Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 22 of 33
Found at i:3517795 original size:19 final size:19
Alignment explanation
Indices: 3517741--3517797 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 19
3517731 AAAAATTATT
*
3517741 AAAATAATA-ATA-TTTTA
1 AAAATAATATTTATTTTTA
* *
3517758 AAATTAAAATTATATTTTTA
1 AAAATAATATT-TATTTTTA
3517778 AAAATAATATTTATTTTTA
1 AAAATAATATTTATTTTTA
3517797 A
1 A
3517798 TATTATTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 7 0.22
19 11 0.34
20 14 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATAATATTTATTTTTA
Found at i:3517804 original size:16 final size:16
Alignment explanation
Indices: 3517780--3517842 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
3517770 TATTTTTAAA
*
3517780 AATAATATTTATTTTT
1 AATAATATTAATTTTT
* * **
3517796 AATATTATTAAATTAA
1 AATAATATTAATTTTT
*
3517812 AATAATATTTATTTTT
1 AATAATATTAATTTTT
*
3517828 AATATTATTAATTTT
1 AATAATATTAATTTT
3517843 AAAATAAAAA
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATAATATTAATTTTT
Found at i:3517819 original size:32 final size:33
Alignment explanation
Indices: 3517778--3517849 Score: 128
Period size: 32 Copynumber: 2.2 Consensus size: 33
3517768 TATATTTTTA
3517778 AAAATAATATTTATTTTTAATATTATTAA-ATT
1 AAAATAATATTTATTTTTAATATTATTAATATT
*
3517810 AAAATAATATTTATTTTTAATATTATTAATTTT
1 AAAATAATATTTATTTTTAATATTATTAATATT
3517843 AAAATAA
1 AAAATAA
3517850 AAAATATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 29 0.76
33 9 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
AAAATAATATTTATTTTTAATATTATTAATATT
Found at i:3517858 original size:33 final size:32
Alignment explanation
Indices: 3517789--3517860 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
3517779 AAATAATATT
* **
3517789 TATTTTTAATATTATTAAATTAAAATAATATT
1 TATTTTTAATATTATTAAATTAAAATAAAAAA
*
3517821 TATTTTTAATATTATTAATTTTAAAATAAAAAA
1 TATTTTTAATATTATTAA-ATTAAAATAAAAAA
3517854 TATTTTT
1 TATTTTT
3517861 CATGTTACCT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
32 18 0.51
33 17 0.49
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
TATTTTTAATATTATTAAATTAAAATAAAAAA
Found at i:3518072 original size:17 final size:16
Alignment explanation
Indices: 3518050--3518097 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
3518040 AGAAAGCTAG
3518050 AAAGGAGAAAAGAAGAA
1 AAAGGA-AAAAGAAGAA
*
3518067 AAAGGAAAAAGGAAAAA
1 AAAGGAAAAA-GAAGAA
*
3518084 AAAAGAAAAA-AAGA
1 AAAGGAAAAAGAAGA
3518098 GAGAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.11
16 4 0.15
17 20 0.74
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAGGAAAAAGAAGAA
Found at i:3518104 original size:18 final size:17
Alignment explanation
Indices: 3518057--3518105 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
3518047 TAGAAAGGAG
*
3518057 AAAAGAAGAAAAAGGAA
1 AAAAGAAGAAAAAGAAA
* *
3518074 AAAGGAAAAAAAAAGAAA
1 AAAAG-AAGAAAAAGAAA
3518092 AAAAGAGAGAAAAA
1 AAAAGA-AGAAAAA
3518106 ATTATTTGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAGAAGAAAAAGAAA
Found at i:3518161 original size:27 final size:26
Alignment explanation
Indices: 3518126--3518204 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 26
3518116 TATATTTGTA
*
3518126 TTATTTTTTATTTAAAATATTATATTT
1 TTATATTTTATTT-AAATATTATATTT
* **
3518153 TTATA-TTT-TTTATATATTA-ATAA
1 TTATATTTTATTTAAATATTATATTT
3518176 TT-TATTTTATTT-AATA-TATATTT
1 TTATATTTTATTTAAATATTATATTT
3518199 TTATAT
1 TTATAT
3518205 GTACGTGTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
22 4 0.10
23 14 0.34
24 13 0.32
25 3 0.07
26 3 0.07
27 4 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTATATTTTATTTAAATATTATATTT
Found at i:3518167 original size:17 final size:17
Alignment explanation
Indices: 3518145--3518204 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
3518135 ATTTAAAATA
3518145 TTATATTTTTATATTTT
1 TTATATTTTTATATTTT
* *
3518162 TTATATATTAATAATTTAT
1 TTATATTTTTAT-ATTT-T
*
3518181 TT-TATTTAATATATATTT
1 TTATATTT-TTATAT-TTT
3518199 TTATAT
1 TTATAT
3518205 GTACGTGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
17 10 0.30
18 13 0.39
19 10 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATTTTTATATTTT
Found at i:3518644 original size:20 final size:20
Alignment explanation
Indices: 3518621--3518677 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
3518611 ATTTAAAATA
*
3518621 TTATATTTTTGTATATTTGT
1 TTATATTTTTGTATATTTAT
* **
3518641 TTATATATTAATA-ATTTAT
1 TTATATTTTTGTATATTTAT
3518660 TT-TATTTTATGTATATTT
1 TTATATTTT-TGTATATTT
3518678 TTATATATAT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
18 5 0.18
19 9 0.32
20 14 0.50
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
TTATATTTTTGTATATTTAT
Found at i:3520618 original size:17 final size:18
Alignment explanation
Indices: 3520585--3520618 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3520575 GGTTTTTATA
*
3520585 ATTTTATATATAATTAAT
1 ATTTTATATAAAATTAAT
3520603 ATTTTA-ATAAAATTAA
1 ATTTTATATAAAATTAA
3520619 CGTCAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTATATAAAATTAAT
Found at i:3520789 original size:17 final size:17
Alignment explanation
Indices: 3520763--3520821 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
3520753 AAATTTATTA
*
3520763 TAAATCATATAAAAAAT
1 TAAATAATATAAAAAAT
3520780 TAAATAATATAAAAAAT
1 TAAATAATATAAAAAAT
* * *
3520797 AAAATATTTTAAATATAAT
1 TAAATAATATAAA-A-AAT
3520816 TAAATA
1 TAAATA
3520822 TATTAATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 26 0.74
18 1 0.03
19 8 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAATAATATAAAAAAT
Found at i:3520792 original size:9 final size:9
Alignment explanation
Indices: 3520761--3520853 Score: 54
Period size: 8 Copynumber: 10.8 Consensus size: 9
3520751 AAAAATTTAT
*
3520761 TATAAATCA
1 TATAAATAA
*
3520770 TATAAAAAA
1 TATAAATAA
3520779 T-TAAATAA
1 TATAAATAA
*
3520787 TATAAAAAA
1 TATAAATAA
*
3520796 TA-AAATAT
1 TATAAATAA
*
3520804 TTTAAAT-A
1 TATAAATAA
3520812 TAATTAAAT-A
1 T-A-TAAATAA
*
3520822 TATTAAT-A
1 TATAAATAA
* *
3520830 TACATATAA
1 TATAAATAA
3520839 TATAAAT-A
1 TATAAATAA
3520847 TATAAAT
1 TATAAAT
3520854 TATCAAATTA
Statistics
Matches: 64, Mismatches: 15, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
8 30 0.47
9 27 0.42
10 7 0.11
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (9 bp):
TATAAATAA
Found at i:3521720 original size:2 final size:2
Alignment explanation
Indices: 3521713--3521749 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3521703 TCTTTAATTC
3521713 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3521750 CAAGATCTCA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3522528 original size:12 final size:12
Alignment explanation
Indices: 3522511--3522535 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3522501 GGTGAGTTAA
3522511 TGTGGCAGCCAG
1 TGTGGCAGCCAG
3522523 TGTGGCAGCCAG
1 TGTGGCAGCCAG
3522535 T
1 T
3522536 TCACTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (12 bp):
TGTGGCAGCCAG
Found at i:3538536 original size:55 final size:55
Alignment explanation
Indices: 3538444--3538567 Score: 142
Period size: 55 Copynumber: 2.3 Consensus size: 55
3538434 GCAACGCCAA
* *
3538444 ATGACGCCAAGTCACCCTCGCCCTGATCGCTAACATGGCGCGTAACTAACCCCAC
1 ATGACGCCAAGTCACCCTCGCCCTGATCGCCAACATGGCACGTAACTAACCCCAC
* * * * * * * *
3538499 GTGATGCCAAGTCACCCTCTCTCT-AGTCGCCACCATGGCATGTAACTAGCCCCAT
1 ATGACGCCAAGTCACCCTCGCCCTGA-TCGCCAACATGGCACGTAACTAACCCCAC
3538554 ATGACGCCAAGTCA
1 ATGACGCCAAGTCA
3538568 TTGGGCCCCC
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
54 1 0.02
55 55 0.98
ACGTcount: A:0.25, C:0.37, G:0.19, T:0.19
Consensus pattern (55 bp):
ATGACGCCAAGTCACCCTCGCCCTGATCGCCAACATGGCACGTAACTAACCCCAC
Found at i:3543148 original size:14 final size:13
Alignment explanation
Indices: 3543115--3543157 Score: 63
Period size: 14 Copynumber: 3.4 Consensus size: 13
3543105 TATTATTTTT
3543115 TAAA-TTAAAT-A
1 TAAATTTAAATAA
3543126 TAAATTTAAATAA
1 TAAATTTAAATAA
3543139 TAATATTTAAATAA
1 TAA-ATTTAAATAA
3543153 TAAAT
1 TAAAT
3543158 AGATGATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.14
12 6 0.21
13 6 0.21
14 13 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAATTTAAATAA
Found at i:3547094 original size:18 final size:18
Alignment explanation
Indices: 3547032--3547107 Score: 95
Period size: 18 Copynumber: 4.4 Consensus size: 18
3547022 CAAGGTCACG
*
3547032 ATCAATATTGTCACTATC
1 ATCAATATCGTCACTATC
* * *
3547050 ATCAATAGCTTCACTAGC
1 ATCAATATCGTCACTATC
3547068 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTATC
3547086 ATCAATATCG--A-TATC
1 ATCAATATCGTCACTATC
3547101 ATCAATA
1 ATCAATA
3547108 AGAAAACCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
15 11 0.22
16 1 0.02
18 39 0.76
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.33
Consensus pattern (18 bp):
ATCAATATCGTCACTATC
Found at i:3554646 original size:27 final size:27
Alignment explanation
Indices: 3554607--3554695 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
3554597 AGTGTGAAAA
3554607 AAAAACATT-AAATTTTTATTTAAATTT
1 AAAAA-ATTAAAATTTTTATTTAAATTT
*
3554634 AAAAAATTAAAATTATTATTTAAATATT
1 AAAAAATTAAAATTTTTATTTAAAT-TT
3554662 AATAAAAATTAAAAATATTTTATATTAACATTT
1 -A-AAAAATT-AAAAT-TTTTAT-TTAA-ATTT
3554695 A
1 A
3554696 TATATTTTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
26 3 0.06
27 20 0.38
28 2 0.04
29 1 0.02
30 7 0.13
31 5 0.10
32 6 0.12
33 6 0.12
34 2 0.04
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
AAAAAATTAAAATTTTTATTTAAATTT
Found at i:3555055 original size:23 final size:25
Alignment explanation
Indices: 3555029--3555078 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
3555019 AAGAAACTTT
3555029 TAAATATTTTT-A-TTATATTTAAA
1 TAAATATTTTTAATTTATATTTAAA
*
3555052 TAAATTTTTTTAATTTTATATTTAAA
1 TAAATATTTTTAA-TTTATATTTAAA
3555078 T
1 T
3555079 CAAACTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 10 0.43
24 1 0.04
26 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TAAATATTTTTAATTTATATTTAAA
Found at i:3555812 original size:20 final size:20
Alignment explanation
Indices: 3555787--3555855 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
3555777 ATAATTAATA
*
3555787 TTATATAAATTTTAATATAT
1 TTATATAAATTTTATTATAT
*
3555807 TTATATAATAATTTTATTATTT
1 TTATAT-A-AATTTTATTATAT
* * *
3555829 TTATTTATATTATATTATAT
1 TTATATAAATTTTATTATAT
3555849 ATTATAT
1 -TTATAT
3555856 TTTAATTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 16 0.41
21 7 0.18
22 16 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATATAAATTTTATTATAT
Found at i:3555849 original size:12 final size:12
Alignment explanation
Indices: 3555801--3555856 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
3555791 ATAAATTTTA
*
3555801 ATATATTTATATA
1 ATATA-TTATATT
*
3555814 ATA-ATTTTATT
1 ATATATTATATT
3555825 AT-T-TT-TATT
1 ATATATTATATT
3555834 -TATATTATATT
1 ATATATTATATT
3555845 ATATATTATATT
1 ATATATTATATT
3555857 TTAATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
8 1 0.03
9 5 0.14
10 4 0.11
11 11 0.31
12 12 0.33
13 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATATTATATT
Found at i:3556654 original size:22 final size:21
Alignment explanation
Indices: 3556626--3556668 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3556616 TATGTATTCA
* *
3556626 TATTATATTATATTATATATTT
1 TATTATATCATAATA-ATATTT
3556648 TATTATATCATAATAATATTT
1 TATTATATCATAATAATATTT
3556669 AAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTATATCATAATAATATTT
Found at i:3556722 original size:32 final size:33
Alignment explanation
Indices: 3556671--3556732 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
3556661 TAATATTTAA
*
3556671 AATATTTTATATTTATATAAAATTTAATATGTT
1 AATAATTTATATTTATATAAAATTTAATATGTT
* *
3556704 AATAATTTATA-TTATATAAATTTTTATAT
1 AATAATTTATATTTATATAAAATTTAATAT
3556733 ATTTATGTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 16 0.62
33 10 0.38
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (33 bp):
AATAATTTATATTTATATAAAATTTAATATGTT
Found at i:3557524 original size:30 final size:31
Alignment explanation
Indices: 3557490--3557551 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
3557480 TTACACTTTA
*
3557490 TTAATAAAATTATTA-A-TTAATATATTTAAT
1 TTAATAAAATTATTATAGATAATATA-TTAAT
**
3557520 TTAATATTATTATTATAGATAATATATTAAT
1 TTAATAAAATTATTATAGATAATATATTAAT
3557551 T
1 T
3557552 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 13 0.48
31 7 0.26
32 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (31 bp):
TTAATAAAATTATTATAGATAATATATTAAT
Found at i:3559542 original size:13 final size:13
Alignment explanation
Indices: 3559524--3559552 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3559514 TGATGTGACT
3559524 TTTAATTAAAATA
1 TTTAATTAAAATA
3559537 TTTAATTAAAATA
1 TTTAATTAAAATA
3559550 TTT
1 TTT
3559553 GATCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTAATTAAAATA
Found at i:3560363 original size:2 final size:2
Alignment explanation
Indices: 3560356--3560381 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3560346 TAAATTCGCT
3560356 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
3560382 ATCTGTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3560490 original size:14 final size:14
Alignment explanation
Indices: 3560434--3560493 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
3560424 AAATAAAATA
* *
3560434 TTTAAATATTTAAA
1 TTTATATATTTAAT
* *
3560448 TTT-GATATTTATT
1 TTTATATATTTAAT
3560461 TATATATATATTTAAT
1 T-T-TATATATTTAAT
3560477 TTTATATATTTAAT
1 TTTATATATTTAAT
3560491 TTT
1 TTT
3560494 TTAAAAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 8 0.21
14 19 0.50
15 2 0.05
16 9 0.24
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TTTATATATTTAAT
Found at i:3560533 original size:19 final size:19
Alignment explanation
Indices: 3560499--3560544 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3560489 ATTTTTTAAA
*
3560499 AAAT-TATTTTATAAATTT
1 AAATATATTTTATAAATAT
3560517 AAATATATTATTA-AAATAT
1 AAATATATT-TTATAAATAT
3560536 AAATATATT
1 AAATATATT
3560545 CAAATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 4 0.16
19 18 0.72
20 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAATATATTTTATAAATAT
Found at i:3560541 original size:17 final size:17
Alignment explanation
Indices: 3560525--3560557 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3560515 TTAAATATAT
3560525 TATTAAAAT-ATAAATA
1 TATTAAAATAATAAATA
*
3560541 TATTCAAATAATAAATA
1 TATTAAAATAATAAATA
3560558 AACTCAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
TATTAAAATAATAAATA
Found at i:3560549 original size:16 final size:16
Alignment explanation
Indices: 3560525--3560568 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
3560515 TTAAATATAT
*
3560525 TATTAAAATATAAATA
1 TATTCAAATATAAATA
3560541 TATTCAAATAATAAATA
1 TATTCAAAT-ATAAATA
* *
3560558 AACTCAAATAT
1 TATTCAAATAT
3560569 TATATAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (16 bp):
TATTCAAATATAAATA
Found at i:3560564 original size:17 final size:17
Alignment explanation
Indices: 3560530--3560586 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
3560520 TATATTATTA
* *
3560530 AAAT-ATAAATATATTC
1 AAATAATAAATAAACTC
3560546 AAATAATAAATAAACTC
1 AAATAATAAATAAACTC
* *
3560563 AAATATTATATAAAC-C
1 AAATAATAAATAAACTC
3560579 AAACTAAT
1 AAA-TAAT
3560587 TCGTATTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 8 0.24
17 26 0.76
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAATAAATAAACTC
Found at i:3560891 original size:24 final size:23
Alignment explanation
Indices: 3560834--3560892 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 23
3560824 AATATTGTTT
*
3560834 ATTTTTTTTATTATATTTAAATAA
1 ATTTTTATT-TTATATTTAAATAA
3560858 A-TTTTATTTTATAATTTAAATAA
1 ATTTTTATTTTAT-ATTTAAATAA
3560881 ATTTTTATTTTA
1 ATTTTTATTTTA
3560893 AAGAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 4 0.12
23 17 0.53
24 11 0.34
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTTTTATTTTATATTTAAATAA
Found at i:3567945 original size:34 final size:32
Alignment explanation
Indices: 3567907--3567980 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 32
3567897 GAAATTTTTG
3567907 TAAATTTGATCTTAAT-ATAAAATAATATTTTATT
1 TAAATTTGAT-TTAATAATAAAAT-AT-TTTTATT
*
3567941 TAAATTATTATTTAATAATAAAATATTTTTATT
1 TAAATT-TGATTTAATAATAAAATATTTTTATT
3567974 TAAATTT
1 TAAATTT
3567981 AATTATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
32 1 0.03
33 13 0.35
34 13 0.35
35 10 0.27
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (32 bp):
TAAATTTGATTTAATAATAAAATATTTTTATT
Found at i:3568305 original size:29 final size:29
Alignment explanation
Indices: 3568238--3568311 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
3568228 TCATTTATAT
* *
3568238 AATATTAATTAATTATATTATTTTATTAA
1 AATAATAATTATTTATATTATTTTATTAA
*
3568267 AATAAAAATTATTTATA-TATTTT-TTAA
1 AATAATAATTATTTATATTATTTTATTAA
*
3568294 AATGACATAATTCTTTAT
1 AAT-A-ATAATTATTTAT
3568312 TAATAATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
27 7 0.18
28 7 0.18
29 24 0.63
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (29 bp):
AATAATAATTATTTATATTATTTTATTAA
Found at i:3568644 original size:3 final size:3
Alignment explanation
Indices: 3568636--3568679 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3568626 ATTTTTACAC
3568636 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3568680 TGAAATTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3568802 original size:2 final size:2
Alignment explanation
Indices: 3568795--3568827 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3568785 TTTGAGATCC
3568795 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
3568828 AGATCAATTT
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:3569068 original size:59 final size:58
Alignment explanation
Indices: 3569005--3569162 Score: 126
Period size: 59 Copynumber: 2.7 Consensus size: 58
3568995 TATAATTATG
* * *
3569005 AAAATATAATATATATAAAAAATAAAATAATAAAATAATATGATATAAATATATTTTAA
1 AAAATATAATATATATAAAAAATAAAATAATAAAATAATAT-AAATAAAAATATATTAA
** * * * *
3569064 AAAAT-T-ATATAATATTAATTATTAATATATTAAAATTATTATAAATAAAAATATATTAA
1 AAAATATAATAT-ATA-TAAAAAATAAAATAATAAAA-TAATATAAATAAAAATATATTAA
*
3569123 ATATAATTATAATATA-ATAAAAAATATAAAT-ATAATATAA
1 A-A-AA-TATAATATATATAAAAAATA-AAATAATAAAATAA
3569163 CTACATAAAA
Statistics
Matches: 74, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
57 4 0.05
58 4 0.05
59 35 0.47
60 8 0.11
61 12 0.16
62 5 0.07
63 2 0.03
64 4 0.05
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (58 bp):
AAAATATAATATATATAAAAAATAAAATAATAAAATAATATAAATAAAAATATATTAA
Found at i:3569087 original size:17 final size:18
Alignment explanation
Indices: 3569067--3569110 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
3569057 ATTTTAAAAA
3569067 ATTATATAATATT-AATT
1 ATTATATAATATTAAATT
3569084 ATTA-AT-ATATTAAAATT
1 ATTATATAATATT-AAATT
3569101 ATTATA-AATA
1 ATTATATAATA
3569111 AAAATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 5 0.22
16 2 0.09
17 12 0.52
18 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTATATAATATTAAATT
Found at i:3569092 original size:20 final size:20
Alignment explanation
Indices: 3569069--3569137 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
3569059 TTTAAAAAAT
3569069 TATATAATATTAATTATTAA
1 TATATAATATTAATTATTAA
* *
3569089 TATATTAAAATT-ATTATAAA
1 TATA-TAATATTAATTATTAA
* * *
3569109 TAAAAATATATTAAATA-TAA
1 TATATA-ATATTAATTATTAA
3569129 T-TATAATAT
1 TATATAATAT
3569138 AATAAAAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
18 4 0.11
19 3 0.08
20 21 0.57
21 9 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATATAATATTAATTATTAA
Found at i:3569121 original size:26 final size:28
Alignment explanation
Indices: 3569087--3569162 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
3569077 ATTAATTATT
*
3569087 AATATATTAAA-ATTATTATAA-ATAAA
1 AATATATTAAATATAATTATAATATAAA
3569113 AATATATTAAATATAATTATAATATAATA
1 AATATATTAAATATAATTATAATATAA-A
*
3569142 AA-AAATATAAATATAA-TATAA
1 AATATAT-TAAATATAATTATAA
3569163 CTACATAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
26 11 0.25
27 9 0.20
28 12 0.27
29 12 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
AATATATTAAATATAATTATAATATAAA
Found at i:3569173 original size:29 final size:30
Alignment explanation
Indices: 3569097--3569175 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
3569087 AATATATTAA
* * *
3569097 AATTATTATAAATAAAAATATATTAAATAT
1 AATTATAATACATAAAAAAATATTAAATAT
*
3569127 AATTATAATATA-ATAAAAAATA-TAAATAT
1 AATTATAATACATA-AAAAAATATTAAATAT
3569156 AA-TATAACTACATAAAAAAA
1 AATTATAA-TACATAAAAAAA
3569176 AATTCAACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 5 0.12
29 19 0.45
30 18 0.43
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (30 bp):
AATTATAATACATAAAAAAATATTAAATAT
Found at i:3569177 original size:32 final size:29
Alignment explanation
Indices: 3569097--3569177 Score: 74
Period size: 30 Copynumber: 2.6 Consensus size: 29
3569087 AATATATTAA
* *
3569097 AATTATTATAAATAAAAATATATTAAATAT
1 AATTATAATAAA-AAAAAAATATTAAATAT
*
3569127 AATTATAATATAATAAAAAATA-TAAATAT
1 AATTATAATA-AAAAAAAAATATTAAATAT
3569156 AATATAACTACATAAAAAAAAA
1 AAT-T-A-TA-ATAAAAAAAAA
3569178 TTCAACATGC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
29 10 0.24
30 17 0.40
31 3 0.07
32 9 0.21
33 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.32
Consensus pattern (29 bp):
AATTATAATAAAAAAAAAATATTAAATAT
Found at i:3569374 original size:15 final size:15
Alignment explanation
Indices: 3569356--3569384 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3569346 TTTTTTATTT
3569356 AAATTTAAATTAATC
1 AAATTTAAATTAATC
3569371 AAATTTAAATTAAT
1 AAATTTAAATTAAT
3569385 TAATTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTTAAATTAATC
Found at i:3570554 original size:2 final size:2
Alignment explanation
Indices: 3570547--3570584 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3570537 ATTAAAAGGG
*
3570547 AT AT AT AT GT 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
3570585 TCAAAAAGAA
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:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3573885 original size:10 final size:10
Alignment explanation
Indices: 3573864--3573903 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
3573854 TTTTATTTTA
3573864 AAATATAATTT
1 AAATA-AATTT
*
3573875 AAGTAAATTT
1 AAATAAATTT
3573885 AAATAAATTT
1 AAATAAATTT
*
3573895 AAATTAATT
1 AAATAAATT
3573904 ATTTATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 22 0.85
11 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (10 bp):
AAATAAATTT
Found at i:3574929 original size:3 final size:3
Alignment explanation
Indices: 3574921--3574947 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3574911 TTCTCGGGTT
3574921 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
3574948 AGTTTTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3576031 original size:3 final size:3
Alignment explanation
Indices: 3576017--3576069 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
3576007 TGGGGAAATG
* *
3576017 AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3576065 AAT AA
1 AAT AA
3576070 CATTAGGAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3582542 original size:4 final size:4
Alignment explanation
Indices: 3582535--3582561 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3582525 TTATCAAAGA
3582535 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
3582562 GAATTGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:3582581 original size:17 final size:17
Alignment explanation
Indices: 3582559--3582591 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3582549 ATAAATAAAT
3582559 AAAGAAT-TGAATAAAAA
1 AAAGAATAT-AATAAAAA
3582576 AAAGAATATAATAAAA
1 AAAGAATATAATAAAA
3582592 TTACATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (17 bp):
AAAGAATATAATAAAAA
Found at i:3582902 original size:8 final size:8
Alignment explanation
Indices: 3582889--3582981 Score: 123
Period size: 8 Copynumber: 11.6 Consensus size: 8
3582879 TTGTTAAAAT
3582889 TATATATA
1 TATATATA
3582897 TATATATA
1 TATATATA
*
3582905 TATGTATA
1 TATATATA
*
3582913 TATGTATA
1 TATATATA
*
3582921 TATATATG
1 TATATATA
*
3582929 TATATATG
1 TATATATA
3582937 TATATATA
1 TATATATA
3582945 TATATATA
1 TATATATA
*
3582953 TGTATATA
1 TATATATA
*
3582961 TGTATATA
1 TATATATA
*
3582969 TATATGTA
1 TATATATA
3582977 TATAT
1 TATAT
3582982 TCAAACATAT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 78 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (8 bp):
TATATATA
Found at i:3582906 original size:12 final size:12
Alignment explanation
Indices: 3582889--3582981 Score: 123
Period size: 12 Copynumber: 7.8 Consensus size: 12
3582879 TTGTTAAAAT
3582889 TATATATATATA
1 TATATATATATA
*
3582901 TATATATGTATA
1 TATATATATATA
*
3582913 TATGTATATATA
1 TATATATATATA
* *
3582925 TATGTATATATG
1 TATATATATATA
3582937 TATATATATATA
1 TATATATATATA
*
3582949 TATATGTATATA
1 TATATATATATA
*
3582961 TGTATATATATA
1 TATATATATATA
*
3582973 TGTATATAT
1 TATATATAT
3582982 TCAAACATAT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 72 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (12 bp):
TATATATATATA
Found at i:3582914 original size:20 final size:20
Alignment explanation
Indices: 3582889--3582981 Score: 136
Period size: 20 Copynumber: 4.8 Consensus size: 20
3582879 TTGTTAAAAT
* *
3582889 TATATATATATATATATATG
1 TATATATGTATATATATATA
*
3582909 TATATATGTATATATATATG
1 TATATATGTATATATATATA
3582929 TATATATG--TATATATATA
1 TATATATGTATATATATATA
*
3582947 TATATATGTATATATGTATA
1 TATATATGTATATATATATA
3582967 TATATATGTATATAT
1 TATATATGTATATAT
3582982 TCAAACATAT
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
18 17 0.25
20 51 0.75
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
TATATATGTATATATATATA
Found at i:3583868 original size:20 final size:20
Alignment explanation
Indices: 3583824--3583869 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
3583814 ATTAATGTTA
3583824 AATTTATTTAAAAATTAAATC
1 AATTTATTT-AAAATTAAATC
*
3583845 -ATTTATTT-AATTTAAACTC
1 AATTTATTTAAAATTAAA-TC
3583864 AATTTA
1 AATTTA
3583870 ATCTAAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 7 0.32
19 2 0.09
20 13 0.59
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTTATTTAAAATTAAATC
Found at i:3585328 original size:3 final size:3
Alignment explanation
Indices: 3585320--3585346 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3585310 AGACGGAGAG
3585320 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
3585347 AAATCTGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3586172 original size:21 final size:21
Alignment explanation
Indices: 3586146--3586186 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3586136 TGTATTTTGC
3586146 AGCAAATA-GAAAAGAAAAGAA
1 AGCAAA-AGGAAAAGAAAAGAA
*
3586167 AGCAAAAGGAAAAGGAAAGA
1 AGCAAAAGGAAAAGAAAAGA
3586187 GTGATGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.68, C:0.05, G:0.24, T:0.02
Consensus pattern (21 bp):
AGCAAAAGGAAAAGAAAAGAA
Found at i:3589070 original size:22 final size:23
Alignment explanation
Indices: 3589040--3589082 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3589030 TATTTATATT
*
3589040 AATATTTTAATT-ATTGAGTTTA
1 AATAATTTAATTAATTGAGTTTA
*
3589062 AATAATTTATTTAATTGAGTT
1 AATAATTTAATTAATTGAGTT
3589083 AATATCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (23 bp):
AATAATTTAATTAATTGAGTTTA
Found at i:3589763 original size:20 final size:19
Alignment explanation
Indices: 3589742--3589780 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
3589732 ATTATATTTA
3589742 AAATATTATATATTTATAT
1 AAATATTATATATTTATAT
*
3589761 AAATTTTAATATATTTATAT
1 AAATATT-ATATATTTATAT
3589781 TATTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AAATATTATATATTTATAT
Found at i:3589774 original size:36 final size:36
Alignment explanation
Indices: 3589711--3589793 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
3589701 ATAGATTAAT
**
3589711 TTATATATTTTATGCATTATAATTATATTTAAAATA
1 TTATATATTTTATAAATTATAATTATATTTAAAATA
* * *
3589747 TTATATATTTATATAAATTTTAA-TATATTTATATTA
1 TTATATATTT-TATAAATTATAATTATATTTAAAATA
*
3589783 TTTTATATTTT
1 TTATATATTTT
3589794 TATTATATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 1 0.03
36 30 0.75
37 9 0.22
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (36 bp):
TTATATATTTTATAAATTATAATTATATTTAAAATA
Found at i:3589790 original size:18 final size:19
Alignment explanation
Indices: 3589747--3589822 Score: 81
Period size: 18 Copynumber: 4.2 Consensus size: 19
3589737 ATTTAAAATA
*
3589747 TTATATATTTATA-TAAATT
1 TTATATATTTATATTATA-T
3589766 TTAATATATTTATATTAT-T
1 TT-ATATATTTATATTATAT
3589785 TTATAT-TTT-TATTATAT
1 TTATATATTTATATTATAT
*
3589802 TTTTATA-TTATATTATAT
1 TTATATATTTATATTATAT
3589820 TTA
1 TTA
3589823 AAATTACTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
16 6 0.12
17 11 0.22
18 14 0.29
19 5 0.10
20 11 0.22
21 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATATATTTATATTATAT
Found at i:3589791 original size:16 final size:16
Alignment explanation
Indices: 3589733--3589822 Score: 63
Period size: 16 Copynumber: 5.2 Consensus size: 16
3589723 TGCATTATAA
* *
3589733 TTATATTTAAAATATT
1 TTATATTTATATTATT
* *
3589749 ATATATTTATATAAATTT
1 TTATATTTATAT-TA-TT
3589767 TAATATATTTATATTATT
1 T--TATATTTATATTATT
*
3589785 TTATATTTTTATTATAT
1 TTATATTTATATTAT-T
*
3589802 TTTTATATTATATTATAT
1 TTATAT-TTATATTAT-T
3589820 TTA
1 TTA
3589823 AAATTACTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
16 22 0.38
17 7 0.12
18 17 0.29
19 1 0.02
20 11 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATATTTATATTATT
Found at i:3589801 original size:11 final size:11
Alignment explanation
Indices: 3589775--3589807 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3589765 TTTAATATAT
*
3589775 TTATATTATT-
1 TTATATTTTTA
3589785 TTATATTTTTA
1 TTATATTTTTA
3589796 TTATATTTTTA
1 TTATATTTTTA
3589807 T
1 T
3589808 ATTATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATATTTTTA
Found at i:3591294 original size:29 final size:29
Alignment explanation
Indices: 3591229--3591297 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
3591219 AATGATTATA
3591229 ATTTTTTAAAATAAAAAAATTTAAATATT
1 ATTTTTTAAAATAAAAAAATTTAAATATT
*** * *
3591258 AAAATTTAAATTAAAATATATTT-AATATT
1 ATTTTTTAAAATAAAA-AAATTTAAATATT
3591287 ATTTTTTAAAA
1 ATTTTTTAAAA
3591298 ATAATTATAT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTTTTTAAAATAAAAAAATTTAAATATT
Found at i:3592029 original size:142 final size:134
Alignment explanation
Indices: 3591776--3592112 Score: 557
Period size: 142 Copynumber: 2.4 Consensus size: 134
3591766 TGCTTAATCA
3591776 AAAACCCACCAAGAATCAGATCAAATTTCACTAAATCTAGGTAATTTTGGGGTCCCATTTCCCTA
1 AAAACCCACCAAGAATCAGATCAAATTTCACTAAATCTAGGTAATTTTGGGGTCCCATTTCCCTA
3591841 AAAATTAGGATTTCCTCAGTCTTAACTGATATCTATATATATATATATATATATACATATTACCT
66 AAAATTAGGATTTCCTCAGTCTTAACTG------ATATATATATATATATATAT--ATATTACCT
3591906 TATTTAATTAAG
123 TATTTAATTAAG
*
3591918 AAAACCCACCAAGAATCAGATCAAATTTCACTAAATCTAGGTAAATTTGGGGTCCCATTTCCCTA
1 AAAACCCACCAAGAATCAGATCAAATTTCACTAAATCTAGGTAATTTTGGGGTCCCATTTCCCTA
*
3591983 AAAATTAGGATTTCTTCAGTCTTAACTGATATATATATATATATATATATATTACCTTATTTAAT
66 AAAATTAGGATTTCCTCAGTCTTAACTGATATATATATATATATATATATATTACCTTATTTAAT
3592048 TAAG
131 TAAG
* *
3592052 AAAACCCACCAAGAATCAGATCAAATTTCACTAAGTCTAGGTATTTTTGAGGGTCCCATTT
1 AAAACCCACCAAGAATCAGATCAAATTTCACTAAATCTAGGTAATTTTG-GGGTCCCATTT
3592113 GACAGAAAAG
Statistics
Matches: 189, Mismatches: 5, Indels: 9
0.93 0.02 0.04
Matches are distributed among these distances:
134 67 0.35
135 11 0.06
136 20 0.11
142 91 0.48
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (134 bp):
AAAACCCACCAAGAATCAGATCAAATTTCACTAAATCTAGGTAATTTTGGGGTCCCATTTCCCTA
AAAATTAGGATTTCCTCAGTCTTAACTGATATATATATATATATATATATATTACCTTATTTAAT
TAAG
Found at i:3594482 original size:10 final size:11
Alignment explanation
Indices: 3594454--3594486 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3594444 TATATATCTC
3594454 TAATTTATTTT
1 TAATTTATTTT
3594465 TAATTTATTTT
1 TAATTTATTTT
*
3594476 TTA-TTATTTT
1 TAATTTATTTT
3594486 T
1 T
3594487 CTTAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TAATTTATTTT
Found at i:3596154 original size:23 final size:22
Alignment explanation
Indices: 3596112--3596155 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3596102 ACTAAAAAAT
*
3596112 TTTAAAAATAATATTTAATAAA
1 TTTAAAAATAATATTCAATAAA
3596134 TTTAAAAATTAA-ATATCAATAA
1 TTTAAAAA-TAATAT-TCAATAA
3596156 CTTTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAAATAATATTCAATAAA
Found at i:3611406 original size:36 final size:37
Alignment explanation
Indices: 3611325--3611398 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
3611315 AGTTTTTAAA
3611325 AAAATAATAAATTAAAATATAAATGAATAATTATTTTT
1 AAAATAATAAATTAAAATATAAAT-AATAATTATTTTT
* *
3611363 AAAATAATAAA-TAAATATTTAAAT-ATGATTATTTTT
1 AAAATAATAAATTAAA-ATATAAATAATAATTATTTTT
3611399 TAGATAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 11 0.33
37 4 0.12
38 18 0.55
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (37 bp):
AAAATAATAAATTAAAATATAAATAATAATTATTTTT
Found at i:3611497 original size:18 final size:19
Alignment explanation
Indices: 3611476--3611517 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
3611466 AATTTTAAAT
*
3611476 TAAATTAATATT-ATTTAA
1 TAAATTAATATTAAATTAA
3611494 TAAA-TAATATTAAATTAA
1 TAAATTAATATTAAATTAA
3611512 TAAATT
1 TAAATT
3611518 GTATTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 7 0.33
18 13 0.62
19 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAATTAATATTAAATTAA
Found at i:3611505 original size:28 final size:30
Alignment explanation
Indices: 3611474--3611547 Score: 91
Period size: 28 Copynumber: 2.5 Consensus size: 30
3611464 AAAATTTTAA
3611474 ATTAAATTAATATTATT-TA-ATAAATAAT
1 ATTAAATTAATATTATTGTATATAAATAAT
*
3611502 ATTAAATTAATA-AATTGTATTATAAATAAT
1 ATTAAATTAATATTATTGTA-TATAAATAAT
*
3611532 ATAAATATTAATATTA
1 ATTAA-ATTAATATTA
3611548 ATACGACTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 3 0.08
28 14 0.37
30 13 0.34
31 7 0.18
32 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (30 bp):
ATTAAATTAATATTATTGTATATAAATAAT
Found at i:3611508 original size:33 final size:33
Alignment explanation
Indices: 3611470--3611550 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 33
3611460 ATTTAAAATT
3611470 TTAAATTAAATTAATATTAT-TTAATAAATAATA
1 TTAAATTAAATTAATATTATATT-ATAAATAATA
*
3611503 TTAAATT-AA-TAA-ATTGTATTATAAATAATA
1 TTAAATTAAATTAATATTATATTATAAATAATA
*
3611533 TAAATATTAATATTAATA
1 TTAA-ATTAA-ATTAATA
3611551 CGACTACTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
30 17 0.43
31 8 0.20
32 3 0.08
33 8 0.20
34 3 0.08
35 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (33 bp):
TTAAATTAAATTAATATTATATTATAAATAATA
Found at i:3612480 original size:2 final size:2
Alignment explanation
Indices: 3612467--3612498 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3612457 ATTATTATTA
*
3612467 TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3612499 GCTAATTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3613604 original size:24 final size:26
Alignment explanation
Indices: 3613570--3613630 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
3613560 ACATAAAATT
* *
3613570 TAAAATTAAATTA-TAATA-ATTTTA
1 TAAAATAAAATTATTAAAATATTTTA
*
3613594 TAAAATAAAA-TATTAAAATATTTTT
1 TAAAATAAAATTATTAAAATATTTTA
3613619 TAAAATAAAATT
1 TAAAATAAAATT
3613631 TAAATACCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 2 0.06
24 13 0.42
25 15 0.48
26 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAAATAAAATTATTAAAATATTTTA
Found at i:3613618 original size:26 final size:25
Alignment explanation
Indices: 3613579--3613634 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
3613569 TTAAAATTAA
*
3613579 ATTATAATAATTTTATAAAATAAAAT
1 ATTAAAATAATTTT-TAAAATAAAAT
*
3613605 ATTAAAATATTTTTTAAAATAAAAT
1 ATTAAAATAATTTTTAAAATAAAAT
3613630 -TTAAA
1 ATTAAA
3613635 TACCTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 5 0.18
25 11 0.39
26 12 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTAAAATAATTTTTAAAATAAAAT
Found at i:3613622 original size:25 final size:26
Alignment explanation
Indices: 3613579--3613634 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
3613569 TTAAAATTAA
*
3613579 ATTATAATAATTTTATAAAATAAAAT
1 ATTAAAATAATTTTATAAAATAAAAT
*
3613605 ATTAAAAT-ATTTTTTAAAATAAAAT
1 ATTAAAATAATTTTATAAAATAAAAT
3613630 -TTAAA
1 ATTAAA
3613635 TACCTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 5 0.18
25 16 0.57
26 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTAAAATAATTTTATAAAATAAAAT
Found at i:3613632 original size:12 final size:12
Alignment explanation
Indices: 3613562--3613634 Score: 58
Period size: 12 Copynumber: 6.0 Consensus size: 12
3613552 GAAAAAATAC
3613562 ATAAAATTTAAA
1 ATAAAATTTAAA
* *
3613574 ATTAAA-TTATA
1 ATAAAATTTAAA
**
3613585 ATAATTTTATAAA
1 ATAAAATT-TAAA
3613598 ATAAAATATTAAA
1 ATAAAAT-TTAAA
***
3613611 ATATTTTTTAAA
1 ATAAAATTTAAA
3613623 ATAAAATTTAAA
1 ATAAAATTTAAA
3613635 TACCTTTTTA
Statistics
Matches: 44, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
11 7 0.16
12 20 0.45
13 16 0.36
14 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAAAATTTAAA
Found at i:3613642 original size:25 final size:23
Alignment explanation
Indices: 3613568--3613645 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 23
3613558 ATACATAAAA
*
3613568 TTTAAAATTAAA-TTATAATAATTT
1 TTTAAAATAAAATTTA-AAT-ATTT
*
3613592 TATAAAATAAAATATTAAAATATTT
1 TTTAAAATAAAAT-TT-AAATATTT
*
3613617 TTTAAAATAAAATTTAAATACCTT
1 TTTAAAATAAAATTTAAATA-TTT
3613641 TTTAA
1 TTTAA
3613646 TTAATTTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
23 5 0.11
24 19 0.41
25 16 0.35
26 5 0.11
27 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAATAAAATTTAAATATTT
Found at i:3614153 original size:23 final size:22
Alignment explanation
Indices: 3614127--3614183 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 22
3614117 TTTATATCAA
3614127 TAAATATAAATAAATAAAATTAT
1 TAAATATAAATAAATAAAA-TAT
3614150 TAAATAT--AT---TAAAATAT
1 TAAATATAAATAAATAAAATAT
3614167 TAAATATAAATACAATA
1 TAAATATAAATA-AATA
3614184 TGTATATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
17 10 0.36
18 5 0.18
19 2 0.07
21 2 0.07
23 9 0.32
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAATATAAATAAATAAAATAT
Found at i:3614155 original size:17 final size:17
Alignment explanation
Indices: 3614128--3614175 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
3614118 TTATATCAAT
3614128 AAATA-TAAATA-AATA
1 AAATATTAAATATAATA
*
3614143 AAATTATTAAATATATTA
1 AAA-TATTAAATATAATA
3614161 AAATATTAAATATAA
1 AAATATTAAATATAA
3614176 ATACAATATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 3 0.11
16 2 0.07
17 17 0.61
18 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATATTAAATATAATA
Found at i:3614425 original size:14 final size:15
Alignment explanation
Indices: 3614408--3614441 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3614398 TCATTTAATT
3614408 TTTAAAA-ATTAAAA
1 TTTAAAACATTAAAA
*
3614422 TTTAAAACTTTAAAA
1 TTTAAAACATTAAAA
3614437 TTTAA
1 TTTAA
3614442 TATTCATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
TTTAAAACATTAAAA
Found at i:3614440 original size:7 final size:7
Alignment explanation
Indices: 3614408--3614441 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
3614398 TCATTTAATT
3614408 TTTAAAA
1 TTTAAAA
*
3614415 ATTAAAA
1 TTTAAAA
3614422 TTTAAAA
1 TTTAAAA
3614429 CTTTAAAA
1 -TTTAAAA
3614437 TTTAA
1 TTTAA
3614442 TATTCATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (7 bp):
TTTAAAA
Found at i:3615534 original size:36 final size:33
Alignment explanation
Indices: 3615474--3615542 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 33
3615464 TACAAGAAAA
3615474 ATATTTTATATTAATATAAAATTAATTAATTTTAT
1 ATATTTTATATTAATATAAAATTAA-T-ATTTTAT
* *
3615509 ATATTTTATAATTTATATAAGATTAATATTTTAT
1 ATATTTTAT-ATTAATATAAAATTAATATTTTAT
3615543 TAAATTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 7 0.23
35 10 0.32
36 14 0.45
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (33 bp):
ATATTTTATATTAATATAAAATTAATATTTTAT
Found at i:3615551 original size:16 final size:17
Alignment explanation
Indices: 3615520--3615556 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
3615510 TATTTTATAA
3615520 TTTATATAAGATTAATAT
1 TTTATATAAGATTAAT-T
3615538 TTTAT-TAA-ATTAATT
1 TTTATATAAGATTAATT
3615553 TTTA
1 TTTA
3615557 AATTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.26
16 6 0.32
17 3 0.16
18 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTATATAAGATTAATT
Found at i:3615789 original size:22 final size:22
Alignment explanation
Indices: 3615720--3615789 Score: 54
Period size: 21 Copynumber: 3.1 Consensus size: 22
3615710 AATATATGAA
*
3615720 TAAAATATAATAATTTAATTAAAT
1 TAAAATAT-AT-ATATAATTAAAT
* * **
3615744 AAAAATAAAT-TATAAATT-TTT
1 TAAAATATATATAT-AATTAAAT
3615765 TAAAATATATATATAATTAAAT
1 TAAAATATATATATAATTAAAT
3615787 TAA
1 TAA
3615790 TCACTTCATG
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
21 15 0.44
22 11 0.32
23 2 0.06
24 6 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAAATATATATATAATTAAAT
Found at i:3616351 original size:21 final size:20
Alignment explanation
Indices: 3616313--3616367 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
3616303 TATTTTTAAA
*
3616313 AATAATATTAAAATTTTTAT
1 AATAATATTTAAATTTTTAT
*
3616333 AATAATATTTATATATTTTAT
1 AATAATATTTAAAT-TTTTAT
3616354 AATTAA-ATTTAAAT
1 AA-TAATATTTAAAT
3616368 AAAAATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.40
21 15 0.50
22 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATATTTAAATTTTTAT
Found at i:3616387 original size:20 final size:20
Alignment explanation
Indices: 3616362--3616401 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3616352 ATAATTAAAT
3616362 TTAAATAAAAATTTTAATTA
1 TTAAATAAAAATTTTAATTA
***
3616382 TTAAATTTTAATTTTAATTA
1 TTAAATAAAAATTTTAATTA
3616402 AATCAATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAATAAAAATTTTAATTA
Found at i:3616417 original size:34 final size:32
Alignment explanation
Indices: 3616374--3616442 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
3616364 AAATAAAAAT
3616374 TTTAATTATT-AAATTTTAATTTTAATTAAATCAA
1 TTTAATTATTAAAATTTTAA-TTTAA--AAATCAA
*
3616408 TTTAATTATTAAAATTTTTATTTAAAAATCAA
1 TTTAATTATTAAAATTTTAATTTAAAAATCAA
3616440 TTT
1 TTT
3616443 GTTCATACGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 10 0.30
34 15 0.45
35 8 0.24
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (32 bp):
TTTAATTATTAAAATTTTAATTTAAAAATCAA
Found at i:3616433 original size:47 final size:47
Alignment explanation
Indices: 3616315--3616433 Score: 120
Period size: 47 Copynumber: 2.5 Consensus size: 47
3616305 TTTTTAAAAA
* *
3616315 TAATATTAAAATTTTTATAATAATATTTATATATTTTATAATTAAATT
1 TAATATTAAAATTTTTATATTAA-ATTTATATATTTTATAAATAAATT
* * *
3616363 TAA-ATAAAAATTTTAATTATTAAATTT-TA-ATTTTAATTAAATCAATT
1 TAATATTAAAATTTTTA-TATTAAATTTATATATTTT-A-TAAATAAATT
3616410 TAATTATTAAAATTTTTAT-TTAAA
1 TAA-TATTAAAATTTTTATATTAAA
3616434 AATCAATTTG
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
45 5 0.08
46 3 0.05
47 31 0.53
48 9 0.15
49 11 0.19
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (47 bp):
TAATATTAAAATTTTTATATTAAATTTATATATTTTATAAATAAATT
Found at i:3617881 original size:20 final size:20
Alignment explanation
Indices: 3617840--3617881 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3617830 CATCAATTAC
*
3617840 TTATTTATCATTTAAATGAT
1 TTATTTATCATTTAAATAAT
3617860 TTATTTAT-ATTTAAACTAAT
1 TTATTTATCATTTAAA-TAAT
3617880 TT
1 TT
3617882 TACTTGAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATTTATCATTTAAATAAT
Found at i:3619250 original size:21 final size:20
Alignment explanation
Indices: 3619220--3619258 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
3619210 GGCATGCTTC
3619220 TAATATATATATATATAATA
1 TAATATATATATATATAATA
3619240 TAATACTATATATATATAA
1 TAATA-TATATATATATAA
3619259 AACAGGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATATATATATATATAATA
Found at i:3619440 original size:21 final size:22
Alignment explanation
Indices: 3619400--3619453 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
3619390 TGAATATATA
3619400 TATATATATAAATTTAATTTAAT
1 TATATAT-TAAATTTAATTTAAT
*
3619423 TTTATATTAAATTT-ATTTAAT
1 TATATATTAAATTTAATTTAAT
*
3619444 TATATTTTAA
1 TATATATTAA
3619454 TTTCATTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 15 0.54
22 7 0.25
23 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATATTAAATTTAATTTAAT
Found at i:3619805 original size:14 final size:14
Alignment explanation
Indices: 3619788--3619825 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
3619778 ATATCATCTC
3619788 ATAATTTTTTAAAG
1 ATAATTTTTTAAAG
*
3619802 ATAA-TTATTAAAG
1 ATAATTTTTTAAAG
3619815 ATAATTTTTTA
1 ATAATTTTTTA
3619826 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (14 bp):
ATAATTTTTTAAAG
Found at i:3621490 original size:27 final size:27
Alignment explanation
Indices: 3621433--3621487 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
3621423 TTATTTACTG
3621433 TTTA-TTTTATAATAAAATATTATAAA
1 TTTATTTTTATAATAAAATATTATAAA
* * *
3621459 TTTATTTTTATATTAATAT-TTATATA
1 TTTATTTTTATAATAAAATATTATAAA
3621485 TTT
1 TTT
3621488 TATAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TTTATTTTTATAATAAAATATTATAAA
Found at i:3623263 original size:20 final size:20
Alignment explanation
Indices: 3623238--3623276 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3623228 TTAACACTTA
3623238 AAAAATTAAATAA-AAATTTT
1 AAAAATTAAA-AATAAATTTT
3623258 AAAAATTAAAAATAAATTT
1 AAAAATTAAAAATAAATTT
3623277 ATATTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTAAAAATAAATTTT
Found at i:3623818 original size:16 final size:16
Alignment explanation
Indices: 3623799--3623835 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3623789 GGTAATAATT
*
3623799 ATATAAAATTATAAAA
1 ATATAAAATAATAAAA
*
3623815 ATATAAAATAATATAA
1 ATATAAAATAATAAAA
3623831 ATATA
1 ATATA
3623836 TCTTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATATAAAATAATAAAA
Found at i:3623885 original size:7 final size:7
Alignment explanation
Indices: 3623875--3623918 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
3623865 AATTTATTTT
3623875 AAATATA
1 AAATATA
*
3623882 AAATAAA
1 AAATATA
3623889 ATAATAT-
1 A-AATATA
3623896 AAATATA
1 AAATATA
*
3623903 TAATATA
1 AAATATA
3623910 AAATATA
1 AAATATA
3623917 AA
1 AA
3623919 TTATCAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
6 5 0.16
7 22 0.71
8 4 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAATATA
Found at i:3623907 original size:13 final size:12
Alignment explanation
Indices: 3623875--3623917 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 12
3623865 AATTTATTTT
*
3623875 AAATATAAAAT-
1 AAATATAATATA
3623886 AAA-ATAATATA
1 AAATATAATATA
3623897 AATATATAATATA
1 AA-ATATAATATA
3623910 AAATATAA
1 AAATATAA
3623918 ATTATCAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 6 0.21
11 5 0.18
12 7 0.25
13 10 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATATAATATA
Found at i:3623931 original size:20 final size:20
Alignment explanation
Indices: 3623874--3623919 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
3623864 TAATTTATTT
* *
3623874 TAAATATAAAATAAAATAATA
1 TAAATATATAATATAA-AATA
3623895 TAAATATATAATATAAAATA
1 TAAATATATAATATAAAATA
3623915 TAAAT
1 TAAAT
3623920 TATCAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAATATATAATATAAAATA
Found at i:3624022 original size:20 final size:21
Alignment explanation
Indices: 3623967--3624025 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
3623957 TATTAATAAA
3623967 TTTTAAAAAA-TAATATATAT
1 TTTTAAAAAATTAATATATAT
** * *
3623987 TTTTATGAGATATAATA-ATTT
1 TTTTAAAAAAT-TAATATATAT
3624008 TTTTAAAAAATTAATATA
1 TTTTAAAAAATTAATATA
3624026 ATTAAAAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
20 12 0.41
21 12 0.41
22 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
TTTTAAAAAATTAATATATAT
Found at i:3624373 original size:20 final size:19
Alignment explanation
Indices: 3624320--3624391 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
3624310 AAATAAAATT
* *
3624320 TTATTATATTTGTATAAAA
1 TTATTATATTTTTATTAAA
* *
3624339 TTATCTTTATATTTATTAAA
1 TTAT-TATATTTTTATTAAA
*
3624359 TATATTATATTTTTATTATA
1 T-TATTATATTTTTATTAAA
*
3624379 TTTTTATATTTTT
1 TTATTATATTTTT
3624392 TCAAAATTAC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 15 0.35
20 25 0.58
21 3 0.07
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (19 bp):
TTATTATATTTTTATTAAA
Found at i:3624375 original size:11 final size:11
Alignment explanation
Indices: 3624361--3624385 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3624351 TTATTAAATA
3624361 TATTATATTTT
1 TATTATATTTT
3624372 TATTATATTTT
1 TATTATATTTT
3624383 TAT
1 TAT
3624386 ATTTTTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTATATTTT
Found at i:3624379 original size:18 final size:18
Alignment explanation
Indices: 3624345--3624391 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3624335 AAAATTATCT
3624345 TTATATTTATTAAATA-TA
1 TTATATTT-TTAAATATTA
* *
3624363 TTATATTTTTATTATATTT
1 TTATATTTTTA-AATATTA
3624382 TTATATTTTT
1 TTATATTTTT
3624392 TCAAAATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 11 0.44
19 11 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATATTTTTAAATATTA
Found at i:3625113 original size:11 final size:12
Alignment explanation
Indices: 3625099--3625130 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3625089 TAAATTACTC
3625099 TTATTTTTAA-T
1 TTATTTTTAAGT
3625110 TTATTTTTAAGT
1 TTATTTTTAAGT
3625122 TT-TTTTTAA
1 TTATTTTTAA
3625131 AATTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (12 bp):
TTATTTTTAAGT
Found at i:3626490 original size:13 final size:13
Alignment explanation
Indices: 3626474--3626498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3626464 TATTATAAAA
3626474 TAATTTTTTTTAT
1 TAATTTTTTTTAT
3626487 TAATTTTTTTTA
1 TAATTTTTTTTA
3626499 GATAAATAAA
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:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TAATTTTTTTTAT
Found at i:3629565 original size:16 final size:18
Alignment explanation
Indices: 3629535--3629568 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
3629525 ATTCTCAATA
3629535 TTTAATATTTAAATTTAT
1 TTTAATATTTAAATTTAT
3629553 TTTAAT-TTT-AATTTAT
1 TTTAATATTTAAATTTAT
3629569 ATAATATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTAATATTTAAATTTAT
Found at i:3635191 original size:20 final size:19
Alignment explanation
Indices: 3635150--3635195 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
3635140 AAATTTAAAT
*
3635150 TAAATTT-AATTTGATTTG
1 TAAATTTAAATTTGATTTA
*
3635168 TAAATTTAAATTATTATTTA
1 TAAATTTAAATT-TGATTTA
3635188 TAAATTTA
1 TAAATTTA
3635196 TAAAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 4 0.17
20 13 0.54
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (19 bp):
TAAATTTAAATTTGATTTA
Found at i:3635206 original size:21 final size:20
Alignment explanation
Indices: 3635163--3635207 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3635153 ATTTAATTTG
* **
3635163 ATTTGTAAATTTAAATTATT
1 ATTTATAAATTTAAAAAATT
3635183 ATTTATAAATTTATAAAAATT
1 ATTTATAAATTTA-AAAAATT
3635204 ATTT
1 ATTT
3635208 TTATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTATAAATTTAAAAAATT
Found at i:3635315 original size:17 final size:16
Alignment explanation
Indices: 3635291--3635325 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
3635281 TTATAATCTG
3635291 TTTTAATTTAATATAA
1 TTTTAATTTAATATAA
3635307 TTTTAAATTTAATATAA
1 TTTT-AATTTAATATAA
3635324 TT
1 TT
3635326 GATTGAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAATTTAATATAA
Found at i:3649655 original size:3 final size:3
Alignment explanation
Indices: 3649647--3649674 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3649637 CATACTCTTC
3649647 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3649675 TTGAGTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3654201 original size:2 final size:2
Alignment explanation
Indices: 3654194--3654234 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
3654184 ATTCCAGTTT
* *
3654194 TA TA TA TA TA TA AA TA TA GA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3654235 TGTTTCAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3655011 original size:20 final size:20
Alignment explanation
Indices: 3654988--3655059 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 20
3654978 ATAAGTTATT
3654988 AATATATTAATATTTATATA
1 AATATATTAATATTTATATA
* *
3655008 AATATA-AAATATATTAAATA
1 AATATATTAATAT-TTATATA
3655028 AGATTATAATATAATA-TTATATA
1 A-A-TAT-AT-TAATATTTATATA
3655051 AAT-TATTAA
1 AATATATTAA
3655060 ATTATTAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
18 3 0.07
19 7 0.17
20 14 0.33
21 2 0.05
22 4 0.10
23 8 0.19
25 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (20 bp):
AATATATTAATATTTATATA
Found at i:3655157 original size:32 final size:29
Alignment explanation
Indices: 3655121--3655181 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
3655111 ATTTTAAAAA
3655121 TTTAATATTTATAATTATTATAATAATATATT
1 TTTAATATTT-TAATT-TT-TAATAATATATT
*
3655153 TTTAATATTTTTATTTTTAATAATATATT
1 TTTAATATTTTAATTTTTAATAATATATT
3655182 AAATAGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 12 0.43
30 2 0.07
31 4 0.14
32 10 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTAATATTTTAATTTTTAATAATATATT
Found at i:3661741 original size:11 final size:11
Alignment explanation
Indices: 3661725--3661824 Score: 61
Period size: 10 Copynumber: 9.3 Consensus size: 11
3661715 TATTTTATAA
3661725 ATTTTAATATT
1 ATTTTAATATT
3661736 ATTTTAATATATTT
1 ATTTT-A-ATA-TT
*
3661750 ATTTT-ATGTT
1 ATTTTAATATT
*
3661760 ATTTTTATATT
1 ATTTTAATATT
*
3661771 A-TATAGTATATT
1 ATTTTA--ATATT
*
3661783 -TTATAATATT
1 ATTTTAATATT
*
3661793 ATTATAATA-T
1 ATTTTAATATT
3661803 ATTTT--TATT
1 ATTTTAATATT
3661812 -TTTTAATATT
1 ATTTTAATATT
3661822 ATT
1 ATT
3661825 AAATTTAATT
Statistics
Matches: 72, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
8 6 0.08
9 1 0.01
10 23 0.32
11 22 0.31
12 10 0.14
13 3 0.04
14 7 0.10
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
ATTTTAATATT
Found at i:3661837 original size:29 final size:29
Alignment explanation
Indices: 3661729--3661825 Score: 99
Period size: 30 Copynumber: 3.4 Consensus size: 29
3661719 TTATAAATTT
*
3661729 TAATATTATTTTAATATA--TTTATTTTA
1 TAATATTATTATAATATATTTTTATTTTA
** * * * *
3661756 TGTTATTTTTATATTATATAGTATATTTTA
1 TAATATTATTATAATATAT-TTTTATTTTA
*
3661786 TAATATTATTATAATATATTTTTATTTTT
1 TAATATTATTATAATATATTTTTATTTTA
3661815 TAATATTATTA
1 TAATATTATTA
3661826 AATTTAATTT
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
27 13 0.24
29 18 0.33
30 23 0.43
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (29 bp):
TAATATTATTATAATATATTTTTATTTTA
Found at i:3662501 original size:14 final size:15
Alignment explanation
Indices: 3662468--3662505 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3662458 ATGTTTATAG
*
3662468 ATATTTATTAAAATA
1 ATATTTATTAAAAAA
*
3662483 TTATTT-TTAAAAAA
1 ATATTTATTAAAAAA
3662497 ATATTTATT
1 ATATTTATT
3662506 CATTTAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTATTAAAAAA
Found at i:3662791 original size:28 final size:30
Alignment explanation
Indices: 3662747--3662812 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 30
3662737 AATCTTTATT
* *
3662747 TAAATTAATTTAAAATA-TA-TATTAAT-A
1 TAAAATAATTTAAAATATTATTATAAATAA
*
3662774 TAAAATAATATTATAATATTATTATAAATAA
1 TAAAATAAT-TTAAAATATTATTATAAATAA
3662805 TAAAATAA
1 TAAAATAA
3662813 ATATATGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 8 0.25
28 7 0.22
29 2 0.06
30 6 0.19
31 9 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
TAAAATAATTTAAAATATTATTATAAATAA
Found at i:3662792 original size:18 final size:17
Alignment explanation
Indices: 3662750--3662786 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3662740 CTTTATTTAA
*
3662750 ATTAATTTAAAATATAT
1 ATTAATATAAAATATAT
3662767 ATTAATATAAAATA-AT
1 ATTAATATAAAATATAT
3662783 ATTA
1 ATTA
3662787 TAATATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTAATATAAAATATAT
Found at i:3662812 original size:23 final size:23
Alignment explanation
Indices: 3662727--3662812 Score: 68
Period size: 23 Copynumber: 3.6 Consensus size: 23
3662717 TTAATATATT
*
3662727 AATAATAAAA-AATCTTTATT-TA
1 AATAATAAAATAAT-ATTATTATA
*
3662749 AATTAATTTAAAATATATATTAATATAA
1 AA-TAA--TAAAATA-ATATTATTAT-A
**
3662777 AATAATATTATAATATTATTATA
1 AATAATAAAATAATATTATTATA
3662800 AATAATAAAATAA
1 AATAATAAAATAA
3662813 ATATATGAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
22 2 0.04
23 15 0.30
24 9 0.18
25 10 0.20
26 5 0.10
27 6 0.12
28 3 0.06
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (23 bp):
AATAATAAAATAATATTATTATA
Found at i:3663909 original size:2 final size:2
Alignment explanation
Indices: 3663904--3663945 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3663894 ACACACACAC
3663904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3663946 TGTATCTCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3665566 original size:4 final size:4
Alignment explanation
Indices: 3665557--3665582 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3665547 ACAAAGAAAA
3665557 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
3665583 TCTATACCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:3668463 original size:339 final size:339
Alignment explanation
Indices: 3667836--3668514 Score: 959
Period size: 339 Copynumber: 2.0 Consensus size: 339
3667826 TCCGAGCCTG
*
3667836 TGCTTCAATGCTAACGAGTTGAGACTCAAGAAGTTGCTTTGATTCATTTGCATTATCTGAGATTT
1 TGCTTCAATGCTAACGAGTTGAGACTCAAGAAGTTGCTTTGATTCATTTGCATTATCTGAAATTT
* * * *
3667901 GCACCAACAGTGCCCTTTCCTCTTCAAGTTCAGCTCCTAATGAGTCAATCTTCGCTAATGTTGTC
66 GCACCAACAATGCCCTTTCCTCTTCAAGTTCAGCTACTAATAAGTCAATCTTCGCTAATATTGTC
* * *
3667966 TCTGCATCTATTTCCATGCTACTGAGCTGAGACTGAAGATGTTGCTTTTCATCATTTGCCATGCA
131 TCTGCATCTATTTCCATGCAACTGAGCTGAGACTGAAGATGTTGCTTTGCATCATTTGCCATGAA
* * * * * *
3668031 GAGCTCTCTTTGCAACTCCTGCAATTTTATTTCAGTGTACTTCAGCTGGACTTTTGTCGCTTTAA
196 GAGCTCTCTTTGCAACTCCTCCAATTTTACTTCAGTGTACCTCAACTGGACTTCTGTCGCTTCAA
* * * *
3668096 GACTTTCTTGACTTTTTGCAAGAGCAATTTCTAGTTCAGCCTTCCCAACTTCTATCTTTTCCAAC
261 GACTTTCTTGACTTTTGGAAAGAGCAATTTCAAGTTCAGCCTTCCCAACTTCTATCTTCTCCAAC
*
3668161 TTCTCTTCAAATTC
326 TTCTCTGCAAATTC
* * *
3668175 TGCTTCGATGCTAATGAGTTGAGACTCAAGAATTTGCTTTGATTCATTTGCATTAAT-TGAAATT
1 TGCTTCAATGCTAACGAGTTGAGACTCAAGAAGTTGCTTTGATTCATTTGCATT-ATCTGAAATT
** * * * * *
3668239 TGCACTGACAATGCCCTTTCCTTTTCAATTTCTGCTACTAATAAGTTAATCTTCGCTGATATTGT
65 TGCACCAACAATGCCCTTTCCTCTTCAAGTTCAGCTACTAATAAGTCAATCTTCGCTAATATTGT
* * *
3668304 CTCTGCATCTGTTTCCATGCAACTGAGTTGAGACTCG-AGATGTTGCTTTGCTTCATTTGCCATG
130 CTCTGCATCTATTTCCATGCAACTGAGCTGAGACT-GAAGATGTTGCTTTGCATCATTTGCCATG
* * * *
3668368 AAGAGCTCTCTTTGCAATTCCTCCACTTTTACTTCAGTGTCCCTCAACTGTACTTCTGAT-GCTT
194 AAGAGCTCTCTTTGCAACTCCTCCAATTTTACTTCAGTGTACCTCAACTGGACTTCTG-TCGCTT
* *
3668432 CGAGACTTTCTTGACTTTTGGAAAGAGCAATTTCAAGTTCAGCCTTCTCAACTTCTATCTTCTCC
258 CAAGACTTTCTTGACTTTTGGAAAGAGCAATTTCAAGTTCAGCCTTCCCAACTTCTATCTTCTCC
*
3668497 AACTTCTCTGCAAGTTC
323 AACTTCTCTGCAAATTC
3668514 T
1 T
3668515 ACCGTTCGAT
Statistics
Matches: 298, Mismatches: 39, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
339 294 0.99
340 4 0.01
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.39
Consensus pattern (339 bp):
TGCTTCAATGCTAACGAGTTGAGACTCAAGAAGTTGCTTTGATTCATTTGCATTATCTGAAATTT
GCACCAACAATGCCCTTTCCTCTTCAAGTTCAGCTACTAATAAGTCAATCTTCGCTAATATTGTC
TCTGCATCTATTTCCATGCAACTGAGCTGAGACTGAAGATGTTGCTTTGCATCATTTGCCATGAA
GAGCTCTCTTTGCAACTCCTCCAATTTTACTTCAGTGTACCTCAACTGGACTTCTGTCGCTTCAA
GACTTTCTTGACTTTTGGAAAGAGCAATTTCAAGTTCAGCCTTCCCAACTTCTATCTTCTCCAAC
TTCTCTGCAAATTC
Found at i:3673611 original size:21 final size:22
Alignment explanation
Indices: 3673564--3673650 Score: 58
Period size: 21 Copynumber: 4.1 Consensus size: 22
3673554 TTATTTTATT
*
3673564 ATTTATTATATAATTAAATTAT
1 ATTTATTATATAATTAAATTAA
* * *
3673586 TTTTA-TATATTATTTAATTAA
1 ATTTATTATATAATTAAATTAA
* *
3673607 ATTTA-AAT-TAA-AAATATTAA
1 ATTTATTATATAATTAA-ATTAA
* *
3673627 ATTTATTAT-TAAATAATTTAA
1 ATTTATTATATAATTAAATTAA
3673648 ATT
1 ATT
3673651 GAACTAATTT
Statistics
Matches: 50, Mismatches: 12, Indels: 7
0.72 0.17 0.10
Matches are distributed among these distances:
19 1 0.02
20 12 0.24
21 31 0.62
22 6 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTATTATATAATTAAATTAA
Done.