Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008772.1 Hibiscus syriacus cultivar Beakdansim tig00111877_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: 3098974
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 16
Found at i:2118294 original size:30 final size:31
Alignment explanation
Indices: 2118222--2118299 Score: 115
Period size: 30 Copynumber: 2.6 Consensus size: 31
2118212 ATTTAACAAA
* **
2118222 AAGGGGGAG-AAATTTAAGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
2118252 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
2118283 AA-GGGGAGTAAGTTTTT
1 AAGGGGGAGTAAGTTTTT
2118300 CAAAATCAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 24 0.55
31 20 0.45
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.32
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
Found at i:2118714 original size:19 final size:19
Alignment explanation
Indices: 2118690--2118728 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2118680 TCGAATGCAT
2118690 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
2118709 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
2118728 T
1 T
2118729 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:2118745 original size:65 final size:64
Alignment explanation
Indices: 2118627--2118771 Score: 163
Period size: 65 Copynumber: 2.2 Consensus size: 64
2118617 TATTCAAAGG
*
2118627 CATGCACCGATGCA-TCAATCCATGCATCGATGCATCGATGAATTAATTGAACATCGAATGCATT
1 CATGCACCGATGCACTC-ATCCATGCATCGATGCATC-ATGAATTAATTAAACATCGAATGCATT
2118691 C
64 C
*
2118692 CATGCACCGATGCACTC-TCCATGCATCGATGCACTC-TGAA-TATTTTCAAAACATCGAATGCA
1 CATGCACCGATGCACTCATCCATGCATCGATGCA-TCATGAATTA-ATT--AAACATCGAATGCA
*
2118754 TTT
62 TTC
* *
2118757 GATGCATCGATGCAC
1 CATGCACCGATGCAC
2118772 CAGGCTATTT
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
62 2 0.03
63 6 0.09
64 16 0.23
65 44 0.63
66 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCATCCATGCATCGATGCATCATGAATTAATTAAACATCGAATGCATTC
Found at i:2118796 original size:45 final size:46
Alignment explanation
Indices: 2118712--2118815 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 46
2118702 TGCACTCTCC
*
2118712 ATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTG
** *
2118758 ATGCATCGATGCAC-CAGGCTATTTTTC-AAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGAATA-TTTTCAAAACATCGAATGCATTTG
2118803 ATGCATCGATGCA
1 ATGCATCGATGCA
2118816 TCCTTAGTGC
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
45 34 0.64
46 19 0.36
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (46 bp):
ATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTG
Found at i:2127917 original size:21 final size:21
Alignment explanation
Indices: 2127847--2127927 Score: 83
Period size: 23 Copynumber: 3.8 Consensus size: 21
2127837 TATTTGGCAG
*
2127847 AGGGAAACGATACCCCC-ATA
1 AGGGAATCGATACCCCCTATA
* * *
2127867 AGGGAACCGATTCCCCCTTTGA
1 AGGGAATCGATACCCCCTAT-A
*
2127889 ATGGGAATCGATTCCCCCTATA
1 A-GGGAATCGATACCCCCTATA
*
2127911 GGGGAATCGATACCCCC
1 AGGGAATCGATACCCCC
2127928 ATGGGGTTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
20 15 0.29
21 16 0.31
22 3 0.06
23 17 0.33
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (21 bp):
AGGGAATCGATACCCCCTATA
Found at i:2128248 original size:14 final size:13
Alignment explanation
Indices: 2128226--2128267 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
2128216 TTATATGATG
2128226 TTTTT-CAAACAT
1 TTTTTCCAAACAT
2128238 TATTTTCCAAACAGT
1 T-TTTTCCAAACA-T
*
2128253 TTTTTCAAAACAT
1 TTTTTCCAAACAT
2128266 TT
1 TT
2128268 CCCTTTAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 1 0.04
13 7 0.27
14 16 0.62
15 2 0.08
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (13 bp):
TTTTTCCAAACAT
Found at i:2131539 original size:37 final size:37
Alignment explanation
Indices: 2131486--2131590 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
2131476 CCTTTTCGTC
* *
2131486 CTACTAGGATTCAAACTCATAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * *
2131523 TTGCTAGGATTTAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* *
2131560 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
2131591 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:2132039 original size:2 final size:2
Alignment explanation
Indices: 2132032--2132061 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2132022 CTTAATTAGT
2132032 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
2132062 CTTGCTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2132243 original size:22 final size:23
Alignment explanation
Indices: 2132217--2132264 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
2132207 ATTCTACTTA
2132217 TTTATATTATA-TATGTA-TATTT
1 TTTATATTATATTAT-TATTATTT
*
2132239 TTTATATTTTATTATTATTATTT
1 TTTATATTATATTATTATTATTT
2132262 TTT
1 TTT
2132265 TTACTTTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTATATTATATTATTATTATTT
Found at i:2132306 original size:12 final size:11
Alignment explanation
Indices: 2132276--2132311 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2132266 TACTTTCTCT
*
2132276 TTCTTTTATTA
1 TTCTTGTATTA
2132287 TTCTTGTATTA
1 TTCTTGTATTA
2132298 TTACTTGTATTA
1 TT-CTTGTATTA
2132310 TT
1 TT
2132312 TTTATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (11 bp):
TTCTTGTATTA
Found at i:2132328 original size:2 final size:2
Alignment explanation
Indices: 2132321--2132367 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2132311 TTTTATATTT
2132321 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
2132363 TA TA T
1 TA TA T
2132368 GCGTATGTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2132839 original size:23 final size:23
Alignment explanation
Indices: 2132794--2132842 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2132784 TTCTTTTCGT
2132794 TATTTAATTTATTAATTTATATA
1 TATTTAATTTATTAATTTATATA
* *
2132817 TATTTACTTT-TTTATTTATTATA
1 TATTTAATTTATTAATTTA-TATA
2132840 TAT
1 TAT
2132843 ATATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTTAATTTATTAATTTATATA
Found at i:2132897 original size:22 final size:20
Alignment explanation
Indices: 2132862--2132936 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
2132852 TTATTCGTAC
*
2132862 TTTGTTATTATTATTTTGTTTA
1 TTTGTT-TTTTTATTTT-TTTA
*
2132884 TTTGTTTTATTTATTTTCTT-
1 TTTGTTTT-TTTATTTTTTTA
* *
2132904 TTTCTTTTTTATATATTTTTA
1 TTTGTTTTTT-TATTTTTTTA
2132925 TTTGTTTTTTTA
1 TTTGTTTTTTTA
2132937 CTTACTATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.05
20 16 0.36
21 13 0.30
22 13 0.30
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTGTTTTTTTATTTTTTTA
Found at i:2137379 original size:7 final size:6
Alignment explanation
Indices: 2137378--2137434 Score: 60
Period size: 6 Copynumber: 9.0 Consensus size: 6
2137368 CAAAAAAGAA
* *
2137378 AAAAAG CAAAAAG AAAAAG AAAAAG AAAAAG AAAGAAC AAAAATC AAAAAG
1 AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAA-AAG AAAAA-G AAAAAG
*
2137429 GAAAAG
1 AAAAAG
2137435 GGACAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
6 28 0.62
7 17 0.38
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:2137380 original size:22 final size:21
Alignment explanation
Indices: 2137354--2137403 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2137344 CAATCAGAAC
*
2137354 AAAAAGGGCAAAAACAAAAAAG
1 AAAAAGAGCAAAAA-AAAAAAG
* *
2137376 AAAAAAAGCAAAAAGAAAAAG
1 AAAAAGAGCAAAAAAAAAAAG
2137397 AAAAAGA
1 AAAAAGA
2137404 AAAAGAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAAAGAGCAAAAAAAAAAAG
Found at i:2137381 original size:15 final size:15
Alignment explanation
Indices: 2137370--2137407 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 15
2137360 GGCAAAAACA
2137370 AAAAAGAAAAAAAGC
1 AAAAAGAAAAAAAGC
2137385 AAAAAG--AAAAAG-
1 AAAAAGAAAAAAAGC
2137397 AAAAAGAAAAA
1 AAAAAGAAAAA
2137408 GAAAGAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 6 0.29
14 3 0.14
15 6 0.29
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAGC
Found at i:2137394 original size:12 final size:12
Alignment explanation
Indices: 2137378--2137434 Score: 60
Period size: 13 Copynumber: 4.5 Consensus size: 12
2137368 CAAAAAAGAA
2137378 AAAAAGCAAAAAG
1 AAAAAG-AAAAAG
2137391 AAAAAGAAAAAG
1 AAAAAGAAAAAG
*
2137403 AAAAAGAAAGAAC
1 AAAAAGAAA-AAG
*
2137416 AAAAATCAAAAAG
1 AAAAA-GAAAAAG
*
2137429 GAAAAG
1 AAAAAG
2137435 GGACAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
12 15 0.41
13 19 0.51
14 3 0.08
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:2138111 original size:22 final size:22
Alignment explanation
Indices: 2138037--2138113 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
2138027 GCTACCCCAT
*
2138037 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
* **
2138059 CAAACCTATGAGCATCCCATGC
1 CAAACCTTTGAGCATCAAATGC
2138081 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
2138103 CAAACCTTTGA
1 CAAACCTTTGA
2138114 CCAAACATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:2139142 original size:106 final size:106
Alignment explanation
Indices: 2138938--2140428 Score: 2120
Period size: 106 Copynumber: 14.0 Consensus size: 106
2138928 ATATCGTGCC
* * * * * * * *
2138938 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTTTCAAC-AACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
2139002 AATTTCGGAGCTAATTTCAACGTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
2139043 ACTCTAGACAACACAAGTTAAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2139108 AATTTTAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2139149 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2139214 AATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
2139255 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2139320 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
2139361 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGAGACCGCTGGTTGTCAATAACCAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2139426 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
2139467 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2139532 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
2139573 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2139638 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
2139679 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2139744 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
2139785 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
2139850 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
2139891 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAATAAACAACTTGCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2139956 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
2139997 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACCAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2140062 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
2140103 ACTCAAGACAACGCAAGTTTACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
1 ACTCCAG---A--C-A----ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
* * *
2140168 ACAACTTCCCAATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGA
56 ACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * ** ** *
2140219 AC-CCAAGGCAACACAAGCTCAACTTCACGACGAATAGG-CAACTAATTGTTAAC-AA-AA-TT-
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAA-GGGACCGCTGGTTGTCAACAAACAACTTC
* * *
2140278 TC-A-TTCAGAGTCAATTTCAACTTCACAGCGAATGATATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
2140319 ACTCGAGATAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCAC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** * * * *
2140384 GGTTCCAAAGCCAATTTCAACTTCAC-GACGGAGGATACTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
2140425 ACTC
1 ACTC
2140429 AGAACAATGC
Statistics
Matches: 1259, Mismatches: 105, Indels: 43
0.89 0.07 0.03
Matches are distributed among these distances:
99 2 0.00
100 70 0.06
101 4 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 49 0.04
106 1025 0.81
107 2 0.00
109 1 0.00
110 1 0.00
111 2 0.00
112 1 0.00
115 1 0.00
116 91 0.07
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:2141198 original size:37 final size:37
Alignment explanation
Indices: 2141146--2141249 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
2141136 CTTTTCGTCA
* *
2141146 TACTAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TACTAGGATTTAAACTCCTAAAAATATGATAGAATTC
* * *
2141183 TGCTAGGATTTAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTTAAACTCCTAAAAATATGATAGAATTC
* * *
2141220 TACTATGATTTAAAATCCTAAAGATATGAT
1 TACTAGGATTTAAACTCCTAAAAATATGAT
2141250 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (37 bp):
TACTAGGATTTAAACTCCTAAAAATATGATAGAATTC
Found at i:2141916 original size:15 final size:15
Alignment explanation
Indices: 2141811--2141920 Score: 61
Period size: 15 Copynumber: 7.3 Consensus size: 15
2141801 TTTTCTTTGC
2141811 ATTT-TTATTATTACT
1 ATTTATTATTATTA-T
2141826 ATTATATTTATTATTAT
1 ATT-TA-TTATTATTAT
* *
2141843 TTTTACTATTA-TAT
1 ATTTATTATTATTAT
* *
2141857 -TTTCCTT-TTATTCT
1 ATTT-ATTATTATTAT
*
2141871 ACTTATT-TATATTAT
1 ATTTATTAT-TATTAT
*
2141886 ATATGTA-TATTTTTAT
1 AT-T-TATTATTATTAT
2141902 ATTTATTATTATTAT
1 ATTTATTATTATTAT
2141917 ATTT
1 ATTT
2141921 TTTTACTTTC
Statistics
Matches: 73, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
13 6 0.08
14 11 0.15
15 29 0.40
16 12 0.16
17 6 0.08
18 9 0.12
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.65
Consensus pattern (15 bp):
ATTTATTATTATTAT
Found at i:2141965 original size:12 final size:11
Alignment explanation
Indices: 2141941--2141981 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2141931 TCTTTTTTTT
2141941 TATTATTCTTG
1 TATTATTCTTG
2141952 TATTATTACTTG
1 TATTATT-CTTG
* *
2141964 TATTATTTTTA
1 TATTATTCTTG
2141975 TATTATT
1 TATTATT
2141982 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:2141982 original size:11 final size:11
Alignment explanation
Indices: 2141935--2141982 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
2141925 ACTTTCTCTT
*
2141935 TTTTTTTATTA
1 TTTTTGTATTA
*
2141946 TTCTTGTATTA
1 TTTTTGTATTA
*
2141957 TTACTTGTATTA
1 TT-TTTGTATTA
*
2141969 TTTTTATATTA
1 TTTTTGTATTA
2141980 TTT
1 TTT
2141983 ATTTTGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (11 bp):
TTTTTGTATTA
Found at i:2142209 original size:2 final size:2
Alignment explanation
Indices: 2142202--2142228 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2142192 TTACTATTAT
2142202 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 T
2142229 TCTACACAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2142502 original size:34 final size:34
Alignment explanation
Indices: 2142458--2142544 Score: 81
Period size: 34 Copynumber: 2.5 Consensus size: 34
2142448 TCTTTTCGTC
*
2142458 ATTTAATTTATTAATTTATATATATT-TACTTT-TT
1 ATTTATTTTATT-ATTTATAT-TATTCTACTTTGTT
*
2142492 ATTTATTTTA-TATATATATTATTCGTACTTTGTT
1 ATTTATTTTATTATTTATATTATTC-TACTTTGTT
2142526 ATTATTATTTTATTTATTT
1 A-T-TTATTTTA-TTATTT
2142545 GTTTTATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
31 4 0.09
32 7 0.16
33 7 0.16
34 12 0.28
35 1 0.02
36 8 0.19
38 4 0.09
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (34 bp):
ATTTATTTTATTATTTATATTATTCTACTTTGTT
Found at i:2142551 original size:13 final size:13
Alignment explanation
Indices: 2142533--2142557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2142523 GTTATTATTA
2142533 TTTTATTTATTTG
1 TTTTATTTATTTG
2142546 TTTTATTTATTT
1 TTTTATTTATTT
2142558 TCTTTTTCTT
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:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTTATTTATTTG
Found at i:2142555 original size:28 final size:27
Alignment explanation
Indices: 2142524--2142618 Score: 76
Period size: 27 Copynumber: 3.6 Consensus size: 27
2142514 TCGTACTTTG
2142524 TTATTATTATTTTATTTATTTGTTTTAT
1 TTATTATTATTTTATTTATTTGTTTT-T
* *
2142552 TTATT-TTCTTTT-TCTT-TTT-CTTTT
1 TTATTATTATTTTAT-TTATTTGTTTTT
2142576 TTA-TATATATTTTA-TTATTTGTTTTTT
1 TTATTAT-TATTTTATTTATTTG-TTTTT
*
2142603 TTACTTACTATTTTAT
1 TTA-TTATTATTTTAT
2142619 CTTTGCTTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 19
0.68 0.07 0.25
Matches are distributed among these distances:
23 1 0.02
24 7 0.13
25 11 0.21
26 4 0.08
27 15 0.29
28 12 0.23
29 2 0.04
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (27 bp):
TTATTATTATTTTATTTATTTGTTTTT
Found at i:2145053 original size:27 final size:27
Alignment explanation
Indices: 2145021--2145074 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
2145011 AAATACTTTA
2145021 GGTCATTTAACACTTTAGGAGCATTTT
1 GGTCATTTAACACTTTAGGAGCATTTT
* *
2145048 GGTCATTTTACACTTTAGGGGCATTTT
1 GGTCATTTAACACTTTAGGAGCATTTT
2145075 TATAAATCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (27 bp):
GGTCATTTAACACTTTAGGAGCATTTT
Found at i:2148762 original size:21 final size:21
Alignment explanation
Indices: 2148727--2148790 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
2148717 GCCGAAAGTT
2148727 ACTGTAGCAAGGGTATCGGTAC
1 ACTGTAGC-AGGGTATCGGTAC
*
2148749 ACTGTAGCAGGGTATCAGTAC
1 ACTGTAGCAGGGTATCGGTAC
* *
2148770 ATTGTAGCAGGATATCGGTAC
1 ACTGTAGCAGGGTATCGGTAC
2148791 CATTGTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
21 30 0.79
22 8 0.21
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGGGTATCGGTAC
Found at i:2153004 original size:48 final size:48
Alignment explanation
Indices: 2152952--2153368 Score: 331
Period size: 48 Copynumber: 8.6 Consensus size: 48
2152942 TAGCCTGCAC
* *
2152952 TTGTTCAAGATGATC-GAAACTCTGATAACTTTTCAGAGGCCGATGCTG
1 TTGTTGAAGATGATCAG-AACTCTGATAACTTTTCAGAGGCTGATGCTG
* * *
2153000 TTGTTGAAGATGATCAGAACTCGGAGAACATTTT-TGAGGCTGATGCTG
1 TTGTTGAAGATGATCAGAACTCTGATAAC-TTTTCAGAGGCTGATGCTG
* * * * ** *
2153048 TTCTTGAAGATGATAAGAACTCTCATTACTTTATCA-AGGATCCTGACACTA
1 TTGTTGAAGATGATCAGAACTCTGATAACTTT-TCAGAGG---CTGATGCTG
* ** * * *
2153099 TTGTTGGAGATGATTGGAACTCTGATAACTTTCCTGAAGCTGATGCTG
1 TTGTTGAAGATGATCAGAACTCTGATAACTTTTCAGAGGCTGATGCTG
* ** * * *
2153147 TTGATGAAGATGATTGGAAGTCATCA-AACTTTTCCGAGGCTGATGCTG
1 TTGTTGAAGATGATCAGAACTC-TGATAACTTTTCAGAGGCTGATGCTG
* * * * *
2153195 TTGTTCAAGATCATCAGAACTCTGATAACTTTCCTGAGGAGTCCGATGCTG
1 TTGTTGAAGATGATCAGAACTCTGATAACTTT--TCA-GAGGCTGATGCTG
* * *
2153246 TTGTTGAAGACGATCAGAAGTCTGATAACTTTCTC-GAGACTGATGCTG
1 TTGTTGAAGATGATCAGAACTCTGATAACTTT-TCAGAGGCTGATGCTG
* * ** * ** * *
2153294 TTGCTGGAGGCGATCAGAACTCTGATAACTTTCCTTAGGATGATGTTG
1 TTGTTGAAGATGATCAGAACTCTGATAACTTTTCAGAGGCTGATGCTG
2153342 TTGTTGAAGATGATCAGAACTCTGATA
1 TTGTTGAAGATGATCAGAACTCTGATA
2153369 TCTGTCCTGA
Statistics
Matches: 290, Mismatches: 65, Indels: 28
0.76 0.17 0.07
Matches are distributed among these distances:
47 6 0.02
48 200 0.69
49 7 0.02
50 4 0.01
51 73 0.25
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (48 bp):
TTGTTGAAGATGATCAGAACTCTGATAACTTTTCAGAGGCTGATGCTG
Found at i:2153243 original size:99 final size:98
Alignment explanation
Indices: 2153115--2153360 Score: 283
Period size: 99 Copynumber: 2.5 Consensus size: 98
2153105 GAGATGATTG
* **
2153115 GAACTCTGATAACTTTCCTGA--AG-CTGATGCTGTTGATGAAGATGATTGGAAGTCATCA-AAC
1 GAACTCTGATAACTTTCCTGAGGAGTC-GATGCTGTTGTTGAAGATGATCAGAAGTC-TCATAAC
* * *
2153176 TTT-TCCGAGGCTGATGCTGTTGTTCAAGATC-ATCA
64 TTTCT-CGAGACTGATGCTGTTGCTCAAG-GCGATCA
* *
2153211 GAACTCTGATAACTTTCCTGAGGAGTCCGATGCTGTTGTTGAAGACGATCAGAAGTCTGATAACT
1 GAACTCTGATAACTTTCCTGAGGAGT-CGATGCTGTTGTTGAAGATGATCAGAAGTCTCATAACT
**
2153276 TTCTCGAGACTGATGCTGTTGCTGGAGGCGATCA
65 TTCTCGAGACTGATGCTGTTGCTCAAGGCGATCA
* *
2153310 GAACTCTGATAACTTTCCTTAGGA-T-GATGTTGTTGTTGAAGATGATCAGAA
1 GAACTCTGATAACTTTCCTGAGGAGTCGATGCTGTTGTTGAAGATGATCAGAA
2153361 CTCTGATATC
Statistics
Matches: 130, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
96 45 0.35
98 6 0.05
99 77 0.59
100 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (98 bp):
GAACTCTGATAACTTTCCTGAGGAGTCGATGCTGTTGTTGAAGATGATCAGAAGTCTCATAACTT
TCTCGAGACTGATGCTGTTGCTCAAGGCGATCA
Found at i:2153250 original size:147 final size:147
Alignment explanation
Indices: 2152952--2153383 Score: 401
Period size: 147 Copynumber: 2.9 Consensus size: 147
2152942 TAGCCTGCAC
* * * * * *
2152952 TTGTTCAAGATGATCGAAACTCTGATAACTTTTCAGAGGCCGATGCTGTTGTTGAAGATGATCAG
1 TTGTTGAAGATGATCGGAACTCTGATAAC-TTTCTGAAGCTGATGCTGTTGATGAAGATGATCAG
* * * * * *
2153017 AACTCGGAGAACATTTT-TGAGGCTGATGCTGTTCTTGAAGATGATAAGAACTCTCATTACTTT-
65 AACTCTGAGAAC-TTTTCCGAGGCTGATGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTTC
* *
2153080 ATCAAGGA-TCCTGACACTA
129 CT-GAGGAGTCCTGACACTA
* * **
2153099 TTGTTGGAGATGATTGGAACTCTGATAACTTTCCTGAAGCTGATGCTGTTGATGAAGATGATTGG
1 TTGTTGAAGATGATCGGAACTCTGATAACTTT-CTGAAGCTGATGCTGTTGATGAAGATGATCAG
* * * *
2153164 AAGTCATCA-AACTTTTCCGAGGCTGATGCTGTTGTTCAAGATCATCAGAACTCTGATAACTTTC
65 AACTC-TGAGAACTTTTCCGAGGCTGATGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTTC
** *
2153228 CTGAGGAGTCC-GATGCTG
129 CTGAGGAGTCCTGACACTA
* * * * * **
2153246 TTGTTGAAGACGATCAGAAGTCTGATAACTTTCTCG-AGACTGATGCTGTTGCTGGAGGCGATCA
1 TTGTTGAAGATGATCGGAACTCTGATAACTTTCT-GAAG-CTGATGCTGTTGATGAAGATGATCA
* * * * * *
2153310 GAACTCTGATAAC-TTTCCTTAGGATGATGTTGTTGTTGAAGATGATCAGAACTCTGATATCTGT
64 GAACTCTGAGAACTTTTCC-GAGGCTGATGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTT
2153374 CCTGAGGAGT
128 CCTGAGGAGT
2153384 TCAAATCAAT
Statistics
Matches: 231, Mismatches: 45, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
146 18 0.08
147 208 0.90
148 5 0.02
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (147 bp):
TTGTTGAAGATGATCGGAACTCTGATAACTTTCTGAAGCTGATGCTGTTGATGAAGATGATCAGA
ACTCTGAGAACTTTTCCGAGGCTGATGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTTCCT
GAGGAGTCCTGACACTA
Found at i:2154860 original size:27 final size:27
Alignment explanation
Indices: 2154830--2154890 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
2154820 AAATATATAT
2154830 TTTTTAAATCAAAATAAAAATAAAATA
1 TTTTTAAATCAAAATAAAAATAAAATA
* ** *
2154857 TTTTTAAATTAAGTTAATAATAAAATA
1 TTTTTAAATCAAAATAAAAATAAAATA
*
2154884 TATTTAA
1 TTTTTAA
2154891 TGAACTACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
TTTTTAAATCAAAATAAAAATAAAATA
Found at i:2165462 original size:9 final size:9
Alignment explanation
Indices: 2165448--2165481 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
2165438 TAAAAGGGAA
2165448 AAATAAAAT
1 AAATAAAAT
2165457 AAATAAAAT
1 AAATAAAAT
2165466 AAAT-AAAT
1 AAATAAAAT
2165474 AAGATAAA
1 AA-ATAAA
2165482 GGAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2165981 original size:18 final size:17
Alignment explanation
Indices: 2165958--2166000 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2165948 ATATATACAT
2165958 ATAATAATAATAACATAA
1 ATAATAATAATAA-ATAA
* *
2165976 ATAATAAAAATAAATGA
1 ATAATAATAATAAATAA
2165993 ATAA-AATA
1 ATAATAATA
2166001 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:2165997 original size:14 final size:13
Alignment explanation
Indices: 2165960--2165998 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
2165950 ATATACATAT
2165960 AATAATAATAACATA
1 AATAATAA-AA-ATA
2165975 AATAATAAAAATA
1 AATAATAAAAATA
2165988 AATGAATAAAA
1 AAT-AATAAAA
2165999 TATCCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:2166434 original size:37 final size:36
Alignment explanation
Indices: 2166391--2166492 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
2166381 ATAGTAGAAC
2166391 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
2166428 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
2166462 TCTATCATATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
2166493 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 32 0.53
37 28 0.47
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:2167348 original size:105 final size:105
Alignment explanation
Indices: 2167040--2167871 Score: 1314
Period size: 105 Copynumber: 8.0 Consensus size: 105
2167030 CATTGTTCCA
* * * ** * * *
2167040 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * *
2167105 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
2167146 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
2167206 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
2167246 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
**
2167311 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCACTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
2167351 AGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
2167416 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
2167456 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
2167521 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
2167561 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
2167626 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
2167666 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
2167731 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
2167771 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
2167836 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
2167872 CCTCGAGTGC
Statistics
Matches: 683, Mismatches: 37, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
100 84 0.12
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.00
105 510 0.75
106 77 0.11
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:2168604 original size:68 final size:65
Alignment explanation
Indices: 2168514--2168671 Score: 199
Period size: 68 Copynumber: 2.4 Consensus size: 65
2168504 AAGATATCTG
* * ** *
2168514 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATT-TGTTTTAAGGGAAATAAATTCAAAG-G
2168579 TT
64 TT
* * * *
2168581 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTTTTTTAGGGGAAATAAATTCAAAGGT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGGT
2168646 T
65 T
*
2168647 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
2168672 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 22 0.28
68 32 0.41
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.33
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGGTT
Found at i:2168698 original size:36 final size:35
Alignment explanation
Indices: 2168647--2168927 Score: 272
Period size: 36 Copynumber: 8.0 Consensus size: 35
2168637 TTCAAAGGTT
* *
2168647 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
2168683 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
2168718 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
2168756 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
2168785 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
2168820 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
2168857 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
2168892 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
2168928 CTCTTCTAGT
Statistics
Matches: 204, Mismatches: 25, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 134 0.66
37 33 0.16
38 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:2168757 original size:138 final size:137
Alignment explanation
Indices: 2168595--2168901 Score: 409
Period size: 138 Copynumber: 2.2 Consensus size: 137
2168585 TTTCAAGAGT
* * ** * * *
2168595 AACTGTCTCAAGGGAGACAAAATTTTTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
2168660 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
2168724 TCCAAAAGA
129 TCCAAAAGA
** * *
2168733 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * *
2168798 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
2168863 CAAGAGA
131 CAAAAGA
*
2168870 AACTGTCTCAAGAGAGACAAAATTTGTTTCAA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAA
2168902 GGGAAACTGT
Statistics
Matches: 146, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
137 44 0.30
138 102 0.70
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:2168949 original size:35 final size:36
Alignment explanation
Indices: 2168789--2168961 Score: 172
Period size: 36 Copynumber: 4.8 Consensus size: 36
2168779 AATATTTTGT
* * **
2168789 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * * * *
2168825 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* *
2168861 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTGC
*
2168897 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * *
2168931 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
2168962 TCTTGTTTTA
Statistics
Matches: 121, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.04
35 23 0.19
36 92 0.76
37 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:2169434 original size:18 final size:18
Alignment explanation
Indices: 2169407--2169442 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2169397 TGTTGAATCC
* *
2169407 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
2169425 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
2169443 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:2169934 original size:22 final size:22
Alignment explanation
Indices: 2169857--2169927 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
2169847 TTGTGTTTGG
*
2169857 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
2169879 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
2169901 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
2169923 TCAAA
1 TCAAA
2169928 AGATTGATGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:2170611 original size:15 final size:15
Alignment explanation
Indices: 2170587--2170653 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 15
2170577 TGATTTTTGC
*
2170587 TCTTTTTTTCTTTTGT
1 TCTTTGTTTCTTTT-T
2170603 TC-TTGTTTCTCTTTT
1 TCTTTGTTTCT-TTTT
2170618 TCTTTGTTT-TTTTT
1 TCTTTGTTTCTTTTT
2170632 TGCTTT-TTTGCTTCTTT
1 T-CTTTGTTT-CTT-TTT
2170649 TCTTT
1 TCTTT
2170654 TTTGTTCTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
14 8 0.18
15 15 0.34
16 17 0.39
17 4 0.09
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (15 bp):
TCTTTGTTTCTTTTT
Found at i:2170639 original size:22 final size:22
Alignment explanation
Indices: 2170590--2170657 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
2170580 TTTTTGCTCT
* *
2170590 TTTTTTCTTTTGTTCTTGTTT-C
1 TTTTTTC-TTTGTTTTTTTTTGC
2170612 TCTTTTTCTTTGTTTTTTTTTGC
1 T-TTTTTCTTTGTTTTTTTTTGC
2170635 TTTTTTGCTTCT-TTTCTTTTTTG
1 TTTTTT-CTT-TGTTT-TTTTTTG
2170658 TTCTTGATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 17 0.44
23 14 0.36
24 8 0.21
ACGTcount: A:0.00, C:0.13, G:0.09, T:0.78
Consensus pattern (22 bp):
TTTTTTCTTTGTTTTTTTTTGC
Found at i:2170640 original size:23 final size:22
Alignment explanation
Indices: 2170555--2170662 Score: 76
Period size: 24 Copynumber: 4.5 Consensus size: 22
2170545 TTGCATGTGC
*
2170555 TTTTTGTCCCTTTTTCTTTTTTT
1 TTTTTG-CTCTTTTTCTTTTTTT
2170578 GATTTTTGCTCTTTTT-TTCTTTTGT
1 --TTTTTGCTCTTTTTCTT-TTTT-T
*
2170603 TCTTGTTTCTCTTTTTCTTTGTTTT
1 T-TT-TTGCTCTTTTTCTTT-TTTT
2170628 TTTTTGCT-TTTTTGCTTCTTTTCT
1 TTTTTGCTCTTTTT-CTT-TTTT-T
*
2170652 TTTTTGTTCTT
1 TTTTTGCTCTT
2170663 GATTGGATCT
Statistics
Matches: 69, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
22 5 0.07
23 13 0.19
24 24 0.35
25 22 0.32
26 5 0.07
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.76
Consensus pattern (22 bp):
TTTTTGCTCTTTTTCTTTTTTT
Found at i:2173767 original size:2 final size:2
Alignment explanation
Indices: 2173760--2173800 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2173750 GAAAAAGAAA
2173760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2173801 CATCAAAGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2174205 original size:12 final size:12
Alignment explanation
Indices: 2174184--2174222 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
2174174 ATATATATAT
2174184 ACATATAATAATA
1 ACATA-AATAATA
2174197 ACATAAATAATA
1 ACATAAATAATA
*
2174209 AAATAAATGAATA
1 ACATAAAT-AATA
2174222 A
1 A
2174223 AATATCCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (12 bp):
ACATAAATAATA
Found at i:2174660 original size:37 final size:36
Alignment explanation
Indices: 2174617--2174718 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
2174607 ATAGTAGAAC
2174617 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
2174654 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
2174688 TCTATCATATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
2174719 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 32 0.53
37 28 0.47
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:2178401 original size:3 final size:3
Alignment explanation
Indices: 2178393--2178426 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2178383 CAATTCATTG
*
2178393 TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2178427 ATTGCCTCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2182168 original size:13 final size:13
Alignment explanation
Indices: 2182152--2182180 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2182142 GAGAGACTAG
2182152 TAATTCCAGATGA
1 TAATTCCAGATGA
2182165 TAATTCCAGATGA
1 TAATTCCAGATGA
2182178 TAA
1 TAA
2182181 GGAGTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (13 bp):
TAATTCCAGATGA
Found at i:2186411 original size:16 final size:17
Alignment explanation
Indices: 2186392--2186429 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2186382 GTTTTATGGA
2186392 TTTATATGTTTTAG-TT
1 TTTATATGTTTTAGATT
* *
2186408 TTTAGATTTTTTAGATT
1 TTTATATGTTTTAGATT
2186425 TTTAT
1 TTTAT
2186430 TAAGTTTTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (17 bp):
TTTATATGTTTTAGATT
Found at i:2190223 original size:34 final size:32
Alignment explanation
Indices: 2190161--2190230 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
2190151 ACCTTACAAC
* *
2190161 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
2190193 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
2190227 TCCC
1 TCCC
2190231 CTTTACAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:2190539 original size:21 final size:21
Alignment explanation
Indices: 2190514--2190555 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2190504 CCAGAATGGG
*
2190514 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2190535 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2190556 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:2190681 original size:19 final size:19
Alignment explanation
Indices: 2190641--2190687 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
2190631 AGCCTCGGGG
*
2190641 TACTGTTCAAACAATAATT
1 TACTGTTCAAACAATAAAT
* *
2190660 TACTGTTCAAATAGTAAAT
1 TACTGTTCAAACAATAAAT
*
2190679 TACTATTCA
1 TACTGTTCA
2190688 TAAAAACATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.38
Consensus pattern (19 bp):
TACTGTTCAAACAATAAAT
Found at i:2190784 original size:29 final size:31
Alignment explanation
Indices: 2190752--2190811 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
2190742 AAATTTTGAA
*
2190752 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
*
2190781 TAAATTTAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
2190812 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 10 0.37
31 7 0.26
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:2193335 original size:23 final size:23
Alignment explanation
Indices: 2193291--2193354 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
2193281 CAACTCTTAT
* *
2193291 AAATGCACCAAAGTGCCACGTAG
1 AAATACACCGAAGTGCCACGTAG
* * *
2193314 AATTATACCGAAGTGCCGCGTAG
1 AAATACACCGAAGTGCCACGTAG
*
2193337 AAATGCACCGAAGTGCCA
1 AAATACACCGAAGTGCCA
2193355 TATAAAATGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATACACCGAAGTGCCACGTAG
Found at i:2194353 original size:2 final size:2
Alignment explanation
Indices: 2194346--2194395 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2194336 TTTACATGTA
2194346 AT AT AT AT AT 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 AT AT AT AT AT
2194388 AT AT AT AT
1 AT AT AT AT
2194396 TGTTATCTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2194981 original size:16 final size:18
Alignment explanation
Indices: 2194960--2195000 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2194950 GCATGTTAAC
2194960 ACATATAA-TCATG-CAT
1 ACATATAATTCATGTCAT
2194976 ACATATAATTCATGTCAT
1 ACATATAATTCATGTCAT
*
2194994 GCATATA
1 ACATATA
2195001 CATATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 9 0.41
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (18 bp):
ACATATAATTCATGTCAT
Found at i:2198282 original size:23 final size:23
Alignment explanation
Indices: 2198253--2198317 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
2198243 CAGCTCGAAT
*
2198253 AAATGCACCGAAGTGCCATGTAG
1 AAATGCACCGAAGTGCCATGTAA
* * **
2198276 AATTGCACCGAAGTGTCGCGTAA
1 AAATGCACCGAAGTGCCATGTAA
2198299 AAATGCACCGAAGTGCCAT
1 AAATGCACCGAAGTGCCAT
2198318 ATGAAATGTC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCATGTAA
Found at i:2198339 original size:22 final size:22
Alignment explanation
Indices: 2198314--2198364 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2198304 CACCGAAGTG
2198314 CCATAT-GAAATGTCCATAAGGA
1 CCATATAGAAAT-TCCATAAGGA
* *
2198336 CCATATAGAAATTCCTTAAGAA
1 CCATATAGAAATTCCATAAGGA
*
2198358 TCATATA
1 CCATATA
2198365 CATATTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (22 bp):
CCATATAGAAATTCCATAAGGA
Found at i:2199418 original size:34 final size:34
Alignment explanation
Indices: 2199375--2199443 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
2199365 AACAATGCCA
*
2199375 AAGGTAAGAGAAGTACCTATACTCCCATGATGGT
1 AAGGTAAGAGAAGTACCTATAATCCCATGATGGT
2199409 AAGGTAAGAGAAGTACCTATAATCCCATGATGGT
1 AAGGTAAGAGAAGTACCTATAATCCCATGATGGT
2199443 A
1 A
2199444 TCGATACTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (34 bp):
AAGGTAAGAGAAGTACCTATAATCCCATGATGGT
Found at i:2199920 original size:15 final size:15
Alignment explanation
Indices: 2199902--2199939 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
2199892 CAATTATTTT
2199902 TCTTGTAAGCTTAAA
1 TCTTGTAAGCTTAAA
2199917 TCTTGTAAGCTTAAA
1 TCTTGTAAGCTTAAA
2199932 TCTTGTAA
1 TCTTGTAA
2199940 ACACATATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (15 bp):
TCTTGTAAGCTTAAA
Found at i:2214930 original size:21 final size:21
Alignment explanation
Indices: 2214886--2214930 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2214876 GATTTCTGGG
* * *
2214886 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
2214907 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
2214928 CAA
1 CAA
2214931 ACGAACCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:2215367 original size:20 final size:20
Alignment explanation
Indices: 2215322--2215359 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2215312 TGAATATGTG
* *
2215322 ATATGTTATGATGATAAACC
1 ATATGATATGATAATAAACC
2215342 ATATGATATGATAATAAA
1 ATATGATATGATAATAAA
2215360 TTATATGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.34
Consensus pattern (20 bp):
ATATGATATGATAATAAACC
Found at i:2215408 original size:2 final size:2
Alignment explanation
Indices: 2215401--2215437 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2215391 AAGATCTTTG
2215401 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2215438 AATGAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2216558 original size:103 final size:103
Alignment explanation
Indices: 2216374--2216588 Score: 376
Period size: 103 Copynumber: 2.1 Consensus size: 103
2216364 GTCGAGGGTC
*
2216374 TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
* *
2216439 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
2216477 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
*
2216542 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2216580 TATGTGGTC
1 TATGTGGTC
2216589 CTTATGGACA
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:2216638 original size:23 final size:23
Alignment explanation
Indices: 2216608--2216667 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
2216598 ATTATTATAT
2216608 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
2216631 GGCACTACGGTGCAATTTTATGT
1 GGCACTACGGTGCAATTCTACGC
*
2216654 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
2216668 TTTATATGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2216675 original size:23 final size:22
Alignment explanation
Indices: 2216597--2216675 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 22
2216587 TCCTTATGGA
*
2216597 CATTATTATATGGCACTACGGTG
1 CATT-TTATGTGGCACTACGGTG
* * *
2216620 CAATTCTACGCGGCACTACGGTG
1 C-ATTTTATGTGGCACTACGGTG
*
2216643 CAATTTTATGTGGCACTTCGGTG
1 C-ATTTTATGTGGCACTACGGTG
2216666 CATTTATATG
1 CATTT-TATG
2216676 AGCTGTGGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
22 4 0.09
23 39 0.85
24 3 0.07
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (22 bp):
CATTTTATGTGGCACTACGGTG
Found at i:2219893 original size:21 final size:21
Alignment explanation
Indices: 2219849--2219893 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2219839 GATTTCTGGG
* * *
2219849 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
2219870 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
2219891 CAA
1 CAA
2219894 ACGAACCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:2221634 original size:103 final size:103
Alignment explanation
Indices: 2221409--2221626 Score: 402
Period size: 103 Copynumber: 2.1 Consensus size: 103
2221399 GTCGAGGGTC
2221409 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2221474 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
2221512 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2221577 TTGAT-CTCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCT-TAGCATATGTATATGATTCTTAAGGAATGA
2221615 TATGTGGTCCTT
1 TATGTGGTCCTT
2221627 ATGGACATTA
Statistics
Matches: 112, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
102 2 0.02
103 110 0.98
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:2221710 original size:23 final size:23
Alignment explanation
Indices: 2221642--2221702 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
2221632 CATTATTATA
*
2221642 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
2221665 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
2221688 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
2221703 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:2222502 original size:1 final size:1
Alignment explanation
Indices: 2222492--2222553 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
2222482 TCGAAGAAAG
* * * * ** * *
2222492 AAAAAGAAAAAAAGAAAAAAGAAAAAAAAAAAAAAGAAAAAGGAAAAAAAGAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2222554 CGTTTAGGGT
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:2222505 original size:8 final size:8
Alignment explanation
Indices: 2222492--2222550 Score: 79
Period size: 7 Copynumber: 7.6 Consensus size: 8
2222482 TCGAAGAAAG
2222492 AAAAAGAA
1 AAAAAGAA
2222500 AAAAAG-A
1 AAAAAGAA
2222507 AAAAAGAA
1 AAAAAGAA
2222515 AAAAA-AA
1 AAAAAGAA
2222522 AAAAAG-A
1 AAAAAGAA
*
2222529 AAAAGGAA
1 AAAAAGAA
2222537 AAAAAGAGA
1 AAAAAGA-A
2222546 AAAAA
1 AAAAA
2222551 AAACGTTTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
7 20 0.44
8 19 0.42
9 6 0.13
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:2222526 original size:30 final size:30
Alignment explanation
Indices: 2222492--2222553 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
2222482 TCGAAGAAAG
2222492 AAAAAGAAAAAA-AGAAAAAAGAAAAAAAAA
1 AAAAAGAAAAAAGA-AAAAAAGAAAAAAAAA
* *
2222522 AAAAAGAAAAAGGAAAAAAAGAGAAAAAAA
1 AAAAAGAAAAAAGAAAAAAAGAAAAAAAAA
2222552 AA
1 AA
2222554 CGTTTAGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (30 bp):
AAAAAGAAAAAAGAAAAAAAGAAAAAAAAA
Found at i:2222552 original size:21 final size:19
Alignment explanation
Indices: 2222492--2222553 Score: 74
Period size: 18 Copynumber: 3.3 Consensus size: 19
2222482 TCGAAGAAAG
2222492 AAAAAGAAAAAAAGAAAAA
1 AAAAAGAAAAAAAGAAAAA
*
2222511 AGAAAA-AAAAAAA-AAAGA
1 A-AAAAGAAAAAAAGAAAAA
*
2222529 AAAAGGAAAAAAAGAGAAAA
1 AAAAAGAAAAAAAGA-AAAA
2222549 AAAAA
1 AAAAA
2222554 CGTTTAGGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
17 3 0.09
18 12 0.34
19 9 0.26
20 11 0.31
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAAAGAAAAA
Found at i:2222553 original size:15 final size:14
Alignment explanation
Indices: 2222492--2222553 Score: 79
Period size: 15 Copynumber: 4.2 Consensus size: 14
2222482 TCGAAGAAAG
2222492 AAAAAGAAAAAAAGA
1 AAAAAGAAAAAAA-A
2222507 AAAAAGAAAAAAAAA
1 AAAAAG-AAAAAAAA
*
2222522 AAAAAGAAAAAGGAA
1 AAAAAGAAAAA-AAA
*
2222537 AAAAAGAGAAAAAA
1 AAAAAGAAAAAAAA
2222551 AAA
1 AAA
2222554 CGTTTAGGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
14 10 0.24
15 25 0.60
16 7 0.17
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAA
Found at i:2222553 original size:22 final size:23
Alignment explanation
Indices: 2222492--2222550 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 23
2222482 TCGAAGAAAG
2222492 AAAAAGAAAAAAAGAAAAAAGAA
1 AAAAAGAAAAAAAGAAAAAAGAA
*
2222515 AAAAA-AAAAAAAGAAAAAGGAA
1 AAAAAGAAAAAAAGAAAAAAGAA
2222537 AAAAAGAGAAAAAA
1 AAAAAGA-AAAAAA
2222551 AAACGTTTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 21 0.64
23 6 0.18
24 6 0.18
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAAAGAAAAAAGAA
Found at i:2225859 original size:13 final size:13
Alignment explanation
Indices: 2225831--2225878 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
2225821 ATTATATATA
2225831 TATTTATATTTC-C
1 TATTT-TATTTCTC
2225844 TATTTTATTTCTC
1 TATTTTATTTCTC
*
2225857 TATTTTATATT-TT
1 TATTTTAT-TTCTC
2225870 TATTTTATT
1 TATTTTATT
2225879 ATTATTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
12 7 0.22
13 23 0.72
14 2 0.06
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTTTATTTCTC
Found at i:2225886 original size:14 final size:14
Alignment explanation
Indices: 2225857--2225895 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2225847 TTTATTTCTC
*
2225857 TATTTTA-TATTTT
1 TATTTTATTATTAT
2225870 TATTTTATTATTAT
1 TATTTTATTATTAT
2225884 TATTTTACTTAT
1 TATTTTA-TTAT
2225896 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.30
14 12 0.52
15 4 0.17
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTTTATTATTAT
Found at i:2225935 original size:13 final size:13
Alignment explanation
Indices: 2225844--2225999 Score: 67
Period size: 13 Copynumber: 11.8 Consensus size: 13
2225834 TTATATTTCC
* *
2225844 TATTTTATTTCTC
1 TATTTTATTTATT
2225857 TATTTTATATT-TT
1 TATTTTAT-TTATT
2225870 TATTTTA-TTA-T
1 TATTTTATTTATT
* *
2225881 TATTAT-TTTACT
1 TATTTTATTTATT
* * *
2225893 TATATATATATATA
1 TAT-TTTATTTATT
2225907 TACTTTTACTTT-TT
1 TA-TTTTA-TTTATT
2225921 TATTTTATTTATT
1 TATTTTATTTATT
*
2225934 TATTTTCTTTTATTTT
1 TATTTT-ATTTA--TT
2225950 TATTCTCTA-TT-TT
1 TATT-T-TATTTATT
*
2225963 TATCTTCATTTTATT
1 TAT-TTTA-TTTATT
*
2225978 TGTTTTATTTATT
1 TATTTTATTTATT
2225991 TA-TTTATTT
1 TATTTTATTT
2226000 GCATTATCAT
Statistics
Matches: 111, Mismatches: 14, Indels: 37
0.69 0.09 0.23
Matches are distributed among these distances:
11 11 0.10
12 15 0.14
13 45 0.41
14 23 0.21
15 7 0.06
16 8 0.07
17 1 0.01
18 1 0.01
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.71
Consensus pattern (13 bp):
TATTTTATTTATT
Found at i:2226121 original size:15 final size:17
Alignment explanation
Indices: 2226091--2226122 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2226081 TATTCTATTC
2226091 ATTTTTATATTTACTTT
1 ATTTTTATATTTACTTT
2226108 ATTTTT-TA-TTACTTT
1 ATTTTTATATTTACTTT
2226123 CTTTATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTTATATTTACTTT
Found at i:2227603 original size:30 final size:30
Alignment explanation
Indices: 2227542--2227609 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
2227532 TTATATAAAA
*
2227542 AATTTAAACTAATAATAAAATTAATTTATAT
1 AATTTAAAC-AATAATAAAATTAATTAATAT
2227573 AATTTAAA-AATAAATAAAA-TAATTAAATAT
1 AATTTAAACAAT-AATAAAATTAATT-AATAT
*
2227603 AAATTAA
1 AATTTAA
2227610 TAAGTGATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 8 0.24
30 17 0.52
31 8 0.24
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (30 bp):
AATTTAAACAATAATAAAATTAATTAATAT
Found at i:2227783 original size:35 final size:35
Alignment explanation
Indices: 2227733--2227802 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
2227723 ACAAGTTATT
2227733 GTTTCACGTGACAACCATATGATTTTTCCTATATC
1 GTTTCACGTGACAACCATATGATTTTTCCTATATC
*
2227768 GTTTCACGTGGCAACCATATGATTTTTCCTATATC
1 GTTTCACGTGACAACCATATGATTTTTCCTATATC
2227803 CATGTGTCCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (35 bp):
GTTTCACGTGACAACCATATGATTTTTCCTATATC
Found at i:2243375 original size:77 final size:77
Alignment explanation
Indices: 2243178--2243474 Score: 326
Period size: 77 Copynumber: 3.9 Consensus size: 77
2243168 GTAAATAAGA
* * * * *
2243178 AGAACGAAAAGAAGCATCACATTTTCGATTCAAGTAGAACGAAATGAGGCATAATACTTTC-ATT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTCGATT
***
2243242 CCCGTATAAAGT
66 CTTATATAAAGT
* * * * * *
2243254 AGAACGAAAGGAAGCATCGCAGTTTCGATTCAAGTATAATGAAAGGAGGCATAACACTTTTGATT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTCGATT
* *
2243319 CTTATTTAATGT
66 CTTATATAAAGT
* ** * * * * *
2243331 ATATTGGAAGGAAGCATCACACTTTCAATTCAAGAAGAACGAAAGAAGACAAAACACTTTCGATT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTCGATT
**
2243396 CTTACCTAAAGT
66 CTTATATAAAGT
* * *
2243408 AGAACGGAAGGAAGTATCACACTTTCGATTCAAGTAGAACAAAAAGAGGCATAACACTTTCGATT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTCGATT
2243473 CT
66 CT
2243475 CGATGATAGA
Statistics
Matches: 179, Mismatches: 41, Indels: 1
0.81 0.19 0.00
Matches are distributed among these distances:
76 53 0.30
77 126 0.70
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (77 bp):
AGAACGGAAGGAAGCATCACACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTCGATT
CTTATATAAAGT
Found at i:2243467 original size:154 final size:152
Alignment explanation
Indices: 2243188--2243474 Score: 371
Period size: 154 Copynumber: 1.9 Consensus size: 152
2243178 AGAACGAAAA
* * * * * *
2243188 GAAGCATCACATTTTCGATTCAAGTAGAACGAAATGAGGCATAATACTTTCATTCCCGTATAAAG
1 GAAGCATCACACTTTCAATTCAAGAAGAACGAAATGAGACAAAACACTTTCATT-CCGTATAAAG
* * * ** * *
2243253 TAGAACGAAAGGAAGCATCGCAGTTTCGATTCAAGTATAATGAAAGGAGGCATAACACTTTTGAT
65 TAGAACGAAAGGAAGCATCACACTTTCGATTCAAGTAGAACAAAAAGAGGCATAACACTTTCGAT
2243318 TCTTATTTAATGTATATTGGAAG
130 TCTTATTTAATGTATATTGGAAG
*
2243341 GAAGCATCACACTTTCAATTCAAGAAGAACGAAA-GAAGACAAAACACTTTCGATT-CTTACCTA
1 GAAGCATCACACTTTCAATTCAAGAAGAACGAAATG-AGACAAAACACTTTC-ATTCCGTA--TA
* *
2243404 AAGTAGAACGGAAGGAAGTATCACACTTTCGATTCAAGTAGAACAAAAAGAGGCATAACACTTTC
62 AAGTAGAACGAAAGGAAGCATCACACTTTCGATTCAAGTAGAACAAAAAGAGGCATAACACTTTC
2243469 GATTCT
127 GATTCT
2243475 CGATGATAGA
Statistics
Matches: 114, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
152 4 0.04
153 43 0.38
154 67 0.59
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (152 bp):
GAAGCATCACACTTTCAATTCAAGAAGAACGAAATGAGACAAAACACTTTCATTCCGTATAAAGT
AGAACGAAAGGAAGCATCACACTTTCGATTCAAGTAGAACAAAAAGAGGCATAACACTTTCGATT
CTTATTTAATGTATATTGGAAG
Found at i:2244924 original size:27 final size:24
Alignment explanation
Indices: 2244890--2244942 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
2244880 CACAATATAC
2244890 TATGATTTAAATACAAATATATTGAA
1 TATGATTTAAAT-CAAA-ATATTGAA
* *
2244916 TATGTATTTTAATCAAAATTTTGAA
1 TATG-ATTTAAATCAAAATATTGAA
2244941 TA
1 TA
2244943 CCTAATTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.38
26 8 0.33
27 7 0.29
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (24 bp):
TATGATTTAAATCAAAATATTGAA
Found at i:2246586 original size:16 final size:15
Alignment explanation
Indices: 2246553--2246583 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2246543 AAATTCTAAA
2246553 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
2246568 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
2246583 T
1 T
2246584 TATCGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:2246595 original size:40 final size:39
Alignment explanation
Indices: 2246551--2246632 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
2246541 TGAAATTCTA
*
2246551 AATA-TTTAAATAAAAATTATTTATATAAAAATTTATCGAT
1 AATATTTTAAATAAAAATTA-TTATAT-AAAATTCATCGAT
2246591 AATATTTTAAATAAAAATTATTATATAAAATTCATCGAT
1 AATATTTTAAATAAAAATTATTATATAAAATTCATCGAT
2246630 AAT
1 AAT
2246633 TTAATTTCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
39 15 0.38
40 10 0.25
41 15 0.38
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (39 bp):
AATATTTTAAATAAAAATTATTATATAAAATTCATCGAT
Found at i:2247062 original size:172 final size:168
Alignment explanation
Indices: 2246762--2247091 Score: 608
Period size: 172 Copynumber: 1.9 Consensus size: 168
2246752 TGCGATCGAC
2246762 AACAAAAATCAACCCATAACAACTGCATTTGACGGAAAAATAAATTCGTTTCAAGAAAAAATATC
1 AACAAAAATCAACCCATAACAACTGCATTTGACGGAAAAATAAATTCGTTTCAAGAAAAAATATC
2246827 TTATGTGATTGATTCAAGACATCCGAATGAATATCAGGTTTAAATTATATTTTAAAAAAGGAGAA
66 TTATGTGATTGATTCAAGACATCCGAATGAATATCAGGTTTAAATTATATTTTAAAAAAGGAGAA
2246892 GATAAATTCCCTTGCGATTTCTCAGCTGTTGCGGATCG
131 GATAAATTCCCTTGCGATTTCTCAGCTGTTGCGGATCG
2246930 AACAAAAATCAAACCCATTAACAACTGCATTTGACGGAAAAATAAATTCGTTTCAAGAAAAAAAT
1 AACAAAAATC-AACCCA-TAACAACTGCATTTGACGGAAAAATAAATTCGTTTCAAG-AAAAAAT
2246995 ATTCTTATGTGATTGATTCAAGACATCCGAATGAATATCAGG-TTAAATTATATTTTAAAAAAAG
63 A-TCTTATGTGATTGATTCAAGACATCCGAATGAATATCAGGTTTAAATTATATTTT-AAAAAAG
2247059 GAGAAGATAAATTCCCTTGCGATTTCTCAGCTG
126 GAGAAGATAAATTCCCTTGCGATTTCTCAGCTG
2247092 AAAAAAAGGA
Statistics
Matches: 157, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
168 10 0.06
169 6 0.04
170 39 0.25
171 22 0.14
172 80 0.51
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (168 bp):
AACAAAAATCAACCCATAACAACTGCATTTGACGGAAAAATAAATTCGTTTCAAGAAAAAATATC
TTATGTGATTGATTCAAGACATCCGAATGAATATCAGGTTTAAATTATATTTTAAAAAAGGAGAA
GATAAATTCCCTTGCGATTTCTCAGCTGTTGCGGATCG
Found at i:2247421 original size:22 final size:23
Alignment explanation
Indices: 2247357--2247422 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 23
2247347 AACTGTTGAA
2247357 AATTAAAATCCACCGAAAGGTGG
1 AATTAAAATCCACCGAAAGGTGG
* * *
2247380 CATTAAACAAATCTATCGAAAGGTGG
1 AATT--A-AAATCCACCGAAAGGTGG
2247406 AATT-AAATCCACCGAAA
1 AATTAAAATCCACCGAAA
2247423 ATAATAAGTC
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
22 11 0.32
23 3 0.09
25 1 0.03
26 19 0.56
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (23 bp):
AATTAAAATCCACCGAAAGGTGG
Found at i:2247542 original size:24 final size:25
Alignment explanation
Indices: 2247498--2247548 Score: 86
Period size: 24 Copynumber: 2.0 Consensus size: 25
2247488 ACTTTAGGGT
2247498 ATTTATAAAATTAGTCCTTAAGCTTC
1 ATTTATAAAA-TAGTCCTTAAGCTTC
2247524 ATTTATAAAA-AGTCCTTAAGCTTC
1 ATTTATAAAATAGTCCTTAAGCTTC
2247548 A
1 A
2247549 ACTATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 15 0.60
26 10 0.40
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (25 bp):
ATTTATAAAATAGTCCTTAAGCTTC
Found at i:2247554 original size:24 final size:25
Alignment explanation
Indices: 2247501--2247556 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
2247491 TTAGGGTATT
**
2247501 TATAAAATTAGTCCTTAAGCTTCATT
1 TATAAAA-TAGTCCTTAAGCTTCAAC
2247527 TATAAAA-AGTCCTTAAGCTTCAAC
1 TATAAAATAGTCCTTAAGCTTCAAC
2247551 TATAAA
1 TATAAA
2247557 TACCCTAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 21 0.75
26 7 0.25
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (25 bp):
TATAAAATAGTCCTTAAGCTTCAAC
Found at i:2251218 original size:29 final size:30
Alignment explanation
Indices: 2251176--2251257 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 30
2251166 CCCAAAGGAC
*
2251176 CTATCCAGATGTCACAAAG-ACCCCGACAA
1 CTATCCAGAGGTCACAAAGAACCCCGACAA
* * *
2251205 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCCCGACAA
* * * *
2251235 CTGTCCATAGGTCCCGAAGAACC
1 CTATCCAGAGGTCACAAAGAACC
2251258 TAGGTAAACT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 17 0.40
30 26 0.60
ACGTcount: A:0.34, C:0.32, G:0.18, T:0.16
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCCCGACAA
Found at i:2251247 original size:30 final size:31
Alignment explanation
Indices: 2251202--2251283 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 31
2251192 AAGACCCCGA
* * * *
2251202 CAACTATCCAGAGGTCATAAAGAACCTCGG-
1 CAACTGTCCATAGGTCACAAAGAACCTAGGT
* *
2251232 CAACTGTCCATAGGTCCCGAAGAACCTAGGT
1 CAACTGTCCATAGGTCACAAAGAACCTAGGT
* * *
2251263 AAACTGTCCATATGTCTCAAA
1 CAACTGTCCATAGGTCACAAA
2251284 AGACATAGGT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 24 0.59
31 17 0.41
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (31 bp):
CAACTGTCCATAGGTCACAAAGAACCTAGGT
Found at i:2254551 original size:26 final size:26
Alignment explanation
Indices: 2254520--2254570 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2254510 TTCAAAATTA
* *
2254520 AAATCCACCAAAAGTTGGCATTAAAC
1 AAATCCACCAAAAGGTGGAATTAAAC
*
2254546 AAATCCACCGAAAGGTGGAATTAAA
1 AAATCCACCAAAAGGTGGAATTAAA
2254571 TCCACCGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.18
Consensus pattern (26 bp):
AAATCCACCAAAAGGTGGAATTAAAC
Found at i:2263577 original size:23 final size:23
Alignment explanation
Indices: 2263547--2263603 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
2263537 AGAGTTCTAA
2263547 TTGTACATTCATATTGATCAGTT
1 TTGTACATTCATATTGATCAGTT
2263570 TTGTACATTCATATTGATCAGTT
1 TTGTACATTCATATTGATCAGTT
*
2263593 TTGTATATTCA
1 TTGTACATTCA
2263604 GATCGAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.49
Consensus pattern (23 bp):
TTGTACATTCATATTGATCAGTT
Found at i:2266008 original size:17 final size:17
Alignment explanation
Indices: 2265986--2266021 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2265976 ATATATTTTA
* *
2265986 AAAATATAAAAATAGAT
1 AAAATACAAAAATAAAT
2266003 AAAATACAAAAATAAAT
1 AAAATACAAAAATAAAT
2266020 AA
1 AA
2266022 TCAATCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (17 bp):
AAAATACAAAAATAAAT
Found at i:2266525 original size:11 final size:11
Alignment explanation
Indices: 2266509--2266533 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2266499 TAAAAATTGA
2266509 TATATATACTT
1 TATATATACTT
2266520 TATATATACTT
1 TATATATACTT
2266531 TAT
1 TAT
2266534 TTTGGGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATACTT
Found at i:2267397 original size:3 final size:3
Alignment explanation
Indices: 2267379--2267426 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
2267369 CTACAAAAAC
*
2267379 ATT A-T ATT ACT ATT ATT A-T ATT ATT ATT A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2267424 ATT
1 ATT
2267427 CTATTAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 6 0.15
3 34 0.85
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:2267398 original size:14 final size:13
Alignment explanation
Indices: 2267379--2267432 Score: 58
Period size: 14 Copynumber: 4.1 Consensus size: 13
2267369 CTACAAAAAC
2267379 ATTATATTACTATT
1 ATTATATT-CTATT
2267393 ATTATA-T-TATT
1 ATTATATTCTATT
*
2267404 ATTATATTATTATT
1 ATTATATT-CTATT
2267418 ATTATTATTCTATT
1 ATTA-TATTCTATT
2267432 A
1 A
2267433 ATTTATATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
11 10 0.29
12 1 0.03
13 1 0.03
14 19 0.54
15 4 0.11
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTATATTCTATT
Found at i:2267432 original size:11 final size:11
Alignment explanation
Indices: 2267389--2267426 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
2267379 ATTATATTAC
2267389 TATTATTATAT
1 TATTATTATAT
2267400 TATTATTATAT
1 TATTATTATAT
2267411 TATTATTATTAT
1 TATTATTA-TAT
2267423 TATT
1 TATT
2267427 CTATTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.73
12 7 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTATTATAT
Found at i:2267443 original size:20 final size:21
Alignment explanation
Indices: 2267392--2267444 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
2267382 ATATTACTAT
*
2267392 TATTATATTATTATTATATTAT
1 TATTATA-TATTATTATATTAA
*
2267414 TATTAT-TATTATTCTATTAA
1 TATTATATATTATTATATTAA
2267434 T-TTATATATTA
1 TATTATATATTA
2267445 CAATTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.14
20 18 0.64
22 6 0.21
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTATATATTATTATATTAA
Found at i:2268383 original size:29 final size:29
Alignment explanation
Indices: 2268341--2268399 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2268331 TTACATACCG
2268341 CTTCCCTTCCCCTATATATTCAACAAACA
1 CTTCCCTTCCCCTATATATTCAACAAACA
2268370 CTTCCCTTCCCCTATATATTCAACAAACA
1 CTTCCCTTCCCCTATATATTCAACAAACA
2268399 C
1 C
2268400 GCTGCTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.39, G:0.00, T:0.31
Consensus pattern (29 bp):
CTTCCCTTCCCCTATATATTCAACAAACA
Found at i:2269339 original size:16 final size:15
Alignment explanation
Indices: 2269316--2269354 Score: 69
Period size: 16 Copynumber: 2.5 Consensus size: 15
2269306 TTTAATTGTA
2269316 TTTTATTATTTCTTT
1 TTTTATTATTTCTTT
2269331 TTATTATTATTTCTTT
1 TT-TTATTATTTCTTT
2269347 TTTTATTA
1 TTTTATTA
2269355 ACTTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTATTTCTTT
Found at i:2269385 original size:22 final size:20
Alignment explanation
Indices: 2269329--2269400 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 20
2269319 TATTATTTCT
*
2269329 TTTTATTATTATT-TCTTT-
1 TTTTATTATTATTGTATTTA
*
2269347 TTTTATTA--ACTTTTATTTA
1 TTTTATTATTA-TTGTATTTA
*
2269366 TCTTTGTTATCTATTGTATTTA
1 T-TTTATTAT-TATTGTATTTA
2269388 TTTTATTATTATT
1 TTTTATTATTATT
2269401 ATACTAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
16 1 0.02
17 2 0.05
18 12 0.28
19 1 0.02
20 10 0.23
21 7 0.16
22 9 0.21
23 1 0.02
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTTATTATTATTGTATTTA
Found at i:2270724 original size:27 final size:27
Alignment explanation
Indices: 2270693--2270757 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
2270683 TTTGTTCGGG
2270693 TCGGGTCGGGTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAGTGTGATAT
*
2270720 TCGGGTCAGGTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAGTGTGATAT
*
2270747 TCAGGTCGGGT
1 TCGGGTCGGGT
2270758 CGGGTTCGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.15, C:0.09, G:0.34, T:0.42
Consensus pattern (27 bp):
TCGGGTCGGGTTTTTTAAGTGTGATAT
Found at i:2270726 original size:32 final size:31
Alignment explanation
Indices: 2270691--2270763 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 31
2270681 ATTTTGTTCG
2270691 GGTCGGGTCGGGTTTTTTAAGTGTGATA-T-
1 GGTCGGGTCGGGTTTTTTAAGTGTGATATTC
*
2270720 --TCGGGTCAGGTTTTTTAAGTGTGATATTC
1 GGTCGGGTCGGGTTTTTTAAGTGTGATATTC
2270749 AGGTCGGGTCGGGTT
1 -GGTCGGGTCGGGTT
2270764 CGGGTTTAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 25 0.68
28 1 0.03
32 11 0.30
ACGTcount: A:0.14, C:0.10, G:0.37, T:0.40
Consensus pattern (31 bp):
GGTCGGGTCGGGTTTTTTAAGTGTGATATTC
Found at i:2271379 original size:18 final size:17
Alignment explanation
Indices: 2271340--2271392 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
2271330 TATGGAATTG
* *
2271340 GATTCCAATTCCTGAAA
1 GATTCCAATTCCTCATA
2271357 GATTCCAATTCCTTCATA
1 GATTCCAATTCC-TCATA
2271375 GATTCCAATTCCCTCATA
1 GATTCCAATT-CCTCATA
2271393 AACATTCCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 12 0.38
18 18 0.56
19 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (17 bp):
GATTCCAATTCCTCATA
Found at i:2272456 original size:18 final size:17
Alignment explanation
Indices: 2272423--2272465 Score: 70
Period size: 18 Copynumber: 2.5 Consensus size: 17
2272413 TTTAGACATA
2272423 TTTTGCA-TTTTTATTT
1 TTTTGCATTTTTTATTT
2272439 TTTTGCATTTTGTTATTT
1 TTTTGCATTTT-TTATTT
2272457 TTTTGCATT
1 TTTTGCATT
2272466 CACATTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 7 0.28
17 3 0.12
18 15 0.60
ACGTcount: A:0.12, C:0.07, G:0.09, T:0.72
Consensus pattern (17 bp):
TTTTGCATTTTTTATTT
Found at i:2275047 original size:20 final size:21
Alignment explanation
Indices: 2275014--2275053 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2275004 TTTTAACGTA
**
2275014 ATTGATATTCATTTT-AAACC
1 ATTGATATAAATTTTCAAACC
2275034 ATTGATATAAATTTTCAAAC
1 ATTGATATAAATTTTCAAAC
2275054 AATTTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTGATATAAATTTTCAAACC
Found at i:2283347 original size:95 final size:93
Alignment explanation
Indices: 2283237--2283480 Score: 307
Period size: 95 Copynumber: 2.7 Consensus size: 93
2283227 TAATATTATA
2283237 TATA-TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
1 TATACTATA-AATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
* *
2283301 AT-AGTATTCAGTTAGCCTGAAAAAGGTGAT
65 ATAAG-ATTCAGCTAACCTGAAAAAGGTG-T
2283331 TATACTATATAATAAAGCTTGAGTTGTCCCTCTA-AGGCAATTGGTTAAACGCCCCGGCTTTATG
1 TATACTATA-AATAAAGCTTGAGTTGTCCCTCTAGA-GCAATTGGTTAAACGCCCCGGCTTTATG
*
2283395 GATAAGATTCAGCTAACCTGATAAAGGTGT
64 GATAAGATTCAGCTAACCTGAAAAAGGTGT
* *
2283425 T-TAC-----AT--A--TTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGGA
1 TATACTATAAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
2283480 T
66 T
2283481 TCAGCTAGCC
Statistics
Matches: 140, Mismatches: 6, Indels: 19
0.85 0.04 0.12
Matches are distributed among these distances:
83 45 0.32
84 1 0.01
85 1 0.01
87 2 0.01
93 3 0.02
94 7 0.05
95 79 0.56
96 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (93 bp):
TATACTATAAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
TAAGATTCAGCTAACCTGAAAAAGGTGT
Found at i:2284589 original size:116 final size:116
Alignment explanation
Indices: 2284462--2285173 Score: 971
Period size: 116 Copynumber: 6.0 Consensus size: 116
2284452 TCATCTTTAG
* * *
2284462 ATTGGATTTCAACTTCACGACGAAGTATATCCAATTCAAGGCTCAACTTCATAACGAA-GGGTTC
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGG-CC
*
2284526 ATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTC
65 ATCCACGGTTTCAACTTCACGACGAAGGGAATCATGCTCACCAGCAACATTC
* *
2284578 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
* * *
2284643 TCCACGGTTTCAACTTTACGATGAAGGGAATCATGCTCACTAGCAACATTC
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCATGCTCACCAGCAACATTC
*
2284694 ATTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
* *
2284759 TCCACGGTGTCAACTTCACGACGAAGGGAATCGTGCTCACCAG-AACATTC
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCATGCTCACCAGCAACATTC
* * ** * *
2284809 ATTGGATTGCAACTTCACGACAAAATATATCC-ATTCAAGGCTCAACATCACAACGAATGGGTCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
*
2284873 TCCACGGTTTCAACTTCACGACGAAGGGAATCATGCTCACCAGTAACATTC
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCATGCTCACCAGCAACATTC
* * * *
2284924 ATATTTAGATTGGATTTCAACTTTACAACGAAGGATATCCAATTTAAGGCTCAACTTCATAACGA
1 --------ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGA
* * * *
2284989 AGGGGCCATCCACGGTTTCAACTTCACGACGGAGGGAATCGTGCTCACCAGTAACATTCATC
58 ATGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCATGCTCACCAGCAACA-T--TC
2285051 TTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATG
1 -----ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATG
* * * *
2285116 GGCCATCCACAGTTTAAACTTCATGACGAAGGGAATCATGCCCACCAGCAACATTC
61 GGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCATGCTCACCAGCAACATTC
2285172 AT
1 AT
2285174 CTTCATTTCA
Statistics
Matches: 535, Mismatches: 47, Indels: 28
0.88 0.08 0.05
Matches are distributed among these distances:
114 71 0.13
115 42 0.08
116 208 0.39
117 3 0.01
121 2 0.00
123 27 0.05
124 179 0.33
125 1 0.00
127 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (116 bp):
ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
TCCACGGTTTCAACTTCACGACGAAGGGAATCATGCTCACCAGCAACATTC
Found at i:2285174 original size:124 final size:124
Alignment explanation
Indices: 2284809--2285176 Score: 558
Period size: 124 Copynumber: 3.0 Consensus size: 124
2284799 CAGAACATTC
* * ** * *
2284809 ATTGGATTGCAACTTCACGACAAAATATATCC-ATTCAAGGCTCAACATCACAACGAATGGGTCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
*
2284873 TCCACGGTTTCAACTTCACGACGAAGGGAATCATGCTCACCAGTAACATTCATATTTAG
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCATGCTCACCAGTAACATTCATCTTTAG
* * * * *
2284932 ATTGGATTTCAACTTTACAACGAAGGATATCCAATTTAAGGCTCAACTTCATAACGAAGGGGCCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
* *
2284997 TCCACGGTTTCAACTTCACGACGGAGGGAATCGTGCTCACCAGTAACATTCATCTTTAG
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCATGCTCACCAGTAACATTCATCTTTAG
2285056 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
* * * * *
2285121 TCCACAGTTTAAACTTCATGACGAAGGGAATCATGCCCACCAGCAACATTCATCTT
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCATGCTCACCAGTAACATTCATCTT
2285177 CATTTCAACA
Statistics
Matches: 218, Mismatches: 26, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
123 26 0.12
124 192 0.88
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (124 bp):
ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
TCCACGGTTTCAACTTCACGACGAAGGGAATCATGCTCACCAGTAACATTCATCTTTAG
Found at i:2285798 original size:79 final size:79
Alignment explanation
Indices: 2285667--2285859 Score: 368
Period size: 79 Copynumber: 2.4 Consensus size: 79
2285657 TTCAAGAGGT
2285667 CCACGATTTCAACTTCACGATGAAGGATATCGTGCACAGGATTTTACAGTTCAGCTCAACTTCAC
1 CCACGATTTCAACTTCACGATGAAGGATATCGTGCACAGGATTTTACAGTTCAGCTCAACTTCAC
2285732 AACGAATGAGTTAC
66 AACGAATGAGTTAC
2285746 CCACGATTTCAACTTCACGATGAAGGATATCGTGCACAGGATTTTACAGTTCAGCTCAACTTCAC
1 CCACGATTTCAACTTCACGATGAAGGATATCGTGCACAGGATTTTACAGTTCAGCTCAACTTCAC
2285811 AACGAATGAGTTAC
66 AACGAATGAGTTAC
* *
2285825 CCACGATTTCAACTTCATGAAGAAGGATATCGTGC
1 CCACGATTTCAACTTCACGATGAAGGATATCGTGC
2285860 TCAATGGATC
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 112 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (79 bp):
CCACGATTTCAACTTCACGATGAAGGATATCGTGCACAGGATTTTACAGTTCAGCTCAACTTCAC
AACGAATGAGTTAC
Found at i:2286043 original size:3 final size:3
Alignment explanation
Indices: 2286024--2286061 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
2286014 TCTACAAAAA
*
2286024 TAT TA- TAT TAC TAT TAT TAT TA- TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2286062 CTATTAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2286046 original size:17 final size:17
Alignment explanation
Indices: 2286024--2286067 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
2286014 TCTACAAAAA
2286024 TATTATATTACTATTAT
1 TATTATATTACTATTAT
*
2286041 TATTATATTATTATTAT
1 TATTATATTACTATTAT
*
2286058 TATTCTATTA
1 TATTATATTA
2286068 ATTTATATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTATATTACTATTAT
Found at i:2287986 original size:46 final size:46
Alignment explanation
Indices: 2287909--2288013 Score: 110
Period size: 46 Copynumber: 2.3 Consensus size: 46
2287899 TTATTTTTTA
* * *
2287909 ATTGTATTTTATTATTATTTCTTTTTTTACTAACTTTTATTTATCT
1 ATTGTATTTTATTATTATTTATTATTATACTAACTTTTATTTATCT
* * * *
2287955 ATTGTATTTATTTTATTA-TTATTATTATACTAATTTTTTTTTA-AT
1 ATTGTATTT-TATTATTATTTATTATTATACTAACTTTTATTTATCT
2288000 ATT-TATTTT-TTATT
1 ATTGTATTTTATTATT
2288014 TTACAATCTA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
42 5 0.10
43 1 0.02
44 5 0.10
45 4 0.08
46 29 0.57
47 7 0.14
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.69
Consensus pattern (46 bp):
ATTGTATTTTATTATTATTTATTATTATACTAACTTTTATTTATCT
Found at i:2290539 original size:16 final size:17
Alignment explanation
Indices: 2290507--2290539 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2290497 TTTAAAATTT
*
2290507 AAATTTTTTTCTATTAA
1 AAATTTATTTCTATTAA
2290524 AAATTTATTT-TATTAA
1 AAATTTATTTCTATTAA
2290540 TGTTATTTAT
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:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATTTATTTCTATTAA
Done.