Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 61 of 206
Found at i:17269377 original size:2 final size:2
Alignment explanation
Indices: 17269370--17269401 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17269360 GTGCATTTTG
17269370 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
17269402 GTCATTATCA
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:17280428 original size:368 final size:367
Alignment explanation
Indices: 17279113--17280587 Score: 2382
Period size: 367 Copynumber: 4.0 Consensus size: 367
17279103 AAAAAGAAAA
17279113 TAAAATTTATTAAAATAAAAAAGGCAAAATTTTCTAAAATTTCATATTTCAACAAGAATGTAAAA
1 TAAAATTTATTAAAATAAAAAAGGCAAAATTTTCTAAAATTTCATATTTCAACAAGAATGTAAAA
* * *
17279178 TTTCTTAAGAGATACTATTGATATTAATTCCTATATTTTGAAATATTGATAGAATGTGAAATTAC
66 TTTCTTAAGAGATACTATTGATATTAATTCCTATATTCTAAAATATTGACAGAATGTGAAATTAC
* * *
17279243 CATCTCATCTAGAGAAACGATTGTATGAAACTGTGGTTCCACGTCATCTTTATCCCTTTTCCAAT
131 CATCTCATCTAGAGAAATGATTGTATAAAACTGTGATTCCACGTCATCTTTATCCC-TTTCCAAT
* * * *
17279308 GGGAGAATGACAAATTAGATTTTTTTTTTCCTGATTTTTAGCTTTTTCTTTTTGAAAAAATTCAA
195 GGGAGAATGACAAATCAGA--TTTTTTCTCCTGATTTTTAGCTTTTTCCTCTTGAAAAAATTCAA
* *
17279373 ATCCAACTAAAAATACTAAAAA-TATGGAGAGAAAAAATATGATTTTTCATTCTCCCATTAGAAA
258 ATCCAACTAAAAATACTAAAAATTA-GGAGAGAAAAAATATGATTTGTCATTCTCCTATTAGAAA
*
17279437 GAGATAAAAATGACGTGAAATCACAATTTCATATTATCTTTTCTCC
322 GAGATAAAAATGACGTGAAATCACAATTTCATATCATCTTTTCTCC
* *
17279483 TAAAATTTATTATAATAGAATAAGGCAAAATTTTCTAAAATTTCATATTTCAACAAGAATGTAAA
1 TAAAATTTATTAAAATA-AAAAAGGCAAAATTTTCTAAAATTTCATATTTCAACAAGAATGTAAA
*
17279548 ATTTCTTAAGAGATACTATTGATATTAATTCTTATATTCTAAAATATTGACAGAATGTGAAATTA
65 ATTTCTTAAGAGATACTATTGATATTAATTCCTATATTCTAAAATATTGACAGAATGTGAAATTA
* * * * *
17279613 CCATCTCATCTAGAGAAATAATTGTATAAAATTGTGATTCCACGTTATTTTTATCTCTTTCCAAT
130 CCATCTCATCTAGAGAAATGATTGTATAAAACTGTGATTCCACGTCATCTTTATCCCTTTCCAAT
17279678 GGGAGAATGACAAATCAGATTTTTTCTCCTGATTTTTAGCTTTTTCCTCTTGAAAAAATTCAAAT
195 GGGAGAATGACAAATCAGATTTTTTCTCCTGATTTTTAGCTTTTTCCTCTTGAAAAAATTCAAAT
* * * *
17279743 CCAACTAAAAATACTAAAAATCAGGA-AAATAAAAATCTGATTTGTCATTCTCTTATTAGAAAGA
260 CCAACTAAAAATACTAAAAATTAGGAGAGA-AAAAATATGATTTGTCATTCTCCTATTAGAAAGA
*
17279807 GATAAAAATGACGTGAAATTACAATTTCATATCATCTTTTCTCC
324 GATAAAAATGACGTGAAATCACAATTTCATATCATCTTTTCTCC
* * *
17279851 TAAATTTTATTAAAATAAAAAAGGCAAAATTTTCTAAAATTTCATATTTTAACAAGAATGTAAAT
1 TAAAATTTATTAAAATAAAAAAGGCAAAATTTTCTAAAATTTCATATTTCAACAAGAATGTAAAA
* *
17279916 TTTCTTAAGAGATAATATTGATATTAATTCCTATATTCTGAAATATTGACAGAATGTGAAATTAC
66 TTTCTTAAGAGATACTATTGATATTAATTCCTATATTCTAAAATATTGACAGAATGTGAAATTAC
17279981 CATCTCATCTAGAGAAATGATTGTATAAAACTGTGATTCCACGTCATCTTTATCCCTTTCCAATG
131 CATCTCATCTAGAGAAATGATTGTATAAAACTGTGATTCCACGTCATCTTTATCCCTTTCCAATG
* *
17280046 GGAGAATGACAAATCAGATTTTTTTTCCTGATTTTTAGCTTTTTCTTCTTGAAAAAATTCAAATC
196 GGAGAATGACAAATCAGATTTTTTCTCCTGATTTTTAGCTTTTTCCTCTTGAAAAAATTCAAATC
* *
17280111 CAACTAAAACTACTAAAAATTAGGAGAGAAAAAATATGATTTGTCATTCTCCAATTAGAAAGAGA
261 CAACTAAAAATACTAAAAATTAGGAGAGAAAAAATATGATTTGTCATTCTCCTATTAGAAAGAGA
*
17280176 TAAAAATGACGTGAAATCACAATTTCATATTATCTTTTCTCC
326 TAAAAATGACGTGAAATCACAATTTCATATCATCTTTTCTCC
* * *
17280218 TAAAATTTATTATAATAGAATAAGGCAATATTTTCTAAAATTTCATATTTCAACAAGAATGTAAA
1 TAAAATTTATTAAAATA-AAAAAGGCAAAATTTTCTAAAATTTCATATTTCAACAAGAATGTAAA
*
17280283 ATTTCTTAAGAGATACTATTGATATTAATTCTTATATTCTAAAATATTGACAGAATGTGAAATTA
65 ATTTCTTAAGAGATACTATTGATATTAATTCCTATATTCTAAAATATTGACAGAATGTGAAATTA
* * * *
17280348 CCATCTCATCTAGAGAAATGATTGTATAAAATTGTGGTTCCACGTCATTTTTATCTCTTTCCAAT
130 CCATCTCATCTAGAGAAATGATTGTATAAAACTGTGATTCCACGTCATCTTTATCCCTTTCCAAT
* *
17280413 GGGAGAATGACAAATCAAATTTTTTCTCCTGATTTTTAGC-TTTTCCTCTTAAAAAAATTCAAAT
195 GGGAGAATGACAAATCAGATTTTTTCTCCTGATTTTTAGCTTTTTCCTCTTGAAAAAATTCAAAT
* * * *
17280477 CCAACTAAAAATACTAAAAATTAGAAGA-AAAAAATCTGATTTATCATTCTCCTATTAAAAAGAG
260 CCAACTAAAAATACTAAAAATTAGGAGAGAAAAAATATGATTTGTCATTCTCCTATTAGAAAGAG
* * *
17280541 ATAAAAATTATGTAAAATCACAATTTCATATCATCTTTTCTCC
325 ATAAAAATGACGTGAAATCACAATTTCATATCATCTTTTCTCC
17280584 TAAA
1 TAAA
17280588 CACGAGTTAT
Statistics
Matches: 1024, Mismatches: 76, Indels: 14
0.92 0.07 0.01
Matches are distributed among these distances:
366 75 0.07
367 391 0.38
368 359 0.35
369 1 0.00
370 42 0.04
371 156 0.15
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37
Consensus pattern (367 bp):
TAAAATTTATTAAAATAAAAAAGGCAAAATTTTCTAAAATTTCATATTTCAACAAGAATGTAAAA
TTTCTTAAGAGATACTATTGATATTAATTCCTATATTCTAAAATATTGACAGAATGTGAAATTAC
CATCTCATCTAGAGAAATGATTGTATAAAACTGTGATTCCACGTCATCTTTATCCCTTTCCAATG
GGAGAATGACAAATCAGATTTTTTCTCCTGATTTTTAGCTTTTTCCTCTTGAAAAAATTCAAATC
CAACTAAAAATACTAAAAATTAGGAGAGAAAAAATATGATTTGTCATTCTCCTATTAGAAAGAGA
TAAAAATGACGTGAAATCACAATTTCATATCATCTTTTCTCC
Found at i:17286797 original size:31 final size:31
Alignment explanation
Indices: 17286751--17286820 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
17286741 TTGTAATTTG
* *
17286751 GTCACTAAATTATTC-AAAAATTTCCATTTAA
1 GTCATTAAACTATTCAAAAAATTT-CATTTAA
* *
17286782 GTTATTAAACTATTCAAAAAATTTTATTTAA
1 GTCATTAAACTATTCAAAAAATTTCATTTAA
17286813 GTCATTAA
1 GTCATTAA
17286821 GTTATTAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 25 0.76
32 8 0.24
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.41
Consensus pattern (31 bp):
GTCATTAAACTATTCAAAAAATTTCATTTAA
Found at i:17291323 original size:5 final size:5
Alignment explanation
Indices: 17291315--17291339 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
17291305 ATTTAATTAA
17291315 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
17291340 TTAAGTAATT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:17300195 original size:42 final size:42
Alignment explanation
Indices: 17300149--17300239 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
17300139 TAACCCTTCC
* * * *
17300149 GGGTTTTAGTTCAACTCTTTTGAGC-TCCAGTTTAACCCTAAT
1 GGGTTTCAGTTCAACTCCTATGAGCTTCC-GTTCAACCCTAAT
* * *
17300191 GGGTTTCCGTTCAGCTCCTATGAGCTTCCGTTCAACCCTTAT
1 GGGTTTCAGTTCAACTCCTATGAGCTTCCGTTCAACCCTAAT
17300233 GGGTTTC
1 GGGTTTC
17300240 CATTTAGTAC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 38 0.93
43 3 0.07
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.38
Consensus pattern (42 bp):
GGGTTTCAGTTCAACTCCTATGAGCTTCCGTTCAACCCTAAT
Found at i:17300233 original size:21 final size:21
Alignment explanation
Indices: 17300157--17300233 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
17300147 CCGGGTTTTA
* *
17300157 GTTCAACTCTTTTGAGC-TCC
1 GTTCAACCCTTATGAGCTTCC
* * * *
17300177 AGTTTAACCCTAATGGGTTTCC
1 -GTTCAACCCTTATGAGCTTCC
*
17300199 GTTCAGCTCC-TATGAGCTTCC
1 GTTCAAC-CCTTATGAGCTTCC
17300220 GTTCAACCCTTATG
1 GTTCAACCCTTATG
17300234 GGTTTCCATT
Statistics
Matches: 41, Mismatches: 12, Indels: 6
0.69 0.20 0.10
Matches are distributed among these distances:
20 2 0.05
21 34 0.83
22 5 0.12
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (21 bp):
GTTCAACCCTTATGAGCTTCC
Found at i:17300240 original size:21 final size:21
Alignment explanation
Indices: 17300182--17300240 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
17300172 GCTCCAGTTT
*
17300182 AACCCTAATGGGTTTCCGTTC
1 AACCCTTATGGGTTTCCGTTC
* * *
17300203 AGCTCC-TATGAGCTTCCGTTC
1 AAC-CCTTATGGGTTTCCGTTC
17300224 AACCCTTATGGGTTTCC
1 AACCCTTATGGGTTTCC
17300241 ATTTAGTACT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.17, C:0.31, G:0.19, T:0.34
Consensus pattern (21 bp):
AACCCTTATGGGTTTCCGTTC
Found at i:17300260 original size:42 final size:42
Alignment explanation
Indices: 17300182--17300269 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
17300172 GCTCCAGTTT
* *
17300182 AACCCTAATGGGTTTCCGTTCAGCTCCTATGAGCTTCCGTTC
1 AACCCTAATGGGTTTCCATTCAGCTCCTATGAGCTTCCGTGC
* * * * *
17300224 AACCCTTATGGGTTTCCATTTAG-TACTTATGTGCTTCTGTGC
1 AACCCTAATGGGTTTCCATTCAGCT-CCTATGAGCTTCCGTGC
17300266 AACC
1 AACC
17300270 TTCGGGATTC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.03
42 37 0.97
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (42 bp):
AACCCTAATGGGTTTCCATTCAGCTCCTATGAGCTTCCGTGC
Found at i:17303476 original size:17 final size:17
Alignment explanation
Indices: 17303454--17303493 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
17303444 AGCAATTAGT
17303454 TCAAAAAGT-TTTTTCTA
1 TCAAAAAGTATTTTT-TA
17303471 TCAAAAAGTATTTTTTA
1 TCAAAAAGTATTTTTTA
17303488 T-AAAAA
1 TCAAAAA
17303494 ATTCAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 12 0.55
18 5 0.23
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (17 bp):
TCAAAAAGTATTTTTTA
Found at i:17307947 original size:18 final size:20
Alignment explanation
Indices: 17307916--17307952 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
17307906 ACATACACAT
*
17307916 AGCATAATAGAAAA-GTTTG
1 AGCATAATAAAAAATGTTTG
17307935 AGCA-AATAAAAAATGTTT
1 AGCATAATAAAAAATGTTT
17307953 AGGGTTAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.27
Consensus pattern (20 bp):
AGCATAATAAAAAATGTTTG
Found at i:17312462 original size:17 final size:17
Alignment explanation
Indices: 17312440--17312497 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
17312430 ATTAAATCAA
17312440 ATACTCGTACAAAAGAT
1 ATACTCGTACAAAAGAT
* *
17312457 ATACTC--ACATTAAATCAA
1 ATACTCGTACA--AAA-GAT
17312475 ATACTCGTACAAAAGAT
1 ATACTCGTACAAAAGAT
17312492 ATACTC
1 ATACTC
17312498 ACAGAAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 3 0.09
17 16 0.50
18 10 0.31
20 3 0.09
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.26
Consensus pattern (17 bp):
ATACTCGTACAAAAGAT
Found at i:17312476 original size:35 final size:35
Alignment explanation
Indices: 17312430--17312500 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
17312420 AATTTAGCAG
17312430 ATTAAATCAAATACTCGTACAAAAGATATACTCAC
1 ATTAAATCAAATACTCGTACAAAAGATATACTCAC
17312465 ATTAAATCAAATACTCGTACAAAAGATATACTCAC
1 ATTAAATCAAATACTCGTACAAAAGATATACTCAC
17312500 A
1 A
17312501 GAAAATGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.25
Consensus pattern (35 bp):
ATTAAATCAAATACTCGTACAAAAGATATACTCAC
Found at i:17322940 original size:29 final size:30
Alignment explanation
Indices: 17322896--17322964 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
17322886 TTTTTTAAAA
* * *
17322896 TTTAAAAAATAAAAA-TATGAAAATATATT
1 TTTAAAAATTAAAAATTATAAAAAAATATT
*
17322925 TTTAAAAATTAGAAATTATAAAAAAATATT
1 TTTAAAAATTAAAAATTATAAAAAAATATT
17322955 TTTAAAAATT
1 TTTAAAAATT
17322965 TAATTATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 13 0.37
30 22 0.63
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (30 bp):
TTTAAAAATTAAAAATTATAAAAAAATATT
Found at i:17332592 original size:11 final size:11
Alignment explanation
Indices: 17332554--17332610 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
17332544 AAGTCTGTTG
*
17332554 TTTTACTATTG
1 TTTTACTATTA
*
17332565 TTTTACTATCA
1 TTTTACTATTA
17332576 TTTTACTATTA
1 TTTTACTATTA
* *
17332587 TATTACAATTA
1 TTTTACTATTA
* *
17332598 CTTTATTATTA
1 TTTTACTATTA
17332609 TT
1 TT
17332611 GTTTGGATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.28, C:0.11, G:0.02, T:0.60
Consensus pattern (11 bp):
TTTTACTATTA
Found at i:17337063 original size:41 final size:42
Alignment explanation
Indices: 17336989--17337103 Score: 151
Period size: 41 Copynumber: 2.7 Consensus size: 42
17336979 TTTTTGTCCT
*
17336989 AATGTGGTTGCTTCCACGTTGCTTCCTTTTTTGTTTGGACATA
1 AATGTGGTTGCTTCCAC-TTGCTTCCTTTTTTGTCTGGACATA
*
17337032 AATGTGGTTGCTTCCA-TTGCTTCCTTTTTTGTCTGGATATA
1 AATGTGGTTGCTTCCACTTGCTTCCTTTTTTGTCTGGACATA
* *
17337073 GATGTGATTGCTTCCACACATTGCTTCCTTT
1 AATGTGGTTGCTT-C-CAC-TTGCTTCCTTT
17337104 ATCTTTTCTT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
41 34 0.53
42 1 0.02
43 18 0.28
45 11 0.17
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (42 bp):
AATGTGGTTGCTTCCACTTGCTTCCTTTTTTGTCTGGACATA
Found at i:17338074 original size:45 final size:45
Alignment explanation
Indices: 17337999--17338116 Score: 197
Period size: 45 Copynumber: 2.7 Consensus size: 45
17337989 TTTTTGTCCT
*
17337999 GATGTGGTTGCTT-C-CACGTTGCTTCCTTTTTTG-TCTGGACGTA
1 GATGTGGTTGCTTCCACACGTTGCTTCCTTTTTTGCT-TGGACATA
17338042 GATGTGGTTGCTTCCACACGTTGCTTCCTTTTTTGCTTGGACATA
1 GATGTGGTTGCTTCCACACGTTGCTTCCTTTTTTGCTTGGACATA
17338087 GATGTGGTTGCTTCCACACGTTGCTTCCTT
1 GATGTGGTTGCTTCCACACGTTGCTTCCTT
17338117 ATTGCTTTTC
Statistics
Matches: 71, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
43 13 0.18
44 1 0.01
45 56 0.79
46 1 0.01
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.42
Consensus pattern (45 bp):
GATGTGGTTGCTTCCACACGTTGCTTCCTTTTTTGCTTGGACATA
Found at i:17338418 original size:164 final size:164
Alignment explanation
Indices: 17338147--17338474 Score: 584
Period size: 164 Copynumber: 2.0 Consensus size: 164
17338137 CCTTTCCCAT
* * * * *
17338147 GTATTTTTTATTTCTTCAATTATGTGTGAGGAAAATCGTCAATCTTCATGTCAGTTGTTTTTTTT
1 GTATTTTTTATTTCTTCAATTATGTGCGAGGAAAATCATCAATCTTCATGTCAATTATCTTTTTT
*
17338212 AATAGTTGAATGGATTATTTACATCTATCATCCTGGCGATATCCAACATCAGCATTATATGCCAA
66 AATAGTTGAAAGGATTATTTACATCTATCATCCTGGCGATATCCAACATCAGCATTATATGCCAA
17338277 TATTCTTCTTCCATCAGACCAAAAGCAATAAGAC
131 TATTCTTCTTCCATCAGACCAAAAGCAATAAGAC
17338311 GTATTTTTTATTTCTTCAATTATGTGCGAGGAAAATCATCAATCTTCATGTCAATTATCTTTTTT
1 GTATTTTTTATTTCTTCAATTATGTGCGAGGAAAATCATCAATCTTCATGTCAATTATCTTTTTT
* *
17338376 AATAGTTGAAAGGATTATTTACATCTATCATCTTGGCGATATCCAACATCAGCATTATATGTCAA
66 AATAGTTGAAAGGATTATTTACATCTATCATCCTGGCGATATCCAACATCAGCATTATATGCCAA
17338441 TATTCTTCTTCCATCAGACCAAAAGCAATAAGAC
131 TATTCTTCTTCCATCAGACCAAAAGCAATAAGAC
17338475 TTTTGTTAAA
Statistics
Matches: 156, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
164 156 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (164 bp):
GTATTTTTTATTTCTTCAATTATGTGCGAGGAAAATCATCAATCTTCATGTCAATTATCTTTTTT
AATAGTTGAAAGGATTATTTACATCTATCATCCTGGCGATATCCAACATCAGCATTATATGCCAA
TATTCTTCTTCCATCAGACCAAAAGCAATAAGAC
Found at i:17348353 original size:3 final size:3
Alignment explanation
Indices: 17348347--17348372 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17348337 AATAGATACT
17348347 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
17348373 TGATGATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:17352080 original size:51 final size:51
Alignment explanation
Indices: 17351984--17352080 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
17351974 CGGTATATGA
* *
17351984 CGTAAGACCATAGATGAAAAACGCTATGGCAATCTAGTATGAGGTACGTCG
1 CGTAAGACCATAGATGAAAAACGCAATGGCAATCTAGTATAAGGTACGTCG
* * *
17352035 CGTAAGATCATAGATGAAAGACGCAATGGCAA-CATGGTATAAGGTA
1 CGTAAGACCATAGATGAAAAACGCAATGGCAATC-TAGTATAAGGTA
17352081 AAAGATATAC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 1 0.03
51 39 0.98
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (51 bp):
CGTAAGACCATAGATGAAAAACGCAATGGCAATCTAGTATAAGGTACGTCG
Found at i:17352324 original size:31 final size:32
Alignment explanation
Indices: 17352249--17352334 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 32
17352239 GGTAGTCCAT
*
17352249 TAGGACAGTAAACACAAAATAGAGATAGTCTA
1 TAGGACAATAAACACAAAATAGAGATAGTCTA
*
17352281 CTAGGACAATAAATACAAAATAGAGATAGT-T-
1 -TAGGACAATAAACACAAAATAGAGATAGTCTA
* *
17352312 TTGGAACAATAAACA-TAAATAGA
1 TAGG-ACAATAAACACAAAATAGA
17352335 ATCTGTCAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
30 10 0.21
31 9 0.19
32 1 0.02
33 27 0.57
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.21
Consensus pattern (32 bp):
TAGGACAATAAACACAAAATAGAGATAGTCTA
Found at i:17354810 original size:62 final size:59
Alignment explanation
Indices: 17354737--17354854 Score: 173
Period size: 62 Copynumber: 1.9 Consensus size: 59
17354727 AAATGATTAT
* * * *
17354737 TTTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTATTTTAATAAGA
1 TTTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATAAGA
17354799 TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
1 TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
17354855 TTAAAGTGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 22 0.42
60 1 0.02
61 1 0.02
62 28 0.54
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (59 bp):
TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAAGA
Found at i:17356933 original size:35 final size:35
Alignment explanation
Indices: 17356861--17356988 Score: 184
Period size: 35 Copynumber: 3.6 Consensus size: 35
17356851 AGTACATCGA
* * * *
17356861 TAATCCAACCGAAACACACAAAATGCTCATAACAGC
1 TAATCCATCTGAAACACAC-CAATGCTCATAAGAGC
*
17356897 TAATCTATCTGAAACACACCAATGCTCATAAGAGC
1 TAATCCATCTGAAACACACCAATGCTCATAAGAGC
*
17356932 TAATCCATCCGAAACACACCAATGCTCATAAGAGC
1 TAATCCATCTGAAACACACCAATGCTCATAAGAGC
*
17356967 TAATCCATTTGAAACACACCAA
1 TAATCCATCTGAAACACACCAA
17356989 AACAGAAAGT
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 67 0.81
36 16 0.19
ACGTcount: A:0.43, C:0.29, G:0.09, T:0.19
Consensus pattern (35 bp):
TAATCCATCTGAAACACACCAATGCTCATAAGAGC
Found at i:17360820 original size:124 final size:125
Alignment explanation
Indices: 17360555--17360824 Score: 416
Period size: 124 Copynumber: 2.2 Consensus size: 125
17360545 CTCACATGTG
* *
17360555 GACGTGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACGCTTCTAAGCAAATAGT
1 GACGCGCTTTTGCTACAGTAGGTCCAGAAAAAATAATTTCGAGTTGACGCTTCTAAGCAAATAGT
* * *
17360620 ATAAAAAACGCTTGAGGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCTCCCACGTA
66 ATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCTCCCACATA
* * *
17360680 GACGCGCTTTTGCTACAGTAGGTCCAGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGT
1 GACGCGCTTTTGCTACAGTAGGTCCAGAAAAAATAATTTCGAGTTGACGCTTCTAAGCAAATAGT
* *
17360745 AT-AAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCTCCCACATG
66 ATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCTCCCACATA
* * *
17360804 GATGCGTTTTTACTACAGTAG
1 GACGCGCTTTTGCTACAGTAG
17360825 CATGTTTCGG
Statistics
Matches: 132, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
124 70 0.53
125 62 0.47
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (125 bp):
GACGCGCTTTTGCTACAGTAGGTCCAGAAAAAATAATTTCGAGTTGACGCTTCTAAGCAAATAGT
ATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCTCCCACATA
Found at i:17364135 original size:48 final size:49
Alignment explanation
Indices: 17364029--17364340 Score: 513
Period size: 49 Copynumber: 6.4 Consensus size: 49
17364019 TAAGAATATT
* *
17364029 AACTATTTTGTATTTCATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATA
*
17364078 AACTATTTTGTATTTTATTAAATGAAATAATATC-AAATATTCAAAATA
1 AACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATA
* *
17364126 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTTAAAATA
1 AACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATA
* *
17364175 AACTATTTTGTA-TTTATTACATCAAATAATATCAAATTATTCAAAATA
1 AACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATA
* *
17364223 AACTATTTTGTATGTTATTACATCAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATA
17364272 AACTATTTTGTATTTTA-TAACATCAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTAA-ATCAAATAATATCAAAATATTCAAAATA
17364321 AACTATTTTGTATTTTATTA
1 AACTATTTTGTATTTTATTA
17364341 CATTAATATA
Statistics
Matches: 249, Mismatches: 10, Indels: 7
0.94 0.04 0.03
Matches are distributed among these distances:
48 94 0.38
49 153 0.61
50 2 0.01
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.42
Consensus pattern (49 bp):
AACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATA
Found at i:17364136 original size:97 final size:97
Alignment explanation
Indices: 17364029--17364340 Score: 520
Period size: 97 Copynumber: 3.2 Consensus size: 97
17364019 TAAGAATATT
*
17364029 AACTATTTTGTATTTCATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTT
1 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTT
*
17364094 ATTAAATGAAATAATATCAAATATTCAAAATA
66 ATTAAATCAAATAATATCAAATATTCAAAATA
*
17364126 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTTAAAATAAACTATTTTGTA-TTT
1 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTT
*
17364190 ATTACATCAAATAATATCAAATTATTCAAAATA
66 ATTAAATCAAATAATATCAAA-TATTCAAAATA
* * *
17364223 AACTATTTTGTATGTTATTACATCAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTT
1 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTT
17364288 A-TAACATCAAATAATATCAAAATATTCAAAATA
66 ATTAA-ATCAAATAATATC-AAATATTCAAAATA
17364321 AACTATTTTGTATTTTATTA
1 AACTATTTTGTATTTTATTA
17364341 CATTAATATA
Statistics
Matches: 201, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
96 22 0.11
97 129 0.64
98 47 0.23
99 3 0.01
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.42
Consensus pattern (97 bp):
AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTT
ATTAAATCAAATAATATCAAATATTCAAAATA
Found at i:17364507 original size:21 final size:21
Alignment explanation
Indices: 17364466--17364523 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
17364456 CTAGCTTCTA
* *
17364466 GCGGGGGTTGTGGTTGCTCCG
1 GCGGGGATTCTGGTTGCTCCG
17364487 GCGGGGATTCTGGTT-CATCCG
1 GCGGGGATTCTGGTTGC-TCCG
*
17364508 GTAGGGGA-TCTGGTTG
1 G-CGGGGATTCTGGTTG
17364524 TCGGTGTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.03
21 25 0.81
22 5 0.16
ACGTcount: A:0.07, C:0.17, G:0.47, T:0.29
Consensus pattern (21 bp):
GCGGGGATTCTGGTTGCTCCG
Found at i:17366653 original size:11 final size:11
Alignment explanation
Indices: 17366637--17366682 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
17366627 TTTAAATAGA
17366637 AATTTGAGAGG
1 AATTTGAGAGG
17366648 AATTTGAGA-G
1 AATTTGAGAGG
17366658 AATATT-AGAGAG
1 AAT-TTGAGAG-G
*
17366670 AAATTGAGAGG
1 AATTTGAGAGG
17366681 AA
1 AA
17366683 GGATTTAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
10 7 0.23
11 16 0.53
12 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.30, T:0.24
Consensus pattern (11 bp):
AATTTGAGAGG
Found at i:17366676 original size:22 final size:22
Alignment explanation
Indices: 17366634--17366679 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
17366624 TCTTTTAAAT
* *
17366634 AGAAATTTGAGAGGAATTTGAG
1 AGAAATTAGAGAGGAAATTGAG
17366656 AGAATATTAGAGA-GAAATTGAG
1 AGAA-ATTAGAGAGGAAATTGAG
17366678 AG
1 AG
17366680 GAAGGATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.30, T:0.24
Consensus pattern (22 bp):
AGAAATTAGAGAGGAAATTGAG
Found at i:17370702 original size:20 final size:20
Alignment explanation
Indices: 17370665--17370702 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17370655 TATTTTTAAA
*
17370665 AAAAATTATTTAATATATAT
1 AAAAATTATTTAAAATATAT
17370685 AAAAA-TATTTACAAATAT
1 AAAAATTATTTA-AAATAT
17370703 CAAACAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATTATTTAAAATATAT
Found at i:17374123 original size:3 final size:3
Alignment explanation
Indices: 17374115--17374168 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
17374105 TTTAGCAACT
17374115 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
17374163 TCA TTA
1 TTA TTA
17374169 CTACTACTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:17374468 original size:40 final size:39
Alignment explanation
Indices: 17374387--17374475 Score: 106
Period size: 40 Copynumber: 2.3 Consensus size: 39
17374377 ATATATTTTG
* * *
17374387 TATATATATTCTTTATATTTTATGATTCCTATGTACCTA
1 TATATATATACTTTATATTTTATGATACCTATATACCTA
** *
17374426 TATATATATACTTTTATATTTTATGATAGTTATATACGTA
1 TATATATATAC-TTTATATTTTATGATACCTATATACCTA
*
17374466 TATATGTATA
1 TATATATATA
17374476 TGCTTACTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 10 0.24
40 32 0.76
ACGTcount: A:0.33, C:0.08, G:0.07, T:0.53
Consensus pattern (39 bp):
TATATATATACTTTATATTTTATGATACCTATATACCTA
Found at i:17380815 original size:45 final size:46
Alignment explanation
Indices: 17380764--17380874 Score: 188
Period size: 46 Copynumber: 2.4 Consensus size: 46
17380754 ATCAATTGTC
*
17380764 CTTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTACCA
1 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
* *
17380809 CTTGATCAGATAAGTGTAGCTGAAGCTTCCACTTATCACTTTATCA
1 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
17380855 CTTGATCAGATAAGTGTAGC
1 CTTGATCAGATAAGTGTAGC
17380875 CACTTATCAC
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
45 21 0.34
46 41 0.66
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (46 bp):
CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
Found at i:17380878 original size:37 final size:37
Alignment explanation
Indices: 17380837--17380983 Score: 258
Period size: 37 Copynumber: 4.0 Consensus size: 37
17380827 GCTGAAGCTT
* ** *
17380837 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
17380874 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
17380911 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
17380948 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
17380984 GCTAAAACTA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 106 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (37 bp):
CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
Found at i:17389158 original size:44 final size:44
Alignment explanation
Indices: 17389048--17389930 Score: 578
Period size: 44 Copynumber: 20.6 Consensus size: 44
17389038 ATTATACAGG
* * *
17389048 TCTTATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATATCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG-ATA-GAGA
* * **
17389094 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGAGA
* **
17389138 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGAGA
* * * *
17389181 TCCTATCTCTCTGAGATTACAGTGGAGCGGAT--TA-A-AG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGAGA
* * * ** * *
17389220 TCTTATATCTCTGA-AGTTACAGTAGAGTGGATCGTA-TTAG-G-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGATAGAGA
* *
17389261 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG-ATAG-AGA
* *
17389307 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTA-A
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAG-AGA
* * * *
17389351 TCCTATCTCCTTGAGATTACAGTGGAGCACAT--TA-A-AG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGAGA
* * * ** *
17389390 TTTTATCTCTCTGA-AGTTACAGTAGAGTGGATCG--TATCAG-G-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGAT-AGAGA
* * *
17389431 TCTTTTCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG-A-TAGAGA
* * *
17389477 TCTTATCTCCCTGAGATTACTGCGGAGCAGATCAAAGATAGTA-A
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAG-AGA
* * * *
17389521 TCCTATCTCCTTGAGATTACAGTGGAGCGGAT--TA-A-AG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGAGA
* * ** *
17389560 TCTTATCTCTCTGA-AGTTACAGTAGAGTGGATCG--TATCAG-G-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGAT-AGAGA
* * *
17389601 TCTTATCTCCCTGAGATTACAGTAGAGCAGACCGAAGAATTACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG-A-TAGAGA
* *
17389647 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTA-A
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAG-AGA
* * * *
17389691 TCCTATCTCCTTGAGATTACAGTGGAGCTGAT--TA-A-AG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGAGA
* * ** *
17389730 TCTTATCTCTCTGA-AGTTACAGTAGAGTGGATCG--TATCAG-G-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGAT-AGAGA
* * *
17389771 TCTTATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG-ATAG-AGA
** *
17389817 TCTTATCTCCCTGAGATTACAACGGAGCAGATCAAAGATAGTA-A
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAG-AGA
* ** * *
17389861 TCTTATCTCCCTGAGATTATAGCAGAACAGATTGAAGATAGTA-A
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAG-AGA
17389905 TCTTATCTCCCTGAGATTACAGTGGA
1 TCTTATCTCCCTGAGATTACAGTGGA
17389931 ATAGATTGAA
Statistics
Matches: 663, Mismatches: 119, Indels: 112
0.74 0.13 0.13
Matches are distributed among these distances:
38 4 0.01
39 102 0.15
40 10 0.02
41 114 0.17
42 19 0.03
43 33 0.05
44 198 0.30
45 19 0.03
46 164 0.25
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGAGA
Found at i:17389388 original size:170 final size:170
Alignment explanation
Indices: 17389087--17389879 Score: 1317
Period size: 170 Copynumber: 4.7 Consensus size: 170
17389077 GACCGAAGAA
* * ** *
17389087 TATCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA--G-AGATCTTATCTCCC
1 TATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAG-AATTGCAGATCTTATCTCCC
* * * *
17389149 TGAGATTACAGTGGAGCAGATCGAAGACACT-ATCCTATCT-CTCTGAGATTACAGTGGAGCGGA
65 TGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCT-TGAGATTACAGTGGAGCGGA
*
17389212 TTAAAGGATCTTATATCTCTGAAGTTACAGTAGAGTGGATCG
129 TTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCG
*
17389254 TATTAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGATCTTATCTCCCT
1 TATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGATCTTATCTCCCT
**
17389319 GAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACAGTGGAGCACATT
66 GAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACAGTGGAGCGGATT
*
17389384 AAAGGATTTTATCTCTCTGAAGTTACAGTAGAGTGGATCG
131 AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCG
* *
17389424 TATCAGGTCTTTTCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAGATCTTATCTCCCT
1 TATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGATCTTATCTCCCT
*
17389489 GAGATTACTGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACAGTGGAGCGGATT
66 GAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACAGTGGAGCGGATT
17389554 AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCG
131 AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCG
* *
17389594 TATCAGGTCTTATCTCCCTGAGATTACAGTAGAGCAGACCGAAGAATTACAGATCTTATCTCCCT
1 TATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGATCTTATCTCCCT
*
17389659 GAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACAGTGGAGCTGATT
66 GAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACAGTGGAGCGGATT
17389724 AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCG
131 AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCG
*
17389764 TATCAGGTCTTATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTGCAGATCTTATCTCCCT
1 TATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGATCTTATCTCCCT
* * *
17389829 GAGATTACAACGGAGCAGATCAAAGATAGTAATCTTATCTCCCTGAGATTA
66 GAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTA
17389880 TAGCAGAACA
Statistics
Matches: 590, Mismatches: 31, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
166 1 0.00
167 39 0.07
168 1 0.00
169 41 0.07
170 506 0.86
171 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (170 bp):
TATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGATCTTATCTCCCT
GAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACAGTGGAGCGGATT
AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCG
Found at i:17390809 original size:19 final size:19
Alignment explanation
Indices: 17390785--17390826 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
17390775 GTTCTTGCGT
*
17390785 TTTTATTTACTTTCTTCTA
1 TTTTATTTACTTTATTCTA
* *
17390804 TTTTATTTATTTTATTTTA
1 TTTTATTTACTTTATTCTA
17390823 TTTT
1 TTTT
17390827 TTGTTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTATTTACTTTATTCTA
Found at i:17391577 original size:3 final size:3
Alignment explanation
Indices: 17391569--17391622 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
17391559 TTTAGCAACT
17391569 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
17391617 TCA TTA
1 TTA TTA
17391623 CTACTACTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:17402332 original size:26 final size:25
Alignment explanation
Indices: 17402251--17402332 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
17402241 CAACTACCTA
* *
17402251 TAAATAATTCAAATAAAAT-TATATT
1 TAAAAAATTAAAATAAAATCTA-ATT
*
17402276 TAGAAAATTAAAAT--AATCTAACTT
1 TAAAAAATTAAAATAAAATCTAA-TT
*
17402300 CGTAAAAGATTAAAATAAAATCTAATT
1 --TAAAAAATTAAAATAAAATCTAATT
17402327 TAAAAA
1 TAAAAA
17402333 TAAATATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
23 4 0.09
24 4 0.09
25 16 0.36
26 12 0.27
27 2 0.04
28 7 0.16
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (25 bp):
TAAAAAATTAAAATAAAATCTAATT
Found at i:17403438 original size:2 final size:2
Alignment explanation
Indices: 17403431--17403458 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17403421 AATTAAACAA
17403431 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
17403459 TGGGTCAAAT
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:17403757 original size:18 final size:20
Alignment explanation
Indices: 17403731--17403769 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
17403721 TTTTAAAAAT
17403731 AAATAATAAAA-ATG-TATA
1 AAATAATAAAATATGTTATA
*
17403749 AAATTATAAAATATGTTATA
1 AAATAATAAAATATGTTATA
17403769 A
1 A
17403770 TTCAAACTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 3 0.17
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AAATAATAAAATATGTTATA
Found at i:17404770 original size:32 final size:30
Alignment explanation
Indices: 17404725--17404784 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
17404715 TGAACGCCGT
* *
17404725 AGTATCTTTAAAGTTTTGGTTTCACCCAATA
1 AGTATCTTTAAAG-TCTGGTTTCAACCAATA
*
17404756 AGTATTTTTGAAAGTCTGGTTTCAACCAA
1 AGTATCTTT-AAAGTCTGGTTTCAACCAA
17404785 GTTCATTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (30 bp):
AGTATCTTTAAAGTCTGGTTTCAACCAATA
Found at i:17405038 original size:62 final size:59
Alignment explanation
Indices: 17404884--17405045 Score: 153
Period size: 60 Copynumber: 2.7 Consensus size: 59
17404874 CCTGTTTCAT
* * * ** *
17404884 TTTCAAAAGTTTTGGTTCTATCCAGTAAGTATTTTTGAAAGTTTGGTTCCGCAAGTTTAT
1 TTTCAAAAGTTCTGGTTCTCT-TAGTAAGTATTTTTGAAAGACTGGTTCCGCAAGTTTAC
* * * * * *
17404944 TTTCAAAAGTTCTAGTTCCACCTAGTAGGTATTTTTGAAAGACTGGTTCCGTCTAGGTTTGC
1 TTTCAAAAGTTCTGGTT-CTCTTAGTAAGTATTTTTGAAAGACTGGTTCCG-C-AAGTTTAC
* *
17405006 TTTCAAAAGTTCTGGTTCTGCTTAGTACGTATTTATGAAA
1 TTTCAAAAGTTCTGGTTCT-CTTAGTAAGTATTTTTGAAA
17405046 CTTTGGTTTC
Statistics
Matches: 81, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
60 40 0.49
61 3 0.04
62 38 0.47
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (59 bp):
TTTCAAAAGTTCTGGTTCTCTTAGTAAGTATTTTTGAAAGACTGGTTCCGCAAGTTTAC
Found at i:17405053 original size:62 final size:60
Alignment explanation
Indices: 17404823--17405053 Score: 198
Period size: 62 Copynumber: 3.8 Consensus size: 60
17404813 AAAACTCATC
* ***
17404823 TTCAAAAGTTCTGGTTCCACCTAGTAAGTATTTATGCAACTTTGGTTTTATCCT-GTTTCATT
1 TTCAAAAGTTCTGGTTCCACCTAGTAAGTATTTATGAAACTTTGGTTCCGT-CTAGTTTC--T
* * * * * *
17404885 TTCAAAAGTTTTGGTTCTATCC-AGTAAGTATTTTTGAAAGTTTGGTTCCG-CAAGTTTATT
1 TTCAAAAGTTCTGGTTCCA-CCTAGTAAGTATTTATGAAACTTTGGTTCCGTCTAGTTT-CT
* * * ***
17404945 TTCAAAAGTTCTAGTTCCACCTAGTAGGTATTTTTGAAAGACTGGTTCCGTCTAGGTTTGCT
1 TTCAAAAGTTCTGGTTCCACCTAGTAAGTATTTATGAAACTTTGGTTCCGTCTA-GTTT-CT
** * *
17405007 TTCAAAAGTTCTGGTTCTGCTTAGTACGTATTTATGAAACTTTGGTT
1 TTCAAAAGTTCTGGTTCCACCTAGTAAGTATTTATGAAACTTTGGTT
17405054 TCACCTAGGT
Statistics
Matches: 135, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
59 2 0.01
60 43 0.32
61 6 0.04
62 82 0.61
63 2 0.01
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.43
Consensus pattern (60 bp):
TTCAAAAGTTCTGGTTCCACCTAGTAAGTATTTATGAAACTTTGGTTCCGTCTAGTTTCT
Found at i:17414548 original size:18 final size:18
Alignment explanation
Indices: 17414525--17414583 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
17414515 AATAAATTTT
17414525 TTAAATATTTTAATATAA
1 TTAAATATTTTAATATAA
* *
17414543 TTAAATA--TAAAAATAA
1 TTAAATATTTTAATATAA
*
17414559 -AAAATATTTTAATATAA
1 TTAAATATTTTAATATAA
17414576 TTAAATAT
1 TTAAATAT
17414584 AAAAATAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
15 5 0.16
16 7 0.22
17 7 0.22
18 13 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAATATTTTAATATAA
Found at i:17414564 original size:33 final size:33
Alignment explanation
Indices: 17414527--17414591 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
17414517 TAAATTTTTT
17414527 AAATATTTTAATATAATTAAATATAAAAATAAA
1 AAATATTTTAATATAATTAAATATAAAAATAAA
17414560 AAATATTTTAATATAATTAAATATAAAAATAA
1 AAATATTTTAATATAATTAAATATAAAAATAA
17414592 TTATATTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (33 bp):
AAATATTTTAATATAATTAAATATAAAAATAAA
Found at i:17414565 original size:25 final size:26
Alignment explanation
Indices: 17414536--17414594 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
17414526 TAAATATTTT
17414536 AATATAATTAAATATAA-AAATAAAA
1 AATATAATTAAATATAATAAATAAAA
* *
17414561 AATAT--TTTAATATAATTAAATATAA
1 AATATAATTAAATATAA-TAAATAAAA
17414586 AA-ATAATTA
1 AATATAATTA
17414595 TATTAAGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
23 9 0.33
24 2 0.07
25 14 0.52
26 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
AATATAATTAAATATAATAAATAAAA
Found at i:17414616 original size:38 final size:37
Alignment explanation
Indices: 17414574--17414653 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 37
17414564 ATTTTAATAT
* *
17414574 AATTAAATATAAAAATAATTATATTAAGAATGTTATTA
1 AATTAAATATAAAAATAATTATATTAA-AATATGATTA
* * *
17414612 AATTATATTTAATAATAATTATATTAAAATATGATTA
1 AATTAAATATAAAAATAATTATATTAAAATATGATTA
17414649 AATTA
1 AATTA
17414654 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 13 0.35
38 24 0.65
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (37 bp):
AATTAAATATAAAAATAATTATATTAAAATATGATTA
Found at i:17414869 original size:46 final size:44
Alignment explanation
Indices: 17414785--17414876 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 44
17414775 ATATCTATTC
* *
17414785 CATTCAACCAAACACAATAATACTATTATAGTTCTATTCCGTTA
1 CATTCAACCAAACACAATAATACTATTATAGCTCTATTCCATTA
*
17414829 CATTCAACCAAACA-ATTGAATTACTGATTATAGCTCTATTCCATTA
1 CATTCAACCAAACACAAT-AA-TACT-ATTATAGCTCTATTCCATTA
17414875 CA
1 CA
17414877 GCTTTATTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 2 0.05
44 16 0.38
45 4 0.10
46 20 0.48
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (44 bp):
CATTCAACCAAACACAATAATACTATTATAGCTCTATTCCATTA
Found at i:17414879 original size:16 final size:16
Alignment explanation
Indices: 17414855--17414921 Score: 89
Period size: 16 Copynumber: 4.2 Consensus size: 16
17414845 TGAATTACTG
*
17414855 ATTATAGCTCTATTCC
1 ATTACAGCTCTATTCC
* *
17414871 ATTACAGCTTTATTAC
1 ATTACAGCTCTATTCC
*
17414887 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCC
*
17414903 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
17414919 ATT
1 ATT
17414922 CTAGTGAACC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.28, C:0.27, G:0.04, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:17418218 original size:44 final size:46
Alignment explanation
Indices: 17418165--17418260 Score: 126
Period size: 44 Copynumber: 2.1 Consensus size: 46
17418155 TATTACAACA
*
17418165 TCTATTCCATTCAACTAAAC-ACAAGAA-TACT-ATTACAACTCTAT
1 TCTATTCCATTCAACCAAACAAC-AGAATTACTAATTACAACTCTAT
* * *
17418209 TCTATTCCATTCAACCAAACAACTGAATTGCTAATTACAATTCTAT
1 TCTATTCCATTCAACCAAACAACAGAATTACTAATTACAACTCTAT
17418255 TCTATT
1 TCTATT
17418261 ACAACTCTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
44 22 0.49
45 5 0.11
46 18 0.40
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (46 bp):
TCTATTCCATTCAACCAAACAACAGAATTACTAATTACAACTCTAT
Found at i:17418263 original size:16 final size:16
Alignment explanation
Indices: 17418242--17418292 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
17418232 TGAATTGCTA
*
17418242 ATTACAATTCTATTCT
1 ATTACAACTCTATTCT
*
17418258 ATTACAACTCTATTCC
1 ATTACAACTCTATTCT
*
17418274 ATTACAGCTCTATTCT
1 ATTACAACTCTATTCT
17418290 ATT
1 ATT
17418293 CTCCCCAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.45
Consensus pattern (16 bp):
ATTACAACTCTATTCT
Found at i:17418702 original size:13 final size:15
Alignment explanation
Indices: 17418670--17418707 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
17418660 ATCTAGAAAA
17418670 AATT-AAATAGAATC
1 AATTAAAATAGAATC
17418684 AATTAAAATA-AAT-
1 AATTAAAATAGAATC
17418697 AATTAAAATAG
1 AATTAAAATAG
17418708 GAAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 7 0.32
15 5 0.23
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (15 bp):
AATTAAAATAGAATC
Found at i:17423748 original size:123 final size:126
Alignment explanation
Indices: 17423529--17423879 Score: 550
Period size: 123 Copynumber: 2.8 Consensus size: 126
17423519 TTATTTTGAG
*
17423529 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 TTGAAGTTTCTGAG-CAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGT
*
17423593 GAAATTGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATA-AT-T-TTT
65 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATATATATTT
* * **
17423652 TTGACGTTTTTGAG-AGAATAGTATAAAATCGCCTCTACCAGGATTATATTTGAGAAGAAATTGT
1 TTGAAGTTTCTGAGCA-AATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGT
* * *
17423716 GAAATCGTGCCCTAGTGGACGCGATTTTGCTACAGTAGGTTATGTAAGAAATATATATATTT
65 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATATATATTT
* *
17423778 TTTAAGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGGGAAGAAATTGTG
1 TTGAAGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
17423843 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
17423880 CAAGTTTGGG
Statistics
Matches: 207, Mismatches: 15, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
122 1 0.00
123 106 0.51
124 3 0.01
125 1 0.00
126 95 0.46
127 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.32
Consensus pattern (126 bp):
TTGAAGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATATATATTT
Found at i:17426998 original size:10 final size:10
Alignment explanation
Indices: 17426983--17427007 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17426973 CAAATCTAAC
17426983 ATTATGTAAA
1 ATTATGTAAA
17426993 ATTATGTAAA
1 ATTATGTAAA
17427003 ATTAT
1 ATTAT
17427008 TAAGTCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:17427066 original size:10 final size:10
Alignment explanation
Indices: 17427051--17427077 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
17427041 TTTTTTTATC
17427051 AAATTATGTA
1 AAATTATGTA
17427061 AAATTATGTA
1 AAATTATGTA
17427071 AAATTAT
1 AAATTAT
17427078 TAAGCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (10 bp):
AAATTATGTA
Found at i:17427167 original size:55 final size:55
Alignment explanation
Indices: 17427099--17427224 Score: 234
Period size: 55 Copynumber: 2.3 Consensus size: 55
17427089 AATTTTAATT
*
17427099 AAATTAGGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
*
17427154 AAATTATGTAAAATTATTAAGTCCAACAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
17427209 AAATTATGTAAAATTA
1 AAATTATGTAAAATTA
17427225 GGTTAGGGTT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 69 1.00
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (55 bp):
AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
Found at i:17427255 original size:18 final size:18
Alignment explanation
Indices: 17427232--17427273 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
17427222 TTAGGTTAGG
17427232 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
17427250 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
17427268 ATTAGG
1 GTTAGG
17427274 TTAGGGTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.48
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:17427288 original size:47 final size:47
Alignment explanation
Indices: 17427219--17427579 Score: 391
Period size: 47 Copynumber: 7.2 Consensus size: 47
17427209 AAATTATGTA
17427219 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
17427266 AAATTAGGTTAGGGTTAGGGTTTTTAATTAATTTATGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGG--TTT--TTAA-TTA----A--GTTAGGGTTTTTAATT
* * *
17427324 AAGTTAAGGTTAGGGTAAGGGTTTTTAATTAAGTTAAGGTTTTTAATT
1 AAATT-AGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
**
17427372 AGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTA-GGTTAGGGTTAGGG--TTT--TT-AATTA----A--GTTAGGGTTTTTAATT
*
17427431 AAATTAGGTTAGGGTAAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
* **
17427478 AAGTTAGGTTAGGGTTA-GGTCCCTTAATTAAGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGT-TTTTAATTAAGTTAGGGTTTTTAATT
* *
17427525 AAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAAAT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
17427572 AAATTAGG
1 AAATTAGG
17427580 GTTTTTATTA
Statistics
Matches: 271, Mismatches: 17, Indels: 52
0.80 0.05 0.15
Matches are distributed among these distances:
46 3 0.01
47 123 0.45
48 35 0.13
49 4 0.01
50 4 0.01
51 4 0.01
52 5 0.02
53 10 0.04
54 5 0.02
55 4 0.01
56 4 0.01
57 4 0.01
58 33 0.12
59 33 0.12
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.45
Consensus pattern (47 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
Found at i:17427338 original size:30 final size:30
Alignment explanation
Indices: 17427250--17427364 Score: 180
Period size: 29 Copynumber: 3.9 Consensus size: 30
17427240 TTTTAATTAA
*
17427250 GTTAGGGTTTTTAATTAAATT-AGGTTAGG
1 GTTAGGGTTTTTAATTAAGTTAAGGTTAGG
* *
17427279 GTTAGGGTTTTTAATTAA-TTTATGTTAGG
1 GTTAGGGTTTTTAATTAAGTTAAGGTTAGG
17427308 GTTAGGGTTTTTAATTAAGTTAAGGTTAGG
1 GTTAGGGTTTTTAATTAAGTTAAGGTTAGG
*
17427338 GTAAGGGTTTTTAATTAAGTTAAGGTT
1 GTTAGGGTTTTTAATTAAGTTAAGGTT
17427365 TTTAATTAGG
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
28 2 0.03
29 43 0.54
30 35 0.44
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (30 bp):
GTTAGGGTTTTTAATTAAGTTAAGGTTAGG
Found at i:17427345 original size:106 final size:103
Alignment explanation
Indices: 17427222--17427579 Score: 500
Period size: 106 Copynumber: 3.5 Consensus size: 103
17427212 TTATGTAAAA
*
17427222 TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
1 TTAGGTTAGGGTAAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
17427287 TTTTAATTAATTTATGTTAGGGTTAGGGTTTTTAATTAAG
66 TTTTAATTAA-TTA-GTTAGGGTTAGGGTTTTTAATTAAG
* **
17427327 TTAAGGTTAGGGTAAGGGTTTTTAATTAAGTTAAGGTTTTTAATTAGGTTAGGGTTAGGGTTAGG
1 TT-AGGTTAGGGTAAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTAGG
*
17427392 GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAA
64 GTTTTTAATT-AATTA-GTTAGGGTTAGGGTTTTTAATTAAG
*
17427434 TTAGGTTAGGGTAAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTA-GG-
1 TTAGGTTAGGGTAAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
***
17427497 --TCCCTTAATTA---A--GTTAGGGTTTTTAATTAAG
66 TTTTAATTAATTAGTTAGGGTTAGGGTTTTTAATTAAG
* *
17427528 TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAAATAAATTAGG
1 TTAGGTTAGGGTAAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAATTAGG
17427580 GTTTTTATTA
Statistics
Matches: 235, Mismatches: 15, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
94 67 0.29
96 1 0.00
100 5 0.02
101 3 0.01
104 2 0.01
105 13 0.06
106 90 0.38
107 52 0.22
108 2 0.01
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.45
Consensus pattern (103 bp):
TTAGGTTAGGGTAAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
TTTTAATTAATTAGTTAGGGTTAGGGTTTTTAATTAAG
Found at i:17427366 original size:18 final size:18
Alignment explanation
Indices: 17427343--17427382 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
17427333 TTAGGGTAAG
17427343 GGTTTTTAATTAAGTTAA
1 GGTTTTTAATTAAGTTAA
* *
17427361 GGTTTTTAATTAGGTTAG
1 GGTTTTTAATTAAGTTAA
17427379 GGTT
1 GGTT
17427383 AGGGTTAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (18 bp):
GGTTTTTAATTAAGTTAA
Found at i:17427412 original size:29 final size:29
Alignment explanation
Indices: 17427356--17427467 Score: 170
Period size: 29 Copynumber: 3.8 Consensus size: 29
17427346 TTTTAATTAA
* **
17427356 GTTAAGGTTTTTAATTAGGTTAGGGTTAGG
1 GTTAGGGTTTTTAATTAAATTA-GGTTAGG
17427386 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
17427415 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* *
17427444 GTAAGGGTTTTTAATTAAGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGG
17427468 GTTTTTAATT
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 58 0.75
30 19 0.25
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (29 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGG
Found at i:17427487 original size:17 final size:18
Alignment explanation
Indices: 17427447--17427586 Score: 96
Period size: 18 Copynumber: 7.6 Consensus size: 18
17427437 GGTTAGGGTA
17427447 AGGGTTTTTAATTAAGTT
1 AGGGTTTTTAATTAAGTT
17427465 AGGGTTTTTAATTAAGTTAGGTT
1 AGGGTTTTTAATT-A---A-GTT
17427488 AGGGTTAGGTCCCTTAATTAAGTT
1 AGGGTT---T---TTAATTAAGTT
17427512 AGGGTTTTTAATTAAGTT
1 AGGGTTTTTAATTAAGTT
**
17427530 A-GG---TT-A--GGGTT
1 AGGGTTTTTAATTAAGTT
17427541 AGGGTTTTTAATTAAGTT
1 AGGGTTTTTAATTAAGTT
* *
17427559 AGGGTTTTTAAATAAATT
1 AGGGTTTTTAATTAAGTT
17427577 AGGGTTTTTA
1 AGGGTTTTTA
17427587 TTACATCAAA
Statistics
Matches: 98, Mismatches: 6, Indels: 36
0.70 0.04 0.26
Matches are distributed among these distances:
11 4 0.04
12 2 0.02
13 1 0.01
14 2 0.02
15 2 0.02
16 1 0.01
17 2 0.02
18 54 0.55
19 1 0.01
21 1 0.01
22 1 0.01
23 9 0.09
24 9 0.09
25 1 0.01
26 1 0.01
28 1 0.01
29 6 0.06
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (18 bp):
AGGGTTTTTAATTAAGTT
Found at i:17427634 original size:25 final size:26
Alignment explanation
Indices: 17427582--17427645 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
17427572 AAATTAGGGT
*
17427582 TTTTATTACATCAAATTGAACTTCTA
1 TTTTATTACATCAAATTAAACTTCTA
* *
17427608 TTTTATTATATTAAA-TAAACTTCTA
1 TTTTATTACATCAAATTAAACTTCTA
17427633 TTTTATTACATCA
1 TTTTATTACATCA
17427646 GATAATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 20 0.61
26 13 0.39
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTATTACATCAAATTAAACTTCTA
Found at i:17428755 original size:7 final size:7
Alignment explanation
Indices: 17428745--17428769 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17428735 CATAATACAT
17428745 AATACTA
1 AATACTA
17428752 AATACTA
1 AATACTA
17428759 AATACTA
1 AATACTA
17428766 AATA
1 AATA
17428770 TCAATCGACT
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:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:17429941 original size:51 final size:51
Alignment explanation
Indices: 17429886--17430046 Score: 304
Period size: 51 Copynumber: 3.2 Consensus size: 51
17429876 TTTAAAAAAT
* *
17429886 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
17429937 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
17429988 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
17430039 GAAATTGA
1 GAAATTGA
17430047 AAGAATTTTG
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 108 1.00
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
Found at i:17430046 original size:22 final size:22
Alignment explanation
Indices: 17430021--17430093 Score: 128
Period size: 22 Copynumber: 3.3 Consensus size: 22
17430011 AAATATGGGT
17430021 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
*
17430043 TTGAAAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
17430065 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
*
17430087 TTAAGAG
1 TTGAGAG
17430094 GATTAGAGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:17430587 original size:20 final size:19
Alignment explanation
Indices: 17430550--17430587 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
17430540 TTTTGCGTTA
*
17430550 TTAAATTTGAATATAATTT
1 TTAAATTTGAATACAATTT
17430569 TTAAATTTGAAATACAATT
1 TTAAATTTG-AATACAATT
17430588 ATCCTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (19 bp):
TTAAATTTGAATACAATTT
Found at i:17431962 original size:191 final size:191
Alignment explanation
Indices: 17431634--17432015 Score: 624
Period size: 191 Copynumber: 2.0 Consensus size: 191
17431624 AATACATTCA
17431634 ATTCATGATAAACAGCTAGATCTAAGTTTAATTGAGCTTACCAATGCTCTTATATTAACCCGAGC
1 ATTCATGATAAACAGCTAGATCTAAGTTTAATTGAGCTTACCAATGCTCTTATATTAACCCGAGC
*
17431699 ACGAAATATAACCAAATTGTAAAGTTTTACAAATGTATGGTTTGACGTCATGACTTCATCTAGTG
66 ACGAAATAGAACCAAATTGTAAAGTTTTACAAATGTATGGTTTGACGTCATGACTTCATCTAGTG
* *
17431764 TTTGTCACGACATGGCAATTACAGTATGTCACGTTGCAACGACACGACAAGTCTTAGCTCG
131 CTTGTCACGACATGGCAATTACAGTATGTCACGTCGCAACGACACGACAAGTCTTAGCTCG
* *
17431825 ATTCATGATAAACA-ATCA-ATCTAAGTCTTAATTGAGCTTACCAATGCTTTTATATTAACCCGA
1 ATTCATGATAAACAGCT-AGATCTAAGT-TTAATTGAGCTTACCAATGCTCTTATATTAACCCGA
* * * **
17431888 GCACGAAATAGGATCAAATTGTAAAGTTTTGCAAATGTATGGTTTGACGTTGTGACTTCATCTAG
64 GCACGAAATAGAACCAAATTGTAAAGTTTTACAAATGTATGGTTTGACGTCATGACTTCATCTAG
* *
17431953 TGCTTGTCACGACATGGCAATTACATTATGTCACGTCGCAACGAGACGACAAGTCTTAGCTCG
129 TGCTTGTCACGACATGGCAATTACAGTATGTCACGTCGCAACGACACGACAAGTCTTAGCTCG
17432016 TCACGACGTC
Statistics
Matches: 177, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
190 9 0.05
191 168 0.95
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (191 bp):
ATTCATGATAAACAGCTAGATCTAAGTTTAATTGAGCTTACCAATGCTCTTATATTAACCCGAGC
ACGAAATAGAACCAAATTGTAAAGTTTTACAAATGTATGGTTTGACGTCATGACTTCATCTAGTG
CTTGTCACGACATGGCAATTACAGTATGTCACGTCGCAACGACACGACAAGTCTTAGCTCG
Found at i:17433415 original size:71 final size:71
Alignment explanation
Indices: 17433295--17433436 Score: 248
Period size: 71 Copynumber: 2.0 Consensus size: 71
17433285 CATATAGGGA
17433295 GAATGAATATTATCCCAAAGAGACTAAGCATACCCTATGAGAGTAACTCATTTATAACAAGGTCA
1 GAATGAATATTATCCCAAAGAGACTAAGCATACCCTATGAGAGTAACTCATTTATAACAAGGTCA
17433360 TTGGAC
66 TTGGAC
* * * *
17433366 GAATGAATATTATCCTAAAGAGATTAAGCATATCCTATGAGAGTCACTCATTTATAACAAGGTCA
1 GAATGAATATTATCCCAAAGAGACTAAGCATACCCTATGAGAGTAACTCATTTATAACAAGGTCA
17433431 TTGGAC
66 TTGGAC
17433437 TAGCACTAGT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (71 bp):
GAATGAATATTATCCCAAAGAGACTAAGCATACCCTATGAGAGTAACTCATTTATAACAAGGTCA
TTGGAC
Found at i:17433760 original size:57 final size:57
Alignment explanation
Indices: 17433675--17433786 Score: 140
Period size: 57 Copynumber: 1.9 Consensus size: 57
17433665 TAGTTGGTGA
* *
17433675 AATGGAGAAATAGGAAACATTTGAAAATG-GT-TAAGGTTTTCTCCAAAATGAAAATGAG
1 AATGGAGAAATA-GAAACATTTGAAAATGAATGT-A-GTTTTCTCCAAAATAAAAATGAG
*
17433733 AATGGAGAAAT-GAAATCATTTGCAAATGAATGTAGTTTTCTCCAAAATAAAAAT
1 AATGGAGAAATAGAAA-CATTTGAAAATGAATGTAGTTTTCTCCAAAATAAAAAT
17433787 AAAAATAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
56 4 0.08
57 30 0.62
58 13 0.27
59 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.28
Consensus pattern (57 bp):
AATGGAGAAATAGAAACATTTGAAAATGAATGTAGTTTTCTCCAAAATAAAAATGAG
Found at i:17433804 original size:19 final size:19
Alignment explanation
Indices: 17433776--17433812 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17433766 AGTTTTCTCC
17433776 AAAATAAAAATAAAAATAA
1 AAAATAAAAATAAAAATAA
* *
17433795 AAAATGAAAATGAAAATA
1 AAAATAAAAATAAAAATA
17433813 TCTTGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAATAAAAATAAAAATAA
Found at i:17438356 original size:32 final size:31
Alignment explanation
Indices: 17438311--17438406 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
17438301 CTTAGATAAT
17438311 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
17438342 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
17438374 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
17438405 TT
1 TT
17438407 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:17438757 original size:4 final size:4
Alignment explanation
Indices: 17438711--17438741 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
17438701 ATCTATCCTT
17438711 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
17438742 ACTAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:17439571 original size:16 final size:17
Alignment explanation
Indices: 17439552--17439592 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
17439542 AAAATAGTAT
17439552 TATAATAAATTTAAA-A
1 TATAATAAATTTAAACA
*
17439568 TATACTAAATTTAAACA
1 TATAATAAATTTAAACA
*
17439585 TAAAATAA
1 TATAATAA
17439593 TGCTAGATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (17 bp):
TATAATAAATTTAAACA
Found at i:17440769 original size:42 final size:41
Alignment explanation
Indices: 17440707--17440830 Score: 153
Period size: 40 Copynumber: 3.0 Consensus size: 41
17440697 CCCATTTTTA
*
17440707 TTTTAAAA-ATTTTAAAAAATTAAAAAAAGGATTTTTAAAATTT
1 TTTTAAAATATTTT--AAAATTAAAAAAAGTA-TTTTAAAATTT
* *
17440750 TTTTAAAATATTTTAAAATTAAAAAAAGTATTTTAAAAATA
1 TTTTAAAATATTTTAAAATTAAAAAAAGTATTTTAAAATTT
***
17440791 TTTTAAAAT-TAAAAAAATTAAAAAAAGTATTTTAAAATTT
1 TTTTAAAATATTTTAAAATTAAAAAAAGTATTTTAAAATTT
17440831 AAAAAAATTA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
40 26 0.36
41 18 0.25
42 15 0.21
43 8 0.11
44 5 0.07
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (41 bp):
TTTTAAAATATTTTAAAATTAAAAAAAGTATTTTAAAATTT
Found at i:17440792 original size:31 final size:29
Alignment explanation
Indices: 17440749--17440839 Score: 112
Period size: 31 Copynumber: 3.1 Consensus size: 29
17440739 TTTTAAAATT
*
17440749 TTTTTAAAATATTTTAAAATTAAAAAAAGTA
1 TTTTAAAAATATTTTAAAATTAAAAAAA--A
17440780 TTTTAAAAATATTTTAAAATT-AAAAAAA
1 TTTTAAAAATATTTTAAAATTAAAAAAAA
** *
17440808 TTAAAAAAAGTATTTTAAAATTTAAAAAAA
1 TTTTAAAAA-TATTTTAAAATTAAAAAAAA
17440838 TT
1 TT
17440840 AAAAAGTATG
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
28 8 0.15
29 12 0.22
30 15 0.27
31 20 0.36
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
TTTTAAAAATATTTTAAAATTAAAAAAAA
Found at i:17440868 original size:39 final size:38
Alignment explanation
Indices: 17440764--17440876 Score: 131
Period size: 40 Copynumber: 2.9 Consensus size: 38
17440754 AAAATATTTT
***
17440764 AAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAATTAAAAAAAGTATTTT-AAAAT-TAAAAAAATTAAA
17440804 AAAATTAAAAAAAGTATTTTAAAATTTAAAAAAATTAAA
1 AAAATTAAAAAAAGTATTTTAAAA-TTAAAAAAATTAAA
*
17440843 AAGTATGT-AAAAAA-TATTTTAAAATTAAAAAAAT
1 AA-AAT-TAAAAAAAGTATTTTAAAATTAAAAAAAT
17440877 AAATATATTT
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
38 10 0.15
39 26 0.39
40 29 0.44
41 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (38 bp):
AAAATTAAAAAAAGTATTTTAAAATTAAAAAAATTAAA
Found at i:17441924 original size:30 final size:30
Alignment explanation
Indices: 17441890--17441951 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
17441880 TTTAACAAGA
17441890 AAATGCCTCTAAAATAATAATAAAATTAAC
1 AAATGCCTCTAAAATAATAATAAAATTAAC
* *
17441920 AAATGTCTTTAAAATAATAATAAAATTAAC
1 AAATGCCTCTAAAATAATAATAAAATTAAC
17441950 AA
1 AA
17441952 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAATAAAATTAAC
Found at i:17449303 original size:33 final size:33
Alignment explanation
Indices: 17449261--17449326 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
17449251 GTCAATAGGA
17449261 AGCACAATAAACCATTGCAGCTTCAGCAAATTC
1 AGCACAATAAACCATTGCAGCTTCAGCAAATTC
17449294 AGCACAATAAACCATTGCAGCTTCAGCAAATTC
1 AGCACAATAAACCATTGCAGCTTCAGCAAATTC
17449327 TAAAGAGACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.21
Consensus pattern (33 bp):
AGCACAATAAACCATTGCAGCTTCAGCAAATTC
Found at i:17452042 original size:44 final size:44
Alignment explanation
Indices: 17451992--17452084 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
17451982 GTAGGTCAAA
*
17451992 TAATATTAAAATAACCTACACTAAT-AAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAA-AGTTTAAGTGAGAAAC
*
17452036 TAATATTAAAATAATCTACACTAATCAAAGTTTAAGTGAGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGAGAAAC
17452080 TAATA
1 TAATA
17452085 ACATAGTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 44 0.96
45 2 0.04
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGAGAAAC
Found at i:17461705 original size:154 final size:154
Alignment explanation
Indices: 17461425--17461706 Score: 395
Period size: 154 Copynumber: 1.8 Consensus size: 154
17461415 CTCCTTTCTG
* *
17461425 AACTGCGCAACCATACCCTTTGAAGGTGGTGGCTTGGATTAGGCTTCCTGGATTGCTTAGAGAAA
1 AACTGCGCAACCATACCCTTTGAAGGTGGTGGCTTGGATTAGGCTTCCTAGATTGCCTAGAGAAA
** * * ***
17461490 TGTTTAAGCGTAGTATCCTGCATGCAATTGGCGAAATGATGGGAAAAATAATCAAGGTGGACTAC
66 TGCATAAGCATAGTATCCTGCATGCAATTGGCGAAACGAAACGAAAAATAATCAAGGTGGACTAC
17461555 ATGTCTGAAAATGGTTTGAAAGTC
131 ATGTCTGAAAATGGTTTGAAAGTC
* * *
17461579 AACTGTGCAGCCATACCCTTTGAAGGTGGTGGCTTGGATTAGGCTTCCTAGATTGCCTAGTGAAA
1 AACTGCGCAACCATACCCTTTGAAGGTGGTGGCTTGGATTAGGCTTCCTAGATTGCCTAGAGAAA
* ** * *
17461644 TGCATAAGCATGGTATTTTGCATGCAATTGGTGAAACGACAACG-AAAGTAATCAAGGTGGACT
66 TGCATAAGCATAGTATCCTGCATGCAATTGGCGAAACGA-AACGAAAAATAATCAAGGTGGACT
17461707 CGAAGACTGA
Statistics
Matches: 110, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
154 109 0.99
155 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (154 bp):
AACTGCGCAACCATACCCTTTGAAGGTGGTGGCTTGGATTAGGCTTCCTAGATTGCCTAGAGAAA
TGCATAAGCATAGTATCCTGCATGCAATTGGCGAAACGAAACGAAAAATAATCAAGGTGGACTAC
ATGTCTGAAAATGGTTTGAAAGTC
Found at i:17466279 original size:38 final size:37
Alignment explanation
Indices: 17466197--17466280 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 37
17466187 ACAATACATA
* *
17466197 AACAGTAGTCATGCTTAAAATGTATTTAGTCCAACAG
1 AACAGTAGACATGCTTAAAATGTATTGAGTCCAACAG
* * *
17466234 AGGCAGTAGACATGCTTAATATGTATTCGA-TTCAACAG
1 A-ACAGTAGACATGCTTAAAATGTATT-GAGTCCAACAG
17466272 TAACAGTAG
1 -AACAGTAG
17466281 GCATACTAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
37 1 0.03
38 35 0.92
39 2 0.05
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (37 bp):
AACAGTAGACATGCTTAAAATGTATTGAGTCCAACAG
Found at i:17470748 original size:26 final size:26
Alignment explanation
Indices: 17470717--17470771 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
17470707 CTTTCATTTT
* *
17470717 CATGTTGAACATCTCTCTGCCTTCAA
1 CATGTTGAACACCTCTCTACCTTCAA
*
17470743 CATGTTGAACACCTTTCTACCTTCAA
1 CATGTTGAACACCTCTCTACCTTCAA
17470769 CAT
1 CAT
17470772 CTCTAATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.31, G:0.09, T:0.35
Consensus pattern (26 bp):
CATGTTGAACACCTCTCTACCTTCAA
Found at i:17480051 original size:21 final size:21
Alignment explanation
Indices: 17480019--17480073 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
17480009 TTTTACTACT
* *
17480019 AGTGGGTCATCCACAATAATGA
1 AGTGGTTCATCCACAACAAT-A
*
17480041 A-TGGTTCATCCACAACGATA
1 AGTGGTTCATCCACAACAATA
17480061 AGTGGTTCATCCA
1 AGTGGTTCATCCA
17480074 TAACGCGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (21 bp):
AGTGGTTCATCCACAACAATA
Found at i:17483957 original size:15 final size:15
Alignment explanation
Indices: 17483937--17483969 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17483927 TATTCTATGG
*
17483937 ATAAATAATATTTAC
1 ATAAATAATAATTAC
17483952 ATAAATAATAATTAC
1 ATAAATAATAATTAC
17483967 ATA
1 ATA
17483970 CGACACATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAAATAATAATTAC
Found at i:17488343 original size:29 final size:30
Alignment explanation
Indices: 17488284--17488341 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
17488274 TCTGAGCCTT
*
17488284 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
17488314 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
17488342 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:17488571 original size:13 final size:13
Alignment explanation
Indices: 17488553--17488584 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
17488543 TTTCCAGCAA
17488553 TTATGAATTTATT
1 TTATGAATTTATT
17488566 TTATGAATTTATT
1 TTATGAATTTATT
*
17488579 TGATGA
1 TTATGA
17488585 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:17488814 original size:50 final size:50
Alignment explanation
Indices: 17488679--17488931 Score: 308
Period size: 50 Copynumber: 4.8 Consensus size: 50
17488669 ATTTGGGTAA
*
17488679 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GA-CATG
* *
17488735 AGAGGTCCCATGTATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCC----ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
*
17488789 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
* * * *
17488839 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
** *
17488889 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
17488932 TGTTATTATC
Statistics
Matches: 177, Mismatches: 15, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
50 87 0.49
51 34 0.19
54 12 0.07
55 2 0.01
56 8 0.05
59 2 0.01
60 32 0.18
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
Found at i:17491412 original size:15 final size:15
Alignment explanation
Indices: 17491394--17491428 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
17491384 GACACATGGG
17491394 TGTGTGACACGAGCA
1 TGTGTGACACGAGCA
*
17491409 TGTGTGACACGAGCG
1 TGTGTGACACGAGCA
17491424 TGTGT
1 TGTGT
17491429 AACAAATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (15 bp):
TGTGTGACACGAGCA
Found at i:17494155 original size:22 final size:22
Alignment explanation
Indices: 17494125--17494194 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 22
17494115 CTTTTTCTTT
17494125 TTTAATTTATT-TCATTTACTTA
1 TTTAATTTATTAT-ATTTACTTA
*
17494147 TTTATTTTATTATATTTACTTTA
1 TTTAATTTATTATATTTAC-TTA
*
17494170 TTATTATATTATATATATTTACTTA
1 TT-TAAT-TTAT-TATATTTACTTA
17494195 AATATTAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 16 0.40
23 6 0.15
24 2 0.05
25 7 0.17
26 9 0.22
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTAATTTATTATATTTACTTA
Found at i:17494164 original size:14 final size:14
Alignment explanation
Indices: 17494145--17494190 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
17494135 TTCATTTACT
17494145 TATTTATTTTATTA
1 TATTTATTTTATTA
*
17494159 TATTTACTTTATTA
1 TATTTATTTTATTA
* *
17494173 T-TATATTATA-TA
1 TATTTATTTTATTA
17494185 TATTTA
1 TATTTA
17494191 CTTAAATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
12 3 0.12
13 9 0.35
14 14 0.54
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTATTTTATTA
Found at i:17494186 original size:26 final size:27
Alignment explanation
Indices: 17494139--17494193 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
17494129 ATTTATTTCA
*
17494139 TTTACTTATTTATTTTATTATATTTAC
1 TTTACTTATTTATTATATTATATTTAC
17494166 TTTA-TTATTATATTATA-TATATTTAC
1 TTTACTTATT-TATTATATTATATTTAC
17494192 TT
1 TT
17494194 AAATATTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTACTTATTTATTATATTATATTTAC
Found at i:17494200 original size:26 final size:25
Alignment explanation
Indices: 17494148--17494201 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
17494138 ATTTACTTAT
* * *
17494148 TTATTTTATTATATTTACTTTATTA
1 TTATATTATTATATTTACTTAAATA
17494173 TTATATTATATATATTTACTTAAATA
1 TTATATTAT-TATATTTACTTAAATA
17494199 TTA
1 TTA
17494202 AGTAATACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATATTATTATATTTACTTAAATA
Found at i:17494213 original size:26 final size:26
Alignment explanation
Indices: 17494158--17494215 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
17494148 TTATTTTATT
* * * *
17494158 ATATTTACTTTATTATTATATTATAT
1 ATATTTACTTAAATATTATATAATAC
17494184 ATATTTACTTAAATATTA-AGTAATAC
1 ATATTTACTTAAATATTATA-TAATAC
17494210 ATATTT
1 ATATTT
17494216 TATTAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATTTACTTAAATATTATATAATAC
Found at i:17494879 original size:24 final size:24
Alignment explanation
Indices: 17494845--17494890 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
17494835 TATATGAAAT
* *
17494845 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
17494869 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
17494891 TTTAATTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:17499269 original size:131 final size:131
Alignment explanation
Indices: 17499035--17499297 Score: 490
Period size: 131 Copynumber: 2.0 Consensus size: 131
17499025 AGGCACTTTT
*
17499035 CAATCAGCTGAAGTTGGAGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGAGGTCT
1 CAATCAGCTGAAGTTGGAGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGAGGTCA
* *
17499100 GGACTGTCAGGTAAAGCTTTAGGCTGAAAAGTTTGGGCATTGAGATGGACCATAGAAGTGTTTTG
66 GGACCGTCAGGTAAAGCTTTAGGCTGAAAAGTTTGGGCATCGAGATGGACCATAGAAGTGTTTTG
17499165 G
131 G
17499166 CAATCAGCTGAAGTTGGAGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGAGGTCA
1 CAATCAGCTGAAGTTGGAGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGAGGTCA
*
17499231 GGACCGTCAGGTAAAGCTTTAGGTTGAAAAGTTTGGGCATCGAGATGGACCATAGAAGTGTTTTG
66 GGACCGTCAGGTAAAGCTTTAGGCTGAAAAGTTTGGGCATCGAGATGGACCATAGAAGTGTTTTG
17499296 G
131 G
17499297 C
1 C
17499298 CTCATACATA
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
131 128 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (131 bp):
CAATCAGCTGAAGTTGGAGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGAGGTCA
GGACCGTCAGGTAAAGCTTTAGGCTGAAAAGTTTGGGCATCGAGATGGACCATAGAAGTGTTTTG
G
Found at i:17501394 original size:17 final size:17
Alignment explanation
Indices: 17501342--17501394 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
17501332 TACAATTGAC
17501342 TTTCATATTTTTTTGTT
1 TTTCATATTTTTTTGTT
*** *
17501359 TTGGGTAATTTATTT-TT
1 TTTCAT-ATTTTTTTGTT
17501376 TTTCATATTTTTTTGTT
1 TTTCATATTTTTTTGTT
17501393 TT
1 TT
17501395 GGGCAATTTA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
16 7 0.27
17 12 0.46
18 7 0.27
ACGTcount: A:0.13, C:0.04, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTCATATTTTTTTGTT
Found at i:17501409 original size:35 final size:34
Alignment explanation
Indices: 17501342--17501422 Score: 126
Period size: 34 Copynumber: 2.4 Consensus size: 34
17501332 TACAATTGAC
*
17501342 TTTCATATTTTTTTGTTTTGGGTAATTTATTTTT
1 TTTCATATTTTTTTGTTTTGGGCAATTTATTTTT
*
17501376 TTTCATATTTTTTTGTTTTGGGCAATTTAATTTT
1 TTTCATATTTTTTTGTTTTGGGCAATTTATTTTT
*
17501410 TTTCTTTATTTTT
1 TTTC-ATATTTTT
17501423 ATTTTGTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
34 36 0.84
35 7 0.16
ACGTcount: A:0.15, C:0.05, G:0.10, T:0.70
Consensus pattern (34 bp):
TTTCATATTTTTTTGTTTTGGGCAATTTATTTTT
Found at i:17502473 original size:6 final size:6
Alignment explanation
Indices: 17502462--17502496 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
17502452 GAAAACTGGG
17502462 GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA -GAGAA
1 GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA
17502497 TGGAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
GGAGAA
Found at i:17502960 original size:14 final size:15
Alignment explanation
Indices: 17502941--17502973 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
17502931 AGGGCTGTTC
17502941 TTAT-AGATTGAATG
1 TTATAAGATTGAATG
17502955 TTATAGAGATTGAATG
1 TTATA-AGATTGAATG
17502971 TTA
1 TTA
17502974 CAGAGAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
16 13 0.76
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (15 bp):
TTATAAGATTGAATG
Found at i:17502966 original size:16 final size:16
Alignment explanation
Indices: 17502945--17502984 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
17502935 CTGTTCTTAT
*
17502945 AGATTGAATGTTATAG
1 AGATTGAATGTTACAG
17502961 AGATTGAATGTTACAG
1 AGATTGAATGTTACAG
*
17502977 AGAATGAA
1 AGATTGAA
17502985 AATAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.30
Consensus pattern (16 bp):
AGATTGAATGTTACAG
Found at i:17507542 original size:43 final size:43
Alignment explanation
Indices: 17507494--17507785 Score: 428
Period size: 43 Copynumber: 6.8 Consensus size: 43
17507484 TTTTAGAAAA
*
17507494 AAACGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
17507537 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
17507579 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
17507622 AAACGCCACTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCAT
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
17507665 AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * ** *
17507708 AAACGGCGCTATAA-ACCATGACCTTTAGCGGCACTTTTATCAA
1 AAACGCCGCTA-AAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
17507751 AAACGCCGTTAAAGAACAA-ACCTTTAGCGGCGCTT
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTT
17507786 CTAGCAAAAA
Statistics
Matches: 227, Mismatches: 19, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
42 59 0.26
43 166 0.73
44 2 0.01
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:17507774 original size:128 final size:127
Alignment explanation
Indices: 17507492--17507785 Score: 430
Period size: 128 Copynumber: 2.3 Consensus size: 127
17507482 GTTTTTAGAA
*
17507492 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTTTCCCACAAACGCCGCTAAAGACCAAG
1 AAAAACGCCGCTAAAGACCAA-ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAG
*
17507557 ACCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCAC
65 ACCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCAC
* * * * *
17507620 ACAAACGCCACTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCATAAACGCCGCTAAAGACCAGG
1 AAAAACGCCGCTAAAGACCA-AACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAG
* *
17507685 ACCTTTAGCGGCGCTTTTCCCACAAACGGCGCTATAA-ACCATGACCTTTAGCGGCACTTTT-AT
65 ACCTTTAGCGGCGC-TTTCCCACAAACGCCGCTA-AAGACCAAGACCTTTAGCGGCACTTTTCA-
17507748 C
127 C
* *
17507749 AAAAACGCCGTTAAAGAACAAACCTTTAGCGGCGCTT
1 AAAAACGCCGCTAAAGACCAAACCTTTAGCGGCGCTT
17507786 CTAGCAAAAA
Statistics
Matches: 148, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
128 89 0.60
129 57 0.39
130 2 0.01
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (127 bp):
AAAAACGCCGCTAAAGACCAAACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGA
CCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCAC
Found at i:17507818 original size:42 final size:42
Alignment explanation
Indices: 17507492--17507818 Score: 243
Period size: 43 Copynumber: 7.7 Consensus size: 42
17507482 GTTTTTAGAA
* * *
17507492 AAAAACGCCGCTAAAGACCA-AGACCTTTAGCGGTGCTTTTCCC
1 AAAAACGCCGCTAAA-AACATA-ACCTTTAGCGGCGCTTTTACC
* * *
17507535 ACAAACGCCGCTAAAGACCA-AGACCTTTAGCGGCGC-TTTCCC
1 AAAAACGCCGCTAAA-AACATA-ACCTTTAGCGGCGCTTTTACC
* *
17507577 ACAAACGCCGCTAAAGACCA-AGACCTTTAGCGGCGCTTTT-CAC
1 AAAAACGCCGCTAAA-AACATA-ACCTTTAGCGGCGCTTTTAC-C
* * * ** *
17507620 ACAAACGCCACTAAAGACCAGGACCTTTAGCGGCGCTTTTCCC
1 AAAAACGCCGCTAAA-AACATAACCTTTAGCGGCGCTTTTACC
* * ** *
17507663 ATAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTCCC
1 AAAAACGCCGCTAAA-AACATAACCTTTAGCGGCGCTTTTACC
* * * * * *
17507706 ACAAACGGCGCTATAAACCATGACCTTTAGCGGCACTTTTATC
1 AAAAACGCCGCTA-AAAACATAACCTTTAGCGGCGCTTTTACC
* * *
17507749 AAAAACGCCGTTAAAGAACA-AACCTTTAGCGGCGCTTCTAGC
1 AAAAACGCCGCTAAA-AACATAACCTTTAGCGGCGCTTTTACC
* *
17507791 AAAAACGTCGCTAAAAACATAATCTTTA
1 AAAAACGCCGCTAAAAACATAACCTTTA
17507819 AAAAAATTAT
Statistics
Matches: 254, Mismatches: 23, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
41 4 0.02
42 83 0.33
43 164 0.65
44 3 0.01
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.20
Consensus pattern (42 bp):
AAAAACGCCGCTAAAAACATAACCTTTAGCGGCGCTTTTACC
Found at i:17509003 original size:16 final size:16
Alignment explanation
Indices: 17508982--17509012 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17508972 AGTCCCAAAC
17508982 TATTGTAAACATCAGT
1 TATTGTAAACATCAGT
17508998 TATTGTAAACATCAG
1 TATTGTAAACATCAG
17509013 ATAGGTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
TATTGTAAACATCAGT
Found at i:17511048 original size:17 final size:17
Alignment explanation
Indices: 17511026--17511060 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
17511016 CTACAGTCTA
17511026 ATTTAAAATATACTAGC
1 ATTTAAAATATACTAGC
17511043 ATTTAAAATATACTAGC
1 ATTTAAAATATACTAGC
17511060 A
1 A
17511061 CACAAAGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (17 bp):
ATTTAAAATATACTAGC
Found at i:17512969 original size:40 final size:40
Alignment explanation
Indices: 17512839--17512970 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 40
17512829 TAGATTTTTT
* ** *
17512839 GCGGCGCTTTTTGAAAAA-CGCCGCTAA-AAATAATCATTA
1 GCGGCG-TTTTTTAAAAAGCGCCGCTAATACTTAATCTTTA
* *
17512878 CCGGCGTTTTTAAAAAAGCGCCGCTAATACTTAATCTTTA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATACTTAATCTTTA
* * * * *
17512918 GCGGCGTTTTTTTAAAAGTGCCGCTAATGCTTGATTTTTA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATACTTAATCTTTA
17512958 GCGGCGTTTTTTA
1 GCGGCGTTTTTTA
17512971 TCCAAACGCC
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
38 10 0.13
39 14 0.18
40 54 0.69
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (40 bp):
GCGGCGTTTTTTAAAAAGCGCCGCTAATACTTAATCTTTA
Found at i:17514431 original size:15 final size:15
Alignment explanation
Indices: 17514403--17514443 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
17514393 AGAATGTGGA
17514403 CTATTAA-T-TTTTT
1 CTATTAATTCTTTTT
17514416 CTATTAATTCTTTTT
1 CTATTAATTCTTTTT
*
17514431 CTAATAATTCTTT
1 CTATTAATTCTTT
17514444 AATCTGTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 7 0.28
14 1 0.04
15 17 0.68
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (15 bp):
CTATTAATTCTTTTT
Found at i:17523047 original size:475 final size:475
Alignment explanation
Indices: 17522157--17523110 Score: 1692
Period size: 475 Copynumber: 2.0 Consensus size: 475
17522147 CTTTCCAATG
* * *
17522157 TAATCTCCGCCCTTGTAGTTGATAAGCTAGTTTGGAAAGGATGCGAAGCATACCTTGCTTTCGTA
1 TAATCTCCACCCTTGTAGTTGATAAGCTAGTTTAGAAAGGATGCGAAGCATACCTTGCCTTCGTA
* * *
17522222 TCTAATTCTGTTCTTATAAAGCTTTCTATAGAAAATATTCATATTGTGAGGGACTTTTCAGACGT
66 TCTAATTCTGTTCCTACAAAGCTTTCTATAGAAAATATTCATATTGTGAAGGACTTTTCAGACGT
17522287 CTTTCTCGAGGAATTGCTCGAAATACCTCCAGATAAAAAGGTTAAATTCGGTATTGATTTGTTAT
131 CTTTCTCGAGGAATTGCTCGAAATACCTCCAGATAAAAAGGTTAAATTCGGTATTGATTTGTTAT
*
17522352 CGGGTACCACTCATGTGTCTATTGTACCTTACCGAATGGCACTGAAAGAACTTGTGGAGTTAAAA
196 CGGGTACCACTCATGTGTCTATTGTACCTTACCGAATGGCACTGAAAGAACTTGTGGAGCTAAAA
*
17522417 GCTCAGCTCTAAGAACTTCTCGATAAAAGGTTCATCCGACCAAGTGTGTCTTCGTGGGGGGCACT
261 GCTCAACTCTAAGAACTTCTCGATAAAAGGTTCATCCGACCAAGTGTGTCTTCGTGGGGGGCACT
17522482 GGTATTTTTTGTTAAGAAGAAGGACAAATCGATGAGAATGTGTATAGATTACCGACAGCTGAACA
326 GGTATTTTTTGTTAAGAAGAAGGACAAATCGATGAGAATGTGTATAGATTACCGACAGCTGAACA
17522547 AGTTGACAGTAAAAAATAAGTATCCGCTATCGAAGATCGACGACTTATTCGACCAGTTTCGTGGG
391 AGTTGACAGTAAAAAATAAGTATCCGCTATCGAAGATCGACGACTTATTCGACCAGTTTCGTGGG
17522612 GCATCTATTTTCTCCAAGAT
456 GCATCTATTTTCTCCAAGAT
* *
17522632 TAATCTCCACCCTTGTAGTTGATAAGCTAGTTTAGAAAGGATGTGAGGCATACCTTGCCTTCGTA
1 TAATCTCCACCCTTGTAGTTGATAAGCTAGTTTAGAAAGGATGCGAAGCATACCTTGCCTTCGTA
* * * *
17522697 TCTGATTCTGTTCCTACAAAGCTTTCTGTAGAAAATATTCATATTGTGAATGACTTTTTAGACGT
66 TCTAATTCTGTTCCTACAAAGCTTTCTATAGAAAATATTCATATTGTGAAGGACTTTTCAGACGT
* *
17522762 CTTTCTTGAGGAATTGCTCGAAATACCTCTAGATAAAAAGGTTAAATTCGGTATTGATTTGTTAT
131 CTTTCTCGAGGAATTGCTCGAAATACCTCCAGATAAAAAGGTTAAATTCGGTATTGATTTGTTAT
* * * *
17522827 CGGGTATCGCTCCTGTGTTTATTGTACCTTACCGAATGGCACTGAAAGAACTTGTGGAGCTAAAA
196 CGGGTACCACTCATGTGTCTATTGTACCTTACCGAATGGCACTGAAAGAACTTGTGGAGCTAAAA
* * *
17522892 GCTCAACTCTAAGAACTTCTCGATAGAGGGTTCATCCGACCGAGTGTGTCTTCGTGGGGGGCACT
261 GCTCAACTCTAAGAACTTCTCGATAAAAGGTTCATCCGACCAAGTGTGTCTTCGTGGGGGGCACT
17522957 GGTATTTTTTGTTAAGAAGAAGGACAAATCGATGAGAATGTGTATAGATTACCGACAGCTGAACA
326 GGTATTTTTTGTTAAGAAGAAGGACAAATCGATGAGAATGTGTATAGATTACCGACAGCTGAACA
*
17523022 AGTTGACAGTGAAAAATAAGTATCCGCTATCGAAGATCGACGACTTATTCGACCAGTTTCGTGGG
391 AGTTGACAGTAAAAAATAAGTATCCGCTATCGAAGATCGACGACTTATTCGACCAGTTTCGTGGG
17523087 GCATCTATTTTCTCCAAGAT
456 GCATCTATTTTCTCCAAGAT
17523107 TAAT
1 TAAT
17523111 TTTTGTTATT
Statistics
Matches: 455, Mismatches: 24, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
475 455 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (475 bp):
TAATCTCCACCCTTGTAGTTGATAAGCTAGTTTAGAAAGGATGCGAAGCATACCTTGCCTTCGTA
TCTAATTCTGTTCCTACAAAGCTTTCTATAGAAAATATTCATATTGTGAAGGACTTTTCAGACGT
CTTTCTCGAGGAATTGCTCGAAATACCTCCAGATAAAAAGGTTAAATTCGGTATTGATTTGTTAT
CGGGTACCACTCATGTGTCTATTGTACCTTACCGAATGGCACTGAAAGAACTTGTGGAGCTAAAA
GCTCAACTCTAAGAACTTCTCGATAAAAGGTTCATCCGACCAAGTGTGTCTTCGTGGGGGGCACT
GGTATTTTTTGTTAAGAAGAAGGACAAATCGATGAGAATGTGTATAGATTACCGACAGCTGAACA
AGTTGACAGTAAAAAATAAGTATCCGCTATCGAAGATCGACGACTTATTCGACCAGTTTCGTGGG
GCATCTATTTTCTCCAAGAT
Found at i:17526533 original size:12 final size:12
Alignment explanation
Indices: 17526518--17526544 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17526508 GTTGTGTGCC
17526518 AGGTCGTGTGGT
1 AGGTCGTGTGGT
17526530 AGGTCGTGTGGT
1 AGGTCGTGTGGT
17526542 AGG
1 AGG
17526545 CCATGTAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.11, C:0.07, G:0.52, T:0.30
Consensus pattern (12 bp):
AGGTCGTGTGGT
Found at i:17527714 original size:33 final size:33
Alignment explanation
Indices: 17527668--17527767 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 33
17527658 TAATTTTAGT
*
17527668 ATTTCTTTGTATTATGACTTTCTAAGATTGTTG
1 ATTTATTTGTATTATGACTTTCTAAGATTGTTG
* **
17527701 ATTTA-TT-TA-TATTA-TTAGT-A-ATT-TTAG
1 ATTTATTTGTATTATGACTTTCTAAGATTGTT-G
*
17527728 TATTTCTTTGTATTATGACTTTCTAAGATTGTTG
1 -ATTTATTTGTATTATGACTTTCTAAGATTGTTG
17527762 ATTTAT
1 ATTTAT
17527768 CGACTAGGTT
Statistics
Matches: 49, Mismatches: 9, Indels: 18
0.64 0.12 0.24
Matches are distributed among these distances:
26 2 0.04
27 4 0.08
28 5 0.10
29 5 0.10
30 6 0.12
31 6 0.12
32 5 0.10
33 10 0.20
34 4 0.08
35 2 0.04
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.57
Consensus pattern (33 bp):
ATTTATTTGTATTATGACTTTCTAAGATTGTTG
Found at i:17527732 original size:28 final size:28
Alignment explanation
Indices: 17527641--17527743 Score: 75
Period size: 28 Copynumber: 3.5 Consensus size: 28
17527631 TTACCACCCC
17527641 TTTATTTATATTATTAGTAATTTTAGTA
1 TTTATTTATATTATTAGTAATTTTAGTA
* * **
17527669 TTTCTTTGTATTATGACTTTCTAAGATTGTT-G-A
1 TTT-ATT-TA-TATTA-TTAGT-A-ATT-TTAGTA
17527702 TTTATTTATATTATTAGTAATTTTAGTA
1 TTTATTTATATTATTAGTAATTTTAGTA
* *
17527730 TTTCTTTGTATTAT
1 TTTATTTATATTAT
17527744 GACTTTCTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
26 2 0.04
27 4 0.07
28 17 0.30
29 5 0.09
30 6 0.11
31 6 0.11
32 5 0.09
33 5 0.09
34 4 0.07
35 2 0.04
ACGTcount: A:0.26, C:0.04, G:0.10, T:0.60
Consensus pattern (28 bp):
TTTATTTATATTATTAGTAATTTTAGTA
Found at i:17527736 original size:61 final size:61
Alignment explanation
Indices: 17527641--17527767 Score: 254
Period size: 61 Copynumber: 2.1 Consensus size: 61
17527631 TTACCACCCC
17527641 TTTATTTATATTATTAGTAATTTTAGTATTTCTTTGTATTATGACTTTCTAAGATTGTTGA
1 TTTATTTATATTATTAGTAATTTTAGTATTTCTTTGTATTATGACTTTCTAAGATTGTTGA
17527702 TTTATTTATATTATTAGTAATTTTAGTATTTCTTTGTATTATGACTTTCTAAGATTGTTGA
1 TTTATTTATATTATTAGTAATTTTAGTATTTCTTTGTATTATGACTTTCTAAGATTGTTGA
17527763 TTTAT
1 TTTAT
17527768 CGACTAGGTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (61 bp):
TTTATTTATATTATTAGTAATTTTAGTATTTCTTTGTATTATGACTTTCTAAGATTGTTGA
Found at i:17528950 original size:21 final size:21
Alignment explanation
Indices: 17528915--17528960 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
17528905 AATTTCACCG
*
17528915 CTACAATATCCAATCTCACTA
1 CTACAATAACCAATCTCACTA
* * *
17528936 CTACAATAACTAATCTTACTC
1 CTACAATAACCAATCTCACTA
17528957 CTAC
1 CTAC
17528961 CGCTGTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (21 bp):
CTACAATAACCAATCTCACTA
Found at i:17531185 original size:16 final size:16
Alignment explanation
Indices: 17531164--17531210 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
17531154 TATATATTTT
17531164 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
17531180 AAACATAAAAAACTT-
1 AAACATAAAAAACTTA
17531195 AAAC-T-AAAAACTTA
1 AAACATAAAAAACTTA
17531209 AA
1 AA
17531211 CCAGTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.27
14 3 0.10
15 4 0.13
16 15 0.50
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19
Consensus pattern (16 bp):
AAACATAAAAAACTTA
Found at i:17531909 original size:14 final size:13
Alignment explanation
Indices: 17531885--17531919 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
17531875 AGAAGAGAGG
17531885 GAAAAGAAAGAAA
1 GAAAAGAAAGAAA
17531898 GAAAAGACAAGAAA
1 GAAAAGA-AAGAAA
17531912 G-AAAGAAA
1 GAAAAGAAA
17531920 TGTTATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.10
13 12 0.57
14 7 0.33
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (13 bp):
GAAAAGAAAGAAA
Found at i:17535098 original size:27 final size:26
Alignment explanation
Indices: 17535067--17535146 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 26
17535057 AACAAAATTT
17535067 ATATTACAAAGTTTGTTCCAATTTTTA
1 ATATTACAAAGTTTGTTCCAA-TTTTA
** * *
17535094 ATATTGTAATGTAT-TT--AA-TTT-
1 ATATTACAAAGTTTGTTCCAATTTTA
17535115 ATATTACAAAGTTTGTTCCAAGTTTTA
1 ATATTACAAAGTTTGTTCCAA-TTTTA
17535142 ATATT
1 ATATT
17535147 GTAATGTATT
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
21 10 0.26
22 5 0.13
24 4 0.10
26 5 0.13
27 15 0.38
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (26 bp):
ATATTACAAAGTTTGTTCCAATTTTA
Found at i:17535101 original size:62 final size:62
Alignment explanation
Indices: 17535000--17535333 Score: 303
Period size: 62 Copynumber: 5.9 Consensus size: 62
17534990 CAATGTGCCT
* * * *
17535000 AATTTATATTATAAAGTTTGTTCCAATTTTTAATGTTGTAATATATTTAATTTATATAACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATTACAA
17535062 AATTTATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATTAC-A
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATTACAA
* * * *
17535123 AAGTT-TGTT-CCAA----G-T----TTT--AATATTGTAATGTATTTAATTTATATTACAT
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATTACAA
* *
17535172 AATTTATATTATAAAATTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATTAC-A
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATTACAA
* * * *
17535233 AAGTT-TGTT-CCAA----G-T----TTT--AATATTGTAATGTATTTAATTTATATTACAT
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATTACAA
* * * *
17535282 AATTTATATTACAAAGTTTGTTCCAAGTTTTAGTGTTGTAATGT-TGTAATTT
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTT
17535334 TAATGCATTA
Statistics
Matches: 219, Mismatches: 25, Indels: 57
0.73 0.08 0.19
Matches are distributed among these distances:
48 58 0.26
49 8 0.04
50 12 0.05
51 5 0.02
54 2 0.01
55 4 0.02
56 2 0.01
59 5 0.02
60 11 0.05
61 16 0.07
62 96 0.44
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.51
Consensus pattern (62 bp):
AATTTATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATTACAA
Found at i:17535113 original size:24 final size:24
Alignment explanation
Indices: 17535086--17535162 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 24
17535076 AGTTTGTTCC
17535086 AATTTTTAATATTGTAATGTATTT
1 AATTTTTAATATTGTAATGTATTT
** * *
17535110 AA--TTT-ATATTACAAAGTTTGTT
1 AATTTTTAATATTGTAATGTAT-TT
*
17535132 CCAAGTTTTAATATTGTAATGTATTT
1 --AATTTTTAATATTGTAATGTATTT
17535158 AATTT
1 AATTT
17535163 ATATTACATA
Statistics
Matches: 38, Mismatches: 9, Indels: 12
0.64 0.15 0.20
Matches are distributed among these distances:
21 10 0.26
22 5 0.13
24 8 0.21
26 5 0.13
27 10 0.26
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (24 bp):
AATTTTTAATATTGTAATGTATTT
Done.