Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 15 of 120
Found at i:4424209 original size:70 final size:69
Alignment explanation
Indices: 4424129--4424262 Score: 205
Period size: 70 Copynumber: 1.9 Consensus size: 69
4424119 TCCGAATAAG
* *
4424129 AAAAGTCAAAACTATGCCGTTTTGATAAATATTTAACTTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGGCAAAACTACGCCGTTTTGATAAATATTTAACTTTTCTAAAGTTAAAAG-CAAAACCATT
4424194 CAGTT
65 CAGTT
* * * *
4424199 AAAAGGCAAAACTACGTCGTTTTTATAAATGTTTAACTTTTCTAAAGTTAAAAGGAAAACCATT
1 AAAAGGCAAAACTACGCCGTTTTGATAAATATTTAACTTTTCTAAAGTTAAAAGCAAAACCATT
4424263 ATATTGTTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
69 9 0.16
70 49 0.84
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (69 bp):
AAAAGGCAAAACTACGCCGTTTTGATAAATATTTAACTTTTCTAAAGTTAAAAGCAAAACCATTC
AGTT
Found at i:4426487 original size:24 final size:24
Alignment explanation
Indices: 4426459--4426510 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4426449 TTAGTAAGTC
*
4426459 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATGCT
* *
4426483 AAATATATTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATGCT
4426507 AAAT
1 AAAT
4426511 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATGCT
Found at i:4431627 original size:12 final size:12
Alignment explanation
Indices: 4431577--4431628 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
4431567 GCATTCCAAA
4431577 GATGAAAG-CTT
1 GATGAAAGACTT
4431588 GATTGAAA-ACTT
1 GA-TGAAAGACTT
* *
4431600 GATTAAAAACTT
1 GATGAAAGACTT
4431612 GATGAAAGACTT
1 GATGAAAGACTT
4431624 GATGA
1 GATGA
4431629 TTAAATGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 6 0.17
12 29 0.83
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (12 bp):
GATGAAAGACTT
Found at i:4432834 original size:18 final size:18
Alignment explanation
Indices: 4432811--4432853 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4432801 ACCCAATCTA
**
4432811 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
4432829 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
4432847 AACCCAA
1 AACCCAA
4432854 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:4432986 original size:18 final size:18
Alignment explanation
Indices: 4432957--4433041 Score: 107
Period size: 18 Copynumber: 4.7 Consensus size: 18
4432947 GTAGTGATTC
* *
4432957 AATTTGGTTAATTCAGAT
1 AATTCGGTTAATTCAGTT
*
4432975 AATTCGGGTAATTCAGTT
1 AATTCGGTTAATTCAGTT
** *
4432993 AATTCGGTTAATTTGGGT
1 AATTCGGTTAATTCAGTT
4433011 AATTCGGTTAATTCAGTT
1 AATTCGGTTAATTCAGTT
*
4433029 AATTTGGTTAATT
1 AATTCGGTTAATT
4433042 TTTAACCAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 56 1.00
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (18 bp):
AATTCGGTTAATTCAGTT
Found at i:4432993 original size:27 final size:27
Alignment explanation
Indices: 4432963--4433041 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
4432953 ATTCAATTTG
* *
4432963 GTTAATTCAGATAATTCGGGTAATTCA
1 GTTAATTCAGTTAATTTGGGTAATTCA
* *
4432990 GTTAATTCGGTTAATTTGGGTAATTCG
1 GTTAATTCAGTTAATTTGGGTAATTCA
*
4433017 GTTAATTCAGTTAATTTGGTTAATT
1 GTTAATTCAGTTAATTTGGGTAATT
4433042 TTTAACCAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (27 bp):
GTTAATTCAGTTAATTTGGGTAATTCA
Found at i:4433042 original size:9 final size:9
Alignment explanation
Indices: 4432957--4433041 Score: 89
Period size: 9 Copynumber: 9.4 Consensus size: 9
4432947 GTAGTGATTC
*
4432957 AATTTGGTT
1 AATTCGGTT
* *
4432966 AATTCAGAT
1 AATTCGGTT
*
4432975 AATTCGGGT
1 AATTCGGTT
*
4432984 AATTCAGTT
1 AATTCGGTT
4432993 AATTCGGTT
1 AATTCGGTT
* *
4433002 AATTTGGGT
1 AATTCGGTT
4433011 AATTCGGTT
1 AATTCGGTT
*
4433020 AATTCAGTT
1 AATTCGGTT
*
4433029 AATTTGGTT
1 AATTCGGTT
4433038 AATT
1 AATT
4433042 TTTAACCAAA
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 61 1.00
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:4433610 original size:5 final size:5
Alignment explanation
Indices: 4433600--4433650 Score: 59
Period size: 5 Copynumber: 10.2 Consensus size: 5
4433590 GGTCTACCTG
* **
4433600 TAAAA TAAAA TAAAA TAGAA -GGAA TAAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA
4433650 T
1 T
4433651 GTGTAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
4 3 0.08
5 34 0.85
6 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:4441392 original size:20 final size:20
Alignment explanation
Indices: 4441367--4441411 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
4441357 CCTTAAATTG
*
4441367 TTTTATGTATAAGATTATTA
1 TTTTATGTATAAAATTATTA
*
4441387 TTTTATTTATAAAATTATTA
1 TTTTATGTATAAAATTATTA
4441407 TTTTA
1 TTTTA
4441412 ATAAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTATGTATAAAATTATTA
Found at i:4441421 original size:20 final size:19
Alignment explanation
Indices: 4441375--4441426 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
4441365 TGTTTTATGT
**
4441375 ATAAGATTATTATTTTATTT
1 ATAA-ATTATTATTTTATAA
4441395 ATAAAATTATTATTTTAATAA
1 AT-AAATTATTATTTT-ATAA
4441416 ATAAATT-TTAT
1 ATAAATTATTAT
4441427 GTTAGAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 4 0.14
20 18 0.64
21 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATAAATTATTATTTTATAA
Found at i:4445468 original size:222 final size:222
Alignment explanation
Indices: 4445082--4445508 Score: 782
Period size: 222 Copynumber: 1.9 Consensus size: 222
4445072 CTAATAGCTC
* *
4445082 ATCAGAGTTTATCACATACATTGCACCTTGAGATGTAAGTACTACTATTGCATCTGCTACAACTT
1 ATCAGAGTCTATCACATACATTGCACCTTGAGATGTAAGTACTACTATTGCATCAGCTACAACTT
4445147 ATCACAAATATTGCTATGCCTACTGCTATCGGGTGATGGTGCAAGAAATGCTGTTTCAATTCCAA
66 ATCACAAATATTGCTATGCCTACTGCTATCGGGTGATGGTGCAAGAAATGCTGTTTCAATTCCAA
* *
4445212 GCACTTATGATCTGAGACTATTGTCCGAAAGTTGCAGGAAATTGTTAATTGAAGAGGAGAATAGA
131 GCACTTATGATCTGAGACTATTGTCCAAAAGTTGCAGGAAATTGTTAATTGAAGAGAAGAATAGA
4445277 GGGAAAGTGTATCTGATGCCTTCTGCT
196 GGGAAAGTGTATCTGATGCCTTCTGCT
* **
4445304 ATCAGAGTCTATCACATACATTGCACCTTGAGATGTAAGTACTTCTATTTTATCAGCTACAACTT
1 ATCAGAGTCTATCACATACATTGCACCTTGAGATGTAAGTACTACTATTGCATCAGCTACAACTT
4445369 ATCACAAATATTGCTATGCCTACTGCTATCGGGTGATGGTGCAAGAAATGCTGTTTCAATTCCAA
66 ATCACAAATATTGCTATGCCTACTGCTATCGGGTGATGGTGCAAGAAATGCTGTTTCAATTCCAA
*
4445434 GCACTTATGTTCTGAGACTATTGTCCAAAAGTTGCAGGAAATTGTTAATTGAAGAGAAGAATAGA
131 GCACTTATGATCTGAGACTATTGTCCAAAAGTTGCAGGAAATTGTTAATTGAAGAGAAGAATAGA
4445499 GGGAAAGTGT
196 GGGAAAGTGT
4445509 TATACCTGAC
Statistics
Matches: 197, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
222 197 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (222 bp):
ATCAGAGTCTATCACATACATTGCACCTTGAGATGTAAGTACTACTATTGCATCAGCTACAACTT
ATCACAAATATTGCTATGCCTACTGCTATCGGGTGATGGTGCAAGAAATGCTGTTTCAATTCCAA
GCACTTATGATCTGAGACTATTGTCCAAAAGTTGCAGGAAATTGTTAATTGAAGAGAAGAATAGA
GGGAAAGTGTATCTGATGCCTTCTGCT
Found at i:4449881 original size:3 final size:3
Alignment explanation
Indices: 4449873--4449906 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4449863 TGGTTTGATC
4449873 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
4449907 TTTGAATGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:4453409 original size:22 final size:21
Alignment explanation
Indices: 4453367--4453409 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4453357 AGGGTTACTA
*
4453367 AAATAATTATTATTTAAAATT
1 AAATAATTATTATTCAAAATT
* *
4453388 AAATTATTATATATTCAGAATT
1 AAATAATTAT-TATTCAAAATT
4453410 TATATTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATAATTATTATTCAAAATT
Found at i:4454937 original size:17 final size:18
Alignment explanation
Indices: 4454917--4454971 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 18
4454907 CATAAATAAA
4454917 AAATATATAAA-ATTATT
1 AAATATATAAATATTATT
**
4454934 AAATAT-TAAATATTAAA
1 AAATATATAAATATTATT
*
4454951 AAATATATAAATATTTTT
1 AAATATATAAATATTATT
4454969 AAA
1 AAA
4454972 AAAAATTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 4 0.13
17 16 0.52
18 11 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATATAAATATTATT
Found at i:4456199 original size:2 final size:2
Alignment explanation
Indices: 4456192--4456221 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4456182 TTTATAACTT
4456192 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4456222 AAGCATCTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4458032 original size:24 final size:24
Alignment explanation
Indices: 4458005--4458061 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
4457995 TATAATAAAA
4458005 ATATTAAATAATAAAAATACATTT-
1 ATATTAAATAATAAAAA-ACATTTG
* * *
4458029 ATATTAACTTATTAAAAACATTTG
1 ATATTAAATAATAAAAAACATTTG
4458053 ATATTAAAT
1 ATATTAAAT
4458062 GATAGTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (24 bp):
ATATTAAATAATAAAAAACATTTG
Found at i:4463041 original size:22 final size:22
Alignment explanation
Indices: 4463015--4463056 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4463005 CCTCAGCTAC
4463015 CCAAACACAACCAAACCCAAAT
1 CCAAACACAACCAAACCCAAAT
* *
4463037 CCAAACAGAACCAGACCCAA
1 CCAAACACAACCAAACCCAA
4463057 CTAGCCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.40, G:0.05, T:0.02
Consensus pattern (22 bp):
CCAAACACAACCAAACCCAAAT
Found at i:4464184 original size:3 final size:3
Alignment explanation
Indices: 4464178--4464220 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
4464168 ATTATTATTA
4464178 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
4464221 CGTCGTCGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:4464883 original size:75 final size:75
Alignment explanation
Indices: 4464798--4464948 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 75
4464788 CTAAGGTGCT
*
4464798 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTAAAAAAAATTTAAAATAAGGC
1 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTAAAAAAAATTTAAAATAAGAC
4464863 AATGTTTTGC
66 AATGTTTTGC
* * *
4464873 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAACAATTTTAAAATAAGAC
1 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTAAAAAAAATTTAAAATAAGAC
4464938 AATGTTTTGC
66 AATGTTTTGC
4464948 G
1 G
4464949 TTTGGGAAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (75 bp):
GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTAAAAAAAATTTAAAATAAGAC
AATGTTTTGC
Found at i:4465213 original size:113 final size:111
Alignment explanation
Indices: 4464873--4465248 Score: 583
Period size: 110 Copynumber: 3.4 Consensus size: 111
4464863 AATGTTTTGC
* * * *
4464873 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAACAATTTTAAAATAAGAC
1 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAAATTTTAAAATAAGGC
* * * *
4464938 AATGTTTTGCGTTTGGGAAATTTGAGAAAACATGGCCTAAGGTGCT
66 AATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
4464984 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT-AAAAATTTTAAAATAAGGC
1 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAAATTTTAAAATAAGGC
* *
4465048 AATGTTTTGCATTTGGGTAATTCGAGAGAACGTGCCCTAAGGTGCT
66 AATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* *
4465094 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAAAATTTTCGAAATAAG
1 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT-AAAAAATTTT-AAAATAAG
4465159 GCAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
64 GCAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* * * *
4465207 GGGTGTCGATTTTTCTCATTTAACCGAATAGCCAAATATCCT
1 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
4465249 CTTGAATTTC
Statistics
Matches: 243, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
110 101 0.42
111 43 0.18
112 9 0.04
113 90 0.37
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (111 bp):
GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAAATTTTAAAATAAGGC
AATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
Found at i:4468720 original size:20 final size:20
Alignment explanation
Indices: 4468695--4468732 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4468685 TGAGCACCGA
*
4468695 AATAACAGATACAAAAATTC
1 AATAACAAATACAAAAATTC
*
4468715 AATAACAAATAGAAAAAT
1 AATAACAAATACAAAAAT
4468733 AACACAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (20 bp):
AATAACAAATACAAAAATTC
Found at i:4473385 original size:27 final size:26
Alignment explanation
Indices: 4473333--4473399 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 26
4473323 ATTATATATT
*
4473333 AAATATATATATTTTTATTTTTAATC
1 AAATATATATATTTTTATTTTCAATC
4473359 AAATATATATATATTTTATTTTCAATC
1 AAATATATATAT-TTTTATTTTCAATC
4473386 AAATATATATATTT
1 AAATATATATATTT
4473400 AATATATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 14 0.36
27 25 0.64
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (26 bp):
AAATATATATATTTTTATTTTCAATC
Found at i:4473405 original size:13 final size:13
Alignment explanation
Indices: 4473387--4473477 Score: 104
Period size: 13 Copynumber: 7.4 Consensus size: 13
4473377 TTTTCAATCA
4473387 AATATATATATTT
1 AATATATATATTT
4473400 AATATATATATTT
1 AATATATATATTT
* * *
4473413 TAT-TTTCA-ATTA
1 AATATAT-ATATTT
4473425 AATATATATATTT
1 AATATATATATTT
4473438 AATATATATATTT
1 AATATATATATTT
4473451 --TATATATA-TT
1 AATATATATATTT
4473461 AA-ATATATATTT
1 AATATATATATTT
4473473 AATAT
1 AATAT
4473478 GGGTTAGACC
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
10 2 0.03
11 15 0.23
12 12 0.18
13 36 0.55
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATATATATTT
Found at i:4473406 original size:11 final size:11
Alignment explanation
Indices: 4473390--4473477 Score: 52
Period size: 11 Copynumber: 7.4 Consensus size: 11
4473380 TCAATCAAAT
4473390 ATATATATTTA
1 ATATATATTTA
4473401 ATATATATATT-
1 ATATATAT-TTA
* * *
4473412 TTATTTTCAATTA
1 ATA-TAT-ATTTA
4473425 AATATATATATTTA
1 -ATATATA--TTTA
*
4473439 ATATATATATTTT
1 ATA--TATATTTA
*
4473452 ATATATATTAA
1 ATATATATTTA
4473463 ATATATATTTA
1 ATATATATTTA
4473474 ATAT
1 ATAT
4473478 GGGTTAGACC
Statistics
Matches: 58, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
11 30 0.52
12 7 0.12
13 12 0.21
14 5 0.09
15 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATATATTTA
Found at i:4473408 original size:38 final size:38
Alignment explanation
Indices: 4473363--4473453 Score: 173
Period size: 38 Copynumber: 2.4 Consensus size: 38
4473353 TTAATCAAAT
4473363 ATATATATATTTTATTTTCAATCAAATATATATATTTA
1 ATATATATATTTTATTTTCAATCAAATATATATATTTA
*
4473401 ATATATATATTTTATTTTCAATTAAATATATATATTTA
1 ATATATATATTTTATTTTCAATCAAATATATATATTTA
4473439 ATATATATATTTTAT
1 ATATATATATTTTAT
4473454 ATATATTAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (38 bp):
ATATATATATTTTATTTTCAATCAAATATATATATTTA
Found at i:4475136 original size:28 final size:28
Alignment explanation
Indices: 4475089--4475148 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
4475079 ATTCCTACTC
*
4475089 TTTTCTAATAGCAGATTGATAAATTAAA
1 TTTTCTAATAGCAGAATGATAAATTAAA
* * *
4475117 TTTTCTAGTAGGAGAATGATAAATTAGA
1 TTTTCTAATAGCAGAATGATAAATTAAA
4475145 TTTT
1 TTTT
4475149 TTTTCCTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (28 bp):
TTTTCTAATAGCAGAATGATAAATTAAA
Found at i:4476430 original size:18 final size:18
Alignment explanation
Indices: 4476407--4476441 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4476397 TGTAAGTGTG
4476407 TGAAGAATCATTAAGGTA
1 TGAAGAATCATTAAGGTA
*
4476425 TGAAGAGTCATTAAGGT
1 TGAAGAATCATTAAGGT
4476442 GGAGGAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.29
Consensus pattern (18 bp):
TGAAGAATCATTAAGGTA
Found at i:4491977 original size:2 final size:2
Alignment explanation
Indices: 4491970--4492015 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4491960 AAATTTCAAA
4491970 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4492012 AT AT
1 AT AT
4492016 CAAAACCCAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4502976 original size:39 final size:39
Alignment explanation
Indices: 4502933--4503012 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
4502923 ACCCCTGTAC
4502933 AAATCTTCGATAATAACCAGCTAAACCCAAGAAACTTCT
1 AAATCTTCGATAATAACCAGCTAAACCCAAGAAACTTCT
4502972 AAATCTTCGATAATAACCAGCTAAACCCAAGAAACTTCT
1 AAATCTTCGATAATAACCAGCTAAACCCAAGAAACTTCT
4503011 AA
1 AA
4503013 CTTCAGATAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.23
Consensus pattern (39 bp):
AAATCTTCGATAATAACCAGCTAAACCCAAGAAACTTCT
Found at i:4523166 original size:18 final size:18
Alignment explanation
Indices: 4523143--4523180 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4523133 CTGATTTACA
4523143 TAGGATTAAAAGTAGGAG
1 TAGGATTAAAAGTAGGAG
**
4523161 TAGGATTAGTAGTAGGAG
1 TAGGATTAAAAGTAGGAG
4523179 TA
1 TA
4523181 TGAGTAGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.34, T:0.26
Consensus pattern (18 bp):
TAGGATTAAAAGTAGGAG
Found at i:4523188 original size:18 final size:18
Alignment explanation
Indices: 4523153--4523188 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4523143 TAGGATTAAA
*
4523153 AGTAGGAGTAGGATTAGT
1 AGTAGGAGTAGGAGTAGT
*
4523171 AGTAGGAGTATGAGTAGT
1 AGTAGGAGTAGGAGTAGT
4523189 GTTAGATGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.39, T:0.28
Consensus pattern (18 bp):
AGTAGGAGTAGGAGTAGT
Found at i:4526512 original size:41 final size:41
Alignment explanation
Indices: 4526461--4526555 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
4526451 TCAAACCGTT
* * *
4526461 TTGATGTTGCAAAGTTCTAG-ATGGGTTC-TCCTCTAGTCATG
1 TTGAAGTTGCAAAGTTC-AGAATGGG-CCATCCTCTAGCCATG
*
4526502 TTGAAGTTGCAAAGTTCGGAATGGGCCATCCTCTAGCCATG
1 TTGAAGTTGCAAAGTTCAGAATGGGCCATCCTCTAGCCATG
4526543 TTGAAGTTGCAAA
1 TTGAAGTTGCAAA
4526556 ATCTTTTCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 2 0.04
41 46 0.96
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (41 bp):
TTGAAGTTGCAAAGTTCAGAATGGGCCATCCTCTAGCCATG
Found at i:4529519 original size:23 final size:23
Alignment explanation
Indices: 4529485--4529559 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
4529475 AACATATTGG
* *
4529485 ATAACACAAAGCACCGAAGTGAT
1 ATAACACAAAGCACCAAAGTGCT
* *
4529508 GTAACACGAAGCA-CAAATGTGCT
1 ATAACACAAAGCACCAAA-GTGCT
*
4529531 ATATCACAAAGCACCAAAGTGCT
1 ATAACACAAAGCACCAAAGTGCT
4529554 ATAACA
1 ATAACA
4529560 TGAAGTACCG
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 3 0.07
23 35 0.83
24 4 0.10
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.16
Consensus pattern (23 bp):
ATAACACAAAGCACCAAAGTGCT
Found at i:4562056 original size:87 final size:87
Alignment explanation
Indices: 4561900--4562059 Score: 268
Period size: 87 Copynumber: 1.8 Consensus size: 87
4561890 AAAGAATTAG
*
4561900 TGGTGCTAACATGATTTGAAAGCAATGCATATACAAATCAAGTACATAATTTAGTTATCCAAATA
1 TGGTGCTAACATGATTTGAAAGCAATGCATATACAAATCAAGTACATAAATTAGTTATCCAAATA
4561965 ATTTATAAGCAAAAGAGCTCAA
66 ATTTATAAGCAAAAGAGCTCAA
* *
4561987 TGGTTCTAACATGATTTGAAAGCAATGCATATACAAATCAAGTGTCA-AAATTAGTTATCCAAAT
1 TGGTGCTAACATGATTTGAAAGCAATGCATATACAAATCAAGT-ACATAAATTAGTTATCCAAAT
*
4562051 GATTTATAA
65 AATTTATAA
4562060 ACATGCTCTT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
87 66 0.97
88 2 0.03
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (87 bp):
TGGTGCTAACATGATTTGAAAGCAATGCATATACAAATCAAGTACATAAATTAGTTATCCAAATA
ATTTATAAGCAAAAGAGCTCAA
Found at i:4562652 original size:22 final size:23
Alignment explanation
Indices: 4562581--4562654 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
4562571 TAACACTCCA
* *
4562581 CAATAATAATCGCATCAAAGTGC
1 CAATAACAATCGCACCAAAGTGC
* * *
4562604 TAGTATCAATCGCACCAAAGTGC
1 CAATAACAATCGCACCAAAGTGC
*
4562627 CAATAACAATCGCACC-AAGTGT
1 CAATAACAATCGCACCAAAGTGC
4562649 CAATAA
1 CAATAA
4562655 GCTCCCACCA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 11 0.26
23 31 0.74
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (23 bp):
CAATAACAATCGCACCAAAGTGC
Found at i:4565832 original size:271 final size:271
Alignment explanation
Indices: 4565349--4565896 Score: 1069
Period size: 271 Copynumber: 2.0 Consensus size: 271
4565339 TGATAAACGA
*
4565349 TGAAATATGAATGATGCTTATATTTGTGCATTATTGGTCATGGTTTAAGCTCATATGTGAAAATA
1 TGAAATATGAATGAAGCTTATATTTGTGCATTATTGGTCATGGTTTAAGCTCATATGTGAAAATA
4565414 AAGTTTCATAGTATGTGTGTATGGTATATTCGGTCTATGATTTGGCATGAAATAATGTCATGAAT
66 AAGTTTCATAGTATGTGTGTATGGTATATTCGGTCTATGATTTGGCATGAAATAATGTCATGAAT
4565479 GGTTTATCATGTGGTTAGTTCCAAAAAGAGTTATGTTTAAATACACTAGCTTGCAACTATGGTTG
131 GGTTTATCATGTGGTTAGTTCCAAAAAGAGTTATGTTTAAATACACTAGCTTGCAACTATGGTTG
4565544 AATGATATGTTTATATCTTGTGTGATGTGCATAGGAACAAGTGTGGAAAGATAATGAAATAGTAA
196 AATGATATGTTTATATCTTGTGTGATGTGCATAGGAACAAGTGTGGAAAGATAATGAAATAGTAA
4565609 GTTCATATGGC
261 GTTCATATGGC
*
4565620 TGAAATATGAATGAAGCTTATATTTGTGCATTATTGGTCATGGTTTAAGCTCATGTGTGAAAATA
1 TGAAATATGAATGAAGCTTATATTTGTGCATTATTGGTCATGGTTTAAGCTCATATGTGAAAATA
*
4565685 AAGTTTCATAGTATGTGTGTATGGTATATTCGGTTTATGATTTGGCATGAAATAATGTCATGAAT
66 AAGTTTCATAGTATGTGTGTATGGTATATTCGGTCTATGATTTGGCATGAAATAATGTCATGAAT
4565750 GGTTTATCATGTGGTTAGTTCCAAAAAGAGTTATGTTTAAATACACTAGCTTGCAACTATGGTTG
131 GGTTTATCATGTGGTTAGTTCCAAAAAGAGTTATGTTTAAATACACTAGCTTGCAACTATGGTTG
4565815 AATGATATGTTTATATCTTGTGTGATGTGCATAGGAACAAGTGTGGAAAGATAATGAAATAGTAA
196 AATGATATGTTTATATCTTGTGTGATGTGCATAGGAACAAGTGTGGAAAGATAATGAAATAGTAA
4565880 GTTCATATGGC
261 GTTCATATGGC
4565891 TGAAAT
1 TGAAAT
4565897 TTAATGATTA
Statistics
Matches: 274, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
271 274 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (271 bp):
TGAAATATGAATGAAGCTTATATTTGTGCATTATTGGTCATGGTTTAAGCTCATATGTGAAAATA
AAGTTTCATAGTATGTGTGTATGGTATATTCGGTCTATGATTTGGCATGAAATAATGTCATGAAT
GGTTTATCATGTGGTTAGTTCCAAAAAGAGTTATGTTTAAATACACTAGCTTGCAACTATGGTTG
AATGATATGTTTATATCTTGTGTGATGTGCATAGGAACAAGTGTGGAAAGATAATGAAATAGTAA
GTTCATATGGC
Found at i:4566099 original size:46 final size:46
Alignment explanation
Indices: 4566032--4566194 Score: 285
Period size: 46 Copynumber: 3.6 Consensus size: 46
4566022 TTTGAGTACT
4566032 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
4566078 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
4566124 TTTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
4566170 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
4566195 ATCATATGTA
Statistics
Matches: 113, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
44 12 0.11
45 5 0.04
46 96 0.85
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:4574750 original size:26 final size:27
Alignment explanation
Indices: 4574702--4574756 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
4574692 GAACAAATGG
**
4574702 AAAGTGATTGTTGCTGTTGTAAAAAAA
1 AAAGTGATTGTTGCACTTGTAAAAAAA
*
4574729 AAAGTGA-TGTTGCACTTTTAAAAAAA
1 AAAGTGATTGTTGCACTTGTAAAAAAA
4574755 AA
1 AA
4574757 TTGCAGCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.31
Consensus pattern (27 bp):
AAAGTGATTGTTGCACTTGTAAAAAAA
Found at i:4575544 original size:6 final size:6
Alignment explanation
Indices: 4575497--4575535 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
4575487 CACCACTATC
* * *
4575497 ATGGTG ATTGTA ACGGTG ATGGTG ATGGTG ATGGTG ATG
1 ATGGTG ATGGTG ATGGTG ATGGTG ATGGTG ATGGTG ATG
4575536 ATGGTGATGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.21, C:0.03, G:0.44, T:0.33
Consensus pattern (6 bp):
ATGGTG
Found at i:4578771 original size:32 final size:31
Alignment explanation
Indices: 4578702--4578772 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
4578692 CAAGTTGAAG
*
4578702 TACCAAA-TAGAACAAAAAAAAAAGATTAAT
1 TACCAAATTAGAACAAAAAAAAAAGATTAAA
*
4578732 TACCAAATTAGAA-AAAAAAAAGTAAGTTTAAA
1 TACCAAATTAGAACAAAAAAAA--AAGATTAAA
*
4578764 TATCAAATT
1 TACCAAATT
4578773 GGATCCCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 15 0.43
31 5 0.14
32 15 0.43
ACGTcount: A:0.62, C:0.08, G:0.07, T:0.23
Consensus pattern (31 bp):
TACCAAATTAGAACAAAAAAAAAAGATTAAA
Found at i:4578858 original size:31 final size:31
Alignment explanation
Indices: 4578790--4578862 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
4578780 AAAAAAGATT
* * *
4578790 AAGTATCAAATTAAGAAAAAGTGCTAACTTT
1 AAGTACCAAATTAAGAAAAAGTACTAACTTC
* * * *
4578821 AGGTACCAAATTAGGAAAAAGTATTAAGTTC
1 AAGTACCAAATTAAGAAAAAGTACTAACTTC
4578852 AAGTACCAAAT
1 AAGTACCAAAT
4578863 ATTATATTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (31 bp):
AAGTACCAAATTAAGAAAAAGTACTAACTTC
Found at i:4579002 original size:22 final size:23
Alignment explanation
Indices: 4578972--4579015 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
4578962 AAATTACATA
4578972 ATATATAAAAA-TAGAATAAAAAC
1 ATATATAAAAAGTA-AATAAAAAC
4578995 ATAT-TAAAAAGTAAATAAAAA
1 ATATATAAAAAGTAAATAAAAA
4579016 TGGACTGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (23 bp):
ATATATAAAAAGTAAATAAAAAC
Found at i:4580305 original size:6 final size:6
Alignment explanation
Indices: 4580281--4580320 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
4580271 TATACTAAGT
4580281 ATATAG ATAGGTA- ATATAG ATATAG ATATAG ATATAG ATA
1 ATATAG ATA--TAG ATATAG ATATAG ATATAG ATATAG ATA
4580321 GGTAAATTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 2 0.06
6 24 0.77
7 3 0.10
8 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:4580374 original size:23 final size:22
Alignment explanation
Indices: 4580348--4580414 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
4580338 GATGTGAGTG
* *
4580348 AAAAATAATTTTTGTAAAAATAT
1 AAAAAAAATTTTTATAAAAAT-T
*
4580371 AAAAAAAATTTATATAAAAATT
1 AAAAAAAATTTTTATAAAAATT
* *
4580393 AAAATAAAATTTTGATTAAAAT
1 AAAA-AAAATTTTTATAAAAAT
4580415 GATAAATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 5 0.14
23 32 0.86
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (22 bp):
AAAAAAAATTTTTATAAAAATT
Found at i:4580421 original size:24 final size:23
Alignment explanation
Indices: 4580362--4580421 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
4580352 ATAATTTTTG
*
4580362 TAAAAATATAAAAAAAATTTATA
1 TAAAAATATAAATAAAATTTATA
4580385 TAAAAAT-TAAAATAAAATTT-TGA
1 TAAAAATAT-AAATAAAATTTAT-A
*
4580408 TTAAAATGATAAAT
1 TAAAAAT-ATAAAT
4580422 TTAAGATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 2 0.06
23 24 0.77
24 4 0.13
25 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (23 bp):
TAAAAATATAAATAAAATTTATA
Found at i:4584201 original size:21 final size:22
Alignment explanation
Indices: 4584163--4584207 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
4584153 GAAAACAGAA
* * *
4584163 AACTAATGTAAGTCATATCTAG
1 AACTAATGAAAGTAATATATAG
4584185 AACTAAT-AAAGTAATATATAG
1 AACTAATGAAAGTAATATATAG
4584206 AA
1 AA
4584208 GTGAAGGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (22 bp):
AACTAATGAAAGTAATATATAG
Found at i:4588034 original size:31 final size:32
Alignment explanation
Indices: 4587999--4588070 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
4587989 ATCAAAGTTA
* * *
4587999 TAATTTGATTAACAAAATTATTCAAAAAT-TT
1 TAATTTAAGTAACAAAACTATTCAAAAATATT
* *
4588030 TAATTTAAGTCACTAAACTATTCAAAAATATT
1 TAATTTAAGTAACAAAACTATTCAAAAATATT
4588062 T-ATTTAAGT
1 TAATTTAAGT
4588071 CACTAGGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 32 0.91
32 3 0.09
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (32 bp):
TAATTTAAGTAACAAAACTATTCAAAAATATT
Found at i:4588071 original size:31 final size:31
Alignment explanation
Indices: 4588017--4588075 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
4588007 TTAACAAAAT
4588017 TATTCAAAAATTTTAATTTAAGTCACTAAAC
1 TATTCAAAAATTTTAATTTAAGTCACTAAAC
4588048 TATTCAAAAATATTT-ATTTAAGTCACTA
1 TATTCAAAAAT-TTTAATTTAAGTCACTA
4588076 GGCTGTAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (31 bp):
TATTCAAAAATTTTAATTTAAGTCACTAAAC
Found at i:4600307 original size:24 final size:22
Alignment explanation
Indices: 4600275--4600335 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
4600265 AACCAAAATA
*
4600275 CCTTATTTTTTTCTTCTTTTCCTT
1 CCTTCTTTTTTTCTTC-TTT-CTT
* *
4600299 CCTTCTTTTCTTCTGCTTTCTT
1 CCTTCTTTTTTTCTTCTTTCTT
*
4600321 CCTTC-TTATTTCTTC
1 CCTTCTTTTTTTCTTC
4600336 CGTTTCTGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 7 0.23
22 8 0.26
23 3 0.10
24 13 0.42
ACGTcount: A:0.03, C:0.30, G:0.02, T:0.66
Consensus pattern (22 bp):
CCTTCTTTTTTTCTTCTTTCTT
Found at i:4600442 original size:27 final size:27
Alignment explanation
Indices: 4600396--4600475 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
4600386 ATCAGAGCAT
4600396 TGGCGCCTCTCAG-TATGGCACCAATAA
1 TGGCGCCTCTCAGATA-GGCACCAATAA
* ** *
4600423 TGGCGCCTCCCAGATAGGCACCACCAT
1 TGGCGCCTCTCAGATAGGCACCAATAA
* *
4600450 TGGCGCCTCTGAGATAGGCGCCAATA
1 TGGCGCCTCTCAGATAGGCACCAATA
4600476 CTATGTATTA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
27 41 0.95
28 2 0.05
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.19
Consensus pattern (27 bp):
TGGCGCCTCTCAGATAGGCACCAATAA
Found at i:4604808 original size:15 final size:16
Alignment explanation
Indices: 4604776--4604809 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4604766 GTTAATGGAA
*
4604776 AAAATAATTTTAATAT
1 AAAATAATTATAATAT
4604792 AAAATAATTAT-ATAT
1 AAAATAATTATAATAT
4604807 AAA
1 AAA
4604810 GTTTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATAATTATAATAT
Found at i:4604906 original size:17 final size:17
Alignment explanation
Indices: 4604884--4604920 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4604874 ATATGATAGC
*
4604884 TTTTTTTATGAAATAAT
1 TTTTTTTATCAAATAAT
*
4604901 TTTTTTTATCAAATTAT
1 TTTTTTTATCAAATAAT
4604918 TTT
1 TTT
4604921 ACCAAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTTTTTATCAAATAAT
Found at i:4608696 original size:2 final size:2
Alignment explanation
Indices: 4608691--4608718 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4608681 TTGTGTGTAA
4608691 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4608719 CAAGTACCCA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4610938 original size:29 final size:28
Alignment explanation
Indices: 4610886--4610940 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
4610876 TCGGATTCTT
*
4610886 TTTAATAGTACAAGATTAAATTGATCTA
1 TTTAATAGTAAAAGATTAAATTGATCTA
*
4610914 TTTAATAGTAGAAATATTAAATTGATC
1 TTTAATAGTA-AAAGATTAAATTGATC
4610941 CAATCTCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (28 bp):
TTTAATAGTAAAAGATTAAATTGATCTA
Found at i:4614426 original size:15 final size:15
Alignment explanation
Indices: 4614406--4614434 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4614396 AGACAAAGCA
4614406 GAAGAAGAAGCAGAT
1 GAAGAAGAAGCAGAT
4614421 GAAGAAGAAGCAGA
1 GAAGAAGAAGCAGA
4614435 AGAAATAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.07, G:0.34, T:0.03
Consensus pattern (15 bp):
GAAGAAGAAGCAGAT
Found at i:4614435 original size:24 final size:24
Alignment explanation
Indices: 4614405--4614476 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
4614395 GAGACAAAGC
*
4614405 AGAAGAAGAAGCAGATGAAGAAGA
1 AGAAGAAGAAGCAGAGGAAGAAGA
* **
4614429 AGCAGAAGAAATAGAGGAAGAAGA
1 AGAAGAAGAAGCAGAGGAAGAAGA
* * *
4614453 GGAAGGAGAAGGAGAGGAAGAAGA
1 AGAAGAAGAAGCAGAGGAAGAAGA
4614477 GAAAGAGAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.56, C:0.03, G:0.39, T:0.03
Consensus pattern (24 bp):
AGAAGAAGAAGCAGAGGAAGAAGA
Found at i:4614477 original size:24 final size:23
Alignment explanation
Indices: 4614441--4614485 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
4614431 CAGAAGAAAT
*
4614441 AGAGGAAGAAGAGGAAGGAGAAGG
1 AGAGGAAGAAGA-GAAAGAGAAGG
4614465 AGAGGAAGAAGAGAAAGAGAA
1 AGAGGAAGAAGAGAAAGAGAA
4614486 AATGATGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (23 bp):
AGAGGAAGAAGAGAAAGAGAAGG
Found at i:4617149 original size:46 final size:48
Alignment explanation
Indices: 4617083--4617179 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 48
4617073 ACCACTATTT
4617083 TTTCTATAAGCCGTCCCCCATGCGTTTAGGG-GCAAGGCCACTTTATTAC
1 TTTCTATAAGCCG-CCCCCATGCGTTT-GGGAGCAAGGCCACTTTATTAC
* * *
4617132 TTTCTATAAG-C-CCCCCATGTGTTTGGGAGCAGGGTCACTTTATTAC
1 TTTCTATAAGCCGCCCCCATGCGTTTGGGAGCAAGGCCACTTTATTAC
4617178 TT
1 TT
4617180 ATTGGGTTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
45 3 0.07
46 30 0.68
48 1 0.02
49 10 0.23
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.34
Consensus pattern (48 bp):
TTTCTATAAGCCGCCCCCATGCGTTTGGGAGCAAGGCCACTTTATTAC
Found at i:4621121 original size:38 final size:38
Alignment explanation
Indices: 4621024--4621142 Score: 134
Period size: 38 Copynumber: 3.1 Consensus size: 38
4621014 ATATATTTGC
*
4621024 GTTATCGAATGGAATAACTCTTATGAGCAAACAGGCGT
1 GTTATCGAATGGAATAACTCTTATGAGCAAACTGGCGT
* * * *
4621062 GATAT-TAGGTGGAATAGCTCTTATGAGCAAACTGGCGT
1 GTTATCGA-ATGGAATAACTCTTATGAGCAAACTGGCGT
* * *
4621100 GTTATCGAAT-GAGATAACTCTTATGAGTAAAATGGTGT
1 GTTATCGAATGGA-ATAACTCTTATGAGCAAACTGGCGT
4621138 GTTAT
1 GTTAT
4621143 TGGGTACCCG
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
37 3 0.05
38 62 0.94
39 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (38 bp):
GTTATCGAATGGAATAACTCTTATGAGCAAACTGGCGT
Found at i:4625396 original size:20 final size:20
Alignment explanation
Indices: 4625349--4625388 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4625339 ATTTAAATTT
* *
4625349 TATCAATATCTATCATTATA
1 TATCTATATCTATCACTATA
4625369 TATCTATATCTAT-ACTATA
1 TATCTATATCTATCACTATA
4625388 T
1 T
4625389 TATTTATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (20 bp):
TATCTATATCTATCACTATA
Found at i:4629778 original size:18 final size:18
Alignment explanation
Indices: 4629755--4629792 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4629745 ATGTTTAAAC
* *
4629755 TTGGATTCTGCTGCTTTA
1 TTGGATTCTACTGATTTA
4629773 TTGGATTCTACTGATTTA
1 TTGGATTCTACTGATTTA
4629791 TT
1 TT
4629793 TAGGAAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.13, G:0.18, T:0.53
Consensus pattern (18 bp):
TTGGATTCTACTGATTTA
Found at i:4635615 original size:23 final size:22
Alignment explanation
Indices: 4635563--4635616 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
4635553 CTAGGTGGTA
* *
4635563 AGTTGAGC-CTTGCTTTACTGG
1 AGTTAAGCACTTGCCTTACTGG
*
4635584 ATTTAAAGCACTTGCCTTACTTGG
1 AGTT-AAGCACTTGCCTTAC-TGG
4635608 AGTTAAGCA
1 AGTTAAGCA
4635617 ACAATGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 3 0.12
23 14 0.54
24 6 0.23
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (22 bp):
AGTTAAGCACTTGCCTTACTGG
Found at i:4636401 original size:19 final size:18
Alignment explanation
Indices: 4636379--4636418 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
4636369 TGAATAAAAC
4636379 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
4636398 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
4636416 TTA
1 TTA
4636419 AAATATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:4639598 original size:13 final size:13
Alignment explanation
Indices: 4639580--4639604 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4639570 TATTTTAATA
4639580 TTATTTTGTGTGT
1 TTATTTTGTGTGT
4639593 TTATTTTGTGTG
1 TTATTTTGTGTG
4639605 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:4641436 original size:41 final size:41
Alignment explanation
Indices: 4641401--4641585 Score: 237
Period size: 41 Copynumber: 4.5 Consensus size: 41
4641391 GTGAAATTGT
* *
4641401 TCAGACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAA
1 TCAGACTATACGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
*
4641442 TCGGACTATACGTCC-AGCAGGCTAAGTGCCGGTGAACTGAA
1 TCAGACTATACG-CCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * *
4641483 TCAGGCTACAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
1 TCAGACTATACGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * * *
4641524 GCAGGCTATAGGCCTAGCAGGCTAAGTGCCGGTGAACGGAA
1 TCAGACTATACGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * *
4641565 TTAGACTATAAGCCTATCAGG
1 TCAGACTATACGCCTAGCAGG
4641586 TGCAGTGCCA
Statistics
Matches: 126, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
40 2 0.02
41 123 0.98
42 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (41 bp):
TCAGACTATACGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
Found at i:4647399 original size:13 final size:13
Alignment explanation
Indices: 4647381--4647405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4647371 TATTTTAATA
4647381 TTATTTTGTGTGT
1 TTATTTTGTGTGT
4647394 TTATTTTGTGTG
1 TTATTTTGTGTG
4647406 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:4648729 original size:41 final size:41
Alignment explanation
Indices: 4648593--4648751 Score: 171
Period size: 41 Copynumber: 3.9 Consensus size: 41
4648583 GTGAAATTGT
* * *
4648593 TCAGACTATACA-TCTAGCAGGCTAAGTGCCGATGAATTGAA
1 TCAGACTATA-AGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
* *
4648634 TCGGACTATACGTCC-AGCAGGCTAAGTGCCGGTGAACTGAA
1 TCAGACTATAAG-CCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * *
4648675 TCAGGCTACAAGCCTAGCAGGCTAAGTGCCGGTGAACGGAA
1 TCAGACTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * *
4648716 TTAGACTATAAGCCTATCAGG-TGAAGTGCCAGTGAA
1 TCAGACTATAAGCCTAGCAGGCT-AAGTGCCGGTGAA
4648752 TCCGTTTAAA
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.03
41 95 0.96
42 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (41 bp):
TCAGACTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
Found at i:4649024 original size:33 final size:34
Alignment explanation
Indices: 4648939--4649025 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 34
4648929 TTTAAGTGTG
*
4648939 TATATGTATGCATTCAGCATAGGTGGATATATATA
1 TATATG-ATGCATTCGGCATAGGTGGATATATATA
*
4648974 TATATGTATGCATTCGGCATAGGTGGGTATA-AGTGA
1 TATATG-ATGCATTCGGCATAGGTGGATATATA-T-A
4649010 -ATATG-TGCATTCGGCA
1 TATATGATGCATTCGGCA
4649026 CTTATAGTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
33 11 0.23
34 1 0.02
35 35 0.73
36 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.34
Consensus pattern (34 bp):
TATATGATGCATTCGGCATAGGTGGATATATATA
Found at i:4658730 original size:42 final size:42
Alignment explanation
Indices: 4658672--4658761 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
4658662 CCTAATTGGA
* *
4658672 AAAATAATTCTCTTATTCTAATCAACTACTAAAACATAAGAG
1 AAAATAATTCTCTTATTCTAATAAACTACTAAAACATAAAAG
* *
4658714 AAAATAATTCTCTTATTCTAATAAACTACTAAAAGATAAAAT
1 AAAATAATTCTCTTATTCTAATAAACTACTAAAACATAAAAG
4658756 AAAATA
1 AAAATA
4658762 TTCCTAGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.31
Consensus pattern (42 bp):
AAAATAATTCTCTTATTCTAATAAACTACTAAAACATAAAAG
Found at i:4667880 original size:15 final size:15
Alignment explanation
Indices: 4667835--4667881 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
4667825 CCGTTAACCG
4667835 TTAACCAAACCAAAAT
1 TTAACCAAA-CAAAAT
***
4667851 TTTTTCAAA-AAAAT
1 TTAACCAAACAAAAT
4667865 TTAACCAAACAAAAT
1 TTAACCAAACAAAAT
4667880 TT
1 TT
4667882 TTTCGGTTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
14 11 0.46
15 7 0.29
16 6 0.25
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (15 bp):
TTAACCAAACAAAAT
Found at i:4672399 original size:12 final size:12
Alignment explanation
Indices: 4672382--4672406 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4672372 CTTGAAATGC
4672382 CTTCTCTTCACT
1 CTTCTCTTCACT
4672394 CTTCTCTTCACT
1 CTTCTCTTCACT
4672406 C
1 C
4672407 CTTTCTGCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (12 bp):
CTTCTCTTCACT
Found at i:4678290 original size:19 final size:19
Alignment explanation
Indices: 4678268--4678304 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4678258 TATTTTAATT
4678268 AATAAAAAATAAAAAAACC
1 AATAAAAAATAAAAAAACC
* *
4678287 AATAAAATATAAATAAAC
1 AATAAAAAATAAAAAAAC
4678305 TAACACAAAA
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (19 bp):
AATAAAAAATAAAAAAACC
Found at i:4690019 original size:16 final size:16
Alignment explanation
Indices: 4690000--4690053 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
4689990 CTAATTAAAC
4690000 TGTTCGACATTTATGT
1 TGTTCGACATTTATGT
* **
4690016 TGTTC-ACCAATTATAC
1 TGTTCGA-CATTTATGT
*
4690032 TGTTCGCCATTTATGT
1 TGTTCGACATTTATGT
4690048 TGTTCG
1 TGTTCG
4690054 TCATGTGTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 1 0.03
16 28 0.97
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.46
Consensus pattern (16 bp):
TGTTCGACATTTATGT
Found at i:4690028 original size:32 final size:32
Alignment explanation
Indices: 4689992--4690052 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
4689982 TGTGTTCGCT
4689992 AATTAAACTGTTCGACATTTATGTTGTTCACC
1 AATTAAACTGTTCGACATTTATGTTGTTCACC
* *
4690024 AATTATACTGTTCGCCATTTATGTTGTTC
1 AATTAAACTGTTCGACATTTATGTTGTTC
4690053 GTCATGTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (32 bp):
AATTAAACTGTTCGACATTTATGTTGTTCACC
Found at i:4699396 original size:12 final size:12
Alignment explanation
Indices: 4699379--4699407 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
4699369 CTAAAGAATC
4699379 TTTATTGGATCA
1 TTTATTGGATCA
4699391 TTTATTGGATCA
1 TTTATTGGATCA
4699403 TTTAT
1 TTTAT
4699408 GGTCACAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (12 bp):
TTTATTGGATCA
Found at i:4704857 original size:15 final size:16
Alignment explanation
Indices: 4704837--4704866 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4704827 ACTAGGTATC
4704837 GTCATCTTC-CTGAGT
1 GTCATCTTCACTGAGT
4704852 GTCATCTTCACTGAG
1 GTCATCTTCACTGAG
4704867 ATGCTTAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.37
Consensus pattern (16 bp):
GTCATCTTCACTGAGT
Found at i:4705854 original size:2 final size:2
Alignment explanation
Indices: 4705847--4705873 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4705837 TACGAAAATG
4705847 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4705874 CACACACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4706831 original size:37 final size:36
Alignment explanation
Indices: 4706753--4706847 Score: 95
Period size: 36 Copynumber: 2.6 Consensus size: 36
4706743 AAAGAATCAG
* * * *
4706753 TATTCTAATATAACAATCAAGTT-AAAAGAAAAATAA
1 TATTCTAAGATAATAATCGA-TTCAAAAAAAAAATAA
*
4706789 TATTCT-AGCATAATAATCGATTCAAAAAAAAAAGTAG
1 TATTCTAAG-ATAATAATCGATTCAAAAAAAAAA-TAA
*
4706826 TATTCTAAGATAATAATTGATT
1 TATTCTAAGATAATAATCGATT
4706848 TAAATATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
35 3 0.06
36 24 0.49
37 20 0.41
38 2 0.04
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (36 bp):
TATTCTAAGATAATAATCGATTCAAAAAAAAAATAA
Found at i:4706869 original size:58 final size:58
Alignment explanation
Indices: 4706800--4706963 Score: 181
Period size: 55 Copynumber: 2.8 Consensus size: 58
4706790 ATTCTAGCAT
* * * *
4706800 AATAATCGATTCAAAAAAAAAAGTAGTATTCTAAGATAATAATTGATTTAAATATATA
1 AATAATCGATTCAAAAAAAAAAGTAGTATTCTAACATAACAATCGATTTAAACATATA
* *
4706858 AATAATCGATTC--AAAAGAAA-CAGTATTCTAACATAACAATCGATTTAAACATATA
1 AATAATCGATTCAAAAAAAAAAGTAGTATTCTAACATAACAATCGATTTAAACATATA
* * * * *
4706913 AACAATTGATTCAAAAGAAGAAGAAGTTGTATTCCACCATAACAATCGATT
1 AATAATCGATTCAAAA-AA-AA-AAGTAGTATTCTAACATAACAATCGATT
4706964 CAAAAGATGT
Statistics
Matches: 87, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
55 40 0.46
56 7 0.08
57 2 0.02
58 14 0.16
59 1 0.01
60 2 0.02
61 21 0.24
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (58 bp):
AATAATCGATTCAAAAAAAAAAGTAGTATTCTAACATAACAATCGATTTAAACATATA
Found at i:4707516 original size:2 final size:2
Alignment explanation
Indices: 4707509--4707533 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4707499 ATAAACATTA
4707509 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4707534 AATTAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4708440 original size:31 final size:30
Alignment explanation
Indices: 4708405--4708469 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
4708395 ACTAAATTGG
* ** *
4708405 ACAACTTGTCTAACGGGAGTGACTAAAATTA
1 ACAACTTATCTAACAAGAATGACTAAAA-TA
4708436 ACAACTTATCTAACAAGAATGACTAAAATA
1 ACAACTTATCTAACAAGAATGACTAAAATA
4708466 ACAA
1 ACAA
4708470 ATTTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (30 bp):
ACAACTTATCTAACAAGAATGACTAAAATA
Found at i:4708944 original size:7 final size:7
Alignment explanation
Indices: 4708934--4708973 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
4708924 ATCTTCAATC
4708934 CCAATTT
1 CCAATTT
4708941 CCAATTT
1 CCAATTT
4708948 CCAATTT
1 CCAATTT
4708955 CCAATTT
1 CCAATTT
4708962 CCAATTT
1 CCAATTT
*
4708969 TCAAT
1 CCAAT
4708974 CCTCAATACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.42
Consensus pattern (7 bp):
CCAATTT
Found at i:4708980 original size:21 final size:21
Alignment explanation
Indices: 4708922--4708980 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
4708912 CTTAAATTCT
*
4708922 CAATCTTCAATCC-CAATTTC
1 CAATTTTCAATCCTCAATTTC
* *
4708942 CAATTTCCAAT-TTCCAATTTC
1 CAATTTTCAATCCT-CAATTTC
4708963 CAATTTTCAATCCTCAAT
1 CAATTTTCAATCCTCAAT
4708981 ACTTAAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 9 0.29
21 21 0.68
22 1 0.03
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.39
Consensus pattern (21 bp):
CAATTTTCAATCCTCAATTTC
Found at i:4710644 original size:64 final size:63
Alignment explanation
Indices: 4710522--4710664 Score: 144
Period size: 64 Copynumber: 2.3 Consensus size: 63
4710512 GATTTTTTGT
* * * * * ***
4710522 CACAACCATCACAACATGCACACTCATTCCCCGCATCAACACCTTCAGTTTCGATTTATTTTTA
1 CACAACCACCACAACACGCACAATCATTCCACGCATCAACACATTCAACATCGATTTA-TTTTA
* *
4710586 CACAACCACCACAACACGTACAATCATTCCATGCATCAACACATTCAACAT-GAGTTTATTTTA
1 CACAACCACCACAACACGCACAATCATTCCACGCATCAACACATTCAACATCGA-TTTATTTTA
* * *
4710649 AATAAGCACCACAACA
1 CACAACCACCACAACA
4710665 TGCGCCATCG
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
63 20 0.31
64 45 0.69
ACGTcount: A:0.36, C:0.32, G:0.06, T:0.25
Consensus pattern (63 bp):
CACAACCACCACAACACGCACAATCATTCCACGCATCAACACATTCAACATCGATTTATTTTA
Found at i:4719407 original size:13 final size:13
Alignment explanation
Indices: 4719389--4719414 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4719379 TTTTTTTTAG
4719389 TTAGCATCTTGAT
1 TTAGCATCTTGAT
4719402 TTAGCATCTTGAT
1 TTAGCATCTTGAT
4719415 CCATATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
TTAGCATCTTGAT
Found at i:4726361 original size:21 final size:21
Alignment explanation
Indices: 4726321--4726366 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4726311 ACAAAATCCT
* ** *
4726321 AAACTCGAAACCTCGTACTCG
1 AAACTCAAAACCTCAAACTCA
4726342 AAACTCAAAACCTCAAACTCA
1 AAACTCAAAACCTCAAACTCA
4726363 AAAC
1 AAAC
4726367 CTTAAGCTCA
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:0.46, C:0.33, G:0.07, T:0.15
Consensus pattern (21 bp):
AAACTCAAAACCTCAAACTCA
Found at i:4726376 original size:14 final size:14
Alignment explanation
Indices: 4726342--4726368 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4726332 CTCGTACTCG
4726342 AAACTCAAAACCTC
1 AAACTCAAAACCTC
4726356 AAACTCAAAACCT
1 AAACTCAAAACCT
4726369 TAAGCTCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (14 bp):
AAACTCAAAACCTC
Found at i:4727545 original size:2 final size:2
Alignment explanation
Indices: 4727538--4727572 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4727528 GTATGGCTAA
4727538 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4727573 AACTAAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4728167 original size:41 final size:41
Alignment explanation
Indices: 4728107--4728293 Score: 297
Period size: 41 Copynumber: 4.6 Consensus size: 41
4728097 TTTAAACAGA
*
4728107 TTCACTGGCACTTCA-CCTGCTAGGCTTATAGCCTGATTCAG
1 TTCACCGGCACTT-AGCCTGCTAGGCTTATAGCCTGATTCAG
4728148 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
4728189 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC-G
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
* *
4728229 AATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCGG
1 -TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
* *
4728271 ATCACCGACACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAG
4728294 ACGTAAAGTC
Statistics
Matches: 140, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
40 2 0.01
41 137 0.98
42 1 0.01
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.28
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
Found at i:4728317 original size:82 final size:82
Alignment explanation
Indices: 4728148--4728321 Score: 235
Period size: 82 Copynumber: 2.1 Consensus size: 82
4728138 CCTGATTCAG
* * *
4728148 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGA
* * **
4728213 CTTATAGCCTGATTCGA
66 CGTAAAGCCTGAAACGA
* *
4728230 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCGGATCACCGACACTTAGCCTGCTAGA
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGA
4728295 CGTAAAGTCC-GAAAC-A
66 CGTAAAG-CCTGAAACGA
4728311 TTTCACCGGCA
1 -TTCACCGGCA
4728322 ATTAATCTGT
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
81 1 0.01
82 77 0.96
83 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (82 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGA
CGTAAAGCCTGAAACGA
Found at i:4729117 original size:2 final size:2
Alignment explanation
Indices: 4729110--4729155 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
4729100 NNNNNNNATA
*
4729110 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4729152 AT AT
1 AT AT
4729156 TCATACCTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4732329 original size:18 final size:18
Alignment explanation
Indices: 4732296--4732330 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4732286 TTGTTTATCC
*
4732296 ACGGTACTATTTACGTAG
1 ACGGTACTATTCACGTAG
*
4732314 ACGGTACTGTTCACGTA
1 ACGGTACTATTCACGTA
4732331 TACAGTAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (18 bp):
ACGGTACTATTCACGTAG
Found at i:4737624 original size:11 final size:11
Alignment explanation
Indices: 4737604--4737710 Score: 63
Period size: 11 Copynumber: 10.4 Consensus size: 11
4737594 TTAAAAATTA
4737604 AAAAAGTATTTT
1 AAAAA-TATTTT
4737616 AAAAATATTTT
1 AAAAATATTTT
4737627 --AAA-A--TT
1 AAAAATATTTT
* *
4737633 AAAAAAAATTT
1 AAAAATATTTT
4737644 AAAAAGTATTTT
1 AAAAA-TATTTT
*
4737656 TAAAATATTTT
1 AAAAATATTTT
*
4737667 --AAA-A-TTA
1 AAAAATATTTT
* *
4737674 AAAAATA-ATA
1 AAAAATATTTT
4737684 AAAAAGTATTTT
1 AAAAA-TATTTT
4737696 AAAAATATTTT
1 AAAAATATTTT
4737707 AAAA
1 AAAA
4737711 TTTAAAAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
6 2 0.03
7 2 0.03
8 5 0.06
9 10 0.13
10 8 0.10
11 31 0.40
12 19 0.25
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:4737633 original size:30 final size:29
Alignment explanation
Indices: 4737590--4737661 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
4737580 ACCAAAAATT
*
4737590 TATTTTAAAAATTAAAAAAGTATTTTAAAAA-
1 TATTTT-AAAATTAAAAAA--AATTTAAAAAG
4737621 TATTTTAAAATTAAAAAAAATTTAAAAAG
1 TATTTTAAAATTAAAAAAAATTTAAAAAG
4737650 TATTTTTAAAAT
1 TA-TTTTAAAAT
4737662 ATTTTAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
28 9 0.24
29 2 0.05
30 21 0.55
31 6 0.16
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (29 bp):
TATTTTAAAATTAAAAAAAATTTAAAAAG
Found at i:4737636 original size:17 final size:17
Alignment explanation
Indices: 4737614--4737647 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4737604 AAAAAGTATT
* *
4737614 TTAAAAATATTTTAAAA
1 TTAAAAAAAATTTAAAA
4737631 TTAAAAAAAATTTAAAA
1 TTAAAAAAAATTTAAAA
4737648 AGTATTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAAATTTAAAA
Found at i:4737648 original size:40 final size:40
Alignment explanation
Indices: 4737596--4737728 Score: 214
Period size: 40 Copynumber: 3.3 Consensus size: 40
4737586 AATTTATTTT
4737596 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
* *
4737636 AAAAATTTAAAAAGTATTTTTAAAATATTTTAAAATTAAA
1 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
*
4737676 AAATAA-TAAAAAAGTATTTTAAAAATATTTTAAAATTTAA
1 AAA-AATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
*
4737716 AAAAATTTAAAAA
1 AAAAATTAAAAAA
4737729 TAAATATATT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
39 2 0.02
40 81 0.95
41 2 0.02
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (40 bp):
AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
Found at i:4738652 original size:7 final size:7
Alignment explanation
Indices: 4738640--4738673 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
4738630 ACTATTGTGA
4738640 CAGTTAG
1 CAGTTAG
4738647 CAGTTAG
1 CAGTTAG
*
4738654 TAGTTAG
1 CAGTTAG
*
4738661 TAGTTAG
1 CAGTTAG
4738668 CAGTTA
1 CAGTTA
4738674 TGGTAGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.35
Consensus pattern (7 bp):
CAGTTAG
Found at i:4738667 original size:21 final size:21
Alignment explanation
Indices: 4738641--4738689 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
4738631 CTATTGTGAC
4738641 AGTTAGCAGTTA-GTAGTTAGT
1 AGTTAGCAGTTAGGTAGTTA-T
4738662 AGTTAGCAGTTATGGTAGTTAT
1 AGTTAGCAGTTA-GGTAGTTAT
4738684 AGTTAG
1 AGTTAG
4738690 TTAACTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.46
22 7 0.27
23 7 0.27
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.39
Consensus pattern (21 bp):
AGTTAGCAGTTAGGTAGTTAT
Found at i:4738854 original size:14 final size:14
Alignment explanation
Indices: 4738835--4738867 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
4738825 GCCTTCTTTG
4738835 TGTTTTCTTGTTTA
1 TGTTTTCTTGTTTA
*
4738849 TGTTTTCTTGTTTG
1 TGTTTTCTTGTTTA
4738863 TGTTT
1 TGTTT
4738868 CTGCCATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.06, G:0.18, T:0.73
Consensus pattern (14 bp):
TGTTTTCTTGTTTA
Found at i:4743366 original size:21 final size:21
Alignment explanation
Indices: 4743340--4743388 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
4743330 TTGTTGTGAC
4743340 AGTTAGCAGTTA-GTAGTTAAT
1 AGTTAGCAGTTAGGTAGTT-AT
4743361 AGTTAGCAGTTATGGTAGTTAT
1 AGTTAGCAGTTA-GGTAGTTAT
4743383 AGTTAG
1 AGTTAG
4743389 TTAACTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.46
22 8 0.31
23 6 0.23
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.39
Consensus pattern (21 bp):
AGTTAGCAGTTAGGTAGTTAT
Found at i:4751045 original size:31 final size:31
Alignment explanation
Indices: 4751002--4751068 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
4750992 TCAATTTAAC
*
4751002 CACTAACATTTTAGATCAGTTT-TACTTTGGT
1 CACTCACATTTTAGATC-GTTTCTACTTTGGT
*
4751033 CACTCACATTTTAGATCGTTTCTATTTTGGT
1 CACTCACATTTTAGATCGTTTCTACTTTGGT
4751064 CACTC
1 CACTC
4751069 TCCGCTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (31 bp):
CACTCACATTTTAGATCGTTTCTACTTTGGT
Found at i:4752647 original size:31 final size:31
Alignment explanation
Indices: 4752612--4752678 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
4752602 TCATTTAAAA
* *
4752612 AAATTCAACTATTTTTAAAAGGCTGATGGTC
1 AAATTCAACTATTTCTAAAAGGCTAATGGTC
* * * *
4752643 AAATTCGACTCTTTCTGAAAGGTTAATGGTC
1 AAATTCAACTATTTCTAAAAGGCTAATGGTC
4752674 AAATT
1 AAATT
4752679 TAATTCTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (31 bp):
AAATTCAACTATTTCTAAAAGGCTAATGGTC
Found at i:4756965 original size:21 final size:22
Alignment explanation
Indices: 4756923--4756965 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4756913 CACTTTGAGG
**
4756923 GTTTTAATGAGAATTTTTAAAA
1 GTTTTAATGAGAATTTACAAAA
4756945 GTTTT-ATGAGAATTTACAAAA
1 GTTTTAATGAGAATTTACAAAA
4756966 CATAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (22 bp):
GTTTTAATGAGAATTTACAAAA
Found at i:4759842 original size:2 final size:2
Alignment explanation
Indices: 4759835--4759868 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4759825 TTAATTTGTA
4759835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4759869 GTAGGATGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4762017 original size:2 final size:2
Alignment explanation
Indices: 4762010--4762043 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4762000 TATTATATGA
4762010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4762044 GAAATGTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4764180 original size:12 final size:12
Alignment explanation
Indices: 4764163--4764188 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4764153 TGAAGGCGAC
4764163 CCTAATCTGAAT
1 CCTAATCTGAAT
4764175 CCTAATCTGAAT
1 CCTAATCTGAAT
4764187 CC
1 CC
4764189 AGAATAAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (12 bp):
CCTAATCTGAAT
Found at i:4765188 original size:2 final size:2
Alignment explanation
Indices: 4765179--4765213 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4765169 GTATATAAGT
4765179 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4765214 AATAATGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4776449 original size:3 final size:3
Alignment explanation
Indices: 4776441--4776468 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4776431 ATGACCAGCC
4776441 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4776469 AGGATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4784294 original size:29 final size:30
Alignment explanation
Indices: 4784251--4784311 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
4784241 ATTAGTCATT
* * *
4784251 TACAAATATAGGAGAGCTTGGATAAAA-TC
1 TACAAATATAAGAGAGATGGGATAAAACTC
4784280 TACAAATATAAGAGAGATGGGATAAAACTC
1 TACAAATATAAGAGAGATGGGATAAAACTC
4784310 TA
1 TA
4784312 GGCTCATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.48, C:0.10, G:0.20, T:0.23
Consensus pattern (30 bp):
TACAAATATAAGAGAGATGGGATAAAACTC
Found at i:4785466 original size:3 final size:3
Alignment explanation
Indices: 4785447--4785490 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
4785437 AAGAGAAAGG
*
4785447 AGA AG- AGA AGG AGA AGA AGA AGA AG- AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
4785491 AGTTTATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:4785472 original size:20 final size:20
Alignment explanation
Indices: 4785447--4785490 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
4785437 AAGAGAAAGG
*
4785447 AGAAGAGAAGGAGAAGAAGA
1 AGAAGAGAAGAAGAAGAAGA
4785467 AGAAGAGAAGAAGAAGAAGA
1 AGAAGAGAAGAAGAAGAAGA
4785487 AGAA
1 AGAA
4785491 AGTTTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (20 bp):
AGAAGAGAAGAAGAAGAAGA
Found at i:4785688 original size:22 final size:21
Alignment explanation
Indices: 4785661--4785846 Score: 154
Period size: 22 Copynumber: 9.0 Consensus size: 21
4785651 TAGATTAGAA
*
4785661 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTGT-AATT
*
4785683 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTGTAATT
*
4785704 TTTT-TAGGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
4785722 TGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* *
4785743 ATTTTATAATTAA-ATTTGT-ATT
1 -TTTTGT-ATGAATA-TTGTAATT
* * * * *
4785765 TATAGTTTTGGAT-TAGTAATT
1 TTTTG-TATGAATATTGTAATT
4785786 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
4785805 TTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGT-AATT
4785827 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
4785847 AATATTATAG
Statistics
Matches: 129, Mismatches: 22, Indels: 27
0.72 0.12 0.15
Matches are distributed among these distances:
18 3 0.02
19 29 0.22
20 22 0.17
21 26 0.20
22 41 0.32
23 8 0.06
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:4785735 original size:19 final size:19
Alignment explanation
Indices: 4785685--4785741 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
4785675 TTTAAATTTT
* *
4785685 TTGTATGAATATTATAATTT
1 TTGTATGAATATTGTAA-TG
* *
4785705 TTTTAGGAATATTGTAATG
1 TTGTATGAATATTGTAATG
4785724 TTGTATGAATATTGTAAT
1 TTGTATGAATATTGTAAT
4785742 TATTTTATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (19 bp):
TTGTATGAATATTGTAATG
Found at i:4785827 original size:41 final size:40
Alignment explanation
Indices: 4785661--4785846 Score: 166
Period size: 41 Copynumber: 4.5 Consensus size: 40
4785651 TAGATTAGAA
*
4785661 TTTTGTATGAATATTTTAAATTTTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTGT-AA--TTTTGTATGAATATTATAATT
* * *
4785704 TTTT-TAGGAATATTGTAATGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTATAATT
* * * *
4785743 ATTTTATAATTAA-ATTTGT-ATTTATAGTTTTG--GATTAGTAATT
1 -TTTTGT-ATGAATA-TTGTAATTT-T-G-TATGAATATTA-TAATT
4785786 TTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTAT-AATT
4785827 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
4785847 AATATTATAG
Statistics
Matches: 116, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
39 22 0.19
40 6 0.05
41 44 0.38
42 31 0.27
43 10 0.09
44 3 0.03
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (40 bp):
TTTTGTATGAATATTGTAATTTTGTATGAATATTATAATT
Found at i:4785968 original size:19 final size:19
Alignment explanation
Indices: 4785944--4786001 Score: 53
Period size: 22 Copynumber: 2.9 Consensus size: 19
4785934 TGAATGTTGT
4785944 AATATTATAATTTTGTATG
1 AATATTATAATTTTGTATG
**
4785963 AATATTGCAATTTTTTTGTATG
1 AATATT---ATAATTTTGTATG
* *
4785985 AATATTGTAATATTGTA
1 AATATTATAATTTTGTA
4786002 ATTTTGCATG
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
19 13 0.43
22 17 0.57
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (19 bp):
AATATTATAATTTTGTATG
Found at i:4785972 original size:97 final size:99
Alignment explanation
Indices: 4785795--4786017 Score: 369
Period size: 97 Copynumber: 2.3 Consensus size: 99
4785785 TTTTTGTATG
*
4785795 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATAATATTATAGTTT
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTG--ATAATATTATAATTT
4785860 TGTATGAATATTGCAATTTTTTTGTATGAATATTGT
64 TGTATGAATATTGCAATTTTTTTGTATGAATATTGT
* * *
4785896 AATTTTGTAATTTTGTATGAATATTAT-ATTTTTTTGTATGAATGTTG-TAATATTATAATTTTG
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGATAATATTATAATTTTG
4785959 TATGAATATTGCAATTTTTTTGTATGAATATTGT
66 TATGAATATTGCAATTTTTTTGTATGAATATTGT
*
4785993 AATATTGTAATTTTGCATGAATATT
1 AATATTGTAATTTTGTATGAATATT
4786018 GTAATGTGAG
Statistics
Matches: 116, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
97 72 0.62
100 18 0.16
101 26 0.22
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (99 bp):
AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGATAATATTATAATTTTG
TATGAATATTGCAATTTTTTTGTATGAATATTGT
Found at i:4786018 original size:49 final size:49
Alignment explanation
Indices: 4785795--4786018 Score: 319
Period size: 49 Copynumber: 4.5 Consensus size: 49
4785785 TTTTTGTATG
** *
4785795 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
4785844 AATAATAT-TATAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AAT-AT-TGTA-A-TTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
* *
4785896 AATTTTGTAATTTTGTATGAATATT--ATATTTTTTTGTATGAATGTTGT
1 AATATTGTAATTTTGTATGAATATTGCA-ATTTTTTTGTATGAATATTGT
*
4785944 AATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
*
4785993 AATATTGTAATTTTGCATGAATATTG
1 AATATTGTAATTTTGTATGAATATTG
4786019 TAATGTGAGG
Statistics
Matches: 157, Mismatches: 10, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
47 1 0.01
48 43 0.27
49 62 0.39
50 7 0.04
51 5 0.03
52 39 0.25
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
Found at i:4786327 original size:38 final size:38
Alignment explanation
Indices: 4786283--4786357 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
4786273 CATATAAAGT
4786283 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTGA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTGA
*
4786321 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTG
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTG
4786358 GGTTTTTTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTGA
Found at i:4786507 original size:15 final size:15
Alignment explanation
Indices: 4786466--4786507 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
4786456 GTTAACTTAT
*
4786466 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
4786481 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
4786497 TTAAATTTTAT
1 TTAAATTTTAT
4786508 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:4788141 original size:6 final size:6
Alignment explanation
Indices: 4788130--4788212 Score: 112
Period size: 6 Copynumber: 13.8 Consensus size: 6
4788120 GCATCATGCA
*
4788130 CCAGAG CCAGAG CCAGGG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG
* * * * *
4788178 CCAGAG CGAGAG GCAGAG CGAGAG CGAGAG GCAGA
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGA
4788213 ACTACATTCT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.33, C:0.28, G:0.40, T:0.00
Consensus pattern (6 bp):
CCAGAG
Done.