Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167826.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_1, 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: 36299135
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 357000 characters in sequence are not A, C, G, or T
File 8 of 402
Found at i:1324303 original size:57 final size:58
Alignment explanation
Indices: 1324185--1324309 Score: 155
Period size: 57 Copynumber: 2.2 Consensus size: 58
1324175 GTTTAGAGTG
* * * * *
1324185 TTTAGGGTTTCGTTTTTAGTGTTTAGAGGGTTTACGGTTTAATTTAGGGTTTAAAGTA
1 TTTAAGGTTTCATTTTTAGGGTTTAGAAGGTTTACGGTTTAATTTAGGGTTTAAAGGA
* *
1324243 TTTAAGGTTTCATTTTTAGGGTTT-GAAGGTTT-GGGTTTAATTTAGGGGTTTGAAGGA
1 TTTAAGGTTTCATTTTTAGGGTTTAGAAGGTTTACGGTTTAATTTA-GGGTTTAAAGGA
*
1324300 TTTAAAGTTT
1 TTTAAGGTTT
1324310 GGAGGTTTGG
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
56 11 0.19
57 26 0.45
58 21 0.36
ACGTcount: A:0.22, C:0.02, G:0.28, T:0.48
Consensus pattern (58 bp):
TTTAAGGTTTCATTTTTAGGGTTTAGAAGGTTTACGGTTTAATTTAGGGTTTAAAGGA
Found at i:1324316 original size:43 final size:44
Alignment explanation
Indices: 1324263--1324353 Score: 125
Period size: 43 Copynumber: 2.1 Consensus size: 44
1324253 CATTTTTAGG
*
1324263 GTTTGAAGGTTT-GGGTTTAA-TTTAGGGGTTTGAAGGATTTAA-A
1 GTTTGAAGGTTTGGGGTTTAATTTTAGAGGTTT-AA-GATTTAAGA
*
1324306 GTTTGGAGGTTTGGGGTTTAATTTTAGAGGTTTAAGATTTAAGA
1 GTTTGAAGGTTTGGGGTTTAATTTTAGAGGTTTAAGATTTAAGA
1324350 GTTT
1 GTTT
1324354 CAAAGCTTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 18 0.42
44 15 0.35
45 10 0.23
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (44 bp):
GTTTGAAGGTTTGGGGTTTAATTTTAGAGGTTTAAGATTTAAGA
Found at i:1324337 original size:21 final size:20
Alignment explanation
Indices: 1324269--1324338 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 20
1324259 TAGGGTTTGA
1324269 AGGTTT-GGGTTTAATTTAG
1 AGGTTTGGGGTTTAATTTAG
* * *
1324288 GGGTTTGAAGGATTTAAAGTTTGG
1 AGGTTTG--GGGTTT-AA-TTTAG
1324312 AGGTTTGGGGTTTAATTTTAG
1 AGGTTTGGGGTTTAA-TTTAG
1324333 AGGTTT
1 AGGTTT
1324339 AAGATTTAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 5 0.13
21 12 0.31
22 10 0.26
23 2 0.05
24 10 0.26
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.44
Consensus pattern (20 bp):
AGGTTTGGGGTTTAATTTAG
Found at i:1324346 original size:21 final size:20
Alignment explanation
Indices: 1324278--1324347 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
1324268 AAGGTTTGGG
*
1324278 TTTAATTTAGGGGTTTGAAGGA
1 TTTAATTTAGAGGTTT-AA-GA
* ** *
1324300 TTTAAAGTTTGGAGGTTTGGGG
1 TTT-AA-TTTAGAGGTTTAAGA
1324322 TTTAATTTTAGAGGTTTAAGA
1 TTTAA-TTTAGAGGTTTAAGA
1324343 TTTAA
1 TTTAA
1324348 GAGTTTCAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
21 18 0.50
22 7 0.19
23 2 0.06
24 9 0.25
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (20 bp):
TTTAATTTAGAGGTTTAAGA
Found at i:1324686 original size:13 final size:13
Alignment explanation
Indices: 1324670--1324711 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
1324660 TTTTACAATC
1324670 ATTTTGTATTTTT
1 ATTTTGTATTTTT
*
1324683 ATTTT-TACTTTT
1 ATTTTGTATTTTT
*
1324695 ATTTTGTATTTGT
1 ATTTTGTATTTTT
1324708 ATTT
1 ATTT
1324712 AACACTTAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (13 bp):
ATTTTGTATTTTT
Found at i:1324687 original size:25 final size:25
Alignment explanation
Indices: 1324659--1324711 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1324649 TATTATTATT
*
1324659 TTTTTACAATCATTTTGTATTTTTA
1 TTTTTACAATCATTTTGTATTTGTA
** *
1324684 TTTTTACTTTTATTTTGTATTTGTA
1 TTTTTACAATCATTTTGTATTTGTA
1324709 TTT
1 TTT
1324712 AACACTTAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.70
Consensus pattern (25 bp):
TTTTTACAATCATTTTGTATTTGTA
Found at i:1325867 original size:18 final size:17
Alignment explanation
Indices: 1325844--1325899 Score: 73
Period size: 16 Copynumber: 3.4 Consensus size: 17
1325834 TTTTTATCTC
1325844 TTTTTTTAATTAATTAA
1 TTTTTTTAATTAATTAA
1325861 TTTTTTTAATTTAA-TAA
1 TTTTTTTAA-TTAATTAA
*
1325878 -TTTTTTAA-TATTTAA
1 TTTTTTTAATTAATTAA
1325893 TTTTTTT
1 TTTTTTT
1325900 GTTGTATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
14 2 0.06
15 3 0.09
16 14 0.40
17 12 0.34
18 4 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTTTAATTAATTAA
Found at i:1335345 original size:13 final size:13
Alignment explanation
Indices: 1335309--1335334 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1335299 AAAAAAATAA
1335309 CAAAATTTAAATT
1 CAAAATTTAAATT
1335322 CAAAATTTAAATT
1 CAAAATTTAAATT
1335335 TATAAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
CAAAATTTAAATT
Found at i:1335771 original size:13 final size:13
Alignment explanation
Indices: 1335735--1335760 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1335725 AAAAAAATAA
1335735 CAAAATTTAAATT
1 CAAAATTTAAATT
1335748 CAAAATTTAAATT
1 CAAAATTTAAATT
1335761 TATAAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
CAAAATTTAAATT
Found at i:1340269 original size:24 final size:24
Alignment explanation
Indices: 1340238--1340285 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1340228 GCTTTACAAG
1340238 TTCTTCCATTGGCAAATGAAAACC
1 TTCTTCCATTGGCAAATGAAAACC
1340262 TTCTTCCATTGGCAAATGAAAACC
1 TTCTTCCATTGGCAAATGAAAACC
1340286 CTGGCAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.29
Consensus pattern (24 bp):
TTCTTCCATTGGCAAATGAAAACC
Found at i:1341299 original size:2 final size:2
Alignment explanation
Indices: 1341292--1341349 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
1341282 GAATCTCAAC
* *
1341292 AT AT AT AT AT AT AT GT AT GT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1341333 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1341350 CACACACCCA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1342639 original size:2 final size:2
Alignment explanation
Indices: 1342632--1342659 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1342622 CACTTGTAAA
1342632 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1342660 TGAGAGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1346192 original size:2 final size:2
Alignment explanation
Indices: 1346185--1346212 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1346175 CAATCTCTTG
1346185 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1346213 TTGAGAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1349725 original size:6 final size:6
Alignment explanation
Indices: 1349709--1349749 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
1349699 GAGCTCATTT
1349709 TTTTAAA TTTTAA TTTTAA -TTTAA -TTTAA TTTTTAA TTTTA
1 TTTT-AA TTTTAA TTTTAA TTTTAA TTTTAA -TTTTAA TTTTA
1349750 TTAATTTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.31
6 13 0.41
7 9 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTTAA
Found at i:1349736 original size:16 final size:16
Alignment explanation
Indices: 1349717--1349757 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
1349707 TTTTTTAAAT
1349717 TTTAATTTTAATTTAA
1 TTTAATTTTAATTTAA
*
1349733 TTTAATTTTTAATTTTA
1 TTTAA-TTTTAATTTAA
1349750 -TTAATTTT
1 TTTAATTTT
1349758 CATTATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 9 0.39
17 10 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTAATTTTAATTTAA
Found at i:1349742 original size:17 final size:17
Alignment explanation
Indices: 1349717--1349757 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1349707 TTTTTTAAAT
1349717 TTTAA-TTTTAATTTAA
1 TTTAATTTTTAATTTAA
*
1349733 TTTAATTTTTAATTTTA
1 TTTAATTTTTAATTTAA
1349750 -TTAATTTT
1 TTTAATTTT
1349758 CATTATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTAATTTTTAATTTAA
Found at i:1349767 original size:3 final size:3
Alignment explanation
Indices: 1349759--1349926 Score: 157
Period size: 3 Copynumber: 55.0 Consensus size: 3
1349749 ATTAATTTTC
* * * *
1349759 ATT ATT ATT ATG ATT ATG ATT ATG ATT ATG ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1349807 ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATCT ATT AAT ATT -TT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT AT-T ATT ATT ATT ATT ATT
*
1349852 ATTT ATAT ATT ATT ATT ATT ATT -TT AGTT ATCT ATT AAT A-T ATT -TT
1 A-TT AT-T ATT ATT ATT ATT ATT ATT A-TT AT-T ATT ATT ATT ATT ATT
* *
1349898 ATT ATTT ATCT ATT ATT TTT ATT TTT ATT
1 ATT A-TT AT-T ATT ATT ATT ATT ATT ATT
1349927 TTTTGTCTTG
Statistics
Matches: 138, Mismatches: 15, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
2 10 0.07
3 104 0.75
4 24 0.17
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1350701 original size:3 final size:3
Alignment explanation
Indices: 1350693--1350724 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1350683 ATTTATTTAT
*
1350693 TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1350725 TCTAAATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1361290 original size:14 final size:16
Alignment explanation
Indices: 1361271--1361302 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1361261 ATTATACTTT
1361271 AAGAAAAA-AAA-AAA
1 AAGAAAAACAAAGAAA
1361285 AAGAAAAACAAAGAAA
1 AAGAAAAACAAAGAAA
1361301 AA
1 AA
1361303 AGAGGAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (16 bp):
AAGAAAAACAAAGAAA
Found at i:1362427 original size:44 final size:43
Alignment explanation
Indices: 1362317--1362607 Score: 303
Period size: 44 Copynumber: 6.7 Consensus size: 43
1362307 AAATTATGGT
* *
1362317 GCCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCGTTAA
1 GCCTCTGTTTAGAGGAGCTTTGTTTATTTTCCAAAGTCGTTGA
* ** * * **
1362360 GACTCTACTTAGAGGAGCATTGTTGATTTATCCAAAGTTTTTGA
1 GCCTCTGTTTAGAGGAGCTTTGTTTATTT-TCCAAAGTCGTTGA
* * * * *
1362404 GCCTCTGTTTAAAAGAACTTTGTTTATTTTTCAAAGTTGTTGA
1 GCCTCTGTTTAGAGGAGCTTTGTTTATTTTCCAAAGTCGTTGA
* * * *
1362447 GCATCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGA
1 GCCTCTGTTTAGAGGAGCTTTGTTTATTTTCCAAAGTCGTTGA
*
1362490 GCCTCTGCTTAGAGGAGCTTTGTTTATTTATCCAAAGTCGTTGA
1 GCCTCTGTTTAGAGGAGCTTTGTTTATTT-TCCAAAGTCGTTGA
* **
1362534 GCCTCTGCTTAGAGGAGCTTTGTTTATCTTTGTAAAGTCGTTGA
1 GCCTCTGTTTAGAGGAGCTTTGTTTAT-TTTCCAAAGTCGTTGA
* * * * * *
1362578 GCTTCTGCTTAAAGGAACCTTATTTATTTT
1 GCCTCTGTTTAGAGGAGCTTTGTTTATTTT
1362608 TTTAAAAAAT
Statistics
Matches: 207, Mismatches: 38, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
43 101 0.49
44 104 0.50
45 2 0.01
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (43 bp):
GCCTCTGTTTAGAGGAGCTTTGTTTATTTTCCAAAGTCGTTGA
Found at i:1362459 original size:87 final size:86
Alignment explanation
Indices: 1362317--1362608 Score: 307
Period size: 87 Copynumber: 3.4 Consensus size: 86
1362307 AAATTATGGT
* * *
1362317 GCCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCGTTAAG-ACTCTACTTAGAGGAGCATT
1 GCCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCGTTGAGCA-TCTGCTTAGAGGAGCTTT
**
1362381 GTTGATTTATCCAAAGTTTTTGA
65 GTTGATTT-TCCAAAGTCATTGA
* * * * * *
1362404 GCCTCTGTTTAAAAGAACTTTGTTTATTTTTCAAAGTTGTTGAGCATCTGTTTAGAGGAGCTTTA
1 GCCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCGTTGAGCATCTGCTTAGAGGAGCTTTG
* *
1362469 TTTATTTTTCAAAGTCATTGA
66 TTGATTTTCCAAAGTCATTGA
* * *
1362490 GCCTCTGCTTAGAGGAGCTTTGTTTATTTATCCAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTT
1 GCCTCTGTTTAGAGGAGCTTTGTTTATTT-TTCAAAGTCGTTGAGCATCTGCTTAGAGGAGCTTT
* ** *
1362555 GTTTATCTTTGTAAAGTCGTTGA
65 GTTGAT-TTTCCAAAGTCATTGA
* * * * * *
1362578 GCTTCTGCTTAAAGGAACCTTATTTATTTTT
1 GCCTCTGTTTAGAGGAGCTTTGTTTATTTTT
1362609 TTAAAAAATT
Statistics
Matches: 171, Mismatches: 31, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
86 36 0.21
87 97 0.57
88 38 0.22
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (86 bp):
GCCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCGTTGAGCATCTGCTTAGAGGAGCTTTG
TTGATTTTCCAAAGTCATTGA
Found at i:1362555 original size:130 final size:131
Alignment explanation
Indices: 1362320--1362608 Score: 384
Period size: 130 Copynumber: 2.2 Consensus size: 131
1362310 TTATGGTGCC
* *
1362320 TCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCGTTAAGACTCTACTTAGAGGAGCATTGTTG
1 TCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCATTAAGACTCTACTTAGAGGAGCATTGTTG
** * *
1362385 ATTTATCCAAAGTTTTTGAGCCTCTGTTTAAAAGAACTTTGTTTAT-TTT-TCAAAGTTGTTGAG
66 ATTTATCCAAAGTCGTTGAGCCTCTGCTTAAAAGAACTTTGTTTATCTTTGT-AAAGTCGTTGAG
1362448 CA
130 CA
* * * * *
1362450 TCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGAGCCTCTGCTTAGAGGAGCTTTGTTT
1 TCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCATTAAGACTCTACTTAGAGGAGCATTGTTG
* * *
1362515 ATTTATCCAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTGTTTATCTTTGTAAAGTCGTTGAGC
66 ATTTATCCAAAGTCGTTGAGCCTCTGCTTAAAAGAACTTTGTTTATCTTTGTAAAGTCGTTGAGC
*
1362580 T
131 A
* * * *
1362581 TCTGCTTAAAGGAACCTTATTTATTTTT
1 TCTGTTTAGAGGAGCTTTATTTATTTTT
1362609 TTAAAAAATT
Statistics
Matches: 138, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
130 98 0.71
131 39 0.28
132 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (131 bp):
TCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCATTAAGACTCTACTTAGAGGAGCATTGTTG
ATTTATCCAAAGTCGTTGAGCCTCTGCTTAAAAGAACTTTGTTTATCTTTGTAAAGTCGTTGAGC
A
Found at i:1362859 original size:5 final size:6
Alignment explanation
Indices: 1362822--1362858 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1362812 GGACTCATTT
1362822 TTTTAA TTTTAA TTTTAA TTTTAA -TTTAA -TTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTT
1362859 ATTATTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:1362890 original size:17 final size:16
Alignment explanation
Indices: 1362852--1362897 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
1362842 TTAATTTAAT
1362852 TTAAT-TTA-TTATTA
1 TTAATATTATTTATTA
*
1362866 TTATTATTATTTATCTA
1 TTAATATTATTTAT-TA
*
1362883 TTAATATTTTTTATT
1 TTAATATTATTTATT
1362898 TATCTATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 3 0.12
16 5 0.19
17 14 0.54
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TTAATATTATTTATTA
Found at i:1362910 original size:16 final size:16
Alignment explanation
Indices: 1362889--1362921 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1362879 TCTATTAATA
*
1362889 TTTTTTATTTATCTAT
1 TTTTTTAGTTATCTAT
1362905 TTTTTTAGTTATCTAT
1 TTTTTTAGTTATCTAT
1362921 T
1 T
1362922 AATAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTTTTAGTTATCTAT
Found at i:1362937 original size:40 final size:38
Alignment explanation
Indices: 1362856--1362952 Score: 128
Period size: 37 Copynumber: 2.6 Consensus size: 38
1362846 TTTAATTTAA
* *
1362856 TTTA-TTAT-TATTATTATTATTTATCTATTAATATTT
1 TTTATTTATCTATTATTTTTAGTTATCTATTAATATTT
1362892 TTTATTTATCTATT-TTTTTAGTTATCTATTAATAAATTT
1 TTTATTTATCTATTATTTTTAGTTATCTATTAAT--ATTT
1362931 TATTATTTATCTATTATTTTTA
1 T-TTATTTATCTATTATTTTTA
1362953 TTTTTATTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
36 4 0.08
37 21 0.40
38 4 0.08
39 5 0.09
40 13 0.25
41 6 0.11
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (38 bp):
TTTATTTATCTATTATTTTTAGTTATCTATTAATATTT
Found at i:1363429 original size:16 final size:15
Alignment explanation
Indices: 1363404--1363433 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1363394 TTTTAGAGAG
1363404 AAAAAGGAGAAAAAA
1 AAAAAGGAGAAAAAA
1363419 AAAAAGAGAGAAAAA
1 AAAAAG-GAGAAAAA
1363434 TGAAAGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAAGGAGAAAAAA
Found at i:1363747 original size:3 final size:3
Alignment explanation
Indices: 1363730--1363772 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
1363720 ATTCATTTAT
*
1363730 TTA TTA -TA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1363773 TCTAAATTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1363869 original size:19 final size:20
Alignment explanation
Indices: 1363845--1363882 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1363835 ATTTTCCATA
*
1363845 AAAAT-AAAGTTTCTAAAAT
1 AAAATAAAAATTTCTAAAAT
1363864 AAAATAAAAATTTCTAAAA
1 AAAATAAAAATTTCTAAAA
1363883 AAATAGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAATAAAAATTTCTAAAAT
Found at i:1363945 original size:61 final size:60
Alignment explanation
Indices: 1363864--1364038 Score: 173
Period size: 61 Copynumber: 2.9 Consensus size: 60
1363854 TTTCTAAAAT
*
1363864 AAAATAAAAAT-TTCTAAAAAAATAGCATTTTAAGGAAAGTTGAAAGTATCAATTTTCCTTA
1 AAAATAAAAATGTTCT-AAAAAATAG-ATTTTAAGAAAAGTTGAAAGTATCAATTTTCCTTA
* * * * *
1363925 AAAATAAAAGTGTTCTAAAAAATA-TTTTTGAAAAAAAAGTTGAAAGTATCAATTTTTTCTTG
1 AAAATAAAAATGTTCTAAAAAATAGATTTT--AAGAAAAGTTGAAAGTATCAA-TTTTCCTTA
* * *
1363987 AAAATAAAATTG-T-TAAAAAGT--ATTTTGAGAAAAAGTTGAAAGTATCAATTTT
1 AAAATAAAAATGTTCTAAAAAATAGATTTTAAG-AAAAGTTGAAAGTATCAATTTT
1364039 TCTTGTACAA
Statistics
Matches: 98, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
57 5 0.05
58 18 0.18
59 8 0.08
60 7 0.07
61 38 0.39
62 22 0.22
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (60 bp):
AAAATAAAAATGTTCTAAAAAATAGATTTTAAGAAAAGTTGAAAGTATCAATTTTCCTTA
Found at i:1367462 original size:60 final size:59
Alignment explanation
Indices: 1367368--1367599 Score: 333
Period size: 60 Copynumber: 3.9 Consensus size: 59
1367358 ATATATATAT
*
1367368 AATAAAATTTTCAAAAAAACATTTTTAAGAAAAAGTTGAAAGTATTAATTTTTCTTGAA
1 AATAAAATTTTCAAAAAAACATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAA
*
1367427 AATAAAATTTTCAAAAAAAACATTTTTAAGGAAAAGTTGAAAGTATCAA-TTTTCTTTGAA
1 AATAAAATTTTC-AAAAAAACATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTC-TTGAA
* * *
1367487 AATAAAATTTTCAAAAAAACATTTTTAAGAAAAAATTAAAAGTATTAATTTTTCTTGAA
1 AATAAAATTTTCAAAAAAACATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAA
** * *
1367546 AATAAAA-TTAAAAAAATATATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTT
1 AATAAAATTTTCAAAAA-A-ACATTTTTAAGAAAAAGTTGAAAGTATCAATTTTT
1367600 AAAAAAAAAT
Statistics
Matches: 155, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
58 7 0.05
59 62 0.40
60 86 0.55
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (59 bp):
AATAAAATTTTCAAAAAAACATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAA
Found at i:1367500 original size:119 final size:119
Alignment explanation
Indices: 1367368--1367598 Score: 394
Period size: 119 Copynumber: 1.9 Consensus size: 119
1367358 ATATATATAT
* *
1367368 AATAAAATTTTCAAAAAAACATTTTTAAGAAAAAGTTGAAAGTATTAATTTTTCTTGAAAATAAA
1 AATAAAATTTTCAAAAAAACATTTTTAAGAAAAAATTAAAAGTATTAATTTTTCTTGAAAATAAA
*
1367433 ATTTTCAAAAAA-A-ACATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCTTTGAA
66 A--TTAAAAAAATATACATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCTTTGAA
1367487 AATAAAATTTTCAAAAAAACATTTTTAAGAAAAAATTAAAAGTATTAATTTTTCTTGAAAATAAA
1 AATAAAATTTTCAAAAAAACATTTTTAAGAAAAAATTAAAAGTATTAATTTTTCTTGAAAATAAA
*
1367552 ATTAAAAAAATATATATTTTTAAGGAAAAGTTGAAAGTATCAATTTT
66 ATTAAAAAAATATACATTTTTAAGGAAAAGTTGAAAGTATCAATTTT
1367599 TAAAAAAAAA
Statistics
Matches: 106, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
117 8 0.08
118 1 0.01
119 97 0.92
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (119 bp):
AATAAAATTTTCAAAAAAACATTTTTAAGAAAAAATTAAAAGTATTAATTTTTCTTGAAAATAAA
ATTAAAAAAATATACATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCTTTGAA
Found at i:1367537 original size:27 final size:27
Alignment explanation
Indices: 1367507--1367626 Score: 91
Period size: 27 Copynumber: 4.2 Consensus size: 27
1367497 TCAAAAAAAC
*
1367507 ATTTTTAAGAAAAAATTAAAAGTATTA
1 ATTTTTAAGAAAAAATTAAAAGTATCA
*
1367534 ATTTTTCTTGAA-AATAAAATTAAAAAAATAT-A
1 A--TTT-TT-AAGAA-AAAATT--AAAAGTATCA
* * *
1367566 TATTTTTAAGGAAAAGTTGAAAGTATCA
1 -ATTTTTAAGAAAAAATTAAAAGTATCA
* *
1367594 ATTTTTAAAAAAAAATTGAAAGTATCA
1 ATTTTTAAGAAAAAATTAAAAGTATCA
1367621 ATTTTT
1 ATTTTT
1367627 CTTGTATAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
27 37 0.49
28 1 0.01
29 10 0.13
30 7 0.09
31 11 0.15
32 1 0.01
33 8 0.11
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (27 bp):
ATTTTTAAGAAAAAATTAAAAGTATCA
Found at i:1367598 original size:26 final size:27
Alignment explanation
Indices: 1367567--1367626 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
1367557 AAAAATATAT
** *
1367567 ATTTTTAAGGAAAAGTTGAAAGTATCA
1 ATTTTTAAAAAAAAATTGAAAGTATCA
1367594 ATTTTTAAAAAAAAATTGAAAGTATCA
1 ATTTTTAAAAAAAAATTGAAAGTATCA
1367621 ATTTTT
1 ATTTTT
1367627 CTTGTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (27 bp):
ATTTTTAAAAAAAAATTGAAAGTATCA
Found at i:1376627 original size:2 final size:2
Alignment explanation
Indices: 1376620--1376658 Score: 60
Period size: 2 Copynumber: 18.5 Consensus size: 2
1376610 TTCTAAAGTG
1376620 TA TA TA TA TA TA TA GTA TA TA TA TA TA TA TA GTA TA TA T
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA T
1376659 TGGTACATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 31 0.89
3 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1376639 original size:15 final size:15
Alignment explanation
Indices: 1376619--1376658 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1376609 CTTCTAAAGT
1376619 GTATATATATATATA
1 GTATATATATATATA
1376634 GTATATATATATATA
1 GTATATATATATATA
1376649 -TAGTATATAT
1 GTA-TATATAT
1376659 TGGTACATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 2 0.08
15 22 0.92
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
GTATATATATATATA
Found at i:1376642 original size:17 final size:17
Alignment explanation
Indices: 1376620--1376658 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1376610 TTCTAAAGTG
1376620 TATATATATATATAGTA
1 TATATATATATATAGTA
1376637 TATATATATATATAGTA
1 TATATATATATATAGTA
1376654 TATAT
1 TATAT
1376659 TGGTACATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
TATATATATATATAGTA
Found at i:1377736 original size:43 final size:44
Alignment explanation
Indices: 1377674--1377760 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 44
1377664 CCCTTGTTGG
1377674 GTACGCATGTTCATGCTCTATAACTCTAAAGTATAAT-AAAAAA
1 GTACGCATGTTCATGCTCTATAACTCTAAAGTATAATGAAAAAA
*
1377717 GTACGCATGTTCATTCTCTATAACTCTAAAGTATAATGAAAAAA
1 GTACGCATGTTCATGCTCTATAACTCTAAAGTATAATGAAAAAA
1377761 AATAAAGGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 36 0.86
44 6 0.14
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (44 bp):
GTACGCATGTTCATGCTCTATAACTCTAAAGTATAATGAAAAAA
Found at i:1384191 original size:65 final size:66
Alignment explanation
Indices: 1384105--1384229 Score: 216
Period size: 65 Copynumber: 1.9 Consensus size: 66
1384095 CTGAAGTAAG
*
1384105 GCTTAGATACTAACGATGATTGTGTTGTTTATCAGACCAAAACTTT-GAAAATTTGTACGAGTCA
1 GCTTAGATACTAACGATGATTGTGTTGCTTATCAGACCAAAACTTTAGAAAATTTGTACGAGTCA
1384169 A
66 A
* *
1384170 GCTTAGATACTCACGGTGATTGTGTTGCTTATCAGACCAAAACTTTAGAAAATTTGTACG
1 GCTTAGATACTAACGATGATTGTGTTGCTTATCAGACCAAAACTTTAGAAAATTTGTACG
1384230 GGGCAAACTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
65 43 0.77
66 13 0.23
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (66 bp):
GCTTAGATACTAACGATGATTGTGTTGCTTATCAGACCAAAACTTTAGAAAATTTGTACGAGTCA
A
Found at i:1389760 original size:23 final size:22
Alignment explanation
Indices: 1389716--1389762 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
1389706 TATGTTGAAC
* *
1389716 AAAAAAATTATTTGTGTAATTT
1 AAAAAAATTATTTATATAATTT
*
1389738 AAAATAAATTATTTATATTATTT
1 AAAA-AAATTATTTATATAATTT
1389761 AA
1 AA
1389763 GTAATCAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
AAAAAAATTATTTATATAATTT
Found at i:1389848 original size:17 final size:17
Alignment explanation
Indices: 1389828--1389870 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1389818 TTTCAGATAA
*
1389828 TTTTAATTTTTAAAT-T
1 TTTTAATTTTAAAATAT
*
1389844 TTTTTATTTTAAAATAT
1 TTTTAATTTTAAAATAT
*
1389861 TATTAATTTT
1 TTTTAATTTT
1389871 GAATAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTAATTTTAAAATAT
Found at i:1389898 original size:22 final size:21
Alignment explanation
Indices: 1389873--1389914 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1389863 TTAATTTTGA
1389873 ATAAATATATTTAAATAAAAAT
1 ATAAA-ATATTTAAATAAAAAT
* *
1389895 ATAAACTGTTTAAATAAAAA
1 ATAAAATATTTAAATAAAAA
1389915 AATATGAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAAAATATTTAAATAAAAAT
Found at i:1389932 original size:23 final size:23
Alignment explanation
Indices: 1389889--1389933 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1389879 ATATTTAAAT
*
1389889 AAAAATATAAACTGTTTAAATAA
1 AAAAATATAAACTGTTAAAATAA
*
1389912 AAAAATATGAA-TGTATAAAATA
1 AAAAATATAAACTGT-TAAAATA
1389934 TCATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (23 bp):
AAAAATATAAACTGTTAAAATAA
Found at i:1392729 original size:16 final size:17
Alignment explanation
Indices: 1392699--1392731 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1392689 ATATATTATA
1392699 TTTAATTATTAAATTTT
1 TTTAATTATTAAATTTT
1392716 TTTAATTA-TAAATTTT
1 TTTAATTATTAAATTTT
1392732 CAAAATCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAATTATTAAATTTT
Found at i:1392731 original size:14 final size:16
Alignment explanation
Indices: 1392699--1392731 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1392689 ATATATTATA
1392699 TTTAATTATTAAATTTT
1 TTTAATTATTAAA-TTT
1392716 TTTAATTA-TAAATTT
1 TTTAATTATTAAATTT
1392731 T
1 T
1392732 CAAAATCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 4 0.25
17 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTAATTATTAAATTT
Found at i:1393337 original size:6 final size:6
Alignment explanation
Indices: 1393328--1393363 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1393318 AAGTTTTATT
* *
1393328 TTTTGC TTTTAC TTTTAT TTTTAC TTTTAC TTTTAC
1 TTTTAC TTTTAC TTTTAC TTTTAC TTTTAC TTTTAC
1393364 ATGTTTATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.69
Consensus pattern (6 bp):
TTTTAC
Found at i:1393354 original size:18 final size:19
Alignment explanation
Indices: 1393321--1393362 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
1393311 ATATTTTAAG
*
1393321 TTTTATTTTTTGCTTTTAC
1 TTTTATTTTTTACTTTTAC
1393340 TTTTA-TTTTTACTTTTAC
1 TTTTATTTTTTACTTTTAC
1393358 TTTTA
1 TTTTA
1393363 CATGTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTATTTTTTACTTTTAC
Found at i:1397994 original size:16 final size:16
Alignment explanation
Indices: 1397968--1398000 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1397958 TTAAGTTCGT
1397968 TTATAAGAAAC-AGCG
1 TTATAAGAAACAAGCG
1397983 TTATAAGAAAACAAGCG
1 TTATAAG-AAACAAGCG
1398000 T
1 T
1398001 GAACCACGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (16 bp):
TTATAAGAAACAAGCG
Found at i:1401949 original size:20 final size:21
Alignment explanation
Indices: 1401925--1401971 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1401915 CAGATATTTT
* *
1401925 TAATTTTATTTTATTATTATA
1 TAATTTAATTTAATTATTATA
*
1401946 -AATTTAATTTAATTTTTATA
1 TAATTTAATTTAATTATTATA
1401966 TAATTT
1 TAATTT
1401972 GTACAATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TAATTTAATTTAATTATTATA
Found at i:1406957 original size:26 final size:26
Alignment explanation
Indices: 1406919--1406975 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
1406909 ATTATATTTG
*
1406919 ATATATATAATAATATAAATTATTAAA
1 ATATAAATAATAATATAAATTA-TAAA
1406946 ATATAAAT-ATAATATAAATTATAAA
1 ATATAAATAATAATATAAATTATAAA
1406971 ATATA
1 ATATA
1406976 TTTAAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 9 0.31
26 13 0.45
27 7 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
ATATAAATAATAATATAAATTATAAA
Found at i:1406961 original size:11 final size:12
Alignment explanation
Indices: 1406928--1406969 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 12
1406918 GATATATATA
1406928 ATAATATAAATT
1 ATAATATAAATT
1406940 ATTAAAATATAAA-T
1 A-T--AATATAAATT
1406954 ATAATATAAATT
1 ATAATATAAATT
1406966 ATAA
1 ATAA
1406970 AATATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 8 0.31
12 6 0.23
13 2 0.08
14 2 0.08
15 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAATATAAATT
Found at i:1406995 original size:19 final size:19
Alignment explanation
Indices: 1406919--1406997 Score: 80
Period size: 18 Copynumber: 4.4 Consensus size: 19
1406909 ATTATATTTG
*
1406919 ATATATATAATAATATAAAT
1 ATATATATAA-ATTATAAAT
1406939 -TAT-TA-AAA-TATAAAT
1 ATATATATAAATTATAAAT
1406954 ATA-ATATAAATTATAAA-
1 ATATATATAAATTATAAAT
* *
1406971 ATATATTTAAATTTTAAAT
1 ATATATATAAATTATAAAT
1406990 ATATATAT
1 ATATATAT
1406998 GTTTAATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
15 7 0.14
16 5 0.10
17 8 0.16
18 20 0.40
19 10 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATATATAAATTATAAAT
Found at i:1407099 original size:19 final size:19
Alignment explanation
Indices: 1407063--1407106 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1407053 TTTAAATATT
*
1407063 ATATAAATAAAAATAAATA
1 ATATAAATAAAAACAAATA
* *
1407082 ATATAAATATACACAAATA
1 ATATAAATAAAAACAAATA
1407101 A-ATAAA
1 ATATAAA
1407107 ATTAATACGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (19 bp):
ATATAAATAAAAACAAATA
Found at i:1407415 original size:17 final size:17
Alignment explanation
Indices: 1407381--1407415 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1407371 AATGTATAGA
*
1407381 ATTAATATTAATATTAT
1 ATTAATATTAATAATAT
*
1407398 ATTAATATTATTAATAT
1 ATTAATATTAATAATAT
1407415 A
1 A
1407416 AAATTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAATATTAATAATAT
Found at i:1408009 original size:16 final size:16
Alignment explanation
Indices: 1407961--1408012 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1407951 TTTAATTAAT
* *
1407961 TTTTTAATTATATATA
1 TTTTTAAATATTTATA
* * * *
1407977 TATTTATATAATGATA
1 TTTTTAAATATTTATA
1407993 TTTTTAAATATTTATA
1 TTTTTAAATATTTATA
1408009 TTTT
1 TTTT
1408013 AAAAATAATA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTTTAAATATTTATA
Found at i:1408024 original size:30 final size:32
Alignment explanation
Indices: 1407957--1408026 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 32
1407947 TTTTTTTAAT
* *
1407957 TAAT-TTTTTAATTATATATATATTTATATAA
1 TAATATTTTTAAATATATATATATTTATAAAA
* *
1407988 TGATATTTTTAAATATTTATAT-TTTA-AAAA
1 TAATATTTTTAAATATATATATATTTATAAAA
1408018 TAATATTTT
1 TAATATTTT
1408027 ATTAATTTCG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 11 0.33
31 7 0.21
32 15 0.45
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (32 bp):
TAATATTTTTAAATATATATATATTTATAAAA
Found at i:1428203 original size:20 final size:21
Alignment explanation
Indices: 1428170--1428214 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
1428160 ATAATATAAA
*
1428170 ATATTAATAATTTATATATTT
1 ATATTAATAATTTATATATTG
*
1428191 ATATT-ATATTTTATATATTG
1 ATATTAATAATTTATATATTG
1428211 ATAT
1 ATAT
1428215 AAAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATATTAATAATTTATATATTG
Found at i:1432851 original size:30 final size:30
Alignment explanation
Indices: 1432745--1432851 Score: 80
Period size: 30 Copynumber: 3.6 Consensus size: 30
1432735 TTTATTACAT
* *
1432745 CTAAATAAGCTCTTAAATT-TTAATTTAAAC
1 CTAAATAAACTCTT-AATTATTAATTTATAC
* *
1432775 GTAAATAAACCCTTAA-TATTTAATCTGTAT-C
1 CTAAATAAACTCTTAATTA-TTAAT-T-TATAC
*
1432806 C-AAAT-AAGTCATTAATTATTAATTTATAC
1 CTAAATAAACTC-TTAATTATTAATTTATAC
*
1432835 CTAAATAAATTCTTAAT
1 CTAAATAAACTCTTAAT
1432852 ATAAATCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
28 4 0.07
29 8 0.13
30 38 0.63
31 8 0.13
32 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (30 bp):
CTAAATAAACTCTTAATTATTAATTTATAC
Found at i:1438946 original size:26 final size:26
Alignment explanation
Indices: 1438897--1438946 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1438887 TGATAGAGGT
*
1438897 TCCTGATATTATCTGATATTTAGTGA
1 TCCTGATATTATCTGATATATAGTGA
1438923 TCCTGATATTAATCTGATA-ATAGT
1 TCCTGATATT-ATCTGATATATAGT
1438947 TCACCACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (26 bp):
TCCTGATATTATCTGATATATAGTGA
Found at i:1443082 original size:5 final size:5
Alignment explanation
Indices: 1443072--1443096 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1443062 ATGATTTATG
1443072 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
1443097 TATTATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:1447603 original size:2 final size:2
Alignment explanation
Indices: 1447596--1447634 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1447586 ACAGTGTAAA
*
1447596 CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1447635 ACTTCTCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:1447917 original size:2 final size:2
Alignment explanation
Indices: 1447910--1447956 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
1447900 GTGCTGTCAT
* * *
1447910 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG GG AG AG AA
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1447952 AG AG A
1 AG AG A
1447957 CCAAAAAGGC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1449332 original size:38 final size:37
Alignment explanation
Indices: 1449290--1449374 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 37
1449280 TACCACACCA
* *
1449290 ATCTATTTGTGTGTTACAAATGGGTATCATATACCTAT
1 ATCTATTT-TGTGTTACAAATGGGTATCACATACCCAT
*
1449328 ATCTATATTTGTGTTTCAAATGGGTATCACATACCCAT
1 ATCTAT-TTTGTGTTACAAATGGGTATCACATACCCAT
1449366 ATCTATTTT
1 ATCTATTTT
1449375 CTATCATAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 3 0.07
38 38 0.88
39 2 0.05
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (37 bp):
ATCTATTTTGTGTTACAAATGGGTATCACATACCCAT
Found at i:1450747 original size:64 final size:64
Alignment explanation
Indices: 1450646--1450771 Score: 216
Period size: 64 Copynumber: 2.0 Consensus size: 64
1450636 ATTAGCTAGT
* * * *
1450646 AAAATAGGTATAATATGGATCTAAGCACATATAGATGGAGAAAATGCTCTAAAAGCCAACCACA
1 AAAATAGGAATAATACGGATCTAAGCACATACAGATGGAGAAAATGCTCAAAAAGCCAACCACA
1450710 AAAATAGGAATAATACGGATCTAAGCACATACAGATGGAGAAAATGCTCAAAAAGCCAACCA
1 AAAATAGGAATAATACGGATCTAAGCACATACAGATGGAGAAAATGCTCAAAAAGCCAACCA
1450772 TGAAGGATTG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (64 bp):
AAAATAGGAATAATACGGATCTAAGCACATACAGATGGAGAAAATGCTCAAAAAGCCAACCACA
Found at i:1467674 original size:18 final size:19
Alignment explanation
Indices: 1467636--1467696 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 19
1467626 TATATATAAT
1467636 AATTATTATATTTTATTTTTA
1 AATTATTATA--TTATTTTTA
*
1467657 TATTATTATATTA-TTTTA
1 AATTATTATATTATTTTTA
* *
1467675 AATTATCATATCTAATTTTA
1 AATTATTATAT-TATTTTTA
1467695 AA
1 AA
1467697 AAAATTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 14 0.40
19 5 0.14
20 7 0.20
21 9 0.26
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTATTATATTATTTTTA
Found at i:1474664 original size:21 final size:21
Alignment explanation
Indices: 1474618--1474658 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1474608 ATATAATACG
1474618 ATAATATAATATAAAAATATA
1 ATAATATAATATAAAAATATA
*
1474639 TTAATA-AATATAAAAA-ATA
1 ATAATATAATATAAAAATATA
1474658 A
1 A
1474659 CATAATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.17
20 10 0.56
21 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAATATAATATAAAAATATA
Found at i:1474780 original size:31 final size:31
Alignment explanation
Indices: 1474722--1474780 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1474712 ATTTTTTATT
* * *
1474722 TTTTTATATTAATATAAATTATTATACATAA
1 TTTTTATATAAATATAAAATATAATACATAA
1474753 TTTTTATATAAAATATAAAATA-AATACA
1 TTTTTATAT-AAATATAAAATATAATACA
1474781 AAAACTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (31 bp):
TTTTTATATAAATATAAAATATAATACATAA
Found at i:1479589 original size:32 final size:32
Alignment explanation
Indices: 1479553--1479616 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1479543 TTGGGTGTTA
* *
1479553 TTTAAGAAATTTGATGTTATTTGAGAGAGAGC
1 TTTAAGAAATTTGAAGTTACTTGAGAGAGAGC
1479585 TTTAAGAAATTTGAAGTTACTTGAGAGAGAGC
1 TTTAAGAAATTTGAAGTTACTTGAGAGAGAGC
1479617 CTCAAGTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (32 bp):
TTTAAGAAATTTGAAGTTACTTGAGAGAGAGC
Found at i:1486449 original size:30 final size:31
Alignment explanation
Indices: 1486408--1486484 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 31
1486398 TTATTTTGGT
1486408 TAAAT-AAGTTTTTATATTTTT-A-TTACAT-
1 TAAATAAAGTTTTTAT-TTTTTGATTTACATC
*
1486436 TAGAATAAAG-TTTTATTTTTTGATTTATATC
1 TA-AATAAAGTTTTTATTTTTTGATTTACATC
*
1486467 TAAATAAATTTTTTATTT
1 TAAATAAAGTTTTTATTT
1486485 CAAACGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
28 7 0.17
29 10 0.24
30 14 0.34
31 10 0.24
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (31 bp):
TAAATAAAGTTTTTATTTTTTGATTTACATC
Found at i:1487075 original size:16 final size:17
Alignment explanation
Indices: 1487049--1487081 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1487039 TCTAGAACAG
1487049 ATAGTTTTCATTTTTCT
1 ATAGTTTTCATTTTTCT
1487066 ATAG-TTTCATTTTTCT
1 ATAGTTTTCATTTTTCT
1487082 TTCTGGTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (17 bp):
ATAGTTTTCATTTTTCT
Found at i:1487212 original size:5 final size:5
Alignment explanation
Indices: 1487193--1487227 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
1487183 ATATGCATGG
1487193 ATAAT ATATAT ATAAT ATAAT ATAATT ATAAT ATA
1 ATAAT ATA-AT ATAAT ATAAT ATAA-T ATAAT ATA
1487228 TGCAATAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
ATAAT
Found at i:1487214 original size:16 final size:16
Alignment explanation
Indices: 1487193--1487227 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1487183 ATATGCATGG
1487193 ATAATAT-ATATATAAT
1 ATAATATAAT-TATAAT
1487209 ATAATATAATTATAAT
1 ATAATATAATTATAAT
1487225 ATA
1 ATA
1487228 TGCAATAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAATATAATTATAAT
Found at i:1488301 original size:2 final size:2
Alignment explanation
Indices: 1488294--1488320 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1488284 TAATTAAGTC
1488294 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1488321 ACGGTATGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1492641 original size:2 final size:2
Alignment explanation
Indices: 1492636--1492665 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1492626 TAACTATAGT
*
1492636 TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1492666 AGTGTGTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1494628 original size:16 final size:16
Alignment explanation
Indices: 1494604--1494637 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1494594 GAAATAGGGA
*
1494604 CATATAAAACAAAAAT
1 CATAGAAAACAAAAAT
1494620 CATAGAAAACAAAAAT
1 CATAGAAAACAAAAAT
1494636 CA
1 CA
1494638 CAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.68, C:0.15, G:0.03, T:0.15
Consensus pattern (16 bp):
CATAGAAAACAAAAAT
Found at i:1494658 original size:15 final size:16
Alignment explanation
Indices: 1494609--1494663 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1494599 AGGGACATAT
* *
1494609 AAAACAAAAATCATAG
1 AAAACAAAAATCACAA
1494625 AAAACAAAAATCACAA
1 AAAACAAAAATCACAA
*
1494641 AAAATAAAAA-CACGAA
1 AAAACAAAAATCAC-AA
*
1494657 AACACAA
1 AAAACAA
1494664 CAAGCAGAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
15 3 0.09
16 30 0.91
ACGTcount: A:0.73, C:0.16, G:0.04, T:0.07
Consensus pattern (16 bp):
AAAACAAAAATCACAA
Found at i:1495289 original size:18 final size:18
Alignment explanation
Indices: 1495268--1495307 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1495258 TTTTTTAGTA
*
1495268 TTTTATTTATTTATTTAT
1 TTTTATTTATGTATTTAT
*
1495286 TTTTATTTATGTGTTTAT
1 TTTTATTTATGTATTTAT
1495304 TTTT
1 TTTT
1495308 TTGGTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTTATTTATGTATTTAT
Found at i:1495294 original size:22 final size:21
Alignment explanation
Indices: 1495269--1495309 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1495259 TTTTTAGTAT
*
1495269 TTTATTTATTTATTTATTTTTA
1 TTTATGTATTTATTT-TTTTTA
*
1495291 TTTATGTGTTTATTTTTTT
1 TTTATGTATTTATTTTTTT
1495310 GGTATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTATGTATTTATTTTTTTTA
Found at i:1495352 original size:9 final size:8
Alignment explanation
Indices: 1495335--1495364 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1495325 TTAAATTTAG
1495335 AATAAAAA
1 AATAAAAA
1495343 AATAAAAA
1 AATAAAAA
1495351 AAT-AAAA
1 AATAAAAA
1495358 AATAAAA
1 AATAAAA
1495365 TTTTCGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AATAAAAA
Found at i:1495411 original size:26 final size:25
Alignment explanation
Indices: 1495390--1495437 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1495380 TTAATTATCC
1495390 AATGATGAAATTTATA-AAAATTTCA
1 AATGAT-AAATTTATATAAAATTTCA
* *
1495415 AATGGTAAATTTTTATAAAATTT
1 AATGATAAATTTATATAAAATTT
1495438 TTAAGTGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (25 bp):
AATGATAAATTTATATAAAATTTCA
Found at i:1495542 original size:8 final size:8
Alignment explanation
Indices: 1495529--1495555 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1495519 TTTTCAAACA
1495529 AAAAATAT
1 AAAAATAT
1495537 AAAAATAT
1 AAAAATAT
1495545 AAAAATAT
1 AAAAATAT
1495553 AAA
1 AAA
1495556 TTTGGGTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAATAT
Found at i:1495630 original size:25 final size:25
Alignment explanation
Indices: 1495594--1495648 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
1495584 CAAGAATGAG
* *
1495594 ATTTTTAAAAATTTCAAA-TGATAA
1 ATTTTTAAAAATCTCAAAGTGAAAA
1495618 ATTTTTAAGAAATCTCAAAGTGAAAA
1 ATTTTTAA-AAATCTCAAAGTGAAAA
1495644 ATTTT
1 ATTTT
1495649 CTTTAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 8 0.30
25 9 0.33
26 10 0.37
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (25 bp):
ATTTTTAAAAATCTCAAAGTGAAAA
Found at i:1495788 original size:17 final size:17
Alignment explanation
Indices: 1495766--1495807 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1495756 ACAAATAGTG
1495766 AAAAATTTAAAAATAAA
1 AAAAATTTAAAAATAAA
**
1495783 AAAAATAAAAAAATAAA
1 AAAAATTTAAAAATAAA
*
1495800 AAGAATTT
1 AAAAATTT
1495808 CTAATATGGT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAAATTTAAAAATAAA
Found at i:1497761 original size:68 final size:68
Alignment explanation
Indices: 1497652--1497786 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 68
1497642 CACCTTAAAA
*
1497652 GATGAGTCTTAAATCTCACATCGAACATAATAGGAGTGTCACTGG-GATATATAAGGGTCACGAG
1 GATGAGTCCTAAATCTCACATCGAACATAATAGGAGTGTCACTGGAG-TATATAAGGGTCACGAG
1497716 GTTG
65 GTTG
1497720 GATGAGTCCTAAATCTCACATCGAACATAATAGGAGTGTCACTGGAGTATATAAGGGTCACGAGG
1 GATGAGTCCTAAATCTCACATCGAACATAATAGGAGTGTCACTGGAGTATATAAGGGTCACGAGG
1497785 TT
66 TT
1497787 AGGTGCCGAA
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
68 64 0.98
69 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (68 bp):
GATGAGTCCTAAATCTCACATCGAACATAATAGGAGTGTCACTGGAGTATATAAGGGTCACGAGG
TTG
Found at i:1497823 original size:19 final size:19
Alignment explanation
Indices: 1497799--1497837 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1497789 GTGCCGAAGA
*
1497799 ATGTCACGGAAGGGTCACG
1 ATGTCACGAAAGGGTCACG
1497818 ATGTCACGAAAGGGTCACG
1 ATGTCACGAAAGGGTCACG
1497837 A
1 A
1497838 GGTTGGGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.33, T:0.15
Consensus pattern (19 bp):
ATGTCACGAAAGGGTCACG
Found at i:1498115 original size:156 final size:156
Alignment explanation
Indices: 1497831--1498118 Score: 531
Period size: 156 Copynumber: 1.8 Consensus size: 156
1497821 TCACGAAAGG
*
1497831 GTCACGAGGTTGGGTGCTAATAGGAGTGTCACTGGGGTATATAAGGGTCACGAGGTTGGATGCGG
1 GTCACGAGGTTGGGTGCTAATAGGAGTGTCACTAGGGTATATAAGGGTCACGAGGTTGGATGCGG
* * *
1497896 GAGAATGTCACGGACCTAAGGATGAGTCCTGAATCTCACATCGAACATAATAGGAGGGTCACTGG
66 AAGAATGTCACGGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCACTGG
1497961 GGTATATAAAGGTTTACACTATTTTC
131 GGTATATAAAGGTTTACACTATTTTC
1497987 GTCACGAGGTTGGGTGCTAATAGGAGTGTCACTAGGGTATATAAGGGTCACGAGGTTGGATGCGG
1 GTCACGAGGTTGGGTGCTAATAGGAGTGTCACTAGGGTATATAAGGGTCACGAGGTTGGATGCGG
*
1498052 AAGAATGTCACGGACCTAAGGATGAGTCATGACTCTCACATCGAACATAATAGGAAGGTCACTGG
66 AAGAATGTCACGGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCACTGG
1498117 GG
131 GG
1498119 CTAATAGGAG
Statistics
Matches: 127, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
156 127 1.00
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (156 bp):
GTCACGAGGTTGGGTGCTAATAGGAGTGTCACTAGGGTATATAAGGGTCACGAGGTTGGATGCGG
AAGAATGTCACGGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCACTGG
GGTATATAAAGGTTTACACTATTTTC
Found at i:1498206 original size:116 final size:114
Alignment explanation
Indices: 1497997--1498341 Score: 492
Period size: 116 Copynumber: 3.0 Consensus size: 114
1497987 GTCACGAGGT
* *
1497997 TGGGTGCTAATAGGAGTGTCACTAGGGTATATAAGGGTCACGAGGTTGGATGCGGAAGAATGTCA
1 TGGG-GCTAATAGGAGTGTCA-T-GGGTATATAAGGGTCACGAGGTTGGGTGCGGGAGAATGTCA
*
1498062 CGGACCTAAGGATGAGTCATGACTCTCACATCGAACATAATAGGAAGGTCAC
63 CGGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCAC
1498114 TGGGGCTAATAGGAGTGTCATTGGGGTATATAAGGGTCACGAGGTTGGGTGCGGGAGAATGTCAC
1 TGGGGCTAATAGGAGTGTCA-T-GGGTATATAAGGGTCACGAGGTTGGGTGCGGGAGAATGTCAC
1498179 GGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCAC
64 GGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCAC
* * * *
1498230 T-GGGATATATAAGG-GTTTCA-----CTAT--GGGTCACGAGGTTGGGTGCGAGAGAATGTCAC
1 TGGGGCTA-AT-AGGAGTGTCATGGGTATATAAGGGTCACGAGGTTGGGTGCGGGAGAATGTCAC
*
1498286 GGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGATCAC
64 GGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCAC
1498337 TGGGG
1 TGGGG
1498342 TATATAAGGG
Statistics
Matches: 215, Mismatches: 10, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
107 82 0.38
108 3 0.01
109 3 0.01
115 5 0.02
116 115 0.53
117 7 0.03
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.23
Consensus pattern (114 bp):
TGGGGCTAATAGGAGTGTCATGGGTATATAAGGGTCACGAGGTTGGGTGCGGGAGAATGTCACGG
ACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCAC
Found at i:1498337 original size:107 final size:107
Alignment explanation
Indices: 1498147--1498360 Score: 401
Period size: 107 Copynumber: 2.0 Consensus size: 107
1498137 GGGTATATAA
*
1498147 GGGTCACGAGGTTGGGTGCGGGAGAATGTCACGGACCTAAGGATGAGTCATGAATCTCACATCGA
1 GGGTCACGAGGTTGGGTGCGAGAGAATGTCACGGACCTAAGGATGAGTCATGAATCTCACATCGA
*
1498212 ACATAATAGGAAGGTCACTGGGATATATAAGGGTTTCACTAT
66 ACATAATAGGAAGATCACTGGGATATATAAGGGTTTCACTAT
1498254 GGGTCACGAGGTTGGGTGCGAGAGAATGTCACGGACCTAAGGATGAGTCATGAATCTCACATCGA
1 GGGTCACGAGGTTGGGTGCGAGAGAATGTCACGGACCTAAGGATGAGTCATGAATCTCACATCGA
*
1498319 ACATAATAGGAAGATCACTGGGGTATATAAGGGTTTCACTAT
66 ACATAATAGGAAGATCACTGGGATATATAAGGGTTTCACTAT
1498361 TTTCGTCTTG
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 104 1.00
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.23
Consensus pattern (107 bp):
GGGTCACGAGGTTGGGTGCGAGAGAATGTCACGGACCTAAGGATGAGTCATGAATCTCACATCGA
ACATAATAGGAAGATCACTGGGATATATAAGGGTTTCACTAT
Found at i:1514814 original size:2 final size:2
Alignment explanation
Indices: 1514807--1514832 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1514797 TGTAATTTGC
1514807 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1514833 TGTAATTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1516672 original size:30 final size:31
Alignment explanation
Indices: 1516631--1516706 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 31
1516621 TTATTTTGGT
1516631 TAAAT-AAGTTTTTATATTTTT-A-TTACAT-
1 TAAATAAAGTTTTTAT-TTTTTGATTTACATC
*
1516659 TAGAATAAAG-TTTTATTTTTTGATTTATATC
1 TA-AATAAAGTTTTTATTTTTTGATTTACATC
1516690 TAAATAAA-TTTTTATTT
1 TAAATAAAGTTTTTATTT
1516707 CAAACGAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
28 7 0.17
29 10 0.24
30 22 0.54
31 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.57
Consensus pattern (31 bp):
TAAATAAAGTTTTTATTTTTTGATTTACATC
Found at i:1516830 original size:24 final size:24
Alignment explanation
Indices: 1516802--1516848 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1516792 TTAAAGGTTT
*
1516802 ATTTAAGTATAATAAAGTA-TAAAA
1 ATTTAACTA-AATAAAGTACTAAAA
*
1516826 ATTTATCTAAATAAAGTACTAAA
1 ATTTAACTAAATAAAGTACTAAA
1516849 GTTTAGGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (24 bp):
ATTTAACTAAATAAAGTACTAAAA
Found at i:1517286 original size:17 final size:17
Alignment explanation
Indices: 1517264--1517297 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1517254 TCTAGAACAG
1517264 ATAGTTTTCATTTTTCT
1 ATAGTTTTCATTTTTCT
1517281 ATAGTTTTCATTTTTCT
1 ATAGTTTTCATTTTTCT
1517298 TTCTGGTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
ATAGTTTTCATTTTTCT
Found at i:1517866 original size:2 final size:2
Alignment explanation
Indices: 1517859--1517884 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1517849 GCCTCAAAGG
1517859 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1517885 GCATATCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1518551 original size:2 final size:2
Alignment explanation
Indices: 1518544--1518575 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1518534 TAATTAAGTC
1518544 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1518576 GTATGGAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1522871 original size:2 final size:2
Alignment explanation
Indices: 1522866--1522895 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1522856 TAACTATAGT
*
1522866 TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1522896 AGTGTGTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1524858 original size:16 final size:16
Alignment explanation
Indices: 1524834--1524867 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1524824 GAAATAGGGA
*
1524834 CATATAAAACAAAAAT
1 CATAGAAAACAAAAAT
1524850 CATAGAAAACAAAAAT
1 CATAGAAAACAAAAAT
1524866 CA
1 CA
1524868 CAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.68, C:0.15, G:0.03, T:0.15
Consensus pattern (16 bp):
CATAGAAAACAAAAAT
Found at i:1524888 original size:15 final size:16
Alignment explanation
Indices: 1524839--1524893 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1524829 AGGGACATAT
* *
1524839 AAAACAAAAATCATAG
1 AAAACAAAAATCACAA
1524855 AAAACAAAAATCACAA
1 AAAACAAAAATCACAA
*
1524871 AAAATAAAAA-CACGAA
1 AAAACAAAAATCAC-AA
*
1524887 AACACAA
1 AAAACAA
1524894 CAAGCAGAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
15 3 0.09
16 30 0.91
ACGTcount: A:0.73, C:0.16, G:0.04, T:0.07
Consensus pattern (16 bp):
AAAACAAAAATCACAA
Found at i:1525536 original size:18 final size:18
Alignment explanation
Indices: 1525498--1525537 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1525488 TTTTTTAGTA
* *
1525498 TTTTATTTATTTATTTGT
1 TTTTATTTATGTATTTAT
*
1525516 TTTTATTTATGTGTTTAT
1 TTTTATTTATGTATTTAT
1525534 TTTT
1 TTTT
1525538 TGGTATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (18 bp):
TTTTATTTATGTATTTAT
Found at i:1525544 original size:22 final size:22
Alignment explanation
Indices: 1525461--1525545 Score: 64
Period size: 22 Copynumber: 3.7 Consensus size: 22
1525451 TCAGTCGAGC
*
1525461 TATTTTTTGGTATATATATATT
1 TATTTTTTGGTATTTATATATT
* *
1525483 TAAAGTTTTTTAGTATTTTATTTATT
1 T--A-TTTTTTGGTA-TTTATATATT
* * *
1525509 TATTTGTTT-TTATTTATGTGTT
1 TATTT-TTTGGTATTTATATATT
1525531 TATTTTTTGGTATTT
1 TATTTTTTGGTATTT
1525546 TTACATGATT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
21 3 0.06
22 19 0.38
23 5 0.10
24 5 0.10
25 9 0.18
26 9 0.18
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (22 bp):
TATTTTTTGGTATTTATATATT
Found at i:1525769 original size:8 final size:8
Alignment explanation
Indices: 1525756--1525782 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1525746 TTTTCAAACA
1525756 AAAAATAT
1 AAAAATAT
1525764 AAAAATAT
1 AAAAATAT
1525772 AAAAATAT
1 AAAAATAT
1525780 AAA
1 AAA
1525783 TTTGGGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAATAT
Found at i:1525862 original size:25 final size:25
Alignment explanation
Indices: 1525821--1525875 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
1525811 CAAGAATGAG
* * *
1525821 ATTTTTAAAAGTTTCAAA-TGATAA
1 ATTTTTAAAAATCTCAAAGTGAAAA
1525845 ATTTTTAAGAAATCTCAAAGTGAAAA
1 ATTTTTAA-AAATCTCAAAGTGAAAA
1525871 ATTTT
1 ATTTT
1525876 CTTTAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 8 0.31
25 8 0.31
26 10 0.38
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.40
Consensus pattern (25 bp):
ATTTTTAAAAATCTCAAAGTGAAAA
Found at i:1526015 original size:17 final size:17
Alignment explanation
Indices: 1525993--1526034 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1525983 ACAAATAGTG
1525993 AAAAATTTAAAAATAAA
1 AAAAATTTAAAAATAAA
**
1526010 AAAAATAAAAAAATAAA
1 AAAAATTTAAAAATAAA
*
1526027 AAGAATTT
1 AAAAATTT
1526035 CTAATATGGT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAAATTTAAAAATAAA
Found at i:1527994 original size:68 final size:68
Alignment explanation
Indices: 1527885--1528019 Score: 236
Period size: 68 Copynumber: 2.0 Consensus size: 68
1527875 CACCTTAAAA
*
1527885 GATGAGTCTTAAATCTCACATCGAACATAATAGGAGTGTCACTGG-GATATATAAGGGTCACGAG
1 GATGAGTCCTAAATCTCACATCGAACATAATAGGAGTGTCACTGGAG-TATATAAGGGTCACGAG
1527949 GTTG
65 GTTG
*
1527953 GATGAGTCCTGAATCTCACATCGAACATAATAGGAGTGTCACTGGAGTATATAAGGGTCACGAGG
1 GATGAGTCCTAAATCTCACATCGAACATAATAGGAGTGTCACTGGAGTATATAAGGGTCACGAGG
1528018 TT
66 TT
1528020 AGGTGCCGAA
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 63 0.98
69 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.26
Consensus pattern (68 bp):
GATGAGTCCTAAATCTCACATCGAACATAATAGGAGTGTCACTGGAGTATATAAGGGTCACGAGG
TTG
Found at i:1528056 original size:19 final size:19
Alignment explanation
Indices: 1528032--1528070 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1528022 GTGCCGAAGA
1528032 ATGTCACGGAAGGGTCACG
1 ATGTCACGGAAGGGTCACG
1528051 ATGTCACGGAAGGGTCACG
1 ATGTCACGGAAGGGTCACG
1528070 A
1 A
1528071 GGTTGGGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.36, T:0.15
Consensus pattern (19 bp):
ATGTCACGGAAGGGTCACG
Found at i:1528348 original size:156 final size:156
Alignment explanation
Indices: 1528064--1528351 Score: 522
Period size: 156 Copynumber: 1.8 Consensus size: 156
1528054 TCACGGAAGG
*
1528064 GTCACGAGGTTGGGTGCTAATAGAAGTGTCACTGGGGTATATAAGGGTCACGAGGTTGGATGCGG
1 GTCACGAGGTTGGGTGCTAATAGAAGTGTCACTAGGGTATATAAGGGTCACGAGGTTGGATGCGG
* * *
1528129 GAGAATGTCACGGACCTAAGGATGAGTCCTGAATCTCACATCGAACATAATAGGAGGGTCACTGG
66 AAGAATGTCACGGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCACTGG
1528194 GGTATATAAAGGTTTACACTATTTTC
131 GGTATATAAAGGTTTACACTATTTTC
*
1528220 GTCACGAGGTTGGGTGCTAATAGGAGTGTCACTAGGGTATATAAGGGTCACGAGGTTGGATGCGG
1 GTCACGAGGTTGGGTGCTAATAGAAGTGTCACTAGGGTATATAAGGGTCACGAGGTTGGATGCGG
*
1528285 AAGAATGTCACGGACCTAAGGATGAGTCATGACTCTCACATCGAACATAATAGGAAGGTCACTGG
66 AAGAATGTCACGGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCACTGG
1528350 GG
131 GG
1528352 CTAATAGGAG
Statistics
Matches: 126, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
156 126 1.00
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (156 bp):
GTCACGAGGTTGGGTGCTAATAGAAGTGTCACTAGGGTATATAAGGGTCACGAGGTTGGATGCGG
AAGAATGTCACGGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCACTGG
GGTATATAAAGGTTTACACTATTTTC
Found at i:1528439 original size:116 final size:116
Alignment explanation
Indices: 1528230--1528467 Score: 422
Period size: 116 Copynumber: 2.0 Consensus size: 116
1528220 GTCACGAGGT
1528230 TGGGTGCTAATAGGAGTGTCACTAGGGTATATAAGGGTCACGAGGTTGGATGCGGAAGAATGTCA
1 TGGG-GCTAATAGGAGTGTCACTAGGGTATATAAGGGTCACGAGGTTGGATGCGGAAGAATGTCA
*
1528295 CGGACCTAAGGATGAGTCATGACTCTCACATCGAACATAATAGGAAGGTCAC
65 CGGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCAC
* * * *
1528347 TGGGGCTAATAGGAGTGTCATTGGGGTATATAAGGGTCACGAGGTTGGGTGCGGGAGAATGTCAC
1 TGGGGCTAATAGGAGTGTCACTAGGGTATATAAGGGTCACGAGGTTGGATGCGGAAGAATGTCAC
1528412 GGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCAC
66 GGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCAC
1528463 TGGGG
1 TGGGG
1528468 TATATAAGGG
Statistics
Matches: 116, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
116 112 0.97
117 4 0.03
ACGTcount: A:0.29, C:0.15, G:0.33, T:0.22
Consensus pattern (116 bp):
TGGGGCTAATAGGAGTGTCACTAGGGTATATAAGGGTCACGAGGTTGGATGCGGAAGAATGTCAC
GGACCTAAGGATGAGTCATGAATCTCACATCGAACATAATAGGAAGGTCAC
Found at i:1531871 original size:2 final size:2
Alignment explanation
Indices: 1531864--1531919 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1531854 GGTACTTCCC
1531864 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1531906 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
1531920 GCCCATTTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1542976 original size:12 final size:12
Alignment explanation
Indices: 1542959--1543032 Score: 114
Period size: 12 Copynumber: 6.2 Consensus size: 12
1542949 CACAATATCT
1542959 TTCTTCTCATCC
1 TTCTTCTCATCC
1542971 TTCTTCTCGA-CC
1 TTCTTCTC-ATCC
1542983 TTCTTCTCATCC
1 TTCTTCTCATCC
*
1542995 TTCTTCTCGTCC
1 TTCTTCTCATCC
*
1543007 TTCTTCTCGTCC
1 TTCTTCTCATCC
1543019 TTCTTCTCATCC
1 TTCTTCTCATCC
1543031 TT
1 TT
1543033 TGCAGCCCCT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
11 1 0.02
12 56 0.97
13 1 0.02
ACGTcount: A:0.05, C:0.41, G:0.04, T:0.50
Consensus pattern (12 bp):
TTCTTCTCATCC
Found at i:1543008 original size:36 final size:36
Alignment explanation
Indices: 1542959--1543032 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
1542949 CACAATATCT
1542959 TTCTTCTCATCCTTCTTCTCGACCTTCTTCTCATCC
1 TTCTTCTCATCCTTCTTCTCGACCTTCTTCTCATCC
* *
1542995 TTCTTCTCGTCCTTCTTCTCGTCCTTCTTCTCATCC
1 TTCTTCTCATCCTTCTTCTCGACCTTCTTCTCATCC
1543031 TT
1 TT
1543033 TGCAGCCCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.05, C:0.41, G:0.04, T:0.50
Consensus pattern (36 bp):
TTCTTCTCATCCTTCTTCTCGACCTTCTTCTCATCC
Found at i:1546160 original size:38 final size:38
Alignment explanation
Indices: 1546109--1546192 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
1546099 CACAAATTGG
* * **
1546109 TCAGGATTAAGAAGAAAATAAAGAGTGGAATTCATTAA
1 TCAGGCTTAAGAAGAAAATAAAAAACGGAATTCATTAA
* *
1546147 TCAGGCTTAAGAAGGAAATAAAAAACGGAATTCATTAG
1 TCAGGCTTAAGAAGAAAATAAAAAACGGAATTCATTAA
*
1546185 TAAGGCTT
1 TCAGGCTT
1546193 TCACACAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.24
Consensus pattern (38 bp):
TCAGGCTTAAGAAGAAAATAAAAAACGGAATTCATTAA
Found at i:1550878 original size:19 final size:19
Alignment explanation
Indices: 1550857--1550892 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1550847 TTATTAATTT
*
1550857 TTTTTAATT-TTTATATTA
1 TTTTAAATTATTTATATTA
1550875 TTTTAAATTATTTATATT
1 TTTTAAATTATTTATATT
1550893 TACATCTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTAAATTATTTATATTA
Found at i:1551326 original size:27 final size:28
Alignment explanation
Indices: 1551277--1551329 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
1551267 TGTTTAATAT
*
1551277 ATAAAATTATGATAAAATAATATTATAA
1 ATAAAATTATAATAAAATAATATTATAA
*
1551305 ATAAAATTA-AATAAAATGATATTAT
1 ATAAAATTATAATAAAATAATATTAT
1551330 TTTATTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (28 bp):
ATAAAATTATAATAAAATAATATTATAA
Found at i:1552626 original size:24 final size:24
Alignment explanation
Indices: 1552599--1552652 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1552589 AGCTTTCGAA
*
1552599 AAGGGGAGTTCCAGAGAGATGTTG
1 AAGGGGAGTTCCAGAGAGAGGTTG
* *
1552623 AAGGGGATTTCGAGAGAGAGGTTG
1 AAGGGGAGTTCCAGAGAGAGGTTG
1552647 AAGGGG
1 AAGGGG
1552653 TATTCTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.30, C:0.06, G:0.46, T:0.19
Consensus pattern (24 bp):
AAGGGGAGTTCCAGAGAGAGGTTG
Found at i:1556133 original size:27 final size:27
Alignment explanation
Indices: 1556084--1556143 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
1556074 ATATAAAATG
1556084 ATATTA-TTTAATTTAACTCTATTTATA
1 ATATTATTTTAATTTAACTCTA-TTATA
* *
1556111 ATATTATTTTATTTTATCT-TATTATA
1 ATATTATTTTAATTTAACTCTATTATA
*
1556137 ATTTTAT
1 ATATTAT
1556144 ATATCAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 11 0.38
27 8 0.28
28 10 0.34
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (27 bp):
ATATTATTTTAATTTAACTCTATTATA
Found at i:1556294 original size:2 final size:2
Alignment explanation
Indices: 1556283--1556326 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1556273 TATAGGAACC
1556283 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1556324 AT A
1 AT A
1556327 GGTAGCTTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1563513 original size:17 final size:17
Alignment explanation
Indices: 1563457--1563515 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
1563447 TTAAAATAAT
* *
1563457 TTATCATTAATAAAATA
1 TTATCATTAATGAATTA
* *
1563474 TTATCA-T-CTGATTTA
1 TTATCATTAATGAATTA
1563489 TT-TCATTAATGAATTA
1 TTATCATTAATGAATTA
1563505 TTATCATTAAT
1 TTATCATTAAT
1563516 TCATTAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 3 0.09
15 7 0.21
16 9 0.27
17 14 0.42
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.49
Consensus pattern (17 bp):
TTATCATTAATGAATTA
Found at i:1569016 original size:11 final size:11
Alignment explanation
Indices: 1568996--1569096 Score: 52
Period size: 11 Copynumber: 9.5 Consensus size: 11
1568986 AATTTAAAAT
1568996 ATTA-ATATAA
1 ATTATATATAA
1569006 ATTATATATAA
1 ATTATATATAA
1569017 ATT-TA-ATAA
1 ATTATATATAA
* * *
1569026 A-AATAAAAAA
1 ATTATATATAA
* *
1569036 TATTTTATAT-T
1 -ATTATATATAA
* *
1569047 TTTTTATATAA
1 ATTATATATAA
*
1569058 ATTAATAGATAA
1 ATT-ATATATAA
*
1569070 TTTATATATATA
1 ATTATATATA-A
1569082 A-TATATATAA
1 ATTATATATAA
1569092 ATTAT
1 ATTAT
1569097 TAATATTTTA
Statistics
Matches: 67, Mismatches: 15, Indels: 17
0.68 0.15 0.17
Matches are distributed among these distances:
9 7 0.10
10 19 0.28
11 29 0.43
12 12 0.18
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (11 bp):
ATTATATATAA
Found at i:1569091 original size:34 final size:33
Alignment explanation
Indices: 1569051--1569121 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 33
1569041 TATATTTTTT
1569051 TATATAAATTAATAGATAATTTATAT-ATATAATA
1 TATATAAATTAATA-ATAATTTATATAATATAA-A
* *
1569085 TATATAAATTATTAATATTTTATATAATATAAA
1 TATATAAATTAATAATAATTTATATAATATAAA
1569118 TATA
1 TATA
1569122 CGGAACATCG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 15 0.44
34 19 0.56
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (33 bp):
TATATAAATTAATAATAATTTATATAATATAAA
Found at i:1570458 original size:13 final size:13
Alignment explanation
Indices: 1570438--1570476 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1570428 ATAAATATCA
1570438 ATTAAATTTATATT
1 ATTAAATTT-TATT
1570452 A-TAAATTTT-TT
1 ATTAAATTTTATT
1570463 ATTAAATTTTATT
1 ATTAAATTTTATT
1570476 A
1 A
1570477 ATTTATCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 3 0.13
12 9 0.39
13 10 0.43
14 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTAAATTTTATT
Found at i:1578240 original size:19 final size:18
Alignment explanation
Indices: 1578219--1578279 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 18
1578209 TTTTAATAAA
1578219 TTTATAATTATTATTAAAAT
1 TTTA-AATTA-TATTAAAAT
1578239 TTTAAATTATATT---AT
1 TTTAAATTATATTAAAAT
* *
1578254 TTT-TATTATATT-ATAT
1 TTTAAATTATATTAAAAT
1578270 TTTAAATTAT
1 TTTAAATTAT
1578280 TAGATTTACT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 8 0.22
15 5 0.14
16 5 0.14
17 5 0.14
18 4 0.11
19 5 0.14
20 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAAATTATATTAAAAT
Done.