Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 40 of 211
Found at i:11886597 original size:50 final size:50
Alignment explanation
Indices: 11886507--11886613 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 50
11886497 GGATACATCA
* * * **
11886507 CAGCTCTTATAAGTTTCCTGTTATTCAACTCGTATAAGCTTCCCGTTATT
1 CAGCTCATATAAGCTTCCCGTTATTCAACTCCCATAAGCTTCCCGTTATT
* * * *
11886557 CAGCTCATATGAGCTTCCCGTTATTCAGCTCCCATGAGCTTCCTGTTATT
1 CAGCTCATATAAGCTTCCCGTTATTCAACTCCCATAAGCTTCCCGTTATT
*
11886607 CAACTCA
1 CAGCTCA
11886614 GAAAAGATTA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.37
Consensus pattern (50 bp):
CAGCTCATATAAGCTTCCCGTTATTCAACTCCCATAAGCTTCCCGTTATT
Found at i:11899129 original size:130 final size:130
Alignment explanation
Indices: 11898968--11899590 Score: 745
Period size: 130 Copynumber: 4.8 Consensus size: 130
11898958 AATAACTCAT
* * **
11898968 TGATTTAATATCACAACTGATATTATTAAGGCTCGTTGATTTACAATCACAATTTAAGTTCATTG
1 TGATTTAATATCACAGCTGATATTATTAAGGCTCGTTGATTTACGATCACAACCTAAGTTCATTG
* * *
11899033 ATTTACTATCATAAACAATTTTCTATGACTTAGTTGATTTACTATCGCTACTCCAAATAGCTCGT
66 ATTTACTATCATAAACAATCTTCTATGAGTTAGTTGATTTACTATCGCTACTCCAAATAGCTCGC
* * * *
11899098 TGAATTAATATCACAGTTGATATTATTAAGGCTCGCTGATTTACGATCACAACCTAAGTTCATTT
1 TGATTTAATATCACAGCTGATATTATTAAGGCTCGTTGATTTACGATCACAACCTAAGTTCATTG
* * ** *
11899163 ATTTACTATTATGAACAATCTTCTATGAGTTAGTTGATTTACTATCAATACTCCAAACAGCTCGC
66 ATTTACTATCATAAACAATCTTCTATGAGTTAGTTGATTTACTATCGCTACTCCAAATAGCTCGC
* * * *
11899228 TGATTTAATATCACAGTTGATATTATTGAGGCTCATTGATTTACGATCGCAACCTAAGTTCATTG
1 TGATTTAATATCACAGCTGATATTATTAAGGCTCGTTGATTTACGATCACAACCTAAGTTCATTG
* * ** * * *
11899293 ATTTACTATCATGAAA-AATCTTCTATGATTTAGTTGATTTACTATTGCTACTTTAAACATCTCA
66 ATTTACTATCAT-AAACAATCTTCTATGAGTTAGTTGATTTACTATCGCTACTCCAAATAGCTCG
11899357 C
130 C
* *
11899358 TGATTTAATATCACAGATGATATTATTAAGGCTCGTTGATTTACGAT-AGCAGCCTAAGTTCATT
1 TGATTTAATATCACAGCTGATATTATTAAGGCTCGTTGATTTACGATCA-CAACCTAAGTTCATT
* * * * *
11899422 GA-TTACTATCATGAACAATCTTCTATAAGTTAGTTGATTTACAATTGCTGCTCCAAATAGCTCG
65 GATTTACTATCATAAACAATCTTCTATGAGTTAGTTGATTTACTATCGCTACTCCAAATAGCTCG
11899486 C
130 C
* * * * * * *
11899487 T-AGTTTAAGATCACAACTGATATTATTAAGGCT-GACTGGTTTAGGAACACAGCCTAAGTTCAT
1 TGA-TTTAATATCACAGCTGATATTATTAAGGCTCG-TTGATTTACGATCACAACCTAAGTTCAT
* * * * *
11899550 TAATTTACAATCATGAATAATCCTTC-CTGAGTTAGTTGATT
64 TGATTTACTATCATAAACAAT-CTTCTATGAGTTAGTTGATT
11899591 CATAGTCATA
Statistics
Matches: 426, Mismatches: 59, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
128 4 0.01
129 102 0.24
130 314 0.74
131 6 0.01
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (130 bp):
TGATTTAATATCACAGCTGATATTATTAAGGCTCGTTGATTTACGATCACAACCTAAGTTCATTG
ATTTACTATCATAAACAATCTTCTATGAGTTAGTTGATTTACTATCGCTACTCCAAATAGCTCGC
Found at i:11905973 original size:23 final size:23
Alignment explanation
Indices: 11905922--11905979 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
11905912 TTTGGAACTG
* *
11905922 TAAATTTTTATATTATGATTTTT
1 TAAATTTTTATATTATGAATTCT
* * *
11905945 TGAATTTTTATTTTATTAATTCT
1 TAAATTTTTATATTATGAATTCT
11905968 TAAATTATTTAT
1 TAAATT-TTTAT
11905980 CAACGTAACA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (23 bp):
TAAATTTTTATATTATGAATTCT
Found at i:11908789 original size:1 final size:1
Alignment explanation
Indices: 11908783--11908811 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
11908773 TGTGAAATGG
11908783 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11908812 CCCAATAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11912491 original size:38 final size:38
Alignment explanation
Indices: 11912440--11912513 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
11912430 GATGCTAGAC
*
11912440 AAGATATTTCCAATAAACAAATTTTTCTAATCAAAATT
1 AAGATATTTCCAATAAACAAATTTCTCTAATCAAAATT
*
11912478 AAGATATTTCCAATAAACAAATTTCTCTTATCAAAA
1 AAGATATTTCCAATAAACAAATTTCTCTAATCAAAA
11912514 CGATTGACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (38 bp):
AAGATATTTCCAATAAACAAATTTCTCTAATCAAAATT
Found at i:11917377 original size:21 final size:21
Alignment explanation
Indices: 11917348--11917506 Score: 135
Period size: 21 Copynumber: 7.6 Consensus size: 21
11917338 GAAGCTTGTA
11917348 AGCTGAACAGAAGCTCATAAG
1 AGCTGAACAGAAGCTCATAAG
* * *
11917369 AGCTAAACAGAAACCCATAA-
1 AGCTGAACAGAAGCTCATAAG
* *
11917389 AGGTTGAACAGAAGCTCGTAAG
1 A-GCTGAACAGAAGCTCATAAG
** * *
11917411 ATTTGAACAGAAACTCTTAAG
1 AGCTGAACAGAAGCTCATAAG
*
11917432 AGTTGAACAGAAGCTCGA-AAG
1 AGCTGAACAGAAGCTC-ATAAG
*
11917453 AGCTGAAC-GAAAACTCATAAG
1 AGCTGAACAG-AAGCTCATAAG
* * * *
11917474 AGTTAAACAAAAGCTCGTAAG
1 AGCTGAACAGAAGCTCATAAG
11917495 AGCTGAACAGAA
1 AGCTGAACAGAA
11917507 AGTAAAACAC
Statistics
Matches: 108, Mismatches: 24, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
20 3 0.03
21 104 0.96
22 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.16
Consensus pattern (21 bp):
AGCTGAACAGAAGCTCATAAG
Found at i:11917399 original size:42 final size:42
Alignment explanation
Indices: 11917351--11917507 Score: 185
Period size: 42 Copynumber: 3.7 Consensus size: 42
11917341 GCTTGTAAGC
* *
11917351 TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAA-AGGT
1 TGAACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGA-GT
* ** *
11917393 TGAACAGAAGCTCGTAAGATTTGAACAGAAACTCTTAAGAGT
1 TGAACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGAGT
11917435 TGAACAGAAGCTCGA-AAGAGCTGAAC-GAAAACTCATAAGAGT
1 TGAACAGAAGCTC-ATAAGAGCTGAACAG-AAACTCATAAGAGT
* * *
11917477 TAAACAAAAGCTCGTAAGAGCTGAACAGAAA
1 TGAACAGAAGCTCATAAGAGCTGAACAGAAA
11917508 GTAAAACACG
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
41 1 0.01
42 94 0.97
43 2 0.02
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.17
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGAGT
Found at i:11917492 original size:84 final size:84
Alignment explanation
Indices: 11917351--11917507 Score: 212
Period size: 84 Copynumber: 1.9 Consensus size: 84
11917341 GCTTGTAAGC
* * **
11917351 TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTGAACAGAAGCTCGTAAGATTTG
1 TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTAAACAAAAGCTCGTAAGAGCTG
11917416 AACAGAAACTCTTAAGAGT
66 AACAGAAACTCTTAAGAGT
* *
11917435 TGAACAGAAGCTCGA-AAGAGCTGAAC-GAAAACTCAT-AAGAGTTAAACAAAAGCTCGTAAGAG
1 TGAACAGAAGCTC-ATAAGAGCTAAACAG-AAACCCATAAAG-GTTAAACAAAAGCTCGTAAGAG
11917497 CTGAACAGAAA
63 CTGAACAGAAA
11917508 GTAAAACACG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
83 4 0.06
84 59 0.92
85 1 0.02
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.17
Consensus pattern (84 bp):
TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTAAACAAAAGCTCGTAAGAGCTG
AACAGAAACTCTTAAGAGT
Found at i:11921179 original size:13 final size:13
Alignment explanation
Indices: 11921163--11921197 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
11921153 TAAAACCCAA
*
11921163 ATATAAAATATAT
1 ATATAAAATAAAT
11921176 ATATAAAATAAAT
1 ATATAAAATAAAT
11921189 ATAATAAAA
1 AT-ATAAAA
11921198 GTCTAATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATAAAATAAAT
Found at i:11922299 original size:18 final size:17
Alignment explanation
Indices: 11922267--11922301 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11922257 GTGTTTTGAA
11922267 TTGTTTTAATTTAATTT
1 TTGTTTTAATTTAATTT
*
11922284 TTGTTATTATTTTAATTT
1 TTGTT-TTAATTTAATTT
11922302 ATATGCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTGTTTTAATTTAATTT
Found at i:11924998 original size:22 final size:24
Alignment explanation
Indices: 11924970--11925013 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
11924960 TATGGCAAGA
11924970 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
11924992 AATTAAGTTAGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
11925014 AACTTAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:11925373 original size:38 final size:36
Alignment explanation
Indices: 11925323--11925414 Score: 96
Period size: 37 Copynumber: 2.5 Consensus size: 36
11925313 ATATGTGTGG
* *
11925323 AATTGAAATGAATAT-TGACTTAAAAATGGAAAAGTGA
1 AATTGAATTGAAT-TGTGA-TTAAAAATGAAAAAGTGA
* * *
11925360 ATTTTGAATTGAATTGTGATTGAAAGTGAAAAAGTGA
1 A-ATTGAATTGAATTGTGATTAAAAATGAAAAAGTGA
*
11925397 AATTGAATTGAAATGTGA
1 AATTGAATTGAATTGTGA
11925415 ATTTGGAGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
36 15 0.33
37 18 0.39
38 13 0.28
ACGTcount: A:0.46, C:0.01, G:0.22, T:0.32
Consensus pattern (36 bp):
AATTGAATTGAATTGTGATTAAAAATGAAAAAGTGA
Found at i:11930304 original size:18 final size:18
Alignment explanation
Indices: 11930267--11930304 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
11930257 AAAAAATCAC
*
11930267 ATTTTTTATATTTAATAT
1 ATTTTTTATATTTAAAAT
11930285 ATTTTTTA-ATTTCAAAAT
1 ATTTTTTATATTT-AAAAT
11930303 AT
1 AT
11930305 ATAGTGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTTATATTTAAAAT
Found at i:11936235 original size:26 final size:26
Alignment explanation
Indices: 11936206--11936266 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
11936196 ATAAGGTTAA
* *
11936206 TTATTTTAAGTT-CTTTATATATTATT
1 TTATTTTAAGTTACTTTACATATTA-C
* *
11936232 TTATTTAAAGTTATTTTACATATTAC
1 TTATTTTAAGTTACTTTACATATTAC
11936258 TTATTTTAA
1 TTATTTTAA
11936267 AATTAACCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (26 bp):
TTATTTTAAGTTACTTTACATATTAC
Found at i:11936265 original size:27 final size:25
Alignment explanation
Indices: 11936205--11936267 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
11936195 TATAAGGTTA
*
11936205 ATTATTTT-AAGTTCTTTATATATT
1 ATTATTTTAAAGTTCTTTACATATT
* *
11936229 ATTTTATTTAAAGTTATTTTACATATT
1 ATTAT-TTTAAAGTT-CTTTACATATT
11936256 ACTTATTTTAAA
1 A-TTATTTTAAA
11936268 ATTAACCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 4 0.13
25 3 0.10
26 5 0.16
27 16 0.52
28 3 0.10
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (25 bp):
ATTATTTTAAAGTTCTTTACATATT
Found at i:11936688 original size:40 final size:41
Alignment explanation
Indices: 11936559--11936744 Score: 146
Period size: 40 Copynumber: 4.4 Consensus size: 41
11936549 TGTTTGGATA
* * * * *
11936559 AAAAATGCCGGTAAAAATCGAGCATTAGTGGCG-CTTTAAG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTAGG
* * * * *
11936599 AAAATCGCCACTAAAGATCGAGCATTAGCAGCGTTTTT-TG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTAGG
*
11936639 AAAAACGCCGCTAAAAAT-AAGCATTAGCGGCGTTTTTAGG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTAGG
*
11936679 AAAAACGCCGAAAACGCCGCAAAAAAT-GAGCATTAGCGGCGTTTTTAGG
1 ----A-----AAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTAGG
*
11936728 AAAAACGCCGCAAAAAA
1 AAAAACGCCGCTAAAAA
11936745 CCAAAGCCCA
Statistics
Matches: 118, Mismatches: 17, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
39 17 0.14
40 59 0.50
41 3 0.03
44 1 0.01
45 1 0.01
49 37 0.31
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (41 bp):
AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTAGG
Found at i:11936693 original size:49 final size:50
Alignment explanation
Indices: 11936640--11936742 Score: 181
Period size: 49 Copynumber: 2.1 Consensus size: 50
11936630 CGTTTTTTGA
*
11936640 AAAACGCCGCTAAAAATAAGCATTAGCGGCGTTTTTAGGAAAAACGCCG-
1 AAAACGCCGCAAAAAATAAGCATTAGCGGCGTTTTTAGGAAAAACGCCGC
*
11936689 AAAACGCCGCAAAAAATGAGCATTAGCGGCGTTTTTAGGAAAAACGCCGC
1 AAAACGCCGCAAAAAATAAGCATTAGCGGCGTTTTTAGGAAAAACGCCGC
11936739 AAAA
1 AAAA
11936743 AACCAAAGCC
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 47 0.92
50 4 0.08
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (50 bp):
AAAACGCCGCAAAAAATAAGCATTAGCGGCGTTTTTAGGAAAAACGCCGC
Found at i:11937018 original size:41 final size:41
Alignment explanation
Indices: 11936783--11937002 Score: 336
Period size: 41 Copynumber: 5.4 Consensus size: 41
11936773 CTTTGGGGGA
* *
11936783 TTTAACGGTGTTTTTG-TAGAAGCGCCGCTAATGCTGGGGTC
1 TTTAGCGGCGTTTTTGATA-AAGCGCCGCTAATGCTGGGGTC
* *
11936824 TTTAGCGGCATTTTTG-TAGAAGCGCCGCTAATACTGGGGTC
1 TTTAGCGGCGTTTTTGATA-AAGCGCCGCTAATGCTGGGGTC
*
11936865 TTTAGCGGCGTTTTTGATAAAGCGCCGCTAGTGCTGGGGTC
1 TTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTGGGGTC
*
11936906 TTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTGGGATC
1 TTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTGGGGTC
*
11936947 TTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTAGGGTC
1 TTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTGGGGTC
*
11936988 TGTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
11937003 AGAGGAGCGC
Statistics
Matches: 166, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
41 164 0.99
42 2 0.01
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTGGGGTC
Found at i:11937231 original size:25 final size:27
Alignment explanation
Indices: 11937177--11937231 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
11937167 AATCCCTAAT
* * *
11937177 TTCAGACTTTTCTTCACTCCCGTTTTC
1 TTCAGACTTTTCATCACTCCCGCTTCC
11937204 TTCAGACTTTTCAT-A-TCCCGCTTCC
1 TTCAGACTTTTCATCACTCCCGCTTCC
11937229 TTC
1 TTC
11937232 TCATTATCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.44
26 1 0.04
27 13 0.52
ACGTcount: A:0.13, C:0.35, G:0.07, T:0.45
Consensus pattern (27 bp):
TTCAGACTTTTCATCACTCCCGCTTCC
Found at i:11940791 original size:43 final size:43
Alignment explanation
Indices: 11940726--11940924 Score: 200
Period size: 43 Copynumber: 4.8 Consensus size: 43
11940716 AAGTCATGTT
* ** *
11940726 TTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGGTC
1 TTTAGCGGCATTTGTGAAAAAAGCGTCGCTAAAGGTCTTGATC
* *
11940769 TTTAGCGGCATTTGTAAAAAAAGTGAT-GCTAAA-G----G-TC
1 TTTAGCGGCATTTGTGAAAAAAGCG-TCGCTAAAGGTCTTGATC
* *
11940806 -TTAGCGGCATTTGTGGGAAAAA-CGCCGCTAAAGGTCTTGATC
1 TTTAGCGGCATTTGT-GAAAAAAGCGTCGCTAAAGGTCTTGATC
* *
11940848 TTTATCGGCGTTTGTGAAAAAAGCGTCGCTAAAGGTCTTGATC
1 TTTAGCGGCATTTGTGAAAAAAGCGTCGCTAAAGGTCTTGATC
** *
11940891 TTTAGCGGCATTTGTGAGCAAAGCGCCGCTAAAG
1 TTTAGCGGCATTTGTGAAAAAAGCGTCGCTAAAG
11940925 TTAGCGCCGC
Statistics
Matches: 127, Mismatches: 18, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
36 21 0.17
37 8 0.06
38 1 0.01
41 1 0.01
42 9 0.07
43 86 0.68
44 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCATTTGTGAAAAAAGCGTCGCTAAAGGTCTTGATC
Found at i:11940862 original size:79 final size:79
Alignment explanation
Indices: 11940727--11940886 Score: 232
Period size: 79 Copynumber: 2.0 Consensus size: 79
11940717 AGTCATGTTT
* * * *
11940727 TTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGGTCTTTAGCGGCATTTGTAAAAAAAG
1 TTAGCGGCATTTGTGGGAAAAACGCCGCTAAAGGTCTTGATCTTTAGCGGCATTTGTAAAAAAAG
*
11940792 TGAT-GCTAAAGGTC
66 CG-TCGCTAAAGGTC
* * *
11940806 TTAGCGGCATTTGTGGGAAAAACGCCGCTAAAGGTCTTGATCTTTATCGGCGTTTGTGAAAAAAG
1 TTAGCGGCATTTGTGGGAAAAACGCCGCTAAAGGTCTTGATCTTTAGCGGCATTTGTAAAAAAAG
11940871 CGTCGCTAAAGGTC
66 CGTCGCTAAAGGTC
11940885 TT
1 TT
11940887 GATCTTTAGC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
78 1 0.01
79 71 0.99
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (79 bp):
TTAGCGGCATTTGTGGGAAAAACGCCGCTAAAGGTCTTGATCTTTAGCGGCATTTGTAAAAAAAG
CGTCGCTAAAGGTC
Found at i:11944927 original size:9 final size:9
Alignment explanation
Indices: 11944913--11944951 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
11944903 AATCATTTTG
11944913 TTTATAATT
1 TTTATAATT
11944922 TTTATATATT
1 TTTATA-ATT
11944932 TTTAATAATT
1 TTT-ATAATT
11944942 TTTA-AATT
1 TTTATAATT
11944950 TT
1 TT
11944952 AAAAGGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 6 0.21
9 7 0.25
10 12 0.43
11 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTATAATT
Found at i:11946854 original size:18 final size:17
Alignment explanation
Indices: 11946831--11946865 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
11946821 ATCTTTTTAG
11946831 ATTAAAACAAAAATAATT
1 ATTAAAA-AAAAATAATT
*
11946849 ATTAAAATAAAATAATT
1 ATTAAAAAAAAATAATT
11946866 CTAAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTAAAAAAAAATAATT
Found at i:11946872 original size:16 final size:17
Alignment explanation
Indices: 11946840--11946872 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11946830 GATTAAAACA
*
11946840 AAAATAATTATTAAAAT
1 AAAATAATTACTAAAAT
11946857 AAAATAATT-CTAAAAT
1 AAAATAATTACTAAAAT
11946873 TTAAAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAATTACTAAAAT
Found at i:11947717 original size:125 final size:124
Alignment explanation
Indices: 11947391--11947767 Score: 576
Period size: 125 Copynumber: 3.0 Consensus size: 124
11947381 TTAGGGTTTT
*** * **
11947391 TAGGTCATGGAAGAAATAATTTCGAGTTGAAGTTTCTGATAAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCATGGAAGAAATAATTT-TTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * * *
11947456 AGAATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTAGTGGACGCGCTTTTGCTATAG
65 AGGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
*
11947516 TAGGTCATGGAAGAAATAA-TTTTTTTGACGTTTCTGAGCAAATAGTATAAAACCGCTTCTAGCA
1 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
* *
11947580 GGATGCTATTTGAGAAGAATTTGTAAAAATTGCGCCCTCGTGGACACGCTTTTGCTACAG
66 GGATGCTATTTGAGAAGAATTTGT-AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * *
11947640 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCAAGGA
1 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
11947705 GGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
66 GGATGCTATTTGAGAAGAATTTGT-AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
11947765 TAG
1 TAG
11947768 CATGTTTGGG
Statistics
Matches: 230, Mismatches: 20, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
123 59 0.26
124 51 0.22
125 120 0.52
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (124 bp):
TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
GGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:11949508 original size:21 final size:21
Alignment explanation
Indices: 11949479--11949741 Score: 280
Period size: 21 Copynumber: 12.0 Consensus size: 21
11949469 GCAAGCCCGT
*
11949479 TTAGTGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
11949500 TTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
*
11949521 TTAGAGTTTTTAAG-TAACGGG
1 TTAGGGTTTTTAAGTTAA-GGG
*
11949542 TTAGGGTTTTTAAGTTTAGGG
1 TTAGGGTTTTTAAGTTAAGGG
*
11949563 TTTAGGGTTTTTAA-TTAAATTAGG
1 -TTAGGGTTTTTAAGTT-AA--GGG
*
11949587 TTAGAGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
* *
11949608 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAA--GGG
11949631 TTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
* * *
11949652 TTAGGATTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAA--GGG
11949675 TTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
* *
11949696 TTTAAGGTTTTTAA-TTAAATTAGG
1 -TTAGGGTTTTTAAGTT-AA--GGG
11949720 TTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
11949741 T
1 T
11949742 ATTAATGGTT
Statistics
Matches: 203, Mismatches: 23, Indels: 32
0.79 0.09 0.12
Matches are distributed among these distances:
20 3 0.01
21 97 0.48
22 30 0.15
23 65 0.32
24 8 0.04
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.46
Consensus pattern (21 bp):
TTAGGGTTTTTAAGTTAAGGG
Found at i:11949628 original size:44 final size:44
Alignment explanation
Indices: 11949498--11949741 Score: 366
Period size: 44 Copynumber: 5.5 Consensus size: 44
11949488 TTAAGTTAAG
* * **
11949498 GGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTTTTAA-GTAA-CG
1 GGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTA
* *
11949540 GGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAATTTAATTA
*
11949585 GGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTA
*
11949629 GGTTAGGGTTTTTAAGTTAAGGGTTAGGATTTTTAATTTAATTA
1 GGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTA
* *
11949673 GGTTAGGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAATTTAATTA
11949718 GGTTAGGGTTTTTAAGTTAAGGGT
1 GGTTAGGGTTTTTAAGTTAAGGGT
11949742 ATTAATGGTT
Statistics
Matches: 184, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
42 22 0.12
43 12 0.07
44 88 0.48
45 62 0.34
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.46
Consensus pattern (44 bp):
GGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTA
Found at i:11949709 original size:89 final size:88
Alignment explanation
Indices: 11949498--11949741 Score: 359
Period size: 89 Copynumber: 2.8 Consensus size: 88
11949488 TTAAGTTAAG
* ** *
11949498 GGTTAGGGTTTTTAAGTTAAGGGTT-AGAGTTTTTAA-GTAA-CGGGTTAGGGTTTTTAAGTTTA
1 GGTTAGGGTTTTTAAGTTAAGGGTTAAG-GTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA
*
11949560 GGGTTTAGGGTTTTTAATTAAATTA
65 GGG-TTAGGATTTTTAATTAAATTA
* *
11949585 GGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
*
11949650 GGTTAGGATTTTTAATTTAATTA
66 GGTTAGGATTTTTAATTAAATTA
*
11949673 GGTTAGGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAA
1 GGTTAGGGTTTTTAAGTTAAGGG-TTAAGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA
11949738 GGGT
65 GGGT
11949742 ATTAATGGTT
Statistics
Matches: 142, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
87 32 0.23
88 45 0.32
89 65 0.46
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.46
Consensus pattern (88 bp):
GGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
GGTTAGGATTTTTAATTAAATTA
Found at i:11949760 original size:133 final size:129
Alignment explanation
Indices: 11949498--11949741 Score: 373
Period size: 133 Copynumber: 1.9 Consensus size: 129
11949488 TTAAGTTAAG
* *
11949498 GGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTTTTAAGTAACGGGTTAGGGTTTTTAAGTTTAGGG
1 GGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTTTTAAGTAACAGGTTAGGGTTTTTAAGTTAAGGG
* *
11949563 TTTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATT
66 TTTAAGGTTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTAAGGGTTAGGG--TTTAATATAATT
11949628 A
129 A
* *
11949629 GGTTAGGGTTTTTAAGTTAAGGGTTAG-GATTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA
1 GGTTAGGGTTTTTAAGTTAAGGGTTAGAG-TTTTTAA-GTAA-CAGGTTAGGGTTTTTAAGTTAA
*
11949693 GGGTTTAAGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGT
63 GGGTTTAAGGTTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTAAGGGT
11949742 ATTAATGGTT
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
130 1 0.01
131 34 0.33
132 3 0.03
133 66 0.63
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.46
Consensus pattern (129 bp):
GGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTTTTAAGTAACAGGTTAGGGTTTTTAAGTTAAGGG
TTTAAGGTTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTAATATAATTA
Found at i:11949831 original size:25 final size:24
Alignment explanation
Indices: 11949790--11949916 Score: 104
Period size: 25 Copynumber: 5.3 Consensus size: 24
11949780 TTCAAAATAT
11949790 TCAAA-AAATTTCTATTTTATTACA
1 TCAAATAAATTT-TATTTTATTACA
11949814 TCAAATAAACTTTTATTTTATTACA
1 TCAAATAAA-TTTTATTTTATTACA
* * ** *
11949839 TCAAAT-AATATCA--AAATAAC-
1 TCAAATAAATTTTATTTTATTACA
*
11949859 T-AAAAAAATTTTCTATTTTATTACA
1 TCAAATAAA-TTT-TATTTTATTACA
*
11949884 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAA-TTTTATTTTATTACA
11949909 TCAAATAA
1 TCAAATAA
11949917 TATCAAAATA
Statistics
Matches: 80, Mismatches: 14, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
19 3 0.04
20 3 0.04
21 6 0.08
22 1 0.01
23 3 0.04
24 11 0.14
25 42 0.52
26 11 0.14
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.42
Consensus pattern (24 bp):
TCAAATAAATTTTATTTTATTACA
Found at i:11949876 original size:70 final size:69
Alignment explanation
Indices: 11949792--11949926 Score: 252
Period size: 70 Copynumber: 1.9 Consensus size: 69
11949782 CAAAATATTC
*
11949792 AAAAAATTTCTATTTTATTACATCAAATAAACTTTTATTTTATTACATCAAATAATATCAAAATA
1 AAAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATA
11949857 ACTA
66 ACTA
11949861 AAAAAATTTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAAT
1 AAAAAA-TTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAAT
11949926 A
65 A
11949927 TTCAAAATAT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
69 6 0.09
70 58 0.91
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (69 bp):
AAAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATA
ACTA
Found at i:11951235 original size:20 final size:21
Alignment explanation
Indices: 11951193--11951236 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
11951183 ATACTTTTAT
*
11951193 TTTTAAAAATCTACATAATAA
1 TTTTAAAAATCTACATAAAAA
11951214 TTTT-AAAATCTA-ATATAAAA
1 TTTTAAAAATCTACATA-AAAA
11951234 TTT
1 TTT
11951237 ACCTCGTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 14 0.67
21 4 0.19
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTTAAAAATCTACATAAAAA
Found at i:11952169 original size:12 final size:11
Alignment explanation
Indices: 11952127--11952169 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
11952117 ATTTTTACGG
*
11952127 TTTAAAAAAAA
1 TTTAAAAAATA
11952138 TTTAAAAAATA
1 TTTAAAAAATA
* *
11952149 TTTTTAAAATTA
1 -TTTAAAAAATA
11952161 TTTAAAAAA
1 TTTAAAAAA
11952170 AGGGAGTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TTTAAAAAATA
Found at i:11952503 original size:63 final size:63
Alignment explanation
Indices: 11952404--11952538 Score: 243
Period size: 63 Copynumber: 2.1 Consensus size: 63
11952394 ACGCGATTTG
* *
11952404 CTGACGTGTCAGCAAATTGCGTCCTAGAGGCCGCGATTTCTTGGCGCGTCCCTTGACATCGCA
1 CTGACGTGGCAGCAAATCGCGTCCTAGAGGCCGCGATTTCTTGGCGCGTCCCTTGACATCGCA
*
11952467 CTGACGTGGCAGCAAATCGCGTCCTAGAGGCTGCGATTTCTTGGCGCGTCCCTTGACATCGCA
1 CTGACGTGGCAGCAAATCGCGTCCTAGAGGCCGCGATTTCTTGGCGCGTCCCTTGACATCGCA
11952530 CTGACGTGG
1 CTGACGTGG
11952539 ATGCGATTTT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 69 1.00
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (63 bp):
CTGACGTGGCAGCAAATCGCGTCCTAGAGGCCGCGATTTCTTGGCGCGTCCCTTGACATCGCA
Found at i:11963287 original size:19 final size:19
Alignment explanation
Indices: 11963263--11963300 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
11963253 AATTTATAAC
*
11963263 TAATTAACCTTAATTACTT
1 TAATTAAACTTAATTACTT
11963282 TAATTAAACTTAATTACTT
1 TAATTAAACTTAATTACTT
11963301 AACCTTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATTAAACTTAATTACTT
Found at i:11975946 original size:35 final size:35
Alignment explanation
Indices: 11975895--11975965 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
11975885 TCTCCTTACA
11975895 CAATCGTGCATTTCAAGTCATGTGTGCCACACGGC
1 CAATCGTGCATTTCAAGTCATGTGTGCCACACGGC
*
11975930 CAATTGTGCATTTCAAGTCATGTGTGCCACACGGC
1 CAATCGTGCATTTCAAGTCATGTGTGCCACACGGC
11975965 C
1 C
11975966 TGCGACACGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.27
Consensus pattern (35 bp):
CAATCGTGCATTTCAAGTCATGTGTGCCACACGGC
Found at i:11977574 original size:3 final size:3
Alignment explanation
Indices: 11977566--11977590 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11977556 AAGTCTAATA
11977566 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
11977591 TTAAAATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:11979388 original size:16 final size:16
Alignment explanation
Indices: 11979319--11979386 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
11979309 TTTGGTTCGC
11979319 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
11979335 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
11979351 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
11979367 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
11979383 TGTA
1 TGTA
11979387 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:11979421 original size:45 final size:44
Alignment explanation
Indices: 11979367--11979461 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
11979357 GGATTAGAGG
* *
11979367 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
11979412 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
11979456 TGTAAT
1 TGTAAT
11979462 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:11979644 original size:18 final size:17
Alignment explanation
Indices: 11979623--11979657 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11979613 TTATTATTTA
*
11979623 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
11979641 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
11979658 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:11979651 original size:28 final size:27
Alignment explanation
Indices: 11979581--11979653 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
11979571 TTTATTATCA
*
11979581 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
11979609 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
11979636 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
11979654 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:11979770 original size:144 final size:147
Alignment explanation
Indices: 11979542--11979813 Score: 478
Period size: 144 Copynumber: 1.9 Consensus size: 147
11979532 ATGATTATTG
11979542 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
* *
11979607 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAACTTAATAAAATTCTTAATAATTAGC
11979672 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
11979691 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
11979753 ATAATTATTATTAAATATATTTTAATTAAAATATATAACTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAACTTAATAAAATTCTTAATAATTA
11979814 ATATTCTTAT
Statistics
Matches: 120, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
144 91 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAACTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:11979883 original size:129 final size:130
Alignment explanation
Indices: 11979750--11979983 Score: 416
Period size: 129 Copynumber: 1.8 Consensus size: 130
11979740 ATCATATTTA
* *
11979750 AACATAATTATTATTAAATATATTTTAATTAAAATATATAACTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAACTTAATAAAATTCTTAATAATTAA
*
11979815 TATTCTTATATGAATTTACTCAAACCATAAT-TATTATTAAATATGATACTGTAAAATATAAAAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATTAAATATGATACTGTAAAATATAAAAT
*
11979879 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAACTTAATAAAATTCTTAATAATTAA
*
11979944 TATTCTTATATGAATTTACTCAAATCATAATATATGATTA
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATTA
11979984 TAACTAATAT
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
129 92 0.93
130 7 0.07
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (130 bp):
AACATAATTATTATTAAATATAATATAATTAAAATATATAACTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAACCATAATATATGATTAAATATGATACTGTAAAATATAAAAT
Found at i:11979917 original size:18 final size:17
Alignment explanation
Indices: 11979896--11979930 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11979886 TTATTATTAA
11979896 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
11979914 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
11979931 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:11979993 original size:17 final size:16
Alignment explanation
Indices: 11979971--11980017 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
11979961 ACTCAAATCA
11979971 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
11979988 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
11980002 TAAATATATGATTTAA
1 T-AATATATGATTTAA
11980018 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:11980018 original size:17 final size:17
Alignment explanation
Indices: 11979990--11980023 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11979980 ATTATAACTA
*
11979990 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
11980007 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
11980024 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:11980166 original size:93 final size:91
Alignment explanation
Indices: 11980056--11980249 Score: 284
Period size: 92 Copynumber: 2.1 Consensus size: 91
11980046 GATTATAGTT
* *
11980056 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTA-ATATAATTAT-ATAATAATATATAATTTC
* *
11980119 ATAAAATTCTTGATAATAAAAATTTTCTTA
63 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
11980149 TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAGTGATATATAATTTCATA
1 TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAATAATATATAATTTCATA
11980214 AAATTCTTAATAATAAAATGTTCTTA
66 AAATTCTTAATAATAAAATGTTCTTA
11980240 TATGAATTTA
1 TATGAATTTA
11980250 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
91 21 0.23
92 40 0.43
93 29 0.31
94 3 0.03
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (91 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAATAATATATAATTTCATA
AAATTCTTAATAATAAAATGTTCTTA
Found at i:11983870 original size:15 final size:15
Alignment explanation
Indices: 11983850--11983880 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11983840 ATATTATGTA
11983850 TAATTGAGGTAAAAT
1 TAATTGAGGTAAAAT
11983865 TAATTGAGGTAAAAT
1 TAATTGAGGTAAAAT
11983880 T
1 T
11983881 TGAAGGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.35
Consensus pattern (15 bp):
TAATTGAGGTAAAAT
Found at i:11988423 original size:12 final size:12
Alignment explanation
Indices: 11988400--11988431 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
11988390 TCTTGTGTTC
11988400 AAAAAAAT--TG
1 AAAAAAATAATG
11988410 AAAAAAATAATG
1 AAAAAAATAATG
11988422 AAAAAAATAA
1 AAAAAAATAA
11988432 AAAATAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.40
12 12 0.60
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (12 bp):
AAAAAAATAATG
Found at i:11989521 original size:27 final size:26
Alignment explanation
Indices: 11989477--11989527 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
11989467 ATATTACAAA
* *
11989477 TTTTCTTTTTATTTTCTTTAATTTCT
1 TTTTCATTTGATTTTCTTTAATTTCT
11989503 TTTTCATTTGATTGTTCTTTAATTT
1 TTTTCATTTGATT-TTCTTTAATTT
11989528 TATGAATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.14, C:0.10, G:0.04, T:0.73
Consensus pattern (26 bp):
TTTTCATTTGATTTTCTTTAATTTCT
Found at i:11992269 original size:12 final size:13
Alignment explanation
Indices: 11992249--11992281 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
11992239 AATATATGTA
11992249 AAATTGAAG-TTT
1 AAATTGAAGCTTT
*
11992261 AATTTGAAGCTTT
1 AAATTGAAGCTTT
11992274 AAATTGAA
1 AAATTGAA
11992282 AGTTATGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.39
Consensus pattern (13 bp):
AAATTGAAGCTTT
Found at i:11998903 original size:17 final size:17
Alignment explanation
Indices: 11998883--11998950 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 17
11998873 ATAAATTGAT
11998883 ATAAATATATAAAAATC
1 ATAAATATATAAAAATC
* *
11998900 ATAAATATTTATAAATATT
1 ATAAATA--TATAAAAATC
*
11998919 ATAAA-AAATAAAAATC
1 ATAAATATATAAAAATC
11998935 GAATAAAT-TATAAAAA
1 --ATAAATATATAAAAA
11998951 ATTATAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 7 0.17
17 7 0.17
18 13 0.32
19 13 0.32
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (17 bp):
ATAAATATATAAAAATC
Found at i:11998920 original size:9 final size:9
Alignment explanation
Indices: 11998882--11998923 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
11998872 TATAAATTGA
11998882 TATAAATA-
1 TATAAATAT
*
11998890 TATAAAAAT
1 TATAAATAT
*
11998899 CATAAATATT
1 TATAAATA-T
11998909 TATAAATAT
1 TATAAATAT
11998918 TATAAA
1 TATAAA
11998924 AAATAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 7 0.25
9 13 0.46
10 8 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (9 bp):
TATAAATAT
Found at i:11998922 original size:19 final size:17
Alignment explanation
Indices: 11998882--11998958 Score: 59
Period size: 19 Copynumber: 4.4 Consensus size: 17
11998872 TATAAATTGA
11998882 TATAAATATATAAAAAT
1 TATAAATATATAAAAAT
* *
11998899 CATAAATATTTATAAATAT
1 TATAAATA--TATAAAAAT
*
11998918 TATAAA-AAATAAAAAT
1 TATAAATATATAAAAAT
*
11998934 CGAATAAAT-TATAAAAAAT
1 --TATAAATATAT-AAAAAT
11998953 TATAAA
1 TATAAA
11998959 ATTAATAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
16 7 0.15
17 12 0.26
18 8 0.17
19 19 0.41
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (17 bp):
TATAAATATATAAAAAT
Found at i:11998959 original size:27 final size:26
Alignment explanation
Indices: 11998865--11998967 Score: 86
Period size: 27 Copynumber: 3.8 Consensus size: 26
11998855 TTAAAAATAA
*
11998865 AAAAAATTATAAATTGATATAAA-TAT
1 AAAAAATTATAAAATGA-ATAAATTAT
* **
11998891 ATAAAAATCATAAATATTTATAAATATTAT
1 A-AAAAATTATAAA-ATGAAT-AA-ATTAT
11998921 AAAAAA-TA-AAAATCGAATAAATTAT
1 AAAAAATTATAAAAT-GAATAAATTAT
*
11998946 AAAAAATTATAAAATTAATAAA
1 AAAAAATTATAAAATGAATAAA
11998968 ACATATTTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
25 11 0.18
26 13 0.21
27 23 0.38
28 4 0.07
29 6 0.10
30 4 0.07
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAAAATTATAAAATGAATAAATTAT
Found at i:12000176 original size:30 final size:30
Alignment explanation
Indices: 12000140--12000198 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
12000130 CCCGAGCTTT
12000140 GAGGCAAAAGTATAATTATGCAAAAGTTTA
1 GAGGCAAAAGTATAATTATGCAAAAGTTTA
* * * *
12000170 GAGGCAAAATTGTAATTTTTCAAAAGTTT
1 GAGGCAAAAGTATAATTATGCAAAAGTTT
12000199 GAGTCAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (30 bp):
GAGGCAAAAGTATAATTATGCAAAAGTTTA
Found at i:12000642 original size:50 final size:50
Alignment explanation
Indices: 12000539--12000770 Score: 157
Period size: 50 Copynumber: 4.5 Consensus size: 50
12000529 GGGAATGAGA
* * * *
12000539 TCCCATGTAAGACCATGTCTGGGACATGTCATTGGTATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCA---AG---ATGAGAGG
** *
12000595 TCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGAGAGG
* * * * **
12000645 TTCCC-CGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAAC
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGAGAGG
* * * ** * **
12000695 TCCCATGTAAGACCA-GATATGGGATATGGCATTGGCAATACAGA--AAACA
1 TCCCATGTAAGACCATG-TCTGGGACATGGCATGGGCACCA-AGATGAGAGG
*
12000744 TCCCATGTAAGACTATGTCTGGGACAT
1 TCCCATGTAAGACCATGTCTGGGACAT
12000771 AGCTTTGGCA
Statistics
Matches: 143, Mismatches: 28, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
49 29 0.20
50 71 0.50
51 6 0.04
53 2 0.01
56 35 0.24
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGAGAGG
Found at i:12001011 original size:16 final size:16
Alignment explanation
Indices: 12000985--12001026 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
12000975 TTATTTAAGT
*
12000985 AAGCAAGTAAGTAAAC
1 AAGCGAGTAAGTAAAC
* *
12001001 AAGTGAGTAAGTAAAG
1 AAGCGAGTAAGTAAAC
12001017 AAGCGAGTAA
1 AAGCGAGTAA
12001027 AGATTCTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.52, C:0.07, G:0.26, T:0.14
Consensus pattern (16 bp):
AAGCGAGTAAGTAAAC
Found at i:12010257 original size:63 final size:63
Alignment explanation
Indices: 12010120--12010259 Score: 156
Period size: 63 Copynumber: 2.2 Consensus size: 63
12010110 TGGCTTGGGT
* * * * * * *
12010120 ACACGTCCATGTCCCTGGCCATATGTTTTTTGTACCATAAACAGTGAGTTACATAGCCTTGAC
1 ACACGTCCGTGTCCCTGGCCATATGGTCTTTGTACCACAAACAGTGAGGTACACAGCCTGGAC
* * * * *
12010183 ACATGTCCGTGTCCCTGGCTATATGGTCTTTGTACCACGAACAGTGAGGTACGCGGCCTGGAC
1 ACACGTCCGTGTCCCTGGCCATATGGTCTTTGTACCACAAACAGTGAGGTACACAGCCTGGAC
12010246 ACACG-CACGTGTCC
1 ACACGTC-CGTGTCC
12010260 TTTGCCCGTG
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
62 1 0.02
63 62 0.98
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (63 bp):
ACACGTCCGTGTCCCTGGCCATATGGTCTTTGTACCACAAACAGTGAGGTACACAGCCTGGAC
Found at i:12014379 original size:9 final size:9
Alignment explanation
Indices: 12014362--12014416 Score: 65
Period size: 9 Copynumber: 6.1 Consensus size: 9
12014352 TATAGTTTGA
12014362 TATTCGAAT
1 TATTCGAAT
*
12014371 TATTTGAAT
1 TATTCGAAT
*
12014380 TATTCGAGT
1 TATTCGAAT
12014389 TATTCGAAT
1 TATTCGAAT
* *
12014398 TATTTGAGT
1 TATTCGAAT
*
12014407 TATTCAAAT
1 TATTCGAAT
12014416 T
1 T
12014417 CGAAAGCTCA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:12014606 original size:24 final size:24
Alignment explanation
Indices: 12014577--12014639 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
12014567 AGTGTTGCGG
* *
12014577 ACAAATTGCCAGAACAGTATTCAA
1 ACAAATTGCCAGAACAATATGCAA
* *
12014601 ACAAATTGCCAAAATAATATGCAA
1 ACAAATTGCCAGAACAATATGCAA
* *
12014625 ACAAATCGCTAGAAC
1 ACAAATTGCCAGAAC
12014640 TCCAAACAGA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.21, G:0.11, T:0.19
Consensus pattern (24 bp):
ACAAATTGCCAGAACAATATGCAA
Found at i:12014692 original size:30 final size:29
Alignment explanation
Indices: 12014646--12014718 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
12014636 GAACTCCAAA
* * *
12014646 CAGAACTCC-AAAATTGCGGATTTACTGC
1 CAGAACTCCAAAAATTGCAGATATACCGC
*
12014674 TAGAACTCCAATAAATTGCAGATATACCGC
1 CAGAACTCCAA-AAATTGCAGATATACCGC
*
12014704 CAGAACTCCACAAAT
1 CAGAACTCCAAAAAT
12014719 CTCCTGTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 8 0.22
29 5 0.14
30 24 0.65
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (29 bp):
CAGAACTCCAAAAATTGCAGATATACCGC
Found at i:12017382 original size:9 final size:9
Alignment explanation
Indices: 12017365--12017431 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
12017355 GTAGTGATTC
*
12017365 AATTCGGTT
1 AATTCGGGT
* *
12017374 AATTTGGTT
1 AATTCGGGT
12017383 AATTCGGGT
1 AATTCGGGT
*
12017392 AATTTGGGT
1 AATTCGGGT
*
12017401 AATTCAGGT
1 AATTCGGGT
12017410 AATTCGGGT
1 AATTCGGGT
*
12017419 AATTCGGTT
1 AATTCGGGT
12017428 AATT
1 AATT
12017432 TTTAACCAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.42
Consensus pattern (9 bp):
AATTCGGGT
Found at i:12017388 original size:18 final size:18
Alignment explanation
Indices: 12017365--12017432 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
12017355 GTAGTGATTC
*
12017365 AATTCGGTTAATTTGGTT
1 AATTCGGTTAATTTGGGT
*
12017383 AATTCGGGTAATTTGGGT
1 AATTCGGTTAATTTGGGT
*
12017401 AATTCAGG-TAATTCGGGT
1 AATTC-GGTTAATTTGGGT
12017419 AATTCGGTTAATTT
1 AATTCGGTTAATTT
12017433 TTAACCAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.05
18 40 0.91
19 2 0.05
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (18 bp):
AATTCGGTTAATTTGGGT
Found at i:12023027 original size:25 final size:25
Alignment explanation
Indices: 12022998--12023045 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
12022988 TGACGTAAAT
*
12022998 TGAATGTGAATAATGTTTAATCGCA
1 TGAATGTGAATAATGGTTAATCGCA
*
12023023 TGAATGTGAATGATGGTTAATCG
1 TGAATGTGAATAATGGTTAATCG
12023046 ATTCTAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.35
Consensus pattern (25 bp):
TGAATGTGAATAATGGTTAATCGCA
Found at i:12028278 original size:2 final size:2
Alignment explanation
Indices: 12028271--12028319 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
12028261 AATGATACAA
12028271 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12028313 AC AC AC A
1 AC AC AC A
12028320 TATTCATTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12030454 original size:9 final size:9
Alignment explanation
Indices: 12030442--12030532 Score: 53
Period size: 9 Copynumber: 9.9 Consensus size: 9
12030432 TTTTGTGAAT
12030442 TTTTATAAA
1 TTTTATAAA
12030451 TTTTA-AATA
1 TTTTATAA-A
* *
12030460 TTGTATATA
1 TTTTATAAA
* *
12030469 TATTATTAA
1 TTTTATAAA
*
12030478 TTTTATAAT
1 TTTTATAAA
12030487 TTATTA-AAA
1 TT-TTATAAA
12030496 TTTT-TATAA
1 TTTTATA-AA
12030505 TATTTATAAA
1 T-TTTATAAA
* *
12030515 TTTTTATGAT
1 -TTTTATAAA
12030525 TTTTATAA
1 TTTTATAA
12030533 TTCTTGTAAG
Statistics
Matches: 61, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
8 5 0.08
9 38 0.62
10 15 0.25
11 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (9 bp):
TTTTATAAA
Found at i:12030500 original size:19 final size:19
Alignment explanation
Indices: 12030423--12030532 Score: 77
Period size: 19 Copynumber: 5.8 Consensus size: 19
12030413 TATGATATTA
* *
12030423 TTTATAAGTTTTTGTGAATT
1 TTTATAA-TTTTTATAAATT
*
12030443 TTTATAA-ATTT-TAAATAT
1 TTTATAATTTTTATAAAT-T
* * *
12030461 TGTAT-ATATATTATTAA-T
1 TTTATAAT-TTTTATAAATT
12030479 TTTATAATTTATTA-AAATT
1 TTTATAATTT-TTATAAATT
*
12030498 TTTATAATATTTATAAATT
1 TTTATAATTTTTATAAATT
*
12030517 TTTATGATTTTTATAA
1 TTTATAATTTTTATAA
12030533 TTCTTGTAAG
Statistics
Matches: 70, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
17 5 0.07
18 19 0.27
19 36 0.51
20 10 0.14
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTATAATTTTTATAAATT
Found at i:12030508 original size:36 final size:37
Alignment explanation
Indices: 12030442--12030518 Score: 88
Period size: 36 Copynumber: 2.1 Consensus size: 37
12030432 TTTTGTGAAT
*
12030442 TTTTATAAATTTTAAATATTGTATATATA-TTATTAA
1 TTTTATAAATTTTAAATATTGTATATATATTTATAAA
* *
12030478 TTTTATAATTTATTAAA-ATT-TTTATAATATTTATAAA
1 TTTTATAAATT-TTAAATATTGTATAT-ATATTTATAAA
12030515 TTTT
1 TTTT
12030519 TATGATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 4 0.11
36 16 0.46
37 15 0.43
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (37 bp):
TTTTATAAATTTTAAATATTGTATATATATTTATAAA
Found at i:12030570 original size:12 final size:12
Alignment explanation
Indices: 12030553--12030577 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12030543 TATATCTCAA
12030553 TTTTACTATTTT
1 TTTTACTATTTT
12030565 TTTTACTATTTT
1 TTTTACTATTTT
12030577 T
1 T
12030578 AATTTTTTAT
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTACTATTTT
Found at i:12030585 original size:17 final size:17
Alignment explanation
Indices: 12030563--12030595 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12030553 TTTTACTATT
12030563 TTTTTTACT-ATTTTTAA
1 TTTTTTA-TAATTTTTAA
12030580 TTTTTTATAATTTTTA
1 TTTTTTATAATTTTTA
12030596 TGAGAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTATAATTTTTAA
Found at i:12031210 original size:19 final size:20
Alignment explanation
Indices: 12031168--12031221 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
12031158 AAAACACCCA
*
12031168 AAATAATTCAAAATAATTTTT
1 AAAT-ATTCAAAATAATTTAT
12031189 AAATATTCAAAAT-ATTTAT
1 AAATATTCAAAATAATTTAT
*
12031208 AAAAATTCCAAAAT
1 AAATATT-CAAAAT
12031222 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 11 0.37
20 15 0.50
21 4 0.13
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATATTCAAAATAATTTAT
Found at i:12031867 original size:18 final size:19
Alignment explanation
Indices: 12031840--12031877 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
12031830 CCAAGAAGGC
12031840 TTTTCTATTTCTATT-TTTT
1 TTTTCTATTTC-ATTCTTTT
12031859 TTTTC-ATTTCATTCTTTT
1 TTTTCTATTTCATTCTTTT
12031877 T
1 T
12031878 CCTCTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.17
18 10 0.56
19 5 0.28
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTATTTCATTCTTTT
Found at i:12031876 original size:17 final size:19
Alignment explanation
Indices: 12031840--12031877 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
12031830 CCAAGAAGGC
*
12031840 TTTTCTATTTCTATTTTTT
1 TTTTCTATTTCTATTCTTT
12031859 TTTTC-ATTTC-ATTCTTT
1 TTTTCTATTTCTATTCTTT
12031876 TT
1 TT
12031878 CCTCTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 5 0.28
19 5 0.28
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTATTTCTATTCTTT
Found at i:12034476 original size:17 final size:18
Alignment explanation
Indices: 12034440--12034474 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12034430 CCAAAATGTA
12034440 AAAAATAAAAAAATCTTT
1 AAAAATAAAAAAATCTTT
* *
12034458 AAAATTAAAAAACTCTT
1 AAAAATAAAAAAATCTT
12034475 AACCCACCTC
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:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATAAAAAAATCTTT
Found at i:12039088 original size:14 final size:14
Alignment explanation
Indices: 12039069--12039096 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12039059 AACTTAGACC
12039069 TAAATCTTGAATCT
1 TAAATCTTGAATCT
12039083 TAAATCTTGAATCT
1 TAAATCTTGAATCT
12039097 CGAACCCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TAAATCTTGAATCT
Found at i:12044019 original size:22 final size:22
Alignment explanation
Indices: 12043993--12044034 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
12043983 CAACCAAATA
12043993 ATCACAGCTTCAACAATTTACT
1 ATCACAGCTTCAACAATTTACT
12044015 ATCACAGCTTCAACAATTTA
1 ATCACAGCTTCAACAATTTA
12044035 TCATTCACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (22 bp):
ATCACAGCTTCAACAATTTACT
Found at i:12045673 original size:11 final size:11
Alignment explanation
Indices: 12045653--12045696 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
12045643 AGATAAATGT
*
12045653 TATTTAATTAA
1 TATTTTATTAA
12045664 TATTTTATTAA
1 TATTTTATTAA
*
12045675 TATTTTTATTAT
1 TA-TTTTATTAA
*
12045687 TACTTTATTA
1 TATTTTATTA
12045697 TTAAATGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:12050091 original size:13 final size:13
Alignment explanation
Indices: 12050054--12050160 Score: 61
Period size: 12 Copynumber: 8.7 Consensus size: 13
12050044 AAAAACTTAA
*
12050054 TGATTAAAA-ACT
1 TGATGAAAAGACT
*
12050066 TGATGGAAA-ACT
1 TGATGAAAAGACT
*
12050078 TTATGAAAAGACT
1 TGATGAAAAGACT
12050091 TGATGAAAAG-CT
1 TGATGAAAAGACT
12050103 T-A--AAAAGAACT
1 TGATGAAAAG-ACT
*
12050114 TGATG-CAA-ACT
1 TGATGAAAAGACT
* * *
12050125 TAATAAAAAAAACT
1 TGAT-GAAAAGACT
12050139 TGAT-AAAAGAACT
1 TGATGAAAAG-ACT
12050152 TGATGAAAA
1 TGATGAAAA
12050161 ACACTTGAAG
Statistics
Matches: 73, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
9 5 0.07
11 10 0.14
12 25 0.34
13 23 0.32
14 10 0.14
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.25
Consensus pattern (13 bp):
TGATGAAAAGACT
Found at i:12050118 original size:23 final size:21
Alignment explanation
Indices: 12050059--12050127 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 21
12050049 CTTAATGATT
12050059 AAAA-ACTTGATGGAAAACTTTA
1 AAAAGACTTGAT-GAAAAC-TTA
12050081 TGAAAAGACTTGATGAAAAGCTTA
1 --AAAAGACTTGATGAAAA-CTTA
*
12050105 AAAAGAACTTGATGCAAACTTA
1 AAAAG-ACTTGATGAAAACTTA
12050127 A
1 A
12050128 TAAAAAAAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
22 10 0.24
23 11 0.27
24 12 0.29
25 8 0.20
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (21 bp):
AAAAGACTTGATGAAAACTTA
Found at i:12050126 original size:22 final size:22
Alignment explanation
Indices: 12050083--12050127 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
12050073 AAACTTTATG
12050083 AAAAGACTTGATGAAAAGCTTA
1 AAAAGACTTGATGAAAAGCTTA
*
12050105 AAAAGAACTTGATGCAAA-CTTA
1 AAAAG-ACTTGATGAAAAGCTTA
12050127 A
1 A
12050128 TAAAAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (22 bp):
AAAAGACTTGATGAAAAGCTTA
Found at i:12050151 original size:27 final size:27
Alignment explanation
Indices: 12050121--12050176 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
12050111 ACTTGATGCA
12050121 AACTTAATAAAAAAAACTTGATA-AAAG
1 AACTTAATAAAAAAAACTTGA-AGAAAG
* * *
12050148 AACTTGATGAAAAACACTTGAAGAAAG
1 AACTTAATAAAAAAAACTTGAAGAAAG
12050175 AA
1 AA
12050177 AACACTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.20
Consensus pattern (27 bp):
AACTTAATAAAAAAAACTTGAAGAAAG
Found at i:12051579 original size:6 final size:6
Alignment explanation
Indices: 12051568--12051625 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
12051558 GTCTCCCTGC
* * *
12051568 AAAATA AAAATA AAAATA AATAAGA AAAATA AATAATA AGAA-A AAATTA
1 AAAATA AAAATA AAAATA AA-AATA AAAATA AA-AATA AAAATA AAAATA
*
12051617 AAATTA AAA
1 AAAATA AAA
12051626 TGTGAATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
5 3 0.07
6 31 0.70
7 10 0.23
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:12051614 original size:13 final size:13
Alignment explanation
Indices: 12051568--12051606 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
12051558 GTCTCCCTGC
12051568 AAAATAAA-AATA
1 AAAATAAATAATA
*
12051580 AAAATAAATAAGA
1 AAAATAAATAATA
12051593 AAAATAAATAATA
1 AAAATAAATAATA
12051606 A
1 A
12051607 GAAAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (13 bp):
AAAATAAATAATA
Found at i:12051614 original size:17 final size:17
Alignment explanation
Indices: 12051569--12051612 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
12051559 TCTCCCTGCA
12051569 AAATAA-AAATAA-AAAT
1 AAATAAGAAA-AATAAAT
12051585 AAATAAGAAAAATAAAT
1 AAATAAGAAAAATAAAT
12051602 -AATAAGAAAAA
1 AAATAAGAAAAA
12051613 ATTAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.16
Consensus pattern (17 bp):
AAATAAGAAAAATAAAT
Found at i:12058451 original size:13 final size:13
Alignment explanation
Indices: 12058430--12058515 Score: 51
Period size: 13 Copynumber: 6.9 Consensus size: 13
12058420 TTGATGGAGA
*
12058430 ACTTTATGAAAAG
1 ACTTGATGAAAAG
12058443 ACTTGATGAAAAG
1 ACTTGATGAAAAG
12058456 -CTT-A--AAAAG
1 ACTTGATGAAAAG
*
12058465 AACTTGATG-CAA-
1 -ACTTGATGAAAAG
* * *
12058477 ACTTAATAAAAAAA
1 ACTTGAT-GAAAAG
12058491 ACTTGAT-AAAAG
1 ACTTGATGAAAAG
12058503 AACTTGATGAAAA
1 -ACTTGATGAAAA
12058516 ACACTTGAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 19
0.68 0.09 0.23
Matches are distributed among these distances:
9 5 0.09
11 10 0.18
12 8 0.14
13 23 0.41
14 10 0.18
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.24
Consensus pattern (13 bp):
ACTTGATGAAAAG
Found at i:12058481 original size:22 final size:22
Alignment explanation
Indices: 12058438--12058482 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
12058428 GAACTTTATG
12058438 AAAAGACTTGATGAAAAGCTTA
1 AAAAGACTTGATGAAAAGCTTA
*
12058460 AAAAGAACTTGATGCAAA-CTTA
1 AAAAG-ACTTGATGAAAAGCTTA
12058482 A
1 A
12058483 TAAAAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (22 bp):
AAAAGACTTGATGAAAAGCTTA
Found at i:12058493 original size:25 final size:25
Alignment explanation
Indices: 12058400--12058501 Score: 79
Period size: 25 Copynumber: 4.2 Consensus size: 25
12058390 GCTTAATTGA
*
12058400 AAAACTTAATAATTAAAAACTTGATGG
1 AAAACTTAATAA-AAAAAACTTGAT-G
* * * *
12058427 AGAACTTTAT-GAAAAGACTTGATG
1 AAAACTTAATAAAAAAAACTTGATG
*
12058451 AAAAGC-T--TAAAAAGAACTTGATG
1 AAAA-CTTAATAAAAAAAACTTGATG
*
12058474 CAAACTTAATAAAAAAAACTTGAT-
1 AAAACTTAATAAAAAAAACTTGATG
12058498 AAAA
1 AAAA
12058502 GAACTTGATG
Statistics
Matches: 58, Mismatches: 12, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
22 2 0.03
23 15 0.26
24 8 0.14
25 25 0.43
27 8 0.14
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.25
Consensus pattern (25 bp):
AAAACTTAATAAAAAAAACTTGATG
Found at i:12058506 original size:27 final size:27
Alignment explanation
Indices: 12058476--12058531 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
12058466 ACTTGATGCA
12058476 AACTTAATAAAAAAAACTTGATA-AAAG
1 AACTTAATAAAAAAAACTTGA-AGAAAG
* * *
12058503 AACTTGATGAAAAACACTTGAAGAAAG
1 AACTTAATAAAAAAAACTTGAAGAAAG
12058530 AA
1 AA
12058532 AACACTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.20
Consensus pattern (27 bp):
AACTTAATAAAAAAAACTTGAAGAAAG
Found at i:12060955 original size:18 final size:18
Alignment explanation
Indices: 12060932--12060966 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12060922 CTCATGGATC
12060932 TGATAAACAAAATAAACT
1 TGATAAACAAAATAAACT
* *
12060950 TGATAAAGATAATAAAC
1 TGATAAACAAAATAAAC
12060967 ATAAAGAGCA
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:0.60, C:0.09, G:0.09, T:0.23
Consensus pattern (18 bp):
TGATAAACAAAATAAACT
Found at i:12067202 original size:26 final size:25
Alignment explanation
Indices: 12067154--12067212 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
12067144 TTTCTCATCC
**
12067154 CAATTTTACCCCAATAATTTTTTGA
1 CAATTTTACCCCAATAAAATTTTGA
*
12067179 CAATTTTACCCCCGATAAAATTTTGA
1 CAATTTTA-CCCCAATAAAATTTTGA
*
12067205 CGATTTTA
1 CAATTTTA
12067213 ACCTTAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 8 0.28
26 21 0.72
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (25 bp):
CAATTTTACCCCAATAAAATTTTGA
Found at i:12067387 original size:6 final size:6
Alignment explanation
Indices: 12067376--12067423 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
12067366 TGCAAGTGTC
*
12067376 CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT CATTTC CATTTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT
12067424 TTGGAAACCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.65
Consensus pattern (6 bp):
CATTTT
Found at i:12072393 original size:21 final size:21
Alignment explanation
Indices: 12072368--12072418 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
12072358 GCGGTGGCGG
*
12072368 TGAGATTAGTTACTGTAACAA
1 TGAGATTAGGTACTGTAACAA
* * *
12072389 TGAGATTGGGTACTGTAGCAG
1 TGAGATTAGGTACTGTAACAA
12072410 TGAGATTAG
1 TGAGATTAG
12072419 AAACAGTGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.31
Consensus pattern (21 bp):
TGAGATTAGGTACTGTAACAA
Found at i:12076282 original size:15 final size:15
Alignment explanation
Indices: 12076262--12076294 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12076252 TATATATATT
12076262 TTTATA-AAAAATTAA
1 TTTATATAAAAA-TAA
12076277 TTTATATAAAAATAA
1 TTTATATAAAAATAA
12076292 TTT
1 TTT
12076295 GATCTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTATATAAAAATAA
Found at i:12077728 original size:20 final size:20
Alignment explanation
Indices: 12077691--12077728 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12077681 ATTGTCAAAA
* *
12077691 AAAATTTAAAAGTAAAAACT
1 AAAATTGAAAAGAAAAAACT
12077711 AAAATTGAAAAGAAAAAA
1 AAAATTGAAAAGAAAAAA
12077729 GGTGAACAAC
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:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (20 bp):
AAAATTGAAAAGAAAAAACT
Found at i:12078356 original size:22 final size:21
Alignment explanation
Indices: 12078331--12078372 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
12078321 TTATGAAAAA
*
12078331 ATTTAAGATTTTTATTTTTTTC
1 ATTTAAGAGTTTT-TTTTTTTC
*
12078353 ATTTTAGAGTTTTTTTTTTT
1 ATTTAAGAGTTTTTTTTTTT
12078373 GTATTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.71
Consensus pattern (21 bp):
ATTTAAGAGTTTTTTTTTTTC
Found at i:12078358 original size:23 final size:24
Alignment explanation
Indices: 12078332--12078399 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 24
12078322 TATGAAAAAA
12078332 TTTAAGA-TTTTTATTTTTTTCA-T
1 TTTAAGAGTTTTTATTTTTTT-ATT
12078355 TTT-AGAGTTTTT-TTTTTTGTATT
1 TTTAAGAGTTTTTATTTTTT-TATT
* * *
12078378 TTTATGATTTTTTATATTTTTA
1 TTTAAGAGTTTTTATTTTTTTA
12078400 AGGAATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
22 10 0.27
23 13 0.35
24 9 0.24
25 5 0.14
ACGTcount: A:0.19, C:0.01, G:0.07, T:0.72
Consensus pattern (24 bp):
TTTAAGAGTTTTTATTTTTTTATT
Found at i:12078408 original size:19 final size:18
Alignment explanation
Indices: 12078368--12078415 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
12078358 AGAGTTTTTT
* * *
12078368 TTTTTGTATTTTTATGAT
1 TTTTTATATTTTTAGGAA
12078386 TTTTTATATTTTTAAGGAA
1 TTTTTATATTTTT-AGGAA
12078405 TTTTTAT-TTTT
1 TTTTTATATTTT
12078416 AAAGTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (18 bp):
TTTTTATATTTTTAGGAA
Found at i:12079085 original size:11 final size:11
Alignment explanation
Indices: 12079066--12079095 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12079056 TATAAAGTGA
12079066 AAAAC-AAGGT
1 AAAACAAAGGT
12079076 AAAACAAAGGT
1 AAAACAAAGGT
12079087 AAAACAAAG
1 AAAACAAAG
12079096 AAGGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.67, C:0.10, G:0.17, T:0.07
Consensus pattern (11 bp):
AAAACAAAGGT
Found at i:12082430 original size:7 final size:7
Alignment explanation
Indices: 12082418--12082450 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
12082408 TAGTCAATTG
12082418 GTATTTA
1 GTATTTA
12082425 GTATTTA
1 GTATTTA
12082432 GTATTTA
1 GTATTTA
12082439 GTATTTA
1 GTATTTA
12082446 GTATT
1 GTATT
12082451 ATGTATTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:12083097 original size:18 final size:18
Alignment explanation
Indices: 12083074--12083116 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12083064 TACCAGGTGC
* *
12083074 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
12083092 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
12083110 GTTTCCT
1 GTATCCT
12083117 TTTTCTAGTC
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:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:12084989 original size:15 final size:15
Alignment explanation
Indices: 12084969--12085000 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12084959 TTAACATTTT
*
12084969 CTTAAAAACCCTAAA
1 CTTAAAAACCCCAAA
12084984 CTTAAAAACCCCAAA
1 CTTAAAAACCCCAAA
12084999 CT
1 CT
12085001 CTAACCCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (15 bp):
CTTAAAAACCCCAAA
Found at i:12085538 original size:20 final size:20
Alignment explanation
Indices: 12085513--12085555 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
12085503 AGCACCACCA
*
12085513 ATTTTTTT-AATAATTTTTTT
1 ATTTTTTTAAAT-ATTATTTT
12085533 ATTTTTTTAAATATTATTTT
1 ATTTTTTTAAATATTATTTT
12085553 ATT
1 ATT
12085556 AGTGGTGCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTTTTTAAATATTATTTT
Found at i:12085738 original size:16 final size:16
Alignment explanation
Indices: 12085717--12085747 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12085707 CCCTCCGCCA
12085717 CGCCCTGCACACTACG
1 CGCCCTGCACACTACG
12085733 CGCCCTGCACACTAC
1 CGCCCTGCACACTAC
12085748 ATTTTACAGT
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:0.19, C:0.52, G:0.16, T:0.13
Consensus pattern (16 bp):
CGCCCTGCACACTACG
Found at i:12086197 original size:106 final size:95
Alignment explanation
Indices: 12086042--12086706 Score: 538
Period size: 103 Copynumber: 6.8 Consensus size: 95
12086032 AAATTATTAG
* * * *
12086042 TAATTTATGATTATGTTATAATTTGTTTGTTCTTTAGTTTAGTGTTTTGTGAATTTTTATTAATG
1 TAATTTATGATTAGGTTATAAATTG-TTG-TGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATG
12086107 TAA-TTTTTTTGTTTTTTTAATTATTTTATAGTTATGTTGTTAA
64 TAATTTTTTTTG-TTTTTT-A--A---T-TA--T-T-TTGTTAA
12086150 TAATTTATGATTAGGTTATAAATTGTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTA
1 TAATTTATGATTAGGTTATAAATTGTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTA
12086215 ATTTTTTTTGTTTTTTAATTATTTTGTTAA
66 ATTTTTTTTGTTTTTTAATTATTTTGTTAA
*
12086245 TAATTTATTATTAGGTTATAAATTGTTGTGTTTAG-TTAGTGTTTTGTGATTTTTTATTAATGTA
1 TAATTTATGATTAGGTTATAAATTGTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTA
** * * * *
12086309 A----AATTATTTTATAGTTATTTTGTTAG
66 ATTTTTTTTGTTTTTTAATTATTTTGTTAA
*
12086335 TAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAGTTTTTTGTGATTTTTTATTAATGT
1 TAATTTATGATTAGGTTATAAATTGTT-GTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGT
** * * *
12086400 AAAATTTTTTAAAAATAATTTTATAGTTATTTTGTTAG
65 --AATTTTTT-----TTGTTTTTTAATTATTTTGTTAA
* *
12086438 TAATTTATGATTAAGTTATAAATTGTTAGTGTTTAGTTTAGTATTTTGTGATTTTTTATTAATGT
1 TAATTTATGATTAGGTTATAAATTGTT-GTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGT
* *
12086503 AAAATTATTTTTTAAAATAATTTTATATAGTTATTTTGTTAG
65 --AATT-TTTTTT---GT--TTTT-TA-A-TTATTTTGTTAA
* **
12086545 TAATTTATGATTAGGTTATAAA----------TCG-TTAGTGTTTTACGATTTTTTATTAATGTA
1 TAATTTATGATTAGGTTATAAATTGTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTA
* * *
12086599 ATTTTTTTAAAATTT-TTTTATAGTTATTTTGTTAG
66 A--TTTTT----TTTGTTTTTTAATTATTTTGTTAA
* * * * * *
12086634 TAATTTATGATTAAGTTATAAATTATTATGTTTAGTTTAATATTTTTTGATTTTTTATTAATGTA
1 TAATTTATGATTAGGTTATAAATTGTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTA
*
12086699 AATTTTTT
66 ATTTTTTT
12086707 ATAACGTAAT
Statistics
Matches: 482, Mismatches: 35, Indels: 94
0.79 0.06 0.15
Matches are distributed among these distances:
89 33 0.07
90 45 0.09
91 10 0.02
92 30 0.06
93 2 0.00
94 38 0.08
95 68 0.14
96 3 0.01
97 1 0.00
98 7 0.01
99 5 0.01
100 27 0.06
102 2 0.00
103 92 0.19
104 7 0.01
105 3 0.01
106 42 0.09
107 44 0.09
108 23 0.05
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (95 bp):
TAATTTATGATTAGGTTATAAATTGTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTA
ATTTTTTTTGTTTTTTAATTATTTTGTTAA
Found at i:12086638 original size:196 final size:195
Alignment explanation
Indices: 12086150--12086722 Score: 698
Period size: 195 Copynumber: 3.0 Consensus size: 195
12086140 ATGTTGTTAA
* *
12086150 TAATTTATGATTAGGTTATAAATTGTT-GTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGT
1 TAATTTATGATTAGGTAATAAATTGTTAGTGTTTAATTTAGTGTTTTGTGATTTTTTATTAATGT
* * *
12086214 AATTTTTTT----TGTTTTTTA-A-TTATTTTGTTAATAATTTATTATTAGGTTATAAATTGTT-
66 AATTTTTTTAAAAT-TTTTTTATAGTTATTTTGTTAGTAATTTATGATTAAGTTATAAATTGTTA
* * * *
12086272 GTGTTTAG-TTAGTGTTTTGTGATTTTTTATTAATGTAAAATTA--TTTTATAGTTATTTTGTTA
130 GTGTTTAGTTTAGTATTTTGTGATTTTTTATTAATGTAAAATTATTTTTTAAAGTAATTTTATTA
12086334 G
195 G
* * *
12086335 TAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAGTTTTTTGTGATTTTTTATTAATGT
1 TAATTTATGATTAGGTAATAAATTGTTAGTGTTTAATTTAGTGTTTTGTGATTTTTTATTAATGT
* **
12086400 AAAATTTTTTAAAAATAATTTTATAGTTATTTTGTTAGTAATTTATGATTAAGTTATAAATTGTT
66 --AATTTTTTTAAAATTTTTTTATAGTTATTTTGTTAGTAATTTATGATTAAGTTATAAATTGTT
*
12086465 AGTGTTTAGTTTAGTATTTTGTGATTTTTTATTAATGTAAAATTATTTTTTAAAATAATTTTATA
129 AGTGTTTAGTTTAGTATTTTGTGATTTTTTATTAATGTAAAATTATTTTTTAAAGTAATTTTAT-
12086530 TAG
193 TAG
* ** **
12086533 TTATTT-TG-TTA-GTAATTTA-TGATTAG-GTTATAAATCGTTAGTGTTTTACGATTTTTTATT
1 TAATTTATGATTAGGTAATAAATTG-TTAGTGTT-T-AAT--TTAGTGTTTTGTGATTTTTTATT
12086593 AATGTAATTTTTTTAAAATTTTTTTATAGTTATTTTGTTAGTAATTTATGATTAAGTTATAAATT
61 AATGTAATTTTTTTAAAATTTTTTTATAGTTATTTTGTTAGTAATTTATGATTAAGTTATAAATT
* * * * *
12086658 ATTA-TGTTTAGTTTAATATTTTTTGATTTTTTATTAATGT-AAATT-TTTTATAACGTAATTTT
126 GTTAGTGTTTAGTTTAGTATTTTGTGATTTTTTATTAATGTAAAATTATTTTTTAAAGTAATTTT
12086720 ATT
191 ATT
12086723 TTATTTTTAT
Statistics
Matches: 340, Mismatches: 29, Indels: 31
0.85 0.07 0.08
Matches are distributed among these distances:
185 27 0.08
186 36 0.11
188 8 0.02
191 5 0.01
192 3 0.01
193 52 0.15
194 18 0.05
195 78 0.23
196 65 0.19
197 15 0.04
198 33 0.10
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.58
Consensus pattern (195 bp):
TAATTTATGATTAGGTAATAAATTGTTAGTGTTTAATTTAGTGTTTTGTGATTTTTTATTAATGT
AATTTTTTTAAAATTTTTTTATAGTTATTTTGTTAGTAATTTATGATTAAGTTATAAATTGTTAG
TGTTTAGTTTAGTATTTTGTGATTTTTTATTAATGTAAAATTATTTTTTAAAGTAATTTTATTAG
Found at i:12087862 original size:38 final size:40
Alignment explanation
Indices: 12087804--12087878 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 40
12087794 ACAAAAAATA
*
12087804 TATTTTAAAAATAAAAAAAT-AAAAAAAATATTTTTAAAG
1 TATTTTAAAAATAAAAAAATAAAAAAAAATATATTTAAAG
*
12087843 TATTTT-AAAATTAAAAAATAAAAAAAAATATATTTA
1 TATTTTAAAAATAAAAAAATAAAAAAAAATATATTTA
12087879 TTATATTCGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 12 0.36
39 21 0.64
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (40 bp):
TATTTTAAAAATAAAAAAATAAAAAAAAATATATTTAAAG
Found at i:12092757 original size:25 final size:26
Alignment explanation
Indices: 12092729--12092777 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
12092719 AATAGCATTA
*
12092729 AACTAA-ACAAATAA-TTTATAATAGT
1 AACTAACA-AAATAACTTTAAAATAGT
12092754 AACTAACAAAATAACTTTAAAATA
1 AACTAACAAAATAACTTTAAAATA
12092778 AATTGAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (26 bp):
AACTAACAAAATAACTTTAAAATAGT
Found at i:12099999 original size:6 final size:6
Alignment explanation
Indices: 12099977--12100017 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
12099967 CTTTACGTCC
* * *
12099977 ATCTTG ATCTTA ATCTTG GTCTTG ATCTTG ATCTTG TTCTT
1 ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG ATCTT
12100018 TCGTGTTAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.54
Consensus pattern (6 bp):
ATCTTG
Found at i:12100001 original size:18 final size:18
Alignment explanation
Indices: 12099978--12100017 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12099968 TTTACGTCCA
12099978 TCTTGATCTTAATCTTGG
1 TCTTGATCTTAATCTTGG
* *
12099996 TCTTGATCTTGATCTTGT
1 TCTTGATCTTAATCTTGG
12100014 TCTT
1 TCTT
12100018 TCGTGTTAGA
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:0.12, C:0.17, G:0.15, T:0.55
Consensus pattern (18 bp):
TCTTGATCTTAATCTTGG
Found at i:12103400 original size:43 final size:43
Alignment explanation
Indices: 12103335--12103472 Score: 120
Period size: 43 Copynumber: 3.3 Consensus size: 43
12103325 TGTGATTTCA
* * *
12103335 TGTAAGACTATGTCTGGGACATTGGCATCAGTATGAGATTACG
1 TGTAAGACCATGTCTAGGACATTGGCATCAATATGAGATTACG
* * **
12103378 TGTAAGACCATGTCTAGAACATTGACA-CCTTAT-ATGATT-CG
1 TGTAAGACCATGTCTAGGACATTGGCATCAATATGA-GATTACG
* * ** * * *
12103419 TGTAAGACCCTGTCTAGGATAGAGGCATCAATATGTGATAACA
1 TGTAAGACCATGTCTAGGACATTGGCATCAATATGAGATTACG
12103462 TGTAAGACCAT
1 TGTAAGACCAT
12103473 ATCTGGGATA
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
41 24 0.33
42 15 0.21
43 34 0.47
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACATTGGCATCAATATGAGATTACG
Found at i:12109626 original size:36 final size:36
Alignment explanation
Indices: 12109585--12109659 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
12109575 GAAAGTAAAG
12109585 AAATGCAAATGAAAATAAGGAAATCATGAAAGAGTA
1 AAATGCAAATGAAAATAAGGAAATCATGAAAGAGTA
*
12109621 AAATGCAAATGAAAATAAGTAAATCATGAAAGAGTA
1 AAATGCAAATGAAAATAAGGAAATCATGAAAGAGTA
12109657 AAA
1 AAA
12109660 CTTGCAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.60, C:0.05, G:0.17, T:0.17
Consensus pattern (36 bp):
AAATGCAAATGAAAATAAGGAAATCATGAAAGAGTA
Found at i:12109643 original size:21 final size:21
Alignment explanation
Indices: 12109585--12109643 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 21
12109575 GAAAGTAAAG
*
12109585 AAATGCAAATGAAAATAAG-G
1 AAATGCAAATGAAAATAAGTA
*
12109605 AAAT-C--ATG-AAA-GAGTA
1 AAATGCAAATGAAAATAAGTA
12109621 AAATGCAAATGAAAATAAGTA
1 AAATGCAAATGAAAATAAGTA
12109642 AA
1 AA
12109644 TCATGAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 11
0.68 0.07 0.25
Matches are distributed among these distances:
15 2 0.07
16 7 0.23
17 4 0.13
19 4 0.13
20 7 0.23
21 6 0.20
ACGTcount: A:0.61, C:0.05, G:0.17, T:0.17
Consensus pattern (21 bp):
AAATGCAAATGAAAATAAGTA
Found at i:12109651 original size:17 final size:17
Alignment explanation
Indices: 12109593--12109651 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
12109583 AGAAATGCAA
*
12109593 ATGAAAATAAGGAAATC
1 ATGAAAATAAGTAAATC
*
12109610 ATG-AAA-GAGTAAAATGC
1 ATGAAAATAAGT-AAAT-C
12109627 AAATGAAAATAAGTAAATC
1 --ATGAAAATAAGTAAATC
12109646 ATGAAA
1 ATGAAA
12109652 GAGTAAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
15 2 0.06
16 7 0.21
17 10 0.30
19 4 0.12
20 7 0.21
21 3 0.09
ACGTcount: A:0.59, C:0.05, G:0.17, T:0.19
Consensus pattern (17 bp):
ATGAAAATAAGTAAATC
Found at i:12113068 original size:8 final size:8
Alignment explanation
Indices: 12113055--12113080 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
12113045 TAATGTTTTT
12113055 AAAGGGTA
1 AAAGGGTA
12113063 AAAGGGTA
1 AAAGGGTA
12113071 AAAGGGTA
1 AAAGGGTA
12113079 AA
1 AA
12113081 TAGGTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.35, T:0.12
Consensus pattern (8 bp):
AAAGGGTA
Found at i:12114030 original size:43 final size:43
Alignment explanation
Indices: 12113962--12114114 Score: 152
Period size: 43 Copynumber: 3.6 Consensus size: 43
12113952 TTTGAGGTGT
* *
12113962 GATTTCGTGTAAGACCATGTTTGGGACATTGGCACCGATATGA
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCACCGATATGA
* *
12114005 GATTACGTGTAAGACCTTGTCTGGGACTTTGGCACCG-TAT-A
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCACCGATATGA
* * ** *
12114046 TGATT-CGTGTAAGACCCTGTTTGGGACAGAGGCATCGATATG-
1 -GATTACGTGTAAGACCATGTCTGGGACATTGGCACCGATATGA
* * *
12114088 GTATAACATGTAAGACCATATCTGGGA
1 G-ATTACGTGTAAGACCATGTCTGGGA
12114115 TATGGCATTG
Statistics
Matches: 90, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
41 28 0.31
42 12 0.13
43 50 0.56
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.29
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGCACCGATATGA
Found at i:12129994 original size:3 final size:3
Alignment explanation
Indices: 12129986--12130017 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12129976 GCGATTATCC
12129986 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
12130018 CAAGTTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:12136428 original size:9 final size:9
Alignment explanation
Indices: 12136391--12136554 Score: 59
Period size: 10 Copynumber: 17.2 Consensus size: 9
12136381 TTAAAATCAT
12136391 TTAAAAATCA
1 TTAAAAAT-A
12136401 TTAAAAATGA
1 TTAAAAAT-A
*
12136411 --ATAAATA
1 TTAAAAATA
*
12136418 TTAAGAATA
1 TTAAAAATA
12136427 TTTAAAATATA
1 -TTAAAA-ATA
*
12136438 TATAATAATA
1 T-TAAAAATA
12136448 TTAATATAA-A
1 TTAA-A-AATA
*
12136458 CTTATAAATA
1 -TTAAAAATA
*
12136468 TTATAAAAAA
1 TTA-AAAATA
* *
12136478 ATAAAAA-C
1 TTAAAAATA
*
12136486 TTATAAATA
1 TTAAAAATA
12136495 TTATACAAATA
1 TTA-A-AAATA
12136506 -TAAAAATA
1 TTAAAAATA
* *
12136514 TAAAAAAAA
1 TTAAAAATA
12136523 TTATAAAATTA
1 TTA-AAAA-TA
*
12136534 ATAAAACATA
1 TTAAAA-ATA
*
12136544 TTTAAAATA
1 TTAAAAATA
12136553 TT
1 TT
12136555 TTAAAATTTT
Statistics
Matches: 114, Mismatches: 23, Indels: 35
0.66 0.13 0.20
Matches are distributed among these distances:
7 1 0.01
8 15 0.13
9 34 0.30
10 43 0.38
11 21 0.18
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (9 bp):
TTAAAAATA
Found at i:12136508 original size:27 final size:27
Alignment explanation
Indices: 12136450--12136511 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
12136440 TAATAATATT
*
12136450 AATATAAACTTATAAATATTATAAAAA
1 AATAAAAACTTATAAATATTATAAAAA
*
12136477 AATAAAAACTTATAAATATTATACAAA
1 AATAAAAACTTATAAATATTATAAAAA
*
12136504 TATAAAAA
1 AATAAAAA
12136512 TATAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.31
Consensus pattern (27 bp):
AATAAAAACTTATAAATATTATAAAAA
Found at i:12136512 original size:8 final size:8
Alignment explanation
Indices: 12136450--12136519 Score: 50
Period size: 8 Copynumber: 8.2 Consensus size: 8
12136440 TAATAATATT
12136450 AATATAAA
1 AATATAAA
**
12136458 CTTATAAA
1 AATATAAA
*
12136466 TATTATAAA
1 -AATATAAA
*
12136475 AAAATAAA
1 AATATAAA
12136483 AACTTATAAA
1 AA--TATAAA
* *
12136493 TATTATACA
1 -AATATAAA
12136502 AATATAAA
1 AATATAAA
12136510 AATATAAA
1 AATATAAA
12136518 AA
1 AA
12136520 AAATTATAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
8 30 0.62
9 12 0.25
10 5 0.10
11 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (8 bp):
AATATAAA
Done.