Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 12 of 135
Found at i:3414348 original size:5 final size:5
Alignment explanation
Indices: 3414338--3414364 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3414328 TACCTGAACG
3414338 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
3414365 TAATTGCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:3425397 original size:15 final size:15
Alignment explanation
Indices: 3425374--3425425 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
3425364 TTGATTTAAA
*
3425374 TTATATTTAAATTAT
1 TTATGTTTAAATTAT
*
3425389 TTATGTTTAAAATA-
1 TTATGTTTAAATTAT
* *
3425403 TTATGTTTTAGTTAT
1 TTATGTTTAAATTAT
3425418 TTATGTTT
1 TTATGTTT
3425426 TTATTTTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 11 0.35
15 20 0.65
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (15 bp):
TTATGTTTAAATTAT
Found at i:3427055 original size:21 final size:23
Alignment explanation
Indices: 3427015--3427056 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
3427005 AACCTAGAGA
*
3427015 TTAAAAATCTTGGACTTGCATGG
1 TTAAAAATATTGGACTTGCATGG
3427038 TTAAAAA-ATTGG-CTTGCAT
1 TTAAAAATATTGGACTTGCAT
3427057 TCAATTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (23 bp):
TTAAAAATATTGGACTTGCATGG
Found at i:3435276 original size:32 final size:32
Alignment explanation
Indices: 3435239--3435308 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
3435229 AGGTGCACTA
3435239 GTGTTTGTAATTTAGTCTACGTGTGTATGTGT
1 GTGTTTGTAATTTAGTCTACGTGTGTATGTGT
3435271 GTGTTTGTAATTTAGTCTACGTGTGTATGTGT
1 GTGTTTGTAATTTAGTCTACGTGTGTATGTGT
3435303 GTGTTT
1 GTGTTT
3435309 TTTAATATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.14, C:0.06, G:0.29, T:0.51
Consensus pattern (32 bp):
GTGTTTGTAATTTAGTCTACGTGTGTATGTGT
Found at i:3439325 original size:30 final size:31
Alignment explanation
Indices: 3439291--3439350 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
3439281 TTTTCGTTTA
* * *
3439291 ATTTAGAGTTAAA-TTGATTTTTTAAATTTT
1 ATTTAAAGTTAAATTTAATTATTTAAATTTT
*
3439321 ATTTAAATTTAAATTTAATTATTTAAATTT
1 ATTTAAAGTTAAATTTAATTATTTAAATTT
3439351 ACTTTGGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (31 bp):
ATTTAAAGTTAAATTTAATTATTTAAATTTT
Found at i:3439340 original size:5 final size:6
Alignment explanation
Indices: 3439311--3439394 Score: 55
Period size: 6 Copynumber: 13.8 Consensus size: 6
3439301 AAATTGATTT
* * **
3439311 TTTAAA TTT-TA TTTAAA TTTAAA TTTAATTA TTTAAA TTT-AC TTTGGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A TTTAAA TTTAAA TTTAAA
** * *
3439359 TTTAAA TTTAAA TAAAAA TTAAAA CATTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAA
3439395 CATTAAAAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
5 8 0.13
6 42 0.70
7 4 0.07
8 6 0.10
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:3439349 original size:31 final size:31
Alignment explanation
Indices: 3439311--3439369 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3439301 AAATTGATTT
3439311 TTTAAATTTTA-TTTAAATTTAAATTTAATTA
1 TTTAAA-TTTACTTTAAATTTAAATTTAATTA
**
3439342 TTTAAATTTACTTTGGATTTAAATTTAA
1 TTTAAATTTACTTTAAATTTAAATTTAA
3439370 ATAAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (31 bp):
TTTAAATTTACTTTAAATTTAAATTTAATTA
Found at i:3440975 original size:34 final size:32
Alignment explanation
Indices: 3440910--3440976 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 32
3440900 TTTGTGCAAG
* *
3440910 TAGTCCTTCCGCATTTTTTATTTGCTTCAATT
1 TAGTCCTTCCGCATTTTTTAATTACTTCAATT
* *
3440942 TAGTCCTTTCTGCATTTTTTAATTATTTGCAATT
1 TAGTCC-TTCCGCATTTTTTAATTACTT-CAATT
3440976 T
1 T
3440977 TGCCATGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 6 0.21
33 17 0.59
34 6 0.21
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.55
Consensus pattern (32 bp):
TAGTCCTTCCGCATTTTTTAATTACTTCAATT
Found at i:3441177 original size:162 final size:162
Alignment explanation
Indices: 3441006--3441485 Score: 811
Period size: 162 Copynumber: 3.0 Consensus size: 162
3440996 CTTTTCAATT
* *
3441006 TAGTCCTTTGACTGTTTAACTGTACCAGAGGTTGCCACGTGTCACTTTTTAGATTATTTATGCAT
1 TAGTCCTTTGACTGTTTGACTGTACCAGAGGTTGCCACGTGTCACTTTTTGGATTATTTATGCAT
3441071 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCAAATCAACTTTATTTTTAATTACAAA
66 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCAAATCAACTTTATTTTTAATTACAAA
3441136 ATTGGCCCGATAATTTTTCAAGGTTTATAAAC
131 ATTGGCCCGATAATTTTTCAAGGTTTATAAAC
3441168 TAGTCCTTTGACTGTTTGACTGTACCAGAGGTTGCCACGTGTCACTTTTTGGATTATTTATGCAT
1 TAGTCCTTTGACTGTTTGACTGTACCAGAGGTTGCCACGTGTCACTTTTTGGATTATTTATGCAT
3441233 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCAAATCAACTTTATTTTTAATTACAAA
66 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCAAATCAACTTTATTTTTAATTACAAA
3441298 ATTGGCCCGATAATTTTTCAAGGTTTATAAAC
131 ATTGGCCCGATAATTTTTCAAGGTTTATAAAC
* * * *
3441330 TAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCAATTTTTGGCTTATTTCTGCAT
1 TAGTCCTTTGACTGTTTGACTGTACCAGAGGTTGCCACGTGTCACTTTTTGGATTATTTATGCAT
* * * * *
3441395 TTAGTCCTTTTTATTTTTAATTTATTTTAATTTAGTCCTTAAATTAACTTT-TATTTAATTACAA
66 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCC-CAAATCAACTTTATTTTTAATTACAA
* *
3441459 AATTGGTCCAGA-AATTTTTCAAAGTTT
130 AATTGG-CCCGATAATTTTTCAAGGTTT
3441486 TCAAATTAGT
Statistics
Matches: 303, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
162 289 0.95
163 14 0.05
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.46
Consensus pattern (162 bp):
TAGTCCTTTGACTGTTTGACTGTACCAGAGGTTGCCACGTGTCACTTTTTGGATTATTTATGCAT
TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCAAATCAACTTTATTTTTAATTACAAA
ATTGGCCCGATAATTTTTCAAGGTTTATAAAC
Found at i:3441619 original size:30 final size:30
Alignment explanation
Indices: 3441585--3441722 Score: 188
Period size: 30 Copynumber: 4.6 Consensus size: 30
3441575 CAAAAATCAT
* *
3441585 ATTTTAACCCCAAAACTTTTCTAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
*
3441615 ATTTTGACCCCAAAACTCTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
*
3441645 ATTTTGACCCTAAAACTTTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
* * *
3441675 ATTTTGGCTCCAAAACTTTTCTAAAATTATC
1 ATTTTGACCCCAAAACTTTTCCAAAATTA-C
*
3441706 ATTTT-ACCCCCAAACTT
1 ATTTTGACCCCAAAACTT
3441723 CCCTAAATCC
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
30 89 0.94
31 6 0.06
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (30 bp):
ATTTTGACCCCAAAACTTTTCCAAAATTAC
Found at i:3441768 original size:59 final size:57
Alignment explanation
Indices: 3441697--3441892 Score: 223
Period size: 59 Copynumber: 3.4 Consensus size: 57
3441687 AAACTTTTCT
* *
3441697 AAAATTATCATTTTACCCCCAAACTTCCCT-AAATCCCATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCAAACTT--CTAAAATTCCATTTTTAACCCCGATTTCACC
* * * *
3441755 AAAATTTACCATTTTACCCCTAAATCTTTTAAAATTCCAATTTTAACCTCGATTTCACC
1 AAAA-TTACCATTTTACCCCCAAA-CTTCTAAAATTCCATTTTTAACCCCGATTTCACC
** * *
3441814 AAAAATTACCATTTTACCCCCGAATTTTCTAAAATTCTATTTTTAACCCCGATTACACC
1 -AAAATTACCATTTTACCCCC-AAACTTCTAAAATTCCATTTTTAACCCCGATTTCACC
* *
3441873 AAAATTACCACTTTGCCCCC
1 AAAATTACCATTTTACCCCC
3441893 GGGTATCCAT
Statistics
Matches: 117, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
58 23 0.20
59 85 0.73
60 9 0.08
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.35
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCCAAACTTCTAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:3441770 original size:30 final size:29
Alignment explanation
Indices: 3441736--3441882 Score: 104
Period size: 29 Copynumber: 5.0 Consensus size: 29
3441726 TAAATCCCAT
3441736 TTTTAACCCCGATTTCACCAAAATTTACCA
1 TTTTAACCCCGATTTCACCAAAA-TTACCA
* ** ***
3441766 TTTT-ACCCCTAAATCTTTTAAAATT-CCAA
1 TTTTAACCCCGATTTC-ACCAAAATTACC-A
*
3441795 TTTTAACCTCGATTTCACCAAAAATTACCA
1 TTTTAACCCCGATTTCACC-AAAATTACCA
* * * *
3441825 TTTTACCCCCGAATTT-TCTAAAATT-CTA
1 TTTTAACCCCG-ATTTCACCAAAATTACCA
*
3441853 TTTTTAACCCCGATTACACCAAAATTACCA
1 -TTTTAACCCCGATTTCACCAAAATTACCA
3441883 CTTTGCCCCC
Statistics
Matches: 85, Mismatches: 23, Indels: 18
0.67 0.18 0.14
Matches are distributed among these distances:
28 7 0.08
29 38 0.45
30 34 0.40
31 6 0.07
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (29 bp):
TTTTAACCCCGATTTCACCAAAATTACCA
Found at i:3443232 original size:12 final size:12
Alignment explanation
Indices: 3443212--3443243 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3443202 CATTTTTATT
3443212 AAACCCAATTAC
1 AAACCCAATTAC
*
3443224 AAGCCCAATTAC
1 AAACCCAATTAC
3443236 AAACCCAA
1 AAACCCAA
3443244 ACCTAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.34, G:0.03, T:0.12
Consensus pattern (12 bp):
AAACCCAATTAC
Found at i:3443777 original size:38 final size:40
Alignment explanation
Indices: 3443718--3443792 Score: 102
Period size: 38 Copynumber: 1.9 Consensus size: 40
3443708 TACGCAGGCA
* *
3443718 TATATCTATATGCATAGACATATAT-TCTGATTTTATTCCT
1 TATATATATATGCATAGACATACATAT-TGATTTTATTCCT
3443758 TATATATATATGCA-A-ACATACATATTGATTTTATT
1 TATATATATATGCATAGACATACATATTGATTTTATT
3443793 TTTTTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 17 0.53
39 2 0.06
40 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (40 bp):
TATATATATATGCATAGACATACATATTGATTTTATTCCT
Found at i:3443783 original size:40 final size:38
Alignment explanation
Indices: 3443718--3443792 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 38
3443708 TACGCAGGCA
*
3443718 TATATCTATATGCATAGACATATATTCTGATTTTATTCCT
1 TATATATATATGCATAGACATATA-T-TGATTTTATTCCT
3443758 TATATATATATGCA-A-ACATACATATTGATTTTATT
1 TATATATATATGCATAGACAT--ATATTGATTTTATT
3443793 TTTTTTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
38 14 0.44
39 2 0.06
40 16 0.50
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (38 bp):
TATATATATATGCATAGACATATATTGATTTTATTCCT
Found at i:3443833 original size:2 final size:2
Alignment explanation
Indices: 3443826--3443859 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3443816 ATGTACGTGC
* *
3443826 AT AT AT AT GT GT 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
3443860 TGATTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3443930 original size:8 final size:8
Alignment explanation
Indices: 3443916--3443948 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
3443906 AACAGATTTG
3443916 AAAAAAAT
1 AAAAAAAT
*
3443924 GAAAAAAT
1 AAAAAAAT
3443932 AAAAAAAT
1 AAAAAAAT
3443940 AAAAAAAT
1 AAAAAAAT
3443948 A
1 A
3443949 TTCAAAACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:3446571 original size:30 final size:29
Alignment explanation
Indices: 3446537--3447013 Score: 326
Period size: 30 Copynumber: 16.1 Consensus size: 29
3446527 TACCTAGAAG
3446537 CCTCAAACTTTCCAAAAATTACATTTTGAC
1 CCTCAAAC-TTCCAAAAATTACATTTTGAC
* *
3446567 CCTCAAACTTTTCAAAAATTATATTTTGAC
1 CCTCAAAC-TTCCAAAAATTACATTTTGAC
* * *
3446597 CCCCAAACTTCTCAAAATTTATATTTTGAGC
1 CCTCAAACTTC-CAAAAATTACATTTTGA-C
* *
3446628 CCT-AAACTTTCCCAAAATTCCATTTTG-C
1 CCTCAAAC-TTCCAAAAATTACATTTTGAC
** *
3446656 CCAAAAATTTCCAAAAATTACATTTTGAC
1 CCTCAAACTTCCAAAAATTACATTTTGAC
*
3446685 TCCT-AAACTTCTCAAAAATTACATTTTAAC
1 -CCTCAAACTTC-CAAAAATTACATTTTGAC
*
3446715 CC-CTAAACTTCTCAAAAATTACATTTTAAC
1 CCTC-AAACTTC-CAAAAATTACATTTTGAC
* *
3446745 CC-CTAAACTTCTTAAAAATTACATTTTAAC
1 CCTC-AAACTTC-CAAAAATTACATTTTGAC
* * * *
3446775 CCTTAAACTTCTTAAAAATTATATTTTAAC
1 CCTCAAACTTC-CAAAAATTACATTTTGAC
* * *
3446805 CCTCAAACTTCTTACAAATTACATTTTAAC
1 CCTCAAACTTC-CAAAAATTACATTTTGAC
*
3446835 CC-CTAAACTTTCCAAAAATTCCATTTTTG-C
1 CCTC-AAAC-TTCCAAAAATTACA-TTTTGAC
** * *
3446865 CCTTGAACTTCCAAAAATCACATTTTTAC
1 CCTCAAACTTCCAAAAATTACATTTTGAC
** * *
3446894 CCTTGAACTTTCCAAAAATTCCATTTTTACCC
1 CCTCAAAC-TTCCAAAAATTACATTTTGA--C
* *
3446926 CCTTAAACTTCCAAAAATTCCATTTTTG--
1 CCTCAAACTTCCAAAAATTACA-TTTTGAC
* * ** *
3446954 CCACAGAACTTCCAAAAACTGTATTTTTA-
1 CCTCA-AACTTCCAAAAATTACATTTTGAC
* * * *
3446983 CCTCGAATTTCCAAAAATGACATTTTTAC
1 CCTCAAACTTCCAAAAATTACATTTTGAC
3447012 CC
1 CC
3447014 CTGAGATATT
Statistics
Matches: 376, Mismatches: 49, Indels: 45
0.80 0.10 0.10
Matches are distributed among these distances:
28 49 0.13
29 55 0.15
30 233 0.62
31 27 0.07
32 12 0.03
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
CCTCAAACTTCCAAAAATTACATTTTGAC
Found at i:3446645 original size:90 final size:88
Alignment explanation
Indices: 3446541--3447015 Score: 387
Period size: 90 Copynumber: 5.3 Consensus size: 88
3446531 TAGAAGCCTC
* * * *
3446541 AAACTTTCCAAAAATTACATTTTGA-CCCTCAAACTTTTCAAAAATTATATTTTGACCCCCAAAC
1 AAAC-TTCCAAAAATTACATTTTAACCCCT-AAACTTTCCAAAAATTACATTTTGACCCCTAAAC
* *
3446605 TTCTCAAAATTTATATTTTGAGCCCT
64 TTCTCAAAAATTATATTTT-AACCCT
* * * * * *
3446631 AAACTTTCCCAAAATTCCATTTT--GCCCAAAAATTTCCAAAAATTACATTTTGACTCCTAAACT
1 AAAC-TTCCAAAAATTACATTTTAACCCCTAAACTTTCCAAAAATTACATTTTGACCCCTAAACT
*
3446694 TCTCAAAAATTACATTTTAACCCCT
65 TCTCAAAAATTATATTTTAA-CCCT
* * *
3446719 AAACTTCTCAAAAATTACATTTTAACCCCTAAAC-TTCTTAAAAATTACATTTTAACCCTTAAAC
1 AAACTTC-CAAAAATTACATTTTAACCCCTAAACTTTC-CAAAAATTACATTTTGACCCCTAAAC
*
3446783 TTCTTAAAAATTATATTTTAACCCT
64 TTCTCAAAAATTATATTTTAACCCT
* * * * *
3446808 CAAACTTCTTACAAATTACATTTTAACCCCTAAACTTTCCAAAAATTCCATTTTTG-CCCTTGAA
1 -AAACTTC-CAAAAATTACATTTTAACCCCTAAACTTTCCAAAAATTACA-TTTTGACCCCTAAA
* * *
3446872 CTTC-CAAAAATCACATTTTTACCCTT
63 CTTCTCAAAAATTATATTTTAACCC-T
* * * * *
3446898 GAACTTTCCAAAAATTCCATTTTTACCCCCTTAAAC-TTCCAAAAATTCCATTTTTG-CCAC-AG
1 AAAC-TTCCAAAAATTACA-TTTTAACCCC-TAAACTTTCCAAAAATTACA-TTTTGACCCCTA-
* * *
3446960 AACTTC-CAAAAACTGTATTTTTA-CCT
61 AACTTCTCAAAAATTATATTTTAACCCT
* * * *
3446986 CGAATTTCCAAAAATGACATTTTTACCCCT
1 -AAACTTCCAAAAATTACATTTTAACCCCT
3447016 GAGATATTCC
Statistics
Matches: 321, Mismatches: 49, Indels: 34
0.79 0.12 0.08
Matches are distributed among these distances:
86 1 0.00
87 12 0.04
88 80 0.25
89 42 0.13
90 174 0.54
91 12 0.04
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (88 bp):
AAACTTCCAAAAATTACATTTTAACCCCTAAACTTTCCAAAAATTACATTTTGACCCCTAAACTT
CTCAAAAATTATATTTTAACCCT
Found at i:3446877 original size:29 final size:29
Alignment explanation
Indices: 3446844--3446971 Score: 161
Period size: 29 Copynumber: 4.3 Consensus size: 29
3446834 CCCCTAAACT
3446844 TTCCAAAAATTCCATTTTTGCCCTTGAAC
1 TTCCAAAAATTCCATTTTTGCCCTTGAAC
*
3446873 TTCCAAAAA-TCACATTTTTACCCTTGAAC
1 TTCCAAAAATTC-CATTTTTGCCCTTGAAC
* *
3446902 TTTCCAAAAATTCCATTTTTACCCCCTTAAAC
1 -TTCCAAAAATTCCATTTTT--GCCCTTGAAC
*
3446934 TTCCAAAAATTCCATTTTTGCCAC-AGAAC
1 TTCCAAAAATTCCATTTTTGCC-CTTGAAC
3446963 TTCCAAAAA
1 TTCCAAAAA
3446972 CTGTATTTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.02
29 39 0.45
30 17 0.20
31 21 0.24
32 8 0.09
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTGCCCTTGAAC
Found at i:3447029 original size:31 final size:30
Alignment explanation
Indices: 3446820--3447029 Score: 121
Period size: 29 Copynumber: 7.1 Consensus size: 30
3446810 AACTTCTTAC
* * *
3446820 AAATTACATTTTAACCCCTAAACT-TTCCAA
1 AAATGACATTTTTACCCCTGAA-TATTCCAA
** * * *
3446850 AAATTCCATTTTTGCCCTTGAA-CTTCCAA
1 AAATGACATTTTTACCCCTGAATATTCCAA
* *
3446879 AAATCACATTTTTACCCTTGAACT-TTCCAA
1 AAATGACATTTTTACCCCTGAA-TATTCCAA
** *
3446909 AAATTCCATTTTTACCCCCTTAA-ACTTCCAA
1 AAATGACATTTTTA-CCCCTGAATA-TTCCAA
** * * * *
3446940 AAATTCCATTTTTGCCACAGAA-CTTCCAA
1 AAATGACATTTTTACCCCTGAATATTCCAA
* *
3446969 AAACTG-TATTTTTACCTC-GAAT-TTCCAA
1 AAA-TGACATTTTTACCCCTGAATATTCCAA
3446997 AAATGACATTTTTACCCCTGAGATATTCCAA
1 AAATGACATTTTTACCCCTGA-ATATTCCAA
3447028 AA
1 AA
3447030 TTATGTTTTA
Statistics
Matches: 145, Mismatches: 23, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
27 2 0.01
28 22 0.15
29 45 0.31
30 43 0.30
31 33 0.23
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (30 bp):
AAATGACATTTTTACCCCTGAATATTCCAA
Found at i:3447246 original size:19 final size:19
Alignment explanation
Indices: 3447222--3447262 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3447212 ACCTTTATCG
*
3447222 TTAA-TTGCATAGCTCGTTT
1 TTAATTTGCATA-CTCATTT
3447241 TTAATTTGCATACTCATTT
1 TTAATTTGCATACTCATTT
3447260 TTA
1 TTA
3447263 TCTATGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.51
Consensus pattern (19 bp):
TTAATTTGCATACTCATTT
Found at i:3447483 original size:97 final size:98
Alignment explanation
Indices: 3447310--3447506 Score: 297
Period size: 97 Copynumber: 2.0 Consensus size: 98
3447300 TCCAAAATAT
* * *
3447310 TTAAAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAATTTGTGTCTTAACTTACTAGGTGC
1 TTAAAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGC
*
3447375 GATTTTTCTTCAAACCGGGATAATCGAATACCC
66 GACTTTTCTTCAAACCGGGATAATCGAATACCC
* * * *
3447408 TTAAAA-CGAGGCAATGTTTCTTTATCTCTGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGT
1 TTAAAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGC
* *
3447472 GACTTTTCTTCAAATCGGGATAATCGAATATCC
66 GACTTTTCTTCAAACCGGGATAATCGAATACCC
3447505 TT
1 TT
3447507 TTCCAAGGTT
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
97 83 0.93
98 6 0.07
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (98 bp):
TTAAAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGC
GACTTTTCTTCAAACCGGGATAATCGAATACCC
Found at i:3463622 original size:49 final size:48
Alignment explanation
Indices: 3463471--3463803 Score: 213
Period size: 49 Copynumber: 6.8 Consensus size: 48
3463461 ATGAAGCATG
* * * * *
3463471 AAGGGAAAGATTTAAGCCGTAACGACGAATCCAGTACCGCGAGGATACA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAGATATA
* * * * * *
3463520 AAGGGAAAGATTTAAGTCGCAATGGCGAA-CCTTA-TACCTCAAAAGCATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCC--AGTACCACAAGA-TATA
* * *
3463569 AAGGGAAAGATTGAAGTCGTAACGGCGAATCCAGTACCACGAAGATATA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAGATATA
* * * * * * * * * *
3463618 AAGGGAAAGGTTTAAGACGCAACAGCCAACCCTGTACCTCAAAAGTGTG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAGA-TATA
* *
3463667 AAGGAAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACGAAGATATA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAGATATA
** * * * * * * *
3463716 AAGAAAAAGGTTTAAGTCGCAACAGCGAA-CCTTGTACCTCAGAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACA-AGATATA
* * **
3463765 AAGGGAAAAATTTAAGCCGTAACGGCGAATTTAGTACCA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
3463804 TGCAGGATGA
Statistics
Matches: 212, Mismatches: 61, Indels: 22
0.72 0.21 0.07
Matches are distributed among these distances:
48 11 0.05
49 192 0.91
50 9 0.04
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (48 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAGATATA
Found at i:3463633 original size:98 final size:98
Alignment explanation
Indices: 3463464--3463803 Score: 448
Period size: 98 Copynumber: 3.5 Consensus size: 98
3463454 CATTACCATG
* * * *
3463464 AAGCATGAAGGGAAAGATTTAAGCCGTAACGACGAATCCAGTACCGCGAGGATACAAAGGGAAAG
1 AAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGATATAAAGGGAAAG
* ** *
3463529 ATTTAAGTCGCAATGGCGAACCTTATACCTCAA
66 GTTTAAGTCGCAACAGCGAACCTTGTACCTCAA
* *
3463562 AAGCATGAAGGGAAAGATTGAAGTCGTAACGGCGAATCCAGTACCACGAAGATATAAAGGGAAAG
1 AAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGATATAAAGGGAAAG
* * *
3463627 GTTTAAGACGCAACAGCCAACCCTGTACCTCAA
66 GTTTAAGTCGCAACAGCGAACCTTGTACCTCAA
** * * * **
3463660 AAGTGTGAAGGAAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACGAAGATATAAAGAAAAAG
1 AAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGATATAAAGGGAAAG
3463725 GTTTAAGTCGCAACAGCGAACCTTGTACCTC-A
66 GTTTAAGTCGCAACAGCGAACCTTGTACCTCAA
* * **
3463757 GAGACATGAAGGGAAAAATTTAAGCCGTAACGGCGAATTTAGTACCA
1 AAG-CATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCA
3463804 TGCAGGATGA
Statistics
Matches: 207, Mismatches: 34, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
97 3 0.01
98 204 0.99
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (98 bp):
AAGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGATATAAAGGGAAAG
GTTTAAGTCGCAACAGCGAACCTTGTACCTCAA
Found at i:3466153 original size:497 final size:486
Alignment explanation
Indices: 3465225--3466207 Score: 1741
Period size: 497 Copynumber: 2.0 Consensus size: 486
3465215 AAAAAAAAGA
*
3465225 TTTAAAGATTTAAATAAAAAAGCTCATTTTTTAAAAAAAAGGAGATCTCCATTCGATCTAAAAAG
1 TTTAAAGATTTAAATAAAAAAGCTCATTTTTTAAAAAAAAGCAGATCTCCATTCGATCTAAAAAG
*
3465290 ATCCGAACCTAAATCTGCACTTTAAGAAAGGAAACTAAAATGGGGGTTGTCGTTTCGCCTACTCG
66 ATCCGAACCTAAATCTGCACTTTAAGAAAGGAAACTAAAAGGGGGGTTGTCGTTTCGCCTACTCG
3465355 GACACCGTGCGTGACGGTTTGGACGACGGAGCCGCGATGACCGAAGGTTAGGCCTGCGTCGGAGA
131 GACACCGTGCGTGACGGTTTGGACGACGGAGCCGCGATGACCGAAGGTTAGGCCTGCGTCGGAGA
3465420 TGGGAAGGTTTCAAAAGAATTCTAGAAAGAAAGAAGGAACAAAAATGAATTTTTGAAAAGGATGG
196 TGGGAAGGTTTCAAAAGAATTCTAGAAAGAAAGAAGGAACAAAAATGAATTTTTGAAAAGGATGG
3465485 GATGAAAAATGAATTTTAAGAGTTATTTTTTTAAATATTACCTCCTGCACGGCGTCGTTTTGGTG
261 GATGAAAAATGAATTTTAAGAGTTATTTTTTTAAATATTACCTCCTGCACGGCGTCGTTTTGGTG
*
3465550 TGCAAGCCTTGGGACCAAACGACGTCGTTTCCTGGAGCTTTGACCCGACCTGAATGGGTCCGTGT
326 TGCAAGCCTTGGGACCAAACGACGTCATTTCCTGGAGCTTTGACCCGACCTGAATGGGTCCGTGT
3465615 GTTTCTGGATATTGGGATATTTATCCCTTTAACCATTCCGCCTTTTAATATTTTCAATTCAATCC
391 GTTTCTGGATATTGGGATATTTATCCCTTTAACCATTCCGCCTTTTAATATTTTCAATTCAATCC
*
3465680 TTCCTGTTACTTTTAATTCATTTGTACTTTT
456 TTCCTGTTACTTTTAATTCATTTGTAATTTT
** *
3465711 TTTAAAGATTTAAATAAAAAAGCTCATTTTTTTTAAAAAAGCAGATCTCGATTCGATCTAAAAAG
1 TTTAAAGATTTAAATAAAAAAGCTCATTTTTTAAAAAAAAGCAGATCTCCATTCGATCTAAAAAG
3465776 ATCCGAACCTAAATCTGCACTTTAAGAAAGGAAACTAAAAGGGGGGTTGTCGTTTCGCCTACTCG
66 ATCCGAACCTAAATCTGCACTTTAAGAAAGGAAACTAAAAGGGGGGTTGTCGTTTCGCCTACTCG
* *
3465841 GACACCGTGCGTGGCGGTTTGGACGACGGAGAAGCGACGGAGCCGCTGTGACCGAAGGTTAGGCC
131 GACACCGTGCGTGACGGTTTGGACGAC-G-G-AGC--C---G-CG--ATGACCGAAGGTTAGGCC
*
3465906 TGTGTCGGAGATGGGAAGGTTTCAAAAGAATTCTAGAAAGAAAGAAGGAACAAAAATGAATTTTT
185 TGCGTCGGAGATGGGAAGGTTTCAAAAGAATTCTAGAAAGAAAGAAGGAACAAAAATGAATTTTT
*
3465971 GGAAAGGATGGGATGAAAAATGAATTTTAAGAGTTATTTTTTTAAATATTACCTCCTGCACGGCG
250 GAAAAGGATGGGATGAAAAATGAATTTTAAGAGTTATTTTTTTAAATATTACCTCCTGCACGGCG
* *
3466036 TCGTTTTGGTGTGCAAGCCTTGGGACCAAACGGCGTCATTTCTTGGAGCTTTGACCCGACCTGAA
315 TCGTTTTGGTGTGCAAGCCTTGGGACCAAACGACGTCATTTCCTGGAGCTTTGACCCGACCTGAA
*
3466101 TGGGTCCGTGTGTTTCTGGATATTGGGATATTTATCCCTTTAACCCTTCCGCCTTTTAATATTTT
380 TGGGTCCGTGTGTTTCTGGATATTGGGATATTTATCCCTTTAACCATTCCGCCTTTTAATATTTT
3466166 CAATTCAATCCTTCCTGTTACTTTTAATTCATTTGTAATTTT
445 CAATTCAATCCTTCCTGTTACTTTTAATTCATTTGTAATTTT
3466208 GCCCTTAAGA
Statistics
Matches: 472, Mismatches: 14, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
486 151 0.32
487 1 0.00
488 1 0.00
489 3 0.01
491 1 0.00
494 1 0.00
495 2 0.00
497 312 0.66
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Consensus pattern (486 bp):
TTTAAAGATTTAAATAAAAAAGCTCATTTTTTAAAAAAAAGCAGATCTCCATTCGATCTAAAAAG
ATCCGAACCTAAATCTGCACTTTAAGAAAGGAAACTAAAAGGGGGGTTGTCGTTTCGCCTACTCG
GACACCGTGCGTGACGGTTTGGACGACGGAGCCGCGATGACCGAAGGTTAGGCCTGCGTCGGAGA
TGGGAAGGTTTCAAAAGAATTCTAGAAAGAAAGAAGGAACAAAAATGAATTTTTGAAAAGGATGG
GATGAAAAATGAATTTTAAGAGTTATTTTTTTAAATATTACCTCCTGCACGGCGTCGTTTTGGTG
TGCAAGCCTTGGGACCAAACGACGTCATTTCCTGGAGCTTTGACCCGACCTGAATGGGTCCGTGT
GTTTCTGGATATTGGGATATTTATCCCTTTAACCATTCCGCCTTTTAATATTTTCAATTCAATCC
TTCCTGTTACTTTTAATTCATTTGTAATTTT
Found at i:3467406 original size:16 final size:15
Alignment explanation
Indices: 3467377--3467411 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
3467367 TTTGATGAAG
3467377 AAAA-ATAAATAAAA
1 AAAAGATAAATAAAA
3467391 AAAAGATAATATAAAA
1 AAAAGATAA-ATAAAA
3467407 AAAAG
1 AAAAG
3467412 CAAAGAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 4 0.21
16 11 0.58
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (15 bp):
AAAAGATAAATAAAA
Found at i:3467445 original size:25 final size:25
Alignment explanation
Indices: 3467377--3467454 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
3467367 TTTGATGAAG
* *
3467377 AAAAATAAATAAAAAAAAGATAATATA
1 AAAAATAAATAAAAAGAAGA-AA-AAA
** *
3467404 AAAAA-AAGCAAAGAGAAGAAAAAA
1 AAAAATAAATAAAAAGAAGAAAAAA
*
3467428 AAAAATAAATAAAAAGAAGAAGAAA
1 AAAAATAAATAAAAAGAAGAAAAAA
3467453 AA
1 AA
3467455 CAAGAACCAG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
24 7 0.17
25 19 0.46
26 10 0.24
27 5 0.12
ACGTcount: A:0.79, C:0.01, G:0.10, T:0.09
Consensus pattern (25 bp):
AAAAATAAATAAAAAGAAGAAAAAA
Found at i:3468530 original size:50 final size:50
Alignment explanation
Indices: 3468407--3468602 Score: 189
Period size: 50 Copynumber: 3.9 Consensus size: 50
3468397 ATGAAGATTC
** * *
3468407 GAAGGGAAAGGTTGAGGCCGCAATAGTGAACCTGGTACCTTAAAAGATGT
1 GAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTTAAAAGAAGT
* *
3468457 GATGGGAAAGGTTAAGGCCGCAACGGCGAACCTGGTACC-TAAGAAGAAGT
1 GAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTTAA-AAGAAGT
* * * * * ** **
3468507 GAAGAGAAAAGTTGAGGCTGCAACGACGAACCCGGTACCACAAAA-ATTT
1 GAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTTAAAAGAAGT
* * * **
3468556 GAAGGGAAAGGTTGAGGCCTCAACGACCAACCCAGTACCTTAAAAGA
1 GAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTTAAAAGA
3468603 TATTATGGGA
Statistics
Matches: 119, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
49 42 0.35
50 75 0.63
51 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.29, T:0.15
Consensus pattern (50 bp):
GAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTTAAAAGAAGT
Found at i:3471902 original size:48 final size:47
Alignment explanation
Indices: 3471779--3472114 Score: 157
Period size: 49 Copynumber: 6.9 Consensus size: 47
3471769 GGATTGAGGT
* ** * *
3471779 CGCAATGGCGAATCCGGTTCCATGAAGATGAAATGGGACAA--TCTAAGC
1 CGCAACGGCGAATCTAGTACCACGAAGATGAAA-GGGA-AAGGT-TAAGC
* * ** * *
3471827 CGCAATGGCAAATCCGGTTCCATGAAGATGAAATGGGAAAGGTTAAGC
1 CGCAACGGCGAATCTAGTACCACGAAGATGAAA-GGGAAAGGTTAAGC
* * *
3471875 CGCAACGGTGAATCTAGTACCACGAAGAT-ATGGAGGGAAAGGTTTAAGT
1 CGCAACGGCGAATCTAGTACCACGAAGATGA--AAGGGAAAGG-TTAAGC
* * * ** * *
3471924 CGCAATGGCGAACCTTGTACCTCAAAAACATG-AAGGGAAAGATTTAAGC
1 CGCAACGGCGAATCTAGTA-C-CACGAAGATGAAAGGGAAAG-GTTAAGC
* * *
3471973 CGCAACGACGAATCTAGTACCACGAAGAT-ATGAGGGGAAAGGTTTAAGT
1 CGCAACGGCGAATCTAGTACCACGAAGATGA--AAGGGAAAGG-TTAAGC
* * * *
3472022 CGCAACGGCGAACCTTA-TACCTCAGAAACATG-AAGGGAAAGATTTAAGC
1 CGCAACGGCGAATC-TAGTACCAC-G-AAGATGAAAGGGAAAG-GTTAAGC
* * * *
3472071 TGTAACGGCTAATCTAGTATCACGAAGAT-ATGAAGGGAAAGGTT
1 CGCAACGGCGAATCTAGTACCACGAAGATGA--AAGGGAAAGGTT
3472115 TAAGTTGCAA
Statistics
Matches: 221, Mismatches: 45, Indels: 44
0.71 0.15 0.14
Matches are distributed among these distances:
47 13 0.06
48 78 0.35
49 116 0.52
50 4 0.02
51 10 0.05
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (47 bp):
CGCAACGGCGAATCTAGTACCACGAAGATGAAAGGGAAAGGTTAAGC
Found at i:3471944 original size:49 final size:49
Alignment explanation
Indices: 3471861--3472140 Score: 280
Period size: 49 Copynumber: 5.7 Consensus size: 49
3471851 AAGATGAAAT
* * * *
3471861 GGGAAAGG-TTAAGCCGCAACGGTGAATCTAGTACCACGAAGATATGGA
1 GGGAAAGGTTTAAGTCGCAACGGCGAACCTAGTACCACGAAGATATGAA
* * * * * *
3471909 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAACATGAA
1 GGGAAAGGTTTAAGTCGCAACGGCGAACCTAGTACCACGAAGATATGAA
* * * * *
3471958 GGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATATGAG
1 GGGAAAGGTTTAAGTCGCAACGGCGAACCTAGTACCACGAAGATATGAA
* *
3472007 GGGAAAGGTTTAAGTCGCAACGGCGAACCTTA-TACCTCAGAA-ACATGAA
1 GGGAAAGGTTTAAGTCGCAACGGCGAACC-TAGTACCAC-GAAGATATGAA
* * * * *
3472056 GGGAAAGATTTAAG-CTGTAACGGCTAATCTAGTATCACGAAGATATGAA
1 GGGAAAGGTTTAAGTC-GCAACGGCGAACCTAGTACCACGAAGATATGAA
* * *
3472105 GGGAAAGGTTTAAGTTGCAACGACGAACCTTGTACC
1 GGGAAAGGTTTAAGTCGCAACGGCGAACCTAGTACC
3472141 TCAAAAACAT
Statistics
Matches: 182, Mismatches: 43, Indels: 13
0.76 0.18 0.05
Matches are distributed among these distances:
48 14 0.08
49 163 0.90
50 5 0.03
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.20
Consensus pattern (49 bp):
GGGAAAGGTTTAAGTCGCAACGGCGAACCTAGTACCACGAAGATATGAA
Found at i:3471986 original size:98 final size:98
Alignment explanation
Indices: 3471861--3472159 Score: 449
Period size: 98 Copynumber: 3.1 Consensus size: 98
3471851 AAGATGAAAT
* *
3471861 GGGAAAG-GTTAAGCCGCAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTC
1 GGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTC
*
3471925 GCAATGGCGAACCTTGTACCTCAAAAACATGAA
66 GCAACGGCGAACCTTGTACCTCAAAAACATGAA
*
3471958 GGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATAT-GAGGGGAAAGGTTTAAGT
1 GGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGA-GGGAAAGGTTTAAGT
* *
3472022 CGCAACGGCGAACCTTATACCTCAGAAACATGAA
65 CGCAACGGCGAACCTTGTACCTCAAAAACATGAA
* * * * * *
3472056 GGGAAAGATTTAAGCTGTAACGGCTAATCTAGTATCACGAAGATATGAAGGGAAAGGTTTAAGTT
1 GGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTC
* *
3472121 GCAACGACGAACCTTGTACCTCAAAAACATAAA
66 GCAACGGCGAACCTTGTACCTCAAAAACATGAA
3472154 GGGAAA
1 GGGAAA
3472160 AGTTGAGGCC
Statistics
Matches: 182, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
97 9 0.05
98 172 0.95
99 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (98 bp):
GGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTC
GCAACGGCGAACCTTGTACCTCAAAAACATGAA
Found at i:3472104 original size:147 final size:147
Alignment explanation
Indices: 3471953--3472225 Score: 332
Period size: 147 Copynumber: 1.9 Consensus size: 147
3471943 CCTCAAAAAC
* * * * * * * *
3471953 ATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATATGAGGGGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCACAAAAACATAAAGGGAAAAGTTG
* * *
3472018 AAGTCGCAACGGCGAACCTTA-TACCTCAGAAACATGAAGGGAAAGATTTAAGCTGTAACGGCTA
66 AAGCCGCAACGGCGAACC-CAGTACCTCAGAAACATGAAGGGAAAGATTGAAGCTGTAACGGCTA
3472082 ATCTAGTATCACGAAGAT
130 ATCTAGTATCACGAAGAT
* ** * *
3472100 ATGAAGGGAAAGGTTTAAGTTGCAACGACGAACCTTGTACCTCAAAAACATAAAGGGAAAAGTTG
1 ATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCACAAAAACATAAAGGGAAAAGTTG
* * * * * *
3472165 AGGCCGCTACGGTGAACCCAGTACCTTAGAAGCATGACGGGAAAGATTGAAGCTGTAACGG
66 AAGCCGCAACGGCGAACCCAGTACCTCAGAAACATGAAGGGAAAGATTGAAGCTGTAACGG
3472226 TAAATCTTAT
Statistics
Matches: 103, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
146 1 0.01
147 102 0.99
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.19
Consensus pattern (147 bp):
ATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCACAAAAACATAAAGGGAAAAGTTG
AAGCCGCAACGGCGAACCCAGTACCTCAGAAACATGAAGGGAAAGATTGAAGCTGTAACGGCTAA
TCTAGTATCACGAAGAT
Found at i:3472534 original size:40 final size:40
Alignment explanation
Indices: 3472479--3472619 Score: 149
Period size: 40 Copynumber: 3.5 Consensus size: 40
3472469 AAGTTATATC
* *
3472479 ACCACCTAATCTCTTACCCCGATCATAGGGCAGGTTGAAA
1 ACCACCCAATCTCTTACCCCGATCATAGGGCAGATTGAAA
* * *
3472519 ACCACCCAATCTCTTACCCCAATCATAAGGCAGATTAAAA
1 ACCACCCAATCTCTTACCCCGATCATAGGGCAGATTGAAA
* * * * * *
3472559 ATCACCAAATCTCTTACCCCGGTCATGGGGTAGATTGAAGCC
1 ACCACCCAATCTCTTACCCCGATCATAGGGCAGATTGAA--A
*
3472601 ACCATCCAATCT-TTACCCC
1 ACCACCCAATCTCTTACCCC
3472620 TAAGTCAAGA
Statistics
Matches: 82, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
40 66 0.80
41 7 0.09
42 9 0.11
ACGTcount: A:0.31, C:0.33, G:0.13, T:0.23
Consensus pattern (40 bp):
ACCACCCAATCTCTTACCCCGATCATAGGGCAGATTGAAA
Found at i:3472643 original size:45 final size:46
Alignment explanation
Indices: 3472592--3472697 Score: 153
Period size: 46 Copynumber: 2.3 Consensus size: 46
3472582 CATGGGGTAG
* *
3472592 ATTGAAGCCACCATCCAATC-TTTACCCCTAAGTCAAGAGGGGCAA
1 ATTGAAGCCAACATCCAATCTTTTACCCCTAAATCAAGAGGGGCAA
*
3472637 ATTGAAGCCAGA-ATCCAATCTTTTACCCCTAAATCAAGATGGGCAA
1 ATTGAAGCCA-ACATCCAATCTTTTACCCCTAAATCAAGAGGGGCAA
*
3472683 GTTGAAGCCAACATC
1 ATTGAAGCCAACATC
3472698 TCACAGAAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
45 19 0.35
46 35 0.65
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (46 bp):
ATTGAAGCCAACATCCAATCTTTTACCCCTAAATCAAGAGGGGCAA
Found at i:3473698 original size:2 final size:2
Alignment explanation
Indices: 3473691--3473733 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
3473681 TATTTATTTT
* * *
3473691 TA TA TA TA TA CA TA TG TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3473733 T
1 T
3473734 GCAAACATAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3476602 original size:15 final size:16
Alignment explanation
Indices: 3476570--3476603 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3476560 AAATTTAGCC
3476570 TTCAATGTTAGTATTT
1 TTCAATGTTAGTATTT
3476586 TTCAAT-TTAGTTATTT
1 TTCAATGTTAG-TATTT
3476602 TT
1 TT
3476604 TAACTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.62
Consensus pattern (16 bp):
TTCAATGTTAGTATTT
Found at i:3481642 original size:9 final size:9
Alignment explanation
Indices: 3481630--3481706 Score: 55
Period size: 9 Copynumber: 7.8 Consensus size: 9
3481620 TTTAATGATT
3481630 TTTTTATAA
1 TTTTTATAA
3481639 TTTTCTATAA
1 TTTT-TATAA
*
3481649 GTTTTATAAGA
1 TTTTTAT-A-A
* *
3481660 TTTTAATAT
1 TTTTTATAA
*
3481669 TTTTTAAAA
1 TTTTTATAA
3481678 TATTTCTAATAA
1 T-TTT-T-ATAA
3481690 TTTTTTATAA
1 -TTTTTATAA
3481700 TTTTTAT
1 TTTTTAT
3481707 GTGAAAAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
9 21 0.40
10 17 0.32
11 8 0.15
12 6 0.11
13 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3481642 original size:10 final size:10
Alignment explanation
Indices: 3481629--3481704 Score: 57
Period size: 10 Copynumber: 7.5 Consensus size: 10
3481619 TTTTAATGAT
3481629 TTTTTTATAA
1 TTTTTTATAA
*
3481639 TTTTCTATAA
1 TTTTTTATAA
*
3481649 -GTTTTATAA
1 TTTTTTATAA
**
3481658 GATTTTA-ATA
1 TTTTTTATA-A
*
3481668 TTTTTTAAAA
1 TTTTTTATAA
*
3481678 TATTTCTAATAA
1 T-TTT-TTATAA
3481690 TTTTTTATAA
1 TTTTTTATAA
3481700 TTTTT
1 TTTTT
3481705 ATGTGAAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
9 8 0.15
10 32 0.62
11 7 0.13
12 5 0.10
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:3481938 original size:20 final size:21
Alignment explanation
Indices: 3481890--3481948 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
3481880 TATTGTACTG
* *
3481890 TATTTTAAAAATTAGAGATAAA
1 TATTTTAAAAA-TAAAAATAAA
*
3481912 AATTTTAAAAATAAAAAT-AA
1 TATTTTAAAAATAAAAATAAA
**
3481932 TATTTTATCAATAAAAA
1 TATTTTAAAAATAAAAA
3481949 GGAGAATGTC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 16 0.52
21 5 0.16
22 10 0.32
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (21 bp):
TATTTTAAAAATAAAAATAAA
Found at i:3482125 original size:9 final size:9
Alignment explanation
Indices: 3482098--3482333 Score: 101
Period size: 9 Copynumber: 25.0 Consensus size: 9
3482088 GGTTTAAATG
3482098 TAATTTTTAA
1 TAATTTTT-A
3482108 TAA--TTTA
1 TAATTTTTA
3482115 TAATTTTTA
1 TAATTTTTA
3482124 TAATTTTTA
1 TAATTTTTA
3482133 -ATATTATTTA
1 TA-ATT-TTTA
* *
3482143 TAAGTTTCA
1 TAATTTTTA
3482152 TCAATTTTTA
1 T-AATTTTTA
*
3482162 TAAGCTTTTA
1 TAA-TTTTTA
*
3482172 -AA-TATTA
1 TAATTTTTA
**
3482179 TAGGTTTTA
1 TAATTTTTA
*
3482188 TTATTTTTA
1 TAATTTTTA
***
3482197 TAAAAGATTA
1 T-AATTTTTA
3482207 TAATTTATTA
1 TAATTT-TTA
3482217 TATATTTTTA
1 TA-ATTTTTA
*
3482227 TAATATTTA
1 TAATTTTTA
*
3482236 TAAGTTTTTG
1 TAA-TTTTTA
**
3482246 TGTTTTTTCA
1 TAATTTTT-A
3482256 TAATTTTTTA
1 TAA-TTTTTA
3482266 TAATTTTT-
1 TAATTTTTA
*
3482274 TAAGTTTATA
1 TAA-TTTTTA
*
3482284 TAAAATTTTA
1 T-AATTTTTA
3482294 -AGATTTTTA
1 TA-ATTTTTA
3482303 -AATATTTCTAA
1 TAAT-TTT-T-A
3482314 TAATTTTTTAA
1 TAA-TTTTT-A
3482325 TAATTTTTA
1 TAATTTTTA
3482334 AGTAAGATTA
Statistics
Matches: 172, Mismatches: 30, Indels: 49
0.69 0.12 0.20
Matches are distributed among these distances:
7 8 0.05
8 11 0.06
9 71 0.41
10 57 0.33
11 19 0.11
12 5 0.03
13 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (9 bp):
TAATTTTTA
Found at i:3482159 original size:28 final size:26
Alignment explanation
Indices: 3482098--3482161 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 26
3482088 GGTTTAAATG
* *
3482098 TAATTTTTAATAATTTATAATTTTTA
1 TAATTTTTAATAATTTATAAGTTTCA
3482124 TAATTTTTAATATTATTTATAAGTTTCA
1 TAATTTTTAATA--ATTTATAAGTTTCA
3482152 TCAATTTTTA
1 T-AATTTTTA
3482162 TAAGCTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 12 0.36
28 13 0.39
29 8 0.24
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (26 bp):
TAATTTTTAATAATTTATAAGTTTCA
Found at i:3482264 original size:11 final size:10
Alignment explanation
Indices: 3482204--3482275 Score: 60
Period size: 10 Copynumber: 7.3 Consensus size: 10
3482194 TTATAAAAGA
*
3482204 TTATAATTTA
1 TTATAATTTT
3482214 TTAT-ATATTT
1 TTATAAT-TTT
*
3482224 TTATAA-TAT
1 TTATAATTTT
*
3482233 TTATAAGTTT
1 TTATAATTTT
* *
3482243 TTGT-GTTTT
1 TTATAATTTT
3482252 TTCATAATTTT
1 TT-ATAATTTT
3482263 TTATAATTTT
1 TTATAATTTT
3482273 TTA
1 TTA
3482276 AGTTTATATA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 15 0.31
10 27 0.55
11 7 0.14
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.65
Consensus pattern (10 bp):
TTATAATTTT
Found at i:3482766 original size:20 final size:18
Alignment explanation
Indices: 3482716--3482788 Score: 60
Period size: 20 Copynumber: 3.9 Consensus size: 18
3482706 GTTTAATTTT
*
3482716 TTTTTCATAA-TTTATATA
1 TTTTT-ATAAGTTTTTATA
*
3482734 TTTTTCTAA-TTTTCTATA
1 TTTTTATAAGTTTT-TATA
3482752 TTATTTATAAGTTTTTATGAA
1 TT-TTTATAAGTTTTTAT--A
*
3482773 TTTTTATAAGCTTTTA
1 TTTTTATAAGTTTTTA
3482789 AATATATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 6 0.13
18 11 0.24
19 9 0.20
20 17 0.37
21 3 0.07
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTTTATAAGTTTTTATA
Found at i:3482766 original size:29 final size:29
Alignment explanation
Indices: 3482725--3482780 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
3482715 TTTTTTCATA
*
3482725 ATTTATATATTTTTCT-AATTTTCTATATT
1 ATTTATATATTTTTATGAATTTT-TATATT
3482754 ATTTATA-AGTTTTTATGAATTTTTATA
1 ATTTATATA-TTTTTATGAATTTTTATA
3482781 AGCTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 1 0.04
29 17 0.71
30 6 0.25
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (29 bp):
ATTTATATATTTTTATGAATTTTTATATT
Found at i:3485646 original size:15 final size:14
Alignment explanation
Indices: 3485624--3485657 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
3485614 TCATTTACAT
3485624 ATTTTTATATATTA
1 ATTTTTATATATTA
*
3485638 ATTTATTATATATTT
1 ATTT-TTATATATTA
3485653 ATTTT
1 ATTTT
3485658 ATGTCATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTTATATATTA
Found at i:3492092 original size:99 final size:97
Alignment explanation
Indices: 3491741--3492078 Score: 297
Period size: 96 Copynumber: 3.5 Consensus size: 97
3491731 TTGCAATGTT
* * * * * * **
3491741 TTCGTGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGCTTTCGAGGTACAAGGTT
1 TTCGTGGTACTGGATTCACCATCGCGGCGTAAATCTTTCCCTACATGC-TTCTAGGTATGAGGTT
* * * * **
3491806 CGTCGTGGCGACTTAAACCTTTCCCTTTGCGTC
65 CGCCATTGCGACTTAAACCTTTCCCTATGTATC
* * * * * * ** * **
3491839 TTCGTGGCACTTGATTCGCCATTGCGGCTTAAATCTTACCCTTTAT--TTTTGAGGTACAAGGTT
1 TTCGTGGTACTGGATTCACCATCGCGGCGTAAATCTTTCCCTACATGCTTCT-AGGTATGAGGTT
* *
3491902 CGCCGTTGCGACTTAAACCTTTCCCTTTGTATC
65 CGCCATTGCGACTTAAACCTTTCCCTATGTATC
* * *
3491935 TTCGTGGTACTGGATTCACCGTCGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATGAGGTT
1 TTCGTGGTACTGGATTCACCATCGCGGCGTAAATCTTTCCCTACATGCTTCT-AGGTATGAGGTT
* *
3492000 CGTCATTGTGACTTAAACCTTTCCCTCCAT-TATC
65 CGCCATTGCGACTTAAACCTTTCCCT--ATGTATC
*
3492034 TTCGTGGTACTGGATTCGCCATCGCGGTCGTAAA-CTTTCCCTACA
1 TTCGTGGTACTGGATTCACCATCGCGG-CGTAAATCTTTCCCTACA
3492079 AATCTTCATG
Statistics
Matches: 206, Mismatches: 28, Indels: 11
0.84 0.11 0.04
Matches are distributed among these distances:
95 2 0.01
96 80 0.39
98 79 0.38
99 39 0.19
100 6 0.03
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.36
Consensus pattern (97 bp):
TTCGTGGTACTGGATTCACCATCGCGGCGTAAATCTTTCCCTACATGCTTCTAGGTATGAGGTTC
GCCATTGCGACTTAAACCTTTCCCTATGTATC
Found at i:3492112 original size:99 final size:97
Alignment explanation
Indices: 3491741--3492124 Score: 269
Period size: 96 Copynumber: 3.9 Consensus size: 97
3491731 TTGCAATGTT
* * * * * * ** **
3491741 TTCGTGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGCTTTCGAGGTACAAGGTT
1 TTCGTGGTACTGGATTCACCATCGCGGCGTAAATCTTTCCCTACATGC-TTCTAGGTATGAGACT
* * * **
3491806 CGTCGTGGCGACTTAAACCTTTCCCTTTGCGTC
65 CGCCGTTGCGACTTAAACCTTTCCCTATGTATC
* * * * * * ** * ** **
3491839 TTCGTGGCACTTGATTCGCCATTGCGGCTTAAATCTTACCCTTTAT--TTTTGAGGTACAAGGTT
1 TTCGTGGTACTGGATTCACCATCGCGGCGTAAATCTTTCCCTACATGCTTCT-AGGTATGAGACT
*
3491902 CGCCGTTGCGACTTAAACCTTTCCCTTTGTATC
65 CGCCGTTGCGACTTAAACCTTTCCCTATGTATC
* * * **
3491935 TTCGTGGTACTGGATTCACCGTCGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATGAGGTT
1 TTCGTGGTACTGGATTCACCATCGCGGCGTAAATCTTTCCCTACATGCTTCT-AGGTATGAGACT
* * *
3492000 CGTCATTGTGACTTAAACCTTTCCCTCCAT-TATC
65 CGCCGTTGCGACTTAAACCTTTCCCT--ATGTATC
*
3492034 TTCGTGGTACTGGATTCGCCATCGCGGTCGTAAA-CTTTCCCTACAAAT-CTTC-ATGGTATCG-
1 TTCGTGGTACTGGATTCACCATCGCGG-CGTAAATCTTTCCCTAC--ATGCTTCTA-GGTAT-GA
* *
3492095 GACTCGCCGTTGCGACTTCAATCTTTCCCT
61 GACTCGCCGTTGCGACTTAAACCTTTCCCT
3492125 TCATGTTTCT
Statistics
Matches: 241, Mismatches: 35, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
95 2 0.01
96 80 0.33
98 80 0.33
99 66 0.27
100 11 0.05
101 2 0.01
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (97 bp):
TTCGTGGTACTGGATTCACCATCGCGGCGTAAATCTTTCCCTACATGCTTCTAGGTATGAGACTC
GCCGTTGCGACTTAAACCTTTCCCTATGTATC
Found at i:3492262 original size:50 final size:49
Alignment explanation
Indices: 3491746--3492274 Score: 266
Period size: 49 Copynumber: 10.8 Consensus size: 49
3491736 ATGTTTTCGT
* * * *
3491746 GGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCT-TCATGCTT-TCGA
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCTCAT-CTTCT-GA
* * * * * *
3491795 GGTACAAGGTTCGTCGTGGCGACTTAAACCTTTCCCTTTGCGTCTTC-GT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCT-CATCTTCTGA
* ** * * * * * *
3491844 GGCACTTGATTCGCCATTGCGGCTTAAATCTTACCCT-TTAT-TTTTGA
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCTCATCTTCTGA
* * * *
3491891 GGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGTATCTTC-GT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCT-CATCTTCTGA
* * * *
3491940 GGTAC-TGGATTCACCGTCGCGGCTTAAATCTTTCCCT-TCATGCTTCTGA
1 GGTACAAGG-TTCGCCGTTGCGACTTAAATCTTTCCCTCTCAT-CTTCTGA
** * * * * * *
3491989 GGTATGAGGTTCGTCATTGTGACTTAAACCTTTCCCTCCATTATCTTC-GT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCT-C-TCATCTTCTGA
* * * * * **
3492039 GGTAC-TGGATTCGCCATCGCGGTCGTAAA-CTTTCCCTACAAATCTTC--A
1 GGTACAAGG-TTCGCCGTTGC-GACTTAAATCTTTCCCT-CTCATCTTCTGA
* * *
3492087 TGGTATC--GGACTCGCCGTTGCGACTTCAATCTTTCCCT-TCATGTTTCTGA
1 -GGTA-CAAGG-TTCGCCGTTGCGACTTAAATCTTTCCCTCTCAT-CTTCTGA
* ** * * *
3492137 GGTACAAGGTTTGTTGTTGCTACTTAAACCTTTCCCTC-CATATCTTC-GT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCTC--ATCTTCTGA
* * * *
3492186 GGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCTCATCTCATCTTCTGA
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTC-CCTCTCATCTTCTGA
*
3492236 GGTACAAGGTTCGCCGTTGCGACTTAAAACTTTCCCTCT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCT
3492275 ATATCTTCGT
Statistics
Matches: 355, Mismatches: 95, Indels: 60
0.70 0.19 0.12
Matches are distributed among these distances:
46 2 0.01
47 35 0.10
48 18 0.05
49 211 0.59
50 71 0.20
51 15 0.04
52 3 0.01
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.36
Consensus pattern (49 bp):
GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCTCATCTTCTGA
Found at i:3492269 original size:148 final size:146
Alignment explanation
Indices: 3491741--3492272 Score: 436
Period size: 148 Copynumber: 3.6 Consensus size: 146
3491731 TTGCAATGTT
3491741 TTCGTGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCT-TCATGCTTTCGAGGTACAAGG-
1 TTCGTGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTCTCAT-C-TTCGAGGTAC-AGGA
* * * *** * * ** * * **
3491804 TTCGTCGTGGCGACTTAAACCTTTCCCTTTGCGTCTTC-GTGGCACTTGATTCGCCATTGCGGCT
63 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGT-TTCTGAGGTACAAGGTTCGTCATTGCTACT
* * * *
3491868 TAAATCTTACCCT--TTATT
127 TAAACCTTTCCCTCCATATC
* * * * * * * * * * *
3491886 TTTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATT
1 TTCGTGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTCT-CATCTTCGAGGTACAGGATT
* * * * **
3491951 CACCGTCGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATGAGGTTCGTCATTG-TGACTTA
65 CGCCGTTGCGACTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGTCATTGCT-ACTTA
3492015 AACCTTTCCCTCCATTATC
129 AACCTTTCCCTCCA-TATC
* * * **
3492034 TTCGTGGTACTGGATTCGCCATCGCGGTCGTAAA-CTTTCCCTACAAATCTTC-ATGGTATC-GG
1 TTCGTGGTACTAGATTCGCCATTGCGG-CTTAAATCTTTCCCT-CTCATCTTCGA-GGTA-CAGG
* * * **
3492096 ACTCGCCGTTGCGACTTCAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTTGTTGTTGCTACT
62 ATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGTCATTGCTACT
3492161 TAAACCTTTCCCTCCATATC
127 TAAACCTTTCCCTCCATATC
* *
3492181 TTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCTCATCTCATCTTCTGAGGTACAAGG-
1 TTCGTGGTACTAGATTCGCCATTGCGGCTTAAATCTTTC-CCTCTCATCTTC-GAGGTAC-AGGA
*
3492245 TTCGCCGTTGCGACTTAAAACTTTCCCT
63 TTCGCCGTTGCGACTTAAATCTTTCCCT
3492273 CTATATCTTC
Statistics
Matches: 302, Mismatches: 66, Indels: 35
0.75 0.16 0.09
Matches are distributed among these distances:
144 5 0.02
145 96 0.32
146 7 0.02
147 43 0.14
148 141 0.47
149 10 0.03
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.37
Consensus pattern (146 bp):
TTCGTGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTCTCATCTTCGAGGTACAGGATTC
GCCGTTGCGACTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGTCATTGCTACTTAAA
CCTTTCCCTCCATATC
Found at i:3492271 original size:99 final size:98
Alignment explanation
Indices: 3492065--3492284 Score: 264
Period size: 99 Copynumber: 2.2 Consensus size: 98
3492055 TCGCGGTCGT
* * * * * *
3492065 AAACTTTCCCTACAAATCTTCATGGTATCGGACTCGCCGTTGCGACTTCAATCTTTCCCTTCATG
1 AAACTTTCCCTCCATATCTTCGTGGTATCAGACTCGCCGTTGCGACTTAAATCTTTCCATTCATG
* * ** *
3492130 TTTCTGAGGTACAAGGTTTGTTGTTGCTACTTA
66 CTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
* * *
3492163 AACCTTTCCCTCCATATCTTCGTGGTA-CTAGATTCGCCGTTGCGGCTTAAATCTTTCTCATCTC
1 AAACTTTCCCTCCATATCTTCGTGGTATC-AGACTCGCCGTTGCGACTTAAATCTTTC-CAT-TC
3492227 AT-CTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
63 ATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
*
3492262 AAACTTTCCCTCTATATCTTCGT
1 AAACTTTCCCTCCATATCTTCGT
3492285 TGTGATGAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
97 1 0.01
98 47 0.46
99 51 0.50
100 4 0.04
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37
Consensus pattern (98 bp):
AAACTTTCCCTCCATATCTTCGTGGTATCAGACTCGCCGTTGCGACTTAAATCTTTCCATTCATG
CTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
Found at i:3496406 original size:23 final size:23
Alignment explanation
Indices: 3496234--3496394 Score: 157
Period size: 23 Copynumber: 6.9 Consensus size: 23
3496224 CGAAGTACTT
3496234 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
* *
3496260 AACAGCAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * * *
3496282 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
3496304 AATCAGTAGGCACACGAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
*
3496328 AACAGTAGGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
3496351 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
3496374 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
3496395 TGAACGGTAA
Statistics
Matches: 116, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
22 18 0.16
23 77 0.66
24 3 0.03
26 13 0.11
27 5 0.04
ACGTcount: A:0.41, C:0.24, G:0.25, T:0.10
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:3506634 original size:21 final size:22
Alignment explanation
Indices: 3506608--3506659 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
3506598 TTTCCAAATA
3506608 TTTTAA-A-AAATGTATTTCCTT
1 TTTTAATACAAATG-ATTTCCTT
*
3506629 TTTTAATACATATGATTTCCTT
1 TTTTAATACAAATGATTTCCTT
3506651 TTCTTAATA
1 TT-TTAATA
3506660 TATAATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 6 0.22
22 11 0.41
23 10 0.37
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTTAATACAAATGATTTCCTT
Found at i:3506696 original size:18 final size:20
Alignment explanation
Indices: 3506675--3506712 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
3506665 TAAAAAAAGG
3506675 AGTGAAAA-TTCA-AAAAAT
1 AGTGAAAATTTCAGAAAAAT
3506693 AGTGAAAATTTCAGAAAAAT
1 AGTGAAAATTTCAGAAAAAT
3506713 CTAATTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 4 0.22
20 6 0.33
ACGTcount: A:0.58, C:0.05, G:0.13, T:0.24
Consensus pattern (20 bp):
AGTGAAAATTTCAGAAAAAT
Found at i:3507890 original size:29 final size:30
Alignment explanation
Indices: 3507851--3507914 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
3507841 TTAAAATGTG
* *
3507851 ATTTTTGGATGC-CCGAGGGCAAAACGGTA
1 ATTTTGGGATGCTCCGAGGGCAAAAAGGTA
* *
3507880 ATTTTGGGATGCTTCGAGGGTAAAAAGGTA
1 ATTTTGGGATGCTCCGAGGGCAAAAAGGTA
3507910 ATTTT
1 ATTTT
3507915 TGGACAGTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.31
Consensus pattern (30 bp):
ATTTTGGGATGCTCCGAGGGCAAAAAGGTA
Found at i:3507910 original size:30 final size:29
Alignment explanation
Indices: 3507851--3508061 Score: 143
Period size: 29 Copynumber: 7.2 Consensus size: 29
3507841 TTAAAATGTG
* * *
3507851 ATTTTTGGATGC-CCGAGGGCAAAACGGTA
1 ATTTTTGGA-GCTTCGAGGGTAAAAAGGTA
*
3507880 ATTTTGGGATGCTTCGAGGGTAAAAAGGTA
1 ATTTTTGGA-GCTTCGAGGGTAAAAAGGTA
* * *
3507910 ATTTTTGGA-CAGTCGAGGG-AAGAAATGTG
1 ATTTTTGGAGC-TTCGAGGGTAA-AAAGGTA
* *
3507939 ATTTTTGGA-CATTCGAGGGTAAAATGGAA
1 ATTTTTGGAGC-TTCGAGGGTAAAAAGGTA
*
3507968 ATTTTTGGAAAG-TTC-AGGGTCAAAAATGTA
1 ATTTTTGG--AGCTTCGAGGGT-AAAAAGGTA
*
3507998 ATTTTTGGAAGTTTCG-GGGTTAAAAATGG-A
1 ATTTTTGG-AGCTTCGAGGG-TAAAAA-GGTA
*
3508028 ATTTTTGGA-CATTCGAGGGTAAAATGGTA
1 ATTTTTGGAGC-TTCGAGGGTAAAAAGGTA
3508057 ATTTT
1 ATTTT
3508062 CGGAAAAGTT
Statistics
Matches: 148, Mismatches: 19, Indels: 30
0.75 0.10 0.15
Matches are distributed among these distances:
28 5 0.03
29 76 0.51
30 64 0.43
31 3 0.02
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.32
Consensus pattern (29 bp):
ATTTTTGGAGCTTCGAGGGTAAAAAGGTA
Found at i:3507942 original size:29 final size:29
Alignment explanation
Indices: 3507893--3508061 Score: 159
Period size: 29 Copynumber: 5.8 Consensus size: 29
3507883 TTGGGATGCT
3507893 TCGAGGGTAAAAAGGTAATTTTTGGACAG
1 TCGAGGGTAAAAAGGTAATTTTTGGACAG
* * *
3507922 TCGAGGG-AAGAAATGTGATTTTTGGACAT
1 TCGAGGGTAA-AAAGGTAATTTTTGGACAG
* * *
3507951 TCGAGGGTAAAATGGAAATTTTTGGAAAG
1 TCGAGGGTAAAAAGGTAATTTTTGGACAG
*
3507980 TTC-AGGGTCAAAAATGTAATTTTTGGA-AG
1 -TCGAGGGT-AAAAAGGTAATTTTTGGACAG
*
3508009 TTTCG-GGGTTAAAAATGG-AATTTTTGGACAT
1 --TCGAGGG-TAAAAA-GGTAATTTTTGGACAG
*
3508040 TCGAGGGTAAAATGGTAATTTT
1 TCGAGGGTAAAAAGGTAATTTT
3508062 CGGAAAAGTT
Statistics
Matches: 114, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
28 4 0.04
29 64 0.56
30 43 0.38
31 3 0.03
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (29 bp):
TCGAGGGTAAAAAGGTAATTTTTGGACAG
Found at i:3507973 original size:58 final size:57
Alignment explanation
Indices: 3507864--3508066 Score: 182
Period size: 59 Copynumber: 3.5 Consensus size: 57
3507854 TTTGGATGCC
** * * *
3507864 CGAGGGCAAAACGGTAATTTTGGGATGCTTCGAGGGTAAAAAGGTAATTTTTGGACAGT
1 CGAGGGCAAAAATGTAATTTTTGGAAG-TTCGAGGGTAAAATGG-AATTTTTGGACAGT
* *
3507923 CGAGGG-AAGAAATGTGATTTTTGGACA-TTCGAGGGTAAAATGGAAATTTTTGGAAAGTT
1 CGAGGGCAA-AAATGTAATTTTTGGA-AGTTCGAGGGTAAAATGG-AATTTTTGGACAG-T
*
3507982 C-AGGGTCAAAAATGTAATTTTTGGAAGTTTCG-GGGTTAAAAATGGAATTTTTGGACATT
1 CGAGGG-CAAAAATGTAATTTTTGGAAG-TTCGAGGG-T-AAAATGGAATTTTTGGACAGT
* *
3508041 CGAGGG-TAAAATGGTAATTTTCGGAA
1 CGAGGGCAAAAAT-GTAATTTTTGGAA
3508067 AAGTTGGGGT
Statistics
Matches: 120, Mismatches: 13, Indels: 22
0.77 0.08 0.14
Matches are distributed among these distances:
58 39 0.32
59 52 0.43
60 22 0.18
61 7 0.06
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.31
Consensus pattern (57 bp):
CGAGGGCAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAATGGAATTTTTGGACAGT
Found at i:3509811 original size:17 final size:17
Alignment explanation
Indices: 3509791--3509830 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3509781 CCAAATGGAT
*
3509791 TTAAATTTAATATAAAC
1 TTAAATTTAAAATAAAC
*
3509808 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAC
3509825 TTAAAT
1 TTAAAT
3509831 ATGTTGGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAAATAAAC
Found at i:3510332 original size:39 final size:39
Alignment explanation
Indices: 3510289--3510414 Score: 103
Period size: 39 Copynumber: 3.2 Consensus size: 39
3510279 CATGATCGGT
** * *
3510289 GTAAGAGATTG-GCTGATGGTGATCTGCCTCAAGTTTGAG
1 GTAAGAGATTGAG-TGATGGCAATCTGCCTCAAGCTCGAG
* * *
3510328 GTAAGAGATCGAGTGGTTGCAATCTGCCTCAAGCTCGAG
1 GTAAGAGATTGAGTGATGGCAATCTGCCTCAAGCTCGAG
* * * * * *
3510367 GTAAGAGATTGAATGGTTGCAATCTACC-CTAGGCTCGGG
1 GTAAGAGATTGAGTGATGGCAATCTGCCTC-AAGCTCGAG
3510406 GTAAGAGAT
1 GTAAGAGAT
3510415 CAAATGGTTG
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
38 1 0.01
39 71 0.97
40 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (39 bp):
GTAAGAGATTGAGTGATGGCAATCTGCCTCAAGCTCGAG
Found at i:3510409 original size:78 final size:76
Alignment explanation
Indices: 3510327--3510533 Score: 224
Period size: 78 Copynumber: 2.7 Consensus size: 76
3510317 TCAAGTTTGA
* * *
3510327 GGTAAGAGATCGAGTGGTTGCAATCTGCCTCAAGCTCGAGGTAAGAGATTG-AATGGTTGCAATC
1 GGTAAGAGATCGAATGGTTGCAATCTGCCCCAAGCTCGAGGTAAGAGATTGCAATGG-AG--ATC
3510391 T-ACCCTAGGCTCGG
63 TGACCCT-GGCTCGG
* * *
3510405 GGTAAGAGATCAAATGGTTGCAATCTGCCCCAGGCTC-ATGGTAAAAGATTGGCTAATGGAGATC
1 GGTAAGAGATCGAATGGTTGCAATCTGCCCCAAGCTCGA-GGTAAGAGATT-GC-AATGGAGATC
*
3510469 TGCCCCTGGCTCGG
63 TGACCCTGGCTCGG
* * *
3510483 GGTAAGAGATCGAATGGTCGTAATCTGCCCCAAGCTCG-GGATAAGAAATTG
1 GGTAAGAGATCGAATGGTTGCAATCTGCCCCAAGCTCGAGG-TAAGAGATTG
3510534 GTTGATGGTG
Statistics
Matches: 109, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
77 4 0.04
78 94 0.86
79 5 0.05
80 1 0.01
81 5 0.05
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (76 bp):
GGTAAGAGATCGAATGGTTGCAATCTGCCCCAAGCTCGAGGTAAGAGATTGCAATGGAGATCTGA
CCCTGGCTCGG
Found at i:3510448 original size:39 final size:39
Alignment explanation
Indices: 3510327--3510528 Score: 171
Period size: 39 Copynumber: 5.2 Consensus size: 39
3510317 TCAAGTTTGA
* * *
3510327 GGTAAGAGATCGAGTGGTTGCAATCTGCCTCAAGCTC-G
1 GGTAAGAGATCGAATGGTTGCAATCTGCCCCAGGCTCAG
* * * *
3510365 AGGTAAGAGATTGAATGGTTGCAATCTACCCTAGGCTCGG
1 -GGTAAGAGATCGAATGGTTGCAATCTGCCCCAGGCTCAG
* *
3510405 GGTAAGAGATCAAATGGTTGCAATCTGCCCCAGGCTCAT
1 GGTAAGAGATCGAATGGTTGCAATCTGCCCCAGGCTCAG
* * * * *
3510444 GGTAAAAGATTGGCTAATGG-AG--ATCTGCCCCTGGCTCGG
1 GGTAAGAGA-T--CGAATGGTTGCAATCTGCCCCAGGCTCAG
* * *
3510483 GGTAAGAGATCGAATGGTCGTAATCTGCCCCAAGCTC-G
1 GGTAAGAGATCGAATGGTTGCAATCTGCCCCAGGCTCAG
3510521 GGATAAGA
1 GG-TAAGA
3510529 AATTGGTTGA
Statistics
Matches: 132, Mismatches: 23, Indels: 16
0.77 0.13 0.09
Matches are distributed among these distances:
36 6 0.05
37 1 0.01
38 4 0.03
39 112 0.85
40 2 0.02
41 1 0.01
42 6 0.05
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (39 bp):
GGTAAGAGATCGAATGGTTGCAATCTGCCCCAGGCTCAG
Found at i:3510812 original size:49 final size:49
Alignment explanation
Indices: 3510759--3511455 Score: 400
Period size: 49 Copynumber: 14.2 Consensus size: 49
3510749 CGTGGGTTCG
* * * *
3510759 ATCTTTCTCGTCATGTTTCTAAGGTACAAGGTTCACCATTGCGGCTTAA
1 ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCATTGCGACTTAA
* * * * **
3510808 ATCTTTCCCTTCATGCTTCCGAGGTAGAAGGTTCGCTGTTGCGACTTAA
1 ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCATTGCGACTTAA
* ** * ** *
3510857 ACCTTTCCCTTTGTGTCTTC-GTGGTA-TTGGATTCGCCATTGCGACTTAA
1 ATCTTTCCCTTCATGT-TTCTGAGGTACAAGG-TTCACCATTGCGACTTAA
* * *
3510906 ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCATCGTTACGACTTAA
1 ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCATTGCGACTTAA
* * * * * * ** **
3510955 ACCTTTCCCTTTATATCTTC-GTGGTAC-TGGATTCGCTGTTGCGGTTTAA
1 ATCTTTCCCTTCATGT-TTCTGAGGTACAAGG-TTCACCATTGCGACTTAA
* *
3511004 ATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCACCATTGCGACTTAA
1 ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCATTGCGACTTAA
* ** * * ** * *
3511053 ACCTTTCCCTTTGTGTCTTC-GTGGTAC-TGGATTCGTCGTTGCGGCTTAA
1 ATCTTTCCCTTCATGT-TTCTGAGGTACAAGG-TTCACCATTGCGACTTAA
* * * * * * *
3511102 ATCTTTCCCTTCAT-ATCCTCGTGGTAC-TGGATTCGCCATTACGGCTTAA
1 ATCTTTCCCTTCATGTTTCT-GAGGTACAAGG-TTCACCATTGCGACTTAA
* ** ** *
3511151 ATCTTTCCCTTCATGTCTTC-GTGGTA-TTGGATTCGTCATTGCGGCTTAA
1 ATCTTTCCCTTCATGT-TTCTGAGGTACAAGG-TTCACCATTGCGACTTAA
* ** * *
3511200 ATCTTTCCCTTCATGTTTCTGTGGTACAAGGTTCGTCGTTGTGACTTAA
1 ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCATTGCGACTTAA
* * * *** * * *
3511249 ACCTTTCCCTT--TGTATCTTTGTGGT-TTTGGATTCGCCGTTGCGGCTTAA
1 ATCTTTCCCTTCATGT-T-TCTGAGGTACAAGG-TTCACCATTGCGACTTAA
* * * *
3511298 ATATTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAA
1 ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCATTGCGACTTAA
* ** * * * *
3511347 ACCTTTCCCTTTGTGTCTTC-GTGGTAC-TGGATTCGCCGTTGCTG-CTTAA
1 ATCTTTCCCTTCATGT-TTCTGAGGTACAAGG-TTCACCATTGC-GACTTAA
* *
3511396 ATCTTTCCCTTCATGTTTTTGAGGTACAAGGTTCACCGTTGCGACTTAA
1 ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCATTGCGACTTAA
*
3511445 ACCTTTCCCTT
1 ATCTTTCCCTT
3511456 TTCTTCCTCA
Statistics
Matches: 505, Mismatches: 114, Indels: 58
0.75 0.17 0.09
Matches are distributed among these distances:
47 5 0.01
48 22 0.04
49 451 0.89
50 22 0.04
51 5 0.01
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.40
Consensus pattern (49 bp):
ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCATTGCGACTTAA
Found at i:3510914 original size:98 final size:98
Alignment explanation
Indices: 3510797--3511456 Score: 874
Period size: 98 Copynumber: 6.7 Consensus size: 98
3510787 AGGTTCACCA
* * * *
3510797 TTGCGGCTTAAATCTTTCCCTTCATGCTTCCGAGGTAGAAGGTTCGCTGTTGCGACTTAAACCTT
1 TTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTT
* *
3510862 TCCCTTTGTGTCTTCGTGGTATTGGATTCGCCA
66 TCCCTTTGTGTCTTCGTGGTACTGGATTCGCCG
* ** *
3510895 TTGCGACTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCATCGTTACGACTTAAACCTT
1 TTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTT
* * *
3510960 TCCCTTTATATCTTCGTGGTACTGGATTCGCTG
66 TCCCTTTGTGTCTTCGTGGTACTGGATTCGCCG
* * * * *
3510993 TTGCGGTTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCACCATTGCGACTTAAACCTT
1 TTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTT
*
3511058 TCCCTTTGTGTCTTCGTGGTACTGGATTCGTCG
66 TCCCTTTGTGTCTTCGTGGTACTGGATTCGCCG
* * * * * * * *
3511091 TTGCGGCTTAAATCTTTCCCTTCAT-ATCCTCGTGGTAC-TGGATTCGCCATTACGGCTTAAATC
1 TTGCGGCTTAAATCTTTCCCTTCATGTTTCT-GAGGTACAAGG-TTCGCCGTTGCGACTTAAACC
** * * *
3511154 TTTCCCTTCATGTCTTCGTGGTATTGGATTCGTCA
64 TTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCG
* * *
3511189 TTGCGGCTTAAATCTTTCCCTTCATGTTTCTGTGGTACAAGGTTCGTCGTTGTGACTTAAACCTT
1 TTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTT
* * **
3511254 TCCCTTTGTATCTTTGTGGTTTTGGATTCGCCG
66 TCCCTTTGTGTCTTCGTGGTACTGGATTCGCCG
* * * *
3511287 TTGCGGCTTAAATATTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTT
1 TTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTT
3511352 TCCCTTTGTGTCTTCGTGGTACTGGATTCGCCG
66 TCCCTTTGTGTCTTCGTGGTACTGGATTCGCCG
* * *
3511385 TTGCTGCTTAAATCTTTCCCTTCATGTTTTTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTT
1 TTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTT
3511450 TCCCTTT
66 TCCCTTT
3511457 TCTTCCTCAT
Statistics
Matches: 485, Mismatches: 73, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
97 4 0.01
98 476 0.98
99 5 0.01
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (98 bp):
TTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTT
TCCCTTTGTGTCTTCGTGGTACTGGATTCGCCG
Found at i:3510993 original size:147 final size:147
Alignment explanation
Indices: 3510759--3511357 Score: 638
Period size: 147 Copynumber: 4.1 Consensus size: 147
3510749 CGTGGGTTCG
* * * * * * * *
3510759 ATCTTTCTCGTCATGTTTCTAAGGTACAAGGTTCACCATTGCGGCTTAAATCTTTCCCTTCAT-G
1 ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCATCGTTGCGACTTAAACCTTTCCCTTCATAT
* ** * * * ** * *
3510823 CTTCCGAGGTAGAAGG-TTCGCTGTTGCGACTTAAACCTTTCCCTTTGTGTCT-TCGTGGTAT-T
66 CTT-CGTGGTA-CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCT-GAGGTATAA
3510885 GGATTCGCCATTGCGACTTAA
128 GG-TTCGCCATTGCGACTTAA
* *
3510906 ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCATCGTTACGACTTAAACCTTTCCCTTTATAT
1 ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCATCGTTGCGACTTAAACCTTTCCCTTCATAT
* *
3510971 CTTCGTGGTACTGGATTCGCTGTTGCGGTTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGT
66 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGT
*
3511036 TCACCATTGCGACTTAA
131 TCGCCATTGCGACTTAA
* ** * * * * *
3511053 ACCTTTCCCTTTGTGTCTTC-GTGGTAC-TGGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCAT
1 ATCTTTCCCTTCATGT-TTCTGAGGTACAAGG-TTCATCGTTGCGACTTAAACCTTTCCCTTCAT
* * * * *
3511116 ATCCTCGTGGTACTGGATTCGCCATTACGGCTTAAATCTTTCCCTTCATGTCT-TCGTGGTAT-T
64 ATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCT-GAGGTATAA
* *
3511179 GGATTCGTCATTGCGGCTTAA
128 GG-TTCGCCATTGCGACTTAA
* * * **
3511200 ATCTTTCCCTTCATGTTTCTGTGGTACAAGGTTCGTCGTTGTGACTTAAACCTTTCCCTTTGTAT
1 ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCATCGTTGCGACTTAAACCTTTCCCTTCATAT
* ** *
3511265 CTTTGTGGTTTTGGATTCGCCGTTGCGGCTTAAATATTTCCCTTCATGTCTCTGAGGTATAAGGT
66 CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGT
3511330 TCGCCATTGCGACTTAA
131 TCGCCATTGCGACTTAA
*
3511347 ACCTTTCCCTT
1 ATCTTTCCCTT
3511358 TGTGTCTTCG
Statistics
Matches: 378, Mismatches: 62, Indels: 24
0.81 0.13 0.05
Matches are distributed among these distances:
146 10 0.03
147 354 0.94
148 14 0.04
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (147 bp):
ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCATCGTTGCGACTTAAACCTTTCCCTTCATAT
CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGT
TCGCCATTGCGACTTAA
Found at i:3511371 original size:147 final size:147
Alignment explanation
Indices: 3510839--3511455 Score: 642
Period size: 147 Copynumber: 4.2 Consensus size: 147
3510829 AGGTAGAAGG
* * * ** * *
3510839 TTCGCTGTTGCGACTTAAACCTTTCCCTTTGTGTCT-TCGTGGTAT-TGGATTCGCCATTGCGAC
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCT-GAGGTATAAGG-TTCGCCATTGCGAC
* * * *
3510902 TTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGG-TTCATCGTTACGACTTAAACCTTTCCCTT
64 TTAAACCTTTCCCTTCATGTTTCTGTGGTAC-AGGATTCGTCGTTGCGACTTAAACCTTTCCCTT
3510966 TATATCTTCGTGGTACTGGA
128 TATATCTTCGTGGTACTGGA
* * *
3510986 TTCGCTGTTGCGGTTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCACCATTGCGACTT
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTT
** * * * *
3511051 AAACCTTTCCCTTTGTGTCTTC-GTGGTACTGGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCA
66 AAACCTTTCCCTTCATGT-TTCTGTGGTACAGGATTCGTCGTTGCGACTTAAACCTTTCCCTTTA
*
3511115 TATCCTCGTGGTACTGGA
130 TATCTTCGTGGTACTGGA
* * * * * *
3511133 TTCGCCATTACGGCTTAAATCTTTCCCTTCATGTCT-TCGTGGTAT-TGGATTCGTCATTGCGGC
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCT-GAGGTATAAGG-TTCGCCATTGCGAC
* *
3511196 TTAAATCTTTCCCTTCATGTTTCTGTGGTACAAGG-TTCGTCGTTGTGACTTAAACCTTTCCCTT
64 TTAAACCTTTCCCTTCATGTTTCTGTGGTAC-AGGATTCGTCGTTGCGACTTAAACCTTTCCCTT
* * **
3511260 TGTATCTTTGTGGTTTTGGA
128 TATATCTTCGTGGTACTGGA
*
3511280 TTCGCCGTTGCGGCTTAAATATTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTT
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTT
** * * * *
3511345 AAACCTTTCCCTTTGTGTCTTC-GTGGTACTGGATTCGCCGTTGCTG-CTTAAATCTTTCCCTTC
66 AAACCTTTCCCTTCATGT-TTCTGTGGTACAGGATTCGTCGTTGC-GACTTAAACCTTTCCCTTT
* * * * *
3511408 ATGTTTTTGAGGTACAAGG-
129 ATATCTTCGTGGTAC-TGGA
* * *
3511427 TTCACCGTTGCGACTTAAACCTTTCCCTT
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTT
3511456 TTCTTCCTCA
Statistics
Matches: 389, Mismatches: 67, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
146 10 0.03
147 362 0.93
148 17 0.04
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.40
Consensus pattern (147 bp):
TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTT
AAACCTTTCCCTTCATGTTTCTGTGGTACAGGATTCGTCGTTGCGACTTAAACCTTTCCCTTTAT
ATCTTCGTGGTACTGGA
Found at i:3512533 original size:21 final size:21
Alignment explanation
Indices: 3512512--3512589 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 21
3512502 CTCTCCTTTT
3512512 CTTTTTCTGTTTTTTCTATTTC
1 CTTTTTCT-TTTTTTCTATTTC
* * *
3512534 CTTTTTCCTTTTTCCTTTTTC
1 CTTTTTCTTTTTTTCTATTTC
*
3512555 CTTTTTTCTTTTTTTCCTTTTTTC
1 C-TTTTTCTTTTTTT-C-TATTTC
3512579 CTTTTTTCTTT
1 C-TTTTTCTTT
3512590 CACTTCTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 12 0.25
22 18 0.38
23 1 0.02
24 17 0.35
ACGTcount: A:0.01, C:0.22, G:0.01, T:0.76
Consensus pattern (21 bp):
CTTTTTCTTTTTTTCTATTTC
Found at i:3512540 original size:7 final size:7
Alignment explanation
Indices: 3512508--3512589 Score: 76
Period size: 7 Copynumber: 11.3 Consensus size: 7
3512498 CGACCTCTCC
3512508 TTTT-CT
1 TTTTCCT
*
3512514 TTTTCTGT
1 TTTTC-CT
*
3512522 TTTTTCT
1 TTTTCCT
*
3512529 ATTTCCT
1 TTTTCCT
3512536 TTTTCCT
1 TTTTCCT
3512543 TTTTCCT
1 TTTTCCT
3512550 TTTTCCTT
1 TTTTCC-T
*
3512558 TTTTCTTT
1 TTTTC-CT
3512566 TTTTCCTT
1 TTTTCC-T
3512574 TTTTCCT
1 TTTTCCT
*
3512581 TTTTTCT
1 TTTTCCT
3512588 TT
1 TT
3512590 CACTTCTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
6 4 0.06
7 34 0.55
8 24 0.39
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.77
Consensus pattern (7 bp):
TTTTCCT
Found at i:3512553 original size:8 final size:8
Alignment explanation
Indices: 3512530--3512586 Score: 84
Period size: 8 Copynumber: 7.5 Consensus size: 8
3512520 GTTTTTTCTA
3512530 TTTCC-TT
1 TTTCCTTT
3512537 TTTCC-TT
1 TTTCCTTT
3512544 TTTCC-TT
1 TTTCCTTT
3512551 TTTCCTTT
1 TTTCCTTT
*
3512559 TTTCTTTT
1 TTTCCTTT
3512567 TTTCCTTT
1 TTTCCTTT
3512575 TTTCCTTT
1 TTTCCTTT
3512583 TTTC
1 TTTC
3512587 TTTCACTTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
7 19 0.40
8 28 0.60
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTCCTTT
Found at i:3512568 original size:16 final size:15
Alignment explanation
Indices: 3512508--3512589 Score: 80
Period size: 15 Copynumber: 5.5 Consensus size: 15
3512498 CGACCTCTCC
*
3512508 TTTTC-TTTTTCTGTT
1 TTTTCTTTTTTC-CTT
*
3512523 TTTTC-TATTTCC-T
1 TTTTCTTTTTTCCTT
*
3512536 TTTTCCTTTTTCCTT
1 TTTTCTTTTTTCCTT
* *
3512551 TTTCCTTTTTTCTTT
1 TTTTCTTTTTTCCTT
3512566 TTTTCCTTTTTTCCTT
1 TTTT-CTTTTTTCCTT
3512582 TTTTCTTT
1 TTTTCTTT
3512590 CACTTCTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
13 6 0.11
14 6 0.11
15 30 0.54
16 14 0.25
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.77
Consensus pattern (15 bp):
TTTTCTTTTTTCCTT
Found at i:3513481 original size:15 final size:16
Alignment explanation
Indices: 3513451--3513483 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3513441 TGACTTTTTC
*
3513451 TTCCTTTTCTTTCTTT
1 TTCCTTTTCTTACTTT
3513467 TTCCTTTT-TTACTTT
1 TTCCTTTTCTTACTTT
3513482 TT
1 TT
3513484 ATTGGGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCCTTTTCTTACTTT
Found at i:3517583 original size:30 final size:29
Alignment explanation
Indices: 3517470--3517584 Score: 99
Period size: 29 Copynumber: 3.9 Consensus size: 29
3517460 GCCCGGGGGC
* * *
3517470 AAAATGGTAATTTTAGGATGCTTCGGGGGGT
1 AAAATGGTAATTTTTGGAAG-TTC-GAGGGT
* * * * *
3517501 AAAAAGGTAAATTTTGGACA-CTCAAGGGCA
1 AAAATGGTAATTTTTGGA-AGTTCGAGGG-T
3517531 AAAATGG-AATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGTTCGAGGGT
3517559 AAAATGGTAATTTTTGGAAAGTTCGA
1 AAAATGGTAATTTTTGG-AAGTTCGA
3517585 CGTCAAAATC
Statistics
Matches: 66, Mismatches: 13, Indels: 11
0.73 0.14 0.12
Matches are distributed among these distances:
28 8 0.12
29 27 0.41
30 16 0.24
31 15 0.23
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.30
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGTTCGAGGGT
Found at i:3517593 original size:30 final size:28
Alignment explanation
Indices: 3517531--3517593 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 28
3517521 CTCAAGGGCA
*
3517531 AAAATGGAATTTTTGGAAGTTCGAGGGT
1 AAAATGGAATTTTTGGAAGTTCGAGCGT
3517559 AAAATGGTAATTTTTGGAAAGTTCGA-CGT
1 AAAATGG-AATTTTTGG-AAGTTCGAGCGT
3517588 CAAAAT
1 -AAAAT
3517594 CTAGTTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 7 0.23
29 11 0.35
30 13 0.42
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGAGCGT
Found at i:3519631 original size:17 final size:17
Alignment explanation
Indices: 3519565--3519650 Score: 64
Period size: 17 Copynumber: 4.9 Consensus size: 17
3519555 TTAATTTAAA
*
3519565 TAAAATTAAAATTAATATT
1 TAAAA-TAAACTTAA-ATT
* *
3519584 TATAATAAATTTAAATT
1 TAAAATAAACTTAAATT
** ** *
3519601 CCAAATGGATTTAAATT
1 TAAAATAAACTTAAATT
*
3519618 TAATATAAACTTAAATT
1 TAAAATAAACTTAAATT
*
3519635 TAAAATAAATTTAAAT
1 TAAAATAAACTTAAAT
3519651 CTGTTGGGCC
Statistics
Matches: 52, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
17 40 0.77
18 8 0.15
19 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (17 bp):
TAAAATAAACTTAAATT
Found at i:3519647 original size:34 final size:34
Alignment explanation
Indices: 3519565--3519650 Score: 84
Period size: 34 Copynumber: 2.5 Consensus size: 34
3519555 TTAATTTAAA
* *
3519565 TAAAATTAAAATTAATATTTATAATAAATTTAAATT
1 TAAAA-TAAATTTAA-ATTTATAATAAACTTAAATT
** **
3519601 CCAAATGGATTTAAATTTA-ATATAAACTTAAATT
1 TAAAATAAATTTAAATTTATA-ATAAACTTAAATT
3519635 TAAAATAAATTTAAAT
1 TAAAATAAATTTAAAT
3519651 CTGTTGGGCC
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
33 1 0.03
34 29 0.74
35 6 0.15
36 3 0.08
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (34 bp):
TAAAATAAATTTAAATTTATAATAAACTTAAATT
Found at i:3519817 original size:19 final size:20
Alignment explanation
Indices: 3519795--3519837 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
3519785 TTTTGGAACA
* *
3519795 TTTTTATATTTTTCTG-ATT
1 TTTTTAGATTTTTCAGCATT
3519814 TTTTTAGATTTTTCAGCATT
1 TTTTTAGATTTTTCAGCATT
3519834 TTTT
1 TTTT
3519838 CTGTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.70
Consensus pattern (20 bp):
TTTTTAGATTTTTCAGCATT
Found at i:3520320 original size:3 final size:3
Alignment explanation
Indices: 3520312--3520347 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3520302 AAATAATCTC
3520312 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3520348 CACTCTACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3520618 original size:20 final size:21
Alignment explanation
Indices: 3520580--3520618 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3520570 CTTAACTGAC
*
3520580 TAACTGACATTAACGAACTTT
1 TAACTGACAATAACGAACTTT
*
3520601 TAACT-ACAATAACTAACT
1 TAACTGACAATAACGAACT
3520619 ACATTGTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
TAACTGACAATAACGAACTTT
Found at i:3520890 original size:22 final size:22
Alignment explanation
Indices: 3520865--3520906 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3520855 AGATTTATTC
*
3520865 TTTGAGTTAAACTCCACAGATA
1 TTTGAATTAAACTCCACAGATA
*
3520887 TTTGAATTAAACTTCACAGA
1 TTTGAATTAAACTCCACAGA
3520907 GATAAGATAT
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:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (22 bp):
TTTGAATTAAACTCCACAGATA
Found at i:3522437 original size:20 final size:20
Alignment explanation
Indices: 3522412--3522450 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3522402 GAAATTATTT
*
3522412 CCATATTCACATGTTTTTCC
1 CCATATTCACATGCTTTTCC
3522432 CCATATTCACATGCTTTTC
1 CCATATTCACATGCTTTTC
3522451 TTTTAGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.31, G:0.05, T:0.44
Consensus pattern (20 bp):
CCATATTCACATGCTTTTCC
Found at i:3526703 original size:3 final size:3
Alignment explanation
Indices: 3526695--3526724 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3526685 GGTCATCCCT
3526695 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3526725 AATATCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3532850 original size:30 final size:30
Alignment explanation
Indices: 3532814--3532975 Score: 118
Period size: 29 Copynumber: 5.5 Consensus size: 30
3532804 ATCCGGGGGC
* *
3532814 AAAATGGTAATTTT-GGTGTAATCGGGGTTA
1 AAAATGG-AATTTTAGATGAAATCGGGGTTA
* * * *
3532844 AAAATGGAATTTTAAAAG-ATTCGGGGGT-
1 AAAATGGAATTTTAGATGAAATCGGGGTTA
* * *
3532872 AAAATGGCAATTTTTGGTAAAATCGGGGTTA
1 AAAATGG-AATTTTAGATGAAATCGGGGTTA
* ** * *
3532903 AAAATGGAATTTTAGAAG-CTTTGGGGGT-
1 AAAATGGAATTTTAGATGAAATCGGGGTTA
*
3532931 AAAATGGTAATTTTCGATGAAATCGGGGTTA
1 AAAATGG-AATTTTAGATGAAATCGGGGTTA
*
3532962 AAAACGGAATTTTA
1 AAAATGGAATTTTA
3532976 AAAGATTCGG
Statistics
Matches: 97, Mismatches: 28, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
28 14 0.14
29 35 0.36
30 35 0.36
31 13 0.13
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (30 bp):
AAAATGGAATTTTAGATGAAATCGGGGTTA
Found at i:3532854 original size:29 final size:29
Alignment explanation
Indices: 3532814--3532915 Score: 84
Period size: 30 Copynumber: 3.5 Consensus size: 29
3532804 ATCCGGGGGC
*
3532814 AAAATGGTAATTTTGGTGTAATCGGGGTTA
1 AAAATGGCAATTTTGGTG-AATCGGGGTTA
*** * *
3532844 AAAATGG-AATTTTAAAAGATTCGGGGGT-
1 AAAATGGCAATTTT-GGTGAATCGGGGTTA
*
3532872 AAAATGGCAATTTTTGGTAAAATCGGGGTTA
1 AAAATGGCAA-TTTTGGT-GAATCGGGGTTA
3532903 AAAATGG-AATTTT
1 AAAATGGCAATTTT
3532916 AGAAGCTTTG
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
28 7 0.12
29 20 0.36
30 22 0.39
31 7 0.12
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.33
Consensus pattern (29 bp):
AAAATGGCAATTTTGGTGAATCGGGGTTA
Found at i:3532905 original size:59 final size:59
Alignment explanation
Indices: 3532807--3533005 Score: 283
Period size: 59 Copynumber: 3.4 Consensus size: 59
3532797 TATGGATATC
* *
3532807 CGGGGGCAAAATGGTAA-TTTTGGTGTAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * * *
3532865 CGGGGGTAAAATGGCAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * * *
3532924 TGGGGGTAAAATGGTAATTTTCGATGAAATCGGGGTTAAAAACGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
3532983 CGGGGGAAAAATGATAATTTTTG
1 CGGGGGTAAAATGGTAATTTTTG
3533006 AAAGTTTTGG
Statistics
Matches: 122, Mismatches: 18, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
58 15 0.12
59 107 0.88
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:3532928 original size:29 final size:29
Alignment explanation
Indices: 3532835--3532995 Score: 105
Period size: 29 Copynumber: 5.5 Consensus size: 29
3532825 TTTGGTGTAA
* *
3532835 TCGGGGTTAAAAATGG-AATTTTAAAAGAT
1 TCGGGGGT-AAAATGGCAATTTTAGAAGAT
* *
3532864 TCGGGGGTAAAATGGCAATTTTTGGTAA-AA
1 TCGGGGGTAAAATGGCAA-TTTTAG-AAGAT
* *
3532894 TCGGGGTTAAAAATGG-AATTTTAGAAGCT
1 TCGGGGGT-AAAATGGCAATTTTAGAAGAT
* * * * *
3532923 TTGGGGGTAAAATGGTAATTTTCGATGAAA
1 TCGGGGGTAAAATGGCAATTTTAGAAG-AT
* * *
3532953 TCGGGGTTAAAAACGG-AATTTTAAAAGAT
1 TCGGGGGT-AAAATGGCAATTTTAGAAGAT
*
3532982 TCGGGGGAAAAATG
1 TCGGGGGTAAAATG
3532996 ATAATTTTTG
Statistics
Matches: 100, Mismatches: 24, Indels: 17
0.71 0.17 0.12
Matches are distributed among these distances:
28 21 0.21
29 36 0.36
30 28 0.28
31 15 0.15
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (29 bp):
TCGGGGGTAAAATGGCAATTTTAGAAGAT
Found at i:3533018 original size:59 final size:58
Alignment explanation
Indices: 3532835--3533308 Score: 304
Period size: 60 Copynumber: 8.0 Consensus size: 58
3532825 TTTGGTGTAA
* * *
3532835 TCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATGGCAATTTTTGGTAAAA--
1 TCGGGGTTAAAAATGGAATTTTAAAAGATTTGGGGGCAAAAT-GTAATTTTT-G-AAAATT
* * * *
3532894 TCGGGGTTAAAAATGGAATTTTAGAAGCTTTGGGGGTAAAATGGTAATTTTCGATGAAA--
1 TCGGGGTTAAAAATGGAATTTTAAAAGATTTGGGGGCAAAAT-GTAATTTTTGA--AAATT
* * * *
3532953 TCGGGGTTAAAAACGGAATTTTAAAAGATTCGGGGGAAAAATGATAATTTTTGAAAGTT
1 TCGGGGTTAAAAATGGAATTTTAAAAGATTTGGGGGCAAAATG-TAATTTTTGAAAATT
* ** * * *
3533012 TTGGGG-TCGAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTGAAAAGTT
1 TCGGGGTTAAAAATGGAATTTT--AAAAGATTTGGGGGCAAAATGTAATTTTTGAAAA-TT
* * * * *
3533072 TCGGGG-TCAAAATGTAATTGTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTGAAAAATT
1 TCGGGGTTAAAAATGGAATT-T-TAAAAGATTTGGGGGCAAAATGTAATTTTTG-AAAATT
* * * * ** * *
3533132 TTGGGGTT-AAAATGTAATTTTAGGAAAGTTTTAGGGTTAAAATGTAATTTTGGGAAAGTT
1 TCGGGGTTAAAAATGGAATTTTA--AAAGATTTGGGGGCAAAATGTAATTTT-TGAAAATT
* * * * **
3533192 TCGGGG-TCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTAGGAAAAGATT
1 TCGGGGTTAAAAATGGAATTTT--AAAAGATTTGGGGGCAAAATGTAATTTTTG-AAA-ATT
* ** *
3533253 T-GGGGTT-AAAATGTAATTTTGAGAAAG-TTTCGGGATCAAAATGTAATTTTGGAAAA
1 TCGGGGTTAAAAATGGAATTTT-A-AAAGATTT-GGGGGCAAAATGTAATTTTTGAAAA
3533309 GTGTTGGGGT
Statistics
Matches: 354, Mismatches: 38, Indels: 47
0.81 0.09 0.11
Matches are distributed among these distances:
57 3 0.01
58 15 0.04
59 125 0.35
60 199 0.56
61 11 0.03
62 1 0.00
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.34
Consensus pattern (58 bp):
TCGGGGTTAAAAATGGAATTTTAAAAGATTTGGGGGCAAAATGTAATTTTTGAAAATT
Found at i:3533040 original size:30 final size:30
Alignment explanation
Indices: 3532990--3533361 Score: 507
Period size: 30 Copynumber: 12.4 Consensus size: 30
3532980 ATTCGGGGGA
*
3532990 AAAATGATAATTTTTG-AAAGTTTTGGGGTC
1 AAAATG-TAATTTTGGAAAAGTTTTGGGGTC
*
3533020 GAAATGTAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* *
3533050 AAAATGTAATTTTTGAAAAGTTTCGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
*
3533080 AAAATGTAATTGTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* * *
3533110 AAAATGTAATTTTTGAAAAATTTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* *
3533140 AAAATGTAATTTTAGG-AAAGTTTTAGGGTT
1 AAAATGTAATTTT-GGAAAAGTTTTGGGGTC
* *
3533170 AAAATGTAATTTTGGGAAAGTTTCGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
3533200 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* * *
3533230 AAAATGTAATTTAGGAAAAGATTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* *
3533260 AAAATGTAATTTT-GAGAAAGTTTCGGGATC
1 AAAATGTAATTTTGGA-AAAGTTTTGGGGTC
*
3533290 AAAATGTAATTTTGGAAAAGTGTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* *
3533320 AAAATATAATTTTGGAAAAGTTTTTGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
*
3533350 AAAAGGTAATTT
1 AAAATGTAATTT
3533362 CTAGACAATT
Statistics
Matches: 301, Mismatches: 36, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
29 12 0.04
30 286 0.95
31 3 0.01
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTTGGGGTC
Found at i:3533578 original size:160 final size:162
Alignment explanation
Indices: 3533395--3533772 Score: 389
Period size: 161 Copynumber: 2.3 Consensus size: 162
3533385 AGCAATAAAA
*
3533395 CCAAAAACAGGTGACACGTGGCAGTCC-CACAG-GCA-TCCAGA-AGTC-AAGAGACTAATTTGA
1 CCAAAAA-A-GTGACACGTGGCAG-CCTC-CAGTGCAGT-CAAACAGTCAAAG-GACTAATTT-A
* *
3533455 -AAATCTTGAAAAATCT-TTGGACCAATTTTGTAATT-AAATAAAAGTTAATTTAAGGACTAAAT
59 TAAACCTTGAAAAAT-TATTGGACCAATTTCGTAATTAAAAT-AAAGTTAATTT-AGGACTAAAT
* * *
3533517 AAAAATAAA-TAAAAATAGAAGGGACTAAATGCAGAAATAAG
121 AAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAG
* ** *
3533558 CC-AAAAATTGACACGTGGCAGCCTCTGGTGCAGTCAAACAGTCAAAGGACTAGTTTATAAACCT
1 CCAAAAAAGTGACACGTGGCAGCCTCCAGTGCAGTCAAACAGTCAAAGGACTAATTTATAAACCT
* * * * * *
3533622 TGAAAAATTATTGGGCCAATTTCGTAATTAAAATAAAGTTGATTTGGGATTAAATTAAAGCAAAT
66 TGAAAAATTATTGGACCAATTTCGTAATTAAAATAAAGTTAATTTAGGACTAAATAAAAACAAAT
* *
3533687 TAAAAATAAAAAGGACTAAATGCATAAATAAT
131 TAAAAATAAAAAGGACTAAATGCAGAAATAAG
*** * *
3533719 CCAAAAAAGTGACACGTGGCAGCCTATGGTACAGTCAAACAGTCAAGGGACTAA
1 CCAAAAAAGTGACACGTGGCAGCCTCCAGTGCAGTCAAACAGTCAAAGGACTAA
3533773 ATTGAAAAGC
Statistics
Matches: 182, Mismatches: 23, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
159 3 0.02
160 36 0.20
161 84 0.46
162 57 0.31
163 2 0.01
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (162 bp):
CCAAAAAAGTGACACGTGGCAGCCTCCAGTGCAGTCAAACAGTCAAAGGACTAATTTATAAACCT
TGAAAAATTATTGGACCAATTTCGTAATTAAAATAAAGTTAATTTAGGACTAAATAAAAACAAAT
TAAAAATAAAAAGGACTAAATGCAGAAATAAG
Found at i:3533643 original size:161 final size:162
Alignment explanation
Indices: 3533459--3533771 Score: 427
Period size: 161 Copynumber: 1.9 Consensus size: 162
3533449 ATTTGAAAAT
* *
3533459 CTTGAAAAATCTTTGGACCAATTTTGTAATT-AAATAAAAGTTAATTTAAGGACTAAATAAAAAT
1 CTTGAAAAATCTTTGGACCAATTTCGTAATTAAAAT-AAAGTTAATTT-AGGACTAAATAAAAAC
* * * *
3533523 AAA-TAAAAATAGAAGGGACTAAATGCAGAAATAAGCC-AAAAATTGACACGTGGCAGCCTCTGG
64 AAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAAAGTGACACGTGGCAGCCTATGG
*
3533586 TGCAGTCAAACAGTCAAAGGACTAGTTTATAAAC
129 TACAGTCAAACAGTCAAAGGACTAGTTTATAAAC
* * * * * *
3533620 CTTGAAAAAT-TATTGGGCCAATTTCGTAATTAAAATAAAGTTGATTTGGGATTAAATTAAAGCA
1 CTTGAAAAATCT-TTGGACCAATTTCGTAATTAAAATAAAGTTAATTTAGGACTAAATAAAAACA
* *
3533684 AATTAAAAATAAAAAGGACTAAATGCATAAATAATCCAAAAAAGTGACACGTGGCAGCCTATGGT
65 AATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAAAGTGACACGTGGCAGCCTATGGT
*
3533749 ACAGTCAAACAGTCAAGGGACTA
130 ACAGTCAAACAGTCAAAGGACTA
3533772 AATTGAAAAG
Statistics
Matches: 132, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
160 15 0.11
161 67 0.51
162 50 0.38
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (162 bp):
CTTGAAAAATCTTTGGACCAATTTCGTAATTAAAATAAAGTTAATTTAGGACTAAATAAAAACAA
ATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAAAGTGACACGTGGCAGCCTATGGTA
CAGTCAAACAGTCAAAGGACTAGTTTATAAAC
Found at i:3534243 original size:22 final size:21
Alignment explanation
Indices: 3534193--3534252 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
3534183 AGAGATAAGC
*
3534193 CTTTCT-TTCTTATTTTTCTT
1 CTTTCTGTTCTTATTCTTCTT
3534213 CTTT-TGTTCTTCATTCTTCATT
1 CTTTCTGTTCTT-ATTCTTC-TT
3534235 -TTTCTGTTCTTTATTCTT
1 CTTTCTGTTC-TTATTCTT
3534253 TAAAAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 1 0.03
20 9 0.26
21 9 0.26
22 13 0.38
23 2 0.06
ACGTcount: A:0.07, C:0.20, G:0.03, T:0.70
Consensus pattern (21 bp):
CTTTCTGTTCTTATTCTTCTT
Found at i:3534648 original size:17 final size:17
Alignment explanation
Indices: 3534622--3534661 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3534612 CTTTATTTAT
*
3534622 TAATTGTTATTTATTAA
1 TAATTATTATTTATTAA
3534639 TAATTATTATTTATTAA
1 TAATTATTATTTATTAA
*
3534656 TTATTA
1 TAATTA
3534662 CCAAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TAATTATTATTTATTAA
Found at i:3534661 original size:14 final size:14
Alignment explanation
Indices: 3534614--3534661 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
3534604 TATTCTCTCT
*
3534614 TTATTTATTAATTG
1 TTATTTATTAATTA
3534628 TTATTTATTAATAATTA
1 TTATTTA-T--TAATTA
3534645 TTATTTATTAATTA
1 TTATTTATTAATTA
3534659 TTA
1 TTA
3534662 CCAAAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 16 0.53
15 1 0.03
16 1 0.03
17 12 0.40
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TTATTTATTAATTA
Found at i:3535267 original size:20 final size:20
Alignment explanation
Indices: 3535235--3535294 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
3535225 CAGGGCATGG
3535235 TGGAGCTTGGTGGTCAGCAGA
1 TGGAGC-TGGTGGTCAGCAGA
3535256 TGGAGCTGGTGGTCAGCAGA
1 TGGAGCTGGTGGTCAGCAGA
*
3535276 TGGAGCTGGTGGCCAGCAG
1 TGGAGCTGGTGGTCAGCAG
3535295 CAGTAGGCAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 32 0.84
21 6 0.16
ACGTcount: A:0.18, C:0.17, G:0.45, T:0.20
Consensus pattern (20 bp):
TGGAGCTGGTGGTCAGCAGA
Found at i:3535478 original size:6 final size:6
Alignment explanation
Indices: 3535463--3535537 Score: 73
Period size: 6 Copynumber: 12.5 Consensus size: 6
3535453 TTTTATTATT
* * *
3535463 AATTTA AATTTT AA-TTA AATTTA AATTTTTA CATTTA AATTTA AA-ATA
1 AATTTA AATTTA AATTTA AATTTA AA--TTTA AATTTA AATTTA AATTTA
**
3535511 AATTTA AATTTA ACCTTA AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AAT
3535538 CTTGTTCAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 8 0.15
6 42 0.76
8 5 0.09
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:3535485 original size:17 final size:17
Alignment explanation
Indices: 3535463--3535537 Score: 77
Period size: 17 Copynumber: 4.5 Consensus size: 17
3535453 TTTTATTATT
3535463 AATTTAAATTTTAATTA
1 AATTTAAATTTTAATTA
3535480 AATTTAAA-TTT--TTA
1 AATTTAAATTTTAATTA
* * *
3535494 CATTTAAATTTAAAATA
1 AATTTAAATTTTAATTA
3535511 AATTTAAA-TTTAACCTTA
1 AATTTAAATTTTAA--TTA
3535529 AATTTAAAT
1 AATTTAAAT
3535538 CTTGTTCAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 10 0.22
15 2 0.04
16 7 0.15
17 17 0.37
18 10 0.22
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTAAATTTTAATTA
Found at i:3535988 original size:68 final size:68
Alignment explanation
Indices: 3535871--3536503 Score: 1149
Period size: 68 Copynumber: 9.3 Consensus size: 68
3535861 CTCATTTCAA
* ** * * *
3535871 CAATTTCAGAGATAAAGACGTGTTATCCATTCTACTTCAATTCCGAGGGGATGACGTTGCCCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCGCTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
3535936 CTT
66 CTT
* *
3535939 CGATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCGCTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
3536004 CTT
66 CTT
3536007 CAATTTCAGAGATGAAGACGTGTTATCCGCTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCGCTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
3536072 CTT
66 CTT
*
3536075 CAATTTCAGAGATGAAGACGTGTTATCCGCTCTACTTCAATTTCAAGGGGATGACGTTACTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCGCTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
3536140 CTT
66 CTT
3536143 CAATTTCAGAGATGAAGACGTGTTATCCGCTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCGCTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
3536208 CTT
66 CTT
*
3536211 CAATTTCAGAGATAAAGACGTGTTATCCGCTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCGCTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
3536276 CTT
66 CTT
*
3536279 CAATTTCAGAGATGAAGACGTGTTATCCGCTCTACTTCAATTTCAAAGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCGCTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
3536344 CTT
66 CTT
*
3536347 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCGCTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
3536412 CTT
66 CTT
*
3536415 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCGCTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
3536480 CTT
66 CTT
3536483 CAATTTCAGAGATGAAGACGT
1 CAATTTCAGAGATGAAGACGT
3536504 TGAGACCTGC
Statistics
Matches: 550, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 550 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (68 bp):
CAATTTCAGAGATGAAGACGTGTTATCCGCTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
CTT
Found at i:3548536 original size:59 final size:59
Alignment explanation
Indices: 3548438--3548695 Score: 340
Period size: 59 Copynumber: 4.4 Consensus size: 59
3548428 TATGGATACC
* * *
3548438 CGGGGGCAAAATGGTAA-TTTTGGT-ATAATCGAGGTTAAAAATAGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGA-AATCGGGGTTAAAAATGGAATTTTAAAAGATT
* ** * * *
3548496 CGGGGGTAAAATGGCAATTTTTGGTGAAATCGGGGTTAAAAGCGAAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * * *
3548555 CGGGGGTAAAATGGCAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
*
3548614 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * *
3548673 CGAGGGAAAAATGATAATTTTTG
1 CGGGGGTAAAATGGTAATTTTTG
3548696 AAAGTTTTGG
Statistics
Matches: 177, Mismatches: 21, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
58 15 0.08
59 161 0.91
60 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:3548648 original size:29 final size:30
Alignment explanation
Indices: 3548495--3548654 Score: 130
Period size: 30 Copynumber: 5.4 Consensus size: 30
3548485 TTTAAAAGAT
* *
3548495 TCGGGGGTAAAATGGCAATTTTTGGTGAAA
1 TCGGGGTTAAAATGGCAATTTTAGGTGAAA
* ** **
3548525 TCGGGGTTAAAA-GCGAAATTTTAGAAG-CT
1 TCGGGGTTAAAATG-GCAATTTTAGGTGAAA
* *
3548554 TCGGGGGTAAAATGGCAATTTTCGGTGAAA
1 TCGGGGTTAAAATGGCAATTTTAGGTGAAA
** **
3548584 TCGGGGTTAAAAATGG-AATTTTAGAAG-CT
1 TCGGGGTT-AAAATGGCAATTTTAGGTGAAA
* * *
3548613 TCGGGGGTAAAATGGTAATTTTTGGTGAAA
1 TCGGGGTTAAAATGGCAATTTTAGGTGAAA
3548643 TCGGGGTTAAAA
1 TCGGGGTTAAAA
3548655 ACGGAATTTT
Statistics
Matches: 97, Mismatches: 27, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
28 7 0.07
29 36 0.37
30 47 0.48
31 7 0.07
ACGTcount: A:0.32, C:0.07, G:0.31, T:0.29
Consensus pattern (30 bp):
TCGGGGTTAAAATGGCAATTTTAGGTGAAA
Found at i:3548663 original size:30 final size:30
Alignment explanation
Indices: 3548445--3548665 Score: 125
Period size: 29 Copynumber: 7.5 Consensus size: 30
3548435 ACCCGGGGGC
*
3548445 AAAATGGTAATTTT-GGT-ATAATCGAGGTTA
1 AAAATGG-AATTTTAGGTGA-AATCGGGGTTA
* *** * *
3548475 AAAATAGAATTTTAAAAG-ATTCGGGGGT-
1 AAAATGGAATTTTAGGTGAAATCGGGGTTA
*
3548503 AAAATGGCAATTTTTGGTGAAATCGGGGTTA
1 AAAATGG-AATTTTAGGTGAAATCGGGGTTA
** * ** ** *
3548534 AAAGCGAAATTTTAGAAG-CTTCGGGGGT-
1 AAAATGGAATTTTAGGTGAAATCGGGGTTA
*
3548562 AAAATGGCAATTTTCGGTGAAATCGGGGTTA
1 AAAATGG-AATTTTAGGTGAAATCGGGGTTA
** ** *
3548593 AAAATGGAATTTTAGAAG-CTTCGGGGGT-
1 AAAATGGAATTTTAGGTGAAATCGGGGTTA
*
3548621 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGG-AATTTTAGGTGAAATCGGGGTTA
*
3548652 AAAACGGAATTTTA
1 AAAATGGAATTTTA
3548666 AAAGATTCGA
Statistics
Matches: 134, Mismatches: 46, Indels: 22
0.66 0.23 0.11
Matches are distributed among these distances:
28 17 0.13
29 50 0.37
30 50 0.37
31 17 0.13
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (30 bp):
AAAATGGAATTTTAGGTGAAATCGGGGTTA
Found at i:3548664 original size:29 final size:29
Alignment explanation
Indices: 3548445--3548664 Score: 109
Period size: 30 Copynumber: 7.4 Consensus size: 29
3548435 ACCCGGGGGC
*
3548445 AAAATGGTAATTTTGGT-ATAATCGAGGTTA
1 AAAATGG-AATTTTGGTGA-AATCGGGGTTA
* ** *
3548475 AAAATAGAATTTT--AAAAGATTCGGGGGT-
1 AAAATGGAATTTTGGTGAA-A-TCGGGGTTA
3548503 AAAATGGCAATTTTTGGTGAAATCGGGGTTA
1 AAAATGG-AA-TTTTGGTGAAATCGGGGTTA
** * * * *
3548534 AAAGCGAAATTTT--AGAAGCTTCGGGGGT-
1 AAAATGGAATTTTGGTGAA--ATCGGGGTTA
3548562 AAAATGGCAATTTTCGGTGAAATCGGGGTTA
1 AAAATGG-AATTTT-GGTGAAATCGGGGTTA
* * *
3548593 AAAATGGAATTTT--AGAAGCTTCGGGGGT-
1 AAAATGGAATTTTGGTGAA--ATCGGGGTTA
3548621 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGG-AA-TTTTGGTGAAATCGGGGTTA
*
3548652 AAAACGGAATTTT
1 AAAATGGAATTTT
3548665 AAAAGATTCG
Statistics
Matches: 141, Mismatches: 27, Indels: 45
0.66 0.13 0.21
Matches are distributed among these distances:
27 7 0.05
28 19 0.13
29 44 0.31
30 45 0.32
31 18 0.13
32 8 0.06
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (29 bp):
AAAATGGAATTTTGGTGAAATCGGGGTTA
Found at i:3548708 original size:59 final size:56
Alignment explanation
Indices: 3548470--3548816 Score: 152
Period size: 59 Copynumber: 5.9 Consensus size: 56
3548460 GTATAATCGA
* * * *
3548470 GGTTAAAAATAGAATTTTAAAAGATTCGGGGGTAAAATGGCAATTTTTGGTGAAA--TCGG
1 GGTTAAAAATGGAATTTTAAAAGATTC-GGGGAAAAAT-GTAA-TTTT--TGAAATTTTGG
** * * * * * *
3548529 GGTTAAAAGCGAAATTTTAGAAGCTTCGGGGGTAAAATGGCAATTTTCGGTGAAA--TCGG
1 GGTTAAAAATGGAATTTTAAAAGATTC-GGGGAAAAAT-GTAATTTT---TGAAATTTTGG
* * * *
3548588 GGTTAAAAATGGAATTTTAGAAGCTTCGGGGGTAAAATGGTAATTTTTGGTGAAA--TCGG
1 GGTTAAAAATGGAATTTTAAAAGATTC-GGGGAAAAAT-GTAA-TTTT--TGAAATTTTGG
*
3548647 GGTTAAAAACGGAATTTTAAAAGATTCGAGGGAAAAATGATAATTTTTGAAAGTTTTGG
1 GGTTAAAAATGGAATTTTAAAAGATTCG-GGGAAAAATG-TAATTTTTGAAA-TTTTGG
** * * * *
3548706 GG-TCGAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTGAAAAATTTTGG
1 GGTTAAAAATGGAATTTT--AAAAGATTCGGGG-AAAAATGTAATTTTTG--AAATTTTGG
* * * ** *
3548766 GGTT-AAAATGTAATTTTAGGAAAGTTTTGGGTTAAAATGTAATTTTGGAAA
1 GGTTAAAAATGGAATTTTA--AAAGATTCGGGGAAAAATGTAATTTTTGAAA
3548817 AGTTTTGGTG
Statistics
Matches: 247, Mismatches: 26, Indels: 32
0.81 0.09 0.10
Matches are distributed among these distances:
56 5 0.02
57 3 0.01
58 22 0.09
59 164 0.66
60 49 0.20
61 4 0.02
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (56 bp):
GGTTAAAAATGGAATTTTAAAAGATTCGGGGAAAAATGTAATTTTTGAAATTTTGG
Found at i:3548730 original size:30 final size:30
Alignment explanation
Indices: 3548680--3549114 Score: 531
Period size: 30 Copynumber: 14.5 Consensus size: 30
3548670 ATTCGAGGGA
*
3548680 AAAATGATAATTTTTG-AAAGTTTTGGGGTC
1 AAAATG-TAATTTTGGAAAAGTTTTGGGGTC
*
3548710 GAAATGTAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* * *
3548740 AAAATGTAATTTTTGAAAAATTTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
*
3548770 AAAATGTAATTTTAGG-AAAGTTTT-GGGTT
1 AAAATGTAATTTT-GGAAAAGTTTTGGGGTC
*
3548799 AAAATGTAATTTTGGAAAAGTTTTGGTGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* * *
3548829 AAAATGTAATTTAGGAAAAAGTTTTAGGGTT
1 AAAATGTAATTTTGG-AAAAGTTTTGGGGTC
* *
3548860 AAAATGTAATTTTGGGAAAGTTTCGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* *
3548890 AAAATGTAATTTTTGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* **
3548920 AAAATGTAATTTTGG-GAAGTTTCAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
*
3548949 AAAATGTAATTTTGGAAAAGTTTTGAGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* ** * *
3548979 AAAATGTAATTTAGGAAAAAATTTGAGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* *
3549009 AAAATGTAATTTT-AAGAAAGTTTCGGGGTC
1 AAAATGTAATTTTGGA-AAAGTTTTGGGGTC
3549039 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
* *
3549069 -AAATATAATTTTGGAAAAGTTTTTGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
*
3549098 AAAAGGTAATTTCTGGA
1 AAAATGTAATTT-TGGA
3549115 CAATTTAGGG
Statistics
Matches: 346, Mismatches: 49, Indels: 19
0.84 0.12 0.05
Matches are distributed among these distances:
28 2 0.01
29 87 0.25
30 225 0.65
31 32 0.09
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTTGGGGTC
Found at i:3548738 original size:89 final size:89
Alignment explanation
Indices: 3548645--3549109 Score: 489
Period size: 89 Copynumber: 5.2 Consensus size: 89
3548635 TGGTGAAATC
* * * *
3548645 GGGGTTAAAAACGGAATTTT-AAAAGATTCGAGGG-AAAAATGATAATTTTTGAAAGTTTTGGGG
1 GGGGTT-AAAATGTAATTTTGAAAAGATTCGAGGGTCAAAATG-TAATTTTGGAAAGTTTTGGGG
*
3548708 TCGAAATGTAATTTTGGAAAAGTTTT
64 TCAAAATGTAATTTTGGAAAAGTTTT
* * *
3548734 GGGGTCAAAATGTAATTTTTGAAAA-ATTTTG-GGGTTAAAATGTAATTTTAGGAAAGTTTT-GG
1 GGGGTTAAAATGTAA-TTTTGAAAAGA-TTCGAGGGTCAAAATGTAATTTT-GGAAAGTTTTGGG
*
3548796 GTTAAAATGTAATTTTGGAAAAGTTTT
63 GTCAAAATGTAATTTTGGAAAAGTTTT
* * * ** * *
3548823 GGTGTCAAAATGTAATTTAGGAAAA-AGTTTTAGGGTTAAAATGTAATTTTGGGAAAGTTTCGGG
1 GGGGTTAAAATGTAATTT-TGAAAAGA-TTCGAGGGTCAAAATGTAATTTT-GGAAAGTTTTGGG
*
3548887 GTCAAAATGTAATTTTTGAAAAGTTTT
63 GTCAAAATGTAATTTTGGAAAAGTTTT
** * *
3548914 GGGGTTAAAATGTAATTTTGGGAAGTTTC-AGGGTCAAAATGTAATTTTGGAAAAGTTTTGAGGT
1 GGGGTTAAAATGTAATTTTGAAAAGATTCGAGGGTCAAAATGTAATTTTGG-AAAGTTTTGGGGT
* **
3548978 CAAAATGTAATTTAGGAAAAAATTT
65 CAAAATGTAATTTTGGAAAAGTTTT
* * *
3549003 GAGGTTAAAATGTAATTTTAAGAAAGTTTCG-GGGTCAAAATGTAATTTTGGAAAAGTTTTGGGG
1 GGGGTTAAAATGTAATTTTGA-AAAGATTCGAGGGTCAAAATGTAATTTTGG-AAAGTTTTGGGG
*
3549067 TC-AAATATAATTTTGGAAAAGTTTT
64 TCAAAATGTAATTTTGGAAAAGTTTT
* * *
3549092 TGGGTCAAAAGGTAATTT
1 GGGGTTAAAATGTAATTT
3549110 CTGGACAATT
Statistics
Matches: 321, Mismatches: 43, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
88 12 0.04
89 171 0.53
90 95 0.30
91 43 0.13
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (89 bp):
GGGGTTAAAATGTAATTTTGAAAAGATTCGAGGGTCAAAATGTAATTTTGGAAAGTTTTGGGGTC
AAAATGTAATTTTGGAAAAGTTTT
Found at i:3548888 original size:150 final size:149
Alignment explanation
Indices: 3548696--3549114 Score: 610
Period size: 150 Copynumber: 2.8 Consensus size: 149
3548686 ATAATTTTTG
* ** * * *
3548696 AAAGTTTTGGGGTCGAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTGAAAAAT
1 AAAGTTTTAGGGTTAAAATGTAATTTTGGGAAAGTTTCGGGGTCAAAATGTAATTTTTGAAAAGT
*
3548761 TTTGGGGTTAAAATGTAATTTTAGGAAAGTTTTGGGTTAAAATGTAATTTTGGAAAAGTTTTG-G
66 TTTGGGGTTAAAATGTAATTTT-GGAAAGTTTTGGGTCAAAATGTAATTTTGGAAAAGTTTTGAG
3548825 TGTCAAAATGTAATTTAGGAA
130 -GTCAAAATGTAATTTAGGAA
3548846 AAAGTTTTAGGGTTAAAATGTAATTTTGGGAAAGTTTCGGGGTCAAAATGTAATTTTTGAAAAGT
1 AAAGTTTTAGGGTTAAAATGTAATTTTGGGAAAGTTTCGGGGTCAAAATGTAATTTTTGAAAAGT
* *
3548911 TTTGGGGTTAAAATGTAATTTTGGGAAGTTTCAGGGTCAAAATGTAATTTTGGAAAAGTTTTGAG
66 TTTGGGGTTAAAATGTAATTTTGGAAAGTTT-TGGGTCAAAATGTAATTTTGGAAAAGTTTTGAG
3548976 GTCAAAATGTAATTTAGGAA
130 GTCAAAATGTAATTTAGGAA
* * ** *
3548996 AAAATTTGA-GGTTAAAATGTAATTTTAAGAAAGTTTCGGGGTCAAAATGTAATTTTGGAAAAGT
1 AAAGTTTTAGGGTTAAAATGTAATTTTGGGAAAGTTTCGGGGTCAAAATGTAATTTTTGAAAAGT
* * *
3549060 TTTGGGG-TCAAATATAATTTTGGAAAAGTTTTTGGGTCAAAAGGTAATTTCTGGA
66 TTTGGGGTTAAAATGTAATTTTGG-AAAG-TTTTGGGTCAAAATGTAATTT-TGGA
3549115 CAATTTAGGG
Statistics
Matches: 245, Mismatches: 19, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
148 14 0.06
149 86 0.35
150 144 0.59
151 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (149 bp):
AAAGTTTTAGGGTTAAAATGTAATTTTGGGAAAGTTTCGGGGTCAAAATGTAATTTTTGAAAAGT
TTTGGGGTTAAAATGTAATTTTGGAAAGTTTTGGGTCAAAATGTAATTTTGGAAAAGTTTTGAGG
TCAAAATGTAATTTAGGAA
Found at i:3549453 original size:161 final size:163
Alignment explanation
Indices: 3549218--3549519 Score: 430
Period size: 162 Copynumber: 1.9 Consensus size: 163
3549208 TTGCAAATCT
* * *
3549218 TTGGACCAATTTTGTAATTAAATAAAAGTTAATTTAAGGACTAAATAAAAATAAATTAAAAATAG
1 TTGGACCAATTTCGTAATTAAATAAAAGTTAATTTAAGGACTAAATAAAAACAAATTAAAAATAA
* * * *
3549283 AAGGGACTAAATGCAGAAATAAGCC-AAAAATTGACACGTGGCAGCCTCTGGTGCAGTCAAACAG
66 AAAGGACTAAATGCAGAAATAAGCCAAAAAAGTGACACGTGGCAGCCTATGGTACAGTCAAACAG
3549347 TCAAAGGACTAGTTTATAAACCTTGAAAAATTA
131 TCAAAGGACTAGTTTATAAACCTTGAAAAATTA
* * * * * *
3549380 TTGGGCCAATTTCGTAATTAAA-ATAAAGTTGATTT-GGGATTAAATTAAAGCAAATTAAAAATA
1 TTGGACCAATTTCGTAATTAAATA-AAAGTTAATTTAAGGACTAAATAAAAACAAATTAAAAATA
* *
3549443 AAAAGGACTAAATGCATAAATAATCCAAAAAAGTGACACGTGGCAGCCTATGGTACAGTCAAACA
65 AAAAGGACTAAATGCAGAAATAAGCCAAAAAAGTGACACGTGGCAGCCTATGGTACAGTCAAACA
*
3549508 GTCAAGGGACTA
130 GTCAAAGGACTA
3549520 AATTGAAAAG
Statistics
Matches: 122, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
161 46 0.38
162 76 0.62
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.25
Consensus pattern (163 bp):
TTGGACCAATTTCGTAATTAAATAAAAGTTAATTTAAGGACTAAATAAAAACAAATTAAAAATAA
AAAGGACTAAATGCAGAAATAAGCCAAAAAAGTGACACGTGGCAGCCTATGGTACAGTCAAACAG
TCAAAGGACTAGTTTATAAACCTTGAAAAATTA
Found at i:3549990 original size:22 final size:21
Alignment explanation
Indices: 3549940--3549999 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
3549930 AGAGATAAGC
*
3549940 CTTTCT-TTCTTATTTTTCTT
1 CTTTCTGTTCTTATTCTTCTT
3549960 CTTT-TGTTCTTCATTCTTCATT
1 CTTTCTGTTCTT-ATTCTTC-TT
3549982 -TTTCTGTTCTTTATTCTT
1 CTTTCTGTTC-TTATTCTT
3550000 TAAAAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 1 0.03
20 9 0.26
21 9 0.26
22 13 0.38
23 2 0.06
ACGTcount: A:0.07, C:0.20, G:0.03, T:0.70
Consensus pattern (21 bp):
CTTTCTGTTCTTATTCTTCTT
Found at i:3550393 original size:17 final size:17
Alignment explanation
Indices: 3550367--3550406 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3550357 CTTTATTTAT
*
3550367 TAATTGTTATTTATTAA
1 TAATTATTATTTATTAA
3550384 TAATTATTATTTATTAA
1 TAATTATTATTTATTAA
*
3550401 TTATTA
1 TAATTA
3550407 CCAAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TAATTATTATTTATTAA
Found at i:3550406 original size:14 final size:14
Alignment explanation
Indices: 3550359--3550406 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
3550349 TATTCTCTCT
*
3550359 TTATTTATTAATTG
1 TTATTTATTAATTA
3550373 TTATTTATTAATAATTA
1 TTATTTA-T--TAATTA
3550390 TTATTTATTAATTA
1 TTATTTATTAATTA
3550404 TTA
1 TTA
3550407 CCAAAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 16 0.53
15 1 0.03
16 1 0.03
17 12 0.40
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TTATTTATTAATTA
Found at i:3551012 original size:20 final size:21
Alignment explanation
Indices: 3550980--3551019 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3550970 CAGGGCATGG
*
3550980 TGGAGCTTGGTGGTCAGCAGA
1 TGGAGCTTGGTGGCCAGCAGA
3551001 TGGAGC-TGGTGGCCAGCAG
1 TGGAGCTTGGTGGCCAGCAG
3551020 CAGTAGGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.20
Consensus pattern (21 bp):
TGGAGCTTGGTGGCCAGCAGA
Found at i:3551211 original size:17 final size:17
Alignment explanation
Indices: 3551189--3551280 Score: 84
Period size: 17 Copynumber: 5.5 Consensus size: 17
3551179 TTTTATTATT
3551189 AATTTAAATTTTAATTA
1 AATTTAAATTTTAATTA
* **
3551206 AATTTAAATTTAAAGCA
1 AATTTAAATTTTAATTA
3551223 AATTTAAA-TTT--TTA
1 AATTTAAATTTTAATTA
* * *
3551237 CATTTAAATTTAAAATA
1 AATTTAAATTTTAATTA
3551254 AATTTAAA-TTTAACCTTA
1 AATTTAAATTTTAA--TTA
3551272 AATTTAAAT
1 AATTTAAAT
3551281 CTTGTTCAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
14 8 0.14
15 2 0.04
16 6 0.11
17 31 0.54
18 10 0.18
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (17 bp):
AATTTAAATTTTAATTA
Found at i:3551212 original size:6 final size:6
Alignment explanation
Indices: 3551189--3551280 Score: 82
Period size: 6 Copynumber: 15.5 Consensus size: 6
3551179 TTTTATTATT
* **
3551189 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA--TTTA
* * **
3551237 CATTTA AATTTA AA-ATA AATTTA AATTTA ACCTTA AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT
3551281 CTTGTTCAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
5 11 0.16
6 51 0.76
8 5 0.07
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:3551496 original size:30 final size:29
Alignment explanation
Indices: 3551472--3551536 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
3551462 AATTTTGAGG
*
3551472 AATTTAGGGATTAAATTTGAAATTTTTGGAA
1 AATTT-GGGATTAAAATTGAAA-TTTTGGAA
*
3551503 AATTTGGGATTAAAATTGAACTTTTGG-A
1 AATTTGGGATTAAAATTGAAATTTTGGAA
3551531 AATTTG
1 AATTTG
3551537 AGGGCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 7 0.22
29 6 0.19
30 14 0.44
31 5 0.16
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.42
Consensus pattern (29 bp):
AATTTGGGATTAAAATTGAAATTTTGGAA
Found at i:3551602 original size:30 final size:29
Alignment explanation
Indices: 3551524--3551622 Score: 99
Period size: 29 Copynumber: 3.4 Consensus size: 29
3551514 AAAATTGAAC
** * * *
3551524 TTTTGGAAATTTGAGGGCAAAATGGTAAC
1 TTTTGGATGTTTGAAGGTAAAATGGTAAT
* **
3551553 TTTTGGTTGTTTGGGGGTAAAAATGGTAAT
1 TTTTGGATGTTTGAAGGT-AAAATGGTAAT
*
3551583 TTTTGGATGTTTGAAGGTAACATGGTAAT
1 TTTTGGATGTTTGAAGGTAAAATGGTAAT
*
3551612 TTTTTGATGTT
1 TTTTGGATGTT
3551623 CGGCAGCAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 33 0.57
30 25 0.43
ACGTcount: A:0.26, C:0.03, G:0.28, T:0.42
Consensus pattern (29 bp):
TTTTGGATGTTTGAAGGTAAAATGGTAAT
Found at i:3551636 original size:29 final size:29
Alignment explanation
Indices: 3551572--3551673 Score: 100
Period size: 29 Copynumber: 3.5 Consensus size: 29
3551562 TTTGGGGGTA
* * * *
3551572 AAAATGGTAATTTTTGGATGTT-TGAAGGT
1 AAAATGGTAATTTTTTGATGTTCGGCA-GC
*
3551601 AACATGGTAATTTTTTGATGTTCGGCAGC
1 AAAATGGTAATTTTTTGATGTTCGGCAGC
* *
3551630 AAAATGGTGA-TTTTTGAAAGTTCGGCAGC
1 AAAATGGTAATTTTTTG-ATGTTCGGCAGC
*
3551659 AAAATGGTGATTTTT
1 AAAATGGTAATTTTT
3551674 GAAAGTTCGA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
28 6 0.10
29 50 0.81
30 6 0.10
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.38
Consensus pattern (29 bp):
AAAATGGTAATTTTTTGATGTTCGGCAGC
Found at i:3551674 original size:29 final size:29
Alignment explanation
Indices: 3551612--3551682 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
3551602 ACATGGTAAT
*
3551612 TTTTTG-ATGTTCGGCAGCAAAATGGTGA
1 TTTTTGAAAGTTCGGCAGCAAAATGGTGA
3551640 TTTTTGAAAGTTCGGCAGCAAAATGGTGA
1 TTTTTGAAAGTTCGGCAGCAAAATGGTGA
3551669 TTTTTGAAAGTTCG
1 TTTTTGAAAGTTCG
3551683 AGGGTAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 6 0.15
29 35 0.85
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.37
Consensus pattern (29 bp):
TTTTTGAAAGTTCGGCAGCAAAATGGTGA
Found at i:3551691 original size:29 final size:30
Alignment explanation
Indices: 3551630--3551721 Score: 100
Period size: 29 Copynumber: 3.1 Consensus size: 30
3551620 GTTCGGCAGC
* *
3551630 AAAATGGTGATTTTTGAAAGTTCG-GCAG-C
1 AAAATGGTGATTTTTGAAAGTTCGAG-GGTA
3551659 AAAATGGTGATTTTTGAAAGTTCGAGGGTA
1 AAAATGGTGATTTTTGAAAGTTCGAGGGTA
* * * *
3551689 AAAAT-ATAATTTTGGAAAGTTCGAGGGTC
1 AAAATGGTGATTTTTGAAAGTTCGAGGGTA
3551718 AAAA
1 AAAA
3551722 CATAATTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
29 49 0.89
30 6 0.11
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (30 bp):
AAAATGGTGATTTTTGAAAGTTCGAGGGTA
Found at i:3551734 original size:30 final size:30
Alignment explanation
Indices: 3551668--3551735 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
3551658 CAAAATGGTG
*
3551668 ATTTTT-GAAAGTTCGAGGGTAAAAATATA
1 ATTTTTGGAAAGTTCGAGGGTAAAAACATA
*
3551697 A-TTTTGGAAAGTTCGAGGGTCAAAACATA
1 ATTTTTGGAAAGTTCGAGGGTAAAAACATA
3551726 ATTTTTGGAA
1 ATTTTTGGAA
3551736 GTTTAGGGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 4 0.11
29 23 0.66
30 8 0.23
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (30 bp):
ATTTTTGGAAAGTTCGAGGGTAAAAACATA
Found at i:3554652 original size:27 final size:29
Alignment explanation
Indices: 3554622--3554677 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
3554612 ACTTTCCTAT
*
3554622 AAATAGTAATA-C-ATAAAAATATTATTA
1 AAATAGTAATATCTAAAAAAATATTATTA
*
3554649 AAATTGTAATATCTTAAAAAAATATTATT
1 AAATAGTAATATC-TAAAAAAATATTATT
3554678 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 10 0.42
28 1 0.04
30 13 0.54
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (29 bp):
AAATAGTAATATCTAAAAAAATATTATTA
Found at i:3554746 original size:34 final size:34
Alignment explanation
Indices: 3554675--3554748 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
3554665 AAAAAATATT
*
3554675 ATTTTTATTAAATTAGATTTTGAATTGGATTTTA
1 ATTTTTATTAAATTAGATTTTGAATTGGATTTAA
* *
3554709 ATTTTTA-TAAATTATA-TTTGAGTATTGTATTTAA
1 ATTTTTATTAAATTAGATTTTGA--ATTGGATTTAA
3554743 ATTTTT
1 ATTTTT
3554749 TTATTCAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 5 0.14
33 8 0.23
34 22 0.63
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.58
Consensus pattern (34 bp):
ATTTTTATTAAATTAGATTTTGAATTGGATTTAA
Found at i:3555555 original size:21 final size:20
Alignment explanation
Indices: 3555529--3555567 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3555519 TCTGGTAGAA
3555529 AATAA-TAGCATATAGCAAAAC
1 AATAATTAG-ATATA-CAAAAC
3555550 AATAATTAGATATACAAA
1 AATAATTAGATATACAAA
3555568 TTTGAAACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 10 0.59
22 3 0.18
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.23
Consensus pattern (20 bp):
AATAATTAGATATACAAAAC
Done.