Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001776.1 Hibiscus syriacus cultivar Beakdansim tig00003584_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 183134
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5080 original size:4 final size:4
Alignment explanation
Indices: 5071--5104 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
5061 ATAAAATAAC
5071 AATA AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
5105 ACTAAAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:6311 original size:29 final size:28
Alignment explanation
Indices: 6267--6322 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
6257 ATATTATGTT
* * *
6267 TTTTGAAAAATGTTTTCAAATTATATAG
1 TTTTCAAAAATGTTTTAAAACTATATAG
6295 TTTTCAAAAATGTTTTTAAAACTATATA
1 TTTTCAAAAATG-TTTTAAAACTATATA
6323 TTATAAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (28 bp):
TTTTCAAAAATGTTTTAAAACTATATAG
Found at i:6484 original size:68 final size:67
Alignment explanation
Indices: 6342--6581 Score: 258
Period size: 68 Copynumber: 3.5 Consensus size: 67
6332 TTTGAAATGA
* *
6342 TTTAAAAACTATATAATATATATATGTTCTTCAAAATATTTTTTAAAAA-ACTATATATAT-TTT
1 TTTAAAAACTATAT-A-ATATATAT-TT-TTCAAAA-AATTTTTAAAAATA-TATATATTTATTT
*
6405 CAAA-ATG
60 CAAATATC
*
6412 TTTAAAAACTATATAATATATATTTTTAAAAAAATGTTTTAAAAATTATATATATTTATTTCAAA
1 TTTAAAAACTATATAATATATATTTTTCAAAAAAT-TTTTAAAAA-TATATATATTTATTTCAAA
6477 TA-C
64 TATC
* *
6480 TTTAAAAACTATATAATATATA-CTTTCAAAAAATATTTAAAAACTATATATATTTATTTTCAAA
1 TTTAAAAACTATATAATATATATTTTTCAAAAAATTTTTAAAAA-TATATATATTTA-TTTC-AA
*
6544 ATATT
63 ATATC
6549 TTTAAAAACTATAT-ATATATAATGTTTTCAAAA
1 TTTAAAAACTATATAATATAT-AT-TTTTCAAAA
6582 CTATATATAT
Statistics
Matches: 149, Mismatches: 10, Indels: 21
0.83 0.06 0.12
Matches are distributed among these distances:
65 2 0.01
66 35 0.23
67 24 0.16
68 49 0.33
69 17 0.11
70 14 0.09
71 8 0.05
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (67 bp):
TTTAAAAACTATATAATATATATTTTTCAAAAAATTTTTAAAAATATATATATTTATTTCAAATA
TC
Found at i:6499 original size:34 final size:36
Alignment explanation
Indices: 6342--6569 Score: 139
Period size: 34 Copynumber: 6.6 Consensus size: 36
6332 TTTGAAATGA
**
6342 TTTAAAAACTATATAATATATATATGTTCTTCAAAATAT
1 TTTAAAAACTATATAATATAT-T-TACT-TTCAAAATAT
** * * * *
6381 TTTTTAAA--A-A-ACTATATATATTTTCAAAAT-G
1 TTTAAAAACTATATAATATATTTACTTTCAAAATAT
* *
6412 TTTAAAAACTATATAATATATATT--TTTAAAAAAATGT
1 TTTAAAAACTATATAATATAT-TTACTTT--CAAAATAT
*
6449 TTTAAAAA-T-TAT-ATATATTTA-TTTC-AAATAC
1 TTTAAAAACTATATAATATATTTACTTTCAAAATAT
*
6480 TTTAAAAACTATATAATATA--TACTTTCAAAAAAT
1 TTTAAAAACTATATAATATATTTACTTTCAAAATAT
*
6514 ATTTAAAAAC--TAT-ATATATTTATTTTCAAAATATT
1 -TTTAAAAACTATATAATATATTTACTTTCAAAATA-T
6549 TTTAAAAACTATATATATATA
1 TTTAAAAACTATATA-ATATA
6570 ATGTTTTCAA
Statistics
Matches: 148, Mismatches: 19, Indels: 45
0.70 0.09 0.21
Matches are distributed among these distances:
31 18 0.12
32 16 0.11
33 16 0.11
34 42 0.28
35 25 0.17
36 11 0.07
37 9 0.06
38 5 0.03
39 6 0.04
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.44
Consensus pattern (36 bp):
TTTAAAAACTATATAATATATTTACTTTCAAAATAT
Found at i:6601 original size:25 final size:24
Alignment explanation
Indices: 6546--6606 Score: 86
Period size: 25 Copynumber: 2.5 Consensus size: 24
6536 TTTTCAAAAT
6546 ATTTTTAAAAACTATATATATATA
1 ATTTTTAAAAACTATATATATATA
*
6570 ATGTTTTCAAAACTATATATATATA
1 AT-TTTTAAAAACTATATATATATA
*
6595 GGTTTTTAAAAA
1 -ATTTTTAAAAA
6607 TTTTTAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.06
25 29 0.91
26 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (24 bp):
ATTTTTAAAAACTATATATATATA
Found at i:6726 original size:24 final size:23
Alignment explanation
Indices: 6699--6751 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
6689 TTTTTACTCA
* **
6699 AAATATATTTTAATTTATAATAAT
1 AAATATATTATAACATA-AATAAT
6723 AAATAATATTATAACATAAATAAT
1 AAAT-ATATTATAACATAAATAAT
6747 AAATA
1 AAATA
6752 ACATATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.04
24 14 0.56
25 10 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATATATTATAACATAAATAAT
Found at i:6729 original size:17 final size:17
Alignment explanation
Indices: 6709--6747 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
6699 AAATATATTT
6709 TAAT-TTATAATAATAAA
1 TAATATTATAA-AATAAA
*
6726 TAATATTATAACATAAA
1 TAATATTATAAAATAAA
6743 TAATA
1 TAATA
6748 AATAACATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATATTATAAAATAAA
Found at i:17429 original size:19 final size:20
Alignment explanation
Indices: 17404--17460 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
17394 TTATATATAC
17404 TTATATTATATATATTTTAT
1 TTATATTATATATATTTTAT
* **
17424 TT-TATTACATATATCGTAT
1 TTATATTATATATATTTTAT
*
17443 TTACATATATATATATTT
1 TTATAT-TATATATATTT
17461 GTTTTGCAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 16 0.57
20 4 0.14
21 8 0.29
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (20 bp):
TTATATTATATATATTTTAT
Found at i:19445 original size:15 final size:15
Alignment explanation
Indices: 19425--19479 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
19415 AAGTTATATT
19425 TTAAAATTTACTAGA
1 TTAAAATTTACTAGA
* **
19440 TTAAAATTTTAAGTATT
1 TTAAAA-TTT-ACTAGA
*
19457 TTTAAATTTACTAGA
1 TTAAAATTTACTAGA
19472 TTAAAATT
1 TTAAAATT
19480 ATAAATCATT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
15 16 0.53
16 6 0.20
17 8 0.27
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (15 bp):
TTAAAATTTACTAGA
Found at i:19548 original size:25 final size:24
Alignment explanation
Indices: 19520--19580 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
19510 GTGACAATCT
* * *
19520 ATTTTTATTTTTTAAAATTTTATAA
1 ATTTATATTTTCTAAAA-TTTAAAA
*
19545 ATTTATCTTTTCTAAAATTTAAAA
1 ATTTATATTTTCTAAAATTTAAAA
19569 ATTTAT-TTTTCT
1 ATTTATATTTTCT
19581 TAACATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 6 0.19
24 12 0.38
25 14 0.44
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTTATATTTTCTAAAATTTAAAA
Found at i:19555 original size:24 final size:23
Alignment explanation
Indices: 19523--19580 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
19513 ACAATCTATT
*
19523 TTTATTTTT-TAAAATTTTATAAA
1 TTTATTTTTCTAAAA-TTTAAAAA
19546 TTTATCTTTTCTAAAATTTAAAAA
1 TTTAT-TTTTCTAAAATTTAAAAA
19570 TTTATTTTTCT
1 TTTATTTTTCT
19581 TAACATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 11 0.34
24 16 0.50
25 5 0.16
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTATTTTTCTAAAATTTAAAAA
Found at i:23485 original size:18 final size:18
Alignment explanation
Indices: 23462--23502 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
23452 GAACTCCTCT
23462 CGAATCCGAACTCTAGCC
1 CGAATCCGAACTCTAGCC
23480 CGAATCCGAACTCTAGCC
1 CGAATCCGAACTCTAGCC
23498 CGAAT
1 CGAAT
23503 TCGGCTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.37, G:0.17, T:0.17
Consensus pattern (18 bp):
CGAATCCGAACTCTAGCC
Found at i:30824 original size:52 final size:52
Alignment explanation
Indices: 30762--30861 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
30752 GGGCACACAG
30762 AAATAGGAAACTAGCCTAGAGTTAGG-GAATTACAACTAATTACAAGGAACAA
1 AAATAGGAAACTAGCCTAGAGTT-GGTGAATTACAACTAATTACAAGGAACAA
* *
30814 AAATAGGAAACTAGCCTAGAGTTGGTGGATTACAACTAATTAGAAGGA
1 AAATAGGAAACTAGCCTAGAGTTGGTGAATTACAACTAATTACAAGGA
30862 TATTATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.04
52 43 0.96
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (52 bp):
AAATAGGAAACTAGCCTAGAGTTGGTGAATTACAACTAATTACAAGGAACAA
Found at i:34846 original size:30 final size:34
Alignment explanation
Indices: 34788--34849 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 34
34778 TTATTTAAGG
*
34788 ATTAAATTGAAATGAATTAAAAATACGAGGATTT
1 ATTAAATTGAAATGAATTAAAAAGACGAGGATTT
34822 ATTAAATT-AAAT-AA-T-AAAAGACGAGGAT
1 ATTAAATTGAAATGAATTAAAAAGACGAGGAT
34850 GAATATGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 12 0.44
31 1 0.04
32 2 0.07
33 4 0.15
34 8 0.30
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.29
Consensus pattern (34 bp):
ATTAAATTGAAATGAATTAAAAAGACGAGGATTT
Found at i:35982 original size:59 final size:59
Alignment explanation
Indices: 35919--36359 Score: 346
Period size: 59 Copynumber: 7.5 Consensus size: 59
35909 TGGCACTATA
*
35919 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
* * * *
35978 TGTGCTAAAGTTATAAGGAAAACATACTGAGTGTATGGATTTCCATATAGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
* * * * * *
36037 TGTACTAAAATGATAAGGAAATCATACTGAATATATGGATTTCCAGATAGG-GCA-TTATA
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATAT-GGAGCACTGA-G
* ** *
36096 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGTA-AAAGCACTAAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCA-TATGGAGCACTGAG
* * * * * * *
36155 GGTGATACAAGGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGG-GCACTTCA-
1 TGTGCTAAAATGATAAGGAAATCATACTGAGT-GTATGGATTTCCATAT-GGAGCAC-TGAG
* * * * **
36214 TGTGACAAAAATGGTAAAGG-AATCATACT-AATGGTATGGA-TTCTCAAATAGG-GCACTTCG
1 TGTG-CTAAAATGAT-AAGGAAATCATACTGAGT-GTATGGATTTC-CATAT-GGAGCACTGAG
* * * * * *
36274 TGTGCTAAAATGAGAAGGAAATCATATTAAGTATAT-GATATTCCAGATAGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGAT-TTCCATATGGAGCACTGAG
* * * * *
36333 AGTCCTAACATTATAAGGAAATTATAC
1 TGTGCTAAAATGATAAGGAAATCATAC
36360 GAATTGTATA
Statistics
Matches: 302, Mismatches: 62, Indels: 36
0.75 0.16 0.09
Matches are distributed among these distances:
58 13 0.04
59 235 0.78
60 50 0.17
61 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
Found at i:36251 original size:60 final size:60
Alignment explanation
Indices: 36169--36299 Score: 178
Period size: 60 Copynumber: 2.2 Consensus size: 60
36159 ATACAAGGAT
* *
36169 AAGGAAATCATACTAATAGTATGGATTTTCATATAGGGCACTTCATGTGACAAAAATGGTA
1 AAGGAAATCATACTAATAGTATGGATTCTCAAATAGGGCACTTCATGTG-CAAAAATGGTA
* * *
36230 AAGG-AATCATACTAATGGTATGGATTCTCAAATAGGGCACTTCGTGTGCTAAAAT-G-A
1 AAGGAAATCATACTAATAGTATGGATTCTCAAATAGGGCACTTCATGTGCAAAAATGGTA
36287 GAAGGAAATCATA
1 -AAGGAAATCATA
36300 TTAAGTATAT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
57 1 0.02
58 5 0.08
59 13 0.21
60 40 0.63
61 4 0.06
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.27
Consensus pattern (60 bp):
AAGGAAATCATACTAATAGTATGGATTCTCAAATAGGGCACTTCATGTGCAAAAATGGTA
Found at i:36351 original size:178 final size:176
Alignment explanation
Indices: 35918--36368 Score: 447
Period size: 178 Copynumber: 2.5 Consensus size: 176
35908 ATGGCACTAT
* * * *
35918 ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGA-ATTTCCATATGGAGCACTGAGTGTG
1 ATGTGCTAAAATGAGAAGGAAATCATACTGAGTGTATGATA-TTCCAGATAGAGCACTGAGAGTG
* * * *
35982 CTAA-AGTTATAAGGAAAACATACTGAGTGTATGGATTTCCATATAGAGCACTGAGTGTACTAAA
65 CTAACA-TTATAAGGAAATCATACT-AATGTATGGATTTCCATATAGAGCACTCAGTGTACAAAA
* *
36046 ATGATAAGGAAATCATACTGAATATATGGATTTCCAGATAGGGCATTAT
128 ATGATAAGGAAATCATACTGAATATATGGATTTCCAAATAGGGCATTAC
* * *
36095 ATGTGCTAAAATG-GTAAGGAAATCATACTGAGTGTATGGAT-TTCCAG-TAAAAGCACTAAGGG
1 ATGTGCTAAAATGAG-AAGGAAATCATACTGAGTGTAT-GATATTCCAGAT-AGAGCACTGAGAG
* ** * *
36157 TGAT-ACAAGGATAAGGAAATCATACTAATAGTATGGATTTTCATATAGGGCACTTCA-TGTGAC
63 TGCTAAC-ATTATAAGGAAATCATACTAAT-GTATGGATTTCCATATAGAGCAC-TCAGTGT-AC
* *
36220 AAAAATGGTAAAGG-AATCATACT-AATGGTATGGA-TTCTCAAATAGGGCACTT-C
124 AAAAATGAT-AAGGAAATCATACTGAAT-ATATGGATTTC-CAAATAGGGCA-TTAC
* * * * *
36273 GTGTGCTAAAATGAGAAGGAAATCATATTAAGTATATGATATTCCAGATAGAGCACTGAGAGTCC
1 ATGTGCTAAAATGAGAAGGAAATCATACTGAGTGTATGATATTCCAGATAGAGCACTGAGAGTGC
* *
36338 TAACATTATAAGGAAATTATACGAATTGTAT
66 TAACATTATAAGGAAATCATACTAA-TGTAT
36369 AAATTTCCTA
Statistics
Matches: 224, Mismatches: 32, Indels: 35
0.77 0.11 0.12
Matches are distributed among these distances:
176 4 0.02
177 100 0.45
178 109 0.49
179 11 0.05
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.29
Consensus pattern (176 bp):
ATGTGCTAAAATGAGAAGGAAATCATACTGAGTGTATGATATTCCAGATAGAGCACTGAGAGTGC
TAACATTATAAGGAAATCATACTAATGTATGGATTTCCATATAGAGCACTCAGTGTACAAAAATG
ATAAGGAAATCATACTGAATATATGGATTTCCAAATAGGGCATTAC
Found at i:36499 original size:44 final size:44
Alignment explanation
Indices: 36436--36656 Score: 334
Period size: 44 Copynumber: 5.0 Consensus size: 44
36426 TCAATGATGC
36436 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
36480 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
36524 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * * *
36568 GAATAATGGTAAGTATATTGGTAAAATAAGGTTACGAGCTTAGG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * * * *
36612 GATTTAATGGTAAGTATATTGTTAAAATAAACTTACGAGTTTATG
1 AAATT-ATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
36657 GATTAAATGG
Statistics
Matches: 164, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
44 130 0.79
45 34 0.21
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (44 bp):
AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
Found at i:37529 original size:18 final size:18
Alignment explanation
Indices: 37506--37557 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
37496 GCGTAGAATT
*
37506 TGTCCCGTATGACCACTA
1 TGTCCCGTAGGACCACTA
37524 TGTCCCGTAGGACCACTA
1 TGTCCCGTAGGACCACTA
*
37542 TGTCCCGAAGGACCAC
1 TGTCCCGTAGGACCAC
37558 ATATCACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGTAGGACCACTA
Found at i:41922 original size:18 final size:18
Alignment explanation
Indices: 41899--41950 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
41889 GCGTAGAATT
*
41899 TATCCCGTAGGACCACTA
1 TATCCCGTAGAACCACTA
41917 TATCCCGTAGAACCACTA
1 TATCCCGTAGAACCACTA
* *
41935 TGTCCCGAAGAACCAC
1 TATCCCGTAGAACCAC
41951 ATTTCACATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.31, C:0.35, G:0.15, T:0.19
Consensus pattern (18 bp):
TATCCCGTAGAACCACTA
Found at i:41986 original size:18 final size:18
Alignment explanation
Indices: 41963--42016 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 18
41953 TTCACATATA
*
41963 TCCCGAATGACCACTATG
1 TCCCGAAGGACCACTATG
41981 TCCCGAAGGACCAACCACTATG
1 TCCCGAAGG----ACCACTATG
42003 TCCCGAAGGACCAC
1 TCCCGAAGGACCAC
42017 ATATCACATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 13 0.42
22 18 0.58
ACGTcount: A:0.30, C:0.37, G:0.19, T:0.15
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:42000 original size:22 final size:22
Alignment explanation
Indices: 41972--42015 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
41962 ATCCCGAATG
41972 ACCACTATGTCCCGAAGGACCA
1 ACCACTATGTCCCGAAGGACCA
41994 ACCACTATGTCCCGAAGGACCA
1 ACCACTATGTCCCGAAGGACCA
42016 CATATCACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.18, T:0.14
Consensus pattern (22 bp):
ACCACTATGTCCCGAAGGACCA
Found at i:42016 original size:66 final size:66
Alignment explanation
Indices: 41927--42058 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
41917 TATCCCGTAG
*
41927 AACCACTATGTCCCGAAGAACCACATTTCACATATATCCCGAATGACCACTATGTCCCGAAGGAC
1 AACCACTATGTCCCGAAGAACCACATATCACATATATCCCGAATGACCACTATGTCCCGAAGGAC
41992 C
66 C
* *
41993 AACCACTATGTCCCGAAGGACCACATATCACATATATCCCGAATGACCACTATGTCCCGAATGAC
1 AACCACTATGTCCCGAAGAACCACATATCACATATATCCCGAATGACCACTATGTCCCGAAGGAC
42058 C
66 C
42059 GCATAGAACC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.20
Consensus pattern (66 bp):
AACCACTATGTCCCGAAGAACCACATATCACATATATCCCGAATGACCACTATGTCCCGAAGGAC
C
Found at i:43713 original size:45 final size:45
Alignment explanation
Indices: 43649--43739 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
43639 ACCCGGTTAT
43649 TGGGATGTTACAGTTGTTGCCCAAAATAGTATGATTGGCTTGTGG
1 TGGGATGTTACAGTTGTTGCCCAAAATAGTATGATTGGCTTGTGG
43694 TGGGATGTTACAGTTGTTGCCCAAAATAGTATGATTGGCTTGTGG
1 TGGGATGTTACAGTTGTTGCCCAAAATAGTATGATTGGCTTGTGG
43739 T
1 T
43740 TGGCGCCAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.22, C:0.11, G:0.31, T:0.36
Consensus pattern (45 bp):
TGGGATGTTACAGTTGTTGCCCAAAATAGTATGATTGGCTTGTGG
Found at i:44510 original size:2 final size:2
Alignment explanation
Indices: 44503--44533 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44493 GTGGCGTAGT
44503 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44534 GAAGGATCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54805 original size:21 final size:21
Alignment explanation
Indices: 54779--54826 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
54769 ATTATTATTT
54779 AAATAACAAAACCGGTAGAAA
1 AAATAACAAAACCGGTAGAAA
*
54800 AAATAACAAAATCGGTAGAAA
1 AAATAACAAAACCGGTAGAAA
*
54821 TAATAA
1 AAATAA
54827 TGTTTCTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.15
Consensus pattern (21 bp):
AAATAACAAAACCGGTAGAAA
Found at i:74348 original size:31 final size:31
Alignment explanation
Indices: 74312--74382 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
74302 CTTACGTAAT
*
74312 AAAGTTAAGGAATCAAATGTACCTAAAATAA
1 AAAGTTAAGGAATCAAATGTACCAAAAATAA
* *
74343 AAAGTTAAGGAATTAAATGTACCAAAAATAT
1 AAAGTTAAGGAATCAAATGTACCAAAAATAA
74374 AAAGTTAAG
1 AAAGTTAAG
74383 AACTAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (31 bp):
AAAGTTAAGGAATCAAATGTACCAAAAATAA
Found at i:76952 original size:19 final size:20
Alignment explanation
Indices: 76914--76952 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
76904 CTAAAACAAA
*
76914 CAATATTTTTATTTAATAAT
1 CAATATTTTAATTTAATAAT
*
76934 CAATA-TTTAATTTATTAAT
1 CAATATTTTAATTTAATAAT
76953 TGATTAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
CAATATTTTAATTTAATAAT
Found at i:82854 original size:27 final size:29
Alignment explanation
Indices: 82802--82864 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
82792 AATTGTTTGA
82802 TTATTTTGATGGTTGGATTTAGATCA-AG
1 TTATTTTGATGGTTGGATTTAGATCATAG
* * *
82830 TTATTTTTAT-GTT-GATTTGATATCATAT
1 TTATTTTGATGGTTGGATTT-AGATCATAG
82858 TTATTTT
1 TTATTTT
82865 AGGGTCGGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 5 0.17
27 8 0.27
28 17 0.57
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (29 bp):
TTATTTTGATGGTTGGATTTAGATCATAG
Found at i:83622 original size:281 final size:287
Alignment explanation
Indices: 83112--83641 Score: 724
Period size: 281 Copynumber: 1.9 Consensus size: 287
83102 TATGATTTTG
* **
83112 AGTAAATTACAAAAATATAAATAAATATGGGTCAATTTTAATAAAAATATAATTTTAAGGACCAA
1 AGTAAATTACAAAAATATAAATAAATATGGGTCAATTTCAATAAAAATATAATTTTAAACACCAA
* * *
83177 ATTGAACAAACATAAAATTACGAATTGAAATTTAAATAAATTAAATAGCACTCATGGATGAGGGA
66 ATTAAACAAACATAAAATTACGAATTGAAATTTAAATAAATTAAATAGCAC-CA-GCATGAGGAA
* * * *
83242 TCAAATCAAAATAATTATAAAATGTTAAGTTGAAATTAATATACAAATAGACTAAATTGAATTCA
129 TCAAATCAAAATAATTATAAAATATGAAGTTGAAACTAATATAAAAATAGACTAAATTGAATTCA
*
83307 TTTAAAAAGTTGGTGAACAAAAGTTTATAAAG-TTTGGAAATTATGATATAATTTATAGAGTTTG
194 TTTAAAAAGTTGGTGAACAAAAGTTTATAAAGTTTTGGAAATTATAATATAATTTATAGAGTTTG
83371 AAGTATATTATGCAATTTATTGGGTTCGA
259 AAGTATATTATGCAATTTATTGGGTTCGA
* * *
83400 AGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTCATATACAAATATAATTTTAAACACTA
1 AGTAAATTACAAAAATATAAATAAATATGGGTCAATTTCA-ATAAAAATATAATTTTAAACACCA
* *
83465 AATTAAACAAATATAAAATTAC-AAGTT-AAGATTT-AATAAATTAAA-CG-A-CA-CAT-AGGA
65 AATTAAACAAACATAAAATTACGAA-TTGAA-ATTTAAATAAATTAAATAGCACCAGCATGAGGA
*
83522 ATCAAATCAAAATAATTGTAAAATATGAAGTTGAAACTAATATAAAAATAGACTAAATT-ACATT
128 ATCAAATCAAAATAATTATAAAATATGAAGTTGAAACTAATATAAAAATAGACTAAATTGA-ATT
** *
83586 CATTTCAAAAA-TTGAG-GAGTAAAAGTTTATAAAGTTTTGGATATTATAATATAATT
192 CATTT-AAAAAGTTG-GTGAACAAAAGTTTATAAAGTTTTGGAAATTATAATATAATT
83642 AATATATATA
Statistics
Matches: 215, Mismatches: 20, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
280 1 0.00
281 84 0.39
282 27 0.13
284 2 0.01
286 1 0.00
287 1 0.00
288 53 0.25
289 46 0.21
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (287 bp):
AGTAAATTACAAAAATATAAATAAATATGGGTCAATTTCAATAAAAATATAATTTTAAACACCAA
ATTAAACAAACATAAAATTACGAATTGAAATTTAAATAAATTAAATAGCACCAGCATGAGGAATC
AAATCAAAATAATTATAAAATATGAAGTTGAAACTAATATAAAAATAGACTAAATTGAATTCATT
TAAAAAGTTGGTGAACAAAAGTTTATAAAGTTTTGGAAATTATAATATAATTTATAGAGTTTGAA
GTATATTATGCAATTTATTGGGTTCGA
Found at i:83650 original size:2 final size:2
Alignment explanation
Indices: 83643--84022 Score: 85
Period size: 2 Copynumber: 192.0 Consensus size: 2
83633 AATATAATTA
** * * *
83643 AT AT AT AT AT AT AT GC AT AA AT AT AT AT ACT -T AT AC AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * **
83685 CT AT A- AGT AT GT AT AT AT GT -T AT ACT -T AT AT ACT -T AT CC
1 AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT
* * * *
83724 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT TT TT TT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
83765 AT AT A- AGT AT AT AT AC CT -T GAT AG AT AG AT A- AT -T AT AT ACT
1 AT AT AT A-T AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT A-T
* * ** * *
83806 -T TT TT AT AT AT AT AT GC AT GAT -T A- AT GAT GT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT -AT AT AT AT AT AT AT
* * * * * * * *
83847 GT AT GAT GT AT AT AC AT A- AGT GT AT AT AA AT AC AT AT AA AT AA
1 AT AT -AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * * ** *
83890 AT AT GT GT AT AT AT AT AT AT AC AT AT GC AT GAT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
* * * * * *
83933 AT AT AC AT TT AT AT AT GT AT AT AT AT AC AT TT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
83975 AT A- AT -T AC AT A- AGT AT AT AT AT GT AT AT AT AT AT -T CAT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT -AT AT
*
84015 TT AT AT AT
1 AT AT AT AT
84023 GTCACAATTT
Statistics
Matches: 263, Mismatches: 83, Indels: 64
0.64 0.20 0.16
Matches are distributed among these distances:
1 18 0.07
2 228 0.87
3 17 0.06
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (2 bp):
AT
Found at i:83681 original size:20 final size:20
Alignment explanation
Indices: 83626--83681 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
83616 AAAGTTTTGG
*
83626 ATAT-TATA-ATATA-ATTA
1 ATATATATATATATACATAA
*
83643 ATATATATATATATGCATAA
1 ATATATATATATATACATAA
83663 ATATATATACT-TATACATA
1 ATATATATA-TATATACATA
83682 TACCTATAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 4 0.12
20 19 0.59
21 1 0.03
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (20 bp):
ATATATATATATATACATAA
Found at i:83915 original size:22 final size:22
Alignment explanation
Indices: 83880--84022 Score: 94
Period size: 22 Copynumber: 6.3 Consensus size: 22
83870 ATATAAATAC
* * *
83880 ATATAAATAAATATGTGTATAT
1 ATATATATACATATGTATATAT
83902 ATATATATACATATGCATGATATATGT
1 ATATATATACATATG--T-ATATA--T
* * *
83929 ATATATATACATTTATATATGT
1 ATATATATACATATGTATATAT
83951 ATATATATACAT-T-TATATAT
1 ATATATATACATATGTATATAT
* *
83971 GTATATAATTACATAAGTATATAT
1 ATATAT-A-TACATATGTATATAT
* * *
83995 ATGTATATATATAT-TCATATTT
1 ATATATATACATATGT-ATATAT
84017 ATATAT
1 ATATAT
84023 GTCACAATTT
Statistics
Matches: 96, Mismatches: 15, Indels: 20
0.73 0.11 0.15
Matches are distributed among these distances:
20 11 0.11
21 3 0.03
22 46 0.48
23 1 0.01
24 16 0.17
25 5 0.05
27 14 0.15
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (22 bp):
ATATATATACATATGTATATAT
Found at i:87644 original size:22 final size:22
Alignment explanation
Indices: 87603--87683 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
87593 CTCGTATAAA
87603 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
87626 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
87648 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
87670 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
87684 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:87679 original size:13 final size:13
Alignment explanation
Indices: 87617--87679 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
87607 CCGAAGTGCC
87617 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
87630 CC---GAAGTGC-
1 CCGTAGAATTGCA
87639 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
87652 CC---GAAGTGC-
1 CCGTAGAATTGCA
87661 CCGTAGAATTGCA
1 CCGTAGAATTGCA
87674 CCGTAG
1 CCGTAG
87680 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:92491 original size:22 final size:22
Alignment explanation
Indices: 92460--92539 Score: 126
Period size: 22 Copynumber: 3.6 Consensus size: 22
92450 CTCGTATAAA
*
92460 TGCACCGAAGTGCCCCGTATAAT
1 TGCACCGAAGTG-CCCGTAGAAT
92483 TG-ACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
92504 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
92526 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
92540 ATATATGATG
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
21 11 0.20
22 41 0.76
23 2 0.04
ACGTcount: A:0.25, C:0.29, G:0.26, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:93927 original size:21 final size:21
Alignment explanation
Indices: 93897--93941 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
93887 TCTTATTCGT
* *
93897 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
93918 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
93939 TTG
1 TTG
93942 CCCAAAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:95192 original size:99 final size:97
Alignment explanation
Indices: 95021--95207 Score: 356
Period size: 99 Copynumber: 1.9 Consensus size: 97
95011 TGATCATGCC
95021 TTAGAGATCATTGGCGTGGGAACCATCAAATTGAAGATGTATGATGGAACAATTAAAGTTGTTCG
1 TTAGAGATCATTGGCGTGGGAACCATCAAATTGAAGATGTATGATGGAACAATTAAAGTTGTTCG
95086 AGATGTGCGGCACGTGAAAGGCCTGAAGAAAAAT
66 AGATGTGC-GC-CGTGAAAGGCCTGAAGAAAAAT
95120 TTAGAGATCATTGGCGTGGGAACCATCAAATTGAAGATGTATGATGGAACAATTAAAGTTGTTCG
1 TTAGAGATCATTGGCGTGGGAACCATCAAATTGAAGATGTATGATGGAACAATTAAAGTTGTTCG
95185 AGATGTGCGCCGTGAAAGGCCTG
66 AGATGTGCGCCGTGAAAGGCCTG
95208 CCTTAGAGAT
Statistics
Matches: 88, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
97 13 0.15
98 2 0.02
99 73 0.83
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (97 bp):
TTAGAGATCATTGGCGTGGGAACCATCAAATTGAAGATGTATGATGGAACAATTAAAGTTGTTCG
AGATGTGCGCCGTGAAAGGCCTGAAGAAAAAT
Found at i:106478 original size:34 final size:34
Alignment explanation
Indices: 106400--106519 Score: 199
Period size: 34 Copynumber: 3.5 Consensus size: 34
106390 CCCGAACTCG
106400 AAAATATTATATATATATAATTAATATAAAAAATAA
1 AAAATA-T-TATATATATAATTAATATAAAAAATAA
106436 AAAA-ATTATATATATAATTAATAT-AAAAATAAA
1 AAAATATTATATATATAATTAATATAAAAAAT-AA
106469 AAAATATTATATATATAATTAATATAAAAAATAA
1 AAAATATTATATATATAATTAATATAAAAAATAA
106503 AAAATATTATATATATA
1 AAAATATTATATATATA
106520 TATATATATA
Statistics
Matches: 81, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
32 6 0.07
33 24 0.30
34 40 0.49
35 7 0.09
36 4 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAA
Found at i:107722 original size:14 final size:13
Alignment explanation
Indices: 107696--107734 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
107686 TCAAACAATT
107696 ATTTAATTGTTTGA
1 ATTTAA-TGTTTGA
*
107710 ATTGTAATGTTTGT
1 ATT-TAATGTTTGA
107724 ATTTAATGTTT
1 ATTTAATGTTT
107735 ATATTTAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 8 0.35
14 12 0.52
15 3 0.13
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (13 bp):
ATTTAATGTTTGA
Found at i:107732 original size:13 final size:13
Alignment explanation
Indices: 107695--107742 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
107685 GTCAAACAAT
107695 TATTTAATTGTTTG
1 TATTTAA-TGTTTG
*
107709 AATTGTAATGTTTG
1 TATT-TAATGTTTG
*
107723 TATTTAATGTTTA
1 TATTTAATGTTTG
107736 TATTTAA
1 TATTTAA
107743 CTTTTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 15 0.50
14 12 0.40
15 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.58
Consensus pattern (13 bp):
TATTTAATGTTTG
Found at i:108913 original size:16 final size:16
Alignment explanation
Indices: 108894--108934 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
108884 TTTTGAGATT
108894 TTGAGAGTTTGAAAGA
1 TTGAGAGTTTGAAAGA
108910 TTGAGAGTTTGAAAGA
1 TTGAGAGTTTGAAAGA
*
108926 TTAAGAGTT
1 TTGAGAGTT
108935 CTATATATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (16 bp):
TTGAGAGTTTGAAAGA
Found at i:109185 original size:16 final size:15
Alignment explanation
Indices: 109155--109192 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
109145 AAATTTGGTT
*
109155 AAATAATTAAATATA
1 AAATAAATAAATATA
109170 AAATAAATATAATATA
1 AAATAAATA-AATATA
109186 AAA-AAAT
1 AAATAAAT
109193 TTACATTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAAATAAATATA
Found at i:112940 original size:22 final size:22
Alignment explanation
Indices: 112890--112945 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
112880 AATATTTAAA
112890 TATATAAACAAGTAAAATTAAAAC
1 TATATAAA-AA-TAAAATTAAAAC
* *
112914 -A-ATAAAAATACAATTAGAAC
1 TATATAAAAATAAAATTAAAAC
112934 TATATAAAAATA
1 TATATAAAAATA
112946 TTTAAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 10 0.36
21 3 0.11
22 14 0.50
23 1 0.04
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.25
Consensus pattern (22 bp):
TATATAAAAATAAAATTAAAAC
Found at i:114215 original size:3 final size:3
Alignment explanation
Indices: 114209--114281 Score: 94
Period size: 3 Copynumber: 24.0 Consensus size: 3
114199 AATAATTATT
* **
114209 TAA TAA TAA T-A TAA TATA TAA TAA TATT TAA TAA TAA TAA TAA TTT
1 TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA
114255 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
114282 ATAAAATGGG
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.03
3 54 0.89
4 5 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:115130 original size:116 final size:113
Alignment explanation
Indices: 114699--115577 Score: 1226
Period size: 116 Copynumber: 7.7 Consensus size: 113
114689 GTTGAACAAA
* * ** * * *
114699 TTCTTCTTCCTTCTTCAGATTAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATCCATCA
* * * *
114764 AGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA-
66 AATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
114811 -T-TTCTT-CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCA
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATCCA
114873 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
63 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* ** * * *
114924 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATCCATCA
* * * *
114989 AATGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAAC
66 AATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
115037 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCA
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATCCA
115102 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
63 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
115153 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCATTGTTAATCCA
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATCCA
*
115218 TCAAATGATGAATTTAAACAAAAGGTTAAACAAATTCTTCTCATTATGAAC
63 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* ** * * *
115269 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATCCATCA
* * * *
115334 AATGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAAC
66 AATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
115382 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCATTGTTAATCCA
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATCCA
115447 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
63 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * * **
115498 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAACCTGGCAATGCTGATCCATTG
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATCCATCA
*
115563 AATGATGGATTTAAA
66 AATGATGAATTTAAA
115578 TCTTTGCTAA
Statistics
Matches: 685, Mismatches: 69, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
109 11 0.02
110 5 0.01
111 1 0.00
112 80 0.12
113 255 0.37
114 1 0.00
115 5 0.01
116 327 0.48
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATCCATCA
AATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
Found at i:115163 original size:229 final size:227
Alignment explanation
Indices: 114699--115577 Score: 1230
Period size: 229 Copynumber: 3.9 Consensus size: 227
114689 GTTGAACAAA
* * ** *
114699 TTCTTCTTCCTTCTTCAGAT-TAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATC
1 TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACCTGGAAAAGCTAATCCATC
* * * *
114763 AAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTC
66 AAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
*
114824 AGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTA
131 AGAT---GAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATCCATCAAATGATGAATTTA
114889 AACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
193 AACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* ** *
114924 TTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATC
1 TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACCTGGAAAAGCTAATCCATC
* * * *
114988 AAATGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
66 AAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
*
115053 AGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTA
131 AGAT---GAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATCCATCAAATGATGAATTTA
115118 AACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
193 AACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* ** *
115153 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCATTGTTAATCCA
1 TTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTACCTGGAAAAGCTAATCCA
*
115218 TCAAATGATGAATTTAAACAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
64 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
* ** * * * * *
115283 TCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
129 TCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATCCATCAAATGATGAATTTAA
* *
115348 GCAAAAAGTTGAACAAATTCTTCTCATTATGAAC
194 ACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* ** *
115382 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCATTGTTAATCCA
1 TTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTACCTGGAAAAGCTAATCCA
*
115447 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCT
64 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
* * ** *
115512 TCAGATGAGTTCTTCTCATTATGAACTCAACCTGGCAATGCTGATCCATTGAATGATGGATTTAA
129 TCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATCCATCAAATGATGAATTTAA
115577 A
194 A
115578 TCTTTGCTAA
Statistics
Matches: 608, Mismatches: 39, Indels: 10
0.93 0.06 0.02
Matches are distributed among these distances:
225 109 0.18
227 1 0.00
228 5 0.01
229 393 0.65
232 100 0.16
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (227 bp):
TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACCTGGAAAAGCTAATCCATC
AAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
AGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATCCATCAAATGATGAATTTAAAC
AAAAGGTTGAACAAATTCTTCTCATTATGAAC
Found at i:115332 original size:345 final size:344
Alignment explanation
Indices: 114699--115577 Score: 1488
Period size: 345 Copynumber: 2.6 Consensus size: 344
114689 GTTGAACAAA
* * ** * * * *
114699 TTCTTCTTCCTTCTTCAGAT---TAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCA
* * * *
114761 TCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTTCTTCTT
66 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTT
114823 CAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTT
131 CAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTT
*
114888 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
196 AAACAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
114953 TCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAAGTTGAACA
261 TCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAAGTTGAACA
115018 AATTCTTCTCATTATGAAC
326 AATTCTTCTCATTATGAAC
115037 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCA
115102 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
66 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCT
*
115167 TCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCATTGTTAATCCATCAAATGATGAATT
130 TCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATT
115232 TAAACAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
195 TAAACAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
115297 CTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAAGTTGAAC
260 CTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAAGTTGAAC
115362 AAATTCTTCTCATTATGAAC
325 AAATTCTTCTCATTATGAAC
*
115382 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCATTGTTAATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCA
115447 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCT
66 TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCTTCT
* * * ** *
115512 TCAGAT---GAGTTCTTCTCATTATGAACTCAACCTGGCAATGCTGATCCATTGAATGATGGATT
130 TCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATT
115574 TAAA
195 TAAA
115578 TCTTTGCTAA
Statistics
Matches: 511, Mismatches: 22, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
338 20 0.04
341 80 0.16
342 53 0.10
343 1 0.00
344 5 0.01
345 350 0.68
346 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (344 bp):
TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCA
TCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTT
CAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTT
AAACAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAAGTTGAACA
AATTCTTCTCATTATGAAC
Found at i:116002 original size:22 final size:22
Alignment explanation
Indices: 115977--116031 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
115967 GATAAAGCTT
*
115977 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
115999 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
116021 TCATCTTTGAA
1 TCATCTTTGAA
116032 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:118762 original size:114 final size:114
Alignment explanation
Indices: 118562--118785 Score: 358
Period size: 114 Copynumber: 2.0 Consensus size: 114
118552 GATCATGCAG
* * * * *
118562 TTCATCTTTCAATTCTAATGATCAGTTTTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCAGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
118627 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* **
118676 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCAGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
118741 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAG
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAG
118786 AACATGGCAC
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCAGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:120837 original size:7 final size:7
Alignment explanation
Indices: 120825--120862 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
120815 TTAAGGGTTC
120825 CTTTTTT
1 CTTTTTT
120832 CTTTTTT
1 CTTTTTT
*
120839 CTTTTTC
1 CTTTTTT
120846 CTTTTTT
1 CTTTTTT
*
120853 -TTTCTT
1 CTTTTTT
120859 CTTT
1 CTTT
120863 CTTTGCTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
CTTTTTT
Found at i:120848 original size:21 final size:20
Alignment explanation
Indices: 120822--120862 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
120812 TGTTTAAGGG
*
120822 TTCCTTTTTTCTTTTTTCTTT
1 TTCCTTTTTT-TTTCTTCTTT
120843 TTCCTTTTTTTTTCTTCTTT
1 TTCCTTTTTTTTTCTTCTTT
120863 CTTTGCTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (20 bp):
TTCCTTTTTTTTTCTTCTTT
Found at i:124171 original size:14 final size:14
Alignment explanation
Indices: 124137--124190 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
124127 TTGTGCAATA
* *
124137 CAAATGCAAAGATG
1 CAAATGTAAATATG
124151 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
124166 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
124180 TAAATGTAAAT
1 CAAATGTAAAT
124191 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:126596 original size:22 final size:22
Alignment explanation
Indices: 126546--126601 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
126536 AATATTTAAA
126546 TATATAAACAAGTAAAATTAAAAC
1 TATATAAA-AA-TAAAATTAAAAC
* *
126570 -A-ATAAAAATACAATTAGAAC
1 TATATAAAAATAAAATTAAAAC
126590 TATATAAAAATA
1 TATATAAAAATA
126602 TTTAAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 10 0.36
21 3 0.11
22 14 0.50
23 1 0.04
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.25
Consensus pattern (22 bp):
TATATAAAAATAAAATTAAAAC
Found at i:127880 original size:3 final size:3
Alignment explanation
Indices: 127874--127937 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
127864 AATAATTATT
* **
127874 TAA TAA TAA T-A TAA TATA TAA TAA TATT TAA TAA TAA TAA TAA TTT
1 TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA
127920 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
127938 ATAAATAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 45 0.87
4 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:127897 original size:18 final size:17
Alignment explanation
Indices: 127874--127941 Score: 86
Period size: 18 Copynumber: 4.0 Consensus size: 17
127864 AATAATTATT
127874 TAATAATAATATAATATA
1 TAATAATAATATAATA-A
*
127892 TAATAAT-ATTTAATAA
1 TAATAATAATATAATAA
*
127908 TAATAATAATTTTAATAA
1 TAATAATAA-TATAATAA
127926 TAATAATAATA-AATAA
1 TAATAATAATATAATAA
127942 ATAAATTGGG
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
16 13 0.28
17 9 0.20
18 24 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATAATAATATAATAA
Found at i:127926 original size:31 final size:28
Alignment explanation
Indices: 127863--127941 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
127853 AATGGGCCTG
127863 TAATAATTATTTAATAATAATATAATATA
1 TAATAA-TATTTAATAATAATATAATATA
*
127892 TAATAATATTTAATAATAATAATAAT-TT
1 TAATAATATTTAATAATAAT-ATAATATA
*
127920 TAATAATA-ATAATAATAA-ATAA
1 TAATAATATTTAATAATAATATAA
127942 ATAAATTGGG
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
25 4 0.09
27 9 0.19
28 23 0.49
29 11 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TAATAATATTTAATAATAATATAATATA
Found at i:129466 original size:54 final size:55
Alignment explanation
Indices: 129384--129492 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 55
129374 TGTAAGATCT
* * *
129384 AAGCTTAAAGTTATTCGGATTTAGCAAGAGGATGTCATTCCATGCTCA-GTGTCG
1 AAGCTTAAACTTATTCGAATTTAGCAAGAGAATGTCATTCCATGCTCAGGTGTCG
* *
129438 AAGCTTTAACTTATTCTAATTTAGCAAGAGAATGTCATTCCATGCTCAGGTGTCG
1 AAGCTTAAACTTATTCGAATTTAGCAAGAGAATGTCATTCCATGCTCAGGTGTCG
129493 GGAAATGACA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 43 0.88
55 6 0.12
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (55 bp):
AAGCTTAAACTTATTCGAATTTAGCAAGAGAATGTCATTCCATGCTCAGGTGTCG
Found at i:141643 original size:7 final size:7
Alignment explanation
Indices: 141631--141657 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
141621 ATGAATAGAC
141631 AAATGGT
1 AAATGGT
141638 AAATGGT
1 AAATGGT
141645 AAATGGT
1 AAATGGT
141652 AAATGG
1 AAATGG
141658 AGCAAGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (7 bp):
AAATGGT
Found at i:143059 original size:21 final size:21
Alignment explanation
Indices: 143033--143082 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
143023 CTGAATGGGA
143033 TATGATAATCTTTCGAGATTT
1 TATGATAATCTTTCGAGATTT
*
143054 TATGATAATTTTTCGAGATTT
1 TATGATAATCTTTCGAGATTT
143075 TATGATAA
1 TATGATAA
143083 AGTTTTATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (21 bp):
TATGATAATCTTTCGAGATTT
Found at i:144439 original size:13 final size:13
Alignment explanation
Indices: 144384--144449 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 13
144374 ATTATAAATA
*
144384 ATATATATTGTAT
1 ATATATATAGTAT
* *
144397 AAATTATATAGTTT
1 ATA-TATATAGTAT
*
144411 AT-TA-ATA-TAA
1 ATATATATAGTAT
*
144421 AT-TATATAGTTT
1 ATATATATAGTAT
144433 ATATATATAGTAT
1 ATATATATAGTAT
144446 ATAT
1 ATAT
144450 GGTTTAGGGT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
10 5 0.12
11 6 0.15
12 5 0.12
13 15 0.38
14 9 0.22
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (13 bp):
ATATATATAGTAT
Found at i:144572 original size:24 final size:24
Alignment explanation
Indices: 144545--144615 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
144535 ATATAATAAG
144545 GTTTATATTTATATATGAACTATA
1 GTTTATATTTATATATGAACTATA
*
144569 G-TT-TA--CATATA--AACTATA
1 GTTTATATTTATATATGAACTATA
* *
144587 GTTAATATTTACATATGAACTATA
1 GTTTATATTTATATATGAACTATA
144611 GTTTA
1 GTTTA
144616 CATATGAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
18 8 0.22
19 1 0.03
20 7 0.19
22 6 0.17
23 2 0.06
24 12 0.33
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (24 bp):
GTTTATATTTATATATGAACTATA
Found at i:144595 original size:42 final size:42
Alignment explanation
Indices: 144549--144628 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
144539 AATAAGGTTT
*
144549 ATATTTATATATGAACTATAGTTTACATATAAACTATAGTTA
1 ATATTTACATATGAACTATAGTTTACATATAAACTATAGTTA
*
144591 ATATTTACATATGAACTATAGTTTACATATGAACTATA
1 ATATTTACATATGAACTATAGTTTACATATAAACTATA
144629 TATATAAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.41
Consensus pattern (42 bp):
ATATTTACATATGAACTATAGTTTACATATAAACTATAGTTA
Found at i:144665 original size:2 final size:2
Alignment explanation
Indices: 144658--144785 Score: 53
Period size: 2 Copynumber: 59.0 Consensus size: 2
144648 ACATATGACC
* *
144658 TA TA TA TA TA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA TA GTT
1 TA TA TA TA TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA -TA
* ** * *
144702 TA CA TA TGA CC TA TA TA TA TA TA CTA TA GTT TA TA TT TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA
* *
144745 CTA TA TA T- TA TA TA TA TA AA CTA TA TG TA CTA TA TA GTA TA
1 -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA
144786 ATTTACATAT
Statistics
Matches: 94, Mismatches: 18, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
1 2 0.02
2 74 0.79
3 18 0.19
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:144677 original size:33 final size:34
Alignment explanation
Indices: 144605--144679 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
144595 TTACATATGA
* *
144605 ACTATAGTTTACATATGAACTATATATATAAACT
1 ACTATAGTTTACATATGACCTATATATATATACT
144639 A-TATAGTTTACATATGACCTATATATATATA-T
1 ACTATAGTTTACATATGACCTATATATATATACT
144671 ACTATAGTT
1 ACTATAGTT
144680 GATATTTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 2 0.05
33 35 0.92
34 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (34 bp):
ACTATAGTTTACATATGACCTATATATATATACT
Found at i:144698 original size:7 final size:7
Alignment explanation
Indices: 144686--144785 Score: 52
Period size: 7 Copynumber: 14.6 Consensus size: 7
144676 AGTTGATATT
144686 TATATAC
1 TATATAC
*
144693 TATATAG
1 TATATAC
144700 T-T-TAC
1 TATATAC
144705 -ATATGACC
1 TATAT-A-C
144713 TATATA-
1 TATATAC
144719 TATATAC
1 TATATAC
*
144726 TATAGT-T
1 TATA-TAC
*
144733 TATAT-T
1 TATATAC
144739 TATATAC
1 TATATAC
*
144746 TATATAT
1 TATATAC
144753 TATATA-
1 TATATAC
*
144759 TATAAAC
1 TATATAC
144766 TATATGTAC
1 TATA--TAC
*
144775 TATATAG
1 TATATAC
144782 TATA
1 TATA
144786 ATTTACATAT
Statistics
Matches: 74, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
5 3 0.04
6 20 0.27
7 38 0.51
8 3 0.04
9 10 0.14
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (7 bp):
TATATAC
Found at i:144740 original size:53 final size:54
Alignment explanation
Indices: 144625--144751 Score: 211
Period size: 53 Copynumber: 2.4 Consensus size: 54
144615 ACATATGAAC
* *
144625 TATATATATAAACTATATAGTTTACATATGACCTATATATATATATACTATAGTT
1 TATATTTATATACTATATAGTTTACATATGACC-ATATATATATATACTATAGTT
*
144680 GATATTTATATACTATATAGTTTACATATGACC-TATATATATATACTATAGTT
1 TATATTTATATACTATATAGTTTACATATGACCATATATATATATACTATAGTT
144733 TATATTTATATACTATATA
1 TATATTTATATACTATATA
144752 TTATATATAT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
53 38 0.56
55 30 0.44
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.46
Consensus pattern (54 bp):
TATATTTATATACTATATAGTTTACATATGACCATATATATATATACTATAGTT
Found at i:144769 original size:18 final size:18
Alignment explanation
Indices: 144660--144785 Score: 71
Period size: 18 Copynumber: 6.7 Consensus size: 18
144650 ATATGACCTA
144660 TATATATATATACTATAGT
1 TATATATATATACTATA-T
*
144679 TGATATTTATATACTATA-
1 T-ATATATATATACTATAT
* *
144697 TAGTTTACATATGACCTATA-
1 TA-TATATATAT-A-CTATAT
* *
144717 TATATATACTATAGTTTA-
1 TATATATA-TATACTATAT
*
144735 TATTTATATACTA-TATAT
1 TATATATATA-TACTATAT
*
144753 TATATATATAAACTATAT
1 TATATATATATACTATAT
144771 GTACTATATAGTATA
1 -TA-TATATA-TATA
144786 ATTTACATAT
Statistics
Matches: 83, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
17 7 0.08
18 33 0.40
19 9 0.11
20 31 0.37
21 3 0.04
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (18 bp):
TATATATATATACTATAT
Found at i:144769 original size:53 final size:53
Alignment explanation
Indices: 144626--144770 Score: 184
Period size: 53 Copynumber: 2.7 Consensus size: 53
144616 CATATGAACT
* * * *
144626 ATATATATAAACTATATAGTTTACATATGACCTATATATATATATACTATAGTTG
1 ATATTTATATACTATATAGTTTACATATAAAC--TATATATATATACTATAGTTG
* * *
144681 ATATTTATATACTATATAGTTTACATATGACCTATATATATATACTATAGTTT
1 ATATTTATATACTATATAGTTTACATATAAACTATATATATATACTATAGTTG
*
144734 ATATTTATATACTATATA-TTATATATATAAACTATAT
1 ATATTTATATACTATATAGTT-TACATATAAACTATAT
144771 GTACTATATA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
52 2 0.02
53 51 0.61
55 30 0.36
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (53 bp):
ATATTTATATACTATATAGTTTACATATAAACTATATATATATACTATAGTTG
Found at i:144778 original size:20 final size:19
Alignment explanation
Indices: 144713--144785 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 19
144703 ACATATGACC
144713 TATATATATATACTATAGTT
1 TATATATATATACTATA-TT
*
144733 TATATTTATATACTATATAT
1 TATATATATATACTATAT-T
* *
144753 TATATATATAAACTATATG
1 TATATATATATACTATATT
144772 TACTATATAGTATA
1 TA-TATATA-TATA
144786 ATTTACATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.07
20 39 0.87
21 3 0.07
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (19 bp):
TATATATATATACTATATT
Found at i:144868 original size:33 final size:33
Alignment explanation
Indices: 144829--145073 Score: 224
Period size: 33 Copynumber: 7.5 Consensus size: 33
144819 TCCTAAACCC
*
144829 TAAACTATACATTATATAGTTTATTAGTATATA
1 TAAACTATACATTATATAGTTCATTAGTATATA
* ** *
144862 TAAACTATATAATATATATA-AACTATATGGTATATA
1 TAAACTATA-CAT-TATATAGTTC-AT-TAGTATATA
144898 TAAACTATACATTATATATAGTTCATTAGTATATA
1 TAAACTATACA-T-TATATAGTTCATTAGTATATA
* *
144933 TAAACTATATATTTTATAGTTCATTAGTATATA
1 TAAACTATACATTATATAGTTCATTAGTATATA
*
144966 TAAACTATATATTATATAGTTCATTAGTATATA
1 TAAACTATACATTATATAGTTCATTAGTATATA
* *
144999 T-AAC----C--TATATAG-T-ATATGGTAGATA
1 TAAACTATACATTATATAGTTCAT-TAGTATATA
* *
145024 CAAACTATA-TTTATATAGTTCATTAGTATATA
1 TAAACTATACATTATATAGTTCATTAGTATATA
* *
145056 TAAACTATATAGTATATA
1 TAAACTATACATTATATA
145074 TAAACTATAT
Statistics
Matches: 174, Mismatches: 21, Indels: 34
0.76 0.09 0.15
Matches are distributed among these distances:
24 2 0.01
25 8 0.05
26 10 0.06
31 7 0.04
32 19 0.11
33 70 0.40
34 3 0.02
35 27 0.16
36 27 0.16
37 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (33 bp):
TAAACTATACATTATATAGTTCATTAGTATATA
Found at i:144879 original size:18 final size:18
Alignment explanation
Indices: 144853--145084 Score: 139
Period size: 18 Copynumber: 13.1 Consensus size: 18
144843 TATAGTTTAT
144853 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
*
144871 TAATATATATAAACTATA
1 TAGTATATATAAACTATA
*
144889 TGGTATATATAAACTATA
1 TAGTATATATAAACTATA
* * **
144907 CATTATATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
144924 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
* **
144942 TA-T-TTTAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
144957 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
**
144975 TA-T-TATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
*
144990 TAGTATATATAACCTATA
1 TAGTATATATAAACTATA
* *
145008 TAGTATATGGTAGATAC-AAA
1 TAGTATAT-ATA-A-ACTATA
* * *
145028 CTA-TATTTATATAGT-TCA
1 -TAGTATATATAAACTAT-A
145046 TTAGTATATATAAACTATA
1 -TAGTATATATAAACTATA
145065 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
145083 TA
1 TA
145085 TTAATTTATT
Statistics
Matches: 159, Mismatches: 34, Indels: 42
0.68 0.14 0.18
Matches are distributed among these distances:
15 8 0.05
16 15 0.09
17 28 0.18
18 83 0.52
19 14 0.09
20 8 0.05
21 3 0.02
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (18 bp):
TAGTATATATAAACTATA
Found at i:145227 original size:60 final size:61
Alignment explanation
Indices: 145144--145272 Score: 190
Period size: 60 Copynumber: 2.1 Consensus size: 61
145134 TATAAGGATC
* * *
145144 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTATAA-CATTAAATTTGGAAT
1 AAATTGAACAAAGTTGAAATATGAAGCTTAAATTAATAAATTA-AATCATTAAATTTAGAAT
* *
145205 AAATTGAA-AAAGTTGAAATATGAAGCTTAAATTAATATATTAAATCATTAAATTTAGACT
1 AAATTGAACAAAGTTGAAATATGAAGCTTAAATTAATAAATTAAATCATTAAATTTAGAAT
145265 AAATTGAA
1 AAATTGAA
145273 TAAATTTAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
59 2 0.03
60 52 0.84
61 8 0.13
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (61 bp):
AAATTGAACAAAGTTGAAATATGAAGCTTAAATTAATAAATTAAATCATTAAATTTAGAAT
Found at i:147996 original size:15 final size:15
Alignment explanation
Indices: 147976--148006 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
147966 AACCTTGTAA
147976 AACCTTAACTATAAG
1 AACCTTAACTATAAG
*
147991 AACCTTAATTATAAG
1 AACCTTAACTATAAG
148006 A
1 A
148007 TCTTAGAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.29
Consensus pattern (15 bp):
AACCTTAACTATAAG
Found at i:148347 original size:13 final size:13
Alignment explanation
Indices: 148328--148365 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
148318 TAATTTAGTG
148328 ATTATAAATAA-A
1 ATTATAAATAAGA
148340 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
148355 ATTATAAATAA
1 ATTATAAATAA
148366 TATAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:148375 original size:19 final size:19
Alignment explanation
Indices: 148344--148461 Score: 76
Period size: 19 Copynumber: 6.5 Consensus size: 19
148334 AATAAAATTT
148344 ATAATAT-AAGAATTATAA
1 ATAATATAAAGAATTATAA
148362 ATAATATAAAGAATT-TGAA
1 ATAATATAAAGAATTAT-AA
* *
148381 TTAATATAAA-AATCA-AA
1 ATAATATAAAGAATTATAA
*
148398 TTTATAATATACA-AA-T-T--
1 ---ATAATATAAAGAATTATAA
148415 ATAATAT-AAGAATTATAA
1 ATAATATAAAGAATTATAA
* *
148433 AAAATATAAAGAATTGTAA
1 ATAATATAAAGAATTATAA
*
148452 TTAATATAAA
1 ATAATATAAA
148462 AACTAAATTT
Statistics
Matches: 77, Mismatches: 10, Indels: 25
0.69 0.09 0.22
Matches are distributed among these distances:
13 1 0.01
14 9 0.12
15 1 0.01
16 1 0.01
17 2 0.03
18 17 0.22
19 36 0.47
20 10 0.13
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (19 bp):
ATAATATAAAGAATTATAA
Found at i:148387 original size:37 final size:36
Alignment explanation
Indices: 148345--148460 Score: 116
Period size: 37 Copynumber: 3.2 Consensus size: 36
148335 ATAAAATTTA
148345 TAATATAAGAATTATAAATAATATAAAGAATTTGAAT
1 TAATATAAGAATTATAAATAATATAAAGAA-TTGAAT
* * *
148382 TAATATAAAAATCA-AATTTATAATATACA-AATT--A-
1 TAATATAAGAATTATAA---ATAATATAAAGAATTGAAT
*
148416 TAATATAAGAATTATAAAAAATATAAAGAATTGTAAT
1 TAATATAAGAATTATAAATAATATAAAGAATTG-AAT
148453 TAATATAA
1 TAATATAA
148461 AAACTAAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
32 8 0.13
33 4 0.06
34 12 0.19
35 3 0.05
36 3 0.05
37 22 0.35
38 2 0.03
39 9 0.14
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (36 bp):
TAATATAAGAATTATAAATAATATAAAGAATTGAAT
Found at i:148418 original size:14 final size:14
Alignment explanation
Indices: 148394--148432 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
148384 ATATAAAAAT
148394 CAAATTTATAATATA
1 CAAA-TTATAATATA
148409 CAAATTATAATATA
1 CAAATTATAATATA
148423 -AGAATTATAA
1 CA-AATTATAA
148433 AAAATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 18 0.78
15 4 0.17
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (14 bp):
CAAATTATAATATA
Found at i:148425 original size:71 final size:70
Alignment explanation
Indices: 148329--148472 Score: 222
Period size: 71 Copynumber: 2.0 Consensus size: 70
148319 AATTTAGTGA
*
148329 TTATAAATAAAATTTATAATATAAGAATTATAAATAATATAAAGAATT-TGAATTAATATAAAAA
1 TTATAAATAAAATTTATAATATAAGAATTATAAAAAATATAAAGAATTGT-AATTAATATAAAAA
148393 -TCAAAT
65 CT-AAAT
148399 TTATAATATACAAA-TTATAATATAAGAATTATAAAAAATATAAAGAATTGTAATTAATATAAAA
1 TTATAA-ATA-AAATTTATAATATAAGAATTATAAAAAATATAAAGAATTGTAATTAATATAAAA
148463 ACTAAAT
64 ACTAAAT
148470 TTA
1 TTA
148473 ATTATCATAA
Statistics
Matches: 69, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
70 6 0.09
71 58 0.84
72 5 0.07
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (70 bp):
TTATAAATAAAATTTATAATATAAGAATTATAAAAAATATAAAGAATTGTAATTAATATAAAAAC
TAAAT
Found at i:148516 original size:27 final size:26
Alignment explanation
Indices: 148465--148517 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
148455 ATATAAAAAC
* *
148465 TAAATTTAATTATCATAAGTTTATTA
1 TAAATTTAAATAGCATAAGTTTATTA
148491 TAAATTTAAAATAGCATAA-TTATATTA
1 TAAATTT-AAATAGCATAAGTT-TATTA
148518 ATTGTAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (26 bp):
TAAATTTAAATAGCATAAGTTTATTA
Found at i:153970 original size:18 final size:18
Alignment explanation
Indices: 153949--153991 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
153939 TAATAATAAA
153949 TTATTATAAAATATATTT
1 TTATTATAAAATATATTT
*
153967 TTATTAT-AATTATATTT
1 TTATTATAAAATATATTT
153984 TTATTATA
1 TTATTATA
153992 GTTTAAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATAAAATATATTT
Found at i:155439 original size:15 final size:15
Alignment explanation
Indices: 155419--155459 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
155409 TAAATAAAAA
155419 TTTATAATTAATAAT
1 TTTATAATTAATAAT
*
155434 TTTATAATAAAATAAT
1 TTTATAAT-TAATAAT
*
155450 TTTAAAATTA
1 TTTATAATTA
155460 TGAATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTATAATTAATAAT
Found at i:155449 original size:16 final size:15
Alignment explanation
Indices: 155407--155453 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 15
155397 TCTATCTTAA
155407 TTTA-AATAAA-AA-
1 TTTATAATAAATAAT
*
155419 TTTATAATTAATAAT
1 TTTATAATAAATAAT
155434 TTTATAATAAAATAAT
1 TTTATAAT-AAATAAT
155450 TTTA
1 TTTA
155454 AAATTATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 4 0.14
13 5 0.17
14 2 0.07
15 8 0.28
16 10 0.34
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTATAATAAATAAT
Found at i:160458 original size:13 final size:13
Alignment explanation
Indices: 160440--160464 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
160430 TCGAATATAC
160440 TTAGAAAATCTTT
1 TTAGAAAATCTTT
160453 TTAGAAAATCTT
1 TTAGAAAATCTT
160465 AAAATTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTAGAAAATCTTT
Found at i:160928 original size:17 final size:17
Alignment explanation
Indices: 160903--160940 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
160893 CAAACAAATT
*
160903 CAAAGTCAAACAATCCA
1 CAAATTCAAACAATCCA
*
160920 CAAATTCAAACATTCCA
1 CAAATTCAAACAATCCA
160937 -AAAT
1 CAAAT
160941 ATCCAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.53, C:0.26, G:0.03, T:0.18
Consensus pattern (17 bp):
CAAATTCAAACAATCCA
Found at i:162862 original size:23 final size:22
Alignment explanation
Indices: 162825--162885 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
162815 GGGGTATCGA
* *
162825 TTCCCCTACAGGGGGGAATCAG
1 TTCCCCTTCAAGGGGGAATCAG
*
162847 TTCCCCTTCAAAGGGGGAATCTG
1 TTCCCCTTC-AAGGGGGAATCAG
162870 TTCCCCTTCAAGGGGG
1 TTCCCCTTCAAGGGGG
162886 TATCGATTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 15 0.43
23 20 0.57
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.23
Consensus pattern (22 bp):
TTCCCCTTCAAGGGGGAATCAG
Found at i:162895 original size:22 final size:22
Alignment explanation
Indices: 162814--162896 Score: 89
Period size: 22 Copynumber: 3.7 Consensus size: 22
162804 AGAACCCTTG
* * *
162814 GGGGGTATCGATTCCCCTACAG
1 GGGGGAATCGATTCCCCTTCAA
162836 GGGGGAATC-AGTTCCCCTTCAAA
1 GGGGGAATCGA-TTCCCCTTC-AA
162859 GGGGGAATCTG-TTCCCCTTCAA
1 GGGGGAATC-GATTCCCCTTCAA
*
162881 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
162897 TCTGCACCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.04
22 31 0.60
23 19 0.37
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:171668 original size:2 final size:2
Alignment explanation
Indices: 171596--171657 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
171586 ATTTTATTCA
171596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
171638 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
171658 TCAGTTATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:172954 original size:74 final size:73
Alignment explanation
Indices: 172861--173009 Score: 171
Period size: 74 Copynumber: 2.0 Consensus size: 73
172851 GATTAAACTC
172861 AAGTTTAGGATAATATTTTAAACATTATAT-TTTATCTTT-GTATTTTAGTTTAAATAGGTTTT-
1 AAGTTTAGGATAATATTTT--ACATTATATCTTTAT-TTTAGTATTTTAGTTTAAATA-GTTTTA
172923 AGTATTTTAATT
62 AGTATTTTAATT
* * * *
172935 AAGTTATAGGATTAT-TTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAG
1 AAGTT-TAGGATAATATTTTACATTATATCTTTATTTTA-GTATTTTAGTTTAAATAGTTTTAAG
*
172999 TGTTTTAATT
64 TATTTTAATT
173009 A
1 A
173010 GGATTTAAGA
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
72 10 0.15
73 9 0.14
74 38 0.58
75 8 0.12
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (73 bp):
AAGTTTAGGATAATATTTTACATTATATCTTTATTTTAGTATTTTAGTTTAAATAGTTTTAAGTA
TTTTAATT
Found at i:173656 original size:19 final size:18
Alignment explanation
Indices: 173605--173653 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
173595 AATCTCTTTA
173605 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
* *
173624 TTTCTTTTATTTAATTCTT
1 ATT-TTTTATTTAATTATT
173643 ATTTTTTATTT
1 ATTTTTTATTT
173654 TAAAAACAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:173718 original size:13 final size:15
Alignment explanation
Indices: 173682--173718 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
173672 AATCTCTCTT
173682 TTATATTTATTACTA
1 TTATATTTATTACTA
173697 TTAATATTTATTA-TA
1 TT-ATATTTATTACTA
173712 -TATATTT
1 TTATATTT
173719 CCTTTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 1 0.05
15 4 0.19
16 10 0.48
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATATTTATTACTA
Found at i:176657 original size:6 final size:6
Alignment explanation
Indices: 176646--176671 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
176636 TTCGTTATAA
176646 TTTTGT TTTTGT TTTTGT TTTTGT TT
1 TTTTGT TTTTGT TTTTGT TTTTGT TT
176672 CATTTCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:176677 original size:5 final size:5
Alignment explanation
Indices: 176669--176705 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
176659 TTTGTTTTTG
176669 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TT
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TT
176706 ATTTTATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTCA
Found at i:176745 original size:21 final size:21
Alignment explanation
Indices: 176706--176747 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
176696 TCATTTCATT
*
176706 ATTTTATTTATTTTATTTTTA
1 ATTTTATTTATATTATTTTTA
*
176727 ATTTTATTTTATATTTTTTTT
1 ATTTTA-TTTATATTATTTTT
176748 CTGAACAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (21 bp):
ATTTTATTTATATTATTTTTA
Found at i:178455 original size:75 final size:75
Alignment explanation
Indices: 178366--178513 Score: 176
Period size: 75 Copynumber: 2.0 Consensus size: 75
178356 TAAACTCAAG
*
178366 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTT-TTATTTTAGTTTAAATATGTTTTAG-T
1 TTTAGGATAATATTTT-AACATTATATCTTTAT-TTTAGTATTTTAGTTTAAATA-GTTTTAGAT
178428 ATTTTAATTAAGT
63 ATTTTAATTAAGT
* * * * * *
178441 TTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAGATGT
1 TTTAGGATAATATTTTAACATTATATCTTTATTTTA-GTATTTTAGTTTAAATAGTTTTAGATAT
178506 TTTAATTA
65 TTTAATTA
178514 GGATTTAAGA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
74 10 0.16
75 26 0.42
76 26 0.42
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATCTTTATTTTAGTATTTTAGTTTAAATAGTTTTAGATATT
TTAATTAAGT
Done.