Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397266.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_20.0, 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: 7441454
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 92215 characters in sequence are not A, C, G, or T
File 3 of 18
Found at i:879698 original size:12 final size:12
Alignment explanation
Indices: 879681--879706 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
879671 AAACACGAAC
879681 CAAGCATTCTGT
1 CAAGCATTCTGT
879693 CAAGCATTCTGT
1 CAAGCATTCTGT
879705 CA
1 CA
879707 GACTCGTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (12 bp):
CAAGCATTCTGT
Found at i:897615 original size:2 final size:2
Alignment explanation
Indices: 897610--897634 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
897600 AGGTGTGTTT
897610 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
897635 AAAGAAAAAA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:899921 original size:2 final size:2
Alignment explanation
Indices: 899914--899939 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
899904 CGCAGATATG
899914 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
899940 TACACATGTA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:913068 original size:231 final size:227
Alignment explanation
Indices: 912658--913080 Score: 557
Period size: 228 Copynumber: 1.8 Consensus size: 227
912648 AAGACTTACC
* * * * * *
912658 GTTATTATGATAATTCAACAGGTTTTACTCAATAGTGCCTCCTTTGTGTTCTTGCTGCACCTCTT
1 GTTATTATGATAATTCAACAGGCTTTACTCAATAGTGCCTCCTCTGTGTTCCTGCTACACCCCTC
* * **
912723 GTATTCAGTGTTCCTTACCAGAATGGGGATGAAGGCTTCATTGAGATTGCCAAGATGGTTGGAGA
66 GTATTCAGTGTACC-TACCAGAATGGGCATGAAAACTTCATTGAGATTGCCAAGATGGTTGGAGA
*
912788 AGGCTATATAATGGTAACTTAAGCAGCCTGCTGTCTCTAAGTTATGTAAATTAC-TTGTTTTGTT
130 AGGCTATATAATGGTAACTTAAGCAACCTGCTGTCTCTAAGTTATGTAAATTACATT-TTTTGTT
912852 AAATCTGACAGCCTTTTTCCTGCTTTCATTTTAA
194 AAATCTGACAGCCTTTTTCCTGCTTTCATTTTAA
* * * * *
912886 GTTATTCTGCTAATTCAACAGGCTTTGCTGAATATTGCCTCCTCTGTGTTCCTGCTACACCCCCT
1 GTTATTATGATAATTCAACAGGCTTTACTCAATAGTGCCTCCTCTGTGTTCCTGCTACA-CCCCT
* *
912951 CGTATTCAGTGGTACC-ACCA-AGTGGGCATGAAAACTTCATTGAGATTGCCAAGATGGTTGGGG
65 CGTATTCAGT-GTACCTACCAGAATGGGCATGAAAACTTCATTGAGATTGCCAAGATGGTTGGAG
* *
913014 AAGGCCATATATTGAATGGTAACTTAAGCAACCTGCTG-CTTGTAATTTATGTAAATTACATTTT
129 AAGG-C-TATA-T-AATGGTAACTTAAGCAACCTGCTGTC-TCTAAGTTATGTAAATTACATTTT
913078 TTG
189 TTG
913081 CATCCTCATA
Statistics
Matches: 167, Mismatches: 20, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
227 42 0.25
228 55 0.33
229 17 0.10
230 6 0.04
231 45 0.27
232 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (227 bp):
GTTATTATGATAATTCAACAGGCTTTACTCAATAGTGCCTCCTCTGTGTTCCTGCTACACCCCTC
GTATTCAGTGTACCTACCAGAATGGGCATGAAAACTTCATTGAGATTGCCAAGATGGTTGGAGAA
GGCTATATAATGGTAACTTAAGCAACCTGCTGTCTCTAAGTTATGTAAATTACATTTTTTGTTAA
ATCTGACAGCCTTTTTCCTGCTTTCATTTTAA
Found at i:936622 original size:28 final size:27
Alignment explanation
Indices: 936574--936656 Score: 68
Period size: 28 Copynumber: 3.1 Consensus size: 27
936564 CCCTTTTTTA
* *
936574 TTAAGTTAATTAAA-TATTTATATTTATT
1 TTAAATTAAATAAATTA-TTATA-TTATT
*
936602 TTAAATTAAATAAATTATTATAATTA-A
1 TTAAATTAAATAAATTATTAT-ATTATT
936629 TTAAA-TAAA-AATATTATT-TATTATT
1 TTAAATTAAATAA-ATTATTATATTATT
936654 TTA
1 TTA
936657 TATTTATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
24 4 0.09
25 6 0.13
26 10 0.21
27 5 0.11
28 19 0.40
29 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (27 bp):
TTAAATTAAATAAATTATTATATTATT
Found at i:964023 original size:30 final size:30
Alignment explanation
Indices: 963987--964046 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
963977 ATTAATTATT
*
963987 AAAATTTATTTAGTAAAAAATTAAAATATA
1 AAAATTTATTTAGTAAAAAATAAAAATATA
* *
964017 AAAATTTATTTTGTATAAAATAAAAATATA
1 AAAATTTATTTAGTAAAAAATAAAAATATA
964047 TTTGATTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTTATTTAGTAAAAAATAAAAATATA
Found at i:964437 original size:33 final size:31
Alignment explanation
Indices: 964389--964460 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 31
964379 GTTTTTCCTC
*
964389 AATTAGTCATGAGCTATTATTATT-AATTTGGAT
1 AATTAGT-ATAAGCTATTATT-TTAAATTT-GAT
*
964422 AATATAGTATAAGCTATTGTTTTAAATTTGAT
1 AAT-TAGTATAAGCTATTATTTTAAATTTGAT
964454 AATTAGT
1 AATTAGT
964461 GATTTTATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 4 0.11
32 8 0.23
33 19 0.54
34 4 0.11
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.46
Consensus pattern (31 bp):
AATTAGTATAAGCTATTATTTTAAATTTGAT
Found at i:968646 original size:8 final size:8
Alignment explanation
Indices: 968624--968657 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
968614 TTTTATTGTA
968624 TATAA-TT
1 TATAATTT
968631 TA-AATTT
1 TATAATTT
968638 TATAATTT
1 TATAATTT
968646 TATAATTT
1 TATAATTT
968654 TATA
1 TATA
968658 TAATTACCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 2 0.08
7 6 0.24
8 17 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATAATTT
Found at i:975217 original size:26 final size:26
Alignment explanation
Indices: 975180--975229 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
975170 AAGTTTTTTG
975180 TTATTTTATTATATTT-AATTAAATTT
1 TTATTTTATTAT-TTTAAATTAAATTT
975206 TTATATTT-TTATTTTAAATTAAAT
1 TTAT-TTTATTATTTTAAATTAAAT
975230 AAAATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 3 0.14
26 16 0.73
27 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTATTTTATTATTTTAAATTAAATTT
Found at i:975245 original size:18 final size:18
Alignment explanation
Indices: 975216--975278 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
975206 TTATATTTTT
*
975216 ATTTTA-AATTAAATAAA
1 ATTTTATAATTAATTAAA
975233 ATTTTATAATTAATTATAA
1 ATTTTATAATTAATTA-AA
*
975252 ATTAATTATTATTAATTAAA
1 ATT--TTATAATTAATTAAA
*
975272 ATATTAT
1 ATTTTAT
975279 TTATCATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 6 0.15
18 12 0.31
19 5 0.13
20 4 0.10
21 12 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTTATAATTAATTAAA
Found at i:975249 original size:10 final size:10
Alignment explanation
Indices: 975236--975269 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
975226 AAATAAAATT
975236 TTATAATTAA
1 TTATAATTAA
975246 TTATAAATTAA
1 TTAT-AATTAA
*
975257 TTATTATTAA
1 TTATAATTAA
975267 TTA
1 TTA
975270 AAATATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTATAATTAA
Found at i:976281 original size:17 final size:17
Alignment explanation
Indices: 976252--976297 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
976242 AAACCATGAG
*
976252 CAATTTCTTTTGTTCCTT
1 CAATTT-TTTTGTTACTT
*
976270 CAATTTTTTTGTTATTT
1 CAATTTTTTTGTTACTT
976287 CAATTATTTTT
1 CAATT-TTTTT
976298 ACAGTAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.17, C:0.13, G:0.04, T:0.65
Consensus pattern (17 bp):
CAATTTTTTTGTTACTT
Found at i:982105 original size:25 final size:25
Alignment explanation
Indices: 982071--982118 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
982061 GGTAATTCCA
982071 ACATAGATTCCTTCCTGGTGCTTCT
1 ACATAGATTCCTTCCTGGTGCTTCT
982096 ACATAGATTCCTTCCTGGTGCTT
1 ACATAGATTCCTTCCTGGTGCTT
982119 TTATTTCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.40
Consensus pattern (25 bp):
ACATAGATTCCTTCCTGGTGCTTCT
Found at i:984078 original size:22 final size:22
Alignment explanation
Indices: 984016--984060 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
984006 AAGTATAAAA
*
984016 TAATAATAAAAT-ATT-TTAAT
1 TAATAATAAATTAATTATTAAT
984036 TAATAATAAATTAATTATTAAT
1 TAATAATAAATTAATTATTAAT
984058 TAA
1 TAA
984061 AAAAATCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 3 0.14
22 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATAATAAATTAATTATTAAT
Found at i:993406 original size:23 final size:23
Alignment explanation
Indices: 993380--993425 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
993370 TGATAAATAT
993380 ATATAAATATTTTAT-TTTTATTA
1 ATATAAAT-TTTTATATTTTATTA
*
993403 ATATTAATTTTTATATTTTATTA
1 ATATAAATTTTTATATTTTATTA
993426 TCAAATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATATAAATTTTTATATTTTATTA
Found at i:994292 original size:42 final size:42
Alignment explanation
Indices: 994233--994413 Score: 176
Period size: 42 Copynumber: 4.4 Consensus size: 42
994223 ATAGTTTAAA
*
994233 TAATATAAATTAATTTTACATTTATTAGCTTACAAGTTCAAT
1 TAATATAAATTAATTTTACATTTATTAACTTACAAGTTCAAT
* *
994275 TAATATAAATTAATTTTATATTTATTAATTTACAAGTTCAAT
1 TAATATAAATTAATTTTACATTTATTAACTTACAAGTTCAAT
* * * *** *
994317 TAATATAAA--AATTTTATATATT-TAAATTTACATCAT-AAG
1 TAATATAAATTAATTTTACAT-TTATTAACTTACAAGTTCAAT
* * * * *
994356 TAATATAAATTAATTTTATATTTGTTAATTTATAAATTCAAT
1 TAATATAAATTAATTTTACATTTATTAACTTACAAGTTCAAT
994398 TAATATAAA--AATTTTA
1 TAATATAAATTAATTTTA
994414 TAAATAATAT
Statistics
Matches: 120, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 11 0.09
40 29 0.24
41 21 0.17
42 59 0.49
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.48
Consensus pattern (42 bp):
TAATATAAATTAATTTTACATTTATTAACTTACAAGTTCAAT
Found at i:995220 original size:30 final size:27
Alignment explanation
Indices: 995186--995259 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 27
995176 ATATTTAATG
*
995186 ATAAATATTTATTTAATTTAAAATAAAAA
1 ATAAAAATTTATTTAATTT--AATAAAAA
*
995215 TATAAAAATTTAATTAAATTTAATAAAAA
1 -ATAAAAATTT-ATTTAATTTAATAAAAA
995244 ATAAAAATTTATTTAA
1 ATAAAAATTTATTTAA
995260 ATTTTTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 5 0.12
28 10 0.25
29 8 0.20
30 9 0.22
31 8 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
ATAAAAATTTATTTAATTTAATAAAAA
Found at i:995251 original size:28 final size:29
Alignment explanation
Indices: 995207--995263 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
995197 TTTAATTTAA
995207 AATAAAAATATAAAAATTTAATTAAATTT
1 AATAAAAATATAAAAATTTAATTAAATTT
*
995236 AATAAAAA-ATAAAAATTTATTTAAATTT
1 AATAAAAATATAAAAATTTAATTAAATTT
995264 TTTTTAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
AATAAAAATATAAAAATTTAATTAAATTT
Found at i:1007695 original size:55 final size:55
Alignment explanation
Indices: 1007611--1007721 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
1007601 TTTGGCAGGA
*
1007611 TTCGGCTGCATTTACTGATATAATAATTTAGTCACAGGGAAGACTGCATATCCTC
1 TTCGGCTGCATTTACTGATATAATAATTTAGTCACAGGAAAGACTGCATATCCTC
1007666 TTCGGCTGCATTTACTGATATAATAATTTAGTCACAGGAAAGACTGCATATCCTC
1 TTCGGCTGCATTTACTGATATAATAATTTAGTCACAGGAAAGACTGCATATCCTC
1007721 T
1 T
1007722 CCGCCAACAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (55 bp):
TTCGGCTGCATTTACTGATATAATAATTTAGTCACAGGAAAGACTGCATATCCTC
Found at i:1008377 original size:24 final size:24
Alignment explanation
Indices: 1008330--1008378 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1008320 TTCGGTTTCA
*
1008330 AATTGTTTAATTTCAAAGTTATTG
1 AATTGTTTAATATCAAAGTTATTG
*
1008354 AATTGTTTAA-ATCAATGTTGATTG
1 AATTGTTTAATATCAAAGTT-ATTG
1008378 A
1 A
1008379 GTTAAGTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (24 bp):
AATTGTTTAATATCAAAGTTATTG
Found at i:1012549 original size:11 final size:10
Alignment explanation
Indices: 1012521--1012563 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
1012511 TTTTAGGTCT
1012521 AATATTTTAA
1 AATATTTTAA
1012531 AATATTTTAA
1 AATATTTTAA
1012541 AATTATTTTAA
1 AA-TATTTTAA
* *
1012552 AAAAATTTAA
1 AATATTTTAA
1012562 AA
1 AA
1012564 GTTTTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 20 0.67
11 10 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AATATTTTAA
Found at i:1012549 original size:21 final size:22
Alignment explanation
Indices: 1012523--1012571 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1012513 TTAGGTCTAA
* *
1012523 TATTTTAAAATATTTTAAAA-T
1 TATTTTAAAAAAATTTAAAAGT
1012544 TATTTTAAAAAAATTTAAAAGT
1 TATTTTAAAAAAATTTAAAAGT
1012566 T-TTTTA
1 TATTTTA
1012572 TTTTTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTTTAAAAAAATTTAAAAGT
Found at i:1019905 original size:3 final size:3
Alignment explanation
Indices: 1019893--1019922 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1019883 AAAGGGGGGG
*
1019893 AGA AGC AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1019923 CAGAGAAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1020099 original size:23 final size:23
Alignment explanation
Indices: 1020073--1020118 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1020063 GCTATTGAGA
1020073 GAGAAAGAAAGAGAAAGAGAATT
1 GAGAAAGAAAGAGAAAGAGAATT
* * *
1020096 GAGAGAGATAGAGAGAGAGAATT
1 GAGAAAGAAAGAGAAAGAGAATT
1020119 TAGCCTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.35, T:0.11
Consensus pattern (23 bp):
GAGAAAGAAAGAGAAAGAGAATT
Found at i:1022619 original size:2 final size:2
Alignment explanation
Indices: 1022612--1022647 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1022602 TTATTTTTCT
1022612 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1022648 ACACCTAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1023263 original size:19 final size:19
Alignment explanation
Indices: 1023232--1023283 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 19
1023222 AACTTCATCT
1023232 ATTAT-TATAAAATATAAAA
1 ATTATGTAT-AAATATAAAA
*
1023251 ATTATGTATAAAT-TAAAT
1 ATTATGTATAAATATAAAA
*
1023269 A-TATGTATATATATA
1 ATTATGTATAAATATA
1023284 TATAATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 10 0.34
18 7 0.24
19 9 0.31
20 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (19 bp):
ATTATGTATAAATATAAAA
Found at i:1023477 original size:17 final size:17
Alignment explanation
Indices: 1023437--1023480 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
1023427 ATTAAGTGTA
1023437 ATAATATAATGTATATAT
1 ATAATAT-ATGTATATAT
*
1023455 -TAAATATATGTATATGT
1 AT-AATATATGTATATAT
1023472 ATAATATAT
1 ATAATATAT
1023481 TACTCTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (17 bp):
ATAATATATGTATATAT
Found at i:1023585 original size:184 final size:190
Alignment explanation
Indices: 1023254--1023630 Score: 502
Period size: 184 Copynumber: 2.0 Consensus size: 190
1023244 TATAAAAATT
*
1023254 ATGTATAAATTAAATATATGTATATATATATATAATATTACTTTATTATATATATGAAATTAATG
1 ATGTATAAATTAAATATATGTATATATATATATAATATTACTCTATTATATATATGAAATTAATG
* * * *
1023319 ATACAACTTTTACGTTATAGTATTTTAATTTTTATATCAAAATCTGTATAAATGATAACTAATTA
66 ATACAAC--TAACGTTATAGTATTGTAATTTTTATATCAAAATCTGTATAAATAATAAATAATTA
*
1023384 TAAATAATATGTTAT-AAAAATTAAAACGATAACTAATAAAATTATTAAGTGTAATAATATA
129 TAAATAATATGTTATAAAAAACTAAAACGATAACTAATAAAATTATTAAGTGTAATAATATA
* *
1023445 ATGTATATATTAAATATATGTATATGTATA-AT-ATATTACTCTATTATGTATATATGAAATTAA
1 ATGTATAAATTAAATATATGTATATATATATATAATATTACTCTATTA--TATATATGAAATTAA
* *
1023508 T-A-AC-AC-AAC-TTATA-TGTTGTAATGTTTTATATCAAAATTTGTATAAATAATAAATAATT
64 TGATACAACTAACGTTATAGTATTGTAAT-TTTTATATCAAAATCTGTATAAATAATAAATAATT
* * * ** *
1023567 ATAAATAATATGTTATAAAAAACTAAGATGATAATTAATAAGGTTATTAAGTGTAATTATATA
128 ATAAATAATATGTTATAAAAAACTAAAACGATAACTAATAAAATTATTAAGTGTAATAATATA
1023630 A
1 A
1023631 ATAAATTTTA
Statistics
Matches: 166, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
183 7 0.04
184 53 0.32
185 42 0.25
188 2 0.01
189 15 0.09
190 3 0.02
191 44 0.27
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (190 bp):
ATGTATAAATTAAATATATGTATATATATATATAATATTACTCTATTATATATATGAAATTAATG
ATACAACTAACGTTATAGTATTGTAATTTTTATATCAAAATCTGTATAAATAATAAATAATTATA
AATAATATGTTATAAAAAACTAAAACGATAACTAATAAAATTATTAAGTGTAATAATATA
Found at i:1026313 original size:21 final size:20
Alignment explanation
Indices: 1026287--1026330 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1026277 AAAGTGAAAA
* *
1026287 ATATTACATGATTATGTTATT
1 ATATTACATCATTAT-TCATT
*
1026308 ATATTATATCATTATTCATT
1 ATATTACATCATTATTCATT
1026328 ATA
1 ATA
1026331 ATATTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (20 bp):
ATATTACATCATTATTCATT
Found at i:1026409 original size:13 final size:14
Alignment explanation
Indices: 1026370--1026412 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
1026360 TAATATGAAA
* *
1026370 TAATAAATAATATTT
1 TAATTAATAATA-AT
1026385 TAATTAATAATAAT
1 TAATTAATAATAAT
1026399 TAATT-ATAATAAT
1 TAATTAATAATAAT
1026412 T
1 T
1026413 TATTTGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 9 0.35
14 6 0.23
15 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTAATAATAAT
Found at i:1030835 original size:2 final size:2
Alignment explanation
Indices: 1030828--1030859 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1030818 TCTAGTTTGA
1030828 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
1030860 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1031483 original size:2 final size:2
Alignment explanation
Indices: 1031476--1031507 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1031466 TTCATTATTT
1031476 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1031508 ATTCTAAAAT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1032796 original size:2 final size:2
Alignment explanation
Indices: 1032789--1032829 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1032779 AAGGAGCTTT
* *
1032789 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TC TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1032830 GCTAGAAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1033998 original size:31 final size:31
Alignment explanation
Indices: 1033963--1034021 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1033953 TTGCAGGATA
*
1033963 ATGCTCAGATCAGATCTTGGGACCATTTATG
1 ATGCTCAGATCAGACCTTGGGACCATTTATG
1033994 ATGCTCAGATCAGACCTTGGGACCATTT
1 ATGCTCAGATCAGACCTTGGGACCATTT
1034022 TTTTCTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (31 bp):
ATGCTCAGATCAGACCTTGGGACCATTTATG
Found at i:1042804 original size:30 final size:29
Alignment explanation
Indices: 1042764--1042865 Score: 132
Period size: 30 Copynumber: 3.4 Consensus size: 29
1042754 TTATGTTAAT
*
1042764 TAAGTTTTTATACTTTTATTTTGAGATGAA
1 TAAGTTTTTATA-TTTTATTTTGAGATAAA
* *
1042794 TAAGTATTTATATGTTTATTTTGAAATAAA
1 TAAGTTTTTATAT-TTTATTTTGAGATAAA
* *
1042824 TAAGTTTTTATATTTTTATTTTAAGTTAAA
1 TAAGTTTTTATA-TTTTATTTTGAGATAAA
1042854 TAAGTTTTTATA
1 TAAGTTTTTATA
1042866 ATTAATAGTT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
29 1 0.02
30 61 0.97
31 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.55
Consensus pattern (29 bp):
TAAGTTTTTATATTTTATTTTGAGATAAA
Found at i:1043128 original size:30 final size:28
Alignment explanation
Indices: 1043094--1043165 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
1043084 AATCATTAAT
*
1043094 TATAATAATTTATTAAACTCAAAATAAAAA
1 TATAAAAATTTATTAAA--CAAAATAAAAA
* *
1043124 TATAAAAATTTGATTGAACATAATAAAAA
1 TATAAAAATTT-ATTAAACAAAATAAAAA
1043153 -ATAAAAATTTATT
1 TATAAAAATTTATT
1043166 TAATTTTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
27 3 0.08
28 10 0.26
29 10 0.26
30 10 0.26
31 5 0.13
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (28 bp):
TATAAAAATTTATTAAACAAAATAAAAA
Found at i:1045026 original size:2 final size:2
Alignment explanation
Indices: 1045019--1045045 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1045009 GGAGATTCAA
1045019 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1045046 AAGGATAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1046113 original size:30 final size:28
Alignment explanation
Indices: 1046045--1046117 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 28
1046035 TAAAGTTAAA
* *
1046045 TAAATAAATTTTTATTTTTTATTATATT
1 TAAATAAATTTTTATTTTTTATTAAAAT
*
1046073 TAATTAAATTTTTATTTTTTATTTTAAAAT
1 TAAATAAATTTTTATTTTTTA--TTAAAAT
1046103 TAAATAAATTTTTAT
1 TAAATAAATTTTTAT
1046118 GATTAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 20 0.51
30 19 0.49
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TAAATAAATTTTTATTTTTTATTAAAAT
Found at i:1046141 original size:24 final size:24
Alignment explanation
Indices: 1046096--1046150 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
1046086 ATTTTTTATT
*
1046096 TTAAAATTAAATAAATTTTTATGA
1 TTAAAATTAAATAAATTATTATGA
* *
1046120 TTAATAATT-AATTAATTATTATTAA
1 TTAA-AATTAAATAAATTATTA-TGA
1046145 TTAAAA
1 TTAAAA
1046151 GTCACTTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TTAAAATTAAATAAATTATTATGA
Found at i:1049137 original size:29 final size:30
Alignment explanation
Indices: 1049105--1049169 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
1049095 AAATTTTATC
*
1049105 AATTTTTTAT-TTTTTA-TTACAATTAATTA
1 AATTTTTTATATTTTTAGTTA-AATTAAATA
1049134 AA-TTTTTATATTTTTAGTTTAAATTAAATA
1 AATTTTTTATATTTTTAG-TTAAATTAAATA
1049164 AATTTT
1 AATTTT
1049170 ATGACTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
28 7 0.23
29 8 0.26
30 10 0.32
31 6 0.19
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (30 bp):
AATTTTTTATATTTTTAGTTAAATTAAATA
Found at i:1072748 original size:2 final size:2
Alignment explanation
Indices: 1072741--1072775 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1072731 ATAAAATTTG
1072741 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1072776 GTATGATTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1075990 original size:2 final size:2
Alignment explanation
Indices: 1075985--1076009 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1075975 TAAATAAATA
1075985 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
1076010 CATTTTGTAT
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:1081312 original size:15 final size:17
Alignment explanation
Indices: 1081292--1081324 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1081282 GATATTTCTA
1081292 TTATAAA-ATA-AAAAT
1 TTATAAATATATAAAAT
1081307 TTATAAATATATAAAAT
1 TTATAAATATATAAAAT
1081324 T
1 T
1081325 GTTACATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTATAAATATATAAAAT
Found at i:1081596 original size:31 final size:31
Alignment explanation
Indices: 1081561--1081620 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
1081551 TTTGTATACG
*
1081561 TTTAATTAA-ATTTTTATATTTTTATTTTAAA
1 TTTAATAAATATTTTTAT-TTTTTATTTTAAA
1081592 TTTAATAAATATTTTTATTTTTTATTTTA
1 TTTAATAAATATTTTTATTTTTTATTTTA
1081621 TTTCAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
TTTAATAAATATTTTTATTTTTTATTTTAAA
Found at i:1081972 original size:29 final size:28
Alignment explanation
Indices: 1081896--1081972 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 28
1081886 ATCATTAGTT
1081896 ATAAAAATTTATTTAACA-TAAAATAAAA
1 ATAAAAATTTATTTAA-ATTAAAATAAAA
*
1081924 ATACAAAATCTTAATTAAATGTAATAA-AAAA
1 ATA-AAAAT-TTATTTAAAT-TAA-AATAAAA
1081955 ATAAAAATTTATTTAAAT
1 ATAAAAATTTATTTAAAT
1081973 ATATTTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
28 3 0.07
29 15 0.36
30 12 0.29
31 10 0.24
32 2 0.05
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (28 bp):
ATAAAAATTTATTTAAATTAAAATAAAA
Found at i:1088384 original size:16 final size:16
Alignment explanation
Indices: 1088363--1088400 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1088353 ATATATTATA
*
1088363 ATAATAATAATATA-AT
1 ATAATAAT-ATAAACAT
1088379 ATAATAATATAAACAT
1 ATAATAATATAAACAT
1088395 ATAATA
1 ATAATA
1088401 TTTTTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAATAATATAAACAT
Found at i:1088389 original size:27 final size:27
Alignment explanation
Indices: 1088335--1088390 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1088325 ATTATATTAA
* * *
1088335 AATAATAATGATATATTGATATATTAT
1 AATAATAATAATATAATGATATAATAT
1088362 AATAATAATAATATAAT-ATAATAATAT
1 AATAATAATAATATAATGAT-ATAATAT
1088389 AA
1 AA
1088391 ACATATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (27 bp):
AATAATAATAATATAATGATATAATAT
Found at i:1088504 original size:18 final size:17
Alignment explanation
Indices: 1088481--1088515 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
1088471 ATCGTCCCTT
1088481 TTTAATTTTATGTTATAA
1 TTTAATTTTAT-TTATAA
1088499 TTTAATTTTATTTATAA
1 TTTAATTTTATTTATAA
1088516 AATAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTAATTTTATTTATAA
Found at i:1088521 original size:17 final size:18
Alignment explanation
Indices: 1088483--1088522 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1088473 CGTCCCTTTT
**
1088483 TAATTTTATGTTATAATT
1 TAATTTTATGTTATAAAA
1088501 TAATTTTAT-TTATAAAA
1 TAATTTTATGTTATAAAA
1088518 TAATT
1 TAATT
1088523 AATTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TAATTTTATGTTATAAAA
Found at i:1099496 original size:25 final size:26
Alignment explanation
Indices: 1099467--1099519 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
1099457 AAATTTTAAA
1099467 ATTTTTAAT-TATTTAA-AAAATTTT
1 ATTTTTAATATATTTAATAAAATTTT
*
1099491 ATTTTTATTATATTTAATTAAAATTTT
1 ATTTTTAATATATTTAA-TAAAATTTT
1099518 AT
1 AT
1099520 ATTATTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 8 0.32
25 7 0.28
27 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTTAATATATTTAATAAAATTTT
Found at i:1099500 original size:23 final size:24
Alignment explanation
Indices: 1099467--1099529 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 24
1099457 AAATTTTAAA
1099467 ATTTTTAATTATTTAA-AAAATTTT
1 ATTTTT-ATTATTTAATAAAATTTT
1099491 ATTTTTATTATATTTAATTAAAATTTT
1 ATTTTTA-T-TATTTAA-TAAAATTTT
*
1099518 A-TATTATTATTT
1 ATTTTTATTATTT
1099530 TAAATTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
23 1 0.03
24 12 0.35
25 8 0.24
26 4 0.12
27 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTTATTATTTAATAAAATTTT
Found at i:1099522 original size:29 final size:26
Alignment explanation
Indices: 1099456--1099529 Score: 71
Period size: 29 Copynumber: 2.8 Consensus size: 26
1099446 TTTAAAAAAG
* *
1099456 AAAATTTTAAAATTTTTAATTATTTAA
1 AAAATTTT-ATATTTTTATTTATTTAA
1099483 AAAA-TTT-TATTTTTATTATATTTAA
1 AAAATTTTATATTTTTATT-TATTTAA
*
1099508 TTAAAATTTTATATTATTATTT
1 --AAAATTTTATATTTTTATTT
1099530 TAAATTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 8 0.21
25 7 0.18
26 3 0.08
27 8 0.21
28 4 0.10
29 9 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
AAAATTTTATATTTTTATTTATTTAA
Found at i:1099535 original size:26 final size:27
Alignment explanation
Indices: 1099476--1099538 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 27
1099466 AATTTTTAAT
*
1099476 TATTTAA--AAAATTTTATTTTTATTA
1 TATTTAATTAAAATTTTATTATTATTA
1099501 TATTTAATTAAAATTTTA-TATTATTA
1 TATTTAATTAAAATTTTATTATTATTA
1099527 T-TTTAAATTAAA
1 TATTT-AATTAAA
1099539 TAAATTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
25 10 0.29
26 15 0.44
27 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TATTTAATTAAAATTTTATTATTATTA
Found at i:1099543 original size:29 final size:28
Alignment explanation
Indices: 1099479--1099554 Score: 79
Period size: 26 Copynumber: 2.8 Consensus size: 28
1099469 TTTTAATTAT
*
1099479 TTAAAAAATTTTATTTTTATTATATTTAA
1 TTAAAAAATTTTA-TATTATTATATTTAA
1099508 TT--AAAATTTTATATTATTAT-TTTAAA
1 TTAAAAAATTTTATATTATTATATTT-AA
*
1099534 TTAAATAAATTTT-TATAATTA
1 TTAAA-AAATTTTATATTATTA
1099555 ATAATAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
25 3 0.07
26 12 0.29
27 9 0.22
28 8 0.20
29 9 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTAAAAAATTTTATATTATTATATTTAA
Found at i:1102442 original size:2 final size:2
Alignment explanation
Indices: 1102435--1102460 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1102425 ATGTATGTTT
1102435 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1102461 ATATGGCTTA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1110339 original size:34 final size:33
Alignment explanation
Indices: 1110301--1110364 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
1110291 ATGTAAAATA
*
1110301 TTATTAAATTTAATAAAACTA-TTTTTATTTAAAG
1 TTATTAAATATAAT-AAAC-AGTTTTTATTTAAAG
* *
1110335 TTATTTAATATAATTAACAGTTTTTATTTA
1 TTATTAAATATAATAAACAGTTTTTATTTA
1110365 TAAATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 1 0.04
33 13 0.50
34 12 0.46
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (33 bp):
TTATTAAATATAATAAACAGTTTTTATTTAAAG
Found at i:1121117 original size:15 final size:15
Alignment explanation
Indices: 1121097--1121140 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1121087 TAATTACTAT
1121097 TATATATATTTTTAA
1 TATATATATTTTTAA
* *
1121112 TATATATACTTTAAA
1 TATATATATTTTTAA
* *
1121127 TATAAATATATTTA
1 TATATATATTTTTA
1121141 CTTTCTATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATATATTTTTAA
Found at i:1121378 original size:34 final size:36
Alignment explanation
Indices: 1121328--1121405 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 36
1121318 ACATATAATG
* *
1121328 TTTAAATTGTTGTTTGA-ATA-TTT-CTTTTTAGTTA
1 TTTAAATTGATATTTGAGATATTTTACTTTTTA-TTA
*
1121362 TTTAAATTGATATTTGAGATATTTTATTTTTTATTA
1 TTTAAATTGATATTTGAGATATTTTACTTTTTATTA
1121398 TTTAAATT
1 TTTAAATT
1121406 TAAATTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 15 0.39
35 3 0.08
36 14 0.37
37 6 0.16
ACGTcount: A:0.28, C:0.01, G:0.09, T:0.62
Consensus pattern (36 bp):
TTTAAATTGATATTTGAGATATTTTACTTTTTATTA
Found at i:1122340 original size:31 final size:30
Alignment explanation
Indices: 1122303--1122362 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
1122293 TTATTAATTA
* * *
1122303 ATTTATATATTATTTAATAGATAAATTAATC
1 ATTTATACATTAATTAATA-AAAAATTAATC
1122334 ATTTATACATTAATTAATAAAAAATTAAT
1 ATTTATACATTAATTAATAAAAAATTAAT
1122363 TTATCAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (30 bp):
ATTTATACATTAATTAATAAAAAATTAATC
Found at i:1122364 original size:27 final size:28
Alignment explanation
Indices: 1122298--1122366 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 28
1122288 GAAATTTATT
* * *
1122298 AATTAATTTATATATTATTTAATAGATA
1 AATTAATTTATACATTAATTAATAGAAA
1122326 AATTAATCATTTATACATTAATTAATA-AAA
1 AATT-A--ATTTATACATTAATTAATAGAAA
1122356 AATTAATTTAT
1 AATTAATTTAT
1122367 CAAGATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
27 6 0.17
28 4 0.11
29 2 0.06
30 6 0.17
31 17 0.49
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (28 bp):
AATTAATTTATACATTAATTAATAGAAA
Found at i:1122843 original size:17 final size:19
Alignment explanation
Indices: 1122823--1122865 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1122813 AATAAAATTA
1122823 TATATATA-ATT-TTAATG
1 TATATATAGATTATTAATG
* *
1122840 TATAAATAGATTATTAATT
1 TATATATAGATTATTAATG
1122859 TATATAT
1 TATATAT
1122866 CAAATAAGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 3 0.14
19 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TATATATAGATTATTAATG
Found at i:1122944 original size:17 final size:18
Alignment explanation
Indices: 1122924--1122961 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1122914 CAAATCGAGA
*
1122924 TTAATTAAAAATATT-AT
1 TTAATCAAAAATATTAAT
*
1122941 TTAATCAAAATTATTAAT
1 TTAATCAAAAATATTAAT
1122959 TTA
1 TTA
1122962 TAAAAGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATCAAAAATATTAAT
Found at i:1126842 original size:22 final size:23
Alignment explanation
Indices: 1126817--1126866 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1126807 CATTAGTTAC
**
1126817 TAATTTTTAATTATTACGAGA-T
1 TAATTTTTAAGCATTACGAGATT
*
1126839 TAATTTTTAAGCATTACGTGATT
1 TAATTTTTAAGCATTACGAGATT
1126862 TAATT
1 TAATT
1126867 ATTATTTCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.50
Consensus pattern (23 bp):
TAATTTTTAAGCATTACGAGATT
Found at i:1134787 original size:46 final size:45
Alignment explanation
Indices: 1134728--1134820 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 45
1134718 ATGACTTAAT
*
1134728 AGGTAATGAGCAAACCTGAGATATTGAAGAAAACTAAGTAATATTA
1 AGGTAATAAGCAAACCTGAGATATTGAAGAAAACTAAGTAAT-TTA
*
1134774 AGGTAATAAGCAAACCTGAGATATTGAAGAAAACTAGGTAATTTA
1 AGGTAATAAGCAAACCTGAGATATTGAAGAAAACTAAGTAATTTA
1134819 AG
1 AG
1134821 CTCTGCTCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 5 0.11
46 40 0.89
ACGTcount: A:0.47, C:0.09, G:0.20, T:0.24
Consensus pattern (45 bp):
AGGTAATAAGCAAACCTGAGATATTGAAGAAAACTAAGTAATTTA
Found at i:1134853 original size:27 final size:27
Alignment explanation
Indices: 1134822--1134875 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1134812 TAATTTAAGC
1134822 TCTGCTCAGACTACCAATTACTTTAAA
1 TCTGCTCAGACTACCAATTACTTTAAA
*
1134849 TCTGCTTAGACTACCAATTACTTTAAA
1 TCTGCTCAGACTACCAATTACTTTAAA
1134876 CAGGAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.35
Consensus pattern (27 bp):
TCTGCTCAGACTACCAATTACTTTAAA
Found at i:1137625 original size:5 final size:5
Alignment explanation
Indices: 1137615--1137646 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1137605 AGATGGTGGC
*
1137615 TTTCT TTTCT TTTCT TTTCG TTTCT TTTCT TT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TT
1137647 CTTCCTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:1140834 original size:3 final size:3
Alignment explanation
Indices: 1140826--1140862 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1140816 CTTACAATTT
1140826 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1140863 AACCACCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1142073 original size:2 final size:2
Alignment explanation
Indices: 1142066--1142110 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1142056 AAAAGAAAAG
*
1142066 GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1142108 GA G
1 GA G
1142111 GGATGGGGCG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1155466 original size:16 final size:16
Alignment explanation
Indices: 1155441--1155471 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1155431 TTCTTCTTAT
*
1155441 AAAAACAAACAAAGAA
1 AAAAAAAAACAAAGAA
1155457 AAAAAAAAACAAAGA
1 AAAAAAAAACAAAGA
1155472 GATTCCAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAAAACAAAGAA
Found at i:1180392 original size:26 final size:25
Alignment explanation
Indices: 1180354--1180423 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
1180344 CAAATTAATA
*
1180354 TTATATATATTAATATATAATAATATAT
1 TTATAT-TTTTAATATATAATAA-A-AT
*
1180382 TTA-ATTTTTAATTTAT-ATAAAAT
1 TTATATTTTTAATATATAATAAAAT
1180405 TTATATTTTTAATAT-TAAT
1 TTATATTTTTAATATATAAT
1180424 TTTAATTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 6 0.16
24 13 0.35
25 4 0.11
26 9 0.24
27 2 0.05
28 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATATTTTTAATATATAATAAAAT
Found at i:1186434 original size:129 final size:129
Alignment explanation
Indices: 1186217--1186450 Score: 371
Period size: 129 Copynumber: 1.8 Consensus size: 129
1186207 GAGTTGAAAT
*
1186217 GGAGAATGCGAATTCAGCCCCCACAGGTTGCTACAAATGCGGACGAACAGGCCACTGGTCAAGTG
1 GGAGAATGCGAATTCAGCCCCAACAGGTTGCTACAAATGCGGACGAACAGGCCACTGGTCAAGTG
* *
1186282 ACTGCCCCGACGCCCCCGAATCCGACCACCCCAATCTCAATCCCAATCCGGGAAGAGTCGCAAC
66 ACTGCCCCGACGCCCCCAAATCCGACCAACCCAATCTCAATCCCAATCCGGGAAGAGTCGCAAC
* * * *
1186346 GGAGAA-GACGAATTCAGCCGCAACAGGTTGCTACAAGTGCGGACGACCAGGCCACTGGTCACGT
1 GGAGAATG-CGAATTCAGCCCCAACAGGTTGCTACAAATGCGGACGAACAGGCCACTGGTCAAGT
* *
1186410 GACTGCCCGGACGCCCCCAAATCCGATCAACCCAATCTCAA
65 GACTGCCCCGACGCCCCCAAATCCGACCAACCCAATCTCAA
1186451 GGCTTCCTCC
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
128 1 0.01
129 94 0.99
ACGTcount: A:0.28, C:0.35, G:0.24, T:0.13
Consensus pattern (129 bp):
GGAGAATGCGAATTCAGCCCCAACAGGTTGCTACAAATGCGGACGAACAGGCCACTGGTCAAGTG
ACTGCCCCGACGCCCCCAAATCCGACCAACCCAATCTCAATCCCAATCCGGGAAGAGTCGCAAC
Found at i:1189237 original size:93 final size:93
Alignment explanation
Indices: 1189067--1189237 Score: 225
Period size: 93 Copynumber: 1.8 Consensus size: 93
1189057 TGCCAAATAA
* ** *
1189067 TGGAGCTGGCTGCTCCACTGAAGTTCATATCACAGAAGAACAGAGAGCTCGGATGGAAGCTAACA
1 TGGAGCTGGCTCCTCCACTGAAACTCAAATCACAGAAGAACAGAGAGCTCGGATGGAAGCTAACA
* *
1189132 AGTTGAAGGCACTACAGAGAGTTGCAGC
66 AGATGAAAGCACTACAGAGAGTTGCAGC
* * * * * *
1189160 TGGAGCTGGCTCCTCTAGTGAAACTCAAATCACAGAAGAGCAGCGTGCTCGGATGGAAGCTAATA
1 TGGAGCTGGCTCCTCCACTGAAACTCAAATCACAGAAGAACAGAGAGCTCGGATGGAAGCTAACA
*
1189225 GGATGAAAGCACT
66 AGATGAAAGCACT
1189238 GGAAAGAGCA
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
93 65 1.00
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.19
Consensus pattern (93 bp):
TGGAGCTGGCTCCTCCACTGAAACTCAAATCACAGAAGAACAGAGAGCTCGGATGGAAGCTAACA
AGATGAAAGCACTACAGAGAGTTGCAGC
Found at i:1190330 original size:11 final size:12
Alignment explanation
Indices: 1190309--1190340 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
1190299 AATTAATATT
1190309 ATTATCTTTATA
1 ATTATCTTTATA
1190321 ATTA-CTTTATA
1 ATTATCTTTATA
1190332 ATTATCTTT
1 ATTATCTTT
1190341 TATTCAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTATCTTTATA
Found at i:1194473 original size:18 final size:16
Alignment explanation
Indices: 1194434--1194472 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
1194424 GGGTGGAGAC
1194434 AGGA-GAGGCGGCGGG
1 AGGAGGAGGCGGCGGG
1194449 AGGAGGAGGCGGC-GG
1 AGGAGGAGGCGGCGGG
1194464 AGGAGGAGG
1 AGGAGGAGG
1194473 AAGCGGTGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.23, C:0.10, G:0.67, T:0.00
Consensus pattern (16 bp):
AGGAGGAGGCGGCGGG
Found at i:1205763 original size:2 final size:2
Alignment explanation
Indices: 1205756--1205787 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1205746 GTATGTACAA
*
1205756 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1205788 TAAATTACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1219534 original size:2 final size:2
Alignment explanation
Indices: 1219527--1219559 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1219517 TATGTATGTA
1219527 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1219560 GTATGTACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1219587 original size:12 final size:12
Alignment explanation
Indices: 1219570--1219594 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1219560 GTATGTACAC
1219570 ACACACACACAT
1 ACACACACACAT
1219582 ACACACACACAT
1 ACACACACACAT
1219594 A
1 A
1219595 TAGATATACA
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:0.52, C:0.40, G:0.00, T:0.08
Consensus pattern (12 bp):
ACACACACACAT
Found at i:1219601 original size:6 final size:6
Alignment explanation
Indices: 1219590--1219632 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
1219580 ATACACACAC
*
1219590 ACATAT AGATAT ACATAT ACATAT ACATAT ACATAT ACATAT A
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT A
1219633 TTTGCTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:1244549 original size:4 final size:4
Alignment explanation
Indices: 1244528--1244588 Score: 77
Period size: 4 Copynumber: 15.2 Consensus size: 4
1244518 TGTGTGTTTG
* * *
1244528 TGTA TATA TATA TATA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* *
1244576 AGTA TGCA TGTA T
1 TGTA TGTA TGTA T
1244589 TTTACCCCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.48
Consensus pattern (4 bp):
TGTA
Found at i:1256465 original size:68 final size:68
Alignment explanation
Indices: 1256339--1256486 Score: 228
Period size: 68 Copynumber: 2.2 Consensus size: 68
1256329 GAGAGAGTTG
* * *
1256339 GGGGGGGGGA-GGTGACTAAAGGTCACTTCTATAGTATCCACCTTTTCTTTCCTAAGAAAAGCAA
1 GGGGAGGGGAGGGGGACTAAAGGTCACTTCTATAGTATCCACCTTTTCTTTCCTAAGAAAAGAAA
1256403 AGA
66 AGA
* * *
1256406 GGGGAGGGGAGGGGGACTAAAGGTCACTTCTTTATTATCCACCTTTTCTTTCCTGAGAAAAGAAA
1 GGGGAGGGGAGGGGGACTAAAGGTCACTTCTATAGTATCCACCTTTTCTTTCCTAAGAAAAGAAA
1256471 AGA
66 AGA
1256474 GGGGA-GGGAGGGG
1 GGGGAGGGGAGGGG
1256487 TGGTGTAGGG
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
67 17 0.23
68 57 0.77
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (68 bp):
GGGGAGGGGAGGGGGACTAAAGGTCACTTCTATAGTATCCACCTTTTCTTTCCTAAGAAAAGAAA
AGA
Found at i:1258060 original size:53 final size:53
Alignment explanation
Indices: 1257980--1258082 Score: 170
Period size: 53 Copynumber: 1.9 Consensus size: 53
1257970 CCAAATATTA
* * * *
1257980 TATTGGTTGCGACTGTATGCTATCTAATGTAAATACGCAGTGTTGATGTTTGG
1 TATTGGTAGCGACTGAATGCTATCTAATGTAAATACCCAGTGGTGATGTTTGG
1258033 TATTGGTAGCGACTGAATGCTATCTAATGTAAATACCCAGTGGTGATGTT
1 TATTGGTAGCGACTGAATGCTATCTAATGTAAATACCCAGTGGTGATGTT
1258083 CGAGAAAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (53 bp):
TATTGGTAGCGACTGAATGCTATCTAATGTAAATACCCAGTGGTGATGTTTGG
Found at i:1270478 original size:3 final size:3
Alignment explanation
Indices: 1270470--1270506 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1270460 TCAATTGGCT
1270470 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1270507 GTTTTAAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1271631 original size:15 final size:15
Alignment explanation
Indices: 1271610--1271647 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1271600 TTTAGTTAAG
*
1271610 AATTATTATTTATATT
1 AATTATTATTAAT-TT
1271626 -ATTATTATTAATTT
1 AATTATTATTAATTT
1271640 AATTATTA
1 AATTATTA
1271648 CATATTGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
AATTATTATTAATTT
Found at i:1280817 original size:27 final size:27
Alignment explanation
Indices: 1280764--1280837 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
1280754 GATTTATGGT
*
1280764 ATATAAATTTAATTAAATATAATTAAAA
1 ATATAAATTT-ATTAAATATTATTAAAA
* *
1280792 ATATAAATTTATTTAATATTTTTAAAA
1 ATATAAATTTATTAAATATTATTAAAA
1280819 A-AT-AATTT-TTAAATATTAT
1 ATATAAATTTATTAAATATTAT
1280838 GTCATAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 9 0.22
25 5 0.12
26 2 0.05
27 15 0.37
28 10 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATATAAATTTATTAAATATTATTAAAA
Found at i:1283310 original size:17 final size:17
Alignment explanation
Indices: 1283290--1283323 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1283280 ATTATTAACT
1283290 TGTAGTTGAATTTAATC
1 TGTAGTTGAATTTAATC
1283307 TGTAGTTGAATTTAATC
1 TGTAGTTGAATTTAATC
1283324 ATATTAGAAT
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:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (17 bp):
TGTAGTTGAATTTAATC
Found at i:1284334 original size:2 final size:2
Alignment explanation
Indices: 1284329--1284361 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1284319 TATATATATA
*
1284329 TG TG TG TG TG TG TG TG TG TG TG TG TC TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1284362 ATGTATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1289520 original size:2 final size:2
Alignment explanation
Indices: 1289513--1289550 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1289503 TCTGATCCAA
1289513 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1289551 GTATGTAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1296978 original size:15 final size:15
Alignment explanation
Indices: 1296943--1296991 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1296933 TTATTATTAA
*
1296943 AATATTAAAAATACT
1 AATATTAAAAATAAT
*
1296958 AATATTAATAATAAT
1 AATATTAAAAATAAT
*
1296973 ATTATTATGAAAATAAT
1 AATATTA--AAAATAAT
1296990 AA
1 AA
1296992 AAATATTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 19 0.70
17 8 0.30
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (15 bp):
AATATTAAAAATAAT
Found at i:1296996 original size:23 final size:24
Alignment explanation
Indices: 1296963--1297007 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1296953 ATACTAATAT
*
1296963 TAATAATAATA-TTATTATGAAAA
1 TAATAAAAATATTTATTATGAAAA
1296986 TAATAAAAATATTTATTATGAA
1 TAATAAAAATATTTATTATGAA
1297008 TAATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
TAATAAAAATATTTATTATGAAAA
Found at i:1312283 original size:21 final size:20
Alignment explanation
Indices: 1312258--1312296 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1312248 TTACAACATG
1312258 AATACACATTTTAAGTAGAAA
1 AATAC-CATTTTAAGTAGAAA
* *
1312279 AATACCTTTTTGAGTAGA
1 AATACCATTTTAAGTAGA
1312297 TACGTAGCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (20 bp):
AATACCATTTTAAGTAGAAA
Found at i:1317307 original size:2 final size:2
Alignment explanation
Indices: 1317300--1317329 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1317290 TATTTACACA
1317300 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
1317330 TAAAAGTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1328138 original size:572 final size:573
Alignment explanation
Indices: 1327054--1328203 Score: 1865
Period size: 572 Copynumber: 2.0 Consensus size: 573
1327044 ATATGTACAT
* * *
1327054 ATTTAAATATAATTAATTAGACTGTGTATAATTTTCTTATTTAAAAAGTAAAATTCAAATTTTCT
1 ATTTAAATACAATTAATTAGACGGTGCATAATTTTCTTATTTAAAAAGTAAAATTCAAATTTTCT
*
1327119 TCTCAAATCATTTTTATAAAAACAACATTGACATCTAACATTGAAATTTGTATTATTTCAATAAT
66 TCTCAAATCATTTTTATAAAAACAACATTGACATCTAACATTGAAATATGTATTATTTCAATAAT
1327184 AAAATTTTAATCTTTACATCAAAATTTTCACCAAATTTAATTTATATACATAATAATCATCGAAA
131 AAAATTTTAATCTTTACATCAAAATTTTCACCAAATTTAATTTATATACATAATAATCATCGAAA
* * * * *
1327249 CTTGGATATTAAATCATTAAATTTATTAACGTGTCAACTTTATTTTAGTTACATAGAGTATATTT
196 CCTAGATATTAAATCATTAAATTTATTAACGTGTCAACTTTATTTTAGTTACATAAAATATAGTT
1327314 TGCTAGCTAACCACTACTTTCGATTATTAATCATTAATTACAGTTGTAAGTATTCAAAATATGTA
261 TGCTAGCTAACCACTACTTTCGATTATTAATCATTAATTACAGTTGTAAGTATTCAAAATATGTA
* *
1327379 ATCAATTTCATTGACTTGAATATTGAATCATTAAATTTATTGACATGACGACATTATATTAGTTA
326 ATCAATTTCATTGACTTAAATATTGAATCATTAAATTTATAGACATGACGACATTATATTAGTTA
* *
1327444 CATCAAGTGTATTTTGCTAGCTAATCACTTCTTTCAATTATTACATTAATTATAGTTGTAAATGT
391 CATCAAGTGTATTTTGCTAGCTAATCACTTCTTTCAATTATTACAGTAATTATAATTGTAAATGT
* *
1327509 TCAAAATATATAATCAATTAATATAAAAATTCATGTGTCACGTTAAATTATTAAGATTACTCCAA
456 TCAAAATATATAATCAATTAATATAAAAATTCATGTGCCACGTTAAATGATTAAGATTACTCCAA
* *
1327574 TCACTTAATATAACAGTTGAATATTCATATTATTATGATAATGATTATTTTTA
521 TCACTTAATATAACAGTCGAATATTCATATTATTATGATAATGATCATTTTTA
* * * * * * *
1327627 ATTTAAATGCAATTCATTGGACGGTGCATAATTTTTTTATTTAAAGAGTAAGATTCAAATTTTTT
1 ATTTAAATACAATTAATTAGACGGTGCATAATTTTCTTATTTAAAAAGTAAAATTCAAATTTTCT
1327692 TCTCAAAT-ATTGTTTATAAAAACAACATTGACATCTAACATTGAAATATGTATTATTTCAATAA
66 TCTCAAATCATT-TTTATAAAAACAACATTGACATCTAACATTGAAATATGTATTATTTCAATAA
* * *
1327756 TAAAGTTTTAATCTTTACATCAAAATTTTCACCGAATTTAATTTATATATATAATAATCATCG-A
130 TAAAATTTTAATCTTTACATCAAAATTTTCACCAAATTTAATTTATATACATAATAATCATCGAA
* * * * * *
1327820 ACCTAGATATTGAATCATTAAATTTATTGATGTGGT-GACTTTATTTTGGTTACATAAAATGTAG
195 ACCTAGATATTAAATCATTAAATTTATTAACGT-GTCAACTTTATTTTAGTTACATAAAATATAG
* *
1327884 TTTGCTAGCTAACCACTACTTTCGATTATTAATCATTAATTATAGTTGTAAGTATTTAAAATATG
259 TTTGCTAGCTAACCACTACTTTCGATTATTAATCATTAATTACAGTTGTAAGTATTCAAAATATG
*
1327949 TAATCAATTTCATTGACTTAAATATTGAATCATTAAATTTATAGACGTGACGACATTATATTAGT
324 TAATCAATTTCATTGACTTAAATATTGAATCATTAAATTTATAGACATGACGACATTATATTAGT
* * *
1328014 TACATCGAGTGTATTTTGCTAGCTAATCATTTCTTTCGATTATTACAGTAATTATAATTGTAAAT
389 TACATCAAGTGTATTTTGCTAGCTAATCACTTCTTTCAATTATTACAGTAATTATAATTGTAAAT
* *
1328079 GTTCAAAATATGTAATCAATTAATATAAAAATTCATGTGCCACGTTAAATGATTAAGATTACTTC
454 GTTCAAAATATATAATCAATTAATATAAAAATTCATGTGCCACGTTAAATGATTAAGATTACTCC
* * *
1328144 AATTACTTAATTTAATAGTCGAATATTCATATTATTATGATAATGATCATTTTTA
519 AATCACTTAATATAACAGTCGAATATTCATATTATTATGATAATGATCATTTTTA
1328199 ATTTA
1 ATTTA
1328204 TTATAGAATA
Statistics
Matches: 531, Mismatches: 44, Indels: 5
0.92 0.08 0.01
Matches are distributed among these distances:
572 355 0.67
573 176 0.33
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (573 bp):
ATTTAAATACAATTAATTAGACGGTGCATAATTTTCTTATTTAAAAAGTAAAATTCAAATTTTCT
TCTCAAATCATTTTTATAAAAACAACATTGACATCTAACATTGAAATATGTATTATTTCAATAAT
AAAATTTTAATCTTTACATCAAAATTTTCACCAAATTTAATTTATATACATAATAATCATCGAAA
CCTAGATATTAAATCATTAAATTTATTAACGTGTCAACTTTATTTTAGTTACATAAAATATAGTT
TGCTAGCTAACCACTACTTTCGATTATTAATCATTAATTACAGTTGTAAGTATTCAAAATATGTA
ATCAATTTCATTGACTTAAATATTGAATCATTAAATTTATAGACATGACGACATTATATTAGTTA
CATCAAGTGTATTTTGCTAGCTAATCACTTCTTTCAATTATTACAGTAATTATAATTGTAAATGT
TCAAAATATATAATCAATTAATATAAAAATTCATGTGCCACGTTAAATGATTAAGATTACTCCAA
TCACTTAATATAACAGTCGAATATTCATATTATTATGATAATGATCATTTTTA
Found at i:1341440 original size:25 final size:24
Alignment explanation
Indices: 1341412--1341507 Score: 76
Period size: 25 Copynumber: 4.0 Consensus size: 24
1341402 TCTTATTAAT
1341412 TATAATTAATTAATAAAAAGTAAAA
1 TATAATTAATTAATAAAAA-TAAAA
* *
1341437 TATACTTATTTAATCTAAAAATAAAA
1 TATAATTAATTAA--TAAAAATAAAA
*
1341463 TAT--TTAATTGAAT-ATAATAAAA
1 TATAATTAATT-AATAAAAATAAAA
1341485 GTATAATT--TTAAATAAAAATAAA
1 -TATAATTAATT-AATAAAAATAAA
1341508 CACTTTAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
22 8 0.14
23 9 0.16
24 12 0.21
25 15 0.26
26 8 0.14
27 6 0.10
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.36
Consensus pattern (24 bp):
TATAATTAATTAATAAAAATAAAA
Found at i:1344504 original size:21 final size:21
Alignment explanation
Indices: 1344480--1344519 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1344470 TATGAAAAAA
* *
1344480 TTAAAATATTTTTTTATAAAT
1 TTAAAATATTATTATATAAAT
1344501 TTAAAATATTATTATATAA
1 TTAAAATATTATTATATAA
1344520 TTTTTTGAAA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAAATATTATTATATAAAT
Found at i:1344614 original size:33 final size:31
Alignment explanation
Indices: 1344564--1344639 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 31
1344554 AGCTCTCTAA
1344564 AATTTTTAA-ATTAATAAAAAATATATAATAAT
1 AATTTTTAATATTAATAAAAAATA-A-AATAAT
*
1344596 AATTTTTAATATTAATAAAAAATAAAATTAT
1 AATTTTTAATATTAATAAAAAATAAAATAAT
*
1344627 -ATTTTCAATATTA
1 AATTTTTAATATTA
1344640 CTACATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 12 0.29
31 5 0.12
32 10 0.24
33 14 0.34
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (31 bp):
AATTTTTAATATTAATAAAAAATAAAATAAT
Found at i:1344945 original size:81 final size:81
Alignment explanation
Indices: 1344855--1345017 Score: 256
Period size: 81 Copynumber: 2.0 Consensus size: 81
1344845 GTTATCTTTT
* *
1344855 TCTATTTTTATTCAAGATATAAAAA-ATTTTTGAATTTAATTTATTAAATAAGAGATACATATAC
1 TCTATTTTTATTCAAGATATAAAAACA-TTTTGAATTTAATTTATTAAATAAGAAATACAAATAC
1344919 TATCATTGAATCAAACG
65 TATCATTGAATCAAACG
* *
1344936 TCTATTTTTATTCAAGATATAAAAACATTTTGAATTTAGTTTATTAAATAAGAAATACAAATATT
1 TCTATTTTTATTCAAGATATAAAAACATTTTGAATTTAATTTATTAAATAAGAAATACAAATACT
* *
1345001 TTCTTTGAATCAAACG
66 ATCATTGAATCAAACG
1345017 T
1 T
1345018 GTAATAGCAC
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
81 74 0.99
82 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (81 bp):
TCTATTTTTATTCAAGATATAAAAACATTTTGAATTTAATTTATTAAATAAGAAATACAAATACT
ATCATTGAATCAAACG
Found at i:1345087 original size:15 final size:16
Alignment explanation
Indices: 1345057--1345093 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
1345047 AAAGTATTTA
1345057 TATAAAAAATATGTTT
1 TATAAAAAATATGTTT
*
1345073 TATATAAAA-ATGTTT
1 TATAAAAAATATGTTT
1345088 TATAAA
1 TATAAA
1345094 TTCTGATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (16 bp):
TATAAAAAATATGTTT
Found at i:1355230 original size:34 final size:36
Alignment explanation
Indices: 1355192--1355260 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
1355182 GATGTATTTT
1355192 TAATA-TGGAA-AATTATGTCTTTTT-GTATGAAAAG
1 TAATATTGGAATAATTATGT-TTTTTCGTATGAAAAG
* *
1355226 TAATATTGTAATAATTATGTTTTTTCGTATTAAAA
1 TAATATTGGAATAATTATGTTTTTTCGTATGAAAA
1355261 AAAAATATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 5 0.17
35 9 0.30
36 16 0.53
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (36 bp):
TAATATTGGAATAATTATGTTTTTTCGTATGAAAAG
Found at i:1360208 original size:30 final size:29
Alignment explanation
Indices: 1360134--1360225 Score: 141
Period size: 29 Copynumber: 3.1 Consensus size: 29
1360124 TTATATAAAA
1360134 AAATTTAAATAAATTTTTATATTTTTATT
1 AAATTTAAATAAATTTTTATATTTTTATT
*
1360163 AAATTTAACTAAATTTTTATATTTTTATTTT
1 AAATTTAAATAAATTTTTATATTTTTA--TT
1360194 AAA-TTAAATAAATTTTTATATTTTTAATT
1 AAATTTAAATAAATTTTTATATTTTT-ATT
1360223 AAA
1 AAA
1360226 ATATTATTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
29 31 0.53
30 21 0.36
31 6 0.10
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (29 bp):
AAATTTAAATAAATTTTTATATTTTTATT
Found at i:1360257 original size:24 final size:23
Alignment explanation
Indices: 1360181--1360257 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 23
1360171 CTAAATTTTT
*
1360181 ATATTTTTATTTTAAATTAAATA
1 ATATTTTTATTTTATATTAAATA
*
1360204 A-ATTTTTATATTTTTAATTAAAATA
1 ATATTTTTAT-TTTAT-ATT-AAATA
* *
1360229 TTATTTATTATTTTATATTATATA
1 ATATTT-TTATTTTATATTAAATA
1360253 ATATT
1 ATATT
1360258 AATTTGACAT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
22 8 0.19
23 4 0.09
24 11 0.26
25 8 0.19
26 8 0.19
27 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATATTTTTATTTTATATTAAATA
Found at i:1360419 original size:18 final size:19
Alignment explanation
Indices: 1360382--1360425 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1360372 AAATAAAAAA
*
1360382 TAATAATAAATATTTTAAT
1 TAATAATAAATATATTAAT
*
1360401 TAATAATAATTA-ATTAAT
1 TAATAATAAATATATTAAT
*
1360419 TATTAAT
1 TAATAAT
1360426 TATAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATAATAAATATATTAAT
Found at i:1360424 original size:25 final size:24
Alignment explanation
Indices: 1360380--1360445 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 24
1360370 ATAAATAAAA
*
1360380 AATAATAA-TAAAT-ATTTTAATT
1 AATAATAATTAATTAATTTTAATT
1360402 AATAATAATTAATTAATTATTAATT
1 AATAATAATTAATTAATT-TTAATT
* *
1360427 -ATAAAAAATTATTTAATTT
1 AAT-AATAATTAATTAATTT
1360446 AAAATAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
22 8 0.22
23 4 0.11
24 6 0.16
25 19 0.51
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AATAATAATTAATTAATTTTAATT
Found at i:1360438 original size:17 final size:17
Alignment explanation
Indices: 1360416--1360449 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1360406 ATAATTAATT
1360416 AATTA-TTAATTATAAAA
1 AATTATTTAATT-TAAAA
1360433 AATTATTTAATTTAAAA
1 AATTATTTAATTTAAAA
1360450 TAAAAATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTATTTAATTTAAAA
Found at i:1365296 original size:23 final size:23
Alignment explanation
Indices: 1365268--1365320 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
1365258 TGTTTAAAAT
1365268 TTTAATTATGTTCAAAAATTTTA
1 TTTAATTATGTTCAAAAATTTTA
1365291 TTTAATTATGTTCAAAAATTTTA
1 TTTAATTATGTTCAAAAATTTTA
1365314 TTTAATT
1 TTTAATT
1365321 CTTTATAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTAATTATGTTCAAAAATTTTA
Found at i:1365613 original size:16 final size:16
Alignment explanation
Indices: 1365592--1365631 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1365582 CGTAAATATA
1365592 TTTATAA-TTAATAATT
1 TTTATAAGTT-ATAATT
*
1365608 TTTATAAGTTATAGTT
1 TTTATAAGTTATAATT
1365624 TTTATAAG
1 TTTATAAG
1365632 GTTAACACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (16 bp):
TTTATAAGTTATAATT
Found at i:1366247 original size:65 final size:65
Alignment explanation
Indices: 1366177--1366376 Score: 231
Period size: 65 Copynumber: 3.1 Consensus size: 65
1366167 TAAATTATCT
* * * * *
1366177 ATATATAAATGCGTATAGAATAAGGTTTGGGTACATATATTATATATTATATAAATAATAACAAA
1 ATATATAAATGGGTATAGAATTAGGTTCGGGTACATTTATTATATATTATATAAATAATAATAAA
* ** * * * *
1366242 ATATATAGATGGGTATAGGGTTCGGTCCAGGTACATTTATTATACATTATATAAATAATAATAAA
1 ATATATAAATGGGTATAGAATTAGGTTCGGGTACATTTATTATATATTATATAAATAATAATAAA
* ** *
1366307 ATATATAAATGGGTATA-AATTTTGAACTCGAGTACATTTATTATATATTATATAAATAATAATA
1 ATATATAAATGGGTATAGAA-TTAG-GTTCGGGTACATTTATTATATATTATATAAATAATAATA
1366371 AA
64 AA
1366373 ATAT
1 ATAT
1366377 TATATAAATT
Statistics
Matches: 111, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
65 72 0.65
66 39 0.35
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (65 bp):
ATATATAAATGGGTATAGAATTAGGTTCGGGTACATTTATTATATATTATATAAATAATAATAAA
Found at i:1378702 original size:4 final size:4
Alignment explanation
Indices: 1378682--1378726 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
1378672 TTCCTTAATT
* *
1378682 TTTC -TTC TCTC TCTC TTTC TTTC TTTC TTTC TTTC TTT- TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1378727 TAGACTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 6 0.16
4 31 0.84
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:1403661 original size:35 final size:34
Alignment explanation
Indices: 1403618--1403784 Score: 174
Period size: 35 Copynumber: 4.8 Consensus size: 34
1403608 AATTAGAATG
* * *
1403618 AGTGAAGCACTATTTCACGCTAAACAACTAGAACA
1 AGTGAAACACTACTTCATGC-AAACAACTAGAACA
* *
1403653 AGT-AAAGCACTACTTCATGCAGAACAACCATAACA
1 AGTGAAA-CACTACTTCATGCA-AACAACTAGAACA
* *
1403688 AATGAAACACTACTTCATGCAAAACAACTAAAACA
1 AGTGAAACACTACTTCATGC-AAACAACTAGAACA
* *
1403723 AGTGAAACACTATTTCATGCGAAACAACTAGAACC
1 AGTGAAACACTACTTCATGC-AAACAACTAGAACA
* *
1403758 AGTGGAACACTACTTCACGCAGAACAA
1 AGTGAAACACTACTTCATGCA-AACAA
1403785 TTAGGATAAG
Statistics
Matches: 111, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
34 4 0.04
35 103 0.93
36 4 0.04
ACGTcount: A:0.46, C:0.24, G:0.13, T:0.18
Consensus pattern (34 bp):
AGTGAAACACTACTTCATGCAAACAACTAGAACA
Found at i:1404022 original size:28 final size:28
Alignment explanation
Indices: 1403979--1404054 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
1403969 TTACCTTGTC
* * * *
1403979 CTCTTGTACCTTTTCACGTGCACTTTCTT
1 CTCTTG-ACCTGTTCACATACACTTTATT
1404008 CTCTTGACCTGTTCACATACACTTTATT
1 CTCTTGACCTGTTCACATACACTTTATT
* * *
1404036 CTCTTAACTTGTTCTCATA
1 CTCTTGACCTGTTCACATA
1404055 TAGCTTTTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 34 0.85
29 6 0.15
ACGTcount: A:0.17, C:0.29, G:0.08, T:0.46
Consensus pattern (28 bp):
CTCTTGACCTGTTCACATACACTTTATT
Found at i:1404377 original size:12 final size:12
Alignment explanation
Indices: 1404347--1404389 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
1404337 CACTCAGAGC
*
1404347 TTCTCTTTCTAA
1 TTCTCTCTCTAA
1404359 CTTCTCTCTCTAA
1 -TTCTCTCTCTAA
1404372 TTCTCTACT-TAA
1 TTCTCT-CTCTAA
1404384 TTCTCT
1 TTCTCT
1404390 TTTTATTCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 15 0.54
13 13 0.46
ACGTcount: A:0.16, C:0.30, G:0.00, T:0.53
Consensus pattern (12 bp):
TTCTCTCTCTAA
Found at i:1415354 original size:32 final size:32
Alignment explanation
Indices: 1415318--1415382 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
1415308 CGAACAGAAT
*
1415318 CACCATATTAGAGGAGAAAGGATCTCAACTAA
1 CACCATATTAGAGGAGAAAGAATCTCAACTAA
*
1415350 CACCATATTAGAGGAGAGAGAATCTCAACTAA
1 CACCATATTAGAGGAGAAAGAATCTCAACTAA
1415382 C
1 C
1415383 TCACATGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (32 bp):
CACCATATTAGAGGAGAAAGAATCTCAACTAA
Found at i:1426514 original size:36 final size:36
Alignment explanation
Indices: 1426473--1426606 Score: 180
Period size: 36 Copynumber: 3.7 Consensus size: 36
1426463 ACAGGGTTGA
* * *
1426473 TGGTGATGAACCAACTAGTATGGATTTGAGGACGGG
1 TGGTGATGAGCCAACTGGTTTGGATTTGAGGACGGG
1426509 TGGTGATGAGCCAACTGGTTTGGATTTGAGGACGGG
1 TGGTGATGAGCCAACTGGTTTGGATTTGAGGACGGG
* **
1426545 TGGTGATGAGCCAACTGGTTTGGATTTGCA-TACAAG
1 TGGTGATGAGCCAACTGGTTTGGATTTG-AGGACGGG
* *
1426581 TGGTGATGTGCCAACTAGTTTGGATT
1 TGGTGATGAGCCAACTGGTTTGGATT
1426607 CACATATAGA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
36 88 0.99
37 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGAGCCAACTGGTTTGGATTTGAGGACGGG
Found at i:1426775 original size:36 final size:37
Alignment explanation
Indices: 1426735--1426849 Score: 157
Period size: 36 Copynumber: 3.2 Consensus size: 37
1426725 TCCTCTAGAG
* * *
1426735 GCCCCATATCCTGCTC-ATAGCACATCTCTGCTTAAA
1 GCCCCACATCATGCTCTAAAGCACATCTCTGCTTAAA
1426771 GCCCCACATCATGC-CTAAAGCACATCTCTGCTTAAA
1 GCCCCACATCATGCTCTAAAGCACATCTCTGCTTAAA
*
1426807 GCCCCACATCATG-TCTAAAGCACATCTCCT-CTTGAA
1 GCCCCACATCATGCTCTAAAGCACATCT-CTGCTTAAA
1426843 GCCCCAC
1 GCCCCAC
1426850 CTCCACCTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
35 1 0.01
36 69 0.96
37 2 0.03
ACGTcount: A:0.27, C:0.38, G:0.11, T:0.23
Consensus pattern (37 bp):
GCCCCACATCATGCTCTAAAGCACATCTCTGCTTAAA
Found at i:1426780 original size:20 final size:20
Alignment explanation
Indices: 1426755--1426816 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
1426745 CTGCTCATAG
1426755 CACATCTCTGCTTAAAGCCC
1 CACATCTCTGCTTAAAGCCC
* *
1426775 CACATC-ATGCCTAAAG---
1 CACATCTCTGCTTAAAGCCC
1426791 CACATCTCTGCTTAAAGCCC
1 CACATCTCTGCTTAAAGCCC
1426811 CACATC
1 CACATC
1426817 ATGTCTAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 6 0.18
17 8 0.24
19 8 0.24
20 12 0.35
ACGTcount: A:0.29, C:0.39, G:0.10, T:0.23
Consensus pattern (20 bp):
CACATCTCTGCTTAAAGCCC
Found at i:1426791 original size:19 final size:19
Alignment explanation
Indices: 1426767--1426827 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
1426757 CATCTCTGCT
1426767 TAAAGCCCCACATCATGCC
1 TAAAGCCCCACATCATGCC
* *
1426786 TAAAG---CACATCTCTGCT
1 TAAAGCCCCACATC-ATGCC
*
1426803 TAAAGCCCCACATCATGTC
1 TAAAGCCCCACATCATGCC
1426822 TAAAGC
1 TAAAGC
1426828 ACATCTCCTC
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 6 0.18
17 8 0.24
19 13 0.39
20 6 0.18
ACGTcount: A:0.33, C:0.34, G:0.11, T:0.21
Consensus pattern (19 bp):
TAAAGCCCCACATCATGCC
Found at i:1426796 original size:16 final size:16
Alignment explanation
Indices: 1426775--1426832 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
1426765 CTTAAAGCCC
1426775 CACATCATGCCTAAAG
1 CACATCATGCCTAAAG
* *
1426791 CACATCTCTGCTTAAAG
1 CACATC-ATGCCTAAAG
*
1426808 CCCCACATCATGTCTAAAG
1 ---CACATCATGCCTAAAG
1426827 CACATC
1 CACATC
1426833 TCCTCTTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 12 0.36
17 8 0.24
19 7 0.21
20 6 0.18
ACGTcount: A:0.33, C:0.34, G:0.10, T:0.22
Consensus pattern (16 bp):
CACATCATGCCTAAAG
Found at i:1426808 original size:17 final size:17
Alignment explanation
Indices: 1426753--1426808 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
1426743 TCCTGCTCAT
1426753 AGCACATCTCTGCTTAA
1 AGCACATCTCTGCTTAA
* *
1426770 AGCCCCACATC-ATGCCTAA
1 AG---CACATCTCTGCTTAA
1426789 AGCACATCTCTGCTTAA
1 AGCACATCTCTGCTTAA
1426806 AGC
1 AGC
1426809 CCCACATCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 6 0.19
17 11 0.35
19 8 0.26
20 6 0.19
ACGTcount: A:0.30, C:0.34, G:0.12, T:0.23
Consensus pattern (17 bp):
AGCACATCTCTGCTTAA
Found at i:1428194 original size:22 final size:22
Alignment explanation
Indices: 1428154--1428196 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1428144 TGCATGATTG
*
1428154 GATATTAGGCATTATGTGACTA
1 GATATTAGGCATTACGTGACTA
*
1428176 GATATTAGGCATTGCGTGACT
1 GATATTAGGCATTACGTGACT
1428197 GTTTTTAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.35
Consensus pattern (22 bp):
GATATTAGGCATTACGTGACTA
Found at i:1428313 original size:44 final size:44
Alignment explanation
Indices: 1428244--1428363 Score: 132
Period size: 44 Copynumber: 2.7 Consensus size: 44
1428234 TCCAGCATTC
* * * *
1428244 CATTACATGACTAGTTTTTAAGTATTACGTGATCATTTTTTCAG
1 CATTACATGACTGGTTTTTAGGTATTACGTGATCAATTTTTAAG
* * * *
1428288 CATTACATGACTGGTTATTAGGTATTGCATGATTAATTTTTAAG
1 CATTACATGACTGGTTTTTAGGTATTACGTGATCAATTTTTAAG
* * * *
1428332 TATTACGTGACTGGTTTTTAGGCATTAGGTGA
1 CATTACATGACTGGTTTTTAGGTATTACGTGA
1428364 CCCCACATCC
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 61 1.00
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (44 bp):
CATTACATGACTGGTTTTTAGGTATTACGTGATCAATTTTTAAG
Found at i:1428349 original size:22 final size:22
Alignment explanation
Indices: 1428245--1428351 Score: 90
Period size: 22 Copynumber: 4.9 Consensus size: 22
1428235 CCAGCATTCC
1428245 ATTACATGACTAGTTTTTAAGT
1 ATTACATGACTAGTTTTTAAGT
* * * *
1428267 ATTACGTGA-TCATTTTTTCAGC
1 ATTACATGACT-AGTTTTTAAGT
* * *
1428289 ATTACATGACTGGTTATTAGGT
1 ATTACATGACTAGTTTTTAAGT
* * *
1428311 ATTGCATGATTAATTTTTAAGT
1 ATTACATGACTAGTTTTTAAGT
* *
1428333 ATTACGTGACTGGTTTTTA
1 ATTACATGACTAGTTTTTA
1428352 GGCATTAGGT
Statistics
Matches: 61, Mismatches: 22, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
21 1 0.02
22 59 0.97
23 1 0.02
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (22 bp):
ATTACATGACTAGTTTTTAAGT
Done.