Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008318.1 Hibiscus syriacus cultivar Beakdansim tig00111016_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: 501449
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:236314 original size:21 final size:21
Alignment explanation
Indices: 236290--236338 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
236280 CCCCTGTCAT
*
236290 CGTTCAATGGGTTCCTCCTAC
1 CGTTCAATGGGTCCCTCCTAC
236311 CGTTCAATGGGTCCCTCCTAC
1 CGTTCAATGGGTCCCTCCTAC
236332 CGTTCAA
1 CGTTCAA
236339 GAGCCTGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.35, G:0.18, T:0.31
Consensus pattern (21 bp):
CGTTCAATGGGTCCCTCCTAC
Found at i:237079 original size:18 final size:17
Alignment explanation
Indices: 237040--237082 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
237030 ATTATATGAA
237040 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
237056 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
237074 TATTATTAT
1 TATTATTAT
237083 ACATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:237101 original size:58 final size:60
Alignment explanation
Indices: 237050--237160 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
237040 TATTTTATTC
*
237050 ATTTAT-TTTTA-TTATT-C-ATGTTATTATTATTATACATATATATATATATATTAAATT
1 ATTTATATTTTATTTATTACTATATT-TTATTATTATACATATATATATATATATTAAATT
* * *
237107 ATTTTTATTTTATTTTTTACTATATTTTATTATTATATATATATATATATATAT
1 ATTTATATTTTATTTATTACTATATTTTATTATTATACATATATATATATATAT
237161 GTGTTTCTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
57 5 0.11
58 5 0.11
59 4 0.09
60 28 0.61
61 4 0.09
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (60 bp):
ATTTATATTTTATTTATTACTATATTTTATTATTATACATATATATATATATATTAAATT
Found at i:237395 original size:20 final size:19
Alignment explanation
Indices: 237340--237396 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 19
237330 TCTTATAACT
237340 TTATATATATATTATTTTATTA
1 TTAT-TATATA-T-TTTTATTA
*
237362 TTATTTTCAT-TTTTTATTCA
1 TTATTAT-ATATTTTTATT-A
237382 TTATTATATATTTTT
1 TTATTATATATTTTT
237397 TTTAAAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
19 9 0.30
20 13 0.43
21 2 0.07
22 6 0.20
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTATATATTTTTATTA
Found at i:240411 original size:26 final size:28
Alignment explanation
Indices: 240373--240426 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
240363 GCTCATAGCT
*
240373 TGAAAAGAAAGTT-TAGGGGCCTGATGA
1 TGAAAAGAAAGTTCGAGGGGCCTGATGA
240400 TGAAAA-AAAGTTCGAGGGGCCTGATGA
1 TGAAAAGAAAGTTCGAGGGGCCTGATGA
240427 GAGAGCCTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.37, C:0.09, G:0.33, T:0.20
Consensus pattern (28 bp):
TGAAAAGAAAGTTCGAGGGGCCTGATGA
Found at i:247212 original size:106 final size:106
Alignment explanation
Indices: 246957--247598 Score: 826
Period size: 106 Copynumber: 6.0 Consensus size: 106
246947 ATATCGCACC
* * * *
246957 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGACTGGTTGTCAACAAACCACTTT-T
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAA-CAATTTCC
* * **
247021 CAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAT
65 CA--AT--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
247067 ACTCGAGACAACACAAGTTCAACTTCAGAACGAAGGGACGGCTGGTTGTCAACAAACCATTACCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
* *
247132 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
247173 ACTCAAGACAACATAAGTTCAACTTCACAATGAAAGGACGGCTGGTTGTCAACAAACCACTTT-T
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAA-CAATTTCC
* *
247237 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * *
247279 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGAAAACTGGTTGTTAGCAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
247344 AATTTCAGAGCCAA-TTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
247384 ACTCAAGACGACACAAGTTCAAATTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
*
247449 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
247490 ACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAATAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
* * *
247555 -AGTTCGGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
247595 ACTC
1 ACTC
247599 GGAACAATAT
Statistics
Matches: 471, Mismatches: 56, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
104 1 0.00
105 141 0.30
106 267 0.57
107 3 0.01
108 1 0.00
109 3 0.01
110 55 0.12
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:247466 original size:211 final size:212
Alignment explanation
Indices: 246957--247598 Score: 889
Period size: 211 Copynumber: 3.0 Consensus size: 212
246947 ATATCGCACC
*
246957 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGACTGGTTGTCAACAAACCACTTTTC
1 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACGACTGGTTGTCAACAAACCACTTTTC
* *
247022 AGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATT-ATACTCGAGACAACACAAGTT
66 A--AT--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA-ACTCGAGACAACACAAGTT
* * *
247086 CAACTTCAGAACGAAGGGACGGCTGGTTGTCAACAAACCATTACCCAATTTCAGAGCCAATTTCA
126 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCA
* *
247151 ACTTCACATCGAAGGATATTAG
191 ACTTCACAGCGAAGGATATTGG
* * *
247173 ACTCAAGACAACATAAGTTCAACTTCACAATGAAAGGACGGCTGGTTGTCAACAAACCACTTTTC
1 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACGACTGGTTGTCAACAAACCACTTTTC
* * * *
247238 AGTTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCAAGACAACACAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACT
*** * *
247303 TCACAACGAAGGGAAAACTGGTTGTTAGCAAACAATTTCCCAATTTCAGAGCCAA-TTCAACTTC
131 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
247367 ACAGCGAAGGATATTGG
196 ACAGCGAAGGATATTGG
* * * * *
247384 ACTCAAGACGACACAAGTTCAAATTCACAACGAAGGGACGACTGGTTGTCAACAAA-CAATTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACGACTGGTTGTCAACAAACCACTTT-T
*
247448 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAAC
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAAC
* * * * * *
247513 TTCACAGCGAAGGGGCGGCTGGCTGTCAACAAATAATTTCCC-AGTTCGGAGCCAATTTCAACTT
130 TTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTT
*
247577 CAC-GACGGAGGATATTGG
195 CACAG-CGAAGGATATTGG
247595 ACTC
1 ACTC
247599 GGAACAATAT
Statistics
Matches: 378, Mismatches: 44, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
210 17 0.04
211 194 0.51
212 104 0.28
214 1 0.00
216 62 0.16
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (212 bp):
ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACGACTGGTTGTCAACAAACCACTTTTC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACT
TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGG
Found at i:247542 original size:317 final size:319
Alignment explanation
Indices: 246957--247598 Score: 866
Period size: 317 Copynumber: 2.0 Consensus size: 319
246947 ATATCGCACC
* * ** * *
246957 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGACTGGTTGTCAACAAACCACTTTTC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGAAAACTGGTTGTCAACAAACCAATTTCC
* * * *
247022 AGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTATACTCGAGACAACACAAGTTC
66 AG-AT-ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGTTC
* * * *
247087 AACTTCAGAACGAAGGGACGGCTGGTTGTCAACAAACCATTACCCAATTTCAGAGCCAATTTCAA
129 AAATTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTACCCAATTTCAGAGCCAATTTCAA
* * * *
247152 CTTCACATCGAAGGATATTAGACTCAAGACAACATAAGTTCAACTTCACAATGAAAGGACGGCTG
194 CTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAAGGACGGCTG
* * * *
247217 GTTGTCAACAAACCACTTT-TCAGTTTCAGAGCCAATTTCAACTTCAC-AGCGAATGATATTGG
259 GCTGTCAACAAA-CAATTTCCCAG-TTCAGAGCCAATTTCAACTTCACGA-CGAAGGATATTGG
* *
247279 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGAAAACTGGTTGTTAGCAAA-CAATTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGAAAACTGGTTGTCAACAAACCAATTT-C
* *
247343 CA-AT-TTCAGAGCCAA-TTCAACTTCACAGCGAAGGATATTGGACTCAAGACGACACAAGTTCA
65 CAGATATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGTTCA
*
247405 AATTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAAC
130 AATTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTACCCAATTTCAGAGCCAATTTCAAC
* * * *
247470 TTCACAGCGAAGGATATT-GAACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTG
195 TTCACAGCGAAGGATATTAG-ACTCAAGACAACACAAGCTCAACTTCACAACGAAAGGACGGCTG
* * *
247534 GCTGTCAACAAATAATTTCCCAGTTCGGAGCCAATTTCAACTTCACGACGGAGGATATTGG
259 GCTGTCAACAAACAATTTCCCAGTTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGG
247595 ACTC
1 ACTC
247599 GGAACAATAT
Statistics
Matches: 282, Mismatches: 34, Indels: 14
0.85 0.10 0.04
Matches are distributed among these distances:
316 42 0.15
317 172 0.61
318 10 0.04
320 1 0.00
321 5 0.02
322 52 0.18
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (319 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGAAAACTGGTTGTCAACAAACCAATTTCC
AGATATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGTTCAA
ATTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTACCCAATTTCAGAGCCAATTTCAACT
TCACAGCGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAAGGACGGCTGGC
TGTCAACAAACAATTTCCCAGTTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGG
Found at i:248925 original size:18 final size:17
Alignment explanation
Indices: 248886--248928 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
248876 ATTATATGGA
248886 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
248902 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
248920 TATTATTAT
1 TATTATTAT
248929 ACGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:248991 original size:2 final size:2
Alignment explanation
Indices: 248986--249016 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
248976 TATATTTTAT
248986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
249017 GTTTCTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:249510 original size:38 final size:37
Alignment explanation
Indices: 249424--249519 Score: 106
Period size: 40 Copynumber: 2.5 Consensus size: 37
249414 AGAGGGTATC
*
249424 TTTTCTATTTTTAAATATTTGTTGTATATATATATAGCT
1 TTTTC-ATTTTTAAATATTTGATGTATATATATATA-CT
*
249463 TATTT-ATTTTATTAATACTTTGATGTATATATATATA-T
1 T-TTTCATTTT-TAAATA-TTTGATGTATATATATATACT
249501 TTTTCATTTTTCAAATATT
1 TTTTCATTTTT-AAATATT
249520 ACTATATATA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
37 6 0.12
38 16 0.33
39 6 0.12
40 21 0.43
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (37 bp):
TTTTCATTTTTAAATATTTGATGTATATATATATACT
Found at i:251113 original size:30 final size:31
Alignment explanation
Indices: 251069--251163 Score: 86
Period size: 31 Copynumber: 3.1 Consensus size: 31
251059 AGACCCCGAC
* ** *
251069 AACTATCCAGAGGTCGTAAAGAACCTCGGT-
1 AACTATCCATAGGTCCCAAAGAACCTAGGTA
* *
251099 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATAGGTCCCAAAGAACCTAGGTA
* * *
251130 AACTATCCATATGTCTCAAA-AGACATAGGTA
1 AACTATCCATAGGTCCCAAAGA-ACCTAGGTA
251161 AAC
1 AAC
251164 CCTCGACTCT
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
30 25 0.48
31 27 0.52
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (31 bp):
AACTATCCATAGGTCCCAAAGAACCTAGGTA
Found at i:252889 original size:3 final size:3
Alignment explanation
Indices: 252881--252938 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
252871 GCTTACGGGG
*
252881 AGA AGA AGA ATA AGA AGA AGA A-A AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
252928 AGA AGA AGA AG
1 AGA AGA AGA AG
252939 GAAATAAGCT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:254204 original size:28 final size:28
Alignment explanation
Indices: 254159--254212 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
254149 GCTTGTTTAA
*
254159 TTGATTTGTAAAAGTTGATTTGTAAAAG
1 TTGATTTGTAAAAGTTGATGTGTAAAAG
** *
254187 TTGATTTGTTTAATTTGATGTGTAAA
1 TTGATTTGTAAAAGTTGATGTGTAAA
254213 TAAGAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.48
Consensus pattern (28 bp):
TTGATTTGTAAAAGTTGATGTGTAAAAG
Found at i:254205 original size:14 final size:14
Alignment explanation
Indices: 254159--254195 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
254149 GCTTGTTTAA
254159 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
254173 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
254187 TTGATTTGT
1 TTGATTTGT
254196 TTAATTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:254234 original size:78 final size:78
Alignment explanation
Indices: 254105--254259 Score: 267
Period size: 78 Copynumber: 2.0 Consensus size: 78
254095 TTTTACATTG
*
254105 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTAA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATAATTTTTTGCTTGTTTAATTGATTTGTAA
254170 AAGTTGATTTGTA
66 AAGTTGATTTGTA
* *
254183 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATAATTTTTT-CTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATAATTTTTTGCTTGTTTAATTGATTTGTA
254247 AAAGTTGATTTGT
65 AAAGTTGATTTGT
254260 TGTTTTAAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
78 49 0.67
79 24 0.33
ACGTcount: A:0.32, C:0.01, G:0.18, T:0.49
Consensus pattern (78 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATAATTTTTTGCTTGTTTAATTGATTTGTAA
AAGTTGATTTGTA
Found at i:254692 original size:18 final size:18
Alignment explanation
Indices: 254669--254704 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
254659 AAGCCGGTTG
*
254669 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
254687 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
254705 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:257929 original size:41 final size:41
Alignment explanation
Indices: 257847--258282 Score: 430
Period size: 41 Copynumber: 10.5 Consensus size: 41
257837 TTGTAAACGT
* * * * *
257847 GCGGCGTTTGTAAACACAAACTCCACTAAAGTATGACTCTTTA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAGTCTATA
* *
257890 GCGGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
* * *
257931 GTGGCGTTTGTATAAAAATGCCACTAAAGCACGAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
* * * * * * *
257972 GCGACATTTGTAAACATAAACACCACTAAAGTATGAGTGTTTA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAGTCTATA
** * *
258015 GCGGAATTTGTATAAAAATGTCACTAAA-TCACGAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGT-ACGAGTCTATA
* *
258056 GAGGCGTTTGAATAAAAACGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
* * * *
258097 ACGGTGTTTGTATAAAAATGTCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
*
258138 GCGGCGTTTGTATAAAAAACGCCACTAAAGTACGATTCTATA
1 GCGGCGTTTGTAT-AAAAACGCCACTAAAGTACGAGTCTATA
** * * * * *
258180 GCATCGTTTGTATTAAAATGCCACTAAATTAC-AGACTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
* *
258220 GCGGCGTTTGTATAAAAACG-CACCTAAAGTAC-ATTCTTTA
1 GCGGCGTTTGTATAAAAACGCCA-CTAAAGTACGAGTCTATA
*
258260 GCGGCGTTTGTTCTAAAAACGCC
1 GCGGCGTTTG-TATAAAAACGCC
258283 GCGACAAATG
Statistics
Matches: 324, Mismatches: 61, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
39 2 0.01
40 46 0.14
41 191 0.59
42 41 0.13
43 44 0.14
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
Found at i:258079 original size:125 final size:125
Alignment explanation
Indices: 257853--258207 Score: 358
Period size: 125 Copynumber: 2.8 Consensus size: 125
257843 ACGTGCGGCG
* **
257853 TTTGTAAACACAAACTCCACTAAAGTATGACTCTTTAGCGGCGTTTGTATAAAAACACCACTAAA
1 TTTGTAAACACAAACACCACTAAAGTATGACTCTTTAGCGGAATTTGTATAAAAACACCACTAAA
* * * *
257918 GTACGAGTCTTTAGTGGCGTTTGTATAAAAATGCCACTAAAGCACGAGTCTATAGCGACA
66 GTACGAGTCTATAGAGGCGTTTGAATAAAAACGCCACTAAAGCACGAGTCTATAGCGACA
* * * ***
257978 TTTGTAAACATAAACACCACTAAAGTATGAGTGTTTAGCGGAATTTGTATAAAAATGTCACTAAA
1 TTTGTAAACACAAACACCACTAAAGTATGACTCTTTAGCGGAATTTGTATAAAAACACCACTAAA
* * ***
258043 -TCACGAGTCTATAGAGGCGTTTGAATAAAAACGCCACTAAAGTACGAGTCTATAACGGTG
66 GT-ACGAGTCTATAGAGGCGTTTGAATAAAAACGCCACTAAAGCACGAGTCTATAGCGACA
* *** * * * ** *
258103 TTTGTATA-A-AAATGTCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAAACGCCACTAA
1 TTTGTAAACACAAACACCACTAAAGTATGACTCTTTAGCGGAATTTGTAT-AAAAACACCACTAA
* * * * *
258166 AGTACGATTCTATAGCA-TCGTTTGTATTAAAATGCCACTAAA
65 AGTACGAGTCTATAG-AGGCGTTTGAATAAAAACGCCACTAAA
258208 TTACAGACTT
Statistics
Matches: 192, Mismatches: 34, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
123 31 0.16
124 47 0.24
125 114 0.59
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (125 bp):
TTTGTAAACACAAACACCACTAAAGTATGACTCTTTAGCGGAATTTGTATAAAAACACCACTAAA
GTACGAGTCTATAGAGGCGTTTGAATAAAAACGCCACTAAAGCACGAGTCTATAGCGACA
Found at i:259436 original size:18 final size:17
Alignment explanation
Indices: 259413--259477 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 17
259403 GTATAAATAC
259413 TAATAATAATTAATCAT
1 TAATAATAATTAATCAT
* *
259430 GTAATAATTATTAATAAT
1 -TAATAATAATTAATCAT
259448 TAATACATAA--AAT-AT
1 TAATA-ATAATTAATCAT
*
259463 TAATATTAATTAATC
1 TAATAATAATTAATC
259478 CTAATTCGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 3 0.08
15 7 0.18
16 6 0.15
17 5 0.13
18 18 0.46
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (17 bp):
TAATAATAATTAATCAT
Found at i:259450 original size:25 final size:24
Alignment explanation
Indices: 259407--259477 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 24
259397 TATAAAGTAT
* *
259407 AAATACTAATAATAATTAATCATG
1 AAATATTAATAATAATTAATCATA
* *
259431 TAATAATTATTAATAATTAATACATA
1 AAAT-ATTAATAATAATTAAT-CATA
*
259457 AAATATTAATATTAATTAATC
1 AAATATTAATAATAATTAATC
259478 CTAATTCGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 4 0.11
25 28 0.74
26 6 0.16
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (24 bp):
AAATATTAATAATAATTAATCATA
Found at i:260346 original size:18 final size:18
Alignment explanation
Indices: 260323--260429 Score: 144
Period size: 18 Copynumber: 5.9 Consensus size: 18
260313 ACTGAATATT
260323 TGTCCCGAAAGACCACTA
1 TGTCCCGAAAGACCACTA
260341 TGTCCCGAAAGACCACTA
1 TGTCCCGAAAGACCACTA
* *
260359 TATCCCGAAGGACCACTA
1 TGTCCCGAAAGACCACTA
* *
260377 TGTCACGAAGGACCACTA
1 TGTCCCGAAAGACCACTA
260395 TGTCCC-AAAGAACCACTA
1 TGTCCCGAAAG-ACCACTA
* *
260413 TGTCCTGAAGGACCACT
1 TGTCCCGAAAGACCACT
260430 GATAATCCCT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
17 3 0.04
18 73 0.92
19 3 0.04
ACGTcount: A:0.33, C:0.32, G:0.18, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:260396 original size:54 final size:54
Alignment explanation
Indices: 260323--260429 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
260313 ACTGAATATT
*
260323 TGTCCCGAAAGACCACTATGTCCCGAAAG-ACCACTATATCCCGAAGGACCACTA
1 TGTCACGAAAGACCACTATGTCCC-AAAGAACCACTATATCCCGAAGGACCACTA
* * *
260377 TGTCACGAAGGACCACTATGTCCCAAAGAACCACTATGTCCTGAAGGACCACT
1 TGTCACGAAAGACCACTATGTCCCAAAGAACCACTATATCCCGAAGGACCACT
260430 GATAATCCCT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
53 4 0.08
54 44 0.92
ACGTcount: A:0.33, C:0.32, G:0.18, T:0.18
Consensus pattern (54 bp):
TGTCACGAAAGACCACTATGTCCCAAAGAACCACTATATCCCGAAGGACCACTA
Found at i:265525 original size:21 final size:20
Alignment explanation
Indices: 265510--265547 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
265500 GATCCCACTG
*
265510 ATCGTGTTTGTCATCCCCTC
1 ATCGTATTTGTCATCCCCTC
265530 ATCGTATTTG--ATCCCCTC
1 ATCGTATTTGTCATCCCCTC
265548 GCAGAGGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.13, C:0.34, G:0.13, T:0.39
Consensus pattern (20 bp):
ATCGTATTTGTCATCCCCTC
Found at i:266614 original size:20 final size:23
Alignment explanation
Indices: 266564--266621 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 23
266554 GCATGGGTAG
266564 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTTAAAGAA
266588 TGCATCGATGCACTG-T-AA-AA
1 TGCATCGATGCACTGTTAAAGAA
*
266608 TGTATCGATGCACT
1 TGCATCGATGCACT
266622 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 15 0.45
21 2 0.06
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (23 bp):
TGCATCGATGCACTGTTAAAGAA
Found at i:270467 original size:21 final size:20
Alignment explanation
Indices: 270441--270479 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
270431 ATCTCACTCA
*
270441 AATTCTAACATTTCTAAATCT
1 AATTCTAACACTTC-AAATCT
270462 AATTCTAACACTTCAAAT
1 AATTCTAACACTTCAAAT
270480 TCCTTAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTCTAACACTTCAAATCT
Found at i:271433 original size:22 final size:19
Alignment explanation
Indices: 271407--271454 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
271397 AGTGTACCCC
271407 GGTGAGTCACCAGAGCTACGGT
1 GGTGAGTCACCAGA--TA-GGT
* *
271429 GGTGACTCACCCGATAGGT
1 GGTGAGTCACCAGATAGGT
271448 GGTGAGT
1 GGTGAGT
271455 TGTGCGGTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 9 0.39
20 2 0.09
22 12 0.52
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (19 bp):
GGTGAGTCACCAGATAGGT
Found at i:271912 original size:14 final size:14
Alignment explanation
Indices: 271860--271915 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
271850 GACCTGTAAA
271860 ATTATAA-AA-ATT
1 ATTATAATAATATT
*
271872 AATTATAA-AATAAT
1 -ATTATAATAATATT
*
271886 AATATAATAATATT
1 ATTATAATAATATT
*
271900 ATTATATTAATATT
1 ATTATAATAATATT
271914 AT
1 AT
271916 AATACTTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
13 15 0.42
14 21 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTATAATAATATT
Found at i:290173 original size:57 final size:57
Alignment explanation
Indices: 290104--290219 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
290094 ATTACCTGAA
290104 GGATCTTCACAAGATCTTGGACTAGGATCAGATTCTTGGTTTTGCTGCAGAGATGCT
1 GGATCTTCACAAGATCTTGGACTAGGATCAGATTCTTGGTTTTGCTGCAGAGATGCT
*
290161 GGATCTTCACAAGATCTTGGACTAGGATCAGATTCTTGGTTTTGCTGCAGAGGTGCT
1 GGATCTTCACAAGATCTTGGACTAGGATCAGATTCTTGGTTTTGCTGCAGAGATGCT
290218 GG
1 GG
290220 TGGTTCCATC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (57 bp):
GGATCTTCACAAGATCTTGGACTAGGATCAGATTCTTGGTTTTGCTGCAGAGATGCT
Found at i:309549 original size:20 final size:20
Alignment explanation
Indices: 309524--309568 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
309514 GTCATCCATT
309524 TTTTTAAAC-CTCAAACCGGA
1 TTTTTAAACTCT-AAACCGGA
*
309544 TTTTTAAACTCTAGACCGGA
1 TTTTTAAACTCTAAACCGGA
309564 TTTTT
1 TTTTT
309569 TTCGGATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (20 bp):
TTTTTAAACTCTAAACCGGA
Found at i:314059 original size:15 final size:16
Alignment explanation
Indices: 314034--314067 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
314024 CTTTACCCAC
314034 AAAAAGAAAAGAAATA
1 AAAAAGAAAAGAAATA
*
314050 AAAAAG-AAAGGAATA
1 AAAAAGAAAAGAAATA
314065 AAA
1 AAA
314068 CCCAAGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (16 bp):
AAAAAGAAAAGAAATA
Found at i:315502 original size:17 final size:19
Alignment explanation
Indices: 315467--315503 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
315457 ATACAAAAGA
315467 AATTTCTAAATTATATGTG
1 AATTTCTAAATTATATGTG
315486 AATTT-TAAATT-TATGTG
1 AATTTCTAAATTATATGTG
315503 A
1 A
315504 GTGTGACCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 6 0.33
19 5 0.28
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.49
Consensus pattern (19 bp):
AATTTCTAAATTATATGTG
Found at i:318466 original size:83 final size:83
Alignment explanation
Indices: 318327--318565 Score: 451
Period size: 83 Copynumber: 2.9 Consensus size: 83
318317 ACTGCAACAC
318327 GATGAACAAAGAAATGCGATGAACTCATGCAGTGAATTGGCTTTGAAACCATGAACGTGTCCATT
1 GATGAACAAAGAAATGCGATGAACTCATGCAGTGAATTGGCTTTGAAACCATGAACGTGTCCATT
318392 TCTGCAACACTCCTACAT
66 TCTGCAACACTCCTACAT
318410 GATGAACAAAGAAATGCGATGAACTCATGCAGTGAATTGGCTTTGAAACCATGAACGTGTCCATT
1 GATGAACAAAGAAATGCGATGAACTCATGCAGTGAATTGGCTTTGAAACCATGAACGTGTCCATT
318475 TCTGCAACACTCCTACAT
66 TCTGCAACACTCCTACAT
* * *
318493 GATGAACAAAGAAATGCGATGAACTCATGCAGTGAATTGGCTTTGAAACCAAGAATGTGTCCGTT
1 GATGAACAAAGAAATGCGATGAACTCATGCAGTGAATTGGCTTTGAAACCATGAACGTGTCCATT
318558 TCTGCAAC
66 TCTGCAAC
318566 GAAAATGGTG
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 153 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (83 bp):
GATGAACAAAGAAATGCGATGAACTCATGCAGTGAATTGGCTTTGAAACCATGAACGTGTCCATT
TCTGCAACACTCCTACAT
Found at i:324306 original size:19 final size:19
Alignment explanation
Indices: 324282--324319 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
324272 TTTTGAATAG
324282 TGAACAATACCCATGAACA
1 TGAACAATACCCATGAACA
*
324301 TGAACAATACCTATGAACA
1 TGAACAATACCCATGAACA
324320 GTGAGGGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.24, G:0.11, T:0.18
Consensus pattern (19 bp):
TGAACAATACCCATGAACA
Found at i:324894 original size:46 final size:46
Alignment explanation
Indices: 324786--324954 Score: 233
Period size: 46 Copynumber: 3.8 Consensus size: 46
324776 ATAAAATCTT
* *
324786 TTACCATTT--ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTA-TTTATCAAAATAC
*
324831 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTATCAACATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTATCAAAATAC
* *
324877 TTTCCATTTAAATTCCATAAGCTCGTAAGCTTATTTATCAATATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTATCAAAATAC
*
324923 TTGCCA-TT--ATT-CATAAGCTCGTAAGCTTATTT
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTT
324955 GCATACTTAC
Statistics
Matches: 116, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
42 21 0.18
43 3 0.03
45 11 0.09
46 60 0.52
47 21 0.18
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (46 bp):
TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTATCAAAATAC
Found at i:336027 original size:15 final size:15
Alignment explanation
Indices: 336007--336038 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
335997 ACACAAACCC
336007 TTAGATTTGGGATCT
1 TTAGATTTGGGATCT
336022 TTAGATTTGGGATCT
1 TTAGATTTGGGATCT
336037 TT
1 TT
336039 GAAATCCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (15 bp):
TTAGATTTGGGATCT
Found at i:339818 original size:46 final size:45
Alignment explanation
Indices: 339753--339861 Score: 166
Period size: 46 Copynumber: 2.4 Consensus size: 45
339743 TGGTATATGG
* *
339753 TTATGGAAT-AATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
*
339797 TTATGGAAATAAATGGTAAGTATATTTATAAAATAAGCTTACGAGC
1 TTATGG-AATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
*
339843 TTATGGGATAAATGGTAAG
1 TTATGGAATAAATGGTAAG
339862 AGATTTTATA
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
44 6 0.10
45 15 0.25
46 38 0.64
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.31
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
Found at i:340189 original size:22 final size:23
Alignment explanation
Indices: 340136--340189 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
340126 CGTATCGATG
340136 CACTATTCACAGATACTATTCAT
1 CACTATTCACAGATACTATTCAT
* * *
340159 CACTGTTCAC-GGTACTGTTCAT
1 CACTATTCACAGATACTATTCAT
*
340181 CGCTATTCA
1 CACTATTCA
340190 TAAAAAATCT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (23 bp):
CACTATTCACAGATACTATTCAT
Found at i:341297 original size:30 final size:30
Alignment explanation
Indices: 341261--341320 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
341251 TATCTTCATT
*
341261 CTGTAGCAGTTATTGTAGCGTATCGATGCA
1 CTGTAGCAGTTACTGTAGCGTATCGATGCA
341291 CTGTAGCAGTTACTGTAGCGTATCGATGCA
1 CTGTAGCAGTTACTGTAGCGTATCGATGCA
341321 TAATATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (30 bp):
CTGTAGCAGTTACTGTAGCGTATCGATGCA
Found at i:345586 original size:41 final size:42
Alignment explanation
Indices: 345517--345604 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
345507 ATTTTGACTA
* * *
345517 TCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCACAAATTCACGTTGCGATTTTCATAAT
**
345559 TCGCATTGCGATTT-ACGTATTCACGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTCACAAATTCACGTTGCGATTTTCATAAT
345600 TCGCA
1 TCGCA
345605 ATGTGAATAC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 27 0.66
42 14 0.34
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (42 bp):
TCGCATTGCGATTTCACAAATTCACGTTGCGATTTTCATAAT
Found at i:345587 original size:20 final size:21
Alignment explanation
Indices: 345517--345603 Score: 86
Period size: 21 Copynumber: 4.2 Consensus size: 21
345507 ATTTTGACTA
* * *
345517 TCGCATTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTACCTAAT
*
345538 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGATTTACCTAAT
* *
345559 TCGCATTGCGATTTACGT-AT
1 TCGCGTTGCGATTTACCTAAT
* * *
345579 TCACGTTGCGATTTTCATAAT
1 TCGCGTTGCGATTTACCTAAT
345600 TCGC
1 TCGC
345604 AATGTGAATA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.30
21 38 0.70
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTACCTAAT
Found at i:345625 original size:20 final size:20
Alignment explanation
Indices: 345600--345693 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
345590 TTTTCATAAT
*
345600 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
345620 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
345640 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
345661 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
345681 TCGCAATGCGAAT
1 TCGCAATGCGAAT
345694 CTGACTATCG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 46 0.72
21 18 0.28
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:345662 original size:41 final size:41
Alignment explanation
Indices: 345600--345693 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
345590 TTTTCATAAT
* * *
345600 TCGCAATGTGAA-TACGTAAATCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATACGTAAA
* *
345640 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATACGTAAA
345681 TCGCAATGCGAAT
1 TCGCAATGCGAAT
345694 CTGACTATCG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 11 0.23
41 37 0.77
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAACGCGAATACGTAAA
Found at i:346298 original size:19 final size:19
Alignment explanation
Indices: 346234--346333 Score: 94
Period size: 14 Copynumber: 5.7 Consensus size: 19
346224 TAGTTTCGAG
346234 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
346254 AATGAAAATCGCAA--CG-
1 AATGAAAATCGCAACGCGA
*
346270 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
*
346287 AATGAAAATCGCAA--TG-
1 AATGAAAATCGCAACGCGA
*
346303 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
346320 AATGAAAATCGCAA
1 AATGAAAATCGCAA
346334 TTTTCATTCT
Statistics
Matches: 64, Mismatches: 6, Indels: 21
0.70 0.07 0.23
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 3 0.05
17 2 0.03
18 3 0.05
19 20 0.31
20 14 0.22
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:346334 original size:33 final size:33
Alignment explanation
Indices: 346240--346334 Score: 172
Period size: 33 Copynumber: 2.8 Consensus size: 33
346230 CGAGAATGAA
*
346240 AATCGCAACGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAATGAGAG
346274 AATCGCAACGCGAAATGAAAATCGCAATGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAATGAGAG
346307 AATCGCAACGCGAAATGAAAATCGCAAT
1 AATCGCAACGCGAAATGAAAATCGCAAT
346335 TTTCATTCTC
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
33 49 0.82
34 11 0.18
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAATGAGAG
Found at i:348245 original size:94 final size:93
Alignment explanation
Indices: 348056--348619 Score: 940
Period size: 94 Copynumber: 6.1 Consensus size: 93
348046 TAGATTGCTT
*
348056 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC----TATT-TATTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCT-TTAACACTGTGAAGTTAG
*
348116 TATTTGTCTTTTGTTTTGTCTTTCGGTTGA
65 TATTTGTC-TTTGTTTTGTCTTTTGGTTGA
348146 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
348211 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
348240 AGTAAATTTGTTCGGTTGCTGCCAATTCTGTTAAACTGTGTATTCTTTAATACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
348305 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
348334 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
348399 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
348428 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
348493 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
348522 AGTAAATTTGTTCGTTTGCTTCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
348587 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
348615 AGTAA
1 AGTAA
348620 TGCAATCCAT
Statistics
Matches: 453, Mismatches: 13, Indels: 13
0.95 0.03 0.03
Matches are distributed among these distances:
90 35 0.08
93 45 0.10
94 352 0.78
95 21 0.05
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:348294 original size:17 final size:17
Alignment explanation
Indices: 348264--348296 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
348254 GTTGCTGCCA
348264 ATTCTGTTAAACTGTGT
1 ATTCTGTTAAACTGTGT
348281 ATTCT-TTAATACTGTG
1 ATTCTGTTAA-ACTGTG
348297 AAGTTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.48
Consensus pattern (17 bp):
ATTCTGTTAAACTGTGT
Found at i:348756 original size:19 final size:19
Alignment explanation
Indices: 348710--348767 Score: 98
Period size: 19 Copynumber: 3.0 Consensus size: 19
348700 TCTTTTGGTT
348710 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
348729 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
348749 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
348768 CAAAATCGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.50, C:0.17, G:0.22, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:348814 original size:19 final size:19
Alignment explanation
Indices: 348792--348886 Score: 101
Period size: 19 Copynumber: 5.2 Consensus size: 19
348782 GAAACTATAA
*
348792 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
*
348811 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
348825 TCTCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
348844 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
348863 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
348883 TCGC
1 TCGC
348887 TCGATAGTCA
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
14 9 0.15
16 2 0.03
17 2 0.03
19 30 0.49
20 18 0.30
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:348872 original size:20 final size:20
Alignment explanation
Indices: 348821--348882 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
348811 TCGCATTGCG
*
348821 ATTCTCTCGTTGCGATTTTT
1 ATTCTCTCGTTGCGATTTTC
*
348841 ATT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
348860 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
348880 ATT
1 ATT
348883 TCGCTCGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.11, C:0.21, G:0.16, T:0.52
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:349395 original size:42 final size:42
Alignment explanation
Indices: 349316--349434 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
349306 GAATCGCCTG
* * * * * * *
349316 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAAAGGCCCCTA
1 TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
*
349358 TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
* * *
349400 TCATT-GTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCACTCCCACCGTTCAAGAG
349435 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.03
42 58 0.91
43 4 0.06
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
Found at i:349397 original size:21 final size:21
Alignment explanation
Indices: 349368--349434 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
349358 TCATTCCTCG
*
349368 AGAGTCCACTCCCACCGTTCA
1 AGAGGCCACTCCCACCGTTCA
** ** *
349389 AGAGGCCACTGTCATTGTTGA
1 AGAGGCCACTCCCACCGTTCA
*
349410 AGAGGTCC-CTCCCACCATTCA
1 AGAGG-CCACTCCCACCGTTCA
349431 AGAG
1 AGAG
349435 CCCGATTCAC
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAGGCCACTCCCACCGTTCA
Found at i:350804 original size:14 final size:14
Alignment explanation
Indices: 350785--350820 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
350775 ATTGTTTAAT
350785 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
350799 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
350813 TGATTTGT
1 TGATTTGT
350821 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:350952 original size:14 final size:14
Alignment explanation
Indices: 350933--350987 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
350923 GACTATCGCA
350933 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
350947 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
350964 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
350980 TTGCGATT
1 TTGCGATT
350988 TTCATTTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:350970 original size:33 final size:33
Alignment explanation
Indices: 350928--351005 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
350918 AAAATGACTA
350928 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
350961 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
350994 TTGCATTGCGAT
1 TCGCATTGCGAT
351006 AGTCATTTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:350971 original size:19 final size:19
Alignment explanation
Indices: 350947--351025 Score: 69
Period size: 19 Copynumber: 4.4 Consensus size: 19
350937 GATTCTCTCG
350947 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
350966 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
350980 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCA
** *
350999 TTGCGATAGTCATTTTCGCG
1 TTGCGATTTTCA-TTTCGCA
351019 TTGCGAT
1 TTGCGAT
351026 AGACATTAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
14 6 0.13
16 7 0.15
17 6 0.13
19 16 0.34
20 12 0.26
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:351024 original size:20 final size:19
Alignment explanation
Indices: 350978--351032 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
350968 GCGATTCTCT
**
350978 CGTTGCGATTTTCATTTTG
1 CGTTGCGATAGTCATTTTG
*
350997 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTT-G
*
351017 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
351033 AAGATGATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTTG
Found at i:353608 original size:24 final size:24
Alignment explanation
Indices: 353557--353608 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
353547 ATCTGAGTAT
** *
353557 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
353581 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
353605 TGAC
1 TGAC
353609 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:354342 original size:27 final size:27
Alignment explanation
Indices: 354304--354364 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
354294 TGGAGATGGA
354304 ATGAGTTGCGATTTAGGGATTTAGGTT
1 ATGAGTTGCGATTTAGGGATTTAGGTT
354331 ATGAGTTGCGATTTAGGGATTTAGGTT
1 ATGAGTTGCGATTTAGGGATTTAGGTT
354358 ATGAGTT
1 ATGAGTT
354365 ACTGCTGCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.23, C:0.03, G:0.33, T:0.41
Consensus pattern (27 bp):
ATGAGTTGCGATTTAGGGATTTAGGTT
Found at i:354544 original size:41 final size:42
Alignment explanation
Indices: 354499--354582 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 42
354489 TCAAAGTACA
* *
354499 AATTAGGAAAATCGCAATGCG-ATTACGTAAATCGCAATGCG
1 AATTAGGAAAATCGCAACGCGAATTACGGAAATCGCAATGCG
**
354540 AATTAGGAAAATCGCAACGCGAATTTGGGAAATCGCAATGCG
1 AATTAGGAAAATCGCAACGCGAATTACGGAAATCGCAATGCG
354582 A
1 A
354583 TAGTCAGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
41 20 0.53
42 18 0.47
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (42 bp):
AATTAGGAAAATCGCAACGCGAATTACGGAAATCGCAATGCG
Found at i:354551 original size:21 final size:21
Alignment explanation
Indices: 354499--354582 Score: 116
Period size: 21 Copynumber: 4.0 Consensus size: 21
354489 TCAAAGTACA
354499 AATTAGGAAAATCGCAATGCG
1 AATTAGGAAAATCGCAATGCG
* *
354520 -ATTACGTAAATCGCAATGCG
1 AATTAGGAAAATCGCAATGCG
*
354540 AATTAGGAAAATCGCAACGCG
1 AATTAGGAAAATCGCAATGCG
* *
354561 AATTTGGGAAATCGCAATGCG
1 AATTAGGAAAATCGCAATGCG
354582 A
1 A
354583 TAGTCAGAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
20 18 0.33
21 36 0.67
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (21 bp):
AATTAGGAAAATCGCAATGCG
Found at i:355955 original size:14 final size:14
Alignment explanation
Indices: 355946--355972 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
355936 GTATGAGTAG
355946 TACCGTATGAACAA
1 TACCGTATGAACAA
355960 TACCGTATGAACA
1 TACCGTATGAACA
355973 GTAATGAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TACCGTATGAACAA
Found at i:356001 original size:22 final size:22
Alignment explanation
Indices: 355952--356016 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
355942 GTAGTACCGT
*
355952 ATGAACAATACCGTATGAACAGTA
1 ATGAACAGTACCG--TGAACAGTA
* * *
355976 ATGAACAGTACTGTGAACATTG
1 ATGAACAGTACCGTGAACAGTA
355998 ATGAACAGTACCGTGAACA
1 ATGAACAGTACCGTGAACA
356017 ATACCAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 25 0.69
24 11 0.31
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.22
Consensus pattern (22 bp):
ATGAACAGTACCGTGAACAGTA
Found at i:356145 original size:13 final size:14
Alignment explanation
Indices: 356120--356148 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
356110 TAAAACGTTC
356120 ATCATTATACATTT
1 ATCATTATACATTT
356134 ATCATT-TACATTT
1 ATCATTATACATTT
356147 AT
1 AT
356149 ACGTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (14 bp):
ATCATTATACATTT
Found at i:358138 original size:12 final size:12
Alignment explanation
Indices: 358123--358157 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
358113 AACCCAACCT
358123 TTAATTCAACAA
1 TTAATTCAACAA
358135 TTAATTCAACAA
1 TTAATTCAACAA
*
358147 ATAA-TCAACAA
1 TTAATTCAACAA
358158 AATAGAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (12 bp):
TTAATTCAACAA
Found at i:361720 original size:22 final size:22
Alignment explanation
Indices: 361679--361735 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
361669 GAAATATGAT
361679 ATGAACAGTATCGTATGAACAATA
1 ATGAACAGTA-C-TATGAACAATA
* *
361703 ATGAATAGTACTATGAACAATG
1 ATGAACAGTACTATGAACAATA
361725 ATGAACAGTAC
1 ATGAACAGTAC
361736 CGTGAACAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 20 0.67
23 1 0.03
24 9 0.30
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.25
Consensus pattern (22 bp):
ATGAACAGTACTATGAACAATA
Found at i:361741 original size:22 final size:22
Alignment explanation
Indices: 361679--361743 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
361669 GAAATATGAT
*
361679 ATGAACAGTATCGTATGAACAATA
1 ATGAACAGTACCG--TGAACAATA
* ** *
361703 ATGAATAGTACTATGAACAATG
1 ATGAACAGTACCGTGAACAATA
361725 ATGAACAGTACCGTGAACA
1 ATGAACAGTACCGTGAACA
361744 GTTCCAAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
22 24 0.73
24 9 0.27
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (22 bp):
ATGAACAGTACCGTGAACAATA
Found at i:362735 original size:21 final size:21
Alignment explanation
Indices: 362711--362764 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
362701 CATATGAAAT
*
362711 TTGTCCCGAATGACCATTGTA
1 TTGTCCCGAATGACCACTGTA
*
362732 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAATGACCACTGTA
362753 TTGTCCCGAATG
1 TTGTCCCGAATG
362765 GCCTATGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (21 bp):
TTGTCCCGAATGACCACTGTA
Found at i:368820 original size:24 final size:24
Alignment explanation
Indices: 368735--368822 Score: 79
Period size: 24 Copynumber: 3.7 Consensus size: 24
368725 GATATCAGAA
* *
368735 ATCAAAACAGAATTCAAAAT-AGAT
1 ATCAAAACAGAATTC-AGATCATAT
* * *
368759 ATCATAACAGAATCCAGATCATAA
1 ATCAAAACAGAATTCAGATCATAT
* * *
368783 ATCAAAACGGAATTCAGGTCATGT
1 ATCAAAACAGAATTCAGATCATAT
*
368807 ATCAGAACAGAATTCA
1 ATCAAAACAGAATTCA
368823 AGTCGGAAAT
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
23 3 0.06
24 47 0.94
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCATAT
Found at i:379164 original size:60 final size:59
Alignment explanation
Indices: 379039--379164 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 59
379029 CATGAAGCCA
* * * * * *
379039 AAGTTCAAGTACCTAATTGGATCCAAAAAAGTTTAGGCATCACATTGAATCTTAAAGCC
1 AAGTTCAAGTACCTAATTGGACCCAAAAAAGTTAAGACATCAAATTGAACCTTAAAACC
* * * *
379098 AAGTTCAAGTACCTAATTGGACCCAAAAAATGTTAAGATATTAAATTGCACCTTAAAATC
1 AAGTTCAAGTACCTAATTGGACCCAAAAAA-GTTAAGACATCAAATTGAACCTTAAAACC
379158 AAGTTCA
1 AAGTTCA
379165 GATACTGAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
59 29 0.52
60 27 0.48
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (59 bp):
AAGTTCAAGTACCTAATTGGACCCAAAAAAGTTAAGACATCAAATTGAACCTTAAAACC
Found at i:382332 original size:20 final size:18
Alignment explanation
Indices: 382303--382419 Score: 108
Period size: 20 Copynumber: 5.9 Consensus size: 18
382293 AAATGACCAA
382303 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACGCGAT-T
* *
382322 CAAATTTCGCAACCCAGGTT
1 CAAA-TTCGCAACGC-GATT
382342 CCAAATTCGCAACGCGATTT
1 -CAAATTCGCAACGCGA-TT
*
382362 TAAGATTCGCAACGCGATAGT
1 CAA-ATTCGCAACGCGAT--T
382383 CAAAATTCGCAACGCGATT
1 C-AAATTCGCAACGCGATT
*
382402 TAAGATTCGCAACGCGAT
1 CAA-ATTCGCAACGCGAT
382420 ACTCCAAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 18
0.77 0.07 0.17
Matches are distributed among these distances:
18 2 0.02
19 23 0.28
20 34 0.41
21 21 0.26
22 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (18 bp):
CAAATTCGCAACGCGATT
Found at i:382371 original size:40 final size:40
Alignment explanation
Indices: 382303--382434 Score: 144
Period size: 40 Copynumber: 3.3 Consensus size: 40
382293 AAATGACCAA
* * *
382303 CAAATTCGCAACGCGATCTCAA-ATTTCGCAACCCAGGT-TC
1 CAAATTCGCAACGCGATTTTAAGA-TTCGCAACCC-GATATC
*
382343 CAAATTCGCAACGCGATTTTAAGATTCGCAACGCGATAGTC
1 CAAATTCGCAACGCGATTTTAAGATTCGCAACCCGATA-TC
* *
382384 AAAATTCGCAACGCGA-TTTAAGATTCGCAACGCGATACTC
1 CAAATTCGCAACGCGATTTTAAGATTCGCAACCCGATA-TC
*
382424 CAAAATCGCAA
1 CAAATTCGCAA
382435 TGCATTTGTT
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
39 2 0.02
40 61 0.75
41 18 0.22
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (40 bp):
CAAATTCGCAACGCGATTTTAAGATTCGCAACCCGATATC
Found at i:382399 original size:41 final size:41
Alignment explanation
Indices: 382344--382434 Score: 150
Period size: 40 Copynumber: 2.2 Consensus size: 41
382334 CCCAGGTTCC
*
382344 AAATTCGCAACGCGATTTTAAGATTCGCAACGCGATAGT-CA
1 AAATTCGCAACGCGA-TTTAAGATTCGCAACGCGATACTCCA
382385 AAATTCGCAACGCGATTTAAGATTCGCAACGCGATACTCCA
1 AAATTCGCAACGCGATTTAAGATTCGCAACGCGATACTCCA
382426 AAA-TCGCAA
1 AAATTCGCAA
382435 TGCATTTGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
40 28 0.58
41 20 0.42
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (41 bp):
AAATTCGCAACGCGATTTAAGATTCGCAACGCGATACTCCA
Found at i:382410 original size:60 final size:60
Alignment explanation
Indices: 382306--382419 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
382296 TGACCAACAA
* *
382306 ATTCGCAACGCGATCTCAAATTTCGCAACCCAGGTTCCAAATTCGCAACGCGATTTTAAG
1 ATTCGCAACGCGATCTCAAAATTCGCAACCCAGATTCCAAATTCGCAACGCGATTTTAAG
* * *
382366 ATTCGCAACGCGATAGTCAAAATTCGCAACGC-GATT-TAAGATTCGCAACGCGAT
1 ATTCGCAACGCGAT-CTCAAAATTCGCAACCCAGATTCCAA-ATTCGCAACGCGAT
382420 ACTCCAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 2 0.04
60 31 0.66
61 14 0.30
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (60 bp):
ATTCGCAACGCGATCTCAAAATTCGCAACCCAGATTCCAAATTCGCAACGCGATTTTAAG
Found at i:383281 original size:6 final size:6
Alignment explanation
Indices: 383263--383294 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
383253 GTCCCGTCCC
*
383263 GTCGTG GTGGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
383295 AATACGTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.12, G:0.53, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:383389 original size:21 final size:21
Alignment explanation
Indices: 383363--383430 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
383353 AACAAATGCA
*
383363 TTGCGATTTTGGAGTATCGCG
1 TTGCGATTTTGGAATATCGCG
* *
383384 TTGCGAATCTT--AAAATCGCG
1 TTGCG-ATTTTGGAATATCGCG
* *
383404 TTACGATTTTGGACTATCGCG
1 TTGCGATTTTGGAATATCGCG
383425 TTGCGA
1 TTGCGA
383431 ATCTTAAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 4 0.11
20 11 0.31
21 17 0.47
22 4 0.11
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (21 bp):
TTGCGATTTTGGAATATCGCG
Found at i:383403 original size:20 final size:20
Alignment explanation
Indices: 383378--383452 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
383368 ATTTTGGAGT
383378 ATCGCGTTGCGAATCTTAAA
1 ATCGCGTTGCGAATCTTAAA
* * **
383398 ATCGCGTTACG-ATTTTGGACT
1 ATCGCGTTGCGAATCTT--AAA
383419 ATCGCGTTGCGAATCTTAAA
1 ATCGCGTTGCGAATCTTAAA
*
383439 ATCGCGCTGCGAAT
1 ATCGCGTTGCGAAT
383453 TTGGAACCTG
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
19 4 0.09
20 24 0.56
21 11 0.26
22 4 0.09
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (20 bp):
ATCGCGTTGCGAATCTTAAA
Found at i:383456 original size:41 final size:41
Alignment explanation
Indices: 383364--383457 Score: 152
Period size: 41 Copynumber: 2.3 Consensus size: 41
383354 ACAAATGCAT
* *
383364 TGCGATTTTGGAGTATCGCGTTGCGAATCTTAAAATCGCGT
1 TGCGATTTTGGACTATCGCGTTGCGAATCTTAAAATCGCGC
*
383405 TACGATTTTGGACTATCGCGTTGCGAATCTTAAAATCGCGC
1 TGCGATTTTGGACTATCGCGTTGCGAATCTTAAAATCGCGC
*
383446 TGCGAATTTGGA
1 TGCGATTTTGGA
383458 ACCTGGGTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (41 bp):
TGCGATTTTGGACTATCGCGTTGCGAATCTTAAAATCGCGC
Found at i:387577 original size:18 final size:18
Alignment explanation
Indices: 387522--387578 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
387512 TGAAATTGAT
*
387522 TTTTTCGATTCGGTTCGA
1 TTTTTCGATTCGGTTCGG
** * *
387540 TTTTTTTA-ACGGTTTGGG
1 TTTTTCGATTCGG-TTCGG
387558 TTTTTCGATTCGGTTCGG
1 TTTTTCGATTCGGTTCGG
387576 TTT
1 TTT
387579 ATCGGTTTTT
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
17 3 0.11
18 22 0.79
19 3 0.11
ACGTcount: A:0.09, C:0.12, G:0.25, T:0.54
Consensus pattern (18 bp):
TTTTTCGATTCGGTTCGG
Found at i:388925 original size:20 final size:20
Alignment explanation
Indices: 388900--388938 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
388890 ATTCTAGTCT
*
388900 TTGTTATTTTTCTATATTAC
1 TTGTTATTCTTCTATATTAC
388920 TTGTTATTCTTCTATATTA
1 TTGTTATTCTTCTATATTA
388939 TTATCTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.10, G:0.05, T:0.64
Consensus pattern (20 bp):
TTGTTATTCTTCTATATTAC
Found at i:389278 original size:4 final size:4
Alignment explanation
Indices: 389271--389298 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
389261 GATGGACCAA
389271 GGAG GGAG GGAG GGAG GGAG GGAG GGAG
1 GGAG GGAG GGAG GGAG GGAG GGAG GGAG
389299 AGGGAGACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:393293 original size:14 final size:15
Alignment explanation
Indices: 393236--393298 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 15
393226 AAATAAAACC
393236 AATTAAAT-TATTAT
1 AATTAAATATATTAT
393250 --TTAAA-ATCATTACT
1 AATTAAATAT-ATTA-T
393264 AATTAAATATATTAT
1 AATTAAATATATTAT
*
393279 AATTAATTA-ATTAT
1 AATTAAATATATTAT
393293 -ATTAAA
1 AATTAAA
393299 ATCTATATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
12 6 0.15
13 9 0.22
14 6 0.15
15 9 0.22
16 9 0.22
17 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:393509 original size:20 final size:20
Alignment explanation
Indices: 393465--393712 Score: 176
Period size: 20 Copynumber: 12.2 Consensus size: 20
393455 AATGACCAAC
*
393465 AAAATCGCAACGCGAAAT-A-
1 AAAATCGCAACGCG-ATTCAG
*
393484 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
393504 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
393524 AAAATCGCAACG-G--TCAAAAG
1 AAAATCGCAACGCGATTC---AG
393544 AAAATCGCAACGCGATATTCCA-
1 AAAATCGCAACGCG--ATT-CAG
* * *
393566 AGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
393586 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
393608 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
393628 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
393648 AGAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
393668 AGAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
393688 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
393708 AAAAT
1 AAAAT
393713 GAGTAAATTC
Statistics
Matches: 196, Mismatches: 14, Indels: 37
0.79 0.06 0.15
Matches are distributed among these distances:
18 3 0.02
19 20 0.10
20 135 0.69
21 5 0.03
22 29 0.15
23 2 0.01
25 1 0.01
26 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:393592 original size:42 final size:40
Alignment explanation
Indices: 393465--393712 Score: 240
Period size: 40 Copynumber: 6.1 Consensus size: 40
393455 AATGACCAAC
* * *
393465 AAAATCGCAACGCGAAAT--AAAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCG-ATTCCAAGAATCGCAACGCGATTAAG
* **** *
393504 AAAATCGCAACGTTGAAAAGAA-AATCGCAACG-G-TCAAAAG
1 AAAATCGCAACG-CGATTCCAAGAATCGCAACGCGAT--TAAG
*
393544 AAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTAAG
* *
393586 AGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTAAG
393628 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT--AAG
*
393670 --AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
393708 AAAAT
1 AAAAT
393713 GAGTAAATTC
Statistics
Matches: 176, Mismatches: 17, Indels: 31
0.79 0.08 0.14
Matches are distributed among these distances:
38 3 0.02
39 16 0.09
40 86 0.49
41 5 0.03
42 64 0.36
43 1 0.01
44 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
Found at i:393658 original size:40 final size:40
Alignment explanation
Indices: 393542--393712 Score: 254
Period size: 40 Copynumber: 4.2 Consensus size: 40
393532 AACGGTCAAA
* *
393542 AGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTA
1 AGAAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTC
*
393584 AGAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTC
393626 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCC
1 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT-C
*
393667 A-AGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
393706 AGAAAAT
1 AGAAAAT
393713 GAGTAAATTC
Statistics
Matches: 119, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
39 2 0.02
40 63 0.53
41 2 0.02
42 52 0.44
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (40 bp):
AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
Found at i:393819 original size:6 final size:6
Alignment explanation
Indices: 393808--393840 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
393798 GACACGTATT
393808 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
393841 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:394352 original size:6 final size:6
Alignment explanation
Indices: 394341--394373 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
394331 TCTCGTCTCG
394341 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
394374 AATACGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:394562 original size:60 final size:60
Alignment explanation
Indices: 394469--394734 Score: 251
Period size: 60 Copynumber: 4.4 Consensus size: 60
394459 GAATTTACTC
* *
394469 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTAAATCGCGTTGCG
*
394529 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTAAATCGCGTTGCG
* * * **
394589 ATTCTT-GGAAGATCGCGTTGCGATTCTCT-TAATCGCATTGCGATTCTTGGAATATCGCGTTGC
1 ATT-TTCTG-A-ATCGCGTTGCGATTCT-TGGAATCGCGTTGCGATT-TTCTAA-ATCGCGTTGC
394652 G
60 G
**** *
394653 ATTTTCTTTTG-A-C-CGTTGCGATT-TTCTTTTCAACGTTGCGATTTTCTAAATCGCGTTGCG
1 ATTTTC---TGAATCGCGTTGCGATTCTTGGAATC-GCGTTGCGATTTTCTAAATCGCGTTGCG
*
394713 ATTTT-T-ATTTCGCGTTGCGATT
1 ATTTTCTGA-ATCGCGTTGCGATT
394735 TTGTTGGTCA
Statistics
Matches: 175, Mismatches: 15, Indels: 33
0.78 0.07 0.15
Matches are distributed among these distances:
56 1 0.01
58 1 0.01
59 10 0.06
60 80 0.46
61 11 0.06
62 49 0.28
63 7 0.04
64 15 0.09
67 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.42
Consensus pattern (60 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTAAATCGCGTTGCG
Found at i:394675 original size:42 final size:41
Alignment explanation
Indices: 394477--394660 Score: 250
Period size: 40 Copynumber: 4.5 Consensus size: 41
394467 TCATTTTCTT
***
394477 AATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATT-TTCTT
1 AATCGCGTTGCGATTTTCTT--AATCGCGTTGCGATTCTTGGA
*
394517 AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGG-
1 AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGA
394557 AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGA
1 AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGA
* *
394598 AGATCGCGTTGCGATTCTCTTAATCGCATTGCGATTCTTGGA
1 A-ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGA
394640 ATATCGCGTTGCGATTTTCTT
1 A-ATCGCGTTGCGATTTTCTT
394661 TTGACCGTTG
Statistics
Matches: 131, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
40 67 0.51
41 3 0.02
42 61 0.47
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.39
Consensus pattern (41 bp):
AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGA
Found at i:394709 original size:20 final size:20
Alignment explanation
Indices: 394469--394736 Score: 215
Period size: 20 Copynumber: 13.2 Consensus size: 20
394459 GAATTTACTC
*
394469 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
394489 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
394509 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
*
394529 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
394549 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
394569 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
394589 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * *
394611 ATTCTCTTAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
394631 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* *
394653 ATTTTCT--TTTGACCGTTGCG
1 ATTTTCTAAATCG--CGTTGCG
** *
394673 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
394693 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
394713 ATTTT-TATTTCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
394732 ATTTT
1 ATTTT
394737 GTTGGTCATT
Statistics
Matches: 203, Mismatches: 32, Indels: 27
0.77 0.12 0.10
Matches are distributed among these distances:
18 2 0.01
19 21 0.10
20 136 0.67
21 17 0.08
22 27 0.13
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:400936 original size:43 final size:43
Alignment explanation
Indices: 400877--400969 Score: 125
Period size: 43 Copynumber: 2.2 Consensus size: 43
400867 GTTTACCCTT
* * *
400877 AAAATATTAAGTGTCTCAATTATAAAGATAGAAAT-AGATATTA
1 AAAAAATTAAGGGTCTCAATTATAAAGATA-AAATGAGAGATTA
* *
400920 AAAAAATTAAGGGTCTCAATTATAAAGGTAAAATGTGAGATTA
1 AAAAAATTAAGGGTCTCAATTATAAAGATAAAATGAGAGATTA
400963 AAAAAAT
1 AAAAAAT
400970 CAGAGGCTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 4 0.09
43 40 0.91
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (43 bp):
AAAAAATTAAGGGTCTCAATTATAAAGATAAAATGAGAGATTA
Found at i:401030 original size:43 final size:42
Alignment explanation
Indices: 400892--401081 Score: 136
Period size: 43 Copynumber: 4.5 Consensus size: 42
400882 ATTAAGTGTC
* *
400892 TCAATTATAAAGAT-AGAAATAGATATTAAAAAAATTA-AGGGT
1 TCAATTATAAAGATAAAAAAT-GAAATTAAAAAAATTAGA-GGT
* ** * *
400934 CTCAATTATAAAGGTAAAATGTGAGATTAAAAAAATCAGAGGCT
1 -TCAATTATAAAGATAAAAAATGAAATTAAAAAAATTAGAGG-T
* * * * *
400978 TTAACTATAAAGGTAAAAAATGAAATTACAAAAATTAGAAGT
1 TCAATTATAAAGATAAAAAATGAAATTAAAAAAATTAGAGGT
* * * *
401020 ATCAATTATAAATATAAAAAATAAAATT-GAAAAATTA-AGGGCA
1 -TCAATTATAAAGATAAAAAATGAAATTAAAAAAATTAGA-GG-T
*
401063 TCAATTATAATGATAAAAA
1 TCAATTATAAAGATAAAAA
401082 GTATGATTGA
Statistics
Matches: 117, Mismatches: 24, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
41 1 0.01
42 27 0.23
43 84 0.72
44 5 0.04
ACGTcount: A:0.55, C:0.05, G:0.13, T:0.27
Consensus pattern (42 bp):
TCAATTATAAAGATAAAAAATGAAATTAAAAAAATTAGAGGT
Found at i:401054 original size:42 final size:43
Alignment explanation
Indices: 400991--401099 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 43
400981 ACTATAAAGG
* * *
400991 TAAAAAATGAAATTACAAAAATTAGA-AGTATCAATTATAAAT-A
1 TAAAAAATAAAATT-GAAAAATTAGAGAGCATCAATTAT-AATGA
*
401034 TAAAAAATAAAATTGAAAAATTA-AGGGCATCAATTATAATGA
1 TAAAAAATAAAATTGAAAAATTAGAGAGCATCAATTATAATGA
* **
401076 TAAAAAGTATGATTGAAAAATTAG
1 TAAAAAATAAAATTGAAAAATTAG
401100 GGGCCCTAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
41 4 0.07
42 39 0.70
43 13 0.23
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.28
Consensus pattern (43 bp):
TAAAAAATAAAATTGAAAAATTAGAGAGCATCAATTATAATGA
Found at i:404837 original size:7 final size:7
Alignment explanation
Indices: 404825--404892 Score: 136
Period size: 7 Copynumber: 9.7 Consensus size: 7
404815 CCAAATAATC
404825 TTTCCTT
1 TTTCCTT
404832 TTTCCTT
1 TTTCCTT
404839 TTTCCTT
1 TTTCCTT
404846 TTTCCTT
1 TTTCCTT
404853 TTTCCTT
1 TTTCCTT
404860 TTTCCTT
1 TTTCCTT
404867 TTTCCTT
1 TTTCCTT
404874 TTTCCTT
1 TTTCCTT
404881 TTTCCTT
1 TTTCCTT
404888 TTTCC
1 TTTCC
404893 GTGTTAAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 61 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTCCTT
Found at i:405309 original size:3 final size:3
Alignment explanation
Indices: 405301--405326 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
405291 CTTCCTTGAA
405301 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
405327 GGCAATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:409772 original size:25 final size:26
Alignment explanation
Indices: 409725--409776 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
409715 TACATTACTG
409725 AAATCAAATTCATATCTGACATGTCTA
1 AAATCAAATTCA-ATCTGACATGTCTA
409752 AAATCAAATTC-ATCTGACATGTCTA
1 AAATCAAATTCAATCTGACATGTCTA
409777 TGAACCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 14 0.56
27 11 0.44
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (26 bp):
AAATCAAATTCAATCTGACATGTCTA
Found at i:409882 original size:18 final size:17
Alignment explanation
Indices: 409845--409891 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
409835 TATGGAATTG
*
409845 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
409862 GATTCCAATTCATTCACA
1 GATTCCAATTC-CTCACA
409880 GATTCCAATTCC
1 GATTCCAATTCC
409892 CTCATAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:410232 original size:22 final size:22
Alignment explanation
Indices: 410207--410248 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
410197 TTGAACGCTT
*
410207 ACACTCCTAACATTCTCAAATC
1 ACACCCCTAACATTCTCAAATC
*
410229 ACACCCCTAATATTCTCAAA
1 ACACCCCTAACATTCTCAAA
410249 AGTGGGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (22 bp):
ACACCCCTAACATTCTCAAATC
Found at i:411695 original size:12 final size:12
Alignment explanation
Indices: 411678--411703 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
411668 AAATGATATG
411678 CTTTTAAAAAAT
1 CTTTTAAAAAAT
411690 CTTTTAAAAAAT
1 CTTTTAAAAAAT
411702 CT
1 CT
411704 ATCAATAATA
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:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (12 bp):
CTTTTAAAAAAT
Found at i:411968 original size:20 final size:20
Alignment explanation
Indices: 411943--411983 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
411933 TTGGGGATAT
411943 GGGTGAGGAGACAGTTGCCG
1 GGGTGAGGAGACAGTTGCCG
411963 GGGTGAGGAGACAGTTGCCG
1 GGGTGAGGAGACAGTTGCCG
411983 G
1 G
411984 TGGCCGTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.51, T:0.15
Consensus pattern (20 bp):
GGGTGAGGAGACAGTTGCCG
Found at i:418674 original size:21 final size:21
Alignment explanation
Indices: 418606--418684 Score: 81
Period size: 23 Copynumber: 3.7 Consensus size: 21
418596 TCGAAATGGA
** *
418606 GTGCATGGATGCACTACA-TG
1 GTGCATGGATGCACTGTAGGG
*
418626 GTGCATCGATGCACTAGT-GGCAG
1 GTGCATGGATGCACT-GTAGG--G
418649 GTGCATGGATGCACTGTAGGG
1 GTGCATGGATGCACTGTAGGG
418670 GTGCATGGATGCACT
1 GTGCATGGATGCACT
418685 TTGACACCCT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
20 14 0.29
21 16 0.33
22 2 0.04
23 17 0.35
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (21 bp):
GTGCATGGATGCACTGTAGGG
Found at i:418935 original size:21 final size:22
Alignment explanation
Indices: 418900--418945 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
418890 AATAAAATGT
418900 TTAATGAAAAAGATACCAATTG
1 TTAATGAAAAAGATACCAATTG
* *
418922 TTAAT-AAAATGATATCAATTG
1 TTAATGAAAAAGATACCAATTG
418943 TTA
1 TTA
418946 CCAATTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (22 bp):
TTAATGAAAAAGATACCAATTG
Found at i:420086 original size:19 final size:20
Alignment explanation
Indices: 420043--420090 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
420033 TCTAAATCCT
*
420043 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
420063 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
420082 TTTTCAAAA
1 TTTTCAAAA
420091 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:421212 original size:3 final size:3
Alignment explanation
Indices: 421204--421258 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
421194 TTTTTATTGA
* *
421204 TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT TAT TAA AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
421251 TAT TAT TA
1 TAT TAT TA
421259 CAAACAGGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:422538 original size:31 final size:31
Alignment explanation
Indices: 422490--422597 Score: 78
Period size: 32 Copynumber: 3.4 Consensus size: 31
422480 TTTAACTACA
*
422490 AGTTTTATTACTT-TTTATATTTTAACATTAT
1 AGTTTTATT-TTTATTTATATTTTAACATTAT
*
422521 AGTTTTATTTTTA-TT-TATTTTAGTCATTATTT
1 AGTTTTATTTTTATTTATATTTTA-ACATTA--T
* * * * *
422553 AGTTATATTTTAATTTAAATATTAATTATTAT
1 AGTTTTATTTTTATTTATATTTTAA-CATTAT
*
422585 TGTTTTATTTTTA
1 AGTTTTATTTTTA
422598 ATATAAATTA
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
29 7 0.12
30 9 0.15
31 9 0.15
32 23 0.39
33 2 0.03
34 9 0.15
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.64
Consensus pattern (31 bp):
AGTTTTATTTTTATTTATATTTTAACATTAT
Found at i:422870 original size:17 final size:17
Alignment explanation
Indices: 422848--422885 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
422838 ATATTTTTTT
422848 TATATTTTATATATAAA
1 TATATTTTATATATAAA
* *
422865 TATATTTTTTATATAAT
1 TATATTTTATATATAAA
422882 TATA
1 TATA
422886 AATTTGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:423430 original size:21 final size:21
Alignment explanation
Indices: 423404--423501 Score: 187
Period size: 21 Copynumber: 4.7 Consensus size: 21
423394 GCGAATAAGT
*
423404 AAATCGCAATGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
423425 AAATCGCAACGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
423446 AAATCGCAACGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
423467 AAATCGCAACGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
423488 AAATCGCAACGCGA
1 AAATCGCAACGCGA
423502 TACTGACTTT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.18
Consensus pattern (21 bp):
AAATCGCAACGCGAATTTGGA
Found at i:423516 original size:20 final size:20
Alignment explanation
Indices: 423491--423563 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
423481 ATTTGGAAAA
423491 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
423511 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
423531 TCGCAACGCGATATTGACTT
1 TCGCAACGCGATACTGACTT
*
423551 TCGCAACGAGATA
1 TCGCAACGCGATA
423564 ATACATAATC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:423778 original size:22 final size:22
Alignment explanation
Indices: 423750--423793 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
423740 CACTCTCTCA
423750 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
423772 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
423794 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:424105 original size:20 final size:20
Alignment explanation
Indices: 424056--424114 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
424046 TTTATTCTCT
* **
424056 TGTTGCGATAGTCAAATTCG
1 TGTTGCGATTGTCATTTTCG
*
424076 CGTTGCGATTGTCATTTTCG
1 TGTTGCGATTGTCATTTTCG
*
424096 TGTTGCGATTTTCATTTTC
1 TGTTGCGATTGTCATTTTC
424115 AGAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (20 bp):
TGTTGCGATTGTCATTTTCG
Found at i:424305 original size:25 final size:24
Alignment explanation
Indices: 424251--424305 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
424241 TGTTTATTAT
* *
424251 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
424275 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
424301 TGTTT
1 TGTTT
424306 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:424994 original size:20 final size:20
Alignment explanation
Indices: 424969--425014 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
424959 TAGTTTACTT
424969 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
424989 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
425009 TCGCAA
1 TCGCAA
425015 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:425023 original size:19 final size:20
Alignment explanation
Indices: 424980--425024 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
424970 CGCAACACGA
424980 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
425000 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
425019 AAATGA
1 AAATGA
425025 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:425030 original size:19 final size:19
Alignment explanation
Indices: 424988--425071 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 19
424978 GAAAATGACT
***
424988 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
425008 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
425027 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
425041 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
425060 ATCGCAATGCGA
1 ATCGCAATGCGA
425072 TTTGTGTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 27 0.51
20 10 0.19
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:425122 original size:33 final size:33
Alignment explanation
Indices: 425078--425157 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
425068 GCGATTTGTG
* *
425078 TTTCGCGTTGCGGTTTTATCGTTGCGATTTTAA
1 TTTCGCATTGCGATTTTATCGTTGCGATTTTAA
* * *
425111 TTTTGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTATCGTTGCGATTTTAA
425144 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
425158 AGCCATTTCC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.12, C:0.16, G:0.23, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTATCGTTGCGATTTTAA
Found at i:425154 original size:19 final size:18
Alignment explanation
Indices: 425061--425157 Score: 57
Period size: 19 Copynumber: 5.7 Consensus size: 18
425051 GAAATGAAAA
* *
425061 TCGCAATGCGATTTGTGTT
1 TCGCATTGCGATTT-TATT
* *
425080 TCGCGTTGCGGTTTTA--
1 TCGCATTGCGATTTTATT
425096 TCG--TTGCGATTTTAATT
1 TCGCATTGCGATTTT-ATT
* *
425113 TTGCATTGCGA-TTT-TG
1 TCGCATTGCGATTTTATT
425129 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
425146 TCGCATTGCGAT
1 TCGCATTGCGAT
425158 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 15 0.25
15 4 0.07
16 6 0.10
17 6 0.10
18 4 0.07
19 24 0.41
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:425176 original size:20 final size:20
Alignment explanation
Indices: 425142--425216 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
425132 TTGCGATTTT
425142 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
425161 CATTTCCGCGTTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* * *
425181 CATTTCCGCGTTGTGATAGT
1 CATTTCCGCATTGCGATAGC
*
425201 CATTTTCGCATTGCGA
1 CATTTCCGCATTGCGA
425217 AAGTAAGTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
19 5 0.10
20 44 0.90
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:425671 original size:40 final size:42
Alignment explanation
Indices: 425582--425671 Score: 130
Period size: 40 Copynumber: 2.2 Consensus size: 42
425572 CCCGACTCAC
* *
425582 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
425624 CTATCATCCCTTAAGAGTCCCC-CC-ACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
425664 CTGTCATC
1 CTGTCATC
425672 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 21 0.49
41 2 0.05
42 20 0.47
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:427115 original size:14 final size:14
Alignment explanation
Indices: 427081--427119 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
427071 TTGATTGTTT
427081 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
427095 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
427109 TGTTGATTTGT
1 AATTGATTTGT
427120 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:427335 original size:34 final size:34
Alignment explanation
Indices: 427296--427400 Score: 102
Period size: 40 Copynumber: 2.9 Consensus size: 34
427286 TGCGATTTTC
* *
427296 ATTTCGCATTGCGATTTTCTCGTTGCGATAGCCA
1 ATTTCGCGTTGCGATTTTCCCGTTGCGATAGCCA
* *
427330 ATTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCA
1 ATTTCGCGTTGC----G--ATTTTCCCGTTGCGATAGCCA
* *
427370 TTTTCGCGTTGCGATTTCCCCGTTGCGATAG
1 ATTTCGCGTTGCGATTTTCCCGTTGCGATAG
427401 TCAAATGAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
34 27 0.46
36 1 0.02
38 1 0.02
40 30 0.51
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (34 bp):
ATTTCGCGTTGCGATTTTCCCGTTGCGATAGCCA
Done.