Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004096.1 Hibiscus syriacus cultivar Beakdansim tig00008957_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: 961865
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:179187 original size:191 final size:196
Alignment explanation
Indices: 178512--179839 Score: 2083
Period size: 190 Copynumber: 6.9 Consensus size: 196
178502 TTTAAATTAG
178512 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
178577 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTAGGATC
66 TTGTACCGGTTAGATTGAAAAATTACA-ATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
*
178642 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGACC-A
130 GACAC-TTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
178706 AAA
194 AAA
*
178709 -ATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
178773 -T-TACCGGTTAGATTGAAAAATTACATATTACA-TATACTTTTGGGTTCGATGATTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACA-ATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
*
178835 GACACTTTT-TATATGGATCGACACTTTATGGGTGCACCCTG-TTT-CATTCATTC-GGACCAAA
130 GACACTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAA
178896 AA
195 AA
*
178898 TATCGACACAAACTAAAACGTGTCGACACA-TATTTAGACATATTCTCTCAT-AAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
178961 TTGTACCGGTTAGATTGAAAAATTAC-ATATACATTATACTTTTGGGTTCGATGA-TTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACAAT-TACATTATACTTTTGGGTTCGATGATTTTGGGATC
179024 GACAC-TTT-TATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAA
130 GACACTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAA
179087 AA
195 AA
179089 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
179154 TTGTATCGGTTAGATTG-AAAATTAC-ATTACATTATAC-TTTGGGTTCGATGATTTTGGGATCG
66 TTGTACCGGTTAGATTGAAAAATTACAATTACATTATACTTTTGGGTTCGATGATTTTGGGATCG
*
179216 ACACTTTTATATATGGATCGACAC-TT-TGGTTGCACCCTGTTTTCCA-TCATTCTGGAACAAAA
131 ACACTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAA
179278 A
196 A
* *
179279 TATCGACACAAACT--AAATTAGTCGACACA-TATTTAGACATA-T-TCTCATAAAA-CGGTAAA
1 TATCGACACAAACTAAAAAGT-GTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
179338 CTTGTA-CGGTTAGATTGAAAAATTACATATTACA-T-TACTTTTGGGTTCGAT-ATTTTGGGAT
65 CTTGTACCGGTTAGATTGAAAAATTACA-ATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * * *
179399 CAACAC--TGATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGAACCAA
129 CGACACTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
179462 AAA
194 AAA
* * *
179465 TATCGACACCAACTAAAAAGTGTCGACACGTTATTTAGACATATTCTCTCATAAAACCGGTAAAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
179530 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACA-ATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
* * *
179595 GAAACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTTCCATTCATTCTGGAACAA
130 GACAC-TTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
179660 AAA
194 AAA
* * *
179663 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTAAA
1 TATCGACACAAACTAAA-AAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
179728 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
65 CTTGTACCGGTTAGATTGAAAAATTACA-ATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
179793 TTGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
128 TCGACAC-TTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
179840 GGCCATATTG
Statistics
Matches: 1060, Mismatches: 34, Indels: 71
0.91 0.03 0.06
Matches are distributed among these distances:
183 17 0.02
184 13 0.01
185 57 0.05
186 51 0.05
187 15 0.01
188 85 0.08
189 66 0.06
190 136 0.13
191 128 0.12
192 68 0.06
193 78 0.07
194 47 0.04
195 14 0.01
196 63 0.06
198 71 0.07
199 91 0.09
200 60 0.06
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (196 bp):
TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
TTGTACCGGTTAGATTGAAAAATTACAATTACATTATACTTTTGGGTTCGATGATTTTGGGATCG
ACACTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAA
A
Found at i:179491 original size:376 final size:392
Alignment explanation
Indices: 178512--179839 Score: 2119
Period size: 376 Copynumber: 3.4 Consensus size: 392
178502 TTTAAATTAG
* *
178512 TATCGACACAAACTAAA-AAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAATTAG-GTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
*
178576 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTAGGAT
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
178641 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGACC-
130 CGACAC--TTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGACCA
178705 AAAA-ATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
193 AAAATATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
178769 ATAC-T-TACCGGTTAGATTGAAAAATTACATATTACA-TATACTTTTGGGTTCGATGATTTTGG
258 ATACTTGTACCGGTTAGATTGAAAAATTACA-ATTACATTATACTTTTGGGTTCGATGATTTTGG
* *
178831 GATCGACACTTTT-TATATGGATCGACACTTTATGGGTGCACCCTG-TTT-CATTCATTC-GGAC
322 GATCGACACTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAA
178892 CAAAAA
387 CAAAAA
*
178898 TATCGACACAAACTAAA--ACGTGTCGACACA-TATTTAGACATATTCTCTCAT-AAACCGGTAT
1 TATCGACACAAACTAAATTA-G-GTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAA
178959 ACTTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTCGATGA-TTTGGGA
64 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
*
179022 TCGACACTTT-TATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
129 TCGACACTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGACCAA
*
179086 AAATATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
194 AAATATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
*
179151 TACTTGTATCGGTTAGATTG-AAAATTAC-ATTACATTATAC-TTTGGGTTCGATGATTTTGGGA
259 TACTTGTACCGGTTAGATTGAAAAATTACAATTACATTATACTTTTGGGTTCGATGATTTTGGGA
179213 TCGACACTTTTATATATGGATCGACAC-TT-TGGTTGCACCCTGTTTTCCA-TCATTCTGGAACA
324 TCGACACTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
179275 AAAA
389 AAAA
179279 TATCGACACAAACTAAATTA-GTCGACACA-TATTTAGACATA-T-TCTCATAAAA-CGGTAAAC
1 TATCGACACAAACTAAATTAGGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAAC
179339 TTGTA-CGGTTAGATTGAAAAATTACATATTACA-T-TACTTTTGGGTTCGAT-ATTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
* * *
179400 AACAC-TGATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGAACCAAAA
131 GACACTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGACCAAAA
* *
179464 ATATCGACACCAACTAAAAAGTGTCGACACGTTATTTAGACATATTCTCTCATAAAACCGGTAAA
196 ATATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
179529 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
261 CTTGTACCGGTTAGATTGAAAAATTACA-ATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
179594 CGAAACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTTCCATTCATTCTGGAACA
325 CGACAC-TTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
179659 AAAA
389 AAAA
*
179663 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTAAA
1 TATCGACACAAACTAAATTAG-GTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
* *
179728 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
* *
179793 TTGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
129 TCGACAC--TTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
179840 GGCCATATTG
Statistics
Matches: 879, Mismatches: 25, Indels: 64
0.91 0.03 0.07
Matches are distributed among these distances:
375 2 0.00
376 162 0.18
377 32 0.04
378 22 0.03
379 79 0.09
380 105 0.12
381 131 0.15
382 24 0.03
383 58 0.07
384 78 0.09
385 22 0.03
386 37 0.04
387 12 0.01
388 1 0.00
389 10 0.01
390 12 0.01
391 28 0.03
392 1 0.00
393 9 0.01
394 6 0.01
395 13 0.01
398 35 0.04
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (392 bp):
TATCGACACAAACTAAATTAGGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAAC
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGACCAAAA
ATATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACAATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAAA
AA
Found at i:179981 original size:18 final size:19
Alignment explanation
Indices: 179958--180001 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
179948 TTATATTCAC
179958 ATACAAAA-TATAAATCGT
1 ATACAAAATTATAAATCGT
*
179976 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
179995 ATACAAA
1 ATACAAA
180002 TTAACCCTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:181810 original size:30 final size:31
Alignment explanation
Indices: 181767--181826 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
181757 CATCTTAATA
181767 TCACCCCTTAACACCCCAACTTCTTTCACCCT
1 TCACCCC-TAACACCCCAACTTCTTTCACCCT
* *
181799 TCACCCC-AACACCTCTACTTCTTTCACC
1 TCACCCCTAACACCCCAACTTCTTTCACC
181827 ACTCCATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 19 0.73
32 7 0.27
ACGTcount: A:0.22, C:0.50, G:0.00, T:0.28
Consensus pattern (31 bp):
TCACCCCTAACACCCCAACTTCTTTCACCCT
Found at i:181889 original size:20 final size:21
Alignment explanation
Indices: 181864--181904 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
181854 CCCTTATGCC
181864 CTCAAGTGTCTC-TCGACTCT
1 CTCAAGTGTCTCTTCGACTCT
*
181884 CTCAAGTTTCTCTTCGACTCT
1 CTCAAGTGTCTCTTCGACTCT
181905 TGATTGTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.15, C:0.34, G:0.12, T:0.39
Consensus pattern (21 bp):
CTCAAGTGTCTCTTCGACTCT
Found at i:184808 original size:214 final size:212
Alignment explanation
Indices: 184348--184909 Score: 860
Period size: 214 Copynumber: 2.6 Consensus size: 212
184338 TACTTTATAC
*
184348 GTATGGACACTTTTATAAAATGATATACTTTTTTTAAAGTTATGTAA-TTATGTTTCAATTTTTT
1 GTATGGACACTTTTAAAAAATGATATAC-TTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTT
184412 TTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA-AAAAATTAT
65 TTAATAGTGTTTCATGTTTTCCACCT---ATA-TAATTTAATAATTTCATTTACACAAAAATTAT
*
184476 TTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATAACCAAAGATAA
126 TTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATAACCAAAGATAA
184541 TAATAAATATGTTTCCACAAAAA
191 TAAT-AATATGTTTCCACAAAAA
184564 -TATGGACACTTTTAAAAAATGATATACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTT
1 GTATGGACACTTTTAAAAAATGATATACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTT
*
184628 TAATAGTG-TTCATGTTTTCCACCTATAATAGTTTAATAATTTCATTTACACAAAAATTATTTGA
66 TAATAGTGTTTCATGTTTTCCACCTAT-ATAATTTAATAATTTCATTTACACAAAAATTATTTGA
*
184692 TTTTTTGATA-TTTATAAAATA-T-TTTA-AATTTAAATTTAACAATATTAACCGAAGATAATAA
130 TTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA-TAACCAAAGATAATAA
184753 T-ATATGTTTTCCACATGAAATAA
194 TAATATG-TTTCCAC---AAA-AA
184776 GTATGGACACTTTTAAAAAATGATATTACTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTT
1 GTATGGACACTTTTAAAAAATGATA-TACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTT
*
184840 TTAATAGTGTTTCATGTTTTCCACCTAT-TAATTTAATAATTTC-TTTACACACAAATTATTTGA
65 TTAATAGTGTTTCATGTTTTCCACCTATATAATTTAATAATTTCATTTACACAAAAATTATTTGA
184903 TATTTTT
130 T-TTTTT
184910 TAAAATATTA
Statistics
Matches: 327, Mismatches: 6, Indels: 30
0.90 0.02 0.08
Matches are distributed among these distances:
207 5 0.02
208 25 0.08
209 20 0.06
210 1 0.00
211 57 0.17
212 44 0.13
213 38 0.12
214 85 0.26
215 52 0.16
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (212 bp):
GTATGGACACTTTTAAAAAATGATATACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTT
TAATAGTGTTTCATGTTTTCCACCTATATAATTTAATAATTTCATTTACACAAAAATTATTTGAT
TTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATAACCAAAGATAATAATA
ATATGTTTCCACAAAAA
Found at i:186530 original size:31 final size:31
Alignment explanation
Indices: 186489--186571 Score: 139
Period size: 31 Copynumber: 2.7 Consensus size: 31
186479 GGACAAACGG
186489 GGCTAATGACTAACGAAAACCGACCCAGACA
1 GGCTAATGACTAACGAAAACCGACCCAGACA
* *
186520 GGGTAATGACTAACGAAAACTGACCCAGACA
1 GGCTAATGACTAACGAAAACCGACCCAGACA
*
186551 GGCTAATGACTAAAGAAAACC
1 GGCTAATGACTAACGAAAACC
186572 AAAACAAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.12
Consensus pattern (31 bp):
GGCTAATGACTAACGAAAACCGACCCAGACA
Found at i:190345 original size:17 final size:16
Alignment explanation
Indices: 190319--190350 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
190309 ATAAAACAAA
190319 CAGACAAAAAAGAAAT
1 CAGACAAAAAAGAAAT
190335 CAGATCAAAAAAGAAA
1 CAGA-CAAAAAAGAAA
190351 GGGAAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.69, C:0.12, G:0.12, T:0.06
Consensus pattern (16 bp):
CAGACAAAAAAGAAAT
Found at i:191851 original size:22 final size:23
Alignment explanation
Indices: 191809--191856 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
191799 CATATTTCTA
* *
191809 TATTTATAATATATTTAATATTT
1 TATTTATAAAATATTTAATATCT
191832 TATTT-TAAAATA-TTATATATCT
1 TATTTATAAAATATTTA-ATATCT
191854 TAT
1 TAT
191857 ATCATATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 3 0.14
22 14 0.64
23 5 0.23
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TATTTATAAAATATTTAATATCT
Found at i:191887 original size:17 final size:16
Alignment explanation
Indices: 191853--191890 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
191843 ATTATATATC
191853 TTATA-TCATATAAAA
1 TTATATTCATATAAAA
*
191868 TTATATTCATAATAATA
1 TTATATTCAT-ATAAAA
191885 TTATAT
1 TTATAT
191891 ATTATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 4 0.20
17 11 0.55
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (16 bp):
TTATATTCATATAAAA
Found at i:193456 original size:120 final size:117
Alignment explanation
Indices: 193224--193464 Score: 306
Period size: 120 Copynumber: 2.0 Consensus size: 117
193214 TTTCGCAACT
* * *
193224 CGAATTCGCCAATTTCGTAACTCAACTATCGATATAGGTAAACACGGTAAAAATCAGGTCAAAAA
1 CGAATTCGCCAATTTCGCAACTCAACTATCGATATAGGTAAACACGGTAAAAATCAGATAAAAAA
* * * * *
193289 TATGAATTCGTCAATTTGGAAACTGAGTTGTGAATTTAGCAAATTCGTGTTG
66 TACGAATTCGCCAATTTGAAAACTGAATTGTAAATTTAGCAAATTCGTGTTG
* *
193341 CGAATTTGACCAATTTCGCAACTCAATTATCGATATAGGTAAACACGGTAGAAAAATTC-GATAA
1 CGAATTCG-CCAATTTCGCAACTCAACTATCGATATAGGTAAACACGGT--AAAAA-TCAGATAA
* * *
193405 AAAATCCGAATTCGCCAATTTGAAAACTGAATT-TCAAATTTGGCAAGTTCGTGTTG
62 AAAATACGAATTCGCCAATTTGAAAACTGAATTGT-AAATTTAGCAAATTCGTGTTG
193461 CGAA
1 CGAA
193465 ATGTAAAATC
Statistics
Matches: 106, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
117 7 0.07
118 38 0.36
119 1 0.01
120 58 0.55
121 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (117 bp):
CGAATTCGCCAATTTCGCAACTCAACTATCGATATAGGTAAACACGGTAAAAATCAGATAAAAAA
TACGAATTCGCCAATTTGAAAACTGAATTGTAAATTTAGCAAATTCGTGTTG
Found at i:194118 original size:20 final size:20
Alignment explanation
Indices: 194080--194120 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
194070 AAAAATTTTA
*
194080 AAAAAATAAATATATAATAT
1 AAAAAATAAAAATATAATAT
194100 AAAAAATAAAAA-ATAAATAT
1 AAAAAATAAAAATAT-AATAT
194120 A
1 A
194121 TATTAACGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAAATAAAAATATAATAT
Found at i:195556 original size:27 final size:24
Alignment explanation
Indices: 195526--195576 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
195516 TACTTACTAA
195526 TTAAACAAATATATATTATTTTAATTT
1 TTAAACAAA-A-AT-TTATTTTAATTT
**
195553 TTAATGAAAAATTTATTTTAATTT
1 TTAAACAAAAATTTATTTTAATTT
195577 ATATTGTCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 12 0.55
25 2 0.09
26 1 0.05
27 7 0.32
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTAAACAAAAATTTATTTTAATTT
Found at i:197072 original size:29 final size:28
Alignment explanation
Indices: 197030--197086 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
197020 ATCTATACTC
*
197030 ATTTTTTTTAATTTAGTGTCAAACGTTT
1 ATTTTTTTCAATTTAGTGTCAAACGTTT
*
197058 ATTTTATTTCAATTTGGTGTCAAACGTTT
1 ATTTT-TTTCAATTTAGTGTCAAACGTTT
197087 GAAGTTCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.54
Consensus pattern (28 bp):
ATTTTTTTCAATTTAGTGTCAAACGTTT
Found at i:200373 original size:2 final size:2
Alignment explanation
Indices: 200366--200414 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
200356 CAAGATAGTG
200366 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
200408 TA TA TA T
1 TA TA TA T
200415 TTTGCAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:207091 original size:15 final size:15
Alignment explanation
Indices: 207071--207109 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
207061 TCGCTCTCCT
207071 TGTTGCTGCTGATGC
1 TGTTGCTGCTGATGC
207086 TGTTGCTGCTGATGC
1 TGTTGCTGCTGATGC
207101 TGTTGCTGC
1 TGTTGCTGC
207110 AGCGGCTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.05, C:0.21, G:0.33, T:0.41
Consensus pattern (15 bp):
TGTTGCTGCTGATGC
Found at i:216875 original size:148 final size:147
Alignment explanation
Indices: 216584--217358 Score: 1077
Period size: 148 Copynumber: 5.2 Consensus size: 147
216574 AACATATTCA
* *
216584 GTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTATTTTACTGTTTACATTATTAGTAATCTTT
1 GTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTT-TTTTACCGTTTACATTATTAGCAA-CTTT
* *
216649 -AAACAAACCGGTAGGTATTTTAATATAATTGGTAGCGCCTATTTTTTTTACCGTTTACATTATT
64 CAAAAAAACCGGTAGGTATTTTAATATAATAGGTAGCGCCTA-TTTTTTTACCGTTTACATTATT
*
216713 ATCAACCTTTAAAAAAAACCG
128 AGCAACC-TTAAAAAAAACCG
* *
216734 ATAGGTAGTTTAATGTAATAGGTAGCGCCTA-TTTTTTTACCGTTTATATTATTAGCAACTTTCA
1 GTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACTTTCA
* * * *
216798 AAAAAACAGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTACC
66 AAAAAACCGGTAGGTATTTTAATATAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAGC
*
216863 AACCTTTAAAAAAACCG
131 AACCTTAAAAAAAACCG
* * ** *
216880 GTAGGTATTTTAATGTAATAGGTAACGCCTATTTTTTTTATTGTTTACATTATTAGCAACCTTCA
1 GTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACTTTC-
* * *
216945 AAAAAAACTGGTAGGTATTTTAATATAATAGGTAACGCCTATTTTTTTACCGTTTACATTATTAA
65 AAAAAAACCGGTAGGTATTTTAATATAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAG
*
217010 CAACCTTAAAAAAAACGG
130 CAACCTTAAAAAAAACCG
* * * * * *
217028 GTAGGTATTTTAATATAATAGGTAGTGCCTATTTTATTTTACCGTTTACATTATTAGTAATTTTT
1 GTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTT-TTTTACCGTTTACATTATTAGCAACTTTC
* ** *
217093 AAACAAACCGGTAGGTATTTTAATATAATATATAGTGCCTATTTTTTTACCGTTTACATTATTAG
65 AAAAAAACCGGTAGGTATTTTAATATAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAG
*
217158 CAACCTTAAAAAAAATCG
130 CAACCTTAAAAAAAACCG
* *
217176 GTATGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTCA
1 GTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACTTTCA
* * * * *
217241 AAAAAACTGGTAGGTATTTTAATGTAATAGGTAACGCTTATTTTTTTTATCGTTTACATTATTAG
66 AAAAAACCGGTAGGTATTTTAATATAATAGGTAGCGCCTA-TTTTTTTACCGTTTACATTATTAG
* *
217306 CAACATTAAAAAAAACCT
130 CAACCTTAAAAAAAACCG
* * *
217324 GTAGGTATTTTAATGTAATAAGTAACGCCTATTTT
1 GTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTT
217359 ATATTTCCAG
Statistics
Matches: 553, Mismatches: 67, Indels: 12
0.88 0.11 0.02
Matches are distributed among these distances:
146 40 0.07
147 118 0.21
148 339 0.61
149 26 0.05
150 30 0.05
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (147 bp):
GTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACTTTCA
AAAAAACCGGTAGGTATTTTAATATAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAGC
AACCTTAAAAAAAACCG
Found at i:216976 original size:221 final size:222
Alignment explanation
Indices: 216584--217358 Score: 1092
Period size: 221 Copynumber: 3.5 Consensus size: 222
216574 AACATATTCA
* * *
216584 GTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTATTTTACTGTTTACATTATTAGTAATCTTT
1 GTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGCAACCTTT
* * *
216649 AAACAAACCGGTAGGTATTTTAATATAATTGGTAGCGCCTATTTTTTTTACCGTTTACATTATTA
66 AAAAAAACCGGTAGGTATTTTAATATAATAGGTAACGCCTATTTTTTTTACCGTTTACATTATTA
* * *
216714 TCAACCTTTAAAAAAAACCGATAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTT
131 GCAACC-TTAAAAAAAACTGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTT
* *
216779 ATATTATTAGCAACTTTCAAAAAAACAG
195 ACATTATTAGCAACCTTCAAAAAAACAG
*
216807 GTAGGTAGTTTAATGTAATAGGTAGCGCCTA-TTT-TTTTACCGTTTACATTATTACCAACCTTT
1 GTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGCAACCTTT
* **
216870 AAAAAAACCGGTAGGTATTTTAATGTAATAGGTAACGCCTATTTTTTTTATTGTTTACATTATTA
66 AAAAAAACCGGTAGGTATTTTAATATAATAGGTAACGCCTATTTTTTTTACCGTTTACATTATTA
* * *
216935 GCAACCTTCAAAAAAAACTGGTAGGTATTTTAATATAATAGGTAACGCCTATTTTTTTACCGTTT
131 GCAACCTT-AAAAAAAACTGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTT
* * *
217000 ACATTATTAACAACCTTAAAAAAAACGG
195 ACATTATTAGCAACCTTCAAAAAAACAG
* * * * **
217028 GTAGGTATTTTAATATAATAGGTAGTGCCTATTTTATTTTACCGTTTACATTATTAGTAATTTTT
1 GTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGCAACCTTT
* ** **
217093 AAACAAACCGGTAGGTATTTTAATATAATATATAGTGCCTA-TTTTTTTACCGTTTACATTATTA
66 AAAAAAACCGGTAGGTATTTTAATATAATAGGTAACGCCTATTTTTTTTACCGTTTACATTATTA
*
217157 GCAACCTTAAAAAAAA-TCGGTATGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTT
131 GCAACCTTAAAAAAAACT-GGTAGGTAGTTTAATGTAATAGGTAGCGCCTA-TTTTTTTACCGTT
*
217221 TACATTATTAGCAACCTTCAAAAAAACTG
194 TACATTATTAGCAACCTTCAAAAAAACAG
* * * * * *
217250 GTAGGTATTTTAATGTAATAGGTAACGCTTATTTT-TTTTATCGTTTACATTATTAGCAACATTA
1 GTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGCAACCTTT
* * *
217314 AAAAAAACCTGTAGGTATTTTAATGTAATAAGTAACGCCTATTTT
66 AAAAAAACCGGTAGGTATTTTAATATAATAGGTAACGCCTATTTT
217359 ATATTTCCAG
Statistics
Matches: 487, Mismatches: 59, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
220 3 0.01
221 285 0.59
222 108 0.22
223 91 0.19
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (222 bp):
GTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGCAACCTTT
AAAAAAACCGGTAGGTATTTTAATATAATAGGTAACGCCTATTTTTTTTACCGTTTACATTATTA
GCAACCTTAAAAAAAACTGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTA
CATTATTAGCAACCTTCAAAAAAACAG
Found at i:218023 original size:2 final size:2
Alignment explanation
Indices: 218016--218042 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
218006 TAAAAGATGA
218016 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
218043 AAACAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:218457 original size:33 final size:33
Alignment explanation
Indices: 218420--218487 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
218410 AATGCTTCGA
* *
218420 TTTTAGTGTTTCAATAGGACTCAAATACGTTGG
1 TTTTAGTATTCCAATAGGACTCAAATACGTTGG
218453 TTTTAGTATTCCAATAGGACTCAAATACGTTGG
1 TTTTAGTATTCCAATAGGACTCAAATACGTTGG
218486 TT
1 TT
218488 AGTTTATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (33 bp):
TTTTAGTATTCCAATAGGACTCAAATACGTTGG
Found at i:218548 original size:3 final size:3
Alignment explanation
Indices: 218542--218582 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
218532 AAAATAAAAA
218542 AAT AAT AAT AA- ATAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA
218583 ATAAATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 1 0.03
3 34 0.94
4 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:218560 original size:12 final size:12
Alignment explanation
Indices: 218534--218599 Score: 60
Period size: 9 Copynumber: 6.2 Consensus size: 12
218524 GGTCTGTAAA
*
218534 AATAA-AAAAAT
1 AATAATAAATAT
218545 AATAATAAATAT
1 AATAATAAATAT
218557 AATAAT--A-AT
1 AATAATAAATAT
218566 AATAAT--A-AT
1 AATAATAAATAT
218575 AATAATAAATA-
1 AATAATAAATAT
218586 AATAA-AAATAT
1 AATAATAAATAT
218597 AAT
1 AAT
218600 GTTTTTGTAG
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
9 17 0.35
10 6 0.12
11 14 0.29
12 12 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:219083 original size:84 final size:82
Alignment explanation
Indices: 218941--220102 Score: 948
Period size: 84 Copynumber: 14.0 Consensus size: 82
218931 AGCTTAATGG
* ** * * * **
218941 AATCGAACTCAAAGGTCTTTG--GCAGATAGTCCTTATTGCCTTGACATATGCTGCAAATGATAG
1 AATCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGAT-G
* *
219004 TGCCTTTGAGCTGAGTGG
65 TGCCTTTGAGCTGAGCGT
* * *
219022 AGTCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATA
1 AATCGAACTCGAAGGTCTTTGTTG-CAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGAT-
* *
219087 GTGCCTTGGAGCTGAGCAT
64 GTGCCTTTGAGCTGAGCGT
* * * * * * * *
219106 AGTCGAACTCGAAGGTCTTTTGTTGGTAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGAT
1 AATCGAACTCGAAGGTC-TTTGTT-GCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGAT
*
219171 GTGCCTTGGAGCTGAGCGT
64 GTGCCTTTGAGCTGAGCGT
* * * * * *
219190 AATCGAACTCGAAGGTCTTTGGTGATAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGTTG
1 AATCGAACTCGAAGGTCTTTGTTG-CAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGAT-
*
219255 GTGCCTTTGAGCTAAGTC-T
64 GTGCCTTTGAGCTGAG-CGT
* * * * * *
219274 AATCGGACTCGAAGGTATTTG--GCAGATAGCCTTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 AATCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGATGT
* *
219337 GCCTTGGAGCTGAGCAT
66 GCCTTTGAGCTGAGCGT
* * * *
219354 AGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGTT
1 AATCGAACTCGAAGGTCTTT-GTT-GCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGAT
* * *
219419 GGTACCTTTGAGTTGAGTGT
64 -GTGCCTTTGAGCTGAGCGT
* * ** * * * * *
219439 AATTGAAATCGAAGGTCTTTG--GCAGATAACCCTTCTAGTATTGAGTTGTACTACAAATGATAT
1 AATCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGATGT
* * * *
219502 ACCCTCGAAGCTGAGTGT
66 GCCTTTG-AGCTGAGCGT
* * * *
219520 AATCGAACTCGAGGGTCTTTG--GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 AATCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGATGT
* *
219583 GTCTTGGAGCTGAGCGT
66 GCCTTTGAGCTGAGCGT
* * * * * *
219600 AGTCGAACTCGAAGGTCTTTGGTTGGCGGATAACCCTTCTCGACTTAAGTTATGCTGTAAATAAT
1 AATCGAACTCGAAGGTCTTT-GTT-GCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGAT
* * *
219665 ATGCCTTGGAGATGAGCGT
64 GTGCCTTTGAGCTGAGCGT
* * * * ** * *
219684 AGTCAAACTCGATGGTATTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
1 AATCGAACTCGAAGGT-CTTT-GTTGCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGAT
* *
219749 GTGCCTTCGAAGCTGAGTGT
64 GTGCCTTTG-AGCTGAGCGT
* * * * * * * * * *
219769 AATCGAACTCGAGGGTCTTTG--GTAGATAGCCCTTATCGACTTAAGTTATGTTGTATATTATGT
1 AATCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGATGT
*
219832 GCC-TTGAAGTTGAGCGT
66 GCCTTTG-AGCTGAGCGT
* * *
219849 AATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCATTCTTGACTTAAGTTATGCTGCAAATGAT
1 AATCGAACTCGAAGGTCTTT-GTT-GCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGAT
* *
219914 ATGCC-TTGAAGCTGAGCGC
64 GTGCCTTTG-AGCTGAGCGT
* ** * * *
219933 AGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGAT
1 AATCGAACTCGAAGGTC-TTT-GTTGCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGAT
* * *
219998 GTGCCCTCGAAGCTGAGTGT
64 GTGCCTTTG-AGCTGAGCGT
* * * * * *
220018 AATCGAACTCGAGGGTATTCGGTTAGCAGATAACCCTTATTA-CCTTAAGTTATGCTGTAAAAGA
1 AATCGAACTCGAAGGTCTT-TGTT-GCAGATAACCCTT-CTAGCCTTAAGTTATGCTGCAAATGA
220082 TGTGCCTTTGAGCTGAGCGT
63 TGTGCCTTTGAGCTGAGCGT
220102 A
1 A
220103 GTTAAACTTG
Statistics
Matches: 885, Mismatches: 166, Indels: 57
0.80 0.15 0.05
Matches are distributed among these distances:
79 1 0.00
80 95 0.11
81 182 0.21
82 2 0.00
83 40 0.05
84 395 0.45
85 167 0.19
86 3 0.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (82 bp):
AATCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGATGT
GCCTTTGAGCTGAGCGT
Found at i:219462 original size:165 final size:165
Alignment explanation
Indices: 218941--220098 Score: 1012
Period size: 165 Copynumber: 7.0 Consensus size: 165
218931 AGCTTAATGG
* * * * * * **
218941 AATCGAACTCAAAGGTCTTTGGCAGATAGTCCTTATTGCCTTGACATATGCTGCAAATGATAGTG
1 AATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGAT-GTG
* * * * * *
219006 CCTTTGAGCTGAGTGGAGTCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTAGCCTTGAG
65 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAG
* * **
219070 TTATGCTGTAAATGATAGTGCCTTGGAGCTGAGCAT
130 TTATGCTGCAAATGATGGTGCCTTGGAGCTGAGTGT
* * * * * * * *
219106 AGTCGAACTCGAAGGTCTTTTGTTGGTAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGAT
1 AATCGAACTCGAAGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGAT
* *
219171 GTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGG-TGATAGATAACCCTTCTAGCCTT
62 GTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTT
* * * * * * *
219235 GAGTTATGTTGTAAATGTTGGTGCCTTTGAGCTAAGTCT
127 AAGTTATGCTGCAAATGATGGTGCCTTGGAGCTGAGTGT
* * *
219274 AATCGGACTCGAAGGTATTTGGCAGATAGCCTTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
1 AATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
* * * *
219339 CTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGT
66 CTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGT
* * * *
219404 TATGCTGCAAATGTTGGTACCTTTGAGTTGAGTGT
131 TATGCTGCAAATGATGGTGCCTTGGAGCTGAGTGT
* * * * * * * * *
219439 AATTGAAATCGAAGGTCTTTGGCAGATAACCCTTCTAGTA-TTGAGTTGTACTACAAATGATATA
1 AATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCG-ACTTAAGTTATGCTGCAAATGATGT-
* * * * * *
219503 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT-G--G-CAGATAACCCTTCTCGACTTAA
64 GCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAA
* * *
219564 GCTATGCTGCAAATGAT-GTGTCTTGGAGCTGAGCGT
129 GTTATGCTGCAAATGATGGTGCCTTGGAGCTGAGTGT
* * * * *
219600 AGTCGAACTCGAAGGTCTTTGGTTGGCGGATAACCCTTCTCGACTTAAGTTATGCTGTAAATAAT
1 AATCGAACTCGAAGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGAT
* * * * * * * *
219665 ATGCCTTGGAGATGAGCGTAGTCAAACTCGATGGTATTTTGG-TCACAGATAACCCTTCTAGCCT
62 GTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGT-CTTTGGTTGACAGATAACCCTTCTAGACT
* * *
219729 TGAGTTATGCTGTAAATGAT-GTGCCTTCGAAGCTGAGTGT
126 TAAGTTATGCTGCAAATGATGGTGCCTT-GGAGCTGAGTGT
* * * * * * *
219769 AATCGAACTCGAGGGTCTTTGGTAGATAGCCCTTATCGACTTAAGTTATGTTGTATATTATGTGC
1 AATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
* * * * *
219834 CTTGAAGTTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCATTCTTGACTTAAGT
66 CTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGT
* * * *
219899 TATGCTGCAAATGAT-ATGCCTTGAAGCTGAGCGC
131 TATGCTGCAAATGATGGTGCCTTGGAGCTGAGTGT
* * * * * * *
219933 AGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGAT
1 AATCGAACTCGAAGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGAT
* * * * * * * *
219998 GTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTATTCGGTT-AGCAGATAACCCTTATTA-C
62 GTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGA-CAGATAACCCTT-CTAGA
* * *
220061 CTTAAGTTATGCTGTAAAAGAT-GTGCCTTTGAGCTGAG
124 CTTAAGTTATGCTGCAAATGATGGTGCCTTGGAGCTGAG
220099 CGTAGTTAAA
Statistics
Matches: 815, Mismatches: 152, Indels: 48
0.80 0.15 0.05
Matches are distributed among these distances:
161 28 0.03
162 37 0.05
163 2 0.00
164 130 0.16
165 266 0.33
166 32 0.04
167 1 0.00
168 178 0.22
169 140 0.17
170 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (165 bp):
AATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
CTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGT
TATGCTGCAAATGATGGTGCCTTGGAGCTGAGTGT
Found at i:219848 original size:249 final size:248
Alignment explanation
Indices: 218978--220124 Score: 1291
Period size: 249 Copynumber: 4.6 Consensus size: 248
218968 AGTCCTTATT
** * * * * *
218978 GCCTTGACATATGCTGCAAATGATAGTGCCTTTG-AGCTGAGTGGAGTCGAACTCGAAGGTCTTT
1 GCCTTGAGTTATGCTGTAAATGAT-GTGCCTTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT
* * * *
219042 GTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATAGTGCCTTGGAGCTGAGCATA
65 G--G-CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT-GTGCCTTGGAGCTGAGCATA
* * * * * * * * * *
219107 GTCGAACTCGAAGGTCTTTTGTTGGTAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATG
126 GTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATA
* * * *
219172 TGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGATAGATAACCCTTCTA
191 TGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTCACAGATAACCCTTCTA
* * * * * * * *
219230 GCCTTGAGTTATGTTGTAAATGTTGGTGCCTTTG-AGCTAAGTCTAATCGGACTCGAAGGTATTT
1 GCCTTGAGTTATGCTGTAAATGAT-GTGCCTTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT
* *
219294 GGCAGATAGCCTTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCG
65 GGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCG
* * *
219359 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGTTGGTAC
130 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT-ATGC
* * * * *
219424 CTTTGAGTTGAGTGTAATTGAAA-TCGAAGGTCTTTGG---CAGATAACCCTTCTA
194 CTTGGAGCTGAGCGT-AGTCAAACTCGAAGGTCTTTGGTCACAGATAACCCTTCTA
** * * ** * * *
219476 GTATTGAGTTGTACTACAAATGATATACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTG
1 GCCTTGAGTTATGCTGTAAATGATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTG
* * *
219541 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCTTGGAGCTGAGCGTAGTCGA
66 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGA
* * *
219606 ACTCGAAGGTCTTTGGTTGGCGGATAACCCTTCTCGACTTAAGTTATGCTGTAAATAATATGCCT
131 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCT
* * *
219671 TGGAGATGAGCGTAGTCAAACTCGATGGTATTTTGGTCACAGATAACCCTTCTA
196 TGGAGCTGAGCGTAGTCAAACTCGAAGGT-CTTTGGTCACAGATAACCCTTCTA
219725 GCCTTGAGTTATGCTGTAAATGATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTG
1 GCCTTGAGTTATGCTGTAAATGATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTG
* * * * * * * * * * *
219790 GTAGATAGCCCTTATCGACTTAAGTTATGTTGTATATTATGTGCCTTGAAGTTGAGCGTAATCGA
66 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGA
* *
219855 ACTCGAAGGTCTTTGGTTGGCAGATAACCATTCTTGACTTAAGTTATGCTGCAAATGATATGCCT
131 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCT
* * *
219920 TGAAGCTGAGCGCAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTA
196 TGGAGCTGAGCGTAGTCAAACTCGAAGGTC-TTTGGTCACAGATAACCCTTCTA
* *
219974 GCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTATTCG
1 GCCTTGAGTTATGCTGTAAATGATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGAGGG---TC-
* * * * * * * *
220039 GTTAGCAGATAACCCTTAT-TACCTTAAGTTATGCTGTAAAAGATGTGCCTTTGAGCTGAGCGTA
62 TTTGGCAGATAACCCTTCTCGA-CTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATA
** * *
220103 GTTAAACTTGAAGGCCTTTGGT
126 GTCGAACTCGAAGGTCTTTGGT
220125 GGGTACGATT
Statistics
Matches: 759, Mismatches: 122, Indels: 27
0.84 0.13 0.03
Matches are distributed among these distances:
244 5 0.01
245 26 0.03
246 176 0.23
248 74 0.10
249 350 0.46
250 5 0.01
252 56 0.07
253 67 0.09
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (248 bp):
GCCTTGAGTTATGCTGTAAATGATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTG
GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGA
ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCT
TGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTCACAGATAACCCTTCTA
Found at i:220459 original size:110 final size:110
Alignment explanation
Indices: 220231--220664 Score: 655
Period size: 110 Copynumber: 4.0 Consensus size: 110
220221 ATCCAAATAT
* * * *
220231 TTGTGTTGTTTCGAGGCCAATATCCTTCG-TCGTGAAGTTAAAATTGACTC----TGAAACT-AG
1 TTGTGTTGTCTCGAGTCCAATATCATTCGCT-GTGAAGTTGAAATTGACTCTGAATGAAACTGA-
* *
220290 AAAGTTATTTGTTGACAGACAGTTGCCCCTTCGCTGTGAAGTTGAGC
64 AAAGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
*
220337 TTGTGTTGTCTCGAGTCCAATATCATTTGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* * *
220402 ATTTGTTTGTTGACAGTCAGTCACCCCTTCGCTGTGAAGTTGAGC
66 AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
* * *
220447 TTGTGTTATCTCGAGTCCAATATCATTCGCTGTGAAGTTGAATTTAACTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* *
220512 AGCTATTTGTTGATAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
66 AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
*
220557 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
*
220622 AGTTATTTGTTGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGA
66 AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
220665 AATTGGCTCT
Statistics
Matches: 296, Mismatches: 26, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
106 43 0.15
107 1 0.00
110 251 0.85
111 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (110 bp):
TTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
Found at i:220688 original size:67 final size:67
Alignment explanation
Indices: 220580--220731 Score: 259
Period size: 67 Copynumber: 2.3 Consensus size: 67
220570 AGTCCAATAT
*
220580 CCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAGTCAGTCG
1 CCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAGTCAGTCC
220645 CC
66 CC
* * *
220647 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCC
1 CCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAGTCAGTCC
220712 CC
66 CC
*
220714 CCTTCGCTGTAAAGTTGA
1 CCTTCGCTGTGAAGTTGA
220732 GCTTGTGTTG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 79 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (67 bp):
CCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAGTCAGTCC
CC
Found at i:220700 original size:177 final size:171
Alignment explanation
Indices: 220472--220835 Score: 548
Period size: 177 Copynumber: 2.1 Consensus size: 171
220462 TCCAATATCA
* * *
220472 TTCGCTGTGAAGTTGAATTTAACTCTGAATGAAACTGAAAAGCTATTTGTTGATAGTCAGTCGCC
1 TTCGCTGTGAAGTTGAAATTAACTCTGAATGAAACTGAAAAGCTATTTGTTGACAGTCAGTCCCC
* *
220537 CCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
66 CCTTCGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATTCGC--T---G-TGAAATT
* **
220602 GACTCTGAATGAAACTGAAAAGTTATTTGTTGACAGTCAGTCGCCCC
125 GACTCTAAATGAAACTGAAAAGTTATTTGTTGACAGTCAACCGCCCC
* ** * *
220649 TTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCCCC
1 TTCGCTGTGAAGTTGAAATTAACTCTGAATGAAACTGAAAAGCTATTTGTTGACAGTCAGTCCCC
220714 CCTTCGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAATTGACTCT
66 CCTTCGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAATTGACTCT
*
220779 AAATGAAACTGAAAAGTTGTTTGTTGACAGTCAACCGCCCC
131 AAATGAAACTGAAAAGTTATTTGTTGACAGTCAACCGCCCC
220820 TTCGCTGTGAAGTTGA
1 TTCGCTGTGAAGTTGA
220836 GCTTGTGTTG
Statistics
Matches: 172, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
171 65 0.38
172 1 0.01
175 1 0.01
177 105 0.61
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (171 bp):
TTCGCTGTGAAGTTGAAATTAACTCTGAATGAAACTGAAAAGCTATTTGTTGACAGTCAGTCCCC
CCTTCGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAATTGACTCT
AAATGAAACTGAAAAGTTATTTGTTGACAGTCAACCGCCCC
Found at i:220903 original size:281 final size:284
Alignment explanation
Indices: 220365--220945 Score: 943
Period size: 281 Copynumber: 2.0 Consensus size: 284
220355 AATATCATTT
*
220365 GCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAATTTGTTTGTTGACAGTCAGTCACCCCT
1 GCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCACCCCT
*
220430 TCGCTGTGAAGTTGAGCTTGTGTTATCTCGAGTCCAATATCATTCGCTGTGAAGTTGAATTTAAC
66 TCGCTGTAAAGTTGAGCTTGTGTTATCTCGAGTCCAATATCATTCGCTGTGAA---GAATTTAAC
* * **
220495 TCTGAATGAAACTGAAAAGCTATTTGTTGATAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
128 TCTAAATGAAACTGAAAAGCTATTTGTTGACAGTCAACCGCCCCTTCGCTGTGAAGTTGAGCTTG
* *
220560 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
193 TGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGT
220625 TATTTGTTGACAGTCAGTCGCCCCTTC
258 TATTTGTTGACAGTCAGTCGCCCCTTC
* * *
220652 GTTGTGAAGTTGAAATTGGCTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCCCCCCT
1 GCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCACCCCT
* *
220717 TCGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTG-A-AA-TTGACTCT
66 TCGCTGTAAAGTTGAGCTTGTGTTATCTCGAGTCCAATATCATTCGCTGTGAAGAATTTAACTCT
* *
220779 AAATGAAACTGAAAAGTTGTTTGTTGACAGTCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGT
131 AAATGAAACTGAAAAGCTATTTGTTGACAGTCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGT
*
220844 TGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGT
196 TGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTAT
* **
220909 TTGTTGACAGTTAGTTTCCCCTTC
261 TTGTTGACAGTCAGTCGCCCCTTC
220933 GCTGTGAAGTTGA
1 GCTGTGAAGTTGA
220946 GCTTGTGTTG
Statistics
Matches: 274, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
281 161 0.59
282 2 0.01
286 1 0.00
287 110 0.40
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (284 bp):
GCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCACCCCT
TCGCTGTAAAGTTGAGCTTGTGTTATCTCGAGTCCAATATCATTCGCTGTGAAGAATTTAACTCT
AAATGAAACTGAAAAGCTATTTGTTGACAGTCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGT
TGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTAT
TTGTTGACAGTCAGTCGCCCCTTC
Found at i:220931 original size:110 final size:110
Alignment explanation
Indices: 220649--221057 Score: 605
Period size: 110 Copynumber: 3.8 Consensus size: 110
220639 CAGTCGCCCC
* * * *
220649 TTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCCCC
1 TTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCACC
*
220714 CCTTCGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCA
66 CCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCA
** *
220759 TTCGC--T---G-TGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGTTGACAGTCAACCGCC
1 TTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCACC
220818 CCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCA
66 CCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCA
* **
220863 TTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGTTGACAGTTAGTTTCC
1 TTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCACC
* *
220928 CCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTTCAATATCC
66 CCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCA
* * * * *
220973 TTCGATGTAAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACTGTCAGTCACC
1 TTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCACC
*
221038 CTTTCGCTGTGAAGTTGAGC
66 CCTTCGCTGTGAAGTTGAGC
221058 AACCACCATC
Statistics
Matches: 270, Mismatches: 23, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
104 96 0.36
105 1 0.00
106 1 0.00
108 1 0.00
109 1 0.00
110 170 0.63
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (110 bp):
TTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCACC
CCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCA
Found at i:220955 original size:391 final size:394
Alignment explanation
Indices: 220281--221055 Score: 1234
Period size: 391 Copynumber: 2.0 Consensus size: 394
220271 AAATTGACTC
** *
220281 TGAAACTAGAAAGTTATTTGTTGACAGACAGTTGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGT
1 TGAAACTAGAAAGTTATTTGTTGACAGACAGTCCCCCCTTCGCTGTAAAGTTGAGCTTGTGTTGT
* * *
220346 CTCGAGTCCAATATCATTTGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAATTTGTTTG
66 CTCGAGTCCAATATCATTCGC-GT--AGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTG
**
220411 TTGACAGTCAGTCACCCCTTCGCTGTGAAGTTGAGCTTGTGTTATCTCGAGTCCAATATCATTCG
128 TTGACAGTCAACCACCCCTTCGCTGTGAAGTTGAGCTTGTGTTATCTCGAGTCCAATATCATTCG
* * *
220476 CTGTGAAGTTGAATTTAACTCTGAATGAAACTGAAAAGCTATTTGTTGATAGTCAGTCGCCCCTT
193 CTGTGAAGTTGAAATTAACTCTAAATGAAACTGAAAAGCTATTTGTTGACAGTCAGTCGCCCCTT
* *
220541 CGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACT
258 CGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGATGTAAAGTTGAAATTGACT
* *
220606 CTGAATGAAACTGAAAAGTTATTTGTTGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAAATTGG
323 CTGAATGAAACTGAAAAGTTATTTGTTGACAGTCAGTCACCCCTTCGCTGTGAAGTTGAAATTGG
220671 CTCTGAA
388 CTCTGAA
* *
220678 TGAAACT-GAAAAGTTGTTTGTTGACAGTCAGTCCCCCCTTCGCTGTAAAGTTGAGCTTGTGTTG
1 TGAAACTAG-AAAGTTATTTGTTGACAGACAGTCCCCCCTTCGCTGTAAAGTTGAGCTTGTGTTG
220742 TCTCGAGTCCAATATCATTCGC-T-G-TGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGTT
65 TCTCGAGTCCAATATCATTCGCGTAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGTT
* *
220804 GACAGTCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATTCGCT
130 GACAGTCAACCACCCCTTCGCTGTGAAGTTGAGCTTGTGTTATCTCGAGTCCAATATCATTCGCT
* * * * **
220869 GTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGTTGACAGTTAGTTTCCCCTTCG
195 GTGAAGTTGAAATTAACTCTAAATGAAACTGAAAAGCTATTTGTTGACAGTCAGTCGCCCCTTCG
*
220934 CTGTGAAGTTGAGCTTGTGTTGTCTCGAGTTCAATATCCTTCGATGTAAAGTTGAAATTGACTCT
260 CTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGATGTAAAGTTGAAATTGACTCT
* *
220999 GAATGAAACTGAAAAGTTATTTGTTGACTGTCAGTCACCCTTTCGCTGTGAAGTTGA
325 GAATGAAACTGAAAAGTTATTTGTTGACAGTCAGTCACCCCTTCGCTGTGAAGTTGA
221056 GCAACCACCA
Statistics
Matches: 349, Mismatches: 28, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
391 268 0.77
392 1 0.00
395 1 0.00
396 1 0.00
397 78 0.22
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (394 bp):
TGAAACTAGAAAGTTATTTGTTGACAGACAGTCCCCCCTTCGCTGTAAAGTTGAGCTTGTGTTGT
CTCGAGTCCAATATCATTCGCGTAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGTTG
ACAGTCAACCACCCCTTCGCTGTGAAGTTGAGCTTGTGTTATCTCGAGTCCAATATCATTCGCTG
TGAAGTTGAAATTAACTCTAAATGAAACTGAAAAGCTATTTGTTGACAGTCAGTCGCCCCTTCGC
TGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGATGTAAAGTTGAAATTGACTCTG
AATGAAACTGAAAAGTTATTTGTTGACAGTCAGTCACCCCTTCGCTGTGAAGTTGAAATTGGCTC
TGAA
Found at i:226980 original size:17 final size:17
Alignment explanation
Indices: 226960--227009 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
226950 GAAAGTCAAC
226960 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
226977 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
226994 GGTCAACGATCGGGTC
1 GGTCAACGGTCGGGTC
227010 AGACTGGTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.14, C:0.24, G:0.44, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:234079 original size:5 final size:5
Alignment explanation
Indices: 234069--234121 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
234059 AACGGTCAAC
* *
234069 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
234118 GGTC
1 GGTC
234122 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:234082 original size:17 final size:17
Alignment explanation
Indices: 234062--234122 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
234052 GAAAGTCAAC
234062 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
234079 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
234101 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
234118 GGTCA
1 GGTCA
234123 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:234097 original size:22 final size:22
Alignment explanation
Indices: 234069--234121 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
234059 AACGGTCAAC
234069 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
234091 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
234113 GGTCGGGTC
1 GGTCGGGTC
234122 AGACCGGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (22 bp):
GGTCGGGTCGGGTCAACGGTCG
Found at i:236975 original size:162 final size:162
Alignment explanation
Indices: 236785--237874 Score: 1182
Period size: 162 Copynumber: 6.7 Consensus size: 162
236775 ACTATTTGTT
*** * * *
236785 GATTCTTTCCCATCCTTTAATGAATTCTTGCCTTCATTC-AAACTCGACTT-CTGGTTCAAACCA
1 GATTCTTTCCCATCCTTTACCAAATTCTTGCCTTCATTCGAACCT-GA-TTGCTGGTTCAAATCG
* * * * *
236848 CCCTTACTTGCATCATTATCATCAACACCTTTTGATCCATCAATTTGATCTACTCCATGATCTTT
64 CTCTTACTTGCATCATTATCAGCACCCCCTTTTGATCCATCAATTTGATCTCCTCCATGATCTTT
236913 CCCACTATTTGTATTTCCTTTCGCTTCACCACTC
129 CCCACTATTTGTATTTCCTTTCGCTTCACCACTC
* * * *
236947 GATTCTTTCCCATCCTTTACCAAATTCTTGCCTTCATTCGAGCCTGACTGTTGGTTCAAATTGCT
1 GATTCTTTCCCATCCTTTACCAAATTCTTGCCTTCATTCGAACCTGATTGCTGGTTCAAATCGCT
* *
237012 CTTACTTGCATCATTATCAGCACCCCCTTCTGATCCATCAATCTGATCTCCTCCATGAT-TATTC
66 CTTACTTGCATCATTATCAGCACCCCCTTTTGATCCATCAATTTGATCTCCTCCATGATCT-TTC
* * *
237076 CCACTATTTGTATTTCCTTTAGCTTCACCATTG
130 CCACTATTTGTATTTCCTTTCGCTTCACCACTC
** * * *
237109 GATGT-TTTCATATCCTTTACCAAATTCTTGCCTTCATTTGAACCCGATTTG-TGGTTCAAATTG
1 GAT-TCTTTCCCATCCTTTACCAAATTCTTGCCTTCATTCGAACCTGA-TTGCTGGTTCAAATCG
** * * * * *
237172 CTCTCGCTTGCTTCATTATCAGCACCCCTTTTTGATCCATCAATTTGATCTCCTCCGTTATCTAT
64 CTCTTACTTGCATCATTATCAGCACCCCCTTTTGATCCATCAATTTGATCTCCTCCATGATCTTT
* ** * *
237237 CCCACTGTCCGTATTTCCTGTT-GCTTCACCAGTT
129 CCCACTATTTGTATTTCCT-TTCGCTTCACCACTC
* * * *
237271 GACTT-TTTCCCATCCTTTATCAAATCCTTGCCTTCATTCGAACCTGATTCCTGATTCAAATCGC
1 GA-TTCTTTCCCATCCTTTACCAAATTCTTGCCTTCATTCGAACCTGATTGCTGGTTCAAATCGC
* * * * ** *
237335 TCTTACTTGTATTATTATCAGCACCTCCTTCTGATCCATCAATTTGATCTCCTCTGTTATCTTTC
65 TCTTACTTGCATCATTATCAGCACCCCCTTTTGATCCATCAATTTGATCTCCTCCATGATCTTTC
* * *
237400 CCACTGCTCT-TATTTCCTTTTGCTTCACCACTC
130 CCACT-ATTTGTATTTCCTTTCGCTTCACCACTC
** * ** * * *
237433 -ATTTCTTTCCCATCCTTTACCAAATTCTTAACTTCATTCGGACCCAATTGCTGTTTTAAACCGC
1 GA-TTCTTTCCCATCCTTTACCAAATTCTTGCCTTCATTCGAACCTGATTGCTGGTTCAAATCGC
* * * *
237497 TATTACTTGCATCATTATCGGCACCCCCTTTTGATCCATCAATTTGATCTCCTCTATTATCTTTC
65 TCTTACTTGCATCATTATCAGCACCCCCTTTTGATCCATCAATTTGATCTCCTCCATGATCTTTC
* *
237562 CCACTA---GTGTTTCCTTTCACTTCACCACTC
130 CCACTATTTGTATTTCCTTTCGCTTCACCACTC
* * *
237592 GATTCTTTCCCATCCTTTATCAAATTCTTGCCTTCATTCGAACCGGATTGCTGGTCCAAATCGCT
1 GATTCTTTCCCATCCTTTACCAAATTCTTGCCTTCATTCGAACCTGATTGCTGGTTCAAATCGCT
* * *
237657 CTTACTTGCATCATTATCAGCACCCCCTTTTGATCCATCAACTTGATCTCCTCCGTGAACTTTCC
66 CTTACTTGCATCATTATCAGCACCCCCTTTTGATCCATCAATTTGATCTCCTCCATGATCTTTCC
* * * *
237722 CACTGTTCGTATTTCCTTTCACTTCACCACTT
131 CACTATTTGTATTTCCTTTCGCTTCACCACTC
* * * * * ** * **
237754 GATTCCTTCCCAACCTTTACCAAACTCTTACCTTCATCCGAACCCAATTGCTGGTTTAGTTCGCT
1 GATTCTTTCCCATCCTTTACCAAATTCTTGCCTTCATTCGAACCTGATTGCTGGTTCAAATCGCT
* * * *
237819 CTTACTTGCACCATTATCA--ACACCCTTCTCTGATCCATCAATTTGACCTCTTCCAT
66 CTTACTTGCATCATTATCAGCACCCCCTT-T-TGATCCATCAATTTGATCTCCTCCAT
237875 CAACTTTAAT
Statistics
Matches: 785, Mismatches: 124, Indels: 38
0.83 0.13 0.04
Matches are distributed among these distances:
159 135 0.17
160 8 0.01
161 10 0.01
162 620 0.79
163 12 0.02
ACGTcount: A:0.20, C:0.31, G:0.09, T:0.39
Consensus pattern (162 bp):
GATTCTTTCCCATCCTTTACCAAATTCTTGCCTTCATTCGAACCTGATTGCTGGTTCAAATCGCT
CTTACTTGCATCATTATCAGCACCCCCTTTTGATCCATCAATTTGATCTCCTCCATGATCTTTCC
CACTATTTGTATTTCCTTTCGCTTCACCACTC
Found at i:243741 original size:29 final size:31
Alignment explanation
Indices: 243709--243774 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
243699 AATAGTTATT
*
243709 ATAATAA-ATATAACATTTTAAT-AAATTTA
1 ATAATAATATAGAACATTTTAATAAAATTTA
* *
243738 ATAATAATTTTAGAATATTTTAATAAAATTTA
1 ATAATAA-TATAGAACATTTTAATAAAATTTA
243770 ATAAT
1 ATAAT
243775 TATTTTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 7 0.23
31 12 0.39
32 12 0.39
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (31 bp):
ATAATAATATAGAACATTTTAATAAAATTTA
Found at i:243746 original size:11 final size:11
Alignment explanation
Indices: 243727--243794 Score: 75
Period size: 11 Copynumber: 6.2 Consensus size: 11
243717 TATAACATTT
243727 TAATAAATTTAA
1 TAAT-AATTTAA
*
243739 TAATAATTTTA
1 TAATAATTTAA
* *
243750 GAATATTTTAA
1 TAATAATTTAA
243761 TAA-AATTTAA
1 TAATAATTTAA
* *
243771 TAATTATTTTA
1 TAATAATTTAA
243782 TAATAATTTAA
1 TAATAATTTAA
243793 TA
1 TA
243795 TTCATTTTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
10 9 0.20
11 32 0.71
12 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (11 bp):
TAATAATTTAA
Found at i:243767 original size:32 final size:32
Alignment explanation
Indices: 243723--243794 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
243713 TAAATATAAC
243723 ATTTTAAT-AAATTTAATAATAATTTTAGAAT
1 ATTTTAATAAAATTTAATAATAATTTTAGAAT
* *
243754 ATTTTAATAAAATTTAATAATTATTTTATAAT
1 ATTTTAATAAAATTTAATAATAATTTTAGAAT
*
243786 AATTTAATA
1 ATTTTAATA
243795 TTCATTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
31 8 0.22
32 29 0.78
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (32 bp):
ATTTTAATAAAATTTAATAATAATTTTAGAAT
Found at i:243793 original size:22 final size:21
Alignment explanation
Indices: 243725--243806 Score: 87
Period size: 22 Copynumber: 3.9 Consensus size: 21
243715 AATATAACAT
*
243725 TTTAATAA-ATTTAATAATAA
1 TTTAATAATATTTTATAATAA
* *
243745 TTTTAGAATATTTTAATAA-AA
1 TTTAATAATATTTT-ATAATAA
243766 TTTAATAATTATTTTATAATAA
1 TTTAATAA-TATTTTATAATAA
*
243788 TTTAATATTCATTTTATAA
1 TTTAATAAT-ATTTTATAA
243807 ATTATAACAT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
20 6 0.12
21 17 0.33
22 28 0.55
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
TTTAATAATATTTTATAATAA
Found at i:245283 original size:156 final size:156
Alignment explanation
Indices: 245062--245782 Score: 1219
Period size: 156 Copynumber: 4.6 Consensus size: 156
245052 TTACCTCTGC
* *
245062 TGATTCCCTTACCTTCCTTAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTTG
1 TGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTTG
* *
245127 CCTGCACTAGCCTTGAATTCGATTCAATCGAATCCTTTAACTTGCATAGCTCAGCTTCACAAGTG
66 CCTGCACTAGCCTTGAATTCGATTCATTCAAATCCTTTAACTTGCATAGCTCAGCTTCACAAGTG
245192 GCAAGCTTCTCGTTAAGTTCTCTATT
131 GCAAGCTTCTCGTTAAGTTCTCTATT
*
245218 TGATTCCCTCACCTTCCTCATCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTTG
1 TGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTTG
245283 CCTGCACTAGCCTTGAATTCGATTCATTCAAATCCTTTAACTTGCATAGCTCAGCTTCACAAGTG
66 CCTGCACTAGCCTTGAATTCGATTCATTCAAATCCTTTAACTTGCATAGCTCAGCTTCACAAGTG
245348 GCAAGCTTCTCGTTAAGTTCTCTATT
131 GCAAGCTTCTCGTTAAGTTCTCTATT
* *
245374 TGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTACTTCATTTA
1 TGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTTG
* *
245439 CCTGCACTAGCCTTGAATTCAATTCATTCAAATCCTTTAACTTGCATAGCTCATCTTCACAAGTG
66 CCTGCACTAGCCTTGAATTCGATTCATTCAAATCCTTTAACTTGCATAGCTCAGCTTCACAAGTG
*
245504 GCAAGCTTCTCGTTAAGTTCTCTACT
131 GCAAGCTTCTCGTTAAGTTCTCTATT
* * * ** *
245530 TGATTCTCTCGCCTTCCTCAGCTCAGCTTCAGAACTTACAAGCTTTTCAGTAAGTGTTTCATTTG
1 TGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTTG
* * *
245595 CCTGCACTAGCCTTGAATTTGATTCATTCGAATCCTTTAATTTGCATA-CTTCAGCTTCACAAGT
66 CCTGCACTAGCCTTGAATTCGATTCATTCAAATCCTTTAACTTGCATAGC-TCAGCTTCACAAGT
*
245659 GGCAAGCTTCTCGTTAAGCTCTCTATT
130 GGCAAGCTTCTCGTTAAGTTCTCTATT
* * *
245686 TGATTCCCGCACCTTCCTCAGCTCCGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTTT
1 TGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTTG
245751 CCTGCACTAGCCTTGAATTCGATTCATTCAAA
66 CCTGCACTAGCCTTGAATTCGATTCATTCAAA
245783 GCATCTGCAT
Statistics
Matches: 527, Mismatches: 37, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
155 1 0.00
156 526 1.00
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (156 bp):
TGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTTG
CCTGCACTAGCCTTGAATTCGATTCATTCAAATCCTTTAACTTGCATAGCTCAGCTTCACAAGTG
GCAAGCTTCTCGTTAAGTTCTCTATT
Found at i:246094 original size:117 final size:117
Alignment explanation
Indices: 245823--246076 Score: 427
Period size: 117 Copynumber: 2.2 Consensus size: 117
245813 CATAGCTCAT
* * *
245823 CTTCACAAGTAGCAAGCTTCTCGTTAAGTTCTCTTTTTGCTTGCTCAAGTCGTGAATTGGATTCA
1 CTTCACAAGAAGCAAGCTTCTCGTTAAGTTCTCTGTTTGCGTGCTCAAGTCGTGAATTGGATTCA
* *
245888 GTCAATGCATTTTGGCTTGCCTCCGTCGAATCCCTCAACATCCTCAGGTCAG
66 GTCAATGCATTTTGGCTTGCCTCAGTCGAATCCATCAACATCCTCAGGTCAG
* *
245940 CTTCACAAGAGGCAAGCTTCTCGTTAAGTTCTCTGTTTGCGTGCTCGAGTCGTGAATTGGATTCA
1 CTTCACAAGAAGCAAGCTTCTCGTTAAGTTCTCTGTTTGCGTGCTCAAGTCGTGAATTGGATTCA
*
246005 GTCAATGCATTTTGGCTTGCCTCAGTTGAATCCATCAACATCCTCAGGTCAG
66 GTCAATGCATTTTGGCTTGCCTCAGTCGAATCCATCAACATCCTCAGGTCAG
*
246057 CTTCACAGGAAGCAAGCTTC
1 CTTCACAAGAAGCAAGCTTC
246077 CTTCTAAGCT
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 127 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (117 bp):
CTTCACAAGAAGCAAGCTTCTCGTTAAGTTCTCTGTTTGCGTGCTCAAGTCGTGAATTGGATTCA
GTCAATGCATTTTGGCTTGCCTCAGTCGAATCCATCAACATCCTCAGGTCAG
Found at i:246120 original size:117 final size:117
Alignment explanation
Indices: 245823--246133 Score: 410
Period size: 117 Copynumber: 2.7 Consensus size: 117
245813 CATAGCTCAT
* * * * *
245823 CTTCACAAGTAGCAAGCTTCTCGTTAAGTTCTCTTTTTGCTTGCTCAAGTCGTGAATTGGATTCA
1 CTTCACAAGAAGCAAGCTTCTCGTTAAGTTCTCTGTTTGCGTGCTCGAGCCGTGAATTGGATTCA
* *
245888 GTCAATGCATTTTGGCTTGCCTCCGTCGAATCCCTCAACATCCTCAGGTCAG
66 GTCAATGCATTTTGGCTTGCCTCAGTCGAATCCATCAACATCCTCAGGTCAG
* *
245940 CTTCACAAGAGGCAAGCTTCTCGTTAAGTTCTCTGTTTGCGTGCTCGAGTCGTGAATTGGATTCA
1 CTTCACAAGAAGCAAGCTTCTCGTTAAGTTCTCTGTTTGCGTGCTCGAGCCGTGAATTGGATTCA
*
246005 GTCAATGCATTTTGGCTTGCCTCAGTTGAATCCATCAACATCCTCAGGTCAG
66 GTCAATGCATTTTGGCTTGCCTCAGTCGAATCCATCAACATCCTCAGGTCAG
* * * * * * * * *
246057 CTTCACAGGAAGCAAGCTTC-CTTCTAAGCTT-TCTGTTTTCTTGTTCTAGCCTTGCATTTGATT
1 CTTCACAAGAAGCAAGCTTCTCGT-TAAG-TTCTCTGTTTGCGTGCTCGAGCCGTGAATTGGATT
*
246120 CAGCCAATGCATTT
64 CAGTCAATGCATTT
246134 GTTCCCGCCT
Statistics
Matches: 172, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
116 2 0.01
117 168 0.98
118 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (117 bp):
CTTCACAAGAAGCAAGCTTCTCGTTAAGTTCTCTGTTTGCGTGCTCGAGCCGTGAATTGGATTCA
GTCAATGCATTTTGGCTTGCCTCAGTCGAATCCATCAACATCCTCAGGTCAG
Found at i:249634 original size:2 final size:2
Alignment explanation
Indices: 249627--249671 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
249617 CCCGATACAA
249627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
249669 AT A
1 AT A
249672 ATTTTAAACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:251374 original size:32 final size:32
Alignment explanation
Indices: 251328--251398 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
251318 AATAATAAAC
* *
251328 TTTGAT-AAATTTAATGATCATTTTATAACAT
1 TTTGATAAAATTTAATGATAAATTTATAACAT
*
251359 TTTGATAAAATTTAATGATAAATTTATAATAT
1 TTTGATAAAATTTAATGATAAATTTATAACAT
*
251391 TTTAATAA
1 TTTGATAA
251399 TTTTATTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 6 0.17
32 29 0.83
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.48
Consensus pattern (32 bp):
TTTGATAAAATTTAATGATAAATTTATAACAT
Found at i:251541 original size:2 final size:2
Alignment explanation
Indices: 251534--251559 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
251524 ATGTATATGC
251534 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
251560 TAAAATCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:252244 original size:25 final size:27
Alignment explanation
Indices: 252156--252260 Score: 160
Period size: 27 Copynumber: 3.9 Consensus size: 27
252146 AAAGAACTCA
*
252156 TTTTCATCAAATTTCTATGTCAATTTTT
1 TTTTCATCAAATTTCTATCTCAA-TTTT
* *
252184 TTTTCATCAAATTTCCATGTCAATTTT
1 TTTTCATCAAATTTCTATCTCAATTTT
252211 TTTTCATCAAATTTCTATCTCAA-TTT
1 TTTTCATCAAATTTCTATCTCAATTTT
252237 TTTT-ATCAAATTTCTATCTCAATT
1 TTTTCATCAAATTTCTATCTCAATT
252261 AACAAAAACT
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
25 18 0.25
26 8 0.11
27 25 0.34
28 22 0.30
ACGTcount: A:0.27, C:0.17, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTTCATCAAATTTCTATCTCAATTTT
Found at i:254368 original size:31 final size:31
Alignment explanation
Indices: 254330--254440 Score: 177
Period size: 31 Copynumber: 3.6 Consensus size: 31
254320 AGAGTCGAGG
* * *
254330 GTTTACCTATGTTCTTAGGGAGATATAGACT
1 GTTTACCTATGTTCTTCGGGAAATATGGACT
*
254361 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGAAATATGGACT
254392 GTTTACCTATGTTCTTCGGGAAATATGGACT
1 GTTTACCTATGTTCTTCGGGAAATATGGACT
*
254423 GTTTACCTAGGTTCTTCG
1 GTTTACCTATGTTCTTCG
254441 AAATCTATGG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGAAATATGGACT
Found at i:254450 original size:31 final size:30
Alignment explanation
Indices: 254330--254454 Score: 128
Period size: 31 Copynumber: 4.0 Consensus size: 30
254320 AGAGTCGAGG
* * *
254330 GTTTACCTATGTTCTTAGGGAGA-TATAGACT
1 GTTTACCTATGTTCTT--CGAAACTATGGACT
**
254361 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGAAAC-TATGGACT
254392 GTTTACCTATGTTCTTCGGGAAA-TATGGACT
1 GTTTACCTATGTTCTTC--GAAACTATGGACT
*
254423 GTTTACCTAGGTTCTTCGAAATCTATGGACT
1 GTTTACCTATGTTCTTCGAAA-CTATGGACT
254454 G
1 G
254455 GTCCTTTGGG
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
29 7 0.09
31 73 0.89
33 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (30 bp):
GTTTACCTATGTTCTTCGAAACTATGGACT
Found at i:254450 original size:62 final size:62
Alignment explanation
Indices: 254330--254454 Score: 180
Period size: 62 Copynumber: 2.0 Consensus size: 62
254320 AGAGTCGAGG
* * **
254330 GTTTACCTATGTTCTTAGGGAGATATAGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTAGGGAAATATAGACTGTTTACCTAGGTTCTTCGAAACATATGGACT
* *
254392 GTTTACCTATGTTCTTCGGGAAATATGGACTGTTTACCTAGGTTCTTCGAAATC-TATGGACT
1 GTTTACCTATGTTCTTAGGGAAATATAGACTGTTTACCTAGGTTCTTCGAAA-CATATGGACT
254454 G
1 G
254455 GTCCTTTGGG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
62 55 0.98
63 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (62 bp):
GTTTACCTATGTTCTTAGGGAAATATAGACTGTTTACCTAGGTTCTTCGAAACATATGGACT
Found at i:255206 original size:22 final size:21
Alignment explanation
Indices: 255160--255206 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
255150 GCAGTACTGT
*
255160 AGCAGGGTATCAGTACCCTGT
1 AGCAGGGTATCAGTACCCTGA
255181 AGCAGGGTATC-GATACCCCTGA
1 AGCAGGGTATCAG-TA-CCCTGA
255203 AGCA
1 AGCA
255207 ATCTGGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 13 0.57
22 9 0.39
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.19
Consensus pattern (21 bp):
AGCAGGGTATCAGTACCCTGA
Found at i:257355 original size:24 final size:24
Alignment explanation
Indices: 257328--257427 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
257318 GATGTCAAAA
*
257328 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
257352 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
257376 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
257400 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
257424 ATCA
1 ATCA
257428 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:257427 original size:48 final size:48
Alignment explanation
Indices: 257326--257429 Score: 118
Period size: 48 Copynumber: 2.2 Consensus size: 48
257316 GAGATGTCAA
* * * ** *
257326 AAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAGGTTAG
1 AAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAAATCAG
* * * *
257374 GAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAAATCAG
1 AAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAAATCAG
257422 AAATCAGA
1 AAATCAGA
257430 TAAAATATTC
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.21
Consensus pattern (48 bp):
AAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAAATCAG
Found at i:259939 original size:15 final size:15
Alignment explanation
Indices: 259919--259952 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
259909 TGTTAACACC
259919 GGTCAACAGTCAACG
1 GGTCAACAGTCAACG
*
259934 GGTCAACGGTCAACG
1 GGTCAACAGTCAACG
259949 GGTC
1 GGTC
259953 GGGTCGGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.15
Consensus pattern (15 bp):
GGTCAACAGTCAACG
Found at i:259968 original size:18 final size:18
Alignment explanation
Indices: 259945--259995 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
259935 GTCAACGGTC
259945 AACGGGTCGGGTCGGGTA
1 AACGGGTCGGGTCGGGTA
*
259963 AACGGGTCGGGTCGGGTC
1 AACGGGTCGGGTCGGGTA
259981 AACGGGTCGGGTCGG
1 AACGGGTCGGGTCGG
259996 TTTGTGACCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.14, C:0.20, G:0.51, T:0.16
Consensus pattern (18 bp):
AACGGGTCGGGTCGGGTA
Found at i:262123 original size:32 final size:31
Alignment explanation
Indices: 262049--262127 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
262039 TCAAACGGTC
262049 GGGGACCATATTGCAAACAGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
*
262080 GGAGACCATATTGCAAACAGACTAAATGTTTG
1 GGGGACCATATTGCAAACAGACTAAATG-TTG
*
262112 GGGGACTATATTGCAA
1 GGGGACCATATTGCAA
262128 GTTTTAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 27 0.61
32 17 0.39
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:262900 original size:16 final size:16
Alignment explanation
Indices: 262857--262901 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
262847 TGAGTCACGC
*
262857 GCTTAATGAGCAACGA
1 GCTTAACGAGCAACGA
* * *
262873 ACATAACAAGCAACGA
1 GCTTAACGAGCAACGA
262889 GCTTAACGAGCAA
1 GCTTAACGAGCAA
262902 TGAGTCGAGT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.13
Consensus pattern (16 bp):
GCTTAACGAGCAACGA
Found at i:269923 original size:3 final size:3
Alignment explanation
Indices: 269915--269968 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
269905 AATTATTTAA
* ** *
269915 ATT ATT ATT TTT AAA ATT GTT ATT ATT ATT ATT ATT ATT ATAT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T AT-T
269962 ATT ATT A
1 ATT ATT A
269969 AATTAAATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 35 0.83
4 7 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:271249 original size:11 final size:11
Alignment explanation
Indices: 271233--271284 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
271223 CTTTTTAATC
271233 ATTATTTTTTT
1 ATTATTTTTTT
*
271244 ATTATTTTGTT
1 ATTATTTTTTT
* *
271255 ATTACTTTTAT
1 ATTATTTTTTT
*
271266 ATTATTTTATT
1 ATTATTTTTTT
271277 ATTATTTT
1 ATTATTTT
271285 CATATTAGTC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (11 bp):
ATTATTTTTTT
Found at i:271263 original size:22 final size:21
Alignment explanation
Indices: 271233--271291 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
271223 CTTTTTAATC
271233 ATTATT-TTTT-TATTATTTT
1 ATTATTATTTTATATTATTTT
*
271252 GTTATTACTTTTATATTATTTT
1 ATTATTA-TTTTATATTATTTT
271274 ATTATTATTTTCATATTA
1 ATTATTATTTT-ATATTA
271292 GTCACATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 5 0.15
21 8 0.24
22 21 0.62
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.69
Consensus pattern (21 bp):
ATTATTATTTTATATTATTTT
Found at i:271290 original size:11 final size:10
Alignment explanation
Indices: 271233--271291 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
271223 CTTTTTAATC
*
271233 ATTATTTTTTT
1 ATTA-TTTTAT
*
271244 ATTATTTTGTT
1 ATTATTTT-AT
271255 ATTACTTTTAT
1 ATTA-TTTTAT
271266 ATTATTTTATT
1 ATTATTTTA-T
271277 ATTATTTTCAT
1 ATTATTTT-AT
271288 ATTA
1 ATTA
271292 GTCACATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 9 0.21
11 29 0.67
12 5 0.12
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.69
Consensus pattern (10 bp):
ATTATTTTAT
Found at i:271422 original size:22 final size:22
Alignment explanation
Indices: 271396--271441 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
271386 GGTATTTTAA
271396 ATAATTAAATATTATAAAAATT
1 ATAATTAAATATTATAAAAATT
* * **
271418 ATAATTTAATTTTATTTAAATT
1 ATAATTAAATATTATAAAAATT
271440 AT
1 AT
271442 TTTTAGGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAATTAAATATTATAAAAATT
Found at i:273689 original size:28 final size:29
Alignment explanation
Indices: 273642--273700 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
273632 TATTAAAAAA
*
273642 TAAAATTATGAAAATATTAAATTTAGTTT
1 TAAAATTATAAAAATATTAAATTTAGTTT
* *
273671 TAAAA-TATAAAAATCTTAAATTTATTTT
1 TAAAATTATAAAAATATTAAATTTAGTTT
273699 TA
1 TA
273701 TTGTAAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (29 bp):
TAAAATTATAAAAATATTAAATTTAGTTT
Found at i:276773 original size:41 final size:41
Alignment explanation
Indices: 276713--276793 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
276703 GTTCGAACTT
**
276713 TGATGTTTGTTAATAGAGCAAATTGTA-TTGAGAGAGTCACC
1 TGATGTTTGCAAATAGAGCAAATTG-AGTTGAGAGAGTCACC
* *
276754 TGATGTTTGCAAATGGAGCAAATTGAGTTGAGAGGGTCAC
1 TGATGTTTGCAAATAGAGCAAATTGAGTTGAGAGAGTCAC
276794 ACTGTCTACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 1 0.03
41 34 0.97
ACGTcount: A:0.31, C:0.10, G:0.28, T:0.31
Consensus pattern (41 bp):
TGATGTTTGCAAATAGAGCAAATTGAGTTGAGAGAGTCACC
Found at i:277677 original size:22 final size:21
Alignment explanation
Indices: 277652--277694 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
277642 GATCAAACCA
*
277652 GCCCCATTACAAAATCTAAATG
1 GCCCAATTACAAAATC-AAATG
* *
277674 GCCCAATTCCTAAATCAAATG
1 GCCCAATTACAAAATCAAATG
277695 AGAGTTCGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.23
Consensus pattern (21 bp):
GCCCAATTACAAAATCAAATG
Found at i:279583 original size:29 final size:29
Alignment explanation
Indices: 279537--279614 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
279527 AACTTCTGTC
*
279537 ATTTACATTTTTGACCTTTAATTTATGTT
1 ATTTACATTTCTGACCTTTAATTTATGTT
*
279566 ATTTACATTTCT-ACCCTTTAATTTTTGTT
1 ATTTACATTTCTGA-CCTTTAATTTATGTT
*
279595 ATTTTA-ATTTGTG-CCTTTAA
1 A-TTTACATTTCTGACCTTTAA
279615 ATTTCATCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 8 0.19
29 31 0.72
30 4 0.09
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (29 bp):
ATTTACATTTCTGACCTTTAATTTATGTT
Found at i:284297 original size:15 final size:16
Alignment explanation
Indices: 284277--284306 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
284267 TAATCAAAAT
284277 GAAAAATA-ATATTTG
1 GAAAAATATATATTTG
284292 GAAAAATATATATTT
1 GAAAAATATATATTT
284307 TAAACACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (16 bp):
GAAAAATATATATTTG
Found at i:285493 original size:2 final size:2
Alignment explanation
Indices: 285486--285544 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
285476 AGATTTGGAA
285486 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
285528 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
285545 CTTTTTCACC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:287063 original size:21 final size:22
Alignment explanation
Indices: 287033--287089 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
287023 TAATACATAA
*
287033 AATAGTATTTAATTTAT-ATTT
1 AATATTATTTAATTTATAATTT
*
287054 AGAT-TTATTTGATTTATAATTT
1 A-ATATTATTTAATTTATAATTT
*
287076 ATTATTATTTAATT
1 AATATTATTTAATT
287090 AAATTAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
AATATTATTTAATTTATAATTT
Found at i:293950 original size:20 final size:20
Alignment explanation
Indices: 293925--293966 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
293915 TTGGCCACCA
* *
293925 CGCCGGCCGCCGCTGATCGG
1 CGCCGGCCACCGCTCATCGG
293945 CGCCGGCCACCGCTCATCGG
1 CGCCGGCCACCGCTCATCGG
293965 CG
1 CG
293967 GCGAACCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.07, C:0.48, G:0.36, T:0.10
Consensus pattern (20 bp):
CGCCGGCCACCGCTCATCGG
Found at i:295284 original size:106 final size:105
Alignment explanation
Indices: 295092--295760 Score: 943
Period size: 105 Copynumber: 6.5 Consensus size: 105
295082 CAATGCAAGA
* * * * * * ** *
295092 TGCGTTGTTTCGAGGCCAATATCCTTTGATGTGAAGTTGAAATTGGCTCTAAAACCGGGAAATTA
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AATTG
* * *
295157 CTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACT
65 TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* * * *
295198 TGTGTTGTCTGGGGCCCAATCTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-TTG
*
295263 TTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACT
65 TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
*
295304 TGCGTTGTCTGGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTC------T-GGAATTGT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTGT
295362 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* *
295402 TGCGTTGTCTGGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCCCTG--A-----AATTGT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTGT
295460 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* *
295500 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTGT
* *
295565 TTGTTGACAACCAGCGGTCCTTTCGTCGTGAAGTTGAACT
66 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* * * *
295605 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGACATTGAGAAATAT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTGT
*
295670 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* *
295710 TACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAATTTGAAATTGGCTCTG
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
295761 GGTAAAACCT
Statistics
Matches: 517, Mismatches: 35, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
98 184 0.36
99 4 0.01
100 2 0.00
105 196 0.38
106 131 0.25
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (105 bp):
TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTGT
TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
Found at i:295437 original size:98 final size:98
Alignment explanation
Indices: 295161--295761 Score: 844
Period size: 98 Copynumber: 5.9 Consensus size: 98
295151 AAATTACTTG
* * * * *
295161 TTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGGGCCCAATCTCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
295226 TTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
66 TTGTGAAGTTGAAATTGGCTC------T-GGAA-TTGTTTA
* *
295267 TTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTTG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
295332 TTGTGAAGTTGAAATTGGCTCTGGAATTGTTTA
66 TTGTGAAGTTGAAATTGGCTCTGGAATTGTTTA
295365 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* * *
295430 TTATGAAGTTGAAATTGGCCCTGAAATTGTTTA
66 TTGTGAAGTTGAAATTGGCTCTGGAATTGTTTA
295463 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* *
295528 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTG
66 TTGTGAAGTTGAAATTGGCTC------TG-GAATTGTTTA
*
295568 TTGACAACCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
295633 TTGTGAAGTTGAAATTGGCTCT-GACATTGAGAAATATTTG
66 TTGTGAAGTTGAAATTGGCTCTGGA-ATT--G-----TTTA
*
295673 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
295738 TTGTGAATTTGAAATTGGCTCTGG
66 TTGTGAAGTTGAAATTGGCTCTGG
295762 GTAAAACCTG
Statistics
Matches: 457, Mismatches: 22, Indels: 32
0.89 0.04 0.06
Matches are distributed among these distances:
97 2 0.00
98 186 0.41
99 5 0.01
100 2 0.00
104 2 0.00
105 180 0.39
106 80 0.18
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (98 bp):
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
TTGTGAAGTTGAAATTGGCTCTGGAATTGTTTA
Found at i:295538 original size:196 final size:200
Alignment explanation
Indices: 295161--295761 Score: 877
Period size: 203 Copynumber: 3.0 Consensus size: 200
295151 AAATTACTTG
* * * * *
295161 TTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGGGCCCAATCTCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* * * *
295226 TTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCAGTCCCTTCGTC
66 TTATGAAGTTGAAATTGGCTC--ACA-TGAGAA-TTGTTTATTGACAACCAGCGGTCCCTTCGTC
*
295291 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGG
127 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGG
*
295356 AATTGTTTA
192 AAATGTTTA
295365 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
295430 TTATGAAGTTGAAATTGGC-C-C-TGA-AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
66 TTATGAAGTTGAAATTGGCTCACATGAGAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
295491 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
131 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC------T
*
295556 GAGAAATGTTTG
190 G-GAAATGTTTA
*
295568 TTGACAACCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* * * *
295633 TTGTGAAGTTGAAATTGGCTCTGACATTGAGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCG
66 TTATGAAGTTGAAATTGGCTC--ACA-TGAGAATTGTTTATTGACAACCAGCGGTCCCTTCGTCG
* *
295698 TGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAATTTGAAATTGGCTCTGG
128 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGG
295762 GTAAAACCTG
Statistics
Matches: 364, Mismatches: 19, Indels: 29
0.88 0.05 0.07
Matches are distributed among these distances:
196 91 0.25
197 2 0.01
198 2 0.01
202 2 0.01
203 92 0.25
204 81 0.22
207 1 0.00
209 3 0.01
210 90 0.25
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (200 bp):
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
TTATGAAGTTGAAATTGGCTCACATGAGAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAAAT
GTTTA
Found at i:305982 original size:20 final size:20
Alignment explanation
Indices: 305943--305986 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
305933 ATGGTTAGTA
*
305943 AAATAAAAATAAATGAAAAT
1 AAATAAAAATAAAAGAAAAT
305963 AAATAAAAATAACAAG-AAAT
1 AAATAAAAATAA-AAGAAAAT
305983 AAAT
1 AAAT
305987 GGCAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAAAGAAAAT
Found at i:307758 original size:20 final size:20
Alignment explanation
Indices: 307733--307774 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
307723 TTGGCCACCA
* *
307733 CGCCGGCCGCCGCTGATCGG
1 CGCCGGCCACCGCTCATCGG
307753 CGCCGGCCACCGCTCATCGG
1 CGCCGGCCACCGCTCATCGG
307773 CG
1 CG
307775 GCGAACCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.07, C:0.48, G:0.36, T:0.10
Consensus pattern (20 bp):
CGCCGGCCACCGCTCATCGG
Found at i:317239 original size:12 final size:12
Alignment explanation
Indices: 317222--317247 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
317212 CTACATTATC
317222 TACTGATAAATT
1 TACTGATAAATT
317234 TACTGATAAATT
1 TACTGATAAATT
317246 TA
1 TA
317248 TTGTTTGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
TACTGATAAATT
Found at i:321461 original size:18 final size:19
Alignment explanation
Indices: 321438--321473 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
321428 CATATCTTTA
*
321438 TTTTATTT-TTTAAATAAT
1 TTTTATTTATTCAAATAAT
321456 TTTTATTTATTCAAATAA
1 TTTTATTTATTCAAATAA
321474 AATAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTATTTATTCAAATAAT
Found at i:322269 original size:8 final size:8
Alignment explanation
Indices: 321693--322268 Score: 684
Period size: 8 Copynumber: 72.0 Consensus size: 8
321683 CCTCACCCTT
321693 ATACATAC
1 ATACATAC
321701 ATACATAC
1 ATACATAC
321709 ATACATAC
1 ATACATAC
321717 ATACATAC
1 ATACATAC
321725 ATACATAC
1 ATACATAC
321733 ATACATAC
1 ATACATAC
321741 ATACATAC
1 ATACATAC
321749 ATACATAC
1 ATACATAC
321757 ATACATAC
1 ATACATAC
321765 ATACATAC
1 ATACATAC
321773 ATACATAC
1 ATACATAC
321781 ATACATAC
1 ATACATAC
321789 ATACATAC
1 ATACATAC
321797 ATACATAC
1 ATACATAC
321805 ATACATAC
1 ATACATAC
321813 ATACATAC
1 ATACATAC
321821 ATACATAC
1 ATACATAC
321829 ATACATAC
1 ATACATAC
321837 ATACATAC
1 ATACATAC
321845 ATACATAC
1 ATACATAC
321853 ATACATAC
1 ATACATAC
321861 ATACATAC
1 ATACATAC
321869 ATACATAC
1 ATACATAC
321877 ATACATAC
1 ATACATAC
321885 ATACATAC
1 ATACATAC
321893 ATACATAC
1 ATACATAC
321901 ATACATAC
1 ATACATAC
321909 ATACATAC
1 ATACATAC
*
321917 ATACCTAC
1 ATACATAC
* *
321925 GTACCTAC
1 ATACATAC
* *
321933 GTACCTAC
1 ATACATAC
* *
321941 GTACCTAC
1 ATACATAC
* *
321949 GTACCTAC
1 ATACATAC
* *
321957 GTACCTAC
1 ATACATAC
* *
321965 GTACCTAC
1 ATACATAC
*
321973 GTACATAC
1 ATACATAC
*
321981 GTACATAC
1 ATACATAC
* *
321989 GTACATAT
1 ATACATAC
321997 ATACATAC
1 ATACATAC
*
322005 GTACATAC
1 ATACATAC
*
322013 ATACATAT
1 ATACATAC
*
322021 ATACGTAC
1 ATACATAC
*
322029 ATACGTAC
1 ATACATAC
** *
322037 ATATGTAT
1 ATACATAC
322045 ATACATAC
1 ATACATAC
322053 ATACATAC
1 ATACATAC
**
322061 ATATGTAC
1 ATACATAC
* *
322069 ATACGTAT
1 ATACATAC
*
322077 ATATATAC
1 ATACATAC
**
322085 ATATGTAC
1 ATACATAC
*
322093 ATATATAC
1 ATACATAC
322101 ATACATAC
1 ATACATAC
*
322109 ATACATAT
1 ATACATAC
*
322117 GTACATAC
1 ATACATAC
322125 ATACATAC
1 ATACATAC
**
322133 ATATGTAC
1 ATACATAC
322141 ATACATAC
1 ATACATAC
322149 ATACATAC
1 ATACATAC
* *
322157 ATACGTAT
1 ATACATAC
* *
322165 GTACGTAC
1 ATACATAC
* *
322173 GTACGTAC
1 ATACATAC
* *
322181 GTACAAAC
1 ATACATAC
322189 ATACATAC
1 ATACATAC
* *
322197 ATACGTGC
1 ATACATAC
322205 ATACATAC
1 ATACATAC
322213 ATACATAC
1 ATACATAC
*
322221 ATATATAC
1 ATACATAC
* *
322229 GTACGTAC
1 ATACATAC
* *
322237 GTACATAT
1 ATACATAC
322245 ATACATAC
1 ATACATAC
322253 ATACATAC
1 ATACATAC
*
322261 GTACATAC
1 ATACATAC
322269 GGGGTTCATG
Statistics
Matches: 513, Mismatches: 55, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 513 1.00
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.27
Consensus pattern (8 bp):
ATACATAC
Found at i:327161 original size:2 final size:2
Alignment explanation
Indices: 327154--327183 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
327144 TTAAAGGTAA
327154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
327184 CTGATTATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:330052 original size:15 final size:15
Alignment explanation
Indices: 330032--330062 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
330022 GCATCTCCCA
*
330032 ATCAAATAAGGGGTC
1 ATCAAATAAGAGGTC
330047 ATCAAATAAGAGGTC
1 ATCAAATAAGAGGTC
330062 A
1 A
330063 AACATGTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (15 bp):
ATCAAATAAGAGGTC
Found at i:350872 original size:43 final size:43
Alignment explanation
Indices: 350815--350897 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
350805 AACTCACTGC
* *
350815 TTGTGCTAGTATTGCTCTTAAATTGC-GTAGGTGATATTGTGCT
1 TTGTGCCAGTATTGCTCTTAAATTGCAAT-GGTGATATTGTGCT
*
350858 TTGTGCCAGTATTGCTCTTGAATTGCAATGGTGATATTGT
1 TTGTGCCAGTATTGCTCTTAAATTGCAATGGTGATATTGT
350898 TGAAAAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 35 0.97
44 1 0.03
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.43
Consensus pattern (43 bp):
TTGTGCCAGTATTGCTCTTAAATTGCAATGGTGATATTGTGCT
Found at i:366375 original size:25 final size:27
Alignment explanation
Indices: 366347--366397 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
366337 TAGGTGAACA
366347 TATAAAATTTTA-A-ATGAAAATAACT
1 TATAAAATTTTAGATATGAAAATAACT
*
366372 TATAGAATTTTAGGATATGAAAATAA
1 TATAAAATTTTA-GATATGAAAATAA
366398 ATTTACAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 11 0.50
27 1 0.05
28 10 0.45
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (27 bp):
TATAAAATTTTAGATATGAAAATAACT
Found at i:366850 original size:14 final size:15
Alignment explanation
Indices: 366831--366863 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
366821 TTTAAATTAT
366831 TTAAATATA-ACTTA
1 TTAAATATATACTTA
*
366845 TTAAATATATATTTA
1 TTAAATATATACTTA
366860 TTAA
1 TTAA
366864 GTGATGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAAATATATACTTA
Found at i:374254 original size:2 final size:2
Alignment explanation
Indices: 374249--374283 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
374239 CAAAAAGACA
*
374249 AG AG AG AG AG AG AG AG TG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
374284 CCCTTCATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (2 bp):
AG
Found at i:375053 original size:2 final size:2
Alignment explanation
Indices: 375046--375077 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
375036 TCTCCCTCCC
375046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
375078 AAAAAAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:376719 original size:31 final size:31
Alignment explanation
Indices: 376684--376742 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
376674 AAATTACGTA
*
376684 TTTAATCATTTAATTATCACATTAATTTCAT
1 TTTAATCATTTAACTATCACATTAATTTCAT
*
376715 TTTAATCATTTAACTATCACTTTAATTT
1 TTTAATCATTTAACTATCACATTAATTT
376743 GGATCATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTAATCATTTAACTATCACATTAATTTCAT
Found at i:378060 original size:37 final size:37
Alignment explanation
Indices: 378019--378126 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
378009 AACATAACGT
378019 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAAGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAAGA
*
378056 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAAGA
* * * * *
378093 TAGAGATCTACTATGATTTAAACTCCTAACAATA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATA
378127 GGATCCAGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAAGA
Found at i:378591 original size:3 final size:3
Alignment explanation
Indices: 378583--378663 Score: 69
Period size: 3 Copynumber: 26.7 Consensus size: 3
378573 AACAGTATAT
* * *
378583 TTA TTA TTA -TA TATA TT- TAA TTA TATA TTT TTA TTA TCTA TTA TTT
1 TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA
*
378629 TTA TTA TTA TTA TTA TTA CTT- TTT TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT
378664 TATTCTTTCG
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
2 5 0.08
3 48 0.75
4 11 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:378599 original size:12 final size:12
Alignment explanation
Indices: 378578--378746 Score: 51
Period size: 12 Copynumber: 14.4 Consensus size: 12
378568 ATTCCAACAG
*
378578 TATATTTATTAT
1 TATATATATTAT
378590 TATATATATTTAAT
1 TATATATA-TT-AT
378604 TATATAT-TT-T
1 TATATATATTAT
*
378614 TATTATCTATTAT
1 TA-TATATATTAT
378627 T-T-T-TATTAT
1 TATATATATTAT
378636 TAT-TATTATTACT
1 TATATA-TATTA-T
* *
378649 T-TTTTTATTAT
1 TATATATATTAT
*
378660 TAT-T-TATTCT
1 TATATATATTAT
* * *
378670 T-TCGTCATTTTAA
1 TAT-AT-ATATTAT
378683 TATATATA-TA-
1 TATATATATTAT
378693 TATATATA-TAT
1 TATATATATTAT
378704 ATATATATATTAT
1 -TATATATATTAT
*
378717 CACTAT-TATATAT
1 TA-TATATAT-TAT
* *
378730 TTTATATATTAC
1 TATATATATTAT
378742 TATAT
1 TATAT
378747 TTTATCACTA
Statistics
Matches: 121, Mismatches: 14, Indels: 44
0.68 0.08 0.25
Matches are distributed among these distances:
9 8 0.07
10 22 0.18
11 11 0.09
12 46 0.38
13 24 0.20
14 10 0.08
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.61
Consensus pattern (12 bp):
TATATATATTAT
Found at i:378599 original size:16 final size:16
Alignment explanation
Indices: 378578--378751 Score: 80
Period size: 16 Copynumber: 10.6 Consensus size: 16
378568 ATTCCAACAG
378578 TATATTTATTATTATA
1 TATATTTATTATTATA
378594 TATATTTA--ATTATA
1 TATATTTATTATTATA
*
378608 TATTTTTATTATCTAT-
1 TATATTTATTAT-TATA
*
378624 TATTTTTATTATTATTA
1 TATATTTATTATTA-TA
378641 TTATTACTTT-TT-TTAT-
1 -TA-TA-TTTATTATTATA
* *
378657 TATTATTTATTCTT-TCG
1 TA-TATTTATTATTAT-A
*
378674 TCAT-TTTAATATATATA
1 T-ATATTTATTAT-TATA
*
378691 TATATATATATATATATA
1 TATATTTAT-TAT-TATA
*
378709 TATATTATCACTATTATA
1 TATATT-T-ATTATTATA
378727 TAT-TTTATATATTACTA
1 TATATTTAT-TATTA-TA
378744 TAT-TTTAT
1 TATATTTAT
378752 CACTATGTAT
Statistics
Matches: 127, Mismatches: 10, Indels: 41
0.71 0.06 0.23
Matches are distributed among these distances:
14 16 0.13
15 11 0.09
16 39 0.31
17 23 0.18
18 27 0.21
19 7 0.06
20 4 0.03
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (16 bp):
TATATTTATTATTATA
Found at i:378605 original size:14 final size:14
Alignment explanation
Indices: 378578--378619 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
378568 ATTCCAACAG
378578 TATATTTATTATTATA
1 TATATTTA--ATTATA
378594 TATATTTAATTATA
1 TATATTTAATTATA
*
378608 TAT-TTTTATTAT
1 TATATTTAATTAT
378620 CTATTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 8 0.32
14 9 0.36
16 8 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATATTTAATTATA
Found at i:378689 original size:2 final size:2
Alignment explanation
Indices: 378682--378738 Score: 66
Period size: 2 Copynumber: 29.0 Consensus size: 2
378672 CGTCATTTTA
378682 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT CACT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -A-T AT AT
*
378724 AT AT AT -T TT AT AT AT
1 AT AT AT AT AT AT AT AT
378739 TACTATATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
1 3 0.06
2 43 0.88
3 2 0.04
4 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:380575 original size:32 final size:32
Alignment explanation
Indices: 380534--380628 Score: 127
Period size: 32 Copynumber: 2.9 Consensus size: 32
380524 TGAAGGCATC
*
380534 TTTGAAGATTCAACAACAAATGTTGGGGTATTT
1 TTTG-AGATTCAACAACAAATGTTGGGGCATTT
* *
380567 TTTGAGATTTAACATCAAATGTTGGGGCATTT
1 TTTGAGATTCAACAACAAATGTTGGGGCATTT
* * *
380599 TTTGAGATTCAACATCGAATATTGGGGCAT
1 TTTGAGATTCAACAACAAATGTTGGGGCAT
380629 CTTTGGGAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
32 52 0.93
33 4 0.07
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.37
Consensus pattern (32 bp):
TTTGAGATTCAACAACAAATGTTGGGGCATTT
Found at i:380641 original size:32 final size:32
Alignment explanation
Indices: 380539--380642 Score: 102
Period size: 32 Copynumber: 3.2 Consensus size: 32
380529 GCATCTTTGA
* * * **
380539 AGATTCAACAACAAATGTTGGGGTATTTTTTG
1 AGATTCAACATCAAATATTGGGGCATTTTGGG
* * **
380571 AGATTTAACATCAAATGTTGGGGCATTTTTTG
1 AGATTCAACATCAAATATTGGGGCATTTTGGG
*
380603 AGATTCAACATCGAATATTGGGGCATCTTTGGG
1 AGATTCAACATCAAATATTGGGGCAT-TTTGGG
380636 A-ATTCAA
1 AGATTCAA
380643 TATCCTGATG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 58 0.92
33 5 0.08
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGGGGCATTTTGGG
Found at i:386261 original size:13 final size:13
Alignment explanation
Indices: 386232--386266 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
386222 ATAACTAATA
*
386232 ATATTAAAT-ATT
1 ATATTAAATAAAT
386244 ATATTAAATAAAT
1 ATATTAAATAAAT
386257 ATATTAAATA
1 ATATTAAATA
386267 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:386792 original size:34 final size:31
Alignment explanation
Indices: 386747--386835 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
386737 TTAATAATTC
* *
386747 TAAATAAATAATAATTATATAAATATTTTTTTAA
1 TAAAAAAATAATAATTATATAAATA---TATTAA
* *
386781 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* *
386812 TATAAAAAATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
386836 AAAATACTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 7 0.15
32 17 0.37
34 22 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:388161 original size:10 final size:10
Alignment explanation
Indices: 388120--388162 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
388110 TTATTAGTTT
*
388120 ATTAAAACTA
1 ATTAAAAATA
388130 ATTAAATAATA
1 ATTAAA-AATA
388141 ATATAAAAAATA
1 AT-T-AAAAATA
388153 ATTAAAAATA
1 ATTAAAAATA
388163 CCACATTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 13 0.45
11 6 0.21
12 7 0.24
13 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (10 bp):
ATTAAAAATA
Found at i:391830 original size:41 final size:41
Alignment explanation
Indices: 391784--391863 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
391774 CACTTTTAGA
* *
391784 CAATTTAAAAGCCAAGTAAGATCTGTACATAATTATTAGGG
1 CAATTTAAAAACCAAGTAAGATCTGTAAATAATTATTAGGG
391825 CAATTTAAAAACCAAGTAAGATCTGTAAATAATTATTAG
1 CAATTTAAAAACCAAGTAAGATCTGTAAATAATTATTAG
391864 AGCACGTAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (41 bp):
CAATTTAAAAACCAAGTAAGATCTGTAAATAATTATTAGGG
Found at i:394055 original size:86 final size:88
Alignment explanation
Indices: 393913--394083 Score: 258
Period size: 85 Copynumber: 2.0 Consensus size: 88
393903 ATATATATAT
* *
393913 TATCTTTATCATCACTTCAAAAATATTTTTTTAAAATATTTTAACTTGAAATATATTTAAATAGT
1 TATCTTTATCATCACTTCAAAAATA-TTCTTTAAAATATCTTAACTTGAAATATATTT-AATAGT
393978 TTATTATTAATTTAAAATAAAAAAC
64 TTATTATTAATTTAAAATAAAAAAC
* *
394003 TATCTTTATTATCACTT-AAAAATA-TCTTT-AAATATCTTAACTTGAAATATATTTAATATTTT
1 TATCTTTATCATCACTTCAAAAATATTCTTTAAAATATCTTAACTTGAAATATATTTAATAGTTT
*
394065 ATTATTAATTTAATATAAA
66 ATTATTAATTTAAAATAAA
394084 TATATATATA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
85 25 0.33
86 24 0.32
87 4 0.05
89 7 0.09
90 16 0.21
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (88 bp):
TATCTTTATCATCACTTCAAAAATATTCTTTAAAATATCTTAACTTGAAATATATTTAATAGTTT
ATTATTAATTTAAAATAAAAAAC
Found at i:394122 original size:29 final size:28
Alignment explanation
Indices: 394089--394180 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 28
394079 ATAAATATAT
394089 ATATATATATATATTATTTTAAATTTAAA
1 ATATATAT-TATATTATTTTAAATTTAAA
* * *
394118 ATATATTTTATTATTATCTTAACTTTTAAA
1 ATATATATTA-TATTATTTTAA-ATTTAAA
* * * *
394148 A-ATATATTAAAATATTTTAACTTCAAA
1 ATATATATTATATTATTTTAAATTTAAA
394175 ATATAT
1 ATATAT
394181 TTTAACTTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
27 6 0.12
28 14 0.27
29 24 0.47
30 7 0.14
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (28 bp):
ATATATATTATATTATTTTAAATTTAAA
Found at i:394153 original size:62 final size:57
Alignment explanation
Indices: 394058--394184 Score: 134
Period size: 57 Copynumber: 2.1 Consensus size: 57
394048 AATATATTTA
*
394058 ATATTTTATTATTAATTTAATATAAATATATATATATATATATATTATTTTAAATTTAAAAT
1 ATATTTTATTATTAATTTAATATAAATATATATAT-TA-A-A-A-TATTTTAAATTCAAAAT
* *
394120 ATATTTTATTATT-ATCTTAACTTTTAAA-A-ATATATTAAAATATTTTAACTTCAAAAT
1 ATATTTTATTATTAAT-TTAA--TATAAATATATATATTAAAATATTTTAAATTCAAAAT
394177 ATATTTTA
1 ATATTTTA
394185 ACTTAAGAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
57 23 0.39
58 1 0.02
59 1 0.02
60 1 0.02
61 4 0.07
62 23 0.39
63 1 0.02
64 5 0.08
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (57 bp):
ATATTTTATTATTAATTTAATATAAATATATATATTAAAATATTTTAAATTCAAAAT
Found at i:394198 original size:23 final size:23
Alignment explanation
Indices: 394172--394215 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
394162 TTTTAACTTC
* *
394172 AAAATATATTTTAACTTAAGAAT
1 AAAATATAATTTAAATTAAGAAT
394195 AAAATATAATTTAAATTAAGA
1 AAAATATAATTTAAATTAAGA
394216 TGTTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (23 bp):
AAAATATAATTTAAATTAAGAAT
Found at i:398534 original size:138 final size:138
Alignment explanation
Indices: 398286--398566 Score: 519
Period size: 138 Copynumber: 2.0 Consensus size: 138
398276 GGACAGCAAG
398286 GCATAGGGAATCTCCCATTGAACAATGGAAATGCATTCCCTTCTGATGAGGTTTAAACCTTACAC
1 GCATAGGGAATCTCCCATTGAACAATGGAAATGCATTCCCTTCTGATGAGGTTTAAACCTTACAC
* *
398351 TTTCTCTTCTAACTATTTCCTTCCACCTATGTGCTTTACTAAAGTAAATTTTGGCTTGTTCTCTG
66 TTTCTCTTCTAACTAATGCCTTCCACCTATGTGCTTTACTAAAGTAAATTTTGGCTTGTTCTCTG
398416 TACCATAT
131 TACCATAT
*
398424 GCATAGGGAATCTCCCATTGAACAATGGAAATGCATTCCCTTCTGATGAGGTTTAAACCTTAGAC
1 GCATAGGGAATCTCCCATTGAACAATGGAAATGCATTCCCTTCTGATGAGGTTTAAACCTTACAC
*
398489 TTTCTCTTCTAACTAATGCCTTTCACCTATGTGCTTTACTAAAGTAAATTTTGGCTTGTTCTCTG
66 TTTCTCTTCTAACTAATGCCTTCCACCTATGTGCTTTACTAAAGTAAATTTTGGCTTGTTCTCTG
398554 TACCATAT
131 TACCATAT
398562 -CATAG
1 GCATAG
398567 TGGGGAGGTA
Statistics
Matches: 139, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
137 5 0.04
138 134 0.96
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (138 bp):
GCATAGGGAATCTCCCATTGAACAATGGAAATGCATTCCCTTCTGATGAGGTTTAAACCTTACAC
TTTCTCTTCTAACTAATGCCTTCCACCTATGTGCTTTACTAAAGTAAATTTTGGCTTGTTCTCTG
TACCATAT
Found at i:402965 original size:20 final size:20
Alignment explanation
Indices: 402942--402988 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
402932 ATGTTTGAAA
402942 AATTAATT-AAATTTAAATAT
1 AATTAATTGAAA-TTAAATAT
*
402962 AATTAATTGTAATTAAATAT
1 AATTAATTGAAATTAAATAT
*
402982 AAATAAT
1 AATTAAT
402989 ATGTTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AATTAATTGAAATTAAATAT
Found at i:403598 original size:23 final size:23
Alignment explanation
Indices: 403556--403601 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
403546 CAATTGTGAG
**
403556 TGATTTAATTAATATCATTTAAA
1 TGATTTAATTAATAAAATTTAAA
*
403579 TGATTTAATTGATAAAATTTAAA
1 TGATTTAATTAATAAAATTTAAA
403602 AAAAAATATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (23 bp):
TGATTTAATTAATAAAATTTAAA
Found at i:413124 original size:13 final size:13
Alignment explanation
Indices: 413108--413147 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
413098 TTACTACTAA
413108 TTTAATAATATTT
1 TTTAATAATATTT
413121 TTTAATAATAATTT
1 TTTAATAAT-ATTT
* *
413135 ATTATTAATATTT
1 TTTAATAATATTT
413148 AATTATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTAATAATATTT
Found at i:413148 original size:24 final size:24
Alignment explanation
Indices: 413121--413252 Score: 112
Period size: 24 Copynumber: 5.6 Consensus size: 24
413111 AATAATATTT
*
413121 TTTAATAATAATTTATTATTAAT-A
1 TTTAATAATAA-TTATTAATAATAA
* *
413145 TTTAAT--TATTTGA-TACTAATAA
1 TTTAATAATAATT-ATTAATAATAA
*
413167 TTTAATAATGATTATTAATAATTAA
1 TTTAATAATAATTATTAATAA-TAA
* * *
413192 ATT-ATAATAATTAATAATAATGA
1 TTTAATAATAATTATTAATAATAA
* *
413215 TTTAATAATGATTATTAATAATTA
1 TTTAATAATAATTATTAATAATAA
*
413239 TTTAATAATGATTA
1 TTTAATAATAATTA
413253 AATATTTAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
21 8 0.09
22 10 0.11
23 5 0.06
24 60 0.68
25 5 0.06
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (24 bp):
TTTAATAATAATTATTAATAATAA
Found at i:413150 original size:21 final size:21
Alignment explanation
Indices: 413126--413191 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
413116 TATTTTTTAA
413126 TAATAATTTATTATTAATATT
1 TAATAATTTATTATTAATATT
* *
413147 TAATTATTTGA-TACTAATAATT
1 TAATAATTT-ATTATTAAT-ATT
* *
413169 TAATAA-TGATTATTAATAAT
1 TAATAATTTATTATTAATATT
413189 TAA
1 TAA
413192 ATTATAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
20 6 0.17
21 21 0.58
22 9 0.25
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (21 bp):
TAATAATTTATTATTAATATT
Found at i:413201 original size:14 final size:15
Alignment explanation
Indices: 413177--413205 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
413167 TTTAATAATG
413177 ATTATTAATAATTAA
1 ATTATTAATAATTAA
413192 ATTA-TAATAATTAA
1 ATTATTAATAATTAA
413206 TAATAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTATTAATAATTAA
Found at i:413204 original size:21 final size:21
Alignment explanation
Indices: 413161--413209 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
413151 TATTTGATAC
* * *
413161 TAATAATTTAATAATGATTAT
1 TAATAATTAAATAATAATAAT
*
413182 TAATAATTAAATTATAATAAT
1 TAATAATTAAATAATAATAAT
413203 TAATAAT
1 TAATAAT
413210 AATGATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TAATAATTAAATAATAATAAT
Found at i:413338 original size:22 final size:22
Alignment explanation
Indices: 413305--413346 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
413295 ATAGCTGAAC
*
413305 TTATAACAAGTCGAATTTATAT
1 TTATAACAAGTCAAATTTATAT
413327 TTATAA-ATAGTCAAATTTAT
1 TTATAACA-AGTCAAATTTAT
413347 TCTTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (22 bp):
TTATAACAAGTCAAATTTATAT
Found at i:414145 original size:17 final size:16
Alignment explanation
Indices: 414125--414181 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
414115 AACTAAAAAC
414125 ATAATGAAAATAAATAA
1 ATAAT-AAAATAAATAA
414142 ATAAT---ATAAATAAA
1 ATAATAAAATAAAT-AA
*
414156 ATAATAAAATAAAAAA
1 ATAATAAAATAAATAA
414172 ATATATAAAA
1 ATA-ATAAAA
414182 AATATAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
13 6 0.18
14 7 0.21
16 5 0.15
17 16 0.47
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (16 bp):
ATAATAAAATAAATAA
Found at i:414150 original size:13 final size:13
Alignment explanation
Indices: 414134--414189 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
414124 CATAATGAAA
414134 ATAAATAAATAAT
1 ATAAATAAATAAT
414147 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
*
414161 A-AAATAAA-AAA
1 ATAAATAAATAAT
* *
414172 ATATATAAAAAAT
1 ATAAATAAATAAT
414185 ATAAA
1 ATAAA
414190 AATGTATGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 3 0.08
12 9 0.25
13 16 0.44
14 8 0.22
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:414156 original size:34 final size:29
Alignment explanation
Indices: 414125--414188 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 29
414115 AACTAAAAAC
*
414125 ATAATGAAAATAAATAAATAATATAAATAAA
1 ATAAT-AAAATAAAAAAAT-ATATAAATAAA
414156 ATAATAAAATAAAAAAATATATAAA-AAA
1 ATAATAAAATAAAAAAATATATAAATAAA
414184 TATAA
1 -ATAA
414189 AAATGTATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 3 0.10
29 11 0.35
30 12 0.39
31 5 0.16
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (29 bp):
ATAATAAAATAAAAAAATATATAAATAAA
Found at i:414251 original size:21 final size:21
Alignment explanation
Indices: 414132--414253 Score: 76
Period size: 21 Copynumber: 5.9 Consensus size: 21
414122 AACATAATGA
*
414132 AAATAAATAAATAATATAAAT
1 AAATAAATAAATAATAAAAAT
414153 AAA-ATAATAAAATAA-AAAAAT
1 AAATA-AAT-AAATAATAAAAAT
*
414174 ATATAAA-AAAT-ATAAAAAT
1 AAATAAATAAATAATAAAAAT
** **
414193 GTATGTATAATATAAT-AAAAT
1 AAATAAATAA-ATAATAAAAAT
* * *
414214 -ACTAAATAGTAACAATAATAAT
1 AAATAAATA--AATAATAAAAAT
414236 AAATAAATAAATAATAAA
1 AAATAAATAAATAATAAA
414254 TATACATATA
Statistics
Matches: 76, Mismatches: 14, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
18 1 0.01
19 14 0.18
20 7 0.09
21 33 0.43
22 14 0.18
23 7 0.09
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATAAATAAATAATAAAAAT
Found at i:414323 original size:2 final size:2
Alignment explanation
Indices: 414316--414350 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
414306 TGAAGTAAGA
*
414316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
414351 ACGTTAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:414415 original size:2 final size:2
Alignment explanation
Indices: 414410--414436 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
414400 AAAAAAAATA
414410 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
414437 AATAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:414504 original size:23 final size:24
Alignment explanation
Indices: 414469--414516 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
414459 ACGCAAAGAA
414469 AAATGAAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAAA-TATAATTAAAT
*
414493 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAAAAAAATATAATTAAAT
414516 A
1 A
414517 TATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (24 bp):
AAATGAAAAAAAATATAATTAAAT
Found at i:414994 original size:37 final size:37
Alignment explanation
Indices: 414953--415033 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
414943 GAATCATATC
* * *
414953 TTTAGGAATTTAAATAATAGTAGAACTCTATCCTATT
1 TTTAGGAATTTAAATAATAGCAAAACTATATCCTATT
* * ** *
414990 TTTAGGAGTTTGAATCCTAGCAAAATTATATCCTATT
1 TTTAGGAATTTAAATAATAGCAAAACTATATCCTATT
415027 TTTAGGA
1 TTTAGGA
415034 GTTTGAATCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (37 bp):
TTTAGGAATTTAAATAATAGCAAAACTATATCCTATT
Found at i:415982 original size:106 final size:106
Alignment explanation
Indices: 415798--417073 Score: 2023
Period size: 106 Copynumber: 12.0 Consensus size: 106
415788 GCATTGTTCC
* * * * *
415798 GAGTCCAATATCCTCCG-TCGTGAAGTTAAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * *
415862 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * * *
415904 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
415969 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
416010 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
416075 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
416116 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
416181 CCAGCGGTCCCTTCATCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
416222 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
416287 CCACCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
416328 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
416393 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
416434 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
416499 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCCTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
416540 GGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
416605 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
416646 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
416711 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
416752 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
416817 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
416858 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
416923 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
416964 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
417029 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
417070 GAGT
1 GAGT
417074 GGCACGATAT
Statistics
Matches: 1085, Mismatches: 84, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
106 1084 1.00
107 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Done.