Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 16 of 130
Found at i:4458144 original size:14 final size:15
Alignment explanation
Indices: 4458120--4458157 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
4458110 AAAAGATAAA
4458120 AAAATAATAAAAAAT-
1 AAAA-AATAAAAAATG
4458135 AAAAAATAAAAAATG
1 AAAAAATAAAAAATG
4458150 AAAAAATA
1 AAAAAATA
4458158 GGTGTTGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:4459182 original size:8 final size:8
Alignment explanation
Indices: 4459171--4459195 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4459161 CCAAAAATAA
4459171 TAATAAAT
1 TAATAAAT
4459179 TAATAAAT
1 TAATAAAT
4459187 TAATAAAT
1 TAATAAAT
4459195 T
1 T
4459196 TTGCTTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAATAAAT
Found at i:4461420 original size:24 final size:23
Alignment explanation
Indices: 4461375--4461427 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
4461365 TGAGCTTTAT
4461375 ATTAT-TGTTTTTAATTAAAATA
1 ATTATATGTTTTTAATTAAAATA
*
4461397 TTTATATGTTTTTAA-TAATCAATA
1 ATTATATGTTTTTAATTAA--AATA
4461421 ATTATAT
1 ATTATAT
4461428 ATTTATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 7 0.27
23 9 0.35
24 10 0.38
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (23 bp):
ATTATATGTTTTTAATTAAAATA
Found at i:4461428 original size:26 final size:24
Alignment explanation
Indices: 4461371--4461429 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 24
4461361 AATATGAGCT
4461371 TTATATTATTGTTTTTAATTAAAATA
1 TTATA-TA-TGTTTTTAATTAAAATA
4461397 TT-TATATGTTTTTAA-TAATCAATAA
1 TTATATATGTTTTTAATTAA--AAT-A
4461422 TTATATAT
1 TTATATAT
4461430 TTATTATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
22 3 0.10
23 9 0.31
24 5 0.17
25 5 0.17
26 7 0.24
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (24 bp):
TTATATATGTTTTTAATTAAAATA
Found at i:4463707 original size:6 final size:6
Alignment explanation
Indices: 4463698--4463740 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
4463688 TATAAAACAT
* *
4463698 AAATAA AAATAA AAACAA AAATAA AAAT-A AAATAA AAACAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AA
4463741 CAAATAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.12
Consensus pattern (6 bp):
AAATAA
Found at i:4463712 original size:18 final size:18
Alignment explanation
Indices: 4463685--4463729 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
4463675 TGCATATATT
*
4463685 AAATATAAAACATAAATAA
1 AAATA-AAAACAAAAATAA
4463704 AAATAAAAACAAAAATAA
1 AAATAAAAACAAAAATAA
4463722 AAATAAAA
1 AAATAAAA
4463730 TAAAAACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (18 bp):
AAATAAAAACAAAAATAA
Found at i:4463753 original size:28 final size:24
Alignment explanation
Indices: 4463696--4463756 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 24
4463686 AATATAAAAC
4463696 ATAAATAAAAATAAAAACAAAAATA
1 ATAAAT-AAAATAAAAACAAAAATA
4463721 A-AAATAAAATAAAAACAAAACA-A
1 ATAAATAAAATAAAAACAAAA-ATA
4463744 ATAAAT-AAATAAA
1 ATAAATAAAATAAA
4463757 TAATGACCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 24 0.71
24 9 0.26
25 1 0.03
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (24 bp):
ATAAATAAAATAAAAACAAAAATA
Found at i:4464805 original size:21 final size:21
Alignment explanation
Indices: 4464781--4464824 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4464771 GGTTGTAGGA
4464781 GTGGCGAT-GACGATAATGGTG
1 GTGGCGATAGACG-TAATGGTG
* *
4464802 GTGGTGATAGATGTAATGGTG
1 GTGGCGATAGACGTAATGGTG
4464823 GT
1 GT
4464825 TAGCGATGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.23, C:0.05, G:0.43, T:0.30
Consensus pattern (21 bp):
GTGGCGATAGACGTAATGGTG
Found at i:4468257 original size:2 final size:2
Alignment explanation
Indices: 4468250--4468282 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4468240 GTTATGTCAC
4468250 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4468283 TACACAGGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4470831 original size:29 final size:29
Alignment explanation
Indices: 4470774--4470833 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
4470764 TGAATCGGAT
*
4470774 AAGAAAAAAAAAAAAGAAAGGAGGAAAGA
1 AAGAAAAAAAAAAAAGAAAGGAAGAAAGA
4470803 AAGAAAAAAAAGAAAA-AAAGAGAAG-AAGA
1 AAGAAAAAAAA-AAAAGAAAG-GAAGAAAGA
4470832 AA
1 AA
4470834 AACGCAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (29 bp):
AAGAAAAAAAAAAAAGAAAGGAAGAAAGA
Found at i:4470877 original size:3 final size:3
Alignment explanation
Indices: 4470871--4470898 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4470861 AAATTAAATA
4470871 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4470899 TAAAGATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4471190 original size:21 final size:21
Alignment explanation
Indices: 4471164--4471205 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4471154 TTAATATAAA
4471164 AATTTTAAAAAATAAAAAAAT
1 AATTTTAAAAAATAAAAAAAT
*
4471185 AATTTTAAAATATAAAAAAAT
1 AATTTTAAAAAATAAAAAAAT
4471206 TAAGATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AATTTTAAAAAATAAAAAAAT
Found at i:4472828 original size:2 final size:2
Alignment explanation
Indices: 4472821--4472853 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4472811 ATTGAATTGT
4472821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4472854 CTTGTGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4475522 original size:11 final size:10
Alignment explanation
Indices: 4475495--4475521 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
4475485 TAAGAGATTA
4475495 GATTTTTAGT
1 GATTTTTAGT
4475505 GATTTTTAGT
1 GATTTTTAGT
4475515 GATTTTT
1 GATTTTT
4475522 TTTTCATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.63
Consensus pattern (10 bp):
GATTTTTAGT
Found at i:4480486 original size:10 final size:11
Alignment explanation
Indices: 4480459--4480493 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
4480449 ATTTAATTTC
4480459 AAAATTTTATT
1 AAAATTTTATT
4480470 AAAATTTTATT
1 AAAATTTTATT
* *
4480481 AAATTTTTTTT
1 AAAATTTTATT
4480492 AA
1 AA
4480494 TTTGAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
AAAATTTTATT
Found at i:4480758 original size:14 final size:14
Alignment explanation
Indices: 4480741--4480774 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4480731 TGGAATAAAC
*
4480741 AAATATAAATAATA
1 AAATAAAAATAATA
*
4480755 AAATAAAAATACTA
1 AAATAAAAATAATA
4480769 AAATAA
1 AAATAA
4480775 GGCACGGCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAAAAATAATA
Found at i:4481822 original size:19 final size:19
Alignment explanation
Indices: 4481772--4481823 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
4481762 AAAAAACAAT
*
4481772 AAAATGAAATAATAAAATAA
1 AAAATTAAA-AATAAAATAA
*
4481792 TAAA-TAATAAATAAAATAA
1 AAAATTAA-AAATAAAATAA
4481811 AAAATTAAAAATA
1 AAAATTAAAAATA
4481824 GGTAATTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAATTAAAAATAAAATAA
Found at i:4482992 original size:528 final size:528
Alignment explanation
Indices: 4481968--4482998 Score: 1755
Period size: 529 Copynumber: 2.0 Consensus size: 528
4481958 ATACACACAC
* * *
4481968 ACACACACCGTATATGAGATTTATATTATTTTTTCAATCCAAATGTTTATATATTTTTAATAATC
1 ACACACACCATATAAGAGATTTATATTATTTTTTCAATCAAAATGTTTATATATTTTTAATAATC
* * *
4482033 AATAATTATATGTTTATTATAGGGTAAGTTTGATATAAATCCATTGGCTTAGGATCGAGTAATGA
66 AATAATTATATATTTATTATAGGGTAAGTTTGACATAAATCCATTGGCTAAGGATCGAGTAATGA
* *
4482098 TGTCTTTGAATAAAAATGGAAGGACTTCAAATCTTAGATAAAAAGTAAATGGTTCAAACACAATA
131 TGTCTTTGAATAAAAATGAAAGGACTTCAAATCTAAGATAAAAAGTAAATGGTTCAAACACAATA
* *
4482163 GAACAAGATCAAAAGGTTCTTGATGATAAATTTGATTGGCTTTTGAAAATTTGAGAATCTACAAA
196 GAACAAGATCAAAAGGTTCTTGATGATAAACTTGATCGGCTTTTGAAAATTTGAGAATCTACAAA
* * *
4482228 AGCGAAGGTATACATTTTTAAAGTTTTGTTTCCTTTATGTATATTTCATAACATTTTTTTCTTTT
261 AGCAAAGGTATACATTTTTAAAGTTTTATTTCCTTTATATATATTTCATAACATTTTTTTCTTTT
*
4482293 ATTTTTCTTCTAACTTTATAGAAAAAGGAAGTTGTTGACAAAAGAAATAGACAAAAGTTGAAGTC
326 ATTTTTCTTCTAACTTTATAAAAAAAGGAAGTTGTTGACAAAAGAAATAGACAAAAGTTGAAGTC
4482358 CACCTCATACTTTAGGCACAAAAAATTTTGCAAAAAAAATAAAGAAAATGGTAATGTAATGTACT
391 CACCTCATACTTTAGGCACAAAAAATTTTGCAAAAAAAATAAAGAAAATGGTAATGTAATGTACT
4482423 TTAATTAAGTAATTTATAAATAAAATTGCCTAAATTATTATAATTATTAAATTGAAAAATTACAA
456 TTAATTAAGTAATTTATAAATAAAATTGCCTAAATTATTATAATTATTAAATTGAAAAATTACAA
4482488 ATTATTAT
521 ATTATTAT
* *
4482496 ACACACA-CATATAAGAGCTTTATATTATTTTTTTCAATCAAAATGTTTATATGTTTTTAATAAT
1 ACACACACCATATAAGAGATTTATATTA-TTTTTTCAATCAAAATGTTTATATATTTTTAATAAT
*
4482560 CAATAATTATATATTTATTATAGGGTAAGTTTGACATAAATCCATTGGCTAAGGATTGAGTAATG
65 CAATAATTATATATTTATTATAGGGTAAGTTTGACATAAATCCATTGGCTAAGGATCGAGTAATG
* * *
4482625 ATGTCTTTGGATAAAAAATGAAAGGACTTCAAGTCTAAGGTAAAAAGTAAATGGTTCAAACACAA
130 ATGTCTTTGAAT-AAAAATGAAAGGACTTCAAATCTAAGATAAAAAGTAAATGGTTCAAACACAA
* *
4482690 TAGAACAAGATCAAAAGGTTCTTGATGATAAACTTGATCGGCTTTTG-ACATTCTGGGAATCTAC
194 TAGAACAAGATCAAAAGGTTCTTGATGATAAACTTGATCGGCTTTTGAAAATT-TGAGAATCTAC
4482754 AAAAGCAAAGGTATACATTTTTAAAGTTTTATTT-CTCTTATATATATTTCATAACATTTTTTTC
258 AAAAGCAAAGGTATACATTTTTAAAGTTTTATTTCCT-TTATATATATTTCATAACATTTTTTTC
4482818 TTTTATTTTTCTTCTAACTTTATAAAAAAAGGAAGTTGTTGACAAAAGAAATAGACAAAAGTTGA
322 TTTTATTTTTCTTCTAACTTTATAAAAAAAGGAAGTTGTTGACAAAAGAAATAGACAAAAGTTGA
* * * *
4482883 AGTCCACCTCATACTTTAGTCAC-AAAAGTTTTGCAAAAAGAATAGAGAAAATGGTAATGTAATG
387 AGTCCACCTCATACTTTAGGCACAAAAAATTTTGCAAAAAAAATAAAGAAAATGGTAATGTAATG
*
4482947 TACTTTAATTAAGTAATTTATAAATAAAATTGCTTAAATTATTATAATTATT
452 TACTTTAATTAAGTAATTTATAAATAAAATTGCCTAAATTATTATAATTATT
4482999 TATTTTAATT
Statistics
Matches: 472, Mismatches: 27, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
527 17 0.04
528 208 0.44
529 247 0.52
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (528 bp):
ACACACACCATATAAGAGATTTATATTATTTTTTCAATCAAAATGTTTATATATTTTTAATAATC
AATAATTATATATTTATTATAGGGTAAGTTTGACATAAATCCATTGGCTAAGGATCGAGTAATGA
TGTCTTTGAATAAAAATGAAAGGACTTCAAATCTAAGATAAAAAGTAAATGGTTCAAACACAATA
GAACAAGATCAAAAGGTTCTTGATGATAAACTTGATCGGCTTTTGAAAATTTGAGAATCTACAAA
AGCAAAGGTATACATTTTTAAAGTTTTATTTCCTTTATATATATTTCATAACATTTTTTTCTTTT
ATTTTTCTTCTAACTTTATAAAAAAAGGAAGTTGTTGACAAAAGAAATAGACAAAAGTTGAAGTC
CACCTCATACTTTAGGCACAAAAAATTTTGCAAAAAAAATAAAGAAAATGGTAATGTAATGTACT
TTAATTAAGTAATTTATAAATAAAATTGCCTAAATTATTATAATTATTAAATTGAAAAATTACAA
ATTATTAT
Found at i:4487347 original size:15 final size:15
Alignment explanation
Indices: 4487327--4487356 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4487317 CAGAAAGCAG
4487327 TGTCTCTTCGACAAA
1 TGTCTCTTCGACAAA
*
4487342 TGTCTCTTTGACAAA
1 TGTCTCTTCGACAAA
4487357 AATCTAAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (15 bp):
TGTCTCTTCGACAAA
Found at i:4488971 original size:2 final size:2
Alignment explanation
Indices: 4488964--4488990 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4488954 ATTGAATTGT
4488964 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4488991 CTTTTATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4490589 original size:25 final size:25
Alignment explanation
Indices: 4490559--4490607 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
4490549 TTTTTATTAA
4490559 ATTTTTTTAATCACAATAATAATAT
1 ATTTTTTTAATCACAATAATAATAT
* *
4490584 ATTTTTTTAATCATAATTATAATA
1 ATTTTTTTAATCACAATAATAATA
4490608 ATAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTTTTTTAATCACAATAATAATAT
Found at i:4494562 original size:20 final size:18
Alignment explanation
Indices: 4494521--4494564 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
4494511 GTTTTATGGT
*
4494521 AATAATTTAATAAATAAA
1 AATAATTAAATAAATAAA
*
4494539 AATAATTAAATGACAATAAC
1 AATAATTAAAT-A-AATAAA
4494559 AATAAT
1 AATAAT
4494565 AAAAATCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
19 1 0.05
20 11 0.50
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (18 bp):
AATAATTAAATAAATAAA
Found at i:4496307 original size:17 final size:16
Alignment explanation
Indices: 4496275--4496308 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4496265 TATTTTTAAA
*
4496275 ATATAAATATATAATT
1 ATATAAAAATATAATT
4496291 ATATAAAAATAATAATT
1 ATATAAAAAT-ATAATT
4496308 A
1 A
4496309 AAAAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAAATATAATT
Found at i:4499899 original size:15 final size:15
Alignment explanation
Indices: 4499879--4499908 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4499869 CAGAAAGCAG
4499879 TGTCTCTTCGACAAA
1 TGTCTCTTCGACAAA
*
4499894 TGTCTCTTTGACAAA
1 TGTCTCTTCGACAAA
4499909 AATCTAAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (15 bp):
TGTCTCTTCGACAAA
Found at i:4500046 original size:2 final size:2
Alignment explanation
Indices: 4500039--4500074 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4500029 GTTATGCCAT
4500039 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4500075 AAACTCAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4500746 original size:21 final size:21
Alignment explanation
Indices: 4500717--4500757 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4500707 TAATATAAAA
*
4500717 ATTTAAAAAAATATAAAAATG
1 ATTTAAAAAAATAAAAAAATG
* *
4500738 ATTTTAAAATATAAAAAAAT
1 ATTTAAAAAAATAAAAAAAT
4500758 TAAGATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
ATTTAAAAAAATAAAAAAATG
Found at i:4504502 original size:18 final size:17
Alignment explanation
Indices: 4504447--4504502 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
4504437 ATGTATATAT
* *
4504447 AAAATATAAAATAAAAAT
1 AAAA-ATAAAACAAAAAC
**
4504465 AAAAATAAAACAAAGCC
1 AAAAATAAAACAAAAAC
4504482 AAAAACTAAAACAAAAAC
1 AAAAA-TAAAACAAAAAC
4504500 AAA
1 AAA
4504503 TAAATAGATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 14 0.45
18 17 0.55
ACGTcount: A:0.77, C:0.11, G:0.02, T:0.11
Consensus pattern (17 bp):
AAAAATAAAACAAAAAC
Found at i:4507837 original size:15 final size:15
Alignment explanation
Indices: 4507817--4507846 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4507807 CAGAAAGCAG
4507817 TGTCTCTTCGACAAA
1 TGTCTCTTCGACAAA
*
4507832 TGTCTCTTTGACAAA
1 TGTCTCTTCGACAAA
4507847 AATCTAAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (15 bp):
TGTCTCTTCGACAAA
Found at i:4508651 original size:18 final size:18
Alignment explanation
Indices: 4508630--4508676 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
4508620 AATGATTTTT
4508630 AATATAAAAAT-TTTAAAA
1 AATATAAAAATATTT-AAA
*
4508648 AATATAAAAATGATTTTAA
1 AATATAAAAAT-ATTTAAA
4508667 AATATAAAAA
1 AATATAAAAA
4508677 AATTAAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.42
19 12 0.46
20 3 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (18 bp):
AATATAAAAATATTTAAA
Found at i:4508665 original size:21 final size:21
Alignment explanation
Indices: 4508639--4508679 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4508629 TAATATAAAA
*
4508639 ATTTTAAAAAATATAAAAATG
1 ATTTTAAAAAATAAAAAAATG
*
4508660 ATTTTAAAATATAAAAAAAT
1 ATTTTAAAAAATAAAAAAAT
4508680 TAAGATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
ATTTTAAAAAATAAAAAAATG
Found at i:4510275 original size:2 final size:2
Alignment explanation
Indices: 4510268--4510296 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4510258 ATTGAATTGT
4510268 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4510297 CTTTTATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4511906 original size:24 final size:24
Alignment explanation
Indices: 4511866--4511920 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
4511856 TTCTTATTAA
*
4511866 ATTTTTTTAAATTATAATAATAAT
1 ATTTTTTTAAATCATAATAATAAT
* *
4511890 ATTTTTTTCAATCATAATTATAAT
1 ATTTTTTTAAATCATAATAATAAT
4511914 ATTTTTT
1 ATTTTTT
4511921 ATTATTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTTTTTAAATCATAATAATAAT
Found at i:4513607 original size:44 final size:44
Alignment explanation
Indices: 4513523--4513610 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
4513513 CCAATTGAAC
* *
4513523 AGAAATTAAGTGCTACACCGTAGAAACCACCTTTAAAATCTTAA
1 AGAAACTAAGTGCTACACAGTAGAAACCACCTTTAAAATCTTAA
* * * *
4513567 AGAAACTAAGTTCTACACAGTATAAGCCA-CTTCTAGAATCTTAA
1 AGAAACTAAGTGCTACACAGTAGAAACCACCTT-TAAAATCTTAA
4513611 CCTGTTACAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
43 3 0.08
44 34 0.92
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.26
Consensus pattern (44 bp):
AGAAACTAAGTGCTACACAGTAGAAACCACCTTTAAAATCTTAA
Found at i:4516600 original size:10 final size:10
Alignment explanation
Indices: 4516587--4516625 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
4516577 ACAAAAAAGG
4516587 AAAAAAATAT
1 AAAAAAATAT
4516597 AAAAATATATAT
1 AAAAA-A-ATAT
*
4516609 AAAAAAATGT
1 AAAAAAATAT
4516619 AAAAAAA
1 AAAAAAA
4516626 GAGGGAGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 15 0.58
11 2 0.08
12 9 0.35
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (10 bp):
AAAAAAATAT
Found at i:4517817 original size:36 final size:36
Alignment explanation
Indices: 4517748--4517930 Score: 120
Period size: 36 Copynumber: 5.0 Consensus size: 36
4517738 ATCAAGGTCA
* * *
4517748 TTTTTATAGTTTTATGACTTGCGATTTAATCCCAATCG
1 TTTTTAT--TTTTTTGACTTGCGGTTTAATCCCAGTCG
* * *
4517786 TTTTTATTTTTTTGACTTGCGGTTCAGTCCCAGTCA
1 TTTTTATTTTTTTGACTTGCGGTTTAATCCCAGTCG
** * * * * *
4517822 TGATTA-ATCTTTGACTTGTGGTTTAATCTC-GAT-A
1 TTTTTATTTTTTTGACTTGCGGTTTAATCCCAG-TCG
** *
4517856 TTTCTATATTTTCCTGACTTGCAGTTTAATCCCAGTCG
1 TTT-T-TATTTTTTTGACTTGCGGTTTAATCCCAGTCG
* * * *
4517894 CTTTTATTTTTTTGACTTGCTGTTCAGTCCCAGTCG
1 TTTTTATTTTTTTGACTTGCGGTTTAATCCCAGTCG
4517930 T
1 T
4517931 CGTTAATCTT
Statistics
Matches: 108, Mismatches: 31, Indels: 14
0.71 0.20 0.09
Matches are distributed among these distances:
34 3 0.03
35 20 0.19
36 56 0.52
37 19 0.18
38 10 0.09
ACGTcount: A:0.18, C:0.19, G:0.15, T:0.48
Consensus pattern (36 bp):
TTTTTATTTTTTTGACTTGCGGTTTAATCCCAGTCG
Found at i:4517905 original size:109 final size:109
Alignment explanation
Indices: 4517688--4518879 Score: 1071
Period size: 109 Copynumber: 11.0 Consensus size: 109
4517678 GTCATTCCTC
* * ** * * * ** * *
4517688 TTGACTTACGGTTCAATTTCAGTCATCGTTAATCTCTGAATCGTGGTTTAATCAAGGTCATTTTT
1 TTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCT
** * * * *
4517753 ATAGTTTTATGACTTGC-GATTTAATCCCAATCGTTTTTATTTTT
66 ATAGTTTCCTGACTTACAG-TTTAATCTCAGTCGCTTTTATTTTT
* * *
4517797 TTGACTTGCGGTTCAGTCCCAGTCAT-GATTAATCTTTGACTTGTGGTTTAATCTCGAT-ATTTC
1 TTGACTTGCGGTTCAGTCCCAGTCGTCG-TTAATCTTTGACTCGTGGTTTAATCCCGATCATTTC
* * *
4517860 TATATTTTCCTGACTTGCAGTTTAATCCCAGTCGCTTTTATTTTT
65 TATAGTTTCCTGACTTACAGTTTAATCTCAGTCGCTTTTATTTTT
* * * *
4517905 TTGACTTGCTGTTCAGTCCCAGTCGTCGTTAATCTTTGACTCATGGTTTAATCCCGATAATTTTT
1 TTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCT
* * * * * *
4517970 ATAGTTTCCTAACTTGCGGTTTAATTTTAGTCACTTTTATTTTT
66 ATAGTTTCCTGACTTACAGTTTAATCTCAGTCGCTTTTATTTTT
* * ** * * *
4518014 TTGACTTGCAGTTCAATCTTAGTCATCGTTAATCTTTGACTCGTGGTTTAATCTC-AGTCATTTT
1 TTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATCCCGA-TCATTTC
* * *
4518078 TATAGTTTCCTGACTTAC-GATTTAATTTTAGTTGCTTTTATTTTT
65 TATAGTTTCCTGACTTACAG-TTTAATCTCAGTCGCTTTTATTTTT
* * * * * * * *
4518123 CTGACTTGTGGTTCAGTCTCAGTTGTCATTAATCTTTGACTTGTTGTTTAATCCCGATCATTTTT
1 TTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCT
* * * * *
4518188 GTAGTTTCTTTACTT-GAGATTTAATCTCAGTTGCTTTTATTTTT
66 ATAGTTTCCTGACTTACAG-TTTAATCTCAGTCGCTTTTATTTTT
** * * * *
4518232 TTGACTTGCGGTTCAGTCTTAGTCATTGTTAATCTCTGACTCGTGATTTAATCCCGATCATTTCT
1 TTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCT
* * *
4518297 ATAGTTTCCTGACTTAC-GATTTAATCCCAATCGCTGTTATTTTT
66 ATAGTTTCCTGACTTACAG-TTTAATCTCAGTCGCTTTTATTTTT
* * * * * * * * *
4518341 ATGATTTACGGTTCAGTCACAGTCGTCGTTAATCTTTGAATCATGATTTAATCCTGATCATTTTT
1 TTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCT
* * **
4518406 ATAGATTT-CTGACTTACTGTTTAATCTCAATTACTTTTATTTTT
66 ATAG-TTTCCTGACTTACAGTTTAATCTCAGTCGCTTTTATTTTT
* * * * * * * * *
4518450 CTGACTTGCGATTCAATCTCAGTCATCGTTATTCTTTGACTCGCGATTTAATCTCGATCATTTCT
1 TTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCT
* * * *
4518515 ATAGTTTCCTAACTTGCAATTTAATAAT-AGTCGCTTTTATTTTT
66 ATAGTTTCCTGACTTACAGTTTAAT-CTCAGTCGCTTTTATTTTT
* * * * * * *
4518559 TTGACTTACGGTTCAATCCCAGTCGTCATTAATATTTGATTCGTGGTTTAATCCTGATCATTTTT
1 TTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCT
* *
4518624 ATAGTTTCTTGACTTA-TGATTTAATCTCAGTCGCTTTTATTTTT
66 ATAGTTTCCTGACTTACAG-TTTAATCTCAGTCGCTTTTATTTTT
* * * * * * * * * * *
4518668 TTGACTTACGATTTAATCCCACTTGTCGTTAATCTCTGACTAGTGGTTTAATCCCGGTCACTCCT
1 TTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCT
* * *
4518733 AT-GTTTCC-AACTTACGGTTTAATCTCAGTCACTTTTATTTTT
66 ATAGTTTCCTGACTTACAGTTTAATCTCAGTCGCTTTTATTTTT
* * * * * * * * *
4518775 TTGATTTGCGATTCAGTCTCAATTGTTGTTAATCTCTGACTCGTGGTTTAATCTCAATCATTTCT
1 TTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCT
** *
4518840 AT-G-TTCCCAACTTACGGTTTAATCTCAGTCGCTTTTATTT
66 ATAGTTTCCTGACTTACAGTTTAATCTCAGTCGCTTTTATTT
4518880 AGTTAGCTTC
Statistics
Matches: 898, Mismatches: 168, Indels: 36
0.81 0.15 0.03
Matches are distributed among these distances:
106 4 0.00
107 115 0.13
108 106 0.12
109 667 0.74
110 6 0.01
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (109 bp):
TTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCT
ATAGTTTCCTGACTTACAGTTTAATCTCAGTCGCTTTTATTTTT
Found at i:4518379 original size:327 final size:327
Alignment explanation
Indices: 4517688--4518879 Score: 1265
Period size: 327 Copynumber: 3.7 Consensus size: 327
4517678 GTCATTCCTC
* *
4517688 TTGACTTACGGTTCAATTTCAGTCATCGTTAATCTCTGAATCGTGGTTTAATCAAGGTCATTTTT
1 TTGACTTACGGTTCAATCTCAGTCATCGTTAATCTCTGAATCGTGGTTTAATCCA-GTCATTTTT
** * * ** * * *
4517753 ATAGTTTTATGACTTGCGATTTAATCCCAATCGTTTTTATTTTTTTGACTTGCGGTTCAGTCCCA
65 ATAGTTTCCTGACTTACGATTTAATCTCAATCACTTTTATTTTTCTGACTTGCGATTCAGTCTCA
* * * *
4517818 GTCATGATTAATCTTTGACTTGTGGTTTAATCTCGAT-ATTTCTATATTTTCCTGACTTGCAG-T
130 GTCATCATTAATCTTTGACTCGTGGTTTAATCTCGATCATTTCTATAGTTTCCTAACTTGCAGAT
* *
4517881 TTAATCCCAGTCGCTTTTATTTTTTTGACTTGCTGTTCAGTCCCAGTCGTCGTTAATCTTTGACT
195 TTAATCTCAGTCGCTTTTATTTTTTTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTGACT
* * * * * * * *
4517946 CATGGTTTAATCCCGATAATTTTTATAGTTTCCTAACTTGCGGTTTAATTTTAGTCACTTTTATT
260 CGTGGTTTAATCCCGATCATTTTTATAGTTTCCTGACTTACGATTTAATCTCAGTCGCTTTTATT
4518011 TTT
325 TTT
* * * * *
4518014 TTGACTTGCAGTTCAATCTTAGTCATCGTTAATCTTTGACTCGTGGTTTAATCTCAGTCATTTTT
1 TTGACTTACGGTTCAATCTCAGTCATCGTTAATCTCTGAATCGTGGTTTAATC-CAGTCATTTTT
* * * ** * *
4518079 ATAGTTTCCTGACTTACGATTTAATTTTAGTTGCTTTTATTTTTCTGACTTGTGGTTCAGTCTCA
65 ATAGTTTCCTGACTTACGATTTAATCTCAATCACTTTTATTTTTCTGACTTGCGATTCAGTCTCA
** * * * * * * *
4518144 GTTGTCATTAATCTTTGACTTGTTGTTTAATCCCGATCATTTTTGTAGTTTCTTTACTTG-AGAT
130 GTCATCATTAATCTTTGACTCGTGGTTTAATCTCGATCATTTCTATAGTTTCCTAACTTGCAGAT
* ** * * *
4518208 TTAATCTCAGTTGCTTTTATTTTTTTGACTTGCGGTTCAGTCTTAGTCATTGTTAATCTCTGACT
195 TTAATCTCAGTCGCTTTTATTTTTTTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTGACT
* * * * *
4518273 CGTGATTTAATCCCGATCATTTCTATAGTTTCCTGACTTACGATTTAATCCCAATCGCTGTTATT
260 CGTGGTTTAATCCCGATCATTTTTATAGTTTCCTGACTTACGATTTAATCTCAGTCGCTTTTATT
4518338 TTT
325 TTT
* * * * * * * * *
4518341 ATGATTTACGGTTCAGTCACAGTCGTCGTTAATCTTTGAATCATGATTTAATCCTGATCATTTTT
1 TTGACTTACGGTTCAATCTCAGTCATCGTTAATCTCTGAATCGTGGTTTAATCCAG-TCATTTTT
* *
4518406 ATAGATTT-CTGACTTACTG-TTTAATCTCAATTACTTTTATTTTTCTGACTTGCGATTCAATCT
65 ATAG-TTTCCTGACTTAC-GATTTAATCTCAATCACTTTTATTTTTCTGACTTGCGATTCAGTCT
* * * *
4518469 CAGTCATCGTTATTCTTTGACTCGCGATTTAATCTCGATCATTTCTATAGTTTCCTAACTTGCA-
128 CAGTCATCATTAATCTTTGACTCGTGGTTTAATCTCGATCATTTCTATAGTTTCCTAACTTGCAG
* * * * *
4518533 ATTTAATAAT-AGTCGCTTTTATTTTTTTGACTTACGGTTCAATCCCAGTCGTCATTAATATTTG
193 ATTTAAT-CTCAGTCGCTTTTATTTTTTTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTG
* * * *
4518597 ATTCGTGGTTTAATCCTGATCATTTTTATAGTTTCTTGACTTATGATTTAATCTCAGTCGCTTTT
257 ACTCGTGGTTTAATCCCGATCATTTTTATAGTTTCCTGACTTACGATTTAATCTCAGTCGCTTTT
4518662 ATTTTT
322 ATTTTT
* * * * ** * * * * **
4518668 TTGACTTACGATTTAATCCCACTTGTCGTTAATCTCTGACTAGTGGTTTAATCCCGGTCACTCCT
1 TTGACTTACGGTTCAATCTCAGTCATCGTTAATCTCTGAATCGTGGTTTAAT-CCAGTCATTTTT
* * * * *
4518733 AT-GTTTCC-AACTTACGGTTTAATCTCAGTCACTTTTATTTTTTTGATTTGCGATTCAGTCTCA
65 ATAGTTTCCTGACTTACGATTTAATCTCAATCACTTTTATTTTTCTGACTTGCGATTCAGTCTCA
* ** ** * * * * *
4518796 ATTGTTGTTAATCTCTGACTCGTGGTTTAATCTCAATCATTTCTAT-G-TTCCCAACTTAC-GGT
130 GTCATCATTAATCTTTGACTCGTGGTTTAATCTCGATCATTTCTATAGTTTCCTAACTTGCAGAT
4518858 TTAATCTCAGTCGCTTTTATTT
195 TTAATCTCAGTCGCTTTTATTT
4518880 AGTTAGCTTC
Statistics
Matches: 715, Mismatches: 138, Indels: 29
0.81 0.16 0.03
Matches are distributed among these distances:
322 1 0.00
323 30 0.04
324 2 0.00
325 87 0.12
326 147 0.21
327 439 0.61
328 9 0.01
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (327 bp):
TTGACTTACGGTTCAATCTCAGTCATCGTTAATCTCTGAATCGTGGTTTAATCCAGTCATTTTTA
TAGTTTCCTGACTTACGATTTAATCTCAATCACTTTTATTTTTCTGACTTGCGATTCAGTCTCAG
TCATCATTAATCTTTGACTCGTGGTTTAATCTCGATCATTTCTATAGTTTCCTAACTTGCAGATT
TAATCTCAGTCGCTTTTATTTTTTTGACTTGCGGTTCAGTCCCAGTCGTCGTTAATCTTTGACTC
GTGGTTTAATCCCGATCATTTTTATAGTTTCCTGACTTACGATTTAATCTCAGTCGCTTTTATTT
TT
Found at i:4519010 original size:3 final size:3
Alignment explanation
Indices: 4519002--4519031 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4518992 AACTTTTGTT
4519002 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4519032 CATTGATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4520068 original size:16 final size:16
Alignment explanation
Indices: 4520041--4520074 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
4520031 TTTTTTTAAA
4520041 TTTTATTATTA-TTAT
1 TTTTATTATTATTTAT
4520056 TTTTATATATTATTTAT
1 TTTTAT-TATTATTTAT
4520073 TT
1 TT
4520075 GTTTCGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 5 0.29
17 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTATTATTATTTAT
Found at i:4521941 original size:16 final size:16
Alignment explanation
Indices: 4521912--4521957 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
4521902 TATTTTTTAA
*
4521912 ATATAAATATATAATT
1 ATATAAATAAATAATT
* *
4521928 ATATATATAAATAATA
1 ATATAAATAAATAATT
4521944 AT-TAAA-AAATAATT
1 ATATAAATAAATAATT
4521958 TTTAATATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 7 0.28
15 3 0.12
16 15 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAAATAAATAATT
Found at i:4527597 original size:16 final size:16
Alignment explanation
Indices: 4527568--4527613 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
4527558 TGTTTTTTAA
*
4527568 ATATAAATATATAATT
1 ATATAAATAAATAATT
* *
4527584 ATATATATAAATAATA
1 ATATAAATAAATAATT
4527600 AT-TAAA-AAATAATT
1 ATATAAATAAATAATT
4527614 TTTAATATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 7 0.28
15 3 0.12
16 15 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAAATAAATAATT
Found at i:4531331 original size:2 final size:2
Alignment explanation
Indices: 4531324--4531353 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4531314 GTTACGCCAC
4531324 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
4531354 ACTCAGCATA
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):
TA
Found at i:4533110 original size:2 final size:2
Alignment explanation
Indices: 4533103--4533133 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4533093 TCTTACTTGT
4533103 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4533134 TTCTTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4533992 original size:13 final size:13
Alignment explanation
Indices: 4533974--4534000 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4533964 TACACTTCAA
4533974 CACTAATTCAACG
1 CACTAATTCAACG
4533987 CACTAATTCAACG
1 CACTAATTCAACG
4534000 C
1 C
4534001 GGTTGTTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.33, G:0.07, T:0.22
Consensus pattern (13 bp):
CACTAATTCAACG
Found at i:4539594 original size:2 final size:2
Alignment explanation
Indices: 4539589--4539631 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
4539579 TTGCCTGTTT
* * *
4539589 TA TA TA CA TA TA TA TA TA TA TA TA TA TA GA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4539631 T
1 T
4539632 TTTTATTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:4542703 original size:19 final size:16
Alignment explanation
Indices: 4542660--4542707 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
4542650 TTTTTAATTA
4542660 ATTAAT-TATTTTTTT
1 ATTAATATATTTTTTT
*
4542675 ATTTATATATATTTTTT
1 ATTAATATAT-TTTTTT
4542692 ATATAATGATATTTTT
1 AT-TAAT-ATATTTTT
4542708 AAATATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 5 0.19
16 3 0.11
17 8 0.30
18 7 0.26
19 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
ATTAATATATTTTTTT
Found at i:4542886 original size:16 final size:16
Alignment explanation
Indices: 4542865--4542896 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4542855 CATAAAATCA
*
4542865 GATCAGATTCGAGACG
1 GATCAGATTAGAGACG
4542881 GATCAGATTAGAGACG
1 GATCAGATTAGAGACG
4542897 AGCAAAATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (16 bp):
GATCAGATTAGAGACG
Found at i:4558978 original size:24 final size:24
Alignment explanation
Indices: 4558946--4558999 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
4558936 GAAACTTGAT
* *
4558946 ATATATAAATGACTATATGCCTCC
1 ATATGTAAATGACTACATGCCTCC
4558970 ATATGTAAATGACTACATGCCTCC
1 ATATGTAAATGACTACATGCCTCC
4558994 ATATGT
1 ATATGT
4559000 TCAGATCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.33
Consensus pattern (24 bp):
ATATGTAAATGACTACATGCCTCC
Found at i:4560288 original size:12 final size:12
Alignment explanation
Indices: 4560268--4560328 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
4560258 TATTTTTAAG
* *
4560268 ATAATAGCAATA
1 ATAACAGCAACA
4560280 ATAACAGCAACA
1 ATAACAGCAACA
* *
4560292 ATAATAACAACA
1 ATAACAGCAACA
* *
4560304 ACAACAACAACA
1 ATAACAGCAACA
* *
4560316 ACAACAACAACA
1 ATAACAGCAACA
4560328 A
1 A
4560329 CAATAATAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.64, C:0.23, G:0.03, T:0.10
Consensus pattern (12 bp):
ATAACAGCAACA
Found at i:4560295 original size:15 final size:15
Alignment explanation
Indices: 4560275--4560343 Score: 75
Period size: 15 Copynumber: 4.6 Consensus size: 15
4560265 AAGATAATAG
*
4560275 CAATAATAACAGCAA
1 CAATAATAACAACAA
4560290 CAATAATAACAACAA
1 CAATAATAACAACAA
* *
4560305 CAACAACAACAACAA
1 CAATAATAACAACAA
* * *
4560320 CAACAACAACAATAA
1 CAATAATAACAACAA
*
4560335 TAATAATAA
1 CAATAATAA
4560344 TAACTTACAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.65, C:0.22, G:0.01, T:0.12
Consensus pattern (15 bp):
CAATAATAACAACAA
Found at i:4560303 original size:3 final size:3
Alignment explanation
Indices: 4560282--4560331 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
4560272 TAGCAATAAT
* * *
4560282 AAC AGC AAC AAT AAT AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
4560330 AA
1 AA
4560332 TAATAATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.66, C:0.28, G:0.02, T:0.04
Consensus pattern (3 bp):
AAC
Found at i:4562350 original size:25 final size:25
Alignment explanation
Indices: 4562305--4562352 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
4562295 TATGACCTAA
*
4562305 AAATTTTATAAAAATTTATCATTTG
1 AAATTTTATAAAAATTCATCATTTG
*
4562330 AAATTTT-TATAAATTCCATCATT
1 AAATTTTATAAAAATT-CATCATT
4562353 GGATAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (25 bp):
AAATTTTATAAAAATTCATCATTTG
Found at i:4562771 original size:22 final size:22
Alignment explanation
Indices: 4562741--4562785 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4562731 TGCTGTCCAG
4562741 TTTTCTTTTTGGTT-CCTTCTTT
1 TTTTCTTTTT-GTTGCCTTCTTT
* *
4562763 TTTTTTTTTTTTTGCCTTCTTT
1 TTTTCTTTTTGTTGCCTTCTTT
4562785 T
1 T
4562786 GGTGCCAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.78
Consensus pattern (22 bp):
TTTTCTTTTTGTTGCCTTCTTT
Found at i:4585835 original size:1 final size:1
Alignment explanation
Indices: 4585829--4585855 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
4585819 ATGCATTGAT
4585829 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
4585856 GAACAGCAGC
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4600149 original size:1 final size:1
Alignment explanation
Indices: 4600145--4600175 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
4600135 TCTTTTTTTT
*
4600145 GGGGGGGGTGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
4600176 AGGGAGGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:4605739 original size:2 final size:2
Alignment explanation
Indices: 4605692--4605720 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4605682 AAAGTGTGTG
4605692 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4605721 GATGTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4607878 original size:19 final size:21
Alignment explanation
Indices: 4607854--4607895 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4607844 TTTTTATTTT
4607854 ATAAAAATT-T-AAAATATAC
1 ATAAAAATTATAAAAATATAC
4607873 ATAAAAATTAATAAAAATATAC
1 ATAAAAATT-ATAAAAATATAC
4607895 A
1 A
4607896 ATTCGATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
21 1 0.05
22 10 0.50
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (21 bp):
ATAAAAATTATAAAAATATAC
Found at i:4617998 original size:16 final size:16
Alignment explanation
Indices: 4617977--4618008 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4617967 TCCGAGCTCT
4617977 CCGGGTAGTAGAATCC
1 CCGGGTAGTAGAATCC
4617993 CCGGGTAGTAGAATCC
1 CCGGGTAGTAGAATCC
4618009 TGACAATGTG
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:0.25, C:0.25, G:0.31, T:0.19
Consensus pattern (16 bp):
CCGGGTAGTAGAATCC
Found at i:4621115 original size:12 final size:12
Alignment explanation
Indices: 4621098--4621123 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4621088 GGAATGAAAT
4621098 AATTTACTTGAA
1 AATTTACTTGAA
4621110 AATTTACTTGAA
1 AATTTACTTGAA
4621122 AA
1 AA
4621124 GAGGACCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (12 bp):
AATTTACTTGAA
Found at i:4626195 original size:35 final size:35
Alignment explanation
Indices: 4626155--4626221 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
4626145 ATAAGCATGC
4626155 ACATAACAAAAAATAAATGAATGTTTTCTACGTCG
1 ACATAACAAAAAATAAATGAATGTTTTCTACGTCG
* *
4626190 ACATAATAAAAAATAAATGAGTGTTTTCTACG
1 ACATAACAAAAAATAAATGAATGTTTTCTACG
4626222 CCGAAGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (35 bp):
ACATAACAAAAAATAAATGAATGTTTTCTACGTCG
Found at i:4629669 original size:346 final size:347
Alignment explanation
Indices: 4628677--4629778 Score: 2062
Period size: 347 Copynumber: 3.2 Consensus size: 347
4628667 AAATTATTAT
*
4628677 ATGTCCAATGGGATAAATACAATACATGAGCCTAACATTTATGTCTTTTAAATGCTTAAGTTGAA
1 ATGTCCAATGGGATAAGTACAATACATGAGCCTAACATTTATGTCTTTTAAATGCTTAAGTTGAA
*
4628742 AGCTCAACTTTACATGGTTTTTCCAACCATTCTTTCAATTTGCAATAATACAAACTTCCCACACT
66 AGCTCAACTTTACATGGTTTTTCCAACCATTCTTTCAATTTGCAATAGTACAAACTTCCCACACT
*
4628807 TTTCATTTTGTTGCTATAACACTAACAAATTATTTCATTTTCTTTTTTCCAATAATTGAGTAAAT
131 TTTCATTTTGTTGCTATAACACTAACAAATTATTTCATTTTCTTTTTTCCAATAATCGAGTAAAT
* *
4628872 TTTTGAAGCCAACAAAATGATTTGGGAATGGTTATTGGTACTTGGTAATCATGGCCTTAAAGGTT
196 TTTCGAAGCCAACAAAATGATTTGGGAATGGTTATTGGTACTTGGTAGTCATGGCCTTAAAGGTT
*
4628937 TACTAATTAAAACCTTTGTATTTGACAAGAACTTTCCTATGGTCCACAATTACTATACAGATGCA
261 TACTAATTAAAACCTTTGTATTTGACAAGAACTTTCCTAGGGTCCACAATTACTATACAGATGCA
4629002 CAATCACAATAACTTAAAAACA
326 CAATCACAATAACTTAAAAACA
* * *
4629024 ATATCTAATGGGATAAGTACAATATATGAGCCTAACATTTATGTCTTTTAAATGCTTAAGTTGAA
1 ATGTCCAATGGGATAAGTACAATACATGAGCCTAACATTTATGTCTTTTAAATGCTTAAGTTGAA
4629089 AGCTCAACTTTACATGGTTTTTCCAACCATTCTTTCAATTTGCAATAGTACAAACTTCCCACACT
66 AGCTCAACTTTACATGGTTTTTCCAACCATTCTTTCAATTTGCAATAGTACAAACTTCCCACACT
4629154 TTTCATTTTGTTGCTATAACACTAACAAATTATTTCATTTTCTTTTTTCCAATAATCGAGTAAAT
131 TTTCATTTTGTTGCTATAACACTAACAAATTATTTCATTTTCTTTTTTCCAATAATCGAGTAAAT
4629219 TTTCGAAGCCAACAAAATGATTTGGGAATGGTTATTGGTACTTGGTAGTCATGGCCTTAAAGGTT
196 TTTCGAAGCCAACAAAATGATTTGGGAATGGTTATTGGTACTTGGTAGTCATGGCCTTAAAGGTT
*
4629284 TACTAATTAAAACCTTTGTATTGGACAAGAACTTTCCTAGGGTCCACAATTACTATACAGATGCA
261 TACTAATTAAAACCTTTGTATTTGACAAGAACTTTCCTAGGGTCCACAATTACTATACAGATGCA
4629349 CAATCACAATAACTTAAAAACA
326 CAATCACAATAACTTAAAAACA
*
4629371 ATGTCCAATGGGATAAGTACAATATATGAGCCTAACATTTATGTCTTTTAAATGCTTAAGTTGAA
1 ATGTCCAATGGGATAAGTACAATACATGAGCCTAACATTTATGTCTTTTAAATGCTTAAGTTGAA
4629436 AGCTCAACTTTACATGGTTTTTCCAACCATTCTTTCAATTTGCAATAGTACAAACTT-CCACACT
66 AGCTCAACTTTACATGGTTTTTCCAACCATTCTTTCAATTTGCAATAGTACAAACTTCCCACACT
* *
4629500 TTTCATTTTGTTGCTATAACAGTAACAAATTATTTCATTTTCTTTTTTCCAATAATCGAGTACAT
131 TTTCATTTTGTTGCTATAACACTAACAAATTATTTCATTTTCTTTTTTCCAATAATCGAGTAAAT
4629565 TTTCGAAGCCAACAAAATGATTTGGGAATGGTTATTGGTACTTGGTAGTCATGGCCTTAAAGGTT
196 TTTCGAAGCCAACAAAATGATTTGGGAATGGTTATTGGTACTTGGTAGTCATGGCCTTAAAGGTT
*
4629630 TACTAATTAAAACCTTTGTATTTGACAAGAACTTTCCTAGGGTCCACAATTACTATACATATGCA
261 TACTAATTAAAACCTTTGTATTTGACAAGAACTTTCCTAGGGTCCACAATTACTATACAGATGCA
*
4629695 CAATCACTATAACTTAAAAACA
326 CAATCACAATAACTTAAAAACA
4629717 ATGTCCAATGGGATAAGTACAATACATGAGCCTAACATTTATGTCTTTTAAATGCTTAAGTT
1 ATGTCCAATGGGATAAGTACAATACATGAGCCTAACATTTATGTCTTTTAAATGCTTAAGTT
4629779 TTAATTTTTT
Statistics
Matches: 737, Mismatches: 18, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
346 280 0.38
347 457 0.62
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (347 bp):
ATGTCCAATGGGATAAGTACAATACATGAGCCTAACATTTATGTCTTTTAAATGCTTAAGTTGAA
AGCTCAACTTTACATGGTTTTTCCAACCATTCTTTCAATTTGCAATAGTACAAACTTCCCACACT
TTTCATTTTGTTGCTATAACACTAACAAATTATTTCATTTTCTTTTTTCCAATAATCGAGTAAAT
TTTCGAAGCCAACAAAATGATTTGGGAATGGTTATTGGTACTTGGTAGTCATGGCCTTAAAGGTT
TACTAATTAAAACCTTTGTATTTGACAAGAACTTTCCTAGGGTCCACAATTACTATACAGATGCA
CAATCACAATAACTTAAAAACA
Found at i:4634287 original size:21 final size:21
Alignment explanation
Indices: 4634263--4634302 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4634253 AAGATGATAT
4634263 TATT-TAATTTAATTTTATTCA
1 TATTATAATTT-ATTTTATTCA
*
4634284 TATTATTATTTATTTTATT
1 TATTATAATTTATTTTATT
4634303 TTATCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTATAATTTATTTTATTCA
Found at i:4634294 original size:27 final size:25
Alignment explanation
Indices: 4634260--4634310 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
4634250 ATAAAGATGA
4634260 TATTATTTAATTTAATTTTATTCATAT
1 TATTATTT-ATTTAATTTTA-TCATAT
*
4634287 TATTATTTATTTTATTTTATCATA
1 TATTATTTATTTAATTTTATCATA
4634311 ATCTTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
26 10 0.43
27 8 0.35
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTATTTATTTAATTTTATCATAT
Found at i:4634774 original size:24 final size:24
Alignment explanation
Indices: 4634742--4634797 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
4634732 GGCTTGAACA
4634742 TATACACATAGCTCTGATACCATT
1 TATACACATAGCTCTGATACCATT
4634766 TATACACATAGCTCTGATACCATT
1 TATACACATAGCTCTGATACCATT
4634790 TATACACA
1 TATACACA
4634798 GCGGCAGGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (24 bp):
TATACACATAGCTCTGATACCATT
Found at i:4641713 original size:19 final size:20
Alignment explanation
Indices: 4641680--4641718 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
4641670 AGGCATGAAA
*
4641680 TATACTTTTTTAAAAATAAT
1 TATACTTTTTGAAAAATAAT
4641700 TATAC-TTTTGAAAAATAAT
1 TATACTTTTTGAAAAATAAT
4641719 AAAACCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (20 bp):
TATACTTTTTGAAAAATAAT
Found at i:4642272 original size:24 final size:23
Alignment explanation
Indices: 4642236--4642303 Score: 57
Period size: 25 Copynumber: 2.8 Consensus size: 23
4642226 ACCTTTTGTG
*
4642236 TAATCA-TGATATTTATAAATAA
1 TAATCATTTATATTTATAAATAA
* * *
4642258 TAATCTATTTATATTCAAATAATTA
1 TAATC-ATTTATATTTATA-AATAA
4642283 TAATCATTTATTATTTGATAA
1 TAATCATTTA-TATTT-ATAA
4642304 TTATTTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
22 5 0.14
23 1 0.03
24 13 0.37
25 14 0.40
26 2 0.06
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (23 bp):
TAATCATTTATATTTATAAATAA
Found at i:4642315 original size:17 final size:18
Alignment explanation
Indices: 4642282--4642315 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4642272 TCAAATAATT
4642282 ATAATCATTTATTATTTG
1 ATAATCATTTATTATTTG
*
4642300 ATAATTATTT-TTATTT
1 ATAATCATTTATTATTT
4642316 AAATATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
ATAATCATTTATTATTTG
Found at i:4642442 original size:407 final size:408
Alignment explanation
Indices: 4641624--4642444 Score: 1001
Period size: 407 Copynumber: 2.0 Consensus size: 408
4641614 TATATTAGAC
* * * *
4641624 AAAATAAATAAGAAAAGAGAAATAATAGAAAAAAATTTTGGCTTTGAGGCATGAAATATACTTTT
1 AAAATAAATAAGAAAAGAAAAATAATAGAAAAAAATTTTAGCTTTAAAGCATGAAATATACTTTT
* * ** * *
4641689 TTAAAAATAATTATACTTTTGAAAAATAATAAAACCTTAAATTCTCTAATTAGAAGCATTCAAAA
66 TTAAAAATAATTATACTTTTGAAAAATAATAAAACCTCAAACTCTAAAATGAGAAGCAGTCAAAA
*
4641754 TAATTATACTGAAAGATTTATTTATAATAAAGAAACAGATATAAATTTTTATTCAAATGATTATG
131 TAATTATACTGAAAGATTTATTTATAATAAAGAAACAGATATAAACTTTTATTCAAATGATTATG
* * * *
4641819 ACATTATGTATAATCATGATATTTATGAATAATAATTTATTTATACTTAAATAGTTATGACCATT
196 ACATTATGTATAATCATGATATTTATAAATAATAATCTATTTATACTTAAATAATTATAACCATT
*
4641884 TATCATATGATAATTATTTTTGTTCAAACATAATTATTTAAAATATAAATAAAATTAATACAAAA
261 TATCATATGATAATTATTTTTATTCAAACATAATTATTTAAAATATAAATAAAATTAATACAAAA
* *
4641949 ATTAATTTTATTCATCTATAATTAAAAATTTCTATCCAATGTGAAATGCATCACATTCTAAACTA
326 ATTAATTTTATTCAACCATAATTAAAAATTTCTATCCAATGTGAAATGCATCACATTCTAAACTA
* **
4642014 CCAATAATAATTATTAAAA
391 ACAATAATAA-TAAAAAAA
* * * *
4642033 AAAATAAATAAGAGAAA-AAAAATAATATAAAAAAA-TTTAGTTTTAAAGCGTGAAGA-ATATTT
1 AAAATAAATAAGA-AAAGAAAAATAATAGAAAAAAATTTTAGCTTTAAAGCATGAA-ATATACTT
** * * * *
4642095 TTTTAAAGGTAATTTTACTTTT-AAGATATAATAAAATCTCAAACTCTAAAATGAGAAGCAGTGA
64 TTTTAAAAATAATTATACTTTTGAA-AAATAATAAAACCTCAAACTCTAAAATGAGAAGCAGTCA
** * * * *
4642159 AAATGGTTATATTGAAATATTTATTTATAATAAA-TAACAGATATAAACTTTTATTCATAT-AGT
128 AAATAATTATACTGAAAGATTTATTTATAATAAAGAAACAGATATAAACTTTTATTCAAATGA-T
* * *
4642222 TATGACCTTTTGTGTAATCATGATATTTATAAATAATAATCTATTTATA-TTCAAATAATTATAA
192 TATGACATTATGTATAATCATGATATTTATAAATAATAATCTATTTATACTT-AAATAATTATAA
* * * * * *
4642286 TCATTTATTATTTGATAATTATTTTTATTTAAATATAATTATTTAAAATATGAATAAAATTAATA
256 CCATTTATCATATGATAATTATTTTTATTCAAACATAATTATTTAAAATATAAATAAAATTAATA
* * ** * * *
4642351 CAAAAATTAATTTTATTCAACCATAATT-AAACTTTTTAATTTAATGTGAGATGCATCATATTTT
321 CAAAAATTAATTTTATTCAACCATAATTAAAAATTTCT-ATCCAATGTGAAATGCATCACATTCT
* * *
4642415 AAATTAACACTATATCAAAAAAAAAA
385 AAACTAACAATA-AT-AATAAAAAAA
4642441 AAAA
1 AAAA
4642445 AGAGAATAAG
Statistics
Matches: 348, Mismatches: 56, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
406 10 0.03
407 194 0.56
408 109 0.31
409 32 0.09
410 3 0.01
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (408 bp):
AAAATAAATAAGAAAAGAAAAATAATAGAAAAAAATTTTAGCTTTAAAGCATGAAATATACTTTT
TTAAAAATAATTATACTTTTGAAAAATAATAAAACCTCAAACTCTAAAATGAGAAGCAGTCAAAA
TAATTATACTGAAAGATTTATTTATAATAAAGAAACAGATATAAACTTTTATTCAAATGATTATG
ACATTATGTATAATCATGATATTTATAAATAATAATCTATTTATACTTAAATAATTATAACCATT
TATCATATGATAATTATTTTTATTCAAACATAATTATTTAAAATATAAATAAAATTAATACAAAA
ATTAATTTTATTCAACCATAATTAAAAATTTCTATCCAATGTGAAATGCATCACATTCTAAACTA
ACAATAATAATAAAAAAA
Found at i:4646665 original size:9 final size:10
Alignment explanation
Indices: 4646646--4646677 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
4646636 CTGAACTGAA
4646646 TTATATATTT
1 TTATATATTT
4646656 TTAT-TATTT
1 TTATATATTT
4646665 TTATATATTT
1 TTATATATTT
4646675 TTA
1 TTA
4646678 AAATTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTATATATTT
Found at i:4646683 original size:19 final size:19
Alignment explanation
Indices: 4646646--4646685 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4646636 CTGAACTGAA
**
4646646 TTATATATTTTTATTATTT
1 TTATATATTTTTAAAATTT
4646665 TTATATATTTTTAAAATTT
1 TTATATATTTTTAAAATTT
4646684 TT
1 TT
4646686 TAAAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATATATTTTTAAAATTT
Found at i:4647268 original size:2 final size:2
Alignment explanation
Indices: 4647261--4647289 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4647251 TTTGTCTTGA
4647261 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 A
4647290 CACGTGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4662242 original size:15 final size:15
Alignment explanation
Indices: 4662222--4662254 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
4662212 CAACCTACAA
4662222 CAAAGTATGGACTTT
1 CAAAGTATGGACTTT
4662237 CAAAGTATGGACTTT
1 CAAAGTATGGACTTT
4662252 CAA
1 CAA
4662255 TAGAATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (15 bp):
CAAAGTATGGACTTT
Found at i:4664401 original size:20 final size:20
Alignment explanation
Indices: 4664378--4664429 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
4664368 ATAAAATATT
*
4664378 AATTATATATATAAATATAA
1 AATTATATATATAAATAAAA
* *
4664398 AATTAAATA-ATTAATTAAAA
1 AATTATATATA-TAAATAAAA
*
4664418 AATAATATATAT
1 AATTATATATAT
4664430 TTATATCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
19 1 0.04
20 23 0.92
21 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTATATATATAAATAAAA
Found at i:4664776 original size:10 final size:10
Alignment explanation
Indices: 4664763--4664803 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
4664753 TTAATTTGAT
4664763 TTTTATAAAA
1 TTTTATAAAA
*
4664773 TTTTATATAA
1 TTTTATAAAA
*
4664783 TATTAT-AAA
1 TTTTATAAAA
4664792 TTTT-TAAAA
1 TTTTATAAAA
4664801 TTT
1 TTT
4664804 GAGCTGATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
8 1 0.04
9 11 0.42
10 14 0.54
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTATAAAA
Found at i:4665033 original size:23 final size:24
Alignment explanation
Indices: 4665007--4665064 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 24
4664997 TTTTTTATAT
*
4665007 TTTAATATGAAATTTTAT-CC-GAA
1 TTTAATAT-AAATTTAATACCTGAA
4665030 TTTAATATAAATTTAATACCTGAA
1 TTTAATATAAATTTAATACCTGAA
4665054 TTTAATCATAA
1 TTTAAT-ATAA
4665065 TCAAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 8 0.26
23 10 0.32
24 9 0.29
25 4 0.13
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (24 bp):
TTTAATATAAATTTAATACCTGAA
Found at i:4666738 original size:25 final size:25
Alignment explanation
Indices: 4666710--4666759 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
4666700 CCACATATCA
4666710 TTAAATTATTACAACCATTCAACCC
1 TTAAATTATTACAACCATTCAACCC
*
4666735 TTAAATTATTATAACCATTCAACCC
1 TTAAATTATTACAACCATTCAACCC
4666760 AAGAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (25 bp):
TTAAATTATTACAACCATTCAACCC
Found at i:4666969 original size:2 final size:2
Alignment explanation
Indices: 4666962--4666988 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4666952 GTTCTTCTAT
4666962 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4666989 TTTGTCGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4667194 original size:19 final size:17
Alignment explanation
Indices: 4667170--4667213 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
4667160 GAATTAATCA
4667170 AAAAATTAAAAAGAATTTT
1 AAAAATTAAAAA-AA-TTT
4667189 AAAAATTTTAAAAAAATTT
1 AAAAA--TTAAAAAAATTT
4667208 AAAAAT
1 AAAAAT
4667214 CTGAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.04
19 13 0.57
20 2 0.09
21 7 0.30
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAAATTAAAAAAATTT
Found at i:4667241 original size:39 final size:38
Alignment explanation
Indices: 4667184--4667279 Score: 122
Period size: 39 Copynumber: 2.5 Consensus size: 38
4667174 ATTAAAAAGA
* * * *
4667184 ATTTTAAAAATTTTAAAAAAATT-TAAAAATCTGAATT
1 ATTTTAAAAATTATAAAAAAATTAAAAAAATATGAAAT
4667221 ATTTTAAAAAATTATAAAAAAATTAAAAAAATATGAAAT
1 ATTTT-AAAAATTATAAAAAAATTAAAAAAATATGAAAT
*
4667260 ATTTTTAGAAATTATAAAAA
1 A-TTTTAAAAATTATAAAAA
4667280 TAAAAAATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
37 5 0.10
38 17 0.33
39 25 0.49
40 4 0.08
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (38 bp):
ATTTTAAAAATTATAAAAAAATTAAAAAAATATGAAAT
Found at i:4675392 original size:2 final size:2
Alignment explanation
Indices: 4675385--4675424 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4675375 TCCCATTCGC
4675385 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4675425 TAGCATAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4678486 original size:20 final size:17
Alignment explanation
Indices: 4678466--4678498 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
4678456 TAAATTTATT
4678466 AATTATAT-TATAATTA
1 AATTATATATATAATTA
4678482 AATTATATATATAATTA
1 AATTATATATATAATTA
4678499 TTTCCTGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTATATATATAATTA
Found at i:4680427 original size:23 final size:22
Alignment explanation
Indices: 4680401--4680547 Score: 78
Period size: 23 Copynumber: 6.7 Consensus size: 22
4680391 TTAGATTTTA
4680401 TTTTTAAAAAATCAATTTTCAAT
1 TTTTTAAAAAATCAATTTT-AAT
** *
4680424 TTTTTTTAGAA--AATTTTCACA-
1 TTTTTAAAAAATCAATTTT-A-AT
* * *
4680445 TTTTGAAAATATTAA-TTTAAT
1 TTTTTAAAAAATCAATTTTAAT
4680466 TTTTT---AAAT--ATTTTAAT
1 TTTTTAAAAAATCAATTTTAAT
* *
4680483 TTTTCAAAAAATTATATTTTTAATTT
1 TTTTTAAAAAATCA-A-TTTTAA--T
4680509 TTTTTAAAAAATCATATTTTAAT
1 TTTTTAAAAAATCA-ATTTTAAT
*
4680532 TTTTTAAAAATTCAAT
1 TTTTTAAAAAATCAAT
4680548 ATTTTAAAAT
Statistics
Matches: 96, Mismatches: 14, Indels: 29
0.69 0.10 0.21
Matches are distributed among these distances:
16 1 0.01
17 10 0.10
18 3 0.03
20 5 0.05
21 19 0.20
22 6 0.06
23 25 0.26
24 6 0.06
25 6 0.06
26 15 0.16
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (22 bp):
TTTTTAAAAAATCAATTTTAAT
Found at i:4680518 original size:26 final size:25
Alignment explanation
Indices: 4680473--4680554 Score: 91
Period size: 24 Copynumber: 3.4 Consensus size: 25
4680463 AATTTTTTAA
*
4680473 ATATTTTAA--TTTTTCAAAAAATT
1 ATATTTTAATTTTTTTCAAAAAATC
*
4680496 ATATTTTTAATTTTTTTTAAAAAATC
1 ATA-TTTTAATTTTTTTCAAAAAATC
*
4680522 ATATTTTAA-TTTTTT-AAAAATTC
1 ATATTTTAATTTTTTTCAAAAAATC
4680545 AATATTTTAA
1 -ATATTTTAA
4680555 AATTTTTTAG
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
23 10 0.19
24 21 0.40
25 6 0.12
26 15 0.29
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATTTTAATTTTTTTCAAAAAATC
Found at i:4680549 original size:24 final size:23
Alignment explanation
Indices: 4680473--4680563 Score: 94
Period size: 26 Copynumber: 3.7 Consensus size: 23
4680463 AATTTTTTAA
*
4680473 ATATTTTAATTTTTCAAAAAATT-
1 ATATTTTAATTTTT-TAAAAATTC
*
4680496 ATATTTTTAATTTTTTTTAAAAAATC
1 ATA-TTTTAA--TTTTTTAAAAATTC
4680522 ATATTTTAATTTTTTAAAAATTC
1 ATATTTTAATTTTTTAAAAATTC
4680545 AATATTTTAAAATTTTTTA
1 -ATATTTT--AATTTTTTA
4680564 GAATTTTTCT
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
23 16 0.28
24 13 0.22
25 12 0.21
26 17 0.29
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATTTTAATTTTTTAAAAATTC
Found at i:4680727 original size:20 final size:20
Alignment explanation
Indices: 4680704--4680751 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
4680694 CCTTTTGAAA
*
4680704 TTTTTATAAAGTTT-TCTATT
1 TTTTTATAAA-TTTATATATT
*
4680724 TTTTTTTAAATTTATATATT
1 TTTTTATAAATTTATATATT
4680744 TTTTTATA
1 TTTTTATA
4680752 TTCAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTATAAATTTATATATT
Found at i:4680987 original size:29 final size:29
Alignment explanation
Indices: 4680954--4681020 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
4680944 CTTTTAAGTT
*
4680954 TTATAAACTATTTT-TAA-AAACATCAAATA
1 TTATAAA-AATTTTCTAACAAACATCAAA-A
*
4680983 TTATAAAAATTTTCTAACAAACATTAAAA
1 TTATAAAAATTTTCTAACAAACATCAAAA
4681012 TTA-AAAAAT
1 TTATAAAAAT
4681021 ATGAAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 11 0.32
29 14 0.41
30 9 0.26
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (29 bp):
TTATAAAAATTTTCTAACAAACATCAAAA
Found at i:4682124 original size:23 final size:21
Alignment explanation
Indices: 4682098--4682160 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 21
4682088 AAATGTATGT
*
4682098 ATTTATATTAAAAATTAAGTTTA
1 ATTT-TATTAAAAATTAA-ATTA
4682121 ATTTTTAACTTAAAAA-TAAATTA
1 A-TTTT-A-TTAAAAATTAAATTA
4682144 ATGTTTATTAAAAATTA
1 AT-TTTATTAAAAATTA
4682161 TTGTTTTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
21 7 0.21
22 4 0.12
23 9 0.26
24 7 0.21
25 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (21 bp):
ATTTTATTAAAAATTAAATTA
Found at i:4683040 original size:20 final size:20
Alignment explanation
Indices: 4683001--4683040 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4682991 TTTTATATAT
* *
4683001 ATATATTTTTAAAGTTTTTA
1 ATATATTTTTAAACTCTTTA
4683021 ATATATTTTTAAACTCTTTA
1 ATATATTTTTAAACTCTTTA
4683041 TCTTATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (20 bp):
ATATATTTTTAAACTCTTTA
Found at i:4684469 original size:56 final size:55
Alignment explanation
Indices: 4684364--4684481 Score: 130
Period size: 56 Copynumber: 2.1 Consensus size: 55
4684354 TATAAATTTG
* * * * *
4684364 TATATTTTAATTTTCTTACCTATATCAACGGCTAACGCCCGTCAGTATAGACTTA
1 TATATTTTAATTTTCTTACCCATATCAACGACTAACACCCGTAAATATAGACTTA
* * ** *
4684419 TATATTTTAATTTTTCTTACCCATATCGACGATTAACACTTGTAAATATAGACTTG
1 TATATTTTAA-TTTTCTTACCCATATCAACGACTAACACCCGTAAATATAGACTTA
4684475 TA-ATTTT
1 TATATTTT
4684482 TTTTGACATA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
55 15 0.29
56 37 0.71
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (55 bp):
TATATTTTAATTTTCTTACCCATATCAACGACTAACACCCGTAAATATAGACTTA
Found at i:4684581 original size:55 final size:55
Alignment explanation
Indices: 4684522--4684657 Score: 150
Period size: 55 Copynumber: 2.5 Consensus size: 55
4684512 TATTATAGAC
* *
4684522 TTGTATTTTTTAATTTTCTTA-CATATACCAAAGGTTAGAGACTATTAATATAAAA
1 TTGTATATTTTAATTTTCTTATC-TATACCAAAGGTTAGAGACTATCAATATAAAA
* * * * * * *
4684577 TTGTATACTTTAATTTTCTTATCTATATCGATGGTTAGAGATTATCAGTATAAAC
1 TTGTATATTTTAATTTTCTTATCTATACCAAAGGTTAGAGACTATCAATATAAAA
* *
4684632 TTATATATTTTAATTTTTTTAT-TATA
1 TTGTATATTTTAATTTTCTTATCTATA
4684658 TTTTATTGAC
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
54 4 0.06
55 63 0.93
56 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.49
Consensus pattern (55 bp):
TTGTATATTTTAATTTTCTTATCTATACCAAAGGTTAGAGACTATCAATATAAAA
Found at i:4684965 original size:15 final size:15
Alignment explanation
Indices: 4684932--4684967 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
4684922 TAGCAAGTCT
*
4684932 GATAAAACAAACATT
1 GATAAAACAAACATA
*
4684947 GATAAAACAAACGTA
1 GATAAAACAAACATA
4684962 GATAAA
1 GATAAA
4684968 GAGTTACACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.17
Consensus pattern (15 bp):
GATAAAACAAACATA
Found at i:4687266 original size:30 final size:30
Alignment explanation
Indices: 4687232--4687334 Score: 89
Period size: 37 Copynumber: 3.2 Consensus size: 30
4687222 AAGCCAAACA
*
4687232 ATAAATAATTTTATATAATATAAACAATAT
1 ATAAATAATTATATATAATATAAACAATAT
*
4687262 ATAAACAATAAACATGTATATATAATGTAAACAATAT
1 AT--A-AAT--A-AT-TATATATAATATAAACAATAT
* * *
4687299 ATAAACAATTATATATAATCTAAATAATTAT
1 ATAAATAATTATATATAATATAAACAA-TAT
4687330 ATAAA
1 ATAAA
4687335 CCTTATTATG
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
30 18 0.30
31 10 0.17
32 2 0.03
33 3 0.05
34 2 0.03
35 2 0.03
36 2 0.03
37 21 0.35
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (30 bp):
ATAAATAATTATATATAATATAAACAATAT
Found at i:4687270 original size:37 final size:37
Alignment explanation
Indices: 4687227--4687307 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
4687217 TGAAAAAGCC
*
4687227 AAACAATAAATAAT-TTTATATAATATAAACAATATAT
1 AAACAATAAA-AATGTATATATAATATAAACAATATAT
* *
4687264 AAACAATAAACATGTATATATAATGTAAACAATATAT
1 AAACAATAAAAATGTATATATAATATAAACAATATAT
4687301 AAACAAT
1 AAACAAT
4687308 TATATATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 2 0.05
37 38 0.95
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (37 bp):
AAACAATAAAAATGTATATATAATATAAACAATATAT
Found at i:4688461 original size:16 final size:15
Alignment explanation
Indices: 4688421--4688469 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
4688411 TGTATCATTC
*
4688421 TTTTAGAAAGAATATT
1 TTTTATAAA-AATATT
*
4688437 TTATATAAAAATATT
1 TTTTATAAAAATATT
4688452 ATTTTATAAAAA-ATT
1 -TTTTATAAAAATATT
4688467 TTT
1 TTT
4688470 ACAAATAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 3 0.10
15 9 0.31
16 17 0.59
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (15 bp):
TTTTATAAAAATATT
Found at i:4690201 original size:16 final size:16
Alignment explanation
Indices: 4690161--4690202 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
4690151 ATTTTATTTA
*
4690161 TTAATAATTATAGTTT
1 TTAAAAATTATAGTTT
*
4690177 TTATCAAATTATAGTTT
1 TTA-AAAATTATAGTTT
4690194 TTAAAAATT
1 TTAAAAATT
4690203 TTTATTAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (16 bp):
TTAAAAATTATAGTTT
Found at i:4698067 original size:2 final size:2
Alignment explanation
Indices: 4698060--4698091 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4698050 GAGATTCTTC
4698060 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
4698092 AAGATTCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4698852 original size:29 final size:29
Alignment explanation
Indices: 4698820--4698894 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
4698810 TTGAAAACAT
* *
4698820 AATGACAAAAATCAATAAAAATAAAGTAC
1 AATGACAAAATTCAATAAAAATAAAATAC
** * * *
4698849 AATGACAATTTTTAATAAAATTAAAATAT
1 AATGACAAAATTCAATAAAAATAAAATAC
4698878 AATGACAAAATTCAATA
1 AATGACAAAATTCAATA
4698895 TTGAATCATA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.60, C:0.08, G:0.05, T:0.27
Consensus pattern (29 bp):
AATGACAAAATTCAATAAAAATAAAATAC
Found at i:4699404 original size:5 final size:5
Alignment explanation
Indices: 4699396--4699438 Score: 68
Period size: 5 Copynumber: 8.2 Consensus size: 5
4699386 TTTTTTTCAT
4699396 TTATA TTATA TTATA TTATA TTATA TTATA TATATA TATATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA T-TATA T-TATA T
4699439 ACATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 26 0.70
6 11 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:4699429 original size:2 final size:2
Alignment explanation
Indices: 4699397--4699459 Score: 82
Period size: 2 Copynumber: 34.0 Consensus size: 2
4699387 TTTTTTCATT
4699397 TA TA T- TA TA T- TA TA T- TA TA T- TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4699434 TA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
4699460 AGATTAACAA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
1 5 0.09
2 49 0.91
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4699954 original size:13 final size:13
Alignment explanation
Indices: 4699938--4699974 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
4699928 ATTATTGATG
4699938 AAATTTATTGACA
1 AAATTTATTGACA
*
4699951 AAA-TT-TCGACA
1 AAATTTATTGACA
4699962 AAATTTATTGACA
1 AAATTTATTGACA
4699975 CATCAGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
11 8 0.40
12 4 0.20
13 8 0.40
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (13 bp):
AAATTTATTGACA
Found at i:4705332 original size:29 final size:29
Alignment explanation
Indices: 4705296--4705352 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
4705286 TCATTGTAAA
* * *
4705296 TTTTAGACTGATCATTTCATATCAAATAT
1 TTTTAGACTAAGCACTTCATATCAAATAT
4705325 TTTTAGACTAAGCACTTCATATCAAATA
1 TTTTAGACTAAGCACTTCATATCAAATA
4705353 CTTCACATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (29 bp):
TTTTAGACTAAGCACTTCATATCAAATAT
Found at i:4707065 original size:27 final size:27
Alignment explanation
Indices: 4707035--4707090 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
4707025 ATGCATACAT
* * *
4707035 TTAAATATTTATA-AAATTATTATCAAA
1 TTAAATAATAATATAAATTATAAT-AAA
4707062 TTAAATAATAATATAAATTATAATAAA
1 TTAAATAATAATATAAATTATAATAAA
4707089 TT
1 TT
4707091 CATAAAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
TTAAATAATAATATAAATTATAATAAA
Found at i:4707337 original size:17 final size:17
Alignment explanation
Indices: 4707315--4707347 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4707305 TTTCTTTTTT
4707315 TTAAAT-TTTCTTTTACC
1 TTAAATGTTT-TTTTACC
4707332 TTAAATGTTTTTTTAC
1 TTAAATGTTTTTTTAC
4707348 AAAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.61
Consensus pattern (17 bp):
TTAAATGTTTTTTTACC
Found at i:4708317 original size:343 final size:343
Alignment explanation
Indices: 4707691--4708371 Score: 1213
Period size: 343 Copynumber: 2.0 Consensus size: 343
4707681 TAAAAATAAA
4707691 GAGTGTTTTCTACATTTACACTCCAATGTACAAGTCAAAGATCAATGTAAATAAGGTTGAAATGA
1 GAGTGTTTTCTACATTTACACTCCAATGTACAAGTCAAAGATCAATGTAAATAAGGTTGAAATGA
*
4707756 GAGAACAATAAAAAAATATTAGTAAAATGGAAATGAAATGATAGTACCTAGGTGTTCGTATTTAT
66 GAGAACAATAAAAAAATATTAGTAAAATGGAAATGAAATGATAGTACCTAGGTGTTCATATTTAT
* * *
4707821 AGGCGGAAGGTGAGGGGTTTTTAAGGCATAATAGTGATGTGACCAAGCGACATGATACTAAGTAT
131 AGGCCGAAGGTGACGGGTTTTTAAGGCATAATAGTGATGTGACCAAGCAACATGATACTAAGTAT
4707886 GTCAGGTCAGTCCAACATATCAACAGTGATTCAAATAGCGGTGTTATAGCGAAATAATGACCACG
196 GTCAGGTCAGTCCAACATATCAACAGTGATTCAAATAGCGGTGTTATAGCGAAATAATGACCACG
*
4707951 AAATTGCAATCGTGCCACCACTCACCACCGCTATCGAGAAAAATATAGTTAAAAATTTAATCACA
261 AAATTACAATCGTGCCACCACTCACCACCGCTATCGAGAAAAATATAGTTAAAAATTTAATCACA
4708016 CTTAAAACGATATGTAAG
326 CTTAAAACGATATGTAAG
4708034 GAGTGTTTTCTACATTTACACTCCAATGTACAAGTCAAAGATCAATGTAAATAAGGTTGAAATGA
1 GAGTGTTTTCTACATTTACACTCCAATGTACAAGTCAAAGATCAATGTAAATAAGGTTGAAATGA
* * *
4708099 GAGAA-AAGTAAAAAAATATTAGTAGAATGGAAATGAAATGATGGTACCTGGGTGTTCATATTTA
66 GAGAACAA-TAAAAAAATATTAGTAAAATGGAAATGAAATGATAGTACCTAGGTGTTCATATTTA
4708163 TAGGCCGAAGGTGACGGGTTTTTAAGGCATAATAGTGATGTGACCAAGCAACATGATACTAAGTA
130 TAGGCCGAAGGTGACGGGTTTTTAAGGCATAATAGTGATGTGACCAAGCAACATGATACTAAGTA
*
4708228 TGTCAGGTCAGTCCAACATATCAACAGTGATTCAAATAGCGGTGTTATAGTGAAATAGA-GACCA
195 TGTCAGGTCAGTCCAACATATCAACAGTGATTCAAATAGCGGTGTTATAGCGAAATA-ATGACCA
* * * *
4708292 CGAAATTACGATCGTGCCACCACTCACTACCGCTATCGAGAAAAATATGGTTGAAAATTTAATCA
259 CGAAATTACAATCGTGCCACCACTCACCACCGCTATCGAGAAAAATATAGTTAAAAATTTAATCA
4708357 CACTTAAAACGATAT
324 CACTTAAAACGATAT
4708372 ATAGTGGCCG
Statistics
Matches: 323, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
342 2 0.01
343 320 0.99
344 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (343 bp):
GAGTGTTTTCTACATTTACACTCCAATGTACAAGTCAAAGATCAATGTAAATAAGGTTGAAATGA
GAGAACAATAAAAAAATATTAGTAAAATGGAAATGAAATGATAGTACCTAGGTGTTCATATTTAT
AGGCCGAAGGTGACGGGTTTTTAAGGCATAATAGTGATGTGACCAAGCAACATGATACTAAGTAT
GTCAGGTCAGTCCAACATATCAACAGTGATTCAAATAGCGGTGTTATAGCGAAATAATGACCACG
AAATTACAATCGTGCCACCACTCACCACCGCTATCGAGAAAAATATAGTTAAAAATTTAATCACA
CTTAAAACGATATGTAAG
Found at i:4709141 original size:10 final size:9
Alignment explanation
Indices: 4709111--4709140 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4709101 AATTTAACAA
*
4709111 TTTATAATT
1 TTTAAAATT
4709120 TTTAAAATT
1 TTTAAAATT
4709129 TTTAAAATT
1 TTTAAAATT
4709138 TTT
1 TTT
4709141 TTAGATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTAAAATT
Found at i:4709469 original size:126 final size:122
Alignment explanation
Indices: 4709328--4709650 Score: 319
Period size: 123 Copynumber: 2.6 Consensus size: 122
4709318 CCAAAAAATT
* * ** *
4709328 TTTTTATGATATGATTACTTAAGGCATTTTTCACTAAAAATATTTTGAATAAT-TCAACAAAAAA
1 TTTTTATAAT-TGATTACTTAATGCATTTTTCACTAAAAATACCTTAAATAATCTCAA-AAAAAA
* *
4709392 TTTTTAATGGGGTTATTGAAGGCGTTTCTGACAAAAAATACCTTCAATAATCTCTTCATAAA
64 -TTTTAATGGGGTTATTGAAGGCG-TT-TGACAAAAAACACCTTCAATAATCCCTTCATAAA
* ** * **
4709454 TTTTTATAATGTGATTACTCAATGCATTTTTTGCTAAAAATGCCTTAAATAATCTTTAAAAAAAT
1 TTTTTATAAT-TGATTACTTAATGCATTTTTCACTAAAAATACCTTAAATAATCTCAAAAAAAAT
* * * *
4709519 TTTAATGGGGTTATTGAAGGCGTTTGGCCAAAAACGCCTTCAATAATCCCTTCATAGA
65 TTTAATGGGGTTATTGAAGGCGTTTGACAAAAAACACCTTCAATAATCCCTTCATAAA
* * * * *
4709577 TTTTTATGACTTGATTATTTCATGCATTTTTCAC-AAAAA-ACGCTTTGAATAATCCTTAAAAAA
1 TTTTTAT-AATTGATTACTTAATGCATTTTTCACTAAAAATAC-C-TTAAATAAT-CTCAAAAAA
*
4709640 TATTTTTAATG
62 -AATTTTAATG
4709651 ATGAAACAAG
Statistics
Matches: 163, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
121 1 0.01
122 6 0.04
123 61 0.37
124 12 0.07
125 32 0.20
126 49 0.30
127 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (122 bp):
TTTTTATAATTGATTACTTAATGCATTTTTCACTAAAAATACCTTAAATAATCTCAAAAAAAATT
TTAATGGGGTTATTGAAGGCGTTTGACAAAAAACACCTTCAATAATCCCTTCATAAA
Found at i:4709602 original size:123 final size:125
Alignment explanation
Indices: 4709386--4709650 Score: 322
Period size: 123 Copynumber: 2.1 Consensus size: 125
4709376 ATAATTCAAC
* * *
4709386 AAAAAATTTTTAATGGGGTTATTGAAGGCGTTTCTGACAAAAAATACCTTCAATAATCTCTTCAT
1 AAAAAAATTTTAATGGGGTTATTGAAGGCGTTTCTGACAAAAAACACCTTCAATAATCCCTTCAT
** * * *
4709451 AAATTTTTATAATGTGATTACTCAATGCATTTTTTGCTAAAAATGCCTTAAATAATCTTT
66 AAATTTTTATAATGTGATTACTCAATGCATTTTTCACAAAAAACGCCTTAAATAATCCTT
* * *
4709511 AAAAAAATTTTAATGGGGTTATTGAAGGCG-TT-TGGCCAAAAACGCCTTCAATAATCCCTTCAT
1 AAAAAAATTTTAATGGGGTTATTGAAGGCGTTTCTGACAAAAAACACCTTCAATAATCCCTTCAT
* * * * *
4709574 AGATTTTTATGACT-TGATTATTTC-ATGCATTTTTCACAAAAAACGCTTTGAATAATCCTT
66 AAATTTTTAT-AATGTGATTA-CTCAATGCATTTTTCACAAAAAACGCCTTAAATAATCCTT
4709634 AAAAAATATTTTTAATG
1 AAAAAA-A-TTTTAATG
4709651 ATGAAACAAG
Statistics
Matches: 120, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
123 76 0.63
124 7 0.06
125 37 0.31
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (125 bp):
AAAAAAATTTTAATGGGGTTATTGAAGGCGTTTCTGACAAAAAACACCTTCAATAATCCCTTCAT
AAATTTTTATAATGTGATTACTCAATGCATTTTTCACAAAAAACGCCTTAAATAATCCTT
Found at i:4710768 original size:18 final size:17
Alignment explanation
Indices: 4710741--4710804 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 17
4710731 TTATCCACCA
*
4710741 CAAATATATCTTTCACAT
1 CAAATGTATCTTT-ACAT
4710759 CAAATGTATCTTTTACAT
1 CAAATGTATC-TTTACAT
4710777 CAAATGTATCATTTACCA-
1 CAAATGTATC-TTTA-CAT
4710795 CAAATGTATC
1 CAAATGTATC
4710805 CCATATCACA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
18 37 0.88
19 5 0.12
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (17 bp):
CAAATGTATCTTTACAT
Found at i:4715391 original size:3 final size:3
Alignment explanation
Indices: 4715385--4715415 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4715375 TTTTGTTTTC
4715385 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
4715416 AATATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4715541 original size:8 final size:7
Alignment explanation
Indices: 4715495--4715540 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
4715485 TTAAAATGAC
4715495 AAAATTA
1 AAAATTA
4715502 AAAATTA
1 AAAATTA
4715509 AAAATT-
1 AAAATTA
*
4715515 -AAATCAA
1 AAAAT-TA
4715522 AAAATTAA
1 AAAATT-A
4715530 AAAATTA
1 AAAATTA
4715537 AAAA
1 AAAA
4715541 AAGTATTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
5 4 0.12
7 18 0.55
8 11 0.33
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:4717164 original size:13 final size:14
Alignment explanation
Indices: 4717142--4717193 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
4717132 TTGATTACAG
4717142 TTTTTATTTAAT-A
1 TTTTTATTTAATGA
*
4717155 TTTTTGTTTAATGA
1 TTTTTATTTAATGA
*
4717169 TTTTTCATTTAACG-
1 TTTTT-ATTTAATGA
*
4717183 TTTTAATTTAA
1 TTTTTATTTAA
4717194 CAATTAACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 17 0.52
14 10 0.30
15 6 0.18
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (14 bp):
TTTTTATTTAATGA
Found at i:4718049 original size:85 final size:89
Alignment explanation
Indices: 4717948--4718120 Score: 196
Period size: 87 Copynumber: 2.0 Consensus size: 89
4717938 ATTTAAAAAA
* * * * **
4717948 AAAATAATCTAACAAAAA-ATTTTATTAATTGATACCAT-AATTAAAAATAATT-ATCAATTAAT
1 AAAATAATCTAACAAAAATAATTAATTAATTG--ACCATAAATAAAAAATAATTAATAAAAAAAT
4718010 A-ATATATAAAACTAATAAAAAAATT
64 ATATATATAAAACTAATAAAAAAATT
* *
4718035 AAAAT-AT-TAACAAAAATAATTAATTATTTGACTATAAATAAAAAATAATTAATAAAAAAATAT
1 AAAATAATCTAACAAAAATAATTAATTAATTGACCATAAATAAAAAATAATTAATAAAAAAATAT
* *
4718098 ATATGTAAAATTAATAAAAAAAT
66 ATATATAAAACTAATAAAAAAAT
4718121 CTACATTCAT
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
84 4 0.06
85 22 0.31
86 20 0.28
87 26 0.36
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (89 bp):
AAAATAATCTAACAAAAATAATTAATTAATTGACCATAAATAAAAAATAATTAATAAAAAAATAT
ATATATAAAACTAATAAAAAAATT
Found at i:4718273 original size:20 final size:19
Alignment explanation
Indices: 4718248--4718285 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
4718238 AGATTAATTA
4718248 TTATATATTAATAAATATAT
1 TTATATATTAAT-AATATAT
*
4718268 TTATATTTTAATAATATA
1 TTATATATTAATAATATA
4718286 AATAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATATATTAATAATATAT
Found at i:4718519 original size:8 final size:8
Alignment explanation
Indices: 4718506--4718545 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
4718496 ATAACTTTAG
4718506 TTAAAATT
1 TTAAAATT
4718514 TTAAAATT
1 TTAAAATT
4718522 TTAAAATAT
1 TTAAAAT-T
* *
4718531 TTATATTT
1 TTAAAATT
4718539 TTAAAAT
1 TTAAAAT
4718546 ATTTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTAAAATT
Found at i:4718540 original size:17 final size:17
Alignment explanation
Indices: 4718506--4718549 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
4718496 ATAACTTTAG
4718506 TTAAAAT-TTTAAAATT
1 TTAAAATATTTAAAATT
* *
4718522 TTAAAATATTTATATTT
1 TTAAAATATTTAAAATT
4718539 TTAAAATATTT
1 TTAAAATATTT
4718550 TTTATTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAAAATATTTAAAATT
Found at i:4719068 original size:5 final size:5
Alignment explanation
Indices: 4719058--4719123 Score: 50
Period size: 5 Copynumber: 13.8 Consensus size: 5
4719048 AAATTTTATA
* ** *
4719058 AATTT AATTT AA-TT AA-TA AAAAT AATTT AATTT AATTT AA-TT ACTTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT
*
4719105 AATTTT AA-AT AATTT AATT
1 AA-TTT AATTT AATTT AATT
4719124 CAAAATTAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
4 13 0.27
5 30 0.62
6 5 0.10
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (5 bp):
AATTT
Found at i:4719073 original size:9 final size:9
Alignment explanation
Indices: 4719061--4719108 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
4719051 TTTTATAAAT
4719061 TTAATTTAA
1 TTAATTTAA
**
4719070 TTAATAAAA
1 TTAATTTAA
*
4719079 ATAATTTAA
1 TTAATTTAA
4719088 TTTAATTTAA
1 -TTAATTTAA
*
4719098 TTACTTTAA
1 TTAATTTAA
4719107 TT
1 TT
4719109 TTAAATAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (9 bp):
TTAATTTAA
Found at i:4719095 original size:10 final size:10
Alignment explanation
Indices: 4719058--4719123 Score: 50
Period size: 9 Copynumber: 6.9 Consensus size: 10
4719048 AAATTTTATA
4719058 AATTTAATTT
1 AATTTAATTT
*
4719068 AA-TTAA-TA
1 AATTTAATTT
**
4719076 AAAATAATTT
1 AATTTAATTT
4719086 AATTTAATTT
1 AATTTAATTT
*
4719096 AA-TTACTTT
1 AATTTAATTT
*
4719105 AATTTTAA-AT
1 AA-TTTAATTT
4719115 AATTTAATT
1 AATTTAATT
4719124 CAAAATTAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
8 3 0.07
9 20 0.48
10 16 0.38
11 3 0.07
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (10 bp):
AATTTAATTT
Found at i:4728361 original size:2 final size:2
Alignment explanation
Indices: 4728349--4728381 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4728339 TAGATAGTAC
*
4728349 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4728382 TCACTTCCGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4735879 original size:13 final size:12
Alignment explanation
Indices: 4735854--4735885 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
4735844 AGATCTATTT
4735854 ATATTAATATAA
1 ATATTAATATAA
4735866 ATATTAAGTATAA
1 ATATTAA-TATAA
4735879 ATATTAA
1 ATATTAA
4735886 CCCTTTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (12 bp):
ATATTAATATAA
Done.