Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 50 of 103
Found at i:18817444 original size:25 final size:24
Alignment explanation
Indices: 18817415--18817493 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 24
18817405 ATTTGTTTAA
18817415 ATTTAAATAAATAAAGATTAATTAC
1 ATTTAAATAAATAAA-ATTAATTAC
* * ** *
18817440 ATTT--A-AAATTAATTTGTTTAA
1 ATTTAAATAAATAAAATTAATTAC
18817461 ATTTAAATAAATAAAAATTAATTAC
1 ATTTAAATAAAT-AAAATTAATTAC
18817486 ATTTAAAT
1 ATTTAAAT
18817494 TTAATTTATT
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
21 9 0.22
22 6 0.15
23 2 0.05
24 4 0.10
25 19 0.47
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (24 bp):
ATTTAAATAAATAAAATTAATTAC
Found at i:18817453 original size:46 final size:46
Alignment explanation
Indices: 18817402--18817513 Score: 197
Period size: 46 Copynumber: 2.4 Consensus size: 46
18817392 AAATTTTAAT
*
18817402 TTAATTTGTTTAAATTTAAATAAATAAAGATTAATTACATTTAAAA
1 TTAATTTGTTTAAATTTAAATAAATAAAAATTAATTACATTTAAAA
*
18817448 TTAATTTGTTTAAATTTAAATAAATAAAAATTAATTACATTTAAAT
1 TTAATTTGTTTAAATTTAAATAAATAAAAATTAATTACATTTAAAA
*
18817494 TTAATTTATTTAAATTTAAA
1 TTAATTTGTTTAAATTTAAA
18817514 AGTAATATCC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (46 bp):
TTAATTTGTTTAAATTTAAATAAATAAAAATTAATTACATTTAAAA
Found at i:18817510 original size:15 final size:15
Alignment explanation
Indices: 18817394--18817512 Score: 69
Period size: 15 Copynumber: 7.8 Consensus size: 15
18817384 TATGATATAA
*
18817394 ATTTTAATTTAATTT
1 ATTTAAATTTAATTT
* *
18817409 GTTTAAATTTAA-AT
1 ATTTAAATTTAATTT
** * *
18817423 AAATAAAGATTAATTAC
1 ATTTAAA-TTTAATT-T
*
18817440 ATTTAAAATTAATTT
1 ATTTAAATTTAATTT
* * *
18817455 GTTTAAATTTAAATA
1 ATTTAAATTTAATTT
* * * *
18817470 AATAAAAATTAATTAC
1 ATTTAAATTTAATT-T
18817486 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
18817501 ATTTAAATTTAA
1 ATTTAAATTTAA
18817513 AAGTAATATC
Statistics
Matches: 74, Mismatches: 26, Indels: 8
0.69 0.24 0.07
Matches are distributed among these distances:
14 5 0.07
15 46 0.62
16 18 0.24
17 5 0.07
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTTAAATTTAATTT
Found at i:18817510 original size:21 final size:21
Alignment explanation
Indices: 18817391--18817513 Score: 66
Period size: 21 Copynumber: 5.5 Consensus size: 21
18817381 AAATATGATA
* *
18817391 TAAATTTTAATTTAATTTGTT
1 TAAATTTAAATTTAATTTATT
* * *
18817412 TAAATTTAAATAAATAAAGATTAAT
1 TAAATTTAAAT---TTAA-TTTATT
* * *
18817437 TACATTTAAAATTAATTTGTT
1 TAAATTTAAATTTAATTTATT
* * *
18817458 TAAATTTAAATAAATAAAAATTAAT
1 TAAATTTAAAT---T-TAATTTATT
*
18817483 TACATTTAAATTTAATTTATT
1 TAAATTTAAATTTAATTTATT
18817504 TAAATTTAAA
1 TAAATTTAAA
18817514 AGTAATATCC
Statistics
Matches: 72, Mismatches: 22, Indels: 16
0.65 0.20 0.15
Matches are distributed among these distances:
21 37 0.51
22 4 0.06
24 4 0.06
25 27 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TAAATTTAAATTTAATTTATT
Found at i:18818019 original size:12 final size:11
Alignment explanation
Indices: 18817995--18818024 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
18817985 AGTAAATAAG
18817995 AGAAAAATCAA
1 AGAAAAATCAA
18818006 AGAAAAATCAAA
1 AGAAAAATC-AA
18818018 AGAAAAA
1 AGAAAAA
18818025 ATGTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.77, C:0.07, G:0.10, T:0.07
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:18825623 original size:28 final size:30
Alignment explanation
Indices: 18825535--18825624 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 30
18825525 CACGTTATAG
*
18825535 GGACTAAATTGAACAAAAGTGTATAGTA-T-AT
1 GGACTAAATT-AACAAAATTG-AT-GTATTGAT
*
18825566 GGACTAAATTAAACAAAATTGATGTGTTGAT
1 GGACTAAATT-AACAAAATTGATGTATTGAT
18825597 GGACTAAATT-A-AAAATTGA-GATATTGAT
1 GGACTAAATTAACAAAATTGATG-TATTGAT
18825625 ATACAATGTC
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
27 1 0.02
28 14 0.27
29 3 0.06
30 3 0.06
31 31 0.60
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (30 bp):
GGACTAAATTAACAAAATTGATGTATTGAT
Found at i:18828488 original size:19 final size:20
Alignment explanation
Indices: 18828438--18828493 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
18828428 AAACATAAAA
*
18828438 ATTAAATATAAAT-AACATT
1 ATTAAACATAAATAAACATT
*
18828457 ATT-AACTTAAAATAAACATT
1 ATTAAACAT-AAATAAACATT
18828477 -TTAAACATAAATTAAAC
1 ATTAAACATAAA-TAAAC
18828494 TTAAAGTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 3 0.10
19 12 0.40
20 15 0.50
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (20 bp):
ATTAAACATAAATAAACATT
Found at i:18833688 original size:17 final size:16
Alignment explanation
Indices: 18833658--18833692 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
18833648 TATATTAATT
*
18833658 ATTTTTTATTTTTTTA
1 ATTTTTTATATTTTTA
18833674 ATTTTTATATATTTTTA
1 ATTTTT-TATATTTTTA
18833691 AT
1 AT
18833693 ATAGTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTTATATTTTTA
Found at i:18834165 original size:28 final size:28
Alignment explanation
Indices: 18834125--18834226 Score: 98
Period size: 28 Copynumber: 3.6 Consensus size: 28
18834115 AGTCGTATTG
* *
18834125 AAAATGTAGTTATTACATGTCATGTTGA
1 AAAATTTAATTATTACATGTCATGTTGA
* * * *
18834153 AAAATATAATTATTACACGTTATATTG-
1 AAAATTTAATTATTACATGTCATGTTGA
* * * *
18834180 AAGATTTAGTTATTACACAGCCATGTTGA
1 AAAATTTAATTATTACA-TGTCATGTTGA
18834209 AAAATTTAATTATTACAT
1 AAAATTTAATTATTACAT
18834227 ACCATAATGA
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
27 14 0.25
28 28 0.49
29 15 0.26
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (28 bp):
AAAATTTAATTATTACATGTCATGTTGA
Found at i:18834219 original size:56 final size:55
Alignment explanation
Indices: 18834120--18834225 Score: 158
Period size: 56 Copynumber: 1.9 Consensus size: 55
18834110 CTAAAAGTCG
* *
18834120 TATTGAAAATGTAGTTATTACATGTCATGTTGAAAAATATAATTATTACACGTTA
1 TATTGAAAATGTAGTTATTACAAGCCATGTTGAAAAATATAATTATTACACGTTA
* * *
18834175 TATTGAAGATTTAGTTATTACACAGCCATGTTGAAAAATTTAATTATTACA
1 TATTGAAAATGTAGTTATTACA-AGCCATGTTGAAAAATATAATTATTACA
18834226 TACCATAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
55 20 0.44
56 25 0.56
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (55 bp):
TATTGAAAATGTAGTTATTACAAGCCATGTTGAAAAATATAATTATTACACGTTA
Found at i:18834231 original size:28 final size:28
Alignment explanation
Indices: 18834149--18834240 Score: 87
Period size: 28 Copynumber: 3.3 Consensus size: 28
18834139 ACATGTCATG
* ***
18834149 TTGAAAAATATAATTATTACACGTTATA
1 TTGAAAAATTTAATTATTACACACCATA
* * *
18834177 TTG-AAGATTTAGTTATTACACAGCCATG
1 TTGAAAAATTTAATTATTACACA-CCATA
*
18834205 TTGAAAAATTTAATTATTACATACCATA
1 TTGAAAAATTTAATTATTACACACCATA
*
18834233 ATGAAAAA
1 TTGAAAAA
18834241 GTTGTTACAT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
27 15 0.30
28 19 0.38
29 16 0.32
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (28 bp):
TTGAAAAATTTAATTATTACACACCATA
Found at i:18838200 original size:14 final size:12
Alignment explanation
Indices: 18838182--18838265 Score: 77
Period size: 12 Copynumber: 6.8 Consensus size: 12
18838172 AGGGAAGGAA
18838182 AAAGAGAGAAAAG
1 AAAGA-AGAAAAG
18838195 ACAAGAAAGAAAAAG
1 A-AAG-AAG-AAAAG
18838210 AAAGAAG-AAAG
1 AAAGAAGAAAAG
18838221 AAAG-A-AAAAG
1 AAAGAAGAAAAG
18838231 AAAGAAGAAAGAG
1 AAAGAAGAAA-AG
18838244 AAA-AAGAATAAG
1 AAAGAAGAA-AAG
18838256 AAAGAGAGAA
1 AAAGA-AGAA
18838266 GGAGCAGCGG
Statistics
Matches: 61, Mismatches: 0, Indels: 19
0.76 0.00 0.24
Matches are distributed among these distances:
10 9 0.15
11 9 0.15
12 13 0.21
13 11 0.18
14 12 0.20
15 7 0.11
ACGTcount: A:0.73, C:0.01, G:0.25, T:0.01
Consensus pattern (12 bp):
AAAGAAGAAAAG
Found at i:18838206 original size:4 final size:4
Alignment explanation
Indices: 18838191--18838265 Score: 56
Period size: 4 Copynumber: 19.5 Consensus size: 4
18838181 AAAAGAGAGA
18838191 AAAG ACAAG AAAG -AA- AAAG AAAG -AAG AAAG AAAG -AA- AAAG AAAG
1 AAAG A-AAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
*
18838235 -AAG AAAG AGAA- AAAG AATAAG AAAG AGAG AA
1 AAAG AAAG A-AAG AAAG -A-AAG AAAG AAAG AA
18838266 GGAGCAGCGG
Statistics
Matches: 58, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
3 16 0.28
4 31 0.53
5 8 0.14
6 3 0.05
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:18838223 original size:21 final size:21
Alignment explanation
Indices: 18838192--18838265 Score: 100
Period size: 21 Copynumber: 3.6 Consensus size: 21
18838182 AAAGAGAGAA
18838192 AAGACAAGAAAGAAAAAGAAAG
1 AAGA-AAGAAAGAAAAAGAAAG
18838214 AAGAAAGAAAGAAAAAGAAAG
1 AAGAAAGAAAGAAAAAGAAAG
*
18838235 AAGAAAG--AGAAAAAG-AAT
1 AAGAAAGAAAGAAAAAGAAAG
*
18838253 AAGAAAGAGAGAA
1 AAGAAAGAAAGAA
18838266 GGAGCAGCGG
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
18 9 0.18
19 8 0.16
20 4 0.08
21 24 0.49
22 4 0.08
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.01
Consensus pattern (21 bp):
AAGAAAGAAAGAAAAAGAAAG
Found at i:18838225 original size:25 final size:26
Alignment explanation
Indices: 18838179--18838265 Score: 82
Period size: 25 Copynumber: 3.6 Consensus size: 26
18838169 AAAAGGGAAG
*
18838179 GAAAAAGAGAG-A-AAAGACAAGAAA
1 GAAAAAGAAAGAAGAAAGACAAGAAA
18838203 GAAAAAG--A-AAG-AAGA-AAGAAA
1 GAAAAAGAAAGAAGAAAGACAAGAAA
*
18838224 GAAAAAGAAAGAAGAAAGAGAA-AAA
1 GAAAAAGAAAGAAGAAAGACAAGAAA
*
18838249 GAATAAGAAAGAGAGAA
1 GAAAAAGAAAGA-AGAA
18838266 GGAGCAGCGG
Statistics
Matches: 54, Mismatches: 1, Indels: 14
0.78 0.01 0.20
Matches are distributed among these distances:
21 13 0.24
22 6 0.11
23 1 0.02
24 10 0.19
25 18 0.33
26 6 0.11
ACGTcount: A:0.72, C:0.01, G:0.25, T:0.01
Consensus pattern (26 bp):
GAAAAAGAAAGAAGAAAGACAAGAAA
Found at i:18838228 original size:35 final size:33
Alignment explanation
Indices: 18838181--18838260 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 33
18838171 AAGGGAAGGA
*
18838181 AAAAGAGAGAAAAGACAAGAAAGAAAAAGAAAGAAG
1 AAAAGAAAGAAAAGA-AAG-AAGAAAAAGAAA-AAG
*
18838217 -AAAGAAAGAAAAAGAAAGAAGAAAGAGAAAAAG
1 AAAAGAAAG-AAAAGAAAGAAGAAAAAGAAAAAG
18838250 AATAAGAAAGA
1 AA-AAGAAAGA
18838261 GAGAAGGAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
33 3 0.08
34 13 0.33
35 17 0.44
36 6 0.15
ACGTcount: A:0.74, C:0.01, G:0.24, T:0.01
Consensus pattern (33 bp):
AAAAGAAAGAAAAGAAAGAAGAAAAAGAAAAAG
Found at i:18838382 original size:69 final size:67
Alignment explanation
Indices: 18838228--18838463 Score: 264
Period size: 69 Copynumber: 3.4 Consensus size: 67
18838218 AAGAAAGAAA
* *
18838228 AAGAAAGAAGAAAGAGAAAAAGAATAAGAAAGAGAGAAGGAGCAGCG-GCTCAAGGAGAAGAATG
1 AAGAAAGAAG-AA-AGAAAAAGAAGAAGAAAGA-AGAAGGAGCAGCGCG-TCAAGGAGAAGAAAG
*
18838292 AGAGGG
62 AGAAGG
*
18838298 AAGGAAA-AAGAAAGAAAAAGAAGAAGAAAGAATGAAGGAGCATCAGCGTCAAGGAGAAGAAAGA
1 AA-GAAAGAAGAAAGAAAAAGAAGAAGAAAGAA-GAAGGAGCAGC-GCGTCAAGGAGAAGAAAGA
*
18838362 GATGG
63 GAAGG
* * *
18838367 AAGAAAGAAGAAAGAAAAAGAAGAAGCAAG-AGAGAGGAAGCAGCGACGTCGAGGAGAAGAAGGA
1 AAGAAAGAAGAAAGAAAAAGAAGAAGAAAGAAGA-AGG-AGCAGCG-CGTCAAGGAGAAGAAAGA
18838431 GAAGG
63 GAAGG
* *
18838436 AAGGAAGAAGAAAGAAAAA-AAAAAGAAA
1 AAGAAAGAAGAAAGAAAAAGAAGAAGAAA
18838464 AAGGGAGGGA
Statistics
Matches: 146, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
67 3 0.02
68 44 0.30
69 89 0.61
70 6 0.04
71 4 0.03
ACGTcount: A:0.58, C:0.06, G:0.33, T:0.03
Consensus pattern (67 bp):
AAGAAAGAAGAAAGAAAAAGAAGAAGAAAGAAGAAGGAGCAGCGCGTCAAGGAGAAGAAAGAGAA
GG
Found at i:18838389 original size:20 final size:20
Alignment explanation
Indices: 18838352--18838391 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
18838342 AGCGTCAAGG
* **
18838352 AGAAGAAAGAGATGGAAGAA
1 AGAAGAAAGAAAAAGAAGAA
18838372 AGAAGAAAGAAAAAGAAGAA
1 AGAAGAAAGAAAAAGAAGAA
18838392 GCAAGAGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (20 bp):
AGAAGAAAGAAAAAGAAGAA
Found at i:18839203 original size:60 final size:60
Alignment explanation
Indices: 18839111--18839389 Score: 328
Period size: 60 Copynumber: 4.7 Consensus size: 60
18839101 TTTGATTTAA
* * * *
18839111 AAAGGGAGACTTGAAGCCCCGATTTATATTGGGTGGCGTGGATAGTTCCCACGAGTAGGA
1 AAAGGGGGACCTGAAGCCCCGATTCATATTGGGTGGCGTGGATAGTTCCCACGAGTAGGT
* * * * * *
18839171 AAAGAGGGACCTAAAACCCCGATTCATATTGGGTGACGT-GAGTAGTTCCCATGAGTAGGG
1 AAAGGGGGACCTGAAGCCCCGATTCATATTGGGTGGCGTGGA-TAGTTCCCACGAGTAGGT
* * * * * *
18839231 AATGGGGGATCTGAAGCCCCTATTCATATTAGATGGCGTGGGTAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTCATATTGGGTGGCGTGGATAGTTCCCACGAGTAGGT
* * * **
18839291 AAAGGGGGACCTGAAGCTCTGATTCATATTGGGTGGTGTGGGCAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTCATATTGGGTGGCGTGGATAGTTCCCACGAGTAGGT
*
18839351 AAAGGGGGACCTGAAGCCCCGATTTATATAT-GGTGGCGT
1 AAAGGGGGACCTGAAGCCCCGATTCATAT-TGGGTGGCGT
18839390 ATGCAGTTCT
Statistics
Matches: 182, Mismatches: 34, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
59 2 0.01
60 178 0.98
61 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (60 bp):
AAAGGGGGACCTGAAGCCCCGATTCATATTGGGTGGCGTGGATAGTTCCCACGAGTAGGT
Found at i:18844115 original size:4 final size:4
Alignment explanation
Indices: 18844106--18844164 Score: 65
Period size: 4 Copynumber: 15.5 Consensus size: 4
18844096 GAGAAAATAC
18844106 AAGA AAGA AATTGA AAGA AA-A AAGA AA-A AA-A AAGA AAG- AAGA AAG-
1 AAGA AAGA AA--GA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
18844151 AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AA
18844165 AAGAGAGAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
3 15 0.31
4 30 0.61
6 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.03
Consensus pattern (4 bp):
AAGA
Found at i:18844131 original size:7 final size:7
Alignment explanation
Indices: 18844119--18844160 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
18844109 AAAGAAATTG
18844119 AAAGAAA
1 AAAGAAA
18844126 AAAGAAA
1 AAAGAAA
18844133 AAA-AAA
1 AAAGAAA
*
18844139 GAAAGAAG
1 -AAAGAAA
*
18844147 AAAGAAG
1 AAAGAAA
18844154 AAAGAAA
1 AAAGAAA
18844161 GAAAAAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 3 0.10
7 26 0.84
8 2 0.06
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:18844132 original size:21 final size:19
Alignment explanation
Indices: 18844106--18844174 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 19
18844096 GAGAAAATAC
18844106 AAGAAAGAAATTGAAAGAAAA
1 AAGAAAGAAA--GAAAGAAAA
*
18844127 AAGAAA-AAA-AAAGAAAG
1 AAGAAAGAAAGAAAGAAAA
*
18844144 AAGAAAG-AAGAAAGAAAG
1 AAGAAAGAAAGAAAGAAAA
*
18844162 AA-AAAGAGAGAAA
1 AAGAAAGAAAGAAA
18844175 AAGTAGCGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
17 19 0.44
18 15 0.35
20 3 0.07
21 6 0.14
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (19 bp):
AAGAAAGAAAGAAAGAAAA
Found at i:18844143 original size:14 final size:14
Alignment explanation
Indices: 18844089--18844176 Score: 70
Period size: 14 Copynumber: 6.1 Consensus size: 14
18844079 AAAGCAAAGG
*
18844089 AAAAAGAGAGAAAA
1 AAAAAGAAAGAAAA
* *
18844103 TACAAGAAAGAAATTGA
1 AAAAAGAAAGAAA---A
18844120 AAGAAA-AAAGAAAA
1 AA-AAAGAAAGAAAA
*
18844134 AAAAAGAAAGAAGA
1 AAAAAGAAAGAAAA
* *
18844148 AAGAAGAAAGAAAG
1 AAAAAGAAAGAAAA
*
18844162 AAAAAGAGAGAAAA
1 AAAAAGAAAGAAAA
18844176 A
1 A
18844177 GTAGCGACAT
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
13 3 0.05
14 43 0.75
17 9 0.16
18 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.20, T:0.03
Consensus pattern (14 bp):
AAAAAGAAAGAAAA
Found at i:18844149 original size:28 final size:28
Alignment explanation
Indices: 18844118--18844177 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
18844108 GAAAGAAATT
18844118 GAAAGAAAAAAGAAAAAAAAAGAAAGAA
1 GAAAGAAAAAAGAAAAAAAAAGAAAGAA
* * *
18844146 GAAAGAAGAAAGAAAGAAAAAGAGAGAA
1 GAAAGAAAAAAGAAAAAAAAAGAAAGAA
18844174 -AAAG
1 GAAAG
18844178 TAGCGACATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (28 bp):
GAAAGAAAAAAGAAAAAAAAAGAAAGAA
Found at i:18844177 original size:10 final size:10
Alignment explanation
Indices: 18844106--18844177 Score: 69
Period size: 10 Copynumber: 7.3 Consensus size: 10
18844096 GAGAAAATAC
18844106 AAGAAAGAAA
1 AAGAAAGAAA
**
18844116 TTGAAAG--A
1 AAGAAAGAAA
18844124 AA-AAAGAAA
1 AAGAAAGAAA
*
18844133 AAAAAAGAAA
1 AAGAAAGAAA
18844143 GAAGAAAGAAGA
1 -AAGAAAGAA-A
18844155 AAGAAAGAAA
1 AAGAAAGAAA
*
18844165 AAGAGAGAAA
1 AAGAAAGAAA
18844175 AAG
1 AAG
18844178 TAGCGACATC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
7 4 0.08
8 1 0.02
9 3 0.06
10 25 0.49
11 17 0.33
12 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:18844264 original size:69 final size:69
Alignment explanation
Indices: 18844141--18844371 Score: 256
Period size: 69 Copynumber: 3.4 Consensus size: 69
18844131 AAAAAAAAGA
* * * * * *
18844141 AAGAAGAAAGAAGAAAGAAAGAA-AAAGAGAGAAAAAGTAGCGACATCGGGGAGAAGAATGAGAA
1 AAGAAGAAAGAA-AAAGAAA-AAGAAAGAGAGAGAGAGCAGCGGCATCGAGGAGAAGAAAGAGAA
18844205 GGAAGG
64 GGAAGG
* *
18844211 AAGAAGAAAGAAAAAGAAAAAGAAAGAGAGAGGGAGCAGCGGCATCGATGAGAAGAAAGAG-AGG
1 AAGAAGAAAGAAAAAGAAAAAGAAAGAGAGAGAGAGCAGCGGCATCGAGGAGAAGAAAGAGAAGG
18844275 AAAGG
66 -AAGG
* ** * * *
18844280 AAGAAGAAAGAAAAAGAAGAAGAAAGAGAGAGAGAGCAATGGCGTCAAGGAGAAGAAGGA-AAGG
1 AAGAAGAAAGAAAAAGAAAAAGAAAGAGAGAGAGAGCAGCGGCATCGAGGAGAAGAAAGAGAA-G
18844344 GAAGG
65 GAAGG
*
18844349 AAAAAGAAAG-AAAA-AAAAAGAAA
1 AAGAAGAAAGAAAAAGAAAAAGAAA
18844372 AAAGAAAAGG
Statistics
Matches: 139, Mismatches: 18, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
67 8 0.06
68 9 0.06
69 108 0.78
70 14 0.10
ACGTcount: A:0.59, C:0.04, G:0.34, T:0.03
Consensus pattern (69 bp):
AAGAAGAAAGAAAAAGAAAAAGAAAGAGAGAGAGAGCAGCGGCATCGAGGAGAAGAAAGAGAAGG
AAGG
Found at i:18844286 original size:20 final size:18
Alignment explanation
Indices: 18844261--18844310 Score: 68
Period size: 16 Copynumber: 2.8 Consensus size: 18
18844251 GGCATCGATG
18844261 AGAAGAAAGAGAGGAAAGGA
1 AGAAGAAAGAGA-GAAA-GA
18844281 AGAAGAAAGA-A-AAAGA
1 AGAAGAAAGAGAGAAAGA
18844297 AGAAGAAAGAGAGA
1 AGAAGAAAGAGAGA
18844311 GAGAGCAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 12 0.43
17 4 0.14
18 1 0.04
19 1 0.04
20 10 0.36
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
AGAAGAAAGAGAGAAAGA
Found at i:18845125 original size:60 final size:60
Alignment explanation
Indices: 18845023--18845260 Score: 264
Period size: 60 Copynumber: 4.0 Consensus size: 60
18845013 TTTGATTTAA
* * * * * * *
18845023 AAAGGGAGACTTGAAGCCCCGATTTATATTGGGTGGCGTGGGTAGTTCCCACGAGTTGGT
1 AAAGGGGGACCTGAAACCCTGATTCATATTGGGTGGCATGGGTAGTTCCCACGAGTAGGT
* *
18845083 AAAGGGGGACCTGAAACCTTGATTCATATTGGGTGGCATGGGTAGTTCCCACAAGTAGGT
1 AAAGGGGGACCTGAAACCCTGATTCATATTGGGTGGCATGGGTAGTTCCCACGAGTAGGT
* * * * *
18845143 AAAAGGGGACCTGAAGCCCTGATTCATATTGGATGGCATGGGCAGTTCCCATGAGTAGGT
1 AAAGGGGGACCTGAAACCCTGATTCATATTGGGTGGCATGGGTAGTTCCCACGAGTAGGT
* * * * * *
18845203 AAAGGGGGACCTGAAGCCTCT-ATTTATATAT-GGTGGCGTAGGCAGTTCCCACTAGTAG
1 AAAGGGGGACCTGAAACC-CTGATTCATAT-TGGGTGGCATGGGTAGTTCCCACGAGTAG
18845261 ATGATGATGT
Statistics
Matches: 153, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
60 150 0.98
61 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (60 bp):
AAAGGGGGACCTGAAACCCTGATTCATATTGGGTGGCATGGGTAGTTCCCACGAGTAGGT
Found at i:18845250 original size:120 final size:121
Alignment explanation
Indices: 18845022--18845260 Score: 313
Period size: 120 Copynumber: 2.0 Consensus size: 121
18845012 ATTTGATTTA
* * * * * *
18845022 AAAAGGGAGACTTGAAGCCCCGATTTATATTGGGTGGCGTGGGTAGTTCCCACGAGTTGGTAAAG
1 AAAAGGGAGACCTGAAGCCCCGATTCATATTGGATGGCATGGGCAGTTCCCACGAGTAGGTAAAG
* *
18845087 GGGGACCTGAAACCTTGATTCATATTGGGTGGCATGGGTAGTTCCCACAAGTAGGT
66 GGGGACCTGAAACCTTGATTCATATTGGGTGGCATAGGCAGTTCCCACAAGTAGGT
* *
18845143 AAAAGGG-GACCTGAAGCCCTGATTCATATTGGATGGCATGGGCAGTTCCCATGAGTAGGTAAAG
1 AAAAGGGAGACCTGAAGCCCCGATTCATATTGGATGGCATGGGCAGTTCCCACGAGTAGGTAAAG
* * * *
18845207 GGGGACCTGAAGCCTCT-ATTTATATAT-GGTGGCGTAGGCAGTTCCCACTAGTAG
66 GGGGACCTGAAACCT-TGATTCATAT-TGGGTGGCATAGGCAGTTCCCACAAGTAG
18845261 ATGATGATGT
Statistics
Matches: 102, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
120 93 0.91
121 9 0.09
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.25
Consensus pattern (121 bp):
AAAAGGGAGACCTGAAGCCCCGATTCATATTGGATGGCATGGGCAGTTCCCACGAGTAGGTAAAG
GGGGACCTGAAACCTTGATTCATATTGGGTGGCATAGGCAGTTCCCACAAGTAGGT
Found at i:18859757 original size:28 final size:29
Alignment explanation
Indices: 18859701--18859781 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 29
18859691 GTCTTTTCAT
* * * *
18859701 TATTTATCCACTTC-TGATAGATTAAAAG
1 TATTCATCCACTTCTTGATGGGTTACAAG
* *
18859729 TATTCATTCACTT-TTGGTGGGTTACAAG
1 TATTCATCCACTTCTTGATGGGTTACAAG
*
18859757 TATTCATCCATTTCTTGATGGGTTA
1 TATTCATCCACTTCTTGATGGGTTA
18859782 TCCAATTCTT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
28 32 0.76
29 10 0.24
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (29 bp):
TATTCATCCACTTCTTGATGGGTTACAAG
Found at i:18859911 original size:26 final size:25
Alignment explanation
Indices: 18859827--18859918 Score: 78
Period size: 26 Copynumber: 3.6 Consensus size: 25
18859817 TTCACTTCAA
*
18859827 GTGGTAAAATTA-TCTATCCATTTCTG
1 GTGGTAAAACTATTC-ATCCA-TTCTG
* * **
18859853 GAGGTAAAACTATTCTTAGATTCTG
1 GTGGTAAAACTATTCATCCATTCTG
*
18859878 ATGGTAAAACTATTCATCCACTTCTG
1 GTGGTAAAACTATTCATCCA-TTCTG
* *
18859904 GTGTTAAAATTATTC
1 GTGGTAAAACTATTC
18859919 TTAGAATTAA
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
25 20 0.39
26 29 0.57
27 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (25 bp):
GTGGTAAAACTATTCATCCATTCTG
Found at i:18861088 original size:2 final size:2
Alignment explanation
Indices: 18861081--18861106 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18861071 TTCTGAATGT
18861081 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
18861107 GAAATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18871346 original size:2 final size:2
Alignment explanation
Indices: 18871339--18871366 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18871329 GTCTTAATTC
18871339 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18871367 TTAATTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18885528 original size:27 final size:26
Alignment explanation
Indices: 18885470--18885560 Score: 92
Period size: 26 Copynumber: 3.5 Consensus size: 26
18885460 TTTAGACATT
* * * * *
18885470 ACGCACTTGAAATGTCACTATGCATT
1 ACGCACTTGGAATGTCCCTAGGCGTC
* *
18885496 ATGCACTTAGGAATGTCCCTAGGTGTC
1 ACGCACTT-GGAATGTCCCTAGGCGTC
* *
18885523 ACGCACTGGGAATGTCCCTAGGCGTT
1 ACGCACTTGGAATGTCCCTAGGCGTC
18885549 ACGCACTTGGAA
1 ACGCACTTGGAA
18885561 CGTTCTTATG
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
26 34 0.65
27 18 0.35
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.26
Consensus pattern (26 bp):
ACGCACTTGGAATGTCCCTAGGCGTC
Found at i:18885593 original size:26 final size:27
Alignment explanation
Indices: 18885441--18885683 Score: 116
Period size: 27 Copynumber: 9.1 Consensus size: 27
18885431 TTCTTTCTTT
** ** * *
18885441 TTACGCACTTGGGAACATCTTTAGACA
1 TTACGCACTTGGGAATGTCCCTAGGCG
* * * *
18885468 TTACGCACTT-GAAATGTCACTATGCA
1 TTACGCACTTGGGAATGTCCCTAGGCG
* * *
18885494 TTATGCACTTAGGAATGTCCCTAGGTG
1 TTACGCACTTGGGAATGTCCCTAGGCG
*
18885521 TCACGCAC-TGGGAATGTCCCTAGGCG
1 TTACGCACTTGGGAATGTCCCTAGGCG
* * * *
18885547 TTACGCACTT-GGAACGTTCTTATGCG
1 TTACGCACTTGGGAATGTCCCTAGGCG
* ** *
18885573 TTATGCACTTGGGAATGTCTTTAGGAG
1 TTACGCACTTGGGAATGTCCCTAGGCG
* * * * * *
18885600 TTACACGCTTAGGATTGTCCCTATGCT
1 TTACGCACTTGGGAATGTCCCTAGGCG
* * * * *
18885627 TTATGCACTTAGGACTATCCCTAGGTG
1 TTACGCACTTGGGAATGTCCCTAGGCG
* * * * *
18885654 TTGCACACTT-GGAATATCCCTGGGTG
1 TTACGCACTTGGGAATGTCCCTAGGCG
18885680 TTAC
1 TTAC
18885684 ACATTTGGAA
Statistics
Matches: 161, Mismatches: 52, Indels: 7
0.73 0.24 0.03
Matches are distributed among these distances:
26 79 0.49
27 82 0.51
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (27 bp):
TTACGCACTTGGGAATGTCCCTAGGCG
Found at i:18885686 original size:26 final size:26
Alignment explanation
Indices: 18885632--18885693 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
18885622 ATGCTTTATG
* *
18885632 CACTTAGGACTATCCCTAGGTGTTGCA
1 CACTT-GGAATATCCCTAGGTGTTACA
*
18885659 CACTTGGAATATCCCTGGGTGTTACA
1 CACTTGGAATATCCCTAGGTGTTACA
*
18885685 CATTTGGAA
1 CACTTGGAA
18885694 CGCCCTTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 26 0.84
27 5 0.16
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (26 bp):
CACTTGGAATATCCCTAGGTGTTACA
Found at i:18887275 original size:2 final size:2
Alignment explanation
Indices: 18887268--18887299 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18887258 CATTATGTTG
18887268 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18887300 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18887612 original size:2 final size:2
Alignment explanation
Indices: 18887605--18887655 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
18887595 NNNNNNNNNN
18887605 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18887647 TA TA TA TA T
1 TA TA TA TA T
18887656 GTTTATGTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18888703 original size:26 final size:26
Alignment explanation
Indices: 18888631--18888703 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 26
18888621 GGTCGTGACG
* *
18888631 ATTATGCACTTGGGAATGTCTTTGGGT
1 ATTATGCACTT-GGAATGTCCTTGGGC
*** *
18888658 ATTACATACTTGGAACGTCCTTGGGC
1 ATTATGCACTTGGAATGTCCTTGGGC
*
18888684 ATTATGCACTTGAAATGTCC
1 ATTATGCACTTGGAATGTCC
18888704 ATATTAGCGT
Statistics
Matches: 35, Mismatches: 11, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
26 27 0.77
27 8 0.23
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (26 bp):
ATTATGCACTTGGAATGTCCTTGGGC
Found at i:18894528 original size:36 final size:36
Alignment explanation
Indices: 18894484--18894575 Score: 148
Period size: 36 Copynumber: 2.6 Consensus size: 36
18894474 TAGTCGAAGT
18894484 CATCGTGTGCACCCCCACATTGCGCACAACTAATAC
1 CATCGTGTGCACCCCCACATTGCGCACAACTAATAC
* * *
18894520 CATTGTGTGCACCCCCACATTGCGCACAGCTAATGC
1 CATCGTGTGCACCCCCACATTGCGCACAACTAATAC
*
18894556 CATCGTGTGCACCCTCACAT
1 CATCGTGTGCACCCCCACAT
18894576 CGTGCATAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.24, C:0.38, G:0.16, T:0.22
Consensus pattern (36 bp):
CATCGTGTGCACCCCCACATTGCGCACAACTAATAC
Found at i:18895868 original size:25 final size:22
Alignment explanation
Indices: 18895805--18895865 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
18895795 AAATATCATC
*
18895805 TTCCAGCAACTTTTTCTCATAT
1 TTCCAGCAGCTTTTTCTCATAT
18895827 TTCCAGCAGCTTTTTCTCATAT
1 TTCCAGCAGCTTTTTCTCATAT
*
18895849 TTCCAGCAGCTTCTTCT
1 TTCCAGCAGCTTTTTCT
18895866 TCTTCTTCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.18, C:0.30, G:0.08, T:0.44
Consensus pattern (22 bp):
TTCCAGCAGCTTTTTCTCATAT
Found at i:18896672 original size:17 final size:19
Alignment explanation
Indices: 18896631--18896672 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
18896621 ATGTATATAT
18896631 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTG-A-TG
18896652 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGATG
18896669 ATGA
1 ATGA
18896673 TGTTGAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (19 bp):
ATGAATATATGTTGTGATG
Found at i:18896709 original size:37 final size:37
Alignment explanation
Indices: 18896679--18896751 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
18896669 ATGATGTTGA
18896679 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
* *
18896716 AGTGTGCGAGTAGGGAGTGCACATATGGTGATGATA
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
18896752 TTACATTGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.29, C:0.10, G:0.38, T:0.23
Consensus pattern (37 bp):
AGTGTGCGAGTAGGGAGTGCACACATGATGATGATAG
Found at i:18896750 original size:40 final size:38
Alignment explanation
Indices: 18896666--18896738 Score: 114
Period size: 37 Copynumber: 1.9 Consensus size: 38
18896656 ATAATGTTGT
*
18896666 GTGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
1 GTGATGATGTAGAAGTGTGCGAGTAGGGAGTGCACACA
18896704 -TGATGATGATAG-AGTGTGCGAGTAGGGAGTGCACA
1 GTGATGATG-TAGAAGTGTGCGAGTAGGGAGTGCACA
18896739 TATGGTGATG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 31 0.94
38 2 0.06
ACGTcount: A:0.27, C:0.10, G:0.40, T:0.23
Consensus pattern (38 bp):
GTGATGATGTAGAAGTGTGCGAGTAGGGAGTGCACACA
Found at i:18897257 original size:19 final size:19
Alignment explanation
Indices: 18897219--18897259 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
18897209 GGGGTTTTAG
*
18897219 TGAGAAACCCTCGGCCAGC
1 TGAGAAACCCTCGACCAGC
*
18897238 TGAGAAACCCTCGACTAGC
1 TGAGAAACCCTCGACCAGC
18897257 TGA
1 TGA
18897260 TAATTTGAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (19 bp):
TGAGAAACCCTCGACCAGC
Found at i:18903533 original size:18 final size:19
Alignment explanation
Indices: 18903506--18903541 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
18903496 TAGAACTCAA
18903506 GGAAGAGGAAGAAAAAGAT
1 GGAAGAGGAAGAAAAAGAT
*
18903525 GGAAG-GGAAGCAAAAGA
1 GGAAGAGGAAGAAAAAGA
18903542 AAAGAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.56, C:0.03, G:0.39, T:0.03
Consensus pattern (19 bp):
GGAAGAGGAAGAAAAAGAT
Found at i:18918418 original size:20 final size:20
Alignment explanation
Indices: 18918390--18918466 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 20
18918380 AATACTAGTG
*
18918390 ATGTATTGATACATTTGGGA
1 ATGTATCGATACATTTGGGA
* * *
18918410 ATATATTGATACTTTTGGGA
1 ATGTATCGATACATTTGGGA
* *
18918430 ATGTATCGATACTTTTGAGA
1 ATGTATCGATACATTTGGGA
*
18918450 ATGCATCGATACATTTG
1 ATGTATCGATACATTTG
18918467 CACGAATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTGGGA
Found at i:18920210 original size:21 final size:19
Alignment explanation
Indices: 18920184--18920222 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
18920174 AATTTAAAAC
18920184 AATAACATAAAATTTAACTAA
1 AATAAC-TAAAA-TTAACTAA
*
18920205 AATAACTTAAATTAACTA
1 AATAACTAAAATTAACTA
18920223 CTAAACATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAACTAAAATTAACTAA
Found at i:18923243 original size:8 final size:8
Alignment explanation
Indices: 18923212--18923242 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
18923202 GAGCTGATCA
18923212 ATATATAC
1 ATATATAC
18923220 ATATATAC
1 ATATATAC
*
18923228 ATATATAT
1 ATATATAC
18923236 ATATATA
1 ATATATA
18923243 TGTATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATATAC
Found at i:18923324 original size:25 final size:25
Alignment explanation
Indices: 18923290--18923342 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
18923280 AATAGATATC
18923290 TCCAATGGTAGGGGCATATAAGTCA
1 TCCAATGGTAGGGGCATATAAGTCA
18923315 TCCAATGGTAGGGGCATATAAGTCA
1 TCCAATGGTAGGGGCATATAAGTCA
18923340 TCC
1 TCC
18923343 TTACGATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (25 bp):
TCCAATGGTAGGGGCATATAAGTCA
Found at i:18927586 original size:21 final size:19
Alignment explanation
Indices: 18927560--18927600 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
18927550 AATTTAAAAC
18927560 AAAATAACATAAAATCTAACT
1 AAAATAAC-TAAAAT-TAACT
*
18927581 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
18927600 A
1 A
18927601 CTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 5 0.26
21 8 0.42
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:18928021 original size:8 final size:8
Alignment explanation
Indices: 18927985--18928019 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
18927975 AATTGGCTAC
18927985 ATACATAT
1 ATACATAT
*
18927993 ATACATAC
1 ATACATAT
18928001 ATACATAT
1 ATACATAT
*
18928009 ATATATAT
1 ATACATAT
18928017 ATA
1 ATA
18928020 TAGCTCTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (8 bp):
ATACATAT
Found at i:18929835 original size:80 final size:80
Alignment explanation
Indices: 18929719--18930107 Score: 471
Period size: 80 Copynumber: 4.9 Consensus size: 80
18929709 GATCATCATA
* * * * * * * *
18929719 CTTAGCCCACAATGTATGTGACTATCTCATCACATACATCTTAAGACATACATTTCATAATCTCA
1 CTTAGCCCATAGTGTATATGACTATTTCAACACATACATCTCATGGCATACATTTCATAATCTCA
*
18929784 TAAATCACTTACATA
66 TAAATCACTTACATG
* * *
18929799 CTTTGCCCATAGTGTAAATGACTATTTCAACACATACATCTCATGGCATACATTTCATAGTCTCA
1 CTTAGCCCATAGTGTATATGACTATTTCAACACATACATCTCATGGCATACATTTCATAATCTCA
18929864 TAAATCACTTACATG
66 TAAATCACTTACATG
* * * * * **
18929879 CTTAGCCTATAGTATATATGACTATTTCAACATATACATCTAATGGCATACATTT-GTAGCCTCA
1 CTTAGCCCATAGTGTATATGACTATTTCAACACATACATCTCATGGCATACATTTCATAATCTCA
18929943 TAAATCACTTACATG
66 TAAATCACTTACATG
* * * * * *
18929958 GTTAGCCCATATTGTATATGACTATCTCAACATATACATCTCATGGCATGCATTTCATAACCTCA
1 CTTAGCCCATAGTGTATATGACTATTTCAACACATACATCTCATGGCATACATTTCATAATCTCA
18930023 TAAATCACTTACATG
66 TAAATCACTTACATG
* * *
18930038 CTTAGCCCATAGTGTACATG-GTATGGTT-AACACATACATCTCATGGCATACATGTT-ACAATC
1 CTTAGCCCATAGTGTATATGACTAT--TTCAACACATACATCTCATGGCATACAT-TTCATAATC
18930100 TCATAAAT
63 TCATAAAT
18930108 GGAACTCATG
Statistics
Matches: 267, Mismatches: 38, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
79 73 0.27
80 191 0.72
81 3 0.01
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.33
Consensus pattern (80 bp):
CTTAGCCCATAGTGTATATGACTATTTCAACACATACATCTCATGGCATACATTTCATAATCTCA
TAAATCACTTACATG
Found at i:18929982 original size:159 final size:158
Alignment explanation
Indices: 18929749--18930090 Score: 445
Period size: 159 Copynumber: 2.1 Consensus size: 158
18929739 ACTATCTCAT
* * ** *
18929749 CACATACATCTTAA-GACATACATTTCATAATCTCATAAATCACTTACATACTTTGCCCATAGTG
1 CACATACATC-TAATGGCATACATTT-GTAGCCTCATAAATCACTTACATACTTAGCCCATAGTG
* **
18929813 TAAATGACTATTTCAACACATACATCTCATGGCATACATTTCATAGTCTCATAAATCACTTACAT
64 TAAATGACTATCTCAACACATACATCTCATGGCATACATTTCATAACCTCATAAATCACTTACAT
* *
18929878 GCTTAGCCTATAGTATATATGACTAT-TTCAA
129 GCTTAGCCCATAGTATACATG-CTATGTT-AA
* ** *
18929909 CATATACATCTAATGGCATACATTTGTAGCCTCATAAATCACTTACATGGTTAGCCCATATTGTA
1 CACATACATCTAATGGCATACATTTGTAGCCTCATAAATCACTTACATACTTAGCCCATAGTGTA
* * *
18929974 TATGACTATCTCAACATATACATCTCATGGCATGCATTTCATAACCTCATAAATCACTTACATGC
66 AATGACTATCTCAACACATACATCTCATGGCATACATTTCATAACCTCATAAATCACTTACATGC
* *
18930039 TTAGCCCATAGTGTACATGGTATGGTTAA
131 TTAGCCCATAGTATACATGCTAT-GTTAA
*
18930068 CACATACATCTCATGGCATACAT
1 CACATACATCTAATGGCATACAT
18930091 GTTACAATCT
Statistics
Matches: 158, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
158 3 0.02
159 134 0.85
160 21 0.13
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.33
Consensus pattern (158 bp):
CACATACATCTAATGGCATACATTTGTAGCCTCATAAATCACTTACATACTTAGCCCATAGTGTA
AATGACTATCTCAACACATACATCTCATGGCATACATTTCATAACCTCATAAATCACTTACATGC
TTAGCCCATAGTATACATGCTATGTTAA
Found at i:18931360 original size:54 final size:54
Alignment explanation
Indices: 18931270--18931539 Score: 364
Period size: 54 Copynumber: 5.0 Consensus size: 54
18931260 ATTCGTATAC
* *
18931270 CACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCTGGA
1 CACCCCATCTCACCCAGCTCATGTGCATTCCCCCACATCGTGCACATAGCCGGA
* * * *
18931324 CACCCCATCTCAACCATCGCATGTGCATTCCTCCACATCGTGCACATAGCCGGA
1 CACCCCATCTCACCCAGCTCATGTGCATTCCCCCACATCGTGCACATAGCCGGA
* *
18931378 CACCCCATCTCAACCAGCTCATGTGCA-TCCTCTCACATCGTGCACATAGCCGGA
1 CACCCCATCTCACCCAGCTCATGTGCATTCC-CCCACATCGTGCACATAGCCGGA
* *
18931432 CACCCCATCTCACCCAGCTCATTTGCA-TCCCCACACATCATGCACATAGCCGGA
1 CACCCCATCTCACCCAGCTCATGTGCATTCCCC-CACATCGTGCACATAGCCGGA
* * * * * *
18931486 CACCCTATCTTACCCAACCCATGTGCATCCCCCCACATTGTGCACATAGCCGGA
1 CACCCCATCTCACCCAGCTCATGTGCATTCCCCCACATCGTGCACATAGCCGGA
18931540 GTCATCGTGT
Statistics
Matches: 191, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
53 4 0.02
54 183 0.96
55 4 0.02
ACGTcount: A:0.24, C:0.43, G:0.14, T:0.20
Consensus pattern (54 bp):
CACCCCATCTCACCCAGCTCATGTGCATTCCCCCACATCGTGCACATAGCCGGA
Found at i:18931728 original size:2 final size:2
Alignment explanation
Indices: 18931721--18931765 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
18931711 TATAACATAG
18931721 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18931763 TA T
1 TA T
18931766 CAACATTATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18939780 original size:20 final size:19
Alignment explanation
Indices: 18939755--18939803 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 19
18939745 TCTTACATTT
*
18939755 TTTTCACTTGTTTCCTTGAA
1 TTTTCACTT-TTCCCTTGAA
18939775 TTTTCACACTTTTCCCTTGAA
1 TTTT--CACTTTTCCCTTGAA
18939796 TTTTCACT
1 TTTTCACT
18939804 CTAGGATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.15
20 4 0.15
21 13 0.50
22 5 0.19
ACGTcount: A:0.16, C:0.24, G:0.06, T:0.53
Consensus pattern (19 bp):
TTTTCACTTTTCCCTTGAA
Found at i:18939792 original size:21 final size:22
Alignment explanation
Indices: 18939759--18939802 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
18939749 ACATTTTTTT
*
18939759 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
18939781 CACTT-TTCCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
18939802 C
1 C
18939803 TCTAGGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.18, C:0.27, G:0.07, T:0.48
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:18940694 original size:35 final size:34
Alignment explanation
Indices: 18940654--18940765 Score: 113
Period size: 35 Copynumber: 3.3 Consensus size: 34
18940644 ATTCATTTCG
*
18940654 TGAAAAACCATTGTTGTAGGTTGTGGTTGAGCCTT
1 TGAAAAACCATTGTTG-AGGTTATGGTTGAGCCTT
* * * **
18940689 TGAAAAATCACT-TTG-GGTTTTGGTTGAGCCGG
1 TGAAAAACCATTGTTGAGGTTATGGTTGAGCCTT
*
18940721 TGAAAAACTATTG-TGAAAGGTTATGGTTGAGCCTT
1 TGAAAAACCATTGTTG--AGGTTATGGTTGAGCCTT
18940756 TGAAAAACCA
1 TGAAAAACCA
18940766 CTTTGTGTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
32 25 0.41
34 3 0.05
35 33 0.54
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.33
Consensus pattern (34 bp):
TGAAAAACCATTGTTGAGGTTATGGTTGAGCCTT
Found at i:18940715 original size:32 final size:32
Alignment explanation
Indices: 18940671--18940770 Score: 96
Period size: 32 Copynumber: 3.0 Consensus size: 32
18940661 CCATTGTTGT
*
18940671 AGGTTGTGGTTGAGCCTTTGAAAAATCACTTTG
1 AGGTTATGGTTGAGCCTTTGAAAAA-CACTTTG
* **
18940704 -GGTTTTGGTTGAGCCGGTGAAAAACTA-TTGTG
1 AGGTTATGGTTGAGCCTTTGAAAAAC-ACTT-TG
18940736 AAAGGTTATGGTTGAGCCTTTGAAAAACCACTTTG
1 --AGGTTATGGTTGAGCCTTTGAAAAA-CACTTTG
18940771 TGTTATAGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
31 3 0.06
32 24 0.44
35 24 0.44
36 3 0.06
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (32 bp):
AGGTTATGGTTGAGCCTTTGAAAAACACTTTG
Found at i:18940793 original size:67 final size:67
Alignment explanation
Indices: 18940671--18940822 Score: 189
Period size: 67 Copynumber: 2.3 Consensus size: 67
18940661 CCATTGTTGT
* * * * * * *
18940671 AGGTTGTGGTTGAGCCTTTGAAAAATCACTTTGGGTTTTGGTTGAGCCGGTGAAAAACTATTGTG
1 AGGTTATGGTTGAGCCTTTGAAAAACCACTTTGGGTTATAGTTAAGCCGGTGAAAAACTAGTGTA
18940736 AA
66 AA
* *
18940738 AGGTTATGGTTGAGCCTTTGAAAAACCACTTTGTGTTATAGTTAAGCTTGG-GAAAAACTAGTGT
1 AGGTTATGGTTGAGCCTTTGAAAAACCACTTTGGGTTATAGTTAAGC-CGGTGAAAAACTAGTGT
18940802 AAA
65 AAA
* *
18940805 AGGTTTTGGCTGAGCCTT
1 AGGTTATGGTTGAGCCTT
18940823 GTAAAAGCTA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
67 71 0.97
68 2 0.03
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.34
Consensus pattern (67 bp):
AGGTTATGGTTGAGCCTTTGAAAAACCACTTTGGGTTATAGTTAAGCCGGTGAAAAACTAGTGTA
AA
Found at i:18951458 original size:32 final size:33
Alignment explanation
Indices: 18951394--18951509 Score: 146
Period size: 35 Copynumber: 3.4 Consensus size: 33
18951384 ATTGATTTAG
*
18951394 TGAAAAACCATTATTGTAGGTTGTGGTTGAGCCTT
1 TGAAAAACCACT-TTG-AGGTTGTGGTTGAGCCTT
* *
18951429 TGAAAAACCACTTTG-GGTTTTGGTTGAGCCTG
1 TGAAAAACCACTTTGAGGTTGTGGTTGAGCCTT
18951461 TGAAAAACCA-TTGTGAAAGGTTGTGGTTGAGCCTT
1 TGAAAAACCACTT-TG--AGGTTGTGGTTGAGCCTT
18951496 TGAAAAACCACTTT
1 TGAAAAACCACTTT
18951510 ATCCTATAGT
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
31 2 0.03
32 27 0.38
34 3 0.04
35 37 0.52
36 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.34
Consensus pattern (33 bp):
TGAAAAACCACTTTGAGGTTGTGGTTGAGCCTT
Found at i:18951534 original size:67 final size:67
Alignment explanation
Indices: 18951393--18951562 Score: 155
Period size: 67 Copynumber: 2.5 Consensus size: 67
18951383 GATTGATTTA
* *** * ** * * *
18951393 GTGAAAAACCATTATTGTAGGTTGTGGTTGAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGC
1 GTGAAAAACCAGTATAAAAGGTTGTGGTTGAGCCTTTGAAAAACCACTTTAGCCTATAGTTAAGC
18951458 CT
66 CT
* * * *
18951460 GTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCACTTTATCCTATAGTTAAG-
1 GTGAAAAACCAGTATAAAAGGTTGTGGTTGAGCCTTTGAAAAACCACTTTAGCCTATAGTTAAGC
18951524 CT
66 CT
* * *
18951526 CG-GAAAAAACTAGTATAAAAGGTTTTGGCTGAGCCTT
1 -GTG-AAAAACCAGTATAAAAGGTTGTGGTTGAGCCTT
18951563 GTAAAAGCCA
Statistics
Matches: 84, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
66 3 0.04
67 81 0.96
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.32
Consensus pattern (67 bp):
GTGAAAAACCAGTATAAAAGGTTGTGGTTGAGCCTTTGAAAAACCACTTTAGCCTATAGTTAAGC
CT
Found at i:18953865 original size:21 final size:21
Alignment explanation
Indices: 18953839--18953879 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
18953829 GGACAGAAAG
*
18953839 TTTCTCCCTACAGCGAGATTT
1 TTTCTCCCTACAACGAGATTT
* *
18953860 TTTCTCGCTGCAACGAGATT
1 TTTCTCCCTACAACGAGATT
18953880 CAAGTGGCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.37
Consensus pattern (21 bp):
TTTCTCCCTACAACGAGATTT
Found at i:18956402 original size:54 final size:54
Alignment explanation
Indices: 18956338--18956442 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
18956328 ATGCGTATAC
* * *
18956338 CACCCTATCTCACCCAGCTCATATGCATCCCCCCATATCATGCACATAGCCAGA
1 CACCCCATCTCACCCAGCCCATATGCATCCCCCCACATCATGCACATAGCCAGA
* * *
18956392 CACCCCATCTCACCCAGCCCATGTGCATCCCCCCACATCGTGCATATAGCC
1 CACCCCATCTCACCCAGCCCATATGCATCCCCCCACATCATGCACATAGCC
18956443 GGAGTCATCG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.25, C:0.46, G:0.10, T:0.19
Consensus pattern (54 bp):
CACCCCATCTCACCCAGCCCATATGCATCCCCCCACATCATGCACATAGCCAGA
Found at i:18960587 original size:19 final size:19
Alignment explanation
Indices: 18960563--18960660 Score: 56
Period size: 19 Copynumber: 5.1 Consensus size: 19
18960553 TGCCCGTGTG
18960563 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
**** *
18960582 CACGATG-GCACTGATTGTG
1 CACGATGTGGGGGGA-TGTA
*
18960601 CACGATGT-GGGGGATGCA
1 CACGATGTGGGGGGATGTA
* * ** *
18960619 CATGATGGTGCCGGCTATGTG
1 CACGAT-GTG-GGGGGATGTA
18960640 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
18960659 CA
1 CA
18960661 TGAGCCGGGA
Statistics
Matches: 52, Mismatches: 22, Indels: 10
0.62 0.26 0.12
Matches are distributed among these distances:
18 10 0.19
19 29 0.56
20 3 0.06
21 10 0.19
ACGTcount: A:0.20, C:0.16, G:0.41, T:0.22
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:18967294 original size:22 final size:22
Alignment explanation
Indices: 18967239--18967304 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
18967229 TTCAGGTGGT
*
18967239 ATCAAAGCTTCT-AGTTTTAAAG
1 ATCAAAGCTTTTGA-TTTTAAAG
*
18967261 ATCAGAGCTTTTGATTTTAAAG
1 ATCAAAGCTTTTGATTTTAAAG
**
18967283 ATCAAAGCTTTTGGGTTTAAAG
1 ATCAAAGCTTTTGATTTTAAAG
18967305 TTGTTTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
22 37 0.97
23 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (22 bp):
ATCAAAGCTTTTGATTTTAAAG
Found at i:18974320 original size:20 final size:20
Alignment explanation
Indices: 18974297--18974337 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
18974287 AATGGTGTGA
18974297 ATGTGGTTTGAATGGGAATG
1 ATGTGGTTTGAATGGGAATG
*
18974317 ATGTGGTTTGGATGGGAATG
1 ATGTGGTTTGAATGGGAATG
18974337 A
1 A
18974338 AGAAAAGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.34
Consensus pattern (20 bp):
ATGTGGTTTGAATGGGAATG
Found at i:18974870 original size:34 final size:33
Alignment explanation
Indices: 18974827--18974924 Score: 117
Period size: 34 Copynumber: 2.9 Consensus size: 33
18974817 AGAAAAATTA
* *
18974827 TGCATAAAATTGGAGCTATTTGCTGTCAATTTG
1 TGCAGAAAATTGGAGCTATTTGCTGCCAATTTG
* *
18974860 TGCAGAAAAATTAGAGCTGTTTGCTGCCAATTTG
1 TGCAG-AAAATTGGAGCTATTTGCTGCCAATTTG
18974894 TGCAGAAAATTGGATAGCT-TTGTGCTGCCAA
1 TGCAGAAAATTGG--AGCTATT-TGCTGCCAA
18974925 AATTGAGGAG
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
33 11 0.20
34 32 0.57
35 13 0.23
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (33 bp):
TGCAGAAAATTGGAGCTATTTGCTGCCAATTTG
Found at i:18975092 original size:19 final size:22
Alignment explanation
Indices: 18975045--18975099 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
18975035 GGAAAGGAAT
*
18975045 AGAGGAAGCCATGGTGGTGAAG
1 AGAGGAAGCCACGGTGGTGAAG
18975067 AGAGGAAGCCACGGTGGTG-A-
1 AGAGGAAGCCACGGTGGTGAAG
18975087 AG-GGAAGCCACGG
1 AGAGGAAGCCACGG
18975100 GCTGGAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 11 0.34
20 2 0.06
21 1 0.03
22 18 0.56
ACGTcount: A:0.31, C:0.15, G:0.45, T:0.09
Consensus pattern (22 bp):
AGAGGAAGCCACGGTGGTGAAG
Found at i:18975129 original size:24 final size:25
Alignment explanation
Indices: 18975105--18975165 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
18975095 CACGGGCTGG
18975105 AAAGAAAAAAA-AGAAGAAACATGGA
1 AAAGAAAAAAAGA-AAGAAACATGGA
* **
18975130 AAAGAGAAAAAGAAAGAAA-AAAGA
1 AAAGAAAAAAAGAAAGAAACATGGA
18975154 AAAGAAATAAAA
1 AAAGAAA-AAAA
18975166 TGAATAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 9 0.30
25 20 0.67
26 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (25 bp):
AAAGAAAAAAAGAAAGAAACATGGA
Found at i:18975152 original size:11 final size:12
Alignment explanation
Indices: 18975105--18975160 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
18975095 CACGGGCTGG
18975105 AAAGAAAAAA-A
1 AAAGAAAAAAGA
**
18975116 AGAAGAAACATGGA
1 A-AAGAAA-AAAGA
18975130 AAAGAGAAAAAG-
1 AAAGA-AAAAAGA
18975142 AAAGAAAAAAGA
1 AAAGAAAAAAGA
18975154 AAAGAAA
1 AAAGAAA
18975161 TAAAATGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
11 7 0.19
12 18 0.50
13 7 0.19
14 4 0.11
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.02
Consensus pattern (12 bp):
AAAGAAAAAAGA
Found at i:18975165 original size:25 final size:24
Alignment explanation
Indices: 18975105--18975165 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
18975095 CACGGGCTGG
**
18975105 AAAGAAAAAAAAGAAGAAACATGGA
1 AAAG-AAAAAAAGAAGAAACAAAGA
*
18975130 AAAGAGAAAAAGAAAGAAA-AAAGA
1 AAAGAAAAAAAG-AAGAAACAAAGA
18975154 AAAGAAATAAAA
1 AAAGAAA-AAAA
18975166 TGAATAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 16 0.53
25 14 0.47
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (24 bp):
AAAGAAAAAAAGAAGAAACAAAGA
Found at i:18975207 original size:25 final size:25
Alignment explanation
Indices: 18975179--18975260 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
18975169 ATAAATAAAT
* *
18975179 AAATAAATGCGCATGACCTAATAGA
1 AAATAAATGGGCATGACCCAATAGA
*
18975204 AAATAAGTGGGCATGACCCAATAGA
1 AAATAAATGGGCATGACCCAATAGA
* *
18975229 AAATAAGTGGGCATGGCCCAATA-A
1 AAATAAATGGGCATGACCCAATAGA
18975253 GAAATAAA
1 -AAATAAA
18975261 AATAAATGGG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
24 1 0.02
25 50 0.98
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.17
Consensus pattern (25 bp):
AAATAAATGGGCATGACCCAATAGA
Found at i:18975271 original size:31 final size:33
Alignment explanation
Indices: 18975223--18975285 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 33
18975213 GGCATGACCC
* *
18975223 AATAGAAAATAAGTGGGCATGGCCC-AATAAGA
1 AATAGAAAATAAATGGGCATAGCCCAAATAAGA
*
18975255 AATA-AAAATAAATGGGCTTAGCCCAAATAAG
1 AATAGAAAATAAATGGGCATAGCCCAAATAAG
18975286 GAAAATGGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.17
Consensus pattern (33 bp):
AATAGAAAATAAATGGGCATAGCCCAAATAAGA
Found at i:18985366 original size:43 final size:43
Alignment explanation
Indices: 18985303--18985414 Score: 154
Period size: 43 Copynumber: 2.6 Consensus size: 43
18985293 TATTGACTAG
* *
18985303 GCTATGTGCGAGTAGGGAGTGCGCATAAGTCGAG-GATGACCCG
1 GCTATGTGCGAGTAGGGAGTGCGCATAACTCG-GTGATGACCCA
*
18985346 GTTATGTGCGAGTAGGGAGTGCGCATAACTCGGTGATGACCCA
1 GCTATGTGCGAGTAGGGAGTGCGCATAACTCGGTGATGACCCA
* * *
18985389 GCCATGTGCGAGTAAGGAGTGTGCAT
1 GCTATGTGCGAGTAGGGAGTGCGCAT
18985415 GAGCTAGTGA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 1 0.02
43 60 0.98
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACTCGGTGATGACCCA
Found at i:18987656 original size:41 final size:41
Alignment explanation
Indices: 18987560--18987725 Score: 209
Period size: 41 Copynumber: 4.1 Consensus size: 41
18987550 ATAGCCAGAG
* *
18987560 TCATCGTGTGCATCCCCTCACATTGTGCAC-AGCTAATA-C-
1 TCATCGTGTGCATCCCCCCACATCGTGCACAAGC-AATATCA
*
18987599 -CATCGTGTGCATCCCCCCACATCGTGCACAAGCAATATAA
1 TCATCGTGTGCATCCCCCCACATCGTGCACAAGCAATATCA
**
18987639 TCATTC-TGTGCATCCCCCCACATCGTGCACAAATAATGA-CA
1 TCA-TCGTGTGCATCCCCCCACATCGTGCACAAGCAAT-ATCA
*
18987680 TCATCGTGTGCATCCCCCCACATCATGCACAAGCAATATCA
1 TCATCGTGTGCATCCCCCCACATCGTGCACAAGCAATATCA
18987721 TCATC
1 TCATC
18987726 CACACTTCCA
Statistics
Matches: 110, Mismatches: 9, Indels: 14
0.83 0.07 0.11
Matches are distributed among these distances:
38 31 0.28
39 3 0.03
40 3 0.03
41 70 0.64
42 3 0.03
ACGTcount: A:0.28, C:0.35, G:0.13, T:0.24
Consensus pattern (41 bp):
TCATCGTGTGCATCCCCCCACATCGTGCACAAGCAATATCA
Found at i:18987703 original size:82 final size:79
Alignment explanation
Indices: 18987566--18987724 Score: 237
Period size: 82 Copynumber: 2.0 Consensus size: 79
18987556 AGAGTCATCG
* * ** *
18987566 TGTGCATCCCCTCACATTGTGCACAGCTAATACCATCGTGTGCATCCCCCCACATCGTGCACAAG
1 TGTGCATCCCCCCACATCGTGCACAAATAATACCATCGTGTGCATCCCCCCACATCATGCACAAG
18987631 CAATATAATCATTC
66 CAATATAATCATTC
18987645 TGTGCATCCCCCCACATCGTGCACAAATAATGACATCATCGTGTGCATCCCCCCACATCATGCAC
1 TGTGCATCCCCCCACATCGTGCACAAATAAT-AC--CATCGTGTGCATCCCCCCACATCATGCAC
*
18987710 AAGCAATATCATCAT
63 AAGCAATATAATCAT
18987725 CCACACTTCC
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
79 27 0.38
80 2 0.03
82 42 0.59
ACGTcount: A:0.28, C:0.35, G:0.13, T:0.24
Consensus pattern (79 bp):
TGTGCATCCCCCCACATCGTGCACAAATAATACCATCGTGTGCATCCCCCCACATCATGCACAAG
CAATATAATCATTC
Found at i:18988370 original size:24 final size:24
Alignment explanation
Indices: 18988343--18988391 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
18988333 GAGAAGGAAG
*
18988343 AAGCAAGA-AAAGAAAGGAAATGAA
1 AAGCAA-ACAAAGAAAGAAAATGAA
*
18988367 AAGCAAACAAGGAAAGAAAATGAA
1 AAGCAAACAAAGAAAGAAAATGAA
18988391 A
1 A
18988392 GAAAACTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.67, C:0.06, G:0.22, T:0.04
Consensus pattern (24 bp):
AAGCAAACAAAGAAAGAAAATGAA
Found at i:19010142 original size:47 final size:47
Alignment explanation
Indices: 19010008--19010280 Score: 379
Period size: 47 Copynumber: 5.8 Consensus size: 47
19009998 TTTGTCATAC
* * *
19010008 AATTTTACTTAACAAATAAGTAAAATAATTGCACCATGCATTTTATA
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATA
** *
19010055 AATTTTACCTTTTCAAATAAGTAAAATAATTACATTATGCATTTTATA
1 AATTTTACC-TAACAAATAAGTAAAATAATTACATCATGCATTTTATA
* **
19010103 AAATTTACCTAACAAATAAGTAAAATAAAAACATCATGCATTTTATA
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATA
* *
19010150 AATTTTACCTAAAAAATAAGTAAAATAAATACATCATGCATTTTATA
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATA
* * *
19010197 AATTTTACCTAACAAATAAGAAAAATAATTATATCATGTATTTTTATA
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCA-TTTTATA
19010245 AATTTTACCTAACAAATAA-TAAAAT-ATTACAATCAT
1 AATTTTACCTAACAAATAAGTAAAATAATTAC-ATCAT
19010281 ACAAAATATA
Statistics
Matches: 201, Mismatches: 22, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
46 4 0.02
47 130 0.65
48 67 0.33
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.36
Consensus pattern (47 bp):
AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATA
Found at i:19010250 original size:95 final size:94
Alignment explanation
Indices: 19010008--19010270 Score: 375
Period size: 95 Copynumber: 2.8 Consensus size: 94
19009998 TTTGTCATAC
* * * **
19010008 AATTTTACTTAACAAATAAGTAAAATAATTGCACCATGCATTTTATAAATTTTACCTTTTCAAAT
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATAAATTTTACC-TAACAAAT
* *
19010073 AAGTAAAATAATTACATTATGCATTTTATA
65 AAGTAAAATAAATACATCATGCATTTTATA
* ** *
19010103 AAATTTACCTAACAAATAAGTAAAATAAAAACATCATGCATTTTATAAATTTTACCTAAAAAATA
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATAAATTTTACCTAACAAATA
19010168 AGTAAAATAAATACATCATGCATTTTATA
66 AGTAAAATAAATACATCATGCATTTTATA
* * *
19010197 AATTTTACCTAACAAATAAGAAAAATAATTATATCATGTATTTTTATAAATTTTACCTAACAAAT
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCA-TTTTATAAATTTTACCTAACAAAT
19010262 AA-TAAAATA
65 AAGTAAAATA
19010271 TTACAATCAT
Statistics
Matches: 149, Mismatches: 18, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
94 74 0.50
95 75 0.50
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (94 bp):
AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATAAATTTTACCTAACAAATA
AGTAAAATAAATACATCATGCATTTTATA
Found at i:19010486 original size:47 final size:47
Alignment explanation
Indices: 19010435--19010663 Score: 345
Period size: 47 Copynumber: 4.9 Consensus size: 47
19010425 TTAATTAACN
*
19010435 TTTACCTAACAAATAAGTAAAATAAAAACATCATGCATTTTATAAAT
1 TTTACCTAACAAATAAGTAAAATAAATACATCATGCATTTTATAAAT
* *
19010482 TTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATAAGT
1 TTTACCTAACAAATAAGTAAAATAAATACATCATGCATTTTATAAAT
* ** * * *
19010529 TTTGCCTTTTCAAATAAGTAAAATAATTACATTATGCATTTTATAAAA
1 TTTACC-TAACAAATAAGTAAAATAAATACATCATGCATTTTATAAAT
19010577 TTTACCTAACAAATAAGTAAAATAAATACATCATGCATTTTATAAAT
1 TTTACCTAACAAATAAGTAAAATAAATACATCATGCATTTTATAAAT
*
19010624 TTTACCTAACAAATAAGTAAAATAATTACAT-A-GCATTTTA
1 TTTACCTAACAAATAAGTAAAATAAATACATCATGCATTTTA
19010664 CTACATATGT
Statistics
Matches: 165, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
45 8 0.05
46 1 0.01
47 115 0.70
48 41 0.25
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (47 bp):
TTTACCTAACAAATAAGTAAAATAAATACATCATGCATTTTATAAAT
Found at i:19010607 original size:95 final size:94
Alignment explanation
Indices: 19010435--19010663 Score: 354
Period size: 95 Copynumber: 2.4 Consensus size: 94
19010425 TTAATTAACN
** * *
19010435 TTTACCTAACAAATAAGTAAAATAAAAACATCATGCATTTTATAAATTTTACCTAACAAATAAGT
1 TTTACCTAACAAATAAGTAAAATAATTACATTATGCATTTTATAAAATTTACCTAACAAATAAGT
* *
19010500 AAAATAATTACATCATGCATTTTATAAGT
66 AAAATAAATACATCATGCATTTTATAAAT
* **
19010529 TTTGCCTTTTCAAATAAGTAAAATAATTACATTATGCATTTTATAAAATTTACCTAACAAATAAG
1 TTTACC-TAACAAATAAGTAAAATAATTACATTATGCATTTTATAAAATTTACCTAACAAATAAG
19010594 TAAAATAAATACATCATGCATTTTATAAAT
65 TAAAATAAATACATCATGCATTTTATAAAT
19010624 TTTACCTAACAAATAAGTAAAATAATTACA-TA-GCATTTTA
1 TTTACCTAACAAATAAGTAAAATAATTACATTATGCATTTTA
19010664 CTACATATGT
Statistics
Matches: 122, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
92 8 0.07
93 2 0.02
94 27 0.22
95 85 0.70
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (94 bp):
TTTACCTAACAAATAAGTAAAATAATTACATTATGCATTTTATAAAATTTACCTAACAAATAAGT
AAAATAAATACATCATGCATTTTATAAAT
Found at i:19011654 original size:15 final size:15
Alignment explanation
Indices: 19011634--19011702 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
19011624 ATAGGAAATT
19011634 TTAAATTTAAACAAA
1 TTAAATTTAAACAAA
19011649 TTAAATTTAAA-AAA
1 TTAAATTTAAACAAA
*** *
19011663 -TAAA--TAATTTTTAT
1 TTAAATTTAA--ACAAA
19011677 TTAAATTTAAACAAA
1 TTAAATTTAAACAAA
19011692 TTAAATTTAAA
1 TTAAATTTAAA
19011703 TTTATCCTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
11 3 0.07
13 4 0.10
14 4 0.10
15 27 0.66
17 3 0.07
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAATTTAAACAAA
Found at i:19011659 original size:21 final size:21
Alignment explanation
Indices: 19011633--19011706 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
19011623 GATAGGAAAT
19011633 TTTAAATTTAAACAAATTAAA
1 TTTAAATTTAAACAAATTAAA
** * * **
19011654 TTTAAAAAATAAATAATTTTTA
1 TTT-AAATTTAAACAAATTAAA
19011676 TTTAAATTTAAACAAATTAAA
1 TTTAAATTTAAACAAATTAAA
19011697 TTTAAATTTA
1 TTTAAATTTA
19011707 TCCTATCTCA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
21 25 0.62
22 15 0.38
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTAAATTTAAACAAATTAAA
Found at i:19012645 original size:39 final size:39
Alignment explanation
Indices: 19012559--19012634 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
19012549 CCAAGCTTTC
*
19012559 AAAATTTATTTTTGTTTTTAGTTATTTTTATTTAATTGT
1 AAAATTTATTTTTGTTTTTAGCTATTTTTATTTAATTGT
19012598 AAAATTTATTTTTGTTTTTAGCTATTTTTATTTAATT
1 AAAATTTATTTTTGTTTTTAGCTATTTTTATTTAATT
19012635 TATATCTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.26, C:0.01, G:0.07, T:0.66
Consensus pattern (39 bp):
AAAATTTATTTTTGTTTTTAGCTATTTTTATTTAATTGT
Found at i:19020094 original size:21 final size:22
Alignment explanation
Indices: 19020061--19020101 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
19020051 AGTCTTCACC
*
19020061 AGAACTGATTCTCGCTGCAGTA
1 AGAACTGAATCTCGCTGCAGTA
19020083 AGAA-TGAATCTCGCTGCAG
1 AGAACTGAATCTCGCTGCAG
19020102 CGAGATAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (22 bp):
AGAACTGAATCTCGCTGCAGTA
Found at i:19022071 original size:34 final size:34
Alignment explanation
Indices: 19022033--19022100 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
19022023 AAAGGATCAA
19022033 GCATAAACTTTACAAACCACTACTTTTCATGGAT
1 GCATAAACTTTACAAACCACTACTTTTCATGGAT
* *
19022067 GCATAACCTTTACAAACCATTACTTTTCATGGAT
1 GCATAAACTTTACAAACCACTACTTTTCATGGAT
19022101 TAAGCATAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.34
Consensus pattern (34 bp):
GCATAAACTTTACAAACCACTACTTTTCATGGAT
Found at i:19022121 original size:29 final size:28
Alignment explanation
Indices: 19022087--19022172 Score: 82
Period size: 30 Copynumber: 3.0 Consensus size: 28
19022077 TACAAACCAT
*
19022087 TACTTTTCATGGATTAAGCATAACCTTAC
1 TACTTTTCAAGGATTAAGCATAACCTT-C
* * *
19022116 TACTTTTTAAAGGCTTAAGCATAACCCTTT
1 TAC-TTTTCAAGGATTAAGCATAA-CCTTC
* * *
19022146 TACCTTTCAAAGATCAAGCATAACCTT
1 TACTTTTCAAGGATTAAGCATAACCTT
19022173 GACAACATTG
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
28 4 0.09
29 18 0.39
30 20 0.43
31 4 0.09
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (28 bp):
TACTTTTCAAGGATTAAGCATAACCTTC
Found at i:19022136 original size:30 final size:30
Alignment explanation
Indices: 19022100--19022207 Score: 85
Period size: 30 Copynumber: 3.5 Consensus size: 30
19022090 TTTTCATGGA
19022100 TTAAGCATAACCTTACTACTTTTTAAAGGC
1 TTAAGCATAACCTTACTACTTTTTAAAGGC
* * * *
19022130 TTAAGCATAACCCTT-TTACCTTTCAAA-GA
1 TTAAGCATAA-CCTTACTACTTTTTAAAGGC
* * *
19022159 TCAAGCATAACCTTGACAACATTGCCTTTCAAGGC
1 TTAAGCATAACCTT-ACTAC-TT---TTTAAAGGC
19022194 TTAAGCATAACCTT
1 TTAAGCATAACCTT
19022208 TCTCTCTCTC
Statistics
Matches: 58, Mismatches: 12, Indels: 11
0.72 0.15 0.14
Matches are distributed among these distances:
28 4 0.07
29 10 0.17
30 21 0.36
31 5 0.09
34 4 0.07
35 14 0.24
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.32
Consensus pattern (30 bp):
TTAAGCATAACCTTACTACTTTTTAAAGGC
Found at i:19022985 original size:55 final size:55
Alignment explanation
Indices: 19022875--19022989 Score: 178
Period size: 55 Copynumber: 2.1 Consensus size: 55
19022865 TTTCTCTTTA
* * *
19022875 AAGCTTCTAGAATTGACTTGTTGTCTTCCAAGTATCGATTCTTGATCTATTCAGT
1 AAGCTTCTAGAATCGACATGTTGTCTTCCAAGTATCGATTCTTGATCTATCCAGT
* *
19022930 AAGCTTCTAGAATCGACATGTTGTCTTCCAAGTGTCGATTCTTGATCTGTCCAGT
1 AAGCTTCTAGAATCGACATGTTGTCTTCCAAGTATCGATTCTTGATCTATCCAGT
19022985 -AGCTT
1 AAGCTT
19022990 ATCTAAGTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 5 0.09
55 50 0.91
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (55 bp):
AAGCTTCTAGAATCGACATGTTGTCTTCCAAGTATCGATTCTTGATCTATCCAGT
Found at i:19028397 original size:36 final size:36
Alignment explanation
Indices: 19028301--19028400 Score: 146
Period size: 36 Copynumber: 2.8 Consensus size: 36
19028291 TGATATTGCT
* *
19028301 TGTGTGCGATGTGGGGGAGCACACAATGGCATTAGC
1 TGTGCGCGATGTGGGGGAGCACACGATGGCATTAGC
* * *
19028337 TATGCACGATGTGGGGGGGCACACGATGGCATTAGC
1 TGTGCGCGATGTGGGGGAGCACACGATGGCATTAGC
*
19028373 TGTGCGCGATGTGGGGGTGCACACGATG
1 TGTGCGCGATGTGGGGGAGCACACGATG
19028401 ACTCTGACTA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.20, C:0.18, G:0.41, T:0.21
Consensus pattern (36 bp):
TGTGCGCGATGTGGGGGAGCACACGATGGCATTAGC
Found at i:19033026 original size:43 final size:43
Alignment explanation
Indices: 19032938--19033060 Score: 131
Period size: 43 Copynumber: 2.9 Consensus size: 43
19032928 CACCATCCCA
* * ** *
19032938 TCATCACC-AGCTCATGCGCAGTCCCTACTCGCACATGGCTAGG
1 TCATCACCGA-CTTATGCGCACTCCCTACTCGCACATAACCAGG
** *
19032981 TCATCACCGGTTTATGCGCACTCCCTACTCGCACATAACCGGG
1 TCATCACCGACTTATGCGCACTCCCTACTCGCACATAACCAGG
* * *
19033024 TCATCATCGACTTATGCACATTCCCTACTCGCACATA
1 TCATCACCGACTTATGCGCACTCCCTACTCGCACATA
19033061 GCCGAGTCCA
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.23, C:0.37, G:0.16, T:0.24
Consensus pattern (43 bp):
TCATCACCGACTTATGCGCACTCCCTACTCGCACATAACCAGG
Found at i:19041226 original size:12 final size:12
Alignment explanation
Indices: 19041193--19041228 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
19041183 TTTTCAATCA
19041193 CAACTTCTTTTT
1 CAACTTCTTTTT
*
19041205 CAACTACTTTTT
1 CAACTTCTTTTT
*
19041217 CAATTTCTTTTT
1 CAACTTCTTTTT
19041229 TATCATAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.58
Consensus pattern (12 bp):
CAACTTCTTTTT
Found at i:19046419 original size:19 final size:19
Alignment explanation
Indices: 19046395--19046489 Score: 57
Period size: 19 Copynumber: 4.9 Consensus size: 19
19046385 TGCCCTTGTG
19046395 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
***** *
19046414 CACGATG-GCACTTATTGTG
1 CACGATGTGGGGGGA-TGTA
*
19046433 CACGATGTGGGGGGATGCA
1 CACGATGTGGGGGGATGTA
* ** *
19046452 CACGATGGTGCCGGTTATGTG
1 CACGAT-GTG-GGGGGATGTA
19046473 CACGATGTGGGGGGATG
1 CACGATGTGGGGGGATG
19046490 CACATGAGCC
Statistics
Matches: 51, Mismatches: 21, Indels: 8
0.64 0.26 0.10
Matches are distributed among these distances:
18 2 0.04
19 30 0.59
20 8 0.16
21 11 0.22
ACGTcount: A:0.19, C:0.16, G:0.42, T:0.23
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:19046432 original size:38 final size:40
Alignment explanation
Indices: 19046390--19046493 Score: 153
Period size: 38 Copynumber: 2.6 Consensus size: 40
19046380 GATAGTGCCC
*
19046390 TTGTGCACGATGTGGGGGGATGTACACGAT-G-GCAC-TTA
1 TTGTGCACGATGTGGGGGGATGCACACGATGGTGC-CGTTA
19046428 TTGTGCACGATGTGGGGGGATGCACACGATGGTGCCGGTTA
1 TTGTGCACGATGTGGGGGGATGCACACGATGGTGCC-GTTA
19046469 -TGTGCACGATGTGGGGGGATGCACA
1 TTGTGCACGATGTGGGGGGATGCACA
19046494 TGAGCCGGGT
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
38 29 0.48
39 2 0.03
40 27 0.44
41 3 0.05
ACGTcount: A:0.19, C:0.16, G:0.40, T:0.24
Consensus pattern (40 bp):
TTGTGCACGATGTGGGGGGATGCACACGATGGTGCCGTTA
Found at i:19063900 original size:2 final size:2
Alignment explanation
Indices: 19063893--19063943 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
19063883 AAATTCTCTA
19063893 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19063935 AT AT AT AT A
1 AT AT AT AT A
19063944 ATTTAANNNN
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19070143 original size:10 final size:10
Alignment explanation
Indices: 19070115--19070143 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
19070105 TAAATCCATT
19070115 TTTCATAAAA
1 TTTCATAAAA
19070125 TTT-ATAAAA
1 TTTCATAAAA
19070134 TTTCATAAAA
1 TTTCATAAAA
19070144 ACTACCTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
TTTCATAAAA
Found at i:19073657 original size:35 final size:34
Alignment explanation
Indices: 19073585--19073686 Score: 111
Period size: 35 Copynumber: 2.9 Consensus size: 34
19073575 TCTATAAGAA
*
19073585 CAAGCACAACCTTTGCAAATGCCTTTTCATAGGAG
1 CAAGCACAACCTTTACAAATGCCTTTTCA-AGGAG
* *
19073620 CAAGCACAACTTTTACAAATGCCTTTTTC-CGGCAG
1 CAAGCACAACCTTTACAAATGCC-TTTTCAAGG-AG
19073655 CAAGCACAATCC-TTACAAATAG-CTTTTCAAGG
1 CAAGCACAA-CCTTTACAAAT-GCCTTTTCAAGG
19073687 TTAAGCTAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
34 7 0.12
35 43 0.75
36 7 0.12
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (34 bp):
CAAGCACAACCTTTACAAATGCCTTTTCAAGGAG
Found at i:19075044 original size:7 final size:7
Alignment explanation
Indices: 19075032--19075056 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19075022 TTTTTGATAT
19075032 TGTGAGA
1 TGTGAGA
19075039 TGTGAGA
1 TGTGAGA
19075046 TGTGAGA
1 TGTGAGA
19075053 TGTG
1 TGTG
19075057 TATAAGGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (7 bp):
TGTGAGA
Found at i:19075207 original size:37 final size:37
Alignment explanation
Indices: 19075147--19075230 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
19075137 TGATGTTGGG
* *
19075147 TGATGATG-TTGAGTGTGCGAGTAGGGAGTGTACACA
1 TGATGATGATGGAGTGTGCGAGTAGGGAGTGCACACA
*
19075183 TGATGATGATGGAGTGTGTGAGTAGGGAGTGCACACA
1 TGATGATGATGGAGTGTGCGAGTAGGGAGTGCACACA
*
19075220 TGATGACGATG
1 TGATGATGATG
19075231 TATGTATATG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 8 0.19
37 35 0.81
ACGTcount: A:0.26, C:0.08, G:0.39, T:0.26
Consensus pattern (37 bp):
TGATGATGATGGAGTGTGCGAGTAGGGAGTGCACACA
Found at i:19082664 original size:7 final size:7
Alignment explanation
Indices: 19082652--19082676 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19082642 TTTTTGATAT
19082652 TGTGAGA
1 TGTGAGA
19082659 TGTGAGA
1 TGTGAGA
19082666 TGTGAGA
1 TGTGAGA
19082673 TGTG
1 TGTG
19082677 TATAAGGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (7 bp):
TGTGAGA
Found at i:19082826 original size:37 final size:36
Alignment explanation
Indices: 19082767--19082845 Score: 122
Period size: 37 Copynumber: 2.2 Consensus size: 36
19082757 TGATGTTGGG
* *
19082767 TGATGATGTTGAGTGTGCGAGTAGGGAGTGCACAGA
1 TGATGATGTGGAGTGTGCGAGTAGGGAGTGCACACA
*
19082803 TGATGATGATGGAGTGTGGGAGTAGGGAGTGCACACA
1 TGATGATG-TGGAGTGTGCGAGTAGGGAGTGCACACA
19082840 TGATGA
1 TGATGA
19082846 CAATGTATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 8 0.21
37 31 0.79
ACGTcount: A:0.27, C:0.08, G:0.42, T:0.24
Consensus pattern (36 bp):
TGATGATGTGGAGTGTGCGAGTAGGGAGTGCACACA
Found at i:19091308 original size:23 final size:22
Alignment explanation
Indices: 19091282--19091326 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
19091272 TTTTGATGAT
*
19091282 TTGATGAATAAAATATTATTTTA
1 TTGAT-AATAAAACATTATTTTA
**
19091305 TTGATTCTAAAACATTATTTTA
1 TTGATAATAAAACATTATTTTA
19091327 ATGAGTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (22 bp):
TTGATAATAAAACATTATTTTA
Found at i:19091969 original size:19 final size:22
Alignment explanation
Indices: 19091947--19091987 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 22
19091937 TGAAAGCAAA
19091947 AAAAAGG-AAGA-AAA-GAGAG
1 AAAAAGGAAAGAGAAAGGAGAG
19091966 -AAAAGGAAAGAGAAAGGAGAG
1 AAAAAGGAAAGAGAAAGGAGAG
19091987 A
1 A
19091988 GAAGAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 3 0.17
21 5 0.28
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (22 bp):
AAAAAGGAAAGAGAAAGGAGAG
Found at i:19091975 original size:23 final size:21
Alignment explanation
Indices: 19091944--19092003 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
19091934 TTTTGAAAGC
*
19091944 AAAAAAAAGGAAGAAAAGAGAG
1 AAAAGAAA-GAAGAAAAGAGAG
*
19091966 AAAAGGAAAG-AGAAAGGAGAG
1 AAAA-GAAAGAAGAAAAGAGAG
* *
19091987 AGAAGAAATAAGAAAAG
1 AAAAGAAAGAAGAAAAG
19092004 CTAGAAGGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 4 0.13
21 19 0.61
22 5 0.16
23 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (21 bp):
AAAAGAAAGAAGAAAAGAGAG
Found at i:19115247 original size:2 final size:2
Alignment explanation
Indices: 19115242--19115269 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19115232 TGTGTGTGTC
19115242 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19115270 CNTTCATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19115352 original size:116 final size:115
Alignment explanation
Indices: 19115152--19115384 Score: 450
Period size: 116 Copynumber: 2.0 Consensus size: 115
19115142 TTCACTCCTC
19115152 TATA-TTCATGAACTTGTCACATCATTAATATACGTCTCATATCAACCATCTATAGCTATTACGC
1 TATACTTCATGAACTTGTCACATCATTAATATACGTCTCATATCAACCATCTATAGCTATTACGC
19115216 ATCATATGTATGTGTGTGTGTGTGTCTATATATATATATATATATATATA
66 ATCATATGTATGTGTGTGTGTGTGTCTATATATATATATATATATATATA
19115266 TATACNTTCATGAACTTGTCACATCATTAATATACGTCTCATATCAACCATCTATAGCTATTACG
1 TATAC-TTCATGAACTTGTCACATCATTAATATACGTCTCATATCAACCATCTATAGCTATTACG
19115331 CATCATATGTATGTGTGTGTGTGTGTCTATATATATATATATATATATATA
65 CATCATATGTATGTGTGTGTGTGTGTCTATATATATATATATATATATATA
19115382 TAT
1 TAT
19115385 CAACTCTGAA
Statistics
Matches: 117, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
114 4 0.03
116 113 0.97
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.41
Consensus pattern (115 bp):
TATACTTCATGAACTTGTCACATCATTAATATACGTCTCATATCAACCATCTATAGCTATTACGC
ATCATATGTATGTGTGTGTGTGTGTCTATATATATATATATATATATATA
Found at i:19115363 original size:2 final size:2
Alignment explanation
Indices: 19115358--19115384 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19115348 TGTGTGTGTC
19115358 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19115385 CAACTCTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19117066 original size:24 final size:24
Alignment explanation
Indices: 19117005--19117056 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
19116995 GTATAGTATC
* *
19117005 AATTCCGTTAAAAATTTTCAACGA
1 AATTCCATTAGAAATTTTCAACGA
*
19117029 AATTCCATTAGAAATTTTTAACGA
1 AATTCCATTAGAAATTTTCAACGA
19117053 AATT
1 AATT
19117057 TTCGTTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (24 bp):
AATTCCATTAGAAATTTTCAACGA
Found at i:19120937 original size:26 final size:28
Alignment explanation
Indices: 19120877--19120945 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 28
19120867 ATATACATAA
*
19120877 AATATTATGTAT-AATGTATATGATTAAT
1 AATA-TATGTATAAATGAATATGATTAAT
19120905 -ATAATATGTATAAAT-AATAT-ATTAAT
1 AAT-ATATGTATAAATGAATATGATTAAT
19120931 AATATATGTATAAAT
1 AATATATGTATAAAT
19120946 TAATTATACA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
26 18 0.49
27 15 0.41
28 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.43
Consensus pattern (28 bp):
AATATATGTATAAATGAATATGATTAAT
Found at i:19120949 original size:27 final size:28
Alignment explanation
Indices: 19120877--19120949 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 28
19120867 ATATACATAA
19120877 AATATTATGTAT-AATGT-ATATGATTAAT
1 AATA-TATGTATAAAT-TAATATGATTAAT
19120905 -ATAATATGTATAAA-TAATAT-ATTAAT
1 AAT-ATATGTATAAATTAATATGATTAAT
19120931 AATATATGTATAAATTAAT
1 AATATATGTATAAATTAAT
19120950 TATACATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
26 18 0.45
27 19 0.47
28 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (28 bp):
AATATATGTATAAATTAATATGATTAAT
Found at i:19121181 original size:14 final size:15
Alignment explanation
Indices: 19121154--19121183 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
19121144 ATATATTAAT
19121154 TTTATATAGTATATA
1 TTTATATAGTATATA
19121169 TTTATAT-GTATATA
1 TTTATATAGTATATA
19121183 T
1 T
19121184 ATAGTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTATATAGTATATA
Found at i:19121823 original size:22 final size:22
Alignment explanation
Indices: 19121798--19121839 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19121788 TAGTATGTAC
*
19121798 TTAAAATATTATTAGTTTTTGT
1 TTAAAATATTATTAGATTTTGT
*
19121820 TTAATATATTATTAGATTTT
1 TTAAAATATTATTAGATTTT
19121840 ATCATCTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (22 bp):
TTAAAATATTATTAGATTTTGT
Found at i:19127820 original size:2 final size:2
Alignment explanation
Indices: 19127815--19127857 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
19127805 TATATATATA
*
19127815 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19127857 T
1 T
19127858 ATGTATATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.02, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:19134093 original size:42 final size:42
Alignment explanation
Indices: 19134047--19134134 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
19134037 CACATGGCTA
* *
19134047 GGTCAAAATCGGCTTATGCATACTCCTACTCGCACATAGTCG
1 GGTCAAAATCGACTTATGCACACTCCTACTCGCACATAGTCG
** * *
19134089 GGTCATCATCGACTTATGCGCACTCCTACTCGCACATAGTTG
1 GGTCAAAATCGACTTATGCACACTCCTACTCGCACATAGTCG
19134131 GGTC
1 GGTC
19134135 CACATCAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (42 bp):
GGTCAAAATCGACTTATGCACACTCCTACTCGCACATAGTCG
Found at i:19135944 original size:16 final size:16
Alignment explanation
Indices: 19135904--19135945 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
19135894 TGTAGACAAT
*
19135904 TAATT-AAAACTAAAT
1 TAATTAAAAACTAAAC
*
19135919 TCAATGAAAAACTAAAC
1 T-AATTAAAAACTAAAC
19135936 TAATTAAAAA
1 TAATTAAAAA
19135946 AAACTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 1 0.05
16 11 0.50
17 10 0.45
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (16 bp):
TAATTAAAAACTAAAC
Found at i:19142562 original size:19 final size:19
Alignment explanation
Indices: 19142538--19142618 Score: 83
Period size: 19 Copynumber: 4.2 Consensus size: 19
19142528 ATAGTGCCTG
19142538 TGTGCACGATGTGGGGGGA
1 TGTGCACGATGTGGGGGGA
*
19142557 TGTGCACGATGTGGGGGAA
1 TGTGCACGATGTGGGGGGA
** **
19142576 TGCACACGATG-GCGCCGGCTA
1 TGTGCACGATGTG-G--GGGGA
19142597 TGTGCACGATGTGGGGGGA
1 TGTGCACGATGTGGGGGGA
19142616 TGT
1 TGT
19142619 ACATGAGCCA
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
18 1 0.02
19 34 0.69
21 13 0.27
22 1 0.02
ACGTcount: A:0.17, C:0.16, G:0.46, T:0.21
Consensus pattern (19 bp):
TGTGCACGATGTGGGGGGA
Found at i:19143395 original size:20 final size:21
Alignment explanation
Indices: 19143354--19143398 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
19143344 CCTAGGTGGA
*
19143354 AAAATTCAAAGGAAAAGTGTG
1 AAAATTCAAAGGAAAAGAGTG
19143375 AAAATTC-AAGGAAACA-AGTG
1 AAAATTCAAAGGAAA-AGAGTG
19143395 AAAA
1 AAAA
19143399 AAAGGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.58, C:0.07, G:0.20, T:0.16
Consensus pattern (21 bp):
AAAATTCAAAGGAAAAGAGTG
Found at i:19143399 original size:21 final size:20
Alignment explanation
Indices: 19143352--19143399 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
19143342 ACCCTAGGTG
19143352 GAAAAATTCAAAGGAAAAGT
1 GAAAAATTCAAAGGAAAAGT
*
19143372 GTGAAAATTC-AAGGAAACAAGT
1 G-AAAAATTCAAAGG-AA-AAGT
19143394 GAAAAA
1 GAAAAA
19143400 AAGGTAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.58, C:0.06, G:0.21, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAAGGAAAAGT
Done.