTGGGCTTTAAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTAGGC
1 TGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGC
* *
143165 TTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTAACTCGTGGGCTTTGAA
66 TTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
* * *
143230 AGGA-TGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTAACTCGTGGGCTTTGAAAGGATG
129 AGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTG
*
143294 CCACTAACT
192 CCACTGACT
* * *
143303 TGTGGGCTTTGAAAGAGTGTCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGC
1 TGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGC
* *
143368 TTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAA
66 TTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
* * * * *
143433 A-GAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCC
129 AGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCC
143497 ACTGACT
194 ACTGACT
* * *
143504 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCA-TCGA-TT-TGTGG
1 TGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAG-GTGCCACT-GACTTGCGTGG
* * *
143566 GCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTAACTTGTGGGCTTTGA
64 GCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGA
* * *
143631 AAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGT
128 AAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGT
*
143696 GCCACTGAAT
191 GCCACTGACT
* * * * * *
143706 TGTGGGCTTCGCAATG-GTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTAACTTGCGTGGG
1 TGTGGGCTTTG-AAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGG
143770 CTTTGAAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
65 CTTTG-AAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
* * * *
143834 AAGAGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTTGAAAGGGGT
129 AGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAA-GGGT
143899 GCCACTGACT
191 GCCACTGACT
* * * * *
143909 TGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGCTTTGAAAAGTGTTGCCACCGACTTGTGT
1 TGTGGGCTTTGAAAGAGTGCCACTGAC-T-CGTGGGCTTTGAAAAG-G-TGCCACTGACTTGCGT
* * *
143974 GGGCTTTGAAATGG-GTTGCCACCGACTTATGTGGGCTTTGAAATGGGTTGCCACCGAATTGTGT
62 GGGCTTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGCTTTGAAA-GGG-TGCCACTG-ACT-TGT
* * ** * * * * **
144038 GGGCTTTGAAATGG-GTGCCACAGAGTTGTGGATTTTAAAAGAGTGCCACGGAGTTGTGGATTTT
119 GGGCTTTGAAA-GGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
* * *
144102 AAAAGGGTGCCACGGAGT
183 GAAAGGGTGCCACTGACT
** * *
144120 TGTGGATTTTTAAAGGGTGCCAC
1 TGTGGGCTTTGAAAGAGTGCCAC
144143 AGAGTTGTGG
Statistics
Matches: 907, Mismatches: 98, Indels: 64
0.85 0.09 0.06
Matches are distributed among these distances:
196 41 0.05
197 15 0.02
198 30 0.03
199 74 0.08
200 72 0.08
201 102 0.11
202 180 0.20
203 221 0.24
204 5 0.01
205 14 0.02
206 4 0.00
207 24 0.03
208 9 0.01
209 1 0.00
210 14 0.02
211 35 0.04
212 17 0.02
213 2 0.00
214 46 0.05
215 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.28
Consensus pattern (200 bp):
TGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGC
TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
GAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
TGACT
Found at i:143677 original size:258 final size:258
Alignment explanation
Indices: 142855--144142 Score: 1435
Period size: 258 Copynumber: 4.9 Consensus size: 258
142845 TAAAAAAAAT
* * *
142855 GTGCCACT-AGCTTGTGTAGGCTTTGAAAAAAGTTGCCACTGACACATGTGGGCTTTGAAAAGAG
1 GTGCCACTGA-CTTGTGTGGGCTTT-AAAAGAG-TGCCACTG--ACTTGTGGGCTTTG-AAAGAG
** * * * *
142919 TGTTACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGATGCCA
60 TGCCACTGAATT--GTGGGCTTTGAAATGGTGCCACTGACTT--GTGGGCTTTGAAAGGGTGCCA
* * * *
142984 CTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAG-GTGCCACTTACTCG
121 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
* * *
143047 TGGGCTTTGAAAAG-GTACCACTGACTTGTGGGC-TTGAAAGGGTGCCACTGACTT-GTGGGCTT
186 TGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTCGTGGGCTT
*
143109 T-AAAAGA
251 TGAAAGGA
* *
143116 GTGCCACTGAC-T-CGTGGGCTTTGAAAAG-GTGCCACTGACTTGCGTAGGCTTTGAAAGGAGTG
1 GTGCCACTGACTTGTGTGGGCTTT-AAAAGAGTGCCACTGACTT--GTGGGCTTTGAAA-GAGTG
* * * * *
143178 CCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTAACTCGTGGGCTTTGAAAGGATGCCACTGA
62 CCACTGA-AT-TGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
* * * *
143243 CTTGTGTGGGCTTTGAAAGGGTGCCACTAACTCGTGGGCTTTGAAAGGA-TGCCACTAACTTGTG
125 C-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
* * * * * * *
143307 GGCTTTG-AAAGAGTGTCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGCTTT
188 GGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTT-CGTGGGCTTT
*
143371 AAAAGGA
252 GAAAGGA
*
143378 GTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCAC
1 GTGCCACTGACTTGTGTGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCAC
* * *
143443 TGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTG
66 TGAATTGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTG
*
143508 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCA-TCGATTTGTGGGCTTTG
131 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACT-GACTTGTGGGCTTTG
143572 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTAACTT-GTGGGCTTTGAAAGGA
195 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGG-GTGCCACTAACTTCGTGGGCTTTGAAAGGA
143636 GTGCCACTGACTTGTGTGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCAC
1 GTGCCACTGACTTGTGTGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCAC
* * * *
143701 TGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTAACTTGCG
66 TGAATTGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--G
*
143766 TGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTT
129 TGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTT
*
143830 TGAAAAGAGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTTGAAAG
193 TGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTT-CGTGGGCTTTGAAAG
*
143895 GG
257 GA
* * * *
143897 GTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGCTTTGAAAAGTGTTG
1 GTGCCACTGACTTGTGTGGGCTTTAAAAGAGTGCCACTGAC-T-TGTGGGCTTTG-AAAGAG-TG
* * *
143960 CCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATGGGTTGC
62 CCACTGA-AT-TGTGGGCTTTGAAAT-GG-TGCCACTGAC-T-TGTGGGCTTTGAAA-GGG-TGC
* * * * * * *
144025 CACCGAATTGTGTGGGCTTTGAAATGGGTGCCACAGAGTTGT-GGATTTTAAAAGAGTGCCACGG
119 CACTG-ACT-TGTGGGCTTTGAAA-GGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTG
* * * * ** * ** *
144089 AGTTGT-GGATTTTAAAAGGGTGCCACGGAGTTGTGGATTTTTAAAGGGTGCCAC
181 ACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCAC
144143 AGAGTTGTGG
Statistics
Matches: 900, Mismatches: 83, Indels: 79
0.85 0.08 0.07
Matches are distributed among these distances:
255 29 0.03
256 4 0.00
257 134 0.15
258 199 0.22
259 147 0.16
260 82 0.09
261 95 0.11
262 34 0.04
263 14 0.02
264 23 0.03
265 13 0.01
266 2 0.00
267 9 0.01
268 1 0.00
269 13 0.01
270 50 0.06
271 48 0.05
272 2 0.00
273 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (258 bp):
GTGCCACTGACTTGTGTGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCAC
TGAATTGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTG
GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGA
AAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTCGTGGGCTTTGAAAGGA
Found at i:152741 original size:20 final size:20
Alignment explanation
Indices: 152694--152768 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
152684 AAAAAGACAT
*
152694 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
152713 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
152734 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
152754 AATGTATCGATACAT
1 AATGTATCGATACAT
152769 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:152762 original size:40 final size:39
Alignment explanation
Indices: 152691--152768 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
152681 GGTAAAAAGA
* *
152691 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
152730 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
152769 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:161255 original size:14 final size:13
Alignment explanation
Indices: 161232--161280 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 13
161222 CTTTACACCT
161232 AAAAAAAACAAAA
1 AAAAAAAACAAAA
161245 AAAATAAAACAAAA
1 AAAA-AAAACAAAA
161259 AAACAAAAA-AAAA
1 AAA-AAAAACAAAA
161272 AAGAAAAAA
1 AA-AAAAAA
161281 TAGCAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
13 15 0.45
14 17 0.52
15 1 0.03
ACGTcount: A:0.90, C:0.06, G:0.02, T:0.02
Consensus pattern (13 bp):
AAAAAAAACAAAA
Found at i:161280 original size:22 final size:22
Alignment explanation
Indices: 161232--161290 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
161222 CTTTACACCT
161232 AAAAAAAACAAAAAAAATAAAA
1 AAAAAAAACAAAAAAAATAAAA
*
161254 CAAAAAAACAAAAAAAA-AAAGA
1 AAAAAAAACAAAAAAAATAAA-A
* *
161276 AAAAATAGCAAAAAA
1 AAAAAAAACAAAAAA
161291 TAGAAGGGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 3 0.09
22 29 0.91
ACGTcount: A:0.86, C:0.07, G:0.03, T:0.03
Consensus pattern (22 bp):
AAAAAAAACAAAAAAAATAAAA
Found at i:161290 original size:1 final size:1
Alignment explanation
Indices: 161232--161280 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
161222 CTTTACACCT
* * * * *
161232 AAAAAAAACAAAAAAAATAAAACAAAAAAACAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
161281 TAGCAAAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.90, C:0.06, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:162545 original size:29 final size:29
Alignment explanation
Indices: 162505--162807 Score: 407
Period size: 29 Copynumber: 10.5 Consensus size: 29
162495 GTTCATCCCT
162505 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
162534 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
162563 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* * *
162592 TTTCAAAGCCCATAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
162621 TTTCAAAGCCCACAAGTCAGTGGCACCCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
162650 TTTCGAAGCCCACAAGTCAGTGGCACCCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
162679 TTTCGAAGCCCACAATTCAGTGGCA--CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
162706 TTTACGAAGCCCACAATTCAGTGGCACT-C
1 TTT-CAAAGCCCACAAGTCAGTGGCACTCC
*
162735 TTTCAAAGCCCACAAGTCAATGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
162763 TTTCAAAGCCCACACAAGTCAGTGGCACTCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCACTCC
*
162794 TTTTAAAGCCCACA
1 TTTCAAAGCCCACA
162808 TTTTCAAAGC
Statistics
Matches: 253, Mismatches: 14, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
27 5 0.02
28 51 0.20
29 171 0.68
30 17 0.07
31 9 0.04
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCC
Found at i:162596 original size:58 final size:57
Alignment explanation
Indices: 162503--163875 Score: 1046
Period size: 56 Copynumber: 24.3 Consensus size: 57
162493 ATGTTCATCC
162503 CTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAATCAGTGGCACT
* * *
162561 CTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCATAAATCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAATCAGTGGCACT
* * *
162619 CTTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCGAAGCCCACAAGTCAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAATCAGTGGCACT
* * * * *
162677 CCTTTCGAAGCCCACAATTCAGTGGCA-CCTTTACGAAGCCCACAATTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTT-CAAAGCCCACAAATCAGTGGCACT
*
162734 C-TTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACA-AA-TCAGTGGCACT
** ** ** * * * ** ** * *
162792 CCTTTT-AAAGCCCACATTTTCA-AAGC-CCACGAGTCAGTAGCACTC-TTTCA-AAGCCCA
1 -CTTTTCAAAGCCCACA-AGTCAGTGGCACC-C-TTTCA-AAGCCCACAAATCAGTGGCACT
*** ** *** ** * *** ** * * ** **
162849 CAAGTCAGTGGCACC-CTTTTCAAAGCCCACAAGTT-AGTG-GCAC---TC-TTTTCAAAG
1 CTTTTCA-AAGC-CCACAAGTCAGTG-GCACCCTTTCAAAGCCCACAAATCAGTGGC-ACT
* * * * * * * *
162903 C-CTACAAA----TC-AGT--G-GCAC-TCTTTTCAAAGCCCACAAGTCAATGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTG-GCACCCTTTCAAAGCCCACAAATCAGTGGCACT
* * * *
162950 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTTAAAGCCCACAAGTCAGTGGTACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAATCAGTGGCACT
* * * *
163008 CTTTTCAAAGCCCAAAAATCAGTGGCGCTCTTTTCAAAGCCCACAAATCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAATCAGTGGCACT
* * *
163066 CTTTTCAAAGCCTACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACT
* * * *
163122 CCTTTCAGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTCAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACT
* * *
163178 CCTTGCGAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACA-AA-TCAGTGGCACT
* * * * *
163236 CTTTTCCAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAATGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACT
* * * * * *
163292 CCTTTC-AAGCCCACGAGTCAGTGGTACCTTTTCAAAGCCCACGAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACT
* * *
163348 C-TTTCAAAGCCCACAAGTCAGTGGCACCTTTTCGAAGCCCACGAATCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACT
* * * *
163404 C-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTC-AAGCCCACGAGTTAGTGGTAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACT
* ** *
163458 CTTTTCAAAGCCCACGAGTCAGTGGCACTTTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACT
* * * ** * *
163514 CCTTTCAAAGCCCACGAGTTAGTGGCATTCTTTCAAAGCCCACGCAAGTCAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAATCAGTGGCACT
* *
163573 CTTTT-AAAGCCCACGCAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCAGTGGCACT
1 CTTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACT
* * *
163631 C-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTC-AAGCCCACGAGTCAGTGGTAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACT
* * * * *
163685 CTTTTCAAAGCCCACGAGTCAGTGGTACCTTTTCAAAGCCCACGAGTCAGTGGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACT
* ** * *
163741 CCTTTCAAAGCCCACAAGTCAGTGGCATTCTTTCAAAGCCCACGCAAGTCAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAATCAGTGGCACT
** * * * ***
163800 CTTTT-AAAGCCCACGCAAGTCAGTAACACTCTTTTAAAGCCCACGCAAGTCAGTAATACT
1 CTTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAATCAGTGGCACT
163860 CTTTTCAAAGCCCACA
1 CTTTTCAAAGCCCACA
163876 CGTGTCAGTG
Statistics
Matches: 1084, Mismatches: 171, Indels: 119
0.79 0.12 0.09
Matches are distributed among these distances:
43 2 0.00
44 5 0.00
45 3 0.00
47 2 0.00
48 9 0.01
49 2 0.00
52 1 0.00
53 8 0.01
54 3 0.00
55 148 0.14
56 355 0.33
57 93 0.09
58 336 0.31
59 28 0.03
60 76 0.07
61 13 0.01
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (57 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACT
Found at i:162836 original size:44 final size:45
Alignment explanation
Indices: 162763--162850 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 45
162753 AATGGCACCC
* *
162763 TTTCAAAGCCCACACAAGTCAGTGGCACTCCTTTTAAAGCCCACAT
1 TTTCAAAGCCCACACAAGTCAGTAGCACT-CTTTCAAAGCCCACAT
*
162809 TTTCAAAG-CC-CACGAGTCAGTAGCACTCTTTCAAAGCCCACA
1 TTTCAAAGCCCACACAAGTCAGTAGCACTCTTTCAAAGCCCACA
162851 AGTCAGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 14 0.36
44 15 0.38
45 2 0.05
46 8 0.21
ACGTcount: A:0.31, C:0.33, G:0.14, T:0.23
Consensus pattern (45 bp):
TTTCAAAGCCCACACAAGTCAGTAGCACTCTTTCAAAGCCCACAT
Found at i:162849 original size:28 final size:28
Alignment explanation
Indices: 162809--163920 Score: 1240
Period size: 28 Copynumber: 38.9 Consensus size: 28
162799 AAGCCCACAT
* *
162809 TTTCAAAGCCCACGAGTCAGTAGCACTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
*
162837 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
*
162865 TTTTCAAAGCCCACAAGTTAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
162894 TTTTCAAAGCCTACAAATCAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
162923 TTTTCAAAGCCCACAAGTCAATGGCACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
162952 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACT-C
* *
162981 TTTTAAAGCCCACAAGTCAGTGGTACTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* * *
163009 TTTTCAAAGCCCAAAAATCAGTGGCGCTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
*
163038 TTTTCAAAGCCCACAAATCAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
163067 TTTTCAAAGCCTACAAGTCAGTGGCACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
163096 TTTCAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
163124 TTTCAGAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
163152 TTTCGAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* * *
163180 TTGCGAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
163208 TTTCAAAGCCCACACAAGTCAGTGGCAC-C
1 TTTCAAAG-CC-CACAAGTCAGTGGCACTC
* *
163237 TTTTCCAAGCCCACGAGTCAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
163266 TTTCAAAGCCCACAAGTCAATGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
163294 TTTC-AAGCCCACGAGTCAGTGGTAC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
*
163320 TTTTCAAAGCCCACGAGTCAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
163349 TTTCAAAGCCCACAAGTCAGTGGCAC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
*
163376 TTTTCGAAGCCCACGAA-TCAGTGGCACTC
1 -TTTCAAAGCCCAC-AAGTCAGTGGCACTC
*
163405 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* * *
163433 TTTC-AAGCCCACGAGTTAGTGGTAC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
163459 TTTTCAAAGCCCACGAGTCAGTGGCACTT
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
163488 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACT-C
* * *
163516 TTTCAAAGCCCACGAGTTAGTGGCATTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
*
163544 TTTCAAAGCCCACGCAAGTCAGTGGCACCC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTC
* *
163574 TTTTAAAGCCCACGCAAGTCAGTGGCACCC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTC
*
163604 TTTCAAAGCCCACGAGTCAGTGGCACTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
*
163632 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
163660 TTTC-AAGCCCACGAGTCAGTGGTAC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
163686 TTTTCAAAGCCCACGAGTCAGTGGTAC-C
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
*
163714 TTTTCAAAGCCCACGAGTCAGTGGCA-TCC
1 -TTTCAAAGCCCACAAGTCAGTGGCACT-C
*
163743 TTTCAAAGCCCACAAGTCAGTGGCATTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
*
163771 TTTCAAAGCCCACGCAAGTCAGTGGCACCC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTC
* **
163801 TTTTAAAGCCCACGCAAGTCAGTAACACTC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTC
* ***
163831 TTTTAAAGCCCACGCAAGTCAGTAATACTC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTC
* *
163861 TTTTCAAAGCCCACACGTGTCAGTGGCAACTTTT
1 -TTTCAAAGCCCACA--AGTCAGTGGC-AC--TC
*
163895 TTTCAAAGCCTACACAAGTTAGTGGC
1 TTTCAAAGCC--CACAAGTCAGTGGC
163921 GCATTTTTTT
Statistics
Matches: 960, Mismatches: 88, Indels: 67
0.86 0.08 0.06
Matches are distributed among these distances:
26 3 0.00
27 71 0.07
28 506 0.53
29 194 0.20
30 144 0.15
31 17 0.02
32 2 0.00
33 18 0.02
34 1 0.00
35 4 0.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTC
Found at i:164510 original size:20 final size:20
Alignment explanation
Indices: 164482--164556 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
164472 TTTTACCTAG
164482 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
164502 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
164522 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
164542 ATGTATCGATACATT
1 ATGTATCGATACATT
164557 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:164542 original size:40 final size:39
Alignment explanation
Indices: 164482--164559 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
164472 TTTTACCTAG
*
164482 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
164522 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
164560 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:169897 original size:25 final size:24
Alignment explanation
Indices: 169846--169893 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
169836 GAAAAAAACC
*
169846 CAAATTAAAAGGAAAAAGTCTGTT
1 CAAATTAAAAAGAAAAAGTCTGTT
169870 CAAATTAAAAAGAAAAAGTCTGTT
1 CAAATTAAAAAGAAAAAGTCTGTT
169894 TCAACTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (24 bp):
CAAATTAAAAAGAAAAAGTCTGTT
Found at i:171686 original size:30 final size:30
Alignment explanation
Indices: 171650--171722 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
171640 GAAACAGACC
**
171650 TAAGTGTTACTAATCTT-AAATCACAAAGGT
1 TAAGTGTTACTAAT-TTAAAATCACAAAAAT
*
171680 TAAGTGTTATTAATTTAAAATCACAAAAAT
1 TAAGTGTTACTAATTTAAAATCACAAAAAT
*
171710 TAAATGTTACTAA
1 TAAGTGTTACTAA
171723 CCTATGAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (30 bp):
TAAGTGTTACTAATTTAAAATCACAAAAAT
Found at i:171783 original size:28 final size:28
Alignment explanation
Indices: 171752--171813 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
171742 TTACTATTTC
* * *
171752 AATATTCACTTTCAA-TATTTACAATTGT
1 AATATTCAATTT-AATTATTTAAAATTAT
171780 AATATTCAATTTAATTATTTAAAATTAT
1 AATATTCAATTTAATTATTTAAAATTAT
171808 AATATT
1 AATATT
171814 AAATAGTCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 28 0.93
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (28 bp):
AATATTCAATTTAATTATTTAAAATTAT
Found at i:172297 original size:3 final size:3
Alignment explanation
Indices: 172289--172314 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
172279 TGTTTATCTT
172289 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
172315 CACTTTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:173830 original size:30 final size:30
Alignment explanation
Indices: 173794--173851 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
173784 GTTGACTTAT
* *
173794 ATTAAAGTTTTATTTAAGTATAAATTAATA
1 ATTAAAGGTTTATTTAAATATAAATTAATA
173824 ATTAAAGGTTTATTTAAATATAAATTAA
1 ATTAAAGGTTTATTTAAATATAAATTAA
173852 ATAGTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (30 bp):
ATTAAAGGTTTATTTAAATATAAATTAATA
Found at i:175863 original size:16 final size:16
Alignment explanation
Indices: 175834--175875 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
175824 ATCGACTCGA
*
175834 AACCTAAAAT-ACCCG
1 AACCCAAAATGACCCG
175849 AACCCAAAATGACCCG
1 AACCCAAAATGACCCG
*
175865 AACCCGAAATG
1 AACCCAAAATG
175876 GCCTGGACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.45, C:0.33, G:0.12, T:0.10
Consensus pattern (16 bp):
AACCCAAAATGACCCG
Found at i:176680 original size:16 final size:16
Alignment explanation
Indices: 176654--176724 Score: 83
Period size: 16 Copynumber: 4.4 Consensus size: 16
176644 CCCGATTGAC
*
176654 CCGAATCTGAAATAA-
1 CCGAACCTGAAATAAT
*
176669 CTCGAACTTGAAATAAT
1 C-CGAACCTGAAATAAT
176686 CCGAACCTGAAATAAT
1 CCGAACCTGAAATAAT
*
176702 CCGAATCC-GAAATAAC
1 CCGAA-CCTGAAATAAT
176718 CCGAACC
1 CCGAACC
176725 CAAAATGACC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.06
16 43 0.88
17 3 0.06
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.18
Consensus pattern (16 bp):
CCGAACCTGAAATAAT
Found at i:176730 original size:16 final size:16
Alignment explanation
Indices: 176679--176755 Score: 55
Period size: 16 Copynumber: 4.8 Consensus size: 16
176669 CTCGAACTTG
* **
176679 AAATAATCCGAACCTG
1 AAATAACCCGAACCCA
* * *
176695 AAATAATCCGAATCCG
1 AAATAACCCGAACCCA
176711 AAATAACCCGAACCCA
1 AAATAACCCGAACCCA
* * *
176727 AAATGACCTGAACTCGA
1 AAATAACCCGAAC-CCA
*
176744 AAATAACTCGAA
1 AAATAACCCGAA
176756 AATTTTAAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
16 38 0.78
17 11 0.22
ACGTcount: A:0.47, C:0.26, G:0.12, T:0.16
Consensus pattern (16 bp):
AAATAACCCGAACCCA
Found at i:176850 original size:19 final size:19
Alignment explanation
Indices: 176826--176863 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
176816 CCCAATTGAC
176826 AAGTCTAGTTGGTAAGGAT
1 AAGTCTAGTTGGTAAGGAT
176845 AAGTCTAGTTGGTAAGGAT
1 AAGTCTAGTTGGTAAGGAT
176864 GTAAAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (19 bp):
AAGTCTAGTTGGTAAGGAT
Found at i:177156 original size:20 final size:19
Alignment explanation
Indices: 177128--177202 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
177118 TCATACCCTG
*
177128 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTAT-A
* *
177148 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTAT-A
*
177168 ATGTATCGATATATTCTATA
1 ATGTATCGATACATT-TATA
177188 ATGTATCGATACATT
1 ATGTATCGATACATT
177203 ATGTCTTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 43 0.93
21 3 0.07
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (19 bp):
ATGTATCGATACATTTATA
Found at i:177195 original size:40 final size:39
Alignment explanation
Indices: 177128--177205 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
177118 TCATACCCTG
*
177128 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTTATCAATATATCGATACAT-TATGA
* *
177168 ATGTATCGATATATTCTAT-AATGTATCGATACATTATG
1 ATGTATCGATACATT-TATCAATATATCGATACATTATG
177206 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 28 0.82
41 2 0.06
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTTATCAATATATCGATACATTATGA
Found at i:178146 original size:23 final size:23
Alignment explanation
Indices: 178113--178169 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
178103 AGCCTTTGAC
*
178113 CATGCATTTTTTTTATTATGTTT
1 CATGCAATTTTTTTATTATGTTT
178136 CATGCAATTTTTTTATTATGTTT
1 CATGCAATTTTTTTATTATGTTT
*
178159 CATGCACTTTT
1 CATGCAATTTT
178170 AACATGTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.19, C:0.12, G:0.09, T:0.60
Consensus pattern (23 bp):
CATGCAATTTTTTTATTATGTTT
Found at i:181128 original size:18 final size:18
Alignment explanation
Indices: 181085--181129 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
181075 AGATATTTTT
* **
181085 TAATATTTTTAATAAATT
1 TAATATTTTTAAAAAAAA
*
181103 TAAAATTTTTAAAAAAAA
1 TAATATTTTTAAAAAAAA
181121 TAATATTTT
1 TAATATTTT
181130 CGAGTAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATATTTTTAAAAAAAA
Done.