Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000907.1 Hibiscus syriacus cultivar Beakdansim tig00001799_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: 656280
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:191974 original size:6 final size:6
Alignment explanation
Indices: 191963--192048 Score: 172
Period size: 6 Copynumber: 14.3 Consensus size: 6
191953 GTTCAAAGCT
191963 CAATCC CAATCC CAATCC CAATCC CAATCC CAATCC CAATCC CAATCC
1 CAATCC CAATCC CAATCC CAATCC CAATCC CAATCC CAATCC CAATCC
192011 CAATCC CAATCC CAATCC CAATCC CAATCC CAATCC CA
1 CAATCC CAATCC CAATCC CAATCC CAATCC CAATCC CA
192049 TATATTGAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 80 1.00
ACGTcount: A:0.34, C:0.50, G:0.00, T:0.16
Consensus pattern (6 bp):
CAATCC
Found at i:193520 original size:10 final size:10
Alignment explanation
Indices: 193507--193554 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
193497 TCTTATGTTC
193507 GTTCATTTAT
1 GTTCATTTAT
193517 GTTCATTTAT
1 GTTCATTTAT
*
193527 GGTCATTCATTTAA
1 -G---TTCATTTAT
193541 GTTCATTTAT
1 GTTCATTTAT
193551 GTTC
1 GTTC
193555 GAACAGAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 22 0.69
11 1 0.03
13 1 0.03
14 8 0.25
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.54
Consensus pattern (10 bp):
GTTCATTTAT
Found at i:193526 original size:24 final size:24
Alignment explanation
Indices: 193480--193555 Score: 91
Period size: 24 Copynumber: 3.1 Consensus size: 24
193470 CGTTCGTGAA
193480 CGTTCGATTATATGTTC-TCTTATGTT
1 CGTTC-ATT-TATGTTCAT-TTATGTT
*
193506 CGTTCATTTATGTTCATTTATGGT
1 CGTTCATTTATGTTCATTTATGTT
* *
193530 CATTCATTTAAGTTCATTTATGTT
1 CGTTCATTTATGTTCATTTATGTT
193554 CG
1 CG
193556 AACAGAGGGC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
24 35 0.80
25 4 0.09
26 5 0.11
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.53
Consensus pattern (24 bp):
CGTTCATTTATGTTCATTTATGTT
Found at i:193831 original size:13 final size:13
Alignment explanation
Indices: 193815--193873 Score: 61
Period size: 13 Copynumber: 4.7 Consensus size: 13
193805 GTGTTTGTGT
*
193815 TGTTCGTTTATTG
1 TGTTCGTTTATTA
193828 TGTTC--TT-TTA
1 TGTTCGTTTATTA
*
193838 TGTTCTTTTATTA
1 TGTTCGTTTATTA
*
193851 TGTTCGTTTATTTT
1 TGTTCGTTTA-TTA
193865 TGTTCGTTT
1 TGTTCGTTT
193874 GTGTTCGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 7 0.18
11 2 0.05
12 2 0.05
13 17 0.44
14 11 0.28
ACGTcount: A:0.08, C:0.08, G:0.15, T:0.68
Consensus pattern (13 bp):
TGTTCGTTTATTA
Found at i:193847 original size:23 final size:23
Alignment explanation
Indices: 193815--193898 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 23
193805 GTGTTTGTGT
* *
193815 TGTTCGTTTATTGTGTTCTTTTA
1 TGTTCGTTTATTATGTTCGTTTA
*
193838 TGTTCTTTTATTATGTTCGTTTA
1 TGTTCGTTTATTATGTTCGTTTA
* * *
193861 TTTTTGTTCGT-TTGTGTTCGTTTA
1 TGTTCGTT--TATTATGTTCGTTTA
*
193885 CGTTCGTTTATTAT
1 TGTTCGTTTATTAT
193899 TTAAATGAAC
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
22 1 0.02
23 28 0.60
24 17 0.36
25 1 0.02
ACGTcount: A:0.10, C:0.10, G:0.17, T:0.64
Consensus pattern (23 bp):
TGTTCGTTTATTATGTTCGTTTA
Found at i:194509 original size:17 final size:17
Alignment explanation
Indices: 194482--194525 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
194472 TAGACTCAAT
*
194482 TTATCATTTTCGTTTATA
1 TTAT-ATTTTCGCTTATA
194500 TTATATTTTCGCTTATA
1 TTATATTTTCGCTTATA
194517 TTATATTTT
1 TTATATTTT
194526 TGCATTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.23, C:0.09, G:0.05, T:0.64
Consensus pattern (17 bp):
TTATATTTTCGCTTATA
Found at i:194817 original size:6 final size:6
Alignment explanation
Indices: 194808--194853 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
194798 AGAAAATATA
* * *
194808 AATTGC AATTGC AATTGC AATTGT AATTGT AATTGT AATTGT AATT
1 AATTGT AATTGT AATTGT AATTGT AATTGT AATTGT AATTGT AATT
194854 CCTTTGTCAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (6 bp):
AATTGT
Found at i:196111 original size:20 final size:20
Alignment explanation
Indices: 196073--196134 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
196063 GGCGTGGTAC
196073 TAGG-AATTTTTTAACATTTT
1 TAGGAAATTTTTTAA-ATTTT
*
196093 TAGTAAATTTTTTAAATTTT
1 TAGGAAATTTTTTAAATTTT
* * *
196113 TAGGGATTTTTTTAATTTTT
1 TAGGAAATTTTTTAAATTTT
196133 TA
1 TA
196135 ATTTTTATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 26 0.72
21 10 0.28
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (20 bp):
TAGGAAATTTTTTAAATTTT
Found at i:196114 original size:8 final size:9
Alignment explanation
Indices: 196077--196140 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 9
196067 TGGTACTAGG
196077 AATTTTTTA
1 AATTTTTTA
196086 ACATTTTTAGTA
1 A-ATTTTT--TA
196098 AATTTTTTA
1 AATTTTTTA
196107 AA-TTTTTA
1 AATTTTTTA
* *
196115 GGGATTTTTTT
1 --AATTTTTTA
196126 AATTTTTT-
1 AATTTTTTA
196134 AATTTTT
1 AATTTTT
196141 ATATTATTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
8 13 0.28
9 12 0.26
10 7 0.15
11 11 0.24
12 3 0.07
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (9 bp):
AATTTTTTA
Found at i:197478 original size:23 final size:23
Alignment explanation
Indices: 197452--197563 Score: 95
Period size: 24 Copynumber: 4.8 Consensus size: 23
197442 AGCTCATATA
197452 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
197475 AATT-TATCCCGAAGTTCCACGTAG
1 AATTGCA--CCGAAGTGCCACGTAG
*
197499 AATTTGTC-CCGAAG-GACCGCGTAG
1 AA-TTG-CACCGAAGTG-CCACGTAG
* *
197523 AAATGCACCGAAGTGTCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
197546 AATTTCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
197564 TATAAGATTG
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
22 2 0.03
23 32 0.46
24 33 0.48
25 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:198625 original size:19 final size:20
Alignment explanation
Indices: 198589--198626 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
198579 TTTCATTTAG
*
198589 GGGGGAATCGATACCCCCCA
1 GGGGGAATCAATACCCCCCA
*
198609 GGGGGAATTAATACCCCC
1 GGGGGAATCAATACCCCC
198627 TGAACATACT
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:0.26, C:0.32, G:0.29, T:0.13
Consensus pattern (20 bp):
GGGGGAATCAATACCCCCCA
Found at i:206259 original size:3 final size:3
Alignment explanation
Indices: 206205--206241 Score: 56
Period size: 3 Copynumber: 11.7 Consensus size: 3
206195 TTCATTTGAA
206205 TAT TATT TAT ATAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TA-T TAT -TAT TAT TAT TAT TAT TAT TAT TAT TA
206242 AATAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 26 0.81
4 6 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:207658 original size:28 final size:26
Alignment explanation
Indices: 207609--207668 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
207599 TTTTATATGT
* * *
207609 TTATTATCAATATATTTAAAATATTA
1 TTATTATAAATATATTAAAAATAATA
207635 TTATTATAAATATATATAAGAAATAATA
1 TTATTATAAATATAT-TAA-AAATAATA
207663 TATATT
1 T-TATT
207669 TTATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 14 0.50
27 2 0.07
28 8 0.29
29 4 0.14
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
TTATTATAAATATATTAAAAATAATA
Found at i:207910 original size:23 final size:23
Alignment explanation
Indices: 207883--207937 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
207873 TCTTTTCTGA
*
207883 TATTTCTAAATAAATAAATATAT
1 TATTTATAAATAAATAAATATAT
** *
207906 TATTTATATTTAAATTAATATAT
1 TATTTATAAATAAATAAATATAT
*
207929 T-TTCATAAA
1 TATTTATAAA
207938 ATTATAAATT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATAT
Found at i:208477 original size:20 final size:21
Alignment explanation
Indices: 208443--208492 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
208433 TATATATATT
208443 TATTATTTTCATAAT-ATTTA
1 TATTATTTTCATAATGATTTA
*
208463 TATTATTTT-ATTAATGTTTTA
1 TATTATTTTCA-TAATGATTTA
*
208484 TTTTATTTT
1 TATTATTTT
208493 TCAAGTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 13 0.50
21 12 0.46
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (21 bp):
TATTATTTTCATAATGATTTA
Found at i:219145 original size:12 final size:12
Alignment explanation
Indices: 219119--219154 Score: 63
Period size: 12 Copynumber: 2.9 Consensus size: 12
219109 TATTATGCTT
219119 GAAGAAAACAAAA
1 GAAGAAAA-AAAA
219132 GAAGAAAAAAAA
1 GAAGAAAAAAAA
219144 GAAGAAAAAAA
1 GAAGAAAAAAA
219155 TGTTGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 15 0.65
13 8 0.35
ACGTcount: A:0.81, C:0.03, G:0.17, T:0.00
Consensus pattern (12 bp):
GAAGAAAAAAAA
Found at i:219550 original size:18 final size:18
Alignment explanation
Indices: 219496--219572 Score: 77
Period size: 18 Copynumber: 4.1 Consensus size: 18
219486 TATTTATTAA
219496 TAAATTCTAAGTTTATTTTCT
1 TAAATTC-AA-TTTATTTT-T
219517 CTAAATTCAA-TT-TTTTT
1 -TAAATTCAATTTATTTTT
*
219534 TAGATTCAATTTATTTTT
1 TAAATTCAATTTATTTTT
*
219552 GAAATTCAATTTATTCTTT
1 TAAATTCAATTTATT-TTT
219571 TA
1 TA
219573 TTTTGTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
16 8 0.17
17 3 0.06
18 22 0.46
19 6 0.12
21 2 0.04
22 7 0.15
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (18 bp):
TAAATTCAATTTATTTTT
Found at i:221140 original size:124 final size:124
Alignment explanation
Indices: 220915--221459 Score: 864
Period size: 124 Copynumber: 4.4 Consensus size: 124
220905 CACTCGATGG
* * * *
220915 ATCAAATTTTCCAGAGAAAGTTCATAATGAGAACAACTTATCTGAAGAA-GAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * * * * *
220979 AATGAGAAGAACTTATTCAACCTTTTGCATGATTCTATCACAAAAGAAGATAAATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAAAAGGAGATAGATCAGC
221038 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
221103 AATGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCATAAAA-GAGATAGATCATC
66 AATGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAAAAGGAGATAGATCAGC
*
221161 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTAAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
221226 AATGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAAAAGGAGATAGATCAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAAAAGGAGATAGATCAGC
221285 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
221350 AATGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAGAAGGAGATAGACCAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAAAAGGAGATAGATCAGC
* ** * *
221409 ATCAA-TATTTTCAGA-AGTGTTCATAATGAGAAAAACTCATCTGAAGAAGGA
1 ATCAACT-TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
221460 GCAAACTTAT
Statistics
Matches: 396, Mismatches: 23, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
123 196 0.49
124 200 0.51
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.26
Consensus pattern (124 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAAAAGGAGATAGATCAGC
Found at i:221290 original size:247 final size:245
Alignment explanation
Indices: 220823--221459 Score: 889
Period size: 247 Copynumber: 2.6 Consensus size: 245
220813 CAGAAGTGTA
* * **
220823 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAAC
1 CATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC-AAC
* * * *** *
220888 CTTTTGTTTGA--AT-TCAT-CACTCGAT-G-GATCA--AATTTTCCAGAGAAAGTTCATAATGA
65 CTTTTGTATGACTCTATCATAAAAGAGATAGACATCATCAATTTTCCAGAGAAAGTTCATAATGA
* * *
220945 GAACAACTTATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCAT
130 GAAAAACTCATCTGAAGAAGGAAGAAGAAGTTAATAATGAGAAGAACTTATTCAACCTTTTGCAT
*
221009 GATTCTATCACAAAAGAAGATAAATCAACATCAACTTTTCCAGAGAAAGTT
195 GACTCTATCACAAAAGAAGATAAATCAACATCAACTTTTCCAGAGAAAGTT
221060 CATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC
1 CATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC
*
221125 TTTTGTATGACTCTATCATAAAAGAGATAGATCATCATCAACTTTTCCAGAGAAAGTTCATAATA
66 TTTTGTATGACTCTATCATAAAAGAGATAGA-CATCATCAA-TTTTCCAGAGAAAGTTCATAATG
* * * *
221190 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTAATAATGAGAAGAGCTTGTTCAACCTTTTGTA
129 AGAAAAACTCATCTGAAGAAGGAAGAAGAAGTTAATAATGAGAAGAACTTATTCAACCTTTTGCA
* * *
221255 TGACTCTATCACAAAAGGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTT
194 TGACTCTATCACAAAAGAAGATAAATCAACATCAACTTTTCCAGAGAAAGTT
221307 CATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC
1 CATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC
* * * * **
221372 TTTTGTATGACTCTATCACAGAAGGAGATAGACCAGCATCAATATTTTCAGA-AGTGTTCATAAT
66 TTTTGTATGACTCTATCATA-AAAGAGATAGA-CATCATCAAT-TTTCCAGAGAAAGTTCATAAT
221436 GAGAAAAACTCATCTGAAGAAGGA
128 GAGAAAAACTCATCTGAAGAAGGA
221460 GCAAACTTAT
Statistics
Matches: 356, Mismatches: 31, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
236 13 0.04
237 57 0.16
238 1 0.00
239 4 0.01
240 4 0.01
241 1 0.00
243 4 0.01
245 2 0.01
246 40 0.11
247 205 0.58
248 25 0.07
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.26
Consensus pattern (245 bp):
CATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC
TTTTGTATGACTCTATCATAAAAGAGATAGACATCATCAATTTTCCAGAGAAAGTTCATAATGAG
AAAAACTCATCTGAAGAAGGAAGAAGAAGTTAATAATGAGAAGAACTTATTCAACCTTTTGCATG
ACTCTATCACAAAAGAAGATAAATCAACATCAACTTTTCCAGAGAAAGTT
Found at i:221740 original size:3 final size:3
Alignment explanation
Indices: 221696--221729 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
221686 TTCATTTGAA
221696 TAT TATT TAT ATAT TAT TAT TAT TAT TAT TAT TA
1 TAT TA-T TAT -TAT TAT TAT TAT TAT TAT TAT TA
221730 AATAATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:223099 original size:25 final size:25
Alignment explanation
Indices: 223029--223099 Score: 62
Period size: 25 Copynumber: 2.9 Consensus size: 25
223019 AGTCATTAAC
*
223029 TTTAAATTAT-TA-GTTTATTA-TT
1 TTTAATTTATATATGTTTATTATTT
*
223051 TTTAATTTCATTTAT-TTTAGTTATTGT
1 TTTAATTT-ATATATGTTTA-TTATT-T
223078 TTTAATTT-TATATGTTTATTAT
1 TTTAATTTATATATGTTTATTAT
223100 CAATATATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
22 7 0.17
23 2 0.05
24 6 0.15
25 11 0.28
26 5 0.12
27 9 0.22
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (25 bp):
TTTAATTTATATATGTTTATTATTT
Found at i:223396 original size:23 final size:23
Alignment explanation
Indices: 223369--223423 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
223359 TCTTTTCTGA
*
223369 TATTTCTAAATAAATAAATATAT
1 TATTTATAAATAAATAAATATAT
** *
223392 TATTTATATTTAAATTAATATAT
1 TATTTATAAATAAATAAATATAT
*
223415 T-TTCATAAA
1 TATTTATAAA
223424 ATTATAAATT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATAT
Found at i:224954 original size:16 final size:17
Alignment explanation
Indices: 224917--224954 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
224907 GGATAAAACC
*
224917 TTAAACAAATTATTTGT
1 TTAAACAAATTATTTAT
224934 TTAAACAAATTA-TTAT
1 TTAAACAAATTATTTAT
224950 TTAAA
1 TTAAA
224955 TTAATTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAAACAAATTATTTAT
Found at i:225157 original size:29 final size:28
Alignment explanation
Indices: 225123--225185 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 28
225113 AAAAAACCGG
225123 TTAATTCGGTTCGGTTAATAATTTTCAAA
1 TTAATTCGGTTCGGTTAATAA-TTTCAAA
225152 TTAATTCGGTTCGGTTAATAATTTCAAA
1 TTAATTCGGTTCGGTTAATAATTTCAAA
*
225180 TAAATT
1 TTAATT
225186 TTAGTTCGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 12 0.36
29 21 0.64
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (28 bp):
TTAATTCGGTTCGGTTAATAATTTCAAA
Found at i:225296 original size:100 final size:104
Alignment explanation
Indices: 225152--225392 Score: 330
Period size: 100 Copynumber: 2.3 Consensus size: 104
225142 AATTTTCAAA
225152 TTAATTCGGTTCGGTTAATAA-TTTCAAATAAATTTTAGTTCGATTAACCGAACCCAATTAACCG
1 TTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTAGTTCGATTAACCGAACCCAATTAACCG
* *
225216 AATTTTGGCTTCGATTAA-T-A-ATTAA-AAAAATTTAG
66 AATTTTGGCTTCGATTAATTGATAATAATAAAAAATTAG
* * * *
225251 TTAATTCAGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAGCCGAATTAACCG
1 TTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTAGTTCGATTAACCGAACCCAATTAACCG
** *
225316 AATTTTTTCTTCGATTAATTTGATTAATAATTAAAAAATTGG
66 AATTTTGGCTTCGATTAA-TTGA-TAATAA-TAAAAAATTAG
*
225358 TTAATTCGGTTCGGTTAATAATTTTCAAATTAATT
1 TTAATTCGGTTCGGTTAATAATTTTCAAATAAATT
225393 CAGTTTGGTT
Statistics
Matches: 123, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
99 20 0.16
100 56 0.46
102 1 0.01
103 1 0.01
105 4 0.03
107 41 0.33
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (104 bp):
TTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTAGTTCGATTAACCGAACCCAATTAACCG
AATTTTGGCTTCGATTAATTGATAATAATAAAAAATTAG
Found at i:225391 original size:29 final size:29
Alignment explanation
Indices: 225358--225413 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
225348 AAAAAATTGG
*
225358 TTAATTCGGTTCGGTTAATAATTTTCAAA
1 TTAATTCAGTTCGGTTAATAATTTTCAAA
*
225387 TTAATTCAGTTTGGTTAATAATTTTCA
1 TTAATTCAGTTCGGTTAATAATTTTCA
225414 GATAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.48
Consensus pattern (29 bp):
TTAATTCAGTTCGGTTAATAATTTTCAAA
Found at i:225421 original size:29 final size:29
Alignment explanation
Indices: 225360--225421 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
225350 AAAATTGGTT
* *
225360 AATTCGGTTCGGTTAATAATTTTCAAATT
1 AATTCAGTTCGGTTAATAATTTTCAAATA
* *
225389 AATTCAGTTTGGTTAATAATTTTCAGATA
1 AATTCAGTTCGGTTAATAATTTTCAAATA
225418 AATT
1 AATT
225422 TTGGTTCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (29 bp):
AATTCAGTTCGGTTAATAATTTTCAAATA
Found at i:225928 original size:30 final size:30
Alignment explanation
Indices: 225892--225954 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
225882 AGAATAAGTA
225892 AATATTAAAGA-CAAAAAGTATAATTATGCC
1 AATATTAAAGACCAAAAA-TATAATTATGCC
* * *
225922 AATATTAAGGACCAAATATATAATTATGTC
1 AATATTAAAGACCAAAAATATAATTATGCC
225952 AAT
1 AAT
225955 TTATTAATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30
Consensus pattern (30 bp):
AATATTAAAGACCAAAAATATAATTATGCC
Found at i:226224 original size:28 final size:26
Alignment explanation
Indices: 226171--226232 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 26
226161 AAACCAAATG
*
226171 TTTATTCTTTATGCTAGTTTTGTTCA
1 TTTATTCTTTATGCTAGTTTTCTTCA
* *
226197 TTTATTCTATTCATTCTGGTTTTCTTCA
1 TTTATTCT-TT-ATGCTAGTTTTCTTCA
*
226225 CTTATTCT
1 TTTATTCT
226233 GGAGAAAAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 8 0.27
27 2 0.07
28 20 0.67
ACGTcount: A:0.15, C:0.16, G:0.08, T:0.61
Consensus pattern (26 bp):
TTTATTCTTTATGCTAGTTTTCTTCA
Found at i:227619 original size:23 final size:23
Alignment explanation
Indices: 227593--227637 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
227583 AACATATTAG
*
227593 GTAGCGCTTATATAATATAATAA
1 GTAGCGCTTATATAATAAAATAA
227616 GTAGCGCTTATATAATAAAATA
1 GTAGCGCTTATATAATAAAATA
227638 GACATTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.33
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAA
Found at i:227701 original size:87 final size:87
Alignment explanation
Indices: 227553--227715 Score: 263
Period size: 87 Copynumber: 1.9 Consensus size: 87
227543 AATGTTATAT
* * *
227553 CATTTAACCGGTAATATTATTAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAAGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATATAATAAGT
227618 AGCGCTTATATAATAAAATAGA
66 AGCGCTTATATAATAAAATAGA
* * * *
227640 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACTCTTATATATTGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATATAATAAGT
227705 AGCGCTTATAT
66 AGCGCTTATAT
227716 TGACCTATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATATAATAAGT
AGCGCTTATATAATAAAATAGA
Found at i:228172 original size:200 final size:196
Alignment explanation
Indices: 227733--228437 Score: 757
Period size: 200 Copynumber: 3.5 Consensus size: 196
227723 TTTTCGAAGT
* * * * * *
227733 AAACCGGTATATTTATACCGGTAACATTGCAAATTTACCTATTACAATATTATTATCAGTTACGA
1 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
** ** *
227798 TGTTTTTTAGATCGATACAATTT-TAAATGTATCGACACTTTATGCTTGCACCTGGTTGGGCATT
66 TGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCT-GTT-----TT
** * * * * *
227862 CATATTTCATTCTGAAAAAAATTATCGACACAAACTAAC--GTGTCGATATATTAT-TTAGACCT
125 GGTA-TTCATTCTGGACAAAAGTATCGACACAAATTAACAAGTGTCGATA-CTTATGTT-GACCT
*
227924 TTATCTCATA
187 TTTTCTCATA
* *
227934 AAACCGGTATATTTATACCGGTTACATTG-AACATTTACCTATTACATTATACTTATGGGTTTCG
1 AAACCGGTATATTTATACCGGTTACATTGTAA-ATTTACCTATTACATTATAATTATCGGTTTCG
*
227998 ATGTTTTCGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCCT-TTTTGGTA
65 ATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCA-CCTGTTTTGGTA
228062 TTCATTCTGGACCAAAAGTATCGACACAAATTTAACAAGTGTCGATACTTGATGTTGACCTATTT
129 TTCATTCTGGA-CAAAAGTATCGACACAAA-TTAACAAGTGTCGATACTT-ATGTTGACCT-TTT
*
228127 TATCATA
190 TCTCATA
* * * *
228134 AAACTGATATATTTATATCGGTTACATTGTAAATTTACCTAATACATTATAATTATCGGTTTCGA
1 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* *
228199 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCG-TGCACCTCG-TTTGTGC
66 TGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATG-GTTGCACCT-GTTTTG-GT
* * *
228262 ATTCATCCTGGACAATAAGTATCGACACAAATTACACAAGTGTCGATACATTATGTTAACATGTT
128 ATTCATTCTGGACAA-AAGTATCGACACAAATTA-ACAAGTGTCGATAC-TTATGTTGACCT-TT
*
228327 TTCTAAT-
189 TTCTCATA
* * * * * *
228334 TAACCGGTATATTTATACCGGTTACATTGTTAACTTACCTATTACATTATAATTATTGATTTTGA
1 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
*
228399 TGTTTTTTGGG-TCGATAC-TTGTATAAAATGTATCGACAC
66 TG-TTTTTGGGATCGATACTTTTTAT-AAATGTATCGACAC
228438 ATATTTAGGT
Statistics
Matches: 435, Mismatches: 49, Indels: 41
0.83 0.09 0.08
Matches are distributed among these distances:
195 10 0.02
196 20 0.05
197 4 0.01
198 2 0.00
199 23 0.05
200 203 0.47
201 142 0.33
202 28 0.06
203 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (196 bp):
AAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
TGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCTGTTTTGGTATT
CATTCTGGACAAAAGTATCGACACAAATTAACAAGTGTCGATACTTATGTTGACCTTTTTCTCAT
A
Found at i:231416 original size:200 final size:199
Alignment explanation
Indices: 230921--231479 Score: 825
Period size: 200 Copynumber: 2.8 Consensus size: 199
230911 TTTATTTACA
* * **
230921 AAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTGACATATTTATACCGGTTATATTA
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTATATTA
* * *
230986 CAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTCGGTATCAACACTTTTAATAAAT
66 CAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTTTAATAAAT
* *
231051 GTATCGACACTTTGTGCGTTCATCCTTTTTGGCATCAATTCTGAAAAAAAGTATCGACACAAATT
131 GTATCGACACTTTATGCGTTCACCCTTTTTGGCATCAATTCTGAAAAAAAGTATCGACACAAATT
231116 TAAC
196 TAAC
* * * *
231120 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAATCGGTATATTTATACCAGTTACATTG
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTATATTA
* * * *
231185 TAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTT-TTAAAA
66 CAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTTTAAT-AAA
* * * * *
231249 TGTATTGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGACATAAATTATCGACAC-AA
130 TGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCAATTCT-GAAAAAAAGTATCGACACAAA
*
231313 TATTAAG
194 T-TTAAC
* * *
231320 AAGTGTCGATAAATATTATAGACCTATTCTCTCATAAAACCGGTATATGTATACCGGTTATATTA
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTATATTA
231385 CAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTTTAATAAAT
66 CAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTTTAATAAAT
*
231450 GTATCGACACTTTATGCGTGCAACCCTTTT
131 GTATCGACACTTTATGCGTTC-ACCCTTTT
231480 GGATCGACAC
Statistics
Matches: 319, Mismatches: 36, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
198 1 0.00
199 154 0.48
200 155 0.49
201 9 0.03
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (199 bp):
AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTATATTA
CAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTTTAATAAAT
GTATCGACACTTTATGCGTTCACCCTTTTTGGCATCAATTCTGAAAAAAAGTATCGACACAAATT
TAAC
Found at i:231584 original size:251 final size:251
Alignment explanation
Indices: 231224--231715 Score: 661
Period size: 251 Copynumber: 2.0 Consensus size: 251
231214 GTTTCGATGT
* * * **
231224 TTTTGGGATCGACACTTTTTTAAAATGTATTGACACTTTATGCGTTCACCCTTTTTGGCATCCAT
1 TTTTGGGATCGACACTCTATGAAAATGTATCAACACTTTATGCGTTCACCCTTTTTGGCATCCAT
* * * *
231289 TCTGGACATAAATTATCGACACAATATTAAGAAGTGTCGATAAATATTATAGACCTATTCTCTCA
66 TCTGGACATAAAGTATCGACACAAAACTAAGAAGTGTCGATAAATATTATAGACATATT-TCTCA
* * *
231354 TAAAACCGGTATATGTATACCGGTTATATT-ACAAAATTACCTATTACATTATAATTATGGGTTT
130 TAAAACCGATATATGTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATTATGGATTT
** *
231418 TGATG-TTTTTGGGATCGACACTTTTAATAAATGTATCGACACTTTATGCGTGCAACCC
194 CAATGTTTTTTGGG-TCGACACTTTTAATAAATGGATCGACACTTTATGCGTGCAACCC
*
231476 TTTT-GGATCGACACTCTATGAAAATGTATCAACACTTTGTAG-GTTCACCCTTTTTGGCATCCA
1 TTTTGGGATCGACACTCTATGAAAATGTATCAACACTTTAT-GCGTTCACCCTTTTTGGCATCCA
* * * *
231539 TTCTGGACA-AAACGTATCGACACAAAACTAATAAGTGTCGATAAATGTTGTAGACATATTTTTC
65 TTCTGGACATAAA-GTATCGACACAAAACTAAGAAGTGTCGATAAATATTATAGACATATTTCTC
* * *
231603 ATAAAATCGATATATTTATACCGGTTACATTGAAAAATTACTTATTACATTATAATTATGGATTT
129 ATAAAACCGATATATGTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGATTT
** * *
231668 CAATGTTTTTTGGGTCGTTACTTTTTATATATGGATCGACACTTTATG
194 CAATGTTTTTTGGGTCGACACTTTTAATAAATGGATCGACACTTTATG
231716 GGAAACTTTA
Statistics
Matches: 209, Mismatches: 27, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
250 95 0.45
251 109 0.52
252 5 0.02
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (251 bp):
TTTTGGGATCGACACTCTATGAAAATGTATCAACACTTTATGCGTTCACCCTTTTTGGCATCCAT
TCTGGACATAAAGTATCGACACAAAACTAAGAAGTGTCGATAAATATTATAGACATATTTCTCAT
AAAACCGATATATGTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGATTTCA
ATGTTTTTTGGGTCGACACTTTTAATAAATGGATCGACACTTTATGCGTGCAACCC
Found at i:232996 original size:6 final size:6
Alignment explanation
Indices: 232985--233030 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
232975 GTTTGGATCA
* * *
232985 TCATCG TCATCG TCATCG TCATCT TCATCG TCATCT TCATCT TCAT
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCAT
233031 TAACCGTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.17, C:0.33, G:0.09, T:0.41
Consensus pattern (6 bp):
TCATCG
Found at i:233002 original size:12 final size:12
Alignment explanation
Indices: 232985--233030 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
232975 GTTTGGATCA
*
232985 TCATCGTCATCG
1 TCATCGTCATCT
232997 TCATCGTCATCT
1 TCATCGTCATCT
233009 TCATCGTCATCT
1 TCATCGTCATCT
*
233021 TCATCTTCAT
1 TCATCGTCAT
233031 TAACCGTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.17, C:0.33, G:0.09, T:0.41
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:233012 original size:18 final size:18
Alignment explanation
Indices: 232985--233030 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
232975 GTTTGGATCA
*
232985 TCATCGTCATCGTCATCG
1 TCATCTTCATCGTCATCG
*
233003 TCATCTTCATCGTCATCT
1 TCATCTTCATCGTCATCG
233021 TCATCTTCAT
1 TCATCTTCAT
233031 TAACCGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.17, C:0.33, G:0.09, T:0.41
Consensus pattern (18 bp):
TCATCTTCATCGTCATCG
Found at i:234844 original size:201 final size:201
Alignment explanation
Indices: 234499--235039 Score: 920
Period size: 201 Copynumber: 2.7 Consensus size: 201
234489 TATTTAAATT
* * *
234499 AGTATCGACATAAAATTAAAAATGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCATAAAACCGGT
*
234564 ATATTTATACCGGTTACATTGAAAATTTACTTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
*
234629 GGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGA
131 GGATCGATACTTTTTATAAATATATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGA
234694 ACCAAA
196 ACCAAA
* *
234700 AGTATCGACACAAAATCAAAAAAGTGTTGATACATGTTGTAGACATATTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCATAAAACCGGT
234765 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
*
234830 GGATCGATACTTTTTATAAATATATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGG
131 GGATCGATACTTTTTATAAATATATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGA
234895 ACCAAA
196 ACCAAA
* * ** *
234901 AGTATCGATACAAAATTAAAAAAGTGTCGATACATATTGTAGAGTTGTTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCATAAAACCGGT
* * * * *
234966 ATATTTATACCGATTACATTGAAAATTTACCTATTACATTATACTTATGGATACAAATATTTATG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
235031 GGATCGATA
131 GGATCGATA
235040 AATTTTACCT
Statistics
Matches: 320, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
201 320 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (201 bp):
AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCATAAAACCGGT
ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
GGATCGATACTTTTTATAAATATATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGA
ACCAAA
Found at i:235391 original size:28 final size:28
Alignment explanation
Indices: 235346--235401 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
235336 TACATTTACA
*
235346 TCATTGCATCCTTTTGTTATTCTTGTGTC
1 TCATTGCATCCTTTTGTTA-TCTTCTGTC
*
235375 TCATTGCA-GCTTTTGTTATCTTCTGTC
1 TCATTGCATCCTTTTGTTATCTTCTGTC
235402 GTCGTTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.32
28 9 0.36
29 8 0.32
ACGTcount: A:0.11, C:0.21, G:0.14, T:0.54
Consensus pattern (28 bp):
TCATTGCATCCTTTTGTTATCTTCTGTC
Found at i:235917 original size:4 final size:4
Alignment explanation
Indices: 235908--235952 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
235898 AATGTCATTT
235908 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
235953 CAATCTCTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:237184 original size:33 final size:33
Alignment explanation
Indices: 237147--237212 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
237137 CATCTTAAGA
237147 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTTAACACCTCAACTTCTTTCACCACT
* **
237180 TCACCCTTTAACACCTTTACTTCTTTCACCACT
1 TCACCCCTTAACACCTCAACTTCTTTCACCACT
237213 CTATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (33 bp):
TCACCCCTTAACACCTCAACTTCTTTCACCACT
Found at i:237233 original size:21 final size:21
Alignment explanation
Indices: 237208--237254 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
237198 ACTTCTTTCA
237208 CCACTCTATCTATTTTTTCTT
1 CCACTCTATCTATTTTTTCTT
237229 CCACTCTATCTATTTTTTCTT
1 CCACTCTATCTATTTTTTCTT
237250 CCACT
1 CCACT
237255 TCCCCCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.32, G:0.00, T:0.53
Consensus pattern (21 bp):
CCACTCTATCTATTTTTTCTT
Found at i:237292 original size:21 final size:21
Alignment explanation
Indices: 237267--237352 Score: 118
Period size: 21 Copynumber: 4.1 Consensus size: 21
237257 CCCCTTATGC
* *
237267 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* **
237288 CTCTCATGTTTCTCTTTAACT
1 CTCTCAAGTTTCTCTTCGACT
*
237309 CTCTCAAGTTTCTCTTTGACT
1 CTCTCAAGTTTCTCTTCGACT
237330 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
237351 CT
1 CT
237353 TGATTGTCTT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.15, C:0.30, G:0.09, T:0.45
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:237455 original size:15 final size:15
Alignment explanation
Indices: 237435--237467 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
237425 ACTCTATTTT
*
237435 CCCTCATCGTCATCC
1 CCCTCACCGTCATCC
237450 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
237465 CCC
1 CCC
237468 AATACAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.61, G:0.06, T:0.21
Consensus pattern (15 bp):
CCCTCACCGTCATCC
Found at i:239641 original size:20 final size:20
Alignment explanation
Indices: 239612--239666 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
239602 GGTAGCGTTT
239612 TACCGGTTTTATCATTTTGA
1 TACCGGTTTTATCATTTTGA
*
239632 TACCGATTTTATCATTTTGA
1 TACCGGTTTTATCATTTTGA
239652 TACCGGTTTTATCAT
1 TACCGGTTTTATCAT
239667 ACTTTTACCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (20 bp):
TACCGGTTTTATCATTTTGA
Found at i:241345 original size:29 final size:29
Alignment explanation
Indices: 241290--241345 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
241280 CCGTTGACCG
* * *
241290 GGTGACATTTTAGTAATTATTTTGAAACT
1 GGTGACATTTGAGTAATTAATTCGAAACT
241319 GGTGACATATTGAG-AATTAATTCGAAA
1 GGTGACAT-TTGAGTAATTAATTCGAAA
241346 AGGGTGCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (29 bp):
GGTGACATTTGAGTAATTAATTCGAAACT
Found at i:241456 original size:29 final size:30
Alignment explanation
Indices: 241418--241475 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
241408 TGTAGTAAAT
*
241418 ATTTTGAAAATCATGCTATATTGGTAATTA
1 ATTTTGAAAATCATGCTATATTCGTAATTA
* *
241448 ATTTT-AAAATGATGCTATTTTCGTAATT
1 ATTTTGAAAATCATGCTATATTCGTAATT
241476 TTGAAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (30 bp):
ATTTTGAAAATCATGCTATATTCGTAATTA
Found at i:241487 original size:110 final size:110
Alignment explanation
Indices: 241292--241490 Score: 251
Period size: 110 Copynumber: 1.8 Consensus size: 110
241282 GTTGACCGGG
* * * ** *
241292 TGACATTTTAGTAATTATTTTGAAACTGGTGACATATTGAGAATTAATTCGAAAAGGGTGCTATT
1 TGACATTGTAGTAAATATTTTGAAAATCATGACATATTGAGAATTAATTCGAAAAGGATGCTATT
* *
241357 TTTGTAATTTTTTAAAATATATATTTTCTTTAAATTTTAAAAAAA
66 TTCGTAATTTTTGAAAATATATATTTTCTTTAAATTTTAAAAAAA
** *
241402 TGACATTGTAGTAAATATTTTGAAAATCATG-CTATATTG-GTAATTAATTTTAAAATGATGCTA
1 TGACATTGTAGTAAATATTTTGAAAATCATGAC-ATATTGAG-AATTAATTCGAAAAGGATGCTA
241465 TTTTCGTAA-TTTTGAAATATATATAT
64 TTTTCGTAATTTTTGAAA-ATATATAT
241491 ATATATTAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
109 9 0.12
110 66 0.88
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.45
Consensus pattern (110 bp):
TGACATTGTAGTAAATATTTTGAAAATCATGACATATTGAGAATTAATTCGAAAAGGATGCTATT
TTCGTAATTTTTGAAAATATATATTTTCTTTAAATTTTAAAAAAA
Found at i:247609 original size:27 final size:27
Alignment explanation
Indices: 247577--247642 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
247567 GTTATTTTGT
* *
247577 AATTTTTT-AAAAATGATATTTCCGTA
1 AATTTTTTAAAAAATGACATTTCAGTA
*
247603 AATTTTTTAAAAAATGACATTTTAGTA
1 AATTTTTTAAAAAATGACATTTCAGTA
* *
247630 AATATTTTGAAAA
1 AATTTTTTAAAAA
247643 TTATGCTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.24
27 26 0.76
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (27 bp):
AATTTTTTAAAAAATGACATTTCAGTA
Found at i:247701 original size:2 final size:2
Alignment explanation
Indices: 247694--247723 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
247684 TGTAATTTTG
247694 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
247724 TTCGTAAAAT
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):
AT
Found at i:253307 original size:2 final size:2
Alignment explanation
Indices: 253297--253517 Score: 60
Period size: 2 Copynumber: 114.0 Consensus size: 2
253287 AATTGAAAAA
*
253297 AT AT A- AT AT AT AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
253337 AA AT -T AT AT AT AA ACT AT AT TT AT AT -T AT AA ACT AT AT A- AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * * *
253378 -T AT -T AT A- AG CT AT AT AT AT AA AT -T AT GT TT AT AT GA- ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T
* * * * * *
253417 AT AT AT AT AA ACT AT AT AC GT A- AA AT AT AT AT GT AT AA ACT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * * * *
253460 AA AA AGT AT AT AGT TT AT AA AT -T AT A- AT TT AT AT -T A- AT AT
1 AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
253500 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
253518 TATTCAAAGT
Statistics
Matches: 157, Mismatches: 37, Indels: 50
0.64 0.15 0.20
Matches are distributed among these distances:
1 16 0.10
2 133 0.85
3 8 0.05
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:253324 original size:13 final size:13
Alignment explanation
Indices: 253297--253517 Score: 80
Period size: 13 Copynumber: 17.2 Consensus size: 13
253287 AATTGAAAAA
253297 ATATAATATATAT
1 ATATAATATATAT
253310 ATAT-ATATATA-
1 ATATAATATATAT
253321 ATATAAGT-T-TAT
1 ATATAA-TATATAT
253333 ATATAA-AT-TAT
1 ATATAATATATAT
253344 ATATAA-ACTATAT
1 ATATAATA-TATAT
* * *
253357 TTATATTATAAACT
1 ATATAATATATA-T
253371 ATATAAT-TAT-T
1 ATATAATATATAT
*
253382 ATA-AGCTATATAT
1 ATATA-ATATATAT
* *
253395 ATA-AATTATGTTT
1 ATATAA-TATATAT
253408 ATATGAACTATATAT
1 ATAT-AA-TATATAT
*
253423 ATA-AACTATATAC
1 ATATAA-TATATAT
* *
253436 GTAAAATATATAT
1 ATATAATATATAT
*
253449 GTATAA-ACTATA-
1 ATATAATA-TATAT
253461 A-A-AAGTATATAGT
1 ATATAA-TATATA-T
* *
253474 TTATAAATTATAATTT
1 ATAT-AA-TAT-ATAT
253490 ATATTAATATATAT
1 ATA-TAATATATAT
253504 ATAT-ATATATAT
1 ATATAATATATAT
253516 AT
1 AT
253518 TATTCAAAGT
Statistics
Matches: 160, Mismatches: 23, Indels: 51
0.68 0.10 0.22
Matches are distributed among these distances:
10 3 0.02
11 27 0.17
12 31 0.19
13 57 0.36
14 16 0.10
15 13 0.08
16 10 0.06
17 3 0.02
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:253485 original size:25 final size:23
Alignment explanation
Indices: 253438--253486 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
253428 CTATATACGT
253438 AAAATATATATGTATAAACTATA
1 AAAATATATATGTATAAACTATA
* *
253461 AAAAGTATATAGTTTATAAATTATA
1 AAAA-TATATA-TGTATAAACTATA
253486 A
1 A
253487 TTTATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 6 0.27
25 12 0.55
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (23 bp):
AAAATATATATGTATAAACTATA
Found at i:253653 original size:19 final size:19
Alignment explanation
Indices: 253631--253695 Score: 96
Period size: 19 Copynumber: 3.4 Consensus size: 19
253621 TTAAGAATAT
253631 AGGGAAATTGAGAATTTAG
1 AGGGAAATTGAGAATTTAG
253650 AGGGAAATTGAGAATTTAG
1 AGGGAAATTGAGAATTTAG
* *
253669 AGAGAAATTGGAAAATTTAG
1 AGGGAAATT-GAGAATTTAG
253689 A-GGAAAT
1 AGGGAAAT
253696 AGAAAATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
19 32 0.76
20 10 0.24
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.25
Consensus pattern (19 bp):
AGGGAAATTGAGAATTTAG
Found at i:253685 original size:46 final size:45
Alignment explanation
Indices: 253597--253685 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 45
253587 TTTATTTGGT
* * *
253597 AATTTAGAGGTAAATTGAGAAAATTTAAGAATATAGGGAAATTGAG
1 AATTTAGAGGGAAATTGAG-AAATTTAAGAAAATAGGAAAATTGAG
*
253643 AATTTAGAGGGAAATTGAG-AATTTAGAGAGAAATTGGAAAATT
1 AATTTAGAGGGAAATTGAGAAATTTA-AGA-AAATAGGAAAATT
253686 TAGAGGAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 6 0.16
45 3 0.08
46 28 0.76
ACGTcount: A:0.47, C:0.00, G:0.25, T:0.28
Consensus pattern (45 bp):
AATTTAGAGGGAAATTGAGAAATTTAAGAAAATAGGAAAATTGAG
Found at i:253700 original size:18 final size:18
Alignment explanation
Indices: 253633--253736 Score: 93
Period size: 19 Copynumber: 5.7 Consensus size: 18
253623 AAGAATATAG
*
253633 GGAAATTGAGAATTTAGA
1 GGAAATTGAAAATTTAGA
*
253651 GGGAAATTGAGAATTTAGA
1 -GGAAATTGAAAATTTAGA
253670 GAGAAATTGGAAAATTTAGA
1 G-GAAATT-GAAAATTTAGA
* *
253690 GGAAATAGAAAATTTTG-
1 GGAAATTGAAAATTTAGA
* * *
253707 GGAAGTTGGAAATTTAAA
1 GGAAATTGAAAATTTAGA
* *
253725 GGGAATAGAAAA
1 GGAAATTGAAAA
253737 ATTTGGGAAG
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
17 12 0.17
18 18 0.26
19 29 0.41
20 11 0.16
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.25
Consensus pattern (18 bp):
GGAAATTGAAAATTTAGA
Found at i:253732 original size:35 final size:35
Alignment explanation
Indices: 253676--253751 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 35
253666 TAGAGAGAAA
* *
253676 TTGGAAAATTTAGAGGAAATAGAAAATTTTGGGAAG
1 TTGG-AAATTTAAAGGAAATAGAAAAATTTGGGAAG
*
253712 TTGGAAATTTAAAGGGAATAGAAAAATTTGGGAAG
1 TTGGAAATTTAAAGGAAATAGAAAAATTTGGGAAG
253747 TTGGA
1 TTGGA
253752 GCAAGGATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 33 0.89
36 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.28
Consensus pattern (35 bp):
TTGGAAATTTAAAGGAAATAGAAAAATTTGGGAAG
Found at i:253958 original size:4 final size:4
Alignment explanation
Indices: 253949--255185 Score: 2432
Period size: 4 Copynumber: 310.8 Consensus size: 4
253939 TCTATACATA
253949 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
253997 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254045 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254093 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254141 TATG TATG TA-- TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254187 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254235 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA--
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254281 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254329 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254377 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254425 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254473 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254521 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254569 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254617 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254665 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254713 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254761 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254809 TATG TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254855 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254903 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254951 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
254999 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
255047 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
255095 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
255143 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
255186 ATATATAAAC
Statistics
Matches: 1227, Mismatches: 0, Indels: 12
0.99 0.00 0.01
Matches are distributed among these distances:
2 6 0.00
4 1221 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:255207 original size:15 final size:15
Alignment explanation
Indices: 255183--255216 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
255173 TGTATGTATG
255183 TATATATATAAACTA
1 TATATATATAAACTA
*
255198 TATATGTATAAACTA
1 TATATATATAAACTA
255213 TATA
1 TATA
255217 AAATATATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (15 bp):
TATATATATAAACTA
Found at i:255385 original size:7 final size:7
Alignment explanation
Indices: 255373--255440 Score: 55
Period size: 7 Copynumber: 9.7 Consensus size: 7
255363 TAAAAAAAAA
255373 CCTAAAC
1 CCTAAAC
255380 CCTAAAC
1 CCTAAAC
255387 CCTAAAC
1 CCTAAAC
**
255394 TTTAAAC
1 CCTAAAC
** *
255401 TATACAC
1 CCTAAAC
* *
255408 ACTAAAT
1 CCTAAAC
255415 CCTAAAC
1 CCTAAAC
255422 CCTAAAC
1 CCTAAAC
* *
255429 CATGAAC
1 CCTAAAC
255436 CCTAA
1 CCTAA
255441 TACAAATGGA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.44, C:0.34, G:0.01, T:0.21
Consensus pattern (7 bp):
CCTAAAC
Found at i:255440 original size:28 final size:27
Alignment explanation
Indices: 255377--255440 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
255367 AAAAAACCTA
** *
255377 AACCCTAAACCCTAAACTTTAAACTAT
1 AACCCTAAACCCTAAACCCTAAACCAT
* *
255404 ACACACTAAATCCTAAACCCTAAACCAT
1 A-ACCCTAAACCCTAAACCCTAAACCAT
255432 GAACCCTAA
1 -AACCCTAA
255441 TACAAATGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
27 1 0.03
28 27 0.93
29 1 0.03
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.20
Consensus pattern (27 bp):
AACCCTAAACCCTAAACCCTAAACCAT
Found at i:255753 original size:15 final size:15
Alignment explanation
Indices: 255735--255779 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
255725 ATAATCATGT
*
255735 TTTATATAATTTATA
1 TTTAAATAATTTATA
255750 TTTAAATAATTT-TA
1 TTTAAATAATTTATA
255764 -TTAAATAATTTTATA
1 TTTAAATAA-TTTATA
255779 T
1 T
255780 AATATGTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 8 0.31
14 5 0.19
15 13 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAATAATTTATA
Found at i:255783 original size:13 final size:13
Alignment explanation
Indices: 255740--255777 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
255730 CATGTTTTAT
255740 ATAATTTATATTTAA
1 ATAATTT-TA-TTAA
255755 ATAATTTTATTAA
1 ATAATTTTATTAA
255768 ATAATTTTAT
1 ATAATTTTAT
255778 ATAATATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 14 0.61
14 2 0.09
15 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATAATTTTATTAA
Found at i:256474 original size:25 final size:23
Alignment explanation
Indices: 256424--256489 Score: 91
Period size: 21 Copynumber: 2.9 Consensus size: 23
256414 ATAAACCATG
256424 TATAGTATATATAAACTATATATA
1 TATA-TATATATAAACTATATATA
* *
256448 TATATATA-ACACA-TATATATA
1 TATATATATATAAACTATATATA
256469 TATATATATATAAACTATATA
1 TATATATATATAAACTATATA
256490 AAGTAAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 16 0.44
22 6 0.17
23 10 0.28
24 4 0.11
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (23 bp):
TATATATATATAAACTATATATA
Found at i:256489 original size:2 final size:2
Alignment explanation
Indices: 256424--256480 Score: 62
Period size: 2 Copynumber: 28.0 Consensus size: 2
256414 ATAAACCATG
* * *
256424 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA -A CA CA 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
256467 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
256481 AACTATATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
1 1 0.02
2 45 0.92
3 3 0.06
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (2 bp):
TA
Found at i:256489 original size:19 final size:19
Alignment explanation
Indices: 256413--256476 Score: 83
Period size: 21 Copynumber: 3.2 Consensus size: 19
256403 AATATGTATG
* *
256413 TATAAACCATGTATAGTATA
1 TATAAACTATATATA-TATA
256433 TATAAACTATATATATATA
1 TATAAACTATATATATATA
256452 TATAACACATATATATATATA
1 TATAA-AC-TATATATATATA
256473 TATA
1 TATA
256477 TATAAACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
19 9 0.22
20 15 0.38
21 16 0.40
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (19 bp):
TATAAACTATATATATATA
Found at i:256601 original size:14 final size:14
Alignment explanation
Indices: 256582--256615 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
256572 AACCTAATCG
*
256582 TAAACTCTAAACCT
1 TAAACTCTAAACCA
*
256596 TAAACTTTAAACCA
1 TAAACTCTAAACCA
256610 TAAACT
1 TAAACT
256616 GTTGAGTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAACTCTAAACCA
Found at i:260030 original size:21 final size:21
Alignment explanation
Indices: 260004--260044 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
259994 ACAGAACCCC
*
260004 TGGGGGGTATCGATTCCCCTG
1 TGGGGGGAATCGATTCCCCTG
*
260025 TGGGGGGAATCGGTTCCCCT
1 TGGGGGGAATCGATTCCCCT
260045 TCAAAGGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.24, G:0.39, T:0.27
Consensus pattern (21 bp):
TGGGGGGAATCGATTCCCCTG
Found at i:260053 original size:23 final size:21
Alignment explanation
Indices: 260027--260084 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
260017 TTCCCCTGTG
260027 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
260050 GGGGGAATCGGTT-CCCTCAA
1 GGGGGAATCGGTTCCCCTCAA
*
260070 GGGGG-ATCGATTCCC
1 GGGGGAATCGGTTCCC
260085 TCCGCACCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 6 0.18
20 9 0.27
21 2 0.06
22 3 0.09
23 13 0.39
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:262599 original size:18 final size:18
Alignment explanation
Indices: 262566--262600 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
262556 AGGCCCGGCC
*
262566 CATGCACCGCGACTTACG
1 CATGCACCGAGACTTACG
*
262584 CATGCACCGAGCCTTAC
1 CATGCACCGAGACTTAC
262601 CCCATGTGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.40, G:0.20, T:0.17
Consensus pattern (18 bp):
CATGCACCGAGACTTACG
Found at i:262906 original size:29 final size:29
Alignment explanation
Indices: 262862--262933 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 29
262852 TTTTATTCTG
262862 TTTAATATTTTGTTAGTATTTTATTTAATTA
1 TTTAAT-TTTT-TTAGTATTTTATTTAATTA
*
262893 TTTAATTTTTTTAGTATTTTATTTTATTA
1 TTTAATTTTTTTAGTATTTTATTTAATTA
*
262922 TTTTATTTTTTT
1 TTTAATTTTTTT
262934 GTAGTTATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 29 0.74
30 4 0.10
31 6 0.15
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (29 bp):
TTTAATTTTTTTAGTATTTTATTTAATTA
Found at i:262917 original size:13 final size:13
Alignment explanation
Indices: 262901--262930 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
262891 TATTTAATTT
262901 TTTTAGTATTTTA
1 TTTTAGTATTTTA
*
262914 TTTTATTATTTTA
1 TTTTAGTATTTTA
262927 TTTT
1 TTTT
262931 TTTGTAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTAGTATTTTA
Found at i:268897 original size:29 final size:29
Alignment explanation
Indices: 268856--268920 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
268846 TATTTACGGA
* * * *
268856 TTGAAAGGTTTGTTGTGTGATTTTT-TGGG
1 TTGAGAGGATTGTTGTG-AATTTTTAGGGG
268885 TTGAGAGGATTGTTGTGAATTTTTAGGGG
1 TTGAGAGGATTGTTGTGAATTTTTAGGGG
268914 TTGAGAG
1 TTGAGAG
268921 CGTATTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (29 bp):
TTGAGAGGATTGTTGTGAATTTTTAGGGG
Found at i:274177 original size:51 final size:50
Alignment explanation
Indices: 274121--274223 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
274111 GGCCAATGCA
* *
274121 CCGCGCATTAC-CCTGCGTGGCACCACATCAGCGTAAGGAGCGATGCATGGG
1 CCGCGCATTACTCC-ACGTGACACCACATCAGCG-AAGGAGCGATGCATGGG
* * * * *
274172 CCGCGCCTTACTCCACGTGACATCACATCAGCGAAGGCGTGGTGCATGGG
1 CCGCGCATTACTCCACGTGACACCACATCAGCGAAGGAGCGATGCATGGG
274222 CC
1 CC
274224 ATGCCTTACC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
50 16 0.36
51 26 0.59
52 2 0.05
ACGTcount: A:0.20, C:0.33, G:0.30, T:0.17
Consensus pattern (50 bp):
CCGCGCATTACTCCACGTGACACCACATCAGCGAAGGAGCGATGCATGGG
Found at i:274230 original size:50 final size:51
Alignment explanation
Indices: 274144--274240 Score: 126
Period size: 50 Copynumber: 1.9 Consensus size: 51
274134 TGCGTGGCAC
*
274144 CACATCAGCGTAAGGAGCGATGCATGGGCCGCGCCTTA-CTCCACGTGACAT
1 CACATCAGCGTAAGGAGCGATGCATGGGCCACGCCTTACCT-CACGTGACAT
* * * *
274195 CACATCAGCG-AAGGCGTGGTGCATGGGCCATGCCTTACCTCACGTG
1 CACATCAGCGTAAGGAGCGATGCATGGGCCACGCCTTACCTCACGTG
274241 GCGCAGCATA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
50 28 0.70
51 12 0.30
ACGTcount: A:0.22, C:0.31, G:0.29, T:0.19
Consensus pattern (51 bp):
CACATCAGCGTAAGGAGCGATGCATGGGCCACGCCTTACCTCACGTGACAT
Found at i:275892 original size:56 final size:56
Alignment explanation
Indices: 275752--275895 Score: 180
Period size: 56 Copynumber: 2.6 Consensus size: 56
275742 TAGGGCCCCA
* * * *
275752 AAAAATAGGAGCTCTGAAATCGAGTATATCTATCAGTTGTTTCTATTAAGAAGCAT
1 AAAAATAGGGGCTCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCAT
* ** * * * *
275808 AAAAATAGAGATTTCAAAATTGAGTATATGTATCAGTTGTTGCCATTAAGAAGCAT
1 AAAAATAGGGGCTCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCAT
*
275864 AAAAATAGGGGCTCCGAAATCGAATATATCTA
1 AAAAATAGGGGCTCCGAAATCGAGTATATCTA
275896 AAAAATAAGG
Statistics
Matches: 69, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
56 69 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (56 bp):
AAAAATAGGGGCTCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCAT
Found at i:277664 original size:29 final size:29
Alignment explanation
Indices: 277622--277696 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
277612 AACCCAACCA
*
277622 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCTAC
* * *
277651 TAGGTCGCCATGCACGCCCGGCGACCTAG
1 TAGGTCGCCATGCACTCCCAGCGACCTAC
*
277680 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
277697 GGGGCGACCA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.17, C:0.40, G:0.27, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCTAC
Found at i:277702 original size:29 final size:29
Alignment explanation
Indices: 277623--277710 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
277613 ACCCAACCAT
* ***
277623 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACTCCCGGCGACCTAGG
*
277652 AGGTCGCCATGCACGCCCGGCGACCTAGG
1 AGGTCGCCATGCACTCCCGGCGACCTAGG
** *
277681 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGGCGACCTAGG
277710 A
1 A
277711 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.19, C:0.38, G:0.31, T:0.12
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGGCGACCTAGG
Found at i:278005 original size:29 final size:29
Alignment explanation
Indices: 277963--278036 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
277953 GGCGAGATGG
277963 GCGTGCATGGCGACCTGGTTGGTCGCCGA
1 GCGTGCATGGCGACCTGGTTGGTCGCCGA
*
277992 GCGTGCATGGCGACCTGGTTGGTCGCCGG
1 GCGTGCATGGCGACCTGGTTGGTCGCCGA
278021 GCGTGCATGGCGACCT
1 GCGTGCATGGCGACCT
278037 ACCCCCGGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.09, C:0.28, G:0.42, T:0.20
Consensus pattern (29 bp):
GCGTGCATGGCGACCTGGTTGGTCGCCGA
Found at i:285484 original size:2 final size:2
Alignment explanation
Indices: 285477--285504 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
285467 GTAATTGATA
285477 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
285505 TATTATCATT
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):
AT
Found at i:290522 original size:32 final size:31
Alignment explanation
Indices: 290485--290545 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
290475 AAATGTTATC
* *
290485 TTTTTAGTCAAAATAGGTACCTAAAGTATTTT
1 TTTTTA-TCAAAATAGATACCTAAACTATTTT
290517 TTTTTATCAAAATAGATACCTAAACTATT
1 TTTTTATCAAAATAGATACCTAAACTATT
290546 CAAACTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (31 bp):
TTTTTATCAAAATAGATACCTAAACTATTTT
Found at i:290734 original size:29 final size:29
Alignment explanation
Indices: 290629--290734 Score: 122
Period size: 29 Copynumber: 3.6 Consensus size: 29
290619 TGAAAAAATG
* * *
290629 AATACTTTAGGTACCTATTTTGACAAAAA
1 AATACTTCAGGTACTTATTTTGACCAAAA
* *
290658 AATACTTCAGATACATATTTTGACCAAAA
1 AATACTTCAGGTACTTATTTTGACCAAAA
*
290687 AGATAACTTCAGGTACTTATTTTGACCAACA
1 A-AT-ACTTCAGGTACTTATTTTGACCAAAA
* *
290718 AATACTTTAGCTACTTA
1 AATACTTCAGGTACTTA
290735 AATAAAAAAG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 38 0.58
30 4 0.06
31 24 0.36
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (29 bp):
AATACTTCAGGTACTTATTTTGACCAAAA
Found at i:290761 original size:60 final size:59
Alignment explanation
Indices: 290600--290768 Score: 164
Period size: 60 Copynumber: 2.8 Consensus size: 59
290590 TTAATGAAAG
* * * *
290600 AATACTTTAGGTACTTAGATGAAAAAATGA-ATACTTTAGGTACCTATTTTGACAAAAA
1 AATACTTTAGATACTTAAATAAAAAAATGATATACTTTAGGTACTTATTTTGACAAAAA
* * ** * * * *
290658 AATACTTCAGATACATATTTTGACCAAAAA-GATA-ACTTCAGGTACTTATTTTGACCAACA
1 AATACTTTAGATACTTA-AAT-A-AAAAAATGATATACTTTAGGTACTTATTTTGACAAAAA
*
290718 AATACTTTAGCTACTTAAATAAAAAAGATGATATACTTTAGGTACTTATTT
1 AATACTTTAGATACTTAAATAAAAAA-ATGATATACTTTAGGTACTTATTT
290769 ATTATATAAA
Statistics
Matches: 86, Mismatches: 18, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
57 4 0.05
58 16 0.19
59 6 0.07
60 54 0.63
61 6 0.07
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (59 bp):
AATACTTTAGATACTTAAATAAAAAAATGATATACTTTAGGTACTTATTTTGACAAAAA
Found at i:290897 original size:29 final size:29
Alignment explanation
Indices: 290865--290930 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
290855 TATGATTTTC
290865 TTTAAATATGAGAATACTATAAACACTTA
1 TTTAAATATGAGAATACTATAAACACTTA
* *
290894 TTTAAATATGATAATACTATAAAGACTTA
1 TTTAAATATGAGAATACTATAAACACTTA
*
290923 TTCAAATA
1 TTTAAATA
290931 AACTATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (29 bp):
TTTAAATATGAGAATACTATAAACACTTA
Found at i:292631 original size:21 final size:20
Alignment explanation
Indices: 292607--292665 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 20
292597 ATTATCCAAT
292607 AAACTTGACATCCATAACAAC
1 AAACTTGA-ATCCATAACAAC
292628 AAACTTGAAATCCATAACAAC
1 AAACTTG-AATCCATAACAAC
*
292649 CAACTTGAACTCCATAA
1 AAACTTGAA-TCCATAA
292666 TAATAAATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 2 0.06
21 32 0.91
22 1 0.03
ACGTcount: A:0.47, C:0.27, G:0.05, T:0.20
Consensus pattern (20 bp):
AAACTTGAATCCATAACAAC
Found at i:296125 original size:27 final size:28
Alignment explanation
Indices: 296064--296126 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
296054 AACCGGCCCA
* * * *
296064 ACCTGACCCGAACAATTGACCTGACTCT
1 ACCTGAACCGAACAATTGACCTAACCCG
296092 ACCTGAACCGAAC-ATTGACCTAACCCG
1 ACCTGAACCGAACAATTGACCTAACCCG
*
296119 ACTTGAAC
1 ACCTGAAC
296127 TGTTGACCCG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 18 0.60
28 12 0.40
ACGTcount: A:0.32, C:0.35, G:0.14, T:0.19
Consensus pattern (28 bp):
ACCTGAACCGAACAATTGACCTAACCCG
Found at i:296201 original size:22 final size:22
Alignment explanation
Indices: 296173--296219 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
296163 TTAACCGTTT
296173 ACCGGTCAGACCATTGACTTTG
1 ACCGGTCAGACCATTGACTTTG
**
296195 ACCGGTCAGACTGTTGACTTTG
1 ACCGGTCAGACCATTGACTTTG
296217 ACC
1 ACC
296220 AAAAAAGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (22 bp):
ACCGGTCAGACCATTGACTTTG
Found at i:296686 original size:13 final size:13
Alignment explanation
Indices: 296668--296693 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
296658 TGTGTGCAAT
296668 ATAACTATTTTAA
1 ATAACTATTTTAA
296681 ATAACTATTTTAA
1 ATAACTATTTTAA
296694 GTATCTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAACTATTTTAA
Found at i:300395 original size:28 final size:28
Alignment explanation
Indices: 300364--300429 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
300354 AGTCAGACCA
300364 TTGACTTTGATC-GATCTGACTGTTAACT
1 TTGACTTTGATCAG-TCTGACTGTTAACT
300392 TTGACTTTGATCAGTCTGACTGTTAACT
1 TTGACTTTGATCAGTCTGACTGTTAACT
300420 TTGACTTTGA
1 TTGACTTTGA
300430 CCGAAAAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 36 0.97
29 1 0.03
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.44
Consensus pattern (28 bp):
TTGACTTTGATCAGTCTGACTGTTAACT
Found at i:302018 original size:41 final size:41
Alignment explanation
Indices: 301918--302089 Score: 159
Period size: 41 Copynumber: 4.2 Consensus size: 41
301908 TTTTTACGTT
* * * * *
301918 AACGCCACTAAAGTACGTGTCTATGGCGGC-TTTTTAAACACA
1 AACGCCACTAAAGTACGAGTCTATAGCGTCGTTTGTATA-A-A
* * *
301960 AACACGACTAAAGTACGAGTCTATAGCGTCGTTTGTGTAAA
1 AACGCCACTAAAGTACGAGTCTATAGCGTCGTTTGTATAAA
*
302001 AACGTCACTAAAGTACGAGTCTATAGCGGT-GTTTGTATAAA
1 AACGCCACTAAAGTACGAGTCTATAGC-GTCGTTTGTATAAA
* * * * * * *
302042 AATGCCACTATAGTAAGATTCTTTAGCGGCGTTTGTATACA
1 AACGCCACTAAAGTACGAGTCTATAGCGTCGTTTGTATAAA
302083 AACGCCA
1 AACGCCA
302090 TGAAATTTTG
Statistics
Matches: 106, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
40 1 0.01
41 72 0.68
42 28 0.26
43 5 0.05
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (41 bp):
AACGCCACTAAAGTACGAGTCTATAGCGTCGTTTGTATAAA
Found at i:312320 original size:14 final size:14
Alignment explanation
Indices: 312301--312362 Score: 97
Period size: 14 Copynumber: 4.4 Consensus size: 14
312291 ACGTTCGTTA
312301 TATGTTCGTTCATT
1 TATGTTCGTTCATT
*
312315 TATGTTTGTTCATT
1 TATGTTCGTTCATT
**
312329 TATGTTCGTTCGGT
1 TATGTTCGTTCATT
312343 TATGTTCGTTCATT
1 TATGTTCGTTCATT
312357 TATGTT
1 TATGTT
312363 TAACTCAATC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.13, C:0.11, G:0.18, T:0.58
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:312334 original size:28 final size:28
Alignment explanation
Indices: 312292--312362 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
312282 ACGTCGTGAA
* *
312292 CGTTCGTTATATGTTCGTTCATTTATGTT
1 CGTTCATT-TATGTTCGTTCAGTTATGTT
* *
312321 TGTTCATTTATGTTCGTTCGGTTATGTT
1 CGTTCATTTATGTTCGTTCAGTTATGTT
312349 CGTTCATTTATGTT
1 CGTTCATTTATGTT
312363 TAACTCAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 31 0.84
29 6 0.16
ACGTcount: A:0.13, C:0.13, G:0.18, T:0.56
Consensus pattern (28 bp):
CGTTCATTTATGTTCGTTCAGTTATGTT
Found at i:316711 original size:99 final size:99
Alignment explanation
Indices: 316579--316891 Score: 544
Period size: 99 Copynumber: 3.2 Consensus size: 99
316569 CGTTTATCGT
* *
316579 TTAAATGAACGAACATGAACAAACTACATTCCTTAATGAACGAACATGAACAAATTTTTTTTCGT
1 TTAAATGAACGAACATAAACAAACTATATTCCTTAATGAACGAACATGAACAAATTTTTTTTCGT
316644 TTATGTTCGTGTTCGTTTATTTGTTCGGTTAAAA
66 TTATGTTCGTGTTCGTTTATTTGTTCGGTTAAAA
*
316678 TTAAATGAACGAACATAAACAAACTATATTCCTTAATAAACGAACATGAAC-AATATTTTTTTCG
1 TTAAATGAACGAACATAAACAAACTATATTCCTTAATGAACGAACATGAACAAAT-TTTTTTTCG
316742 TTTATGTTCGTGTTCGTTTATTTGTTCGGTTAAAA
65 TTTATGTTCGTGTTCGTTTATTTGTTCGGTTAAAA
*
316777 TTAAATGAACGAACATGAACAAACTATATTCCTTAATGAACGAACATGAACAAATTTTTTTTCGT
1 TTAAATGAACGAACATAAACAAACTATATTCCTTAATGAACGAACATGAACAAATTTTTTTTCGT
*
316842 TTATGTTCGTGTTCGTTTATTTGTTCAGTTAAAA
66 TTATGTTCGTGTTCGTTTATTTGTTCGGTTAAAA
316876 TT-AA--AACGAACATAAA
1 TTAAATGAACGAACATAAA
316892 TATATTTTTA
Statistics
Matches: 205, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
96 11 0.05
98 5 0.02
99 186 0.91
100 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (99 bp):
TTAAATGAACGAACATAAACAAACTATATTCCTTAATGAACGAACATGAACAAATTTTTTTTCGT
TTATGTTCGTGTTCGTTTATTTGTTCGGTTAAAA
Found at i:319473 original size:54 final size:54
Alignment explanation
Indices: 319342--319690 Score: 517
Period size: 54 Copynumber: 6.5 Consensus size: 54
319332 AAACTCATTG
* * *
319342 TGAATTTCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAAC-TATTA
1 TGAATTTCGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGA
* *
319395 TG-ATTAT-GTGGGTTGAACACTTAGTG-CTGATACAGTCGTTCATCAACATATGA
1 TGAATT-TCGTGGGTTGCACACTTAGTGCCT-ATACGGTCGTTCATCAACATATGA
* * *
319448 TGAATTCCGTAGGTTGCACACTTAGTGCCTATACGGTCGTTCATCGACATATGA
1 TGAATTTCGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGA
* *
319502 TGAATTCCGTGGGTTGCACACTTAGTGCCTATAAGGTCGTTCATCAACATATGA
1 TGAATTTCGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGA
** * *
319556 TGAATTTCGTGGGTTGCACACTTAGTGTTTATACGGTTGTTCATCAATATATGA
1 TGAATTTCGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGA
*
319610 TGAATTTCGTGGGTTGTACACTTAGTGCCTATACGGTCGTTCATCAACATATGA
1 TGAATTTCGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGA
319664 TGAATTTCGTGGGTTGCACACTTAGTG
1 TGAATTTCGTGGGTTGCACACTTAGTG
319691 TCGATAATAT
Statistics
Matches: 265, Mismatches: 25, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
51 1 0.00
52 37 0.14
53 9 0.03
54 216 0.82
55 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (54 bp):
TGAATTTCGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGA
Found at i:322020 original size:142 final size:145
Alignment explanation
Indices: 321859--322134 Score: 461
Period size: 146 Copynumber: 1.9 Consensus size: 145
321849 CTCATACAAG
321859 TATACATTATACTTATAATGTATATATATA-ATAA-ATG-TGATGAATATCATGATAATATAATT
1 TATACATTATACTTATAATGTATATATATATATAATATGATGATGAATATCATGATAATATAATT
* *
321921 TATGTATAT-ATAATGTATATTATATATTTATACTTATGCATTCATTATATGTATATACTTATAT
66 CATGTATATCA-AATGTATATTATACATTTATACTTATGCATTCATTATATGTATATACTTATAT
321985 AAGTATATAATATAAT
130 AAGTATATAATATAAT
*
322001 TATACATTATACTTATAATGTATATATATATATAATATGTATGATGAATGTCATGATAATATAAT
1 TATACATTATACTTATAATGTATATATATATATAATATG-ATGATGAATATCATGATAATATAAT
* *
322066 TCATGTATATCAAATGTATATTATGCATTTATCCTTATGCATTCATTATATGTATATACTTATAT
65 TCATGTATATCAAATGTATATTATACATTTATACTTATGCATTCATTATATGTATATACTTATAT
322131 AAGT
130 AAGT
322135 GTAATGTATA
Statistics
Matches: 124, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
142 30 0.24
143 4 0.03
144 3 0.02
146 86 0.69
147 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (145 bp):
TATACATTATACTTATAATGTATATATATATATAATATGATGATGAATATCATGATAATATAATT
CATGTATATCAAATGTATATTATACATTTATACTTATGCATTCATTATATGTATATACTTATATA
AGTATATAATATAAT
Found at i:322953 original size:19 final size:19
Alignment explanation
Indices: 322929--322968 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
322919 TATAAATTCA
*
322929 AAAATCTCACAACTTCGTC
1 AAAATCTCACAACTTCATC
*
322948 AAAATCTCATAACTTCATC
1 AAAATCTCACAACTTCATC
322967 AA
1 AA
322969 TTATAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.28, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAATCTCACAACTTCATC
Found at i:324254 original size:42 final size:42
Alignment explanation
Indices: 324220--324318 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
324210 CGTTTCTTGT
* *
324220 ACAAACGCTGTAATAGAGTAGTAATTTCGCGGCGTTTTTAGC
1 ACAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTTTAGC
*
324262 CCAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTTTAGC
1 ACAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTTTAGC
* * *
324304 AAAAATGCCGCAATA
1 ACAAACGCCGTAATA
324319 AGGTTTTTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (42 bp):
ACAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTTTAGC
Found at i:324408 original size:207 final size:207
Alignment explanation
Indices: 324056--324434 Score: 605
Period size: 207 Copynumber: 1.8 Consensus size: 207
324046 GTTTATTGTA
* * *
324056 CAAATGCCGTAATAGAGTAGTAATTTAGCGACATTTTTACCATAAATGCCGCAATAGGGTTGTTT
1 CAAACGCCGTAATAGAGTAGTAATTTAGCGACATTTTTACCAAAAATGCCGCAATAAGGTTGTTT
* * * *
324121 ATAGTGGCATTTTCCCAACAAACGCCGCAATAAAGATTACTTTAGCATCGTTTTTAGACAAATGC
66 AAAGTGGCATTTTCCCAACAAACGCCACAATAAAGAATACTTTAGCATCATTTTTAGACAAATGC
*
324186 CACAGTAGGGTTAATCAATAGTGGCGTTTCTTGTACAAACGCTGTAATAGAGTAGTAATTTCGCG
131 CACAATAGGGTTAATCAATAGTGGCGTTTCTTGTACAAACGCTGTAATAGAGTAGTAATTTCGCG
324251 GCGTTTTTAGCC
196 GCGTTTTTAGCC
* * * *
324263 CAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTTTAGCAAAAATGCCGCAATAAGGTTTTTT
1 CAAACGCCGTAATAGAGTAGTAATTTAGCGACATTTTTACCAAAAATGCCGCAATAAGGTTGTTT
* * * *
324328 AAAGTGGCGTTTTTCGAACAAACGCCACAATAAAGAATACTTTAGCGTCATTTTTAGACAAATGC
66 AAAGTGGCATTTTCCCAACAAACGCCACAATAAAGAATACTTTAGCATCATTTTTAGACAAATGC
*
324393 CACAATAGTGTTAATCAATAGTGGCGTTTCTTGTACAAACGC
131 CACAATAGGGTTAATCAATAGTGGCGTTTCTTGTACAAACGC
324435 CGCAAAAACA
Statistics
Matches: 155, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
207 155 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (207 bp):
CAAACGCCGTAATAGAGTAGTAATTTAGCGACATTTTTACCAAAAATGCCGCAATAAGGTTGTTT
AAAGTGGCATTTTCCCAACAAACGCCACAATAAAGAATACTTTAGCATCATTTTTAGACAAATGC
CACAATAGGGTTAATCAATAGTGGCGTTTCTTGTACAAACGCTGTAATAGAGTAGTAATTTCGCG
GCGTTTTTAGCC
Found at i:324868 original size:22 final size:22
Alignment explanation
Indices: 324840--324892 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
324830 GTTTTACTGC
*
324840 TTTCGAATAGAAAAATAATAGA
1 TTTCGAAAAGAAAAATAATAGA
*
324862 TTTCGAAAAGGAAAATAATAGA
1 TTTCGAAAAGAAAAATAATAGA
*
324884 TTTTGAAAA
1 TTTCGAAAA
324893 CGCGAACAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (22 bp):
TTTCGAAAAGAAAAATAATAGA
Found at i:334826 original size:21 final size:21
Alignment explanation
Indices: 334818--334868 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
334808 GAAAGCAGAG
334818 AGAGCAGCAACGGAAGCACAA
1 AGAGCAGCAACGGAAGCACAA
* *
334839 AGAGCAGCAACTGAAGCACAT
1 AGAGCAGCAACGGAAGCACAA
*
334860 AGAGAAGCA
1 AGAGCAGCA
334869 TCATATCAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.22, G:0.27, T:0.04
Consensus pattern (21 bp):
AGAGCAGCAACGGAAGCACAA
Found at i:337184 original size:29 final size:29
Alignment explanation
Indices: 337152--337287 Score: 137
Period size: 29 Copynumber: 4.7 Consensus size: 29
337142 CTTTTTTTAA
* * ***
337152 TAATTACCAAAATAACACCCATTTCGAAT
1 TAATTACCAAAATAGCACCAAAACCGAAT
*
337181 TAATTACCAGAATAGCACCAAAACCGAAT
1 TAATTACCAAAATAGCACCAAAACCGAAT
* **
337210 TATTTACCAAAATAGCACCAAAACTAAAT
1 TAATTACCAAAATAGCACCAAAACCGAAT
* * * *
337239 TATTTACCATAATAGCACCAAAACTGGAT
1 TAATTACCAAAATAGCACCAAAACCGAAT
* *
337268 TATTTACCAAAATAACACCA
1 TAATTACCAAAATAGCACCA
337288 GACAACGATC
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 92 1.00
ACGTcount: A:0.47, C:0.23, G:0.06, T:0.24
Consensus pattern (29 bp):
TAATTACCAAAATAGCACCAAAACCGAAT
Found at i:337223 original size:58 final size:59
Alignment explanation
Indices: 337155--337286 Score: 169
Period size: 58 Copynumber: 2.3 Consensus size: 59
337145 TTTTTAATAA
*** *
337155 TTACCAAAATAACACCCATTTC-GAATTAATTACCAGAATAGCACCAAAACCGAATTAT
1 TTACCAAAATAACACCCAAAACTAAATTAATTACCAGAATAGCACCAAAACCGAATTAT
* * * * *
337213 TTACCAAAATAGCA-CCAAAACTAAATTATTTACCATAATAGCACCAAAACTGGATTAT
1 TTACCAAAATAACACCCAAAACTAAATTAATTACCAGAATAGCACCAAAACCGAATTAT
337271 TTACCAAAATAACACC
1 TTACCAAAATAACACC
337287 AGACAACGAT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
57 4 0.06
58 57 0.92
59 1 0.02
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.24
Consensus pattern (59 bp):
TTACCAAAATAACACCCAAAACTAAATTAATTACCAGAATAGCACCAAAACCGAATTAT
Found at i:337287 original size:58 final size:58
Alignment explanation
Indices: 337178--337287 Score: 175
Period size: 58 Copynumber: 1.9 Consensus size: 58
337168 ACCCATTTCG
*
337178 AATTAATTACCAGAATAGCACCAAAACCGAATTATTTACCAAAATAGCACCAAAACTA
1 AATTAATTACCAGAATAGCACCAAAACCGAATTATTTACCAAAATAACACCAAAACTA
* * * *
337236 AATTATTTACCATAATAGCACCAAAACTGGATTATTTACCAAAATAACACCA
1 AATTAATTACCAGAATAGCACCAAAACCGAATTATTTACCAAAATAACACCA
337288 GACAACGATC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.48, C:0.22, G:0.06, T:0.24
Consensus pattern (58 bp):
AATTAATTACCAGAATAGCACCAAAACCGAATTATTTACCAAAATAACACCAAAACTA
Found at i:337345 original size:18 final size:18
Alignment explanation
Indices: 337296--337346 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
337286 CAGACAACGA
337296 TCAAC-GGTCGGGTCGGG
1 TCAACGGGTCGGGTCGGG
** *
337313 TCAACGGGTAAGGTCGGT
1 TCAACGGGTCGGGTCGGG
337331 TCAACGGGTCGGGTCG
1 TCAACGGGTCGGGTCG
337347 TGACCGGTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.16, C:0.22, G:0.43, T:0.20
Consensus pattern (18 bp):
TCAACGGGTCGGGTCGGG
Found at i:343163 original size:29 final size:29
Alignment explanation
Indices: 343121--343255 Score: 135
Period size: 29 Copynumber: 4.7 Consensus size: 29
343111 CCTTTTTAAA
* * **
343121 TAATAACCAAAATAGCACCCATTTCGAAT
1 TAATTACCAAAATAGCACCAAAATCGAAT
* * *
343150 TAATTACCACAATAGCTCTAAAATCGAAT
1 TAATTACCAAAATAGCACCAAAATCGAAT
* * *
343179 TATTTACCAAAATAGCACCAAAACCAAAT
1 TAATTACCAAAATAGCACCAAAATCGAAT
* * *
343208 TATTTACCAGAATAGCACCAAAACCGAAT
1 TAATTACCAAAATAGCACCAAAATCGAAT
* *
343237 TACTTACCAAAATAACACC
1 TAATTACCAAAATAGCACC
343256 GGTCAACGGT
Statistics
Matches: 88, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 88 1.00
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.23
Consensus pattern (29 bp):
TAATTACCAAAATAGCACCAAAATCGAAT
Found at i:343297 original size:18 final size:18
Alignment explanation
Indices: 343263--343315 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
343253 ACCGGTCAAC
*
343263 GGTCAAC-GGTTGGGTCG
1 GGTCAACGGGTAGGGTCG
343280 GGTCAACGGGTAGGGTCG
1 GGTCAACGGGTAGGGTCG
* *
343298 GTTCAACGGGTCGGGTCG
1 GGTCAACGGGTAGGGTCG
343316 TGACCGGTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 7 0.22
18 25 0.78
ACGTcount: A:0.13, C:0.19, G:0.47, T:0.21
Consensus pattern (18 bp):
GGTCAACGGGTAGGGTCG
Found at i:349097 original size:29 final size:29
Alignment explanation
Indices: 349053--349117 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
349043 CATTTTACAC
* *
349053 AAATAGCACCCTTTTTTAAATAATAACCA
1 AAATAGCACCCATTTTGAAATAATAACCA
* *
349082 AAATAGCACCCATTTTGAATTAATTACCA
1 AAATAGCACCCATTTTGAAATAATAACCA
*
349111 TAATAGC
1 AAATAGC
349118 TCTAAAATCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (29 bp):
AAATAGCACCCATTTTGAAATAATAACCA
Found at i:349130 original size:29 final size:29
Alignment explanation
Indices: 349098--349207 Score: 139
Period size: 29 Copynumber: 3.8 Consensus size: 29
349088 CACCCATTTT
* * * * *
349098 GAATTAATTACCATAATAGCTCTAAAATC
1 GAATTATTTACCAAAATAGCACCAAAACC
349127 GAATTATTTACCAAAATAGCACCAAAACC
1 GAATTATTTACCAAAATAGCACCAAAACC
* *
349156 AAATTATTTACCAGAATAGCACCAAAACC
1 GAATTATTTACCAAAATAGCACCAAAACC
* *
349185 GAATTACTTACCAAAATAACACC
1 GAATTATTTACCAAAATAGCACC
349208 GGTCAACGGT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.47, C:0.23, G:0.06, T:0.24
Consensus pattern (29 bp):
GAATTATTTACCAAAATAGCACCAAAACC
Found at i:349219 original size:7 final size:7
Alignment explanation
Indices: 349207--349231 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
349197 AAAATAACAC
349207 CGGTCAA
1 CGGTCAA
349214 CGGTCAA
1 CGGTCAA
349221 CGGTCAA
1 CGGTCAA
349228 CGGT
1 CGGT
349232 TGGGTCGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (7 bp):
CGGTCAA
Found at i:349256 original size:18 final size:18
Alignment explanation
Indices: 349222--349274 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
349212 AACGGTCAAC
*
349222 GGTCAAC-GGTTGGGTCG
1 GGTCAACGGGTAGGGTCG
349239 GGTCAACGGGTAGGGTCG
1 GGTCAACGGGTAGGGTCG
* *
349257 GTTCAACGGGTCGGGTCG
1 GGTCAACGGGTAGGGTCG
349275 TGACCGGTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 7 0.22
18 25 0.78
ACGTcount: A:0.13, C:0.19, G:0.47, T:0.21
Consensus pattern (18 bp):
GGTCAACGGGTAGGGTCG
Found at i:360535 original size:10 final size:10
Alignment explanation
Indices: 360520--360575 Score: 58
Period size: 10 Copynumber: 5.2 Consensus size: 10
360510 TCGTGAACGC
360520 TCGGTTATGT
1 TCGGTTATGT
360530 TCGGTTATGT
1 TCGGTTATGT
*
360540 TCGTTTATGT
1 TCGGTTATGT
360550 TCGTTCGATTATGT
1 TCG---G-TTATGT
*
360564 TCGTTTATGT
1 TCGGTTATGT
360574 TC
1 TC
360576 ATTCATTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 30 0.77
14 9 0.23
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (10 bp):
TCGGTTATGT
Found at i:360561 original size:14 final size:14
Alignment explanation
Indices: 360538--360568 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
360528 GTTCGGTTAT
*
360538 GTTCGTTTATGTTC
1 GTTCGATTATGTTC
360552 GTTCGATTATGTTC
1 GTTCGATTATGTTC
360566 GTT
1 GTT
360569 TATGTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGATTATGTTC
Found at i:360561 original size:24 final size:24
Alignment explanation
Indices: 360528--360588 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
360518 GCTCGGTTAT
*
360528 GTTCGGTTATGTTCGTTTATGTTC
1 GTTCGATTATGTTCGTTTATGTTC
360552 GTTCGATTATGTTCGTTTATGTTC
1 GTTCGATTATGTTCGTTTATGTTC
*
360576 ATTC-ATTTATGTT
1 GTTCGA-TTATGTT
360589 TAACTCAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.13, C:0.11, G:0.20, T:0.56
Consensus pattern (24 bp):
GTTCGATTATGTTCGTTTATGTTC
Found at i:361679 original size:16 final size:16
Alignment explanation
Indices: 361658--361730 Score: 105
Period size: 16 Copynumber: 4.7 Consensus size: 16
361648 CCAACGTTTA
361658 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
361674 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
* *
361690 TGTTCGTTTAAGTTCG
1 TGTTCATTTATGTTCG
*
361706 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
361722 T-TT-ATTTAT
1 TGTTCATTTAT
361731 TAAATGAACG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
14 5 0.09
15 2 0.04
16 46 0.87
ACGTcount: A:0.12, C:0.11, G:0.19, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:364425 original size:2 final size:2
Alignment explanation
Indices: 364374--364413 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
364364 TGATAAATTA
364374 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
364414 TAAAGTTATA
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:366450 original size:3 final size:3
Alignment explanation
Indices: 366442--366485 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
366432 ATATGTAATT
366442 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
366486 TTTTTTATAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:366938 original size:128 final size:131
Alignment explanation
Indices: 366676--367025 Score: 431
Period size: 128 Copynumber: 2.7 Consensus size: 131
366666 GTTCTAGTCG
* * * * * *
366676 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATTTGGTTGGTGGATGACATGGTTCCTACGC
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTTTGG-T-GAGGATGACACGGTTCCTACGT
* * * *
366741 GATGATGACGACTGGCCATCTTTAGGAAGGGTGATAACACAGTTCATACGCGATGAGGACGGCTG
64 GATGAGGACGGCAGGCCATCTTTAGG-AGGATGATAACACAGTTCATACGCGATGAGGACGGCTG
366806 GTTA
128 GTTA
*
366810 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTTTGGT-AGGATGACACGATTCCTACGTGA
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTTTGGTGAGGATGACACGGTTCCTACGTGA
* * * * *
366874 TGAGGATGGCAGACCATCTTTA-G-GGATGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
66 TGAGGACGGCAGGCCATCTTTAGGAGGATGATAACACAGTTCATACGCGATGAGGACGGCTGGTT
366937 A
131 A
* * * *
366938 TCT-GAGGTTCACTCGGCTCCTACGTGATGAGGAGG-TTGGTCGGGGGATGACACGGTTCCTACG
1 TCTAG-GGGTGACACGGCTCCTACGTGATGAGGAGGTTTGGT--GAGGATGACACGGTTCCTACG
367001 TGATGAGGACGGCAGGCCATCTTTA
63 TGATGAGGACGGCAGGCCATCTTTA
367026 TAGATAATGG
Statistics
Matches: 189, Mismatches: 23, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
127 6 0.03
128 67 0.35
130 42 0.22
131 36 0.19
133 1 0.01
134 37 0.20
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (131 bp):
TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTTTGGTGAGGATGACACGGTTCCTACGTGA
TGAGGACGGCAGGCCATCTTTAGGAGGATGATAACACAGTTCATACGCGATGAGGACGGCTGGTT
A
Found at i:367009 original size:39 final size:41
Alignment explanation
Indices: 366905--367013 Score: 123
Period size: 39 Copynumber: 2.7 Consensus size: 41
366895 AGGGATGATA
* *
366905 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGAGGTTC
1 ACACGGTTCCTACGTGATGAGGACGGCTGG-T-TCGGAGGATC
* * * * *
366948 ACTCGGCTCCTACGTGATGAGGA-GGTTGG-TCGGGGGATG
1 ACACGGTTCCTACGTGATGAGGACGGCTGGTTCGGAGGATC
366987 ACACGGTTCCTACGTGATGAGGACGGC
1 ACACGGTTCCTACGTGATGAGGACGGC
367014 AGGCCATCTT
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
39 27 0.49
40 2 0.04
42 5 0.09
43 21 0.38
ACGTcount: A:0.18, C:0.21, G:0.37, T:0.24
Consensus pattern (41 bp):
ACACGGTTCCTACGTGATGAGGACGGCTGGTTCGGAGGATC
Found at i:367284 original size:62 final size:64
Alignment explanation
Indices: 367077--367328 Score: 305
Period size: 66 Copynumber: 3.9 Consensus size: 64
367067 CAATAAAAGT
* * * * ** *
367077 TGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-CGATCTCAAAGATGGGTATTTCAAGAGAA
1 TGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAATAGA-CTCAAAGATTTG-CTTT-AAGAGAA
367141 AC
63 AC
* * * *
367143 TGTCTCAAGGGAGACAAAACTTGTTTCAAGGTAAACAGACTAAAAGATTTGCTTTAAGAGAAAC
1 TGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAATAGACTCAAAGATTTGCTTTAAGAGAAAC
* *
367207 TGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAGTAGTCTCAAAGATTT-C-TTAAGA-AAAC
1 TGTCTCAAGAGAGACAAAAC-TTGTTTCAAGGGAAATAGACTCAAAGATTTGCTTTAAGAGAAAC
* *
367269 TGTCCCAAGAGAGACAAAACTTGTTTCAAGGGAAATAGACTCAAAGATTTGTTTTAAGAG
1 TGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAATAGACTCAAAGATTTGCTTTAAGAG
367329 TGTAACACTC
Statistics
Matches: 163, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
61 28 0.17
62 23 0.14
63 12 0.07
64 29 0.18
65 28 0.17
66 41 0.25
67 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (64 bp):
TGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAATAGACTCAAAGATTTGCTTTAAGAGAAAC
Found at i:367296 original size:126 final size:128
Alignment explanation
Indices: 367077--367328 Score: 336
Period size: 126 Copynumber: 2.0 Consensus size: 128
367067 CAATAAAAGT
* *
367077 TGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAACGATCTCAAAGATGGGTATTTCAAGAGAAA
1 TGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGAT--GTATTTCAAGAGAAA
* * *
367142 CTGTCTCAAGGGAGACAAAACTTGTTTCAAGGTAAACAGACTAAAAGATTTGCTTTAAGAGAAAC
64 CTGTCCCAAGAGAGACAAAACTTGTTTCAAGGGAAACAGACTAAAAGATTTGCTTTAAGAGAAAC
367207 TGTCTCAAGAGAGACAAAACTTTGTTTCAAGGG-AA-GTAGTCTCAAAGAT-T-TCTT-AAGA-A
1 TGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACG-A-TCTCAAAGATGTAT-TTCAAGAGA
* * *
367266 AACTGTCCCAAGAGAGACAAAACTTGTTTCAAGGGAAATAGACTCAAAGATTTGTTTTAAGAG
62 AACTGTCCCAAGAGAGACAAAACTTGTTTCAAGGGAAACAGACTAAAAGATTTGCTTTAAGAG
367329 TGTAACACTC
Statistics
Matches: 110, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
126 58 0.53
127 5 0.05
128 3 0.03
129 1 0.01
130 21 0.19
131 22 0.20
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (128 bp):
TGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGTATTTCAAGAGAAACT
GTCCCAAGAGAGACAAAACTTGTTTCAAGGGAAACAGACTAAAAGATTTGCTTTAAGAGAAAC
Done.