Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 35 of 190
Found at i:9997031 original size:33 final size:33
Alignment explanation
Indices: 9996992--9997068 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
9996982 ATAAATATGG
* *
9996992 ATTTGAGAGAAATTTTGAAGGAATTTGAGAGCAA
1 ATTTGAGAGAAATTTAGAA-GAAATTGAGAGCAA
*
9997026 A-TTGAGAGGAAATTTAGAAGAAATTGAGAGGAA
1 ATTTGAGA-GAAATTTAGAAGAAATTGAGAGCAA
9997059 ATTTGAGAGA
1 ATTTGAGAGA
9997069 GGATTAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 21 0.55
34 17 0.45
ACGTcount: A:0.44, C:0.01, G:0.29, T:0.26
Consensus pattern (33 bp):
ATTTGAGAGAAATTTAGAAGAAATTGAGAGCAA
Found at i:9998609 original size:14 final size:14
Alignment explanation
Indices: 9998590--9998622 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
9998580 AATTTGATTT
9998590 TCAAGTTAATCGAA
1 TCAAGTTAATCGAA
*
9998604 TCAAGTTATTCGAA
1 TCAAGTTAATCGAA
9998618 T-AAGT
1 TCAAGT
9998623 AATTCGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (14 bp):
TCAAGTTAATCGAA
Found at i:9998834 original size:19 final size:22
Alignment explanation
Indices: 9998811--9998857 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
9998801 TATATTTTTT
9998811 AAAAAAT-TATAAA-AAA-TTC
1 AAAAAATATATAAAGAAAGTTC
9998830 TAAAAAATATATAAAGAAAGTTC
1 -AAAAAATATATAAAGAAAGTTC
9998853 AAAAA
1 AAAAA
9998858 TAATGATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 8 0.33
23 3 0.12
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.23
Consensus pattern (22 bp):
AAAAAATATATAAAGAAAGTTC
Found at i:9998835 original size:11 final size:10
Alignment explanation
Indices: 9998810--9998844 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
9998800 TTATATTTTT
9998810 TAAAAAATTA
1 TAAAAAATTA
*
9998820 TAAAAAATTC
1 TAAAAAATTA
9998830 TAAAAAATATA
1 TAAAAAAT-TA
9998841 TAAA
1 TAAA
9998845 GAAAGTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:9998842 original size:21 final size:22
Alignment explanation
Indices: 9998810--9998857 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
9998800 TTATATTTTT
9998810 TAAAAAATTATAAA-AAA-TTC
1 TAAAAAATTATAAAGAAAGTTC
9998830 TAAAAAATATATAAAGAAAGTTC
1 TAAAAAAT-TATAAAGAAAGTTC
9998853 -AAAAA
1 TAAAAA
9998858 TAATGATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.32
21 6 0.24
22 8 0.32
23 3 0.12
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (22 bp):
TAAAAAATTATAAAGAAAGTTC
Found at i:10000682 original size:5 final size:5
Alignment explanation
Indices: 10000674--10000798 Score: 71
Period size: 6 Copynumber: 24.0 Consensus size: 5
10000664 CAACTTTTTT
10000674 TTTCA TTTCA -TTCA TTTCCA TTTCCA TTTCCA TTTCA TTTACA TTTACA
1 TTTCA TTTCA TTTCA TTT-CA TTT-CA TTT-CA TTTCA TTT-CA TTT-CA
* * ** *
10000723 TTTACA TTTCCA TTTCA TTTAA ATT-A TTTTT TTTCA TTTAAA TTT-A
1 TTT-CA TTT-CA TTTCA TTTCA TTTCA TTTCA TTTCA TTT-CA TTTCA
*
10000769 TTT-A TTTCTCA TTTCA TTT-T TTTCA TTTCA
1 TTTCA -TT-TCA TTTCA TTTCA TTTCA TTTCA
10000799 GTTTTTGTTT
Statistics
Matches: 101, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
4 15 0.15
5 39 0.39
6 46 0.46
7 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.59
Consensus pattern (5 bp):
TTTCA
Found at i:10000697 original size:6 final size:6
Alignment explanation
Indices: 10000686--10000742 Score: 73
Period size: 6 Copynumber: 9.8 Consensus size: 6
10000676 TCATTTCATT
* * *
10000686 CATTTC CATTTC CATTTC CATTT- CATTTA CATTTA CATTTA CATTTC
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
10000733 CATTT- CATTT
1 CATTTC CATTT
10000743 AAATTATTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
5 10 0.20
6 39 0.80
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.53
Consensus pattern (6 bp):
CATTTC
Found at i:10000724 original size:29 final size:29
Alignment explanation
Indices: 10000677--10000743 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
10000667 CTTTTTTTTT
* *
10000677 CATTTCA-TT-CATTTCCATTTCCATTTC
1 CATTTCATTTACATTTACATTTACATTTC
10000704 CATTTCATTTACATTTACATTTACATTTC
1 CATTTCATTTACATTTACATTTACATTTC
10000733 CATTTCATTTA
1 CATTTCATTTA
10000744 AATTATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 7 0.19
28 2 0.06
29 27 0.75
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (29 bp):
CATTTCATTTACATTTACATTTACATTTC
Found at i:10000759 original size:19 final size:21
Alignment explanation
Indices: 10000735--10000782 Score: 73
Period size: 19 Copynumber: 2.4 Consensus size: 21
10000725 TACATTTCCA
10000735 TTTCATTTAAA-TTATTT-TT
1 TTTCATTTAAATTTATTTATT
10000754 TTTCATTTAAATTTATTTATT
1 TTTCATTTAAATTTATTTATT
*
10000775 TCTCATTT
1 TTTCATTT
10000783 CATTTTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 11 0.42
20 6 0.23
21 9 0.35
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTCATTTAAATTTATTTATT
Found at i:10000794 original size:14 final size:15
Alignment explanation
Indices: 10000764--10000804 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
10000754 TTTCATTTAA
10000764 ATTT-ATTTATTTCTC
1 ATTTCATTT-TTTCTC
10000779 ATTTCATTTTTT-TC
1 ATTTCATTTTTTCTC
10000793 ATTTCAGTTTTT
1 ATTTCA-TTTTT
10000805 GTTTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.33
15 12 0.50
16 4 0.17
ACGTcount: A:0.17, C:0.12, G:0.02, T:0.68
Consensus pattern (15 bp):
ATTTCATTTTTTCTC
Found at i:10000874 original size:19 final size:19
Alignment explanation
Indices: 10000850--10000901 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
10000840 ACTTTCATTC
10000850 CATTTCATAATCATAATTT
1 CATTTCATAATCATAATTT
*
10000869 CATTTCATAATCATAGTTT
1 CATTTCATAATCATAATTT
*
10000888 CATTTCATATTCAT
1 CATTTCATAATCAT
10000902 TTAACATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (19 bp):
CATTTCATAATCATAATTT
Found at i:10000918 original size:23 final size:23
Alignment explanation
Indices: 10000885--10000969 Score: 98
Period size: 23 Copynumber: 3.5 Consensus size: 23
10000875 ATAATCATAG
10000885 TTTCATTTCATATTCATTTAACA
1 TTTCATTTCATATTCATTTAACA
* * *
10000908 TTTTATTTCATATTAATTACAAATTACA
1 TTTCATTTCATATTCATT-----TAACA
10000936 TTTCATTTCATATTCATTTAACA
1 TTTCATTTCATATTCATTTAACA
10000959 TTTCATTTCAT
1 TTTCATTTCAT
10000970 TAATTTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
23 31 0.61
28 20 0.39
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTCATTTCATATTCATTTAACA
Found at i:10001388 original size:5 final size:5
Alignment explanation
Indices: 10001380--10001680 Score: 98
Period size: 5 Copynumber: 55.4 Consensus size: 5
10001370 TTGTTTTTTT
* *
10001380 TTTCA TTTCA TTCCTA TTTCCA TTTCA TTTCA TTTGTA TTTCCA TTTCA
1 TTTCA TTTCA TTTC-A TTT-CA TTTCA TTTCA TTT-CA TTT-CA TTTCA
* *
10001429 TTTCA TTTCA TTTTCA TTTTCA TTTCA TTT-A ATT-A TTT-T TTTCTA
1 TTTCA TTTCA -TTTCA -TTTCA TTTCA TTTCA TTTCA TTTCA TTTC-A
* * ** **
10001474 TTTAAA TTT-A ATT-A TTTCTCA TTTTCAAA TTTTT TTTCA TTTCA GTTTTTG
1 TTT-CA TTTCA TTTCA -TT-TCA -TTTC--A TTTCA TTTCA TTTCA --TTTCA
* *
10001525 TCTTCA TTTCAA TTT-A TAATTTA TTTTCA TTTAAA CTTTCA -TTCTA TTTCA
1 T-TTCA TTTC-A TTTCA T--TTCA -TTTCA TTT-CA -TTTCA TTTC-A TTTCA
* *
10001576 TAATCA --TAA TTTCA TTTCA TATTCA TTTAACA TTTCA TTTCA TTTCA
1 T-TTCA TTTCA TTTCA TTTCA T-TTCA TTT--CA TTTCA TTTCA TTTCA
* *
10001623 TTTCA TATTCA TTATAAA TTACA TTTCA TTTCA TATTCA TTTAACA TTTCA
1 TTTCA T-TTCA TT-T-CA TTTCA TTTCA TTTCA T-TTCA TTT--CA TTTCA
10001674 TTTCA TT
1 TTTCA TT
10001681 AATTTTTTTC
Statistics
Matches: 230, Mismatches: 30, Indels: 72
0.69 0.09 0.22
Matches are distributed among these distances:
3 2 0.01
4 18 0.08
5 108 0.47
6 72 0.31
7 28 0.12
8 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.01, T:0.58
Consensus pattern (5 bp):
TTTCA
Found at i:10001407 original size:22 final size:22
Alignment explanation
Indices: 10001380--10001458 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
10001370 TTGTTTTTTT
*
10001380 TTTCATTTCATTCCTATTTCCA
1 TTTCATTTCATTTCTATTTCCA
*
10001402 TTTCATTTCATTTGTATTTCCA
1 TTTCATTTCATTTCTATTTCCA
*
10001424 TTTCATTTCATTTC-ATTTTCA
1 TTTCATTTCATTTCTATTTCCA
10001445 TTTTCATTTCATTT
1 -TTTCATTTCATTT
10001459 AATTATTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
21 6 0.12
22 46 0.88
ACGTcount: A:0.18, C:0.20, G:0.01, T:0.61
Consensus pattern (22 bp):
TTTCATTTCATTTCTATTTCCA
Found at i:10001449 original size:28 final size:27
Alignment explanation
Indices: 10001395--10001680 Score: 123
Period size: 28 Copynumber: 10.5 Consensus size: 27
10001385 TTTCATTCCT
*
10001395 ATTTCCATTTCATTTCATTTGT-ATTTCC
1 ATTT-CATTTCATTTCATTT-TCATTTTC
10001423 ATTTCATTTCATTTCATTTTCATTTTC
1 ATTTCATTTCATTTCATTTTCATTTTC
*
10001450 ATTTCATTT-AATT-A-TTT--TTTTC
1 ATTTCATTTCATTTCATTTTCATTTTC
* *
10001472 TATTTAAATTT-AATT-ATTTCTCATTTTC
1 -ATTT-CATTTCATTTCATTT-TCATTTTC
** ** *
10001500 AAATTTTTTTTCATTTCAGTTTTTGTCTTC
1 --ATTTCATTTCATTTCA-TTTTCATTTTC
* **
10001530 ATTTCAATTT-ATAATTTATTTTCATTTAA
1 ATTTC-ATTTCAT--TTCATTTTCATTTTC
** *
10001559 ACTTTCA-TTCTATTTCATAATCA---TA
1 A-TTTCATTTC-ATTTCATTTTCATTTTC
*
10001584 ATTTCATTTCATATTCATTTAACA-TTTC
1 ATTTCATTTCAT-TTCATTT-TCATTTTC
* **
10001612 ATTTCATTTCATTTCATATTCATTATAA
1 ATTTCATTTCATTTCATTTTCATT-TTC
* * *
10001640 ATTACATTTCATTTCATATTCATTTAAC
1 ATTTCATTTCATTTCATTTTCATTT-TC
10001668 ATTTCATTTCATT
1 ATTTCATTTCATT
10001681 AATTTTTTTC
Statistics
Matches: 200, Mismatches: 33, Indels: 50
0.71 0.12 0.18
Matches are distributed among these distances:
22 5 0.03
23 4 0.02
24 19 0.09
25 13 0.06
26 9 0.05
27 37 0.19
28 77 0.38
29 18 0.09
30 15 0.08
31 3 0.01
ACGTcount: A:0.26, C:0.15, G:0.01, T:0.58
Consensus pattern (27 bp):
ATTTCATTTCATTTCATTTTCATTTTC
Found at i:10001469 original size:27 final size:27
Alignment explanation
Indices: 10001380--10001462 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 27
10001370 TTGTTTTTTT
*
10001380 TTTCA-TTTCA-TTCCTATTTCCATTTCA
1 TTTCATTTTCATTTCC-ATTT-CATTTAA
*
10001407 TTTCATTTGT-ATTTCCATTTCATTTCA
1 TTTCATTT-TCATTTCCATTTCATTTAA
*
10001434 TTTCATTTTCATTTTCATTTCATTTAA
1 TTTCATTTTCATTTCCATTTCATTTAA
10001461 TT
1 TT
10001463 ATTTTTTTCT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
26 1 0.02
27 37 0.74
28 7 0.14
29 5 0.10
ACGTcount: A:0.19, C:0.19, G:0.01, T:0.60
Consensus pattern (27 bp):
TTTCATTTTCATTTCCATTTCATTTAA
Found at i:10001470 original size:22 final size:22
Alignment explanation
Indices: 10001424--10001490 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
10001414 TGTATTTCCA
* *
10001424 TTTCATTTCATTTCATT-TTCAT
1 TTTCATTTCATTTAATTATT-TT
10001446 TTTCATTTCATTTAATTATTTT
1 TTTCATTTCATTTAATTATTTT
*
10001468 TTTCTATTTAAATTTAATTATTT
1 TTTC-ATTT-CATTTAATTATTT
10001491 CTCATTTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
22 21 0.54
23 6 0.15
24 12 0.31
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTCATTTCATTTAATTATTTT
Found at i:10002071 original size:5 final size:5
Alignment explanation
Indices: 10002063--10002146 Score: 96
Period size: 5 Copynumber: 15.6 Consensus size: 5
10002053 TTTCTTTTTT
*
10002063 TTTCA TTTCA TTTCTA TTTCCA TTTCA TTTCA TTTCA TTTGTA TTTCCA
1 TTTCA TTTCA TTTC-A TTT-CA TTTCA TTTCA TTTCA TTT-CA TTT-CA
*
10002112 TTTCA TTTCA TTTAA TTTTCA TTTCCA TTTCA TTT
1 TTTCA TTTCA TTTCA -TTTCA TTT-CA TTTCA TTT
10002147 AAATTATCTT
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
5 43 0.62
6 25 0.36
7 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.01, T:0.61
Consensus pattern (5 bp):
TTTCA
Found at i:10002089 original size:22 final size:20
Alignment explanation
Indices: 10002063--10002148 Score: 100
Period size: 22 Copynumber: 4.0 Consensus size: 20
10002053 TTTCTTTTTT
*
10002063 TTTCATTTCATTTCTATTTCCA
1 TTTCATTTCATTTC-ATTT-AA
*
10002085 TTTCATTTCATTTCATTTGTA
1 TTTCATTTCATTTCATTT-AA
10002106 TTTCCATTTCATTTCATTTAA
1 TTT-CATTTCATTTCATTTAA
10002127 TTTTCATTTCCATTTCATTTAA
1 -TTTCATTT-CATTTCATTTAA
10002149 ATTATCTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.24
22 44 0.76
ACGTcount: A:0.21, C:0.19, G:0.01, T:0.59
Consensus pattern (20 bp):
TTTCATTTCATTTCATTTAA
Found at i:10002093 original size:27 final size:26
Alignment explanation
Indices: 10002063--10002169 Score: 133
Period size: 27 Copynumber: 3.9 Consensus size: 26
10002053 TTTCTTTTTT
10002063 TTTCATTTCATTTCTATTTCCATTTCA
1 TTTCATTTCATTT-TATTTCCATTTCA
10002090 TTTCATTTCATTTGTATTTCCATTTCA
1 TTTCATTTCATTT-TATTTCCATTTCA
*
10002117 TTTCATTTAATTTTCATTTCCATTTCA
1 TTTCATTTCATTTT-ATTTCCATTTCA
* * *
10002144 TTTAAATTATCTTTTTTTTTCCATTT
1 TTT-CATT-TCATTTTATTTCCATTT
10002170 AAATTTAATT
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
26 1 0.01
27 53 0.75
28 12 0.17
29 5 0.07
ACGTcount: A:0.20, C:0.18, G:0.01, T:0.62
Consensus pattern (26 bp):
TTTCATTTCATTTTATTTCCATTTCA
Found at i:10002164 original size:22 final size:22
Alignment explanation
Indices: 10002139--10002191 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
10002129 TTCATTTCCA
*
10002139 TTTCATTTAAA-TTATCTTTTTT
1 TTTCATTTAAATTTA-ATTTTTT
10002161 TTTCCATTTAAATTTAATTTTTT
1 TTT-CATTTAAATTTAATTTTTT
*
10002184 TCTCATTT
1 TTTCATTT
10002192 TATTTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.30
23 16 0.59
24 3 0.11
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTCATTTAAATTTAATTTTTT
Found at i:10002260 original size:56 final size:57
Alignment explanation
Indices: 10002165--10002272 Score: 175
Period size: 56 Copynumber: 1.9 Consensus size: 57
10002155 TTTTTTTTTC
10002165 CATTTAAATTTAATTTTTTTCTCATTTTATTTAAATTATCTATCTTCCCATTCATTT
1 CATTTAAATTTAATTTTTTTCTCATTTTATTTAAATTATCTATCTTCCCATTCATTT
* *
10002222 CATTTAAATTTAA-TTTTTTCTC-TTTTCATTTAATTTATCTTTCTTCCCATT
1 CATTTAAATTTAATTTTTTTCTCATTTT-ATTTAAATTATCTATCTTCCCATT
10002273 TTAATTTACG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
55 4 0.08
56 31 0.65
57 13 0.27
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (57 bp):
CATTTAAATTTAATTTTTTTCTCATTTTATTTAAATTATCTATCTTCCCATTCATTT
Found at i:10005652 original size:33 final size:33
Alignment explanation
Indices: 10005610--10005837 Score: 215
Period size: 33 Copynumber: 6.4 Consensus size: 33
10005600 GTAGATTCAA
10005610 CACTTAGCAACCACCAATGAGTCGGGGAATCAG
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAG
* *
10005643 CACTTAGCAACC-CTTTTCACATTTAAGATACGGTGGGATCAG
1 CACTTAGCAACCAC----CA-A--TGAG-T-CGG-GGAATCAG
*
10005685 CACTTAGCAACCACCAATGATTCGGGGAATCAG
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAG
* *
10005718 CACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAG
1 CACTTAGCAA-CCAC--CA-A--TGAG-T-CGG-GGAATCAG
10005760 CACTTAGCAACCACCAATGAGTCGGGGAATCAG
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAG
* *
10005793 TACTTAGCAACCACCAATGAATCGGGGAATCAG
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAG
10005826 CACTTAGCAACC
1 CACTTAGCAACC
10005838 CCTTGGGGGA
Statistics
Matches: 162, Mismatches: 13, Indels: 40
0.75 0.06 0.19
Matches are distributed among these distances:
32 1 0.01
33 79 0.49
34 9 0.06
35 2 0.01
36 9 0.06
37 2 0.01
38 2 0.01
39 9 0.06
40 2 0.01
41 9 0.06
42 37 0.23
43 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (33 bp):
CACTTAGCAACCACCAATGAGTCGGGGAATCAG
Found at i:10005737 original size:75 final size:75
Alignment explanation
Indices: 10005610--10005804 Score: 345
Period size: 75 Copynumber: 2.6 Consensus size: 75
10005600 GTAGATTCAA
**
10005610 CACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCTTTTCACATTTAAGATACG
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACG
*
10005675 GTGGGATCAG
66 GTGGAATCAG
*
10005685 CACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACG
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACG
10005750 GTGGAATCAG
66 GTGGAATCAG
*
10005760 CACTTAGCAACCACCAATGAGTCGGGGAATCAGTACTTAGCAACC
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACC
10005805 ACCAATGAAT
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 114 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (75 bp):
CACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACG
GTGGAATCAG
Found at i:10005850 original size:27 final size:28
Alignment explanation
Indices: 10005816--10005869 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
10005806 CCAATGAATC
10005816 GGGGAATCAGCACTTAGCAACC-CCTTG
1 GGGGAATCAGCACTTAGCAACCTCCTTG
*
10005843 GGGGAATCAGCGCTTAGCAACCTCCTT
1 GGGGAATCAGCACTTAGCAACCTCCTT
10005870 TATATTCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.24, C:0.30, G:0.26, T:0.20
Consensus pattern (28 bp):
GGGGAATCAGCACTTAGCAACCTCCTTG
Found at i:10007837 original size:29 final size:28
Alignment explanation
Indices: 10007804--10007865 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
10007794 AAAGCCGTTT
10007804 TTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTCAAAATTTACCGAAATGGGCC-A
* ** *
10007833 TTTTTTGATTATTTACCGGAATGGGCCA
1 TTTTTTCAAAATTTACCGAAATGGGCCA
10007861 TTTTT
1 TTTTT
10007866 CGCGAAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.44
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:10015674 original size:44 final size:44
Alignment explanation
Indices: 10015407--10015674 Score: 172
Period size: 44 Copynumber: 6.2 Consensus size: 44
10015397 GAGAAAGCAA
* * * *
10015407 ATCTTATCCCCCTAAAGTTGCAGTGCG-GCAGATTAAAGATGGC-G
1 ATCTTATCTCCCTAAGGTTGCAGTG-GAGCAGATTAAACAT-CCAG
* *
10015451 AATCTTATCTCCCTGAA-GTTGGAGTGGAGTAGATTAAAGCCAAT--AG
1 -ATCTTATCTCCCT-AAGGTTGCAGTGGAGCAGATTAAA--C-ATCCAG
* * *
10015497 -TCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAA-AT-CAG
1 ATCTTATCTCCCTAAGGTTGCAGTGGAGCAGATTAAACATCCAG
* * *
10015538 ATCTTATCTCCCTAAGGTTGCAG-AGAGCAGA-T-CACATCAAG
1 ATCTTATCTCCCTAAGGTTGCAGTGGAGCAGATTAAACATCCAG
* *
10015579 -TCTTATCTCCCTGAA-GTTGCAGTGGAGCAGACTGAAA-A-CCTAA
1 ATCTTATCTCCCT-AAGGTTGCAGTGGAGCAGA-TTAAACATCC-AG
* **
10015622 ATCCTATCTCCCTAAGGTTGCAGTGGAGTGGATTAAAACATCCAG
1 ATCTTATCTCCCTAAGGTTGCAGTGGAGCAGATT-AAACATCCAG
10015667 AT-TTATCT
1 ATCTTATCT
10015675 TTAAAGTTGC
Statistics
Matches: 175, Mismatches: 26, Indels: 45
0.71 0.11 0.18
Matches are distributed among these distances:
39 1 0.01
40 24 0.14
41 19 0.11
42 21 0.12
43 6 0.03
44 64 0.37
45 33 0.19
46 5 0.03
48 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGGTTGCAGTGGAGCAGATTAAACATCCAG
Found at i:10015684 original size:126 final size:129
Alignment explanation
Indices: 10015453--10015741 Score: 335
Period size: 126 Copynumber: 2.3 Consensus size: 129
10015443 AGATGGCGAA
* * * * *
10015453 TCTTATCTCCCTGAAGTTGGAGTGGAGTAGA-TTAAAGCCAATAGTCCTATCTCCCTGAGGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAACCAATAGTCCTATCTCCCTAAGGTTGC
* *
10015517 AGTGGAGCGGATTAAAATCAGATCTTATCTCCCTAAGGTTGCAG-AG-AGCAGATCACA-T-CAA
66 AGTGGAGCGGATTAAAATCAGATCTTATCT-CCTAAAGTTGCAGTAGAAGAAGATCA-AGTACAA
10015578 G
129 G
10015579 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAACCTAA-A-TCCTATCTCCCTAAGGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAACC-AATAGTCCTATCTCCCTAAGGTTG
* * * * *
10015642 CAGTGGAGTGGATTAAAACATCCAGAT-TTATCT-TTAAAGTTGCAGTAGAATAAGTTGAAGTCA
65 CAGTGGAGCGGATT-AAA-AT-CAGATCTTATCTCCTAAAGTTGCAGTAGAAGAAGATCAAGT-A
10015705 CAAG
126 CAAG
*
10015709 TCTTATCTCCCTGAAGTTGCAGTGCAGCAGACT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT
10015742 AAAGATAGCA
Statistics
Matches: 140, Mismatches: 13, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
126 70 0.50
127 13 0.09
128 16 0.11
129 5 0.04
130 36 0.26
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (129 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAACCAATAGTCCTATCTCCCTAAGGTTGC
AGTGGAGCGGATTAAAATCAGATCTTATCTCCTAAAGTTGCAGTAGAAGAAGATCAAGTACAAG
Found at i:10017084 original size:14 final size:13
Alignment explanation
Indices: 10017065--10017103 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
10017055 ACTGTTAAAT
10017065 TGTATTATTATTA
1 TGTATTATTATTA
10017078 CTGTATTATTATTA
1 -TGTATTATTATTA
10017092 -GTATTTATTATT
1 TGTA-TTATTATT
10017104 GTGGTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 3 0.12
13 8 0.33
14 13 0.54
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (13 bp):
TGTATTATTATTA
Found at i:10021869 original size:24 final size:25
Alignment explanation
Indices: 10021841--10021894 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
10021831 TGCGATCTTT
10021841 TTTTTGAACCAA-TATACTTTCGGTC
1 TTTTTGAA-CAATTATACTTTCGGTC
* * *
10021866 TTTTTGAATAATTATTCTTTCGTTC
1 TTTTTGAACAATTATACTTTCGGTC
10021891 TTTT
1 TTTT
10021895 GGATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.20, C:0.15, G:0.09, T:0.56
Consensus pattern (25 bp):
TTTTTGAACAATTATACTTTCGGTC
Found at i:10022696 original size:16 final size:16
Alignment explanation
Indices: 10022675--10022754 Score: 67
Period size: 16 Copynumber: 4.9 Consensus size: 16
10022665 AGATTCAATC
*
10022675 CAAAAAAAACAAAAAA
1 CAAAAAAAAGAAAAAA
10022691 CAAAAAAAA-AACAAAA
1 CAAAAAAAAGAA-AAAA
*
10022707 -AAAAGAAAGAAAAAA
1 CAAAAAAAAGAAAAAA
*
10022722 GAAAAGAAAAGAAAAGAA
1 CAAAA-AAAAGAAAA-AA
*
10022740 -AGAGAAAAAGAAAAA
1 CA-AAAAAAAGAAAAA
10022755 TAGGAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
15 13 0.24
16 20 0.36
17 18 0.33
18 4 0.07
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (16 bp):
CAAAAAAAAGAAAAAA
Found at i:10022719 original size:11 final size:11
Alignment explanation
Indices: 10022676--10022752 Score: 54
Period size: 10 Copynumber: 6.8 Consensus size: 11
10022666 GATTCAATCC
*
10022676 AAAAA-AAACA
1 AAAAAGAAAGA
*
10022686 AAAAACAAA-A
1 AAAAAGAAAGA
10022696 AAAAA-ACAA-A
1 AAAAAGA-AAGA
10022706 AAAAAGAAAGA
1 AAAAAGAAAGA
10022717 AAAAAGAAAAGAAA
1 AAAAAG-AAAG--A
10022731 AGAAAAGAAAGA
1 A-AAAAGAAAGA
10022743 GAAAAAGAAA
1 -AAAAAGAAA
10022753 AATAGGAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
9 1 0.02
10 21 0.36
11 11 0.19
12 13 0.22
13 1 0.02
14 6 0.10
15 5 0.09
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:10022728 original size:5 final size:5
Alignment explanation
Indices: 10022693--10022753 Score: 61
Period size: 5 Copynumber: 11.8 Consensus size: 5
10022683 ACAAAAAACA
* * *
10022693 AAAAA AAAAC AAAA- AAAAG AAAGAA AAAAG AAAAG AAAAG AAAAG AAAGAG
1 AAAAG AAAAG AAAAG AAAAG AAA-AG AAAAG AAAAG AAAAG AAAAG AAA-AG
10022744 AAAAAG AAAA
1 -AAAAG AAAA
10022754 ATAGGAATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
4 4 0.08
5 34 0.69
6 8 0.16
7 3 0.06
ACGTcount: A:0.84, C:0.02, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:10022745 original size:21 final size:20
Alignment explanation
Indices: 10022676--10022753 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 20
10022666 GATTCAATCC
* *
10022676 AAAAAAAACAAAA-AACA-A
1 AAAAAAAAGAAAAGAAAAGA
*
10022694 AAAAAAAACAAAA-AAAAGA
1 AAAAAAAAGAAAAGAAAAGA
10022713 AAGAAAAAAGAAAAGAAAAGA
1 AA-AAAAAAGAAAAGAAAAGA
*
10022734 AAAGAAAGAGAAAAAGAAAA
1 AAA-AAAAAG-AAAAGAAAA
10022754 ATAGGAATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
18 16 0.31
19 3 0.06
20 11 0.21
21 13 0.25
22 9 0.17
ACGTcount: A:0.85, C:0.04, G:0.12, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGAAAAGAAAAGA
Found at i:10022754 original size:1 final size:1
Alignment explanation
Indices: 10022676--10022736 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
10022666 GATTCAATCC
* * * * * * * *
10022676 AAAAAAAACAAAAAACAAAAAAAAAACAAAAAAAAGAAAGAAAAAAGAAAAGAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10022737 GAAAGAGAAA
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:10023281 original size:6 final size:7
Alignment explanation
Indices: 10023269--10023310 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
10023259 AAAATAACGA
10023269 AAAAATG
1 AAAAATG
10023276 -AAAATG
1 AAAAATG
10023282 AAAAATG
1 AAAAATG
10023289 AAAAATG
1 AAAAATG
*
10023296 AAAAAAG
1 AAAAATG
10023303 TAAAAATG
1 -AAAAATG
10023311 GAGAGGCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
6 6 0.19
7 19 0.61
8 6 0.19
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:10023286 original size:14 final size:15
Alignment explanation
Indices: 10023253--10023310 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 15
10023243 GTAAAAAATG
10023253 AAATGAAAAATAACGAAA
1 AAATGAAAAAT---GAAA
10023271 AAATG-AAAATG-AA
1 AAATGAAAAATGAAA
10023284 AAATGAAAAATGAAA
1 AAATGAAAAATGAAA
10023299 AAA-GTAAAAATG
1 AAATG-AAAAATG
10023311 GAGAGGCTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 7 0.19
14 8 0.22
15 12 0.32
17 5 0.14
18 5 0.14
ACGTcount: A:0.71, C:0.02, G:0.14, T:0.14
Consensus pattern (15 bp):
AAATGAAAAATGAAA
Found at i:10024579 original size:88 final size:88
Alignment explanation
Indices: 10024466--10025344 Score: 1382
Period size: 88 Copynumber: 10.0 Consensus size: 88
10024456 CGGTGAAACT
* * * * *
10024466 TCAGCCTTGTCTCCTTGAGTAGTAGTAGAATAGGTTGAAAATAGTAGATCTTGTCTTCCTGTATT
1 TCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
* ** *
10024531 GACAGTAAAGTAGATCAAAGACC
66 GGCAGCGAAGTAGATCGAAGACC
* * *
10024554 TAAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTAAAAATAGCAGATATTGTCTTCCTGTATT
1 TCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
10024619 GGCAGCGAAGTAGATCGAAGACC
66 GGCAGCGAAGTAGATCGAAGACC
* *
10024642 TCAACCTTGTCTCCTTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
1 TCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
*
10024707 GGCAGCGAAGTAGATCGAAGACA
66 GGCAGCGAAGTAGATCGAAGACC
* * *
10024730 TCAGCCTTGTCTCCTTGAGTAGTAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGTATT
1 TCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
*
10024795 GGTAGCGAAGTAGATCGAAGACC
66 GGCAGCGAAGTAGATCGAAGACC
*
10024818 TCAGCCTTGTCTTCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
1 TCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
10024883 GGCAGCGAAGTAGATCGAAGACC
66 GGCAGCGAAGTAGATCGAAGACC
* * *
10024906 TCAGCCTTGTCTCCCTGAGTAGTAGTGGGGTAGGTTGAAAATAGCAGATCTTGTCTTTCTGTATT
1 TCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
*
10024971 GGCAGCGAAGTAGATCAAAGACC
66 GGCAGCGAAGTAGATCGAAGACC
* *
10024994 TCAGCCTTGTCTCCCTGAGTAGTAATGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
1 TCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
10025059 GGCAGCGAAGTAGATCGAAGACC
66 GGCAGCGAAGTAGATCGAAGACC
* * * * *
10025082 TCAGCCTTGTATCCCTAAGTAGTAGTGGAGTAAGTTGAAAATAGCAGATCTTGTCTTCCTATATT
1 TCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
10025147 GGCAGCGAAGTAGATCGAAGACC
66 GGCAGCGAAGTAGATCGAAGACC
* *
10025170 TCAACCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCCTGTCTTCCTGTATT
1 TCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
10025235 GGCAGCGAAGTAGATCGAAGACC
66 GGCAGCGAAGTAGATCGAAGACC
* * * *
10025258 TCAGCCTTGTCTCTCTGAGCAGTAATGGAGTAGGTTGAATATAGCAGATCTTG-CATTCCTGTAC
1 TCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTC-TTCCTGTAT
* * *
10025322 TGGTAGTGAAGCAGATCGAAGAC
65 TGGCAGCGAAGTAGATCGAAGAC
10025345 ACCAGTTTTA
Statistics
Matches: 732, Mismatches: 58, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
87 1 0.00
88 731 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (88 bp):
TCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
GGCAGCGAAGTAGATCGAAGACC
Found at i:10025775 original size:44 final size:41
Alignment explanation
Indices: 10025742--10025905 Score: 116
Period size: 42 Copynumber: 3.9 Consensus size: 41
10025732 AAGCCAATAG
* *
10025742 TCCTATCTCCCTGAGGTTGCAGAAGAGCGGATTAAAATCAGA
1 TCCTATCTCCCTAAGGTTGCAG-AGAGCGGATTAAAACCAGA
* * * * * *
10025784 TCTTATCTCCCTAAGGTTGCAGAGAGCAGATCACATCAAG-
1 TCCTATCTCCCTAAGGTTGCAGAGAGCGGATTAAAACCAGA
* * * * * *
10025824 TCTTAGCTCCCTGAA-GTTGCAGTAGAGCAGACTGAAGACCTAAA
1 TCCTATCTCCCT-AAGGTTGCAG-AGAGCGGA-TTAAAACC-AGA
* *
10025868 TCCTATCTCCCTAAGGTTGCAGTGGAGTGGATTAAAAC
1 TCCTATCTCCCTAAGGTTGCAG-AGAGCGGATTAAAAC
10025906 ATTCAGATTT
Statistics
Matches: 94, Mismatches: 22, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
40 18 0.19
41 22 0.23
42 23 0.24
43 8 0.09
44 23 0.24
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (41 bp):
TCCTATCTCCCTAAGGTTGCAGAGAGCGGATTAAAACCAGA
Found at i:10025843 original size:40 final size:42
Alignment explanation
Indices: 10025748--10025854 Score: 114
Period size: 40 Copynumber: 2.6 Consensus size: 42
10025738 ATAGTCCTAT
* * *
10025748 CTCCCTGAGGTTGCAGAAGAGCGGATTAAAATCAGATCTTAT
1 CTCCCTGAAGTTGCAGAAGAGCAGATTAAAATCAGATCTTAG
* *
10025790 CTCCCT-AAGGTTGCAG-AGAGCAGA-TCACATCA-AGTCTTAG
1 CTCCCTGAA-GTTGCAGAAGAGCAGATTAAAATCAGA-TCTTAG
*
10025830 CTCCCTGAAGTTGCAGTAGAGCAGA
1 CTCCCTGAAGTTGCAGAAGAGCAGA
10025855 CTGAAGACCT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
39 1 0.02
40 24 0.43
41 18 0.32
42 13 0.23
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.23
Consensus pattern (42 bp):
CTCCCTGAAGTTGCAGAAGAGCAGATTAAAATCAGATCTTAG
Found at i:10025929 original size:126 final size:129
Alignment explanation
Indices: 10025698--10025991 Score: 318
Period size: 126 Copynumber: 2.3 Consensus size: 129
10025688 AGATGGTGAA
* * * *
10025698 TCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTAAAG-CCAATAGTCCTATCTCCCTGAGGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACCAATAGTCCTATCTCCCTAAGGTTGC
* *
10025762 AGAAGAGCGGATTAAAATCAGATCTTATCTCCCTAAGGTTGCAG-AG-AGCAGATCACA-T-CAA
66 AGAAGAGCGGATTAAAATCAGATCTTATCT-CCTAAAGTTGCAGTAGAAGAAGATCA-AGTACAA
10025823 G
129 G
* * *
10025824 TCTTAGCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGACCTAA-A-TCCTATCTCCCTAAGGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACC-AATAGTCCTATCTCCCTAAGGTTG
** * * * * *
10025887 CAGTGGAGTGGATTAAAACATTCAGAT-TTATCT-TTAAAGTTGCAGTAGAATAAGTTGAAGTCA
65 CAGAAGAGCGGATT-AAA-A-TCAGATCTTATCTCCTAAAGTTGCAGTAGAAGAAGATCAAGT-A
10025950 CAAG
126 CAAG
10025954 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGA
10025992 TAGCAAATTT
Statistics
Matches: 139, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
126 70 0.50
127 9 0.06
128 15 0.11
129 6 0.04
130 39 0.28
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (129 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACCAATAGTCCTATCTCCCTAAGGTTGC
AGAAGAGCGGATTAAAATCAGATCTTATCTCCTAAAGTTGCAGTAGAAGAAGATCAAGTACAAG
Found at i:10027324 original size:14 final size:13
Alignment explanation
Indices: 10027305--10027345 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
10027295 ACTGTTAAAT
10027305 TGTATTATTATTA
1 TGTATTATTATTA
10027318 CTGTATTATTATTA
1 -TGTATTATTATTA
10027332 -GTATTTATTATTA
1 TGTA-TTATTATTA
10027345 T
1 T
10027346 TATGGTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 9 0.36
14 13 0.52
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.61
Consensus pattern (13 bp):
TGTATTATTATTA
Found at i:10027356 original size:19 final size:16
Alignment explanation
Indices: 10027307--10027347 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
10027297 TGTTAAATTG
* *
10027307 TATTATTATTACTGTAT
1 TATTATTAGTA-TTTAT
10027324 TATTATTAGTATTTAT
1 TATTATTAGTATTTAT
10027340 TATTATTA
1 TATTATTA
10027348 TGGTTATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (16 bp):
TATTATTAGTATTTAT
Found at i:10030290 original size:14 final size:14
Alignment explanation
Indices: 10030271--10030297 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10030261 CTTTTTCACA
10030271 AAACTTTATTGGAC
1 AAACTTTATTGGAC
10030285 AAACTTTATTGGA
1 AAACTTTATTGGA
10030298 ATTTGGTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (14 bp):
AAACTTTATTGGAC
Found at i:10030956 original size:24 final size:23
Alignment explanation
Indices: 10030903--10030956 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
10030893 ATTTTCATAT
*
10030903 ATTTTATGTTTTAATTTTTTTGA
1 ATTTTATGTTTAAATTTTTTTGA
*
10030926 AGATTTATGTTTAAATATTTGTTTG-
1 A-TTTTATGTTTAAAT-TTT-TTTGA
10030951 ATTTTA
1 ATTTTA
10030957 AAAATATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 1 0.04
24 16 0.64
25 4 0.16
26 4 0.16
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (23 bp):
ATTTTATGTTTAAATTTTTTTGA
Found at i:10031420 original size:18 final size:18
Alignment explanation
Indices: 10031375--10031434 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 18
10031365 TAATTATTTA
* *
10031375 TTAAATTTAATTAGAATA-
1 TTAAATATATTTA-AATAT
10031393 TTAAACTATATTTAAATAT
1 TTAAA-TATATTTAAATAT
10031412 TTAAATATAATAATTAAATAT
1 TTAAATAT-AT--TTAAATAT
10031433 TT
1 TT
10031435 GTAATTAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 12 0.34
19 13 0.37
21 10 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAAATATATTTAAATAT
Found at i:10033179 original size:38 final size:38
Alignment explanation
Indices: 10033128--10033203 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
10033118 TTATGAATAG
10033128 TAGTCAAAGTAATTGGAAAAAATGCAGATCCTTTCTTT
1 TAGTCAAAGTAATTGGAAAAAATGCAGATCCTTTCTTT
10033166 TAGTCAAAGTAATTGGAAAAAATGCAGATCCTTTCTTT
1 TAGTCAAAGTAATTGGAAAAAATGCAGATCCTTTCTTT
10033204 GAAAGATGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (38 bp):
TAGTCAAAGTAATTGGAAAAAATGCAGATCCTTTCTTT
Found at i:10036947 original size:13 final size:13
Alignment explanation
Indices: 10036929--10036954 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10036919 ACTAACTTCG
10036929 TAAATATTTATGA
1 TAAATATTTATGA
10036942 TAAATATTTATGA
1 TAAATATTTATGA
10036955 GTCCAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TAAATATTTATGA
Found at i:10038086 original size:27 final size:27
Alignment explanation
Indices: 10038039--10038105 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
10038029 ACAAATGGGG
* * *
10038039 GGTGCCGCCTGTGGCAGTGGCACCTTT
1 GGTGCCGCCTGTGCCACTGGCACCATT
*
10038066 GGTGCCGCCTTTGCCACTGGCACCATT
1 GGTGCCGCCTGTGCCACTGGCACCATT
*
10038093 GGTACCGCCTGTG
1 GGTGCCGCCTGTG
10038106 GCGGTCCCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.09, C:0.33, G:0.33, T:0.25
Consensus pattern (27 bp):
GGTGCCGCCTGTGCCACTGGCACCATT
Found at i:10040727 original size:20 final size:20
Alignment explanation
Indices: 10040702--10040741 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
10040692 GGTCAAACAT
10040702 GCACCACTTAAGCATCGATA
1 GCACCACTTAAGCATCGATA
10040722 GCACCACTTAAGCATCGATA
1 GCACCACTTAAGCATCGATA
10040742 CTTTGTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.30, G:0.15, T:0.20
Consensus pattern (20 bp):
GCACCACTTAAGCATCGATA
Found at i:10054881 original size:10 final size:10
Alignment explanation
Indices: 10054859--10054891 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
10054849 ATAATAATAC
*
10054859 AATA-TTAAA
1 AATATTTAAT
10054868 AATATTTAAT
1 AATATTTAAT
10054878 AATATTTAAT
1 AATATTTAAT
10054888 AATA
1 AATA
10054892 ATACAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATTTAAT
Found at i:10059153 original size:29 final size:29
Alignment explanation
Indices: 10059077--10059157 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
10059067 ATTTGTTAAT
* * *
10059077 GCACTTCGGTGCCACTCTGTTTTGATAAA
1 GCACTTCGATGCCACTCTATTCTGATAAA
** * **
10059106 GCACTTCGATGTTATTCTATTCTGATATT
1 GCACTTCGATGCCACTCTATTCTGATAAA
*
10059135 GTACTTCGATGCCACTCTATTCT
1 GCACTTCGATGCCACTCTATTCT
10059158 ATGATTACAC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (29 bp):
GCACTTCGATGCCACTCTATTCTGATAAA
Found at i:10060779 original size:22 final size:23
Alignment explanation
Indices: 10060753--10060796 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
10060743 AATCCTTAAA
*
10060753 AAATAAATATTAAA-ACTAAAAC
1 AAATAAATACTAAATACTAAAAC
10060775 AAATAAATACTAAATACTAAAA
1 AAATAAATACTAAATACTAAAA
10060797 TATTCATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (23 bp):
AAATAAATACTAAATACTAAAAC
Found at i:10064683 original size:2 final size:2
Alignment explanation
Indices: 10064676--10064700 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10064666 CCTAAATCAT
10064676 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 T
10064701 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:10065552 original size:17 final size:18
Alignment explanation
Indices: 10065532--10065565 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
10065522 AGTGATAATA
*
10065532 TAAAATATAGA-TTATAG
1 TAAAAGATAGACTTATAG
10065549 TAAAAGATAGACTTATA
1 TAAAAGATAGACTTATA
10065566 TAATATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (18 bp):
TAAAAGATAGACTTATAG
Found at i:10073260 original size:23 final size:23
Alignment explanation
Indices: 10073220--10073286 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
10073210 ATAAATAGAT
* *
10073220 ATTATTAATATATGAAAATACAA
1 ATTATAAATATATAAAAATACAA
* *
10073243 ATTATAAATTTATAAAAAATATAA
1 ATTATAAATATAT-AAAAATACAA
*
10073267 ATATATAAAATGTATAAAAA
1 AT-TAT-AAATATATAAAAA
10073287 ATTTGTTGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 11 0.31
24 10 0.28
25 8 0.22
26 7 0.19
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (23 bp):
ATTATAAATATATAAAAATACAA
Found at i:10073282 original size:17 final size:16
Alignment explanation
Indices: 10073241--10073284 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
10073231 ATGAAAATAC
*
10073241 AAATTATAAATTTATAA
1 AAATTATAAATATAT-A
*
10073258 AAAATATAAATATATA
1 AAATTATAAATATATA
10073274 AAATGTATAAA
1 AAAT-TATAAA
10073285 AAATTTGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AAATTATAAATATATA
Found at i:10082514 original size:30 final size:30
Alignment explanation
Indices: 10082480--10082583 Score: 77
Period size: 30 Copynumber: 3.4 Consensus size: 30
10082470 TATCTATAAT
10082480 TAAATTTGAGGATCAAATTGATTGAATTTG
1 TAAATTTGAGGATCAAATTGATTGAATTTG
* * ** * *
10082510 TAAATGTGAAGGGTTTAATTTATTGAATTATT
1 TAAATTTG-AGGATCAAATTGATTGAATT-TG
* *
10082542 TAGAA-TT-AGGATCAAATTGATAGAATATG
1 TA-AATTTGAGGATCAAATTGATTGAATTTG
*
10082571 TAAGTATTGAGGA
1 TAAAT-TTGAGGA
10082584 CTAAATATAT
Statistics
Matches: 53, Mismatches: 15, Indels: 11
0.67 0.19 0.14
Matches are distributed among these distances:
28 1 0.02
29 3 0.06
30 23 0.43
31 20 0.38
32 4 0.08
33 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (30 bp):
TAAATTTGAGGATCAAATTGATTGAATTTG
Found at i:10089575 original size:9 final size:9
Alignment explanation
Indices: 10089558--10089588 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
10089548 TCGAGTTGAT
10089558 TCGAATAAC
1 TCGAATAAC
*
10089567 TCGATTAAC
1 TCGAATAAC
10089576 TCGAATAAC
1 TCGAATAAC
10089585 TCGA
1 TCGA
10089589 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:10090520 original size:29 final size:29
Alignment explanation
Indices: 10090487--10090543 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
10090477 AGTTTTTTCA
*
10090487 GCCTAATCCTATAAATTTT-TGAAAAATAG
1 GCCTAATCCGATAAATTTTCT-AAAAATAG
*
10090516 GCCTAATTCGATAAATTTTCTAAAAATA
1 GCCTAATCCGATAAATTTTCTAAAAATA
10090544 CGACATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (29 bp):
GCCTAATCCGATAAATTTTCTAAAAATAG
Found at i:10096993 original size:18 final size:19
Alignment explanation
Indices: 10096970--10097027 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
10096960 TCCTAGACCA
10096970 TTTTTAAGGGTTT-GGATT
1 TTTTTAAGGGTTTAGGATT
*
10096988 TTTTTAAGAGTTTAAGG-TT
1 TTTTTAAGGGTTT-AGGATT
*
10097007 TTTCT-AGGGTTTAGGATT
1 TTTTTAAGGGTTTAGGATT
10097025 TTT
1 TTT
10097028 GTTTTTTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.09
18 23 0.68
19 6 0.18
20 2 0.06
ACGTcount: A:0.19, C:0.02, G:0.24, T:0.55
Consensus pattern (19 bp):
TTTTTAAGGGTTTAGGATT
Found at i:10102510 original size:22 final size:22
Alignment explanation
Indices: 10102485--10102562 Score: 138
Period size: 22 Copynumber: 3.5 Consensus size: 22
10102475 TTTCACAAAC
10102485 AAATTCTCTCAATTTCCTTCAA
1 AAATTCTCTCAATTTCCTTCAA
*
10102507 AAATTCTCTCAATTCCCTTCAA
1 AAATTCTCTCAATTTCCTTCAA
*
10102529 AAATTCTCTCAATTTCCTTCCA
1 AAATTCTCTCAATTTCCTTCAA
10102551 AAATTCTCTCAA
1 AAATTCTCTCAA
10102563 ACTCTCAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTCTCTCAATTTCCTTCAA
Found at i:10102568 original size:30 final size:30
Alignment explanation
Indices: 10102534--10102592 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
10102524 TTCAAAAATT
* *
10102534 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
10102564 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
10102593 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:10102569 original size:52 final size:51
Alignment explanation
Indices: 10102512--10102614 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 51
10102502 TTCAAAAATT
* * *
10102512 CTCTC-AATTCCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATT-CCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
*
10102564 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
10102615 TCCATATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
51 4 0.09
52 38 0.83
53 4 0.09
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (51 bp):
CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:10102603 original size:21 final size:22
Alignment explanation
Indices: 10102564--10102605 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
10102554 TTCTCTCAAA
10102564 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
10102586 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
10102606 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:10102701 original size:28 final size:29
Alignment explanation
Indices: 10102648--10102703 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
10102638 TTAAATTTCA
*
10102648 TTTTTTAAGAAAATTTTACAATTTTTTAT
1 TTTTTTAAGAAAATTTTACAAATTTTTAT
10102677 TTTTTTAA-AATAATTTTA-AAATTTTTA
1 TTTTTTAAGAA-AATTTTACAAATTTTTA
10102704 ANNNNNNNNN
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTTTAAGAAAATTTTACAAATTTTTAT
Found at i:10102846 original size:14 final size:15
Alignment explanation
Indices: 10102817--10102850 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10102807 AAATTTTATA
10102817 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
10102832 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
10102846 TTTTA
1 TTTTA
10102851 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:10102872 original size:24 final size:23
Alignment explanation
Indices: 10102815--10102872 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 23
10102805 TTAAATTTTA
10102815 TATTTTATTTAAGATATTTTTATT
1 TATTTT-TTTAAGATATTTTTATT
10102839 TATGTATTTTT-AGATATTTATTAATT
1 TAT-T-TTTTTAAGATATTT-TT-ATT
10102865 TATTTTTT
1 TATTTTTT
10102873 GTTATAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
24 15 0.50
25 7 0.23
26 8 0.27
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (23 bp):
TATTTTTTTAAGATATTTTTATT
Found at i:10105029 original size:23 final size:23
Alignment explanation
Indices: 10105003--10105655 Score: 525
Period size: 23 Copynumber: 26.8 Consensus size: 23
10104993 AAAACCCTAA
*
10105003 CCTAACTTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
10105026 CCTAACCTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
10105049 CCTAACCTAACTTAATTTAATTAAAAAC
1 CCTAA-C---C-TAATTTAATTAAAAAC
10105077 CCTAACCTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
10105100 CCTAACCTAACTTAATTTAATTAAAAACCC
1 CCTAA-C---C-TAATTTAATTAAAAA--C
10105130 TAACCTAACCTAATTTAATTAAAAAC
1 ---CCTAACCTAATTTAATTAAAAAC
10105156 CCTAACCTAACTTAATTTAATTAAAAAC
1 CCTAA-C---C-TAATTTAATTAAAAAC
10105184 CCTAACCTAATTTAATGT-AAAAC
1 CCTAACCTAATTTAAT-TAAAAAC
10105207 CCTAACCTAACTTAATTTAATTAAAAAC
1 CCTAA-C---C-TAATTTAATTAAAAAC
* *
10105235 TCTAACCTAATTGAATTAAAAACCC
1 CCTAACCTAATTTAATTAAAAA--C
10105260 TAACCTAACCTAATTTAATTAAAAACCC
1 ---CCTAACCTAATTTAATTAAAAA--C
10105288 TAACCTAACCTAATTTAATTAAAAAC
1 ---CCTAACCTAATTTAATTAAAAAC
* *
10105314 CCTAACCTAATTGAATTTAAAACCCAAA
1 CCTAACCTAATTTAA-TT-AAA---AAC
* *
10105342 CCTAACTTAATTTAAATAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
10105365 CCTAACCTAATTGAATT--AAA-
1 CCTAACCTAATTTAATTAAAAAC
*
10105385 ---AACCTAATTTAATCAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
10105405 CCTAACCTAACTTAATTTAATTAAAAAC
1 CCTAA-C---C-TAATTTAATTAAAAAC
*
10105433 CCTAACCTAACTTAATGT-AAAAC
1 CCTAACCTAATTTAAT-TAAAAAC
*
10105456 CCTAACTTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
10105479 CCTAACCTAATTTAATT--AAA-
1 CCTAACCTAATTTAATTAAAAAC
10105499 ---AACCTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
10105519 CCTAACCTAATTGAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
**
10105542 CCTAACCTAACCTAATTGAATTAAA-
1 CCTAACCTAATTTAATT-AA--AAAC
10105567 ---AACCTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
10105587 CCTAACCTAACTTAATGT-AAAAC
1 CCTAACCTAATTTAAT-TAAAAAC
10105610 CCTAACCTAACTTAATTTAATTAAAAAC
1 CCTAA-C---C-TAATTTAATTAAAAAC
*
10105638 CCTAACCTAATTGAATTA
1 CCTAACCTAATTTAATTA
10105656 TAGTTTTACA
Statistics
Matches: 530, Mismatches: 30, Indels: 140
0.76 0.04 0.20
Matches are distributed among these distances:
17 26 0.05
19 9 0.02
21 8 0.02
22 13 0.02
23 231 0.44
24 18 0.03
25 4 0.01
26 8 0.02
27 14 0.03
28 191 0.36
29 1 0.00
30 1 0.00
32 1 0.00
33 5 0.01
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.30
Consensus pattern (23 bp):
CCTAACCTAATTTAATTAAAAAC
Found at i:10105049 original size:51 final size:51
Alignment explanation
Indices: 10104984--10105647 Score: 728
Period size: 51 Copynumber: 13.5 Consensus size: 51
10104974 TTTTGACATT
*
10104984 ATTTGATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
10105035 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
10105086 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAA--C---CCTAACCTA
10105142 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
*
10105193 ATTTAATGT-AAAACCCTAACCTAACTTAATTTAATTAAAAACTCTAACCTA
1 ATTTAAT-TAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
* *
10105244 ATTGAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAA--C---CCTAACCTA
*
10105300 ATTTAATTAAAAACCCTAACCTAA-TTGAATTTAA--AACCCAAA-CCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTT-AATTTAATTAA---AAACCCTAACCTA
* *
10105351 ATTTAAATAAAAACCCTAA-C---C-TAATTGAATT--AAA----AACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
*
10105391 ATTTAATCAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
*
10105442 ACTTAATGT-AAAA--C---CCTAACTTAATTTAATTAAAAACCCTAACCTA
1 ATTTAAT-TAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
10105488 ATTTAATT--AAA----AA-C---C-TAATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
* * *
10105528 ATTGAATTAAAAACCCTAACCTAACCTAATTGAATT--AAA----AACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
* * *
10105573 ATTTAATTAAAAACCCTAACCTAACTTAATGTAA--AACCCTAA-CCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAA---AAACCCTAACCTA
10105624 ATTTAATTAAAAACCCTAACCTAA
1 ATTTAATTAAAAACCCTAACCTAA
10105648 TTGAATTATA
Statistics
Matches: 536, Mismatches: 25, Indels: 104
0.81 0.04 0.16
Matches are distributed among these distances:
40 54 0.10
41 2 0.00
42 3 0.01
43 3 0.01
44 5 0.01
45 46 0.09
46 46 0.09
47 5 0.01
48 2 0.00
49 4 0.01
50 3 0.01
51 265 0.49
52 1 0.00
53 2 0.00
54 3 0.01
55 1 0.00
56 88 0.16
57 3 0.01
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.30
Consensus pattern (51 bp):
ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
Found at i:10105381 original size:28 final size:28
Alignment explanation
Indices: 10104984--10105374 Score: 503
Period size: 28 Copynumber: 14.9 Consensus size: 28
10104974 TTTTGACATT
*
10104984 ATTTGATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
10105012 ATTTAATTAAAAACCCTAA-C---C-TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
10105035 ATTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
10105063 ATTTAATTAAAAACCCTAA-C---C-TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
10105086 ATTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
10105114 ATTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
10105142 ATTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
10105170 ATTTAATTAAAAACCCTAA-C---C-TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
10105193 ATTTAATGT-AAAACCCTAACCTAACTTA
1 ATTTAAT-TAAAAACCCTAACCTAACTTA
*
10105221 ATTTAATTAAAAA--CT---CTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
10105244 ATTGAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
10105272 ATTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
10105300 ATTTAATTAAAAACCCTAACCTAA-TTGA
1 ATTTAATTAAAAACCCTAACCTAACTT-A
*
10105328 A--T--TT-AAAACCCAAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
10105351 ATTTAAATAAAAACCCTAACCTAA
1 ATTTAATTAAAAACCCTAACCTAA
10105375 TTGAATTAAA
Statistics
Matches: 324, Mismatches: 10, Indels: 58
0.83 0.03 0.15
Matches are distributed among these distances:
23 96 0.30
24 11 0.03
25 3 0.01
26 3 0.01
27 9 0.03
28 202 0.62
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.30
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAACTTA
Found at i:10105403 original size:91 final size:91
Alignment explanation
Indices: 10105294--10105655 Score: 381
Period size: 91 Copynumber: 4.0 Consensus size: 91
10105284 ACCCTAACCT
10105294 AACCTAATTTAATTAAAAACCCTAACCTAA-TTGAATTTAAAACCCAAACCTAACTTAATTTAAA
1 AACCTAATTTAATTAAAAACCCTAACCTAACTT-AATTTAAAACCCAAACCTAACTTAATTTAAA
10105358 TAAAAACCCTAACCTAATTGAATTAAA
65 TAAAAACCCTAACCTAATTGAATTAAA
* * *
10105385 AACCTAATTTAATCAAAAACCCTAACCTAACTTAATTTAATTAA---AAACCCTAACCTAACTT-
1 AACCTAATTTAATTAAAAACCCTAACCTAACTTAATTTAA--AACCCAAA-CCTAACTTAATTTA
* * *
10105446 AATGTAAAACCCTAACTTAATTTAATTAAA
63 AAT-AAAAACCCTAACCTAATTGAATTAAA
** * * *
10105476 AACCCTAACCTAATTTAATTAAA----AACCTAATTTAATTAAAAACCCTAACCTAA-TTGAA-T
1 AA-CCTAATTTAA-TTAA--AAACCCTAACCTAACTTAATTTAAAACCCAAACCTAACTT-AATT
*
10105535 TAAA-AACCCTAA-CCTAACCTAATTGAATTAAA
61 TAAATAA---AAACCCTAACCTAATTGAATTAAA
* * *
10105567 AACCTAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTAACCTAACTTAATTTAATT
1 AACCTAATTTAATTAAAAACCCTAACCTAACTTAATTTAAAACCCAAACCTAACTTAATTTAAAT
10105632 AAAAACCCTAACCTAATTGAATTA
66 AAAAACCCTAACCTAATTGAATTA
10105656 TAGTTTTACA
Statistics
Matches: 222, Mismatches: 24, Indels: 50
0.75 0.08 0.17
Matches are distributed among these distances:
87 3 0.01
89 7 0.03
90 19 0.09
91 163 0.73
92 20 0.09
93 7 0.03
95 3 0.01
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.30
Consensus pattern (91 bp):
AACCTAATTTAATTAAAAACCCTAACCTAACTTAATTTAAAACCCAAACCTAACTTAATTTAAAT
AAAAACCCTAACCTAATTGAATTAAA
Found at i:10105406 original size:68 final size:67
Alignment explanation
Indices: 10105238--10105655 Score: 345
Period size: 68 Copynumber: 6.0 Consensus size: 67
10105228 TAAAAACTCT
*
10105238 AACCTAATTGAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATT
1 AACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAA--C---CCTAACCTAA-T
10105303 TAATTAAA
60 TAATTAAA
* * * *
10105311 AACCCTAACCTAATTGAATTTAAAACCCAAACCTAACTTAATTTAAATAAAAACCCTAACCTAAT
1 AA-CCTAA--T--TT-AATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAAT
10105376 TGAATTAAA
60 T-AATTAAA
* *
10105385 AACCTAATTTAATCAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTAACTTAATG
1 AACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAA-TTAAT-
10105450 TAAA
64 TAAA
* * **
10105454 ACCCTAACTTAATTTAATTAAA----AACCCTAACCTAATTTAATTAAAAA-CCTAATTTAATTA
1 AACCTAATTTAA-TTAA--AAACCCTAA-CCTAACCTAATTTAATTAAAAACCCTAACCTAATTA
10105514 A--AAA
62 ATTAAA
* * **
10105518 CCCTAACCTAATTGAATTAAAAACCCTAACCTAACCTAATTGAATTAAAAA-CCTAATTTAATTA
1 ----AACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAATTA
10105582 A--AAA
62 ATTAAA
* *
10105586 CCCTAACCTAACTTAATGT-AAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTAATT
1 ----AACCTAATTTAAT-TAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAATT
10105650 GAATTA
61 -AATTA
10105656 TAGTTTTACA
Statistics
Matches: 294, Mismatches: 25, Indels: 53
0.79 0.07 0.14
Matches are distributed among these distances:
64 3 0.01
65 3 0.01
67 8 0.03
68 149 0.51
69 52 0.18
70 5 0.02
71 1 0.00
72 4 0.01
73 9 0.03
74 24 0.08
76 1 0.00
77 1 0.00
78 1 0.00
79 33 0.11
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (67 bp):
AACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAATTAATTA
AA
Found at i:10105409 original size:18 final size:17
Alignment explanation
Indices: 10105368--10105405 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
10105358 TAAAAACCCT
*
10105368 AACCTAATTGAATTAAA
1 AACCTAATTGAATCAAA
*
10105385 AACCTAATTTAATCAAA
1 AACCTAATTGAATCAAA
10105402 AACC
1 AACC
10105406 CTAACCTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (17 bp):
AACCTAATTGAATCAAA
Found at i:10105430 original size:28 final size:28
Alignment explanation
Indices: 10105389--10105495 Score: 117
Period size: 28 Copynumber: 4.2 Consensus size: 28
10105379 ATTAAAAACC
*
10105389 TAATTTAATCAAAAACCCTAACCTAACT
1 TAATTTAATTAAAAACCCTAACCTAACT
10105417 TAATTTAATTAAAAACCCTAACCTAACT
1 TAATTTAATTAAAAACCCTAACCTAACT
*
10105445 TAA--T--GT-AAAACCCTAA-C----T
1 TAATTTAATTAAAAACCCTAACCTAACT
*
10105463 TAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAACT
10105491 TAATT
1 TAATT
10105496 AAAAACCTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 20
0.74 0.03 0.22
Matches are distributed among these distances:
18 4 0.06
20 1 0.02
22 2 0.03
23 20 0.30
24 2 0.03
26 1 0.02
28 36 0.55
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.33
Consensus pattern (28 bp):
TAATTTAATTAAAAACCCTAACCTAACT
Found at i:10105504 original size:17 final size:17
Alignment explanation
Indices: 10105482--10105519 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
10105472 TAAAAACCCT
10105482 AACCTAATTTAATTAAA
1 AACCTAATTTAATTAAA
10105499 AACCTAATTTAATTAAA
1 AACCTAATTTAATTAAA
10105516 AACC
1 AACC
10105520 CTAACCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (17 bp):
AACCTAATTTAATTAAA
Found at i:10105572 original size:17 final size:17
Alignment explanation
Indices: 10105550--10105587 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
10105540 ACCCTAACCT
10105550 AACCTAATTGAATTAAA
1 AACCTAATTGAATTAAA
*
10105567 AACCTAATTTAATTAAA
1 AACCTAATTGAATTAAA
10105584 AACC
1 AACC
10105588 CTAACCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.29
Consensus pattern (17 bp):
AACCTAATTGAATTAAA
Found at i:10105618 original size:28 final size:28
Alignment explanation
Indices: 10105587--10105647 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
10105577 AATTAAAAAC
10105587 CCTAACCTAACTTAATGT-AAAACCCTAA
1 CCTAACCTAACTTAAT-TAAAAACCCTAA
* *
10105615 CCTAACTTAATTTAATTAAAAACCCTAA
1 CCTAACCTAACTTAATTAAAAACCCTAA
10105643 CCTAA
1 CCTAA
10105648 TTGAATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.28
Consensus pattern (28 bp):
CCTAACCTAACTTAATTAAAAACCCTAA
Found at i:10113905 original size:27 final size:27
Alignment explanation
Indices: 10113871--10113959 Score: 106
Period size: 27 Copynumber: 3.3 Consensus size: 27
10113861 TCCTTAAATA
* * *
10113871 GCCACAAAGGCTTCTATCTCATAGATT
1 GCCACAAAGACTTCCATTTCATAGATT
* *
10113898 GCCACAAAAACTTCCATTTTATAGATT
1 GCCACAAAGACTTCCATTTCATAGATT
* *
10113925 GCCATAAAGACTTCCATTTCATAAATT
1 GCCACAAAGACTTCCATTTCATAGATT
*
10113952 GTCACAAA
1 GCCACAAA
10113960 AGGCTTCTAT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (27 bp):
GCCACAAAGACTTCCATTTCATAGATT
Found at i:10115699 original size:41 final size:41
Alignment explanation
Indices: 10115666--10115811 Score: 229
Period size: 41 Copynumber: 3.6 Consensus size: 41
10115656 CCGACTTTTG
* **
10115666 GCCTGCTAGACTTAAAGTCCAAAATGTTTCACCGGCATCAA
1 GCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCAA
10115707 GCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCAA
1 GCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCAA
* *
10115748 GCCTGCTAGACATAAAGTCTGAATTGTTTCACCGGCATCTA
1 GCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCAA
* *
10115789 GCCTACTAGACATAGAGTCTGAA
1 GCCTGCTAGACATAAAGTCTGAA
10115812 TTATCTCACT
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 98 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (41 bp):
GCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCAA
Found at i:10115832 original size:82 final size:82
Alignment explanation
Indices: 10115666--10115838 Score: 222
Period size: 82 Copynumber: 2.1 Consensus size: 82
10115656 CCGACTTTTG
* *
10115666 GCCTGCTAGACTTAAAGTCCAAAATGTTTCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAA
1 GCCTGCTAGACATAAAGTCCAAAATGTTTCACCGGCATCAAGCCTACTAGACATAAAGTCTGAAA
* *
10115731 TGTTTCACCGGCATCAA
66 TATCTCACCGGCATCAA
** * * * *
10115748 GCCTGCTAGACATAAAGTCTGAATTGTTTCACCGGCATCTAGCCTACTAGACATAGAGTCTGAAT
1 GCCTGCTAGACATAAAGTCCAAAATGTTTCACCGGCATCAAGCCTACTAGACATAAAGTCTGAAA
*
10115813 TATCTCACTGGCAAT-AA
66 TATCTCACCGGC-ATCAA
*
10115830 GCCTTCTAG
1 GCCTGCTAG
10115839 GCACTGAGCT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
82 76 0.97
83 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (82 bp):
GCCTGCTAGACATAAAGTCCAAAATGTTTCACCGGCATCAAGCCTACTAGACATAAAGTCTGAAA
TATCTCACCGGCATCAA
Found at i:10123569 original size:18 final size:17
Alignment explanation
Indices: 10123546--10123591 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
10123536 ATTTAAATTG
10123546 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCG-TTT
*
10123564 CGGTCGC-GTTGCGTTT
1 CGGTCGCGGTCGCGTTT
10123580 --GTCGCGGTCGCG
1 CGGTCGCGGTCGCG
10123592 GACATAACGG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 5 0.20
15 5 0.20
16 3 0.12
17 5 0.20
18 7 0.28
ACGTcount: A:0.00, C:0.28, G:0.41, T:0.30
Consensus pattern (17 bp):
CGGTCGCGGTCGCGTTT
Found at i:10124876 original size:3 final size:3
Alignment explanation
Indices: 10124870--10124916 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
10124860 GAGAGAAAGG
*
10124870 AGA AGA AG- AGA AGG AGA AGA AGA AGA AG- AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
10124916 A
1 A
10124917 AGAAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:10124880 original size:17 final size:16
Alignment explanation
Indices: 10124858--10124913 Score: 71
Period size: 17 Copynumber: 3.5 Consensus size: 16
10124848 AGAAAAAAAA
10124858 AAGAGAGAAAGGAGAAG
1 AAGA-AGAAAGGAGAAG
10124875 AAG-AG-AAGGAGAAG
1 AAGAAGAAAGGAGAAG
*
10124889 AAGAAGAAGAGAAGAAG
1 AAGAAGAA-AGGAGAAG
10124906 AAGAAGAA
1 AAGAAGAA
10124914 GAAAGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
14 12 0.34
15 4 0.11
16 1 0.03
17 18 0.51
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
AAGAAGAAAGGAGAAG
Found at i:10124895 original size:20 final size:20
Alignment explanation
Indices: 10124870--10124920 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
10124860 GAGAGAAAGG
*
10124870 AGAAGAAGAGAAGGAGAAGA
1 AGAAGAAGAGAAGAAGAAGA
10124890 AGAAGAAGAGAAGAAGAAGA
1 AGAAGAAGAGAAGAAGAAGA
10124910 AGAAGAA-AGAA
1 AGAAGAAGAGAA
10124921 AAAAAAAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
AGAAGAAGAGAAGAAGAAGA
Found at i:10124929 original size:17 final size:20
Alignment explanation
Indices: 10124870--10124929 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
10124860 GAGAGAAAGG
* *
10124870 AGAAGAAGAGAAGGAGAAGA
1 AGAAGAAGAGAAGAAGAAAA
*
10124890 AGAAGAAGAGAAGAAGAAGA
1 AGAAGAAGAGAAGAAGAAAA
10124910 AGAAGAA-AGAA-AA-AAAA
1 AGAAGAAGAGAAGAAGAAAA
10124927 AGA
1 AGA
10124930 TAATGTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 6 0.16
18 2 0.05
19 4 0.11
20 26 0.68
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (20 bp):
AGAAGAAGAGAAGAAGAAAA
Found at i:10125041 original size:7 final size:7
Alignment explanation
Indices: 10125029--10125053 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
10125019 GAATTTTTTG
10125029 TTATTAA
1 TTATTAA
10125036 TTATTAA
1 TTATTAA
10125043 TTATTAA
1 TTATTAA
10125050 TTAT
1 TTAT
10125054 CTATATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATTAA
Found at i:10125111 original size:22 final size:21
Alignment explanation
Indices: 10125085--10125416 Score: 164
Period size: 22 Copynumber: 15.0 Consensus size: 21
10125075 TAGATTAGAA
* *
10125085 TTTTGAATGAATATTTTAACTT
1 TTTTGTATGAATATTATAA-TT
10125107 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTATAATT
*
10125128 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTATAATT
* *
10125146 TGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTATAATT
*
10125167 ATTT-TAT--A-ATTA-AATT
1 TTTTGTATGAATATTATAATT
**
10125183 TGTATT-TATAGTTTTGGATTAGTAATT
1 T-T-TTGTAT-G-AAT--ATTA-TAATT
*
10125210 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTATAATT
10125229 TTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTAT-AATT
*
10125251 TTTTGTATGAATATTGTAATATTATAG
1 TTTTGTATGAATA-T-T-ATA--AT-T
*
10125278 TTTTGTATGAATATTACAATTT
1 TTTTGTATGAATATTATAA-TT
* *
10125300 TTTTGTATGAATTTTGTAATTTTGT
1 TTTTGTATGAATATTATAA---T-T
*
10125325 AATTTTGTATGAATATTATATTT
1 --TTTTGTATGAATATTATAATT
*
10125348 TTTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATA-T-T-ATA--AT-T
**
10125375 TTTTGTATGAATATTGCAATTT
1 TTTTGTATGAATATTATAA-TT
*
10125397 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTATAAT
10125417 ATTGTAATTT
Statistics
Matches: 245, Mismatches: 28, Indels: 75
0.70 0.08 0.22
Matches are distributed among these distances:
16 4 0.02
17 4 0.02
18 9 0.04
19 30 0.12
20 18 0.07
21 25 0.10
22 70 0.29
23 5 0.02
24 12 0.05
25 12 0.05
26 9 0.04
27 47 0.19
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTTGTATGAATATTATAATT
Found at i:10125156 original size:19 final size:19
Alignment explanation
Indices: 10125109--10125165 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
10125099 TTTAACTTTT
* *
10125109 TTGTATGAATATTATAATTT
1 TTGTATGAATATTGTAA-TG
*
10125129 TTTTATGAATATTGTAATG
1 TTGTATGAATATTGTAATG
10125148 TTGTATGAATATTGTAAT
1 TTGTATGAATATTGTAAT
10125166 TATTTTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (19 bp):
TTGTATGAATATTGTAATG
Found at i:10125234 original size:19 final size:19
Alignment explanation
Indices: 10125210--10125270 Score: 86
Period size: 19 Copynumber: 3.1 Consensus size: 19
10125200 ATTAGTAATT
10125210 TTTTGTATGAATATTGTAA
1 TTTTGTATGAATATTGTAA
*
10125229 TTTTGTATGAATATTATAAA
1 TTTTGTATGAATATTGT-AA
10125249 TTTTTTGTATGAATATTGTAA
1 --TTTTGTATGAATATTGTAA
10125270 T
1 T
10125271 ATTATAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 17 0.46
20 2 0.05
21 2 0.05
22 16 0.43
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (19 bp):
TTTTGTATGAATATTGTAA
Found at i:10125287 original size:27 final size:25
Alignment explanation
Indices: 10125219--10125443 Score: 217
Period size: 27 Copynumber: 9.1 Consensus size: 25
10125209 TTTTTGTATG
*
10125219 AATATTGTAATTTTGTATGAATATTAT
1 AATATT-T-ATTTTGTATGAATATTGT
10125246 AA-A-TT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
10125268 AATATTATAGTTTTGTATGAATA-T-T
1 AATATT-TA-TTTTGTATGAATATTGT
*
10125293 ACA-ATTT-TTTTGTATGAATTTTGT
1 A-ATATTTATTTTGTATGAATATTGT
*
10125317 AATTTTGTAATTTTGTATGAATA-T-T
1 AATATT-T-ATTTTGTATGAATATTGT
10125342 -ATATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
10125365 AATATTATAATTTTGTATGAATATTG-
1 AATATT-T-ATTTTGTATGAATATTGT
*
10125391 CA-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
10125414 AATATTGTAATTTTGTATGAATATTGT
1 AATATT-T-ATTTTGTATGAATATTGT
10125441 AAT
1 AAT
10125444 GTGGGGGTAT
Statistics
Matches: 168, Mismatches: 7, Indels: 46
0.76 0.03 0.21
Matches are distributed among these distances:
21 13 0.08
22 47 0.28
23 6 0.04
24 20 0.12
25 14 0.08
26 5 0.03
27 63 0.38
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54
Consensus pattern (25 bp):
AATATTTATTTTGTATGAATATTGT
Found at i:10125322 original size:8 final size:8
Alignment explanation
Indices: 10125309--10125333 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
10125299 TTTTTGTATG
10125309 AATTTTGT
1 AATTTTGT
10125317 AATTTTGT
1 AATTTTGT
10125325 AATTTTGT
1 AATTTTGT
10125333 A
1 A
10125334 TGAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (8 bp):
AATTTTGT
Found at i:10125382 original size:97 final size:98
Alignment explanation
Indices: 10125219--10125438 Score: 388
Period size: 97 Copynumber: 2.3 Consensus size: 98
10125209 TTTTTGTATG
*
10125219 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAGTTTTGT
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGT
*
10125284 ATGAATATTACAATTTTTTTGTATGAATTTTGT
66 ATGAATATTACAATTTTTTTGTATGAATATTGT
* *
10125317 AATTTTGTAATTTTGTATGAATATTAT-ATTTTTTTGTATGAATATTGTAATATTATAATTTTGT
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGT
*
10125381 ATGAATATTGCAATTTTTTTGTATGAATATTGT
66 ATGAATATTACAATTTTTTTGTATGAATATTGT
10125414 AATATTGTAATTTTGTATGAATATT
1 AATATTGTAATTTTGTATGAATATT
10125439 GTAATGTGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
97 90 0.78
98 26 0.22
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (98 bp):
AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGT
ATGAATATTACAATTTTTTTGTATGAATATTGT
Found at i:10125389 original size:19 final size:19
Alignment explanation
Indices: 10125365--10125422 Score: 53
Period size: 22 Copynumber: 2.9 Consensus size: 19
10125355 TGAATATTGT
10125365 AATATTATAATTTTGTATG
1 AATATTATAATTTTGTATG
**
10125384 AATATTGCAATTTTTTTGTATG
1 AATATT---ATAATTTTGTATG
* *
10125406 AATATTGTAATATTGTA
1 AATATTATAATTTTGTA
10125423 ATTTTGTATG
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
19 13 0.43
22 17 0.57
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (19 bp):
AATATTATAATTTTGTATG
Found at i:10125439 original size:49 final size:49
Alignment explanation
Indices: 10125219--10125438 Score: 352
Period size: 49 Copynumber: 4.5 Consensus size: 49
10125209 TTTTTGTATG
* *
10125219 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
* * *
10125268 AATATTATAGTTTTGTATGAATATTACAATTTTTTTGTATGAATTTTGT
1 AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
* *
10125317 AATTTTGTAATTTTGTATGAATATTA-TATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
* *
10125365 AATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
10125414 AATATTGTAATTTTGTATGAATATT
1 AATATTGTAATTTTGTATGAATATT
10125439 GTAATGTGGG
Statistics
Matches: 155, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
48 43 0.28
49 112 0.72
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
Found at i:10125555 original size:60 final size:60
Alignment explanation
Indices: 10125484--10125605 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 60
10125474 TGTATGAATA
* * * * * * *
10125484 TTGTAATTATTTTATAA-TTAATTTGTTTGTAATTTGGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
*
10125544 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
10125604 TT
1 TT
10125606 AGTTTAGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 6 0.11
60 47 0.89
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.55
Consensus pattern (60 bp):
TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:10125684 original size:38 final size:38
Alignment explanation
Indices: 10125639--10125720 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
10125629 CATATAAAGT
10125639 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
* *
10125677 TTATAAAAAAATTAAAAATTATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
10125715 TTATAA
1 TTATAA
10125721 CTGACTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:10125798 original size:15 final size:15
Alignment explanation
Indices: 10125757--10125798 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
10125747 GTTAACTCAT
*
10125757 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
10125772 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
10125788 TTAAATTTTAT
1 TTAAATTTTAT
10125799 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:10127435 original size:6 final size:6
Alignment explanation
Indices: 10127424--10127473 Score: 82
Period size: 6 Copynumber: 8.3 Consensus size: 6
10127414 TCATGCACCG
* *
10127424 GAGCCA GAGCCA GAGCCA GAGCCA GAGCCG GAGCCA GAGCCA GACCCA
1 GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA
10127472 GA
1 GA
10127474 ACTACATTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.32, C:0.34, G:0.34, T:0.00
Consensus pattern (6 bp):
GAGCCA
Found at i:10130763 original size:22 final size:22
Alignment explanation
Indices: 10130735--10130777 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
10130725 ATACCTAATT
**
10130735 TTTTCTTTTTTTTCCTTCCTTC
1 TTTTCTTTTCCTTCCTTCCTTC
10130757 TTTTCTTTTCCTTCCTTCCTT
1 TTTTCTTTTCCTTCCTTCCTT
10130778 ATTATTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTCTTTTCCTTCCTTCCTTC
Found at i:10130767 original size:18 final size:17
Alignment explanation
Indices: 10130737--10130774 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
10130727 ACCTAATTTT
10130737 TTCTTTTTTTTCCTTCC
1 TTCTTTTTTTTCCTTCC
10130754 TTCTTTTCTTTTCCTTCC
1 TTCTTTT-TTTTCCTTCC
10130772 TTC
1 TTC
10130775 CTTATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
TTCTTTTTTTTCCTTCC
Found at i:10130895 original size:27 final size:27
Alignment explanation
Indices: 10130846--10130948 Score: 136
Period size: 27 Copynumber: 3.8 Consensus size: 27
10130836 AAAATAACAG
* *
10130846 CATTGGCGCCTCTCA-GAATGGCACCAC
1 CATTGGCGCCTCCCAGGTA-GGCACCAC
*
10130873 CATTGGCGCTTCCCAGGTAGGCACCAC
1 CATTGGCGCCTCCCAGGTAGGCACCAC
*
10130900 CATTGGCGCCTCCTAGGTAGGCACCAC
1 CATTGGCGCCTCCCAGGTAGGCACCAC
* *
10130927 TATTGGCGCCTCCCAGATAGGC
1 CATTGGCGCCTCCCAGGTAGGC
10130949 GCCAATACTA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 65 0.97
28 2 0.03
ACGTcount: A:0.19, C:0.36, G:0.25, T:0.19
Consensus pattern (27 bp):
CATTGGCGCCTCCCAGGTAGGCACCAC
Found at i:10135902 original size:3 final size:3
Alignment explanation
Indices: 10135894--10135934 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
10135884 TTTCCAATAT
*
10135894 TTA TTA TTA -TA TTA TTTA TTA TCA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
10135935 TCTATATTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:10135992 original size:22 final size:23
Alignment explanation
Indices: 10135960--10136024 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
10135950 ACGCATTGTT
*
10135960 TTTTTTATATAATATATATATGCA
1 TTTTTT-TATAATATATATACGCA
*
10135984 -TTTTTTAT-ATAGTATACACGCA
1 TTTTTTTATAATA-TATATACGCA
10136006 TTATTTTTATAATATATAT
1 TT-TTTTTATAATATATAT
10136025 GTATATATGC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
21 3 0.09
22 11 0.32
23 6 0.18
24 11 0.32
25 3 0.09
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.54
Consensus pattern (23 bp):
TTTTTTTATAATATATATACGCA
Found at i:10135992 original size:24 final size:24
Alignment explanation
Indices: 10135960--10136024 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
10135950 ACGCATTGTT
*
10135960 TTTTTTATATAATATATATATGCA
1 TTTTTTATATAATATATATACGCA
* *
10135984 TTTTTTATAT-A-GTATACACGCA
1 TTTTTTATATAATATATATACGCA
10136006 TTATTTT-TATAATATATAT
1 TT-TTTTATATAATATATAT
10136025 GTATATATGC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
22 13 0.39
23 6 0.18
24 14 0.42
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.54
Consensus pattern (24 bp):
TTTTTTATATAATATATATACGCA
Found at i:10136037 original size:30 final size:28
Alignment explanation
Indices: 10135989--10136060 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 28
10135979 ATGCATTTTT
10135989 TATATAGTATACACGCATTAT-TTTTATAA
1 TATATAGTATACACGCATT-TCTTTTAT-A
* *
10136018 TATATATGTATATATGCATTTCTTTTATA
1 TATATA-GTATACACGCATTTCTTTTATA
10136047 TAGTATACGTATAC
1 TA-TATA-GTATAC
10136061 CTGTATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 10 0.28
30 26 0.72
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (28 bp):
TATATAGTATACACGCATTTCTTTTATA
Found at i:10136051 original size:54 final size:51
Alignment explanation
Indices: 10135948--10136054 Score: 151
Period size: 51 Copynumber: 2.0 Consensus size: 51
10135938 ATATTCATAC
* * *
10135948 ACACGCATTGTTTTTTTTATATAATATATATATGCATTTTTTATATAGTAT
1 ACACGCATTATTTTTATAATATAATATATATATGCATTTTTTATATAGTAT
*
10135999 ACACGCATTATTTTTATAATATATATGTATATATGCATTTCTTTTATATAGTAT
1 ACACGCATTATTTTTATAATATA-ATATATATATGCA-TT-TTTTATATAGTAT
10136053 AC
1 AC
10136055 GTATACCTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
51 20 0.41
52 12 0.24
53 2 0.04
54 15 0.31
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.50
Consensus pattern (51 bp):
ACACGCATTATTTTTATAATATAATATATATATGCATTTTTTATATAGTAT
Found at i:10137532 original size:3 final size:3
Alignment explanation
Indices: 10137524--10137555 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
10137514 GATTTTGTCC
10137524 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
10137556 CCTACTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:10138715 original size:2 final size:2
Alignment explanation
Indices: 10138710--10138734 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10138700 TGGTGTCAAC
10138710 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
10138735 CATTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10138840 original size:16 final size:16
Alignment explanation
Indices: 10138796--10138841 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 16
10138786 TCCATTATTT
10138796 TATATACATATTGTAAA
1 TATATACATATT-TAAA
10138813 TATATA-AGTATTTAAA
1 TATATACA-TATTTAAA
10138829 TATATACATATTT
1 TATATACATATTT
10138842 TCATGATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (16 bp):
TATATACATATTTAAA
Found at i:10141633 original size:41 final size:41
Alignment explanation
Indices: 10141581--10141676 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
10141571 GATCCTGTCT
*
10141581 CATCATGAACATGGTTGCTTCAACTTTGCATTGTCTTCTCA
1 CATCATGAACATGGTTGCTTCAACGTTGCATTGTCTTCTCA
* *
10141622 CATCATGAACATGGTTGCTTCCACGTTGCATTGTCTTGTCA
1 CATCATGAACATGGTTGCTTCAACGTTGCATTGTCTTCTCA
10141663 CATCATGAACATGG
1 CATCATGAACATGG
10141677 GCATTGTCTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (41 bp):
CATCATGAACATGGTTGCTTCAACGTTGCATTGTCTTCTCA
Found at i:10150832 original size:5 final size:5
Alignment explanation
Indices: 10150822--10150846 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
10150812 CATAATTATG
10150822 AGCTA AGCTA AGCTA AGCTA AGCTA
1 AGCTA AGCTA AGCTA AGCTA AGCTA
10150847 GCTCATTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (5 bp):
AGCTA
Found at i:10157473 original size:246 final size:247
Alignment explanation
Indices: 10157018--10157509 Score: 842
Period size: 246 Copynumber: 2.0 Consensus size: 247
10157008 TTGTTAACTA
*
10157018 AGGAGGGACATAAATTATACATAAGCCCAAAATGAGATATTTTGGGTGGCATAAGCTGAGAAAAA
1 AGGAGGGACATAAATTATACATAAGCCCAAAAGGAGATATTTTGGGTGGCATAAGCTGAGAAAAA
* * * *
10157083 TCAGGAGAATTGGTGAAATAATGGCAAAATGGGAAAATAACAAAATTTACTAAAATAAAAATGAG
66 TCAGGAGAATTGATGAAATAAGGGAAAAATAGGAAAATAACAAAATTTACTAAAATAAAAATGAG
**
10157148 ACCAAATTAGAATATCTAGAATTATCTTCATATTTTGTTCATTATCATCAACCAAAAATGTCCTA
131 ACCAAATTAGAATATCTAGAATTATCTTCATATTTTGTTCATTATCATCAACCAAAAACATCCTA
*
10157213 AGGGTTTATTCAAGCTGGTATTTCATAATTTTTGCACCAAAAAATTTAAATG
196 AGGGTTTATTCAAGCTGGTATTTCATAATTTTTGCACCAAAAAATTCAAATG
* *
10157265 AGGAGGGACATAAATTGTA-TTAAGCCCAAAAGGAGATATTTTGGGTGGCATAAGCTGAGAAAAA
1 AGGAGGGACATAAATTATACATAAGCCCAAAAGGAGATATTTTGGGTGGCATAAGCTGAGAAAAA
10157329 TCAGGAGAATTGATGAAATAAGGGAAAAATAGGAAAATAACAAAATTTACTAAAATAAAAATGAG
66 TCAGGAGAATTGATGAAATAAGGGAAAAATAGGAAAATAACAAAATTTACTAAAATAAAAATGAG
* * * * *
10157394 ACTAAATTATAATATCTGGAATTCTCTTCATATTTTGTTCATTATCATCAGCCAAAAACATCCTA
131 ACCAAATTAGAATATCTAGAATTATCTTCATATTTTGTTCATTATCATCAACCAAAAACATCCTA
10157459 AGGGTTTATTCAAGCTGGTATTTCATAATTTTTGCACCAAAAAATTCAAAT
196 AGGGTTTATTCAAGCTGGTATTTCATAATTTTTGCACCAAAAAATTCAAAT
10157510 ACGAAGCTAG
Statistics
Matches: 230, Mismatches: 15, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
246 212 0.92
247 18 0.08
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (247 bp):
AGGAGGGACATAAATTATACATAAGCCCAAAAGGAGATATTTTGGGTGGCATAAGCTGAGAAAAA
TCAGGAGAATTGATGAAATAAGGGAAAAATAGGAAAATAACAAAATTTACTAAAATAAAAATGAG
ACCAAATTAGAATATCTAGAATTATCTTCATATTTTGTTCATTATCATCAACCAAAAACATCCTA
AGGGTTTATTCAAGCTGGTATTTCATAATTTTTGCACCAAAAAATTCAAATG
Found at i:10157616 original size:21 final size:20
Alignment explanation
Indices: 10157590--10157653 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
10157580 GTTCGTGTAA
10157590 CTTGAATTATATTCTTAAATG
1 CTTGAA-TATATTCTTAAATG
* *
10157611 CTTGAAGTATATT-TTTATTG
1 CTTGAA-TATATTCTTAAATG
*
10157631 ATGTGAATATATTCTTAAATG
1 CT-TGAATATATTCTTAAATG
10157652 CT
1 CT
10157654 CAACCCGAGG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 12 0.35
21 22 0.65
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.48
Consensus pattern (20 bp):
CTTGAATATATTCTTAAATG
Found at i:10174201 original size:20 final size:21
Alignment explanation
Indices: 10174162--10174201 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
10174152 CACCAAGTGA
10174162 AAACATTTACATGAACAACTTC
1 AAACATTTACAT-AACAACTTC
*
10174184 AAACATTTATAT-ACAACT
1 AAACATTTACATAACAACT
10174202 ATGTGTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (21 bp):
AAACATTTACATAACAACTTC
Found at i:10174734 original size:35 final size:36
Alignment explanation
Indices: 10174688--10174852 Score: 173
Period size: 34 Copynumber: 4.8 Consensus size: 36
10174678 TAAAGAGTGT
10174688 GCCCAACACTAGTCAGATAAACTGACAGA-AGTTAC
1 GCCCAACACTAGTCAGATAAACTGACAGATAGTTAC
* * **
10174723 GCCCAACACTAGTCAGA-GAACCGA-AGATAGTTGT
1 GCCCAACACTAGTCAGATAAACTGACAGATAGTTAC
* *
10174757 GCCCAGCACTAGTCAGATAAACTAACAGA-AGTTAC
1 GCCCAACACTAGTCAGATAAACTGACAGATAGTTAC
* * * * *
10174792 GCCCAGCACTAGTCGGAT-AACCGAC-GATAATTAT
1 GCCCAACACTAGTCAGATAAACTGACAGATAGTTAC
10174826 GCCCAGA-ACTAGTCAGATAAACTGACA
1 GCCCA-ACACTAGTCAGATAAACTGACA
10174853 AAATTGCGCC
Statistics
Matches: 105, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
33 5 0.05
34 49 0.47
35 48 0.46
36 3 0.03
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (36 bp):
GCCCAACACTAGTCAGATAAACTGACAGATAGTTAC
Found at i:10174796 original size:69 final size:69
Alignment explanation
Indices: 10174685--10174907 Score: 288
Period size: 69 Copynumber: 3.2 Consensus size: 69
10174675 ATATAAAGAG
* * * *
10174685 TGTGCCCAACACTAGTCAGATAAACTGACAGAAGTTACGCCCAACACTAGTCAGAGAACCGAAGA
1 TGTGCCCAGCACTAGTCAGATAAACTGACAGAAGTTACGCCCAACACTAGTCGGATAACCGACGA
10174750 TAGT
66 TAGT
* *
10174754 TGTGCCCAGCACTAGTCAGATAAACTAACAGAAGTTACGCCCAGCACTAGTCGGATAACCGACGA
1 TGTGCCCAGCACTAGTCAGATAAACTGACAGAAGTTACGCCCAACACTAGTCGGATAACCGACGA
*
10174819 TAAT
66 TAGT
* * * * * * *
10174823 TATGCCCAGAACTAGTCAGATAAACTGACA-AAATTGCG-CCAAGCGCTAGTTGGATAACCGGCG
1 TGTGCCCAGCACTAGTCAGATAAACTGACAGAAGTTACGCCCAA-CACTAGTCGGATAACCGACG
*
10174886 ATGGT
65 ATAGT
10174891 TGTGCCCAGCACTAGTC
1 TGTGCCCAGCACTAGTC
10174908 GAATGAATCA
Statistics
Matches: 133, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
67 3 0.02
68 41 0.31
69 89 0.67
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (69 bp):
TGTGCCCAGCACTAGTCAGATAAACTGACAGAAGTTACGCCCAACACTAGTCGGATAACCGACGA
TAGT
Found at i:10178045 original size:18 final size:18
Alignment explanation
Indices: 10178005--10178045 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
10177995 TTAATCTTTG
10178005 ATTTA-TTATTTTATTTT
1 ATTTATTTATTTTATTTT
*
10178022 AGTTATTTATTTTAATTTT
1 ATTTATTTATTTT-ATTTT
10178041 -TTTAT
1 ATTTAT
10178046 CTGACTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 11 0.55
19 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTATTTATTTTATTTT
Found at i:10183401 original size:42 final size:42
Alignment explanation
Indices: 10183325--10183411 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 42
10183315 CTAGAAGCAC
* * ** *
10183325 TTTCTTGCAACGTATGCTGAAAACATGTCTAGCTTAATGCAT
1 TTTCTTGCAAAGTACGCTGAAAACACATCCAGCTTAATGCAT
* *
10183367 TTTCTTGCAAAGTACGCTGAAAACACATCCAGCTTAGTGCGT
1 TTTCTTGCAAAGTACGCTGAAAACACATCCAGCTTAATGCAT
10183409 TTT
1 TTT
10183412 AAAAAATCTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (42 bp):
TTTCTTGCAAAGTACGCTGAAAACACATCCAGCTTAATGCAT
Found at i:10189176 original size:15 final size:16
Alignment explanation
Indices: 10189151--10189192 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
10189141 TAAACTAAAA
10189151 CAAAGGAGAAATGAA-G
1 CAAA-GAGAAATGAATG
*
10189167 CAAAGAGAAACGAATG
1 CAAAGAGAAATGAATG
10189183 CAAAGA-AAAT
1 CAAAGAGAAAT
10189193 TGATCAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.60, C:0.10, G:0.24, T:0.07
Consensus pattern (16 bp):
CAAAGAGAAATGAATG
Done.