Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold174
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: 2085601
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 9 of 15
Found at i:1036540 original size:30 final size:30
Alignment explanation
Indices: 1036504--1036567 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
1036494 GAGTGGGAGC
* *
1036504 CTTGGTTGGTGGTGCTGGAGTTGTTGGCGG
1 CTTGGTTGGAGGGGCTGGAGTTGTTGGCGG
*
1036534 CTTGGTTGGAGGGGCTGGAGTTGTTGGTGG
1 CTTGGTTGGAGGGGCTGGAGTTGTTGGCGG
1036564 CTTG
1 CTTG
1036568 AACGGCGGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.05, C:0.09, G:0.50, T:0.36
Consensus pattern (30 bp):
CTTGGTTGGAGGGGCTGGAGTTGTTGGCGG
Found at i:1036605 original size:132 final size:131
Alignment explanation
Indices: 1036343--1036617 Score: 290
Period size: 132 Copynumber: 2.1 Consensus size: 131
1036333 GGGTGAAGAA
*
1036343 GTTGGTGGCTTATATGGCGGAGAGGGAACCTTGGTTGGTGGTGCTGGCGTTGTTGGCGGCTTATA
1 GTTGGTGGCTTATATGGCGGAGAGGGAACCTTGGTTGGTGGTGCTGGAGTTGTTGGCGGCTTATA
* ** * * * * * *
1036408 TGGCGGAGTGGGAGCCTTGGTTGGTGGTACTGGAGTTGTTGGCGGCTTGGTTGGAGGGGCTGGAG
66 TGGAGGAGTGGGAG-CTTGGTTGGTGGTACTGGAGGAGTAGGAGCCTTGATCGGAGGGGCAGGAG
*
1036473 TT
130 TG
* * *
1036475 GTTGGTGGCTTATATGGCGGAGTGGGAGCCTTGGTTGGTGGTGCTGGAGTTGTTGGCGGCTTGGT
1 GTTGGTGGCTTATATGGCGGAGAGGGAACCTTGGTTGGTGGTGCTGGAGTTGTTGGCGGCTT-AT
* * * *
1036540 -TGGAGGGGCT-GGAG-TT-GTTGGTGGCTTGAAC-GGCGGAGTAGGAGCCTTGATCGGTGGTGC
65 ATGGAGGAG-TGGGAGCTTGGTTGGTGG--T--ACTGGAGGAGTAGGAGCCTTGATCGGAGGGGC
1036600 AGGAGTG
125 AGGAGTG
1036607 GTTGGTGGCTT
1 GTTGGTGGCTT
1036618 GGTTGGGGGT
Statistics
Matches: 119, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
129 8 0.07
130 2 0.02
131 1 0.01
132 104 0.87
133 4 0.03
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.31
Consensus pattern (131 bp):
GTTGGTGGCTTATATGGCGGAGAGGGAACCTTGGTTGGTGGTGCTGGAGTTGTTGGCGGCTTATA
TGGAGGAGTGGGAGCTTGGTTGGTGGTACTGGAGGAGTAGGAGCCTTGATCGGAGGGGCAGGAGT
G
Found at i:1036698 original size:48 final size:47
Alignment explanation
Indices: 1036646--1036777 Score: 183
Period size: 48 Copynumber: 2.7 Consensus size: 47
1036636 TGGCGGCTTG
1036646 TATGGCGGAGTGGGAGCCTTGGTTGGTGGTGCAGGAACTGGGGGTTTA
1 TATGG-GGAGTGGGAGCCTTGGTTGGTGGTGCAGGAACTGGGGGTTTA
** * * *
1036694 TATGGGGGAGTGGGAGCCTCAGTTGGTGGGGTAGGAATTGGGGGTTTA
1 TAT-GGGGAGTGGGAGCCTTGGTTGGTGGTGCAGGAACTGGGGGTTTA
*
1036742 TACGTGGGAGTGGGAGCCTTGGTTGGTGGTGCAGGA
1 TATG-GGGAGTGGGAGCCTTGGTTGGTGGTGCAGGA
1036778 CTTGGCGGAA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
47 1 0.01
48 69 0.96
49 2 0.03
ACGTcount: A:0.15, C:0.09, G:0.49, T:0.27
Consensus pattern (47 bp):
TATGGGGAGTGGGAGCCTTGGTTGGTGGTGCAGGAACTGGGGGTTTA
Found at i:1037868 original size:19 final size:19
Alignment explanation
Indices: 1037840--1037886 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1037830 ATGATACTAA
1037840 TTAA-AAATAATAT-ATAT
1 TTAATAAATAATATGATAT
*
1037857 TTAATTAAATAATTTGATAT
1 TTAA-TAAATAATATGATAT
1037877 TTAATAAATA
1 TTAATAAATA
1037887 TTAAACAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 4 0.15
19 14 0.54
20 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
TTAATAAATAATATGATAT
Found at i:1037975 original size:8 final size:9
Alignment explanation
Indices: 1037960--1037984 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1037950 GTAAAATTTA
1037960 ATTTTTTTT
1 ATTTTTTTT
1037969 ATTTTTTTT
1 ATTTTTTTT
1037978 ATTTTTT
1 ATTTTTT
1037985 AAGTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:1038460 original size:13 final size:13
Alignment explanation
Indices: 1038422--1038454 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1038412 ATATCAATTC
1038422 TTAATTAAATTAAT
1 TTAATT-AATTAAT
1038436 TTAATTAATTAAT
1 TTAATTAATTAAT
1038449 TTAATT
1 TTAATT
1038455 TTTTAACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAATTAATTAAT
Found at i:1038540 original size:13 final size:13
Alignment explanation
Indices: 1038524--1038610 Score: 56
Period size: 13 Copynumber: 6.5 Consensus size: 13
1038514 TCACATAAAT
1038524 ATATAATATATAA
1 ATATAATATATAA
*
1038537 ATATAATAAAATAAAA
1 ATATAAT---ATATAA
*
1038553 ATATAATATA-AT
1 ATATAATATATAA
1038565 ATAATAATATATAA
1 AT-ATAATATATAA
*
1038579 A-AT-TTATATAA
1 ATATAATATATAA
*
1038590 AT-TATATAAATAA
1 ATATA-ATATATAA
1038603 GATATAAT
1 -ATATAAT
1038611 CGTACTAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
11 9 0.16
12 5 0.09
13 24 0.41
14 6 0.10
15 2 0.03
16 12 0.21
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (13 bp):
ATATAATATATAA
Found at i:1038544 original size:5 final size:5
Alignment explanation
Indices: 1038524--1038570 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
1038514 TCACATAAAT
* *
1038524 ATATA ATAT- ATA-A ATATA ATAAA ATAAAA ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA ATATA ATA
1038571 ATATATAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 6 0.16
5 26 0.70
6 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
ATATA
Found at i:1038554 original size:16 final size:15
Alignment explanation
Indices: 1038520--1038581 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 15
1038510 AATATCACAT
* *
1038520 AAATATATAATATAT
1 AAATATATAAAATAA
1038535 AAATATAATAAAATAA
1 AAATAT-ATAAAATAA
1038551 AAATATAATATAATATAA
1 AAATAT-ATA-AA-ATAA
*
1038569 TAATATATAAAAT
1 AAATATATAAAAT
1038582 TTATATAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
15 8 0.20
16 19 0.46
17 5 0.12
18 9 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATATATAAAATAA
Found at i:1038834 original size:6 final size:6
Alignment explanation
Indices: 1038823--1038890 Score: 83
Period size: 6 Copynumber: 12.0 Consensus size: 6
1038813 ATTTAAAAAT
1038823 TTTAAA TTTAAA TTTAAA TTT-AA TTT-AA TTT-AA TTT-AA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
1038866 TTTAAA TTAAAA TTTAAAA TTTAAA
1 TTTAAA TTTAAA TTT-AAA TTTAAA
1038891 ATTATTTAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
5 25 0.43
6 27 0.47
7 6 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:1038849 original size:5 final size:5
Alignment explanation
Indices: 1038827--1038875 Score: 71
Period size: 5 Copynumber: 9.4 Consensus size: 5
1038817 AAAAATTTTA
*
1038827 AATTT AAATTT AAATTT AATTT AATTT AATTT AATTT AATTT AAATT AA
1 AATTT -AATTT -AATTT AATTT AATTT AATTT AATTT AATTT AATTT AA
1038876 AATTTAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
5 31 0.74
6 11 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (5 bp):
AATTT
Found at i:1038913 original size:16 final size:16
Alignment explanation
Indices: 1038833--1038977 Score: 99
Period size: 16 Copynumber: 9.3 Consensus size: 16
1038823 TTTAAATTTA
*
1038833 AATTTAAATTT-AATTT
1 AATTTAAATTTGAA-AT
*
1038849 AATTT-AATTT-AATTT
1 AATTTAAATTTGAA-AT
1038864 AATTTAAA-TT--AA-
1 AATTTAAATTTGAAAT
*
1038876 AATTTAAAATTTAAAAT
1 AATTT-AAATTTGAAAT
* *
1038893 TATTTAATTTTGAAAT
1 AATTTAAATTTGAAAT
*
1038909 AATTTAAATTTGAGAT
1 AATTTAAATTTGAAAT
1038925 AATTTAAATTTGAGAA-
1 AATTTAAATTTGA-AAT
* * *
1038941 AGTTTGAATTTGAAAA
1 AATTTAAATTTGAAAT
* *
1038957 AATTTAAACTTGAAAG
1 AATTTAAATTTGAAAT
1038973 AATTT
1 AATTT
1038978 GAATCCAAGA
Statistics
Matches: 107, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
12 5 0.05
13 3 0.03
14 3 0.03
15 19 0.18
16 72 0.67
17 5 0.05
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.46
Consensus pattern (16 bp):
AATTTAAATTTGAAAT
Found at i:1039148 original size:12 final size:11
Alignment explanation
Indices: 1039130--1039164 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1039120 GTTAAATGAG
1039130 TTTTTAAATAT
1 TTTTTAAATAT
1039141 TTTATTAAATAT
1 TTT-TTAAATAT
*
1039153 ATTTTAAATAT
1 TTTTTAAATAT
1039164 T
1 T
1039165 AATTTGGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTTAAATAT
Found at i:1039341 original size:18 final size:18
Alignment explanation
Indices: 1039320--1039354 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1039310 ATTATTTAAA
* *
1039320 AAATTGATTTTATATAAC
1 AAATTAATTATATATAAC
1039338 AAATTAATTATATATAA
1 AAATTAATTATATATAA
1039355 ATATAGATAT
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:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
AAATTAATTATATATAAC
Found at i:1039794 original size:35 final size:36
Alignment explanation
Indices: 1039723--1039800 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 36
1039713 TTTTATTTTT
*
1039723 AAAAT-TATAATTTAATAATTTAAATTTAAATTTAAA
1 AAAATATATAATTTAATAAATTAAATTTAAA-TTAAA
*
1039759 AAAATATATAATTTAA-AAATTAATTTTTAAA-TAAA
1 AAAATATATAATTTAATAAATTAA-ATTTAAATTAAA
*
1039794 ATAATAT
1 AAAATAT
1039801 TATTGTTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 10 0.27
36 11 0.30
37 16 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (36 bp):
AAAATATATAATTTAATAAATTAAATTTAAATTAAA
Found at i:1039880 original size:20 final size:20
Alignment explanation
Indices: 1039823--1039881 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
1039813 TATATTTAAT
*
1039823 AATTCAAAATAAATTTAAATAA
1 AATT-AAAA-AAATTAAAATAA
* *
1039845 AATTTTATAAAA-TAAAATAA
1 AA-TTAAAAAAATTAAAATAA
1039865 AATTAAAAAAATTAAAA
1 AATTAAAAAAATTAAAA
1039882 AGCTGATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 7 0.23
20 14 0.47
21 3 0.10
22 4 0.13
23 2 0.07
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AATTAAAAAAATTAAAATAA
Found at i:1040267 original size:8 final size:8
Alignment explanation
Indices: 1040224--1040388 Score: 55
Period size: 8 Copynumber: 20.8 Consensus size: 8
1040214 GACTTATAAG
1040224 TTATATAT
1 TTATATAT
*
1040232 TAAT-TAT
1 TTATATAT
1040239 TTATATAT
1 TTATATAT
*
1040247 ATATATCACAT
1 -T-TAT-ATAT
1040258 TTATATAT
1 TTATATAT
*
1040266 TT-TATAA
1 TTATATAT
*
1040273 TAATATA-
1 TTATATAT
*
1040280 ATA-ATAT
1 TTATATAT
1040287 TTATAT-T
1 TTATATAT
*
1040294 TTTTAATAT
1 TTAT-ATAT
* *
1040303 TCATATTAA
1 TTATA-TAT
1040312 TTATATTAATT
1 TTATA-T-A-T
*
1040323 TTAAAATAT
1 TT-ATATAT
1040332 TTATATAT
1 TTATATAT
1040340 TTATAT-T
1 TTATATAT
*
1040347 ATAT-TAT
1 TTATATAT
1040354 ATTATAT-T
1 -TTATATAT
1040362 TTA-AT-T
1 TTATATAT
*
1040368 TTTTATA-
1 TTATATAT
*
1040375 TTATATAA
1 TTATATAT
1040383 TTATAT
1 TTATAT
1040389 TATGTTGAAT
Statistics
Matches: 117, Mismatches: 21, Indels: 38
0.66 0.12 0.22
Matches are distributed among these distances:
6 9 0.08
7 34 0.29
8 41 0.35
9 19 0.16
10 6 0.05
11 6 0.05
12 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (8 bp):
TTATATAT
Found at i:1040302 original size:16 final size:16
Alignment explanation
Indices: 1040280--1040356 Score: 61
Period size: 16 Copynumber: 4.9 Consensus size: 16
1040270 TAATAATATA
1040280 ATAATATTTATATTTT
1 ATAATATTTATATTTT
* * *
1040296 TTAATATTCATA-TTA
1 ATAATATTTATATTTT
*
1040311 ATTATA-TTA-ATTTT
1 ATAATATTTATATTTT
*
1040325 AAAATATTTATATATTT
1 ATAATATTTATAT-TTT
*
1040342 ATATTATATTATATT
1 ATAATAT-TTATATT
1040357 ATATTTTAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 9
0.69 0.17 0.14
Matches are distributed among these distances:
13 1 0.02
14 8 0.18
15 9 0.20
16 12 0.27
17 9 0.20
18 6 0.13
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAATATTTATATTTT
Found at i:1040360 original size:43 final size:42
Alignment explanation
Indices: 1040282--1040391 Score: 116
Period size: 43 Copynumber: 2.5 Consensus size: 42
1040272 ATAATATAAT
*
1040282 AATATTTATATTTTTTAATATTCATATTAATTATA-TTAATTTTAA
1 AATATTTATA-TATTT-ATATT-ATATTAATTATATTTAATTTT-A
*
1040327 AATATTTATATATTTATATTATATTATATTATATTTTAATTTTT
1 AATATTTATATATTTATATTATATTA-ATTATA-TTTAATTTTA
* *
1040371 TATA-TTATATAATTATATTAT
1 AATATTTATATATTTATATTAT
1040392 GTTGAATGAG
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
42 6 0.10
43 27 0.47
44 7 0.12
45 18 0.31
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (42 bp):
AATATTTATATATTTATATTATATTAATTATATTTAATTTTA
Found at i:1041416 original size:14 final size:16
Alignment explanation
Indices: 1041386--1041417 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1041376 TTAAATTTTA
1041386 ATTTTTCAAATAATTT
1 ATTTTTCAAATAATTT
1041402 ATTTTT-AAA-AATTT
1 ATTTTTCAAATAATTT
1041416 AT
1 AT
1041418 AAAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTTCAAATAATTT
Found at i:1041445 original size:24 final size:24
Alignment explanation
Indices: 1041416--1041462 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1041406 TTAAAAATTT
*
1041416 ATAAAAATAAATTAAATATATATG
1 ATAAAAATAAATTAAATAAATATG
* *
1041440 ATAAAATTTAATTAAATAAATAT
1 ATAAAAATAAATTAAATAAATAT
1041463 TTTAATAAAA
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:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
ATAAAAATAAATTAAATAAATATG
Found at i:1041481 original size:29 final size:27
Alignment explanation
Indices: 1041440--1041493 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 27
1041430 AATATATATG
1041440 ATAAAATTTAATT-AAATAAATATTTTA
1 ATAAAATTTAATTAAAAT-AATATTTTA
1041467 ATAAAATTTTAAATTAAAATAATATTT
1 ATAAAA-TTT-AATTAAAATAATATTT
1041494 AAAAATATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.25
28 3 0.12
29 11 0.46
30 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
ATAAAATTTAATTAAAATAATATTTTA
Found at i:1041494 original size:28 final size:26
Alignment explanation
Indices: 1041423--1041495 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 26
1041413 TTTATAAAAA
* *
1041423 TAAATTAAAT-ATATATGATAAAATT
1 TAAATTAAATAATATTTAATAAAATT
1041448 T-AATTAAATAAATATTTTAATAAAATTT
1 TAAATTAAAT-AATA-TTTAATAAAA-TT
1041476 TAAATTAAAATAATATTTAA
1 TAAATT-AAATAATATTTAA
1041496 AAATATCCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
24 8 0.20
25 1 0.03
26 3 0.08
27 8 0.20
28 8 0.20
29 8 0.20
30 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (26 bp):
TAAATTAAATAATATTTAATAAAATT
Found at i:1043438 original size:16 final size:17
Alignment explanation
Indices: 1043417--1043454 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1043407 AAATTTGATT
1043417 TAAAA-TGAGTTAAAAA
1 TAAAATTGAGTTAAAAA
* *
1043433 TAAAATTGAGTTTAAAT
1 TAAAATTGAGTTAAAAA
1043450 TAAAA
1 TAAAA
1043455 AAGCAAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.32
Consensus pattern (17 bp):
TAAAATTGAGTTAAAAA
Found at i:1043671 original size:5 final size:5
Alignment explanation
Indices: 1043661--1043747 Score: 56
Period size: 5 Copynumber: 17.0 Consensus size: 5
1043651 AAGACAATGC
* *
1043661 TATAA TATAA TATAAA AATAA TTAAAA TATAA TATAAAA TATAA TAT-A
1 TATAA TATAA TAT-AA TATAA -TATAA TATAA TAT--AA TATAA TATAA
* *
1043709 TATACA TA-AA TA-AA TATAA TAAAA T-TTA TATAAA TATAA
1 TATA-A TATAA TATAA TATAA TATAA TATAA TAT-AA TATAA
1043748 ATTATTTTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
4 13 0.20
5 33 0.51
6 14 0.22
7 5 0.08
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (5 bp):
TATAA
Found at i:1043899 original size:19 final size:18
Alignment explanation
Indices: 1043861--1043917 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1043851 ATTTCAAAAA
*
1043861 AAATTAAATAAATATA-TT
1 AAATTAAA-AAATAAATTT
1043879 AAATTTAAAAAATAAATTT
1 AAA-TTAAAAAATAAATTT
*
1043898 AAATAAAAAAATAAAATTT
1 AAATTAAAAAAT-AAATTT
1043917 A
1 A
1043918 TTTTTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 17 0.50
19 17 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTAAAAAATAAATTT
Found at i:1043915 original size:32 final size:30
Alignment explanation
Indices: 1043851--1043917 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 30
1043841 TTTGTTTGAT
* * * *
1043851 ATTTCAAAAAAAATTAAATAAATATATTAA
1 ATTTAAAAAAAAATTAAATAAAAAAATAAA
1043881 ATTTAAAAAATAAATTTAAATAAAAAAATAAA
1 ATTTAAAAAA-AAA-TTAAATAAAAAAATAAA
1043913 ATTTA
1 ATTTA
1043918 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 9 0.29
31 3 0.10
32 19 0.61
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (30 bp):
ATTTAAAAAAAAATTAAATAAAAAAATAAA
Found at i:1047268 original size:19 final size:20
Alignment explanation
Indices: 1047233--1047280 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1047223 TGGAGATTCC
* *
1047233 ATAATATTAAATGTAATTAT
1 ATAATATTAAATATAATTAA
1047253 ATAATA-TAAATATAATTAA
1 ATAATATTAAATATAATTAA
1047272 ATAA-ATTAA
1 ATAATATTAA
1047281 TATTTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 18 0.72
20 6 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
ATAATATTAAATATAATTAA
Found at i:1047345 original size:17 final size:19
Alignment explanation
Indices: 1047319--1047353 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1047309 AAAAATTATA
1047319 TTTAACTTATT-TTAAAAT
1 TTTAACTTATTATTAAAAT
1047337 TTTAA-TTATTATTAAAA
1 TTTAACTTATTATTAAAA
1047354 ATATTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAACTTATTATTAAAAT
Found at i:1047457 original size:20 final size:20
Alignment explanation
Indices: 1047400--1047474 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
1047390 TTTATAATTA
1047400 AATTTAAA-TAAAA-ATATT
1 AATTTAAATTAAAATATATT
*
1047418 --TTT-AATTAATAA-ATAAT
1 AATTTAAATTAA-AATATATT
* *
1047435 AATTTTAATTAAATTATATT
1 AATTTAAATTAAAATATATT
1047455 AATTTAAATTAAAATATATT
1 AATTTAAATTAAAATATATT
1047475 TTATATAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
15 2 0.04
16 6 0.13
17 6 0.13
19 4 0.09
20 28 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTTAAATTAAAATATATT
Found at i:1047542 original size:3 final size:3
Alignment explanation
Indices: 1047534--1047573 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1047524 AAAGGTCTAC
1047534 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1047574 AGAATGGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1047703 original size:20 final size:20
Alignment explanation
Indices: 1047665--1047703 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1047655 AATTATTTTT
*
1047665 ATGTTATAATTATATATAAG
1 ATGTTATAATTATAAATAAG
1047685 ATGTTATATATT-TAAATAA
1 ATGTTATA-ATTATAAATAA
1047704 ATTTTAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (20 bp):
ATGTTATAATTATAAATAAG
Found at i:1047785 original size:24 final size:24
Alignment explanation
Indices: 1047758--1047827 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
1047748 TTATATATTC
1047758 ATATTATATTTATATTTTATTTTT
1 ATATTATATTTATATTTTATTTTT
* *
1047782 ATATCATA-TTATTTTTTACTTTTT
1 ATATTATATTTATATTTTA-TTTTT
* * * *
1047806 TTGTTATATTCATATTATATTT
1 ATATTATATTTATATTTTATTT
1047828 AAAATTATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
23 9 0.25
24 20 0.56
25 7 0.19
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (24 bp):
ATATTATATTTATATTTTATTTTT
Found at i:1047788 original size:29 final size:31
Alignment explanation
Indices: 1047751--1047828 Score: 110
Period size: 29 Copynumber: 2.6 Consensus size: 31
1047741 AATATAATTA
1047751 TATATTCATATTATATTTATA-TTTTATTT-T
1 TATATTCATATTATATTTATACTTTT-TTTGT
*
1047781 TATA-TCATATTAT-TTTTTACTTTTTTTGT
1 TATATTCATATTATATTTATACTTTTTTTGT
1047810 TATATTCATATTATATTTA
1 TATATTCATATTATATTTA
1047829 AAATTATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 8 0.19
29 18 0.43
30 13 0.31
31 3 0.07
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.65
Consensus pattern (31 bp):
TATATTCATATTATATTTATACTTTTTTTGT
Found at i:1049136 original size:29 final size:30
Alignment explanation
Indices: 1049094--1049160 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 30
1049084 ATGTTAAGGG
* *
1049094 TTTATTTATATATAGATTAAAAATT-AATA
1 TTTATTTAAATATAAATTAAAAATTAAATA
*
1049123 TTTATTTAAATATAAATTAAATATTAAATA
1 TTTATTTAAATATAAATTAAAAATTAAATA
1049153 TTTATTTA
1 TTTATTTA
1049161 GGTATAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TTTATTTAAATATAAATTAAAAATTAAATA
Found at i:1049175 original size:30 final size:29
Alignment explanation
Indices: 1049094--1049175 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 29
1049084 ATGTTAAGGG
* *
1049094 TTTATTTATATATAGATTAAAA-ATTAATA
1 TTTATTTAAATATA-ATAAAAATATTAATA
*
1049123 TTTATTTAAATATAA-ATTAAATATTAAATA
1 TTTATTTAAATATAATA-AAAATATT-AATA
**
1049153 TTTATTTAGGTATAATAAAAATA
1 TTTATTTAAATATAATAAAAATA
1049176 AAATTTGTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 4 0.09
29 16 0.37
30 22 0.51
31 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (29 bp):
TTTATTTAAATATAATAAAAATATTAATA
Found at i:1053030 original size:15 final size:16
Alignment explanation
Indices: 1053001--1053031 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1052991 ATCATTCCTC
1053001 TTTCCCGATTTAAGAT
1 TTTCCCGATTTAAGAT
1053017 TTTCCCGA-TTAAGAT
1 TTTCCCGATTTAAGAT
1053032 ATAATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (16 bp):
TTTCCCGATTTAAGAT
Found at i:1058859 original size:20 final size:18
Alignment explanation
Indices: 1058834--1058878 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1058824 TAAAAAATAA
*
1058834 ATATTTAATTATTTATAATT
1 ATATTTAATTA--TATAAAT
*
1058854 ATATTTGATTATATAAAT
1 ATATTTAATTATATAAAT
1058872 ATATTTA
1 ATATTTA
1058879 TTTAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 12 0.55
20 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
ATATTTAATTATATAAAT
Found at i:1062466 original size:20 final size:20
Alignment explanation
Indices: 1062441--1062483 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1062431 TAAATATTGC
1062441 ATATATAATTTTGACATTAA
1 ATATATAATTTTGACATTAA
*
1062461 ATATATAATTTTGATATTAA
1 ATATATAATTTTGACATTAA
1062481 ATA
1 ATA
1062484 AGTATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (20 bp):
ATATATAATTTTGACATTAA
Found at i:1062917 original size:22 final size:23
Alignment explanation
Indices: 1062857--1062914 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 23
1062847 ATTTAGATTG
1062857 ATTTAATT-TAAATTATTTTTTAA
1 ATTTAATTATAAATTA-TTTTTAA
*
1062880 ATTTAA--AAAAATTATTTTTAA
1 ATTTAATTATAAATTATTTTTAA
1062901 ATTTAATTATAAAT
1 ATTTAATTATAAAT
1062915 ATTAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 13 0.43
22 6 0.20
23 11 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTAATTATAAATTATTTTTAA
Found at i:1064025 original size:17 final size:17
Alignment explanation
Indices: 1064004--1064038 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1063994 TTACAACACA
*
1064004 AAAAATAATATTAATATT
1 AAAAA-AATATAAATATT
1064022 AAAAAAATATAAATATT
1 AAAAAAATATAAATATT
1064039 TTAAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAAAATATAAATATT
Found at i:1064103 original size:22 final size:22
Alignment explanation
Indices: 1064075--1064116 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1064065 AAAATTTGTT
**
1064075 ATATATATTTATGATATAAAAA
1 ATATATAAATATGATATAAAAA
1064097 ATATATAAATATGATATAAA
1 ATATATAAATATGATATAAA
1064117 TTATTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (22 bp):
ATATATAAATATGATATAAAAA
Found at i:1064211 original size:2 final size:2
Alignment explanation
Indices: 1064204--1064255 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
1064194 ACATTTCCAA
* ** *
1064204 AT AT AT AT AT AT AT TT CC AA 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
1064246 AT AT AT AT AT
1 AT AT AT AT AT
1064256 CTTGCAGGAG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1064221 original size:20 final size:20
Alignment explanation
Indices: 1064196--1064255 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
1064186 TTTCTCTTAC
1064196 ATTTCCAAATATATATATAT
1 ATTTCCAAATATATATATAT
1064216 ATTTCCAAATATATATATAT
1 ATTTCCAAATATATATATAT
* *
1064236 ATAT--ATATATATATATAT
1 ATTTCCAAATATATATATAT
1064254 AT
1 AT
1064256 CTTGCAGGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.39
20 23 0.61
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTCCAAATATATATATAT
Found at i:1064360 original size:3 final size:3
Alignment explanation
Indices: 1064352--1064380 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1064342 GTGTGATAGT
1064352 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1064381 TTTTGACCAA
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:1065356 original size:11 final size:11
Alignment explanation
Indices: 1065336--1065368 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
1065326 AGATTGTAGG
1065336 TTTTTAATTTTA
1 TTTTT-ATTTTA
1065348 TTTTTATTTTA
1 TTTTTATTTTA
1065359 -TTTTATTTTA
1 TTTTTATTTTA
1065369 ATTGGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 6 0.29
12 5 0.24
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:1065907 original size:52 final size:52
Alignment explanation
Indices: 1065807--1065907 Score: 125
Period size: 52 Copynumber: 1.9 Consensus size: 52
1065797 ATAACTATGA
* **
1065807 AAAGTTTAGGTAATTTGTCATATTCATACTCTGTGTTTTTACATAAAAATTT
1 AAAGTTTAGGTAATTTGTCATAATCATACTCTGTAATTTTACATAAAAATTT
* *
1065859 AAAGTTTAGGTAATTTGTCA-AATGATACAT-TTTAATTTTACATGAAAAA
1 AAAGTTTAGGTAATTTGTCATAATCATAC-TCTGTAATTTTACAT-AAAAA
1065908 AGTTTTAAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
51 16 0.38
52 26 0.62
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.43
Consensus pattern (52 bp):
AAAGTTTAGGTAATTTGTCATAATCATACTCTGTAATTTTACATAAAAATTT
Found at i:1066861 original size:11 final size:11
Alignment explanation
Indices: 1066845--1066874 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1066835 ACCCACCGAA
1066845 AAGCCCAACAT
1 AAGCCCAACAT
1066856 AAGCCCAACAT
1 AAGCCCAACAT
*
1066867 AAGTCCAA
1 AAGCCCAA
1066875 ACTAAAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.33, G:0.10, T:0.10
Consensus pattern (11 bp):
AAGCCCAACAT
Found at i:1070672 original size:24 final size:23
Alignment explanation
Indices: 1070640--1070692 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
1070630 TTAATTATGA
*
1070640 ATATAAAAATATAAAATTTTAAAT
1 ATATAAAAATATAAAA-ATTAAAT
*
1070664 ATATAAAAAATTTAAAAATTAAAT
1 ATAT-AAAAATATAAAAATTAAAT
1070688 ATATA
1 ATATA
1070693 TTTATATACC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 1 0.04
24 14 0.54
25 11 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
ATATAAAAATATAAAAATTAAAT
Found at i:1071306 original size:15 final size:14
Alignment explanation
Indices: 1071281--1071320 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
1071271 ATTAACAGCG
1071281 ATTATTAATTAAATA
1 ATTA-TAATTAAATA
*
1071296 ATTCATAATTATATA
1 ATT-ATAATTAAATA
1071311 ATTATAATTA
1 ATTATAATTA
1071321 TATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 15 0.65
16 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTATAATTAAATA
Found at i:1071319 original size:21 final size:21
Alignment explanation
Indices: 1071294--1071340 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
1071284 ATTAATTAAA
1071294 TAATTCATAATT-ATATAA-TTA
1 TAATT-ATAATTAATA-AATTTA
*
1071315 TAATTATATTTAATAAATTTA
1 TAATTATAATTAATAAATTTA
1071336 TAATT
1 TAATT
1071341 TAAATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATTATAATTAATAAATTTA
Found at i:1076539 original size:25 final size:26
Alignment explanation
Indices: 1076478--1076554 Score: 74
Period size: 24 Copynumber: 3.1 Consensus size: 26
1076468 AATTTAAAAA
*
1076478 AATTAT-AAATTTTA-TTT-AATTAT
1 AATTATAAAATTATATTTTAAATTAT
* *
1076501 AATAATAATA-TATATTTTAAATT-T
1 AATTATAAAATTATATTTTAAATTAT
*
1076525 AATTATAAAATTATATTTTAATAATAT
1 AATTATAAAATTATATTTTAA-ATTAT
1076552 AAT
1 AAT
1076555 AAATTTTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
23 8 0.19
24 14 0.33
25 14 0.33
26 2 0.05
27 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
AATTATAAAATTATATTTTAAATTAT
Found at i:1076542 original size:48 final size:43
Alignment explanation
Indices: 1076443--1076575 Score: 119
Period size: 43 Copynumber: 3.0 Consensus size: 43
1076433 TTATTTAATT
* * *
1076443 TTATAATTTTAATTTATATAAATAAAATTTAAAA-AAATTAT-AAA
1 TTAT-ATTTTAA-TAATAT-AATAAATTTTAAAATTAATTATAAAA
* * *
1076487 TTTTATTTAATTATAATAATAATATATATTTTAAATTTAATTATAAAA
1 TTATATTT--TAATAAT-ATAATA-A-ATTTTAAAATTAATTATAAAA
1076535 TTATATTTTAATAATATAATAAATTTTAAAATTAATT-TAAA
1 TTATATTTTAATAATATAATAAATTTTAAAATTAATTATAAA
1076576 TTGTGACTCG
Statistics
Matches: 73, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
42 4 0.05
43 18 0.25
44 11 0.15
45 11 0.15
46 13 0.18
47 6 0.08
48 10 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (43 bp):
TTATATTTTAATAATATAATAAATTTTAAAATTAATTATAAAA
Found at i:1078826 original size:8 final size:9
Alignment explanation
Indices: 1078808--1078861 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
1078798 TTTTTGAATT
*
1078808 TATATAATA
1 TATATATTA
1078817 TAT-TATTA
1 TATATATTA
1078825 TATATATATA
1 TATATAT-TA
1078835 TATATATTA
1 TATATATTA
*
1078844 TGTA-ATT-
1 TATATATTA
*
1078851 TATATCTTA
1 TATATATTA
1078860 TA
1 TA
1078862 AACATTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 3 0.08
8 12 0.32
9 13 0.35
10 9 0.24
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (9 bp):
TATATATTA
Found at i:1078829 original size:10 final size:11
Alignment explanation
Indices: 1078807--1078844 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
1078797 ATTTTTGAAT
1078807 TTATATAATATA
1 TTATAT-ATATA
1078819 TTAT-TATATA
1 TTATATATATA
1078829 TATATATATATA
1 T-TATATATATA
1078841 TTAT
1 TTAT
1078845 GTAATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.25
11 7 0.29
12 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTATATATATA
Found at i:1080757 original size:19 final size:19
Alignment explanation
Indices: 1080735--1080774 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1080725 TTGATAAAAA
1080735 TTAATTAAATTTAGTTAAT
1 TTAATTAAATTTAGTTAAT
* *
1080754 TTAATTAGATTTATTTAAT
1 TTAATTAAATTTAGTTAAT
1080773 TT
1 TT
1080775 GAAAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TTAATTAAATTTAGTTAAT
Found at i:1083443 original size:20 final size:20
Alignment explanation
Indices: 1083418--1083460 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1083408 AGTAATAAAT
1083418 ATTAATTATATACATAACAC
1 ATTAATTATATACATAACAC
*
1083438 ATTAATTATATACGTAACAC
1 ATTAATTATATACATAACAC
1083458 ATT
1 ATT
1083461 TGTCTTACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (20 bp):
ATTAATTATATACATAACAC
Found at i:1085633 original size:2 final size:2
Alignment explanation
Indices: 1085628--1085660 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1085618 TAAAAATGTA
1085628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1085661 AAATGTATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1088727 original size:32 final size:33
Alignment explanation
Indices: 1088673--1088737 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
1088663 ATTTTTTCAT
*
1088673 AAATATATTATTTTTATATTA-TTATAATATTTA
1 AAATATATTATTTTAATATTATTTAT-ATATTTA
1088706 AAATA-ATATATTTTAAT-TTATTTATATATTTA
1 AAATATAT-TATTTTAATATTATTTATATATTTA
1088738 TGTAATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
AAATATATTATTTTAATATTATTTATATATTTA
Found at i:1088738 original size:12 final size:13
Alignment explanation
Indices: 1088712--1088793 Score: 57
Period size: 12 Copynumber: 6.4 Consensus size: 13
1088702 TTTAAAATAA
*
1088712 TATATTTTA-ATT
1 TATATTATATATT
1088724 TAT-TTATATATT
1 TATATTATATATT
*
1088736 TAT-GTA-ATATT
1 TATATTATATATT
*
1088747 TATATTAT-TTTT
1 TATATTATATATT
1088759 TATATTATATTATAT
1 TATATTATA-TAT-T
*
1088774 TATAATTATTATTTT
1 TAT-ATTA-TATATT
1088789 TATAT
1 TATAT
1088794 AATTATGTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
11 12 0.21
12 24 0.43
14 4 0.07
15 8 0.14
16 6 0.11
17 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (13 bp):
TATATTATATATT
Found at i:1088755 original size:28 final size:30
Alignment explanation
Indices: 1088726--1088809 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 30
1088716 TTTTAATTTA
1088726 TTTATATATTTATGTAATATTTA-TATTAT
1 TTTATATATTTATGTAATATTTATTATTAT
*
1088755 TTTTTATATTATAT-T-ATATTATAATTATTATT
1 TTTATATATT-TATGTAATATT-T-ATTATTA-T
* *
1088787 TTTATATAATTATGTAACATTTA
1 TTTATATATTTATGTAATATTTA
1088810 AAAATATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
28 5 0.11
29 11 0.25
30 4 0.09
31 9 0.20
32 11 0.25
33 4 0.09
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATATATTTATGTAATATTTATTATTAT
Found at i:1088766 original size:17 final size:17
Alignment explanation
Indices: 1088676--1088771 Score: 54
Period size: 17 Copynumber: 5.5 Consensus size: 17
1088666 TTTTCATAAA
1088676 TATATTATTTTTATATTAT
1 TATATTATTTTT-TA-TAT
* *** *
1088695 TATAATATTTAAAATAA
1 TATATTATTTTTTATAT
*
1088712 TATATT-TTAATTTAT-T
1 TATATTATT-TTTTATAT
*
1088728 TATA-TATTTATGTAATATT
1 TATATTATTT-T-TTATA-T
1088747 TATATTATTTTTTATAT
1 TATATTATTTTTTATAT
1088764 TATATTAT
1 TATATTAT
1088772 ATTATAATTA
Statistics
Matches: 56, Mismatches: 14, Indels: 16
0.65 0.16 0.19
Matches are distributed among these distances:
15 1 0.02
16 9 0.16
17 21 0.38
18 5 0.09
19 15 0.27
20 5 0.09
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (17 bp):
TATATTATTTTTTATAT
Found at i:1088786 original size:17 final size:16
Alignment explanation
Indices: 1088749--1088799 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
1088739 GTAATATTTA
1088749 TATTATTTTTTAT-AT
1 TATTATTTTTTATAAT
*
1088764 TA-TATTATATTATAAT
1 TATTATT-TTTTATAAT
1088780 TATTATTTTTATATAAT
1 TATTATTTTT-TATAAT
1088797 TAT
1 TAT
1088800 GTAACATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 4 0.13
15 7 0.23
16 6 0.20
17 13 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTATTTTTTATAAT
Found at i:1088847 original size:19 final size:19
Alignment explanation
Indices: 1088806--1088891 Score: 61
Period size: 20 Copynumber: 4.4 Consensus size: 19
1088796 TTATGTAACA
*
1088806 TTTAA-AAATATTTAATTTAT
1 TTTAATAAATTTTTAA-TT-T
*
1088826 TTTTATAAATTTTTATATTT
1 TTTAATAAATTTTTA-ATTT
*
1088846 TTTAATATATTTTTAA--T
1 TTTAATAAATTTTTAATTT
*
1088863 TTTAATTTTAATTTATTAATTT
1 TTTAA--TAAATTT-TTAATTT
1088885 TTTAATA
1 TTTAATA
1088892 TATATAAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
17 6 0.12
19 6 0.12
20 23 0.44
21 10 0.19
22 7 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTAATAAATTTTTAATTT
Found at i:1088945 original size:20 final size:20
Alignment explanation
Indices: 1088922--1089026 Score: 70
Period size: 20 Copynumber: 5.0 Consensus size: 20
1088912 AAATATATTA
1088922 AAATATTTTATATTATAAAT
1 AAATATTTTATATTATAAAT
* * *
1088942 AAATAATATA-AATATAAAAT
1 AAATATTTTATATTAT-AAAT
*
1088962 AAATATATTAATATTTATATAAT
1 AAATAT-TTTATA-TTATA-AAT
1088985 ATAA-ACTTTTATATTATAAAT
1 A-AATA-TTTTATATTATAAAT
* * * *
1089006 ATATATATAATATTTTAAAT
1 AAATATTTTATATTATAAAT
1089026 A
1 A
1089027 TAATTATCAT
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
19 4 0.06
20 31 0.48
21 7 0.11
22 7 0.11
23 13 0.20
24 3 0.05
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATATTTTATATTATAAAT
Found at i:1088959 original size:19 final size:19
Alignment explanation
Indices: 1088938--1088975 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1088928 TTTATATTAT
1088938 AAATAAATAATATAAATATA
1 AAATAAAT-ATATAAATATA
*
1088958 AAATAAATATATTAATAT
1 AAATAAATATATAAATAT
1088976 TTATATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATAAATATATAAATATA
Found at i:1088981 original size:25 final size:25
Alignment explanation
Indices: 1088912--1089029 Score: 80
Period size: 25 Copynumber: 5.1 Consensus size: 25
1088902 AAATTAATTA
*
1088912 AAATATATTAAAATATTT-TATATTAT
1 AAATATATT--AATATTTATATAATAT
* ** *
1088938 AAATA-AATAATATAAATATAAAAT
1 AAATATATTAATATTTATATAATAT
1088962 AAATATATTAATATTTATATAATAT
1 AAATATATTAATATTTATATAATAT
1088987 AAACT-T-TT-ATA-TTATA-AATAT
1 AAA-TATATTAATATTTATATAATAT
1089008 --ATATA-TAATATTT-TA-AATAT
1 AAATATATTAATATTTATATAATAT
1089028 AA
1 AA
1089030 TTATCATACT
Statistics
Matches: 74, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
18 1 0.01
19 3 0.04
20 10 0.14
21 7 0.09
22 5 0.07
23 8 0.11
24 13 0.18
25 21 0.28
26 6 0.08
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATATATTAATATTTATATAATAT
Found at i:1088986 original size:17 final size:17
Alignment explanation
Indices: 1088966--1089019 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
1088956 TAAAATAAAT
1088966 ATATTAATATTTATATA
1 ATATTAATATTTATATA
1088983 ATA-TAA-ACTTT-TATA
1 ATATTAATA-TTTATATA
* * *
1088998 TTATAAATATATATATA
1 ATATTAATATTTATATA
1089015 ATATT
1 ATATT
1089020 TTAAATATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
15 7 0.25
16 10 0.36
17 11 0.39
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTAATATTTATATA
Found at i:1089043 original size:40 final size:44
Alignment explanation
Indices: 1088958--1089044 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 44
1088948 TATAAATATA
* *
1088958 AAATAAATATATTAATATTTATATAATATAAACTTTTATATTAT
1 AAATAAATATATTAATATTTATATAATATAAACTTTCATACTAT
*
1089002 AAATATATATA-TAATATTT-TA-AATAT-AA-TTATCATACTAT
1 AAATAAATATATTAATATTTATATAATATAAACTT-TCATACTAT
1089042 AAA
1 AAA
1089045 CCATAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
39 2 0.05
40 12 0.31
41 5 0.13
42 2 0.05
43 8 0.21
44 10 0.26
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (44 bp):
AAATAAATATATTAATATTTATATAATATAAACTTTCATACTAT
Found at i:1089958 original size:3 final size:3
Alignment explanation
Indices: 1089950--1089977 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1089940 AACCCTTCAC
1089950 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1089978 TTCTGGTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:1091722 original size:25 final size:25
Alignment explanation
Indices: 1091694--1091746 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1091684 ATCTTTTAAA
*
1091694 TATAATTATGAATAAATATTATCAT
1 TATAATTATGAATAAATATTATAAT
* * * *
1091719 TATATTTATTATTAATTATTATAAT
1 TATAATTATGAATAAATATTATAAT
1091744 TAT
1 TAT
1091747 TAAATAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
TATAATTATGAATAAATATTATAAT
Found at i:1092032 original size:23 final size:23
Alignment explanation
Indices: 1092015--1092083 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
1092005 TATATGAGAT
1092015 AAATATAATATAAAATATAATTA
1 AAATATAATATAAAATATAATTA
1092038 AAATATAATAT--AATATAA--A
1 AAATATAATATAAAATATAATTA
*
1092057 AAAT-T-ATAT-AAATATAATTT
1 AAATATAATATAAAATATAATTA
1092077 AAATATA
1 AAATATA
1092084 TATTTATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
17 4 0.10
18 8 0.20
19 5 0.12
20 4 0.10
21 8 0.20
23 11 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATATAATATAAAATATAATTA
Found at i:1092047 original size:28 final size:28
Alignment explanation
Indices: 1092016--1092196 Score: 101
Period size: 28 Copynumber: 6.4 Consensus size: 28
1092006 ATATGAGATA
*
1092016 AATATAATATAAAATATAATTAAAATAT
1 AATATAATATAAAATATTATTAAAATAT
*
1092044 AATATAATATAAAAAATTA-TATAAATAT
1 AATATAATATAAAATATTATTA-AAATAT
* *
1092072 AATTTAA-AT-ATATATTTATTAAAAT-T
1 AATATAATATAAAATA-TTATTAAAATAT
* *
1092098 TATATAATAT-AAATA--ATTAAATTAT
1 AATATAATATAAAATATTATTAAAATAT
* * * *
1092123 ATTAAAATTTAAATAATTATATATTTTAAATAT
1 AATATAATAT-AA-AA-TAT-TA-TTAAAATAT
*
1092156 AATTATTATATATAAA-ATTA-TACAAATAT
1 AA-TATAATATA-AAATATTATTA-AAATAT
1092185 AATATAAATATA
1 AATAT-AATATA
1092197 TATTTAACTA
Statistics
Matches: 115, Mismatches: 21, Indels: 33
0.68 0.12 0.20
Matches are distributed among these distances:
24 7 0.06
25 7 0.06
26 9 0.08
27 18 0.16
28 37 0.32
29 15 0.13
30 2 0.02
31 2 0.02
32 1 0.01
33 11 0.10
34 6 0.05
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
AATATAATATAAAATATTATTAAAATAT
Found at i:1092079 original size:40 final size:40
Alignment explanation
Indices: 1092022--1092198 Score: 140
Period size: 42 Copynumber: 4.6 Consensus size: 40
1092012 GATAAATATA
*
1092022 ATATAAAATATAA-TTAAAATATAATATAATATAAAAAATT
1 ATAT-AAATATAATTTAAAATATAATATTATATAAAAAATT
* *
1092062 ATATAAATATAATTT-AAATAT-ATATT-TATTAAAATTT
1 ATATAAATATAATTTAAAATATAATATTATATAAAAAATT
* * *
1092099 ATAT-AATATAA---ATAAT-TAA-ATTATATTAAAATTT
1 ATATAAATATAATTTAAAATATAATATTATATAAAAAATT
* * * *
1092133 AAATAATTATATATTTTAAATATAATTATTATATATAAAATT
1 ATATAAATATA-ATTTAAAATATAA-TATTATATAAAAAATT
* *
1092175 ATACAAATATAATATAAATATATA
1 ATATAAATATAATTTAAA-ATATA
1092199 TTTAACTATC
Statistics
Matches: 108, Mismatches: 16, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
33 4 0.04
34 18 0.17
35 5 0.05
36 8 0.07
37 13 0.12
38 4 0.04
39 17 0.16
40 9 0.08
41 5 0.05
42 25 0.23
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (40 bp):
ATATAAATATAATTTAAAATATAATATTATATAAAAAATT
Found at i:1092131 original size:34 final size:31
Alignment explanation
Indices: 1092068--1092139 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 31
1092058 AATTATATAA
* *
1092068 ATATAATTTAAATATATATTTATTAAAATTT
1 ATATAATATAAATATAAATTTATTAAAATTT
1092099 ATATAATATAAATAATTAAATTATATTAAAATTT
1 ATATAATATAAAT-A-TAAATT-TATTAAAATTT
*
1092133 AAATAAT
1 ATATAAT
1092140 TATATATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 12 0.34
32 1 0.03
33 5 0.14
34 17 0.49
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
ATATAATATAAATATAAATTTATTAAAATTT
Found at i:1092195 original size:11 final size:11
Alignment explanation
Indices: 1092013--1092196 Score: 87
Period size: 11 Copynumber: 17.8 Consensus size: 11
1092003 GATATATGAG
1092013 ATAAATATAAT
1 ATAAATATAAT
1092024 ATAAAATATAAT
1 AT-AAATATAAT
1092036 -TAAAATATAAT
1 AT-AAATATAAT
1092047 AT-AATATAA-
1 ATAAATATAAT
1092056 A-AAAT-T-AT
1 ATAAATATAAT
1092064 ATAAATATAAT
1 ATAAATATAAT
*
1092075 TTAAATAT-AT
1 ATAAATATAAT
** *
1092085 ATTTAT-TAAA
1 ATAAATATAAT
**
1092095 ATTTATATAAT
1 ATAAATATAAT
1092106 AT-AA-ATAAT
1 ATAAATATAAT
*
1092115 -TAAATTATATT
1 ATAAA-TATAAT
*
1092126 A-AAATTTAA-
1 ATAAATATAAT
*
1092135 ATAATTATATATT
1 ATAA--ATATAAT
*
1092148 TTAAATATAAT
1 ATAAATATAAT
*
1092159 -T-ATTAT-AT
1 ATAAATATAAT
*
1092167 ATAAA-ATTAT
1 ATAAATATAAT
*
1092177 ACAAATATAAT
1 ATAAATATAAT
1092188 ATAAATATA
1 ATAAATATA
1092197 TATTTAACTA
Statistics
Matches: 133, Mismatches: 19, Indels: 42
0.69 0.10 0.22
Matches are distributed among these distances:
7 1 0.01
8 5 0.04
9 24 0.18
10 34 0.26
11 52 0.39
12 14 0.11
13 3 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.42
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:1092331 original size:2 final size:2
Alignment explanation
Indices: 1092324--1092384 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1092314 TGTTGAAACC
1092324 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
1092366 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1092385 CTTAATTTAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1092920 original size:17 final size:19
Alignment explanation
Indices: 1092889--1092923 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1092879 AAATATTATT
1092889 AAATATAAATATTAATATA
1 AAATATAAATATTAATATA
1092908 AAATA-AAAT-TTAATAT
1 AAATATAAATATTAATAT
1092924 TATTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATATAAATATTAATATA
Found at i:1092922 original size:23 final size:23
Alignment explanation
Indices: 1092896--1092947 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1092886 ATTAAATATA
*
1092896 AATATTA-ATATAAAATAAAATTT
1 AATATTATATAAAAAATAAAA-TT
*
1092919 AATATTATTTAAAAAATAAAATT
1 AATATTATATAAAAAATAAAATT
1092942 AATATT
1 AATATT
1092948 TAAATTCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AATATTATATAAAAAATAAAATT
Found at i:1093084 original size:21 final size:21
Alignment explanation
Indices: 1093058--1093104 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1093048 TGTTAATTTA
1093058 TATATTTTATTATATTATAAT
1 TATATTTTATTATATTATAAT
* *
1093079 TATATTTTATTATTTTATATT
1 TATATTTTATTATATTATAAT
1093100 TATAT
1 TATAT
1093105 AAATTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TATATTTTATTATATTATAAT
Found at i:1093424 original size:20 final size:19
Alignment explanation
Indices: 1093383--1093427 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1093373 TTTGATTATA
* **
1093383 TTATTTAAATTTTTTATTT
1 TTATTTAAATTTTTAAAAT
1093402 TTATTTAAAATTTTTAAAAT
1 TTATTT-AAATTTTTAAAAT
1093422 TTATTT
1 TTATTT
1093428 TTATATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTAAATTTTTAAAAT
Found at i:1093814 original size:19 final size:18
Alignment explanation
Indices: 1093790--1093828 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1093780 TATTAAATAA
1093790 ATTTATATAATTTTATTAT
1 ATTTATATAATTTT-TTAT
*
1093809 ATTTATATTATTTTTTAT
1 ATTTATATAATTTTTTAT
1093827 AT
1 AT
1093829 GATTGAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTATATAATTTTTTAT
Found at i:1096287 original size:3 final size:3
Alignment explanation
Indices: 1096279--1096306 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1096269 TGGTTAACAT
1096279 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1096307 GACTATAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1097035 original size:21 final size:20
Alignment explanation
Indices: 1096985--1097042 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
1096975 AATTTTATTT
*
1096985 TTTAAAAATAATTAAATAAA
1 TTTAAAATTAATTAAATAAA
*
1097005 TTTATGAATTAATTAAATTAAA
1 TTTA-AAATTAATTAAA-TAAA
*
1097027 TTTAAAATTAAATAAA
1 TTTAAAATTAATTAAA
1097043 AATATCACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 4 0.12
21 20 0.62
22 8 0.25
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TTTAAAATTAATTAAATAAA
Found at i:1097507 original size:41 final size:39
Alignment explanation
Indices: 1097462--1097552 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 39
1097452 ACATGTAATT
1097462 ATATGAATATAATATTTATAAAATATT-TAAAATATAATTTA
1 ATATGAATAT-ATATTT-TAAAAT-TTATAAAATATAATTTA
* * *
1097503 ATATGAATATTTATTTTAAAATTTATATAATATAAATT-
1 ATATGAATATATATTTTAAAATTTATAAAATATAATTTA
1097541 AT-T-AATATATAT
1 ATATGAATATATAT
1097553 AAATATATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
36 8 0.18
37 1 0.02
38 4 0.09
39 17 0.38
40 5 0.11
41 10 0.22
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (39 bp):
ATATGAATATATATTTTAAAATTTATAAAATATAATTTA
Found at i:1099325 original size:164 final size:163
Alignment explanation
Indices: 1099041--1099340 Score: 456
Period size: 164 Copynumber: 1.8 Consensus size: 163
1099031 GCTCCTGATC
** * * *
1099041 ATCTCCGCCATGTTGTTAGGAAACCCGGCGTTTCTAGTCAAGGAGGGCAAGGATTTCGACTCGAT
1 ATCTCCGCCATGTTGTTAGGAAACCCAACGGTCCTAGCCAAGGAGGGCAAGGATTTCGACTCGAT
* *
1099106 GAAGTTTTCGAAGTTCTTGATCTTTTGGGAATCAAGGATTCTTCCGGACCAAGTAATGGTGGAGA
66 GAAGTTTTCGAAGTTCTCGATCTTTTGGGAATCAAGGATTCTTCCGGACCAAGTAATGGCGGAGA
*
1099171 AGGGCACTGAAGCTCGTACTTTTGCTTCAAATT
131 AAGGCACTGAAGCTCGTACTTTTGCTTCAAATT
* * *
1099204 ATCTGCGCCATGTTGTTAGGAAACCCAACGGTCCTAGCCAAGGAGGGTAGGGATTTCGACTCTGA
1 ATCTCCGCCATGTTGTTAGGAAACCCAACGGTCCTAGCCAAGGAGGGCAAGGATTTCGACTC-GA
* * **
1099269 TGAAGTTTTCGAAGTTCTCGATCTTTTGGGGATCTAGGATTCTTCCGGGTCAAGTAATGGCGGAG
65 TGAAGTTTTCGAAGTTCTCGATCTTTTGGGAATCAAGGATTCTTCCGGACCAAGTAATGGCGGAG
1099334 AAAGGCA
130 AAAGGCA
1099341 TTTGAAGTTT
Statistics
Matches: 121, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
163 54 0.45
164 67 0.55
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (163 bp):
ATCTCCGCCATGTTGTTAGGAAACCCAACGGTCCTAGCCAAGGAGGGCAAGGATTTCGACTCGAT
GAAGTTTTCGAAGTTCTCGATCTTTTGGGAATCAAGGATTCTTCCGGACCAAGTAATGGCGGAGA
AAGGCACTGAAGCTCGTACTTTTGCTTCAAATT
Found at i:1099971 original size:30 final size:30
Alignment explanation
Indices: 1099935--1099995 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
1099925 TCTGGATCAG
*
1099935 TTAAGATGTTTTTAATTACATTGCTCTTGT
1 TTAAGATATTTTTAATTACATTGCTCTTGT
1099965 TTAAGATATTTTTAATTACATTGCTCTTGT
1 TTAAGATATTTTTAATTACATTGCTCTTGT
1099995 T
1 T
1099996 GACAGTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.10, G:0.11, T:0.54
Consensus pattern (30 bp):
TTAAGATATTTTTAATTACATTGCTCTTGT
Found at i:1103459 original size:2 final size:2
Alignment explanation
Indices: 1103452--1103477 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1103442 TGAAAGTGTA
1103452 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
1103478 CTTAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1106845 original size:22 final size:21
Alignment explanation
Indices: 1106817--1106857 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1106807 TAATACAATT
1106817 ATAATTAAATAAAATTAAAAAA
1 ATAATTAAA-AAAATTAAAAAA
*
1106839 ATAATTAAAAAGATTAAAA
1 ATAATTAAAAAAATTAAAA
1106858 CGGAATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
ATAATTAAAAAAATTAAAAAA
Found at i:1107304 original size:14 final size:16
Alignment explanation
Indices: 1107285--1107321 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1107275 TTTAAATATT
1107285 TATATTT-GATA-AAA
1 TATATTTAGATATAAA
1107299 TATATTTAGATATAAA
1 TATATTTAGATATAAA
*
1107315 TTTATTT
1 TATATTT
1107322 TTGGATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 4 0.20
16 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
TATATTTAGATATAAA
Found at i:1108364 original size:19 final size:19
Alignment explanation
Indices: 1108342--1108385 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1108332 ATCCGTCTAA
1108342 AAAATTATAAT-TTAAAAAT
1 AAAATTA-AATATTAAAAAT
* *
1108361 AAAAATAAATATTAAAATT
1 AAAATTAAATATTAAAAAT
1108380 AAAATT
1 AAAATT
1108386 TATTAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTAAATATTAAAAAT
Found at i:1109153 original size:25 final size:26
Alignment explanation
Indices: 1109125--1109174 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1109115 GTTATTCGAT
1109125 TTTTAAAT-AAATCT-TAATAAAAATA
1 TTTTAAATGAAAT-TATAATAAAAATA
*
1109150 TTTTAAATGTAATTATAATAAAAAT
1 TTTTAAATGAAATTATAATAAAAAT
1109175 TATATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (26 bp):
TTTTAAATGAAATTATAATAAAAATA
Found at i:1110584 original size:16 final size:16
Alignment explanation
Indices: 1110559--1110606 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
1110549 AATAAATCTT
1110559 AATATATATTATTTGA
1 AATATATATTATTTGA
* * *
1110575 ATTTTATATT-TTTTA
1 AATATATATTATTTGA
1110590 AATATATATTTATTTGA
1 AATATATA-TTATTTGA
1110607 TTTATGTTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
15 10 0.42
16 10 0.42
17 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
AATATATATTATTTGA
Found at i:1110760 original size:29 final size:25
Alignment explanation
Indices: 1110723--1110795 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 25
1110713 TATTTAAGTT
*
1110723 TAAT-TATAAATATATAATAATTATTAT
1 TAATATATAAATA-ATAA-AATT-TTAA
1110750 TAATAATATAAA-AATAAAATTTTAA
1 TAAT-ATATAAATAATAAAATTTTAA
1110775 TAATATAATAAATAATAAAAT
1 TAATAT-ATAAATAATAAAAT
1110796 ATGCTTTTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
24 2 0.05
25 12 0.29
26 12 0.29
27 8 0.20
28 1 0.02
29 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATATATAAATAATAAAATTTTAA
Found at i:1111106 original size:2 final size:2
Alignment explanation
Indices: 1111099--1111149 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
1111089 ACAATGTTAA
*
1111099 AT AT AT AT AT AT AT AT AT A- AT -T AT -T GT AT -T CAT 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
1111138 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1111150 TAGGACAGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
1 4 0.09
2 38 0.88
3 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1112919 original size:16 final size:16
Alignment explanation
Indices: 1112892--1112929 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1112882 GAAATTTTTA
*
1112892 AATATA-ATTAAACAT
1 AATATATATTAAAAAT
1112907 AATATATATTAAAAAT
1 AATATATATTAAAAAT
*
1112923 AAAATAT
1 AATATAT
1112930 TCAATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
AATATATATTAAAAAT
Found at i:1115874 original size:20 final size:20
Alignment explanation
Indices: 1115846--1115886 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1115836 TATTAAATAA
*
1115846 ATTTATAT-TTT-AAAATTT
1 ATTTATATATTTAAAAAATT
1115864 ATTTATATATTTAAAAAATT
1 ATTTATATATTTAAAAAATT
1115884 ATT
1 ATT
1115887 AAAAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 9 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTATATATTTAAAAAATT
Found at i:1117163 original size:25 final size:26
Alignment explanation
Indices: 1117135--1117194 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
1117125 TTAAAAATTT
1117135 TAATTAATA-TTTACAT-AATATTTTA
1 TAATTAATATTTTA-ATAAATATTTTA
*
1117160 TAATTAA-ATTTTAATAAATTTTTTA
1 TAATTAATATTTTAATAAATATTTTA
1117185 TAATTGAATA
1 TAATT-AATA
1117195 ATAATTCAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 3 0.10
25 24 0.80
26 2 0.07
27 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
TAATTAATATTTTAATAAATATTTTA
Found at i:1117177 original size:10 final size:10
Alignment explanation
Indices: 1117116--1117181 Score: 55
Period size: 9 Copynumber: 6.2 Consensus size: 10
1117106 TGAATCATTA
1117116 TTAA-AAATT
1 TTAATAAATT
1117125 TTAA-AAATT
1 TTAATAAATT
*
1117134 TTAATTAATAT
1 TTAATAAAT-T
1117145 TTACATAATATTT
1 TTA-ATAA-A-TT
1117158 TATAATTAAATT
1 T-TAA-TAAATT
1117170 TTAATAAATT
1 TTAATAAATT
1117180 TT
1 TT
1117182 TTATAATTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
9 13 0.27
10 11 0.23
11 7 0.15
12 6 0.12
13 5 0.10
14 6 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (10 bp):
TTAATAAATT
Found at i:1118033 original size:2 final size:2
Alignment explanation
Indices: 1118028--1118063 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1118018 AGACACACAC
*
1118028 AT AT AT AG 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
1118064 TCCCTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1118975 original size:15 final size:16
Alignment explanation
Indices: 1118955--1118986 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1118945 TTAACAATCA
1118955 ATTTTT-AAAAATTTT
1 ATTTTTGAAAAATTTT
1118970 ATTTTTGAAAAATTTT
1 ATTTTTGAAAAATTTT
1118986 A
1 A
1118987 AAAATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
ATTTTTGAAAAATTTT
Found at i:1120920 original size:2 final size:2
Alignment explanation
Indices: 1120913--1120949 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1120903 TTTTGTACTT
* *
1120913 TA TA TA TA TA TA TA TA TA TT TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1120950 TAGTTGGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1128463 original size:28 final size:28
Alignment explanation
Indices: 1128431--1128494 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1128421 AATTTTTTTA
* *
1128431 ATTTTATAAAT-TATATTAAAAATTTAT
1 ATTTTTTAAATATATATTAAAAATATAT
* *
1128458 ATTTTTTAAATATATTTTTAAAATATAT
1 ATTTTTTAAATATATATTAAAAATATAT
1128486 ATTATTTTA
1 ATT-TTTTA
1128495 TTAATTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 10 0.32
28 16 0.52
29 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTTTTAAATATATATTAAAAATATAT
Found at i:1128471 original size:13 final size:13
Alignment explanation
Indices: 1128455--1128485 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1128445 ATTAAAAATT
*
1128455 TATATTTTTTAAA
1 TATATTTTTAAAA
1128468 TATATTTTTAAAA
1 TATATTTTTAAAA
1128481 TATAT
1 TATAT
1128486 ATTATTTTAT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATATTTTTAAAA
Found at i:1128613 original size:13 final size:13
Alignment explanation
Indices: 1128595--1128619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1128585 TGATTTGTTA
1128595 AAAATAAATAAAT
1 AAAATAAATAAAT
1128608 AAAATAAATAAA
1 AAAATAAATAAA
1128620 GTTTTATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:1130543 original size:15 final size:16
Alignment explanation
Indices: 1130525--1130570 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
1130515 ATAAAATTTT
1130525 TTTAATAAATA-AATA
1 TTTAATAAATATAATA
* *
1130540 TTTAAT-GATATAATC
1 TTTAATAAATATAATA
*
1130555 TTTAATAAATTTAATA
1 TTTAATAAATATAATA
1130571 CTACTACTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
14 3 0.12
15 15 0.62
16 6 0.25
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
TTTAATAAATATAATA
Found at i:1134313 original size:23 final size:19
Alignment explanation
Indices: 1134265--1134304 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1134255 TCATGTCCAC
1134265 TATACTAAGCATAATTTCT
1 TATACTAAGCATAATTTCT
1134284 TATACTAAGCATAATTTCT
1 TATACTAAGCATAATTTCT
1134303 TA
1 TA
1134305 CTCAAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (19 bp):
TATACTAAGCATAATTTCT
Found at i:1135177 original size:5 final size:5
Alignment explanation
Indices: 1135135--1135175 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
1135125 GTGCTACTAC
* *
1135135 TTTCC TTTCC TTTCT TTTCT TTTCT TTTCT TTT-T TTT-T TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1135176 TTAAAAAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
4 8 0.23
5 27 0.77
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:1136018 original size:3 final size:3
Alignment explanation
Indices: 1136010--1136039 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1136000 GCCTTAATTG
1136010 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1136040 AATTTTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1136304 original size:13 final size:14
Alignment explanation
Indices: 1136276--1136308 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1136266 ATCTTGAATA
1136276 TAAATTTTAATAATT
1 TAAATTTT-ATAATT
1136291 TAAATTTT-TAATT
1 TAAATTTTATAATT
1136304 TAAAT
1 TAAAT
1136309 AAATATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
15 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAAATTTTATAATT
Found at i:1136337 original size:18 final size:18
Alignment explanation
Indices: 1136294--1136342 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 18
1136284 AATAATTTAA
1136294 ATTTTTAATTTAAATAAAT
1 ATTTTT-ATTTAAATAAAT
1136313 A--TTTATTT-AATAAAAT
1 ATTTTTATTTAAAT-AAAT
1136329 ATTTTTATTTAAAT
1 ATTTTTATTTAAAT
1136343 TTAATTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 3 0.12
16 9 0.35
17 3 0.12
18 7 0.27
19 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTTATTTAAATAAAT
Found at i:1136658 original size:16 final size:16
Alignment explanation
Indices: 1136606--1136660 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1136596 TATTATATAT
*
1136606 TTATATAAATTTTAAT
1 TTATATAAATTTTAAA
* *
1136622 TTAT-TAATAATTTATA
1 TTATATAA-ATTTTAAA
1136638 TTATATAAATTTTAAA
1 TTATATAAATTTTAAA
*
1136654 ATATATA
1 TTATATA
1136661 TTTATATAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 25 0.81
17 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATATAAATTTTAAA
Found at i:1137368 original size:13 final size:13
Alignment explanation
Indices: 1137350--1137395 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
1137340 AACAAATATT
1137350 TATATTATATTTA
1 TATATTATATTTA
*
1137363 TATATTTTA-TTA
1 TATATTATATTTA
1137375 TATAATTATATTTA
1 TAT-ATTATATTTA
1137389 -ATATTAT
1 TATATTAT
1137396 CGAATCTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 11 0.38
13 15 0.52
14 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATATTATATTTA
Found at i:1137384 original size:18 final size:19
Alignment explanation
Indices: 1137345--1137395 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
1137335 ATAAAAACAA
*
1137345 ATATTTATATTATATTTAT
1 ATATTTATATTATATATAT
1137364 ATATTT-TATTATATA-ATT
1 ATATTTATATTATATATA-T
1137382 ATATTTAATATTAT
1 ATATTT-ATATTAT
1137396 CGAATCTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 1 0.04
18 15 0.54
19 6 0.21
20 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTTATATTATATATAT
Found at i:1137393 original size:20 final size:17
Alignment explanation
Indices: 1137345--1137395 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
1137335 ATAAAAACAA
1137345 ATATTTATATTATATTT
1 ATATTTATATTATATTT
*
1137362 ATATATTTTATTATATAATT
1 ATAT-TTATATTATAT--TT
1137382 ATATTTAATATTAT
1 ATATTT-ATATTAT
1137396 CGAATCTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 4 0.14
18 10 0.36
19 2 0.07
20 12 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATTTATATTATATTT
Found at i:1138119 original size:39 final size:40
Alignment explanation
Indices: 1138051--1138134 Score: 109
Period size: 39 Copynumber: 2.1 Consensus size: 40
1138041 TCGGATAGAA
* * *
1138051 TAATAATTTAAATTTTTTTATAAATTTAAATTAAATTAATT
1 TAATAATTT-AATTTTTTTATAAACTTAAATTAAATCAAAT
1138092 TAATAATTT-ATTTTTGTT-TAAACTTAAATTAAATCAAAT
1 TAATAATTTAATTTTT-TTATAAACTTAAATTAAATCAAAT
1138131 TAAT
1 TAAT
1138135 TTAAAGTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
39 28 0.72
40 2 0.05
41 9 0.23
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (40 bp):
TAATAATTTAATTTTTTTATAAACTTAAATTAAATCAAAT
Found at i:1138512 original size:2 final size:2
Alignment explanation
Indices: 1138505--1138529 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1138495 ATTGATCTTT
1138505 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1138530 TGATATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1140086 original size:2 final size:2
Alignment explanation
Indices: 1140079--1140109 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1140069 AATGTAAAAT
1140079 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1140110 GTGTCAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1141310 original size:20 final size:21
Alignment explanation
Indices: 1141285--1141327 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1141275 ATTATTTTAT
1141285 TTAAAT-TTAAT-TATAAAATA
1 TTAAATATTAATATA-AAAATA
1141305 TTAAATATTAATATAAAAATA
1 TTAAATATTAATATAAAAATA
1141326 TT
1 TT
1141328 TTTAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 13 0.62
22 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAATATTAATATAAAAATA
Found at i:1141682 original size:2 final size:2
Alignment explanation
Indices: 1141675--1141701 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1141665 CCTTTTCCTT
1141675 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
1141702 GTATGTATGT
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
Done.