Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 5 of 20
Found at i:658958 original size:11 final size:10
Alignment explanation
Indices: 658901--658959 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
658891 GTTACCTCTG
658901 ATATATTAAT
1 ATATATTAAT
*
658911 ATAT-TGAAT
1 ATATATTAAT
*
658920 GTAT-TTAAAT
1 ATATATT-AAT
658930 ATATATTCAAT
1 ATATATT-AAT
658941 ATA-ATTAATT
1 ATATATTAA-T
658951 ATATATTAA
1 ATATATTAA
658960 ATTTTTATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
9 10 0.25
10 17 0.43
11 13 0.32
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (10 bp):
ATATATTAAT
Found at i:659071 original size:22 final size:22
Alignment explanation
Indices: 659046--659091 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
659036 ATAAGCCCTA
*
659046 TTTTTTT-ATTA-TTGACTTTC
1 TTTTTTTCATTAGTTGACTTGC
659066 TTTTTTTCATTAGTTGACTTGC
1 TTTTTTTCATTAGTTGACTTGC
659088 TTTT
1 TTTT
659092 CTCAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
21 4 0.17
22 12 0.52
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTTTTTTCATTAGTTGACTTGC
Found at i:659415 original size:16 final size:16
Alignment explanation
Indices: 659396--659434 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
659386 TCTGAAATAA
* *
659396 TTCGAACCTGAGAAAG
1 TTCGAACCTAAAAAAG
659412 TTCGAACCTAAAAAAG
1 TTCGAACCTAAAAAAG
*
659428 CTCGAAC
1 TTCGAAC
659435 TCGAAAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (16 bp):
TTCGAACCTAAAAAAG
Found at i:660461 original size:24 final size:23
Alignment explanation
Indices: 660431--660478 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
660421 TTTAATTAAG
*
660431 ATTAAATGGATTTTTAAATATTTT
1 ATTAAATCGA-TTTTAAATATTTT
* *
660455 ATTAAATCTATTTTAAATTTTTT
1 ATTAAATCGATTTTAAATATTTT
660478 A
1 A
660479 AATATTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
ATTAAATCGATTTTAAATATTTT
Found at i:660755 original size:27 final size:30
Alignment explanation
Indices: 660701--660758 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 30
660691 ATTAAATATA
660701 TTAAAAATATAATAATATAATAAATATTTAC
1 TTAAAAATATAATAATAT-ATAAATATTTAC
*
660732 TTAAAAAT-TAATAAT-T-TAATTATTTAC
1 TTAAAAATATAATAATATATAAATATTTAC
660759 ATTTTAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 10 0.38
29 1 0.04
30 7 0.27
31 8 0.31
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
TTAAAAATATAATAATATATAAATATTTAC
Found at i:661932 original size:38 final size:39
Alignment explanation
Indices: 661870--661958 Score: 112
Period size: 38 Copynumber: 2.3 Consensus size: 39
661860 AAAAAATGAT
661870 TATTTATTATATATTATATATAATAA-TTTAATAATAAA
1 TATTTATTATATATTATATATAATAATTTTAATAATAAA
*
661908 TATTTATGT-TAT-TTATATATTAATAATTTTTATAATAAA
1 TATTTAT-TATATATTATATA-TAATAATTTTAATAATAAA
*
661947 TAATTTTTTATA
1 T-ATTTATTATA
661959 ATTTTCATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
37 7 0.16
38 16 0.36
39 14 0.32
40 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (39 bp):
TATTTATTATATATTATATATAATAATTTTAATAATAAA
Found at i:661950 original size:16 final size:17
Alignment explanation
Indices: 661919--661960 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
661909 ATTTATGTTA
*
661919 TTTATATATTAATAA-TT
1 TTTATA-ATAAATAATTT
661936 TTTATAATAAATAATTT
1 TTTATAATAAATAATTT
661953 TTTATAAT
1 TTTATAAT
661961 TTTCATTACG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTATAATAAATAATTT
Found at i:661953 original size:15 final size:17
Alignment explanation
Indices: 661919--661958 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
661909 ATTTATGTTA
*
661919 TTTATATATTAATAATT
1 TTTATATATAAATAATT
661936 TTTATA-ATAAATAATT
1 TTTATATATAAATAATT
661952 TTT-TATA
1 TTTATATA
661959 ATTTTCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 13 0.62
17 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTATATATAAATAATT
Found at i:665305 original size:49 final size:50
Alignment explanation
Indices: 665235--665376 Score: 146
Period size: 49 Copynumber: 2.9 Consensus size: 50
665225 GTCTAAACTC
* * * * *
665235 AAATCAATTAAAATCTAAAATAATTTAGATTTTAAAAAAATTTATATCTA
1 AAATAAATTCAAATTTAAAATAATTTAGATTTTAAAAAAATATAAATCTA
* * * * *
665285 AAATGAA-TCGAATTTTAAATAATTTA-AATTTAAAATAATATAAATCTA
1 AAATAAATTCAAATTTAAAATAATTTAGATTTTAAAAAAATATAAATCTA
* *
665333 AAATAAATTTAAATTTAAAATAATTTAGA-TCTAAAAATAATATA
1 AAATAAATTCAAATTTAAAATAATTTAGATTTTAAAAA-AATATA
665377 TCCGAACCTG
Statistics
Matches: 74, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
48 24 0.32
49 37 0.50
50 13 0.18
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (50 bp):
AAATAAATTCAAATTTAAAATAATTTAGATTTTAAAAAAATATAAATCTA
Found at i:665314 original size:16 final size:16
Alignment explanation
Indices: 665235--665373 Score: 109
Period size: 16 Copynumber: 8.4 Consensus size: 16
665225 GTCTAAACTC
* *
665235 AAATCAATTAAAATCTA
1 AAAT-AATTTAAATTTA
*
665252 AAATAATTTAGATTTTA
1 AAATAATTTA-AATTTA
* * *
665269 AAAAAATTTATATCTA
1 AAATAATTTAAATTTA
** *
665285 AAATGAA-TCGAATTTT
1 AAAT-AATTTAAATTTA
665301 AAATAATTTAAATTTA
1 AAATAATTTAAATTTA
* *
665317 AAATAATATAAATCTA
1 AAATAATTTAAATTTA
665333 AAATAAATTTAAATTTA
1 AAAT-AATTTAAATTTA
* *
665350 AAATAATTTAGATCTAA
1 AAATAATTTAAAT-TTA
665367 AAATAAT
1 AAATAAT
665374 ATATCCGAAC
Statistics
Matches: 95, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
15 2 0.02
16 51 0.54
17 42 0.44
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.37
Consensus pattern (16 bp):
AAATAATTTAAATTTA
Found at i:665347 original size:33 final size:32
Alignment explanation
Indices: 665301--665373 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 32
665291 ATCGAATTTT
665301 AAATAATTTAAATTTAAAATAATATAAATCTA
1 AAATAATTTAAATTTAAAATAATATAAATCTA
* *
665333 AAATAAATTTAAATTTAAAATAATTTAGATCTAA
1 AAAT-AATTTAAATTTAAAATAATATAAATCT-A
665367 AAATAAT
1 AAATAAT
665374 ATATCCGAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 4 0.11
33 28 0.76
34 5 0.14
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (32 bp):
AAATAATTTAAATTTAAAATAATATAAATCTA
Found at i:667791 original size:2 final size:2
Alignment explanation
Indices: 667784--667820 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
667774 TAGTCAATGT
*
667784 TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
667821 TTTAACCTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:668006 original size:35 final size:35
Alignment explanation
Indices: 667925--668014 Score: 94
Period size: 35 Copynumber: 2.5 Consensus size: 35
667915 CTTTTTAATT
* *
667925 TAATATAATAAATAAATTTTGTTAGTATATAATCAAC
1 TAATA-AATAAATAAATTTTATTA-TATATAATAAAC
*
667962 TAATTAATAAATAAATTTTAATT-TATA-AGATAAAC
1 TAATAAATAAATAAATTTT-ATTATATATA-ATAAAC
*
667997 TAATAAATAAATCAATTT
1 TAATAAATAAATAAATTT
668015 AATCATTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
34 1 0.02
35 25 0.54
36 14 0.30
37 6 0.13
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.40
Consensus pattern (35 bp):
TAATAAATAAATAAATTTTATTATATATAATAAAC
Found at i:668332 original size:21 final size:20
Alignment explanation
Indices: 668306--668347 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
668296 TTATCATTGA
*
668306 TTTTAATTTTATCATTATAAT
1 TTTTAATTTAAT-ATTATAAT
668327 TTTTAATCTTAATATTATAAT
1 TTTTAAT-TTAATATTATAAT
668348 AATTAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTAATTTAATATTATAAT
Found at i:671357 original size:2 final size:2
Alignment explanation
Indices: 671350--671386 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
671340 TAGTCAATGT
671350 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
671387 TTTTAACCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:671578 original size:36 final size:36
Alignment explanation
Indices: 671497--671580 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 36
671487 TTTTTAATTC
** *
671497 AATATAATAAATAAATTTTGTTAATATATAATCAAAT
1 AATA-AATAAATAAATTTCATTAATATAAAATCAAAT
* **
671534 AATTAATAAATAAATTTCATTTTTATAAAAT-AAACT
1 AATAAATAAATAAATTTCATTAATATAAAATCAAA-T
671570 AATAAATAAAT
1 AATAAATAAAT
671581 CTAATCATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
35 3 0.08
36 33 0.85
37 3 0.08
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (36 bp):
AATAAATAAATAAATTTCATTAATATAAAATCAAAT
Found at i:672249 original size:17 final size:19
Alignment explanation
Indices: 672213--672251 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
672203 TTAAGTCAAG
672213 TATAAATATCTAAAATAAA
1 TATAAATATCTAAAATAAA
*
672232 TATAAAT-T-TAATATAAA
1 TATAAATATCTAAAATAAA
672249 TAT
1 TAT
672252 GTATAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 1 0.05
19 7 0.37
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TATAAATATCTAAAATAAA
Found at i:672329 original size:17 final size:18
Alignment explanation
Indices: 672289--672329 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
672279 AAGTATATAG
**
672289 AATATAAAATATTTTAAA
1 AATATAAAATATTAAAAA
672307 AA-ATAAAA-ATTAAAAA
1 AATATAAAATATTAAAAA
672323 AATATAA
1 AATATAA
672330 TCCGAAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
17 10 0.50
18 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATAAAATATTAAAAA
Found at i:673676 original size:12 final size:12
Alignment explanation
Indices: 673659--673700 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
673649 TTTAAAATTT
673659 TAAATATTTATA
1 TAAATATTTATA
673671 TAAATA-TT-T-
1 TAAATATTTATA
673680 TAAATATTTATA
1 TAAATATTTATA
673692 TAAATATTT
1 TAAATATTT
673701 TAAATTTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 6 0.22
10 3 0.11
11 3 0.11
12 15 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAATATTTATA
Found at i:673718 original size:21 final size:21
Alignment explanation
Indices: 673651--673705 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
673641 TGATGAATTT
673651 TAAA-ATTTTAAATATTTATA
1 TAAATATTTTAAATATTTATA
673671 TAAATATTTTAAATATTTATA
1 TAAATATTTTAAATATTTATA
673692 TAAATATTTTAAAT
1 TAAATATTTTAAAT
673706 TTATCATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.12
21 30 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAATATTTTAAATATTTATA
Found at i:674309 original size:31 final size:32
Alignment explanation
Indices: 674271--674383 Score: 86
Period size: 35 Copynumber: 3.5 Consensus size: 32
674261 GGCTTAGGTG
*
674271 TAAAATTTTTTTATTTAGATTTAAATTAAT-C
1 TAAAATTTTTTTATTTAGATTTAAAATAATAC
* ** *
674302 TAAAA-TTTTATATTTTTATTTAAAATAATAT
1 TAAAATTTTTTTATTTAGATTTAAAATAATAC
* * * *
674333 TAAAATTATTTTTATATTAATATTTATAATAAAAT
1 TAAAATT-TTTTTAT-TT-AGATTTAAAATAATAC
*
674368 TTAAATTATTTTTATT
1 TAAAATT-TTTTTATT
674384 ATATATACAA
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
30 20 0.30
31 10 0.15
32 1 0.01
33 6 0.09
34 3 0.04
35 27 0.40
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (32 bp):
TAAAATTTTTTTATTTAGATTTAAAATAATAC
Found at i:674323 original size:30 final size:31
Alignment explanation
Indices: 674271--674339 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
674261 GGCTTAGGTG
* *
674271 TAAAATTTTTTTATTTAGATTTAAATTAAT-C
1 TAAAA-TTTTATATTTAGATTTAAAATAATAC
** *
674302 TAAAATTTTATATTTTTATTTAAAATAATAT
1 TAAAATTTTATATTTAGATTTAAAATAATAC
674333 TAAAATT
1 TAAAATT
674340 ATTTTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 20 0.62
31 12 0.38
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (31 bp):
TAAAATTTTATATTTAGATTTAAAATAATAC
Found at i:674357 original size:35 final size:35
Alignment explanation
Indices: 674307--674382 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
674297 TAATCTAAAA
** *
674307 TTTTATATTTTTATTTAAAATAATATTAAAATTAT
1 TTTTATATTAATATTTAAAATAAAATTAAAATTAT
* *
674342 TTTTATATTAATATTTATAATAAAATTTAAATTAT
1 TTTTATATTAATATTTAAAATAAAATTAAAATTAT
674377 TTTTAT
1 TTTTAT
674383 TATATATACA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (35 bp):
TTTTATATTAATATTTAAAATAAAATTAAAATTAT
Found at i:676016 original size:16 final size:19
Alignment explanation
Indices: 675991--676032 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 19
675981 CGCCACATGG
*
675991 ATAAACTTTTTT-TT-TT-
1 ATAAATTTTTTTGTTATTA
676007 ATAAATTTTTTTGTTATTA
1 ATAAATTTTTTTGTTATTA
676026 ATAAATT
1 ATAAATT
676033 AAATAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 11 0.50
17 2 0.09
18 2 0.09
19 7 0.32
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
ATAAATTTTTTTGTTATTA
Found at i:676017 original size:15 final size:16
Alignment explanation
Indices: 675991--676023 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
675981 CGCCACATGG
*
675991 ATAAACTTTTTTTTTT
1 ATAAACTTTTTTTGTT
676007 ATAAA-TTTTTTTGTT
1 ATAAACTTTTTTTGTT
676022 AT
1 AT
676024 TAATAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (16 bp):
ATAAACTTTTTTTGTT
Found at i:697817 original size:20 final size:21
Alignment explanation
Indices: 697786--697825 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
697776 TTTGGTGATT
697786 TTTAATTAAAAAAATATTATA
1 TTTAATTAAAAAAATATTATA
697807 TTTAA-TAAAAAAATATTAT
1 TTTAATTAAAAAAATATTAT
697826 TGAAGATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTAATTAAAAAAATATTATA
Found at i:697834 original size:20 final size:20
Alignment explanation
Indices: 697792--697834 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
697782 GATTTTTAAT
**
697792 TAAAAAAATATTATATTTAA
1 TAAAAAAATATTATATGAAA
697812 TAAAAAAATATTAT-TGAAGA
1 TAAAAAAATATTATATGAA-A
697832 TAA
1 TAA
697835 TAATATACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (20 bp):
TAAAAAAATATTATATGAAA
Found at i:704445 original size:63 final size:64
Alignment explanation
Indices: 704378--704502 Score: 180
Period size: 63 Copynumber: 2.0 Consensus size: 64
704368 ATTTATTTAG
*
704378 AACCAAACAAAAATCTAATTGCAACAATACATCAAACAACTAGAAGACA-ACAAAAAGCGCTAA
1 AACCAAACAAAAATCTAATTGCAACAATACATCAAACAAATAGAAGACACACAAAAAGCGCTAA
* * ** *
704441 AACCAAACAAATATCTCATTGCCCCAATTCATCAAACAAATAGAAGACACGACAAAAAGCGC
1 AACCAAACAAAAATCTAATTGCAACAATACATCAAACAAATAGAAGACAC-ACAAAAAGCGC
704503 CCATTCTTGA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 43 0.80
65 11 0.20
ACGTcount: A:0.53, C:0.25, G:0.09, T:0.14
Consensus pattern (64 bp):
AACCAAACAAAAATCTAATTGCAACAATACATCAAACAAATAGAAGACACACAAAAAGCGCTAA
Found at i:706238 original size:137 final size:137
Alignment explanation
Indices: 705992--706257 Score: 442
Period size: 137 Copynumber: 1.9 Consensus size: 137
705982 TAAAAAATGC
705992 AGAACCAGTGAAACACACAGCTCCAATGGTGTAAAGTACAAAAATATAAGGATAAAACAACTAGC
1 AGAACCAGTGAAACACACAGCTCCAATGGTGTAAAGTACAAAAATATAAGGATAAAACAACTAGC
* *
706057 GTAAGGAACTATAAATTCCCCAGCTATTCCTCTAGAGTATAATCAACTGATGCATTAAATCAAAG
66 GTAAAGAACTATAAATTCCCCAGCTATTCCTCTAGAGTATAATCAACTGATGCATTAAAACAAAG
706122 AAAAGGA
131 AAAAGGA
* * * ** * *
706129 AGAACCAGTGAATCCCACAGCTTCAATGGTGTACGGTACAAAAATGTAAGGATAAAACAACTAGT
1 AGAACCAGTGAAACACACAGCTCCAATGGTGTAAAGTACAAAAATATAAGGATAAAACAACTAGC
*
706194 GTAAAGAACTATAAATTCCCCAGCTATTCCTCTGGAGTATAATCAACTGATGCATTAAAACAAA
66 GTAAAGAACTATAAATTCCCCAGCTATTCCTCTAGAGTATAATCAACTGATGCATTAAAACAAA
706258 AGGTATGATG
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
137 119 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (137 bp):
AGAACCAGTGAAACACACAGCTCCAATGGTGTAAAGTACAAAAATATAAGGATAAAACAACTAGC
GTAAAGAACTATAAATTCCCCAGCTATTCCTCTAGAGTATAATCAACTGATGCATTAAAACAAAG
AAAAGGA
Found at i:707203 original size:16 final size:16
Alignment explanation
Indices: 707182--707223 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
707172 TGTAATTGTT
* *
707182 ATAATAACTTTTATAA
1 ATAATAAATTATATAA
707198 ATAATAAATTATATAA
1 ATAATAAATTATATAA
*
707214 ACAA-AAATTA
1 ATAATAAATTA
707224 AAGATTGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATAAATTATATAA
Found at i:707419 original size:33 final size:31
Alignment explanation
Indices: 707348--707419 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
707338 ATTTATATTT
*
707348 AAAATTATAAAATAAAATAAAATATAACTCG
1 AAAATTATAAAATAAAATAAAATATAACTCA
** * * *
707379 ATGATTATCATATATAATAATAATAATAACTCA
1 AAAATTATAAAATAAAATAA-AAT-ATAACTCA
707412 AAAATTAT
1 AAAATTAT
707420 TTGACATAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
31 15 0.48
32 3 0.10
33 13 0.42
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAATTATAAAATAAAATAAAATATAACTCA
Found at i:707665 original size:2 final size:2
Alignment explanation
Indices: 707660--707690 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
707650 GCGCACATGC
707660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
707691 AACCAAGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:714989 original size:6 final size:6
Alignment explanation
Indices: 714978--715020 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
714968 CTTTTTTAAA
* * *
714978 TAAATT TAAATT TAAATT TAAATA TAATTTT TTAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAA-ATT TAAATT TAAATT
715021 AATCAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
6 27 0.90
7 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TAAATT
Found at i:716282 original size:31 final size:33
Alignment explanation
Indices: 716230--716302 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 33
716220 TATAATTTAA
* *
716230 AATATATT-AATTTATATTAATATTAATATTTT
1 AATAAATTAAATTTATAATAATATTAATATTTT
* *
716262 TAT-AATTAAATTTA-AATAATATTATTATTTT
1 AATAAATTAAATTTATAATAATATTAATATTTT
716293 AATAAATTAA
1 AATAAATTAA
716303 TAATAATACA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
31 20 0.59
32 14 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
AATAAATTAAATTTATAATAATATTAATATTTT
Found at i:716295 original size:28 final size:28
Alignment explanation
Indices: 716247--716310 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
716237 TAATTTATAT
* * *
716247 TAATATTAATATTTTTATAATTAAATTTA
1 TAATAATATTATTTTTATAA-TAAATTAA
716276 -AATAATATTATTATTT-TAATAAATTAA
1 TAATAATATTATT-TTTATAATAAATTAA
716303 TAATAATA
1 TAATAATA
716311 CAAATTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 7 0.23
28 20 0.67
29 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TAATAATATTATTTTTATAATAAATTAA
Found at i:718876 original size:2 final size:2
Alignment explanation
Indices: 718869--718901 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
718859 GCAAATACAA
718869 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
718902 ATGTGAGGAG
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:719887 original size:2 final size:2
Alignment explanation
Indices: 719880--719908 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
719870 CCTTTTCATT
719880 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 T
719909 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:719913 original size:2 final size:2
Alignment explanation
Indices: 719908--719937 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
719898 TCTCTCTCTC
719908 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
719938 TAAAACTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:720643 original size:6 final size:6
Alignment explanation
Indices: 720632--720661 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
720622 CGAGTGCAGA
720632 GCATGT GCATGT GCATGT GCATGT GCATGT
1 GCATGT GCATGT GCATGT GCATGT GCATGT
720662 ACATTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
GCATGT
Found at i:720891 original size:17 final size:17
Alignment explanation
Indices: 720869--720902 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
720859 TTTAAAAAGT
720869 AAAATATAAATAATTTA
1 AAAATATAAATAATTTA
*
720886 AAAATATAAATATTTTA
1 AAAATATAAATAATTTA
720903 CTTTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATATAAATAATTTA
Found at i:720935 original size:3 final size:3
Alignment explanation
Indices: 720927--720962 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
720917 AATTAATTTA
720927 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
720963 GAGATGATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:725020 original size:2 final size:2
Alignment explanation
Indices: 725009--725043 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
724999 AGACGAGACC
725009 AT AT -T 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
725044 TGAAGAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:726849 original size:20 final size:20
Alignment explanation
Indices: 726826--726863 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
726816 ACATAAATAT
726826 ATTTA-ATATTTATTAAAAAA
1 ATTTATATATTTA-TAAAAAA
726846 ATTTATATATTTATAAAA
1 ATTTATATATTTATAAAA
726864 TTATATCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTATATATTTATAAAAAA
Found at i:727407 original size:39 final size:38
Alignment explanation
Indices: 727336--727411 Score: 91
Period size: 38 Copynumber: 1.9 Consensus size: 38
727326 CTCGCTCGAA
*
727336 TTATTTTTTAAAAAATTTAAATTTAATTATAAATATAAAT
1 TTATTTTTT-AAAAATTTAAATTTAATAATAAA-ATAAAT
* *
727376 TTATTTTTT-AAAATTTTATTTTAAATAATAAAATAA
1 TTATTTTTTAAAAATTTAAATTT-AATAATAAAATAA
727412 TTTTTAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 15 0.47
39 8 0.25
40 9 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (38 bp):
TTATTTTTTAAAAATTTAAATTTAATAATAAAATAAAT
Found at i:727415 original size:33 final size:31
Alignment explanation
Indices: 727354--727431 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 31
727344 TAAAAAATTT
* *
727354 AAATTTAATTATAAATATAAATTTATTTTTTA
1 AAATTTAATTATAAATATAAA-ATAATTTTTA
* *
727386 AAATTTTATTTTAAATAATAAAATAATTTTTA
1 AAATTTAATTATAAAT-ATAAAATAATTTTTA
727418 AAA-TTAATT-TAAAT
1 AAATTTAATTATAAAT
727432 GTTTTAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 5 0.12
31 5 0.12
32 25 0.62
33 5 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
AAATTTAATTATAAATATAAAATAATTTTTA
Found at i:728792 original size:3 final size:3
Alignment explanation
Indices: 728784--728841 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
728774 TTACCGGGTA
*
728784 TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
728832 TTC TTC TTC T
1 TTC TTC TTC T
728842 GGGGAATAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:729692 original size:3 final size:3
Alignment explanation
Indices: 729684--729723 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
729674 ATTTATTTAC
* *
729684 TAT TAT TAT TGT TAT TAT TAT TAAT AAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
729724 GTTACTGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 30 0.94
4 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:729702 original size:22 final size:22
Alignment explanation
Indices: 729676--729735 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
729666 ATGCTTTTAT
*
729676 TTATTTACTATTATTATTGTTA
1 TTATTTACTATTATTATTATTA
* *
729698 TTA-TTATTAATAATTATTATTA
1 TTATTTACT-ATTATTATTATTA
*
729720 TTATGTTACTGTTATT
1 TTAT-TTACTATTATT
729736 CAGGTATTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.14
22 17 0.59
23 4 0.14
24 4 0.14
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (22 bp):
TTATTTACTATTATTATTATTA
Found at i:731092 original size:50 final size:50
Alignment explanation
Indices: 731012--731117 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 50
731002 ATCTTTTTAT
*
731012 AACTTTAGTGGATTTAGAATACGGTATGGAACCTATGCCTTGATGGAAAC
1 AACTGTAGTGGATTTAGAATACGGTATGGAACCTATGCCTTGATGGAAAC
*
731062 AACTGTAGTGGGTTTAGAATACGGTATGGAACCTATGCCTTGATGGAAAC
1 AACTGTAGTGGATTTAGAATACGGTATGGAACCTATGCCTTGATGGAAAC
731112 AACTGT
1 AACTGT
731118 TTACTCACTC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (50 bp):
AACTGTAGTGGATTTAGAATACGGTATGGAACCTATGCCTTGATGGAAAC
Found at i:733839 original size:19 final size:19
Alignment explanation
Indices: 733815--733852 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
733805 AGACATTCAT
733815 AAATCTTATAAAAATTAAC
1 AAATCTTATAAAAATTAAC
733834 AAATCTTATAAAAATTAAC
1 AAATCTTATAAAAATTAAC
733853 TTTCAACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATCTTATAAAAATTAAC
Found at i:737509 original size:15 final size:14
Alignment explanation
Indices: 737455--737509 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
737445 TAATAAAAAA
737455 ATATATAAAATGATT
1 ATATATAAAAT-ATT
*
737470 AT-TA-AAAAAATT
1 ATATATAAAATATT
* *
737482 ATATTTAAGATATGT
1 ATATATAAAATAT-T
737497 ATATATAAAATAT
1 ATATATAAAATAT
737510 AAATAATTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
12 5 0.16
13 5 0.16
14 7 0.23
15 14 0.45
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (14 bp):
ATATATAAAATATT
Found at i:737866 original size:20 final size:20
Alignment explanation
Indices: 737838--737914 Score: 93
Period size: 21 Copynumber: 3.8 Consensus size: 20
737828 TATAATAATA
* *
737838 ATAATATTAATTATTATAGT
1 ATAAAATTAAATATTATAGT
* *
737858 ATAAAATTAAATATTGTAAT
1 ATAAAATTAAATATTATAGT
737878 GATAAAATTAAATATTATAGTT
1 -ATAAAATTAAATATTATAG-T
737900 ATAAAATT-AATATTA
1 ATAAAATTAAATATTA
737915 AAAAATAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 23 0.47
21 25 0.51
22 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (20 bp):
ATAAAATTAAATATTATAGT
Found at i:737912 original size:41 final size:41
Alignment explanation
Indices: 737833--737913 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
737823 ATGATTATAA
* *
737833 TAATAATAATATTAATTATTATAGTATAAAATTAAATATTG
1 TAATAATAAAATTAAATATTATAGTATAAAATTAAATATTG
*
737874 TAATGATAAAATTAAATATTATAGTTATAAAATT-AATATT
1 TAATAATAAAATTAAATATTATAG-TATAAAATTAAATATT
737914 AAAAAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 27 0.75
42 9 0.25
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (41 bp):
TAATAATAAAATTAAATATTATAGTATAAAATTAAATATTG
Found at i:738613 original size:2 final size:2
Alignment explanation
Indices: 738602--738649 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
738592 TGGAAGAAAA
* *
738602 AT AT -T AT AT AT AT AT AT AT AC AT AC 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
*
738643 AC AT AT A
1 AT AT AT A
738650 ATTAGAAGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:739221 original size:20 final size:21
Alignment explanation
Indices: 739193--739233 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
739183 ATGAGAATTC
* *
739193 AATATTTAAATTTAAT-TGTA
1 AATAGTTAAATATAATATGTA
739213 AATAGTTAAATATAATATGTA
1 AATAGTTAAATATAATATGTA
739234 TTTAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
AATAGTTAAATATAATATGTA
Found at i:742364 original size:28 final size:28
Alignment explanation
Indices: 742300--742354 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
742290 TAAATGCCAC
742300 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
742328 CCTTTGTATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
742355 ATTTTTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.11, G:0.22, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:742395 original size:24 final size:24
Alignment explanation
Indices: 742336--742404 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
742326 TTCCTTTGTA
* * *
742336 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATGGTGG--CTTGTTG
* *
742362 TATGTAAAAAATGGTGGCTTGTTG
1 TTTGTCAAAAATGGTGGCTTGTTG
*
742386 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAAATGGTGGCT
742405 AATTTTTATT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 21 0.60
26 14 0.40
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCTTGTTG
Found at i:744956 original size:21 final size:22
Alignment explanation
Indices: 744927--744972 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
744917 TGTTCAGACA
** *
744927 AGTAGTACTCCGTAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
744949 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
744970 AGT
1 AGT
744973 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:746941 original size:28 final size:28
Alignment explanation
Indices: 746880--746944 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
746870 CAAATGCTAC
746880 CTTTTGTATTTGTCAAATATGGTGGTTT
1 CTTTTGTATTTGTCAAATATGGTGGTTT
*
746908 CCTTTGTATTTGTCAAATATGGTGGTTAT
1 CTTTTGTATTTGTCAAATATGGTGGTT-T
746937 -TTTTGTAT
1 CTTTTGTAT
746945 GTAAAAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.18, C:0.08, G:0.20, T:0.54
Consensus pattern (28 bp):
CTTTTGTATTTGTCAAATATGGTGGTTT
Found at i:746975 original size:24 final size:24
Alignment explanation
Indices: 746916--746984 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
746906 TTCCTTTGTA
* * *
746916 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATGGTGG--CTTGTTG
* *
746942 TATGTAAAAAATGGTGGCTTGTTG
1 TTTGTCAAAAATGGTGGCTTGTTG
*
746966 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAAATGGTGGCT
746985 AATTTTTATT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 21 0.60
26 14 0.40
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCTTGTTG
Found at i:748524 original size:4 final size:4
Alignment explanation
Indices: 748515--748574 Score: 59
Period size: 4 Copynumber: 15.2 Consensus size: 4
748505 TTAAAGGCTA
* * * * *
748515 ATAT ATAT ATAT ATAT GTAT GTAT GTAT ATAT ATAT ATAT GTAT GTAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
748563 GTAT ATAT -TAT A
1 ATAT ATAT ATAT A
748575 ACAAAGCCTC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 3 0.06
4 48 0.94
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:748528 original size:8 final size:8
Alignment explanation
Indices: 748516--748574 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
748506 TAAAGGCTAA
*
748516 TATATATA
1 TATATATG
748524 TATATATG
1 TATATATG
*
748532 TATGTATG
1 TATATATG
*
748540 TATATATA
1 TATATATG
748548 TATATATG
1 TATATATG
*
748556 TATGTATG
1 TATATATG
748564 TATATAT-
1 TATATATG
748571 TATA
1 TATA
748575 ACAAAGCCTC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
7 4 0.09
8 40 0.91
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (8 bp):
TATATATG
Found at i:748545 original size:20 final size:20
Alignment explanation
Indices: 748520--748570 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
748510 GGCTAATATA
*
748520 TATATATATATGTATGTATG
1 TATATATATATATATGTATG
748540 TATATATATATATATGTATG
1 TATATATATATATATGTATG
*
748560 TATGTATATAT
1 TATATATATAT
748571 TATAACAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (20 bp):
TATATATATATATATGTATG
Found at i:748548 original size:24 final size:24
Alignment explanation
Indices: 748516--748574 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
748506 TAAAGGCTAA
748516 TATATATATATATATGTATGTATG
1 TATATATATATATATGTATGTATG
748540 TATATATATATATATGTATGTATG
1 TATATATATATATATGTATGTATG
748564 TATATAT-TATA
1 TATATATATATA
748575 ACAAAGCCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.11
24 31 0.89
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (24 bp):
TATATATATATATATGTATGTATG
Found at i:749423 original size:2 final size:2
Alignment explanation
Indices: 749416--749441 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
749406 ATAGACAATA
749416 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
749442 GAATACTGAT
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:750738 original size:20 final size:21
Alignment explanation
Indices: 750698--750738 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
750688 TTTTCAATGG
*
750698 ATTATGTTGGAATTCTAATCA
1 ATTATGTGGGAATTCTAATCA
*
750719 ATTATGTGGGGATT-TAATCA
1 ATTATGTGGGAATTCTAATCA
750739 TTTTCTATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (21 bp):
ATTATGTGGGAATTCTAATCA
Found at i:752862 original size:2 final size:2
Alignment explanation
Indices: 752855--752885 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
752845 GTTAATAGTT
752855 TA TA 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 TA TA T
752886 TAGCCCTTTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:759109 original size:16 final size:16
Alignment explanation
Indices: 759077--759210 Score: 92
Period size: 16 Copynumber: 7.9 Consensus size: 16
759067 AAAATTGATC
*
759077 AATTCAAATTCTAAAAT
1 AATTTAAATT-TAAAAT
*
759094 AATTTAAACTTAAAAT
1 AATTTAAATTTAAAAT
*
759110 AATTTAAATTCAAAAT
1 AATTTAAATTTAAAAT
*
759126 GATTTAAATTTAAATTGATT
1 AATTTAAATTTAAA---A-T
759146 CAAATAATT-AATTTAAAAT
1 --AAT--TTAAATTTAAAAT
* *
759165 GATTT-AACTTAAAAT
1 AATTTAAATTTAAAAT
* **
759180 AACTTAAAAATAAAAT
1 AATTTAAATTTAAAAT
759196 AATTTAAATTTAAAA
1 AATTTAAATTTAAAA
759211 ATTTAAAATA
Statistics
Matches: 92, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
15 14 0.15
16 52 0.57
17 10 0.11
19 2 0.02
20 2 0.02
22 2 0.02
23 8 0.09
24 2 0.02
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.38
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:759221 original size:24 final size:22
Alignment explanation
Indices: 759183--759226 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
759173 TTAAAATAAC
*
759183 TTAAAAATAAAATAATTTAAAT
1 TTAAAAATAAAATAAATTAAAT
759205 TTAAAAATTTAAAATAAATTAA
1 TTAAAAA--TAAAATAAATTAA
759227 TTCACCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TTAAAAATAAAATAAATTAAAT
Found at i:759225 original size:70 final size:71
Alignment explanation
Indices: 759083--759229 Score: 176
Period size: 70 Copynumber: 2.1 Consensus size: 71
759073 GATCAATTCA
* * * * *
759083 AATTCTAAAATAATTTAAACTTAAAATAATTTAAATTCAAAATGATTTAAATTTAAATTGATTCA
1 AATTCTAAAATAATTTAAACTTAAAATAATTAAAAATCAAAATAATTTAAATTTAAAAT-ATTAA
759148 AATAATT
65 AATAATT
*
759155 AATT-TAAAATGATTT-AACTTAAAATAACTTAAAAAT-AAAATAATTTAAATTTAAAA-ATTTA
1 AATTCTAAAATAATTTAAACTTAAAATAA-TTAAAAATCAAAATAATTTAAATTTAAAATA-TTA
759216 AAATAAATT
64 AAAT-AATT
759225 AATTC
1 AATTC
759230 ACCTAATTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
68 1 0.02
69 6 0.09
70 38 0.58
71 16 0.25
72 4 0.06
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (71 bp):
AATTCTAAAATAATTTAAACTTAAAATAATTAAAAATCAAAATAATTTAAATTTAAAATATTAAA
ATAATT
Found at i:761485 original size:20 final size:20
Alignment explanation
Indices: 761462--761511 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
761452 GCAATCAAAT
*
761462 TAAGCAAAGATTTTTTTTTA
1 TAAGCAAAGATATTTTTTTA
* * *
761482 TAAGTATATATATTTTTTTA
1 TAAGCAAAGATATTTTTTTA
761502 TAAAGCAAAG
1 T-AAGCAAAG
761512 TTTAGTTCTA
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (20 bp):
TAAGCAAAGATATTTTTTTA
Found at i:765296 original size:20 final size:22
Alignment explanation
Indices: 765253--765297 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
765243 TTGAGATATA
**
765253 AAAAAAATTATCTAATTTTTTT
1 AAAAAAATTATCTAATTTAATT
765275 AAAAAAA-TATC-AATTTAATT
1 AAAAAAATTATCTAATTTAATT
765295 AAA
1 AAA
765298 TTTATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 4 0.19
22 7 0.33
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAAAATTATCTAATTTAATT
Found at i:765431 original size:22 final size:22
Alignment explanation
Indices: 765403--765448 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
765393 ATATAAAATT
765403 TATTTTTACA-TTAATATTTATA
1 TATTTTTACATTTAAT-TTTATA
*
765425 TATTTTTATATTTAATTTTATA
1 TATTTTTACATTTAATTTTATA
765447 TA
1 TA
765449 AAAATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTTTACATTTAATTTTATA
Found at i:766731 original size:20 final size:21
Alignment explanation
Indices: 766685--766731 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
766675 ACTAAAATTA
766685 TTTTTTTATTAATCGAATTTT
1 TTTTTTTATTAATCGAATTTT
* * *
766706 ATTTTTTGTTGATC-AATTTT
1 TTTTTTTATTAATCGAATTTT
766726 TTTTTT
1 TTTTTT
766732 CACAAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.70
Consensus pattern (21 bp):
TTTTTTTATTAATCGAATTTT
Found at i:767487 original size:3 final size:3
Alignment explanation
Indices: 767479--767510 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
767469 TCTTTTTCTT
767479 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
767511 TATTTTGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:767925 original size:13 final size:14
Alignment explanation
Indices: 767907--767944 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
767897 TAAATATTAA
767907 TAAAATTAAT-TTT
1 TAAAATTAATATTT
767920 TAAAATT-ATATTT
1 TAAAATTAATATTT
767933 TAAAATATAATA
1 TAAAAT-TAATA
767945 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.09
13 16 0.73
14 1 0.05
15 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAAATTAATATTT
Found at i:768897 original size:24 final size:23
Alignment explanation
Indices: 768870--768948 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 23
768860 AAAAATTATT
768870 TAAATTTATTTATAAATATTAATA
1 TAAATTTATTT-TAAATATTAATA
* *
768894 TAAAAATATT-TTTTTAATATT-TTA
1 T--AAAT-TTATTTTAAATATTAATA
* *
768918 TATA-TTATTTTAAATAATAATA
1 TAAATTTATTTTAAATATTAATA
768940 TAAAATTTA
1 T-AAATTTA
768949 AAATTAATTC
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
20 2 0.05
21 9 0.22
22 5 0.12
23 2 0.05
24 7 0.17
25 7 0.17
26 7 0.17
27 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAATTTATTTTAAATATTAATA
Found at i:769242 original size:14 final size:13
Alignment explanation
Indices: 769225--769268 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
769215 ATAGTTTTTT
769225 ATTTTTAAATTATA
1 ATTTTTAAATTA-A
**
769239 ATTTAAAAATTAA
1 ATTTTTAAATTAA
769252 ATTATTTAAATTAA
1 ATT-TTTAAATTAA
769266 ATT
1 ATT
769269 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTTTAAATTAA
Found at i:769255 original size:5 final size:5
Alignment explanation
Indices: 769245--769293 Score: 52
Period size: 5 Copynumber: 10.6 Consensus size: 5
769235 TATAATTTAA
* *
769245 AAATT AAATT -ATTT AAATT AAATT AAAAT AAA-- AAA-T AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT
769291 AAA
1 AAA
769294 ATTTTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
3 3 0.08
4 6 0.16
5 29 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
AAATT
Found at i:769280 original size:27 final size:27
Alignment explanation
Indices: 769228--769293 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
769218 GTTTTTTATT
** *
769228 TTTAAATTATAATTTAAAAATTAAATTA
1 TTTAAATTA-AATTTAAAAAAAAAATAA
769256 TTTAAATTAAA-TTAAAATAAAAAATAA
1 TTTAAATTAAATTTAAAA-AAAAAATAA
*
769283 ATTAAATTAAA
1 TTTAAATTAAA
769294 ATTTTATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 6 0.18
27 18 0.55
28 9 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TTTAAATTAAATTTAAAAAAAAAATAA
Found at i:774692 original size:21 final size:22
Alignment explanation
Indices: 774668--774710 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
774658 TAAATATATT
* *
774668 ATTTGATAATTTTAA-TTATAA
1 ATTTGAAAAATTTAATTTATAA
*
774689 ATTTTAAAAATTTAATTTATAA
1 ATTTGAAAAATTTAATTTATAA
774711 TGGAAGACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTTGAAAAATTTAATTTATAA
Found at i:776242 original size:36 final size:36
Alignment explanation
Indices: 776202--776287 Score: 163
Period size: 36 Copynumber: 2.4 Consensus size: 36
776192 CAATATTTGA
*
776202 ACTCCTCTAGTCCTTTTGGTGCGAAAGAACTCTGCT
1 ACTCCTCTAGTCCTTTTGGTGCGAAAGAAATCTGCT
776238 ACTCCTCTAGTCCTTTTGGTGCGAAAGAAATCTGCT
1 ACTCCTCTAGTCCTTTTGGTGCGAAAGAAATCTGCT
776274 ACTCCTCTAGTCCT
1 ACTCCTCTAGTCCT
776288 AACCTCTTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (36 bp):
ACTCCTCTAGTCCTTTTGGTGCGAAAGAAATCTGCT
Found at i:778059 original size:18 final size:20
Alignment explanation
Indices: 778038--778081 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
778028 ATGCATAAGT
778038 TATTTATATATTATT-C-TA
1 TATTTATATATTATTACATA
* *
778056 TATTAATGTATTATTACATA
1 TATTTATATATTATTACATA
778076 TATTTA
1 TATTTA
778082 ATTACTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 13 0.62
19 1 0.05
20 7 0.33
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (20 bp):
TATTTATATATTATTACATA
Found at i:778487 original size:56 final size:57
Alignment explanation
Indices: 778413--778519 Score: 171
Period size: 56 Copynumber: 1.9 Consensus size: 57
778403 AATTAGTAAA
* * *
778413 AATTCTTTAATTCTTAATTTATAAAAT-AAAAAAGTTCAAATATATAATAATAGTAC
1 AATTCTTTAATTCGTAATTTAAAAAATAAAAAAAATTCAAATATATAATAATAGTAC
*
778469 AATTGTTTAATTCGTAATTTAAAAAATAAAAAAAATTCAAATATATAATAA
1 AATTCTTTAATTCGTAATTTAAAAAATAAAAAAAATTCAAATATATAATAA
778520 AAGAATAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
56 24 0.52
57 22 0.48
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (57 bp):
AATTCTTTAATTCGTAATTTAAAAAATAAAAAAAATTCAAATATATAATAATAGTAC
Found at i:778767 original size:10 final size:10
Alignment explanation
Indices: 778752--778788 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
778742 CATAATTTAT
778752 TTATATATTA
1 TTATATATTA
778762 TTATATATTA
1 TTATATATTA
778772 --ATATATTA
1 TTATATATTA
778780 TTTATATAT
1 -TTATATAT
778789 ATTTAATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.33
10 10 0.42
11 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTATATATTA
Found at i:778770 original size:18 final size:19
Alignment explanation
Indices: 778749--778788 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
778739 ATGCATAATT
*
778749 TATTTATATATTA-TTATA
1 TATTAATATATTATTTATA
778767 TATTAATATATTATTTATA
1 TATTAATATATTATTTATA
778786 TAT
1 TAT
778789 ATTTAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTAATATATTATTTATA
Found at i:778791 original size:10 final size:10
Alignment explanation
Indices: 778746--778793 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
778736 ATAATGCATA
*
778746 ATTTATTTAT
1 ATTTATATAT
778756 ATATTATTATAT
1 AT-TTA-TATAT
*
778768 ATTAATATATT
1 ATTTATATA-T
778779 ATTTATATAT
1 ATTTATATAT
778789 ATTTA
1 ATTTA
778794 ATTACTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 12 0.38
11 14 0.44
12 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTATATAT
Found at i:778797 original size:18 final size:18
Alignment explanation
Indices: 778776--778822 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
778766 ATATTAATAT
778776 ATTATTTATATATATTTA
1 ATTATTTATATATATTTA
*
778794 ATTACTTTTATATATGTTTA
1 ATTA--TTTATATATATTTA
778814 A--ATTTATAT
1 ATTATTTATAT
778823 TTTAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 7 0.27
18 5 0.19
20 14 0.54
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
ATTATTTATATATATTTA
Found at i:778939 original size:31 final size:28
Alignment explanation
Indices: 778904--778965 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 28
778894 CAAAATATAA
778904 AAATAAAAATAAAAATTTATAATTCAATATT
1 AAATAAAAATAAAAATTT-TAATT-AAT-TT
* * *
778935 AAATATAATTAAATATTTTAATTAATTT
1 AAATAAAAATAAAAATTTTAATTAATTT
778963 AAA
1 AAA
778966 CAATGTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.18
29 3 0.11
30 5 0.18
31 15 0.54
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (28 bp):
AAATAAAAATAAAAATTTTAATTAATTT
Found at i:779238 original size:55 final size:56
Alignment explanation
Indices: 779136--779244 Score: 148
Period size: 55 Copynumber: 2.0 Consensus size: 56
779126 TTAACGAAAT
* *
779136 TAGTAAAATTGTTTAATTCTTAATTTATAAAATAAAAAAATTCAAATAAATAATAA
1 TAGTAAAATTATTTAATTCTTAATTCATAAAATAAAAAAATTCAAATAAATAATAA
* * * * *
779192 TAGTAAATTTATTTAATTCTT-ATTCATATAATAAAAAATTTTAAATATATAAT
1 TAGTAAAATTATTTAATTCTTAATTCATAAAATAAAAAAATTCAAATAAATAAT
779245 GAAAAATGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
55 27 0.59
56 19 0.41
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (56 bp):
TAGTAAAATTATTTAATTCTTAATTCATAAAATAAAAAAATTCAAATAAATAATAA
Found at i:779339 original size:729 final size:714
Alignment explanation
Indices: 777801--780178 Score: 2945
Period size: 712 Copynumber: 3.3 Consensus size: 714
777791 ATAAACATTG
* * * * *
777801 ATAAAGAATAACAGGCATTTTCACATATATTACTCAAAAAATAATACAGTATGTTTAGTAACTTT
1 ATAAAAAATAACAGGCATTTTCACATATATTACTCAAAAAATAATACAATATATTTAATCACTTT
* * ** *
777866 AAATTAAATATATTTTGATTCTATTATTATAAGCATACAATTCACGGGAGATAGATATAAATCAA
66 AAATTAAATATATTTTGATTCTATTGTTACAAGCATACAATTCAC-AAATATAGATATAAATCAA
* *
777931 ATCAAATACTCATATATCACCCTTTTCAAGAATGAAAATATAATATTAGATATATAAAATATAAT
130 ATCAAATACTCATATATCACCCTTCTCAAGAATGAAAATATAACATTAGATATAT--AATATAAT
* * * *
777996 ATCATAC-ATTAATTTATAATTAGTTATATATAATGCATAAGTTATTTATATATTATTCTATATT
193 ATAATACAATAAATTTATAATTAGTTATATATAATGCATAATTTATTTATATATTATTATATATT
* * *
778060 AATGTATTATTACATATATTTAATTACTTTT-TATATGTTTAAATTCATGTATTTAAATAATAAA
258 AATATATTATTATATATATTTAATTACTTTTATATATGTTTAAATTTATGTATTTAAATAATAAA
* * *
778124 GAAATAATAATAAAACGAAAATAAAATCGTTTAATTGTTTTACAAAATAATATGTTAAGCAAAAG
323 AAAATAATAATAAAA--TAAATAAAATCGTTAAATTGTTTTACAAAATAATATGTTAAGCAAAAG
* *
778189 AT-A-AAAAATAAATATTTATAAATTAATATTAAATATAATTAAATGTTTTAATTAATTTAAGC-
386 ATAATAAAAATAAAAATTTAT-AATTAATATTAAATATAATTAAATGTTTTAATTAATTTAAACA
* * * *
778251 -G-ATATCAT-CAA--T-AAAATGCACATGT-TCTATATTTATATT-TTTTCAGAGCTCAAAAAT
450 TGTATAT-ATAAAATTTAAAAATGCA-ATATATATATA-TTATATTATTTTCATAGCTCAAAAAT
* * * * * *
778308 TTAAAACCTAGCATAACCACAAAACAAAGATATTAGGAGATACAATTTTCAACTTTTATACTTTT
512 TTAAAACCTAGTATAACTAAAAAACAAATATATTAGAAGATACAATTTTCAACTTTTATATTTTT
* *
778373 AATTTATTTACATTATATCTTTCTTAACAAAATTAGTAAAAATTCTTTAATTCTTAATTTATAAA
577 AATTTATTTACTTTATATC-TTCTTAACAAAATTAGT-AAAATTGTTTAATTCTTAATTTATAAA
* * * *
778438 ATAAAAAAGTTCAAATATATAATAATAGTACAATTGTTTAATTCGTAATTTAAAAAATAAAAAAA
640 ATAAAAAAATTCAAATATATAATAATAGTA-AATTGTTTAATTC-TTATTCATAAAAT-AAAAAA
*
778503 ATTCAAATATATA
702 ATTTAAATATATA
* * * *
778516 ATAAAAGAATAAAAGTC-GTTTCACATATATTACT--AAAAA-AATACAATATGTTTAATCACTT
1 ATAAAA-AATAACAGGCATTTTCACATATATTACTCAAAAAATAATACAATATATTTAATCACTT
* * *
778577 TAAATTAAATATATTTTGTTTCTATTTTTACAAGCATACAATTTACGAAATATAGATATAAATCA
65 TAAATTAAATATATTTTGATTCTATTGTTACAAGCATACAATTCAC-AAATATAGATATAAATCA
* * * *
778642 AATCAAATACTCATTTATCACCCTTCTCAAAAATGAAAATATAACATTAGATGTATAATAAAATA
129 AATCAAATACTCATATATCACCCTTCTCAAGAATGAAAATATAACATTAGATATATAATATAATA
*
778707 TAATACAATAAATTTATAATTAGTTATACATAATGCATAATTTATTTATATATTATTATATATTA
194 TAATACAATAAATTTATAATTAGTTATATATAATGCATAATTTATTTATATATTATTATATATTA
*
778772 ATATATTATTTATATATATTTAATTACTTTTATATATGTTTAAATTTATAT-TTTAAATAATAAA
259 ATATATTA-TTATATATATTTAATTACTTTTATATATGTTTAAATTTATGTATTTAAATAATAAA
* * * * * *
778836 TAAATAATAATAAAATAAGATTAAATTGTTAAATTGTTTTACAAAATATTATGTCAAGCAAAATA
323 AAAATAATAATAAAATAA-ATAAAATCGTTAAATTGTTTTACAAAATAATATGTTAAGCAAAAGA
*
778901 TAAAAATAAAAATAAAAATTTATAATTCAATATTAAATATAATTAAATATTTTAATTAATTTAAA
387 T---AATAAAAATAAAAATTTATAATT-AATATTAAATATAATTAAATGTTTTAATTAATTTAAA
*
778966 CAATGTCATATATAAAATTTTAAAATATTCTATATATATATATATATATATCTATTTTCATAGCT
448 C-ATGT-ATATATAAAA-TTTAAAA-ATGC-A-ATATATATATAT-TATAT-TATTTTCATAGCT
* *
779031 CAAAAATTTAAAACCTAGTATATA-TAAAAAACAAATATATTAGAAGATAAAATTTTGAACTTTT
505 CAAAAATTTAAAACCTAGTATA-ACTAAAAAACAAATATATTAGAAGATACAATTTTCAACTTTT
*
779095 ATATTTTTAATTTATTTACTTTATATCTTGCTTAACGAAATTAGTAAAATTGTTTAATTCTTAAT
569 ATATTTTTAATTTATTTACTTTATATCTT-CTTAACAAAATTAGTAAAATTGTTTAATTCTTAAT
* * *
779160 TTATAAAATAAAAAAATTCAAATAAATAATAATAGTAAATTTATTTAATTCTTATTCATATAATA
633 TTATAAAATAAAAAAATTCAAATATATAATAATAGTAAA-TTGTTTAATTCTTATTCATAAAATA
*
779225 AAAAATTTTAAATATATA
697 AAAAAATTTAAATATATA
* * *
779243 ATGAAAAATGACAGGCA-TTTCACATATATTAGTCAAAAAATAATACAATATATTTAATCACTTT
1 ATAAAAAATAACAGGCATTTTCACATATATTACTCAAAAAATAATACAATATATTTAATCACTTT
* *
779307 AAATTAAATATATTTTGATACTATTGTTACAAGGATACAA---A-AAAT-T--ATATAAATCAAA
66 AAATTAAATATATTTTGATTCTATTGTTACAAGCATACAATTCACAAATATAGATATAAATCAAA
* *
779365 TCAAATACTCATATATCA-CCTTCTCAAGAACGAAAATATAACATTCGATATATAATATAATATA
131 TCAAATACTCATATATCACCCTTCTCAAGAATGAAAATATAACATTAGATATATAATATAATATA
* * * * * *
779429 ATATATTAAATTTATAATTTA-TAATTTATAATGCATAATTTATTTATATATTATTTTATATTTA
196 ATACAATAAATTTATAA-TTAGTTATATATAATGCATAATTTATTTATATATTATTATATATTAA
*
779493 TATATTA-TATATATATTTAATTACTTTTATATATGTTCAAATTTATGTATTTAAATAATAAAAA
260 TATATTATTATATATATTTAATTACTTTTATATATGTTTAAATTTATGTATTTAAATAATAAAAA
* * * *
779557 AATACTAAT-AAATGAATAAAAATCATTAAATTGTTTTA-AAAAGTAATATATTAAGCAAAAGAT
325 AATAATAATAAAATAAAT-AAAATCGTTAAATTGTTTTACAAAA-TAATATGTTAAGCAAAAGAT
*
779620 AATAACAA-AAAAA-TTATAATTTAATATTAAATATAATTAAATGTTTTAATTAATTTAAACGAT
388 AATAAAAATAAAAATTTATAA-TTAATATTAAATATAATTAAATGTTTTAATTAATTTAAAC-AT
*
779683 GTTATATATAAAAATTTATAAAATGC---A-A-ATAT-TT-TA-TA--TT--TAGCTCAAAATTT
451 G-TATATAT-AAAATTTA-AAAATGCAATATATATATATTATATTATTTTCATAGCTCAAAAATT
*
779736 TAAAACCTAATATAACTAAAAAAACAAATATATTAGAAGATACAATTTTCAACTTTTATATTTTT
513 TAAAACCTAGTATAACT-AAAAAACAAATATATTAGAAGATACAATTTTCAACTTTTATATTTTT
779801 AATTTATTTA-TGTTATA---TCTTAACAAAATTAGTAAAATTGTTTAATTCTTAATTTATAAAA
577 AATTTATTTACT-TTATATCTTCTTAACAAAATTAGTAAAATTGTTTAATTCTTAATTTATAAAA
* * *
779862 TAAAAAAATTTAAATATATAATAATAGTAAAATTGTTTAATT-TGTATTCATAAAATACAAAAGT
641 TAAAAAAATTCAAATATATAATAATAGT-AAATTGTTTAATTCT-TATTCATAAAATAAAAAAAT
*
779926 TTAAATATAAA
704 TTAAATATATA
** * * * * * *
779937 ATAAAAAATAATGGGTATTTTCATATATATTACTTAAAAACTAATACAATACATTTAACCACTTT
1 ATAAAAAATAACAGGCATTTTCACATATATTACTCAAAAAATAATACAATATATTTAATCACTTT
*
780002 AAATTAAATATATTTTGATTCTATTGTTACAAGCATACAATTCACAAGA-A-AAATATAAATCAA
66 AAATTAAATATATTTTGATTCTATTGTTACAAGCATACAATTCACAA-ATATAGATATAAATCAA
* ** ** * *
780065 ATCAAATACTTATATATCACTTTTCTTGAGAATTAAAATATAACATTCGATATATAATATAATAT
130 ATCAAATACTCATATATCACCCTTCTCAAGAATGAAAATATAACATTAGATATATAATATAATAT
* * * *
780130 AATACATTAAATTTATAATTTGTTATGTATAATGTATAATTTATTTATA
195 AATACAATAAATTTATAATTAGTTATATATAATGCATAATTTATTTATA
780179 CATATTAATT
Statistics
Matches: 1463, Mismatches: 142, Indels: 129
0.84 0.08 0.07
Matches are distributed among these distances:
693 1 0.00
694 116 0.08
695 83 0.06
696 1 0.00
697 27 0.02
698 61 0.04
699 4 0.00
700 1 0.00
701 33 0.02
702 80 0.05
703 2 0.00
704 1 0.00
705 1 0.00
706 4 0.00
707 1 0.00
708 1 0.00
710 15 0.01
711 102 0.07
712 176 0.12
713 81 0.06
714 15 0.01
715 33 0.02
716 59 0.04
717 6 0.00
718 77 0.05
719 23 0.02
720 103 0.07
721 38 0.03
723 1 0.00
724 5 0.00
725 3 0.00
726 26 0.02
727 27 0.02
728 26 0.02
729 125 0.09
730 104 0.07
731 1 0.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (714 bp):
ATAAAAAATAACAGGCATTTTCACATATATTACTCAAAAAATAATACAATATATTTAATCACTTT
AAATTAAATATATTTTGATTCTATTGTTACAAGCATACAATTCACAAATATAGATATAAATCAAA
TCAAATACTCATATATCACCCTTCTCAAGAATGAAAATATAACATTAGATATATAATATAATATA
ATACAATAAATTTATAATTAGTTATATATAATGCATAATTTATTTATATATTATTATATATTAAT
ATATTATTATATATATTTAATTACTTTTATATATGTTTAAATTTATGTATTTAAATAATAAAAAA
ATAATAATAAAATAAATAAAATCGTTAAATTGTTTTACAAAATAATATGTTAAGCAAAAGATAAT
AAAAATAAAAATTTATAATTAATATTAAATATAATTAAATGTTTTAATTAATTTAAACATGTATA
TATAAAATTTAAAAATGCAATATATATATATTATATTATTTTCATAGCTCAAAAATTTAAAACCT
AGTATAACTAAAAAACAAATATATTAGAAGATACAATTTTCAACTTTTATATTTTTAATTTATTT
ACTTTATATCTTCTTAACAAAATTAGTAAAATTGTTTAATTCTTAATTTATAAAATAAAAAAATT
CAAATATATAATAATAGTAAATTGTTTAATTCTTATTCATAAAATAAAAAAATTTAAATATATA
Found at i:779456 original size:14 final size:14
Alignment explanation
Indices: 779437--779471 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
779427 TAATATATTA
**
779437 AATTTATAATTTAT
1 AATTTATAATGCAT
779451 AATTTATAATGCAT
1 AATTTATAATGCAT
779465 AATTTAT
1 AATTTAT
779472 TTATATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (14 bp):
AATTTATAATGCAT
Found at i:779490 original size:18 final size:19
Alignment explanation
Indices: 779469--779511 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
779459 ATGCATAATT
*
779469 TATTTATATATTAT-TTTA
1 TATTTATATATTATATATA
779487 TATTTATATATTATATATA
1 TATTTATATATTATATATA
779506 TATTTA
1 TATTTA
779512 ATTACTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTATATATTATATATA
Found at i:779934 original size:55 final size:56
Alignment explanation
Indices: 779830--779940 Score: 163
Period size: 55 Copynumber: 2.0 Consensus size: 56
779820 TTAACAAAAT
* *
779830 TAGTAAAATTGTTTAATTCTTAATTTATAAAATAAAAAAATTTAAATATATAATAA
1 TAGTAAAATTGTTTAATTCTTAATTCATAAAATAAAAAAATTTAAATATAAAATAA
* *
779886 TAGTAAAATTGTTTAATT-TGT-ATTCATAAAATACAAAAGTTTAAATATAAAATAA
1 TAGTAAAATTGTTTAATTCT-TAATTCATAAAATAAAAAAATTTAAATATAAAATAA
779941 AAAATAATGG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
55 31 0.62
56 19 0.38
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (56 bp):
TAGTAAAATTGTTTAATTCTTAATTCATAAAATAAAAAAATTTAAATATAAAATAA
Found at i:788031 original size:6 final size:6
Alignment explanation
Indices: 788020--788053 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
788010 GTTGATTTAA
* *
788020 AAATTT AAATTT AGATTT AAATTT GAATTT AAAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAAT
788054 GAAAATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:789356 original size:29 final size:28
Alignment explanation
Indices: 789311--789379 Score: 74
Period size: 29 Copynumber: 2.6 Consensus size: 28
789301 AATTTTTATA
* *
789311 AATATAAATAAA-T-TTTTGATAATTTT
1 AATATAAAAAAATTATTTTGAAAATTTT
*
789337 ATATATAAAAAAATTATTTTTAAAATTTT
1 A-ATATAAAAAAATTATTTTGAAAATTTT
789366 AAT-T-AAAAAATTAT
1 AATATAAAAAAATTAT
789380 ATTATATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 11 0.30
27 11 0.30
28 3 0.08
29 12 0.32
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
AATATAAAAAAATTATTTTGAAAATTTT
Found at i:790345 original size:109 final size:106
Alignment explanation
Indices: 790216--790430 Score: 394
Period size: 109 Copynumber: 2.0 Consensus size: 106
790206 CTGTTGATGC
790216 TTGCTTAGATCTTTCTGTTAAGTATTAACTAATGAATTCCTCATCCAATTTTACAGTACGTTTTG
1 TTGCTTAGATCTTTCTGTTAAGTATTAACTAATGAATT-CTCATCCAATTTTACAGTACGTTTTG
790281 TTGTTATGTATGTATGTTTATAAATTTGTTTGTTTTAATAAAAT
65 TTGTTATGTATG--TGTTTATAAATTTGTTTGTTTTAATAAAAT
*
790325 TTGCTTAGATCTTTCTGTTAAGTATTAACTAATGAATTCTCATCCAATTTTACAGTACTTTTTGT
1 TTGCTTAGATCTTTCTGTTAAGTATTAACTAATGAATTCTCATCCAATTTTACAGTACGTTTTGT
790390 TGTTATGTATGTGTTTATAAATTTGTTTGTTTTAATAAAAT
66 TGTTATGTATGTGTTTATAAATTTGTTTGTTTTAATAAAAT
790431 GTGTATGCAT
Statistics
Matches: 105, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
106 30 0.29
108 37 0.35
109 38 0.36
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50
Consensus pattern (106 bp):
TTGCTTAGATCTTTCTGTTAAGTATTAACTAATGAATTCTCATCCAATTTTACAGTACGTTTTGT
TGTTATGTATGTGTTTATAAATTTGTTTGTTTTAATAAAAT
Found at i:795703 original size:15 final size:15
Alignment explanation
Indices: 795683--795715 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
795673 CCCCCCCCAA
795683 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
*
795698 AAAAAAGAAAAAAAG
1 AAAAAAAAAAAAAAG
795713 AAA
1 AAA
795716 TTGGCATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:795712 original size:8 final size:8
Alignment explanation
Indices: 795682--795715 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
795672 CCCCCCCCCA
*
795682 AAAAAAAA
1 AAAAAAAG
795690 AAAAAAAG
1 AAAAAAAG
795698 -AAAAAAG
1 AAAAAAAG
795705 AAAAAAAG
1 AAAAAAAG
795713 AAA
1 AAA
795716 TTGGCATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:798522 original size:19 final size:20
Alignment explanation
Indices: 798495--798546 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
798485 CCCAGACCTT
798495 TAAAT-TTAAATCATAATAC
1 TAAATATTAAATCATAATAC
* * * *
798514 T-AATCTTAAACCCTAATTC
1 TAAATATTAAATCATAATAC
798533 TAAATATTAAATCA
1 TAAATATTAAATCA
798547 AACCGACGAT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
18 3 0.12
19 13 0.52
20 9 0.36
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAATATTAAATCATAATAC
Found at i:800279 original size:17 final size:17
Alignment explanation
Indices: 800257--800292 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
800247 AAGCTTCAGT
800257 TACTGAATGGTATTAAA
1 TACTGAATGGTATTAAA
800274 TACTGAATGGTATTAAA
1 TACTGAATGGTATTAAA
800291 TA
1 TA
800293 AGCATGAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (17 bp):
TACTGAATGGTATTAAA
Found at i:803355 original size:21 final size:22
Alignment explanation
Indices: 803322--803367 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
803312 TTTATTTGCA
* *
803322 TTTTTGAGCCTTGTAA-TCAAG
1 TTTTAGAGACTTGTAAGTCAAG
*
803343 TTTTAGAGACTTGTAAGTCACG
1 TTTTAGAGACTTGTAAGTCAAG
803365 TTT
1 TTT
803368 CTCTGAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (22 bp):
TTTTAGAGACTTGTAAGTCAAG
Found at i:804122 original size:2 final size:2
Alignment explanation
Indices: 804115--804139 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
804105 AATTTATTGA
804115 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
804140 GAGCATCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:806118 original size:2 final size:2
Alignment explanation
Indices: 806111--806139 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
806101 TTGGCTAATG
806111 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
806140 GATGAATCTT
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:806688 original size:4 final size:4
Alignment explanation
Indices: 806679--806705 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
806669 TAACTCCATC
806679 TGTT TGTT TGTT TGTT TGTT TGTT TGT
1 TGTT TGTT TGTT TGTT TGTT TGTT TGT
806706 CTTTTTCAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (4 bp):
TGTT
Found at i:807358 original size:3 final size:3
Alignment explanation
Indices: 807350--807388 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
807340 TAGATTCCCC
807350 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
807389 ATATTCTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:809615 original size:24 final size:23
Alignment explanation
Indices: 809571--809619 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
809561 TCCTTTTTCC
* *
809571 ATTTTCTTTTTTTTTTTTTTTTA
1 ATTTTCTTTTTTGTTTGTTTTTA
*
809594 ATTTTGTTTGTTTGTTTGTTTTTA
1 ATTTTCTTT-TTTGTTTGTTTTTA
809618 AT
1 AT
809620 GATAAATCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.10, C:0.02, G:0.08, T:0.80
Consensus pattern (23 bp):
ATTTTCTTTTTTGTTTGTTTTTA
Found at i:810136 original size:2 final size:2
Alignment explanation
Indices: 810129--810157 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
810119 TTGTTAGCAT
810129 TA 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 TA T
810158 CACCATGTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:813289 original size:5 final size:5
Alignment explanation
Indices: 813279--813303 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
813269 TAGCAACTAC
813279 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
813304 TCGGAATGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:815038 original size:5 final size:5
Alignment explanation
Indices: 815019--815048 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
815009 ACAAAGAAAG
815019 AAAAT AAATAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAA-AT AAAAT AAAAT AAAAT AAAA
815049 GAAAGACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:816132 original size:21 final size:21
Alignment explanation
Indices: 816108--816147 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
816098 AAATTTTATT
*
816108 TAAAT-TTAATTAAAGAATATA
1 TAAATATTAA-TAAAAAATATA
816129 TAAATATTAATAAAAAATA
1 TAAATATTAATAAAAAATA
816148 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
TAAATATTAATAAAAAATATA
Found at i:818415 original size:29 final size:29
Alignment explanation
Indices: 818355--818416 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
818345 AGTCAAATTT
*
818355 TTTATTTAAATATAATTTAAAAAATAAAAA
1 TTTATTTAAATATAA-TTAAAAAACAAAAA
818385 TTTATTTAAATATAA-TAAAAATACAAAAA
1 TTTATTTAAATATAATTAAAAA-ACAAAAA
818414 TTT
1 TTT
818417 TTAAAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 6 0.20
29 9 0.30
30 15 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
TTTATTTAAATATAATTAAAAAACAAAAA
Found at i:818640 original size:2 final size:2
Alignment explanation
Indices: 818633--818674 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
818623 CACTTATCTT
818633 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
818675 AAACCCACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:818930 original size:18 final size:20
Alignment explanation
Indices: 818892--818935 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
818882 TATAATTTTA
818892 TATTTTAATAAATTAATAAT
1 TATTTTAATAAATTAATAAT
818912 TAATTTTAAT-AA-T-ATAAT
1 T-ATTTTAATAAATTAATAAT
818930 TATTTT
1 TATTTT
818936 TTTGTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 1 0.04
20 3 0.13
21 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTTAATAAATTAATAAT
Found at i:819136 original size:29 final size:29
Alignment explanation
Indices: 819082--819137 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
819072 ATTTATGTAC
* *
819082 ATAATTATTTAAATAGAATATGAAATAAA
1 ATAATTAATTAAATAGAATATAAAATAAA
*
819111 ATAATTAAATTAAATA-AATTTAAAATA
1 ATAATT-AATTAAATAGAATATAAAATA
819138 TATATAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 15 0.65
30 8 0.35
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (29 bp):
ATAATTAATTAAATAGAATATAAAATAAA
Found at i:819161 original size:19 final size:18
Alignment explanation
Indices: 819126--819167 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
819116 TAAATTAAAT
*
819126 AAATTTAAAATATATATA
1 AAATTTAAAAAATATATA
819144 AAATTTATAAAAATATATA
1 AAATTTA-AAAAATATATA
819163 AAATT
1 AAATT
819168 AAATAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATTTAAAAAATATATA
Found at i:820936 original size:17 final size:15
Alignment explanation
Indices: 820896--820962 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 15
820886 ACCATTATTT
*
820896 TTAATTTATATCTAAA
1 TTAATTT-TATTTAAA
820912 TTAATTTTAATTTAAA
1 TTAATTTT-ATTTAAA
820928 TTAATTTTTTATTTAAAA
1 TTAA--TTTTATTT-AAA
*
820946 TAAAATTTTATTTAAA
1 T-TAATTTTATTTAAA
820962 T
1 T
820963 ATAAATTAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
15 1 0.02
16 21 0.48
17 12 0.27
18 8 0.18
19 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATTTTATTTAAA
Found at i:820966 original size:18 final size:18
Alignment explanation
Indices: 820914--820967 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 18
820904 TATCTAAATT
820914 AATTTTAATTTAAAT-TAA
1 AATTTT-ATTTAAATATAA
**
820932 TTTTTTATTTAAA-ATAA
1 AATTTTATTTAAATATAA
820949 AATTTTATTTAAATATAA
1 AATTTTATTTAAATATAA
820967 A
1 A
820968 TTAAGAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 21 0.70
18 9 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTTTATTTAAATATAA
Found at i:824200 original size:6 final size:6
Alignment explanation
Indices: 824185--824217 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
824175 ATAATGTTTG
824185 AAAA-A AAAAGA AAAAGA AAAAGAA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAG-A AAAAGA AAA
824218 TAAATAAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.15
6 16 0.62
7 6 0.23
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:824206 original size:12 final size:13
Alignment explanation
Indices: 824185--824217 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
824175 ATAATGTTTG
824185 AAAA-AAAAAG-A
1 AAAAGAAAAAGAA
824196 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
824209 AAAAGAAAA
1 AAAAGAAAA
824218 TAAATAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 6 0.30
13 10 0.50
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Done.