Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 27 of 33
Found at i:4839723 original size:23 final size:22
Alignment explanation
Indices: 4839687--4839730 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
4839677 TAATTTTATT
*
4839687 TAAATTTAATTATAAAAATAAA
1 TAAATTTAAATATAAAAATAAA
4839709 TAAATATTAAATATAAAAATAA
1 TAAAT-TTAAATATAAAAATAA
4839731 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAATTTAAATATAAAAATAAA
Found at i:4840474 original size:24 final size:24
Alignment explanation
Indices: 4840447--4840546 Score: 82
Period size: 28 Copynumber: 4.0 Consensus size: 24
4840437 GATAAATGTG
4840447 ATATAATAAAATAATTAAAATATAAT
1 ATATAATAAAATAATTAAAATAT--T
*
4840473 ATAATATAAAAAATAATGT-AAATATT
1 AT-ATA-ATAAAATAAT-TAAAATATT
4840499 ATAT-AT-AAATATATTAAAAT-TT
1 ATATAATAAAATA-ATTAAAATATT
* *
4840521 ATATAATATAAATTATTAATATATT
1 ATATAATA-AAATAATTAAAATATT
4840546 A
1 A
4840547 AAAATTTATA
Statistics
Matches: 61, Mismatches: 4, Indels: 19
0.73 0.05 0.23
Matches are distributed among these distances:
22 12 0.20
23 9 0.15
24 7 0.11
25 9 0.15
26 5 0.08
27 3 0.05
28 15 0.25
29 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (24 bp):
ATATAATAAAATAATTAAAATATT
Found at i:4840590 original size:13 final size:13
Alignment explanation
Indices: 4840572--4840610 Score: 55
Period size: 11 Copynumber: 3.1 Consensus size: 13
4840562 ATATAACACC
4840572 TAATATATAATTA
1 TAATATATAATTA
4840585 TAATATA-AA-TA
1 TAATATATAATTA
4840596 TAATATATATATTA
1 TAATATATA-ATTA
4840610 T
1 T
4840611 TAAATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 9 0.39
12 3 0.13
13 8 0.35
14 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATATATAATTA
Found at i:4841814 original size:41 final size:41
Alignment explanation
Indices: 4841763--4841840 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
4841753 AAATTAGATC
** *
4841763 AATTTGAATTATTATTTATGTAATA-AAAAATATTTTTATTTA
1 AATTTGAATTA-TAAATAT-TAATATAAAAATAATTTTATTTA
4841805 AATTT-AATTATAAATATTAATATAAAAATAATTTTA
1 AATTTGAATTATAAATATTAATATAAAAATAATTTTA
4841841 AATTTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 5 0.16
40 17 0.53
41 5 0.16
42 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (41 bp):
AATTTGAATTATAAATATTAATATAAAAATAATTTTATTTA
Found at i:4841856 original size:20 final size:19
Alignment explanation
Indices: 4841827--4841866 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
4841817 AATATTAATA
* *
4841827 TAAAAATAATTTTAAATTT
1 TAAAAATAATATGAAATTT
4841846 TAAATAATAATATGAAATTT
1 TAAA-AATAATATGAAATTT
4841866 T
1 T
4841867 GATCAATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
TAAAAATAATATGAAATTT
Found at i:4842547 original size:17 final size:19
Alignment explanation
Indices: 4842534--4842609 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 19
4842524 TTAATAATTT
4842534 TAAATATAATATAATTATA
1 TAAATATAATATAATTATA
4842553 TAAATATAATATAA--A-A
1 TAAATATAATATAATTATA
4842569 TAAATAT-ATA-AA-TATA
1 TAAATATAATATAATTATA
*
4842585 TAATTTATAA-AT-ATTATA
1 TAA-ATATAATATAATTATA
4842603 TAAATAT
1 TAAATAT
4842610 TTTAAAAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
14 2 0.04
15 4 0.08
16 12 0.24
17 9 0.18
18 8 0.16
19 14 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATATAATATAATTATA
Found at i:4842563 original size:24 final size:23
Alignment explanation
Indices: 4842536--4842624 Score: 81
Period size: 24 Copynumber: 3.7 Consensus size: 23
4842526 AATAATTTTA
4842536 AATATAATATAATTATATAAATAT
1 AATATAA-ATAATTATATAAATAT
*
4842560 AATATAAAATAAATATATAAATATAT
1 AATAT-AAATAATTATAT-AA-ATAT
4842586 AATTTATAAAT-ATTATATAAATAT
1 AA--TATAAATAATTATATAAATAT
** *
4842610 TTTAAAAATAATTAT
1 AATATAAATAATTAT
4842625 GACGTATATA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
22 6 0.11
23 5 0.09
24 18 0.33
25 6 0.11
26 12 0.22
27 4 0.07
28 3 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AATATAAATAATTATATAAATAT
Found at i:4842564 original size:11 final size:11
Alignment explanation
Indices: 4842534--4842609 Score: 62
Period size: 11 Copynumber: 7.6 Consensus size: 11
4842524 TTAATAATTT
4842534 TAAATATAATA
1 TAAATATAATA
4842545 T-AAT-T-ATA
1 TAAATATAATA
4842553 TAAATATAATA
1 TAAATATAATA
4842564 TAAA-ATAA-A
1 TAAATATAATA
*
4842573 TATATA-AATA
1 TAAATATAATA
4842583 TATAAT-T--TA
1 TA-AATATAATA
*
4842592 TAAATATTATA
1 TAAATATAATA
4842603 TAAATAT
1 TAAATAT
4842610 TTTAAAAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 20
0.71 0.03 0.27
Matches are distributed among these distances:
8 7 0.13
9 15 0.28
10 12 0.23
11 19 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAATATAATA
Found at i:4842610 original size:11 final size:11
Alignment explanation
Indices: 4842537--4842624 Score: 59
Period size: 11 Copynumber: 7.2 Consensus size: 11
4842527 ATAATTTTAA
4842537 ATATAATATAATT
1 ATATAA-AT-ATT
*
4842550 ATATAAATATA
1 ATATAAATATT
*
4842561 ATATAAAATAAAT
1 ATAT-AAAT-ATT
4842574 ATATAAATATAT
1 ATATAAATAT-T
4842586 AATTTATAAATATT
1 -A--TATAAATATT
4842600 ATATAAATATT
1 ATATAAATATT
* *
4842611 TTAAAAATAATT
1 ATATAAAT-ATT
4842623 AT
1 AT
4842625 GACGTATATA
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
11 23 0.38
12 15 0.25
13 13 0.21
14 1 0.02
15 9 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATAAATATT
Found at i:4842620 original size:26 final size:26
Alignment explanation
Indices: 4842547--4842620 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 26
4842537 ATATAATATA
*
4842547 ATTATATAAATATAATATAAAAT-AA-
1 ATTATATAAATATTATA-AAAATAAAT
**
4842572 A-TATATAAATA-TATAATTTATAAAT
1 ATTATATAAATATTATAA-AAATAAAT
*
4842597 ATTATATAAATATTTTAAAAATAA
1 ATTATATAAATATTATAAAAATAA
4842621 TTATGACGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
22 1 0.03
23 5 0.13
24 12 0.32
25 2 0.05
26 14 0.37
27 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
ATTATATAAATATTATAAAAATAAAT
Found at i:4843036 original size:2 final size:2
Alignment explanation
Indices: 4843029--4843059 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4843019 TACTAGAATC
4843029 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4843060 GTTTGAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4845049 original size:20 final size:19
Alignment explanation
Indices: 4845015--4845074 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
4845005 ATTTTTTAAA
4845015 ATTAAAATT-TATAAATAT
1 ATTAAAATTATATAAATAT
4845033 ATTAAAATTTATATAAATAT
1 ATTAAAA-TTATATAAATAT
* *
4845053 AATATAAATTAT-TAAATTT
1 ATTA-AAATTATATAAATAT
4845072 ATT
1 ATT
4845075 TTTTTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 7 0.19
19 10 0.28
20 16 0.44
21 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAAAATTATATAAATAT
Found at i:4845052 original size:18 final size:18
Alignment explanation
Indices: 4845011--4845052 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4845001 AAATATTTTT
4845011 TAAA-ATTAAAATTTATA
1 TAAATATTAAAATTTATA
4845028 -AATATATTAAAATTTATA
1 TAA-ATATTAAAATTTATA
4845046 TAAATAT
1 TAAATAT
4845053 AATATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.09
17 1 0.05
18 17 0.77
19 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAATATTAAAATTTATA
Found at i:4849728 original size:4 final size:4
Alignment explanation
Indices: 4849719--4849743 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4849709 TTGAGGACAG
4849719 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
4849744 CATTGTGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:4849929 original size:14 final size:15
Alignment explanation
Indices: 4849910--4849948 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
4849900 ATATTATGAG
4849910 TATTTTTTTCTTTT-
1 TATTTTTTTCTTTTA
*
4849924 TATTTTTTTTTTTTA
1 TATTTTTTTCTTTTA
4849939 TATTTTTTTC
1 TATTTTTTTC
4849949 CTCTCAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (15 bp):
TATTTTTTTCTTTTA
Found at i:4849946 original size:13 final size:13
Alignment explanation
Indices: 4849914--4849947 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
4849904 TATGAGTATT
*
4849914 TTTTTCTTTTTATT
1 TTTTT-TTTTTATA
4849928 TTTTTTTTTTATA
1 TTTTTTTTTTATA
4849941 TTTTTTT
1 TTTTTTT
4849948 CCTCTCAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTATA
Found at i:4850475 original size:28 final size:27
Alignment explanation
Indices: 4850405--4850476 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
4850395 GTTTACCATC
* * *
4850405 AATTAATAATATTT-TAATTAAAAAAT
1 AATTAAAAATATTTAAAATAAAAAAAT
* *
4850431 AATTAAAATTAAATTAAAATAAAAAAAT
1 AATTAAAAAT-ATTTAAAATAAAAAAAT
4850459 AAATTAAAAATATTTAAA
1 -AATTAAAAATATTTAAA
4850477 CTTTTAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 8 0.22
27 3 0.08
28 16 0.44
29 9 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
AATTAAAAATATTTAAAATAAAAAAAT
Found at i:4851127 original size:42 final size:38
Alignment explanation
Indices: 4851046--4851129 Score: 96
Period size: 42 Copynumber: 2.1 Consensus size: 38
4851036 AAGTTGATAA
* *
4851046 TAAAAAATAATTAATATTTTATTATTAAATATTATATT
1 TAAAAAATAATTAATATTTAATTATTAAATATTAAATT
* *
4851084 TAAAAAATAATATTATTATTTAATTAAATTAAATTTTAAATT
1 TAAAAAAT-A-ATTAATATTTAATT--ATTAAATATTAAATT
4851126 TAAA
1 TAAA
4851130 TTTATAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
38 8 0.21
39 1 0.03
40 12 0.32
42 17 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (38 bp):
TAAAAAATAATTAATATTTAATTATTAAATATTAAATT
Found at i:4853567 original size:11 final size:11
Alignment explanation
Indices: 4853553--4853614 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
4853543 AACTATAATG
4853553 TTTATATTATA
1 TTTATATTATA
*
4853564 TTTATATTATTTT
1 TTTATATTA--TA
4853577 TTTATATTATA
1 TTTATATTATA
4853588 TTT-TAATTAT-
1 TTTAT-ATTATA
4853598 TTT-T-TTATAA
1 TTTATATTAT-A
4853608 TTTATAT
1 TTTATAT
4853615 CATAAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
8 4 0.10
10 8 0.19
11 19 0.45
12 1 0.02
13 10 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTATATTATA
Found at i:4853582 original size:13 final size:13
Alignment explanation
Indices: 4853564--4853606 Score: 63
Period size: 12 Copynumber: 3.5 Consensus size: 13
4853554 TTATATTATA
4853564 TTTATATTATTTT
1 TTTATATTATTTT
*
4853577 TTTATATTA-TAT
1 TTTATATTATTTT
4853589 TTTA-ATTATTTT
1 TTTATATTATTTT
4853601 TTTATA
1 TTTATA
4853607 ATTTATATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 12 0.46
13 10 0.38
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATATTATTTT
Found at i:4853614 original size:26 final size:25
Alignment explanation
Indices: 4853553--4853606 Score: 94
Period size: 24 Copynumber: 2.2 Consensus size: 25
4853543 AACTATAATG
4853553 TTTATATTATA-TTTATATTATTTT
1 TTTATATTATATTTTATATTATTTT
4853577 TTTATATTATATTTTA-ATTATTTT
1 TTTATATTATATTTTATATTATTTT
4853601 TTTATA
1 TTTATA
4853607 ATTTATATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTATATTATATTTTATATTATTTT
Found at i:4854720 original size:2 final size:2
Alignment explanation
Indices: 4854713--4854749 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4854703 TAATGTTCTA
*
4854713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4854750 CCTGATGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4856291 original size:19 final size:19
Alignment explanation
Indices: 4856267--4856307 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
4856257 TTTTGAAAAT
4856267 AAAAAATT-TTAATTATCTA
1 AAAAAATTATTAATTAT-TA
4856286 AAAAAATTACTTAATTATTA
1 AAAAAATTA-TTAATTATTA
4856306 AA
1 AA
4856308 CTGAATAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 4 0.20
21 8 0.40
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAAATTATTAATTATTA
Found at i:4858104 original size:17 final size:16
Alignment explanation
Indices: 4858082--4858116 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
4858072 AATAAAAGAG
*
4858082 TATTATTTTTTATATTA
1 TATTATATTTTA-ATTA
4858099 TATTATATTTTAATTA
1 TATTATATTTTAATTA
4858115 TA
1 TA
4858117 AATATTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTATATTTTAATTA
Found at i:4858581 original size:16 final size:15
Alignment explanation
Indices: 4858553--4858591 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
4858543 AATATTAAAT
*
4858553 AATTAATTTAATTTA
1 AATTAATTAAATTTA
4858568 AATTAAATTAAATTTA
1 AATT-AATTAAATTTA
4858584 AATATAAT
1 AAT-TAAT
4858592 ATATTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 16 0.76
17 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAATTAAATTTA
Found at i:4861337 original size:15 final size:16
Alignment explanation
Indices: 4861301--4861353 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
4861291 GTTCATATTA
* * *
4861301 ATAATAAAAATTTATA
1 ATAATAAAAAATAATG
*
4861317 ATAATAAATAATAAT-
1 ATAATAAAAAATAATG
4861332 ATAATAAAAAATAATG
1 ATAATAAAAAATAATG
4861348 ATAATA
1 ATAATA
4861354 GTAATATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 14 0.44
16 18 0.56
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
ATAATAAAAAATAATG
Found at i:4861463 original size:24 final size:25
Alignment explanation
Indices: 4861387--4861467 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 25
4861377 TAATTAAAAA
* *
4861387 TATAAAAAAATTAATTTTATTTTAAAT
1 TATATAAAAATTAATTTT-TTAT-AAT
* *
4861414 TATATAATAAA--AATATTTTAAAAAT
1 TATATAA-AAATTAAT-TTTTTATAAT
4861439 TAT-TAAAAATTAATTTTTTATAAT
1 TATATAAAAATTAATTTTTTATAAT
4861463 TATAT
1 TATAT
4861468 TTATAATTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
23 3 0.07
24 14 0.33
25 10 0.23
26 4 0.09
27 9 0.21
28 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TATATAAAAATTAATTTTTTATAAT
Found at i:4862141 original size:25 final size:26
Alignment explanation
Indices: 4862081--4862141 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
4862071 GCGTGTGATT
*
4862081 TTTTTATTATAATTATATTTAAAATA
1 TTTTTATTATAATCATATTTAAAATA
** *
4862107 -TTTTATT-TATATCATATTTTTATTA
1 TTTTTATTATA-ATCATATTTAAAATA
4862132 TTTTTATTAT
1 TTTTTATTAT
4862142 TTATATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
24 2 0.07
25 18 0.64
26 7 0.25
27 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTTTATTATAATCATATTTAAAATA
Found at i:4864262 original size:17 final size:18
Alignment explanation
Indices: 4864240--4864281 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
4864230 TTAATAGTTA
4864240 TTAAAAAAA-ATTTGTAG
1 TTAAAAAAATATTTGTAG
*
4864257 TTAAAAAAATATTTTTAG
1 TTAAAAAAATATTTGTAG
4864275 -TAAAAAA
1 TTAAAAAA
4864282 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (18 bp):
TTAAAAAAATATTTGTAG
Found at i:4864265 original size:18 final size:17
Alignment explanation
Indices: 4864242--4864281 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
4864232 AATAGTTATT
4864242 AAAAAAAATTTGTAGTTA
1 AAAAAAAATTTGTAG-TA
* *
4864260 AAAAAATATTTTTAGTA
1 AAAAAAAATTTGTAGTA
4864277 AAAAA
1 AAAAA
4864282 TAAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (17 bp):
AAAAAAAATTTGTAGTA
Found at i:4864433 original size:208 final size:202
Alignment explanation
Indices: 4864199--4864573 Score: 486
Period size: 208 Copynumber: 1.8 Consensus size: 202
4864189 ATGTCCACTA
* * *
4864199 GAATGAGAATATAATTTAATTATAATTTAAATTAATAGTTATTAAA-AAAAATTTGTAGTTAAAA
1 GAATGAGAATATAATTTAATTATAATTTAAATTAATAGTAATTAAAGAAAAATTTATAATT-AAA
* *
4864263 AAATATTTTTAGTAAAAAATAAAAAAATTTAAAAATAAAAAAAATAATTGACAATTGATAAA-AG
65 AAATATTATGAGTAAAAAATAAAAAAA--T--AAAT---AAAAATAATTGACAATTGATAAAGA-
* *
4864327 GCATATTTAT-TTTTTATTTAAAATTAACTGATAAATAATACTTTAGGAGTAAGTATATTTTGTA
122 GCATATTTATCTTTCTATTTAAAATTAACTGATAAATAATAATTTAGGAGTAAGTATATTTTGTA
4864391 TCTAGCATGTTTATTT
187 TCTAGCATGTTTATTT
* * *
4864407 GAATGAGAATATAATTTAATTATAATTTAAGTTAATAGTAATTAAAGATAATTTTATAATTAAAA
1 GAATGAGAATATAATTTAATTATAATTTAAATTAATAGTAATTAAAGAAAAATTTATAATTAAAA
* * * * * *
4864472 AATATTATGATTAAAAAATTAAAAAATAAATATAAATAATTGATAATTGATAAAGAGTATGTTTA
66 AATATTATGAGTAAAAAATAAAAAAATAAATAAAAATAATTGACAATTGATAAAGAGCATATTTA
* *
4864537 TCTTTCTATTTAAAATTAATTTATAAATAATAATTTA
131 TCTTTCTATTTAAAATTAACTGATAAATAATAATTTA
4864574 AATAATAAAT
Statistics
Matches: 146, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
201 29 0.20
202 32 0.22
204 4 0.03
206 1 0.01
208 70 0.48
209 10 0.07
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (202 bp):
GAATGAGAATATAATTTAATTATAATTTAAATTAATAGTAATTAAAGAAAAATTTATAATTAAAA
AATATTATGAGTAAAAAATAAAAAAATAAATAAAAATAATTGACAATTGATAAAGAGCATATTTA
TCTTTCTATTTAAAATTAACTGATAAATAATAATTTAGGAGTAAGTATATTTTGTATCTAGCATG
TTTATTT
Found at i:4864484 original size:16 final size:16
Alignment explanation
Indices: 4864445--4864490 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
4864435 AAGTTAATAG
*
4864445 TAATTAAAGATAATTTTA
1 TAATTAAA-A-AATATTA
4864463 TAATTAAAAAATATTA
1 TAATTAAAAAATATTA
*
4864479 TGATTAAAAAAT
1 TAATTAAAAAAT
4864491 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 17 0.65
17 1 0.04
18 8 0.31
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (16 bp):
TAATTAAAAAATATTA
Found at i:4866133 original size:130 final size:129
Alignment explanation
Indices: 4865901--4866154 Score: 436
Period size: 130 Copynumber: 2.0 Consensus size: 129
4865891 ATTGTACTAC
4865901 GACAAACAACATACAAGGAGCAATTTCATGGCAGACATCATATCCAAAACTCAGCCTCTAATCAT
1 GACAAACAACATACAAGGAGCAATTTCATGGCAGACATCATATCCAAAACTCAGCCTCTAATCAT
* * *
4865966 CACACTGTGGGTTTAAAAGTTAAAAACTTTTTAACATACATATGTACAATGACATGCCTCCTAA
66 CACACTGTAGGTTTAAAAGTCAAAAACTTTTAAACATACATATGTACAATGACATGCCTCCTAA
* * *
4866030 GACAAACAGCGTACAAGGAGCAATTTCATGGCTGACATCATAATCCAAAACTCAGCCTCTAATCA
1 GACAAACAACATACAAGGAGCAATTTCATGGCAGACATCAT-ATCCAAAACTCAGCCTCTAATCA
*
4866095 TCACACTGTAGGTTTAAACGTCAAAAACTTTTAAACATACATATGTACAATGACATGCCT
65 TCACACTGTAGGTTTAAAAGTCAAAAACTTTTAAACATACATATGTACAATGACATGCCT
4866155 AGATTTTACA
Statistics
Matches: 117, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
129 38 0.32
130 79 0.68
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (129 bp):
GACAAACAACATACAAGGAGCAATTTCATGGCAGACATCATATCCAAAACTCAGCCTCTAATCAT
CACACTGTAGGTTTAAAAGTCAAAAACTTTTAAACATACATATGTACAATGACATGCCTCCTAA
Found at i:4869692 original size:27 final size:28
Alignment explanation
Indices: 4869656--4869725 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
4869646 TTTTTAAAAA
* *
4869656 TTTAATAAAAA-TAATGTATTAAATAATT
1 TTTAATAAAAATTAAT-AATTAAATAAAT
4869684 TTTAA-AAAAATTAATAATTAAATAAAT
1 TTTAATAAAAATTAATAATTAAATAAAT
*
4869711 TTTAATTAATAATTA
1 TTTAA-TAAAAATTA
4869726 TAGACATCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 20 0.56
28 9 0.25
29 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (28 bp):
TTTAATAAAAATTAATAATTAAATAAAT
Found at i:4871337 original size:16 final size:16
Alignment explanation
Indices: 4871291--4871342 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
4871281 TCTAAATCCG
*
4871291 AAATAGTTTAAACTCA
1 AAATAGTTTAAACTTA
**
4871307 AAATAGTCAAAACTTA
1 AAATAGTTTAAACTTA
*
4871323 AAATATTTTAAACTTGA
1 AAATAGTTTAAACTT-A
4871340 AAA
1 AAA
4871343 AACTTAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
16 25 0.86
17 4 0.14
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.31
Consensus pattern (16 bp):
AAATAGTTTAAACTTA
Found at i:4874145 original size:15 final size:14
Alignment explanation
Indices: 4874106--4874147 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
4874096 AAGGATTAAA
4874106 TTTTTTAT-ATTAT
1 TTTTTTATAATTAT
*
4874119 TTTTTTAAAATTAT
1 TTTTTTATAATTAT
4874133 TTTTTTCATAATTAT
1 TTTTTT-ATAATTAT
4874148 AAAAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 7 0.28
14 11 0.44
15 7 0.28
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTTATAATTAT
Found at i:4874429 original size:24 final size:23
Alignment explanation
Indices: 4874406--4874472 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 23
4874396 ATTATGTTAT
4874406 TTTTATTTAAAATAAATTAATTA
1 TTTTATTTAAAATAAATTAATTA
*
4874429 --TTATTTAAAAATAAATTTAA-AA
1 TTTTATTT-AAAATAAA-TTAATTA
4874451 TATTTA-TTAATAATAAATTAAT
1 T-TTTATTTAA-AATAAATTAAT
4874473 ATTAGTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 13
0.72 0.02 0.26
Matches are distributed among these distances:
21 6 0.17
22 9 0.25
23 10 0.28
24 8 0.22
25 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTTATTTAAAATAAATTAATTA
Found at i:4874434 original size:21 final size:21
Alignment explanation
Indices: 4874408--4874489 Score: 87
Period size: 21 Copynumber: 3.8 Consensus size: 21
4874398 TATGTTATTT
4874408 TTATTTAA-AATAAATTAATTA
1 TTATTTAATAATAAATTAA-TA
*
4874429 TTATTTAAAAATAAATTTAAAATA
1 TTATTTAATAATAAA-TT--AATA
4874453 TT-TATTAATAATAAATTAATA
1 TTAT-TTAATAATAAATTAATA
*
4874474 TTAGTTAATAATAAAT
1 TTATTTAATAATAAAT
4874490 ATCTTTAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
21 26 0.49
22 6 0.11
23 5 0.09
24 14 0.26
25 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (21 bp):
TTATTTAATAATAAATTAATA
Found at i:4877113 original size:2 final size:2
Alignment explanation
Indices: 4877106--4877134 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4877096 ACTTGACCCC
4877106 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4877135 CCTGTGTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4885545 original size:61 final size:61
Alignment explanation
Indices: 4885470--4885592 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 61
4885460 ATACATATAC
*
4885470 ATAGTTATTAATTAGTGGCTTAAATTAGCTCTCTTTTAAAAATTAAGTTCGTGCTTACAGA
1 ATAGTTATTAATTAGTGGCTTAAATCAGCTCTCTTTTAAAAATTAAGTTCGTGCTTACAGA
*
4885531 ATAGTTATTAATTAGTGGCTTAAATCAGCTCTCTTTTAAAAATTAAGTTCGTGTTTACAGA
1 ATAGTTATTAATTAGTGGCTTAAATCAGCTCTCTTTTAAAAATTAAGTTCGTGCTTACAGA
4885592 A
1 A
4885593 AGACCACAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (61 bp):
ATAGTTATTAATTAGTGGCTTAAATCAGCTCTCTTTTAAAAATTAAGTTCGTGCTTACAGA
Found at i:4886788 original size:2 final size:2
Alignment explanation
Indices: 4886781--4886806 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4886771 TGCCATGTGA
4886781 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
4886807 GCCATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4908987 original size:17 final size:18
Alignment explanation
Indices: 4908962--4909007 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
4908952 CAAATAAAAT
*
4908962 AATATAATAATAT-TTTA
1 AATAAAATAATATATTTA
4908979 AATAAAAT-ATATATTTA
1 AATAAAATAATATATTTA
4908996 AATATAAATAAT
1 AATA-AAATAAT
4909008 TTATATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 4 0.16
17 15 0.60
18 4 0.16
19 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATAAAATAATATATTTA
Found at i:4908994 original size:18 final size:16
Alignment explanation
Indices: 4908942--4909038 Score: 59
Period size: 14 Copynumber: 6.4 Consensus size: 16
4908932 TATTTTATTT
4908942 TATTTAAATACAAATAA
1 TATTTAAATA-AAATAA
* *
4908959 -A-AT-AATATAATAA
1 TATTTAAATAAAATAA
4908972 TATTTTAAATAAAATATA
1 TA-TTTAAATAAAATA-A
4908990 TATTTAAATATAAAT-A
1 TATTTAAATA-AAATAA
*
4909006 -ATTTATATAAAAT--
1 TATTTAAATAAAATAA
*
4909019 TATATAAAT-AAAT-A
1 TATTTAAATAAAATAA
4909033 TATTTA
1 TATTTA
4909039 TATACAATAT
Statistics
Matches: 64, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
13 9 0.14
14 20 0.31
15 9 0.14
16 3 0.05
17 16 0.25
18 7 0.11
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (16 bp):
TATTTAAATAAAATAA
Found at i:4909031 original size:33 final size:32
Alignment explanation
Indices: 4908943--4909034 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 32
4908933 ATTTTATTTT
*
4908943 ATTTAAATACAA-ATA-AAAT-AATATAATAATA
1 ATTTAAATAAAATATATAAATAAATAT-A-AATA
* **
4908974 TTTTAAATAAAATATATATTTAAATATAAATA
1 ATTTAAATAAAATATATAAATAAATATAAATA
*
4909006 ATTTATATAAAATTATATAAATAAATATA
1 ATTTAAATAAAA-TATATAAATAAATATA
4909035 TTTATATACA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
31 10 0.20
32 17 0.35
33 17 0.35
34 5 0.10
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
ATTTAAATAAAATATATAAATAAATATAAATA
Found at i:4909053 original size:28 final size:27
Alignment explanation
Indices: 4908955--4909052 Score: 83
Period size: 32 Copynumber: 3.4 Consensus size: 27
4908945 TTAAATACAA
* * *
4908955 ATAAAATAATAT-AAT-AATATTTTAA
1 ATAAAATTATATAAATAAATAATTTAT
4908980 ATAAAATATATATTTAAATATAAATAATTTAT
1 ATAAAAT-TATA--T-AA-ATAAATAATTTAT
4909012 ATAAAATTATATAAATAAATATATTTAT
1 ATAAAATTATATAAATAAATA-ATTTAT
4909040 ATACAATATTATA
1 ATA-AA-ATTATA
4909053 ATTTTTGTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
25 7 0.12
26 3 0.05
27 7 0.12
28 12 0.20
29 3 0.05
30 7 0.12
31 6 0.10
32 15 0.25
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (27 bp):
ATAAAATTATATAAATAAATAATTTAT
Found at i:4909264 original size:23 final size:25
Alignment explanation
Indices: 4909204--4909265 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 25
4909194 GAGTATAAAA
4909204 TTTTATTTATAATATTTAAAATAATT
1 TTTTATTTA-AATATTTAAAATAATT
*
4909230 TTTTATTT--ATATTT-ATAT-A-T
1 TTTTATTTAAATATTTAAAATAATT
4909250 TTTTATTTAAAATATT
1 TTTTATTT-AAATATT
4909266 ATCACATATG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
20 9 0.28
21 1 0.03
22 3 0.09
23 11 0.34
26 8 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTATTTAAATATTTAAAATAATT
Found at i:4909386 original size:31 final size:26
Alignment explanation
Indices: 4909330--4909382 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
4909320 AATTCAATTC
4909330 AATTCAATTCAATTGAAGATTATGTT
1 AATTCAATTCAATTGAAGATTATGTT
4909356 AATTCAATTCAATTGAAGATTATGTT
1 AATTCAATTCAATTGAAGATTATGTT
4909382 A
1 A
4909383 TGTTTAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.42
Consensus pattern (26 bp):
AATTCAATTCAATTGAAGATTATGTT
Found at i:4911570 original size:15 final size:16
Alignment explanation
Indices: 4911546--4911587 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
4911536 TTTTCATAAA
4911546 TTAA-AAATATTAATT
1 TTAATAAATATTAATT
4911561 TT-ATAAATATT-ATT
1 TTAATAAATATTAATT
*
4911575 TTAATCAATATTA
1 TTAATAAATATTA
4911588 TTAAATATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAATAAATATTAATT
Found at i:4915945 original size:43 final size:41
Alignment explanation
Indices: 4915897--4915990 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 41
4915887 ATTTATCATG
*
4915897 TATTTATAT-ATTATTATGTTATAATTATTTTTAAAATATTT-TA
1 TATTTATATAATT-TTA-ATTATAA-TA-TTTTAAAATATTTATA
4915940 TATTTATATAAATTTTAATTATAATATTTTAAAATATTTATA
1 TATTTATAT-AATTTTAATTATAATATTTTAAAATATTTATA
4915982 TATTTATAT
1 TATTTATAT
4915991 TATCTTATAA
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
41 13 0.28
42 13 0.28
43 15 0.32
44 3 0.06
45 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (41 bp):
TATTTATATAATTTTAATTATAATATTTTAAAATATTTATA
Found at i:4915948 original size:41 final size:41
Alignment explanation
Indices: 4915903--4915993 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 41
4915893 CATGTATTTA
*
4915903 TATATTATTAT-GTTATAATTATTTTTAAAATATTT-TATATT
1 TATATTATTATAATTATAA-TA-TTTTAAAATATTTATATATT
* *
4915944 TATATAAATTTTAATTATAATATTTTAAAATATTTATATATT
1 TATAT-TATTATAATTATAATATTTTAAAATATTTATATATT
4915986 TATATTAT
1 TATATTAT
4915994 CTTATAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
41 20 0.47
42 17 0.40
43 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (41 bp):
TATATTATTATAATTATAATATTTTAAAATATTTATATATT
Found at i:4916002 original size:27 final size:26
Alignment explanation
Indices: 4915950--4916018 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
4915940 TATTTATATA
* *
4915950 AATTTTA-ATTATAATATTTTAAAAT
1 AATTTTATATTATATTATCTTAAAAT
*
4915975 -ATTTATATATTTATATTATCTTATAAT
1 AATTT-TATA-TTATATTATCTTAAAAT
4916002 AAATTTTATATTATATT
1 -AATTTTATATTATATT
4916019 TTTAATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 4 0.11
25 2 0.06
26 1 0.03
27 21 0.58
28 4 0.11
29 4 0.11
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (26 bp):
AATTTTATATTATATTATCTTAAAAT
Found at i:4917130 original size:25 final size:25
Alignment explanation
Indices: 4917073--4917153 Score: 78
Period size: 25 Copynumber: 3.4 Consensus size: 25
4917063 TTATATATAT
* *
4917073 TAAAAAAAT-TATATTATATATATA
1 TAAAAAAATATATATTAAATATAAA
***
4917097 TATTTAAATATATATTAAATATAAA
1 TAAAAAAATATATATTAAATATAAA
* *
4917122 TACAAAAATATAT-TTAAA-AAAAA
1 TAAAAAAATATATATTAAATATAAA
4917145 TAAAAAAAT
1 TAAAAAAAT
4917154 TAAATAATAT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
23 12 0.26
24 11 0.24
25 23 0.50
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (25 bp):
TAAAAAAATATATATTAAATATAAA
Found at i:4917132 original size:23 final size:23
Alignment explanation
Indices: 4917102--4917153 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
4917092 ATATATATTT
* *
4917102 AAATATATATTAAATATAAATACAA
1 AAATATAT-TTAAA-AAAAATAAAA
4917127 AAATATATTTAAAAAAAATAAAA
1 AAATATATTTAAAAAAAATAAAA
4917150 AAAT
1 AAAT
4917154 TAAATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.48
24 5 0.20
25 8 0.32
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATATATTTAAAAAAAATAAAA
Found at i:4917866 original size:28 final size:29
Alignment explanation
Indices: 4917812--4917867 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
4917802 TCGCCGACTA
**
4917812 ATTTTAAACATCACATTAGGATAAAAAAT
1 ATTTTAAACATCACATTAAAATAAAAAAT
*
4917841 ATTTTAAA-ATCACA-TAAAATATAAAAT
1 ATTTTAAACATCACATTAAAATAAAAAAT
4917868 GGTATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.42
28 6 0.25
29 8 0.33
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (29 bp):
ATTTTAAACATCACATTAAAATAAAAAAT
Found at i:4918525 original size:59 final size:59
Alignment explanation
Indices: 4918441--4918554 Score: 139
Period size: 59 Copynumber: 1.9 Consensus size: 59
4918431 TGTTTACAGG
*
4918441 AATTGAATTATATTAATAAATTTATTT-ATAAATTAA-A-TTATTTATTTAATTTAAATTAA
1 AATTGAATTATATTAATAAAATTATTTAATAAA--AATATTTA-TTATTTAATTTAAATTAA
4918500 AATTGAACTTA-ATTTAA-AAAATTATTTAATAAAAATATTTATTATTTAATTTAAA
1 AATTGAA-TTATA-TTAATAAAATTATTTAATAAAAATATTTATTATTTAATTTAAA
4918555 AATATATATT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
58 2 0.04
59 32 0.65
60 15 0.31
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (59 bp):
AATTGAATTATATTAATAAAATTATTTAATAAAAATATTTATTATTTAATTTAAATTAA
Found at i:4918557 original size:22 final size:20
Alignment explanation
Indices: 4918520--4918576 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 20
4918510 AATTTAAAAA
*
4918520 ATTATTTAATAAAAATATTT
1 ATTATTTAATAAAAATATAT
4918540 ATTATTTAATTTAAAAATATAT
1 ATTATTTAA--TAAAAATATAT
4918562 ATT-TTTAA-AAAAATA
1 ATTATTTAATAAAAATA
4918577 CTAAACTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 7 0.21
20 9 0.26
21 5 0.15
22 13 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTATTTAATAAAAATATAT
Found at i:4919163 original size:23 final size:23
Alignment explanation
Indices: 4919137--4919188 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
4919127 CAGTTAAATC
*
4919137 TTTAAATTTTTTTTAT-ATTAATA
1 TTTAAATTATTTTTATAATTAA-A
*
4919160 TTTATA-TATTTTTATAATTAAA
1 TTTAAATTATTTTTATAATTAAA
*
4919182 TTAAAAT
1 TTTAAAT
4919189 AAAAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTAAATTATTTTTATAATTAAA
Found at i:4928117 original size:23 final size:22
Alignment explanation
Indices: 4928054--4928128 Score: 56
Period size: 23 Copynumber: 3.5 Consensus size: 22
4928044 TAAAGTTATC
*
4928054 AAATATTA-TATT-TAAT-AAT
1 AAATATTATTATTATTATAAAT
4928073 AATATATTATTATTATTATAAAT
1 AA-ATATTATTATTATTATAAAT
4928096 AAGATATTAATTAATT-TT-TAAA-
1 AA-ATATT-ATT-ATTATTATAAAT
4928118 AAATATT-TTAT
1 AAATATTATTAT
4928129 AAATACTTGT
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
18 2 0.04
19 4 0.08
20 6 0.12
21 9 0.19
22 5 0.10
23 14 0.29
24 5 0.10
25 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (22 bp):
AAATATTATTATTATTATAAAT
Found at i:4935448 original size:20 final size:22
Alignment explanation
Indices: 4935425--4935477 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
4935415 CCTCTATTTT
*
4935425 CTTTTTTTCTT-TT-TTTTCTC
1 CTTTCTTTCTTCTTCTTTTCTC
*
4935445 CTTTCTTTCTTCTTCTTTTCTTT
1 CTTTCTTTCTTCTTCTTTTC-TC
4935468 CTTTCTTTCT
1 CTTTCTTTCT
4935478 CAGCTCCCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 10 0.36
21 2 0.07
22 5 0.18
23 11 0.39
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
CTTTCTTTCTTCTTCTTTTCTC
Found at i:4935457 original size:23 final size:23
Alignment explanation
Indices: 4935422--4935477 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 23
4935412 TTTCCTCTAT
*
4935422 TTTCTTTTTTTCTT-TT-TTTTC
1 TTTCTTTCTTTCTTCTTCTTTTC
*
4935443 -TCCTTTCTTTCTTCTTCTTTTC
1 TTTCTTTCTTTCTTCTTCTTTTC
4935465 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
4935478 CAGCTCCCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 5 0.17
23 11 0.38
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTCTTTCTTTCTTCTTCTTTTC
Found at i:4935786 original size:18 final size:17
Alignment explanation
Indices: 4935759--4935823 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 17
4935749 TAACATAAAT
4935759 ATATATTTAAAATT-TTA
1 ATATA-TTAAAATTATTA
4935776 TATAATATT--AATTATTA
1 -AT-ATATTAAAATTATTA
4935793 ATATATTAAAATTAATTAA
1 ATATATTAAAATT-ATT-A
4935812 ATATATATAAAA
1 ATATAT-TAAAA
4935824 AATAATTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
15 5 0.12
16 6 0.15
17 7 0.17
18 7 0.17
19 10 0.25
20 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATTAAAATTATTA
Found at i:4935807 original size:21 final size:19
Alignment explanation
Indices: 4935782--4935837 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 19
4935772 TTTATATAAT
4935782 ATTAATTATTAATATATTAAA
1 ATTAATTA--AATATATTAAA
4935803 ATTAATTAAATATATATAAAA
1 ATTAATTAAATATAT-T-AAA
*
4935824 AATAATTAAATATA
1 ATTAATTAAATATA
4935838 AAGTATCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 7 0.22
20 1 0.03
21 24 0.75
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTAATTAAATATATTAAA
Found at i:4935982 original size:2 final size:2
Alignment explanation
Indices: 4935977--4936002 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4935967 TCTCTCTCTC
4935977 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
4936003 AAACTTAGTA
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:4943339 original size:8 final size:9
Alignment explanation
Indices: 4943324--4943355 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
4943314 GCCCTTTCAC
4943324 TATTTTATT
1 TATTTTATT
4943333 T-TTTTATT
1 TATTTTATT
4943341 TATTTT-TT
1 TATTTTATT
4943349 TATTTTA
1 TATTTTA
4943356 AGTTCCCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TATTTTATT
Found at i:4943355 original size:13 final size:13
Alignment explanation
Indices: 4943324--4943355 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
4943314 GCCCTTTCAC
4943324 TATTTTATTTTTT
1 TATTTTATTTTTT
4943337 TA-TTTATTTTTT
1 TATTTTATTTTTT
4943349 TATTTTA
1 TATTTTA
4943356 AGTTCCCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TATTTTATTTTTT
Found at i:4949732 original size:31 final size:33
Alignment explanation
Indices: 4949697--4949763 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 33
4949687 TTTATTATTA
* * *
4949697 TTATTTTGTGTAATTA-GTTAATAGTAATT-GT
1 TTATTATGTGAAATTAGGTTAAGAGTAATTAGT
*
4949728 TTATTATGTGAAATTAGGTTTAGAGTAATTAGT
1 TTATTATGTGAAATTAGGTTAAGAGTAATTAGT
4949761 TTA
1 TTA
4949764 GGGGTAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 14 0.47
32 11 0.37
33 5 0.17
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (33 bp):
TTATTATGTGAAATTAGGTTAAGAGTAATTAGT
Found at i:4949759 original size:15 final size:15
Alignment explanation
Indices: 4949739--4949778 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4949729 TATTATGTGA
4949739 AATTAGGTTTA-GAGT
1 AATTA-GTTTAGGAGT
*
4949754 AATTAGTTTAGGGGT
1 AATTAGTTTAGGAGT
4949769 AATTAGTTTA
1 AATTAGTTTA
4949779 AAGCTTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (15 bp):
AATTAGTTTAGGAGT
Found at i:4954826 original size:27 final size:27
Alignment explanation
Indices: 4954792--4954849 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
4954782 CACCATATTT
* **
4954792 TCCTACTCAATCTCCATACCTGTCATA
1 TCCTACTCAACCTCCATACCCATCATA
4954819 TCCTACTCAACCTCCATACCCATCATA
1 TCCTACTCAACCTCCATACCCATCATA
4954846 TCCT
1 TCCT
4954850 GCCACGACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.26, C:0.41, G:0.02, T:0.31
Consensus pattern (27 bp):
TCCTACTCAACCTCCATACCCATCATA
Found at i:4955246 original size:75 final size:75
Alignment explanation
Indices: 4955122--4955500 Score: 560
Period size: 75 Copynumber: 5.0 Consensus size: 75
4955112 TTATTGATTA
* * *
4955122 TAGTTGTTGATAGTAGTAATGTGAAATATGTAGAAACATTTGTTGATTGTAGTTATCGTGCAGAT
1 TAGTTGTTGATAGTAGTACTGTGAAATATGCAGAAACATTTGTTAATTGTAGTTATCGTGCAGAT
* *
4955187 TATCTCGGGT
66 TATCTCAGAT
* *
4955197 TAGTTGTTGATAGTAGTACTGTGAAATATGCAAAAACATTTGTTAATTGTAATTATCGTGCAGAT
1 TAGTTGTTGATAGTAGTACTGTGAAATATGCAGAAACATTTGTTAATTGTAGTTATCGTGCAGAT
* *
4955262 TATCTCGGGT
66 TATCTCAGAT
* * * * *
4955272 TAGTTGTTCATAGTAGTACTGTGAAATATGCTGAAACATTTGTTCATTGTAGTTATCATGCATAT
1 TAGTTGTTGATAGTAGTACTGTGAAATATGCAGAAACATTTGTTAATTGTAGTTATCGTGCAGAT
4955337 TATCTCAGAT
66 TATCTCAGAT
* * * *
4955347 TAGTTGTTGATAGTAGTAATGTGAAATACGCAGTAACATTTGTTAATTGTAGTTATCGTGCATAT
1 TAGTTGTTGATAGTAGTACTGTGAAATATGCAGAAACATTTGTTAATTGTAGTTATCGTGCAGAT
4955412 TATCTCAGAT
66 TATCTCAGAT
* *
4955422 TAGTTGTTGATAGTAGTACTTGTGAAATATGCAAAAACATTTGTTGATTGTAGTTATCGTGCAGA
1 TAGTTGTTGATAGTAGTAC-TGTGAAATATGCAGAAACATTTGTTAATTGTAGTTATCGTGCAGA
*
4955487 TTATTTCAGAT
65 TTATCTCAGAT
4955498 TAG
1 TAG
4955501 AGTTTCATCT
Statistics
Matches: 275, Mismatches: 28, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
75 222 0.81
76 53 0.19
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (75 bp):
TAGTTGTTGATAGTAGTACTGTGAAATATGCAGAAACATTTGTTAATTGTAGTTATCGTGCAGAT
TATCTCAGAT
Found at i:4955354 original size:39 final size:39
Alignment explanation
Indices: 4955311--4955438 Score: 120
Period size: 39 Copynumber: 3.4 Consensus size: 39
4955301 GCTGAAACAT
* * *
4955311 TTGTTCATTGTAGTTATCATGCATATTATCTCAGATTAG
1 TTGTTGATAGTAGTTATCGTGCATATTATCTCAGATTAG
* * * ** *
4955350 TTGTTGATAGTAGTAAT-GTG-A-AATA-CGCAGTAACAT
1 TTGTTGATAGTAGTTATCGTGCATATTATCTCAG-ATTAG
* *
4955386 TTGTTAATTGTAGTTATCGTGCATATTATCTCAGATTAG
1 TTGTTGATAGTAGTTATCGTGCATATTATCTCAGATTAG
4955425 TTGTTGATAGTAGT
1 TTGTTGATAGTAGT
4955439 ACTTGTGAAA
Statistics
Matches: 65, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
35 4 0.06
36 19 0.29
37 4 0.06
38 3 0.05
39 31 0.48
40 4 0.06
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (39 bp):
TTGTTGATAGTAGTTATCGTGCATATTATCTCAGATTAG
Found at i:4956171 original size:23 final size:23
Alignment explanation
Indices: 4956145--4956193 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
4956135 TTGATTTGGG
* * *
4956145 AATTCTTTTATTTTAATTTACTT
1 AATTATTTTATTTTAAATAACTT
4956168 AATTATTTTATTTTAAATAACTT
1 AATTATTTTATTTTAAATAACTT
4956191 AAT
1 AAT
4956194 ATGAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (23 bp):
AATTATTTTATTTTAAATAACTT
Found at i:4957100 original size:32 final size:30
Alignment explanation
Indices: 4957064--4957123 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
4957054 AAATCGCAAA
4957064 TAACTTAAAAATCAGAATGCGTTTCAAAATTT
1 TAACTTAAAAATCAGAAT--GTTTCAAAATTT
* * *
4957096 TAACTTTAATATCAGCATGTTTCAAAAT
1 TAACTTAAAAATCAGAATGTTTCAAAAT
4957124 CTCATTGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.40
32 15 0.60
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (30 bp):
TAACTTAAAAATCAGAATGTTTCAAAATTT
Found at i:4958165 original size:66 final size:67
Alignment explanation
Indices: 4958060--4958194 Score: 173
Period size: 66 Copynumber: 2.0 Consensus size: 67
4958050 TTTTGAACTC
* * ** ** * *
4958060 TTTTCAGCTCTGAAATTTGAGAATAAGCGGAAGCGGCAGTTTTTCTTAAGACAGGTTAGGGTAAT
1 TTTTCAGCTCTGAAATTTGAGAACAAGAGGAAGAAGCAGTTTTTCCCAAGACAGGTCAAGGTAAT
4958125 CT
66 CT
* *
4958127 TTTTGAGCTCTGAAATTTGAGGACAAGAGG-AGAAGCAGTTTTTCCCAAGACAGGTCAAGGTAAT
1 TTTTCAGCTCTGAAATTTGAGAACAAGAGGAAGAAGCAGTTTTTCCCAAGACAGGTCAAGGTAAT
4958191 CT
66 CT
4958193 TT
1 TT
4958195 GTACTCGATA
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
66 32 0.55
67 26 0.45
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (67 bp):
TTTTCAGCTCTGAAATTTGAGAACAAGAGGAAGAAGCAGTTTTTCCCAAGACAGGTCAAGGTAAT
CT
Found at i:4958376 original size:2 final size:2
Alignment explanation
Indices: 4958369--4958395 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4958359 TTATTTTCTT
4958369 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4958396 TGGAACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4963800 original size:2 final size:2
Alignment explanation
Indices: 4963753--4963787 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4963743 TAGCTTTTGG
4963753 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 A
4963788 AACACTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4967700 original size:2 final size:2
Alignment explanation
Indices: 4967695--4967737 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
4967685 AAAAACAGCA
*
4967695 AG AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4967737 A
1 A
4967738 TGGATTTGAT
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:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (2 bp):
AG
Found at i:4968682 original size:16 final size:16
Alignment explanation
Indices: 4968658--4968699 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
4968648 TATATATTAG
*
4968658 ATTAATTTAAGTTTAA-
1 ATTATTTTAAG-TTAAT
4968674 ATTATTTTAAGTTAAT
1 ATTATTTTAAGTTAAT
4968690 ATTATTTTAA
1 ATTATTTTAA
4968700 ATTTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
ATTATTTTAAGTTAAT
Found at i:4968737 original size:16 final size:16
Alignment explanation
Indices: 4968700--4968869 Score: 78
Period size: 16 Copynumber: 10.1 Consensus size: 16
4968690 ATTATTTTAA
*
4968700 ATTTTAAAATTTAAGTTT
1 ATTTT-AAATTTAA-ATT
4968718 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
* **
4968734 ATTTTAAATTAAAAAA
1 ATTTTAAATTTAAATT
* *
4968750 ATTTATATTATTTAAATC
1 ATTT-TA-AATTTAAATT
* *
4968768 AATTTAAATTTGAGA-T
1 ATTTTAAATTT-AAATT
4968784 A--TTAAGAGTTTTAAATT
1 ATTTTAA-A--TTTAAATT
*
4968801 -TTTAAATCAATTTAAATTT
1 ATTT---TAAATTTAAA-TT
* *
4968820 ATATCAAATTTAAATT
1 ATTTTAAATTTAAATT
* *
4968836 ATTTTGAATTTAAATA
1 ATTTTAAATTTAAATT
4968852 ATTTTTAAATTTAAATT
1 A-TTTTAAATTTAAATT
4968869 A
1 A
4968870 AGAGTTTTAA
Statistics
Matches: 114, Mismatches: 23, Indels: 31
0.68 0.14 0.18
Matches are distributed among these distances:
14 4 0.04
15 1 0.01
16 41 0.36
17 40 0.35
18 21 0.18
19 2 0.02
20 3 0.03
21 2 0.02
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (16 bp):
ATTTTAAATTTAAATT
Found at i:4968761 original size:41 final size:40
Alignment explanation
Indices: 4968673--4968766 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 40
4968663 TTTAAGTTTA
* **
4968673 AATTATTTT-AAGTTAATATTATTTTAAATTTTAAAATTT
1 AATTATTTTAAATTTAATATTATTTTAAATTAAAAAATTT
4968712 AAGTTTATTTTAAATTTAA-ATTATTTTAAATTAAAAAAATTT
1 AA--TTATTTTAAATTTAATATTATTTTAAATT-AAAAAATTT
4968754 ATATTA-TTTAAAT
1 A-ATTATTTTAAAT
4968767 CAATTTAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
39 2 0.04
40 7 0.15
41 23 0.49
42 14 0.30
43 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (40 bp):
AATTATTTTAAATTTAATATTATTTTAAATTAAAAAATTT
Found at i:4968776 original size:25 final size:26
Alignment explanation
Indices: 4968720--4968778 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
4968710 TTAAGTTTAT
*
4968720 TTTAAATTTAAATTATTTTAAATTAA
1 TTTAAATTTAAATTATTTTAAATCAA
** *
4968746 -AAAAATTTATATTA-TTTAAATCAA
1 TTTAAATTTAAATTATTTTAAATCAA
4968770 TTTAAATTT
1 TTTAAATTT
4968779 GAGATATTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTAAATTTAAATTATTTTAAATCAA
Found at i:4968858 original size:27 final size:28
Alignment explanation
Indices: 4968797--4968928 Score: 81
Period size: 27 Copynumber: 4.5 Consensus size: 28
4968787 AAGAGTTTTA
* *
4968797 AATTTTTAAATCAATTTAAATTTATATC
1 AATTTTTAAATTAATTTAAATTTAAATC
* * *
4968825 AA-ATTTAAATTATTTTGAATTTAAAT-
1 AATTTTTAAATTAATTTAAATTTAAATC
*
4968851 AATTTTTAAATTTAAATTAAGAGTTTTAAATC
1 AATTTTTAAA-TTAATTTAA-A--TTTAAATC
* *
4968883 TACTTCGTATTAAAATTATTTTAAATTTAAAT-
1 -AATT--T-TT-AAATTAATTTAAATTTAAATC
*
4968915 AATTTTCAAATTAA
1 AATTTTTAAATTAA
4968929 GAGTTTAAGT
Statistics
Matches: 78, Mismatches: 15, Indels: 23
0.67 0.13 0.20
Matches are distributed among these distances:
26 2 0.03
27 31 0.40
28 9 0.12
29 2 0.03
31 10 0.13
33 10 0.13
35 2 0.03
36 9 0.12
37 3 0.04
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (28 bp):
AATTTTTAAATTAATTTAAATTTAAATC
Found at i:4972223 original size:2 final size:2
Alignment explanation
Indices: 4972216--4972253 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4972206 GCCTTTGGGG
4972216 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4972254 GGTGGATGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4973877 original size:23 final size:23
Alignment explanation
Indices: 4973836--4973906 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 23
4973826 ATCTCCTAGT
4973836 TTTAAATATAATT-ATATATAATA
1 TTTAAA-ATAATTAATATATAATA
*
4973859 TTTAAAATAATTAAAATATAATAAA
1 TTTAAAATAATTAATATATAAT--A
4973884 TATTAAAA-AATTAATATA-AATA
1 T-TTAAAATAATTAATATATAATA
4973906 T
1 T
4973907 ATTATAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
22 8 0.19
23 14 0.33
24 3 0.07
25 11 0.26
26 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTAAAATAATTAATATATAATA
Found at i:4974655 original size:18 final size:18
Alignment explanation
Indices: 4974624--4974674 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
4974614 GAATGAAAAT
*
4974624 ATATTTCAAAATAAGTAGA
1 ATATTT-AAAATAAATAGA
4974643 AT-TTTAGAAATAAATAGA
1 ATATTTA-AAATAAATAGA
*
4974661 TTATTTAAAATAAA
1 ATATTTAAAATAAA
4974675 ATATTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 1 0.04
18 21 0.75
19 6 0.21
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (18 bp):
ATATTTAAAATAAATAGA
Found at i:4978819 original size:2 final size:2
Alignment explanation
Indices: 4978812--4978836 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4978802 TTAAAAGAAG
4978812 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 T
4978837 GCTTAAAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4979514 original size:23 final size:23
Alignment explanation
Indices: 4979471--4979516 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4979461 GATAAATTAT
*
4979471 AAAAATAAAAAATAAACTAATAA
1 AAAAATAAAAAACAAACTAATAA
*
4979494 AAAAATAATAAAACATA-TAATAA
1 AAAAATAA-AAAACAAACTAATAA
4979517 TTTTTTAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (23 bp):
AAAAATAAAAAACAAACTAATAA
Found at i:4989847 original size:16 final size:16
Alignment explanation
Indices: 4989812--4989852 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
4989802 GAAGTAGAAC
4989812 AAAATTTTTATTATTT
1 AAAATTTTTATTATTT
*
4989828 -AAATTTTTATTTTTT
1 AAAATTTTTATTATTT
*
4989843 AAAATATTTA
1 AAAATTTTTA
4989853 CGTATAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AAAATTTTTATTATTT
Found at i:4991516 original size:114 final size:112
Alignment explanation
Indices: 4991313--4991539 Score: 330
Period size: 114 Copynumber: 2.0 Consensus size: 112
4991303 AGAGCCTAGA
* * * *
4991313 ACTAGAATGTCAAGGCCCAAATAGAGTTTCCTTATACTTGGTTCCTCTGCTAGGGGAATTCTAAC
1 ACTAGAAGGCCAAGGCCCAAATACAGTTTCCTTAGACTTGGTTCCTCTGCTAGGGGAATTCT-AC
* *
4991378 ATTCTAACATTTCCTTATTAATGTCTTGGTTTTCTGATATTAGAACTT
65 ATTCTAACATTTCCTTATTAATGTCTTGCTTTTCTGATATTAAAACTT
* *
4991426 ACTAGAAGGCCAAGGCCCAAATATCAGTTTCCTTAGATTTGGTTCCTCTGTTAGGGGAATTCT-C
1 ACTAGAAGGCCAAGGCCCAAATA-CAGTTTCCTTAGACTTGGTTCCTCTGCTAGGGGAATTCTAC
*
4991490 ATTCTAACATTTCCTTGTTAATATGTCTTGCTTTTCTGATATTAAAACTT
65 ATTCTAACATTTCCTTATT-A-ATGTCTTGCTTTTCTGATATTAAAACTT
4991540 TCTTTTTAAT
Statistics
Matches: 102, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
112 19 0.19
113 22 0.22
114 61 0.60
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (112 bp):
ACTAGAAGGCCAAGGCCCAAATACAGTTTCCTTAGACTTGGTTCCTCTGCTAGGGGAATTCTACA
TTCTAACATTTCCTTATTAATGTCTTGCTTTTCTGATATTAAAACTT
Found at i:4996919 original size:2 final size:2
Alignment explanation
Indices: 4996912--4996944 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4996902 AAAGACGCCA
4996912 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4996945 AAAGAAAAAC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5005511 original size:18 final size:18
Alignment explanation
Indices: 5005488--5005536 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
5005478 CTCCTCCCTA
* *
5005488 TTTATATTTTTTTAATAT
1 TTTATATTTATTTAAAAT
*
5005506 TTTATAATTATTTAAAAT
1 TTTATATTTATTTAAAAT
5005524 ATTATATATTTAT
1 -TT-TATATTTAT
5005537 ATATTATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 15 0.60
19 2 0.08
20 8 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATATTTATTTAAAAT
Found at i:5005581 original size:34 final size:31
Alignment explanation
Indices: 5005521--5005595 Score: 87
Period size: 34 Copynumber: 2.3 Consensus size: 31
5005511 AATTATTTAA
5005521 AATATTATATATTTATATATTATAATAAATT
1 AATATTATATATTTATATATTATAATAAATT
* * *
5005552 AATAATATATATTATATATCATTTCTAATATATT
1 AATATTATATATT-TATAT-A-TTATAATAAATT
*
5005586 TATATTATAT
1 AATATTATAT
5005596 TTTTTATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 12 0.33
32 5 0.14
33 1 0.03
34 18 0.50
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (31 bp):
AATATTATATATTTATATATTATAATAAATT
Found at i:5005597 original size:11 final size:11
Alignment explanation
Indices: 5005500--5005597 Score: 71
Period size: 11 Copynumber: 8.9 Consensus size: 11
5005490 TATATTTTTT
5005500 TAATAT-TTTA
1 TAATATATTTA
5005510 TAAT-TATTTA
1 TAATATATTTA
5005520 -AA-ATATTATA
1 TAATATATT-TA
*
5005530 TATTTATATATTA
1 TA-ATATAT-TTA
* *
5005543 TAATAAATTAA
1 TAATATATTTA
5005554 TAATATATATTA
1 TAATATAT-TTA
*
5005566 T-ATATCATTTC
1 TAATAT-ATTTA
5005577 TAATATATTTA
1 TAATATATTTA
*
5005588 TATTATATTT
1 TAATATATTT
5005598 TTTATTATTT
Statistics
Matches: 69, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
9 7 0.10
10 10 0.14
11 30 0.43
12 13 0.19
13 8 0.12
14 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
TAATATATTTA
Found at i:5006063 original size:30 final size:30
Alignment explanation
Indices: 5006006--5006067 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 30
5005996 TTTAAAGTTA
5006006 ATATTTAATAAAAAATATTAAATTTAAAAAT
1 ATATTTAATAAAAAATA-TAAATTTAAAAAT
*
5006037 ATATTTAAATAAAAAATA-ATATTTAAAAAT
1 ATATTT-AATAAAAAATATAAATTTAAAAAT
5006067 A
1 A
5006068 AATTAAACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 12 0.41
31 6 0.21
32 11 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (30 bp):
ATATTTAATAAAAAATATAAATTTAAAAAT
Found at i:5006069 original size:20 final size:17
Alignment explanation
Indices: 5006006--5006063 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
5005996 TTTAAAGTTA
5006006 ATATTT-AAT-AAAAA-
1 ATATTTAAATAAAAAAT
*
5006020 ATA-TTAAATTTAAAAAT
1 ATATTTAAA-TAAAAAAT
5006037 ATATTTAAATAAAAAAT
1 ATATTTAAATAAAAAAT
5006054 AATATTTAAA
1 -ATATTTAAA
5006064 AATAAATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
13 2 0.05
14 5 0.14
15 1 0.03
16 5 0.14
17 10 0.27
18 14 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATTTAAATAAAAAAT
Found at i:5006516 original size:20 final size:20
Alignment explanation
Indices: 5006484--5006531 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
5006474 TTATTAAATA
5006484 TTAATTT-TAAATAAATAAT
1 TTAATTTATAAATAAATAAT
* **
5006503 TTAATTTATAAATAATTTTT
1 TTAATTTATAAATAAATAAT
5006523 TTAATTTAT
1 TTAATTTAT
5006532 TAAAAAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTTATAAATAAATAAT
Found at i:5007497 original size:40 final size:40
Alignment explanation
Indices: 5007452--5007567 Score: 142
Period size: 40 Copynumber: 2.9 Consensus size: 40
5007442 AAATATTTTA
*
5007452 ATTTTTTAAATTTATCATAATTTTTTTAGACTCGTCATTT
1 ATTTTTTAAGTTTATCATAATTTTTTTAGACTCGTCATTT
* * * **
5007492 ATTTTTTAAGTTTATCTTAACTTTTTAAGACTTATCATTT
1 ATTTTTTAAGTTTATCATAATTTTTTTAGACTCGTCATTT
* * *
5007532 ATCTTTTTAAGTTCATCATAATCTTTTTAAACTCGT
1 AT-TTTTTAAGTTTATCATAATTTTTTTAGACTCGT
5007568 TATTACTTTT
Statistics
Matches: 61, Mismatches: 14, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
40 36 0.59
41 25 0.41
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (40 bp):
ATTTTTTAAGTTTATCATAATTTTTTTAGACTCGTCATTT
Found at i:5007540 original size:22 final size:21
Alignment explanation
Indices: 5007486--5007561 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 21
5007476 TTTAGACTCG
*
5007486 TCATTTAT-TTTTTAAGTTTA
1 TCATTTATCTTTTTAAGCTTA
*
5007506 TC--TTAACTTTTTAAGACTTA
1 TCATTTATCTTTTTAAG-CTTA
5007526 TCATTTATCTTTTTAAG-TTCA
1 TCATTTATCTTTTTAAGCTT-A
*
5007547 TCA-TAATCTTTTTAA
1 TCATTTATCTTTTTAA
5007562 ACTCGTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
18 3 0.06
19 8 0.17
20 20 0.43
21 4 0.09
22 12 0.26
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.57
Consensus pattern (21 bp):
TCATTTATCTTTTTAAGCTTA
Found at i:5008401 original size:11 final size:12
Alignment explanation
Indices: 5008373--5008404 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5008363 GAATAATAAT
5008373 ATAATA-ATTAA
1 ATAATATATTAA
5008384 ATAATATATTAA
1 ATAATATATTAA
5008396 AT-ATATATT
1 ATAATATATT
5008405 TTATTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATAATATATTAA
Found at i:5010002 original size:44 final size:44
Alignment explanation
Indices: 5009940--5010034 Score: 174
Period size: 44 Copynumber: 2.2 Consensus size: 44
5009930 GGTTGTTCTT
5009940 TCTAAC-TTAAACTCTTTAACCCTTATTCTATTTACATTATCTC
1 TCTAACTTTAAACTCTTTAACCCTTATTCTATTTACATTATCTC
*
5009983 TCTAACTTTAAACTCTTTAACCTTTATTCTATTTACATTATCTC
1 TCTAACTTTAAACTCTTTAACCCTTATTCTATTTACATTATCTC
5010027 TCTAACTT
1 TCTAACTT
5010035 CTATAGAGAT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 6 0.12
44 44 0.88
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.48
Consensus pattern (44 bp):
TCTAACTTTAAACTCTTTAACCCTTATTCTATTTACATTATCTC
Found at i:5013795 original size:29 final size:31
Alignment explanation
Indices: 5013751--5013811 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
5013741 CCCTTCGTTC
*
5013751 AGAACTCGAAACGAATTTGAT-AG-TTAATA
1 AGAACTCGAAACGAATATGATAAGTTTAATA
*
5013780 AGAACTCGAAAGGAATATGATAAGTTTAATA
1 AGAACTCGAAACGAATATGATAAGTTTAATA
5013811 A
1 A
5013812 ATATAATATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 19 0.68
30 2 0.07
31 7 0.25
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26
Consensus pattern (31 bp):
AGAACTCGAAACGAATATGATAAGTTTAATA
Found at i:5013874 original size:9 final size:9
Alignment explanation
Indices: 5013826--5013875 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
5013816 AATATGATAC
5013826 ATTTAATAT
1 ATTTAATAT
* *
5013835 ATGTATTAT
1 ATTTAATAT
5013844 ATTT-ATAT
1 ATTTAATAT
*
5013852 -TTTAAAAT
1 ATTTAATAT
5013860 -TTTAATAT
1 ATTTAATAT
5013868 ATTTAATA
1 ATTTAATA
5013876 ATTATGAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 3 0.09
8 13 0.39
9 17 0.52
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (9 bp):
ATTTAATAT
Found at i:5014262 original size:21 final size:20
Alignment explanation
Indices: 5014197--5014264 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 20
5014187 TTTTTTTAAA
*
5014197 ATTATAAATATAATATAAATT
1 ATTATAAATATTATA-AAATT
*
5014218 ATTA-AAATATT-TAAATTTT
1 ATTATAAATATTATAAA-ATT
5014237 AATTATAAATATTATAAAATAT
1 -ATTATAAATATTATAAAAT-T
5014259 ATTATA
1 ATTATA
5014265 TTAATCACAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 10 0.26
21 18 0.46
22 5 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTATAAATATTATAAAATT
Found at i:5017940 original size:13 final size:13
Alignment explanation
Indices: 5017901--5017943 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
5017891 TAAATAAAAA
5017901 TATTAAATAAATATT
1 TATT-AATAAA-ATT
*
5017916 TTTTAA-AAAATT
1 TATTAATAAAATT
5017928 TATTAATAAAATT
1 TATTAATAAAATT
5017941 TAT
1 TAT
5017944 AAAGTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 2 0.08
15 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TATTAATAAAATT
Found at i:5018506 original size:27 final size:25
Alignment explanation
Indices: 5018476--5018537 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 25
5018466 AAATAAAAAT
5018476 AAAATTATAATTTT-TTATAATAAATTA
1 AAAATTAT-ATTTTATTA-AAT-AATTA
5018503 AAAA--ATATTTTATTAAATAATTA
1 AAAATTATATTTTATTAAATAATTA
*
5018526 ATAATTAT-TTTT
1 AAAATTATATTTT
5018538 GATTTATCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
23 8 0.26
24 12 0.39
25 7 0.23
27 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AAAATTATATTTTATTAAATAATTA
Found at i:5018524 original size:23 final size:24
Alignment explanation
Indices: 5018485--5018537 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
5018475 TAAAATTATA
5018485 ATTTTTTATAATAAATTAAAAAAT
1 ATTTTTTATAATAAATTAAAAAAT
* *
5018509 ATTTTATTA-AAT-AATTAATAATT
1 ATTTT-TTATAATAAATTAAAAAAT
5018532 ATTTTT
1 ATTTTT
5018538 GATTTATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 1 0.04
23 14 0.54
24 8 0.31
25 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTTTTATAATAAATTAAAAAAT
Found at i:5020970 original size:1 final size:1
Alignment explanation
Indices: 5020954--5021621 Score: 1309
Period size: 1 Copynumber: 668.0 Consensus size: 1
5020944 TTCAAGAAAG
* *
5020954 AAAACAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5021019 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5021084 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5021149 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5021214 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5021279 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5021344 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5021409 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5021474 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5021539 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
5021604 AAAAAAAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAA
5021622 CCCTAATAAT
Statistics
Matches: 661, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
1 661 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5022076 original size:18 final size:18
Alignment explanation
Indices: 5022053--5022101 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
5022043 CTCCTCCCTA
* *
5022053 TTTATATTTTTTTAATAT
1 TTTATATTTATTTAAAAT
*
5022071 TTTATAATTATTTAAAAT
1 TTTATATTTATTTAAAAT
5022089 ATTATATATTTAT
1 -TT-TATATTTAT
5022102 ATATTATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 15 0.60
19 2 0.08
20 8 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATATTTATTTAAAAT
Found at i:5022146 original size:34 final size:31
Alignment explanation
Indices: 5022086--5022178 Score: 91
Period size: 34 Copynumber: 3.0 Consensus size: 31
5022076 AATTATTTAA
5022086 AATATTATATATTTATATATTATAATAAATT
1 AATATTATATATTTATATATTATAATAAATT
* * *
5022117 AATAATATATATTATATATCATTTCTAATATATT
1 AATATTATATATT-TATAT-A-TTATAATAAATT
* * *
5022151 TATATTATATTTTTAT-TATTTTAA-AAAT
1 AATATTATATATTTATATATTATAATAAAT
5022179 AATTTAAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
29 3 0.06
30 5 0.10
31 13 0.25
32 6 0.12
33 4 0.08
34 20 0.39
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (31 bp):
AATATTATATATTTATATATTATAATAAATT
Found at i:5022162 original size:11 final size:11
Alignment explanation
Indices: 5022065--5022162 Score: 71
Period size: 11 Copynumber: 8.9 Consensus size: 11
5022055 TATATTTTTT
5022065 TAATAT-TTTA
1 TAATATATTTA
5022075 TAAT-TATTTA
1 TAATATATTTA
5022085 -AA-ATATTATA
1 TAATATATT-TA
*
5022095 TATTTATATATTA
1 TA-ATATAT-TTA
* *
5022108 TAATAAATTAA
1 TAATATATTTA
5022119 TAATATATATTA
1 TAATATAT-TTA
*
5022131 T-ATATCATTTC
1 TAATAT-ATTTA
5022142 TAATATATTTA
1 TAATATATTTA
*
5022153 TATTATATTT
1 TAATATATTT
5022163 TTATTATTTT
Statistics
Matches: 69, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
9 7 0.10
10 10 0.14
11 30 0.43
12 13 0.19
13 8 0.12
14 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
TAATATATTTA
Found at i:5022167 original size:11 final size:11
Alignment explanation
Indices: 5022087--5022173 Score: 52
Period size: 11 Copynumber: 7.6 Consensus size: 11
5022077 ATTATTTAAA
5022087 ATATTATATATTT
1 ATATT-TATA-TT
*
5022100 ATATATTATAAT
1 ATAT-TTATATT
* * *
5022112 AAATTAATAAT
1 ATATTTATATT
5022123 ATATATTATA-T
1 ATAT-TTATATT
* *
5022134 ATCATTTCTAAT
1 AT-ATTTATATT
5022146 ATATTTATATT
1 ATATTTATATT
*
5022157 ATATTTTTATT
1 ATATTTATATT
5022168 AT-TTTA
1 ATATTTA
5022174 AAAATAATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
10 3 0.05
11 35 0.58
12 13 0.22
13 8 0.13
14 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATTTATATT
Found at i:5022600 original size:17 final size:17
Alignment explanation
Indices: 5022578--5022669 Score: 68
Period size: 17 Copynumber: 5.5 Consensus size: 17
5022568 TAATATTTAA
5022578 TAAAAATATATTAAATT
1 TAAAAATATATTAAATT
5022595 TAAAAATATATTTAAA--
1 TAAAAATATA-TTAAATT
*
5022611 TAAAAA-ATA--ATATT
1 TAAAAATATATTAAATT
*
5022625 TAAAAATAAATTAAACTT
1 TAAAAATATATTAAA-TT
* **
5022643 TTAATTTAATATTAAAATT
1 TAAAAAT-ATATT-AAATT
5022662 TAAAAATA
1 TAAAAATA
5022670 AATTTATTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 17
0.67 0.12 0.20
Matches are distributed among these distances:
12 2 0.04
14 6 0.11
15 5 0.09
16 6 0.11
17 12 0.21
18 12 0.21
19 10 0.18
20 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAAATATATTAAATT
Found at i:5022626 original size:30 final size:31
Alignment explanation
Indices: 5022570--5022632 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 31
5022560 TTTAAAGTTA
5022570 ATATTTAATAAAAATATATTAAATTTAAAAAT
1 ATATTTAATAAAAATATA-TAAATTTAAAAAT
*
5022602 ATATTTAAATAAAAA-ATA-ATATTTAAAAAT
1 ATATTT-AATAAAAATATATAAATTTAAAAAT
5022632 A
1 A
5022633 AATTAAACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 12 0.41
32 9 0.31
33 8 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (31 bp):
ATATTTAATAAAAATATATAAATTTAAAAAT
Found at i:5022634 original size:20 final size:17
Alignment explanation
Indices: 5022570--5022628 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
5022560 TTTAAAGTTA
5022570 ATATTT-AAT-AAAAAT
1 ATATTTAAATAAAAAAT
*
5022585 ATA-TTAAATTTAAAAAT
1 ATATTTAAA-TAAAAAAT
5022602 ATATTTAAATAAAAAAT
1 ATATTTAAATAAAAAAT
5022619 AATATTTAAA
1 -ATATTTAAA
5022629 AATAAATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
14 2 0.05
15 5 0.13
16 1 0.03
17 16 0.42
18 14 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATTTAAATAAAAAAT
Found at i:5023082 original size:20 final size:20
Alignment explanation
Indices: 5023050--5023097 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
5023040 TTATTAAATA
5023050 TTAATTT-TAAATAAATAAT
1 TTAATTTATAAATAAATAAT
* **
5023069 TTAATTTATAAATAATTTTT
1 TTAATTTATAAATAAATAAT
5023089 TTAATTTAT
1 TTAATTTAT
5023098 TAAAAAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTTATAAATAAATAAT
Found at i:5024043 original size:20 final size:20
Alignment explanation
Indices: 5024015--5024127 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
5024005 TTAAATATTT
5024015 TAAT-TTTTTAAATTTATCA
1 TAATCTTTTTAAATTTATCA
* * * **
5024034 TAATTTTTTTAGACTCGTCA
1 TAATCTTTTTAAATTTATCA
* *
5024054 TTTAT-TTTTTAAATTTATCT
1 -TAATCTTTTTAAATTTATCA
5024074 TAA-CTTTTTAAGATTTATCA
1 TAATCTTTTTAA-ATTTATCA
* *
5024094 TTTATCTTTTTAAATTCATCA
1 -TAATCTTTTTAAATTTATCA
5024115 TAATCTTTTTAAA
1 TAATCTTTTTAAA
5024128 CTCGTTATTA
Statistics
Matches: 73, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.18
20 40 0.55
21 12 0.16
22 8 0.11
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.57
Consensus pattern (20 bp):
TAATCTTTTTAAATTTATCA
Found at i:5024062 original size:40 final size:40
Alignment explanation
Indices: 5024017--5024132 Score: 142
Period size: 40 Copynumber: 2.9 Consensus size: 40
5024007 AAATATTTTA
5024017 ATTTTTTAAATTTATCATAATTTTTTTAGACTCGTCATTT
1 ATTTTTTAAATTTATCATAATTTTTTTAGACTCGTCATTT
* * * * **
5024057 ATTTTTTAAATTTATCTTAACTTTTTAAGATTTATCATTT
1 ATTTTTTAAATTTATCATAATTTTTTTAGACTCGTCATTT
* * *
5024097 ATCTTTTTAAATTCATCATAATCTTTTTAAACTCGT
1 AT-TTTTTAAATTTATCATAATTTTTTTAGACTCGT
5024133 TATTACTTTT
Statistics
Matches: 60, Mismatches: 15, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
40 36 0.60
41 24 0.40
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.56
Consensus pattern (40 bp):
ATTTTTTAAATTTATCATAATTTTTTTAGACTCGTCATTT
Found at i:5024082 original size:21 final size:21
Alignment explanation
Indices: 5024058--5024124 Score: 50
Period size: 22 Copynumber: 3.2 Consensus size: 21
5024048 TCGTCATTTA
5024058 TTTTTTAAATTTATCTTAAC-
1 TTTTTTAAATTTATCTTAACT
*
5024078 -TTTTTAAGATTTATCATTTA-T
1 TTTTTTAA-ATTTATC-TTAACT
* * *
5024099 CTTTTTAAATTCATCATAATCT
1 TTTTTTAAATTTATCTTAA-CT
5024121 TTTT
1 TTTT
5024125 AAACTCGTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
19 7 0.19
20 9 0.25
21 9 0.25
22 11 0.31
ACGTcount: A:0.28, C:0.10, G:0.01, T:0.60
Consensus pattern (21 bp):
TTTTTTAAATTTATCTTAACT
Found at i:5024965 original size:11 final size:12
Alignment explanation
Indices: 5024937--5024968 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5024927 GAATAATAAT
5024937 ATAATA-ATTAA
1 ATAATATATTAA
5024948 ATAATATATTAA
1 ATAATATATTAA
5024960 AT-ATATATT
1 ATAATATATT
5024969 TTATTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATAATATATTAA
Found at i:5026566 original size:44 final size:44
Alignment explanation
Indices: 5026504--5026598 Score: 174
Period size: 44 Copynumber: 2.2 Consensus size: 44
5026494 GGTTGTTCTT
5026504 TCTAAC-TTAAACTCTTTAACCCTTATTCTATTTACATTATCTC
1 TCTAACTTTAAACTCTTTAACCCTTATTCTATTTACATTATCTC
*
5026547 TCTAACTTTAAACTCTTTAACCTTTATTCTATTTACATTATCTC
1 TCTAACTTTAAACTCTTTAACCCTTATTCTATTTACATTATCTC
5026591 TCTAACTT
1 TCTAACTT
5026599 CTATAGAGAT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 6 0.12
44 44 0.88
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.48
Consensus pattern (44 bp):
TCTAACTTTAAACTCTTTAACCCTTATTCTATTTACATTATCTC
Found at i:5030426 original size:9 final size:9
Alignment explanation
Indices: 5030378--5030427 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
5030368 AATATGATAC
5030378 ATTTAATAT
1 ATTTAATAT
* *
5030387 ATGTATTAT
1 ATTTAATAT
5030396 ATTT-ATAT
1 ATTTAATAT
*
5030404 -TTTAAAAT
1 ATTTAATAT
5030412 -TTTAATAT
1 ATTTAATAT
5030420 ATTTAATA
1 ATTTAATA
5030428 ATTATGAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 3 0.09
8 13 0.39
9 17 0.52
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (9 bp):
ATTTAATAT
Done.