Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013262.1 Kokia drynarioides strain JFW-HI SEQ_128283, whole genome shotgun sequence
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: 264704
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 147 characters in sequence are not A, C, G, or T
Found at i:194 original size:14 final size:15
Alignment explanation
Indices: 175--248 Score: 55
Period size: 14 Copynumber: 5.0 Consensus size: 15
165 AACCTAGCTA
175 ATTAATTACCAAAAT
1 ATTAATTACCAAAAT
*
190 A-TAATATA-AAAAAT
1 ATTAAT-TACCAAAAT
204 AATTAATTACCAAAAT
1 -ATTAATTACCAAAAT
* * **
220 AAT-ATCACCATCAT
1 ATTAATTACCAAAAT
*
234 ATTATTTACCAAAAT
1 ATTAATTACCAAAAT
249 GGTACAAAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 10
0.67 0.17 0.16
Matches are distributed among these distances:
14 19 0.44
15 15 0.35
16 9 0.21
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (15 bp):
ATTAATTACCAAAAT
Found at i:218 original size:16 final size:16
Alignment explanation
Indices: 173--222 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
163 TAAACCTAGC
173 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
*
189 T-A-TAATATA-AAAAA
1 TAATTAAT-TACCAAAA
203 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
219 TAAT
1 TAAT
223 ATCACCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:1594 original size:43 final size:43
Alignment explanation
Indices: 1510--1594 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
1500 ATTAACATGT
* * * *
1510 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCGTGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTACATGTTAC
* *
1553 TAAATTATATTACTTTACTCTTATTAATAT-CTTCACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTT-ACATGTTA
1595 TTAATTGTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 2 0.06
43 33 0.94
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTACATGTTAC
Found at i:2257 original size:21 final size:21
Alignment explanation
Indices: 2231--2274 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2221 GAGTCACTGT
2231 AATACTCTACTCCTCCCGGGC
1 AATACTCTACTCCTCCCGGGC
* *
2252 AATACTCTACTCTTCCGGGGC
1 AATACTCTACTCCTCCCGGGC
2273 AA
1 AA
2275 ATAGACCCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.25
Consensus pattern (21 bp):
AATACTCTACTCCTCCCGGGC
Found at i:2517 original size:14 final size:13
Alignment explanation
Indices: 2494--2567 Score: 62
Period size: 14 Copynumber: 5.4 Consensus size: 13
2484 TTTCATAACA
2494 TTAAACCCTAAACC
1 TTAAA-CCTAAACC
2508 TTAAATCCTAAA-C
1 TTAAA-CCTAAACC
2521 TTAAACCATAAACC
1 TTAAACC-TAAACC
* *
2535 CTAAACATTAAA-C
1 TTAAAC-CTAAACC
2548 TTAAAACCTTAAACC
1 TT-AAACC-TAAACC
2563 TTAAA
1 TTAAA
2568 TATTATACAT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
12 2 0.04
13 12 0.24
14 32 0.65
15 3 0.06
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (13 bp):
TTAAACCTAAACC
Found at i:2526 original size:27 final size:28
Alignment explanation
Indices: 2494--2568 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 28
2484 TTTCATAACA
*
2494 TTAAACCCTAAACCTTAAATC-CTAAAC
1 TTAAACCATAAACCTTAAATCACTAAAC
* *
2521 TTAAACCATAAACCCTAAA-CATTAAAC
1 TTAAACCATAAACCTTAAATCACTAAAC
*
2548 TTAAAACCTTAAACCTTAAAT
1 TT-AAACCATAAACCTTAAAT
2569 ATTATACATG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.03
27 24 0.60
28 15 0.38
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (28 bp):
TTAAACCATAAACCTTAAATCACTAAAC
Found at i:2527 original size:20 final size:20
Alignment explanation
Indices: 2502--2567 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
2492 CATTAAACCC
*
2502 TAAACCTTAAATCCTAAACT
1 TAAACCTTAAAACCTAAACT
* *
2522 TAAACCATAAACCCTAAACAT
1 TAAACCTTAAAACCTAAAC-T
2543 TAAA-CTTAAAACCTTAAACCT
1 TAAACCTTAAAACC-TAAA-CT
2564 TAAA
1 TAAA
2568 TATTATACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
20 24 0.62
21 14 0.36
22 1 0.03
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAACCTTAAAACCTAAACT
Found at i:5574 original size:4 final size:4
Alignment explanation
Indices: 5565--5622 Score: 82
Period size: 4 Copynumber: 14.5 Consensus size: 4
5555 AAACACATTA
*
5565 TCTT TCTT TCAT TC-T TCTT TCTT TCTT TCTT TCTT TCTT TCTTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TC-TT TCTT
*
5613 TATT TCTT TC
1 TCTT TCTT TC
5623 CCGTTTATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
3 3 0.06
4 42 0.86
5 4 0.08
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.72
Consensus pattern (4 bp):
TCTT
Found at i:10612 original size:24 final size:24
Alignment explanation
Indices: 10578--10624 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
10568 TTTAGAATTT
*
10578 TTTTTAAATATTTATTGTTTTTTA
1 TTTTTAAATATTTATTATTTTTTA
* *
10602 TTTTTATATATTTTTTATTTTTT
1 TTTTTAAATATTTATTATTTTTT
10625 GAATAGTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (24 bp):
TTTTTAAATATTTATTATTTTTTA
Found at i:12262 original size:29 final size:30
Alignment explanation
Indices: 12230--12290 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
12220 TAAATAAATA
12230 TAAGTATTTA-TTTAAATTGTGTTTAACTT
1 TAAGTATTTATTTTAAATTGTGTTTAACTT
12259 TAAGTATTTATTTTAAATTGTGTTTAACTT
1 TAAGTATTTATTTTAAATTGTGTTTAACTT
12289 TA
1 TA
12291 TTTATCACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (30 bp):
TAAGTATTTATTTTAAATTGTGTTTAACTT
Found at i:12939 original size:5 final size:6
Alignment explanation
Indices: 12923--12947 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12913 TTCGTCAAAA
12923 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
12948 CTTCGCGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:17910 original size:22 final size:23
Alignment explanation
Indices: 17866--17910 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
17856 AAAAATAAAA
* *
17866 AATAATAAAAATTATTAAATTTT
1 AATAATAAAAACTATGAAATTTT
*
17889 AATAA-AAAAACTATGAATTTTT
1 AATAATAAAAACTATGAAATTTT
17911 TTAATTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AATAATAAAAACTATGAAATTTT
Found at i:17944 original size:20 final size:19
Alignment explanation
Indices: 17921--17966 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
17911 TTAATTTTAT
17921 TAAAATTAGAAAAAAAATTA
1 TAAAATTAG-AAAAAAATTA
* *
17941 TAAAAATAGTAAAAAATTA
1 TAAAATTAGAAAAAAATTA
17960 TAAAATT
1 TAAAATT
17967 TTATAAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (19 bp):
TAAAATTAGAAAAAAATTA
Found at i:17945 original size:10 final size:10
Alignment explanation
Indices: 17932--18010 Score: 53
Period size: 10 Copynumber: 8.2 Consensus size: 10
17922 AAAATTAGAA
17932 AAAAAATTAT
1 AAAAAATTAT
17942 -AAAAA-TAGT
1 AAAAAATTA-T
17951 AAAAAATTAT
1 AAAAAATTAT
*
17961 --AAAATTTT
1 AAAAAATTAT
* **
17969 ATAAAATCGT
1 AAAAAATTAT
17979 AAGAAAATTAT
1 AA-AAAATTAT
17990 AAAAAATGTA-
1 AAAAAAT-TAT
18000 AAAAAA-TAT
1 AAAAAATTAT
18009 AA
1 AA
18011 TTTTTTTTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
8 11 0.20
9 8 0.15
10 24 0.44
11 12 0.22
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:17986 original size:21 final size:20
Alignment explanation
Indices: 17961--18010 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
17951 AAAAAATTAT
* * *
17961 AAAATTTTATAAAATCGTAAG
1 AAAATTATAAAAAAT-GTAAA
17982 AAAATTATAAAAAATGTAAA
1 AAAATTATAAAAAATGTAAA
18002 AAAA-TATAA
1 AAAATTATAA
18011 TTTTTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 5 0.19
20 8 0.31
21 13 0.50
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (20 bp):
AAAATTATAAAAAATGTAAA
Found at i:18004 original size:19 final size:18
Alignment explanation
Indices: 17932--18010 Score: 61
Period size: 19 Copynumber: 4.1 Consensus size: 18
17922 AAAATTAGAA
17932 AAAAAATTATAAAAA-TAGT
1 AAAAAATTA-AAAAATTA-T
* *
17951 AAAAAATTATAAAATTTT
1 AAAAAATTAAAAAATTAT
*
17969 ATAAAATCGTAAGAAAATTAT
1 AAAAAAT--TAA-AAAATTAT
*
17990 AAAAAATGTAAAAAAATAT
1 AAAAAAT-TAAAAAATTAT
18009 AA
1 AA
18011 TTTTTTTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
18 11 0.22
19 19 0.39
20 6 0.12
21 13 0.27
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAAAATTAAAAAATTAT
Found at i:18250 original size:21 final size:20
Alignment explanation
Indices: 18226--18267 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
18216 TTTATAAAAG
18226 TTTACAATTTTTTATAATTTT
1 TTTACAA-TTTTTATAATTTT
* *
18247 TTTACGATTTTTATTATTTT
1 TTTACAATTTTTATAATTTT
18267 T
1 T
18268 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTACAATTTTTATAATTTT
Found at i:18274 original size:18 final size:18
Alignment explanation
Indices: 18234--18304 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 18
18224 AGTTTACAAT
*
18234 TTTTTATAATTTTTTTACGA
1 TTTTTATAATTTTTATA--A
*
18254 TTTTTATTATTTTTATAA
1 TTTTTATAATTTTTATAA
*
18272 TTTTTAATAAATTTTATAA
1 TTTTT-ATAATTTTTATAA
*
18291 CTTTTATATATTTT
1 TTTTTATA-ATTTT
18305 ATTTATAGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 9 0.21
19 19 0.44
20 15 0.35
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (18 bp):
TTTTTATAATTTTTATAA
Found at i:18281 original size:10 final size:9
Alignment explanation
Indices: 18234--18304 Score: 70
Period size: 9 Copynumber: 7.4 Consensus size: 9
18224 AGTTTACAAT
18234 TTTTTATAA
1 TTTTTATAA
*
18243 TTTTTTTACGA
1 TTTTTATA--A
*
18254 TTTTTATTA
1 TTTTTATAA
18263 TTTTTATAA
1 TTTTTATAA
18272 TTTTTAATAA
1 TTTTT-ATAA
*
18282 ATTTTATAA
1 TTTTTATAA
*
18291 CTTTTATATA
1 TTTTTATA-A
18301 TTTT
1 TTTT
18305 ATTTATAGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
9 32 0.63
10 12 0.24
11 7 0.14
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:18285 original size:29 final size:28
Alignment explanation
Indices: 18214--18304 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 28
18204 TTTTTATGCT
* * *
18214 TTTTTATAAAAGTTTACAATTTTTTATAA
1 TTTTTATACAATTTTATAA-TTTTTATAA
* * *
18243 TTTTTTTACGATTTTTATTATTTTTATAA
1 TTTTTATAC-AATTTTATAATTTTTATAA
*
18272 TTTTTAATA-AATTTTATAACTTTTATATA
1 TTTTT-ATACAATTTTATAATTTTTATA-A
18301 TTTT
1 TTTT
18305 ATTTATAGTT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
28 15 0.31
29 26 0.53
30 8 0.16
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTTTATACAATTTTATAATTTTTATAA
Found at i:18596 original size:89 final size:88
Alignment explanation
Indices: 18420--18643 Score: 316
Period size: 89 Copynumber: 2.6 Consensus size: 88
18410 ATGACCAGAA
* * * *
18420 GGTCGTTTTGATGTA-TTT-AACAGTTCAAGTATCCAATTGAGTG--AAAAAAACAGGGGTTTAA
1 GGTCTTTTTGATGCATTTTGAA-AGTTCAAGTATCCAATTGAGTGCAAAAAAAACAGGAGCTTAA
*
18481 TTGCTTTTTTTGAAAAAGTTTGAG
65 TTGATTTTTTTGAAAAAGTTTGAG
18505 GGT-TCTTTTGATGCATTTTGAAAGTTCAAGTATCCAATTGAGTGCAAAAAAAGGACAGGAGCTT
1 GGTCT-TTTTGATGCATTTTGAAAGTTCAAGTATCCAATTGAGTGCAAAAAAA--ACAGGAGCTT
18569 AATT-ATTTTTTTGAAAAAGTTTGAG
63 AATTGATTTTTTTGAAAAAGTTTGAG
*
18594 GGTCTTTTTGATGCATTTTGAAAGTTCAAGTATTCAATTGAGTGCAAAAA
1 GGTCTTTTTGATGCATTTTGAAAGTTCAAGTATCCAATTGAGTGCAAAAA
18644 GAAAGGCTTT
Statistics
Matches: 125, Mismatches: 6, Indels: 12
0.87 0.04 0.08
Matches are distributed among these distances:
85 12 0.10
86 25 0.20
87 2 0.02
88 6 0.05
89 67 0.54
90 13 0.10
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (88 bp):
GGTCTTTTTGATGCATTTTGAAAGTTCAAGTATCCAATTGAGTGCAAAAAAAACAGGAGCTTAAT
TGATTTTTTTGAAAAAGTTTGAG
Found at i:23926 original size:23 final size:24
Alignment explanation
Indices: 23883--23927 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
23873 ACCCAAATCT
* *
23883 AATTTTAAAAATTACTTTTATACA
1 AATTATAAAAATTACTATTATACA
23907 AATTATAAAAATTA-TATTATA
1 AATTATAAAAATTACTATTATA
23928 AGCATGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
AATTATAAAAATTACTATTATACA
Found at i:37163 original size:3 final size:3
Alignment explanation
Indices: 37155--37183 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
37145 CTCTACATGT
37155 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
37184 TGCCAATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:37660 original size:42 final size:42
Alignment explanation
Indices: 37613--37886 Score: 178
Period size: 42 Copynumber: 6.5 Consensus size: 42
37603 TCGGTTTAGC
* **
37613 CGATGATGCACTTATGTGCTAGTATAATTGCTTCGGCATATT
1 CGATGATGCACTTATGTGCCAGTATAATTGCTTCGATATATT
** * ** * *
37655 CGATGATGCACTTACATGCCAATAT-ATTTTTTCGGTACA-T
1 CGATGATGCACTTATGTGCCAGTATAATTGCTTCGATATATT
* * * *
37695 CTGATGATGCACTAACGTGCTAGTATAATTGCATCGATATATT
1 C-GATGATGCACTTATGTGCCAGTATAATTGCTTCGATATATT
* * * * * * * * *
37738 CAATGATGCA-GTATGTACTAGTATATTTTCTTCAATACATC
1 CGATGATGCACTTATGTGCCAGTATAATTGCTTCGATATATT
* * * *
37779 CGATGATGCACTTACGTACCAATATAATTGCTTCAATATATT
1 CGATGATGCACTTATGTGCCAGTATAATTGCTTCGATATATT
* * * ** * *
37821 CAATGATGTACTTACT-TGCCAGTATATTTTTTTCGGATACATC
1 CGATGATGCACTTA-TGTGCCAGTATAATTGCTTC-GATATATT
*
37864 CAATGATGCACTTATGTGCCAGT
1 CGATGATGCACTTATGTGCCAGT
37887 GTGATTACTT
Statistics
Matches: 176, Mismatches: 49, Indels: 13
0.74 0.21 0.05
Matches are distributed among these distances:
40 2 0.01
41 60 0.34
42 87 0.49
43 27 0.15
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (42 bp):
CGATGATGCACTTATGTGCCAGTATAATTGCTTCGATATATT
Found at i:37737 original size:83 final size:83
Alignment explanation
Indices: 37612--37882 Score: 301
Period size: 83 Copynumber: 3.2 Consensus size: 83
37602 TTCGGTTTAG
* ** * *
37612 CCGATGATGCACTTATGTGCTAGTATAATTGCTTCGGCATATTCGATGATGCACTTACATGCCAA
1 CCGATGATGCACTTACGTGCTAGTATAATTGCTTCGATATATTCAATGATGCACTTACATGCCAG
37677 TATATTTTTTCGGTACAT
66 TATATTTTTTCGGTACAT
* * * * ** * *
37695 CTGATGATGCACTAACGTGCTAGTATAATTGCATCGATATATTCAATGATGCA-GTATGTACTAG
1 CCGATGATGCACTTACGTGCTAGTATAATTGCTTCGATATATTCAATGATGCACTTACATGCCAG
**
37759 TATATTTTCTTCAATACAT
66 TATATTTT-TTCGGTACAT
* * * * * *
37778 CCGATGATGCACTTACGTACCAATATAATTGCTTCAATATATTCAATGATGTACTTACTTGCCAG
1 CCGATGATGCACTTACGTGCTAGTATAATTGCTTCGATATATTCAATGATGCACTTACATGCCAG
37843 TATATTTTTTTCGGATACAT
66 TATA-TTTTTTCGG-TACAT
* *
37863 CCAATGATGCACTTATGTGC
1 CCGATGATGCACTTACGTGC
37883 CAGTGTGATT
Statistics
Matches: 151, Mismatches: 33, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
82 13 0.09
83 99 0.66
84 13 0.09
85 26 0.17
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (83 bp):
CCGATGATGCACTTACGTGCTAGTATAATTGCTTCGATATATTCAATGATGCACTTACATGCCAG
TATATTTTTTCGGTACAT
Found at i:37912 original size:85 final size:84
Alignment explanation
Indices: 37657--37922 Score: 198
Period size: 83 Copynumber: 3.2 Consensus size: 84
37647 GGCATATTCG
* * ** ** * * * *
37657 ATGATGCACTTACATGCCAATATATTTT-TTCGGTACATCTGATGATGCACTAACGTGCTAGTAT
1 ATGATGCACTTACTTGCCAGTATATTTTCTTCAATACATCCAATGATGCACTTACGTACCAATAT
* * * *
37721 AATTGCATCGATATATTCA
66 AATTACTTCAATATACTCA
* * * *
37740 ATGATGCA-GTA-TGTACTAGTATATTTTCTTCAATACATCCGATGATGCACTTACGTACCAATA
1 ATGATGCACTTACT-TGCCAGTATATTTTCTTCAATACATCCAATGATGCACTTACGTACCAATA
* *
37803 TAATTGCTTCAATATATTCA
65 TAATTACTTCAATATACTCA
* * * * * * *
37823 ATGATGTACTTACTTGCCAGTATATTTTTTTCGGATACATCCAATGATGCACTTATGTGCCAGTG
1 ATGATGCACTTACTTGCCAGTATATTTTCTTC-AATACATCCAATGATGCACTTACGTACCAATA
* * *
37888 TGATTACTTCAATTTAACT-G
65 TAATTACTTCAATAT-ACTCA
*
37908 ATGATGCATTTACTT
1 ATGATGCACTTACTT
37923 ACCATGAATA
Statistics
Matches: 145, Mismatches: 32, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
82 13 0.09
83 61 0.42
84 17 0.12
85 52 0.36
86 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (84 bp):
ATGATGCACTTACTTGCCAGTATATTTTCTTCAATACATCCAATGATGCACTTACGTACCAATAT
AATTACTTCAATATACTCA
Found at i:41005 original size:11 final size:11
Alignment explanation
Indices: 40986--41019 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
40976 ATTTTGTTTA
40986 ATTTAATTTTT
1 ATTTAATTTTT
*
40997 ATTTTATTTTTT
1 A-TTTAATTTTT
41009 ATTTAATTTTT
1 ATTTAATTTTT
41020 TTATTTAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
ATTTAATTTTT
Found at i:41020 original size:12 final size:12
Alignment explanation
Indices: 40970--41026 Score: 62
Period size: 13 Copynumber: 4.6 Consensus size: 12
40960 TTATTTTAAG
*
40970 TTATTTATTTTGT
1 TTATTTAATTT-T
40983 TTAATTTAA-TTT
1 TT-ATTTAATTTT
*
40995 TTATTTTATTTT
1 TTATTTAATTTT
41007 TTATTTAATTTTT
1 TTATTTAA-TTTT
41020 TTATTTA
1 TTATTTA
41027 GTTTAGTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
11 5 0.13
12 13 0.34
13 15 0.39
14 5 0.13
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (12 bp):
TTATTTAATTTT
Found at i:41339 original size:47 final size:47
Alignment explanation
Indices: 41253--41342 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 47
41243 GGTGTGGATA
* *
41253 CCATTTTGGTATATAAATATTTATTTTATATCATTTTGATAAATAAC
1 CCATTTTGATATATAAATATTTATTTTATATCATATTGATAAATAAC
* * *
41300 CCATTTTGATATATAATTA-TTATTTTTTTATTATATTGATAAA
1 CCATTTTGATATATAAATATTTA-TTTTATATCATATTGATAAA
41343 AAATTATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
46 3 0.08
47 34 0.92
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.52
Consensus pattern (47 bp):
CCATTTTGATATATAAATATTTATTTTATATCATATTGATAAATAAC
Found at i:43288 original size:43 final size:42
Alignment explanation
Indices: 43224--43327 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 42
43214 TGTTATTCAC
* *
43224 TGACATGTTATTAAATTATATTACTTGACTAGTCTTAATATGG
1 TGACATGTTA-TAAATTATATTACTTGACTAGTATTAATATCG
* * **
43267 TGGCATGTTACTAAATTATATTACTTTACTCTTATTAATATCG
1 TGACATGTTA-TAAATTATATTACTTGACTAGTATTAATATCG
*
43310 TGACATGTTATTAATTAT
1 TGACATGTTATAAATTAT
43328 GCAGTTCATC
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
42 7 0.13
43 45 0.87
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.46
Consensus pattern (42 bp):
TGACATGTTATAAATTATATTACTTGACTAGTATTAATATCG
Found at i:43793 original size:6 final size:6
Alignment explanation
Indices: 43784--43830 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
43774 CCTCAGAGCT
* * *
43784 AGAGCA AGAGCA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA GGAGG
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGG
43831 CATCGAATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.47, C:0.04, G:0.49, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:43799 original size:12 final size:12
Alignment explanation
Indices: 43778--43825 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
43768 CTCCTACCTC
* *
43778 AGAGCTAGAGCA
1 AGAGCAAGAGGA
43790 AGAGCAAGAGGA
1 AGAGCAAGAGGA
*
43802 AGAGGAAGAGGA
1 AGAGCAAGAGGA
*
43814 AGAGGAAGAGGA
1 AGAGCAAGAGGA
43826 GGAGGCATCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.48, C:0.06, G:0.44, T:0.02
Consensus pattern (12 bp):
AGAGCAAGAGGA
Found at i:44360 original size:7 final size:7
Alignment explanation
Indices: 44348--44532 Score: 75
Period size: 7 Copynumber: 24.7 Consensus size: 7
44338 TATGCATAAA
44348 TTAAACC
1 TTAAACC
44355 TTAAA-C
1 TTAAACC
44361 TCTAAACC
1 T-TAAACC
*
44369 CTAAACC
1 TTAAACC
*
44376 TTAAATC
1 TTAAACC
44383 TTAAAAACC
1 TT--AAACC
**
44392 CAAAACC
1 TTAAACC
*
44399 TTAAAACA
1 TT-AAACC
*
44407 TTAAACT
1 TTAAACC
44414 TTAAAAACC
1 TT--AAACC
44423 TTAAACC
1 TTAAACC
*
44430 TTAAATC
1 TTAAACC
* *
44437 TAAAATC
1 TTAAACC
44444 TTAAAACC
1 TT-AAACC
**
44452 CAAAACC
1 TTAAACC
**
44459 CAAAACC
1 TTAAACC
*
44466 TTAAAACA
1 TT-AAACC
44474 TTAAACC
1 TTAAACC
44481 TTGAAAACC
1 TT--AAACC
44490 TTAAATCC
1 TTAAA-CC
* *
44498 TAAATAATC
1 T-TA-AACC
*
44507 ATAAACC
1 TTAAACC
44514 TTAAACC
1 TTAAACC
*
44521 TTGAACC
1 TTAAACC
*
44528 ATAAA
1 TTAAA
44533 AATCCACGAA
Statistics
Matches: 134, Mismatches: 30, Indels: 28
0.70 0.16 0.15
Matches are distributed among these distances:
6 2 0.01
7 90 0.67
8 21 0.16
9 19 0.14
10 2 0.01
ACGTcount: A:0.50, C:0.24, G:0.01, T:0.25
Consensus pattern (7 bp):
TTAAACC
Found at i:44420 original size:16 final size:16
Alignment explanation
Indices: 44371--44434 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 16
44361 TCTAAACCCT
* *
44371 AAACCTTAAATCTTAA
1 AAACATTAAACCTTAA
***
44387 AAACCCAAAACCTT-A
1 AAACATTAAACCTTAA
*
44402 AAACATTAAACTTTAA
1 AAACATTAAACCTTAA
*
44418 AAACCTTAAACCTTAA
1 AAACATTAAACCTTAA
44434 A
1 A
44435 TCTAAAATCT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
15 11 0.29
16 27 0.71
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (16 bp):
AAACATTAAACCTTAA
Found at i:44450 original size:22 final size:22
Alignment explanation
Indices: 44393--44494 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
44383 TTAAAAACCC
*
44393 AAAACCTTAAAACATTAAACTTT
1 AAAACCTTAAAACATTAAA-TCT
*
44416 AAAAACCTT-AAACCTTAAATCT
1 -AAAACCTTAAAACATTAAATCT
* *** * *
44438 AAAATCTTAAAACCCAAAACCC
1 AAAACCTTAAAACATTAAATCT
*
44460 AAAACCTTAAAACATTAAACCTT
1 AAAACCTTAAAACATTAAATC-T
44483 GAAAACCTTAAA
1 -AAAACCTTAAA
44495 TCCTAAATAA
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
21 7 0.11
22 28 0.44
23 9 0.14
24 19 0.30
ACGTcount: A:0.53, C:0.23, G:0.01, T:0.24
Consensus pattern (22 bp):
AAAACCTTAAAACATTAAATCT
Found at i:44471 original size:15 final size:15
Alignment explanation
Indices: 44350--44501 Score: 82
Period size: 15 Copynumber: 10.1 Consensus size: 15
44340 TGCATAAATT
44350 AAACCTT-AAACTCT-
1 AAACCTTAAAAC-CTA
* *
44364 AAACCCT-AAACCTT
1 AAACCTTAAAACCTA
* *
44378 AAATCTTAAAAACCCA
1 AAACCTT-AAAACCTA
* *
44394 AAACCTTAAAACATT
1 AAACCTTAAAACCTA
* *
44409 AAACTTTAAAAACCTT
1 AAACCTT-AAAACCTA
*
44425 AAACCTT-AAATCTA
1 AAACCTTAAAACCTA
* *
44439 AAATCTTAAAACCCA
1 AAACCTTAAAACCTA
*
44454 AAACC-CAAAACCTTA
1 AAACCTTAAAACC-TA
*
44469 AAACATT-AAACCTTGA
1 AAACCTTAAAACC-T-A
*
44485 AAACCTTAAATCCTA
1 AAACCTTAAAACCTA
44500 AA
1 AA
44502 TAATCATAAA
Statistics
Matches: 105, Mismatches: 24, Indels: 17
0.72 0.16 0.12
Matches are distributed among these distances:
13 2 0.02
14 32 0.30
15 35 0.33
16 32 0.30
17 4 0.04
ACGTcount: A:0.51, C:0.25, G:0.01, T:0.24
Consensus pattern (15 bp):
AAACCTTAAAACCTA
Found at i:44478 original size:30 final size:30
Alignment explanation
Indices: 44364--44478 Score: 92
Period size: 30 Copynumber: 3.8 Consensus size: 30
44354 CTTAAACTCT
* *
44364 AAACCCTAAACCTTAAATCTTAAAAACCCA
1 AAACCCAAAACCTTAAAACTTAAAAACCCA
* * **
44394 AAACCTTAAAACATT-AAACTTTAAAAACCTT
1 AAACC-CAAAACCTTAAAAC-TTAAAAACCCA
** *
44425 AAACCTTAAATC-TAAAATCTT-AAAACCCA
1 AAACCCAAAACCTTAAAA-CTTAAAAACCCA
44454 AAACCCAAAACCTTAAAACATTAAA
1 AAACCCAAAACCTTAAAAC-TTAAA
44479 CCTTGAAAAC
Statistics
Matches: 64, Mismatches: 14, Indels: 13
0.70 0.15 0.14
Matches are distributed among these distances:
29 17 0.27
30 24 0.38
31 23 0.36
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.23
Consensus pattern (30 bp):
AAACCCAAAACCTTAAAACTTAAAAACCCA
Found at i:44478 original size:60 final size:59
Alignment explanation
Indices: 44347--44501 Score: 163
Period size: 60 Copynumber: 2.6 Consensus size: 59
44337 TTATGCATAA
* * * * *
44347 ATTAAACCTTAAA-CTCTAAACCCTAAACCTTAAATCTTAAAAACCCAAAACCTTAAAAC
1 ATTAAACATTAAACCT-TAAACCTTAAATCTAAAATCTTAAAAACCCAAAACCTCAAAAC
*
44406 ATTAAACTTTAAAAACCTTAAACCTTAAATCTAAAATCTT-AAAACCCAAAACC-CAAAAC
1 ATTAAACATT--AAACCTTAAACCTTAAATCTAAAATCTTAAAAACCCAAAACCTCAAAAC
*
44465 CTTAAAACATTAAACCTTGAAAACCTTAAATCCTAAA
1 ATT-AAACATTAAACCTT--AAACCTTAAAT-CTAAA
44502 TAATCATAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
58 7 0.09
59 16 0.20
60 30 0.37
61 27 0.33
62 2 0.02
ACGTcount: A:0.50, C:0.25, G:0.01, T:0.25
Consensus pattern (59 bp):
ATTAAACATTAAACCTTAAACCTTAAATCTAAAATCTTAAAAACCCAAAACCTCAAAAC
Found at i:44490 original size:9 final size:8
Alignment explanation
Indices: 44371--44494 Score: 77
Period size: 7 Copynumber: 16.2 Consensus size: 8
44361 TCTAAACCCT
44371 AAACCTT-
1 AAACCTTA
*
44378 AAATCTTAA
1 AAACCTT-A
*
44387 AAACC-CA
1 AAACCTTA
44394 AAACCTTA
1 AAACCTTA
*
44402 AAACATT-
1 AAACCTTA
*
44409 AAACTTTAA
1 AAACCTT-A
44418 AAACCTT-
1 AAACCTTA
44425 AAACCTT-
1 AAACCTTA
*
44432 AAATC-TA
1 AAACCTTA
*
44439 AAATCTTA
1 AAACCTTA
*
44447 AAACC-CA
1 AAACCTTA
*
44454 AAACC-CA
1 AAACCTTA
44461 AAACCTTA
1 AAACCTTA
*
44469 AAACATT-
1 AAACCTTA
44476 AAACCTTGA
1 AAACCTT-A
44485 AAACCTTA
1 AAACCTTA
44493 AA
1 AA
44495 TCCTAAATAA
Statistics
Matches: 94, Mismatches: 13, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
6 1 0.01
7 53 0.56
8 23 0.24
9 17 0.18
ACGTcount: A:0.52, C:0.23, G:0.01, T:0.23
Consensus pattern (8 bp):
AAACCTTA
Found at i:44493 original size:16 final size:15
Alignment explanation
Indices: 44461--44518 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
44451 CCAAAACCCA
44461 AAACCTTAAAACATT
1 AAACCTTAAAACATT
*
44476 AAACCTTGAAAACCTT
1 AAACCTT-AAAACATT
*
44492 AAATCCTAAATAATCA-T
1 AAA-CCTTAA-AA-CATT
44509 AAACCTTAAA
1 AAACCTTAAA
44519 CCTTGAACCA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 8 0.23
16 17 0.49
17 9 0.26
18 1 0.03
ACGTcount: A:0.52, C:0.21, G:0.02, T:0.26
Consensus pattern (15 bp):
AAACCTTAAAACATT
Found at i:44711 original size:26 final size:26
Alignment explanation
Indices: 44671--44722 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
44661 CCCTAAACCA
*
44671 AAATACAAACATAAAAATTATTAATT
1 AAATACAAACATAAAAATAATTAATT
** *
44697 AAATACAAATTTAAACATAATTAATT
1 AAATACAAACATAAAAATAATTAATT
44723 CCAAATTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATACAAACATAAAAATAATTAATT
Found at i:48587 original size:24 final size:23
Alignment explanation
Indices: 48560--48619 Score: 93
Period size: 24 Copynumber: 2.6 Consensus size: 23
48550 CTAATGTGAG
48560 AAAAAATTAAAATCAATATGAGAA
1 AAAAAATTAAAATCAATATGA-AA
48584 AAAAAATTAAAATCAATATGAAA
1 AAAAAATTAAAATCAATATGAAA
* *
48607 AAAAGACTAAAAT
1 AAAAAATTAAAAT
48620 ATTACTTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 13 0.38
24 21 0.62
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (23 bp):
AAAAAATTAAAATCAATATGAAA
Found at i:56874 original size:31 final size:30
Alignment explanation
Indices: 56801--56874 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
56791 AATTAGGATT
** * *
56801 AATAAAACATTTTGAATAATTCGTAATTAA
1 AATAAAATTTTTTGAATAATTCATAATCAA
56831 AATAAAATTTTTTGAATAATTCAATAATCAA
1 AATAAAATTTTTTGAATAATTC-ATAATCAA
* *
56862 ATTATAATTTTTT
1 AATAAAATTTTTT
56875 TAATTAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 20 0.54
31 17 0.46
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (30 bp):
AATAAAATTTTTTGAATAATTCATAATCAA
Found at i:59503 original size:33 final size:30
Alignment explanation
Indices: 59440--59514 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 30
59430 AAAAAAATTT
*
59440 GAATTTTGAGTTAATCGAATCGAGTTATTC
1 GAATTTTGAGTTAATCGAATCGACTTATTC
59470 GAATTATTCGAGTTAATTCGAAT-GACTTGATTC
1 GAATT-TT-GAGTTAA-TCGAATCGACTT-ATTC
**
59503 GAGCTTTGAGTT
1 GAATTTTGAGTT
59515 CGAGTCGAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
30 5 0.13
31 7 0.18
32 13 0.34
33 13 0.34
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (30 bp):
GAATTTTGAGTTAATCGAATCGACTTATTC
Found at i:65128 original size:14 final size:14
Alignment explanation
Indices: 65105--65143 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
65095 TTGTTCCATT
65105 GAAAATGATTTTCG
1 GAAAATGATTTTCG
* *
65119 GAATATGATTTTTG
1 GAAAATGATTTTCG
65133 GAAAATGATTT
1 GAAAATGATTT
65144 ACTTTTTCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.41
Consensus pattern (14 bp):
GAAAATGATTTTCG
Found at i:65366 original size:21 final size:20
Alignment explanation
Indices: 65324--65384 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
65314 AGTTTATTTA
* **
65324 TATTTTAATTAATCATGTTT
1 TATTTTAATTAATCTTAATT
65344 TAGTTTTAATTAATCTTAATT
1 TA-TTTTAATTAATCTTAATT
* *
65365 TA-CTTAATTAAGCTTAATT
1 TATTTTAATTAATCTTAATT
65384 T
1 T
65385 CTAATTTCGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 16 0.46
20 2 0.06
21 17 0.49
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
TATTTTAATTAATCTTAATT
Found at i:86614 original size:21 final size:22
Alignment explanation
Indices: 86590--86630 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
86580 TTTTGACACT
*
86590 TTATTTTAT-AAATTTCAAATA
1 TTATTTGATAAAATTTCAAATA
86611 TTATTTGATAAAATTTCAAA
1 TTATTTGATAAAATTTCAAA
86631 ACTTTTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (22 bp):
TTATTTGATAAAATTTCAAATA
Found at i:99528 original size:237 final size:238
Alignment explanation
Indices: 99086--99545 Score: 701
Period size: 237 Copynumber: 1.9 Consensus size: 238
99076 AAAAATAAAA
*
99086 ATCAATCTAGCCCATCTCAAGGAAGGCTATACACATGATGGCTTAAAATAAAAACAAACAATAAT
1 ATCAATCTAGCCCATCTCAAGGAAGGCTATACACATAATGGCTTAAAATAAAAACAAACAATAAT
* *
99151 TGTGCACAGCACAGTAATTAGGTCCATGTTACACCAAAGCTAAATATTTTGCTAAATACCCAGGA
66 TGTGCACAGCACAGTAATTAGGTCCATATTACACCAAAGCTAAATATTTTGATAAATACCCAGGA
* *
99216 TACATATTTGCTATAGAAGTGCATGTAATAACGAACAACATGTAATTTATACCTACAAAAGGAAC
131 TACATATTTGCTAGAGAAGTACATGTAATAACGAACAACATGTAATTTATACCTACAAAAGGAAC
99281 CCTAAAGAATACAAAAGAATCTACTCTAATACAAATAATGAAT
196 CCTAAAGAATACAAAAGAATCTACTCTAATACAAATAATGAAT
* * * * *
99324 ATCAATCTAGCCTATCTTAAGGAA-GTTATACACATAATGG-TTAAAAATACAAAGAAACAATAA
1 ATCAATCTAGCCCATCTCAAGGAAGGCTATACACATAATGGCTT-AAAATAAAAACAAACAATAA
* * *
99387 TTGTTCACAGCATAGTAATTAGGTCCATATTACA-CAGAGCTAAATATTTTGATAAATACCCAGG
65 TTGTGCACAGCACAGTAATTAGGTCCATATTACACCAAAGCTAAATATTTTGATAAATACCCAGG
** * * * *
99451 ATATTGTCTTTGCTAGAGAAGTACATGTAATAATGAACAATATGTCATTTATACCTACAAAAGGA
130 ATA-CATATTTGCTAGAGAAGTACATGTAATAACGAACAACATGTAATTTATACCTACAAAAGGA
*
99516 ACCCTAAAGAATACAAAAGAATCTTCTCTA
194 ACCCTAAAGAATACAAAAGAATCTACTCTA
99546 TTGTAGTATA
Statistics
Matches: 200, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
236 33 0.17
237 145 0.73
238 22 0.11
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (238 bp):
ATCAATCTAGCCCATCTCAAGGAAGGCTATACACATAATGGCTTAAAATAAAAACAAACAATAAT
TGTGCACAGCACAGTAATTAGGTCCATATTACACCAAAGCTAAATATTTTGATAAATACCCAGGA
TACATATTTGCTAGAGAAGTACATGTAATAACGAACAACATGTAATTTATACCTACAAAAGGAAC
CCTAAAGAATACAAAAGAATCTACTCTAATACAAATAATGAAT
Found at i:109904 original size:25 final size:24
Alignment explanation
Indices: 109876--109922 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
109866 TTTTATATTA
* *
109876 ATATTAATATTAAATAAATATAACT
1 ATATTAAGATTAAACAAA-ATAACT
109901 ATATTAAGATTAAACAAAATAA
1 ATATTAAGATTAAACAAAATAA
109923 AAATCCCCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (24 bp):
ATATTAAGATTAAACAAAATAACT
Found at i:109965 original size:6 final size:6
Alignment explanation
Indices: 109956--109999 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
109946 TCCACCTCCG
* *
109956 CCTCTC CCTCTC CCTCTC CCTCTA CCTCTA CCTCTTC CC-CTC CC
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTC-TC CCTCTC CC
110000 CTTCACATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
5 4 0.11
6 28 0.80
7 3 0.09
ACGTcount: A:0.05, C:0.64, G:0.00, T:0.32
Consensus pattern (6 bp):
CCTCTC
Found at i:109971 original size:18 final size:18
Alignment explanation
Indices: 109943--109990 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
109933 CCCCACCCCC
*
109943 ACCTCCACCTC-CGCCTCT
1 ACCTCTACCTCTC-CCTCT
* *
109961 CCCTCTCCCTCTCCCTCT
1 ACCTCTACCTCTCCCTCT
109979 ACCTCTACCTCT
1 ACCTCTACCTCT
109991 TCCCCTCCCC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.08, C:0.60, G:0.02, T:0.29
Consensus pattern (18 bp):
ACCTCTACCTCTCCCTCT
Found at i:110108 original size:17 final size:17
Alignment explanation
Indices: 110086--110136 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
110076 GTAAAACGGG
110086 GGAGGGAGAGGGACGAA
1 GGAGGGAGAGGGACGAA
**
110103 GGAGGGA-AGTGGACGGT
1 GGAGGGAGAG-GGACGAA
*
110120 GG-GGGAGAGGGAGGAA
1 GGAGGGAGAGGGACGAA
110136 G
1 G
110137 ATGGGGTGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.29, C:0.04, G:0.63, T:0.04
Consensus pattern (17 bp):
GGAGGGAGAGGGACGAA
Found at i:122854 original size:15 final size:15
Alignment explanation
Indices: 122834--122863 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
122824 TTATTCATGC
*
122834 AAAATATAAAAGACA
1 AAAATACAAAAGACA
122849 AAAATACAAAAGACA
1 AAAATACAAAAGACA
122864 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.10, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAATACAAAAGACA
Found at i:124276 original size:41 final size:41
Alignment explanation
Indices: 124231--124313 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
124221 ATTCAAACAT
*
124231 TCCCAAAATACACAATTCAAAATAAACATTACAAAAATACA
1 TCCCAAAATACACAATACAAAATAAACATTACAAAAATACA
*
124272 TCCCAAAATACACAATACAAATTAAACATTACAAAAATACA
1 TCCCAAAATACACAATACAAAATAAACATTACAAAAATACA
124313 T
1 T
124314 AGGATTATAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.58, C:0.22, G:0.00, T:0.20
Consensus pattern (41 bp):
TCCCAAAATACACAATACAAAATAAACATTACAAAAATACA
Found at i:124304 original size:14 final size:14
Alignment explanation
Indices: 124234--124307 Score: 62
Period size: 14 Copynumber: 5.4 Consensus size: 14
124224 CAAACATTCC
*
124234 CAAAATACACAATT-
1 CAAAATAAAC-ATTA
124248 CAAAATAAACATTA
1 CAAAATAAACATTA
* **
124262 CAAAA-ATACATCC
1 CAAAATAAACATTA
* *
124275 CAAAATACACAATA
1 CAAAATAAACATTA
*
124289 CAAATTAAACATTA
1 CAAAATAAACATTA
124303 CAAAA
1 CAAAA
124308 ATACATAGGA
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
13 13 0.28
14 33 0.72
ACGTcount: A:0.61, C:0.20, G:0.00, T:0.19
Consensus pattern (14 bp):
CAAAATAAACATTA
Found at i:125115 original size:13 final size:14
Alignment explanation
Indices: 125090--125121 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
125080 TTTAAAATTA
125090 TTAAAATTATTTTT
1 TTAAAATTATTTTT
125104 TTAAAA-TATTTTT
1 TTAAAATTATTTTT
125117 TTAAA
1 TTAAA
125122 TATAACATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAAATTATTTTT
Found at i:126131 original size:29 final size:27
Alignment explanation
Indices: 126083--126137 Score: 92
Period size: 29 Copynumber: 2.0 Consensus size: 27
126073 ATGATGACTA
126083 TATTTTAAAATAATTTTAATAATTTTG
1 TATTTTAAAATAATTTTAATAATTTTG
126110 TATTTTAAAAATTAATTTTAATAATTTT
1 TATTTT-AAAA-TAATTTTAATAATTTT
126138 AAAATCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 6 0.23
28 4 0.15
29 16 0.62
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TATTTTAAAATAATTTTAATAATTTTG
Found at i:130664 original size:22 final size:22
Alignment explanation
Indices: 130639--130682 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
130629 ATTAAGAAAA
130639 AAAATTACAATCAAACTAAGTG
1 AAAATTACAATCAAACTAAGTG
*
130661 AAAATTACAATCAGACTAAGTG
1 AAAATTACAATCAAACTAAGTG
130683 TGTACATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.23
Consensus pattern (22 bp):
AAAATTACAATCAAACTAAGTG
Found at i:135007 original size:6 final size:6
Alignment explanation
Indices: 134996--135032 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
134986 ATCAAAATTT
* *
134996 AAAGTG AAAGTG AAAGTG AAATTG AAATTG AAAGTG A
1 AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG A
135033 TATGAATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (6 bp):
AAAGTG
Found at i:141777 original size:43 final size:43
Alignment explanation
Indices: 141708--141791 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
141698 TTGAGGTCAG
*
141708 AAAATGAAATCTAGATCCTTCATTAATTTAATAAAATGATTTC
1 AAAATGAAAGCTAGATCCTTCATTAATTTAATAAAATGATTTC
* *
141751 AAAATTGAAAGCTAGATGCTT-ATTAATTTAATACAATGATT
1 AAAA-TGAAAGCTAGATCCTTCATTAATTTAATAAAATGATT
141792 CGCTTGTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 23 0.62
44 14 0.38
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (43 bp):
AAAATGAAAGCTAGATCCTTCATTAATTTAATAAAATGATTTC
Found at i:146500 original size:20 final size:20
Alignment explanation
Indices: 146475--146515 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
146465 AGTATATTTG
*
146475 ATTTTTTTTTAGAATTTTTA
1 ATTTTTTTTTAAAATTTTTA
146495 ATTTTTTTTTAAAATTTTTA
1 ATTTTTTTTTAAAATTTTTA
146515 A
1 A
146516 AATATGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
ATTTTTTTTTAAAATTTTTA
Found at i:171364 original size:33 final size:33
Alignment explanation
Indices: 171327--171454 Score: 150
Period size: 33 Copynumber: 3.8 Consensus size: 33
171317 GGAAGAACCC
* *
171327 AAGAAAG-AGGAGCCCAAGAAGGAGGAGGAGCCG
1 AAGAAAGAAGAAG-CCAAGAAGGAAGAGGAGCCG
*
171360 AAGAAAGAAGAAGCCAAGAAGGAAGAGGAGCCA
1 AAGAAAGAAGAAGCCAAGAAGGAAGAGGAGCCG
* *
171393 AAGAAAGAAGAAGCCAAGAAGGAAGAGGAACCC
1 AAGAAAGAAGAAGCCAAGAAGGAAGAGGAGCCG
* *
171426 AAGAAGGAAGAGGAGCCAAAGAAAGAAGA
1 AAGAAAGAAGA--AGCC-AAGAAGGAAGA
171455 AGAGAAACAG
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 66 0.79
34 4 0.05
35 4 0.05
36 10 0.12
ACGTcount: A:0.52, C:0.12, G:0.35, T:0.00
Consensus pattern (33 bp):
AAGAAAGAAGAAGCCAAGAAGGAAGAGGAGCCG
Found at i:171380 original size:18 final size:18
Alignment explanation
Indices: 171359--171456 Score: 91
Period size: 18 Copynumber: 5.8 Consensus size: 18
171349 AGGAGGAGCC
171359 GAAGAAAGAAGAAGCCAA
1 GAAGAAAGAAGAAGCCAA
* *
171377 GAAGGAAG-AGGAGCC-A
1 GAAGAAAGAAGAAGCCAA
171393 -AAGAAAGAAGAAGCCAA
1 GAAGAAAGAAGAAGCCAA
* * *
171410 GAAGGAAGAGGAACCCAA
1 GAAGAAAGAAGAAGCCAA
* *
171428 GAAGGAAG-AGGAGCC-A
1 GAAGAAAGAAGAAGCCAA
171444 -AAGAAAGAAGAAG
1 GAAGAAAGAAGAAG
171457 AGAAACAGCC
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
15 12 0.19
16 12 0.19
17 11 0.17
18 29 0.45
ACGTcount: A:0.55, C:0.11, G:0.34, T:0.00
Consensus pattern (18 bp):
GAAGAAAGAAGAAGCCAA
Found at i:171391 original size:51 final size:50
Alignment explanation
Indices: 171295--171448 Score: 174
Period size: 51 Copynumber: 3.1 Consensus size: 50
171285 AAACCGCCGG
*
171295 AGAAGAAGGAGGAGCCGAA-AAAGGAAGAACCCAAG-A--AAGAGGAGCCCA
1 AGAAG-AGGAGGAGCCGAAGAAA-GAAGAACCCAAGAAGGAAGAGGAGCCAA
*
171343 AGAAGGAGGAGGAGCCGAAGAAAGAAGAAGCCAAGAAGGAAGAGGAGCCAA
1 AGAA-GAGGAGGAGCCGAAGAAAGAAGAACCCAAGAAGGAAGAGGAGCCAA
* * * *
171394 AGAA-AGAAGAAGCCAAGAAGGAAGAGGAACCCAAGAAGGAAGAGGAGCCAA
1 AGAAGAGGAGGAGCC--GAAGAAAGAAGAACCCAAGAAGGAAGAGGAGCCAA
171445 AGAA
1 AGAA
171449 AGAAGAAGAG
Statistics
Matches: 92, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
48 28 0.30
49 13 0.14
51 51 0.55
ACGTcount: A:0.51, C:0.14, G:0.35, T:0.00
Consensus pattern (50 bp):
AGAAGAGGAGGAGCCGAAGAAAGAAGAACCCAAGAAGGAAGAGGAGCCAA
Found at i:171470 original size:6 final size:6
Alignment explanation
Indices: 171461--171495 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
171451 AAGAAGAGAA
171461 ACAGCC ACAGCC ACAGCC ACAGCC AGCAGCC -CAGC
1 ACAGCC ACAGCC ACAGCC ACAGCC A-CAGCC ACAGC
171496 AGCAGCCGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.14
6 19 0.68
7 5 0.18
ACGTcount: A:0.31, C:0.49, G:0.20, T:0.00
Consensus pattern (6 bp):
ACAGCC
Found at i:171484 original size:18 final size:18
Alignment explanation
Indices: 171461--171507 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
171451 AAGAAGAGAA
171461 ACAGCCA-CAGCCACAGCC
1 ACAGCCAGCAGCC-CAGCC
171479 ACAGCCAGCAGCCCAG-C
1 ACAGCCAGCAGCCCAGCC
171496 AGCAGCC-GCAGC
1 A-CAGCCAGCAGC
171508 TGGTGCCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 7 0.26
18 15 0.56
19 5 0.19
ACGTcount: A:0.30, C:0.47, G:0.23, T:0.00
Consensus pattern (18 bp):
ACAGCCAGCAGCCCAGCC
Found at i:172952 original size:12 final size:12
Alignment explanation
Indices: 172935--172968 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
172925 TATAACCATT
172935 ATAATTTATTTA
1 ATAATTTATTTA
172947 ATAATTTATTTA
1 ATAATTTATTTA
* *
172959 TTAATATATT
1 ATAATTTATT
172969 AATTATGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATAATTTATTTA
Found at i:176224 original size:113 final size:113
Alignment explanation
Indices: 176069--176298 Score: 340
Period size: 113 Copynumber: 2.0 Consensus size: 113
176059 CCATTAACCC
* *
176069 AAAGAAACTTAACGGGAATAAGATATTGAAACCAAAGGTATTGAATCTTTTGGTTAATGA-GTTT
1 AAAGAAACTTAACGGGAAGAAGATATTGAAACCAAAGATATTGAATCTTTTGGTTAAT-ATGTTT
* * *
176133 TAAAAATTCAAGCTTT-AGAACAGATTTATAACTAAATATATTGGAATCA
65 CAAAAATTCAAGCTTTGA-AACAAATTTATAACTAAAAATATTGGAATCA
*
176182 AAAGAAACTTAACGGGAAGAAGATATT-ATAACCAAATATATTGAATCTTTTGGTTAATATGTTT
1 AAAGAAACTTAACGGGAAGAAGATATTGA-AACCAAAGATATTGAATCTTTTGGTTAATATGTTT
* *
176246 CAAAGATTCAAGCTTTGAAACAAATTTGTAACTAAAAATATTGGAATCA
65 CAAAAATTCAAGCTTTGAAACAAATTTATAACTAAAAATATTGGAATCA
176295 AAAG
1 AAAG
176299 GGAAGAAGAA
Statistics
Matches: 106, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
112 2 0.02
113 103 0.97
114 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.31
Consensus pattern (113 bp):
AAAGAAACTTAACGGGAAGAAGATATTGAAACCAAAGATATTGAATCTTTTGGTTAATATGTTTC
AAAAATTCAAGCTTTGAAACAAATTTATAACTAAAAATATTGGAATCA
Found at i:177183 original size:4 final size:4
Alignment explanation
Indices: 177170--177216 Score: 69
Period size: 4 Copynumber: 11.8 Consensus size: 4
177160 AAAATTGAAG
*
177170 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAA
177217 GAAGGAAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 3 0.08
4 33 0.85
5 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:177939 original size:16 final size:16
Alignment explanation
Indices: 177894--177943 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
177884 TAAATCTAGC
*
177894 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
177910 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
177924 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
177940 TAAT
1 TAAT
177944 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:179281 original size:43 final size:42
Alignment explanation
Indices: 179199--179291 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 42
179189 ATTAACATGT
* *
179199 TAAATTATATTACTTGACTTGTGTTAATATGGTTGCATGTTA
1 TAAATTATATTACTTGACTTGTATTAATATGCTTGCATGTTA
*
179241 CTAAATTATATTACTTTACTCT-TATTAATAT-CTTGACATGTTA
1 -TAAATTATATTACTTGACT-TGTATTAATATGCTTG-CATGTTA
*
179284 TTAATTAT
1 TAAATTAT
179292 GCAGTTCATC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
42 10 0.23
43 33 0.75
44 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (42 bp):
TAAATTATATTACTTGACTTGTATTAATATGCTTGCATGTTA
Found at i:179952 original size:45 final size:45
Alignment explanation
Indices: 179851--179987 Score: 163
Period size: 45 Copynumber: 3.0 Consensus size: 45
179841 GCATAGCTCA
*
179851 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGTCACCACAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC
179896 TCAAGCCAAGGATATCAGCCTCTA-TTTGACGAGCCACCACAATAC
1 TCAAGCCAAGGATATCAGCCTC-AGTTTGACGAGCCACCACAATAC
* * * * * *
179941 TCAAAG-GAAGGATGTCAAG-CTGAGTTTGATGAGCCATCACGATAC
1 TC-AAGCCAAGGATATC-AGCCTCAGTTTGACGAGCCACCACAATAC
179986 TC
1 TC
179988 TATTCCTCCT
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
44 1 0.01
45 74 0.91
46 6 0.07
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC
Found at i:180008 original size:21 final size:20
Alignment explanation
Indices: 179982--180021 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
179972 AGCCATCACG
*
179982 ATACTCTATTCCTCCTGGGCA
1 ATACTCTACTCCTCC-GGGCA
180003 ATACTCTACTCCTCCGGGC
1 ATACTCTACTCCTCCGGGC
180022 CAAATGGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.17, C:0.38, G:0.15, T:0.30
Consensus pattern (20 bp):
ATACTCTACTCCTCCGGGCA
Found at i:181805 original size:13 final size:13
Alignment explanation
Indices: 181787--181816 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
181777 CAGGTTTCTT
181787 AAGAAGAATTCCC
1 AAGAAGAATTCCC
181800 AAGAAGAATTCCC
1 AAGAAGAATTCCC
181813 AAGA
1 AAGA
181817 TTCCATGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.20, G:0.17, T:0.13
Consensus pattern (13 bp):
AAGAAGAATTCCC
Found at i:183354 original size:19 final size:18
Alignment explanation
Indices: 183323--183367 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
183313 AATAAATCTG
*
183323 TTAAAAATTAAATAAAAT
1 TTAAAAATAAAATAAAAT
*
183341 TTAATAAATAAAATACAATT
1 TTAA-AAATAAAATA-AAAT
183361 TTAAAAA
1 TTAAAAA
183368 GATATCATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.17
19 12 0.52
20 7 0.30
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAAAATAAAATAAAAT
Found at i:183427 original size:4 final size:4
Alignment explanation
Indices: 183407--183470 Score: 67
Period size: 4 Copynumber: 15.8 Consensus size: 4
183397 CACATTACAC
* * * *
183407 TTCT TTCC TTC- TTCT TTCT TTCCT CTAT TTCT TCCT TTCT TTCT TTCTT
1 TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TTC-T
183456 TTCT TTCT TTCT TTC
1 TTCT TTCT TTCT TTC
183471 CCATTTATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
3 3 0.06
4 40 0.80
5 7 0.14
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.69
Consensus pattern (4 bp):
TTCT
Found at i:183446 original size:21 final size:19
Alignment explanation
Indices: 183415--183471 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 19
183405 ACTTCTTTCC
183415 TTCTTCTTTCTTTCCTCTAT
1 TTCTTCTTTCTTTCCTCT-T
*
183435 TTCTTCCTTTCTTTCTTTCTT
1 TTCTT-CTTTCTTTC-CTCTT
183456 TTCTTTCTTTCTTTCC
1 TTC-TTCTTTCTTTCC
183472 CATTTATTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 5 0.16
21 22 0.69
22 5 0.16
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (19 bp):
TTCTTCTTTCTTTCCTCTT
Found at i:183461 original size:17 final size:16
Alignment explanation
Indices: 183407--183470 Score: 67
Period size: 17 Copynumber: 3.9 Consensus size: 16
183397 CACATTACAC
*
183407 TTCTTTCCTTC-TTCT
1 TTCTTTCTTTCTTTCT
* *
183422 TTCTTTCCTCTATTTCT
1 TTCTTT-CTTTCTTTCT
*
183439 TCCTTTCTTTCTTTCTT
1 TTCTTTCTTTCTTTC-T
183456 TTCTTTCTTTCTTTC
1 TTCTTTCTTTCTTTC
183471 CCATTTATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
15 6 0.15
16 9 0.23
17 24 0.62
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCTTTCTTTCTTTCT
Found at i:187083 original size:15 final size:16
Alignment explanation
Indices: 187059--187102 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
187049 TTTTTTTTTT
187059 GTAATCACATTCTTCA
1 GTAATCACATTCTTCA
*
187075 -TAATTACATT-TTCA
1 GTAATCACATTCTTCA
*
187089 GGAATCACATTCTT
1 GTAATCACATTCTT
187103 TTGATTAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 4 0.17
15 17 0.74
16 2 0.09
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (16 bp):
GTAATCACATTCTTCA
Found at i:188720 original size:15 final size:15
Alignment explanation
Indices: 188700--188731 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
188690 AGCATTTCAA
188700 ATGCTTAGTAAGTTC
1 ATGCTTAGTAAGTTC
188715 ATGCTTAGTAAGTTC
1 ATGCTTAGTAAGTTC
188730 AT
1 AT
188732 TGGTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (15 bp):
ATGCTTAGTAAGTTC
Found at i:189080 original size:22 final size:22
Alignment explanation
Indices: 189052--189114 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
189042 TACACCACAC
*
189052 CAGAGAGCATCGTAGTGCTAAA
1 CAGAGAGCATCGAAGTGCTAAA
* * * *
189074 CAGAGAGCATAGAATTACTAAG
1 CAGAGAGCATCGAAGTGCTAAA
189096 CAGAGAGCATCGAAGTGCT
1 CAGAGAGCATCGAAGTGCT
189115 GATTAGAGAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.17
Consensus pattern (22 bp):
CAGAGAGCATCGAAGTGCTAAA
Found at i:189432 original size:17 final size:17
Alignment explanation
Indices: 189410--189442 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
189400 CATTTACAGA
189410 CAAACA-ATTTCATAATT
1 CAAACACATTT-ATAATT
189427 CAAACACATTTATAAT
1 CAAACACATTTATAAT
189443 AATATTACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (17 bp):
CAAACACATTTATAATT
Found at i:190558 original size:19 final size:17
Alignment explanation
Indices: 190535--190581 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
190525 TTAATTTCAA
190535 TCCACATTTTCGTGGGTT-
1 TCCACATTTT-GT-GGTTG
190553 TCCCACAATTTTGTGGTTG
1 T-CCAC-ATTTTGTGGTTG
190572 TCCACATTTT
1 TCCACATTTT
190582 TGTGATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 5 0.19
18 9 0.35
19 7 0.27
20 5 0.19
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (17 bp):
TCCACATTTTGTGGTTG
Found at i:191350 original size:26 final size:26
Alignment explanation
Indices: 191319--191370 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
191309 ATATTTTAAA
* *
191319 ATAAAACCATGGTTTTAAATAATTTT
1 ATAAAACCATAGTCTTAAATAATTTT
* *
191345 ATAAAACTATAGTCTTAAATGATTTT
1 ATAAAACCATAGTCTTAAATAATTTT
191371 CGCATAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (26 bp):
ATAAAACCATAGTCTTAAATAATTTT
Found at i:207686 original size:21 final size:21
Alignment explanation
Indices: 207660--207728 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
207650 TCACTTCGTT
207660 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
* *
207681 TCTTTTTGTTCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
* * * *
207702 TCTTTGTGTCTAACTCACTTC
1 TCTTTTTGTCCAAGTTACTTC
207723 -CTTTTT
1 TCTTTTT
207729 TCTTTGTGAG
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 5 0.13
21 34 0.87
ACGTcount: A:0.12, C:0.23, G:0.10, T:0.55
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:214865 original size:31 final size:28
Alignment explanation
Indices: 214801--214869 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 28
214791 CAATCAAAAT
214801 TTCATGTATAAATTGCACAAAAACAAAG
1 TTCATGTATAAATTGCACAAAAACAAAG
* *
214829 TTCATGTATACAATTGCACATTAAACCATAG
1 TTCATGTATA-AATTGCACA--AAAACAAAG
214860 TTCATGTATA
1 TTCATGTATA
214870 GTTTTGAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 10 0.28
29 9 0.25
31 17 0.47
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (28 bp):
TTCATGTATAAATTGCACAAAAACAAAG
Found at i:215438 original size:17 final size:17
Alignment explanation
Indices: 215416--215502 Score: 104
Period size: 17 Copynumber: 5.1 Consensus size: 17
215406 CAACATTTAA
215416 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAATTT
*
215433 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
215450 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* *
215467 ATTTTTGAGTTTAAATTT
1 A-TTTTAAATTTAAATTT
*
215485 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
215502 A
1 A
215503 AAATTTAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
16 6 0.10
17 41 0.67
18 14 0.23
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:215450 original size:6 final size:6
Alignment explanation
Indices: 215410--215510 Score: 57
Period size: 6 Copynumber: 17.0 Consensus size: 6
215400 CCGACCCAAC
* * *
215410 ATTTAA ATTTTAA ATTTTAA A-TT-A TTTTAA GTTTAA ATTT-A TTTTAA
1 ATTTAA A-TTTAA A-TTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * * * * *
215457 ATTTAA ACTTAT TTTTGA GTTTAA ATTT-A TTTTGA ATTTAA ATTTAAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
215505 ATTTAA
1 ATTTAA
215511 TTAAAAGTCC
Statistics
Matches: 72, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
4 1 0.01
5 12 0.17
6 40 0.56
7 19 0.26
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (6 bp):
ATTTAA
Found at i:215485 original size:35 final size:33
Alignment explanation
Indices: 215416--215500 Score: 125
Period size: 35 Copynumber: 2.5 Consensus size: 33
215406 CAACATTTAA
215416 ATTTTAAATTTTAAATTATTTTAAGTTTAAATTT
1 ATTTTAAA-TTTAAATTATTTTAAGTTTAAATTT
*
215450 ATTTTAAATTTAAACTTATTTTTGAGTTTAAATTT
1 ATTTTAAATTTAAA-TTA-TTTTAAGTTTAAATTT
*
215485 ATTTTGAATTTAAATT
1 ATTTTAAATTTAAATT
215501 TAAAATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
33 6 0.13
34 13 0.28
35 28 0.60
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (33 bp):
ATTTTAAATTTAAATTATTTTAAGTTTAAATTT
Found at i:216174 original size:22 final size:23
Alignment explanation
Indices: 216135--216179 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
216125 TGCATTTATT
216135 ATATATTAAATATAATT-ATTAA
1 ATATATTAAATATAATTAATTAA
216157 ATATATTAAATA-ATATTAATTAA
1 ATATATTAAATATA-ATTAATTAA
216180 TTAATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.05
22 15 0.71
23 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATATTAAATATAATTAATTAA
Found at i:216540 original size:61 final size:61
Alignment explanation
Indices: 216472--216596 Score: 205
Period size: 61 Copynumber: 2.0 Consensus size: 61
216462 CCCCTTTTTT
* * *
216472 AATGTTGAAGCCCAAATTTTGACCGAGTCCCAAGCTCCCCTTTAAATTTATTTTAAGATTA
1 AATGTTGAAGCCCAAATTTTGACCGAGCCCCAAGCTCACCTTTAAATTTATTTTAAAATTA
* *
216533 AATGTTGAAGCTCAAATTTTGACCGGGCCCCAAGCTCACCTTTAAATTTATTTTAAAATTA
1 AATGTTGAAGCCCAAATTTTGACCGAGCCCCAAGCTCACCTTTAAATTTATTTTAAAATTA
216594 AAT
1 AAT
216597 TTGTTTAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (61 bp):
AATGTTGAAGCCCAAATTTTGACCGAGCCCCAAGCTCACCTTTAAATTTATTTTAAAATTA
Found at i:216614 original size:6 final size:6
Alignment explanation
Indices: 216605--216694 Score: 75
Period size: 6 Copynumber: 15.5 Consensus size: 6
216595 ATTTGTTTAA
* * *
216605 AAATTT AAATTT -ATTTT AAATTT AAATGT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
216651 AAGTTT AAATTT --ATTAT CAAATTT AAATTT --ATTAT AAATTT AAA
1 AAATTT AAATTT AAATT-T -AAATTT AAATTT AAATT-T AAATTT AAA
216695 ATAAATAAAG
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
4 6 0.09
5 9 0.13
6 45 0.67
7 4 0.06
8 3 0.04
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:216658 original size:35 final size:35
Alignment explanation
Indices: 216573--216694 Score: 123
Period size: 35 Copynumber: 3.7 Consensus size: 35
216563 CAAGCTCACC
* * *
216573 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAATTTAAATGTATTTAAAAA
*
216608 TTTAAATTTATTTTAAATTTAAATGTATTT-TAAA
1 TTTAAATTTATTTTAAATTTAAATGTATTTAAAAA
* *
216642 TTTAAATTTAAGTTTAAATTT--AT-TA--T-CAAA
1 TTTAAATTT-ATTTTAAATTTAAATGTATTTAAAAA
*
216672 TTTAAATTTATTATAAATTTAAA
1 TTTAAATTTATTTTAAATTTAAA
216695 ATAAATAAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
29 9 0.12
30 13 0.17
31 1 0.01
32 2 0.03
33 2 0.03
34 12 0.16
35 37 0.49
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATGTATTTAAAAA
Found at i:216675 original size:18 final size:17
Alignment explanation
Indices: 216573--216694 Score: 128
Period size: 17 Copynumber: 7.4 Consensus size: 17
216563 CAAGCTCACC
216573 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
216590 ATTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
216608 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
216625 TTTAAATGTATTTTAAA
1 TTTAAATTTATTTTAAA
*
216642 TTT-AA---A-TTTAAG
1 TTTAAATTTATTTTAAA
*
216654 TTTAAATTTATTATCAAA
1 TTTAAATTTATT-TTAAA
*
216672 TTTAAATTTATTATAAA
1 TTTAAATTTATTTTAAA
216689 TTTAAA
1 TTTAAA
216695 ATAAATAAAG
Statistics
Matches: 86, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
12 8 0.09
13 3 0.03
16 3 0.03
17 43 0.50
18 29 0.34
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:217411 original size:24 final size:24
Alignment explanation
Indices: 217384--217450 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
217374 TCATTAAGGT
* *
217384 TAATATTGAT-TATTATATTATTAA
1 TAATATTGATATAATA-ATAATTAA
*
217408 TAATATTTATATAATAATAATTAA
1 TAATATTGATATAATAATAATTAA
*
217432 TAATAAT-A-ATAATAATAAT
1 TAATATTGATATAATAATAAT
217451 GACACTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.29
23 1 0.03
24 22 0.58
25 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (24 bp):
TAATATTGATATAATAATAATTAA
Found at i:217459 original size:27 final size:24
Alignment explanation
Indices: 217405--217465 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
217395 ATTATATTAT
* * *
217405 TAATAATATTTATATAATAATAAT
1 TAATAATAATAATATAATAATAAC
217429 TAATAATAATAATAATAATAATGACAC
1 TAATAATAATAAT-ATAATAAT-A-AC
217456 TAATAATAAT
1 TAATAATAAT
217466 TTTTAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.35
25 8 0.26
26 1 0.03
27 11 0.35
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (24 bp):
TAATAATAATAATATAATAATAAC
Found at i:217476 original size:3 final size:3
Alignment explanation
Indices: 217405--217465 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
217395 ATTATATTAT
* *
217405 TAA TAA TAT TTA T-A TAA TAA TAA TTAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
* * *
217450 TGA CAC TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
217466 TTTTAATAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:218616 original size:29 final size:29
Alignment explanation
Indices: 218569--218674 Score: 106
Period size: 29 Copynumber: 3.6 Consensus size: 29
218559 CGAAACTTCC
* * *
218569 AAAAATCCCATTTTTACCCCCGAAGCTTGT
1 AAAAATCCCA-ATTTAACCCCAAAGCTTGT
* * **
218599 AAAAAT-CCAATTTAACCCTAAAACTTCC
1 AAAAATCCCAATTTAACCCCAAAGCTTGT
*
218627 AAAAATCCCATTTTAACCCCAAAGCTTGT
1 AAAAATCCCAATTTAACCCCAAAGCTTGT
*
218656 AAAATTCCCAATTTTAACC
1 AAAAATCCCAA-TTTAACC
218675 TCGAAACTTC
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
28 18 0.30
29 29 0.48
30 13 0.22
ACGTcount: A:0.39, C:0.28, G:0.05, T:0.28
Consensus pattern (29 bp):
AAAAATCCCAATTTAACCCCAAAGCTTGT
Found at i:218724 original size:59 final size:59
Alignment explanation
Indices: 218542--218819 Score: 271
Period size: 59 Copynumber: 4.7 Consensus size: 59
218532 ATTGTTCAAC
* **
218542 AATCCCATTTTTAACCTCGAAACTTCCAAAAATCCCATTTTTACCCCCGAAGCTTGTAAA
1 AATCCCATTTTTAACC-CGAAACTTCCAAAAATTCCATTTTTACCCCCGAAGCTTCCAAA
* * * * * **
218602 AAT-CCA-ATTTAACCCTAAAACTTCCAAAAATCCCA-TTTTAACCCCAAAGCTTGTAAA
1 AATCCCATTTTTAACCC-GAAACTTCCAAAAATTCCATTTTTACCCCCGAAGCTTCCAAA
* * * *
218659 ATTCCCAATTTTAACCTCGAAACTTCCAAAAATTCCATTTTTACCCCTGAA-CTACCAAA
1 AATCCCATTTTTAACC-CGAAACTTCCAAAAATTCCATTTTTACCCCCGAAGCTTCCAAA
* * * *
218718 AATCCCATTTTTAACACCGAAGCTTTCAAAAATTCCATCTTTACCCCCGAA-CCTCCAAA
1 AATCCCATTTTTAAC-CCGAAACTTCCAAAAATTCCATTTTTACCCCCGAAGCTTCCAAA
* * *
218777 AATCCCATTTTTGACCCCAAAATTACCAAAAA-TCTCATTTTTA
1 AATCCCATTTTTAACCCGAAACTT-CCAAAAATTC-CATTTTTA
218820 ACCTCAAAAC
Statistics
Matches: 182, Mismatches: 28, Indels: 17
0.80 0.12 0.07
Matches are distributed among these distances:
57 23 0.13
58 36 0.20
59 108 0.59
60 15 0.08
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.29
Consensus pattern (59 bp):
AATCCCATTTTTAACCCGAAACTTCCAAAAATTCCATTTTTACCCCCGAAGCTTCCAAA
Found at i:218886 original size:29 final size:29
Alignment explanation
Indices: 218542--218886 Score: 259
Period size: 30 Copynumber: 11.7 Consensus size: 29
218532 ATTGTTCAAC
*
218542 AATCCCATTTTTAACCTCGAAACTTCCAAA
1 AATCCCATTTTTAACCCCG-AACTTCCAAA
* **
218572 AATCCCATTTTTACCCCCGAAGCTTGTAAA
1 AATCCCATTTTTAACCCCGAA-CTTCCAAA
* **
218602 AAT-CCA-ATTTAACCCTAAAACTTCCAAA
1 AATCCCATTTTTAACCC-CGAACTTCCAAA
* **
218630 AATCCCA-TTTTAACCCCAAAGCTTGTAAA
1 AATCCCATTTTTAACCCCGAA-CTTCCAAA
* * *
218659 ATTCCCAATTTTAACCTCGAAACTTCCAAA
1 AATCCCATTTTTAACCCCG-AACTTCCAAA
* *
218689 AATTCCATTTTT-ACCCCTGAACTACCAAA
1 AATCCCATTTTTAACCCC-GAACTTCCAAA
* *
218718 AATCCCATTTTTAACACCGAAGCTTTCAAA
1 AATCCCATTTTTAACCCCGAA-CTTCCAAA
* * * *
218748 AATTCCATCTTTACCCCCGAACCTCCAAA
1 AATCCCATTTTTAACCCCGAACTTCCAAA
* * *
218777 AATCCCATTTTTGACCCCAAAATTACCAAA
1 AATCCCATTTTTAACCCCGAACTT-CCAAA
* ** *
218807 AATCTCATTTTTAACCTCAAAACTTTCAAA
1 AATCCCATTTTTAACC-CCGAACTTCCAAA
* * * * *
218837 AGGT-CTATTTTTATCCTCGAACTTCTAAA
1 A-ATCCCATTTTTAACCCCGAACTTCCAAA
*
218866 AATCCCATTTTTGACCCCGAA
1 AATCCCATTTTTAACCCCGAA
218887 TTTTCCTAAA
Statistics
Matches: 242, Mismatches: 60, Indels: 27
0.74 0.18 0.08
Matches are distributed among these distances:
28 20 0.08
29 102 0.42
30 111 0.46
31 9 0.04
ACGTcount: A:0.36, C:0.29, G:0.05, T:0.30
Consensus pattern (29 bp):
AATCCCATTTTTAACCCCGAACTTCCAAA
Found at i:218898 original size:89 final size:88
Alignment explanation
Indices: 218625--218888 Score: 268
Period size: 89 Copynumber: 3.0 Consensus size: 88
218615 CCTAAAACTT
* * * *
218625 CCAAAAATCCCA-TTTTAACCCCAAAGCTTGT--AAAATTCCCAATTTTAACCTCGAAACTTCCA
1 CCAAAAATCCCATTTTTAACACCAAAACTT-TCAAAAAGT-CCATTTTTAACCTCG-AACTTCCA
* *
218687 AAAATTCCATTTTT-ACCCCTGAACTA
63 AAAATCCCATTTTTGACCCC-GAATTA
* * * * * * *
218713 CCAAAAATCCCATTTTTAACACCGAAGCTTTCAAAAATTCCATCTTTACCCCCGAACCTCCAAAA
1 CCAAAAATCCCATTTTTAACACCAAAACTTTCAAAAAGTCCATTTTTAACCTCGAACTTCCAAAA
*
218778 ATCCCATTTTTGACCCCAAAATTA
66 ATCCCATTTTTGACCCC-GAATTA
* * * * *
218802 CCAAAAATCTCATTTTTAAC-CTCAAAACTTTCAAAAGGTCTATTTTTATCCTCGAACTTCTAAA
1 CCAAAAATCCCATTTTTAACAC-CAAAACTTTCAAAAAGTCCATTTTTAACCTCGAACTTCCAAA
218866 AATCCCATTTTTGACCCCGAATT
65 AATCCCATTTTTGACCCCGAATT
218889 TTCCTAAAAT
Statistics
Matches: 148, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
88 38 0.26
89 104 0.70
90 6 0.04
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (88 bp):
CCAAAAATCCCATTTTTAACACCAAAACTTTCAAAAAGTCCATTTTTAACCTCGAACTTCCAAAA
ATCCCATTTTTGACCCCGAATTA
Found at i:220715 original size:30 final size:30
Alignment explanation
Indices: 220663--220950 Score: 165
Period size: 30 Copynumber: 9.9 Consensus size: 30
220653 AAGTATCCTG
* * *
220663 AACTGTCCAAAAATCACGTTTTGACCCCTA
1 AACTTTCCAAAAATTACATTTTGACCCCTA
* * *
220693 AACTTTCCAATAATTATATTTTGACTCCTA
1 AACTTTCCAAAAATTACATTTTGACCCCTA
** *
220723 AACTTTCCAAAAATTACATTTTGACCTTTG
1 AACTTTCCAAAAATTACATTTTGACCCCTA
* * *
220753 AAC--TCCTAAAATTACATTTTTGCCCCCAA
1 AACTTTCCAAAAATTACA-TTTTGACCCCTA
*
220782 AAC-TTCC-AAAATTACAATTTTGTCCCC-A
1 AACTTTCCAAAAATTAC-ATTTTGACCCCTA
* * *
220810 AAC-TTCCAAAAATCACATTTT--TCCCTCG
1 AACTTTCCAAAAATTACATTTTGACCCCT-A
* **
220838 AAC-TTCCAAAAATCACATTTT-ACCCCCG
1 AACTTTCCAAAAATTACATTTTGACCCCTA
* * *
220866 TACTTT-CAAAAATCACATTTTTATCCCCGT-
1 AACTTTCCAAAAATTACATTTTGA-CCCC-TA
* * *
220896 -AC-TTCAAAAAATCACATTTT-ACCCCCA
1 AACTTTCCAAAAATTACATTTTGACCCCTA
* * *
220923 AAATTCTCAAAAAATTACATTTTTACCC
1 AACTT-TCCAAAAATTACATTTTGACCC
220951 TTGAACTTAC
Statistics
Matches: 211, Mismatches: 30, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
26 3 0.01
27 4 0.02
28 68 0.32
29 57 0.27
30 75 0.36
31 4 0.02
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (30 bp):
AACTTTCCAAAAATTACATTTTGACCCCTA
Found at i:220829 original size:28 final size:28
Alignment explanation
Indices: 220663--220950 Score: 172
Period size: 28 Copynumber: 9.9 Consensus size: 28
220653 AAGTATCCTG
*
220663 AACTGTCCAAAAATCACGTTTTGACCCCTA
1 AACT-TCCAAAAATCACATTTTGACCCC-A
* * * *
220693 AACTTTCCAATAATTATATTTTGACTCCTA
1 AAC-TTCCAAAAATCACATTTTGAC-CCCA
* ***
220723 AACTTTCCAAAAATTACATTTTGACCTTTG
1 AAC-TTCCAAAAATCACATTTTGACC-CCA
* * *
220753 AAC-TCCTAAAATTACATTTTTGCCCCCAA
1 AACTTCCAAAAATCACA-TTTTGACCCC-A
* *
220782 AACTTCC-AAAATTACAATTTTGTCCCCA
1 AACTTCCAAAAATCAC-ATTTTGACCCCA
* *
220810 AACTTCCAAAAATCACATTTT-TCCCTCG
1 AACTTCCAAAAATCACATTTTGACCC-CA
*
220838 AACTTCCAAAAATCACATTTT-ACCCCCG
1 AACTTCCAAAAATCACATTTTGA-CCCCA
* * * *
220866 TACTTTCAAAAATCACATTTTTATCCCCG
1 AACTTCCAAAAATCACATTTTGA-CCCCA
* *
220895 TACTTCAAAAAATCACATTTT-ACCCCCA
1 AACTTCCAAAAATCACATTTTGA-CCCCA
* * *
220923 AAATTCTCAAAAAATTACATTTTTACCC
1 AACTTC-C-AAAAATCACATTTTGACCC
220951 TTGAACTTAC
Statistics
Matches: 215, Mismatches: 29, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
27 4 0.02
28 77 0.36
29 63 0.29
30 67 0.31
31 4 0.02
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (28 bp):
AACTTCCAAAAATCACATTTTGACCCCA
Found at i:220918 original size:57 final size:56
Alignment explanation
Indices: 220811--220978 Score: 180
Period size: 57 Copynumber: 2.9 Consensus size: 56
220801 TTGTCCCCAA
*
220811 ACTTCCAAAAATCACATTTTTCCCTCGAACTTCCAAAAATCACATTTTACCCCCGT
1 ACTTCCAAAAATCACATTTTTCCCTCGAACTTCAAAAAATCACATTTTACCCCCGT
* * **
220867 ACTTTCAAAAATCACATTTTTATCCC-CGTACTTCAAAAAATCACATTTTACCCCCAA
1 ACTTCCAAAAATCACA-TTTT-TCCCTCGAACTTCAAAAAATCACATTTTACCCCCGT
* * *
220924 AATTCTCAAAAAATTACATTTTTACCCTTGAACTT-ACAAAAAT-ATCATTTTACCC
1 ACTTC-C-AAAAATCACATTTTT-CCCTCGAACTTCA-AAAAATCA-CATTTTACCC
220979 TTGAGCATCC
Statistics
Matches: 94, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
56 15 0.16
57 35 0.37
58 14 0.15
59 30 0.32
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (56 bp):
ACTTCCAAAAATCACATTTTTCCCTCGAACTTCAAAAAATCACATTTTACCCCCGT
Found at i:220975 original size:28 final size:28
Alignment explanation
Indices: 220943--221006 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
220933 AAAATTACAT
* *
220943 TTTTACCCTTGAACTTACAAAAATATCA
1 TTTTACCCTTGAACATACAAAAATACCA
* * *
220971 TTTTACCCTTGAGCATCCAAAATTACCA
1 TTTTACCCTTGAACATACAAAAATACCA
220999 TTTTACCC
1 TTTTACCC
221007 CCAATCTTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.36
Consensus pattern (28 bp):
TTTTACCCTTGAACATACAAAAATACCA
Found at i:224158 original size:25 final size:25
Alignment explanation
Indices: 224123--224171 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
224113 AATATTTAAG
*
224123 TTTTATGTAAAAATAAATTAATTATA
1 TTTTATGTAAAAACAAA-TAATTATA
*
224149 TTTTAT-TAAATACAAATAATTAT
1 TTTTATGTAAAAACAAATAATTAT
224172 TAATAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 8 0.38
26 6 0.29
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTTATGTAAAAACAAATAATTATA
Found at i:229636 original size:11 final size:11
Alignment explanation
Indices: 229616--229644 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
229606 TTAATAGTAA
229616 AAAATA-ATTT
1 AAAATATATTT
229626 AAAATATATTT
1 AAAATATATTT
229637 AAAATATA
1 AAAATATA
229645 AAGTTAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATATATTT
Found at i:230069 original size:2 final size:2
Alignment explanation
Indices: 230064--230102 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
230054 ACACACACAC
230064 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
230103 ATAAGAGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:230258 original size:2 final size:2
Alignment explanation
Indices: 230251--230277 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
230241 GTGCAAAAGT
230251 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
230278 GTAAGGTTAT
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:240149 original size:59 final size:59
Alignment explanation
Indices: 240056--240173 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
240046 TTCATAGAAT
*
240056 TATGGATAGAGATTATATAAATTAAACTTTTTAATAAAAATCAAATCAAATTTCAAAAG
1 TATGGATAGAGATTATATAAATTAAACTTCTTAATAAAAATCAAATCAAATTTCAAAAG
240115 TATGGATAGAGATTATATAAATTAAACTTCTTAATAAAAATCAAATCAAATTTCAAAAG
1 TATGGATAGAGATTATATAAATTAAACTTCTTAATAAAAATCAAATCAAATTTCAAAAG
240174 AAGTTGATTA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (59 bp):
TATGGATAGAGATTATATAAATTAAACTTCTTAATAAAAATCAAATCAAATTTCAAAAG
Found at i:243608 original size:18 final size:18
Alignment explanation
Indices: 243574--243608 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
243564 TTTTCAAATG
*
243574 ATTATTAAAAATTATAAA
1 ATTATTAAAAATAATAAA
*
243592 ATTATTAAATATAATAA
1 ATTATTAAAAATAATAA
243609 CAAAATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTATTAAAAATAATAAA
Found at i:246142 original size:70 final size:70
Alignment explanation
Indices: 246060--246202 Score: 286
Period size: 70 Copynumber: 2.0 Consensus size: 70
246050 CGTTCATAAA
246060 CATCTAAGGAAGAAGAAGACACATAGATGAGACAAAATTAAAAGTTGACACTTGATCAGCTTCCA
1 CATCTAAGGAAGAAGAAGACACATAGATGAGACAAAATTAAAAGTTGACACTTGATCAGCTTCCA
246125 CCCAC
66 CCCAC
246130 CATCTAAGGAAGAAGAAGACACATAGATGAGACAAAATTAAAAGTTGACACTTGATCAGCTTCCA
1 CATCTAAGGAAGAAGAAGACACATAGATGAGACAAAATTAAAAGTTGACACTTGATCAGCTTCCA
246195 CCCAC
66 CCCAC
246200 CAT
1 CAT
246203 GCATCTCTTT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.19
Consensus pattern (70 bp):
CATCTAAGGAAGAAGAAGACACATAGATGAGACAAAATTAAAAGTTGACACTTGATCAGCTTCCA
CCCAC
Found at i:248838 original size:18 final size:18
Alignment explanation
Indices: 248811--248846 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
248801 ACATTACACG
* *
248811 TTAAAGTATAGAAATTAA
1 TTAAAATATAAAAATTAA
248829 TTAAAATATAAAAATTAA
1 TTAAAATATAAAAATTAA
248847 ATTGACAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
TTAAAATATAAAAATTAA
Found at i:250354 original size:21 final size:21
Alignment explanation
Indices: 250330--250371 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
250320 TTTAAAAAAA
*
250330 AAGTTAAAAGTCAAAACCATT
1 AAGTTAAAAGGCAAAACCATT
250351 AAGTTAAAAGGCAAAACCATT
1 AAGTTAAAAGGCAAAACCATT
250372 TAGTATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.21
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACCATT
Found at i:251359 original size:11 final size:12
Alignment explanation
Indices: 251338--251364 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
251328 AACTAGGTTC
251338 TTTTTCTTTTTT
1 TTTTTCTTTTTT
251350 TTTTTCTTTTTT
1 TTTTTCTTTTTT
251362 TTT
1 TTT
251365 GATAAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:260712 original size:4 final size:4
Alignment explanation
Indices: 260703--260764 Score: 63
Period size: 4 Copynumber: 15.0 Consensus size: 4
260693 AAATAAACGG
* *
260703 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GGAAG GAGAG GAAA GAAA -AAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA -GAAA GA-AA GAAA GAAA GAAA
*
260753 GAAT GAAA GAAA
1 GAAA GAAA GAAA
260765 AGTAATGTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
3 3 0.06
4 36 0.72
5 11 0.22
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:260722 original size:13 final size:13
Alignment explanation
Indices: 260704--260764 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
260694 AATAAACGGG
260704 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
260717 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
* * * *
260730 AAGGAAGGAGAGG
1 AAAGAAAGAAAGA
260743 AAAGAAA-AAAG-
1 AAAGAAAGAAAGA
*
260754 AATGAAAGAAA
1 AAAGAAAGAAA
260765 AGTAATGTGT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
11 6 0.15
12 6 0.15
13 27 0.69
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:264042 original size:45 final size:45
Alignment explanation
Indices: 263993--264086 Score: 161
Period size: 45 Copynumber: 2.1 Consensus size: 45
263983 TATCGTTCTT
* *
263993 TTGAGTATTGCGGTGGCTCGTCAAATTGAGGCTGATATCCTTAGC
1 TTGAGTATTACGGTGGCTCGTCAAATTGAAGCTGATATCCTTAGC
*
264038 TTGAGTATTACGGTGGCTCGTCAAATTGAAGCTGATATCCTTGGC
1 TTGAGTATTACGGTGGCTCGTCAAATTGAAGCTGATATCCTTAGC
264083 TTGA
1 TTGA
264087 TGAGCTATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (45 bp):
TTGAGTATTACGGTGGCTCGTCAAATTGAAGCTGATATCCTTAGC
Done.