Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold9
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: 3883850
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 144036 characters in sequence are not A, C, G, or T
File 15 of 24
Found at i:2226163 original size:89 final size:90
Alignment explanation
Indices: 2225831--2227342 Score: 1734
Period size: 89 Copynumber: 16.9 Consensus size: 90
2225821 AAAAAGGTGA
* * * * * * *
2225831 CACTAACTTGTGTGAGCTTTGAAAAGAGTTGCCACTGGC-T-CGTGGGTTTTGAAAAGAGTTACC
1 CACTGACTTGTG-G-GCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGA--TGCC
** * *
2225894 ACTGGCTTATGGGCTTTGAAAAGAG-TGC
62 ACTAACTTGTGGGCTTTAAAAAGAGATGC
** * *
2225922 CACTGACTTGTGGGCTTTGAAAGGA--TGCCACTAAC-T-TGTGGACTTTGAAAGGATGCCACTA
1 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTA
* *
2225983 ACTTGTGGGTTTTGAAAAA-AG-TGT
66 ACTTGTGGGCTTT-AAAAAGAGATGC
* * * ** * * * *
2226007 CACTAACTGGTGGGTTTTGCTAAA--AG-TGCCACTAAC-T-TATGGGCTTTGAAATGGTGTCAC
1 CACTGACTTGTGGGCTTTG--AAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCAC
2226067 TAACTTGTGGGCTTTAAAAAGAG-TGC
64 TAACTTGTGGGCTTTAAAAAGAGATGC
* * * *
2226093 CACTGACTTATGGGCTTTGAAAGGAGTTGCCACCAACTTGTGTGGGTTTTAAAAAGATGCCACTA
1 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTA
*
2226158 ACTTGTGGGCTTT-GAAAGAGATGC
66 ACTTGTGGGCTTTAAAAAGAGATGC
* * *
2226182 CACTGACTTATGGGCTTTGAAAGGAGTTGCCATCGACTTGTGTGGGCTTTGAAAAGATGCCACTG
1 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTA
*
2226247 ACTTGTGGGCTTTGAAAAA-AGTTGC
66 ACTTGTGGGCTTT-AAAAAGAGATGC
** * * **
2226272 CACCAACTTGTGTGGGCTTTGAAAGGAGTTTCCACTGACTTGTGCAGGCTTTGAAAAGATGCCAC
1 CACTGAC-T-TGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCAC
2226337 TAACTTGTGGGCTTTAAAAAGAG-TGC
64 TAACTTGTGGGCTTTAAAAAGAGATGC
* * *
2226363 CACTGACTTATGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTAAAAAGATGCCACTA
1 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTA
*
2226428 ACTTGTGGGCTTTGAAAA-AGATGC
66 ACTTGTGGGCTTTAAAAAGAGATGC
* * * * * *
2226452 CACTAACTTATGGGCCTTGAAAGGAGTTGCCACCGACTTGTATGGGTTTTGAAAAGATGCCACTG
1 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTA
* * *
2226517 ACTTGTGGGCTTTGAAAAGAGTTAC
66 ACTTGTGGGCTTTAAAAAGAGATGC
* *
2226542 CACCGACTTGTGTGGGCTTTGAAAGGAGTTACCACCGACTTGTGTGGGCTTTGAAAAGATGCCAC
1 CACTGAC-T-TGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCAC
*
2226607 TAACTTGTGGGCTTT-GAAAGAGATGC
64 TAACTTGTGGGCTTTAAAAAGAGATGC
* *
2226633 CACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTG
1 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTA
*
2226698 ACTTGTGGGCTTTAAAAAGAGTTGC
66 ACTTGTGGGCTTTAAAAAGAGATGC
* *
2226723 CACCGACTTGTGTGGGCTTTGAAAGGAGTTACCACCGACTTGTGTGGGCTTTGAAAAGATGCCAC
1 CACTGAC-T-TGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCAC
* *
2226788 TGACTTGTGGGCTTT-GAAAGAGATGC
64 TAACTTGTGGGCTTTAAAAAGAGATGC
* * * *
2226814 CACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAAGGGTGCCACTG
1 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTA
* *
2226879 ACTTGTGGGCTTTGAAAAGAGTTGC
66 ACTTGTGGGCTTTAAAAAGAGATGC
* *
2226904 CACCGACTTGTGTGGGCTTTGAAAGGAGTTGCCACTGACTTGTGTGGGCTTTGAAAAAGATGCCA
1 CACTGAC-T-TGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTG-AAAAGATGCCA
* *
2226969 CTGACTTGTGGGCTTT-GAAAGAGATGC
63 CTAACTTGTGGGCTTTAAAAAGAGATGC
** * *
2226996 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCATTGACTTGTGTGGGCTTTGAAAGGGTGCCACTA
1 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTA
* *
2227061 ACTTGTGGGCTTTGAAAAGAGTTGC
66 ACTTGTGGGCTTTAAAAAGAGATGC
* * *
2227086 TACCGACTTGTGTGGGCTTTGAAAGGAGTTGCTACCGACTTGTGTGGGCTTTGAAAAGATGCCAC
1 CACTGAC-T-TGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCAC
*
2227151 TAACTTGTGGGCTTT-GAAAGAGATGC
64 TAACTTGTGGGCTTTAAAAAGAGATGC
* * * *
2227177 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCAACTTGTGTGGGCTTTGAAAGGGTGCCACTG
1 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTA
* * *
2227242 ATTTGTGGGCTTT-GAAAG-GGTGC
66 ACTTGTGGGCTTTAAAAAGAGATGC
* * * * * *
2227265 CACTAACTTGTGGGCTTTGGAAGG-G-TGCCACTGA-TT-TGT-GGATTTTAAAATGATGCCATT
1 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAA-GATGCCACT
* * *
2227325 GAGTTGTGGACTTTAAAA
65 AACTTGTGGGCTTTAAAA
2227343 GTGAAAGCTC
Statistics
Matches: 1244, Mismatches: 145, Indels: 70
0.85 0.10 0.05
Matches are distributed among these distances:
83 8 0.01
84 25 0.02
85 46 0.04
86 75 0.06
87 35 0.03
88 35 0.03
89 491 0.39
90 110 0.09
91 76 0.06
92 318 0.26
93 25 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (90 bp):
CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTA
ACTTGTGGGCTTTAAAAAGAGATGC
Found at i:2226331 original size:181 final size:180
Alignment explanation
Indices: 2225836--2227304 Score: 1838
Period size: 181 Copynumber: 8.2 Consensus size: 180
2225826 GGTGACACTA
* * * * * * * **
2225836 ACTTGTGTGAGCTTTGAAAAGAGTTGCCACTGGC-T-CGTGGGTTTTGAAAAGAGTTACCACTGG
1 ACTTGTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGA--TGCCACTAA
* **
2225899 CTTATGGGCTTTGAAA-AGAGTGCCACTGACTTGTGGGCTTTGAAAGGA--TGCCACTAAC-T-T
64 CTTGTGGGCTTTGAAAGAGA-TGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGT
* * * * * **
2225959 GTGGACTTTGAAAGGATGCCACTAACTTGTGGGTTTTGAAAAAAG-TGTCACTA
128 GTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTG-AAAGAGTTGCCACCG
* ** * * * *
2226012 AC-TG-GTGGGTTTTGCTAAA--AG-TGCCACTAAC-T-TATGGGCTTTGAAATGGTGTCACTAA
1 ACTTGTGTGGGCTTTG--AAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAA
* * *
2226070 CTTGTGGGCTTT-AAAAAGAGTGCCACTGACTTATGGGCTTTGAAAGGAGTTGCCACCAACTTGT
64 CTTGTGGGCTTTGAAAGAGA-TGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGT
* * * *
2226134 GTGGGTTTTAAAAAGATGCCACTAACTTGTGGGCTTTGAAAGAGATGCCACTG
128 GTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTGAAAGAGTTGCCACCG
* * *
2226187 AC-T-TATGGGCTTTGAAAGGAGTTGCCATCGACTTGTGTGGGCTTTGAAAAGATGCCACTGACT
1 ACTTGTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACT
* * ** * *
2226250 TGTGGGCTTTGAAAAAAGTTGCCACCAACTTGTGTGGGCTTTGAAAGGAGTTTCCACTGACTTGT
66 TGTGGGCTTTG-AAAGAGATGCCACTGAC-T-TGTGGGCTTTGAAAGGAGTTGCCACCGACTTGT
** * *
2226315 GCAGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTAAAAAGAG-TGCCACTG
128 GTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTT-GAAAGAGTTGCCACCG
* * *
2226368 AC-T-TATGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTAAAAAGATGCCACTAACT
1 ACTTGTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACT
* * * * *
2226431 TGTGGGCTTTGAAAAAGATGCCACTAACTTATGGGCCTTGAAAGGAGTTGCCACCGACTTGTATG
66 TGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTG
* * *
2226496 GGTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTACCACCG
131 GGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTG-AAAGAGTTGCCACCG
*
2226547 ACTTGTGTGGGCTTTGAAAGGAGTTACCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACT
1 ACTTGTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACT
*
2226612 TGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTG
66 TGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTG
* *
2226677 GGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTAAAAAGAGTTGCCACCG
131 GGCTTTGAAAAGATGCCACTAACTTGTGGGCTTT-GAAAGAGTTGCCACCG
* *
2226728 ACTTGTGTGGGCTTTGAAAGGAGTTACCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTGACT
1 ACTTGTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACT
*
2226793 TGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTG
66 TGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTG
* * *
2226858 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCG
131 GGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTG-AAAGAGTTGCCACCG
* *
2226909 ACTTGTGTGGGCTTTGAAAGGAGTTGCCACTGACTTGTGTGGGCTTTGAAAAAGATGCCACTGAC
1 ACTTGTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTG-AAAAGATGCCACTAAC
**
2226974 TTGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCATTGACTTGTGT
65 TTGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGT
* * *
2227039 GGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCTACCG
130 GGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTG-AAAGAGTTGCCACCG
*
2227091 ACTTGTGTGGGCTTTGAAAGGAGTTGCTACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACT
1 ACTTGTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACT
*
2227156 TGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCAACTTGTGTG
66 TGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTG
* * * * * **
2227221 GGCTTTGAAAGGGTGCCACTGATTTGTGGGCTTTGAAAG-GGTGCCACTA
131 GGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTGAAAGAGTTGCCACCG
* * *
2227270 AC-T-TGTGGGCTTTGGAAGG-G-TGCCACTGATTTGTG
1 ACTTGTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTG
2227305 GATTTTAAAA
Statistics
Matches: 1163, Mismatches: 104, Indels: 53
0.88 0.08 0.04
Matches are distributed among these distances:
170 3 0.00
171 47 0.04
173 33 0.03
174 16 0.01
175 67 0.06
176 13 0.01
177 16 0.01
178 101 0.09
179 25 0.02
180 27 0.02
181 635 0.55
182 180 0.15
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (180 bp):
ACTTGTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACT
TGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTG
GGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTGAAAGAGTTGCCACCG
Found at i:2226374 original size:270 final size:270
Alignment explanation
Indices: 2225831--2227343 Score: 1892
Period size: 270 Copynumber: 5.6 Consensus size: 270
2225821 AAAAAGGTGA
* * * * * * * *
2225831 CACTAACTTGTGTGAGCTTTGAAAAGAGTTGCCACTGGC-T-CGTGGGTTTTGAAAAGAGTTACC
1 CACTGACTTGTG-G-GCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTT-AAAA-AGATGCC
* * **
2225894 ACTGGCTTATGGGCTTTGAAA-AGAGTGCCACTGACTTGTGGGCTTTGAAAGGA--TGCCACTAA
62 ACTGACTTGTGGGCTTTGAAAGAGA-TGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGA
* * * * * * **
2225956 C-T-TGTGGACTTTGAAAGGATGCCACTAACTTGTGGGTTTTGAAAAAAG-TGTCACTAAC-TG-
126 CTTGTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGT
* ** * * * *
2226016 GTGGGTTTTGCTAAA--AG-TGCCACTAAC-T-TATGGGCTTTGAAATGGTGTCACTAACTTGTG
191 GTGGGCTTTG--AAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACTTGTG
2226076 GGCTTTAAAA-AGAGTGC
254 GGCTTTAAAAGAGA-TGC
* * * *
2226093 CACTGACTTATGGGCTTTGAAAGGAGTTGCCACCAACTTGTGTGGGTTTTAAAAAGATGCCACTA
1 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTAAAAAGATGCCACTG
* *
2226158 ACTTGTGGGCTTTGAAAGAGATGCCACTGACTTATGGGCTTTGAAAGGAGTTGCCATCGACTTGT
66 ACTTGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGT
* *
2226223 GTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAAAGTTGCCACCAACTTGTGTGGG
131 GTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGG
* * **
2226288 CTTTGAAAGGAGTTTCCACTGACTTGTGCAGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTA
196 CTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTA
2226353 AAA-AGAGTGC
261 AAAGAGA-TGC
* * *
2226363 CACTGACTTATGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTAAAAAGATGCCACTA
1 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTAAAAAGATGCCACTG
* * * *
2226428 ACTTGTGGGCTTTGAAAAAGATGCCACTAACTTATGGGCCTTGAAAGGAGTTGCCACCGACTTGT
66 ACTTGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGT
* * *
2226493 ATGGGTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTACCACCGACTTGTGTGGG
131 GTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGG
* *
2226558 CTTTGAAAGGAGTTACCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTG
196 CTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTA
2226623 AAAGAGATGC
261 AAAGAGATGC
* *
2226633 CACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTG
1 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTAAAAAGATGCCACTG
* * * *
2226698 ACTTGTGGGCTTTAAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAAGGAGTTACCACCGACT
66 ACTTGTGGGCTTT-GAAAGAGATGCCACTGAC-T-TGTGGGCTTTGAAAGGAGTTGCCACCGACT
* *
2226763 TGTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTG-AAAGAGATGCCACTGAC-T-TGT
128 TGTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGT
* * * *
2226825 GGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
193 GGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCT
*
2226890 TTGAAAAGAGTTGC
258 TT-AAAAGAGATGC
* *
2226904 CACCGACTTGTGTGGGCTTTGAAAGGAGTTGCCACTGACTTGTGTGGGCTTTGAAAAAGATGCCA
1 CACTGAC-T-TGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTT-AAAAAGATGCCA
**
2226969 CTGACTTGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCATTGACT
63 CTGACTTGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACT
* * * *
2227034 TGTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCTACCGACTTGTGT
128 TGTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGT
*
2227099 GGGCTTTGAAAGGAGTTGCTACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCT
193 GGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCT
*
2227164 TTGAAAGAGATGC
258 TTAAAAGAGATGC
* * * *
2227177 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCAACTTGTGTGGGCTTTGAAAGGGTGCCACTG
1 CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTAAAAAGATGCCACTG
* * * * *
2227242 ATTTGTGGGCTTTGAAAG-GGTGCCACTAACTTGTGGGCTTTGGAAGG-G-TGCCACTGA-TT-T
66 ACTTGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGT
* * * * *
2227302 GT-GGATTTTAAAATGATGCCATTGAGTTGTGGACTTT-AAAAG
131 GTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGAAAAG
2227344 TGAAAGCTCA
Statistics
Matches: 1111, Mismatches: 113, Indels: 52
0.87 0.09 0.04
Matches are distributed among these distances:
260 70 0.06
261 9 0.01
262 26 0.02
263 1 0.00
264 55 0.05
265 32 0.03
266 4 0.00
267 19 0.02
268 9 0.01
269 27 0.02
270 461 0.41
271 137 0.12
272 32 0.03
273 137 0.12
274 92 0.08
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (270 bp):
CACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTAAAAAGATGCCACTG
ACTTGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGT
GTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGG
CTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTA
AAAGAGATGC
Found at i:2228102 original size:21 final size:21
Alignment explanation
Indices: 2228076--2228130 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
2228066 GTTATAAGCA
*
2228076 ATGTATCGATACAATT-TCCTC
1 ATGTATCGATACAATTGTAC-C
2228097 ATGTATCGATAC-ATTGTACC
1 ATGTATCGATACAATTGTACC
2228117 ATGTATCGATACAA
1 ATGTATCGATACAA
2228131 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACAATTGTACC
Found at i:2228206 original size:19 final size:20
Alignment explanation
Indices: 2228159--2228214 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
2228149 CTACCAATCT
* *
2228159 CATGTATTGATACAATTATC
1 CATGTATCGATACAATGATC
* *
2228179 CACGTATCGATACAATGA-G
1 CATGTATCGATACAATGATC
2228198 CATGTATCGATACAATG
1 CATGTATCGATACAATG
2228215 TATCGATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATGATC
Found at i:2228217 original size:13 final size:13
Alignment explanation
Indices: 2228199--2228225 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2228189 TACAATGAGC
2228199 ATGTATCGATACA
1 ATGTATCGATACA
2228212 ATGTATCGATACA
1 ATGTATCGATACA
2228225 A
1 A
2228226 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2228241 original size:33 final size:32
Alignment explanation
Indices: 2228182--2228244 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
2228172 AATTATCCAC
* *
2228182 GTATCGATACAATGAGCATGTATCGATACAAT
1 GTATCGATACAAAGAGAATGTATCGATACAAT
*
2228214 GTATCGATACAAAGCATAATGTATCGATACA
1 GTATCGATACAAAG-AGAATGTATCGATACA
2228245 TCTAGGTGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (32 bp):
GTATCGATACAAAGAGAATGTATCGATACAAT
Found at i:2228571 original size:27 final size:28
Alignment explanation
Indices: 2228533--2228608 Score: 127
Period size: 27 Copynumber: 2.8 Consensus size: 28
2228523 GATCATAACA
*
2228533 AAAAGGATGCCACAGAGTTGTGGAC-TT
1 AAAAGGATGCCACGGAGTTGTGGACTTT
2228560 AAAAGGATGCCACGGAGTTGTGGACTTT
1 AAAAGGATGCCACGGAGTTGTGGACTTT
*
2228588 AAAAAGATGCCACGGAGTTGT
1 AAAAGGATGCCACGGAGTTGT
2228609 AGAGTTTGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 24 0.52
28 22 0.48
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.22
Consensus pattern (28 bp):
AAAAGGATGCCACGGAGTTGTGGACTTT
Found at i:2229909 original size:16 final size:16
Alignment explanation
Indices: 2229869--2229912 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2229859 TCCCTTTTTA
2229869 TTTTGCTTTTGCACTT
1 TTTTGCTTTTGCACTT
* *
2229885 TTTTCCTTTT-CATTT
1 TTTTGCTTTTGCACTT
2229900 TTTGTGCTTTTGC
1 TTT-TGCTTTTGC
2229913 TTTTGACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 7 0.30
16 15 0.65
17 1 0.04
ACGTcount: A:0.05, C:0.18, G:0.11, T:0.66
Consensus pattern (16 bp):
TTTTGCTTTTGCACTT
Found at i:2236969 original size:20 final size:20
Alignment explanation
Indices: 2236944--2237020 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
2236934 GTAAAAAGAT
*
2236944 AGAATGTATCAATACATTGA
1 AGAATGTATCGATACATTGA
*
2236964 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
2236984 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
2237004 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
2237021 CTGGGTACTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:2237878 original size:167 final size:165
Alignment explanation
Indices: 2237534--2238119 Score: 424
Period size: 167 Copynumber: 3.5 Consensus size: 165
2237524 GGTGTCTACA
* * * * * * * * *
2237534 GTTTATAATTTTTAAAATTTATTAAATGTTGTCATTTAATTTTTATTAAATCAATTTTGAAAAAT
1 GTTTAAAATTTTTAAAATTCATCAAATATTATCA-TTAATTATCATTTAATCAGTTTTGAAAAAT
* * * ** ** * * *
2237599 TCCTTT-TATTTCATGA-GTTATTGA-TTTTCTTTTGGAATTCTTCTTATTTTTGAAATACGGAG
65 TCATTTAT-TTTCAT-ATGTTTTTCATTTTTCCCTTAAAATTCCT-TTATTTTTGAAAAACTGAG
*
2237661 TTTTCT-TCTCTATAAAT-TTTTTCG--GGAGGATTTTCATCG
127 TTTTCTAT-TCTATAAATGTTTTT-GAAGGA-GTTTTTC-TCG
* *
2237700 GATTAAAATTTTTAAAATTCATCAAATATTATTATCTAATTATCATTTAATCAGTTTTGAAAAAT
1 GTTTAAAATTTTTAAAATTCATCAAATATTATCAT-TAATTATCATTTAATCAGTTTTGAAAAAT
** * * ** *
2237765 TCATTTATTTTTTTGAAT-TTTTTTATTTTT-TCTTAAAATTTTTTTTATTTTTGAAAAACTGAT
65 TCATTTATTTTCAT--ATGTTTTTCATTTTTCCCTTAAAA-TTCCTTTATTTTTGAAAAACTGAG
2237828 TTTTCTATTCTATAAATGTTTTTGAAGGAGTTTTTCTCG
127 TTTTCTATTCTATAAATGTTTTTGAAGGAGTTTTTCTCG
* * * * * * * *
2237867 GTTTGAAATTTTTAATATTCATTAACTATCACCATTTAA--ATCATAGTAAGTTAGTTTTGAAAA
1 GTTTAAAATTTTTAAAATTCATCAAATATTATCA-TTAATTATCAT-TTAA-TCAGTTTTGAAAA
* * * *
2237930 ATTCATTAATTTTCATATGTTTTTCATTTTTCCCTTGAAATTCCTCTATTTTTAAAAAAACTGAG
63 ATTCATTTATTTTCATATGTTTTTCATTTTTCCCTTAAAATTCCTTTATTTTT-GAAAAACTGAG
* * * *
2237995 TTTCCTATTCCATAAAGGTTTTTGAGAGGA-TTTTTCTCA
127 TTTTCTATTCTATAAATGTTTTTGA-AGGAGTTTTTCTCG
* * * * * * * *
2238034 GTTTTAAATTTTTATAATTTATCTAATGTTGTCATTGAATTCTCATTAAATCAGTTTTGAAAAAT
1 GTTTAAAATTTTTAAAATTCATCAAATATTATCATT-AATTATCATTTAATCAGTTTTGAAAAAT
*
2238099 TCAATTTATTTT-ATGTGTTTT
65 TC-ATTTATTTTCATATGTTTT
2238120 GAAATTTTTG
Statistics
Matches: 332, Mismatches: 67, Indels: 41
0.75 0.15 0.09
Matches are distributed among these distances:
165 8 0.02
166 87 0.26
167 195 0.59
168 35 0.11
169 7 0.02
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (165 bp):
GTTTAAAATTTTTAAAATTCATCAAATATTATCATTAATTATCATTTAATCAGTTTTGAAAAATT
CATTTATTTTCATATGTTTTTCATTTTTCCCTTAAAATTCCTTTATTTTTGAAAAACTGAGTTTT
CTATTCTATAAATGTTTTTGAAGGAGTTTTTCTCG
Found at i:2239852 original size:139 final size:140
Alignment explanation
Indices: 2239543--2240018 Score: 499
Period size: 139 Copynumber: 3.5 Consensus size: 140
2239533 TTATTTTACC
* * * * *
2239543 ACTAAATGAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCTTACAGTTTTTCGTA-A-G
1 ACTAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTA-TGATTTTCATATAGG
* * *
2239606 GGTATAAAAATCTTCAAAACTTTTCGTATCTTTTCGGTTCTTCATTACT-GTACAAAATGAATTT
65 GGTATAGAAATCTTCAAAACTTTTCGTATCTTTT-GGTTCTCCATTA-TGGTACGAAATGAATTT
**
2239670 TT-AGAAATTAACG
128 TTGA-AAATTAAAA
* * * *
2239683 ATTACATAAAAATTATTATCTTAATATTTCAAAATTTCTAATATTCCTATGATTTTC-TATAGGG
1 ACTAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGATTTTCATATAGGG
* *
2239747 GTATAGAAATCTTTAAAACTTTTCGTATCTTTTGGTTCTCCATTATGGTATGAAATGAATTTTTG
66 GTATAGAAATCTTCAAAACTTTTCGTATCTTTTGGTTCTCCATTATGGTACGAAATGAATTTTTG
2239812 AAAATTAAAA
131 AAAATTAAAA
* * *
2239822 ACTAAATAAAAATTATTATCTTAATTTTTCAATATTTCTAATATTTCTAT-AGTTTTCAATAGAG
1 ACTAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGA-TTTTC-ATATA-
* *
2239886 GTGGGTATAGAAATCTTCAAAACTTTTC--A-----------TCCATTAAGGTACGAAATGAAGT
63 G-GGGTATAGAAATCTTCAAAACTTTTCGTATCTTTTGGTTCTCCATTATGGTACGAAATGAATT
2239938 TTTGAAAATTAAAA
127 TTTGAAAATTAAAA
* * * *
2239952 A-TCAAATAAAAATTATTATATTAATTTTTCAAGATTTCTATTATTCCTATGGTTTTC-TGTAGG
1 ACT-AAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGATTTTCATATAGG
2240015 GGTA
65 GGTA
2240019 AAGTTTTTAA
Statistics
Matches: 293, Mismatches: 32, Indels: 36
0.81 0.09 0.10
Matches are distributed among these distances:
126 5 0.02
127 1 0.00
128 2 0.01
129 1 0.00
130 83 0.28
138 4 0.01
139 90 0.31
140 77 0.26
141 4 0.01
142 1 0.00
143 25 0.09
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (140 bp):
ACTAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGATTTTCATATAGGG
GTATAGAAATCTTCAAAACTTTTCGTATCTTTTGGTTCTCCATTATGGTACGAAATGAATTTTTG
AAAATTAAAA
Found at i:2241077 original size:38 final size:38
Alignment explanation
Indices: 2241025--2241141 Score: 148
Period size: 38 Copynumber: 3.1 Consensus size: 38
2241015 ACAAGCTACG
2241025 AACAAAAACCACTATTTTAAACCGGTGGCACGGTTAGA
1 AACAAAAACCACTATTTTAAACCGGTGGCACGGTTAGA
* * *
2241063 AACAAAAACTACTATTCTAAATCGGTGGCACGGTTA-A
1 AACAAAAACCACTATTTTAAACCGGTGGCACGGTTAGA
* * *
2241100 ATACAAAAACCACTATTCTT-ATCCGATGGCACGGTTTGA
1 A-ACAAAAACCACTATT-TTAAACCGGTGGCACGGTTAGA
2241139 AAC
1 AAC
2241142 CTGTTTCTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
37 2 0.03
38 62 0.93
39 3 0.04
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (38 bp):
AACAAAAACCACTATTTTAAACCGGTGGCACGGTTAGA
Found at i:2242030 original size:22 final size:22
Alignment explanation
Indices: 2241987--2242029 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2241977 AAATTAATAA
*
2241987 AACTGAAATTTATGTTATTTTT
1 AACTGAAATATATGTTATTTTT
*
2242009 AACT-AAATATATTTTATTTTT
1 AACTGAAATATATGTTATTTTT
2242030 TCTGAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (22 bp):
AACTGAAATATATGTTATTTTT
Found at i:2245045 original size:3 final size:3
Alignment explanation
Indices: 2245033--2245062 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2245023 ATAGATATAC
2245033 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2245063 TTGTGGGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:2248643 original size:20 final size:20
Alignment explanation
Indices: 2248618--2248687 Score: 140
Period size: 20 Copynumber: 3.5 Consensus size: 20
2248608 TTCTTTATAA
2248618 GTATCGATACATTTGGTCAT
1 GTATCGATACATTTGGTCAT
2248638 GTATCGATACATTTGGTCAT
1 GTATCGATACATTTGGTCAT
2248658 GTATCGATACATTTGGTCAT
1 GTATCGATACATTTGGTCAT
2248678 GTATCGATAC
1 GTATCGATAC
2248688 TGTGCAATCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.39
Consensus pattern (20 bp):
GTATCGATACATTTGGTCAT
Found at i:2248671 original size:40 final size:39
Alignment explanation
Indices: 2248618--2248712 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 39
2248608 TTCTTTATAA
* *
2248618 GTATCGATACATTTGGTCATGTATCGATACATTTG-GTCAT
1 GTATCGATACATTTGGTCATGTATCGATAC-TGTGAATC-T
2248658 GTATCGATACATTTGGTCATGTATCGATACTGTGCAATCT
1 GTATCGATACATTTGGTCATGTATCGATACTGTG-AATCT
2248698 GTATCGATACATTTG
1 GTATCGATACATTTG
2248713 AAGGTGTATC
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
39 3 0.06
40 46 0.90
41 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (39 bp):
GTATCGATACATTTGGTCATGTATCGATACTGTGAATCT
Found at i:2249269 original size:22 final size:22
Alignment explanation
Indices: 2249242--2249286 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
2249232 TTTTCTTTTC
2249242 TCTCCCCCTTAATCAAAA-AATT
1 TCTCCCCCTTAAT-AAAATAATT
2249264 TCTCCCCCTTAATAAAATAATT
1 TCTCCCCCTTAATAAAATAATT
2249286 T
1 T
2249287 AACAATTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAATAATT
Found at i:2250612 original size:21 final size:21
Alignment explanation
Indices: 2250581--2250632 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
2250571 GCTACTAGTG
*
2250581 TGGGGGCTGCCCGGTTGCAACC
1 TGGGGG-TGCCCGGTCGCAACC
*
2250603 TGGGGGTG-CCGGTCGCGACC
1 TGGGGGTGCCCGGTCGCAACC
2250623 TGGTGGGTGC
1 TGG-GGGTGC
2250633 TGCCTAAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 13 0.50
21 7 0.27
22 6 0.23
ACGTcount: A:0.06, C:0.27, G:0.48, T:0.19
Consensus pattern (21 bp):
TGGGGGTGCCCGGTCGCAACC
Found at i:2251294 original size:8 final size:8
Alignment explanation
Indices: 2251281--2251306 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2251271 AACATCATTC
2251281 ATCACAAA
1 ATCACAAA
2251289 ATCACAAA
1 ATCACAAA
2251297 ATCACAAA
1 ATCACAAA
2251305 AT
1 AT
2251307 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:2257248 original size:19 final size:20
Alignment explanation
Indices: 2257203--2257254 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2257193 TTACAAGTCA
*
2257203 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATATTGGG
*
2257223 ATGTATCGATACATATTGTG
1 ATGTATCGATACATATTGGG
2257243 -TGTATCGATACA
1 ATGTATCGATACA
2257255 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATATTGGG
Found at i:2257343 original size:20 final size:21
Alignment explanation
Indices: 2257296--2257345 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2257286 GCCAGTGACC
*
2257296 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
2257317 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
2257337 TGTATCGAT
1 TGTATCGAT
2257346 GCAATGTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:2259093 original size:25 final size:26
Alignment explanation
Indices: 2259065--2259116 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
2259055 TTACTAAATT
2259065 TTATATATTATAATAT-AATAG-TATA
1 TTATATATTA-AATATCAATAGTTATA
*
2259090 TTATATATTACATATCAATAGTTATA
1 TTATATATTAAATATCAATAGTTATA
2259116 T
1 T
2259117 AATTGTGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 15 0.62
26 5 0.21
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (26 bp):
TTATATATTAAATATCAATAGTTATA
Found at i:2259176 original size:26 final size:24
Alignment explanation
Indices: 2259134--2259207 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 24
2259124 TATAACACAG
*
2259134 ATATATAATATTA--TATAAATATT
1 ATATATAACATTATTTATAAATA-T
*
2259157 TTATTATAACATTATTTATAAATA-
1 ATA-TATAACATTATTTATAAATAT
2259181 ATATATAACATTATTTGATATAATAT
1 ATATATAACATTATTT-ATA-AATAT
2259207 A
1 A
2259208 ATCTTATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
23 15 0.36
24 14 0.33
25 4 0.10
26 9 0.21
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (24 bp):
ATATATAACATTATTTATAAATAT
Found at i:2262500 original size:5 final size:5
Alignment explanation
Indices: 2262490--2262514 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2262480 AAATTAACAG
2262490 CTAGA CTAGA CTAGA CTAGA CTAGA
1 CTAGA CTAGA CTAGA CTAGA CTAGA
2262515 AGCAGACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (5 bp):
CTAGA
Found at i:2265571 original size:20 final size:20
Alignment explanation
Indices: 2265546--2265583 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2265536 CTCACGACAT
2265546 TGTATCAATACATTACTTAA
1 TGTATCAATACATTACTTAA
2265566 TGTATCAATACATTACTT
1 TGTATCAATACATTACTT
2265584 TAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (20 bp):
TGTATCAATACATTACTTAA
Found at i:2265671 original size:20 final size:20
Alignment explanation
Indices: 2265607--2265677 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
2265597 ATTGAACTCA
***
2265607 ATGTATCGATACATTTATGG
1 ATGTATCGATACATTTAAAT
2265627 ATGTATCGATACATTCTAAAT
1 ATGTATCGATACATT-TAAAT
**
2265648 -TGTATCGATACATTTACCT
1 ATGTATCGATACATTTAAAT
*
2265667 ATGTATTGATA
1 ATGTATCGATA
2265678 TAAATGAGGG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.07
20 38 0.88
21 2 0.05
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTAAAT
Found at i:2267064 original size:13 final size:13
Alignment explanation
Indices: 2267046--2267071 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2267036 CAATTTTTTG
2267046 TGTATCGATACAT
1 TGTATCGATACAT
2267059 TGTATCGATACAT
1 TGTATCGATACAT
2267072 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2267086 original size:32 final size:33
Alignment explanation
Indices: 2267026--2267089 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2267016 TACAAGCCAA
** *
2267026 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
2267059 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
2267090 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:2269171 original size:21 final size:20
Alignment explanation
Indices: 2269142--2269184 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2269132 GGCTAGTGTG
**
2269142 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTTACGACCT
*
2269163 GGGAGTGCCGGTTACGACCT
1 GGGACTGCCGGTTACGACCT
2269183 GG
1 GG
2269185 TGATGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.12, C:0.26, G:0.42, T:0.21
Consensus pattern (20 bp):
GGGACTGCCGGTTACGACCT
Found at i:2269497 original size:20 final size:20
Alignment explanation
Indices: 2269460--2269503 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2269450 TGATGCTGGT
2269460 TTTGATGAAAAACGAAGTAA
1 TTTGATGAAAAACGAAGTAA
*
2269480 TTTGAGTGAAAAAC-AAGTAT
1 TTTGA-TGAAAAACGAAGTAA
2269500 TTTG
1 TTTG
2269504 CAAAAGATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (20 bp):
TTTGATGAAAAACGAAGTAA
Found at i:2269642 original size:13 final size:13
Alignment explanation
Indices: 2269624--2269649 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2269614 ATAATCACCC
2269624 TGTATCGATACAA
1 TGTATCGATACAA
2269637 TGTATCGATACAA
1 TGTATCGATACAA
2269650 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2271736 original size:15 final size:15
Alignment explanation
Indices: 2271716--2271746 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2271706 ATTTCGTTTA
*
2271716 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2271731 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2271746 G
1 G
2271747 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2275824 original size:13 final size:13
Alignment explanation
Indices: 2275806--2275831 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2275796 CAATTTTTTG
2275806 TGTATCGATACAT
1 TGTATCGATACAT
2275819 TGTATCGATACAT
1 TGTATCGATACAT
2275832 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2275846 original size:32 final size:33
Alignment explanation
Indices: 2275786--2275849 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2275776 TACAAGCCAA
** *
2275786 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
2275819 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
2275850 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:2288649 original size:12 final size:11
Alignment explanation
Indices: 2288634--2288688 Score: 53
Period size: 12 Copynumber: 4.9 Consensus size: 11
2288624 CTAATGAAGA
2288634 AAAAGATGAGAG
1 AAAAGA-GAGAG
2288646 AAAATGA-A-AG
1 AAAA-GAGAGAG
2288656 ATAAAGAGAGAG
1 A-AAAGAGAGAG
2288668 AATAAGAGAGAG
1 AA-AAGAGAGAG
2288680 -AAAGAGAGA
1 AAAAGAGAGA
2288689 AAGAGAGGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
10 13 0.34
11 7 0.18
12 16 0.42
13 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.07
Consensus pattern (11 bp):
AAAAGAGAGAG
Found at i:2288666 original size:22 final size:23
Alignment explanation
Indices: 2288625--2288688 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
2288615 GGTTTAAGGC
2288625 TAATG-AAGAAAAAGATGAGAGAA
1 TAATGAAAGAAAAAGA-GAGAGAA
*
2288648 -AATGAAAGATAAAGAGAGAGAA
1 TAATGAAAGAAAAAGAGAGAGAA
* *
2288670 TAA-GAGAGAGAAAGAGAGA
1 TAATGAAAGAAAAAGAGAGA
2288689 AAGAGAGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 25 0.69
23 11 0.31
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (23 bp):
TAATGAAAGAAAAAGAGAGAGAA
Found at i:2288707 original size:18 final size:18
Alignment explanation
Indices: 2288671--2288708 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2288661 GAGAGAGAAT
*
2288671 AAGAGAGAGAAAGAGAGA
1 AAGAGAGAGAAAGAAAGA
2288689 AAGAGAG-GAAAGGAAAGA
1 AAGAGAGAGAAA-GAAAGA
2288707 AA
1 AA
2288709 TTAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (18 bp):
AAGAGAGAGAAAGAAAGA
Found at i:2291640 original size:16 final size:16
Alignment explanation
Indices: 2291616--2291670 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
2291606 TTGGATTTGT
* *
2291616 GTTCAAGCTCGTTCGG
1 GTTCGAGCTCATTCGG
*
2291632 GTTCGAGCTTATTCGG
1 GTTCGAGCTCATTCGG
* * *
2291648 GTTCGGGCTTATTCAG
1 GTTCGAGCTCATTCGG
2291664 GTTCGAG
1 GTTCGAG
2291671 TTTTTTCGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.13, C:0.20, G:0.33, T:0.35
Consensus pattern (16 bp):
GTTCGAGCTCATTCGG
Found at i:2294233 original size:20 final size:20
Alignment explanation
Indices: 2294189--2294233 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2294179 GTTAGCAGCC
2294189 CATG-TTCATGCATTTTGAG
1 CATGTTTCATGCATTTTGAG
2294208 CTATGTTTCATGCATTTAT-AG
1 C-ATGTTTCATGCATTT-TGAG
2294229 CATGT
1 CATGT
2294234 CCAGCACCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.04
20 7 0.30
21 14 0.61
22 1 0.04
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (20 bp):
CATGTTTCATGCATTTTGAG
Found at i:2299719 original size:90 final size:90
Alignment explanation
Indices: 2299625--2299797 Score: 199
Period size: 90 Copynumber: 1.9 Consensus size: 90
2299615 ATCCTTCAAG
* * *
2299625 AAACTCCATCCACATTCCTCAGAGGCGATATTCTAACC-CTATTCTATAAAAAAATT-CAAATTT
1 AAACTCCAACCACATTACTCAGAGGCGATACTCTAACCAC-ATTCTA-AAAAAAATTACAAATTT
2299688 TCTTTTCT-CATAATTTTATCACAGGGA
64 TCTTTT-TGCATAATTTTATCACAGGGA
* * * * * * *
2299715 AAACTCTAACCCCATTACTCTGAGGGGATACTCTAACCACATTCTACACAAAATTATAAATTTTC
1 AAACTCCAACCACATTACTCAGAGGCGATACTCTAACCACATTCTAAAAAAAATTACAAATTTTC
*
2299780 TTTTTGTATAATTTTATC
66 TTTTTGCATAATTTTATC
2299798 TTTGGGGAAC
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
89 8 0.12
90 60 0.87
91 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.36
Consensus pattern (90 bp):
AAACTCCAACCACATTACTCAGAGGCGATACTCTAACCACATTCTAAAAAAAATTACAAATTTTC
TTTTTGCATAATTTTATCACAGGGA
Found at i:2301159 original size:20 final size:20
Alignment explanation
Indices: 2301129--2301189 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
2301119 ATTTGTACCG
2301129 ATACAATAAGTGAATGTATCA
1 ATAC-ATAAGTGAATGTATCA
2301150 ATACATAAGTGAATGTATCA
1 ATACATAAGTGAATGTATCA
**
2301170 ATACATGTGTGCAATGTATC
1 ATACATAAGTG-AATGTATC
2301190 GATATAGGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 25 0.68
21 12 0.32
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.31
Consensus pattern (20 bp):
ATACATAAGTGAATGTATCA
Found at i:2301258 original size:19 final size:20
Alignment explanation
Indices: 2301234--2301281 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2301224 GGAAAGAAAA
*
2301234 TGTATCGATAC-TTTTTCAT
1 TGTATCGATACATATTTCAT
2301253 TGTATCGATACATATTTCAT
1 TGTATCGATACATATTTCAT
*
2301273 TATATCGAT
1 TGTATCGAT
2301282 GTATTCTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (20 bp):
TGTATCGATACATATTTCAT
Found at i:2309994 original size:20 final size:19
Alignment explanation
Indices: 2309969--2310078 Score: 96
Period size: 20 Copynumber: 5.6 Consensus size: 19
2309959 TGCCAATTTC
2309969 ATGTATCGATACAATTAAAT
1 ATGTATCGATACAA-TAAAT
* **
2309989 ATGTATCGATACAATGAGC
1 ATGTATCGATACAATAAAT
**
2310008 ATGTATCGATACAATAAGC
1 ATGTATCGATACAATAAAT
* *
2310027 ATATATCGATACAA-AGCAT
1 ATGTATCGATACAATA-AAT
* *
2310046 AATGTATCGATACATCTAGAT
1 -ATGTATCGATACA-ATAAAT
2310067 ATGTATCGATAC
1 ATGTATCGATAC
2310079 TTTCTAGGGT
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
18 1 0.01
19 33 0.44
20 38 0.51
21 2 0.03
22 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (19 bp):
ATGTATCGATACAATAAAT
Found at i:2310013 original size:19 final size:19
Alignment explanation
Indices: 2309968--2310040 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
2309958 CTGCCAATTT
*
2309968 CATGTATCGATACAATTAAA
1 CATGTATCGATACAA-TAAG
* *
2309988 TATGTATCGATACAATGAG
1 CATGTATCGATACAATAAG
2310007 CATGTATCGATACAATAAG
1 CATGTATCGATACAATAAG
*
2310026 CATATATCGATACAA
1 CATGTATCGATACAA
2310041 AGCATAATGT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 33 0.70
20 14 0.30
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATAAG
Found at i:2310021 original size:39 final size:40
Alignment explanation
Indices: 2309968--2310078 Score: 129
Period size: 39 Copynumber: 2.8 Consensus size: 40
2309958 CTGCCAATTT
*
2309968 CATGTATCGATACAATTAAATATGTATCGATACAATG-AG
1 CATGTATCGATACAATTAAATATGTATCGATACAAAGCAG
** * *
2310007 CATGTATCGATACAA-TAAGCATATATCGATACAAAGCAT
1 CATGTATCGATACAATTAAATATGTATCGATACAAAGCAG
* *
2310046 AATGTATCGATAC-ATCTAGATATGTATCGATAC
1 CATGTATCGATACAAT-TAAATATGTATCGATAC
2310079 TTTCTAGGGT
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
38 18 0.31
39 28 0.47
40 13 0.22
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (40 bp):
CATGTATCGATACAATTAAATATGTATCGATACAAAGCAG
Found at i:2310045 original size:17 final size:17
Alignment explanation
Indices: 2309992--2310046 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 17
2309982 ATTAAATATG
*
2309992 TATCGATACAATGAGCATG
1 TATCGATACAA--AGCATA
2310011 TATCGATACAATAAGCATA
1 TATCGATAC-A-AAGCATA
2310030 TATCGATACAAAGCATA
1 TATCGATACAAAGCATA
2310047 ATGTATCGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.21
18 1 0.03
19 23 0.70
20 1 0.03
21 1 0.03
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (17 bp):
TATCGATACAAAGCATA
Found at i:2313105 original size:31 final size:31
Alignment explanation
Indices: 2313062--2313126 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
2313052 CTTTTTGTAC
2313062 ATGATCTTTAATAAAGTGATGTCTAATTTCA
1 ATGATCTTTAATAAAGTGATGTCTAATTTCA
2313093 ATGAT-TTATAATAAAGTGATGTCTAATTTCA
1 ATGATCTT-TAATAAAGTGATGTCTAATTTCA
2313124 ATG
1 ATG
2313127 TGCTTAGTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.42
Consensus pattern (31 bp):
ATGATCTTTAATAAAGTGATGTCTAATTTCA
Found at i:2315509 original size:13 final size:13
Alignment explanation
Indices: 2315491--2315515 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2315481 ATAATGCACA
2315491 GTATCGATACATT
1 GTATCGATACATT
2315504 GTATCGATACAT
1 GTATCGATACAT
2315516 GACCACTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2315622 original size:13 final size:13
Alignment explanation
Indices: 2315604--2315629 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2315594 ACATACAAGA
2315604 TGTATCGATACAT
1 TGTATCGATACAT
2315617 TGTATCGATACAT
1 TGTATCGATACAT
2315630 AACCAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2315652 original size:34 final size:32
Alignment explanation
Indices: 2315584--2315652 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
2315574 CCTTAACTGT
2315584 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
*
2315616 TTGTATCGATACATAACCAA-ATTGTATCGATGCA
1 TTGTATCGATACAT-A-CAAGA-TGTATCGATACA
2315650 TTG
1 TTG
2315653 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 14 0.42
33 2 0.06
34 17 0.52
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:2322779 original size:18 final size:17
Alignment explanation
Indices: 2322752--2322785 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2322742 CAAAGAGGGC
*
2322752 TCGATTCCTCGAAACAT
1 TCGATTCCTCAAAACAT
2322769 TCGAGTTCCTCAAAACA
1 TCGA-TTCCTCAAAACA
2322786 AAGCCACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.26
Consensus pattern (17 bp):
TCGATTCCTCAAAACAT
Found at i:2324399 original size:13 final size:13
Alignment explanation
Indices: 2324381--2324406 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2324371 ACATACAAGA
2324381 TGTATCGATACAT
1 TGTATCGATACAT
2324394 TGTATCGATACAT
1 TGTATCGATACAT
2324407 AACCAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2324402 original size:32 final size:34
Alignment explanation
Indices: 2324361--2324429 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
2324351 CCTTAACTAT
*
2324361 TTGTATCGATACAT-A-CAAGA-TGTATCGATACA
1 TTGTATCGATACATAACCAA-ATTATATCGATACA
2324393 TTGTATCGATACATAACCAAATTATATCGATACA
1 TTGTATCGATACATAACCAAATTATATCGATACA
2324427 TTG
1 TTG
2324430 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 14 0.42
33 2 0.06
34 17 0.52
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (34 bp):
TTGTATCGATACATAACCAAATTATATCGATACA
Found at i:2328149 original size:42 final size:43
Alignment explanation
Indices: 2328048--2329255 Score: 308
Period size: 42 Copynumber: 28.7 Consensus size: 43
2328038 TGTTTCGAAA
*
2328048 TCTGCCTATCAGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
* * * *
2328091 TCTGCCTATTGACTTTGACCTTGGAGGCTT-TCTTACCTTC-AG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCT-TTACCCTCAAG
* * * * *
2328133 TCTGCTTATCGGCTTTGACCATAGAGA-TTGCCTTA-TCTCAAG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTT-CTTTACCCTCAAG
* * * * *
2328175 TCTGCCT-GCTAGATTTGACCTTGGAGACTTTTTTACCTTC-AG
1 TCTGCCTATC-GGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
* * **** ** * * * * *
2328217 TCTGCTTGTTAATTTTGACCTAAGAGACTACCTCA-TCTAAAG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
* * * * **
2328259 TCTG-CT-TGCTGACTTT-AACTCTAGAGACTTTTTTA-CCTTTAG
1 TCTGCCTAT-C-GGCTTTGACCT-TGGAGACTTCTTTACCCTCAAG
* * * * * * *
2328301 TCTACCTGTCGGCTTTGACCCTGGAGACTACCTCA-TCTCAAG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
* * * * * *
2328343 TCTACCTGTTGGCTTTAACCTTGGAGACTT-TCTTATCTTC-AG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCT-TTACCCTCAAG
* ** * * * * * * *
2328385 TTTGCCTATCGATTTTAACCCTAGAGACTGCCTCA-TCTCAAG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
* * * * *
2328427 TCTACCTATCGACTTTGACTTTGGAGACTTTTTTACCTTC-AG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
* * * * *
2328469 T-TTCCTTATCGGCTTTGACCTTGGAAACTGGC-TGA-TCTCAAG
1 TCTGCC-TATCGGCTTTGACCTTGGAGACT-TCTTTACCCTCAAG
* * * * ** * * *
2328511 TTTGCCTGTCAGCTTTGACCCTAAATACTT-TCATACCTTC-AG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCT-TTACCCTCAAG
* * ** * * * * * ** *
2328553 TCTACCTGTCAACTTTGACCCTAGAGACTGCCTCA-TGTCAAA
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
* * * * * * *
2328595 TCTACTTGTTGGCGTTGACCCTGAAGACTTCTTTACCCTCAAG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
* * *
2328638 TCTGCCTGTCGGCTTTGACCTTGGAGA-TTTTCTTACCTTC-AG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCT-TTACCCTCAAG
* * * * * * * * *
2328680 TCTGCTTGTTGGCTTTGACCCT-AAAAATTGCCTTA-TCTCAAG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTT-CTTTACCCTCAAG
* * **
2328722 TCTGCCTATCGACTTTGACCTTAGAGACTT-TATTACATTCAA-
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCT-TTACCCTCAAG
* * * * * * * *
2328764 TCTTCTTGTCGGCTTTGA-CTTGAAGACTGCCTCA-TCTCAAG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
* * * * * * *
2328805 TCTACCTGTCGGCGTTGACCCTAGAGACTTTTTTACCATCAAG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
* * * * * *
2328848 TTTGCTTGTCAGCTTTGACCCTGGAGACTT-TCTTACCTTC-AG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCT-TTACCCTCAAG
*
2328890 TCTGCCTATCGG-TGTTGACCTTGGAAACTT-TCTTACCCTCAAG
1 TCTGCCTATCGGCT-TTGACCTTGGAGACTTCT-TTACCCTCAAG
* * * * * * *
2328933 TTTGCTTACCGGCTTTAACCCTGGAAACTT-TCTTACCTTC-AG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCT-TTACCCTCAAG
* * * * * * *
2328975 TCTACCTATCAGCTTTGTCCTTGGAGACTACCTCA-TCTCAAG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
* * * * *
2329017 TCTACCTATTGGCTTTGACCTTGGAGACTT-TCTTATCTTC-GG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCT-TTACCCTCAAG
* ** * *
2329059 TCGGCCTATCGGCTTAAACCTTGGAGACTTCCTTA-TCTCAAG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
* * * * * * *
2329101 TCTACCTGTTGACTTTGACCTTGGAGGCTTTTTTACCTTC-AG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
* * * * * *
2329143 TTTGCTTATCGGCTTTGACCTTGGAGACTACCTGA-TCTCAAG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
* * * * * * *
2329185 TCTGCTTGTCAGCTTTGACCCTAGAGACTT-TCATACCTTC-AG
1 TCTGCCTATCGGCTTTGACCTTGGAGACTTCT-TTACCCTCAAG
* * * *
2329227 TCTACCTATCGACTTTGACCCTAGAGACT
1 TCTGCCTATCGGCTTTGACCTTGGAGACT
2329256 GCTATCACAA
Statistics
Matches: 823, Mismatches: 287, Indels: 111
0.67 0.24 0.09
Matches are distributed among these distances:
40 5 0.01
41 55 0.07
42 594 0.72
43 167 0.20
44 2 0.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.37
Consensus pattern (43 bp):
TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTTACCCTCAAG
Found at i:2328192 original size:84 final size:84
Alignment explanation
Indices: 2328085--2329255 Score: 510
Period size: 84 Copynumber: 13.9 Consensus size: 84
2328075 CTTCTTTACC
* *
2328085 CTCAAGTCTGCCT-ATTGACTTTGACCTTGGAGGCTTTCTTACCTTCAGTCTGCTTATCGGCTTT
1 CTCAAGTCTGCCTGA-TGACTTTGACCTTGGAGACTTTTTTACCTTCAGTCTGCTTATCGGCTTT
* * * *
2328149 GACCATAGAGATTGCCTTAT
65 GACCCTAGAGACTACCTCAT
* * ****
2328169 CTCAAGTCTGCCTGCTAGA-TTTGACCTTGGAGACTTTTTTACCTTCAGTCTGCTTGTTAATTTT
1 CTCAAGTCTGCCTGAT-GACTTTGACCTTGGAGACTTTTTTACCTTCAGTCTGCTTATCGGCTTT
2328233 GA-CCTAAGAGACTACCTCAT
65 GACCCT-AGAGACTACCTCAT
* * * * * * * * *
2328253 CTAAAGTCTGCTTGCTGACTTT-AACTCTAGAGACTTTTTTACCTTTAGTCTACCTGTCGGCTTT
1 CTCAAGTCTGCCTGATGACTTTGACCT-TGGAGACTTTTTTACCTTCAGTCTGCTTATCGGCTTT
*
2328317 GACCCTGGAGACTACCTCAT
65 GACCCTAGAGACTACCTCAT
* * * * * * * * ** *
2328337 CTCAAGTCTACCTGTTGGCTTTAACCTTGGAGACTTTCTTATCTTCAGTTTGCCTATCGATTTTA
1 CTCAAGTCTGCCTGATGACTTTGACCTTGGAGACTTTTTTACCTTCAGTCTGCTTATCGGCTTTG
*
2328402 ACCCTAGAGACTGCCTCAT
66 ACCCTAGAGACTACCTCAT
* * * *
2328421 CTCAAGTCTACCT-ATCGACTTTGACTTTGGAGACTTTTTTACCTTCAGTTTCCTTATCGGCTTT
1 CTCAAGTCTGCCTGAT-GACTTTGACCTTGGAGACTTTTTTACCTTCAGTCTGCTTATCGGCTTT
* * * ** *
2328485 GACCTTGGAAACTGGCTGAT
65 GACCCTAGAGACTACCTCAT
* * * ** * ** * * * **
2328505 CTCAAGTTTGCCTG-TCAGCTTTGACCCTAAATACTTTCATACCTTCAGTCTACCTGTCAACTTT
1 CTCAAGTCTGCCTGATGA-CTTTGACCTTGGAGACTTTTTTACCTTCAGTCTGCTTATCGGCTTT
*
2328569 GACCCTAGAGACTGCCTCAT
65 GACCCTAGAGACTACCTCAT
* * * * * * * * * * * * *
2328589 GTCAAATCTACTTGTTGGCGTTGACCCTGAAGACTTCTTTACCCTCAAGTCTGCCTGTCGGCTTT
1 CTCAAGTCTGCCTGATGACTTTGACCTTGGAGACTTTTTTACCTTC-AGTCTGCTTATCGGCTTT
* * * ** * *
2328654 GACCTTGGAGATTTTCTTAC
65 GACCCTAGAGACTACCTCAT
* * * * * * * ** * * *
2328674 CTTC-AGTCTGCTTGTTGGCTTTGACCCT-AAAAATTGCCTTATC-TCAAGTCTGCCTATCGACT
1 C-TCAAGTCTGCCTGATGACTTTGACCTTGGAGACTT-TTTTACCTTC-AGTCTGCTTATCGGCT
* *
2328736 TTGACCTTAGAGACTTTA-TTACAT
63 TTGACCCTAGAGAC--TACCT-CAT
* * * * *** * * * * * *
2328760 -TCAA-TCTTCTTG-TCGGCTTTGA-CTTGAAGACTGCCTCATC-TCAAGTCTACCTGTCGGCGT
1 CTCAAGTCTGCCTGAT-GACTTTGACCTTGGAGACTTTTTTACCTTC-AGTCTGCTTATCGGCTT
*** * *
2328820 TGACCCTAGAGACTTTTTTAC
64 TGACCCTAGAGACTACCTCAT
* * * * * *
2328841 CATCAAGTTTGCTTG-TCAGCTTTGACCCTGGAGACTTTCTTACCTTCAGTCTGCCTATCGG-TG
1 C-TCAAGTCTGCCTGATGA-CTTTGACCTTGGAGACTTTTTTACCTTCAGTCTGCTTATCGGCT-
* * * ** * *
2328904 TTGACCTTGGAAACTTTCTTACC
63 TTGACCCTAGAGACTACCTCA-T
* * * * * * * * * * *
2328927 CTCAAGTTTG-CTTACCGGCTTTAACCCTGGAAACTTTCTTACCTTCAGTCTACCTATCAGCTTT
1 CTCAAGTCTGCCTGA-TGACTTTGACCTTGGAGACTTTTTTACCTTCAGTCTGCTTATCGGCTTT
* * *
2328991 GTCCTTGGAGACTACCTCAT
65 GACCCTAGAGACTACCTCAT
* * * * * * * *
2329011 CTCAAGTCTACCT-ATTGGCTTTGACCTTGGAGACTTTCTTATCTTCGGTCGGCCTATCGGCTTA
1 CTCAAGTCTGCCTGA-TGACTTTGACCTTGGAGACTTTTTTACCTTCAGTCTGCTTATCGGCTTT
* * * * *
2329075 AACCTTGGAGACTTCCTTAT
65 GACCCTAGAGACTACCTCAT
* * * *
2329095 CTCAAGTCTACCTGTTGACTTTGACCTTGGAGGCTTTTTTACCTTCAGTTTGCTTATCGGCTTTG
1 CTCAAGTCTGCCTGATGACTTTGACCTTGGAGACTTTTTTACCTTCAGTCTGCTTATCGGCTTTG
* * *
2329160 ACCTTGGAGACTACCTGAT
66 ACCCTAGAGACTACCTCAT
* * * * ** * * *
2329179 CTCAAGTCTGCTTG-TCAGCTTTGACCCTAGAGACTTTCATACCTTCAGTCTACCTATCGACTTT
1 CTCAAGTCTGCCTGATGA-CTTTGACCTTGGAGACTTTTTTACCTTCAGTCTGCTTATCGGCTTT
2329243 GACCCTAGAGACT
65 GACCCTAGAGACT
2329256 GCTATCACAA
Statistics
Matches: 843, Mismatches: 209, Indels: 70
0.75 0.19 0.06
Matches are distributed among these distances:
81 2 0.00
82 2 0.00
83 52 0.06
84 607 0.72
85 171 0.20
86 9 0.01
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (84 bp):
CTCAAGTCTGCCTGATGACTTTGACCTTGGAGACTTTTTTACCTTCAGTCTGCTTATCGGCTTTG
ACCCTAGAGACTACCTCAT
Found at i:2328866 original size:295 final size:295
Alignment explanation
Indices: 2328337--2329109 Score: 693
Period size: 295 Copynumber: 2.6 Consensus size: 295
2328327 ACTACCTCAT
* * * *
2328337 CTCAAGTCTACCTGTTGGCTTTAACCTTGGAGACTTTCTTATCTTCAGTTTGCCTATCGATTTTA
1 CTCAAGTCTACCTGTCGGCTTTAACCTTGGAGACTTTCTTACCTTCAGTCTGCCTATCGACTTTA
* * * * * *
2328402 ACCCTAGAGACTGCCTCATCTCAAGTCTACCTATCGACTTTGACTTTGGAGACTTTTTTACCTTC
66 ACCCTAAAAACTGCCTCATCTCAAGTCTACCTATCGACTTTGACCTTAGAGACTTTATTACATTC
* * * * * *
2328467 AGTTTCCTTATCGGCTTTGACCTTGGAAACTGGCTGATCTCAAGTTTGCCTGTCAGCTTTGACCC
131 AATTTCCTTATCGGCTTTGACCTTGGAAACTGCCTCATCTCAAGTCTACCTGTCAGCGTTGACCC
* *
2328532 TAAATACTTTCATACCTTCAGTCTACCTGTCAACTTTGACCCTAGAGACTGCCTCATGTCAAATC
196 TAAAGACTTTCATACCATCAGTCTACCTGTCAACTTTGACCCTAGAGACTGCCTCATGTCAAATC
2328597 TACTTGTTGGCGTTGACCCTGAAGACTTCTTTACC
261 TACTTGTTGGCGTTGACCCTGAAGACTTCTTTACC
* * * * * * * *
2328632 CTCAAGTCTGCCTGTCGGCTTTGACCTTGGAGATTTTCTTACCTTCAGTCTGCTTGTTGGCTTTG
1 CTCAAGTCTACCTGTCGGCTTTAACCTTGGAGACTTTCTTACCTTCAGTCTGCCTATCGACTTTA
* * *
2328697 ACCCTAAAAATTGCCTTATCTCAAGTCTGCCTATCGACTTTGACCTTAGAGACTTTATTACATTC
66 ACCCTAAAAACTGCCTCATCTCAAGTCTACCTATCGACTTTGACCTTAGAGACTTTATTACATTC
* *
2328762 AATCTT-CTTGTCGGCTTTGA-CTT-GAAGACTGCCTCATCTCAAGTCTACCTGTCGGCGTTGAC
131 AAT-TTCCTTATCGGCTTTGACCTTGGAA-ACTGCCTCATCTCAAGTCTACCTGTCAGCGTTGAC
* ** * * * * * * * *
2328824 CCTAGAGACTTTTTTACCATCAAGTTTGCTTGTCAGCTTTGACCCTGGAGACTTTCTTACCT-TC
194 CCTAAAGACTTTCATACCATC-AGTCTACCTGTCAACTTTGACCCTAGAGAC-TGCCT-CATGTC
* * * * * * *
2328888 -AGTCTGCCTATCGGTGTTGACCTTGGAA-ACTT-TCTTACC
256 AAATCTACTTGTTGGCGTTGACCCT-GAAGACTTCT-TTACC
* * * ** * * *
2328927 CTCAAGTTTGCTTACCGGCTTTAACCCTGGAAACTTTCTTACCTTCAGTCTACCTATC-AGCTTT
1 CTCAAGTCTACCTGTCGGCTTTAACCTTGGAGACTTTCTTACCTTCAGTCTGCCTATCGA-CTTT
** * ** * * * * * *
2328991 GTCCTTGGAGACTACCTCATCTCAAGTCTACCTATTGGCTTTGACCTTGGAGACTTTCTTATC-T
65 AACCCTAAAAACTGCCTCATCTCAAGTCTACCTATCGACTTTGACCTTAGAGACTTTATTA-CAT
** ** ** * * *
2329055 TCGGTCGGCC-TATCGGCTTAAACCTTGGAGACTTCCTTATCTCAAGTCTACCTGT
129 TCAAT-TTCCTTATCGGCTTTGACCTTGGAAACTGCCTCATCTCAAGTCTACCTGT
2329110 TGACTTTGAC
Statistics
Matches: 381, Mismatches: 85, Indels: 23
0.78 0.17 0.05
Matches are distributed among these distances:
293 3 0.01
294 49 0.13
295 287 0.75
296 38 0.10
297 4 0.01
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.37
Consensus pattern (295 bp):
CTCAAGTCTACCTGTCGGCTTTAACCTTGGAGACTTTCTTACCTTCAGTCTGCCTATCGACTTTA
ACCCTAAAAACTGCCTCATCTCAAGTCTACCTATCGACTTTGACCTTAGAGACTTTATTACATTC
AATTTCCTTATCGGCTTTGACCTTGGAAACTGCCTCATCTCAAGTCTACCTGTCAGCGTTGACCC
TAAAGACTTTCATACCATCAGTCTACCTGTCAACTTTGACCCTAGAGACTGCCTCATGTCAAATC
TACTTGTTGGCGTTGACCCTGAAGACTTCTTTACC
Found at i:2329183 original size:168 final size:168
Alignment explanation
Indices: 2328048--2329255 Score: 854
Period size: 168 Copynumber: 7.2 Consensus size: 168
2328038 TGTTTCGAAA
* * * * * *
2328048 TCTGCCTATC-AGCTTTGACCTTGGAGACTTCTTTACCCTCAAGTCTGCCTATTGACTTTGACCT
1 TCTGCCTATCGA-CTTTGACCTTAGAGACTTCCTTA-TCTCAAGTCTACTTGTTGACTTTGACCT
* * * * * * * *
2328112 TGGAGGCTTTCTTACCTTCAGTCTGCTTATCGGCTTTGACCATAGAGATTGCCTTATCTCAAGTC
64 TGGAGACTTTTTTACCTTCAGTCTACCTATCGGCTTTGACCTTGGAGACTACCTTATCTCAAGTC
* * * *
2328177 TGCCTGCTAGATTTGACCTTGGAGACTTTTTTACCTTCAG
129 TGCCTGTTAGCTTTGACCCTGGAGACTTTCTTACCTTCAG
* * ** * * * * * * * *
2328217 TCTGCTTGTTAATTTTGACCTAAGAGACTACCTCATCTAAAGTCTGCTTGCTGACTTT-AACTCT
1 TCTGCCTATCGACTTTGACCTTAGAGACTTCCTTATCTCAAGTCTACTTGTTGACTTTGACCT-T
* * * * *
2328281 AGAGACTTTTTTACCTTTAGTCTACCTGTCGGCTTTGACCCTGGAGACTACCTCATCTCAAGTCT
65 GGAGACTTTTTTACCTTCAGTCTACCTATCGGCTTTGACCTTGGAGACTACCTTATCTCAAGTCT
* * * * *
2328346 ACCTGTTGGCTTTAACCTTGGAGACTTTCTTATCTTCAG
130 GCCTGTTAGCTTTGACCCTGGAGACTTTCTTACCTTCAG
* * * * * * * * * *
2328385 TTTGCCTATCGATTTTAACCCTAGAGACTGCCTCATCTCAAGTCTACCTATCGACTTTGACTTTG
1 TCTGCCTATCGACTTTGACCTTAGAGACTTCCTTATCTCAAGTCTACTTGTTGACTTTGACCTTG
* * ** * *
2328450 GAGACTTTTTTACCTTCAGT-TTCCTTATCGGCTTTGACCTTGGAAACTGGCTGATCTCAAGTTT
66 GAGACTTTTTTACCTTCAGTCTACC-TATCGGCTTTGACCTTGGAGACTACCTTATCTCAAGTCT
* ** * *
2328514 GCCTGTCAGCTTTGACCCTAAATACTTTCATACCTTCAG
130 GCCTGTTAGCTTTGACCCTGGAGACTTTCTTACCTTCAG
* * * * * * * * * * *
2328553 TCTACCTGTCAACTTTGACCCTAGAGACTGCCTCATGTCAAATCTACTTGTTGGCGTTGACCCTG
1 TCTGCCTATCGACTTTGACCTTAGAGACTTCCTTATCTCAAGTCTACTTGTTGACTTTGACCTTG
* * * * * * ** *
2328618 AAGACTTCTTTACCCTCAAGTCTGCCTGTCGGCTTTGACCTTGGAGATTTTCTTACCTTC-AGTC
66 GAGACTTTTTTACCTTC-AGTCTACCTATCGGCTTTGACCTTGGAGACTACCTTATC-TCAAGTC
* * * * * * *
2328682 TGCTTGTTGGCTTTGACCCT-AAAAATTGCCTTATC-TCAAG
129 TGCCTGTTAGCTTTGACCCTGGAGACTT-TCTTACCTTC-AG
** * * *
2328722 TCTGCCTATCGACTTTGACCTTAGAGACTTTATTA-CATTCAA-TCTTCTTGTCGGCTTTGA-CT
1 TCTGCCTATCGACTTTGACCTTAGAGACTTCCTTATC--TCAAGTCTACTTGTTGACTTTGACCT
* *** * * * * * * *** *
2328784 TGAAGACTGCCTCATC-TCAAGTCTACCTGTCGGCGTTGACCCTAGAGACTTTTTTACCATCAAG
64 TGGAGACTTTTTTACCTTC-AGTCTACCTATCGGCTTTGACCTTGGAGACTACCTTATC-TCAAG
* * *
2328848 TTTGCTTGTCAGCTTTGACCCTGGAGACTTTCTTACCTTCAG
127 TCTGCCTGTTAGCTTTGACCCTGGAGACTTTCTTACCTTCAG
* * * * * * * *** * * *
2328890 TCTGCCTATCG-GTGTTGACCTTGGAAACTTTCTTACCCTCAAGTTTGCTTACCGGCTTTAACCC
1 TCTGCCTATCGACT-TTGACCTTAGAGACTTCCTTA-TCTCAAGTCTACTTGTTGACTTTGACCT
* * * * *
2328954 TGGAAACTTTCTTACCTTCAGTCTACCTATCAGCTTTGTCCTTGGAGACTACCTCATCTCAAGTC
64 TGGAGACTTTTTTACCTTCAGTCTACCTATCGGCTTTGACCTTGGAGACTACCTTATCTCAAGTC
* * * * * *
2329019 TACCTATTGGCTTTGACCTTGGAGACTTTCTTATCTTCGG
129 TGCCTGTTAGCTTTGACCCTGGAGACTTTCTTACCTTCAG
* * ** * *
2329059 TCGGCCTATCGGCTTAAACCTTGGAGACTTCCTTATCTCAAGTCTACCTGTTGACTTTGACCTTG
1 TCTGCCTATCGACTTTGACCTTAGAGACTTCCTTATCTCAAGTCTACTTGTTGACTTTGACCTTG
* * * * *
2329124 GAGGCTTTTTTACCTTCAGTTTGCTTATCGGCTTTGACCTTGGAGACTACCTGATCTCAAGTCTG
66 GAGACTTTTTTACCTTCAGTCTACCTATCGGCTTTGACCTTGGAGACTACCTTATCTCAAGTCTG
* * * *
2329189 CTTGTCAGCTTTGACCCTAGAGACTTTCATACCTTCAG
131 CCTGTTAGCTTTGACCCTGGAGACTTTCTTACCTTCAG
* *
2329227 TCTACCTATCGACTTTGACCCTAGAGACT
1 TCTGCCTATCGACTTTGACCTTAGAGACT
2329256 GCTATCACAA
Statistics
Matches: 802, Mismatches: 216, Indels: 43
0.76 0.20 0.04
Matches are distributed among these distances:
167 45 0.06
168 499 0.62
169 205 0.26
170 51 0.06
171 2 0.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.37
Consensus pattern (168 bp):
TCTGCCTATCGACTTTGACCTTAGAGACTTCCTTATCTCAAGTCTACTTGTTGACTTTGACCTTG
GAGACTTTTTTACCTTCAGTCTACCTATCGGCTTTGACCTTGGAGACTACCTTATCTCAAGTCTG
CCTGTTAGCTTTGACCCTGGAGACTTTCTTACCTTCAG
Found at i:2332353 original size:20 final size:20
Alignment explanation
Indices: 2332328--2332402 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
2332318 ATTTGCCTGC
2332328 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
* *
2332348 ATGTATAGATACATTGAGTA
1 ATGTATCGATACATTGAATA
* *
2332368 ATGTATCGATACA--AAACTT
1 ATGTATCGATACATTGAA-TA
2332387 ATGTATCGATACATTG
1 ATGTATCGATACATTG
2332403 TATCAATACA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 1 0.02
19 14 0.31
20 30 0.67
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:2333121 original size:61 final size:61
Alignment explanation
Indices: 2333026--2333141 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 61
2333016 AAGTAGAGAG
*
2333026 TGATAAAGATGCCAATATGCTAATTTAGAGCCAGCGATATTAGG-CTTAAAGATGAGAAGGA
1 TGATAAAGATGCCAATATGCTAATTAAGAGCCAGCGATA-TAGGACTTAAAGATGAGAAGGA
* * *
2333087 TGATAAAGGA-GCCAATATGCTGATTCAAG-GCCAGCTATATCGGACTTAAAGATGA
1 TGATAAA-GATGCCAATATGCTAATT-AAGAGCCAGCGATATAGGACTTAAAGATGA
2333142 AGGTGCCAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
60 3 0.06
61 41 0.85
62 4 0.08
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (61 bp):
TGATAAAGATGCCAATATGCTAATTAAGAGCCAGCGATATAGGACTTAAAGATGAGAAGGA
Found at i:2333284 original size:43 final size:43
Alignment explanation
Indices: 2333097--2333283 Score: 189
Period size: 43 Copynumber: 4.2 Consensus size: 43
2333087 TGATAAAGGA
* *
2333097 GCCAATATGCTGATTCAAGGCCAGCT-ATATCGGACTTAAAGATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAG-TGATATTGGGCTT--AGA--AA--T
* * * * *
2333146 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAGGAAT
1 GCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTTAGAAAT
* * *
2333189 GTCAATATACTGATTCAAGGCCAATGATATTGGGCTTA-AGAAT
1 GCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTTAGA-AAT
*
2333232 GCCAATATGTTGATTCAAGGCCAGTGATATTGGGCTTAGAAAT
1 GCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTTAGAAAT
2333275 GCCAATATG
1 GCCAATATG
2333284 TGTTGACACC
Statistics
Matches: 118, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
43 81 0.69
44 1 0.01
45 2 0.02
47 2 0.02
49 32 0.27
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
GCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTTAGAAAT
Found at i:2333531 original size:5 final size:5
Alignment explanation
Indices: 2333521--2333578 Score: 55
Period size: 5 Copynumber: 11.2 Consensus size: 5
2333511 TTTATTCGAT
* *
2333521 ATAAA ATAAA ATAAA AGTAAA AAAATA AAAAA ATAAA ATAAA AGTAAA
1 ATAAA ATAAA ATAAA A-TAAA ATAA-A ATAAA ATAAA ATAAA A-TAAA
*
2333569 A-AAA TTAAA A
1 ATAAA ATAAA A
2333579 AATAAAAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 3 0.07
5 27 0.60
6 15 0.33
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:2333547 original size:14 final size:14
Alignment explanation
Indices: 2333528--2333578 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
2333518 GATATAAAAT
2333528 AAAATAAAAGTAAA
1 AAAATAAAAGTAAA
2333542 AAAATAAAA--AAA
1 AAAATAAAAGTAAA
2333554 TAAAATAAAAGTAAA
1 -AAAATAAAAGTAAA
2333569 AAAATTAAAA
1 AAAA-TAAAA
2333579 AATAAAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
12 3 0.09
13 9 0.27
14 13 0.39
15 8 0.24
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (14 bp):
AAAATAAAAGTAAA
Found at i:2333553 original size:27 final size:27
Alignment explanation
Indices: 2333523--2333592 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
2333513 TATTCGATAT
2333523 AAAATAAAATAAAAGTAAAAAAATAAA
1 AAAATAAAATAAAAGTAAAAAAATAAA
*
2333550 AAAATAAAATAAAAGTAAAAAAATTAA
1 AAAATAAAATAAAAGTAAAAAAATAAA
2333577 AAAATAAAAGTAAAAG
1 AAAATAAAA-TAAAAG
2333593 AAACCATCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 35 0.85
28 6 0.15
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.16
Consensus pattern (27 bp):
AAAATAAAATAAAAGTAAAAAAATAAA
Found at i:2333572 original size:22 final size:22
Alignment explanation
Indices: 2333523--2333591 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
2333513 TATTCGATAT
*
2333523 AAAATAAAATAAAAGTAAAA--A
1 AAAAAAAAATAAAA-TAAAAGTA
2333544 AATAAAAAAATAAAATAAAAGTA
1 AA-AAAAAAATAAAATAAAAGTA
*
2333567 AAAAAATTAA-AAAATAAAAGTA
1 AAAAAA-AAATAAAATAAAAGTA
2333589 AAA
1 AAA
2333592 GAAACCATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 7 0.17
22 30 0.71
23 5 0.12
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (22 bp):
AAAAAAAAATAAAATAAAAGTA
Found at i:2334094 original size:20 final size:21
Alignment explanation
Indices: 2334069--2334119 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
2334059 CGATACATTA
**
2334069 TATCGATACATG-ACCGAATG
1 TATCGATACATGCAAAGAATG
*
2334089 TATCGATACTTGCAAAGAATG
1 TATCGATACATGCAAAGAATG
2334110 TATCGATACA
1 TATCGATACA
2334120 GGTGATTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (21 bp):
TATCGATACATGCAAAGAATG
Found at i:2334192 original size:15 final size:14
Alignment explanation
Indices: 2334172--2334204 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2334162 GTATCGATAC
2334172 ATACAAGATGTATCG
1 ATACAA-ATGTATCG
2334187 ATAC-AATGTATCG
1 ATACAAATGTATCG
2334200 ATACA
1 ATACA
2334205 TGACCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.71
14 1 0.06
15 4 0.24
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (14 bp):
ATACAAATGTATCG
Found at i:2334197 original size:13 final size:13
Alignment explanation
Indices: 2334179--2334204 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2334169 TACATACAAG
2334179 ATGTATCGATACA
1 ATGTATCGATACA
2334192 ATGTATCGATACA
1 ATGTATCGATACA
2334205 TGACCAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2334223 original size:34 final size:32
Alignment explanation
Indices: 2334161--2334225 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 32
2334151 CTTAACTATT
2334161 TGTATCGATACATACAAGATGTATCGATACAA
1 TGTATCGATACATACAAGATGTATCGATACAA
2334193 TGTATCGATACATGACCAA-ATTGTATCGATACA
1 TGTATCGATACAT-A-CAAGA-TGTATCGATACA
2334226 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 13 0.43
33 2 0.07
34 15 0.50
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (32 bp):
TGTATCGATACATACAAGATGTATCGATACAA
Found at i:2339654 original size:13 final size:13
Alignment explanation
Indices: 2339636--2339661 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2339626 TACACCAAGT
2339636 ATGTATCGATACA
1 ATGTATCGATACA
2339649 ATGTATCGATACA
1 ATGTATCGATACA
2339662 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2339659 original size:32 final size:33
Alignment explanation
Indices: 2339618--2339681 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2339608 TAGCCAAACT
* **
2339618 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2339650 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2339682 TTGGCTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2341218 original size:8 final size:8
Alignment explanation
Indices: 2341205--2341235 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
2341195 ATTCGATTAA
2341205 ATTTTGTG
1 ATTTTGTG
2341213 ATTTTGTG
1 ATTTTGTG
2341221 ATTTTGTG
1 ATTTTGTG
2341229 ATGTTTG
1 AT-TTTG
2341236 ATGTTGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (8 bp):
ATTTTGTG
Found at i:2341451 original size:13 final size:13
Alignment explanation
Indices: 2341433--2341457 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2341423 CAGCATTCTC
2341433 TGTATCGATACAG
1 TGTATCGATACAG
2341446 TGTATCGATACA
1 TGTATCGATACA
2341458 AAGGGTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2342401 original size:20 final size:21
Alignment explanation
Indices: 2342358--2342401 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
2342348 GTGAATAAAG
2342358 GAAATTGTTTTATTAAGGGGGA
1 GAAATTGTTTTA-TAAGGGGGA
2342380 GAAATT-TTTTA-AAGGGGAGA
1 GAAATTGTTTTATAAGGGG-GA
2342400 GA
1 GA
2342402 GAAAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.29
20 4 0.19
21 5 0.24
22 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (21 bp):
GAAATTGTTTTATAAGGGGGA
Found at i:2342994 original size:20 final size:21
Alignment explanation
Indices: 2342969--2343019 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2342959 CGATACATTA
*
2342969 TATCGATACATG-ACCA-AATG
1 TATCGATACATGCA-AAGAATG
*
2342989 TATCGATACTTGCAAAGAATG
1 TATCGATACATGCAAAGAATG
2343010 TATCGATACA
1 TATCGATACA
2343020 GGTGATTGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (21 bp):
TATCGATACATGCAAAGAATG
Found at i:2344351 original size:27 final size:28
Alignment explanation
Indices: 2344288--2344363 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
2344278 GAAATAAAGT
*
2344288 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
2344316 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
2344343 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2344364 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2344454 original size:51 final size:53
Alignment explanation
Indices: 2344347--2344469 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 53
2344337 GATTAACGGG
* * * * *
2344347 GTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAAAAAAATCGGA
2344401 GTTGGAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAAAAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAAAAAAATCGGA
*
2344452 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
2344470 GTGGAGAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
51 34 0.55
52 2 0.03
53 8 0.13
54 18 0.29
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAAAAAAATCGGA
Found at i:2346023 original size:13 final size:13
Alignment explanation
Indices: 2346005--2346030 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2345995 ACAAAGATCC
2346005 ATGTATCGATACA
1 ATGTATCGATACA
2346018 ATGTATCGATACA
1 ATGTATCGATACA
2346031 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2346026 original size:33 final size:33
Alignment explanation
Indices: 2345984--2346049 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2345974 AAAATTTCTA
***
2345984 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2346017 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2346050 TTTTCCTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2346110 original size:13 final size:13
Alignment explanation
Indices: 2346092--2346116 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2346082 ACAATACTTA
2346092 TGTATCGATACAT
1 TGTATCGATACAT
2346105 TGTATCGATACA
1 TGTATCGATACA
2346117 AATTGTTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2346944 original size:119 final size:116
Alignment explanation
Indices: 2346736--2346947 Score: 252
Period size: 119 Copynumber: 1.8 Consensus size: 116
2346726 GGGTGTCCAC
* * * * *
2346736 TTTTCAAGGACAAAGGAAAAGAGAATGAAATAGGTCTTGCTCCTTGAGGACCAAGGAAGAGAAGA
1 TTTTCAAGGACAAAGGAAAAGAGAATGAAATACGTCCTACTCCTTGAGGACAAAAGAAGAGAAGA
2346801 AAAGGAAAGTGTCCTGCTTCTTGAGGACAACGTGAAAAAGAGTACGTCCCA
66 AAAGGAAAGTGTCCTGCTTCTTGAGGACAACGTGAAAAAGAGTACGTCCCA
* *
2346852 TTTTCCAAGGACAAAGGAAAAAGGGAAATGAAATACGTCCTACT-CTCTGAGGATAAAAGAA-AG
1 TTTT-CAAGGACAAAGG-AAAAGAG-AATGAAATACGTCCTACTCCT-TGAGGACAAAAGAAGAG
* *
2346915 AGGAAAA-TAAAGTGTATCCTGC-TCTTTGAGGAC
62 AAGAAAAGGAAAGTG--TCCTGCTTC-TTGAGGAC
2346948 TAAAAAGTGC
Statistics
Matches: 80, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
116 4 0.05
117 18 0.22
118 18 0.22
119 40 0.50
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (116 bp):
TTTTCAAGGACAAAGGAAAAGAGAATGAAATACGTCCTACTCCTTGAGGACAAAAGAAGAGAAGA
AAAGGAAAGTGTCCTGCTTCTTGAGGACAACGTGAAAAAGAGTACGTCCCA
Found at i:2347423 original size:116 final size:115
Alignment explanation
Indices: 2346930--2347812 Score: 1101
Period size: 116 Copynumber: 7.7 Consensus size: 115
2346920 AATAAAGTGT
** *
2346930 ATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT---GAA-AA-GCGTCCT
1 ATCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAGAAGAAGGCGTCCT
* ** * *
2346990 GCTCTTTGAGTACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGT
66 GCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGC
* * * **
2347040 GTTCTGCTCTTTGAGGA-TTGGAAAACGCCACCAACTTGTGTGGGCTTTGAAAGAAGAAGGCGTC
1 ATCCTGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTT-AAAGAAGAAGGCGTC
*
2347104 CTGCTCTTTGAGGACT--GAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGC
64 CTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTT-----AAAAGGC
* * * * * *
2347160 GTCCTGCTCTTTGGGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAA-AAAGCATC
1 ATCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT--AAAGAAGAAGGCGTC
*
2347224 CTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGGC
64 CTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGC
* *
2347275 ATCCTGCTCTTTGAGGA-TTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAGAAGGCGTC
1 ATCCTGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTT-AAAGAAGAAGGCGTC
* *
2347339 CTGCTCTTTGAGGACTGGGAAGTGCTACCAACTTGTGTGGGCTTTAAAAGGT
64 CTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
* *
2347391 ATCCTGCTCTTTGAGGATTAGGAAGTGCCACCAACTTGTGTGGGCTTT----AAG-AGGTGTCCT
1 ATCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAGAAGAAGGCGTCCT
* * *
2347451 ACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGC
66 GCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
* *
2347501 ATCCTGCTCTTTGAGGACTAAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCC
1 ATCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT-AAAGAAGAAGGCGTCC
*
2347566 TGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGC
65 TGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
* * * *
2347617 GTCCTGCTCTTTGAGGACTAGGAAGTGCCACTAACTTGTGTGGGCTTTAAAAGGAGAAGGCATCC
1 ATCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT-AAAGAAGAAGGCGTCC
2347682 TGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
65 TGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
* *
2347733 GTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT----AA-AAGGCATCCT
1 ATCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAGAAGAAGGCGTCCT
*
2347793 GCTCTTTGAGGACTAGGAAG
66 GCTCTTTGAGGACTGGGAAG
2347813 GGCTAAAAGA
Statistics
Matches: 691, Mismatches: 57, Indels: 50
0.87 0.07 0.06
Matches are distributed among these distances:
109 1 0.00
110 166 0.24
111 4 0.01
114 11 0.02
115 100 0.14
116 302 0.44
117 6 0.01
120 93 0.13
121 8 0.01
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (115 bp):
ATCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAGAAGAAGGCGTCCT
GCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
Found at i:2347470 original size:171 final size:168
Alignment explanation
Indices: 2346931--2347811 Score: 1041
Period size: 171 Copynumber: 5.1 Consensus size: 168
2346921 ATAAAGTGTA
* *
2346931 TCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTT---GAAAA-GCGTCCTG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCGTCCTG
* * * ** *
2346991 CTCTTTGAGTACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTTCTGCTCTTTGAG
65 CTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAG
* **
2347055 GATTGGAAAACGCCACCAACTTGTGTGGGCTTTGAAAGAAGAAGGCG
129 GACTGG-AAGTGCCACCAACTTGTGTGGGCTTT-----AAG-AGGCG
** *
2347102 TCCTGCTCTTTGAGGACT-GAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAGAAAAGGCGTCCTG
* * *
2347166 CTCTTTGGGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCT
65 CTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT-AAAAG-----GCATCCTGCTCT
* * *
2347231 TTGAGGACT-GAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGGCA
124 TTGAGGACTGGAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGCG
*
2347276 TCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAGAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAGAA-AAGGCGTCCT
* * *
2347341 GCTCTTTGAGGACTGGGAAGTGCTACCAACTTGTGTGGGCTTTAAAAGGTATCCTGCTCTTTGAG
64 GCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAG
* *
2347406 GATTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
129 GACT-GGAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGCG
* *
2347447 TCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----AAAAGGCATCCTGC
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCGTCCTGC
* *
2347508 TCTTTGAGGACTAAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCTCTT
66 TCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT---A--A-AAGGCATCCTGCTCTT
2347573 TGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGCG
125 TGAGGACT-GGAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGCG
* * * *
2347618 TCCTGCTCTTTGAGGACTAGG-AAGTGCCACTAACTTGTGTGGGCTTTAAAAGGAGAAGGCATCC
1 TCCTGCTCTTTGAGGACT-GGAAAATGCCACCAACTTGTGTGGGCTTT-AAA-GAAAAGGCGTCC
* *
2347682 TGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGA
63 TGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGA
* *
2347747 GGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCA
128 GGACT-GGAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGCG
2347789 TCCTGCTCTTTGAGGACTAGGAA
1 TCCTGCTCTTTGAGGACT-GGAA
2347812 GGGCTAAAAG
Statistics
Matches: 625, Mismatches: 54, Indels: 61
0.84 0.07 0.08
Matches are distributed among these distances:
165 49 0.08
166 2 0.00
168 1 0.00
170 41 0.07
171 269 0.43
172 7 0.01
174 27 0.04
175 81 0.13
176 55 0.09
177 52 0.08
179 2 0.00
180 22 0.04
181 17 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (168 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCGTCCTGC
TCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGA
CTGGAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGCG
Found at i:2347809 original size:55 final size:55
Alignment explanation
Indices: 2346931--2347812 Score: 990
Period size: 55 Copynumber: 15.4 Consensus size: 55
2346921 ATAAAGTGTA
** *
2346931 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAA-GCG
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGCG
* * * *
2346986 TCCTGCTCTTTGAGTACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
* * **
2347041 TTCTGCTCTTTGAGGA-TTGGAAAACGCCACCAACTTGTGTGGGCTTTGAAAGAAGAAGGCG
1 TCCTGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTT-----AA-AAGGCG
*
2347102 TCCTGCTCTTTGAGGACT--GAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTT-----AAAAGGCG
* * * *
2347161 TCCTGCTCTTTGGGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT-AAAAG-----GCG
* *
2347222 TCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
* *
2347276 TCCTGCTCTTTGAGGA-TTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAGAAGGCG
1 TCCTGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTT-----AA-AAGGCG
* * **
2347337 TCCTGCTCTTTGAGGACTGGGAAGTGCTACCAACTTGTGTGGGCTTTAAAAGGTA
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
* * *
2347392 TCCTGCTCTTTGAGGATTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
* * *
2347447 TCCTACTCTTTGAGGACT-GGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
*
2347502 TCCTGCTCTTTGAGGACTAAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT---A--A-AAGGCG
* *
2347563 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGCG
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
* *
2347618 TCCTGCTCTTTGAGGACTAGGAAGTGCCACTAACTTGTGTGGGCTTTAAAAGGAGAAGGCA
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT---A--A-AAGGCG
*
2347679 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
*
2347734 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
2347789 TCCTGCTCTTTGAGGACTAGGAAG
1 TCCTGCTCTTTGAGGACTAGGAAG
2347813 GGCTAAAAGA
Statistics
Matches: 722, Mismatches: 61, Indels: 88
0.83 0.07 0.10
Matches are distributed among these distances:
53 1 0.00
54 28 0.04
55 376 0.52
56 15 0.02
58 4 0.01
59 32 0.04
60 77 0.11
61 185 0.26
62 4 0.01
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
Found at i:2354236 original size:54 final size:51
Alignment explanation
Indices: 2354169--2354299 Score: 129
Period size: 51 Copynumber: 2.5 Consensus size: 51
2354159 GATTAACGGG
* ** * * *
2354169 GTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATT--ACTATTTTGAAAATAAAATCAGA
*
2354223 GTTGGAGTATCCCCGATTAT-AGAAAATTACTATTTTGAAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTACTATTTTGAAAATAAAATCAGA
* *
2354274 GTTGGAATATCCTCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
2354300 TTGAGAAACT
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
51 35 0.55
52 4 0.06
53 7 0.11
54 18 0.28
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTACTATTTTGAAAATAAAATCAGA
Found at i:2356694 original size:33 final size:33
Alignment explanation
Indices: 2356636--2356702 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2356626 AAAATTTCCA
***
2356636 AATGTATCGATACAAAGATCCATGTATCAATAC
1 AATGTATCGATACAAAGAAAAATGTATCAATAC
* *
2356669 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCAATAC
2356702 A
1 A
2356703 TTTCCTTAGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCAATAC
Found at i:2356746 original size:19 final size:18
Alignment explanation
Indices: 2356722--2356789 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
2356712 CAGTAGCTAA
2356722 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2356741 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
*
2356756 -T-TGTATCAATACAAAAC
1 TTATGTATCGATAC-AAAC
2356773 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2356790 TTGTTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.59
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2356768 original size:32 final size:32
Alignment explanation
Indices: 2356725--2356787 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
2356715 TAGCTAATTA
* *
2356725 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCAATACAAAACTTATGTATCGATACAT
2356757 TGTATCAATACAAAACTTATGTATCGATACA
1 TGTATCAATACAAAACTTATGTATCGATACA
2356788 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (32 bp):
TGTATCAATACAAAACTTATGTATCGATACAT
Found at i:2356851 original size:21 final size:22
Alignment explanation
Indices: 2356825--2356882 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
2356815 GTTGGGACCC
* *
2356825 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGCACAAA
*
2356846 TGTATCGATACA-TTCCACAAA
1 TGTATCGATACATTTGCACAAA
2356867 TGTATCGATACATTTG
1 TGTATCGATACATTTG
2356883 GAATTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 26 0.84
22 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
TGTATCGATACATTTGCACAAA
Found at i:2358248 original size:13 final size:13
Alignment explanation
Indices: 2358230--2358255 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2358220 CAATTTTTTG
2358230 TGTATCGATACAT
1 TGTATCGATACAT
2358243 TGTATCGATACAT
1 TGTATCGATACAT
2358256 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2358995 original size:21 final size:21
Alignment explanation
Indices: 2358954--2358997 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2358944 CTCCCCTTTA
* *
2358954 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
2358975 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
2358996 TC
1 TC
2358998 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:2362926 original size:15 final size:15
Alignment explanation
Indices: 2362890--2362927 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2362880 TTCATCAATT
* *
2362890 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
2362905 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
2362920 TCATTTTG
1 TCATTTTG
2362928 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:2364758 original size:21 final size:21
Alignment explanation
Indices: 2364729--2364773 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2364719 AAGTTTTCAT
*
2364729 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2364749 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2364771 TTT
1 TTT
2364774 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2366932 original size:13 final size:13
Alignment explanation
Indices: 2366914--2366939 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2366904 CAATTTTTTG
2366914 TGTATCGATACAT
1 TGTATCGATACAT
2366927 TGTATCGATACAT
1 TGTATCGATACAT
2366940 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2367326 original size:25 final size:25
Alignment explanation
Indices: 2367297--2367346 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
2367287 CAATCCTTTG
2367297 TTATATCAAAACCAAGATCCTAACA
1 TTATATCAAAACCAAGATCCTAACA
2367322 TTATATCAAAACCAAGATCCTAACA
1 TTATATCAAAACCAAGATCCTAACA
2367347 GTTGTGTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.04, T:0.24
Consensus pattern (25 bp):
TTATATCAAAACCAAGATCCTAACA
Found at i:2368142 original size:33 final size:33
Alignment explanation
Indices: 2368066--2368142 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
2368056 AAAAGAAAAA
* *
2368066 AAAAAAAAAGGTAACTCACAGCTAGTGGGAAAGG
1 AAAAAAAAA-GTAACTCACAGCAAGTAGGAAAGG
* * *
2368100 AGAAAAAAAGTAACTCACGGCAAGTAGGAGA-G
1 AAAAAAAAAGTAACTCACAGCAAGTAGGAAAGG
2368132 AAAAACAAAAG
1 AAAAA-AAAAG
2368143 AAAGGAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 5 0.14
33 23 0.64
34 8 0.22
ACGTcount: A:0.55, C:0.12, G:0.25, T:0.09
Consensus pattern (33 bp):
AAAAAAAAAGTAACTCACAGCAAGTAGGAAAGG
Found at i:2368497 original size:25 final size:25
Alignment explanation
Indices: 2368468--2368525 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
2368458 CATCCACCAC
2368468 CAGCAGCTTCCAGGGCAGCAATGAA
1 CAGCAGCTTCCAGGGCAGCAATGAA
*
2368493 TAGCAGCTTCCAGGGCAGCAATGAA
1 CAGCAGCTTCCAGGGCAGCAATGAA
2368518 CAGCAGCT
1 CAGCAGCT
2368526 CCAACAAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.14
Consensus pattern (25 bp):
CAGCAGCTTCCAGGGCAGCAATGAA
Found at i:2384049 original size:52 final size:52
Alignment explanation
Indices: 2383901--2384029 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
2383891 CCGAAATATG
*
2383901 AAATTTGCCTGCACGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
2383953 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
2384005 AAATTTGTCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2384030 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:2384056 original size:13 final size:13
Alignment explanation
Indices: 2384038--2384062 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2384028 CAAAGATCAG
2384038 TGTATCGATACAA
1 TGTATCGATACAA
2384051 TGTATCGATACA
1 TGTATCGATACA
2384063 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2384128 original size:19 final size:19
Alignment explanation
Indices: 2384104--2384169 Score: 90
Period size: 19 Copynumber: 3.8 Consensus size: 19
2384094 AGTAGCTTCA
2384104 TATGTATCGATACAACACT
1 TATGTATCGATACAACACT
2384123 TATGTATCGAT---ACA--
1 TATGTATCGATACAACACT
2384137 T-TGTATCGATACAACACT
1 TATGTATCGATACAACACT
2384155 TATGTATCGATACAA
1 TATGTATCGATACAA
2384170 ATCGTTGACA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 9 0.22
14 1 0.02
16 6 0.15
18 1 0.02
19 24 0.59
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TATGTATCGATACAACACT
Found at i:2384143 original size:13 final size:13
Alignment explanation
Indices: 2384125--2384149 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2384115 ACAACACTTA
2384125 TGTATCGATACAT
1 TGTATCGATACAT
2384138 TGTATCGATACA
1 TGTATCGATACA
2384150 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2384147 original size:32 final size:32
Alignment explanation
Indices: 2384106--2384168 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
2384096 TAGCTTCATA
2384106 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
2384138 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
2384169 AATCGTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:2385915 original size:127 final size:128
Alignment explanation
Indices: 2385611--2386496 Score: 900
Period size: 127 Copynumber: 7.0 Consensus size: 128
2385601 TTAAACTTTG
* *** * *
2385611 AGAGAC-TTCCTATCCCTTAGTATATATGTTGGCTTTGACCTTAGAGACTTTCTTATCCCTTAGT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTATCCCTTAGT
* * * * * * * *
2385675 CTACCTGTCGGATTTGACCTTGGAAACTTTTCTATCCCTTAGTCTGCCTATTGGCTTTGACCTT
66 CTGCCTGTCAGCTTTGACCCTAGAGACTTTTCT-TCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* * * * * * *
2385739 AAAGACTAT-CTTTCCCTTAGTCTGCATGTCGACTTTGACCCTAGAGACTTTCTTATCCCTTAGT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTATCCCTTAGT
* * * *
2385803 CTGCTTGTCAGCTTTGACCCT-GAAGACTTTTCTTCCCTTAG-CTGCCTATTGGCTTTGACCCT
66 CTGCCTGTCAGCTTTGACCCTAG-AGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCTT
** *
2385865 AGAGACTTTCCTATCCCTTAGTCTGTTTGTCGGCTTTGACCTTGGAGACTTTCCTATCCCTTAGT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTATCCCTTAGT
* * * * * * * * *
2385930 CTACTTGTCAGTTTTGACCTTAGAGACTTTCCTTCCTTTAGTTTGCCTATCAGG-TTTGATCTT
66 CTGCCTGTCAGCTTTGACCCTAGAGACTTTTCTTCCCTTAGTCTGCCTGTC-GGCTTTGACCTT
* * * * *
2385993 AGAGACTTT-ATTTCCCTTAGTCTGCCTGTCGGCTTTAACCTTAGAGACTTTCCTATCCCTTAGT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTATCCCTTAGT
* * * * *
2386057 ATACCTGTC-GATTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACTTT
66 CTGCCTGTCAG-CTTTGACCCTAGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* ** * *
2386120 GGAGACTTTCCTATCTTTTAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCCTT-T-CCTTAG
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTT-CTTATCCCTTAG
* ** * * *
2386183 TTTGCCTGTTGGCTTTTACCCTAGAGACTTTTCTTCCCTTAGTCTACCTGTCGACTTTGACCTT
65 TCTGCCTGTCAGCTTTGACCCTAGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* *
2386247 AAAGACTTTCCTATCCCTTAGTCTGCCTATCGGCTTTGACCCTTGG-GA-TTTCTT-TCCCTTAG
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGA-CCTTGGAGACTTTCTTATCCCTTAG
* * * * * * * *
2386309 TCTGCTTATCAGCTTTGACCTTGGAGAC-TTTCTTATCTCTTAGTCTGCTTGTCGACTTTGACCC
65 TCTGCCTGTCAGCTTTGACCCTAGAGACTTTTC-T-TCCCTTAGTCTGCCTGTCGGCTTTGACCT
2386373 T
128 T
* *** * *
2386374 GGAGACTTTCCT-TGCCCTTAGTCTATTTGTCAGCTTTGACCTTGGAGACTTTCCTATCCCTTAG
1 AGAGACTTTCCTAT-CCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTATCCCTTAG
* *
2386438 TCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTATCCCTCAGTCTGCCTGTCGGCTTT
65 TCTGCCTGTCAGCTTTGACCCTAGAGACTTTTCT-TCCCTTAGTCTGCCTGTCGGCTTT
2386497 AACCCTGAAG
Statistics
Matches: 635, Mismatches: 103, Indels: 39
0.82 0.13 0.05
Matches are distributed among these distances:
125 8 0.01
126 67 0.11
127 350 0.55
128 148 0.23
129 58 0.09
130 4 0.01
ACGTcount: A:0.16, C:0.27, G:0.17, T:0.40
Consensus pattern (128 bp):
AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTATCCCTTAGT
CTGCCTGTCAGCTTTGACCCTAGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCTT
Found at i:2386054 original size:212 final size:213
Alignment explanation
Indices: 2385641--2386502 Score: 959
Period size: 212 Copynumber: 4.1 Consensus size: 213
2385631 TATATATGTT
* * * * * *
2385641 GGCTTTGACCTTAGAGACTTTCTTATCCCTTAGTCTACCTGTCGGATTTGACCTTGGAAACTTTT
1 GGCTTTGACCCTAGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTC
* * * * * * * *
2385706 CTATCCCTTAGTCTGCCTATTGGCTTTGACCTTAAAGACTATCTTTCCCTTAGTCTGCATGTC-G
66 CTATCCCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTGCCTGTCAG
* * *
2385770 ACTTTGACCCTAGAGACTTTCTTATCCCTTAGTCTGCTTGTCAGCTTTGACCCT-GAAGACTTTT
131 -CTTTGACCCTAGAGACTTTCTT-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG-AGACTTTC
*
2385834 CT-TCCCTTAG-CTGCCTATT
193 CTATCCCTTAGTCTGCCTATC
**
2385853 GGCTTTGACCCTAGAGACTTTCCTATCCCTTAGTCTGTTTGTCGGCTTTGACCTTGGAGACTTTC
1 GGCTTTGACCCTAGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTC
* * * * * * *
2385918 CTATCCCTTAGTCTACTTGTC-AGTTTTGACCTTAGAGACTTTCCTTCCTTTAGTTTGCCTATCA
66 CTATCCCTTAGTCTGCCTGTCGA-CTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTGCCTGTCA
* * * * * *
2385982 GGTTTGATCTTAGAGACTTTATTTCCCTTAGTCTGCCTGTCGGCTTTAACCTTAGAGACTTTCCT
130 GCTTTGACCCTAGAGACTTTCTTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCT
* * *
2386047 ATCCCTTAGTATACCTGTC
195 ATCCCTTAGTCTGCCTATC
** *
2386066 GATTTTGACCCTAGAGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACTTTGGAGACTTTC
1 GGCTTTGACCCTAGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTC
** * * * **
2386130 CTATCTTTTAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCCTTTCCTTAGTTTGCCTGTTGG
66 CTATCCCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTGCCTGTCAG
* * * * *
2386195 CTTTTACCCTAGAGACTTT-TCTTCCCTTAGTCTACCTGTCGACTTTGACCTTAAAGACTTTCCT
131 CTTTGACCCTAGAGACTTTCT-TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCT
2386259 ATCCCTTAGTCTGCCTATC
195 ATCCCTTAGTCTGCCTATC
* * * * * *
2386278 GGCTTTGACCCTTGGGA-TTT-CTTTCCCTTAGTCTGCTTATCAGCTTTGACCTTGGAGACTTTC
1 GGCTTTGACCCTAGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTC
* * * * ***
2386341 TTATCTCTTAGTCTGCTTGTCGACTTTGACCCTGGAGACTTTCCTTGCCCTTAGTCTATTTGTCA
66 CTATCCCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTTTCCTT-CCCTTAGTCTGCCTGTCA
* * * *
2386406 GCTTTGACCTTGGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTC
130 GCTTTGACCCTAGAGACTTT-CTTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCC
* *
2386471 TATCCCTCAGTCTGCCTGTC
194 TATCCCTTAGTCTGCCTATC
*
2386491 GGCTTTAACCCT
1 GGCTTTGACCCT
2386503 GAAGACCGCC
Statistics
Matches: 547, Mismatches: 92, Indels: 21
0.83 0.14 0.03
Matches are distributed among these distances:
210 2 0.00
211 118 0.22
212 332 0.61
213 94 0.17
214 1 0.00
ACGTcount: A:0.15, C:0.27, G:0.17, T:0.40
Consensus pattern (213 bp):
GGCTTTGACCCTAGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTC
CTATCCCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTGCCTGTCAG
CTTTGACCCTAGAGACTTTCTTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTA
TCCCTTAGTCTGCCTATC
Found at i:2386502 original size:43 final size:43
Alignment explanation
Indices: 2385611--2386496 Score: 884
Period size: 43 Copynumber: 20.9 Consensus size: 43
2385601 TTAAACTTTG
* *** *
2385611 AGAGAC-TTCCTATCCCTTAGTATATATGTTGGCTTTGACCTT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* * *
2385653 AGAGACTTTCTTATCCCTTAGTCTACCTGTCGGATTTGACCTT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* * * * *
2385696 GGAAACTTTTCTATCCCTTAGTCTGCCTATTGGCTTTGACCTT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* * * * * *
2385739 AAAGACTAT-CTTTCCCTTAGTCTGCATGTCGACTTTGACCCT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* * * *
2385781 AGAGACTTTCTTATCCCTTAGTCTGCTTGTCAGCTTTGACCCT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* * * *
2385824 -GAAGACTTTTCT-TCCCTTAG-CTGCCTATTGGCTTTGACCCT
1 AG-AGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
**
2385865 AGAGACTTTCCTATCCCTTAGTCTGTTTGTCGGCTTTGACCTT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* * * * *
2385908 GGAGACTTTCCTATCCCTTAGTCTACTTGTCAGTTTTGACCTT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* * * *
2385951 AGAGACTTTCCT-TCCTTTAGTTTGCCTATCAGG-TTTGATCTT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTC-GGCTTTGACCTT
* * *
2385993 AGAGACTTT-ATTTCCCTTAGTCTGCCTGTCGGCTTTAACCTT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* * ** *
2386035 AGAGACTTTCCTATCCCTTAGTATACCTGTCGATTTTGACCCT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
*
2386078 AGAGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACTTT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* ** * *
2386120 GGAGACTTTCCTATCTTTTAGTCTGCCTGTCGACTTTGACCCT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* * * * * *
2386163 GGAGACTTTCCT-TTCCTTAGTTTGCCTGTTGGCTTTTACCCT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* * *
2386205 AGAGACTTTTCT-TCCCTTAGTCTACCTGTCGACTTTGACCTT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* *
2386247 AAAGACTTTCCTATCCCTTAGTCTGCCTATCGGCTTTGACCCTT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGA-CCTT
* * * * *
2386291 -GGGA-TTT-CTTTCCCTTAGTCTGCTTATCAGCTTTGACCTT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* * * * * *
2386331 GGAGACTTTCTTATCTCTTAGTCTGCTTGTCGACTTTGACCCT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* *** *
2386374 GGAGACTTTCCT-TGCCCTTAGTCTATTTGTCAGCTTTGACCTT
1 AGAGACTTTCCTAT-CCCTTAGTCTGCCTGTCGGCTTTGACCTT
* *
2386417 GGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCCT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
* *
2386460 AGAGACTTTTCTATCCCTCAGTCTGCCTGTCGGCTTT
1 AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTT
2386497 AACCCTGAAG
Statistics
Matches: 695, Mismatches: 131, Indels: 35
0.81 0.15 0.04
Matches are distributed among these distances:
40 4 0.01
41 58 0.08
42 227 0.33
43 401 0.58
44 5 0.01
ACGTcount: A:0.16, C:0.27, G:0.17, T:0.40
Consensus pattern (43 bp):
AGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTT
Found at i:2386999 original size:5 final size:5
Alignment explanation
Indices: 2386989--2387043 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
2386979 TTTATTCGAT
2386989 ATAAA ATAAA ATAAA AGT-AA A-AAA ATAAA ATAAA AGTAAA A-AATA
1 ATAAA ATAAA ATAAA A-TAAA ATAAA ATAAA ATAAA A-TAAA ATAA-A
*
2387034 AAAAA ATAAA
1 ATAAA ATAAA
2387044 GGTAAAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
4 5 0.12
5 30 0.70
6 8 0.19
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (5 bp):
ATAAA
Found at i:2387015 original size:14 final size:13
Alignment explanation
Indices: 2386996--2387053 Score: 64
Period size: 14 Copynumber: 4.3 Consensus size: 13
2386986 GATATAAAAT
2386996 AAAATAAAAGTAAA
1 AAAATAAAA-TAAA
2387010 AAAATAAAATAAA
1 AAAATAAAATAAA
*
2387023 AGTAA-AAAATAAA
1 A-AAATAAAATAAA
*
2387036 AAAATAAAGGTAAA
1 AAAATAAA-ATAAA
2387050 AAAA
1 AAAA
2387054 ATCATCATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
12 2 0.05
13 17 0.45
14 19 0.50
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:2387016 original size:24 final size:26
Alignment explanation
Indices: 2386989--2387043 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
2386979 TTTATTCGAT
*
2386989 ATAAAATAAAA-T-AAAAGTAAAAAA
1 ATAAAATAAAAGTAAAAAATAAAAAA
2387013 ATAAAATAAAAGTAAAAAATAAAAAA
1 ATAAAATAAAAGTAAAAAATAAAAAA
2387039 ATAAA
1 ATAAA
2387044 GGTAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 11 0.39
25 1 0.04
26 16 0.57
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (26 bp):
ATAAAATAAAAGTAAAAAATAAAAAA
Found at i:2387029 original size:18 final size:19
Alignment explanation
Indices: 2386991--2387053 Score: 90
Period size: 19 Copynumber: 3.2 Consensus size: 19
2386981 TATTCGATAT
2386991 AAAATAAAATAAAAGTAAA
1 AAAATAAAATAAAAGTAAA
2387010 AAAATAAAATAAAAGTAAAA
1 AAAATAAAATAAAAGT-AAA
* *
2387030 AATAAAAAAATAAAGGTAAA
1 AA-AATAAAATAAAAGTAAA
2387050 AAAA
1 AAAA
2387054 ATCATCATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.45
20 10 0.25
21 12 0.30
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.14
Consensus pattern (19 bp):
AAAATAAAATAAAAGTAAA
Found at i:2387610 original size:33 final size:33
Alignment explanation
Indices: 2387529--2387642 Score: 131
Period size: 33 Copynumber: 3.4 Consensus size: 33
2387519 GCACGGCAAA
* *
2387529 AGGAGAAAAAAAACGTAACTCACAGTAAG-AGGAAA
1 AGGAG-AAAAAAA-GTAACTCACAGCAAGTAGG-AG
* * * *
2387564 AGAAAAAAAAAAGTAACTCACGGCAAGTGGGAG
1 AGGAGAAAAAAAGTAACTCACAGCAAGTAGGAG
*
2387597 AGGAGAAATAAAGTAACTCACAGCAAGTAGGAG
1 AGGAGAAAAAAAGTAACTCACAGCAAGTAGGAG
2387630 AGGAGAAAAAAAG
1 AGGAGAAAAAAAG
2387643 AAGAGAATAA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
33 54 0.82
34 9 0.14
35 3 0.05
ACGTcount: A:0.54, C:0.11, G:0.26, T:0.09
Consensus pattern (33 bp):
AGGAGAAAAAAAGTAACTCACAGCAAGTAGGAG
Found at i:2387873 original size:122 final size:122
Alignment explanation
Indices: 2387652--2387879 Score: 298
Period size: 122 Copynumber: 1.9 Consensus size: 122
2387642 GAAGAGAATA
* *
2387652 AACAGTAGCTTCCAGCTCCAACAAAGCACCCAAAACTAGCAATTCGAGTTTCTTCCAACACCCAC
1 AACAGTAGCTTCCAGCTCCAACAAAGCACCCAAAACCAGCAATTAGAGTTTCTTCCAACACCCAC
** * *
2387717 GACAGTAGCAGCTTCCATGAGTGCTTGCTACTCGAGCACTCTAGCAGCAGCACCCACC
66 GACAACAGCAACTTCCACGAGTGCTTGCTACTCGAGC-CTCTAGCAGCAGCACCCACC
* * * * * *
2387775 AACAGTAGCTTCCAGCTCCAACAAAGCA-TCAAAACCAGTAGTTAGAGTTTCTTTCAGCATCCAC
1 AACAGTAGCTTCCAGCTCCAACAAAGCACCCAAAACCAGCAATTAGAGTTTCTTCCAACACCCAC
**
2387839 GGTAACAGCAACTTCCACGAGTGCTTGC-AGCTCGAGCCTCT
66 GACAACAGCAACTTCCACGAGTGCTTGCTA-CTCGAGCCTCT
2387880 TCCAGCTTTT
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
121 5 0.06
122 57 0.63
123 28 0.31
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (122 bp):
AACAGTAGCTTCCAGCTCCAACAAAGCACCCAAAACCAGCAATTAGAGTTTCTTCCAACACCCAC
GACAACAGCAACTTCCACGAGTGCTTGCTACTCGAGCCTCTAGCAGCAGCACCCACC
Found at i:2388016 original size:30 final size:31
Alignment explanation
Indices: 2387960--2388017 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
2387950 AGCTTCCACG
*
2387960 GCAGCAACGAATAGCAACTCCAACAAGCTCA
1 GCAGCAACGAACAGCAACTCCAACAAGCTCA
* *
2387991 GCAGCAAC-AACAGCATCTTCAACAAGC
1 GCAGCAACGAACAGCAACTCCAACAAGC
2388018 AATGTCAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.41, C:0.33, G:0.16, T:0.10
Consensus pattern (31 bp):
GCAGCAACGAACAGCAACTCCAACAAGCTCA
Found at i:2388443 original size:10 final size:9
Alignment explanation
Indices: 2388424--2388449 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2388414 AAATGCAATA
2388424 TTTTTCTTT
1 TTTTTCTTT
2388433 TTTTTCTTT
1 TTTTTCTTT
2388442 TTTTTCTT
1 TTTTTCTT
2388450 GGTAATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:2390341 original size:32 final size:31
Alignment explanation
Indices: 2390305--2390488 Score: 210
Period size: 32 Copynumber: 5.8 Consensus size: 31
2390295 ACTTAAAAGA
* *
2390305 GTTGCCACTAACTTGTGTCGGCTTTAAGAAGG
1 GTTGCCACCAACTTGTGTGGGCTTT-AGAAGG
*
2390337 GTTGCCACCAACTTGTGTAGGCTTCT-GAAGAG
1 GTTGCCACCAACTTGTGTGGGCTT-TAGAAG-G
2390369 GTTGCCACCAACTTGTGTGGGCTTTA-AAGAAG
1 GTTGCCACCAACTTGTGTGGGCTTTAGAAG--G
*
2390401 GTTGCCACCAACTTGTGTGGGCTTTGGAAAGG
1 GTTGCCACCAACTTGTGTGGGCTTTAG-AAGG
* * * *
2390433 GTTACCACCGACTTGCGTGGGCTTTGGAAAGG
1 GTTGCCACCAACTTGTGTGGGCTTTAG-AAGG
*
2390465 GTTGCCACCGACTTGTGTGGGCTT
1 GTTGCCACCAACTTGTGTGGGCTT
2390489 CAAAAAAGGT
Statistics
Matches: 137, Mismatches: 9, Indels: 12
0.87 0.06 0.08
Matches are distributed among these distances:
31 8 0.06
32 125 0.91
33 1 0.01
34 3 0.02
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.29
Consensus pattern (31 bp):
GTTGCCACCAACTTGTGTGGGCTTTAGAAGG
Found at i:2390469 original size:96 final size:96
Alignment explanation
Indices: 2390299--2390499 Score: 255
Period size: 96 Copynumber: 2.1 Consensus size: 96
2390289 TATTGGACTT
* * *
2390299 AAAAGAGTTGCCACTAACTTGTGTCGGCTTTAAGAAGGGTTGCCACCAACTTGTGTAGGCTTCTG
1 AAAAG-GTTGCCACCAACTTGTGTCGGCTTTAAGAAGGGTTACCACCAACTTGCGTAGGCTTCTG
*
2390364 AAGAGGTTGCCACCAACTTGTGTGGGCTTTAA
65 AAGAGGTTGCCACCAACTTGTGTGGGCTTCAA
* * * * *
2390396 AGAAGGTTGCCACCAACTTGTGTGGGCTTT-GGAAAGGGTTACCACCGACTTGCGTGGGCTT-TG
1 AAAAGGTTGCCACCAACTTGTGTCGGCTTTAAG-AAGGGTTACCACCAACTTGCGTAGGCTTCT-
*
2390459 GAA-AGGGTTGCCACCGACTTGTGTGGGCTTCAA
64 GAAGA-GGTTGCCACCAACTTGTGTGGGCTTCAA
2390492 AAAAGGTT
1 AAAAGGTT
2390500 TCTCCACTGG
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
95 3 0.03
96 83 0.92
97 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.27
Consensus pattern (96 bp):
AAAAGGTTGCCACCAACTTGTGTCGGCTTTAAGAAGGGTTACCACCAACTTGCGTAGGCTTCTGA
AGAGGTTGCCACCAACTTGTGTGGGCTTCAA
Found at i:2390666 original size:33 final size:32
Alignment explanation
Indices: 2390629--2390956 Score: 283
Period size: 33 Copynumber: 10.2 Consensus size: 32
2390619 GCTTTAGAGG
* *
2390629 AAGGTGCCACGTAGTTGTGGGCTTAAAAGGAA
1 AAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * * *
2390661 CAAGGTGCTACAGAGTTGTGAACTTTAAAGGAA
1 -AAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * ** *
2390694 AAGATGCCATGGAGTTGTGGGTTTTAAAA-AAA
1 AAGGTGCCACGGAGTTGT-GGACTTAAAAGGAA
2390726 AACGGTGCCACGGAGTTGTGGACTTAAAAGGAA
1 AA-GGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
2390759 CAAGGTGCCACAGAGTTGTAGACTTAAAAGGAA
1 -AAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * * **
2390792 AAGATGTCATGGAGTTGTGGACTTTGAAAAAAAA
1 AAGGTGCCACGGAGTTGTGGAC-TT-AAAAGGAA
* *
2390826 AAGGTGCCATGGAGTTTTGGACTT-AAA-G--
1 AAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
2390854 --GGTGCCACGGAGTTATGGACTTAAAAGGAA
1 AAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
2390884 AAGATGCCACGGAGTTGTGGGCTTTGAAAAGAAA
1 AAGGTGCCACGGAGTTGTGGAC-TT-AAAAGGAA
* **
2390918 AAGGTGTCACAAAGTTGTGGACTTAAAAGGAA
1 AAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
2390950 TAAGGTG
1 -AAGGTG
2390957 GTATTTTGGT
Statistics
Matches: 235, Mismatches: 45, Indels: 30
0.76 0.15 0.10
Matches are distributed among these distances:
26 20 0.09
27 3 0.01
28 1 0.00
31 3 0.01
32 67 0.29
33 90 0.38
34 51 0.22
ACGTcount: A:0.36, C:0.11, G:0.30, T:0.23
Consensus pattern (32 bp):
AAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:2390752 original size:98 final size:97
Alignment explanation
Indices: 2390629--2390956 Score: 393
Period size: 98 Copynumber: 3.4 Consensus size: 97
2390619 GCTTTAGAGG
* * * *
2390629 AAGGTGCCACGTAGTTGTGGGCTTAAAAGGAACAAGGTGCTACAGAGTTGTGAACTTTAAAGGAA
1 AAGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACAGAGTTGTGAACTTAAAAGGAA
*
2390694 AAGATGCCATGGAGTTGTGGGTTTTAAAAAAA
66 AAGATGCCATGGAGTTGTGGGTTTGAAAAAAA
2390726 AACGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACAGAGTTGT-AGACTTAAAAGG
1 AA-GGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACAGAGTTGTGA-ACTTAAAAGG
* *
2390790 AAAAGATGTCATGGAGTTGTGGACTTTGAAAAAAAA
64 AAAAGATGCCATGGAGTTGTGG-GTTTG-AAAAAAA
* * * * *
2390826 AAGGTGCCATGGAGTTTTGGACTT-AAA-G-----GGTGCCACGGAGTTATGGACTTAAAAGGAA
1 AAGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACAGAGTTGTGAACTTAAAAGGAA
*
2390884 AAGATGCCACGGAGTTGTGGGCTTTGAAAAGAAA
66 AAGATGCCATGGAGTTGTGGG-TTTGAAAA-AAA
* ** *
2390918 AAGGTGTCACAAAGTTGTGGACTTAAAAGGAATAAGGTG
1 AAGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTG
2390957 GTATTTTGGT
Statistics
Matches: 197, Mismatches: 20, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
91 4 0.02
92 70 0.36
93 3 0.02
94 1 0.01
97 4 0.02
98 79 0.40
99 27 0.14
100 9 0.05
ACGTcount: A:0.36, C:0.11, G:0.30, T:0.23
Consensus pattern (97 bp):
AAGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACAGAGTTGTGAACTTAAAAGGAA
AAGATGCCATGGAGTTGTGGGTTTGAAAAAAA
Found at i:2390857 original size:26 final size:26
Alignment explanation
Indices: 2390828--2390878 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
2390818 AAAAAAAAAA
* *
2390828 GGTGCCATGGAGTTTTGGACTTAAAG
1 GGTGCCACGGAGTTATGGACTTAAAG
2390854 GGTGCCACGGAGTTATGGACTTAAA
1 GGTGCCACGGAGTTATGGACTTAAA
2390879 AGGAAAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.27
Consensus pattern (26 bp):
GGTGCCACGGAGTTATGGACTTAAAG
Found at i:2390920 original size:34 final size:32
Alignment explanation
Indices: 2390856--2390946 Score: 92
Period size: 34 Copynumber: 2.8 Consensus size: 32
2390846 ACTTAAAGGG
*
2390856 TGCCACGGAGTTATGGACTTAAAAGGAAAAGA
1 TGCCACGGAGTTATGGACTTAAAAGAAAAAGA
* * *
2390888 TGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGG
1 TGCCACGGAGTTATGGAC-TT-AAAAGAAAAAGA
* ** *
2390922 TGTCACAAAGTTGTGGACTTAAAAG
1 TGCCACGGAGTTATGGACTTAAAAG
2390947 GAATAAGGTG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
32 21 0.43
33 4 0.08
34 24 0.49
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (32 bp):
TGCCACGGAGTTATGGACTTAAAAGAAAAAGA
Found at i:2390939 original size:92 final size:92
Alignment explanation
Indices: 2390762--2390944 Score: 258
Period size: 92 Copynumber: 2.0 Consensus size: 92
2390752 AAAGGAACAA
* * *
2390762 GGTGCCACAGAGTTGTAGACTTAAAAGGAAAAGATGTCATGGAGTTGTGGACTTTGAAAAAAAAA
1 GGTGCCACAGAGTTATAGACTTAAAAGGAAAAGATGCCACGGAGTTGTGGACTTTGAAAAAAAAA
*** *
2390827 AGGTGCCATGGAGTTTTGGACTTAAAG
66 AGGTGCCACAAAGTTGTGGACTTAAAG
* * * *
2390854 GGTGCCACGGAGTTATGGACTTAAAAGGAAAAGATGCCACGGAGTTGTGGGCTTTGAAAAGAAAA
1 GGTGCCACAGAGTTATAGACTTAAAAGGAAAAGATGCCACGGAGTTGTGGACTTTGAAAAAAAAA
*
2390919 AGGTGTCACAAAGTTGTGGACTTAAA
66 AGGTGCCACAAAGTTGTGGACTTAAA
2390945 AGGAATAAGG
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
92 79 1.00
ACGTcount: A:0.36, C:0.11, G:0.30, T:0.23
Consensus pattern (92 bp):
GGTGCCACAGAGTTATAGACTTAAAAGGAAAAGATGCCACGGAGTTGTGGACTTTGAAAAAAAAA
AGGTGCCACAAAGTTGTGGACTTAAAG
Done.