Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold63
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: 2211945
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 524 characters in sequence are not A, C, G, or T
File 10 of 16
Found at i:1464143 original size:29 final size:29
Alignment explanation
Indices: 1464080--1464149 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
1464070 TAAAAATTTA
*
1464080 TATAA-ATATAAAATATTTTAAATATAAT
1 TATAATATATAAAATATTATAAATATAAT
*
1464108 TATAATATTATAAAATA-TATAAATATACT
1 TATAATA-TATAAAATATTATAAATATAAT
1464137 GTA-AATATATAAA
1 -TATAATATATAAA
1464150 TTATCATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 11 0.30
29 15 0.41
30 11 0.30
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (29 bp):
TATAATATATAAAATATTATAAATATAAT
Found at i:1465556 original size:22 final size:23
Alignment explanation
Indices: 1465503--1465558 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
1465493 AAAATATTCA
1465503 AAATTTAAAATGATTAAATTAGAT
1 AAATTT-AAATGATTAAATTAGAT
*
1465527 AAAATTAAAT-ATTAAATATA-AT
1 AAATTTAAATGATTAAAT-TAGAT
*
1465549 TAATTTAAAT
1 AAATTTAAAT
1465559 CTAAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 17 0.61
23 6 0.21
24 5 0.18
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
AAATTTAAATGATTAAATTAGAT
Found at i:1466203 original size:2 final size:2
Alignment explanation
Indices: 1466196--1466223 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1466186 ATGCATAATC
1466196 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
1466224 ATTTTAATGC
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):
TA
Found at i:1466764 original size:4 final size:4
Alignment explanation
Indices: 1466755--1466793 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
1466745 TTAGGCTAAA
* *
1466755 AAAG AAAG AAAG AAAA AAAG AAAG AAAG GAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1466794 TGAGAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1470701 original size:26 final size:25
Alignment explanation
Indices: 1470672--1470740 Score: 59
Period size: 26 Copynumber: 2.6 Consensus size: 25
1470662 AAAAAAATTT
1470672 ATTATATTAATATTTATATATTTTTA
1 ATTA-ATTAATATTTATATATTTTTA
** * *
1470698 ATTAAATTTAA-ATAAAAATATTTTTT
1 ATT-AA-TTAATATTTATATATTTTTA
1470724 ATTAATTAAATATTTAT
1 ATTAATT-AATATTTAT
1470741 TTAAATCAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
24 2 0.06
25 4 0.12
26 21 0.66
27 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTAATTAATATTTATATATTTTTA
Found at i:1471174 original size:16 final size:16
Alignment explanation
Indices: 1471153--1471204 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1471143 ATCAATTTTT
1471153 TTAAAAGATATATTTA
1 TTAAAAGATATATTTA
* *
1471169 TTAAAAATGATAAAATT-
1 TT-AAAA-GATATATTTA
*
1471186 TTAAAATATATATTTA
1 TTAAAAGATATATTTA
1471202 TTA
1 TTA
1471205 TCATTACAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 6 0.21
18 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (16 bp):
TTAAAAGATATATTTA
Found at i:1471391 original size:24 final size:25
Alignment explanation
Indices: 1471336--1471391 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
1471326 ATTTTATAAG
*
1471336 TTTATATTTAATATATTTGTAATTTT
1 TTTA-ATTTAATATATTTGTAAATTT
*
1471362 TTTAATTTTATATATTT-TAAATTT
1 TTTAATTTAATATATTTGTAAATTT
1471386 TTTAAT
1 TTTAAT
1471392 ATATTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 12 0.43
25 12 0.43
26 4 0.14
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (25 bp):
TTTAATTTAATATATTTGTAAATTT
Found at i:1472064 original size:21 final size:22
Alignment explanation
Indices: 1472017--1472058 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1472007 ATAATTTAAA
*
1472017 ATTAAATTTGATTTAATTGTAT
1 ATTAAATTTGATTTAATTATAT
*
1472039 ATTAAATTT-ATTTAGTTATA
1 ATTAAATTTGATTTAATTATA
1472059 AGTTAATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
ATTAAATTTGATTTAATTATAT
Found at i:1472144 original size:18 final size:18
Alignment explanation
Indices: 1472121--1472155 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1472111 CTAATATTTG
* *
1472121 ATTATAATATTAATTTTT
1 ATTATAAGAGTAATTTTT
1472139 ATTATAAGAGTAATTTT
1 ATTATAAGAGTAATTTT
1472156 ATAAACAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
ATTATAAGAGTAATTTTT
Found at i:1472639 original size:16 final size:16
Alignment explanation
Indices: 1472618--1472651 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1472608 TATCATACTT
1472618 TTATTTTCATATTATA
1 TTATTTTCATATTATA
*
1472634 TTATTTTTATATTATA
1 TTATTTTCATATTATA
1472650 TT
1 TT
1472652 TTAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTTCATATTATA
Found at i:1472643 original size:11 final size:11
Alignment explanation
Indices: 1472629--1472664 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
1472619 TATTTTCATA
1472629 TTATATTATTT
1 TTATATTATTT
1472640 TTATATTATATT
1 TTATATTAT-TT
1472652 TTA-ATTATTT
1 TTATATTATTT
1472662 TTA
1 TTA
1472665 ATAATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.21
11 14 0.58
12 5 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATATTATTT
Found at i:1472643 original size:22 final size:22
Alignment explanation
Indices: 1472616--1472673 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1472606 TATATCATAC
*
1472616 TTTTATTTTCATATTAT-ATTAT
1 TTTTATATT-ATATTATAATTAT
*
1472638 TTTTATATTATATTTTAATTAT
1 TTTTATATTATATTATAATTAT
*
1472660 TTTTAATAATATAT
1 TTTT-ATATTATAT
1472674 ATGTCATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 17 0.55
23 8 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATATTATATTATAATTAT
Found at i:1472804 original size:12 final size:12
Alignment explanation
Indices: 1472787--1472876 Score: 59
Period size: 10 Copynumber: 7.8 Consensus size: 12
1472777 TATTTTATTT
1472787 TTATATTATAAA
1 TTATATTATAAA
*
1472799 TTATATT-TAAG
1 TTATATTATAAA
*
1472810 TTGATATAATAAA
1 TT-ATATTATAAA
1472823 TTATA-T-TAAA
1 TTATATTATAAA
*
1472833 TTA-A-TATATA
1 TTATATTATAAA
1472843 TT-TA-TATAAA
1 TTATATTATAAA
* *
1472853 TTTTAATATAATA
1 TTATATTATAA-A
1472866 TTTATATTATA
1 -TTATATTATA
1472877 TAAATTTTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
9 2 0.03
10 20 0.32
11 7 0.11
12 19 0.31
13 6 0.10
14 8 0.13
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
TTATATTATAAA
Found at i:1472839 original size:23 final size:22
Alignment explanation
Indices: 1472797--1472874 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
1472787 TTATATTATA
* *
1472797 AATTATATTTAAGTTGATATAAT
1 AATTATA-TTAAATTAATATAAT
1472820 AAATTATATTAAATTAATAT-AT
1 -AATTATATTAAATTAATATAAT
*
1472842 ATTTATA-TAAATTTTAATATAAT
1 AATTATATTAAA--TTAATATAAT
*
1472865 ATTTATATTA
1 AATTATATTA
1472875 TATAAATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
20 4 0.09
21 6 0.13
22 9 0.19
23 19 0.40
24 9 0.19
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (22 bp):
AATTATATTAAATTAATATAAT
Found at i:1473270 original size:16 final size:15
Alignment explanation
Indices: 1473229--1473271 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1473219 ACCCTTAGAT
*
1473229 GATATAATATATATG
1 GATATAATATATATA
1473244 GATA-AATATATATA
1 GATATAATATATATA
*
1473258 TATATAATGATATA
1 GATATAAT-ATATA
1473272 AAATTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.50
15 7 0.29
16 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (15 bp):
GATATAATATATATA
Found at i:1473930 original size:30 final size:29
Alignment explanation
Indices: 1473896--1474009 Score: 88
Period size: 30 Copynumber: 3.8 Consensus size: 29
1473886 TATTATAGAT
*
1473896 TTATTTTAATATAAATTAAAAGTTAAAAA
1 TTATTTAAATATAAATTAAAAGTTAAAAA
** * * *
1473925 CTTATTTTGATATAATTTACAAGTTAAGAGTTA
1 -TTATTTAAATATAAATTAAAAGTTAA-A--AA
* *
1473958 TTATTGTAAATATAACTTAAAAATTAAAAA
1 TTATT-TAAATATAAATTAAAAGTTAAAAA
1473988 TTTATTTAAATAT-AA-TAAAAGT
1 -TTATTTAAATATAAATTAAAAGT
1474010 ATAACACGTA
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
28 6 0.09
29 1 0.01
30 31 0.46
31 6 0.09
32 6 0.09
33 17 0.25
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (29 bp):
TTATTTAAATATAAATTAAAAGTTAAAAA
Found at i:1474632 original size:17 final size:17
Alignment explanation
Indices: 1474612--1474646 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1474602 TTTATTATAC
1474612 TCAAATAAATA-TTTATT
1 TCAAATAAA-AGTTTATT
1474629 TCAAATAAAAGTTTATT
1 TCAAATAAAAGTTTATT
1474646 T
1 T
1474647 AGGTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (17 bp):
TCAAATAAAAGTTTATT
Found at i:1474702 original size:29 final size:28
Alignment explanation
Indices: 1474631--1474703 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
1474621 TATTTATTTC
*
1474631 AAATAAAAGTTTATTTAGGTAAAATTAA
1 AAATAAAAGATTATTTAGGTAAAATTAA
* * *
1474659 AAGTTAAAA-ACTTATTTTGGTACAATTTAA
1 AA-ATAAAAGA-TTATTTAGGTA-AAATTAA
1474689 AAATAAAAGATTATT
1 AAATAAAAGATTATT
1474704 ATTTGAATAC
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
28 2 0.06
29 25 0.69
30 9 0.25
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.37
Consensus pattern (28 bp):
AAATAAAAGATTATTTAGGTAAAATTAA
Found at i:1476678 original size:19 final size:19
Alignment explanation
Indices: 1476646--1476702 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
1476636 ATTATTTTTT
*
1476646 TATTATAATTATATTTAAAA
1 TATTAT-ATAATATTTAAAA
* *
1476666 TATTATATAATATATTTATA
1 TATTATATAATAT-TTAAAA
*
1476686 TACTTATATCATATTTA
1 TA-TTATATAATATTTA
1476703 TTATTATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 6 0.20
20 14 0.47
21 10 0.33
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTATATAATATTTAAAA
Found at i:1477812 original size:15 final size:15
Alignment explanation
Indices: 1477757--1477834 Score: 57
Period size: 13 Copynumber: 5.7 Consensus size: 15
1477747 TTTCTTTAGC
*
1477757 AATATATTCA-ATTT
1 AATATATTTATATTT
*
1477771 AAT-TATTTAAATTT
1 AATATATTTATATTT
1477785 --T-TATTT-T-TTT
1 AATATATTTATATTT
1477795 AATATATTTATATTT
1 AATATATTTATATTT
1477810 -A-ATATTTATATTT
1 AATATATTTATATTT
1477823 GATATATATTTA
1 -A-ATATATTTA
1477835 AATATGAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
10 3 0.06
12 7 0.13
13 22 0.42
14 9 0.17
15 3 0.06
16 1 0.02
17 7 0.13
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (15 bp):
AATATATTTATATTT
Found at i:1478397 original size:28 final size:27
Alignment explanation
Indices: 1478357--1478413 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
1478347 TACTATTTAA
**
1478357 TTTTAATTATAAATATTAATAAAATAAT
1 TTTTAATTATAAATAAAAATAAAA-AAT
1478385 TTTTAAATT-TAAATAAAAATAAAAAAT
1 TTTT-AATTATAAATAAAAATAAAAAAT
1478412 TT
1 TT
1478414 AAATTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 5 0.19
28 17 0.65
29 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TTTTAATTATAAATAAAAATAAAAAAT
Found at i:1478729 original size:22 final size:22
Alignment explanation
Indices: 1478698--1478751 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1478688 TTTCTTTTTG
1478698 AAAAAAATAAATAAGCA-ATTA
1 AAAAAAATAAATAAGCACATTA
*
1478719 AAAGAAAAT-AATAAGTACATTA
1 AAA-AAAATAAATAAGCACATTA
1478741 AAAATAAATAA
1 AAAA-AAATAA
1478752 TTATCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 11 0.39
22 16 0.57
23 1 0.04
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.20
Consensus pattern (22 bp):
AAAAAAATAAATAAGCACATTA
Found at i:1478752 original size:22 final size:20
Alignment explanation
Indices: 1478698--1478809 Score: 66
Period size: 21 Copynumber: 5.3 Consensus size: 20
1478688 TTTCTTTTTG
1478698 AAAAAAATAAATAAGCAATTA
1 AAAAAAAT-AATAAGCAATTA
*
1478719 AAAGAAAATAATAAGTACATTA
1 AAA-AAAATAATAAGCA-ATTA
* * **
1478741 AAAATAAATAATTATCTTTTTA
1 AAAA-AAATAATAAGC-AATTA
* *
1478763 TATTAAAAAGAA-AA-CAATTA
1 -A-AAAAAATAATAAGCAATTA
*
1478783 AAAAAAATAAATAAACAATTA
1 AAAAAAAT-AATAAGCAATTA
1478804 AAAAAA
1 AAAAAA
1478810 TAAATAAACA
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
18 5 0.07
19 3 0.04
20 5 0.07
21 24 0.35
22 24 0.35
23 6 0.09
24 2 0.03
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (20 bp):
AAAAAAATAATAAGCAATTA
Found at i:1478808 original size:20 final size:21
Alignment explanation
Indices: 1478774--1478828 Score: 85
Period size: 20 Copynumber: 2.6 Consensus size: 21
1478764 ATTAAAAAGA
1478774 AAACAATTAAAAAAAATAAAT
1 AAACAATTAAAAAAAATAAAT
1478795 AAACAATT-AAAAAAATAAAT
1 AAACAATTAAAAAAAATAAAT
1478815 AAACATATATAAAA
1 AAACA-AT-TAAAA
1478829 TAATTATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.55
21 10 0.32
22 1 0.03
23 3 0.10
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (21 bp):
AAACAATTAAAAAAAATAAAT
Found at i:1478873 original size:23 final size:23
Alignment explanation
Indices: 1478847--1478904 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
1478837 TTTTTATATT
1478847 AAAAATAATAATT-TTACATTAA
1 AAAAATAATAATTATTACATTAA
*
1478869 AAAAAGCAAT--TTGATTACATTAA
1 AAAAA-TAATAATT-ATTACATTAA
1478892 AAAAATAATAATT
1 AAAAATAATAATT
1478905 CAAAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
21 2 0.07
22 8 0.28
23 17 0.59
24 2 0.07
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (23 bp):
AAAAATAATAATTATTACATTAA
Found at i:1478873 original size:85 final size:84
Alignment explanation
Indices: 1478698--1478851 Score: 228
Period size: 80 Copynumber: 1.9 Consensus size: 84
1478688 TTTCTTTTTG
*
1478698 AAAAAAATAAATAAGCAATTAAAAGAAAATAATAAGTACATTAAAAATAAATAATTATCTTTTTA
1 AAAAAAATAAATAAACAATTAAAAGAAAATAATAAG-ACATTAAAAATAAATAATTATCTTTTTA
1478763 TATTAAAAAGAAAACAATTA
65 TATTAAAAAGAAAACAATTA
* *
1478783 AAAAAAATAAATAAACAATT-AAA-AAAATAAATAA-ACA-TATATA-AAATAATTATCTTTTTA
1 AAAAAAATAAATAAACAATTAAAAGAAAAT-AATAAGACATTAAAAATAAATAATTATCTTTTTA
1478843 TATTAAAAA
65 TATTAAAAA
1478852 TAATAATTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
80 26 0.40
81 4 0.06
82 3 0.05
83 5 0.08
84 8 0.12
85 19 0.29
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.29
Consensus pattern (84 bp):
AAAAAAATAAATAAACAATTAAAAGAAAATAATAAGACATTAAAAATAAATAATTATCTTTTTAT
ATTAAAAAGAAAACAATTA
Found at i:1478879 original size:20 final size:20
Alignment explanation
Indices: 1478837--1478896 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
1478827 AATAATTATC
* *
1478837 TTTTTATATTAAAAATAATAA
1 TTTTTACATTAAAAA-AACAA
1478858 -TTTTACATTAAAAAAAGCAA
1 TTTTTACATTAAAAAAA-CAA
1478878 TTTGATTACATTAAAAAAA
1 TTT--TTACATTAAAAAAA
1478897 TAATAATTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 2 0.06
20 15 0.45
21 2 0.06
23 14 0.42
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (20 bp):
TTTTTACATTAAAAAAACAA
Found at i:1479246 original size:22 final size:21
Alignment explanation
Indices: 1479219--1479281 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
1479209 TTAGACTTAG
1479219 AAATTATTTTATATTAATATTT
1 AAATTATTTTATATTAA-ATTT
* *
1479241 ATATTATATTATAATTAAATTT
1 AAATTATTTTAT-ATTAAATTT
* *
1479263 AAATAATTTTTTATTAAAT
1 AAATTATTTTATATTAAAT
1479282 AATAATTTCG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 7 0.21
22 22 0.65
23 5 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATTATTTTATATTAAATTT
Found at i:1480450 original size:2 final size:2
Alignment explanation
Indices: 1480443--1480499 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
1480433 ATATTATTAT
* *
1480443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TG TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1480484 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
1480500 AACTTCCATT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1480605 original size:2 final size:2
Alignment explanation
Indices: 1480598--1480630 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1480588 CATTCCAAAG
*
1480598 AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1480631 AATCAGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1483985 original size:25 final size:25
Alignment explanation
Indices: 1483957--1484040 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 25
1483947 ATTAAAAATC
1483957 TAAGTTGATAATAAATAATTATATT
1 TAAGTTGATAATAAATAATTATATT
* * * *
1483982 TAAG-TGATGATGAATTATTTCAGAAATT
1 TAAGTTGATAAT-AAATAATT---ATATT
*
1484010 TAAATTGATAATAAATAATTATATT
1 TAAGTTGATAATAAATAATTATATT
1484035 TAAGTT
1 TAAGTT
1484041 TTAATATATT
Statistics
Matches: 44, Mismatches: 10, Indels: 10
0.69 0.16 0.16
Matches are distributed among these distances:
24 6 0.14
25 19 0.43
28 13 0.30
29 6 0.14
ACGTcount: A:0.45, C:0.01, G:0.11, T:0.43
Consensus pattern (25 bp):
TAAGTTGATAATAAATAATTATATT
Found at i:1484340 original size:25 final size:24
Alignment explanation
Indices: 1484307--1484362 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
1484297 ATTTTATAAG
*
1484307 TTTATATTTGATATATTCATAATTTT
1 TTTA-ATTTGATATATT-ATAAATTT
* *
1484333 TTTAATTTTATATATTTTAAATTT
1 TTTAATTTGATATATTATAAATTT
1484357 TTTAAT
1 TTTAAT
1484363 ATATTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 12 0.44
25 11 0.41
26 4 0.15
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTAATTTGATATATTATAAATTT
Found at i:1484661 original size:3 final size:3
Alignment explanation
Indices: 1484653--1484697 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1484643 TATTTTTATC
1484653 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1484698 TGTTTCATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1484938 original size:9 final size:9
Alignment explanation
Indices: 1484924--1484954 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
1484914 AAAAATAATT
1484924 TTAAAATAA
1 TTAAAATAA
1484933 TTAAAATAA
1 TTAAAATAA
1484942 TTAAAATAA
1 TTAAAATAA
1484951 TTAA
1 TTAA
1484955 TATTAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TTAAAATAA
Found at i:1485075 original size:21 final size:21
Alignment explanation
Indices: 1485028--1485069 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1485018 ATAATTTAAA
*
1485028 ATTAAATTTGATTTAATTGTAT
1 ATTAAATTT-ATTTAATTATAT
*
1485050 ATTAAATTTATTTAGTTATA
1 ATTAAATTTATTTAATTATA
1485070 AGTTAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTAAATTTATTTAATTATAT
Found at i:1485668 original size:20 final size:19
Alignment explanation
Indices: 1485611--1485668 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 19
1485601 TTTAAATATA
1485611 TTTATATCATATT--TTATT
1 TTTATAT-ATATTAATTATT
*
1485629 TTCATATATATT-A-T-TT
1 TTTATATATATTAATTATT
1485645 TTTATATATATTTAATTATT
1 TTTATATATA-TTAATTATT
1485665 TTTA
1 TTTA
1485669 ATAATACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
16 11 0.33
17 8 0.24
18 7 0.21
19 1 0.03
20 6 0.18
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATATATATTAATTATT
Found at i:1485680 original size:20 final size:21
Alignment explanation
Indices: 1485638--1485680 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1485628 TTTCATATAT
* **
1485638 ATTATTTTTTATATATATTTA
1 ATTATTTTTAATATATACATA
1485659 ATTATTTTTAATA-ATACATA
1 ATTATTTTTAATATATACATA
1485679 AT
1 AT
1485681 GTATCATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTATTTTTAATATATACATA
Found at i:1485823 original size:24 final size:22
Alignment explanation
Indices: 1485789--1485841 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 22
1485779 TTTATTTTTT
*
1485789 TTATATCATAAATTATATTTAAA
1 TTATATAATAAATTATA-TTAAA
1485812 TTGATATAATAAATTATATTAAA
1 TT-ATATAATAAATTATATTAAA
1485835 TTATATA
1 TTATATA
1485842 TATTTATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 5 0.18
23 9 0.32
24 14 0.50
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TTATATAATAAATTATATTAAA
Found at i:1485834 original size:10 final size:10
Alignment explanation
Indices: 1485797--1485840 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 10
1485787 TTTTATATCA
1485797 TAAATTATATT
1 TAAATTATA-T
1485808 TAAATTGATAT
1 TAAATT-ATAT
1485819 AATAAATTATAT
1 --TAAATTATAT
1485831 TAAATTATAT
1 TAAATTATAT
1485841 ATATTTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.33
11 7 0.23
12 7 0.23
13 6 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (10 bp):
TAAATTATAT
Found at i:1485912 original size:28 final size:26
Alignment explanation
Indices: 1485830--1485915 Score: 100
Period size: 28 Copynumber: 3.2 Consensus size: 26
1485820 ATAAATTATA
1485830 TTAAATTATATATATTTATATAAATT
1 TTAAATTATATATATTTATATAAATT
* *
1485856 TTGAATATATATTTATATTATATAAATT
1 TTAAAT-TATATATAT-TTATATAAATT
* *
1485884 TTAAATTTTATACTATTTATATTATATT
1 TTAAATTATATA-TATTTATA-TAAATT
1485912 TTAA
1 TTAA
1485916 TTTAATTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
26 5 0.10
27 17 0.34
28 28 0.56
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (26 bp):
TTAAATTATATATATTTATATAAATT
Found at i:1486332 original size:29 final size:29
Alignment explanation
Indices: 1486299--1486361 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1486289 TATTTACAAT
1486299 AATAA-CTCTTAACTTGTAAATTATATCAA
1 AATAAGCTCTTAACTTG-AAATTATATCAA
* * * *
1486328 AATAAGTTTTTAACTTGAATTTATATTAA
1 AATAAGCTCTTAACTTGAAATTATATCAA
1486357 AATAA
1 AATAA
1486362 ATCATAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (29 bp):
AATAAGCTCTTAACTTGAAATTATATCAA
Found at i:1490123 original size:6 final size:6
Alignment explanation
Indices: 1490114--1490160 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
1490104 AAGTAATCTC
1490114 AAATTT AAATTTT AAACTGTT AAATTT -AATTT -AATTT AAATTT AAAT
1 AAATTT AAA-TTT AAA-T-TT AAATTT AAATTT AAATTT AAATTT AAAT
1490161 AATATATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 10 0.27
6 14 0.38
7 8 0.22
8 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:1490155 original size:11 final size:12
Alignment explanation
Indices: 1490114--1490160 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 12
1490104 AAGTAATCTC
1490114 AAATTTAAATTTT
1 AAATTTAAA-TTT
1490127 AAACTGTTAAATTT
1 AAA-T-TTAAATTT
1490141 -AATTT-AATTT
1 AAATTTAAATTT
1490151 AAATTTAAAT
1 AAATTTAAAT
1490161 AATATATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
10 5 0.17
11 7 0.23
12 4 0.13
13 5 0.17
14 4 0.13
15 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (12 bp):
AAATTTAAATTT
Found at i:1490413 original size:28 final size:29
Alignment explanation
Indices: 1490355--1490414 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
1490345 GAGTTAATTT
*
1490355 ATTTTAATATTAATATATTTTTATAATTAA
1 ATTTTAATA-TAAAATATTTTTATAATTAA
1490385 ATTTTAATA-AAAATATTTTTATTAA-TAA
1 ATTTTAATATAAAATATTTTTA-TAATTAA
1490413 AT
1 AT
1490415 AATAATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 16 0.57
29 3 0.11
30 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTTTAATATAAAATATTTTTATAATTAA
Found at i:1490426 original size:28 final size:28
Alignment explanation
Indices: 1490359--1490427 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
1490349 TAATTTATTT
**
1490359 TAATATTAATATATTTTTATAATTAAATTT
1 TAAT-TTAA-ATATTTTTATAATTAAATAA
**
1490389 TAATAAAAATATTTTTATTAA-TAAATAA
1 TAATTTAAATATTTTTA-TAATTAAATAA
1490417 TAATTTAAATA
1 TAATTTAAATA
1490428 AAATTAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
28 23 0.72
29 5 0.16
30 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TAATTTAAATATTTTTATAATTAAATAA
Found at i:1490467 original size:25 final size:25
Alignment explanation
Indices: 1490417--1490469 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
1490407 TAATAAATAA
*
1490417 TAATTTAAATAAAATTAATTTAATT
1 TAATTTAAATAAAATAAATTTAATT
1490442 TAATTTAAATTTAAAA-AAATTT-ATT
1 TAATTTAAA--TAAAATAAATTTAATT
1490467 TAA
1 TAA
1490470 GACTCGACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 15 0.60
26 5 0.20
27 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TAATTTAAATAAAATAAATTTAATT
Found at i:1490721 original size:48 final size:45
Alignment explanation
Indices: 1490645--1490747 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 45
1490635 CAGACCAATT
*
1490645 ATTTACATTT-TTTATATTATTTAAATTTATATAAGTA-T-TTTAAA
1 ATTTAAATTTATTTATATTATTTAAATTTATAT-AGTACTATTT-AA
*
1490689 ATTTAAATTTATTTATCATTTATATTAAATTTATATATTACTATTTAA
1 ATTTAAATTTATTTAT-A-TTAT-TTAAATTTATATAGTACTATTTAA
1490737 ATTTAAATTTA
1 ATTTAAATTTA
1490748 AATTAAATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
44 9 0.18
45 5 0.10
46 1 0.02
47 7 0.14
48 26 0.51
49 3 0.06
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (45 bp):
ATTTAAATTTATTTATATTATTTAAATTTATATAGTACTATTTAA
Found at i:1490742 original size:26 final size:25
Alignment explanation
Indices: 1490663--1490747 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 25
1490653 TTTTTATATT
*
1490663 ATTTAAATTTATATA-AGTATTTTAAA
1 ATTTAAATTTATATATACTA-TTT-AA
* *
1490689 ATTTAAATTTATTTAT-C-ATTTAT
1 ATTTAAATTTATATATACTATTTAA
1490712 A-TTAAATTTATATATTACTATTTAA
1 ATTTAAATTTATATA-TACTATTTAA
1490737 ATTTAAATTTA
1 ATTTAAATTTA
1490748 AATTAAATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
22 12 0.24
23 3 0.06
24 4 0.08
25 7 0.14
26 23 0.47
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (25 bp):
ATTTAAATTTATATATACTATTTAA
Found at i:1491222 original size:25 final size:25
Alignment explanation
Indices: 1491188--1491238 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1491178 TATAAAAAAA
*
1491188 TAAGAAAACATTTACAGACATTTCT
1 TAAGAAAACATTTACAAACATTTCT
*
1491213 TAAGAAAACATTTGCAAACATTTCT
1 TAAGAAAACATTTACAAACATTTCT
1491238 T
1 T
1491239 CTACTCATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (25 bp):
TAAGAAAACATTTACAAACATTTCT
Found at i:1491598 original size:19 final size:19
Alignment explanation
Indices: 1491555--1491600 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1491545 AATATCTTTA
*
1491555 ATATTTTTATTATACTTAT
1 ATATTTTTATTATACGTAT
1491574 ATTATTTTTATTAT-CGTAT
1 A-TATTTTTATTATACGTAT
1491593 CATATTTT
1 -ATATTTT
1491601 ATGTTATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (19 bp):
ATATTTTTATTATACGTAT
Found at i:1491665 original size:17 final size:18
Alignment explanation
Indices: 1491632--1491665 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1491622 TATATAATAT
1491632 TTATAGTTAATAATTATG
1 TTATAGTTAATAATTATG
*
1491650 TTATATTTAA-AATTAT
1 TTATAGTTAATAATTAT
1491666 TAAATATATG
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:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
TTATAGTTAATAATTATG
Found at i:1491821 original size:24 final size:24
Alignment explanation
Indices: 1491792--1491840 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1491782 ATATAATTTT
1491792 ATATATATAAATTTTAAAATTATTAA
1 ATATA-AT-AATTTTAAAATTATTAA
* *
1491818 ATATAATATTTTTAAAATAATTA
1 ATATAATAATTTTAAAATTATTA
1491841 TATAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 2 0.10
26 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATAATAATTTTAAAATTATTAA
Found at i:1491855 original size:22 final size:20
Alignment explanation
Indices: 1491795--1491848 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
1491785 TAATTTTATA
*
1491795 TATATAAATTTTAAAATTAT
1 TATATAAATTTTAAAATAAT
1491815 TAAATATAATATTTTTAAAATAAT
1 T--ATATAA-A-TTTTAAAATAAT
1491839 TATATAAATT
1 TATATAAATT
1491849 AATTAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
20 3 0.10
21 1 0.03
22 12 0.41
23 1 0.03
24 12 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATAAATTTTAAAATAAT
Found at i:1495502 original size:18 final size:18
Alignment explanation
Indices: 1495481--1495537 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
1495471 AGTCACATAC
* *
1495481 TTTTTAAAAATTTTAATT
1 TTTTTAAAAATTATAAAT
1495499 TTTTTAAAAATTATAAAT
1 TTTTTAAAAATTATAAAT
* *
1495517 TTTTCAAAAATCATTAAAT
1 TTTTTAAAAATTA-TAAAT
1495536 TT
1 TT
1495538 CTGTAGTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 27 0.79
19 7 0.21
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTTAAAAATTATAAAT
Found at i:1497542 original size:2 final size:2
Alignment explanation
Indices: 1497537--1497570 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1497527 TCTCTCTCTC
*
1497537 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1497571 AAGCAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1498506 original size:2 final size:2
Alignment explanation
Indices: 1498501--1498538 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1498491 ACACACACAC
*
1498501 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1498539 TTATTGGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1498927 original size:24 final size:24
Alignment explanation
Indices: 1498900--1498948 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1498890 ATAAATAAAT
* *
1498900 AAATAAATGAAGCCTTTTATTTGA
1 AAATAAAAGAAGCATTTTATTTGA
1498924 AAATAAAAGAAGCATTTTATTTGA
1 AAATAAAAGAAGCATTTTATTTGA
1498948 A
1 A
1498949 CCCTATAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (24 bp):
AAATAAAAGAAGCATTTTATTTGA
Found at i:1501165 original size:2 final size:2
Alignment explanation
Indices: 1501158--1501184 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1501148 GGAAGGGAGG
1501158 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 A
1501185 ATGGAATTTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1501728 original size:16 final size:16
Alignment explanation
Indices: 1501709--1501743 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1501699 AAAAAGTGAT
1501709 ATTTA-ATAAATATAAA
1 ATTTATATAAA-ATAAA
1501725 ATTTATATAAAATAAA
1 ATTTATATAAAATAAA
1501741 ATT
1 ATT
1501744 CGAAAGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTTATATAAAATAAA
Found at i:1506004 original size:16 final size:18
Alignment explanation
Indices: 1505985--1506017 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1505975 TTTTGACTGC
1505985 AATA-TATTTT-TTAAAT
1 AATATTATTTTGTTAAAT
1506001 AATATTATTTTGTTAAA
1 AATATTATTTTGTTAAA
1506018 ATTTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
AATATTATTTTGTTAAAT
Found at i:1506661 original size:2 final size:2
Alignment explanation
Indices: 1506654--1506694 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1506644 GAATTATCTG
1506654 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1506695 GACTTCTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1509053 original size:24 final size:25
Alignment explanation
Indices: 1509023--1509071 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
1509013 TTCACCCAAC
1509023 AAAAAATAT-TTCAATTTTT-TTTAA
1 AAAAAATATATT-AATTTTTATTTAA
1509047 AAAAAATATATTAATTTTTATTTAA
1 AAAAAATATATTAATTTTTATTTAA
1509072 TTTTATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAAAATATATTAATTTTTATTTAA
Found at i:1509897 original size:23 final size:24
Alignment explanation
Indices: 1509831--1509899 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 24
1509821 ATGGTGAATT
*
1509831 AAAATATAACATGAATACAACATAG
1 AAAA-ATAACATTAATACAACATAG
*
1509856 AAAAAT-A-ATTAAAACACAACAT-G
1 AAAAATAACATT--AATACAACATAG
*
1509879 AAAACTAACATTAATACAACA
1 AAAAATAACATTAATACAACA
1509900 CGAATAGTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
22 2 0.06
23 15 0.42
24 12 0.33
25 7 0.19
ACGTcount: A:0.62, C:0.14, G:0.04, T:0.19
Consensus pattern (24 bp):
AAAAATAACATTAATACAACATAG
Found at i:1510242 original size:5 final size:5
Alignment explanation
Indices: 1510192--1510284 Score: 53
Period size: 5 Copynumber: 17.8 Consensus size: 5
1510182 TACATAATTT
* * * * * *
1510192 TTTTC TATTTA TTTTC TTTTTT TTTTC TTTAC TTTAC TGTAC TTTTC TTTTTC
1 TTTTC T-TTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC
* * *
1510245 TTTTTC TTTCTC TTTCC TTTTC TTTTG ATTT- TTTTC TTTT
1 -TTTTC TTT-TC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1510285 TAAAAAATTA
Statistics
Matches: 70, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
4 3 0.04
5 43 0.61
6 24 0.34
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:1510260 original size:16 final size:16
Alignment explanation
Indices: 1510235--1510269 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1510225 TTACTGTACT
* *
1510235 TTTCTTTTTCTTTTTC
1 TTTCTCTTTCCTTTTC
1510251 TTTCTCTTTCCTTTTC
1 TTTCTCTTTCCTTTTC
1510267 TTT
1 TTT
1510270 TGATTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTCTTTCCTTTTC
Found at i:1514813 original size:13 final size:15
Alignment explanation
Indices: 1514781--1514811 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1514771 TCTTCTATAT
1514781 TATTTTTTAATAAAA
1 TATTTTTTAATAAAA
*
1514796 TATTTTTTAAAAAAA
1 TATTTTTTAATAAAA
1514811 T
1 T
1514812 TTATTCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTTTTAATAAAA
Found at i:1516400 original size:13 final size:13
Alignment explanation
Indices: 1516362--1516401 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
1516352 CCGAATTACT
1516362 ATTTAATAATAAA
1 ATTTAATAATAAA
*
1516375 ATTT-TTAATAAA
1 ATTTAATAATAAA
*
1516387 ATTTAATCATAAA
1 ATTTAATAATAAA
1516400 AT
1 AT
1516402 ATATAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTTAATAATAAA
Found at i:1516832 original size:2 final size:2
Alignment explanation
Indices: 1516825--1516851 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1516815 AGCAATGCAA
1516825 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 A
1516852 ATGTTTTAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1517542 original size:2 final size:2
Alignment explanation
Indices: 1517535--1517571 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1517525 CTCACAGTTA
1517535 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1517572 TTTAAAGCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1523346 original size:16 final size:17
Alignment explanation
Indices: 1523310--1523356 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
1523300 GCTTTATTTT
*
1523310 AATTAAATTTATTCA-TA
1 AATTAAATTTAAT-ATTA
1523327 AATTAAA-TTAATATTA
1 AATTAAATTTAATATTA
1523343 AATTAAATTTAATA
1 AATTAAATTTAATA
1523357 ATCAATCGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 1 0.04
16 13 0.48
17 13 0.48
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTAAATTTAATATTA
Found at i:1525189 original size:18 final size:19
Alignment explanation
Indices: 1525163--1525221 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 19
1525153 TATTTTAATA
*
1525163 TAATTAATA-AATTATATT
1 TAATAAATATAATTATATT
1525181 TAATAAATATATAATTATATT
1 TAAT-AA-ATATAATTATATT
*
1525202 TAA-AAATTTTAA-TATATT
1 TAATAAA-TATAATTATATT
1525220 TA
1 TA
1525222 TATTTACCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
18 13 0.37
19 7 0.20
20 3 0.09
21 12 0.34
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAAATATAATTATATT
Found at i:1525196 original size:21 final size:19
Alignment explanation
Indices: 1525172--1525221 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 19
1525162 ATAATTAATA
1525172 AATTATATTTAATAAATATAT
1 AATTATATTTAA-AAAT-TAT
*
1525193 AATTATATTTAAAAATTTT
1 AATTATATTTAAAAATTAT
1525212 AA-TATATTTA
1 AATTATATTTA
1525222 TATTTACCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 8 0.29
19 4 0.14
20 4 0.14
21 12 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTATATTTAAAAATTAT
Found at i:1525445 original size:35 final size:36
Alignment explanation
Indices: 1525401--1525471 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 36
1525391 AAATTATTTT
* *
1525401 ATATCAATATTTATATATTA-TATAAT-TTAATTTAA
1 ATATAAATATTTATAAATTATTA-AATATTAATTTAA
*
1525436 ATATAAATATTTTTAAATTATTAAATATTAATTTAA
1 ATATAAATATTTATAAATTATTAAATATTAATTTAA
1525472 TTTAAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (36 bp):
ATATAAATATTTATAAATTATTAAATATTAATTTAA
Found at i:1525462 original size:18 final size:16
Alignment explanation
Indices: 1525431--1525464 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
1525421 TATAATTTAA
1525431 TTTAAATATAAATATT
1 TTTAAATATAAATATT
1525447 TTTAAATTATTAAATATT
1 TTTAAA-TA-TAAATATT
1525465 AATTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAATATAAATATT
Found at i:1525476 original size:10 final size:10
Alignment explanation
Indices: 1525447--1525495 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
1525437 TATAAATATT
1525447 TTTAAATT-A
1 TTTAAATTAA
*
1525456 TTAAATATTAA
1 TTTAA-ATTAA
*
1525467 TTTAATTTAA
1 TTTAAATTAA
*
1525477 ATTAAATTAA
1 TTTAAATTAA
1525487 TTTAAATTA
1 TTTAAATTA
1525496 TAAAAATACA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
9 4 0.12
10 23 0.72
11 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TTTAAATTAA
Found at i:1525480 original size:15 final size:15
Alignment explanation
Indices: 1525448--1525495 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
1525438 ATAAATATTT
*
1525448 TTAAATT-ATTAAATA
1 TTAAATTAATTTAA-A
*
1525463 TTAATTTAATTTAAA
1 TTAAATTAATTTAAA
1525478 TTAAATTAATTTAAA
1 TTAAATTAATTTAAA
1525493 TTA
1 TTA
1525496 TAAAAATACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAAATTAATTTAAA
Found at i:1525503 original size:41 final size:41
Alignment explanation
Indices: 1525423--1525500 Score: 115
Period size: 40 Copynumber: 1.9 Consensus size: 41
1525413 ATATATTATA
* *
1525423 TAATTTAATTTAAATATAAATATTTTTAAATTATTAAATAT
1 TAATTTAATTTAAATATAAATATATTTAAATTATAAAATAT
1525464 TAATTTAATTTAAAT-TAAAT-TAATTTAAATTATAAAA
1 TAATTTAATTTAAATATAAATAT-ATTTAAATTATAAAA
1525501 ATACATAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 1 0.03
40 18 0.53
41 15 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (41 bp):
TAATTTAATTTAAATATAAATATATTTAAATTATAAAATAT
Found at i:1525705 original size:22 final size:22
Alignment explanation
Indices: 1525687--1525735 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1525677 AAAATAAATT
* *
1525687 TAATTTTATTATTATATAAAAA
1 TAATTATATTAATATATAAAAA
*
1525709 TAATTATATTAATATATAATAA
1 TAATTATATTAATATATAAAAA
1525731 -AATTA
1 TAATTA
1525736 AAATTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATTATATTAATATATAAAAA
Found at i:1525741 original size:22 final size:22
Alignment explanation
Indices: 1525694--1525742 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1525684 ATTTAATTTT
* *
1525694 ATTATTATATAAAAATAATTAT
1 ATTAATATATAAAAATAATTAA
*
1525716 ATTAATATATAATAA-AATTAAA
1 ATTAATATATAAAAATAATT-AA
1525738 ATTAA
1 ATTAA
1525743 AAAATTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATATATAAAAATAATTAA
Found at i:1525771 original size:17 final size:17
Alignment explanation
Indices: 1525751--1525785 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1525741 AAAAAATTAT
*
1525751 TAATTTAATCAATTTAA
1 TAATTAAATCAATTTAA
*
1525768 TAATTAAATTAATTTAA
1 TAATTAAATCAATTTAA
1525785 T
1 T
1525786 TTAATAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTAAATCAATTTAA
Found at i:1525786 original size:9 final size:9
Alignment explanation
Indices: 1525749--1525786 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1525739 TTAAAAAATT
1525749 ATTAATTTA
1 ATTAATTTA
*
1525758 ATCAATTTA
1 ATTAATTTA
*
1525767 A-TAATTAA
1 ATTAATTTA
1525775 ATTAATTTA
1 ATTAATTTA
1525784 ATT
1 ATT
1525787 TAATAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
8 6 0.25
9 18 0.75
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (9 bp):
ATTAATTTA
Found at i:1525848 original size:12 final size:13
Alignment explanation
Indices: 1525831--1525876 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
1525821 CACTCTAATA
1525831 ATTTATTTATT-T
1 ATTTATTTATTAT
1525843 ATTTATATTATATTAT
1 A-TT-TATT-TATTAT
1525859 ATTTATTT-TTAT
1 ATTTATTTATTAT
1525871 ATTTAT
1 ATTTAT
1525877 ATAATTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 11 0.37
13 3 0.10
14 8 0.27
15 6 0.20
16 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTTATTTATTAT
Found at i:1525864 original size:6 final size:6
Alignment explanation
Indices: 1525842--1525878 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1525832 TTTATTTATT
*
1525842 TATTTA TA-TTA TA-TTA TATTTA TTTTTA TATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TAT
1525879 AATTTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:1528897 original size:20 final size:20
Alignment explanation
Indices: 1528872--1528911 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1528862 TTCCTAGGTC
1528872 GACTTGTTATTATTAATTAA
1 GACTTGTTATTATTAATTAA
1528892 GACTTGTTATTATTAATTAA
1 GACTTGTTATTATTAATTAA
1528912 TAAAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (20 bp):
GACTTGTTATTATTAATTAA
Found at i:1530316 original size:14 final size:15
Alignment explanation
Indices: 1530297--1530325 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1530287 TTCAGTTGAT
1530297 TGTCTGGTT-CTTGG
1 TGTCTGGTTACTTGG
1530311 TGTCTGGTTACTTGG
1 TGTCTGGTTACTTGG
1530326 AAGGTCCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.03, C:0.14, G:0.34, T:0.48
Consensus pattern (15 bp):
TGTCTGGTTACTTGG
Found at i:1531798 original size:18 final size:18
Alignment explanation
Indices: 1531775--1531835 Score: 86
Period size: 18 Copynumber: 3.3 Consensus size: 18
1531765 TTCAAAATAA
1531775 TATTAAAATTTTATTTTT
1 TATTAAAATTTTATTTTT
* * *
1531793 TATTAATATTATATATTTA
1 TATTAAAATTTTAT-TTTT
1531812 TATTAAAATTTTATTTTT
1 TATTAAAATTTTATTTTT
1531830 TATTAA
1 TATTAA
1531836 TATTATATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
18 21 0.58
19 15 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTAAAATTTTATTTTT
Found at i:1531816 original size:37 final size:37
Alignment explanation
Indices: 1531774--1531855 Score: 155
Period size: 37 Copynumber: 2.2 Consensus size: 37
1531764 ATTCAAAATA
1531774 ATATTAAAATTTTATTTTTTATTAATATTATATATTT
1 ATATTAAAATTTTATTTTTTATTAATATTATATATTT
1531811 ATATTAAAATTTTATTTTTTATTAATATTATATATTT
1 ATATTAAAATTTTATTTTTTATTAATATTATATATTT
*
1531848 ATTTTAAA
1 ATATTAAA
1531856 TAAAATTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (37 bp):
ATATTAAAATTTTATTTTTTATTAATATTATATATTT
Found at i:1531865 original size:35 final size:37
Alignment explanation
Indices: 1531774--1531875 Score: 118
Period size: 37 Copynumber: 2.8 Consensus size: 37
1531764 ATTCAAAATA
** *
1531774 ATATTAAAATTTTATTTTTTATTAATATTATATATTT
1 ATATTAAAATTAAAATTTTTATTAATATTATATATTT
** *
1531811 ATATTAAAATTTTATTTTTTATTAATATTATATATTT
1 ATATTAAAATTAAAATTTTTATTAATATTATATATTT
* *
1531848 AT-TTTAAA-TAAAATTTTTATTATTATTA
1 ATATTAAAATTAAAATTTTTATTAATATTA
1531876 ATTTGAATCG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 16 0.27
36 5 0.08
37 39 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (37 bp):
ATATTAAAATTAAAATTTTTATTAATATTATATATTT
Found at i:1532110 original size:22 final size:21
Alignment explanation
Indices: 1532064--1532117 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
1532054 ATTTAACCCG
*
1532064 TTTTAAA-TT-ATTATATTTT
1 TTTTAAATTTAATTATAATTT
1532083 TATTTAAATTTAATTATAAATTT
1 T-TTTAAATTTAATTAT-AATTT
*
1532106 TTTTATATTTAA
1 TTTTAAATTTAA
1532118 AATTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 1 0.03
20 6 0.21
21 2 0.07
22 15 0.52
23 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAAATTTAATTATAATTT
Found at i:1537424 original size:12 final size:11
Alignment explanation
Indices: 1537409--1537516 Score: 85
Period size: 12 Copynumber: 9.3 Consensus size: 11
1537399 ATTGCTATTA
1537409 TAAATTGAAAAT
1 TAAATT-AAAAT
1537421 TAAATT-AAAT
1 TAAATTAAAAT
1537431 TAAATATATTAAAT
1 TAAAT-TA--AAAT
*
1537445 TAATATTCAAAT
1 TAA-ATTAAAAT
1537457 TAAAATTAAAAT
1 T-AAATTAAAAT
1537469 TAAAATT-AAAT
1 T-AAATTAAAAT
*
1537480 TAAATAAAAAT
1 TAAATTAAAAT
* *
1537491 TTAATAAAAAT
1 TAAATTAAAAT
*
1537502 TAAATCAAATAT
1 TAAATTAAA-AT
1537514 TAA
1 TAA
1537517 TCGATTTTTT
Statistics
Matches: 82, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
10 13 0.16
11 27 0.33
12 30 0.37
13 2 0.02
14 8 0.10
15 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (11 bp):
TAAATTAAAAT
Found at i:1537427 original size:5 final size:5
Alignment explanation
Indices: 1537417--1537484 Score: 75
Period size: 5 Copynumber: 12.8 Consensus size: 5
1537407 TATAAATTGA
*
1537417 AAATT AAATT AAATT AAA-T ATATT AAATT AATATT CAAATT AAAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AA-ATT -AAATT -AAATT
1537464 AAAATT AAAATT AAATT AAAT
1 -AAATT -AAATT AAATT AAAT
1537485 AAAAATTTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
4 3 0.05
5 29 0.51
6 23 0.40
7 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:1537464 original size:6 final size:6
Alignment explanation
Indices: 1537405--1537505 Score: 77
Period size: 6 Copynumber: 17.0 Consensus size: 6
1537395 AATAATTGCT
* * *
1537405 ATTATAA ATTGAAA ATT-AA ATT-AA ATTAAA TATATTAA ATTAAT ATTCAA
1 ATTA-AA ATT-AAA ATTAAA ATTAAA ATTAAA -AT-TAAA ATTAAA ATTAAA
* * *
1537455 ATTAAA ATTAAA ATTAAA ATT-AA ATT-AA ATAAAA ATT-TA ATAAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1537500 ATTAAA
1 ATTAAA
1537506 TCAAATATTA
Statistics
Matches: 76, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
5 22 0.29
6 38 0.50
7 12 0.16
8 4 0.05
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (6 bp):
ATTAAA
Found at i:1537464 original size:18 final size:17
Alignment explanation
Indices: 1537405--1537505 Score: 89
Period size: 17 Copynumber: 5.7 Consensus size: 17
1537395 AATAATTGCT
1537405 ATTATAAATTGAAAATTAA
1 ATTA-AAATT-AAAATTAA
1537424 ATT-AAATTAAATATATTAA
1 ATTAAAATT-AA-A-ATTAA
* *
1537443 ATTAATATTCAAATTAAA
1 ATTAAAATTAAAATT-AA
1537461 ATTAAAATTAAAATTAA
1 ATTAAAATTAAAATTAA
* *
1537478 ATT-AAATAAAAATTTA
1 ATTAAAATTAAAATTAA
*
1537494 ATAAAAATTAAA
1 ATTAAAATTAAA
1537506 TCAAATATTA
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
16 13 0.19
17 22 0.32
18 17 0.25
19 12 0.18
20 4 0.06
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (17 bp):
ATTAAAATTAAAATTAA
Found at i:1539858 original size:82 final size:82
Alignment explanation
Indices: 1539758--1540161 Score: 551
Period size: 82 Copynumber: 4.9 Consensus size: 82
1539748 CTACCTTGTA
* * * *
1539758 CCACATAAATTACCAAGTTTCACATCACAAAACTTGACCCTTAATTCAATTCTTAACATCGAAAA
1 CCACAGAAATTACCAAGTTCCACAGCACAAAACTTGACCCTTAATTCAATTCTCAACATCGAAAA
* *
1539823 CCTCGAAGTAACAGTTT
66 CCTCAAAGCAACAGTTT
* * *
1539840 CCACAGAAACTACCAAGTTTCCACAGCACAAAACTTGACCATCAATTCAATTCTCAACATC-AAA
1 CCACAGAAATTACCAAG-TTCCACAGCACAAAACTTGACCCTTAATTCAATTCTCAACATCGAAA
**
1539904 ACCTCAAAGCAATGGTTT
65 ACCTCAAAGCAACAGTTT
* * * * *
1539922 CAACGGAAATTACCAAGTTCCACAGCACAAAACTTGACCCTTAATTCATTTCTTAACATCGGAAA
1 CCACAGAAATTACCAAGTTCCACAGCACAAAACTTGACCCTTAATTCAATTCTCAACATCGAAAA
1539987 CCTCAAAGCAACAGTTT
66 CCTCAAAGCAACAGTTT
* * * *
1540004 CCACAGAAACTACCATGTTCCACAGCACAAAACTTGACCCTTGATTCAATTGTCAACATCGAAAA
1 CCACAGAAATTACCAAGTTCCACAGCACAAAACTTGACCCTTAATTCAATTCTCAACATCGAAAA
*
1540069 CCTCGAAGCAACAGTTT
66 CCTCAAAGCAACAGTTT
* * *
1540086 CAACAGAAATTAGCAAGTTCCACAGCACAAAACTTGACCC-TAATTTCAATTCTCAGCATCGAAA
1 CCACAGAAATTACCAAGTTCCACAGCACAAAACTTGACCCTTAA-TTCAATTCTCAACATCGAAA
*
1540150 ACCACAAAGCAA
65 ACCTCAAAGCAA
1540162 TGGTTTTCCA
Statistics
Matches: 279, Mismatches: 40, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
81 41 0.15
82 200 0.72
83 38 0.14
ACGTcount: A:0.39, C:0.28, G:0.10, T:0.23
Consensus pattern (82 bp):
CCACAGAAATTACCAAGTTCCACAGCACAAAACTTGACCCTTAATTCAATTCTCAACATCGAAAA
CCTCAAAGCAACAGTTT
Found at i:1547186 original size:2 final size:2
Alignment explanation
Indices: 1547179--1547217 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1547169 CCTCCTCAAT
* *
1547179 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1547218 TTACCCAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:1547469 original size:20 final size:20
Alignment explanation
Indices: 1547433--1547499 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
1547423 TTACGCTTTG
* *
1547433 ATTTA-ATTTTTAGTTTAAT
1 ATTTATATTTATATTTTAAT
1547452 ATTTATATTTATATTTT-AT
1 ATTTATATTTATATTTTAAT
* *
1547471 CATATATATTAATATTTTAA-
1 -ATTTATATTTATATTTTAAT
*
1547491 ATTAATATT
1 ATTTATATT
1547500 ATTAGTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 14 0.36
20 24 0.62
21 1 0.03
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (20 bp):
ATTTATATTTATATTTTAAT
Found at i:1548017 original size:18 final size:17
Alignment explanation
Indices: 1547994--1548073 Score: 63
Period size: 18 Copynumber: 4.4 Consensus size: 17
1547984 TGTATTGAAA
1547994 TTAATATAATATAAATT
1 TTAATATAATATAAATT
*
1548011 GTTAATATATTA-AAATT
1 -TTAATATAATATAAATT
*
1548028 TATATAAATATATATAATATT
1 T-TA-ATATA-ATATAA-ATT
1548049 TTAAATATAATTATAAATT
1 TT-AATATAA-TATAAATT
*
1548068 ATAATA
1 TTAATA
1548074 GGTAATATGA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
16 1 0.02
17 7 0.14
18 18 0.36
19 7 0.14
20 12 0.24
21 5 0.10
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (17 bp):
TTAATATAATATAAATT
Found at i:1548070 original size:29 final size:29
Alignment explanation
Indices: 1547996--1548070 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
1547986 TATTGAAATT
*
1547996 AATATAA-TATAAATTGT-TAATATATTA
1 AATATAATTATAAATTATATAATATATTA
* *
1548023 AA-AT-TTATATAAATATATATAATATTTTA
1 AATATAAT-TATAAAT-TATATAATATATTA
1548052 AATATAATTATAAATTATA
1 AATATAATTATAAATTATA
1548071 ATAGGTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
26 2 0.05
27 9 0.24
28 2 0.05
29 15 0.39
30 9 0.24
31 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (29 bp):
AATATAATTATAAATTATATAATATATTA
Found at i:1548516 original size:5 final size:5
Alignment explanation
Indices: 1548501--1548541 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
1548491 TATAAATTGA
* * *
1548501 TTAAA TTAAT TAAAT TAAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
1548542 GATCAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
TTAAT
Found at i:1548995 original size:3 final size:3
Alignment explanation
Indices: 1548987--1549023 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1548977 TCCCTCACTA
*
1548987 TCT TCT TCT TCT TCT TCT TCT TCG TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1549024 GTAGTGATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:1550963 original size:19 final size:19
Alignment explanation
Indices: 1550936--1550995 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
1550926 AGGATAAGTA
*
1550936 TTATATAAATATATATTTT
1 TTATTTAAATATATATTTT
*
1550955 TTATTTAAAT-T-TTTTTT
1 TTATTTAAATATATATTTT
*
1550972 ATGTATTTAAAGATTATATTTT
1 -T-TATTTAAATA-TATATTTT
1550994 TT
1 TT
1550996 TAATTGAGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
17 5 0.16
18 2 0.06
19 17 0.53
20 1 0.03
21 2 0.06
22 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TTATTTAAATATATATTTT
Found at i:1552727 original size:2 final size:2
Alignment explanation
Indices: 1552720--1552746 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1552710 TCATTTTATG
1552720 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 A
1552747 GTTAATGTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1553332 original size:14 final size:14
Alignment explanation
Indices: 1553313--1553343 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1553303 TAAATAAAAA
1553313 AAATATAATTTTTT
1 AAATATAATTTTTT
1553327 AAATATAATTTTTT
1 AAATATAATTTTTT
1553341 AAA
1 AAA
1553344 AAATTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATATAATTTTTT
Found at i:1556402 original size:32 final size:33
Alignment explanation
Indices: 1556361--1556436 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
1556351 AAAACTGTCG
*
1556361 TATATTTATATAAA-TTTAAATATATTTAT-AATT
1 TATA-TTATATAAATTTTAAA-AAATTTATGAATT
* *
1556394 TATATTATACAAATTTTAAAAAATTTATGTATT
1 TATATTATATAAATTTTAAAAAATTTATGAATT
*
1556427 CATATTATAT
1 TATATTATAT
1556437 TAGTATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
32 15 0.42
33 21 0.58
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (33 bp):
TATATTATATAAATTTTAAAAAATTTATGAATT
Found at i:1562427 original size:37 final size:37
Alignment explanation
Indices: 1562386--1562556 Score: 96
Period size: 37 Copynumber: 4.8 Consensus size: 37
1562376 ATTTAAAGAG
1562386 TTAAATTAATTTATTTAAATTAAATTAAATTAAATTT
1 TTAAATTAATTTATTTAAATTAAATTAAATTAAATTT
* * *
1562423 TT-AA--AATAT-TTTAAATTTAAATT-ATTTTAATTT
1 TTAAATTAATTTATTTAAA-TTAAATTAAATTAAATTT
* *
1562456 TT-AATTAATTAGATTTATCATTTAAATT-AATTAAA--T
1 TTAAATTAATT-TATTTA--AATTAAATTAAATTAAATTT
* * *
1562492 TTAAATT-ATTTAAATTTAAATT-AATTAAGTTTAATAT
1 TTAAATTAATTT--ATTTAAATTAAATTAAATTAAATTT
* * *
1562529 TTAATTTAATTAAATTTAAGTT-AATTAA
1 TTAAATTAATT-TATTTAAATTAAATTAA
1562557 TTTATATTCA
Statistics
Matches: 104, Mismatches: 15, Indels: 30
0.70 0.10 0.20
Matches are distributed among these distances:
33 18 0.17
34 15 0.14
35 11 0.11
36 8 0.08
37 36 0.35
38 15 0.14
39 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.52
Consensus pattern (37 bp):
TTAAATTAATTTATTTAAATTAAATTAAATTAAATTT
Found at i:1562454 original size:15 final size:15
Alignment explanation
Indices: 1562422--1562679 Score: 93
Period size: 15 Copynumber: 16.6 Consensus size: 15
1562412 AAATTAAATT
*
1562422 TTTAAAATATTTTAAA
1 TTTAAATTATTTT-AA
1562438 TTTAAATTATTTTAA
1 TTTAAATTATTTTAA
*
1562453 TTTTTAATTAATTAGATTTATCA
1 --TTT-A--AATT--ATTT-TAA
* *
1562476 TTTAAATTAATTAAA
1 TTTAAATTATTTTAA
*
1562491 TTTAAATTATTTAAA
1 TTTAAATTATTTTAA
*
1562506 TTTAAATTA-ATTAA
1 TTTAAATTATTTTAA
1562520 GTTT-AA-TA-TTTAA
1 -TTTAAATTATTTTAA
*
1562533 TTT-AATTAAATTTAA
1 TTTAAATT-ATTTTAA
* *
1562548 GTT-AATTAATTTATA
1 TTTAAATTATTTTA-A
* *
1562563 TTCAAATT-TATTAA
1 TTTAAATTATTTTAA
* * *
1562577 GATTAAA-TATTTGAG
1 -TTTAAATTATTTTAA
* *
1562592 TGTAAATTATTTTGAG
1 TTTAAATTATTTT-AA
* * * *
1562608 TGTGAACTACTTTATA
1 TTTAAATTATTTTA-A
*
1562624 TTTGAATTATTTTAAA
1 TTTAAATTATTTT-AA
*
1562640 TTTAAATTATTTTTTA
1 TTTAAATTA-TTTTAA
1562656 TTT-AATTATTTTAAA
1 TTTAAATTATTTT-AA
1562671 TTTAAATTA
1 TTTAAATTA
1562680 ATTGACTTCA
Statistics
Matches: 187, Mismatches: 32, Indels: 46
0.71 0.12 0.17
Matches are distributed among these distances:
12 5 0.03
13 7 0.04
14 22 0.12
15 67 0.36
16 59 0.32
17 8 0.04
18 5 0.03
20 5 0.03
21 3 0.02
22 4 0.02
23 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (15 bp):
TTTAAATTATTTTAA
Found at i:1562459 original size:23 final size:23
Alignment explanation
Indices: 1562386--1562445 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
1562376 ATTTAAAGAG
* * **
1562386 TTAAATTAATTTATTTAAATTAAA
1 TTAAATTAAATT-TTTAAAATATT
1562410 TTAAATTAAATTTTTAAAATATT
1 TTAAATTAAATTTTTAAAATATT
1562433 TTAAATTTAAATT
1 TTAAA-TTAAATT
1562446 ATTTTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAAATTAAATTTTTAAAATATT
Found at i:1562461 original size:16 final size:16
Alignment explanation
Indices: 1562418--1562462 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1562408 AATTAAATTA
*
1562418 AATTTTTAAAATATTTT
1 AATTTTT-AATTATTTT
* *
1562435 AAATTTAAATTATTTT
1 AATTTTTAATTATTTT
1562451 AATTTTTAATTA
1 AATTTTTAATTA
1562463 ATTAGATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTTTAATTATTTT
Found at i:1562471 original size:22 final size:22
Alignment explanation
Indices: 1562446--1562545 Score: 58
Period size: 22 Copynumber: 4.2 Consensus size: 22
1562436 AATTTAAATT
*
1562446 ATTTTAATTTTTAATTAATTAG
1 ATTTTAATTTTTAATTAATTAA
* *
1562468 ATTTATCA-TTTAAATTAATTAA
1 ATTT-TAATTTTTAATTAATTAA
*
1562490 ATTTAAATTATTTAAATTTAAATTAATTA
1 ATTTTAATT-TTT-AA-TT-AATT-A--A
* *
1562519 AGTTTAATATTTAATTTAATTAA
1 ATTTTAATTTTTAA-TTAATTAA
1562542 ATTT
1 ATTT
1562546 AAGTTAATTA
Statistics
Matches: 59, Mismatches: 10, Indels: 17
0.69 0.12 0.20
Matches are distributed among these distances:
21 1 0.02
22 21 0.36
23 8 0.14
24 2 0.03
25 3 0.05
26 8 0.14
27 6 0.10
28 3 0.05
29 7 0.12
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTTTAATTTTTAATTAATTAA
Found at i:1562512 original size:21 final size:24
Alignment explanation
Indices: 1562427--1562547 Score: 55
Period size: 22 Copynumber: 5.1 Consensus size: 24
1562417 AAATTTTTAA
*
1562427 AATATTTTAAATTTAAATT-ATTTT
1 AATA-TTTAAATTTAAATTAAGTTT
*
1562451 AAT-TTTTAA-TT-AATT-AGATTT
1 AATATTTAAATTTAAATTAAG-TTT
*
1562472 -ATCATTTAAA-TT-AATTAAATTT
1 AAT-ATTTAAATTTAAATTAAGTTT
1562494 AAATTATTTAAATTTAAATTAATTAAGTTT
1 -AA-TATTTAAATTT--A--AATTAAGTTT
*
1562524 AATATTT-AATTT-AATTAAATTT
1 AATATTTAAATTTAAATTAAGTTT
1562546 AA
1 AA
1562548 GTTAATTAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
20 7 0.09
21 5 0.06
22 30 0.38
23 1 0.01
24 11 0.14
25 3 0.04
27 5 0.06
28 5 0.06
29 2 0.03
30 9 0.12
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (24 bp):
AATATTTAAATTTAAATTAAGTTT
Found at i:1562576 original size:57 final size:53
Alignment explanation
Indices: 1562386--1562588 Score: 157
Period size: 52 Copynumber: 3.8 Consensus size: 53
1562376 ATTTAAAGAG
* * * *
1562386 TTAAATTAATTT--ATTTAAATTAAATTAA-ATTAAATTTTTAAAATATTTTAAAT
1 TTAAATT-ATTTAAATTCAAATT-AATTAAGATTAAATATTTAAATTA-ATTAAAT
* ** *
1562439 TTAAATTATTTTAATTTTTAATTAATT-AGATT-TATCATTTAAATTAATTAAAT
1 TTAAATTA-TTTAAATTCAAATTAATTAAGATTAAAT-ATTTAAATTAATTAAAT
* * *
1562492 TTAAATTATTTAAATTTAAATTAATTAAG-TTTAATATTTAATTTAATTAAAT
1 TTAAATTATTTAAATTCAAATTAATTAAGATTAAATATTTAAATTAATTAAAT
* *
1562544 TTAAGTTAATTAATTTATATTCAAATTTATTAAGATTAAATATTT
1 TT-A---AATT-ATTTAAATTCAAATTAATTAAGATTAAATATTT
1562589 GAGTGTAAAT
Statistics
Matches: 123, Mismatches: 14, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
52 37 0.30
53 32 0.26
54 15 0.12
55 7 0.06
56 4 0.03
57 19 0.15
58 9 0.07
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (53 bp):
TTAAATTATTTAAATTCAAATTAATTAAGATTAAATATTTAAATTAATTAAAT
Found at i:1562637 original size:16 final size:16
Alignment explanation
Indices: 1562618--1562679 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
1562608 TGTGAACTAC
* *
1562618 TTTATATTTGAATTAT
1 TTTAAATTTAAATTAT
1562634 TTTAAATTTAAATTAT
1 TTTAAATTTAAATTAT
**
1562650 TTTTTATTT-AATTAT
1 TTTAAATTTAAATTAT
1562665 TTTAAATTTAAATTA
1 TTTAAATTTAAATTA
1562680 ATTGACTTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
15 13 0.33
16 26 0.67
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTAAATTTAAATTAT
Found at i:1562694 original size:31 final size:30
Alignment explanation
Indices: 1562628--1562696 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
1562618 TTTATATTTG
* * *
1562628 AATTATTTTAAATTTAAATTATTTTTTATTT
1 AATTATTTTAAATTTAAATTA-TATTGATTA
1562659 AATTATTTTAAATTTAAATTA-ATTGACTTCA
1 AATTATTTTAAATTTAAATTATATTGA-TT-A
1562690 AATTATT
1 AATTATT
1562697 AATTTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 3 0.09
30 2 0.06
31 28 0.85
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (30 bp):
AATTATTTTAAATTTAAATTATATTGATTA
Found at i:1563535 original size:9 final size:9
Alignment explanation
Indices: 1563523--1563548 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1563513 TAATATAATG
1563523 TATATTTAA
1 TATATTTAA
1563532 TATATTTAA
1 TATATTTAA
1563541 TATATTTA
1 TATATTTA
1563549 TTAAAAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TATATTTAA
Found at i:1567678 original size:13 final size:13
Alignment explanation
Indices: 1567660--1567684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1567650 ATGTGCAAAG
1567660 CATGACTGAGTCA
1 CATGACTGAGTCA
1567673 CATGACTGAGTC
1 CATGACTGAGTC
1567685 CGAGTCTATT
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:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (13 bp):
CATGACTGAGTCA
Found at i:1569310 original size:20 final size:21
Alignment explanation
Indices: 1569285--1569325 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1569275 TATTTAAATT
*
1569285 TTAATTATATTAAAT-ATTAA
1 TTAATTATATAAAATAATTAA
*
1569305 TTAATTTTATAAAATAATTAA
1 TTAATTATATAAAATAATTAA
1569326 ATTATTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATTATATAAAATAATTAA
Found at i:1569482 original size:14 final size:16
Alignment explanation
Indices: 1569462--1569504 Score: 63
Period size: 14 Copynumber: 2.8 Consensus size: 16
1569452 TTATTAAAAA
1569462 ATTAAATTTTAAT-AT
1 ATTAAATTTTAATCAT
1569477 -TTAAATTTTAATCAT
1 ATTAAATTTTAATCAT
*
1569492 ATTAAATATTAAT
1 ATTAAATTTTAAT
1569505 TGATTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 12 0.48
15 2 0.08
16 11 0.44
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTAAATTTTAATCAT
Found at i:1569636 original size:198 final size:200
Alignment explanation
Indices: 1569256--1569657 Score: 673
Period size: 198 Copynumber: 2.0 Consensus size: 200
1569246 CTTTTTATCA
* * *
1569256 TAAAAATTATAAATATTAATATTTAAATTTTAATTATATTAAATATTAATTAATTTTATAAAATA
1 TAAAAAATATAAATATTAATATTTAAATTTTAATCATATTAAATATTAATTAATTATATAAAATA
* *
1569321 ATTAAATTATTTAATTTTTACGAAATTAAAAAATTTTGATTTTAATATATTTAATTAATATCAAA
66 ATTAAATTATTTAATTTTTACGAAATTAAAAAATATTAATTTTAATATATTTAATTAATATCAAA
1569386 ATTTTAATTTTTAATAAAATTAATGTTCATTGGTTTTAATATCAAAATATAAAAAATCATAAAAA
131 ATTTTAATTTTTAATAAAATTAATGTTCATTGGTTTTAATATCAAAATATAAAAAATCATAAAAA
1569451 ATTAT
196 ATTAT
* *
1569456 TAAAAAAT-TAAATTTTAATATTTAAATTTTAATCATATTAAATATTAATTGATTATATAAAATA
1 TAAAAAATATAAATATTAATATTTAAATTTTAATCATATTAAATATTAATTAATTATATAAAATA
** * *
1569520 ATTAAATTATTTAATTTTTGTGAAGTTAAAAAA-ATTAATTTTAATATATTTAATTAATATGAAA
66 ATTAAATTATTTAATTTTTACGAAATTAAAAAATATTAATTTTAATATATTTAATTAATATCAAA
* *
1569584 ATTTTAATTTTTAATAAAATTGATGTTCGTTGGTTTTAATATCAAAATATAAAAAATCATAAAAA
131 ATTTTAATTTTTAATAAAATTAATGTTCATTGGTTTTAATATCAAAATATAAAAAATCATAAAAA
1569649 ATTAT
196 ATTAT
1569654 TAAA
1 TAAA
1569658 TTTTTTTTTT
Statistics
Matches: 189, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
198 100 0.53
199 82 0.43
200 7 0.04
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (200 bp):
TAAAAAATATAAATATTAATATTTAAATTTTAATCATATTAAATATTAATTAATTATATAAAATA
ATTAAATTATTTAATTTTTACGAAATTAAAAAATATTAATTTTAATATATTTAATTAATATCAAA
ATTTTAATTTTTAATAAAATTAATGTTCATTGGTTTTAATATCAAAATATAAAAAATCATAAAAA
ATTAT
Found at i:1570593 original size:24 final size:25
Alignment explanation
Indices: 1570555--1570625 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 25
1570545 ATATGAGTGT
1570555 GAAAAGGAAGGAGGAGATGGAGAAGAG
1 GAAAAGGAA-GAGGAGA-GGAGAAGAG
1570582 G-AAA-GAAGAGGAGAGG-G-AGAG
1 GAAAAGGAAGAGGAGAGGAGAAGAG
1570603 GAAAAGGAAGATGGAGAAGGAGA
1 GAAAAGGAAGA-GGAG-AGGAGA
1570626 GGGTGGAGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
21 5 0.13
22 4 0.11
23 7 0.18
24 11 0.29
25 6 0.16
26 4 0.11
27 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.48, T:0.03
Consensus pattern (25 bp):
GAAAAGGAAGAGGAGAGGAGAAGAG
Found at i:1574267 original size:17 final size:19
Alignment explanation
Indices: 1574235--1574274 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
1574225 ATTTTATAAA
1574235 TTATTTTATTATTTAAAAT
1 TTATTTTATTATTTAAAAT
*
1574254 TTATTTTA-TA-TTAATAT
1 TTATTTTATTATTTAAAAT
1574271 TTAT
1 TTAT
1574275 ATATTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 2 0.10
19 8 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTTTATTATTTAAAAT
Done.