Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 9 of 28
Found at i:1404293 original size:22 final size:23
Alignment explanation
Indices: 1404243--1404290 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1404233 AAACATTGTG
1404243 AAATTTTAAAGTTTTTTAAAAAT
1 AAATTTTAAAGTTTTTTAAAAAT
1404266 AAATTTTAAAGTTTTTTAAAAAT
1 AAATTTTAAAGTTTTTTAAAAAT
1404289 AA
1 AA
1404291 TTTACTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
AAATTTTAAAGTTTTTTAAAAAT
Found at i:1404617 original size:16 final size:16
Alignment explanation
Indices: 1404584--1404714 Score: 64
Period size: 17 Copynumber: 8.1 Consensus size: 16
1404574 GATTACGACG
1404584 TTAAATATAAT-T--A
1 TTAAATATAATATAAA
1404597 TTAAATATAATATAAA
1 TTAAATATAATATAAA
*
1404613 TTAAAATTTAATA-AAA
1 TT-AAATATAATATAAA
1404629 TATAAATTATTAAAATATAAAA
1 T-TAAA-TA-T--AATAT-AAA
*
1404651 TT-ATTATAAATATAAA
1 TTAAATAT-AATATAAA
* *
1404667 --AAATTTAA-ATATTA
1 TTAAATATAATATA-AA
1404681 TTATAATATAATA-AAA
1 TTA-AATATAATATAAA
1404697 TATAAATATAATATAAA
1 T-TAAATATAATATAAA
1404714 T
1 T
1404715 ATATGTATTA
Statistics
Matches: 91, Mismatches: 8, Indels: 34
0.68 0.06 0.26
Matches are distributed among these distances:
13 14 0.15
14 4 0.04
15 3 0.03
16 25 0.27
17 30 0.33
18 3 0.03
19 2 0.02
20 5 0.05
21 1 0.01
22 4 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAATATAATATAAA
Found at i:1404642 original size:15 final size:15
Alignment explanation
Indices: 1404586--1404666 Score: 75
Period size: 15 Copynumber: 5.6 Consensus size: 15
1404576 TTACGACGTT
1404586 AAATAT-AATTATT-
1 AAATATAAATTATTA
1404599 AAATAT-AA-TA-TA
1 AAATATAAATTATTA
* *
1404611 AATTA-AAATTTAATA
1 AAATATAAA-TTATTA
1404626 AAATATAAATTATTA
1 AAATATAAATTATTA
1404641 AAATATAAAATTATTA
1 AAATAT-AAATTATTA
1404657 TAAATATAAA
1 -AAATATAAA
1404667 AAATTTAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
11 1 0.02
12 8 0.14
13 8 0.14
14 2 0.04
15 17 0.30
16 15 0.26
17 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATATAAATTATTA
Found at i:1404650 original size:32 final size:32
Alignment explanation
Indices: 1404610--1404717 Score: 85
Period size: 36 Copynumber: 3.2 Consensus size: 32
1404600 AATATAATAT
1404610 AAAT-TAAAATTTAATAAAATATAAATTATTA
1 AAATATAAAATTTAATAAAATATAAATTATTA
* **
1404641 AAATATAAAA-TTATTATAAATATAAAAAATTTA
1 AAATATAAAATTTAATA-AAATATAAATTA-TTA
* * *
1404674 AATATTATTATAATATAATAAAATATAAATATAATA
1 AA-A-TA-TAAAATTTAATAAAATATAAAT-TATTA
1404710 TAAATATA
1 -AAATATA
1404718 TGTATTATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
31 9 0.15
32 15 0.25
33 5 0.08
34 3 0.05
35 4 0.07
36 16 0.27
37 7 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (32 bp):
AAATATAAAATTTAATAAAATATAAATTATTA
Found at i:1404671 original size:19 final size:16
Alignment explanation
Indices: 1404610--1404667 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
1404600 AATATAATAT
*
1404610 AAAT-TAAAATTTAATA
1 AAATATAAAA-TTATTA
1404626 AAATAT-AAATTATTA
1 AAATATAAAATTATTA
1404641 AAATATAAAATTATTA
1 AAATATAAAATTATTA
1404657 TAAATATAAAA
1 -AAATATAAAA
1404668 AATTTAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
15 11 0.29
16 16 0.42
17 11 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATATAAAATTATTA
Found at i:1404677 original size:15 final size:15
Alignment explanation
Indices: 1404626--1404678 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
1404616 AAATTTAATA
* *
1404626 AAATATAAATTATTA
1 AAATATAAAATATTT
1404641 AAATATAAAATTATTAT
1 AAATATAAAA-TATT-T
*
1404658 AAATATAAAAAATTT
1 AAATATAAAATATTT
1404673 AAATAT
1 AAATAT
1404679 TATTATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 16 0.48
16 7 0.21
17 10 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATATAAAATATTT
Found at i:1404696 original size:27 final size:28
Alignment explanation
Indices: 1404629--1404717 Score: 116
Period size: 26 Copynumber: 3.4 Consensus size: 28
1404619 TTTAATAAAA
*
1404629 TATAAAT-TATTAAAATATAAA-ATTAT
1 TATAAATATAATAAAATATAAATATTAT
*
1404655 TATAAATATAA-AAAATTTAAATATTAT
1 TATAAATATAATAAAATATAAATATTAT
*
1404682 TAT-AATATAATAAAATATAAATA-TAA
1 TATAAATATAATAAAATATAAATATTAT
1404708 TATAAATATA
1 TATAAATATA
1404718 TGTATTATTA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
26 28 0.51
27 27 0.49
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
TATAAATATAATAAAATATAAATATTAT
Found at i:1404697 original size:21 final size:21
Alignment explanation
Indices: 1404585--1404712 Score: 71
Period size: 21 Copynumber: 5.7 Consensus size: 21
1404575 ATTACGACGT
*
1404585 TAAATATAATTATTAAATATAATA
1 TAAATATAA-TA-T-AATAAAATA
* *
1404609 TAAATTAAAATTTAATAAAATA
1 TAAA-TATAATATAATAAAATA
*
1404631 TAAATTATTAAAATATAA-AATTATTA
1 TAAA-TA-T--AATATAATAA--AATA
* *
1404657 TAAATATAA-AAAATTTAAATA
1 TAAATATAATATAA-TAAAATA
* *
1404678 TTATTATAATATAATAAAATA
1 TAAATATAATATAATAAAATA
1404699 TAAATATAATATAA
1 TAAATATAATATAA
1404713 ATATATGTAT
Statistics
Matches: 80, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
21 31 0.39
22 20 0.25
23 2 0.03
24 8 0.10
25 12 0.15
26 7 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATATAATATAATAAAATA
Found at i:1408774 original size:2 final size:2
Alignment explanation
Indices: 1408769--1408794 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1408759 GGGTTGGCTC
1408769 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
1408795 TTGGAGAGAT
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):
AT
Found at i:1409379 original size:18 final size:17
Alignment explanation
Indices: 1409356--1409396 Score: 66
Period size: 16 Copynumber: 2.4 Consensus size: 17
1409346 GCTTGGATTT
1409356 TTTTTATTTTTTTTAAAA
1 TTTTTATTTTTTTT-AAA
1409374 TTTTTA-TTTTTTTAAA
1 TTTTTATTTTTTTTAAA
1409390 TTTTTAT
1 TTTTTAT
1409397 AAAAATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.41
17 7 0.32
18 6 0.27
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTATTTTTTTTAAA
Found at i:1409382 original size:27 final size:27
Alignment explanation
Indices: 1409352--1409409 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1409342 ACATGCTTGG
* * * * *
1409352 ATTTTTTTTATTTTTTTTAAAATTTTT
1 ATTTTTTTAAATTTTTATAAAAATTTC
1409379 ATTTTTTTAAATTTTTATAAAAATTTC
1 ATTTTTTTAAATTTTTATAAAAATTTC
1409406 ATTT
1 ATTT
1409410 ATTTCTTAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (27 bp):
ATTTTTTTAAATTTTTATAAAAATTTC
Found at i:1409620 original size:21 final size:21
Alignment explanation
Indices: 1409596--1409642 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
1409586 ATAATGAAAA
*
1409596 TTTAGTAATT-TTAAAATTATT
1 TTTAATAATTGTT-AAATTATT
*
1409617 TTTAATTATTGTTAAATTATT
1 TTTAATAATTGTTAAATTATT
*
1409638 ATTAA
1 TTTAA
1409643 ATTATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
TTTAATAATTGTTAAATTATT
Found at i:1409634 original size:11 final size:10
Alignment explanation
Indices: 1409603--1409647 Score: 54
Period size: 11 Copynumber: 4.2 Consensus size: 10
1409593 AAATTTAGTA
1409603 ATTTTAAAATT
1 ATTTT-AAATT
*
1409614 ATTTTTAATT
1 ATTTTAAATT
1409624 ATTGTTAAATT
1 ATT-TTAAATT
1409635 ATTATTAAATT
1 ATT-TTAAATT
1409646 AT
1 AT
1409648 ATTTTAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
10 7 0.23
11 23 0.77
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (10 bp):
ATTTTAAATT
Found at i:1409882 original size:30 final size:29
Alignment explanation
Indices: 1409818--1409885 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 29
1409808 TAAAAATATT
1409818 TTTTATTTT-TTAAAAAATTAATTATGTA
1 TTTTATTTTATTAAAAAATTAATTATGTA
*
1409846 --ATATTTTATTAATAAAATTAA-TATGTA
1 TTTTATTTTATTAA-AAAATTAATTATGTA
1409873 TTTTAATTTTATT
1 TTTT-ATTTTATT
1409886 TTAAAGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
26 6 0.18
27 10 0.30
28 8 0.24
29 1 0.03
30 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (29 bp):
TTTTATTTTATTAAAAAATTAATTATGTA
Found at i:1412727 original size:28 final size:27
Alignment explanation
Indices: 1412669--1412728 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
1412659 AAATGATATT
*
1412669 ATTTAATTTGTTTGATTTAAATATTAT
1 ATTTAATTTGTTTGATTTAAATATTAA
1412696 ATTTATATTTGTAATTGATTTAAA-A-TAA
1 ATTTA-ATTTGT--TTGATTTAAATATTAA
1412724 ATTTA
1 ATTTA
1412729 GATATGAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.17
28 13 0.45
29 1 0.03
30 10 0.34
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (27 bp):
ATTTAATTTGTTTGATTTAAATATTAA
Found at i:1413959 original size:33 final size:33
Alignment explanation
Indices: 1413917--1413979 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
1413907 AAAGAAAATG
1413917 AATCAAATATCATTATAATGGTAACATTTAATA
1 AATCAAATATCATTATAATGGTAACATTTAATA
*
1413950 AATCAAATATCATTTTAATGGTAACATTTA
1 AATCAAATATCATTATAATGGTAACATTTA
1413980 TGTTGGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (33 bp):
AATCAAATATCATTATAATGGTAACATTTAATA
Found at i:1421595 original size:12 final size:12
Alignment explanation
Indices: 1421580--1421605 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1421570 CTTCAAATCA
1421580 AATTCAAAATTT
1 AATTCAAAATTT
1421592 AATTCAAAATTT
1 AATTCAAAATTT
1421604 AA
1 AA
1421606 CTTAATTGAT
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:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTCAAAATTT
Found at i:1426169 original size:57 final size:57
Alignment explanation
Indices: 1426106--1426220 Score: 196
Period size: 57 Copynumber: 2.0 Consensus size: 57
1426096 TTTGGTATTC
*
1426106 AAATATATATTGCATATAAAAAGAAAGTGAG-AAATATGAAAAATACAAAGGATGTTT
1 AAATATATATTACATATAAAAAGAAAGTGAGAAAATA-GAAAAATACAAAGGATGTTT
*
1426163 AAATATATATTACATATATAAAGAAAGTGAGAAAATAGAAAAATACAAAGGATGTTT
1 AAATATATATTACATATAAAAAGAAAGTGAGAAAATAGAAAAATACAAAGGATGTTT
1426220 A
1 A
1426221 TAGTTTTGCT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
57 50 0.91
58 5 0.09
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (57 bp):
AAATATATATTACATATAAAAAGAAAGTGAGAAAATAGAAAAATACAAAGGATGTTT
Found at i:1439084 original size:28 final size:27
Alignment explanation
Indices: 1439038--1439093 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
1439028 AAAATAAATT
1439038 TTATTATTAAAATTATAATATATAAAAA
1 TTATTATTAAAATTATAAT-TATAAAAA
*
1439066 TTATTATTAAAA-TAGTAATTTTAAAAA
1 TTATTATTAAAATTA-TAATTATAAAAA
1439093 T
1 T
1439094 ATTTAACCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
TTATTATTAAAATTATAATTATAAAAA
Found at i:1441728 original size:26 final size:28
Alignment explanation
Indices: 1441669--1441773 Score: 81
Period size: 31 Copynumber: 3.6 Consensus size: 28
1441659 TATATATTTG
* * *
1441669 TATTATTTTTTTATTATAACAATATTTAAAA
1 TATTATATATTTATTAT-A-AAT-TTTAATA
*
1441700 TATTATATATTTA-TATAAA-TTTGATA
1 TATTATATATTTATTATAAATTTTAATA
1441726 TATT-TATTATTTATTTTATAAATTTTAATA
1 TATTATA-TATTTA--TTATAAATTTTAATA
*
1441756 TATTAATATATTTTTTAT
1 TATT-ATATATTTATTAT
1441774 TTTTATTTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
25 2 0.03
26 15 0.25
28 2 0.03
29 11 0.18
30 13 0.21
31 16 0.26
32 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (28 bp):
TATTATATATTTATTATAAATTTTAATA
Found at i:1441734 original size:30 final size:30
Alignment explanation
Indices: 1441700--1441773 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
1441690 ATATTTAAAA
*
1441700 TATTATATATTTATATAAA-TTTGATATATT
1 TATTATATATTT-TATAAATTTTAATATATT
*
1441730 TATTATTTATTTTATAAATTTTAATATA-T
1 TATTATATATTTTATAAATTTTAATATATT
* *
1441759 TAATATATTTTTTAT
1 TATTATATATTTTAT
1441774 TTTTATTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 19 0.50
30 19 0.50
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (30 bp):
TATTATATATTTTATAAATTTTAATATATT
Found at i:1441801 original size:27 final size:25
Alignment explanation
Indices: 1441763--1441815 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
1441753 ATATATTAAT
*
1441763 ATATTTTTTATT-TTTATTTTATTTA
1 ATATTTTTTATTATTT-TTGTATTTA
1441788 ATATTTTTCATATTATTTTTGTATTTA
1 ATATTTTT--TATTATTTTTGTATTTA
1441815 A
1 A
1441816 ATTACTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.33
27 13 0.54
28 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (25 bp):
ATATTTTTTATTATTTTTGTATTTA
Found at i:1441999 original size:4 final size:4
Alignment explanation
Indices: 1441990--1442016 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1441980 AGTTATCTAT
1441990 ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATT
1442017 TAACGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:1442456 original size:6 final size:6
Alignment explanation
Indices: 1442447--1442476 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1442437 TATTTAAATC
1442447 ATATTT ATATTT ATTATTT ATATTT ATATT
1 ATATTT ATATTT A-TATTT ATATTT ATATT
1442477 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATATTT
Found at i:1442466 original size:13 final size:13
Alignment explanation
Indices: 1442448--1442473 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1442438 ATTTAAATCA
1442448 TATTTATATTTAT
1 TATTTATATTTAT
1442461 TATTTATATTTAT
1 TATTTATATTTAT
1442474 ATTAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTTATATTTAT
Found at i:1443782 original size:24 final size:24
Alignment explanation
Indices: 1443754--1443806 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1443744 ATTCAATAAA
1443754 AAATATAA-ACAAAAATAATATATT
1 AAATA-AATACAAAAATAATATATT
* **
1443778 TAATAAATATGAAAATAATATATT
1 AAATAAATACAAAAATAATATATT
1443802 AAATA
1 AAATA
1443807 CATCATGATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATAAATACAAAAATAATATATT
Found at i:1443936 original size:2 final size:2
Alignment explanation
Indices: 1443926--1443957 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
1443916 TAACAAAAAA
1443926 AT AT GAT 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
1443958 AATTATTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1444275 original size:3 final size:3
Alignment explanation
Indices: 1444267--1444294 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1444257 TATTTTTTGT
1444267 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1444295 TAAAAAAAAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1444573 original size:29 final size:29
Alignment explanation
Indices: 1444541--1444598 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1444531 CGAGTGAATT
1444541 AAATAAATATAATATTATAAAAATATATA
1 AAATAAATATAATATTATAAAAATATATA
* * * **
1444570 AAATTAATTTAATTTTATATTAATATATA
1 AAATAAATATAATATTATAAAAATATATA
1444599 TGAAGTATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
AAATAAATATAATATTATAAAAATATATA
Found at i:1444629 original size:27 final size:26
Alignment explanation
Indices: 1444581--1444634 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
1444571 AATTAATTTA
1444581 ATTTTATATTAATATATATGAAGTATT
1 ATTTTATATTAATATATATGAAG-ATT
* *
1444608 ATTTTATATATATTTTAT-TGAAGATT
1 ATTTTATAT-TAATATATATGAAGATT
1444634 A
1 A
1444635 AAAAAATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.17
27 14 0.58
28 6 0.25
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (26 bp):
ATTTTATATTAATATATATGAAGATT
Found at i:1444678 original size:26 final size:24
Alignment explanation
Indices: 1444644--1444693 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1444634 AAAAAAATTG
*
1444644 TTTTAAAATGTATTTTTTATTTATAA
1 TTTTAAAAT-TA-TTTTTATATATAA
*
1444670 TTTTTAAATTATTTTTATATATAA
1 TTTTAAAATTATTTTTATATATAA
1444694 AATATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 12 0.55
25 2 0.09
26 8 0.36
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTTAAAATTATTTTTATATATAA
Found at i:1444837 original size:15 final size:17
Alignment explanation
Indices: 1444808--1444849 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
1444798 TAAAAAGTGA
* *
1444808 TATATATAAATTTAA-T
1 TATATATATAGTTAATT
1444824 TAT-TATATAGTTAATT
1 TATATATATAGTTAATT
1444840 TATATATATA
1 TATATATATA
1444850 TATATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TATATATATAGTTAATT
Found at i:1449742 original size:16 final size:17
Alignment explanation
Indices: 1449699--1449742 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
1449689 AATCATATTA
1449699 AATAATTATTATTTATTTG
1 AATAATT-TT-TTTATTTG
*
1449718 AATAATTTTTTTATTTT
1 AATAATTTTTTTATTTG
1449735 AA-AATTTT
1 AATAATTTT
1449743 ATGTAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
18 2 0.08
19 7 0.29
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
AATAATTTTTTTATTTG
Found at i:1450605 original size:21 final size:23
Alignment explanation
Indices: 1450581--1450664 Score: 63
Period size: 23 Copynumber: 3.7 Consensus size: 23
1450571 TATAATATTT
1450581 TAAAATATATAAAA-AA-TAATA
1 TAAAATATATAAAATAATTAATA
*
1450602 TAAATATGACATAAAATAATTAATA
1 TAAA-AT-ATATAAAATAATTAATA
*
1450627 TATAATATA-AAAATGAA-T-ATGA
1 TAAAATATATAAAAT-AATTAAT-A
1450649 TACAAATATA-AAAATA
1 TA-AAATATATAAAATA
1450665 TATAGATATA
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
21 6 0.12
22 12 0.23
23 22 0.42
24 4 0.08
25 8 0.15
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
TAAAATATATAAAATAATTAATA
Found at i:1450617 original size:32 final size:32
Alignment explanation
Indices: 1450581--1450642 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1450571 TATAATATTT
*
1450581 TAAAAT-ATATAAAAAATAATATAAATATGACA
1 TAAAATAAT-TAAAAAATAATATAAAAATGACA
* *
1450613 TAAAATAATTAATATATAATATAAAAATGA
1 TAAAATAATTAAAAAATAATATAAAAATGA
1450643 ATATGATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (32 bp):
TAAAATAATTAAAAAATAATATAAAAATGACA
Found at i:1453662 original size:21 final size:19
Alignment explanation
Indices: 1453633--1453689 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1453623 TAAATTAATA
**
1453633 TTATTTTTATTAATAATTT
1 TTATTTTTATTAATAAAAT
* *
1453652 TTAGTTTTTTAATATTAAAAT
1 TTA--TTTTTATTAATAAAAT
1453673 TTATTTTTATTAATAAA
1 TTATTTTTATTAATAAA
1453690 TGTTCAACCA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 15 0.50
21 15 0.50
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTATTTTTATTAATAAAAT
Found at i:1455912 original size:2 final size:2
Alignment explanation
Indices: 1455905--1455932 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1455895 AACACATGTG
1455905 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
1455933 GTGGTCTCGT
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:1456599 original size:19 final size:19
Alignment explanation
Indices: 1456572--1456608 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1456562 TTTATAAATT
1456572 AATAAATATTAATTTATTC
1 AATAAATATTAATTTATTC
*
1456591 AATACATATTAATTTATT
1 AATAAATATTAATTTATT
1456609 TTTAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
AATAAATATTAATTTATTC
Found at i:1464621 original size:3 final size:3
Alignment explanation
Indices: 1464613--1464638 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1464603 TATAATATCT
1464613 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1464639 TTGCTTTGTT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1464734 original size:45 final size:45
Alignment explanation
Indices: 1464671--1464766 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 45
1464661 CTTTGTTATT
* *
1464671 TTTTTAATTGTGTTTTAATTAGG-TTTGAGTCTAAGTTTATATAGA
1 TTTTTAATTGAGTTTTAATT-GGATTTGAGTCTAAGTTCATATAGA
* * * *
1464716 TTTTTAGTTGAGTTTTAATTGGATTTGGGTTTAAGTTCATATGGA
1 TTTTTAATTGAGTTTTAATTGGATTTGAGTCTAAGTTCATATAGA
1464761 TTTTTA
1 TTTTTA
1464767 CTTTGTGTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
44 2 0.05
45 42 0.95
ACGTcount: A:0.24, C:0.02, G:0.20, T:0.54
Consensus pattern (45 bp):
TTTTTAATTGAGTTTTAATTGGATTTGAGTCTAAGTTCATATAGA
Found at i:1465261 original size:18 final size:18
Alignment explanation
Indices: 1465222--1465269 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
1465212 TATCAATTAT
* * *
1465222 TTATTTTTATTTTTTAAA
1 TTATTTTTAATTATAAAA
1465240 -TATTTTTAATTATAAAA
1 TTATTTTTAATTATAAAA
1465257 TTATTTTTAATTA
1 TTATTTTTAATTA
1465270 ACATCAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTTTAATTATAAAA
Found at i:1467670 original size:20 final size:19
Alignment explanation
Indices: 1467645--1467735 Score: 92
Period size: 20 Copynumber: 4.6 Consensus size: 19
1467635 ACCCTTTAAA
*
1467645 GTATCGATACATATCCAGAT
1 GTATCGATACATATTCA-AT
* **
1467665 GTATCGATACATCATGCTTT
1 GTATCGATACAT-ATTCAAT
* *
1467685 GTATCGATACATGTTCATT
1 GTATCGATACATATTCAAT
1467704 GTATCGATACATATTCAATT
1 GTATCGATACATATTCAA-T
*
1467724 ATATCGATACAT
1 GTATCGATACAT
1467736 GAAAGTGGCA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
19 20 0.33
20 37 0.62
21 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (19 bp):
GTATCGATACATATTCAAT
Found at i:1467729 original size:39 final size:40
Alignment explanation
Indices: 1467646--1467736 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 40
1467636 CCCTTTAAAG
* * *
1467646 TATCGATACATATCCAGATGTATCGATACATCATGCTTTG
1 TATCGATACATGTCCAGATGTATCGATACATCATGCATTA
* * *
1467686 TATCGATACATGTTCA-TTGTATCGATACAT-ATTCAATTA
1 TATCGATACATGTCCAGATGTATCGATACATCATGC-ATTA
1467725 TATCGATACATG
1 TATCGATACATG
1467737 AAAGTGGCAG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
38 3 0.07
39 27 0.61
40 14 0.32
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (40 bp):
TATCGATACATGTCCAGATGTATCGATACATCATGCATTA
Found at i:1470450 original size:52 final size:51
Alignment explanation
Indices: 1470355--1470474 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 51
1470345 GAGATAATAA
* * *
1470355 CGGGGCTGGAGTATCCCCGATTATGAAAAATCGATTTTCTAGAAATAAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCGATCTTCTAGAAAT-AAAAC
* * * * *
1470407 CGGGGTTGGAGTATCCTCGATTGTGGAAAATCGATGCTT-TAGAAATGAGAC
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCGAT-CTTCTAGAAATAAAAC
1470458 CGGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
1470475 GTGAAAATAG
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
51 18 0.31
52 38 0.66
53 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATCGATCTTCTAGAAATAAAAC
Found at i:1470544 original size:78 final size:78
Alignment explanation
Indices: 1470407--1470552 Score: 195
Period size: 78 Copynumber: 1.9 Consensus size: 78
1470397 AAATAAAAAT
* * * * * *
1470407 CGGGGTTGGAGTATCCTCGATTGTGGAAAATCGATGCTTTAGAAATGAGACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATAGAAAATCGATGCTTTAGAAATAAAACCGGAGTTGGAGTAT
1470472 CCCGTGAAAATAG
66 CCCGTGAAAATAG
* * *
1470485 CGGGGTTGGAGTATCCCCGATTATA-AGAAATTGATGCTTTGGAAATAAAATCGGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTATAGA-AAATCGATGCTTTAGAAATAAAACCGGAGTTGGAGTA
1470549 TCCC
65 TCCC
1470553 TGATTGTGAA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
77 1 0.02
78 57 0.98
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.27
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCGATTATAGAAAATCGATGCTTTAGAAATAAAACCGGAGTTGGAGTAT
CCCGTGAAAATAG
Found at i:1470552 original size:51 final size:51
Alignment explanation
Indices: 1470489--1470602 Score: 144
Period size: 51 Copynumber: 2.2 Consensus size: 51
1470479 AAATAGCGGG
*
1470489 GTTGGAGTATCCCCGATTAT-AAGAAATT-G-ATGCTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAA-AAATTAGTAT--TTTAGAAATAAAATCGGA
* * *
1470540 GTTGGAGTATCCCTGATTGTGAAAAATTAGTATTTTAGAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAATCGGA
1470591 GTTGGAGTATCC
1 GTTGGAGTATCC
1470603 TTTCGAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
51 51 0.91
52 3 0.05
53 2 0.04
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAATCGGA
Found at i:1470591 original size:129 final size:130
Alignment explanation
Indices: 1470350--1470635 Score: 325
Period size: 130 Copynumber: 2.2 Consensus size: 130
1470340 TTTTGGAGAT
* * *
1470350 AATAACGGGGCTGGAGTATCCCCGATTATGAAAAATCGATTTTCTAGAAATAAAAATCGGGGTTG
1 AATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATCTTCTAGAAATAAAAATCGGAGTTG
* * * *
1470415 GAGTATCCTCGATTGTGGAAAATCGATGCTTTAGAAATGAGACCGGGGTTGGAGTATCCCGT-GA
66 GAGTATCCTCGATTGTGAAAAATAGAT-CTTTAGAAATAAAACCGGGGTTGGAGTATCCCGTCGA
1470479 A
130 A
* * *
1470480 AATAGCGGGGTTGGAGTATCCCCGATTAT-AAGAAATTGATGCTT-TGGAAAT-AAAATCGGAGT
1 AATAACGGGGTTGGAGTATCCCCGATTATGAA-AAATCGAT-CTTCTAGAAATAAAAATCGGAGT
* **
1470542 TGGAGTATCC-CTGATTGTGAAAAATTAGTAT-TTTAGAAATAAAATCGGGGTTGGAGTATCCTT
64 TGGAGTATCCTC-GATTGTGAAAAA-TAG-ATCTTTAGAAATAAAACCGGGGTTGGAGTATCCCG
1470605 TCGAA
126 TCGAA
* *
1470610 AA-AACCAGGATTGGAGTATCCCCGAT
1 AATAA-CGGGGTTGGAGTATCCCCGAT
1470636 GACATAACGG
Statistics
Matches: 133, Mismatches: 16, Indels: 14
0.82 0.10 0.09
Matches are distributed among these distances:
128 1 0.01
129 62 0.47
130 66 0.50
131 4 0.03
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (130 bp):
AATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATCTTCTAGAAATAAAAATCGGAGTTG
GAGTATCCTCGATTGTGAAAAATAGATCTTTAGAAATAAAACCGGGGTTGGAGTATCCCGTCGAA
Found at i:1470891 original size:51 final size:51
Alignment explanation
Indices: 1470727--1470870 Score: 184
Period size: 51 Copynumber: 2.8 Consensus size: 51
1470717 AAATAACGGG
* * * *
1470727 GTTGGAGCATCCCCAATT-GTGAAAAATTGGTGTTTTGGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTAG-GAAAAATTGATGTTTTGGAAATAAAATCGGA
* * * *
1470778 GTTGAAGTATCCCCGATTACGG-TAAATTGATGCTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTA-GGAAAAATTGATGTTTTGGAAATAAAATCGGA
1470829 GTTGGAGTATCCCCGATTAGGAAAAATTGATGTTTTGGAAAT
1 GTTGGAGTATCCCCGATTAGGAAAAATTGATGTTTTGGAAAT
1470871 GGAACCGGGA
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
50 2 0.03
51 74 0.95
52 1 0.01
53 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTAGGAAAAATTGATGTTTTGGAAATAAAATCGGA
Found at i:1473201 original size:20 final size:19
Alignment explanation
Indices: 1473176--1473295 Score: 104
Period size: 20 Copynumber: 6.7 Consensus size: 19
1473166 AAAATACCTG
1473176 AATGTATCGATACAATTAGC
1 AATGTATCGATACAA-TAGC
1473196 AATGTATCG-----ATA-C
1 AATGTATCGATACAATAGC
1473209 AATGTATCGATACAATAAGC
1 AATGTATCGATACAAT-AGC
1473229 AATGTATCG-----ATA-C
1 AATGTATCGATACAATAGC
1473242 AATGTATCGATACAATGAGC
1 AATGTATCGATACAAT-AGC
1473262 AATGTATCGATACAAT-GC
1 AATGTATCGATACAATAGC
1473280 AAAATGTATCGATACA
1 --AATGTATCGATACA
1473296 TCTGGGTAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 32
0.72 0.00 0.28
Matches are distributed among these distances:
13 20 0.24
14 3 0.04
15 3 0.04
18 6 0.07
19 2 0.02
20 50 0.60
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.28
Consensus pattern (19 bp):
AATGTATCGATACAATAGC
Found at i:1473218 original size:33 final size:33
Alignment explanation
Indices: 1473176--1473278 Score: 188
Period size: 33 Copynumber: 3.1 Consensus size: 33
1473166 AAAATACCTG
*
1473176 AATGTATCGATACAATTAGCAATGTATCGATAC
1 AATGTATCGATACAATAAGCAATGTATCGATAC
1473209 AATGTATCGATACAATAAGCAATGTATCGATAC
1 AATGTATCGATACAATAAGCAATGTATCGATAC
*
1473242 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATAAGCAATGTATCGATAC
1473275 AATG
1 AATG
1473279 CAAAATGTAT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (33 bp):
AATGTATCGATACAATAAGCAATGTATCGATAC
Found at i:1473277 original size:13 final size:13
Alignment explanation
Indices: 1473195--1473258 Score: 77
Period size: 13 Copynumber: 5.4 Consensus size: 13
1473185 ATACAATTAG
1473195 CAATGTATCGATA
1 CAATGTATCGATA
1473208 CAATGTATCGATA
1 CAATGTATCGATA
*
1473221 CAA--TA---A-G
1 CAATGTATCGATA
1473228 CAATGTATCGATA
1 CAATGTATCGATA
1473241 CAATGTATCGATA
1 CAATGTATCGATA
1473254 CAATG
1 CAATG
1473259 AGCAATGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 3 0.07
8 1 0.02
9 2 0.05
11 2 0.05
12 1 0.02
13 34 0.79
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1473373 original size:24 final size:20
Alignment explanation
Indices: 1473242--1473365 Score: 88
Period size: 20 Copynumber: 5.8 Consensus size: 20
1473232 GTATCGATAC
**
1473242 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAAT
1473262 AATGTATCGATACAATGCAA-
1 AATGTATCGATACAATG-AAT
* *
1473282 AATGTATCGATACATCTGGGTAAACCCAG
1 AATGTATCGATACA-AT--G---A---AT
* **
1473311 AATGTATTGATACAATGAGC
1 AATGTATCGATACAATGAAT
1473331 AATGTATCGATACAATGAAT
1 AATGTATCGATACAATGAAT
1473351 AATGTATCGATACAA
1 AATGTATCGATACAA
1473366 ATTGTGAAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 20
0.74 0.09 0.18
Matches are distributed among these distances:
20 63 0.75
21 2 0.02
23 2 0.02
25 1 0.01
26 1 0.01
28 2 0.02
29 13 0.15
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGAAT
Found at i:1474638 original size:59 final size:59
Alignment explanation
Indices: 1474520--1474646 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
1474510 ACAAATTTAT
* * *
1474520 ACAAATTTCTCTAATTTCTCCGTTTATAACACTTTTATTTCTCTATTTCTCCTCGTTAA
1 ACAAATTTCTCCAATTTCTCCGTTTATAACACTTCTATTTCTCTATTTCTCCTCCTTAA
**
1474579 ACAAATTTCTCCAATTTCTCTTTTTATAACACTTCTATTTCTCTATTTCTTCC-CCTTAA
1 ACAAATTTCTCCAATTTCTCCGTTTATAACACTTCTATTTCTCTATTTC-TCCTCCTTAA
1474638 A-ATAATTTC
1 ACA-AATTTC
1474647 CCTCTAATTT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
58 1 0.02
59 57 0.93
60 3 0.05
ACGTcount: A:0.25, C:0.24, G:0.02, T:0.49
Consensus pattern (59 bp):
ACAAATTTCTCCAATTTCTCCGTTTATAACACTTCTATTTCTCTATTTCTCCTCCTTAA
Found at i:1479813 original size:154 final size:153
Alignment explanation
Indices: 1479584--1480544 Score: 730
Period size: 154 Copynumber: 6.3 Consensus size: 153
1479574 TCATAAGAGG
* * * * * *
1479584 GATGAACTTATCCCAAATGCCCACTTTCGGCAT-AAAG-CAGACCCGGTGACGACTTAGGAGTTG
1 GATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAGTGA-ACCCGGTGACGACCTAGGAGTCG
* * * *
1479647 ATTTTAAAAAATTACCAAAATGCCCCTAAGAG-ATACCTTCGACGTGAAAGTACCCGATACCTCT
65 ATTCTAAGAAATTACAAAAATGCCCCTAAGAGTATACCTTCGACGTAAAAGTACCCGA-ACCTCT
* *
1479711 AAAGGACTTAGAAAAACTAGAGATGG
129 AAAGGACTTA-AAAAACTAGAAATGC
* * * * * * *
1479737 GATTAACCTATTCTAAATGCCCACTTTCTGCATAAAAGTGAACCCGGTGACAACCTATGACTCGA
1 GATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAGTGAACCCGGTGACGACCTAGGAGTCGA
* ** * * *
1479802 TTTTAAGAAATTATGAAAATGCTCCTATG-GTATATCTTCGACGTAAAA-TGA--C-AACC-CT-
66 TTCTAAGAAATTACAAAAATGCCCCTAAGAGTATACCTTCGACGTAAAAGT-ACCCGAACCTCTA
* *
1479860 -A--A---AAAAGACTAGAAAAGC
130 AAGGACTTAAAAAACTAGAAATGC
* * ** *** ** * * *
1479878 GATGAACCTACCCTAAATGCCCACCTTCGACATAAAAGCAAATTTGGTGATAACTTAAGACTCGA
1 GATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAGTGAACCCGGTGACGACCTAGGAGTCGA
* * * *
1479943 TTCTAAGAAAGTACGAAAATGCCCCTATAG-GTATACTTTTGACGTAAAAGTATCCCGGCAACC-
66 TTCTAAGAAATTACAAAAATGCCCCTA-AGAGTATACCTTCGACGTAAAAGTA-CCC-G-AACCT
*
1480006 CTAAAGGACTT-AAAGACTAGAAATGC
127 CTAAAGGACTTAAAAAACTAGAAATGC
* * * *
1480032 GATGAACCTATCCTAAATGCCCACCTTCGACATAAAAATGGACCCGGTGATGACCTAGGAGTCGA
1 GATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAGTGAACCCGGTGACGACCTAGGAGTCGA
* ** * *
1480097 TTCTAAAAAATTACAAAAATATCCCTATA-AATATACCTTCGACGTAAAAGTACCTCG-ACAATC
66 TTCTAAGAAATTACAAAAATGCCCCTA-AGAGTATACCTTCGACGTAAAAGTACC-CGAAC-CT-
1480160 CTAAAGGACTTAAAAAGACTAGAAATGC
127 CTAAAGGACTTAAAAA-ACTAGAAATGC
* * * *
1480188 GACGAACCTATCCTAAAT-CCCACCTTCGGCATAAAAGCGAACCTGGTGACGACCTAGGAGTCAA
1 GATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAGTGAACCCGGTGACGACCTAGGAGTCGA
** * * *
1480252 TTCTAAGAAATTACAAAAATATCCCTATGAGTATACATTCGACGTAAAAGTACTCTGGTAACCT-
66 TTCTAAGAAATTACAAAAATGCCCCTAAGAGTATACCTTCGACGTAAAAGTAC-C-CG-AACCTC
* * *
1480316 TAAAGGACTTAAAAAGACTCATAAAAGG
128 TAAAGGACTTAAAAA-ACT-AGAAATGC
* * * *
1480344 GATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAATGGACCCCGGTGATGACCTAGGAGTTG
1 GATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAGT-GAACCCGGTGACGACCTAGGAGTCG
* * * * * * * * *
1480409 GTTCT-AGAAAAATACAAAAATGCCCGTAAG-GGATACGTTCGACGTGAAAGTATCCTAGTACCC
65 ATTCTAAG-AAATTACAAAAATGCCCCTAAGAGTATACCTTCGACGTAAAAGTA-CC-CGAACCT
* ** ** * *
1480472 CTAAAAGACTTTAAAAAGGTTTTAAAAGG
127 CTAAAGGAC-TTAAAAA-ACTAGAAATGC
* ** *
1480501 GATGAACCTATCCTAAATGCCTACCTTTAGCATAAAAGAGAACC
1 GATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAGTGAACC
1480545 TGACAATGAC
Statistics
Matches: 657, Mismatches: 114, Indels: 71
0.78 0.14 0.08
Matches are distributed among these distances:
141 85 0.13
142 19 0.03
143 1 0.00
145 2 0.00
147 1 0.00
148 6 0.01
149 2 0.00
150 4 0.01
151 3 0.00
152 2 0.00
153 33 0.05
154 185 0.28
155 110 0.17
156 60 0.09
157 91 0.14
158 53 0.08
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (153 bp):
GATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAGTGAACCCGGTGACGACCTAGGAGTCGA
TTCTAAGAAATTACAAAAATGCCCCTAAGAGTATACCTTCGACGTAAAAGTACCCGAACCTCTAA
AGGACTTAAAAAACTAGAAATGC
Found at i:1480459 original size:157 final size:154
Alignment explanation
Indices: 1479861--1480644 Score: 672
Period size: 157 Copynumber: 5.0 Consensus size: 154
1479851 GACAACCCTA
* * ***
1479861 AAAAAGACTAGAAAAGCGATGAACCTACCCTAAATGCCCACCTTCGACATAAAAGCA-AATTTGG
1 AAAAAGACTAGAAAAGCGATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAG-AGAACCCGG
* * * * * * * *
1479925 TGATAACTTAAGACTCGATTCTAAGAAAGTACGAAAATGCCCCTATAGGTATACTTTTGACGTAA
65 TGATGACCTAGGAGTCGATTCTAAAAAATTACAAAAATG-CCCTA-AGGTATACTTTCGACGTAA
* *
1479990 AAGTA-TCCCGGCAACCCTAAAGGACTT
128 AAGTACT-CTGGTAACCCTAAAGGACTT
* * *
1480017 --AAAGACTAGAAATGCGATGAACCTATCCTAAATGCCCACCTTCGACATAAAA-ATGGACCCGG
1 AAAAAGACTAGAAAAGCGATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAGA-GAACCCGG
* ** *
1480079 TGATGACCTAGGAGTCGATTCTAAAAAATTACAAAAATATCCCTATAAATATACCTTCGACGTAA
65 TGATGACCTAGGAGTCGATTCTAAAAAATTACAAAAAT-GCCCTA-AGGTATACTTTCGACGTAA
** *
1480144 AAGTAC-CTCGACAATCCTAAAGGACTT
128 AAGTACTCT-GGTAACCCTAAAGGACTT
* * * *
1480171 AAAAAGACTAGAAATGCGACGAACCTATCCTAAAT-CCCACCTTCGGCATAAAAGCGAACCTGGT
1 AAAAAGACTAGAAAAGCGATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAGAGAACCCGGT
* * * * * *
1480235 GACGACCTAGGAGTCAATTCTAAGAAATTACAAAAATATCCCTATGAGTATACATTCGACGTAAA
66 GATGACCTAGGAGTCGATTCTAAAAAATTACAAAAAT-GCCCTAAG-GTATACTTTCGACGTAAA
*
1480300 AGTACTCTGGTAACCTTAAAGGACTT
129 AGTACTCTGGTAACCCTAAAGGACTT
* * *
1480326 AAAAAGACTCATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCGGCATAAAA-ATGGACCCC
1 AAAAAGACT-AGAAAAGCGATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAGA--GAACCC
* * * *
1480390 GGTGATGACCTAGGAGTTGGTTCTAGAAAAA-TACAAAAATGCCCGTAAGGGATACGTTCGACGT
63 GGTGATGACCTAGGAGTCGATTCTA-AAAAATTACAAAAATGCCC-TAAGGTATACTTTCGACGT
* * * *
1480454 GAAAGTA-TCCTAGTACCCCTAAAAGACTTT
126 AAAAGTACT-CTGGTAACCCTAAAGGAC-TT
** ** * * ** * **
1480484 AAAAAGGTTTTAAAAGGGATGAACCTATCCTAAATGCCTACCTTTAGCATAAAAGAGAACCTGAC
1 AAAAAGACTAGAAAAGCGATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAGAGAACCCGGT
* * * * * ** * * * *
1480549 AATGACCTAGGACTTGGTTTTATAAAAATTATGAAAATACTCCCAAGGGATACTTTCGACGTGAA
66 GATGACCTAGGAGTCGATTCTA-AAAAATTACAAAAATGC-CCTAAGGTATACTTTCGACGTAAA
* *
1480614 AGTAAC-CTGATATCCCTAAAGGACTT
129 AGT-ACTCTGGTAACCCTAAAGGACTT
1480640 AAAAA
1 AAAAA
1480645 TGATAGGTAT
Statistics
Matches: 524, Mismatches: 81, Indels: 46
0.80 0.12 0.07
Matches are distributed among these distances:
152 1 0.00
153 1 0.00
154 126 0.24
155 109 0.21
156 93 0.18
157 140 0.27
158 50 0.10
159 4 0.01
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (154 bp):
AAAAAGACTAGAAAAGCGATGAACCTATCCTAAATGCCCACCTTCGGCATAAAAGAGAACCCGGT
GATGACCTAGGAGTCGATTCTAAAAAATTACAAAAATGCCCTAAGGTATACTTTCGACGTAAAAG
TACTCTGGTAACCCTAAAGGACTT
Found at i:1481845 original size:25 final size:22
Alignment explanation
Indices: 1481817--1481867 Score: 57
Period size: 25 Copynumber: 2.2 Consensus size: 22
1481807 TTATTCGTAA
*
1481817 GCTTCTTTTTTTTTCCTTTGCTTTT
1 GCTTCTTGTTTTTT-CTTT-C-TTT
*
1481842 GCTTGTTGTTTTTTCTTTCTTT
1 GCTTCTTGTTTTTTCTTTCTTT
1481864 GCTT
1 GCTT
1481868 GCTATTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 1 0.04
24 4 0.17
25 12 0.50
ACGTcount: A:0.00, C:0.18, G:0.12, T:0.71
Consensus pattern (22 bp):
GCTTCTTGTTTTTTCTTTCTTT
Found at i:1482867 original size:16 final size:16
Alignment explanation
Indices: 1482846--1482878 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1482836 ATATTTTTTT
1482846 TTTCTTCTCCTTCTCC
1 TTTCTTCTCCTTCTCC
*
1482862 TTTCTTCTTCTTCTCC
1 TTTCTTCTCCTTCTCC
1482878 T
1 T
1482879 CCTTATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTCTTCTCCTTCTCC
Found at i:1482999 original size:18 final size:19
Alignment explanation
Indices: 1482978--1483014 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1482968 CGTGTGTGGC
*
1482978 TTTTCTTTTC-TTTTTTTT
1 TTTTCATTTCATTTTTTTT
1482996 TTTTCATTTCATTTTTTTT
1 TTTTCATTTCATTTTTTTT
1483015 GTCATTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTCATTTCATTTTTTTT
Found at i:1487845 original size:33 final size:33
Alignment explanation
Indices: 1487803--1487865 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1487793 CATTTTATGG
1487803 TGTATCGATAC-AAAACAATTTGTATCGATATAA
1 TGTATCGATACTAAAA-AATTTGTATCGATATAA
* *
1487836 TGTATCGATACTTAGAAATTTGTATCGATA
1 TGTATCGATACTAAAAAATTTGTATCGATA
1487866 CATCTAGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (33 bp):
TGTATCGATACTAAAAAATTTGTATCGATATAA
Found at i:1488299 original size:2 final size:2
Alignment explanation
Indices: 1488292--1488322 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1488282 TTTAATTCAA
*
1488292 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1488323 AAATGGTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1489881 original size:16 final size:16
Alignment explanation
Indices: 1489862--1489908 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1489852 AGCTAAACCC
*
1489862 CGAAAGAACTCGAACT
1 CGAAAGAACACGAACT
1489878 CGAAAGAACACGAACT
1 CGAAAGAACACGAACT
* *
1489894 CGAGAGAACCCGAAC
1 CGAAAGAACACGAAC
1489909 CCTAGATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.45, C:0.28, G:0.21, T:0.06
Consensus pattern (16 bp):
CGAAAGAACACGAACT
Found at i:1490880 original size:24 final size:24
Alignment explanation
Indices: 1490853--1490898 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1490843 TACGTGGGCT
**
1490853 TTTAGATTTAAATGGGCTTTTAAG
1 TTTAGATGGAAATGGGCTTTTAAG
*
1490877 TTTAGATGGACATGGGCTTTTA
1 TTTAGATGGAAATGGGCTTTTA
1490899 TTTAAGATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (24 bp):
TTTAGATGGAAATGGGCTTTTAAG
Found at i:1491355 original size:16 final size:16
Alignment explanation
Indices: 1491336--1491396 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 16
1491326 GCCCGAATCC
*
1491336 GAAAAAACTTAAACTT
1 GAAAAAACTCAAACTT
* ** *
1491352 GAAAAAGC-CCGACTC
1 GAAAAAACTCAAACTT
*
1491367 GAAAAAGCTCAAACTT
1 GAAAAAACTCAAACTT
*
1491383 GAAAAAACTTAAAC
1 GAAAAAACTCAAAC
1491397 CTAAACGAGT
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
15 11 0.32
16 23 0.68
ACGTcount: A:0.52, C:0.20, G:0.11, T:0.16
Consensus pattern (16 bp):
GAAAAAACTCAAACTT
Found at i:1491389 original size:32 final size:32
Alignment explanation
Indices: 1491324--1491388 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 32
1491314 GAACCCGAAT
*
1491324 AAGCCCGAATCCGAAAAAACTTAAACTTGAAA
1 AAGCCCGAATCCGAAAAAACTCAAACTTGAAA
* *
1491356 AAGCCCGACT-CGAAAAAGCTCAAACTTGAAA
1 AAGCCCGAATCCGAAAAAACTCAAACTTGAAA
1491387 AA
1 AA
1491389 ACTTAAACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 21 0.70
32 9 0.30
ACGTcount: A:0.49, C:0.23, G:0.14, T:0.14
Consensus pattern (32 bp):
AAGCCCGAATCCGAAAAAACTCAAACTTGAAA
Found at i:1492362 original size:19 final size:19
Alignment explanation
Indices: 1492340--1492382 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1492330 ATAATTAAAT
*
1492340 TAAATAAATAT-AAATTATA
1 TAAA-AAATATAAAAATATA
*
1492359 TAAAAATTATAAAAATATA
1 TAAAAAATATAAAAATATA
1492378 TAAAA
1 TAAAA
1492383 CTAATTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAAATATAAAAATATA
Found at i:1492367 original size:11 final size:10
Alignment explanation
Indices: 1492341--1492382 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1492331 TAATTAAATT
*
1492341 AAATAAATATA
1 AAATATATA-A
*
1492352 AATTATATAA
1 AAATATATAA
1492362 AAAT-TATAA
1 AAATATATAA
1492371 AAATATATAA
1 AAATATATAA
1492381 AA
1 AA
1492383 CTAATTTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 9 0.33
10 11 0.41
11 7 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATATATAA
Found at i:1494722 original size:12 final size:12
Alignment explanation
Indices: 1494700--1494734 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1494690 ACGGGAGTTA
*
1494700 TATTTTACTTTT
1 TATTTTTCTTTT
*
1494712 TTTTTTTCTTTT
1 TATTTTTCTTTT
1494724 TATTTTTCTTT
1 TATTTTTCTTT
1494735 ATTTAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (12 bp):
TATTTTTCTTTT
Found at i:1501640 original size:23 final size:25
Alignment explanation
Indices: 1501614--1501673 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 25
1501604 ACCTATCATA
*
1501614 ATAAAATTTAA-GAT-ATAATTTAT
1 ATAAATTTTAATGATAATAATTTAT
1501637 ATAAATTTTAATTCGATAATAATTTAT
1 ATAAATTTTAA-T-GATAATAATTTAT
1501664 ATAAATTTTA
1 ATAAATTTTA
1501674 TATAAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 10 0.31
26 3 0.09
27 19 0.59
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (25 bp):
ATAAATTTTAATGATAATAATTTAT
Found at i:1501673 original size:11 final size:11
Alignment explanation
Indices: 1501659--1501689 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
1501649 TCGATAATAA
1501659 TTTATATAAAT
1 TTTATATAAAT
1501670 TTTATATAAAT
1 TTTATATAAAT
1501681 TTTAATATA
1 TTT-ATATA
1501690 TTTATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTATATAAAT
Found at i:1503051 original size:2 final size:2
Alignment explanation
Indices: 1503044--1503077 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1503034 CTATTTTTGC
1503044 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
1503078 GTGTGTGTGT
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):
AT
Found at i:1504417 original size:68 final size:68
Alignment explanation
Indices: 1504307--1504433 Score: 218
Period size: 68 Copynumber: 1.9 Consensus size: 68
1504297 CAACATAATG
*
1504307 ACCTTACAGTGCAAGCAAAGCACGGCAATGGCATTACGGTTCCACAATTCAACCAAAATAACGTA
1 ACCTTACAGTGCAAGCAAAGCACGGCAATGGCATTACAGTTCCACAATTCAACCAAAATAACGTA
1504372 AGA
66 AGA
* * *
1504375 ACCTTACAGTGCACGGAAAGCATGGCAATGGCATTACAGTTCCACAATTCAACCAAAAT
1 ACCTTACAGTGCAAGCAAAGCACGGCAATGGCATTACAGTTCCACAATTCAACCAAAAT
1504434 TGCTCCAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 55 1.00
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (68 bp):
ACCTTACAGTGCAAGCAAAGCACGGCAATGGCATTACAGTTCCACAATTCAACCAAAATAACGTA
AGA
Found at i:1509568 original size:2 final size:2
Alignment explanation
Indices: 1509561--1509591 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1509551 TTTATGATAC
1509561 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
1509592 GAAATTCAAA
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:1513102 original size:25 final size:23
Alignment explanation
Indices: 1513072--1513126 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1513062 TAATTATATA
1513072 AATATATAAAATAAAAATTATTTTT
1 AATATATAAAAT-AAAATT-TTTTT
* * *
1513097 AATATATATACTAATATTTTTTT
1 AATATATAAAATAAAATTTTTTT
1513120 AATATAT
1 AATATAT
1513127 TTTTAGTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 12 0.44
24 5 0.19
25 10 0.37
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
AATATATAAAATAAAATTTTTTT
Found at i:1513901 original size:32 final size:33
Alignment explanation
Indices: 1513865--1513933 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 33
1513855 AGATAATACC
* * *
1513865 TATATTTTTTAATTTTAAAT-TTAA-AAATAAA
1 TATATTCTTAAATTTTAAATATAAATAAATAAA
1513896 -ATATATCTTAAATTTTAAATATAAATAAATAAA
1 TATAT-TCTTAAATTTTAAATATAAATAAATAAA
1513929 TATAT
1 TATAT
1513934 GAATAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 4 0.13
31 13 0.42
32 3 0.10
33 7 0.23
34 4 0.13
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (33 bp):
TATATTCTTAAATTTTAAATATAAATAAATAAA
Found at i:1513969 original size:21 final size:21
Alignment explanation
Indices: 1513944--1513988 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1513934 GAATAATTTT
1513944 TAATGATAAGATTAAATTTGA
1 TAATGATAAGATTAAATTTGA
1513965 TAATGATAAGATTAAATTTGA
1 TAATGATAAGATTAAATTTGA
1513986 TAA
1 TAA
1513989 ATCGAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (21 bp):
TAATGATAAGATTAAATTTGA
Found at i:1514755 original size:50 final size:50
Alignment explanation
Indices: 1514679--1514876 Score: 245
Period size: 50 Copynumber: 4.0 Consensus size: 50
1514669 GATTTGGTGG
* * *
1514679 TCTTCACCGACCTTTGACAA-CAGAGAGAGTTGGCCGTAATTGTTGACTAT
1 TCTTCACCAACCTTTGACAATC-GAGAGAGATGGCCATAATTGTTGACTAT
* * * * *
1514729 TCTTCACCAACCTTTGATAATCGAGAGAGGTGACCATTATTATTGACTAT
1 TCTTCACCAACCTTTGACAATCGAGAGAGATGGCCATAATTGTTGACTAT
* *
1514779 TCTTTATCAACCTTTGACAATCGAGAGAGATGGCCATAATTGTTGACTAT
1 TCTTCACCAACCTTTGACAATCGAGAGAGATGGCCATAATTGTTGACTAT
* * * * *
1514829 TTTTCACCAACCTTTGATAATAGAGAGAGATAGCCGTAATTGTTGACT
1 TCTTCACCAACCTTTGACAATCGAGAGAGATGGCCATAATTGTTGACT
1514877 CTAAGCAACT
Statistics
Matches: 126, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
50 125 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (50 bp):
TCTTCACCAACCTTTGACAATCGAGAGAGATGGCCATAATTGTTGACTAT
Found at i:1514875 original size:100 final size:100
Alignment explanation
Indices: 1514688--1514876 Score: 274
Period size: 100 Copynumber: 1.9 Consensus size: 100
1514678 GTCTTCACCG
* * *
1514688 ACCTTTGACAACAGAGAGAGTTGGCCGTAATTGTTGACTATTCTTCACCAACCTTTGATAATCGA
1 ACCTTTGACAACAGAGAGAGATGGCCATAATTGTTGACTATTCTTCACCAACCTTTGATAATAGA
* *
1514753 GAGAGGTGACCATTATTATTGACTATTCTTTATCA
66 GAGAGATGACCATAATTATTGACTATTCTTTATCA
*
1514788 ACCTTTGACAATC-GAGAGAGATGGCCATAATTGTTGACTATTTTTCACCAACCTTTGATAATAG
1 ACCTTTGACAA-CAGAGAGAGATGGCCATAATTGTTGACTATTCTTCACCAACCTTTGATAATAG
* *
1514852 AGAGAGAT-AGCCGTAATTGTTGACT
65 AGAGAGATGA-CCATAATTATTGACT
1514877 CTAAGCAACT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
99 1 0.01
100 77 0.97
101 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (100 bp):
ACCTTTGACAACAGAGAGAGATGGCCATAATTGTTGACTATTCTTCACCAACCTTTGATAATAGA
GAGAGATGACCATAATTATTGACTATTCTTTATCA
Found at i:1519399 original size:50 final size:50
Alignment explanation
Indices: 1519317--1519459 Score: 198
Period size: 50 Copynumber: 2.9 Consensus size: 50
1519307 GGTGGTCTTT
* *
1519317 ACCAACCTTTGACAATAGAAAG-AGTTGGCCGTAATTGTTGACTATTATTC
1 ACCAACCTTTGACAATAGAGAGAAG-TGACCGTAATTGTTGACTATTATTC
* * * *
1519367 ACCAACTTTTGACAATCGAGAGAAGTGACCGTAATTGTTGACTATTCTTT
1 ACCAACCTTTGACAATAGAGAGAAGTGACCGTAATTGTTGACTATTATTC
* *
1519417 ACTAACCTTTGATAATAGAGAGAAGTGACCGTAATTGTTGACT
1 ACCAACCTTTGACAATAGAGAGAAGTGACCGTAATTGTTGACT
1519460 CTAAGCAACT
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 80 0.98
51 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (50 bp):
ACCAACCTTTGACAATAGAGAGAAGTGACCGTAATTGTTGACTATTATTC
Found at i:1521317 original size:16 final size:18
Alignment explanation
Indices: 1521282--1521320 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
1521272 TATCTTAAAT
1521282 TTTATACTTTAAATTTTA
1 TTTATACTTTAAATTTTA
1521300 TTTATA-TTTAAA-TTTA
1 TTTATACTTTAAATTTTA
1521316 TTTAT
1 TTTAT
1521321 TCAAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.43
17 6 0.29
18 6 0.29
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATACTTTAAATTTTA
Found at i:1528216 original size:29 final size:29
Alignment explanation
Indices: 1528174--1528235 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
1528164 CAATTGTAAC
1528174 TTGTATATCTGTAGGACTTAGAATAAACA
1 TTGTATATCTGTAGGACTTAGAATAAACA
1528203 TTGTATATCTGTAGGACTTAGAATAAACA
1 TTGTATATCTGTAGGACTTAGAATAAACA
1528232 TTGT
1 TTGT
1528236 GCTGCGGCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (29 bp):
TTGTATATCTGTAGGACTTAGAATAAACA
Found at i:1529715 original size:14 final size:15
Alignment explanation
Indices: 1529692--1529724 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1529682 ATATCACTCC
*
1529692 AAAAACAAAAA-CAA
1 AAAAAAAAAAACCAA
1529706 AAAAAAAAAAACCAA
1 AAAAAAAAAAACCAA
1529721 AAAA
1 AAAA
1529725 TGATGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAACCAA
Found at i:1530547 original size:32 final size:33
Alignment explanation
Indices: 1530511--1530589 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 33
1530501 ATTATTTTTA
*
1530511 TATATTATATATATTTTAATGT-ATTA-ATAATT
1 TATATTATATATATTTTAATATAATTATAT-ATT
* *
1530543 TATATTTTATAAATTTTAATATAATTATATATT
1 TATATTATATATATTTTAATATAATTATATATT
* *
1530576 CATATAATATATAT
1 TATATTATATATAT
1530590 ATATATTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 19 0.50
33 17 0.45
34 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (33 bp):
TATATTATATATATTTTAATATAATTATATATT
Found at i:1530603 original size:15 final size:15
Alignment explanation
Indices: 1530585--1530635 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
1530575 TCATATAATA
1530585 TATATATATATTTTT
1 TATATATATATTTTT
*
1530600 TATA-AAATTATTTTT
1 TATATATA-TATTTTT
1530615 TATAT-TATATTCGTTT
1 TATATATATATT--TTT
1530631 TATAT
1 TATAT
1530636 TTAAAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 6 0.20
15 16 0.53
16 8 0.27
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (15 bp):
TATATATATATTTTT
Found at i:1530603 original size:17 final size:17
Alignment explanation
Indices: 1530583--1530624 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
1530573 ATTCATATAA
1530583 TATATATATATATTTTT
1 TATATATATATATTTTT
*
1530600 TATA-AAAT-TATTTTT
1 TATATATATATATTTTT
1530615 TATAT-TATAT
1 TATATATATAT
1530625 TCGTTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATATATATATTTTT
Found at i:1531388 original size:17 final size:17
Alignment explanation
Indices: 1531339--1531378 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1531329 ATTTATTTTC
*
1531339 TATTAAA-AATATTTACT
1 TATTAAATAA-ATTTAAT
1531356 TATTAAATAAATTTAAT
1 TATTAAATAAATTTAAT
1531373 TATTAA
1 TATTAA
1531379 GTAATCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTAAATAAATTTAAT
Found at i:1532880 original size:21 final size:22
Alignment explanation
Indices: 1532854--1532901 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1532844 TTATTGAAAG
1532854 ATAAAAA-AAAAATCAAAA-ATT
1 ATAAAAATAAAAAT-AAAATATT
1532875 ATAAAAAATAAAAATAAAATATT
1 AT-AAAAATAAAAATAAAATATT
1532898 ATAA
1 ATAA
1532902 CTATTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.08
22 11 0.46
23 11 0.46
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (22 bp):
ATAAAAATAAAAATAAAATATT
Found at i:1532887 original size:23 final size:22
Alignment explanation
Indices: 1532856--1532901 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
1532846 ATTGAAAGAT
1532856 AAAAAAAAAATCAAAA-ATTATA
1 AAAAAAAAAAT-AAAATATTATA
1532878 AAAAATAAAAATAAAATATTATA
1 AAAAA-AAAAATAAAATATTATA
1532901 A
1 A
1532902 CTATTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAAAAAAAATAAAATATTATA
Found at i:1533514 original size:37 final size:35
Alignment explanation
Indices: 1533460--1533528 Score: 84
Period size: 37 Copynumber: 1.9 Consensus size: 35
1533450 ATTTTTTTTA
* *
1533460 AAAAAATAAATTATTTAATTTTTTATTAATTATTT
1 AAAAAATAAATTATTTAAATTTATATTAATTATTT
* *
1533495 AAAAAATAATATTTTTTTAAATTTATATTTATTA
1 AAAAAATAA-A-TTATTTAAATTTATATTAATTA
1533529 ATATAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 9 0.32
36 1 0.04
37 18 0.64
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
AAAAAATAAATTATTTAAATTTATATTAATTATTT
Found at i:1534533 original size:21 final size:21
Alignment explanation
Indices: 1534486--1534544 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
1534476 ATTAAATTAG
* *
1534486 TAATTTTGTTAAA-ATTTATTT
1 TAATTTT-TAAAATATTTACTT
1534507 TAATTTTTAAAACTATTTACTT
1 TAATTTTTAAAA-TATTTACTT
*
1534529 T-ATTTTTCAAATATTT
1 TAATTTTTAAAATATTT
1534545 TAATTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 9 0.27
21 16 0.48
22 8 0.24
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (21 bp):
TAATTTTTAAAATATTTACTT
Found at i:1534546 original size:21 final size:21
Alignment explanation
Indices: 1534499--1534551 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1534489 TTTTGTTAAA
*
1534499 ATTTATTTTAATTTTTAAAACT
1 ATTTAATTT-ATTTTTAAAACT
* *
1534521 ATTTACTTTATTTTTCAAA-T
1 ATTTAATTTATTTTTAAAACT
1534541 ATTTTAATTTA
1 A-TTTAATTTA
1534552 AAAAAAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 17 0.63
22 8 0.30
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTAATTTATTTTTAAAACT
Found at i:1535636 original size:26 final size:25
Alignment explanation
Indices: 1535592--1535641 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
1535582 ATTAAATATA
1535592 ATTTATATATTTTTATTATATTTTT
1 ATTTATATATTTTTATTATATTTTT
1535617 ATTT-TATATTTTATATTTATATTTT
1 ATTTATATATTTT-TA-TTATATTTT
1535642 AAATATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.35
25 6 0.26
26 9 0.39
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (25 bp):
ATTTATATATTTTTATTATATTTTT
Found at i:1535642 original size:13 final size:12
Alignment explanation
Indices: 1535597--1535641 Score: 65
Period size: 13 Copynumber: 3.7 Consensus size: 12
1535587 ATATAATTTA
1535597 TATATTTTTA-T
1 TATATTTTTATT
1535608 TATATTTTTATTT
1 TATATTTTTA-TT
1535621 TATATTTTATATT
1 TATATTTT-TATT
1535634 TATATTTT
1 TATATTTT
1535642 AAATATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.32
13 19 0.61
14 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TATATTTTTATT
Found at i:1537652 original size:3 final size:3
Alignment explanation
Indices: 1537644--1537698 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
1537634 AAGATAAAGC
1537644 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1537692 ATA ATA A
1 ATA ATA A
1537699 AAGTCTAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1537845 original size:2 final size:2
Alignment explanation
Indices: 1537828--1537876 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
1537818 TCATAATAAA
* *
1537828 AT AT GT AT AA 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 AT
1537870 AT AT AT A
1 AT AT AT A
1537877 ACCCCAAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1538299 original size:14 final size:14
Alignment explanation
Indices: 1538280--1538307 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1538270 TTTGAATAAG
1538280 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
1538294 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
1538308 AATATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:1547253 original size:13 final size:13
Alignment explanation
Indices: 1547235--1547259 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1547225 TACTATATAC
1547235 ACTGTATCGATAT
1 ACTGTATCGATAT
1547248 ACTGTATCGATA
1 ACTGTATCGATA
1547260 CATGAATAGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
ACTGTATCGATAT
Found at i:1547339 original size:10 final size:10
Alignment explanation
Indices: 1547326--1547388 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
1547316 GTTATGAACA
1547326 ATGAACAGTG
1 ATGAACAGTG
1547336 ATGAACAGTG
1 ATGAACAGTG
* *
1547346 ATGTATC-GATAT
1 ATG-AACAG-T-G
1547358 ATGAACAGTG
1 ATGAACAGTG
* *
1547368 ATAAATAGTG
1 ATGAACAGTG
1547378 ATGAACAGTG
1 ATGAACAGTG
1547388 A
1 A
1547389 AAAATGAGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
10 31 0.76
11 6 0.15
12 4 0.10
ACGTcount: A:0.41, C:0.08, G:0.25, T:0.25
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1547442 original size:20 final size:20
Alignment explanation
Indices: 1547417--1547468 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1547407 TGCCAATGCT
1547417 ATGTATCGATACTTAGCAAA
1 ATGTATCGATACTTAGCAAA
1547437 ATGTATCGATACTTAGCAAA
1 ATGTATCGATACTTAGCAAA
*
1547457 ATCTATCGATAC
1 ATGTATCGATAC
1547469 ATCTGAGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACTTAGCAAA
Found at i:1548469 original size:19 final size:20
Alignment explanation
Indices: 1548447--1548485 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1548437 TTAAAACGTG
1548447 TAAAATTA-ATTTTTCATTA
1 TAAAATTATATTTTTCATTA
1548466 TAAAATTATATTTTTCATTA
1 TAAAATTATATTTTTCATTA
1548486 ATTAATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAAATTATATTTTTCATTA
Found at i:1549542 original size:17 final size:17
Alignment explanation
Indices: 1549516--1549560 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1549506 TTACGACTTC
* *
1549516 TGCCTTTGGTTTGCTTT
1 TGCCTCTGGTTTGATTT
1549533 TGCCTCTGGTTTGATTT
1 TGCCTCTGGTTTGATTT
*
1549550 TGCTTCTGGTT
1 TGCCTCTGGTT
1549561 GCTGTTGCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.02, C:0.18, G:0.24, T:0.56
Consensus pattern (17 bp):
TGCCTCTGGTTTGATTT
Found at i:1549638 original size:48 final size:48
Alignment explanation
Indices: 1549577--1549683 Score: 151
Period size: 48 Copynumber: 2.2 Consensus size: 48
1549567 GCTGATCTGT
*
1549577 TTCTGGTTACTAATTTGCTTCTGGTTGCTGTTGTTATTGCCGAGCTGC
1 TTCTAGTTACTAATTTGCTTCTGGTTGCTGTTGTTATTGCCGAGCTGC
* * * ** *
1549625 TTCTAGTTACTAATTTGTTTCTGGTTGCTTTTGTTGTTGCCGATTTGT
1 TTCTAGTTACTAATTTGCTTCTGGTTGCTGTTGTTATTGCCGAGCTGC
1549673 TTCTAGTTACT
1 TTCTAGTTACT
1549684 GTTGCTATTG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.11, C:0.16, G:0.21, T:0.51
Consensus pattern (48 bp):
TTCTAGTTACTAATTTGCTTCTGGTTGCTGTTGTTATTGCCGAGCTGC
Found at i:1549935 original size:45 final size:45
Alignment explanation
Indices: 1549884--1550000 Score: 207
Period size: 45 Copynumber: 2.6 Consensus size: 45
1549874 TTTGTTATTT
* *
1549884 TTTTAATTGAGTTTGGGTTTAAGTTTATATAGATTTTTAGTTGGG
1 TTTTAATTGGGTTTGGGTTTAAGTTTATATAGATTTTGAGTTGGG
*
1549929 TTTTAATTGGGTTTAGGTTTAAGTTTATATAGATTTTGAGTTGGG
1 TTTTAATTGGGTTTGGGTTTAAGTTTATATAGATTTTGAGTTGGG
1549974 TTTTAATTGGGTTTGGGTTTAAGTTTA
1 TTTTAATTGGGTTTGGGTTTAAGTTTA
1550001 AATTTTTGTT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (45 bp):
TTTTAATTGGGTTTGGGTTTAAGTTTATATAGATTTTGAGTTGGG
Found at i:1549999 original size:23 final size:23
Alignment explanation
Indices: 1549928--1550004 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 23
1549918 TTTTAGTTGG
*
1549928 GTTTTAATTGGGTTTAGGTTTAA
1 GTTTTAATTGGGTTTGGGTTTAA
* ** * **
1549951 G-TTTATATAGATTTTGAG-TTGG
1 GTTTTA-ATTGGGTTTGGGTTTAA
1549973 GTTTTAATTGGGTTTGGGTTTAA
1 GTTTTAATTGGGTTTGGGTTTAA
*
1549996 GTTTAAATT
1 GTTTTAATT
1550005 TTTGTTTTAT
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 15 0.41
23 22 0.59
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (23 bp):
GTTTTAATTGGGTTTGGGTTTAA
Found at i:1561805 original size:2 final size:2
Alignment explanation
Indices: 1561798--1561823 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1561788 CGCCAATTGG
1561798 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
1561824 GTTTCCTAGT
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):
AT
Found at i:1561946 original size:19 final size:18
Alignment explanation
Indices: 1561924--1561967 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
1561914 TAATTTTTTA
1561924 TTAATTTATAAATAATAAT
1 TTAATTTATAAAT-ATAAT
* *
1561943 TTAAATTTTTAAATTTAAT
1 TT-AATTTATAAATATAAT
1561962 TTAATT
1 TTAATT
1561968 AAAAACTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 8 0.36
20 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTTATAAATATAAT
Found at i:1562509 original size:6 final size:6
Alignment explanation
Indices: 1562491--1562525 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1562481 TTTTTTAAAA
* *
1562491 AAATTT AATTTT AAATTT AAATTT GAATTT AAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT
1562526 AATTTAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:1562596 original size:32 final size:31
Alignment explanation
Indices: 1562545--1562633 Score: 85
Period size: 31 Copynumber: 2.8 Consensus size: 31
1562535 TGTAAGCTCG
*
1562545 AATTTATTATTTTTATTAAAAATATTAAA-AAA
1 AATTT-TTATTTTAATT-AAAATATTAAATAAA
*
1562577 TATTTTTATTTATAATT-AAAT-TTAAATAAA
1 AATTTTTATTT-TAATTAAAATATTAAATAAA
*
1562607 AATATATTATTTTAATTTAAAATATTA
1 AAT-TTTTATTTTAA-TTAAAATATTA
1562634 TTCAAGTTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
29 5 0.11
30 12 0.26
31 15 0.32
32 12 0.26
33 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
AATTTTTATTTTAATTAAAATATTAAATAAA
Found at i:1566517 original size:27 final size:27
Alignment explanation
Indices: 1566486--1566629 Score: 74
Period size: 27 Copynumber: 5.4 Consensus size: 27
1566476 ATAAAAGAAC
1566486 ATATTTAAAATTTTATATAAATATAAA
1 ATATTTAAAATTTTATATAAATATAAA
* * *
1566513 ATATTTTAAATATAAT-TATAATAT--A
1 ATATTTAAAATTTTATATA-AATATAAA
* * *
1566538 ATA---AAATATATAATATAAATA-AAT
1 ATATTTAAA-ATTTTATATAAATATAAA
*
1566562 AT-TTTAAAATTTATATTATTTAAAT-TATTA
1 ATATTTAAAATTT-TA-TA--TAAATATA-AA
1566592 ATATATTAAAATTTT-TATAAATATAAA
1 ATAT-TTAAAATTTTATATAAATATAAA
*
1566619 ATATTTTAAAT
1 ATATTTAAAAT
1566630 AAAATTAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 35
0.66 0.08 0.26
Matches are distributed among these distances:
22 2 0.02
23 11 0.12
24 4 0.04
25 7 0.08
26 12 0.13
27 30 0.34
28 2 0.02
29 8 0.09
30 2 0.02
31 2 0.02
32 9 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATATTTAAAATTTTATATAAATATAAA
Found at i:1566561 original size:17 final size:17
Alignment explanation
Indices: 1566519--1566563 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
1566509 TAAAATATTT
1566519 TAAATATAAT-TATAATA
1 TAAATA-AATATATAATA
1566536 T-AATAAAATATATAATA
1 TAAAT-AAATATATAATA
1566553 TAAATAAATAT
1 TAAATAAATAT
1566564 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.24
17 16 0.64
18 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATAAATATATAATA
Found at i:1566630 original size:16 final size:17
Alignment explanation
Indices: 1566491--1566630 Score: 63
Period size: 16 Copynumber: 8.0 Consensus size: 17
1566481 AGAACATATT
*
1566491 TAAAATTTTATATAAATA
1 TAAAATATT-TATAAATA
1566509 TAAAATATTT-TAAATA
1 TAAAATATTTATAAATA
* *
1566525 TAATTATAATATAATAAAATA
1 TAA-AAT-AT-TTAT-AAATA
* **
1566546 TATAATATAAATAAATA
1 TAAAATATTTATAAATA
* * *
1566563 TTTTAAA-ATTTATATTATT
1 --TAAAATATTTATA-AATA
* * *
1566582 TAAATTATTAATATAT-
1 TAAAATATTTATAAATA
*
1566598 TAAAATTTTTATAAATA
1 TAAAATATTTATAAATA
1566615 TAAAATATTT-TAAATA
1 TAAAATATTTATAAATA
1566631 AAATTAAAAC
Statistics
Matches: 92, Mismatches: 20, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
16 27 0.29
17 23 0.25
18 24 0.26
19 8 0.09
20 3 0.03
21 7 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAATATTTATAAATA
Found at i:1567085 original size:22 final size:22
Alignment explanation
Indices: 1567057--1567101 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1567047 ATATATCATA
*
1567057 TAAATTA-TATATTATATATTTT
1 TAAATTATTATA-TATATAATTT
1567079 TAAATTATTATATATATAATTT
1 TAAATTATTATATATATAATTT
1567101 T
1 T
1567102 CTTTTGATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TAAATTATTATATATATAATTT
Found at i:1567271 original size:6 final size:5
Alignment explanation
Indices: 1567242--1567295 Score: 62
Period size: 5 Copynumber: 11.2 Consensus size: 5
1567232 TAAAATTTAA
1567242 TATAT T-TA- TATACT TATAT TATAT TCATAT TAT-T T-TAT TATAT TATAT
1 TATAT TATAT TATA-T TATAT TATAT T-ATAT TATAT TATAT TATAT TATAT
1567290 TATAT T
1 TATAT T
1567296 TAAAATTATC
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
3 2 0.05
4 8 0.19
5 24 0.56
6 9 0.21
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:1567282 original size:8 final size:9
Alignment explanation
Indices: 1567236--1567297 Score: 56
Period size: 10 Copynumber: 6.6 Consensus size: 9
1567226 ATTTTATAAA
*
1567236 ATTTAATAT
1 ATTTATTAT
1567245 ATTTA-TAT
1 ATTTATTAT
1567253 ACTTATATTAT
1 A-TT-TATTAT
1567264 ATTCATATTAT
1 ATT--TATTAT
1567275 -TTTATTAT
1 ATTTATTAT
1567283 ATTATATTAT
1 ATT-TATTAT
1567293 ATTTA
1 ATTTA
1567298 AAATTATCGA
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
8 10 0.21
9 11 0.23
10 15 0.32
11 11 0.23
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTTATTAT
Found at i:1567297 original size:19 final size:19
Alignment explanation
Indices: 1567170--1567297 Score: 72
Period size: 19 Copynumber: 6.7 Consensus size: 19
1567160 GGGATTTTTT
*
1567170 TTATAATTATATTTA-AATTA
1 TTAT-ATTATATTTATTA-TA
1567190 TTATA-TAT-TTTATTAATA
1 TTATATTATATTTATT-ATA
* * *
1567208 TTAAATTATTAATAATT-TA
1 TTATATTA-TATTTATTATA
* * * *
1567227 TTTTATAAAATTTAATATA
1 TTATATTATATTTATTATA
1567246 TT-TA-TATACTTATATTATA
1 TTATATTATA-TT-TATTATA
1567265 TTCATATTAT-TTTATTATA
1 TT-ATATTATATTTATTATA
1567284 TTATATTATATTTA
1 TTATATTATATTTA
1567298 AAATTATCGA
Statistics
Matches: 82, Mismatches: 14, Indels: 25
0.68 0.12 0.21
Matches are distributed among these distances:
17 6 0.07
18 24 0.29
19 36 0.44
20 7 0.09
21 6 0.07
22 3 0.04
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATATTATATTTATTATA
Found at i:1568169 original size:30 final size:29
Alignment explanation
Indices: 1568135--1568204 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 29
1568125 GCAATTCAAC
1568135 CAAAATAGTATTAAATTTAAAATAAATTAT
1 CAAAATAGTATT-AATTTAAAATAAATTAT
* *
1568165 CAAAATAGT-TT-TTTTAAAATAATTTAT
1 CAAAATAGTATTAATTTAAAATAAATTAT
* *
1568192 CAAATTAATATTA
1 CAAAATAGTATTA
1568205 TTTTTTTGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 21 0.62
28 2 0.06
29 2 0.06
30 9 0.26
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.41
Consensus pattern (29 bp):
CAAAATAGTATTAATTTAAAATAAATTAT
Found at i:1572431 original size:13 final size:13
Alignment explanation
Indices: 1572410--1572439 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1572400 ATACATTGTT
1572410 CATTGTATCGATA
1 CATTGTATCGATA
*
1572423 CATTTTATCGATA
1 CATTGTATCGATA
1572436 CATT
1 CATT
1572440 CTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1572480 original size:20 final size:19
Alignment explanation
Indices: 1572455--1572562 Score: 102
Period size: 20 Copynumber: 5.8 Consensus size: 19
1572445 TTTACCCAGA
*
1572455 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTCT-CAT
*
1572475 TGTATCGATATATTGCTCAT
1 TGTATCGATACATT-CTCAT
1572495 TGTATCGAT--A---T-AT
1 TGTATCGATACATTCTCAT
1572508 TGTATCGATACATTACTCAT
1 TGTATCGATACATT-CTCAT
* *
1572528 TGTATCGATACATTTTACAA
1 TGTATCGATACATTCT-CAT
1572548 TGTATCGATACATTC
1 TGTATCGATACATTC
1572563 AGGCATTTTT
Statistics
Matches: 74, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
13 11 0.15
14 1 0.01
15 1 0.01
18 1 0.01
19 2 0.03
20 57 0.77
21 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTCTCAT
Found at i:1572511 original size:13 final size:13
Alignment explanation
Indices: 1572493--1572517 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1572483 TATATTGCTC
1572493 ATTGTATCGATAT
1 ATTGTATCGATAT
1572506 ATTGTATCGATA
1 ATTGTATCGATA
1572518 CATTACTCAT
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:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:1572515 original size:33 final size:33
Alignment explanation
Indices: 1572473--1572537 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
1572463 TACATTTTGC
* *
1572473 ATTGTATCGATATATTGCTCATTGTATCGATAT
1 ATTGTATCGATACATTACTCATTGTATCGATAT
1572506 ATTGTATCGATACATTACTCATTGTATCGATA
1 ATTGTATCGATACATTACTCATTGTATCGATA
1572538 CATTTTACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (33 bp):
ATTGTATCGATACATTACTCATTGTATCGATAT
Found at i:1572552 original size:53 final size:53
Alignment explanation
Indices: 1572455--1572557 Score: 138
Period size: 53 Copynumber: 1.9 Consensus size: 53
1572445 TTTACCCAGA
* * *
1572455 TGTATCGATACATTTTGCATTGTATCGATATATTGCTCATTGTATCGATATAT
1 TGTATCGATACATTCTGCATTGTATCGATACATTGCTCAATGTATCGATATAT
*
1572508 TGTATCGATACATTACT-CATTGTATCGATACATT-TTACAATGTATCGATA
1 TGTATCGATACATT-CTGCATTGTATCGATACATTGCT-CAATGTATCGATA
1572558 CATTCAGGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
52 1 0.02
53 42 0.95
54 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.43
Consensus pattern (53 bp):
TGTATCGATACATTCTGCATTGTATCGATACATTGCTCAATGTATCGATATAT
Done.