Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397264.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_130.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8132550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 35170 characters in sequence are not A, C, G, or T
File 7 of 14
Found at i:3120740 original size:2 final size:2
Alignment explanation
Indices: 3120733--3120763 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3120723 ATTTCCCTCC
3120733 CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3120764 TTCCTTCCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:3127390 original size:49 final size:52
Alignment explanation
Indices: 3127333--3127437 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 52
3127323 AATGTCATCT
*
3127333 GTTTTATTTGTGGAGGAATGGTGGGTTTC-A-T-TAAGATCTTCATTTAAAA
1 GTTTTATTTGTAGAGGAATGGTGGGTTTCGATTATAAGATCTTCATTTAAAA
3127382 GTTTTATTTGTAGAGGAATGGTGGGTTTCGTATTTCATAAGATCTTCATTTAAAA
1 GTTTTATTTGTAGAGGAATGGTGGGTTTCG-A-TT-ATAAGATCTTCATTTAAAA
3127437 G
1 G
3127438 ACTCTGTATC
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
49 28 0.57
51 1 0.02
53 1 0.02
55 19 0.39
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.43
Consensus pattern (52 bp):
GTTTTATTTGTAGAGGAATGGTGGGTTTCGATTATAAGATCTTCATTTAAAA
Found at i:3152028 original size:2 final size:2
Alignment explanation
Indices: 3152015--3152048 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3152005 CAAAAGAAAA
*
3152015 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3152049 CTTCAGCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3154786 original size:3 final size:3
Alignment explanation
Indices: 3154778--3154805 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3154768 TGATTATAGC
3154778 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3154806 GCTAATCACA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3157903 original size:70 final size:70
Alignment explanation
Indices: 3157790--3157930 Score: 237
Period size: 70 Copynumber: 2.0 Consensus size: 70
3157780 AACTGGATTC
* * *
3157790 AAGCAAGTTTAAACAAAGACAGACCGAGTACACAAACATTTCCATTAGTCACTAAATGCTTGAAA
1 AAGCAAGTTCAAACAAAGACAGACCCAGTACACAAACATTTCCATTACTCACTAAATGCTTGAAA
3157855 AATGG
66 AATGG
*
3157860 AAGCAAGTTCAAACAAAGACAGACCCAGTACACAAACATTTCCATTACTCACTAAATTCTTGAAA
1 AAGCAAGTTCAAACAAAGACAGACCCAGTACACAAACATTTCCATTACTCACTAAATGCTTGAAA
*
3157925 GATGG
66 AATGG
3157930 A
1 A
3157931 CAAAACCCTG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.21
Consensus pattern (70 bp):
AAGCAAGTTCAAACAAAGACAGACCCAGTACACAAACATTTCCATTACTCACTAAATGCTTGAAA
AATGG
Found at i:3179383 original size:24 final size:23
Alignment explanation
Indices: 3179355--3179410 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
3179345 AGGGATGTTA
*
3179355 GGGTTTTGAGGAAGGAAATTATTG
1 GGGTTTTGAAGAA-GAAATTATTG
*
3179379 GGGTTTTGGAAGAAGAAATTATTT
1 GGGTTTT-GAAGAAGAAATTATTG
3179403 GGGTTTTG
1 GGGTTTTG
3179411 TTGAAGAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 1 0.03
24 23 0.79
25 5 0.17
ACGTcount: A:0.27, C:0.00, G:0.36, T:0.38
Consensus pattern (23 bp):
GGGTTTTGAAGAAGAAATTATTG
Found at i:3179404 original size:25 final size:24
Alignment explanation
Indices: 3179355--3179425 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 24
3179345 AGGGATGTTA
*
3179355 GGGTTTT-GAGGAAGGAAATTATT
1 GGGTTTTGGAAGAAGGAAATTATT
3179378 GGGGTTTTGGAAGAA-GAAATTATTT
1 -GGGTTTTGGAAGAAGGAAATTA-TT
*
3179403 GGGTTTTGTTGAAGAGGGAAATT
1 GGGTTTTG--GAAGAAGGAAATT
3179426 TGGTTGGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 22 0.55
25 7 0.17
26 5 0.12
27 6 0.15
ACGTcount: A:0.30, C:0.00, G:0.35, T:0.35
Consensus pattern (24 bp):
GGGTTTTGGAAGAAGGAAATTATT
Found at i:3181144 original size:210 final size:210
Alignment explanation
Indices: 3180767--3181461 Score: 1007
Period size: 210 Copynumber: 3.3 Consensus size: 210
3180757 CAATGGCTTG
* * * ** **
3180767 AAACCAGATGTCATCACCTACAACTCTTTAATTCGA-GGATTTTGTTTTTCAGGCTTATGGAAAG
1 AAACCTGATGTTATCACCTACAACTCTTTAATAC-ATGGATTTTGCCTTTCAGGCCAATGGAAAG
* * ** *
3180831 AAGCAGCAAGCTTGTTTCACAGAATGATGGATGAAGGAATTCATCCCTTTGTAGTAACTTTCAGC
65 AGGCAGCAAGCTTGTTCCACAGAATGATGGATGAAGGAATTCATCCCAATGTAGTAACTTTCAAC
3180896 TCTTTAATTGATGCTTTGTGCAAACAAAAGAGAGTGAAAGAAGCCCTTACAATGTTGGAGCTAAT
130 TCTTTAATTGATGCTTTGTGCAAACAAAAGAGAGTGAAAGAAGCCCTTACAATGTTGGAGCTAAT
3180961 GAGTGAAAGAGGTGTA
195 GAGTGAAAGAGGTGTA
* * *
3180977 AAAGCTGATGTTATCACCTACAGCTCTTTAATATATGGATTTTGCCTTTCAGGCCAATGGAAAGA
1 AAACCTGATGTTATCACCTACAACTCTTTAATACATGGATTTTGCCTTTCAGGCCAATGGAAAGA
* * *
3181042 GGCAGCAAGCTTCTTCCACAGACA-GATGGATGAAGGGATCCATCCCAATGTAGTAACTTTCAAC
66 GGCAGCAAGCTTGTTCCACAGA-ATGATGGATGAAGGAATTCATCCCAATGTAGTAACTTTCAAC
* * * *
3181106 TCTTTAATTGATGCTTTGTGCAAACAAAGGAAAGTGAAAGAAGCCCATAGAATGTTGGAGCTAAT
130 TCTTTAATTGATGCTTTGTGCAAACAAAAGAGAGTGAAAGAAGCCCTTACAATGTTGGAGCTAAT
*
3181171 GAGTGAAAGAGATGTA
195 GAGTGAAAGAGGTGTA
* * *
3181187 AAACCTGATGTTATCACTTACAACTCTTTAATACATGGATTTTGTCTGTCAGGCCAATGGAAAGA
1 AAACCTGATGTTATCACCTACAACTCTTTAATACATGGATTTTGCCTTTCAGGCCAATGGAAAGA
* * * *
3181252 GGCAGAAAGCTTGTTCCACAAAATGACGGATGAAGGAATTCATCCCGATGTAGTAACTTTCAACT
66 GGCAGCAAGCTTGTTCCACAGAATGATGGATGAAGGAATTCATCCCAATGTAGTAACTTTCAACT
* * * *
3181317 CTTTAATTGATGCTTTGTGCAAACAAAATAGAGTGAAAGAAGCCTTTACAATGTTGGAACAAATG
131 CTTTAATTGATGCTTTGTGCAAACAAAAGAGAGTGAAAGAAGCCCTTACAATGTTGGAGCTAATG
3181382 AGTGAAAGAGGTGTA
196 AGTGAAAGAGGTGTA
* * * * *
3181397 AAACCTGATGTTATCACTTACAATTCTTTAATACATGGATTGTGCCGTTCAGGTCAATGGAAAGA
1 AAACCTGATGTTATCACCTACAACTCTTTAATACATGGATTTTGCCTTTCAGGCCAATGGAAAGA
3181462 AGCAACAAAC
Statistics
Matches: 431, Mismatches: 51, Indels: 6
0.88 0.10 0.01
Matches are distributed among these distances:
209 2 0.00
210 428 0.99
211 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (210 bp):
AAACCTGATGTTATCACCTACAACTCTTTAATACATGGATTTTGCCTTTCAGGCCAATGGAAAGA
GGCAGCAAGCTTGTTCCACAGAATGATGGATGAAGGAATTCATCCCAATGTAGTAACTTTCAACT
CTTTAATTGATGCTTTGTGCAAACAAAAGAGAGTGAAAGAAGCCCTTACAATGTTGGAGCTAATG
AGTGAAAGAGGTGTA
Found at i:3195601 original size:27 final size:27
Alignment explanation
Indices: 3195539--3195602 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
3195529 ATTTTGCGTT
* * * *
3195539 CTTTTGCTGCTTGCTTTTTATTGTTTG
1 CTTTTGCTTCTTGCTTTATATAGTTTC
3195566 CTTTTGCTTCTTGCTTTATATAGTTTC
1 CTTTTGCTTCTTGCTTTATATAGTTTC
3195593 CTTTTGCTTC
1 CTTTTGCTTC
3195603 CTTAAAATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.06, C:0.19, G:0.14, T:0.61
Consensus pattern (27 bp):
CTTTTGCTTCTTGCTTTATATAGTTTC
Found at i:3220770 original size:22 final size:21
Alignment explanation
Indices: 3220740--3220780 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3220730 AGATTTGGGC
*
3220740 GTGGATTTGGCGGAGTTGGAGG
1 GTGGATTTGGAGGA-TTGGAGG
*
3220762 GTGGTTTTGGAGGATTGGA
1 GTGGATTTGGAGGATTGGA
3220781 TGAGAGAGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.15, C:0.02, G:0.51, T:0.32
Consensus pattern (21 bp):
GTGGATTTGGAGGATTGGAGG
Found at i:3227485 original size:36 final size:36
Alignment explanation
Indices: 3227436--3227718 Score: 198
Period size: 36 Copynumber: 7.9 Consensus size: 36
3227426 AATCCAGCAC
* * * *
3227436 AAAAGCAAGACTTTCAATTTACAGCCAATTCAATTA
1 AAAAGCAAAACTTTCAATTTAAACCCAATTCAATGA
* *
3227472 AAAAGTAAAACTTTCAATTTAAACCCAATTCAATGC
1 AAAAGCAAAACTTTCAATTTAAACCCAATTCAATGA
* ** * *
3227508 AAAAGCAAAAGTTTCAATTCCAACTCAATTCAGT-A
1 AAAAGCAAAACTTTCAATTTAAACCCAATTCAATGA
* * * *
3227543 GAAAAGCAACACTTTCAAATTAAACCCGATTCAATGC
1 -AAAAGCAAAACTTTCAATTTAAACCCAATTCAATGA
* * * * **
3227580 AAAAGCAAAAGTTTTAATTTCAACTCAATTCGGT-A
1 AAAAGCAAAACTTTCAATTTAAACCCAATTCAATGA
* ** *
3227615 GAAAAGCGACGCTTTCAAATTAAACCCAATTCAA-GA
1 -AAAAGCAAAACTTTCAATTTAAACCCAATTCAATGA
* * * * *
3227651 AGAAGAAAAACTTTCCAA-TCAAGCCCAATTCAA-AA
1 AAAAGCAAAACTTT-CAATTTAAACCCAATTCAATGA
* * *
3227686 CAAAATCAACATTTTCAATTTAAACCCAATTCA
1 -AAAAGCAAAACTTTCAATTTAAACCCAATTCA
3227719 GTAAAATAAA
Statistics
Matches: 183, Mismatches: 57, Indels: 14
0.72 0.22 0.06
Matches are distributed among these distances:
35 26 0.14
36 157 0.86
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (36 bp):
AAAAGCAAAACTTTCAATTTAAACCCAATTCAATGA
Found at i:3227537 original size:72 final size:72
Alignment explanation
Indices: 3227352--3227648 Score: 264
Period size: 72 Copynumber: 4.2 Consensus size: 72
3227342 GTCCTTAAGG
* * * * *
3227352 ACCCAATTCGATGCAAAAGC-AAAGCTTTCAA--ACTAACCCAATTCAGCACAAAAGCACAACTT
1 ACCCAATTCAATGCAAAAGCAAAAG-TTTCAATTAC-AACTCAATTCAGTAGAAAAGCAAAACTT
* *
3227414 TTAAATCAA
64 TCAAATTAA
** * *** * * * * *
3227423 A-TTAATCCAGCACAAAAGCAAGACTTTCAATTTACAGC-CAATTCAATTA-AAAAGTAAAACTT
1 ACCCAATTCAATGCAAAAGCAAAAGTTTCAA-TTACAACTCAATTC-AGTAGAAAAGCAAAACTT
*
3227485 TCAATTTAA
64 TCAAATTAA
* *
3227494 ACCCAATTCAATGCAAAAGCAAAAGTTTCAATTCCAACTCAATTCAGTAGAAAAGCAACACTTTC
1 ACCCAATTCAATGCAAAAGCAAAAGTTTCAATTACAACTCAATTCAGTAGAAAAGCAAAACTTTC
3227559 AAATTAA
66 AAATTAA
* * * * * **
3227566 ACCCGATTCAATGCAAAAGCAAAAGTTTTAATTTCAACTCAATTCGGTAGAAAAGCGACGCTTTC
1 ACCCAATTCAATGCAAAAGCAAAAGTTTCAATTACAACTCAATTCAGTAGAAAAGCAAAACTTTC
3227631 AAATTAA
66 AAATTAA
3227638 ACCCAATTCAA
1 ACCCAATTCAA
3227649 GAAGAAGAAA
Statistics
Matches: 180, Mismatches: 38, Indels: 15
0.77 0.16 0.06
Matches are distributed among these distances:
70 17 0.09
71 35 0.19
72 126 0.70
73 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.24
Consensus pattern (72 bp):
ACCCAATTCAATGCAAAAGCAAAAGTTTCAATTACAACTCAATTCAGTAGAAAAGCAAAACTTTC
AAATTAA
Found at i:3228858 original size:30 final size:30
Alignment explanation
Indices: 3228819--3228884 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
3228809 ACCCATTAAT
*
3228819 TATAAAAATTT-ATTTAATCTAAAATAAAAA
1 TATAAAAATTTGATTGAATCTAAAA-AAAAA
* * *
3228849 TATACAAATTTGATTGAATGTAATAAAAAA
1 TATAAAAATTTGATTGAATCTAAAAAAAAA
3228879 TATAAA
1 TATAAA
3228885 TTTTTTCAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.35
Consensus pattern (30 bp):
TATAAAAATTTGATTGAATCTAAAAAAAAA
Found at i:3231344 original size:119 final size:119
Alignment explanation
Indices: 3231133--3231372 Score: 480
Period size: 119 Copynumber: 2.0 Consensus size: 119
3231123 GTGTTATCAT
3231133 TTATTTGGCTGGATGCCTTTGTTTAATTGGATCAAAGCCCTTTTATTTCGGGATTTATTACCATT
1 TTATTTGGCTGGATGCCTTTGTTTAATTGGATCAAAGCCCTTTTATTTCGGGATTTATTACCATT
3231198 TGTACCCGATATATTTGTTGTTTCTATTTAATTCCTTTCCCCCCTTTTAAGTTC
66 TGTACCCGATATATTTGTTGTTTCTATTTAATTCCTTTCCCCCCTTTTAAGTTC
3231252 TTATTTGGCTGGATGCCTTTGTTTAATTGGATCAAAGCCCTTTTATTTCGGGATTTATTACCATT
1 TTATTTGGCTGGATGCCTTTGTTTAATTGGATCAAAGCCCTTTTATTTCGGGATTTATTACCATT
3231317 TGTACCCGATATATTTGTTGTTTCTATTTAATTCCTTTCCCCCCTTTTAAGTTC
66 TGTACCCGATATATTTGTTGTTTCTATTTAATTCCTTTCCCCCCTTTTAAGTTC
3231371 TT
1 TT
3231373 TTCTTTCCAC
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 121 1.00
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.48
Consensus pattern (119 bp):
TTATTTGGCTGGATGCCTTTGTTTAATTGGATCAAAGCCCTTTTATTTCGGGATTTATTACCATT
TGTACCCGATATATTTGTTGTTTCTATTTAATTCCTTTCCCCCCTTTTAAGTTC
Found at i:3231596 original size:2 final size:2
Alignment explanation
Indices: 3231589--3231618 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3231579 CTGTCTATAC
3231589 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3231619 GTGGGATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3236367 original size:40 final size:42
Alignment explanation
Indices: 3236296--3236381 Score: 97
Period size: 40 Copynumber: 2.1 Consensus size: 42
3236286 GTAGAGAGTT
* * * *
3236296 GAGAATAGGGTTAGAATATGATATAAGAGGG-CTAAATAGGA
1 GAGAATAGGATTAGAATATGATAGAAGAGGGCCAAAATAGAA
*
3236337 GAGAA-AGGATTAGAATATGGTAGGAA-AGGGCCAAAATAGAA
1 GAGAATAGGATTAGAATATGATA-GAAGAGGGCCAAAATAGAA
3236378 GAGA
1 GAGA
3236382 TTTAGAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
40 19 0.50
41 19 0.50
ACGTcount: A:0.47, C:0.03, G:0.33, T:0.17
Consensus pattern (42 bp):
GAGAATAGGATTAGAATATGATAGAAGAGGGCCAAAATAGAA
Found at i:3240350 original size:14 final size:14
Alignment explanation
Indices: 3240315--3240360 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
3240305 TAACATTTCA
3240315 ATTATTAATAATTAT
1 ATTATTAA-AATTAT
*
3240330 A-TA-TAAAATTTT
1 ATTATTAAAATTAT
3240342 ATTATTAAAATGTAT
1 ATTATTAAAAT-TAT
3240357 ATTA
1 ATTA
3240361 AAAAGTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 6 0.23
13 5 0.19
14 8 0.31
15 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
ATTATTAAAATTAT
Found at i:3248692 original size:2 final size:2
Alignment explanation
Indices: 3248685--3248731 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3248675 GAAAAACTTT
3248685 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
3248727 TA TA T
1 TA TA T
3248732 GTAGGGCAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3264463 original size:50 final size:48
Alignment explanation
Indices: 3264409--3264580 Score: 147
Period size: 50 Copynumber: 3.5 Consensus size: 48
3264399 TTTATTATTA
* * *
3264409 ATTTTTATATAATATCATCTCTTAAATGTATTTTTAATGTCATATATTTT
1 ATTTTTATATATTATCATATCTT-AAT-TATTTTTAATATCATATATTTT
* * *
3264459 ATTTTTATTTATTATTATAATCTT--TTATATTTT-ATAT--TTTATTATT
1 ATTTTTATATATTATCAT-ATCTTAATTAT-TTTTAATATCATATATT-TT
3264505 AATTTTTATATATTATCATATCTTCAATATATTTTTAATATCATATATTTT
1 -ATTTTTATATATTATCATATCTT-AAT-TATTTTTAATATCATATATTTT
* * *
3264556 ATTTTCATTTATTATTATAATCTTA
1 ATTTTTATATATTATCAT-ATCTTA
3264581 TATATTTATT
Statistics
Matches: 98, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
45 5 0.05
46 7 0.07
47 22 0.22
48 5 0.05
49 5 0.05
50 38 0.39
51 11 0.11
52 5 0.05
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.60
Consensus pattern (48 bp):
ATTTTTATATATTATCATATCTTAATTATTTTTAATATCATATATTTT
Found at i:3264491 original size:27 final size:27
Alignment explanation
Indices: 3264455--3264520 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
3264445 ATGTCATATA
3264455 TTTTAT-TTTTAT-TTATTATTA-TAAT
1 TTTTATATTTTATATT-TTATTATTAAT
3264480 CTTTTATATTTTATATTTTATTATTAAT
1 -TTTTATATTTTATATTTTATTATTAAT
*
3264508 TTTTATATATTAT
1 TTTTATATTTTAT
3264521 CATATCTTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
26 6 0.17
27 24 0.67
28 6 0.17
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTATATTTTATATTTTATTATTAAT
Found at i:3264511 original size:97 final size:98
Alignment explanation
Indices: 3264385--3264589 Score: 331
Period size: 97 Copynumber: 2.1 Consensus size: 98
3264375 TACAAGTTTA
* * * *
3264385 ATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATGTATTTTTAATGTC
1 ATATATTTATATATTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAATATC
*
3264450 ATATATTTTATTTTTATTTATTATTATAATCTT
66 ATATATTTTATTTTCATTTATTATTATAATCTT
* * *
3264483 TTATATTT-TATATTTTATTATTAATTTTTATATATTATCATATCTTCAATATATTTTTAATATC
1 ATATATTTATATATTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAATATC
3264547 ATATATTTTATTTTCATTTATTATTATAATCTT
66 ATATATTTTATTTTCATTTATTATTATAATCTT
3264580 ATATATTTAT
1 ATATATTTAT
3264590 TTTCATTTCT
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
97 89 0.92
98 8 0.08
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.61
Consensus pattern (98 bp):
ATATATTTATATATTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAATATC
ATATATTTTATTTTCATTTATTATTATAATCTT
Found at i:3264519 original size:47 final size:47
Alignment explanation
Indices: 3264440--3264587 Score: 158
Period size: 47 Copynumber: 3.1 Consensus size: 47
3264430 TTAAATGTAT
* *
3264440 TTTTAATGTCATATATTTTATTTTTATTTATTATTATAATCTTTTATA
1 TTTTAATAT-ATATATTTTATTTTTATTTATTATTATAATCTTATATA
* * *
3264488 TTTT-ATAT-TTTATTATTAATTTTTATATATTATCAT-ATCTTCAATATA
1 TTTTAATATATATATT-TT-ATTTTTATTTATTATTATAATCTT--ATATA
*
3264536 TTTTTAATATCATATATTTTATTTTCATTTATTATTATAATCTTATATA
1 -TTTTAATAT-ATATATTTTATTTTTATTTATTATTATAATCTTATATA
3264585 TTT
1 TTT
3264588 ATTTTCATTT
Statistics
Matches: 82, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
45 5 0.06
46 7 0.09
47 19 0.23
48 11 0.13
49 9 0.11
50 19 0.23
51 7 0.09
52 5 0.06
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (47 bp):
TTTTAATATATATATTTTATTTTTATTTATTATTATAATCTTATATA
Found at i:3264618 original size:32 final size:32
Alignment explanation
Indices: 3264450--3264607 Score: 87
Period size: 33 Copynumber: 4.8 Consensus size: 32
3264440 TTTTAATGTC
* *
3264450 ATATATTTTATTTTTATTTATTATTATAATCTT
1 ATATA-TTTATTTTCATTTATTAATATAATCTT
* *
3264483 TTATATTTTATATTTTA-TTATTAAT-T--T-TT
1 ATATA-TTTAT-TTTCATTTATTAATATAATCTT
* * * *
3264512 ATATATTATCATATCTTCAATATATT--TTTAATATC
1 ATATATT-T-AT-T-TTC-ATTTATTAATATAATCTT
*
3264547 ATATATTTTATTTTCATTTATTATTATAATCTT
1 ATATA-TTTATTTTCATTTATTAATATAATCTT
*
3264580 ATATATTTATTTTCATTTCTTTAATATA
1 ATATATTTATTTTCATTT-ATTAATATA
3264608 GTTTTTATAT
Statistics
Matches: 99, Mismatches: 12, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
28 2 0.02
29 7 0.07
30 5 0.05
31 9 0.09
32 19 0.19
33 40 0.40
34 8 0.08
35 7 0.07
36 2 0.02
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.63
Consensus pattern (32 bp):
ATATATTTATTTTCATTTATTAATATAATCTT
Found at i:3264630 original size:5 final size:5
Alignment explanation
Indices: 3264622--3264737 Score: 58
Period size: 5 Copynumber: 22.4 Consensus size: 5
3264612 TTATATTATA
* * * * * * *
3264622 TATTT TATTT TATTT TGTTT TACCTA TATTA TATAT AATTT TAATTT T-TTA
1 TATTT TATTT TATTT TATTT TA-TTT TATTT TATTT TATTT T-ATTT TATTT
* * *
3264673 TATTT TATTT TATTT TATTT T-TTGAT TATTA TATTA TATATA TATTT
1 TATTT TATTT TATTT TATTT TATT--T TATTT TATTT TAT-TT TATTT
3264720 TAATATT T-TTT TATTT TA
1 T-AT-TT TATTT TATTT TA
3264738 ATTATAATAT
Statistics
Matches: 87, Mismatches: 14, Indels: 20
0.72 0.12 0.17
Matches are distributed among these distances:
4 8 0.09
5 57 0.66
6 17 0.20
7 5 0.06
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (5 bp):
TATTT
Found at i:3264750 original size:41 final size:40
Alignment explanation
Indices: 3264683--3264765 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 40
3264673 TATTTTATTT
* * *
3264683 TATTTTATTTTTTGATTATTATATTAT-ATATATATTTTAA
1 TATTTTATTTTTTAATTATAATATTATAAAATAT-TTTTAA
*
3264723 TATTTTTTTATTTTAATTATAATATTATAAAATATTTTTAA
1 TATTTTATT-TTTTAATTATAATATTATAAAATATTTTTAA
3264764 TA
1 TA
3264766 AAGTAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
40 8 0.22
41 24 0.65
42 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (40 bp):
TATTTTATTTTTTAATTATAATATTATAAAATATTTTTAA
Found at i:3265067 original size:28 final size:27
Alignment explanation
Indices: 3265016--3265068 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
3265006 AATTTTTTTA
*
3265016 TATAATTTTAAATTTTAATTAAATATT
1 TATAATTTTAAATTTTAATAAAATATT
3265043 TATAAGTTTTAATATTTT-ATAAAATA
1 TATAA-TTTTAA-ATTTTAATAAAATA
3265069 ATAAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.22
28 13 0.57
29 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TATAATTTTAAATTTTAATAAAATATT
Found at i:3268613 original size:24 final size:25
Alignment explanation
Indices: 3268586--3268632 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
3268576 TAGGGATCCC
*
3268586 GATTTGGGGC-CCCTTGGAAAGCTT
1 GATTTAGGGCTCCCTTGGAAAGCTT
3268610 GATTTAGGGCTCCCTTGGAAAGC
1 GATTTAGGGCTCCCTTGGAAAGC
3268633 CCAATATGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.28
Consensus pattern (25 bp):
GATTTAGGGCTCCCTTGGAAAGCTT
Found at i:3271084 original size:54 final size:54
Alignment explanation
Indices: 3271002--3271128 Score: 218
Period size: 54 Copynumber: 2.4 Consensus size: 54
3270992 ACTAGTAGGG
* *
3271002 GAACGAAGTTCTGGTAAGGCCCCAATTATATATAAAAACCAAAAACAAGAACAA
1 GAACGAAGTTCTGGTAAGACCCCAATTATATAAAAAAACCAAAAACAAGAACAA
* *
3271056 GAACGAAGTTCTGGTAAGACCCTAATTATATAAAAAAACTAAAAACAAGAACAA
1 GAACGAAGTTCTGGTAAGACCCCAATTATATAAAAAAACCAAAAACAAGAACAA
3271110 GAACGAAGTTCTGGTAAGA
1 GAACGAAGTTCTGGTAAGA
3271129 TTAATCCTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.50, C:0.16, G:0.17, T:0.18
Consensus pattern (54 bp):
GAACGAAGTTCTGGTAAGACCCCAATTATATAAAAAAACCAAAAACAAGAACAA
Found at i:3276527 original size:23 final size:24
Alignment explanation
Indices: 3276501--3276550 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3276491 AAAATAAAGG
*
3276501 AAAAAAGAAAG-AAGAAA-AGGGA
1 AAAAAAAAAAGAAAGAAAGAGGGA
* *
3276523 AAAAATAAACGAAAGAAAGAGGGA
1 AAAAAAAAAAGAAAGAAAGAGGGA
3276547 AAAA
1 AAAA
3276551 TAGTAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 6 0.26
24 9 0.39
ACGTcount: A:0.72, C:0.02, G:0.24, T:0.02
Consensus pattern (24 bp):
AAAAAAAAAAGAAAGAAAGAGGGA
Found at i:3276541 original size:22 final size:22
Alignment explanation
Indices: 3276498--3276552 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
3276488 GAAAAAATAA
*
3276498 AGGAAAAAAGAAAGAAGAAAAG
1 AGGAAAAAATAAAGAAGAAAAG
3276520 -GGAAAAAATAAACGAA-AGAAAG
1 AGGAAAAAATAAA-GAAGA-AAAG
*
3276542 AGGGAAAAATA
1 AGGAAAAAATA
3276553 GTAAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 12 0.43
22 7 0.25
23 9 0.32
ACGTcount: A:0.69, C:0.02, G:0.25, T:0.04
Consensus pattern (22 bp):
AGGAAAAAATAAAGAAGAAAAG
Found at i:3278127 original size:43 final size:43
Alignment explanation
Indices: 3278079--3278167 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
3278069 CAAAACTCGT
* *
3278079 TAAATACTTCGAATCCAACTCAACTTTTTCTTCAACTCAAAAG
1 TAAATACTTCCAATCCAACTCAACTTTTTCTTCAACACAAAAG
*
3278122 TAAATACTTCCAGTCCAACTCAACTTTTTCTTCAACACAAAAG
1 TAAATACTTCCAATCCAACTCAACTTTTTCTTCAACACAAAAG
3278165 TAA
1 TAA
3278168 CCCTGGCGGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.31
Consensus pattern (43 bp):
TAAATACTTCCAATCCAACTCAACTTTTTCTTCAACACAAAAG
Found at i:3278577 original size:26 final size:26
Alignment explanation
Indices: 3278541--3278596 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
3278531 GAAGAAGAAA
3278541 AAAAGCAAGAATTTTGGGTCATATCC
1 AAAAGCAAGAATTTTGGGTCATATCC
3278567 AAAAGCAAGAATTTTGGGTCATATCC
1 AAAAGCAAGAATTTTGGGTCATATCC
3278593 AAAA
1 AAAA
3278597 TAAAGAATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (26 bp):
AAAAGCAAGAATTTTGGGTCATATCC
Found at i:3278602 original size:26 final size:26
Alignment explanation
Indices: 3278541--3278604 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
3278531 GAAGAAGAAA
*
3278541 AAAAGCAAGAATTTTGGGTCATATCC
1 AAAAGAAAGAATTTTGGGTCATATCC
*
3278567 AAAAGCAAGAATTTTGGGTCATATCC
1 AAAAGAAAGAATTTTGGGTCATATCC
*
3278593 AAAATAAAGAAT
1 AAAAGAAAGAAT
3278605 GCAGCAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (26 bp):
AAAAGAAAGAATTTTGGGTCATATCC
Found at i:3278870 original size:18 final size:18
Alignment explanation
Indices: 3278849--3278960 Score: 134
Period size: 18 Copynumber: 6.2 Consensus size: 18
3278839 TCCGGCAGCA
* *
3278849 CCTTCTCGCCCGGGATCG
1 CCTTCTCGCCCAGGAGCG
*
3278867 CCTTCTCGCCCGGGAGCG
1 CCTTCTCGCCCAGGAGCG
* * *
3278885 CCTTCTGGCCCTGCAGCG
1 CCTTCTCGCCCAGGAGCG
*
3278903 CCTTCTCGCCCAGGAACG
1 CCTTCTCGCCCAGGAGCG
*
3278921 CCTTCCCGCCCAGGAGCG
1 CCTTCTCGCCCAGGAGCG
* *
3278939 CCTTCCCTCCCAGGAGCG
1 CCTTCTCGCCCAGGAGCG
3278957 CCTT
1 CCTT
3278961 TTAGTGCACA
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 83 1.00
ACGTcount: A:0.09, C:0.46, G:0.26, T:0.19
Consensus pattern (18 bp):
CCTTCTCGCCCAGGAGCG
Found at i:3281020 original size:28 final size:28
Alignment explanation
Indices: 3280925--3281005 Score: 153
Period size: 28 Copynumber: 2.9 Consensus size: 28
3280915 TCAACCGCCA
3280925 AGGACAACAGCAAGGAATTCATGTCTTT
1 AGGACAACAGCAAGGAATTCATGTCTTT
3280953 AGGACAACAGCAAGGAATTCATGTCTTT
1 AGGACAACAGCAAGGAATTCATGTCTTT
*
3280981 AGGACAGCAGCAAGGAATTCATGTC
1 AGGACAACAGCAAGGAATTCATGTC
3281006 CTTAAGCTTC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (28 bp):
AGGACAACAGCAAGGAATTCATGTCTTT
Found at i:3281106 original size:17 final size:17
Alignment explanation
Indices: 3281084--3281121 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
3281074 TGTGCCCAGC
3281084 AGTGAATATCAACCATT
1 AGTGAATATCAACCATT
3281101 AGTGAATATCAACCATT
1 AGTGAATATCAACCATT
3281118 -GTGA
1 AGTGA
3281122 TGCCTTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (17 bp):
AGTGAATATCAACCATT
Found at i:3289686 original size:18 final size:18
Alignment explanation
Indices: 3289663--3289702 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3289653 CTAATAATCA
3289663 TATTTTTAAGCATTTTTG
1 TATTTTTAAGCATTTTTG
*
3289681 TATTTTTAAGTATTTTTG
1 TATTTTTAAGCATTTTTG
3289699 TATT
1 TATT
3289703 AAAAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.65
Consensus pattern (18 bp):
TATTTTTAAGCATTTTTG
Found at i:3309137 original size:56 final size:56
Alignment explanation
Indices: 3309051--3309166 Score: 178
Period size: 56 Copynumber: 2.1 Consensus size: 56
3309041 AATGATTGTG
* * *
3309051 AAAAGAGATGAAACCAATGGTAGTTTGGTTAATGGTGTGTCAAAGATAAGATTGCA
1 AAAAGAGATGAAACCAAAGGCAGTTCGGTTAATGGTGTGTCAAAGATAAGATTGCA
* * *
3309107 AAAAGAGATGAAACCAAAGGCAGTTCGGTTATTGGTGTGTCGAAGATAATATTGCA
1 AAAAGAGATGAAACCAAAGGCAGTTCGGTTAATGGTGTGTCAAAGATAAGATTGCA
3309163 AAAA
1 AAAA
3309167 CTTGTCAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.25
Consensus pattern (56 bp):
AAAAGAGATGAAACCAAAGGCAGTTCGGTTAATGGTGTGTCAAAGATAAGATTGCA
Found at i:3312797 original size:29 final size:30
Alignment explanation
Indices: 3312763--3312844 Score: 73
Period size: 29 Copynumber: 2.8 Consensus size: 30
3312753 ATTCAAAAAA
3312763 ATTTAAATAAGTCTTTATATTTTTATTGTG
1 ATTTAAATAAGTCTTTATATTTTTATTGTG
* *
3312793 -TTT-AATCAAG-CTCTTAT-GTTTTATTTTG
1 ATTTAAAT-AAGTCT-TTATATTTTTATTGTG
* * *
3312821 AGTTAAATAAATTTTTATATTTTT
1 ATTTAAATAAGTCTTTATATTTTT
3312845 TATTTTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
28 14 0.35
29 18 0.45
30 8 0.20
ACGTcount: A:0.29, C:0.05, G:0.09, T:0.57
Consensus pattern (30 bp):
ATTTAAATAAGTCTTTATATTTTTATTGTG
Found at i:3313421 original size:31 final size:30
Alignment explanation
Indices: 3313387--3313446 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3313377 AAAAAAATAT
* *
3313387 TTTTTGATTATG-TTTAATTAAGTCTTTATA
1 TTTTT-ATTATGAATTAAATAAGTCTTTATA
*
3313417 TTTTTATTTTGAATTAAATAAGTCTTTATA
1 TTTTTATTATGAATTAAATAAGTCTTTATA
3313447 ATTGACGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.58
Consensus pattern (30 bp):
TTTTTATTATGAATTAAATAAGTCTTTATA
Found at i:3335389 original size:66 final size:66
Alignment explanation
Indices: 3335279--3335411 Score: 203
Period size: 66 Copynumber: 2.0 Consensus size: 66
3335269 GTTCCTGGTT
* *
3335279 CAAGGTAATCCATCCAAGTAAAACCATCTGCCCCAGCTGCATTTTCCTCCAGCGTATTCTCCATT
1 CAAGGTAATCCATCCAAGCAAAACCATCTGCCCCAGCTGCATTTTCCTCCACCGTATTCTCCATT
3335344 A
66 A
* * * * *
3335345 CAAGGTAATCCATCCAAGCAAAATCATCTGCCGCAGCTGTATTTTCCTTCACCGTATTGTCCATT
1 CAAGGTAATCCATCCAAGCAAAACCATCTGCCCCAGCTGCATTTTCCTCCACCGTATTCTCCATT
3335410 A
66 A
3335411 C
1 C
3335412 TTGCTCATTC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.27, C:0.32, G:0.13, T:0.29
Consensus pattern (66 bp):
CAAGGTAATCCATCCAAGCAAAACCATCTGCCCCAGCTGCATTTTCCTCCACCGTATTCTCCATT
A
Found at i:3338396 original size:32 final size:32
Alignment explanation
Indices: 3338360--3338426 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
3338350 AAATCATGTT
*
3338360 ATTTAAACTTCCAAAGCAAAAATTATGCCCAA
1 ATTTAAACCTCCAAAGCAAAAATTATGCCCAA
* * * * *
3338392 ATTTAGACCTCTAGAGCAAAAGTTATGCCTAA
1 ATTTAAACCTCCAAAGCAAAAATTATGCCCAA
3338424 ATT
1 ATT
3338427 ACCAAAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.28
Consensus pattern (32 bp):
ATTTAAACCTCCAAAGCAAAAATTATGCCCAA
Found at i:3341099 original size:28 final size:28
Alignment explanation
Indices: 3341059--3341115 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3341049 AAAAAATAAA
3341059 ATTGATCTATAATTCAAGCTTAGTACCT
1 ATTGATCTATAATTCAAGCTTAGTACCT
3341087 ATTGATCTATAATTCAAGCTTAGTACCT
1 ATTGATCTATAATTCAAGCTTAGTACCT
3341115 A
1 A
3341116 CTATCCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39
Consensus pattern (28 bp):
ATTGATCTATAATTCAAGCTTAGTACCT
Found at i:3351147 original size:22 final size:23
Alignment explanation
Indices: 3351117--3351161 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
3351107 ATAGAGTTAC
3351117 TTGAGCTTAATT-TTGATAGTAAT
1 TTGAGCTTAATTCTTG-TAGTAAT
*
3351140 TTGA-CTTAGTTCTTGTAGTAAT
1 TTGAGCTTAATTCTTGTAGTAAT
3351162 GCAGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.49
Consensus pattern (23 bp):
TTGAGCTTAATTCTTGTAGTAAT
Found at i:3351807 original size:19 final size:19
Alignment explanation
Indices: 3351771--3351812 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
3351761 TATTAAAATT
3351771 AAGAAGAATTTGAGAGATTC
1 AAGAAGAATTTGAGAGA-TC
3351791 AAGAAG-ATTTG-GTAGATC
1 AAGAAGAATTTGAG-AGATC
3351809 AAGA
1 AAGA
3351813 TTACAGTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 7 0.33
19 8 0.38
20 6 0.29
ACGTcount: A:0.45, C:0.05, G:0.26, T:0.24
Consensus pattern (19 bp):
AAGAAGAATTTGAGAGATC
Found at i:3353774 original size:10 final size:12
Alignment explanation
Indices: 3353747--3353788 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
3353737 CATGTATGCG
*
3353747 TATACATATAT-
1 TATATATATATA
3353758 TATATAT-TATA
1 TATATATATATA
3353769 -ATATATATATA
1 TATATATATATA
3353780 TATATATAT
1 TATATATAT
3353789 TAATTTGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 9 0.33
11 10 0.37
12 8 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATATATATA
Found at i:3353805 original size:2 final size:2
Alignment explanation
Indices: 3353747--3353788 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
3353737 CATGTATGCG
*
3353747 TA TA CA TA TA T- TA TA TA T- TA TA -A 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
3353786 TA T
1 TA T
3353789 TAATTTGAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3354558 original size:2 final size:2
Alignment explanation
Indices: 3354551--3354579 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3354541 TAAATCTTAT
3354551 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
3354580 TTGGGCGACA
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:3355048 original size:4 final size:4
Alignment explanation
Indices: 3355041--3355082 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
3355031 TATATATTTT
* * *
3355041 TATC TATC TAT- TATC TATC TATC TGTC TGTC TATC TGTC TAT
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
3355083 AAGTATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.19, C:0.21, G:0.07, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:3358280 original size:2 final size:2
Alignment explanation
Indices: 3358273--3358302 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3358263 AGGACAAAAG
3358273 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3358303 ATGCATCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3363964 original size:27 final size:27
Alignment explanation
Indices: 3363930--3363983 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
3363920 ACTTAATACA
*
3363930 ATAATCTCTTAAATCACAGAACTCAAT
1 ATAATCTCTTAAACCACAGAACTCAAT
* *
3363957 ATAATCTCTTGAACCACAGAATTCAAT
1 ATAATCTCTTAAACCACAGAACTCAAT
3363984 TACAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.30
Consensus pattern (27 bp):
ATAATCTCTTAAACCACAGAACTCAAT
Found at i:3369553 original size:6 final size:7
Alignment explanation
Indices: 3369536--3369560 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3369526 ACATACAAGG
3369536 AAAAAAT
1 AAAAAAT
3369543 AAAAAAT
1 AAAAAAT
3369550 AAAAAAT
1 AAAAAAT
3369557 AAAA
1 AAAA
3369561 CGAATAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:3369990 original size:2 final size:2
Alignment explanation
Indices: 3369983--3370009 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3369973 AATGTATGTG
3369983 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
3370010 GCATGCATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3370469 original size:7 final size:7
Alignment explanation
Indices: 3370457--3370481 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3370447 CTTAAATAAA
3370457 AGAATAG
1 AGAATAG
3370464 AGAATAG
1 AGAATAG
3370471 AGAATAG
1 AGAATAG
3370478 AGAA
1 AGAA
3370482 ATCCCAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (7 bp):
AGAATAG
Found at i:3371499 original size:2 final size:2
Alignment explanation
Indices: 3371492--3371530 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3371482 TCTTTCTCTT
3371492 TA TA TA TA 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 TA TA TA TA T
3371531 CTATTTTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3380244 original size:39 final size:38
Alignment explanation
Indices: 3380200--3380274 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 38
3380190 TTGTTTGGAA
3380200 GGCATCTAAAACAAG-TCACTTTTCTTTAATTTCAAATAT
1 GGCATCTAAAACAAGCT-ACTTTTC-TTAATTTCAAATAT
*
3380239 GGCATCTAAAACAAGCTACTTTTCTTAGTTTCAAAT
1 GGCATCTAAAACAAGCTACTTTTCTTAATTTCAAAT
3380275 CAGGATACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
38 11 0.32
39 22 0.65
40 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (38 bp):
GGCATCTAAAACAAGCTACTTTTCTTAATTTCAAATAT
Found at i:3381120 original size:15 final size:14
Alignment explanation
Indices: 3381096--3381144 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3381086 TTAAACATAC
* *
3381096 TAAAATAAAACAAA
1 TAAAACAAAAAAAA
*
3381110 TAAACCAAAAAAATA
1 TAAAACAAAAAAA-A
3381125 TAATAACAAAAAAAA
1 TAA-AACAAAAAAAA
3381140 TAAAA
1 TAAAA
3381145 AAATGAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 12 0.41
15 8 0.28
16 9 0.31
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (14 bp):
TAAAACAAAAAAAA
Found at i:3381134 original size:25 final size:24
Alignment explanation
Indices: 3381100--3381159 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
3381090 ACATACTAAA
* *
3381100 ATAAAACAAATAAACCAAAAAAAT
1 ATAAAACAAAAAAAACAAAAAAAT
*
3381124 ATAATAACAAAAAAAATAAAAAAAT
1 ATAA-AACAAAAAAAACAAAAAAAT
*
3381149 GAGAAAACAAA
1 -ATAAAACAAA
3381160 CGAAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 4 0.13
25 23 0.77
26 3 0.10
ACGTcount: A:0.77, C:0.08, G:0.03, T:0.12
Consensus pattern (24 bp):
ATAAAACAAAAAAAACAAAAAAAT
Found at i:3391094 original size:227 final size:227
Alignment explanation
Indices: 3390629--3391325 Score: 954
Period size: 227 Copynumber: 3.0 Consensus size: 227
3390619 TCATCTAGTT
* *
3390629 CATCCACAATAGTATGCAGGTTCAAAACA-GAAAAGCCTTTTGACTACGAATATTTAAAACATTT
1 CATCCACCATAGTATGCAGGGTCAAAA-AGGAAAAGCCTTTTGACTACGAATATTTAAAACATTT
* * *
3390693 TCCTAGAGAC-TATAGAATAGAGAAGAAAAGAAAGGGAAAGGGGAAGGATGGTTATATGAATTAT
65 TTCTAGAGACGT-TAGAGTAGAGAAGAAAAGAAAAGG-AAGGGGAAGGATGGTTATATGAATTAT
** * *
3390757 CATGGGTGGGTGGGTCTGTCTGCAACCATGCCTATGTGCTTCTACACACACAATATGTACTAGAA
128 TTTGGGTGGGTGTGTCTGTCTGCAACCATGCCTATGTGCTTCTACACTCAC--TATGTACTAGAA
*
3390822 GGATGATTGTATCAACCATTGTGTTAGAACATGTGTG
191 GGATGATTGTATCAACCATTGTGTTAGTACATGTGTG
* *
3390859 CGTCCACCATAGTATGCAGGGTCAAAAAGGAAAAGCCTTTTGACTATGAATATTTAAAATCATTT
1 CATCCACCATAGTATGCAGGGTCAAAAAGGAAAAGCCTTTTGACTACGAATATTTAAAA-CATTT
*
3390924 TTCTAGAAACGTTAGAGTAGAGAAGAAAAGAAAAGGAAGGGGAAGG-TGGTTATATGAATTATTT
65 TTCTAGAGACGTTAGAGTAGAGAAGAAAAGAAAAGGAAGGGGAAGGATGGTTATATGAATTATTT
* * *
3390988 TGGATGGGTGTGTCTGTCTGCCACCATGTCTATGTGCTTCTACACTCACTATGTACTAGAAGGAT
130 TGGGTGGGTGTGTCTGTCTGCAACCATGCCTATGTGCTTCTACACTCACTATGTACTAGAAGGAT
3391053 GATTGTATCAACCATTGTGTTAGTACATGTGTG
195 GATTGTATCAACCATTGTGTTAGTACATGTGTG
* * *
3391086 CATCCACCATAGTCTGCAGGGTCAAAAAGGACAAGCCTTTTGACTACGAATATTCAAAAGCATTT
1 CATCCACCATAGTATGCAGGGTCAAAAAGGAAAAGCCTTTTGACTACGAATATTTAAAA-CATTT
* *
3391151 TTCTGGAGACGTTAGAGTAGAGAAGAAAAGAAAGGGAAGGGGAAGGGGAAGGATGTTTATATGAA
65 TTCTAGAGACGTTAGAGTAGAGAAGAAAAG-AA---AA--GGAAGGGGAAGGATGGTTATATGAA
* * * *
3391216 TTATTTTGGGTGGGTTTAGCTCT-T-TGCAACCATGCCTATCTGCTTCTACACTCGCAATTTTGT
124 TTATTTTGGGTGGGTGT-G-TCTGTCTGCAACCATGCCTATGTGCTTCTACACT--C-ACTATGT
* *
3391279 AGTAGAAGGATGATAGTATCAACCATTGTGTTAGTACATGTGTG
184 ACTAGAAGGATGATTGTATCAACCATTGTGTTAGTACATGTGTG
3391323 CAT
1 CAT
3391326 GTTCACCTGC
Statistics
Matches: 418, Mismatches: 34, Indels: 23
0.88 0.07 0.05
Matches are distributed among these distances:
227 135 0.32
228 2 0.00
229 61 0.15
230 63 0.15
231 37 0.09
232 1 0.00
233 12 0.03
234 51 0.12
235 2 0.00
236 4 0.01
237 50 0.12
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (227 bp):
CATCCACCATAGTATGCAGGGTCAAAAAGGAAAAGCCTTTTGACTACGAATATTTAAAACATTTT
TCTAGAGACGTTAGAGTAGAGAAGAAAAGAAAAGGAAGGGGAAGGATGGTTATATGAATTATTTT
GGGTGGGTGTGTCTGTCTGCAACCATGCCTATGTGCTTCTACACTCACTATGTACTAGAAGGATG
ATTGTATCAACCATTGTGTTAGTACATGTGTG
Found at i:3393455 original size:14 final size:14
Alignment explanation
Indices: 3393436--3393479 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3393426 TTATTTATAT
*
3393436 TTAAATTTAAAATA
1 TTAAATATAAAATA
3393450 TTAAATATAAAACTA
1 TTAAATATAAAA-TA
3393465 -TAAATATATAAATA
1 TTAAATATA-AAATA
3393479 T
1 T
3393480 GATATATAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAATATAAAATA
Found at i:3393524 original size:16 final size:17
Alignment explanation
Indices: 3393494--3393533 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3393484 TATAAGATTT
*
3393494 TATACAATAGTTAAAT-A
1 TATA-AATAGCTAAATAA
3393511 TATAAATAGCTAAATAA
1 TATAAATAGCTAAATAA
3393528 TATAAA
1 TATAAA
3393534 CAAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (17 bp):
TATAAATAGCTAAATAA
Found at i:3395475 original size:19 final size:19
Alignment explanation
Indices: 3395437--3395475 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3395427 ATTCTTCATG
* *
3395437 GCTACATTTTCTTTAGTTT
1 GCTACATTATCTATAGTTT
*
3395456 GCTACATTATCTATATTTT
1 GCTACATTATCTATAGTTT
3395475 G
1 G
3395476 ATTTTCATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.10, T:0.54
Consensus pattern (19 bp):
GCTACATTATCTATAGTTT
Found at i:3402626 original size:27 final size:27
Alignment explanation
Indices: 3402577--3402634 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
3402567 CCTTAATATA
*
3402577 TAACAAAGTGATTCATACCTTGATGTG
1 TAACAAAGTGATTCATACCTTGACGTG
***
3402604 TAACAAAGTGATTCATGTTTTGACGTG
1 TAACAAAGTGATTCATACCTTGACGTG
3402631 TAAC
1 TAAC
3402635 CTTAGTATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (27 bp):
TAACAAAGTGATTCATACCTTGACGTG
Found at i:3406058 original size:2 final size:2
Alignment explanation
Indices: 3406051--3406077 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3406041 TAGTTAGTGT
3406051 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
3406078 GTATTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3406629 original size:24 final size:24
Alignment explanation
Indices: 3406591--3406636 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3406581 ATAGTTAAGT
* *
3406591 TGTTACACGTAATGTTTAAAAACA
1 TGTTACACGCAATGTTGAAAAACA
*
3406615 TGTTACACGCCATGTTGAAAAA
1 TGTTACACGCAATGTTGAAAAA
3406637 AAATACTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (24 bp):
TGTTACACGCAATGTTGAAAAACA
Found at i:3406748 original size:31 final size:30
Alignment explanation
Indices: 3406687--3406749 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
3406677 CATCATAGTT
* *
3406687 AAAAAATATTGTTATACGCCATATTGAAAA
1 AAAAAATATTGTTACACGCCATATTAAAAA
* * *
3406717 AAAAAATAATTGTTACATGCTATGTTAAAAA
1 AAAAAAT-ATTGTTACACGCCATATTAAAAA
3406748 AA
1 AA
3406750 TATTGTTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (30 bp):
AAAAAATATTGTTACACGCCATATTAAAAA
Found at i:3406776 original size:28 final size:29
Alignment explanation
Indices: 3406745--3406815 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 29
3406735 GCTATGTTAA
*
3406745 AAAAATATTGTTGTTACACATT-ATATTT
1 AAAAATATTGTTGTTACACATTAATACTT
* * *
3406773 AAAAACA-T-TTATTACACTTTAATACTT
1 AAAAATATTGTTGTTACACATTAATACTT
*
3406800 -AAAATGTTGTTGTTAC
1 AAAAATATTGTTGTTAC
3406816 TTACGAACCA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
26 14 0.42
27 7 0.21
28 12 0.36
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (29 bp):
AAAAATATTGTTGTTACACATTAATACTT
Found at i:3412420 original size:2 final size:2
Alignment explanation
Indices: 3412376--3412403 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3412366 CTATACATAC
3412376 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
3412404 GTTGTAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3422480 original size:50 final size:50
Alignment explanation
Indices: 3422405--3422503 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
3422395 ACGTTGCCGA
3422405 AATCGGGTGGGAGAGAGTGTCACGAAGAAAGTACCTCTATCCCACATTGG
1 AATCGGGTGGGAGAGAGTGTCACGAAGAAAGTACCTCTATCCCACATTGG
3422455 AATCGGGTGGGAGAGAGTGTCACGAAGAAAGTACCTCTATCCCACATTG
1 AATCGGGTGGGAGAGAGTGTCACGAAGAAAGTACCTCTATCCCACATTG
3422504 AACAAGAACG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.20
Consensus pattern (50 bp):
AATCGGGTGGGAGAGAGTGTCACGAAGAAAGTACCTCTATCCCACATTGG
Found at i:3426318 original size:114 final size:113
Alignment explanation
Indices: 3426113--3426320 Score: 299
Period size: 114 Copynumber: 1.8 Consensus size: 113
3426103 ATCAGGAAAT
* * * * * *
3426113 AGATTAGAGAGACAGAAATAAAAATAATCAGTACTAATTTATTGTTTTGATAGAATTTCTTGAAT
1 AGATTAAAGAGACAGAAAAAAAAATAATCAGTACTAATTTAATGTTTTAATAGAATATCTAGAAT
*
3426178 TTATATCATTTGAAAGATAACAGTAATGATATGTGACATGATACAAAA
66 TTATATCATTTGAAAGAAAACAGTAATGATATGTGACATGATACAAAA
* * *
3426226 AGATTAAAGGGACAGAAAAAAAAATATTCAGTACTAATTTTAATGTTTTAATAGAATATCTAGTA
1 AGATTAAAGAGACAGAAAAAAAAATAATCAGTACTAA-TTTAATGTTTTAATAGAATATCTAGAA
* *
3426291 TTTGTTTCATTTGAAAGAAAACAGTAATGA
65 TTTATATCATTTGAAAGAAAACAGTAATGA
3426321 CATATGAACT
Statistics
Matches: 82, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
113 33 0.40
114 49 0.60
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.34
Consensus pattern (113 bp):
AGATTAAAGAGACAGAAAAAAAAATAATCAGTACTAATTTAATGTTTTAATAGAATATCTAGAAT
TTATATCATTTGAAAGAAAACAGTAATGATATGTGACATGATACAAAA
Found at i:3435811 original size:1 final size:1
Alignment explanation
Indices: 3435807--3435852 Score: 74
Period size: 1 Copynumber: 46.0 Consensus size: 1
3435797 CTAAAAAGAA
**
3435807 GGGGGGGGGGGGGGGCAGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
3435853 AATCACGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.02, C:0.02, G:0.96, T:0.00
Consensus pattern (1 bp):
G
Found at i:3441049 original size:2 final size:2
Alignment explanation
Indices: 3441042--3441069 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3441032 CACCACTAAA
3441042 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
3441070 GTTTGTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3443640 original size:2 final size:2
Alignment explanation
Indices: 3443624--3443660 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3443614 GCTGTGCTTT
*
3443624 TA TA TA -A TA TG 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
3443661 CTTTTTCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3445695 original size:15 final size:15
Alignment explanation
Indices: 3445675--3445704 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3445665 TGTATGACAT
3445675 CTACAAAAAGTAGAC
1 CTACAAAAAGTAGAC
*
3445690 CTACAAAATGTAGAC
1 CTACAAAAAGTAGAC
3445705 TCTGTTTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.20, G:0.13, T:0.17
Consensus pattern (15 bp):
CTACAAAAAGTAGAC
Found at i:3473631 original size:23 final size:21
Alignment explanation
Indices: 3473605--3473646 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
3473595 AATAAAATAA
3473605 TTTTTTAAATATTAATATTTTCT
1 TTTTTTAAAT-TTAA-ATTTTCT
*
3473628 TTTTTTTAATTTAAATTTT
1 TTTTTTAAATTTAAATTTT
3473647 AAATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 4 0.22
23 9 0.50
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTTAAATTTAAATTTTCT
Found at i:3475835 original size:17 final size:17
Alignment explanation
Indices: 3475814--3475849 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3475804 TAAATAAATT
*
3475814 TAAAAATTAAATA-TTA
1 TAAAAAATAAATATTTA
3475830 TAAAAAATAAATATTTA
1 TAAAAAATAAATATTTA
3475847 TAA
1 TAA
3475850 TGCTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAAATAAATATTTA
Found at i:3480190 original size:32 final size:32
Alignment explanation
Indices: 3480149--3480213 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 32
3480139 AACATAAAGG
3480149 AGTAAAGACCACTAAC-AGAATAAAACTCAGTT
1 AGTAAAGACCACTAACAAG-ATAAAACTCAGTT
3480181 AGTAAAGACCACTAACAAGATAAAACTCAGTT
1 AGTAAAGACCACTAACAAGATAAAACTCAGTT
3480213 A
1 A
3480214 AAAAGAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.18
Consensus pattern (32 bp):
AGTAAAGACCACTAACAAGATAAAACTCAGTT
Found at i:3485406 original size:19 final size:19
Alignment explanation
Indices: 3485382--3485421 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3485372 TAAAACATAA
3485382 TTTAAAAAAAAATAATTTT
1 TTTAAAAAAAAATAATTTT
**
3485401 TTTAAAATTAAATAATTTT
1 TTTAAAAAAAAATAATTTT
3485420 TT
1 TT
3485422 ATTCTTTTAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAAAAAAAAATAATTTT
Found at i:3495791 original size:28 final size:28
Alignment explanation
Indices: 3495760--3495814 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
3495750 GATAATTCTA
*
3495760 AAACTTTCCCAGCACAAAAGCACTGCAG
1 AAACTTTCCCAGCACAAAAACACTGCAG
* *
3495788 AAACTTTCCTAGCAGAAAAACACTGCA
1 AAACTTTCCCAGCACAAAAACACTGCA
3495815 ACGACTGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.42, C:0.29, G:0.13, T:0.16
Consensus pattern (28 bp):
AAACTTTCCCAGCACAAAAACACTGCAG
Found at i:3499373 original size:16 final size:16
Alignment explanation
Indices: 3499342--3499385 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
3499332 TTTAAATTTT
3499342 TAATAT-ATTTTT-AA
1 TAATATAATTTTTAAA
3499356 TAATATAATTTTTAAA
1 TAATATAATTTTTAAA
* *
3499372 TAAAATATTTTTTA
1 TAATATAATTTTTA
3499386 TATTAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 6 0.23
15 6 0.23
16 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATATAATTTTTAAA
Found at i:3499382 original size:30 final size:29
Alignment explanation
Indices: 3499346--3499405 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
3499336 AATTTTTAAT
3499346 ATATTTTTAATAATATAATTT-TTAAATAAA
1 ATATTTTTAAT-AT-TAATTTATTAAATAAA
* *
3499376 ATATTTTTTATATTAATTTATTAATTAAA
1 ATATTTTTAATATTAATTTATTAAATAAA
3499405 A
1 A
3499406 GATAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 6 0.22
29 11 0.41
30 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
ATATTTTTAATATTAATTTATTAAATAAA
Found at i:3503599 original size:25 final size:24
Alignment explanation
Indices: 3503569--3503666 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 24
3503559 TTGAAACGAT
3503569 AAAAATAAAAATTTTAATATTTAAA
1 AAAAATAAAAATTTTAA-ATTTAAA
*
3503594 AAAAATAAAATTTTTAAACTTTTAAA
1 AAAAATAAAAATTTTAAA--TTTAAA
* *
3503620 AAGTAAAAATAAAATTTTAAA-ATAAA
1 AA--AAATA-AAAATTTTAAATTTAAA
**
3503646 AAAAATAAATGTTTTAAATTT
1 AAAAATAAAAATTTTAAATTT
3503667 TGAGGCGGCA
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
23 9 0.15
24 6 0.10
25 16 0.27
26 14 0.24
28 4 0.07
29 10 0.17
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAAATAAAAATTTTAAATTTAAA
Found at i:3504958 original size:21 final size:21
Alignment explanation
Indices: 3504915--3504954 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
3504905 TGTTTTTTAT
*
3504915 TTTTTTAAAATATAATAATAA
1 TTTTTTAAAATATAATAAAAA
3504936 TTTTTT-AAAT-TAATAAAAA
1 TTTTTTAAAATATAATAAAAA
3504955 AATTATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTTTTAAAATATAATAAAAA
Found at i:3505081 original size:9 final size:8
Alignment explanation
Indices: 3505050--3505081 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
3505040 AATTTTGATT
3505050 AAAATTTA
1 AAAATTTA
3505058 AAAATTTA
1 AAAATTTA
3505066 AAAATTTA
1 AAAATTTA
3505074 AAATATTT
1 AAA-ATTT
3505082 TATCTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
AAAATTTA
Found at i:3523963 original size:45 final size:45
Alignment explanation
Indices: 3523899--3523988 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
3523889 AGGTCAAACG
3523899 GCGGAGGCAGTCTAGATCTACAGCCAAATTATGATCCAAGTAATA
1 GCGGAGGCAGTCTAGATCTACAGCCAAATTATGATCCAAGTAATA
3523944 GCGGAGGCAGTCTAGATCTACAGCCAAATTATGATCCAAGTAATA
1 GCGGAGGCAGTCTAGATCTACAGCCAAATTATGATCCAAGTAATA
3523989 TTAATTCAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (45 bp):
GCGGAGGCAGTCTAGATCTACAGCCAAATTATGATCCAAGTAATA
Found at i:3526628 original size:81 final size:81
Alignment explanation
Indices: 3526465--3526707 Score: 452
Period size: 81 Copynumber: 3.0 Consensus size: 81
3526455 TCAACATCAC
* *
3526465 TGGTGTTGACTGTGGACCGGGCCACGGTATCAGGT-TGTGTTGAATACCCTGTTTTCTTTCATTC
1 TGGTGTTGACTGTGGACCGGGCCACGGTATCAGGTCTCTGTTCAATACCCTGTTTTCTTTCATTC
3526529 TTGAAACAAAAAACTT
66 TTGAAACAAAAAACTT
3526545 TGGTGTTGACTGTGGACCGGGCCACGGTATCAGGTCTCTGTTCAATACCCTGTTTTCTTTCATTC
1 TGGTGTTGACTGTGGACCGGGCCACGGTATCAGGTCTCTGTTCAATACCCTGTTTTCTTTCATTC
*
3526610 CTGAAACAAAAAACTT
66 TTGAAACAAAAAACTT
3526626 TGGTGTTGACTGTGGACCGGGCCACGGTATCAGGTCTCTGTTCAATACCCTGTTTTCTTTCATTC
1 TGGTGTTGACTGTGGACCGGGCCACGGTATCAGGTCTCTGTTCAATACCCTGTTTTCTTTCATTC
3526691 TTGAAACAAAAAACTT
66 TTGAAACAAAAAACTT
3526707 T
1 T
3526708 CTTTGCTAGC
Statistics
Matches: 158, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
80 35 0.22
81 123 0.78
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (81 bp):
TGGTGTTGACTGTGGACCGGGCCACGGTATCAGGTCTCTGTTCAATACCCTGTTTTCTTTCATTC
TTGAAACAAAAAACTT
Found at i:3529012 original size:23 final size:22
Alignment explanation
Indices: 3528957--3529061 Score: 73
Period size: 23 Copynumber: 5.0 Consensus size: 22
3528947 GTGGTGGCAC
3528957 TGGTGGAGGTTTT--GGT-G-G
1 TGGTGGAGGTTTTGGGGTGGTG
* * *
3528975 TGGCGGTGGTCTTGGGGGTGGTG
1 TGGTGGAGGT-TTTGGGGTGGTG
3528998 TGGTGGAGGTTTT--GGT-G-G
1 TGGTGGAGGTTTTGGGGTGGTG
*
3529016 TGGTGGAGGTTTTGGGGTGGCGG
1 TGGTGGAGGTTTTGGGGTGG-TG
* *
3529039 TGGTGGAGGGTTAGGAGGTGGTG
1 TGGTGGAGGTTTTGG-GGTGGTG
3529062 GAGGCCTAGG
Statistics
Matches: 67, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
18 22 0.33
19 3 0.04
20 6 0.09
21 4 0.06
22 3 0.04
23 24 0.36
24 5 0.07
ACGTcount: A:0.06, C:0.03, G:0.59, T:0.32
Consensus pattern (22 bp):
TGGTGGAGGTTTTGGGGTGGTG
Found at i:3529020 original size:18 final size:18
Alignment explanation
Indices: 3528898--3529142 Score: 103
Period size: 18 Copynumber: 12.4 Consensus size: 18
3528888 TGGTGGTCTA
* * *
3528898 GGTGGTGGTTTTGGGGGA
1 GGTGGAGGTTTTGGTGGT
* *
3528916 GGTGGAGGTTTAGGTGGA
1 GGTGGAGGTTTTGGTGGT
*
3528934 GGAGGAGGTATTGGTGGTGGCACT
1 GGTGGAGGT-TT--TGGTGG---T
3528958 GGTGGAGGTTTTGGTGGT
1 GGTGGAGGTTTTGGTGGT
* * *
3528976 GGCGGTGGTCTTGGGGGTGGTGT
1 GGTGGAGGT-TT--TGGT-G-GT
3528999 GGTGGAGGTTTTGGTGGT
1 GGTGGAGGTTTTGGTGGT
3529017 GGTGGAGGTTTTGGGGTGGCGGT
1 GGTGGAGGTTTT--GGT---GGT
* * *
3529040 GGTGGAGGGTTAGGAGGT
1 GGTGGAGGTTTTGGTGGT
** *
3529058 GGTGGAGGCCTAGGTGGT
1 GGTGGAGGTTTTGGTGGT
* **
3529076 GGTGGTGGGCTTGGTGGT
1 GGTGGAGGTTTTGGTGGT
*
3529094 GGTGCAGGAGGTGGCTTAGGTGGT
1 GGT---GGAGGT---TTTGGTGGT
**
3529118 GGTGGAGGCCTTGGTGGT
1 GGTGGAGGTTTTGGTGGT
3529136 GGTGGAG
1 GGTGGAG
3529143 CCTTGGTGGT
Statistics
Matches: 176, Mismatches: 29, Indels: 44
0.71 0.12 0.18
Matches are distributed among these distances:
18 95 0.54
19 5 0.03
20 6 0.03
21 25 0.14
22 3 0.02
23 24 0.14
24 18 0.10
ACGTcount: A:0.09, C:0.05, G:0.58, T:0.29
Consensus pattern (18 bp):
GGTGGAGGTTTTGGTGGT
Found at i:3529059 original size:41 final size:41
Alignment explanation
Indices: 3528916--3529065 Score: 158
Period size: 41 Copynumber: 3.6 Consensus size: 41
3528906 TTTTGGGGGA
* * * *
3528916 GGTGGAGGTTTAGGTGGAGGAGGAGGTATTGGTGGTGGCACT
1 GGTGGAGGTTTAGGTGGTGGTGGAGGTTTTGG-GGTGGCAGT
* * * * *
3528958 GGTGGAGGTTTTGGTGGTGGCGGTGGTCTTGGGGGTGG-TGT
1 GGTGGAGGTTTAGGTGGTGGTGGAGGT-TTTGGGGTGGCAGT
* *
3528999 GGTGGAGGTTTTGGTGGTGGTGGAGGTTTTGGGGTGGCGGT
1 GGTGGAGGTTTAGGTGGTGGTGGAGGTTTTGGGGTGGCAGT
* *
3529040 GGTGGAGGGTTAGGAGGTGGTGGAGG
1 GGTGGAGGTTTAGGTGGTGGTGGAGG
3529066 CCTAGGTGGT
Statistics
Matches: 91, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
40 9 0.10
41 51 0.56
42 28 0.31
43 3 0.03
ACGTcount: A:0.09, C:0.03, G:0.58, T:0.29
Consensus pattern (41 bp):
GGTGGAGGTTTAGGTGGTGGTGGAGGTTTTGGGGTGGCAGT
Found at i:3529147 original size:17 final size:18
Alignment explanation
Indices: 3529037--3529154 Score: 105
Period size: 18 Copynumber: 6.3 Consensus size: 18
3529027 TTGGGGTGGC
* *
3529037 GGTGGTGGAGG-GTTAGGA
1 GGTGGTGGAGGCCTT-GGT
*
3529055 GGTGGTGGAGGCCTAGGT
1 GGTGGTGGAGGCCTTGGT
* *
3529073 GGTGGTGGTGGGCTTGGT
1 GGTGGTGGAGGCCTTGGT
*
3529091 GGTGGTGCAGGAGGTGGCTTAGGT
1 GGTGGT---GGA-G-GCCTT-GGT
3529115 GGTGGTGGAGGCCTTGGT
1 GGTGGTGGAGGCCTTGGT
3529133 GGTGGTGGA-GCCTTGGT
1 GGTGGTGGAGGCCTTGGT
3529150 GGTGG
1 GGTGG
3529155 AGCAGGAGTA
Statistics
Matches: 85, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
17 13 0.15
18 46 0.54
19 5 0.06
20 1 0.01
21 5 0.06
22 1 0.01
23 5 0.06
24 9 0.11
ACGTcount: A:0.08, C:0.08, G:0.58, T:0.26
Consensus pattern (18 bp):
GGTGGTGGAGGCCTTGGT
Found at i:3529190 original size:59 final size:57
Alignment explanation
Indices: 3529072--3529198 Score: 134
Period size: 59 Copynumber: 2.2 Consensus size: 57
3529062 GAGGCCTAGG
* ** *
3529072 TGGTGGTGGTGGGCTTGGTGGTGGTGCAGGAGGTGGCTTAGGTGGTGGTGGAGGCCT
1 TGGTGGTGGTGGGCTTGGTGGTGGAGCAGGAGGTGGCTTAGGTGGTGGCAGAAGCCT
*
3529129 TGGTGGTGGTGGAGCCTTGGTGGTGGAGCAGGA-GTAGGGC-TAGGTGGTGGCCATAAG-CT
1 TGGTGGTGGTGG-G-CTTGGTGGTGGAGCAGGAGGT--GGCTTAGGTGGTGG-CAGAAGCCT
*
3529188 TGGTGGAGGTG
1 TGGTGGTGGTG
3529199 CAGGAGGTGG
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
57 12 0.20
58 3 0.05
59 39 0.66
60 5 0.08
ACGTcount: A:0.11, C:0.09, G:0.54, T:0.26
Consensus pattern (57 bp):
TGGTGGTGGTGGGCTTGGTGGTGGAGCAGGAGGTGGCTTAGGTGGTGGCAGAAGCCT
Found at i:3529222 original size:18 final size:18
Alignment explanation
Indices: 3529201--3529238 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3529191 TGGAGGTGCA
*
3529201 GGAGGTGGACTAGGTGGT
1 GGAGGAGGACTAGGTGGT
*
3529219 GGAGGAGGACTTGGTGGT
1 GGAGGAGGACTAGGTGGT
3529237 GG
1 GG
3529239 CCACAAGCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.05, G:0.58, T:0.21
Consensus pattern (18 bp):
GGAGGAGGACTAGGTGGT
Found at i:3529247 original size:60 final size:60
Alignment explanation
Indices: 3529171--3529452 Score: 395
Period size: 60 Copynumber: 4.7 Consensus size: 60
3529161 AGTAGGGCTA
3529171 GGTGGTGGCCATAAGCTTGGTGGAGGTGCAGGAGGTGGACTAGGTGGTGGAGGAGGACTT
1 GGTGGTGGCCATAAGCTTGGTGGAGGTGCAGGAGGTGGACTAGGTGGTGGAGGAGGACTT
* *
3529231 GGTGGTGGCCACAAGCTGGTGTGGAGGTGCAGGAGGTGGACTAGGTGGTGGAGGAGGACTT
1 GGTGGTGGCCATAAGCTTG-GTGGAGGTGCAGGAGGTGGACTAGGTGGTGGAGGAGGACTT
* * * * * *
3529292 GGTGGTGGCCACAAGCTGGGTGGAGGTGCAGGAGGAGGATTAGGTGGTGGTGGAGGGCTT
1 GGTGGTGGCCATAAGCTTGGTGGAGGTGCAGGAGGTGGACTAGGTGGTGGAGGAGGACTT
* * * * * *
3529352 GGTGGTGGCCATAGGCTTGGTGGAGGTGCTGGAGGTGGATTAGGGGGTGGAGGTGGCCTT
1 GGTGGTGGCCATAAGCTTGGTGGAGGTGCAGGAGGTGGACTAGGTGGTGGAGGAGGACTT
* *
3529412 GGTGGTGGCCATAGGCTTGGTGGA-GTGGCAGGTGGTGGACT
1 GGTGGTGGCCATAAGCTTGGTGGAGGT-GCAGGAGGTGGACT
3529453 TGGAGGAGGT
Statistics
Matches: 202, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
59 2 0.01
60 140 0.69
61 60 0.30
ACGTcount: A:0.16, C:0.11, G:0.52, T:0.22
Consensus pattern (60 bp):
GGTGGTGGCCATAAGCTTGGTGGAGGTGCAGGAGGTGGACTAGGTGGTGGAGGAGGACTT
Found at i:3529283 original size:18 final size:18
Alignment explanation
Indices: 3529262--3529299 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3529252 TGGAGGTGCA
*
3529262 GGAGGTGGACTAGGTGGT
1 GGAGGAGGACTAGGTGGT
*
3529280 GGAGGAGGACTTGGTGGT
1 GGAGGAGGACTAGGTGGT
3529298 GG
1 GG
3529300 CCACAAGCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.05, G:0.58, T:0.21
Consensus pattern (18 bp):
GGAGGAGGACTAGGTGGT
Found at i:3529446 original size:30 final size:30
Alignment explanation
Indices: 3529339--3529449 Score: 99
Period size: 30 Copynumber: 3.7 Consensus size: 30
3529329 GATTAGGTGG
3529339 TGGTGGAGGGCTTGGTGGTGGCCATAGGCT
1 TGGTGGAGGGCTTGGTGGTGGCCATAGGCT
*
3529369 TGGTGGAGGTGC-TGGAGGTGG--ATTAGG--
1 TGGTGGAGG-GCTTGGTGGTGGCCA-TAGGCT
*
3529396 GGGTGGAGGTGGCCTTGGTGGTGGCCATAGGCT
1 TGGTGGA-G-GG-CTTGGTGGTGGCCATAGGCT
*
3529429 TGGTGGAGTGGC-AGGTGGTGG
1 TGGTGGAG-GGCTTGGTGGTGG
3529450 ACTTGGAGGA
Statistics
Matches: 66, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
27 6 0.09
28 3 0.05
29 6 0.09
30 33 0.50
31 7 0.11
32 5 0.08
33 6 0.09
ACGTcount: A:0.11, C:0.10, G:0.54, T:0.25
Consensus pattern (30 bp):
TGGTGGAGGGCTTGGTGGTGGCCATAGGCT
Found at i:3529592 original size:18 final size:18
Alignment explanation
Indices: 3529542--3529593 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
3529532 GTGGAGGCCT
* *
3529542 TGGTGGTGGTGCTGGGGG
1 TGGTGGTGGAGTTGGGGG
* * * *
3529560 TGGAGGAGGATTTGGTGG
1 TGGTGGTGGAGTTGGGGG
3529578 TGGTGGTGGAGTTGGG
1 TGGTGGTGGAGTTGGG
3529594 TAGGGTTTGG
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.08, C:0.02, G:0.62, T:0.29
Consensus pattern (18 bp):
TGGTGGTGGAGTTGGGGG
Found at i:3539368 original size:19 final size:19
Alignment explanation
Indices: 3539346--3539382 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3539336 TAAGTTAATT
3539346 ATTATATTTTT-TATATTTA
1 ATTA-ATTTTTATATATTTA
3539365 ATTAATTTTTATATATTT
1 ATTAATTTTTATATATTT
3539383 TAATATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTAATTTTTATATATTTA
Found at i:3539369 original size:26 final size:27
Alignment explanation
Indices: 3539324--3539393 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 27
3539314 TATTTATCTA
3539324 ATTTGTTTAT-TTTAAGTTAATTATTAT
1 ATTT-TTTATATTTAAGTTAATTATTAT
*
3539351 ATTTTTTATATTTAA-TTAATTTTTAT
1 ATTTTTTATATTTAAGTTAATTATTAT
*
3539377 ATATTTTA-ATATTAAGT
1 ATTTTTTATAT-TTAAGT
3539394 CAAATAAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
25 2 0.05
26 26 0.68
27 10 0.26
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (27 bp):
ATTTTTTATATTTAAGTTAATTATTAT
Found at i:3543499 original size:31 final size:31
Alignment explanation
Indices: 3543454--3543528 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
3543444 TGATGCTATG
3543454 TGACATGTTAAATATATTAT-ATTGATATGAGA
1 TGACATGTT-AATATATTATAATTGATAT-AGA
* *
3543486 TGACATGTTAATATATTATAATTGATGTATA
1 TGACATGTTAATATATTATAATTGATATAGA
*
3543517 TGACATGCTAAT
1 TGACATGTTAAT
3543529 TTGACATGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 23 0.59
32 16 0.41
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (31 bp):
TGACATGTTAATATATTATAATTGATATAGA
Found at i:3543961 original size:28 final size:28
Alignment explanation
Indices: 3543905--3543957 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
3543895 ATATGTATTT
3543905 TTTTTCAATTTAAACAATAATTTTATAA
1 TTTTTCAATTTAAACAATAATTTTATAA
3543933 TTTTT-AATTTGAAACAA-AATTTTAT
1 TTTTTCAATTT-AAACAATAATTTTAT
3543958 TAATATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (28 bp):
TTTTTCAATTTAAACAATAATTTTATAA
Found at i:3563686 original size:21 final size:21
Alignment explanation
Indices: 3563641--3563711 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
3563631 TTTCTCGTCT
* * **
3563641 AGCCACCGCTGCTCTTCTCTT
1 AGCCACCGTTGCTCTTCCCGA
* *
3563662 AGCCAGCGTTGCTCTTCCCGG
1 AGCCACCGTTGCTCTTCCCGA
* *
3563683 AGCCACCGTTGTTCTTCGCGA
1 AGCCACCGTTGCTCTTCCCGA
3563704 AGCCACCG
1 AGCCACCG
3563712 GCTTTCTTCG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.13, C:0.39, G:0.23, T:0.25
Consensus pattern (21 bp):
AGCCACCGTTGCTCTTCCCGA
Found at i:3595486 original size:37 final size:35
Alignment explanation
Indices: 3595444--3595550 Score: 137
Period size: 37 Copynumber: 3.1 Consensus size: 35
3595434 TTGAATTTTA
3595444 AGACTATAAATCAGAACTGACAGCCCAACTTGAAGGG
1 AGACTATAAATCAGAACTGACAGCCCAACTTGAA--G
* * *
3595481 AGACTATAAATCAGAACTGACGGCCTACCTTGAAG
1 AGACTATAAATCAGAACTGACAGCCCAACTTGAAG
* *
3595516 AG--TATGAATCAGAACTGACAGCCCAACTTGGAG
1 AGACTATAAATCAGAACTGACAGCCCAACTTGAAG
3595549 AG
1 AG
3595551 TATGAAGTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
33 28 0.45
35 3 0.05
37 31 0.50
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.18
Consensus pattern (35 bp):
AGACTATAAATCAGAACTGACAGCCCAACTTGAAG
Found at i:3595531 original size:33 final size:33
Alignment explanation
Indices: 3595443--3595553 Score: 132
Period size: 33 Copynumber: 3.2 Consensus size: 33
3595433 TTTGAATTTT
*
3595443 AAGACTATAAATCAGAACTGACAGCCCAACTTG
1 AAGAGTATAAATCAGAACTGACAGCCCAACTTG
* * *
3595476 AAGGGAGACTATAAATCAGAACTGACGGCCTACCTTG
1 AA--GAG--TATAAATCAGAACTGACAGCCCAACTTG
*
3595513 AAGAGTATGAATCAGAACTGACAGCCCAACTTG
1 AAGAGTATAAATCAGAACTGACAGCCCAACTTG
*
3595546 GAGAGTAT
1 AAGAGTAT
3595554 GAAGTTATTC
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
33 33 0.51
35 5 0.08
37 27 0.42
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.19
Consensus pattern (33 bp):
AAGAGTATAAATCAGAACTGACAGCCCAACTTG
Found at i:3601989 original size:27 final size:26
Alignment explanation
Indices: 3601957--3602186 Score: 120
Period size: 27 Copynumber: 8.4 Consensus size: 26
3601947 AATTTACACA
3601957 TTATATTAAAAATTTAATTATTACAT
1 TTATATTAAAAATTTAATTATTACAT
* * * *
3601983 TTCATATTGAAAAATGTAAATATTATACC
1 TT-ATATT-AAAAATTTAATTATTACA-T
* * * *
3602012 TTATGTTTGAAAATTTAGTTGTTATACA-
1 TTAT-ATTAAAAATTTAATT-AT-TACAT
* * * *
3602040 TTATCTTAAAAAAATATAGTTATTATAT
1 TTATATT--AAAAATTTAATTATTACAT
* * * *
3602068 ATCATGTTGAATATTTAATTATTACAT
1 -TTATATTAAAAATTTAATTATTACAT
* **
3602095 GTTATGTTAAAAATTTAATTATTGTAT
1 -TTATATTAAAAATTTAATTATTACAT
* * *
3602122 ATAATATTAAAAATATAGTTATTACAT
1 -TTATATTAAAAATTTAATTATTACAT
* *
3602149 ATTATGTTAAAAATATAATTATTACAT
1 -TTATATTAAAAATTTAATTATTACAT
3602176 GTTATATTAAA
1 -TTATATTAAA
3602187 GAGTTTATTG
Statistics
Matches: 153, Mismatches: 41, Indels: 19
0.72 0.19 0.09
Matches are distributed among these distances:
26 2 0.01
27 98 0.64
28 30 0.20
29 20 0.13
30 3 0.02
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (26 bp):
TTATATTAAAAATTTAATTATTACAT
Found at i:3602123 original size:54 final size:54
Alignment explanation
Indices: 3602049--3602186 Score: 159
Period size: 54 Copynumber: 2.6 Consensus size: 54
3602039 ATTATCTTAA
* * * * * * *
3602049 AAAAATATAGTTATTATATATCATGTTGAATATTTAATTATTACATGTTATGTT
1 AAAAATATAATTATTATATATAATATTAAAAATATAATTATTACATATTATGTT
* * *
3602103 AAAAATTTAATTATTGTATATAATATTAAAAATATAGTTATTACATATTATGTT
1 AAAAATATAATTATTATATATAATATTAAAAATATAATTATTACATATTATGTT
* * *
3602157 AAAAATATAATTATTACATGTTATATTAAA
1 AAAAATATAATTATTATATATAATATTAAA
3602187 GAGTTTATTG
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (54 bp):
AAAAATATAATTATTATATATAATATTAAAAATATAATTATTACATATTATGTT
Found at i:3602241 original size:28 final size:27
Alignment explanation
Indices: 3602157--3602244 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 27
3602147 ATATTATGTT
* * * *
3602157 AAAAATATAATTATTACATGTTATATT
1 AAAAATTTAATTGTTACACGTTATATG
* * * *
3602184 AAAGAGTTT-ATTGTTATACGTTCTGTTG
1 AAA-AATTTAATTGTTACACGTTAT-ATG
3602212 AAAAATTTAATTGTTACACGTTATAATG
1 AAAAATTTAATTGTTACACGTTAT-ATG
3602240 AAAAA
1 AAAAA
3602245 ATTGTTACAC
Statistics
Matches: 45, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
27 18 0.40
28 27 0.60
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (27 bp):
AAAAATTTAATTGTTACACGTTATATG
Found at i:3606471 original size:17 final size:17
Alignment explanation
Indices: 3606449--3606483 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3606439 GACGCATTAA
3606449 TTTAGCCCTTATTCAAG
1 TTTAGCCCTTATTCAAG
3606466 TTTAGCCCTTATTCAAG
1 TTTAGCCCTTATTCAAG
3606483 T
1 T
3606484 ATAAATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (17 bp):
TTTAGCCCTTATTCAAG
Found at i:3640322 original size:3 final size:3
Alignment explanation
Indices: 3640314--3640354 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
3640304 TAGCCAATCC
* * *
3640314 TCT TCT TCT TCT TCT TTT TCT TTT TCT TCT TCT TCC TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
3640355 CTCGATCTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:3641450 original size:20 final size:21
Alignment explanation
Indices: 3641420--3641460 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
3641410 TTTATTTTGA
3641420 AAAAAATGAATAATATAAAAT
1 AAAAAATGAATAATATAAAAT
*
3641441 AAAAAA-GAATAATGTAAAAT
1 AAAAAATGAATAATATAAAAT
3641461 CAAGTCTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (21 bp):
AAAAAATGAATAATATAAAAT
Found at i:3643015 original size:12 final size:12
Alignment explanation
Indices: 3642998--3643028 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3642988 CCTCCCTCGC
*
3642998 TCTCTCTCTCTT
1 TCTCTCTCTCTA
3643010 TCTCTCTCTCTA
1 TCTCTCTCTCTA
3643022 TCTCTCT
1 TCTCTCT
3643029 ATTTTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.55
Consensus pattern (12 bp):
TCTCTCTCTCTA
Found at i:3661131 original size:42 final size:42
Alignment explanation
Indices: 3661072--3661153 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
3661062 CAGGTAATGT
*
3661072 ACTACATATATGCTCATCCTAGTTTATGTCTAACGGAGATGC
1 ACTACATATATGCTCATCCCAGTTTATGTCTAACGGAGATGC
* *
3661114 ACTACATATATTCTCATCCCAGTTTATGTCTAATGGAGAT
1 ACTACATATATGCTCATCCCAGTTTATGTCTAACGGAGAT
3661154 AAGTCAAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (42 bp):
ACTACATATATGCTCATCCCAGTTTATGTCTAACGGAGATGC
Found at i:3663721 original size:2 final size:2
Alignment explanation
Indices: 3663714--3663740 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3663704 TGACAATGTT
3663714 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
3663741 GTTAGGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3667826 original size:21 final size:22
Alignment explanation
Indices: 3667780--3667829 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
3667770 TGAAAAATCT
* *
3667780 TTATTTTATAAATTACTGTTAA
1 TTATTTTATAAATTAATGCTAA
*
3667802 -TATTTTTTAAA-TAATGCTAA
1 TTATTTTATAAATTAATGCTAA
3667822 TTATTTTA
1 TTATTTTA
3667830 ATCGATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (22 bp):
TTATTTTATAAATTAATGCTAA
Found at i:3677160 original size:21 final size:20
Alignment explanation
Indices: 3677132--3677170 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3677122 TTCAATTATA
*
3677132 ATTAATAAATTTTAAAATAT
1 ATTAATAAATATTAAAATAT
*
3677152 ATTATATAACTATTAAAAT
1 ATTA-ATAAATATTAAAAT
3677171 TTGTATGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTAATAAATATTAAAATAT
Found at i:3677263 original size:2 final size:2
Alignment explanation
Indices: 3677256--3677286 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3677246 TACGACGGAA
*
3677256 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3677287 AATTTGATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3681315 original size:15 final size:15
Alignment explanation
Indices: 3681291--3681325 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3681281 GTTTGGAATG
3681291 TAATTATTGAAAATA
1 TAATTATTGAAAATA
*
3681306 TAATTGTTGAAAATA
1 TAATTATTGAAAATA
3681321 TAATT
1 TAATT
3681326 TTGTAACGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTATTGAAAATA
Found at i:3688420 original size:20 final size:18
Alignment explanation
Indices: 3688391--3688432 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
3688381 AAAAAAGTAA
3688391 TTTTGGTTTT-TTTATGAAT
1 TTTTGGTTTTGTTT-T-AAT
3688410 TTTTGGGTTTTGTTTTAAT
1 TTTT-GGTTTTGTTTTAAT
3688429 TTTT
1 TTTT
3688433 TTAATTTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 11 0.52
20 7 0.33
21 3 0.14
ACGTcount: A:0.12, C:0.00, G:0.17, T:0.71
Consensus pattern (18 bp):
TTTTGGTTTTGTTTTAAT
Found at i:3692324 original size:17 final size:17
Alignment explanation
Indices: 3692302--3692335 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3692292 AAAAAGAAAG
3692302 CTGCTTTCCTATGGCAA
1 CTGCTTTCCTATGGCAA
3692319 CTGCTTTCCTATGGCAA
1 CTGCTTTCCTATGGCAA
3692336 AGGCAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (17 bp):
CTGCTTTCCTATGGCAA
Found at i:3696086 original size:2 final size:2
Alignment explanation
Indices: 3696079--3696107 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3696069 AGGGTTAAAA
3696079 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
3696108 GAAAGAAATA
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:3703997 original size:20 final size:20
Alignment explanation
Indices: 3703944--3703997 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
3703934 AAATTACATA
*
3703944 TTGATAAATACATGGGATTTT
1 TTGATAAATATAT-GGATTTT
* * *
3703965 TTCAT-AATCTATGGTTTTT
1 TTGATAAATATATGGATTTT
3703984 TTGATAAATATATG
1 TTGATAAATATATG
3703998 AGCAATGAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
19 10 0.38
20 12 0.46
21 4 0.15
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (20 bp):
TTGATAAATATATGGATTTT
Done.