Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold229
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: 643502
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 5
Found at i:415504 original size:22 final size:22
Alignment explanation
Indices: 415479--415520 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
415469 ATTTTTTATT
415479 TAAAT-TTAATTATAAAAATATG
1 TAAATATTAA-TATAAAAATATG
415501 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
415521 ATATATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATG
Found at i:415524 original size:11 final size:11
Alignment explanation
Indices: 415489--415546 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
415479 TAAATTTAAT
415489 TATAAAAAT-A
1 TATAAAAATAA
* *
415499 TGTAAATATTAA
1 TATAAA-AATAA
415511 TATAAAAATAA
1 TATAAAAATAA
**
415522 TATATTAATAA
1 TATAAAAATAA
415533 TATAATAAATAA
1 TATAA-AAATAA
415545 TA
1 TA
415547 AAATAAAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 5 0.14
11 19 0.51
12 13 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
TATAAAAATAA
Found at i:416784 original size:25 final size:25
Alignment explanation
Indices: 416756--416810 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
416746 TGTTATATAA
*
416756 TTAAAGGAAAAGTCTAACTCAAGTC
1 TTAAAGGAAAAATCTAACTCAAGTC
416781 TTAAAGGAAAAATCTAACTCAAGTC
1 TTAAAGGAAAAATCTAACTCAAGTC
416806 TTAAA
1 TTAAA
416811 TGCTAGAGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.25
Consensus pattern (25 bp):
TTAAAGGAAAAATCTAACTCAAGTC
Found at i:431164 original size:21 final size:20
Alignment explanation
Indices: 431140--431197 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
431130 AAAAATATTA
*
431140 ATAACAATAAAATTAATAAAT
1 ATAATAATAAAATTAAT-AAT
* *
431161 ATAATAGTAAAATTGAATATT
1 ATAATAATAAAATT-AATAAT
*
431182 GTAATAATAAAATTAA
1 ATAATAATAAAATTAA
431198 AATTAATGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.06
21 26 0.84
22 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (20 bp):
ATAATAATAAAATTAATAAT
Found at i:432454 original size:8 final size:9
Alignment explanation
Indices: 432421--432457 Score: 51
Period size: 8 Copynumber: 4.2 Consensus size: 9
432411 AATAAATACA
432421 AATATAAA-
1 AATATAAAT
432429 AATATAAAAT
1 AATAT-AAAT
432439 AATATAAAT
1 AATATAAAT
432448 AAT-TAAAT
1 AATATAAAT
432456 AA
1 AA
432458 ATTATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 12 0.44
9 10 0.37
10 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AATATAAAT
Found at i:432549 original size:18 final size:20
Alignment explanation
Indices: 432516--432554 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
432506 ATTTTTAAAC
432516 AAATAAAAATTTAAAATATT
1 AAATAAAAATTTAAAATATT
432536 AAAT-AAAA-TTAAAATATT
1 AAATAAAAATTTAAAATATT
432554 A
1 A
432555 TGCATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.58
19 4 0.21
20 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAAAAATTTAAAATATT
Found at i:432724 original size:17 final size:16
Alignment explanation
Indices: 432702--432733 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
432692 ACCAATACAT
432702 TTAATTTTACTTATTAA
1 TTAATTTTA-TTATTAA
432719 TTAATTTTATTATTA
1 TTAATTTTATTATTA
432734 TTATTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TTAATTTTATTATTAA
Found at i:434931 original size:14 final size:13
Alignment explanation
Indices: 434899--434933 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
434889 TAAATTATCG
434899 TTAAATTTTTTTT
1 TTAAATTTTTTTT
*
434912 TAAAATTTTTTTAT
1 TTAAATTTTTTT-T
434926 TTAAATTT
1 TTAAATTT
434934 AAACGGATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTAAATTTTTTTT
Found at i:435055 original size:35 final size:33
Alignment explanation
Indices: 434987--435056 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 33
434977 AAAAATTATT
*
434987 TTTTATTAATATTTATAATTAAATTTAAATAAA
1 TTTTATTAATATTTATAATAAAATTTAAATAAA
*
435020 TTTT-TTATTATTTATAAATAATAATTTAAATTAAA
1 TTTTATTAATATTTAT-AATAA-AATTTAAA-TAAA
435055 TT
1 TT
435057 AACTTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 8 0.25
34 8 0.25
35 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TTTTATTAATATTTATAATAAAATTTAAATAAA
Found at i:436753 original size:34 final size:33
Alignment explanation
Indices: 436672--436789 Score: 173
Period size: 33 Copynumber: 3.5 Consensus size: 33
436662 TGGTAAAAAC
*
436672 CACCATTTAATCAACAATGGTAAGCTACCAAAT
1 CACCATTTAATCAACAATGGTAAACTACCAAAT
* * * *
436705 CTCCATTTAGTCAACAATGGCAAACCACCAAAT
1 CACCATTTAATCAACAATGGTAAACTACCAAAT
*
436738 CACCCATTTAATCAACAATGGTAAACTACTAAAT
1 CA-CCATTTAATCAACAATGGTAAACTACCAAAT
436772 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
436790 TCTCCCACTT
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
33 45 0.61
34 29 0.39
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:441278 original size:34 final size:33
Alignment explanation
Indices: 441197--441312 Score: 169
Period size: 33 Copynumber: 3.5 Consensus size: 33
441187 TGGTAAAAAC
*
441197 CACCATTTAATCAACAATGGTAAGCTACCAAAT
1 CACCATTTAATCAACAATGGTAAACTACCAAAT
* * * *
441230 CTCCATTTAGTCAACAATGGCAAACCACCAAAT
1 CACCATTTAATCAACAATGGTAAACTACCAAAT
*
441263 CACCCATTTAATCAACAATGGTAAACTACTAAAT
1 CA-CCATTTAATCAACAATGGTAAACTACCAAAT
441297 CACCATTTAATCAACA
1 CACCATTTAATCAACA
441313 TATTGCACAA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
33 43 0.60
34 29 0.40
ACGTcount: A:0.42, C:0.27, G:0.07, T:0.24
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:443684 original size:36 final size:34
Alignment explanation
Indices: 443643--443710 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 34
443633 CGTGAAAAGG
* *
443643 GAAAAATGAGGGGAGAAAGCAACGCACAAACAAATA
1 GAAAAATAAGGGGAGAAA-CAAAG-ACAAACAAATA
* *
443679 GAAAAATAAGGTGAGCAACAAAGACAAACAAA
1 GAAAAATAAGGGGAGAAACAAAGACAAACAAA
443711 AACGAAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 9 0.32
35 4 0.14
36 15 0.54
ACGTcount: A:0.59, C:0.13, G:0.22, T:0.06
Consensus pattern (34 bp):
GAAAAATAAGGGGAGAAACAAAGACAAACAAATA
Found at i:443970 original size:13 final size:13
Alignment explanation
Indices: 443952--443997 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
443942 AATCAATACG
443952 AGCAAAGGAGAGC
1 AGCAAAGGAGAGC
*
443965 AGCAAAGG-GCG-
1 AGCAAAGGAGAGC
* *
443976 AGCAAAAGAGAAC
1 AGCAAAGGAGAGC
443989 AGCAAAGGA
1 AGCAAAGGA
443998 CGGGCAAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
11 7 0.27
12 3 0.12
13 16 0.62
ACGTcount: A:0.50, C:0.15, G:0.35, T:0.00
Consensus pattern (13 bp):
AGCAAAGGAGAGC
Found at i:443977 original size:24 final size:24
Alignment explanation
Indices: 443949--444007 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
443939 AACAATCAAT
* *
443949 ACGAGCAAAGGAGAGCAGCAAAGG
1 ACGAGCAAAAGAGAACAGCAAAGG
*
443973 GCGAGCAAAAGAGAACAGCAAAGG
1 ACGAGCAAAAGAGAACAGCAAAGG
*
443997 ACGGGCAAAAG
1 ACGAGCAAAAG
444008 GGAAGATGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.47, C:0.17, G:0.36, T:0.00
Consensus pattern (24 bp):
ACGAGCAAAAGAGAACAGCAAAGG
Found at i:453183 original size:15 final size:15
Alignment explanation
Indices: 453163--453239 Score: 79
Period size: 15 Copynumber: 5.3 Consensus size: 15
453153 GAGGCAAACC
453163 CAGCAACAACAACAG
1 CAGCAACAACAACAG
*
453178 CAGCAACAGC-A-A-
1 CAGCAACAACAACAG
*
453190 CAGCAACAGCAACAG
1 CAGCAACAACAACAG
* * *
453205 CGGCAGCAACAGCAG
1 CAGCAACAACAACAG
*
453220 CAGCAACAACAGCAG
1 CAGCAACAACAACAG
453235 CAGCA
1 CAGCA
453240 GCAGCCGCCC
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
12 10 0.19
13 2 0.04
14 2 0.04
15 38 0.73
ACGTcount: A:0.45, C:0.34, G:0.21, T:0.00
Consensus pattern (15 bp):
CAGCAACAACAACAG
Found at i:453184 original size:12 final size:12
Alignment explanation
Indices: 453163--453236 Score: 64
Period size: 12 Copynumber: 6.4 Consensus size: 12
453153 GAGGCAAACC
*
453163 CAGCAACAACAA
1 CAGCAACAACAG
*
453175 CAGCAGC-A-A-
1 CAGCAACAACAG
* *
453184 CAGCAACAGCAA
1 CAGCAACAACAG
* *
453196 CAGCAACAGCGG
1 CAGCAACAACAG
*
453208 CAGCAACAGCAG
1 CAGCAACAACAG
453220 CAGCAACAACAG
1 CAGCAACAACAG
453232 CAGCA
1 CAGCA
453237 GCAGCAGCCG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
9 6 0.12
10 1 0.02
11 2 0.04
12 43 0.83
ACGTcount: A:0.46, C:0.34, G:0.20, T:0.00
Consensus pattern (12 bp):
CAGCAACAACAG
Found at i:453222 original size:3 final size:3
Alignment explanation
Indices: 453175--453244 Score: 68
Period size: 3 Copynumber: 23.3 Consensus size: 3
453165 GCAACAACAA
* * * * * *
453175 CAG CAG CAA CAG CAA CAG CAA CAG CAA CAG CGG CAG CAA CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* *
453223 CAA CAA CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG C
453245 CGCCCCAACA
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.41, C:0.34, G:0.24, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:453244 original size:6 final size:6
Alignment explanation
Indices: 453178--453242 Score: 76
Period size: 6 Copynumber: 10.8 Consensus size: 6
453168 ACAACAACAG
** *
453178 CAGCAA CAGCAA CAGCAA CAGCAA CAGCGG CAGCAA CAGCAG CAGCAA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA
* * *
453226 CAACAG CAGCAG CAGCA
1 CAGCAA CAGCAA CAGCA
453243 GCCGCCCCAA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.43, C:0.34, G:0.23, T:0.00
Consensus pattern (6 bp):
CAGCAA
Found at i:453244 original size:12 final size:12
Alignment explanation
Indices: 453178--453244 Score: 89
Period size: 12 Copynumber: 5.6 Consensus size: 12
453168 ACAACAACAG
*
453178 CAGCAACAGCAA
1 CAGCAGCAGCAA
*
453190 CAGCAACAGCAA
1 CAGCAGCAGCAA
*
453202 CAGCGGCAGCAA
1 CAGCAGCAGCAA
453214 CAGCAGCAGCAA
1 CAGCAGCAGCAA
* *
453226 CAACAGCAGCAG
1 CAGCAGCAGCAA
453238 CAGCAGC
1 CAGCAGC
453245 CGCCCCAACA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 49 1.00
ACGTcount: A:0.42, C:0.34, G:0.24, T:0.00
Consensus pattern (12 bp):
CAGCAGCAGCAA
Found at i:464029 original size:14 final size:14
Alignment explanation
Indices: 464007--464042 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
463997 TTTATTTTTA
464007 TTAAATAAATAAAC
1 TTAAATAAATAAAC
* *
464021 TTAATTAAATAAAT
1 TTAAATAAATAAAC
464035 TTAAATAA
1 TTAAATAA
464043 CTTAATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAAATAAATAAAC
Found at i:465885 original size:24 final size:26
Alignment explanation
Indices: 465849--465898 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
465839 TAAAATAGTA
465849 TTAAAAAATATTTTTA-TAATTAAAT
1 TTAAAAAATATTTTTATTAATTAAAT
* *
465874 TTAAATAA-ATTTTTATTATTTAAAT
1 TTAAAAAATATTTTTATTAATTAAAT
465899 AATAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAAAAAATATTTTTATTAATTAAAT
Found at i:467135 original size:6 final size:6
Alignment explanation
Indices: 467124--467151 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
467114 AAATATTTTT
467124 ATATTA ATATTA ATATTA ATATTA ATAT
1 ATATTA ATATTA ATATTA ATATTA ATAT
467152 ATTTTAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:471772 original size:16 final size:16
Alignment explanation
Indices: 471748--471861 Score: 90
Period size: 16 Copynumber: 7.2 Consensus size: 16
471738 CAAGTTAATT
*
471748 GTTCGGGTCATTTCGA
1 GTTCAGGTCATTTCGA
* *
471764 GTTCAGGTCATTTTGG
1 GTTCAGGTCATTTCGA
* *
471780 GTTCAGGTCATTTTGG
1 GTTCAGGTCATTTCGA
471796 GTTC-GAGTCA-TTCGA
1 GTTCAG-GTCATTTCGA
** * *
471811 -TTTTGAGTCATTTTGG
1 GTTCAG-GTCATTTCGA
*
471827 GTTCGGGTCATTTCGA
1 GTTCAGGTCATTTCGA
*
471843 GTTCAAGTCATTTCGA
1 GTTCAGGTCATTTCGA
471859 GTT
1 GTT
471862 TGGATAATTT
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
14 2 0.03
15 10 0.12
16 65 0.81
17 3 0.04
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.42
Consensus pattern (16 bp):
GTTCAGGTCATTTCGA
Found at i:471822 original size:47 final size:48
Alignment explanation
Indices: 471754--471863 Score: 143
Period size: 47 Copynumber: 2.3 Consensus size: 48
471744 AATTGTTCGG
* * * *
471754 GTCATTTCGAG-TTCAGGTCATTTTGGGTTCAGGTCATTTTGGGTTCGA
1 GTCATTTCGAGTTTGA-GTCATTTTGGGTTCAGGTCATTTCGAGTTCAA
* *
471802 GTCA-TTCGATTTTGAGTCATTTTGGGTTCGGGTCATTTCGAGTTCAA
1 GTCATTTCGAGTTTGAGTCATTTTGGGTTCAGGTCATTTCGAGTTCAA
471849 GTCATTTCGAGTTTG
1 GTCATTTCGAGTTTG
471864 GATAATTTTC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 37 0.70
48 16 0.30
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.43
Consensus pattern (48 bp):
GTCATTTCGAGTTTGAGTCATTTTGGGTTCAGGTCATTTCGAGTTCAA
Found at i:475437 original size:2 final size:2
Alignment explanation
Indices: 475430--475459 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
475420 TTTTCCAATT
*
475430 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
475460 AAAGTAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:475686 original size:21 final size:20
Alignment explanation
Indices: 475662--475725 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
475652 AATTATATTA
475662 ATATTTATATAATATATAATT
1 ATATTTATATAA-ATATAATT
* * *
475683 ATATTTAAATAAAATTTATTTT
1 ATATTTATAT-AAATATA-ATT
*
475705 ATAATTATATAAATAATAATT
1 ATATTTATATAAAT-ATAATT
475726 TAAACCGAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTTATATAAATATAATT
Found at i:475713 original size:43 final size:43
Alignment explanation
Indices: 475640--475725 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 43
475630 AAATTTATTA
*
475640 ATATATTAAAAAAATTATATTAATATTTATAT-AATATATAATT
1 ATATATTAAAAAAATTATATTAATAATTATATAAATA-ATAATT
*
475683 ATAT-TTAAATAAAATT-TATTTTATAATTATATAAATAATAATT
1 ATATATTAAA-AAAATTATA-TTAATAATTATATAAATAATAATT
475726 TAAACCGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
42 7 0.18
43 27 0.71
44 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (43 bp):
ATATATTAAAAAAATTATATTAATAATTATATAAATAATAATT
Found at i:477349 original size:20 final size:20
Alignment explanation
Indices: 477326--477364 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
477316 AAAGATAAAT
*
477326 TAAATAATTCATAAAATTAA
1 TAAATAATTAATAAAATTAA
477346 TAAATAATTAATAAAATTA
1 TAAATAATTAATAAAATTA
477365 TACATATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAATAATTAATAAAATTAA
Found at i:477589 original size:19 final size:19
Alignment explanation
Indices: 477565--477608 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
477555 TAAACTAAAC
477565 AAATCACTAATTTTTAATT
1 AAATCACTAATTTTTAATT
477584 AAATCACTAATTTTTAATT
1 AAATCACTAATTTTTAATT
*
477603 TAATCA
1 AAATCA
477609 ATCTAACCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATCACTAATTTTTAATT
Found at i:477873 original size:14 final size:14
Alignment explanation
Indices: 477827--477874 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
477817 ATTATTTATT
*
477827 TTTATACTATTAAA
1 TTTATACTTTTAAA
*
477841 TTTAATA-TTTTAAT
1 TTT-ATACTTTTAAA
477855 TTTATACTTTTAAA
1 TTTATACTTTTAAA
*
477869 ATTATA
1 TTTATA
477875 AAAAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 3 0.11
14 22 0.79
15 3 0.11
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTATACTTTTAAA
Found at i:479712 original size:18 final size:18
Alignment explanation
Indices: 479689--479735 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
479679 TTTTTTTTTT
479689 AATTTTTTTATATATTTA
1 AATTTTTTTATATATTTA
* *
479707 AATTTTTTAAAATATTTA
1 AATTTTTTTATATATTTA
*
479725 TATTTTTTTAT
1 AATTTTTTTAT
479736 TCGTGTTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
AATTTTTTTATATATTTA
Found at i:481333 original size:16 final size:16
Alignment explanation
Indices: 481312--481345 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
481302 AAATAAATAA
481312 TAATGGAGTTGCCTCT
1 TAATGGAGTTGCCTCT
481328 TAATGGAGTTGCCTCT
1 TAATGGAGTTGCCTCT
481344 TA
1 TA
481346 CATTTGACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (16 bp):
TAATGGAGTTGCCTCT
Found at i:482086 original size:25 final size:24
Alignment explanation
Indices: 482048--482095 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
482038 ATAATTTAAA
* *
482048 TCAAATCAATTTAATTTAAATTAT
1 TCAAATCAACTTAATATAAATTAT
482072 TCAAACTCAACTTAATATAAATTA
1 TCAAA-TCAACTTAATATAAATTA
482096 AATTTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (24 bp):
TCAAATCAACTTAATATAAATTAT
Found at i:482674 original size:15 final size:16
Alignment explanation
Indices: 482656--482685 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
482646 ATTAAGTATG
482656 AATT-TTTTAAATTTT
1 AATTATTTTAAATTTT
482671 AATTATTTTAAATTT
1 AATTATTTTAAATTT
482686 AACTCGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTATTTTAAATTTT
Found at i:485165 original size:2 final size:2
Alignment explanation
Indices: 485158--485193 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
485148 CTTGAAAAGC
*
485158 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
485194 TTACAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:486926 original size:2 final size:2
Alignment explanation
Indices: 486919--486954 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
486909 GCCAAACATA
486919 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
486955 TCATTTTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:487877 original size:5 final size:5
Alignment explanation
Indices: 487867--487909 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
487857 GACGAAATAG
* *
487867 ATATA ATATAA AAATA ATTAAA ATATA ATATA ATATA ATATA A
1 ATATA ATAT-A ATATA A-TATA ATATA ATATA ATATA ATATA A
487910 ATTTATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 25 0.78
6 7 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
ATATA
Found at i:487912 original size:27 final size:29
Alignment explanation
Indices: 487867--487922 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
487857 GACGAAATAG
487867 ATATAATATAAAAATAA-TTA-AAATATA
1 ATATAATATAAAAATAATTTATAAATATA
*
487894 ATATAATAT-AATATAAATTTATAAATATA
1 ATATAATATAAAAAT-AATTTATAAATATA
487923 TTAAATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 4 0.16
27 11 0.44
28 3 0.12
29 7 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
ATATAATATAAAAATAATTTATAAATATA
Found at i:487918 original size:40 final size:39
Alignment explanation
Indices: 487873--487977 Score: 97
Period size: 40 Copynumber: 2.7 Consensus size: 39
487863 ATAGATATAA
487873 TATAAAAATAATTAAA-ATATAATATAATATAATATAAATT
1 TATAAAAAT-ATTAAATATATAATATAATATAATA-AAATT
* * * * *
487913 TATAAATATATTAAATTTATATTATATTATATTAAAATT
1 TATAAAAATATTAAATATATAATATAATATAATAAAATT
* * * *
487952 TATATAAAT-TTATATTTGTAATATAA
1 TATAAAAATATTAAATATATAATATAA
487978 AAATAATATA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
38 13 0.25
39 18 0.34
40 22 0.42
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (39 bp):
TATAAAAATATTAAATATATAATATAATATAATAAAATT
Found at i:487920 original size:19 final size:17
Alignment explanation
Indices: 487907--487965 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 17
487897 TAATATAATA
487907 TAAATTTATAAATATAT
1 TAAATTTATAAATATAT
*
487924 TAAATTTAT-ATTATAT
1 TAAATTTATAAATATAT
* *
487940 TATA-TTA-AAATTTAT
1 TAAATTTATAAATATAT
487955 ATAAATTTATA
1 -TAAATTTATA
487966 TTTGTAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
15 8 0.24
16 12 0.36
17 12 0.36
18 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAAATTTATAAATATAT
Found at i:487960 original size:10 final size:10
Alignment explanation
Indices: 487904--487966 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
487894 ATATAATATA
487904 ATATAAA-TT
1 ATATAAATTT
*
487913 -TATAAATAT
1 ATATAAATTT
487922 AT-TAAATTT
1 ATATAAATTT
*
487931 ATAT-TATATT
1 ATATAAAT-TT
487941 ATATTAAAATTT
1 ATA-T-AAATTT
487953 ATATAAATTT
1 ATATAAATTT
487963 ATAT
1 ATAT
487967 TTGTAATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
8 6 0.14
9 11 0.26
10 17 0.40
11 2 0.05
12 5 0.12
13 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
ATATAAATTT
Found at i:487964 original size:22 final size:21
Alignment explanation
Indices: 487894--487967 Score: 70
Period size: 22 Copynumber: 3.7 Consensus size: 21
487884 TTAAAATATA
*
487894 ATATAATATAATA-TAAA-TT
1 ATATAATATTATATTAAATTT
487913 -TATAA-A-TATATTAAATTT
1 ATATAATATTATATTAAATTT
*
487931 ATATTATATTATATTAAAATTT
1 ATATAATATTATATT-AAATTT
487953 ATATAA-ATTTATATT
1 ATATAATA-TTATATT
487968 TGTAATATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
16 3 0.07
17 5 0.11
18 7 0.16
19 4 0.09
20 1 0.02
21 7 0.16
22 18 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATAATATTATATTAAATTT
Found at i:488069 original size:78 final size:78
Alignment explanation
Indices: 487975--488132 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
487965 ATTTGTAATA
487975 TAAAAATAATATAAATATAATTTGAATACGTTAATCGTTAAATTTAAATTAAATCACTTAACTAG
1 TAAAAATAATATAAATATAATTTGAATACGTTAATCGTTAAATTTAAATTAAATCACTTAACTAG
488040 AACTAGTTAATTT
66 AACTAGTTAATTT
488053 TAAAAATAATATAAATATAATTTGAATACGTTAATCGTTAAATTTAAATTAAATCACTTAACTAG
1 TAAAAATAATATAAATATAATTTGAATACGTTAATCGTTAAATTTAAATTAAATCACTTAACTAG
488118 AACTAGTTAATTT
66 AACTAGTTAATTT
488131 TA
1 TA
488133 CTATTTGTGC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (78 bp):
TAAAAATAATATAAATATAATTTGAATACGTTAATCGTTAAATTTAAATTAAATCACTTAACTAG
AACTAGTTAATTT
Found at i:488523 original size:24 final size:25
Alignment explanation
Indices: 488496--488543 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
488486 AACATTAATT
*
488496 AAAAACACTT-AAAATATTATTTTC
1 AAAAACAATTCAAAATATTATTTTC
*
488520 AAAAACAATTCAATATATTATTTT
1 AAAAACAATTCAAAATATTATTTT
488544 TTATTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAAACAATTCAAAATATTATTTTC
Found at i:494809 original size:8 final size:8
Alignment explanation
Indices: 494772--494817 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
494762 AGTAATTAAG
494772 AAAAATAA
1 AAAAATAA
494780 AAATAATTAA
1 AAA-AA-TAA
*
494790 AAAAATAG
1 AAAAATAA
*
494798 AAAAACAA
1 AAAAATAA
494806 AAAAATAA
1 AAAAATAA
494814 AAAA
1 AAAA
494818 TAATTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 22 0.69
9 4 0.12
10 6 0.19
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (8 bp):
AAAAATAA
Found at i:495699 original size:14 final size:14
Alignment explanation
Indices: 495682--495709 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
495672 ATATTATTAA
495682 AATATTTTTATATT
1 AATATTTTTATATT
495696 AATATTTTTATATT
1 AATATTTTTATATT
495710 TTTAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:496867 original size:16 final size:17
Alignment explanation
Indices: 496836--496869 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
496826 ATAATTTAAA
496836 TTTAAATAAAAGATTAT
1 TTTAAATAAAAGATTAT
*
496853 TTTAATTAAAA-ATTAT
1 TTTAAATAAAAGATTAT
496869 T
1 T
496870 ATTTCATGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTAAATAAAAGATTAT
Found at i:497057 original size:69 final size:69
Alignment explanation
Indices: 496942--497072 Score: 210
Period size: 69 Copynumber: 1.9 Consensus size: 69
496932 ATCCGTTTAG
496942 TGGTATGGCATGATGAAGAGAATTCCACCATGCCATACCATGTTATCTAAATGCATTGCAAAGGT
1 TGGTATGGCATGATGAAGAGAATTCCACCATGCCATACCATGTTATCTAAATGCATTGCAAAGGT
497007 CTAT
66 CTAT
* * * *
497011 TGGTATGGCATGATGGAGAGAATTCTA-CATGCCTTACCATTTTTATCTAAATGCATTGCAAA
1 TGGTATGGCATGATGAAGAGAATTCCACCATGCCATACCA-TGTTATCTAAATGCATTGCAAA
497073 CCATGGCTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
68 11 0.19
69 46 0.81
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (69 bp):
TGGTATGGCATGATGAAGAGAATTCCACCATGCCATACCATGTTATCTAAATGCATTGCAAAGGT
CTAT
Found at i:497482 original size:36 final size:36
Alignment explanation
Indices: 497435--497508 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
497425 CGAAAGCATG
497435 AATATAACATAGAGATACTACTAATTAATTTAATTA
1 AATATAACATAGAGATACTACTAATTAATTTAATTA
497471 AATATAACATAGAGATACTACTAATTAATTTAATTA
1 AATATAACATAGAGATACTACTAATTAATTTAATTA
497507 AA
1 AA
497509 GGAAATGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (36 bp):
AATATAACATAGAGATACTACTAATTAATTTAATTA
Found at i:497855 original size:24 final size:23
Alignment explanation
Indices: 497807--497855 Score: 55
Period size: 24 Copynumber: 2.0 Consensus size: 23
497797 TATTAAACTC
497807 AAATAATTATTTATTAATTAATTA
1 AAATAATTATTTATTAATT-ATTA
*
497831 AAATAATATTTTTATTTAATT-TTA
1 AAATAAT-TATTTA-TTAATTATTA
497855 A
1 A
497856 TTATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 11 0.50
25 5 0.23
26 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AAATAATTATTTATTAATTATTA
Found at i:503540 original size:2 final size:2
Alignment explanation
Indices: 503533--503557 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
503523 AACAGTGGAA
503533 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
503558 TTTTTTGCGT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:504544 original size:19 final size:19
Alignment explanation
Indices: 504520--504568 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
504510 ATATATATAT
*
504520 ATATATATAGATCAAATTC
1 ATATATACAGATCAAATTC
* *
504539 ATATATACGGATTAAATTC
1 ATATATACAGATCAAATTC
504558 ATATATACAGA
1 ATATATACAGA
504569 GAAAATTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (19 bp):
ATATATACAGATCAAATTC
Found at i:504574 original size:19 final size:19
Alignment explanation
Indices: 504533--504575 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
504523 TATATAGATC
* **
504533 AAATTCATATATACGGATT
1 AAATTCATATATACAGAGA
504552 AAATTCATATATACAGAGA
1 AAATTCATATATACAGAGA
504571 AAATT
1 AAATT
504576 GAACTTGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (19 bp):
AAATTCATATATACAGAGA
Found at i:504740 original size:2 final size:2
Alignment explanation
Indices: 504733--504759 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
504723 TATTAAGAAA
504733 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
504760 TCGTTTAATT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:505816 original size:21 final size:23
Alignment explanation
Indices: 505791--505835 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
505781 GATAAATGTG
505791 ATTATGTTATT-AAAT-TTAATA
1 ATTATGTTATTAAAATATTAATA
*
505812 ATTATTTTATTAAAATATTAATA
1 ATTATGTTATTAAAATATTAATA
505835 A
1 A
505836 AAATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 4 0.19
23 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTATGTTATTAAAATATTAATA
Found at i:505841 original size:23 final size:21
Alignment explanation
Indices: 505797--505841 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
505787 TGTGATTATG
**
505797 TTATTAAATTTAATAATTATT
1 TTATTAAATTTAATAAAAATT
505818 TTATTAAAATATTAATAAAAATT
1 TTATT-AAAT-TTAATAAAAATT
505841 T
1 T
505842 AAAAATATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 4 0.20
23 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATTAAATTTAATAAAAATT
Found at i:506657 original size:21 final size:21
Alignment explanation
Indices: 506617--506657 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
506607 TTTTTTCATT
*
506617 TGTAAGTTCTTGTTATTTTTG
1 TGTAAGTTCATGTTATTTTTG
506638 TGTAATGTTCATGTTATTTT
1 TGTAA-GTTCATGTTATTTT
506658 AACAACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.17, C:0.05, G:0.17, T:0.61
Consensus pattern (21 bp):
TGTAAGTTCATGTTATTTTTG
Found at i:507059 original size:19 final size:18
Alignment explanation
Indices: 507014--507061 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
507004 GTATTTTATA
*
507014 ATTAAAAATTTTAATATT
1 ATTAATAATTTTAATATT
*
507032 ATTAGATAATTTTAAATTTT
1 ATTA-ATAATTTT-AATATT
*
507052 TTTAATAATT
1 ATTAATAATT
507062 GAATATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 13 0.52
20 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAATAATTTTAATATT
Found at i:508304 original size:20 final size:20
Alignment explanation
Indices: 508277--508319 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
508267 ATGATTTATT
*
508277 TAAAAAATAGATTCTTTTTAA
1 TAAAAATTA-ATTCTTTTTAA
508298 TAAAAATTAATTCTTTTTAA
1 TAAAAATTAATTCTTTTTAA
508318 TA
1 TA
508320 GAGATAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (20 bp):
TAAAAATTAATTCTTTTTAA
Found at i:509821 original size:25 final size:25
Alignment explanation
Indices: 509793--509865 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
509783 TGATATAATA
509793 ATCAACAATTGACATAAATAAAAAT
1 ATCAACAATTGACATAAATAAAAAT
* *
509818 ATCAA-AA--G--AT-GAT-ATAAT
1 ATCAACAATTGACATAAATAAAAAT
509836 AATCAACAATTGACATAAATAAAAAT
1 -ATCAACAATTGACATAAATAAAAAT
509862 ATCA
1 ATCA
509866 TGTCATTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 4 0.11
19 7 0.19
20 4 0.11
22 2 0.06
24 4 0.11
25 11 0.31
26 4 0.11
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (25 bp):
ATCAACAATTGACATAAATAAAAAT
Found at i:509838 original size:44 final size:44
Alignment explanation
Indices: 509775--509865 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
509765 ACATTGTTAG
509775 TCAAAAGATGATATAATAATCAACAATTGACATAAATAAAAATA
1 TCAAAAGATGATATAATAATCAACAATTGACATAAATAAAAATA
509819 TCAAAAGATGATATAATAATCAACAATTGACATAAATAAAAATA
1 TCAAAAGATGATATAATAATCAACAATTGACATAAATAAAAATA
509863 TCA
1 TCA
509866 TGTCATTATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.58, C:0.10, G:0.07, T:0.25
Consensus pattern (44 bp):
TCAAAAGATGATATAATAATCAACAATTGACATAAATAAAAATA
Found at i:510198 original size:24 final size:24
Alignment explanation
Indices: 510155--510200 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
510145 TAAATAACAC
**
510155 TATATGTATTTATTTTTAAAATTT
1 TATATGTATTTATTAATAAAATTT
*
510179 TATATTTATTTATTAATAAAAT
1 TATATGTATTTATTAATAAAAT
510201 AAGATCATAA
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:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TATATGTATTTATTAATAAAATTT
Found at i:510587 original size:2 final size:2
Alignment explanation
Indices: 510580--510609 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
510570 AGCATTTTCC
510580 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
510610 GTGTGGAAGA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:511100 original size:24 final size:25
Alignment explanation
Indices: 511067--511122 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
511057 GTATTAATAA
*
511067 ATAAATATTTTTATTTAAAATTAAT
1 ATAAATATTTTAATTTAAAATTAAT
* *
511092 ATAAA-ATTTTAATTTAATATTATT
1 ATAAATATTTTAATTTAAAATTAAT
*
511116 GTAAATA
1 ATAAATA
511123 ATAAAACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
ATAAATATTTTAATTTAAAATTAAT
Found at i:511596 original size:19 final size:18
Alignment explanation
Indices: 511564--511603 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
511554 CATTTTTTAA
*
511564 TTAAATAATATATATTGT
1 TTAAATAATATATATTAT
*
511582 TTAATATAATTTATATTAT
1 TTAA-ATAATATATATTAT
511601 TTA
1 TTA
511604 TAAAATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TTAAATAATATATATTAT
Found at i:511618 original size:22 final size:22
Alignment explanation
Indices: 511584--511637 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
511574 TATATTGTTT
* *
511584 AATATAATTTATATTAT-TTATAA
1 AATA-AATATATATAATATTAT-A
511607 AATAAATATATATAATATTATA
1 AATAAATATATATAATATTATA
*
511629 TATAAATAT
1 AATAAATAT
511638 TAAAAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATAAATATATATAATATTATA
Found at i:514473 original size:27 final size:27
Alignment explanation
Indices: 514438--514500 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
514428 CCTTTGACAT
*
514438 TTTTTAAAAAT-AAT-AATCTTTCATCA
1 TTTTAAAAAATAAATAAAT-TTTCATCA
*
514464 TTTTAAAAAATAAATCAAATTTTGATCA
1 TTTTAAAAAATAAAT-AAATTTTCATCA
514492 TTTTAAAAA
1 TTTTAAAAA
514501 TGAATTACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 10 0.31
27 3 0.09
28 16 0.50
29 3 0.09
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.43
Consensus pattern (27 bp):
TTTTAAAAAATAAATAAATTTTCATCA
Found at i:515525 original size:2 final size:2
Alignment explanation
Indices: 515518--515550 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
515508 ATGGAACATC
515518 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
515551 ATGTGAGGCC
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:515768 original size:2 final size:2
Alignment explanation
Indices: 515761--515810 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
515751 GTGGAACATC
*
515761 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
515802 AT AT A- AT AT
1 AT AT AT AT AT
515811 GACGCCTACG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:516073 original size:2 final size:2
Alignment explanation
Indices: 516066--516101 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
516056 ATGAAACATC
516066 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
516102 GACGCCTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:521432 original size:18 final size:17
Alignment explanation
Indices: 521404--521468 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 17
521394 ACTTCATCAA
521404 ATATAAAATATCAAAATTT
1 ATAT-AAATAT-AAAATTT
521423 ATATAAATATAAAATATT
1 ATATAAATATAAAAT-TT
**
521441 -T-TAAATATAATAAAAT
1 ATATAAATATAA-AATTT
521457 ATATAAATATAA
1 ATATAAATATAA
521469 TATAAATACA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 10 0.25
17 9 0.22
18 17 0.43
19 4 0.10
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATAAATATAAAATTT
Found at i:521433 original size:8 final size:8
Alignment explanation
Indices: 521422--521504 Score: 50
Period size: 7 Copynumber: 10.2 Consensus size: 8
521412 TATCAAAATT
521422 TATATAAA
1 TATATAAA
521430 TATA-AAA
1 TATATAAA
*
521437 TATTTTAAA
1 TA-TATAAA
521446 TATAATAAAA
1 TAT-AT-AAA
521456 TATATAAATA
1 TATAT-AA-A
521466 TAATATAAA
1 T-ATATAAA
*
521475 TACATAAA
1 TATATAAA
*
521483 T-TATCAA
1 TATATAAA
521490 -AT-TAAA
1 TATATAAA
521496 TA-ATAAA
1 TATATAAA
521503 TA
1 TA
521505 AATACTAATG
Statistics
Matches: 60, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
6 3 0.05
7 17 0.28
8 13 0.22
9 13 0.22
10 10 0.17
11 4 0.07
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (8 bp):
TATATAAA
Found at i:521441 original size:19 final size:19
Alignment explanation
Indices: 521404--521474 Score: 58
Period size: 19 Copynumber: 3.7 Consensus size: 19
521394 ACTTCATCAA
*
521404 ATATAAAATATCAAA-ATTT
1 ATAT-AAATATAAAATATTT
521423 ATATAAATATAAAATATTT
1 ATATAAATATAAAATATTT
*
521442 -TA-AATATAATAAAATATAT
1 ATATAA-AT-ATAAAATATTT
*
521461 AAATATAATATAAA
1 ATATA-AATATAAA
521475 TACATAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
17 2 0.05
18 13 0.30
19 18 0.42
20 6 0.14
21 3 0.07
22 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATAAATATAAAATATTT
Found at i:521453 original size:25 final size:25
Alignment explanation
Indices: 521340--521466 Score: 80
Period size: 25 Copynumber: 4.8 Consensus size: 25
521330 ATAATTATAT
*
521340 ATATAATACAA-ATAAAATAATTAAA
1 ATATAATA-AATATAAAATATTTAAA
*
521365 ATATAATATGATATTAATACATATTTTAAA
1 ATATAATA-AATA-TAA-A-ATA-TTTAAA
* * *
521395 CT-TCATCAAATATAAAATA-TCAAA
1 ATATAAT-AAATATAAAATATTTAAA
* *
521419 ATTTATATAAATATAAAATATTTTAA
1 ATATA-ATAAATATAAAATATTTAAA
521445 ATATAATAAAATATATAAATAT
1 ATATAAT-AAATATA-AAATAT
521467 AATATAAATA
Statistics
Matches: 79, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
24 5 0.06
25 24 0.30
26 20 0.25
27 10 0.13
28 4 0.05
29 9 0.11
30 7 0.09
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (25 bp):
ATATAATAAATATAAAATATTTAAA
Found at i:521469 original size:18 final size:18
Alignment explanation
Indices: 521422--521483 Score: 74
Period size: 18 Copynumber: 3.5 Consensus size: 18
521412 TATCAAAATT
*
521422 TATATAAATATAA-AATA
1 TATATAAATATAATAAAA
*
521439 T-TTTAAATATAATAAAA
1 TATATAAATATAATAAAA
521456 TATATAAATATAATATAAA
1 TATATAAATATAATA-AAA
*
521475 TACATAAAT
1 TATATAAAT
521484 TATCAAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
16 10 0.26
17 5 0.13
18 12 0.32
19 11 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
TATATAAATATAATAAAA
Found at i:522306 original size:14 final size:14
Alignment explanation
Indices: 522284--522317 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
522274 TATTTTACAC
* *
522284 ATATTTAAATATGA
1 ATATATAAATATAA
522298 ATATATAAATATAA
1 ATATATAAATATAA
522312 ATATAT
1 ATATAT
522318 TCTTTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
ATATATAAATATAA
Found at i:522361 original size:2 final size:2
Alignment explanation
Indices: 522356--522384 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
522346 AAAAATTAAG
522356 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
522385 CCAACACATA
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:526312 original size:14 final size:15
Alignment explanation
Indices: 526295--526336 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
526285 ATTAATTAAA
*
526295 TAAATAAGCA-TATT
1 TAAATAAGAATTATT
*
526309 TAAATATGAATTATT
1 TAAATAAGAATTATT
526324 TAAATAA-AATTAT
1 TAAATAAGAATTAT
526337 ATGCATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (15 bp):
TAAATAAGAATTATT
Found at i:526736 original size:21 final size:20
Alignment explanation
Indices: 526710--526750 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
526700 ATTTATCCTT
*
526710 TTATTTTATTTTGTTAGTTTA
1 TTATTTAATTTTGTTA-TTTA
*
526731 TTATTTAATTTTTTTATTTA
1 TTATTTAATTTTGTTATTTA
526751 AATACTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (20 bp):
TTATTTAATTTTGTTATTTA
Found at i:527861 original size:33 final size:32
Alignment explanation
Indices: 527810--527901 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 32
527800 TTATTTTTTT
*
527810 ATTTTAATTATATAAATAATATATATCTAAATAA
1 ATTTTAA-TATATTAATAATATATAT-TAAATAA
* **
527844 ATTTTAATATATTAATAATTTATATTTTATAA
1 ATTTTAATATATTAATAATATATATTAAATAA
* * *
527876 AATTTAACATATTTATATATATATAT
1 ATTTTAATATATTAATA-ATATATAT
527902 ATATATAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
32 19 0.39
33 23 0.47
34 7 0.14
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (32 bp):
ATTTTAATATATTAATAATATATATTAAATAA
Found at i:528810 original size:2 final size:2
Alignment explanation
Indices: 528805--528831 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
528795 TTTTAGTGTG
528805 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
528832 TATTTTAAGT
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:528925 original size:13 final size:14
Alignment explanation
Indices: 528901--528929 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
528891 ATATTATGAT
528901 ATTTTTATAAAAAA
1 ATTTTTATAAAAAA
528915 ATTTTTA-AAAAAA
1 ATTTTTATAAAAAA
528928 AT
1 AT
528930 CTCTTGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTTTTATAAAAAA
Found at i:529064 original size:20 final size:21
Alignment explanation
Indices: 529026--529064 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
529016 TTTGATAATT
* *
529026 AAAATTAAATATTTTAATTAG
1 AAAATTAAATAATTAAATTAG
529047 AAAATT-AATAATTAAATT
1 AAAATTAAATAATTAAATT
529065 TTTATTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
AAAATTAAATAATTAAATTAG
Found at i:529102 original size:17 final size:16
Alignment explanation
Indices: 529068--529121 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
529058 TTAAATTTTT
*
529068 ATTTTAATTTATTAAA
1 ATTTTAATATATTAAA
529084 ATTTT-ATATAATATAAA
1 ATTTTAATAT-AT-TAAA
529101 ATTATTAATATATTAAA
1 ATT-TTAATATATTAAA
529118 ATTT
1 ATTT
529122 AGAGGAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 3 0.09
16 8 0.24
17 14 0.42
18 4 0.12
19 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTAATATATTAAA
Found at i:530727 original size:20 final size:20
Alignment explanation
Indices: 530685--530765 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 20
530675 ATTTGATAAT
530685 TTTAAAATATT-TATTTTATTA
1 TTTAAAATATTAT-TTTTA-TA
530706 TTTAAAATATTATTTTTATA
1 TTTAAAATATTATTTTTATA
* *
530726 -TTAATAATTATATATTATTAAA
1 TTTAA-AA-TAT-TATTTTTATA
*
530748 TTTAAAA-ATAATTTTTAT
1 TTTAAAATATTATTTTTAT
530766 TGATTAAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
19 10 0.20
20 6 0.12
21 19 0.38
22 11 0.22
23 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTAAAATATTATTTTTATA
Found at i:531277 original size:5 final size:5
Alignment explanation
Indices: 531267--531305 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
531257 TTTAATAAAT
*
531267 TTATA TTATA TTAATA TTATTT TTATA TTATA TTATA TT
1 TTATA TTATA TT-ATA TTA-TA TTATA TTATA TTATA TT
531306 TTAACTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 21 0.70
6 9 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:531294 original size:17 final size:17
Alignment explanation
Indices: 531172--531308 Score: 60
Period size: 17 Copynumber: 8.4 Consensus size: 17
531162 TATTAAAAAA
*
531172 ATTTTATATATATATCA-
1 ATTTTATAT-TATATTAT
531189 ATTTTTATATTTATATTAT
1 A-TTTTATA-TTATATTAT
* **
531208 A-ATTATATT-TAAAAT
1 ATTTTATATTATATTAT
*
531223 ATTTTA-A-TACATTACT
1 ATTTTATATTATATTA-T
* * **
531239 AATTCATATTATA-TCG
1 ATTTTATATTATATTAT
*
531255 ATTTTA-A-TAAATT-T
1 ATTTTATATTATATTAT
*
531269 ATATTATATTAATATTAT
1 ATTTTATATT-ATATTAT
531287 -TTTTATATTATATTAT
1 ATTTTATATTATATTAT
531303 ATTTTA
1 ATTTTA
531309 ACTATTTTTT
Statistics
Matches: 86, Mismatches: 20, Indels: 28
0.64 0.15 0.21
Matches are distributed among these distances:
14 9 0.10
15 11 0.13
16 22 0.26
17 25 0.29
18 17 0.20
19 2 0.02
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (17 bp):
ATTTTATATTATATTAT
Found at i:531304 original size:27 final size:28
Alignment explanation
Indices: 531267--531323 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
531257 TTTAATAAAT
531267 TTATATTATA-TTAA-TATTATTTTTATA
1 TTATATTATATTTAACTATT-TTTTTATA
531294 TTATATTATATTTTAACTATTTTTTTATA
1 TTATATTATA-TTTAACTATTTTTTTATA
531323 T
1 T
531324 GTATCATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 10 0.37
29 13 0.48
30 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (28 bp):
TTATATTATATTTAACTATTTTTTTATA
Found at i:531457 original size:17 final size:16
Alignment explanation
Indices: 531431--531462 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
531421 TTTTTATTTA
531431 AATTTATTTATAAATT
1 AATTTATTTATAAATT
531447 AATTTAGTTTATAAAT
1 AATTTA-TTTATAAAT
531463 ATTATTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
AATTTATTTATAAATT
Found at i:531472 original size:13 final size:13
Alignment explanation
Indices: 531429--531486 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 13
531419 GATTTTTATT
531429 TAAAT-TTATTTA
1 TAAATATTATTTA
531441 TAAATTAATTTAGTTTA
1 TAAA-T-A-TTA-TTTA
531458 TAAATATTATTTA
1 TAAATATTATTTA
**
531471 TATTTATTATTTA
1 TAAATATTATTTA
531484 TAA
1 TAA
531487 TTAATAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
12 4 0.11
13 18 0.47
14 3 0.08
15 1 0.03
16 4 0.11
17 8 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:533959 original size:26 final size:27
Alignment explanation
Indices: 533930--533980 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
533920 TATCATAAAT
533930 TTAATATTATTAAAATA-AATTTTATC
1 TTAATATTATTAAAATATAATTTTATC
* *
533956 TTAATTTTTTTAAAATATAATTTTA
1 TTAATATTATTAAAATATAATTTTA
533981 AAATATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (27 bp):
TTAATATTATTAAAATATAATTTTATC
Found at i:533998 original size:15 final size:13
Alignment explanation
Indices: 533963--533997 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
533953 ATCTTAATTT
533963 TTTTAAAATATAA
1 TTTTAAAATATAA
533976 TTTTAAAATATAA
1 TTTTAAAATATAA
533989 TTATTAAAA
1 TT-TTAAAA
533998 AAAATTACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTTAAAATATAA
Found at i:537113 original size:22 final size:22
Alignment explanation
Indices: 537079--537143 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 22
537069 ATTTAAATAT
*
537079 TAAAATTATTTTTTATAAATTAA
1 TAAAAATA-TTTTTATAAATTAA
*
537102 TAAAAATA-TTTTAT--ATTAT
1 TAAAAATATTTTTATAAATTAA
537121 TAAAAGATAATTTTTATTAAATT
1 TAAAA-AT-ATTTTTA-TAAATT
537144 TACTTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
19 9 0.26
20 2 0.06
21 7 0.21
22 5 0.15
23 8 0.24
25 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TAAAAATATTTTTATAAATTAA
Found at i:537124 original size:19 final size:20
Alignment explanation
Indices: 537097--537140 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
537087 TTTTTTATAA
537097 ATTAATAAAA-AT-ATTTTAT
1 ATTAATAAAAGATAATTTT-T
*
537116 ATTATTAAAAGATAATTTTT
1 ATTAATAAAAGATAATTTTT
537136 ATTAA
1 ATTAA
537141 ATTTACTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 9 0.43
20 7 0.33
21 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTAATAAAAGATAATTTTT
Found at i:537427 original size:2 final size:2
Alignment explanation
Indices: 537422--537460 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
537412 GTTCTCTCAG
537422 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- 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 TA T
537461 GTATGCATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:537470 original size:23 final size:23
Alignment explanation
Indices: 537422--537470 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
537412 GTTCTCTCAG
*
537422 TATATAATATATATATATATATA
1 TATATAATATATATATATATACA
* * *
537445 TATATATTATATATATGTATGCA
1 TATATAATATATATATATATACA
537468 TAT
1 TAT
537471 CAGATTGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
TATATAATATATATATATATACA
Found at i:538505 original size:16 final size:16
Alignment explanation
Indices: 538467--538510 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
538457 TAAAAACTTA
538467 TTTTTTTTAAACAAAT
1 TTTTTTTTAAACAAAT
**
538483 TTATTTTTTATTCAAAT
1 TT-TTTTTTAAACAAAT
538500 TTTTTTTTAAA
1 TTTTTTTTAAA
538511 ATTTAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTTTTAAACAAAT
Found at i:540689 original size:5 final size:5
Alignment explanation
Indices: 540675--540741 Score: 50
Period size: 5 Copynumber: 13.2 Consensus size: 5
540665 TACTCGAATT
* *
540675 ATTT- ATTTA ATTTA ATTTA GATTAA ATTTAA ATTTA TTTTTA A-TTA
1 ATTTA ATTTA ATTTA ATTTA -ATTTA ATTT-A ATTTA -ATTTA ATTTA
*
540721 GA-TTA ATTTA ATTCA ATTTA A
1 -ATTTA ATTTA ATTTA ATTTA A
540742 ATTATTATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
4 8 0.16
5 30 0.59
6 13 0.25
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (5 bp):
ATTTA
Found at i:540729 original size:37 final size:37
Alignment explanation
Indices: 540672--540766 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 37
540662 TAATACTCGA
* *
540672 ATTAT-TTATTTAATTTAATTTAGATTAAATTTAAATTT
1 ATTATATTAATTAAATTAATTTA-ATTAAATTTAAA-TT
* *
540710 ATT-T-TTAATTAGATTAATTTAATTCAATTTAAATT
1 ATTATATTAATTAAATTAATTTAATTAAATTTAAATT
*
540745 ATTATATTAATTAAAATAATTT
1 ATTATATTAATTAAATTAATTT
540767 TTTTATTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
35 5 0.10
36 12 0.24
37 29 0.59
38 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (37 bp):
ATTATATTAATTAAATTAATTTAATTAAATTTAAATT
Found at i:541042 original size:16 final size:15
Alignment explanation
Indices: 541023--541062 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
541013 GTTATAAATA
541023 TTAAAATTAAAATTT
1 TTAAAATTAAAATTT
* *
541038 TTTAAATGTCAAATTT
1 TTAAAAT-TAAAATTT
541054 TTAAAATTA
1 TTAAAATTA
541063 TTGTATGAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAAAATTAAAATTT
Found at i:541504 original size:20 final size:21
Alignment explanation
Indices: 541467--541505 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
541457 ATTTTTTAAA
* *
541467 AAAAATTATTTTTTAATTATT
1 AAAAATTATTCTTAAATTATT
541488 AAAAA-TATTCTTAAATTA
1 AAAAATTATTCTTAAATTA
541506 AAAACTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAAATTATTCTTAAATTATT
Found at i:541564 original size:16 final size:16
Alignment explanation
Indices: 541545--541591 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
541535 ATTTTATTTT
541545 AATTTAATTTTTTAAA
1 AATTTAATTTTTTAAA
* * *
541561 AATTAAATATTATAAA
1 AATTTAATTTTTTAAA
*
541577 TATTT-ATTTTTTAAA
1 AATTTAATTTTTTAAA
541592 TAAATCAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTTAATTTTTTAAA
Found at i:541932 original size:2 final size:2
Alignment explanation
Indices: 541925--541965 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
541915 TGGTACGATC
541925 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
541966 CCCCCCCTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:545013 original size:24 final size:27
Alignment explanation
Indices: 544963--545018 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
544953 AAGAACTAAT
* *
544963 AAATCAATATATAATTATTTCTTTAAA
1 AAATTAATATATAATTATTTCTATAAA
544990 AAATTAATATATAA-T-TTTC-ATAAA
1 AAATTAATATATAATTATTTCTATAAA
545014 AAATT
1 AAATT
545019 TCCTTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 9 0.33
25 4 0.15
26 1 0.04
27 13 0.48
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (27 bp):
AAATTAATATATAATTATTTCTATAAA
Found at i:545224 original size:65 final size:65
Alignment explanation
Indices: 545120--545248 Score: 195
Period size: 65 Copynumber: 2.0 Consensus size: 65
545110 TTCCTTCTAC
* * * * *
545120 TCTCACACTCTTAGCTTCTTTACTCTTGTTGTTGGTTTTCACCACGTAAGTGCACGTATCGTAAA
1 TCTCACACTCTTAGCATCTTGACTATTGTTGTTGGTTTTCACCACGCAAGTGCACATATCGTAAA
* *
545185 TCTCACACTCTTATCATCTTGACTATTGTTGTTGGTTTTCACCATGCAAGTGCACATATCGTAA
1 TCTCACACTCTTAGCATCTTGACTATTGTTGTTGGTTTTCACCACGCAAGTGCACATATCGTAA
545249 CAAGTAATGT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.40
Consensus pattern (65 bp):
TCTCACACTCTTAGCATCTTGACTATTGTTGTTGGTTTTCACCACGCAAGTGCACATATCGTAAA
Found at i:549384 original size:8 final size:8
Alignment explanation
Indices: 549331--549392 Score: 52
Period size: 8 Copynumber: 7.8 Consensus size: 8
549321 TGTGTGTATG
*
549331 TATATGTA
1 TATATATA
*
549339 TATGTATA
1 TATATATA
* *
549347 TGTATATG
1 TATATATA
*
549355 TATATGTA
1 TATATATA
* *
549363 TGTGTATA
1 TATATATA
*
549371 TATATATT
1 TATATATA
549379 TATATATA
1 TATATATA
549387 TATATA
1 TATATA
549393 GTGATATAAA
Statistics
Matches: 39, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (8 bp):
TATATATA
Found at i:549392 original size:6 final size:6
Alignment explanation
Indices: 549327--549389 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
549317 CATATGTGTG
* *
549327 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TGTGTA TATATA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
* *
549375 TATTTA TATATA TAT
1 TATGTA TATGTA TAT
549390 ATAGTGATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TATGTA
Found at i:550553 original size:30 final size:34
Alignment explanation
Indices: 550494--550555 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
550484 GAAATAAAAT
550494 TAAAATAAAATAATTATAATAATAATTTAATTCAA
1 TAAAATAAAATAATTATAATAAT-ATTTAATTCAA
550529 TAAAATAAAAT-A-TAT-ATAAT-TTTAATT
1 TAAAATAAAATAATTATAATAATATTTAATT
550556 TTCAACAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 7 0.26
32 5 0.19
33 3 0.11
34 1 0.04
35 11 0.41
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (34 bp):
TAAAATAAAATAATTATAATAATATTTAATTCAA
Found at i:550744 original size:2 final size:2
Alignment explanation
Indices: 550737--550768 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
550727 AACTGAAATA
550737 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
550769 CAAACATGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:557107 original size:40 final size:41
Alignment explanation
Indices: 557054--557137 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 41
557044 GTGAAGAATA
557054 AAAGTAAATGCGCATCATTCAACCATCACAAGCACAAG-AT
1 AAAGTAAATGCGCATCATTCAACCATCACAAGCACAAGCAT
557094 AAAGTAAATGCGCATCATTCAACCATCACAAGCACAAGCAT
1 AAAGTAAATGCGCATCATTCAACCATCACAAGCACAAGCAT
557135 AAA
1 AAA
557138 CTGCACACAC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 38 0.88
41 5 0.12
ACGTcount: A:0.46, C:0.25, G:0.12, T:0.17
Consensus pattern (41 bp):
AAAGTAAATGCGCATCATTCAACCATCACAAGCACAAGCAT
Found at i:560516 original size:40 final size:40
Alignment explanation
Indices: 560422--560541 Score: 129
Period size: 40 Copynumber: 3.0 Consensus size: 40
560412 TTAACATTTT
* * *
560422 ATTTATATTTATTTAAAATT-TATTA-ATTTTAAAAAATAA
1 ATTTATATTTATTTAAAGTTAT-TTATATTTTAAATAATTA
* *
560461 ATTATAAATTGTATTTAAAGTTATTTATATTATAAATAATTA
1 ATT-TATATT-TATTTAAAGTTATTTATATTTTAAATAATTA
*
560503 ATTTATATTTATTT-AAGTTTATTTATATTTTTAATAATT
1 ATTTATATTTATTTAAAG-TTATTTATATTTTAAATAATT
560542 TAATATTTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
39 6 0.09
40 29 0.43
41 18 0.26
42 15 0.22
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (40 bp):
ATTTATATTTATTTAAAGTTATTTATATTTTAAATAATTA
Found at i:560526 original size:20 final size:20
Alignment explanation
Indices: 560472--560532 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
560462 TTATAAATTG
560472 TATTTAAAG-TTATTTATATT
1 TATTT-AAGTTTATTTATATT
** *
560492 ATAAATAA-TTAATTTATATT
1 -TATTTAAGTTTATTTATATT
560512 TATTTAAGTTTATTTATATT
1 TATTTAAGTTTATTTATATT
560532 T
1 T
560533 TTAATAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATTTAAGTTTATTTATATT
Found at i:560543 original size:20 final size:20
Alignment explanation
Indices: 560481--560543 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
560471 GTATTTAAAG
* *
560481 TTATTTATATTATAAATAAT
1 TTATTTATATTTTTAATAAT
*
560501 TAATTTATATTTATT--TAAGT
1 TTATTTATATTT-TTAATAA-T
560521 TTATTTATATTTTTAATAAT
1 TTATTTATATTTTTAATAAT
560541 TTA
1 TTA
560544 ATATTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 5 0.14
20 26 0.74
21 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATTTATATTTTTAATAAT
Found at i:560603 original size:25 final size:24
Alignment explanation
Indices: 560526--560605 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 24
560516 TAAGTTTATT
* *
560526 TATATTTTTAATAATTTAATATTTTAT
1 TATATTTTAAAT-ATTT-ATA-TTTAA
* * *
560553 TAAATTTTAAATATTAAAAATTTAA
1 TATATTTTAAATATT-TATATTTAA
560578 TATATTTTAAATATTTATATTATAA
1 TATATTTTAAATATTTATATT-TAA
560603 TAT
1 TAT
560606 TATATTTATT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 4 0.09
25 24 0.56
26 5 0.12
27 10 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATATTTTAAATATTTATATTTAA
Found at i:561072 original size:26 final size:25
Alignment explanation
Indices: 561043--561097 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
561033 AATAATATTG
*
561043 AAAAGTATATTTAACAATATTTTGAA
1 AAAAGTATATTTAA-AATATTTTAAA
* *
561069 AAAATTATATTTTAAATATTTTAAA
1 AAAAGTATATTTAAAATATTTTAAA
561094 AAAA
1 AAAA
561098 ATTATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (25 bp):
AAAAGTATATTTAAAATATTTTAAA
Found at i:561098 original size:26 final size:26
Alignment explanation
Indices: 561043--561105 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
561033 AATAATATTG
* *
561043 AAAAGTATATTTAACAATATTTTGAA
1 AAAATTATATTTAACAATATTTTAAA
*
561069 AAAATTATATTTTA-AATATTTTAAAA
1 AAAATTATATTTAACAATATTTT-AAA
561095 AAAATTATATT
1 AAAATTATATT
561106 ATATTTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 8 0.24
26 25 0.76
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (26 bp):
AAAATTATATTTAACAATATTTTAAA
Found at i:561135 original size:24 final size:25
Alignment explanation
Indices: 561097--561144 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
561087 TTTTAAAAAA
* *
561097 AATTATATTATA-TTTAATTTTTTT
1 AATTATATTAAATTTTAATATTTTT
*
561121 AATTATTTTAAATTTTAATATTTT
1 AATTATATTAAATTTTAATATTTT
561145 ATATACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
AATTATATTAAATTTTAATATTTTT
Found at i:573729 original size:14 final size:14
Alignment explanation
Indices: 573710--573736 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
573700 AATTAAAATA
573710 TTATTATATATTTT
1 TTATTATATATTTT
573724 TTATTATATATTT
1 TTATTATATATTT
573737 AAAAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATTATATATTTT
Found at i:574174 original size:18 final size:17
Alignment explanation
Indices: 574146--574195 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
574136 AAAAATCAAT
574146 TAATA-TATTATTTATAA
1 TAATATTATTATTTA-AA
574163 TAATATTATTATATTAAA
1 TAATATTATTAT-TTAAA
*
574181 T-ATGATAATTATTTA
1 TAAT-ATTATTATTTA
574196 CATTTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 10 0.34
18 16 0.55
19 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TAATATTATTATTTAAA
Found at i:574188 original size:23 final size:23
Alignment explanation
Indices: 574144--574189 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
574134 TTAAAAATCA
**
574144 ATTAATATATTATTTATAATAAT
1 ATTAATATATTAAATATAATAAT
* *
574167 ATTATTATATTAAATATGATAAT
1 ATTAATATATTAAATATAATAAT
574190 TATTTACATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTAATATATTAAATATAATAAT
Done.