Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007748.1 Hibiscus syriacus cultivar Beakdansim tig00110013_pilon, 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: 4568288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 24
Found at i:1202684 original size:12 final size:12
Alignment explanation
Indices: 1202667--1202691 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1202657 AAAAAATAAA
1202667 CGATATTCTGAG
1 CGATATTCTGAG
1202679 CGATATTCTGAG
1 CGATATTCTGAG
1202691 C
1 C
1202692 TGAACGTTAA
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:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (12 bp):
CGATATTCTGAG
Found at i:1214431 original size:18 final size:18
Alignment explanation
Indices: 1214400--1214492 Score: 96
Period size: 18 Copynumber: 4.9 Consensus size: 18
1214390 ACTGAATATT
*
1214400 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
*
1214418 TGTCCTGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
1214437 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
1214456 TGTCCCGAAGGACCACTGTT
1 TGTCCCGAAGGACCAC--TA
*
1214476 TATCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1214493 GATAATCCCT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
18 30 0.48
19 2 0.03
20 30 0.48
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1214452 original size:20 final size:20
Alignment explanation
Indices: 1214399--1214495 Score: 112
Period size: 20 Copynumber: 5.0 Consensus size: 20
1214389 CACTGAATAT
*
1214399 TTGTCCCGAAAGACCACT-A
1 TTGTCCCGAAGGACCACTGA
*
1214418 -TGTCCTGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
1214437 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
*
1214456 -TGTCCCGAAGGACCACTGT
1 TTGTCCCGAAGGACCACTGA
*
1214475 TTATCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
1214495 T
1 T
1214496 AATCCCTCGA
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
18 30 0.47
19 2 0.03
20 32 0.50
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.23
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:1214453 original size:38 final size:38
Alignment explanation
Indices: 1214402--1214492 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 38
1214392 TGAATATTTG
* *
1214402 TCCCGAA-AGACCACTATGTCCTGAAGGACCACTGATTG
1 TCCCGAAGA-ACCACTATGTCCCGAAGGACCACTGATTA
* *
1214440 TTCCGAAGAACCACTATGTCCCGAAGGACCACTGTTTA
1 TCCCGAAGAACCACTATGTCCCGAAGGACCACTGATTA
*
1214478 TCCCGAAGGACCACT
1 TCCCGAAGAACCACT
1214493 GATAATCCCT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 45 0.98
39 1 0.02
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.21
Consensus pattern (38 bp):
TCCCGAAGAACCACTATGTCCCGAAGGACCACTGATTA
Found at i:1216681 original size:13 final size:14
Alignment explanation
Indices: 1216658--1216697 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
1216648 GAGATACGGG
1216658 AGGAGAGGAAGAAGA
1 AGGA-AGGAAGAAGA
1216673 A-GAAGGAAGAAGA
1 AGGAAGGAAGAAGA
1216686 AGGAA-GAAGAAG
1 AGGAAGGAAGAAG
1216698 TTATGGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 18 0.75
14 5 0.21
15 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (14 bp):
AGGAAGGAAGAAGA
Found at i:1216683 original size:10 final size:10
Alignment explanation
Indices: 1216668--1216697 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1216658 AGGAGAGGAA
1216668 GAAGAAGAAG
1 GAAGAAGAAG
1216678 GAAGAAGAAG
1 GAAGAAGAAG
1216688 GAAGAAGAAG
1 GAAGAAGAAG
1216698 TTATGGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:1217788 original size:20 final size:20
Alignment explanation
Indices: 1217763--1217801 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1217753 AATTCTCGGA
*
1217763 TGGGCACCATCAGTAAAATG
1 TGGGCACCATCAATAAAATG
1217783 TGGGCACCATCAATAAAAT
1 TGGGCACCATCAATAAAAT
1217802 AAACAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TGGGCACCATCAATAAAATG
Found at i:1226473 original size:16 final size:16
Alignment explanation
Indices: 1226452--1226483 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1226442 TGGATCCAGG
1226452 GATCGAACATGTCTAA
1 GATCGAACATGTCTAA
1226468 GATCGAACATGTCTAA
1 GATCGAACATGTCTAA
1226484 AAGATATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (16 bp):
GATCGAACATGTCTAA
Found at i:1230469 original size:87 final size:87
Alignment explanation
Indices: 1230328--1230529 Score: 225
Period size: 87 Copynumber: 2.3 Consensus size: 87
1230318 AGCCTTAAAC
* * * *
1230328 TATAAAAGTAAAAAGT-ATGATTG-AAAAAATTAAGGACCCCAATTATAAAGGTAAAAAGTGATA
1 TATAAAGGTAAAAAGTGA-GATTGAAAAAAATTAAGGACCCAAATTATAAAGGTAAAAAATGAGA
1230391 TT-AAAATAAATAGGGGCATCAAT
65 TTGAAAA-AAATAGGGGCATCAAT
* * * * *
1230414 TTTAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGGCCCAAATTAT-ATGAGTAAAAAATGGGA
1 TATAAAGGTAAAAAGTGAGATTGAAAAAAATTAAGGACCCAAATTATAAAG-GTAAAAAATGAGA
* * *
1230478 TTGAAAAAATTATGGGCCTCAAT
65 TTGAAAAAAATAGGGGCATCAAT
*
1230501 TATAAAGGT-CAAAGTGAGATTGAAAAAAA
1 TATAAAGGTAAAAAGTGAGATTGAAAAAAA
1230530 CATGAGTTTA
Statistics
Matches: 98, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
86 40 0.41
87 54 0.55
88 4 0.04
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.24
Consensus pattern (87 bp):
TATAAAGGTAAAAAGTGAGATTGAAAAAAATTAAGGACCCAAATTATAAAGGTAAAAAATGAGAT
TGAAAAAAATAGGGGCATCAAT
Found at i:1230529 original size:43 final size:44
Alignment explanation
Indices: 1230328--1230687 Score: 228
Period size: 43 Copynumber: 8.3 Consensus size: 44
1230318 AGCCTTAAAC
* * * *
1230328 TATAAAAGTAAAAAGT-ATGATTG-AAAAAATTAAGGACCCCAAT
1 TATAAAGGTAAAAAGTGA-GATTGAAAAAAATTAGGGGCCTCAAT
* *
1230371 TATAAAGGTAAAAAGTGATATT-AAAATAAA-TAGGGGCATCAAT
1 TATAAAGGTAAAAAGTGAGATTGAAAA-AAATTAGGGGCCTCAAT
*
1230414 TTTAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGGCC-CAAAT
1 TATAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGGCCTC-AAT
* * * *
1230458 TAT-ATGAGTAAAAAATGGGATTG-AAAAAATTATGGGCCTCAAT
1 TATAAAG-GTAAAAAGTGAGATTGAAAAAAATTAGGGGCCTCAAT
* * * * * *
1230501 TATAAAGGT-CAAAGTGAGATTGAAAAAAA-CATGAG-TTTAAT
1 TATAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGGCCTCAAT
* * * * ** *
1230542 TATAAAGGTACAATGTGGGATT-AAAAAATTTAGGATCATCAAT
1 TATAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGGCCTCAAT
* * * ***
1230585 TATAAATGTAAAATAAATGGGATT-AAAAAATATTAAAAGCCTCAAT
1 TATAAAGGT-AAA-AAGTGAGATTGAAAAAA-ATTAGGGGCCTCAAT
* * * *
1230631 TATAATGATAAAAAGT-AGGATT-ACAAAAATTAGGGACCTCAAT
1 TATAAAGGTAAAAAGTGA-GATTGAAAAAAATTAGGGGCCTCAAT
1230674 TAT-AAGGATAAAAA
1 TATAAAGG-TAAAAA
1230688 ACTAAAATTA
Statistics
Matches: 248, Mismatches: 51, Indels: 36
0.74 0.15 0.11
Matches are distributed among these distances:
41 19 0.08
42 29 0.12
43 116 0.47
44 51 0.21
45 17 0.07
46 16 0.06
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (44 bp):
TATAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGGCCTCAAT
Found at i:1230633 original size:46 final size:45
Alignment explanation
Indices: 1230557--1230643 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
1230547 AGGTACAATG
** *
1230557 TGGGATTAAAAAATTTAGGATCATCAATTATAAATG-TAAAATAAA
1 TGGGATTAAAAAATTTAAAAGCATCAATTAT-AATGATAAAATAAA
*
1230602 TGGGATTAAAAAATATTAAAAGCCTCAATTATAATGATAAAA
1 TGGGATTAAAAAAT-TTAAAAGCATCAATTATAATGATAAAA
1230644 AGTAGGATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 18 0.50
46 18 0.50
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.30
Consensus pattern (45 bp):
TGGGATTAAAAAATTTAAAAGCATCAATTATAATGATAAAATAAA
Found at i:1230960 original size:20 final size:20
Alignment explanation
Indices: 1230935--1230972 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1230925 AATTTTAATA
* *
1230935 AAAATAATAATTAAATAACC
1 AAAATAAAAATAAAATAACC
1230955 AAAATAAAAATAAAATAA
1 AAAATAAAAATAAAATAA
1230973 TAGATGAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATAAAAATAAAATAACC
Found at i:1240785 original size:21 final size:21
Alignment explanation
Indices: 1240748--1240790 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1240738 ATGTTTTCGG
*
1240748 TCTTCATCATCTATCTTTGTT
1 TCTTCATCATCTATCTTAGTT
* *
1240769 TCTTCATCATTTTTCTTAGTT
1 TCTTCATCATCTATCTTAGTT
1240790 T
1 T
1240791 GGGATATTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.21, G:0.05, T:0.60
Consensus pattern (21 bp):
TCTTCATCATCTATCTTAGTT
Found at i:1241261 original size:32 final size:32
Alignment explanation
Indices: 1241214--1241282 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
1241204 AGTTTTTTAT
* * *
1241214 TTTCTGAAATGAAGTGATATATT-ACTGAAAAA
1 TTTCTAAAATAAAGTGATAT-TTCAATGAAAAA
*
1241246 TTTCTAAAATAAAGTGATATTTCAATGAAAAG
1 TTTCTAAAATAAAGTGATATTTCAATGAAAAA
1241278 TTTCT
1 TTTCT
1241283 GAAGTGAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 2 0.06
32 30 0.94
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (32 bp):
TTTCTAAAATAAAGTGATATTTCAATGAAAAA
Found at i:1241346 original size:145 final size:144
Alignment explanation
Indices: 1241164--1241531 Score: 372
Period size: 143 Copynumber: 2.6 Consensus size: 144
1241154 AAAATAGGAT
1241164 GTTTTTGTCATTGTATATTAAATGGTGTATGAGAAAATGAAGTTTTTTATTTTCTGAAATGAAGT
1 GTTTTTGTCATTGTATATTAAATGGTGTATGAGAAAATGAAG-TTTTTATTTTCTGAAATGAAGT
* * *
1241229 GATATATTACTGAAAAATTTCTAAAATAAAGTGATATTTCAATGAAAAGTTTCTGAAGTGAAGTA
65 GATATATTACTGAAAAGTTTCTAAAACAAAGTGATATATCAATGAAAAGTTTCTGAAGTGAAGTA
1241294 ATT-GGAAACTGAAAA
130 ATTAGG-AACTGAAAA
* * * * ** ** *
1241309 GTTTTTGTCATTATTTATTAAATGGTGTATGAAAAAATGACGTATTAAATGGTCATTGATGAT-A
1 GTTTTTGTCATTGTATATTAAATGGTGTATGAGAAAATGAAGT-TTTTATTTTC--TGA-AATGA
* * * * *
1241373 ACTCG-T-T-TT--TTAAAAGTTACTGAAACAAAGTGATATATCACTGAAAAGTTTCTGAAGTGA
62 AGT-GATATATTACTGAAAAGTTTCTAAAACAAAGTGATATATCAATGAAAAGTTTCTGAAGTGA
* *
1241433 AGTAATTATGCACTGAAAA
126 AGTAATTAGGAACTGAAAA
*
1241452 G--TTTGTCATTGTGTATTAAATGGTGTATGAGAAAATG-A---TTT-TTTT-T-AAATGAAGTG
1 GTTTTTGTCATTGTATATTAAATGGTGTATGAGAAAATGAAGTTTTTATTTTCTGAAATGAAGTG
*
1241508 ATATATCACTGAAAAGTTTCTAAA
66 ATATATTACTGAAAAGTTTCTAAA
1241532 GTGAAGTAAT
Statistics
Matches: 178, Mismatches: 33, Indels: 34
0.73 0.13 0.14
Matches are distributed among these distances:
130 3 0.02
131 5 0.03
132 2 0.01
133 1 0.01
135 14 0.08
136 1 0.01
141 33 0.19
143 60 0.34
144 2 0.01
145 46 0.26
146 1 0.01
147 7 0.04
148 3 0.02
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (144 bp):
GTTTTTGTCATTGTATATTAAATGGTGTATGAGAAAATGAAGTTTTTATTTTCTGAAATGAAGTG
ATATATTACTGAAAAGTTTCTAAAACAAAGTGATATATCAATGAAAAGTTTCTGAAGTGAAGTAA
TTAGGAACTGAAAA
Found at i:1241420 original size:32 final size:32
Alignment explanation
Indices: 1241384--1241454 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
1241374 CTCGTTTTTT
*
1241384 AAAAGTTACTGAAACAAAGTGATATAT-CACTG
1 AAAAGTTACTGAAACAAAGTAAT-TATGCACTG
* ***
1241416 AAAAGTTTCTGAAGTGAAGTAATTATGCACTG
1 AAAAGTTACTGAAACAAAGTAATTATGCACTG
1241448 AAAAGTT
1 AAAAGTT
1241455 TGTCATTGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 3 0.09
32 30 0.91
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (32 bp):
AAAAGTTACTGAAACAAAGTAATTATGCACTG
Found at i:1241539 original size:103 final size:108
Alignment explanation
Indices: 1241400--1241635 Score: 351
Period size: 103 Copynumber: 2.2 Consensus size: 108
1241390 TACTGAAACA
* *
1241400 AAGTGATATATCACTGAAAAGTTTCTGAAGTGAAGTAATTATG-CACTGAAAAGTT-T-GTCATT
1 AAGTGATATATCACTGAAAAGTTTCTAAAGTGAAGTAATT-GGACACTGAAAAGTTCTCGTCATT
*
1241462 GTGTATTAAATGGTGTATGAGAAAATG-ATTTTTTT-T-AAATG
65 GTGTATTAAATGGTGTATGAGAAAAGGAATTTTTTTATGAAATG
1241503 AAGTGATATATCACTGAAAAGTTTCTAAAGTGAAGTAATTGGACACTGAAAAGTTCTCGTCATTG
1 AAGTGATATATCACTGAAAAGTTTCTAAAGTGAAGTAATTGGACACTGAAAAGTTCTCGTCATTG
*
1241568 TTTATTAAATGGTGTATGAGAAAAGGACATTTTTTTATGAAATG
66 TGTATTAAATGGTGTATGAGAAAAGGA-ATTTTTTTATGAAATG
*
1241612 AAGTGAAATATCACT-AAAACGTTT
1 AAGTGATATATCACTGAAAA-GTTT
1241636 ATGAAACAAT
Statistics
Matches: 120, Mismatches: 5, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
102 1 0.01
103 51 0.43
104 1 0.01
105 31 0.26
107 8 0.07
108 5 0.04
109 23 0.19
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (108 bp):
AAGTGATATATCACTGAAAAGTTTCTAAAGTGAAGTAATTGGACACTGAAAAGTTCTCGTCATTG
TGTATTAAATGGTGTATGAGAAAAGGAATTTTTTTATGAAATG
Found at i:1241638 original size:32 final size:32
Alignment explanation
Indices: 1241601--1241667 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
1241591 AGGACATTTT
*
1241601 TTTATGAAATGAA-GTGAAATATCACT-AAAACG
1 TTTATGAAA-CAATGTGAAATATCACTGAAAA-G
*
1241633 TTTATGAAACAATGTGATATATCACTGAAAAG
1 TTTATGAAACAATGTGAAATATCACTGAAAAG
1241665 TTT
1 TTT
1241668 CTTTCACCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 2 0.06
32 25 0.81
33 4 0.13
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (32 bp):
TTTATGAAACAATGTGAAATATCACTGAAAAG
Found at i:1241666 original size:109 final size:101
Alignment explanation
Indices: 1241400--1241667 Score: 274
Period size: 103 Copynumber: 2.5 Consensus size: 101
1241390 TACTGAAACA
* * * *
1241400 AAGTGATATATCACTGAAAAGTTTCTGAAGTGAAGTAATT-ATGCACTGAAAAGTTTGTCATTGT
1 AAGTGAAATATCACTGAAAAGTTTATAAAG-CAAGTAATTGA--CACTGAAAAGTTTGTCATTGT
*
1241464 GTATTAAATGGTGTATGAGAAAATGATTTTTTTTAAATG
63 GTATTAAATGGTGTATGAGAAAAGGATTTTTTTTAAATG
* * *
1241503 AAGTGATATATCACTGAAAAGTTTCTAAAGTGAAGTAATTGGACACTGAAAAGTTCTCGTCATTG
1 AAGTGAAATATCACTGAAAAGTTTATAAAG-CAAGTAATT-GACACTGAAAAGTT-T-GTCATTG
*
1241568 TTTATTAAATGGTGTATGAGAAAAGGACATTTTTTTATGAAATG
62 TGTATTAAATGGTGTATGAGAAAAGG--ATTTTTTT-T-AAATG
*
1241612 AAGTGAAATATCACT-AAAACGTTTATGAAA-CAATGTGATAT-ATCACTGAAAAGTTT
1 AAGTGAAATATCACTGAAAA-GTTTAT-AAAGCAA-GTAAT-TGA-CACTGAAAAGTTT
1241668 CTTTCACCGA
Statistics
Matches: 145, Mismatches: 7, Indels: 21
0.84 0.04 0.12
Matches are distributed among these distances:
103 51 0.35
104 1 0.01
105 32 0.22
107 8 0.06
108 9 0.06
109 40 0.28
110 4 0.03
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (101 bp):
AAGTGAAATATCACTGAAAAGTTTATAAAGCAAGTAATTGACACTGAAAAGTTTGTCATTGTGTA
TTAAATGGTGTATGAGAAAAGGATTTTTTTTAAATG
Found at i:1249629 original size:24 final size:23
Alignment explanation
Indices: 1249602--1249698 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 23
1249592 ATTTCCGACT
**
1249602 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTCTGATAC-TGATA
* *
1249626 TGAATTTTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGA-TACTGATA
* *
1249650 TGAATTATGTTCTGATATCTGATT
1 TGAATTCTGTTCTGATA-CTGATA
* *
1249674 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGA-TACTGATA
1249698 T
1 T
1249699 CTCTGTTTAC
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
23 1 0.02
24 55 0.93
25 3 0.05
ACGTcount: A:0.23, C:0.11, G:0.16, T:0.49
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTGATA
Found at i:1249644 original size:48 final size:48
Alignment explanation
Indices: 1249588--1249698 Score: 127
Period size: 48 Copynumber: 2.3 Consensus size: 48
1249578 AAATATTTTA
* *
1249588 TCTGATTTCCGACT-TGAATTCTGTTCTGATA-CATGACCTGAATTTTGT
1 TCTGATTTCCGA-TATGAATTATGTTCTGATATC-TGACCTGAATTCTGT
* **
1249636 TCTGATTTCTGATATGAATTATGTTCTGATATCTGATTTGAATTCTGT
1 TCTGATTTCCGATATGAATTATGTTCTGATATCTGACCTGAATTCTGT
* *
1249684 TTTGATTTCTGATAT
1 TCTGATTTCCGATAT
1249699 CTCTGTTTAC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 1 0.02
48 53 0.96
49 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (48 bp):
TCTGATTTCCGATATGAATTATGTTCTGATATCTGACCTGAATTCTGT
Found at i:1249887 original size:2 final size:2
Alignment explanation
Indices: 1249874--1249980 Score: 205
Period size: 2 Copynumber: 53.5 Consensus size: 2
1249864 TGTTTTAAAA
*
1249874 AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1249916 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1249958 AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC A
1249981 TATATATATA
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 103 1.00
ACGTcount: A:0.50, C:0.49, G:0.00, T:0.01
Consensus pattern (2 bp):
AC
Found at i:1249985 original size:2 final size:2
Alignment explanation
Indices: 1249980--1250007 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1249970 ACACACACAC
1249980 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
1250008 GTTTTAAAAG
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:1252177 original size:7 final size:7
Alignment explanation
Indices: 1252165--1252198 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1252155 GATTATACCA
1252165 TAAACCC
1 TAAACCC
1252172 TAAACCC
1 TAAACCC
1252179 TAAACCC
1 TAAACCC
*
1252186 TTAACCC
1 TAAACCC
*
1252193 TTAACC
1 TAAACC
1252199 TTTAACATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:1252203 original size:14 final size:14
Alignment explanation
Indices: 1252165--1252204 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1252155 GATTATACCA
*
1252165 TAAACCCTAAACCC
1 TAAACCCTTAACCC
1252179 TAAACCCTTAACCC
1 TAAACCCTTAACCC
* *
1252193 TTAACCTTTAAC
1 TAAACCCTTAAC
1252205 ATTAGATCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCCTTAACCC
Found at i:1253004 original size:20 final size:20
Alignment explanation
Indices: 1252979--1253017 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1252969 ATCAAGAATC
1252979 ATACAAATGCAT-TTATTATG
1 ATACAAAT-CATATTATTATG
1252999 ATACAAATCATATTATTAT
1 ATACAAATCATATTATTAT
1253018 TACATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (20 bp):
ATACAAATCATATTATTATG
Found at i:1256463 original size:891 final size:891
Alignment explanation
Indices: 1254742--1257408 Score: 5084
Period size: 891 Copynumber: 3.0 Consensus size: 891
1254732 AAATGACAAA
* *
1254742 AAGTTTTGTTGCGGAAAAACTTTGAATCAATTACTGGGAGCAGAAAATGACATAGAAGCTTATAT
1 AAGTTTTGCTGCGGAAAAACTTTGCATCAATTACTGGGAGCAGAAAATGACATAGAAGCTTATAT
1254807 AATGTTGTCAGTTGTCCAAGGCTCACGTGAATACACTAACCTGCTGATATTTTTGGGACCACTTG
66 AATGTTGTCAGTTGTCCAAGGCTCACGTGAATACACTAACCTGCTGATATTTTTGGGACCACTTG
**
1254872 TTAGCCTATCTTATATTCACGTGTAGAGTATTGCTCTTAGGGTATAAAGGGAATTTTAAGGGCAT
131 CCAGCCTATCTTATATTCACGTGTAGAGTATTGCTCTTAGGGTATAAAGGGAATTTTAAGGGCAT
*
1254937 AAAACCATAGAAATTCCTCACTATAAATACTTAAGGATACTCTACATTTAAGAGAGCTTTTGGAG
196 AAAACCTTAGAAATTCCTCACTATAAATACTTAAGGATACTCTACATTTAAGAGAGCTTTTGGAG
** *
1255002 GATTTATTTTGAGCTTTTAAGAGAGAGACGACATCACCATTTTTATATTCTTCTTCTTTTCTCTA
261 GATTTATTTTGAGCTTTTAAGAGAGAGACGACATCACCATTTCCATATTCTTCTTCTTTTCTCCA
1255067 TCATTTTTTATGGTGTCCTTCATAGCCGAGCTTCAAGGGATAGCGACTAGGCCCTCGAGAGAGGC
326 TCATTTTTTATGGTGTCCTTCATAGCCGAGCTTCAAGGGATAGCGACTAGGCCCTCGAGAGAGGC
1255132 TAGCTCACTGGAGTGTTTCACGATGGTGGTTCTAGGCTTCACGGCGGCAGCCCTTTAGGAGTTTT
391 TAGCTCACTGGAGTGTTTCACGATGGTGGTTCTAGGCTTCACGGCGGCAGCCCTTTAGGAGTTTT
*
1255197 TCTTTTCATTGTGCTTTTATTTTCTTACTTTGATGGGTTTCTACTTAAGGGATGATTATGGATGA
456 TCTTTTCATTGTGCTTTTATTTTCTTACTTTGATGGGTTTGTACTTAAGGGATGATTATGGATGA
1255262 ACTTAGCCCCACCATGAACTAATTTATTTGGTGTTGGGTTTGTTATGGATGATGTTTTTTTTATG
521 ACTTAGCCCCACCATGAACTAATTTATTTGGTGTTGGGTTTGTTATGGATGATGTTTTTTTTATG
1255327 TTAATGGATGATTAATTATTTTCATGTTTAAATGTTGTTTTGCTCATTTTTTATATTTTTAAGTG
586 TTAATGGATGATTAATTATTTTCATGTTTAAATGTTGTTTTGCTCATTTTTTATATTTTTAAGTG
*
1255392 TTGAATCTTGTAAGAGCCTTGGGAGATAGCCATTTTCTAAATATATATATCTAATATCGAGAGAG
651 TTGAATCTTGTAAGAGCCTTGGGAGATAGCCATTTTCTAAATATATATACCTAATATCGAGAGAG
1255457 TTAAGTTAAATTTACTTGAGTAAGGGAACTAAACCAGGAC-AGTTATATTCTAATCCATTTTAGA
716 TTAAGTTAAATTTACTTGAGTAAGGGAACTAAACCAGGACGA-TTATATTCTAATCCATTTTAGA
1255521 GATAAGGAGAGGGTTTCAAATGACTAAAAGGGATAGAATTTAATCGATAAGATACTGTTGCAGTT
780 GATAAGGAGAGGGTTTCAAATGACTAAAAGGGATAGAATTTAATCGATAAGATACTGTTGCAGTT
1255586 CAAGATGAGAAATATTGTCGTAGAAATAGTTTTATCAGGCCCCATAT
845 CAAGATGAGAAATATTGTCGTAGAAATAGTTTTATCAGGCCCCATAT
1255633 AAGTTTTGCTGCGGAAAAACTTTGCATCAATTACTGGGAGCAGAAAATGACATAGAAGCTTATAT
1 AAGTTTTGCTGCGGAAAAACTTTGCATCAATTACTGGGAGCAGAAAATGACATAGAAGCTTATAT
1255698 AATGTTGTCAGTTGTCCAAGGCTCACGTGAATACACTAACCTGCTGATATTTTTGGGACCACTTG
66 AATGTTGTCAGTTGTCCAAGGCTCACGTGAATACACTAACCTGCTGATATTTTTGGGACCACTTG
1255763 CCAGCCTATCTTATATTCACGTGTAGAGTATTGCTCTTAGGGTATAAAGGGAATTTTAAGGGCAT
131 CCAGCCTATCTTATATTCACGTGTAGAGTATTGCTCTTAGGGTATAAAGGGAATTTTAAGGGCAT
1255828 AAAACCTTAGAAATTCCTCACTATAAATACTTAAGGATACTCTACATTTAAGAGAGCTTTTGGAG
196 AAAACCTTAGAAATTCCTCACTATAAATACTTAAGGATACTCTACATTTAAGAGAGCTTTTGGAG
*
1255893 GATTTATTTTGAGCTTTTAAGAGAGATACGACATCACCATTTCCATATTCTTCTTCTTTTCTCCA
261 GATTTATTTTGAGCTTTTAAGAGAGAGACGACATCACCATTTCCATATTCTTCTTCTTTTCTCCA
1255958 TCATTTTTTATGGTGTCCTTCATAGCCGAGCTTCAAGGGATAGCGACTAGGCCCTCGAGAGAGGC
326 TCATTTTTTATGGTGTCCTTCATAGCCGAGCTTCAAGGGATAGCGACTAGGCCCTCGAGAGAGGC
1256023 TAGCTCACTGGAGTGTTTCACGATGGTGGTTCTAGGCTTCACGGCGGCAGCCCTTTAGGAGTTTT
391 TAGCTCACTGGAGTGTTTCACGATGGTGGTTCTAGGCTTCACGGCGGCAGCCCTTTAGGAGTTTT
1256088 TCTTTTCATTGTGCTTTTATTTTCTTACTTTGATGGGTTTGTACTTAAGGGATGATTATGGATGA
456 TCTTTTCATTGTGCTTTTATTTTCTTACTTTGATGGGTTTGTACTTAAGGGATGATTATGGATGA
*
1256153 ACTTAGCCCCACCGTGAACTAATTTATTTGGTGTTGGGTTTGTTATGGATGATGTTTTTTTTATG
521 ACTTAGCCCCACCATGAACTAATTTATTTGGTGTTGGGTTTGTTATGGATGATGTTTTTTTTATG
1256218 TTAATGGATGATTAATTATTTTCATGTTTAAATGTTGTTTTGCTCATTTTTTATATTTTTAAGTG
586 TTAATGGATGATTAATTATTTTCATGTTTAAATGTTGTTTTGCTCATTTTTTATATTTTTAAGTG
1256283 TTGAATCTTGTAAGAGCCTTGGGAGATAGCCATTTTCTAAATATATATACCTAATATCGAGAGAG
651 TTGAATCTTGTAAGAGCCTTGGGAGATAGCCATTTTCTAAATATATATACCTAATATCGAGAGAG
1256348 TTAAGTTAAATTTACTTGAGTAAGGGAACTAAACCAGGACGATTATATTCTAATCCATTTTAGAG
716 TTAAGTTAAATTTACTTGAGTAAGGGAACTAAACCAGGACGATTATATTCTAATCCATTTTAGAG
1256413 ATAAGGAGAGGGTTTCAAATGACTAAAAGGGATAGAATTTAATCGATAAGATACTGTTGCAGTTC
781 ATAAGGAGAGGGTTTCAAATGACTAAAAGGGATAGAATTTAATCGATAAGATACTGTTGCAGTTC
*
1256478 AAGATGAGAAATATTGTCGTAGCAATAGTTTTATCAGGCCCCATAT
846 AAGATGAGAAATATTGTCGTAGAAATAGTTTTATCAGGCCCCATAT
*
1256524 AAGTTTTGCTGCGAAAAAACTTTGCATCAATTACTGGGAGCAGAAAATGACATAGAAGCTTATAT
1 AAGTTTTGCTGCGGAAAAACTTTGCATCAATTACTGGGAGCAGAAAATGACATAGAAGCTTATAT
*
1256589 AATGTTGTCAGTTGTCCAAGGCTCACGTGAATACACTAACCTGCTGATATTTTTGGGACAACTTG
66 AATGTTGTCAGTTGTCCAAGGCTCACGTGAATACACTAACCTGCTGATATTTTTGGGACCACTTG
1256654 CCAGCCTATCTTATATTCACGTGTAGAGTATTGCTCTTAGGGTATAAAGGGAATTTTAAGGGCAT
131 CCAGCCTATCTTATATTCACGTGTAGAGTATTGCTCTTAGGGTATAAAGGGAATTTTAAGGGCAT
*
1256719 AAAACCTTAGAAATTCCTCACTATAAATACTTAAGGATACTCTATATTTAAGAGAGCTTTTGGAG
196 AAAACCTTAGAAATTCCTCACTATAAATACTTAAGGATACTCTACATTTAAGAGAGCTTTTGGAG
1256784 GATTTATTTTGAGCTTTTAAGAGAGAGACGACATCACCATTTCCATATTCTTCTTCTTTTCTCCA
261 GATTTATTTTGAGCTTTTAAGAGAGAGACGACATCACCATTTCCATATTCTTCTTCTTTTCTCCA
1256849 TCATTTTTTATGGTGTCCTTCATAGCCGAGCTTCAAGGGATAGCGACTAGGCCCTCGAGAGAGGC
326 TCATTTTTTATGGTGTCCTTCATAGCCGAGCTTCAAGGGATAGCGACTAGGCCCTCGAGAGAGGC
* *
1256914 TAGCTCACTGGAGTGTTTCACGATGGTGGTTCTAGGCTTCACGGTGGCAACCCTTTAGGAGTTTT
391 TAGCTCACTGGAGTGTTTCACGATGGTGGTTCTAGGCTTCACGGCGGCAGCCCTTTAGGAGTTTT
1256979 TCTTTTCATTGTGCTTTTATTTTCTTACTTTGATGGGTTTGTACTTAAGGGATGATTATGGATGA
456 TCTTTTCATTGTGCTTTTATTTTCTTACTTTGATGGGTTTGTACTTAAGGGATGATTATGGATGA
1257044 ACTTAGCCCCACCATGAACTAATTTATTTGGTGTTGGGTTTGTTATGGATGATGTTTTTTTTTAT
521 ACTTAGCCCCACCATGAACTAATTTATTTGGTGTTGGGTTTGTTATGGATGATG-TTTTTTTTAT
* *
1257109 GTTAATGGATGATTAATTATTTTCATGTTTAAATGTTGTGTTGCTCATTTTTTATGTTTTTAAGT
585 GTTAATGGATGATTAATTATTTTCATGTTTAAATGTTGTTTTGCTCATTTTTTATATTTTTAAGT
1257174 GTTGAATCTTGTAAGAGCCTTGGGAGATAGCCATTTTCTAAATATATATACCTAATATCGAGAGA
650 GTTGAATCTTGTAAGAGCCTTGGGAGATAGCCATTTTCTAAATATATATACCTAATATCGAGAGA
** *
1257239 GTTAAGTTAAATTTACTTGAGTAAGGGAACTAAAATAGGACGGTTATATTCTAATCCATTTTAGA
715 GTTAAGTTAAATTTACTTGAGTAAGGGAACTAAACCAGGACGATTATATTCTAATCCATTTTAGA
*
1257304 GATAAGGAGAGGGTTTCAAATGACTAAAAGGGATAGAATTTAATCGATAAGATACTGTTGAAGTT
780 GATAAGGAGAGGGTTTCAAATGACTAAAAGGGATAGAATTTAATCGATAAGATACTGTTGCAGTT
*
1257369 CAAGATGAGAAATATTGTCGTAGGAATAGTTTTATCAGGC
845 CAAGATGAGAAATATTGTCGTAGAAATAGTTTTATCAGGC
1257409 TCCTTACTAG
Statistics
Matches: 1747, Mismatches: 27, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
891 1443 0.83
892 304 0.17
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (891 bp):
AAGTTTTGCTGCGGAAAAACTTTGCATCAATTACTGGGAGCAGAAAATGACATAGAAGCTTATAT
AATGTTGTCAGTTGTCCAAGGCTCACGTGAATACACTAACCTGCTGATATTTTTGGGACCACTTG
CCAGCCTATCTTATATTCACGTGTAGAGTATTGCTCTTAGGGTATAAAGGGAATTTTAAGGGCAT
AAAACCTTAGAAATTCCTCACTATAAATACTTAAGGATACTCTACATTTAAGAGAGCTTTTGGAG
GATTTATTTTGAGCTTTTAAGAGAGAGACGACATCACCATTTCCATATTCTTCTTCTTTTCTCCA
TCATTTTTTATGGTGTCCTTCATAGCCGAGCTTCAAGGGATAGCGACTAGGCCCTCGAGAGAGGC
TAGCTCACTGGAGTGTTTCACGATGGTGGTTCTAGGCTTCACGGCGGCAGCCCTTTAGGAGTTTT
TCTTTTCATTGTGCTTTTATTTTCTTACTTTGATGGGTTTGTACTTAAGGGATGATTATGGATGA
ACTTAGCCCCACCATGAACTAATTTATTTGGTGTTGGGTTTGTTATGGATGATGTTTTTTTTATG
TTAATGGATGATTAATTATTTTCATGTTTAAATGTTGTTTTGCTCATTTTTTATATTTTTAAGTG
TTGAATCTTGTAAGAGCCTTGGGAGATAGCCATTTTCTAAATATATATACCTAATATCGAGAGAG
TTAAGTTAAATTTACTTGAGTAAGGGAACTAAACCAGGACGATTATATTCTAATCCATTTTAGAG
ATAAGGAGAGGGTTTCAAATGACTAAAAGGGATAGAATTTAATCGATAAGATACTGTTGCAGTTC
AAGATGAGAAATATTGTCGTAGAAATAGTTTTATCAGGCCCCATAT
Found at i:1265933 original size:14 final size:14
Alignment explanation
Indices: 1265916--1265964 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
1265906 GTTTGTCCGC
1265916 TTATGTTCGTTCAT
1 TTATGTTCGTTCAT
*
1265930 TTATGTTCGTTCGT
1 TTATGTTCGTTCAT
* * *
1265944 TTATGTGCATTTAT
1 TTATGTTCGTTCAT
1265958 TTATGTT
1 TTATGTT
1265965 TAGCCCAATC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.14, C:0.10, G:0.16, T:0.59
Consensus pattern (14 bp):
TTATGTTCGTTCAT
Found at i:1265935 original size:28 final size:28
Alignment explanation
Indices: 1265903--1265965 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1265893 TGTTATGTAA
* *
1265903 TATGTTTGTCCGCTTATGTTCGTTCATT
1 TATGTTTGTCCGCTTATGTGCATTCATT
* * * *
1265931 TATGTTCGTTCGTTTATGTGCATTTATT
1 TATGTTTGTCCGCTTATGTGCATTCATT
1265959 TATGTTT
1 TATGTTT
1265966 AGCCCAATCT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (28 bp):
TATGTTTGTCCGCTTATGTGCATTCATT
Found at i:1266182 original size:23 final size:23
Alignment explanation
Indices: 1266140--1266183 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1266130 TTTTCATTTA
*
1266140 TGTTCGTTTATATTCATTTATTG
1 TGTTCGTTTACATTCATTTATTG
* *
1266163 TGTTCGTTTACGTTCGTTTAT
1 TGTTCGTTTACATTCATTTAT
1266184 ATTCGTTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.16, T:0.59
Consensus pattern (23 bp):
TGTTCGTTTACATTCATTTATTG
Found at i:1266182 original size:33 final size:34
Alignment explanation
Indices: 1266136--1266206 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
1266126 TCTATTTTCA
* *
1266136 TTTATGTTCGTTTATATTCATTTA-TTGTGTTCG
1 TTTACGTTCGTTTATATTCATTCATTTGTGTTCG
*
1266169 TTTACGTTCGTTTATATTCGTTCATTTGTGTTCG
1 TTTACGTTCGTTTATATTCATTCATTTGTGTTCG
1266203 TTTA
1 TTTA
1266207 TCATTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 21 0.62
34 13 0.38
ACGTcount: A:0.14, C:0.11, G:0.15, T:0.59
Consensus pattern (34 bp):
TTTACGTTCGTTTATATTCATTCATTTGTGTTCG
Found at i:1266993 original size:29 final size:29
Alignment explanation
Indices: 1266951--1267006 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1266941 AGTACAACGT
*
1266951 GATGATGCAAAGTGAACCTGCAGATTAAC
1 GATGATGCAAAGTGAACCAGCAGATTAAC
1266980 GATGATGCAAAGTGAACCAGCAGATTA
1 GATGATGCAAAGTGAACCAGCAGATTA
1267007 GCTGCAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (29 bp):
GATGATGCAAAGTGAACCAGCAGATTAAC
Found at i:1268285 original size:18 final size:18
Alignment explanation
Indices: 1268261--1268300 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1268251 ATGATTTTGA
* *
1268261 AAAAAAAAATATTTAAAAT
1 AAAAAAAAA-CTTAAAAAT
1268280 AAAAAAAAACTTAAAAAT
1 AAAAAAAAACTTAAAAAT
1268298 AAA
1 AAA
1268301 GTTTTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAAAAAACTTAAAAAT
Found at i:1268918 original size:7 final size:8
Alignment explanation
Indices: 1268894--1268930 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
1268884 TTCTTAAAAA
1268894 TTTAATTT
1 TTTAATTT
1268902 TTTAATTT
1 TTTAATTT
1268910 TTTAATTT
1 TTTAATTT
* *
1268918 TTAAAATT
1 TTTAATTT
1268926 TTTAA
1 TTTAA
1268931 ATTTAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTAATTT
Found at i:1275055 original size:22 final size:22
Alignment explanation
Indices: 1275030--1275080 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1275020 AGGAGTTACG
*
1275030 GGAGTTACATGATTTAATTTCA
1 GGAGTTACATGATATAATTTCA
*
1275052 GGAGTTACATGATATAATTTTA
1 GGAGTTACATGATATAATTTCA
1275074 GGAGTTA
1 GGAGTTA
1275081 TAACAGCTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (22 bp):
GGAGTTACATGATATAATTTCA
Found at i:1280162 original size:2 final size:2
Alignment explanation
Indices: 1280157--1280187 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1280147 GTGTGTGTGT
1280157 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1280188 CGCATCGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1280885 original size:22 final size:22
Alignment explanation
Indices: 1280860--1280909 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
1280850 GGAGTTACGA
*
1280860 GAGTTACATGATTTAATATCAG
1 GAGTTACATGATATAATATCAG
*
1280882 GAGTTACATGATATAATTTCAG
1 GAGTTACATGATATAATATCAG
1280904 GAGTTA
1 GAGTTA
1280910 TAACAGCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (22 bp):
GAGTTACATGATATAATATCAG
Found at i:1288243 original size:2 final size:2
Alignment explanation
Indices: 1288236--1288265 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1288226 AAAGCCATGC
1288236 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
1288266 CAACACACAT
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:1289771 original size:55 final size:54
Alignment explanation
Indices: 1289721--1290218 Score: 375
Period size: 55 Copynumber: 9.1 Consensus size: 54
1289711 AGTATAAGAT
* *
1289721 TCGAACAATCTTCAGTAAACGTGTCTGCTCCCTATTTGTTCAGGGTGTATA-AGAC
1 TCGAACAATCTTCA-TAAACGTGTCTGCTCCCTATTTATTCAGGGAGTATAGA-AC
* *
1289776 TCGAACAATCTTCATAAA-ATAGGT-TCGCTCCCTATTTATTCAAGGAGTATAGAAC
1 TCGAACAATCTTCATAAACGT--GTCT-GCTCCCTATTTATTCAGGGAGTATAGAAC
* * * * **
1289831 TCGAACAATCTTCATAAAACGAGTCCGCTCTCTATTTCTTCAAAGAGTATAGAAC
1 TCGAACAATCTTCAT-AAACGTGTCTGCTCCCTATTTATTCAGGGAGTATAGAAC
* * * ** *
1289886 TCGAACAATCTTCAACAAACG-GTCTTCTCTCTATTCCTTCAGAGAGTATAGAAC
1 TCGAACAATCTTC-ATAAACGTGTCTGCTCCCTATTTATTCAGGGAGTATAGAAC
* * * *
1289940 TCGAACAATCTTCAACAAACGGGTCTACTCCCTATTCATTCAGGGAGTATAGAAC
1 TCGAACAATCTTC-ATAAACGTGTCTGCTCCCTATTTATTCAGGGAGTATAGAAC
* * * * * ** *
1289995 TCGAAAAATCTTTATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAAC
1 TCGAACAATCTTCAT-AAACGTGTCTGCTCCCTATTTATTCAGGGAGTATAGAAC
* * * * *
1290050 TCGAACAATCTTCAACAAACGGGCCCGCTCCCTATTCTA-TCAGAGAGTATAGAAC
1 TCGAACAATCTTC-ATAAACGTGTCTGCTCCCTATT-TATTCAGGGAGTATAGAAC
* * * * * *
1290105 TCAAAAAATCTTCAATAAATGGGT-TCGCACCCTATTCTA-TCAGAGAGTATAGAAC
1 TCGAACAATCTTC-ATAAACGTGTCT-GCTCCCTATT-TATTCAGGGAGTATAGAAC
* * * * * *
1290160 TCAAACAATCTTCAACAAACG-GATCCGCTCCCTATTCTA-TCTGAGAGTATAGGAC
1 TCGAACAATCTTC-ATAAACGTG-TCTGCTCCCTATT-TATTCAGGGAGTATAGAAC
1290215 TCGA
1 TCGA
1290219 TCTTCATAAA
Statistics
Matches: 379, Mismatches: 49, Indels: 30
0.83 0.11 0.07
Matches are distributed among these distances:
53 1 0.00
54 57 0.15
55 315 0.83
56 6 0.02
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (54 bp):
TCGAACAATCTTCATAAACGTGTCTGCTCCCTATTTATTCAGGGAGTATAGAAC
Found at i:1289842 original size:110 final size:109
Alignment explanation
Indices: 1289721--1290218 Score: 508
Period size: 110 Copynumber: 4.5 Consensus size: 109
1289711 AGTATAAGAT
** * * * * *
1289721 TCGAACAATCTTCAGTAAACGTGTCTGCTCCCTATTTGTTCAGGGTGTATA-AGACTCGAACAAT
1 TCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTT-TTCAGAGAGTATAGA-ACTCGAAAAAT
* *
1289785 CTTCATA-AAATAGGTTCGCTCCCTATTTATTCA-AGGAGTATAGAAC
64 CTTCA-ACAAATGGGTTCGCTCCCTATTCATTCAGA-GAGTATAGAAC
* * * *
1289831 TCGAACAATCTTCATA-AAACGAGTCCGCTCTCTATTTCTTCAAAGAGTATAGAACTCGAACAAT
1 TCGAACAATCTTCA-ACAAACGGGTCCGCTCCCTATTT-TTCAGAGAGTATAGAACTCGAAAAAT
* * * *
1289895 CTTCAACAAA-CGG-TCTTCTCTCTATTCCTTCAGAGAGTATAGAAC
64 CTTCAACAAATGGGTTC-GCTCCCTATTCATTCAGAGAGTATAGAAC
** * *
1289940 TCGAACAATCTTCAACAAACGGGTCTACTCCCTATTCATTCAGGGAGTATAGAACTCGAAAAATC
1 TCGAACAATCTTCAACAAACGGGTCCGCTCCCTATT-TTTCAGAGAGTATAGAACTCGAAAAATC
* * * * *
1290005 TTTATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAAC
65 TTCA-ACAAATGGGTTCGCTCCCTATTCATTCAGAGAGTATAGAAC
* * *
1290050 TCGAACAATCTTCAACAAACGGGCCCGCTCCCTATTCTATCAGAGAGTATAGAACTCAAAAAATC
1 TCGAACAATCTTCAACAAACGGGTCCGCTCCCTATT-TTTCAGAGAGTATAGAACTCGAAAAATC
* *
1290115 TTCAATAAATGGGTTCGCACCCTATTC-TATCAGAGAGTATAGAAC
65 TTCAACAAATGGGTTCGCTCCCTATTCAT-TCAGAGAGTATAGAAC
* * * * *
1290160 TCAAACAATCTTCAACAAACGGATCCGCTCCCTATTCTATCTGAGAGTATAGGACTCGA
1 TCGAACAATCTTCAACAAACGGGTCCGCTCCCTATT-TTTCAGAGAGTATAGAACTCGA
1290219 TCTTCATAAA
Statistics
Matches: 333, Mismatches: 43, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
108 3 0.01
109 88 0.26
110 240 0.72
111 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (109 bp):
TCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTTTTCAGAGAGTATAGAACTCGAAAAATCT
TCAACAAATGGGTTCGCTCCCTATTCATTCAGAGAGTATAGAAC
Found at i:1290099 original size:219 final size:219
Alignment explanation
Indices: 1289721--1290218 Score: 587
Period size: 219 Copynumber: 2.3 Consensus size: 219
1289711 AGTATAAGAT
** * * * *
1289721 TCGAACAATCTTCAGTAAACGTGTCTGCTCCCTATTTGTTCAGGGTGTATA-AGACTCGAACAAT
1 TCGAACAATCTTCAACAAACGGGTCTGCTCCCTA-TTCTTCAGGGAGTATAGA-ACTCGAAAAAT
* * *
1289785 CTTCATAAAATAGGTTCGCTCCCTATTTATTCAAGGAGTATAGAACTCGAACAATCTTCATAAAA
64 CTTCATAAAACAGGTCCGCTCCCTATTCATTCAAGGAGTATAGAACTCGAACAATCTTCATAAAA
* * * * *
1289850 CGAGTCCGCTCTCTATTTCTTCAAAGAGTATAGAACTCGAACAATCTTCAACAAA-CGG-TCTTC
129 CGAGCCCGCTCCCTATTTCTTCAAAGAGTATAGAACTCAAAAAATCTTCAACAAATCGGTTC-GC
* *
1289913 TCTCTATTCCT-TCAGAGAGTATAGAAC
193 ACCCTATT-CTATCAGAGAGTATAGAAC
*
1289940 TCGAACAATCTTCAACAAACGGGTCTACTCCCTATTCATTCAGGGAGTATAGAACTCGAAAAATC
1 TCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTC-TTCAGGGAGTATAGAACTCGAAAAATC
* * * *
1290005 TTTATAAAACGGGTCCGCTCTCTATTCCTTC-AGAGAGTATAGAACTCGAACAATCTTCA-ACAA
65 TTCATAAAACAGGTCCGCTCCCTATTCATTCAAG-GAGTATAGAACTCGAACAATCTTCATA-AA
* * * *
1290068 ACGGGCCCGCTCCCTA-TTCTATCAGAGAGTATAGAACTCAAAAAATCTTCAATAAATGGGTTCG
128 ACGAGCCCGCTCCCTATTTCT-TCAAAGAGTATAGAACTCAAAAAATCTTCAACAAATCGGTTCG
1290132 CACCCTATTCTATCAGAGAGTATAGAAC
192 CACCCTATTCTATCAGAGAGTATAGAAC
* * * * * *
1290160 TCAAACAATCTTCAACAAACGGATCCGCTCCCTATTCTATCTGAGAGTATAGGACTCGA
1 TCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTCT-TCAGGGAGTATAGAACTCGA
1290219 TCTTCATAAA
Statistics
Matches: 238, Mismatches: 32, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
218 9 0.04
219 151 0.63
220 76 0.32
221 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (219 bp):
TCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTCTTCAGGGAGTATAGAACTCGAAAAATCT
TCATAAAACAGGTCCGCTCCCTATTCATTCAAGGAGTATAGAACTCGAACAATCTTCATAAAACG
AGCCCGCTCCCTATTTCTTCAAAGAGTATAGAACTCAAAAAATCTTCAACAAATCGGTTCGCACC
CTATTCTATCAGAGAGTATAGAAC
Found at i:1290284 original size:37 final size:38
Alignment explanation
Indices: 1290229--1290300 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 38
1290219 TCTTCATAAA
*
1290229 ATGAGTTTGCTTCACTACTATTCCGTGAAGGCTTATAT
1 ATGAGTTTGCTTCACTACTATTCCGCGAAGGCTTATAT
*
1290267 ATGA-TTTGCTTCACTACTCTTCCGCGAAGGCTTA
1 ATGAGTTTGCTTCACTACTATTCCGCGAAGGCTTA
1290301 AGATTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 28 0.88
38 4 0.12
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (38 bp):
ATGAGTTTGCTTCACTACTATTCCGCGAAGGCTTATAT
Found at i:1291606 original size:7 final size:7
Alignment explanation
Indices: 1291594--1291741 Score: 56
Period size: 7 Copynumber: 21.7 Consensus size: 7
1291584 TTTTCTCTAT
1291594 TTTTTCA
1 TTTTTCA
1291601 TTTTTCA
1 TTTTTCA
1291608 TTTTTC-
1 TTTTTCA
* *
1291614 TCTTTCT
1 TTTTTCA
1291621 TTTTTC-
1 TTTTTCA
1291627 TTTTT--
1 TTTTTCA
1291632 TTTTT-A
1 TTTTTCA
1291638 TTTTTTCA
1 -TTTTTCA
1291646 -TTTTCA
1 TTTTTCA
1291652 -TTTTC-
1 TTTTTCA
1291657 TCTTTT-A
1 T-TTTTCA
1291664 TTTTTTC-
1 -TTTTTCA
*
1291671 TTCTT--
1 TTTTTCA
1291676 TTTTTCA
1 TTTTTCA
1291683 TTTTT--
1 TTTTTCA
1291688 TTCTTTCACCA
1 TT-TTT---CA
1291699 TTTTTCA
1 TTTTTCA
1291706 TTTTTTCTCA
1 --TTTT-TCA
1291716 TTTTTC-
1 TTTTTCA
*
1291722 CTTTTCA
1 TTTTTCA
1291729 TTTTTTCA
1 -TTTTTCA
1291737 TTTTT
1 TTTTT
1291742 TTTATTTCTT
Statistics
Matches: 113, Mismatches: 6, Indels: 44
0.69 0.04 0.27
Matches are distributed among these distances:
5 11 0.10
6 33 0.29
7 45 0.40
8 12 0.11
9 4 0.04
10 6 0.05
11 2 0.02
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCA
Found at i:1291645 original size:45 final size:45
Alignment explanation
Indices: 1291591--1291688 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
1291581 TATTTTTCTC
*
1291591 TATTTTTTCATTTTTCATTTT-TCTCTTTCTTTTTTCTT-TTTTTTT
1 TATTTTTTCA-TTTTCATTTTCTCT-TTTATTTTTTCTTCTTTTTTT
1291636 TATTTTTTCATTTTCATTTTCTCTTTTATTTTTTCTTCTTTTTTT
1 TATTTTTTCATTTTCATTTTCTCTTTTATTTTTTCTTCTTTTTTT
*
1291681 CATTTTTT
1 TATTTTTT
1291689 TCTTTCACCA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
44 22 0.45
45 27 0.55
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (45 bp):
TATTTTTTCATTTTCATTTTCTCTTTTATTTTTTCTTCTTTTTTT
Found at i:1291686 original size:9 final size:8
Alignment explanation
Indices: 1291616--1291693 Score: 56
Period size: 8 Copynumber: 9.9 Consensus size: 8
1291606 CATTTTTCTC
1291616 TTTC-TTT
1 TTTCTTTT
1291623 TTTCTTTT
1 TTTCTTTT
1291631 TTT-TTTAT
1 TTTCTTT-T
*
1291639 TTT-TTCAT
1 TTTCTT-TT
*
1291647 TTTCATTT
1 TTTCTTTT
*
1291655 TCTCTTTT
1 TTTCTTTT
*
1291663 ATT-TTTT
1 TTTCTTTT
*
1291670 CTTCTTTT
1 TTTCTTTT
1291678 TTTCATTTT
1 TTTC-TTTT
1291687 TTTCTTT
1 TTTCTTT
1291694 CACCATTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
7 13 0.23
8 34 0.61
9 9 0.16
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTCTTTT
Found at i:1291694 original size:13 final size:12
Alignment explanation
Indices: 1291601--1291695 Score: 61
Period size: 13 Copynumber: 7.6 Consensus size: 12
1291591 TATTTTTTCA
1291601 TTTTTCATTTTT
1 TTTTTCATTTTT
*
1291613 CTCTTTC-TTTTT
1 -TTTTTCATTTTT
**
1291625 TCTTTTTTTTTTAT
1 T-TTTTCATTTT-T
1291639 TTTTTCATTTTCAT
1 TTTTTCATTTT--T
*
1291653 TTTCTC-TTTTAT
1 TTTTTCATTTT-T
*
1291665 TTTTTC-TTCTT
1 TTTTTCATTTTT
1291676 TTTTTCATTTTT
1 TTTTTCATTTTT
1291688 TTCTTTCA
1 TT-TTTCA
1291696 CCATTTTTCA
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
11 8 0.12
12 24 0.36
13 26 0.39
14 9 0.13
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTCATTTTT
Found at i:1291695 original size:44 final size:43
Alignment explanation
Indices: 1291583--1291739 Score: 124
Period size: 44 Copynumber: 3.5 Consensus size: 43
1291573 TCCCCTTTTA
* *
1291583 TTTTTCTCTATTTTTTCATTTTTCATTTTTCTCTTTCTTTTTTCTT
1 TTTTTTTC-ATTTTTTCA--TTTCATTTTTCTCTTTATTTTTTCTT
*
1291629 TTTTTTTTATTTTTTCATTTTCA-TTTTCTCTTTTATTTTTTCTT
1 TTTTTTTCATTTTTTCA-TTTCATTTTTCTC-TTTATTTTTTCTT
* * *
1291673 CTTTTTTTCATTTTTTTC-TTTCACCATTTT-TCATT-TTTTCTCATT
1 -TTTTTTTCA-TTTTTTCATTTCA--TTTTTCTCTTTATTTTTTC-TT
1291718 TTTCCTTTTCATTTTTTCATTT
1 TTT--TTTTCATTTTTTCATTT
1291740 TTTTTATTTC
Statistics
Matches: 95, Mismatches: 6, Indels: 20
0.79 0.05 0.17
Matches are distributed among these distances:
43 7 0.07
44 32 0.34
45 28 0.29
46 24 0.25
47 4 0.04
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.75
Consensus pattern (43 bp):
TTTTTTTCATTTTTTCATTTCATTTTTCTCTTTATTTTTTCTT
Found at i:1302984 original size:2 final size:2
Alignment explanation
Indices: 1302977--1303001 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1302967 TGTCAGTACG
1302977 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1303002 CGATATTATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1305401 original size:17 final size:17
Alignment explanation
Indices: 1305354--1305402 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
1305344 ATCGACATAC
* *
1305354 TATTTTT-ATTATCTTT
1 TATTTTTAAATATTTTT
1305370 TATTTTTAAATATTTTT
1 TATTTTTAAATATTTTT
1305387 TATTTTTTAAA-ATTTT
1 TA-TTTTTAAATATTTT
1305403 CATTTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 7 0.24
17 14 0.48
18 8 0.28
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTTAAATATTTTT
Found at i:1305402 original size:16 final size:18
Alignment explanation
Indices: 1305367--1305402 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1305357 TTTTATTATC
1305367 TTTTA-TTTTTAAATATT
1 TTTTATTTTTTAAATATT
1305384 TTTTATTTTTTAAA-ATT
1 TTTTATTTTTTAAATATT
1305401 TT
1 TT
1305403 CATTTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTATTTTTTAAATATT
Found at i:1308334 original size:22 final size:22
Alignment explanation
Indices: 1308307--1308361 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1308297 TGTATGAACA
1308307 GTATCGATACCAT-A-TGGAAGAG
1 GTATCGATACCATAAGTGG-AG-G
*
1308329 GTATCGATGCC-TAAGTGGAGG
1 GTATCGATACCATAAGTGGAGG
1308350 GTATCGATACCA
1 GTATCGATACCA
1308362 GGGAACATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 12 0.43
22 13 0.46
23 3 0.11
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (22 bp):
GTATCGATACCATAAGTGGAGG
Found at i:1310719 original size:14 final size:14
Alignment explanation
Indices: 1310700--1310731 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1310690 CATAAGATAT
1310700 ATATATATATATTC
1 ATATATATATATTC
*
1310714 ATATATATATATTT
1 ATATATATATATTC
1310728 ATAT
1 ATAT
1310732 GATTTGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATATATATATTC
Found at i:1311099 original size:23 final size:23
Alignment explanation
Indices: 1311066--1311133 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
1311056 CATATTATAT
1311066 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * * **
1311089 GGCACTACGGTCCAATTCTACAT
1 GGCACTTCGGTGCATTTCTACGC
* *
1311112 GGAACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
1311134 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1311661 original size:179 final size:174
Alignment explanation
Indices: 1311339--1311691 Score: 636
Period size: 179 Copynumber: 2.0 Consensus size: 174
1311329 TAAGTATAAA
*
1311339 TAGATAACTAAAATATAAATGGATGGAATATTGATTATGAAATGAGGCTATTGATTAAGATAAGA
1 TAGATAACTAAAAGATAAATGGATGGAATATTGATTATGAAATGAGGCTATTGATTAAGATAAGA
1311404 TTTATCTATTTGTATGCATGTGATTATATGGAATTATATTGATTTGTATGATATTATTGTATGAT
66 TTTATCTATTTGTATGCATGTGATTATATGGAATTATATTGATTTGTATGATATTATTGTATGAT
1311469 ATGTTCATGCATGTTTAGGAATTA-AGTTTCAATTCTGAGTTTT
131 ATGTTCATGCATGTTTAGGAATTAGAGTTTCAATTCTGAGTTTT
1311512 TAGATAACTAAAAGATATAATGGATGGAATATTGATTATGAAATGAGGCTATTGATAATTAAGAT
1 TAGATAACTAAAAGATA-AATGGATGGAATATTGATTATGAAATGAGGCTATTG---ATTAAGAT
1311577 AAGATTTATCTATTTGTATGCATGTGATTATATGGAATGTTATATTGATTTGTATGATATTATTG
62 AAGATTTATCTATTTGTATGCATGTGATTATATGGAA--TTATATTGATTTGTATGATATTATTG
1311642 TATGATATGTTCATGCATGTTTAGGAATTAGAGTTTCAATTCTGAGTTTT
125 TATGATATGTTCATGCATGTTTAGGAATTAGAGTTTCAATTCTGAGTTTT
1311692 ATATGCCTCA
Statistics
Matches: 172, Mismatches: 1, Indels: 7
0.96 0.01 0.04
Matches are distributed among these distances:
173 16 0.09
174 36 0.21
177 45 0.26
179 56 0.33
180 19 0.11
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (174 bp):
TAGATAACTAAAAGATAAATGGATGGAATATTGATTATGAAATGAGGCTATTGATTAAGATAAGA
TTTATCTATTTGTATGCATGTGATTATATGGAATTATATTGATTTGTATGATATTATTGTATGAT
ATGTTCATGCATGTTTAGGAATTAGAGTTTCAATTCTGAGTTTT
Found at i:1313286 original size:18 final size:18
Alignment explanation
Indices: 1313263--1313299 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1313253 GTTCTTAAGG
1313263 AGTGGTCATTCGGGACAA
1 AGTGGTCATTCGGGACAA
*
1313281 AGTGGTCATTCGGGTCAA
1 AGTGGTCATTCGGGACAA
1313299 A
1 A
1313300 TTCTACGCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.24
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAA
Found at i:1314507 original size:20 final size:20
Alignment explanation
Indices: 1314464--1314518 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1314454 CTACTCAAGT
* *
1314464 ATATCGATACT-AAGACCTA
1 ATATCGATACTCAGGGCCTA
*
1314483 GTATCGATACTCAGGGCCTA
1 ATATCGATACTCAGGGCCTA
1314503 ATATCGATACTCAGGG
1 ATATCGATACTCAGGG
1314519 TCTTGATCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
ATATCGATACTCAGGGCCTA
Found at i:1314688 original size:21 final size:21
Alignment explanation
Indices: 1314664--1314706 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1314654 ATTGGCACTC
1314664 AATG-GAGTATCGATAACTAAG
1 AATGTGAGTATCGAT-ACTAAG
*
1314685 AATGTGTGTATCGATACTAAG
1 AATGTGAGTATCGATACTAAG
1314706 A
1 A
1314707 TGATTTCCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (21 bp):
AATGTGAGTATCGATACTAAG
Found at i:1316661 original size:23 final size:23
Alignment explanation
Indices: 1316643--1316693 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
1316633 TAAAATTTTT
1316643 AATCCCTAAAATCTTAAATACTC
1 AATCCCTAAAATCTTAAATACTC
* *
1316666 AATCTCTAAAATCTCAAATACTC
1 AATCCCTAAAATCTTAAATACTC
1316689 AATCC
1 AATCC
1316694 TTCAAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.29
Consensus pattern (23 bp):
AATCCCTAAAATCTTAAATACTC
Found at i:1317024 original size:24 final size:23
Alignment explanation
Indices: 1316987--1317033 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1316977 TATTTATTTA
1316987 TGAGTTATAAATTTTAATTAAATC
1 TGAGTTATAAA-TTTAATTAAATC
** *
1317011 TGAGTTATTTATTTATTTAAATC
1 TGAGTTATAAATTTAATTAAATC
1317034 CAACAGTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (23 bp):
TGAGTTATAAATTTAATTAAATC
Found at i:1319006 original size:157 final size:163
Alignment explanation
Indices: 1318684--1319010 Score: 553
Period size: 157 Copynumber: 2.0 Consensus size: 163
1318674 TTGCCTTTCA
*
1318684 TGGACCTACAGAAATACCAAAAATCAAATGCCAAAAAGATGTTCATTGATGAATCTGTTAAAAAA
1 TGGATCTACAGAAATACCAAAAATCAAAT-CCAAAAAGATGTTCATTGATGAATCTGTTAAAAAA
1318749 ACAGGTTTCTTCTTCCCACTTTACAGGTTCAAATTACAAATAGTGTAGAAGTGTTTCCAGGTTAA
65 ACAGGTTTCTTCTTCCCACTTTACAGGTTCAAATTACAAATAGTGTAGAAGTGTTTCCAGGTTAA
1318814 AATAGATTCGAGAAACTGAGTCTCAAGAAATAAT
130 AATAGATTCGAGAAACTGAGTCTCAAGAAATAAT
1318848 TGGATCTACAGAAATACCAAAAAATCAAAT-CAAAAAGAT-TTC-TTGATGAATCTGTT-AAAAA
1 TGGATCTACAGAAATACC-AAAAATCAAATCCAAAAAGATGTTCATTGATGAATCTGTTAAAAAA
*
1318909 ACAGGTTTTCTTCTTCCCACTTTACAGTTTC-AATTAC-AATAG-GTAGAAGTGTTTCCA-GTTA
65 ACAGG-TTTCTTCTTCCCACTTTACAGGTTCAAATTACAAATAGTGTAGAAGTGTTTCCAGGTTA
1318970 AAATAGATTCGAGAAACTGAGTCTCAAGAAATAAT
129 AAATAGATTCGAGAAACTGAGTCTCAAGAAATAAT
1319005 TGGATC
1 TGGATC
1319011 ATGTAAGTCA
Statistics
Matches: 159, Mismatches: 2, Indels: 11
0.92 0.01 0.06
Matches are distributed among these distances:
157 45 0.28
158 15 0.09
159 5 0.03
160 16 0.10
161 38 0.24
162 3 0.02
163 9 0.06
164 17 0.11
165 11 0.07
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (163 bp):
TGGATCTACAGAAATACCAAAAATCAAATCCAAAAAGATGTTCATTGATGAATCTGTTAAAAAAA
CAGGTTTCTTCTTCCCACTTTACAGGTTCAAATTACAAATAGTGTAGAAGTGTTTCCAGGTTAAA
ATAGATTCGAGAAACTGAGTCTCAAGAAATAAT
Found at i:1328802 original size:21 final size:20
Alignment explanation
Indices: 1328776--1328844 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
1328766 TGACCTATCA
1328776 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATGT-ATCTGTG
* ** *
1328797 TCCCGAATGACCTATC---A
1 TCCCGAAGGATGTATCTGTG
1328814 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGT-ATCTGTG
*
1328835 TCCTGAAGGA
1 TCCCGAAGGA
1328845 CCTATCATAT
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
17 10 0.29
18 3 0.09
20 3 0.09
21 19 0.54
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (20 bp):
TCCCGAAGGATGTATCTGTG
Found at i:1328813 original size:38 final size:38
Alignment explanation
Indices: 1328757--1328852 Score: 156
Period size: 38 Copynumber: 2.5 Consensus size: 38
1328747 GTATAAACTA
* *
1328757 TGTCTCGAATGACCTATCATCCCGAAGGATGTCATCTG
1 TGTCCCGAATGACCTATCATCCCGAAGGATGTAATCTG
1328795 TGTCCCGAATGACCTATCATCCCGAAGGATGTAATCTG
1 TGTCCCGAATGACCTATCATCCCGAAGGATGTAATCTG
* *
1328833 TGTCCTGAAGGACCTATCAT
1 TGTCCCGAATGACCTATCAT
1328853 ATGTCTCGTA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (38 bp):
TGTCCCGAATGACCTATCATCCCGAAGGATGTAATCTG
Found at i:1329794 original size:31 final size:31
Alignment explanation
Indices: 1329756--1329825 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
1329746 ACAACATTCC
* *
1329756 CAACTTTTTCCAAAATTACGAATTGGTCCCT
1 CAACTTTTTCCAAAATTACAAAATGGTCCCT
*
1329787 CAAC-TTTTCGAAAATTACAAAATGGTCCCT
1 CAACTTTTTCCAAAATTACAAAATGGTCCCT
*
1329817 -AAATTTTTC
1 CAACTTTTTC
1329826 TAAAGCTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.06
30 28 0.82
31 4 0.12
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.36
Consensus pattern (31 bp):
CAACTTTTTCCAAAATTACAAAATGGTCCCT
Found at i:1330783 original size:29 final size:30
Alignment explanation
Indices: 1330750--1330810 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1330740 TATTTATAAC
*
1330750 TTTTTAAA-ATTATATTTTAGTC-CCTAAAT
1 TTTTTAAAGATTATACTTTAGTCACC-AAAT
*
1330779 TTTTTAAAGTTTATACTTTAGTCACCAAAT
1 TTTTTAAAGATTATACTTTAGTCACCAAAT
1330809 TT
1 TT
1330811 ATAACATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 8 0.29
30 18 0.64
31 2 0.07
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.51
Consensus pattern (30 bp):
TTTTTAAAGATTATACTTTAGTCACCAAAT
Found at i:1333647 original size:99 final size:99
Alignment explanation
Indices: 1333476--1333673 Score: 387
Period size: 99 Copynumber: 2.0 Consensus size: 99
1333466 CAGGAAGCTC
*
1333476 CTTTATATCGACCTCAAGCCTTTCCTAAACCTGAAACCAAATTAACAAAAGTTATTAAACAAAAA
1 CTTTATATCGACCTCAAACCTTTCCTAAACCTGAAACCAAATTAACAAAAGTTATTAAACAAAAA
1333541 TGACTAATCAGTTCTATTAATATATATATATATA
66 TGACTAATCAGTTCTATTAATATATATATATATA
1333575 CTTTATATCGACCTCAAACCTTTCCTAAACCTGAAACCAAATTAACAAAAGTTATTAAACAAAAA
1 CTTTATATCGACCTCAAACCTTTCCTAAACCTGAAACCAAATTAACAAAAGTTATTAAACAAAAA
1333640 TGACTAATCAGTTCTATTAATATATATATATATA
66 TGACTAATCAGTTCTATTAATATATATATATATA
1333674 TATATATATA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (99 bp):
CTTTATATCGACCTCAAACCTTTCCTAAACCTGAAACCAAATTAACAAAAGTTATTAAACAAAAA
TGACTAATCAGTTCTATTAATATATATATATATA
Found at i:1333666 original size:2 final size:2
Alignment explanation
Indices: 1333659--1333691 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1333649 AGTTCTATTA
1333659 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 A
1333692 AAGTACAGAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1341107 original size:17 final size:18
Alignment explanation
Indices: 1341085--1341124 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1341075 CCGTTATAAG
1341085 ACTA-GGTGAATCGGTAC
1 ACTAGGGTGAATCGGTAC
*
1341102 ACTAGGGGTGCATCGGTAC
1 ACTA-GGGTGAATCGGTAC
1341121 ACTA
1 ACTA
1341125 ATTACATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
19 16 0.80
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (18 bp):
ACTAGGGTGAATCGGTAC
Found at i:1341223 original size:65 final size:65
Alignment explanation
Indices: 1341109--1341265 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 65
1341099 TACACTAGGG
* * * * * *
1341109 GTGCATCGGTACACTAATTACATTCGATGTTTCAAAAGAGCCAGAAGTGCATCGATGCATG-GTA
1 GTGCATCGATACACAAAATGCATTCGATGTTTCAAAAGAGCAAGAAGTGCATCGATGCATGACT-
1341173 T
65 T
* * *
1341174 GTGCATCGATACACAAAATGCATTTGATGTTTCAAAATATTCAAG-AGTGCATCGATGCATGACT
1 GTGCATCGATACACAAAATGCATTCGATGTTTCAAAAGA-GCAAGAAGTGCATCGATGCATGACT
1341238 T
65 T
1341239 GTGCATCGATACACAAAATGCATTCGA
1 GTGCATCGATACACAAAATGCATTCGA
1341266 AATGGGTGTG
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 76 0.95
66 4 0.05
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (65 bp):
GTGCATCGATACACAAAATGCATTCGATGTTTCAAAAGAGCAAGAAGTGCATCGATGCATGACTT
Found at i:1342513 original size:21 final size:21
Alignment explanation
Indices: 1342487--1342529 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1342477 AAATTGGCAT
* * *
1342487 GGGGGTATCAGTACCATCTGG
1 GGGGGTACCAATACCATATGG
1342508 GGGGGTACCAATACCATATGG
1 GGGGGTACCAATACCATATGG
1342529 G
1 G
1342530 CAATCTGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (21 bp):
GGGGGTACCAATACCATATGG
Found at i:1344718 original size:14 final size:13
Alignment explanation
Indices: 1344678--1344718 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
1344668 ATGGGCAAAT
*
1344678 TTTGAAAACTATG
1 TTTGAAAACAATG
1344691 TTTGAAAACAATG
1 TTTGAAAACAATG
1344704 TTTGAAAATCAATG
1 TTTGAAAA-CAATG
1344718 T
1 T
1344719 GCAGTTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:1344782 original size:22 final size:21
Alignment explanation
Indices: 1344742--1344787 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1344732 CAATATAATT
* *
1344742 AAATCAAAAACAATAATTTTA
1 AAATCAAAAAAAATAATTTCA
*
1344763 AAATCAAAAAAAAATTATTTCA
1 AAATC-AAAAAAAATAATTTCA
1344785 AAA
1 AAA
1344788 ATTTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATCAAAAAAAATAATTTCA
Found at i:1345248 original size:23 final size:22
Alignment explanation
Indices: 1345196--1345256 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
1345186 TACCCTCATG
1345196 GGGGGTATCGGTACCCATTCAA
1 GGGGGTATCGGTACCCATTCAA
*
1345218 GGATGGTATCGGTACCCATTCAAA
1 GG-GGGTATCGGTACCCATTC-AA
*
1345242 GGGGGTATCGATACC
1 GGGGGTATCGGTACC
1345257 TAGCTCGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.06
23 28 0.82
24 4 0.12
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (22 bp):
GGGGGTATCGGTACCCATTCAA
Found at i:1350147 original size:21 final size:21
Alignment explanation
Indices: 1350122--1350163 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1350112 AAATTGGCAT
*
1350122 GGGGTATCGATACCATCTGGG
1 GGGGTACCGATACCATCTGGG
*
1350143 GGGGTACCGGTACCATCTGGG
1 GGGGTACCGATACCATCTGGG
1350164 CAATATGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.21
Consensus pattern (21 bp):
GGGGTACCGATACCATCTGGG
Found at i:1351889 original size:24 final size:24
Alignment explanation
Indices: 1351862--1351912 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1351852 GATTAATTCG
*
1351862 GGTTAGTTTGGATTTGGATTTTAT
1 GGTTAGTTTAGATTTGGATTTTAT
*
1351886 GGTTAGTTTAGATTTGGATTTTGT
1 GGTTAGTTTAGATTTGGATTTTAT
1351910 GGT
1 GGT
1351913 AGAGGAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (24 bp):
GGTTAGTTTAGATTTGGATTTTAT
Found at i:1352208 original size:16 final size:16
Alignment explanation
Indices: 1352187--1352222 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1352177 AAAACATCAA
*
1352187 TTAAAACAATACTTTT
1 TTAAAACAATAATTTT
*
1352203 TTAAAATAATAATTTT
1 TTAAAACAATAATTTT
1352219 TTAA
1 TTAA
1352223 CATTTTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAACAATAATTTT
Found at i:1352653 original size:21 final size:20
Alignment explanation
Indices: 1352604--1352656 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
1352594 AAACCCGATG
* *
1352604 GGTGTATCAATGCATATCAT
1 GGTGTATCGATGCACATCAT
* *
1352624 TGTGCATCGATGCACATTCAT
1 GGTGTATCGATGCACA-TCAT
1352645 GGTGTATCGATG
1 GGTGTATCGATG
1352657 AATATTCAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (20 bp):
GGTGTATCGATGCACATCAT
Found at i:1352663 original size:21 final size:21
Alignment explanation
Indices: 1352604--1352703 Score: 71
Period size: 20 Copynumber: 4.8 Consensus size: 21
1352594 AAACCCGATG
*
1352604 GGTGTATCAATGCATA-TCAT
1 GGTGTATCGATGCATATTCAT
* * *
1352624 TGTGCATCGATGCACATTCAT
1 GGTGTATCGATGCATATTCAT
* *
1352645 GGTGTATCGATGAATATTCAAG
1 GGTGTATCGATGCATATTC-AT
*
1352667 GGATGCATCGATGCAT-TGTC-T
1 GG-TGTATCGATGCATAT-TCAT
* *
1352688 AGTGTATCAATGCATA
1 GGTGTATCGATGCATA
1352704 GTGTACAAAA
Statistics
Matches: 60, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
20 23 0.38
21 20 0.33
22 4 0.07
23 13 0.22
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (21 bp):
GGTGTATCGATGCATATTCAT
Found at i:1358559 original size:65 final size:65
Alignment explanation
Indices: 1358472--1358595 Score: 203
Period size: 65 Copynumber: 1.9 Consensus size: 65
1358462 ATTACATTCG
* *
1358472 ATGTTTCAAAAGAGTCAGGAGTGCATCGATGCATGGTCTGTGCATCGGTACACAAAATGTGTTCA
1 ATGTTTCAAAAGAGTCAAGAGTGCATCGATGCATGGTCTGTGCATCGATACACAAAATGTGTTCA
* * *
1358537 ATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGTTTGTGCATCGATACACAAAATG
1 ATGTTTCAAAAGAGTCAAGAGTGCATCGATGCATGGTCTGTGCATCGATACACAAAATG
1358596 CATTCGAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (65 bp):
ATGTTTCAAAAGAGTCAAGAGTGCATCGATGCATGGTCTGTGCATCGATACACAAAATGTGTTCA
Found at i:1359253 original size:2 final size:2
Alignment explanation
Indices: 1359246--1359302 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1359236 ATCCTATCCC
1359246 TA TA TA 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 TA TA TA
1359288 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1359303 GCAAATACAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1359468 original size:25 final size:25
Alignment explanation
Indices: 1359429--1359496 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
1359419 GTGGATTTTG
1359429 AAAAATG--TTTTTAAAAGTATTGT
1 AAAAATGAATTTTTAAAAGTATTGT
1359452 AAAAATGAATTTTTAAAAGTATTGT
1 AAAAATGAATTTTTAAAAGTATTGT
1359477 AAAAATGAATTTTTAAAAGT
1 AAAAATGAATTTTTAAAAGT
1359497 TTTATATAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.16
25 36 0.84
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.40
Consensus pattern (25 bp):
AAAAATGAATTTTTAAAAGTATTGT
Found at i:1366738 original size:20 final size:20
Alignment explanation
Indices: 1366715--1366766 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1366705 CCTATAGGGA
1366715 GTATCGATACTCTATCGTTG
1 GTATCGATACTCTATCGTTG
1366735 GTATCGATACTCTATCGTTG
1 GTATCGATACTCTATCGTTG
1366755 GTATCGATACTC
1 GTATCGATACTC
1366767 ATTCGAGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
GTATCGATACTCTATCGTTG
Found at i:1367922 original size:14 final size:14
Alignment explanation
Indices: 1367903--1367929 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1367893 TTTGTTATAT
1367903 ATGTCTATATTTAC
1 ATGTCTATATTTAC
1367917 ATGTCTATATTTA
1 ATGTCTATATTTA
1367930 TTTTATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (14 bp):
ATGTCTATATTTAC
Found at i:1369061 original size:2 final size:2
Alignment explanation
Indices: 1369056--1369088 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1369046 TTCTATTAAT
1369056 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1369089 TTATTTATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1369724 original size:28 final size:27
Alignment explanation
Indices: 1369675--1369795 Score: 92
Period size: 28 Copynumber: 4.6 Consensus size: 27
1369665 GAAAAAAATG
*
1369675 AAAATAAATAAAATAAAGAAAGACAAA
1 AAAATAAAGAAAATAAAGAAAGACAAA
* *
1369702 AGAAATAAA-AAAATAACATAAAGATAAA
1 A-AAATAAAGAAAATAA-AGAAAGACAAA
* ** *
1369730 AAGATAAAGAAAATAAA-AAAGGGATA
1 AAAATAAAGAAAATAAAGAAAGACAAA
*
1369756 AAAAT--AGAAAAAAAAGAAA-A-AATA
1 AAAATAAAGAAAATAAAGAAAGACAA-A
1369780 ATAAATAAAGAAAATA
1 A-AAATAAAGAAAATA
1369796 GCAACAATCT
Statistics
Matches: 75, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
23 1 0.01
24 11 0.15
25 7 0.09
26 10 0.13
27 22 0.29
28 24 0.32
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (27 bp):
AAAATAAAGAAAATAAAGAAAGACAAA
Found at i:1369728 original size:19 final size:17
Alignment explanation
Indices: 1369662--1369795 Score: 71
Period size: 18 Copynumber: 7.6 Consensus size: 17
1369652 GAAATGTGTA
1369662 AAAGAAAA-AAATGAAAAT
1 AAAGAAAATAAA--AAAAT
* *
1369680 AAATAAAATAAAGAAAGAC
1 AAAGAAAATAAA-AAA-AT
1369699 AAA-AGAAATAAAAAAAT
1 AAAGA-AAATAAAAAAAT
* *
1369716 AACATAAAGATAAAAAGAT
1 AA-AGAAA-ATAAAAAAAT
**
1369735 AAAGAAAATAAAAAAGGG
1 AAAGAAAATAAAAAA-AT
* *
1369753 ATA-AAAATAGAAAAA-
1 AAAGAAAATAAAAAAAT
1369768 AAAGAAAA-AATAATAAAT
1 AAAGAAAATAA-AA-AAAT
1369786 AAAGAAAATA
1 AAAGAAAATA
1369796 GCAACAATCT
Statistics
Matches: 91, Mismatches: 13, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
15 3 0.03
16 6 0.07
17 23 0.25
18 32 0.35
19 27 0.30
ACGTcount: A:0.76, C:0.01, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAGAAAATAAAAAAAT
Found at i:1369733 original size:36 final size:35
Alignment explanation
Indices: 1369661--1369749 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 35
1369651 AGAAATGTGT
*
1369661 AAAAGAAAAAAATGAAAATAAATAAAATAAAGAAAGA
1 AAAAGAAATAAA--AAAATAAATAAAATAAAGAAAGA
1369698 CAAAAGAAATAAAAAAATAACATAAAGAT-AA-AAAGA
1 -AAAAGAAATAAAAAAATAA-ATAAA-ATAAAGAAAGA
*
1369734 TAAAGAAAATAAAAAA
1 AAAAG-AAATAAAAAA
1369750 GGGATAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
35 4 0.09
36 22 0.48
37 7 0.15
38 13 0.28
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (35 bp):
AAAAGAAATAAAAAAATAAATAAAATAAAGAAAGA
Found at i:1369903 original size:26 final size:26
Alignment explanation
Indices: 1369874--1369923 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1369864 AACATCAAGG
1369874 GAATAA-AAATAAAGTAAAAATAAAGA
1 GAATAATAAA-AAAGTAAAAATAAAGA
*
1369900 GAATAATAAAAAATTAAAAATAAA
1 GAATAATAAAAAAGTAAAAATAAA
1369924 TACACAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (26 bp):
GAATAATAAAAAAGTAAAAATAAAGA
Found at i:1370108 original size:14 final size:14
Alignment explanation
Indices: 1370091--1370117 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1370081 TATAGTGCTT
1370091 AAATAAAAATAATC
1 AAATAAAAATAATC
1370105 AAATAAAAATAAT
1 AAATAAAAATAAT
1370118 AAAAATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATAAAAATAATC
Found at i:1370149 original size:16 final size:16
Alignment explanation
Indices: 1370097--1370154 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
1370087 GCTTAAATAA
*
1370097 AAATAATCAAATA-A-
1 AAATAATAAAATATAT
1370111 AAATAATAAAAATATAT
1 AAATAAT-AAAATATAT
* *
1370128 ATATAATAAAATATTT
1 AAATAATAAAATATAT
*
1370144 AAATAAGAAAA
1 AAATAATAAAA
1370155 AAAATATGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 7 0.19
15 5 0.14
16 18 0.50
17 6 0.17
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (16 bp):
AAATAATAAAATATAT
Found at i:1372341 original size:41 final size:41
Alignment explanation
Indices: 1372271--1372395 Score: 135
Period size: 43 Copynumber: 3.0 Consensus size: 41
1372261 GTAGAGTTGA
* ** * *
1372271 CACGATATCCTTCACCGTGAAGTTAAAATCGTGGATGTGTC
1 CACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGTC
* * **
1372312 CACGATATCCTCCGTCGTGGAGTTGAAATCATGGCTTTGTGGG
1 CACGATATCCTCCGTCGTGGAGTTGAAATCGTGG--ATGTGTC
*
1372355 TACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATG-GTC
1 CACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGTC
1372395 C
1 C
1372396 CTTTGTTGCG
Statistics
Matches: 67, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
40 1 0.01
41 30 0.45
43 36 0.54
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.30
Consensus pattern (41 bp):
CACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGTC
Found at i:1385743 original size:14 final size:14
Alignment explanation
Indices: 1385724--1385764 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1385714 GACAAAGGAA
1385724 ATAAAGAAAATAAC
1 ATAAAGAAAATAAC
*
1385738 ATAAAGATAAA-AAG
1 ATAAAGA-AAATAAC
1385752 ATAAAGAAAATAA
1 ATAAAGAAAATAA
1385765 AAAAAGGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.12
14 18 0.75
15 3 0.12
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (14 bp):
ATAAAGAAAATAAC
Found at i:1385743 original size:37 final size:37
Alignment explanation
Indices: 1385679--1385769 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
1385669 AAAAAATGTT
*
1385679 AAAGAAAAAAAATGAAAATAAATTAAAGA-AAGAAAGAC
1 AAAGAAAATAAA-GAAAATAAATTAAAGATAA-AAAGAC
* *
1385717 AAAGGAAATAAAGAAAATAACA-TAAAGATAAAAAGAT
1 AAAGAAAATAAAGAAAATAA-ATTAAAGATAAAAAGAC
1385754 AAAGAAAATAAA-AAAA
1 AAAGAAAATAAAGAAAA
1385770 GGATAAACAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
36 4 0.09
37 30 0.64
38 13 0.28
ACGTcount: A:0.75, C:0.02, G:0.12, T:0.11
Consensus pattern (37 bp):
AAAGAAAATAAAGAAAATAAATTAAAGATAAAAAGAC
Found at i:1385793 original size:26 final size:26
Alignment explanation
Indices: 1385764--1385818 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
1385754 AAAGAAAATA
*
1385764 AAAAAAGG-ATAAA-CATAAA-AATAG
1 AAAAAAGGAATAAATAATAAATAA-AG
1385788 AGAAAAAGGAATAAATAATAAATAAAG
1 A-AAAAAGGAATAAATAATAAATAAAG
1385815 AAAA
1 AAAA
1385819 TGGTAACAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 1 0.04
25 7 0.27
26 8 0.31
27 8 0.31
28 2 0.08
ACGTcount: A:0.73, C:0.02, G:0.13, T:0.13
Consensus pattern (26 bp):
AAAAAAGGAATAAATAATAAATAAAG
Found at i:1385810 original size:25 final size:25
Alignment explanation
Indices: 1385758--1385818 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
1385748 AAAGATAAAG
1385758 AAAAT-AA-AAAAAGGATAAACATA
1 AAAATAAAGAAAAAGGATAAACATA
*
1385781 AAAATAGAGAAAAAGGA-ATAA-ATA
1 AAAATAAAGAAAAAGGATA-AACATA
1385805 ATAAATAAAGAAAA
1 A-AAATAAAGAAAA
1385819 TGGTAACAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 5 0.16
24 6 0.19
25 21 0.66
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (25 bp):
AAAATAAAGAAAAAGGATAAACATA
Found at i:1386164 original size:16 final size:16
Alignment explanation
Indices: 1386112--1386169 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
1386102 CTTAAATAAA
*
1386112 AAATAATCAAATA-A-
1 AAATAATAAAATATAT
1386126 AAATAATAAAAATATAT
1 AAATAAT-AAAATATAT
* *
1386143 ATATAATAAAATATTT
1 AAATAATAAAATATAT
*
1386159 AAATAAGAAAA
1 AAATAATAAAA
1386170 AAAATACGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 7 0.19
15 5 0.14
16 18 0.50
17 6 0.17
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (16 bp):
AAATAATAAAATATAT
Found at i:1388708 original size:34 final size:34
Alignment explanation
Indices: 1388670--1388735 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
1388660 CGTTTAAATG
* * *
1388670 TTTGTGAATGTGTTTATTTAGAGTTCGTTTATCT
1 TTTGTGAATATATTCATTTAGAGTTCGTTTATCT
* *
1388704 TTTGTGAATATATTCGTTTAGTGTTCGTTTAT
1 TTTGTGAATATATTCATTTAGAGTTCGTTTAT
1388736 TGTTAATGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.18, C:0.06, G:0.20, T:0.56
Consensus pattern (34 bp):
TTTGTGAATATATTCATTTAGAGTTCGTTTATCT
Found at i:1394787 original size:2 final size:2
Alignment explanation
Indices: 1394780--1394819 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1394770 TATTTCAAAC
1394780 AT 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 AT
1394820 CGTAACCAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1395502 original size:2 final size:2
Alignment explanation
Indices: 1395497--1395527 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1395487 TTAAAAAAAA
*
1395497 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1395528 AATAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1396907 original size:3 final size:3
Alignment explanation
Indices: 1396899--1396987 Score: 126
Period size: 3 Copynumber: 29.0 Consensus size: 3
1396889 TTTATTTATC
1396899 TAA TAA TAA TAA TAA TATA TAA TTAA TAA TAA TAA T-A TATA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA -TAA TAA TAA TAA TAA TA-A TAA TAA
**
1396946 TAA TAA TTT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1396988 AAAGAAAACT
Statistics
Matches: 78, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.03
3 67 0.86
4 9 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1397236 original size:45 final size:45
Alignment explanation
Indices: 1397171--1397602 Score: 693
Period size: 45 Copynumber: 9.6 Consensus size: 45
1397161 AGATGACCCG
* * * *
1397171 AAACATCATGCACTAAAGGTCTTATAGATGACTCGAAGGTTTTGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGA
* * **
1397216 AAACATCATGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGA
*
1397261 AAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGA
*
1397306 AAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGA
*
1397351 AAAAATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGA
* * *
1397396 AAACATCATACATTGAAGGGCTTACAGATGACCCGAAGGCTTTGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGA
1397441 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGA
* * * *
1397486 AAACATCATACACTGAAGGGCTTACAGATGACCCAAAGGCTTTGC
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGA
*
1397531 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGA
1397576 AAACATCATGCACTGAAGGGCTTACAG
1 AAACATCATGCACTGAAGGGCTTACAG
1397603 TTGTGGGAAA
Statistics
Matches: 360, Mismatches: 27, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 360 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (45 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGA
Found at i:1397298 original size:20 final size:20
Alignment explanation
Indices: 1397273--1397344 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 20
1397263 ACATCATGCA
1397273 CTGAAGGGCTTACAGATGAC
1 CTGAAGGGCTTACAGATGAC
** *
1397293 CTGAAGGTTTTGAAAACATCATG-C
1 CTGAAGGGCTT----ACA-GATGAC
1397317 ACTGAAGGGCTTACAGATGAC
1 -CTGAAGGGCTTACAGATGAC
1397338 CTGAAGG
1 CTGAAGG
1397345 TTTTGAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
20 19 0.49
21 4 0.10
24 4 0.10
25 12 0.31
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (20 bp):
CTGAAGGGCTTACAGATGAC
Found at i:1397883 original size:19 final size:19
Alignment explanation
Indices: 1397846--1397883 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1397836 TTGTAAGGTA
*
1397846 TTTTTCATCACGAATCTTC
1 TTTTTCATCACGAAACTTC
1397865 TTTTTCAT-ACGAAAACTTC
1 TTTTTCATCACG-AAACTTC
1397884 ATGTTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (19 bp):
TTTTTCATCACGAAACTTC
Found at i:1398306 original size:22 final size:22
Alignment explanation
Indices: 1398251--1398307 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
1398241 AATAAAGCTT
* *
1398251 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATATA
1398273 TCATCTTTGAAGAGAGAATATA
1 TCATCTTTGAAGAGAGAATATA
1398295 TCATCTTTGAAGA
1 TCATCTTTGAAGA
1398308 ATGTAGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATATA
Found at i:1408110 original size:2 final size:2
Alignment explanation
Indices: 1408103--1408154 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
1408093 ATGTAAACAA
1408103 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1408142 AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT
1408155 TAAAGTAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 4 0.09
2 42 0.91
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1408127 original size:19 final size:19
Alignment explanation
Indices: 1408103--1408154 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
1408093 ATGTAAACAA
1408103 ATATATATATATATATAAT
1 ATATATATATATATATAAT
1408122 ATATATATATATATATAAT
1 ATATATATATATATATAAT
1408141 A-ATATATATA-ATAT
1 ATATATATATATATAT
1408155 TAAAGTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.12
18 9 0.27
19 20 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATATATATATATATAAT
Found at i:1408134 original size:150 final size:148
Alignment explanation
Indices: 1407810--1408140 Score: 398
Period size: 150 Copynumber: 2.2 Consensus size: 148
1407800 AGTTTTAAGA
* * * *
1407810 AAATATAT-TAATATATATATATATATTTTATTTTTATAAATAAGATATTTATTTACTTAAAAAT
1 AAATATATATAATATATATATATATATATAATTTATAAAAATAAGATATTTATTTACTTAAAAAT
*
1407874 ATCAGAAAAAGACTTCTAGGTGCTTTAAGACAGCTCATTTCTTAATATAAAAAAATAAATAAATA
66 ATCAGAAAAAGACTTCTAGGTGCTTTAAGACAGCCCATTTCTTAATATAAAAAAATAAATAAATA
** *
1407939 TTAATAAAACATTTCTAT
131 TTAATAAAACAAATATAT
* * * * ** * *
1407957 AAAAAAATAATTAAAATAAAT-TAATATATATAATTTATAAAAATATTATATTTATTTATTTAAG
1 AAATATAT-A-TAATATATATAT-ATATATATAATTTATAAAAATAAGATATTTATTTACTTAAA
* * *
1408021 AATATCAGAAAAGGACTTCTAGGTGCTTTAAGACATCCCATTTCTTAATATTAAAAAAT-AATAA
63 AATATCAGAAAAAGACTTCTAGGTGCTTTAAGACAGCCCATTTCTTAATATAAAAAAATAAATAA
*
1408085 ATATTAAAATGTAAACAAATATAT
128 ATATT--AAT-AAAACAAATATAT
*
1408109 ATATATATATAATATATATATATATATATAAT
1 AAATATATATAATATATATATATATATATAAT
1408141 AATATATATA
Statistics
Matches: 151, Mismatches: 25, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
147 6 0.04
149 11 0.07
150 115 0.76
151 5 0.03
152 14 0.09
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (148 bp):
AAATATATATAATATATATATATATATATAATTTATAAAAATAAGATATTTATTTACTTAAAAAT
ATCAGAAAAAGACTTCTAGGTGCTTTAAGACAGCCCATTTCTTAATATAAAAAAATAAATAAATA
TTAATAAAACAAATATAT
Found at i:1409479 original size:3 final size:3
Alignment explanation
Indices: 1409471--1409535 Score: 94
Period size: 3 Copynumber: 21.0 Consensus size: 3
1409461 TTTATTTATC
**
1409471 TAA TAA TAA TAA TAA TATA TAA TTAA TAA TAA TAA TAA TTT TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA -TAA TAA TAA TAA TAA TAA TAA TAA
1409518 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1409536 GCAAACTTGA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
3 50 0.89
4 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1412663 original size:14 final size:15
Alignment explanation
Indices: 1412639--1412667 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1412629 AATTTTTTGC
1412639 ATAGTTTTAGGGTTT
1 ATAGTTTTAGGGTTT
1412654 ATAG-TTTAGGGTTT
1 ATAGTTTTAGGGTTT
1412668 GGAATTTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (15 bp):
ATAGTTTTAGGGTTT
Found at i:1412716 original size:20 final size:21
Alignment explanation
Indices: 1412670--1412716 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1412660 TAGGGTTTGG
*
1412670 AATTTAGGGGTTATGGTTTAT
1 AATTTAGGGGTTATGGTTTAA
* *
1412691 AGTTTAGGGTTTA-GGTTTAA
1 AATTTAGGGGTTATGGTTTAA
1412711 AATTTA
1 AATTTA
1412717 AGGTGTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (21 bp):
AATTTAGGGGTTATGGTTTAA
Found at i:1415753 original size:19 final size:19
Alignment explanation
Indices: 1415729--1415770 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1415719 AAAATAAAAG
1415729 CATGTATTCTTACTCTTAC
1 CATGTATTCTTACTCTTAC
*
1415748 CATGTATTCTTACTCTTAG
1 CATGTATTCTTACTCTTAC
1415767 CATG
1 CATG
1415771 AATTAAACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.24, G:0.10, T:0.45
Consensus pattern (19 bp):
CATGTATTCTTACTCTTAC
Found at i:1416108 original size:24 final size:24
Alignment explanation
Indices: 1416060--1416108 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1416050 AAATAAAAAT
*
1416060 AATTAAATAGTATTTATAAATTTTA
1 AATTAAATA-TATTTAAAAATTTTA
1416085 AATTAAAT-TATTCTAAAAATTTTA
1 AATTAAATATATT-TAAAAATTTTA
1416109 TTTATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 10 0.45
25 8 0.36
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
AATTAAATATATTTAAAAATTTTA
Found at i:1416183 original size:23 final size:23
Alignment explanation
Indices: 1416157--1416206 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1416147 TTTTAAAATT
1416157 ATATTATTTATTTATTTGAAACA
1 ATATTATTTATTTATTTGAAACA
*
1416180 ATATTATTTATTTATTTGAAATA
1 ATATTATTTATTTATTTGAAACA
1416203 ATAT
1 ATAT
1416207 CACTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (23 bp):
ATATTATTTATTTATTTGAAACA
Found at i:1417358 original size:73 final size:74
Alignment explanation
Indices: 1417274--1417463 Score: 201
Period size: 73 Copynumber: 2.6 Consensus size: 74
1417264 AAACAATTCA
* * *
1417274 AAATTTTAAATATTGATACTTAATAT-ATGATGATCGATATTTTTAAATATTGGAAAAA-TTGAA
1 AAATTTAAAATATTGATACTTAATATGATAATGATCGATACTTTTAAATATT-GAAAAAGTT-AA
*
1417337 T-ATAAGATCG
64 TAAAAAGATCG
* * * *
1417347 AAATTTAAAATATTGATACTT-ATGTGGTAATGATTGATACTTTTAAATATTGAAAAAGTTTATA
1 AAATTTAAAATATTGATACTTAATATGATAATGATCGATACTTTTAAATATTGAAAAAGTTAATA
1417411 AAAAGATCG
66 AAAAGATCG
* * ** * *
1417420 AAATTTGAAATACTGATACTT-ATGCGATGATGATTGATACTTTT
1 AAATTTAAAATATTGATACTTAATATGATAATGATCGATACTTTT
1417464 CTATTTTGAA
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
72 11 0.11
73 90 0.89
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (74 bp):
AAATTTAAAATATTGATACTTAATATGATAATGATCGATACTTTTAAATATTGAAAAAGTTAATA
AAAAGATCG
Found at i:1417476 original size:73 final size:73
Alignment explanation
Indices: 1417303--1417463 Score: 209
Period size: 73 Copynumber: 2.2 Consensus size: 73
1417293 TTAATATATG
* * * * *
1417303 ATGATCGATATTTTTAAATATTGGAAAAA-TTGA-ATATAAGATCGAAATTTAAAATATTGATAC
1 ATGATTGATACTTTTAAATATT-GAAAAAGTTTATA-AAAAGATCGAAATTTAAAATACTGATAC
* *
1417366 TTATGTGGTA
64 TTATGCGATA
*
1417376 ATGATTGATACTTTTAAATATTGAAAAAGTTTATAAAAAGATCGAAATTTGAAATACTGATACTT
1 ATGATTGATACTTTTAAATATTGAAAAAGTTTATAAAAAGATCGAAATTTAAAATACTGATACTT
*
1417441 ATGCGATG
66 ATGCGATA
1417449 ATGATTGATACTTTT
1 ATGATTGATACTTTT
1417464 CTATTTTGAA
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
72 6 0.08
73 70 0.91
74 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.39
Consensus pattern (73 bp):
ATGATTGATACTTTTAAATATTGAAAAAGTTTATAAAAAGATCGAAATTTAAAATACTGATACTT
ATGCGATA
Found at i:1417484 original size:33 final size:33
Alignment explanation
Indices: 1417447--1417518 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
1417437 ACTTATGCGA
1417447 TGATGATTGATACTTTTCTATTTTGAAAAAAAT
1 TGATGATTGATACTTTTCTATTTTGAAAAAAAT
1417480 TGATGATTGATACTTTTCTATTTTGAAAAAAAT
1 TGATGATTGATACTTTTCTATTTTGAAAAAAAT
1417513 TGATGA
1 TGATGA
1417519 AGATGATCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (33 bp):
TGATGATTGATACTTTTCTATTTTGAAAAAAAT
Found at i:1417719 original size:2 final size:2
Alignment explanation
Indices: 1417712--1417748 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1417702 TCTCATTTTC
1417712 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1417749 TAAATTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1418719 original size:170 final size:169
Alignment explanation
Indices: 1418522--1418839 Score: 388
Period size: 170 Copynumber: 1.9 Consensus size: 169
1418512 GAAACTCTGG
* *
1418522 TAATATTTTAGGCACAACTAATTTTATTAAAAAGAAAATGAACATTCCAGATCTCAACCTACTTT
1 TAATATTTTAGGCACAACCAATTTTATTAAAAAGAAAATGAACATTCCAGATCACAACCTACTTT
* * * * * *
1418587 CTTGGTGAA-CCTTAATATTCTTGGGCGCAA-CTGAATTTCTTATAGATACTCATAACATTTTCA
66 CTTAG-CAAGCCATAATATTCTTGGGCACAACCAG-ATTTCTTATAGATACTCATAACATTTCCA
* *
1418650 GCTTTTAACTTATTTTGTTATCGTGAGAATGTCTAATGCTGA
129 GC-TTTAAATAATTTTGTTATCGTGAGAATGTCTAATGCTGA
** * * * * * *
1418692 TAATATTTTAGGTGCAACCGATTTTATTATAAAGAAAATTAACATTTCATATCACAACTTACTTT
1 TAATATTTTAGGCACAACCAATTTTATTAAAAAGAAAATGAACATTCCAGATCACAACCTACTTT
* ** * *
1418757 CTTAGCAAGCGATAATATTCTTGGGCATTACCAGATTTCTTATAGATATTCATTACATTTCCAGC
66 CTTAGCAAGCCATAATATTCTTGGGCACAACCAGATTTCTTATAGATACTCATAACATTTCCAGC
1418822 TTTAAATAATTTTGTTAT
131 TTTAAATAATTTTGTTAT
1418840 TGATACTTAC
Statistics
Matches: 123, Mismatches: 23, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
169 18 0.15
170 103 0.84
171 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (169 bp):
TAATATTTTAGGCACAACCAATTTTATTAAAAAGAAAATGAACATTCCAGATCACAACCTACTTT
CTTAGCAAGCCATAATATTCTTGGGCACAACCAGATTTCTTATAGATACTCATAACATTTCCAGC
TTTAAATAATTTTGTTATCGTGAGAATGTCTAATGCTGA
Found at i:1419266 original size:22 final size:21
Alignment explanation
Indices: 1419227--1419280 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 21
1419217 ATATATGTTT
*
1419227 AAAATATTTTAAAATAATATA
1 AAAATATTATAAAATAATATA
* *
1419248 AAAATATTCATAAAGTAATCTA
1 AAAATATT-ATAAAATAATATA
*
1419270 AATAT-TTATAA
1 AAAATATTATAA
1419281 TATTTAGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 4 0.14
21 10 0.36
22 14 0.50
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAATATTATAAAATAATATA
Found at i:1420401 original size:42 final size:43
Alignment explanation
Indices: 1420288--1420405 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
1420278 GTCATGACAA
* * * *
1420288 TTAGTGGTGTTTGTTCCCAAAATGCCACTAAAAGACCTATCCT
1 TTAGTTGTGTTTGTTCCCAAAATGCCGCTAAATGACCTATACT
*
1420331 TTAGTTGTGTTTGTTCCCAAAATACCGCTAAATGACCT-TACT
1 TTAGTTGTGTTTGTTCCCAAAATGCCGCTAAATGACCTATACT
* *
1420373 TTTGCTT-TGTTTGTTCCCAAAACGCCGCTAAAT
1 TTAG-TTGTGTTTGTTCCCAAAATGCCGCTAAAT
1420406 ATCTTAACCT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
42 30 0.45
43 36 0.55
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.36
Consensus pattern (43 bp):
TTAGTTGTGTTTGTTCCCAAAATGCCGCTAAATGACCTATACT
Found at i:1423331 original size:25 final size:25
Alignment explanation
Indices: 1423297--1423349 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1423287 CCTCCATGGT
1423297 GAGCGGCGTTCGTGAGATGGAGAGG
1 GAGCGGCGTTCGTGAGATGGAGAGG
*
1423322 GAGCTGCGTTCGTGAGATGGAGAGG
1 GAGCGGCGTTCGTGAGATGGAGAGG
1423347 GAG
1 GAG
1423350 AGAAATAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.21, C:0.11, G:0.51, T:0.17
Consensus pattern (25 bp):
GAGCGGCGTTCGTGAGATGGAGAGG
Done.