Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold87
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: 1020132
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.24
Warning! 278509 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:229405 original size:13 final size:13
Alignment explanation
Indices: 229389--229413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
229379 TATCAAGAAC
229389 ATGTATCGATACA
1 ATGTATCGATACA
229402 ATGTATCGATAC
1 ATGTATCGATAC
229414 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:229412 original size:32 final size:33
Alignment explanation
Indices: 229371--229434 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
229361 TATTTCAAGG
229371 TGTATCGATA-TCAAG-AACATGTATCGATACAA
1 TGTATCGATACT-AAGCAACATGTATCGATACAA
*
229403 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACTAAGCAACATGTATCGATACA
229435 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (33 bp):
TGTATCGATACTAAGCAACATGTATCGATACAA
Found at i:229525 original size:91 final size:91
Alignment explanation
Indices: 229421--229615 Score: 336
Period size: 91 Copynumber: 2.1 Consensus size: 91
229411 TACTAAGCAA
* *
229421 TATGTATCGATACATCTGGGTGTGTATCGATATATTCTAAGGTTTTAACCTTTGTAGCTTAAGTC
1 TATGTATCGATACATCTGGGTGTGTATCGATACATTCTAAGGTTTTAACCTTTATAGCTTAAGTC
*
229486 AACTTTTATGTGTTGATACAAATACC
66 AACTTTTATGTGTCGATACAAATACC
* * *
229512 TATGTATCGATACATCTGGGTGTGTATCGATACATTCTAAGGTTTTGATCTTTATAGCTTAAGTT
1 TATGTATCGATACATCTGGGTGTGTATCGATACATTCTAAGGTTTTAACCTTTATAGCTTAAGTC
229577 AACTTTTATGTGTCGATACAAATACC
66 AACTTTTATGTGTCGATACAAATACC
229603 TATGTATCGATAC
1 TATGTATCGATAC
229616 TTTGAATTAT
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 98 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (91 bp):
TATGTATCGATACATCTGGGTGTGTATCGATACATTCTAAGGTTTTAACCTTTATAGCTTAAGTC
AACTTTTATGTGTCGATACAAATACC
Found at i:229946 original size:20 final size:20
Alignment explanation
Indices: 229904--229947 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
229894 TATGCATTTG
* *
229904 TTATTATATGAATTTACATT
1 TTATTATATGAATTTAAAAT
229924 TTATTATA-GAGATTTAAAAT
1 TTATTATATGA-ATTTAAAAT
229944 TTAT
1 TTAT
229948 AAAATCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (20 bp):
TTATTATATGAATTTAAAAT
Found at i:231005 original size:21 final size:20
Alignment explanation
Indices: 230974--231013 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
230964 AAACTTTTTC
*
230974 AAATTTAATTTTTTTAATTT
1 AAATTTAATTTTTTAAATTT
230994 AAATTATAATTTTTTAAATT
1 AAATT-TAATTTTTTAAATT
231014 AATTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
AAATTTAATTTTTTAAATTT
Found at i:231006 original size:20 final size:20
Alignment explanation
Indices: 230974--231020 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
230964 AAACTTTTTC
*
230974 AAATTTAATTTTTTTAATTT
1 AAATTTAATTTTTTTAAATT
230994 AAATTATAA-TTTTTTAAATT
1 AAATT-TAATTTTTTTAAATT
231014 -AATTTAA
1 AAATTTAA
231021 ATTGAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 3 0.12
19 4 0.16
20 15 0.60
21 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAATTTAATTTTTTTAAATT
Found at i:231247 original size:7 final size:7
Alignment explanation
Indices: 231237--231261 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
231227 TTATTAGCAA
231237 AGTCCGC
1 AGTCCGC
231244 AGTCCGC
1 AGTCCGC
231251 AGTCCGC
1 AGTCCGC
231258 AGTC
1 AGTC
231262 GCACGCGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.40, G:0.28, T:0.16
Consensus pattern (7 bp):
AGTCCGC
Found at i:231371 original size:2 final size:2
Alignment explanation
Indices: 231364--231392 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
231354 GTATTCCACG
231364 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
231393 CCCTTGACAA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:232855 original size:16 final size:17
Alignment explanation
Indices: 232818--232855 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
232808 TTTATCATTA
232818 TTAAAG-GTAAATGTTT
1 TTAAAGAGTAAATGTTT
232834 TT-AAGAGTAAAT-TTT
1 TTAAAGAGTAAATGTTT
232849 TTAAAGA
1 TTAAAGA
232856 AAAATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (17 bp):
TTAAAGAGTAAATGTTT
Found at i:237371 original size:2 final size:2
Alignment explanation
Indices: 237364--237393 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
237354 CTGATTTTGT
237364 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
237394 GTTGTGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:237410 original size:18 final size:18
Alignment explanation
Indices: 237389--237428 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
237379 ATATATATAT
*
237389 ATATAGTTGTGTTTTTTA
1 ATATAGTTGCGTTTTTTA
237407 ATATAGTTGCGTTTTTTA
1 ATATAGTTGCGTTTTTTA
237425 ATAT
1 ATAT
237429 GTTTCCGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (18 bp):
ATATAGTTGCGTTTTTTA
Found at i:239569 original size:33 final size:32
Alignment explanation
Indices: 239507--239574 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
239497 GTAGCTAAAC
**
239507 TTGTATCGATACACACAGTATGTAACGATACA
1 TTGTATCGATACACACAAAATGTAACGATACA
* *
239539 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTAACGATACA
239572 TTG
1 TTG
239575 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTAACGATACA
Found at i:245887 original size:22 final size:21
Alignment explanation
Indices: 245844--245884 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
245834 CAAATTTCTT
245844 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAATACATC
245866 GTTTTTCA-TCAAAAT-CATC
1 GTTTTTCACTCAAAATACATC
245885 ATCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (21 bp):
GTTTTTCACTCAAAATACATC
Found at i:246192 original size:21 final size:21
Alignment explanation
Indices: 246148--246189 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
246138 CCCCTAGGCA
*
246148 GCACCCACCAGGTCGCGACCG
1 GCACCCACCAGGTCGCAACCG
246169 GCACCC-CCAGGTCGCAACCG
1 GCACCCACCAGGTCGCAACCG
246189 G
1 G
246190 GCAGTCCCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.19, C:0.48, G:0.29, T:0.05
Consensus pattern (21 bp):
GCACCCACCAGGTCGCAACCG
Found at i:246459 original size:24 final size:24
Alignment explanation
Indices: 246427--246479 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
246417 TGTCGCGCTG
246427 TCGACATGAAATATCTCAAGTCTT
1 TCGACATGAAATATCTCAAGTCTT
246451 TCGACATGAAATATCTCAAGTCTT
1 TCGACATGAAATATCTCAAGTCTT
246475 TCGAC
1 TCGAC
246480 TTCCTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (24 bp):
TCGACATGAAATATCTCAAGTCTT
Found at i:248161 original size:13 final size:13
Alignment explanation
Indices: 248143--248167 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
248133 AACTTGCACA
248143 GTATCGATACATT
1 GTATCGATACATT
248156 GTATCGATACAT
1 GTATCGATACAT
248168 GACTAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:248180 original size:20 final size:20
Alignment explanation
Indices: 248155--248206 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
248145 ATCGATACAT
**
248155 TGTATCGATACATGACTAAA
1 TGTATCGATACATGAAAAAA
*
248175 TGTATCGATACTTGAAAAAA
1 TGTATCGATACATGAAAAAA
248195 TGTATCGATACA
1 TGTATCGATACA
248207 AGTCATTAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:248835 original size:13 final size:13
Alignment explanation
Indices: 248817--248841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
248807 ATTACTCACA
248817 TGTATCGATACAT
1 TGTATCGATACAT
248830 TGTATCGATACA
1 TGTATCGATACA
248842 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:248949 original size:47 final size:51
Alignment explanation
Indices: 248830--248963 Score: 197
Period size: 47 Copynumber: 2.7 Consensus size: 51
248820 ATCGATACAT
***
248830 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
248882 TGTATCGATACA-TATAAATGTATCGATACATGCAGGC-AA-TTG-CCAGA
1 TGTATCGATACACTATAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
248929 TGTATCGATACACTAT-AATGTATCGATACATGCAG
1 TGTATCGATACACTATAAATGTATCGATACATGCAG
248964 ATAAATTTTC
Statistics
Matches: 78, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
47 36 0.46
48 6 0.08
49 2 0.03
50 21 0.27
51 1 0.01
52 12 0.15
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:253470 original size:32 final size:33
Alignment explanation
Indices: 253434--253496 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
253424 TCAAAATACG
*
253434 AACGTATCAAAATCTATATAAAATTA-AATATT
1 AACGTATAAAAATCTATATAAAATTATAATATT
* * *
253466 AACGTGTAAAAATTTATATAAATTTATAATA
1 AACGTATAAAAATCTATATAAAATTATAATA
253497 CTATAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 22 0.85
33 4 0.15
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37
Consensus pattern (33 bp):
AACGTATAAAAATCTATATAAAATTATAATATT
Found at i:254195 original size:23 final size:23
Alignment explanation
Indices: 254123--254196 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
254113 TTAATAAAAT
254123 AAAATAATATTTAATTAAATTTTAA
1 AAAATAATATTT-ATTAAA-TTTAA
* *
254148 AATAATCAAT-TTT-TT--ATATAG
1 AA-AAT-AATATTTATTAAATTTAA
254169 AAAATAATATTTATTAAATTTAA
1 AAAATAATATTTATTAAATTTAA
254192 AAAAT
1 AAAAT
254197 TTACATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 3 0.08
20 6 0.15
21 7 0.18
22 1 0.03
23 9 0.23
24 2 0.05
25 2 0.05
26 6 0.15
27 3 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (23 bp):
AAAATAATATTTATTAAATTTAA
Found at i:254238 original size:30 final size:30
Alignment explanation
Indices: 254202--254265 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
254192 AAAATTTACA
*
254202 TTAAAAATTAAAA-TATTAATTATTA-TATTT
1 TTAAAAATAAAAAGTATT--TTATTATTATTT
254232 TTAAAAATAAAAAGTATTTTATTATTATTT
1 TTAAAAATAAAAAGTATTTTATTATTATTT
254262 TTAA
1 TTAA
254266 TAAAATAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 6 0.19
30 21 0.68
31 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
TTAAAAATAAAAAGTATTTTATTATTATTT
Found at i:254580 original size:20 final size:22
Alignment explanation
Indices: 254555--254595 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
254545 ATATAAACAG
254555 TTGAAT-ATG-AAATTTTTTAT
1 TTGAATAATGAAAATTTTTTAT
254575 TTGAATAATGATAAATTTTTT
1 TTGAATAATGA-AAATTTTTT
254596 TAATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
23 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.54
Consensus pattern (22 bp):
TTGAATAATGAAAATTTTTTAT
Found at i:254619 original size:22 final size:21
Alignment explanation
Indices: 254565--254639 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 21
254555 TTGAATATGA
*
254565 AATTTTTT-ATTTGAATAATGAT
1 AATTTTTTAATTTG-TTAAT-AT
*
254587 AAATTTTTTTAATTTTTTAAATAT
1 -AA-TTTTTTAATTTGTT-AATAT
*
254611 TATTTTTTAATTTGTTAATAT
1 AATTTTTTAATTTGTTAATAT
254632 AATTTTTT
1 AATTTTTT
254640 TAAAAAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
21 12 0.27
22 13 0.30
23 3 0.07
24 9 0.20
25 7 0.16
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (21 bp):
AATTTTTTAATTTGTTAATAT
Found at i:254640 original size:22 final size:21
Alignment explanation
Indices: 254588--254642 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
254578 AATAATGATA
*
254588 AATTTTTTTAATTTTTTAAAT
1 AATTTTTTTAATTTGTTAAAT
*
254609 ATTATTTTTTAATTTGTTAATAT
1 AAT-TTTTTTAATTTGTTAA-AT
254632 AATTTTTTTAA
1 AATTTTTTTAA
254643 AAAATTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 23 0.79
23 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
AATTTTTTTAATTTGTTAAAT
Found at i:254676 original size:22 final size:22
Alignment explanation
Indices: 254591--254678 Score: 63
Period size: 22 Copynumber: 3.8 Consensus size: 22
254581 AATGATAAAT
254591 TTTTTTAATTTT-TTAAATATTA
1 TTTTTT-ATTTTATTAAATATTA
* *
254613 TTTTTTAATTTGTTAATATAATT-
1 TTTTTTATTTTATTAA-AT-ATTA
* *
254636 TTTTTAAAAAATTTAATTAAATATTA
1 TTTTT----TATTTTATTAAATATTA
254662 TTTTTTATTTTATTAAA
1 TTTTTTATTTTATTAAA
254679 AAATAATAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 16
0.69 0.09 0.22
Matches are distributed among these distances:
21 4 0.08
22 20 0.39
23 7 0.14
24 3 0.06
25 3 0.06
26 7 0.14
27 7 0.14
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (22 bp):
TTTTTTATTTTATTAAATATTA
Found at i:254724 original size:24 final size:24
Alignment explanation
Indices: 254683--254729 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
254673 ATTAAAAAAT
* *
254683 AATAATAAATACTTTTTATTTTAA
1 AATAATAAATACTATTTAATTTAA
* *
254707 AATAATAATTAGTATTTAATTTA
1 AATAATAAATACTATTTAATTTA
254730 TTAATGTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
AATAATAAATACTATTTAATTTAA
Found at i:254891 original size:22 final size:22
Alignment explanation
Indices: 254849--254892 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
254839 TATAATCAAA
* *
254849 TAAATTATTTTTAAAACTTAAT
1 TAAATTATTATTAAAAATTAAT
254871 TAAA-TATTATTAAAATATTAAT
1 TAAATTATTATTAAAA-ATTAAT
254893 AATAACCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAATTATTATTAAAAATTAAT
Found at i:260129 original size:21 final size:21
Alignment explanation
Indices: 260101--260168 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
260091 TCAAAACATT
*
260101 ATTT-TATAATATTTTATCTC
1 ATTTCTATATTATTTTATCTC
* ***
260121 ATTTCTATATTA-TATATGAA
1 ATTTCTATATTATTTTATCTC
260141 ATTTTCTATATTATTTTATCTC
1 A-TTTCTATATTATTTTATCTC
260163 ATTTCT
1 ATTTCT
260169 TGGATTATTG
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
20 9 0.25
21 22 0.61
22 5 0.14
ACGTcount: A:0.29, C:0.10, G:0.01, T:0.59
Consensus pattern (21 bp):
ATTTCTATATTATTTTATCTC
Found at i:261113 original size:24 final size:23
Alignment explanation
Indices: 261086--261136 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
261076 TTTTCATCAT
*
261086 TTATAACTTTATAATTTTTAAAAA
1 TTATAA-TGTATAATTTTTAAAAA
261110 TTAT-ATGTATAATTTTTAAAAA
1 TTATAATGTATAATTTTTAAAAA
261132 TTATA
1 TTATA
261137 TTTTAATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 20 0.80
23 1 0.04
24 4 0.16
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TTATAATGTATAATTTTTAAAAA
Found at i:261123 original size:22 final size:22
Alignment explanation
Indices: 261095--261137 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
261085 TTTATAACTT
261095 TATAATTTTTAAAAATTATATG
1 TATAATTTTTAAAAATTATATG
261117 TATAATTTTTAAAAATTATAT
1 TATAATTTTTAAAAATTATAT
261138 TTTAATATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TATAATTTTTAAAAATTATATG
Found at i:261632 original size:2 final size:2
Alignment explanation
Indices: 261625--261650 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
261615 TAAAATATGT
261625 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
261651 AAGCACATAT
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):
TA
Found at i:261773 original size:54 final size:56
Alignment explanation
Indices: 261670--261778 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 56
261660 TAACTAAAAA
261670 TTATTTTTGAAAAAAATTATTTTTTAAATTATCTGACTTAACACCTTTAAATTTAG
1 TTATTTTTGAAAAAAATTATTTTTTAAATTATCTGACTTAACACCTTTAAATTTAG
* * *
261726 TTATTTTTGAAAAAAA-TATTATTTT-AATTAT-TTACTTATCATCTTTAAATTTA
1 TTATTTTTGAAAAAAATTATT-TTTTAAATTATCTGACTTAACACCTTTAAATTTA
261779 CAGTACGTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
54 19 0.39
55 10 0.20
56 20 0.41
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (56 bp):
TTATTTTTGAAAAAAATTATTTTTTAAATTATCTGACTTAACACCTTTAAATTTAG
Found at i:262132 original size:62 final size:63
Alignment explanation
Indices: 262063--262211 Score: 176
Period size: 62 Copynumber: 2.4 Consensus size: 63
262053 TTACTTTTAT
* * * * *
262063 ATTAAATATAAAATAATAACATTAACTTTCATTTTAAAATAATATTTAAAAGT-TTTTTATAA
1 ATTAAATAAAAAATAATAACATTAACTCTCATTTTAAAATAATATTAAAAAATATTTGTATAA
* * * *
262125 ATTAAATAAAAAATTATAACATTTACTCTCATTTTAAAGTAATATTAAAAAATATTTGTATAT
1 ATTAAATAAAAAATAATAACATTAACTCTCATTTTAAAATAATATTAAAAAATATTTGTATAA
*
262188 ATT-AATACAATTAATAATAACATT
1 ATTAAATA-AA-AAATAATAACATT
262212 TACATATTAA
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
62 50 0.68
63 12 0.16
64 11 0.15
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (63 bp):
ATTAAATAAAAAATAATAACATTAACTCTCATTTTAAAATAATATTAAAAAATATTTGTATAA
Found at i:263513 original size:14 final size:14
Alignment explanation
Indices: 263486--263536 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
263476 TTGAGAAGAG
**
263486 TATTTTAATTTTTA
1 TATTTTAAGATTTA
263500 TATTATT-AGATTTAA
1 TATT-TTAAGATTT-A
*
263515 TATTTTAATATTTA
1 TATTTTAAGATTTA
263529 TATTTTAA
1 TATTTTAA
263537 AAATTGTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
TATTTTAAGATTTA
Found at i:264843 original size:20 final size:21
Alignment explanation
Indices: 264826--264872 Score: 73
Period size: 19 Copynumber: 2.4 Consensus size: 21
264816 ATATTAATTT
264826 AATTAAAAA-ATAATTAATAA
1 AATTAAAAATATAATTAATAA
264846 AATTAAAAATATAA--AATAA
1 AATTAAAAATATAATTAATAA
264865 AATTAAAA
1 AATTAAAA
264873 CTTAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.50
20 9 0.35
21 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AATTAAAAATATAATTAATAA
Found at i:264919 original size:14 final size:14
Alignment explanation
Indices: 264900--264933 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
264890 TATTATTTTT
264900 TAATTTAAAAAATA
1 TAATTTAAAAAATA
*
264914 TAATTTAAAATATA
1 TAATTTAAAAAATA
*
264928 TTATTT
1 TAATTT
264934 TTATTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTTAAAAAATA
Found at i:266356 original size:11 final size:11
Alignment explanation
Indices: 266331--266379 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
266321 CTCAATATAT
*
266331 TAATTTTTTTC
1 TAATTTTTTTA
266342 T--TTTTTTT-
1 TAATTTTTTTA
266350 TAATTTTTTTA
1 TAATTTTTTTA
*
266361 TAATTATTTTA
1 TAATTTTTTTA
*
266372 TAGTTTTT
1 TAATTTTT
266380 AGTTTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
8 1 0.03
9 7 0.22
10 7 0.22
11 17 0.53
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (11 bp):
TAATTTTTTTA
Found at i:266546 original size:20 final size:19
Alignment explanation
Indices: 266521--266566 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
266511 GATCTTGTAA
*
266521 TTTTTTCGATTTTACTTTAT
1 TTTTTTCG-TTTTACATTAT
* *
266541 TTTTTTAGTTTTGCATTAT
1 TTTTTTCGTTTTACATTAT
266560 TTTTTTC
1 TTTTTTC
266567 ATTAAGTCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.13, C:0.09, G:0.07, T:0.72
Consensus pattern (19 bp):
TTTTTTCGTTTTACATTAT
Found at i:270291 original size:89 final size:89
Alignment explanation
Indices: 269928--270281 Score: 413
Period size: 89 Copynumber: 4.1 Consensus size: 89
269918 TTTGTCGTGT
* * *
269928 CATTAGTCAAATATTTTTCATCGTGTTAGAA-G-----GATACCCATATGCATCTATTACATCTT
1 CATTAGTCAAATATTTTTCATCGTGTTAGAAGGAATCTGATACTCACATGCATCTATCACATCTT
*
269987 TCGAGTTCCAAGAAATTTATTAGG
66 TCGAGTTTCAAGAAATTTATTAGG
* * * * *
270011 CATTAGTCAAATATTTTTCATCGT-TTCAGAAGGAATATGATATTTACATACATCTGTCACATCT
1 CATTAGTCAAATATTTTTCATCGTGTT-AGAAGGAATCTGATACTCACATGCATCTATCACATCT
270075 TTCGAGTTTCAAGAAATTTATTAGG
65 TTCGAGTTTCAAGAAATTTATTAGG
* * * * * * *
270100 CATT-GTCGAATA-TTTTCTGTCATGTCAAAAAGAATCTGATA-TCCACATGCATCTATCATATC
1 CATTAGTCAAATATTTTTC-ATCGTGTTAGAAGGAATCTGATACT-CACATGCATCTATCACATC
* *
270162 TTTCGAGTTTTAAGAATTTTATTAGG
64 TTTCGAGTTTCAAGAAATTTATTAGG
* *
270188 CATTAGTCAAATATTTTTCATCGTGTTAGAAGGAATCTAATACTCACATGCATCTGTCACATCTT
1 CATTAGTCAAATATTTTTCATCGTGTTAGAAGGAATCTGATACTCACATGCATCTATCACATCTT
*
270253 TCGAGTTTCAAGAATTTTATTAGG
66 TCGAGTTTCAAGAAATTTATTAGG
*
270277 TATTA
1 CATTA
270282 AACACATATT
Statistics
Matches: 226, Mismatches: 32, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
82 2 0.01
83 28 0.12
84 1 0.00
87 6 0.03
88 65 0.29
89 118 0.52
90 6 0.03
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (89 bp):
CATTAGTCAAATATTTTTCATCGTGTTAGAAGGAATCTGATACTCACATGCATCTATCACATCTT
TCGAGTTTCAAGAAATTTATTAGG
Found at i:276179 original size:27 final size:28
Alignment explanation
Indices: 276143--276206 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
276133 AATCGGATTT
276143 GAGTAT-CCCGTG--AATAATAGGGGTTG
1 GAGTATCCCCGTGAAAATAAT-GGGGTTG
276169 GAGTATCCCCGTGAAAATAATGGGGTTG
1 GAGTATCCCCGTGAAAATAATGGGGTTG
276197 GAGTATCCCC
1 GAGTATCCCC
276207 ATTATGATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
26 6 0.17
27 6 0.17
28 17 0.49
29 6 0.17
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (28 bp):
GAGTATCCCCGTGAAAATAATGGGGTTG
Found at i:276422 original size:49 final size:48
Alignment explanation
Indices: 276367--276493 Score: 159
Period size: 48 Copynumber: 2.6 Consensus size: 48
276357 GTGTTTTGGA
* * * *
276367 AATAAAATCGGAGTTGAATATCTCCGATTGTGGAGAATTGGGTATTTAG
1 AATAAAATCGGAGTTGAGTATCCCCGATTATGGA-AAATGGGTATTTAG
*
276416 AATAAAA-CGGAGTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTAG
1 AATAAAATCGGAGTT-GAGTATCCCCGATTATGGAAAATGGGTATTTAG
*
276464 AA-ATAAATCAGAGTTGAGTATCCCCGATTA
1 AATA-AAATCGGAGTTGAGTATCCCCGATTA
276494 AGAAAATTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
47 1 0.01
48 39 0.57
49 29 0.42
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (48 bp):
AATAAAATCGGAGTTGAGTATCCCCGATTATGGAAAATGGGTATTTAG
Found at i:276429 original size:48 final size:48
Alignment explanation
Indices: 276365--276493 Score: 161
Period size: 49 Copynumber: 2.6 Consensus size: 48
276355 TAGTGTTTTG
* * * *
276365 GAAATAAAATCGGAGTTGAATATCTCCGATTGTGGAGAATTGGGTATTTA
1 GAAATAAAA-CGGAGTTGAGTATCCCCGATTATGGA-AAATGGGTATTTA
*
276415 G-AATAAAACGGAGTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTA
1 GAAATAAAACGGAGTT-GAGTATCCCCGATTATGGAAAATGGGTATTTA
* *
276463 GAAATAAATCAGAGTTGAGTATCCCCGATTA
1 GAAATAAAACGGAGTTGAGTATCCCCGATTA
276494 AGAAAATTGA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
48 34 0.49
49 35 0.50
50 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.29
Consensus pattern (48 bp):
GAAATAAAACGGAGTTGAGTATCCCCGATTATGGAAAATGGGTATTTA
Found at i:276509 original size:48 final size:48
Alignment explanation
Indices: 276411--276538 Score: 125
Period size: 49 Copynumber: 2.6 Consensus size: 48
276401 GAATTGGGTA
* * *
276411 TTTAGAATAAAACGGAGTTGGAGTATCCCCGATTATGGAAAATGGGTG
1 TTTAGAATAAAACAGAGTTGGAGTATCCCCGATTATAGAAAATGAGTG
* *
276459 TTTAGAAATAAATCAGAGTT-GAGTATCCCCGATTA-AGAAAATTGATTG
1 TTTAG-AATAAAACAGAGTTGGAGTATCCCCGATTATAGAAAA-TGAGTG
* * *
276507 TTTTGGAAATGAAACTGAGATTGGAGTATCCC
1 -TTTAG-AATAAAACAGAG-TTGGAGTATCCC
276539 TGTGATGAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
47 5 0.08
48 24 0.36
49 26 0.39
50 2 0.03
51 9 0.14
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (48 bp):
TTTAGAATAAAACAGAGTTGGAGTATCCCCGATTATAGAAAATGAGTG
Found at i:276516 original size:49 final size:48
Alignment explanation
Indices: 276411--276538 Score: 127
Period size: 48 Copynumber: 2.6 Consensus size: 48
276401 GAATTGGGTA
* * *
276411 TTTAG-AATAAAACGGAGTTGGAGTATCCCCGATTATGGAAAATGGGTG
1 TTTAGAAAT-AAACAGAGTTGGAGTATCCCCGATTATAGAAAATGAGTG
*
276459 TTTAGAAATAAATCAGAGTT-GAGTATCCCCGATTA-AGAAAATTGATTG
1 TTTAGAAATAAA-CAGAGTTGGAGTATCCCCGATTATAGAAAA-TGAGTG
* *
276507 TTTTGGAAATGAAACTGAGATTGGAGTATCCC
1 -TTTAGAAAT-AAACAGAG-TTGGAGTATCCC
276539 TGTGATGAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
47 5 0.07
48 27 0.40
49 21 0.31
50 5 0.07
51 9 0.13
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (48 bp):
TTTAGAAATAAACAGAGTTGGAGTATCCCCGATTATAGAAAATGAGTG
Found at i:557360 original size:20 final size:19
Alignment explanation
Indices: 557335--557406 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
557325 AAAATGCCTG
557335 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTG-AA
* * *
557355 AATGTATCGATGCAATGAGC
1 AATGTATCGATACATTGA-A
*
557375 AATGTATCGATACAATTCAA
1 AATGTATCGATAC-ATTGAA
557395 AATGTATCGATA
1 AATGTATCGATA
557407 TATCTGGGTA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.02
20 39 0.91
21 3 0.07
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:557619 original size:21 final size:20
Alignment explanation
Indices: 557590--557628 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
557580 TGTATCGAAA
557590 ATGTCAATTCGTCC-CCACAT
1 ATGTCAATTC-TCCACCACAT
557610 ATGTCCAATTCTCCACCAC
1 ATGT-CAATTCTCCACCAC
557629 TAGCTAGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.38, G:0.08, T:0.28
Consensus pattern (20 bp):
ATGTCAATTCTCCACCACAT
Found at i:562328 original size:60 final size:61
Alignment explanation
Indices: 562090--562312 Score: 412
Period size: 61 Copynumber: 3.7 Consensus size: 61
562080 AAGATGCGAG
*
562090 AATAATAAAGGTGCCAATATGCTGATTCACGGCCAACGATAACGAGCTTGAAGATGAGAAA
1 AATAATAAAGGTGCTAATATGCTGATTCACGGCCAACGATAACGAGCTTGAAGATGAGAAA
562151 AATAATAAAGGTGCTAATATGCTGATTCACGGCCAACGATAACGAGCTTGAAGATGAGAAA
1 AATAATAAAGGTGCTAATATGCTGATTCACGGCCAACGATAACGAGCTTGAAGATGAGAAA
562212 AATAATAAAGGTGCTAATATGCTGATTCACGGCCAACGATAACGAGCTTGAAGATGAG-AA
1 AATAATAAAGGTGCTAATATGCTGATTCACGGCCAACGATAACGAGCTTGAAGATGAGAAA
* *
562272 AATAATAAAGGTGCTAATATGCTGATTCAAGGCCAGCGATA
1 AATAATAAAGGTGCTAATATGCTGATTCACGGCCAACGATA
562313 GTGGGCTTAA
Statistics
Matches: 159, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
60 41 0.26
61 118 0.74
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (61 bp):
AATAATAAAGGTGCTAATATGCTGATTCACGGCCAACGATAACGAGCTTGAAGATGAGAAA
Found at i:562374 original size:52 final size:50
Alignment explanation
Indices: 562282--562462 Score: 193
Period size: 52 Copynumber: 3.5 Consensus size: 50
562272 AATAATAAAG
* * * *
562282 GTGCTAATATGCTGATTCAAGGCCAGCGATAGTGGGCTTAACGATGACAAA
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAA-GATGACAAA
* *
562333 TGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGACAAA
1 -GTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTT-AAGATGACAAA
* * *
562385 G-GCATCAATATGCTGATTCAAGGCCAGTGATATTAGACTTAAGAAAGAAAAA
1 GTGC--CAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAG-ATGACAAA
* *
562437 GGTGCCAATGTGTTGATTCAAGGCCA
1 -GTGCCAATATGCTGATTCAAGGCCA
562463 ACAACAATGG
Statistics
Matches: 110, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 99 0.90
53 3 0.03
54 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (50 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAGATGACAAA
Found at i:562458 original size:104 final size:103
Alignment explanation
Indices: 562287--562488 Score: 271
Period size: 104 Copynumber: 2.0 Consensus size: 103
562277 TAAAGGTGCT
* * * * *
562287 AATATGCTGATTCAAGGCCAGCGATAGTGGGCTTAACGATGACAAATGTGCCAATGTGCTGATTC
1 AATATGCTGATTCAAGGCCAGCGATAGTAGACTTAACGAAGAAAAAGGTGCCAATGTGCTGATTC
* * *
562352 AAGGCCAGCGACATTAGACTTAAAGATGACAAAGGCATC
66 AAGGCCAACAACAATAGACTTAAAGAT-ACAAAGGCATC
* * *
562391 AATATGCTGATTCAAGGCCAGTGATATTAGACTTAA-GAAAGAAAAAGGTGCCAATGTGTTGATT
1 AATATGCTGATTCAAGGCCAGCGATAGTAGACTTAACG-AAGAAAAAGGTGCCAATGTGCTGATT
*
562455 CAAGGCCAACAACAATGGACTTAAAGATACAAAG
65 CAAGGCCAACAACAATAGACTTAAAGATACAAAG
562489 AATGATAAAG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
103 7 0.08
104 78 0.92
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (103 bp):
AATATGCTGATTCAAGGCCAGCGATAGTAGACTTAACGAAGAAAAAGGTGCCAATGTGCTGATTC
AAGGCCAACAACAATAGACTTAAAGATACAAAGGCATC
Found at i:562646 original size:36 final size:36
Alignment explanation
Indices: 562599--562669 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
562589 GTAGGGCTTA
*
562599 AAAATGGTAAAAGTGCCAATATGTTGATTCAAGGCC
1 AAAATGGTAAAAGTGCCAATATGCTGATTCAAGGCC
562635 AAAATGGTAAAAGTGCCAATATGCTGATTCAAGGC
1 AAAATGGTAAAAGTGCCAATATGCTGATTCAAGGC
562670 TAGCAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (36 bp):
AAAATGGTAAAAGTGCCAATATGCTGATTCAAGGCC
Found at i:562909 original size:112 final size:111
Alignment explanation
Indices: 562754--562975 Score: 284
Period size: 110 Copynumber: 2.0 Consensus size: 111
562744 TGAATATGAG
* * * * * *
562754 AAAAATGATAAAAGTGCCAATATGCTGATTTAAGGCCATCGATATTAGACTTAAAGATGATAAGG
1 AAAAATGATAAAAGTGCCAATATGCTGATTCAAGACCAGCGATATCAGACTTAAAGA-AAGAA-G
*
562819 ATGAGAAGGATGCCAATGTGCTGATTCAAGGCCAATGACATTGGGCTA
64 ATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAATGACATTGGGCTA
* * *
562867 AAAAATGGT-AAAGTGCTAATATGCTGATTCAAGACCAGCGATATCGGACTTAAAGAAAGAAGAT
1 AAAAATGATAAAAGTGCCAATATGCTGATTCAAGACCAGCGATATCAGACTTAAAGAAAGAAGAT
** * * *
562931 TTGATGAATGCCAATGTGTTGATTTAAGGCCAATGACATTGGGCT
66 GAGAAGAATGCCAATGTGCTGATTCAAGGCCAATGACATTGGGCT
562976 TAGATGGGTT
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
110 42 0.45
111 3 0.03
112 41 0.44
113 8 0.09
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (111 bp):
AAAAATGATAAAAGTGCCAATATGCTGATTCAAGACCAGCGATATCAGACTTAAAGAAAGAAGAT
GAGAAGAATGCCAATGTGCTGATTCAAGGCCAATGACATTGGGCTA
Found at i:563021 original size:32 final size:32
Alignment explanation
Indices: 562982--563679 Score: 587
Period size: 32 Copynumber: 22.0 Consensus size: 32
562972 GGCTTAGATG
* *
562982 GGTTGCCACTAACTTGCGTGGGCTTTAGAGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
*
563014 TGTTGCCACCAACTTGTGTGGGCTTTAGA-AA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
* * *
563045 GGAGGTGCCACGAACTTGTGTGGGCTTTAGA-AGG
1 -G-GTTGCCACCAACTTGTGTGGGCTTTAGAGA-A
** * *
563079 GGTTTACACCGACTTATGTGGGCTTT-GAGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
* * *
563110 GGGTTGCCACTAACTTGTGTGGGTTTTAGA-AG
1 -GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
* * *
563142 GGTTCCCACCCACTTGTGTAGGCTTTAGAGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
** *
563174 GGTTGCCATGAACTTGTGTGGGCATT-GAAGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAG-AGAA
* *
563206 GGTTGCCACCGACTTGTGTGGGCTTTAGAG-G
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
* *
563237 GGTTGCCACCAAGTTGTGTGGGCTTTGGAGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
* *
563269 GGTTGCCACCTACTTGTGTGGGCTTTGGA-AA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
* * *
563300 GGTTACCACCAGCTTGTGTGGGCTTTAGAG-G
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
* * * *
563331 GGTTACCACCAGCTTATGTGGGCTTTGGAGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
* * * *
563363 GGTTGCCACCTGACTTGTGTCGGCTTTAAAG-G
1 GGTTGCCACC-AACTTGTGTGGGCTTTAGAGAA
* * *
563395 GGTTGCCACCAGCTTGTGTGGGCTTTGGAG-G
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
* * *
563426 GGTTGCCACCAGCTTATGTAGGCTTTAGAGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
* * **** * *
563458 GATTACCATTGGCTTGTGTGGGCTTTGGAG-G
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
* *
563489 GGTTGCCACCAGA-TTGTATGGGCTTTAGAGAG
1 GGTTGCCACCA-ACTTGTGTGGGCTTTAGAGAA
* * * *
563521 GGTTGCCACCGATTTATGTGGGCTTTAGAG-G
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
* * *
563552 GGTTGCCATCGACTTGCTGTGGGCTTTTGAGAA
1 GGTTGCCACCAACTTG-TGTGGGCTTTAGAGAA
* * * *
563585 GGTTGCTATCGACTTGTGTGGGCTTTAGAG-G
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
* * * *
563616 GGTTACCACCAGCTTGTGTGGGCTTTGGGGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
* * * *
563648 GGTTGCCATCAGCTTGTATGGGCTTTAAAGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
563680 AAAAGATGCC
Statistics
Matches: 535, Mismatches: 111, Indels: 40
0.78 0.16 0.06
Matches are distributed among these distances:
31 213 0.40
32 262 0.49
33 60 0.11
ACGTcount: A:0.19, C:0.17, G:0.34, T:0.30
Consensus pattern (32 bp):
GGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
Found at i:563214 original size:95 final size:95
Alignment explanation
Indices: 562982--563679 Score: 638
Period size: 95 Copynumber: 7.3 Consensus size: 95
562972 GGCTTAGATG
* * *
562982 GGTTGCCACTAACTTGCGTGGGCTTT-AGAGAATGTTGCCACCAACTTGTGTGGGCTTTAGAAAG
1 GGTTGCCACTGACTTGTGTGGGCTTTGA-AGAAGGTTGCCACCAACTTGTGTGGGCTTTAG--AG
** *
563046 GAGG-TGCCACGAACTTGTGTGGGCTTTAGA-AGG
63 G-GGTTGCCACCCACTTGTGTGGGCTTTAGAGA-A
** * * * * *
563079 GGTTTACACCGACTTATGTGGGCTTTG-AGAAGGGTTGCCACTAACTTGTGTGGGTTTTAGAAGG
1 GGTTGCCACTGACTTGTGTGGGCTTTGAAGAA-GGTTGCCACCAACTTGTGTGGGCTTTAGAGGG
* *
563143 GTTCCCACCCACTTGTGTAGGCTTTAGAGAA
65 GTTGCCACCCACTTGTGTGGGCTTTAGAGAA
* *
563174 GGTTGCCA-TGAACTTGTGTGGGCATTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGGG
1 GGTTGCCACTG-ACTTGTGTGGGCTTTGAAGAAGGTTGCCACCAACTTGTGTGGGCTTTAGAGGG
* * *
563238 GTTGCCACCAAGTTGTGTGGGCTTTGGAGAA
65 GTTGCCACCCACTTGTGTGGGCTTTAGAGAA
* * *
563269 GGTTGCCACCT-ACTTGTGTGGGCTTTGGA-AAGGTTACCACCAGCTTGTGTGGGCTTTAGAGGG
1 GGTTGCCA-CTGACTTGTGTGGGCTTTGAAGAAGGTTGCCACCAACTTGTGTGGGCTTTAGAGGG
* * *
563332 GTTACCA-CCAGCTTATGTGGGCTTTGGAGAA
65 GTTGCCACCCA-CTTGTGTGGGCTTTAGAGAA
* * * * *
563363 GGTTGCCACCTGACTTGTGTCGGCTTTAAAG-GGGTTGCCACCAGCTTGTGTGGGCTTTGGAGGG
1 GGTTGCCA-CTGACTTGTGTGGGCTTTGAAGAAGGTTGCCACCAACTTGTGTGGGCTTTAGAGGG
* *
563427 GTTGCCA-CCAGCTTATGTAGGCTTTAGAGAA
65 GTTGCCACCCA-CTTGTGTGGGCTTTAGAGAA
* * * * * * *
563458 GATTACCATTGGCTTGTGTGGGCTTTGGAG-GGGTTGCCACCAGA-TTGTATGGGCTTTAGAGAG
1 GGTTGCCACTGACTTGTGTGGGCTTTGAAGAAGGTTGCCACCA-ACTTGTGTGGGCTTTAGAG-G
* * * *
563521 GGTTGCCACCGATTTATGTGGGCTTTAGAG-G
64 GGTTGCCACCCACTTGTGTGGGCTTTAGAGAA
* * *
563552 GGTTGCCA-TCGACTTGCTGTGGGCTTTTG-AGAAGGTTGCTATCGACTTGTGTGGGCTTTAGAG
1 GGTTGCCACT-GACTTG-TGTGGGC-TTTGAAGAAGGTTGCCACCAACTTGTGTGGGCTTTAGAG
* * *
563615 GGGTTACCA-CCAGCTTGTGTGGGCTTTGGGGAA
63 GGGTTGCCACCCA-CTTGTGTGGGCTTTAGAGAA
* * *
563648 GGTTGCCA-TCAGCTTGTATGGGCTTTAAAGAA
1 GGTTGCCACTGA-CTTGTGTGGGCTTTGAAGAA
563680 AAAAGATGCC
Statistics
Matches: 499, Mismatches: 79, Indels: 48
0.80 0.13 0.08
Matches are distributed among these distances:
93 3 0.01
94 129 0.26
95 269 0.54
96 52 0.10
97 46 0.09
ACGTcount: A:0.19, C:0.17, G:0.34, T:0.30
Consensus pattern (95 bp):
GGTTGCCACTGACTTGTGTGGGCTTTGAAGAAGGTTGCCACCAACTTGTGTGGGCTTTAGAGGGG
TTGCCACCCACTTGTGTGGGCTTTAGAGAA
Found at i:563664 original size:63 final size:63
Alignment explanation
Indices: 562970--563674 Score: 560
Period size: 63 Copynumber: 11.1 Consensus size: 63
562960 CCAATGACAT
* * * * * * *
562970 TGGGC-TTAGATGGGTTGCCACTAACTTGCGTGGGCTTTAGAGAATGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGGGGTTGCCACCAGCTTGTGTGGGCTTTGGAGAAGGTTGCCACCAGCTTGTG
* * **
563032 TGGGCTTTAGAAAGGAGG-TGCCACGAACTTGTGTGGGCTTT--AGAAGGGGTTTACACC-GACT
1 TGGGCTTTAG--AGG-GGTTGCCACCAGCTTGTGTGGGCTTTGGAGAA--GGTTGCCACCAG-CT
*
563093 TATG
60 TGTG
* * * * *
563097 TGGGCTTTGAGAAGGGTTGCCACTAACTTGTGTGGG-TTT-TAGAAGGGTTCCCACCCA-CTTGT
1 TGGGCTTT-AGAGGGGTTGCCACCAGCTTGTGTGGGCTTTGGAGAA-GGTTGCCA-CCAGCTTGT
563159 G
63 G
* * ** * * *
563160 TAGGCTTTAGAGAAGGTTGCCATGAACTTGTGTGGGCATTGAAGAAGGTTGCCACC-GACTTGTG
1 TGGGCTTTAGAG-GGGTTGCCACCAGCTTGTGTGGGCTTTGGAGAAGGTTGCCACCAG-CTTGTG
563224 TGGGCTTTAGAGGGGTTGCCACCAAG-TTGTGTGGGCTTTGGAGAAGGTTGCCACCTA-CTTGTG
1 TGGGCTTTAGAGGGGTTGCCACC-AGCTTGTGTGGGCTTTGGAGAAGGTTGCCACC-AGCTTGTG
* ** * * * * *
563287 TGGGCTTTGGAAAGGTTACCACCAGCTTGTGTGGGCTTTAGAG-GGGTTACCACCAGCTTATG
1 TGGGCTTTAGAGGGGTTGCCACCAGCTTGTGTGGGCTTTGGAGAAGGTTGCCACCAGCTTGTG
* * * * ** *
563349 TGGGCTTTGGAGAAGGTTGCCACCTGACTTGTGTCGGCTTTAAAG-GGGTTGCCACCAGCTTGTG
1 TGGGCTTTAGAG-GGGTTGCCACCAG-CTTGTGTGGGCTTTGGAGAAGGTTGCCACCAGCTTGTG
* * * * * * ***
563413 TGGGCTTTGGAGGGGTTGCCACCAGCTTATGTAGGCTTTAGAGAAGATTACCATTGGCTTGTG
1 TGGGCTTTAGAGGGGTTGCCACCAGCTTGTGTGGGCTTTGGAGAAGGTTGCCACCAGCTTGTG
* * * * * * *
563476 TGGGCTTTGGAGGGGTTGCCACCAGATTGTATGGGCTTTAGAGAGGGTTGCCACC-GATTTATG
1 TGGGCTTTAGAGGGGTTGCCACCAGCTTGTGTGGGCTTTGGAGAAGGTTGCCACCAG-CTTGTG
* * * *
563539 TGGGCTTTAGAGGGGTTGCCATC-GACTTGCTGTGGGCTTTTGAGAAGGTTGCTATC-GACTTGT
1 TGGGCTTTAGAGGGGTTGCCACCAG-CTTG-TGTGGGCTTTGGAGAAGGTTGCCACCAG-CTTGT
563602 G
63 G
* * * *
563603 TGGGCTTTAGAGGGGTTACCACCAGCTTGTGTGGGCTTTGGGGAAGGTTGCCATCAGCTTGTA
1 TGGGCTTTAGAGGGGTTGCCACCAGCTTGTGTGGGCTTTGGAGAAGGTTGCCACCAGCTTGTG
563666 TGGGCTTTA
1 TGGGCTTTA
563675 AAGAAAAAAG
Statistics
Matches: 532, Mismatches: 81, Indels: 59
0.79 0.12 0.09
Matches are distributed among these distances:
61 1 0.00
62 52 0.10
63 276 0.52
64 151 0.28
65 48 0.09
66 4 0.01
ACGTcount: A:0.18, C:0.17, G:0.34, T:0.30
Consensus pattern (63 bp):
TGGGCTTTAGAGGGGTTGCCACCAGCTTGTGTGGGCTTTGGAGAAGGTTGCCACCAGCTTGTG
Found at i:563893 original size:63 final size:63
Alignment explanation
Indices: 563821--564356 Score: 419
Period size: 63 Copynumber: 8.5 Consensus size: 63
563811 CTTTTTTTTC
* * * * * *
563821 AAAGCCCATATAAGCCGATGGCAACCTTCCCCAATGCCCATACAAGCTGGTGGCAACCCCTCT
1 AAAGCCCACACAAGCCGGTGGCAACCTTCTCCAAAGCCCACACAAGCTGGTGGCAACCCCTCT
* ** *
563884 AAAGCCCATACAAGTTGGTGGCAACCTTCTCAAAAGCCCACACAAG-TCGGTGGCAACCCCTCT
1 AAAGCCCACACAAGCCGGTGGCAACCTTCTCCAAAGCCCACACAAGCT-GGTGGCAACCCCTCT
* ** * * * * * *
563947 AAAGCCCACACAAGTCAATGGCAACCATATCTAAAGCCCATACAAGCTGGT-GCAACCCTTCC
1 AAAGCCCACACAAGCCGGTGGCAACCTTCTCCAAAGCCCACACAAGCTGGTGGCAACCCCTCT
* * * * * *
564009 AAAGCCAACACAAGCTGGGGGCAATCC--CTCCAAAGCCTATACAAGCTAGTGGCAACCCCTCT
1 AAAGCCCACACAAGCCGGTGGCAA-CCTTCTCCAAAGCCCACACAAGCTGGTGGCAACCCCTCT
* * * * * *
564071 AAAGCCTATACAAGTCGGTGGCAACCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCCCTTT
1 AAAGCCCACACAAGCCGGTGGCAACCTTCTCCAAAGCCCACACAAGCTGGTGGCAACCCCTCT
* * * * *
564134 AAAGCCCACATAAGCTGGTGGCAA-CTTTTCCAAAGCCCACACAAG-TAGGTGGCAACCTTCTCC
1 AAAGCCCACACAAGCCGGTGGCAACCTTCTCCAAAGCCCACACAAGCT-GGTGGCAACC-CCTCT
* * * * * *
564197 AAAG-CCACA-AAACTTGGTGGCAACCTTTTCCAATGCCCACACAAG-TCGGTGGTAACCCTTCT
1 AAAGCCCACACAAGC-CGGTGGCAACCTTCTCCAAAGCCCACACAAGCT-GGTGGCAACCCCTC-
564259 T
63 T
* * * * **
564260 CAAAGGCCACATAAGTCGGTGGCAACCCTTCT-CAAAGCCCACACAAG-TCGATGGCAAGCTTTC
1 -AAAGCCCACACAAGCCGGTGGCAA-CCTTCTCCAAAGCCCACACAAGCT-GGTGGCAA-C-CCC
564323 TCT
61 TCT
* * **
564326 AAAACTCACACAAGTTGGTGGCAACCTTCTC
1 AAAGCCCACACAAGCCGGTGGCAACCTTCTC
564357 TGAAAGCTCA
Statistics
Matches: 382, Mismatches: 73, Indels: 34
0.78 0.15 0.07
Matches are distributed among these distances:
61 25 0.07
62 101 0.26
63 180 0.47
64 11 0.03
65 54 0.14
66 9 0.02
67 2 0.01
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.19
Consensus pattern (63 bp):
AAAGCCCACACAAGCCGGTGGCAACCTTCTCCAAAGCCCACACAAGCTGGTGGCAACCCCTCT
Found at i:563929 original size:32 final size:32
Alignment explanation
Indices: 563839--564363 Score: 428
Period size: 31 Copynumber: 16.6 Consensus size: 32
563829 TATAAGCCGA
* * * * *
563839 TGGCAACCTTCCCCAATGCCCATACAAGCTGG
1 TGGCAACCTTCTCTAAAGCCCACACAAGTTGG
* *
563871 TGGCAACC-CCTCTAAAGCCCATACAAGTTGG
1 TGGCAACCTTCTCTAAAGCCCACACAAGTTGG
* *
563902 TGGCAACCTTCTCAAAAGCCCACACAAGTCGG
1 TGGCAACCTTCTCTAAAGCCCACACAAGTTGG
* ***
563934 TGGCAACC-CCTCTAAAGCCCACACAAGTCAA
1 TGGCAACCTTCTCTAAAGCCCACACAAGTTGG
* * * *
563965 TGGCAACCATATCTAAAGCCCATACAAGCTGG
1 TGGCAACCTTCTCTAAAGCCCACACAAGTTGG
* *
563997 T-GCAACCCTTC-C-AAAGCCAACACAAGCTGG
1 TGGCAA-CCTTCTCTAAAGCCCACACAAGTTGG
* * * * * *
564027 GGGCAATCC--CTCCAAAGCCTATACAAGCTAG
1 TGGCAA-CCTTCTCTAAAGCCCACACAAGTTGG
* * * *
564058 TGGCAACC-CCTCTAAAGCCTATACAAGTCGG
1 TGGCAACCTTCTCTAAAGCCCACACAAGTTGG
564089 TGGCAACCTTCTCTAAAGCCCACACAAGTTGG
1 TGGCAACCTTCTCTAAAGCCCACACAAGTTGG
* * * *
564121 TGGCAACC-CCTTTAAAGCCCACATAAGCTGG
1 TGGCAACCTTCTCTAAAGCCCACACAAGTTGG
* * *
564152 TGGCAA-CTTTTCCAAAGCCCACACAAGTAGG
1 TGGCAACCTTCTCTAAAGCCCACACAAGTTGG
* * *
564183 TGGCAACCTTCTCCAAAG-CCACAAAACTTGG
1 TGGCAACCTTCTCTAAAGCCCACACAAGTTGG
* * * *
564214 TGGCAACCTTTTCCAATGCCCACACAAGTCGG
1 TGGCAACCTTCTCTAAAGCCCACACAAGTTGG
* * * *
564246 TGGTAACCCTTCT-TCAAAGGCCACATAAGTCGG
1 TGGCAA-CCTTCTCT-AAAGCCCACACAAGTTGG
* *
564279 TGGCAACCCTTCTC-AAAGCCCACACAAGTCGA
1 TGGCAA-CCTTCTCTAAAGCCCACACAAGTTGG
* * *
564311 TGGCAAGCTTTCTCTAAAACTCACACAAGTTGG
1 TGGCAA-CCTTCTCTAAAGCCCACACAAGTTGG
564344 TGGCAACCTTCTCTGAAAGC
1 TGGCAACCTTCTCT-AAAGC
564364 TCAAGGAATA
Statistics
Matches: 401, Mismatches: 76, Indels: 31
0.79 0.15 0.06
Matches are distributed among these distances:
29 1 0.00
30 20 0.05
31 183 0.46
32 141 0.35
33 56 0.14
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.19
Consensus pattern (32 bp):
TGGCAACCTTCTCTAAAGCCCACACAAGTTGG
Found at i:565093 original size:20 final size:20
Alignment explanation
Indices: 565068--565118 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
565058 GTTTGAAGCA
565068 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ATC
*
565088 ATGTATCGATACAATGTGTC
1 ATGTATCGATACAATGTATC
565108 ATGTATCGATA
1 ATGTATCGATA
565119 TAAACAGTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATGTATC
Found at i:565194 original size:19 final size:19
Alignment explanation
Indices: 565150--565205 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
565140 CTGCCAGTTT
**
565150 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
565170 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
565189 CATGTATCGATACAATG
1 CATGTATCGATACAATG
565206 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:565208 original size:13 final size:13
Alignment explanation
Indices: 565190--565216 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
565180 TACAATGAAC
565190 ATGTATCGATACA
1 ATGTATCGATACA
565203 ATGTATCGATACA
1 ATGTATCGATACA
565216 A
1 A
565217 AGCATAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:565809 original size:21 final size:22
Alignment explanation
Indices: 565783--565826 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
565773 GGCTCTCGTT
*
565783 AAAAAATTT-TCCCTTTAATAA
1 AAAAAATTTCTCCCCTTAATAA
*
565804 AAAAAATTTCTCCCCTTGATAA
1 AAAAAATTTCTCCCCTTAATAA
565826 A
1 A
565827 CGGTTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAAAATTTCTCCCCTTAATAA
Found at i:573038 original size:21 final size:20
Alignment explanation
Indices: 573013--573085 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
573003 TTATAAATTA
573013 TATCGATACAAATAGTAAATG
1 TATCGATAC-AATAGTAAATG
*
573034 TATCGATAC-ATGAGTGAATG
1 TATCGATACAAT-AGTAAATG
* * **
573054 TATCAATACATTCCTGAAATG
1 TATCGATACAATAGT-AAATG
573075 TATCGATACAA
1 TATCGATACAA
573086 AACCACTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
19 2 0.05
20 16 0.39
21 23 0.56
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (20 bp):
TATCGATACAATAGTAAATG
Found at i:573055 original size:20 final size:21
Alignment explanation
Indices: 573029--573084 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
573019 TACAAATAGT
*
573029 AAATGTATCGATACATGAGTG
1 AAATGTATCGATACATGACTG
* **
573050 -AATGTATCAATACATTCCTG
1 AAATGTATCGATACATGACTG
573070 AAATGTATCGATACA
1 AAATGTATCGATACA
573085 AAACCACTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (21 bp):
AAATGTATCGATACATGACTG
Found at i:573674 original size:22 final size:23
Alignment explanation
Indices: 573631--573676 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
573621 CTAAAAAATA
573631 CTATTCCATTAGCCTCTAAAAAC
1 CTATTCCATTAGCCTCTAAAAAC
*
573654 CTATTCTCA-TAG-CTCTCAAAAC
1 CTATTC-CATTAGCCTCTAAAAAC
573676 C
1 C
573677 ACCACTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 9 0.43
24 2 0.10
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.30
Consensus pattern (23 bp):
CTATTCCATTAGCCTCTAAAAAC
Found at i:575739 original size:23 final size:23
Alignment explanation
Indices: 575706--575753 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
575696 ACATTATGGG
*
575706 TTGTCCCTATTCTTATTCATCAT
1 TTGTCCATATTCTTATTCATCAT
575729 TTGTCCATATTCTTATTCATCAT
1 TTGTCCATATTCTTATTCATCAT
575752 TT
1 TT
575754 TTCTTGTGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.23, G:0.04, T:0.54
Consensus pattern (23 bp):
TTGTCCATATTCTTATTCATCAT
Found at i:577341 original size:26 final size:27
Alignment explanation
Indices: 577291--577348 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
577281 AAAGTCTTCA
*
577291 AGTTTTAACATTCCTATTAAAAAAAGT
1 AGTTTTAACATTCCCATTAAAAAAAGT
* *
577318 AGTTTTAA-ATTCCCATTGAGAAAAGT
1 AGTTTTAACATTCCCATTAAAAAAAGT
577344 AGTTT
1 AGTTT
577349 CAAGTTCAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (27 bp):
AGTTTTAACATTCCCATTAAAAAAAGT
Found at i:594425 original size:13 final size:13
Alignment explanation
Indices: 594407--594433 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
594397 AAATTATGCT
594407 TTGTATCGATACA
1 TTGTATCGATACA
594420 TTGTATCGATACA
1 TTGTATCGATACA
594433 T
1 T
594434 GCACAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:600676 original size:13 final size:13
Alignment explanation
Indices: 600658--600683 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
600648 ACAATATTCT
600658 TTGTATCGATACA
1 TTGTATCGATACA
600671 TTGTATCGATACA
1 TTGTATCGATACA
600684 AGGGTTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:600816 original size:21 final size:22
Alignment explanation
Indices: 600792--600841 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
600782 ATCAAATCTT
* *
600792 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
600813 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
600835 --TCAAAAT
1 CTTCAAAAT
600842 TATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:605809 original size:13 final size:13
Alignment explanation
Indices: 605791--605815 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
605781 CAAAGATCAG
605791 TGTATCGATACAA
1 TGTATCGATACAA
605804 TGTATCGATACA
1 TGTATCGATACA
605816 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:605881 original size:19 final size:19
Alignment explanation
Indices: 605857--605922 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
605847 AGTAGCTTCA
*
605857 TATGTATTGATACAACACT
1 TATGTATCGATACAACACT
605876 TATGTATCGAT---ACA--
1 TATGTATCGATACAACACT
605890 T-TGTATCGATACAACACT
1 TATGTATCGATACAACACT
605908 TATGTATCGATACAA
1 TATGTATCGATACAA
605923 ATCGTTGACA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
16 6 0.15
18 1 0.03
19 23 0.57
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (19 bp):
TATGTATCGATACAACACT
Found at i:605896 original size:13 final size:13
Alignment explanation
Indices: 605878--605902 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
605868 ACAACACTTA
605878 TGTATCGATACAT
1 TGTATCGATACAT
605891 TGTATCGATACA
1 TGTATCGATACA
605903 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:605901 original size:32 final size:32
Alignment explanation
Indices: 605859--605921 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
605849 TAGCTTCATA
*
605859 TGTATTGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
605891 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
605922 AATCGTTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:608347 original size:20 final size:20
Alignment explanation
Indices: 608322--608394 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
608312 AAAGACAGAT
608322 TGTATCGATACATTGAAAAA
1 TGTATCGATACATTGAAAAA
* * *
608342 TGTATCGATACATTCATACA
1 TGTATCGATACATTGAAAAA
* *
608362 TGTATCAATATATTGAAAAA
1 TGTATCGATACATTGAAAAA
608382 TGTATCGATACAT
1 TGTATCGATACAT
608395 CGGGTAAAAG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATTGAAAAA
Found at i:608423 original size:89 final size:91
Alignment explanation
Indices: 608267--608443 Score: 277
Period size: 89 Copynumber: 2.0 Consensus size: 91
608257 TAATTTTAAC
* *
608267 TACATGTATCGACACATTAAAAAATATATCGATACATCTGGGTAAAAAGACAGATTGTATCGATA
1 TACATGTATCAACACATTAAAAAATATATCGATACATCTGGGTAAAAAGACAGAATGTATCGATA
*
608332 CATTGAAAAATGTATCGATACATTCA
66 CATTAAAAAATGTATCGATACATTCA
* * * *
608358 TACATGTATCAATATATTGAAAAATGTATCGATACATC-GGGT-AAAAGACAGAATGTATCGATA
1 TACATGTATCAACACATTAAAAAATATATCGATACATCTGGGTAAAAAGACAGAATGTATCGATA
608421 CATTAAAAAATGTATCGATACAT
66 CATTAAAAAATGTATCGATACAT
608444 ATGGGTAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
89 42 0.53
90 4 0.05
91 33 0.42
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.29
Consensus pattern (91 bp):
TACATGTATCAACACATTAAAAAATATATCGATACATCTGGGTAAAAAGACAGAATGTATCGATA
CATTAAAAAATGTATCGATACATTCA
Found at i:610938 original size:13 final size:13
Alignment explanation
Indices: 610897--610945 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
610887 CGTTACAAGC
610897 CAATGTATCGATA
1 CAATGTATCGATA
*
610910 CAAT-T-T-G-TT
1 CAATGTATCGATA
610919 C-ATGTATCGATA
1 CAATGTATCGATA
610931 CAATGTATCGATA
1 CAATGTATCGATA
610944 CA
1 CA
610946 TCTTATATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 2 0.07
9 3 0.10
10 2 0.07
11 2 0.07
12 3 0.10
13 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:610940 original size:34 final size:32
Alignment explanation
Indices: 610897--610965 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
610887 CGTTACAAGC
*
610897 CAATGTATCGATACAAT-TTGTTCATGTATCGATA
1 CAATGTATCGATAC-ATCTT-AT-ATGTATCGATA
610931 CAATGTATCGATACATCTTATATGTATCGATA
1 CAATGTATCGATACATCTTATATGTATCGATA
610963 CAA
1 CAA
610966 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 14 0.42
33 3 0.09
34 16 0.48
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (32 bp):
CAATGTATCGATACATCTTATATGTATCGATA
Found at i:617642 original size:3 final size:3
Alignment explanation
Indices: 617634--617664 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
617624 TCTGAGTCAC
*
617634 CAT CAT CAT CAT CAT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
617665 CTTGATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:619284 original size:13 final size:13
Alignment explanation
Indices: 619243--619291 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
619233 CATTACAAGC
619243 CAATGTATCGATA
1 CAATGTATCGATA
*
619256 CAAT-T-T-GGT-
1 CAATGTATCGATA
619265 C-ATGTATCGATA
1 CAATGTATCGATA
619277 CAATGTATCGATA
1 CAATGTATCGATA
619290 CA
1 CA
619292 TCTTGTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 2 0.07
9 2 0.07
10 3 0.10
11 3 0.10
12 2 0.07
13 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:619286 original size:34 final size:32
Alignment explanation
Indices: 619243--619311 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
619233 CATTACAAGC
619243 CAATGTATCGATACAAT-TTGGTCATGTATCGATA
1 CAATGTATCGATAC-ATCTT-GT-ATGTATCGATA
*
619277 CAATGTATCGATACATCTTGTATGTATTGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
619309 CAA
1 CAA
619312 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 13 0.39
33 4 0.12
34 16 0.48
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:624142 original size:26 final size:26
Alignment explanation
Indices: 624090--624162 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
624080 CAAGAAATGG
* *
624090 TTGTCAAGAAAT-TATTATCAAGAACTT
1 TTGTCAAGAAATGT-TTGTCAAAAAC-T
*
624117 TTGTCGAG-AATGTTTGTCAAAAACT
1 TTGTCAAGAAATGTTTGTCAAAAACT
*
624142 TTGTCAAGAAATTTTTGTCAA
1 TTGTCAAGAAATGTTTGTCAA
624163 TACAACCTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 8 0.21
26 23 0.59
27 8 0.21
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (26 bp):
TTGTCAAGAAATGTTTGTCAAAAACT
Found at i:624160 original size:14 final size:14
Alignment explanation
Indices: 624075--624162 Score: 76
Period size: 14 Copynumber: 6.6 Consensus size: 14
624065 CAATTCGCCA
*
624075 TTTGTCAAGAAATG
1 TTTGTCAAGAAATT
*
624089 GTTGTCAAGAAATT
1 TTTGTCAAGAAATT
* * *
624103 ATTATCAAG-AACT
1 TTTGTCAAGAAATT
* *
624116 TTTGTCGAG-AATG
1 TTTGTCAAGAAATT
*
624129 TTTGTCAA-AAA-C
1 TTTGTCAAGAAATT
624141 TTTGTCAAGAAATT
1 TTTGTCAAGAAATT
624155 TTTGTCAA
1 TTTGTCAA
624163 TACAACCTCT
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
12 8 0.14
13 23 0.40
14 27 0.47
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (14 bp):
TTTGTCAAGAAATT
Found at i:624211 original size:28 final size:28
Alignment explanation
Indices: 624171--624520 Score: 316
Period size: 28 Copynumber: 12.4 Consensus size: 28
624161 AATACAACCT
*
624171 CTTTTCAAAGCTCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
624199 CTTTTTAAAGCTCACATGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
*
624228 C-TTTCAAAGCCCACAAGTCAGTGGCGC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
624255 CTTCTCAAAGCCCATAAGTTAGTTGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
624283 CTTCTCAAAACCCACATGTCAGTGGCAAC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-AC
* ** *
624312 C-TTTCAAAGACCACAAGTCAACGACATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
624340 C-TTTCAAAGCCCACAAGTCAGTGGTAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
624367 CTTTTCAAAGCCCATAAGTCAATGGCA-
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
624394 CTTTCTC-AAGCCCATATGTCGGTGGCATC
1 CTTT-TCAAAGCCCACAAGTCAGTGGCA-C
* *
624423 C-TTTCAAAGCCCATAAGTAAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
624450 CTTTTCAAAGCCCACAAGTCAGCGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
624478 CTTTTCAAAGCCCACACAAGTCGGTGGCAA
1 CTTTTCAAAG-CC-CACAAGTCAGTGGCAC
624508 CTTTCTCTAAAGC
1 CTTT-TC-AAAGC
624521 TAATGCAAGT
Statistics
Matches: 263, Mismatches: 45, Indels: 25
0.79 0.14 0.08
Matches are distributed among these distances:
27 29 0.11
28 202 0.77
29 8 0.03
30 17 0.06
31 3 0.01
32 4 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:624480 original size:111 final size:113
Alignment explanation
Indices: 624183--624491 Score: 362
Period size: 112 Copynumber: 2.8 Consensus size: 113
624173 TTTCAAAGCT
* * *
624183 CACAAGTCAGTGGC-ACCTTTTTAAAG-CTCACATGTC-AGTGGCATCCTTTCAAAGCCCACAAG
1 CACATGTCAGTGGCAACC-TTTCAAAGAC-CACAAGTCAAGTGGCATCCTTTCAAAGCCCACAAG
** * * * *
624245 TCAGTGGCGCCTTCTCAAAGCCCATAAGTTAGTTGCACCTTCTCAAAACC
64 TCAGTGGCATCTTTTCAAAGCCCATAAGTCAATGGCACCTTCTCAAAACC
* *
624295 CACATGTCAGTGGCAACCTTTCAAAGACCACAAGTCAA-CGACATCCTTTCAAAGCCCACAAGTC
1 CACATGTCAGTGGCAACCTTTCAAAGACCACAAGTCAAGTGGCATCCTTTCAAAGCCCACAAGTC
* * *
624359 AGTGGTATCTTTTCAAAGCCCATAAGTCAATGGCACTTTCTC-AAGCC
66 AGTGGCATCTTTTCAAAGCCCATAAGTCAATGGCACCTTCTCAAAACC
* * * * *
624406 CATATGTCGGTGGCATCCTTTCAAAGCCCATAAGT-AAGTGGCA-CCTTTTCAAAGCCCACAAGT
1 CACATGTCAGTGGCAACCTTTCAAAGACCACAAGTCAAGTGGCATCC-TTTCAAAGCCCACAAGT
*
624469 CAGCGGCATCTTTTCAAAGCCCA
65 CAGTGGCATCTTTTCAAAGCCCA
624492 CACAAGTCGG
Statistics
Matches: 169, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
110 4 0.02
111 75 0.44
112 85 0.50
113 5 0.03
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (113 bp):
CACATGTCAGTGGCAACCTTTCAAAGACCACAAGTCAAGTGGCATCCTTTCAAAGCCCACAAGTC
AGTGGCATCTTTTCAAAGCCCATAAGTCAATGGCACCTTCTCAAAACC
Found at i:626571 original size:20 final size:20
Alignment explanation
Indices: 626542--626582 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
626532 TAGCCTTTGA
* *
626542 TCATGCATTTTCACTATGTT
1 TCATGAATTTTCAATATGTT
*
626562 TCATGAATTTTTAATATGTT
1 TCATGAATTTTCAATATGTT
626582 T
1 T
626583 GGCATCTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.54
Consensus pattern (20 bp):
TCATGAATTTTCAATATGTT
Found at i:628247 original size:13 final size:13
Alignment explanation
Indices: 628229--628257 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
628219 CAGAGAGCAT
628229 TTGTATCGATACA
1 TTGTATCGATACA
628242 TTGTATCGATACA
1 TTGTATCGATACA
628255 TTG
1 TTG
628258 ATCTTTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:630481 original size:24 final size:26
Alignment explanation
Indices: 630454--630503 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
630444 TAGAAAAATT
630454 TATTCAT-C-GGGGACACTCCAACCC
1 TATTCATCCAGGGGACACTCCAACCC
*
630478 TATTCCTCCGAGGGGACACTCCAACC
1 TATTCATCC-AGGGGACACTCCAACC
630504 TCGTTTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 1 0.05
27 15 0.68
ACGTcount: A:0.24, C:0.38, G:0.18, T:0.20
Consensus pattern (26 bp):
TATTCATCCAGGGGACACTCCAACCC
Found at i:642979 original size:52 final size:52
Alignment explanation
Indices: 642831--642959 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
642821 CGAAATATGA
*
642831 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGTCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
**
642883 AAATTT-TCCTATATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGT-CTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
642935 AAATTTGTCTGCATGTATCGATACA
1 AAATTTGTCTGCATGTATCGATACA
642960 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
52 69 0.99
53 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGTCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:642986 original size:13 final size:13
Alignment explanation
Indices: 642968--642992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
642958 CAAAGATCAG
642968 TGTATCGATACAA
1 TGTATCGATACAA
642981 TGTATCGATACA
1 TGTATCGATACA
642993 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:643055 original size:13 final size:13
Alignment explanation
Indices: 643037--643088 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
643027 AGCTTCATAG
643037 CGATACATTGTAT
1 CGATACATTGTAT
643050 CGATACAACCCTTATGTAT
1 CGATAC-A---TT--GTAT
643069 CGATACATTGTAT
1 CGATACATTGTAT
643082 CGATACA
1 CGATACA
643089 AATCATTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
14 1 0.03
15 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:645790 original size:10 final size:10
Alignment explanation
Indices: 645777--645845 Score: 70
Period size: 10 Copynumber: 6.9 Consensus size: 10
645767 CGTCCTCCAC
645777 AAAAAA-AAA
1 AAAAAACAAA
*
645786 CAAAAACAAA
1 AAAAAACAAA
*
645796 ACAAAACAAA
1 AAAAAACAAA
*
645806 CAAAAGA-AAA
1 -AAAAAACAAA
*
645816 AAAAAAGAAA
1 AAAAAACAAA
645826 AAACAAACAAA
1 AAA-AAACAAA
645837 AAAAAACAA
1 AAAAAACAA
645846 CGACAAAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
9 10 0.20
10 26 0.53
11 13 0.27
ACGTcount: A:0.86, C:0.12, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:645854 original size:1 final size:1
Alignment explanation
Indices: 645777--645842 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
645767 CGTCCTCCAC
* * * * * * * * *
645777 AAAAAAAAACAAAAACAAAACAAAACAAACAAAAGAAAAAAAAAAGAAAAAACAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
645842 A
1 A
645843 CAACGACAAA
Statistics
Matches: 47, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:645854 original size:14 final size:14
Alignment explanation
Indices: 645775--645845 Score: 83
Period size: 14 Copynumber: 5.0 Consensus size: 14
645765 GGCGTCCTCC
645775 ACAAAAAAAAACAAAA
1 ACAAAAAAAAAC--AA
*
645791 ACAAAACAAAACAA
1 ACAAAAAAAAACAA
645805 ACAAAAGAAAAA-AA
1 ACAAAA-AAAAACAA
*
645819 A-AAGAAAAAACAA
1 ACAAAAAAAAACAA
645832 ACAAAAAAAAACAA
1 ACAAAAAAAAACAA
645846 CGACAAAAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
12 5 0.10
13 6 0.12
14 22 0.46
15 4 0.08
16 11 0.23
ACGTcount: A:0.85, C:0.13, G:0.03, T:0.00
Consensus pattern (14 bp):
ACAAAAAAAAACAA
Found at i:645854 original size:37 final size:37
Alignment explanation
Indices: 645775--645854 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 37
645765 GGCGTCCTCC
*
645775 ACAAAAAAAAACAAAAACAAAACAAAACAAACAAAAG
1 ACAAAAAAAAAAAAAAACAAAACAAAACAAACAAAAG
645812 A-AAAAAAAAAGAAAAAAC-AAACAAAA-AAA-AACAACG
1 ACAAAAAAAAA-AAAAAACAAAACAAAACAAACAA-AA-G
645848 ACAAAAA
1 ACAAAAA
645855 GAGTCCGGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
34 2 0.05
35 5 0.13
36 19 0.50
37 12 0.32
ACGTcount: A:0.82, C:0.14, G:0.04, T:0.00
Consensus pattern (37 bp):
ACAAAAAAAAAAAAAAACAAAACAAAACAAACAAAAG
Found at i:647330 original size:34 final size:32
Alignment explanation
Indices: 647287--647611 Score: 296
Period size: 34 Copynumber: 10.0 Consensus size: 32
647277 ATTCCTCACC
*
647287 CTTTTAAAGCCCACAACTCTGTGACACCTTTTT
1 CTTTT-AAGCCCACAACTCTGTGGCACCTTTTT
*
647320 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1 CTTTT--AAGCCCACAACTCTGTGGCACCTTTTT
**
647354 CTTTTCAAAGCCCACAACTCCATGGCACCTTTTT
1 CTTTT--AAGCCCACAACTCTGTGGCACCTTTTT
* * *
647388 CTTTTCAAAGTCTACAACTCCGTGGCACC-----
1 CTTTT--AAGCCCACAACTCTGTGGCACCTTTTT
647417 CTTTTAAGCCCACAACTCTGTGGCACTCTTTTT
1 CTTTTAAGCCCACAACTCTGTGGCAC-CTTTTT
*
647450 CTTTTTAAGTCCACAACTCTGTGGCA-C-----
1 C-TTTTAAGCCCACAACTCTGTGGCACCTTTTT
647477 CTTTTAAGCCCACAACT-TCGTGGCACTCTTTTT
1 CTTTTAAGCCCACAACTCT-GTGGCAC-CTTTTT
647510 CCTTTTAAGCCCACAACTCTGTGGCACTCTTTTT
1 -CTTTTAAGCCCACAACTCTGTGGCAC-CTTTTT
* *
647544 CCTTTTAAGTCCATAACTCTGTGGCACTCTTTTT
1 -CTTTTAAGCCCACAACTCTGTGGCAC-CTTTTT
* * * *
647578 CCTTTTAAGCCTACAAGTCAGTGGCACCCTTTT
1 -CTTTTAAGCCCACAACTCTGTGGCACCTTTTT
647611 C
1 C
647612 AAAAGCCCAT
Statistics
Matches: 255, Mismatches: 19, Indels: 37
0.82 0.06 0.12
Matches are distributed among these distances:
25 1 0.00
26 21 0.08
27 19 0.07
28 2 0.01
29 5 0.02
32 2 0.01
33 11 0.04
34 193 0.76
35 1 0.00
ACGTcount: A:0.21, C:0.32, G:0.12, T:0.36
Consensus pattern (32 bp):
CTTTTAAGCCCACAACTCTGTGGCACCTTTTT
Found at i:647482 original size:26 final size:27
Alignment explanation
Indices: 647452--647508 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 27
647442 CTCTTTTTCT
*
647452 TTTTAAGTCCACAAC-TCTGTGGCAC-C
1 TTTTAAGCCCACAACTTC-GTGGCACTC
647478 TTTTAAGCCCACAACTTCGTGGCACTC
1 TTTTAAGCCCACAACTTCGTGGCACTC
647505 TTTT
1 TTTT
647509 TCCTTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.35
Consensus pattern (27 bp):
TTTTAAGCCCACAACTTCGTGGCACTC
Found at i:647718 original size:30 final size:28
Alignment explanation
Indices: 647584--647706 Score: 183
Period size: 28 Copynumber: 4.3 Consensus size: 28
647574 TTTTCCTTTT
* *
647584 AAGCCTACAAGTCAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC--TTCAA
*
647614 AAGCCCATAAGTCAGTGGCAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTCAA
*
647642 AAGCCCATAAGTCAGTGGCAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTCAA
*
647670 AAGCCCACAAGTCAGTGGCAACATTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTCAA
647698 AAGCCCACA
1 AAGCCCACA
647707 CAAGTTGGTG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 68 0.77
30 20 0.23
ACGTcount: A:0.36, C:0.30, G:0.17, T:0.17
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACCTTCAA
Found at i:647849 original size:49 final size:49
Alignment explanation
Indices: 647726--648232 Score: 414
Period size: 49 Copynumber: 10.7 Consensus size: 49
647716 GGCGTTTTCT
* * * * * *
647726 TTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATT-ATCACCTTCACC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGT-ATCTTCATC
*
647775 TTTAA-ACCAATGTCGCTGGCCTTGAATCAGCACATTGGTATCTTCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGTATCTTCATC
* * *
647823 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG------CACC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGTATCTTCATC
*
647866 TTTAAGTCCAATGTCG-TCAGCCTTGAATCAGCACATTGGTATCTTCATC
1 TTTAAGTCCAATGTCGCT-GGCCTTGAATCAGCACATTGGTATCTTCATC
* * *
647915 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG------CACC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGTATCTTCATC
* *
647958 TTTAAGTCCAATGTC-ATCGGCGTTGAATCAGCACATTGGTATCTTCATC
1 TTTAAGTCCAATGTCGCT-GGCCTTGAATCAGCACATTGGTATCTTCATC
* * * * ** *
648007 TTTAAGTCCAATATCACTGGCCTTGAATCA--ATA-T--AAT-GGCACC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGTATCTTCATC
*
648050 TTTAAGTCCAATGTCGCCGGCCTTGAATCAGCACATTGGTATCTTCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGTATCTTCATC
* * * ** * * * * *
648099 TTTAAGTTCGATATCATTGGCCTTGAATCAGCATATTAGCATCTTTAAC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGTATCTTCATC
* ** * *
648148 ATTCCTAAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTGGCA--TTCTTC
1 -TT--TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGTATCTTCATC
* * *
648198 TTCAAGTCTAATGTCGCTGGCCATGAATCAGCACA
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
648233 GTGTCATTCT
Statistics
Matches: 361, Mismatches: 70, Indels: 56
0.74 0.14 0.11
Matches are distributed among these distances:
42 2 0.01
43 103 0.29
44 2 0.01
45 2 0.01
46 2 0.01
47 29 0.08
48 41 0.11
49 144 0.40
50 7 0.02
52 29 0.08
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (49 bp):
TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGTATCTTCATC
Found at i:647889 original size:43 final size:43
Alignment explanation
Indices: 647726--648088 Score: 264
Period size: 43 Copynumber: 7.9 Consensus size: 43
647716 GGCGTTTTCT
* * **
647726 TTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTATCACCTTCACC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACA-T-T----GGCACC
* * *
647775 TTTAA-ACCAATGTCGCTGGCCTTGAATCAGCACATTGGTATCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGG------CACC
*
647823 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC
* * *
647866 TTTAAGTCCAATGTCG-TCAGCCTTGAATCAGCACATTGGTATCTTCATC
1 TTTAAGTCCAATATCGCT-GGCCTTGAATCAGCACATTGG------CACC
*
647915 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC
* * * *
647958 TTTAAGTCCAATGTC-ATCGGCGTTGAATCAGCACATTGGTATCTTCATC
1 TTTAAGTCCAATATCGCT-GGCCTTGAATCAGCACATTGG------CACC
* ** * *
648007 TTTAAGTCCAATATCACTGGCCTTGAATCAATATAATGGCACC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC
* *
648050 TTTAAGTCCAATGTCGCCGGCCTTGAATCAGCACATTGG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGG
648089 TATCTTCATC
Statistics
Matches: 252, Mismatches: 39, Indels: 52
0.73 0.11 0.15
Matches are distributed among these distances:
42 2 0.01
43 108 0.43
46 1 0.00
47 1 0.00
48 33 0.13
49 105 0.42
50 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (43 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC
Found at i:647917 original size:92 final size:92
Alignment explanation
Indices: 647726--648146 Score: 603
Period size: 92 Copynumber: 4.5 Consensus size: 92
647716 GGCGTTTTCT
* ** *
647726 TTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTATCACCTTCACCTTTAA-ACCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA-T-T----GGCACCTTTAAGTCCAATGTCG
647790 -CTGGCCTTGAATCAGCACATTGGTATCTTCATC
60 TC-GGCCTTGAATCAGCACATTGGTATCTTCATC
*
647823 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTCGTCAGCC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTCGTCGGCC
647888 TTGAATCAGCACATTGGTATCTTCATC
66 TTGAATCAGCACATTGGTATCTTCATC
* *
647915 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTCATCGGCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTCGTCGGCC
647980 TTGAATCAGCACATTGGTATCTTCATC
66 TTGAATCAGCACATTGGTATCTTCATC
* ** * *
648007 TTTAAGTCCAATATCACTGGCCTTGAATCAATATAATGGCACCTTTAAGTCCAATGTCGCCGGCC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTCGTCGGCC
648072 TTGAATCAGCACATTGGTATCTTCATC
66 TTGAATCAGCACATTGGTATCTTCATC
* * ** * *
648099 TTTAAGTTCGATATCATTGGCCTTGAATCAGCATATTAGCATCTTTAA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAA
648147 CATTCCTAAG
Statistics
Matches: 299, Mismatches: 23, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
91 9 0.03
92 253 0.85
93 1 0.00
95 1 0.00
96 1 0.00
97 34 0.11
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.33
Consensus pattern (92 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTCGTCGGCC
TTGAATCAGCACATTGGTATCTTCATC
Found at i:648913 original size:21 final size:21
Alignment explanation
Indices: 648889--648937 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
648879 CAACAATTAG
*
648889 TATCGATGCAAACAGTAAATC
1 TATCAATGCAAACAGTAAATC
*
648910 TATCAATGCAAACAGTAAATG
1 TATCAATGCAAACAGTAAATC
648931 TATCAAT
1 TATCAAT
648938 ACATAAGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (21 bp):
TATCAATGCAAACAGTAAATC
Found at i:648953 original size:19 final size:19
Alignment explanation
Indices: 648929--648991 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
648919 AAACAGTAAA
*
648929 TGTATCAATACATAAGTGT
1 TGTATCGATACATAAGTGT
648948 TGTATCGAT--ATAA----
1 TGTATCGATACATAAGTGT
648961 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
648980 TGTATCGATACA
1 TGTATCGATACA
648992 ATGCTACTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
15 4 0.11
17 4 0.11
19 20 0.54
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:648972 original size:32 final size:32
Alignment explanation
Indices: 648927--648994 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
648917 GCAAACAGTA
*
648927 AATGTATCAATACATAAGTGTTGTATCGATAT
1 AATGTATCAATACATAAGTGTTGTATCGATAC
*
648959 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCAATACATAAGTGTTGTATCGATAC
648991 AATG
1 AATG
648995 CTACTGCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (32 bp):
AATGTATCAATACATAAGTGTTGTATCGATAC
Found at i:649048 original size:13 final size:13
Alignment explanation
Indices: 649030--649057 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
649020 CATTACTCAA
649030 TGTATCGATACAT
1 TGTATCGATACAT
649043 TGTATCGATACAT
1 TGTATCGATACAT
649056 TG
1 TG
649058 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:649051 original size:33 final size:33
Alignment explanation
Indices: 649010--649076 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
649000 GCCAAGGAAA
649010 TGTATCGATACATT-ACTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCAATGTATCGATACAT
**
649043 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
649076 T
1 T
649077 TGGGAATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATGTATCGATACAT
Found at i:653313 original size:13 final size:13
Alignment explanation
Indices: 653295--653319 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
653285 TACCCAAATA
653295 TATCGATACATTG
1 TATCGATACATTG
653308 TATCGATACATT
1 TATCGATACATT
653320 TTACAGCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:653918 original size:32 final size:34
Alignment explanation
Indices: 653877--653939 Score: 103
Period size: 32 Copynumber: 1.9 Consensus size: 34
653867 CAAGTGATTG
653877 AGAGGTTCTATCTTAACCT-TG-AAAGATAGTGT
1 AGAGGTTCTATCTTAACCTATGAAAAGATAGTGT
*
653909 AGAGGTTCTATCTTAGCCTATGAAAAGATAG
1 AGAGGTTCTATCTTAACCTATGAAAAGATAG
653940 GGTTATAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 18 0.64
33 2 0.07
34 8 0.29
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (34 bp):
AGAGGTTCTATCTTAACCTATGAAAAGATAGTGT
Found at i:655645 original size:20 final size:20
Alignment explanation
Indices: 655620--655662 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
655610 CAAGTATAAT
655620 TTCATAGTATTAAGAATTAC
1 TTCATAGTATTAAGAATTAC
*
655640 TTCATAGTATTTAGAATTAC
1 TTCATAGTATTAAGAATTAC
655660 TTC
1 TTC
655663 TCAATTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (20 bp):
TTCATAGTATTAAGAATTAC
Found at i:657143 original size:38 final size:38
Alignment explanation
Indices: 657092--657168 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
657082 CTAAGACCAA
*
657092 AATTAAATCTCCTCAATTTCTAGAAATAATTCACGGAG
1 AATTAAATCTCCTCAATTTCTAGAAAGAATTCACGGAG
* *
657130 AATTACATCTCCTCAATTTCTAGAAAGAATTCATGGAG
1 AATTAAATCTCCTCAATTTCTAGAAAGAATTCACGGAG
657168 A
1 A
657169 TATATGTGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (38 bp):
AATTAAATCTCCTCAATTTCTAGAAAGAATTCACGGAG
Found at i:661069 original size:22 final size:20
Alignment explanation
Indices: 661037--661077 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
661027 CATTTTCCAT
661037 TTAAAAAAAGGTGGAAAATTAG
1 TTAAAAAAA-G-GGAAAATTAG
*
661059 TTAAAATAAGGGAAAATTA
1 TTAAAAAAAGGGAAAATTA
661078 AGGGGATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 1 0.06
22 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (20 bp):
TTAAAAAAAGGGAAAATTAG
Found at i:665491 original size:2 final size:2
Alignment explanation
Indices: 665472--665523 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
665462 ACTACAAAAG
* * *
665472 AT AT AC AT AT AT AA AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
665514 AT AT AT AT AT
1 AT AT AT AT AT
665524 TTGCTGAAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:669750 original size:13 final size:13
Alignment explanation
Indices: 669732--669756 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
669722 CATTTTAATT
669732 TGTATCGATACAA
1 TGTATCGATACAA
669745 TGTATCGATACA
1 TGTATCGATACA
669757 TTGAAACTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:669755 original size:33 final size:33
Alignment explanation
Indices: 669710--669809 Score: 119
Period size: 33 Copynumber: 3.0 Consensus size: 33
669700 ACTTTCACAT
* ** *
669710 AATGTATTGATACATTTTAATTTGTATCGATAC
1 AATGTATCGATACATTGAAACTTGTATCGATAC
*
669743 AATGTATCGATACATTGAAACTTGTATCGATAT
1 AATGTATCGATACATTGAAACTTGTATCGATAC
* * * *
669776 AATGTATCGATATATTGCAACTTATATTGATAC
1 AATGTATCGATACATTGAAACTTGTATCGATAC
669809 A
1 A
669810 TCTGCATGTG
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (33 bp):
AATGTATCGATACATTGAAACTTGTATCGATAC
Found at i:669783 original size:13 final size:13
Alignment explanation
Indices: 669765--669789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
669755 CATTGAAACT
669765 TGTATCGATATAA
1 TGTATCGATATAA
669778 TGTATCGATATA
1 TGTATCGATATA
669790 TTGCAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTATCGATATAA
Found at i:672862 original size:2 final size:2
Alignment explanation
Indices: 672857--672891 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
672847 TTAAGTTTTG
672857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
672892 TTAAAGATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:674697 original size:20 final size:20
Alignment explanation
Indices: 674674--674711 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
674664 ATACATATTC
674674 TTATTAATTATTTAATATAT
1 TTATTAATTATTTAATATAT
674694 TTATTAATTATTTAATAT
1 TTATTAATTATTTAATAT
674712 TAAAATTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATTAATTATTTAATATAT
Found at i:674719 original size:20 final size:20
Alignment explanation
Indices: 674676--674737 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
674666 ACATATTCTT
**
674676 ATTAATTATTTAATA-TATTT
1 ATTAATTATTTAATATTA-AA
674696 ATTAATTATTTAATATTAAA
1 ATTAATTATTTAATATTAAA
* *
674716 ATTACTTTTTTAATATTTAAA
1 ATTAATTATTTAATA-TTAAA
674737 A
1 A
674738 ATATTTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 28 0.78
21 8 0.22
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTAATTATTTAATATTAAA
Found at i:674750 original size:22 final size:20
Alignment explanation
Indices: 674704--674744 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
674694 TTATTAATTA
*
674704 TTTAATATTAAAATTACTTT
1 TTTAATATTAAAAATACTTT
674724 TTTAATATTTAAAAATA-TTT
1 TTTAATA-TTAAAAATACTTT
674744 T
1 T
674745 AATTAAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAATATTAAAAATACTTT
Found at i:675308 original size:30 final size:29
Alignment explanation
Indices: 675272--675341 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 29
675262 AATAAAAGTC
*
675272 TTTAATTTTTAATTTGAATTCAAATAAACT
1 TTTAATTTTTAATTTAAATTCAAATAAA-T
675302 TTTAATTTTTAATTTAAATTCAAATAAAT
1 TTTAATTTTTAATTTAAATTCAAATAAAT
675331 TCTTAATTTTT
1 T-TTAATTTTT
675342 CAACTTCTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 2 0.05
30 36 0.95
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (29 bp):
TTTAATTTTTAATTTAAATTCAAATAAAT
Found at i:675755 original size:13 final size:13
Alignment explanation
Indices: 675732--675777 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
675722 AGATTTGGCG
675732 ATATGTATATTTAT
1 ATAT-TATATTTAT
675746 ATATTATA-TT-T
1 ATATTATATTTAT
* *
675757 ATATTATTTTTAA
1 ATATTATATTTAT
675770 ATATTATA
1 ATATTATA
675778 ACTATATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
11 8 0.30
12 4 0.15
13 11 0.41
14 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
ATATTATATTTAT
Done.