Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397283.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_31.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1333793
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 10515 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:22435 original size:21 final size:22
Alignment explanation
Indices: 22410--22450 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
22400 TCAATTGCGA
22410 AAATTG-TGAAAAGG-TAAGAGG
1 AAATTGATG-AAAGGTTAAGAGG
22431 AAATTGATGAAAGGTTAAGA
1 AAATTGATGAAAGGTTAAGA
22451 CTTTGAACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (22 bp):
AAATTGATGAAAGGTTAAGAGG
Found at i:26334 original size:249 final size:249
Alignment explanation
Indices: 25895--26369 Score: 776
Period size: 249 Copynumber: 1.9 Consensus size: 249
25885 GAGTATTTGA
25895 CATAATTTCTCTACTTAAAAGAACAAAGTTCCTACTACTAATTTCAAAAAAAATATTAATTTATT
1 CATAATTTCTCTACTTAAAAGAACAAAGTTCCTACTACTAATTTCAAAAAAAATATTAATTTATT
* * *
25960 GATTAAATAATATTTTGATTAGTAACTAAATTTTCGTAATCCAACGATATTAAATGTTTAGAGGA
66 AATTAAATAATATTTCGATTAGTAACTAAATTTTCATAATCCAACGATATTAAATGTTTAGAGGA
* ** * *
26025 TTTATTATAATTAGAGAAACTAGCATTATCTTTTAAGTTTTTTAATAACATAATGACATGAACAT
131 TTTATTATAATTAGAGAAAATAAAATTATCTTTTAAATTTTTTAATAACATAACGACATGAA-AT
*
26090 GACATGTTGGTTTATCATAATAAATATTGATAAATTAATTATTTATTAGTTGGTG
195 GACATGTTGGTATATCATAATAAATATTGATAAATTAATTATTTATTAGTTGGTG
* *
26145 CATAATTTCTCTACTTAAAAGAACAAAGTTCTTACTACTAATTT-TAAAAAAATATTAATTTATT
1 CATAATTTCTCTACTTAAAAGAACAAAGTTCCTACTACTAATTTCAAAAAAAATATTAATTTATT
*
26209 AATTAAATAATATTTCGATTAGTTACTAAATTTTCATAATCCAACGATATTAAAT-TTCTAGAAG
66 AATTAAATAATATTTCGATTAGTAACTAAATTTTCATAATCCAACGATATTAAATGTT-TAG-AG
26273 G-TTTATTATAATTAGAGAAAATAAAATTATCTTTTAAATTTTTTAATAACATAACGACATGAAA
129 GATTTATTATAATTAGAGAAAATAAAATTATCTTTTAAATTTTTTAATAACATAACGACATGAAA
* *
26337 TGACATGTTGGTATGTCATAATAAATGTTGATA
194 TGACATGTTGGTATATCATAATAAATATTGATA
26370 TAGTTTGATA
Statistics
Matches: 209, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
248 33 0.16
249 130 0.62
250 46 0.22
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (249 bp):
CATAATTTCTCTACTTAAAAGAACAAAGTTCCTACTACTAATTTCAAAAAAAATATTAATTTATT
AATTAAATAATATTTCGATTAGTAACTAAATTTTCATAATCCAACGATATTAAATGTTTAGAGGA
TTTATTATAATTAGAGAAAATAAAATTATCTTTTAAATTTTTTAATAACATAACGACATGAAATG
ACATGTTGGTATATCATAATAAATATTGATAAATTAATTATTTATTAGTTGGTG
Found at i:41944 original size:3 final size:3
Alignment explanation
Indices: 41936--41964 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41926 TAGATTTAAG
41936 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
41965 TAGATTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:43726 original size:24 final size:21
Alignment explanation
Indices: 43676--43733 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
43666 CAATTAGAAC
43676 AGCAGCAGCTTGGCCACCTAA
1 AGCAGCAGCTTGGCCACCTAA
43697 AGCAGCAGCTTGGCCACCTAA
1 AGCAGCAGCTTGGCCACCTAA
* *
43718 AGTACCAGCTTGGCCA
1 AGCAGCAGCTTGGCCA
43734 TGTACAGTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.28, C:0.33, G:0.24, T:0.16
Consensus pattern (21 bp):
AGCAGCAGCTTGGCCACCTAA
Found at i:43813 original size:3 final size:3
Alignment explanation
Indices: 43791--43829 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
43781 GCCATGCACA
* *
43791 CTT CTT CTG CTT CTT TTT CTT CTT CTT CTT CTTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CT
43830 GCAACACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:45212 original size:108 final size:108
Alignment explanation
Indices: 45023--45278 Score: 365
Period size: 108 Copynumber: 2.4 Consensus size: 108
45013 GATATCGTTT
* * *
45023 ACTGCTTCCACTACCCTCACTTGAATTCTTACTGCTTCCGGTTTCATGATCAAGCTCTAGATGTC
1 ACTGCTTCCACTACCCTCACTTGAATGCTTACTGCTTCCAGTTTCATCATCAAGCTCTAGATGTC
45088 TTCTTGAATGCCCACTGCTTCCACTGC-CCTCACTTAAACGCTC
66 TTCTTGAATGCCCACTGCTTCCACT-CTCCTCACTTAAACGCTC
* * *
45131 ACTGCTTCCACTACCCTCACTTGAATGATTAC-GTCTTTCAGTTTCATCATCAAGTTCTAGATGT
1 ACTGCTTCCACTACCCTCACTTGAATGCTTACTG-CTTCCAGTTTCATCATCAAGCTCTAGATGT
* * * * *
45195 CTTCTTGAATGCTCACTGCTTCCACTCTCCTCGCTTGAATGCTT
65 CTTCTTGAATGCCCACTGCTTCCACTCTCCTCACTTAAACGCTC
45239 ACTGCTTCCACT-CTCCTCACTTGAATGCTTACTGCTTCCA
1 ACTGCTTCCACTAC-CCTCACTTGAATGCTTACTGCTTCCA
45279 CTTCCCTCAC
Statistics
Matches: 131, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
107 3 0.02
108 127 0.97
109 1 0.01
ACGTcount: A:0.19, C:0.33, G:0.12, T:0.36
Consensus pattern (108 bp):
ACTGCTTCCACTACCCTCACTTGAATGCTTACTGCTTCCAGTTTCATCATCAAGCTCTAGATGTC
TTCTTGAATGCCCACTGCTTCCACTCTCCTCACTTAAACGCTC
Found at i:45234 original size:30 final size:30
Alignment explanation
Indices: 45198--45306 Score: 150
Period size: 30 Copynumber: 3.6 Consensus size: 30
45188 TAGATGTCTT
*
45198 CTTGAATGCTCACTGCTTCCACTCTCCTCG
1 CTTGAATGCTCACTGCTTCCACTCTCCTCA
*
45228 CTTGAATGCTTACTGCTTCCACTCTCCTCA
1 CTTGAATGCTCACTGCTTCCACTCTCCTCA
*
45258 CTTGAATGCTTACTGCTTCCACT-TCCCTCA
1 CTTGAATGCTCACTGCTTCCACTCT-CCTCA
*
45288 CTCGAATGC-CTACTGCTTC
1 CTTGAATGCTC-ACTGCTTC
45307 TGCTTCCAAC
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
29 1 0.01
30 72 0.99
ACGTcount: A:0.16, C:0.38, G:0.12, T:0.35
Consensus pattern (30 bp):
CTTGAATGCTCACTGCTTCCACTCTCCTCA
Found at i:45342 original size:138 final size:138
Alignment explanation
Indices: 45090--45359 Score: 323
Period size: 138 Copynumber: 2.0 Consensus size: 138
45080 TAGATGTCTT
*
45090 CTTGAATGCCCACTGCTTCCACTGCCCTCACTTAAACGCTCACTGCTTCCACTACCCTCACTTGA
1 CTTGAATGCCCACTGCTTCCACTGCCCTCACTTAAACGCTCACTGCTTCCACTACCCTCACTCGA
* * * * * * *
45155 ATGATTACGTCTTTCAGTTTCATCATCAAGTTCTAGATGTCTTCTTGAATGCTCACTGCTTCCAC
66 ATGACTACGTCTTTCAGTTCCAACATCAAGTTCCAGACGTCTCCCTGAATGCTCACTGCTTCCAC
45220 TCTCCTCG
131 TCTCCTCG
** * * * *
45228 CTTGAATGCTTACTGCTTCCACT-CTCCTCACTTGAATGCTTACTGCTTCCACTTCCCTCACTCG
1 CTTGAATGCCCACTGCTTCCACTGC-CCTCACTTAAACGCTCACTGCTTCCACTACCCTCACTCG
* * *
45292 AATGCCTAC-TGC-TTCTGCTTCCAACGA-CAAGTTCCAGACGTCTCCCTGAATGCTTACTGCTT
65 AATGACTACGT-CTTTCAG-TTCCAAC-ATCAAGTTCCAGACGTCTCCCTGAATGCTCACTGCTT
45354 CCACTC
127 CCACTC
45360 CCATCACTTT
Statistics
Matches: 111, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
137 6 0.05
138 104 0.94
139 1 0.01
ACGTcount: A:0.19, C:0.35, G:0.13, T:0.33
Consensus pattern (138 bp):
CTTGAATGCCCACTGCTTCCACTGCCCTCACTTAAACGCTCACTGCTTCCACTACCCTCACTCGA
ATGACTACGTCTTTCAGTTCCAACATCAAGTTCCAGACGTCTCCCTGAATGCTCACTGCTTCCAC
TCTCCTCG
Found at i:50756 original size:19 final size:18
Alignment explanation
Indices: 50705--50756 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
50695 TCTCTCTAGT
*
50705 TCCTTTCTTCTCCCTTTCC
1 TCCTTTCTT-TCTCTTTCC
* **
50724 TCTTTTCTCCCTCTTTCTC
1 TCCTTTCTTTCTCTTTC-C
50743 TCCTTTCTTTCTCT
1 TCCTTTCTTTCTCT
50757 ATAGAGTGAG
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (18 bp):
TCCTTTCTTTCTCTTTCC
Found at i:72603 original size:97 final size:96
Alignment explanation
Indices: 72466--72640 Score: 323
Period size: 97 Copynumber: 1.8 Consensus size: 96
72456 ATTTTTAATA
*
72466 TTAATATTGTAGTTTTTATTTTTATATTTTTGAAATTTTGGTTTTTTTACTAAAGAATTTTTTTT
1 TTAATATTGTAGTTTTTATTTTTATATTTTTGAAATTTTGGTTTTTTTACTAAAGAATTTTTTTC
72531 CAATTTTTGTTTTTTATATCTTTGAAAAAATT
66 CAATTTTT-TTTTTTATATCTTTGAAAAAATT
*
72563 TTAATATTGTAGTTTTTATTTTTATATTTTTTAAATTTTGGTTTTTTTACTAAAGAATTTTTTTC
1 TTAATATTGTAGTTTTTATTTTTATATTTTTGAAATTTTGGTTTTTTTACTAAAGAATTTTTTTC
72628 CAATTTTTTTTTT
66 CAATTTTTTTTTT
72641 CAATTTTTGG
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
96 5 0.07
97 71 0.93
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.64
Consensus pattern (96 bp):
TTAATATTGTAGTTTTTATTTTTATATTTTTGAAATTTTGGTTTTTTTACTAAAGAATTTTTTTC
CAATTTTTTTTTTTATATCTTTGAAAAAATT
Found at i:73074 original size:79 final size:78
Alignment explanation
Indices: 72929--73117 Score: 299
Period size: 79 Copynumber: 2.4 Consensus size: 78
72919 TTTTTTGGAA
*
72929 ATTTTTCTTTAATTTTTTAAAAA-TATTTTTTTCCAATTTGTTTTTCAATTTTTGGGTTTACTAA
1 ATTTTTCTTTAATTTTTTAAAAAGAATTTTTTTCCAATTTGTTTTTCAATTTTTGGGTTTACTAA
72993 TTTTCCTTTGATT
66 TTTTCCTTTGATT
* *
73006 ATTTTTCTTTAATTTTCTAAAAAGAATTTTTTTCCAATTTTTTTTTTCAATTTTTGGGTTTACTA
1 ATTTTTCTTTAATTTTTTAAAAAGAATTTTTTTCCAA-TTTGTTTTTCAATTTTTGGGTTTACTA
*
73071 ATTTTTCTTTGATT
65 ATTTTCCTTTGATT
* * *
73085 ATTTTTCTTTATTTTTTTAGAAGGAATTTTTTT
1 ATTTTTCTTTAATTTTTTAAAAAGAATTTTTTT
73118 TTTAATTTTT
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
77 22 0.22
78 12 0.12
79 68 0.67
ACGTcount: A:0.22, C:0.08, G:0.07, T:0.63
Consensus pattern (78 bp):
ATTTTTCTTTAATTTTTTAAAAAGAATTTTTTTCCAATTTGTTTTTCAATTTTTGGGTTTACTAA
TTTTCCTTTGATT
Found at i:84822 original size:18 final size:18
Alignment explanation
Indices: 84801--84839 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
84791 AGGAAATCAA
84801 GTTGCTAAGTCAAATAAC
1 GTTGCTAAGTCAAATAAC
84819 GTTGCTAAGTCAAATAAC
1 GTTGCTAAGTCAAATAAC
84837 GTT
1 GTT
84840 TAACAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (18 bp):
GTTGCTAAGTCAAATAAC
Found at i:87880 original size:591 final size:588
Alignment explanation
Indices: 86472--87932 Score: 1729
Period size: 603 Copynumber: 2.4 Consensus size: 588
86462 GACTTTCTTT
* * * * ** * * * *
86472 TTTTTTCGAGGCAAAACCAATTTCGAACGAGATGCAGCTTTCACAGCAAGAGCTGAATTATTTCC
1 TTTTTGCGAGACAAAACCAAGTTGGAACTTGATGCAGCATTGACAGCAAGAGCTAAATTACTTCC
* *
86537 AGGGCAATCTCCTTTCTTAGTTGCT-CTCCGGGTTTTTTTTAAAGACTGTAGTTTAGAAGTCAAA
66 AGGGCCATCTCCTTTCTTAGTTG-TACTCTGGG-TTTTTTT--A-A---T--TTTAGAAGTCAAA
* * * ** * * * *
86601 TGGAACTTCTTACTACCTTTTACGTGAACTGC-CTGTTTTGGTGGAGCAGGAGACGACGAATTTA
121 TGAAACTTCTCACTATCTGCTACATGAACTGCTCTG--TTGGTGGAGCAGGAGAGGAAGAATTTG
*
86665 CATTTTCTGTTG-GCTGGAGACACTTGGAACTAGCAGGCTTTGTTAGAGCTTGACTCCTCTTAGA
184 CATTTTCTGTTGTG-TGGAGACACTTGGAACTGGCA-GCTTTGTTAGAGCTTGACTCCTCTTAGA
* * * * *
86729 ACCCAGATTACCCCGTCTAATCTGTTTTGCTATTTGAGTGCCAGAGTTTAGTTTGTTGAGTAGAG
247 ACCCAGATTACCCCATCCAATCTGTATCGCTATTTGAATGCCAGAGTTTAGTTTGTTGAGTAGAG
*** * * *
86794 TAGTGGAGGAAAAACGACCTTTCAGGCACACAGTTTCTTTACCTGGCACAATAGCTGAGATATAT
312 TACCAGAGGAAAAACGACCTTTCAGGCACACAATTTCTTTACCTCGCACAATAGCTCAGATATAT
* ** * **
86859 CGTAAGTTAACAGCGTGGGAGCAACAAAGGAGAATTTATAAAATCGAAAAAATACACAACACACA
377 CGTAAGTTAACAGCATAAGAGCAACAAAGGAGAATTTAAAAAAGAGAAAAAATACACAACACACA
*
86924 ACATAACATTGCAATGATACTCTCAGAAATAAGGCATCCGTTACCTGCTTCTCCCTGAGTGGATC
442 ACATAACATTGCAACGATACTCTCAGAAATAAGGCATCCGTTACCTGCTTCTCCCTGAGTGGATC
* *
86989 CCGAATTCACCTTCTGCTTAGACCTACTATCACTTGTATTCTTTTGTTTTATATCTTTTGAGGAA
507 CCGAATTCACCTTCTGCTTAGACCTACCATCACTTGTATGCTTTTGTTTTATATCTTTTGAGGAA
87054 ACCTCAAAGTCAGAGTTACAAACTCTAATC
572 ACCTC--A--C------ACAAACTC--A-C
** * *
87084 TTTTTTTGAGGCAAAACCAAGTTGGAACTTGATGAAGCATTGACAGCAAGAGCTAAATTACTTCC
1 TTTTTGCGAGACAAAACCAAGTTGGAACTTGATGCAGCATTGACAGCAAGAGCTAAATTACTTCC
* * * * * * *
87149 AAGGCCATCTCCTTCCTCAGTTGTACTTTGGGTGTCTTTAATTTTAGAAGTCAAAGGAAACTTCT
66 AGGGCCATCTCCTTTCTTAGTTGTACTCTGGGTTTTTTTAATTTTAGAAGTCAAATGAAACTTCT
* *
87214 CACTATCTGCTACATGAGCTGC-CCGTTCAGGTGGAGCAGGAGAGGAAGAATTTGCATTTTCTGT
131 CACTATCTGCTACATGAACTGCTCTGTT--GGTGGAGCAGGAGAGGAAGAATTTGCATTTTCTGT
* * * *
87278 TGTCTGGAGACACTTGGAACGGGCAGACTTTGTCAGAGCTCGACTCCTCTTAGAACCCAGATTAC
194 TGTGTGGAGACACTTGGAACTGGCAG-CTTTGTTAGAGCTTGACTCCTCTTAGAACCCAGATTAC
* * *
87343 CCCATCCAATTTGTATCGCTGTTTGAATGCCGGAGTTTAGTTTGTTGAGTAGAGTACCAGAGGAA
258 CCCATCCAATCTGTATCGCTATTTGAATGCCAGAGTTTAGTTTGTTGAGTAGAGTACCAGAGGAA
* * * * *
87408 AAACTACCTTTTAGGCTCACAATTTTTTTCCCTCGCACAATAGCTCAGATATATCGTAAGTTAAC
323 AAACGACCTTTCAGGCACACAATTTCTTTACCTCGCACAATAGCTCAGATATATCGTAAGTTAAC
87473 AGCATAAGAGCAACAAAGGAGAAATTATAAAAAAGAGAAAAAAAATACACAACATAACACAACAT
388 AGCATAAGAGCAACAAAGGAG-AATT-TAAAAAAGAG--AAAAAATACACAAC---ACACAACAT
* * * *
87538 AACATTGTAGCGATACTCTCA-AAGATGAGGCATCCG-TACCTGCTTCTCCCTGAGTGGATCCTG
446 AACATTGCAACGATACTCTCAGAA-ATAAGGCATCCGTTACCTGCTTCTCCCTGAGTGGATCCCG
* *
87601 AATTCACCTTCTGCTTTGACCTACCATCACTTGTATGCTTTTGTTTTATATGTTTTGAGGAAA-C
510 AATTCACCTTCTGCTTAGACCTACCATCACTTGTATGCTTTTGTTTTATATCTTTTGAGGAAACC
*
87665 -C-C-CAAAGTC-C
575 TCACACAAACTCAC
*
87675 TTTTTGCGAGACAAAGCCAAGTTGGAACTTGATGCAGCATTGACAGCAAGAGCTAAATTACTTCC
1 TTTTTGCGAGACAAAACCAAGTTGGAACTTGATGCAGCATTGACAGCAAGAGCTAAATTACTTCC
* *
87740 AGGGCCATCTCCTTTCTTAGTTGTACTCTGGGTTTTTTTAATTTTAGAAGTCAAATGCAACTCCT
66 AGGGCCATCTCCTTTCTTAGTTGTACTCTGGGTTTTTTTAATTTTAGAAGTCAAATGAAACTTCT
*
87805 CACTATCTGCTACATGAACTGACTCTGTTGGTGGAGCAAGAGAGGAAGAATTTGCATTTTCTGTT
131 CACTATCTGCTACATGAACTG-CTCTGTTGGTGGAGCAGGAGAGGAAGAATTTGCATTTTCTGTT
* * * * * *
87870 GTGGGGAGACACTTGGAATTGGCAGGTTTAGTTAGAGCTTGACTCCTGTTACAACGCAGATTA
195 GTGTGGAGACACTTGGAACTGGCAGCTTT-GTTAGAGCTTGACTCCTCTTAGAACCCAGATTA
87933 ATCCGTCCAA
Statistics
Matches: 736, Mismatches: 97, Indels: 53
0.83 0.11 0.06
Matches are distributed among these distances:
590 3 0.00
591 221 0.30
592 1 0.00
593 4 0.01
595 6 0.01
601 2 0.00
602 2 0.00
603 257 0.35
604 4 0.01
605 8 0.01
607 15 0.02
608 2 0.00
609 88 0.12
610 38 0.05
611 6 0.01
612 79 0.11
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (588 bp):
TTTTTGCGAGACAAAACCAAGTTGGAACTTGATGCAGCATTGACAGCAAGAGCTAAATTACTTCC
AGGGCCATCTCCTTTCTTAGTTGTACTCTGGGTTTTTTTAATTTTAGAAGTCAAATGAAACTTCT
CACTATCTGCTACATGAACTGCTCTGTTGGTGGAGCAGGAGAGGAAGAATTTGCATTTTCTGTTG
TGTGGAGACACTTGGAACTGGCAGCTTTGTTAGAGCTTGACTCCTCTTAGAACCCAGATTACCCC
ATCCAATCTGTATCGCTATTTGAATGCCAGAGTTTAGTTTGTTGAGTAGAGTACCAGAGGAAAAA
CGACCTTTCAGGCACACAATTTCTTTACCTCGCACAATAGCTCAGATATATCGTAAGTTAACAGC
ATAAGAGCAACAAAGGAGAATTTAAAAAAGAGAAAAAATACACAACACACAACATAACATTGCAA
CGATACTCTCAGAAATAAGGCATCCGTTACCTGCTTCTCCCTGAGTGGATCCCGAATTCACCTTC
TGCTTAGACCTACCATCACTTGTATGCTTTTGTTTTATATCTTTTGAGGAAACCTCACACAAACT
CAC
Found at i:89298 original size:2 final size:2
Alignment explanation
Indices: 89293--89318 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
89283 GAGAGACCCC
89293 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
89319 TGATGTGTTA
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:95419 original size:16 final size:15
Alignment explanation
Indices: 95398--95442 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
95388 ATTAATAAAA
95398 AATAATAAAATTA-T
1 AATAATAAAATTATT
95412 -ATAATAATAATTATT
1 AATAATAA-AATTATT
95427 AATTAATAAAATTATT
1 AA-TAATAAAATTATT
95443 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 7 0.26
14 5 0.19
15 1 0.04
16 8 0.30
17 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAATAAAATTATT
Found at i:95425 original size:14 final size:14
Alignment explanation
Indices: 95399--95435 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
95389 TTAATAAAAA
95399 ATAATAA-AATTAT
1 ATAATAATAATTAT
95412 ATAATAATAATTAT
1 ATAATAATAATTAT
95426 -TAATTAATAA
1 ATAA-TAATAA
95436 AATTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTAT
Found at i:107435 original size:79 final size:79
Alignment explanation
Indices: 107304--107464 Score: 313
Period size: 79 Copynumber: 2.0 Consensus size: 79
107294 AAGATTCAAA
107304 TCCAGTTATAAGTAATAAAACACCTTTGCTAATGATAATCAAGTATGCTACAAGGCTATATCAAT
1 TCCAGTTATAAGTAATAAAACACCTTTGCTAATGATAATCAAGTATGCTACAAGGCTATATCAAT
107369 CACATCAGAAATAT
66 CACATCAGAAATAT
*
107383 TCCAGTTATAAGTAATAAAATACCTTTGCTAATGATAATCAAGTATGCTACAAGGCTATATCAAT
1 TCCAGTTATAAGTAATAAAACACCTTTGCTAATGATAATCAAGTATGCTACAAGGCTATATCAAT
107448 CACATCAGAAATAT
66 CACATCAGAAATAT
107462 TCC
1 TCC
107465 TTGCCAACTA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (79 bp):
TCCAGTTATAAGTAATAAAACACCTTTGCTAATGATAATCAAGTATGCTACAAGGCTATATCAAT
CACATCAGAAATAT
Found at i:107492 original size:36 final size:36
Alignment explanation
Indices: 107446--107518 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
107436 GGCTATATCA
107446 ATCACATCAGAAATATTCCTTGCCAACTACAAATTT
1 ATCACATCAGAAATATTCCTTGCCAACTACAAATTT
107482 ATCACATCAGAAATATTCCTTGCCAACTACAAATTT
1 ATCACATCAGAAATATTCCTTGCCAACTACAAATTT
107518 A
1 A
107519 CTTAGGAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.30
Consensus pattern (36 bp):
ATCACATCAGAAATATTCCTTGCCAACTACAAATTT
Found at i:110334 original size:71 final size:71
Alignment explanation
Indices: 110249--110392 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 71
110239 AGGAAAAGAA
*
110249 AACCACCACATTTTACAGATGAAACCAATGAACAAATGTAGAAGATTTTCTGCCTTTAGTTTCTG
1 AACCACCACATTTTACAGATGAAACCAATGAACAAATGTAGAAGATTTTCTGCCTTTAGTTTCTA
110314 CTAACC
66 CTAACC
110320 AACCACCACATTTTACAGATGAAACCAATGAACAAATGTAGAAGATTTTCTGCCTTTAGTTTCTA
1 AACCACCACATTTTACAGATGAAACCAATGAACAAATGTAGAAGATTTTCTGCCTTTAGTTTCTA
110385 CTAACC
66 CTAACC
110391 AA
1 AA
110393 AAGCATTATC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (71 bp):
AACCACCACATTTTACAGATGAAACCAATGAACAAATGTAGAAGATTTTCTGCCTTTAGTTTCTA
CTAACC
Found at i:117877 original size:29 final size:29
Alignment explanation
Indices: 117833--117894 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
117823 GTCCGATATG
* *
117833 AAATGCATTATTTAACAGGCTTGACACCA
1 AAATGCAGTATCTAACAGGCTTGACACCA
117862 AAATGCAGTATCTAACAGGCTTGACACCA
1 AAATGCAGTATCTAACAGGCTTGACACCA
117891 AAAT
1 AAAT
117895 TCCATGGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (29 bp):
AAATGCAGTATCTAACAGGCTTGACACCA
Found at i:132143 original size:2 final size:2
Alignment explanation
Indices: 132136--132164 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
132126 ACATACGTAC
132136 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
132165 GTTCTCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:136123 original size:88 final size:88
Alignment explanation
Indices: 135974--136154 Score: 362
Period size: 88 Copynumber: 2.1 Consensus size: 88
135964 CCTAAGATGC
135974 ATGCTGCTGCCTGTTTAGGAGAGTTTGCCTACTTAATCTTAGTTGCGTTGGTGCTAGTGTCACAC
1 ATGCTGCTGCCTGTTTAGGAGAGTTTGCCTACTTAATCTTAGTTGCGTTGGTGCTAGTGTCACAC
136039 GAAGCGTTTCAAAAGTAGGTGGG
66 GAAGCGTTTCAAAAGTAGGTGGG
136062 ATGCTGCTGCCTGTTTAGGAGAGTTTGCCTACTTAATCTTAGTTGCGTTGGTGCTAGTGTCACAC
1 ATGCTGCTGCCTGTTTAGGAGAGTTTGCCTACTTAATCTTAGTTGCGTTGGTGCTAGTGTCACAC
136127 GAAGCGTTTCAAAAGTAGGTGGG
66 GAAGCGTTTCAAAAGTAGGTGGG
136150 ATGCT
1 ATGCT
136155 TCAATCTTGT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 93 1.00
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.33
Consensus pattern (88 bp):
ATGCTGCTGCCTGTTTAGGAGAGTTTGCCTACTTAATCTTAGTTGCGTTGGTGCTAGTGTCACAC
GAAGCGTTTCAAAAGTAGGTGGG
Found at i:141443 original size:29 final size:29
Alignment explanation
Indices: 141410--141477 Score: 73
Period size: 32 Copynumber: 2.2 Consensus size: 29
141400 TTAAATACGA
141410 CGTGTAACAATAAAATTTTTTTAACATGG
1 CGTGTAACAATAAAATTTTTTTAACATGG
* * **
141439 TGTGTAATAACAGTAATTTTTTTTTAACATGG
1 CGTG---TAACAATAAAATTTTTTTAACATGG
141471 CGTGTAA
1 CGTGTAA
141478 TAATTTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
29 6 0.19
32 25 0.81
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (29 bp):
CGTGTAACAATAAAATTTTTTTAACATGG
Found at i:141643 original size:66 final size:66
Alignment explanation
Indices: 141537--141684 Score: 201
Period size: 66 Copynumber: 2.3 Consensus size: 66
141527 AGTATTTTTT
* * *
141537 TTAA-CATGACGTGTAACAACCTAATTATAGCGTGTAACATATTTTTGTACAT-AGCGTGTAACA
1 TTAACCATGATGTGTAACAACCTAAATATAACGTGTAACATATTTTTGTACATGA-CGTGTAACA
*
141600 AT
65 AC
* ** *
141602 TTAACCATGGTGTGTAACAATTTAAATATAACGTGTCACATATTTTTGTACATGACGTGTAACAA
1 TTAACCATGATGTGTAACAACCTAAATATAACGTGTAACATATTTTTGTACATGACGTGTAACAA
141667 C
66 C
141668 TTAACCATGATGTGTAA
1 TTAACCATGATGTGTAA
141685 TATGTTTTGT
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
65 4 0.06
66 67 0.93
67 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (66 bp):
TTAACCATGATGTGTAACAACCTAAATATAACGTGTAACATATTTTTGTACATGACGTGTAACAA
C
Found at i:141735 original size:17 final size:15
Alignment explanation
Indices: 141700--141737 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
141690 TTTGTACATG
141700 GTGTGTAACATCATA
1 GTGTGTAACATCATA
141715 GTGTGTAACATCATA
1 GTGTGTAACATCATA
141730 GTGTGTAA
1 GTGTGTAA
141738 TTTTATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (15 bp):
GTGTGTAACATCATA
Found at i:148631 original size:3 final size:3
Alignment explanation
Indices: 148625--148668 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
148615 TAGTTATTTG
148625 ATA ATA 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 ATA ATA AT
148669 CCTTTGGGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:181710 original size:3 final size:3
Alignment explanation
Indices: 181702--181754 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
181692 TAAGGTATTG
181702 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
181750 ATA AT
1 ATA AT
181755 TGGCTTTAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:190034 original size:9 final size:10
Alignment explanation
Indices: 189996--190035 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
189986 TTATGGTAAA
189996 TTATTATTATT
1 TTATTATT-TT
190007 ATTATTATTTT
1 -TTATTATTTT
190018 TTATTATTTT
1 TTATTATTTT
190028 TTA-TATTT
1 TTATTATTT
190036 AGGGCCTGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 5 0.18
10 13 0.46
11 2 0.07
12 8 0.29
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TTATTATTTT
Found at i:203561 original size:10 final size:10
Alignment explanation
Indices: 203533--203563 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
203523 GGGAAAGGCT
*
203533 AGAGAGAGAG
1 AGAGAGAGTG
203543 AGAGAGAGTG
1 AGAGAGAGTG
203553 AGAGAGAGTG
1 AGAGAGAGTG
203563 A
1 A
203564 TGGTGTGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.48, T:0.06
Consensus pattern (10 bp):
AGAGAGAGTG
Found at i:211134 original size:2 final size:2
Alignment explanation
Indices: 211127--211157 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
211117 TATTCAAGTA
*
211127 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
211158 AAATATCAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:213468 original size:2 final size:2
Alignment explanation
Indices: 213463--213495 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
213453 GAAAAGGGGG
213463 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
213496 GAAATATATT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:213705 original size:2 final size:2
Alignment explanation
Indices: 213698--213730 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
213688 GAGTTGTTCC
213698 AT AT AT AT A- AT GAT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT A
213731 AGAACTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:222452 original size:26 final size:26
Alignment explanation
Indices: 222416--222466 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
222406 TGATTTTTTT
*
222416 TATCATTATTAAAAAACAATAAAAAC
1 TATCATAATTAAAAAACAATAAAAAC
* *
222442 TATCATAATTAACAAATAATAAAAA
1 TATCATAATTAAAAAACAATAAAAA
222467 TTTATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (26 bp):
TATCATAATTAAAAAACAATAAAAAC
Found at i:230245 original size:3 final size:3
Alignment explanation
Indices: 230239--230265 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
230229 CATCATCATC
230239 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
230266 TAAAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:239412 original size:82 final size:82
Alignment explanation
Indices: 239267--239417 Score: 209
Period size: 82 Copynumber: 1.8 Consensus size: 82
239257 GATAAGCATT
* * *
239267 AGTTCAATTTGACTTGACATGAAACAGTCAAGTTCATAGATTCACAGAGATTCTGATTTTTCATT
1 AGTTCAATTCGACTTGACATGAAACAGTCAAGTTAATAGATTCACAGAGATTCTAATTTTTCATT
239332 GTTACATATATATATAC
66 GTTACATATATATATAC
* *
239349 AGTTCAATTCGACTTGATATGAAACAGTC-AGTTTAATAGATTCAC-TAGA-TCATAATTTCTTC
1 AGTTCAATTCGACTTGACATGAAACAGTCAAG-TTAATAGATTCACAGAGATTC-TAATTT-TTC
239411 ATTGTTA
63 ATTGTTA
239418 TCAATTTTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
80 2 0.03
81 10 0.16
82 49 0.80
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (82 bp):
AGTTCAATTCGACTTGACATGAAACAGTCAAGTTAATAGATTCACAGAGATTCTAATTTTTCATT
GTTACATATATATATAC
Found at i:244533 original size:42 final size:42
Alignment explanation
Indices: 244445--244586 Score: 144
Period size: 42 Copynumber: 3.4 Consensus size: 42
244435 CCAGAAAGTG
* * * * **
244445 CAGCGCCAAAACCTGATCTCCCTACCAAAAAACGTGAAAGGG
1 CAGCACCAAAACCTGATCTCCCCACCATAAAACCTGAAAGCA
* *
244487 CAGCACCAAAACCTGATCTCCCCACCATAGAACCTGTAAGCA
1 CAGCACCAAAACCTGATCTCCCCACCATAAAACCTGAAAGCA
* *
244529 CAGCACCAAAACCCGATCAT-CCCACCATAAAACCTGGAA-CTA
1 CAGCACCAAAACCTGATC-TCCCCACCATAAAACCTGAAAGC-A
* *
244571 CAGCAACACAACCTGA
1 CAGCACCAAAACCTGA
244587 ACAGCCTCCT
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.01
42 82 0.98
43 1 0.01
ACGTcount: A:0.39, C:0.36, G:0.13, T:0.12
Consensus pattern (42 bp):
CAGCACCAAAACCTGATCTCCCCACCATAAAACCTGAAAGCA
Found at i:247652 original size:2 final size:2
Alignment explanation
Indices: 247645--247675 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
247635 ATTTCGGATT
*
247645 TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
247676 GTTCTTCCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:261038 original size:34 final size:34
Alignment explanation
Indices: 260993--261058 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
260983 CCACAAAGTT
* * *
260993 CAAAACTTGACACCATAAATTGTCATCTACTGAC
1 CAAAACGTGACACCATAAACTATCATCTACTGAC
261027 CAAAACGTGACACCATAAACTATCATCTACTG
1 CAAAACGTGACACCATAAACTATCATCTACTG
261059 CTTGTGCGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (34 bp):
CAAAACGTGACACCATAAACTATCATCTACTGAC
Found at i:270072 original size:61 final size:62
Alignment explanation
Indices: 269974--270143 Score: 274
Period size: 61 Copynumber: 2.8 Consensus size: 62
269964 TGTACTTAAA
269974 CACATTTAAAAGCTATGCACTTTATGAAGGGTGGTTTTTAATGAAATATC-CTTTGCCTGTC
1 CACATTTAAAAGCTATGCACTTTATGAAGGGTGGTTTTTAATGAAATATCGCTTTGCCTGTC
* * *
270035 CATATTTAAAAGTTATGGACTTTATGAAGGGTGGTTTTTAATGAAATA-CGCTTTGCCTGTC
1 CACATTTAAAAGCTATGCACTTTATGAAGGGTGGTTTTTAATGAAATATCGCTTTGCCTGTC
* *
270096 CACA-TTAAAAGCTATGCACCTTATAAAGGGTGGTTTTTAATGAAATAT
1 CACATTTAAAAGCTATGCACTTTATGAAGGGTGGTTTTTAATGAAATAT
270144 GAATTGCTTT
Statistics
Matches: 99, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
60 40 0.40
61 59 0.60
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.37
Consensus pattern (62 bp):
CACATTTAAAAGCTATGCACTTTATGAAGGGTGGTTTTTAATGAAATATCGCTTTGCCTGTC
Found at i:278063 original size:17 final size:17
Alignment explanation
Indices: 278043--278076 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
278033 ATCATAATAA
278043 ATAATAAAATAATATAT
1 ATAATAAAATAATATAT
*
278060 ATAATATAATAATATAT
1 ATAATAAAATAATATAT
278077 TCACGTAATA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATAAAATAATATAT
Found at i:278066 original size:5 final size:5
Alignment explanation
Indices: 278013--278070 Score: 50
Period size: 5 Copynumber: 11.6 Consensus size: 5
278003 TTTTTATTTT
* *
278013 ATATT ATATA ATATTA ATAT- ATCATA ATA-A ATAATA AAATA ATAT-
1 ATATA ATATA ATA-TA ATATA AT-ATA ATATA AT-ATA ATATA ATATA
278058 ATATA ATATA ATA
1 ATATA ATATA ATA
278071 ATATATTCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
4 9 0.20
5 26 0.59
6 9 0.20
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:278074 original size:8 final size:8
Alignment explanation
Indices: 278020--278075 Score: 62
Period size: 8 Copynumber: 7.0 Consensus size: 8
278010 TTTATATTAT
278020 ATAATATTA
1 ATAATA-TA
*
278029 AT-ATATC
1 ATAATATA
278036 ATAATA-A
1 ATAATATA
*
278043 ATAATAAA
1 ATAATATA
278051 ATAATATA
1 ATAATATA
278059 TATAATATA
1 -ATAATATA
278068 ATAATATA
1 ATAATATA
278076 TTCACGTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
7 9 0.22
8 22 0.54
9 10 0.24
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAATATA
Found at i:286351 original size:25 final size:25
Alignment explanation
Indices: 286318--286367 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
286308 ATCTGCACTA
286318 AAACACAAGAAGAGCTCTCACGGTT
1 AAACACAAGAAGAGCTCTCACGGTT
286343 AAACACAAGAAGAGCTCTCACGGTT
1 AAACACAAGAAGAGCTCTCACGGTT
286368 TTCACAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (25 bp):
AAACACAAGAAGAGCTCTCACGGTT
Found at i:294180 original size:2 final size:2
Alignment explanation
Indices: 294173--294212 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
294163 TTTCTTCACT
*
294173 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
294213 CTCGCACATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:299255 original size:26 final size:24
Alignment explanation
Indices: 299221--299271 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
299211 TCATATGATT
*
299221 ATGTTATCATGTTACATGAATATGTC
1 ATGTCATCAT-TTACATG-ATATGTC
*
299247 ATGTCATCATTTATATGATATGTC
1 ATGTCATCATTTACATGATATGTC
299271 A
1 A
299272 ATATATTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 8 0.35
25 6 0.26
26 9 0.39
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (24 bp):
ATGTCATCATTTACATGATATGTC
Found at i:301088 original size:113 final size:116
Alignment explanation
Indices: 300940--301157 Score: 289
Period size: 113 Copynumber: 1.9 Consensus size: 116
300930 GCTATGAAAA
* * * * * *
300940 AAAAAAAATTCAAAGTGTATATATTTGTCGGGTTTTTACAAAAATTTTTATTCGACATTTGTTAT
1 AAAAAAAATTCAAAGTGTATATATTTATCGAGTTTTTACAAAAATTTTTACTCGACAGTTATCAT
* * * *
301005 GATTTTTATGTTT-AAGAATATGATTCAAAATCTCATTTTTTATTTGTGTG
66 AATTTTTATATTTAAAAAATAAGATTCAAAATCTCATTTTTTATTTGTGTG
* ** *
301055 AAAAAAAA-TC-AAGTGTATATATTTATTGAGTTTTTATGAAAATTTTTACTCGTCAGTTATCAT
1 AAAAAAAATTCAAAGTGTATATATTTATCGAGTTTTTACAAAAATTTTTACTCGACAGTTATCAT
301118 AATTTTTATATTTAAAAAATAAGATTCAAAATCTCATTTT
66 AATTTTTATATTTAAAAAATAAGATTCAAAATCTCATTTT
301158 GATACTTCGA
Statistics
Matches: 88, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
113 54 0.61
114 26 0.30
115 8 0.09
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (116 bp):
AAAAAAAATTCAAAGTGTATATATTTATCGAGTTTTTACAAAAATTTTTACTCGACAGTTATCAT
AATTTTTATATTTAAAAAATAAGATTCAAAATCTCATTTTTTATTTGTGTG
Found at i:301219 original size:16 final size:16
Alignment explanation
Indices: 301194--301225 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
301184 GTATATACAT
*
301194 CAAGTTTTTGTTGAAG
1 CAAGTGTTTGTTGAAG
301210 CAAGTGTTTGTTGAAG
1 CAAGTGTTTGTTGAAG
301226 ACTTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.06, G:0.28, T:0.41
Consensus pattern (16 bp):
CAAGTGTTTGTTGAAG
Found at i:305694 original size:25 final size:25
Alignment explanation
Indices: 305649--305697 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
305639 TTTATTTTTG
*
305649 AATTAAGTACATTTTTATAATTAAT
1 AATTAAGTACATTATTATAATTAAT
*
305674 AATTAATTA-ATTATTATTAATTAA
1 AATTAAGTACATTATTA-TAATTAA
305698 AATATCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
AATTAAGTACATTATTATAATTAAT
Found at i:305995 original size:3 final size:3
Alignment explanation
Indices: 305981--306020 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
305971 TTATGTTAAT
*
305981 TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
306021 CCATTTACCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:306855 original size:15 final size:16
Alignment explanation
Indices: 306835--306868 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
306825 CATGATTAAC
*
306835 TTAATTAAA-ATATTT
1 TTAATTAAATATAATT
306850 TTAATTAAATATAATT
1 TTAATTAAATATAATT
306866 TTA
1 TTA
306869 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTAAATATAATT
Found at i:312090 original size:22 final size:23
Alignment explanation
Indices: 312065--312113 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
312055 TTTTTACTGT
*
312065 TTTATATTA-AAAATATT-AAATA
1 TTTATATTATAAAAAATTCAAA-A
312087 TTTATATTATAAAAAATTCAAAA
1 TTTATATTATAAAAAATTCAAAA
312110 TTTA
1 TTTA
312114 ACATAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 9 0.38
23 12 0.50
24 3 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTATATTATAAAAAATTCAAAA
Found at i:315384 original size:26 final size:26
Alignment explanation
Indices: 315355--315405 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
315345 CCTTTATTTA
315355 TACTGATATGAGATCAATGATTTTTG
1 TACTGATATGAGATCAATGATTTTTG
315381 TACTGATATGAGATCAATGATTTTT
1 TACTGATATGAGATCAATGATTTTT
315406 CCCCATCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (26 bp):
TACTGATATGAGATCAATGATTTTTG
Found at i:316016 original size:158 final size:153
Alignment explanation
Indices: 315658--316208 Score: 527
Period size: 157 Copynumber: 3.5 Consensus size: 153
315648 TAGTACTTTG
* *
315658 TAATTTTAGTAATATCTCGTCAAATCTGGTAAATTTTGTAATAATTTTGATAATGTCACGTCAAT
1 TAATTTTAGTAATATCTCGTCAAATCTGATAAATTTTGTAATAATTTTGATAATGTCACGTCAGT
* * * *
315723 TTTTATTCTTATTTTCACAATA-AATATTTGT-TCAATTGCTTACCAAAATCATATAATATATAC
66 TTTTATTCTTATTTTCACAATATAAAATTTTTATCAATTACTTACAAAAATCATATAATATAT--
* *
315786 CATTTATTATTGTAAGTAATAAATTA
129 CATTTATTATTATAAATAAT-AATTA
* * * * ** * *
315812 TAATTTTAGTAATATTTCGTTAAAT-TCGATATATGTTGTAGCAATTTTGGTAATGCCACGTCAG
1 TAATTTTAGTAATATCTCGTCAAATCT-GATAAATTTTGTAATAATTTTGATAATGTCACGTCAG
* * * *
315876 TTTTTATTTTTATTTTTACAATAACTAGAAATTTTTAATCAATCACTTACAAAAATCACATAATA
65 TTTTTATTCTTATTTTCACAAT-A-TA-AAATTTTT-ATCAATTACTTACAAAAATCATATAATA
315941 TATCATTTATTATTATAAATAATAATTCA
126 TATCATTTATTATTATAAATAATAATT-A
* * * * *
315970 TAATTTTATTTATAACTCGTCAAATCTGATACATTTTGTAATAATTTTGATAATATCACGTCAGT
1 TAATTTTAGTAATATCTCGTCAAATCTGATAAATTTTGTAATAATTTTGATAATGTCACGTCAGT
* * * * *
316035 GTTAATTCTAATATTCACAATAGTAAAAATCTTTTATCAATTACTTACTAAAAT--TATAATAAT
66 TTTTATTCTTATTTTCACAATA-T-AAAAT-TTTTATCAATTACTTACAAAAATCATATAAT-AT
* * *
316098 AACTAGTTATTATTATAATTAATAATTAA
127 ATC-ATTTATTATTATAAATAATAATT-A
* * * * * * * **
316127 TAATTTTGGTAATATCGCTTCAAATCTAATAAATTCTATAATACTTTTGATAATGTCACACCAAA
1 TAATTTTAGTAATATCTCGTCAAATCTGATAAATTTTGTAATAATTTTGATAATGTCACGTC--A
*
316192 TTTTTTATTCTTATTTT
64 GTTTTTATTCTTATTTT
316209 ATCATTAGTC
Statistics
Matches: 317, Mismatches: 65, Indels: 25
0.78 0.16 0.06
Matches are distributed among these distances:
153 1 0.00
154 72 0.23
155 6 0.02
156 4 0.01
157 98 0.31
158 96 0.30
159 14 0.04
160 26 0.08
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (153 bp):
TAATTTTAGTAATATCTCGTCAAATCTGATAAATTTTGTAATAATTTTGATAATGTCACGTCAGT
TTTTATTCTTATTTTCACAATATAAAATTTTTATCAATTACTTACAAAAATCATATAATATATCA
TTTATTATTATAAATAATAATTA
Found at i:316150 original size:157 final size:155
Alignment explanation
Indices: 315658--316208 Score: 497
Period size: 158 Copynumber: 3.5 Consensus size: 155
315648 TAGTACTTTG
* * *
315658 TAATTTTAGTAATATCTCGTCAAATCTGGTAAATTTTGTAATAATTTTGATAATGTCACGTCAAT
1 TAATTTTAGTAATATCGCGTCAAATCTGATAAATTTTGTAATAATTTTGATAATGTCACGTCAGT
* * * *
315723 TTTTATTCTTATTTTCAC-A-ATAAATATTTGT-TCAATTGCTTACCAAAATCATATAAT-ATAT
66 TTTTATTCTTATTTTCACAATATAAAAATTTTTATCAATTACTTACAAAAAT--TATAATAATAT
* * *
315784 ACCATTTATTATTGTAAGTAATAAATTA
129 ACTATTTATTATTATAAATAAT-AATTA
** * * * ** * *
315812 TAATTTTAGTAATATTTCGTTAAAT-TCGATATATGTTGTAGCAATTTTGGTAATGCCACGTCAG
1 TAATTTTAGTAATATCGCGTCAAATCT-GATAAATTTTGTAATAATTTTGATAATGTCACGTCAG
* * * * * *
315876 TTTTTATTTTTATTTTTACAATAACTAGAAATTTTTAATCAATCACTTACAAAAATCA-CATAAT
65 TTTTTATTCTTATTTTCACAAT-A-TAAAAATTTTT-ATCAATTACTTACAAAAATTATAATAAT
315940 ATA-TCATTTATTATTATAAATAATAATTCA
127 ATACT-ATTTATTATTATAAATAATAATT-A
* * * * * *
315970 TAATTTTATTTATAACTCGTCAAATCTGATACATTTTGTAATAATTTTGATAATATCACGTCAGT
1 TAATTTTAGTAATATCGCGTCAAATCTGATAAATTTTGTAATAATTTTGATAATGTCACGTCAGT
* * * * *
316035 GTTAATTCTAATATTCACAATAGTAAAAATCTTTTATCAATTACTTACTAAAATTATAATAATA-
66 TTTTATTCTTATTTTCACAATA-TAAAAAT-TTTTATCAATTACTTACAAAAATTATAATAATAT
* *
316099 ACTAGTTATTATTATAATTAATAATTAA
129 ACTATTTATTATTATAAATAATAATT-A
* * * * * * **
316127 TAATTTTGGTAATATCGCTTCAAATCTAATAAATTCTATAATACTTTTGATAATGTCACACCAAA
1 TAATTTTAGTAATATCGCGTCAAATCTGATAAATTTTGTAATAATTTTGATAATGTCACGTC--A
*
316192 TTTTTTATTCTTATTTT
64 GTTTTTATTCTTATTTT
316209 ATCATTAGTC
Statistics
Matches: 312, Mismatches: 69, Indels: 27
0.76 0.17 0.07
Matches are distributed among these distances:
153 1 0.00
154 69 0.22
155 1 0.00
157 103 0.33
158 109 0.35
159 14 0.04
160 15 0.05
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (155 bp):
TAATTTTAGTAATATCGCGTCAAATCTGATAAATTTTGTAATAATTTTGATAATGTCACGTCAGT
TTTTATTCTTATTTTCACAATATAAAAATTTTTATCAATTACTTACAAAAATTATAATAATATAC
TATTTATTATTATAAATAATAATTA
Found at i:316647 original size:63 final size:64
Alignment explanation
Indices: 316513--316678 Score: 192
Period size: 63 Copynumber: 2.6 Consensus size: 64
316503 ATAATGGTCA
* * * *
316513 CACATTAATGAAGATTTAGATAAGTTTTGATATCACTTATCATTAGTATCTCTCATGAGGACTC
1 CACATTAGTGAAGATTTAGATAAGTTCTGATACCACTTATCAGTAGTATCTCTCATGAGGACTC
* * * *
316577 CAGATTAGTGAA-AATTAGATAAGTTCTGATACCACTTATCAGTAGTATCTCTCATGA-GAGTTT
1 CACATTAGTGAAGATTTAGATAAGTTCTGATACCACTTATCAGTAGTATCTCTCATGAGGA-CTC
* * * * *
316640 TACATTAGTGAAGTTTTGGATAAGTTCTAAAACCACTTA
1 CACATTAGTGAAGATTTAGATAAGTTCTGATACCACTTA
316679 CCAAAGATTA
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
62 2 0.02
63 52 0.61
64 31 0.36
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (64 bp):
CACATTAGTGAAGATTTAGATAAGTTCTGATACCACTTATCAGTAGTATCTCTCATGAGGACTC
Found at i:319291 original size:151 final size:152
Alignment explanation
Indices: 318998--319319 Score: 373
Period size: 151 Copynumber: 2.1 Consensus size: 152
318988 AAAGACTTAT
* * * *
318998 GTAAGCTCTGATACCACTTATTATAAGTTCACATTTTGTGAATGAAAGTGTCACGAATCCATGTT
1 GTAAGCTTTGATACCATTTATTATAAGCTCACATTTTATGAATGAAAGTGTCACGAATCCATGTT
* * * * * *
319063 TTTAATTCAAAAGAAATGCCCGATAGGAGATGGAGTACCTATGTTTATACATCTAAGACCAATCA
66 TTTAACTCAAAAGAAATGCCCGATAGAAGATAGAATACCTATGTTTATACACCAAAGACCAATCA
*
319128 TATCTCATTAGTGAAGATTCAA
131 TATCTCATTAGTGAAAATTCAA
* *
319150 GTAGGCTTTGATACCATTTATTATAAGCTCACATTTTATGAAT-AAAGGTGTCAC-AATTCACT-
1 GTAAGCTTTGATACCATTTATTATAAGCTCACATTTTATGAATGAAA-GTGTCACGAATCCA-TG
* ** * * * *
319212 TTTTTAACTCCAAAGAAATGCTTGATA-AATGATAGAATACTTATGTTTATATACCAAATACCCA
64 TTTTTAACTCAAAAGAAATGCCCGATAGAA-GATAGAATACCTATGTTTATACACCAAAGACCAA
* * *
319276 TTATATCTCATTAGTGAAAATTTAG
128 TCATATCTCATTAGTGAAAATTCAA
*
319301 GTAAGCTTTGATGCCATTT
1 GTAAGCTTTGATACCATTT
319320 GTCATATATA
Statistics
Matches: 142, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
150 1 0.01
151 95 0.67
152 46 0.32
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (152 bp):
GTAAGCTTTGATACCATTTATTATAAGCTCACATTTTATGAATGAAAGTGTCACGAATCCATGTT
TTTAACTCAAAAGAAATGCCCGATAGAAGATAGAATACCTATGTTTATACACCAAAGACCAATCA
TATCTCATTAGTGAAAATTCAA
Found at i:319801 original size:20 final size:20
Alignment explanation
Indices: 319771--319826 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
319761 GGAATAATTT
319771 ATAATTTTGGTAATATTAAGTA
1 ATAATTTTGGTAATATT--GTA
319793 A-AA-TTTGGTAAATATTGTA
1 ATAATTTTGGT-AATATTGTA
319812 ATAATTTTGGTAATA
1 ATAATTTTGGTAATA
319827 CCATGTCAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 4 0.13
20 12 0.39
21 14 0.45
22 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (20 bp):
ATAATTTTGGTAATATTGTA
Found at i:319857 original size:90 final size:90
Alignment explanation
Indices: 319763--320094 Score: 326
Period size: 90 Copynumber: 3.7 Consensus size: 90
319753 TCTTTTGAGG
*
319763 AATAATTTATAATTTTGGTAATATTAAGTAAAATTTGGTAAATATTGTAATAATTTTGGTAATAC
1 AATAATTTATAATTTTGGTAATATTAAGTAAAATCTGGTAAATATTGTAATAATTTTGGTAATAC
*
319828 CATGTCAGTTTTTATTATTATAAGT
66 CAAGTCAGTTTTTATTATTATAAGT
* * * * * ** *
319853 AATAATTTGTAATTATGGTAATATCTCAA--AAAATTTGCTAAATGTCCTAATAATTTTGCTAAT
1 AATAATTTATAATTTTGGTAATAT-T-AAGTAAAATCTGGTAAATATTGTAATAATTTTGGTAAT
* * * *
319916 GCCAAGTCAATTTTTATTATTGTAAAT
64 ACCAAGTCAGTTTTTATTATTATAAGT
* * ** * * ** * *
319943 ATTAATTTATAATTTTGGTGATATTTTGTAAAATCTGATAAATGTTGTAATAATTTTAATACTAT
1 AATAATTTATAATTTTGGTAATATTAAGTAAAATCTGGTAAATATTGTAATAATTTTGGTAATAC
* **
320008 CACGTCAGTTTTTAACATTATAAGT
66 CAAGTCAGTTTTTATTATTATAAGT
* * ** * * *
320033 AATAATTTATAATTTTGATCATATTCCGTAAAATCTGGTTAATATTGTGATTATTTTGGTAA
1 AATAATTTATAATTTTGGTAATATTAAGTAAAATCTGGTAAATATTGTAATAATTTTGGTAA
320095 CCATCATCAA
Statistics
Matches: 192, Mismatches: 46, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
89 1 0.01
90 188 0.98
91 1 0.01
92 2 0.01
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (90 bp):
AATAATTTATAATTTTGGTAATATTAAGTAAAATCTGGTAAATATTGTAATAATTTTGGTAATAC
CAAGTCAGTTTTTATTATTATAAGT
Found at i:321640 original size:5 final size:5
Alignment explanation
Indices: 321630--321659 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
321620 CAAATGTCCA
321630 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
321660 CCCTCCTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TCCTT
Found at i:329881 original size:80 final size:80
Alignment explanation
Indices: 329716--329883 Score: 250
Period size: 80 Copynumber: 2.1 Consensus size: 80
329706 ACAAATCAAA
* * * *
329716 CAAGCCTT-TTTTCTTTTAAAAGAAAAAAAAATCTCATCTTGAATGTCCATTGAACTAAAAACAC
1 CAAG-CTTCTTTTCTATGAAAAGAAAAAAAAATCTCATCTTGAATATCCACTGAACTAAAAACAC
*
329780 AATACCCAGAAACATC
65 AATACCCAGAAACACC
*
329796 CAAGCTTCTTTTCTATGAAAAGAAGAGAAAAATCTCATCTTGAATAT-CACTGAACTAAAAACAC
1 CAAGCTTCTTTTCTATGAAAAGAA-AAAAAAATCTCATCTTGAATATCCACTGAACTAAAAACAC
329860 AATACCCAGAAACACC
65 AATACCCAGAAACACC
329876 CAAGCTTC
1 CAAGCTTC
329884 AAAACTGAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
79 3 0.04
80 57 0.71
81 20 0.25
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (80 bp):
CAAGCTTCTTTTCTATGAAAAGAAAAAAAAATCTCATCTTGAATATCCACTGAACTAAAAACACA
ATACCCAGAAACACC
Found at i:331277 original size:28 final size:29
Alignment explanation
Indices: 331204--331282 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 29
331194 ATCATATTTT
331204 AATA-TTAATATATAACTTATATCATTTCA
1 AATATTTAATATATAA-TTATATCATTTCA
* * *
331233 AATATATAATCTGTAATTATAT-ATTTCA
1 AATATTTAATATATAATTATATCATTTCA
* *
331261 TGAT-TTTAATATATAATCATAT
1 -AATATTTAATATATAATTATAT
331283 TATATTATTA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
28 20 0.50
29 12 0.30
30 8 0.20
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47
Consensus pattern (29 bp):
AATATTTAATATATAATTATATCATTTCA
Found at i:333716 original size:34 final size:34
Alignment explanation
Indices: 333673--333747 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
333663 CTCTTCCCGG
* *
333673 CTTCTCCCTAATATTAGGTTCAGTCTCCTCTCGC
1 CTTCTCCCTAACATTAGCTTCAGTCTCCTCTCGC
*
333707 CTTCTCCCTACCATTAGCTTCAGTCTCCTCTCGC
1 CTTCTCCCTAACATTAGCTTCAGTCTCCTCTCGC
333741 CTTCTCC
1 CTTCTCC
333748 AGCTCTTNNN
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.12, C:0.41, G:0.09, T:0.37
Consensus pattern (34 bp):
CTTCTCCCTAACATTAGCTTCAGTCTCCTCTCGC
Found at i:334823 original size:20 final size:21
Alignment explanation
Indices: 334798--334839 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
334788 TTTGTATACA
*
334798 AATTAAAAGATGTAT-ATTAT
1 AATTAAAAGATATATAATTAT
*
334818 AATTAATAGATATATAATTAT
1 AATTAAAAGATATATAATTAT
334839 A
1 A
334840 CAATTATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
AATTAAAAGATATATAATTAT
Found at i:334971 original size:23 final size:24
Alignment explanation
Indices: 334943--334989 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
334933 TAATATCAAC
334943 ATATAAT-TTATATCATTTA-AAAT
1 ATATAATATTATAT-ATTTAGAAAT
334966 ATATAATATTATATATTTAGAAAT
1 ATATAATATTATATATTTAGAAAT
334990 GAAAATACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
ATATAATATTATATATTTAGAAAT
Found at i:338786 original size:18 final size:18
Alignment explanation
Indices: 338741--338794 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
338731 CTTTATGAAA
* *
338741 AATAAATATATTTATATT
1 AATATATATATATATATT
338759 AATATATATATATATATT
1 AATATATATATATATATT
* *
338777 -ATAT-TTTATATAAATT
1 AATATATATATATATATT
338793 AA
1 AA
338795 AATTTTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 10 0.32
17 5 0.16
18 16 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATATATATATATATATT
Found at i:338973 original size:44 final size:43
Alignment explanation
Indices: 338907--338994 Score: 99
Period size: 44 Copynumber: 2.0 Consensus size: 43
338897 TATTTATCTA
* * *
338907 AAATTATAAAATTTATTAAAAAT-TACTTTTTATTAGTATAAATT
1 AAATTATAAAATTAAATAAAAATATA-ATTTTA-TAGTATAAATT
*
338951 AAATTATTAAAATTAAAT-AAAATATAATTTTATATTATAAATT
1 AAATTA-TAAAATTAAATAAAAATATAATTTTATAGTATAAATT
338994 A
1 A
338995 TTAGGTTCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
43 11 0.29
44 16 0.42
45 11 0.29
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (43 bp):
AAATTATAAAATTAAATAAAAATATAATTTTATAGTATAAATT
Found at i:341207 original size:23 final size:25
Alignment explanation
Indices: 341166--341211 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
341156 CTAATAACTA
*
341166 TATATCAATATTAACATATATAATT
1 TATATCAATATTAAAATATATAATT
341191 TATATC-AT-TTAAAATATATAA
1 TATATCAATATTAAAATATATAA
341212 CTTGTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 2 0.10
25 6 0.30
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (25 bp):
TATATCAATATTAAAATATATAATT
Found at i:341608 original size:40 final size:40
Alignment explanation
Indices: 341553--341721 Score: 234
Period size: 40 Copynumber: 4.2 Consensus size: 40
341543 AGTTGGTAAA
* *
341553 TCCTTTGCTTGCTTTTCCTCGCTTCTCTTAATGAATGTTC
1 TCCTTTGCTTGCTTTTCCCCGCTTCTCTTAACGAATGTTC
* *
341593 TCCTTTGCTTGCTTTTCCCCGATAT-TCTTAATGAATGTTC
1 TCCTTTGCTTGCTTTTCCCCGCT-TCTCTTAACGAATGTTC
* * *
341633 TCGTTTGCTTGCCTTTCCCCCGCTTTTCTTAACGAATGTTC
1 TCCTTTGCTTG-CTTTTCCCCGCTTCTCTTAACGAATGTTC
341674 TCCTTTGCTTGC-TTTCCCCGGCTTCTCTTAACGAATGTTC
1 TCCTTTGCTTGCTTTTCCCC-GCTTCTCTTAACGAATGTTC
341714 TCCTTTGC
1 TCCTTTGC
341722 AAAAAAAAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
39 6 0.05
40 75 0.65
41 35 0.30
ACGTcount: A:0.11, C:0.30, G:0.14, T:0.46
Consensus pattern (40 bp):
TCCTTTGCTTGCTTTTCCCCGCTTCTCTTAACGAATGTTC
Found at i:341670 original size:81 final size:80
Alignment explanation
Indices: 341553--341721 Score: 234
Period size: 81 Copynumber: 2.1 Consensus size: 80
341543 AGTTGGTAAA
* * *
341553 TCCTTTGCTTGCTTTTCCTCGCTTCTCTTAATGAATGTTCTCCTTTGCTTGCTTTTCCCC-GATA
1 TCCTTTGCTTGCTTTCCCCCGCTTCTCTTAACGAATGTTCTCCTTTGCTTGC-TTTCCCCGGAT-
*
341617 T-TCTTAATGAATGTTC
64 TCTCTTAACGAATGTTC
* * *
341633 TCGTTTGCTTGCCTTTCCCCCGCTTTTCTTAACGAATGTTCTCCTTTGCTTGCTTTCCCCGGCTT
1 TCCTTTGCTTG-CTTTCCCCCGCTTCTCTTAACGAATGTTCTCCTTTGCTTGCTTTCCCCGGATT
341698 CTCTTAACGAATGTTC
65 CTCTTAACGAATGTTC
341714 TCCTTTGC
1 TCCTTTGC
341722 AAAAAAAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
80 18 0.23
81 60 0.77
ACGTcount: A:0.11, C:0.30, G:0.14, T:0.46
Consensus pattern (80 bp):
TCCTTTGCTTGCTTTCCCCCGCTTCTCTTAACGAATGTTCTCCTTTGCTTGCTTTCCCCGGATTC
TCTTAACGAATGTTC
Found at i:346304 original size:28 final size:29
Alignment explanation
Indices: 346272--346362 Score: 98
Period size: 29 Copynumber: 3.1 Consensus size: 29
346262 CAGTTCAAAA
346272 AATTTAAA-ATAATTTTTAT-TTTT-TATT
1 AATTTAAATA-AATTTTTATATTTTATATT
*
346299 ACATTTAATTAAATTTTTATATTTTATATT
1 A-ATTTAAATAAATTTTTATATTTTATATT
* * *
346329 AAATTAAATAAATTTTTATAATTAATAATT
1 AATTTAAATAAATTTTTATATTTTAT-ATT
346359 AATT
1 AATT
346363 AATTATCGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.02
28 15 0.28
29 26 0.49
30 11 0.21
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (29 bp):
AATTTAAATAAATTTTTATATTTTATATT
Found at i:362332 original size:7 final size:7
Alignment explanation
Indices: 362296--362338 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
362286 TAAACAAAAG
362296 AAGGAAA
1 AAGGAAA
*
362303 AATGAAA
1 AAGGAAA
*
362310 AAAGAAA
1 AAGGAAA
*
362317 AAAGAAA
1 AAGGAAA
362324 AATGGAAA
1 AA-GGAAA
362332 AAGGAAA
1 AAGGAAA
362339 GGGAAAGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
7 26 0.81
8 6 0.19
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (7 bp):
AAGGAAA
Found at i:362332 original size:14 final size:14
Alignment explanation
Indices: 362291--362334 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
362281 AAATGTAAAC
362291 AAAAGAAGGAAAAATG
1 AAAA-AAGGAAAAA-G
*
362307 AAAAAAGAAAAAAG
1 AAAAAAGGAAAAAG
*
362321 AAAAATGGAAAAAG
1 AAAAAAGGAAAAAG
362335 GAAAGGGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.52
15 8 0.32
16 4 0.16
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (14 bp):
AAAAAAGGAAAAAG
Found at i:362344 original size:21 final size:21
Alignment explanation
Indices: 362296--362344 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
362286 TAAACAAAAG
362296 AAGGAAAAATGAAAAAAGAAA
1 AAGGAAAAATGAAAAAAGAAA
* * *
362317 AAAGAAAAATGGAAAAAGGAA
1 AAGGAAAAATGAAAAAAGAAA
*
362338 AGGGAAA
1 AAGGAAA
362345 GAGAGAAAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.04
Consensus pattern (21 bp):
AAGGAAAAATGAAAAAAGAAA
Found at i:369257 original size:2 final size:2
Alignment explanation
Indices: 369250--369297 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
369240 GCACAAACAT
369250 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
369292 GA GA GA
1 GA GA GA
369298 ACCTGTATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:372894 original size:119 final size:119
Alignment explanation
Indices: 372723--372947 Score: 346
Period size: 119 Copynumber: 1.9 Consensus size: 119
372713 GAAAAGAATA
*
372723 CTAACTTCAGTTCTAATTAAATATATGCTAAATTTAAATCAGAAGAAAAATGAACAATAAAATGA
1 CTAACTTCAGTTCTAATTAAAGATATGCTAAATTTAAATCAGAAGAAAAATGAACAATAAAATGA
* *
372788 TCATATCAAAAATCATTAAATTTAAGGAATATATACATATATAAATATATAATG
66 TCATATCAAAAATCATCAAATATAAGGAATATATACATATATAAATATATAATG
* *
372842 CTAACTTCGGTTTCTAATTAAAGATATGCTAAA-TTAAATCAGAA-AAAGAATGAATAATAAAAT
1 CTAACTTCAG-TTCTAATTAAAGATATGCTAAATTTAAATCAGAAGAAA-AATGAACAATAAAAT
* * *
372905 GATCATCTCAAATATCATCAAATATAAGGAATATATATATATA
64 GATCATATCAAAAATCATCAAATATAAGGAATATATACATATA
372948 ATTAGCAAAG
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
118 3 0.03
119 72 0.75
120 21 0.22
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32
Consensus pattern (119 bp):
CTAACTTCAGTTCTAATTAAAGATATGCTAAATTTAAATCAGAAGAAAAATGAACAATAAAATGA
TCATATCAAAAATCATCAAATATAAGGAATATATACATATATAAATATATAATG
Found at i:374975 original size:29 final size:28
Alignment explanation
Indices: 374943--374999 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
374933 TATTTCAAAA
*
374943 AAATTTAAATAAATTATTATTATTTTTAT
1 AAATTCAAATAAATTATTA-TATTTTTAT
* *
374972 AAATTCAATTAAATTTTTATATTTTTAT
1 AAATTCAAATAAATTATTATATTTTTAT
375000 TTTGAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
AAATTCAAATAAATTATTATATTTTTAT
Found at i:377112 original size:300 final size:301
Alignment explanation
Indices: 376565--377167 Score: 1100
Period size: 300 Copynumber: 2.0 Consensus size: 301
376555 AAACTTAGCT
* *
376565 ACAAGAGCACTGAGCAAAACCTTTTCAATCTTCTTCTCTGCCTGTCCAAATCCATACCAAATTTA
1 ACAACAGCACTGAGCAAAACCTTTTCAATCTTCTTCTCTGCCTATCCAAATCCATACCAAATTTA
*
376630 ATGGAAAACCTAGTAGTAAAAAACAGGGCTAGAGATGCCTAATCAGAAAGCTCCTGAGGGCTACA
66 ATGGAAAACCTAATAGTAAAAAACAGGGCTAGAGATGCCTAATCAGAAAGCTCCTGAGGGCTACA
* *
376695 TCATTTTTACTCCAATTATTGCACAATTTTGAGCTTCCAGGAGTTTCAGGAGACTGATATTATTG
131 TCATTTTTACTCCAATTATTGCACAATTTTGAGCTTCCAGGAGTTTCAGGACACTGATATTATTA
376760 TTCCAGGCCCCTGGAATATTGTACATTTAACATGCGAACCTGACAATAGTTCAAGATCCAAGACT
196 TTCCAGGCCCCTGGAATATTGTACATTTAACATGCGAACCTGACAATAGTTCAAGATCCAAGACT
376825 GGGGAAAGCTTTGTTTTCATGGGGGTGGAAAAA-GGTTTTG
261 GGGGAAAGCTTTGTTTTCATGGGGGTGGAAAAAGGGTTTTG
*
376865 ACAACAGCACTGAGCAAAACCTTTTCAGTCTTCTTCTCTGCCTATCCAAATCCATACCAAATTTA
1 ACAACAGCACTGAGCAAAACCTTTTCAATCTTCTTCTCTGCCTATCCAAATCCATACCAAATTTA
* *
376930 ATGGAAAACCTAATAGTAAAAGACAGGGCTAGAGATGCCTAATCAGAAAGCTCCTGAGGGCTATA
66 ATGGAAAACCTAATAGTAAAAAACAGGGCTAGAGATGCCTAATCAGAAAGCTCCTGAGGGCTACA
*
376995 TCATTTTTTCTCCAATTATTGCACAATTTTGAGCTTCCAGGAGTTTCAGGACACTGATATTATTA
131 TCATTTTTACTCCAATTATTGCACAATTTTGAGCTTCCAGGAGTTTCAGGACACTGATATTATTA
* *
377060 TTCCAGGCCCCTGGAATATTGTACATTTAACATGCTAACCTGGCAATAGTTCAAGATCCAAGACT
196 TTCCAGGCCCCTGGAATATTGTACATTTAACATGCGAACCTGACAATAGTTCAAGATCCAAGACT
377125 GGGGAAAGCTTTGTTTTCATGGGGGTGGAAAAAGGGTTTTG
261 GGGGAAAGCTTTGTTTTCATGGGGGTGGAAAAAGGGTTTTG
377166 AC
1 AC
377168 CATAAAGATG
Statistics
Matches: 291, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
300 282 0.97
301 9 0.03
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (301 bp):
ACAACAGCACTGAGCAAAACCTTTTCAATCTTCTTCTCTGCCTATCCAAATCCATACCAAATTTA
ATGGAAAACCTAATAGTAAAAAACAGGGCTAGAGATGCCTAATCAGAAAGCTCCTGAGGGCTACA
TCATTTTTACTCCAATTATTGCACAATTTTGAGCTTCCAGGAGTTTCAGGACACTGATATTATTA
TTCCAGGCCCCTGGAATATTGTACATTTAACATGCGAACCTGACAATAGTTCAAGATCCAAGACT
GGGGAAAGCTTTGTTTTCATGGGGGTGGAAAAAGGGTTTTG
Found at i:377825 original size:76 final size:76
Alignment explanation
Indices: 377735--377879 Score: 218
Period size: 76 Copynumber: 1.9 Consensus size: 76
377725 CTAATACAGC
* *
377735 CACAAAAATTAACTAATTCAATACTTCATGTGATATGAAAATTTGAACATTAGAATCACTTTAGC
1 CACAAAAATTAACTAATTCAATACCTCATGTGACATGAAAATTTGAACATTAGAATCACTTTAGC
377800 CCATAACATAT
66 CCATAACATAT
* * * * * *
377811 CACAAAAATTAACTAATTGAGTACCTCATGTGACATGAAAATTTGGACATTGGAGTTACTTTAGC
1 CACAAAAATTAACTAATTCAATACCTCATGTGACATGAAAATTTGAACATTAGAATCACTTTAGC
377876 CCAT
66 CCAT
377880 TACCCAAAGC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 61 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (76 bp):
CACAAAAATTAACTAATTCAATACCTCATGTGACATGAAAATTTGAACATTAGAATCACTTTAGC
CCATAACATAT
Found at i:382568 original size:12 final size:12
Alignment explanation
Indices: 382551--382575 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
382541 TATTCTTAAA
382551 TTATTTTATTTT
1 TTATTTTATTTT
382563 TTATTTTATTTT
1 TTATTTTATTTT
382575 T
1 T
382576 CCCATATGTC
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:383117 original size:13 final size:13
Alignment explanation
Indices: 383086--383123 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
383076 ATTATATTTT
383086 TTAAAATTAATTAA
1 TTAAAATT-ATTAA
*
383100 ATAAAATTATTAA
1 TTAAAATTATTAA
383113 TTAAAA-TATTA
1 TTAAAATTATTA
383124 TATATCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 5 0.23
13 10 0.45
14 7 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TTAAAATTATTAA
Found at i:383139 original size:17 final size:17
Alignment explanation
Indices: 383117--383149 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
383107 TATTAATTAA
*
383117 AATATTATATATCATTT
1 AATATTATATAGCATTT
383134 AATATTATATAGCATT
1 AATATTATATAGCATT
383150 GACATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (17 bp):
AATATTATATAGCATTT
Found at i:383805 original size:16 final size:16
Alignment explanation
Indices: 383769--383805 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
383759 TATAAAATTA
383769 TAAATAATATTTAAAT
1 TAAATAATATTTAAAT
383785 T-AATAATTATTT-AAT
1 TAAATAA-TATTTAAAT
383800 TAAATA
1 TAAATA
383806 TAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATAATATTTAAAT
Found at i:402082 original size:2 final size:2
Alignment explanation
Indices: 402075--402102 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
402065 AGAAAGTGAA
402075 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
402103 GTCTTTGCAT
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:414898 original size:2 final size:2
Alignment explanation
Indices: 414893--414931 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
414883 TATTCTTCAA
414893 TC TC 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 TC TC T
414932 GTGTTTCTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:424577 original size:29 final size:30
Alignment explanation
Indices: 424515--424579 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
424505 TAACAAAAAT
* * * *
424515 TTATTATTTTATTTATACTCAATTGAGTTT
1 TTATTTTTTTATTTATACTCAATTAAATTC
*
424545 TTATTTTTTTATTT-TATTCAATTAAATTC
1 TTATTTTTTTATTTATACTCAATTAAATTC
424574 TTATTT
1 TTATTT
424580 CATGACTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (30 bp):
TTATTTTTTTATTTATACTCAATTAAATTC
Found at i:429615 original size:27 final size:26
Alignment explanation
Indices: 429579--429661 Score: 89
Period size: 29 Copynumber: 3.0 Consensus size: 26
429569 TAAAAATTAA
429579 ATTAAA-TTTTATTTTTATTATAATT
1 ATTAAATTTTTATTTTTATTATAATT
429604 ACTTAAATTTTTATATTTTTATTA-AATT
1 A-TTAAA-TTTT-TATTTTTATTATAATT
*
429632 ATTAAATTTTTAATTAATTATTATTAATT
1 ATTAAATTTTT-ATT-TTTATTA-TAATT
429661 A
1 A
429662 AAATATTATA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
25 2 0.04
26 12 0.24
27 11 0.22
28 8 0.16
29 16 0.33
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTAAATTTTTATTTTTATTATAATT
Found at i:429630 original size:19 final size:20
Alignment explanation
Indices: 429606--429654 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
429596 TTATAATTAC
* *
429606 TTAAATTTTTATATTTTT-A
1 TTAAATTATTAAATTTTTAA
429625 TTAAATTATTAAATTTTTAA
1 TTAAATTATTAAATTTTTAA
429645 TT-AATTATTA
1 TTAAATTATTA
429655 TTAATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 24 0.89
20 3 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAAATTATTAAATTTTTAA
Found at i:429751 original size:18 final size:19
Alignment explanation
Indices: 429728--429771 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
429718 TATTATTTGT
*
429728 TATAATATGTTAAT-ATAA
1 TATAATATGTAAATAATAA
*
429746 TATAAT-GGTAAATAATAA
1 TATAATATGTAAATAATAA
429764 TATAATAT
1 TATAATAT
429772 AAAATTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (19 bp):
TATAATATGTAAATAATAA
Found at i:429804 original size:30 final size:29
Alignment explanation
Indices: 429761--429822 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
429751 TGGTAAATAA
* *
429761 TAATATAATATAAAATTATTAA-AATTTATT
1 TAATATAAAATAAAA-TA-TAATAATTTAAT
*
429791 TAATTTAAAATAAAATATAATAATTTAAT
1 TAATATAAAATAAAATATAATAATTTAAT
429820 TAA
1 TAA
429823 AAATAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.11
29 12 0.43
30 13 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TAATATAAAATAAAATATAATAATTTAAT
Found at i:429816 original size:20 final size:18
Alignment explanation
Indices: 429791--429831 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
429781 AAAATTTATT
429791 TAATTTAAAATAAAATATAA
1 TAATTT-AAATAAAA-ATAA
*
429811 TAATTTAATTAAAAATAA
1 TAATTTAAATAAAAATAA
429829 TAA
1 TAA
429832 AAAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 7 0.35
20 6 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATTTAAATAAAAATAA
Found at i:429837 original size:25 final size:25
Alignment explanation
Indices: 429788--429837 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
429778 ATTAAAATTT
* *
429788 ATTTAATTTAAAATAAAATATAATA
1 ATTTAATTAAAAATAAAATAAAATA
429813 ATTTAATTAAAAATAATAA-AAAATA
1 ATTTAATTAAAAATAA-AATAAAATA
429838 TTTTTGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
ATTTAATTAAAAATAAAATAAAATA
Found at i:443753 original size:2 final size:2
Alignment explanation
Indices: 443746--443781 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
443736 ATTGAGCTCT
443746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
443782 CGTGTGCATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:446810 original size:16 final size:16
Alignment explanation
Indices: 446789--446823 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
446779 AACTATACTT
446789 AAAAATTATAACTCTA
1 AAAAATTATAACTCTA
*
446805 AAAAATTATAACTTTA
1 AAAAATTATAACTCTA
446821 AAA
1 AAA
446824 CTAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAATTATAACTCTA
Found at i:455259 original size:9 final size:9
Alignment explanation
Indices: 455247--455279 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
455237 TCAAGACGTC
455247 TATATTTTA
1 TATATTTTA
455256 TATATTTTA
1 TATATTTTA
455265 TAT-TTTT-
1 TATATTTTA
455272 TATATTTT
1 TATATTTT
455280 CTCCCAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 3 0.13
8 8 0.35
9 12 0.52
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TATATTTTA
Found at i:455268 original size:16 final size:16
Alignment explanation
Indices: 455247--455279 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
455237 TCAAGACGTC
455247 TATATTTTATATATTT
1 TATATTTTATATATTT
*
455263 TATATTTTTTATATTT
1 TATATTTTATATATTT
455279 T
1 T
455280 CTCCCAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TATATTTTATATATTT
Found at i:456667 original size:3 final size:3
Alignment explanation
Indices: 456627--456656 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
456617 AGCTGCTGAC
*
456627 GAT GAC GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
456657 AAACATGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:459528 original size:20 final size:21
Alignment explanation
Indices: 459505--459543 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
459495 CTTTTGCTGT
459505 TTCTTTGTTT-TTT-TTTTTTC
1 TTCTTT-TTTGTTTATTTTTTC
459525 TTCTTTTTTGTTTATTTTT
1 TTCTTTTTTGTTTATTTTT
459544 GTTCAATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 9 0.53
21 5 0.29
ACGTcount: A:0.03, C:0.08, G:0.05, T:0.85
Consensus pattern (21 bp):
TTCTTTTTTGTTTATTTTTTC
Found at i:463105 original size:19 final size:18
Alignment explanation
Indices: 463074--463116 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
463064 AGTTTCTCCC
*
463074 ATTTTTCACATTT-TATTA
1 ATTTTTAACATTTAT-TTA
463092 ATTTTTAACTATTTATTTA
1 ATTTTTAAC-ATTTATTTA
463111 ATTTTT
1 ATTTTT
463117 TATTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 13 0.59
20 1 0.05
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTAACATTTATTTA
Found at i:473809 original size:12 final size:12
Alignment explanation
Indices: 473792--473820 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
473782 TCATGTATGA
473792 TCTTGCTGCCCT
1 TCTTGCTGCCCT
473804 TCTTGCTGCCCT
1 TCTTGCTGCCCT
473816 TCTTG
1 TCTTG
473821 ATGCAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.38, G:0.17, T:0.45
Consensus pattern (12 bp):
TCTTGCTGCCCT
Found at i:489060 original size:9 final size:9
Alignment explanation
Indices: 489046--489080 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
489036 TTTTAACATA
489046 TTTTTATTT
1 TTTTTATTT
489055 TTTTTA-TT
1 TTTTTATTT
*
489063 TTTTTAATT
1 TTTTTATTT
489072 TTTTTATTT
1 TTTTTATTT
489081 GATTAGATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTATTT
Found at i:489066 original size:17 final size:17
Alignment explanation
Indices: 489046--489080 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
489036 TTTTAACATA
*
489046 TTTTTATTTTTTTTATT
1 TTTTTAATTTTTTTATT
489063 TTTTTAATTTTTTTATT
1 TTTTTAATTTTTTTATT
489080 T
1 T
489081 GATTAGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTAATTTTTTTATT
Found at i:490551 original size:16 final size:18
Alignment explanation
Indices: 490525--490560 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
490515 TATTAATTTT
490525 AAATAATATTTA-TTAAA
1 AAATAATATTTATTTAAA
490542 AAATAA-ATTTATTTAAA
1 AAATAATATTTATTTAAA
490559 AA
1 AA
490561 GGTTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATAATATTTATTTAAA
Found at i:493376 original size:2 final size:2
Alignment explanation
Indices: 493371--493421 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
493361 ATCTTATGCT
* * *
493371 TA TA TA TA TA TA CA TC TA TG TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
493412 TA TG TA TA TA
1 TA TA TA TA TA
493422 AGCAAAAGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:495661 original size:21 final size:22
Alignment explanation
Indices: 495637--495677 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
495627 GTTTCTTTTT
495637 AAATT-TTTATTTTTTTAAAAA
1 AAATTGTTTATTTTTTTAAAAA
495658 AAATTGTTTATTTTTTTAAA
1 AAATTGTTTATTTTTTTAAA
495678 GAATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
AAATTGTTTATTTTTTTAAAAA
Found at i:510699 original size:10 final size:11
Alignment explanation
Indices: 510672--510704 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
510662 CATGATATAC
510672 ATATATATATT
1 ATATATATATT
510683 ATAATATATATT
1 AT-ATATATATT
510695 -TATATATATT
1 ATATATATATT
510705 CTCAATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.43
11 3 0.14
12 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATATATATT
Found at i:510957 original size:2 final size:2
Alignment explanation
Indices: 510950--510997 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
510940 GTTGAAGTCC
* * *
510950 TA TA TA TA TA CA TA TG CA 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
510992 TA TA TA
1 TA TA TA
510998 AAATACAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:513334 original size:1 final size:1
Alignment explanation
Indices: 513328--513361 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
513318 CCATTTGTAA
513328 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
513362 AAGGTCCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:517704 original size:63 final size:63
Alignment explanation
Indices: 517567--517693 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
517557 CATCTAGAGA
517567 AATACTCAAAAAACTCGCTTTTACAAATTTGACGAGTAAATCTCATCATCAGAGTTGTCGTTT
1 AATACTCAAAAAACTCGCTTTTACAAATTTGACGAGTAAATCTCATCATCAGAGTTGTCGTTT
517630 AATACTCAAAAAACTCGCTTTTACAAATTTGACGAGTAAATCTCATCATCAGAGTTGTCGTTT
1 AATACTCAAAAAACTCGCTTTTACAAATTTGACGAGTAAATCTCATCATCAGAGTTGTCGTTT
517693 A
1 A
517694 CAAGTGAAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (63 bp):
AATACTCAAAAAACTCGCTTTTACAAATTTGACGAGTAAATCTCATCATCAGAGTTGTCGTTT
Found at i:518409 original size:20 final size:21
Alignment explanation
Indices: 518371--518415 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
518361 CATTGAAAGT
*
518371 TTTATTATTGTTTACTATTTA
1 TTTATTATTGTTCACTATTTA
* *
518392 TTTATTA-TGTTCATTATTTC
1 TTTATTATTGTTCACTATTTA
518412 TTTA
1 TTTA
518416 CTTTTTTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTATTATTGTTCACTATTTA
Found at i:531328 original size:6 final size:6
Alignment explanation
Indices: 531313--531350 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
531303 GTTGGTAGAC
*
531313 GGCGTG GGCGTT GGCGTT GGCGTT GGCGTT GGCGTT GG
1 GGCGTT GGCGTT GGCGTT GGCGTT GGCGTT GGCGTT GG
531351 AGTAGGAGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.55, T:0.29
Consensus pattern (6 bp):
GGCGTT
Found at i:532407 original size:2 final size:2
Alignment explanation
Indices: 532400--532433 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
532390 ATAGATTCTT
532400 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
532434 AGTCAGTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:538440 original size:2 final size:2
Alignment explanation
Indices: 538433--538458 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
538423 TCTTTGGATA
538433 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
538459 TGTTCTCGTG
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:548631 original size:18 final size:18
Alignment explanation
Indices: 548608--548642 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
548598 GCGCTCTCGT
548608 TCTCTCTCCTTCTCCCGC
1 TCTCTCTCCTTCTCCCGC
548626 TCTCTCTCCTTCTCCCG
1 TCTCTCTCCTTCTCCCG
548643 TCGCTCCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.54, G:0.06, T:0.40
Consensus pattern (18 bp):
TCTCTCTCCTTCTCCCGC
Found at i:548679 original size:6 final size:6
Alignment explanation
Indices: 548662--548708 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
548652 GATGCGCAAA
* * **
548662 CGTTCG CGTTCT CTTTCT CGTTCT CGTTCT CGTAGT CGTTCT CGTTC
1 CGTTCT CGTTCT CGTTCT CGTTCT CGTTCT CGTTCT CGTTCT CGTTC
548709 CCGCTCCCTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.02, C:0.32, G:0.19, T:0.47
Consensus pattern (6 bp):
CGTTCT
Found at i:549990 original size:38 final size:39
Alignment explanation
Indices: 549940--550031 Score: 123
Period size: 38 Copynumber: 2.4 Consensus size: 39
549930 ATCAAATCCA
* *
549940 AAATTCAATCAACAAATGTAAATAATATTCTTCATTACC
1 AAATTCAATCAACAAATGTAAATAATATTCTCCATAACC
* *
549979 AAATT-AATCAACAAATGTAAATGATATTGTCCATAACC
1 AAATTCAATCAACAAATGTAAATAATATTCTCCATAACC
*
550017 AAATTCCAATTAACA
1 AAATT-CAATCAACA
550032 CACAGAGTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 34 0.74
39 5 0.11
40 7 0.15
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.30
Consensus pattern (39 bp):
AAATTCAATCAACAAATGTAAATAATATTCTCCATAACC
Found at i:552802 original size:17 final size:18
Alignment explanation
Indices: 552767--552804 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
552757 ATTTGGGTAA
552767 ATCAATTCAGTCTAATTG
1 ATCAATTCAGTCTAATTG
*
552785 ATCAATTGAGTC-AATTG
1 ATCAATTCAGTCTAATTG
552802 ATC
1 ATC
552805 TAAAATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (18 bp):
ATCAATTCAGTCTAATTG
Found at i:554559 original size:21 final size:19
Alignment explanation
Indices: 554535--554590 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
554525 TCCTTGTATT
554535 TTTCATAAATATATATGATAA
1 TTTCATAAATATATAT-A-AA
* *
554556 TTTCTTAAATATATCATAAT
1 TTTCATAAATATAT-ATAAA
*
554576 TTTCCTAAATATATA
1 TTTCATAAATATATA
554591 CAACTGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 14 0.45
21 14 0.45
22 2 0.06
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (19 bp):
TTTCATAAATATATATAAA
Found at i:554569 original size:19 final size:20
Alignment explanation
Indices: 554545--554589 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
554535 TTTCATAAAT
* *
554545 ATATATGATAA-TTTCTTAA
1 ATATATCATAATTTTCCTAA
554564 ATATATCATAATTTTCCTAA
1 ATATATCATAATTTTCCTAA
554584 ATATAT
1 ATATAT
554590 ACAACTGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATATCATAATTTTCCTAA
Found at i:577845 original size:15 final size:14
Alignment explanation
Indices: 577820--577851 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
577810 ATTGTTATCG
577820 ATTAATTAATTATT
1 ATTAATTAATTATT
577834 ATTAATTAAATTATT
1 ATTAATT-AATTATT
577849 ATT
1 ATT
577852 TATTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTAATTAATTATT
Found at i:598418 original size:167 final size:168
Alignment explanation
Indices: 598146--598457 Score: 434
Period size: 167 Copynumber: 1.9 Consensus size: 168
598136 CTGCTGCCAG
* * *
598146 ACAAAGCTGGCTGCGTTTGCTTTTCAGATTGCAATCTTTGCTCACACCACCAAAGGATGCAAGTA
1 ACAAAGCTGGCTGCGCTTGCTTTTAAAATTGCAATCTTTGCT-ACACCACCAAAGGATGCAAGTA
* * * * *
598211 CCATTCACAATTGAAGTGATGGAAGAAAACCCATAATGCCATTCCATGC-AAGATTCACAGTTGT
65 CCATTCACAATAGAAGTAAAGGAAGAAAACCCAAAATGCCAATCCATGCAAAGATTCACAGTT-T
598275 TCCAAGAACTGATATTCCTGAAATTCCTAGCTCCTAGACA
129 TCCAAGAACTGATATTCCTGAAATTCCTAGCTCCTAGACA
* * *
598315 ACAAAGCTTGGCTGTGCTTGCTCTTTAAAATTGCAGTCTTTGCT-CACCACCATA-GATGCAA-T
1 ACAAAGC-TGGCTGCGCTTGCT-TTTAAAATTGCAATCTTTGCTACACCACCAAAGGATGCAAGT
* *
598377 ACCATTCACAATAGAAGTAAAGGAGGAAAACCCAAAATGCCAATCCATGCAAAGATTTACAGTTT
64 ACCATTCACAATAGAAGTAAAGGAAGAAAACCCAAAATGCCAATCCATGCAAAGATTCACAGTTT
*
598442 TTCAAGAACTGATATT
129 TCCAAGAACTGATATT
598458 ATACATAAAA
Statistics
Matches: 126, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
167 61 0.48
168 19 0.15
169 16 0.13
170 12 0.10
171 18 0.14
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (168 bp):
ACAAAGCTGGCTGCGCTTGCTTTTAAAATTGCAATCTTTGCTACACCACCAAAGGATGCAAGTAC
CATTCACAATAGAAGTAAAGGAAGAAAACCCAAAATGCCAATCCATGCAAAGATTCACAGTTTTC
CAAGAACTGATATTCCTGAAATTCCTAGCTCCTAGACA
Done.