Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 70 of 120
Found at i:20553216 original size:23 final size:24
Alignment explanation
Indices: 20553163--20553216 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
20553153 GATATATAGT
*
20553163 ATATTTTTAATTGAATCAGATATA
1 ATATTTTTAATTGAATCAAATATA
*
20553187 AT-GTTTTAA-TGAGATCAAAT-TA
1 ATATTTTTAATTGA-ATCAAATATA
20553209 ATATTTTT
1 ATATTTTT
20553217 TATAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 7 0.28
23 16 0.64
24 2 0.08
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (24 bp):
ATATTTTTAATTGAATCAAATATA
Found at i:20554304 original size:41 final size:41
Alignment explanation
Indices: 20554257--20554350 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
20554247 GAATTTTATT
* *
20554257 TTAACAAGAATTCTAGTCATCCAATTCTAACAATTTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
20554298 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
20554339 TTAACAAGAATT
1 TTAACAAGAATT
20554351 TTCTACGAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:20554363 original size:17 final size:17
Alignment explanation
Indices: 20554341--20554380 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
20554331 TCTCCACCTT
* * *
20554341 AACAAGAATTTTCTACG
1 AACAAGAACTCTCAACG
20554358 AACAAGAACTCTCAACG
1 AACAAGAACTCTCAACG
20554375 AACAAG
1 AACAAG
20554381 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.23, G:0.12, T:0.17
Consensus pattern (17 bp):
AACAAGAACTCTCAACG
Found at i:20558774 original size:17 final size:18
Alignment explanation
Indices: 20558736--20558776 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20558726 CTTTACTTTT
* *
20558736 ATTTTATTTTACCACCGA
1 ATTTTATTTTAACACAGA
20558754 ATTTTATTTTAACA-AGA
1 ATTTTATTTTAACACAGA
20558771 ATTTTA
1 ATTTTA
20558777 GTCACCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTTTATTTTAACACAGA
Found at i:20566201 original size:14 final size:15
Alignment explanation
Indices: 20566177--20566205 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20566167 AGTGAAGAGC
20566177 ATTTCCTTCTTTTCT
1 ATTTCCTTCTTTTCT
20566192 ATTT-CTTCTTTTCT
1 ATTTCCTTCTTTTCT
20566206 CCCTTCGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTCCTTCTTTTCT
Found at i:20566571 original size:66 final size:66
Alignment explanation
Indices: 20566465--20566594 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
20566455 AAGACGTGGA
* *
20566465 TTCGAATGTGTTGAAATGCATTATCCTCTTATTTATGGGTTGAGAGAGATTATGGGTAGTTCAGG
1 TTCGAATGCGTTGAAACGCATTATCCTCTTATTTATGGGTTGAGAGAGATTATGGGTAGTTCAGG
20566530 C
66 C
*
20566531 TTCGAGTGCGTTGAAACGCATTATCCTCTTATTTATGGGTTGAGAGAGATTATGGGTAGTTCAG
1 TTCGAATGCGTTGAAACGCATTATCCTCTTATTTATGGGTTGAGAGAGATTATGGGTAGTTCAG
20566595 ATCCGATCCT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.37
Consensus pattern (66 bp):
TTCGAATGCGTTGAAACGCATTATCCTCTTATTTATGGGTTGAGAGAGATTATGGGTAGTTCAGG
C
Found at i:20572209 original size:12 final size:12
Alignment explanation
Indices: 20572192--20572216 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20572182 ATTAAAGAAT
20572192 TAATAGCATTCA
1 TAATAGCATTCA
20572204 TAATAGCATTCA
1 TAATAGCATTCA
20572216 T
1 T
20572217 CATAACAACA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:20576991 original size:21 final size:21
Alignment explanation
Indices: 20576944--20577014 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
20576934 AATAGTGCAG
20576944 ACTTCTACC-AATACAAGTGAT
1 ACTTCTACCGAA-ACAAGTGAT
*
20576965 AGTTCTACCGAAACAAGTGACT
1 ACTTCTACCGAAACAAGTGA-T
**
20576987 -CTTCTACCGAAACAAGTCTT
1 ACTTCTACCGAAACAAGTGAT
20577007 ACTTCTAC
1 ACTTCTAC
20577015 TGATACTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
20 1 0.02
21 39 0.91
22 3 0.07
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.28
Consensus pattern (21 bp):
ACTTCTACCGAAACAAGTGAT
Found at i:20579024 original size:19 final size:19
Alignment explanation
Indices: 20579000--20579037 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20578990 CCTAATTAAC
20579000 TATCCTAACGATAAAATTT
1 TATCCTAACGATAAAATTT
20579019 TATCCTAACGATAAAATTT
1 TATCCTAACGATAAAATTT
20579038 CATAATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (19 bp):
TATCCTAACGATAAAATTT
Found at i:20582278 original size:22 final size:21
Alignment explanation
Indices: 20582244--20582306 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
20582234 ACCGTACTTA
*
20582244 CTGTTCAGACTATGTGTGCTT
1 CTGTTTAGACTATGTGTGCTT
*
20582265 CTGTTTAGAACTATGTGTACTT
1 CTGTTTAG-ACTATGTGTGCTT
* *
20582287 CTATTTAGCACTGTGTGTGC
1 CTGTTTAG-ACTATGTGTGC
20582307 CTATTATTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 7 0.20
22 28 0.80
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.43
Consensus pattern (21 bp):
CTGTTTAGACTATGTGTGCTT
Found at i:20582350 original size:25 final size:25
Alignment explanation
Indices: 20582322--20582388 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
20582312 ATTTCCTAGT
*
20582322 ACTTATGTGCTTTTGTTTCTCCAGC
1 ACTTATGTGCTTTTGTTTCCCCAGC
*
20582347 ACTTATGTGCTTCTGTTTCCCCAGC
1 ACTTATGTGCTTTTGTTTCCCCAGC
* *
20582372 ATTTATGCGCTTTTGTT
1 ACTTATGTGCTTTTGTT
20582389 AAGTACTTCG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.12, C:0.24, G:0.16, T:0.48
Consensus pattern (25 bp):
ACTTATGTGCTTTTGTTTCCCCAGC
Found at i:20588296 original size:18 final size:18
Alignment explanation
Indices: 20588273--20588308 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20588263 GTGTTTAATT
20588273 ATAAATATTGATTATATG
1 ATAAATATTGATTATATG
20588291 ATAAATATTGATTATATG
1 ATAAATATTGATTATATG
20588309 TAGACTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (18 bp):
ATAAATATTGATTATATG
Found at i:20588396 original size:22 final size:22
Alignment explanation
Indices: 20588366--20588454 Score: 97
Period size: 22 Copynumber: 4.0 Consensus size: 22
20588356 ACGCTACCGC
20588366 GCTTACTGTTCAGCACTGTGTGT
1 GCTT-CTGTTCAGCACTGTGTGT
* *
20588389 GCTTCTGTTTAGCACTATGTGT
1 GCTTCTGTTCAGCACTGTGTGT
* ** *
20588411 TCTTCTGTTCAATATTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
* *
20588433 GCTTCTATTTAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
20588455 TCCTACTGTT
Statistics
Matches: 52, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
22 48 0.92
23 4 0.08
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.46
Consensus pattern (22 bp):
GCTTCTGTTCAGCACTGTGTGT
Found at i:20588505 original size:25 final size:25
Alignment explanation
Indices: 20588460--20588521 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
20588450 TGTGTTCCTA
*
20588460 CTGTTTCT-CAGAACTTATGTGCTT
1 CTGTTTCTCCAGCACTTATGTGCTT
20588484 CTGTTTCTCCAGCACTTATGTGCTT
1 CTGTTTCTCCAGCACTTATGTGCTT
*
20588509 CTGTTTCCCCAGC
1 CTGTTTCTCCAGC
20588522 TTCTGTTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 8 0.23
25 27 0.77
ACGTcount: A:0.13, C:0.29, G:0.16, T:0.42
Consensus pattern (25 bp):
CTGTTTCTCCAGCACTTATGTGCTT
Found at i:20595328 original size:21 final size:21
Alignment explanation
Indices: 20595302--20595341 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20595292 TAGTGTAAAC
*
20595302 TTTTACCGATACATGTGACCG
1 TTTTACCGATACAAGTGACCG
20595323 TTTTACCGATACAAGTGAC
1 TTTTACCGATACAAGTGAC
20595342 TCTTCTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.33
Consensus pattern (21 bp):
TTTTACCGATACAAGTGACCG
Found at i:20598418 original size:28 final size:28
Alignment explanation
Indices: 20598378--20598433 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
20598368 GATATCCGAT
20598378 TTACTCCCTGTTGACCCAAAGGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
20598406 TTACTCCCTGTTGACCCAAAGGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
20598434 CTGTTACCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (28 bp):
TTACTCCCTGTTGACCCAAAGGTCATGC
Found at i:20602420 original size:15 final size:15
Alignment explanation
Indices: 20602400--20602431 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
20602390 AAGGGTATAA
20602400 TTACCATTTAAGGGC
1 TTACCATTTAAGGGC
20602415 TTACCATTTAAGGGC
1 TTACCATTTAAGGGC
20602430 TT
1 TT
20602432 TTCTAGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (15 bp):
TTACCATTTAAGGGC
Found at i:20609624 original size:17 final size:17
Alignment explanation
Indices: 20609602--20609635 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20609592 AGTAAACATA
*
20609602 ACCACAGATCGTTTGTC
1 ACCACAGATAGTTTGTC
20609619 ACCACAGATAGTTTGTC
1 ACCACAGATAGTTTGTC
20609636 TTTGGGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (17 bp):
ACCACAGATAGTTTGTC
Found at i:20610959 original size:124 final size:124
Alignment explanation
Indices: 20610737--20610980 Score: 391
Period size: 124 Copynumber: 2.0 Consensus size: 124
20610727 GTTGCTTGCA
* * * *
20610737 GCTAATCAAATATCACCAGGAGGGTGCTAAAGGTTTTTGCTAAGGTAACTCCACAATCACCAACT
1 GCTAATCAAATATCACCAGGAGGATGCTAAAGATTTTTGCCAAAGTAACTCCACAATCACCAACT
* * *
20610802 TGTTTAATTGTGCAAGGCAAGGAGAAAAGGCTAAGTCCAGACTTC-GAAACCAACTTGAT
66 TGTCTAATTGTGCAAGGCAAGGAGAAAAAGCTAAGTCCAGACCTCAG-AACCAACTTGAT
* *
20610861 GCTAATCAAATATCACCGGGAGGATGCTAAAGATTTTTGCCAAAGTAACTCCACAATCACCAATT
1 GCTAATCAAATATCACCAGGAGGATGCTAAAGATTTTTGCCAAAGTAACTCCACAATCACCAACT
20610926 TGTCTAATTGTGCAAGGCAAGGAGAAAAAGCTAAGTCCAGACCTCAGAACCAACT
66 TGTCTAATTGTGCAAGGCAAGGAGAAAAAGCTAAGTCCAGACCTCAGAACCAACT
20610981 GAAGCAATTA
Statistics
Matches: 110, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
124 109 0.99
125 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (124 bp):
GCTAATCAAATATCACCAGGAGGATGCTAAAGATTTTTGCCAAAGTAACTCCACAATCACCAACT
TGTCTAATTGTGCAAGGCAAGGAGAAAAAGCTAAGTCCAGACCTCAGAACCAACTTGAT
Found at i:20613526 original size:19 final size:18
Alignment explanation
Indices: 20613504--20613539 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20613494 TGAATCAATT
20613504 TTTTCTATTTTTTAATAAA
1 TTTTCTA-TTTTTAATAAA
*
20613523 TTTTTTATTTTTAATAA
1 TTTTCTATTTTTAATAA
20613540 TTTATTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCTATTTTTAATAAA
Found at i:20616518 original size:20 final size:19
Alignment explanation
Indices: 20616493--20616536 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
20616483 TGAAGTGGCA
* *
20616493 TGTACCTAAGTAGAGTTGGG
1 TGTACCCAAGTAGAATT-GG
*
20616513 TGTACCCAATTAGAATTGG
1 TGTACCCAAGTAGAATTGG
20616532 TGTAC
1 TGTAC
20616537 GTATAGAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (19 bp):
TGTACCCAAGTAGAATTGG
Found at i:20628115 original size:23 final size:23
Alignment explanation
Indices: 20628089--20628132 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
20628079 AATTCAACGA
*
20628089 TCAGTCAAAGTCAACGGTTCGAT
1 TCAGTCAAAGTCAACAGTTCGAT
*
20628112 TCAGTCAAAGTTAACAGTTCG
1 TCAGTCAAAGTCAACAGTTCG
20628133 GGTTAGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (23 bp):
TCAGTCAAAGTCAACAGTTCGAT
Found at i:20629523 original size:21 final size:22
Alignment explanation
Indices: 20629488--20629541 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
20629478 TTTTTGTTTC
**
20629488 AATTAATTTCAAACT-AATCTTA
1 AATTAATTTTTAACTCAAT-TTA
20629510 AATT-ATTTTTAACTCAATTTA
1 AATTAATTTTTAACTCAATTTA
*
20629531 ATTTAATTTTT
1 AATTAATTTTT
20629542 GAATATTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTAATTTTTAACTCAATTTA
Found at i:20631927 original size:37 final size:37
Alignment explanation
Indices: 20631886--20631959 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
20631876 GCTTAGATTG
* * *
20631886 TGTCAATGTATGAAAAGTCTATTAAGTGAGTCTGTGT
1 TGTCAATGCATGAAAAGTCTATAAAGCGAGTCTGTGT
* * *
20631923 TGTCAGTGCATGAAGAGTCTGTAAAGCGAGTCTGTGT
1 TGTCAATGCATGAAAAGTCTATAAAGCGAGTCTGTGT
20631960 CTGTTCTTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.34
Consensus pattern (37 bp):
TGTCAATGCATGAAAAGTCTATAAAGCGAGTCTGTGT
Found at i:20638505 original size:20 final size:20
Alignment explanation
Indices: 20638456--20638505 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
20638446 GTCACTATAT
* *
20638456 TTTTTTAATAGGAGCTTATA
1 TTTTTTAATTGGAGCTAATA
*
20638476 TTTTTTAATTGTAGCTAATA
1 TTTTTTAATTGGAGCTAATA
20638496 TTTTTTAATT
1 TTTTTTAATT
20638506 TTTAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.58
Consensus pattern (20 bp):
TTTTTTAATTGGAGCTAATA
Found at i:20641730 original size:42 final size:42
Alignment explanation
Indices: 20641683--20641904 Score: 268
Period size: 42 Copynumber: 5.3 Consensus size: 42
20641673 TCAAGTCATA
* * * *
20641683 AGTCTTCCTTTAATTATACTTTCATTCTCATCTCGAGGCATG
1 AGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATG
20641725 AGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATG
1 AGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATG
20641767 AGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATG
1 AGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATG
* * * * * *
20641809 AGTCTTCCTTTAATCATATTTTCATGCTCATTTCGAGCCACG
1 AGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATG
* * * *
20641851 AGTCTTCCATTT-ATACA-AATTCTCATGCTCAACCCGAGATATG
1 AGTCTTCC-TTTAAT-CATAA-TCTCATTCTCATCTCGAGACATG
*
20641894 AGCCTTCCTTT
1 AGTCTTCCTTT
20641905 TTATACAACA
Statistics
Matches: 158, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
42 130 0.82
43 28 0.18
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (42 bp):
AGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATG
Found at i:20643239 original size:42 final size:42
Alignment explanation
Indices: 20643117--20643239 Score: 160
Period size: 42 Copynumber: 3.0 Consensus size: 42
20643107 GAAACGAGCG
* *
20643117 TGAGGATAT-ATTTAAAGAAGACTCATGTCTCA-AGATGAGAA
1 TGAGAATATGATTAAAAGAAGACTCATGTCTCAGA-ATGAGAA
* * *
20643158 TGAGAATATGATTAAAGGAAGACTCATGTCTCGGGATGAGAA
1 TGAGAATATGATTAAAAGAAGACTCATGTCTCAGAATGAGAA
* *
20643200 TGAGAATATGATTAAAAAAAGACTCATGGCTCAGAATGAG
1 TGAGAATATGATTAAAAGAAGACTCATGTCTCAGAATGAG
20643240 CGTAGGGTTA
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 8 0.11
42 62 0.89
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (42 bp):
TGAGAATATGATTAAAAGAAGACTCATGTCTCAGAATGAGAA
Found at i:20653299 original size:21 final size:21
Alignment explanation
Indices: 20653262--20653304 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
20653252 ATAAAGATTG
*
20653262 ATTGTGTGATTAATTGATGAA
1 ATTGTGTGATTAATTGAGGAA
*
20653283 ATTGTG-GATTTATTTGAGGAA
1 ATTGTGTGA-TTAATTGAGGAA
20653304 A
1 A
20653305 CAAAGGTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.42
Consensus pattern (21 bp):
ATTGTGTGATTAATTGAGGAA
Found at i:20653379 original size:6 final size:6
Alignment explanation
Indices: 20653368--20653406 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
20653358 TGATCAAAAT
* * *
20653368 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
20653407 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:20658267 original size:62 final size:62
Alignment explanation
Indices: 20658170--20658431 Score: 452
Period size: 62 Copynumber: 4.2 Consensus size: 62
20658160 TAGAAAATGA
20658170 AAAGGTCCGATGTCTTCGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
1 AAAGGTCCGATGTCTTCGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
* * *
20658232 AAAGGTCTGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTAATACGGATT
1 AAAGGTCCGATGTCTTCGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
* * *
20658294 AAAGGTCCGATGTCTTCATGATATCGTGAGCATTACATGAGAAATCAATCCTATTACGGATT
1 AAAGGTCCGATGTCTTCGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
*
20658356 AAAGGTCTGATGTCTTCGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
1 AAAGGTCCGATGTCTTCGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
*
20658418 TAAGGTCCGATGTC
1 AAAGGTCCGATGTC
20658432 GAAAATCTTG
Statistics
Matches: 185, Mismatches: 15, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
62 185 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (62 bp):
AAAGGTCCGATGTCTTCGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
Found at i:20662314 original size:2 final size:2
Alignment explanation
Indices: 20662307--20662373 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
20662297 TTAATTAATG
20662307 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
20662349 TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
20662374 AAAGATTAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20666678 original size:16 final size:17
Alignment explanation
Indices: 20666657--20666691 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
20666647 TCTGATTCCC
20666657 CTTTCTCTTT-CATTTT
1 CTTTCTCTTTCCATTTT
*
20666673 CTTTCTTTTTCCATTTT
1 CTTTCTCTTTCCATTTT
20666690 CT
1 CT
20666692 CCAAGGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.69
Consensus pattern (17 bp):
CTTTCTCTTTCCATTTT
Found at i:20669145 original size:14 final size:14
Alignment explanation
Indices: 20669122--20669205 Score: 69
Period size: 14 Copynumber: 5.7 Consensus size: 14
20669112 ATATACCTGA
*
20669122 AAAAAATGAGGAAG
1 AAAATATGAGGAAG
* *
20669136 AAAATGTGAGAAATG
1 AAAATATGAGGAA-G
*
20669151 AAGAAAATGAGGAAG
1 AA-AATATGAGGAAG
*
20669166 AAAATATGAGAAATG
1 AAAATATGAGGAA-G
*
20669181 AAAAAAATGAGGAAG
1 -AAAATATGAGGAAG
*
20669196 AAAATGTGAG
1 AAAATATGAG
20669206 AAATAATGTT
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
14 27 0.50
15 8 0.15
16 19 0.35
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.13
Consensus pattern (14 bp):
AAAATATGAGGAAG
Found at i:20669151 original size:21 final size:20
Alignment explanation
Indices: 20669125--20669210 Score: 54
Period size: 21 Copynumber: 4.2 Consensus size: 20
20669115 TACCTGAAAA
20669125 AAATGAGGAAGAAAATGTGAG
1 AAAT-AGGAAGAAAATGTGAG
*
20669146 AAAT--GAAGAAAATGAGGAAG
1 AAATAGGAAGAAAATG-TG-AG
* ** *
20669166 AAAATATG-AG-AAATGAAAA
1 -AAATAGGAAGAAAATGTGAG
20669185 AAATGAGGAAGAAAATGTGAG
1 AAAT-AGGAAGAAAATGTGAG
20669206 AAATA
1 AAATA
20669211 ATGTTCACAT
Statistics
Matches: 49, Mismatches: 8, Indels: 17
0.66 0.11 0.23
Matches are distributed among these distances:
18 14 0.29
19 4 0.08
20 5 0.10
21 23 0.47
22 2 0.04
23 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.27, T:0.14
Consensus pattern (20 bp):
AAATAGGAAGAAAATGTGAG
Found at i:20669160 original size:30 final size:30
Alignment explanation
Indices: 20669119--20669209 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
20669109 ATAATATACC
20669119 TGAAAAAAATGAGGAAGAAAATGTGAGAAA
1 TGAAAAAAATGAGGAAGAAAATGTGAGAAA
* *
20669149 TGAAGAAAATGAGGAAGAAAATATGAGAAA
1 TGAAAAAAATGAGGAAGAAAATGTGAGAAA
20669179 TGAAAAAAATGAGGAAGAAAATGTGAGAAA
1 TGAAAAAAATGAGGAAGAAAATGTGAGAAA
20669209 T
1 T
20669210 AATGTTCACA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.14
Consensus pattern (30 bp):
TGAAAAAAATGAGGAAGAAAATGTGAGAAA
Found at i:20669232 original size:18 final size:18
Alignment explanation
Indices: 20669206--20669257 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
20669196 AAAATGTGAG
*
20669206 AAATAATGTTCACATTTT
1 AAATAATGTTCACATTTC
* *
20669224 AAATCATGTTTACATTTC
1 AAATAATGTTCACATTTC
* *
20669242 AAATTATATTCACATT
1 AAATAATGTTCACATT
20669258 GATGGAAATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.44
Consensus pattern (18 bp):
AAATAATGTTCACATTTC
Found at i:20675570 original size:10 final size:10
Alignment explanation
Indices: 20675538--20675599 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
20675528 AAGATTTTAG
20675538 AAATTATAAA
1 AAATTATAAA
*
20675548 AAA-TAAAAA
1 AAATTATAAA
20675557 AAATTATAAA
1 AAATTATAAA
20675567 AAATCT-T-AA
1 AAAT-TATAAA
20675576 AAATCT-TAAA
1 AAAT-TATAAA
*
20675586 AATATTTTAAA
1 AA-ATTATAAA
20675597 AAA
1 AAA
20675600 ACAAAATGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
9 17 0.38
10 19 0.42
11 9 0.20
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATTATAAA
Found at i:20675577 original size:19 final size:18
Alignment explanation
Indices: 20675507--20675598 Score: 69
Period size: 19 Copynumber: 4.9 Consensus size: 18
20675497 ATTAGATAGA
*
20675507 TTAAAAAA-TTCAAAAAT
1 TTAAAAAATTTTAAAAAT
* * *
20675524 TCAAAAGATTTTAGAAAT
1 TTAAAAAATTTTAAAAAT
***
20675542 TATAAAAAATAAAAAAAAT
1 T-TAAAAAATTTTAAAAAT
*
20675561 TATAAAAAATCTTAAAAAT
1 T-TAAAAAATTTTAAAAAT
20675580 CTTAAAAATATTTTAAAAA
1 -TTAAAAA-ATTTTAAAAA
20675599 AACAAAATGT
Statistics
Matches: 57, Mismatches: 14, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
17 6 0.11
18 8 0.14
19 33 0.58
20 10 0.18
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
TTAAAAAATTTTAAAAAT
Found at i:20683463 original size:41 final size:41
Alignment explanation
Indices: 20683406--20683742 Score: 320
Period size: 41 Copynumber: 8.2 Consensus size: 41
20683396 GGACAAAAAA
* * * * *
20683406 CGCCGCAAAAGGT-AGGGCAATAGCGGCGTTTATAGGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGAAAG
* * * *
20683446 CGCCGCTAAAGGTTAGGGCAATAGTGACGCTCATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGAAAG
* * *
20683487 CGTCGCTAAAGGTCAGAGCAATAGCGACTCTTATAGGCAAA-
1 CGCCGCTAAAGGTCAGAGCAATAGCGACGCTTAT-GGGAAAG
* * * * *
20683528 TGCCGCTAAAGGTTAGATCAATAGTGACGCTTATGGGCAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGAAAG
* * *
20683569 CGCCGCTAAAGGTCAGAGTAATAGCGGCGCTTATGGGCAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGAAAG
* *
20683610 TGCCGCTAAAGGTCAGAGCAATAGCGATGCTTATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGAAAG
* * * * * ***
20683651 CGTCGCTAAAAGTCAGAGCAATAACGGCTCTTATTAAAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGAAAG
* * * *
20683692 CGCCACTAAAGGTCAGAGCATTAACGACGCTTATAAGG-AAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGACGCTTAT-GGGAAAG
*
20683733 CACCGCTAAA
1 CGCCGCTAAA
20683743 ACTCAATAAT
Statistics
Matches: 240, Mismatches: 53, Indels: 7
0.80 0.18 0.02
Matches are distributed among these distances:
40 16 0.07
41 219 0.91
42 5 0.02
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (41 bp):
CGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGAAAG
Found at i:20683877 original size:34 final size:35
Alignment explanation
Indices: 20683801--20683877 Score: 124
Period size: 34 Copynumber: 2.3 Consensus size: 35
20683791 TAATATTAAC
20683801 AATTATTTTAAAACTTATATAAACTAAAAAAATTTA
1 AATTATTTTAAAACTTATATAAACTAAAAAAA-TTA
20683837 AA--ATTTTAAAACTTATATAAACTAAAAAAA-TA
1 AATTATTTTAAAACTTATATAAACTAAAAAAATTA
20683869 AATTATTTT
1 AATTATTTT
20683878 GGTCTTATGG
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
32 4 0.10
34 33 0.85
36 2 0.05
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (35 bp):
AATTATTTTAAAACTTATATAAACTAAAAAAATTA
Found at i:20688529 original size:24 final size:24
Alignment explanation
Indices: 20688501--20688559 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
20688491 TAGAGTAATA
* *
20688501 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
20688525 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
*
20688549 AGAATTTAACT
1 AGAGTTTAACT
20688560 GAAAGATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:20688562 original size:24 final size:24
Alignment explanation
Indices: 20688517--20688563 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
20688507 TGACTCAAAT
* *
20688517 AAATAAACAGAGTTTAATTGAAAC
1 AAATAAACAGAATTTAACTGAAAC
20688541 AAATAAACAGAATTTAACTGAAA
1 AAATAAACAGAATTTAACTGAAA
20688564 GATTATTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (24 bp):
AAATAAACAGAATTTAACTGAAAC
Found at i:20690478 original size:43 final size:43
Alignment explanation
Indices: 20690429--20690512 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
20690419 TAATGTTAGT
* *
20690429 GGCGTTTGTGGGAAAAGCACCGCTAAAGACCATGTTCTTTAAC
1 GGCGTTTGTAGGAAAAGCACCGCTAAAGAACATGTTCTTTAAC
*
20690472 GGCGTTTGTAGGAAAAGCGCCGCTAAAGAACATGTTCTTTA
1 GGCGTTTGTAGGAAAAGCACCGCTAAAGAACATGTTCTTTA
20690513 GTGGGGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (43 bp):
GGCGTTTGTAGGAAAAGCACCGCTAAAGAACATGTTCTTTAAC
Found at i:20694520 original size:26 final size:26
Alignment explanation
Indices: 20694482--20694531 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
20694472 TAAGCTTTTC
* *
20694482 ATAGCTTAGCAAA-TTCATAGAGTTAA
1 ATAGATTACCAAACTTCA-AGAGTTAA
20694508 ATAGATTACCAAACTTCAAGAGTT
1 ATAGATTACCAAACTTCAAGAGTT
20694532 GTACAATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (26 bp):
ATAGATTACCAAACTTCAAGAGTTAA
Found at i:20694810 original size:52 final size:52
Alignment explanation
Indices: 20694724--20695014 Score: 474
Period size: 52 Copynumber: 5.6 Consensus size: 52
20694714 TTCTCATTTA
* * ** *
20694724 ATACTCACGATGACACATAGTCGTCAGATATCATAATCCGTAAAGGATGCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
20694776 ATACTCACGATGACACATAGTCACCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* ** *
20694828 ATGCTCACGATGACACATAGTCATCGGACCTCATAATTTGTAAAGGATTCGT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
20694880 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
20694932 ATACTCACGATGACACATAATCATCGGATCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
20694984 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
20695015 TTTTCATTTA
Statistics
Matches: 220, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 220 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:20699367 original size:11 final size:11
Alignment explanation
Indices: 20699352--20699384 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
20699342 CCGTTAATCG
20699352 ACCGTTGACCA
1 ACCGTTGACCA
*
20699363 GCCGTTGACCA
1 ACCGTTGACCA
20699374 ACCGTTGACCA
1 ACCGTTGACCA
20699385 TTGATAGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.18
Consensus pattern (11 bp):
ACCGTTGACCA
Found at i:20699420 original size:20 final size:20
Alignment explanation
Indices: 20699374--20699443 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
20699364 CCGTTGACCA
20699374 ACCGTTGACCATTGA-TAGTTG
1 ACCGTTGACCATTGACT--TTG
20699395 ACCGTTGACCATTGACTTTG
1 ACCGTTGACCATTGACTTTG
* * *
20699415 ATCGTTAACCGTTGACTTTG
1 ACCGTTGACCATTGACTTTG
*
20699435 ACCATTGAC
1 ACCGTTGAC
20699444 TTTCTCGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.62
21 15 0.36
22 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (20 bp):
ACCGTTGACCATTGACTTTG
Found at i:20699442 original size:27 final size:28
Alignment explanation
Indices: 20699378--20699442 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
20699368 TGACCAACCG
*
20699378 TTGACCATTGATAGTTGACCGTTGACCA
1 TTGACCATTGATAGTTAACCGTTGACCA
* * *
20699406 TTGA-CTTTGATCGTTAACCGTTGA-CT
1 TTGACCATTGATAGTTAACCGTTGACCA
20699432 TTGACCATTGA
1 TTGACCATTGA
20699443 CTTTCTCGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 5 0.16
27 22 0.71
28 4 0.13
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (28 bp):
TTGACCATTGATAGTTAACCGTTGACCA
Found at i:20708538 original size:41 final size:41
Alignment explanation
Indices: 20708493--20708578 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
20708483 TCAATTTTGT
*
20708493 AATGAATTAAACCTAACCTATGATCTAGTTCTCATAAAAGA
1 AATGAATTAAACCGAACCTATGATCTAGTTCTCATAAAAGA
20708534 AATGAATTAAACCGAACCTATGATCTAGTTCTCATAAAAGA
1 AATGAATTAAACCGAACCTATGATCTAGTTCTCATAAAAGA
20708575 AATG
1 AATG
20708579 TTGTTTTGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (41 bp):
AATGAATTAAACCGAACCTATGATCTAGTTCTCATAAAAGA
Found at i:20711384 original size:14 final size:14
Alignment explanation
Indices: 20711355--20711392 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
20711345 TGTTTGACTG
*
20711355 AAAATGACTTTCGA
1 AAAATGAATTTCGA
20711369 AAAAT-AATTTCTGA
1 AAAATGAATTTC-GA
20711383 AAAATGAATT
1 AAAATGAATT
20711393 ACTTTTCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 5 0.24
14 12 0.57
15 4 0.19
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (14 bp):
AAAATGAATTTCGA
Found at i:20714759 original size:2 final size:2
Alignment explanation
Indices: 20714752--20714781 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20714742 GATTCCCAAC
*
20714752 AT AT AT AT AT AC 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
20714782 GAAAATCACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20717615 original size:14 final size:14
Alignment explanation
Indices: 20717578--20717618 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
20717568 GGTGTGGCAA
20717578 GGAAAGGG-AAA-G
1 GGAAAGGGAAAAGG
*
20717590 GGAAAGGAAAAAGG
1 GGAAAGGGAAAAGG
*
20717604 GGGAAGGGAAAAGG
1 GGAAAGGGAAAAGG
20717618 G
1 G
20717619 AAATAGGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 7 0.29
13 3 0.12
14 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (14 bp):
GGAAAGGGAAAAGG
Found at i:20717628 original size:21 final size:19
Alignment explanation
Indices: 20717580--20717628 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
20717570 TGTGGCAAGG
*
20717580 AAAGGGAAAGGGAAAGGAA
1 AAAGGGGAAGGGAAAGGAA
20717599 AAAGGGGGAAGGGAAAAGGGAA
1 AAA-GGGGAAGGG-AAA-GGAA
*
20717621 ATAGGGGA
1 AAAGGGGA
20717629 GAGGCTTCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 3 0.12
20 8 0.32
21 8 0.32
22 6 0.24
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (19 bp):
AAAGGGGAAGGGAAAGGAA
Found at i:20721717 original size:15 final size:15
Alignment explanation
Indices: 20721677--20721720 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
20721667 GAAAAGTTTA
20721677 TATCCGAAAGGATAT
1 TATCCGAAAGGATAT
*
20721692 TAT-TGAAAAGGATAT
1 TATCCG-AAAGGATAT
*
20721707 TATCCGGAAGGATA
1 TATCCGAAAGGATA
20721721 ATTAATGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (15 bp):
TATCCGAAAGGATAT
Found at i:20721718 original size:30 final size:29
Alignment explanation
Indices: 20721638--20721733 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 29
20721628 TTTAAAATAT
* * *
20721638 TTGAAAATGTTATATTCGAAAGGATA-T-
1 TTGAAAAGGATATATCCGAAAGGATATTA
**
20721665 TTGAAAAGTTTATATCCGAAAGGATATTA
1 TTGAAAAGGATATATCCGAAAGGATATTA
*
20721694 TTGAAAAGGATATTATCCGGAAGGATAATTA
1 TTGAAAAGGATA-TATCCGAAAGGAT-ATTA
*
20721725 ATGAAAAGG
1 TTGAAAAGG
20721734 TTGAAAAGGA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
27 23 0.40
28 1 0.02
29 10 0.17
30 12 0.21
31 12 0.21
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (29 bp):
TTGAAAAGGATATATCCGAAAGGATATTA
Found at i:20721743 original size:40 final size:40
Alignment explanation
Indices: 20721694--20721780 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 40
20721684 AAGGATATTA
* * *
20721694 TTGAAAAGGATATTATCCGGAAGGATAATTAATGAAAAGG
1 TTGAAAAGGACATTATCCGAAAGGATAATAAATGAAAAGG
* *
20721734 TTGAAAAGGACGTTATCCGAAAGGATACTAAATGAAAAGG
1 TTGAAAAGGACATTATCCGAAAGGATAATAAATGAAAAGG
*
20721774 TCGAAAA
1 TTGAAAA
20721781 TGTAAATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.46, C:0.08, G:0.24, T:0.22
Consensus pattern (40 bp):
TTGAAAAGGACATTATCCGAAAGGATAATAAATGAAAAGG
Found at i:20725102 original size:14 final size:14
Alignment explanation
Indices: 20725050--20725108 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
20725040 AAACAAAAGA
*
20725050 AAAAAAATTAGAAT
1 AAAAAAATTAAAAT
** * *
20725064 GTAACAATTAAATT
1 AAAAAAATTAAAAT
*
20725078 AAAAACA--AAAAT
1 AAAAAAATTAAAAT
20725090 AAAAAAATTAAAAT
1 AAAAAAATTAAAAT
20725104 AAAAA
1 AAAAA
20725109 TGACTAAATT
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
12 10 0.31
14 22 0.69
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.20
Consensus pattern (14 bp):
AAAAAAATTAAAAT
Found at i:20729376 original size:29 final size:29
Alignment explanation
Indices: 20729344--20729402 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
20729334 TCTTATTCCC
20729344 AAGGTTAGTAGAGCTCATTCTATTAAATA
1 AAGGTTAGTAGAGCTCATTCTATTAAATA
20729373 AAGGTTAGTAGAGCTCATTCTATTAAATA
1 AAGGTTAGTAGAGCTCATTCTATTAAATA
20729402 A
1 A
20729403 TTTAGACCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (29 bp):
AAGGTTAGTAGAGCTCATTCTATTAAATA
Found at i:20735927 original size:19 final size:18
Alignment explanation
Indices: 20735887--20735931 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
20735877 ACTGTAAACC
*
20735887 TATAAAAAATTTAGAAAC
1 TATAAAAAATTTAGAAAA
20735905 TATAAAAAATTGTA-ATAAA
1 TATAAAAAATT-TAGA-AAA
20735924 TATAAAAA
1 TATAAAAA
20735932 TATAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (18 bp):
TATAAAAAATTTAGAAAA
Found at i:20736683 original size:20 final size:21
Alignment explanation
Indices: 20736636--20736697 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
20736626 ACTCAATTTC
20736636 TTGTAAAAACTCAGGTTTTTA
1 TTGTAAAAACTCAGGTTTTTA
* *
20736657 CTATAAAAAC-CAAGGTTTTT-
1 TTGTAAAAACTC-AGGTTTTTA
*
20736677 TTGTAAAGAACTCAGGATTTT
1 TTGTAAA-AACTCAGGTTTTT
20736698 CCCTTTTTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
20 6 0.18
21 26 0.79
22 1 0.03
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (21 bp):
TTGTAAAAACTCAGGTTTTTA
Found at i:20738330 original size:6 final size:6
Alignment explanation
Indices: 20738319--20738351 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
20738309 GTACAGGGTC
*
20738319 TGAAAA TGAAAA TGAAAA TGAAAA TGAGAA TGA
1 TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA TGA
20738352 TCATAGGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (6 bp):
TGAAAA
Found at i:20757215 original size:18 final size:20
Alignment explanation
Indices: 20757178--20757216 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20757168 AAAATCTATG
*
20757178 AATTTGTAAAACATTATTAA
1 AATTTATAAAACATTATTAA
20757198 AATTTATAAAA-A-TATTAA
1 AATTTATAAAACATTATTAA
20757216 A
1 A
20757217 TAAAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
20 10 0.56
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
AATTTATAAAACATTATTAA
Found at i:20758989 original size:13 final size:13
Alignment explanation
Indices: 20758971--20759001 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
20758961 TGTTGAGGTT
*
20758971 AAGATTGTCGATG
1 AAGATTGACGATG
20758984 AAGATTGACGATG
1 AAGATTGACGATG
20758997 AAGAT
1 AAGAT
20759002 CATATAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.29, T:0.26
Consensus pattern (13 bp):
AAGATTGACGATG
Found at i:20761452 original size:18 final size:18
Alignment explanation
Indices: 20761426--20761460 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20761416 AGAAAGCAAT
20761426 TTTGGTATTGATATTGAC
1 TTTGGTATTGATATTGAC
*
20761444 TTTGTTATTGATATTGA
1 TTTGGTATTGATATTGA
20761461 AGGCTAGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.20, T:0.54
Consensus pattern (18 bp):
TTTGGTATTGATATTGAC
Found at i:20763145 original size:19 final size:21
Alignment explanation
Indices: 20763100--20763146 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
20763090 ATAATAATTA
*
20763100 TAAAAAGTCATTAAATTTAAT
1 TAAAAAGTCATAAAATTTAAT
*
20763121 TAAAAA-TCATAAAATTTATT
1 TAAAAAGTCATAAAATTTAAT
20763141 TAAAAA
1 TAAAAA
20763147 TATTTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAAAGTCATAAAATTTAAT
Found at i:20763341 original size:12 final size:12
Alignment explanation
Indices: 20763324--20763350 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20763314 ATAAATTATT
20763324 TTTTAGCATTTA
1 TTTTAGCATTTA
20763336 TTTTAGCATTTA
1 TTTTAGCATTTA
20763348 TTT
1 TTT
20763351 GTTTTCTGGA
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:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTTAGCATTTA
Found at i:20765195 original size:7 final size:7
Alignment explanation
Indices: 20765172--20765225 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
20765162 TTTCAAAAAA
20765172 GTCAACG
1 GTCAACG
*
20765179 GTCAA-A
1 GTCAACG
20765185 GTCAACG
1 GTCAACG
20765192 GTCAACG
1 GTCAACG
*
20765199 ATCAACG
1 GTCAACG
* *
20765206 ATCAACA
1 GTCAACG
*
20765213 GTCAATG
1 GTCAACG
20765220 GTCAAC
1 GTCAAC
20765226 AGTCGATCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
6 5 0.13
7 33 0.87
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:20765224 original size:21 final size:20
Alignment explanation
Indices: 20765171--20765225 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
20765161 TTTTCAAAAA
*
20765171 AGTCAACGGTCAAAGTCAAC
1 AGTCAACGGTCAACGTCAAC
* *
20765191 GGTCAACGATCAACGATCAAC
1 AGTCAACGGTCAACG-TCAAC
*
20765212 AGTCAATGGTCAAC
1 AGTCAACGGTCAAC
20765226 AGTCGATCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.16
Consensus pattern (20 bp):
AGTCAACGGTCAACGTCAAC
Found at i:20765226 original size:14 final size:14
Alignment explanation
Indices: 20765171--20765229 Score: 77
Period size: 14 Copynumber: 4.3 Consensus size: 14
20765161 TTTTCAAAAA
20765171 AGTCAACGGTCAA-
1 AGTCAACGGTCAAC
20765184 AGTCAACGGTCAAC
1 AGTCAACGGTCAAC
*
20765198 -GATCAACGATCAAC
1 AG-TCAACGGTCAAC
*
20765212 AGTCAATGGTCAAC
1 AGTCAACGGTCAAC
20765226 AGTC
1 AGTC
20765230 GATCAACGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
13 14 0.35
14 25 0.62
15 1 0.03
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.17
Consensus pattern (14 bp):
AGTCAACGGTCAAC
Found at i:20765247 original size:22 final size:22
Alignment explanation
Indices: 20765219--20765293 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
20765209 AACAGTCAAT
*
20765219 GGTCAACAGTCGATCAACGGAC
1 GGTCAACAGCCGATCAACGGAC
*
20765241 GGTCAACAGCCGATCAACGGTC
1 GGTCAACAGCCGATCAACGGAC
* * *
20765263 GATCAAC-GACCGATTAACGGTC
1 GGTCAACAG-CCGATCAACGGAC
*
20765285 GGTCGACAG
1 GGTCAACAG
20765294 TTTGACTTGG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 1 0.02
22 43 0.96
23 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.15
Consensus pattern (22 bp):
GGTCAACAGCCGATCAACGGAC
Found at i:20766573 original size:28 final size:29
Alignment explanation
Indices: 20766540--20766609 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
20766530 ATTAAAATTA
* **
20766540 TTTAATAATTTTAT-TATTT-CAAAATTTT
1 TTTAATAATTTTATAT-TTTAAAAAATAAT
20766568 TTTAATAATTTTATATTTTAAAAAATAAT
1 TTTAATAATTTTATATTTTAAAAAATAAT
20766597 TTTAATAATTTTA
1 TTTAATAATTTTA
20766610 AAATCATTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.46
29 20 0.54
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTAATAATTTTATATTTTAAAAAATAAT
Found at i:20766594 original size:20 final size:22
Alignment explanation
Indices: 20766571--20766612 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
20766561 AAATTTTTTT
20766571 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
20766591 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
20766613 TCATTTGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:20780106 original size:18 final size:19
Alignment explanation
Indices: 20780083--20780120 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
20780073 TTTTTTAGTT
20780083 ATTTTTAAA-AAAATTTAA
1 ATTTTTAAACAAAATTTAA
20780101 ATTTTTAAACAAAATTTAA
1 ATTTTTAAACAAAATTTAA
20780120 A
1 A
20780121 CATTTTAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTTTAAACAAAATTTAA
Found at i:20780126 original size:20 final size:18
Alignment explanation
Indices: 20780085--20780128 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
20780075 TTTTAGTTAT
*
20780085 TTTTAAAAAAATTTAAAT
1 TTTTAAAAAAATTTAAAA
20780103 TTTTAAACAAAATTTAAACA
1 TTTTAAA-AAAATTTAAA-A
20780123 TTTTAA
1 TTTTAA
20780129 CTATTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 10 0.43
20 6 0.26
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTTAAAAAAATTTAAAA
Found at i:20780210 original size:144 final size:144
Alignment explanation
Indices: 20780028--20780300 Score: 394
Period size: 144 Copynumber: 1.9 Consensus size: 144
20780018 TTTTGGATTT
*
20780028 TTTTTATAAAAAAAGAAAATTTAGATTTTTAAAAATAAAAACCTAT-TTTTTAGTTATTTT-TA-
1 TTTTTATAAAAAAAGAAAATTTAGATTTTTAAAAATAAAAA--TATGTTTTTAGTTATTTTAAAG
* *
20780090 AAAAAATTTAAATTTTTAAACAAAATTTAAACATTTTAACTATTTCAAAATAAAAGTTTTGATTT
64 AAAAAATTTAAAATTTTAAACAAAATTTAAA-ATTTTAACCATTTCAAAATAAAAGTTTTGATTT
20780155 TTTTTAAAAAATAGTGA
128 TTTTTAAAAAATAGTGA
*
20780172 TTTTTA-AAAAAAA-AAAAGTTTAGATTTTTTTAAAATAAAAATATGTTTTTAGTTATTTTAAAG
1 TTTTTATAAAAAAAGAAAA-TTTAGA-TTTTTAAAAATAAAAATATGTTTTTAGTTATTTTAAAG
* * * *
20780235 AAAAAATTTAAAATTTTAAACAAAGTTTGAATTTTTAACCATTTCGAAATAAAAGTTTTGATTTT
64 AAAAAATTTAAAATTTTAAACAAAATTTAAAATTTTAACCATTTCAAAATAAAAGTTTTGATTTT
20780300 T
129 T
20780301 AAGAAAAGTA
Statistics
Matches: 116, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
142 7 0.06
143 27 0.23
144 54 0.47
145 28 0.24
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (144 bp):
TTTTTATAAAAAAAGAAAATTTAGATTTTTAAAAATAAAAATATGTTTTTAGTTATTTTAAAGAA
AAAATTTAAAATTTTAAACAAAATTTAAAATTTTAACCATTTCAAAATAAAAGTTTTGATTTTTT
TTAAAAAATAGTGA
Found at i:20780329 original size:144 final size:140
Alignment explanation
Indices: 20780026--20780331 Score: 368
Period size: 144 Copynumber: 2.1 Consensus size: 140
20780016 AGTTTTGGAT
*
20780026 TTTTTTTATAAAAAAAGAAAATTTAGATTTTTAAAAATAAAAACCTATTTTTTAGTTATTTTTAA
1 TTTTTTTAT--AAAAA-AAAATTTAGATTTTTAAAAATAAAAA-CTATTTTTTAGTTATTTTAAA
* *
20780091 AAAAATTTAAATTTTTAAACAAAATTTAAACATTTTAACTATTTCAAAATAAAAGTTTTGATTTT
62 AAAAATTTAAAATTTTAAACAAAATTTAAACATTTTAACCATTTCAAAATAAAAGTTTTGA--TT
20780156 TTTTAAAAAATAGTGA
125 TTTTAAAAAATAGTGA
* * *
20780172 -TTTTTAAAAAAAAAAAAGTTTAGATTTTTTTAAAATAAAAA-TATGTTTTTAGTTATTTTAAAG
1 TTTTTTTATAAAAAAAAA-TTTAGA-TTTTTAAAAATAAAAACTAT-TTTTTAGTTATTTT-AA-
* * * *
20780235 AAAAAATTTAAAATTTTAAACAAAGTTTGAA-TTTTTAACCATTTCGAAATAAAAGTTTTGA-TT
61 AAAAAATTTAAAATTTTAAACAAAATTTAAACATTTTAACCATTTCAAAATAAAAGTTTTGATTT
20780298 TTTAAGAAAAGTAGTGA
126 TTTAA-AAAA-TAGTGA
20780315 TTTTGTTTATAAAAAAA
1 TTTT-TTTATAAAAAAA
20780332 TTTAATTTTG
Statistics
Matches: 139, Mismatches: 12, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
141 7 0.05
142 11 0.08
143 31 0.22
144 46 0.33
145 44 0.32
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (140 bp):
TTTTTTTATAAAAAAAAATTTAGATTTTTAAAAATAAAAACTATTTTTTAGTTATTTTAAAAAAA
ATTTAAAATTTTAAACAAAATTTAAACATTTTAACCATTTCAAAATAAAAGTTTTGATTTTTTAA
AAAATAGTGA
Found at i:20780932 original size:16 final size:16
Alignment explanation
Indices: 20780885--20780932 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
20780875 TTTATTCTTA
20780885 TTTCATTGTTTATTTAT
1 TTTCA-TGTTTATTTAT
*
20780902 TTTCATGTCTATTTAT
1 TTTCATGTTTATTTAT
*
20780918 ATTT-ATGTTTTTTTA
1 -TTTCATGTTTATTTA
20780933 CACACTCCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 19 0.70
17 8 0.30
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTCATGTTTATTTAT
Found at i:20783353 original size:25 final size:27
Alignment explanation
Indices: 20783299--20783353 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 27
20783289 TGGTTCATCA
**
20783299 GAAATGAGTAAATGGAAATGGTTACTT
1 GAAATGAGTAAATGGAAATGGTTAAAT
20783326 GAAATG-G-AAATGGTAAAT-GTTAAAT
1 GAAATGAGTAAATGG-AAATGGTTAAAT
20783351 GAA
1 GAA
20783354 TATGTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 14 0.56
26 5 0.20
27 6 0.24
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.27
Consensus pattern (27 bp):
GAAATGAGTAAATGGAAATGGTTAAAT
Found at i:20785937 original size:3 final size:3
Alignment explanation
Indices: 20785929--20785966 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
20785919 TTATCTTTGT
20785929 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
20785967 CTCTCCAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:20799803 original size:19 final size:17
Alignment explanation
Indices: 20799779--20799826 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
20799769 TTCCTAACAC
20799779 TTTTTATAAATAAGATAAT
1 TTTTTATAAA-AAG-TAAT
*
20799798 TTTTTATCATAAAAGTTAT
1 TTTTTAT-A-AAAAGTAAT
20799817 TTTTTATAAA
1 TTTTTATAAA
20799827 CAAATTATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.08
18 1 0.04
19 17 0.65
20 4 0.15
21 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (17 bp):
TTTTTATAAAAAGTAAT
Found at i:20801099 original size:23 final size:23
Alignment explanation
Indices: 20801063--20801110 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
20801053 TAGATAATAT
* *
20801063 ATTTTAGTATATTGTATTAACAA
1 ATTTTAGTACATTGCATTAACAA
* *
20801086 ATTTTAGTGCATTGCATTACCAA
1 ATTTTAGTACATTGCATTAACAA
20801109 AT
1 AT
20801111 CGTTTCATTT
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:0.35, C:0.10, G:0.10, T:0.44
Consensus pattern (23 bp):
ATTTTAGTACATTGCATTAACAA
Found at i:20814728 original size:24 final size:25
Alignment explanation
Indices: 20814686--20814734 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
20814676 TTAATCATTC
*
20814686 ATTTTATCTTTTTAAAATTTATTTT
1 ATTTTATCTTTTTAAAATTAATTTT
* *
20814711 ATTTTTTC-TTTTAGAATTAATTTT
1 ATTTTATCTTTTTAAAATTAATTTT
20814735 TGTTATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (25 bp):
ATTTTATCTTTTTAAAATTAATTTT
Found at i:20820518 original size:10 final size:10
Alignment explanation
Indices: 20820503--20820530 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
20820493 GGTTGATACG
20820503 ATTTCCTACA
1 ATTTCCTACA
20820513 ATTTCCTACA
1 ATTTCCTACA
20820523 ATTTCCTA
1 ATTTCCTA
20820531 TTGCTATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (10 bp):
ATTTCCTACA
Found at i:20820832 original size:21 final size:21
Alignment explanation
Indices: 20820807--20820848 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
20820797 TCCTATTGTC
20820807 GTATTGGAGCTTTTACATGTT
1 GTATTGGAGCTTTTACATGTT
**
20820828 GTATTTTAGCTTTTACATGTT
1 GTATTGGAGCTTTTACATGTT
20820849 CTGATGCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (21 bp):
GTATTGGAGCTTTTACATGTT
Found at i:20822039 original size:56 final size:58
Alignment explanation
Indices: 20821903--20822056 Score: 181
Period size: 56 Copynumber: 2.7 Consensus size: 58
20821893 TATATTATGA
*
20821903 TTTTTATT-AATTCATATTTTAATAATAATTATATTAAAA-ATGTTATTAAATTATATACT
1 TTTTTATTAAATT-ATA-TTTAATAATAATCATATTAAAATATG-TATTAAATTATATACT
* * * * **
20821962 ATTTTATTAAAGTGTATTTAATAATAATCATGTTAAAATATG-ATTAAATTAT-TTGT
1 TTTTTATTAAATTATATTTAATAATAATCATATTAAAATATGTATTAAATTATATACT
*
20822018 TTTTTATTAAATTATATTTAATAATAATCTTATTAAAAT
1 TTTTTATTAAATTATATTTAATAATAATCATATTAAAAT
20822057 TTAACAACAA
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
56 36 0.44
57 10 0.12
58 20 0.25
59 12 0.15
60 3 0.04
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (58 bp):
TTTTTATTAAATTATATTTAATAATAATCATATTAAAATATGTATTAAATTATATACT
Found at i:20822256 original size:16 final size:16
Alignment explanation
Indices: 20822216--20822274 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
20822206 AACAATGAAA
* *
20822216 TATTA-ATTATAGCCC
1 TATTACATTACAGCTC
*
20822231 TATT-CAATTACAGCTT
1 TATTAC-ATTACAGCTC
*
20822247 TATTACATTATAGCTC
1 TATTACATTACAGCTC
*
20822263 TATTTCATTACA
1 TATTACATTACA
20822275 ACCAACCAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 4 0.12
16 29 0.85
17 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (16 bp):
TATTACATTACAGCTC
Found at i:20822531 original size:27 final size:27
Alignment explanation
Indices: 20822493--20822556 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
20822483 AAACCAAAAC
* * *
20822493 AAAATTTCCATAAAACATTAAGCCCAA
1 AAAATTTTCATAAAACACTAAACCCAA
* *
20822520 AAAATTTTCATAGAACACTAAACTCAA
1 AAAATTTTCATAAAACACTAAACCCAA
*
20822547 AAAAATTTCA
1 AAAATTTTCA
20822557 AAACCCTAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.25
Consensus pattern (27 bp):
AAAATTTTCATAAAACACTAAACCCAA
Found at i:20834130 original size:62 final size:63
Alignment explanation
Indices: 20834019--20834154 Score: 204
Period size: 62 Copynumber: 2.2 Consensus size: 63
20834009 TTAATATAAC
20834019 ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTAGTACCTAAAC-TTTTTTTT-AGACTCA
1 ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTAGTACCTAAACTTTTTTTTTAAGACTCA
* * * * *
20834080 ATTTGGTGCCTGAACTTGATATTTTTTTCCTAATTTGGTACCTAAGCTTTTTTTTTAAGATTCA
1 ATTTGGTACCTGAACTTGACA-TTTTTTCCTAATTTAGTACCTAAACTTTTTTTTTAAGACTCA
20834144 ATTTGGTACCT
1 ATTTGGTACCT
20834155 TCAATTAAGA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
61 19 0.29
62 23 0.35
63 8 0.12
64 16 0.24
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (63 bp):
ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTAGTACCTAAACTTTTTTTTTAAGACTCA
Found at i:20841266 original size:15 final size:15
Alignment explanation
Indices: 20841248--20841282 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
20841238 ATGTCATATA
20841248 TATATATATGTGTAC
1 TATATATATGTGTAC
*
20841263 TATATATGTGTGTAC
1 TATATATATGTGTAC
20841278 T-TATA
1 TATATA
20841283 AATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (15 bp):
TATATATATGTGTAC
Found at i:20843092 original size:39 final size:40
Alignment explanation
Indices: 20843038--20843140 Score: 118
Period size: 39 Copynumber: 2.6 Consensus size: 40
20843028 AAACACCACA
** * **
20843038 AAAGGTAGAATAATAGTGGCGCTTAT-GGCAAGCGCCGCT
1 AAAGGTAGAGCAATAGCGGCGCTTATAGAAAAGCGCCGCT
* *
20843077 AAAGGTAGAGCAATAGCGACGCTTATATAAAAGCGCCGCT
1 AAAGGTAGAGCAATAGCGGCGCTTATAGAAAAGCGCCGCT
*
20843117 AAAGGTCGAAGCAATAGCGGCGCT
1 AAAGGTAG-AGCAATAGCGGCGCT
20843141 ATCTCATAAG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 22 0.42
40 17 0.32
41 14 0.26
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.17
Consensus pattern (40 bp):
AAAGGTAGAGCAATAGCGGCGCTTATAGAAAAGCGCCGCT
Found at i:20846253 original size:21 final size:21
Alignment explanation
Indices: 20846227--20846277 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
20846217 CTACAACTTA
20846227 AAGCGGAGGTAGCAGCGAGGC
1 AAGCGGAGGTAGCAGCGAGGC
*
20846248 AAGCGGAGGTAGCAGCGAGGG
1 AAGCGGAGGTAGCAGCGAGGC
*
20846269 AAGCAGAGG
1 AAGCGGAGG
20846278 CTACAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.49, T:0.04
Consensus pattern (21 bp):
AAGCGGAGGTAGCAGCGAGGC
Found at i:20861659 original size:10 final size:9
Alignment explanation
Indices: 20861632--20861656 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
20861622 GATTTGTCTA
20861632 GAAAAAATT
1 GAAAAAATT
20861641 GAAAAAATT
1 GAAAAAATT
20861650 GAAAAAA
1 GAAAAAA
20861657 ATTTGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (9 bp):
GAAAAAATT
Found at i:20867322 original size:22 final size:22
Alignment explanation
Indices: 20867297--20867352 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
20867287 ATTTAATAAA
* *
20867297 TAAAAATAAAAATCTAAAAGGC
1 TAAAACTAAAAATCTAAAAGAC
* *
20867319 TAAAACTAAAAGTCTAAAAGAT
1 TAAAACTAAAAATCTAAAAGAC
20867341 TAAAACTAAAAA
1 TAAAACTAAAAA
20867353 ATCCCAATCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (22 bp):
TAAAACTAAAAATCTAAAAGAC
Found at i:20867327 original size:14 final size:15
Alignment explanation
Indices: 20867305--20867337 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
20867295 AATAAAAATA
20867305 AAAATCTAAAAGGCT
1 AAAATCTAAAAGGCT
*
20867320 AAAA-CTAAAAGTCT
1 AAAATCTAAAAGGCT
20867334 AAAA
1 AAAA
20867338 GATTAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.61, C:0.12, G:0.09, T:0.18
Consensus pattern (15 bp):
AAAATCTAAAAGGCT
Found at i:20874664 original size:27 final size:26
Alignment explanation
Indices: 20874633--20874691 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
20874623 AACTCGACTT
*
20874633 GTTGACCGTTAACTATGGACTTTGACA
1 GTTGACCATTAACT-TGGACTTTGACA
* *
20874660 GTTGACCATTAACTTTGACTTTGACC
1 GTTGACCATTAACTTGGACTTTGACA
20874686 GTTGAC
1 GTTGAC
20874692 TTTTTCGACC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 16 0.55
27 13 0.45
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (26 bp):
GTTGACCATTAACTTGGACTTTGACA
Found at i:20874693 original size:19 final size:20
Alignment explanation
Indices: 20874650--20874694 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
20874640 GTTAACTATG
20874650 GACTTTGACAGTTGACCATT
1 GACTTTGACAGTTGACCATT
* * *
20874670 AACTTTGAC-TTTGACCGTT
1 GACTTTGACAGTTGACCATT
20874689 GACTTT
1 GACTTT
20874695 TTCGACCAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (20 bp):
GACTTTGACAGTTGACCATT
Found at i:20878570 original size:55 final size:55
Alignment explanation
Indices: 20878496--20878660 Score: 235
Period size: 55 Copynumber: 3.0 Consensus size: 55
20878486 TGAGCTGAAT
*
20878496 TAGCTTTACGCTCTAACCGAGACGTAAGTAGTCCAAAGCTCTA-TATGAGCTATAA
1 TAGCTTTACGCTCTAACCGAGACGTAAGTAGTCCAAAGCTCTACT-CGAGCTATAA
*
20878551 TAGCTTTACGCTCTAACCGAGATGTAAGTAGTCCAAAGCTCTACTCGAGCTATAA
1 TAGCTTTACGCTCTAACCGAGACGTAAGTAGTCCAAAGCTCTACTCGAGCTATAA
* * * **
20878606 TAGGTTTATGCTCTAACCGAGACATAAGTAGTTAAAAGCTCTAC-CAGAGCTATAA
1 TAGCTTTACGCTCTAACCGAGACGTAAGTAGTCCAAAGCTCTACTC-GAGCTATAA
20878661 ATAGGTCAAA
Statistics
Matches: 100, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
54 1 0.01
55 98 0.98
56 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (55 bp):
TAGCTTTACGCTCTAACCGAGACGTAAGTAGTCCAAAGCTCTACTCGAGCTATAA
Found at i:20878660 original size:28 final size:27
Alignment explanation
Indices: 20878520--20878687 Score: 103
Period size: 28 Copynumber: 6.1 Consensus size: 27
20878510 AACCGAGACG
* **
20878520 TAAGTAGTCCAAAGCTCTATATGAGCTA
1 TAAGTAGTTCAAAGCTCTA-CCGAGCTA
* * * *
20878548 TAA-TAGCTT-TACGCTCTAACCGAGATG
1 TAAGTAG-TTCAAAGCTCT-ACCGAGCTA
*
20878575 TAAGTAGTCCAAAGCTCTACTCGAGCTA
1 TAAGTAGTTCAAAGCTCTAC-CGAGCTA
* *
20878603 TAA-TAGGTT-TATGCTCTAACCGAGAC-A
1 TAAGTA-GTTCAAAGCTCT-ACCGAG-CTA
*
20878630 TAAGTAGTTAAAAGCTCTACCAGAGCTA
1 TAAGTAGTTCAAAGCTCTACC-GAGCTA
* *
20878658 TAAATAGGTCAAAGCTCTACCCGAGCTA
1 TAAGTAGTTCAAAGCTCTA-CCGAGCTA
20878686 TA
1 TA
20878688 TTAGAGTATT
Statistics
Matches: 107, Mismatches: 20, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
27 42 0.39
28 63 0.59
29 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (27 bp):
TAAGTAGTTCAAAGCTCTACCGAGCTA
Found at i:20879428 original size:20 final size:20
Alignment explanation
Indices: 20879399--20879438 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
20879389 ATTCCACTAC
*
20879399 TAAACTAATTAACAATCGAA
1 TAAACCAATTAACAATCGAA
20879419 TAAACCAATTAACAATCGAA
1 TAAACCAATTAACAATCGAA
20879439 ATTATAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.17, G:0.05, T:0.23
Consensus pattern (20 bp):
TAAACCAATTAACAATCGAA
Found at i:20879501 original size:6 final size:6
Alignment explanation
Indices: 20879490--20879621 Score: 54
Period size: 6 Copynumber: 23.3 Consensus size: 6
20879480 GTTATTATCA
**
20879490 ATTAAT ATTAAT -TT-AT ATT-AT -TTGTT ATTAAT ATTAAGT A--AAT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAA-T ATTAAT
* * * *
20879533 AATAAT CTTTAT ATTAAGT AATT-A- A-TAAT ATTTAT ATTAAT ATT-AT
1 ATTAAT ATTAAT ATTAA-T -ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT
* * * *
20879579 ATTTAT ATTAAT AATTAAT A-T-AT TTTTAT ATTTAT ATTAAT AT
1 ATTAAT ATTAAT -ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT AT
20879622 ATTTCGATTA
Statistics
Matches: 97, Mismatches: 14, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
3 1 0.01
4 10 0.10
5 17 0.18
6 56 0.58
7 10 0.10
8 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (6 bp):
ATTAAT
Found at i:20879550 original size:23 final size:23
Alignment explanation
Indices: 20879515--20879610 Score: 89
Period size: 23 Copynumber: 4.4 Consensus size: 23
20879505 TATTATTTGT
*
20879515 TATTAATATTAAGTAAATAATAA
1 TATTTATATTAAGTAAATAATAA
* *
20879538 TCTTTATATTAAGTAATTAATAA
1 TATTTATATTAAGTAAATAATAA
20879561 TATTTATATTAA-T--AT--T-A
1 TATTTATATTAAGTAAATAATAA
*
20879578 TATTTATATTAA-TAATTAATATA
1 TATTTATATTAAGTAAATAATA-A
*
20879601 TTTTTATATT
1 TATTTATATT
20879611 TATATTAATA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
17 14 0.23
18 1 0.02
19 1 0.02
20 1 0.02
21 1 0.02
22 1 0.02
23 41 0.68
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTTATATTAAGTAAATAATAA
Found at i:20879562 original size:40 final size:38
Alignment explanation
Indices: 20879500--20879602 Score: 93
Period size: 40 Copynumber: 2.7 Consensus size: 38
20879490 ATTAATATTA
* ** *
20879500 ATTTATATTATTTGTTATTAATATTA-AGTAAATAATAAT
1 ATTTATATTAATAATTAATAATATTATA-TAAAT-ATAAT
* * *
20879539 CTTTATATTAAGTAATTAATAATATTTATATTAATATTAT
1 ATTTATATTAA-TAATTAATAATA-TTATATAAATATAAT
20879579 ATTTATATTAATAATTAAT-ATATT
1 ATTTATATTAATAATTAATAATATT
20879603 TTTATATTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
37 2 0.04
38 3 0.06
39 17 0.32
40 23 0.43
41 7 0.13
42 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (38 bp):
ATTTATATTAATAATTAATAATATTATATAAATATAAT
Found at i:20879580 original size:17 final size:17
Alignment explanation
Indices: 20879560--20879621 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
20879550 GTAATTAATA
20879560 ATATTTATATTAATATT
1 ATATTTATATTAATATT
20879577 ATATTTATATTAATAATT
1 ATATTTATATTAAT-ATT
20879595 A-A--TATATT--T-TT
1 ATATTTATATTAATATT
20879606 ATATTTATATTAATAT
1 ATATTTATATTAATAT
20879622 ATTTCGATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
11 3 0.08
12 1 0.03
13 1 0.03
14 6 0.16
15 6 0.16
16 1 0.03
17 16 0.42
18 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTATATTAATATT
Found at i:20879590 original size:29 final size:29
Alignment explanation
Indices: 20879558--20879621 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
20879548 AAGTAATTAA
20879558 TAATATTT-ATATTAATATTATATTTATAT
1 TAATATTTAATA-TAATATTATATTTATAT
* * *
20879587 TAATAATTAATATATTTTTATATTTATAT
1 TAATATTTAATATAATATTATATTTATAT
20879616 TAATAT
1 TAATAT
20879622 ATTTCGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 27 0.90
30 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TAATATTTAATATAATATTATATTTATAT
Found at i:20894577 original size:60 final size:60
Alignment explanation
Indices: 20894507--20894637 Score: 210
Period size: 60 Copynumber: 2.2 Consensus size: 60
20894497 GTAAATGTTG
20894507 AGGCTGAATTTGTTAA-ATTTTTAGAATTAACACCAAAATGACAAACTATATAAACATTGA
1 AGGCTGAATTTG-TAATATTTTTAGAATTAACACCAAAATGACAAACTATATAAACATTGA
* * **
20894567 AGGCTAAATTTGTAATTTTTTTAGAATTAAGGCCAAAATGACAAACTATATAAACATTGA
1 AGGCTGAATTTGTAATATTTTTAGAATTAACACCAAAATGACAAACTATATAAACATTGA
20894627 AGGCTGAATTT
1 AGGCTGAATTT
20894638 ATTATTATAT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 3 0.05
60 62 0.95
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.33
Consensus pattern (60 bp):
AGGCTGAATTTGTAATATTTTTAGAATTAACACCAAAATGACAAACTATATAAACATTGA
Found at i:20896148 original size:12 final size:12
Alignment explanation
Indices: 20896131--20896186 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
20896121 CCCTAAACCC
20896131 TAAAACTATATT
1 TAAAACTATATT
* *
20896143 TAAAACTTTTTTT
1 TAAAAC-TATATT
20896156 TGACAAACTATATT
1 T-A-AAACTATATT
20896170 TAAAACT-TAATT
1 TAAAACTAT-ATT
20896182 TAAAA
1 TAAAA
20896187 AAAGAACCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
11 1 0.03
12 19 0.53
13 6 0.17
14 6 0.17
15 4 0.11
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (12 bp):
TAAAACTATATT
Found at i:20896753 original size:13 final size:13
Alignment explanation
Indices: 20896735--20896765 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
20896725 AAAAATTTAA
20896735 AAAAACTTAAAAG
1 AAAAACTTAAAAG
20896748 AAAAACTTAAAAG
1 AAAAACTTAAAAG
20896761 AAAAA
1 AAAAA
20896766 TACAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (13 bp):
AAAAACTTAAAAG
Found at i:20896765 original size:19 final size:19
Alignment explanation
Indices: 20896743--20896781 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
20896733 AAAAAAACTT
20896743 AAAAGAAAAACTTAAAAGA
1 AAAAGAAAAACTTAAAAGA
* * *
20896762 AAAATACAAATTTAAAAGA
1 AAAAGAAAAACTTAAAAGA
20896781 A
1 A
20896782 TTTTTTTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.15
Consensus pattern (19 bp):
AAAAGAAAAACTTAAAAGA
Found at i:20898588 original size:2 final size:2
Alignment explanation
Indices: 20898581--20898648 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
20898571 GACATGTTTT
20898581 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
20898623 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
20898649 GCACATGCTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20899783 original size:22 final size:23
Alignment explanation
Indices: 20899757--20899817 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
20899747 TTATTAACAT
20899757 TGTTCGTAAACATGTTCAATT-A
1 TGTTCGTAAACATGTTCAATTAA
* * * **
20899779 TGTTCATGAACATATTCGTTTAA
1 TGTTCGTAAACATGTTCAATTAA
*
20899802 TGTTCGTCAACATGTT
1 TGTTCGTAAACATGTT
20899818 TGTGAATATT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
22 16 0.53
23 14 0.47
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (23 bp):
TGTTCGTAAACATGTTCAATTAA
Found at i:20903336 original size:12 final size:12
Alignment explanation
Indices: 20903306--20903349 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
20903296 CAATTCATAT
*
20903306 CACTTTCAATTC
1 CACTTTCACTTC
* *
20903318 CAATTTCACTTT
1 CACTTTCACTTC
*
20903330 CACTTTCACTCC
1 CACTTTCACTTC
20903342 CACTTTCA
1 CACTTTCA
20903350 ATTTTGATCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.23, C:0.36, G:0.00, T:0.41
Consensus pattern (12 bp):
CACTTTCACTTC
Found at i:20906285 original size:2 final size:2
Alignment explanation
Indices: 20906278--20906304 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20906268 GACTCAAAAC
20906278 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
20906305 CAAAAAAGGA
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:20909024 original size:56 final size:56
Alignment explanation
Indices: 20908918--20909163 Score: 341
Period size: 56 Copynumber: 4.4 Consensus size: 56
20908908 TGAAATAACC
* * * * * *
20908918 TTACGTTCTAACCGAGACGTAGGCA-AACCAGATCTCTACCCGAGCTATAATAGCA
1 TTACGCTCTAACCGAGACGTAAGTATATCCAAAGCTCTACCCGAGCTATAATAGCA
** *
20908973 TTACGCTCTAATTGAGACGTAAGTATGTCCAAAGCTCTACCCGAGCTATAATAGCA
1 TTACGCTCTAACCGAGACGTAAGTATATCCAAAGCTCTACCCGAGCTATAATAGCA
* *
20909029 TTACGCTCTAACCGAGACGTAAATATATCCAAAGCTTTACCCGAGCTATAATAGCA
1 TTACGCTCTAACCGAGACGTAAGTATATCCAAAGCTCTACCCGAGCTATAATAGCA
* * *
20909085 TTATGCTCTAATCGAGCCGTAAGTATATCCAAAGCTCTACCCGAGCTATAATAGCA
1 TTACGCTCTAACCGAGACGTAAGTATATCCAAAGCTCTACCCGAGCTATAATAGCA
* *
20909141 TTATGCTCTAACTGAGACGTAAG
1 TTACGCTCTAACCGAGACGTAAG
20909164 CAGATCGGAG
Statistics
Matches: 168, Mismatches: 22, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
55 20 0.12
56 148 0.88
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (56 bp):
TTACGCTCTAACCGAGACGTAAGTATATCCAAAGCTCTACCCGAGCTATAATAGCA
Found at i:20909038 original size:27 final size:27
Alignment explanation
Indices: 20909004--20909150 Score: 93
Period size: 27 Copynumber: 5.3 Consensus size: 27
20908994 AGTATGTCCA
20909004 AAGCTCTACCCGAGCTATAATAGCATT
1 AAGCTCTACCCGAGCTATAATAGCATT
* * * *
20909031 ACGCTCTAACCGAGACGTA-AATA-TATCCA
1 AAGCTCTACCCGAG-C-TATAATAGCAT--T
*
20909060 AAGCTTTACCCGAGCTATAATAGCATT
1 AAGCTCTACCCGAGCTATAATAGCATT
* ** ** * *
20909087 ATGCTCTAATCGAGCCGTAAGTA-TATCCA
1 AAGCTCTACCCGAGCTATAA-TAGCAT--T
20909116 AAGCTCTACCCGAGCTATAATAGCATT
1 AAGCTCTACCCGAGCTATAATAGCATT
*
20909143 ATGCTCTA
1 AAGCTCTA
20909151 ACTGAGACGT
Statistics
Matches: 85, Mismatches: 25, Indels: 20
0.65 0.19 0.15
Matches are distributed among these distances:
27 39 0.46
28 14 0.16
29 32 0.38
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (27 bp):
AAGCTCTACCCGAGCTATAATAGCATT
Found at i:20909205 original size:112 final size:111
Alignment explanation
Indices: 20908918--20909213 Score: 319
Period size: 112 Copynumber: 2.6 Consensus size: 111
20908908 TGAAATAACC
* ** * * * * *
20908918 TTACGTTCTAACCGAGACGTAGGCA-AACCAGATCTCTACCCGAGCTATAATAGCATTACGCTCT
1 TTACGCTCTAACCGAGACGTAAACAGATCCAAAGCGCTACCCGAGCTATAATAG-ATTAAGCTCT
* * *
20908982 AATTGAGACGTAAGTATGTCCAAAGCTCTACCCGAGCTATAATAGCA
65 AATCGAGCCGTAAGTATATCCAAAGCTCTACCCGAGCTATAATAGCA
* * ** *
20909029 TTACGCTCTAACCGAGACGTAAATATATCCAAAGCTTTACCCGAGCTATAATAGCATTATGCTCT
1 TTACGCTCTAACCGAGACGTAAACAGATCCAAAGCGCTACCCGAGCTATAATAG-ATTAAGCTCT
20909094 AATCGAGCCGTAAGTATATCCAAAGCTCTACCCGAGCTATAATAGCA
65 AATCGAGCCGTAAGTATATCCAAAGCTCTACCCGAGCTATAATAGCA
* * * ** * *
20909141 TTATGCTCTAACTGAGACGTAAGCAGAT-CGGAGCGCTACCCGAGCTGTATGTA-AGTTAAAGCT
1 TTACGCTCTAACCGAGACGTAAACAGATCCAAAGCGCTACCCGAGCTATA-ATAGA-TT-AAGCT
20909204 CTAATCGAGC
63 CTAATCGAGC
20909214 TATCTTTCGA
Statistics
Matches: 157, Mismatches: 24, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
110 1 0.01
111 39 0.25
112 117 0.75
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (111 bp):
TTACGCTCTAACCGAGACGTAAACAGATCCAAAGCGCTACCCGAGCTATAATAGATTAAGCTCTA
ATCGAGCCGTAAGTATATCCAAAGCTCTACCCGAGCTATAATAGCA
Found at i:20911075 original size:20 final size:20
Alignment explanation
Indices: 20911052--20911130 Score: 76
Period size: 20 Copynumber: 3.9 Consensus size: 20
20911042 GCAATGTCCC
20911052 ATTAAATTTAGTTAATTATG
1 ATTAAATTTAGTTAATTATG
20911072 ATTAAGGATTT-GTTAATTAT-
1 ATTAA--ATTTAGTTAATTATG
*
20911092 AGTTTAATTATA-TTAATTATG
1 A-TTAAATT-TAGTTAATTATG
20911113 ATT-AATTTAGTTTAATTA
1 ATTAAATTTAG-TTAATTA
20911131 AAGTATATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
18 2 0.04
19 7 0.14
20 24 0.48
21 13 0.26
22 4 0.08
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (20 bp):
ATTAAATTTAGTTAATTATG
Found at i:20916467 original size:26 final size:26
Alignment explanation
Indices: 20916435--20916492 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
20916425 TTAATATTTA
*
20916435 ATTATTTTTAAATAA-AAT-TATCAAT
1 ATTATTTATAAATAATAATATATC-AT
20916460 ATATATTTATAAATAATAATATATCAT
1 AT-TATTTATAAATAATAATATATCAT
20916487 ATTATT
1 ATTATT
20916493 ATTACCGACC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 2 0.07
26 16 0.55
27 7 0.24
28 4 0.14
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTATTTATAAATAATAATATATCAT
Found at i:20921989 original size:34 final size:34
Alignment explanation
Indices: 20921951--20922015 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
20921941 AAACCAGATT
20921951 TTGATATAATATTATACTGTATTTAATTAGAATA
1 TTGATATAATATTATACTGTATTTAATTAGAATA
20921985 TTGATATAATATTATACTGTATTTAATTAGA
1 TTGATATAATATTATACTGTATTTAATTAGA
20922016 GTATAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (34 bp):
TTGATATAATATTATACTGTATTTAATTAGAATA
Found at i:20922011 original size:17 final size:17
Alignment explanation
Indices: 20921957--20922011 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
20921947 GATTTTGATA
20921957 TAATATTATACTGTATT
1 TAATATTATACTGTATT
** * *
20921974 TAATTAGAATATTG-ATA
1 TAA-TATTATACTGTATT
20921991 TAATATTATACTGTATT
1 TAATATTATACTGTATT
20922008 TAAT
1 TAAT
20922012 TAGAGTATAA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
16 7 0.25
17 14 0.50
18 7 0.25
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (17 bp):
TAATATTATACTGTATT
Found at i:20927486 original size:36 final size:36
Alignment explanation
Indices: 20927407--20927495 Score: 105
Period size: 34 Copynumber: 2.6 Consensus size: 36
20927397 AAAATAATAG
* * *
20927407 CAAATCATT-TAAAATATTTTTAAAAAATATAATTTT
1 CAAAT-ATTATAAAAAATTATTAAAAAATAGAATTTT
*
20927443 -AAA-ATTATAAAAAATTATTAAAAATTAGAATTTT
1 CAAATATTATAAAAAATTATTAAAAAATAGAATTTT
20927477 CAAATATTAT-AAAAATTAT
1 CAAATATTATAAAAAATTAT
20927496 AGAAATGCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
33 3 0.07
34 23 0.50
35 15 0.33
36 5 0.11
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (36 bp):
CAAATATTATAAAAAATTATTAAAAAATAGAATTTT
Done.