Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009461.1 Hibiscus syriacus cultivar Beakdansim tig00113724_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: 2346588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:233767 original size:20 final size:20
Alignment explanation
Indices: 233739--233776 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
233729 TGATACTCAC
233739 CCATAGTATCGATACCAACA
1 CCATAGTATCGATACCAACA
*
233759 CCATGGTATCGATACCAA
1 CCATAGTATCGATACCAA
233777 ATTTGTCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (20 bp):
CCATAGTATCGATACCAACA
Found at i:234344 original size:32 final size:32
Alignment explanation
Indices: 234267--234345 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 32
234257 AAATGATGTT
*
234267 TTTCTGAAATGAAGTGATATATCACCGAAAAG
1 TTTCTGAAATGAAGTGATATATCACCAAAAAG
* * * *
234299 TTTTTAAAATGAAGTTATATATCACTAAAAAG
1 TTTCTGAAATGAAGTGATATATCACCAAAAAG
*
234331 TTTCTGAAGTGAAGT
1 TTTCTGAAATGAAGT
234346 AATTGGACAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (32 bp):
TTTCTGAAATGAAGTGATATATCACCAAAAAG
Found at i:234465 original size:32 final size:32
Alignment explanation
Indices: 234415--234487 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
234405 TTTTTTCCTG
234415 AAATAAAGTGATATATCATTGAAAAGTTTCTA
1 AAATAAAGTGATATATCATTGAAAAGTTTCTA
* *
234447 AAATGAAGTTATATATCATTGAAAAGTTTCTA
1 AAATAAAGTGATATATCATTGAAAAGTTTCTA
*
234479 AAGTAAAGT
1 AAATAAAGT
234488 AATTGGGTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (32 bp):
AAATAAAGTGATATATCATTGAAAAGTTTCTA
Found at i:234526 original size:142 final size:139
Alignment explanation
Indices: 234265--234615 Score: 510
Period size: 142 Copynumber: 2.5 Consensus size: 139
234255 GAAAATGATG
* * * *
234265 TTTTTCTGAAATGAAGTGATATATCACCGAAAAGTTTTTAAAATGAAGTTATATATCACTAAAAA
1 TTTTTCTGAAATAAAGTGATATATCACTGAAAAGTTTCTAAAATGAAGTTATATATCACTGAAAA
* * *
234330 GTTTCTGAAGTGAAGTAATTGGACACTGAATTTTTTTTGTCATTGCGCATTAAATGGTGC-ATGA
66 GTTTCTAAAGTAAAGTAATTGGACACTGAAATTTTTTTGTCATTGCGCATTAAATGGT-CTATGA
*
234394 GAAAATGCCGTT
130 GAAAATGCC--A
* *
234406 TTTTTCCTGAAATAAAGTGATATATCATTGAAAAGTTTCTAAAATGAAGTTATATATCATTGAAA
1 TTTTT-CTGAAATAAAGTGATATATCACTGAAAAGTTTCTAAAATGAAGTTATATATCACTGAAA
** *
234471 AGTTTCTAAAGTAAAGTAATTGGGTACTGAAATTTTTTTGTCATTGTGCATTAAATGGTCTATGA
65 AGTTTCTAAAGTAAAGTAATTGGACACTGAAATTTTTTTGTCATTGCGCATTAAATGGTCTATGA
234536 GAAAATGCCA
130 GAAAATGCCA
*
234546 TTTTT-TGAAATGAAA-TGATATATCACTGAAAATTTTCTAAAATGAAGTTATATATCACTGAAA
1 TTTTTCTGAAAT-AAAGTGATATATCACTGAAAAGTTTCTAAAATGAAGTTATATATCACTGAAA
234609 AGTTTCT
65 AGTTTCT
234616 GAAATGAAGT
Statistics
Matches: 191, Mismatches: 16, Indels: 9
0.88 0.07 0.04
Matches are distributed among these distances:
138 58 0.30
139 3 0.02
140 5 0.03
141 6 0.03
142 119 0.62
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (139 bp):
TTTTTCTGAAATAAAGTGATATATCACTGAAAAGTTTCTAAAATGAAGTTATATATCACTGAAAA
GTTTCTAAAGTAAAGTAATTGGACACTGAAATTTTTTTGTCATTGCGCATTAAATGGTCTATGAG
AAAATGCCA
Found at i:234581 original size:32 final size:32
Alignment explanation
Indices: 234545--234647 Score: 143
Period size: 32 Copynumber: 3.2 Consensus size: 32
234535 AGAAAATGCC
* *
234545 ATTTTTTGAAATGAAATGATATATCACTGAAA
1 ATTTTCTGAAATGAAGTGATATATCACTGAAA
* *
234577 ATTTTCTAAAATGAAGTTATATATCACTGAAA
1 ATTTTCTGAAATGAAGTGATATATCACTGAAA
* *
234609 AGTTTCTGAAATGAAGTGATATATCAATGAAA
1 ATTTTCTGAAATGAAGTGATATATCACTGAAA
*
234641 AGTTTCT
1 ATTTTCT
234648 ATCACCAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.37
Consensus pattern (32 bp):
ATTTTCTGAAATGAAGTGATATATCACTGAAA
Found at i:237020 original size:54 final size:52
Alignment explanation
Indices: 236935--237050 Score: 187
Period size: 52 Copynumber: 2.2 Consensus size: 52
236925 TTACAAAGGG
*
236935 ATGTACCGATACACTCTTGAATGCATTGATACACACCAACATCGAATGCATTTT
1 ATGTACCGATACACTCTTGAATGCATCGAT--ACACCAACATCGAATGCATTTT
* *
236989 ATGTACTGATACACTCTTGAATGCATCGATACACTAACATCGAATGCATTTT
1 ATGTACCGATACACTCTTGAATGCATCGATACACCAACATCGAATGCATTTT
237041 ATGTACCGAT
1 ATGTACCGAT
237051 GCACAGCCAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
52 30 0.52
54 28 0.48
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (52 bp):
ATGTACCGATACACTCTTGAATGCATCGATACACCAACATCGAATGCATTTT
Found at i:245278 original size:20 final size:20
Alignment explanation
Indices: 245241--245279 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
245231 AGATTGAGTG
* * *
245241 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
245261 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
245280 AGTTTTGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:245488 original size:24 final size:22
Alignment explanation
Indices: 245435--245517 Score: 82
Period size: 21 Copynumber: 3.8 Consensus size: 22
245425 CCAGAACCCC
* * *
245435 AGGGGGGTATCGATTCCCCT-G
1 AGGGGGGAATCGGTTCCCCTCA
*
245456 TGGGGGGAATCGGTTCCCCTTCA
1 AGGGGGGAATCGGTTCCCC-TCA
245479 CAGGGGGGAATCGGTT-CCCTCA
1 -AGGGGGGAATCGGTTCCCCTCA
*
245501 AGGGGGG-ATCGATTCCC
1 AGGGGGGAATCGGTTCCC
245518 TCTGCACCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
20 6 0.12
21 25 0.48
22 4 0.08
23 3 0.06
24 14 0.27
ACGTcount: A:0.16, C:0.25, G:0.37, T:0.22
Consensus pattern (22 bp):
AGGGGGGAATCGGTTCCCCTCA
Found at i:245511 original size:20 final size:22
Alignment explanation
Indices: 245457--245519 Score: 85
Period size: 24 Copynumber: 2.9 Consensus size: 22
245447 ATTCCCCTGT
245457 GGGGGGAATCGGTTCCCCTTCACA
1 GGGGGGAATCGGTT-CCC-TCACA
245481 GGGGGGAATCGGTTCCCTCA-A
1 GGGGGGAATCGGTTCCCTCACA
*
245502 GGGGGG-ATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
245520 TGCACCAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
20 11 0.29
21 7 0.18
22 3 0.08
23 3 0.08
24 14 0.37
ACGTcount: A:0.16, C:0.27, G:0.37, T:0.21
Consensus pattern (22 bp):
GGGGGGAATCGGTTCCCTCACA
Found at i:253091 original size:12 final size:12
Alignment explanation
Indices: 253062--253096 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
253052 ATATTATGAT
*
253062 TTTTCAAATATTG
1 TTTTCAAA-ATAG
253075 TTTTCAAAATAG
1 TTTTCAAAATAG
253087 TTTTCAAAAT
1 TTTTCAAAAT
253097 TTTGCCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.49
Consensus pattern (12 bp):
TTTTCAAAATAG
Found at i:254869 original size:13 final size:13
Alignment explanation
Indices: 254847--254880 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
254837 AAGGGGAGTA
*
254847 ATTTTCAAAATTG
1 ATTTTCAAAAATG
254860 A-TTTCAAAAATG
1 ATTTTCAAAAATG
254872 ATTTTCAAA
1 ATTTTCAAA
254881 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:256915 original size:26 final size:26
Alignment explanation
Indices: 256884--256935 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
256874 AATAACAATT
256884 TTTTATTGAATATAAGTACCTAATAC
1 TTTTATTGAATATAAGTACCTAATAC
256910 TTTTATTGAATATAAGTACCTAATAC
1 TTTTATTGAATATAAGTACCTAATAC
256936 AGAACTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
TTTTATTGAATATAAGTACCTAATAC
Found at i:262091 original size:136 final size:133
Alignment explanation
Indices: 261814--262074 Score: 402
Period size: 136 Copynumber: 1.9 Consensus size: 133
261804 GGTTGCGGAG
*
261814 ATCTTCAATAATTTTTTAATTTAGGTTGAGAGTTATGACTAATTATCTTGTAGAGGGAGAGAAGA
1 ATCTTCAATAATTTTTTAATTTAGGTTGAGAATTATGACTAATTATCTTGTAGAGGGAGAGAAGA
*
261879 GAATAGACACACTAAAGATTTTCATACTTCTTATAAGTCGTTTTCTATGTCGGATCGGTAAGTTT
66 GAAT--A-ACACTAAAGATTTTCATACTTCTTATAAGTCGTTTGCTATGTCGGATCGGTAAGTTT
261944 TCATTT
128 TCATTT
* * *
261950 ATCTTCAATAATTTTTTAGTTTAGGTTGAGAATTATGACTAATTATCTTGTAGAGGGTGAGGAGA
1 ATCTTCAATAATTTTTTAATTTAGGTTGAGAATTATGACTAATTATCTTGTAGAGGGAGAGAAGA
262015 GAAT-A-A-TAAAGATTTTCATACTTTTTCTTATAAGTCGTTTGCTATGTCGGATCGGTAAGT
66 GAATAACACTAAAGATTTTCATAC---TTCTTATAAGTCGTTTGCTATGTCGGATCGGTAAGT
262075 CTTTATACTT
Statistics
Matches: 117, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
130 15 0.13
131 1 0.01
132 1 0.01
133 35 0.30
136 65 0.56
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (133 bp):
ATCTTCAATAATTTTTTAATTTAGGTTGAGAATTATGACTAATTATCTTGTAGAGGGAGAGAAGA
GAATAACACTAAAGATTTTCATACTTCTTATAAGTCGTTTGCTATGTCGGATCGGTAAGTTTTCA
TTT
Found at i:266722 original size:31 final size:32
Alignment explanation
Indices: 266678--266739 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 32
266668 TGCTATGCTA
266678 GCCACTTTTTTTTGCATCTTTCTACATTTCCT
1 GCCACTTTTTTTTGCATCTTTCTACATTTCCT
266710 GCCAC-TTTTTTTGCATCTTTCTACATTTCC
1 GCCACTTTTTTTTGCATCTTTCTACATTTCC
266740 GAAGGCATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.13, C:0.29, G:0.06, T:0.52
Consensus pattern (32 bp):
GCCACTTTTTTTTGCATCTTTCTACATTTCCT
Found at i:270879 original size:18 final size:18
Alignment explanation
Indices: 270856--270923 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
270846 ACTGAATATT
270856 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
270874 TGTCCCGAAGGACCAATGA
1 TGTCCCGAAGGACCACT-A
* * *
270893 TTGTTCCAAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
270912 TGTCCCGAAGGA
1 TGTCCCGAAGGA
270924 ATATTGTTTG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 25 0.62
19 2 0.05
20 13 0.32
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:270947 original size:38 final size:37
Alignment explanation
Indices: 270854--270948 Score: 109
Period size: 38 Copynumber: 2.5 Consensus size: 37
270844 GCACTGAATA
*
270854 TTTGTCCCGAAGGACCACTATGTCCCGAAGGACCAATG
1 TTTGT-CCGAAGGACCACTATGTCCCGAAGGAACAATG
* * * * *
270892 ATTGTTCCAAAGAACCACTATGTCCCGAAGGAATATTG
1 TTTG-TCCGAAGGACCACTATGTCCCGAAGGAACAATG
270930 TTTGTCCTGAAGGACCACT
1 TTTGTCC-GAAGGACCACT
270949 CATAATCCCT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
37 3 0.07
38 42 0.91
39 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (37 bp):
TTTGTCCGAAGGACCACTATGTCCCGAAGGAACAATG
Found at i:273050 original size:3 final size:3
Alignment explanation
Indices: 273044--273079 Score: 54
Period size: 3 Copynumber: 11.3 Consensus size: 3
273034 GGGAGGAGAG
273044 GAA GAA GAA GAA GGAA GAA GAA GAA GGAA GAA GAA G
1 GAA GAA GAA GAA -GAA GAA GAA GAA -GAA GAA GAA G
273080 TTCTGGAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 25 0.81
4 6 0.19
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:273060 original size:13 final size:13
Alignment explanation
Indices: 273042--273079 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
273032 ACGGGAGGAG
273042 AGGAAGAAGAAGA
1 AGGAAGAAGAAGA
273055 AGGAAGAAGAAGA
1 AGGAAGAAGAAGA
273068 AGGAAGAAGAAG
1 AGGAAGAAGAAG
273080 TTCTGGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (13 bp):
AGGAAGAAGAAGA
Found at i:273062 original size:10 final size:9
Alignment explanation
Indices: 273044--273079 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
273034 GGGAGGAGAG
273044 GAAGAAGAA
1 GAAGAAGAA
273053 GAAGGAAGAA
1 GAA-GAAGAA
273063 GAAGAAGGAA
1 GAAGAA-GAA
273073 GAAGAAG
1 GAAGAAG
273080 TTCTGGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 7 0.28
10 18 0.72
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (9 bp):
GAAGAAGAA
Found at i:279136 original size:2 final size:2
Alignment explanation
Indices: 279124--279155 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
279114 AAAAATTATG
279124 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
279156 GAAAACTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:290445 original size:2 final size:2
Alignment explanation
Indices: 290438--290462 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
290428 ATATTATGTG
290438 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
290463 CAAAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:290792 original size:9 final size:9
Alignment explanation
Indices: 290772--290969 Score: 130
Period size: 9 Copynumber: 21.9 Consensus size: 9
290762 CGGACAAATT
290772 TATATA-TA
1 TATATATTA
290780 TATATATTA
1 TATATATTA
290789 TATATA-TA
1 TATATATTA
290797 TATATATTA
1 TATATATTA
290806 TATATA-TA
1 TATATATTA
*
290814 T-TATATTG
1 TATATATTA
290822 TATATATTA
1 TATATATTA
*
290831 TATTAGTAATA
1 TA-TA-TATTA
290842 TATTATATT-
1 TA-TATATTA
290851 TAGTATATTA
1 TA-TATATTA
290861 T-TATTATTA
1 TATA-TATTA
*
290870 T-TATAGTA
1 TATATATTA
290878 TAGTATATTTA
1 TA-TATA-TTA
*
290889 TATGTATTA
1 TATATATTA
*
290898 TATGTA-TA
1 TATATATTA
290906 TATTATATT-
1 TA-TATATTA
*
290915 TATATTTTA
1 TATATATTA
290924 TATAT-TGGTA
1 TATATAT--TA
* *
290934 TTTGTATTA
1 TATATATTA
290943 TATAGTATTA
1 TATA-TATTA
*
290953 T-TATTATTT
1 TATA-TATTA
290962 TATATATT
1 TATATATT
290970 TTTATTTATT
Statistics
Matches: 155, Mismatches: 16, Indels: 37
0.75 0.08 0.18
Matches are distributed among these distances:
7 4 0.03
8 36 0.23
9 74 0.48
10 27 0.17
11 14 0.09
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (9 bp):
TATATATTA
Found at i:290810 original size:28 final size:29
Alignment explanation
Indices: 290771--290968 Score: 106
Period size: 30 Copynumber: 6.5 Consensus size: 29
290761 TCGGACAAAT
290771 TTATATATATATATATTATATATATATATATA
1 TTATAT-TATATATA-TAT-TATATATATATA
*
290803 TTATA-TATATATTATATTGTATATATTATA
1 TTATATTATATA-TATATTATATATA-TATA
*
290833 TTAGTAATATAT-TATATT-TAGTATAT-TA
1 TTA-TATTATATATATATTATA-TATATATA
* *
290861 TTATTATTATTATAGTATAGTATATTTATATGTA
1 TTA-TATTA-TATA-TATA-T-TATATATATATA
*
290895 TTATATGTATATATTATATT-TATAT-TTTA
1 TTATAT-TATATA-TATATTATATATATATA
* * *
290924 -TATATTGGTATTTGTATTATATAGTAT-TA
1 TTATATT-ATATATATATTATATA-TATATA
*
290953 TTATTATTTTATATAT
1 TTA-TATTATATATAT
290969 TTTTATTTAT
Statistics
Matches: 134, Mismatches: 13, Indels: 40
0.72 0.07 0.21
Matches are distributed among these distances:
27 6 0.04
28 21 0.16
29 19 0.14
30 38 0.28
31 13 0.10
32 12 0.09
33 17 0.13
34 8 0.06
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (29 bp):
TTATATTATATATATATTATATATATATA
Found at i:290946 original size:2 final size:2
Alignment explanation
Indices: 290772--290928 Score: 103
Period size: 2 Copynumber: 84.5 Consensus size: 2
290762 CGGACAAATT
290772 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA T- 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
*
290812 TA T- TA TA T- TG TA TA TA T- TA TA T- TA GTA -A TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
290849 TT TA GTA TA T- TA T- TA T- TA T- TA T- TA TA GTA TA GTA TA TT
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA
* * * *
290887 TA TA TG TA T- TA TA TG TA TA TA T- TA TA TT TA TA T- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
290926 TA T
1 TA T
290929 TGGTATTTGT
Statistics
Matches: 123, Mismatches: 12, Indels: 40
0.70 0.07 0.23
Matches are distributed among these distances:
1 16 0.13
2 99 0.80
3 8 0.07
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.56
Consensus pattern (2 bp):
TA
Found at i:290953 original size:92 final size:91
Alignment explanation
Indices: 290789--290965 Score: 218
Period size: 92 Copynumber: 1.9 Consensus size: 91
290779 ATATATATTA
290789 TATATATATATATATTATATATATATTATATTGTATATATTATATTAGTAATATATTATATTTAG
1 TATATATATATATATTATATATATATTATATTGTATATATTATATTAGTAATATATTATATTTAG
290854 TATATTATTATTATTATTATAGTATAG
66 TATATTATTATTATT-TTATAGTATAG
* * * * ** *
290881 TATATTTATATGTATTATATGTATATATTATATT-TATATTTTATA-TATTGGTAT-TTGTATTA
1 TATATATATATATATTATA--TATATATTATATTGTATATATTATATTAGTAATATATTATATT-
290943 TA-TAGTATTATTATTATTTTATA
63 TAGTA-TATTATTATTATTTTATA
290966 TATTTTTATT
Statistics
Matches: 74, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
91 13 0.18
92 38 0.51
93 10 0.14
94 13 0.18
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (91 bp):
TATATATATATATATTATATATATATTATATTGTATATATTATATTAGTAATATATTATATTTAG
TATATTATTATTATTTTATAGTATAG
Found at i:290969 original size:28 final size:27
Alignment explanation
Indices: 290770--290969 Score: 114
Period size: 25 Copynumber: 7.4 Consensus size: 27
290760 TTCGGACAAA
290770 TTTATATA-TATATATATTA-TA-TAT
1 TTTATATATTATATATATTATTATTAT
*
290794 ATATATATATTATATATA-TATTA-TAT
1 -TTTATATATTATATATATTATTATTAT
* * *
290820 TGTATATATTATAT-TAGTAATA-TAT
1 TTTATATATTATATATATTATTATTAT
* * *
290845 TATATTTAGTATAT-TATTATTATTAT
1 TTTATATATTATATATATTATTATTAT
* * *
290871 TATAGTATAGTATATTTA-TATGTATTAT
1 TTTA-TATATTATATATATTAT-TATTAT
*
290899 ATGTATATATTATATTTATATT-TTATATAT
1 -TTTATATATTATA--TATATTATTAT-TAT
* *
290929 TGGTATTTGTATTATATAGTATTATTATTAT
1 T--T-TATATATTATATA-TATTATTATTAT
290960 TTTATATATT
1 TTTATATATT
290970 TTTATTTATT
Statistics
Matches: 141, Mismatches: 17, Indels: 31
0.75 0.09 0.16
Matches are distributed among these distances:
24 2 0.01
25 46 0.33
26 20 0.14
27 12 0.09
28 22 0.16
29 8 0.06
30 9 0.06
31 9 0.06
32 13 0.09
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (27 bp):
TTTATATATTATATATATTATTATTAT
Found at i:290978 original size:19 final size:19
Alignment explanation
Indices: 290902--290980 Score: 63
Period size: 19 Copynumber: 4.0 Consensus size: 19
290892 GTATTATATG
290902 TATATATTA-TATTTATATTT
1 TATATATTATTA-TT-TATTT
** *
290922 TATATATTGGTATTTGTATTA
1 TATATATTATTA-TT-TATTT
290943 TATAGTATTATTA-TTATTT
1 TATA-TATTATTATTTATTT
*
290962 TATATATTTTTATTTATTT
1 TATATATTATTATTTATTT
290981 AATTAGTTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.14
19 14 0.29
20 9 0.18
21 13 0.27
22 6 0.12
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
TATATATTATTATTTATTT
Found at i:292816 original size:31 final size:31
Alignment explanation
Indices: 292762--292820 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
292752 TGGCTACAAT
* *
292762 ACTTACATTATTGGTTTATTAAGTTTTGGTC
1 ACTTACATTATCGGTTTAATAAGTTTTGGTC
* *
292793 ACTTACGTTATCGTTTTAATAAGTTTTG
1 ACTTACATTATCGGTTTAATAAGTTTTG
292821 AACACTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.51
Consensus pattern (31 bp):
ACTTACATTATCGGTTTAATAAGTTTTGGTC
Found at i:292827 original size:31 final size:31
Alignment explanation
Indices: 292762--292827 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
292752 TGGCTACAAT
* * **
292762 ACTTACATTATTGGTTTATTAAGTTTTGGTC
1 ACTTACATTATCGGTTTAATAAGTTTTGAAC
* *
292793 ACTTACGTTATCGTTTTAATAAGTTTTGAAC
1 ACTTACATTATCGGTTTAATAAGTTTTGAAC
292824 ACTT
1 ACTT
292828 TGACATTGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (31 bp):
ACTTACATTATCGGTTTAATAAGTTTTGAAC
Found at i:296913 original size:13 final size:13
Alignment explanation
Indices: 296895--296919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
296885 ATCGAGTATT
296895 TACATGTTGTTTA
1 TACATGTTGTTTA
296908 TACATGTTGTTT
1 TACATGTTGTTT
296920 TCGATGATAA
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:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (13 bp):
TACATGTTGTTTA
Found at i:301050 original size:2 final size:2
Alignment explanation
Indices: 301043--301078 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
301033 TTTAAACTTA
301043 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
301079 TAGTTTGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:301806 original size:45 final size:46
Alignment explanation
Indices: 301757--301845 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
301747 AAACATCGAA
* * *
301757 TGCATTTTATGCATCGATACA-CATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATACATAAGACCATGCATCGATGCACTCAG
*
301802 TGCATTTGATGCATCGATGCATAAGACCATGCATCGATGCACTC
1 TGCATTTGATGCATCGATACATAAGACCATGCATCGATGCACTC
301846 CGGCTTTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 19 0.49
46 20 0.51
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (46 bp):
TGCATTTGATGCATCGATACATAAGACCATGCATCGATGCACTCAG
Found at i:306112 original size:20 final size:20
Alignment explanation
Indices: 306089--306128 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
306079 TCTCAAATGG
306089 TCTCAACATACTTCAACATA
1 TCTCAACATACTTCAACATA
*
306109 TCTCAACATATTTCAACATA
1 TCTCAACATACTTCAACATA
306129 ATATCTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.33
Consensus pattern (20 bp):
TCTCAACATACTTCAACATA
Found at i:306142 original size:10 final size:11
Alignment explanation
Indices: 306091--306171 Score: 59
Period size: 10 Copynumber: 7.5 Consensus size: 11
306081 TCAAATGGTC
306091 TCAACATA-CT
1 TCAACATATCT
306101 TCAACATATC-
1 TCAACATATCT
306111 TCAACATAT-T
1 TCAACATATCT
306121 TCAACATAATATCT
1 TCAAC---ATATCT
306135 T-AACATAT-T
1 TCAACATATCT
306144 TCATAGCATAT-T
1 TCA-A-CATATCT
*
306156 TCATCATATC-
1 TCAACATATCT
306166 TCAACA
1 TCAACA
306172 AAAATATTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 20
0.73 0.02 0.25
Matches are distributed among these distances:
9 2 0.03
10 37 0.63
11 2 0.03
12 9 0.15
13 7 0.12
14 2 0.03
ACGTcount: A:0.40, C:0.23, G:0.01, T:0.36
Consensus pattern (11 bp):
TCAACATATCT
Found at i:308061 original size:15 final size:14
Alignment explanation
Indices: 308033--308067 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
308023 ACATTATCCA
308033 TTTCTACAACACCAC
1 TTTC-ACAACACCAC
308048 TTTCACAACTACCAC
1 TTTCACAAC-ACCAC
308063 TTTCA
1 TTTCA
308068 GTTATACCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.31, C:0.37, G:0.00, T:0.31
Consensus pattern (14 bp):
TTTCACAACACCAC
Found at i:311864 original size:3 final size:3
Alignment explanation
Indices: 311856--311881 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
311846 CATGTTAAAC
311856 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
311882 GACGTGACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:311906 original size:53 final size:53
Alignment explanation
Indices: 311826--311927 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 53
311816 GTTAGTTTTA
* ** *
311826 TCTGACGTGGCACGTTACCTCATGTTAAACCTTCTTCTTCTTCTTCTTCTTCT
1 TCTGACGTGACAAATTACCTCATGTTAAACCTTCTCCTTCTTCTTCTTCTTCT
* *
311879 TCTGACGTGACAAATTACCTCATGTTAACCCTTCTCCTTCTTTTTCTTC
1 TCTGACGTGACAAATTACCTCATGTTAAACCTTCTCCTTCTTCTTCTTC
311928 GAGCGACTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.16, C:0.30, G:0.10, T:0.44
Consensus pattern (53 bp):
TCTGACGTGACAAATTACCTCATGTTAAACCTTCTCCTTCTTCTTCTTCTTCT
Found at i:314686 original size:13 final size:14
Alignment explanation
Indices: 314668--314703 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
314658 TTACTATTAT
314668 TTAGGATTTT-AGG
1 TTAGGATTTTGAGG
314681 TTAGGATTTTGAGG
1 TTAGGATTTTGAGG
314695 TTAAGGATT
1 TT-AGGATT
314704 ATAATTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.48
14 5 0.24
15 6 0.29
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (14 bp):
TTAGGATTTTGAGG
Found at i:315490 original size:44 final size:43
Alignment explanation
Indices: 315428--315515 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 43
315418 AACCACCATT
* * *
315428 AATGTATATGAAGTGAATACAATTATCATCATCATTAATTTGA
1 AATGTATATGAAATGAATACAATTATCATCAACATTAATGTGA
* *
315471 AATGTTATATGAAATGAATACAATTCTTATCAACATTAATGTGA
1 AATG-TATATGAAATGAATACAATTATCATCAACATTAATGTGA
315515 A
1 A
315516 TCATAAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 4 0.10
44 35 0.90
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (43 bp):
AATGTATATGAAATGAATACAATTATCATCAACATTAATGTGA
Found at i:315699 original size:44 final size:44
Alignment explanation
Indices: 315633--315724 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
315623 ATTTTTGATG
* ** * **
315633 TGAAATGATATATGAAGTGAATATAATTGTTACCATCATTAATA
1 TGAAATGATACATGAAAAGAATACAATTCATACCATCATTAATA
**
315677 TGAAATGATACATGAAAAGAATACAATTCATATTATCATTAATA
1 TGAAATGATACATGAAAAGAATACAATTCATACCATCATTAATA
315721 TGAA
1 TGAA
315725 TCATGAAGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.34
Consensus pattern (44 bp):
TGAAATGATACATGAAAAGAATACAATTCATACCATCATTAATA
Found at i:315743 original size:209 final size:201
Alignment explanation
Indices: 315285--315745 Score: 512
Period size: 201 Copynumber: 2.3 Consensus size: 201
315275 ATATATAAGT
* * *
315285 GAATACAATTCTTATCATCACTAATGTGAATCATAAAGTTAGAGGAAATTCACTCCTAATGTTAA
1 GAATACAATTCTTATCATCATTAATGTGAATCATAAAGTTAGAGAAAATTCACTCATAATGTTAA
* * *
315350 TTTATGGTCATAACTTTTTCTTTAGTTTATGACCAATACTTTAATTAGTAGAAAAACAACCATAC
66 TTTATGATCATAACTTTTTCTTTAATTTATGACCAATACTTTAATGAGTAGAAAAACAACCATAC
* * * *
315415 ACCAACCACCATTAATGTATATGAAGTGAATACAATTATCATCATCATTAATTTGAAATGTTATA
131 ACCAACCACCATTAATGTATATGAAGTGAATACAATTATCACCATCATTAATATGAAATGATACA
*
315480 TGAAAT
196 TGAAAA
* ** * * *
315486 GAATACAATTCTTATCAACATTAATGTGAATCATAAAAATAAAGAAAATTCACTCATATTTTTAA
1 GAATACAATTCTTATCATCATTAATGTGAATCATAAAGTTAGAGAAAATTCACTCATAATGTTAA
* ***
315551 TTTATGATCATAACTTTTTCTTTAATTTATG-CCCATAACTTTAATGAGTAAGAAATTAACATTT
66 TTTATGATCATAACTTTTTCTTTAATTTATGACCAAT-ACTTTAATGAGT-AGAAA--AACAACC
****** * * *
315615 A-ACTTACCATTTTTGATGTGAAATGATATATGAAGTGAATATAATTGTTACCATCATTAATATG
127 ATAC--ACCAACCACCAT-T--AATG-TATATGAAGTGAATACAATTATCACCATCATTAATATG
315679 AAATGATACATGAAAA
186 AAATGATACATGAAAA
* * * *
315695 GAATACAATTCATATTATCATTAATATGAATCATGAAGTTAGAGAAAATTC
1 GAATACAATTCTTATCATCATTAATGTGAATCATAAAGTTAGAGAAAATTC
315746 TCTTATCAAC
Statistics
Matches: 212, Mismatches: 38, Indels: 12
0.81 0.15 0.05
Matches are distributed among these distances:
200 4 0.02
201 96 0.45
202 5 0.02
203 2 0.01
204 5 0.02
205 6 0.03
206 1 0.00
208 4 0.02
209 89 0.42
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (201 bp):
GAATACAATTCTTATCATCATTAATGTGAATCATAAAGTTAGAGAAAATTCACTCATAATGTTAA
TTTATGATCATAACTTTTTCTTTAATTTATGACCAATACTTTAATGAGTAGAAAAACAACCATAC
ACCAACCACCATTAATGTATATGAAGTGAATACAATTATCACCATCATTAATATGAAATGATACA
TGAAAA
Found at i:320025 original size:29 final size:29
Alignment explanation
Indices: 319993--320140 Score: 108
Period size: 29 Copynumber: 5.2 Consensus size: 29
319983 TTTTTTTAAC
*
319993 ATTACGAAAATAACACCATTTT-AAAATTA
1 ATTACAAAAATAACACCATTTTCAAAA-TA
* *
320022 ATTATC-AAAATAGCATCATTTTCAAAATA
1 ATTA-CAAAAATAACACCATTTTCAAAATA
* * *
320051 ATTACAAAAATATCACTCTTTTTAAAAAT-
1 ATTACAAAAATAACAC-CATTTTCAAAATA
* * * ** *
320080 TTTACGAAATTGTCACC-TTTT-AAAAAA
1 ATTACAAAAATAACACCATTTTCAAAATA
* *
320107 AATACAAAAATAACACCCTTTTCAAAATA
1 ATTACAAAAATAACACCATTTTCAAAATA
320136 ATTAC
1 ATTAC
320141 CAGAATAGTA
Statistics
Matches: 93, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
26 4 0.04
27 15 0.16
28 6 0.06
29 53 0.57
30 15 0.16
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.33
Consensus pattern (29 bp):
ATTACAAAAATAACACCATTTTCAAAATA
Found at i:326535 original size:24 final size:24
Alignment explanation
Indices: 326508--326565 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
326498 CAGATTAGAT
* *
326508 TCCATGTCAAGTATCATATAAAAA
1 TCCACGTCAAGTACCATATAAAAA
* * *
326532 TCCAGGTCGAGTACCATATCAAAA
1 TCCACGTCAAGTACCATATAAAAA
326556 TCCACGTCAA
1 TCCACGTCAA
326566 AAATCAAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (24 bp):
TCCACGTCAAGTACCATATAAAAA
Found at i:327292 original size:29 final size:28
Alignment explanation
Indices: 327254--327404 Score: 90
Period size: 29 Copynumber: 5.2 Consensus size: 28
327244 ATTTTTTAAC
*
327254 ATTACGAAAATAACACCTTTTTAAAATTA
1 ATTACTAAAATAACACCTTTTTAAAA-TA
* * *
327283 ATTA-TCAAAATAGCATCATTTTCAAAATA
1 ATTACT-AAAATAACA-CCTTTTTAAAATA
*
327312 ATTACTAAAATATCACTCTTTTTAAAA-A
1 ATTACTAAAATAACAC-CTTTTTAAAATA
* * * * * *
327340 TTTTACGAAATTATCACTTTTTTATAAAAAAA
1 -ATTACTAAAATAACAC-CTTTT-T-AAAATA
* * *
327372 AATACAAAAATAACACCTTTTCAAAATA
1 ATTACTAAAATAACACCTTTTTAAAATA
327400 ATTAC
1 ATTAC
327405 CAGAATAGCA
Statistics
Matches: 94, Mismatches: 20, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
28 11 0.12
29 52 0.55
30 15 0.16
31 15 0.16
32 1 0.01
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (28 bp):
ATTACTAAAATAACACCTTTTTAAAATA
Found at i:327411 original size:28 final size:29
Alignment explanation
Indices: 327380--327435 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
327370 AAAATACAAA
*
327380 AATAACACC-TTTTCAAAATAATTACCAG
1 AATAACACCATTTCCAAAATAATTACCAG
* *
327408 AATAGCACCATTTCCCAAATAATTACCA
1 AATAACACCATTTCCAAAATAATTACCA
327436 AAATGTCACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.45, C:0.25, G:0.04, T:0.27
Consensus pattern (29 bp):
AATAACACCATTTCCAAAATAATTACCAG
Found at i:328405 original size:117 final size:116
Alignment explanation
Indices: 328186--328405 Score: 262
Period size: 117 Copynumber: 1.9 Consensus size: 116
328176 TTACACACCT
* * * * *
328186 CCTTTTGTGATGGATGATCCAAGTTGAATAAGTTCTTCTCATTAGGAATTTAGTCTCCGTTATCA
1 CCTTCTGTGATGGATGAACCAAGTTGAATAAGTTATTCTCATTAGGAATTTAGTCTCCCTCATCA
* * * * * * *
328251 GACTAGTTCTTCTCATTATGAACCTTTCCGTTGGAAATATTGATCTACCCC
66 GACGACTTCTTATCATTATAAACCCTTCCATTAGAAATATTGATCTACCCC
* **
328302 CCTTCTGTGATGGATGAACCAAGGTTGAATAAGTTATTCTCATTATG-ATCTTTTTCTCCCTCAT
1 CCTTCTGTGATGGATGAACCAA-GTTGAATAAGTTATTCTCATTAGGAAT-TTAGTCTCCCTCAT
* *
328366 CATACGACTTGTTATCATTATAAACCCTTCCATTAGAAAT
64 CAGACGACTTCTTATCATTATAAACCCTTCCATTAGAAAT
328406 GTTTGGTCTA
Statistics
Matches: 85, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
116 22 0.26
117 63 0.74
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.39
Consensus pattern (116 bp):
CCTTCTGTGATGGATGAACCAAGTTGAATAAGTTATTCTCATTAGGAATTTAGTCTCCCTCATCA
GACGACTTCTTATCATTATAAACCCTTCCATTAGAAATATTGATCTACCCC
Found at i:332468 original size:12 final size:12
Alignment explanation
Indices: 332451--332488 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
332441 AGATGTAAGG
332451 ATGTGAATGCAA
1 ATGTGAATGCAA
332463 ATGTGAAGTGCAA
1 ATGTGAA-TGCAA
*
332476 ATGTAAATGCAA
1 ATGTGAATGCAA
332488 A
1 A
332489 ATGGTGTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.45, C:0.08, G:0.24, T:0.24
Consensus pattern (12 bp):
ATGTGAATGCAA
Found at i:333808 original size:24 final size:24
Alignment explanation
Indices: 333781--333842 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
333771 GTAACAAATC
*
333781 AAAATCCATGTCAAGTATCATATA
1 AAAATCCAGGTCAAGTATCATATA
* *
333805 AAAATTCAGGTCAAGTATCATATT
1 AAAATCCAGGTCAAGTATCATATA
**
333829 TGAATCCAGGTCAA
1 AAAATCCAGGTCAA
333843 CAATCAGGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (24 bp):
AAAATCCAGGTCAAGTATCATATA
Found at i:334595 original size:29 final size:30
Alignment explanation
Indices: 334553--334627 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
334543 CATTTTATAT
* *
334553 AAATAGCACCCTTTT-TAAAATAATAACCA
1 AAATAGCACCCTTTTCAAAAAAAATAACCA
* *
334582 AAATAGCAGCCTTTTCAAAAAAAATTACCA
1 AAATAGCACCCTTTTCAAAAAAAATAACCA
334612 AAATAGCACCCATTTT
1 AAATAGCACCC-TTTT
334628 GAATTAATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 14 0.36
30 21 0.54
31 4 0.10
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.27
Consensus pattern (30 bp):
AAATAGCACCCTTTTCAAAAAAAATAACCA
Found at i:341091 original size:24 final size:24
Alignment explanation
Indices: 341016--341094 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 24
341006 AAACATAATT
* * * *
341016 CAGGTCAGGTAACAAATCAGAATC
1 CAGGTCAAGTATCATATAAGAATC
* * *
341040 CATGTCAAGTATCATATAAAAATT
1 CAGGTCAAGTATCATATAAGAATC
**
341064 CAGGTCAAGTATCATATTTGAATC
1 CAGGTCAAGTATCATATAAGAATC
341088 CAGGTCA
1 CAGGTCA
341095 GCAATCAGGT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (24 bp):
CAGGTCAAGTATCATATAAGAATC
Found at i:341848 original size:29 final size:29
Alignment explanation
Indices: 341806--341900 Score: 120
Period size: 29 Copynumber: 3.3 Consensus size: 29
341796 CATTTTACAT
*
341806 AAATAGCACCCTTTTTAAAATAATAACCA
1 AAATAGCACCCTTTTTAAAATAATTACCA
*
341835 AAATAGCACCCTTTTCAAAA-AATTACCA
1 AAATAGCACCCTTTTTAAAATAATTACCA
* * * * *
341863 AAATAACACCCATTTTGAATTAATTCCCA
1 AAATAGCACCCTTTTTAAAATAATTACCA
341892 AAATAGCAC
1 AAATAGCAC
341901 AAAAATCGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 22 0.39
29 34 0.61
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.26
Consensus pattern (29 bp):
AAATAGCACCCTTTTTAAAATAATTACCA
Found at i:341995 original size:19 final size:19
Alignment explanation
Indices: 341971--342010 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
341961 GTCAGGTCGG
341971 ACCGGTTC-AGACCGATCAA
1 ACCGGTTCGA-ACCGATCAA
*
341990 ACCGGTTCGAACCGGTCAA
1 ACCGGTTCGAACCGATCAA
342009 AC
1 AC
342011 AAGTCAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.30, C:0.33, G:0.23, T:0.15
Consensus pattern (19 bp):
ACCGGTTCGAACCGATCAA
Found at i:349013 original size:30 final size:30
Alignment explanation
Indices: 348956--349033 Score: 113
Period size: 30 Copynumber: 2.6 Consensus size: 30
348946 CATTTTACAT
* * *
348956 AAATAGCACCATTTT-TAAAATAATAACCA
1 AAATAGCACCCTTTTCAAAAAAAATAACCA
348985 AAATAGCACCCTTTTCAAAAAAAATAACCA
1 AAATAGCACCCTTTTCAAAAAAAATAACCA
*
349015 AAATAGCACCCATTTCAAA
1 AAATAGCACCCTTTTCAAA
349034 TTAATTCCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 14 0.32
30 30 0.68
ACGTcount: A:0.51, C:0.22, G:0.04, T:0.23
Consensus pattern (30 bp):
AAATAGCACCCTTTTCAAAAAAAATAACCA
Found at i:351520 original size:4 final size:4
Alignment explanation
Indices: 351511--351574 Score: 96
Period size: 4 Copynumber: 16.5 Consensus size: 4
351501 ATAAAGAAAC
* *
351511 CATA CATA CATA CATA CATA CATA CAT- -ATA TATA TATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
351557 CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CA
351575 CATATATATA
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
2 2 0.04
4 55 0.96
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:351587 original size:8 final size:8
Alignment explanation
Indices: 351511--351588 Score: 70
Period size: 8 Copynumber: 10.0 Consensus size: 8
351501 ATAAAGAAAC
*
351511 CATACATA
1 CATATATA
*
351519 CATACATA
1 CATATATA
*
351527 CATACATA
1 CATATATA
351535 CATATAT-
1 CATATATA
351542 -ATATATA
1 CATATATA
*
351549 CATACATA
1 CATATATA
*
351557 CATACATA
1 CATATATA
*
351565 CATACATA
1 CATATATA
*
351573 CACATATA
1 CATATATA
*
351581 TATATATA
1 CATATATA
351589 AGTACAAGGA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
6 6 0.10
8 56 0.90
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (8 bp):
CATATATA
Found at i:353321 original size:229 final size:233
Alignment explanation
Indices: 352889--353353 Score: 737
Period size: 229 Copynumber: 2.0 Consensus size: 233
352879 GTGGCGACTG
*
352889 AGGCAACTAGGGTTTGTTACCCTAATCACAAATTGATCCATACCGTTAGATTAAGTGTTAGATCT
1 AGGCAACTAGGGTTTGTTACCCTAATCACAAATTGATCCATACCGTTAGATCAAGTGTTAGATCT
* * *
352954 AACGGTTGAGGACTGACGACGTGTATGGCTTAGAGATAGACTATGGTTTCATTGGTTGTTGGACC
66 AACGGTTGAGGACTGACGACGGGTATGGCTTAGAGATAGACTAGGGTTTCATTGGTTGTTCGACC
*
353019 TCTAAACTTGGGATTTGTAAAATATATTGATTTAATTGTTTTTGGACTTGGGTTTGTTAATTGTA
131 TCTAAACTTGGGATTTGTAAAATAGATTGATTTAATTGTTTTTGGACTTGGGTTTGTTAATTGTA
353084 ATAATAATAAC-A-A-CAACAATAATAATGGTAGTAAT
196 ATAATAATAACAATAGCAACAATAATAATGGTAGTAAT
* * *
353119 AGGCAACTAGGGTTTGTTACCCTAATCACGAATTGATTCATATCGTTAGATCAAGTGTTAGATCT
1 AGGCAACTAGGGTTTGTTACCCTAATCACAAATTGATCCATACCGTTAGATCAAGTGTTAGATCT
* *
353184 AATGGTTGAGGACT-A-G-CGGGCCATATGGCTTAGAGAT-GACTAGGGTTTCTTTGGTTGTTCG
66 AACGGTTGAGGACTGACGACGGG---TATGGCTTAGAGATAGACTAGGGTTTCATTGGTTGTTCG
* *
353245 ACCTCTAAACTTGGGCTTTGTAAAATAGATTGATTTAATTGTTTTTGGATTTGGGTTTGTTAATT
128 ACCTCTAAACTTGGGATTTGTAAAATAGATTGATTTAATTGTTTTTGGACTTGGGTTTGTTAATT
*
353310 GTAATAATAATAACAATAGCAACAATAATAATTGTAGTAAT
193 GTAATAATAATAACAATAGCAACAATAATAATGGTAGTAAT
353351 AGG
1 AGG
353354 GATGGTTGAA
Statistics
Matches: 216, Mismatches: 13, Indels: 10
0.90 0.05 0.04
Matches are distributed among these distances:
227 3 0.01
228 1 0.00
229 98 0.45
230 89 0.41
231 1 0.00
232 24 0.11
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (233 bp):
AGGCAACTAGGGTTTGTTACCCTAATCACAAATTGATCCATACCGTTAGATCAAGTGTTAGATCT
AACGGTTGAGGACTGACGACGGGTATGGCTTAGAGATAGACTAGGGTTTCATTGGTTGTTCGACC
TCTAAACTTGGGATTTGTAAAATAGATTGATTTAATTGTTTTTGGACTTGGGTTTGTTAATTGTA
ATAATAATAACAATAGCAACAATAATAATGGTAGTAAT
Found at i:353637 original size:25 final size:25
Alignment explanation
Indices: 353592--353639 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
353582 TCACCCATAA
* *
353592 TTTTAATTTATGTTCATAACTTTTT
1 TTTTAATTTATGTACACAACTTTTT
353617 TTTTAATTTATG-ACAACAACTTT
1 TTTTAATTTATGTAC-ACAACTTT
353640 AATGGCAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.56
Consensus pattern (25 bp):
TTTTAATTTATGTACACAACTTTTT
Found at i:353842 original size:164 final size:160
Alignment explanation
Indices: 353513--354053 Score: 625
Period size: 163 Copynumber: 3.4 Consensus size: 160
353503 TTATTACAAC
* * * *
353513 TATTAATTTGAAATGATATATGAAATGAATACAATTCTTAACATCATTAATGTGAATCATAAAG-
1 TATTAATGTGAAATGATATATGAAGTGAATACAATTCTTATCACCATTAATGTGAATCATAAAGT
* * *
353577 ----AAAATTCACCCATAATTTTAATTTATGTTCATAACTTTTTTTTTAATTTATGACAACAACT
66 TAAAAAAATTCACTCATAACTTTAATTTATGGTCATAAC-TTTTTTTTAATTTATGAC-ACAACT
*
353638 TTAA-TGGCAGGAAAATGACATTACACCTATCA
129 TTAATTGGTAGG-AAATGACATTACACCTATCA
* * *
353670 CCATTAATGTGAAATGATATATGAAGTGAATATAATTCTCATCACCATTAATGTGAATCATAAAG
1 -TATTAATGTGAAATGATATATGAAGTGAATACAATTCTTATCACCATTAATGTGAATCATAAAG
353735 TTAAATAAAATTCACTCATAACTTTAATTTATGGTCATAACTTTTTTTTAATTTACT-ATCACAA
65 TTAAA-AAAATTCACTCATAACTTTAATTTATGGTCATAACTTTTTTTTAATTTA-TGA-CACAA
* * *
353799 CTTTAATTGATAGGAAAGTGACATTACACTTACCA
127 CTTTAATTGGTAGGAAA-TGACATTACACCTATCA
* * * * *
353834 TAATTAATGTGAAATGATATATGAAGTGAATACAATACTTATTACTATTAAAG-GAAATTATAAA
1 T-ATTAATGTGAAATGATATATGAAGTGAATACAATTCTTATCACCATTAATGTG-AATCATAAA
*
353898 CTTAAAAAAA-TCACTCATAACTTTAATTTATGGTCATAA-TTATTTCTTTAATTTATGACCACA
64 GTTAAAAAAATTCACTCATAACTTTAATTTATGGTCATAACTT-TTT-TTTAATTTATGA-CACA
* * *
353961 ACTTTAATTGGTAGGAAATCAACCTTTCACCTATCA
126 ACTTTAATTGGTAGGAAAT-GACATTACACCTATCA
* * * * *
353997 CTATTAATGTGAAATGATATATAAAGTGAATACAATTGTTACCATCATTAATTTGAA
1 -TATTAATGTGAAATGATATATGAAGTGAATACAATTCTTATCACCATTAATGTGAA
354054 ATGATATATG
Statistics
Matches: 326, Mismatches: 39, Indels: 31
0.82 0.10 0.08
Matches are distributed among these distances:
158 57 0.17
161 2 0.01
162 34 0.10
163 119 0.37
164 114 0.35
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (160 bp):
TATTAATGTGAAATGATATATGAAGTGAATACAATTCTTATCACCATTAATGTGAATCATAAAGT
TAAAAAAATTCACTCATAACTTTAATTTATGGTCATAACTTTTTTTTAATTTATGACACAACTTT
AATTGGTAGGAAATGACATTACACCTATCA
Found at i:354062 original size:44 final size:44
Alignment explanation
Indices: 353999--354165 Score: 239
Period size: 44 Copynumber: 3.8 Consensus size: 44
353989 ACCTATCACT
*
353999 ATTAATGTGAAATGATATAT-AAAGTGAATACAATTGTTACCATC
1 ATTAATTTGAAATGATATATGAAA-TGAATACAATTGTTACCATC
* * * *
354043 ATTAATTTGAAATGATATATGAAATAAATACAATTATTATCACC
1 ATTAATTTGAAATGATATATGAAATGAATACAATTGTTACCATC
*
354087 ATTAATATGAAATGATATA-GAAAGTGAATACAATTGTTACCATC
1 ATTAATTTGAAATGATATATGAAA-TGAATACAATTGTTACCATC
*
354131 ATTAATTTGAAACGATATATGAAATGAATACAATT
1 ATTAATTTGAAATGATATATGAAATGAATACAATT
354166 ATTATCATAA
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
43 4 0.04
44 97 0.90
45 7 0.06
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.34
Consensus pattern (44 bp):
ATTAATTTGAAATGATATATGAAATGAATACAATTGTTACCATC
Found at i:354124 original size:88 final size:88
Alignment explanation
Indices: 353992--354172 Score: 317
Period size: 88 Copynumber: 2.1 Consensus size: 88
353982 ACCTTTCACC
* * * *
353992 TATCACTATTAATGTGAAATGATATATAAAGTGAATACAATTGTTACCATCATTAATTTGAAATG
1 TATCACCATTAATATGAAATGATATAGAAAGTGAATACAATTGTTACCATCATTAATTTGAAACG
354057 ATATATGAAATAAATACAATTAT
66 ATATATGAAATAAATACAATTAT
354080 TATCACCATTAATATGAAATGATATAGAAAGTGAATACAATTGTTACCATCATTAATTTGAAACG
1 TATCACCATTAATATGAAATGATATAGAAAGTGAATACAATTGTTACCATCATTAATTTGAAACG
*
354145 ATATATGAAATGAATACAATTAT
66 ATATATGAAATAAATACAATTAT
354168 TATCA
1 TATCA
354173 TAACTTTAAT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.35
Consensus pattern (88 bp):
TATCACCATTAATATGAAATGATATAGAAAGTGAATACAATTGTTACCATCATTAATTTGAAACG
ATATATGAAATAAATACAATTAT
Found at i:354221 original size:25 final size:25
Alignment explanation
Indices: 354176--354223 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
354166 ATTATCATAA
* *
354176 CTTTAATTTATGCTCATAACTTTTT
1 CTTTAATTCATGCTCACAACTTTTT
354201 CTTTAATTCATGACT-ACAACTTT
1 CTTTAATTCATG-CTCACAACTTT
354224 AATTGGTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.27, C:0.19, G:0.04, T:0.50
Consensus pattern (25 bp):
CTTTAATTCATGCTCACAACTTTTT
Found at i:363839 original size:4 final size:4
Alignment explanation
Indices: 363830--363866 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
363820 TTTCCATTCT
*
363830 TTTA TTTA TTTA TTTA TTTA TTTA TTT- TTTA TATA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
363867 ATTAGTTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:367444 original size:22 final size:23
Alignment explanation
Indices: 367419--367472 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
367409 AAAATGAATG
*
367419 AAAAAAAGG-AAAAAGGAAAGAA
1 AAAAAAAGGAAAAAAGAAAAGAA
*
367441 AAAATAAGGAAAAAAGAAAAGAA
1 AAAAAAAGGAAAAAAGAAAAGAA
367464 AAATAAAAG
1 AAA-AAAAG
367473 AAGGGTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 8 0.30
23 15 0.56
24 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (23 bp):
AAAAAAAGGAAAAAAGAAAAGAA
Found at i:368738 original size:66 final size:66
Alignment explanation
Indices: 368632--369591 Score: 1753
Period size: 66 Copynumber: 14.6 Consensus size: 66
368622 TTCGATCCCA
368632 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
368697 G
66 G
*
368698 ATTCAATGAATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
368763 G
66 G
*
368764 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAATAAGTCTGCTTC
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
*
368829 A
66 G
*
368830 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAAAGTAAGTGGAACAAGTCTGCTTC
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
368895 G
66 G
368896 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
368961 G
66 G
368962 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
369027 G
66 G
369028 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
369093 G
66 G
*
369094 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTACTTC
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
369159 G
66 G
*
369160 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTATGCTTC
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
369225 G
66 G
369226 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
369291 G
66 G
369292 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
369357 G
66 G
*
369358 ATTCAATGGACCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
369423 G
66 G
* * *
369424 ATTCAATTGATCAATTTCTCCAAGATTTGATATTCCATTCAGAGTAAGTGGAACAAGTCTGCTTC
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
369489 G
66 G
* *
369490 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTTAAAGTAAGTGGAA-AAGTCTGCTTC
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
369554 G
66 G
* * * * *
369555 ATTCAACGGATCAACATC-CCCATATGTGATATTCCCT
1 ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCT
369592 GAGTGGCAGT
Statistics
Matches: 867, Mismatches: 27, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
64 16 0.02
65 28 0.03
66 823 0.95
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (66 bp):
ATTCAATGGATCAACTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
G
Found at i:373782 original size:44 final size:44
Alignment explanation
Indices: 373719--373803 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
373709 ACCTTCGACA
* *
373719 TACCATTATTAACATGAAATGATATGTGAAGTGAATACAATTGT
1 TACCAGTATTAACATGAAATGATATATGAAGTGAATACAATTGT
**
373763 TACCAGTATTAATTTGAAATGATATATGAAGTGAATACAAT
1 TACCAGTATTAACATGAAATGATATATGAAGTGAATACAAT
373804 CCTTATAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.34
Consensus pattern (44 bp):
TACCAGTATTAACATGAAATGATATATGAAGTGAATACAATTGT
Found at i:373818 original size:44 final size:44
Alignment explanation
Indices: 373726--373824 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
373716 ACATACCATT
* * ** * **
373726 ATTAACATGAAATGATATGTGAAGTGAATACAATTGTTACCAGT
1 ATTAATATGAAATGATATATGAAGTGAATACAATCCTTACAACC
* *
373770 ATTAATTTGAAATGATATATGAAGTGAATACAATCCTTATAACC
1 ATTAATATGAAATGATATATGAAGTGAATACAATCCTTACAACC
373814 ATTAATATGAA
1 ATTAATATGAA
373825 TCATAAAGTT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.33
Consensus pattern (44 bp):
ATTAATATGAAATGATATATGAAGTGAATACAATCCTTACAACC
Found at i:374085 original size:44 final size:44
Alignment explanation
Indices: 374022--374127 Score: 158
Period size: 44 Copynumber: 2.4 Consensus size: 44
374012 ATCTTTCACC
* * *
374022 TACCATTATTAATGTGAAATGATATGTGAAGTGAATACAATTGT
1 TACCATCATTAATATGAAATGATATATGAAGTGAATACAATTGT
* *
374066 TACCATCATTAATTTGAAATGATATATGAAGTGAATACAATTTT
1 TACCATCATTAATATGAAATGATATATGAAGTGAATACAATTGT
*
374110 TACCACCATTAATATGAA
1 TACCATCATTAATATGAA
374128 TCATAAAGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (44 bp):
TACCATCATTAATATGAAATGATATATGAAGTGAATACAATTGT
Found at i:374233 original size:303 final size:303
Alignment explanation
Indices: 373665--374236 Score: 864
Period size: 303 Copynumber: 1.9 Consensus size: 303
373655 TGGTCATTAT
* * *
373665 TTTTTATTTAGTTTATGACTATAACTTTAATGGGTAGGAAATTGACCTTCGACATACCATTATTA
1 TTTTTATTTAATTTATGACCACAACTTTAATGGGTAGGAAATTGACCTTCGACATACCATTATTA
373730 ACATGAAATGATATGTGAAGTGAATACAATTGTTACCAGTATTAATTTGAAATGATATATGAAGT
66 ACATGAAATGATATGTGAAGTGAATACAATTGTTACCAGTATTAATTTGAAATGATATATGAAGT
* *
373795 GAATACAATCCTTATAACCATTAATATGAATCATAAAGTTAAAGAAAATTCACTTATAACTTTAA
131 GAATACAATCCTTACAACCATTAATATGAATCATAAAGTTAAAGAAAATTCACTCATAACTTTAA
* * *
373860 TTTATGACCATAATTTTTTCTTTAATTTATTATCACAACTTTAAATAGTAGGAAAGTGACATTAC
196 TTTATGACCATAAATTTTTCTCTAATTTATGATCACAACTTTAAATAGTAGGAAAGTGACATTAC
373925 ACCTACCACCATTAATGTGAATACAATCTTTATCACTCACAAC
261 ACCTACCACCATTAATGTGAATACAATCTTTATCACTCACAAC
* * * * *
373968 TTTTTCTTTAATTTATGACCACAACTTTAATTGGTGGGAAATTGATCTTTC-ACCTACCATTATT
1 TTTTTATTTAATTTATGACCACAACTTTAATGGGTAGGAAATTGA-CCTTCGACATACCATTATT
**
374032 AATGTGAAATGATATGTGAAGTGAATACAATTGTTACCA-TCATTAATTTGAAATGATATATGAA
65 AACATGAAATGATATGTGAAGTGAATACAATTGTTACCAGT-ATTAATTTGAAATGATATATGAA
** *
374096 GTGAATACAATTTTTACCACCATTAATATGAATCATAAAGTTAAAGAAAATTCACTCATAACTTT
129 GTGAATACAATCCTTACAACCATTAATATGAATCATAAAGTTAAAGAAAATTCACTCATAACTTT
* * * * *
374161 AATTTATG-CTCATAAATTTTTCTCTAATTTATGA-CTACAATTTTAATTGGTAGGAAATTGACC
194 AATTTATGAC-CATAAATTTTTCTCTAATTTATGATC-ACAACTTTAAATAGTAGGAAAGTGACA
*
374224 TTTCACCTACCAC
257 TTACACCTACCAC
374237 TTTTAATATA
Statistics
Matches: 241, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
302 3 0.01
303 234 0.97
304 4 0.02
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (303 bp):
TTTTTATTTAATTTATGACCACAACTTTAATGGGTAGGAAATTGACCTTCGACATACCATTATTA
ACATGAAATGATATGTGAAGTGAATACAATTGTTACCAGTATTAATTTGAAATGATATATGAAGT
GAATACAATCCTTACAACCATTAATATGAATCATAAAGTTAAAGAAAATTCACTCATAACTTTAA
TTTATGACCATAAATTTTTCTCTAATTTATGATCACAACTTTAAATAGTAGGAAAGTGACATTAC
ACCTACCACCATTAATGTGAATACAATCTTTATCACTCACAAC
Found at i:374999 original size:24 final size:25
Alignment explanation
Indices: 374946--375004 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
374936 CACTCATAAT
*
374946 TTTAATTTATAGTTATAATTGTTTC
1 TTTAATTTATAGTCATAATTGTTTC
374971 TTTAATTTATAGTCATAATT-TTTC
1 TTTAATTTATAGTCATAATTGTTTC
374995 TTTAATTTAT
1 TTTAATTTAT
375005 GAACACAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 14 0.42
25 19 0.58
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (25 bp):
TTTAATTTATAGTCATAATTGTTTC
Found at i:375109 original size:44 final size:44
Alignment explanation
Indices: 375043--375132 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
375033 ATATTACACG
* * *
375043 TACCGCCATTAATGTGAGATGATATACAAAGTGAATACAATTCT
1 TACCGCCATTAATGTAAAATGATATACAAAGTGAATAAAATTCT
* * *
375087 TACCGGCATTAATTTAAAATGATATATAAAGTGAATAAAATTCT
1 TACCGCCATTAATGTAAAATGATATACAAAGTGAATAAAATTCT
375131 TA
1 TA
375133 TCACTATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.32
Consensus pattern (44 bp):
TACCGCCATTAATGTAAAATGATATACAAAGTGAATAAAATTCT
Found at i:380148 original size:384 final size:383
Alignment explanation
Indices: 379436--380234 Score: 1526
Period size: 384 Copynumber: 2.1 Consensus size: 383
379426 TAGGTGTTAC
379436 AAAATTCACTCATAACTTTAATTTATGGTCATCGATCTTTCACCTATTACTATTAATGTGAAATG
1 AAAATTCACTCATAACTTTAATTTATGGTCATCGATCTTTCACCTATTACTATTAATGTGAAATG
379501 ATATATGAAGTGAATACAATTCTTACCACTATTAATGTAAATCATAAAGTTAAAGGAAATTCACT
66 ATATATGAAGTGAATACAATTCTTACCACTATTAATGTAAATCATAAAGTTAAAGGAAATTCACT
* *
379566 CCTAATTTTTTTATTATGCTAAGTTGATTAGAAAGTAGTATTTGTTCTAAATACTATCAATCATT
131 CCTAATTTTTTTATTATGCTAAGTTGATTAGAAAGTAGTATTTATTCTAAATACTAGCAATCATT
379631 TAACAATGAATGTTCAATCATCCCTGTTGCATTTGCTAACTTTAATTTATGGTCCCAATTTTTCT
196 TAACAATGAATGTTCAATCATCCCTGTTGCATTTGCTAACTTTAATTTATGGTCCCAATTTTTCT
*
379696 TTAATTTATGACTACAACTTTAATTAGTAGGAAAATGACCTTTCACCTACCACCATCAATGTGAA
261 TTAATTTATGACTACAACTTTAATTAGTAGGAAAAGGACCTTTCACCTACCACCATCAATGTGAA
* *
379761 ATGAAATATAAAGTGAATATAATCTTATCACTATTAATGTGAATCACAAAGTTACAAA
326 ATGAAATATAAAGTGAATATAATATTACCACTATTAATGTGAATCACAAAGTTACAAA
*
379819 AAATATTCACTCATAACTTTAATTTCTGGTCATCGATCTTTCACCTATTACTATTAATGTGAAAT
1 AAA-ATTCACTCATAACTTTAATTTATGGTCATCGATCTTTCACCTATTACTATTAATGTGAAAT
379884 GATATATGAAGTGAATACAATTCTTACCACTATTAATGTAAATCATAAAGTTAAAGGAAATTCAC
65 GATATATGAAGTGAATACAATTCTTACCACTATTAATGTAAATCATAAAGTTAAAGGAAATTCAC
379949 TCCTAATTTTTTTATTATGCTAAGTTGATTAGAAAGTAGTATTTATTCTAAATACTAGCAATCAT
130 TCCTAATTTTTTTATTATGCTAAGTTGATTAGAAAGTAGTATTTATTCTAAATACTAGCAATCAT
*
380014 TTAACAATGAATGTTCAATCATTCCTGTTGCATTTGCTAACTTTAATTTATGGTCCCAATTTTTC
195 TTAACAATGAATGTTCAATCATCCCTGTTGCATTTGCTAACTTTAATTTATGGTCCCAATTTTTC
380079 TTTAATTTATGACTACAACTTTAATTAGTAGGAAAAGGACCTTTCACCTACCACCATCAATGTGA
260 TTTAATTTATGACTACAACTTTAATTAGTAGGAAAAGGACCTTTCACCTACCACCATCAATGTGA
380144 AATGAAATATAAAGTGAATATAATATTACCACTATTAATGTGAATCACAAAGTTACAAA
325 AATGAAATATAAAGTGAATATAATATTACCACTATTAATGTGAATCACAAAGTTACAAA
380203 AAAATTCACTCATAACTTTAATTTATGGTCAT
1 AAAATTCACTCATAACTTTAATTTATGGTCAT
380235 AATTTTTTTA
Statistics
Matches: 407, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
383 31 0.08
384 376 0.92
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (383 bp):
AAAATTCACTCATAACTTTAATTTATGGTCATCGATCTTTCACCTATTACTATTAATGTGAAATG
ATATATGAAGTGAATACAATTCTTACCACTATTAATGTAAATCATAAAGTTAAAGGAAATTCACT
CCTAATTTTTTTATTATGCTAAGTTGATTAGAAAGTAGTATTTATTCTAAATACTAGCAATCATT
TAACAATGAATGTTCAATCATCCCTGTTGCATTTGCTAACTTTAATTTATGGTCCCAATTTTTCT
TTAATTTATGACTACAACTTTAATTAGTAGGAAAAGGACCTTTCACCTACCACCATCAATGTGAA
ATGAAATATAAAGTGAATATAATATTACCACTATTAATGTGAATCACAAAGTTACAAA
Found at i:381123 original size:26 final size:26
Alignment explanation
Indices: 381094--381144 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
381084 GTAGGATCTT
*
381094 ATTTAATGTT-TTAAGTGTGTAAACTC
1 ATTTAAT-TTATTAAGTGGGTAAACTC
*
381120 ATTTAATTTATTTAGTGGGTAAACT
1 ATTTAATTTATTAAGTGGGTAAACT
381145 GGTTTGTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (26 bp):
ATTTAATTTATTAAGTGGGTAAACTC
Found at i:381604 original size:2 final size:2
Alignment explanation
Indices: 381597--381706 Score: 220
Period size: 2 Copynumber: 55.0 Consensus size: 2
381587 CTAAAGAAGT
381597 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
381639 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
381681 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
381707 GATTTACTAT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 108 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:381889 original size:11 final size:11
Alignment explanation
Indices: 381875--381916 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
381865 ATTTATTGTA
381875 ATTATATTTTT
1 ATTATATTTTT
381886 ATTATATTTCTT
1 ATTATATTT-TT
381898 -TTATATTTTT
1 ATTATATTTTT
381908 ATTATATTT
1 ATTATATTT
381917 AAATTGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.07
11 25 0.86
12 2 0.07
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTATATTTTT
Found at i:392821 original size:20 final size:20
Alignment explanation
Indices: 392796--392854 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
392786 TTTGCTGCAG
*
392796 AGGGAATCGATCCCCCCTTA
1 AGGGAATCGATCCCCCCTCA
* *
392816 AGGGAACCGATTCCCCCCACA
1 AGGGAATCGA-TCCCCCCTCA
* *
392837 GGGGAATCGATACCCCCT
1 AGGGAATCGATCCCCCCT
392855 GGGGTTCTGG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.25, C:0.37, G:0.22, T:0.15
Consensus pattern (20 bp):
AGGGAATCGATCCCCCCTCA
Found at i:408549 original size:26 final size:26
Alignment explanation
Indices: 408520--408596 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 26
408510 TGAGCCAGAT
* *
408520 GGGCAACGGCCCAGGGTAGCATTTAA
1 GGGCGACGGCCCAGGGTAGCATGTAA
*
408546 GGGCGACGGCCCAGGGTAGCATGTAG
1 GGGCGACGGCCCAGGGTAGCATGTAA
* * *
408572 GGGCGACGACCCAGGGCAACATGTA
1 GGGCGACGGCCCAGGGTAGCATGTA
408597 GGGGATTCAG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.25, C:0.25, G:0.39, T:0.12
Consensus pattern (26 bp):
GGGCGACGGCCCAGGGTAGCATGTAA
Found at i:410429 original size:21 final size:22
Alignment explanation
Indices: 410388--410443 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
410378 TGTACGTGTA
* *
410388 TAAATATTA-GTTCATATTGCT
1 TAAATATTATTTTCATAGTGCT
410409 TAAATATTATTTTCA-AGTGCT
1 TAAATATTATTTTCATAGTGCT
410430 TCAAAATATTATTT
1 T--AAATATTATTT
410444 ATTACAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 15 0.50
22 4 0.13
23 11 0.37
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (22 bp):
TAAATATTATTTTCATAGTGCT
Found at i:412660 original size:31 final size:31
Alignment explanation
Indices: 412622--412682 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
412612 GAAAATAAAT
*
412622 CAACGTATTTGAGTCCTATTGAAACACTAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAC
*
412653 CAACGTATTTGAGTCTTATTAAAACACTAA
1 CAACGTATTTGAGTCCTATTAAAACACTAA
412683 AACTAAAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (31 bp):
CAACGTATTTGAGTCCTATTAAAACACTAAC
Found at i:413012 original size:26 final size:25
Alignment explanation
Indices: 412983--413046 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
412973 CTTTTTATTT
*
412983 TATTTTTTATTTATT-TACTTTATATA
1 TATTTTTTATTTATTCTAATTT-TA-A
* *
413009 TATTTTTCATTTTCTTCTAATTTTAA
1 TATTTTTTA-TTTATTCTAATTTTAA
413035 TATTTTTTATTT
1 TATTTTTTATTT
413047 CTTTTTACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
25 3 0.09
26 17 0.53
27 7 0.22
28 5 0.16
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (25 bp):
TATTTTTTATTTATTCTAATTTTAA
Found at i:417265 original size:32 final size:30
Alignment explanation
Indices: 417229--417344 Score: 97
Period size: 32 Copynumber: 3.6 Consensus size: 30
417219 GGAACAATGA
*
417229 GGGCATCTTTGAAGATTCAACATCAAATGCTG
1 GGGCATCTTTG-AGATTCAACATCAAAT-TTG
* * *
417261 GGGCATTTTTTGAGATTTAACATCAAAATTTT
1 GGGCA-TCTTTGAGATTCAACATC-AAATTTG
* * *
417293 GGGCATTTTTTTAGATTCAACATCGAATATTG
1 GGGCA-TCTTTGAGATTCAACATCAAAT-TTG
*
417325 GGGCATCTTTGGGAATTCAA
1 GGGCATCTTTGAG-ATTCAA
417345 TATCCTGATG
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
31 8 0.12
32 52 0.75
33 9 0.13
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (30 bp):
GGGCATCTTTGAGATTCAACATCAAATTTG
Found at i:418556 original size:37 final size:37
Alignment explanation
Indices: 418507--418611 Score: 194
Period size: 36 Copynumber: 2.9 Consensus size: 37
418497 CAAGTTTTGC
418507 CTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTGT
1 CTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTGT
*
418544 CTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGT
1 CTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTGT
418580 CTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
1 CTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
418612 CTTTGAATAT
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
36 35 0.53
37 31 0.47
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (37 bp):
CTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTGT
Found at i:418711 original size:31 final size:32
Alignment explanation
Indices: 418650--418711 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
418640 TTCGTCTCCA
418650 TTGAGACAGTTTCTTTTAGAACTAAATTTTTC
1 TTGAGACAGTTTCTTTTAGAACTAAATTTTTC
418682 TTGAGACAGTTTCTTTT-GAAAC-AAATTTTT
1 TTGAGACAGTTTCTTTTAG-AACTAAATTTTT
418712 TCCCTCTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (32 bp):
TTGAGACAGTTTCTTTTAGAACTAAATTTTTC
Found at i:418780 original size:31 final size:30
Alignment explanation
Indices: 418742--418803 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
418732 CTTGAAACAC
*
418742 AAAAAAACCCCTCG-AAATTGTTTCTCTTGA
1 AAAAAAAACCCTCGAAAATT-TTTCTCTTGA
* *
418772 AAAAAAAACCTTTGAAAATTTTTCTCTTGA
1 AAAAAAAACCCTCGAAAATTTTTCTCTTGA
418802 AA
1 AA
418804 CATCAAACCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (30 bp):
AAAAAAAACCCTCGAAAATTTTTCTCTTGA
Found at i:418949 original size:83 final size:83
Alignment explanation
Indices: 418810--419054 Score: 337
Period size: 83 Copynumber: 2.9 Consensus size: 83
418800 GAAACATCAA
* *
418810 ACCTTCGAGTTCGACTACGCTCAGCTTCAAGACACATCATTTACAGCATAACTCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
*
418875 AGTTATCTGCCAACAAAG
66 GGTTATCTGCCAACAAAG
418893 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
* * *
418958 GGCTATCTGTCAACAAGG
66 GGTTATCTGCCAACAAAG
* * * * * * * ** *
418976 ACCTCCGAGTTTGACTCCACTCAGGTCAAATGCACCATCATTTGTAGCATAACTCAAGGCAAGAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTACAGCATAACTCAAGGCTAGAA
419041 GGGTTATCTGCCAA
65 GGGTTATCTGCCAA
419055 ATACCTTCGA
Statistics
Matches: 143, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
83 104 0.73
84 39 0.27
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (83 bp):
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
GGTTATCTGCCAACAAAG
Found at i:419430 original size:10 final size:10
Alignment explanation
Indices: 419411--419465 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
419401 GTCTACAAAA
*
419411 ATATTTTATT
1 ATATTATATT
419421 ATATTATATT
1 ATATTATATT
419431 ATATT-TATT
1 ATATTATATT
419440 -TATT-TATT
1 ATATTATATT
419448 ATTATTATTATT
1 A-TATTA-TATT
419460 AT-TTAT
1 ATATTAT
419466 TTTTTTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
8 8 0.20
9 5 0.12
10 21 0.52
11 1 0.03
12 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
ATATTATATT
Found at i:419436 original size:20 final size:20
Alignment explanation
Indices: 419411--419465 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
419401 GTCTACAAAA
419411 ATATTTTATTATATTATATT
1 ATATTTTATTATATTATATT
419431 ATA-TTTATT-TATT-TATT
1 ATATTTTATTATATTATATT
419448 ATTATTATTATTAT-TTAT
1 A-TATT-TTATTATATTAT
419466 TTTTTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
17 5 0.17
18 6 0.20
19 7 0.23
20 10 0.33
21 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATATTTTATTATATTATATT
Found at i:419453 original size:23 final size:23
Alignment explanation
Indices: 419415--419474 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
419405 ACAAAAATAT
419415 TTTATTATATTA-TATTA-TATTTA
1 TTTATT-TATTATTATTATTA-TTA
419438 TTTATTTATTATTATTATTATTA
1 TTTATTTATTATTATTATTATTA
419461 TTTATTT-TT-TTATT
1 TTTATTTATTATTATT
419475 TTTTGCAGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.14
22 7 0.20
23 21 0.60
24 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTATTTATTATTATTATTATTA
Found at i:419462 original size:27 final size:25
Alignment explanation
Indices: 419415--419474 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 25
419405 ACAAAAATAT
419415 TTTA-TTA-TATTATATTATATTTA
1 TTTATTTATTATTATATTATATTTA
419438 TTTATTTATTATTATTATTATTATTTA
1 TTTATTTATTATTA-TATTA-TATTTA
*
419465 TTTTTTTATT
1 TTTATTTATT
419475 TTTTGCAGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 4 0.12
24 3 0.09
25 5 0.16
26 5 0.16
27 15 0.47
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTATTTATTATTATATTATATTTA
Found at i:419566 original size:33 final size:33
Alignment explanation
Indices: 419529--419594 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
419519 AAAAATAAAT
*
419529 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
419562 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
419595 TGAAGCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (33 bp):
CAACGTATTTGAGTCCTATTAAAACACTAAAAC
Found at i:419605 original size:33 final size:33
Alignment explanation
Indices: 419529--419610 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
419519 AAAAATAAAT
* *
419529 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
1 CAACGCATTTGAGTCCTATTAAAACACTAAAAC
*
419562 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1 CAACGCATTTGAGTCCTATTAAAACACTAAAAC
*
419595 TGAA-GCATTTGAGTCC
1 -CAACGCATTTGAGTCC
419611 AAGTAGGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 43 0.96
34 2 0.04
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (33 bp):
CAACGCATTTGAGTCCTATTAAAACACTAAAAC
Found at i:421655 original size:2 final size:2
Alignment explanation
Indices: 421648--421687 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
421638 TACCTCACAA
421648 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
421688 TTCCAACAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:427015 original size:10 final size:10
Alignment explanation
Indices: 427000--427039 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
426990 ATTTTTAAAT
427000 AAAACAAAAA
1 AAAACAAAAA
427010 AAAACAAAAA
1 AAAACAAAAA
**
427020 AAGGC-AAAA
1 AAAACAAAAA
427029 AAAACAAAAA
1 AAAACAAAAA
427039 A
1 A
427040 GCCAAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 7 0.28
10 18 0.72
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAACAAAAA
Found at i:427040 original size:18 final size:19
Alignment explanation
Indices: 427006--427046 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
426996 AAATAAAACA
*
427006 AAAAAAAACAAAAAAAGGC
1 AAAAAAAACAAAAAAAGCC
427025 AAAAAAAAC-AAAAAAGCC
1 AAAAAAAACAAAAAAAGCC
427043 AAAA
1 AAAA
427047 TTTCAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.80, C:0.12, G:0.07, T:0.00
Consensus pattern (19 bp):
AAAAAAAACAAAAAAAGCC
Found at i:434589 original size:247 final size:247
Alignment explanation
Indices: 434055--434643 Score: 842
Period size: 247 Copynumber: 2.4 Consensus size: 247
434045 CTTATTCATA
434055 TATTGAATAAAAAT-ATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGG
* * * **
434119 TGAAACTTTATTTTGGT--T-GGGTCGGTTTTTTTGAGTGTGATATTCGGGTCGAGTTTGGGTTT
66 TGAAACTTTATTTTGGTGGTCGGGTCAGTTTTTTTAAGTGTGATATTCAGGTCGAGTTCAGGTTT
* * *
434181 AGGGTGAAAATACATGACCCGACCCGAAAATATATAATTTTACCTTATATATTTAGGAATAATTA
131 AGGCTGAAAATACATGACCCGACCCAAAAATATATAAATTTACCTTATATATTTAGGAATAATTA
434246 CAATAATACCCCTCTATATATATATAATTTTTTTTCAATTAAGCCATTGTTTT
196 CAATAATACCCCTCTATATATATATAATTTTTTTTCAATTAAGCCA-TGTTTT
*
434299 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCAGGTTTCTAATTCATATATTCGGGTCGGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGG
*
434364 TGAAACTTTATTTTGGTCGGGTCGGGTCAGTTTTTTTAAGTGTGATATTCAGGTCGGGTTCAGGT
66 TGAAACTTTATTTTGGT--GGTCGGGTCAGTTTTTTTAAGTGTGATATTCAGGTCGAGTTCAGGT
434429 TTAGGCTG-AAA-A-AT-ACCCGACCCAAAAAATATATAAATTTACCTTATATATTTAGGAATAA
129 TTAGGCTGAAAATACATGACCCGACCC-AAAAATATATAAATTTACCTTATATATTTAGGAATAA
* *
434490 TTACAATAATACCCCTC-A-ATATATA-ATTTTTTTTTCAATTAAGTC-TGTTTT
193 TTACAATAATACCCCTCTATATATATATAATTTTTTTTCAATTAAGCCATGTTTT
434541 TATTGAATAAAAATAATTTTTTTATTATTTCAGGTCTGGTCGGGTTTCTAATTCATATATTCGGG
1 TATTGAATAAAAATAATTTTTTTATTATTTC--G---GGTCGGGTTTCTAATTCATATATT----
434606 ACGGGTCGGGTGAAACTTTATTTTGGTTGAGTCGGGTC
57 -CGGGTCGGGTGAAACTTTATTTTGG-TG-GTCGGGTC
434644 TCAGATGGAG
Statistics
Matches: 313, Mismatches: 13, Indels: 30
0.88 0.04 0.08
Matches are distributed among these distances:
242 37 0.12
244 33 0.11
245 73 0.23
246 10 0.03
247 77 0.25
248 1 0.00
249 4 0.01
250 43 0.14
251 1 0.00
252 33 0.11
253 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.42
Consensus pattern (247 bp):
TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGG
TGAAACTTTATTTTGGTGGTCGGGTCAGTTTTTTTAAGTGTGATATTCAGGTCGAGTTCAGGTTT
AGGCTGAAAATACATGACCCGACCCAAAAATATATAAATTTACCTTATATATTTAGGAATAATTA
CAATAATACCCCTCTATATATATATAATTTTTTTTCAATTAAGCCATGTTTT
Found at i:435032 original size:17 final size:18
Alignment explanation
Indices: 435007--435053 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
434997 TAAGGAATTG
435007 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTGACA
* *
435024 GATTTCAATTCCTTTACA
1 GATTCCAATTCCTTGACA
435042 GATTCCAATTCC
1 GATTCCAATTCC
435054 CTCAGAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCTTGACA
Found at i:449382 original size:35 final size:35
Alignment explanation
Indices: 449319--449385 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
449309 CTTAGATCCG
*
449319 TAAGGAATTACCAGCTCGATCAGTCTGAACCTATA
1 TAAGGAATTACCAGCTCGACCAGTCTGAACCTATA
* *
449354 TAAGGAATTACCAGTTTGACCAAG-CTGAACCT
1 TAAGGAATTACCAGCTCGACC-AGTCTGAACCT
449386 GTAGAAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 26 0.93
36 2 0.07
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (35 bp):
TAAGGAATTACCAGCTCGACCAGTCTGAACCTATA
Found at i:454920 original size:21 final size:21
Alignment explanation
Indices: 454891--454943 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
454881 ATTTTGACTA
454891 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
454912 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
454933 TCGCAATGCGA
1 TCGCATTGCGA
454944 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:454958 original size:20 final size:20
Alignment explanation
Indices: 454933--455039 Score: 144
Period size: 20 Copynumber: 5.3 Consensus size: 20
454923 TTTTCCTAAT
454933 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
454953 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
454974 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
454994 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
455014 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
455034 TCGCAA
1 TCGCAA
455040 CGAGATTCTG
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
19 1 0.01
20 59 0.79
21 15 0.20
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:454979 original size:41 final size:40
Alignment explanation
Indices: 454933--455041 Score: 148
Period size: 41 Copynumber: 2.7 Consensus size: 40
454923 TTTTCCTAAT
**
454933 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAA-TACGAAAA
* * *
454974 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
455014 TCGCAATGCGAAT-CTGTAAATCGCAACG
1 TCGCAATGCGAATAC-GTAAATCGCAACG
455042 AGATTCTGAC
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.02
40 29 0.48
41 30 0.50
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
Found at i:455057 original size:40 final size:39
Alignment explanation
Indices: 454933--455060 Score: 120
Period size: 40 Copynumber: 3.2 Consensus size: 39
454923 TTTTCCTAAT
*
454933 TCGCAATGCGAATACGTAAATCGCAACGCGAATT-TGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGAG-ATTCT-G-AAA
* *
454974 TCGCAATGCGATTACGTAAATCGCAATGCGA-ATAC-GTAAA
1 TCGCAATGCGAATACGTAAATCGCAA--CGAGATTCTG-AAA
*
455014 TCGCAATGCGAAT-CTGTAAATCGCAACGAGATTCTGACTA
1 TCGCAATGCGAATAC-GTAAATCGCAACGAGATTCTGA-AA
455054 TCGCAAT
1 TCGCAAT
455061 ACTGAATTTC
Statistics
Matches: 73, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
38 3 0.04
39 5 0.07
40 36 0.49
41 27 0.37
43 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (39 bp):
TCGCAATGCGAATACGTAAATCGCAACGAGATTCTGAAA
Found at i:458395 original size:20 final size:20
Alignment explanation
Indices: 458370--458463 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
458360 GACATTCATT
458370 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
458390 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* *
458410 TGACTATCGCAATGCGGAAT
1 TGACTATCGCAACGCGGAAA
*
458430 TGACTATCGCAACGCAGAAA
1 TGACTATCGCAACGCGGAAA
*
458450 TGACTATTGCAACG
1 TGACTATCGCAACG
458464 AGAGAATCGC
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 62 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.20
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:458557 original size:33 final size:34
Alignment explanation
Indices: 458500--458595 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 34
458490 CGCAACGTCG
458500 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* * *
458534 CGTTGCTATTTTTA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
458567 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
458596 AGTCTGTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 28 0.54
34 24 0.46
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:458716 original size:14 final size:14
Alignment explanation
Indices: 458697--458733 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
458687 CATCAATTAA
458697 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
458711 ACAAATCATCTTTT
1 ACAAATCAACATTT
458725 ACAAATCAA
1 ACAAATCAA
458734 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:460193 original size:42 final size:43
Alignment explanation
Indices: 460086--460196 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 43
460076 TCTAGAATAT
* * * *
460086 TGGGAG-GGACCTCTTCAACAATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGGACCTCTTGAACGATGACAGAGGCCTCTTGAACGA
** *
460128 TGGGAGAGGA-CTCTTGAGGGATGATAGAGGCCTCTTGAACGA
1 TGGGAGAGGACCTCTTGAACGATGACAGAGGCCTCTTGAACGA
460170 TAGGG-GA-GACCTCTTGAACGATGACAG
1 T-GGGAGAGGACCTCTTGAACGATGACAG
460197 GTGAGTCGGG
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
41 2 0.04
42 48 0.86
43 6 0.11
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (43 bp):
TGGGAGAGGACCTCTTGAACGATGACAGAGGCCTCTTGAACGA
Found at i:460723 original size:34 final size:34
Alignment explanation
Indices: 460676--460789 Score: 149
Period size: 34 Copynumber: 3.4 Consensus size: 34
460666 TGAAACTTAA
*
460676 AATCGCAAAGCGAAAATGACTATCGCAACGAGAG
1 AATCGCAATGCGAAAATGACTATCGCAACGAGAG
** * * *
460710 AATCGCAATGCG-AAATGAAAATCGCAACAACAA
1 AATCGCAATGCGAAAATGACTATCGCAACGAGAG
* *
460743 AATCGCAACGCGAAAATGACTATCTCAACGAGAG
1 AATCGCAATGCGAAAATGACTATCGCAACGAGAG
460777 AATCGCAATGCGA
1 AATCGCAATGCGA
460790 TTTTCATTTC
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
33 27 0.42
34 38 0.58
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.13
Consensus pattern (34 bp):
AATCGCAATGCGAAAATGACTATCGCAACGAGAG
Found at i:460842 original size:20 final size:20
Alignment explanation
Indices: 460817--460960 Score: 113
Period size: 20 Copynumber: 7.5 Consensus size: 20
460807 GATTCTTTCG
*
460817 TTGCGATAGTCAAATTCGTA
1 TTGCGATAGTCAAATTCGCA
*
460837 TTGCGATAGTCAAATTCACA
1 TTGCGATAGTCAAATTCGCA
**
460857 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
460877 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCAAATTCGCA
460897 TTGCGAT--TC---TCTCG--
1 TTGCGATAGTCAAAT-TCGCA
** **
460911 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAAATTCGCA
**
460931 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
460951 TTGCGATAGT
1 TTGCGATAGT
460961 AAACTATTCT
Statistics
Matches: 107, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
14 7 0.07
15 1 0.01
16 4 0.04
18 5 0.05
19 1 0.01
20 89 0.83
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:460880 original size:40 final size:40
Alignment explanation
Indices: 460779--460960 Score: 156
Period size: 40 Copynumber: 4.9 Consensus size: 40
460769 AACGAGAGAA
* **
460779 TCGCAATGCGATTTTCA-TTTCGCATTGCGAT--TC--TT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
** * **
460814 TCG--TTGCGATAGTCAAATTCGTATTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
460852 TCACATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
* *
460892 TTGCATTGCGAT--TC--TCTCG--TTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
**
460926 TCGTGTTGCGATAGTCATTTTCGCATTGCGATAGT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
460961 AAACTATTCT
Statistics
Matches: 115, Mismatches: 19, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
33 9 0.08
34 36 0.31
35 3 0.03
36 8 0.07
38 9 0.08
40 50 0.43
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
Found at i:462868 original size:20 final size:20
Alignment explanation
Indices: 462845--462884 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
462835 CTGAAACTTT
462845 AAATCACAACACGAAAATGA
1 AAATCACAACACGAAAATGA
*
462865 AAATCGCAACACGAAAATGA
1 AAATCACAACACGAAAATGA
462885 CTATCGCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.10
Consensus pattern (20 bp):
AAATCACAACACGAAAATGA
Found at i:462890 original size:20 final size:20
Alignment explanation
Indices: 462851--462914 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
462841 CTTTAAATCA
**
462851 CAACACGAAAATGAAAATCG
1 CAACACGAAAATGACTATCG
462871 CAACACGAAAATGACTATCG
1 CAACACGAAAATGACTATCG
* **
462891 CAACGCGAATTTGACTATCG
1 CAACACGAAAATGACTATCG
462911 CAAC
1 CAAC
462915 GCAAGAATCG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.44, C:0.25, G:0.16, T:0.16
Consensus pattern (20 bp):
CAACACGAAAATGACTATCG
Found at i:462983 original size:20 final size:20
Alignment explanation
Indices: 462958--463006 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
462948 GTGATTCTCT
462958 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCAAATTCG
**
462978 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCAAATTCG
*
462998 CGTTGCGAT
1 CATTGCGAT
463007 TCACTCGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
CATTGCGATAGTCAAATTCG
Found at i:463648 original size:21 final size:21
Alignment explanation
Indices: 463624--463669 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
463614 TATTCGCATT
463624 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
463645 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
463666 GCGA
1 GCGA
463670 TAGTGAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:465662 original size:2 final size:2
Alignment explanation
Indices: 465655--465682 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
465645 TCTATTAATT
465655 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
465683 AGATATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:471839 original size:15 final size:12
Alignment explanation
Indices: 471802--471838 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
471792 TATATAACCC
*
471802 TTTTTTTAATAA
1 TTTTTATAATAA
471814 TTTTTATAATAA
1 TTTTTATAATAA
471826 TTTTTATAATAA
1 TTTTTATAATAA
471838 T
1 T
471839 ATAATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTTATAATAA
Found at i:475323 original size:12 final size:12
Alignment explanation
Indices: 475306--475353 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
475296 ATTTTTGTCA
*
475306 TTTTTATTAATT
1 TTTTTATTTATT
475318 TTTTTATTTATT
1 TTTTTATTTATT
* *
475330 GTTTAATTTATT
1 TTTTTATTTATT
*
475342 TTTAT-TTTATT
1 TTTTTATTTATT
475353 T
1 T
475354 CCTATTATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 7 0.23
12 23 0.77
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (12 bp):
TTTTTATTTATT
Found at i:475453 original size:17 final size:16
Alignment explanation
Indices: 475431--475466 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
475421 TTTAAATATA
475431 TTTTTGTTATTATCTTT
1 TTTTTGTTATTAT-TTT
*
475448 TTTTTGTTTTTATTTT
1 TTTTTGTTATTATTTT
475464 TTT
1 TTT
475467 CTTCTTTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.08, C:0.03, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTTGTTATTATTTT
Found at i:475486 original size:23 final size:23
Alignment explanation
Indices: 475433--475489 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
475423 TAAATATATT
* * * *
475433 TTTGTTATTATCTTTTTTTTGTT
1 TTTGTTTTTATCTTCTTTTCGTC
* *
475456 TTTATTTTTTTCTTCTTTTCGTC
1 TTTGTTTTTATCTTCTTTTCGTC
475479 TTTGTTTTTAT
1 TTTGTTTTTAT
475490 TATTATATAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.77
Consensus pattern (23 bp):
TTTGTTTTTATCTTCTTTTCGTC
Found at i:475623 original size:30 final size:30
Alignment explanation
Indices: 475587--475648 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
475577 TTGTTTTAGC
**
475587 TTTTTCAACCTTTTCAAAAT-TTTCAACTTT
1 TTTTTCAAAATTTTC-AAATCTTTCAACTTT
475617 TTTTTCAAAATTTTCAAATCTTTCAACTTT
1 TTTTTCAAAATTTTCAAATCTTTCAACTTT
475647 TT
1 TT
475649 CTTTTTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTTTCAAAATTTTCAAATCTTTCAACTTT
Found at i:476736 original size:21 final size:21
Alignment explanation
Indices: 476685--476736 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
476675 ATACATAATT
*
476685 ATAAATTAGTTAAAATGTAAAA
1 ATAAATTATTTAAAA-GTAAAA
476707 ATAAATTATTTAAAA-TAAAA
1 ATAAATTATTTAAAAGTAAAA
*
476727 TATTAATTAT
1 -ATAAATTAT
476737 ATTATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 5 0.19
21 8 0.30
22 14 0.52
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
ATAAATTATTTAAAAGTAAAA
Found at i:476792 original size:2 final size:2
Alignment explanation
Indices: 476785--476821 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
476775 AATTTTCTTT
476785 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
476822 TTCAATACAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:477945 original size:41 final size:38
Alignment explanation
Indices: 477884--477961 Score: 111
Period size: 41 Copynumber: 2.0 Consensus size: 38
477874 TCTATCATAC
*
477884 ATAAATAAAAAATTATTTAATTAGTTTGTTTGATAGTT
1 ATAAATAAAAAATTAATTAATTAGTTTGTTTGATAGTT
*
477922 ATAAATTAAAAAATAATAATTAATTAGTTTGTTTGTTAGT
1 ATAAA-TAAAAAAT--TAATTAATTAGTTTGTTTGATAGT
477962 CGTTAGTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 5 0.14
39 8 0.23
41 22 0.63
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (38 bp):
ATAAATAAAAAATTAATTAATTAGTTTGTTTGATAGTT
Done.