Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007836.1 Hibiscus syriacus cultivar Beakdansim tig00110185_pilon, 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: 183289
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5521 original size:40 final size:39
Alignment explanation
Indices: 5460--5545 Score: 136
Period size: 40 Copynumber: 2.2 Consensus size: 39
5450 AGTAGCCACG
* *
5460 TTGGTGCTAAAGCTTATGCATCCTAGGAGCCTTGAGGGC
1 TTGGTTCTAAAGCTTACGCATCCTAGGAGCCTTGAGGGC
*
5499 TTGGTTCTAAAAGCTTCCGCATCCTAGGAGCCTTGAGGGC
1 TTGGTTCT-AAAGCTTACGCATCCTAGGAGCCTTGAGGGC
5539 TTGGTTC
1 TTGGTTC
5546 CAACTTTGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
39 7 0.16
40 36 0.84
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (39 bp):
TTGGTTCTAAAGCTTACGCATCCTAGGAGCCTTGAGGGC
Found at i:12135 original size:29 final size:28
Alignment explanation
Indices: 12101--12183 Score: 121
Period size: 29 Copynumber: 2.9 Consensus size: 28
12091 GCGACCTCCT
*
12101 AGGTCGCCATGCACTCCGGGCGACCAAGG
1 AGGTCGCCATGCACGCC-GGCGACCAAGG
*
12130 ATGTCGCCATGCACGCTCGGCGACCAAGG
1 AGGTCGCCATGCACGC-CGGCGACCAAGG
12159 AGGTCGCCATGCACGCCCGGCGACC
1 AGGTCGCCATGCACG-CCGGCGACC
12184 TTGTCTCCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 47 0.96
30 2 0.04
ACGTcount: A:0.19, C:0.37, G:0.33, T:0.11
Consensus pattern (28 bp):
AGGTCGCCATGCACGCCGGCGACCAAGG
Found at i:12374 original size:29 final size:29
Alignment explanation
Indices: 12327--12383 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
12317 GGGTTAAAAG
*
12327 CTTGGTCGCCGGGCATGCATGGCGACCTC
1 CTTGGTCGCCCGGCATGCATGGCGACCTC
12356 CTTGGTCGCCCGG-AGTGCATGGCGACCT
1 CTTGGTCGCCCGGCA-TGCATGGCGACCT
12384 ATGGGTTGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.11, C:0.33, G:0.35, T:0.21
Consensus pattern (29 bp):
CTTGGTCGCCCGGCATGCATGGCGACCTC
Found at i:17263 original size:9 final size:8
Alignment explanation
Indices: 17232--17261 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
17222 ACAGAAGCTC
17232 AAAAAAGA
1 AAAAAAGA
17240 AAAAAAGA
1 AAAAAAGA
17248 AAAAAAGA
1 AAAAAAGA
17256 AAAAAA
1 AAAAAA
17262 AGGGCATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:41379 original size:58 final size:56
Alignment explanation
Indices: 41289--41403 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 56
41279 ATCCTAGGAG
* *
41289 AGTTTGTGAATGATACTAGAAGTCTGTTAAGAGAACAGTTTCAAGATCAGAGAGTGTT
1 AGTTTGTGAAGGATACTAGAAGTCTGTTAAGAGAACAG--TCAAGATCAAAGAGTGTT
*
41347 AGTTTGTGAAGGATACTAGAAGTCTGTTAAGAGAACCGTCAAGATCAAAGAGTGTT
1 AGTTTGTGAAGGATACTAGAAGTCTGTTAAGAGAACAGTCAAGATCAAAGAGTGTT
41403 A
1 A
41404 AAGAAAACAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
56 18 0.33
58 36 0.67
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.29
Consensus pattern (56 bp):
AGTTTGTGAAGGATACTAGAAGTCTGTTAAGAGAACAGTCAAGATCAAAGAGTGTT
Found at i:42904 original size:24 final size:24
Alignment explanation
Indices: 42877--42991 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
42867 TCGATTTGAT
*
42877 TTCTGATCTGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
42901 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
* *
42925 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
* * *
42949 TTATGATATGTTACTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
*
42973 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
42992 GTGAATTATG
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 78 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:42929 original size:12 final size:12
Alignment explanation
Indices: 42892--42930 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
42882 ATCTGATACT
42892 TGACATGGATTC
1 TGACATGGATTC
*
42904 TGATAT-GATATC
1 TGACATGGAT-TC
42916 TGACATGGATTC
1 TGACATGGATTC
42928 TGA
1 TGA
42931 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:42929 original size:48 final size:48
Alignment explanation
Indices: 42877--43008 Score: 167
Period size: 48 Copynumber: 2.8 Consensus size: 48
42867 TCGATTTGAT
*
42877 TTCTGATCTGATACTTGACATGGATTCTGATATGATA-TCTGACATGGA
1 TTCTGATCTGATACTTGACATGGATTATGATATGATACT-TGACATGGA
* * *
42925 TTCTGATCTGATACTTGACTTGGATTATGATATGTTACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGATTATGATATGATACTTGACATGGA
* * * * *
42973 TTTTGATATGATACTTGACGTGAATTATGATTTGAT
1 TTCTGATCTGATACTTGACATGGATTATGATATGAT
43009 TTTTGATATA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
48 72 0.99
49 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (48 bp):
TTCTGATCTGATACTTGACATGGATTATGATATGATACTTGACATGGA
Found at i:43003 original size:24 final size:24
Alignment explanation
Indices: 42880--43008 Score: 143
Period size: 24 Copynumber: 5.4 Consensus size: 24
42870 ATTTGATTTC
* *
42880 TGATCTGATACTTGACATGGATTC
1 TGATATGATACTTGACATGGATTA
*
42904 TGATATGATA-TCTGACATGGATTC
1 TGATATGATACT-TGACATGGATTA
* *
42928 TGATCTGATACTTGACTTGGATTA
1 TGATATGATACTTGACATGGATTA
* * *
42952 TGATATGTTACTTGACCTGGATTT
1 TGATATGATACTTGACATGGATTA
* *
42976 TGATATGATACTTGACGTGAATTA
1 TGATATGATACTTGACATGGATTA
*
43000 TGATTTGAT
1 TGATATGAT
43009 TTTTGATATA
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.01
24 88 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTA
Found at i:46231 original size:15 final size:15
Alignment explanation
Indices: 46211--46239 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46201 TGGTCGACCG
46211 AACCGAATTAATTAT
1 AACCGAATTAATTAT
46226 AACCGAATTAATTA
1 AACCGAATTAATTA
46240 AACTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (15 bp):
AACCGAATTAATTAT
Found at i:46667 original size:183 final size:184
Alignment explanation
Indices: 46357--46743 Score: 620
Period size: 183 Copynumber: 2.1 Consensus size: 184
46347 TTTTCTAATT
* * * *
46357 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
*
46421 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* *
46486 GGATCTTAAATTATTAATTGAGCTTTAAATGGTTTGGGCTT-AGACCATATGTTA
131 GGATCTTAAATTATTAATTGAGCTTTAAATGATTTAGG-TTGAGACCATATGTTA
46540 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAAATAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAAATAATTTAAATAATATATAA
* *
46604 TTATAAAATAAAAAATTTATAT-ATTTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
* * *
46668 TGGATCTTAAATTATTAATTGGGTTTTAAATGATTTAGGTTGAGCCCATATGTTA
130 TGGATCTTAAATTATTAATTGAGCTTTAAATGATTTAGGTTGAGACCATATGTTA
46723 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
46744 AAAATTTAAT
Statistics
Matches: 189, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
182 2 0.01
183 122 0.65
184 65 0.34
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
GGATCTTAAATTATTAATTGAGCTTTAAATGATTTAGGTTGAGACCATATGTTA
Found at i:46780 original size:9 final size:9
Alignment explanation
Indices: 46749--46782 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
46739 TATTTAAAAT
46749 TTAATTTCGG
1 TTAA-TTCGG
*
46759 TTATTTCGG
1 TTAATTCGG
46768 TTAATTCGG
1 TTAATTCGG
46777 TTAATT
1 TTAATT
46783 AACCGAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 19 0.86
10 3 0.14
ACGTcount: A:0.21, C:0.09, G:0.18, T:0.53
Consensus pattern (9 bp):
TTAATTCGG
Found at i:57885 original size:2 final size:2
Alignment explanation
Indices: 57878--57902 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57868 CTCAGTCATT
57878 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
57903 GCAAATGATA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:58667 original size:6 final size:6
Alignment explanation
Indices: 58656--58709 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
58646 ATCCATGACT
* * *
58656 CCCATG CCCATG CCCATG CCCATC CCCATC CCCATC CCCATC CCCATC
1 CCCATC CCCATC CCCATC CCCATC CCCATC CCCATC CCCATC CCCATC
58704 CCCATC
1 CCCATC
58710 TGCGACATCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.17, C:0.61, G:0.06, T:0.17
Consensus pattern (6 bp):
CCCATC
Found at i:60531 original size:18 final size:18
Alignment explanation
Indices: 60508--60551 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
60498 CCATTGCAGG
60508 ATCCCACCCTAGTGGAGC
1 ATCCCACCCTAGTGGAGC
60526 ATCCCACCCTAGTGGAGC
1 ATCCCACCCTAGTGGAGC
60544 ATCCCACC
1 ATCCCACC
60552 ACGCATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.23, C:0.43, G:0.18, T:0.16
Consensus pattern (18 bp):
ATCCCACCCTAGTGGAGC
Found at i:81624 original size:17 final size:19
Alignment explanation
Indices: 81592--81626 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
81582 TTGAGATCCC
81592 ATAAGCAAACACAAAGACA
1 ATAAGCAAACACAAAGACA
81611 ATAA-CAAA-ACAAAGAC
1 ATAAGCAAACACAAAGAC
81627 TACCTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.66, C:0.20, G:0.09, T:0.06
Consensus pattern (19 bp):
ATAAGCAAACACAAAGACA
Found at i:81765 original size:16 final size:16
Alignment explanation
Indices: 81744--81778 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
81734 TGAGTCAGAA
81744 AGCAAAAATAAATGCC
1 AGCAAAAATAAATGCC
81760 AGCAAAAATAAATGCC
1 AGCAAAAATAAATGCC
81776 AGC
1 AGC
81779 TTTTAGCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.20, G:0.14, T:0.11
Consensus pattern (16 bp):
AGCAAAAATAAATGCC
Found at i:82329 original size:39 final size:39
Alignment explanation
Indices: 82275--82354 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
82265 TATCCAAAGT
82275 ATTGATAAAGATTGTCACTTGGGATAAAAGTCCTAAAAC
1 ATTGATAAAGATTGTCACTTGGGATAAAAGTCCTAAAAC
82314 ATTGATAAAGATTGTCACTTGGGATAAAAGTCCTAAAAC
1 ATTGATAAAGATTGTCACTTGGGATAAAAGTCCTAAAAC
82353 AT
1 AT
82355 CGCTAGCAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (39 bp):
ATTGATAAAGATTGTCACTTGGGATAAAAGTCCTAAAAC
Found at i:82909 original size:238 final size:238
Alignment explanation
Indices: 82491--83074 Score: 1044
Period size: 238 Copynumber: 2.5 Consensus size: 238
82481 AACAATAATA
*
82491 CTATCCAAAGCACGGATAAAGCTTGTTATTTAGGATAAAAGTTTTAAAACATCGCTAGCAGTAAC
1 CTATCCAAAGCACGGATAAAGCTTGTTATTTGGGATAAAAGTTTTAAAACATCGCTAGCAGTAAC
*
82556 TAAGGTTGTGCCTGTATTCTTCCAACTCGATGAGAGTGTTCTCCCTGATCATATTTGTTGCATCA
66 TAAGGTTGTGCTTGTATTCTTCCAACTCGATGAGAGTGTTCTCCCTGATCATATTTGTTGCATCA
82621 ACTCTCTTATTTGAAGAACCCTATGAGAAAAAAGTGAACAATAACTTAACACAATAATATATGCA
131 ACTCTCTTATTTGAAGAACCCTATGAGAAAAAAGTGAACAATAACTTAACACAATAATATATGCA
82686 ATTTAAATAAAATGTACTAAGAGGAGTGAACAACAGTTCCCTG
196 ATTTAAATAAAATGTACTAAGAGGAGTGAACAACAGTTCCCTG
*
82729 CTATCCAAAGCATGGATAAAGCTTGTTATTTGGGATAAAAGTTTTAAAACATCGCTAGCAGTAAC
1 CTATCCAAAGCACGGATAAAGCTTGTTATTTGGGATAAAAGTTTTAAAACATCGCTAGCAGTAAC
82794 TAAGGTTGTGCTTGTATTCTTCCAACTCGATGAGAGTGTTCTCCCTGATCATATTTGTTGCATCA
66 TAAGGTTGTGCTTGTATTCTTCCAACTCGATGAGAGTGTTCTCCCTGATCATATTTGTTGCATCA
* *
82859 ACTCTCTTATTTGAAGAACCCTATGAGAAAAAAGTGAACAATGACTTAACACAATAATATATGTA
131 ACTCTCTTATTTGAAGAACCCTATGAGAAAAAAGTGAACAATAACTTAACACAATAATATATGCA
*
82924 ATTTAAATAAAATGTACTAAGAGGAGTGAGCAACAGTTCCCTG
196 ATTTAAATAAAATGTACTAAGAGGAGTGAACAACAGTTCCCTG
* * * * *
82967 CTATCCAAAGTACGGATAAAGATTGTCACTTGGGATAAAAGTTTTAAAACATCGCTAGCAGGAAC
1 CTATCCAAAGCACGGATAAAGCTTGTTATTTGGGATAAAAGTTTTAAAACATCGCTAGCAGTAAC
*
83032 TAAGGTTGTG-TCTGCATTCTTCCAACTCGATGAGAGTGTTCTC
66 TAAGGTTGTGCT-TGTATTCTTCCAACTCGATGAGAGTGTTCTC
83075 GCATTTAAAG
Statistics
Matches: 332, Mismatches: 13, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
237 1 0.00
238 331 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (238 bp):
CTATCCAAAGCACGGATAAAGCTTGTTATTTGGGATAAAAGTTTTAAAACATCGCTAGCAGTAAC
TAAGGTTGTGCTTGTATTCTTCCAACTCGATGAGAGTGTTCTCCCTGATCATATTTGTTGCATCA
ACTCTCTTATTTGAAGAACCCTATGAGAAAAAAGTGAACAATAACTTAACACAATAATATATGCA
ATTTAAATAAAATGTACTAAGAGGAGTGAACAACAGTTCCCTG
Found at i:83230 original size:207 final size:210
Alignment explanation
Indices: 82867--83280 Score: 555
Period size: 207 Copynumber: 2.0 Consensus size: 210
82857 CAACTCTCTT
* * * * * *
82867 ATTTGAAGAACCCTATGAGAAAAAAGTGAACAATGACTTAACACAATAATATATGTAATTTAAAT
1 ATTTAAAGAACCCTATGAGAAAAAACTGAACAATGACTTAAAACAAGAATATAAGCAATTTAAAT
* * * * **
82932 AAAATGTACTAAGAGGAGTGAGCAACAGTTCCCTGCTATCCAAAGTACGGATAAAGATTGTCACT
66 AAAAAGTACTAAGAGGAGTAAGCAACAATTCCATGCTATCCAAAGTACAAATAAAGATTGTCACT
* * * * * *
82997 TGGGATAAAAGTTTTAAAACATCGCTAGCAGGAACTAAGGTTGTGTCTGCATTCTTCCAACTCGA
131 TGGGATAAAAGGTTTAAAACATCGCTAGCAGGAACTAAGGTTATGCCTGCATTATTCCAAATCAA
*
83062 TGAGAGTGTTCTCGC
196 AGAGAGTGTTCTCGC
* * * *
83077 ATTTAAAGAACCCTATGAGAAAGAACTTAACAATGATTTAAAACAAGCATATAAGCAATTTAAAT
1 ATTTAAAGAACCCTATGAGAAAAAACTGAACAATGACTTAAAACAAGAATATAAGCAATTTAAAT
** *
83142 AAAAAGTA-T-TTA-GAGTAAGCAACAATTCTATGCTATCCAAAGTACAAATAAAGATTGTCACT
66 AAAAAGTACTAAGAGGAGTAAGCAACAATTCCATGCTATCCAAAGTACAAATAAAGATTGTCACT
* *
83204 TGGGATGATAGGTTTAAAACATCGCTAGCAGGAACTAAGGTTATGCCTGCATTATTCCAAATCAA
131 TGGGATAAAAGGTTTAAAACATCGCTAGCAGGAACTAAGGTTATGCCTGCATTATTCCAAATCAA
83269 AGAGAGTGTTCT
196 AGAGAGTGTTCT
83281 TCCTGTTCAT
Statistics
Matches: 176, Mismatches: 28, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
207 112 0.64
208 1 0.01
209 1 0.01
210 62 0.35
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (210 bp):
ATTTAAAGAACCCTATGAGAAAAAACTGAACAATGACTTAAAACAAGAATATAAGCAATTTAAAT
AAAAAGTACTAAGAGGAGTAAGCAACAATTCCATGCTATCCAAAGTACAAATAAAGATTGTCACT
TGGGATAAAAGGTTTAAAACATCGCTAGCAGGAACTAAGGTTATGCCTGCATTATTCCAAATCAA
AGAGAGTGTTCTCGC
Found at i:83536 original size:234 final size:236
Alignment explanation
Indices: 83077--83949 Score: 1023
Period size: 234 Copynumber: 3.7 Consensus size: 236
83067 GTGTTCTCGC
* * * * *
83077 ATTTAAAGAACCCTATGAGAAAGAACTTAACAATGATTTAAAACAAGCATATAAGCAATTTAAAT
1 ATTTAAAGAACCCTATG-GAAAAAAGTAAACAATGATTTAAAACAAGAATATATGCAATTTAAAT
* ** * * * ** ** *
83142 AAAAAGTAT-TTA-GAGTAAGCAACAATTCTATGCTATCCAAAGTACAAATAAAGATTGTCACTT
65 AAAATGTATGAGAGGAGTGAGCAGCAGTTCCCTGCTATCCAAAGTACTGATAAAGAATGTCACTT
* * * * * * *
83205 GGGATGATAGGTTTAAAACATCGCTAGCAGGAACTAAGGTTATGCCTGCATTATTCCAAATCAAA
130 GGGATAAAAGTTTTAAAACATCGCTAGCAGGAACTAAGGTTGTGCCTGCATTCTTCCAACTCAAT
* * *
83270 GAGAGTGTTCTTCCTGTTCATATCTACTGCAACGACTCTCCT
195 GAGAGTGTTCTCCCTGTTCATATATGCTGCAACGACTCTCCT
* * * * *
83312 ATTTAAAGAATCCAATGGAAAAATGTAAACAATGATTTAAAACAAGAATATATGAAATTAAAATA
1 ATTTAAAGAACCCTATGGAAAAAAGTAAACAATGATTTAAAACAAGAATATATGCAATTTAAATA
*
83377 AAATGTATGAGAGGAGTGAGCAGCAGTTACCTGCTAT-CAAAGTACTGATAAAGAATGTCACTTG
66 AAATGTATGAGAGGAGTGAGCAGCAGTTCCCTGCTATCCAAAGTACTGATAAAGAATGTCACTTG
* * * *
83441 GGATAAAAGTTTTAAAACATCCCTAGCGGGAACTAA-GTTGTGTCTGCATTCTTCCAACTCGATG
131 GGATAAAAGTTTTAAAACATCGCTAGCAGGAACTAAGGTTGTGCCTGCATTCTTCCAACTCAATG
* * *
83505 AGAGTGTTCTCCCTATTCATATTTGCTGCAACGACTCTCTT
196 AGAGTGTTCTCCCTGTTCATATATGCTGCAACGACTCTCCT
*
83546 ATTTAAAGAACCCTAT-GAAAAAAATAAACAATGATTTAAAACAAGAATATATGCAATTTAAATA
1 ATTTAAAGAACCCTATGGAAAAAAGTAAACAATGATTTAAAACAAGAATATATGCAATTTAAATA
* ** * * *
83610 AATTGTAATGAGAGGAGTGATAAGCAGTTCCCTGCTATCCAAAGT--T-TTAAA-ACATCTC-CA
66 AAATGT-ATGAGAGGAGTGAGCAGCAGTTCCCTGCTATCCAAAGTACTGATAAAGA-ATGTCACT
*** * * * * *
83670 TGTTTTAAAAGTTTTAAAGCATCGCTAGCAAGAACAAAGGTTGTGCCAGCATTCTTCAAACTCAA
129 TGGGATAAAAGTTTTAAAACATCGCTAGCAGGAACTAAGGTTGTGCCTGCATTCTTCCAACTCAA
* * *
83735 TGAGAGTGTTCTCCTTGTTCATATATGTTGCAACAACTCTCCT
194 TGAGAGTGTTCTCCCTGTTCATATATGCTGCAACGACTCTCCT
* * * * * *
83778 A-CTAATGAACCCTATGAAAAAAAGTAAAAAATTATTTAAAACAAGAATATATGCAATTCAAATA
1 ATTTAAAGAACCCTATGGAAAAAAGTAAACAATGATTTAAAACAAGAATATATGCAATTTAAATA
* *
83842 AAATGTACTGAGAGGAGTCAGCAGCAGTTCCCCTGCTATCCAAAGTACTGATAAAGATTGTCACT
66 AAATGTA-TGAGAGGAGTGAGCAGCAGTT-CCCTGCTATCCAAAGTACTGATAAAGAATGTCACT
*
83907 TGGGATAAAAGTTTTAAAACATTGCTAGCAGGAACTAA-GTTGT
129 TGGGATAAAAGTTTTAAAACATCGCTAGCAGGAACTAAGGTTGT
83950 CGAGAACAAA
Statistics
Matches: 533, Mismatches: 91, Indels: 27
0.82 0.14 0.04
Matches are distributed among these distances:
231 45 0.08
232 134 0.25
233 66 0.12
234 147 0.28
235 78 0.15
236 30 0.06
237 33 0.06
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (236 bp):
ATTTAAAGAACCCTATGGAAAAAAGTAAACAATGATTTAAAACAAGAATATATGCAATTTAAATA
AAATGTATGAGAGGAGTGAGCAGCAGTTCCCTGCTATCCAAAGTACTGATAAAGAATGTCACTTG
GGATAAAAGTTTTAAAACATCGCTAGCAGGAACTAAGGTTGTGCCTGCATTCTTCCAACTCAATG
AGAGTGTTCTCCCTGTTCATATATGCTGCAACGACTCTCCT
Found at i:90574 original size:411 final size:411
Alignment explanation
Indices: 89805--90627 Score: 1601
Period size: 411 Copynumber: 2.0 Consensus size: 411
89795 AAGTAACATT
89805 TATGAAAAATTATTTACTTAATCAGACATTGTTGACAAAAGTTTCTATCTTATGAAAGAACATTT
1 TATGAAAAATTATTTACTTAATCAGACATTGTTGACAAAAGTTTCTATCTTATGAAAGAACATTT
89870 GAAAGGATATTCTTGGTGACAATGGAATCAGACATTGTTTGAAACCTAGATTGCTGCAAACAAAA
66 GAAAGGATATTCTTGGTGACAATGGAATCAGACATTGTTTGAAACCTAGATTGCTGCAAACAAAA
89935 TTCCGTCAACACAAATAAAAAACCTAACAAAAGAGGGTCTAATTATAACTCACCATTTGTTGAAG
131 TTCCGTCAACACAAATAAAAAACCTAACAAAAGAGGGTCTAATTATAACTCACCATTTGTTGAAG
90000 AAGATTTTGCAACTATAAAAATCAAAGAATTTGTTATCAAACACTAGCAATAAAGGAAATTAGAA
196 AAGATTTTGCAACTATAAAAATCAAAGAATTTGTTATCAAACACTAGCAATAAAGGAAATTAGAA
90065 AACCAAAGCAACTAATTACTGATTTACATTCATTAGAGAGTATTATCCGACAAAGGCAATCTTAA
261 AACCAAAGCAACTAATTACTGATTTACATTCATTAGAGAGTATTATCCGACAAAGGCAATCTTAA
90130 TAGTTCAAAATAAATCAAAATCAGCAATGATTATGCCATCATGGTACTAGCATAAACATCATACT
326 TAGTTCAAAATAAATCAAAATCAGCAATGATTATGCCATCATGGTACTAGCATAAACATCATACT
90195 TTAAAAATCAGTTCTTTCATC
391 TTAAAAATCAGTTCTTTCATC
*
90216 TATGACAAATTATTTACTTAATCAGACATTGTTGACAAAAGTTTCTATCTTATGAAAGAACATTT
1 TATGAAAAATTATTTACTTAATCAGACATTGTTGACAAAAGTTTCTATCTTATGAAAGAACATTT
90281 GAAAGGATATTCTTGGTGACAATGGAATCAGACATTGTTTGAAACCTAGATTGCTGCAAACAAAA
66 GAAAGGATATTCTTGGTGACAATGGAATCAGACATTGTTTGAAACCTAGATTGCTGCAAACAAAA
90346 TTCCGTCAACACAAATAAAAAACCTAACAAAAGAGGGTCTAATTATAACTCACCATTTGTTGAAG
131 TTCCGTCAACACAAATAAAAAACCTAACAAAAGAGGGTCTAATTATAACTCACCATTTGTTGAAG
* *
90411 AAGATTTTGCAGCTATAAAAATCAAAGAATTTGTTATCAAACACTTGCAATAAAGGAAATTAGAA
196 AAGATTTTGCAACTATAAAAATCAAAGAATTTGTTATCAAACACTAGCAATAAAGGAAATTAGAA
*
90476 AACCAAAGCAACTGATTACTGATTTACATTCATTAGAGAGTATTATCCGACAAAGGCAATCTTAA
261 AACCAAAGCAACTAATTACTGATTTACATTCATTAGAGAGTATTATCCGACAAAGGCAATCTTAA
*
90541 TAGTTCAAAATAAATCAAAATCAGCAGTGATTATGCCATCATGGTACTAGCATAAACATCATACT
326 TAGTTCAAAATAAATCAAAATCAGCAATGATTATGCCATCATGGTACTAGCATAAACATCATACT
90606 TTAAAAATCAGTTCTTTCATC
391 TTAAAAATCAGTTCTTTCATC
90627 T
1 T
90628 TACAAAGAAA
Statistics
Matches: 407, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
411 407 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (411 bp):
TATGAAAAATTATTTACTTAATCAGACATTGTTGACAAAAGTTTCTATCTTATGAAAGAACATTT
GAAAGGATATTCTTGGTGACAATGGAATCAGACATTGTTTGAAACCTAGATTGCTGCAAACAAAA
TTCCGTCAACACAAATAAAAAACCTAACAAAAGAGGGTCTAATTATAACTCACCATTTGTTGAAG
AAGATTTTGCAACTATAAAAATCAAAGAATTTGTTATCAAACACTAGCAATAAAGGAAATTAGAA
AACCAAAGCAACTAATTACTGATTTACATTCATTAGAGAGTATTATCCGACAAAGGCAATCTTAA
TAGTTCAAAATAAATCAAAATCAGCAATGATTATGCCATCATGGTACTAGCATAAACATCATACT
TTAAAAATCAGTTCTTTCATC
Found at i:95766 original size:22 final size:21
Alignment explanation
Indices: 95718--95776 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 21
95708 ACATTTAATA
95718 TATATTAACTTAAAAATATTT
1 TATATTAACTTAAAAATATTT
95739 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA--AAA-ATATTT
95763 TATTATTAACTTAA
1 TA-TATTAACTTAA
95777 TTTAAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.35
23 4 0.12
24 8 0.24
25 10 0.29
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
TATATTAACTTAAAAATATTT
Found at i:96080 original size:41 final size:41
Alignment explanation
Indices: 96007--96373 Score: 278
Period size: 41 Copynumber: 9.0 Consensus size: 41
95997 TAGCGGCATT
* * *
96007 TTTAGTGGTGTTTT-TTATCAAACGCCAG-TAAATACCCGTAC
1 TTTAGTGGCGTTTTAATA-CAAACGCC-GCTAAATACTCGTAC
* * * * *
96048 TTTAGTGGCGTTTTCATATAAATGCCACTAAATA-TTGTAC
1 TTTAGTGGCGTTTTAATACAAACGCCGCTAAATACTCGTAC
* ** * * *
96088 TTTAGTGGTGTTTTTGTACAAACACCGCTAAAGACTCGCAC
1 TTTAGTGGCGTTTTAATACAAACGCCGCTAAATACTCGTAC
* * *
96129 -TTAGTGGCGTTTTAAGCACAAACGCCACTAAATACTCATAC
1 TTTAGTGGCGTTTTAA-TACAAACGCCGCTAAATACTCGTAC
* * * * * *
96170 TTTAGTGGCGTTTTTATATAAATGTCGTTAAATA-TTGTAC
1 TTTAGTGGCGTTTTAATACAAACGCCGCTAAATACTCGTAC
* ** * * * *
96210 TTTAGCGATGTTTGT-ATACAAATGCCGCCAAAGACTCGTAT
1 TTTAGTGGCGTTT-TAATACAAACGCCGCTAAATACTCGTAC
*
96251 TTTAGTGGCGTTTTAATACAAACGCCGCTAAAGACTCGTAC
1 TTTAGTGGCGTTTTAATACAAACGCCGCTAAATACTCGTAC
** * *** * *
96292 TTTAGTGGAATTTTTATACAAATATCGTTAAAGACTCGTAC
1 TTTAGTGGCGTTTTAATACAAACGCCGCTAAATACTCGTAC
* *
96333 TTTAGTGGCGTTTTAATCATAAACGTCGCTAAATACTCGTA
1 TTTAGTGGCGTTTTAAT-ACAAACGCCGCTAAATACTCGTA
96374 TGTTAGTAGT
Statistics
Matches: 251, Mismatches: 66, Indels: 17
0.75 0.20 0.05
Matches are distributed among these distances:
40 71 0.28
41 146 0.58
42 34 0.14
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (41 bp):
TTTAGTGGCGTTTTAATACAAACGCCGCTAAATACTCGTAC
Found at i:96156 original size:81 final size:82
Alignment explanation
Indices: 96007--96184 Score: 202
Period size: 81 Copynumber: 2.2 Consensus size: 82
95997 TAGCGGCATT
* * * * * * *
96007 TTTAGTGGTGTTTTTTATCAAACGCCAGTAAATACCCGTACTTTAGTGGCGTTTTCATATAAATG
1 TTTAGTGGTGTTTTTTATCAAACACCAGTAAAGACCCGCACTTTAGTGGCGTTTTAACACAAACG
**
96072 CCACTAAATA-TTGTAC
66 CCACTAAATACTCATAC
*
96088 TTTAGTGGTGTTTTTGTA-CAAACACC-GCTAAAGACTCGCAC-TTAGTGGCGTTTTAAGCACAA
1 TTTAGTGGTGTTTTT-TATCAAACACCAG-TAAAGACCCGCACTTTAGTGGCGTTTTAA-CACAA
96150 ACGCCACTAAATACTCATAC
63 ACGCCACTAAATACTCATAC
*
96170 TTTAGTGGCGTTTTT
1 TTTAGTGGTGTTTTT
96185 ATATAAATGT
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
80 15 0.18
81 47 0.57
82 20 0.24
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (82 bp):
TTTAGTGGTGTTTTTTATCAAACACCAGTAAAGACCCGCACTTTAGTGGCGTTTTAACACAAACG
CCACTAAATACTCATAC
Found at i:96243 original size:122 final size:122
Alignment explanation
Indices: 96025--96337 Score: 376
Period size: 122 Copynumber: 2.6 Consensus size: 122
96015 TGTTTTTTAT
* * * * **
96025 CAAACGCCAGTAAATACCCGTACTTTAGTGGCGTTTTCATATAAATGCCACTAAATATTGTACTT
1 CAAACGCCACTAAATACTCGTACTTTAGTGGCGTTTTTATATAAATGTCGTTAAATATTGTACTT
* * * * *
96090 TAGTGGTGTTTTTGTACAAACACCGCTAAAGACTCGCA-CTTAGTGGCGTTTTAAGCA
66 TAGCGATGTTTGTATACAAACACCGCCAAAGACTCGCATCTTAGTGGCGTTTTAA-CA
*
96147 CAAACGCCACTAAATACTCATACTTTAGTGGCGTTTTTATATAAATGTCGTTAAATATTGTACTT
1 CAAACGCCACTAAATACTCGTACTTTAGTGGCGTTTTTATATAAATGTCGTTAAATATTGTACTT
** * * *
96212 TAGCGATGTTTGTATACAAATGCCGCCAAAGACTCGTATTTTAGTGGCGTTTTAATA
66 TAGCGATGTTTGTATACAAACACCGCCAAAGACTCGCATCTTAGTGGCGTTTTAACA
* * ** * * * *
96269 CAAACGCCGCTAAAGACTCGTACTTTAGTGGAATTTTTATACAAATATCGTTAAAGACTCGTACT
1 CAAACGCCACTAAATACTCGTACTTTAGTGGCGTTTTTATATAAATGTCGTTAAATA-TTGTACT
96334 TTAG
65 TTAG
96338 TGGCGTTTTA
Statistics
Matches: 163, Mismatches: 26, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
122 138 0.85
123 25 0.15
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (122 bp):
CAAACGCCACTAAATACTCGTACTTTAGTGGCGTTTTTATATAAATGTCGTTAAATATTGTACTT
TAGCGATGTTTGTATACAAACACCGCCAAAGACTCGCATCTTAGTGGCGTTTTAACA
Found at i:99049 original size:23 final size:23
Alignment explanation
Indices: 98994--99054 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
98984 ACATTTTATA
* *
98994 TGGCACTTCAGTACAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
99017 CGGCACTTCGGTGCAATTCTATG
1 TGGCACTTCGGTGCAATTCTACG
99040 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
99055 TTTATACGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:104196 original size:21 final size:19
Alignment explanation
Indices: 104159--104197 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
104149 TGTCGATAAA
*
104159 AGAGAGTGTTTATTATGTT
1 AGAGAGTGTTTAATATGTT
104178 AGAGAGTGTATTAAATATGT
1 AGAGAGTGT-TT-AATATGT
104198 AGAAATAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (19 bp):
AGAGAGTGTTTAATATGTT
Found at i:107187 original size:18 final size:19
Alignment explanation
Indices: 107153--107189 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
107143 CACGGAATGT
107153 AAGATTACCAGAGGGAATAA
1 AAGATTACCA-AGGGAATAA
107173 AAGATTACC-AGGGAATA
1 AAGATTACCAAGGGAATA
107190 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.11, G:0.24, T:0.16
Consensus pattern (19 bp):
AAGATTACCAAGGGAATAA
Found at i:113816 original size:13 final size:13
Alignment explanation
Indices: 113798--113822 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
113788 GAGACGGTGA
113798 AGAAAATAAAAAT
1 AGAAAATAAAAAT
113811 AGAAAATAAAAA
1 AGAAAATAAAAA
113823 GAATTAATGC
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:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AGAAAATAAAAAT
Found at i:121375 original size:313 final size:303
Alignment explanation
Indices: 120813--121727 Score: 1439
Period size: 299 Copynumber: 3.0 Consensus size: 303
120803 ATAAAACCAT
* *
120813 AACACCAGCTGCAACAATGAAAATACTGGAACTTCTGCTAGAAAATAGAGGGAGCTGTAAAGGGT
1 AACACCAGCTCCAACAATGAAAATACTGGAAATTCTGCTAGAAAATAGAGGGAGCTGTAAAGGGT
*
120878 AGGCAATTGGACTCCTTAGCAG-AATAAAAATGAAGATAACATAAAGCTCCAAATAGGGAATAGA
66 AGGCAATTGGACTCCTTAGCAGAAATAAAAATGAAGATAGCATAAAGCTCCAAA-AGGGAATAGA
**
120942 AAACAATCTATTACAAAGAGATCTTTGAACTAACCAGCATAATTGGGAATAAAACTAGCATGCCC
130 AAACAATCTATTATGAAGAGATCTTTGAACTAACCAGCATAATTGGGAATAAAACTAGCATGCCC
* *
121007 TAATTTCCAATTACTAATTTCGACATACAATACAATCAAAATTAGGAATACGAAAAAAAGAAGAA
195 TAATTTCCAATTACTAATTTTGAGATACAATACAATCAAAATTAGGAATACG---AAAAGAA-AA
*
121072 AAAAAACTCACTTCATAAGAATATCATAGTACTCAGGATTCAAAGAAA
256 AAAAAACTCACTTCATAAGAATATCATAGTACTCAGGATCCAAAGAAA
* *
121120 AACACCAGCTCCAACAATGAAAATACTGGAAATTCTGCTAGAAAATAAAGGGAGCTGTACAGGGT
1 AACACCAGCTCCAACAATGAAAATACTGGAAATTCTGCTAGAAAATAGAGGGAGCTGTAAAGGGT
* * *
121185 TGGCAATTGGACTCCTTAGCAGAAATAAAAATGAAGATAGCATAAATCTCCAAACATGGAATACT
66 AGGCAATTGGACTCCTTAGCAGAAATAAAAATGAAGATAGCATAAAGCTCCAAA-A-GG--GA--
*
121250 ATAGAAAACAATCTATTATGAAGAGATATTTGAACTAACCAGCATAATTGGGAATAAAACTAGCA
125 ATAGAAAACAATCTATTATGAAGAGATCTTTGAACTAACCAGCATAATTGGGAATAAAACTAGCA
121315 TGCCCTAATTTCCAATTACTAATTTTGAGATACAATACAATCAAAATTAGGAATAC-----G-AA
190 TGCCCTAATTTCCAATTACTAATTTTGAGATACAATACAATCAAAATTAGGAATACGAAAAGAAA
* *
121374 AAAAAAACTCACTTCATAAGAATACCATGGTACTCAGGATCCAAAGAAAA
255 AAAAAAACTCACTTCATAAGAATATCATAGTACTCAGGATCCAAAG-AAA
* *
121424 AACACCAGCTCCAACAATGAAAGTACTGGAAATTCTGCTAGAAAATTGAGGGAGCTGTAAAGGGT
1 AACACCAGCTCCAACAATGAAAATACTGGAAATTCTGCTAGAAAATAGAGGGAGCTGTAAAGGGT
*
121489 ACGCAATTGGACTCCTTAGCAGAAATAAAAATGAAGATAGCATAAAGCTCCAAAAAGGGAATAGA
66 AGGCAATTGGACTCCTTAGCAGAAATAAAAATGAAGATAGCATAAAGCTCC-AAAAGGGAATAGA
* *
121554 AAACAATCTATTATGAAGAGATCCTTGAACTAACCAGCATAACTGGGAATAAAACTAGCATGCCC
130 AAACAATCTATTATGAAGAGATCTTTGAACTAACCAGCATAATTGGGAATAAAACTAGCATGCCC
* * *
121619 GAATTTCCAATTACTACTTTTGAGATACAATACAATCAAAATTAGGAATACGGAAAAGAAAAGAA
195 TAATTTCCAATTACTAATTTTGAGATACAATACAATCAAAATTAGGAATAC-GAAAAGAAAAAAA
121684 AAACTCACTTCATAAGAATATCATAGTACTCAGGATCCAAAGAA
259 AAACTCACTTCATAAGAATATCATAGTACTCAGGATCCAAAGAA
121728 GAGAACATTC
Statistics
Matches: 560, Mismatches: 33, Indels: 32
0.90 0.05 0.05
Matches are distributed among these distances:
299 116 0.21
301 1 0.00
303 46 0.08
304 114 0.20
305 7 0.01
306 45 0.08
307 82 0.15
308 30 0.05
309 2 0.00
311 1 0.00
313 116 0.21
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (303 bp):
AACACCAGCTCCAACAATGAAAATACTGGAAATTCTGCTAGAAAATAGAGGGAGCTGTAAAGGGT
AGGCAATTGGACTCCTTAGCAGAAATAAAAATGAAGATAGCATAAAGCTCCAAAAGGGAATAGAA
AACAATCTATTATGAAGAGATCTTTGAACTAACCAGCATAATTGGGAATAAAACTAGCATGCCCT
AATTTCCAATTACTAATTTTGAGATACAATACAATCAAAATTAGGAATACGAAAAGAAAAAAAAA
ACTCACTTCATAAGAATATCATAGTACTCAGGATCCAAAGAAA
Found at i:122456 original size:21 final size:21
Alignment explanation
Indices: 122432--122474 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
122422 ACTTCAACTA
* *
122432 TCGCATTGCGATTTTCTAAAT
1 TCGCATTACGATTTTCCAAAT
*
122453 TCGCGTTACGATTTTCCAAAT
1 TCGCATTACGATTTTCCAAAT
122474 T
1 T
122475 TGCAATGTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (21 bp):
TCGCATTACGATTTTCCAAAT
Found at i:122516 original size:21 final size:21
Alignment explanation
Indices: 122492--122567 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
122482 TGAATATGTA
122492 AATCGCAACGCGATAATACAT
1 AATCGCAACGCGATAATACAT
**
122513 AATCGCAACGCGATTCTGAC-T
1 AATCGCAACGCGATAAT-ACAT
* *
122534 -ATCGCAACGTGATAATACAA
1 AATCGCAACGCGATAATACAT
*
122554 AATCGCAATGCGAT
1 AATCGCAACGCGAT
122568 TTTTAAAGCG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 27 0.61
22 2 0.05
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (21 bp):
AATCGCAACGCGATAATACAT
Found at i:122737 original size:22 final size:22
Alignment explanation
Indices: 122712--122758 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
122702 CTACGGCGAC
122712 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
122734 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
122756 ATC
1 ATC
122759 TGTCTATCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.45, G:0.15, T:0.19
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:123206 original size:39 final size:40
Alignment explanation
Indices: 123152--123239 Score: 151
Period size: 39 Copynumber: 2.2 Consensus size: 40
123142 GTTTAATTTA
*
123152 CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCA-TTTCG
1 CGTTGCGATAGTCATTTTCGTATTGCGATTTTCATTTTCG
123191 CGTTGCGATAGTCATTTTCGTATTGCGATTTTCATTTTCG
1 CGTTGCGATAGTCATTTTCGTATTGCGATTTTCATTTTCG
*
123231 TGTTGCGAT
1 CGTTGCGAT
123240 TTTAAGTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 33 0.72
40 13 0.28
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.47
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTTCGTATTGCGATTTTCATTTTCG
Found at i:123249 original size:20 final size:20
Alignment explanation
Indices: 123153--123242 Score: 119
Period size: 20 Copynumber: 4.5 Consensus size: 20
123143 TTTAATTTAC
**
123153 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
123173 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
**
123192 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
123212 ATTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
123232 GTTGCGATTTT
1 GTTGCGATTTT
123243 AAGTTTCAGA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.27
20 43 0.73
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:125167 original size:20 final size:20
Alignment explanation
Indices: 125142--125210 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
125132 AAACTTAAAA
125142 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
125162 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
125182 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
125202 ATCGCAACG
1 ATCGCAACG
125211 GGATAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:125228 original size:34 final size:37
Alignment explanation
Indices: 125141--125229 Score: 103
Period size: 40 Copynumber: 2.4 Consensus size: 37
125131 GAAACTTAAA
125141 AATCGCAACGCGAAAATGACTATCGCAACGCGGAAATG
1 AATCGCAACGCGAAAATGACTATCGCAACGCGG-AATG
**
125179 ACTATCGCAACGCGAATTTGACTATCGCAACG-GG-AT-
1 A--ATCGCAACGCGAAAATGACTATCGCAACGCGGAATG
*
125215 AATCGCAATGCGAAA
1 AATCGCAACGCGAAA
125230 TAAAAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
34 12 0.27
36 1 0.02
37 2 0.04
38 1 0.02
39 2 0.04
40 27 0.60
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (37 bp):
AATCGCAACGCGAAAATGACTATCGCAACGCGGAATG
Found at i:125239 original size:19 final size:19
Alignment explanation
Indices: 125215--125272 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
125205 GCAACGGGAT
125215 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATAAA
**
125234 AATCGCAATGCGAAACCAA
1 AATCGCAATGCGAAATAAA
*
125253 AATCGCAACGCGAAACTAAA
1 AATCGCAATGCGAAA-TAAA
125273 TTCACGCTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 31 0.94
20 2 0.06
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATAAA
Found at i:125309 original size:14 final size:14
Alignment explanation
Indices: 125290--125319 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
125280 TGTGATAGTC
125290 ATTTTCGCATTGCG
1 ATTTTCGCATTGCG
*
125304 ATTTTCGCGTTGCG
1 ATTTTCGCATTGCG
125318 AT
1 AT
125320 AGTCAAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.43
Consensus pattern (14 bp):
ATTTTCGCATTGCG
Found at i:125332 original size:20 final size:19
Alignment explanation
Indices: 125307--125359 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
125297 CATTGCGATT
125307 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTC-AA
*
125327 TTCGCGTTGCGATAGTCAT
1 TTCGCGTTGCGATAGTCAA
125346 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
125360 TTAAGTTTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (19 bp):
TTCGCGTTGCGATAGTCAA
Found at i:125368 original size:20 final size:21
Alignment explanation
Indices: 125345--125388 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
125335 GCGATAGTCA
125345 TTTCCGCGTTGCGA-TTTAAG
1 TTTCCGCGTTGCGATTTTAAG
*
125365 TTT-CGTGTTGCGATTTTAAG
1 TTTCCGCGTTGCGATTTTAAG
125385 TTTC
1 TTTC
125389 AGAAACTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.48
Consensus pattern (21 bp):
TTTCCGCGTTGCGATTTTAAG
Found at i:125956 original size:21 final size:21
Alignment explanation
Indices: 125867--125983 Score: 67
Period size: 21 Copynumber: 5.6 Consensus size: 21
125857 ACTTACATGT
* *
125867 CATCGTTTAAGA-GCCTCT-C
1 CATCGTTCAAGAGGCCCCTAC
** *
125886 CTATCGTTCAAGAGGCCTTTAT
1 C-ATCGTTCAAGAGGCCCCTAC
** * * *
125908 CATCCCTCAAGAGTCTCCTCC
1 CATCGTTCAAGAGGCCCCTAC
* *
125929 CACCGTTCAAGAGGCCCCTAT
1 CATCGTTCAAGAGGCCCCTAC
* * *
125950 CATCGTTGAAGAGGTCCCTCC
1 CATCGTTCAAGAGGCCCCTAC
*
125971 CATCATTCAAGAG
1 CATCGTTCAAGAG
125984 CCTGATTCAT
Statistics
Matches: 70, Mismatches: 25, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
19 1 0.01
20 10 0.14
21 58 0.83
22 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.26
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTAC
Found at i:125962 original size:42 final size:42
Alignment explanation
Indices: 125866--125983 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 42
125856 GACTTACATG
* * * **
125866 TCATCGTTTAAGAGCCT-CTCCTATCGTTCAAGAGGCCTTTA
1 TCATCGTTCAAGAGTCTCCTCCCATCGTTCAAGAGGCCCCTA
** *
125907 TCATCCCTCAAGAGTCTCCTCCCACCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGTCTCCTCCCATCGTTCAAGAGGCCCCTA
* *
125949 TCATCGTTGAAGAGGTC-CCTCCCATCATTCAAGAG
1 TCATCGTTCAAGA-GTCTCCTCCCATCGTTCAAGAG
125984 CCTGATTCAT
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
41 13 0.21
42 46 0.74
43 3 0.05
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.27
Consensus pattern (42 bp):
TCATCGTTCAAGAGTCTCCTCCCATCGTTCAAGAGGCCCCTA
Found at i:127407 original size:15 final size:14
Alignment explanation
Indices: 127372--127419 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
127362 TTGCTTGTTT
127372 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
127386 AATTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
127401 TATTGATGTGTAAA
1 AATTGATTTGTAAA
127415 TAATT
1 -AATT
127420 CTTATTTGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:127449 original size:36 final size:36
Alignment explanation
Indices: 127393--127520 Score: 107
Period size: 36 Copynumber: 3.4 Consensus size: 36
127383 AAAAATTGAT
127393 TTGTTTAATATTGATGTGTAAATAATTCTTATTTGTGC
1 TTGTTT-A-ATTGATGTGTAAATAATTCTTATTTGTGC
* * * * *
127431 TTGTTTAATTGATTTGTAAA-AGTTGGTT-TGTAAAAGTTGAT
1 TTGTTTAATTGATGTGTAAATAATT-CTTAT-T---TG-TG-C
127472 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTGC
1 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTGC
*
127508 TTATTTAATTGAT
1 TTGTTTAATTGAT
127521 TGAAATGTAA
Statistics
Matches: 70, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
35 4 0.06
36 27 0.39
37 3 0.04
38 7 0.10
39 1 0.01
40 2 0.03
41 22 0.31
42 4 0.06
ACGTcount: A:0.27, C:0.03, G:0.17, T:0.52
Consensus pattern (36 bp):
TTGTTTAATTGATGTGTAAATAATTCTTATTTGTGC
Found at i:127462 original size:14 final size:14
Alignment explanation
Indices: 127439--127475 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
127429 GCTTGTTTAA
127439 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
127453 TTGGTTTGTAAAAG
1 TTGATTTGTAAAAG
127467 TTGATTTGT
1 TTGATTTGT
127476 TTAATTGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:127478 original size:79 final size:77
Alignment explanation
Indices: 127378--127521 Score: 252
Period size: 77 Copynumber: 1.8 Consensus size: 77
127368 GTTTAATTGA
*
127378 TTTGTAAAAATTGATTTGTTTAATATTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGA
1 TTTGTAAAAATTGATTTGTTT-A-ATTGATGTGTAAATAATTCTTATTTGTGCTTATTTAATTGA
127443 TTTGTAAAAGTTGG
64 TTTGTAAAAGTTGG
*
127457 TTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTTATTTAATTGATT
1 TTTGTAAAAATTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTTATTTAATTGATT
127522 GAAATGTAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
77 42 0.67
78 1 0.02
79 20 0.32
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (77 bp):
TTTGTAAAAATTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTTATTTAATTGATT
TGTAAAAGTTGG
Found at i:127620 original size:20 final size:20
Alignment explanation
Indices: 127595--127648 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
127585 AGGTACACTT
*
127595 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
*
127615 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
127635 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
127649 TTAATTCGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:127664 original size:19 final size:20
Alignment explanation
Indices: 127642--127684 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
127632 AAATCGCAAC
*
127642 GCGAAAGT-TAATTCGCTTT
1 GCGAAAGTCTAATACGCTTT
*
127661 GCGATAGTCTAATACGCTTT
1 GCGAAAGTCTAATACGCTTT
127681 GCGA
1 GCGA
127685 TTTTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
GCGAAAGTCTAATACGCTTT
Found at i:127716 original size:20 final size:20
Alignment explanation
Indices: 127691--127855 Score: 120
Period size: 20 Copynumber: 8.8 Consensus size: 20
127681 GCGATTTTCT
*
127691 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
127711 CGTTGCAATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
127731 AGTTGCGATAGCCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
127751 CATTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
127765 TGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
127785 CGTTGC-A-A-T---TTTTG
1 CGTTGCGATAGTCAAATTCG
* *
127799 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
127819 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
127839 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
127856 GAATGTGTAA
Statistics
Matches: 108, Mismatches: 25, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
14 17 0.16
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 1 0.01
20 84 0.78
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:127781 original size:34 final size:34
Alignment explanation
Indices: 127730--127827 Score: 133
Period size: 34 Copynumber: 2.9 Consensus size: 34
127720 AGTCAAATTC
* * *
127730 GAGTTGCGATAGCCAAATTCGCATTGCGATTTTT
1 GAGTTACGATAGTCAAATTCGCGTTGCGATTTTT
* *
127764 GTGTTACGATAGTCAAATTCGCGTTGCAATTTTT
1 GAGTTACGATAGTCAAATTCGCGTTGCGATTTTT
* *
127798 GAGTTGCGATAATCAAATTCGCGTTGCGAT
1 GAGTTACGATAGTCAAATTCGCGTTGCGAT
127828 AGTTAAATTC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.36
Consensus pattern (34 bp):
GAGTTACGATAGTCAAATTCGCGTTGCGATTTTT
Found at i:128078 original size:140 final size:140
Alignment explanation
Indices: 127826--128108 Score: 494
Period size: 140 Copynumber: 2.0 Consensus size: 140
127816 TCGCGTTGCG
* *
127826 ATAGTTAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
1 ATAGTCAAATTCGCGTTGCGATAATCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
* * **
127891 TATCGATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATACTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
127956 AATACACATA
131 AATACACATA
* *
127966 ATAGTCAAATTCGCGTTGCGATAATCAAATGAATGTGTAATAAGTGATAACAACTTAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATAATCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
128031 TAGCAATACTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATACTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
128096 AATACACATA
131 AATACACATA
128106 ATA
1 ATA
128109 CAACGTTTGC
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
140 135 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATAATCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
TAGCAATACTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:128189 original size:18 final size:18
Alignment explanation
Indices: 128166--128200 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
128156 AAGCCGGTTG
*
128166 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
128184 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
128201 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:131355 original size:20 final size:20
Alignment explanation
Indices: 131330--131420 Score: 103
Period size: 20 Copynumber: 4.5 Consensus size: 20
131320 TTGAAATTCA
*
131330 GCGTTGCGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
131350 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
* * * **
131370 ACATTGTGATTATGT-ATTATC
1 GCGTTGCGA-TA-GTCAGAATC
131391 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
131411 GCGTTGCGAT
1 GCGTTGCGAT
131421 TTACATATTC
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.04
20 41 0.72
21 12 0.21
22 2 0.04
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:132206 original size:29 final size:29
Alignment explanation
Indices: 132106--132208 Score: 98
Period size: 29 Copynumber: 3.5 Consensus size: 29
132096 TTCATCTAAG
* * *
132106 TATTTAAAATACTTTTTGATCAAAATAAG
1 TATTTAAAATATTTTTTAATCAAAATAAA
* * *
132135 TATATAAATTTATCTTTTTAATCAAAATATA
1 TATTTAAA-ATAT-TTTTTAATCAAAATAAA
** * *
132166 TACGTCAAATATTTTTTTATCAAAATAAA
1 TATTTAAAATATTTTTTAATCAAAATAAA
132195 TATTTAAAATATTT
1 TATTTAAAATATTT
132209 AATCTTTTTC
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
29 33 0.58
30 5 0.09
31 19 0.33
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.46
Consensus pattern (29 bp):
TATTTAAAATATTTTTTAATCAAAATAAA
Found at i:136871 original size:100 final size:99
Alignment explanation
Indices: 136691--136875 Score: 298
Period size: 100 Copynumber: 1.9 Consensus size: 99
136681 CAATAAGTTT
* *
136691 TAAAAAATTCATACAAACGACGTGTTCAAACCTAAATCCTCTAAACGTAATAAATTAATAATCAT
1 TAAAAAATTCATACAAACAACGTGTTCAAACCTAAATCCTCTAAACGTAACAAATTAATAATCAT
*
136756 CTCTTTAATCGGATCACTTGGTTTGCATAAATGC
66 CTCTTTAATCAGATCACTTGGTTTGCATAAATGC
* * *
136790 TAAAAAATTCCTTACAAACAACGTGTTCAAACTTAACTCCTCTAAACGTAACAAATTAATAATCA
1 TAAAAAATT-CATACAAACAACGTGTTCAAACCTAAATCCTCTAAACGTAACAAATTAATAATCA
*
136855 TCTCTTTACTCAGATCACTTG
65 TCTCTTTAATCAGATCACTTG
136876 ATTTATATAT
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
99 9 0.12
100 69 0.88
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.31
Consensus pattern (99 bp):
TAAAAAATTCATACAAACAACGTGTTCAAACCTAAATCCTCTAAACGTAACAAATTAATAATCAT
CTCTTTAATCAGATCACTTGGTTTGCATAAATGC
Found at i:137197 original size:20 final size:20
Alignment explanation
Indices: 137174--137218 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
137164 TATATACTAT
137174 TAATAGTTT-TAATAATATAA
1 TAATA-TTTCTAATAATATAA
* *
137194 TAATATTTCTAGTATTATAA
1 TAATATTTCTAATAATATAA
137214 TAATA
1 TAATA
137219 ATACATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
TAATATTTCTAATAATATAA
Found at i:137457 original size:34 final size:31
Alignment explanation
Indices: 137419--137494 Score: 73
Period size: 31 Copynumber: 2.4 Consensus size: 31
137409 ATTTTAATAA
137419 ATAATTAATATATTTTTTATTTTAATAAAATATT
1 ATAATTAATATA-TTTTTA-TTT-ATAAAATATT
* *
137453 ATAATCTTA-ATATTTTTATTTATAAAATTTT
1 ATAAT-TAATATATTTTTATTTATAAAATATT
* *
137484 AGAAATAATAT
1 ATAATTAATAT
137495 TTAAATAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
30 2 0.06
31 14 0.40
32 3 0.09
33 6 0.17
34 8 0.23
35 2 0.06
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (31 bp):
ATAATTAATATATTTTTATTTATAAAATATT
Found at i:142289 original size:2 final size:2
Alignment explanation
Indices: 142276--142311 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
142266 GAGTAGGAGT
*
142276 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
142312 GTAGCCATAA
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:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:153316 original size:80 final size:80
Alignment explanation
Indices: 153178--153489 Score: 475
Period size: 80 Copynumber: 3.9 Consensus size: 80
153168 TGTAAGTCCT
* *
153178 TACGGATCTAAGGATGTCCTTGGGTAGAACCAAGGTATATCCTTATGTTGGTTCCCTTTGCTGTG
1 TACGAATCTAAGGATGTCCTTGGGTAGAACCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
153243 TGCTTAAGGTAACCC
66 TGCTTAAGGTAACCC
*
153258 TACGAATCTAAGGATGTCCTTGGGTAGAACCAAGGTATATCCTTAGGTTGGTTCCCTTTGATGTG
1 TACGAATCTAAGGATGTCCTTGGGTAGAACCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
153323 TGCTTAAGGTAACCC
66 TGCTTAAGGTAACCC
* * **
153338 TACTG-ATCTAAGGATGTCCTTGGGTAGAACCAAGGTATATCATTAGGTTGGTTTCCTTAACTGT
1 TAC-GAATCTAAGGATGTCCTTGGGTAGAACCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGT
153402 GTGCTTAAGGTAACCC
65 GTGCTTAAGGTAACCC
* * *
153418 TACGAATCTAAGGATGTCCTCGGGTAGACCCAAGGTATATCCTTAAGTT-GTCTCCCCTTTTTGC
1 TACGAATCTAAGGATGTCCTTGGGTAGAACCAAGGTATATCCTTAGGTTGGT-T-CCC--TTTGC
153482 TGTGTGCT
62 TGTGTGCT
153490 GAGGGCAAGC
Statistics
Matches: 211, Mismatches: 15, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
79 3 0.01
80 194 0.92
81 3 0.01
83 11 0.05
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (80 bp):
TACGAATCTAAGGATGTCCTTGGGTAGAACCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
TGCTTAAGGTAACCC
Found at i:153929 original size:28 final size:27
Alignment explanation
Indices: 153855--153929 Score: 64
Period size: 28 Copynumber: 2.7 Consensus size: 27
153845 ATAAATTACA
* *
153855 AATTTAATCATTAAATTTTATTTTTCT
1 AATTTAATCACTAAATTTAATTTTTCT
* *
153882 -ATTTCACTCACTGAATTTTAATTGTTT-T
1 AATTT-AATCACT-AAATTTAATT-TTTCT
153910 AATTTAATCACTAAACTTTA
1 AATTTAATCACTAAA-TTTA
153930 CACATTAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
26 4 0.11
27 7 0.19
28 19 0.51
29 7 0.19
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (27 bp):
AATTTAATCACTAAATTTAATTTTTCT
Found at i:156986 original size:20 final size:20
Alignment explanation
Indices: 156963--157014 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
156953 AACGCGATCC
156963 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
156983 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
157003 CCAAAATCGCAA
1 CCAGAATCGCAA
157015 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:157164 original size:20 final size:20
Alignment explanation
Indices: 157070--157438 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
157060 GATTTTCCAT
* ** *
157070 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
157090 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
157110 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
157130 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
157150 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
157170 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
157190 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
157210 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
157230 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
157250 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
157270 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
157290 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
157310 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
157330 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
157350 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
157370 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
157390 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
157410 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
157430 AATCACAAC
1 AATCGCAAC
157439 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:160667 original size:19 final size:19
Alignment explanation
Indices: 160645--160970 Score: 414
Period size: 19 Copynumber: 18.4 Consensus size: 19
160635 CGGAAAATAC
*
160645 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
160664 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
160678 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
160698 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
160712 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
160731 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
160750 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
160764 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
160783 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
160802 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
160816 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
160835 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
160854 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
160873 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
160892 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
160911 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
160925 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
160944 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
160963 AATCGCAA
1 AATCGCAA
160971 CGAGATAATC
Statistics
Matches: 271, Mismatches: 10, Indels: 52
0.81 0.03 0.16
Matches are distributed among these distances:
14 48 0.18
15 2 0.01
16 16 0.06
17 14 0.05
18 3 0.01
19 175 0.65
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:160732 original size:33 final size:34
Alignment explanation
Indices: 160645--160970 Score: 321
Period size: 33 Copynumber: 9.2 Consensus size: 34
160635 CGGAAAATAC
* *
160645 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
160678 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
160712 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
160750 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
* *
160783 AATCGCAATGCGAAATGAAAATCGCAACGA-CAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
160816 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
160854 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
160892 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
160924 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
160963 AATCGCAA
1 AATCGCAA
160971 CGAGATAATC
Statistics
Matches: 257, Mismatches: 12, Indels: 43
0.82 0.04 0.14
Matches are distributed among these distances:
32 2 0.01
33 109 0.42
34 32 0.12
35 9 0.04
36 6 0.02
37 4 0.02
38 93 0.36
39 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:160906 original size:161 final size:156
Alignment explanation
Indices: 160676--161008 Score: 551
Period size: 161 Copynumber: 2.1 Consensus size: 156
160666 TCCCAACATG
*
160676 AAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATG
1 AAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAATG
*
160741 CGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATC
65 CGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATC
160806 GCAACGACAGAATCGCAATGCGAAATT
130 GCAACGACAGAATCGCAATGCGAAATT
160833 AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGC
1 AAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAAATCGC
160898 AATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
61 AATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
160963 AATCGCAACGAGATAATCGCAATGCGAAATT
126 AATCGCAACGACAGAATCGCAATGCGAAATT
*
160994 ATAAA-CGCATTGCGA
1 A-AAATCGCAATGCGA
161009 TTTTCATTTC
Statistics
Matches: 165, Mismatches: 5, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
156 16 0.10
157 13 0.08
158 2 0.01
160 1 0.01
161 130 0.79
162 3 0.02
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (156 bp):
AAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAATGC
GAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG
CAACGACAGAATCGCAATGCGAAATT
Found at i:161008 original size:52 final size:52
Alignment explanation
Indices: 160673--160992 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
160663 AAATCCCAAC
160673 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
160726 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
160778 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
160830 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
160887 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
160939 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
160991 AT
1 AT
160993 TATAAACGCA
Statistics
Matches: 253, Mismatches: 9, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
52 185 0.73
53 17 0.07
54 2 0.01
55 2 0.01
56 1 0.00
57 46 0.18
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:161089 original size:19 final size:19
Alignment explanation
Indices: 160999--161081 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
160989 AAATTATAAA
160999 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
161018 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
161038 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
161054 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
161071 CGCATTGCGAT
1 CGCATTGCGAT
161082 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:161207 original size:14 final size:14
Alignment explanation
Indices: 161188--161224 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
161178 CATCAATTAC
161188 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
161202 ACAAATCATCTTTT
1 ACAAATCAACTTTT
161216 ACAAATCAA
1 ACAAATCAA
161225 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:163226 original size:33 final size:33
Alignment explanation
Indices: 163180--163272 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
163170 GCGAAACCAA
**
163180 AATCGCAACGCGAAATGAAAATCGCAACGGCAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
163213 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
163246 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
163273 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:163237 original size:19 final size:19
Alignment explanation
Indices: 163143--163277 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
163133 TAGTTTACTT
* *
163143 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
163163 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
163182 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
163201 TCGCAACG-G-CA-G--AA
1 TCGCAACGCGAAATGAAAA
*
163215 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
163234 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
163248 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
163267 TCGCAATGCGA
1 TCGCAACGCGA
163278 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 17 0.18
15 1 0.01
16 8 0.08
17 8 0.08
18 1 0.01
19 49 0.51
20 12 0.12
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:163251 original size:14 final size:14
Alignment explanation
Indices: 163199--163255 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
163189 GCGAAATGAA
**
163199 AATCGCAACGGCAG
1 AATCGCAACGAAAG
163213 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
163230 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
163246 AATCGCAACG
1 AATCGCAACG
163256 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 4 0.11
17 6 0.17
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:163295 original size:19 final size:19
Alignment explanation
Indices: 163273--163401 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
163263 AAAATCGCAA
163273 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
163292 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
163306 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
163325 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
163339 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
163358 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
163377 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
163397 TGCGA
1 TGCGA
163402 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:163315 original size:33 final size:33
Alignment explanation
Indices: 163273--163364 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
163263 AAAATCGCAA
163273 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
163306 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
163339 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
163365 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:163730 original size:92 final size:93
Alignment explanation
Indices: 163445--163915 Score: 903
Period size: 92 Copynumber: 5.1 Consensus size: 93
163435 TTGAATGGAT
163445 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
163510 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
163538 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
163603 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
163631 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
163695 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
163723 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
163787 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
163815 AAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAAGACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
163879 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
163907 AAATTTACT
1 AAATTTACT
163916 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 2, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
91 9 0.02
92 234 0.63
93 131 0.35
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:165635 original size:14 final size:14
Alignment explanation
Indices: 165616--165705 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
165606 TTGAAATGAA
165616 AATCGCAACGAGAG
1 AATCGCAACGAGAG
165630 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
165647 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
165663 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
165682 AATCGCAACGAGAG
1 AATCGCAACGAGAG
165696 AATCGCAACG
1 AATCGCAACG
165706 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:165653 original size:33 final size:33
Alignment explanation
Indices: 165608--165722 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
165598 TCTTTTGGTT
165608 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
165641 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
165674 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
165707 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
165723 TGCGATTTGG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:165654 original size:19 final size:18
Alignment explanation
Indices: 165615--165727 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
165605 GTTGAAATGA
165615 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
165630 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
165647 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
165663 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
165680 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
165696 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
165713 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
165728 TTTGGTTTCG
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:165757 original size:14 final size:14
Alignment explanation
Indices: 165738--165792 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
165728 TTTGGTTTCG
165738 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
165752 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
165771 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
165785 CGTTGCGA
1 CGTTGCGA
165793 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:165800 original size:33 final size:33
Alignment explanation
Indices: 165733--165814 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
165723 TGCGATTTGG
***
165733 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
165766 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
165799 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
165815 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:165819 original size:20 final size:20
Alignment explanation
Indices: 165745--165833 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
165735 TCGCGTTGCG
165745 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
165765 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
165778 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
165798 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
165818 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
165834 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:165954 original size:33 final size:33
Alignment explanation
Indices: 165912--165982 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
165902 AATACTAACT
*
165912 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
165945 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
165978 TGAAA
1 TGAAA
165983 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:166214 original size:22 final size:22
Alignment explanation
Indices: 166162--166216 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
166152 TGGTTGTGAG
**
166162 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
166184 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
166206 GGATTTCTTCG
1 GGATTTCTTCG
166217 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:166387 original size:20 final size:20
Alignment explanation
Indices: 166362--166554 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
166352 CTTTAAATAT
166362 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
166382 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
166404 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
166423 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
166443 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
166463 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
166483 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
166503 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
166523 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
166543 CGCGTTGCGATT
1 CGCGTTGCGATT
166555 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:166549 original size:60 final size:60
Alignment explanation
Indices: 166362--166554 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
166352 CTTTAAATAT
**
166362 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
166423 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
166483 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
166543 CGCGTTGCGATT
1 CGCGTTGCGATT
166555 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:166635 original size:20 final size:20
Alignment explanation
Indices: 166610--166661 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
166600 AAGAATCGCG
*
166610 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
166630 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
166650 TTGCGATTCTGG
1 TTGCGATTCTGG
166662 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:171930 original size:42 final size:43
Alignment explanation
Indices: 171871--171953 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 43
171861 AATTAGATGA
*
171871 CCGGATTTTTTACCGGATTAAAAACCGTTTTTTTTA-AAACTG
1 CCGGATTTTTTACCGGATTAAAAACCGATTTTTTTATAAACTG
*
171913 CCGGATTTTTTACCGGATTAAAAACTGATTTTTTTATAAAC
1 CCGGATTTTTTACCGGATTAAAAACCGATTTTTTTATAAAC
171954 CGGTTTTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 34 0.89
43 4 0.11
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (43 bp):
CCGGATTTTTTACCGGATTAAAAACCGATTTTTTTATAAACTG
Done.