Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007351.1 Hibiscus syriacus cultivar Beakdansim tig00019699_pilon, 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: 256012
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 1 of 2
Found at i:5313 original size:40 final size:40
Alignment explanation
Indices: 5269--5457 Score: 272
Period size: 40 Copynumber: 4.8 Consensus size: 40
5259 AGGACACTAA
* * *
5269 GTGTACATGGTGGGCATGACTTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
5309 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
* *
5349 GTGAATATGGT-GGTACGACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
* * * *
5388 GTGAATATTGTGGGCACAACCTTATGTGTAATATACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
**
5428 GTGTATATGGTGGGCACGATTTTATGTGTA
1 GTGTATATGGTGGGCACGACCTTATGTGTA
5458 GCACTACGGT
Statistics
Matches: 134, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
39 37 0.28
40 97 0.72
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (40 bp):
GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
Found at i:5377 original size:79 final size:79
Alignment explanation
Indices: 5290--5440 Score: 257
Period size: 79 Copynumber: 1.9 Consensus size: 79
5280 GGGCATGACT
* *
5290 TTATGTGTAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGGTGAAT
1 TTATGTGTAATACACTTCGGTGAATATGGTGGGCACAACCTTATGTGTAATACACTTCGGTGAAT
5355 ATGGTGGTACGACC
66 ATGGTGGTACGACC
* * *
5369 TTATGTGTAATACACTTCGGTGAATATTGTGGGCACAACCTTATGTGTAATATACTTCGGTGTAT
1 TTATGTGTAATACACTTCGGTGAATATGGTGGGCACAACCTTATGTGTAATACACTTCGGTGAAT
5434 ATGGTGG
66 ATGGTGG
5441 GCACGATTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 67 1.00
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.35
Consensus pattern (79 bp):
TTATGTGTAATACACTTCGGTGAATATGGTGGGCACAACCTTATGTGTAATACACTTCGGTGAAT
ATGGTGGTACGACC
Found at i:11667 original size:8 final size:8
Alignment explanation
Indices: 11656--11684 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
11646 ACATATAATA
11656 TATATAAG
1 TATATAAG
11664 TATATAAG
1 TATATAAG
11672 TATATAA-
1 TATATAAG
11679 TATATA
1 TATATA
11685 TTATGTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (8 bp):
TATATAAG
Found at i:11806 original size:38 final size:37
Alignment explanation
Indices: 11710--11806 Score: 96
Period size: 36 Copynumber: 2.6 Consensus size: 37
11700 AAATCATTTA
*
11710 AAAAAACCATATA-TATATGTTTTCAAAATACGTTTT
1 AAAAAACTATATATTATATGTTTTCAAAATACGTTTT
* *
11746 -CAAAA-T-TATATTATATACGTTTTCAAAAT-TGTTTTTT
1 AAAAAACTATATATTATAT--GTTTTCAAAATACG--TTTT
11783 AAAAAACTATATATTATATGTTTT
1 AAAAAACTATATATTATATGTTTT
11807 TTTTAAATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
33 4 0.08
34 5 0.10
35 5 0.10
36 11 0.22
37 4 0.08
38 9 0.18
39 1 0.02
40 10 0.20
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.45
Consensus pattern (37 bp):
AAAAAACTATATATTATATGTTTTCAAAATACGTTTT
Found at i:11915 original size:15 final size:15
Alignment explanation
Indices: 11895--11924 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11885 TACAGCTGCC
11895 CCTCTTTACCCATTT
1 CCTCTTTACCCATTT
11910 CCTCTTTACCCATTT
1 CCTCTTTACCCATTT
11925 ATCGTGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.40, G:0.00, T:0.47
Consensus pattern (15 bp):
CCTCTTTACCCATTT
Found at i:12450 original size:32 final size:32
Alignment explanation
Indices: 12412--12492 Score: 137
Period size: 32 Copynumber: 2.5 Consensus size: 32
12402 GGGTACGATA
12412 TCCTTCATCGTGAAGTTCAAATCATGGGTGACT
1 TCCTTCATCGTGAAGTTCAAATCATGGGTGA-T
12445 T-CTTCATCGTGAAGTTCAAATCATGGGTGAT
1 TCCTTCATCGTGAAGTTCAAATCATGGGTGAT
*
12476 TCCTTCGTCGTGAAGTT
1 TCCTTCATCGTGAAGTT
12493 AAGTCCAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
31 2 0.04
32 43 0.93
33 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (32 bp):
TCCTTCATCGTGAAGTTCAAATCATGGGTGAT
Found at i:24578 original size:4 final size:4
Alignment explanation
Indices: 24569--24623 Score: 56
Period size: 4 Copynumber: 13.0 Consensus size: 4
24559 GACCTGAAAA
* * *
24569 AAAT AAAT AATAT ATAT AATAA AAAG AAAT AAAT AAAT AAAT AAAT AATAT
1 AAAT AAAT AA-AT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT
24620 AAAT
1 AAAT
24624 TATATTAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
4 33 0.77
5 10 0.23
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:24598 original size:22 final size:22
Alignment explanation
Indices: 24567--24613 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
24557 TGGACCTGAA
* *
24567 AAAAATAAAT-AATATATATAAT
1 AAAAAGAAATAAATAAATA-AAT
24589 AAAAAGAAATAAATAAATAAAT
1 AAAAAGAAATAAATAAATAAAT
24611 AAA
1 AAA
24614 TAATATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (22 bp):
AAAAAGAAATAAATAAATAAAT
Found at i:24615 original size:26 final size:25
Alignment explanation
Indices: 24565--24616 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
24555 TTTGGACCTG
*
24565 AAAAAAATAAATAATATATATAATA
1 AAAAAAATAAATAATAAATATAATA
24590 AAAAGAAATAAATAAATAAATA-AATA
1 AAAA-AAATAAAT-AATAAATATAATA
24616 A
1 A
24617 TATAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 13 0.54
27 7 0.29
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (25 bp):
AAAAAAATAAATAATAAATATAATA
Found at i:24623 original size:9 final size:9
Alignment explanation
Indices: 24571--24640 Score: 52
Period size: 9 Copynumber: 7.3 Consensus size: 9
24561 CCTGAAAAAA
24571 ATAAATAAT
1 ATAAATAAT
*
24580 ATATATAAT
1 ATAAATAAT
* *
24589 AAAAAGAA-
1 ATAAATAAT
24597 ATAAATAAAT
1 ATAAAT-AAT
24607 AAATAAATAAT
1 --ATAAATAAT
*
24618 ATAAATTAT
1 ATAAATAAT
24627 ATTAATATAAT
1 A-TAA-ATAAT
24638 ATA
1 ATA
24641 TAAGGTAATG
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
8 4 0.09
9 24 0.51
10 5 0.11
11 8 0.17
12 6 0.13
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (9 bp):
ATAAATAAT
Found at i:24673 original size:15 final size:15
Alignment explanation
Indices: 24653--24698 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
24643 AGGTAATGGA
24653 AATATATGAAC-ATAT
1 AATATAT-AACTATAT
24668 AATATATAACTATAT
1 AATATATAACTATAT
24683 AACTATATAA-TATAT
1 AA-TATATAACTATAT
24698 A
1 A
24699 CTATGTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.10
15 19 0.66
16 7 0.24
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (15 bp):
AATATATAACTATAT
Found at i:24681 original size:8 final size:8
Alignment explanation
Indices: 24655--24702 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
24645 GTAATGGAAA
24655 TATATGAAC
1 TATAT-AAC
24664 -ATATAA-
1 TATATAAC
24670 TATATAAC
1 TATATAAC
24678 TATATAAC
1 TATATAAC
24686 TATATAA-
1 TATATAAC
24693 TATAT-AC
1 TATATAAC
24700 TAT
1 TAT
24703 GTTTTCAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 1 0.03
7 16 0.44
8 19 0.53
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (8 bp):
TATATAAC
Found at i:24690 original size:23 final size:22
Alignment explanation
Indices: 24655--24702 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 22
24645 GTAATGGAAA
24655 TATATGAACATATAATATATAAC
1 TATATGAACATATAATATAT-AC
24678 TATAT-AACTATATAATATATAC
1 TATATGAAC-ATATAATATATAC
24700 TAT
1 TAT
24703 GTTTTCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (22 bp):
TATATGAACATATAATATATAC
Found at i:26276 original size:22 final size:20
Alignment explanation
Indices: 26244--26293 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 20
26234 AAAACTTACA
26244 ATAAACATCATATATATTCAGG
1 ATAAACATC--ATATATTCAGG
*
26266 ATAAACGTCATATATTCAGG
1 ATAAACATCATATATTCAGG
26286 ATAAACAT
1 ATAAACAT
26294 TTAGAATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 18 0.69
22 8 0.31
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (20 bp):
ATAAACATCATATATTCAGG
Found at i:27508 original size:19 final size:20
Alignment explanation
Indices: 27482--27527 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
27472 CAAAATGGCC
27482 TAATTTC-ACA-TCCTAACAT
1 TAATTTCAACACT-CTAACAT
*
27501 TGATTTCAACACTCTAACAT
1 TAATTTCAACACTCTAACAT
27521 TAATTTC
1 TAATTTC
27528 CAGCATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.26
20 16 0.70
21 1 0.04
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (20 bp):
TAATTTCAACACTCTAACAT
Found at i:34176 original size:21 final size:21
Alignment explanation
Indices: 34150--34189 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34140 CCCCCTTTGA
*
34150 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
34171 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
34190 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:36442 original size:18 final size:18
Alignment explanation
Indices: 36419--36455 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
36409 GGGGAGAAGA
36419 ATAAGTGTTTAATGTTTT
1 ATAAGTGTTTAATGTTTT
36437 ATAAGTGTTTAATGTTTT
1 ATAAGTGTTTAATGTTTT
36455 A
1 A
36456 CATGATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (18 bp):
ATAAGTGTTTAATGTTTT
Found at i:38377 original size:29 final size:30
Alignment explanation
Indices: 38317--38379 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
38307 AATACATATA
* * *
38317 TTTTGAAAATTACACTTTTGTTCTCTGAAC
1 TTTTAAAAATTACACTTTTGATCTCTAAAC
*
38347 TTTTAAAAATTACCCTTTTGATC-CTAAAC
1 TTTTAAAAATTACACTTTTGATCTCTAAAC
38376 TTTT
1 TTTT
38380 CCAAACTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (30 bp):
TTTTAAAAATTACACTTTTGATCTCTAAAC
Found at i:39832 original size:149 final size:149
Alignment explanation
Indices: 39562--40011 Score: 855
Period size: 149 Copynumber: 3.0 Consensus size: 149
39552 TAACAATATC
39562 AAAATCAAGCTGCTTAAGATTAGGTTCCTACTTTCTCAAAAATAACAATTTGTTCTGAAAATGCA
1 AAAATCAAGCTGCTTAAGATTAGGTTCCTACTTTCTCAAAAATAACAATTTGTTCTGAAAATGCA
39627 AAGGACCTCCCTCGAGAATCCAATCCCACATAGTGGAATTCACAAATGAAAAAAATACAGACTAG
66 AAGGACCTCCCTCGAGAATCCAATCCCACATAGTGGAATTCACAAATGAAAAAAATACAGACTAG
39692 GACCAGCCAAACTAACCTT
131 GACCAGCCAAACTAACCTT
*
39711 AAAATCAAGTTGCTTAAGATTAGGTTCCTACTTTCTCAAAAATAACAATTTGTTCTGAAAATGCA
1 AAAATCAAGCTGCTTAAGATTAGGTTCCTACTTTCTCAAAAATAACAATTTGTTCTGAAAATGCA
39776 AAGGACCTCCCTCGAGAATCCAATCCCACATAGTGGAATTCACAAATGAAAAAAATACAGACTAG
66 AAGGACCTCCCTCGAGAATCCAATCCCACATAGTGGAATTCACAAATGAAAAAAATACAGACTAG
39841 GACCAGCCAAACTAACCTT
131 GACCAGCCAAACTAACCTT
39860 AAAATCAAGCTGCTTAAGATTAGGTTCCTACTTTCTCAAAAATAACAATTTGTTCTGAAAATGCA
1 AAAATCAAGCTGCTTAAGATTAGGTTCCTACTTTCTCAAAAATAACAATTTGTTCTGAAAATGCA
*
39925 AAGGACCTCCCTCGAGAATCCAATCCCACATAGTGGAATTCACAAATGAAAAAAATTATAGACTA
66 AAGGACCTCCCTCGAGAATCCAATCCCACATAGTGGAATTCACAAATGAAAAAAA-TACAGACTA
* *
39990 GGACTAACCAAACTAACCTT
130 GGACCAGCCAAACTAACCTT
40010 AA
1 AA
40012 CTGGCGAATC
Statistics
Matches: 295, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
149 267 0.91
150 28 0.09
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (149 bp):
AAAATCAAGCTGCTTAAGATTAGGTTCCTACTTTCTCAAAAATAACAATTTGTTCTGAAAATGCA
AAGGACCTCCCTCGAGAATCCAATCCCACATAGTGGAATTCACAAATGAAAAAAATACAGACTAG
GACCAGCCAAACTAACCTT
Found at i:41018 original size:15 final size:15
Alignment explanation
Indices: 40998--41027 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40988 ACTATAATAT
40998 AATGAAATACATGTA
1 AATGAAATACATGTA
*
41013 AATGAAATACTTGTA
1 AATGAAATACATGTA
41028 TCATACAAAG
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:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (15 bp):
AATGAAATACATGTA
Found at i:42582 original size:3 final size:3
Alignment explanation
Indices: 42565--42643 Score: 108
Period size: 3 Copynumber: 26.3 Consensus size: 3
42555 ATGTAATTAA
42565 AAT AAT CAA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
42610 AAT AAT AAT AAT AAAT AAT -AT AAC GAT AAT AAT A
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT A
42644 TTAAAAAAAG
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.06
3 59 0.87
4 5 0.07
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:46336 original size:2 final size:2
Alignment explanation
Indices: 46329--46366 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
46319 TTGATCACTA
46329 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46367 GTTATGCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46599 original size:59 final size:59
Alignment explanation
Indices: 46523--46646 Score: 194
Period size: 59 Copynumber: 2.1 Consensus size: 59
46513 AGCAGACTGA
* * *
46523 ATATTCGGGAGTGCACTAAAGGATACCTAGTGCATATGATAGGCACGACCTTATGTGTC
1 ATATTCAGGAGTGCACTAAAGGATACCTAGTGCATATGACAGGCACGACCTTATGTATC
* * *
46582 ATATTCAGGATTGCACTAAAGGGTACCTAGTGCATATGGCAGGCACGACCTTATGTATC
1 ATATTCAGGAGTGCACTAAAGGATACCTAGTGCATATGACAGGCACGACCTTATGTATC
46641 ATATTC
1 ATATTC
46647 GATTTAGCAC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (59 bp):
ATATTCAGGAGTGCACTAAAGGATACCTAGTGCATATGACAGGCACGACCTTATGTATC
Found at i:53819 original size:59 final size:59
Alignment explanation
Indices: 53727--53911 Score: 307
Period size: 59 Copynumber: 3.1 Consensus size: 59
53717 GCCCAAGTTG
*
53727 CATATTCGGGATTACACTAAAGGATACCTAGTGCATATGATGGGCACGACCTTATGTGT
1 CATATTCGGGATTGCACTAAAGGATACCTAGTGCATATGATGGGCACGACCTTATGTGT
53786 CATATTCGGGATTGCACTAAAGGATACCTAGTGCATATGATGGGCACGACCTTATGTGT
1 CATATTCGGGATTGCACTAAAGGATACCTAGTGCATATGATGGGCACGACCTTATGTGT
* * * * * *
53845 CATATTTGAGATTGCACTAAAGGATACCTAGTGCTTATGGTGGGCATGACCTTATGTAT
1 CATATTCGGGATTGCACTAAAGGATACCTAGTGCATATGATGGGCACGACCTTATGTGT
53904 CATATTCG
1 CATATTCG
53912 ATTTTGCACT
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 118 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (59 bp):
CATATTCGGGATTGCACTAAAGGATACCTAGTGCATATGATGGGCACGACCTTATGTGT
Found at i:55847 original size:13 final size:13
Alignment explanation
Indices: 55804--55850 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
55794 TCTCTTTTAT
55804 TTTTACTTTTCAAG
1 TTTTA-TTTTCAAG
* *
55818 TTTT-TATTC-AC
1 TTTTATTTTCAAG
55829 TTTTATTTTCAAG
1 TTTTATTTTCAAG
55842 TTTTATTTT
1 TTTTATTTT
55851 TAATATGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
11 5 0.19
12 8 0.30
13 10 0.37
14 4 0.15
ACGTcount: A:0.19, C:0.11, G:0.04, T:0.66
Consensus pattern (13 bp):
TTTTATTTTCAAG
Found at i:61418 original size:26 final size:26
Alignment explanation
Indices: 61388--61442 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
61378 TTATAAAAGC
*
61388 TTTCTCTTTTAT-TTTTAATTTTCAAG
1 TTTCTCTTTTATCTATT-ATTTTCAAG
* *
61414 TTTCTTTTTTCTCTATTATTTTCAAG
1 TTTCTCTTTTATCTATTATTTTCAAG
61440 TTT
1 TTT
61443 TGTTTTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.16, C:0.13, G:0.04, T:0.67
Consensus pattern (26 bp):
TTTCTCTTTTATCTATTATTTTCAAG
Found at i:64851 original size:16 final size:16
Alignment explanation
Indices: 64830--64861 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
64820 TGGATTAAAG
64830 CGTGAAATAGAAAATT
1 CGTGAAATAGAAAATT
64846 CGTGAAATAGAAAATT
1 CGTGAAATAGAAAATT
64862 ATTCTATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (16 bp):
CGTGAAATAGAAAATT
Found at i:65396 original size:31 final size:32
Alignment explanation
Indices: 65356--65415 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 32
65346 GAGTGTTGAA
65356 ATTGATGTAATTGTTTAATAGTTAATGGAATC
1 ATTGATGTAATTGTTTAATAGTTAATGGAATC
65388 ATTG-TGTAATTGTTTAATAGTTAATGGA
1 ATTGATGTAATTGTTTAATAGTTAATGGA
65416 CTATGCTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (32 bp):
ATTGATGTAATTGTTTAATAGTTAATGGAATC
Found at i:77557 original size:66 final size:66
Alignment explanation
Indices: 77368--77593 Score: 303
Period size: 66 Copynumber: 3.4 Consensus size: 66
77358 GAGAGCCATA
* * * *
77368 GGTGCATTATCGACATAAAAGGTGTCAATAATGAAAATTATCGATCGATTTTGATTAATGCATAA
1 GGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGTTTAATGCATAA
77433 C
66 C
* * * * * * *
77434 TGTACATTATCGGTATAAAA-ATGCCACTATTAAAAATTATCTATCGATTTT-TATTAATGCATA
1 GGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGT-TTAATGCATA
77497 AC
65 AC
77499 GGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGTTTAATGCATAA
1 GGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGTTTAATGCATAA
77564 C
66 C
* * *
77565 GATGCATTATCAGCATAAAATGTGCCACT
1 GGTGCATTATCGGCATAAAAGGTGCCACT
77594 CATGGTATTC
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
65 54 0.40
66 81 0.60
67 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (66 bp):
GGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGTTTAATGCATAA
C
Found at i:89561 original size:28 final size:27
Alignment explanation
Indices: 89469--89562 Score: 73
Period size: 29 Copynumber: 3.3 Consensus size: 27
89459 CTTGACTTTG
* * * *
89469 CATGGGTTTATATCACCGTCCTGATTCTG
1 CATGGGATTATATC-TCGTCTTG-TTCTT
* *
89498 CATAGGATTATATCCTCATCTATGTTCTGT
1 CATGGGATTATAT-CTCGTCT-TGTTCT-T
89528 -ATGGGATTATATCTCGTCTTGTTTCTT
1 CATGGGATTATATCTCGTCTTG-TTCTT
89555 CATGGGAT
1 CATGGGAT
89563 CCTCTATGGA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
27 3 0.06
28 17 0.33
29 29 0.56
30 3 0.06
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (27 bp):
CATGGGATTATATCTCGTCTTGTTCTT
Found at i:92712 original size:24 final size:24
Alignment explanation
Indices: 92680--92727 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
92670 AAAGAGTAAG
92680 TTTAGAAAATAACCATAAATTCTA
1 TTTAGAAAATAACCATAAATTCTA
92704 TTTAGAAAATAACCATAAATTCTA
1 TTTAGAAAATAACCATAAATTCTA
92728 CAAAAATGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
TTTAGAAAATAACCATAAATTCTA
Found at i:93350 original size:2 final size:2
Alignment explanation
Indices: 93343--93376 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
93333 GATTACTAAC
93343 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
93377 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93642 original size:59 final size:59
Alignment explanation
Indices: 93558--93673 Score: 187
Period size: 59 Copynumber: 2.0 Consensus size: 59
93548 TGCATATTCG
* *
93558 GGATTGCGCTAAAGGATACCTAGTGCATATGATAGGCACGACCTTATGTGTCATATTTA
1 GGATTGCACTAAAGGATACCTAGTGCATATGATAGGCACGACCTTATGTATCATATTTA
* * *
93617 GGATTGCACTAAAGGATACCTAGTGCATATGGTGGGCATGACCTTATGTATCATATT
1 GGATTGCACTAAAGGATACCTAGTGCATATGATAGGCACGACCTTATGTATCATATT
93674 CGGTTTTGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.31
Consensus pattern (59 bp):
GGATTGCACTAAAGGATACCTAGTGCATATGATAGGCACGACCTTATGTATCATATTTA
Found at i:93683 original size:59 final size:58
Alignment explanation
Indices: 93550--93685 Score: 182
Period size: 59 Copynumber: 2.3 Consensus size: 58
93540 TAGCAAGTTG
* *
93550 CATATTCGGGATTGCGCTAAAGGATACCTAGTGCATATGATAGGCACGACCTTATGTGT
1 CATATTC-GGATTGCACTAAAGGATACCTAGTGCATATGATAGGCACGACCTTATGTAT
* * * *
93609 CATATTTAGGATTGCACTAAAGGATACCTAGTGCATATGGTGGGCATGACCTTATGTAT
1 CATA-TTCGGATTGCACTAAAGGATACCTAGTGCATATGATAGGCACGACCTTATGTAT
*
93668 CATATTCGGTTTTGCACT
1 CATATTCGG-ATTGCACT
93686 TCAGTGCATA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 4 0.06
59 61 0.91
60 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (58 bp):
CATATTCGGATTGCACTAAAGGATACCTAGTGCATATGATAGGCACGACCTTATGTAT
Found at i:98424 original size:19 final size:20
Alignment explanation
Indices: 98381--98426 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
98371 GACTATGCTG
* * *
98381 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGAT
98401 GAAATTGATGTTAGAAT-AT
1 GAAATTGATGTTAGAATGAT
98420 GAAATTG
1 GAAATTG
98427 GACCATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGAT
Found at i:98681 original size:3 final size:3
Alignment explanation
Indices: 98673--98809 Score: 238
Period size: 3 Copynumber: 45.7 Consensus size: 3
98663 TTTTTATCCA
*
98673 TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
98721 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
98769 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
98810 ATTTATATTA
Statistics
Matches: 126, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 126 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:99319 original size:18 final size:18
Alignment explanation
Indices: 99283--99331 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
99273 AGAGACGGAA
*
99283 AAACAGAAAGAAAAGACAG
1 AAACA-AAAAAAAAGACAG
*
99302 AAACAAAAAAAAATACAG
1 AAACAAAAAAAAAGACAG
99320 AGAA-AAAAAAAA
1 A-AACAAAAAAAA
99332 CAAACTATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.78, C:0.08, G:0.12, T:0.02
Consensus pattern (18 bp):
AAACAAAAAAAAAGACAG
Found at i:100936 original size:18 final size:17
Alignment explanation
Indices: 100913--100963 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
100903 ATCTTTTCAA
100913 ATTTTTTATTTATTTAT
1 ATTTTTTATTTATTTAT
*
100930 -TATTTTTATAATATTTAT
1 AT-TTTTTAT-TTATTTAT
*
100948 ATGTTTTATTTTATTT
1 ATTTTTTA-TTTATTT
100964 GCAAGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 17 0.63
19 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTTTTTATTTATTTAT
Found at i:111575 original size:13 final size:13
Alignment explanation
Indices: 111553--111626 Score: 59
Period size: 13 Copynumber: 5.8 Consensus size: 13
111543 TATTATGCTT
*
111553 GAAGAAAAAAAAA
1 GAAGAGAAAAAAA
111566 GAAGAGAAAAAAA
1 GAAGAGAAAAAAA
111579 GAAGA-AAAAATATA
1 GAAGAGAAAAA-A-A
*
111593 GAA-A-ATGAAAAA
1 GAAGAGA-AAAAAA
*
111605 GAAAAG-AAAAAA
1 GAAGAGAAAAAAA
111617 GAAG-GAAAAA
1 GAAGAGAAAAA
111627 GGAAAAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
11 1 0.02
12 21 0.41
13 22 0.43
14 7 0.14
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (13 bp):
GAAGAGAAAAAAA
Found at i:111577 original size:12 final size:12
Alignment explanation
Indices: 111560--111626 Score: 57
Period size: 12 Copynumber: 5.4 Consensus size: 12
111550 CTTGAAGAAA
111560 AAAAAAGAAGAG
1 AAAAAAGAAGAG
*
111572 AAAAAAAGAAGAA
1 -AAAAAAGAAGAG
*
111585 AAAATATAGAAAATG
1 AAAA-A-AGAAGA-G
*
111600 -AAAAAGAAAAG
1 AAAAAAGAAGAG
111611 AAAAAAGAAG-G
1 AAAAAAGAAGAG
111622 AAAAA
1 AAAAA
111627 GGAAAAAAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
11 7 0.15
12 18 0.39
13 13 0.28
14 8 0.17
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (12 bp):
AAAAAAGAAGAG
Found at i:111583 original size:26 final size:29
Alignment explanation
Indices: 111553--111625 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 29
111543 TATTATGCTT
*
111553 GAAGAAAAAA-AAAGAAGA-GAAAAA-AA
1 GAAGAAAAAATAAAGAAAATGAAAAAGAA
*
111579 GAAGAAAAAATATAGAAAATGAAAAAGAA
1 GAAGAAAAAATAAAGAAAATGAAAAAGAA
* *
111608 -AAGAAAAAAGAAGGAAAA
1 GAAGAAAAAATAAAGAAAA
111626 AGGAAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 10 0.26
27 6 0.15
28 21 0.54
29 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (29 bp):
GAAGAAAAAATAAAGAAAATGAAAAAGAA
Found at i:111624 original size:28 final size:25
Alignment explanation
Indices: 111553--111637 Score: 73
Period size: 28 Copynumber: 3.1 Consensus size: 25
111543 TATTATGCTT
*
111553 GAAGAAAAAAAAAGAAGAGAAAAAAA
1 GAAG-AAAAAAAAGAAAAGAAAAAAA
111579 GAAGAAAAAATATAGAAAATGAAAAAGAA
1 GAAGAAAAAA-A-AGAAAA-GAAAAA-AA
111608 -AAGAAAAAAGAAGGAAAAAGGAAAAAAA
1 GAAGAAAAAA-AA-G-AAAA-GAAAAAAA
111636 GA
1 GA
111638 GGGTCAAGGT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
25 6 0.12
26 5 0.10
27 6 0.12
28 19 0.39
29 13 0.27
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (25 bp):
GAAGAAAAAAAAGAAAAGAAAAAAA
Found at i:111984 original size:16 final size:16
Alignment explanation
Indices: 111965--112006 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
111955 TTTCAAGTGT
*
111965 AATTTATTTGAGATTC
1 AATTTATTTGAAATTC
111981 AATTTATTTTTGAAATTC
1 AATTTA--TTTGAAATTC
111999 AATTTATT
1 AATTTATT
112007 CTTTTCTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 8 0.35
18 15 0.65
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (16 bp):
AATTTATTTGAAATTC
Found at i:111998 original size:18 final size:18
Alignment explanation
Indices: 111971--112006 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
111961 GTGTAATTTA
*
111971 TTTGAGATTCAATTTATT
1 TTTGAAATTCAATTTATT
111989 TTTGAAATTCAATTTATT
1 TTTGAAATTCAATTTATT
112007 CTTTTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (18 bp):
TTTGAAATTCAATTTATT
Found at i:113724 original size:113 final size:113
Alignment explanation
Indices: 113526--114072 Score: 920
Period size: 113 Copynumber: 4.8 Consensus size: 113
113516 TTAGCAAAGA
113526 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
113591 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
113639 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* *
113704 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* * * * *
113752 TGAATTCATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGA
1 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGA
113816 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
113865 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* *
113930 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* * * * *
113978 TGAATTCATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGA
1 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGA
114042 AGAAGGAAG-AGAAAGTTCATAATGAGAAGAA
65 AGAAGGAAGAAG-AAGTTCATAATGAGAAGAA
114073 CTCATCAAGA
Statistics
Matches: 409, Mismatches: 21, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
112 4 0.01
113 404 0.99
114 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
Found at i:113926 original size:226 final size:226
Alignment explanation
Indices: 113526--114072 Score: 1017
Period size: 226 Copynumber: 2.4 Consensus size: 226
113516 TTAGCAAAGA
* * * * *
113526 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGA
1 TGAATTCATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGA
113590 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
113655 TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
130 TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
113720 CATAATGAGAAGAATTTGTTCAACCTTTTGCT
195 CATAATGAGAAGAATTTGTTCAACCTTTTGCT
113752 TGAATTCATCATTTGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATTCATCATTTGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAA
113817 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGT
113882 GGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
131 GGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
113947 ATAATGAGAAGAATTTGTTCAACCTTTTGCT
196 ATAATGAGAAGAATTTGTTCAACCTTTTGCT
113978 TGAATTCATCATTTGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATTCATCATTTGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAA
114043 GAAGGAAG-AGAAAGTTCATAATGAGAAGAA
66 GAAGGAAGAAG-AAGTTCATAATGAGAAGAA
114073 CTCATCAAGA
Statistics
Matches: 314, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
225 3 0.01
226 311 0.99
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (226 bp):
TGAATTCATCATTTGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGT
GGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
ATAATGAGAAGAATTTGTTCAACCTTTTGCT
Found at i:114330 original size:3 final size:3
Alignment explanation
Indices: 114322--114461 Score: 253
Period size: 3 Copynumber: 46.7 Consensus size: 3
114312 TTTTTATCCA
*
114322 TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
114370 TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
114418 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
114462 ATTTATATTA
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 131 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:114971 original size:18 final size:18
Alignment explanation
Indices: 114935--114983 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
114925 AGAGACGGAA
*
114935 AAACAGAAAGAAAAGACAG
1 AAACA-AAAAAAAAGACAG
*
114954 AAACAAAAAAAAATACAG
1 AAACAAAAAAAAAGACAG
114972 AGAA-AAAAAAAA
1 A-AACAAAAAAAA
114984 CAAACTATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.78, C:0.08, G:0.12, T:0.02
Consensus pattern (18 bp):
AAACAAAAAAAAAGACAG
Found at i:129634 original size:139 final size:139
Alignment explanation
Indices: 129384--129664 Score: 526
Period size: 139 Copynumber: 2.0 Consensus size: 139
129374 TGGGTGAAGA
129384 AAACTCTTCAAAAACCTTTGTTCCAAAACAATGATACATAAGTAATAATGTCTAAGAGTGCACAA
1 AAACTCTTCAAAAACCTTTGTTCCAAAACAATGATACATAAGTAATAATGTCTAAGAGTGCACAA
* * *
129449 ATATAGAACAAGCGTACTCTTGTCGCTGATATTTCACCCACTCCTTGAGGAGTTTGATATTGATT
66 ATATAGAACAAGCGCACTCTAGTCGCTAATATTTCACCCACTCCTTGAGGAGTTTGATATTGATT
129514 TTCTGATCT
131 TTCTGATCT
129523 AAACTCTTCAAAAACCTTTGTTCCAAAACAATGATACATAAGTAATAATGTCTAAGAGTGCACAA
1 AAACTCTTCAAAAACCTTTGTTCCAAAACAATGATACATAAGTAATAATGTCTAAGAGTGCACAA
*
129588 ATATAGAACAAGTGCACTCTAGTCGCTAATATTTCACCCACTCCTTGAGGAGTTTGATATTGATT
66 ATATAGAACAAGCGCACTCTAGTCGCTAATATTTCACCCACTCCTTGAGGAGTTTGATATTGATT
129653 TTCTGATCT
131 TTCTGATCT
129662 AAA
1 AAA
129665 ACTTGCTTAG
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 138 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (139 bp):
AAACTCTTCAAAAACCTTTGTTCCAAAACAATGATACATAAGTAATAATGTCTAAGAGTGCACAA
ATATAGAACAAGCGCACTCTAGTCGCTAATATTTCACCCACTCCTTGAGGAGTTTGATATTGATT
TTCTGATCT
Found at i:130784 original size:20 final size:19
Alignment explanation
Indices: 130759--130798 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
130749 TTTTTGATGC
130759 TATATTTTTTGTAATTATTT
1 TATATTTTTTGTAATT-TTT
*
130779 TATATTTTTTTTAATTTTT
1 TATATTTTTTGTAATTTTT
130798 T
1 T
130799 GAATATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (19 bp):
TATATTTTTTGTAATTTTT
Found at i:132447 original size:15 final size:15
Alignment explanation
Indices: 132427--132457 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
132417 TGAAGAAAAT
*
132427 AAAGTAAAAACTTAA
1 AAAGTAAAAACGTAA
132442 AAAGTAAAAACGTAA
1 AAAGTAAAAACGTAA
132457 A
1 A
132458 GGAAAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.06, G:0.10, T:0.16
Consensus pattern (15 bp):
AAAGTAAAAACGTAA
Found at i:146722 original size:18 final size:18
Alignment explanation
Indices: 146695--146742 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
146685 TGATGCAATT
146695 AGTATCGATACTGATATG
1 AGTATCGATACTGATATG
*
146713 AGTATTGATACTGATATG
1 AGTATCGATACTGATATG
146731 AGTATCGATACT
1 AGTATCGATACT
146743 AAGAGAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.35
Consensus pattern (18 bp):
AGTATCGATACTGATATG
Found at i:147236 original size:54 final size:53
Alignment explanation
Indices: 147172--147422 Score: 263
Period size: 54 Copynumber: 4.7 Consensus size: 53
147162 GAACTGTGTG
* * * * *
147172 TGCAAGTTAAGAAATTCATATTAAGTTTATAAATTTTCGTATTAGCATTGTGTC
1 TGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATT-GCATTATGTC
* * *
147226 TGCAACTTAAGAAATTCATAATGAGTTTGTGAATTTCCGTATTG-ATAGTATGTG
1 TGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGCAT--TATGTC
*
147280 TGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATG-C
1 TGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATT-GCATTATGTC
* * * *
147333 GTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTTCGTATTGGCACTATGTG
1 -TGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATT-GCATTATGTC
* * * * * *
147388 TGCACCCTACGTAATTCATAATGAGGTTGTGAATT
1 TGCAACTTAAGAAATTCATAATGAGTTTATGAATT
147423 ACAGTATCAG
Statistics
Matches: 170, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
52 2 0.01
53 1 0.01
54 165 0.97
55 1 0.01
56 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (53 bp):
TGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGCATTATGTC
Found at i:147345 original size:108 final size:108
Alignment explanation
Indices: 147155--147422 Score: 315
Period size: 108 Copynumber: 2.5 Consensus size: 108
147145 TTGTATTTAT
* * * * *
147155 CGTATTGGA-ACTGTGTGTGCAAGTTAAGAAATTCATATTAAGTTTATAAATTTTCGTATTAGCA
1 CGTATT-GACACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTAGCA
* * * *
147219 TTGTGTCTGCAACTTAAGAAATTCATAATGAGTTTGTGAATTTC
65 CTATGTCTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTC
* * *
147263 CGTATTGATAGTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCAC
1 CGTATTGACACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTAGCAC
* *
147328 TATG-CGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTT
66 TATGTC-TGCAACCTAAGAAATTCATAATGAGTTTATGAATTTC
* * * * * * *
147371 CGTATTGGCACTATGTGTGCACCCTACGTAATTCATAATGAGGTTGTGAATT
1 CGTATTGACACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATT
147423 ACAGTATCAG
Statistics
Matches: 136, Mismatches: 22, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
107 3 0.02
108 133 0.98
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (108 bp):
CGTATTGACACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTAGCAC
TATGTCTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTC
Found at i:162141 original size:45 final size:46
Alignment explanation
Indices: 162090--162239 Score: 238
Period size: 45 Copynumber: 3.3 Consensus size: 46
162080 AAATAGAGGT
*
162090 TTAGGAAATAAGTTTGGTAATGTCT-GTAATAGCTCCAACATAGTC
1 TTAGGAAATAAGTTGGGTAATGTCTGGTAATAGCTCCAACATAGTC
162135 TTAGGAAATAAGTTGGGTAATGT-TGGTAATAGCTCCAACATAGTC
1 TTAGGAAATAAGTTGGGTAATGTCTGGTAATAGCTCCAACATAGTC
162180 TTAGGAAATAAGTTGGGTAATG-CTGGTAATAGCTCCAACATAG--
1 TTAGGAAATAAGTTGGGTAATGTCTGGTAATAGCTCCAACATAGTC
*
162223 TAAGAGAAATAAGTTGG
1 TTAG-GAAATAAGTTGG
162240 AATTCCAACA
Statistics
Matches: 100, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
43 3 0.03
44 13 0.13
45 84 0.84
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (46 bp):
TTAGGAAATAAGTTGGGTAATGTCTGGTAATAGCTCCAACATAGTC
Found at i:174234 original size:139 final size:138
Alignment explanation
Indices: 173927--174311 Score: 391
Period size: 139 Copynumber: 2.8 Consensus size: 138
173917 TAAAGGATTA
* * * * *** * * * *
173927 AACCTAAAATGTAGGCCCTAATATTAAATCACATTGAATTTTATCAATTTATTAAATCGAATAAT
1 AACCTAAAATGAAGGCTCTAATACT-AATCATAACCAATTTTAACAAATTATTGAATCAAATAAT
* * * *
173992 TAATATGGAACCTCGGGCATAAAAAGTGAGAACCAAATAAAACATTCACTTAAAGTAAAGGACTA
65 TAATATGGAACCTCAGGCAT-AAAAGCGAGAACCAAATAAAACATCCACCTAAAGTAAAGGACTA
** *
174057 TGGTGAAGTT
129 AAGTGAAATT
* * * *
174067 AATCTAAAATGGAGGCTCTAATACTAATCCTAACCAATTTTAATAAATTATTGAATCAAATAATT
1 AACCTAAAATGAAGGCTCTAATACTAATCATAACCAATTTTAACAAATTATTGAATCAAATAATT
* * * * *
174132 AATATGGAACTTCAGGCATAAACGCGAGGATCAAATTAAAA-ATCCACCT-AATTAAAGGACTAA
66 AATATGGAACCTCAGGCATAAAAGCGAGAACCAAA-TAAAACATCCACCTAAAGTAAAGGACTAA
174195 AGTGAAATT
130 AGTGAAATT
* * *
174204 AAACCTAATATGAAGGCTCTAATTATTAATCATAACCAATTTTAACAAATTATTGGAT-AGAATA
1 -AACCTAAAATGAAGGCTCTAA-TACTAATCATAACCAATTTTAACAAATTATTGAATCA-AATA
*
174268 ATTAATATGGAACCTCAGGCATAAAAGTGA-ATACCAAATCAAAA
63 ATTAATATGGAACCTCAGGCATAAAAGCGAGA-ACCAAAT-AAAA
174312 ATTCTCCCAA
Statistics
Matches: 201, Mismatches: 38, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
137 19 0.09
138 38 0.19
139 123 0.61
140 21 0.10
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (138 bp):
AACCTAAAATGAAGGCTCTAATACTAATCATAACCAATTTTAACAAATTATTGAATCAAATAATT
AATATGGAACCTCAGGCATAAAAGCGAGAACCAAATAAAACATCCACCTAAAGTAAAGGACTAAA
GTGAAATT
Found at i:174368 original size:23 final size:23
Alignment explanation
Indices: 174339--174385 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
174329 ACCTTAGCGA
174339 TTAAATTAAAAAGAAACTAAATT
1 TTAAATTAAAAAGAAACTAAATT
*
174362 TTAAATTAAAAGGAAACTAAATT
1 TTAAATTAAAAAGAAACTAAATT
174385 T
1 T
174386 AAGGACATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (23 bp):
TTAAATTAAAAAGAAACTAAATT
Found at i:174649 original size:29 final size:29
Alignment explanation
Indices: 174594--174649 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
174584 AAAATGCATA
* *
174594 AAAATATTAGAAATTAAAGAACTGAAAGT
1 AAAATACTAGAAATTAAAGAAATGAAAGT
*
174623 AAAATACTGGAAATTAAA-AAATAGAAA
1 AAAATACTAGAAATTAAAGAAAT-GAAA
174650 ATTAATGGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.21
Consensus pattern (29 bp):
AAAATACTAGAAATTAAAGAAATGAAAGT
Found at i:177485 original size:20 final size:19
Alignment explanation
Indices: 177437--177651 Score: 112
Period size: 20 Copynumber: 10.8 Consensus size: 19
177427 CGAATTTGAC
*
177437 AATTTCGCAACACAAATTT
1 AATTTCGCAACACAATTTT
**
177456 CTTTTCCGCAACACAATTTTT
1 AATTT-CGCAACACAA-TTTT
***
177477 AATTTCGCAACTTGATTTT
1 AATTTCGCAACACAATTTT
* *
177496 AGAATTCGCAACACGATTTTCT
1 A-ATTTCGCAACAC-AATTT-T
* *
177518 AA-TTCGCAA-AGCACGTTTC
1 AATTTCGCAACA-CA-ATTTT
* *
177537 AATTTCACAACTCGAATTTT
1 AATTTCGCAACAC-AATTTT
* * *
177557 ATTTTCGCAACTCGATTTTT
1 AATTTCGCAACAC-AATTTT
*
177577 GAA-TTCGCAGCACGAATTTT
1 -AATTTCGCAACAC-AATTTT
*
177597 AATTTCGCAACATGAATTTT
1 AATTTCGCAACA-CAATTTT
* *
177617 AATTTCGCAAAACAGCTTTT
1 AATTTCGCAACACA-ATTTT
*
177637 ATTTTCGCAACACAA
1 AATTTCGCAACACAA
177652 ATGTAAATAG
Statistics
Matches: 148, Mismatches: 34, Indels: 28
0.70 0.16 0.13
Matches are distributed among these distances:
19 15 0.10
20 119 0.80
21 12 0.08
22 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (19 bp):
AATTTCGCAACACAATTTT
Found at i:177526 original size:60 final size:59
Alignment explanation
Indices: 177437--177626 Score: 181
Period size: 60 Copynumber: 3.2 Consensus size: 59
177427 CGAATTTGAC
* * *
177437 AATTTCGCAACACAAATTTCT-TTTCCGCAACACAATTTTTAATTTCGCAACTTG-ATTTT
1 AATTTCGCAACACGATTTTCTAATT-CGCAACACAA-TTTTAATTTCGCAACTTGAATTTT
* * * * *
177496 AGAATTCGCAACACGATTTTCTAATTCGCAA-AGCACGTTTCAATTTCACAACTCGAATTTT
1 A-ATTTCGCAACACGATTTTCTAATTCGCAACA-CA-ATTTTAATTTCGCAACTTGAATTTT
* * * *
177557 ATTTTCGCAACTCGATTTT-TGAATTCGCAGCACGAATTTTAATTTCGCAACATGAATTTT
1 AATTTCGCAACACGATTTTCT-AATTCGCAACAC-AATTTTAATTTCGCAACTTGAATTTT
177617 AATTTCGCAA
1 AATTTCGCAA
177627 AACAGCTTTT
Statistics
Matches: 105, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
59 3 0.03
60 92 0.88
61 10 0.10
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (59 bp):
AATTTCGCAACACGATTTTCTAATTCGCAACACAATTTTAATTTCGCAACTTGAATTTT
Found at i:177759 original size:22 final size:22
Alignment explanation
Indices: 177734--177788 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
177724 TCTCTCACTC
*
177734 TCTCCGGCGACATCCATCTCCA
1 TCTCCGGCGACATCCATCCCCA
* *
177756 TCTCCGGTGACATCCGTCCCCA
1 TCTCCGGCGACATCCATCCCCA
*
177778 TATCCGGCGAC
1 TCTCCGGCGAC
177789 CCCCTCCATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.16, C:0.44, G:0.18, T:0.22
Consensus pattern (22 bp):
TCTCCGGCGACATCCATCCCCA
Found at i:178189 original size:33 final size:34
Alignment explanation
Indices: 178145--178217 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 34
178135 CTTGAAACTT
* * *
178145 AAATTCGCAACAC-GAAATCGCAACTCGAAAATG
1 AAATTCACAACACAAAAATCGCAACTCGAAAAAG
*
178178 AAATTCACAACACAAAAATTGCAACTCGAAAAAG
1 AAATTCACAACACAAAAATCGCAACTCGAAAAAG
178212 AAATTC
1 AAATTC
178218 GCGTTGCGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
33 12 0.34
34 23 0.66
ACGTcount: A:0.51, C:0.22, G:0.11, T:0.16
Consensus pattern (34 bp):
AAATTCACAACACAAAAATCGCAACTCGAAAAAG
Found at i:178230 original size:53 final size:54
Alignment explanation
Indices: 178173--178281 Score: 166
Period size: 53 Copynumber: 2.0 Consensus size: 54
178163 CGCAACTCGA
** * *
178173 AAATGAAATTCACAACACAAAAATTGCAACTCGAAAAA-GAAATTCGCGTTGCG
1 AAATGAAATTCACAACACAAAAAGCGCAACTCAAAAAATGAAATTCACGTTGCG
*
178226 AAATGAAATTCGCAACACAAAAAGCGCAACTCAAAAAATGAAATTCACGTTGCG
1 AAATGAAATTCACAACACAAAAAGCGCAACTCAAAAAATGAAATTCACGTTGCG
178280 AA
1 AA
178282 TTCAAAATTC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 34 0.68
54 16 0.32
ACGTcount: A:0.49, C:0.19, G:0.15, T:0.17
Consensus pattern (54 bp):
AAATGAAATTCACAACACAAAAAGCGCAACTCAAAAAATGAAATTCACGTTGCG
Found at i:178291 original size:20 final size:20
Alignment explanation
Indices: 178266--178303 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
178256 TCAAAAAATG
178266 AAATTC-ACGTTGCGAATTCA
1 AAATTCGAC-TTGCGAATTCA
178286 AAATTCGACTTGCGAATT
1 AAATTCGACTTGCGAATT
178304 TCATTTTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (20 bp):
AAATTCGACTTGCGAATTCA
Found at i:179723 original size:14 final size:15
Alignment explanation
Indices: 179687--179724 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
179677 GAAATCATTG
179687 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
179702 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
179717 AAAAATTA
1 AAAAATTA
179725 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:179938 original size:20 final size:20
Alignment explanation
Indices: 179924--180212 Score: 279
Period size: 20 Copynumber: 14.5 Consensus size: 20
179914 CGAAAATTGA
179924 GTTGCGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAATTCGT
179944 GTTGCGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAATTCGT
* *** * *
179964 TTTGCGAATTCGAAAATCGA
1 GTTGCGAAAAAGAAATTCGT
179984 GTTGCGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAATTCGT
180004 GTTGCGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAATTCGT
* *
180024 GTTGCAAAAAAGAAAATC-T
1 GTTGCGAAAAAGAAATTCGT
180043 AGTTGCGAAAAAGAAATTCGT
1 -GTTGCGAAAAAGAAATTCGT
* *
180064 GTTGCAAAAAAGAAATTCAT
1 GTTGCGAAAAAGAAATTCGT
** * *
180084 GTTGC-AAATTCGAAAATCGA
1 GTTGCGAAA-AAGAAATTCGT
* *
180104 GTTGCGAAATTATAAA-TCGT
1 GTTGCGAAA-AAGAAATTCGT
180124 GTTGCGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAATTCGT
* *
180144 GTTGCGAATTCAA-AAA-TCGA
1 GTTGCGAA--AAAGAAATTCGT
*
180164 CTTGCGAAATTAA-AAA-TCGT
1 GTTGCGAAA--AAGAAATTCGT
*
180184 GTTGTGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAATTCGT
180204 GTTGC-AAAA
1 GTTGCGAAAA
180213 TTGTCAAATT
Statistics
Matches: 222, Mismatches: 36, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
18 2 0.01
19 15 0.07
20 191 0.86
21 12 0.05
22 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.26
Consensus pattern (20 bp):
GTTGCGAAAAAGAAATTCGT
Found at i:179986 original size:60 final size:60
Alignment explanation
Indices: 179896--180208 Score: 434
Period size: 60 Copynumber: 5.2 Consensus size: 60
179886 TACGAAATTA
* *
179896 AAATTCGTGTTACGAATTCGAAAATTGAGTTGCGAAAAAGAAATTCGTGTTGCGAAAAAG
1 AAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAAAGAAATTCGTGTTGCGAAAAAG
*
179956 AAATTCGTTTTGCGAATTCGAAAATCGAGTTGCGAAAAAGAAATTCGTGTTGCGAAAAAG
1 AAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAAAGAAATTCGTGTTGCGAAAAAG
* *** * *
180016 AAATTCGTGTTGCAAAAAAGAAAATCTAGTTGCGAAAAAGAAATTCGTGTTGCAAAAAAG
1 AAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAAAGAAATTCGTGTTGCGAAAAAG
* * * *
180076 AAATTCATGTTGCAAATTCGAAAATCGAGTTGCGAAATTATAAA-TCGTGTTGCGAAAAAG
1 AAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAA-AAGAAATTCGTGTTGCGAAAAAG
* * *
180136 AAATTCGTGTTGCGAATTCAAAAATCGACTTGCGAAATTAA-AAA-TCGTGTTGTGAAAAAG
1 AAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAA--AAGAAATTCGTGTTGCGAAAAAG
180196 AAATTCGTGTTGC
1 AAATTCGTGTTGC
180209 AAAATTGTCA
Statistics
Matches: 227, Mismatches: 24, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
60 221 0.97
61 6 0.03
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.27
Consensus pattern (60 bp):
AAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAAAGAAATTCGTGTTGCGAAAAAG
Found at i:180273 original size:41 final size:40
Alignment explanation
Indices: 180199--180313 Score: 108
Period size: 41 Copynumber: 2.8 Consensus size: 40
180189 GAAAAAGAAA
* * * *
180199 TTCGTGTTGCAAAATTGTCAAATTCGAGTTGCG-AATTTGACT
1 TTCGTGTTGC-GAATT-CCAAATTCGAGTTGCGAAATTGGA-G
* *
180241 TTTGTGTTGCGAATTCCAAATTCTGTGTTGCGAAATTGGAG
1 TTCGTGTTGCGAATTCCAAATTC-GAGTTGCGAAATTGGAG
* *
180282 TTCGTGTTGCGAATT-CAAAATCGAGTTACGAA
1 TTCGTGTTGCGAATTCCAAATTCGAGTTGCGAA
180314 TTCGTTGGTT
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
39 8 0.13
40 13 0.21
41 25 0.41
42 15 0.25
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (40 bp):
TTCGTGTTGCGAATTCCAAATTCGAGTTGCGAAATTGGAG
Found at i:181463 original size:8 final size:9
Alignment explanation
Indices: 181444--181475 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
181434 CTACACCTCT
181444 AAAAACTAA
1 AAAAACTAA
181453 AAAAACTAA
1 AAAAACTAA
*
181462 AAAAACCAA
1 AAAAACTAA
181471 AAAAA
1 AAAAA
181476 AACCCTGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.81, C:0.12, G:0.00, T:0.06
Consensus pattern (9 bp):
AAAAACTAA
Found at i:183818 original size:45 final size:45
Alignment explanation
Indices: 183707--183825 Score: 193
Period size: 45 Copynumber: 2.6 Consensus size: 45
183697 TTATGTGTTT
* * * *
183707 GTGTGCATTTCATAAAATATAAATAATTTATTATTATTTTGTGCA
1 GTGTGCATTTCATAAAATATACACATTTTATTATTATTTCGTGCA
*
183752 GTGTGCTTTTCATAAAATATACACATTTTATTATTATTTCGTGCA
1 GTGTGCATTTCATAAAATATACACATTTTATTATTATTTCGTGCA
183797 GTGTGCATTTCATAAAATATACACATTTT
1 GTGTGCATTTCATAAAATATACACATTTT
183826 TCGTGCATTG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (45 bp):
GTGTGCATTTCATAAAATATACACATTTTATTATTATTTCGTGCA
Found at i:187019 original size:150 final size:150
Alignment explanation
Indices: 186723--186999 Score: 328
Period size: 150 Copynumber: 1.8 Consensus size: 150
186713 AAGTGGTTGT
* * *
186723 TTCAATAGAGAATTCCTGTGAAAAACATAAGAGGCAAAAGGATGAAAAAGGAAATTAAAGCAGAA
1 TTCAATAGAGAATTCCTGTGAAAAACATAAGACGCAAAAGGATGAAAAAGGAAATCAAAGCAAAA
* * * *
186788 GGGCCTCCATAAATGTAATCCGAGACTGGACCGTGGGTTTGAGAATGGATGGGACAGATGTAGCC
66 GGGCCTCCATAAATGTAATCCGAGACTGGACCGTGGGTTTAAGAATGCATGGGACAAATGCAGCC
*
186853 AAGAAGACACCTCAAACTAC
131 AAGAAAACACCTCAAACTAC
* * *
186873 TTCAATAGAGGATTCCTGTGAAAAACATTAAG-CGCAAGAGGAT-AAGAAAGGAAATCCAAGCAA
1 TTCAATAGAGAATTCCTGTGAAAAACA-TAAGACGCAAAAGGATGAA-AAAGGAAATCAAAGCAA
* * * ** * *
186936 AAGGGCTTCCATGAATGTAGTTTGATACT-GACTTGTGGGTTTAAGAAT-CACTGGGACAAATGC
64 AAGGGCCTCCATAAATGTAATCCGAGACTGGAC-CGTGGGTTTAAGAATGCA-TGGGACAAATGC
186999 A
127 A
187000 TCTTTGAAAA
Statistics
Matches: 106, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
149 6 0.06
150 96 0.91
151 4 0.04
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (150 bp):
TTCAATAGAGAATTCCTGTGAAAAACATAAGACGCAAAAGGATGAAAAAGGAAATCAAAGCAAAA
GGGCCTCCATAAATGTAATCCGAGACTGGACCGTGGGTTTAAGAATGCATGGGACAAATGCAGCC
AAGAAAACACCTCAAACTAC
Found at i:188372 original size:64 final size:63
Alignment explanation
Indices: 188301--188528 Score: 210
Period size: 64 Copynumber: 3.6 Consensus size: 63
188291 TTGAAGGTGT
* *
188301 ATCGATGCATTGGTAGTGCATCGATGCACT-CTTTTAAAATAAATACATCGAATGCAATTCGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCA-TACTTTTAAAATAAA-ACATCGAATGCAATTAGTGC
* * * ** ** *
188365 ATTGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCAAATGCAATTAGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATACTTTTAA-AATAAAACATCGAATGCAATTAGTGC
* * ** * * * *
188429 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTGATAATACAACATCGAATGCATTTTA-TG
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT-ACTTTTAAAATAAAACATCGAATGCA-ATTAGTG
188492 C
63 C
*
188493 ATCGATGCATCGGTAGTGCATCGATGCATACTTTTA
1 ATCGATGCATAGGTAGTGCATCGATGCATACTTTTA
188529 TTGAAAGATG
Statistics
Matches: 131, Mismatches: 27, Indels: 13
0.77 0.16 0.08
Matches are distributed among these distances:
63 7 0.05
64 110 0.84
65 14 0.11
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (63 bp):
ATCGATGCATAGGTAGTGCATCGATGCATACTTTTAAAATAAAACATCGAATGCAATTAGTGC
Found at i:189749 original size:31 final size:31
Alignment explanation
Indices: 189676--189802 Score: 130
Period size: 31 Copynumber: 4.1 Consensus size: 31
189666 AGAGTCGAGG
* *
189676 GTATACCTATGTTCTAAGGAACATATGAATA
1 GTATACCTATGTTCTAAGGAACATATGGACA
* ***
189707 GAATTACCTATG-TCTTTTGAGACATATGGACA
1 GTA-TACCTATGTTCTAAGGA-ACATATGGACA
189739 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACA
* * ** *
189770 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACA
189801 GT
1 GT
189803 TGCCGAGGAT
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
31 54 0.69
32 24 0.31
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (31 bp):
GTATACCTATGTTCTAAGGAACATATGGACA
Found at i:189841 original size:30 final size:30
Alignment explanation
Indices: 189790--189861 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
189780 GTTCTTCGGA
* * *
189790 ACCTATGGACAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
189820 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
189850 ACCTCTGGATAG
1 ACCTCTGGATAG
189862 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:193218 original size:64 final size:64
Alignment explanation
Indices: 193106--193235 Score: 156
Period size: 64 Copynumber: 2.0 Consensus size: 64
193096 TTGAAGGTGT
** ** * * *
193106 ATCGATGCATTGGTAGTGCATCGATGCACTCTTTTAAAATAAATACATCGAATGCAATTCGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCACTCCATTAAAAGAAATACATCAAATGCAATTAGTGC
*
193170 ATCGATGCATAAGTAGTGCATCGATGCA-TCCCATTAATAAGGAA-ACATCAAATGCAATTAGTG
1 ATCGATGCATAAGTAGTGCATCGATGCACT-CCATTAA-AAGAAATACATCAAATGCAATTAGTG
193233 C
64 C
193234 AT
1 AT
193236 TTGATAATAC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
63 1 0.02
64 51 0.91
65 4 0.07
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCACTCCATTAAAAGAAATACATCAAATGCAATTAGTGC
Found at i:194504 original size:31 final size:31
Alignment explanation
Indices: 194431--194557 Score: 148
Period size: 31 Copynumber: 4.1 Consensus size: 31
194421 AGAGTCGAGG
194431 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACA
* ***
194462 GAATTACCTATG-TCTTTTGAGACATATGGACA
1 GTA-TACCTATGTTCTAAGGA-ACATATGGACA
194494 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACA
* * ** *
194525 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACA
194556 GT
1 GT
194558 TGCCGAGGAT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
31 54 0.68
32 26 0.32
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTAAGGAACATATGGACA
Found at i:194596 original size:30 final size:30
Alignment explanation
Indices: 194545--194616 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
194535 GTTCTTCGGA
* * *
194545 ACCTATGGACAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
194575 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
194605 ACCTCTGGATAG
1 ACCTCTGGATAG
194617 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:197122 original size:86 final size:86
Alignment explanation
Indices: 196977--197278 Score: 471
Period size: 86 Copynumber: 3.5 Consensus size: 86
196967 AAGAACATCT
* * *
196977 CACATGACTTTCCCGTGAAGGGGAGTCATTCAAAGATCATCTCACCTGGTTCAGACCCGCTAAAG
1 CACATGACTTTCCCATGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCTAAGG
*
197042 GGAACCACCTAAGGAATATAC
66 GGAACCACCTGAGGAATATAC
* * *
197063 CACATGACTTTCCCATGAATGGGAGTCATCCAAAGATCGTCTCACCTGGTTCAAACCCGCTAAGG
1 CACATGACTTTCCCATGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCTAAGG
*
197128 GGAACCGCCTGAGGAATATAC
66 GGAACCACCTGAGGAATATAC
* *
197149 CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTAGTTCAGACCCGCTAAGG
1 CACATGACTTTCCCATGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCTAAGG
197214 GGAACCACCTGAGGAATATAC
66 GGAACCACCTGAGGAATATAC
* * **
197235 CACAT-AATTTCTCATGAAGGAAAGTCATCCAAAGATCATCTCAC
1 CACATGACTTTCCCATGAAGGGGAGTCATCCAAAGATCATCTCAC
197279 GAACCACATG
Statistics
Matches: 197, Mismatches: 19, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
85 34 0.17
86 163 0.83
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (86 bp):
CACATGACTTTCCCATGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCTAAGG
GGAACCACCTGAGGAATATAC
Found at i:197507 original size:82 final size:82
Alignment explanation
Indices: 197408--197574 Score: 264
Period size: 82 Copynumber: 2.0 Consensus size: 82
197398 TACCATAAAA
* *
197408 AAACCTTCTAGTTCGATTCCATTTAGCTCAAGGGCAGCCAAATTCATAGCATAGCTCGAGGCGAG
1 AAACCTTCTAGTTCGATTCCATTCAGCTCAAGGGCAGCCAAATTCATAGCATAGCTCAAGGCGAG
*
197473 AATGGCTATCTGTCAAC
66 AAGGGCTATCTGTCAAC
197490 AAACCTT-TGAGTTCGATTCCATTCAGCTCAAGGGCAGCCAAATTCATAGCATAGCTCAAGGCGA
1 AAACCTTCT-AGTTCGATTCCATTCAGCTCAAGGGCAGCCAAATTCATAGCATAGCTCAAGGCGA
* * *
197554 TAAGGGCTATTTGTCAGC
65 GAAGGGCTATCTGTCAAC
197572 AAA
1 AAA
197575 AAACCTTTGA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
81 1 0.01
82 77 0.99
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (82 bp):
AAACCTTCTAGTTCGATTCCATTCAGCTCAAGGGCAGCCAAATTCATAGCATAGCTCAAGGCGAG
AAGGGCTATCTGTCAAC
Found at i:197717 original size:87 final size:87
Alignment explanation
Indices: 197528--197750 Score: 227
Period size: 87 Copynumber: 2.6 Consensus size: 87
197518 CAAGGGCAGC
* * * * * * *
197528 CAAATTCATAGCATAGCTCAAGGCGATAAGGGCTATTTGTCAGC-AAAAAACCTTTGAGTTTAAT
1 CAAATTCACAGCATAGCTCAAGGCAAAAAGGGCTATATGTCAGCAAAAAAAACTTTCAGTTCAAT
* *
197592 TACATTCAACTCAAGGACGTAT
66 TACATTCAACTCAAGAACATAT
* * * * *
197614 CAAATTTACAGTATAGCTCAAGGCAAGAAGGGTTATATGTCAGCAAAAAAAAC-TTCATGTTCGA
1 CAAATTCACAGCATAGCTCAAGGCAAAAAGGGCTATATGTCAGCAAAAAAAACTTTCA-GTTCAA
*
197678 TTACACTT-AGCTCAAGAACATAT
65 TTACA-TTCAACTCAAGAACATAT
* * * * *
197701 CAAATTGACAGCATAGCTCGATGCAAAAAGGGCTATCTGTCAACAAAAAA
1 CAAATTCACAGCATAGCTCAAGGCAAAAAGGGCTATATGTCAGCAAAAAA
197751 TGTCTAGTTT
Statistics
Matches: 112, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
86 40 0.36
87 70 0.62
88 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25
Consensus pattern (87 bp):
CAAATTCACAGCATAGCTCAAGGCAAAAAGGGCTATATGTCAGCAAAAAAAACTTTCAGTTCAAT
TACATTCAACTCAAGAACATAT
Found at i:198871 original size:8 final size:8
Alignment explanation
Indices: 198848--198885 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
198838 GAGGAAACCG
198848 AAAAGAAA
1 AAAAGAAA
198856 AAAGAGAAA
1 AAA-AGAAA
198865 AAAAGAAA
1 AAAAGAAA
198873 AAAA-AAA
1 AAAAGAAA
*
198880 AGAAGA
1 AAAAGA
198886 GAGGGGAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
7 6 0.22
8 13 0.48
9 8 0.30
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:199450 original size:15 final size:16
Alignment explanation
Indices: 199423--199452 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
199413 TGTCTATTAT
199423 TATTTTCTTTGGGTCC
1 TATTTTCTTTGGGTCC
199439 TATTTT-TTTGGGTC
1 TATTTTCTTTGGGTC
199453 GATTTTCGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.07, C:0.13, G:0.20, T:0.60
Consensus pattern (16 bp):
TATTTTCTTTGGGTCC
Found at i:199653 original size:45 final size:45
Alignment explanation
Indices: 199604--199738 Score: 207
Period size: 45 Copynumber: 3.0 Consensus size: 45
199594 TTATGTGTTT
* *
199604 GTGTGCATTTCAGAAAATATACATATTTTATTATTATTTCGTGCA
1 GTGTGCATTTCATAAAATATACATATTTTATTATTATTTCATGCA
* * *
199649 GTGTGCATTTCATAAAATATACAAAATTTATTATTATTTCATGTA
1 GTGTGCATTTCATAAAATATACATATTTTATTATTATTTCATGCA
* *
199694 GTGTGCATTTCATAAAATATATATATTTTATTGTTATTTCATGCA
1 GTGTGCATTTCATAAAATATACATATTTTATTATTATTTCATGCA
199739 TTCTGTTCCC
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (45 bp):
GTGTGCATTTCATAAAATATACATATTTTATTATTATTTCATGCA
Found at i:199937 original size:13 final size:13
Alignment explanation
Indices: 199919--199948 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
199909 AATCGAGTTT
*
199919 TTTTAATTTTTTA
1 TTTTAATTTTTAA
199932 TTTTAATTTTTAA
1 TTTTAATTTTTAA
199945 TTTT
1 TTTT
199949 TCGCAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:208454 original size:2 final size:2
Alignment explanation
Indices: 208447--208510 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
208437 AAGGAGAAAA
208447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
208489 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
208511 TAATATAATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:208728 original size:2 final size:2
Alignment explanation
Indices: 208723--208751 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
208713 ATAAAAAACA
208723 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 A
208752 AAAAAGAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:209894 original size:3 final size:3
Alignment explanation
Indices: 209881--209934 Score: 54
Period size: 3 Copynumber: 16.3 Consensus size: 3
209871 AATAAGAAAA
*
209881 AAT AAT AAAT AAT AAT AAT AAT AAAT AAGT AAAT AAA AAT AAT AAT AAAT
1 AAT AAT -AAT AAT AAT AAT AAT -AAT AA-T -AAT AAT AAT AAT AAT -AAT
209931 AAT A
1 AAT A
209935 TACTTGTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
3 31 0.70
4 11 0.25
5 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:209896 original size:10 final size:10
Alignment explanation
Indices: 209864--209934 Score: 74
Period size: 10 Copynumber: 7.1 Consensus size: 10
209854 ACAAACACCG
*
209864 AATAAAAAAT
1 AATAAATAAT
* *
209874 AAGAAAAAAT
1 AATAAATAAT
209884 AATAAATAAT
1 AATAAATAAT
209894 AAT-AATAAT
1 AATAAATAAT
*
209903 AAATAAGTAAAT
1 -AATAAAT-AAT
209915 AA-AAATAAT
1 AATAAATAAT
209924 AATAAATAAT
1 AATAAATAAT
209934 A
1 A
209935 TACTTGTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
9 11 0.21
10 34 0.65
11 4 0.08
12 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (10 bp):
AATAAATAAT
Found at i:209913 original size:24 final size:23
Alignment explanation
Indices: 209868--209934 Score: 98
Period size: 24 Copynumber: 2.9 Consensus size: 23
209858 ACACCGAATA
* *
209868 AAAAATAAGAAAAAATAATAAAT
1 AAAAATAATAATAAATAATAAAT
*
209891 AATAATAATAATAAATAAGTAAAT
1 AAAAATAATAATAAATAA-TAAAT
209915 AAAAATAATAATAAATAATA
1 AAAAATAATAATAAATAATA
209935 TACTTGTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 17 0.44
24 22 0.56
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (23 bp):
AAAAATAATAATAAATAATAAAT
Found at i:210087 original size:12 final size:12
Alignment explanation
Indices: 210070--210095 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
210060 TATAATATAT
210070 AAATGTTTTCAA
1 AAATGTTTTCAA
210082 AAATGTTTTCAA
1 AAATGTTTTCAA
210094 AA
1 AA
210096 CTATATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (12 bp):
AAATGTTTTCAA
Found at i:210096 original size:39 final size:39
Alignment explanation
Indices: 209941--210282 Score: 399
Period size: 39 Copynumber: 9.0 Consensus size: 39
209931 AATATACTTG
* *
209941 TAAAAAC-ATATAATATATAGA--TTTT--AAAATGCTT
1 TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTT
* * *
209975 TAAAAATTATAT-AT-TATATATGTTTTCAAAAATATTT
1 TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTT
* *
210012 AAAAAACTATAT-AT-TAT--ATCTTTTC-AAAATGTTTTTTTT
1 TAAAAACTATATAATATATAAATGTTTTCAAAAATG-----TTT
*
210051 TTAAAACTATATAATATATAAATGTTTTCAAAAATGTTT
1 TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTT
* *
210090 TCAAAACTATATAATATATATATGTTTTC-AAAATGTTT
1 TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTT
*
210128 TAAAAACTATATATTATATAAATGTTTTCAAAAATGTTT
1 TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTT
210167 TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTT
1 TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTT
* * *
210206 TCAAAACTATATATTATATAAAAGTTTTCAAAAATGTTT
1 TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTT
*
210245 T--AAACTATATAATATATAAATGTTTTCAGAAATGTTT
1 TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTT
210282 T
1 T
210283 TCAAAACCAT
Statistics
Matches: 269, Mismatches: 23, Indels: 29
0.84 0.07 0.09
Matches are distributed among these distances:
33 5 0.02
34 13 0.05
35 15 0.06
37 56 0.21
38 35 0.13
39 127 0.47
40 2 0.01
41 3 0.01
43 7 0.03
44 6 0.02
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (39 bp):
TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTT
Found at i:210143 original size:116 final size:113
Alignment explanation
Indices: 209941--210261 Score: 376
Period size: 116 Copynumber: 2.9 Consensus size: 113
209931 AATATACTTG
* * * *
209941 TAAAAAC-ATATAATATATAGA--TTTT--AAAATGCTTTAAAAATTATAT-AT-TATATATGTT
1 TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTCAAAACTATATAATATATATATGTT
* *
209999 TTCAAAAATATTTAAAAAACTATATATTATATCTTTTC-AAAATGTTTTTTTT
66 TTCAAAAATGTTTTAAAAACTATATATTATATCTTTTCAAAAATG-----TTT
*
210051 TTAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTCAAAACTATATAATATATATATGTT
1 TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTCAAAACTATATAATATATATATGTT
*
210116 TTC-AAAATGTTTTAAAAACTATATATTATATAAATGTTTTCAAAAATGTTT
66 TTCAAAAATGTTTTAAAAACTATATA-T-TAT--ATCTTTTCAAAAATGTTT
* * *
210167 TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTCAAAACTATATATTATATAAAAGTT
1 TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTCAAAACTATATAATATATATATGTT
*
210232 TTCAAAAATGTTTT--AAACTATATAATATAT
66 TTCAAAAATGTTTTAAAAACTATATATTATAT
210262 AAATGTTTTC
Statistics
Matches: 185, Mismatches: 13, Indels: 25
0.83 0.06 0.11
Matches are distributed among these distances:
110 6 0.03
111 15 0.08
113 7 0.04
115 28 0.15
116 89 0.48
117 24 0.13
118 3 0.02
120 7 0.04
121 6 0.03
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (113 bp):
TAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTCAAAACTATATAATATATATATGTT
TTCAAAAATGTTTTAAAAACTATATATTATATCTTTTCAAAAATGTTT
Found at i:210164 original size:12 final size:12
Alignment explanation
Indices: 210147--210211 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
210137 TATATTATAT
210147 AAATGTTTTCAA
1 AAATGTTTTCAA
210159 AAATGTTTT-AA
1 AAATGTTTTCAA
* *
210170 AAACTATATAATAT-AT
1 AAA-TGT-T--T-TCAA
210186 AAATGTTTTCAA
1 AAATGTTTTCAA
210198 AAATGTTTTCAA
1 AAATGTTTTCAA
210210 AA
1 AA
210212 CTATATATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
11 6 0.14
12 27 0.63
13 1 0.02
14 1 0.02
15 3 0.07
16 5 0.12
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (12 bp):
AAATGTTTTCAA
Found at i:210289 original size:116 final size:116
Alignment explanation
Indices: 210047--210303 Score: 394
Period size: 116 Copynumber: 2.2 Consensus size: 116
210037 AAAATGTTTT
* *
210047 TTTTTTAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTCAAAACTATATAATATATATA
1 TTTTTAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTCAAAACTATATAATATATAAA
* *
210112 TGTTTTCAAAATGTTTTAAAAACTATATATTATATAAATGTTTTCAAAAATG
66 AGTTTTCAAAATGTTTT-AAAACTATATAATATATAAATGTTTTCAAAAATG
*
210164 -TTTTAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTCAAAACTATATATTATATAAA
1 TTTTTAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTCAAAACTATATAATATATAAA
*
210228 AGTTTTCAAAAATGTTTT-AAACTATATAATATATAAATGTTTTCAGAAATG
66 AGTTTTC-AAAATGTTTTAAAACTATATAATATATAAATGTTTTCAAAAATG
* * *
210279 TTTTTCAAAACCATAT-ATGTATAAA
1 TTTTTAAAAACTATATAATATATAAA
210304 AACAAAATAA
Statistics
Matches: 129, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
115 39 0.30
116 80 0.62
117 10 0.08
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (116 bp):
TTTTTAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTCAAAACTATATAATATATAAA
AGTTTTCAAAATGTTTTAAAACTATATAATATATAAATGTTTTCAAAAATG
Found at i:211006 original size:84 final size:83
Alignment explanation
Indices: 210905--211873 Score: 867
Period size: 84 Copynumber: 11.6 Consensus size: 83
210895 GTTCACCTCT
* * * * * * *
210905 GAGCTGAGTGTAATCAAACTCGAAGGT-TTTCGGTGGGCATATAGCCTTTCTCGACTTAAGCTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GGT-GGCAGATAACCCTTCTCGACTTAAGTTAT
*
210969 GCTGCAAATGCTGTGCCTTG
64 GCTGCAAATGATGTGCCTTG
* * ** * * *
210989 GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTGATAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATG
* **
211054 TTATAAATGATGTGCCCTTG
65 CTGCAAATGATGTG-CCTTG
* * * * * *
211074 AAGCTGAGTGTAATCAAACTC-AAGGGTC-TT--TGGCAGATAGCCCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATG
* *
211135 CTGCAAATGATATACCTTG
65 CTGCAAATGATGTGCCTTG
* * * *
211154 GAGCTAAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCTACTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTATG
**
211219 CTGCAAATGATGTGCCCTCA
65 CTGCAAATGATGTG-CCTTG
* * * * * * *
211239 AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGGTGGTAGATAGCCCTTCTCGACTTAAGTTATT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GGTGGCAGATAACCCTTCTCGACTTAAGTTATG
*
211304 CTGCAAATGATGTGCCTTT
65 CTGCAAATGATGTGCCTTG
* ** * * * * * *
211323 GAGCTGAGTGTAGTCGAACTCGAATATCCTTGGGTGGAAGATAACCATTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGT-CTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * *
211388 TTGCAAATGATGTGCCCTC
65 CTGCAAATGATGTGCCTTG
* * * * * * *
211407 GACGCTGAGTGTAATCGAACTC-AAGGGTATTTGGTTGGCAAATATCCCTTATCGACTTAAGCTA
1 GA-GCTGAGCGTAGTCGAACTCGAA-GGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTA
* * *
211471 TACTGTAAATGATGTGTCGTT-
63 TGCTGCAAATGATGTG-CCTTG
* * * * * * *
211492 GAGCTAAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGTAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * * *
211557 TTGTAAATGATGTGCCCTC
65 CTGCAAATGATGTGCCTTG
* * * * * *
211576 GACGCTGAGTGTAATCAAACTCGAGGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTGT
1 GA-GCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTAT
*
211641 GCTGTAAATGATGTGCCTTG
64 GCTGCAAATGATGTGCCTTG
* * *
211661 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATAC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGC
* * *
211726 TACAAATGATATGCCTTA
66 TGCAAATGATGTGCCTTG
* * * * * *
211744 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TCGGTGGCAGATAACCCCTCTAGCCTTGAGCTATGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGC
211808 TGCAAATGATGTGCCTTG
66 TGCAAATGATGTGCCTTG
* * *
211826 GAGCTGAGCGTAGTCGAACTCGAAGATC-TTGGCTGACAGACAACCCTT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTT
211874 GAGTTATGCT
Statistics
Matches: 708, Mismatches: 155, Indels: 45
0.78 0.17 0.05
Matches are distributed among these distances:
80 25 0.04
81 37 0.05
82 73 0.10
83 86 0.12
84 255 0.36
85 225 0.32
86 7 0.01
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (83 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGC
TGCAAATGATGTGCCTTG
Found at i:211383 original size:169 final size:169
Alignment explanation
Indices: 210906--211846 Score: 1096
Period size: 169 Copynumber: 5.6 Consensus size: 169
210896 TTCACCTCTG
* * * *
210906 AGCTGAGTGTAATCAAACTCGAAGGT-TTTCGGTGGGCATATAGCCTTTCTCGACTTAAGCTATG
1 AGCTGAGTGTAATCAAACTCGAGGGTCTTTGGGT-GGCAGATAGCCCTTCTCGACTTAAGCTATG
* * *
210970 CTGCAAATGCTGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGG-T-GATAGATAA
65 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-CTTGGTTGGA-AGATAA
** *
211033 CCCTTCTAGCCTTGAGTTATGTTATAAATGATGTGCCCTTGA
128 CCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCCTCGA
*
211075 AGCTGAGTGTAATCAAACTCAAGGGTC-TT---TGGCAGATAGCCCTTCTCGACTTAAGCTATGC
1 AGCTGAGTGTAATCAAACTCGAGGGTCTTTGGGTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
* * * * *
211136 TGCAAATGATATACCTTGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCC
66 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCCTTGGTTGGAAGATAACCC
*** * *
211201 TTCTCTACTTGAGTTATGCTGCAAATGATGTGCCCTCAA
131 TTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCCTCGA
* * * *
211240 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGGTGGTAGATAGCCCTTCTCGACTTAAGTTATTC
1 AGCTGAGTGTAATCAAACTCGAGGGTCTTTGGGTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
* * * ** * *
211305 TGCAAATGATGTGCCTTTGAGCTGAGTGTAGTCGAACTCGAATATCCTTGGGTGGAAGATAACCA
66 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCCTTGGTTGGAAGATAACCC
211370 TTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCCTCGA
131 TTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCCTCGA
* * * * * * * * *
211409 CGCTGAGTGTAATCGAACTCAAGGGTATTTGGTTGGCAAATATCCCTTATCGACTTAAGCTATAC
1 AGCTGAGTGTAATCAAACTCGAGGGTCTTTGGGTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
* * * * * *
211474 TGTAAATGATGTGTCGTT-GAGCTAAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGTAGATAACC
66 TGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCCTTGGTTGGAAGATAACC
*
211538 CTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGA
130 CTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCCTCGA
* * * *
211578 CGCTGAGTGTAATCAAACTCGAGGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTGTGC
1 AGCTGAGTGTAATCAAACTCGAGGGTCTTTGGGTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
* * *
211643 TGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGT-CTTTGTTGGCAGATAACCC
66 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCCTTGGTTGGAAGATAACCC
* * * ** * * * *
211707 TTCTCGACTTAAGTTATACTACAAATGATATGCCTTAG-
131 TTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCCTCGA
* * * * * * * * * *
211745 AGCTGAGCGTAGTCGAACTCGAAGGTC--TCGGTGGCAGATAACCCCTCTAGCCTTGAGCTATGC
1 AGCTGAGTGTAATCAAACTCGAGGGTCTTTGGGTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
211808 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
66 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
211847 GAAGATCTTG
Statistics
Matches: 667, Mismatches: 96, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
164 5 0.01
165 202 0.30
166 5 0.01
167 22 0.03
168 48 0.07
169 382 0.57
170 3 0.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (169 bp):
AGCTGAGTGTAATCAAACTCGAGGGTCTTTGGGTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCCTTGGTTGGAAGATAACCC
TTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCCTCGA
Found at i:218508 original size:7 final size:7
Alignment explanation
Indices: 218492--218568 Score: 77
Period size: 7 Copynumber: 10.7 Consensus size: 7
218482 ACAAACACCG
218492 AATAAAA
1 AATAAAA
*
218499 AATAAGA
1 AATAAAA
218506 AATAATAA
1 AATAA-AA
218514 TAAT-AAA
1 -AATAAAA
218521 AATAAATA
1 AATAAA-A
218529 AATAAAA
1 AATAAAA
218536 AATAAATA
1 AATAAA-A
*
218544 AATAAAT
1 AATAAAA
*
218551 AA-AAAT
1 AATAAAA
218557 AATAAAA
1 AATAAAA
218564 AATAA
1 AATAA
218569 TATACTTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
6 9 0.15
7 32 0.53
8 16 0.27
9 3 0.05
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (7 bp):
AATAAAA
Found at i:218519 original size:23 final size:21
Alignment explanation
Indices: 218492--218568 Score: 79
Period size: 23 Copynumber: 3.6 Consensus size: 21
218482 ACAAACACCG
218492 AATAAAAAATAAGAAATAATAAT
1 AATAAAAAATAA-AAATAA-AAT
218515 AAT-AAAAATAAATAAATAAAA-
1 AATAAAAAAT-AA-AAATAAAAT
*
218536 AATAAATAAATAAATA-AAAAT
1 AATAAA-AAATAAAAATAAAAT
218557 AATAAAAAATAA
1 AATAAAAAATAA
218569 TATACTTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
20 10 0.21
21 11 0.23
22 12 0.25
23 15 0.31
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (21 bp):
AATAAAAAATAAAAATAAAAT
Found at i:218525 original size:15 final size:16
Alignment explanation
Indices: 218492--218568 Score: 79
Period size: 16 Copynumber: 4.8 Consensus size: 16
218482 ACAAACACCG
*
218492 AATAAAAAATAAGAAAT
1 AATAATAAATAA-AAAT
218509 AATAAT-AATAAAAAT
1 AATAATAAATAAAAAT
218524 -A-AATAAATAAAAAAT
1 AATAATAAAT-AAAAAT
218539 AAATAAATAAATAAAAAT
1 -AAT-AATAAATAAAAAT
*
218557 AATAAAAAATAA
1 AATAATAAATAA
218569 TATACTTTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
13 3 0.06
14 4 0.08
15 10 0.19
16 13 0.25
17 9 0.17
18 6 0.12
19 7 0.13
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (16 bp):
AATAATAAATAAAAAT
Found at i:218529 original size:4 final size:4
Alignment explanation
Indices: 218492--218568 Score: 67
Period size: 4 Copynumber: 20.2 Consensus size: 4
218482 ACAAACACCG
* *
218492 AATA AA-A AAT- AAGA AAT- AAT- AATA ATAAA AATA AATA AATA AA-A
1 AATA AATA AATA AATA AATA AATA AATA A-ATA AATA AATA AATA AATA
*
218536 AATA AATA AATA AATA AAAA TAATA AA-A AATA A
1 AATA AATA AATA AATA AATA -AATA AATA AATA A
218569 TATACTTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
3 17 0.28
4 37 0.62
5 6 0.10
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:218570 original size:19 final size:19
Alignment explanation
Indices: 218492--218570 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 19
218482 ACAAACACCG
* *
218492 AATAA-AAAATAAGAAAT-
1 AATAATAAAAAAATAAATA
218509 AATAATAATAAAAATAAATA
1 AATAATAA-AAAAATAAATA
218529 AATAA-AAAATAAATAAATA
1 AATAATAAAA-AAATAAATA
*
218548 AAT-A-AAAATAATAAA-A
1 AATAATAAAAAAATAAATA
218564 AATAATA
1 AATAATA
218571 TACTTTTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
16 4 0.08
17 12 0.23
18 10 0.19
19 22 0.42
20 5 0.09
ACGTcount: A:0.77, C:0.00, G:0.01, T:0.22
Consensus pattern (19 bp):
AATAATAAAAAAATAAATA
Found at i:218570 original size:23 final size:22
Alignment explanation
Indices: 218496--218570 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
218486 ACACCGAATA
* *
218496 AAAAATAAGAAATAATAATAAT
1 AAAAATAATAAATAAAAATAAT
218518 AAAAATAAATAAAT-AAAA-AAT
1 AAAAAT-AATAAATAAAAATAAT
*
218539 AAATA-AATAAATAAAAATAAT
1 AAAAATAATAAATAAAAATAAT
218560 AAAAAATAATA
1 -AAAAATAATA
218571 TACTTTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
19 7 0.16
20 4 0.09
21 10 0.23
22 13 0.30
23 10 0.23
ACGTcount: A:0.77, C:0.00, G:0.01, T:0.21
Consensus pattern (22 bp):
AAAAATAATAAATAAAAATAAT
Found at i:218643 original size:37 final size:36
Alignment explanation
Indices: 218574--218783 Score: 178
Period size: 37 Copynumber: 5.9 Consensus size: 36
218564 AATAATATAC
* *
218574 TTTTAAAAACCTATA-A-TATAT-GGATTTCAAAAATG
1 TTTTAAAAA-CTATATATTATATATGTTTTC-AAAATG
* *
218609 TTTTAAAAATTATATATTATATATGTTTTCAAAAATA
1 TTTTAAAAACTATATATTATATATGTTTTC-AAAATG
*
218646 TTTAAAAAACTATATATTATATA--TTTTCAAAATG
1 TTTTAAAAACTATATATTATATATGTTTTCAAAATG
218680 TTTTTTTAAAAACTATATA--ATATA-----T--AAATG
1 ---TTTTAAAAACTATATATTATATATGTTTTCAAAATG
*
218710 TTTTCAAAACTATATAATATATATATGTTTTCAAAATG
1 TTTTAAAAACTATAT-AT-TATATATGTTTTCAAAATG
218748 TTTTAAAAACTATATATTATATAAATGTTTTCAAAA
1 TTTTAAAAACTATATATTATAT--ATGTTTTCAAAA
218784 CTATATATTA
Statistics
Matches: 146, Mismatches: 10, Indels: 35
0.76 0.05 0.18
Matches are distributed among these distances:
27 14 0.10
28 1 0.01
30 5 0.03
31 5 0.03
32 1 0.01
34 9 0.06
35 20 0.14
36 11 0.08
37 49 0.34
38 31 0.21
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATATGTTTTCAAAATG
Found at i:218721 original size:27 final size:27
Alignment explanation
Indices: 218683--218745 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
218673 CAAAATGTTT
*
218683 TTTTAAAAACTATATAATATATAAATG
1 TTTTCAAAACTATATAATATATAAATG
*
218710 TTTTCAAAACTATATAATATATATATG
1 TTTTCAAAACTATATAATATATAAATG
218737 TTTTCAAAA
1 TTTTCAAAA
218746 TGTTTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (27 bp):
TTTTCAAAACTATATAATATATAAATG
Found at i:218747 original size:38 final size:38
Alignment explanation
Indices: 218705--218783 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
218695 TATAATATAT
* *
218705 AAATGTTTTCAAAACTATATAATATATATATGTTTTCA
1 AAATGTTTTAAAAACTATATAATATATAAATGTTTTCA
*
218743 AAATGTTTTAAAAACTATATATTATATAAATGTTTTCA
1 AAATGTTTTAAAAACTATATAATATATAAATGTTTTCA
218781 AAA
1 AAA
218784 CTATATATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (38 bp):
AAATGTTTTAAAAACTATATAATATATAAATGTTTTCA
Found at i:218761 original size:27 final size:27
Alignment explanation
Indices: 218743--218811 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 27
218733 TATGTTTTCA
218743 AAATGTTTTAAAAACTATATATTATAT
1 AAATGTTTTAAAAACTATATATTATAT
*
218770 AAATGTTTTCAAAACTATATATTATAT
1 AAATGTTTTAAAAACTATATATTATAT
*
218797 AACTGTTTTGAAAAA
1 AAATGTTTT-AAAAA
218812 TGTTTTAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 34 0.89
28 4 0.11
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (27 bp):
AAATGTTTTAAAAACTATATATTATAT
Found at i:218769 original size:65 final size:65
Alignment explanation
Indices: 218651--218866 Score: 266
Period size: 65 Copynumber: 3.3 Consensus size: 65
218641 AAATATTTAA
218651 AAAACTATAT-AT-TATATA--TTTTCAAAATGTTTTTTTAAAAACTATATAATATATAAATGTT
1 AAAACTATATAATATATATATGTTTTCAAAATG---TTTTAAAAACTATATAATATATAAATGTT
218712 TTC
63 TTC
*
218715 AAAACTATATAATATATATATGTTTTCAAAATGTTTTAAAAACTATATATTATATAAATGTTTTC
1 AAAACTATATAATATATATATGTTTTCAAAATGTTTTAAAAACTATATAATATATAAATGTTTTC
* * *
218780 AAAACTATATATTATATA-ACTGTTTTGAAAAATGTTTT--AAACTATAAAATATATAAATGTTT
1 AAAACTATATAATATATATA-TGTTTT-CAAAATGTTTTAAAAACTATATAATATATAAATG-TT
218842 TTC
63 TTC
* *
218845 AAACCATATATTATATATATAT
1 AAAAC-TATATAATATATATAT
218867 ATATATATAT
Statistics
Matches: 135, Mismatches: 8, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
64 30 0.22
65 65 0.48
66 28 0.21
67 1 0.01
68 11 0.08
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (65 bp):
AAAACTATATAATATATATATGTTTTCAAAATGTTTTAAAAACTATATAATATATAAATGTTTTC
Found at i:218833 original size:37 final size:38
Alignment explanation
Indices: 218770--218842 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
218760 TATATTATAT
* * *
218770 AAATGTTTTCAAAACTATATATTATATAACTGTTTTGAA
1 AAATGTTTT-AAAACTATAAAATATATAAATGTTTTGAA
218809 AAATGTTTT-AAACTATAAAATATATAAATGTTTT
1 AAATGTTTTAAAACTATAAAATATATAAATGTTTT
218843 TCAAACCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 22 0.71
39 9 0.29
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (38 bp):
AAATGTTTTAAAACTATAAAATATATAAATGTTTTGAA
Found at i:218861 original size:2 final size:2
Alignment explanation
Indices: 218850--218895 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
218840 TTTTCAAACC
218850 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
218891 AT AT A
1 AT AT A
218896 AAAATGTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:219014 original size:2 final size:2
Alignment explanation
Indices: 219007--219057 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
218997 AAATAAATAA
219007 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
219048 AT AT AT AT AT
1 AT AT AT AT AT
219058 GTATGTATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:220785 original size:21 final size:21
Alignment explanation
Indices: 220746--220784 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
220736 TAAAATTATT
*
220746 TAAAAATAATATTATAAAATA
1 TAAAAATAATAATATAAAATA
220767 TAAAAAT-ATAATATAAAA
1 TAAAAATAATAATATAAAA
220785 ACATTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAAATAATAATATAAAATA
Found at i:221982 original size:21 final size:21
Alignment explanation
Indices: 221956--221995 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
221946 TAAAGAGTAC
*
221956 AATAATAATATTTTCGGTAGA
1 AATAATAATATTTCCGGTAGA
*
221977 AATAATAATGTTTCCGGTA
1 AATAATAATATTTCCGGTA
221996 ATTTTTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (21 bp):
AATAATAATATTTCCGGTAGA
Found at i:224909 original size:13 final size:13
Alignment explanation
Indices: 224868--224910 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
224858 TAACTATTTA
224868 AATATTATCAATT
1 AATATTATCAATT
* *
224881 AAGCTACTAGCAATT
1 AA--TATTATCAATT
224896 AATATTATCAATT
1 AATATTATCAATT
224909 AA
1 AA
224911 GATACTATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 13 0.54
15 11 0.46
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.37
Consensus pattern (13 bp):
AATATTATCAATT
Found at i:224921 original size:15 final size:15
Alignment explanation
Indices: 224873--224921 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
224863 ATTTAAATAT
*
224873 TATCAATTAAGCTAC
1 TATCAATTAAGATAC
* *
224888 TAGCAATT-A-ATAT
1 TATCAATTAAGATAC
224901 TATCAATTAAGATAC
1 TATCAATTAAGATAC
224916 TATCAA
1 TATCAA
224922 AAATTAGGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
13 9 0.33
14 2 0.07
15 16 0.59
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (15 bp):
TATCAATTAAGATAC
Found at i:226309 original size:22 final size:22
Alignment explanation
Indices: 226284--226350 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
226274 CTTGGAAAAT
*
226284 AATTTAATT-TTTAAAATTTTAA
1 AATTGAATTATTT-AAATTTTAA
226306 AATTGAATTATTT-AATTTCTAA
1 AATTGAATTATTTAAATTT-TAA
*
226328 AATTGAATTATTTAATTTTTAA
1 AATTGAATTATTTAAATTTTAA
226350 A
1 A
226351 GTTCCTCTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.12
22 28 0.70
23 7 0.17
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (22 bp):
AATTGAATTATTTAAATTTTAA
Found at i:232460 original size:42 final size:42
Alignment explanation
Indices: 232347--232460 Score: 108
Period size: 42 Copynumber: 2.7 Consensus size: 42
232337 GCTCGAAGTT
* * *
232347 CTTATGGATGGCCC-AAAAGACTT-ATCGTCATGCTCAAAAGA
1 CTTATAGATGGCCCGAAGA-ACTTAATCATCATGCTCAAAAGA
* * * * * *
232388 CTTATAGATGACCCGAAGGATTTAAGCATCATTCTCATAAGA
1 CTTATAGATGGCCCGAAGAACTTAATCATCATGCTCAAAAGA
232430 CTTACT-GATGGCCCGAAGAACTTAATCATCA
1 CTTA-TAGATGGCCCGAAGAACTTAATCATCA
232461 AGAAAATCTT
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
41 15 0.26
42 41 0.72
43 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (42 bp):
CTTATAGATGGCCCGAAGAACTTAATCATCATGCTCAAAAGA
Found at i:232545 original size:58 final size:58
Alignment explanation
Indices: 232455--232568 Score: 149
Period size: 58 Copynumber: 2.0 Consensus size: 58
232445 AAGAACTTAA
* *
232455 TCATCAAGAAAATCTTGAAAATCAAGCTTAGTTTCTTATAAAAATTC-ATTGAAAATCG
1 TCATCAAGAAAACCCTGAAAATCAAGCTTAGTTTCTT-TAAAAATTCTATTGAAAATCG
* * * * *
232513 TCATCAAGAAACCCCTGAAAATTAGGTTTAGTTTCTTTAAAAATTCTTTTGAAAAT
1 TCATCAAGAAAACCCTGAAAATCAAGCTTAGTTTCTTTAAAAATTCTATTGAAAAT
232569 ATCATGTTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
57 9 0.19
58 39 0.81
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (58 bp):
TCATCAAGAAAACCCTGAAAATCAAGCTTAGTTTCTTTAAAAATTCTATTGAAAATCG
Found at i:233272 original size:2 final size:2
Alignment explanation
Indices: 233265--233319 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
233255 TTCGATCTAA
233265 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
233307 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
233320 AAGGGAGAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:235918 original size:15 final size:14
Alignment explanation
Indices: 235898--235939 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
235888 TTTACGTACA
235898 TTATTATATATTACT
1 TTATTATATA-TACT
235913 TTATTATATATA-T
1 TTATTATATATACT
235926 TTA-TATATAATACT
1 TTATTATAT-ATACT
235940 ACATGTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.20
13 7 0.28
14 3 0.12
15 10 0.40
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATTATATATACT
Found at i:238337 original size:13 final size:13
Alignment explanation
Indices: 238319--238349 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
238309 CCAACACGAG
238319 ACAGTGGATGGTA
1 ACAGTGGATGGTA
238332 ACAGTGGATGGTA
1 ACAGTGGATGGTA
*
238345 TCAGT
1 ACAGT
238350 CGCATATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.10, G:0.35, T:0.26
Consensus pattern (13 bp):
ACAGTGGATGGTA
Done.