Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 28 of 147
Found at i:5749654 original size:26 final size:26
Alignment explanation
Indices: 5749626--5749674 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
5749616 TAAAAAATAA
*
5749626 AAAATATAGGTTTGAAAA-TTTTATT
1 AAAATATAAGTTTGAAAACTTTTATT
5749651 AAAATATAAGTTTGAAAACTTTTA
1 AAAATATAAGTTTGAAAACTTTTA
5749675 ATTTTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATATAAGTTTGAAAACTTTTATT
Found at i:5753080 original size:6 final size:6
Alignment explanation
Indices: 5753071--5753137 Score: 107
Period size: 6 Copynumber: 11.2 Consensus size: 6
5753061 TTTAAGTCCA
* * *
5753071 GATGAT GATGGT GATGGA GATGGT GATGGT GATGGA GATGGT GATGGT
1 GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT
5753119 GATGGT GATGGT GATGGT G
1 GATGGT GATGGT GATGGT G
5753138 CGAATTTTGG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.21, C:0.00, G:0.49, T:0.30
Consensus pattern (6 bp):
GATGGT
Found at i:5753097 original size:18 final size:18
Alignment explanation
Indices: 5753070--5753137 Score: 118
Period size: 18 Copynumber: 3.8 Consensus size: 18
5753060 GTTTAAGTCC
*
5753070 AGATGATGATGGTGATGG
1 AGATGGTGATGGTGATGG
5753088 AGATGGTGATGGTGATGG
1 AGATGGTGATGGTGATGG
5753106 AGATGGTGATGGTGATGG
1 AGATGGTGATGGTGATGG
*
5753124 TGATGGTGATGGTG
1 AGATGGTGATGGTG
5753138 CGAATTTTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.22, C:0.00, G:0.49, T:0.29
Consensus pattern (18 bp):
AGATGGTGATGGTGATGG
Found at i:5753503 original size:18 final size:18
Alignment explanation
Indices: 5753480--5753604 Score: 105
Period size: 18 Copynumber: 6.9 Consensus size: 18
5753470 ATGGTTATTA
5753480 TCCACCTCAAATGTATCC
1 TCCACCTCAAATGTATCC
*
5753498 TCCACCTCCTCAAATATATCC
1 TCCA---CCTCAAATGTATCC
*
5753519 TCCACCTCAAATGTATCAG
1 TCCACCTCAAATGTATC-C
* * *
5753538 T-TACCACAAATGTACCC
1 TCCACCTCAAATGTATCC
* * *
5753555 ACCACCACAAATGTATCA
1 TCCACCTCAAATGTATCC
*
5753573 T---CCTCAAATATATCC
1 TCCACCTCAAATGTATCC
5753588 TCCACCTCAAATGTATC
1 TCCACCTCAAATGTATC
5753605 AAGAACAAAG
Statistics
Matches: 83, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
15 12 0.14
18 53 0.64
19 1 0.01
21 17 0.20
ACGTcount: A:0.33, C:0.36, G:0.05, T:0.26
Consensus pattern (18 bp):
TCCACCTCAAATGTATCC
Found at i:5753510 original size:21 final size:21
Alignment explanation
Indices: 5753484--5753526 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5753474 TTATTATCCA
*
5753484 CCTCAAATGTATCCTCCACCT
1 CCTCAAATATATCCTCCACCT
5753505 CCTCAAATATATCCTCCACCT
1 CCTCAAATATATCCTCCACCT
5753526 C
1 C
5753527 AAATGTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.44, G:0.02, T:0.28
Consensus pattern (21 bp):
CCTCAAATATATCCTCCACCT
Found at i:5754569 original size:18 final size:18
Alignment explanation
Indices: 5754543--5754581 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5754533 GATTTTATGC
*
5754543 AAAAAAGAGGAAGGAACT
1 AAAAAAGAGGAAGAAACT
* *
5754561 AAAAGAGAGGGAGAAACT
1 AAAAAAGAGGAAGAAACT
5754579 AAA
1 AAA
5754582 GGTGACTGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.05, G:0.28, T:0.05
Consensus pattern (18 bp):
AAAAAAGAGGAAGAAACT
Found at i:5766152 original size:21 final size:22
Alignment explanation
Indices: 5766128--5766168 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5766118 ATAAAATATA
*
5766128 TATTTTTTA-TTTTATTAAATT
1 TATTTATTATTTTTATTAAATT
5766149 TATTTATTATTTTTATTAAA
1 TATTTATTATTTTTATTAAA
5766169 ATTTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTTATTATTTTTATTAAATT
Found at i:5767368 original size:17 final size:16
Alignment explanation
Indices: 5767348--5767383 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
5767338 ATTTCAAAAA
5767348 TTTTTATATTTTTTTGT
1 TTTTTA-ATTTTTTTGT
5767365 TTTTTAATTTTTTTGT
1 TTTTTAATTTTTTTGT
5767381 TTT
1 TTT
5767384 GAAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTTAATTTTTTTGT
Found at i:5768466 original size:4 final size:4
Alignment explanation
Indices: 5768459--5768512 Score: 60
Period size: 4 Copynumber: 14.2 Consensus size: 4
5768449 AAAGAAGAAA
* * *
5768459 AAAT AAAT AAAT AAAT AAAT -AAC AAAT -AAT ATAT AAA- ATAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
5768504 AAAT AAAT A
1 AAAT AAAT A
5768513 TTTGGGCCTA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
3 7 0.17
4 34 0.83
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:5768494 original size:14 final size:15
Alignment explanation
Indices: 5768467--5768509 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
5768457 AAAAATAAAT
5768467 AAATAAATAAATAAC
1 AAATAAATAAATAAC
*
5768482 AAAT-AATATATAA-
1 AAATAAATAAATAAC
5768495 AATATAAATAAATAA
1 AA-ATAAATAAATAA
5768510 ATATTTGGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 2 0.08
14 10 0.42
15 12 0.50
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAAATAAATAAC
Found at i:5768694 original size:21 final size:21
Alignment explanation
Indices: 5768661--5768711 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5768651 TTGTTAGAAG
*
5768661 TTTAATAATCTTCGACAAAAT
1 TTTAATAACCTTCGACAAAAT
* * *
5768682 TTTAGTAACCTTCTACATAAT
1 TTTAATAACCTTCGACAAAAT
*
5768703 TTTGATAAC
1 TTTAATAAC
5768712 TTTTGATATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (21 bp):
TTTAATAACCTTCGACAAAAT
Found at i:5768780 original size:21 final size:20
Alignment explanation
Indices: 5768698--5768793 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 20
5768688 AACCTTCTAC
*
5768698 ATAATTTTGATAACTTTTGAT
1 ATAATTTTGATAA-TCTTGAT
* * *
5768719 ATTAGTTTGATAATTTATGAT
1 ATAATTTTGATAATCT-TGAT
* *
5768740 ATAA-TTTGGTAAATATTGAT
1 ATAATTTTGAT-AATCTTGAT
5768760 ATAATTTTGATAATCTGTGAT
1 ATAATTTTGATAATCT-TGAT
*
5768781 -TAAATTTTAATAA
1 AT-AATTTTGATAA
5768794 CATCTTAATG
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
20 21 0.34
21 41 0.66
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (20 bp):
ATAATTTTGATAATCTTGAT
Found at i:5769153 original size:22 final size:21
Alignment explanation
Indices: 5769114--5769207 Score: 66
Period size: 22 Copynumber: 4.3 Consensus size: 21
5769104 AAGTTATAAT
*
5769114 TGATTTACTA-TCATATTATCGA
1 TGATTTACTACT-AAATTAT-GA
5769136 TGATTTACTACTAAATTA-GTA
1 TGATTTACTACTAAATTATG-A
* * *
5769157 TTGATTTACAACTAATTTATATA
1 -TGATTTACTACTAAATTAT-GA
* *
5769180 TGATTTACTACAAAATAATGAA
1 TGATTTACTACTAAATTATG-A
5769202 TGATTT
1 TGATTT
5769208 TTCATTAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 53 0.93
23 2 0.04
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.44
Consensus pattern (21 bp):
TGATTTACTACTAAATTATGA
Found at i:5769905 original size:17 final size:18
Alignment explanation
Indices: 5769868--5769906 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5769858 TGAACGCGGT
*
5769868 CAATCTCTTATTTACCAA
1 CAATCTCTCATTTACCAA
*
5769886 CAATCTCTCA-TTAGCAA
1 CAATCTCTCATTTACCAA
5769903 CAAT
1 CAAT
5769907 ACTGGGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (18 bp):
CAATCTCTCATTTACCAA
Found at i:5770127 original size:22 final size:22
Alignment explanation
Indices: 5770102--5770171 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
5770092 TGCCAACAAA
5770102 GTTATTATTAATTTACTATTAT
1 GTTATTATTAATTTACTATTAT
*
5770124 GTTATT-TATGATTTACTATTAAT
1 GTTATTAT-TAATTTACTATT-AT
* * *
5770147 -TTATTACTAA-TAACTATTAA
1 GTTATTATTAATTTACTATTAT
5770167 GTTAT
1 GTTAT
5770172 CGATGATTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.03
21 12 0.31
22 24 0.62
23 2 0.05
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (22 bp):
GTTATTATTAATTTACTATTAT
Found at i:5770183 original size:21 final size:20
Alignment explanation
Indices: 5770100--5770192 Score: 69
Period size: 21 Copynumber: 4.3 Consensus size: 20
5770090 TCTGCCAACA
*
5770100 AAGTTATTATTAATTTACTATT
1 AAGTTATTA-TGA-TTACTATT
*
5770122 ATGTTATTTATGATTTACTATT
1 AAGTTA-TTATGA-TTACTATT
* * *
5770144 AATTTATTACTAATAACTATT
1 AAGTTATTA-TGATTACTATT
* *
5770165 AAGTTATCGATGATTACTACT
1 AAGTTAT-TATGATTACTATT
5770186 AAGTTAT
1 AAGTTAT
5770193 ATTGATCACT
Statistics
Matches: 57, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
21 31 0.54
22 23 0.40
23 3 0.05
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (20 bp):
AAGTTATTATGATTACTATT
Found at i:5772164 original size:21 final size:21
Alignment explanation
Indices: 5772124--5772166 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
5772114 TATTATCTAA
*
5772124 TATAGTAACTTTAAAATTTTT
1 TATAGTAACCTTAAAATTTTT
5772145 TATAG-AACCTTAAAATTTTT
1 TATAGTAACCTTAAAATTTTT
5772165 TA
1 TA
5772167 ACTTATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.49
Consensus pattern (21 bp):
TATAGTAACCTTAAAATTTTT
Found at i:5776930 original size:13 final size:13
Alignment explanation
Indices: 5776912--5776945 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
5776902 TAAAATTATT
*
5776912 ATTTAATACTTTA
1 ATTTAATACATTA
5776925 ATTTAATACATTA
1 ATTTAATACATTA
5776938 ATTTAATA
1 ATTTAATA
5776946 AAAATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTAATACATTA
Found at i:5777579 original size:20 final size:19
Alignment explanation
Indices: 5777554--5777597 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
5777544 CCAAACTAAA
* *
5777554 TTATATATTTTTATTAGTTT
1 TTATATATATTT-TTAATTT
5777574 TTATATATATTTTTAATTT
1 TTATATATATTTTTAATTT
5777593 TTATA
1 TTATA
5777598 AAATAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TTATATATATTTTTAATTT
Found at i:5777651 original size:12 final size:12
Alignment explanation
Indices: 5777619--5777672 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
5777609 GTATTTAATA
5777619 TAAAAATCTAT-T
1 TAAAAAT-TATAT
5777631 T-AAAA-TATAT
1 TAAAAATTATAT
5777641 TAAAAATTATAT
1 TAAAAATTATAT
*
5777653 TAAAATAATATAT
1 TAAAA-ATTATAT
5777666 ATAAAAA
1 -TAAAAA
5777673 ACAATTTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
9 3 0.08
10 2 0.06
11 8 0.22
12 11 0.31
13 7 0.19
14 5 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
TAAAAATTATAT
Found at i:5778157 original size:11 final size:11
Alignment explanation
Indices: 5778141--5778310 Score: 62
Period size: 11 Copynumber: 15.7 Consensus size: 11
5778131 TAACTTATAT
5778141 ATTTATTACTA
1 ATTTATTACTA
* * *
5778152 ATTTATAAATG
1 ATTTATTACTA
5778163 ATTTATTA-TAA
1 ATTTATTACT-A
* * *
5778174 AATTATCAATA
1 ATTTATTACTA
5778185 A-TTA--ACTA
1 ATTTATTACTA
*
5778193 ATTTACTACTA
1 ATTTATTACTA
* *
5778204 AATTATCACTA
1 ATTTATTACTA
* * *
5778215 ATGTATAATTA
1 ATTTATTACTA
* *
5778226 AATTATTAGTA
1 ATTTATTACTA
5778237 ATTTATTACTA
1 ATTTATTACTA
* * *
5778248 CA-TTGTTAGTG
1 -ATTTATTACTA
*
5778259 ATTTATTATTA
1 ATTTATTACTA
* * *
5778270 AGTTATCAATA
1 ATTTATTACTA
*
5778281 ATTTACTACTA
1 ATTTATTACTA
* * *
5778292 AATTATTAATG
1 ATTTATTACTA
5778303 ATTTATTA
1 ATTTATTA
5778311 TTATATTATT
Statistics
Matches: 113, Mismatches: 39, Indels: 14
0.68 0.23 0.08
Matches are distributed among these distances:
8 4 0.04
9 3 0.03
10 5 0.04
11 99 0.88
12 2 0.02
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (11 bp):
ATTTATTACTA
Found at i:5778169 original size:26 final size:26
Alignment explanation
Indices: 5778115--5778169 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
5778105 GTAATTAATA
* *
5778115 ATTTATTACAAAGTTATAACTTATAT
1 ATTTATTACAAAGTTATAAATGATAT
* * *
5778141 ATTTATTACTAATTTATAAATGATTT
1 ATTTATTACAAAGTTATAAATGATAT
5778167 ATT
1 ATT
5778170 ATAAAATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (26 bp):
ATTTATTACAAAGTTATAAATGATAT
Found at i:5778215 original size:22 final size:22
Alignment explanation
Indices: 5778189--5778297 Score: 76
Period size: 22 Copynumber: 5.0 Consensus size: 22
5778179 TCAATAATTA
5778189 ACTAATTTACTACTAAATTATC
1 ACTAATTTACTACTAAATTATC
* * *
5778211 ACTAATGTA-TAATTAAATTATT
1 ACTAATTTACT-ACTAAATTATC
* * * * *
5778233 AGTAATTTATTACTACATTGTT
1 ACTAATTTACTACTAAATTATC
* * * * *
5778255 AGTGATTTATTATTAAGTTATC
1 ACTAATTTACTACTAAATTATC
*
5778277 AATAATTTACTACTAAATTAT
1 ACTAATTTACTACTAAATTAT
5778298 TAATGATTTA
Statistics
Matches: 66, Mismatches: 19, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
21 1 0.02
22 64 0.97
23 1 0.02
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (22 bp):
ACTAATTTACTACTAAATTATC
Found at i:5778239 original size:44 final size:43
Alignment explanation
Indices: 5778191--5778503 Score: 171
Period size: 44 Copynumber: 7.2 Consensus size: 43
5778181 AATAATTAAC
* * * * *
5778191 TAATTTACTACTAAATTATCACTAATGTATAATTAAATTATTA
1 TAATTTACTACTAAATTATTAATGATTTATTATTAAATTATTA
* * * * * *
5778234 GTAATTTATTACTACATTGTTAGTGATTTATTATTAAGTTATCAA
1 -TAATTTACTACTAAATTATTAATGATTTATTATTAAATTAT-TA
*
5778279 TAATTTACTACTAAATTATTAATGATTTATTATTATATTATTA
1 TAATTTACTACTAAATTATTAATGATTTATTATTAAATTATTA
* ** ** * *
5778322 TATATTTACTATTATGTTA-TAATTGATTTACAACTAAATTTTTA
1 TA-ATTTACTACTAAATTATTAA-TGATTTATTATTAAATTATTA
* * * ** * * *
5778366 TTATTTACTACAAAATTATCACCGATCTACTATTAAATTATCCA
1 TAATTTACTACTAAATTATTAATGATTTATTATTAAATTAT-TA
* * * * * *
5778410 TGATTCACTACCAAGTTATCATTGATTTA-TATTAAATTATTCA
1 TAATTTACTACTAAATTATTAATGATTTATTATTAAATTATT-A
* * * * * * * *
5778453 TGATTTATTATTAAGTTATCATTGATTAATAATTAAATTATTGA
1 TAATTTACTACTAAATTATTAATGATTTATTATTAAATTATT-A
*
5778497 TGATTTA
1 TAATTTA
5778504 TTATTAAGTT
Statistics
Matches: 209, Mismatches: 53, Indels: 14
0.76 0.19 0.05
Matches are distributed among these distances:
43 68 0.33
44 140 0.67
45 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.48
Consensus pattern (43 bp):
TAATTTACTACTAAATTATTAATGATTTATTATTAAATTATTA
Found at i:5778306 original size:22 final size:22
Alignment explanation
Indices: 5778222--5778515 Score: 139
Period size: 22 Copynumber: 13.5 Consensus size: 22
5778212 CTAATGTATA
* * *
5778222 ATTAAATTATTAGTAATTTATT
1 ATTAAATTATTAATGATTTACT
* * * * *
5778244 ACTACATTGTTAGTGATTTATT
1 ATTAAATTATTAATGATTTACT
* * *
5778266 ATTAAGTTATCAATAATTTACT
1 ATTAAATTATTAATGATTTACT
* *
5778288 ACTAAATTATTAATGATTTATT
1 ATTAAATTATTAATGATTTACT
*
5778310 ATTATATTATTATAT-ATTTACT
1 ATTAAATTATTA-ATGATTTACT
** *
5778332 ATTATGTTA-TAATTGATTTACA
1 ATTAAATTATTAA-TGATTTACT
* * *
5778354 ACTAAATT-TTTATTATTTACT
1 ATTAAATTATTAATGATTTACT
** * ** *
5778375 ACAAAATTATCACCGATCTACT
1 ATTAAATTATTAATGATTTACT
** *
5778397 ATTAAATTATCCATGATTCACT
1 ATTAAATTATTAATGATTTACT
** * * *
5778419 ACCAAGTTATCATTGATTTA-T
1 ATTAAATTATTAATGATTTACT
* *
5778440 ATTAAATTATTCATGATTTATT
1 ATTAAATTATTAATGATTTACT
* * * *
5778462 ATTAAGTTATCATTGA-TTAAT
1 ATTAAATTATTAATGATTTACT
* *
5778483 AATTAAATTATTGATGATTTATT
1 -ATTAAATTATTAATGATTTACT
*
5778506 ATTAAGTTAT
1 ATTAAATTAT
5778516 ATTGATTGAC
Statistics
Matches: 199, Mismatches: 65, Indels: 16
0.71 0.23 0.06
Matches are distributed among these distances:
20 1 0.01
21 36 0.18
22 156 0.78
23 6 0.03
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (22 bp):
ATTAAATTATTAATGATTTACT
Found at i:5778520 original size:43 final size:43
Alignment explanation
Indices: 5778396--5778522 Score: 175
Period size: 43 Copynumber: 3.0 Consensus size: 43
5778386 ACCGATCTAC
* * * ** *
5778396 TATTAAATTATCCATGATTCACTACCAAGTTATCATTGATTTA
1 TATTAAATTATTCATGATTTATTATTAAGTTATCATTGATTAA
5778439 TATTAAATTATTCATGATTTATTATTAAGTTATCATTGATTAA
1 TATTAAATTATTCATGATTTATTATTAAGTTATCATTGATTAA
*
5778482 TAATTAAATTATTGATGATTTATTATTAAGTTAT-ATTGATT
1 T-ATTAAATTATTCATGATTTATTATTAAGTTATCATTGATT
5778523 GACATTTAAG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
43 45 0.59
44 31 0.41
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (43 bp):
TATTAAATTATTCATGATTTATTATTAAGTTATCATTGATTAA
Found at i:5778672 original size:22 final size:22
Alignment explanation
Indices: 5778647--5778707 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
5778637 ACTAAAATCG
5778647 ATTTACTATTAAATTATCAATA
1 ATTTACTATTAAATTATCAATA
*
5778669 ATTTGCTATTAAATTATCAATA
1 ATTTACTATTAAATTATCAATA
* *
5778691 ATTTATTATTAAGTTAT
1 ATTTACTATTAAATTAT
5778708 TAATGATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (22 bp):
ATTTACTATTAAATTATCAATA
Found at i:5778736 original size:19 final size:18
Alignment explanation
Indices: 5778714--5778776 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 18
5778704 TTATTAATGA
5778714 TTATTTTTTAAATTATTAC
1 TTATTTTTTAAATTATT-C
5778733 TTATTTTTCATTAAATTATTC
1 TTA-TTTT--TTAAATTATTC
* * *
5778754 TTGATTTATTAATTTATTT
1 TT-ATTTTTTAAATTATTC
5778773 TTAT
1 TTAT
5778777 GTATTTACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 2 0.05
19 14 0.38
20 4 0.11
21 6 0.16
22 11 0.30
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (18 bp):
TTATTTTTTAAATTATTC
Found at i:5778816 original size:22 final size:22
Alignment explanation
Indices: 5778791--5778839 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
5778781 TTACAATTAC
5778791 ATTATAATTA-ATTTACTACTAA
1 ATTATAA-TACATTTACTACTAA
*
5778813 ATTATTATACATTTACTACTAA
1 ATTATAATACATTTACTACTAA
*
5778835 GTTAT
1 ATTAT
5778840 CAAGAAGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTATAATACATTTACTACTAA
Found at i:5780048 original size:15 final size:15
Alignment explanation
Indices: 5780028--5780069 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
5780018 TATTTGTGTC
5780028 TTATTTGTGTTAAAA
1 TTATTTGTGTTAAAA
* *
5780043 TTATTTATGTTAAGA
1 TTATTTGTGTTAAAA
5780058 TTATTTGTGTTA
1 TTATTTGTGTTA
5780070 TATCTAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (15 bp):
TTATTTGTGTTAAAA
Found at i:5783897 original size:14 final size:14
Alignment explanation
Indices: 5783875--5783908 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5783865 GTAATTTATA
5783875 TTTAAAAATAATAT
1 TTTAAAAATAATAT
*
5783889 TTTATAAATAATAT
1 TTTAAAAATAATAT
*
5783903 ATTAAA
1 TTTAAA
5783909 TTAAAATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTAAAAATAATAT
Found at i:5784486 original size:19 final size:19
Alignment explanation
Indices: 5784464--5784513 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
5784454 ATACATAGTT
5784464 TAATT-TTTATAAATAAAAA
1 TAATTATTT-TAAATAAAAA
*
5784483 TAATTATTTTATATAAAAA
1 TAATTATTTTAAATAAAAA
5784502 T--TTA-TTTAAATA
1 TAATTATTTTAAATA
5784514 TATTAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 7 0.25
17 3 0.11
19 15 0.54
20 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATTATTTTAAATAAAAA
Found at i:5784527 original size:12 final size:12
Alignment explanation
Indices: 5784491--5784548 Score: 54
Period size: 11 Copynumber: 5.2 Consensus size: 12
5784481 AATAATTATT
5784491 TTATA-TAAAAA
1 TTATATTAAAAA
*
5784502 TT-TATT-TAAA
1 TTATATTAAAAA
5784512 -TATATTAAAAA
1 TTATATTAAAAA
5784523 TTATATT-AAAA
1 TTATATTAAAAA
*
5784534 TAATATATAAAAA
1 TTATAT-TAAAAA
5784547 TT
1 TT
5784549 TTAAATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
9 1 0.03
10 9 0.24
11 15 0.41
12 7 0.19
13 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TTATATTAAAAA
Found at i:5784552 original size:21 final size:22
Alignment explanation
Indices: 5784492--5784549 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
5784482 ATAATTATTT
*
5784492 TATATAAAAATTTATTTAAATA
1 TATATAAAAATTTATTAAAATA
5784514 TAT-TAAAAATTATATTAAAATAA
1 TATATAAAAATT-TATTAAAAT-A
5784537 TATATAAAAATTT
1 TATATAAAAATTT
5784550 TAAATTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 8 0.25
22 11 0.34
23 5 0.16
24 8 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATATAAAAATTTATTAAAATA
Found at i:5785447 original size:19 final size:19
Alignment explanation
Indices: 5785423--5785466 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
5785413 AACGTGCGAG
*
5785423 TTTAATCGAATTTT-TATAT
1 TTTAATAGAATTTTAT-TAT
*
5785442 TTTAATATAATTTTATTAT
1 TTTAATAGAATTTTATTAT
5785461 TTTAAT
1 TTTAAT
5785467 TAATAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTAATAGAATTTTATTAT
Found at i:5785457 original size:18 final size:18
Alignment explanation
Indices: 5785434--5785470 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5785424 TTAATCGAAT
5785434 TTTTA-TATTTTAATATAA
1 TTTTATTATTTTAAT-TAA
5785452 TTTTATTATTTTAATTAA
1 TTTTATTATTTTAATTAA
5785470 T
1 T
5785471 AAAATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTATTATTTTAATTAA
Found at i:5785894 original size:34 final size:32
Alignment explanation
Indices: 5785821--5785886 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 32
5785811 TTTCAAAAAT
* * *
5785821 AAATTTTGAAAAATCATAAATCTTTTTGTAAAT
1 AAATTTTGAAAAATCATAAAAC-TTTTCTAAAG
5785854 AAATTTTCGAAAAATCATAAAAC-TTTCTAAAG
1 AAATTTT-GAAAAATCATAAAACTTTTCTAAAG
5785886 A
1 A
5785887 GAGATTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 8 0.28
33 7 0.24
34 14 0.48
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (32 bp):
AAATTTTGAAAAATCATAAAACTTTTCTAAAG
Found at i:5785996 original size:18 final size:18
Alignment explanation
Indices: 5785973--5786009 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5785963 TCAAAAATTT
5785973 ATTTTAAAAAATTATAAA
1 ATTTTAAAAAATTATAAA
*
5785991 ATTTTAAAAATTTATAAA
1 ATTTTAAAAAATTATAAA
5786009 A
1 A
5786010 AAATATAATT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTTAAAAAATTATAAA
Found at i:5786159 original size:26 final size:26
Alignment explanation
Indices: 5786129--5786181 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5786119 TCTTATTAAA
* * *
5786129 ATTTTTTTAATCATAATTACAATAAT
1 ATTTTTTCAATAACAATTACAATAAT
*
5786155 ATTTTTTCAATAACAATTATAATAAT
1 ATTTTTTCAATAACAATTACAATAAT
5786181 A
1 A
5786182 ATAATTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTTTTCAATAACAATTACAATAAT
Found at i:5801125 original size:22 final size:22
Alignment explanation
Indices: 5801083--5801126 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5801073 ATTGGGTTAA
*
5801083 AATTTACAAAAAAATATAAATG
1 AATTTACAAAAAAATAAAAATG
*
5801105 AATTTA-AAAAAATTTAAAAATG
1 AATTTACAAAAAA-ATAAAAATG
5801127 TATCTATCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (22 bp):
AATTTACAAAAAAATAAAAATG
Found at i:5802586 original size:55 final size:55
Alignment explanation
Indices: 5802502--5802611 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
5802492 TGGAAAAGGT
5802502 GTCCATGGGAAAATTTTAGGGGTATCCAGAGAAAATTTTCCTTCAAATTTTCTTA
1 GTCCATGGGAAAATTTTAGGGGTATCCAGAGAAAATTTTCCTTCAAATTTTCTTA
*
5802557 GTCCATGGGAAAATTTTAGGGGTGTCCAGAGAAAATTTTCCTTCAAATTTTCTTA
1 GTCCATGGGAAAATTTTAGGGGTATCCAGAGAAAATTTTCCTTCAAATTTTCTTA
5802612 TTTTCCAATC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (55 bp):
GTCCATGGGAAAATTTTAGGGGTATCCAGAGAAAATTTTCCTTCAAATTTTCTTA
Found at i:5805459 original size:21 final size:21
Alignment explanation
Indices: 5805412--5805460 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
5805402 AAAATTAATT
* *
5805412 TTAATCTTATCATTATAATAT
1 TTAATTTTATCATTATAATAA
*
5805433 TTAATTTTATCATTATTATAA
1 TTAATTTTATCATTATAATAA
5805454 TTAATTT
1 TTAATTT
5805461 CATCGTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATTTTATCATTATAATAA
Found at i:5805471 original size:21 final size:21
Alignment explanation
Indices: 5805433--5805472 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5805423 ATTATAATAT
* *
5805433 TTAATTTTATCATTATTATAA
1 TTAATTTCATCATAATTATAA
*
5805454 TTAATTTCATCGTAATTAT
1 TTAATTTCATCATAATTAT
5805473 TATTCTTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TTAATTTCATCATAATTATAA
Found at i:5811212 original size:20 final size:19
Alignment explanation
Indices: 5811189--5811236 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
5811179 TATTTATATC
5811189 ATATAAAATATTAATAATTT
1 ATATAAAATATT-ATAATTT
** *
5811209 ATATATTTATATTATATTTT
1 ATATA-AAATATTATAATTT
5811229 ATATAAAA
1 ATATAAAA
5811237 GTTATGTGTT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
19 1 0.05
20 16 0.73
21 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATAAAATATTATAATTT
Found at i:5811353 original size:15 final size:15
Alignment explanation
Indices: 5811322--5811370 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
5811312 TTTATTAAAA
5811322 TTTTA-ATTTATATTAT
1 TTTTATATTT-TA-TAT
5811338 TTTTATATTTTATAT
1 TTTTATATTTTATAT
5811353 TTTTATTATTTTTATAT
1 TTTTA-TA-TTTTATAT
5811370 T
1 T
5811371 GTATCATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.27
16 9 0.30
17 13 0.43
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATATTTTATAT
Found at i:5811364 original size:9 final size:9
Alignment explanation
Indices: 5811327--5811367 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
5811317 TAAAATTTTA
*
5811327 ATTTATATT
1 ATTTTTATT
5811336 ATTTTTA-T
1 ATTTTTATT
5811344 A-TTTTA-T
1 ATTTTTATT
5811351 ATTTTTATT
1 ATTTTTATT
5811360 ATTTTTAT
1 ATTTTTAT
5811368 ATTGTATCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 7 0.24
8 7 0.24
9 15 0.52
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
ATTTTTATT
Found at i:5814314 original size:18 final size:18
Alignment explanation
Indices: 5814291--5814329 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
5814281 ATGTAATTTT
5814291 TAAAAA-TATGTTATTAAA
1 TAAAAATTAT-TTATTAAA
5814309 TAAAAATTTATTTATTAAA
1 TAAAAA-TTATTTATTAAA
5814328 TA
1 TA
5814330 TATATATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 10 0.53
20 3 0.16
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TAAAAATTATTTATTAAA
Found at i:5817533 original size:16 final size:16
Alignment explanation
Indices: 5817514--5817576 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 16
5817504 ATATAATGTA
5817514 ATATATTAAAATTTAT
1 ATATATTAAAATTTAT
*
5817530 ATAT-TTATAATTTAT
1 ATATATTAAAATTTAT
* *
5817545 -TTTATATAAAA-AT-T
1 ATATAT-TAAAATTTAT
*
5817559 ATATATTATAATTTAT
1 ATATATTAAAATTTAT
5817575 AT
1 AT
5817577 TGACATGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
14 7 0.20
15 17 0.49
16 11 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATATTAAAATTTAT
Found at i:5817539 original size:30 final size:30
Alignment explanation
Indices: 5817505--5817570 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
5817495 CGTATATTCA
*
5817505 TATAATGTAATATAT-TAAAATTTATATATT
1 TATAATGTAATATATATAAAAATTATATA-T
* * *
5817535 TATAATTTATTTTATATAAAAATTATATAT
1 TATAATGTAATATATATAAAAATTATATAT
5817565 TATAAT
1 TATAAT
5817571 TTATATTGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
TATAATGTAATATATATAAAAATTATATAT
Found at i:5817571 original size:30 final size:32
Alignment explanation
Indices: 5817515--5817574 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
5817505 TATAATGTAA
*
5817515 TATATTAAAATTTATATATTTATAATTTATTT
1 TATATTAAAAATTATATATTTATAATTTATTT
5817547 TATA-TAAAAATTATATA-TTATAATTTAT
1 TATATTAAAAATTATATATTTATAATTTAT
5817575 ATTGACATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 11 0.41
31 12 0.44
32 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TATATTAAAAATTATATATTTATAATTTATTT
Found at i:5817593 original size:31 final size:29
Alignment explanation
Indices: 5817527--5817595 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
5817517 TATTAAAATT
* *
5817527 TATATATTTATAATTTAT-TTTATATAAA
1 TATATATTTATAATTTATATTGACATAAA
*
5817555 AATTATATATTATAATTTATATTGACATGAAA
1 TA-TATAT-TTATAATTTATATTGACAT-AAA
5817587 TATATATTT
1 TATATATTT
5817596 TTTAATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
28 1 0.03
29 5 0.15
30 13 0.39
31 10 0.30
32 4 0.12
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (29 bp):
TATATATTTATAATTTATATTGACATAAA
Found at i:5832389 original size:134 final size:134
Alignment explanation
Indices: 5832149--5832417 Score: 423
Period size: 134 Copynumber: 2.0 Consensus size: 134
5832139 TCAATAACAC
* * * * *
5832149 GATCTCAAAAAGCATTAACCCACTTTCGCATTCTCCATGAAGTACTTCTGGGTCACAAAAAAATT
1 GATCTCAAAAACCATTAACCAACTTTCACATTCTCCATAAAGTACTTCTGGGTCACAAAAAAATC
* *
5832214 CACTTTTCAGGTACAAACATAACATGTTCATCAGACATCATAGTAAAAGCCATTGCTAAACCAAC
66 CACTTTTCACGTACAAACATAACAAGTTCATCAGACATCATAGTAAAAGCCATTGCTAAACCAAC
5832279 AAAA
131 AAAA
* * *
5832283 GATCTCAAAAACCATTAACCAACTTTCATATTCTCCTTAAAAGTACTTCTGGGTCACAACAAAAT
1 GATCTCAAAAACCATTAACCAACTTTCACATTCTCCAT-AAAGTACTTCTGGGTCACAAAAAAAT
*
5832348 CCAC-TTTCACGTACAAACATAACAAGTTCATCAGAGATCATAGTAAAAGCCATTGCTAAACCAA
65 CCACTTTTCACGTACAAACATAACAAGTTCATCAGACATCATAGTAAAAGCCATTGCTAAACCAA
5832412 CAAAA
130 CAAAA
5832417 G
1 G
5832418 TTAATCATCA
Statistics
Matches: 123, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
134 96 0.78
135 27 0.22
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.25
Consensus pattern (134 bp):
GATCTCAAAAACCATTAACCAACTTTCACATTCTCCATAAAGTACTTCTGGGTCACAAAAAAATC
CACTTTTCACGTACAAACATAACAAGTTCATCAGACATCATAGTAAAAGCCATTGCTAAACCAAC
AAAA
Found at i:5835875 original size:23 final size:22
Alignment explanation
Indices: 5835849--5835891 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5835839 ATATGCCAAA
5835849 AGTTTTTGCAAAGAACAATTGGG
1 AGTTTTT-CAAAGAACAATTGGG
* *
5835872 AGTTTTTTAAATAACAATTG
1 AGTTTTTCAAAGAACAATTG
5835892 AAGTAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (22 bp):
AGTTTTTCAAAGAACAATTGGG
Found at i:5839750 original size:5 final size:6
Alignment explanation
Indices: 5839724--5839766 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
5839714 GATTTTAATT
* * *
5839724 TTTAAA TTTAAA TTTAAA TTT-AA TTTAAA ATAAAA ATTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
5839767 ATTCGAATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:5839930 original size:25 final size:25
Alignment explanation
Indices: 5839873--5839936 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 25
5839863 GAATTAATAC
* * *
5839873 ATATAAAAATTTAAATAATAATAAT
1 ATATTAAAATTAAAATAATAAAAAT
*
5839898 -T-TT-TAATTAAAATAATAAAAAT
1 ATATTAAAATTAAAATAATAAAAAT
5839920 ATATTAAAATTTAAAAT
1 ATATTAAAA-TTAAAAT
5839937 TTTAATTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
22 16 0.53
23 2 0.07
24 3 0.10
25 2 0.07
26 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATATTAAAATTAAAATAATAAAAAT
Found at i:5839944 original size:19 final size:20
Alignment explanation
Indices: 5839880--5839946 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 20
5839870 TACATATAAA
*
5839880 AATTTAAATAATAATAATTTTT
1 AATTAAAATAATAA-AA-TTTT
* *
5839902 AATTAAAATAATAAAAATAT
1 AATTAAAATAATAAAATTTT
*
5839922 -ATTAAAAT-TTAAAATTTT
1 AATTAAAATAATAAAATTTT
5839940 AATTAAA
1 AATTAAA
5839947 CTTATAAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 7 0.18
19 14 0.37
20 2 0.05
21 2 0.05
22 13 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTAAAATAATAAAATTTT
Found at i:5840931 original size:242 final size:243
Alignment explanation
Indices: 5840480--5840944 Score: 691
Period size: 242 Copynumber: 1.9 Consensus size: 243
5840470 CTCCTTCCAC
* * * *
5840480 TAGAGACCTTGATTTCTATAGTCAATTCAACTTTGGTGACAATGGCTGATGCTATGAAGCAGAAG
1 TAGAGAACTTAATATCTATAGTCAATTCAACTTGGGTGACAATGGCTGATGCTAT-----AGAAG
* * *
5840545 CTCCAACAATCATTGCAGGAAAGCAGTGTTCTTGACACCACAAAAACTGAAATTGGTGCTGCAAT
61 CTCCAACAACCATTGCAGGAAAGCAGTGTCCTTGACACCACAAAAACTGAAATTGGTGCTGAAAT
* *
5840610 GGAGGTATATAATCATATATTAGTTGATAATCTGAAATGGGTTTTGACGAATTTGCTTAATTGGT
126 GGAGGTATATAATCATATATTAGCTGATAATCTAAAATGGGTTTTGACGAATTTGCTTAATTGGT
* *
5840675 TCATTGATTAATGGTTTCAATTATGTTATTGAAACCACTGTCCAATTTTGCAT
191 TCATTAACTAATGGTTTCAATTATGTTATTGAAACCACTGTCCAATTTTGCAT
* * *
5840728 TAGAGAACTTAATATCTATAGTCAATTTAACTTGGGTGACAATGGCTTATGCTAT-GAAGCTTCA
1 TAGAGAACTTAATATCTATAGTCAATTCAACTTGGGTGACAATGGCTGATGCTATAGAAGCTCCA
* *
5840792 ACAACCATTGCAGGAAAGCAGTGTCCTTGACACTC-CCAAAAGTGAAATTGGTGCTGAAATGGAG
66 ACAACCATTGCAGGAAAGCAGTGTCCTTGACAC-CACAAAAACTGAAATTGGTGCTGAAATGGAG
* * *
5840856 GTATATAATCATATATTAGCTGATAATTTAAAATGGGTTTTGACGCATTTGGTTAATTGGTTCAT
130 GTATATAATCATATATTAGCTGATAATCTAAAATGGGTTTTGACGAATTTGCTTAATTGGTTCAT
5840921 TAACTAATGGTTTCAATTATGTTA
195 TAACTAATGGTTTCAATTATGTTA
5840945 ATTCTTGTAT
Statistics
Matches: 197, Mismatches: 19, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
242 147 0.75
243 1 0.01
248 49 0.25
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (243 bp):
TAGAGAACTTAATATCTATAGTCAATTCAACTTGGGTGACAATGGCTGATGCTATAGAAGCTCCA
ACAACCATTGCAGGAAAGCAGTGTCCTTGACACCACAAAAACTGAAATTGGTGCTGAAATGGAGG
TATATAATCATATATTAGCTGATAATCTAAAATGGGTTTTGACGAATTTGCTTAATTGGTTCATT
AACTAATGGTTTCAATTATGTTATTGAAACCACTGTCCAATTTTGCAT
Found at i:5845819 original size:16 final size:16
Alignment explanation
Indices: 5845798--5845828 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5845788 TAAAATATTT
*
5845798 TTAGTATTTTATTGAA
1 TTAGTATTTGATTGAA
5845814 TTAGTATTTGATTGA
1 TTAGTATTTGATTGA
5845829 GTTAAAAGTT
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:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (16 bp):
TTAGTATTTGATTGAA
Found at i:5845835 original size:68 final size:68
Alignment explanation
Indices: 5845726--5845858 Score: 230
Period size: 68 Copynumber: 2.0 Consensus size: 68
5845716 TGTTATATTA
5845726 ATTTTTAGTATTTTATTAAATTAGTATTTGACGGAGTTAAAAGTTAAAGTAATACGTGCAATTAA
1 ATTTTTAGTATTTTATTAAATTAGTATTTGACGGAGTTAAAAGTTAAAGTAATACGTGCAATTAA
5845791 AAT
66 AAT
* ** *
5845794 ATTTTTAGTATTTTATTGAATTAGTATTTGATTGAGTTAAAAGTTAAAGTAATATGTGCAATTAA
1 ATTTTTAGTATTTTATTAAATTAGTATTTGACGGAGTTAAAAGTTAAAGTAATACGTGCAATTAA
5845859 CATAAAATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (68 bp):
ATTTTTAGTATTTTATTAAATTAGTATTTGACGGAGTTAAAAGTTAAAGTAATACGTGCAATTAA
AAT
Found at i:5847858 original size:8 final size:8
Alignment explanation
Indices: 5847841--5848132 Score: 207
Period size: 8 Copynumber: 37.6 Consensus size: 8
5847831 TTAGGGTCTC
5847841 GTTTTAAG
1 GTTTTAAG
*
5847849 GTTTTGAG
1 GTTTTAAG
5847857 GTTTTAAG
1 GTTTTAAG
5847865 GTTTT--G
1 GTTTTAAG
*
5847871 GATTTTAGG
1 G-TTTTAAG
*
5847880 GTTCT-AG
1 GTTTTAAG
*
5847887 ATTTT-AG
1 GTTTTAAG
*
5847894 TGTTTT-GG
1 -GTTTTAAG
*
5847902 GTTTTAGG
1 GTTTTAAG
**
5847910 GTTTCGAG
1 GTTTTAAG
*
5847918 GTTTCAAG
1 GTTTTAAG
5847926 G-TTTAAG
1 GTTTTAAG
*
5847933 GTTTTAGG
1 GTTTTAAG
* **
5847941 GTATCGA-
1 GTTTTAAG
5847948 GTTTTAAG
1 GTTTTAAG
*
5847956 GTTTTGAG
1 GTTTTAAG
*
5847964 ATTTTAAG
1 GTTTTAAG
* *
5847972 ATTTTGAG
1 GTTTTAAG
5847980 GTTTTAAG
1 GTTTTAAG
5847988 G-TTTAAG
1 GTTTTAAG
5847995 GTTTT-AG
1 GTTTTAAG
*
5848002 AATTTTAAG
1 -GTTTTAAG
*
5848011 GTTTTAGG
1 GTTTTAAG
5848019 GTTTTAAG
1 GTTTTAAG
*
5848027 G-TTTAGG
1 GTTTTAAG
5848034 GTTTTAAG
1 GTTTTAAG
*
5848042 G-TTTATG
1 GTTTTAAG
5848049 GTTTTAAG
1 GTTTTAAG
*
5848057 GTTTTATG
1 GTTTTAAG
*
5848065 GTTTTAGG
1 GTTTTAAG
5848073 GTTTTAAG
1 GTTTTAAG
*
5848081 GTTTCAA-
1 GTTTTAAG
5848088 GTTTTGAA-
1 GTTTT-AAG
5848096 GTTTTAAG
1 GTTTTAAG
5848104 GTTTT-AG
1 GTTTTAAG
*
5848111 AGTTTCAAG
1 -GTTTTAAG
*
5848120 GTTTTAGG
1 GTTTTAAG
5848128 GTTTT
1 GTTTT
5848133 TGAAGTTTTT
Statistics
Matches: 225, Mismatches: 43, Indels: 32
0.75 0.14 0.11
Matches are distributed among these distances:
6 2 0.01
7 54 0.24
8 163 0.72
9 6 0.03
ACGTcount: A:0.21, C:0.02, G:0.28, T:0.49
Consensus pattern (8 bp):
GTTTTAAG
Found at i:5847882 original size:15 final size:15
Alignment explanation
Indices: 5847842--5847913 Score: 72
Period size: 15 Copynumber: 4.7 Consensus size: 15
5847832 TAGGGTCTCG
* *
5847842 TTTTAAGGTTTTGAGG
1 TTTTAGGGTTTTG-GA
*
5847858 TTTTAAGGTTTTGGA
1 TTTTAGGGTTTTGGA
* *
5847873 TTTTAGGGTTCTAGA
1 TTTTAGGGTTTTGGA
* *
5847888 TTTTAGTGTTTTGGG
1 TTTTAGGGTTTTGGA
5847903 TTTTAGGGTTT
1 TTTTAGGGTTT
5847914 CGAGGTTTCA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
15 34 0.72
16 13 0.28
ACGTcount: A:0.15, C:0.01, G:0.29, T:0.54
Consensus pattern (15 bp):
TTTTAGGGTTTTGGA
Found at i:5847939 original size:31 final size:31
Alignment explanation
Indices: 5847841--5848141 Score: 217
Period size: 31 Copynumber: 9.7 Consensus size: 31
5847831 TTAGGGTCTC
* *
5847841 GTTTTAAGGTTTTGAGGTTTTAAGGTTT-TG
1 GTTTTAGGGTTTTGAGGTTTTAAGGTTTAAG
* * **
5847871 GATTTTAGGGTTCT-AGATTTT-AGTGTTTTGG
1 G-TTTTAGGGTTTTGAGGTTTTAAG-GTTTAAG
* *
5847902 GTTTTAGGGTTTCGAGGTTTCAAGGTTTAAG
1 GTTTTAGGGTTTTGAGGTTTTAAGGTTTAAG
* * *
5847933 GTTTTAGGGTATCGA-GTTTTAAGGTTTTGAG
1 GTTTTAGGGTTTTGAGGTTTTAAGG-TTTAAG
* * *
5847964 ATTTTAAGATTTTGAGGTTTTAAGGTTTAAG
1 GTTTTAGGGTTTTGAGGTTTTAAGGTTTAAG
** * *
5847995 GTTTTAGAATTTTAAGGTTTTAGGGTTTTAAG
1 GTTTTAGGGTTTTGAGGTTTTAAGG-TTTAAG
* *
5848027 G-TTTAGGGTTTTAAGG-TTTATGGTTTTAAG
1 GTTTTAGGGTTTTGAGGTTTTAAGG-TTTAAG
*
5848057 GTTTTATGGTTTT-AGGGTTTTAAGGTTTCAA-
1 GTTTTAGGGTTTTGA-GGTTTTAAGGTTT-AAG
* *
5848088 GTTTT-GAAGTTTTAAGGTTTT-AGAGTTTCAAG
1 GTTTTAG-GGTTTTGAGGTTTTAAG-GTTT-AAG
*
5848120 GTTTTAGGGTTTTTGAAGTTTT
1 GTTTTAGGG-TTTTGAGGTTTT
5848142 TCTTATGAGA
Statistics
Matches: 219, Mismatches: 34, Indels: 33
0.77 0.12 0.12
Matches are distributed among these distances:
29 2 0.01
30 46 0.21
31 127 0.58
32 33 0.15
33 11 0.05
ACGTcount: A:0.21, C:0.02, G:0.28, T:0.50
Consensus pattern (31 bp):
GTTTTAGGGTTTTGAGGTTTTAAGGTTTAAG
Found at i:5847993 original size:39 final size:39
Alignment explanation
Indices: 5847841--5848141 Score: 174
Period size: 39 Copynumber: 7.7 Consensus size: 39
5847831 TTAGGGTCTC
* * * *
5847841 GTTTTAAGGTTTTGAGGTTTTAAGGTTTT--GGATTTTAGG
1 GTTTTAAGATTTTAAGGTTTTGAGGTTTTAAGG--TTTAAG
* * *
5847880 GTTCT-AGATTTT-AGTGTTTTG-GGTTTTAGGGTTTCGAG
1 GTTTTAAGATTTTAAG-GTTTTGAGGTTTTAAGGTTT-AAG
* * * ** *
5847918 GTTTCAAG-GTTTAAGGTTTT-AGGGTATCGAGTTTTAAG
1 GTTTTAAGATTTTAAGGTTTTGA-GGTTTTAAGGTTTAAG
* *
5847956 GTTTTGAGATTTTAAGATTTTGAGGTTTTAAGGTTTAAG
1 GTTTTAAGATTTTAAGGTTTTGAGGTTTTAAGGTTTAAG
*
5847995 GTTTT-AGAATTTTAAGGTTTT-AGGGTTTTAAGGTTTAGG
1 GTTTTAAG-ATTTTAAGGTTTTGA-GGTTTTAAGGTTTAAG
* * * * *
5848034 GTTTTAAG-GTTTATGGTTTTAAGGTTTTATGGTTTTAGG
1 GTTTTAAGATTTTAAGGTTTTGAGGTTTTAAGG-TTTAAG
* * * *
5848073 GTTTTAAGGTTTCAA-GTTTTGAAGTTTTAAGGTTTTAG
1 GTTTTAAGATTTTAAGGTTTTGAGGTTTTAAGGTTTAAG
* * * *
5848111 AGTTTCAAGGTTTTAGGGTTTTTGAAGTTTT
1 -GTTTTAAGATTTTAAGG-TTTTGAGGTTTT
5848142 TCTTATGAGA
Statistics
Matches: 205, Mismatches: 38, Indels: 36
0.73 0.14 0.13
Matches are distributed among these distances:
37 11 0.05
38 57 0.28
39 118 0.58
40 7 0.03
41 12 0.06
ACGTcount: A:0.21, C:0.02, G:0.28, T:0.50
Consensus pattern (39 bp):
GTTTTAAGATTTTAAGGTTTTGAGGTTTTAAGGTTTAAG
Found at i:5848099 original size:23 final size:22
Alignment explanation
Indices: 5847948--5848125 Score: 110
Period size: 23 Copynumber: 7.6 Consensus size: 22
5847938 AGGGTATCGA
*
5847948 GTTTTAAGGTTTTGAGATTTTAA
1 GTTTTAAGGTTTTAAG-TTTTAA
* *
5847971 GATTTTGAGGTTTTAAGGTTTAA
1 G-TTTTAAGGTTTTAAGTTTTAA
* *
5847994 GGTTTT-AGAATTTTAAGGTTTTAGG
1 -GTTTTAAG-GTTTTAA-GTTTTA-A
*
5848019 GTTTTAAGG-TTTAGGGTTTTAA
1 GTTTTAAGGTTTTA-AGTTTTAA
* * *
5848041 GGTTTATGGTTTTAAGGTTTTATG
1 GTTTTAAGGTTTTAA-GTTTTA-A
* *
5848065 GTTTTAGGGTTTTAAGGTTTCAA
1 GTTTTAAGGTTTTAA-GTTTTAA
5848088 GTTTTGAA-GTTTTAAGGTTTTAGA
1 GTTTT-AAGGTTTTAA-GTTTTA-A
*
5848112 GTTTCAAGGTTTTA
1 GTTTTAAGGTTTTA
5848126 GGGTTTTTGA
Statistics
Matches: 122, Mismatches: 20, Indels: 25
0.73 0.12 0.15
Matches are distributed among these distances:
22 9 0.07
23 56 0.46
24 55 0.45
25 2 0.02
ACGTcount: A:0.23, C:0.01, G:0.26, T:0.50
Consensus pattern (22 bp):
GTTTTAAGGTTTTAAGTTTTAA
Found at i:5850353 original size:23 final size:26
Alignment explanation
Indices: 5850307--5850353 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
5850297 GTATTTTTTT
*
5850307 TTTTTTTATGTTTTTGATAGTTTACC
1 TTTTTTTATGTTTTTGATAATTTACC
5850333 TTTTTTT-T-TTTTTG-TAATTTA
1 TTTTTTTATGTTTTTGATAATTTA
5850354 TCAATTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 1 0.05
26 7 0.35
ACGTcount: A:0.15, C:0.04, G:0.09, T:0.72
Consensus pattern (26 bp):
TTTTTTTATGTTTTTGATAATTTACC
Found at i:5850408 original size:10 final size:10
Alignment explanation
Indices: 5850378--5850410 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
5850368 TAATTGAATG
5850378 TAAATATATA
1 TAAATATATA
5850388 T--ATATATA
1 TAAATATATA
5850396 TAAATATATA
1 TAAATATATA
5850406 TAAAT
1 TAAAT
5850411 TTGGGCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TAAATATATA
Found at i:5852971 original size:2 final size:2
Alignment explanation
Indices: 5852964--5852998 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5852954 ATTTAAAGAT
*
5852964 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5852999 GTATGTCAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5856794 original size:22 final size:22
Alignment explanation
Indices: 5856746--5856792 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5856736 AATTTAAAAT
* * *
5856746 TTTAATAAAAATTATATATAAA
1 TTTAATAAAAATAAAAAATAAA
5856768 TTTAATAAAAATAAAAAATATAA
1 TTTAATAAAAATAAAAAATA-AA
5856791 TT
1 TT
5856793 AACGTATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAATAAAAATAAAAAATAAA
Found at i:5876342 original size:18 final size:18
Alignment explanation
Indices: 5876297--5876354 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
5876287 TAAAATTACT
*
5876297 TATTAATATTTTTAAAT-A
1 TATT-ATATTTATAAATAA
*
5876315 TAATTTTATTTATAAATAA
1 T-ATTATATTTATAAATAA
* *
5876334 TATTATATTAATAAACAA
1 TATTATATTTATAAATAA
5876352 TAT
1 TAT
5876355 ATTAATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 28 0.85
19 5 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTATATTTATAAATAA
Found at i:5876357 original size:15 final size:15
Alignment explanation
Indices: 5876332--5876462 Score: 125
Period size: 15 Copynumber: 9.0 Consensus size: 15
5876322 ATTTATAAAT
*
5876332 AATATTATATTAATA
1 AATAATATATTAATA
*
5876347 AACAATATATTAATA
1 AATAATATATTAATA
5876362 AAT-AT-TATT-ATA
1 AATAATATATTAATA
5876374 AATAA-ATATT-AT-
1 AATAATATATTAATA
5876386 AATAATATATTAATA
1 AATAATATATTAATA
*
5876401 AATAATATATTATTAATG
1 AAT-A-ATA-TATTAATA
* *
5876419 AATAATATACTACTA
1 AATAATATATTAATA
5876434 ATATAATATATTAATA
1 A-ATAATATATTAATA
5876450 AAT-AT-TATTAATA
1 AATAATATATTAATA
5876463 TACTAACATA
Statistics
Matches: 98, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
12 11 0.11
13 24 0.24
14 6 0.06
15 26 0.27
16 17 0.17
17 4 0.04
18 10 0.10
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (15 bp):
AATAATATATTAATA
Found at i:5876373 original size:18 final size:18
Alignment explanation
Indices: 5876309--5876459 Score: 81
Period size: 18 Copynumber: 8.7 Consensus size: 18
5876299 TTAATATTTT
* * *
5876309 TAAATATAATTTTATTTA
1 TAAATATTATTATATTAA
*
5876327 TAAATAATATTATATTAA
1 TAAATATTATTATATTAA
*
5876345 TAAACA--A-TATATTAA
1 TAAATATTATTATATTAA
5876360 TAAATATTATTATA--AA
1 TAAATATTATTATATTAA
5876376 TAAATATTATAATAATATATTAA
1 TAAATA-T-T-AT--TATATTAA
*
5876399 TAAATAATA-TATTATTAA
1 TAAATATTATTA-TATTAA
* * *
5876417 TGAATA--A-TATACTAC
1 TAAATATTATTATATTAA
*
5876432 T-AATA-TAATATATTAA
1 TAAATATTATTATATTAA
5876448 TAAATATTATTA
1 TAAATATTATTA
5876460 ATATACTAAC
Statistics
Matches: 105, Mismatches: 13, Indels: 30
0.71 0.09 0.20
Matches are distributed among these distances:
14 4 0.04
15 19 0.18
16 19 0.18
17 8 0.08
18 39 0.37
19 2 0.02
20 1 0.01
21 5 0.05
23 8 0.08
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (18 bp):
TAAATATTATTATATTAA
Found at i:5876415 original size:72 final size:73
Alignment explanation
Indices: 5876321--5876462 Score: 182
Period size: 72 Copynumber: 2.0 Consensus size: 73
5876311 AATATAATTT
* * *
5876321 TATTTATAAATAATATTATATTAATAAACAATATATTAATAA-ATATTATTATAAATAAATATTA
1 TATTAATAAATAATATTATATTAATAAACAATATACTAATAATATAATA-TATAAATAAATATTA
5876385 -TAATAATA
65 TTAATAATA
* * * *
5876393 TATTAATAAATAATA-TATTATTAATGAATAATATACTACTAATATAATATATTAATAAATATTA
1 TATTAATAAATAATATTA-TATTAATAAACAATATACTAATAATATAATATATAAATAAATATTA
5876457 TTAATA
65 TTAATA
5876463 TACTAACATA
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
71 2 0.03
72 48 0.80
73 10 0.17
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (73 bp):
TATTAATAAATAATATTATATTAATAAACAATATACTAATAATATAATATATAAATAAATATTAT
TAATAATA
Found at i:5876426 original size:44 final size:41
Alignment explanation
Indices: 5876350--5876462 Score: 117
Period size: 44 Copynumber: 2.7 Consensus size: 41
5876340 ATTAATAAAC
*
5876350 AATATATTAATAAAT-AT-TATTATAAATAAATATTA-TAAT
1 AATATATTAATAAATAATATATTATTAATAAATA-TACTAAT
*
5876389 AATATATTAATAAATAATATATTATTAATGAATAATATACTACT
1 AATATATTAATAAATAATATATTATTAAT--A-AATATACTAAT
* *
5876433 AATATAATATATTAATAA-ATATTATTAATA
1 AATATATTA-ATAAATAATATATTATTAATA
5876463 TACTAACATA
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
39 15 0.24
40 2 0.03
41 9 0.14
42 1 0.02
43 3 0.05
44 26 0.41
45 7 0.11
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (41 bp):
AATATATTAATAAATAATATATTATTAATAAATATACTAAT
Found at i:5876456 original size:10 final size:11
Alignment explanation
Indices: 5876350--5876464 Score: 51
Period size: 10 Copynumber: 11.5 Consensus size: 11
5876340 ATTAATAAAC
5876350 AATATATTAAT
1 AATATATTAAT
5876361 AA-ATATT-AT
1 AATATATTAAT
* * *
5876370 TATAAATAAAT
1 AATATATTAAT
5876381 -AT-TA-TAAT
1 AATATATTAAT
5876389 AATATATTAAT
1 AATATATTAAT
*
5876400 AA-ATAAT-AT
1 AATATATTAAT
5876409 -AT-TATTAAT
1 AATATATTAAT
5876418 GAATA-A-T-AT
1 -AATATATTAAT
* *
5876427 ACTACTAAT-AT
1 AATA-TATTAAT
5876438 AATATATTAAT
1 AATATATTAAT
*
5876449 AA-ATATTATT
1 AATATATTAAT
5876459 AATATA
1 AATATA
5876465 CTAACATAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 30
0.66 0.09 0.25
Matches are distributed among these distances:
8 10 0.13
9 12 0.15
10 30 0.38
11 26 0.33
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (11 bp):
AATATATTAAT
Found at i:5876474 original size:72 final size:71
Alignment explanation
Indices: 5876326--5876479 Score: 170
Period size: 72 Copynumber: 2.1 Consensus size: 71
5876316 AATTTTATTT
* *
5876326 ATAAATAATATTATATTAATAAACAATATATTAATAAATATTATTATAAATAAATATTATAATAA
1 ATAAATAATATTATATTAATAAACAATATACTAATAAATAATATTATAAATAAATATTAT-ATAA
*
5876391 TATATTA
65 TATATAA
* * * *
5876398 ATAAATAATA-TATTATTAATGAATAATATACTACTAATATAATA-TATTAATAAATATTAT-TA
1 ATAAATAATATTA-TATTAATAAACAATATACTAATAA-ATAATATTATAAATAAATATTATATA
5876460 ATATACTAA
64 ATATA-TAA
*
5876469 CATAAAGAATA
1 -ATAAATAATA
5876480 ATAAATAGTT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
70 7 0.10
71 4 0.06
72 54 0.77
73 5 0.07
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (71 bp):
ATAAATAATATTATATTAATAAACAATATACTAATAAATAATATTATAAATAAATATTATATAAT
ATATAA
Found at i:5876545 original size:19 final size:19
Alignment explanation
Indices: 5876498--5876545 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
5876488 TTTTATTTTA
*
5876498 AATATTTTTATATTAACAT
1 AATATTTTAATATTAACAT
5876517 AATATTTTAATATTAA-AT
1 AATATTTTAATATTAACAT
*
5876535 ATTATTATTAA
1 AATATT-TTAA
5876546 ACTATAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
AATATTTTAATATTAACAT
Found at i:5876601 original size:26 final size:26
Alignment explanation
Indices: 5876568--5876623 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
5876558 TGTTAAAATT
*
5876568 AATAATTTTAATAATATATA-ATTTC
1 AATAATTTTAATAATAAATATATTTC
*
5876593 AATATATTTTAATAATAAATATATTTT
1 AATA-ATTTTAATAATAAATATATTTC
5876620 AATA
1 AATA
5876624 GTTATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 4 0.15
26 15 0.56
27 8 0.30
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AATAATTTTAATAATAAATATATTTC
Found at i:5876633 original size:29 final size:26
Alignment explanation
Indices: 5876575--5876635 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 26
5876565 ATTAATAATT
* *
5876575 TTAATAATATATAATTTCAATATATT
1 TTAATAATAAATAATTTCAATATATA
*
5876601 TTAATAATAAATATATTTTAATAGTTATA
1 TTAATAATAAATA-ATTTCAATA--TATA
5876630 TTAATA
1 TTAATA
5876636 TTATTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 12 0.41
27 8 0.28
29 9 0.31
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
TTAATAATAAATAATTTCAATATATA
Found at i:5876771 original size:14 final size:14
Alignment explanation
Indices: 5876738--5876778 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
5876728 AATGTAAATA
5876738 TTTTTGAGAAATCAT
1 TTTTTGA-AAATCAT
*
5876753 TTTTTGAAAATTAT
1 TTTTTGAAAATCAT
5876767 TTTTTGCAAAAT
1 TTTTTG-AAAAT
5876779 AAACGAAGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (14 bp):
TTTTTGAAAATCAT
Found at i:5880892 original size:21 final size:18
Alignment explanation
Indices: 5880855--5880889 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5880845 TATTAATACT
5880855 TAAAAATAATATTTTATA
1 TAAAAATAATATTTTATA
5880873 TAAAAATAATATTTTAT
1 TAAAAATAATATTTTAT
5880890 TATTTTGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAAATAATATTTTATA
Found at i:5881223 original size:18 final size:18
Alignment explanation
Indices: 5881197--5881231 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5881187 TTAACATAAA
5881197 AATAATTTAGTAATTTTT
1 AATAATTTAGTAATTTTT
* *
5881215 AATATTTTATTAATTTT
1 AATAATTTAGTAATTTT
5881232 ATAAATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
AATAATTTAGTAATTTTT
Found at i:5884338 original size:13 final size:13
Alignment explanation
Indices: 5884320--5884347 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5884310 CATATCAAGT
5884320 TTCTTGGCTGGTG
1 TTCTTGGCTGGTG
5884333 TTCTTGGCTGGTG
1 TTCTTGGCTGGTG
5884346 TT
1 TT
5884348 TTAGGATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.36, T:0.50
Consensus pattern (13 bp):
TTCTTGGCTGGTG
Found at i:5885583 original size:146 final size:147
Alignment explanation
Indices: 5885422--5885715 Score: 500
Period size: 146 Copynumber: 2.0 Consensus size: 147
5885412 AAAAACCACC
*
5885422 AAATAGTGAAAAGATAAATAAAATGGCAACTTAATTAAGTATATATGATATCTTGATAGTTGAAT
1 AAATAGTGAAAAGATAAATAAAATGACAACTTAATTAAGTATATATGATATCTTGATAGTTGAAT
* * * *
5885487 GAGATATTCTTTAATAAAAGAATGCATACTTGCATATGGTAGGGGTGATAAGAATCAA-AAGAAA
66 GAGATATTCTTTAATAAAAGAATGCATACTTGCACATGATAGGGGTGATAAGAATAAATAAAAAA
5885551 TAAAAAATTATCACCAT
131 TAAAAAATTATCACCAT
* *
5885568 AAATAGTGAAAAGATAAATGAAATGACAACTTAATTAAGTATATATGATATCTTGATAGTTTAAT
1 AAATAGTGAAAAGATAAATAAAATGACAACTTAATTAAGTATATATGATATCTTGATAGTTGAAT
* *
5885633 GAGATATTCTTTAATAAAAGAATGCATGCTTGCACATGATAGGGGTGATAATAATAAATAAAAAA
66 GAGATATTCTTTAATAAAAGAATGCATACTTGCACATGATAGGGGTGATAAGAATAAATAAAAAA
5885698 TAAAAAATTATCACCAT
131 TAAAAAATTATCACCAT
5885715 A
1 A
5885716 GTGTTGTAAG
Statistics
Matches: 138, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
146 115 0.83
147 23 0.17
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (147 bp):
AAATAGTGAAAAGATAAATAAAATGACAACTTAATTAAGTATATATGATATCTTGATAGTTGAAT
GAGATATTCTTTAATAAAAGAATGCATACTTGCACATGATAGGGGTGATAAGAATAAATAAAAAA
TAAAAAATTATCACCAT
Found at i:5889151 original size:13 final size:13
Alignment explanation
Indices: 5889120--5889160 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
5889110 TATCTGCTTA
5889120 AATATATTAAAAT
1 AATATATTAAAAT
**
5889133 TTTATATTAAAAT
1 AATATATTAAAAT
*
5889146 AATATATAAAAAT
1 AATATATTAAAAT
5889159 AA
1 AA
5889161 AAAATTTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATATATTAAAAT
Found at i:5890336 original size:30 final size:30
Alignment explanation
Indices: 5890285--5890341 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5890275 ATAAGACATT
*
5890285 TTATTTTAATTAATCAAATA-TTAAATTTA
1 TTATTTTAATCAATCAAATATTTAAATTTA
*
5890314 TTATTTTGAATCAATTAAATATTTAAAT
1 TTATTTT-AATCAATCAAATATTTAAAT
5890342 ATCTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.29
30 11 0.46
31 6 0.25
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (30 bp):
TTATTTTAATCAATCAAATATTTAAATTTA
Found at i:5890349 original size:30 final size:28
Alignment explanation
Indices: 5890285--5890370 Score: 75
Period size: 30 Copynumber: 2.9 Consensus size: 28
5890275 ATAAGACATT
* *
5890285 TTATTTTAATTAATCAAATATTAAATTTA
1 TTATTTTAATCAATTAAATATTAAA-TTA
5890314 TTATTTTGAATCAATTAAATATTTAAA-TA
1 TTATTTT-AATCAATTAAATA-TTAAATTA
* *
5890343 TCTATTTTTATTCAATTGAATTATTAAA
1 T-TA-TTTTAATCAATT-AAATATTAAA
5890371 CATCAATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
29 10 0.21
30 25 0.52
31 13 0.27
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (28 bp):
TTATTTTAATCAATTAAATATTAAATTA
Found at i:5899211 original size:17 final size:19
Alignment explanation
Indices: 5899171--5899211 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
5899161 TCAAATTAAA
*
5899171 TTATATATTTGTTTAGTTT
1 TTATATATTTGTTTAATTT
*
5899190 ATATATA-TT-TTTAATTT
1 TTATATATTTGTTTAATTT
5899207 TTATA
1 TTATA
5899212 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
17 11 0.58
18 2 0.11
19 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TTATATATTTGTTTAATTT
Found at i:5901040 original size:16 final size:16
Alignment explanation
Indices: 5901019--5901050 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5901009 TTTATTTGTA
5901019 ATTATAAAAAGTTTTC
1 ATTATAAAAAGTTTTC
5901035 ATTATAAAAAGTTTTC
1 ATTATAAAAAGTTTTC
5901051 TTTTTTTGTT
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:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTATAAAAAGTTTTC
Found at i:5901149 original size:14 final size:15
Alignment explanation
Indices: 5901097--5901163 Score: 52
Period size: 14 Copynumber: 4.7 Consensus size: 15
5901087 TAAAAATTTT
5901097 AATAAAT-AATTATA
1 AATAAATAAATTATA
**
5901111 AAT-AATATTTTA-A
1 AATAAATAAATTATA
** *
5901124 AATTTATTAATTA-A
1 AATAAATAAATTATA
5901138 AATAAATAAATTATA
1 AATAAATAAATTATA
5901153 AATATAATAAA
1 AATA-AATAAA
5901164 ATTTATTCAT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
13 7 0.17
14 22 0.55
15 5 0.12
16 6 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATAAATAAATTATA
Found at i:5901545 original size:17 final size:17
Alignment explanation
Indices: 5901525--5901565 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5901515 ATTTTCTTAC
5901525 CAAAAAAA-TGTAAAAAA
1 CAAAAAAAGT-TAAAAAA
*
5901542 CAAAAGAAGTTAAAAAA
1 CAAAAAAAGTTAAAAAA
5901559 -AAAAAAA
1 CAAAAAAA
5901566 AAAAAACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 6 0.29
17 14 0.67
18 1 0.05
ACGTcount: A:0.78, C:0.05, G:0.07, T:0.10
Consensus pattern (17 bp):
CAAAAAAAGTTAAAAAA
Found at i:5901789 original size:11 final size:11
Alignment explanation
Indices: 5901769--5901809 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
5901759 AGGTGTAATG
5901769 ATAT-ATATAA
1 ATATAATATAA
5901779 ATATAATAT-A
1 ATATAATATAA
5901789 A-ATAATATAA
1 ATATAATATAA
*
5901799 AAATAATATAA
1 ATATAATATAA
5901810 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 7 0.25
10 8 0.29
11 13 0.46
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
ATATAATATAA
Found at i:5907755 original size:11 final size:10
Alignment explanation
Indices: 5907722--5907753 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
5907712 TCGAATCAAA
*
5907722 TTATATATTT
1 TTATTTATTT
5907732 TTATTTATTT
1 TTATTTATTT
5907742 TTATTTATTT
1 TTATTTATTT
5907752 TT
1 TT
5907754 TAAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TTATTTATTT
Found at i:5912243 original size:13 final size:13
Alignment explanation
Indices: 5912227--5912251 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5912217 TTAAGTTTAG
5912227 ATATTAAATTTGT
1 ATATTAAATTTGT
5912240 ATATTAAATTTG
1 ATATTAAATTTG
5912252 AATCAAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
ATATTAAATTTGT
Found at i:5912374 original size:20 final size:21
Alignment explanation
Indices: 5912349--5912389 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5912339 ATAATTATTT
* *
5912349 TATATTTAAATTTAT-TTAAA
1 TATATTAAAAATTATATTAAA
5912369 TATATTAAAAATTATATTAAA
1 TATATTAAAAATTATATTAAA
5912390 ATAATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATATTAAAAATTATATTAAA
Found at i:5912386 original size:12 final size:12
Alignment explanation
Indices: 5912366--5912406 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
5912356 AAATTTATTT
5912366 AAATATATTAAA
1 AAATATATTAAA
*
5912378 AATTATATTAAA
1 AAATATATTAAA
5912390 ATAATATATATAAA
1 A-AATATAT-TAAA
5912404 AAA
1 AAA
5912407 ATAAAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 12 0.48
13 8 0.32
14 5 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATATATTAAA
Found at i:5913281 original size:13 final size:13
Alignment explanation
Indices: 5913248--5913286 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
5913238 TAATTTTTTA
*
5913248 AAAATAATTTAAT
1 AAAATATTTTAAT
5913261 AAAA-ATTTTAAT
1 AAAATATTTTAAT
*
5913273 AAAATATTTAAAT
1 AAAATATTTTAAT
5913286 A
1 A
5913287 GATAGATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATATTTTAAT
Found at i:5913398 original size:14 final size:15
Alignment explanation
Indices: 5913368--5913401 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5913358 ATTTTTTTAG
*
5913368 TATTTTTATTAAAAA
1 TATTTATATTAAAAA
5913383 TATTTATATT-AAAA
1 TATTTATATTAAAAA
5913397 TATTT
1 TATTT
5913402 TTAAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTATATTAAAAA
Found at i:5916858 original size:24 final size:25
Alignment explanation
Indices: 5916831--5916878 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
5916821 TTTAAATATC
* *
5916831 TATTTTCTCTCAATTGAA-CTTTTA
1 TATTTTCACTCAATTAAACCTTTTA
5916855 TATTTTCACTCAATTAAACCTTTT
1 TATTTTCACTCAATTAAACCTTTT
5916879 GATTGAACGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.27, C:0.19, G:0.02, T:0.52
Consensus pattern (25 bp):
TATTTTCACTCAATTAAACCTTTTA
Found at i:5919577 original size:18 final size:19
Alignment explanation
Indices: 5919554--5919595 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
5919544 TTAAACCAAA
*
5919554 TTATATATATTTT-AGTTT
1 TTATATATATTTTAAATTT
*
5919572 TTATATATTTTTTAAATTT
1 TTATATATATTTTAAATTT
5919591 TTATA
1 TTATA
5919596 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATATATATTTTAAATTT
Found at i:5919652 original size:13 final size:13
Alignment explanation
Indices: 5919633--5919672 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
5919623 ATTTACTTAA
5919633 ATATATTAAAATT
1 ATATATTAAAATT
* *
5919646 TTATATTAAAATA
1 ATATATTAAAATT
*
5919659 ATATATAAAAATT
1 ATATATTAAAATT
5919672 A
1 A
5919673 AAAACCATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATATTAAAATT
Found at i:5922472 original size:2 final size:2
Alignment explanation
Indices: 5922417--5922455 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5922407 GGTGTCTATT
5922417 TA TA TA -A 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
5922456 ATTATCAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5922790 original size:28 final size:28
Alignment explanation
Indices: 5922737--5922791 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
5922727 TTAAAACTAA
* *
5922737 ATTAATCAAATTATTTTATTTTATTTTC
1 ATTAATCAAATTAATTTATTTAATTTTC
*
5922765 ATTAATTAAATTAAATTT-TTTAATTTT
1 ATTAATCAAATT-AATTTATTTAATTTT
5922792 AAAATTTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTAATCAAATTAATTTATTTAATTTTC
Found at i:5925793 original size:84 final size:84
Alignment explanation
Indices: 5925652--5925814 Score: 272
Period size: 84 Copynumber: 1.9 Consensus size: 84
5925642 TTGCAGCAAA
** *
5925652 ATAGAAATTACTCTAATAATACCTCTTAAAGGACAGCAACAACTACAGCAGAAATACAAGGAATC
1 ATAGAAATTACTCTAATAATACCTCAGAAAGCACAGCAACAACTACAGCAGAAATACAAGGAATC
*
5925717 TGTTCAGCAAGTTGGAAAT
66 TCTTCAGCAAGTTGGAAAT
* *
5925736 ATAGAAATTACTCTAATGATACCTCAGAAAGCAGAGCAACAACTACAGCAGAAATACAAGGAATC
1 ATAGAAATTACTCTAATAATACCTCAGAAAGCACAGCAACAACTACAGCAGAAATACAAGGAATC
5925801 TCTTCAGCAAGTTG
66 TCTTCAGCAAGTTG
5925815 AAAGATGACA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 73 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (84 bp):
ATAGAAATTACTCTAATAATACCTCAGAAAGCACAGCAACAACTACAGCAGAAATACAAGGAATC
TCTTCAGCAAGTTGGAAAT
Found at i:5930846 original size:21 final size:22
Alignment explanation
Indices: 5930802--5930846 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
5930792 ATATTTATAA
**
5930802 TTTTTATCTTAAAAATTATGATT
1 TTTTTATC-TAAAAATTAACATT
5930825 TTTTTATC-AAAAATTAACATT
1 TTTTTATCTAAAAATTAACATT
5930846 T
1 T
5930847 AATCAAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
23 8 0.40
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTATCTAAAAATTAACATT
Found at i:5931246 original size:35 final size:35
Alignment explanation
Indices: 5931206--5931273 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
5931196 AAAAACTATA
*
5931206 TTAAAATAAT-ATATAAAAA-CAATAAAAATTTAAAT
1 TTAAAA-AATCATAAAAAAATCAAT-AAAATTTAAAT
*
5931241 TTAAAAATTCATAAAAAAATCAATAAAATTTAA
1 TTAAAAAATCATAAAAAAATCAATAAAATTTAA
5931274 TTCAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 2 0.07
35 23 0.79
36 4 0.14
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (35 bp):
TTAAAAAATCATAAAAAAATCAATAAAATTTAAAT
Found at i:5931324 original size:24 final size:24
Alignment explanation
Indices: 5931290--5931342 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
5931280 TTAAACCGTA
*
5931290 CAAAAATTCTGTTTAAATTCAAAT
1 CAAAAAATCTGTTTAAATTCAAAT
5931314 CAAAAAATCTGTTTAAATTCAAAT
1 CAAAAAATCTGTTTAAATTCAAAT
5931338 CAAAA
1 CAAAA
5931343 TTTATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (24 bp):
CAAAAAATCTGTTTAAATTCAAAT
Found at i:5932945 original size:13 final size:12
Alignment explanation
Indices: 5932923--5932955 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5932913 TTTTTTAGGG
5932923 TTTTAAAAAAAA
1 TTTTAAAAAAAA
*
5932935 TTTTGAAAAAAA
1 TTTTAAAAAAAA
5932947 -TTTAAAAAA
1 TTTTAAAAAA
5932956 TTCTCAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
TTTTAAAAAAAA
Found at i:5933235 original size:26 final size:26
Alignment explanation
Indices: 5933206--5933259 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
5933196 AATGATGGAA
* *
5933206 TTTATAAAAATTTCTA-ATGATAAATT
1 TTTAT-AAAATTCCTAGATGAGAAATT
5933232 TTTATAAAATTCCTAGATGAGAAATT
1 TTTATAAAATTCCTAGATGAGAAATT
5933258 TT
1 TT
5933260 GTCTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (26 bp):
TTTATAAAATTCCTAGATGAGAAATT
Found at i:5933240 original size:25 final size:24
Alignment explanation
Indices: 5933188--5933259 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 24
5933178 AATAAATATT
* *
5933188 AATTATCTAATGATGGAATTTATAAA
1 AATT-TCTAATGAT-AAATTTTTAAA
5933214 AATTTCTAATGATAAATTTTTATAA
1 AATTTCTAATGATAAATTTTTA-AA
* *
5933239 AATTCCTAGATGAGAAATTTT
1 AATTTCTA-ATGATAAATTTT
5933260 GTCTAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.17
25 18 0.45
26 15 0.38
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.42
Consensus pattern (24 bp):
AATTTCTAATGATAAATTTTTAAA
Found at i:5937908 original size:23 final size:21
Alignment explanation
Indices: 5937861--5937914 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
5937851 TGTAAAAAAA
5937861 AAAAGAAAAAAATGAAAGAATG
1 AAAA-AAAAAAATGAAAGAATG
5937883 AAAAAAAAAAATG-AA-AATG
1 AAAAAAAAAAATGAAAGAATG
*
5937902 AGAGAAAAAAAAT
1 A-AAAAAAAAAAT
5937915 ACTCAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 5 0.17
20 12 0.40
21 9 0.30
22 4 0.13
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (21 bp):
AAAAAAAAAAATGAAAGAATG
Found at i:5937913 original size:27 final size:25
Alignment explanation
Indices: 5937854--5937913 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
5937844 AATGGATTGT
*
5937854 AAAAAAAAAAAGAAAAAAATGAAAG
1 AAAAAAAAAAAAAAAAAAATGAAAG
** *
5937879 AATGAAAAAAAAAAATGAAAATGAGAG
1 AA--AAAAAAAAAAAAAAAAATGAAAG
5937906 AAAAAAAA
1 AAAAAAAA
5937914 TACTCAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 8 0.28
27 21 0.72
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (25 bp):
AAAAAAAAAAAAAAAAAAATGAAAG
Found at i:5939203 original size:21 final size:20
Alignment explanation
Indices: 5939168--5939226 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
5939158 TTTTTAGTTC
5939168 TCAAATGA-AAGTCTTTGAATT
1 TCAAATGAGAA-TCTTTGAA-T
** * *
5939189 TTGAATGTGAATCTTCGAAT
1 TCAAATGAGAATCTTTGAAT
5939209 TCAAATGAGAATCTTTGA
1 TCAAATGAGAATCTTTGA
5939227 GGTGTAAAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
20 15 0.52
21 12 0.41
22 2 0.07
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (20 bp):
TCAAATGAGAATCTTTGAAT
Found at i:5939255 original size:58 final size:59
Alignment explanation
Indices: 5939189--5939306 Score: 186
Period size: 58 Copynumber: 2.0 Consensus size: 59
5939179 TCTTTGAATT
* *
5939189 TTGAATGTGAATCTTCGAA-TTCAAATGAGAATCTTTGAGGTGT-AAAATCTAAAATTTG
1 TTGAATGTGAATCTTCAAACTT-AAATGAGAATCTTTGAGGTGTGAAAACCTAAAATTTG
*
5939247 TTGAATGTGAATCTTCAAACTTAAATGAGAATCTTTGAGGTGTGAAACCCTAAAATTTG
1 TTGAATGTGAATCTTCAAACTTAAATGAGAATCTTTGAGGTGTGAAAACCTAAAATTTG
5939306 T
1 T
5939307 CAAATGTAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 39 0.71
59 16 0.29
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (59 bp):
TTGAATGTGAATCTTCAAACTTAAATGAGAATCTTTGAGGTGTGAAAACCTAAAATTTG
Found at i:5942488 original size:87 final size:86
Alignment explanation
Indices: 5942390--5942562 Score: 310
Period size: 86 Copynumber: 2.0 Consensus size: 86
5942380 ATTGACATTA
5942390 TATAAAATTTATATATTGATAATATATCAAATATAAATTTTTTTTACATATGATTTTTTGTACGT
1 TATAAAATTTATATATTGATAATATATCAAATATAAA-TTTTTTTACATATGATTTTTTGTACGT
5942455 TAACCACATTGACTAGCATAGT
65 TAACCACATTGACTAGCATAGT
*
5942477 TATAAAATTTATATATTGATAATGTATCAAATATAAATTTTTTTACATATGATTTTTTGTACGTT
1 TATAAAATTTATATATTGATAATATATCAAATATAAATTTTTTTACATATGATTTTTTGTACGTT
* *
5942542 AACCACGTTGGCTAGCATAGT
66 AACCACATTGACTAGCATAGT
5942563 CTTGATATGT
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
86 47 0.57
87 36 0.43
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (86 bp):
TATAAAATTTATATATTGATAATATATCAAATATAAATTTTTTTACATATGATTTTTTGTACGTT
AACCACATTGACTAGCATAGT
Found at i:5944530 original size:6 final size:6
Alignment explanation
Indices: 5944515--5944548 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5944505 CTCCAAATGA
* *
5944515 TAGGGT TAGGGC TAGGGC TAGGGC TAGAGC TAGG
1 TAGGGC TAGGGC TAGGGC TAGGGC TAGGGC TAGG
5944549 CTGACGTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.12, G:0.47, T:0.21
Consensus pattern (6 bp):
TAGGGC
Found at i:5946805 original size:18 final size:18
Alignment explanation
Indices: 5946782--5946819 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5946772 TTTTATTAAA
*
5946782 ATTTTAAATTATTTTTAT
1 ATTTTAAATGATTTTTAT
*
5946800 ATTTTATATGATTTTTAT
1 ATTTTAAATGATTTTTAT
5946818 AT
1 AT
5946820 CATGTCATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
ATTTTAAATGATTTTTAT
Found at i:5947097 original size:18 final size:20
Alignment explanation
Indices: 5947070--5947113 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
5947060 TATTTTATTT
5947070 TATA-AAAAATTAA-AA-AA
1 TATATAAAAATTAATAATAA
5947087 TATATAAAAATTAATAATAA
1 TATATAAAAATTAATAATAA
5947107 TATATAA
1 TATATAA
5947114 TTTGATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.17
18 9 0.38
19 2 0.08
20 9 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TATATAAAAATTAATAATAA
Found at i:5948194 original size:62 final size:55
Alignment explanation
Indices: 5948053--5948194 Score: 128
Period size: 56 Copynumber: 2.4 Consensus size: 55
5948043 TATTTAAAAT
* *
5948053 ATAATATAATGATATGATATA-AAAATATAAAAATAATATAATTTAAAATTTTTATA
1 ATAATATAAT-ATA-AATATATAAAATAAAAAAATAATATAATTTAAAATTTTTATA
*
5948109 ATAAT-TATATATAAATTTAATAAAATAAAAAAATTAATATAAATTATAACATAATTTTTAAGTA
1 ATAATATA-ATATAAATAT-ATAAAATAAAAAAA-TAATAT-AATT-T-A-A-AATTTTT-A-TA
5948173 A-AATATAATATAAATATATAAA
1 ATAATATAATATAAATATATAAA
5948195 TTTTAATATT
Statistics
Matches: 70, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
54 3 0.04
55 6 0.09
56 18 0.26
57 6 0.09
58 4 0.06
59 1 0.01
60 1 0.01
61 1 0.01
62 12 0.17
63 13 0.19
64 5 0.07
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (55 bp):
ATAATATAATATAAATATATAAAATAAAAAAATAATATAATTTAAAATTTTTATA
Found at i:5951278 original size:19 final size:18
Alignment explanation
Indices: 5951241--5951279 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
5951231 TACCACGACA
*
5951241 TTCCAAAATATTTGGAGT
1 TTCCAAAATATTTAGAGT
*
5951259 TTCCAATAATATTTATAGT
1 TTCCAA-AATATTTAGAGT
5951278 TT
1 TT
5951280 TGTATGTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (18 bp):
TTCCAAAATATTTAGAGT
Found at i:5952932 original size:20 final size:23
Alignment explanation
Indices: 5952907--5952951 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 23
5952897 ATTATATATA
*
5952907 TATTTAGTAA-AT-AATTT-TTT
1 TATTTAATAATATAAATTTATTT
5952927 TATTTAATAATATAAATTTATTT
1 TATTTAATAATATAAATTTATTT
5952950 TA
1 TA
5952952 GATTAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 2 0.10
22 5 0.24
23 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTTAATAATATAAATTTATTT
Done.