Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, 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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 35 of 117
Found at i:5903750 original size:18 final size:19
Alignment explanation
Indices: 5903714--5903751 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5903704 AAAGTTTTAA
5903714 AATTTCAAAATAAATATTT
1 AATTTCAAAATAAATATTT
5903733 AATTT-AAAATTAAA-ATTT
1 AATTTCAAAA-TAAATATTT
5903751 A
1 A
5903752 TCCATCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTTCAAAATAAATATTT
Found at i:5907020 original size:12 final size:13
Alignment explanation
Indices: 5907003--5907034 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5906993 GCCAGGTTTC
5907003 TTTTTTTCTT-CT
1 TTTTTTTCTTCCT
5907015 TTTTTTT-TTCCT
1 TTTTTTTCTTCCT
5907027 TTTTTTTC
1 TTTTTTTC
5907035 AAATTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 16 0.89
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTCTTCCT
Found at i:5910033 original size:23 final size:23
Alignment explanation
Indices: 5910006--5910052 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
5909996 ATCATTATGA
*
5910006 TGAAGTTTACATGATATGGATGT
1 TGAAGTTTACATGATATGAATGT
* *
5910029 TGAAGTTTATATGATGTGAATGT
1 TGAAGTTTACATGATATGAATGT
5910052 T
1 T
5910053 TTAAATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.43
Consensus pattern (23 bp):
TGAAGTTTACATGATATGAATGT
Found at i:5920673 original size:21 final size:20
Alignment explanation
Indices: 5920633--5920682 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
5920623 ATTGAAATTA
5920633 ATAAAATATTATTTTTAAAT
1 ATAAAATATTATTTTTAAAT
5920653 ATAAAATATTATTTTTAAA-
1 ATAAAATATTATTTTTAAAT
5920672 ATATAAATATT
1 ATA-AAATATT
5920683 TAATTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAAAATATTATTTTTAAAT
Found at i:5925699 original size:27 final size:27
Alignment explanation
Indices: 5925644--5925699 Score: 62
Period size: 29 Copynumber: 2.0 Consensus size: 27
5925634 TGCAAATAAA
*
5925644 AAAAATTAAGAGTTTATTTGAGTATAAT
1 AAAAATTAAGAGTTTATTTGAG-AGAAT
5925672 AAAAATATAAGAGTTTTATTT-A-AGAAT
1 AAAAAT-TAAGAG-TTTATTTGAGAGAAT
5925699 A
1 A
5925700 GTAAAGAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 5 0.20
28 6 0.24
29 7 0.28
30 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (27 bp):
AAAAATTAAGAGTTTATTTGAGAGAAT
Found at i:5928235 original size:30 final size:30
Alignment explanation
Indices: 5928201--5928258 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5928191 TAATTGAATA
* *
5928201 CAAATTAAAGGTTAATAATTTATTTCAGAG
1 CAAATTAAAGATAAATAATTTATTTCAGAG
**
5928231 CAAATTAAAGATAAATGGTTTATTTCAG
1 CAAATTAAAGATAAATAATTTATTTCAG
5928259 TATTATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (30 bp):
CAAATTAAAGATAAATAATTTATTTCAGAG
Found at i:5929629 original size:9 final size:9
Alignment explanation
Indices: 5929611--5929639 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5929601 ATGATATGAT
5929611 AAAAAA-TA
1 AAAAAATTA
5929619 AAAAAATTA
1 AAAAAATTA
5929628 AAAAAATTA
1 AAAAAATTA
5929637 AAA
1 AAA
5929640 TTTTTACGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAAAATTA
Found at i:5939613 original size:107 final size:108
Alignment explanation
Indices: 5939427--5939643 Score: 346
Period size: 107 Copynumber: 2.0 Consensus size: 108
5939417 TCCCATCAGA
* * * *
5939427 AACCGCCTATATGCCATGATCAAAATAACCATGGTTAGAACCAGAACAGAAAACACCTAAGTTTC
1 AACCGCCTAGATGCCATGATAAAAAAAACCATGGTTAGAACCAGAACAGAAAACACCCAAGTTTC
5939492 AGGTTAGACAATAAAGAAAAATA-TAACTACAAAGTTATATTG
66 AGGTTAGACAATAAAGAAAAATATTAACTACAAAGTTATATTG
* * * * *
5939534 AACCGCCTAGCTGTCATGATAAAAAAAACCATGGTTAGAACTAGAACGGAAAACACCCAAGTTTT
1 AACCGCCTAGATGCCATGATAAAAAAAACCATGGTTAGAACCAGAACAGAAAACACCCAAGTTTC
5939599 AGGTTAGACAATAAAGAAAAATATTAACTACAAAGTTATATTG
66 AGGTTAGACAATAAAGAAAAATATTAACTACAAAGTTATATTG
5939642 AA
1 AA
5939644 TTATCAATTG
Statistics
Matches: 100, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
107 79 0.79
108 21 0.21
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.23
Consensus pattern (108 bp):
AACCGCCTAGATGCCATGATAAAAAAAACCATGGTTAGAACCAGAACAGAAAACACCCAAGTTTC
AGGTTAGACAATAAAGAAAAATATTAACTACAAAGTTATATTG
Found at i:5941913 original size:19 final size:19
Alignment explanation
Indices: 5941875--5941913 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5941865 GACAATAGAG
***
5941875 ATTATTACATGGATTTAAA
1 ATTATTACATGGAGAAAAA
5941894 ATTATTACATGGAGAAAAA
1 ATTATTACATGGAGAAAAA
5941913 A
1 A
5941914 AAACAACAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (19 bp):
ATTATTACATGGAGAAAAA
Found at i:5952441 original size:2 final size:2
Alignment explanation
Indices: 5952434--5952465 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5952424 CAGCCAACAA
5952434 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
5952466 TAACTTTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5963373 original size:10 final size:10
Alignment explanation
Indices: 5963355--5963390 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
5963345 CCTCGATGAG
5963355 AAAAA-AATT
1 AAAAATAATT
5963364 AAAAATAATT
1 AAAAATAATT
5963374 AAAAAATAATT
1 -AAAAATAATT
5963385 AAAAAT
1 AAAAAT
5963391 TATATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.20
10 10 0.40
11 10 0.40
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
AAAAATAATT
Found at i:5963380 original size:11 final size:11
Alignment explanation
Indices: 5963355--5963389 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
5963345 CCTCGATGAG
5963355 AAAAA-AATT-
1 AAAAATAATTA
5963364 AAAAATAATTA
1 AAAAATAATTA
5963375 AAAAATAATTA
1 AAAAATAATTA
5963386 AAAA
1 AAAA
5963390 TTATATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 5 0.21
10 4 0.17
11 15 0.62
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAATAATTA
Found at i:5963486 original size:12 final size:11
Alignment explanation
Indices: 5963429--5963488 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
5963419 TTTTTTATTT
*
5963429 AATTTAGATCA
1 AATTTAGATTA
*
5963440 AAGTTAGATATTA
1 AATTTAG--ATTA
* *
5963453 AATATATATTA
1 AATTTAGATTA
5963464 AATTTAGATTA
1 AATTTAGATTA
5963475 AATTTCAGATTA
1 AATTT-AGATTA
5963487 AA
1 AA
5963489 ATGTGAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 24 0.62
12 8 0.21
13 7 0.18
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.40
Consensus pattern (11 bp):
AATTTAGATTA
Found at i:5963549 original size:20 final size:20
Alignment explanation
Indices: 5963524--5963565 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5963514 TGAATCAAAT
*
5963524 TATATAT-TTTTATTAATTTA
1 TATATATATTTTA-AAATTTA
5963544 TATATATATTTTAAAATTTA
1 TATATATATTTTAAAATTTA
5963564 TA
1 TA
5963566 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATATATTTTAAAATTTA
Found at i:5963643 original size:79 final size:79
Alignment explanation
Indices: 5963554--5963715 Score: 297
Period size: 79 Copynumber: 2.1 Consensus size: 79
5963544 TATATATATT
*
5963554 TTAAAATTTATAAAATAAAAATAATTAATTTATGTATAAAATTATTTAAATATATTAAAATAATA
1 TTAAAATTTATAAAATAAAAATAATTAATTTATATATAAAATTATTTAAATATATTAAAATAATA
5963619 TATAAAAATAAAAA
66 TATAAAAATAAAAA
* *
5963633 TTAAATTTTATAAAATAAAAATAATTAATTTATATATAAATTTATTTAAATATATTAAAATAATA
1 TTAAAATTTATAAAATAAAAATAATTAATTTATATATAAAATTATTTAAATATATTAAAATAATA
5963698 TATAAAAATAAAAA
66 TATAAAAATAAAAA
5963712 TTAA
1 TTAA
5963716 TAAACAGAAT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.40
Consensus pattern (79 bp):
TTAAAATTTATAAAATAAAAATAATTAATTTATATATAAAATTATTTAAATATATTAAAATAATA
TATAAAAATAAAAA
Found at i:5963664 original size:22 final size:22
Alignment explanation
Indices: 5963612--5963666 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
5963602 AATATATTAA
*
5963612 AATAATATATAAAAATAAAAATT
1 AATAATTTAT-AAAATAAAAATT
*
5963635 AA-ATTTTATAAAATAAAAA-T
1 AATAATTTATAAAATAAAAATT
5963655 AATTAATTTATA
1 AA-TAATTTATA
5963667 TATAAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 3 0.11
21 10 0.37
22 12 0.44
23 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAATTTATAAAATAAAAATT
Found at i:5964404 original size:21 final size:20
Alignment explanation
Indices: 5964354--5964405 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
5964344 AATATTTTGT
*
5964354 TAATATTATTAAATTATATA
1 TAATATTATTAAATTATAAA
*
5964374 TAATAGTTATTAAAATTTTAAA
1 TAATA-TTATT-AAATTATAAA
*
5964396 TTATATTATT
1 TAATATTATT
5964406 TTTAAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 10 0.37
22 12 0.44
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATATTATTAAATTATAAA
Found at i:5964411 original size:45 final size:44
Alignment explanation
Indices: 5964357--5964460 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 44
5964347 ATTTTGTTAA
* *
5964357 TATTATTAAATTATATATAATAGTTATTAAAATTTTA-AATTATAT
1 TATTTTTAAATTATATAT-AT-GTTATTAAAATTATATAATTATAT
* * * *
5964402 TATTTTTAAATTATTTATATTTTATTAATATTATATTATTATAT
1 TATTTTTAAATTATATATATGTTATTAAAATTATATAATTATAT
*
5964446 CATATTTTAAATTAT
1 TAT-TTTTAAATTAT
5964461 CAAATTTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 12 0.24
44 11 0.22
45 27 0.54
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (44 bp):
TATTTTTAAATTATATATATGTTATTAAAATTATATAATTATAT
Found at i:5964419 original size:15 final size:17
Alignment explanation
Indices: 5964388--5964460 Score: 72
Period size: 16 Copynumber: 4.7 Consensus size: 17
5964378 AGTTATTAAA
5964388 ATTTTAAATTATATTAT
1 ATTTTAAATTATATTAT
5964405 -TTTTAAATTAT-TTAT
1 ATTTTAAATTATATTAT
5964420 ATTTT--ATTAATATTAT
1 ATTTTAAATT-ATATTAT
*
5964436 A--TT--ATTATATCAT
1 ATTTTAAATTATATTAT
5964449 ATTTTAAATTAT
1 ATTTTAAATTAT
5964461 CAAATTTAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
13 7 0.15
14 8 0.17
15 8 0.17
16 20 0.42
17 5 0.10
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTAAATTATATTAT
Found at i:5975840 original size:28 final size:25
Alignment explanation
Indices: 5975809--5975869 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
5975799 AAAGTTTTTA
5975809 ATTAAATATTTAAACTTTATTTTTATAT
1 ATTAAATATTTAAA--TT-TTTTTATAT
*
5975837 ATTAAATTATTTCAATTTTTTTATAT
1 ATTAAA-TATTTAAATTTTTTTATAT
*
5975863 TTTAAAT
1 ATTAAAT
5975870 TAAAATTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 1 0.03
26 14 0.47
27 2 0.07
28 6 0.20
29 7 0.23
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTAAATATTTAAATTTTTTTATAT
Found at i:5976088 original size:27 final size:27
Alignment explanation
Indices: 5976031--5976089 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
5976021 TATCCACAGC
* ** *
5976031 ATTTAAGTATTTGATTAAAAAAATTTT
1 ATTTAAGGATTTGATTAAAAAAAAATA
5976058 ATTTAAGGATTAT-ATTAAAAAAAAATA
1 ATTTAAGGATT-TGATTAAAAAAAAATA
5976085 ATTTA
1 ATTTA
5976090 GGAGACAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (27 bp):
ATTTAAGGATTTGATTAAAAAAAAATA
Found at i:5977692 original size:16 final size:15
Alignment explanation
Indices: 5977651--5977698 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
5977641 ACAATGATAT
*
5977651 GATATAAACATAATACA
1 GATATAAA-AT-ATAAA
5977668 GATATAAAATATAAA
1 GATATAAAATATAAA
*
5977683 GATAATAAAATTTAAA
1 GAT-ATAAAATATAAA
5977699 ATTTTAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.25
16 13 0.46
17 8 0.29
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (15 bp):
GATATAAAATATAAA
Found at i:5988418 original size:15 final size:18
Alignment explanation
Indices: 5988381--5988419 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 18
5988371 TTTAAAATTT
5988381 TATTATATCTTATAAATA
1 TATTATATCTTATAAATA
5988399 TATTA-ATCTT-TAAA-A
1 TATTATATCTTATAAATA
5988414 TATTAT
1 TATTAT
5988420 TTGTTCATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.30
16 4 0.20
17 5 0.25
18 5 0.25
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTATATCTTATAAATA
Found at i:5988420 original size:18 final size:19
Alignment explanation
Indices: 5988371--5988420 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
5988361 TTTAAAGAAT
*
5988371 TTTAAAATTTTATTATATC
1 TTTAAAATATTATTATATC
5988390 -TTATAAATA-TATTA-ATC
1 TTTA-AAATATTATTATATC
5988407 TTTAAAATATTATT
1 TTTAAAATATTATT
5988421 TGTTCATACT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 8 0.30
18 15 0.56
19 4 0.15
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAAAATATTATTATATC
Found at i:5988837 original size:20 final size:20
Alignment explanation
Indices: 5988812--5988852 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5988802 AGCTGGAAGA
5988812 TAGCCATATTTCATTCGGCT
1 TAGCCATATTTCATTCGGCT
5988832 TAGCCATATTTCATTCGGCT
1 TAGCCATATTTCATTCGGCT
5988852 T
1 T
5988853 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (20 bp):
TAGCCATATTTCATTCGGCT
Found at i:5989389 original size:26 final size:24
Alignment explanation
Indices: 5989353--5989403 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 24
5989343 TTTATATGTA
*
5989353 TTTATTTAAATTAT-TATTTATTTG
1 TTTATTTAAA-TATGAATTTATTTG
5989377 TTTATTATAAAATATGAATTTATTTG
1 TTTATT-T-AAATATGAATTTATTTG
5989403 T
1 T
5989404 CATTTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 6 0.26
25 4 0.17
26 13 0.57
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATTTAAATATGAATTTATTTG
Found at i:5989473 original size:20 final size:19
Alignment explanation
Indices: 5989436--5989478 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
5989426 ATATTTTAAT
*
5989436 AAAAAAATAAAACTAAAAAC
1 AAAAAAATAAAAC-AAAAAA
5989456 AAAAAAATGAAAA-AAAAAA
1 AAAAAAAT-AAAACAAAAAA
5989475 AAAA
1 AAAA
5989479 CCAAGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 8 0.38
21 4 0.19
ACGTcount: A:0.86, C:0.05, G:0.02, T:0.07
Consensus pattern (19 bp):
AAAAAAATAAAACAAAAAA
Found at i:5989477 original size:15 final size:14
Alignment explanation
Indices: 5989433--5989477 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
5989423 TAAATATTTT
*
5989433 AATAAAAAAATAAA
1 AATAAAAAAAAAAA
* *
5989447 ACTAAAAACAAAAA
1 AATAAAAAAAAAAA
5989461 AATGAAAAAAAAAAA
1 AAT-AAAAAAAAAAA
5989476 AA
1 AA
5989478 ACCAAGAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.84, C:0.04, G:0.02, T:0.09
Consensus pattern (14 bp):
AATAAAAAAAAAAA
Found at i:5990716 original size:177 final size:177
Alignment explanation
Indices: 5990218--5990794 Score: 953
Period size: 177 Copynumber: 3.3 Consensus size: 177
5990208 GCATCGTCAA
*
5990218 TGCAGAAAATACGTTCCGACGTTACAACACTCTTGGCGATGGTGTAGCAGGTGGTGCTAGTGCTC
1 TGCAGAAAATATGTTCCGACGTTACAACACTCTTGGCGATGGTGTAGCAGGTGGTGCTAGTGCTC
5990283 AAGGCAATCCAGGCGGTCGCGTTCAAGGAGGTTATAGAGGTCATGACGCTTATGATGAAGGCAAT
66 AAGGCAATCCAGGCGGTCGCGTTCAAGGAGGTTATAGAGGTCATGACGCTTATGATGAAGGCAAT
5990348 TGGGGAGGCGGTGATTCCGGTGTCGGCGGTGATGGCTTTGGAGTACT
131 TGGGGAGGCGGTGATTCCGGTGTCGGCGGTGATGGCTTTGGAGTACT
*** * *
5990395 TG--G-TTTTCTGCTCCGACGTTACAACACTCTTGGCGATGGTGTAGCAGGTGGTGCTAGTGCTC
1 TGCAGAAAATATGTTCCGACGTTACAACACTCTTGGCGATGGTGTAGCAGGTGGTGCTAGTGCTC
5990457 AAGGCAATCCAGGCGGTCGCGTTCAAGGAGGTTATAGAGGTCATGACGCTTATGATGAAGGCAAT
66 AAGGCAATCCAGGCGGTCGCGTTCAAGGAGGTTATAGAGGTCATGACGCTTATGATGAAGGCAAT
5990522 TGGGGAGGCGGTGATTCCGGTGTCGGCGGTGATGGCTTTGGAGTACT
131 TGGGGAGGCGGTGATTCCGGTGTCGGCGGTGATGGCTTTGGAGTACT
5990569 TGCAGAAAATATGTTCCGACGTTACAACACTCTTGGCGATGGTGTAGCAGGTGGTGCTAGTGCTC
1 TGCAGAAAATATGTTCCGACGTTACAACACTCTTGGCGATGGTGTAGCAGGTGGTGCTAGTGCTC
*
5990634 AAGGCAATCCAGGAGGTCGCGTTCAAGGAGGTTATAGAGGTCATGACGCTTATGATGAAGGCAAT
66 AAGGCAATCCAGGCGGTCGCGTTCAAGGAGGTTATAGAGGTCATGACGCTTATGATGAAGGCAAT
* ** ** * *
5990699 TGGCGAGGCCCTGATTCCTATGTCCGCCGTGATGGCTTTGGAGTACT
131 TGGGGAGGCGGTGATTCCGGTGTCGGCGGTGATGGCTTTGGAGTACT
* * * * * *
5990746 TGCAGAAAATATGTTGCGAGGTGACGACACTCGTGACGATGGTGTAGCA
1 TGCAGAAAATATGTTCCGACGTTACAACACTCTTGGCGATGGTGTAGCA
5990795 CCACCTGCAG
Statistics
Matches: 372, Mismatches: 25, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
174 167 0.45
175 1 0.00
176 1 0.00
177 203 0.55
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.26
Consensus pattern (177 bp):
TGCAGAAAATATGTTCCGACGTTACAACACTCTTGGCGATGGTGTAGCAGGTGGTGCTAGTGCTC
AAGGCAATCCAGGCGGTCGCGTTCAAGGAGGTTATAGAGGTCATGACGCTTATGATGAAGGCAAT
TGGGGAGGCGGTGATTCCGGTGTCGGCGGTGATGGCTTTGGAGTACT
Found at i:5991057 original size:127 final size:126
Alignment explanation
Indices: 5990819--5991073 Score: 501
Period size: 127 Copynumber: 2.0 Consensus size: 126
5990809 CACTGCTATT
5990819 CTCGCTCCAGCTCCACTAGACCAGAACTTGAGTTTTATGGACTTGCCACCTGCACAAAGAGTCGT
1 CTCGCTCCAGCTCCACTAGACCAGAACTTGAGTTTTATGGACTTGCCACCTGCACAAAGAGTCGT
5990884 AGGAGATTCAGAATTGGTTAGTTTGAGTGAAGACGAAGCAATTCAGCTAATTGGCCGTGAG
66 AGGAGATTCAGAATTGGTTAGTTTGAGTGAAGACGAAGCAATTCAGCTAATTGGCCGTGAG
5990945 CTCGCTCCAGCTACCACTAGACCAGAACTTGAGTTTTATGGACTTGCCACCTGCACAAAGAGTCG
1 CTCGCTCCAGCT-CCACTAGACCAGAACTTGAGTTTTATGGACTTGCCACCTGCACAAAGAGTCG
5991010 TAGGAGATTCAGAATTGGTTAGTTTGAGTGAAGACGAAGCAATTCAGCTAATTGGCCGTGAG
65 TAGGAGATTCAGAATTGGTTAGTTTGAGTGAAGACGAAGCAATTCAGCTAATTGGCCGTGAG
5991072 CT
1 CT
5991074 GTACAGCCTA
Statistics
Matches: 128, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
126 12 0.09
127 116 0.91
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (126 bp):
CTCGCTCCAGCTCCACTAGACCAGAACTTGAGTTTTATGGACTTGCCACCTGCACAAAGAGTCGT
AGGAGATTCAGAATTGGTTAGTTTGAGTGAAGACGAAGCAATTCAGCTAATTGGCCGTGAG
Found at i:5992721 original size:13 final size:13
Alignment explanation
Indices: 5992703--5992727 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5992693 TCAATTGTTT
5992703 AAAAAATTAAATA
1 AAAAAATTAAATA
5992716 AAAAAATTAAAT
1 AAAAAATTAAAT
5992728 TAAATTATAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAAATTAAATA
Found at i:5992819 original size:16 final size:17
Alignment explanation
Indices: 5992772--5992819 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
5992762 TTCTATCAAC
5992772 AATTATTTTTTTATT-T
1 AATTATTTTTTTATTAT
*
5992788 AATT-TTTTAATTATTAT
1 AATTATTTT-TTTATTAT
5992805 -ATTATTTTTTTATTA
1 AATTATTTTTTTATTA
5992820 CTTGTATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 4 0.15
16 18 0.67
17 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
AATTATTTTTTTATTAT
Found at i:5994075 original size:22 final size:20
Alignment explanation
Indices: 5994042--5994084 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
5994032 TATTTTTATA
* *
5994042 TCTTTAATTTTTTATTATTT
1 TCTTTAATTTTTAAATATTT
5994062 TCTTTATATATTTTAAATATTT
1 TCTTTA-AT-TTTTAAATATTT
5994084 T
1 T
5994085 AATTCATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 2 0.11
22 11 0.58
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (20 bp):
TCTTTAATTTTTAAATATTT
Found at i:5995746 original size:28 final size:28
Alignment explanation
Indices: 5995670--5995734 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
5995660 ATATTTTTTT
* *
5995670 ATAAA-TTT-TTTT-AATCGTAATTATA
1 ATAAATTTTATTTTGAATCTTAATTACA
5995695 ATAAATTTTATTTTGAATCTTAATTACA
1 ATAAATTTTATTTTGAATCTTAATTACA
*
5995723 ATAATTTTTATT
1 ATAAATTTTATT
5995735 ATTATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.15
26 3 0.09
27 4 0.12
28 22 0.65
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (28 bp):
ATAAATTTTATTTTGAATCTTAATTACA
Found at i:6000837 original size:14 final size:15
Alignment explanation
Indices: 6000813--6000843 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
6000803 CATTAAAATG
6000813 TATTGAAATTATTAT
1 TATTGAAATTATTAT
6000828 TATT-AAATTATTAT
1 TATTGAAATTATTAT
6000842 TA
1 TA
6000844 AAAAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TATTGAAATTATTAT
Found at i:6000930 original size:9 final size:10
Alignment explanation
Indices: 6000916--6001032 Score: 59
Period size: 10 Copynumber: 11.9 Consensus size: 10
6000906 GAAATAAAAC
6000916 TATTTATTAT
1 TATTTATTAT
6000926 T-TTTA-TAT
1 TATTTATTAT
*
6000934 TATTTATTAA
1 TATTTATTAT
*
6000944 TATATTATAAAT
1 TAT-TTAT-TAT
6000956 TATTTATTAAT
1 TATTTATT-AT
* *
6000967 ATAATATAATAT
1 -T-ATTTATTAT
6000979 TATTTA-T-T
1 TATTTATTAT
*
6000987 TATTTAATAT
1 TATTTATTAT
*
6000997 TCTTTATTA-
1 TATTTATTAT
*
6001006 -ATATATTAT
1 TATTTATTAT
* *
6001015 T-TATAATAT
1 TATTTATTAT
6001024 TATTTATTA
1 TATTTATTA
6001033 ATATAATATT
Statistics
Matches: 81, Mismatches: 14, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
8 17 0.21
9 18 0.22
10 23 0.28
11 11 0.14
12 7 0.09
13 5 0.06
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTTATTAT
Found at i:6000939 original size:18 final size:18
Alignment explanation
Indices: 6000916--6001048 Score: 69
Period size: 18 Copynumber: 7.4 Consensus size: 18
6000906 GAAATAAAAC
6000916 TATTTATTATTTTTATAT
1 TATTTATTATTTTTATAT
*
6000934 TATTTATTA---ATATAT
1 TATTTATTATTTTTATAT
**
6000949 TATAAATTATTTATTAATAT
1 TATTTATTATTT-TT-ATAT
* * *
6000969 AATATAATATTATTTAT-T
1 TATTTATTATT-TTTATAT
*
6000987 TATTTAATATTCTTTAT-T
1 TATTTATTATT-TTTATAT
* * *
6001005 AATATATTATTTATAATAT
1 TATTTATTATTT-TTATAT
* * *
6001024 TATTTATTAATATAATAT
1 TATTTATTATTTTTATAT
6001042 TATTTAT
1 TATTTAT
6001049 AAGTAAAATT
Statistics
Matches: 89, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
15 12 0.13
17 1 0.01
18 49 0.55
19 12 0.13
20 14 0.16
21 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTATTATTTTTATAT
Found at i:6000940 original size:15 final size:15
Alignment explanation
Indices: 6000922--6001048 Score: 82
Period size: 15 Copynumber: 8.3 Consensus size: 15
6000912 AAACTATTTA
*
6000922 TTATTTTTATATTAT
1 TTATTATTATATTAT
*
6000937 TTATTAATATATTAT
1 TTATTATTATATTAT
**
6000952 AAATTATT-TATTAAT
1 TTATTATTATATT-AT
* * *
6000967 ATAATATAATATTAT
1 TTATTATTATATTAT
*
6000982 TTATTTATTTAATATTCT
1 TTA-TTA-TT-ATATTAT
*
6001000 TTATTAATATATTAT
1 TTATTATTATATTAT
6001015 TTA-TA--ATATTAT
1 TTATTATTATATTAT
6001027 TTATTAATATAATATTAT
1 TTATT-AT-T-ATATTAT
6001045 TTAT
1 TTAT
6001049 AAGTAAAATT
Statistics
Matches: 87, Mismatches: 14, Indels: 19
0.73 0.12 0.16
Matches are distributed among these distances:
12 10 0.11
13 1 0.01
14 7 0.08
15 38 0.44
16 7 0.08
17 4 0.05
18 20 0.23
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTATTATATTAT
Found at i:6000997 original size:63 final size:64
Alignment explanation
Indices: 6000916--6001048 Score: 182
Period size: 63 Copynumber: 2.1 Consensus size: 64
6000906 GAAATAAAAC
* *
6000916 TATTTA-TTATTTTTATATTATTTATTAATATATTATAAATTAT-TTATTAATATAATATAATAT
1 TATTTATTTATTTTAATATTATTTATTAATATATTATAAATAATATTATTAAT-TAATATAATAT
* ** *
6000979 TATTTATTTA-TTTAATATTCTTTATTAATATATTATTTATAATATTATTTATTAATATAATAT
1 TATTTATTTATTTTAATATTATTTATTAATATATTATAAATAATATTATTAATTAATATAATAT
6001042 TATTTAT
1 TATTTAT
6001049 AAGTAAAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
63 52 0.84
64 10 0.16
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (64 bp):
TATTTATTTATTTTAATATTATTTATTAATATATTATAAATAATATTATTAATTAATATAATAT
Found at i:6001033 original size:27 final size:28
Alignment explanation
Indices: 6000929--6001042 Score: 109
Period size: 27 Copynumber: 4.3 Consensus size: 28
6000919 TTATTATTTT
6000929 TATATTATTTATTAATA-TA-TTA-T-A
1 TATATTATTTATTAATATTATTTATTAA
* * * *
6000953 -A-ATTATTTATTAATATAATATAATAT
1 TATATTATTTATTAATATTATTTATTAA
*
6000979 TAT-TTATTTATTTAATATTCTTTATTAA
1 TATATTATTTA-TTAATATTATTTATTAA
6001007 TATATTATTTA-TAATATTATTTATTAA
1 TATATTATTTATTAATATTATTTATTAA
*
6001034 TATAATATT
1 TATATTATT
6001043 ATTTATAAGT
Statistics
Matches: 72, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
22 14 0.19
23 2 0.03
24 2 0.03
25 1 0.01
27 31 0.43
28 15 0.21
29 7 0.10
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (28 bp):
TATATTATTTATTAATATTATTTATTAA
Found at i:6001040 original size:45 final size:45
Alignment explanation
Indices: 6000920--6001048 Score: 151
Period size: 45 Copynumber: 2.9 Consensus size: 45
6000910 TAAAACTATT
*
6000920 TATTATTT-TTATATTATTTATTAATATATTATAAATTATTTATTAATA
1 TATTATTTATAATATTATTTATTAATATA--AT--ATTATTTATTAATA
* * *
6000968 TA--A--TATAATATTATTTATTTATTTAATATTCTTTATTAATA
1 TATTATTTATAATATTATTTATTAATATAATATTATTTATTAATA
6001009 TATTATTTATAATATTATTTATTAATATAATATTATTTAT
1 TATTATTTATAATATTATTTATTAATATAATATTATTTAT
6001049 AAGTAAAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 13
0.78 0.08 0.15
Matches are distributed among these distances:
41 15 0.22
43 3 0.04
44 1 0.01
45 47 0.68
46 1 0.01
48 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.60
Consensus pattern (45 bp):
TATTATTTATAATATTATTTATTAATATAATATTATTTATTAATA
Found at i:6006508 original size:24 final size:24
Alignment explanation
Indices: 6006477--6006528 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
6006467 TAAGAGTTAT
* *
6006477 AAATAAAAAAAATATTTGATA-AA
1 AAATAAAAAAAAAATTTAATATAA
6006500 AAATAAAAAAAAAATTTAATATAA
1 AAATAAAAAAAAAATTTAATATAA
6006524 AAATA
1 AAATA
6006529 CATAAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (24 bp):
AAATAAAAAAAAAATTTAATATAA
Found at i:6009143 original size:6 final size:6
Alignment explanation
Indices: 6009134--6009169 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
6009124 ATAATTTTTA
*
6009134 TTTATT TTTATT TTTATT TTTATT TTT-TT GTTATT T
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT T
6009170 AGGAATCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:6010264 original size:2 final size:2
Alignment explanation
Indices: 6010259--6010292 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6010249 AAAATTATTT
6010259 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
6010293 AAAGCAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6017868 original size:16 final size:16
Alignment explanation
Indices: 6017847--6017878 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6017837 CCCATGGTTA
6017847 TTAATTATTGAAGTTT
1 TTAATTATTGAAGTTT
6017863 TTAATTATTGAAGTTT
1 TTAATTATTGAAGTTT
6017879 GTGAAACTGA
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:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (16 bp):
TTAATTATTGAAGTTT
Found at i:6024251 original size:31 final size:30
Alignment explanation
Indices: 6024208--6024265 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
6024198 ACATTCTCAT
6024208 TTTATAAATTTATTTATTTGTATATCATATGA
1 TTTATAAATTTATTTA-TT-TATATCATATGA
6024240 TTTAT-AATTTATTTATTTATATCATA
1 TTTATAAATTTATTTATTTATATCATA
6024266 GACTATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 9 0.35
30 2 0.08
31 10 0.38
32 5 0.19
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (30 bp):
TTTATAAATTTATTTATTTATATCATATGA
Found at i:6024272 original size:27 final size:31
Alignment explanation
Indices: 6024214--6024272 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
6024204 TCATTTTATA
*
6024214 AATTTATTTATTTGTATATCATATGATTTAT
1 AATTTATTTATTTGTATATCATATGATCTAT
6024245 AATTTATTTA-TT-TATATCATA-GA-CTAT
1 AATTTATTTATTTGTATATCATATGATCTAT
6024272 A
1 A
6024273 TTAATTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 4 0.15
28 2 0.07
29 9 0.33
30 2 0.07
31 10 0.37
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (31 bp):
AATTTATTTATTTGTATATCATATGATCTAT
Found at i:6026814 original size:2 final size:2
Alignment explanation
Indices: 6026803--6026852 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
6026793 ATCCTTGTCC
* * *
6026803 TA TA -A TA TA TA TA TA TA TA TA TA TA TC TA TA TC TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
6026844 TA TC TA TA T
1 TA TA TA TA T
6026853 GTCTTCCTCC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6032959 original size:27 final size:28
Alignment explanation
Indices: 6032929--6033000 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
6032919 TTTTCAAATC
6032929 TTTTGTTTATTTTTTGAAATGGG-ATTT
1 TTTTGTTTATTTTTTGAAATGGGTATTT
*
6032956 TTTT-TTTATTGTTTTAAAATGGGTATTT
1 TTTTGTTTATT-TTTTGAAATGGGTATTT
* *
6032984 GTTGGTTT-TTTATTTGA
1 TTTTGTTTATTT-TTTGA
6033001 GGCTGTGTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
26 6 0.16
27 16 0.43
28 12 0.32
29 3 0.08
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (28 bp):
TTTTGTTTATTTTTTGAAATGGGTATTT
Found at i:6035648 original size:15 final size:16
Alignment explanation
Indices: 6035624--6035656 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
6035614 TATACATATT
*
6035624 ATATATTATATGATTA
1 ATATATTATATAATTA
6035640 ATATA-TATATAATTA
1 ATATATTATATAATTA
6035655 AT
1 AT
6035657 TCGTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
ATATATTATATAATTA
Found at i:6035707 original size:25 final size:24
Alignment explanation
Indices: 6035679--6035770 Score: 65
Period size: 23 Copynumber: 4.0 Consensus size: 24
6035669 GATATGAATA
6035679 AATATGAATAATATTAATATATATT
1 AATATG-ATAATATTAATATATATT
* *
6035704 AATA-GATAAAATTAATACATA-T
1 AATATGATAATATTAATATATATT
*
6035726 -ATAT-A-AATATAAATATA-ATT
1 AATATGATAATATTAATATATATT
*
6035746 AACATGA-ATATATATAATA-ATATT
1 AATATGATA-ATAT-TAATATATATT
6035770 A
1 A
6035771 TTAAAATAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 10 0.19
21 7 0.13
22 3 0.06
23 19 0.36
24 9 0.17
25 4 0.08
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (24 bp):
AATATGATAATATTAATATATATT
Found at i:6035750 original size:27 final size:28
Alignment explanation
Indices: 6035720--6035794 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 28
6035710 TAAAATTAAT
6035720 ACAT-ATATATAAATATAAATATAATTA
1 ACATAATATATAAATATAAATATAATTA
* *
6035747 ACATGAATATATATA-AT-AATATTATTA
1 ACAT-AATATATAAATATAAATATAATTA
* * *
6035774 AAATAATAAATAATTATAAAT
1 ACATAATATATAAATATAAAT
6035795 TATTTATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
26 7 0.18
27 18 0.47
28 5 0.13
29 8 0.21
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (28 bp):
ACATAATATATAAATATAAATATAATTA
Found at i:6036217 original size:20 final size:19
Alignment explanation
Indices: 6036174--6036222 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
6036164 AATAGATATA
6036174 AAAAATATATTAAATGCCT
1 AAAAATATATTAAATGCCT
*
6036193 -TAAATATATTAAATATG-CT
1 AAAAATATATT-AA-ATGCCT
6036212 AAAAATATATT
1 AAAAATATATT
6036223 CATATAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 9 0.36
19 4 0.16
20 12 0.48
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (19 bp):
AAAAATATATTAAATGCCT
Found at i:6044608 original size:2 final size:2
Alignment explanation
Indices: 6044601--6044636 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6044591 ATAAATGCTC
6044601 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6044637 AAAAGATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6053165 original size:20 final size:22
Alignment explanation
Indices: 6053136--6053175 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
6053126 TGATATTGAA
6053136 TTTATCATTT-TTTA-ATAATT
1 TTTATCATTTATTTATATAATT
*
6053156 TTTATTATTTATTTATATAA
1 TTTATCATTTATTTATATAA
6053176 ATAAGAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 4 0.24
22 4 0.24
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATCATTTATTTATATAATT
Found at i:6057219 original size:29 final size:29
Alignment explanation
Indices: 6057181--6057246 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 29
6057171 TTTCCGCATT
6057181 TAAATTAATTTTTAATT-TTTAATTTATATC
1 TAAA-TAATTTTT-ATTATTTAATTTATATC
*
6057211 TAAATAATTTTTATTATTTAATTTATATT
1 TAAATAATTTTTATTATTTAATTTATATC
6057240 TAAATAA
1 TAAATAA
6057247 ACTCTTTACA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 3 0.09
29 27 0.79
30 4 0.12
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
TAAATAATTTTTATTATTTAATTTATATC
Found at i:6057552 original size:16 final size:17
Alignment explanation
Indices: 6057531--6057568 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
6057521 TATACTTTAA
6057531 ATTTTTA-ATTTATATT
1 ATTTTTATATTTATATT
*
6057547 ATTTTTATTTTTTATATT
1 ATTTTTA-TATTTATATT
6057565 ATTT
1 ATTT
6057569 CGTATCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
18 12 0.63
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTTTTATATTTATATT
Found at i:6057986 original size:13 final size:13
Alignment explanation
Indices: 6057968--6058018 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
6057958 GATATTATCT
6057968 AAATATAATATAA
1 AAATATAATATAA
6057981 AAATATAACT-TAA
1 AAATATAA-TATAA
*
6057994 AAATAATACATTTAA
1 AAAT-ATA-ATATAA
*
6058009 AATTATAATA
1 AAATATAATA
6058019 ATTATTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 17 0.53
14 8 0.25
15 7 0.22
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:6060133 original size:31 final size:30
Alignment explanation
Indices: 6060068--6060138 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 30
6060058 GTAACTTACT
*
6060068 TATATA-TAAATATTTTTTTATTAAATTAA
1 TATATATTAAATATATTTTTATTAAATTAA
6060097 -A-ATATTAAATAGTATTTTTATT-AATATAA
1 TATATATTAAATA-TATTTTTATTAAAT-TAA
6060126 TATATATTAAATA
1 TATATATTAAATA
6060139 AATAATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
27 3 0.08
28 10 0.28
29 12 0.33
30 1 0.03
31 10 0.28
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TATATATTAAATATATTTTTATTAAATTAA
Found at i:6061808 original size:19 final size:22
Alignment explanation
Indices: 6061758--6061823 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 22
6061748 AAATTTTAAG
6061758 TTAATTATTTTATATAATTATTA
1 TTAATT-TTTTATATAATTATTA
*
6061781 TTAA-ATTTTA-AT-ATTATTA
1 TTAATTTTTTATATAATTATTA
* *
6061800 -TAATTTTTT-TAAAATTATGA
1 TTAATTTTTTATATAATTATTA
6061820 TTAA
1 TTAA
6061824 GTCAAAATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 3 0.09
19 12 0.34
20 8 0.23
21 8 0.23
23 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTAATTTTTTATATAATTATTA
Found at i:6061913 original size:21 final size:22
Alignment explanation
Indices: 6061876--6061918 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
6061866 TATGGTTATC
6061876 ACAATAATTCGGTTCATATTGA
1 ACAATAATTCGGTTCATATTGA
6061898 ACAATAATTC-GTTCATATTGA
1 ACAATAATTCGGTTCATATTGA
6061919 TTTTTCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (22 bp):
ACAATAATTCGGTTCATATTGA
Found at i:6062261 original size:23 final size:23
Alignment explanation
Indices: 6062232--6062287 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 23
6062222 CATATTTGAT
6062232 ATATATAATAATATAAATTATTAAA
1 ATATAT-ATAATATAAATTA-TAAA
6062257 ATATAAATATAATATAAATTATAAA
1 ATAT--ATATAATATAAATTATAAA
6062282 ATATAT
1 ATATAT
6062288 TTAAATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
23 2 0.07
25 12 0.41
26 13 0.45
27 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATATATAATATAAATTATAAA
Found at i:6062272 original size:11 final size:12
Alignment explanation
Indices: 6062239--6062280 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 12
6062229 GATATATATA
6062239 ATAATATAAATT
1 ATAATATAAATT
6062251 ATTAAAATATAAA-T
1 A-T--AATATAAATT
6062265 ATAATATAAATT
1 ATAATATAAATT
6062277 ATAA
1 ATAA
6062281 AATATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 8 0.31
12 6 0.23
13 2 0.08
14 2 0.08
15 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAATATAAATT
Found at i:6062285 original size:19 final size:18
Alignment explanation
Indices: 6062230--6062300 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
6062220 ATCATATTTG
*
6062230 ATATATAT-AATAATATAA
1 ATATATATAAATTATA-AA
*
6062248 AT-TAT-TAAAATAT-AA
1 ATATATATAAATTATAAA
6062263 ATATAATATAAATTATAAA
1 ATAT-ATATAAATTATAAA
* *
6062282 ATATATTTAAATTTTAAA
1 ATATATATAAATTATAAA
6062300 A
1 A
6062301 ACGAATATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
15 4 0.09
16 2 0.05
17 9 0.21
18 22 0.51
19 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATATATAAATTATAAA
Found at i:6068454 original size:22 final size:22
Alignment explanation
Indices: 6068427--6068484 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
6068417 TGATGTTGAC
*
6068427 TTTTATAATGTTTAAGAA-AAAT
1 TTTTATAATGTTTAA-AATAAAG
6068449 TTTTAT-A-GTTTAAAATTAAAG
1 TTTTATAATGTTTAAAA-TAAAG
*
6068470 TTTTATAATTTTTAA
1 TTTTATAATGTTTAA
6068485 TGTAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 2 0.07
20 6 0.20
21 10 0.33
22 7 0.23
23 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
TTTTATAATGTTTAAAATAAAG
Found at i:6071701 original size:10 final size:10
Alignment explanation
Indices: 6071688--6071720 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
6071678 CAAAAAGAAA
6071688 GAAAACAGAG
1 GAAAACAGAG
6071698 GAAAACAGAG
1 GAAAACAGAG
*
6071708 G-AAACAGGG
1 GAAAACAGAG
6071717 GAAA
1 GAAA
6071721 GAAACCGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.58, C:0.09, G:0.33, T:0.00
Consensus pattern (10 bp):
GAAAACAGAG
Found at i:6073519 original size:111 final size:111
Alignment explanation
Indices: 6073321--6073546 Score: 398
Period size: 111 Copynumber: 2.0 Consensus size: 111
6073311 AAAATTTTAT
*
6073321 CATTGGAAATACATGATTTCAATATTCCATTCTAAATACAAAGTGTGGGTTTTGAAGCTATCAAG
1 CATTGGAAATACATGATTTCAACATTCCATTCTAAATACAAAGTGTGGGTTTTGAAGCTATCAAG
* *
6073386 TTTTGTATCGATGACAAGAAAAATGTTTTGAAATTTTTAAGTTTTG
66 TTTTGTATCAATGACAAAAAAAATGTTTTGAAATTTTTAAGTTTTG
*
6073432 CATTGGAAATACATGATTTCAACATTCCATTCTAAATACAAAGTGTGGGTTTTGGAGCTATCAAG
1 CATTGGAAATACATGATTTCAACATTCCATTCTAAATACAAAGTGTGGGTTTTGAAGCTATCAAG
* *
6073497 TTTTGTATCAATGATAAAAAAAATGTTTTGAAATTTTTAGGTTTTG
66 TTTTGTATCAATGACAAAAAAAATGTTTTGAAATTTTTAAGTTTTG
6073543 CATT
1 CATT
6073547 CAAATTTTAT
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (111 bp):
CATTGGAAATACATGATTTCAACATTCCATTCTAAATACAAAGTGTGGGTTTTGAAGCTATCAAG
TTTTGTATCAATGACAAAAAAAATGTTTTGAAATTTTTAAGTTTTG
Found at i:6076516 original size:18 final size:19
Alignment explanation
Indices: 6076486--6076540 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
6076476 TTGACATGAT
6076486 AATATAATAAAAAATTATAA
1 AATATAAT-AAAAATTATAA
*
6076506 AA-ATGAT-AAAATT-TAA
1 AATATAATAAAAATTATAA
6076522 AATTATAATAAAAATTATA
1 AA-TATAATAAAAATTATA
6076541 TATATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 5 0.17
17 6 0.21
18 4 0.14
19 10 0.34
20 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
AATATAATAAAAATTATAA
Found at i:6077350 original size:41 final size:40
Alignment explanation
Indices: 6077305--6077383 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 40
6077295 TTGTATAAAT
*
6077305 ATATATAAAATATAAAA-AT-TATTATATTATAATTTTTATTG
1 ATATATAAAATACAAAATATATATT-T-TT-TAATTTTTATTG
*
6077346 ATATATTAAATACAAAATATATATTTTTTAATTTTTAT
1 ATATATAAAATACAAAATATATATTTTTTAATTTTTAT
6077384 CAAATTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 10 0.29
41 17 0.50
42 3 0.09
43 4 0.12
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (40 bp):
ATATATAAAATACAAAATATATATTTTTTAATTTTTATTG
Found at i:6077363 original size:40 final size:41
Alignment explanation
Indices: 6077305--6077383 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 41
6077295 TTGTATAAAT
6077305 ATATATAAAATATAAAAAT-TATTATATTATAATTTTTATTG
1 ATATATAAAATATAAAAATATA-TATATTATAATTTTTATTG
* * * *
6077346 ATATATTAAATA-CAAAATATATATTTTTTAATTTTTAT
1 ATATATAAAATATAAAAATATATATATTATAATTTTTAT
6077384 CAAATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 20 0.61
41 13 0.39
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (41 bp):
ATATATAAAATATAAAAATATATATATTATAATTTTTATTG
Found at i:6081909 original size:16 final size:15
Alignment explanation
Indices: 6081888--6081921 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
6081878 CATCTATGGG
*
6081888 ATTTATTTACTTTTGT
1 ATTTATTTAATTTT-T
6081904 ATTTATTTAATTTTT
1 ATTTATTTAATTTTT
6081919 ATT
1 ATT
6081922 AAAAAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTTATTTAATTTTT
Found at i:6081947 original size:3 final size:3
Alignment explanation
Indices: 6081937--6081973 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
6081927 AAGAATTACC
6081937 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
6081974 AAGTTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:6087512 original size:27 final size:27
Alignment explanation
Indices: 6087454--6087522 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
6087444 TATTAACTAA
6087454 ATCACATTTGTATAAAGGCCAAAAAAG
1 ATCACATTTGTATAAAGGCCAAAAAAG
*
6087481 ATCACAATTGTATAAAGGCCAAAAATA-
1 ATCACATTTGTATAAAGGCCAAAAA-AG
* *
6087508 TTCACATTTGCATAA
1 ATCACATTTGTATAA
6087523 TTCATAGATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (27 bp):
ATCACATTTGTATAAAGGCCAAAAAAG
Found at i:6088259 original size:2 final size:2
Alignment explanation
Indices: 6088252--6088281 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6088242 AAGAAACCAA
6088252 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
6088282 GAAATGAAGG
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:6091023 original size:24 final size:23
Alignment explanation
Indices: 6090970--6091024 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
6090960 TTTATCATAG
* *
6090970 AAAAT-TTTAAAAATATTCCTTT
1 AAAATATTTAAAAATAATCATTT
**
6090992 AATTTATTTATAAAATAATCATTT
1 AAAATATTTA-AAAATAATCATTT
6091016 AAAATATTT
1 AAAATATTT
6091025 TTGTTTATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 3 0.12
23 4 0.16
24 18 0.72
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAATATTTAAAAATAATCATTT
Found at i:6091058 original size:63 final size:63
Alignment explanation
Indices: 6090989--6091166 Score: 175
Period size: 63 Copynumber: 2.8 Consensus size: 63
6090979 AAAATATTCC
* *
6090989 TTTAATTTATTTATAAAATAATCATTTAAAATATTTTTGTTTATAAAACGT-CTTAAATAATTT
1 TTTAATTTATTTATAAAATAATCATTTAAAATATTTTTATTTATAAAA-ATACTTAAATAATTT
** **
6091052 TTTAATTTATTTATAAAATAATTGTTTAAGGTATTTTCTA--TATAAAAATACCTTAAATAATTT
1 TTTAATTTATTTATAAAATAATCATTTAAAATATTTT-TATTTATAAAAATA-CTTAAATAATTT
* **
6091115 TTTTATTT-TTTATATTATGAATCATTTAATAATTATCTTTTAATTTATAAAA
1 TTTAATTTATTTATAAAAT-AATCATTTAA-AA-TAT-TTTT-ATTTATAAAA
6091167 TAATTATTTA
Statistics
Matches: 92, Mismatches: 13, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
61 1 0.01
62 15 0.16
63 60 0.65
64 1 0.01
65 4 0.04
66 4 0.04
68 7 0.08
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.52
Consensus pattern (63 bp):
TTTAATTTATTTATAAAATAATCATTTAAAATATTTTTATTTATAAAAATACTTAAATAATTT
Found at i:6091489 original size:62 final size:62
Alignment explanation
Indices: 6091327--6091485 Score: 205
Period size: 61 Copynumber: 2.6 Consensus size: 62
6091317 CTATTTAAGA
* * *
6091327 TATTTTCTGTATAGAAATACTTTAAATAATTAATTTATATTTTTATAAAAAAATTATTGAAAG
1 TATTTTCTGTACAAAAATACTTTAAATAA-TCATTTATATTTTTATAAAAAAATTATTGAAAG
* * * *
6091390 TGTTTTTTGTACAAAAATAC-TTAAATAATCCATTTATATTTTTAT-AAAAGATTATTGAATG
1 TATTTTCTGTACAAAAATACTTTAAATAAT-CATTTATATTTTTATAAAAAAATTATTGAAAG
* *
6091451 TATTTTCTATACAAAAATGCTTTAAATAATCATTT
1 TATTTTCTGTACAAAAATACTTTAAATAATCATTT
6091486 TATAAAAATA
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
61 36 0.43
62 31 0.37
63 16 0.19
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (62 bp):
TATTTTCTGTACAAAAATACTTTAAATAATCATTTATATTTTTATAAAAAAATTATTGAAAG
Found at i:6091519 original size:94 final size:94
Alignment explanation
Indices: 6091409--6091583 Score: 248
Period size: 94 Copynumber: 1.9 Consensus size: 94
6091399 TACAAAAATA
*
6091409 CTTAAATAATCCATTTATATTTTTATA-AAAGATTATTGAATG-TATTTTCTATACAAAA-ATGC
1 CTTAAATAATCCATTTATATTTTTATAGAAAGATTATTAAATGCTATTTTCTATA-AAAATAT-C
*
6091471 TTTAAATAATCATTTTATAAAAATAAAAACGC
64 -TTAAATAATCAATTTATAAAAATAAAAACGC
* * * *
6091503 CTTAAATAATCTATTTATATTTTTATAGAAATATTATTAAATGCTTTTTTGTATAAAAATATCTT
1 CTTAAATAATCCATTTATATTTTTATAGAAAGATTATTAAATGCTATTTTCTATAAAAATATCTT
6091568 AAATAATCAATTTATA
66 AAATAATCAATTTATA
6091584 TTTTTATAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
94 43 0.60
95 18 0.25
96 11 0.15
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (94 bp):
CTTAAATAATCCATTTATATTTTTATAGAAAGATTATTAAATGCTATTTTCTATAAAAATATCTT
AAATAATCAATTTATAAAAATAAAAACGC
Found at i:6091640 original size:58 final size:61
Alignment explanation
Indices: 6091503--6091655 Score: 171
Period size: 58 Copynumber: 2.6 Consensus size: 61
6091493 ATAAAAACGC
* *
6091503 CTTAAATAATCTATTTATATTTTTATAGAAATATTATTAAATGCTTTTTTGTATAAAAATAT
1 CTTAAATAATCTATTTATATTTTTATAGAAATATTA-TAAATGCTTTTCTGTACAAAAATAT
* *
6091565 CTTAAATAATCAATTTATATTTTTATA-AAA-GTTA-AAAT-CGTTTTCTGTACAAAAACT-T
1 CTTAAATAATCTATTTATATTTTTATAGAAATATTATAAATGC-TTTTCTGTACAAAAA-TAT
6091623 CTTAAATAATCT-TTT-TA-TTTTATA-AAATGATTA
1 CTTAAATAATCTATTTATATTTTTATAGAAAT-ATTA
6091656 CTTAATATAA
Statistics
Matches: 81, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
55 10 0.12
56 2 0.02
57 7 0.09
58 29 0.36
59 1 0.01
60 3 0.04
61 3 0.04
62 26 0.32
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (61 bp):
CTTAAATAATCTATTTATATTTTTATAGAAATATTATAAATGCTTTTCTGTACAAAAATAT
Found at i:6091650 original size:156 final size:154
Alignment explanation
Indices: 6091348--6091640 Score: 402
Period size: 156 Copynumber: 1.9 Consensus size: 154
6091338 TAGAAATACT
6091348 TTAAATAATTAATTTATATTTTTATAAAAAAATTATTGAAAGTGTTTTTTGTACAAAAATACTTA
1 TTAAATAATTAATTTATATTTTTATAAAAAAATTATTGAAAGTGTTTTTTGTACAAAAATACTTA
* *
6091413 AATAATCCATTTATATTTTTATAAAAGATTATTGAATGTATTTTCTATACAAAAATGCTTTAAAT
66 AATAATCAATTTATATTTTTATAAAAGATTA-TAAATG-ATTTTCTATACAAAAATGCTTTAAAT
6091478 AATCATTTTATAAAAATAAAAACGCC
129 AATCATTTTATAAAAATAAAAACGCC
* * *
6091504 TTAAATAATCT-ATTTATATTTTTATAGAAATATTATT-AAA-TGCTTTTTTGTATAAAAATATC
1 TTAAATAAT-TAATTTATATTTTTATAAAAAAATTATTGAAAGTG-TTTTTTGTACAAAAATA-C
* *
6091566 TTAAATAATCAATTTATATTTTTATAAAAG-TTA-AAATCG-TTTTCTGTACAAAAACTTC-TTA
63 TTAAATAATCAATTTATATTTTTATAAAAGATTATAAAT-GATTTTCTATACAAAAA-TGCTTTA
*
6091627 AATAATCTTTTTAT
126 AATAATCATTTTAT
6091641 TTTATAAAAT
Statistics
Matches: 124, Mismatches: 8, Indels: 14
0.85 0.05 0.10
Matches are distributed among these distances:
152 30 0.24
153 5 0.04
154 3 0.02
155 22 0.18
156 63 0.51
157 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (154 bp):
TTAAATAATTAATTTATATTTTTATAAAAAAATTATTGAAAGTGTTTTTTGTACAAAAATACTTA
AATAATCAATTTATATTTTTATAAAAGATTATAAATGATTTTCTATACAAAAATGCTTTAAATAA
TCATTTTATAAAAATAAAAACGCC
Found at i:6097053 original size:1 final size:1
Alignment explanation
Indices: 6097009--6097035 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
6096999 AAACTTTGAG
6097009 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
6097036 AAGTCTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6099317 original size:3 final size:3
Alignment explanation
Indices: 6099309--6099340 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6099299 TTTTCTTAAG
6099309 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
6099341 TAGCAAGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:6100174 original size:2 final size:2
Alignment explanation
Indices: 6100167--6100192 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6100157 TGGTCACAAC
6100167 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
6100193 CATACACGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6107235 original size:3 final size:3
Alignment explanation
Indices: 6107227--6107252 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6107217 AAAAGAAAGA
6107227 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
6107253 AGAAGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:6110525 original size:14 final size:14
Alignment explanation
Indices: 6110503--6110539 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
6110493 AGACATAAGC
*
6110503 ATAAAATAATTAAA
1 ATAACATAATTAAA
6110517 ATAACATAATTAAA
1 ATAACATAATTAAA
6110531 ATAACATAA
1 ATAACATAA
6110540 CAAGAGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAACATAATTAAA
Found at i:6111070 original size:16 final size:18
Alignment explanation
Indices: 6111042--6111094 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
6111032 TTCTTACATG
*
6111042 TATATAATACAATTTA-T
1 TATATAATTCAATTTATT
*
6111059 TA-ATAATTCAATTGATT
1 TATATAATTCAATTTATT
*
6111076 TATATAATT-AATTTTTT
1 TATATAATTCAATTTATT
6111093 TA
1 TA
6111095 AAAATATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 11 0.37
17 13 0.43
18 6 0.20
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
TATATAATTCAATTTATT
Found at i:6117512 original size:6 final size:6
Alignment explanation
Indices: 6117503--6117527 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6117493 AAAAAAAAAC
6117503 ATAGAA ATAGAA ATAGAA ATAGAA A
1 ATAGAA ATAGAA ATAGAA ATAGAA A
6117528 AAGGAAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
ATAGAA
Found at i:6120613 original size:34 final size:34
Alignment explanation
Indices: 6120573--6120639 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
6120563 GTTCAAGCTT
6120573 TTCGAAGGTTGCGCCAATGGTCACCATATGGAGC
1 TTCGAAGGTTGCGCCAATGGTCACCATATGGAGC
6120607 TTCGAAGGTTGCGCCAATGGTCACCATATGGAG
1 TTCGAAGGTTGCGCCAATGGTCACCATATGGAG
6120640 ATAACCCGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (34 bp):
TTCGAAGGTTGCGCCAATGGTCACCATATGGAGC
Found at i:6121061 original size:2 final size:2
Alignment explanation
Indices: 6121054--6121086 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
6121044 TCAAGAAGGT
*
6121054 TA TA TA TA TA TA TA TA TA CA 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
6121087 TAAAGTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6121388 original size:13 final size:14
Alignment explanation
Indices: 6121362--6121390 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6121352 AAAATTTATA
6121362 TAATTATAATATTT
1 TAATTATAATATTT
6121376 TAATTAT-ATATTT
1 TAATTATAATATTT
6121389 TA
1 TA
6121391 TTCATGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATAATATTT
Found at i:6133310 original size:24 final size:25
Alignment explanation
Indices: 6133282--6133346 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 25
6133272 ATGTTGATTT
6133282 ATGATTTACAAAATGTTTT-ACATA
1 ATGATTTACAAAATGTTTTGACATA
*** *
6133306 ATGATGATTTTGAAATGTTTTGACATT
1 ATGAT--TTACAAAATGTTTTGACATA
6133333 ATGATTTGACAAAA
1 ATGATTT-ACAAAA
6133347 GTATTTAATG
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
24 5 0.17
25 2 0.07
26 14 0.47
27 9 0.30
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (25 bp):
ATGATTTACAAAATGTTTTGACATA
Found at i:6133315 original size:27 final size:27
Alignment explanation
Indices: 6133282--6133337 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
6133272 ATGTTGATTT
6133282 ATGATTTACAAAATGTTTT-ACATAATG
1 ATGATTT-CAAAATGTTTTGACATAATG
** *
6133309 ATGATTTTGAAATGTTTTGACATTATG
1 ATGATTTCAAAATGTTTTGACATAATG
6133336 AT
1 AT
6133338 TTGACAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (27 bp):
ATGATTTCAAAATGTTTTGACATAATG
Found at i:6133805 original size:16 final size:15
Alignment explanation
Indices: 6133775--6133803 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6133765 AAAGTAAAAT
6133775 CAATCATATTTTTTA
1 CAATCATATTTTTTA
6133790 CAATCATATTTTTT
1 CAATCATATTTTTT
6133804 TATGCACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (15 bp):
CAATCATATTTTTTA
Found at i:6143893 original size:2 final size:2
Alignment explanation
Indices: 6143880--6143909 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6143870 TATTTACTAA
*
6143880 AT AT AA 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
6143910 GAAGAGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6151115 original size:32 final size:33
Alignment explanation
Indices: 6151079--6151163 Score: 86
Period size: 32 Copynumber: 2.6 Consensus size: 33
6151069 AAAAAAAATA
* * * *
6151079 TTATTATTATAATAAGATAAT-GTTCATTTGTT
1 TTATTATTATAATAGGATAATGGTCCACTTGCT
*
6151111 TTATTTTTTATAAT-GGAT-ATGGTCCACTTGCT
1 TTA-TTATTATAATAGGATAATGGTCCACTTGCT
6151143 TTATTATCTATAATAGGATAA
1 TTATTAT-TATAATAGGATAA
6151164 AACTCAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
31 5 0.12
32 23 0.55
33 13 0.31
34 1 0.02
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (33 bp):
TTATTATTATAATAGGATAATGGTCCACTTGCT
Found at i:6152894 original size:33 final size:32
Alignment explanation
Indices: 6152856--6152935 Score: 76
Period size: 33 Copynumber: 2.5 Consensus size: 32
6152846 TTTTGTTTTT
*
6152856 AATTTTTAATTTTTAA-TATATTATTTAATATAA
1 AATTTTTAATTTTTAAGTA-AAT-TTTAATATAA
*
6152889 AA-TTTTAATATATTTAAGTAAATTTTGATATAA
1 AATTTTTAAT-T-TTTAAGTAAATTTTAATATAA
*
6152922 AATTATT-ATTTTTA
1 AATTTTTAATTTTTA
6152936 TTTTATAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
31 4 0.10
32 8 0.20
33 16 0.40
34 10 0.25
35 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (32 bp):
AATTTTTAATTTTTAAGTAAATTTTAATATAA
Found at i:6152970 original size:18 final size:19
Alignment explanation
Indices: 6152939--6152980 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
6152929 ATTTTTATTT
*
6152939 TATAAAAATTTAAAAAATA
1 TATAAAAATCTAAAAAATA
6152958 TATAAAAA-CTAAAAAATA
1 TATAAAAATCTAAAAAATA
6152976 TATAA
1 TATAA
6152981 TTCGGTTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
TATAAAAATCTAAAAAATA
Found at i:6153320 original size:2 final size:2
Alignment explanation
Indices: 6153313--6153343 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6153303 TTTTTCATAA
6153313 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 A
6153344 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6153793 original size:252 final size:252
Alignment explanation
Indices: 6153348--6154103 Score: 1426
Period size: 252 Copynumber: 3.0 Consensus size: 252
6153338 TATATACACA
*
6153348 CACACACACACGCATTGGTGTTAGTATTATAGATAAAGAAAACCTATTACTCTA-TTTCTTTC-A
1 CACACACACACACATTGGTGTTAGTATTATAGATAAAGAAAACCTATTACTCTATTTTCTTTCAA
6153411 AATTCCTCCTTTTTACCTTCAAAGTGAGAGAGTTCAATAATGGAAGAAGTTACTAACAATAGCAA
66 AATT--TCCTTTTTACCTTCAAAGTGAGAGAGTTCAATAATGGAAGAAGTTACTAACAATAGCAA
6153476 TGGCTTAGTGCTACCAAAGCCTATAAACCTTCCCTTGATGACCGCCGAGCAGGAGAGAGATGAAG
129 TGGCTTAGTGCTACCAAAGCCTATAAACCTTCCCTTGATGACCGCCGAGCAGGAGAGAGATGAAG
6153541 CATTCCTAAAATCAATGCCTCCTGGTTATCGGTTCAAGCAACGTGATGATGAGCATGTT
194 CATTCCTAAAATCAATGCCTCCTGGTTATCGGTTCAAGCAACGTGATGATGAGCATGTT
6153600 CACACACACACACATTGGTGTTAGTATTATAGATAAAGAAAACCTATTACTCTATTTTCTTTCAA
1 CACACACACACACATTGGTGTTAGTATTATAGATAAAGAAAACCTATTACTCTATTTTCTTTCAA
6153665 AATTTCCTTTTTACCTTCAAAGTGAGAGAGTTCAATAATGGAAGAAGTTACTAACAATAGCAATG
66 AATTTCCTTTTTACCTTCAAAGTGAGAGAGTTCAATAATGGAAGAAGTTACTAACAATAGCAATG
*
6153730 GCTTAGTGCTACCAAAGCCTATAAACCTTCCCTTGATGACCGCCAAGCAGGAGAGAGATGAAGCA
131 GCTTAGTGCTACCAAAGCCTATAAACCTTCCCTTGATGACCGCCGAGCAGGAGAGAGATGAAGCA
6153795 TTCCTAAAATCAATGCCTCCTGGTTATCGGTTCAAGCAACGTGATGATGAGCATGTT
196 TTCCTAAAATCAATGCCTCCTGGTTATCGGTTCAAGCAACGTGATGATGAGCATGTT
6153852 CACACACACACACATTGGTGTTAGTATTATAGATAAAGAAAACCTATTACTCTATTTTCTTTCAA
1 CACACACACACACATTGGTGTTAGTATTATAGATAAAGAAAACCTATTACTCTATTTTCTTTCAA
6153917 AATTTCCTTTTTACCTTCAAAGTGAGAGAGTTCAATAATGGAAGAAGTTACTAACAATAGCAATG
66 AATTTCCTTTTTACCTTCAAAGTGAGAGAGTTCAATAATGGAAGAAGTTACTAACAATAGCAATG
* *
6153982 GCTTTGTGCTATCAAAGCCTATAAACCTTCCCTTGATGACCGCCGAGCAGGAGAGAGATGAAGCA
131 GCTTAGTGCTACCAAAGCCTATAAACCTTCCCTTGATGACCGCCGAGCAGGAGAGAGATGAAGCA
* *
6154047 TTCCTAAAATCAATGCCTCCTGGTTATCGGTTCAAGCAACGTGATGAGGAGCTTGTT
196 TTCCTAAAATCAATGCCTCCTGGTTATCGGTTCAAGCAACGTGATGATGAGCATGTT
6154104 AAGTATTATT
Statistics
Matches: 495, Mismatches: 7, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
252 482 0.97
253 8 0.02
254 5 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (252 bp):
CACACACACACACATTGGTGTTAGTATTATAGATAAAGAAAACCTATTACTCTATTTTCTTTCAA
AATTTCCTTTTTACCTTCAAAGTGAGAGAGTTCAATAATGGAAGAAGTTACTAACAATAGCAATG
GCTTAGTGCTACCAAAGCCTATAAACCTTCCCTTGATGACCGCCGAGCAGGAGAGAGATGAAGCA
TTCCTAAAATCAATGCCTCCTGGTTATCGGTTCAAGCAACGTGATGATGAGCATGTT
Found at i:6154443 original size:17 final size:17
Alignment explanation
Indices: 6154418--6154452 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6154408 ATCCATTAAC
*
6154418 TCTATTGAAGTCTATTA
1 TCTACTGAAGTCTATTA
6154435 TCTACTGAAGTCTATTA
1 TCTACTGAAGTCTATTA
6154452 T
1 T
6154453 GTGATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (17 bp):
TCTACTGAAGTCTATTA
Found at i:6162280 original size:33 final size:32
Alignment explanation
Indices: 6162242--6162321 Score: 76
Period size: 33 Copynumber: 2.5 Consensus size: 32
6162232 TTTTGTTTTT
*
6162242 AATTTTTAATTTTTAA-TATATTATTTAATATAA
1 AATTTTTAATTTTTAAGTA-AAT-TTTAATATAA
*
6162275 AA-TTTTAATATATTTAAGTAAATTTTGATATAA
1 AATTTTTAAT-T-TTTAAGTAAATTTTAATATAA
*
6162308 AATTATT-ATTTTTA
1 AATTTTTAATTTTTA
6162322 TTTTATAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
31 4 0.10
32 8 0.20
33 16 0.40
34 10 0.25
35 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (32 bp):
AATTTTTAATTTTTAAGTAAATTTTAATATAA
Found at i:6162356 original size:18 final size:19
Alignment explanation
Indices: 6162325--6162366 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
6162315 ATTTTTATTT
*
6162325 TATAAAAATTTAAAAAATA
1 TATAAAAATCTAAAAAATA
6162344 TATAAAAA-CTAAAAAATA
1 TATAAAAATCTAAAAAATA
6162362 TATAA
1 TATAA
6162367 TTCGGTTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
TATAAAAATCTAAAAAATA
Found at i:6163170 original size:252 final size:252
Alignment explanation
Indices: 6162725--6163479 Score: 1449
Period size: 252 Copynumber: 3.0 Consensus size: 252
6162715 CACACACACA
*
6162725 CACACACACACGCATTGGTGTTAGTATTATAGATAAAGAAAACCTATTACTCTATTTTCTTTCAA
1 CACACACACACACATTGGTGTTAGTATTATAGATAAAGAAAACCTATTACTCTATTTTCTTTCAA
6162790 AATTTCCTTTTTACCTTCAAAGTGAGAGAGTTCAATAATGGAAGAAGTTACTAACAATAGCAATG
66 AATTTCCTTTTTACCTTCAAAGTGAGAGAGTTCAATAATGGAAGAAGTTACTAACAATAGCAATG
6162855 GCTTAGTGCTACCAAAGCCTATAAACCTTCCCTTGATGACCGCCGAGCAGGAGAGAGATGAAGCA
131 GCTTAGTGCTACCAAAGCCTATAAACCTTCCCTTGATGACCGCCGAGCAGGAGAGAGATGAAGCA
6162920 TTCCTAAAATCAATGCCTCCTGGTTATCGGTTCAAGCAACGTGATGATGAGCATGTT
196 TTCCTAAAATCAATGCCTCCTGGTTATCGGTTCAAGCAACGTGATGATGAGCATGTT
6162977 CACACACACACACATTGGTGTTAGTATTATAGATAAAGAAAACCTATTACTCTATTTTCTTTCAA
1 CACACACACACACATTGGTGTTAGTATTATAGATAAAGAAAACCTATTACTCTATTTTCTTTCAA
6163042 AATTTCCTTTTTACCTTCAAAGTGAGAGAGTTCAATAATGGAAGAAGTTACTAACAATAGCAATG
66 AATTTCCTTTTTACCTTCAAAGTGAGAGAGTTCAATAATGGAAGAAGTTACTAACAATAGCAATG
*
6163107 GCTTAGTGCTACCAAAGCCTATAAACCTTCCCTTGATGACCGCCAAGCAGGAGAGAGATGAAGCA
131 GCTTAGTGCTACCAAAGCCTATAAACCTTCCCTTGATGACCGCCGAGCAGGAGAGAGATGAAGCA
6163172 TTCCTAAAATCAATGCCTCCTGGTTATCGGTTCAAGCAACGTGATGATGAGCATGTT
196 TTCCTAAAATCAATGCCTCCTGGTTATCGGTTCAAGCAACGTGATGATGAGCATGTT
6163229 CACACACACACACATTGGTGTTAGTATTATAGATAAAGAAAACCTATTACTCTATTTTCTTTCAA
1 CACACACACACACATTGGTGTTAGTATTATAGATAAAGAAAACCTATTACTCTATTTTCTTTCAA
6163294 AATTTCCTTTTTACCTTCAAAGTGAGAGAGTTCAATAATGGAAGAAGTTACTAACAATAGCAATG
66 AATTTCCTTTTTACCTTCAAAGTGAGAGAGTTCAATAATGGAAGAAGTTACTAACAATAGCAATG
* *
6163359 GCTTTGTGCTATCAAAGCCTATAAACCTT-CCTTGATGACCGCCGAGCAGGAGAGAGATGAAGCA
131 GCTTAGTGCTACCAAAGCCTATAAACCTTCCCTTGATGACCGCCGAGCAGGAGAGAGATGAAGCA
* *
6163423 TTCCTAAAATCAATGCCTCCTGGTTATCGGTTCAAGCAACGTGATGAGGAGCTTGTT
196 TTCCTAAAATCAATGCCTCCTGGTTATCGGTTCAAGCAACGTGATGATGAGCATGTT
6163480 AAGTATTATT
Statistics
Matches: 496, Mismatches: 7, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
251 89 0.18
252 407 0.82
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (252 bp):
CACACACACACACATTGGTGTTAGTATTATAGATAAAGAAAACCTATTACTCTATTTTCTTTCAA
AATTTCCTTTTTACCTTCAAAGTGAGAGAGTTCAATAATGGAAGAAGTTACTAACAATAGCAATG
GCTTAGTGCTACCAAAGCCTATAAACCTTCCCTTGATGACCGCCGAGCAGGAGAGAGATGAAGCA
TTCCTAAAATCAATGCCTCCTGGTTATCGGTTCAAGCAACGTGATGATGAGCATGTT
Found at i:6163616 original size:13 final size:13
Alignment explanation
Indices: 6163598--6163622 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6163588 TTTCAGATCC
6163598 TTGTTTTTTTTTT
1 TTGTTTTTTTTTT
6163611 TTGTTTTTTTTT
1 TTGTTTTTTTTT
6163623 CTTGGTGTTT
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTGTTTTTTTTTT
Found at i:6163819 original size:17 final size:17
Alignment explanation
Indices: 6163794--6163828 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6163784 ATCCATTAAC
*
6163794 TCTATTGAAGTCTATTA
1 TCTACTGAAGTCTATTA
6163811 TCTACTGAAGTCTATTA
1 TCTACTGAAGTCTATTA
6163828 T
1 T
6163829 GTGATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (17 bp):
TCTACTGAAGTCTATTA
Found at i:6168878 original size:15 final size:16
Alignment explanation
Indices: 6168848--6168881 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
6168838 ACATCTCAAA
*
6168848 ATTATAATTATTTTAT
1 ATTATAAATATTTTAT
6168864 ATTATAAAT-TTTTAT
1 ATTATAAATATTTTAT
6168879 ATT
1 ATT
6168882 TTCAAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTATAAATATTTTAT
Found at i:6168982 original size:19 final size:19
Alignment explanation
Indices: 6168939--6168982 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
6168929 TTTCACTATT
6168939 TTTAATATTTTATATATAA
1 TTTAATATTTTATATATAA
* *
6168958 TATAATTTTTTAT-TATGAA
1 TTTAATATTTTATATAT-AA
6168977 TTTAAT
1 TTTAAT
6168983 GGATTGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTAATATTTTATATATAA
Found at i:6172160 original size:2 final size:2
Alignment explanation
Indices: 6172153--6172180 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6172143 TCTTGCATTG
6172153 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
6172181 GTATGTATGT
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:6172565 original size:2 final size:2
Alignment explanation
Indices: 6172558--6172595 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
6172548 TCTATCCAGG
* *
6172558 AT AT AT AT AC AT AT AT AG 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
6172596 GGTTTCTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6192688 original size:15 final size:14
Alignment explanation
Indices: 6192664--6192723 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 14
6192654 AAAAAATAAT
*
6192664 TTTTATTAAACAATA
1 TTTTAATAAA-AATA
6192679 TTTTAATAAAAATA
1 TTTTAATAAAAATA
*
6192693 TTTTTTATAAAAATAA
1 -TTTTAATAAAAAT-A
6192709 TATTTAAATAAAAAT
1 T-TTT-AATAAAAAT
6192724 TTCAACATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
14 4 0.11
15 22 0.58
16 4 0.11
17 8 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTTAATAAAAATA
Found at i:6192690 original size:31 final size:32
Alignment explanation
Indices: 6192655--6192723 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
6192645 GTATAAATGA
* *
6192655 AAAAATAATTTTTAT-TAAACAATATTTTAAT
1 AAAAATAATTTTTATAAAAACAATATTTAAAT
* *
6192686 AAAAATATTTTTTATAAAAATAATATTTAAAT
1 AAAAATAATTTTTATAAAAACAATATTTAAAT
6192718 AAAAAT
1 AAAAAT
6192724 TTCAACATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 14 0.42
32 19 0.58
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (32 bp):
AAAAATAATTTTTATAAAAACAATATTTAAAT
Found at i:6192690 original size:32 final size:33
Alignment explanation
Indices: 6192648--6192722 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 33
6192638 AGAATGAGTA
*
6192648 TAAATGAAAAAATAATTTTTAT-TAAACAATATT
1 TAAAT-AAAAAATAATTTTTATAAAAACAATATT
* * *
6192681 TTAAT-AAAAATATTTTTTATAAAAATAATATT
1 TAAATAAAAAATAATTTTTATAAAAACAATATT
6192713 TAAATAAAAA
1 TAAATAAAAA
6192723 TTTCAACATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 14 0.40
32 13 0.37
33 8 0.23
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (33 bp):
TAAATAAAAAATAATTTTTATAAAAACAATATT
Found at i:6193564 original size:21 final size:20
Alignment explanation
Indices: 6193530--6193572 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
6193520 ATGAAATATA
*
6193530 AATTTTATTTTTTAAT-AAAT
1 AATTTTATTGTTT-ATCAAAT
6193550 AATTTTAGTTGTTTATCAAAT
1 AATTTTA-TTGTTTATCAAAT
6193571 AA
1 AA
6193573 CCTTATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (20 bp):
AATTTTATTGTTTATCAAAT
Found at i:6194770 original size:16 final size:16
Alignment explanation
Indices: 6194749--6194805 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
6194739 ATTTTTAAAT
6194749 ATAAATATAAAATTAA
1 ATAAATATAAAATTAA
* *
6194765 ATAAATAACAAAAAT-A
1 ATAAAT-ATAAAATTAA
*
6194781 TTAAATATATATAATTAA
1 ATAAATATA-A-AATTAA
6194799 ATAAATA
1 ATAAATA
6194806 ATAATAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 2 0.06
16 13 0.42
17 9 0.29
18 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAATATAAAATTAA
Found at i:6194797 original size:34 final size:36
Alignment explanation
Indices: 6194745--6194828 Score: 115
Period size: 36 Copynumber: 2.5 Consensus size: 36
6194735 TATTATTTTT
*
6194745 AAATA-TAAATATA-A-AATTAAATAAATAA-CA-A
1 AAATATTAAATATATATAATTAAATAAATAATAATA
6194776 AAATATTAAATATATATAATTAAATAAATAATAATA
1 AAATATTAAATATATATAATTAAATAAATAATAATA
*
6194812 AAATATTATATATATAT
1 AAATATTAAATATATAT
6194829 CTTAGATAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
31 5 0.11
32 8 0.17
33 1 0.02
34 14 0.30
35 1 0.02
36 17 0.37
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (36 bp):
AAATATTAAATATATATAATTAAATAAATAATAATA
Found at i:6194799 original size:14 final size:14
Alignment explanation
Indices: 6194780--6194823 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
6194770 TAACAAAAAT
6194780 ATTAAATATATATA
1 ATTAAATATATATA
*
6194794 ATTAAATAAATAATA
1 ATTAAATATAT-ATA
*
6194809 ATAAAATATTATATA
1 ATTAAATA-TATATA
6194824 TATATCTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 10 0.40
15 13 0.52
16 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATTAAATATATATA
Found at i:6195395 original size:54 final size:54
Alignment explanation
Indices: 6195326--6195434 Score: 148
Period size: 54 Copynumber: 2.0 Consensus size: 54
6195316 CCTTTAAAAA
* ** *
6195326 TGTCTTTAGGACAGAAA-TTTAATTTGTTATTTTTGAGTATTTAATTCAATAATG
1 TGTCCTTAGGACAGAAACTTT-ATTTGTTATTTTCAAGTATTTAATTCAACAATG
* *
6195380 TGTCCTTAGGTCAGAAACTTTATTTTTTATTTTCAAGTATTTAATTCAACAATG
1 TGTCCTTAGGACAGAAACTTTATTTGTTATTTTCAAGTATTTAATTCAACAATG
6195434 T
1 T
6195435 TATCAGTACG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
54 45 0.94
55 3 0.06
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (54 bp):
TGTCCTTAGGACAGAAACTTTATTTGTTATTTTCAAGTATTTAATTCAACAATG
Found at i:6195675 original size:13 final size:13
Alignment explanation
Indices: 6195659--6195683 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6195649 TATTTTCTTA
6195659 AATATTTTTTATT
1 AATATTTTTTATT
6195672 AATATTTTTTAT
1 AATATTTTTTAT
6195684 AAAAAAAAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
AATATTTTTTATT
Found at i:6210264 original size:15 final size:15
Alignment explanation
Indices: 6210246--6210280 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
6210236 AATAGTATAT
6210246 AATAAAA-ATGATAAA
1 AATAAAATAT-ATAAA
6210261 AATAAAATATATAAA
1 AATAAAATATATAAA
6210276 AATAA
1 AATAA
6210281 TATAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
AATAAAATATATAAA
Found at i:6217384 original size:114 final size:114
Alignment explanation
Indices: 6217179--6217388 Score: 285
Period size: 114 Copynumber: 1.8 Consensus size: 114
6217169 AAGAGACTTT
* * ** *
6217179 GCAAAGCCTTTATGGGATACCTCACCCATTGGGCTTTGGCAGGTTGGGTTGTATCTATTTCCTTA
1 GCAAAGCCTTTATGGGATACCTCACCCATCGGGCCTCAGCAGGTTGGATTGTATCTATTTCCTTA
* ** *
6217244 TTCTTTTTTGGTAGCGCAAAGCCTCGTACTAAACGTTTCCTTATTCTCC
66 TTCTCTTTTGACAGCACAAAGCCTCGTACTAAACGTTTCCTTATTCTCC
* **
6217293 GCAAAGCTTTTATGGGATACCTCATTCATCGGGCCTCAGCAGGTTGGATTGTATCTATTTCCTTA
1 GCAAAGCCTTTATGGGATACCTCACCCATCGGGCCTCAGCAGGTTGGATTGTATCTATTTCCTTA
* * *
6217358 TTCTCTTTTGACAGCATAGAGTCTCGTACTA
66 TTCTCTTTTGACAGCACAAAGCCTCGTACTA
6217389 CGTGACAGAT
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
114 81 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (114 bp):
GCAAAGCCTTTATGGGATACCTCACCCATCGGGCCTCAGCAGGTTGGATTGTATCTATTTCCTTA
TTCTCTTTTGACAGCACAAAGCCTCGTACTAAACGTTTCCTTATTCTCC
Done.