Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009635.1 Hibiscus syriacus cultivar Beakdansim tig00117038_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: 1009897
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:527269 original size:15 final size:14
Alignment explanation
Indices: 527249--527351 Score: 61
Period size: 13 Copynumber: 7.1 Consensus size: 14
527239 ATATACTTTT
527249 TATAGTTTATACATA
1 TATAGTTTATA-ATA
527264 TATAGTTTAT-ATA
1 TATAGTTTATAATA
*
527277 CATAGTTTAT-ATA
1 TATAGTTTATAATA
* *
527290 TATACTTCACATAA-A
1 TATAGTT--TATAATA
* *
527305 CATAATTTAT-ATA
1 TATAGTTTATAATA
*
527318 TATATCTTATAATAATTA
1 TATA-GTT-T-ATAA-TA
527336 TATAGTTTATAATA
1 TATAGTTTATAATA
527350 TA
1 TA
527352 AATATAGTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 19
0.70 0.10 0.19
Matches are distributed among these distances:
12 1 0.01
13 26 0.38
14 6 0.09
15 23 0.33
16 4 0.06
17 3 0.04
18 6 0.09
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.47
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:527369 original size:17 final size:18
Alignment explanation
Indices: 527335--527370 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
527325 TATAATAATT
527335 ATATAGTTTATAATATAA
1 ATATAGTTTATAATATAA
527353 ATATAGTTTAT-ATATAA
1 ATATAGTTTATAATATAA
527370 A
1 A
527371 CTTATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
ATATAGTTTATAATATAA
Found at i:527395 original size:18 final size:18
Alignment explanation
Indices: 527311--527396 Score: 55
Period size: 19 Copynumber: 5.1 Consensus size: 18
527301 TAAACATAAT
*
527311 TTATATATATATCTTATA
1 TTATATATATATATTATA
527329 --ATA-AT-TATA-TAGT-
1 TTATATATATATATTA-TA
*
527342 TTATA-ATATA-AATATA
1 TTATATATATATATTATA
*
527358 GTT-TATATATAAACTTATA
1 -TTATATATATATA-TTATA
527377 TTATATATATATATTATA
1 TTATATATATATATTATA
527395 TT
1 TT
527397 TTTCAAATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 22
0.68 0.04 0.28
Matches are distributed among these distances:
13 2 0.04
14 4 0.07
15 9 0.17
16 9 0.17
17 7 0.13
18 10 0.19
19 13 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
TTATATATATATATTATA
Found at i:530234 original size:37 final size:36
Alignment explanation
Indices: 530188--530292 Score: 160
Period size: 34 Copynumber: 2.9 Consensus size: 36
530178 ATAATAGTAT
530188 AACTCTATCCTATTTTTAGGAGTTTGAATCCTAGCAA
1 AACTCTATCCTATTTTTAGGAGTTTGAATCCTAG-AA
* *
530225 AATTTTATCCTATTTTTAGGAGTTTGAATCCT--AA
1 AACTCTATCCTATTTTTAGGAGTTTGAATCCTAGAA
*
530259 AACTCTATCCTATTTTTAGTAGTTTGAATCCTAG
1 AACTCTATCCTATTTTTAGGAGTTTGAATCCTAG
530293 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
34 31 0.51
37 30 0.49
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (36 bp):
AACTCTATCCTATTTTTAGGAGTTTGAATCCTAGAA
Found at i:531127 original size:105 final size:105
Alignment explanation
Indices: 530827--531587 Score: 1044
Period size: 105 Copynumber: 7.3 Consensus size: 105
530817 CATTGTTCCA
* * * * ** * *
530827 AGTCTAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAG
* * *
530892 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
530933 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
530993 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
531033 AATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
* *
531098 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTATGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
531138 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGAA-TGGGAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAGTTGTTGTTGACAAG
* *
531202 CAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
531243 AGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAAAT---AAGTT-TT-TTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
531303 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
531343 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
*
531408 AGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
531448 AGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAG
* * *
531513 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
531554 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
531588 CGCAGATGGC
Statistics
Matches: 594, Mismatches: 43, Indels: 33
0.89 0.06 0.05
Matches are distributed among these distances:
99 1 0.00
100 170 0.29
101 3 0.01
102 12 0.02
103 5 0.01
104 9 0.02
105 287 0.48
106 82 0.14
107 4 0.01
109 21 0.04
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:531300 original size:205 final size:205
Alignment explanation
Indices: 530826--531587 Score: 959
Period size: 205 Copynumber: 3.6 Consensus size: 205
530816 GCATTGTTCC
* * * * *
530826 AAGTCTAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGA-AATTGTTTGTTGACA
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAA----AATAAGT-TTTGTTGACA
* * *
530890 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGA
60 ACCAGTCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
** *
530955 AGTTGAAATTGAATCT--GAAT-GAAATT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
125 AGTTGAAATTGGCTCTGAGAATGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
531016 GAACTTGCGTTGTCTGG
190 GAACTTGCGTTGTCT-G
* * * *
531033 AA-TCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAAT---AAGTT-TTGTTGACAAC
* *
531097 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTATGGAGTCCAATATCCTTCGTTGTGAA
62 CAGTC-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
*
531161 GTTGAAATTGGCTCTGAGAATGGGAAGTTGTTGTTGACAAGCAACGGTCCCTTCGTCGTGAAGTT
126 GTTGAAATTGGCTCTGAGAAT-GGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
531226 GAACTTGCGTTGTCTG
190 GAACTTGCGTTGTCTG
* *
531242 AAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAAATAAGTTTT-TTGACAAGCAG-
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAATAAGTTTTGTTGACAACCAGT
531305 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 C-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
* *
531370 AAATTGGCTCTGA-AATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGCCGTGAAGTTGAA
130 AAATTGGCTCTGAGAA-TG-GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
531434 CTTGCGTTGTCTG
193 CTTGCGTTGTCTG
* * *
531447 GAGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA---ATAAG-T-TTTGTTGACAA
* * * * *
531512 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCGT
61 CCAGTCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT-CCA--ATATCCTTCGTTGT
*
531577 GGAGTTGAAAT
123 GAAGTTGAAAT
531588 CGCAGATGGC
Statistics
Matches: 493, Mismatches: 38, Indels: 41
0.86 0.07 0.07
Matches are distributed among these distances:
204 5 0.01
205 268 0.54
206 34 0.07
207 11 0.02
208 4 0.01
209 9 0.02
210 90 0.18
211 46 0.09
212 4 0.01
214 22 0.04
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (205 bp):
AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAATAAGTTTTGTTGACAACCAGT
CGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
AATTGGCTCTGAGAATGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTG
Found at i:531379 original size:310 final size:312
Alignment explanation
Indices: 530827--531587 Score: 1160
Period size: 310 Copynumber: 2.4 Consensus size: 312
530817 CATTGTTCCA
* * * * *
530827 AGTCTAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGAACTGGGAAGTTGTTTGTTGACAA
530891 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
66 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
530956 GTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
131 GTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* *
531021 TGCGTTGTCTGGAATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAGATTGGGAAGTTG
196 TGCGTTGTCTGGAATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAAATTGAGAAGTTG
*
531086 TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTATGG
261 TTGTTGACAAGCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCATTGTATGG
531138 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGAA-TGGGAAGTTG-TTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGAACTGGGAAGTTGTTTGTTGACAA
* * * * *
531201 GCA-ACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAAGTCCAATATCCTTTGTTGTG
66 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG-AGTCCAATATCCTTCGTTGTG
** *
531264 AAGTTGAAATTGGCTCTGAAAAT-AAGTTTT-TTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
129 AAGTTGAAATTGAATCTG--AATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
* *
531327 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA
192 AACTTGCGTTGTCTGGAATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAAATTGAGAA
* * *
531392 GTTGTTGTTGACAGGCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGG
257 GTTGTTGTTGACAAGCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCATTGTATGG
* * *
531448 AGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGAGAAGTTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGAACTGGGAAGTTGTTTGTTGACAA
* *
531512 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCGT
66 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-CCA--ATATCCTTCGTTGT
*
531577 GGAGTTGAAAT
128 GAAGTTGAAAT
531588 CGCAGATGGC
Statistics
Matches: 407, Mismatches: 31, Indels: 21
0.89 0.07 0.05
Matches are distributed among these distances:
309 4 0.01
310 274 0.67
311 97 0.24
312 11 0.03
314 21 0.05
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (312 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGAACTGGGAAGTTGTTTGTTGACAA
CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
TGCGTTGTCTGGAATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAAATTGAGAAGTTG
TTGTTGACAAGCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCATTGTATGG
Found at i:532315 original size:67 final size:65
Alignment explanation
Indices: 532183--532576 Score: 268
Period size: 65 Copynumber: 5.8 Consensus size: 65
532173 AAGATATCTG
* * * *
532183 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAATAAATTTAAAGA-
532248 TT
64 TT
* * *
532250 TGTGTTTCAAGAGTAATTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTTAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTTAAAGAT
532315 T
65 T
* ** * * **
532316 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAAATTTGTTTTAAGGGAAA-----T-AA-ATT
* * *
532380 GACAAAACT
58 TA-AAGATT
* * * * * * * * * *
532389 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTTAAAGATT
* * * * * **
532454 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----TAAATTTA-
* *
532519 ACGAAAT
60 AAG-ATT
* *
532526 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
532577 CTGTCTCAAG
Statistics
Matches: 254, Mismatches: 55, Indels: 31
0.75 0.16 0.09
Matches are distributed among these distances:
65 84 0.33
66 9 0.04
67 26 0.10
68 31 0.12
70 3 0.01
71 3 0.01
72 57 0.22
73 41 0.16
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTTAAAGATT
Found at i:532367 original size:36 final size:36
Alignment explanation
Indices: 532315--532596 Score: 323
Period size: 36 Copynumber: 8.0 Consensus size: 36
532305 ATTTAAAGAT
* *
532315 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
532352 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
532387 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
532424 TTTGTTTCAA-AGAAAACATAT-TC-----A-A-ATAT
1 TTTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
532453 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
532489 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
532525 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
532561 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
532597 CTCTTCTAGT
Statistics
Matches: 209, Mismatches: 23, Indels: 27
0.81 0.09 0.10
Matches are distributed among these distances:
28 2 0.01
29 18 0.09
30 2 0.01
31 1 0.00
34 1 0.00
35 7 0.03
36 145 0.69
37 33 0.16
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:532425 original size:138 final size:137
Alignment explanation
Indices: 532267--532577 Score: 444
Period size: 138 Copynumber: 2.3 Consensus size: 137
532257 CAAGAGTAAT
* * * *
532267 TGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTTAAAGATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
* *
532332 TGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCC
66 TGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCC
532396 AAAAGAAAC
129 AAAAGAAAC
* * * *
532405 TGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
* * * * *
532470 TGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTCAA
66 TGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAA
*
532535 GAGAAAC
131 AAGAAAC
*
532542 TGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
532578 TGTCTCAAGA
Statistics
Matches: 153, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
137 51 0.33
138 102 0.67
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
TGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAA
AAGAAAC
Found at i:532618 original size:35 final size:36
Alignment explanation
Indices: 532458--532630 Score: 172
Period size: 36 Copynumber: 4.8 Consensus size: 36
532448 AATATTTTGT
* * **
532458 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * * * *
532494 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* *
532530 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTGC
*
532566 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * *
532600 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
532631 TCTTGTTTTA
Statistics
Matches: 121, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.04
35 23 0.19
36 92 0.76
37 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:533103 original size:18 final size:18
Alignment explanation
Indices: 533076--533111 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
533066 TGTTGAATCC
* *
533076 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
533094 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
533112 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:533540 original size:22 final size:22
Alignment explanation
Indices: 533514--533568 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
533504 TTGTGTTTGG
533514 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
533536 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
533558 TCAAAGGTTTG
1 TCAAAGGTTTG
533569 ATGGGATAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:534258 original size:34 final size:32
Alignment explanation
Indices: 534208--534273 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 32
534198 GATTTTGCTC
534208 TTTTTTTTGTTCTTGTTCTCTTT-TTCTTTGTT
1 TTTTTTTTGTTCTTGTTCT-TTTCTTCTTTGTT
* *
534240 TTTTTTTTGCTTTTTTGTTCTTTTCTTTTTTGTT
1 TTTTTTTTG--TTCTTGTTCTTTTCTTCTTTGTT
534274 CTTGATGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 9 0.31
33 3 0.10
34 17 0.59
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.80
Consensus pattern (32 bp):
TTTTTTTTGTTCTTGTTCTTTTCTTCTTTGTT
Found at i:534269 original size:15 final size:15
Alignment explanation
Indices: 534229--534276 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
534219 CTTGTTCTCT
*
534229 TTTTCTTTGTTT-TTT
1 TTTTCTTT-TTTGTTC
534244 TTTTGCTTTTTTGTTC
1 TTTT-CTTTTTTGTTC
534260 TTTTCTTTTTTGTTC
1 TTTTCTTTTTTGTTC
534275 TT
1 TT
534277 GATGGATCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 20 0.67
16 10 0.33
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTTTGTTC
Found at i:535336 original size:65 final size:67
Alignment explanation
Indices: 535255--535391 Score: 260
Period size: 67 Copynumber: 2.1 Consensus size: 67
535245 ATATGTGGAC
535255 TTTTTCTCAGATCATCTTGGCAGG-TTAGTCGT-CAACCAGCTGATTGGGCTCATTCGTTGTGAT
1 TTTTTCTCAGATCATCTTGGCAGGTTTAGTCGTACAACCAGCTGATTGGGCTCATTCGTTGTGAT
535318 AG
66 AG
535320 TTTTTCTCAGATCATCTTGGCAGGTTTAGTCGTACAACCAGCTGATTGGGCTCATTCGTTGTGAT
1 TTTTTCTCAGATCATCTTGGCAGGTTTAGTCGTACAACCAGCTGATTGGGCTCATTCGTTGTGAT
535385 AG
66 AG
535387 TTTTT
1 TTTTT
535392 TTATGATGTT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
65 24 0.34
66 8 0.11
67 38 0.54
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.39
Consensus pattern (67 bp):
TTTTTCTCAGATCATCTTGGCAGGTTTAGTCGTACAACCAGCTGATTGGGCTCATTCGTTGTGAT
AG
Found at i:538456 original size:2 final size:2
Alignment explanation
Indices: 538449--538478 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
538439 ATATTAAAGA
538449 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
538479 ATAGTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:538468 original size:13 final size:13
Alignment explanation
Indices: 538450--538475 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
538440 TATTAAAGAA
538450 TATATATATATAT
1 TATATATATATAT
538463 TATATATATATAT
1 TATATATATATAT
538476 ATAATAGTAA
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:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:538469 original size:15 final size:15
Alignment explanation
Indices: 538449--538477 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
538439 ATATTAAAGA
538449 ATATATATATATATT
1 ATATATATATATATT
538464 ATATATATATATAT
1 ATATATATATATAT
538478 AATAGTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:538559 original size:61 final size:60
Alignment explanation
Indices: 538455--538568 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 60
538445 AAGAATATAT
* * *
538455 ATATATATTATATATATATATATAATAGTAAAATATAGTAAAAATAAATGAAATAATTTA
1 ATATATATTATATATATACATATAATAATAAAATATAATAAAAATAAATGAAATAATTTA
*
538515 ATATATA-TATATATATACATATAATAATAACATGAATAATAAAAATAAATGAAA
1 ATATATATTATATATATACATATAATAATAAAAT--ATAATAAAAATAAATGAAA
538569 AATATCCATA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
59 23 0.48
60 7 0.15
61 18 0.38
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (60 bp):
ATATATATTATATATATACATATAATAATAAAATATAATAAAAATAAATGAAATAATTTA
Found at i:539003 original size:36 final size:36
Alignment explanation
Indices: 538954--539053 Score: 136
Period size: 36 Copynumber: 2.9 Consensus size: 36
538944 ATAGTATAAC
*
538954 TCTATCTTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCATATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
538991 T-TATCCTATTTTTAGGAGTTTG-ATCCT--AAAAT
1 TCTATCATATTTTTAGGAGTTTGAATCCTAGAAAAT
*
539023 TCTATCATATTTTTAGTAGTTTGAATCCTAG
1 TCTATCATATTTTTAGGAGTTTGAATCCTAG
539054 TAGACGAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
32 6 0.11
33 19 0.34
34 5 0.09
35 5 0.09
36 20 0.36
37 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (36 bp):
TCTATCATATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:540620 original size:89 final size:89
Alignment explanation
Indices: 540468--540638 Score: 290
Period size: 89 Copynumber: 1.9 Consensus size: 89
540458 CTCTTGATCC
*
540468 ATCCATCCCTGAATACAGGTGGTAGATGTATATGGAGTTAGGGCTAAAAAGTCCAAGTACTAGAA
1 ATCCATCCCTGAATACAGGTGGTAGATGAATATGGAGTTAGGGCTAAAAAGTCCAAGTACTAGAA
*
540533 GATGGAATGTTGTGTGCTGGATTT
66 GATGGAAAGTTGTGTGCTGGATTT
*
540557 ATCCAT-CCTGAATACAGGTGGTAGATGAATGATGGAGTTAGGGCTAAAAAGTCCAAGTGCTAGA
1 ATCCATCCCTGAATACAGGTGGTAGATGAAT-ATGGAGTTAGGGCTAAAAAGTCCAAGTACTAGA
*
540621 TGATGGAAAGTTGTGTGC
65 AGATGGAAAGTTGTGTGC
540639 AGATGCAAAT
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
88 23 0.30
89 54 0.70
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.27
Consensus pattern (89 bp):
ATCCATCCCTGAATACAGGTGGTAGATGAATATGGAGTTAGGGCTAAAAAGTCCAAGTACTAGAA
GATGGAAAGTTGTGTGCTGGATTT
Found at i:540900 original size:37 final size:37
Alignment explanation
Indices: 540859--540939 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
540849 TTTGTCCTGG
540859 AAACTGCACTACATTCATG-TGCTTATCCTACTCATGA
1 AAACTGCACTACATTCATGCT-CTTATCCTACTCATGA
540896 AAACTGCACTACATTCATGCTCTTATCCTACTCATGA
1 AAACTGCACTACATTCATGCTCTTATCCTACTCATGA
540933 AAACTGC
1 AAACTGC
540940 TTTCTCATGC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
37 42 0.98
38 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (37 bp):
AAACTGCACTACATTCATGCTCTTATCCTACTCATGA
Found at i:544584 original size:22 final size:22
Alignment explanation
Indices: 544543--544585 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
544533 AGGTATAATA
*
544543 AAAAAATAATATATAAAAAAGG
1 AAAAAATAATATAAAAAAAAGG
*
544565 AAAAAATAATAAAAATAAAAA
1 AAAAAATAATATAAA-AAAAA
544586 TTAATAGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (22 bp):
AAAAAATAATATAAAAAAAAGG
Found at i:544804 original size:233 final size:236
Alignment explanation
Indices: 544501--544969 Score: 794
Period size: 234 Copynumber: 2.0 Consensus size: 236
544491 TCTTGATTTT
544501 AGGAAAAGATAGAATTCCAGGTAAAGTAGAAAAGGTATAATAAAAAAATAATATATAAAAAAGGA
1 AGGAAAAGATAGAATTCCAGGTAAAGTAGAAAAGGTATAATAAAAAAATAATATATAAAAAAGGA
544566 AAAAATAAT-AAA-AATAAAAATTAATAGTAATAAATATAAAAAGGGATTTTTAAAAGTTG-TTT
66 AAAAATAATAAAATAATAAAAATTAATAGTAATAAATAT-AAAAGGGATTTTT-AAAGTTGTTTT
*
544628 TAAAATAAAAGATAAGAATTAAATAAACAAA-TAAAGAGATTGAGAT-CAGAGAAACTTATTGTG
129 TAAAAT-AAAGATAAGAATTAAATAAACAAATTAAAGAGATTGAGATAAAGAGAAACTTATTGTG
544691 AAAGCAAACCTCAGACTTCAGCTTCGCCTCAAATT-CTCGGATCA
193 AAAGC-AACCTCAGACTTCAGCTTCGCCTCAAATTCCTCGGATCA
*
544735 AGGAAAAGATAGAATTCCAGGT-AAGTAGAAAAGGTATAA-AAATAAATAAT-TATAAAAAAAGG
1 AGGAAAAGATAGAATTCCAGGTAAAGTAGAAAAGGTATAATAAAAAAATAATATAT-AAAAAAGG
*
544797 AAAAAAATAATAAAATAATAAATATTAATAGTAATAAATATAAAAGGGATTTTTAAAGTTGTTTT
65 -AAAAAATAATAAAATAATAAAAATTAATAGTAATAAATATAAAAGGGATTTTTAAAGTTGTTTT
544862 TAAAATAAAGATAAGAATTAAATAAACAAATTAAAGAGATTGAGATAAAGAGAAACTTATTGTGA
129 TAAAATAAAGATAAGAATTAAATAAACAAATTAAAGAGATTGAGATAAAGAGAAACTTATTGTGA
544927 AAGCAACCTCAGACTTCAGCTTCGCCTCAAATTCCTCGGATCA
194 AAGCAACCTCAGACTTCAGCTTCGCCTCAAATTCCTCGGATCA
544970 TCGAAATAAA
Statistics
Matches: 224, Mismatches: 3, Indels: 15
0.93 0.01 0.06
Matches are distributed among these distances:
231 3 0.01
232 18 0.08
233 58 0.26
234 91 0.41
235 54 0.24
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.25
Consensus pattern (236 bp):
AGGAAAAGATAGAATTCCAGGTAAAGTAGAAAAGGTATAATAAAAAAATAATATATAAAAAAGGA
AAAAATAATAAAATAATAAAAATTAATAGTAATAAATATAAAAGGGATTTTTAAAGTTGTTTTTA
AAATAAAGATAAGAATTAAATAAACAAATTAAAGAGATTGAGATAAAGAGAAACTTATTGTGAAA
GCAACCTCAGACTTCAGCTTCGCCTCAAATTCCTCGGATCA
Found at i:544817 original size:28 final size:28
Alignment explanation
Indices: 544763--544818 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
544753 AGGTAAGTAG
* * *
544763 AAAAGGTATAAAAATAAATAATTATAAA
1 AAAAGGTAAAAAAATAAAAAATAATAAA
544791 AAAAGG-AAAAAAATAATAAAATAATAAA
1 AAAAGGTAAAAAAATAA-AAAATAATAAA
544819 TATTAATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (28 bp):
AAAAGGTAAAAAAATAAAAAATAATAAA
Found at i:545740 original size:27 final size:30
Alignment explanation
Indices: 545704--545760 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
545694 AAATATATAT
545704 AAAAACATATAG-AACAAAAT-ATAATAAC
1 AAAAACATATAGAAACAAAATAATAATAAC
*
545732 AAAAA-ATATAGTAAACTAAATAATAATAA
1 AAAAACATATAG-AAACAAAATAATAATAA
545761 TACATCTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 6 0.24
28 5 0.20
29 7 0.28
30 7 0.28
ACGTcount: A:0.68, C:0.07, G:0.04, T:0.21
Consensus pattern (30 bp):
AAAAACATATAGAAACAAAATAATAATAAC
Found at i:549827 original size:67 final size:68
Alignment explanation
Indices: 549658--549848 Score: 226
Period size: 69 Copynumber: 2.8 Consensus size: 68
549648 TTGTCTTAAA
* * * * *
549658 AGACAGAATTCGTTTCAAGGGAAACGATCTTAAAGATATATGTTGTTTCATGAG-AAACGGCCTC
1 AGACAGAATTTGTTTCAAGGGAAACAATCTCAAAGAT-TTTG-TGTTTCAAGAGAAAACGGCCTC
549722 AAGGG
64 AAGGG
* * * * * *
549727 AGACAAAATTTTGTTTTAAGGGAAATAAACTCAAAGATTTTGTGTTTCAAGAGAAAACTGTCTCA
1 AGACAGAA-TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAAACGGCCTCA
549792 AGGG
65 AGGG
*
549796 AGAC-GAATTTGTTTCAAGGGAAACAATCTC-AAGGTTTTGTGTTTCAAGAGAAA
1 AGACAGAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAA
549849 CATTTTCAAA
Statistics
Matches: 104, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
66 22 0.21
67 20 0.19
68 12 0.12
69 27 0.26
70 23 0.22
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.29
Consensus pattern (68 bp):
AGACAGAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAAACGGCCTCAA
GGG
Found at i:549910 original size:36 final size:34
Alignment explanation
Indices: 549805--549919 Score: 148
Period size: 34 Copynumber: 3.4 Consensus size: 34
549795 GAGACGAATT
* *
549805 TGTTTCAAGGGAAACAATCTC-AAGG---TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTG
* *
549835 TGTTTCAAGAGAAACATTTTCAAATGTTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTG
549869 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG-TT-TTTTTG
549905 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
549920 TGTATCAAGG
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.25
31 3 0.04
34 29 0.40
35 2 0.03
36 21 0.29
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.39
Consensus pattern (34 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTG
Found at i:550059 original size:36 final size:36
Alignment explanation
Indices: 549959--550073 Score: 151
Period size: 36 Copynumber: 3.1 Consensus size: 36
549949 CAAGGATTGA
* *
549959 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
549996 TGTTTTAAGAA-AAACATGTCTTAAGAGAGACAAAATT
1 TGTTTCAA-AAGAAAC-TGTCTCAAGAGAGACAAAATT
*
550033 TGTTTCAAAAGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
550069 TGTTT
1 TGTTT
550074 AATGTAAAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
36 26 0.38
37 24 0.35
38 18 0.26
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (36 bp):
TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:550123 original size:30 final size:30
Alignment explanation
Indices: 550087--550145 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
550077 GTAAAACATA
*
550087 TTCAAAGATTT-TGTTTCAAGGGAAACTGTT
1 TTCAAAG-TTTATGTTTCAAGAGAAACTGTT
*
550117 TTCAAAGTTTATGTTTCAATAGAAACTGT
1 TTCAAAGTTTATGTTTCAAGAGAAACTGT
550146 CTCAAATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (30 bp):
TTCAAAGTTTATGTTTCAAGAGAAACTGTT
Found at i:550212 original size:35 final size:36
Alignment explanation
Indices: 550138--550212 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
550128 TGTTTCAATA
* **
550138 GAAACTGTCTCAAATGAGACAAAATTTGTTTCAAGG
1 GAAACTATCTCAAATGAGACAAAATTCATTTCAAGG
550174 GAAACTATCTCAAGA-GAGACAAAA-TCATTTCAAGG
1 GAAACTATCTCAA-ATGAGACAAAATTCATTTCAAGG
550209 GAAA
1 GAAA
550213 TGTTTTCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 13 0.37
36 21 0.60
37 1 0.03
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.23
Consensus pattern (36 bp):
GAAACTATCTCAAATGAGACAAAATTCATTTCAAGG
Found at i:550325 original size:99 final size:101
Alignment explanation
Indices: 550100--550377 Score: 445
Period size: 100 Copynumber: 2.8 Consensus size: 101
550090 AAAGATTTTG
* * **
550100 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAATAGAAACTGTCTCAAATGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
550164 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCA
*
550201 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTC-AGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
* *
550265 GTTTCAAGGGAAACTATCTCAAGAGAGAC-AATTTA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCA
*
550300 TTTCAAGGGAAATGCTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
550365 GTTCCAAGGGAAA
66 GTTTCAAGGGAAA
550378 TGTTTTCAAT
Statistics
Matches: 165, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
99 60 0.36
100 93 0.56
101 12 0.07
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (101 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCA
Found at i:550394 original size:165 final size:164
Alignment explanation
Indices: 550164--550534 Score: 584
Period size: 165 Copynumber: 2.2 Consensus size: 164
550154 AGACAAAATT
* * **
550164 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCAT-TTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTCAAGGGAAATGTTTTCAATGTTTA
* *
550228 TGTTTCAAGAGAAATTGTCTC-AGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAC
* *
550292 ACAATTTATTTCAAGGGAAATGCTTTCAATGTTTA
131 AAAATTAATTTCAA-GGAAATGCTTTCAATGTTTA
*
550327 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTT-CAAGGGAAATGTTTTCAATGTTT
550392 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
65 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
*
550457 CAAAATTAATTTCAAGGAAATGTTTTCAATGTTTA
130 CAAAATTAATTTCAAGGAAATGCTTTCAATGTTTA
* *
550492 TGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTTCTGTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTT-TGTT
550535 TCGAGGAAAC
Statistics
Matches: 191, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
163 33 0.17
164 2 0.01
165 95 0.50
166 57 0.30
167 4 0.02
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (164 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAC
AAAATTAATTTCAAGGAAATGCTTTCAATGTTTA
Found at i:550398 original size:66 final size:65
Alignment explanation
Indices: 550264--550443 Score: 276
Period size: 66 Copynumber: 2.8 Consensus size: 65
550254 GACAAAATTT
* * *
550264 TGTTTCAAGGGAAACTATCTCAAGAGAGAC--AATTTAT-TTCAAGGGAAATGCTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT-TGTTCAAGGGAAATGCTTTCAATGTTT
550326 A
65 A
*
550327 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTT-CAAGGGAAATGCTTTCAATGTTT
550392 A
65 A
550393 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG-TTCAAGGGAAA
550444 CTATCTCAAG
Statistics
Matches: 108, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
63 27 0.25
64 1 0.01
65 7 0.06
66 71 0.66
67 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCAAGGGAAATGCTTTCAATGTTTA
Found at i:550493 original size:99 final size:103
Alignment explanation
Indices: 550327--550553 Score: 331
Period size: 99 Copynumber: 2.2 Consensus size: 103
550317 TCAATGTTTA
* * *
550327 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGGGAAACTATCTCAA--GAGACAAAATTATGTTCCAAGGGAAATGTTTTCAATGTTT
*
550392 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT-
64 ATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTC
550430 TGTTTCAAGGGAAACTATCTCAAGAGACAAAATTAAT-TT-CAA-GGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGACAAAATT-ATGTTCCAAGGGAAATGTTTTCAATGTTTA
*
550492 TGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTTC
65 TGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTC
*
550531 TGTTTCGA-GGAAACTATCTCAAG
1 TGTTTCAAGGGAAACTATCTCAAG
550554 CGAGATAAAA
Statistics
Matches: 115, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
99 52 0.45
100 21 0.18
101 20 0.17
102 1 0.01
103 21 0.18
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.31
Consensus pattern (103 bp):
TGTTTCAAGGGAAACTATCTCAAGAGACAAAATTATGTTCCAAGGGAAATGTTTTCAATGTTTAT
GTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTC
Found at i:552069 original size:181 final size:180
Alignment explanation
Indices: 551759--552101 Score: 589
Period size: 181 Copynumber: 1.9 Consensus size: 180
551749 TTTAACTAAA
*
551759 GGTTCATCTCATCACAAAGTCTTTGGCCTGATAAAAGCAGTGGAGCAAACACCGAATTGCCAAGT
1 GGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCAAGT
* * **
551824 GTCCGAGCATGTCATGGTTTGAATGTAATCTATCATAAAGCCAGGGCTTCCGAGTTTCCTCTATA
66 GTCCCAG-ATGTCATAGTTTGAACATAATCTATCATAAAGCCAGGGCTTCCGAGTTTCCTCTATA
551889 ACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGATAAATCACTGAAG
130 ACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGATAAATCACTGAAG
*
551940 GGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGGAGCAAACACCGAATTGCCAAG
1 GGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGT-GGAGCAAACACCGAATTGCCAAG
*
552005 TGTCCCAG-TGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCTCTAT
65 TGTCCCAGATGTCATAGTTTGAACATAATCTA-TCATAAAGCCAGGGCTTCCGAGTTTCCTCTAT
552069 AACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
129 AACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
552102 CGGATTTAAT
Statistics
Matches: 153, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
180 20 0.13
181 103 0.67
182 30 0.20
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (180 bp):
GGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCAAGT
GTCCCAGATGTCATAGTTTGAACATAATCTATCATAAAGCCAGGGCTTCCGAGTTTCCTCTATAA
CCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGATAAATCACTGAAG
Found at i:556235 original size:21 final size:20
Alignment explanation
Indices: 556198--556238 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
556188 ACAAAATAAT
* *
556198 AAAAAGAATATATATAATAG
1 AAAAATAATATAAATAATAG
556218 AAAAATAATAATAAATAATAG
1 AAAAATAAT-ATAAATAATAG
556239 TAAACATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (20 bp):
AAAAATAATATAAATAATAG
Found at i:558686 original size:5 final size:5
Alignment explanation
Indices: 558676--558797 Score: 54
Period size: 5 Copynumber: 23.8 Consensus size: 5
558666 TTTTCAGAGA
* * * * *
558676 AAAAT AAAAT AAATT AAAAC AAAAT -AAAT AGAAT AAAAAT AAAGT GCTAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT --AAAAT
* * * *
558728 AATAA- AAAAA ACAAAT AAAAT -GAAT AAAAT AAATAA AAAAA AAAAT
1 AA-AAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT
* *
558774 GAAAAT AAAAT -GAAT AAACT AAAA
1 -AAAAT AAAAT AAAAT AAAAT AAAA
558798 AATAGAACGA
Statistics
Matches: 87, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
4 12 0.14
5 53 0.61
6 19 0.22
7 3 0.03
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:558714 original size:20 final size:20
Alignment explanation
Indices: 558676--558791 Score: 57
Period size: 18 Copynumber: 5.8 Consensus size: 20
558666 TTTTCAGAGA
*
558676 AAAATAAAATAAATTAAAAC
1 AAAATAAAATAAATAAAAAC
*
558696 AAAAT-AAATAGAATAAAAAT
1 AAAATAAAATA-AATAAAAAC
*
558716 AAAGTGCTAAATAATAAA-AAAAAC
1 AAA---AT-AA-AATAAATAAAAAC
*
558740 -AAATAAAATGAAT-AAAA-
1 AAAATAAAATAAATAAAAAC
* **
558757 TAAATAAAA-AAA-AAAATG
1 AAAATAAAATAAATAAAAAC
*
558775 AAAATAAAATGAATAAA
1 AAAATAAAATAAATAAA
558792 CTAAAAAATA
Statistics
Matches: 73, Mismatches: 10, Indels: 26
0.67 0.09 0.24
Matches are distributed among these distances:
17 5 0.07
18 25 0.34
19 9 0.12
20 19 0.26
23 3 0.04
24 5 0.07
25 3 0.04
26 4 0.05
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAATAAAATAAATAAAAAC
Found at i:558753 original size:9 final size:9
Alignment explanation
Indices: 558741--558791 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
558731 AAAAAAAACA
558741 AATAAAATG
1 AATAAAATG
*
558750 AATAAAATA
1 AATAAAATG
558759 AATAAAA--
1 AATAAAATG
*
558766 AAAAAAATG
1 AATAAAATG
558775 AAAATAAAATG
1 --AATAAAATG
558786 AATAAA
1 AATAAA
558792 CTAAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
7 6 0.17
9 21 0.60
11 8 0.23
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (9 bp):
AATAAAATG
Found at i:558769 original size:22 final size:21
Alignment explanation
Indices: 558724--558782 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
558714 ATAAAGTGCT
* *
558724 AAATAATAAAAAAAACAAATA
1 AAATAATAAAATAAACAAAAA
*
558745 AAATGAATAAAATAAATAAAAA
1 AAAT-AATAAAATAAACAAAAA
*
558767 AAAAAATGAAAATAAA
1 AAATAAT-AAAATAAA
558783 ATGAATAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 7 0.22
22 25 0.78
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15
Consensus pattern (21 bp):
AAATAATAAAATAAACAAAAA
Found at i:558780 original size:36 final size:34
Alignment explanation
Indices: 558723--558796 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 34
558713 AATAAAGTGC
* *
558723 TAAATAATAAAAAAAACAAATAAAATGAATAAAA
1 TAAATAAAAAAAAAAAAAAATAAAATGAATAAAA
*
558757 TAAATAAAAAAAAAAATGAAAATAAAATGAATAAAC
1 TAAATAAAAAAAAAAA--AAAATAAAATGAATAAAA
558793 TAAA
1 TAAA
558797 AAATAGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
34 15 0.43
36 20 0.57
ACGTcount: A:0.76, C:0.03, G:0.04, T:0.18
Consensus pattern (34 bp):
TAAATAAAAAAAAAAAAAAATAAAATGAATAAAA
Found at i:561859 original size:18 final size:18
Alignment explanation
Indices: 561836--561877 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
561826 ATCTAAAATA
*
561836 TCAACAGAATTAATTCTT
1 TCAACAAAATTAATTCTT
561854 TCAACAAAATTAATTCTT
1 TCAACAAAATTAATTCTT
561872 TCAACA
1 TCAACA
561878 TGATAAGGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (18 bp):
TCAACAAAATTAATTCTT
Found at i:564206 original size:18 final size:18
Alignment explanation
Indices: 564185--564227 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
564175 GTTGTTTTTA
*
564185 AAATAAAAGATAATAATT
1 AAATAAAAGAAAATAATT
564203 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
564221 AAATAAA
1 AAATAAA
564228 CAAATTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:576891 original size:22 final size:22
Alignment explanation
Indices: 576866--576921 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
576856 TATCCTCAGA
576866 TGGTATTGATACTACTATATAG
1 TGGTATTGATACTACTATATAG
576888 TGGTATTGATACTACTATATAG
1 TGGTATTGATACTACTATATAG
*
576910 TGGTATCGATAC
1 TGGTATTGATAC
576922 CCCTCTGATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (22 bp):
TGGTATTGATACTACTATATAG
Found at i:578538 original size:45 final size:45
Alignment explanation
Indices: 578483--578642 Score: 225
Period size: 44 Copynumber: 3.6 Consensus size: 45
578473 TTTGTATCAA
* *
578483 TTATCCCATAAGCTTGTAAGCTTATTTTACCAAAATACTTACCAT
1 TTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
* * *
578528 TTAACCCATAATCTCGTAAGC-TATTTTAACAATATACTTACCAT
1 TTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
* *
578572 TTGTTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA-
1 TTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
* *
578616 TTATTCCATAAGCTCGGAAGCTTATTT
1 TTATCCCATAAGCTCGTAAGCTTATTT
578643 CATGCTTACC
Statistics
Matches: 102, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
44 63 0.62
45 39 0.38
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (45 bp):
TTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
Found at i:578806 original size:40 final size:40
Alignment explanation
Indices: 578751--578904 Score: 238
Period size: 40 Copynumber: 3.9 Consensus size: 40
578741 CGTGCTATAT
* *
578751 ATAAGGTTGTGCCCACCATATACAGCGAAGTGTATTACAA
1 ATAAGGTCGTGCCCACCATATACACCGAAGTGTATTACAA
*
578791 ATAAGGTCGTGCCCACCATATACACCGAAGTGTATTACAC
1 ATAAGGTCGTGCCCACCATATACACCGAAGTGTATTACAA
* *
578831 ATAAGGTTGTGCCCACTATATACACCGAAGTGTATTACACA
1 ATAAGGTCGTGCCCACCATATACACCGAAGTGTATTACA-A
*
578872 A-AAGGGCGTGCCCACCATATACACCGAAGTGTA
1 ATAAGGTCGTGCCCACCATATACACCGAAGTGTA
578905 AACCTGCAAC
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 103 0.99
41 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (40 bp):
ATAAGGTCGTGCCCACCATATACACCGAAGTGTATTACAA
Found at i:578845 original size:80 final size:80
Alignment explanation
Indices: 578751--578904 Score: 265
Period size: 80 Copynumber: 1.9 Consensus size: 80
578741 CGTGCTATAT
* *
578751 ATAAGGTTGTGCCCACCATATACAGCGAAGTGTATTACA-AATAAGGTCGTGCCCACCATATACA
1 ATAAGGTTGTGCCCACCATATACACCGAAGTGTATTACACAA-AAGGGCGTGCCCACCATATACA
578815 CCGAAGTGTATTACAC
65 CCGAAGTGTATTACAC
*
578831 ATAAGGTTGTGCCCACTATATACACCGAAGTGTATTACACAAAAGGGCGTGCCCACCATATACAC
1 ATAAGGTTGTGCCCACCATATACACCGAAGTGTATTACACAAAAGGGCGTGCCCACCATATACAC
578896 CGAAGTGTA
66 CGAAGTGTA
578905 AACCTGCAAC
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
80 68 0.97
81 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (80 bp):
ATAAGGTTGTGCCCACCATATACACCGAAGTGTATTACACAAAAGGGCGTGCCCACCATATACAC
CGAAGTGTATTACAC
Found at i:582778 original size:6 final size:6
Alignment explanation
Indices: 582762--582876 Score: 56
Period size: 6 Copynumber: 17.8 Consensus size: 6
582752 TCTCTCATTG
*
582762 TTTTCTC TTTTTC -TTTTC -TTATC TTTTTC TATATATAT- TTTTTC TTTTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC T-T-T-T-TC TTTTTC TTTTTC
* * * * *
582812 ATTTTATT TTTGTTC ATTGTC TTTTTT TCTTTTC TTTTTC TGTTTTT TTTTTC
1 -TTTT-TC TTT-TTC TTTTTC TTTTTC T-TTTTC TTTTTC T-TTTTC TTTTTC
582865 TTGTTTC TTTTT
1 TT-TTTC TTTTT
582877 TTATAATATT
Statistics
Matches: 84, Mismatches: 12, Indels: 25
0.69 0.10 0.21
Matches are distributed among these distances:
5 10 0.12
6 35 0.42
7 32 0.38
8 4 0.05
9 2 0.02
10 1 0.01
ACGTcount: A:0.07, C:0.13, G:0.03, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:582815 original size:14 final size:13
Alignment explanation
Indices: 582799--582876 Score: 56
Period size: 13 Copynumber: 5.9 Consensus size: 13
582789 TCTATATATA
582799 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
582812 ATTTTATT-TTTGTTC
1 -TTTT-TTCTTT-TTC
* *
582827 -ATTGTCTTTTT-
1 TTTTTTCTTTTTC
582838 TTCTTTTCTTTTTC
1 TT-TTTTCTTTTTC
582852 TGTTTTT-TTTTTC
1 T-TTTTTCTTTTTC
*
582865 TTGTTTCTTTTT
1 TTTTTTCTTTTT
582877 TTATAATATT
Statistics
Matches: 51, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
12 7 0.14
13 26 0.51
14 12 0.24
15 6 0.12
ACGTcount: A:0.04, C:0.12, G:0.05, T:0.79
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:582821 original size:19 final size:18
Alignment explanation
Indices: 582762--582875 Score: 70
Period size: 19 Copynumber: 5.9 Consensus size: 18
582752 TCTCTCATTG
*
582762 TTTTCTCTTTTTC-TTT-
1 TTTTTTCTTTTTCTTTTA
* *
582778 TCTTATCTTTTTCTATATATA
1 TTTTTTCTTTTTCT-T-T-TA
582799 TTTTTTCTTTTTCATTTTA
1 TTTTTTCTTTTTC-TTTTA
* * *
582818 TTTTTGTTCATTGTCTTTTT
1 -TTTT-TTCTTTTTCTTTTA
*
582838 TTCTTTTCTTTTTCTGTTTT
1 TT-TTTTCTTTTTCT-TTTA
582858 TTTTTTCTTGTTTCTTTT
1 TTTTTTCTT-TTTCTTTT
582876 TTTATAATAT
Statistics
Matches: 78, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
16 11 0.14
18 1 0.01
19 23 0.29
20 23 0.29
21 19 0.24
22 1 0.01
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTTTCTTTTTCTTTTA
Found at i:582829 original size:15 final size:14
Alignment explanation
Indices: 582806--582878 Score: 57
Period size: 15 Copynumber: 5.4 Consensus size: 14
582796 ATATTTTTTC
*
582806 TTTTTCATTTTATT
1 TTTTTCATTTTCTT
*
582820 TTTGTTCATTGTCTT
1 TTT-TTCATTTTCTT
582835 TTTTTC-TTTTC--
1 TTTTTCATTTTCTT
582846 TTTTTC-TGTTT-TT
1 TTTTTCAT-TTTCTT
*
582859 TTTTTCTTGTTTCTT
1 TTTTTCAT-TTTCTT
582874 TTTTT
1 TTTTT
582879 ATAATATTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
11 7 0.14
12 3 0.06
13 10 0.20
14 11 0.22
15 19 0.38
ACGTcount: A:0.04, C:0.11, G:0.05, T:0.79
Consensus pattern (14 bp):
TTTTTCATTTTCTT
Found at i:582876 original size:19 final size:18
Alignment explanation
Indices: 582799--582878 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 18
582789 TCTATATATA
582799 TTTTTTCTTTTTCATTTTAT
1 TTTTTTCTTTTTC-TTTT-T
* *
582819 TTTTGTTCATTGTCTTTTT
1 TTTT-TTCTTTTTCTTTTT
582838 TTCTTTTCTTTTTCTGTTTT
1 TT-TTTTCTTTTTCT-TTTT
582858 TTTTTTCTTGTTTCTTTTT
1 TTTTTTCTT-TTTCTTTTT
582877 TT
1 TT
582879 ATAATATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
19 24 0.46
20 21 0.40
21 7 0.13
ACGTcount: A:0.04, C:0.11, G:0.05, T:0.80
Consensus pattern (18 bp):
TTTTTTCTTTTTCTTTTT
Found at i:582877 original size:14 final size:13
Alignment explanation
Indices: 582834--582877 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 13
582824 TTCATTGTCT
582834 TTTTTTCT-TTTC
1 TTTTTTCTGTTTC
*
582846 -TTTTTCTGTTTT
1 TTTTTTCTGTTTC
582858 TTTTTTCTTGTTTC
1 TTTTTTC-TGTTTC
582872 TTTTTT
1 TTTTTT
582878 TATAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.26
12 3 0.11
13 6 0.22
14 11 0.41
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (13 bp):
TTTTTTCTGTTTC
Found at i:585773 original size:44 final size:46
Alignment explanation
Indices: 585693--585877 Score: 151
Period size: 52 Copynumber: 3.9 Consensus size: 46
585683 TATCAATTAT
* * * *
585693 CCCATAAGCTTGTAAGCTTATTTTACCAAAATACTTACCATTT-AA
1 CCCATAAACTAGTAAGCTTATTTTACCAATATACTTAACATTTGAA
* * **
585738 CCCATAAACTCGTAAGC-TATTTTAACAATATACTTAACATTTGTT
1 CCCATAAACTAGTAAGCTTATTTTACCAATATACTTAACATTTGAA
* * *
585783 CCAATATACTTAGTAAGCTTATTTTACCAATATACTTAGTAAGCTTATTT-TA
1 CCCATAAAC-TAGTAAGCTTATTTTACCAATATAC-T--TAA-C--ATTTGAA
* * *
585835 CCAATATACTTAGTAAGCTTATTTTACCAATATACTTACCATT
1 CCCATAAAC-TAGTAAGCTTATTTTACCAATATACTTAACATT
585878 ATTCCATAAG
Statistics
Matches: 118, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
44 22 0.19
45 22 0.19
46 10 0.08
47 15 0.13
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
52 36 0.31
53 4 0.03
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (46 bp):
CCCATAAACTAGTAAGCTTATTTTACCAATATACTTAACATTTGAA
Found at i:585813 original size:26 final size:26
Alignment explanation
Indices: 585783--585872 Score: 180
Period size: 26 Copynumber: 3.5 Consensus size: 26
585773 AACATTTGTT
585783 CCAATATACTTAGTAAGCTTATTTTA
1 CCAATATACTTAGTAAGCTTATTTTA
585809 CCAATATACTTAGTAAGCTTATTTTA
1 CCAATATACTTAGTAAGCTTATTTTA
585835 CCAATATACTTAGTAAGCTTATTTTA
1 CCAATATACTTAGTAAGCTTATTTTA
585861 CCAATATACTTA
1 CCAATATACTTA
585873 CCATTATTCC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 64 1.00
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.41
Consensus pattern (26 bp):
CCAATATACTTAGTAAGCTTATTTTA
Found at i:586062 original size:40 final size:40
Alignment explanation
Indices: 586007--586128 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
585997 ATCGTAGTGC
*
586007 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
586047 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
586087 TACACATAAGGTCATGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
586127 TA
1 TA
586129 TAAACCTGCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:587560 original size:58 final size:58
Alignment explanation
Indices: 587476--587825 Score: 218
Period size: 59 Copynumber: 6.0 Consensus size: 58
587466 ATGGCACTTT
* *
587476 GTGTGCTAGAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGA
1 GTGTGCTA-AATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGAGCACTAA
* * *
587535 GTGTGCTAAATGATAAGGAAATCATATTGAAAT-TAAGGATTTCCAGATAGG-GCA-TATTA
1 GTGTGCTAAATGATAAGGAAATCATACTG-AGTGTATGGATTTCCAGAT-GGAGCACTA--A
* * * ** *
587594 -TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGGTTTCCAGATAAAGTACTAA
1 GTGTGCT-AAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGAGCACTAA
* * *** *
587652 GGGTGCTAAATGATAAGGAAATCATATTGAAAATATGGATTTACAGATAGG-GCA-TATTA
1 GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGAT-GGAGCACTA--A
* ** * * * **
587711 -TGTGCTAAAATGGTAACAAAATCATACT-AATGGTGTGGATTTTCTA-ATAGG-GCACTTT
1 GTGTGCT-AAATGATAAGGAAATCATACTGAGT-GTATGGA-TTTCCAGAT-GGAGCACTAA
* * * * *
587769 GTGTGCTAAAATGAAAAGGGAAGCATACTAAGTGTAT-GATTTTCCAGATAGAGCACT
1 GTGTGCT-AAATGATAAGGAAATCATACTGAGTGTATGGA-TTTCCAGATGGAGCACT
587826 GATAGTGCTA
Statistics
Matches: 223, Mismatches: 48, Indels: 40
0.72 0.15 0.13
Matches are distributed among these distances:
57 3 0.01
58 96 0.43
59 115 0.52
60 9 0.04
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (58 bp):
GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGAGCACTAA
Found at i:587683 original size:117 final size:117
Alignment explanation
Indices: 587477--587738 Score: 389
Period size: 117 Copynumber: 2.2 Consensus size: 117
587467 TGGCACTTTG
* * * ** * *
587477 TGTGCTAGAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGGTGCT
* *
587542 AAATGATAAGGAAATCATATTGAAATTAAGGATTTCCAGATAGGGCATATTA
66 AAATGATAAGGAAATCATATTGAAAATAAGGATTTACAGATAGGGCATATTA
* * *
587594 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGGTTTCCAGATAAAGTACTAAGGGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGGTGCT
*
587659 AAATGATAAGGAAATCATATTGAAAATATGGATTTACAGATAGGGCATATTA
66 AAATGATAAGGAAATCATATTGAAAATAAGGATTTACAGATAGGGCATATTA
**
587711 TGTGCTAAAATGGTAACAAAATCATACT
1 TGTGCTAAAATGGTAAGGAAATCATACT
587739 AATGGTGTGG
Statistics
Matches: 129, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 129 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.29
Consensus pattern (117 bp):
TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGGTGCT
AAATGATAAGGAAATCATATTGAAAATAAGGATTTACAGATAGGGCATATTA
Found at i:588343 original size:21 final size:21
Alignment explanation
Indices: 588284--588349 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
588274 TGCAGATATT
*
588284 ACTATAGCAGTGTATCGATGC
1 ACTATAGCAGTGTATCGATAC
* *
588305 ACTGCTAGAAGTGTATCGATAC
1 ACT-ATAGCAGTGTATCGATAC
*
588327 ACTATAGCAGTGCATCGATAC
1 ACTATAGCAGTGTATCGATAC
588348 AC
1 AC
588350 ATTTTCTTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (21 bp):
ACTATAGCAGTGTATCGATAC
Found at i:594778 original size:58 final size:60
Alignment explanation
Indices: 594652--594995 Score: 225
Period size: 59 Copynumber: 5.8 Consensus size: 60
594642 ATGACACTTT
* * ** * * *
594652 GTGTGATAGAATGATAAGGAAATCATATTGTGTGTATGGATTTCCATAT-GGAGCA-CTGA
1 GTGTGCTAAAATGATAAGGAAATCATATTGAATGTATGGATTTCCAGATAGG-GCATATTA
* * *
594711 GTGTACT-AAATGATAAGGAAATCATATTGAAAT-TATGGATTTCCATATATGGCATATTA
1 GTGTGCTAAAATGATAAGGAAATCATATTG-AATGTATGGATTTCCAGATAGGGCATATTA
* * * * * * **
594770 -TGTGCTAAAATGGTAAGGGAATCATACTGAGTGT-TTGAGTTTCCAGAGAAAGCACTA--A
1 GTGTGCTAAAATGATAAGGAAATCATATTGAATGTATGGA-TTTCCAGATAGGGCA-TATTA
* ** *
594828 GGGTGCT-AAATGATAAGGAAATCATATTGAAAATATGGATTTCTAGATAGGGCATATTA
1 GTGTGCTAAAATGATAAGGAAATCATATTGAATGTATGGATTTCCAGATAGGGCATATTA
** * *
594887 -TGTGCTAAAATGATAACAAAATCATACT-AATGGTATGGATTTTCTA-ATAGGGCACT-TT-
1 GTGTGCTAAAATGATAAGGAAATCATATTGAAT-GTATGGA-TTTCCAGATAGGGCA-TATTA
* * * *
594945 GTGTGCTAAAATGAAAAGGGAAGCATACT-AAGTGTAT-GATTTTCCAGATAG
1 GTGTGCTAAAATGATAAGGAAATCATATTGAA-TGTATGGA-TTTCCAGATAG
594996 AGCACTGATA
Statistics
Matches: 225, Mismatches: 42, Indels: 36
0.74 0.14 0.12
Matches are distributed among these distances:
57 2 0.01
58 97 0.43
59 116 0.52
60 10 0.04
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (60 bp):
GTGTGCTAAAATGATAAGGAAATCATATTGAATGTATGGATTTCCAGATAGGGCATATTA
Found at i:594954 original size:117 final size:117
Alignment explanation
Indices: 594703--594916 Score: 311
Period size: 117 Copynumber: 1.8 Consensus size: 117
594693 TTCCATATGG
* * * * *
594703 AGCACTGAGTGTACTAAATGATAAGGAAATCATATTGAAATTATGGATTTCCATATATGGCATAT
1 AGCACTAAGTGTGCTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATAT
* *** * *
594768 TATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTTTGAGTTTCCAGAGAA
66 TATGTGCTAAAATGATAACAAAATCATACTAAGTGTTGGAGTTTCCAGAGAA
* *
594820 AGCACTAAGGGTGCTAAATGATAAGGAAATCATATTGAAAATATGGATTTCTAGATAGGGCATAT
1 AGCACTAAGTGTGCTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATAT
594885 TATGTGCTAAAATGATAACAAAATCATACTAA
66 TATGTGCTAAAATGATAACAAAATCATACTAA
594917 TGGTATGGAT
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
117 85 1.00
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (117 bp):
AGCACTAAGTGTGCTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATAT
TATGTGCTAAAATGATAACAAAATCATACTAAGTGTTGGAGTTTCCAGAGAA
Found at i:598014 original size:14 final size:14
Alignment explanation
Indices: 597969--598014 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
597959 CTTTTGTGAA
597969 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
*
597985 CATTCATTTATGTT
1 CGTTCATTTATGTT
597999 CGTTCATTTATGTT
1 CGTTCATTTATGTT
598013 CG
1 CG
598015 AATTGAGGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 21 0.75
15 3 0.11
16 4 0.14
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.52
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:598338 original size:20 final size:20
Alignment explanation
Indices: 598313--598362 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
598303 CGTTCGTTTG
598313 TGTTCGTTTACATTCATTTA
1 TGTTCGTTTACATTCATTTA
*
598333 TGTTCGTTTACATTCGTTTA
1 TGTTCGTTTACATTCATTTA
598353 TGTTCGTTTA
1 TGTTCGTTTA
598363 TTATTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.56
Consensus pattern (20 bp):
TGTTCGTTTACATTCATTTA
Found at i:598363 original size:10 final size:10
Alignment explanation
Indices: 598304--598363 Score: 66
Period size: 10 Copynumber: 6.0 Consensus size: 10
598294 TATTATGTTC
*
598304 GTTCGTTTGT
1 GTTCGTTTAT
*
598314 GTTCGTTTAC
1 GTTCGTTTAT
* *
598324 ATTCATTTAT
1 GTTCGTTTAT
*
598334 GTTCGTTTAC
1 GTTCGTTTAT
*
598344 ATTCGTTTAT
1 GTTCGTTTAT
598354 GTTCGTTTAT
1 GTTCGTTTAT
598364 TATTTAAATG
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
10 39 1.00
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:598710 original size:16 final size:16
Alignment explanation
Indices: 598689--598720 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
598679 TTTTTCTACA
598689 GATGCTTTGGATGAAC
1 GATGCTTTGGATGAAC
598705 GATGCTTTGGATGAAC
1 GATGCTTTGGATGAAC
598721 AATGATTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.31, T:0.31
Consensus pattern (16 bp):
GATGCTTTGGATGAAC
Found at i:598731 original size:15 final size:16
Alignment explanation
Indices: 598690--598731 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
598680 TTTTCTACAG
* *
598690 ATGCTTTGGATGAACG
1 ATGCATTGGATGAACA
*
598706 ATGCTTTGGATGAACA
1 ATGCATTGGATGAACA
598722 ATG-ATTGGAT
1 ATGCATTGGAT
598732 TCGATGGGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.33
Consensus pattern (16 bp):
ATGCATTGGATGAACA
Found at i:599716 original size:12 final size:13
Alignment explanation
Indices: 599690--599722 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
599680 ACAGCAGTTC
599690 AAAAAGAAAACGAA
1 AAAAAG-AAACGAA
599704 AAAAAGAAA-GAA
1 AAAAAGAAACGAA
599716 AAAAAGA
1 AAAAAGA
599723 TGTTGTTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 3 0.16
14 6 0.32
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAGAAACGAA
Found at i:601174 original size:25 final size:25
Alignment explanation
Indices: 601130--601180 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
601120 TCCATTTTCA
*
601130 ACTTTAAATATTTTCTTTATT-TTT
1 ACTTCAAATATTTTCTTTATTATTT
601154 ACTTCAAATCATTTT-TATTATTATTT
1 ACTTCAAAT-ATTTTCT-TTATTATTT
601180 A
1 A
601181 AATATCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 9 0.39
25 10 0.43
26 4 0.17
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (25 bp):
ACTTCAAATATTTTCTTTATTATTT
Found at i:601190 original size:22 final size:22
Alignment explanation
Indices: 601132--601193 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
601122 CATTTTCAAC
* *
601132 TTTAAATATTTTCTTTATTTTTA
1 TTTAAATATCTT-TTTATTATTA
* *
601155 CTTCAA-ATCATTTTTATTATTA
1 TTTAAATATC-TTTTTATTATTA
601177 TTTAAATATCTTTTTAT
1 TTTAAATATCTTTTTAT
601194 CAAACCCCCC
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
22 22 0.71
23 9 0.29
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTAAATATCTTTTTATTATTA
Found at i:610284 original size:20 final size:20
Alignment explanation
Indices: 610259--610309 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
610249 AATCCTCTCT
610259 GTATCGATACTAACCATTCA
1 GTATCGATACTAACCATTCA
* * * *
610279 GTATCGATACCACCCCTTTA
1 GTATCGATACTAACCATTCA
610299 GTATCGATACT
1 GTATCGATACT
610310 CATCTCAAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (20 bp):
GTATCGATACTAACCATTCA
Found at i:621843 original size:3 final size:3
Alignment explanation
Indices: 621826--621869 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
621816 ACAAAAAACG
*
621826 ATA ATA AGA ATTA ATA ATA ATA ATA ATA ATA AT- ATAA ATA ATA A
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA A
621870 AATTATTGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 30 0.83
4 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:622728 original size:257 final size:256
Alignment explanation
Indices: 622036--623160 Score: 1393
Period size: 257 Copynumber: 4.4 Consensus size: 256
622026 AATATAACCT
* * * * *
622036 GAAGGATTTAATCATCACGCTCGAAAGAGTTACTGATGACCCAAAGGACTTACTA-ATTTTGGAA
1 GAAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCAAAGGACTTA-TATATTTGGGAA
* *
622100 ATAATTTACTGGGTAAGAAACTTTCGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTA-A
65 ATAATTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTC-AGA
* * * * ** **
622164 ATACATTAAATGAGAAACTTTGAAAATTGTTTTCTCATTTTTCGAAAATCATGTGGTAATGTCCT
129 AAACATTAAATGAGAAACTTTGGAAACTGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCCT
* *
622229 GCCCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTCCTCTAAAGACTGACAGATGACCC
194 GCCC-AAGGTCTTATAGATGGCCCAAAGG-CTTATCATCTTACTCGAAAGACTGACAGATGACCC
* * ** *
622294 GAAGGATTTAATCATCATACTTGAAAGACTTACTAATGGCCTGAAGGACTTATCTATTTGGGAAA
1 GAAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCAAAGGACTTATATATTTGGGAAA
* * * *
622359 TAATTTATTGGGTAAAAAACTTTGAAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCATAAA
66 TAATTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCAGAAA
*
622424 ACATTAAATGAGAAACTTTGGAAATCT-CTTTCACATTTTT-GAAAATCATGTGAAAACATCCTG
131 ACATTAAATGAGAAACTTTGGAAA-CTGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTG
* * * *
622487 CCCAAAGGTCTTATAGATGGCTCAAAGGTCTTATCATCTTTCTCGAAAGACTGATAGATGACAC
195 CCC-AAGGTCTTATAGATGGCCCAAAGG-CTTATCATCTTACTCGAAAGACTGACAGATGACCC
* * *
622551 GAAGGATTTAATAATCATTCTTGAAAGAC-TAGTGATGGCCCAAAGGACTTATATATTTGGGAAA
1 GAAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCAAAGGACTTATATATTTGGGAAA
* * * * *
622615 TAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTGCTTTCCAAAAATTTAATTTTTAGAAA
66 TAATTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCAGAAA
* *
622680 ACATTAAATGAGAAACTTTTGAAACTGCTTTCTCATTTTTCAAAAATCATGTG-AAACATCCTGC
131 ACATTAAATGAGAAACTTTGGAAACTGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGC
* * * * *
622744 CTTAAGGTCTTATAGACGGCCCGAAGGGCTTATCATCTTGCTTGAAAGACTGACAGATGACCC
196 C-CAAGGTCTTATAGATGGCCC-AAAGGCTTATCATCTTACTCGAAAGACTGACAGATGACCC
** *
622807 GAAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCAAAGGACTTATCTATTTGGGAAA
1 GAAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCAAAGGACTTATATATTTGGGAAA
622872 TAATTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCAGAAA
66 TAATTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCAGAAA
* * *
622937 ACATTAAATCATAAACTTTGGAAA-TCGCTTTCTCATTTTTTGAAAATCATGTGAAAAACATCCT
131 ACATTAAATGAGAAACTTTGGAAACT-GCTTTCTCATTTTTCGAAAATCATGTG-AAAACATCCT
*
623001 GCCC---G------A-A-GG-----A--CTTATCATCTTACTCGAAAGATTGACAGATGACCC
194 GCCCAAGGTCTTATAGATGGCCCAAAGGCTTATCATCTTACTCGAAAGACTGACAGATGACCC
* * * * *
623046 GAAGGATTTAATTATCATGCTTGAAAGACTTATTGATGACCCGAAGGACTTACCA-ATTTGGGAA
1 GAAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCAAAGGACTTA-TATATTTGGGAA
* * * * *
623110 ATAGTTTACTGGATAAGAAACTTTGGAAATCATTTTCTTGCTTTTGAAAAA
65 ATAATTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAA
623161 AAAATAGAAA
Statistics
Matches: 763, Mismatches: 92, Indels: 43
0.85 0.10 0.05
Matches are distributed among these distances:
239 133 0.17
247 2 0.00
248 1 0.00
249 1 0.00
255 3 0.00
256 207 0.27
257 259 0.34
258 144 0.19
259 13 0.02
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (256 bp):
GAAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCAAAGGACTTATATATTTGGGAAA
TAATTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCAGAAA
ACATTAAATGAGAAACTTTGGAAACTGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGC
CCAAGGTCTTATAGATGGCCCAAAGGCTTATCATCTTACTCGAAAGACTGACAGATGACCC
Found at i:637794 original size:21 final size:22
Alignment explanation
Indices: 637768--637809 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
637758 AGTGAAAAAA
637768 CCGGATCG-GTTTTTATCCGAT
1 CCGGATCGAGTTTTTATCCGAT
*
637789 CCGGATCGATTTTTTATCCGA
1 CCGGATCGAGTTTTTATCCGA
637810 ATTTGTGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (22 bp):
CCGGATCGAGTTTTTATCCGAT
Found at i:639604 original size:24 final size:24
Alignment explanation
Indices: 639577--639625 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
639567 AGAAATGAGG
639577 AGTAAACGATATGAAGAGAGAATA
1 AGTAAACGATATGAAGAGAGAATA
*
639601 AGTAAACGATATGAGGAGAGAATA
1 AGTAAACGATATGAAGAGAGAATA
639625 A
1 A
639626 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.27, T:0.16
Consensus pattern (24 bp):
AGTAAACGATATGAAGAGAGAATA
Found at i:648229 original size:13 final size:12
Alignment explanation
Indices: 648192--648239 Score: 55
Period size: 11 Copynumber: 4.1 Consensus size: 12
648182 CACTTTTCTA
*
648192 TTTTT-TTCTTG
1 TTTTTCTTCTTT
648203 TTTTTCTT-TTT
1 TTTTTCTTCTTT
648214 TTTTTCTTCATTT
1 TTTTTCTTC-TTT
*
648227 TTTCTCTTCTTT
1 TTTTTCTTCTTT
648239 T
1 T
648240 GTTCCCCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 15 0.47
12 6 0.19
13 11 0.34
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTTCTTCTTT
Found at i:657561 original size:162 final size:160
Alignment explanation
Indices: 657370--657691 Score: 626
Period size: 162 Copynumber: 2.0 Consensus size: 160
657360 GTTGGCGGGA
657370 CGGCAGCCCTTGAAATTTCAAATTCTGCTATAATTAAATTTTTTTTCTTTGTATTTTCTATAGAT
1 CGGCAGCCCTTGAAATTTCAAATTCTGCTATAATTAAATTTTTTTTCTTTGTATTTTCTATAGAT
657435 AATCTGTTTTTCTCCTAAAATTCTTTAAGTTCGATCCCCCTAAAATTTTTGTAAGCCCCTAGGAT
66 AATCTGTTTTTCTCCTAAAATTCTTTAAGTTCGATCCCCCTAAAATTTTTGTAAGCCCCTAGGAT
657500 AAAATTCTAGGTCCTTCCCTGATTCGTATG
131 AAAATTCTAGGTCCTTCCCTGATTCGTATG
657530 CGGCAGCCCCTTGAAAATTTCAAATTCTGCTATAATTAAATTTTTTTTCTTTGTATTTTCTATAG
1 CGGCAG-CCCTTG-AAATTTCAAATTCTGCTATAATTAAATTTTTTTTCTTTGTATTTTCTATAG
657595 ATAATCTGTTTTTCTCCTAAAATTCTTTAAGTTCGATCCCCCTAAAATTTTTGTAAGCCCCTAGG
64 ATAATCTGTTTTTCTCCTAAAATTCTTTAAGTTCGATCCCCCTAAAATTTTTGTAAGCCCCTAGG
657660 ATAAAATTCTAGGTCCTTCCCTGATTCGTATG
129 ATAAAATTCTAGGTCCTTCCCTGATTCGTATG
657692 ATCTCTATAA
Statistics
Matches: 160, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
160 6 0.04
161 6 0.04
162 148 0.93
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (160 bp):
CGGCAGCCCTTGAAATTTCAAATTCTGCTATAATTAAATTTTTTTTCTTTGTATTTTCTATAGAT
AATCTGTTTTTCTCCTAAAATTCTTTAAGTTCGATCCCCCTAAAATTTTTGTAAGCCCCTAGGAT
AAAATTCTAGGTCCTTCCCTGATTCGTATG
Found at i:661223 original size:21 final size:20
Alignment explanation
Indices: 661181--661220 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
661171 CTCGAATTTA
661181 AAATTTTATCACAAAGAGTT
1 AAATTTTATCACAAAGAGTT
661201 AAATTTTATCACAAAGAGTT
1 AAATTTTATCACAAAGAGTT
661221 TAAGTTAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
AAATTTTATCACAAAGAGTT
Found at i:662713 original size:3 final size:3
Alignment explanation
Indices: 662707--662756 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
662697 GGTAAAAAAA
662707 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
662755 TA
1 TA
662757 CATCATTGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:665272 original size:26 final size:24
Alignment explanation
Indices: 665236--665294 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
665226 AAATCGTTCA
*
665236 TTTTTCAAATAAAAGTCATAATTGTT
1 TTTTTAAAATAAAA-T-ATAATTGTT
* *
665262 TTTTTAAAATAATATTTAATTGTT
1 TTTTTAAAATAAAATATAATTGTT
*
665286 TTTCTAAAA
1 TTTTTAAAA
665295 AAATGGTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 16 0.55
25 1 0.03
26 12 0.41
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (24 bp):
TTTTTAAAATAAAATATAATTGTT
Found at i:675265 original size:29 final size:31
Alignment explanation
Indices: 675198--675271 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 31
675188 AAAATTACCC
* * *
675198 TTTTGGTCCCTAAACTTTTCTAAAGTTTATA
1 TTTTGGTCACTAAACTTTTCTAAAATTTACA
* *
675229 ATTT-GTCACAAAAC-TTTC-AAAATTTACA
1 TTTTGGTCACTAAACTTTTCTAAAATTTACA
675257 TTTTGGTCACTAAAC
1 TTTTGGTCACTAAAC
675272 AAAATTTTGG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
28 11 0.31
29 13 0.37
30 8 0.23
31 3 0.09
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (31 bp):
TTTTGGTCACTAAACTTTTCTAAAATTTACA
Found at i:676912 original size:46 final size:45
Alignment explanation
Indices: 676846--677017 Score: 274
Period size: 46 Copynumber: 3.8 Consensus size: 45
676836 GATAAAATCT
*
676846 CTTACCATTTATCCTATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
676891 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCCAAATA
1 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
676937 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
676983 CTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTTT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTT
677018 CCAGTTTATC
Statistics
Matches: 120, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
44 25 0.21
45 12 0.10
46 83 0.69
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:681117 original size:20 final size:20
Alignment explanation
Indices: 681094--681139 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
681084 CATCTCTCAT
*
681094 TTTTTTCT-CTTTTTCCTTTC
1 TTTTTTCTAATTTTTCC-TTC
*
681114 TTTTTTCTAATTTTTTCTTC
1 TTTTTTCTAATTTTTCCTTC
681134 TTTTTT
1 TTTTTT
681140 TCTGTTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTCTAATTTTTCCTTC
Found at i:681117 original size:21 final size:21
Alignment explanation
Indices: 681093--681142 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
681083 TCATCTCTCA
*
681093 TTTTTTTCT-CTTTTTCCTT-
1 TTTTTTTCTAATTTTTCCTTC
*
681112 TCTTTTTTCTAATTTTTTCTTC
1 T-TTTTTTCTAATTTTTCCTTC
681134 TTTTTTTCT
1 TTTTTTTCT
681143 GTTTCATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 8 0.31
21 16 0.62
22 1 0.04
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTTTCTAATTTTTCCTTC
Found at i:683926 original size:44 final size:45
Alignment explanation
Indices: 683804--683929 Score: 182
Period size: 46 Copynumber: 2.8 Consensus size: 45
683794 GATAAAATTT
*
683804 CTTACCATTTATCCCATAAGCTTGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
683849 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTAGCAATATA
1 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
** *
683895 CTTGTCA-TTATTCCATAAGCTCGTAAGCTTATTTT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTT
683930 CCAGTTTATC
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
44 25 0.34
45 12 0.16
46 37 0.50
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:688301 original size:16 final size:15
Alignment explanation
Indices: 688276--688322 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 15
688266 AAACATAATG
688276 AAAT-AAATAATAGTA
1 AAATAAAATAATA-TA
688291 AAATAAAAT-A-ATA
1 AAATAAAATAATATA
688304 AAATAAAATATATATA
1 AAATAAAATA-ATATA
688320 AAA
1 AAA
688323 ATATAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 11 0.39
14 1 0.04
15 6 0.21
16 10 0.36
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (15 bp):
AAATAAAATAATATA
Found at i:688305 original size:13 final size:13
Alignment explanation
Indices: 688270--688313 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
688260 AACTTAAAAC
*
688270 ATAATGAAATAAATA
1 ATAATAAAAT-AA-A
*
688285 ATAGTAAAATAAA
1 ATAATAAAATAAA
688298 ATAATAAAATAAA
1 ATAATAAAATAAA
688311 ATA
1 ATA
688314 TATATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 16 0.62
14 2 0.08
15 8 0.31
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (13 bp):
ATAATAAAATAAA
Found at i:688531 original size:2 final size:2
Alignment explanation
Indices: 688526--688576 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
688516 AAAATAATAA
*
688526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
688568 AT AT AT AT A
1 AT AT AT AT A
688577 AATAGGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:689096 original size:36 final size:36
Alignment explanation
Indices: 689056--689148 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 36
689046 ATGCTTATGG
* * *
689056 ATCCTATCTTTAGGAGTTTAATAATAGTAGAACTAT
1 ATCCTATTTTTAGGAGTTTAATAATAGCAAAACTAT
** * *
689092 ATCCTATTTTTAGGA-TTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTT-AATAATAGCAAAACTAT
689128 ATCCTATTTTTAGGAGTTTAA
1 ATCCTATTTTTAGGAGTTTAA
689149 ATCCTAGTAC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
35 3 0.06
36 42 0.88
37 3 0.06
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTAATAATAGCAAAACTAT
Found at i:690432 original size:105 final size:106
Alignment explanation
Indices: 690248--691685 Score: 2134
Period size: 106 Copynumber: 13.7 Consensus size: 106
690238 ATCCCTCTCC
* * *
690248 GAAATTGGGAAATTATTTGTTGACAACCA--GGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTC
1 GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* *
690311 TCGAGTCCAATATCCTTCTATGTGAAGTTGAAATTGGCTCT
66 TGGAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCT
*
690352 GAAATTAGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG-ACTTGCGTTGTC
1 GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
690416 TGGAGTCCAATATCCTTCGT-TGTGAAGTTGAAATTGGCTCT
66 TGGAGTCCAATATCCTTC-TCTGTGAAGTTGAAATTGGCTCT
* * * *
690457 GAAATTGAGAA-TTGTTTGTTGACAACCAGCGGTTCCTTCGTCGTAAAGTTGAACTTGCATTGTC
1 GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* *
690521 TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTAT
66 TGGAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCT
* * * *
690562 GAAATTGGGAAGTTCTTT-ATGATAACCA-CGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTC
1 GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* *
690625 TTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
66 TGGAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCT
* *
690666 GAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTC
1 GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
690731 TGGAGTCCAATATCCTTCGTC-GTGAAGTTGAAATTGGCTCT
66 TGGAGTCCAATATCCTTC-TCTGTGAAGTTGAAATTGGCTCT
* ** *
690772 GAAA-TGAGAAGTTGTTTGTTGACAACCAGTAGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTC
1 GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
690836 TGGAGTCCAATATCCTTCGT-TGTGAAGTTGAAATTGGCTCC
66 TGGAGTCCAATATCCTTC-TCTGTGAAGTTGAAATTGGCTCT
* *
690877 GAAATTGGGAAATTGTTTGTTAACAACCAGCGGTCCCTTCGTCGTGAAG-TGAACTTGCGTTGTC
1 GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* * *
690941 TGGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCC
66 TGGAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCT
* ** *
690982 GAAATTGGGAAATTAATTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTC
1 GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* *
691047 TCGAGTCCAATATCCTTCTATGTGAAGTTGAAATTGGCTCT
66 TGGAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCT
*
691088 GAAATTAGGAAGTTGTTTGTTGAC-ACCAGCGGTCCC-TCGTCGTGAAGTTGAACTTGCGTTGTC
1 GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
691151 TGGAGTCCAATATCCTTCGT-TGTGAAGTTGAAATTGGCTCT
66 TGGAGTCCAATATCCTTC-TCTGTGAAGTTGAAATTGGCTCT
* * * *
691192 GAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTTCCTTCGTCGTAAAGTTGAACTTGCATTGTC
1 GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* *
691257 TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTAT
66 TGGAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCT
* * * *
691298 G-AATTGGGAAGTTCTTTATTGATAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTC
1 GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* *
691362 TTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
66 TGGAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCT
* * *
691403 GAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTC
1 GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
691468 TGGAGTCCAATATCCTTCGT-TGTGAAGTTGAAAATGGCTCT
66 TGGAGTCCAATATCCTTC-TCTGTGAAGTTGAAATTGGCTCT
* * * *
691509 GAAATTGAGAAGTTGTTTGTTGAGAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGTGTTGTC
1 GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
691574 TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
66 TGGAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCT
* * ** * *
691615 GAATTTGGGAAGTTGTTTGTTGACAACCAACCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
1 GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
691680 TCGAGT
66 TGGAGT
691686 GGCACGATAT
Statistics
Matches: 1212, Mismatches: 102, Indels: 38
0.90 0.08 0.03
Matches are distributed among these distances:
104 236 0.19
105 448 0.37
106 527 0.43
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCT
Found at i:691269 original size:526 final size:525
Alignment explanation
Indices: 690263--691685 Score: 2205
Period size: 526 Copynumber: 2.7 Consensus size: 525
690253 TGGGAAATTA
*
690263 TTTGTTGACAACCAGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTCGAGTCCAATATCCTT
1 TTTGTTGACAACCAGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTT
* *
690328 C-TATGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTC
66 CGT-TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTC
690392 GTCGTGAAGTTG-ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
130 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
690456 TGAAATTGAG-AATTGTTTGTTGACAACCAGCGGTTCCTTCGTCGTAAAGTTGAACTTGCA-TTG
195 TGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG-AGTTG
* * *
690519 TCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTCTTT-ATG
259 TCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTG
* * *
690583 ATAACCACGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGT
324 A-CACCACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGT
* *
690648 GAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGA
388 GAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTAA
** *
690713 AGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCG-TCGTGAAGTTGAAATTGGCTCTGAAAT
453 AGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTATGAAAT
*
690777 GAGAAGTTG
517 GAGAAGTTC
* *
690786 TTTGTTGACAACCAGTAGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
1 TTTGTTGACAACCAG--GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCC
* *
690851 TTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTAACAACCAGCGGTCCCTT
64 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTT
* *
690916 CGTCGTGAAG-TGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCT
129 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* * **
690980 CCGAAATTGGGAAATTAATTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTG
194 CTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTG
* ** *
691045 TCTCGAGTCCAATATCCTTCTATGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTGTTG
259 TCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTG
* *
691110 ACACCAGCGGTCCC-TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
324 ACACCA-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGT
* *
691174 GAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTTCCTTCGTCGTAA
388 GAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTAA
*
691239 AGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAATTG
453 AGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATG
*
691304 GGAAGTTC
518 AGAAGTTC
* * * *
691312 TTTATTGATAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCC
1 TTTGTTGACAACCA--GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCC
* *
691377 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTT
64 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTT
* *
691442 CGTCGTGAAGTTGAACTTGAGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAATGGCT
129 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* * * *
691507 CTGAAATTGAGAAGTTGTTTGTTGAGAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGTGTTG
194 CTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTG
*
691572 TCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTG
259 TCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTG
** * *
691637 ACAACCAACCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
324 AC-ACC-ACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGT
691686 GGCACGATAT
Statistics
Matches: 818, Mismatches: 67, Indels: 24
0.90 0.07 0.03
Matches are distributed among these distances:
523 15 0.02
524 2 0.00
525 173 0.21
526 408 0.50
527 180 0.22
528 9 0.01
529 31 0.04
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (525 bp):
TTTGTTGACAACCAGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTT
CGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCG
TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
GAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTC
TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAC
ACCACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTAAAGT
TGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATGAGA
AGTTC
Found at i:692637 original size:22 final size:22
Alignment explanation
Indices: 692611--692663 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
692601 GTGTTTGGTC
692611 AAAGGTTTGGCATTTGATGCTA
1 AAAGGTTTGGCATTTGATGCTA
*
692633 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTA
692655 AAAGGTTTG
1 AAAGGTTTG
692664 ATGGGTAGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.09, G:0.28, T:0.36
Consensus pattern (22 bp):
AAAGGTTTGGCATTTGATGCTA
Found at i:693290 original size:15 final size:15
Alignment explanation
Indices: 693278--693329 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
693268 TTATTTTTTA
693278 TTTTTGTTC-TTT-T
1 TTTTTGTTCTTTTCT
693291 TTTTTGTT-TTCTTCT
1 TTTTTGTTCTT-TTCT
693306 TTTTTGCTTCTTTTCT
1 TTTTTG-TTCTTTTCT
693322 TTTTTGTT
1 TTTTTGTT
693330 TTTGCCCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
13 9 0.26
14 2 0.06
15 9 0.26
16 12 0.35
17 2 0.06
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.81
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Found at i:693292 original size:18 final size:18
Alignment explanation
Indices: 693279--693333 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
693269 TATTTTTTAT
*
693279 TTTTGTTCTTTTTTTTTG
1 TTTTCTTCTTTTTTTTTG
* *
693297 TTTTCTTCTTTTTTGCTTC
1 TTTTCTTCTTTTTT-TTTG
693316 TTTTCTT-TTTTGTTTTTG
1 TTTTCTTCTTTT-TTTTTG
693334 CCCTTTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 19 0.63
19 11 0.37
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.80
Consensus pattern (18 bp):
TTTTCTTCTTTTTTTTTG
Found at i:697095 original size:12 final size:13
Alignment explanation
Indices: 697078--697106 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
697068 TTTATTTGCA
697078 AAAATTAAAA-TT
1 AAAATTAAAATTT
697090 AAAATTAAAATTT
1 AAAATTAAAATTT
697103 AAAA
1 AAAA
697107 AACCGATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:697446 original size:42 final size:42
Alignment explanation
Indices: 697385--697495 Score: 159
Period size: 42 Copynumber: 2.6 Consensus size: 42
697375 GGGAGAAGGC
697385 AAAGCCATGGAATTTAATAATTAAAGCACTATGGAATAAGAA
1 AAAGCCATGGAATTTAATAATTAAAGCACTATGGAATAAGAA
* * * * * *
697427 AAAGCCATGAAATTCAATAATTAAAGTATTATGGAATAATAC
1 AAAGCCATGGAATTTAATAATTAAAGCACTATGGAATAAGAA
*
697469 AAAGCCATGGACTTTAATAATTAAAGC
1 AAAGCCATGGAATTTAATAATTAAAGC
697496 TTTATAATAG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (42 bp):
AAAGCCATGGAATTTAATAATTAAAGCACTATGGAATAAGAA
Found at i:700015 original size:39 final size:37
Alignment explanation
Indices: 699972--700054 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
699962 GAGCAAGATG
699972 AATTTTTGTCTTTAAG-AAAACAAATCTCAAGTAAGAAAA
1 AATTTTTGTC--TAAGAAAAAC-AATCTCAAGTAAGAAAA
* * *
700011 AATTTGTGTCTAAGAAAAACAATCTCAAGTGAGATAA
1 AATTTTTGTCTAAGAAAAACAATCTCAAGTAAGAAAA
*
700048 GATTTTT
1 AATTTTT
700055 TTTACTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
37 24 0.63
38 5 0.13
39 9 0.24
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.33
Consensus pattern (37 bp):
AATTTTTGTCTAAGAAAAACAATCTCAAGTAAGAAAA
Found at i:700419 original size:116 final size:115
Alignment explanation
Indices: 700239--700539 Score: 361
Period size: 116 Copynumber: 2.6 Consensus size: 115
700229 ATTGAAAAAG
** * * * * * * **
700239 TTCTCATTATAAACTTCTTATCCATTATTGGACGAGTTTTTCTCATTATGAACCCATCTGTTGGA
1 TTCTCATTAGGAACTTCTTCTCC-CTATCGGACGAGTTCTTCTCATTATGAATCCTTCCATTGGA
* * * *
700304 AAT-TCTAAACGACCTTCTTCTGTGATGGACGTGTCAAAGTTGAACAAGTTC
65 AATGT-TAAACCACCTCCTTCTGTGATGGACGAGTCAAAGATGAACAAGTTC
* *
700355 TTCTTATTAGGAACTTCTTCTCCCTAATCGGACGAGTTCTTCTCATTTTGAATCCTTCCATTGGA
1 TTCTCATTAGGAACTTCTTCTCCCT-ATCGGACGAGTTCTTCTCATTATGAATCCTTCCATTGGA
* * *
700420 AATGTTGATCCACCTCCTTCTGTGATGGACGAGTCAAGGATGAACAAGTTC
65 AATGTTAAACCACCTCCTTCTGTGATGGACGAGTCAAAGATGAACAAGTTC
* * *
700471 TTCTCATTAGGAACTTTTTCTCCCGTATCGGATGAGTTGTTCTCATTATGAATCCTTCCATTGGA
1 TTCTCATTAGGAACTTCTTCTCCC-TATCGGACGAGTTCTTCTCATTATGAATCCTTCCATTGGA
700536 AATG
65 AATG
700540 ATTGGTCTAT
Statistics
Matches: 158, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
115 1 0.01
116 155 0.98
117 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (115 bp):
TTCTCATTAGGAACTTCTTCTCCCTATCGGACGAGTTCTTCTCATTATGAATCCTTCCATTGGAA
ATGTTAAACCACCTCCTTCTGTGATGGACGAGTCAAAGATGAACAAGTTC
Found at i:701422 original size:20 final size:20
Alignment explanation
Indices: 701397--701442 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
701387 ACCTGGACCG
*
701397 TTGATCGTTGACCATTGACT
1 TTGATCGTTGACCATTAACT
* *
701417 TTGATCGTTGATCGTTAACT
1 TTGATCGTTGACCATTAACT
701437 TTGATC
1 TTGATC
701443 TTTTACTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (20 bp):
TTGATCGTTGACCATTAACT
Found at i:702053 original size:29 final size:29
Alignment explanation
Indices: 701985--702063 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
701975 ATTCATGTAT
*
701985 TCCTGATTCTGCATTAAGGATTATATCCCCA
1 TCCTGATTCTGCA-T-AGGATCATATCCCCA
* * *
702016 TCGT-ATTCTACATAGGATCATATTCCCA
1 TCCTGATTCTGCATAGGATCATATCCCCA
*
702044 TCCTGATTCTGCATGGGATC
1 TCCTGATTCTGCATAGGATC
702064 TTCTATGGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 16 0.40
29 14 0.35
30 7 0.17
31 3 0.08
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.35
Consensus pattern (29 bp):
TCCTGATTCTGCATAGGATCATATCCCCA
Found at i:703668 original size:17 final size:17
Alignment explanation
Indices: 703628--703669 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
703618 GGTCTAAAGA
703628 TTGAAGGTTTGAAAGTC
1 TTGAAGGTTTGAAAGTC
* * *
703645 TTAAAGGTTTGAAGGTT
1 TTGAAGGTTTGAAAGTC
703662 TTGAAGGT
1 TTGAAGGT
703670 CGTGCATTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.02, G:0.31, T:0.38
Consensus pattern (17 bp):
TTGAAGGTTTGAAAGTC
Found at i:706068 original size:6 final size:6
Alignment explanation
Indices: 706054--706102 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
706044 GACACGTATT
* * **
706054 ACCACG ACCATG ACCACG ACCTCG ACCTTG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
706102 A
1 A
706103 GCCGAGCCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.31, C:0.45, G:0.16, T:0.08
Consensus pattern (6 bp):
ACCACG
Found at i:706085 original size:18 final size:18
Alignment explanation
Indices: 706054--706099 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
706044 GACACGTATT
706054 ACCACGACCATGACCACG
1 ACCACGACCATGACCACG
* *
706072 ACCTCGACCTTGACCACG
1 ACCACGACCATGACCACG
706090 ACCACGACCA
1 ACCACGACCA
706100 CGAGCCGAGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.46, G:0.15, T:0.09
Consensus pattern (18 bp):
ACCACGACCATGACCACG
Found at i:713646 original size:6 final size:6
Alignment explanation
Indices: 713635--713665 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
713625 TCCATTGCTC
713635 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
713666 GCCGAGCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:713673 original size:5 final size:5
Alignment explanation
Indices: 713663--713701 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
713653 ACCACGACCA
* * *
713663 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
713702 ATGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:721564 original size:21 final size:22
Alignment explanation
Indices: 721540--721581 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
721530 AGTGAAAAAA
*
721540 CCGGATTG-GTTTTTATCCGAT
1 CCGGATCGAGTTTTTATCCGAT
*
721561 CCGGATCGATTTTTTATCCGA
1 CCGGATCGAGTTTTTATCCGA
721582 CTTTGTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.40
Consensus pattern (22 bp):
CCGGATCGAGTTTTTATCCGAT
Found at i:723386 original size:24 final size:24
Alignment explanation
Indices: 723340--723388 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
723330 AGAAAAGAGG
723340 AGTAAACGATATGAAGAGAGAATA
1 AGTAAACGATATGAAGAGAGAATA
*
723364 AGTAAACGATATGAATAGAGAATA
1 AGTAAACGATATGAAGAGAGAATA
723388 A
1 A
723389 TTTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.04, G:0.22, T:0.18
Consensus pattern (24 bp):
AGTAAACGATATGAAGAGAGAATA
Found at i:725714 original size:17 final size:18
Alignment explanation
Indices: 725692--725725 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
725682 CCAATTTTGT
*
725692 TATCGATAC-CAAGGGTG
1 TATCGACACTCAAGGGTG
725709 TATCGACACTCAAGGGT
1 TATCGACACTCAAGGGT
725726 AAGTATTGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (18 bp):
TATCGACACTCAAGGGTG
Found at i:726587 original size:146 final size:148
Alignment explanation
Indices: 726322--726615 Score: 574
Period size: 146 Copynumber: 2.0 Consensus size: 148
726312 TTTAGAGAGG
726322 GCCTCAATATTGACAATCACACCCAGTTGGTAGCCAATCCCCTGCGAGTTGTGAGAACCAGGGTG
1 GCCTCAATATTGACAATCACACCCAGTTGGTAGCCAATCCCCTGCGAGTTGTGAGAACCAGGGTG
726387 TTGACCAACTTCGTAGGGCATAATCAAAGAACATCAAAGCTGGATAGGACACATCACACTTTAGC
66 TTGACCAACTTCGTAGGGCATAATCAAAGAACATCAAAGCTGGATAGGACACATCACACTTTAGC
726452 CAAGA-GGCTAGGGATTT
131 CAAGAGGGCTAGGGATTT
726469 GCCTCAATATTGACAATCACACCCAGTTGGTAGCCAATCCCCTGCGAGTTGTGAG-ACCAGGGTG
1 GCCTCAATATTGACAATCACACCCAGTTGGTAGCCAATCCCCTGCGAGTTGTGAGAACCAGGGTG
726533 TTGACCAACTTCGTAGGGCATAATCAAAGAACATCAAAGCTGGATAGGACACATCACACTTTAGC
66 TTGACCAACTTCGTAGGGCATAATCAAAGAACATCAAAGCTGGATAGGACACATCACACTTTAGC
726598 CAAGAGGGCTAGGGATTT
131 CAAGAGGGCTAGGGATTT
726616 TCATGGATAT
Statistics
Matches: 146, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
146 79 0.54
147 67 0.46
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (148 bp):
GCCTCAATATTGACAATCACACCCAGTTGGTAGCCAATCCCCTGCGAGTTGTGAGAACCAGGGTG
TTGACCAACTTCGTAGGGCATAATCAAAGAACATCAAAGCTGGATAGGACACATCACACTTTAGC
CAAGAGGGCTAGGGATTT
Found at i:732008 original size:16 final size:16
Alignment explanation
Indices: 731978--732008 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
731968 CCAAAGTCAA
*
731978 TATTTGATTTGAAAAC
1 TATTTGATTTAAAAAC
731994 TATTTGATTTAAAAA
1 TATTTGATTTAAAAA
732009 AAATAAGCGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (16 bp):
TATTTGATTTAAAAAC
Found at i:735396 original size:21 final size:21
Alignment explanation
Indices: 735367--735406 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
735357 CTTTAGACTT
* *
735367 AGAAAGAATCGAAAGTAAATC
1 AGAAAGAATAGAAAATAAATC
*
735388 AGAATGAATAGAAAATAAA
1 AGAAAGAATAGAAAATAAA
735407 GTTTCCAACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.05, G:0.17, T:0.15
Consensus pattern (21 bp):
AGAAAGAATAGAAAATAAATC
Found at i:743422 original size:21 final size:20
Alignment explanation
Indices: 743394--743432 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
743384 CACTGCAGGA
*
743394 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
743414 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
743433 GACTTTTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:749632 original size:104 final size:103
Alignment explanation
Indices: 749454--749662 Score: 393
Period size: 104 Copynumber: 2.0 Consensus size: 103
749444 TATTTTTAAA
749454 TTTTTTTCATACTATTTGCATTTAGTTTCATGTAGTTTTATTTTTCATGCATTGAGGATAATGCA
1 TTTTTTTCATACTATTTGCATTTAGTTTCATGTAGTTTTATTTTTCATGCATTGAGGATAATGCA
749519 TCCCTTAAGTTTGGGGAGGTATTGC-TCTCACACTTTG
66 TCCCTTAAGTTTGGGGAGGTATTGCGTCTCACACTTTG
749556 TTTTTTTCATACTATATTTGCATTTAGTTTCATGTAGTTTTATTTTTCATGCATTGAGGATAATG
1 TTTTTTTCATAC--TATTTGCATTTAGTTTCATGTAGTTTTATTTTTCATGCATTGAGGATAATG
749621 CATCCCTTAAGTTTGGGGAGGTATTGCGTCTCACACTTTG
64 CATCCCTTAAGTTTGGGGAGGTATTGCGTCTCACACTTTG
749661 TT
1 TT
749663 AATAGTAATT
Statistics
Matches: 104, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
102 12 0.12
104 78 0.75
105 14 0.13
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (103 bp):
TTTTTTTCATACTATTTGCATTTAGTTTCATGTAGTTTTATTTTTCATGCATTGAGGATAATGCA
TCCCTTAAGTTTGGGGAGGTATTGCGTCTCACACTTTG
Found at i:752546 original size:13 final size:13
Alignment explanation
Indices: 752528--752558 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
752518 TGAAACCTCT
752528 TAACTTCACTATC
1 TAACTTCACTATC
752541 TAACTTCACTATC
1 TAACTTCACTATC
752554 TAACT
1 TAACT
752559 CAGACACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (13 bp):
TAACTTCACTATC
Found at i:757787 original size:23 final size:25
Alignment explanation
Indices: 757756--757802 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
757746 GGGATTAAAA
* *
757756 GTAAGAAATTTAGGTGAAA-ATGTG
1 GTAAGAAATTGAAGTGAAATATGTG
757780 GTAA-AAATTGAAGTGAAATATGT
1 GTAAGAAATTGAAGTGAAATATGT
757803 AAAACTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.30
Consensus pattern (25 bp):
GTAAGAAATTGAAGTGAAATATGTG
Found at i:781444 original size:17 final size:17
Alignment explanation
Indices: 781422--781460 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
781412 CTTCATGATT
*
781422 GGGTTGGGCCTTCTTTG
1 GGGTTGGGCCTTCTTTA
781439 GGGTTGGGCCTTCTTTA
1 GGGTTGGGCCTTCTTTA
781456 GGGTT
1 GGGTT
781461 CTACCAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.03, C:0.15, G:0.41, T:0.41
Consensus pattern (17 bp):
GGGTTGGGCCTTCTTTA
Found at i:783183 original size:21 final size:21
Alignment explanation
Indices: 783158--783198 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
783148 CATCAAGGTC
* * *
783158 TTTGTTGAGGCCATGAATTCT
1 TTTGTCGAGGACATAAATTCT
783179 TTTGTCGAGGACATAAATTC
1 TTTGTCGAGGACATAAATTC
783199 GTGCAATGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (21 bp):
TTTGTCGAGGACATAAATTCT
Found at i:792058 original size:21 final size:21
Alignment explanation
Indices: 792032--792072 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
792022 TATTGTTTCA
*
792032 TCTAATGGAATTTCCGTTGAG
1 TCTAATGGAATTTCCATTGAG
792053 TCTAATGGAATTTCCATTGA
1 TCTAATGGAATTTCCATTGA
792073 TAGAGCATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (21 bp):
TCTAATGGAATTTCCATTGAG
Found at i:798577 original size:36 final size:35
Alignment explanation
Indices: 798530--798667 Score: 195
Period size: 36 Copynumber: 3.9 Consensus size: 35
798520 TGAATAAGAA
798530 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTC-AAGT
* * *
798566 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGAA
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAG-T
* *
798602 GAACGAAAGGAAGCACCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT
* *
798637 GAACGGAAGGAAGCGTCAGCACTTTCGATTC
1 GAACGAAAGGAAGCATCAGCACTTTCGATTC
798668 GGTTGTTCAT
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
35 30 0.33
36 61 0.67
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.18
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT
Done.