Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, 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: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 1 of 31
Found at i:261 original size:21 final size:21
Alignment explanation
Indices: 223--262 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
213 TCTATTAAAA
* *
223 ACCTTAAATATACTTAAAAGG
1 ACCTTAAAAATACATAAAAGG
*
244 ACCTTAAAAATGCATAAAA
1 ACCTTAAAAATACATAAAA
263 ATTAATGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (21 bp):
ACCTTAAAAATACATAAAAGG
Found at i:570 original size:21 final size:21
Alignment explanation
Indices: 528--573 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
518 TTTAAAAGCA
**
528 TAAAAAATCTATCAAATTCCT
1 TAAAAAATCTATCAAAAACCT
* *
549 TAAAAAATCTCTTAAAAACCT
1 TAAAAAATCTATCAAAAACCT
570 TAAA
1 TAAA
574 TATACTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAAAATCTATCAAAAACCT
Found at i:1198 original size:21 final size:22
Alignment explanation
Indices: 1174--1221 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1164 AAACATTGTT
1174 AAAAAGAGCATAAAAAAACTC-A
1 AAAAAGA-CATAAAAAAACTCTA
* *
1196 AAAAAGACTTAAAAAATCTCTA
1 AAAAAGACATAAAAAAACTCTA
1218 AAAA
1 AAAA
1222 TCGGAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.67, C:0.12, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAAAGACATAAAAAAACTCTA
Found at i:2148 original size:22 final size:21
Alignment explanation
Indices: 2123--2164 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2113 AAAAGAGCAT
*
2123 AAAAATACTTGAAAAAGTCTTA
1 AAAAATACTTCAAAAA-TCTTA
*
2145 AAAAATGCTTCAAAAATCTT
1 AAAAATACTTCAAAAATCTT
2165 TGATAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAAATACTTCAAAAATCTTA
Found at i:5645 original size:21 final size:21
Alignment explanation
Indices: 5619--5659 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5609 NNNNCTTAAA
5619 AACCTT-AAATATACTTAAAAG
1 AACCTTGAAA-ATACTTAAAAG
*
5640 AACCTTGAAAATGCTTAAAA
1 AACCTTGAAAATACTTAAAA
5660 ATCAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.27
Consensus pattern (21 bp):
AACCTTGAAAATACTTAAAAG
Found at i:5888 original size:20 final size:21
Alignment explanation
Indices: 5846--5888 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5836 AAAAGAACGT
*
5846 AAAAATACTTAAAAATTATAA
1 AAAAATACTTAAAAATTAGAA
5867 AAAAAT-CTCTAAAAA-TAGAA
1 AAAAATACT-TAAAAATTAGAA
5887 AA
1 AA
5889 TAATTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.23
Consensus pattern (21 bp):
AAAAATACTTAAAAATTAGAA
Found at i:21293 original size:15 final size:15
Alignment explanation
Indices: 21266--21298 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
21256 ACTTCAATGG
21266 TTAAATCTTGAGATC
1 TTAAATCTTGAGATC
21281 TTAAA-CTTGGAGATC
1 TTAAATCTT-GAGATC
21296 TTA
1 TTA
21299 GGTTTGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (15 bp):
TTAAATCTTGAGATC
Found at i:28839 original size:114 final size:113
Alignment explanation
Indices: 28588--28817 Score: 343
Period size: 114 Copynumber: 2.0 Consensus size: 113
28578 TTGATGGCTG
* * **
28588 GGAAAGCTTCTTATGCCCTGCTAGCCACGGTCTGTCTTTGGAATATGCCTTCTTATGACATCATT
1 GGAAAGCTACTTAT-CCCTGCTGGCCAAAGTCTGTCTTTGGAATATGCCTTCTTATGACATCATT
*
28653 ATAACATCTTAAGTGCACACAGAACTGATTCAAAGTCAGTTTAATGCTT
65 ATAACATCTTAAGTGCACACAAAACTGATTCAAAGTCAGTTTAATGCTT
**
28702 GGAAAGCTACTTATGCCCTGCTGGCCAAAGTCTGTCTTTGGAATATGCCTTCTTATGACATTGTT
1 GGAAAGCTACTTAT-CCCTGCTGGCCAAAGTCTGTCTTTGGAATATGCCTTCTTATGACATCATT
* *
28767 ATAACATCTTAAGTGTACACTGAAAATTGATTCAAAGTCAGTTTAATGCTT
65 ATAACATCTTAAGTGCACAC--AAAACTGATTCAAAGTCAGTTTAATGCTT
28818 TTTTAGTACT
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
114 78 0.74
116 27 0.26
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (113 bp):
GGAAAGCTACTTATCCCTGCTGGCCAAAGTCTGTCTTTGGAATATGCCTTCTTATGACATCATTA
TAACATCTTAAGTGCACACAAAACTGATTCAAAGTCAGTTTAATGCTT
Found at i:39558 original size:48 final size:48
Alignment explanation
Indices: 39500--39614 Score: 167
Period size: 48 Copynumber: 2.4 Consensus size: 48
39490 GCTTATTTGA
* ** *
39500 CATTACGTGATTGAATATTTATTGAGCATAGTATGACTTGTTTGTAGG
1 CATTATGTGATTGAATATTTATTGAGCATACCATAACTTGTTTGTAGG
* *
39548 CATTATGTGATTGGATATTTGTTGAGCATACCATAACTTGTTTGTAGG
1 CATTATGTGATTGAATATTTATTGAGCATACCATAACTTGTTTGTAGG
*
39596 CATTATGTGACTGAATATT
1 CATTATGTGATTGAATATT
39615 ACGTGACTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.42
Consensus pattern (48 bp):
CATTATGTGATTGAATATTTATTGAGCATACCATAACTTGTTTGTAGG
Found at i:39620 original size:15 final size:15
Alignment explanation
Indices: 39597--39629 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
39587 GTTTGTAGGC
*
39597 ATTATGTGACTGAAT
1 ATTACGTGACTGAAT
39612 ATTACGTGACTGAAT
1 ATTACGTGACTGAAT
39627 ATT
1 ATT
39630 TGTTGAGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (15 bp):
ATTACGTGACTGAAT
Found at i:39662 original size:22 final size:22
Alignment explanation
Indices: 39636--39693 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
39626 TATTTGTTGA
*
39636 GCATTGCGTGACTTGTTTGTAG
1 GCATTGCGTGACTTGTTTATAG
* *
39658 GCATTACGTGACTTGTTTATGG
1 GCATTGCGTGACTTGTTTATAG
*
39680 GCAGTGCGTGACTT
1 GCATTGCGTGACTT
39694 TATCTACCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.31, T:0.38
Consensus pattern (22 bp):
GCATTGCGTGACTTGTTTATAG
Found at i:41508 original size:203 final size:202
Alignment explanation
Indices: 41182--41758 Score: 674
Period size: 203 Copynumber: 2.8 Consensus size: 202
41172 GTTAAGCCAG
* * * * *
41182 TACGTGACTGGTTATGTTGGTATAATGTGAGTGGATATTAGACATCGAGTGACTTATTATTAAGT
1 TACGTGACTGGTTATGTTAGCATAATGTGAATGGATATTACACATTGAGTGACTTATTATTAAGT
* * * * *
41247 ATTACGAGACTGGAGGTGCGTGACCTATGCAATTCGTCTCTTGTTTTGAAG-TTTTTGTTCCGTA
66 ATTACGAGACTGGAGGTGCGTGACTTGTGCAATTCATCTCTTGTTTTG-AGCATTTTGTTCAGTA
*** * * * * * *
41311 GTTTGTAGGTGTTGTGTGACTGATTTTTATATATTGCGTGACTTCTTGTTATGTATTGCGTTATA
130 GTTTGTAGGTG-TACATGACTAATTTTTATATATTGCGTGACCTCTTGTTATGTAATACGTAACA
41376 TTGGACCGT
194 TTGGACCGT
* *
41385 TACGTGACTGGTTATGTTAGCGTAATGTGAATGGATATTACACATTGCA-TGACTTATTATTAGG
1 TACGTGACTGGTTATGTTAGCATAATGTGAATGGATATTACACATTG-AGTGACTTATTATTAAG
* * * * *
41449 TATTATGAGACTGGAGGTGTGTGACTTGTGCAACTCATCTATTGTTTTGGGCATTTTGTTCAGTA
65 TATTACGAGACTGGAGGTGCGTGACTTGTGCAATTCATCTCTTGTTTTGAGCATTTTGTTCAGTA
* *
41514 GTTTGTAGGCTGTACATGACTAATTTTTATGTATTGCGTGACCTGTTGTTATGTAATACGTAACA
130 GTTTGTAGG-TGTACATGACTAATTTTTATATATTGCGTGACCTCTTGTTATGTAATACGTAACA
41579 TTGGACCGT
194 TTGGACCGT
* * * ** * *
41588 GACATGACTAGTTATGTTAGCATAATGTGAATGGATATTATGCATTGAGTAACTTATTATTAACT
1 TACGTGACTGGTTATGTTAGCATAATGTGAATGGATATTACACATTGAGTGACTTATTATTAAGT
* * * * * *
41653 ATTGCGAGATTGGAGGTGCGTGACTTGTGCAATTCATTTCTTATTTTAAGCATTTTGCTCTA-TA
66 ATTACGAGACTGGAGGTGCGTGACTTGTGCAATTCATCTCTTGTTTTGAGCATTTTGTTC-AGTA
* * * *
41717 GTTTGTAGGTACTCCAAGACTAATTTTTATGTATTGCGTGAC
130 GTTTGTAGGT-GTACATGACTAATTTTTATATATTGCGTGAC
41759 GTTGGGCTAT
Statistics
Matches: 317, Mismatches: 51, Indels: 12
0.83 0.13 0.03
Matches are distributed among these distances:
202 3 0.01
203 310 0.98
204 4 0.01
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.41
Consensus pattern (202 bp):
TACGTGACTGGTTATGTTAGCATAATGTGAATGGATATTACACATTGAGTGACTTATTATTAAGT
ATTACGAGACTGGAGGTGCGTGACTTGTGCAATTCATCTCTTGTTTTGAGCATTTTGTTCAGTAG
TTTGTAGGTGTACATGACTAATTTTTATATATTGCGTGACCTCTTGTTATGTAATACGTAACATT
GGACCGT
Found at i:42049 original size:181 final size:180
Alignment explanation
Indices: 41579--42087 Score: 553
Period size: 182 Copynumber: 2.8 Consensus size: 180
41569 ATACGTAACA
* * * * * * *
41579 TTGGACCGTGACATGACTAGTTATGTTAGCATAATGTGAATGGATATTATGCATTGAGTAACTTA
1 TTGGGCCGTGACATTACTGGTTATGTTAGCATAATGTGAGT-GATATTACGCATTAAGTGACTTA
** *
41644 TTATTAACTATTGCGAGATTGGAGGTGCGTGACTTGTGCAATTCATTTCTTATTTTAA-GCATTT
65 TTATTAGGTATTGCGAGAATGGAGGTGCGTGACTTGTGCAATTCATTTCTTATTTTAAGGC-TTT
* ** *
41708 TGCTCTA-TAGTTTGT-AGGTACTCCAAGACTAATTTTTATGTATTGCGTGACG
129 TG-TTTACTAGTTT-TAAGAAACTCCAAGACTAATTTTTATATATTGCGTGACG
** * ** *
41760 TTGGGCTATGGCATTTGTTGGTTATGTTGGCATAATGTGAGTGACTATTACGCATTAAGTGACTT
1 TTGGGCCGTGACA-TTACTGGTTATGTTAGCATAATGTGAGTGA-TATTACGCATTAAGTGACTT
* *
41825 ATTATT-GGATATTGCAAGAATGGAGGTGCGTGATTTGTGCAATTCATTTCTTATTTTAAGGCTT
64 ATTATTAGG-TATTGCGAGAATGGAGGTGCGTGACTTGTGCAATTCATTTCTTATTTTAAGGCTT
* * **
41889 TTGTTTACTAGTTTTAAGAAACTGCATGACTGGTTTTTATATATTGCGTGACAG
128 TTGTTTACTAGTTTTAAGAAACTCCAAGACTAATTTTTATATATTGCGTGAC-G
* * *
41943 -TGGGCCGTTACATTACTGGTTATGTTCGCATAATGTGAGTAGATATTACACATTAAGTGACTTA
1 TTGGGCCGTGACATTACTGGTTATGTTAGCATAATGTGAGT-GATATTACGCATTAAGTGACTTA
* * * * * * *
42007 TTATTAGGTATTGCGAGACT-GACGGTGAGTGACTTATGCAATTAATCTCTTGTTTTGAGGCTTT
65 TTATTAGGTATTGCGAGAATGGA-GGTGCGTGACTTGTGCAATTCATTTCTTATTTTAAGGCTTT
*
42071 TGTTCACTAGTTTTAAG
129 TGTTTACTAGTTTTAAG
42088 CATTGCATGA
Statistics
Matches: 274, Mismatches: 44, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
180 2 0.01
181 125 0.46
182 144 0.53
183 3 0.01
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (180 bp):
TTGGGCCGTGACATTACTGGTTATGTTAGCATAATGTGAGTGATATTACGCATTAAGTGACTTAT
TATTAGGTATTGCGAGAATGGAGGTGCGTGACTTGTGCAATTCATTTCTTATTTTAAGGCTTTTG
TTTACTAGTTTTAAGAAACTCCAAGACTAATTTTTATATATTGCGTGACG
Found at i:43103 original size:42 final size:42
Alignment explanation
Indices: 43056--43151 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
43046 CAGTATAGGA
* * *
43056 CATGCCATAATTGTTGTGTTAGAA-GAGGTTCAATTCGATGAC
1 CATGCCATAACTGTTGTG-TAAAAGGAGGTTCAATTCGACGAC
*
43098 CATGCCATAACTGTTGTGTAAAAGGAGGTTCAGTTCGACGAC
1 CATGCCATAACTGTTGTGTAAAAGGAGGTTCAATTCGACGAC
*
43140 CATGCCACAACT
1 CATGCCATAACT
43152 ATTGAATTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 4 0.08
42 44 0.92
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (42 bp):
CATGCCATAACTGTTGTGTAAAAGGAGGTTCAATTCGACGAC
Found at i:43345 original size:42 final size:42
Alignment explanation
Indices: 43286--43370 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
43276 GGGTAAATAC
43286 AAGGGTATCCCATTAATGGATTATTCCCAAGGTAGATATGAT
1 AAGGGTATCCCATTAATGGATTATTCCCAAGGTAGATATGAT
*
43328 AAGGGTATCCCATTAATGGATTATTCCTAAGGTAGATATGAT
1 AAGGGTATCCCATTAATGGATTATTCCCAAGGTAGATATGAT
43370 A
1 A
43371 TCCTTTCAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (42 bp):
AAGGGTATCCCATTAATGGATTATTCCCAAGGTAGATATGAT
Found at i:44866 original size:2 final size:2
Alignment explanation
Indices: 44856--44888 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
44846 TTTTAAGACC
*
44856 AT AT A- AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44889 TAATCTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:48063 original size:23 final size:23
Alignment explanation
Indices: 48037--48091 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
48027 TTCCTCGACA
* * *
48037 AAATAAATAATTTATTAAAAAAT
1 AAATAAATAACTAATTAAAAAAG
48060 AAATAAATAACTAATTAAAAAAG
1 AAATAAATAACTAATTAAAAAAG
*
48083 AAAAAAATA
1 AAATAAATA
48092 CAGAAGCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (23 bp):
AAATAAATAACTAATTAAAAAAG
Found at i:52566 original size:62 final size:64
Alignment explanation
Indices: 52468--52592 Score: 209
Period size: 62 Copynumber: 2.0 Consensus size: 64
52458 ACTTATAAAG
52468 ATGTTATCAGTGGATATGCTATGTTTCTGACTAGGCCTCTA-GTTTTGTATGTTCATGATATGT
1 ATGTTATCAGTGGATATGCTATGTTTCTGACTAGGCCTCTATGTTTTGTATGTTCATGATATGT
* *
52531 ATGTTATCAGTGG-TATGCTATGTTTCTGACTAGGCCTTTATTGTTTTGTATGTTTATGATAT
1 ATGTTATCAGTGGATATGCTATGTTTCTGACTAGGCCTCTA-TGTTTTGTATGTTCATGATAT
52593 TGATCTATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
62 26 0.45
63 13 0.22
64 19 0.33
ACGTcount: A:0.20, C:0.11, G:0.22, T:0.47
Consensus pattern (64 bp):
ATGTTATCAGTGGATATGCTATGTTTCTGACTAGGCCTCTATGTTTTGTATGTTCATGATATGT
Found at i:61864 original size:2 final size:2
Alignment explanation
Indices: 61857--61881 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61847 GGTGTATAGC
61857 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 T
61882 TTCAATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64273 original size:2 final size:2
Alignment explanation
Indices: 64266--64304 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
64256 TCTCAGAAAA
* *
64266 CT CT CT CT TT CT TT 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 CT CT CT CT CT C
64305 ACACACACAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
CT
Found at i:73687 original size:2 final size:2
Alignment explanation
Indices: 73680--73712 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
73670 ACAAGTGTGC
73680 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73713 GTTTACACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:91712 original size:17 final size:20
Alignment explanation
Indices: 91692--91730 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
91682 GATTAATATA
91692 TTTAT-TAAAA-AA-ATAAT
1 TTTATATAAAATAACATAAT
91709 TTTATATAAAATAACATAAT
1 TTTATATAAAATAACATAAT
91729 TT
1 TT
91731 ACAATCTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 2 0.11
20 7 0.37
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTATATAAAATAACATAAT
Found at i:92961 original size:4 final size:4
Alignment explanation
Indices: 92952--92979 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
92942 GGATAGGGGA
92952 AAGG AAGG AAGG AAGG AAGG AAGG AAGG
1 AAGG AAGG AAGG AAGG AAGG AAGG AAGG
92980 GATCTGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (4 bp):
AAGG
Found at i:93850 original size:2 final size:2
Alignment explanation
Indices: 93783--93835 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
93773 NNNNNNNNNN
93783 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
93825 TA TA CA TA TA T
1 TA TA TA TA TA T
93836 TAATTTATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:94221 original size:2 final size:2
Alignment explanation
Indices: 94214--94241 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
94204 AAATTATTCT
94214 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
94242 CACACTCTAT
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):
TA
Found at i:107030 original size:59 final size:59
Alignment explanation
Indices: 106938--107053 Score: 223
Period size: 59 Copynumber: 2.0 Consensus size: 59
106928 TAAGCAACTT
*
106938 TCGTGTAATTATTGAACAAATACATGGACTGTGATGAAAATATTCAAAAACAAATAACG
1 TCGTGTAATTATTGAACAAATACATGGAATGTGATGAAAATATTCAAAAACAAATAACG
106997 TCGTGTAATTATTGAACAAATACATGGAATGTGATGAAAATATTCAAAAACAAATAA
1 TCGTGTAATTATTGAACAAATACATGGAATGTGATGAAAATATTCAAAAACAAATAA
107054 TGTTTTTTTC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (59 bp):
TCGTGTAATTATTGAACAAATACATGGAATGTGATGAAAATATTCAAAAACAAATAACG
Found at i:107056 original size:28 final size:28
Alignment explanation
Indices: 106967--107056 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
106957 ATACATGGAC
106967 TGTGATGAAAATATTCAAAAACAAATAA
1 TGTGATGAAAATATTCAAAAACAAATAA
* * * * * *
106995 CGTCG-TGTAATTATTGAACAAATACATGGAA
1 TGT-GATGAAAATATTCAA-AAACAAAT--AA
107026 TGTGATGAAAATATTCAAAAACAAATAA
1 TGTGATGAAAATATTCAAAAACAAATAA
107054 TGT
1 TGT
107057 TTTTTTCTTT
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
28 17 0.38
29 7 0.16
30 7 0.16
31 14 0.31
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (28 bp):
TGTGATGAAAATATTCAAAAACAAATAA
Found at i:110484 original size:7 final size:7
Alignment explanation
Indices: 110471--110506 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
110461 CATTTTCCTC
110471 TGGCATT
1 TGGCATT
*
110478 CGGCATT
1 TGGCATT
110485 TGGCATT
1 TGGCATT
110492 TGGCATT
1 TGGCATT
110499 TGGCATT
1 TGGCATT
110506 T
1 T
110507 ACAAAGAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.14, C:0.17, G:0.28, T:0.42
Consensus pattern (7 bp):
TGGCATT
Found at i:119624 original size:3 final size:3
Alignment explanation
Indices: 119616--119640 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
119606 AAATGTTTTA
119616 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
119641 GTGAGAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:131334 original size:16 final size:16
Alignment explanation
Indices: 131268--131335 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 16
131258 TTTTTTAATT
*
131268 AATAAAAAAATTAAAA
1 AATAATAAAATTAAAA
131284 AATAATAAAATTATATAATA
1 AATAATAAAA-T-TA-AA-A
*
131304 CTAATTATAAAAATTAAAA
1 --AATAAT-AAAATTAAAA
131323 AATAATAAAATTA
1 AATAATAAAATTA
131336 TTTTTTTATC
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
16 16 0.38
17 6 0.14
18 2 0.05
19 3 0.07
20 3 0.07
21 2 0.05
22 6 0.14
23 4 0.10
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAATAAAATTAAAA
Found at i:132077 original size:32 final size:33
Alignment explanation
Indices: 132015--132085 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
132005 GAAAATTTAT
*
132015 TATTTTCTGTTATTTAGATAAATTATTG-AAAA
1 TATTTTCTGTTATTTAAATAAATTATTGAAAAA
* *
132047 TATTTTCTGTTATTTAAAT-CATTTTATGAAAAA
1 TATTTTCTGTTATTTAAATAAATTAT-TGAAAAA
132080 TATTTT
1 TATTTT
132086 TCATCATAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 4 0.12
32 20 0.59
33 10 0.29
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (33 bp):
TATTTTCTGTTATTTAAATAAATTATTGAAAAA
Found at i:132439 original size:74 final size:74
Alignment explanation
Indices: 132359--132499 Score: 210
Period size: 74 Copynumber: 1.9 Consensus size: 74
132349 AATCTATACT
** *
132359 TATAAATATGTATTAATTAAATGACAATTGTTGAAATATTTTTTATTATAATTATTAGTAAGGTT
1 TATAAATATGTATTAATTAAATGACAATCATTGAAATATTTTTTATTATAATTATTAGTAAGATT
132424 TAAAACTAA
66 TAAAACTAA
* * ** *
132433 TATAAATGTGTATTTATTAAATGATGATCATTGAAATATTTTTTATTATGATTATTAGTAAGATT
1 TATAAATATGTATTAATTAAATGACAATCATTGAAATATTTTTTATTATAATTATTAGTAAGATT
132498 TA
66 TA
132500 TTCCATTTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 59 1.00
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (74 bp):
TATAAATATGTATTAATTAAATGACAATCATTGAAATATTTTTTATTATAATTATTAGTAAGATT
TAAAACTAA
Found at i:132581 original size:19 final size:20
Alignment explanation
Indices: 132557--132609 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
132547 AAAATACTTT
132557 TTTAATTTTAATAGT-ATTG
1 TTTAATTTTAATAGTAATTG
* * *
132576 TTTAATTTAAATATTAATTT
1 TTTAATTTTAATAGTAATTG
132596 TTTAATTTTTAATA
1 TTTAA-TTTTAATA
132610 TTTTAAGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 13 0.46
20 8 0.29
21 7 0.25
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTAATTTTAATAGTAATTG
Found at i:134220 original size:2 final size:2
Alignment explanation
Indices: 134213--134241 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
134203 NNNNNNNNNN
134213 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
134242 TGCTGTTAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:139179 original size:15 final size:13
Alignment explanation
Indices: 139146--139173 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
139136 GTTGTTCATT
139146 CATGATTATCAAG
1 CATGATTATCAAG
139159 CATGATTATCAAG
1 CATGATTATCAAG
139172 CA
1 CA
139174 CATGATCACA
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:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CATGATTATCAAG
Found at i:150790 original size:40 final size:40
Alignment explanation
Indices: 150735--150815 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
150725 CCGTAGAGTA
150735 TGTCCACCTTCCCCTCTGATCCTGTTGTTATGGTCTCCAT
1 TGTCCACCTTCCCCTCTGATCCTGTTGTTATGGTCTCCAT
150775 TGTCCACCTTCCCCTCTGATCCTGTTGTTATGGTCTCCAT
1 TGTCCACCTTCCCCTCTGATCCTGTTGTTATGGTCTCCAT
150815 T
1 T
150816 TTCTGTCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.10, C:0.35, G:0.15, T:0.41
Consensus pattern (40 bp):
TGTCCACCTTCCCCTCTGATCCTGTTGTTATGGTCTCCAT
Found at i:152280 original size:16 final size:16
Alignment explanation
Indices: 152259--152293 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
152249 AATCAAATCG
* *
152259 TTTATTTTAATATTAT
1 TTTATTATAAAATTAT
152275 TTTATTATAAAATTAT
1 TTTATTATAAAATTAT
152291 TTT
1 TTT
152294 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATTATAAAATTAT
Found at i:197518 original size:22 final size:22
Alignment explanation
Indices: 197490--197546 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
197480 TGAAGGCAGC
*
197490 AACAACTTGAATTCTAAAGTCA
1 AACAACTTGAACTCTAAAGTCA
197512 AACAACTTGAACTCTAAAGTCA
1 AACAACTTGAACTCTAAAGTCA
197534 AACAACTTGAACT
1 AACAACTTGAACT
197547 TTATTTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.46, C:0.21, G:0.09, T:0.25
Consensus pattern (22 bp):
AACAACTTGAACTCTAAAGTCA
Found at i:202135 original size:16 final size:16
Alignment explanation
Indices: 202114--202159 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
202104 AATGATCAGA
*
202114 CGTTATTAGTTAAGAT
1 CGTTATTCGTTAAGAT
*
202130 CGTTATTCGTTATGAT
1 CGTTATTCGTTAAGAT
*
202146 CATTATTCGTTAAG
1 CGTTATTCGTTAAG
202160 GTTATAGATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (16 bp):
CGTTATTCGTTAAGAT
Found at i:203761 original size:25 final size:25
Alignment explanation
Indices: 203728--203777 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
203718 TATGCTTGAA
203728 TCAATTTTAAAGTT-TTTTTATGTTTT
1 TCAATTTTAAA-TTATTTTTAT-TTTT
*
203754 TCAA-TTTATATTATTTTTATTTTT
1 TCAATTTTAAATTATTTTTATTTTT
203778 ATTTTGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 6 0.27
25 12 0.55
26 4 0.18
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.68
Consensus pattern (25 bp):
TCAATTTTAAATTATTTTTATTTTT
Found at i:204680 original size:16 final size:17
Alignment explanation
Indices: 204659--204691 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
204649 AAATAAATCT
204659 ATAATA-TAAAAAACAC
1 ATAATATTAAAAAACAC
*
204675 ATAATATTTAAAAACAC
1 ATAATATTAAAAAACAC
204692 CCCTAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAATATTAAAAAACAC
Found at i:218126 original size:3 final size:3
Alignment explanation
Indices: 218120--218145 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
218110 CTCCTCCTCG
218120 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
218146 TTGGGGTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:226013 original size:15 final size:15
Alignment explanation
Indices: 225993--226041 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
225983 GCCAAAGTTC
225993 CCAAAATATTTCCTT
1 CCAAAATATTTCCTT
*
226008 CCAAAATATTTCCCT
1 CCAAAATATTTCCTT
**
226023 CCAAAGCATTT-CTT
1 CCAAAATATTTCCTT
226037 CCAAA
1 CCAAA
226042 CATTTGGGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 7 0.23
15 23 0.77
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.33
Consensus pattern (15 bp):
CCAAAATATTTCCTT
Found at i:228549 original size:51 final size:51
Alignment explanation
Indices: 228312--228552 Score: 292
Period size: 51 Copynumber: 4.7 Consensus size: 51
228302 GTCTGGCTCT
* *
228312 CTGTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTG-GGCCCT-CTTAGAATC
1 CTGTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTGTGCCCCTGC-TAGCATC
* *
228362 CTGTCGGGCTAGCTTGCCCAGGGGCCTGTGCTGTACT-CCCCTGCTAGCATC
1 CTGTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGT-GTGCCCCTGCTAGCATC
* * * ***
228413 CTGTCGAGCTAGCTCACCCAGAGGCCTGTGCTGTACACCCCTGCTAGCATC
1 CTGTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTGTGCCCCTGCTAGCATC
* *
228464 CTGTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTGTGCCCCTGTTGGCATTC
1 CTGTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTGTGCCCCTGCTAGCA-TC
* * *
228516 C-GTCGGGCTGGTTCGCCCATGGGCCTGTGCTGTGTGC
1 CTGTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTGTGC
228553 TCCTAATGGC
Statistics
Matches: 165, Mismatches: 21, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
50 33 0.20
51 128 0.78
52 4 0.02
ACGTcount: A:0.10, C:0.34, G:0.32, T:0.25
Consensus pattern (51 bp):
CTGTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTGTGCCCCTGCTAGCATC
Found at i:228585 original size:51 final size:51
Alignment explanation
Indices: 228314--228600 Score: 147
Period size: 51 Copynumber: 5.6 Consensus size: 51
228304 CTGGCTCTCT
* * * * * * *
228314 GTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTGGGCCCTCT--TAGAATCCT
1 GTCGGGCTGGTTCGCCCAAGGGCCTGTGCTGTGTGCCC-CTAATGGCATCCC
* * * ** * *
228364 GTCGGGCTAGCTT-GCCCAGGGGCCTGTGCTGTACT-CCCCTGCTAGCATCCT
1 GTCGGGCT-GGTTCGCCCAAGGGCCTGTGCTGT-GTGCCCCTAATGGCATCCC
* * * * *** ** * *
228415 GTCGAGCTAGCTCACCC-AGAGGCCTGTGCTGTACACCCCTGCTAGCATCCT
1 GTCGGGCTGGTTCGCCCAAG-GGCCTGTGCTGTGTGCCCCTAATGGCATCCC
* * * ** *
228466 GTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTGTGCCCCTGTTGGCATTCC
1 GTCGGGCTGGTTCGCCCAAGGGCCTGTGCTGTGTGCCCCTAATGGCATCCC
* *
228517 GTCGGGCTGGTTCGCCCATGGGCCTGTGCTGTGTGCTCCTAATGGCATCCC
1 GTCGGGCTGGTTCGCCCAAGGGCCTGTGCTGTGTGCCCCTAATGGCATCCC
* * *
228568 GTTGGGAC-GGCTT-GCCCAAAGGCCTGTGATGTG
1 GTCGGG-CTGG-TTCGCCCAAGGGCCTGTGCTGTG
228601 CACCTTTGTT
Statistics
Matches: 192, Mismatches: 35, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
49 2 0.01
50 32 0.17
51 154 0.80
52 4 0.02
ACGTcount: A:0.11, C:0.32, G:0.32, T:0.25
Consensus pattern (51 bp):
GTCGGGCTGGTTCGCCCAAGGGCCTGTGCTGTGTGCCCCTAATGGCATCCC
Found at i:228591 original size:153 final size:152
Alignment explanation
Indices: 228312--228636 Score: 334
Period size: 153 Copynumber: 2.1 Consensus size: 152
228302 GTCTGGCTCT
*
228312 CTGTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTGGGCCCTCTTAGAATCCTGTCGGGCTAGCTT
1 CTGTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTGGCCCCTCTTAGAATCCTGTCGGGCTAGCTT
** * *
228377 GCCCAGGGGCCTGTGCTGTACTCCCCTGCTAGCATCCTGTCGAGCTAGCTCACCCAGAGGCCTGT
66 GCCCAGGGGCCTGTGCTGTACTCCCCTAATAGCATCCCGTCGAGCTAGCTCACCCAAAGGCCTGT
* *
228442 GCTGTACACCCCTGCTAGCATC
131 GATGTACACCCCTGCTAGCACC
* * * *
228464 CTGTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTGTGCCCCTGTTGGCATTCC-GTCGGGCT-GG
1 CTGTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTG-GCCCCTCTTAG-AATCCTGTCGGGCTAGC
* * * * * * * **
228527 TTCGCCCATGGGCCTGTGCTGT-GTGCTCCTAATGGCATCCCGTTGGGAC-GGCTTGCCCAAAGG
64 TT-GCCCAGGGGCCTGTGCTGTACT-CCCCTAATAGCATCCCGTCGAG-CTAGCTCACCCAAAGG
* ** * * *
228590 CCTGTGATGTGCACCTTTGTTGGCGCC
126 CCTGTGATGTACACCCCTGCTAGCACC
*
228617 CTGTCGGGCTGGCTCGCCCA
1 CTGTCGGGCTAGCTCGCCCA
228637 AGGTCTTGTG
Statistics
Matches: 141, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
152 39 0.28
153 97 0.69
154 5 0.04
ACGTcount: A:0.10, C:0.33, G:0.32, T:0.25
Consensus pattern (152 bp):
CTGTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTGGCCCCTCTTAGAATCCTGTCGGGCTAGCTT
GCCCAGGGGCCTGTGCTGTACTCCCCTAATAGCATCCCGTCGAGCTAGCTCACCCAAAGGCCTGT
GATGTACACCCCTGCTAGCACC
Found at i:230067 original size:48 final size:49
Alignment explanation
Indices: 229964--230069 Score: 162
Period size: 48 Copynumber: 2.2 Consensus size: 49
229954 AGTTTCAGTG
229964 CTTTTGGATCGTAATTCCATGCATATATTGAAAAGATTTGGGTACCATA
1 CTTTTGGATCGTAATTCCATGCATATATTGAAAAGATTTGGGTACCATA
** * *
230013 -AGTTGGATCGTAATTCCATGCATATATTGAAAAGATTTGGG-ATCGTA
1 CTTTTGGATCGTAATTCCATGCATATATTGAAAAGATTTGGGTACCATA
230060 CTTTTGGATC
1 CTTTTGGATC
230070 CCATAAGTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
47 4 0.08
48 46 0.92
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (49 bp):
CTTTTGGATCGTAATTCCATGCATATATTGAAAAGATTTGGGTACCATA
Found at i:234625 original size:15 final size:16
Alignment explanation
Indices: 234609--234646 Score: 62
Period size: 14 Copynumber: 2.5 Consensus size: 16
234599 ATAATATTTT
234609 AATTTATAAAATATTA
1 AATTTATAAAATATTA
234625 AATTT-T-AAATATTA
1 AATTTATAAAATATTA
234639 AATTTATA
1 AATTTATA
234647 TGTCTATAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 13 0.65
15 2 0.10
16 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTATAAAATATTA
Found at i:250377 original size:18 final size:20
Alignment explanation
Indices: 250342--250379 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
250332 TTAAATTATC
*
250342 AATTATATATATTTTTAATA
1 AATTATATATATTATTAATA
250362 AATTATA-A-ATTATTAATA
1 AATTATATATATTATTAATA
250380 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTATATATATTATTAATA
Found at i:250423 original size:15 final size:16
Alignment explanation
Indices: 250400--250437 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
250390 AAATGAAAGA
250400 AAATAATTAATAATTT
1 AAATAATTAATAATTT
250416 AAAT-ATTAATAATTT
1 AAATAATTAATAATTT
*
250431 AATTAAT
1 AAATAAT
250438 ATTTTACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATAATTAATAATTT
Found at i:250474 original size:17 final size:17
Alignment explanation
Indices: 250435--250474 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
250425 TAATTTAATT
250435 AATA-TTTTACTAATCA
1 AATATTTTTACTAATCA
250451 AATTATTTTTACTAATCA
1 AA-TATTTTTACTAATCA
250469 AATATT
1 AATATT
250475 GTAATAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.09
17 6 0.27
18 14 0.64
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATTTTTACTAATCA
Found at i:251773 original size:32 final size:32
Alignment explanation
Indices: 251724--251784 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
251714 AAATTTCAAT
251724 TTTATTTCATCTTTATTTTATTTTCACAAAATA
1 TTTATTTCATCTTTATTTTATTTT-ACAAAATA
*
251757 TTTATTTTAT-TTTATTTTATTTTACAAA
1 TTTATTTCATCTTTATTTTATTTTACAAA
251785 CCGAATTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 5 0.19
32 13 0.48
33 9 0.33
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (32 bp):
TTTATTTCATCTTTATTTTATTTTACAAAATA
Found at i:261594 original size:30 final size:30
Alignment explanation
Indices: 261558--261616 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
261548 ATTATTAGTT
*
261558 ATAAAAATTTATTTGATTCAAAATAAAAAA
1 ATAAAAATTTATTTAATTCAAAATAAAAAA
*
261588 ATAAAAATTTATTTAATTTAAAATAAAAA
1 ATAAAAATTTATTTAATTCAAAATAAAAA
261617 TAATTTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (30 bp):
ATAAAAATTTATTTAATTCAAAATAAAAAA
Found at i:261622 original size:21 final size:22
Alignment explanation
Indices: 261585--261630 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
261575 TCAAAATAAA
*
261585 AAAATAAAAATTTATTTAATTT
1 AAAATAAAAATTAATTTAATTT
261607 AAAATAAAAA-TAATTTAATTT
1 AAAATAAAAATTAATTTAATTT
261628 AAA
1 AAA
261631 TTTTTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATAAAAATTAATTTAATTT
Found at i:273646 original size:8 final size:8
Alignment explanation
Indices: 273633--273657 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
273623 TCTTAGGCCT
273633 ACAGCTTG
1 ACAGCTTG
273641 ACAGCTTG
1 ACAGCTTG
273649 ACAGCTTG
1 ACAGCTTG
273657 A
1 A
273658 TCACTGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (8 bp):
ACAGCTTG
Found at i:319746 original size:40 final size:40
Alignment explanation
Indices: 319702--319782 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
319692 AAAGAAAGAT
319702 TAATGGTTAGAGTTGTGTACTGAATCTTTAAAACATGACA
1 TAATGGTTAGAGTTGTGTACTGAATCTTTAAAACATGACA
319742 TAATGGTTAGAGTTGTGTACTGAATCTTTAAAACATGACA
1 TAATGGTTAGAGTTGTGTACTGAATCTTTAAAACATGACA
319782 T
1 T
319783 GCTTTATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.36
Consensus pattern (40 bp):
TAATGGTTAGAGTTGTGTACTGAATCTTTAAAACATGACA
Found at i:322050 original size:3 final size:3
Alignment explanation
Indices: 322044--322083 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
322034 AATGCTGCTG
322044 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
322084 CTCGCTCCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:324059 original size:12 final size:12
Alignment explanation
Indices: 324022--324072 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
324012 ACCAGGAGCG
*
324022 GGATCTCGACCT
1 GGATCTAGACCT
*
324034 AGATCTAGACCT
1 GGATCTAGACCT
*
324046 GGATCTAGATCT
1 GGATCTAGACCT
324058 GGATCGT-GACCT
1 GGATC-TAGACCT
324070 GGA
1 GGA
324073 CTGCTCTCTC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
12 32 0.97
13 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (12 bp):
GGATCTAGACCT
Found at i:335681 original size:42 final size:41
Alignment explanation
Indices: 335635--335727 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
335625 CGCAAGAGAT
* *
335635 GGACTGTACTTGGCTGACTGT-GGATTGTAACTTGGAGAGGTA
1 GGACTGTACTTGG-TGA-TGTGGGACTATAACTTGGAGAGGTA
* * *
335677 GGACTATAGCTTGGTGATGTGGGACTATAACTTGGTGAGGTT
1 GGACTGTA-CTTGGTGATGTGGGACTATAACTTGGAGAGGTA
335719 GGACTGTAC
1 GGACTGTAC
335728 CCTGGAGAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
41 4 0.09
42 34 0.79
43 5 0.12
ACGTcount: A:0.22, C:0.12, G:0.35, T:0.31
Consensus pattern (41 bp):
GGACTGTACTTGGTGATGTGGGACTATAACTTGGAGAGGTA
Found at i:335701 original size:21 final size:21
Alignment explanation
Indices: 335662--335723 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
335652 CTGTGGATTG
* *
335662 TAACTTGGAGAGGTAGGACTA
1 TAACTTGGTGAGGTGGGACTA
* *
335683 TAGCTTGGTGATGTGGGACTA
1 TAACTTGGTGAGGTGGGACTA
*
335704 TAACTTGGTGAGGTTGGACT
1 TAACTTGGTGAGGTGGGACT
335724 GTACCCTGGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.10, G:0.35, T:0.31
Consensus pattern (21 bp):
TAACTTGGTGAGGTGGGACTA
Found at i:335768 original size:42 final size:42
Alignment explanation
Indices: 335730--335936 Score: 193
Period size: 42 Copynumber: 4.9 Consensus size: 42
335720 GACTGTACCC
* * *
335730 TGGAGAAGTCGGGCTATAAGCTGGTGAAGTAGGGCTGTATGA
1 TGGAGAAGTGGGGCTATAAGCGGGTGAAGTGGGGCTGTATGA
* * * * * *
335772 TGGAGATGTGGGGCTATAGGAGGGTGAGGTTGGGCTGTAGGA
1 TGGAGAAGTGGGGCTATAAGCGGGTGAAGTGGGGCTGTATGA
* * * * * * * *
335814 AGGAGATGTAGGGCTGTATGATGGG-GATGTTGGGCTGTATGA
1 TGGAGAAGTGGGGCTATAAG-CGGGTGAAGTGGGGCTGTATGA
* * *
335856 TGGAGAAGTGGGGCTATATGCCGGTGAAGTGGGGCTGTATGC
1 TGGAGAAGTGGGGCTATAAGCGGGTGAAGTGGGGCTGTATGA
*
335898 TGGTGAAGTGGGGCTATATA-CGGGTGAAGTGGGGCTGTA
1 TGGAGAAGTGGGGCTATA-AGCGGGTGAAGTGGGGCTGTA
335937 GCTAGGTGAA
Statistics
Matches: 135, Mismatches: 27, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
41 2 0.01
42 130 0.96
43 3 0.02
ACGTcount: A:0.21, C:0.08, G:0.46, T:0.25
Consensus pattern (42 bp):
TGGAGAAGTGGGGCTATAAGCGGGTGAAGTGGGGCTGTATGA
Found at i:335785 original size:21 final size:21
Alignment explanation
Indices: 335730--335936 Score: 137
Period size: 21 Copynumber: 9.9 Consensus size: 21
335720 GACTGTACCC
* * * *
335730 TGGAGAAGTCGGGCTATAAGC
1 TGGAGAAGTGGGGCTGTATGA
* *
335751 TGGTGAAGTAGGGCTGTATGA
1 TGGAGAAGTGGGGCTGTATGA
* * *
335772 TGGAGATGTGGGGCTATAGGA
1 TGGAGAAGTGGGGCTGTATGA
* * * * *
335793 GGGTGAGGTTGGGCTGTAGGA
1 TGGAGAAGTGGGGCTGTATGA
* * *
335814 AGGAGATGTAGGGCTGTATGA
1 TGGAGAAGTGGGGCTGTATGA
* * *
335835 TGGGGATGTTGGGCTGTATGA
1 TGGAGAAGTGGGGCTGTATGA
* *
335856 TGGAGAAGTGGGGCTATATGC
1 TGGAGAAGTGGGGCTGTATGA
* * *
335877 CGGTGAAGTGGGGCTGTATGC
1 TGGAGAAGTGGGGCTGTATGA
* *
335898 TGGTGAAGTGGGGCTATAT-A
1 TGGAGAAGTGGGGCTGTATGA
* *
335918 CGGGTGAAGTGGGGCTGTA
1 -TGGAGAAGTGGGGCTGTA
335937 GCTAGGTGAA
Statistics
Matches: 149, Mismatches: 36, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
21 149 1.00
ACGTcount: A:0.21, C:0.08, G:0.46, T:0.25
Consensus pattern (21 bp):
TGGAGAAGTGGGGCTGTATGA
Found at i:335789 original size:84 final size:84
Alignment explanation
Indices: 335692--335873 Score: 193
Period size: 84 Copynumber: 2.2 Consensus size: 84
335682 ATAGCTTGGT
* ** ** * * *
335692 GATGTGGGACTATAACTTGGTGAGGTTGGACTGTACCCTGGAGAAGTCGGGCTATAAGCTGGTGA
1 GATGTGGGGCTATAACAGGGTGAGGTTGGACTGTACCAAGGAGAAGTAGGGCTATAAGATGGGGA
335757 AGTAGGGCTGTATGATGGA
66 AGTAGGGCTGTATGATGGA
** * ** * * *
335776 GATGTGGGGCTATAGGAGGGTGAGGTTGGGCTGTAGGAAGGAGATGTAGGGCTGTATGATGGGGA
1 GATGTGGGGCTATAACAGGGTGAGGTTGGACTGTACCAAGGAGAAGTAGGGCTATAAGATGGGGA
* *
335841 TGTTGGGCTGTATGATGGA
66 AGTAGGGCTGTATGATGGA
*
335860 GAAGTGGGGCTATA
1 GATGTGGGGCTATA
335874 TGCCGGTGAA
Statistics
Matches: 79, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.23, C:0.08, G:0.43, T:0.26
Consensus pattern (84 bp):
GATGTGGGGCTATAACAGGGTGAGGTTGGACTGTACCAAGGAGAAGTAGGGCTATAAGATGGGGA
AGTAGGGCTGTATGATGGA
Found at i:335927 original size:63 final size:62
Alignment explanation
Indices: 335734--335948 Score: 189
Period size: 63 Copynumber: 3.4 Consensus size: 62
335724 GTACCCTGGA
* * *
335734 GAAGTCGGGCTATAAGCTGGTGAAGTAGGGCTGTATGATGGAGATGTGGGGCTATAGGAGGGT
1 GAAGTGGGGCTATAAGCAGGTGAAGTAGGGCTGTATGATGGAGATGTGGGGCTATA-TAGGGT
* * * * * * * * * * * *
335797 GAGGTTGGGCTGTAGGAAGGAGATGTAGGGCTGTATGATGGGGATGTTGGGCTGTATGATGGA
1 GAAGTGGGGCTATAAGCAGGTGAAGTAGGGCTGTATGATGGAGATGTGGGGCTATAT-AGGGT
* * * * * *
335860 GAAGTGGGGCTATATGCCGGTGAAGTGGGGCTGTATGCTGGTGAAGTGGGGCTATATACGGGT
1 GAAGTGGGGCTATAAGCAGGTGAAGTAGGGCTGTATGATGGAGATGTGGGGCTATATA-GGGT
*
335923 GAAGTGGGGCTGT-AGCTAGGTGAAGT
1 GAAGTGGGGCTATAAGC-AGGTGAAGT
335949 TGGACTATAG
Statistics
Matches: 116, Mismatches: 33, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
62 3 0.03
63 113 0.97
ACGTcount: A:0.21, C:0.08, G:0.46, T:0.25
Consensus pattern (62 bp):
GAAGTGGGGCTATAAGCAGGTGAAGTAGGGCTGTATGATGGAGATGTGGGGCTATATAGGGT
Found at i:335945 original size:42 final size:42
Alignment explanation
Indices: 335845--335957 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
335835 TGGGGATGTT
* * *
335845 GGGCTGTATGATGGAGAAGTGGGGCTATATGCCGGTGAAGTG
1 GGGCTGTATGCTGGTGAAGTGGGGCTATATACCGGTGAAGTG
*
335887 GGGCTGTATGCTGGTGAAGTGGGGCTATATACGGGTGAAGTG
1 GGGCTGTATGCTGGTGAAGTGGGGCTATATACCGGTGAAGTG
* *
335929 GGGCTGTA-GCTAGGTGAAGTTGGACTATA
1 GGGCTGTATGCT-GGTGAAGTGGGGCTATA
335958 GCTAGGAGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 3 0.05
42 61 0.95
ACGTcount: A:0.21, C:0.10, G:0.43, T:0.26
Consensus pattern (42 bp):
GGGCTGTATGCTGGTGAAGTGGGGCTATATACCGGTGAAGTG
Found at i:335972 original size:42 final size:40
Alignment explanation
Indices: 335881--336020 Score: 111
Period size: 42 Copynumber: 3.4 Consensus size: 40
335871 ATATGCCGGT
* *
335881 GAAGTGGGGCTGTATGCTGGTGAAGTGGGGCTATA-TACGGGT
1 GAAGTGGGGCTGTA-GCTGGTGAAGTGGGACTATACTA--GGA
*
335923 GAAGTGGGGCTGTAGCTAGGTGAAGTTGGACTATAGCTAGGA
1 GAAGTGGGGCTGTAGCT-GGTGAAGTGGGACTATA-CTAGGA
* * * * * *
335965 GATGTGGGACTATAACTCGGTGAAGTGGGACTGTAACTTGGA
1 GAAGTGGGGCTGTAGCT-GGTGAAGTGGGACTAT-ACTAGGA
* *
336007 GAGGTAGGGCTGTA
1 GAAGTGGGGCTGTA
336021 ACTTGGAGAG
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
41 3 0.04
42 73 0.92
43 1 0.01
44 2 0.03
ACGTcount: A:0.24, C:0.10, G:0.41, T:0.25
Consensus pattern (40 bp):
GAAGTGGGGCTGTAGCTGGTGAAGTGGGACTATACTAGGA
Found at i:335996 original size:21 final size:21
Alignment explanation
Indices: 335860--335993 Score: 114
Period size: 21 Copynumber: 6.4 Consensus size: 21
335850 GTATGATGGA
*
335860 GAAGTGGGGCTATATGC-CGGT
1 GAAGTGGGGCTATA-GCTAGGT
*
335881 GAAGTGGGGCTGTATGCT-GGT
1 GAAGTGGGGCTATA-GCTAGGT
335902 GAAGTGGGGCTATA--TACGGGT
1 GAAGTGGGGCTATAGCTA--GGT
*
335923 GAAGTGGGGCTGTAGCTAGGT
1 GAAGTGGGGCTATAGCTAGGT
* * *
335944 GAAGTTGGACTATAGCTAGGA
1 GAAGTGGGGCTATAGCTAGGT
* * * *
335965 GATGTGGGACTATAACTCGGT
1 GAAGTGGGGCTATAGCTAGGT
335986 GAAGTGGG
1 GAAGTGGG
335994 ACTGTAACTT
Statistics
Matches: 94, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
18 1 0.01
21 91 0.97
23 2 0.02
ACGTcount: A:0.22, C:0.10, G:0.43, T:0.25
Consensus pattern (21 bp):
GAAGTGGGGCTATAGCTAGGT
Found at i:336019 original size:21 final size:21
Alignment explanation
Indices: 335995--336038 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
335985 TGAAGTGGGA
335995 CTGTAACTTGGAGAGGTAGGG
1 CTGTAACTTGGAGAGGTAGGG
336016 CTGTAACTTGGAGAGGTAGGG
1 CTGTAACTTGGAGAGGTAGGG
336037 CT
1 CT
336039 ATAGCTCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.11, G:0.41, T:0.25
Consensus pattern (21 bp):
CTGTAACTTGGAGAGGTAGGG
Found at i:336052 original size:21 final size:21
Alignment explanation
Indices: 335974--336053 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
335964 AGATGTGGGA
* *
335974 CTATAACTCGGTGAAGT-GGG
1 CTATAACTCGGAGAGGTAGGG
* *
335994 ACTGTAACTTGGAGAGGTAGGG
1 -CTATAACTCGGAGAGGTAGGG
* *
336016 CTGTAACTTGGAGAGGTAGGG
1 CTATAACTCGGAGAGGTAGGG
* *
336037 CTATAGCTCGGTGAGGT
1 CTATAACTCGGAGAGGT
336054 CGGAGAATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
21 47 0.94
22 3 0.06
ACGTcount: A:0.24, C:0.12, G:0.39, T:0.25
Consensus pattern (21 bp):
CTATAACTCGGAGAGGTAGGG
Found at i:359123 original size:16 final size:17
Alignment explanation
Indices: 359094--359126 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
359084 AAAAAGAAAA
359094 GAATAGAGTAAAAATAT
1 GAATAGAGTAAAAATAT
359111 GAATAGA-TAAAAATAT
1 GAATAGAGTAAAAATAT
359127 CTTTTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (17 bp):
GAATAGAGTAAAAATAT
Found at i:362356 original size:22 final size:21
Alignment explanation
Indices: 362323--362364 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
362313 CTTCATATTT
*
362323 TTATTATATTAAATATAAAAG
1 TTATTATATTAAAAATAAAAG
*
362344 TTATGTATTTTAAAAATAAAA
1 TTAT-TATATTAAAAATAAAA
362365 CAAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
TTATTATATTAAAAATAAAAG
Found at i:375279 original size:6 final size:6
Alignment explanation
Indices: 375265--375319 Score: 65
Period size: 6 Copynumber: 8.8 Consensus size: 6
375255 GCCAAGCCTC
* * *
375265 TCTCCG TCTCTG TCTCTG TCTCTG TCTCTG TCTCTCTG TCTCTC TCTCTC
1 TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG --TCTCTG TCTCTG TCTCTG
375315 TCTCT
1 TCTCT
375320 CGTGTGTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 39 0.87
8 6 0.13
ACGTcount: A:0.00, C:0.40, G:0.11, T:0.49
Consensus pattern (6 bp):
TCTCTG
Found at i:375320 original size:8 final size:8
Alignment explanation
Indices: 375262--375320 Score: 57
Period size: 8 Copynumber: 7.4 Consensus size: 8
375252 GCAGCCAAGC
375262 CTCTCTC-
1 CTCTCTCT
*
375269 CGTCTCTGT
1 C-TCTCTCT
*
375278 CTCTGTCT
1 CTCTCTCT
*
375286 CTGTCTCT
1 CTCTCTCT
*
375294 GTCTCTCT
1 CTCTCTCT
*
375302 GTCTCTCT
1 CTCTCTCT
375310 CTCTCTCT
1 CTCTCTCT
375318 CTC
1 CTC
375321 GTGTGTTCAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
7 1 0.02
8 40 0.95
9 1 0.02
ACGTcount: A:0.00, C:0.42, G:0.10, T:0.47
Consensus pattern (8 bp):
CTCTCTCT
Found at i:382998 original size:17 final size:17
Alignment explanation
Indices: 382976--383013 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
382966 AAGATTTTCG
*
382976 AATTTAAATTTTATCAA
1 AATTTAAATTTGATCAA
*
382993 AATTTAAATTTGATTAA
1 AATTTAAATTTGATCAA
383010 AATT
1 AATT
383014 AACAAAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
AATTTAAATTTGATCAA
Found at i:383658 original size:13 final size:13
Alignment explanation
Indices: 383640--383665 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
383630 TTTACACAAC
383640 GTGACATATTAAT
1 GTGACATATTAAT
383653 GTGACATATTAAT
1 GTGACATATTAAT
383666 ATATCATAAT
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:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
GTGACATATTAAT
Found at i:397264 original size:4 final size:4
Alignment explanation
Indices: 397255--397279 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
397245 AAAGTGTAAT
397255 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
397280 GGAATAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:411897 original size:2 final size:2
Alignment explanation
Indices: 411892--411930 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
411882 GGGAAAAATA
* *
411892 AG AG AG AG AA AG AG TG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
411931 AGCAGAGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (2 bp):
AG
Found at i:421490 original size:7 final size:8
Alignment explanation
Indices: 421478--421519 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
421468 AATCTCTCCT
421478 TCTTTC-C
1 TCTTTCTC
421485 TCTTTCTC
1 TCTTTCTC
*
421493 TCTCTCTC
1 TCTTTCTC
*
421501 TCTCTCTC
1 TCTTTCTC
*
421509 TCTCTCTC
1 TCTTTCTC
421517 TCT
1 TCT
421520 AAGAGCAGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 6 0.18
8 27 0.82
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (8 bp):
TCTTTCTC
Found at i:421494 original size:2 final size:2
Alignment explanation
Indices: 421484--421519 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
421474 TCCTTCTTTC
*
421484 CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
421520 AAGAGCAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:422676 original size:3 final size:3
Alignment explanation
Indices: 422660--422693 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
422650 GACTTTGATT
422660 TAA T-A TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
422694 ATTCGACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:430849 original size:3 final size:3
Alignment explanation
Indices: 430843--430871 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
430833 CTCCTCCCCC
430843 TCT TCT TC- TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
430872 CTCTCTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:435633 original size:6 final size:6
Alignment explanation
Indices: 435622--435648 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
435612 GGGAAAGGAG
435622 TGGGGA TGGGGA TGGGGA TGGGGA TGG
1 TGGGGA TGGGGA TGGGGA TGGGGA TGG
435649 TAGGAGTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.67, T:0.19
Consensus pattern (6 bp):
TGGGGA
Found at i:449380 original size:17 final size:18
Alignment explanation
Indices: 449350--449385 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
449340 AAAGATTTTA
449350 TTTTATTATAAAAATAAT
1 TTTTATTATAAAAATAAT
*
449368 TTTTTTTAT-AAAATAAT
1 TTTTATTATAAAAATAAT
449385 T
1 T
449386 ATTAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTATTATAAAAATAAT
Found at i:449476 original size:13 final size:14
Alignment explanation
Indices: 449458--449492 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
449448 TATATTTCTT
449458 AATAATTTTTTA-A
1 AATAATTTTTTATA
449471 AATAATTTTTTATTA
1 AATAATTTTTTA-TA
449486 AATAATT
1 AATAATT
449493 AATATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.60
15 8 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATAATTTTTTATA
Found at i:449563 original size:9 final size:9
Alignment explanation
Indices: 449536--449577 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
449526 AACCTCATTC
449536 AATTTTATTCA
1 AATTTT-TT-A
449547 AA-TTTTTA
1 AATTTTTTA
*
449555 ATTTTTTTA
1 AATTTTTTA
449564 AATTTTTTA
1 AATTTTTTA
449573 AATTT
1 AATTT
449578 CACCATCCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 2 0.07
9 21 0.75
10 3 0.11
11 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (9 bp):
AATTTTTTA
Found at i:449573 original size:18 final size:18
Alignment explanation
Indices: 449536--449570 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
449526 AACCTCATTC
449536 AATTTTATTCAAATTTTT
1 AATTTTATTCAAATTTTT
*
449554 AATTTT-TTTAAATTTTT
1 AATTTTATTCAAATTTTT
449571 TAAATTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
AATTTTATTCAAATTTTT
Found at i:451737 original size:59 final size:60
Alignment explanation
Indices: 451669--451782 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
451659 TGTTGTTTTT
* * **
451669 AAAATATATTTTGAATTATTAC-AGCAGTGTATTCACTATATTCATTGATTTTAACCCAA
1 AAAAAATATTTCGAATTACGACAAGCAGTGTATTCACTATATTCATTGATTTTAACCCAA
**
451728 AAAAAATATTTCGAATTACGACAATTAGTGTATTCACTATATTCATTGATTTTAA
1 AAAAAATATTTCGAATTACGACAAGCAGTGTATTCACTATATTCATTGATTTTAA
451783 AAAATTTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 18 0.38
60 30 0.62
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (60 bp):
AAAAAATATTTCGAATTACGACAAGCAGTGTATTCACTATATTCATTGATTTTAACCCAA
Found at i:455832 original size:53 final size:53
Alignment explanation
Indices: 455752--455853 Score: 195
Period size: 53 Copynumber: 1.9 Consensus size: 53
455742 ACTTTCGCTT
*
455752 CTTTGAACATGAAAATGTCTGTACTTCGTTTGTTTAGTCAGTGATGGAGGTGG
1 CTTTGAACATGAAAATGTCTGTACTTCGTTTGTTTACTCAGTGATGGAGGTGG
455805 CTTTGAACATGAAAATGTCTGTACTTCGTTTGTTTACTCAGTGATGGAG
1 CTTTGAACATGAAAATGTCTGTACTTCGTTTGTTTACTCAGTGATGGAG
455854 ATGGTGGTGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (53 bp):
CTTTGAACATGAAAATGTCTGTACTTCGTTTGTTTACTCAGTGATGGAGGTGG
Found at i:482628 original size:33 final size:33
Alignment explanation
Indices: 482586--482651 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
482576 TCATGTCTCT
482586 TTCTTAATTTGGAAGGTGAGTCAGAAAAAGAGG
1 TTCTTAATTTGGAAGGTGAGTCAGAAAAAGAGG
*
482619 TTCTTAATTTGGAAGGTGAGTCAGAATAAGAGG
1 TTCTTAATTTGGAAGGTGAGTCAGAAAAAGAGG
482652 AAAGACTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.06, G:0.30, T:0.29
Consensus pattern (33 bp):
TTCTTAATTTGGAAGGTGAGTCAGAAAAAGAGG
Found at i:486725 original size:13 final size:13
Alignment explanation
Indices: 486707--486734 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
486697 GTATATTATT
486707 ATAAATTAAATTA
1 ATAAATTAAATTA
486720 ATAAATTAAATTA
1 ATAAATTAAATTA
486733 AT
1 AT
486735 TCATAAAAAA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAAATTAAATTA
Found at i:497603 original size:58 final size:58
Alignment explanation
Indices: 497513--497627 Score: 212
Period size: 58 Copynumber: 2.0 Consensus size: 58
497503 CTTGCATAGC
*
497513 AAGCTACAGATAGTATGAATATTTTACTTGTAGAAATCATTCAAAACAATTAAGTGAA
1 AAGCTACAGATAGTATGAATATTTTACTTGTAGAAATCATTCAAAAAAATTAAGTGAA
*
497571 AAGCTACAGATAGTATGAATATTTTACTTGTAGGAATCATTCAAAAAAATTAAGTGA
1 AAGCTACAGATAGTATGAATATTTTACTTGTAGAAATCATTCAAAAAAATTAAGTGA
497628 CAAAAAGGAC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (58 bp):
AAGCTACAGATAGTATGAATATTTTACTTGTAGAAATCATTCAAAAAAATTAAGTGAA
Found at i:500337 original size:14 final size:13
Alignment explanation
Indices: 500296--500328 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
500286 ACGTTTAAAG
500296 TTATATGAATTT-A
1 TTATAT-AATTTAA
500309 TTATATAATTTAA
1 TTATATAATTTAA
500322 TTATATA
1 TTATATA
500329 CCTTTAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (13 bp):
TTATATAATTTAA
Found at i:538705 original size:132 final size:132
Alignment explanation
Indices: 538458--538722 Score: 431
Period size: 132 Copynumber: 2.0 Consensus size: 132
538448 CCAGTTGTTG
538458 AAATCAATAGCCATTACCAAACTAAAGGAAGGAGACACCTGTATAACATAATTCATGAAACTAAA
1 AAATCAATAGCCATTACCAAACTAAAGGAAGGAGACACCTGTATAACATAATTCATGAAACTAAA
* * * * * *
538523 ATCCTGGCCATACTCAATCAAATTGACAGCTATCATCACTAGACCCCTAAAGCAAGGCTGCACTT
66 ATCCTGGCCAGACTCAATCAAATTGACAACCATCATCACTAAACCACTAAAGAAAGGCTGCACTT
538588 CA
131 CA
* *
538590 AAATCAATAGCCATTACCAAACTAAAGGAAGGATACACCTGTATACCATAATTCATGAAACTAAA
1 AAATCAATAGCCATTACCAAACTAAAGGAAGGAGACACCTGTATAACATAATTCATGAAACTAAA
* * *
538655 ATCCTGGCCAGACTTAATCAAATTGACAACCATCATGACTAAACCACTAAAGAAATGCTGCACTT
66 ATCCTGGCCAGACTCAATCAAATTGACAACCATCATCACTAAACCACTAAAGAAAGGCTGCACTT
538720 CA
131 CA
538722 A
1 A
538723 TTTCCAATCA
Statistics
Matches: 122, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 122 1.00
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.22
Consensus pattern (132 bp):
AAATCAATAGCCATTACCAAACTAAAGGAAGGAGACACCTGTATAACATAATTCATGAAACTAAA
ATCCTGGCCAGACTCAATCAAATTGACAACCATCATCACTAAACCACTAAAGAAAGGCTGCACTT
CA
Found at i:551798 original size:15 final size:15
Alignment explanation
Indices: 551778--551812 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
551768 GGTCGATGAA
*
551778 TATTTTCCTTTATTT
1 TATTTTACTTTATTT
*
551793 TATTTTATTTTATTT
1 TATTTTACTTTATTT
551808 TATTT
1 TATTT
551813 GTTTATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTTACTTTATTT
Found at i:551824 original size:4 final size:5
Alignment explanation
Indices: 551786--551812 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
551776 AATATTTTCC
551786 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT
551813 GTTTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:552009 original size:2 final size:2
Alignment explanation
Indices: 552002--552033 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
551992 GTTATGAGTA
552002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
552034 TAGTTTAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:552441 original size:2 final size:2
Alignment explanation
Indices: 552436--552466 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
552426 CCCTTTTTTC
*
552436 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
552467 ATTTAGGAGG
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:557076 original size:71 final size:71
Alignment explanation
Indices: 556960--557098 Score: 269
Period size: 71 Copynumber: 2.0 Consensus size: 71
556950 CTGGAAGTTT
556960 TAAAATCCATGATAGAGCTTGAAATTGACAAACGAAAGGGACGTGCACTTAGTTGAATTTGAACC
1 TAAAATCCATGATAGAGCTTGAAATTGACAAACGAAAGGGACGTGCACTTAGTTGAATTTGAACC
557025 GCTGTA
66 GCTGTA
*
557031 TAAAATCCATGATAGAGCTTGTAATTGACAAACGAAAGGGACGTGCACTTAGTTGAATTTGAACC
1 TAAAATCCATGATAGAGCTTGAAATTGACAAACGAAAGGGACGTGCACTTAGTTGAATTTGAACC
557096 GCT
66 GCT
557099 TTCAGGTCTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (71 bp):
TAAAATCCATGATAGAGCTTGAAATTGACAAACGAAAGGGACGTGCACTTAGTTGAATTTGAACC
GCTGTA
Found at i:564803 original size:15 final size:16
Alignment explanation
Indices: 564772--564807 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
564762 TTAATCAATA
*
564772 AAAAATAATTTTAAAT
1 AAAATTAATTTTAAAT
564788 AAAATTAATTTT-AAT
1 AAAATTAATTTTAAAT
564803 AAAAT
1 AAAAT
564808 CGATCTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATTAATTTTAAAT
Found at i:565372 original size:22 final size:22
Alignment explanation
Indices: 565338--565391 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
565328 TTAGGTATTG
* **
565338 CTTAAAATC-AATCACGTAATA
1 CTTAAAAACTAATCACACAATA
565359 CTTAAAAACTAATCACACAATA
1 CTTAAAAACTAATCACACAATA
*
565381 CCTAAAAACTA
1 CTTAAAAACTA
565392 TAAATGTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.24
Consensus pattern (22 bp):
CTTAAAAACTAATCACACAATA
Found at i:565482 original size:22 final size:22
Alignment explanation
Indices: 565437--565483 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
565427 TTAAACTTAT
* *
565437 AATACTTAAAAACTAGTTACAC
1 AATACCTAAAAACTAGTAACAC
* *
565459 AATACCTAAAAATTAGTAATAC
1 AATACCTAAAAACTAGTAACAC
565481 AAT
1 AAT
565484 GTCTAATAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.15, G:0.04, T:0.28
Consensus pattern (22 bp):
AATACCTAAAAACTAGTAACAC
Found at i:568090 original size:2 final size:2
Alignment explanation
Indices: 568083--568113 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
568073 GTATTAAATT
568083 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
568114 GTATTATTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:570207 original size:2 final size:2
Alignment explanation
Indices: 570200--570238 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
570190 ATGATTAAGT
570200 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
570239 GAGTGCTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:576490 original size:14 final size:14
Alignment explanation
Indices: 576451--576485 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
576441 TTCCTAATTC
*
576451 CAGGCAAATAAAAT
1 CAGGAAAATAAAAT
576465 CAGGAAAATAAAAT
1 CAGGAAAATAAAAT
576479 CATGGAA
1 CA-GGAA
576486 GTAAATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.14
Consensus pattern (14 bp):
CAGGAAAATAAAAT
Found at i:600492 original size:24 final size:24
Alignment explanation
Indices: 600418--600504 Score: 76
Period size: 24 Copynumber: 3.7 Consensus size: 24
600408 TTATAGTACC
600418 ATATTATAATATAATTTTAA-TAA
1 ATATTATAATATAATTTTAATTAA
* **
600441 GATATTATAATCTAATTAAACATT-A
1 -ATATTATAATATAATTTTA-ATTAA
600466 ATATTAT-ATAATAATTTTAATTAA
1 ATATTATAAT-ATAATTTTAATTAA
600490 ATAATT-T-ATATAATT
1 AT-ATTATAATATAATT
600505 ATTTTAACTC
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
23 11 0.21
24 35 0.67
25 5 0.10
26 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (24 bp):
ATATTATAATATAATTTTAATTAA
Found at i:605378 original size:174 final size:175
Alignment explanation
Indices: 604841--605576 Score: 1113
Period size: 174 Copynumber: 4.2 Consensus size: 175
604831 CACTTATTCG
* * *
604841 TACCATCAGCAGTTGAAGCGATTGCCATGGCTGAGCTATGTCTGATTTTGATGGCACCTTCCATG
1 TACCATCAGCAGTTGAAGGGATTGTCATGGCTGAGCTATGTCGGATTTTGATGGCACCTTCCATG
* * * * **
604906 ACTGATCTATTCCGGATCTTGTTGCT-TATGCCCTCGCTCCGATTAAGCTCCTCTTCTGCCTGTT
66 ACTGAGCTATTCCGAATCTTGATGCTCTATACCCTCTTTCCGATTAAGCTCCTCTTCTGCCTGTT
* * * *
604970 GTCGTCTAGCTCGTCGTTCTTCACTCACTGGAAAAAACTTCTTTA
131 TTCGTCTAGCTCTTCGTTCTTCACTCACTGGAAAAACCTTCTTAA
*
605015 TACCATCAGCAGTTGAAGGCATTGTCATGGCTGAGCTATGTCGGATTTTGATGGCACCTTCCATG
1 TACCATCAGCAGTTGAAGGGATTGTCATGGCTGAGCTATGTCGGATTTTGATGGCACCTTCCATG
*
605080 ACTGAGCTATTCCGAATCTTGAT-CTCTATATTCCTCTTTCCGATTAAGCTCCTCTTCTGCCTGT
66 ACTGAGCTATTCCGAATCTTGATGCTCTATA-CCCTCTTTCCGATTAAGCTCCTCTTCTGCCTGT
* * *
605144 TTTCGTCGAGCTCTTCGTTCTTCACTCGCTGGAAAAACCTTCTTGA
130 TTTCGTCTAGCTCTTCGTTCTTCACTCACTGGAAAAACCTTCTTAA
*
605190 TACCATCAGCAGTTGAAGGGATTGTCATGGCTGAGCTATGTCGGATTTTGATAGCACCTTCCATG
1 TACCATCAGCAGTTGAAGGGATTGTCATGGCTGAGCTATGTCGGATTTTGATGGCACCTTCCATG
*
605255 ACTGACCTATTCCGAATCTTGATGCTCT-TACCCTCTTTCCGATTAAGCTCCTCTTCTGCCTGTT
66 ACTGAGCTATTCCGAATCTTGATGCTCTATACCCTCTTTCCGATTAAGCTCCTCTTCTGCCTGTT
* *
605319 TTCCTCTAGCTCTTCGTTCTTCACTCGCTGGAAAAACCTTCTTAA
131 TTCGTCTAGCTCTTCGTTCTTCACTCACTGGAAAAACCTTCTTAA
* * *
605364 CACCATCAGCAGTTGAAGGGATCGTCATGGCTGAGCTATGTCGGATTCTGATGGCACCTTCCATG
1 TACCATCAGCAGTTGAAGGGATTGTCATGGCTGAGCTATGTCGGATTTTGATGGCACCTTCCATG
605429 ACTGAGCTATTCCGAATCTTGATGCTCT-TACCCTCTTTCCGATTAAGCTCCTCTTCTGCCTGTT
66 ACTGAGCTATTCCGAATCTTGATGCTCTATACCCTCTTTCCGATTAAGCTCCTCTTCTGCCTGTT
* **
605493 TTCGTCTAGCTCTTCGTTCCTCACTCACTGGAAAAAACC-TCTTGG
131 TTCGTCTAGCTCTTCGTTCTTCACTCACTGG-AAAAACCTTCTTAA
* * *
605538 TACCATCAACAGCTGATGAAGCGATTGCCATGGCTGAGC
1 TACCATCAGCAG-T--TGAAGGGATTGTCATGGCTGAGC
605577 CAGGCATGGT
Statistics
Matches: 516, Mismatches: 39, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
173 2 0.00
174 325 0.63
175 165 0.32
176 4 0.01
177 20 0.04
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.34
Consensus pattern (175 bp):
TACCATCAGCAGTTGAAGGGATTGTCATGGCTGAGCTATGTCGGATTTTGATGGCACCTTCCATG
ACTGAGCTATTCCGAATCTTGATGCTCTATACCCTCTTTCCGATTAAGCTCCTCTTCTGCCTGTT
TTCGTCTAGCTCTTCGTTCTTCACTCACTGGAAAAACCTTCTTAA
Found at i:605531 original size:349 final size:348
Alignment explanation
Indices: 604841--605576 Score: 1154
Period size: 349 Copynumber: 2.1 Consensus size: 348
604831 CACTTATTCG
* *
604841 TACCATCAGCAGTTGAAGCGATTGCCATGGCTGAGCTATGTCTGATTTTGATGGCACCTTCCATG
1 TACCATCAGCAGTTGAAGCGATTGCCATGGCTGAGCTATGTCGGATTTTGATAGCACCTTCCATG
* * * *
604906 ACTGATCTATTCCGGATCTTGTTGCTTATGCCCTCGCTCCGATTAAGCTCCTCTTCTGCCTGTTG
66 ACTGACCTATTCCGAATCTTGATGCTTATACCCTCGCTCCGATTAAGCTCCTCTTCTGCCTGTTG
* * *
604971 TCGTCTAGCTCGTCGTTCTTCACTCACTGGAAAAAACTTCTTTATACCATCAGCAGTTGAAGGCA
131 TCCTCTAGCTCGTCGTTCTTCACTCACTGGAAAAAACTTCTTAACACCATCAGCAGTTGAAGGCA
* *
605036 TTGTCATGGCTGAGCTATGTCGGATTTTGATGGCACCTTCCATGACTGAGCTATTCCGAATCTTG
196 TCGTCATGGCTGAGCTATGTCGGATTCTGATGGCACCTTCCATGACTGAGCTATTCCGAATCTTG
* *
605101 ATCTCTATATTCCTCTTTCCGATTAAGCTCCTCTTCTGCCTGTTTTCGTCGAGCTCTTCGTTCTT
261 ATCTCTATATCCCTCTTTCCGATTAAGCTCCTCTTCTGCCTGTTTTCGTCGAGCTCTTCGTTCCT
*
605166 CACTCGCTGGAAAAACCTTCTTGA
326 CACTCACTGGAAAAACC-TCTTGA
* *
605190 TACCATCAGCAGTTGAAGGGATTGTCATGGCTGAGCTATGTCGGATTTTGATAGCACCTTCCATG
1 TACCATCAGCAGTTGAAGCGATTGCCATGGCTGAGCTATGTCGGATTTTGATAGCACCTTCCATG
**
605255 ACTGACCTATTCCGAATCTTGATGCTCT-TACCCTCTTTCCGATTAAGCTCCTCTTCTGCCTGTT
66 ACTGACCTATTCCGAATCTTGATGCT-TATACCCTCGCTCCGATTAAGCTCCTCTTCTGCCTGTT
* * * * *
605319 TTCCTCTAGCTCTTCGTTCTTCACTCGCTGGAAAAACCTTCTTAACACCATCAGCAGTTGAAGGG
130 GTCCTCTAGCTCGTCGTTCTTCACTCACTGGAAAAAACTTCTTAACACCATCAGCAGTTGAAGGC
605384 ATCGTCATGGCTGAGCTATGTCGGATTCTGATGGCACCTTCCATGACTGAGCTATTCCGAATCTT
195 ATCGTCATGGCTGAGCTATGTCGGATTCTGATGGCACCTTCCATGACTGAGCTATTCCGAATCTT
*
605449 GATGCTCT-TA-CCCTCTTTCCGATTAAGCTCCTCTTCTGCCTGTTTTCGTCTAGCTCTTCGTTC
260 GAT-CTCTATATCCCTCTTTCCGATTAAGCTCCTCTTCTGCCTGTTTTCGTCGAGCTCTTCGTTC
*
605512 CTCACTCACTGGAAAAAACCTCTTGG
324 CTCACTCACTGG-AAAAACCTCTTGA
*
605538 TACCATCAACAGCTGATGAAGCGATTGCCATGGCTGAGC
1 TACCATCAGCAG-T--TGAAGCGATTGCCATGGCTGAGC
605577 CAGGCATGGT
Statistics
Matches: 353, Mismatches: 28, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
348 77 0.22
349 250 0.71
350 5 0.01
351 21 0.06
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.34
Consensus pattern (348 bp):
TACCATCAGCAGTTGAAGCGATTGCCATGGCTGAGCTATGTCGGATTTTGATAGCACCTTCCATG
ACTGACCTATTCCGAATCTTGATGCTTATACCCTCGCTCCGATTAAGCTCCTCTTCTGCCTGTTG
TCCTCTAGCTCGTCGTTCTTCACTCACTGGAAAAAACTTCTTAACACCATCAGCAGTTGAAGGCA
TCGTCATGGCTGAGCTATGTCGGATTCTGATGGCACCTTCCATGACTGAGCTATTCCGAATCTTG
ATCTCTATATCCCTCTTTCCGATTAAGCTCCTCTTCTGCCTGTTTTCGTCGAGCTCTTCGTTCCT
CACTCACTGGAAAAACCTCTTGA
Found at i:606506 original size:20 final size:20
Alignment explanation
Indices: 606483--606520 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
606473 AGAGTGTGTC
606483 GAAAACAAG-AACAAGAAATG
1 GAAAAC-AGCAACAAGAAATG
*
606503 GAAAGCAGCAACAAGAAA
1 GAAAACAGCAACAAGAAA
606521 GGTCTGCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.63, C:0.13, G:0.21, T:0.03
Consensus pattern (20 bp):
GAAAACAGCAACAAGAAATG
Found at i:648332 original size:3 final size:3
Alignment explanation
Indices: 648324--648361 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
648314 TTGATGTTGC
*
648324 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT GCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
648362 CTCAAGCTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:649845 original size:27 final size:27
Alignment explanation
Indices: 649787--649845 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
649777 GAAATGTCTT
*
649787 AAAATAAATTTTGTATTTTTTATATTA
1 AAAATAAATTTTGTATTTTTCATATTA
*
649814 CAAATAAATTTT-TCATATTTTCATA-TA
1 AAAATAAATTTTGT-AT-TTTTCATATTA
649841 AAAAT
1 AAAAT
649846 TAAAATCTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 1 0.04
27 19 0.70
28 7 0.26
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAATAAATTTTGTATTTTTCATATTA
Found at i:655085 original size:45 final size:45
Alignment explanation
Indices: 655000--655087 Score: 104
Period size: 45 Copynumber: 2.0 Consensus size: 45
654990 GTTATACGCT
* * *
655000 ATATACAAAAATATGTTACATACTATGGTTAAGTTGTTACACGTC
1 ATATACAAAAATATGTTACACACTATGATTAAGTTATTACACGTC
* ** * *
655045 ATATACGAAAATATGTTACACGTTATTATTAGGTTATTACACG
1 ATATACAAAAATATGTTACACACTATGATTAAGTTATTACACG
655088 CACAAAAACA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (45 bp):
ATATACAAAAATATGTTACACACTATGATTAAGTTATTACACGTC
Found at i:667293 original size:39 final size:40
Alignment explanation
Indices: 667221--667335 Score: 214
Period size: 39 Copynumber: 2.9 Consensus size: 40
667211 ACAATATTTT
*
667221 CTAGATAGCCAAATCCATTTAGGAGTTCATCACTTGTTTC
1 CTAGATAGACAAATCCATTTAGGAGTTCATCACTTGTTTC
667261 CTAGATAGACAAATCCA-TTAGGAGTTCATCACTTGTTTC
1 CTAGATAGACAAATCCATTTAGGAGTTCATCACTTGTTTC
667300 CTAGATAGACAAATCCATTTAGGAGTTCATCACTTG
1 CTAGATAGACAAATCCATTTAGGAGTTCATCACTTG
667336 CCTTCTTGAC
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
39 39 0.53
40 34 0.47
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (40 bp):
CTAGATAGACAAATCCATTTAGGAGTTCATCACTTGTTTC
Found at i:677510 original size:22 final size:22
Alignment explanation
Indices: 677467--677516 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
677457 CGTTACGTCT
* * *
677467 TTAGTTTGTAGTTATTATGTGA
1 TTAGATTGTAGATATTACGTGA
*
677489 TTAGATTGTAGATATTGCGTGA
1 TTAGATTGTAGATATTACGTGA
677511 TT-GATT
1 TTAGATT
677517 TTTAAGCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.50
Consensus pattern (22 bp):
TTAGATTGTAGATATTACGTGA
Found at i:677597 original size:22 final size:22
Alignment explanation
Indices: 677557--677599 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
677547 AAAAACTAGT
**
677557 CTAATCACGTAATGTTTAAAAG
1 CTAATCACGTAATACTTAAAAG
*
677579 CTAATCATGTAATACTTAAAA
1 CTAATCACGTAATACTTAAAA
677600 ACTAGTTACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (22 bp):
CTAATCACGTAATACTTAAAAG
Found at i:677961 original size:16 final size:16
Alignment explanation
Indices: 677928--677957 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
677918 TTGAGACGTG
677928 AATGTGAATTTTATTA
1 AATGTGAATTTTATTA
677944 AATGT-AATTTTATT
1 AATGTGAATTTTATT
677958 TAAAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (16 bp):
AATGTGAATTTTATTA
Found at i:688634 original size:3 final size:3
Alignment explanation
Indices: 688626--688654 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
688616 TCATTAGTTT
688626 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
688655 TGCATGATTT
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:689577 original size:20 final size:20
Alignment explanation
Indices: 689554--689597 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
689544 AAAATTTATA
*
689554 AAAAAACAAAA-TAACTCTTC
1 AAAAAACAAAACTAAATC-TC
*
689574 AAAAAATAAAACTAAATCTC
1 AAAAAACAAAACTAAATCTC
689594 AAAA
1 AAAA
689598 TTAATGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.18
Consensus pattern (20 bp):
AAAAAACAAAACTAAATCTC
Found at i:717420 original size:24 final size:24
Alignment explanation
Indices: 717389--717454 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
717379 GAAGCCTGTC
*
717389 AAGGAGAAGAAACCGAGAGCGCCG
1 AAGGAGAAGAAACCGAAAGCGCCG
**
717413 AAGGAGAAGAAACCGAAAGTTCCG
1 AAGGAGAAGAAACCGAAAGCGCCG
717437 AAGGAGAAGAAACCGAAA
1 AAGGAGAAGAAACCGAAA
717455 CAGCCAAAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.48, C:0.17, G:0.32, T:0.03
Consensus pattern (24 bp):
AAGGAGAAGAAACCGAAAGCGCCG
Found at i:717464 original size:24 final size:23
Alignment explanation
Indices: 717389--717464 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 23
717379 GAAGCCTGTC
*
717389 AAGGAGAAGAAACCGAGAGCGCCG
1 AAGGAGAAGAAACCGA-AACGCCG
717413 AAGGAGAAGAAACCGAAA-GTTCCG
1 AAGGAGAAGAAACCGAAACG--CCG
*
717437 AAGGAGAAGAAACCGAAACAGCCA
1 AAGGAGAAGAAACCGAAAC-GCCG
717461 AAGG
1 AAGG
717465 CCGCTGCACA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
22 1 0.02
23 1 0.02
24 43 0.93
26 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.32, T:0.03
Consensus pattern (23 bp):
AAGGAGAAGAAACCGAAACGCCG
Found at i:730215 original size:3 final size:3
Alignment explanation
Indices: 730202--730253 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
730192 CAAGAGGAAT
* *
730202 GAA GGA GAA GAA GACA -AA CGAA G-A GAA GGA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GA-A GAA -GAA GAA GAA GAA GAA GAA GAA GAA GAA
730247 GAA GAA G
1 GAA GAA G
730254 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 3 0.07
3 35 0.85
4 3 0.07
ACGTcount: A:0.60, C:0.04, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Done.