Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 12 of 93
Found at i:5999638 original size:23 final size:23
Alignment explanation
Indices: 5999581--5999654 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
5999571 TAAATTACAA
* * *
5999581 ATAAAATATTAATACTTAAATA-
1 ATAAATTATTAATATTTAAAAAT
* *
5999603 ATCAACTATTAATATTTAAAAAT
1 ATAAATTATTAATATTTAAAAAT
5999626 ATAAATTATTAATATTTAAAAGAT
1 ATAAATTATTAATATTTAAAA-AT
5999650 A-AAAT
1 ATAAAT
5999655 AAAATAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 18 0.41
23 23 0.52
24 3 0.07
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (23 bp):
ATAAATTATTAATATTTAAAAAT
Found at i:5999651 original size:22 final size:21
Alignment explanation
Indices: 5999579--5999655 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 21
5999569 ATTAAATTAC
*
5999579 AAATAAAATATTAATACTTAA
1 AAATAAAATATTAATATTTAA
* *
5999600 ATAATCAACTATTAATATTTAA
1 A-AATAAAATATTAATATTTAA
5999622 AAATATAAATTATTAATATTTAA
1 AAATA-AAA-TATTAATATTTAA
5999645 AAGATAAAATA
1 AA-ATAAAATA
5999656 AAATAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.09
22 22 0.47
23 18 0.38
24 3 0.06
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (21 bp):
AAATAAAATATTAATATTTAA
Found at i:5999698 original size:127 final size:130
Alignment explanation
Indices: 5999558--5999821 Score: 360
Period size: 127 Copynumber: 2.1 Consensus size: 130
5999548 TAGTATTTTA
*
5999558 TAATATTAATGATTAAATTACAAATAAAATATTAATACTTAAA-TAATCAACTATTAATA-TTT-
1 TAATATTAATGATTAAAGTACAAATAAAATATTAATACTTAAACT-ATCAACTATTAATATTTTA
5999620 AA-AAA-TATAAATTATTAATATTTAAAAGATAAAATAAAATAAAAATAAATAATCACAATAACA
65 AATAAATTATAAATTATTAATATTTAAAA-ATAAAATAAAATAAAAATAAATAATCACAATAACA
5999683 TT
129 TT
* * * * *
5999685 TAATATTAGTGATTAAAGTATAAATAAAATATTAATATTTAAACTATCAATTTTTAATATTTTAA
1 TAATATTAATGATTAAAGTACAAATAAAATATTAATACTTAAACTATCAACTATTAATATTTTAA
* * ** **
5999750 ATAAATTATACATTATTAATGTTTAAAAATAAAATAATTTAAAAATAAATAATCATTATAACATT
66 ATAAATTATAAATTATTAATATTTAAAAATAAAATAAAATAAAAATAAATAATCACAATAACATT
5999815 TAA-ATTA
1 TAATATTA
5999822 TAAATAAAAT
Statistics
Matches: 120, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
127 51 0.43
128 4 0.03
129 6 0.05
130 39 0.32
131 20 0.17
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (130 bp):
TAATATTAATGATTAAAGTACAAATAAAATATTAATACTTAAACTATCAACTATTAATATTTTAA
ATAAATTATAAATTATTAATATTTAAAAATAAAATAAAATAAAAATAAATAATCACAATAACATT
Found at i:5999799 original size:15 final size:16
Alignment explanation
Indices: 5999771--5999802 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5999761 ATTATTAATG
5999771 TTTAAAAATAAAATAA
1 TTTAAAAATAAAATAA
5999787 TTTAAAAAT-AAATAA
1 TTTAAAAATAAAATAA
5999802 T
1 T
5999803 CATTATAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTTAAAAATAAAATAA
Found at i:6003848 original size:40 final size:40
Alignment explanation
Indices: 6003775--6003856 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 40
6003765 TTTTAAAGGA
* *
6003775 AAAAAATTAAAATAAAATATGTAATATAGAAAAT-TATCTT
1 AAAAAATGAAAATAAAATATATAATATAGAAAATATAT-TT
*
6003815 AAAAAATGAAAATAAAATATATGATATTA-AAAATATATTT
1 AAAAAATGAAAATAAAATATATAATA-TAGAAAATATATTT
6003855 AA
1 AA
6003857 GAGATGATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 32 0.86
41 5 0.14
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (40 bp):
AAAAAATGAAAATAAAATATATAATATAGAAAATATATTT
Found at i:6004034 original size:23 final size:23
Alignment explanation
Indices: 6003984--6004036 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
6003974 TAAACACTGT
* * *
6003984 AATATTA-TTTCTTTATATTTTA
1 AATATTATTTTATTTATATATCA
*
6004006 ATTATTATTTTATTTATATATCA
1 AATATTATTTTATTTATATATCA
6004029 AATATTAT
1 AATATTAT
6004037 AATATTATCT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
AATATTATTTTATTTATATATCA
Found at i:6007263 original size:21 final size:20
Alignment explanation
Indices: 6007239--6007277 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
6007229 TAAAGAAAAC
* *
6007239 ATATTTCATCTTTAGATATAA
1 ATATGTCATCATTA-ATATAA
6007260 ATATGTCATCATTAATAT
1 ATATGTCATCATTAATAT
6007278 TTATCTCCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.46
Consensus pattern (20 bp):
ATATGTCATCATTAATATAA
Found at i:6007290 original size:22 final size:22
Alignment explanation
Indices: 6007264--6007305 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6007254 ATATAAATAT
6007264 GTCATCATTAATATTTATCTCC
1 GTCATCATTAATATTTATCTCC
** *
6007286 GTCATTGTTTATATTTATCT
1 GTCATCATTAATATTTATCT
6007306 TTTATTCTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (22 bp):
GTCATCATTAATATTTATCTCC
Found at i:6021809 original size:16 final size:16
Alignment explanation
Indices: 6021786--6021823 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6021776 AGAAACTTTA
*
6021786 ATATATTTCTCATTTGT
1 ATATATTTAT-ATTTGT
6021803 A-ATATTTATATTTGT
1 ATATATTTATATTTGT
6021818 ATATAT
1 ATATAT
6021824 AAATTAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.37
16 11 0.58
17 1 0.05
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (16 bp):
ATATATTTATATTTGT
Found at i:6023173 original size:42 final size:42
Alignment explanation
Indices: 6023125--6023209 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
6023115 GAGGACATAG
* *
6023125 GCGTGATATTAAGGTGTACTATGTGCTACTGCCAAGAATCAA
1 GCGTGATATTAAGCTGTACTATGTGCCACTGCCAAGAATCAA
* * *
6023167 GCGTGATGTTATGCTGTACTGTGTGCCACTGCCAAGAATCAA
1 GCGTGATATTAAGCTGTACTATGTGCCACTGCCAAGAATCAA
6023209 G
1 G
6023210 ATCAAATCGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (42 bp):
GCGTGATATTAAGCTGTACTATGTGCCACTGCCAAGAATCAA
Found at i:6029240 original size:26 final size:26
Alignment explanation
Indices: 6029131--6029269 Score: 105
Period size: 26 Copynumber: 5.5 Consensus size: 26
6029121 TTTATTATTT
*
6029131 ATATTATTA-TTTATTTTATTTTTTA
1 ATATTATTATTTTATTTTATTTTTAA
* *
6029156 ATATTAATATTTTA-TTTATAATTTAA
1 ATATTATTATTTTATTTTAT-TTTTAA
* * *
6029182 ATGTTATTATAATTA-TTTATTTGT--
1 ATATTATTAT-TTTATTTTATTTTTAA
*
6029206 ATA-T-GTATTTTATTTTATTTTTAA
1 ATATTATTATTTTATTTTATTTTTAA
* *
6029230 ATATTAATATTTTATTATT-TATTTAAA
1 ATATTATTATTTTATT-TTAT-TTTTAA
6029257 ATATTATTATTTT
1 ATATTATTATTTT
6029270 GATAATTTAA
Statistics
Matches: 89, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
21 3 0.03
22 11 0.12
23 1 0.01
24 5 0.06
25 14 0.16
26 28 0.31
27 27 0.30
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
ATATTATTATTTTATTTTATTTTTAA
Found at i:6029300 original size:26 final size:25
Alignment explanation
Indices: 6029225--6029305 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
6029215 TTATTTTATT
* *
6029225 TTTAAATATTAATATTT-TATTATTTA
1 TTTAAAAATTAATATTTAT-TTA-TAA
* *
6029251 TTTAAAATATTATTA-TT-TTGATAA
1 TTTAAAA-ATTAATATTTATTTATAA
6029275 TTTAAAAATTAATATTTGATTTATAA
1 TTTAAAAATTAATATTT-ATTTATAA
6029301 TTTAA
1 TTTAA
6029306 TCATTTAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
23 6 0.13
24 11 0.24
25 2 0.04
26 20 0.44
27 6 0.13
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTAAAAATTAATATTTATTTATAA
Found at i:6029652 original size:16 final size:16
Alignment explanation
Indices: 6029631--6029714 Score: 63
Period size: 16 Copynumber: 5.4 Consensus size: 16
6029621 ATCACTTAAA
6029631 ATTTTAAAATTAATAT
1 ATTTTAAAATTAATAT
6029647 ATTTTAAAATATTAATAT
1 ATTTT-AAA-ATTAATAT
6029665 ATTTT---ATT--TAT
1 ATTTTAAAATTAATAT
* *
6029676 AATTTAAAATTATTAT
1 ATTTTAAAATTAATAT
* *
6029692 AGTTAAAATATTAATAT
1 ATTTTAAA-ATTAATAT
6029709 -TTTTAA
1 ATTTTAA
6029715 TTTTTAATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
11 7 0.13
13 3 0.06
14 3 0.06
16 18 0.33
17 10 0.19
18 13 0.24
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (16 bp):
ATTTTAAAATTAATAT
Found at i:6029662 original size:18 final size:17
Alignment explanation
Indices: 6029631--6029670 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
6029621 ATCACTTAAA
6029631 ATTTT-AAAATTAATAT
1 ATTTTAAAAATTAATAT
6029647 ATTTTAAAATATTAATAT
1 ATTTTAAAA-ATTAATAT
6029665 ATTTTA
1 ATTTTA
6029671 TTTATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 5 0.23
17 3 0.14
18 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTAAAAATTAATAT
Found at i:6029703 original size:44 final size:45
Alignment explanation
Indices: 6029633--6029733 Score: 136
Period size: 44 Copynumber: 2.3 Consensus size: 45
6029623 CACTTAAAAT
*
6029633 TTTAAAATTAATATATTTTAAAATATTAATATATTTT-ATTTATAA
1 TTTAAAATTAATATATGTTAAAATATTAATAT-TTTTAATTTATAA
* *
6029678 TTTAAAATTATTATA-GTTAAAATATTAATATTTTTAATTTTTAA
1 TTTAAAATTAATATATGTTAAAATATTAATATTTTTAATTTATAA
*
6029722 TATAAAA-TAATA
1 TTTAAAATTAATA
6029734 ATTTTATAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
43 8 0.16
44 28 0.56
45 14 0.28
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (45 bp):
TTTAAAATTAATATATGTTAAAATATTAATATTTTTAATTTATAA
Found at i:6029840 original size:17 final size:17
Alignment explanation
Indices: 6029815--6029847 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6029805 TTCTCATGGG
*
6029815 CATGGAATAGCTAATAC
1 CATGAAATAGCTAATAC
6029832 CATGAAATAGCTAATA
1 CATGAAATAGCTAATA
6029848 TCGTTAGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
CATGAAATAGCTAATAC
Found at i:6031351 original size:20 final size:19
Alignment explanation
Indices: 6031315--6031354 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
6031305 TATTTTTTAT
* *
6031315 TTATTAAATTAATATCATA
1 TTATTAAATAAAAATCATA
6031334 TTATTAACATAAAAATCATA
1 TTATTAA-ATAAAAATCATA
6031354 T
1 T
6031355 ATAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
TTATTAAATAAAAATCATA
Found at i:6032571 original size:2 final size:2
Alignment explanation
Indices: 6032564--6032596 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6032554 TTATGACATA
6032564 AT 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 AT A
6032597 CACTTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6033912 original size:15 final size:13
Alignment explanation
Indices: 6033873--6033903 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6033863 TATATTATAT
6033873 ATTTTTT-AATAA
1 ATTTTTTAAATAA
6033885 ATTTTTTAAATAA
1 ATTTTTTAAATAA
6033898 ATTTTT
1 ATTTTT
6033904 ATTAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTTTTTAAATAA
Found at i:6034076 original size:13 final size:14
Alignment explanation
Indices: 6034058--6034112 Score: 58
Period size: 18 Copynumber: 3.7 Consensus size: 14
6034048 AAAGGTAAAG
6034058 TTTTTATTTA-ATT
1 TTTTTATTTATATT
6034071 TTTTTATTTATATT
1 TTTTTATTTATATT
6034085 ATCATTATTATTTATATT
1 -T--TT-TTATTTATATT
*
6034103 TATTTATTTA
1 TTTTTATTTA
6034113 ATTATATTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 10 0.28
14 10 0.28
15 2 0.06
17 3 0.08
18 11 0.31
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTATTTATATT
Found at i:6034241 original size:15 final size:16
Alignment explanation
Indices: 6034221--6034250 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6034211 CTATTATGTG
6034221 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
6034236 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
6034251 AATTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:6034665 original size:40 final size:41
Alignment explanation
Indices: 6034621--6034709 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 41
6034611 ATATTATATA
* *
6034621 ATATTTTTAAAATTTTTATATATTAGAT-AT-TTTAAATTTT
1 ATATTTTTAAAA-TATTATATATTAGATAATATTTAAAATTT
*
6034661 ATA-TTTTAAAATATTATATATTATATAATATTTAAAATTT
1 ATATTTTTAAAATATTATATATTAGATAATATTTAAAATTT
*
6034701 AAATTTTTA
1 ATATTTTTA
6034710 TATTATATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 13 0.31
39 10 0.24
40 14 0.33
41 5 0.12
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (41 bp):
ATATTTTTAAAATATTATATATTAGATAATATTTAAAATTT
Found at i:6034677 original size:15 final size:14
Alignment explanation
Indices: 6034647--6034717 Score: 51
Period size: 15 Copynumber: 5.3 Consensus size: 14
6034637 TATATATTAG
*
6034647 ATATTTTAAATTTT
1 ATATTTTAAATATT
6034661 ATATTTTAAAATATT
1 ATATTTT-AAATATT
* *
6034676 ATATATT--ATATA
1 ATATTTTAAATATT
*
6034688 ATATTTAAAAT-TT
1 ATATTTTAAATATT
* *
6034701 AAATTTT-TATATT
1 ATATTTTAAATATT
6034714 ATAT
1 ATAT
6034718 AATATTTTCA
Statistics
Matches: 43, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
12 11 0.26
13 11 0.26
14 9 0.21
15 12 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATTTTAAATATT
Found at i:6034709 original size:41 final size:40
Alignment explanation
Indices: 6034623--6034709 Score: 106
Period size: 38 Copynumber: 2.2 Consensus size: 40
6034613 ATTATATAAT
* * *
6034623 ATTTTTAAAATTTTTATATATTAGATATTTTAAATTTTAT
1 ATTTTTAAAATTATTATATATTAGATATTTTAAAATTTAA
*
6034663 A-TTTTAAAA-TATTATATATTATATAATATTTAAAATTTAA
1 ATTTTTAAAATTATTATATATTAGAT-AT-TTTAAAATTTAA
6034703 ATTTTTA
1 ATTTTTA
6034710 TATTATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 13 0.32
39 10 0.25
40 12 0.30
41 5 0.12
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (40 bp):
ATTTTTAAAATTATTATATATTAGATATTTTAAAATTTAA
Found at i:6034712 original size:31 final size:35
Alignment explanation
Indices: 6034602--6034775 Score: 145
Period size: 31 Copynumber: 5.1 Consensus size: 35
6034592 TAAATTTAAA
* *
6034602 AAATATTATATATTATATAATATTTTTAAAATTTTT
1 AAATTTTATATATTATATAATATTTTCAAAA-TTTT
* * * *
6034638 ATATATTAGATATT-T-TAA-ATTTT--ATATTTT
1 AAATTTTATATATTATATAATATTTTCAAAATTTT
*
6034668 AAAATATTATATATTATATAATA-TTT-AAAA-TTT
1 -AAATTTTATATATTATATAATATTTTCAAAATTTT
6034701 AAATTTT-TATATTATATAATATTTTCAAAATTTTT
1 AAATTTTATATATTATATAATATTTTCAAAA-TTTT
* *
6034736 AAATTTTATATATTTTAT-AT-TTTTAATAAATTTTT
1 AAATTTTATATATTATATAATATTTTCA-AAA-TTTT
6034771 AAATT
1 AAATT
6034776 AATTTTTGAA
Statistics
Matches: 118, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
30 4 0.03
31 28 0.24
32 10 0.08
33 18 0.15
34 11 0.09
35 26 0.22
36 21 0.18
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.56
Consensus pattern (35 bp):
AAATTTTATATATTATATAATATTTTCAAAATTTT
Found at i:6034713 original size:38 final size:37
Alignment explanation
Indices: 6034636--6034756 Score: 99
Period size: 38 Copynumber: 3.2 Consensus size: 37
6034626 TTTAAAATTT
* *
6034636 TTATATATTAGATATTTTAAATTTTATATTTTAAAATA
1 TTATATATTAGATATTTTAAAATTTAAATTTT-AAATA
* *
6034674 TTATATATTATATAATATTTAAAATTTAAATTTT-TATA
1 TTATATATTAGAT-AT-TTTAAAATTTAAATTTTAAATA
*
6034712 -T-TATA-TA-ATATTTTCAAAATTTTTAAATTTTATATA
1 TTATATATTAGATATTTT-AAAA--TTTAAATTTTAAATA
*
6034748 TTTTATATT
1 TTATATATT
6034757 TTTAATAAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
32 3 0.04
33 6 0.09
34 2 0.03
35 12 0.17
36 8 0.11
37 2 0.03
38 19 0.27
39 3 0.04
40 15 0.21
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (37 bp):
TTATATATTAGATATTTTAAAATTTAAATTTTAAATA
Found at i:6034734 original size:67 final size:64
Alignment explanation
Indices: 6034601--6034771 Score: 167
Period size: 67 Copynumber: 2.6 Consensus size: 64
6034591 ATAAATTTAA
6034601 AAAATATTATATATTATATAATATTTTTAAAATTTTTATATATTAGATATTTTAAATTTTATATT
1 AAAATATTATATATTATATAATATTTTTAAAATTTTTATATATTAGATATTTTAAA---TATATT
6034666 TT
63 TT
*
6034668 AAAATATTATATATTATATAATATTTAAAATTTAAATTTTTATATTATATA-ATATTTTCAAA-A
1 AAAATATTATATATTATATAATATTT----TTAAAATTTTTATA-TAT-TAGATATTTT-AAATA
6034731 T-TTTT
59 TATTTT
*
6034736 -AAATTTTATATATT-T-T-ATATTTTTAATAAATTTTTA
1 AAAATATTATATATTATATAATATTTTT-A-AAATTTTTA
6034772 AATTAATTTT
Statistics
Matches: 92, Mismatches: 3, Indels: 23
0.78 0.03 0.19
Matches are distributed among these distances:
60 2 0.02
62 9 0.10
64 6 0.07
65 1 0.01
66 1 0.01
67 39 0.42
68 4 0.04
69 2 0.02
71 13 0.14
72 10 0.11
73 5 0.05
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.56
Consensus pattern (64 bp):
AAAATATTATATATTATATAATATTTTTAAAATTTTTATATATTAGATATTTTAAATATATTTT
Found at i:6047622 original size:19 final size:21
Alignment explanation
Indices: 6047577--6047627 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
6047567 CCTAAAACAA
*
6047577 ATTCAATAAACCCTTAAACTG
1 ATTCAATAAACCCTTAAACCG
* *
6047598 AATCAATAAA-TC-TAAACCG
1 ATTCAATAAACCCTTAAACCG
6047617 ATTCAATAAAC
1 ATTCAATAAAC
6047628 TTTTAACTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 15 0.60
20 1 0.04
21 9 0.36
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.25
Consensus pattern (21 bp):
ATTCAATAAACCCTTAAACCG
Found at i:6047879 original size:21 final size:21
Alignment explanation
Indices: 6047854--6047901 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
6047844 GGTCTTACTC
6047854 AACAAACACTAAAATCGATTT
1 AACAAACACTAAAATCGATTT
*
6047875 AACAAACCCTAAAATCGATTT
1 AACAAACACTAAAATCGATTT
6047896 AACAAA
1 AACAAA
6047902 TCCTAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.54, C:0.21, G:0.04, T:0.21
Consensus pattern (21 bp):
AACAAACACTAAAATCGATTT
Found at i:6047906 original size:21 final size:20
Alignment explanation
Indices: 6047854--6047907 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 20
6047844 GGTCTTACTC
6047854 AACAAACACTAAAATCGATTT
1 AACAAAC-CTAAAATCGATTT
6047875 AACAAACCCTAAAATCGATTT
1 AACAAA-CCTAAAATCGATTT
6047896 AACAAATCCTAA
1 AACAAA-CCTAA
6047908 CTCAATTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.52, C:0.22, G:0.04, T:0.22
Consensus pattern (20 bp):
AACAAACCTAAAATCGATTT
Found at i:6048026 original size:21 final size:21
Alignment explanation
Indices: 6047974--6048101 Score: 64
Period size: 21 Copynumber: 6.2 Consensus size: 21
6047964 AATTTAATTT
** *
6047974 AATTCAATGAACTATAAACT-
1 AATTCAAAAAACTTTAAACTC
* *
6047994 AGTTCAACAAACTTTAAACTC
1 AATTCAAAAAACTTTAAACTC
** *
6048015 AATTCAAAAAACCCCT-AATTC
1 AATTCAAAAAA-CTTTAAACTC
** * * *
6048036 TGTTCATAAAACTGTAAAATC
1 AATTCAAAAAACTTTAAACTC
* * **
6048057 AATTTAAAAAGCTTT-TCCTC
1 AATTCAAAAAACTTTAAACTC
*
6048077 AATTCAAAAAACTTTAAAATC
1 AATTCAAAAAACTTTAAACTC
6048098 AATT
1 AATT
6048102 TAATTTTTCC
Statistics
Matches: 75, Mismatches: 29, Indels: 7
0.68 0.26 0.06
Matches are distributed among these distances:
20 33 0.44
21 40 0.53
22 2 0.03
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31
Consensus pattern (21 bp):
AATTCAAAAAACTTTAAACTC
Found at i:6049073 original size:35 final size:36
Alignment explanation
Indices: 6049025--6049145 Score: 122
Period size: 35 Copynumber: 3.3 Consensus size: 36
6049015 TAACTACTAC
* *
6049025 TTAAATTAA-TAAAAACAAA-ATAATAAAATTTAAAT
1 TTAAA-TAATTAAAAACAAATATCATAAAATATAAAT
* *
6049060 TTAAATAATTAAAAACAAATATCTTAAAA-ATAAAC
1 TTAAATAATTAAAAACAAATATCATAAAATATAAAT
* *
6049095 TTAAATAACTAAAAATAAATATTCATACAACGATATAAAT
1 TTAAATAATTAAAAACAAATA-TCATA-AA--ATATAAAT
6049135 TTAAATAATTA
1 TTAAATAATTA
6049146 GTACATAAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
34 3 0.04
35 38 0.54
36 11 0.16
37 2 0.03
39 1 0.01
40 15 0.21
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.31
Consensus pattern (36 bp):
TTAAATAATTAAAAACAAATATCATAAAATATAAAT
Found at i:6049668 original size:15 final size:17
Alignment explanation
Indices: 6049648--6049680 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
6049638 ATTAAAATTA
6049648 ATAATTT-TATAA-GTT
1 ATAATTTGTATAATGTT
6049663 ATAATTTGTATAATGTT
1 ATAATTTGTATAATGTT
6049680 A
1 A
6049681 ACATAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (17 bp):
ATAATTTGTATAATGTT
Found at i:6049760 original size:23 final size:23
Alignment explanation
Indices: 6049716--6049760 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
6049706 ATATTTAATA
* *
6049716 TATATATATACTAAAAGTATTAG
1 TATATATATAATAAAAGAATTAG
* *
6049739 TATATATATAATATAGGAATTA
1 TATATATATAATAAAAGAATTA
6049761 TATTTCTTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (23 bp):
TATATATATAATAAAAGAATTAG
Found at i:6062087 original size:18 final size:18
Alignment explanation
Indices: 6062060--6062098 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
6062050 TTTTCATTAT
*
6062060 TTATCTACTTCTGGTGAG
1 TTATCCACTTCTGGTGAG
*
6062078 TTATCCACTTCTGGTGGG
1 TTATCCACTTCTGGTGAG
6062096 TTA
1 TTA
6062099 GTGGGTTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.44
Consensus pattern (18 bp):
TTATCCACTTCTGGTGAG
Found at i:6062145 original size:28 final size:28
Alignment explanation
Indices: 6062109--6062187 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
6062099 GTGGGTTAAG
* **
6062109 GTATCCATCTACTTTTGGTGCGTTAAAA
1 GTATACATCTACTTTTGGTAAGTTAAAA
* * *
6062137 GTATTCATCTACTTGTGGTAAGTTACAA
1 GTATACATCTACTTTTGGTAAGTTAAAA
* *
6062165 GTATACATCCATTTTTGGTAAGT
1 GTATACATCTACTTTTGGTAAGT
6062188 GATCCACATA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.41
Consensus pattern (28 bp):
GTATACATCTACTTTTGGTAAGTTAAAA
Found at i:6062280 original size:25 final size:26
Alignment explanation
Indices: 6062252--6062351 Score: 80
Period size: 25 Copynumber: 4.0 Consensus size: 26
6062242 TTACGGCATT
*
6062252 CATCCACTTTTGATGGT-AAATTATC
1 CATCCACTTATGATGGTAAAATTATC
* *
6062277 CATCCACTTATGGTGGTAAAATTATT
1 CATCCACTTATGATGGTAAAATTATC
* ** * *
6062303 CTTAGA-TTCTGTTGGTAAAATTAT-
1 CATCCACTTATGATGGTAAAATTATC
* * *
6062327 TATCCACTTTTGGTGGTAAAATTAT
1 CATCCACTTATGATGGTAAAATTAT
6062352 AATTAAAATT
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
24 2 0.03
25 47 0.80
26 10 0.17
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (26 bp):
CATCCACTTATGATGGTAAAATTATC
Found at i:6062829 original size:21 final size:22
Alignment explanation
Indices: 6062792--6062839 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
6062782 AAGATAACTT
*
6062792 GAAAG-AATAATTAAGGA-GAA
1 GAAAGAAAGAATTAAGGAGGAA
*
6062812 GAAAGAAAGAATTTAGGAGGAA
1 GAAAGAAAGAATTAAGGAGGAA
*
6062834 AAAAGA
1 GAAAGA
6062840 GATCTTATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.12
Consensus pattern (22 bp):
GAAAGAAAGAATTAAGGAGGAA
Found at i:6063403 original size:18 final size:19
Alignment explanation
Indices: 6063380--6063417 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
6063370 GTAAATAATA
*
6063380 TTTTAATTATT-TTTTTAT
1 TTTTAATAATTATTTTTAT
6063398 TTTTAATAATTATTTTTAT
1 TTTTAATAATTATTTTTAT
6063417 T
1 T
6063418 AATATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTAATAATTATTTTTAT
Found at i:6065850 original size:21 final size:21
Alignment explanation
Indices: 6065817--6065857 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6065807 AAGAAAAAGT
* *
6065817 ATATCTAATATCAATAAATTA
1 ATATATAAAATCAATAAATTA
*
6065838 ATATATAAAATCAATTAATT
1 ATATATAAAATCAATAAATT
6065858 TAAGTGAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATATAAAATCAATAAATTA
Found at i:6071375 original size:26 final size:26
Alignment explanation
Indices: 6071326--6071385 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
6071316 TATTTTTCTT
* *
6071326 ATTATTTTTAAAAAGATTAGGCTTTGA
1 ATTA-TTTAAAAAAGATTAAGCTTTGA
* *
6071353 GTTATTTAAAAAATATTAAGCTTTGA
1 ATTATTTAAAAAAGATTAAGCTTTGA
6071379 ATTATTT
1 ATTATTT
6071386 TTTAAGGACC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 25 0.89
27 3 0.11
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (26 bp):
ATTATTTAAAAAAGATTAAGCTTTGA
Found at i:6073437 original size:22 final size:22
Alignment explanation
Indices: 6073398--6073448 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
6073388 TGTTCATTTC
6073398 TATTGTTTAATGTTTATT-TATT
1 TATT-TTTAATGTTTATTCTATT
*
6073420 TATTTTTAATTTTATATTCTATT
1 TATTTTTAATGTT-TATTCTATT
*
6073443 AATTTT
1 TATTTT
6073449 ATGCTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.32
22 8 0.32
23 9 0.36
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (22 bp):
TATTTTTAATGTTTATTCTATT
Found at i:6082474 original size:21 final size:20
Alignment explanation
Indices: 6082449--6082507 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
6082439 TTAAAAAAAT
6082449 TAATTACCATCATTTCTTAAC
1 TAATTACCATCA-TTCTTAAC
* *
6082470 TAATTATCATC-TTCTTAAT
1 TAATTACCATCATTCTTAAC
6082489 TGAA--ACCATCATTCTTAAC
1 T-AATTACCATCATTCTTAAC
6082508 AAAAAAAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 5 0.16
19 15 0.47
20 2 0.06
21 10 0.31
ACGTcount: A:0.34, C:0.22, G:0.02, T:0.42
Consensus pattern (20 bp):
TAATTACCATCATTCTTAAC
Found at i:6087463 original size:20 final size:21
Alignment explanation
Indices: 6087429--6087467 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
6087419 TCCATCTCTT
*
6087429 TTTCCTTTCATTTTCCCACAC
1 TTTCCTTTCACTTTCCCACAC
6087450 TTTCC-TTCACTTTCCCAC
1 TTTCCTTTCACTTTCCCAC
6087468 TACCCAGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.13, C:0.41, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTCCTTTCACTTTCCCACAC
Found at i:6089978 original size:21 final size:21
Alignment explanation
Indices: 6089936--6089978 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6089926 ATTTCTTCTC
* *
6089936 AATAAAGTCCTTGCTTAGTGA
1 AATAAAGTCCTTGCTGACTGA
*
6089957 AATAAAGTCCTTGCTGCCTGA
1 AATAAAGTCCTTGCTGACTGA
6089978 A
1 A
6089979 CTTTTTGTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (21 bp):
AATAAAGTCCTTGCTGACTGA
Found at i:6091043 original size:14 final size:13
Alignment explanation
Indices: 6091021--6091050 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
6091011 TCCCCCAAAT
6091021 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
6091034 AAAAAGAAAAAAAG
1 AAAAA-AAAAAAAG
6091048 AAA
1 AAA
6091051 GGAGACGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:6101380 original size:10 final size:9
Alignment explanation
Indices: 6101356--6101447 Score: 63
Period size: 8 Copynumber: 10.4 Consensus size: 9
6101346 TTTGATATTG
6101356 ATATAATAT
1 ATATAATAT
6101365 AT-TAATAT
1 ATATAATAT
6101373 ATTATAATA-
1 A-TATAATAT
6101382 A-ATAATA-
1 ATATAATAT
* *
6101389 ACATAACAT
1 ATATAATAT
*
6101398 ACTCA-AAGAT
1 A-T-ATAATAT
6101408 CATATAATAT
1 -ATATAATAT
6101418 ATAT-ATAT
1 ATATAATAT
6101426 ATATATATAT
1 ATATA-ATAT
6101436 ATATAA-AT
1 ATATAATAT
6101444 ATAT
1 ATAT
6101448 TTTAATAACT
Statistics
Matches: 69, Mismatches: 4, Indels: 21
0.73 0.04 0.22
Matches are distributed among these distances:
7 7 0.10
8 26 0.38
9 11 0.16
10 23 0.33
11 2 0.03
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.39
Consensus pattern (9 bp):
ATATAATAT
Found at i:6101421 original size:2 final size:2
Alignment explanation
Indices: 6101409--6101447 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
6101399 CTCAAAGATC
*
6101409 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6101448 TTTAATAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6106599 original size:50 final size:51
Alignment explanation
Indices: 6106504--6106601 Score: 121
Period size: 51 Copynumber: 1.9 Consensus size: 51
6106494 TATAACTAAA
* * *
6106504 ATTTAAGTATTAATATATAAATTATTTTTAATAAATTTATTTTTTGATAAT
1 ATTTAAATATTAATATATAAATTATTTTTAATAAATCTATCTTTTGATAAT
*
6106555 ATTTAAATATTATTA-ATATAATT-TTTTTAATAAAATCTA-CTTTTGAT
1 ATTTAAATATTAATATATA-AATTATTTTTAAT-AAATCTATCTTTTGAT
6106602 CCCATTCTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
50 18 0.44
51 23 0.56
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (51 bp):
ATTTAAATATTAATATATAAATTATTTTTAATAAATCTATCTTTTGATAAT
Found at i:6108613 original size:22 final size:22
Alignment explanation
Indices: 6108583--6108645 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
6108573 GTGACTTAAT
6108583 CATTGCGTGACTGATTTTTAGG
1 CATTGCGTGACTGATTTTTAGG
* * *
6108605 CATTACGTGATTG-GTTTTAGG
1 CATTGCGTGACTGATTTTTAGG
*
6108626 CATTGCGTGACTAATTTTTA
1 CATTGCGTGACTGATTTTTA
6108646 AGTAATACCT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.21, C:0.13, G:0.24, T:0.43
Consensus pattern (22 bp):
CATTGCGTGACTGATTTTTAGG
Found at i:6108725 original size:46 final size:45
Alignment explanation
Indices: 6108658--6108764 Score: 135
Period size: 46 Copynumber: 2.4 Consensus size: 45
6108648 TAATACCTAC
* * *
6108658 GTCACACAATACCTTATTAACAAGTCACACAATACCT-TACTAACAA
1 GTCACGCAATGCCTTACTAACAAGTCACACAATACCTAT-C-AACAA
* *
6108704 GTCACGCAATGCCTTACTAACAAGTCACACAATGCCTATCAACTA
1 GTCACGCAATGCCTTACTAACAAGTCACACAATACCTATCAACAA
*
6108749 GTCACGCAATGTCTTA
1 GTCACGCAATGCCTTA
6108765 TCAGAAATCA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 19 0.35
46 34 0.63
47 1 0.02
ACGTcount: A:0.37, C:0.29, G:0.09, T:0.24
Consensus pattern (45 bp):
GTCACGCAATGCCTTACTAACAAGTCACACAATACCTATCAACAA
Found at i:6108740 original size:23 final size:23
Alignment explanation
Indices: 6108658--6108736 Score: 131
Period size: 23 Copynumber: 3.4 Consensus size: 23
6108648 TAATACCTAC
*
6108658 GTCACACAATACCTTATTAACAA
1 GTCACACAATACCTTACTAACAA
6108681 GTCACACAATACCTTACTAACAA
1 GTCACACAATACCTTACTAACAA
* *
6108704 GTCACGCAATGCCTTACTAACAA
1 GTCACACAATACCTTACTAACAA
6108727 GTCACACAAT
1 GTCACACAAT
6108737 GCCTATCAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.41, C:0.29, G:0.08, T:0.23
Consensus pattern (23 bp):
GTCACACAATACCTTACTAACAA
Found at i:6108810 original size:26 final size:26
Alignment explanation
Indices: 6108703--6108906 Score: 136
Period size: 26 Copynumber: 8.5 Consensus size: 26
6108693 CTTACTAACA
* *
6108703 AGTCACGCAATGCCTTA-C--TAACA
1 AGTCACGCAATGCCTTATCAAAAACT
*
6108726 AGTCACACAATGCC-TATC---AACT
1 AGTCACGCAATGCCTTATCAAAAACT
* *
6108748 AGTCACGCAATGTCTTATCAGAAA-T
1 AGTCACGCAATGCCTTATCAAAAACT
*
6108773 CAATCACGCAATGCCTTATCAAAAACT
1 -AGTCACGCAATGCCTTATCAAAAACT
* * * **
6108800 AGTAACACAATACC----CAAAGTC-
1 AGTCACGCAATGCCTTATCAAAAACT
*
6108821 AGTCACGTAATGCC-TATC---AACT
1 AGTCACGCAATGCCTTATCAAAAACT
** * *
6108843 AGTCACATAATGTCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
6108869 AGTCACGCAATGCCTTATCAAAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
6108895 AGTCACGCAATG
1 AGTCACGCAATG
6108907 TCCAAAGTCA
Statistics
Matches: 141, Mismatches: 25, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
21 11 0.08
22 34 0.24
23 22 0.16
24 1 0.01
25 1 0.01
26 71 0.50
27 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (26 bp):
AGTCACGCAATGCCTTATCAAAAACT
Found at i:6108838 original size:95 final size:95
Alignment explanation
Indices: 6108734--6108927 Score: 309
Period size: 95 Copynumber: 2.0 Consensus size: 95
6108724 CAAGTCACAC
*
6108734 AATGCCTATCAACTAGTCACGCAATGTCTTATCAGAAA-TCAATCACGCAATGCCTTATCAAAAA
1 AATGCCTATCAACTAGTCACACAATGTCTTATCAGAAACT-AATCACGCAATGCCTTATCAAAAA
6108798 CTAGTAACACAATACCCAAAGTCAGTCACGT
65 CTAGTAACACAATACCCAAAGTCAGTCACGT
* *
6108829 AATGCCTATCAACTAGTCACATAATGTCTTATCAGAAACTAGTCACGCAATGCCTTATCAAAAAC
1 AATGCCTATCAACTAGTCACACAATGTCTTATCAGAAACTAATCACGCAATGCCTTATCAAAAAC
* * **
6108894 TAGTCACGCAATGTCCAAAGTCAGTCACGT
66 TAGTAACACAATACCCAAAGTCAGTCACGT
6108924 AATG
1 AATG
6108928 TCTAAAAACT
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 90 0.99
96 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (95 bp):
AATGCCTATCAACTAGTCACACAATGTCTTATCAGAAACTAATCACGCAATGCCTTATCAAAAAC
TAGTAACACAATACCCAAAGTCAGTCACGT
Found at i:6111294 original size:2 final size:2
Alignment explanation
Indices: 6111287--6111367 Score: 153
Period size: 2 Copynumber: 40.5 Consensus size: 2
6111277 GGATACATAC
*
6111287 AT AT AT AT AT AT AT AT AC 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
6111329 AT AT AT AT 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 AT AT AT AT A
6111368 AATGTGTTTA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6112013 original size:33 final size:33
Alignment explanation
Indices: 6111947--6112014 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
6111937 AATCTATTTA
* ** *
6111947 AATAAATATATAAGTATATTACATTTATCATAT
1 AATAAACATATAAACATATTACATTTAACATAT
*
6111980 AATAAACATATAAACATATTACATTTAAGATAT
1 AATAAACATATAAACATATTACATTTAACATAT
6112013 AA
1 AA
6112015 AAATAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (33 bp):
AATAAACATATAAACATATTACATTTAACATAT
Found at i:6113698 original size:2 final size:2
Alignment explanation
Indices: 6113691--6113733 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
6113681 CTTAACATGG
*
6113691 AT AT AT AT AT AT CT 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
6113733 A
1 A
6113734 CTACATGTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6119915 original size:35 final size:35
Alignment explanation
Indices: 6119819--6119986 Score: 241
Period size: 35 Copynumber: 4.8 Consensus size: 35
6119809 ACCCATTTTC
* *
6119819 ACCGGCGGCAAACACCCCAGCTATTACTCCT-CTC
1 ACCGGCGGCAAACACCCCAGCTTTTACTCCTCCTA
* *
6119853 ACCAGCGGCAAAC-CCCCAAGCTATTACTCCTCCTA
1 ACCGGCGGCAAACACCCC-AGCTTTTACTCCTCCTA
* *
6119888 ACCGACGGCAAAAACCCCAGCTTTTACTCCTCCTA
1 ACCGGCGGCAAACACCCCAGCTTTTACTCCTCCTA
*
6119923 ACCGGCGGCAAACACCCCAGCTTTAACTCCTCCTA
1 ACCGGCGGCAAACACCCCAGCTTTTACTCCTCCTA
*
6119958 ACCGGCGGCAAACACCCCAGCTTTAACTC
1 ACCGGCGGCAAACACCCCAGCTTTTACTC
6119987 TCCCTGCACA
Statistics
Matches: 122, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
33 4 0.03
34 25 0.20
35 89 0.73
36 4 0.03
ACGTcount: A:0.27, C:0.42, G:0.14, T:0.17
Consensus pattern (35 bp):
ACCGGCGGCAAACACCCCAGCTTTTACTCCTCCTA
Found at i:6120312 original size:12 final size:12
Alignment explanation
Indices: 6120295--6120332 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
6120285 TCATTTTTCA
6120295 TTTTTTTATATT
1 TTTTTTTATATT
*
6120307 TTTTTTTATATA
1 TTTTTTTATATT
*
6120319 TATTTTTA-ATT
1 TTTTTTTATATT
6120330 TTT
1 TTT
6120333 CTTGTTTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTTATATT
Found at i:6120342 original size:24 final size:23
Alignment explanation
Indices: 6120297--6120346 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
6120287 ATTTTTCATT
*
6120297 TTTTTATATTTTTTTTTATATATA
1 TTTTTATATTTTTTTGTATATA-A
*
6120321 TTTTTA-ATTTTTCTTGTTTATAA
1 TTTTTATATTTTT-TTGTATATAA
6120344 TTT
1 TTT
6120347 AGTGTCTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTTTATATTTTTTTGTATATAA
Found at i:6135468 original size:2 final size:2
Alignment explanation
Indices: 6135461--6135495 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6135451 NNNNNNNNNN
*
6135461 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6135496 TTATTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:6135496 original size:8 final size:8
Alignment explanation
Indices: 6135465--6135505 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
6135455 NNNNNNTATA
*
6135465 TATATATA
1 TATATATT
*
6135473 TATATATA
1 TATATATT
6135481 TATATATT
1 TATATATT
6135489 TATATATT
1 TATATATT
*
6135497 TATTTATT
1 TATATATT
6135505 T
1 T
6135506 TTTTGTTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATATATT
Found at i:6135500 original size:12 final size:12
Alignment explanation
Indices: 6135465--6135503 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
6135455 NNNNNNTATA
*
6135465 TATATATATATA
1 TATATATATATT
6135477 TATATATATATT
1 TATATATATATT
*
6135489 TATATATTTATT
1 TATATATATATT
6135501 TAT
1 TAT
6135504 TTTTTTGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATATATATATT
Found at i:6136311 original size:17 final size:18
Alignment explanation
Indices: 6136277--6136321 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
6136267 AAAGCTCTTA
*
6136277 AAAAAAAGTAAAATTTTTT
1 AAAAAAA-TAAAATTTTTG
*
6136296 TAAAAAATAAAA-TTTTG
1 AAAAAAATAAAATTTTTG
6136313 AAAAAAATA
1 AAAAAAATA
6136322 GCTTTTGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (18 bp):
AAAAAAATAAAATTTTTG
Found at i:6136318 original size:18 final size:19
Alignment explanation
Indices: 6136276--6136319 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
6136266 AAAAGCTCTT
*
6136276 AAAAAAAAGTAAAATTTTT
1 AAAAAAAAGTAAAATTTTG
**
6136295 TTAAAAAA-TAAAATTTTG
1 AAAAAAAAGTAAAATTTTG
6136313 AAAAAAA
1 AAAAAAA
6136320 TAGCTTTTGG
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAAAAAAGTAAAATTTTG
Found at i:6137626 original size:22 final size:22
Alignment explanation
Indices: 6137598--6137650 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
6137588 AATTAAAGTT
* *
6137598 AAAGGAAGAAAGAGTAAATGAG
1 AAAGGAAGAAAGAGCAAACGAG
6137620 AAAGGAAGAAAGAGCAAACGAG
1 AAAGGAAGAAAGAGCAAACGAG
6137642 AAAGGAAGA
1 AAAGGAAGA
6137651 TTTCAAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.60, C:0.04, G:0.32, T:0.04
Consensus pattern (22 bp):
AAAGGAAGAAAGAGCAAACGAG
Found at i:6138471 original size:13 final size:13
Alignment explanation
Indices: 6138453--6138477 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6138443 AAAGAGCATA
6138453 TTTTATATGTATC
1 TTTTATATGTATC
6138466 TTTTATATGTAT
1 TTTTATATGTAT
6138478 AATACACATA
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:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (13 bp):
TTTTATATGTATC
Found at i:6151105 original size:28 final size:27
Alignment explanation
Indices: 6151044--6151106 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
6151034 GAGTACTGAA
*
6151044 GTTTTGACTTTGGCGTGTAACATTTTTT
1 GTTTTGACTTTGGCGTGTAACA-TTTTG
* *
6151072 GCTTTGGCTTTGGTGCGTGTAACA-TTTG
1 GTTTTGACTTT-G-GCGTGTAACATTTTG
6151100 GTTTTGA
1 GTTTTGA
6151107 AGTTTTGGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
28 17 0.61
29 1 0.04
30 10 0.36
ACGTcount: A:0.13, C:0.11, G:0.27, T:0.49
Consensus pattern (27 bp):
GTTTTGACTTTGGCGTGTAACATTTTG
Found at i:6151243 original size:34 final size:34
Alignment explanation
Indices: 6151200--6151288 Score: 115
Period size: 34 Copynumber: 2.6 Consensus size: 34
6151190 CATCTTCTGT
6151200 TTTGACTTTGACGTGTAACATCTGGTGATGAAGC
1 TTTGACTTTGACGTGTAACATCTGGTGATGAAGC
** * * * *
6151234 TTTGACTTTGGTGTATAATATCTGGTGCTGAATC
1 TTTGACTTTGACGTGTAACATCTGGTGATGAAGC
*
6151268 TTTGACTTTGACATGTAACAT
1 TTTGACTTTGACGTGTAACAT
6151289 TTGCTGTTGA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.40
Consensus pattern (34 bp):
TTTGACTTTGACGTGTAACATCTGGTGATGAAGC
Found at i:6152017 original size:21 final size:20
Alignment explanation
Indices: 6151986--6152024 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
6151976 TTAAAAGTAA
6151986 TTTTATTAAAAAAAATTATT
1 TTTTATTAAAAAAAATTATT
*
6152006 TTTTAGTTAAAAACAATTA
1 TTTTA-TTAAAAAAAATTA
6152025 AAATTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (20 bp):
TTTTATTAAAAAAAATTATT
Found at i:6156051 original size:15 final size:15
Alignment explanation
Indices: 6156031--6156061 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6156021 TACAATAATT
6156031 AAATTCACCAATTTA
1 AAATTCACCAATTTA
*
6156046 AAATTCACCACTTTA
1 AAATTCACCAATTTA
6156061 A
1 A
6156062 TAGAATATAT
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:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATTCACCAATTTA
Found at i:6157343 original size:5 final size:5
Alignment explanation
Indices: 6157333--6157359 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6157323 GTAACAAATG
6157333 CTAAT CTAAT CTAAT CTAAT CTAAT CT
1 CTAAT CTAAT CTAAT CTAAT CTAAT CT
6157360 CCTTAATGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (5 bp):
CTAAT
Found at i:6161991 original size:19 final size:19
Alignment explanation
Indices: 6161967--6162006 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
6161957 TAATTTACTT
6161967 TGTGCTAAAGACGAGAGGA
1 TGTGCTAAAGACGAGAGGA
6161986 TGTGCTAAAGACGAGAGGA
1 TGTGCTAAAGACGAGAGGA
6162005 TG
1 TG
6162007 GTGTTACACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.38, T:0.17
Consensus pattern (19 bp):
TGTGCTAAAGACGAGAGGA
Found at i:6174538 original size:9 final size:9
Alignment explanation
Indices: 6174524--6174553 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
6174514 TTTACTTTAT
*
6174524 TTTATTTTA
1 TTTATTTCA
6174533 TTTATTTCA
1 TTTATTTCA
6174542 TTTATTTCA
1 TTTATTTCA
6174551 TTT
1 TTT
6174554 TCTACGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTATTTCA
Found at i:6185919 original size:15 final size:15
Alignment explanation
Indices: 6185899--6185932 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6185889 TTTCCTTTAT
6185899 AAAAAGAAAGACAAA
1 AAAAAGAAAGACAAA
* *
6185914 AAAAAGGAAGATAAA
1 AAAAAGAAAGACAAA
6185929 AAAA
1 AAAA
6185933 TTTTGTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAGACAAA
Found at i:6198227 original size:32 final size:31
Alignment explanation
Indices: 6198191--6198252 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
6198181 CCAAAGTTGA
* *
6198191 AGTGATGAACAGCAAAAAGGGGAATGGATTGG
1 AGTGATCAACAGCAAAAA-CGGAATGGATTGG
**
6198223 AGTGATCAGTAGCAAAAACGGAATGGATTG
1 AGTGATCAACAGCAAAAACGGAATGGATTG
6198253 ACATGTTGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.40, C:0.08, G:0.34, T:0.18
Consensus pattern (31 bp):
AGTGATCAACAGCAAAAACGGAATGGATTGG
Found at i:6198400 original size:49 final size:49
Alignment explanation
Indices: 6198285--6198413 Score: 172
Period size: 49 Copynumber: 2.6 Consensus size: 49
6198275 TACAGCAACA
* *
6198285 AAGATATTGCAGAACGAGCAAAAGTGAAAGCTGAAAGTAAAACAACAGC
1 AAGATATTGCGGAACGAGCAAAAGAGAAAGCTGAAAGTAAAACAACAGC
* *
6198334 AACCATATTG-GAGAACGAGCAAAAGAGAAAGCTGAAAG-AAAAGAACAGC
1 AA-GATATTGCG-GAACGAGCAAAAGAGAAAGCTGAAAGTAAAACAACAGC
*
6198383 AGAGATATTGCGGAACGAGCGAAAGAGAAAG
1 A-AGATATTGCGGAACGAGCAAAAGAGAAAG
6198414 TCAGAAAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
49 37 0.53
50 33 0.47
ACGTcount: A:0.50, C:0.13, G:0.26, T:0.10
Consensus pattern (49 bp):
AAGATATTGCGGAACGAGCAAAAGAGAAAGCTGAAAGTAAAACAACAGC
Found at i:6216789 original size:20 final size:20
Alignment explanation
Indices: 6216766--6216804 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6216756 TATTTATATA
6216766 TACATATATATGAATACATG
1 TACATATATATGAATACATG
*
6216786 TACATATATATGTATACAT
1 TACATATATATGAATACAT
6216805 ATGTATGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (20 bp):
TACATATATATGAATACATG
Found at i:6229861 original size:104 final size:105
Alignment explanation
Indices: 6229674--6229875 Score: 271
Period size: 104 Copynumber: 1.9 Consensus size: 105
6229664 ATTGGCAACG
* * * * *
6229674 GCTATGATGCTAGTCAACAATAAAATTTGAGTAAAATAAATCTTTTTTACAGTTTACAACTAGTA
1 GCTATGATGCTAGTCAACAACAAAATTTGAGTAAAATAAAACTTTTTTACAATCTACAACAAGTA
* * * * *
6229739 AAATTTATCATTACGACAGCAGTTAGACTTATAGGCAAAA
66 AAATCTACCAATACGACAGAAGTTAAACTTATAGGCAAAA
* * *
6229779 GCTATGATGCTAGTCAACAACAAGA-TTGAGTGATATAAAACTTTTTTACAATCTACAACAAGTA
1 GCTATGATGCTAGTCAACAACAAAATTTGAGTAAAATAAAACTTTTTTACAATCTACAACAAGTA
*
6229843 AAATCTACCAATATGACAGAAGTTAAACTTATA
66 AAATCTACCAATACGACAGAAGTTAAACTTATA
6229876 TACAATGTGG
Statistics
Matches: 83, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
104 60 0.72
105 23 0.28
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (105 bp):
GCTATGATGCTAGTCAACAACAAAATTTGAGTAAAATAAAACTTTTTTACAATCTACAACAAGTA
AAATCTACCAATACGACAGAAGTTAAACTTATAGGCAAAA
Found at i:6231248 original size:15 final size:16
Alignment explanation
Indices: 6231224--6231263 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
6231214 TTGATGGCTT
*
6231224 ACATCACAACC-ACCA
1 ACATCCCAACCAACCA
*
6231239 ACATCCCAACCAACTA
1 ACATCCCAACCAACCA
6231255 ACATCCCAA
1 ACATCCCAA
6231264 GTCCTAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.45, C:0.45, G:0.00, T:0.10
Consensus pattern (16 bp):
ACATCCCAACCAACCA
Found at i:6234697 original size:33 final size:33
Alignment explanation
Indices: 6234642--6234709 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
6234632 TAAGATCCCA
* * *
6234642 TGTTAAGATTTTTTTTTGTTTTGTTTTTTTAAT
1 TGTTAAGATCTTTTCTTATTTTGTTTTTTTAAT
*
6234675 TGTTGAGATCTTTTCTTATTTTGTTTTTTTAAT
1 TGTTAAGATCTTTTCTTATTTTGTTTTTTTAAT
6234708 TG
1 TG
6234710 AATAATAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.15, C:0.03, G:0.13, T:0.69
Consensus pattern (33 bp):
TGTTAAGATCTTTTCTTATTTTGTTTTTTTAAT
Found at i:6235119 original size:13 final size:14
Alignment explanation
Indices: 6235092--6235124 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
6235082 GAATAATATT
6235092 ATTTTTATACATAA
1 ATTTTTATACATAA
*
6235106 ATTTTTCTAC-TAA
1 ATTTTTATACATAA
6235119 ATTTTT
1 ATTTTT
6235125 GAGTTGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTTTATACATAA
Found at i:6236594 original size:20 final size:21
Alignment explanation
Indices: 6236564--6236602 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
6236554 AATAAGTTTT
*
6236564 TAAATTTTTTATTTTTTTAAA
1 TAAATTTTTTATTCTTTTAAA
6236585 TAAA-TTTTTATTCTTTTA
1 TAAATTTTTTATTCTTTTA
6236603 TTATATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (21 bp):
TAAATTTTTTATTCTTTTAAA
Found at i:6237762 original size:31 final size:31
Alignment explanation
Indices: 6237721--6237791 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
6237711 CTTTTTTATA
* **
6237721 ACATGACATTGAGATGATGATGTGGC-ATGCC
1 ACATGGCATTGAG-TGATGACATGGCAATGCC
6237752 ACATGGCATTGAGTGATGACATGGCAATGCC
1 ACATGGCATTGAGTGATGACATGGCAATGCC
6237783 ACATGGCAT
1 ACATGGCAT
6237792 CATATGATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 10 0.28
31 26 0.72
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (31 bp):
ACATGGCATTGAGTGATGACATGGCAATGCC
Found at i:6240150 original size:19 final size:20
Alignment explanation
Indices: 6240116--6240156 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
6240106 TAAGCAGTGG
6240116 ATATCAAATAGATATCACAAC
1 ATATCAAATAGATATCA-AAC
6240137 ATATC-AAT-GATATCAAAC
1 ATATCAAATAGATATCAAAC
6240155 AT
1 AT
6240157 TATAATTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 7 0.35
20 3 0.15
21 5 0.25
ACGTcount: A:0.51, C:0.17, G:0.05, T:0.27
Consensus pattern (20 bp):
ATATCAAATAGATATCAAAC
Found at i:6240362 original size:43 final size:40
Alignment explanation
Indices: 6240315--6240421 Score: 106
Period size: 43 Copynumber: 2.5 Consensus size: 40
6240305 AGTACCCCAG
*
6240315 ATCAAATATATCAAGCATTAGGCTTAGAATTGTAGCACTACAA
1 ATCAAACATATCAAGCATTA---TTAGAATTGTAGCACTACAA
* * * * *
6240358 ATCAAAGATATCAAGTCTAATTATTTGAATTGTATCACTATAG
1 ATCAAACATATCAAG-C--ATTATTAGAATTGTAGCACTACAA
6240401 ATCAAACATATCAAGCATTAT
1 ATCAAACATATCAAGCATTAT
6240422 ACTTGGTACT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
40 5 0.09
42 1 0.02
43 44 0.80
44 1 0.02
46 4 0.07
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (40 bp):
ATCAAACATATCAAGCATTATTAGAATTGTAGCACTACAA
Found at i:6243486 original size:43 final size:42
Alignment explanation
Indices: 6243395--6243492 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 42
6243385 ATATTATGAT
*
6243395 AAATCAAAGATATCAAACATTATAATTGAAATGTAGTACCTC
1 AAATCAAAGATATCAAACATTATAATTGAAATGTAGCACCTC
* * ** **
6243437 ATATCAAATATATCAAGTATTATGCTTGGAAATGTAGCA-CTAC
1 AAATCAAAGATATCAAACATTATAATT-GAAATGTAGCACCT-C
*
6243480 AAATCAATGATAT
1 AAATCAAAGATAT
6243493 AATTAAGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
42 23 0.52
43 21 0.48
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (42 bp):
AAATCAAAGATATCAAACATTATAATTGAAATGTAGCACCTC
Found at i:6256646 original size:23 final size:23
Alignment explanation
Indices: 6256616--6256663 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
6256606 TACTAAGTTA
*
6256616 GATAAACGTTGGAGCAAAACCAG
1 GATAAACGTTAGAGCAAAACCAG
*
6256639 GATAAACGTTAGAGCAAAACTAG
1 GATAAACGTTAGAGCAAAACCAG
6256662 GA
1 GA
6256664 GAACTAGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.25, T:0.15
Consensus pattern (23 bp):
GATAAACGTTAGAGCAAAACCAG
Found at i:6260988 original size:16 final size:16
Alignment explanation
Indices: 6260967--6260999 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6260957 GTTCAAATAC
6260967 TATTTTTTTCCTATTT
1 TATTTTTTTCCTATTT
*
6260983 TATTTTTTTCCTCTTT
1 TATTTTTTTCCTATTT
6260999 T
1 T
6261000 CCCTTTTCCT
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:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTTTTTTCCTATTT
Found at i:6265372 original size:18 final size:19
Alignment explanation
Indices: 6265339--6265374 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6265329 TTGAATGTTT
6265339 TTTTAAAATATAATAATTA
1 TTTTAAAATATAATAATTA
*
6265358 TTTTAATAT-TAATAATT
1 TTTTAAAATATAATAATT
6265375 TAGATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAAAATATAATAATTA
Found at i:6266851 original size:29 final size:28
Alignment explanation
Indices: 6266805--6266901 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 28
6266795 AAACAAATTT
* * * *
6266805 AAATAAAATTTTAGATTTTTTATTATATT
1 AAATAAATTTTTATATTTTTT-TTAAATC
* *
6266834 TAATTAATTTTTATATTTTATTTTAAATC
1 AAATAAATTTTTATATTTT-TTTTAAATC
* *
6266863 AAATAAATTTTTATATTTTTATTTTGAGTC
1 AAATAAATTTTTATA-TTTT-TTTTAAATC
6266893 AAATAAATT
1 AAATAAATT
6266902 CTTTTAATTA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
29 33 0.59
30 23 0.41
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (28 bp):
AAATAAATTTTTATATTTTTTTTAAATC
Found at i:6266885 original size:30 final size:29
Alignment explanation
Indices: 6266839--6266901 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 29
6266829 ATATTTAATT
6266839 AATTTTTATATTTTATTTTAAATCAAATA
1 AATTTTTATATTTTATTTTAAATCAAATA
* *
6266868 AATTTTTATATTTTTATTTTGAGTCAAATA
1 AATTTTTATA-TTTTATTTTAAATCAAATA
6266898 AATT
1 AATT
6266902 CTTTTAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (29 bp):
AATTTTTATATTTTATTTTAAATCAAATA
Found at i:6268201 original size:92 final size:90
Alignment explanation
Indices: 6268044--6268225 Score: 328
Period size: 92 Copynumber: 2.0 Consensus size: 90
6268034 CAGCAAGGGA
* *
6268044 AGTATGTTGCTAAATGCTAACTATCAAATATCTTGAAGTGCTAAAAAGGCATATATATAGGATTA
1 AGTATGTTGCTAAATGCTAACCATCAAATATCTTGAACTGCTAAAAAGGCATATATATAGGATTA
6268109 ATCACCATTCTTTATTTTTATAATATT
66 ATCACCATTC-TT-TTTTTATAATATT
6268136 AGTATGTTGCTAAATGCTAACCATCAAATATCTTGAACTGCTAAAAAGGCATATATATAGGATTA
1 AGTATGTTGCTAAATGCTAACCATCAAATATCTTGAACTGCTAAAAAGGCATATATATAGGATTA
6268201 ATCACCATTCTTTTTTTATAATATT
66 ATCACCATTCTTTTTTTATAATATT
6268226 TTTTAAAAAA
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
90 13 0.15
91 2 0.02
92 73 0.83
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (90 bp):
AGTATGTTGCTAAATGCTAACCATCAAATATCTTGAACTGCTAAAAAGGCATATATATAGGATTA
ATCACCATTCTTTTTTTATAATATT
Found at i:6270974 original size:18 final size:19
Alignment explanation
Indices: 6270942--6270980 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
6270932 GCCCTTGATA
* *
6270942 TTTTCTTTTCTTTTCTTTG
1 TTTTCTTTTCCTTTCCTTG
6270961 TTTT-TTTTCCTTTCCTTG
1 TTTTCTTTTCCTTTCCTTG
6270979 TT
1 TT
6270981 GCTAAAAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTTCTTTTCCTTTCCTTG
Found at i:6282958 original size:12 final size:12
Alignment explanation
Indices: 6282941--6282974 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6282931 CTGACCGTGG
6282941 TCGTGGTCGTAA
1 TCGTGGTCGTAA
*
6282953 TCGTGGTCATAA
1 TCGTGGTCGTAA
*
6282965 TCATGGTCGT
1 TCGTGGTCGT
6282975 GGAAAAGGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (12 bp):
TCGTGGTCGTAA
Found at i:6283397 original size:45 final size:45
Alignment explanation
Indices: 6283348--6283438 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
6283338 CCCAATAATG
*
6283348 AAATTTCTTAAATTATTTGTTGATGTGTTTTAGTACAACTTTATT
1 AAATTTCTTAAATTATTTGTTGATGTCTTTTAGTACAACTTTATT
6283393 AAATTTCTTAAATTATTTGTTGATGTCTTTTAGTACAACTTTATT
1 AAATTTCTTAAATTATTTGTTGATGTCTTTTAGTACAACTTTATT
6283438 A
1 A
6283439 GGACCTTGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.53
Consensus pattern (45 bp):
AAATTTCTTAAATTATTTGTTGATGTCTTTTAGTACAACTTTATT
Found at i:6291691 original size:29 final size:29
Alignment explanation
Indices: 6291638--6291693 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
6291628 TTTGATTCAA
*
6291638 AATAAAAATATAAACACTTAGTTAAATGT
1 AATAAAAATATAAAAACTTAGTTAAATGT
* *
6291667 AATAAAAATATAAAAATTTATTTAAAT
1 AATAAAAATATAAAAACTTAGTTAAAT
6291694 TTTTTGAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.34
Consensus pattern (29 bp):
AATAAAAATATAAAAACTTAGTTAAATGT
Found at i:6291980 original size:16 final size:16
Alignment explanation
Indices: 6291959--6291989 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6291949 TTTGGTTTAA
*
6291959 TGGAATAGCTATTCTT
1 TGGAATAGCCATTCTT
6291975 TGGAATAGCCATTCT
1 TGGAATAGCCATTCT
6291990 AAGAGAAGCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (16 bp):
TGGAATAGCCATTCTT
Found at i:6292237 original size:18 final size:20
Alignment explanation
Indices: 6292212--6292259 Score: 73
Period size: 18 Copynumber: 2.5 Consensus size: 20
6292202 AACATATAGT
*
6292212 TAAATATTATTTAA-TATAA
1 TAAATATTATTTAACAATAA
6292231 T-AATATTATTTAACAATAA
1 TAAATATTATTTAACAATAA
6292250 TAAATATTAT
1 TAAATATTAT
6292260 AAAGAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 12 0.46
19 6 0.23
20 8 0.31
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAATATTATTTAACAATAA
Found at i:6292267 original size:19 final size:19
Alignment explanation
Indices: 6292214--6292282 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 19
6292204 CATATAGTTA
* *
6292214 AATATTATTTAA-TATAAT
1 AATATTATTAAACAATAAT
*
6292232 AATATTATTTAACAATAAT
1 AATATTATTAAACAATAAT
*
6292251 AAATATTA-TAAAGAATATATTT
1 -AATATTATTAAACAATA-A--T
6292273 AATATTATTA
1 AATATTATTA
6292283 TTTGAATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
18 12 0.29
19 12 0.29
20 8 0.19
21 7 0.17
22 3 0.07
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (19 bp):
AATATTATTAAACAATAAT
Found at i:6292282 original size:44 final size:45
Alignment explanation
Indices: 6292228--6292326 Score: 130
Period size: 44 Copynumber: 2.2 Consensus size: 45
6292218 TTATTTAATA
* *
6292228 TAATAATATTATTT-AACAATAATAAATATTATAAAGAATA-TATT
1 TAATATTATTATTTGAA-AATAATAAATATAATAAAGAATATTATT
* *
6292272 TAATATTATTATTTGAATATAATAAATGTAATAAAGAATATTATT
1 TAATATTATTATTTGAAAATAATAAATATAATAAAGAATATTATT
*
6292317 TAGTATTATT
1 TAATATTATT
6292327 TAAATTTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 33 0.69
45 15 0.31
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.44
Consensus pattern (45 bp):
TAATATTATTATTTGAAAATAATAAATATAATAAAGAATATTATT
Found at i:6292429 original size:23 final size:22
Alignment explanation
Indices: 6292364--6292437 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 22
6292354 NTTTAATATT
*
6292364 AAATATTATTTAATTATAATAA
1 AAATATTATTAAATTATAATAA
* ** *
6292386 AAGGT-TTAATTATCTTCTAATACA
1 AA-ATATT-ATTAAATTATAATA-A
*
6292410 AAATATTATTAAATTATAATGA
1 AAATATTATTAAATTATAATAA
6292432 AAATAT
1 AAATAT
6292438 ATTTGTATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
22 11 0.29
23 22 0.58
24 5 0.13
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (22 bp):
AAATATTATTAAATTATAATAA
Found at i:6294317 original size:14 final size:15
Alignment explanation
Indices: 6294299--6294337 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
6294289 AAAATAATAA
6294299 AATTATATAATAATT
1 AATTATATAATAATT
6294314 -ATTATA-AA-AATT
1 AATTATATAATAATT
6294326 AATTA-ATAATAA
1 AATTATATAATAA
6294338 AATTATCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
12 5 0.24
13 8 0.38
14 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTATATAATAATT
Found at i:6301913 original size:15 final size:15
Alignment explanation
Indices: 6301891--6301932 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
6301881 TTGGGCTATT
6301891 GAAAGAAAAGAAAAA
1 GAAAGAAAAGAAAAA
*
6301906 GGAAGAAAAGAAAAA
1 GAAAGAAAAGAAAAA
6301921 GAAAGAGAAAGA
1 GAAAGA-AAAGA
6301933 GAGAGTCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (15 bp):
GAAAGAAAAGAAAAA
Found at i:6302641 original size:14 final size:12
Alignment explanation
Indices: 6302602--6302636 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
6302592 TTTTAACATG
*
6302602 CCCCTCGCTCTC
1 CCCCTCCCTCTC
*
6302614 CCTCTCCCTCTC
1 CCCCTCCCTCTC
6302626 CCCCTCCCTCT
1 CCCCTCCCTCT
6302637 TTCCCATGCA
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:0.00, C:0.69, G:0.03, T:0.29
Consensus pattern (12 bp):
CCCCTCCCTCTC
Found at i:6323659 original size:199 final size:199
Alignment explanation
Indices: 6323319--6323711 Score: 741
Period size: 199 Copynumber: 2.0 Consensus size: 199
6323309 TTAGTAAGTG
*
6323319 TAGACTTGTTATACATCTCAGACAGGTATCAGTATCCTTTCTCCAAAGGTGTTAAAATTGATAGT
1 TAGACTTGTTATACATCTCAGACAGGTATCAATATCCTTTCTCCAAAGGTGTTAAAATTGATAGT
6323384 AATATGGTCTTGTTTTCTTTTTCTCTGTAATTCTGAGATCTATATTAGGAAAAAGTTGAGAATAT
66 AATATGGTCTTGTTTTCTTTTTCTCTGTAATTCTGAGATCTATATTAGGAAAAAGTTGAGAATAT
*
6323449 GAGGTAGACACATGGCCGCATAGTGTGTTGTACATGCCTGCTGTTTGAATGTATAATTTGCATCA
131 GAGGTAGACACATGGCCACATAGTGTGTTGTACATGCCTGCTGTTTGAATGTATAATTTGCATCA
6323514 GGTT
196 GGTT
*
6323518 TAGACTTGTTATACATCTCAGACAGGTATCAATATCCTTTCTCCAAAGGTGTTTAAATTGATAGT
1 TAGACTTGTTATACATCTCAGACAGGTATCAATATCCTTTCTCCAAAGGTGTTAAAATTGATAGT
* *
6323583 AATATGGTCTTGTTTTCTTTTTCTTTGTAATTCTGAGATCTGTATTAGGAAAAAGTTGAGAATAT
66 AATATGGTCTTGTTTTCTTTTTCTCTGTAATTCTGAGATCTATATTAGGAAAAAGTTGAGAATAT
6323648 GAGGTAGACACATGGCCACATAGTGTGTTGTACATGCCTGCTGTTTGAATGTATAATTTGCATC
131 GAGGTAGACACATGGCCACATAGTGTGTTGTACATGCCTGCTGTTTGAATGTATAATTTGCATC
6323712 TGACTATAGT
Statistics
Matches: 189, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
199 189 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (199 bp):
TAGACTTGTTATACATCTCAGACAGGTATCAATATCCTTTCTCCAAAGGTGTTAAAATTGATAGT
AATATGGTCTTGTTTTCTTTTTCTCTGTAATTCTGAGATCTATATTAGGAAAAAGTTGAGAATAT
GAGGTAGACACATGGCCACATAGTGTGTTGTACATGCCTGCTGTTTGAATGTATAATTTGCATCA
GGTT
Found at i:6324363 original size:30 final size:30
Alignment explanation
Indices: 6324327--6324384 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
6324317 CAGAGGAGTG
6324327 TCAGCACCAGCACCCTCAAACTGTAACATT
1 TCAGCACCAGCACCCTCAAACTGTAACATT
6324357 TCAGCACCAGCACCCTCAAACTGTAACA
1 TCAGCACCAGCACCCTCAAACTGTAACA
6324385 CAAGTGAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.38, G:0.10, T:0.17
Consensus pattern (30 bp):
TCAGCACCAGCACCCTCAAACTGTAACATT
Found at i:6341930 original size:28 final size:29
Alignment explanation
Indices: 6341890--6341955 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
6341880 TTAAATGTTC
* *
6341890 AAATATAATTTATTATTTATAC-TTAAAT
1 AAATATAATTTATCATATATACATTAAAT
*
6341918 AAAT-TAATTTTATCATATCTACATTAAAT
1 AAATATAA-TTTATCATATATACATTAAAT
6341947 -AATATAATT
1 AAATATAATT
6341956 CTAATAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
27 3 0.09
28 20 0.62
29 9 0.28
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (29 bp):
AAATATAATTTATCATATATACATTAAAT
Found at i:6341954 original size:29 final size:28
Alignment explanation
Indices: 6341891--6341955 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
6341881 TAAATGTTCA
* *
6341891 AATATAA-TTTATTATTTATACTTAAAT
1 AATATAATTTTATCATATATACTTAAAT
*
6341918 AA-ATTAATTTTATCATATCTACATTAAAT
1 AATA-TAATTTTATCATATATAC-TTAAAT
6341947 AATATAATT
1 AATATAATT
6341956 CTAATAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.03
27 5 0.16
28 11 0.35
29 13 0.42
30 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (28 bp):
AATATAATTTTATCATATATACTTAAAT
Found at i:6351652 original size:224 final size:225
Alignment explanation
Indices: 6351210--6351667 Score: 798
Period size: 224 Copynumber: 2.0 Consensus size: 225
6351200 TAATTTCTTC
* *
6351210 AAAAAATTATTTACATGTTCAAATGCATGCAGGTTATATTTTAGCTATTTACTCATTTTTAATCA
1 AAAAAAATATTTACATGCTCAAATGCATGCAGGTTATATTTTAGCTATTTACTCATTTTTAATCA
6351275 AACATAGTTTTCCTTTTACCATTTGCTTTTGCATTTTTATCAGATTATCACTCAAAATAAACCAA
66 AACATAGTTTTCCTTTTACCATTTGCTTTTGCATTTTTATCAGATTATCACTCAAAATAAACCAA
6351340 ATTTACCACACACACACACACACAAAAACTATCTGATAACCAAAATTGAACAATTTTCATTTAAA
131 ATTTACCACACACACACACACACAAAAACTATCTGATAACCAAAATTGAACAATTTTCATTTAAA
6351405 ATGAAAATGAAATAAATGAT-GAAGTCCTG
196 ATGAAAATGAAATAAATGATAGAAGTCCTG
*
6351434 AAAAAAATATTTATC-TGCTCAAATGCATGCAGGTTATATTTTAGCTATTTGCTCATTTTTAATC
1 AAAAAAATATTTA-CATGCTCAAATGCATGCAGGTTATATTTTAGCTATTTACTCATTTTTAATC
6351498 AAACAT-GCTTTTCCTTTTACCATTTGCTTTTGCATTTTTATCAGATTATCACTCAAAATAAACC
65 AAACATAG-TTTTCCTTTTACCATTTGCTTTTGCATTTTTATCAGATTATCACTCAAAATAAACC
*
6351562 AAATTTACCACACACACACACACACACAAAAACTATCTGATAACCAAAATTGAATAATTTTCATT
129 AAATTTA-C-CACACACACACACACACAAAAACTATCTGATAACCAAAATTGAACAATTTTCATT
*
6351627 TAAAATGAAAATGAAAATAGATGA-AGAAGTCCTG
192 TAAAATGAAAATG-AAATAAATGATAGAAGTCCTG
6351661 AAAAAAA
1 AAAAAAA
6351668 ACAACCCTAA
Statistics
Matches: 223, Mismatches: 5, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
223 1 0.00
224 128 0.57
225 2 0.01
226 67 0.30
227 25 0.11
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.34
Consensus pattern (225 bp):
AAAAAAATATTTACATGCTCAAATGCATGCAGGTTATATTTTAGCTATTTACTCATTTTTAATCA
AACATAGTTTTCCTTTTACCATTTGCTTTTGCATTTTTATCAGATTATCACTCAAAATAAACCAA
ATTTACCACACACACACACACACAAAAACTATCTGATAACCAAAATTGAACAATTTTCATTTAAA
ATGAAAATGAAATAAATGATAGAAGTCCTG
Found at i:6353466 original size:30 final size:29
Alignment explanation
Indices: 6353430--6353500 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
6353420 CATTATAAAA
*
6353430 TTGAACAAGGCTTTTCGTGGTTTCATTAT-T
1 TTGAAC-AGGCTTTT-GTGATTTCATTATCT
* *
6353460 TTGAACAGGGTTTTTTGATTTCATTATCT
1 TTGAACAGGCTTTTGTGATTTCATTATCT
*
6353489 ATGAACAGGCTT
1 TTGAACAGGCTT
6353501 CCTATTTCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 11 0.31
29 18 0.51
30 6 0.17
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.45
Consensus pattern (29 bp):
TTGAACAGGCTTTTGTGATTTCATTATCT
Found at i:6353727 original size:28 final size:27
Alignment explanation
Indices: 6353645--6353770 Score: 121
Period size: 27 Copynumber: 4.7 Consensus size: 27
6353635 ACATTGCATG
* *
6353645 TAACAACTAAATTTTGAATATAGAC--A
1 TAACAATTAAATTTTTAATATA-ACATA
*
6353671 TAACAATTAAATTTTTAATATAACGTA
1 TAACAATTAAATTTTTAATATAACATA
* * *
6353698 TAGCAATTATATTTTTTAATATGACATA
1 TAACAATTA-AATTTTTAATATAACATA
* * **
6353726 TAATAATTAAATTTTCAGCATAACATA
1 TAACAATTAAATTTTTAATATAACATA
*
6353753 TAACAATTATATTTTTAA
1 TAACAATTAAATTTTTAA
6353771 CATGATTTTT
Statistics
Matches: 80, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
25 2 0.03
26 20 0.25
27 36 0.45
28 22 0.28
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (27 bp):
TAACAATTAAATTTTTAATATAACATA
Found at i:6355492 original size:17 final size:17
Alignment explanation
Indices: 6355470--6355507 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
6355460 CATTCCGAGA
6355470 AGGGTGTGGACCTAACT
1 AGGGTGTGGACCTAACT
6355487 AGGGTGTGGACCTAACT
1 AGGGTGTGGACCTAACT
6355504 AGGG
1 AGGG
6355508 AATTTGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.39, T:0.21
Consensus pattern (17 bp):
AGGGTGTGGACCTAACT
Found at i:6357246 original size:33 final size:33
Alignment explanation
Indices: 6357205--6357271 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
6357195 TTTTCGCATG
6357205 ATTAATTAACAAAAATCAAGATCTAATCACTAA
1 ATTAATTAACAAAAATCAAGATCTAATCACTAA
6357238 ATTAATTAACAAAAATCAAGATCTAATCACTAA
1 ATTAATTAACAAAAATCAAGATCTAATCACTAA
6357271 A
1 A
6357272 CAGTTAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.55, C:0.15, G:0.03, T:0.27
Consensus pattern (33 bp):
ATTAATTAACAAAAATCAAGATCTAATCACTAA
Found at i:6360118 original size:2 final size:2
Alignment explanation
Indices: 6360113--6360137 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6360103 ATGATAATGA
6360113 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 A
6360138 AAGCAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6361868 original size:21 final size:21
Alignment explanation
Indices: 6361843--6361911 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
6361833 AGTTTGAATA
6361843 TAGGAATAGGATCACATGGAT
1 TAGGAATAGGATCACATGGAT
* *
6361864 TAGGAATCAAGG-T---TTGAAT
1 TAGGAAT--AGGATCACATGGAT
6361883 ATAGGAATAGGATCACATGGAT
1 -TAGGAATAGGATCACATGGAT
6361905 TAGGAAT
1 TAGGAAT
6361912 CAAGGTGAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
18 3 0.08
19 5 0.14
20 7 0.19
21 14 0.38
22 5 0.14
23 3 0.08
ACGTcount: A:0.39, C:0.07, G:0.28, T:0.26
Consensus pattern (21 bp):
TAGGAATAGGATCACATGGAT
Found at i:6361891 original size:41 final size:41
Alignment explanation
Indices: 6361834--6361917 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
6361824 TAGAATAAAA
6361834 GTTTGAATATAGGAATAGGATCACATGGATTAGGAATCAAG
1 GTTTGAATATAGGAATAGGATCACATGGATTAGGAATCAAG
6361875 GTTTGAATATAGGAATAGGATCACATGGATTAGGAATCAAG
1 GTTTGAATATAGGAATAGGATCACATGGATTAGGAATCAAG
6361916 GT
1 GT
6361918 GAGGCGATAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.27
Consensus pattern (41 bp):
GTTTGAATATAGGAATAGGATCACATGGATTAGGAATCAAG
Found at i:6377786 original size:21 final size:20
Alignment explanation
Indices: 6377737--6377787 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
6377727 CTACATAAAA
6377737 TTAATAATTTAGTTATCAATT
1 TTAAT-ATTTAGTTATCAATT
* *
6377758 GTATTATTTAGTTTAT-ATATT
1 TTAATATTTAG-TTATCA-ATT
6377779 TTAATATTT
1 TTAATATTT
6377788 TTAATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (20 bp):
TTAATATTTAGTTATCAATT
Found at i:6378080 original size:28 final size:26
Alignment explanation
Indices: 6378040--6378093 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
6378030 AAAAATTTAA
*
6378040 ATTTTATTTATGTTATTTATTTGTTT
1 ATTTTATTTATGTAATTTATTTGTTT
6378066 ATTTATATTTGATGTAATTTATTTGTTT
1 ATTT-TATTT-ATGTAATTTATTTGTTT
6378094 GTAACATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.16
27 5 0.20
28 16 0.64
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (26 bp):
ATTTTATTTATGTAATTTATTTGTTT
Found at i:6380948 original size:10 final size:10
Alignment explanation
Indices: 6380933--6380963 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6380923 ATTTTCAGTA
6380933 CTATATATAT
1 CTATATATAT
6380943 CTATATATAT
1 CTATATATAT
*
6380953 ATATATATAT
1 CTATATATAT
6380963 C
1 C
6380964 ACTTATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (10 bp):
CTATATATAT
Done.