Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, whole genome shotgun sequence
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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 30 of 121
Found at i:5225595 original size:20 final size:20
Alignment explanation
Indices: 5225540--5225595 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
5225530 TTTTTACAAC
* **
5225540 AAAATTTAAAATAATTGTTT
1 AAAATTTAAAATTATTACTT
* *
5225560 AAAATTTAATACTATTACTT
1 AAAATTTAAAATTATTACTT
5225580 AAAATTTAAAATTATT
1 AAAATTTAAAATTATT
5225596 TCATTTCATT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAATTTAAAATTATTACTT
Found at i:5226073 original size:12 final size:12
Alignment explanation
Indices: 5226056--5226080 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5226046 AATAAAATTG
5226056 ATTTATATATCT
1 ATTTATATATCT
5226068 ATTTATATATCT
1 ATTTATATATCT
5226080 A
1 A
5226081 AACATATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATATATCT
Found at i:5229414 original size:20 final size:20
Alignment explanation
Indices: 5229376--5229414 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5229366 CGATTTTAAA
* *
5229376 ATTTGAGGTTTGGGGTTTTG
1 ATTTAAGGTTTGGGATTTTG
*
5229396 ATTTAAGGTTTTGGATTTT
1 ATTTAAGGTTTGGGATTTT
5229415 AGGGGTTTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (20 bp):
ATTTAAGGTTTGGGATTTTG
Found at i:5229423 original size:16 final size:16
Alignment explanation
Indices: 5229402--5229519 Score: 141
Period size: 16 Copynumber: 7.4 Consensus size: 16
5229392 TTTGATTTAA
5229402 GGTTTTGGATTTTAGG
1 GGTTTTGGATTTTAGG
*
5229418 GGTTTTGGATTTTAAG
1 GGTTTTGGATTTTAGG
*
5229434 GG-TTTGGATTTAAGG
1 GGTTTTGGATTTTAGG
* *
5229449 GATTTTAGATTTTAGG
1 GGTTTTGGATTTTAGG
* *
5229465 GATTTCGGATTTTA-G
1 GGTTTTGGATTTTAGG
*
5229480 GATTTTGGATTTTAAGG
1 GGTTTTGGATTTT-AGG
5229497 GGATTTTGGATTTTAGG
1 GG-TTTTGGATTTTAGG
5229514 GGTTTT
1 GGTTTT
5229520 AGAAACCTAG
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
15 25 0.28
16 45 0.51
17 7 0.08
18 11 0.12
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.48
Consensus pattern (16 bp):
GGTTTTGGATTTTAGG
Found at i:5229440 original size:31 final size:32
Alignment explanation
Indices: 5229387--5229519 Score: 152
Period size: 31 Copynumber: 4.2 Consensus size: 32
5229377 TTTGAGGTTT
*
5229387 GGGGTTTT-GA-TTTAA-GGTTTTGGATTTTA
1 GGGGTTTTGGATTTTAAGGGATTTGGATTTTA
*
5229416 GGGGTTTTGGATTTTAAGGG-TTTGGATTTAA
1 GGGGTTTTGGATTTTAAGGGATTTGGATTTTA
* *
5229447 GGGATTTTAGATTTT-AGGGATTTCGGATTTTA
1 GGGGTTTTGGATTTTAAGGGATTT-GGATTTTA
*
5229479 -GGATTTTGGATTTTAAGGGGATTTTGGATTTTA
1 GGGGTTTTGGATTTTAA-GGGA-TTTGGATTTTA
5229512 GGGGTTTT
1 GGGGTTTT
5229520 AGAAACCTAG
Statistics
Matches: 89, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
29 8 0.09
30 6 0.07
31 44 0.49
32 10 0.11
33 12 0.13
34 9 0.10
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.48
Consensus pattern (32 bp):
GGGGTTTTGGATTTTAAGGGATTTGGATTTTA
Found at i:5229955 original size:17 final size:18
Alignment explanation
Indices: 5229918--5229959 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
5229908 CATCAATATT
*
5229918 TAAAAAAAATACTTAAAA
1 TAAAAAAAATACATAAAA
*
5229936 TAAAAAAAATA-ATAATA
1 TAAAAAAAATACATAAAA
5229953 TAAAAAA
1 TAAAAAA
5229960 TTTTAGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (18 bp):
TAAAAAAAATACATAAAA
Found at i:5230375 original size:13 final size:13
Alignment explanation
Indices: 5230357--5230381 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5230347 CAGCCACCTG
5230357 GGTCACTGTCGGC
1 GGTCACTGTCGGC
5230370 GGTCACTGTCGG
1 GGTCACTGTCGG
5230382 TAGTTTTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.28, G:0.40, T:0.24
Consensus pattern (13 bp):
GGTCACTGTCGGC
Found at i:5230633 original size:20 final size:19
Alignment explanation
Indices: 5230601--5230638 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5230591 GAAGACTGTT
5230601 TGTTTTTATTTTTTGTTTC
1 TGTTTTTATTTTTTGTTTC
*
5230620 TGTTTTTGTGTTTTTGTTT
1 TGTTTTTAT-TTTTTGTTT
5230639 GGGTATGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.03, C:0.03, G:0.16, T:0.79
Consensus pattern (19 bp):
TGTTTTTATTTTTTGTTTC
Found at i:5231296 original size:22 final size:23
Alignment explanation
Indices: 5231268--5231320 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
5231258 TTATGCCCAA
5231268 AGGTCTTA-AAAATCAT-TCCCGG
1 AGGTCTTACAAAATCATGT-CCGG
*
5231290 AGGTCTTACAAAATTATGTCCGG
1 AGGTCTTACAAAATCATGTCCGG
5231313 AGGTCTTA
1 AGGTCTTA
5231321 TAGAATCGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 8 0.29
23 19 0.68
24 1 0.04
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (23 bp):
AGGTCTTACAAAATCATGTCCGG
Found at i:5231479 original size:88 final size:87
Alignment explanation
Indices: 5231298--5231495 Score: 263
Period size: 88 Copynumber: 2.3 Consensus size: 87
5231288 GGAGGTCTTA
* * * *
5231298 CAAAATTATGTCCGGAGGTCTTATAGAATCGACTGGATAACATCGTAAGTCAAAAGATAAGGAAT
1 CAAAATTATGCCCAGAGGTCTTACAGAATCGACTGGATAACATCGCAAGTCAAAAGATAAGGAAT
***
5231363 CGATCGGGATAACACCGTGAAT
66 CGATCGGGATAACACCACCAAT
* *
5231385 CAAAATTATGCCTAGAGGTCTTACAGAATCGACTGGGATAACA-CAGCAAGTCGAAAGATAAGGA
1 CAAAATTATGCCCAGAGGTCTTACAGAATCGACT-GGATAACATC-GCAAGTCAAAAGATAAGGA
*
5231449 ATCGATCGGGATAACATCACCAAT
64 ATCGATCGGGATAACACCACCAAT
* *
5231473 CGAAATTATGCCCAAAGGTCTTA
1 CAAAATTATGCCCAGAGGTCTTA
5231496 GAAATCATGT
Statistics
Matches: 96, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
87 31 0.32
88 65 0.68
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (87 bp):
CAAAATTATGCCCAGAGGTCTTACAGAATCGACTGGATAACATCGCAAGTCAAAAGATAAGGAAT
CGATCGGGATAACACCACCAAT
Found at i:5231617 original size:22 final size:22
Alignment explanation
Indices: 5231583--5231626 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5231573 ATCGTGAATC
*
5231583 AAAATTATACCCGGAGGTCTTA
1 AAAATCATACCCGGAGGTCTTA
*
5231605 AAAATCATGCCCGGAGGTCTTA
1 AAAATCATACCCGGAGGTCTTA
5231627 CAGAATTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (22 bp):
AAAATCATACCCGGAGGTCTTA
Found at i:5231809 original size:110 final size:110
Alignment explanation
Indices: 5231399--5232028 Score: 682
Period size: 109 Copynumber: 5.8 Consensus size: 110
5231389 ATTATGCCTA
* ** *
5231399 GAGGTCTTACAGAATCGACTGGGATAACA-CAGCAAGTCGAAAGATAAGGAATCGATCGGGATAA
1 GAGGTCTTACAGAATCGACTGGGATAACATCA-CAAGTCGAAAAATAAAAAATCGATCGAGATAA
* * * * * *
5231463 CATCACCAATCGAAATTATGC-CCAAAGGTCTTAGAAATCATGTCCG
65 CACCGCGAATCAAAATTATGCTCGAAA-GTCTTAGAAATCATGCCCG
* * * * * * * *
5231509 AAAGCCTTATAAAATCGACTGGGATAACATCA-TAGTCGAAAGATAAAAAATTGATCGAGATAAC
1 GAGGTCTTACAGAATCGACTGGGATAACATCACAAGTCGAAAAATAAAAAATCGATCGAGATAAC
* * * * * * *
5231573 ATCGTGAATCAAAATTATACCCGGAGGTCTTAAAAATCATGCCCG
66 ACCGCGAATCAAAATTATGCTCGAAAGTCTTAGAAATCATGCCCG
* * ** * * *
5231618 GAGGTCTTACAGAATTGATTGGGATAACATTGCAATTCG-AAAATAAAGAATCGATCGGGATAAC
1 GAGGTCTTACAGAATCGACTGGGATAACATCACAAGTCGAAAAATAAAAAATCGATCGAGATAAC
5231682 ACCGCGAATCAAAATTATGCTCGAAAGTCTTAGAAATCATGCCCG
66 ACCGCGAATCAAAATTATGCTCGAAAGTCTTAGAAATCATGCCCG
** * * *
5231727 GAGGTCTTACAGAATCGACTAAGATAACACCACAAGTCAAAAAATAAAAAATCGATCAAGATAAC
1 GAGGTCTTACAGAATCGACTGGGATAACATCACAAGTCGAAAAATAAAAAATCGATCGAGATAAC
*
5231792 ACCGCGAATCAAAATTATGCTCGAAAGTCTTAGAAATCATGCCCA
66 ACCGCGAATCAAAATTATGCTCGAAAGTCTTAGAAATCATGCCCG
* * *
5231837 GAGGTCTTACAGAATCGATTGGGATAACATCAC-AGTCGAAAGAT-AAAAATTGATCTG-GATAA
1 GAGGTCTTACAGAATCGACTGGGATAACATCACAAGTCGAAAAATAAAAAATCGATC-GAGATAA
* * * *
5231899 TACCGCGAATCAAAATTATGTTCGGAGGTCTTA-AAATCATGCCCG
65 CACCGCGAATCAAAATTATGCTCGAAAGTCTTAGAAATCATGCCCG
* * ** * * * * *
5231944 GAGGTCTTACAGAATCGACTGAGATAACACCGTAAGTCAAAAAATAAGAGATCAATCGAGAAAAC
1 GAGGTCTTACAGAATCGACTGGGATAACATCACAAGTCGAAAAATAAAAAATCGATCGAGATAAC
*
5232009 ACCGCGAATTAAAATTATGC
66 ACCGCGAATCAAAATTATGC
5232029 CTAGAGGTCT
Statistics
Matches: 429, Mismatches: 83, Indels: 17
0.81 0.16 0.03
Matches are distributed among these distances:
107 39 0.09
108 54 0.13
109 209 0.49
110 125 0.29
111 2 0.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.22
Consensus pattern (110 bp):
GAGGTCTTACAGAATCGACTGGGATAACATCACAAGTCGAAAAATAAAAAATCGATCGAGATAAC
ACCGCGAATCAAAATTATGCTCGAAAGTCTTAGAAATCATGCCCG
Found at i:5231831 original size:219 final size:218
Alignment explanation
Indices: 5231386--5232029 Score: 785
Period size: 219 Copynumber: 2.9 Consensus size: 218
5231376 ACCGTGAATC
* * * * *
5231386 AAAATTATGCCTAGAGGTCTTACAGAATCGACTGGGATAACACAGCAAGTCGAAAGATAAGGAAT
1 AAAATCATGCCCAGAGGTCTTACAGAATCGATTGGGATAACA-TGCAAGTCGAAAGATAAAGAAT
* * * * * * * * *
5231451 CGATCGGGATAACATCACCAATCGAAATTATGC-CCAAAGGTCTTAGAAATCATGTCCGAAAGCC
65 CGATCGGGATAACACCGCGAATCAAAATTATGCTCGAAA-GTCTTAGAAATCATGCCCGGAGGTC
* * * * * * * * * *
5231515 TTATAAAATCGACTGGGATAACATCATAGTCGAAAGATAAAAAATTGATCGAGATAACATCGTGA
129 TTACAGAATCGACTGAGATAACACCAAAGTCAAAAAATAAAAAATCGATCGAGATAACACCGCGA
* * *
5231580 ATCAAAATTATACCCGGAGGTCTTA
194 ATCAAAATTATGCCCGAAAGTCTTA
* * *
5231605 AAAATCATGCCCGGAGGTCTTACAGAATTGATTGGGATAACATTGCAATTCGAAA-ATAAAGAAT
1 AAAATCATGCCCAGAGGTCTTACAGAATCGATTGGGATAACA-TGCAAGTCGAAAGATAAAGAAT
5231669 CGATCGGGATAACACCGCGAATCAAAATTATGCTCGAAAGTCTTAGAAATCATGCCCGGAGGTCT
65 CGATCGGGATAACACCGCGAATCAAAATTATGCTCGAAAGTCTTAGAAATCATGCCCGGAGGTCT
* *
5231734 TACAGAATCGACTAAGATAACACCACAAGTCAAAAAATAAAAAATCGATCAAGATAACACCGCGA
130 TACAGAATCGACTGAGATAACACCA-AAGTCAAAAAATAAAAAATCGATCGAGATAACACCGCGA
*
5231799 ATCAAAATTATGCTCGAAAGTCTTA
194 ATCAAAATTATGCCCGAAAGTCTTA
*
5231824 GAAATCATGCCCAGAGGTCTTACAGAATCGATTGGGATAACAT-CACAGTCGAAAGATAAA-AAT
1 AAAATCATGCCCAGAGGTCTTACAGAATCGATTGGGATAACATGCA-AGTCGAAAGATAAAGAAT
* * * * * *
5231887 TGATCTGGATAATACCGCGAATCAAAATTATGTTCGGAGGTCTTA-AAATCATGCCCGGAGGTCT
65 CGATCGGGATAACACCGCGAATCAAAATTATGCTCGAAAGTCTTAGAAATCATGCCCGGAGGTCT
* * * * *
5231951 TACAGAATCGACTGAGATAACACCGTAAGTCAAAAAATAAGAGATCAATCGAGAAAACACCGCGA
130 TACAGAATCGACTGAGATAACACC-AAAGTCAAAAAATAAAAAATCGATCGAGATAACACCGCGA
*
5232016 ATTAAAATTATGCC
194 ATCAAAATTATGCC
5232030 TAGAGGTCTT
Statistics
Matches: 367, Mismatches: 53, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
217 90 0.25
218 129 0.35
219 148 0.40
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (218 bp):
AAAATCATGCCCAGAGGTCTTACAGAATCGATTGGGATAACATGCAAGTCGAAAGATAAAGAATC
GATCGGGATAACACCGCGAATCAAAATTATGCTCGAAAGTCTTAGAAATCATGCCCGGAGGTCTT
ACAGAATCGACTGAGATAACACCAAAGTCAAAAAATAAAAAATCGATCGAGATAACACCGCGAAT
CAAAATTATGCCCGAAAGTCTTA
Found at i:5232393 original size:41 final size:41
Alignment explanation
Indices: 5232308--5232403 Score: 124
Period size: 41 Copynumber: 2.3 Consensus size: 41
5232298 AGGTTCCCTC
* *
5232308 TAAACAAAGGCTTTGAAATCTTGATTGAAATTGGTTCTTAT
1 TAAACAGAGGCTTTGAAATCTTGATTGAAATCGGTTCTTAT
*
5232349 TAAACAGAGGCTTTGAAATCTTGATTGAGAA-CGGTTGC-TCT
1 TAAACAGAGGCTTTGAAATCTTGATTGA-AATCGGTT-CTTAT
*
5232390 TAAACAGAGACTTT
1 TAAACAGAGGCTTT
5232404 AAAACTTTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
41 46 0.94
42 3 0.06
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.34
Consensus pattern (41 bp):
TAAACAGAGGCTTTGAAATCTTGATTGAAATCGGTTCTTAT
Found at i:5234162 original size:25 final size:25
Alignment explanation
Indices: 5234134--5234181 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
5234124 ATTTTATTTG
5234134 TTTTTT-TCTCTTTTTTTTTTTTTAC
1 TTTTTTGT-TCTTTTTTTTTTTTTAC
5234159 TTTTTTGTTCTTTTTTTTTTTTT
1 TTTTTTGTTCTTTTTTTTTTTTT
5234182 TTTTGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.02, C:0.08, G:0.02, T:0.88
Consensus pattern (25 bp):
TTTTTTGTTCTTTTTTTTTTTTTAC
Found at i:5234164 original size:27 final size:28
Alignment explanation
Indices: 5234125--5234183 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
5234115 AATATGTCCA
* *
5234125 TTTTATTTGTTTTTTTCTCTTTTTTTTT
1 TTTTACTTGTTTTGTTCTCTTTTTTTTT
*
5234153 TTTTACTT-TTTTGTTCTTTTTTTTTTT
1 TTTTACTTGTTTTGTTCTCTTTTTTTTT
5234180 TTTT
1 TTTT
5234184 TTGTGATACC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.03, C:0.07, G:0.03, T:0.86
Consensus pattern (28 bp):
TTTTACTTGTTTTGTTCTCTTTTTTTTT
Found at i:5234174 original size:21 final size:21
Alignment explanation
Indices: 5234148--5234187 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5234138 TTTCTCTTTT
5234148 TTTTTTTTTACTTTTTTGTTC
1 TTTTTTTTTACTTTTTTGTTC
**
5234169 TTTTTTTTTTTTTTTTTGT
1 TTTTTTTTTACTTTTTTGT
5234188 GATACCTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.05, G:0.05, T:0.88
Consensus pattern (21 bp):
TTTTTTTTTACTTTTTTGTTC
Found at i:5234205 original size:1 final size:1
Alignment explanation
Indices: 5234134--5234185 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
5234124 ATTTTATTTG
* * ** * *
5234134 TTTTTTTCTCTTTTTTTTTTTTTACTTTTTTGTTCTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5234186 GTGATACCTC
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.02, C:0.08, G:0.02, T:0.88
Consensus pattern (1 bp):
T
Found at i:5240761 original size:30 final size:30
Alignment explanation
Indices: 5240665--5240800 Score: 104
Period size: 30 Copynumber: 4.6 Consensus size: 30
5240655 TGGAGATTCG
* *
5240665 GATTTTAAGGGTTTGGA-TTT-AAGTTTTGAG
1 GATTTT-AGGGTTTTGATTTTAAAG-TTTGAA
* *
5240695 GATTTTAGGG-TTTGGTTTTAAAGTATGAA
1 GATTTTAGGGTTTTGATTTTAAAGTTTGAA
* *
5240724 -AGGTTTAGGGTTTTGATTTTAGAGTTTGAA
1 GA-TTTTAGGGTTTTGATTTTAAAGTTTGAA
* * *
5240754 GATTTTAGGGTTTCGGTTTTAAAATTTG-A
1 GATTTTAGGGTTTTGATTTTAAAGTTTGAA
* *
5240783 G-GTTTGGGGTTTTGATTT
1 GATTTTAGGGTTTTGATTT
5240801 AAGGGTTTGA
Statistics
Matches: 84, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
28 17 0.20
29 20 0.24
30 46 0.55
31 1 0.01
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.48
Consensus pattern (30 bp):
GATTTTAGGGTTTTGATTTTAAAGTTTGAA
Found at i:5240809 original size:58 final size:58
Alignment explanation
Indices: 5240672--5240811 Score: 176
Period size: 58 Copynumber: 2.4 Consensus size: 58
5240662 TCGGATTTTA
* * * *
5240672 AGGGTTTGGATTTAA-GTTTTGAGGATTTTAGGGTTTGGTTTTAAAGTATGAAAGGTTT
1 AGGGTTTTGATTTAAGGGTTTGAAGATTTTAGGGTTTGGTTTTAAAATATG-AAGGTTT
* * *
5240730 AGGGTTTTGATTTTAGAGTTTGAAGATTTTAGGGTTTCGGTTTTAAAATTTG-AGGTTT
1 AGGGTTTTGATTTAAGGGTTTGAAGATTTTAGGGTTT-GGTTTTAAAATATGAAGGTTT
*
5240788 GGGGTTTTGATTTAAGGGTTTGAA
1 AGGGTTTTGATTTAAGGGTTTGAA
5240812 TTTAAGAGTT
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 40 0.57
59 18 0.26
60 12 0.17
ACGTcount: A:0.23, C:0.01, G:0.31, T:0.46
Consensus pattern (58 bp):
AGGGTTTTGATTTAAGGGTTTGAAGATTTTAGGGTTTGGTTTTAAAATATGAAGGTTT
Found at i:5240875 original size:16 final size:16
Alignment explanation
Indices: 5240835--5240895 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
5240825 AGGTTTGGGA
*
5240835 TTTCGAATTTTATGAGG
1 TTTCGAATTTTA-GGGG
* *
5240852 TTTTGAATGTTAGGGG
1 TTTCGAATTTTAGGGG
5240868 TTTCGAATTTTAGGGG
1 TTTCGAATTTTAGGGG
*
5240884 TTTCGGATTTTA
1 TTTCGAATTTTA
5240896 AGGGATTTGG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
16 28 0.74
17 10 0.26
ACGTcount: A:0.20, C:0.05, G:0.28, T:0.48
Consensus pattern (16 bp):
TTTCGAATTTTAGGGG
Found at i:5240907 original size:16 final size:17
Alignment explanation
Indices: 5240863--5240918 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 17
5240853 TTTGAATGTT
* *
5240863 AGGGGTTTCGAATTTT-
1 AGGGATTTCGGATTTTA
*
5240879 AGGGGTTTCGGATTTTA
1 AGGGATTTCGGATTTTA
5240896 AGGGATTT-GGA-TTTA
1 AGGGATTTCGGATTTTA
5240911 AGGGATTT
1 AGGGATTT
5240919 TAGGAGTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 12 0.32
16 18 0.49
17 7 0.19
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.41
Consensus pattern (17 bp):
AGGGATTTCGGATTTTA
Found at i:5240960 original size:40 final size:40
Alignment explanation
Indices: 5240874--5240961 Score: 106
Period size: 41 Copynumber: 2.2 Consensus size: 40
5240864 GGGGTTTCGA
* **
5240874 ATTTTAGGGGTTTCGGATTTTAAGGGATTTGGATTTAAGGG
1 ATTTTAGGAGTTTCAAATTTTAA-GGATTTGGATTTAAGGG
*
5240915 ATTTTAGGAGTTTCAAATTTTAA-GATTTTGGATTTTAGGG
1 ATTTTAGGAGTTTCAAATTTTAAGGA-TTTGGATTTAAGGG
*
5240955 GTTTTAG
1 ATTTTAG
5240962 AAATCTAGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 2 0.05
40 19 0.46
41 20 0.49
ACGTcount: A:0.24, C:0.02, G:0.28, T:0.45
Consensus pattern (40 bp):
ATTTTAGGAGTTTCAAATTTTAAGGATTTGGATTTAAGGG
Found at i:5242787 original size:13 final size:13
Alignment explanation
Indices: 5242769--5242806 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
5242759 ATCAGAAATA
5242769 AGTGATGAGTCAT
1 AGTGATGAGTCAT
5242782 AGTGATGAGTCAT
1 AGTGATGAGTCAT
5242795 AGTGATGAGTCA
1 AGTGATGAGTCA
5242807 CCTTACTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.29
Consensus pattern (13 bp):
AGTGATGAGTCAT
Found at i:5245600 original size:16 final size:16
Alignment explanation
Indices: 5245579--5245610 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5245569 TGTTGCTTTA
*
5245579 TAAAAAAAGTTATAAT
1 TAAAAAAAATTATAAT
5245595 TAAAAAAAATTATAAT
1 TAAAAAAAATTATAAT
5245611 AAATTATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
TAAAAAAAATTATAAT
Found at i:5245613 original size:15 final size:15
Alignment explanation
Indices: 5245578--5245613 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
5245568 ATGTTGCTTT
*
5245578 ATAAAAAAAGTTATA
1 ATAAAAAAAATTATA
5245593 ATTAAAAAAAATTATA
1 A-TAAAAAAAATTATA
5245609 ATAAA
1 ATAAA
5245614 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
ATAAAAAAAATTATA
Found at i:5248967 original size:37 final size:37
Alignment explanation
Indices: 5248926--5248997 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
5248916 TTTTAAATTA
*
5248926 AATTTTGATTTTATTCGAATTAAATCGAATCAAATCG
1 AATTTTGATTTTATTCAAATTAAATCGAATCAAATCG
* * * *
5248963 AATTTTTATTTTATTTAAATTGAATCGAATTAAAT
1 AATTTTGATTTTATTCAAATTAAATCGAATCAAAT
5248998 TTTATTAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (37 bp):
AATTTTGATTTTATTCAAATTAAATCGAATCAAATCG
Found at i:5249072 original size:13 final size:13
Alignment explanation
Indices: 5249050--5249088 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5249040 AAAATTTTTA
*
5249050 ATTTTTATATATT
1 ATTTTAATATATT
**
5249063 ATTTTAATATAAA
1 ATTTTAATATATT
5249076 ATTTTAATATATT
1 ATTTTAATATATT
5249089 TAAATAAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTAATATATT
Found at i:5249104 original size:31 final size:34
Alignment explanation
Indices: 5249066--5249138 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 34
5249056 ATATATTATT
*
5249066 TTAATATAAAATT-TTAATATA-TTTA-AATAAA
1 TTAATATAAAATTATTAATATATTTTATAAAAAA
* *
5249097 TTAATATAAAATTATTATTTTATTTTATAAAAAA
1 TTAATATAAAATTATTAATATATTTTATAAAAAA
5249131 TTAATATA
1 TTAATATA
5249139 TATATATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 13 0.36
32 6 0.17
33 4 0.11
34 13 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
TTAATATAAAATTATTAATATATTTTATAAAAAA
Found at i:5258045 original size:15 final size:15
Alignment explanation
Indices: 5258016--5258047 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
5258006 CAAATATTCA
5258016 TATAAAATAATTTTT
1 TATAAAATAATTTTT
5258031 TATAATAATAATTTTT
1 TATAA-AATAATTTTT
5258047 T
1 T
5258048 TCTTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAAAATAATTTTT
Found at i:5258077 original size:11 final size:10
Alignment explanation
Indices: 5258050--5258085 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
5258040 AATTTTTTTC
5258050 TTAAAATATA
1 TTAAAATATA
5258060 -TAAAATATA
1 TTAAAATATA
5258069 TTAATAATATA
1 TTAA-AATATA
5258080 TTAAAA
1 TTAAAA
5258086 AAATTTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.38
10 5 0.21
11 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TTAAAATATA
Found at i:5258215 original size:15 final size:15
Alignment explanation
Indices: 5258178--5258206 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5258168 TTACATGTTC
5258178 TTATTATAACATTTT
1 TTATTATAACATTTT
5258193 TTATTATAA-ATTTT
1 TTATTATAACATTTT
5258207 ATTTTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTATAACATTTT
Found at i:5258514 original size:9 final size:9
Alignment explanation
Indices: 5258487--5258520 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
5258477 CTAAAAATCT
5258487 TTTTATATA
1 TTTTATATA
5258496 TTATTAATATA
1 TT-TT-ATATA
5258507 TTTTATATA
1 TTTTATATA
5258516 TTTTA
1 TTTTA
5258521 AGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 12 0.52
10 4 0.17
11 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTATATA
Found at i:5258654 original size:253 final size:243
Alignment explanation
Indices: 5258097--5258701 Score: 806
Period size: 253 Copynumber: 2.4 Consensus size: 243
5258087 AATTTTAGGT
* * * * *
5258097 TCAATATATTAAAA-AAAATTCACAATCACAAATAATATTTTTTTCAATCAAATATTTTTT-CTG
1 TCAATATATAAAAACAAAATTCACAATTATAAATAACATTTTTTTCAACCAAATATTTTTTCCT-
*
5258160 ATTACATGTTACATGTTCTTATTATAACA-TTTTTTATTATAAATTTTATTTTTATATATTGCAC
65 ATTATATGTTACATGTTCTTATTATAACATTTTTTTATTATAAATTTTATTTTTATATATTGCAC
5258224 CTAAAAATCTTTTTATATATTACTAATATATTTTTATATTTTAAGAAAAAATTATTATTATAAAT
130 CTAAAAATCTTTTTATATATTACTAATATATTTTTATATTTTAAGAAAAAATTATTATTATAAAT
* *
5258289 AATTATTTTATGTGAGTATTTGCTTATTATATTTACATTTTCTTATAGA
195 AATTATTTTATATGAGTATTTGCTTATTATATTTACATGTTCTTATAGA
*
5258338 TGCAATATATAAAAACAAAATTCACAATTATAAATAACATATTTTTCAACCAAATATTTTTTTCC
1 T-CAATATATAAAAACAAAATTCACAATTATAAATAACATTTTTTTCAACCAAATA-TTTTTTCC
* *
5258403 TATTATATGTCACATGTTCTTATTATAACATTTTTTTAATTAAAATTTTTAAATTTTGTTTTTAT
64 TATTATATGTTACATGTTCTTATTATAACATTTTTTT-ATT---A----TAAATTTTATTTTTAT
*
5258468 ATATTGCACCTAAAAATCTTTTTATATATTATTAATATATTTTATATATTTTAAGAAAAAAATTA
121 ATATTGCACCTAAAAATCTTTTTATATATTACTAATATATTTT-TATATTTTAAG-AAAAAATTA
* *
5258533 TTATTATAAATAATTATTTTATATGAGTATTTGCTTATTATATGTTGCATGTTCTTAT-TA
184 TTATTATAAATAATTATTTTATATGAGTATTTGCTTATTATAT-TTACATGTTCTTATAGA
* *** ** * *
5258593 T-AATATTTTTTTATTATAATTCACAATTATAAATAACATTTTTTTCAACCAAATATTTTTTCTT
1 TCAATA-TATAAAAACAAAATTCACAATTATAAATAACATTTTTTTCAACCAAATATTTTTTCCT
* *
5258657 ATTATATGTTACATATTCTTATTATAATATTTTTTCTTATTATAA
65 ATTATATGTTACATGTTCTTATTATAACA-TTTTT-TTATTATAA
5258702 TTCACGATTA
Statistics
Matches: 319, Mismatches: 26, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
241 1 0.00
242 12 0.04
243 35 0.11
244 33 0.10
245 8 0.03
246 3 0.01
247 3 0.01
249 1 0.00
251 1 0.00
253 95 0.30
254 60 0.19
255 55 0.17
256 12 0.04
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.50
Consensus pattern (243 bp):
TCAATATATAAAAACAAAATTCACAATTATAAATAACATTTTTTTCAACCAAATATTTTTTCCTA
TTATATGTTACATGTTCTTATTATAACATTTTTTTATTATAAATTTTATTTTTATATATTGCACC
TAAAAATCTTTTTATATATTACTAATATATTTTTATATTTTAAGAAAAAATTATTATTATAAATA
ATTATTTTATATGAGTATTTGCTTATTATATTTACATGTTCTTATAGA
Found at i:5258666 original size:88 final size:91
Alignment explanation
Indices: 5258566--5258794 Score: 392
Period size: 91 Copynumber: 2.5 Consensus size: 91
5258556 TGAGTATTTG
*
5258566 CTTATTATATGTTGCATGTTCTTATTATAATA-TTTTT-TTATTATAATTCACAATTATAAATAA
1 CTTATTATATGTTACATGTTCTTATTATAATATTTTTTCTTATTATAATTCACAATTATAAATAA
5258629 CATT-TTTTTCAACCAAATATTTTTT
66 CATTCTTTTTCAACCAAATATTTTTT
* *
5258654 CTTATTATATGTTACATATTCTTATTATAATATTTTTTCTTATTATAATTCACGATTATAAATAA
1 CTTATTATATGTTACATGTTCTTATTATAATATTTTTTCTTATTATAATTCACAATTATAAATAA
5258719 CATTCTTTTTCAACCAAATATTTTTT
66 CATTCTTTTTCAACCAAATATTTTTT
* *
5258745 CTTATTATATGTTACATGTTTTTATTATAACATTTTTTCTTATTATAATT
1 CTTATTATATGTTACATGTTCTTATTATAATATTTTTTCTTATTATAATT
5258795 TTGAATTTTG
Statistics
Matches: 132, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
88 30 0.23
89 5 0.04
90 29 0.22
91 68 0.52
ACGTcount: A:0.32, C:0.10, G:0.03, T:0.55
Consensus pattern (91 bp):
CTTATTATATGTTACATGTTCTTATTATAATATTTTTTCTTATTATAATTCACAATTATAAATAA
CATTCTTTTTCAACCAAATATTTTTT
Found at i:5258695 original size:18 final size:18
Alignment explanation
Indices: 5258644--5258702 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
5258634 TTTTCAACCA
5258644 AATATTTTTTCTTATTAT
1 AATATTTTTTCTTATTAT
* *
5258662 -ATGTTACATATTCTTATTAT
1 AATATT---TTTTCTTATTAT
5258682 AATATTTTTTCTTATTAT
1 AATATTTTTTCTTATTAT
5258700 AAT
1 AAT
5258703 TCACGATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 4 0.12
18 14 0.42
20 11 0.33
21 4 0.12
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
AATATTTTTTCTTATTAT
Found at i:5258935 original size:163 final size:155
Alignment explanation
Indices: 5258745--5259062 Score: 458
Period size: 163 Copynumber: 2.0 Consensus size: 155
5258735 AATATTTTTT
* * *
5258745 CTTATTATATGTTACATGTTTTTATTATAACATTTTTTCTTATTATAATTTTGAATTTTGCTTTT
1 CTTACTATATGTTACATGTTATTATTATAACATTTTTTCTTATTATAATTGTGAATTTTGCTTTT
*
5258810 ATATATTGCAACTAAAAATCTTTTTTATATATTATTAATGTATTTTATATATTTTAAGAAAAAA-
66 ATATATTGCAACTAAAAATCTCTTTT-T-TA-TATT-AT-TA----ATATATTTTAAGAAAAAAT
5258874 ACTATTATAAATAATTATTTTATGTGAGTATTTG
122 ACTATTATAAATAATTATTTTATGTGAGTATTTG
* *
5258908 CTTACTATATTTTACATGTTATTATTATAACATTTTTTCTTATTATAATTGTGAATTTTGTTTTT
1 CTTACTATATGTTACATGTTATTATTATAACATTTTTTCTTATTATAATTGTGAATTTTGCTTTT
* * *
5258973 ATATATTTCATCTAAAAATCTCTTTTTTATATTATTAATATATTTTAAGAAAAAATTATTATTAT
66 ATATATTGCAACTAAAAATCTCTTTTTTATATTATTAATATATTTTAAGAAAAAA-TACTATTAT
5259038 AAATAATTATTTTATGTGAGTATTT
130 AAATAATTATTTTATGTGAGTATTT
5259063 AAAGATATAA
Statistics
Matches: 144, Mismatches: 9, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
154 18 0.12
156 32 0.22
158 2 0.01
159 2 0.01
160 4 0.03
161 2 0.01
162 1 0.01
163 83 0.58
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (155 bp):
CTTACTATATGTTACATGTTATTATTATAACATTTTTTCTTATTATAATTGTGAATTTTGCTTTT
ATATATTGCAACTAAAAATCTCTTTTTTATATTATTAATATATTTTAAGAAAAAATACTATTATA
AATAATTATTTTATGTGAGTATTTG
Found at i:5271054 original size:29 final size:29
Alignment explanation
Indices: 5271022--5271077 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
5271012 AAAATTTAAT
*
5271022 AATTATTTAAATTGTT-AATATTTTATTAC
1 AATTAATTAAATT-TTAAATATTTTATTAC
*
5271051 AATTAATTAAGTTTTAAATATTTTATT
1 AATTAATTAAATTTTAAATATTTTATT
5271078 TTAAATCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (29 bp):
AATTAATTAAATTTTAAATATTTTATTAC
Found at i:5271216 original size:15 final size:16
Alignment explanation
Indices: 5271196--5271225 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5271186 ATAAAATTTT
5271196 TTTCTTTT-CTTAATA
1 TTTCTTTTGCTTAATA
5271211 TTTCTTTTGCTTAAT
1 TTTCTTTTGCTTAAT
5271226 GCAATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.13, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTCTTTTGCTTAATA
Found at i:5273861 original size:23 final size:23
Alignment explanation
Indices: 5273831--5273874 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
5273821 TTTGATAAAA
5273831 TTTTTTAAAATTT-ATATATAAT
1 TTTTTTAAAATTTAATATATAAT
5273853 TTTTATTAAAATTTAATATATA
1 TTTT-TTAAAATTTAATATATA
5273875 TTAGTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 9 0.45
24 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTTTAAAATTTAATATATAAT
Found at i:5274735 original size:12 final size:12
Alignment explanation
Indices: 5274687--5274746 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 12
5274677 AAATGTATTT
5274687 TAATTTTTTTAA
1 TAATTTTTTTAA
5274699 -AATTTTTTATAA
1 TAATTTTTT-TAA
* *
5274711 GTGAAATTATTTAA
1 -T-AATTTTTTTAA
*
5274725 TTATTTTTTT-A
1 TAATTTTTTTAA
5274736 TAATTTTTTTA
1 TAATTTTTTTA
5274747 CATTTTATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
11 18 0.49
12 9 0.24
13 1 0.03
14 3 0.08
15 6 0.16
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (12 bp):
TAATTTTTTTAA
Found at i:5274771 original size:18 final size:18
Alignment explanation
Indices: 5274732--5274772 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5274722 TAATTATTTT
* * *
5274732 TTTATAATTTTTTTACAT
1 TTTATAATTTTTTAAAAA
5274750 TTTATAATTTTTTAAAAA
1 TTTATAATTTTTTAAAAA
5274768 TTTAT
1 TTTAT
5274773 TTTCAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATAATTTTTTAAAAA
Found at i:5274932 original size:18 final size:17
Alignment explanation
Indices: 5274877--5274932 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
5274867 TAAAATGAAT
5274877 TTTTGAAAAAATTTATAA
1 TTTTG-AAAAATTTATAA
* *
5274895 TCTTGCAAAAA--TATAT
1 TTTTG-AAAAATTTATAA
5274911 TTTTGAAAAGATTTATAA
1 TTTTGAAAA-ATTTATAA
5274929 TTTT
1 TTTT
5274933 TTGAAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 4 0.13
16 9 0.30
18 17 0.57
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (17 bp):
TTTTGAAAAATTTATAA
Found at i:5274940 original size:34 final size:33
Alignment explanation
Indices: 5274852--5274958 Score: 105
Period size: 34 Copynumber: 3.3 Consensus size: 33
5274842 TTTTTTTTCT
*
5274852 AAAATTTA-ACTTTTTTAAAATGA-ATTTTTGAA
1 AAAATTTATAATTTTTTAAAAT-ATATTTTTGAA
***
5274884 AAAATTTATAATCTTGCAAAAATATATTTTTGAA
1 AAAATTTATAAT-TTTTTAAAATATATTTTTGAA
* *
5274918 AAGATTTATAATTTTTTGAAAATTTA-TTTT-AA
1 AAAATTTATAATTTTTT-AAAATATATTTTTGAA
5274950 AAAATTTAT
1 AAAATTTAT
5274959 GTGAAAGAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
32 18 0.30
33 9 0.15
34 34 0.56
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (33 bp):
AAAATTTATAATTTTTTAAAATATATTTTTGAA
Found at i:5281433 original size:106 final size:104
Alignment explanation
Indices: 5281246--5281455 Score: 282
Period size: 106 Copynumber: 2.0 Consensus size: 104
5281236 GAAGTGACAA
*
5281246 AAGCTTTTAAAGTGTGAATTATCCTTTTTAAATTCATTTTTAATTTATTTGTTGATATGACACTT
1 AAGCTTTTAAAGTGTGAATTATCCTTTTTAAATCCATTTTTAATTTATTTGTTGATATGACACTT
*
5281311 GACTATGACCCCAGCAA-CTATGATAGGAAGCTCATAACT
66 GACTATGACCCCAGCAAGC-ACGATAGGAAGCTCATAACT
* * *
5281350 AAGCTTTTAAAGTGTGATTTATCCCCTTTTT-AATCCTTTTTTTAATTTATTTGTTTG-TATGAT
1 AAGCTTTTAAAGTGTGAATTAT--CCTTTTTAAATCC-ATTTTTAATTTATTTG-TTGATATGAC
* * *
5281413 ACTTGAGTATGACCCTAGCAAGCACGATAGGAAGTTCATAACT
62 ACTTGACTATGACCCCAGCAAGCACGATAGGAAGCTCATAACT
5281456 GGCACTTTTG
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
104 21 0.23
105 4 0.04
106 64 0.69
107 4 0.04
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (104 bp):
AAGCTTTTAAAGTGTGAATTATCCTTTTTAAATCCATTTTTAATTTATTTGTTGATATGACACTT
GACTATGACCCCAGCAAGCACGATAGGAAGCTCATAACT
Found at i:5287034 original size:46 final size:46
Alignment explanation
Indices: 5286967--5287058 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
5286957 AGGCTACGGT
5286967 CATGGACTCTTTATCAGTAGAAGGTCCTTCTGGTCTAGGGAAGGTA
1 CATGGACTCTTTATCAGTAGAAGGTCCTTCTGGTCTAGGGAAGGTA
5287013 CATGGACTCTTTATCAGTAGAAGGTCCTTCTGGTCTAGGGAAGGTA
1 CATGGACTCTTTATCAGTAGAAGGTCCTTCTGGTCTAGGGAAGGTA
5287059 TCTTGTAGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (46 bp):
CATGGACTCTTTATCAGTAGAAGGTCCTTCTGGTCTAGGGAAGGTA
Found at i:5298219 original size:39 final size:39
Alignment explanation
Indices: 5298152--5298226 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
5298142 TTGCCGCCCC
* * **
5298152 ACAATTTTGTTTTATAATTGCATCTTTAAAAATTTACAA
1 ACAATTGTATTTTATAATTAAATCTTTAAAAATTTACAA
* *
5298191 ACAATTGTATTTTATAATTAAATTTTTAATAATTTA
1 ACAATTGTATTTTATAATTAAATCTTTAAAAATTTA
5298227 ATTATAAAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (39 bp):
ACAATTGTATTTTATAATTAAATCTTTAAAAATTTACAA
Found at i:5301276 original size:25 final size:25
Alignment explanation
Indices: 5301232--5301295 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
5301222 TAATTTAAAA
*
5301232 TATA-AAAATATTATGATTTAAAATTT
1 TATACAAAA-ATTAT-ATTTTAAATTT
* *
5301258 TA-ATAAAAATTATATTTTATATTT
1 TATACAAAAATTATATTTTAAATTT
5301282 TATACAAAAATTAT
1 TATACAAAAATTAT
5301296 GAGATAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 11 0.33
25 16 0.48
26 6 0.18
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
TATACAAAAATTATATTTTAAATTT
Found at i:5301766 original size:12 final size:12
Alignment explanation
Indices: 5301749--5301802 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
5301739 TATAAATATG
5301749 TAAATTTATAAT
1 TAAATTTATAAT
*
5301761 TAAATTTAATAAA
1 TAAATTT-ATAAT
* *
5301774 TAAAATTATCAT
1 TAAATTTATAAT
* *
5301786 TAATTTTTTAAT
1 TAAATTTATAAT
5301798 TAAAT
1 TAAAT
5301803 GTGATTAATC
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
12 22 0.69
13 10 0.31
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAATTTATAAT
Found at i:5302420 original size:25 final size:25
Alignment explanation
Indices: 5302375--5302422 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5302365 TCTCATCTAA
* *
5302375 AAATTTCTTAGAAATTTATCATTTG
1 AAATTTCTTAAAAATTAATCATTTG
5302400 AAATTTC-TAAAAATCTAATCATT
1 AAATTTCTTAAAAAT-TAATCATT
5302423 GGATAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (25 bp):
AAATTTCTTAAAAATTAATCATTTG
Found at i:5312660 original size:2 final size:2
Alignment explanation
Indices: 5312655--5312687 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5312645 AATGGACTCC
5312655 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5312688 AACATACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5316700 original size:16 final size:17
Alignment explanation
Indices: 5316679--5316710 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5316669 ATGGTTTCAA
5316679 TGTCAA-ATTAATTGAT
1 TGTCAACATTAATTGAT
5316695 TGTCAACATTAATTGA
1 TGTCAACATTAATTGA
5316711 GATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (17 bp):
TGTCAACATTAATTGAT
Found at i:5316719 original size:2 final size:2
Alignment explanation
Indices: 5316712--5316736 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5316702 ATTAATTGAG
5316712 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5316737 AGATGTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5323933 original size:105 final size:105
Alignment explanation
Indices: 5323748--5323952 Score: 286
Period size: 105 Copynumber: 2.0 Consensus size: 105
5323738 TTATTTATAG
* * *
5323748 AGATTAAATCCTAAGGTTGTGACTCTTTGATTGTGTTATTTCAATTATAGATTACTTTTTTTGAT
1 AGATTAAATCCTAAGGTTGTGACTCTTTGATTATGTCATTTCAATTAAAGATTACTTTTTTTGAT
* ** *
5323813 AAAAAATTATTTTTTTAATTAAAGATAAAGTGATTTACAA
66 AAAAAAATACCTTTTTAAGTAAAGATAAAGTGATTTACAA
* *
5323853 AGATTAAATCTTAAGGTTGTGACTCTTTGATTATGTCATTTCAATTAAAGATTA-TTTTTTTTAT
1 AGATTAAATCCTAAGGTTGTGACTCTTTGATTATGTCATTTCAATTAAAGATTACTTTTTTTGA-
* **
5323917 TAAAAAAATACCTTTTTGAGTAATTATAAAGTGATT
65 TAAAAAAATACCTTTTTAAGTAAAGATAAAGTGATT
5323953 CATTTGAATA
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
104 8 0.09
105 79 0.91
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (105 bp):
AGATTAAATCCTAAGGTTGTGACTCTTTGATTATGTCATTTCAATTAAAGATTACTTTTTTTGAT
AAAAAAATACCTTTTTAAGTAAAGATAAAGTGATTTACAA
Found at i:5333880 original size:13 final size:13
Alignment explanation
Indices: 5333862--5333886 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5333852 TTGAATTACT
5333862 AAAAAATTTTAAA
1 AAAAAATTTTAAA
5333875 AAAAAATTTTAA
1 AAAAAATTTTAA
5333887 TGGGGTGACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAATTTTAAA
Found at i:5338327 original size:12 final size:11
Alignment explanation
Indices: 5338296--5338329 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
5338286 TTGAATTATA
5338296 AATAATTTTTT
1 AATAATTTTTT
5338307 AATAATTTTTT
1 AATAATTTTTT
5338318 ACAT-ATTTTTT
1 A-ATAATTTTTT
5338329 A
1 A
5338330 TTTTTACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 20 0.91
12 2 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
AATAATTTTTT
Found at i:5340078 original size:15 final size:15
Alignment explanation
Indices: 5340058--5340102 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
5340048 TTAAATTAAA
5340058 AAAATTATAAATATT
1 AAAATTATAAATATT
5340073 AAAATT-TAAA-ATT
1 AAAATTATAAATATT
*
5340086 TAAATTATTAAATATT
1 AAAATTA-TAAATATT
5340102 A
1 A
5340103 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 8 0.32
14 4 0.16
15 10 0.40
16 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:5343306 original size:13 final size:13
Alignment explanation
Indices: 5343288--5343312 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5343278 ATTTTTAAAA
5343288 ATAAAATTATTTT
1 ATAAAATTATTTT
5343301 ATAAAATTATTT
1 ATAAAATTATTT
5343313 GAATGTGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATAAAATTATTTT
Found at i:5343544 original size:22 final size:22
Alignment explanation
Indices: 5343519--5343573 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
5343509 TATAAATTTT
5343519 TATAAATT-TTTT-CAAATGAAAA
1 TATAAATTATTTTCCAAA--AAAA
5343541 TATAAAATTATTTTCCAAAAAAA
1 TAT-AAATTATTTTCCAAAAAAA
5343564 -ATAAATTATT
1 TATAAATTATT
5343574 CTCAGCTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 8 0.27
22 5 0.17
23 9 0.30
24 4 0.13
25 4 0.13
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (22 bp):
TATAAATTATTTTCCAAAAAAA
Found at i:5349236 original size:15 final size:15
Alignment explanation
Indices: 5349216--5349249 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5349206 GTTTTGAATT
5349216 TTATAAAATTTTATC
1 TTATAAAATTTTATC
* *
5349231 TTATAATATTTTATT
1 TTATAAAATTTTATC
5349246 TTAT
1 TTAT
5349250 TAATTGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATAAAATTTTATC
Found at i:5349296 original size:14 final size:15
Alignment explanation
Indices: 5349277--5349305 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5349267 GAAATCTTAC
5349277 TTTATTTTTG-TAAT
1 TTTATTTTTGCTAAT
5349291 TTTATTTTTGCTAAT
1 TTTATTTTTGCTAAT
5349306 CACTAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.03, G:0.07, T:0.69
Consensus pattern (15 bp):
TTTATTTTTGCTAAT
Found at i:5359731 original size:23 final size:23
Alignment explanation
Indices: 5359702--5359749 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
5359692 AACCCATAAC
*
5359702 AAAAATCAATAAATCGACAGATT
1 AAAAATCAATAAATCAACAGATT
*
5359725 AAAAATCAATAAATTAACAGATT
1 AAAAATCAATAAATCAACAGATT
5359748 AA
1 AA
5359750 CTCAAAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.60, C:0.10, G:0.06, T:0.23
Consensus pattern (23 bp):
AAAAATCAATAAATCAACAGATT
Found at i:5363152 original size:23 final size:22
Alignment explanation
Indices: 5363125--5363182 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
5363115 TTATAATTTA
* *
5363125 AATTTTAATATTGATATTTTTTT
1 AATTTTAA-ATTGAGATATTTTT
5363148 AATTTTTAAATTGAGATATTTTT
1 AA-TTTTAAATTGAGATATTTTT
*
5363171 ATATTTAAAATT
1 A-ATTTTAAATT
5363183 ATTAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 23 0.77
24 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (22 bp):
AATTTTAAATTGAGATATTTTT
Found at i:5367445 original size:79 final size:79
Alignment explanation
Indices: 5367295--5367448 Score: 209
Period size: 79 Copynumber: 1.9 Consensus size: 79
5367285 AAGTTGTGCA
* * * * ***
5367295 AAATAGAAAAAAATTCACGACCGCGATGAGTGCGATTATTGCTATGTTATCCATTATAGCTGTAA
1 AAATAGAAAAAAATTCACGACCGCAATAAGTGCGACTACTGCTATGTTATCCATTATAGCCACAA
*
5367360 CTGCAATAAATGCG
66 CAGCAATAAATGCG
* * *
5367374 AAATAGAAAAAAATTCACGATCGCAATAAGTGCGACTACTGCTGTTTTATCCATTATAGCCACAA
1 AAATAGAAAAAAATTCACGACCGCAATAAGTGCGACTACTGCTATGTTATCCATTATAGCCACAA
5367439 CAGCAATAAA
66 CAGCAATAAA
5367449 CATGATGCGA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 64 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (79 bp):
AAATAGAAAAAAATTCACGACCGCAATAAGTGCGACTACTGCTATGTTATCCATTATAGCCACAA
CAGCAATAAATGCG
Found at i:5370790 original size:15 final size:18
Alignment explanation
Indices: 5370770--5370807 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5370760 GATTTTCAGG
5370770 AGAAGCA-AA-AA-GAGA
1 AGAAGCATAAGAAGGAGA
5370785 AGAAGCATAAGAAGGAGA
1 AGAAGCATAAGAAGGAGA
5370803 AGAAG
1 AGAAG
5370808 GACAAGGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 2 0.10
17 2 0.10
18 9 0.45
ACGTcount: A:0.61, C:0.05, G:0.32, T:0.03
Consensus pattern (18 bp):
AGAAGCATAAGAAGGAGA
Found at i:5374619 original size:9 final size:9
Alignment explanation
Indices: 5374605--5374629 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5374595 AATGTATAAT
5374605 TTTATTTAG
1 TTTATTTAG
5374614 TTTATTTAG
1 TTTATTTAG
5374623 TTTATTT
1 TTTATTT
5374630 TTTAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (9 bp):
TTTATTTAG
Found at i:5374686 original size:11 final size:11
Alignment explanation
Indices: 5374630--5374689 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
5374620 TAGTTTATTT
5374630 TTTAATTTAAAA
1 TTTAATTT-AAA
*
5374642 TTTAACTTAAA
1 TTTAATTTAAA
* * *
5374653 CTTAATATATA
1 TTTAATTTAAA
5374664 TTTATTATTTAAA
1 TTTA--ATTTAAA
5374677 TTTAATTTAAA
1 TTTAATTTAAA
5374688 TT
1 TT
5374690 GAATAAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
11 22 0.58
12 7 0.18
13 9 0.24
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:5375209 original size:28 final size:27
Alignment explanation
Indices: 5375169--5375221 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
5375159 TCCAATAATT
*
5375169 TTTTTATAATAAATTAATAAATAAACA
1 TTTTTATAATAAATAAATAAATAAACA
* *
5375196 TTTTTATAGTTAAATAAATAATTAAA
1 TTTTTATA-ATAAATAAATAAATAAA
5375222 ATAAATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (27 bp):
TTTTTATAATAAATAAATAAATAAACA
Found at i:5375225 original size:13 final size:13
Alignment explanation
Indices: 5375207--5375231 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5375197 TTTTATAGTT
5375207 AAATAAATAATTA
1 AAATAAATAATTA
5375220 AAATAAATAATT
1 AAATAAATAATT
5375232 GCATAAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATAAATAATTA
Found at i:5375720 original size:14 final size:14
Alignment explanation
Indices: 5375703--5375749 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
5375693 TTAATAAAAT
5375703 AAAAATAATATTTA
1 AAAAATAATATTTA
** *
5375717 AAAAA-GGTAATTA
1 AAAAATAATATTTA
*
5375730 AAAAATAATATTTT
1 AAAAATAATATTTA
5375744 AAAAAT
1 AAAAAT
5375750 TTAATTGGAT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (14 bp):
AAAAATAATATTTA
Found at i:5376475 original size:3 final size:3
Alignment explanation
Indices: 5376467--5376510 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
5376457 CAATATATCA
5376467 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5376511 AGCAACAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5376763 original size:13 final size:14
Alignment explanation
Indices: 5376747--5376787 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
5376737 ATATTCTGTT
*
5376747 AAAATTTTTAT-TA
1 AAAATATTTATCTA
5376760 AAAATATTTATCTA
1 AAAATATTTATCTA
*
5376774 AAAA-ATATATCTA
1 AAAATATTTATCTA
5376787 A
1 A
5376788 TTTTATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATATTTATCTA
Found at i:5377563 original size:47 final size:48
Alignment explanation
Indices: 5377469--5377565 Score: 187
Period size: 47 Copynumber: 2.0 Consensus size: 48
5377459 TAACATTCTA
5377469 ACAATAAATCACATAATTCTTGACTATTATTGTTTGTATTAAGTTCAG
1 ACAATAAATCACATAATTCTTGACTATTATTGTTTGTATTAAGTTCAG
5377517 ACAATAAATCACATAATTCTTGAC-ATTATTGTTTGTATTAAGTTCAG
1 ACAATAAATCACATAATTCTTGACTATTATTGTTTGTATTAAGTTCAG
5377564 AC
1 AC
5377566 TGGATGAAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 25 0.51
48 24 0.49
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (48 bp):
ACAATAAATCACATAATTCTTGACTATTATTGTTTGTATTAAGTTCAG
Found at i:5378425 original size:13 final size:13
Alignment explanation
Indices: 5378407--5378431 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5378397 GAACTCTTTT
5378407 ATTAAGTTAAGCA
1 ATTAAGTTAAGCA
5378420 ATTAAGTTAAGC
1 ATTAAGTTAAGC
5378432 TAAAATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
ATTAAGTTAAGCA
Found at i:5378945 original size:56 final size:56
Alignment explanation
Indices: 5378839--5378945 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 56
5378829 AAGGTGACCC
* *
5378839 AACTAAGCCTTTATGTAATCAATTTATCGAGATAAGCTCTTTAACTGAGGTTGTTG
1 AACTAAGCCTTTATGTAAGCAATTTATCGAGATAAGCTCTTTAACCGAGGTTGTTG
* * * * *
5378895 AACTAAGTCTTTATG-AGAGCAATTTATTGAGATGAGCTTTTTGACCGAGGT
1 AACTAAGCCTTTATGTA-AGCAATTTATCGAGATAAGCTCTTTAACCGAGGT
5378946 GGCTGAGATA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
55 1 0.02
56 42 0.98
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (56 bp):
AACTAAGCCTTTATGTAAGCAATTTATCGAGATAAGCTCTTTAACCGAGGTTGTTG
Found at i:5379001 original size:18 final size:19
Alignment explanation
Indices: 5378975--5379022 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
5378965 GACTAATATG
* *
5378975 AGCTCTTTTGGTTGAG-TA
1 AGCTTTTTTGGTCGAGTTA
* *
5378993 AGCTTTTTTGATCGAGTTG
1 AGCTTTTTTGGTCGAGTTA
5379012 AGCTTTTTTGG
1 AGCTTTTTTGG
5379023 CCAAGCTGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.15, C:0.10, G:0.27, T:0.48
Consensus pattern (19 bp):
AGCTTTTTTGGTCGAGTTA
Found at i:5379429 original size:83 final size:83
Alignment explanation
Indices: 5379276--5379511 Score: 229
Period size: 83 Copynumber: 2.8 Consensus size: 83
5379266 GTCCGAGCTC
* * * * * * *
5379276 TTAGGCTAAGTTATTTTGTTGAGTTGGGCCTTTATGAAGGTATTTTGTAGATCCGAGCTCTTTTG
1 TTAGGCTAAGCTATTTTGTTGAATT-GGACTTTATAAAGATA-TTTATAGATTCGAGCTCTTTTG
*
5379341 GCTGAGCTAAATTCAAACTT
64 ACTGAGCTAAATTCAAACTT
* *
5379361 TTAGGCTGAGCTATTTTGTTGAATTGGACTTTATAAAGATATTTATAGATTCGAACTCTTTTGAC
1 TTAGGCTAAGCTATTTTGTTGAATTGGACTTTATAAAGATATTTATAGATTCGAGCTCTTTTGAC
* * * ** *
5379426 TGAGTTGAGTTTGATCTT
66 TGAGCTAAATTCAAACTT
** * * * *
5379444 TTAAACTAAGCTATTTTGTTGAATTAGACCTTTACAAAAGTATTTTTATAGATTTGAGCTCTTTT
1 TTAGGCTAAGCTATTTTGTTGAATTGGA-CTTTA-TAAAG-ATATTTATAGATTCGAGCTCTTTT
5379509 GAC
63 GAC
5379512 CAAGCTAAGT
Statistics
Matches: 124, Mismatches: 24, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
83 56 0.45
84 18 0.15
85 26 0.21
86 24 0.19
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.43
Consensus pattern (83 bp):
TTAGGCTAAGCTATTTTGTTGAATTGGACTTTATAAAGATATTTATAGATTCGAGCTCTTTTGAC
TGAGCTAAATTCAAACTT
Found at i:5383958 original size:9 final size:10
Alignment explanation
Indices: 5383930--5383962 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5383920 TTCTTTTCTA
5383930 TTATTATTTT
1 TTATTATTTT
*
5383940 TAATTATTTT
1 TTATTATTTT
5383950 TTATT-TTTT
1 TTATTATTTT
5383959 TTAT
1 TTAT
5383963 CAAAATTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTATTATTTT
Found at i:5384383 original size:28 final size:28
Alignment explanation
Indices: 5384345--5384407 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
5384335 GACTAAGATT
* *
5384345 AAAAAAAAGTTATTATAGCTGTGATTGA
1 AAAAAAAAGTTACTATAGCTGCGATTGA
*
5384373 AAAAAAAAGTTACTATAGTTGCGATTGA
1 AAAAAAAAGTTACTATAGCTGCGATTGA
5384401 AAAAAAA
1 AAAAAAA
5384408 TCTAATGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.27
Consensus pattern (28 bp):
AAAAAAAAGTTACTATAGCTGCGATTGA
Found at i:5387109 original size:17 final size:17
Alignment explanation
Indices: 5387089--5387132 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
5387079 GTTATATTTG
*
5387089 TTATTATTATGTTATCA
1 TTATTATTATATTATCA
*
5387106 TTATTATTATATTATTA
1 TTATTATTATATTATCA
*
5387123 TTATCATTAT
1 TTATTATTAT
5387133 CATTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (17 bp):
TTATTATTATATTATCA
Found at i:5387110 original size:14 final size:12
Alignment explanation
Indices: 5387100--5387132 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
5387090 TATTATTATG
5387100 TTATCATTATTA
1 TTATCATTATTA
5387112 TTAT-ATTATTA
1 TTATCATTATTA
5387123 TTATCATTAT
1 TTATCATTAT
5387133 CATTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATCATTATTA
Found at i:5388129 original size:11 final size:10
Alignment explanation
Indices: 5388120--5388187 Score: 73
Period size: 10 Copynumber: 6.6 Consensus size: 10
5388110 TCTTTTTATC
5388120 TTTATTTTATT
1 TTTATTTT-TT
5388131 TTTATTTTTGT
1 TTTATTTTT-T
* *
5388142 TTTACTTTTC
1 TTTATTTTTT
*
5388152 TTTATTTATT
1 TTTATTTTTT
*
5388162 TTTATTTTTA
1 TTTATTTTTT
5388172 TTTATTTTTT
1 TTTATTTTTT
*
5388182 ATTATT
1 TTTATT
5388188 CTATTTTCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
10 30 0.64
11 17 0.36
ACGTcount: A:0.16, C:0.03, G:0.01, T:0.79
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:5388133 original size:6 final size:6
Alignment explanation
Indices: 5388112--5388194 Score: 66
Period size: 6 Copynumber: 13.7 Consensus size: 6
5388102 TTTAATATTC
* *
5388112 TTTTTA TCTTTA -TTTTA TTTTTA TTTTT- GTTTTA CTTTTCT- TTATTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTT-TA TT-TTTA
*
5388160 TTTTTA TTTTTA TTTAT- TTTTTA TTATTCTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TT-TT-TA TTTT
5388195 CTTTAAATAA
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
5 12 0.19
6 34 0.55
7 11 0.18
8 5 0.08
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:5388193 original size:31 final size:31
Alignment explanation
Indices: 5388118--5388194 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
5388108 ATTCTTTTTA
*
5388118 TCTTTATTTTATTTTTATTTTTGTTTTACTTT
1 TCTTTA-TTTATTTTTATTTTTGATTTACTTT
5388150 TCTTTATTTATTTTTATTTTT-ATTTA-TTT
1 TCTTTATTTATTTTTATTTTTGATTTACTTT
*
5388179 TTTATTATTCTATTTT
1 TCT-TTATT-TATTTT
5388195 CTTTAAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
29 5 0.12
30 9 0.22
31 21 0.51
32 6 0.15
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (31 bp):
TCTTTATTTATTTTTATTTTTGATTTACTTT
Found at i:5388283 original size:57 final size:57
Alignment explanation
Indices: 5388221--5388616 Score: 485
Period size: 57 Copynumber: 6.7 Consensus size: 57
5388211 AAAATTCCAA
* ** *
5388221 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGGAAATCAAAGTTTC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC
* *
5388279 AAAAAAAAAATATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 ----AAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
5388340 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
5388397 AAAAAAAAAAAGATTTTTTA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAATAAATTTTC
1 -----AAAAAATA-TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT--AAAAATAAATTTTC
*
5388461 AAAAAAAAGATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTC
1 --AAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* *
5388519 AAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAGTAAATTTTC
1 -AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
5388577 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 -AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
5388617 TCCTACACAA
Statistics
Matches: 307, Mismatches: 13, Indels: 32
0.87 0.04 0.09
Matches are distributed among these distances:
57 101 0.33
58 48 0.16
59 9 0.03
60 5 0.02
61 45 0.15
62 80 0.26
63 5 0.02
64 14 0.05
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (57 bp):
AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:5388350 original size:119 final size:116
Alignment explanation
Indices: 5388220--5388616 Score: 577
Period size: 119 Copynumber: 3.3 Consensus size: 116
5388210 AAAAATTCCA
* * **
5388220 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGGAAATCAAAGTTTCAAAAAA
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTCAAAAAA
5388285 AAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTC
64 AAAATATTTTT-AGGAAAAGTTGAAAGTATCAATTTTCCTTA-AAATAAATTTTC
*
5388339 CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAA
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTC-AAAAAA
*
5388404 AAAAGATTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAATAAATTTTC
64 AAAATA-TTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTT---AAAATAAATTTTC
* *
5388461 AAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTC---AAAA
1 -AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAA
5388523 AAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAGTAAATTTTC
65 AAATATTTTTAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAA-TAAATTTTC
5388577 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
5388617 TCCTACACAA
Statistics
Matches: 256, Mismatches: 13, Indels: 22
0.88 0.04 0.08
Matches are distributed among these distances:
115 42 0.16
116 9 0.04
117 8 0.03
118 41 0.16
119 85 0.33
120 5 0.02
121 7 0.03
122 9 0.04
123 50 0.20
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.35
Consensus pattern (116 bp):
AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAAA
AATATTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAATTTTC
Found at i:5388483 original size:180 final size:177
Alignment explanation
Indices: 5388218--5388616 Score: 590
Period size: 180 Copynumber: 2.2 Consensus size: 177
5388208 TAAAAAATTC
* **
5388218 CAAAAAAAATA-TTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTGGAAATCAAAGTTTCAAA
1 CAAAAAAAATATTTTTTA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTC-AA
* * *
5388282 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAAT
64 AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAAT
* *
5388347 ATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
129 ATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
* *
5388396 CAAAAAAAAAAAGATTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAAT-AAATTTT
1 C---AAAAAAAATATTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTT--AAAAATCAAAGTTT
5388460 C-AAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAA
61 CAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAA
*
5388524 AATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAGTAAATTTT
126 AATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
**
5388576 C-AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 CAAAAAAAATATTTTTTAGGAAAAGTTGAAAGTATCAATTTT
5388617 TCCTACACAA
Statistics
Matches: 201, Mismatches: 14, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
176 37 0.18
178 1 0.00
180 110 0.55
181 36 0.18
182 13 0.06
183 4 0.02
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (177 bp):
CAAAAAAAATATTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCAAAA
AAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAATAT
TTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
Found at i:5388664 original size:6 final size:6
Alignment explanation
Indices: 5388653--5388681 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5388643 CTTCCTTTCT
5388653 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
5388682 TCTTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (6 bp):
ATTTTG
Found at i:5392528 original size:13 final size:13
Alignment explanation
Indices: 5392510--5392552 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
5392500 ATGAAAAATG
*
5392510 AAAAAAGATGATAA
1 AAAAAAGAAGA-AA
5392524 AAAAAA-AAGAAA
1 AAAAAAGAAGAAA
5392536 AAAAAAGAAAGAAA
1 AAAAAAG-AAGAAA
5392550 AAA
1 AAA
5392553 GAAAAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 8 0.31
13 3 0.12
14 15 0.58
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.05
Consensus pattern (13 bp):
AAAAAAGAAGAAA
Found at i:5392536 original size:11 final size:11
Alignment explanation
Indices: 5392522--5392560 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
5392512 AAAAGATGAT
5392522 AAAAAAAAAAG
1 AAAAAAAAAAG
5392533 -AAAAAAAAAG
1 AAAAAAAAAAG
*
5392543 AAAGAAAAAAG
1 AAAAAAAAAAG
5392554 AAAAAAA
1 AAAAAAA
5392561 TGAGAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:5392546 original size:14 final size:13
Alignment explanation
Indices: 5392522--5392559 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
5392512 AAAAGATGAT
5392522 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
5392535 AAAAAAAGAAAGAA
1 AAAAAAA-AAAGAA
5392549 AAAAGAAAAAA
1 AAAA-AAAAAA
5392560 ATGAGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.30
14 13 0.57
15 3 0.13
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:5392566 original size:11 final size:11
Alignment explanation
Indices: 5392522--5392568 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
5392512 AAAAGATGAT
*
5392522 AAAAAAAAAAG
1 AAAAAAATAAG
5392533 AAAAAAA-AAG
1 AAAAAAATAAG
5392543 AAAGAAAA-AAG
1 AAA-AAAATAAG
*
5392554 AAAAAAATGAG
1 AAAAAAATAAG
5392565 AAAA
1 AAAA
5392569 TGAAAAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
10 10 0.30
11 23 0.70
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (11 bp):
AAAAAAATAAG
Found at i:5392568 original size:16 final size:15
Alignment explanation
Indices: 5392500--5392576 Score: 63
Period size: 15 Copynumber: 5.0 Consensus size: 15
5392490 TCAACAATGG
5392500 ATGAAAAATGAAAAAA
1 ATGAAAAA-GAAAAAA
*
5392516 GATGATAAA-AAAAAA
1 -ATGAAAAAGAAAAAA
5392531 A-GAAAAA-AAAAGAA
1 ATGAAAAAGAAAA-AA
5392545 A-GAAAAAAGAAAAAA
1 ATG-AAAAAGAAAAAA
5392560 ATGAGAAAATGAAAAAA
1 ATGA-AAAA-GAAAAAA
5392577 TGAGATTCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
13 9 0.17
14 5 0.10
15 15 0.29
16 9 0.17
17 14 0.27
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (15 bp):
ATGAAAAAGAAAAAA
Found at i:5393814 original size:41 final size:41
Alignment explanation
Indices: 5393763--5394097 Score: 539
Period size: 41 Copynumber: 8.1 Consensus size: 41
5393753 ATGATTGTCA
*
5393763 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
5393804 AGGAGAAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
5393845 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
5393886 AGGAGCAATTTAATTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
5393927 AGGAGCAATTTACTTTCCCAAAGTCGTGGTACCT-TGTTTAG
1 AGGAGCAATTTACTTT-TCAAAGTCGTGGTGCCTCTGTTTAG
5393968 AGGAGCAATTTAC-TTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
5394008 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * ***
5394049 AGGAGCAATTTATGTTTCTCAAAGTAGTTAAGCCTCTGTTTAG
1 AGGAGCAATTTA-CTTT-TCAAAGTCGTGGTGCCTCTGTTTAG
5394092 AGGAGC
1 AGGAGC
5394098 TTTGGTAAAA
Statistics
Matches: 275, Mismatches: 14, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
39 15 0.05
40 22 0.08
41 193 0.70
42 18 0.07
43 27 0.10
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:5394110 original size:1 final size:1
Alignment explanation
Indices: 5394104--5394215 Score: 98
Period size: 1 Copynumber: 112.0 Consensus size: 1
5394094 GAGCTTTGGT
* * * * * * *
5394104 AAAAAAAAAACAAAAAAACAAAAAAAAAACAAAAAAAATAAAAAAACAAAAACAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
5394169 CAAAAAACAAAACAAAAAAACAAAAAAACACAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5394216 TGACAATGTT
Statistics
Matches: 83, Mismatches: 28, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 83 1.00
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.01
Consensus pattern (1 bp):
A
Found at i:5394120 original size:8 final size:8
Alignment explanation
Indices: 5394107--5394213 Score: 112
Period size: 8 Copynumber: 12.9 Consensus size: 8
5394097 CTTTGGTAAA
5394107 AAAAAAAC
1 AAAAAAAC
5394115 AAAAAAAC
1 AAAAAAAC
5394123 AAAAAAA-
1 AAAAAAAC
*
5394130 AAACAAAAA
1 AAA-AAAAC
*
5394139 AAATAAAAA
1 AAA-AAAAC
5394148 AACAAAAAC
1 AA-AAAAAC
5394157 AAAAAAA-
1 AAAAAAAC
5394164 AAGAACAAA-
1 AA-AA-AAAC
5394173 AAACAAAAC
1 AAA-AAAAC
5394182 AAAAAAAC
1 AAAAAAAC
5394190 AAAAAAAC
1 AAAAAAAC
5394198 ACAAAAAAC
1 A-AAAAAAC
5394207 AAAAAAA
1 AAAAAAA
5394214 AATGACAATG
Statistics
Matches: 89, Mismatches: 2, Indels: 16
0.83 0.02 0.15
Matches are distributed among these distances:
7 5 0.06
8 50 0.56
9 33 0.37
10 1 0.01
ACGTcount: A:0.87, C:0.11, G:0.01, T:0.01
Consensus pattern (8 bp):
AAAAAAAC
Found at i:5394221 original size:20 final size:18
Alignment explanation
Indices: 5394104--5394212 Score: 125
Period size: 17 Copynumber: 5.9 Consensus size: 18
5394094 GAGCTTTGGT
5394104 AAAAAAAAAACAAAAAAAC
1 AAAAAAAAAAC-AAAAAAC
5394123 AAAAAAAAAACAAAAAA-
1 AAAAAAAAAACAAAAAAC
*
5394140 AATAAAAAAAC-AAAAAC
1 AAAAAAAAAACAAAAAAC
5394157 AAAAAAAAAGAACAAAAAAC
1 -AAAAAAAA-AACAAAAAAC
5394177 AAAACAAAAAAACAAAAAA-
1 -AAA-AAAAAAACAAAAAAC
* *
5394196 ACACAAAAAACAAAAAA
1 AAAAAAAAAACAAAAAA
5394213 AAATGACAAT
Statistics
Matches: 81, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.06
17 23 0.28
18 15 0.19
19 14 0.17
20 19 0.23
21 5 0.06
ACGTcount: A:0.87, C:0.11, G:0.01, T:0.01
Consensus pattern (18 bp):
AAAAAAAAAACAAAAAAC
Found at i:5394398 original size:16 final size:16
Alignment explanation
Indices: 5394379--5394526 Score: 60
Period size: 16 Copynumber: 9.1 Consensus size: 16
5394369 TCTTTTGTAT
5394379 TTTATGTATT-TTATTA
1 TTTAT-TATTATTATTA
*
5394395 TTTATTATTATTATTG
1 TTTATTATTATTATTA
* *
5394411 TGTATTAATATATATATA
1 TTTATTATTAT-TAT-TA
*
5394429 TTTATT-TT-TT-TTC
1 TTTATTATTATTATTA
*
5394442 TGTTAATATT-TATATGTA
1 T-TTATTATTAT-TAT-TA
5394460 TTTTATTTATATAGTTA-TA
1 -TTTA-TTAT-TA-TTATTA
*
5394479 TTTGTTATTATTA-T-
1 TTTATTATTATTATTA
* *
5394493 GTTATCATTATTATTA
1 TTTATTATTATTATTA
*
5394509 TTATATTATTATCATTA
1 TT-TATTATTATTATTA
5394526 T
1 T
5394527 CATTTTTTTT
Statistics
Matches: 99, Mismatches: 17, Indels: 31
0.67 0.12 0.21
Matches are distributed among these distances:
13 2 0.02
14 15 0.15
15 13 0.13
16 24 0.24
17 22 0.22
18 13 0.13
19 6 0.06
20 1 0.01
21 2 0.02
22 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:5394497 original size:11 final size:11
Alignment explanation
Indices: 5394473--5394520 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
5394463 TATTTATATA
5394473 GTTA-TATT-T
1 GTTATTATTAT
5394482 GTTATTATTAT
1 GTTATTATTAT
*
5394493 GTTATCATTA-
1 GTTATTATTAT
5394503 -TTATTATTAT
1 GTTATTATTAT
*
5394513 ATTATTAT
1 GTTATTAT
5394521 CATTATCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 12 0.36
10 4 0.12
11 17 0.52
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.62
Consensus pattern (11 bp):
GTTATTATTAT
Found at i:5394503 original size:17 final size:14
Alignment explanation
Indices: 5394484--5394526 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5394474 TTATATTTGT
*
5394484 TATTATTA-TGTTA
1 TATTATTATTATTA
5394497 TCATTATTATTATTA
1 T-ATTATTATTATTA
*
5394512 TATTATTATCATTA
1 TATTATTATTATTA
5394526 T
1 T
5394527 CATTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 1 0.04
14 20 0.77
15 5 0.19
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:5394525 original size:20 final size:20
Alignment explanation
Indices: 5394483--5394526 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5394473 GTTATATTTG
* *
5394483 TTATTATTATGTTATCATTA
1 TTATTATTATATTATCATCA
*
5394503 TTATTATTATATTATTATCA
1 TTATTATTATATTATCATCA
5394523 TTAT
1 TTAT
5394527 CATTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (20 bp):
TTATTATTATATTATCATCA
Found at i:5395545 original size:11 final size:10
Alignment explanation
Indices: 5395536--5395603 Score: 73
Period size: 10 Copynumber: 6.6 Consensus size: 10
5395526 TCTTTTTATC
5395536 TTTATTTTATT
1 TTTATTTT-TT
5395547 TTTATTTTTGT
1 TTTATTTTT-T
* *
5395558 TTTACTTTTC
1 TTTATTTTTT
*
5395568 TTTATTTATT
1 TTTATTTTTT
*
5395578 TTTATTTTTA
1 TTTATTTTTT
5395588 TTTATTTTTT
1 TTTATTTTTT
*
5395598 ATTATT
1 TTTATT
5395604 CTATTTTCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
10 30 0.64
11 17 0.36
ACGTcount: A:0.16, C:0.03, G:0.01, T:0.79
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:5395549 original size:6 final size:6
Alignment explanation
Indices: 5395528--5395610 Score: 66
Period size: 6 Copynumber: 13.7 Consensus size: 6
5395518 TTTAATATTC
* *
5395528 TTTTTA TCTTTA -TTTTA TTTTTA TTTTT- GTTTTA CTTTTCT- TTATTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTT-TA TT-TTTA
*
5395576 TTTTTA TTTTTA TTTAT- TTTTTA TTATTCTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TT-TT-TA TTTT
5395611 CTTTAAATAA
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
5 12 0.19
6 34 0.55
7 11 0.18
8 5 0.08
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:5395609 original size:31 final size:31
Alignment explanation
Indices: 5395534--5395610 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
5395524 ATTCTTTTTA
*
5395534 TCTTTATTTTATTTTTATTTTTGTTTTACTTT
1 TCTTTA-TTTATTTTTATTTTTGATTTACTTT
5395566 TCTTTATTTATTTTTATTTTT-ATTTA-TTT
1 TCTTTATTTATTTTTATTTTTGATTTACTTT
*
5395595 TTTATTATTCTATTTT
1 TCT-TTATT-TATTTT
5395611 CTTTAAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
29 5 0.12
30 9 0.22
31 21 0.51
32 6 0.15
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (31 bp):
TCTTTATTTATTTTTATTTTTGATTTACTTT
Found at i:5395767 original size:118 final size:116
Alignment explanation
Indices: 5395635--5396089 Score: 609
Period size: 118 Copynumber: 3.8 Consensus size: 116
5395625 AAAAAATTCC
5395635 AAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTC-AAAAA
1 AAAAAAAATATTTTT-AGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAA
* * *
5395698 GGGTTTTT-GAGAAGAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCA
65 AGATTTTTAGAGAA-AAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTCA
* *
5395752 AAAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTCCAAAA
1 AAAAAAA-ATATTTTT-AGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAA
* *
5395816 AATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAA
64 AAGATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTC---A
*
5395873 AAAAAAAAGATATTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAATAAATTTTCAAAA
1 AAAAAAAATAT-TTTTAGGAAAAGTTGAAAGTATCAATTTTCCTT--AAAAATAAATTTTC-AAA
5395938 AAAAGATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTC-
62 AAAAGATTTTTAGA-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCA
*
5395992 -AAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAGTAAATTTTCAAAAAA
1 AAAAAAAATATTTTTAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAA
* * *
5396056 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
65 AGATTTTTAGAGAAAAGTTGAAAGTATCAATTTT
5396090 TCCTACACAA
Statistics
Matches: 307, Mismatches: 17, Indels: 30
0.87 0.05 0.08
Matches are distributed among these distances:
115 36 0.12
116 14 0.05
117 14 0.05
118 91 0.30
119 39 0.13
120 36 0.12
121 12 0.04
122 8 0.03
123 9 0.03
124 48 0.16
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (116 bp):
AAAAAAAATATTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAA
GATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCA
Found at i:5395847 original size:57 final size:58
Alignment explanation
Indices: 5395636--5396089 Score: 589
Period size: 57 Copynumber: 7.7 Consensus size: 58
5395626 AAAAATTCCA
*
5395636 AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTC
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*** * * *
5395693 -AAAAAGGGTTTTT-GAGAAGAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAAATATTTTTAGGGAA-AAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC
* *
5395751 AAAAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTC
1 -AAAAAAATAT-TTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
5395811 CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
5395869 AAAAAAAAAAAAGATATTTTA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAATAAATTTT
1 -----AAAAAAATAT-TTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT--AAAAATAAATTTT
5395933 C
58 C
*
5395934 AAAAAAAAGATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTC
1 -AAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* *
5395992 AAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAGTAAATTTTC
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
5396050 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
5396090 TCCTACACAA
Statistics
Matches: 354, Mismatches: 22, Indels: 41
0.85 0.05 0.10
Matches are distributed among these distances:
55 3 0.01
56 39 0.11
57 87 0.25
58 60 0.17
59 18 0.05
60 14 0.04
61 46 0.13
62 29 0.08
63 39 0.11
64 5 0.01
65 14 0.04
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (58 bp):
AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:5395999 original size:181 final size:182
Alignment explanation
Indices: 5395712--5396056 Score: 588
Period size: 181 Copynumber: 1.9 Consensus size: 182
5395702 TTTTGAGAAG
* *
5395712 AAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAAAAAAATATATTTTTGAGGAAAAG
1 AAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCAAAAAAAATAGATTTTTGAGGAAAAG
* * *
5395777 TTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGT
66 TTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAATATTTTTAGGAAAAAGTTGAAAGT
5395842 ATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAAAAAGATATTTTAGGAA
131 ATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAAAAAGATATTTTAGGAA
*
5395894 AAGTTGAAAGTATCAATTTTCCTTAAAAAAAT-AAATTTTC-AAAAAAA-AGATTTTTGAGGAAA
1 AAGTTGAAAGTATCAATTTTCCTT--AAAAATCAAAGTTTCAAAAAAAATAGATTTTTGAGGAAA
5395956 AGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAATATTTTTAGGAAAAAGTTGAAA
64 AGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAATATTTTTAGGAAAAAGTTGAAA
*
5396021 GTATCAATTTTCCTTAAAAGTAAATTTTCAAAAAAA
129 GTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAA
5396057 TATTTTTGGG
Statistics
Matches: 154, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
181 111 0.72
182 31 0.20
183 7 0.05
184 5 0.03
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.34
Consensus pattern (182 bp):
AAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCAAAAAAAATAGATTTTTGAGGAAAAG
TTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAATATTTTTAGGAAAAAGTTGAAAGT
ATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAAAAAGATATTTTAGGAA
Found at i:5396137 original size:6 final size:6
Alignment explanation
Indices: 5396126--5396154 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5396116 CTTCCTTTCT
5396126 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
5396155 TCTTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (6 bp):
ATTTTG
Found at i:5397671 original size:211 final size:211
Alignment explanation
Indices: 5397305--5397719 Score: 521
Period size: 211 Copynumber: 2.0 Consensus size: 211
5397295 ATTTGGAATC
* * * *
5397305 AATTATTCAAAGTGATATTAAGAAAAAGGATGCAAATCATAGGATTCAACTAGAATGGTGGGGTG
1 AATTATTCAAAGTGATATTAAGAAAAAGGATGCAAATCATAAGATTCAACCAGAATGGTGAGGTA
* * * * *
5397370 ACAAATGCATCAAGTATGTAGTGTGATCATAACATGCCTTTAAAACTAAAAGCAAGGTTGTTTAA
66 AAAAATGCATCAAGCATGTAGTATGATCATAACATGCCTTTAAAACTAAAAGCAAAGTTATTTAA
** *
5397435 AACAACTATAAAATCTATGTTGTTATAT-GGAACTGGGTGTCAAGTCATTAAAAAACAACATGAA
131 AACAACTATAAAATCTACATTGTTATATGGGAA-TGGGTGTCAAGTCACTAAAAAACAACATGAA
5397499 AAGAAAATGATGGGATT
195 AAGAAAATGATGGGATT
* *
5397516 AATTATTCAGAGTGATATTAAGAAAAA-GATGTAAATCATAAGATTCAACCAGAATGGTGAGGTA
1 AATTATTCAAAGTGATATTAAGAAAAAGGATGCAAATCATAAGATTCAACCAGAATGGTGAGGTA
* * * * ** ** *
5397580 ATAAAATTCGTCGAGCATGTTGTATGATTGTAACATGCCTTTAAAGTTAAAGGCAAAGTTATTTA
66 A-AAAATGCATCAAGCATGTAGTATGATCATAACATGCCTTTAAAACTAAAAGCAAAGTTATTTA
* * ** * *
5397645 AAACAATTGTAAAA-CTTACATTGTTATATGGGAATGGGTGTCGGGTCACTAAAAAATAACATGG
130 AAACAACTATAAAATC-TACATTGTTATATGGGAATGGGTGTCAAGTCACTAAAAAACAACATGA
5397709 AAAGAAAATGA
194 AAAGAAAATGA
5397720 GCGTAACTAA
Statistics
Matches: 172, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
210 34 0.20
211 134 0.78
212 4 0.02
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (211 bp):
AATTATTCAAAGTGATATTAAGAAAAAGGATGCAAATCATAAGATTCAACCAGAATGGTGAGGTA
AAAAATGCATCAAGCATGTAGTATGATCATAACATGCCTTTAAAACTAAAAGCAAAGTTATTTAA
AACAACTATAAAATCTACATTGTTATATGGGAATGGGTGTCAAGTCACTAAAAAACAACATGAAA
AGAAAATGATGGGATT
Found at i:5397800 original size:55 final size:55
Alignment explanation
Indices: 5397713--5397816 Score: 156
Period size: 55 Copynumber: 1.9 Consensus size: 55
5397703 ACATGGAAAG
*
5397713 AAAATGAGCGTAACTAAGATAAGGATGCTTAGATGGATGTGTGGTAAGATTAAAA
1 AAAATGAGCGTAACTAAGATAAGGATGCTTAGATGGATATGTGGTAAGATTAAAA
* * *
5397768 AAAATGAGCGTAGCTGAGATGAA-GATGTTTAGATGGATATGTGGTAAGA
1 AAAATGAGCGTAACTAAGAT-AAGGATGCTTAGATGGATATGTGGTAAGA
5397817 CTAGAAGAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
55 42 0.95
56 2 0.05
ACGTcount: A:0.39, C:0.05, G:0.30, T:0.26
Consensus pattern (55 bp):
AAAATGAGCGTAACTAAGATAAGGATGCTTAGATGGATATGTGGTAAGATTAAAA
Found at i:5400380 original size:2 final size:2
Alignment explanation
Indices: 5400373--5400397 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5400363 TATTCTTTTA
5400373 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5400398 ATTGAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5402015 original size:10 final size:9
Alignment explanation
Indices: 5401989--5402013 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5401979 ATAAATAAAA
5401989 TTTAAAATT
1 TTTAAAATT
5401998 TTTAAAATT
1 TTTAAAATT
5402007 TTTAAAA
1 TTTAAAA
5402014 ATAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTAAAATT
Found at i:5404391 original size:16 final size:15
Alignment explanation
Indices: 5404370--5404435 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
5404360 TTCATAATAA
5404370 ATAAAATACTTTTTAT
1 ATAAAATA-TTTTTAT
5404386 ATAAAATATTTTTAT
1 ATAAAATATTTTTAT
*** *
5404401 ATAATAAATAAAATTCT
1 AT-A-AAATATTTTTAT
5404418 ATAAAATA-TTTTAT
1 ATAAAATATTTTTAT
5404432 ATAA
1 ATAA
5404436 TTAAAATTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
14 7 0.17
15 14 0.34
16 10 0.24
17 10 0.24
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAAAATATTTTTAT
Found at i:5404410 original size:17 final size:16
Alignment explanation
Indices: 5404370--5404404 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
5404360 TTCATAATAA
5404370 ATAAAATACTTTTTAT
1 ATAAAATACTTTTTAT
5404386 ATAAAATA-TTTTTAT
1 ATAAAATACTTTTTAT
5404401 ATAA
1 ATAA
5404405 TAAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAAATACTTTTTAT
Found at i:5404443 original size:28 final size:30
Alignment explanation
Indices: 5404382--5404452 Score: 101
Period size: 28 Copynumber: 2.4 Consensus size: 30
5404372 AAAATACTTT
5404382 TTATATAAAATATTTTTATATAATAAATAAAA
1 TTATATAAAATATTTTTATATAAT--ATAAAA
*
5404414 TTCTATAAAATA-TTTTATATAAT-TAAAA
1 TTATATAAAATATTTTTATATAATATAAAA
5404442 TTATATAAAAT
1 TTATATAAAAT
5404453 GCTTCAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 15 0.41
31 11 0.30
32 11 0.30
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (30 bp):
TTATATAAAATATTTTTATATAATATAAAA
Found at i:5405113 original size:52 final size:52
Alignment explanation
Indices: 5405048--5405192 Score: 170
Period size: 52 Copynumber: 2.8 Consensus size: 52
5405038 AGACAAGAAA
* * * *
5405048 ACTTGCAAAAGAAGAATTCCAAGAGAAAGAAGATTCTTAAT-AGATAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGATTCTTAATAAG-CAAGTTTG
*
5405100 ACTTGCAAGAGAAGAATTCTAAAAGGAAAG-GGATTCTTAATAAGCAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGA-GAAAGAGGATTCTTAATAAGCAAGTTTG
* * *
5405152 ACTTACAGGAAAAGAATTCTAAGAG-AAGAGGGATTCTTAAT
1 ACTTGCAAGAGAAGAATTCTAAGAGAAAGA-GGATTCTTAAT
5405193 GGGCAAATTT
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
50 3 0.04
51 1 0.01
52 69 0.86
53 7 0.09
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (52 bp):
ACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGATTCTTAATAAGCAAGTTTG
Found at i:5406097 original size:11 final size:11
Alignment explanation
Indices: 5406078--5406119 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
5406068 AATCCCATAA
5406078 GAGATTTGTTT
1 GAGATTTGTTT
* *
5406089 GAAATTTGTTA
1 GAGATTTGTTT
5406100 GAGATTTGTTT
1 GAGATTTGTTT
5406111 GAGATTTGT
1 GAGATTTGT
5406120 CAGATATTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:5406102 original size:22 final size:22
Alignment explanation
Indices: 5406077--5406119 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5406067 AAATCCCATA
5406077 AGAGATTTGTTTGAAATTTGTT
1 AGAGATTTGTTTGAAATTTGTT
*
5406099 AGAGATTTGTTTGAGATTTGT
1 AGAGATTTGTTTGAAATTTGT
5406120 CAGATATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTGAAATTTGTT
Found at i:5410499 original size:13 final size:13
Alignment explanation
Indices: 5410464--5410500 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
5410454 TGTCAATATT
5410464 TTTATTAAAAATA
1 TTTATTAAAAATA
*
5410477 TATATCTAAAAATA
1 TTTAT-TAAAAATA
5410491 TTTATTAAAA
1 TTTATTAAAA
5410501 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTATTAAAAATA
Found at i:5414226 original size:13 final size:13
Alignment explanation
Indices: 5414208--5414240 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
5414198 TATACATTTC
5414208 TATATATAAATAA
1 TATATATAAATAA
5414221 TATATAT-AATAA
1 TATATATAAATAA
5414233 TA-ATATAA
1 TATATATAA
5414241 TGATAATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 8 0.42
13 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATATATAAATAA
Done.