Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 124 of 130
Found at i:24917791 original size:2 final size:2
Alignment explanation
Indices: 24917784--24917823 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
24917774 AAATGTACAA
24917784 AT AT AT AT AT AT AT AT AT AT AT AT A- 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 AT AT AT AT A
24917824 GACTACTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24921858 original size:3 final size:3
Alignment explanation
Indices: 24921822--24921869 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
24921812 ATCTCGAAAC
* * * * *
24921822 AAT AAT AAC AAC AAC AAT AAT AAC AAT AAC AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24921870 TTATGTATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (3 bp):
AAT
Found at i:24921864 original size:15 final size:15
Alignment explanation
Indices: 24921819--24921865 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
24921809 ATCATCTCGA
*
24921819 AACAATAATAACAAC
1 AACAATAATAACAAT
24921834 AACAATAATAACAAT
1 AACAATAATAACAAT
*
24921849 AACAATAATAATAAT
1 AACAATAATAACAAT
24921864 AA
1 AA
24921866 TAATTTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19
Consensus pattern (15 bp):
AACAATAATAACAAT
Found at i:24931145 original size:12 final size:12
Alignment explanation
Indices: 24931128--24931154 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
24931118 CTGCCAAACA
24931128 AAAACATGTAAT
1 AAAACATGTAAT
24931140 AAAACATGTAAT
1 AAAACATGTAAT
24931152 AAA
1 AAA
24931155 TGTTATTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (12 bp):
AAAACATGTAAT
Found at i:24934691 original size:22 final size:22
Alignment explanation
Indices: 24934663--24934706 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
24934653 TGATTAAAAA
24934663 CTACTGGTATAGCAGCAATTGT
1 CTACTGGTATAGCAGCAATTGT
24934685 CTACTGGTATAGCAGCAATTGT
1 CTACTGGTATAGCAGCAATTGT
24934707 GAGGTCATAC
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:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (22 bp):
CTACTGGTATAGCAGCAATTGT
Found at i:24948476 original size:380 final size:380
Alignment explanation
Indices: 24947775--24948533 Score: 1500
Period size: 380 Copynumber: 2.0 Consensus size: 380
24947765 GGAATTCCAC
24947775 TAAGCATCCAATCCTTTCAGATACAACCACAACCACCAAAGGACTTTACTAGCTTGGCTAGCAGA
1 TAAGCATCCAATCCTTTCAGATACAACCACAACCACCAAAGGACTTTACTAGCTTGGCTAGCAGA
24947840 TATCTTCACAAAGGTTGTGTCCTGGAAATTGCTTTATATCTTTTATATGATATGACTTCGAATTT
66 TATCTTCACAAAGGTTGTGTCCTGGAAATTGCTTTATATCTTTTATATGATATGACTTCGAATTT
24947905 TATGGGACCCAATTGATCAATCAATCTCGGCAAAAGCCAATATCCTTCTACTTTTCCATTTTCTC
131 TATGGGACCCAATTGATCAATCAATCTCGGCAAAAGCCAATATCCTTCTACTTTTCCATTTTCTC
24947970 CTTTCTCATTGAGTTTTAACTATGAAAAGTACTTCTTAACTTCAAGGTTTTCCTCCAAGAAAATC
196 CTTTCTCATTGAGTTTTAACTATGAAAAGTACTTCTTAACTTCAAGGTTTTCCTCCAAGAAAATC
*
24948035 CCTTTCTTTTTCCATTTATTCAAACAAAACAAGCAGAAAAAACATACAAAATCCGAAAGCAGAAA
261 CCTTTCTTTTTCCAGTTATTCAAACAAAACAAGCAGAAAAAACATACAAAATCCGAAAGCAGAAA
*
24948100 AGAGTAATCTCTATATTACTGAAACTGTGGAATAACCTAGTAATGTTTGCCTCAG
326 AGAGTAATCTCTATATTACCGAAACTGTGGAATAACCTAGTAATGTTTGCCTCAG
24948155 TAAGCATCCAATCCTTTCAGATACAACCACAACCACCAAAGGACTTTACTAGCTTGGCTAGCAGA
1 TAAGCATCCAATCCTTTCAGATACAACCACAACCACCAAAGGACTTTACTAGCTTGGCTAGCAGA
24948220 TATCTTCACAAAGGTTGTGTCCTGGAAATTGCTTTATATCTTTTATATGATATGACTTCGAATTT
66 TATCTTCACAAAGGTTGTGTCCTGGAAATTGCTTTATATCTTTTATATGATATGACTTCGAATTT
24948285 TATGGGACCCAATTGATCAATCAATCTCGGCAAAAGCCAATATCCTTCTACTTTTCCATTTTCTC
131 TATGGGACCCAATTGATCAATCAATCTCGGCAAAAGCCAATATCCTTCTACTTTTCCATTTTCTC
24948350 CTTTCTCATTGAGTTTTAACTATGAAAAGTACTTCTTAACTTCAAGGTTTTCCTCCAAGAAAATC
196 CTTTCTCATTGAGTTTTAACTATGAAAAGTACTTCTTAACTTCAAGGTTTTCCTCCAAGAAAATC
24948415 CCTTTCTTTTTCCAGTTATTCAAACAAAACAAGCAGAAAAAACATACAAAATCCGAAAGCAGAAA
261 CCTTTCTTTTTCCAGTTATTCAAACAAAACAAGCAGAAAAAACATACAAAATCCGAAAGCAGAAA
24948480 AGAGTAATCTCTATATTACCGAAACTGTGGAATAACCTAGTAATGTTTGCCTCA
326 AGAGTAATCTCTATATTACCGAAACTGTGGAATAACCTAGTAATGTTTGCCTCA
24948534 CCTTGATTAT
Statistics
Matches: 377, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
380 377 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (380 bp):
TAAGCATCCAATCCTTTCAGATACAACCACAACCACCAAAGGACTTTACTAGCTTGGCTAGCAGA
TATCTTCACAAAGGTTGTGTCCTGGAAATTGCTTTATATCTTTTATATGATATGACTTCGAATTT
TATGGGACCCAATTGATCAATCAATCTCGGCAAAAGCCAATATCCTTCTACTTTTCCATTTTCTC
CTTTCTCATTGAGTTTTAACTATGAAAAGTACTTCTTAACTTCAAGGTTTTCCTCCAAGAAAATC
CCTTTCTTTTTCCAGTTATTCAAACAAAACAAGCAGAAAAAACATACAAAATCCGAAAGCAGAAA
AGAGTAATCTCTATATTACCGAAACTGTGGAATAACCTAGTAATGTTTGCCTCAG
Found at i:24949573 original size:20 final size:22
Alignment explanation
Indices: 24949525--24949569 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
24949515 TTTTTAATTA
24949525 TTAAATATAATATATATTATTT
1 TTAAATATAATATATATTATTT
* *
24949547 TTAAATATGATATATTTTATTT
1 TTAAATATAATATATATTATTT
24949569 T
1 T
24949570 AATACATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTAAATATAATATATATTATTT
Found at i:24949905 original size:22 final size:22
Alignment explanation
Indices: 24949880--24949921 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
24949870 GCACTATATT
24949880 ATAAAATCAATATTAACAAAAA
1 ATAAAATCAATATTAACAAAAA
* *
24949902 ATAAAATTAATTTTAACAAA
1 ATAAAATCAATATTAACAAA
24949922 TTGAAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (22 bp):
ATAAAATCAATATTAACAAAAA
Found at i:24950710 original size:31 final size:31
Alignment explanation
Indices: 24950656--24950731 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
24950646 AAATTAACTA
* *
24950656 TATTATAAAT-AAATATCACATTAAATATAAT
1 TATTATAATTAAAATATAACATTAAATAT-AT
* *
24950687 T-TTATAATTAAAATATAATATTAAATATTT
1 TATTATAATTAAAATATAACATTAAATATAT
24950717 TATTATAATTTAAAA
1 TATTATAA-TTAAAA
24950732 AGCATTAGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
30 9 0.24
31 23 0.61
32 6 0.16
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (31 bp):
TATTATAATTAAAATATAACATTAAATATAT
Found at i:24967447 original size:13 final size:13
Alignment explanation
Indices: 24967423--24967472 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
24967413 TTAATAATCT
24967423 AAAATATAATATA
1 AAAATATAATATA
* *
24967436 ATAATATGATATA
1 AAAATATAATATA
*
24967449 AAAATAATACAAATA
1 AAAAT-ATA-ATATA
24967464 AAAATATAA
1 AAAATATAA
24967473 AAATAATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 16 0.53
14 5 0.17
15 9 0.30
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (13 bp):
AAAATATAATATA
Found at i:24967476 original size:14 final size:15
Alignment explanation
Indices: 24967446--24967478 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
24967436 ATAATATGAT
*
24967446 ATAAAAATAATACAA
1 ATAAAAATAATAAAA
24967461 ATAAAAAT-ATAAAA
1 ATAAAAATAATAAAA
24967475 ATAA
1 ATAA
24967479 TATATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAAAAATAATAAAA
Found at i:24967524 original size:33 final size:35
Alignment explanation
Indices: 24967460--24967525 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
24967450 AAATAATACA
* *
24967460 AATAAAAATATAAAAATAATATATTTTAAATTTTT
1 AATAAAAATATAAAAATAATATATATAAAATTTTT
* *
24967495 AATAAAAATATAAATA-AATTTA-ATAAAATTT
1 AATAAAAATATAAAAATAATATATATAAAATTT
24967526 AAAAAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 7 0.26
34 5 0.19
35 15 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (35 bp):
AATAAAAATATAAAAATAATATATATAAAATTTTT
Found at i:24982289 original size:17 final size:18
Alignment explanation
Indices: 24982264--24982300 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
24982254 AATTTCGAAG
*
24982264 AAAATAATCA-AAAAGTA
1 AAAAGAATCAGAAAAGTA
24982281 AAAAGAATCAGAAAAGTA
1 AAAAGAATCAGAAAAGTA
24982299 AA
1 AA
24982301 TGCAATCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (18 bp):
AAAAGAATCAGAAAAGTA
Found at i:24983610 original size:37 final size:36
Alignment explanation
Indices: 24983569--24983647 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
24983559 TTTTAATCAA
* *
24983569 ATTAACCGAAAATCAAAATTTTTTTAAAATAATTTTC
1 ATTAACAGAAAA-CAAAATTATTTTAAAATAATTTTC
* * *
24983606 ATTAATAGAAAACTAAATTATTTTAAAATTATTTTC
1 ATTAACAGAAAACAAAATTATTTTAAAATAATTTTC
24983642 ATTAAC
1 ATTAAC
24983648 TGTCTAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 26 0.72
37 10 0.28
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.42
Consensus pattern (36 bp):
ATTAACAGAAAACAAAATTATTTTAAAATAATTTTC
Found at i:24986940 original size:14 final size:14
Alignment explanation
Indices: 24986912--24986971 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
24986902 TTTTAATTAA
24986912 TTAATTAT-T-TAT
1 TTAATTATATATAT
24986924 TTAATTATATATAT
1 TTAATTATATATAT
* *
24986938 TTATATAATGATATTT
1 TTA-ATTAT-ATATAT
* *
24986954 TTAAATATTTATAT
1 TTAATTATATATAT
24986968 TTAA
1 TTAA
24986972 AAAATAAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 8 0.21
13 1 0.03
14 14 0.37
15 7 0.18
16 8 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TTAATTATATATAT
Found at i:24986995 original size:22 final size:20
Alignment explanation
Indices: 24986955--24987008 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 20
24986945 ATGATATTTT
24986955 TAAATATTTATATTTAAAAAA
1 TAAAT-TTTATATTTAAAAAA
24986976 TAAATTTTATATTTTTAAAAAA
1 TAAATTTTATA--TTTAAAAAA
24986998 TAATATTTTAT
1 TAA-ATTTTAT
24987009 TAATTTCGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.20
21 5 0.17
22 12 0.40
23 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAATTTTATATTTAAAAAA
Found at i:24993479 original size:17 final size:17
Alignment explanation
Indices: 24993457--24993498 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
24993447 TCTCCTGATG
24993457 GCTGTCTGGACAAATAT
1 GCTGTCTGGACAAATAT
24993474 GCTGTCTGGACAAATAT
1 GCTGTCTGGACAAATAT
*
24993491 TCTGTCTG
1 GCTGTCTG
24993499 AATGGATGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (17 bp):
GCTGTCTGGACAAATAT
Found at i:25004505 original size:16 final size:16
Alignment explanation
Indices: 25004484--25004514 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25004474 TATTTAATTT
25004484 ATTTAAAATATAAAAA
1 ATTTAAAATATAAAAA
*
25004500 ATTTAAAATTTAAAA
1 ATTTAAAATATAAAA
25004515 TATAATATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTTAAAATATAAAAA
Found at i:25008292 original size:357 final size:357
Alignment explanation
Indices: 25007637--25008352 Score: 1423
Period size: 357 Copynumber: 2.0 Consensus size: 357
25007627 AATAGTAGGG
25007637 AAGGGAAGGGAAGGAGTGGGTACCCTCTCCCTTATTTGGCAAACATTTCAATTGAAAGAAGAGAC
1 AAGGGAAGGGAAGGAGTGGGTACCCTCTCCCTTATTTGGCAAACATTTCAATTGAAAGAAGAGAC
25007702 AATTTGGGGCTATTCATCGTTCAAATTAACCATCATTTCATAAAACTATCAGCATCGAATTTTTA
66 AATTTGGGGCTATTCATCGTTCAAATTAACCATCATTTCATAAAACTATCAGCATCGAATTTTTA
25007767 AACTGTTGTTAATTTCACGATAAAATTGGAAATAATAGATGTATATATCTTATATATTCAGAGAT
131 AACTGTTGTTAATTTCACGATAAAATTGGAAATAATAGATGTATATATCTTATATATTCAGAGAT
*
25007832 TTATTTAAGTTCAAATTCTTTTTTTAAAATCAAATTTAAAGGACAATGCCACTTTTGAAACGTTG
196 TTATTTAAGTTCAAATTCTTTTTTTAAAATCAAATTTAAAGGACAATGCCACTTTTGAAACGTTA
25007897 TAAAACAAGAGAGGACGTTATGGTTAATTGATTAAGAATGCTCAAGAATGGTGTTACTACATGAG
261 TAAAACAAGAGAGGACGTTATGGTTAATTGATTAAGAATGCTCAAGAATGGTGTTACTACATGAG
25007962 TTTTGTATGGTATTTGTAACAAAAATAAAGTA
326 TTTTGTATGGTATTTGTAACAAAAATAAAGTA
25007994 AAGGGAAGGGAAGGAGTGGGTACCCTCTCCCTTATTTGGCAAACATTTCAATTGAAAGAAGAGAC
1 AAGGGAAGGGAAGGAGTGGGTACCCTCTCCCTTATTTGGCAAACATTTCAATTGAAAGAAGAGAC
25008059 AATTTGGGGCTATTCATCGTTCAAATTAACCATCATTTCATAAAACTATCAGCATCGAATTTTTA
66 AATTTGGGGCTATTCATCGTTCAAATTAACCATCATTTCATAAAACTATCAGCATCGAATTTTTA
25008124 AACTGTTGTTAATTTCACGATAAAATTGGAAATAATAGATGTATATATCTTATATATTCAGAGAT
131 AACTGTTGTTAATTTCACGATAAAATTGGAAATAATAGATGTATATATCTTATATATTCAGAGAT
25008189 TTATTTAAGTTCAAATTCTTTTTTTAAAATCAAATTTAAAGGACAATGCCACTTTTGAAACGTTA
196 TTATTTAAGTTCAAATTCTTTTTTTAAAATCAAATTTAAAGGACAATGCCACTTTTGAAACGTTA
25008254 TAAAACAAGAGAGGACGTTATGGTTAATTGATTAAGAATGCTCAAGAATGGTGTTACTACATGAG
261 TAAAACAAGAGAGGACGTTATGGTTAATTGATTAAGAATGCTCAAGAATGGTGTTACTACATGAG
25008319 TTTTGTATGGTATTTGTAACAAAAATAAAGTA
326 TTTTGTATGGTATTTGTAACAAAAATAAAGTA
25008351 AA
1 AA
25008353 ATGAAATGAT
Statistics
Matches: 358, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
357 358 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (357 bp):
AAGGGAAGGGAAGGAGTGGGTACCCTCTCCCTTATTTGGCAAACATTTCAATTGAAAGAAGAGAC
AATTTGGGGCTATTCATCGTTCAAATTAACCATCATTTCATAAAACTATCAGCATCGAATTTTTA
AACTGTTGTTAATTTCACGATAAAATTGGAAATAATAGATGTATATATCTTATATATTCAGAGAT
TTATTTAAGTTCAAATTCTTTTTTTAAAATCAAATTTAAAGGACAATGCCACTTTTGAAACGTTA
TAAAACAAGAGAGGACGTTATGGTTAATTGATTAAGAATGCTCAAGAATGGTGTTACTACATGAG
TTTTGTATGGTATTTGTAACAAAAATAAAGTA
Found at i:25012422 original size:2 final size:2
Alignment explanation
Indices: 25012417--25012449 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
25012407 TATGTGTGTG
25012417 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25012450 TGAAGTTTGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25012486 original size:5 final size:5
Alignment explanation
Indices: 25012476--25012504 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
25012466 ATTAGTAAAA
25012476 GAAAG GAAAG GAAAG GAAAG GAAAG GAAA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAA
25012505 CTAGAGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:25022390 original size:15 final size:15
Alignment explanation
Indices: 25022372--25022408 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
25022362 TCACAAATAA
25022372 ATTTATTTAAAATTT
1 ATTTATTTAAAATTT
**
25022387 ATTTATTTATTATTT
1 ATTTATTTAAAATTT
25022402 ATTTATT
1 ATTTATT
25022409 ACTCATTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTATTTAAAATTT
Found at i:25022399 original size:11 final size:11
Alignment explanation
Indices: 25022385--25022409 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25022375 TATTTAAAAT
25022385 TTATTTATTTA
1 TTATTTATTTA
25022396 TTATTTATTTA
1 TTATTTATTTA
25022407 TTA
1 TTA
25022410 CTCATTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:25022516 original size:15 final size:15
Alignment explanation
Indices: 25022498--25022549 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
25022488 GATTAATGTA
*
25022498 TATTTGTTTAAAATT
1 TATTTATTTAAAATT
25022513 TATTTATTT-AAATT
1 TATTTATTTAAAATT
* *
25022527 TATTTAATTATAATT
1 TATTTATTTAAAATT
25022542 TATTTATT
1 TATTTATT
25022550 ATTTATAGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 13 0.41
15 19 0.59
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
TATTTATTTAAAATT
Found at i:25022550 original size:14 final size:15
Alignment explanation
Indices: 25022508--25022551 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
25022498 TATTTGTTTA
25022508 AAATTTATTTATT-T
1 AAATTTATTTATTAT
25022522 AAATTTATTTAATTAT
1 AAATTTATTT-ATTAT
25022538 -AATTTATTTATTAT
1 AAATTTATTTATTAT
25022552 TTATAGACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 15 0.54
15 12 0.43
16 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
AAATTTATTTATTAT
Found at i:25022555 original size:18 final size:18
Alignment explanation
Indices: 25022510--25022556 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 18
25022500 TTTGTTTAAA
25022510 ATTTATTTATTTA-AATTT
1 ATTTA-TTATTTATAATTT
25022528 ATTTA--A-TTATAATTT
1 ATTTATTATTTATAATTT
25022543 ATTTATTATTTATA
1 ATTTATTATTTATA
25022557 GACATATTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.12
15 11 0.44
17 1 0.04
18 10 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTATTATTTATAATTT
Found at i:25023024 original size:13 final size:14
Alignment explanation
Indices: 25022998--25023026 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
25022988 TTTTAAATTA
25022998 ATTTAAATTTTTTT
1 ATTTAAATTTTTTT
25023012 ATTTAAATTTTTTT
1 ATTTAAATTTTTTT
25023026 A
1 A
25023027 ATATTTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTAAATTTTTTT
Found at i:25031466 original size:24 final size:23
Alignment explanation
Indices: 25031430--25031477 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
25031420 ACAAATCCAC
*
25031430 ACATGGACAGTTATAGAATATAA
1 ACATGGACAGTTACAGAATATAA
* *
25031453 ACATGTACAAGTTACAGTATATAA
1 ACATGGAC-AGTTACAGAATATAA
25031477 A
1 A
25031478 GGGGTGACAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (23 bp):
ACATGGACAGTTACAGAATATAA
Found at i:25041053 original size:23 final size:23
Alignment explanation
Indices: 25041021--25041099 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
25041011 TAATTTATGT
25041021 TAAAAGTTTATTTAAATATAAATA
1 TAAAA-TTTATTTAAATATAAATA
* **
25041045 TAAATTTTATTTTGATATAAAAGTA
1 TAAAATTTATTTAAATAT-AAA-TA
25041070 TAAAAATTTATTTAAATA-AAATAA
1 T-AAAATTTATTTAAATATAAAT-A
25041094 TAAAAT
1 TAAAAT
25041100 GTAAAAATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
23 17 0.38
24 12 0.27
25 3 0.07
26 13 0.29
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
TAAAATTTATTTAAATATAAATA
Found at i:25053206 original size:90 final size:90
Alignment explanation
Indices: 25053052--25053274 Score: 311
Period size: 90 Copynumber: 2.5 Consensus size: 90
25053042 ATGGTAATAT
* * * * * * *
25053052 CAAGTTTTATCGAAGAGAGTTTATAATATTTTAATATTATATTGAAATATTTTAATAATTTTTTA
1 CAAGTTTTATCGAAGAAAGCTTATAATATTTTAATATCATATCGAAAGATTCTAATAATCTTTTA
* *
25053117 TGATATATAAGTAAATATTTAAACA
66 TAATATATAAGTAAAGATTTAAACA
* *
25053142 CAAGTTTTGTCGAAAAAAGCTTATAATATTTTAATATCATATCGAAAGATTCTAATAATCTTTTA
1 CAAGTTTTATCGAAGAAAGCTTATAATATTTTAATATCATATCGAAAGATTCTAATAATCTTTTA
25053207 TAATATATAAGTAAAGATTTAAACA
66 TAATATATAAGTAAAGATTTAAACA
* * * *
25053232 CAAATTTTATCGAAGAAAGCTTATGATATTCTAATCTCATATC
1 CAAGTTTTATCGAAGAAAGCTTATAATATTTTAATATCATATC
25053275 AAAATATTTT
Statistics
Matches: 116, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 116 1.00
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (90 bp):
CAAGTTTTATCGAAGAAAGCTTATAATATTTTAATATCATATCGAAAGATTCTAATAATCTTTTA
TAATATATAAGTAAAGATTTAAACA
Found at i:25058639 original size:19 final size:19
Alignment explanation
Indices: 25058615--25058655 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
25058605 GGATCCAGAT
25058615 CAACTACGTTTTCTCCGTA
1 CAACTACGTTTTCTCCGTA
25058634 CAACTACGTTTTCTCCGTA
1 CAACTACGTTTTCTCCGTA
25058653 CAA
1 CAA
25058656 TTCATTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.34
Consensus pattern (19 bp):
CAACTACGTTTTCTCCGTA
Found at i:25061928 original size:31 final size:32
Alignment explanation
Indices: 25061867--25061946 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 32
25061857 GATTGTATTT
* * *
25061867 TTTTTTTTTAAATATCCAAATAAACTCTTGA-A
1 TTTTATTTTAAA-ATACAAATAAACCCTTGATA
*
25061899 TTTTATTTTAAAATACAAATAGACCCTTGATA
1 TTTTATTTTAAAATACAAATAAACCCTTGATA
25061931 TTTTATTATATAAAAT
1 TTTTATT-T-TAAAAT
25061947 TAAAATTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 15 0.37
32 19 0.46
33 1 0.02
34 6 0.15
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (32 bp):
TTTTATTTTAAAATACAAATAAACCCTTGATA
Found at i:25066223 original size:28 final size:29
Alignment explanation
Indices: 25066164--25066232 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
25066154 TAATAATTAT
25066164 TTAAATTTTTAATATTTTATTTCAATCAA
1 TTAAATTTTTAATATTTTATTTCAATCAA
* * * * *
25066193 TTAATTTTTTAAT-TTTTTTTTTACTCGA
1 TTAAATTTTTAATATTTTATTTCAATCAA
*
25066221 TTAAATTCTTAA
1 TTAAATTTTTAA
25066233 ATGGATGAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
28 21 0.64
29 12 0.36
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.59
Consensus pattern (29 bp):
TTAAATTTTTAATATTTTATTTCAATCAA
Found at i:25068856 original size:21 final size:21
Alignment explanation
Indices: 25068818--25068864 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
25068808 TCATATATTT
25068818 TAATT-TTTTATAAATAAA-A
1 TAATTATTTTATAAATAAATA
**
25068837 GTAATTATTTTATATTTAAATA
1 -TAATTATTTTATAAATAAATA
25068859 TAATTA
1 TAATTA
25068865 AATATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 17 0.74
22 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TAATTATTTTATAAATAAATA
Found at i:25068889 original size:22 final size:20
Alignment explanation
Indices: 25068847--25068901 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
25068837 GTAATTATTT
* *
25068847 TATATTTAAATATAATTAAA
1 TATATTAAAATTTAATTAAA
25068867 TATATTAAAATTTATATTAAA
1 TATATTAAAATTTA-ATTAAA
25068888 -ATAATATAAAATTT
1 TAT-AT-TAAAATTT
25068902 TTAAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.47
21 8 0.27
22 8 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATATTAAAATTTAATTAAA
Found at i:25068919 original size:14 final size:15
Alignment explanation
Indices: 25068893--25068925 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
25068883 TTAAAATAAT
25068893 ATAAAATTTTTAAAA
1 ATAAAATTTTTAAAA
25068908 ATAAAA-TTTTAAAA
1 ATAAAATTTTTAAAA
25068922 ATAA
1 ATAA
25068926 TTAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAAAATTTTTAAAA
Found at i:25069275 original size:23 final size:24
Alignment explanation
Indices: 25069248--25069297 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
25069238 TATTTTTTAC
25069248 ATTAAATATACCTATATCATAT-T
1 ATTAAATATACCTATATCATATAT
**
25069271 ATTAAATATAGTTATATCATATAT
1 ATTAAATATACCTATATCATATAT
25069295 ATT
1 ATT
25069298 TTTTAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (24 bp):
ATTAAATATACCTATATCATATAT
Found at i:25069792 original size:21 final size:21
Alignment explanation
Indices: 25069768--25069819 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
25069758 GTCTTTTGTG
*
25069768 TATTAATTTGATTTAATTTTA
1 TATTAATTTGATTTAATTATA
25069789 TATTAAATTT-ATTTAATTATA
1 TATT-AATTTGATTTAATTATA
*
25069810 TGTTAATTTG
1 TATTAATTTG
25069820 TTAGTTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.19
21 17 0.63
22 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (21 bp):
TATTAATTTGATTTAATTATA
Found at i:25075649 original size:19 final size:19
Alignment explanation
Indices: 25075621--25075668 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
25075611 TTTTAACGTC
*
25075621 AAAAACTAAA-GAAAATCAT
1 AAAAAATAAATGAAAAT-AT
*
25075640 AAAAAATAAATTTAAAATAT
1 AAAAAATAAA-TGAAAATAT
25075660 AAAAAATAA
1 AAAAAATAA
25075669 GAGTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
20 11 0.44
21 5 0.20
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAAAATAAATGAAAATAT
Found at i:25075661 original size:20 final size:22
Alignment explanation
Indices: 25075632--25075690 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 22
25075622 AAAACTAAAG
25075632 AAAATCATAAAAAATAA-A-TTT
1 AAAAT-ATAAAAAATAAGAGTTT
25075653 AAAATATAAAAAATAAGAGTTT
1 AAAATATAAAAAATAAGAGTTT
*
25075675 TAAATATTAAAAAATA
1 AAAATA-TAAAAAATA
25075691 TATAATTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 11 0.32
21 6 0.18
22 8 0.24
23 9 0.26
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (22 bp):
AAAATATAAAAAATAAGAGTTT
Found at i:25091050 original size:2 final size:2
Alignment explanation
Indices: 25091006--25091033 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25090996 AACGAAAGGA
25091006 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
25091034 TAATTGACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25092353 original size:17 final size:17
Alignment explanation
Indices: 25092331--25092385 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
25092321 TGAATCAAAA
25092331 TAAATTCAAGATAATAT
1 TAAATTCAAGATAATAT
* *
25092348 TAAATT-TA-ATAAAAT
1 TAAATTCAAGATAATAT
25092363 TAAATTCAAGATAATAT
1 TAAATTCAAGATAATAT
25092380 TAAATT
1 TAAATT
25092386 TAATAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 12 0.38
16 2 0.06
17 18 0.56
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (17 bp):
TAAATTCAAGATAATAT
Found at i:25092364 original size:15 final size:15
Alignment explanation
Indices: 25092341--25092392 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
25092331 TAAATTCAAG
*
25092341 ATAATATTAAATTTA
1 ATAAAATTAAATTTA
*
25092356 ATAAAATTAAATTCAA
1 ATAAAATTAAATT-TA
*
25092372 GATAATATTAAATTTA
1 -ATAAAATTAAATTTA
25092388 ATAAA
1 ATAAA
25092393 TTTGATTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 16 0.53
16 2 0.07
17 12 0.40
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAATTAAATTTA
Found at i:25092367 original size:32 final size:31
Alignment explanation
Indices: 25092327--25092392 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 31
25092317 ACTTTGAATC
25092327 AAAATAAATTCAAGATAATATTAAATTTAAT
1 AAAATAAATTCAAGATAATATTAAATTTAAT
25092358 AAAATTAAATTCAAGATAATATTAAATTTAAT
1 AAAA-TAAATTCAAGATAATATTAAATTTAAT
25092390 AAA
1 AAA
25092393 TTTGATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.12
32 30 0.88
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (31 bp):
AAAATAAATTCAAGATAATATTAAATTTAAT
Found at i:25104848 original size:1 final size:1
Alignment explanation
Indices: 25104842--25104871 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
25104832 GCATAATTTC
25104842 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
25104872 CTGCTGACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:25107310 original size:2 final size:2
Alignment explanation
Indices: 25107303--25107331 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25107293 GTAAATACAT
25107303 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
25107332 TTTACAACAA
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:25109661 original size:2 final size:2
Alignment explanation
Indices: 25109654--25109679 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25109644 GGCGTCCATT
25109654 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
25109680 AACGAGAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:25110924 original size:3 final size:3
Alignment explanation
Indices: 25110916--25110945 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
25110906 TCAGAGGTTG
25110916 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25110946 TATTGACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25113205 original size:22 final size:22
Alignment explanation
Indices: 25113167--25113212 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
25113157 AAACCTACAT
*
25113167 AATTAAATAAATTCAA-TAAAA
1 AATTAAATAAATACAATTAAAA
25113188 AATTAAATTAAATACAATTAAAA
1 AATTAAA-TAAATACAATTAAAA
25113211 AA
1 AA
25113213 AAACTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 8 0.36
23 7 0.32
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (22 bp):
AATTAAATAAATACAATTAAAA
Found at i:25119243 original size:22 final size:23
Alignment explanation
Indices: 25119210--25119253 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
25119200 GAAGTCATGA
*
25119210 AAATAAAATAAAAAAAAGAAAAT
1 AAATAAAATAAAAAAAACAAAAT
*
25119233 AAAT-AAATAAACAAAACAAAA
1 AAATAAAATAAAAAAAACAAAA
25119254 CACAGATGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.82, C:0.05, G:0.02, T:0.11
Consensus pattern (23 bp):
AAATAAAATAAAAAAAACAAAAT
Found at i:25120981 original size:21 final size:21
Alignment explanation
Indices: 25120935--25120982 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
25120925 TGTCGACGTC
*
25120935 TTTATTTCTTTTGTTTACTTTA
1 TTTA-TTCTTTTGTTTACCTTA
*
25120957 TTTATTCTTTTGTGTTTCCTT-
1 TTTATTCTTTTGT-TTACCTTA
25120978 TTTAT
1 TTTAT
25120983 ATTTCCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.73
Consensus pattern (21 bp):
TTTATTCTTTTGTTTACCTTA
Found at i:25120985 original size:23 final size:21
Alignment explanation
Indices: 25120935--25120985 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
25120925 TGTCGACGTC
25120935 TTTAT-TTCTTTTGTTTACTT
1 TTTATATTCTTTTGTTTACTT
*
25120955 TATT-TATTCTTTTGTGTTTCCTT
1 T-TTATATTC-TTT-TGTTTACTT
25120978 TTTATATT
1 TTTATATT
25120986 TCCCAATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 2 0.08
21 5 0.20
22 5 0.20
23 13 0.52
ACGTcount: A:0.12, C:0.10, G:0.06, T:0.73
Consensus pattern (21 bp):
TTTATATTCTTTTGTTTACTT
Found at i:25127101 original size:20 final size:19
Alignment explanation
Indices: 25127073--25127111 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
25127063 ATATTTTTTA
*
25127073 AATTTTTATAAAATAAAAAT
1 AATTATTAT-AAATAAAAAT
*
25127093 AATTATTATATATAAAAAT
1 AATTATTATAAATAAAAAT
25127112 TTTATTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTATTATAAATAAAAAT
Found at i:25127160 original size:26 final size:28
Alignment explanation
Indices: 25127108--25127184 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 28
25127098 TTATATATAA
*
25127108 AAATTTTATTAAATTAATATAAAAAA-T
1 AAATTTTATAAAATTAATATAAAAAATT
*
25127135 AAATTTTA-AAAATTAATA-AATCAAATT
1 AAATTTTATAAAATTAATATAA-AAAATT
* *
25127162 AAA-TTGATAAAATTCGATATAAA
1 AAATTTTATAAAATT-AATATAAA
25127185 TCGTTTTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
25 2 0.05
26 15 0.38
27 18 0.45
28 3 0.08
29 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (28 bp):
AAATTTTATAAAATTAATATAAAAAATT
Found at i:25133506 original size:2 final size:2
Alignment explanation
Indices: 25133499--25133533 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25133489 GACCAAATAG
25133499 AT 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 AT A
25133534 AGAAAGTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25134282 original size:84 final size:83
Alignment explanation
Indices: 25134141--25134306 Score: 296
Period size: 84 Copynumber: 2.0 Consensus size: 83
25134131 TGTCTCCTCT
* *
25134141 AGATTAAGCTCCCGAGCAATCACTCTTATTGCTATGTCCTTCAGACATTAAAAAAATCCATAAAT
1 AGATTAAGCTCCCAAGCAATCACTCTTATTGCTATGTCCTTCAGACATAAAAAAAAT-CATAAAT
25134206 AAGAGACATCATAGTTGTC
65 AAGAGACATCATAGTTGTC
*
25134225 AGATTAAGCTCCCAAGCAATCACTTTTATTGCTATGTCCTTCAGACATAAAAAAAATCATAAATA
1 AGATTAAGCTCCCAAGCAATCACTCTTATTGCTATGTCCTTCAGACATAAAAAAAATCATAAATA
25134290 AGAGACATCATAGTTGT
66 AGAGACATCATAGTTGT
25134307 TATAGTTCAC
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
83 25 0.32
84 54 0.68
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.29
Consensus pattern (83 bp):
AGATTAAGCTCCCAAGCAATCACTCTTATTGCTATGTCCTTCAGACATAAAAAAAATCATAAATA
AGAGACATCATAGTTGTC
Found at i:25137814 original size:30 final size:30
Alignment explanation
Indices: 25137773--25137829 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
25137763 ATTTTTTATT
* * *
25137773 ATATATATATTTATATAATGATATTTTTAA
1 ATATATATATTTAAAAAATAATATTTTTAA
*
25137803 ATATTTATATTTAAAAAATAATATTTT
1 ATATATATATTTAAAAAATAATATTTT
25137830 ATATTTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
ATATATATATTTAAAAAATAATATTTTTAA
Found at i:25137832 original size:21 final size:21
Alignment explanation
Indices: 25137802--25137852 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
25137792 GATATTTTTA
25137802 AATA-TTTATATTTAAAAAAT
1 AATATTTTATATTTAAAAAAT
25137822 AATATTTTATATTTAAAAAAT
1 AATATTTTATATTTAAAAAAT
25137843 AATATTTTAT
1 AATATTTTAT
25137853 TAATTTCGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATTTTATATTTAAAAAAT
Found at i:25138122 original size:14 final size:13
Alignment explanation
Indices: 25138098--25138145 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
25138088 GAAGTTTGTG
*
25138098 AAAATTTTAATAT
1 AAAAATTTAATAT
25138111 AAATAATTTAAT-T
1 AAA-AATTTAATAT
*
25138124 AAAATTTTAATA-
1 AAAAATTTAATAT
25138136 AAAAATTTAA
1 AAAAATTTAA
25138146 ATTAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 16 0.53
13 7 0.23
14 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAAAATTTAATAT
Found at i:25138129 original size:26 final size:25
Alignment explanation
Indices: 25138098--25138150 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
25138088 GAAGTTTGTG
25138098 AAAATTTTAATATAAATAATTT-AATT
1 AAAATTTTAATA-AAA-AATTTAAATT
25138124 AAAATTTTAATAAAAAATTTAAATT
1 AAAATTTTAATAAAAAATTTAAATT
25138149 AA
1 AA
25138151 TAAATTGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 5 0.19
25 9 0.35
26 12 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AAAATTTTAATAAAAAATTTAAATT
Found at i:25138132 original size:12 final size:13
Alignment explanation
Indices: 25138098--25138143 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
25138088 GAAGTTTGTG
25138098 AAAATTTTAATAT
1 AAAATTTTAATAT
*
25138111 AAATAATTTAAT-T
1 AAA-ATTTTAATAT
*
25138124 AAAATTTTAATAA
1 AAAATTTTAATAT
25138137 AAAATTT
1 AAAATTT
25138144 AAATTAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 7 0.25
13 14 0.50
14 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAATTTTAATAT
Found at i:25138370 original size:20 final size:20
Alignment explanation
Indices: 25138345--25138386 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
25138335 TGTAACAAAA
25138345 TATTTTAATCT-ATTAATTTT
1 TATTTTAATCTAATT-ATTTT
*
25138365 TATTTTAATTTAATTATTTT
1 TATTTTAATCTAATTATTTT
25138385 TA
1 TA
25138387 ATAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTTAATCTAATTATTTT
Found at i:25141831 original size:37 final size:38
Alignment explanation
Indices: 25141765--25141836 Score: 87
Period size: 37 Copynumber: 1.9 Consensus size: 38
25141755 ATAATTTTTC
* *
25141765 ATATATTAAATATGAATTTAACATGTATCATATATGAG
1 ATATATTAAATATAAATTTAACATGTATCAAATATGAG
25141803 ATATA-TAAATATAAATATGTAA-AT-TATCAAATAT
1 ATATATTAAATATAAAT-T-TAACATGTATCAAATAT
25141837 ACTTTCAACC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
37 19 0.63
38 8 0.27
39 3 0.10
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (38 bp):
ATATATTAAATATAAATTTAACATGTATCAAATATGAG
Found at i:25144879 original size:2 final size:2
Alignment explanation
Indices: 25144866--25144903 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
25144856 ACATACGTAC
* *
25144866 AT AT AT AG AT AT AT AG 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
25144904 CAGAGAACTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:25145940 original size:51 final size:50
Alignment explanation
Indices: 25145812--25145940 Score: 125
Period size: 51 Copynumber: 2.5 Consensus size: 50
25145802 AATTCAATAT
*
25145812 AATAAATAAAATATGATAATTATATAATAAAAATAATTAATAAATAATTAAAA
1 AATAAAT-AAAT-TG-TAATTATATAATAAAAATAAATAATAAATAATTAAAA
* ** * * * *
25145865 ATTAAATAAATACTAAATTTTATAAT-CAAATAAATATTTAATAAATTAAAA
1 AATAAATAAATTGT-AATTATATAATAAAAATAAATAATAAAT-AATTAAAA
25145916 AATAAATAAATTGTAATTAATATAA
1 AATAAATAAATTGTAATT-ATATAA
25145941 GTTAACAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
50 17 0.28
51 34 0.56
52 4 0.07
53 6 0.10
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (50 bp):
AATAAATAAATTGTAATTATATAATAAAAATAAATAATAAATAATTAAAA
Found at i:25149490 original size:20 final size:21
Alignment explanation
Indices: 25149447--25149490 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
25149437 TCAAATTAAT
25149447 TATATATTTTTATTAATTTATA
1 TATATATTTTTA-TAATTTATA
25149469 TATATATATTTTA-AATTT-TA
1 TATATAT-TTTTATAATTTATA
25149489 TA
1 TA
25149491 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.19
21 5 0.24
22 7 0.33
23 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATATTTTTATAATTTATA
Found at i:25151947 original size:277 final size:277
Alignment explanation
Indices: 25151453--25152012 Score: 1111
Period size: 277 Copynumber: 2.0 Consensus size: 277
25151443 AGGGAAAAAA
25151453 ACTTGTAGTTGTGAGTTCCAATGAAATGTAATATAATTTGCAACGGAAGGATCTTGTCCTTGTGA
1 ACTTGTAGTTGTGAGTTCCAATGAAATGTAATATAATTTGCAACGGAAGGATCTTGTCCTTGTGA
25151518 ACTAATGTCTTTTGTGTGCTGAGCACATTACTTGTTCACTGTTTTTGCCCATTGTGATAGCTTTG
66 ACTAATGTCTTTTGTGTGCTGAGCACATTACTTGTTCACTGTTTTTGCCCATTGTGATAGCTTTG
25151583 GTTGAACTATAAAATTGCCAGCTTTCTTATCATCAAACATAAGTAATCTTTATTGCAACTCCAGT
131 GTTGAACTATAAAATTGCCAGCTTTCTTATCATCAAACATAAGTAATCTTTATTGCAACTCCAGT
25151648 CATCCCAAACATCAATCCTGTTACTGCTAATTAGAATCAGACCAATGGGTTGGACCATTTCCTTT
196 CATCCCAAACATCAATCCTGTTACTGCTAATTAGAATCAGACCAATGGGTTGGACCATTTCCTTT
25151713 GATCTTTCACTTTTCCG
261 GATCTTTCACTTTTCCG
*
25151730 ACTTGTAGTTGTGAGTTCCAATGAAATGTAATATAGTTTGCAACGGAAGGATCTTGTCCTTGTGA
1 ACTTGTAGTTGTGAGTTCCAATGAAATGTAATATAATTTGCAACGGAAGGATCTTGTCCTTGTGA
25151795 ACTAATGTCTTTTGTGTGCTGAGCACATTACTTGTTCACTGTTTTTGCCCATTGTGATAGCTTTG
66 ACTAATGTCTTTTGTGTGCTGAGCACATTACTTGTTCACTGTTTTTGCCCATTGTGATAGCTTTG
25151860 GTTGAACTATAAAATTGCCAGCTTTCTTATCATCAAACATAAGTAATCTTTATTGCAACTCCAGT
131 GTTGAACTATAAAATTGCCAGCTTTCTTATCATCAAACATAAGTAATCTTTATTGCAACTCCAGT
25151925 CATCCCAAACATCAATCCTGTTACTGCTAATTAGAATCAGACCAATGGGTTGGACCATTTCCTTT
196 CATCCCAAACATCAATCCTGTTACTGCTAATTAGAATCAGACCAATGGGTTGGACCATTTCCTTT
25151990 GATCTTTCACTTTTCCG
261 GATCTTTCACTTTTCCG
25152007 ACTTGT
1 ACTTGT
25152013 GTTATTCCAA
Statistics
Matches: 282, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
277 282 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (277 bp):
ACTTGTAGTTGTGAGTTCCAATGAAATGTAATATAATTTGCAACGGAAGGATCTTGTCCTTGTGA
ACTAATGTCTTTTGTGTGCTGAGCACATTACTTGTTCACTGTTTTTGCCCATTGTGATAGCTTTG
GTTGAACTATAAAATTGCCAGCTTTCTTATCATCAAACATAAGTAATCTTTATTGCAACTCCAGT
CATCCCAAACATCAATCCTGTTACTGCTAATTAGAATCAGACCAATGGGTTGGACCATTTCCTTT
GATCTTTCACTTTTCCG
Found at i:25153635 original size:2 final size:2
Alignment explanation
Indices: 25153628--25153658 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25153618 GAAAGTTTAC
25153628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25153659 AGAGATTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25154399 original size:21 final size:21
Alignment explanation
Indices: 25154367--25154407 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
25154357 GTCTAAAATA
25154367 TCTTGCTTGTGATCAAAGATT
1 TCTTGCTTGTGATCAAAGATT
25154388 TCTTG-TTCGTGATCAAAGAT
1 TCTTGCTT-GTGATCAAAGAT
25154408 CTTGGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (21 bp):
TCTTGCTTGTGATCAAAGATT
Found at i:25154845 original size:2 final size:2
Alignment explanation
Indices: 25154840--25154874 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25154830 CTTCCACTGA
25154840 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
25154875 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:25154879 original size:2 final size:2
Alignment explanation
Indices: 25154874--25154915 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
25154864 TCTCTCTCTC
25154874 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25154916 ACTCTCTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25165238 original size:2 final size:2
Alignment explanation
Indices: 25165231--25165257 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25165221 TGGAAGCAAA
25165231 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 A
25165258 GAAAAGTACT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25167252 original size:9 final size:8
Alignment explanation
Indices: 25167232--25167263 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
25167222 TTCTATTTCG
25167232 TTTTTTAT
1 TTTTTTAT
25167240 TTTTTTAT
1 TTTTTTAT
25167248 ATTTTTTAT
1 -TTTTTTAT
25167257 TTTTTTA
1 TTTTTTA
25167264 ATCAGATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTAT
Found at i:25167639 original size:11 final size:11
Alignment explanation
Indices: 25167623--25167664 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
25167613 ATGAAAGGAT
25167623 ATAATATAAAA
1 ATAATATAAAA
25167634 ATAATATTAATTAA
1 ATAATA-TAA--AA
25167648 A-AATATAAAA
1 ATAATATAAAA
25167658 ATAATAT
1 ATAATAT
25167665 GATTTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 3 0.11
11 11 0.41
12 6 0.22
13 4 0.15
14 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:25167686 original size:27 final size:24
Alignment explanation
Indices: 25167625--25167673 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
25167615 GAAAGGATAT
*
25167625 AATATAAAAATAATATTAATTAAA
1 AATATAAAAATAATATGAATTAAA
*
25167649 AATATAAAAATAATATGATTTAAA
1 AATATAAAAATAATATGAATTAAA
25167673 A
1 A
25167674 TTTTAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
AATATAAAAATAATATGAATTAAA
Found at i:25167791 original size:33 final size:33
Alignment explanation
Indices: 25167728--25167792 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
25167718 TATTTTATAT
*
25167728 TTTTATATTAATATAAATTATAATATATAAATA
1 TTTTATATTAATATAAATTATAATACATAAATA
*
25167761 TTTTATATT-TTATATAA-TATGAATACATAAAT
1 TTTTATATTAATATA-AATTAT-AATACATAAAT
25167793 TATCGAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 7 0.25
33 21 0.75
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (33 bp):
TTTTATATTAATATAAATTATAATACATAAATA
Found at i:25168988 original size:28 final size:29
Alignment explanation
Indices: 25168956--25169024 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 29
25168946 TATCAATTAA
25168956 ATTTAAATATTAA-TTTTTAATT-AAATTT
1 ATTTAAATA-TAAGTTTTTAATTGAAATTT
* *
25168984 ATTT-AATATAAGTTTTTTATTGAATTTT
1 ATTTAAATATAAGTTTTTAATTGAAATTT
*
25169012 TTTTAAATTATAA
1 ATTTAAA-TATAA
25169025 TTATAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 3 0.09
27 12 0.35
28 12 0.35
29 2 0.06
30 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (29 bp):
ATTTAAATATAAGTTTTTAATTGAAATTT
Found at i:25169044 original size:24 final size:24
Alignment explanation
Indices: 25169009--25169070 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
25168999 TTTATTGAAT
**
25169009 TTTTTTTAAATTATAATTATAATAA
1 TTTTTTT-AATTATAACAATAATAA
*
25169034 TTTTTTTAATTACAACAATAATAA
1 TTTTTTTAATTATAACAATAATAA
25169058 TTTTTATT-ATTAT
1 TTTTT-TTAATTAT
25169071 TTCAATCTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTTTTAATTATAACAATAATAA
Found at i:25178541 original size:20 final size:20
Alignment explanation
Indices: 25178504--25178544 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
25178494 TTCTTACCAG
* **
25178504 AAGAAAAAAACATTACAAAA
1 AAGAAAAAAAAAAAACAAAA
25178524 AAGAAAAAAAAAAAACAAAA
1 AAGAAAAAAAAAAAACAAAA
25178544 A
1 A
25178545 TATATAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.83, C:0.07, G:0.05, T:0.05
Consensus pattern (20 bp):
AAGAAAAAAAAAAAACAAAA
Found at i:25181838 original size:15 final size:14
Alignment explanation
Indices: 25181815--25181847 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
25181805 ATATTCGTAA
25181815 ATAATAAATAAATT
1 ATAATAAATAAATT
25181829 ATAATCAAATAAATT
1 ATAAT-AAATAAATT
25181844 ATAA
1 ATAA
25181848 AATTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAAATAAATT
Found at i:25190892 original size:62 final size:62
Alignment explanation
Indices: 25190787--25190905 Score: 184
Period size: 62 Copynumber: 1.9 Consensus size: 62
25190777 AAAAATAAAA
* * *
25190787 AAAATAAAATTTGTAAGTGTGCATTCGAGAATAAATTTTAATTTTATTATAATTTATTTAGG
1 AAAATAAAATTTGTAAGTGTGCATTCGAAAATAAATATCAATTTTATTATAATTTATTTAGG
* * *
25190849 AAAATAAATTTTGTAAGTGTGCGTTCGAAAATGAATATCAATTTTATTATAATTTAT
1 AAAATAAAATTTGTAAGTGTGCATTCGAAAATAAATATCAATTTTATTATAATTTAT
25190906 ATTTTTTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (62 bp):
AAAATAAAATTTGTAAGTGTGCATTCGAAAATAAATATCAATTTTATTATAATTTATTTAGG
Found at i:25191836 original size:10 final size:10
Alignment explanation
Indices: 25191823--25191864 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
25191813 ATGAATTGAA
25191823 TTATATATTT
1 TTATATATTT
25191833 TTAT-TAATTT
1 TTATAT-ATTT
25191843 TTATATATTT
1 TTATATATTT
25191853 TTA-A-ATTT
1 TTATATATTT
25191861 TTAT
1 TTAT
25191865 GAAATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 7 0.24
9 2 0.07
10 19 0.66
11 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTATATATTT
Found at i:25191859 original size:18 final size:19
Alignment explanation
Indices: 25191823--25191864 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
25191813 ATGAATTGAA
25191823 TTATATATTTTTATTAATTT
1 TTATATATTTTTA-TAATTT
25191843 TTATATATTTTTA-AATTT
1 TTATATATTTTTATAATTT
25191861 TTAT
1 TTAT
25191865 GAAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATATATTTTTATAATTT
Found at i:25191937 original size:33 final size:33
Alignment explanation
Indices: 25191880--25191946 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
25191870 AAAAATAATT
** * *
25191880 ATTTTATTTAAAATTTTATTTAAATATATCAAAA
1 ATTTTATTTAAAATAATATATAAATA-ACCAAAA
25191914 ATTTTA-TTAAAATAATATATAAATAACCAAAA
1 ATTTTATTTAAAATAATATATAAATAACCAAAA
25191946 A
1 A
25191947 AATTAAACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 7 0.24
33 16 0.55
34 6 0.21
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (33 bp):
ATTTTATTTAAAATAATATATAAATAACCAAAA
Found at i:25192347 original size:17 final size:16
Alignment explanation
Indices: 25192325--25192363 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
25192315 GATGTAAAAA
25192325 ATATATAAAAAAATAAT
1 ATATATAAAAAAAT-AT
**
25192342 ATATATTTAAAAATAT
1 ATATATAAAAAAATAT
25192358 ATATAT
1 ATATAT
25192364 TTCAGTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATATAAAAAAATAT
Found at i:25192359 original size:16 final size:17
Alignment explanation
Indices: 25192333--25192365 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
25192323 AAATATATAA
25192333 AAAAATAATATATATTT
1 AAAAATAATATATATTT
25192350 AAAAAT-ATATATATTT
1 AAAAATAATATATATTT
25192366 CAGTTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAAATAATATATATTT
Found at i:25192502 original size:18 final size:18
Alignment explanation
Indices: 25192476--25192510 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25192466 TCATATAAAT
*
25192476 ATACATTTAATATATTTA
1 ATACATTTAACATATTTA
*
25192494 ATACGTTTAACATATTT
1 ATACATTTAACATATTT
25192511 TTTATATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.49
Consensus pattern (18 bp):
ATACATTTAACATATTTA
Found at i:25192921 original size:63 final size:65
Alignment explanation
Indices: 25192784--25192921 Score: 201
Period size: 63 Copynumber: 2.2 Consensus size: 65
25192774 TGGTTATATA
* *
25192784 ATATAAATATAAATTTAAATATATATATTAAATACATATTAAATGAGTATTAAAATTAATGTAGT
1 ATATAAATATAAATATAAATATATATATTAAATACATATTAAATGAGTATTAAAATTAATGTAAT
** *
25192849 -TATATAATATAAATAT-AA-ATATATATTAAATACATATTAAATGAGTATTAAAATTTTTTTAA
1 ATATA-AATATAAATATAAATATATATATTAAATACATATTAAATGAGTATTAAAATTAATGTAA
25192911 T
65 T
25192912 ATATAAATAT
1 ATATAAATAT
25192922 CTTTTTATAC
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
63 46 0.70
64 10 0.15
65 10 0.15
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (65 bp):
ATATAAATATAAATATAAATATATATATTAAATACATATTAAATGAGTATTAAAATTAATGTAAT
Found at i:25192939 original size:19 final size:19
Alignment explanation
Indices: 25192894--25192940 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
25192884 ATTAAATGAG
* *
25192894 TATTAAAATTTTTTTAATA
1 TATTAATATCTTTTTAATA
*
25192913 TATAAATATCTTTTT-ATA
1 TATTAATATCTTTTTAATA
25192931 CTATTAATAT
1 -TATTAATAT
25192941 GTCAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTAATATCTTTTTAATA
Found at i:25194750 original size:2 final size:2
Alignment explanation
Indices: 25194743--25194768 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25194733 TCAGTTTTGA
25194743 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
25194769 CACAGTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25196003 original size:23 final size:23
Alignment explanation
Indices: 25195968--25196015 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
25195958 ATATATATAT
* * *
25195968 ATATCATTTTATGATCAAAATAA
1 ATATAATTATATGAACAAAATAA
*
25195991 ATATAATTATATGAACAAATTAA
1 ATATAATTATATGAACAAAATAA
25196014 AT
1 AT
25196016 GAAATCCGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (23 bp):
ATATAATTATATGAACAAAATAA
Found at i:25198582 original size:12 final size:12
Alignment explanation
Indices: 25198565--25198603 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
25198555 TTATATATTT
25198565 ATATTATATAAA
1 ATATTATATAAA
25198577 ATATTATATAAA
1 ATATTATATAAA
* *
25198589 AAATTATATATA
1 ATATTATATAAA
25198601 ATA
1 ATA
25198604 ATTTACATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATTATATAAA
Found at i:25199401 original size:13 final size:13
Alignment explanation
Indices: 25199385--25199409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25199375 ATATATTAAG
25199385 AATATATAAAAAT
1 AATATATAAAAAT
25199398 AATATATAAAAA
1 AATATATAAAAA
25199410 CAAAAAAATA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATATATAAAAAT
Found at i:25199455 original size:5 final size:5
Alignment explanation
Indices: 25199441--25199474 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
25199431 TTATTGAATG
*
25199441 AAATT AAATT GAATT -AATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT
25199475 TAATATGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
AAATT
Found at i:25199459 original size:14 final size:14
Alignment explanation
Indices: 25199442--25199471 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25199432 TATTGAATGA
*
25199442 AATTAAATTGAATT
1 AATTAAATTAAATT
25199456 AATTAAATTAAATT
1 AATTAAATTAAATT
25199470 AA
1 AA
25199472 ATTTAATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (14 bp):
AATTAAATTAAATT
Found at i:25199538 original size:16 final size:17
Alignment explanation
Indices: 25199517--25199550 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
25199507 TTAAATCGAT
25199517 ATTTTAAAAATT-TATA
1 ATTTTAAAAATTATATA
*
25199533 ATTTTATAAATTATATA
1 ATTTTAAAAATTATATA
25199550 A
1 A
25199551 AAAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTAAAAATTATATA
Found at i:25200043 original size:6 final size:6
Alignment explanation
Indices: 25200032--25200081 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
25200022 ATAATAAAAT
* * * *
25200032 TTTAAA TTTAAA TTTTAA TTTAAA TATAAA TATAAA -TTAAA TTTATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
25200079 TTT
1 TTT
25200082 GATTTATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
5 4 0.11
6 34 0.89
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:25200131 original size:24 final size:24
Alignment explanation
Indices: 25200104--25200164 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 24
25200094 ATCGAACTAA
*
25200104 ATATTATTTTAAATTTAAAATTTT
1 ATATTATTTTAAATATAAAATTTT
25200128 ATATTATTTT-AATATAAAATTTT
1 ATATTATTTTAAATATAAAATTTT
25200151 A-A-TATATTTAAATA
1 ATATTAT-TTTAAATA
25200165 AATTTATACA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
21 3 0.09
22 4 0.12
23 17 0.50
24 10 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATATTATTTTAAATATAAAATTTT
Found at i:25200280 original size:19 final size:17
Alignment explanation
Indices: 25200240--25200285 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
25200230 ATTTAATTCG
*
25200240 ATTTAAATTTTTTTTAA
1 ATTTTAATTTTTTTTAA
*
25200257 TTTTTAATTTTTACTTTAA
1 ATTTTAATTTTT--TTTAA
25200276 ATTTTAATTT
1 ATTTTAATTT
25200286 GAATTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
19 14 0.58
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTAATTTTTTTTAA
Found at i:25203271 original size:15 final size:16
Alignment explanation
Indices: 25203242--25203275 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
25203232 TTTGAAAGAC
25203242 TTTGATAAATATAAAA
1 TTTGATAAATATAAAA
*
25203258 TTTGA-AAATTTAAAA
1 TTTGATAAATATAAAA
25203273 TTT
1 TTT
25203276 TTATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
TTTGATAAATATAAAA
Found at i:25216219 original size:23 final size:23
Alignment explanation
Indices: 25216192--25216238 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
25216182 ACTCATAAAC
25216192 AAACATACAAACCCATAAGACGT
1 AAACATACAAACCCATAAGACGT
25216215 AAACATACAAACCCATAAGACGT
1 AAACATACAAACCCATAAGACGT
25216238 A
1 A
25216239 GAGCCCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.26, G:0.09, T:0.13
Consensus pattern (23 bp):
AAACATACAAACCCATAAGACGT
Found at i:25216431 original size:52 final size:51
Alignment explanation
Indices: 25216345--25216500 Score: 186
Period size: 52 Copynumber: 3.0 Consensus size: 51
25216335 TATAACCAAA
* * * **
25216345 CAAACTTGCCCATTAAGAATCCCTCTCTTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTACCCATTAAGAATCTCTTTCTT-TTAGAATTCTTCTATTGTAAGT
* *
25216397 TAAACTTACCCATTAAGAATCTCTTTCCTTTTAGAATTCTTCTATTGCAAGT
1 CAAACTTACCCATTAAGAATCTCTTT-CTTTTAGAATTCTTCTATTGTAAGT
* * * *
25216449 CAAACTTACCTATTAAGAATCTTCTTTCTCTTGGAATTCTTCTTTTGTAAGT
1 CAAACTTACCCATTAAGAATC-TCTTTCTTTTAGAATTCTTCTATTGTAAGT
25216501 ATTCTTGTCC
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 81 0.91
53 8 0.09
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (51 bp):
CAAACTTACCCATTAAGAATCTCTTTCTTTTAGAATTCTTCTATTGTAAGT
Found at i:25216551 original size:22 final size:22
Alignment explanation
Indices: 25216526--25216568 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
25216516 GCAATATCTG
*
25216526 ACAAATCCCAAATAAATCTCTA
1 ACAAATCCCAAACAAATCTCTA
25216548 ACAAATCCCAAACAAATCTCT
1 ACAAATCCCAAACAAATCTCT
25216569 TATGGGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (22 bp):
ACAAATCCCAAACAAATCTCTA
Found at i:25231468 original size:24 final size:23
Alignment explanation
Indices: 25231414--25231488 Score: 80
Period size: 25 Copynumber: 3.1 Consensus size: 23
25231404 ATATATTGTT
* *
25231414 AAATTTT-TATAAAATACAAATA
1 AAATTTTATATAAAATATATATA
*
25231436 ATAATTTTATATCAAAATATATTTA
1 A-AATTTTATAT-AAAATATATATA
25231461 AAATTTTATATTAAAATAATATATA
1 AAATTTTATA-TAAAAT-ATATATA
25231486 AAA
1 AAA
25231489 ATTAAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
22 1 0.02
23 6 0.14
24 17 0.39
25 20 0.45
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATTTTATATAAAATATATATA
Found at i:25231476 original size:13 final size:13
Alignment explanation
Indices: 25231438--25231492 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
25231428 TACAAATAAT
* *
25231438 AATTTTATATCAA
1 AATTATATATTAA
25231451 AA-TATAT-TTAA
1 AATTATATATTAA
*
25231462 AATTTTATATTAA
1 AATTATATATTAA
* *
25231475 AATAATATATAAA
1 AATTATATATTAA
25231488 AATTA
1 AATTA
25231493 AAAAAAATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
11 5 0.15
12 8 0.24
13 20 0.61
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTATATATTAA
Found at i:25231488 original size:25 final size:25
Alignment explanation
Indices: 25231414--25231488 Score: 79
Period size: 24 Copynumber: 3.1 Consensus size: 25
25231404 ATATATTGTT
25231414 AAATTTT-TA-TAAAATACA-A-ATA
1 AAATTTTATATTAAAATA-ATATATA
* *
25231436 ATAATTTTATATCAAAAT-ATATTTA
1 A-AATTTTATATTAAAATAATATATA
25231461 AAATTTTATATTAAAATAATATATA
1 AAATTTTATATTAAAATAATATATA
25231486 AAA
1 AAA
25231489 ATTAAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
22 1 0.02
23 7 0.16
24 18 0.42
25 17 0.40
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (25 bp):
AAATTTTATATTAAAATAATATATA
Found at i:25235563 original size:21 final size:22
Alignment explanation
Indices: 25235528--25235573 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
25235518 TATTAGAATA
*
25235528 AAAAGTTTTAAAAATAAATTAT
1 AAAAGTTTAAAAAATAAATTAT
*
25235550 AAAA-TTTAAAAAATATATTAT
1 AAAAGTTTAAAAAATAAATTAT
25235571 AAA
1 AAA
25235574 TGTAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAAGTTTAAAAAATAAATTAT
Found at i:25236026 original size:2 final size:2
Alignment explanation
Indices: 25236014--25236049 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
25236004 ACCATAGGTA
*
25236014 CT CT CT ACT CT CT CT GT 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 C
25236050 GATCTTTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.03, C:0.47, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:25236843 original size:15 final size:15
Alignment explanation
Indices: 25236823--25236852 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
25236813 ATTGAGTACG
25236823 GCTTAGAACTTGGTT
1 GCTTAGAACTTGGTT
25236838 GCTTAGAACTTGGTT
1 GCTTAGAACTTGGTT
25236853 AAATTTAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (15 bp):
GCTTAGAACTTGGTT
Found at i:25246690 original size:16 final size:17
Alignment explanation
Indices: 25246671--25246702 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25246661 ATAAATTTAT
25246671 ATAAAT-ATAAAAAAAA
1 ATAAATAATAAAAAAAA
25246687 ATAAATAATAAAAAAA
1 ATAAATAATAAAAAAA
25246703 TTATATATAT
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
ATAAATAATAAAAAAAA
Found at i:25248262 original size:12 final size:12
Alignment explanation
Indices: 25248245--25248269 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25248235 TAATAATATG
25248245 TAAAAAAATTAT
1 TAAAAAAATTAT
25248257 TAAAAAAATTAT
1 TAAAAAAATTAT
25248269 T
1 T
25248270 TTTAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAAAAATTAT
Found at i:25248441 original size:13 final size:13
Alignment explanation
Indices: 25248423--25248454 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
25248413 AATATATTAT
25248423 TTTTAATTTTTAA
1 TTTTAATTTTTAA
25248436 TTTTAA-TTTTAA
1 TTTTAATTTTTAA
25248448 -TTTAATT
1 TTTTAATT
25248455 ATTTTTAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 7 0.39
13 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:25249101 original size:27 final size:26
Alignment explanation
Indices: 25249054--25249106 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
25249044 TTTTAAATGA
** *
25249054 AATTTATAAAATTTTTTATTAAAAAT
1 AATTTATAAAATCCTTAATTAAAAAT
25249080 AATTTAATAAAATCCTTAATTAAAAAT
1 AATTT-ATAAAATCCTTAATTAAAAAT
25249107 TCAAATAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (26 bp):
AATTTATAAAATCCTTAATTAAAAAT
Found at i:25249500 original size:13 final size:13
Alignment explanation
Indices: 25249469--25249494 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25249459 CCACTACTTA
25249469 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
25249482 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
25249495 GGAAAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:25252312 original size:105 final size:105
Alignment explanation
Indices: 25252129--25252341 Score: 349
Period size: 105 Copynumber: 2.0 Consensus size: 105
25252119 ACTTGACATT
*
25252129 AATAAATGTCACTTGCAAATAGTGAATTTCAACTATAAACTATAATTTATTACTGGAGTTTAAAA
1 AATAAATGTCACTTGCAAATAGTGAATTTCAACTATAAACTATAATTTATTACTGGAATTTAAAA
25252194 AAAAAATGTAGACTATTATAGCTTAGAACATACATTTAAAA
66 AAAAAATGTAGACTATTATAGCTTAGAAC-TACATTTAAAA
* *
25252235 AATAAA-GTCACTTGCAAATAGTGAATTTCAACTATCAACTATAATTTATTGCT-GAATTTAAAA
1 AATAAATGTCACTTGCAAATAGTGAATTTCAACTATAAACTATAATTTATTACTGGAATTT-AAA
* *
25252298 AAAAAAATGTAGACTATTATAGCTTAGTACTTCATTTAAAA
65 AAAAAAATGTAGACTATTATAGCTTAGAACTACATTTAAAA
25252339 AAT
1 AAT
25252342 TTGTGCATGA
Statistics
Matches: 101, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
104 18 0.18
105 77 0.76
106 6 0.06
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.34
Consensus pattern (105 bp):
AATAAATGTCACTTGCAAATAGTGAATTTCAACTATAAACTATAATTTATTACTGGAATTTAAAA
AAAAAATGTAGACTATTATAGCTTAGAACTACATTTAAAA
Found at i:25252829 original size:24 final size:24
Alignment explanation
Indices: 25252788--25252843 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 24
25252778 AATAAAATAA
*
25252788 AAAATATATTTTATATTTTTATATT
1 AAAATATATTTTATATTTTCATA-T
25252813 AAAATA-A-TTTATAATTTTCATAT
1 AAAATATATTTTAT-ATTTTCATAT
25252836 AAAATATA
1 AAAATATA
25252844 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 12 0.43
24 10 0.36
25 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
AAAATATATTTTATATTTTCATAT
Found at i:25253243 original size:14 final size:15
Alignment explanation
Indices: 25253215--25253243 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25253205 CTAATGAACA
25253215 AAAAATATTATAATT
1 AAAAATATTATAATT
25253230 AAAAATATTA-AATT
1 AAAAATATTATAATT
25253244 GAATTCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAAATATTATAATT
Found at i:25254720 original size:17 final size:17
Alignment explanation
Indices: 25254700--25254734 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25254690 CTTATGAACA
*
25254700 TGAATTTCTTGCAAATT
1 TGAATCTCTTGCAAATT
*
25254717 TGAATCTCTTGCGAATT
1 TGAATCTCTTGCAAATT
25254734 T
1 T
25254735 TTGAAACCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (17 bp):
TGAATCTCTTGCAAATT
Found at i:25254919 original size:16 final size:17
Alignment explanation
Indices: 25254890--25254923 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
25254880 TTTACAACCT
25254890 TTGCGAATTTTGAAATC
1 TTGCGAATTTTGAAATC
25254907 TTGCGAA-TTTGAAATC
1 TTGCGAATTTTGAAATC
25254923 T
1 T
25254924 CTGTGGAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (17 bp):
TTGCGAATTTTGAAATC
Found at i:25255008 original size:18 final size:18
Alignment explanation
Indices: 25254985--25255065 Score: 76
Period size: 18 Copynumber: 4.6 Consensus size: 18
25254975 ATTTAAAAAC
*
25254985 TTTTGAAATCTTTGCAAA
1 TTTTGAAATCTTTGCGAA
25255003 TTTTGAAAT-TCTTGCGAA
1 TTTTGAAATCT-TTGCGAA
* ** *
25255021 TCTAAAAACCTTTGCGAA
1 TTTTGAAATCTTTGCGAA
**
25255039 TTTT-AAATCTTTATGAA
1 TTTTGAAATCTTTGCGAA
25255056 TTTTGAAATC
1 TTTTGAAATC
25255066 ATAACAAATT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
17 15 0.30
18 34 0.68
19 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.43
Consensus pattern (18 bp):
TTTTGAAATCTTTGCGAA
Done.