Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008236.1 Hibiscus syriacus cultivar Beakdansim tig00110882_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: 1100419
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:283264 original size:7 final size:7
Alignment explanation
Indices: 283252--283276 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
283242 GAAATGAATG
283252 TAAAGAA
1 TAAAGAA
283259 TAAAGAA
1 TAAAGAA
283266 TAAAGAA
1 TAAAGAA
283273 TAAA
1 TAAA
283277 TAATGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (7 bp):
TAAAGAA
Found at i:291474 original size:24 final size:24
Alignment explanation
Indices: 291447--291493 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
291437 AATGGAACAT
291447 TATACTTATTAAATAAATGATAAC
1 TATACTTATTAAATAAATGATAAC
291471 TATACTTATTAAATAAATGATAA
1 TATACTTATTAAATAAATGATAA
291494 AGAATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
TATACTTATTAAATAAATGATAAC
Found at i:291774 original size:53 final size:54
Alignment explanation
Indices: 291675--291790 Score: 198
Period size: 53 Copynumber: 2.1 Consensus size: 54
291665 TGTTAAACAA
*
291675 ATATATATATATATGAACAAAAAAAAATCAGTTTCCAAGACACATTAAATAAATAT
1 ATATATATATATATGAAC--AAAAAAATCAGTTTCCAAGACACATTAAATAAAAAT
291731 ATATATATATATATGAAC-AAAAAATCAGTTTCCAAGACACATTAAATAAAAAT
1 ATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAAAAT
291784 ATATATA
1 ATATATA
291791 CGTTTAACAA
Statistics
Matches: 59, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
53 41 0.69
56 18 0.31
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.29
Consensus pattern (54 bp):
ATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAAAAT
Found at i:292157 original size:45 final size:45
Alignment explanation
Indices: 292040--292164 Score: 144
Period size: 45 Copynumber: 2.7 Consensus size: 45
292030 ATGGCTATTC
* *
292040 TTCCTAAGACACATTAAACAAATATATATGTATATGAACAAAGAATCAGT
1 TTCC-AAGACACATTAAA-TAA-ATATA--TATATGAACAAAAAATCAGT
** *
292090 TTCCAAGACATGTTAAACAAATATATATATGAACAAAAAAATCAGT
1 TTCCAAGACACATTAAATAAATATATATATGAAC-AAAAAATCAGT
292136 TTCCAAGACACATT-AATAAATATATATAT
1 TTCCAAGACACATTAAATAAATATATATAT
292165 ATATATATAT
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
45 23 0.34
46 22 0.33
47 5 0.07
48 2 0.03
49 11 0.16
50 4 0.06
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.29
Consensus pattern (45 bp):
TTCCAAGACACATTAAATAAATATATATATGAACAAAAAATCAGT
Found at i:292162 original size:2 final size:2
Alignment explanation
Indices: 292155--292207 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
292145 ACATTAATAA
*
292155 AT AT AT AT AT AT AT AT AT AT AT AT AA 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
292197 AT AT AT AT AT A
1 AT AT AT AT AT A
292208 CACGTTTAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:292179 original size:195 final size:194
Alignment explanation
Indices: 291773--292177 Score: 751
Period size: 195 Copynumber: 2.1 Consensus size: 194
291763 CAAGACACAT
* *
291773 TAAATAAAAATATATATACGTTTAACAAATATCCAACTAAGCTATATGTTAACAAATAAATAATG
1 TAAATATATATATATATACGTTTAACAAATATCCAACTAAGCTATATGTTAACAAATAAATAATG
291838 GCTATTCTTCCTAAGACACATTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGA
66 GCTATTCTTCCTAAGACACATTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGA
291903 CATGTTAAACAATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATAAA
131 CATGTTAAACAATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATAAA
291967 TAAATATATATATATATACGTTTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAAT
1 TAAATATATATATATATACGTTTAACAAATATCCAACTAAGCTATATGTT-AACAAATAAATAAT
292032 GGCTATTCTTCCTAAGACACATTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAG
65 GGCTATTCTTCCTAAGACACATTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAG
*
292097 ACATGTTAAACAA-ATATATATATGAACAAAAAAATCAGTTTCCAAGACACATT-AATAAATATA
130 ACATGTTAAACAATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATAAA
*
292160 TATATATATATATATATA
1 TAAATATATATATATATA
292178 TAAATATATA
Statistics
Matches: 206, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
193 26 0.13
194 88 0.43
195 92 0.45
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.30
Consensus pattern (194 bp):
TAAATATATATATATATACGTTTAACAAATATCCAACTAAGCTATATGTTAACAAATAAATAATG
GCTATTCTTCCTAAGACACATTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGA
CATGTTAAACAATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATAAA
Found at i:293470 original size:3 final size:3
Alignment explanation
Indices: 293462--293531 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
293452 TAAACACACT
293462 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
293510 TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
293532 TTTTTTAACT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 1 0.02
3 63 0.98
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:295633 original size:3 final size:3
Alignment explanation
Indices: 295625--295686 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
295615 TATATCCTTC
295625 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
295673 ATA AT- TTA ATA ATA
1 ATA ATA ATA ATA ATA
295687 TTTTTTAACT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 1 0.02
3 55 0.98
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:301038 original size:7 final size:7
Alignment explanation
Indices: 301026--301050 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
301016 GAAATGAATG
301026 TAAAGAA
1 TAAAGAA
301033 TAAAGAA
1 TAAAGAA
301040 TAAAGAA
1 TAAAGAA
301047 TAAA
1 TAAA
301051 TAATGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (7 bp):
TAAAGAA
Found at i:309257 original size:24 final size:24
Alignment explanation
Indices: 309230--309275 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
309220 AATGGAACAT
309230 TATACTTATTAAATAAATGATAAC
1 TATACTTATTAAATAAATGATAAC
309254 TATACTTATTAAATAAATGATA
1 TATACTTATTAAATAAATGATA
309276 TAAAGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (24 bp):
TATACTTATTAAATAAATGATAAC
Found at i:309566 original size:57 final size:53
Alignment explanation
Indices: 309450--309574 Score: 184
Period size: 52 Copynumber: 2.4 Consensus size: 53
309440 CTAAGACATG
* ** *
309450 TTAAACAAATATATATATATATGA-ACAAAAAAAAAATCAGTTTCCAAGACACA
1 TTAAATAAATATATATATATAT-ATATGAACAAAAAATCAGTTTCCAAGACACA
309503 TTAAATAAATATATATATATATATATGAAC-AAAAATCAGTTTCCAAGACACA
1 TTAAATAAATATATATATATATATATGAACAAAAAATCAGTTTCCAAGACACA
309555 TTAAATAAA-ATATATATATA
1 TTAAATAAATATATATATATA
309575 CGTTTAACAA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
51 11 0.16
52 32 0.48
53 24 0.36
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (53 bp):
TTAAATAAATATATATATATATATATGAACAAAAAATCAGTTTCCAAGACACA
Found at i:309931 original size:48 final size:47
Alignment explanation
Indices: 309832--309961 Score: 188
Period size: 48 Copynumber: 2.7 Consensus size: 47
309822 ATGGCTATTC
*
309832 TTCCTAAGACACATTAAACAAATATATATGTATATGAACAAAGAATCAGT
1 TTCC-AAGACACATTAAACAAATATATA--TATATGAACAAAAAATCAGT
**
309882 TTCCAAGACATGTTAAACAAATATATATATATGAACAAAAAAATCAGT
1 TTCCAAGACACATTAAACAAATATATATATATGAAC-AAAAAATCAGT
*
309930 TTCCAAGACACATTAAATAAATATATATATAT
1 TTCCAAGACACATTAAACAAATATATATATAT
309962 ATATATATAT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
47 9 0.12
48 39 0.53
49 21 0.29
50 4 0.05
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (47 bp):
TTCCAAGACACATTAAACAAATATATATATATGAACAAAAAATCAGT
Found at i:309957 original size:2 final size:2
Alignment explanation
Indices: 309950--310000 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
309940 CATTAAATAA
309950 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
309992 AT AT AT AT A
1 AT AT AT AT A
310001 CACGTTTAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:309979 original size:204 final size:202
Alignment explanation
Indices: 309564--309978 Score: 780
Period size: 202 Copynumber: 2.1 Consensus size: 202
309554 ATTAAATAAA
309564 ATATATATATACGTTTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATT
1 ATATATATATACGTTTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATT
309629 CTTCCTAAGACACATTAAACAAATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTTAA
66 CTTCCTAAGACACATTAAACAAATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTTAA
309694 ACAAATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATAAATAAATA
131 ACAAATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATAAATAAATA
309759 TATATAT
196 TATATAT
309766 ATATATATATACGTTTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATT
1 ATATATATATACGTTTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATT
309831 CTTCCTAAGACACATTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTT
66 CTTCCTAAGACACATTAAAC-AA-ATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTT
* *
309896 AAAC-AA-ATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATATATATA
129 AAACAAATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATAAATAAA
309959 TATATATAT
194 TATATATAT
309968 ATATATATATA
1 ATATATATATA
309979 TATATATATA
Statistics
Matches: 209, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
202 160 0.77
203 4 0.02
204 45 0.22
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (202 bp):
ATATATATATACGTTTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATT
CTTCCTAAGACACATTAAACAAATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTTAA
ACAAATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATAAATAAATA
TATATAT
Found at i:311262 original size:3 final size:3
Alignment explanation
Indices: 311254--311326 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
311244 TAAACACACT
311254 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
311302 TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
311327 TTTTTTAACT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 1 0.01
3 66 0.99
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:316256 original size:16 final size:16
Alignment explanation
Indices: 316232--316262 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
316222 AAAAGATACA
*
316232 TATCTTTTTAAAACAG
1 TATCATTTTAAAACAG
316248 TATCATTTTAAAACA
1 TATCATTTTAAAACA
316263 TATTTACCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (16 bp):
TATCATTTTAAAACAG
Found at i:316336 original size:18 final size:18
Alignment explanation
Indices: 316313--316349 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
316303 GAAAGGTTTT
316313 ACCCTTGCACATAGCAAA
1 ACCCTTGCACATAGCAAA
316331 ACCCTTGCACATAGCAAA
1 ACCCTTGCACATAGCAAA
316349 A
1 A
316350 GAGCATGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.32, G:0.11, T:0.16
Consensus pattern (18 bp):
ACCCTTGCACATAGCAAA
Found at i:316392 original size:43 final size:43
Alignment explanation
Indices: 316331--316572 Score: 315
Period size: 43 Copynumber: 5.6 Consensus size: 43
316321 ACATAGCAAA
* * * * *
316331 ACCCTTGCACATAGCAAAAGAGCAT-GGGAAACTATAAGGTCTT
1 ACCCTTGCACACAACAAAAGAACCTGGGGAAACTGTAAGG-CTT
* *
316374 ACCCTTGCACACAACAAAAGAACCTAGGGAAACTGTAAGGCTC
1 ACCCTTGCACACAACAAAAGAACCTGGGGAAACTGTAAGGCTT
* * *
316417 ACCATTGAACACAACAAACGAACCTGGGGGAAACTGTAAGGCTT
1 ACCCTTGCACACAACAAAAGAACCT-GGGGAAACTGTAAGGCTT
*
316461 ACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTT
1 ACCCTTGCACACAACAAAAGAACCTGGGGAAACTGTAAGGCTT
* * *
316504 ACCCTTGCAAACAGCAAAGGAACCTGGGGAAACTGTAAGGCTT
1 ACCCTTGCACACAACAAAAGAACCTGGGGAAACTGTAAGGCTT
* *
316547 ACCCTTGCACACAGCAAAGGAACCTG
1 ACCCTTGCACACAACAAAAGAACCTG
316573 CGGTAACGGT
Statistics
Matches: 180, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
43 129 0.72
44 51 0.28
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (43 bp):
ACCCTTGCACACAACAAAAGAACCTGGGGAAACTGTAAGGCTT
Found at i:316470 original size:87 final size:86
Alignment explanation
Indices: 316356--316571 Score: 326
Period size: 87 Copynumber: 2.5 Consensus size: 86
316346 AAAAGAGCAT
* *
316356 GGGAAACTATAAGGTCTTACCCTTGCACACAACAAAAGAACCTAGGGAAACTGTAAGGCTCACCA
1 GGGAAACTGTAAGG-CTTACCCTTGCACACAACAAAGGAACCTAGGGAAACTGTAAGGCTCACCA
316421 TTG-AACACAACAAACGAACCTGG
65 TTGCAA-ACAACAAACGAACCT-G
* * *
316444 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACCCT
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTAGGGAAACTGTAAGGCTCACCAT
* *
316509 TGCAAACAGCAAAGGAACCTG
66 TGCAAACAACAAACGAACCTG
*
316530 GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCT
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCT
316572 GCGGTAACGG
Statistics
Matches: 119, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
86 42 0.35
87 62 0.52
88 15 0.13
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (86 bp):
GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTAGGGAAACTGTAAGGCTCACCAT
TGCAAACAACAAACGAACCTG
Found at i:320534 original size:18 final size:18
Alignment explanation
Indices: 320511--320556 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
320501 CAGTGAATGG
320511 GTCGGGTCAATGGGTCGA
1 GTCGGGTCAATGGGTCGA
320529 GTCGGGTCAATGGGTCGA
1 GTCGGGTCAATGGGTCGA
320547 GTCGGGTCAA
1 GTCGGGTCAA
320557 ATCGGGTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.43, T:0.22
Consensus pattern (18 bp):
GTCGGGTCAATGGGTCGA
Found at i:320565 original size:10 final size:10
Alignment explanation
Indices: 320512--320578 Score: 52
Period size: 10 Copynumber: 7.0 Consensus size: 10
320502 AGTGAATGGG
320512 TCGGGTC-AA
1 TCGGGTCAAA
* *
320521 T-GGGTCGAG
1 TCGGGTCAAA
320530 TCGGGTC-AA
1 TCGGGTCAAA
* *
320539 T-GGGTCGAG
1 TCGGGTCAAA
320548 TCGGGTCAAA
1 TCGGGTCAAA
320558 TCGGGTCAAA
1 TCGGGTCAAA
*
320568 ACTGGGTCAAA
1 TC-GGGTCAAA
320579 CTATCCCAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
8 10 0.21
9 7 0.15
10 22 0.47
11 8 0.17
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (10 bp):
TCGGGTCAAA
Found at i:322652 original size:85 final size:87
Alignment explanation
Indices: 322530--322698 Score: 227
Period size: 85 Copynumber: 2.0 Consensus size: 87
322520 AAAAGAGCCT
* * *
322530 GGGAAACTATAAGGTCTTGCCCTTGCACACAACAAAGGAACCTAGGA-AAACTGTAAAGCTCACC
1 GGGAAACTATAAGGACTTACCCTTGCACACAACAAAGGAACCT-GGAGAAACTATAAAGCTCACC
322594 CTTGC-CACAACAAAGGAACATG
65 CTTGCACACAACAAAGGAACATG
* ** * *
322616 GGGAAACTGTAA-GACTTACCCTTGCACACAGTAAAGGAACCTGGAGAAACTATAAGGCTTACCC
1 GGGAAACTATAAGGACTTACCCTTGCACACAACAAAGGAACCTGGAGAAACTATAAAGCTCACCC
*
322680 TTGCACACAGCAAAGGAAC
66 TTGCACACAACAAAGGAAC
322699 CTGCGGTAAC
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
84 3 0.04
85 45 0.62
86 24 0.33
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (87 bp):
GGGAAACTATAAGGACTTACCCTTGCACACAACAAAGGAACCTGGAGAAACTATAAAGCTCACCC
TTGCACACAACAAAGGAACATG
Found at i:322701 original size:43 final size:43
Alignment explanation
Indices: 322496--322701 Score: 238
Period size: 43 Copynumber: 4.8 Consensus size: 43
322486 GCAAAAACGG
* * *
322496 TAAGGTCTTACCCTTGCACATAGCAAAAGAGCCTGG-GAAACTA
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGAGAAACTA
* * *
322539 TAAGGTCTTGCCCTTGCACACAACAAAGGAACCTAGGA-AAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCT-GGAGAAACTA
* * * * * *
322583 TAAAGCTCACCCTTGC-CACAACAAAGGAACATGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGAGAAACTA
* *
322625 TAAGACTTACCCTTGCACACAGTAAAGGAACCTGGAGAAACTA
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGAGAAACTA
322668 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTG
322702 CGGTAACGAC
Statistics
Matches: 138, Mismatches: 21, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
41 2 0.01
42 34 0.25
43 91 0.66
44 11 0.08
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGAGAAACTA
Found at i:325450 original size:7 final size:7
Alignment explanation
Indices: 325440--325474 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
325430 CAGTCAACGG
325440 CGGTCAA
1 CGGTCAA
325447 CGGTCAA
1 CGGTCAA
*
325454 CAGTCAA
1 CGGTCAA
325461 CGGTCAA
1 CGGTCAA
325468 CAGGTCA
1 C-GGTCA
325475 GGTCAACAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 20 0.80
8 5 0.20
ACGTcount: A:0.31, C:0.29, G:0.26, T:0.14
Consensus pattern (7 bp):
CGGTCAA
Found at i:325461 original size:14 final size:14
Alignment explanation
Indices: 325442--325488 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
325432 GTCAACGGCG
325442 GTCAACGGTCAACA
1 GTCAACGGTCAACA
325456 GTCAACGGTCAACA
1 GTCAACGGTCAACA
325470 GGTC-A-GGTCAACA
1 -GTCAACGGTCAACA
325483 GCTCAA
1 G-TCAA
325489 GTCAGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.03
13 10 0.33
14 16 0.53
15 3 0.10
ACGTcount: A:0.34, C:0.28, G:0.23, T:0.15
Consensus pattern (14 bp):
GTCAACGGTCAACA
Found at i:325497 original size:31 final size:27
Alignment explanation
Indices: 325448--325511 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 27
325438 GGCGGTCAAC
325448 GGTCAACAGTCAACGGTCAACAGGTCA
1 GGTCAACAGTCAACGGTCAACAGGTCA
*
325475 GGTCAACAGCTCAAGTCAGGTCAACGGGTCA
1 GGTCAACAG-TCAA--C-GGTCAACAGGTCA
*
325506 GATCAA
1 GGTCAA
325512 ATCGGGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 9 0.29
28 4 0.13
30 1 0.03
31 17 0.55
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.16
Consensus pattern (27 bp):
GGTCAACAGTCAACGGTCAACAGGTCA
Found at i:326726 original size:14 final size:14
Alignment explanation
Indices: 326692--326732 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
326682 GTGAATGGGT
*
326692 CGGGTTGGGTC-AA
1 CGGGTCGGGTCAAA
*
326705 CGGATCGGGTCAAA
1 CGGGTCGGGTCAAA
326719 CGGGTCGGGTCAAA
1 CGGGTCGGGTCAAA
326733 ACTGTGTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.22, C:0.20, G:0.41, T:0.17
Consensus pattern (14 bp):
CGGGTCGGGTCAAA
Found at i:326883 original size:43 final size:43
Alignment explanation
Indices: 326814--327062 Score: 286
Period size: 43 Copynumber: 5.8 Consensus size: 43
326804 TAGTGCTACG
** * * * *
326814 GTAAGGTCTTACCCTTGTGCATAGCAAAAGAGCCT-GGGAAACT
1 GTAAGG-CTTACCCTTGCACACAACAAAGGAACCTAGGGAAACT
* ** * *
326857 ATAAGGTCTTATTCTTGCACACAGCAAAGGAACCTAGGTAAACT
1 GTAAGG-CTTACCCTTGCACACAACAAAGGAACCTAGGGAAACT
* *
326901 GTAACGCTCACCCTTGCACACAACAAAGGAACCT-GGGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTAGGGAAACT
* *
326943 GTAAGGCTTACCCTTGCACACATCAAAGGAACCTGGGGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTAGGGAAACT
* * *
326986 GTAAGGCTTACCCTTGCACACAACAAAGGAACATATGGAAATT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTAGGGAAACT
* *
327029 GTAAGGCTTACCCTTGCACACATCAAAAGAACCT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCT
327063 GCGGTAACGG
Statistics
Matches: 177, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
42 38 0.21
43 128 0.72
44 11 0.06
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (43 bp):
GTAAGGCTTACCCTTGCACACAACAAAGGAACCTAGGGAAACT
Found at i:326985 original size:85 final size:85
Alignment explanation
Indices: 326846--327063 Score: 310
Period size: 85 Copynumber: 2.5 Consensus size: 85
326836 AGCAAAAGAG
* ** * * *
326846 CCTGGGAAACTATAAGGTCTTATTCTTGCACACAGCAAAGGAACCTAGGTAAACTGTAACGCTCA
1 CCTGGGAAACTGTAAGG-CTTACCCTTGCACACATCAAAGGAACCTGGGGAAACTGTAACGCTCA
326911 CCCTTGCACACAACAAAGGAA
65 CCCTTGCACACAACAAAGGAA
* *
326932 CCTGGGAAACTGTAAGGCTTACCCTTGCACACATCAAAGGAACCTGGGGAAACTGTAAGGCTTAC
1 CCTGGGAAACTGTAAGGCTTACCCTTGCACACATCAAAGGAACCTGGGGAAACTGTAACGCTCAC
326997 CCTTGCACACAACAAAGGAA
66 CCTTGCACACAACAAAGGAA
* * * *
327017 CATATGGAAATTGTAAGGCTTACCCTTGCACACATCAAAAGAACCTG
1 CCT-GGGAAACTGTAAGGCTTACCCTTGCACACATCAAAGGAACCTG
327064 CGGTAACGGT
Statistics
Matches: 119, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
85 63 0.53
86 56 0.47
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (85 bp):
CCTGGGAAACTGTAAGGCTTACCCTTGCACACATCAAAGGAACCTGGGGAAACTGTAACGCTCAC
CCTTGCACACAACAAAGGAA
Found at i:327043 original size:128 final size:129
Alignment explanation
Indices: 326814--327063 Score: 317
Period size: 128 Copynumber: 1.9 Consensus size: 129
326804 TAGTGCTACG
** * * **
326814 GTAAGGTCTTACCCTTGTGCATAGCAAAAGAGCCTGGGAAACTATAAGGTCTTATTCTTGCACAC
1 GTAAGGTCTTACCCTTGCACACAGCAAAAGAACCTGGGAAACTATAAGGTCTTACCCTTGCACAC
* * *
326879 AGCAAAGGAACCTAGGTAAACTGTAACGCTCACCCTTGCACACAACAAAGGAACCTGGGAAACT
66 AACAAAGGAACATAGGTAAACTGTAACGCTCACCCTTGCACACAACAAAAGAACCTGGGAAACT
* * *
326943 GTAAGG-CTTACCCTTGCACACATCAAAGGAACCTGGGGAAACTGTAAGG-CTTACCCTTGCACA
1 GTAAGGTCTTACCCTTGCACACAGCAAAAGAACCT-GGGAAACTATAAGGTCTTACCCTTGCACA
* * * *
327006 CAACAAAGGAACATATGG-AAATTGTAAGGCTTACCCTTGCACACATCAAAAGAACCTG
65 CAACAAAGGAACATA-GGTAAACTGTAACGCTCACCCTTGCACACAACAAAAGAACCTG
327064 CGGTAACGGT
Statistics
Matches: 103, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
128 82 0.80
129 21 0.20
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (129 bp):
GTAAGGTCTTACCCTTGCACACAGCAAAAGAACCTGGGAAACTATAAGGTCTTACCCTTGCACAC
AACAAAGGAACATAGGTAAACTGTAACGCTCACCCTTGCACACAACAAAAGAACCTGGGAAACT
Found at i:336747 original size:3 final size:3
Alignment explanation
Indices: 336739--336797 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
336729 AAATTCGGAA
336739 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
336787 AAT AAT AAT AA
1 AAT AAT AAT AA
336798 AACTTCTTAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:338561 original size:16 final size:16
Alignment explanation
Indices: 338532--338565 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
338522 TTTGATAACA
338532 TTTCTATCACTTTCCT
1 TTTCTATCACTTTCCT
338548 TTTCTTATCA-TTTCCT
1 TTTC-TATCACTTTCCT
338564 TT
1 TT
338566 CTTCTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTCTATCACTTTCCT
Found at i:338797 original size:25 final size:24
Alignment explanation
Indices: 338769--338815 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
338759 TAACAAAAGC
*
338769 AACAAAAATAAAAAGAAAGAAGAAA
1 AACAAAAAGAAAAAGAAA-AAGAAA
*
338794 AACAAAAAGAGAAAGAAAAAGA
1 AACAAAAAGAAAAAGAAAAAGA
338816 CTCCTACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (24 bp):
AACAAAAAGAAAAAGAAAAAGAAA
Found at i:338800 original size:19 final size:18
Alignment explanation
Indices: 338772--338813 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
338762 CAAAAGCAAC
*
338772 AAAAATAAAAAGAAAGAAG
1 AAAAACAAAAAGAAA-AAG
*
338791 AAAAACAAAAAGAGAAAG
1 AAAAACAAAAAGAAAAAG
338809 AAAAA
1 AAAAA
338814 GACTCCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (18 bp):
AAAAACAAAAAGAAAAAG
Found at i:338808 original size:6 final size:6
Alignment explanation
Indices: 338772--338815 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
338762 CAAAAGCAAC
* * *
338772 AAAAAT AAAAAG AAAGAAG AAAAAC AAAAAG AGAAAG AAAAAG A
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
338816 CTCCTACAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:347909 original size:130 final size:130
Alignment explanation
Indices: 347768--348015 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
347758 TATTTATATA
*
347768 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
347833 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
*
347898 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAATTTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
347963 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
348016 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:348046 original size:130 final size:129
Alignment explanation
Indices: 347782--348046 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
347772 ATTTGGTCCT
* *
347782 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
347847 TGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
347912 AAATTAAATAAAATTTAATAATTTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
347977 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
348041 -A
128 CA
348042 AAATT
1 AAATT
348047 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:348374 original size:28 final size:26
Alignment explanation
Indices: 348343--348403 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
348333 AGTTGATACA
*
348343 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTT-AAA-AATAAATTTAAGAATT
* * *
348371 ATATTTTTAAACTAAATTTAATAATT
1 ATATTTTAAAAATAAATTTAAGAATT
348397 ATATTTT
1 ATATTTT
348404 CATATTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 20 0.69
27 2 0.07
28 7 0.24
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (26 bp):
ATATTTTAAAAATAAATTTAAGAATT
Found at i:348503 original size:16 final size:18
Alignment explanation
Indices: 348482--348515 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
348472 ATTTCTTATT
348482 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
348498 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
348516 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:348662 original size:21 final size:21
Alignment explanation
Indices: 348638--348680 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
348628 TATTACCTTA
348638 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
*
348659 AATTGAAGTTTTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
348680 A
1 A
348681 GGGTTTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:350240 original size:23 final size:26
Alignment explanation
Indices: 350183--350248 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 26
350173 TGATAATGGC
*
350183 TCTGAATCATTCAGAATGTACTTTTG
1 TCTGAATCATTCAGCATGTACTTTTG
*
350209 TGCTGAATCATTCAGCAT-T-GTTTTG
1 T-CTGAATCATTCAGCATGTACTTTTG
*
350234 T-TGAATCAGTCAGCA
1 TCTGAATCATTCAGCA
350249 CTGAATCATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 13 0.36
25 6 0.17
26 2 0.06
27 15 0.42
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (26 bp):
TCTGAATCATTCAGCATGTACTTTTG
Found at i:352213 original size:2 final size:2
Alignment explanation
Indices: 352206--352236 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
352196 ACCTCACTTT
352206 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
352237 GGTAAAGTTT
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:358539 original size:14 final size:14
Alignment explanation
Indices: 358515--358555 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
358505 TCGATTATAT
*
358515 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
*
358529 TTTCATTTATGTTC
1 GTTCATTTATGTTC
358543 GTTCATTTATGTT
1 GTTCATTTATGTT
358556 TGAACAGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.61
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:358838 original size:14 final size:14
Alignment explanation
Indices: 358810--358849 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
358800 TTTTCTGTGT
358810 GTTTGTGTT-GTTC
1 GTTTGTGTTCGTTC
*
358823 GTTTATGTTCGTTC
1 GTTTGTGTTCGTTC
*
358837 GTTCGTGTTCGTT
1 GTTTGTGTTCGTT
358850 TATGTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.03, C:0.12, G:0.28, T:0.57
Consensus pattern (14 bp):
GTTTGTGTTCGTTC
Found at i:359154 original size:12 final size:12
Alignment explanation
Indices: 359137--359161 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
359127 TTTAATCAAA
359137 TTTGAGTATTAC
1 TTTGAGTATTAC
359149 TTTGAGTATTAC
1 TTTGAGTATTAC
359161 T
1 T
359162 AAATTCAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (12 bp):
TTTGAGTATTAC
Found at i:365957 original size:31 final size:30
Alignment explanation
Indices: 365885--365964 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 30
365875 ATTTTACGTA
365885 ATAA-ATAATATTAATAAGATATATCATGTC
1 ATAAGATAATATTAATAA-ATATATCATGTC
*
365915 ATAAGAAAATATTAATAGAATATATCATGTC
1 ATAAGATAATATTAATA-AATATATCATGTC
* *
365946 AT-TGCGTAATATTAATAAA
1 ATAAG-ATAATATTAATAAA
365965 ATAAGTCATG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
30 7 0.16
31 35 0.81
32 1 0.02
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (30 bp):
ATAAGATAATATTAATAAATATATCATGTC
Found at i:367683 original size:76 final size:75
Alignment explanation
Indices: 367576--367723 Score: 217
Period size: 76 Copynumber: 2.0 Consensus size: 75
367566 TAAACTCAAA
367576 TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTAT
1 TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTAT
367641 TTTAATTAAAT
65 TTTAATTAAAT
* * * * * *
367652 TTTAGGATATTATTTT-TATATTTTATCTTTATTTTTGTATTTTAGTTTAAATATGTTTTAGTAT
1 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
367716 TTTAATTA
65 TTTAATTA
367724 GGATTTAGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
75 24 0.37
76 41 0.63
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (75 bp):
TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAAT
Found at i:368413 original size:21 final size:21
Alignment explanation
Indices: 368388--368433 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
368378 CTTTAATTTG
*
368388 TTTATTTAATTATTTTTTTCT
1 TTTATTTAATTATTTTTTTAT
*
368409 TTTATTTAATTCTTTTTTTAT
1 TTTATTTAATTATTTTTTTAT
368430 TTTA
1 TTTA
368434 ACTATAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTATTTAATTATTTTTTTAT
Found at i:368525 original size:16 final size:17
Alignment explanation
Indices: 368458--368526 Score: 60
Period size: 16 Copynumber: 4.4 Consensus size: 17
368448 AAAAATACCC
*
368458 ATTTTATATTTATTACT
1 ATTTTATATTTATTATT
*
368475 A-TTAATATTTATTATT
1 ATTTTATATTTATTATT
*
368491 ATATTAT-TTT-TCT-TT
1 ATTTTATATTTAT-TATT
368506 -TTTTATATTTATT-TT
1 ATTTTATATTTATTATT
368521 ATTTTA
1 ATTTTA
368527 ATATATCTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
14 5 0.12
15 9 0.21
16 24 0.57
17 4 0.10
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTATATTTATTATT
Found at i:368536 original size:31 final size:31
Alignment explanation
Indices: 368479--368537 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
368469 ATTACTATTA
* *
368479 ATATTTATTATTATATTATTTTTCTTTTTTT
1 ATATTTATTATTATATTATATATCTTTTTTT
*
368510 ATATTTATT-TTATTTTAATATATCTTTT
1 ATATTTATTATTATATT-ATATATCTTTT
368538 CAACTTCATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.71
Consensus pattern (31 bp):
ATATTTATTATTATATTATATATCTTTTTTT
Found at i:373041 original size:1 final size:1
Alignment explanation
Indices: 373035--373078 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
373025 TTTCGTTATA
* * * *
373035 TTTTTTTTATTTTTTATTTTTTTTTTTATTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
373079 AGCAAACTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:373047 original size:9 final size:9
Alignment explanation
Indices: 373033--373078 Score: 74
Period size: 9 Copynumber: 5.0 Consensus size: 9
373023 CATTTCGTTA
373033 TATTTTTTT
1 TATTTTTTT
373042 TATTTTTTAT
1 TATTTTTT-T
*
373052 TTTTTTTTT
1 TATTTTTTT
373061 TATTTTTTT
1 TATTTTTTT
373070 TATTTTTTT
1 TATTTTTTT
373079 AGCAAACTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 26 0.76
10 8 0.24
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TATTTTTTT
Found at i:373057 original size:19 final size:19
Alignment explanation
Indices: 373030--373078 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
373020 ACCCATTTCG
373030 TTATATTTTTTTTATTTTTT
1 TTAT-TTTTTTTTATTTTTT
373050 ATT-TTTTTTTTTATTTTTT
1 -TTATTTTTTTTTATTTTTT
373069 TTATTTTTTT
1 TTATTTTTTT
373079 AGCAAACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 2 0.07
19 22 0.81
20 1 0.04
21 2 0.07
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (19 bp):
TTATTTTTTTTTATTTTTT
Found at i:373223 original size:29 final size:29
Alignment explanation
Indices: 373168--373238 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
373158 TTAACAAAAA
*
373168 AACAGTGC--AAAAAACTGACTTGGTTCG
1 AACAGTGCAGAAAAAACTGAATTGGTTCG
*
373195 AACAGTGCAGAAAAAACTGAATTGTTTCG
1 AACAGTGCAGAAAAAACTGAATTGGTTCG
373224 AACAGTGCAGAAAAA
1 AACAGTGCAGAAAAA
373239 TACACAGCAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 8 0.20
29 32 0.80
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (29 bp):
AACAGTGCAGAAAAAACTGAATTGGTTCG
Found at i:375678 original size:21 final size:22
Alignment explanation
Indices: 375653--375693 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
375643 CTTTAATTTA
375653 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
375674 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
375694 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:375749 original size:16 final size:15
Alignment explanation
Indices: 375728--375764 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
375718 ATCCCCTTTT
375728 ATATTTATTACTATTA
1 ATATTTATTA-TATTA
375744 ATATTTATTATATTA
1 ATATTTATTATATTA
*
375759 TTATTT
1 ATATTT
375765 TTCTTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTATTATATTA
Found at i:392296 original size:36 final size:36
Alignment explanation
Indices: 392249--392327 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
392239 ATTTTTCCAT
* *
392249 TAGGGTTTCTTTACACGAATCAAAACGCTTCCCCAC
1 TAGGGTTTCTTTACACAAATCAAAAAGCTTCCCCAC
*
392285 TAGGGTTTCTTTACACAAATCAAAAAGCTTTCCCAC
1 TAGGGTTTCTTTACACAAATCAAAAAGCTTCCCCAC
392321 TAGGGTT
1 TAGGGTT
392328 CTAAATGTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (36 bp):
TAGGGTTTCTTTACACAAATCAAAAAGCTTCCCCAC
Found at i:397085 original size:30 final size:30
Alignment explanation
Indices: 397044--397108 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
397034 TTCAAGGGGC
397044 AAATTGATATTT-ACCTAAAGTTT-AGGTGTT
1 AAATTGATATTTCACCTAAA-TTTAAGG-GTT
* *
397074 AAATTGGTATTTCATCTAAATTTAAGGGTT
1 AAATTGATATTTCACCTAAATTTAAGGGTT
397104 AAATT
1 AAATT
397109 AAAAATTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.43
Consensus pattern (30 bp):
AAATTGATATTTCACCTAAATTTAAGGGTT
Found at i:402352 original size:98 final size:98
Alignment explanation
Indices: 402175--402352 Score: 252
Period size: 98 Copynumber: 1.8 Consensus size: 98
402165 TTTTCTTTAT
* * *
402175 GGGTAAATATACAAATGGTCACTAAACTTTTTAGATACTTACATTTAGTCTCCAAACTTTTAAAA
1 GGGTAAATATACAAATGGTCACTAAACATTTCAGATAATTACATTTAGTCTCCAAACTTTTAAAA
* *
402240 CATGCAATAGAGTCACCAACATTTAGTTCATTA
66 CATGCAACACAGTCACCAACATTTAGTTCATTA
* *
402273 GGGTAAATTATATAAATGGTCACTAAACATTTCAGA-AATTACATTTAGGTC-CCTAACTTTTAA
1 GGGTAAA-TATACAAATGGTCACTAAACATTTCAGATAATTACATTTA-GTCTCCAAACTTTTAA
*
402336 AACTTGCAACACAGTCA
64 AACATGCAACACAGTCA
402353 TCAATTACAT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
98 42 0.60
99 28 0.40
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (98 bp):
GGGTAAATATACAAATGGTCACTAAACATTTCAGATAATTACATTTAGTCTCCAAACTTTTAAAA
CATGCAACACAGTCACCAACATTTAGTTCATTA
Found at i:402411 original size:35 final size:35
Alignment explanation
Indices: 402353--402447 Score: 110
Period size: 35 Copynumber: 2.7 Consensus size: 35
402343 AACACAGTCA
402353 TCAATTACATT-TAAACC-CTAAATTCCAAAATGC-TT
1 TCAATTACATTCTAAACCTC-AAATTCCAAAA--CATT
402388 T-AATTACATTCTAAACCTCAAATTCCAAAACATT
1 TCAATTACATTCTAAACCTCAAATTCCAAAACATT
*
402422 TCAATTACATATC-CAACCTCAAATTC
1 TCAATTACAT-TCTAAACCTCAAATTC
402448 ATAATCATTA
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
33 1 0.02
34 12 0.22
35 38 0.70
36 3 0.06
ACGTcount: A:0.41, C:0.25, G:0.01, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCTCAAATTCCAAAACATT
Found at i:403195 original size:148 final size:148
Alignment explanation
Indices: 402927--403219 Score: 478
Period size: 148 Copynumber: 2.0 Consensus size: 148
402917 AAACTATTTA
* * * *
402927 AATTAGAATCAATTAATATTATAGTATTATAAATATTTATAATTAAATTAAAACAGAAACTCGAA
1 AATTAGAATCAAATAATATTATACTATGATAAATATTTATAATTAAATTAAAACAGAAACTCAAA
* * *
402992 AATTCAATTCAATTTAACTTGATTTAAATTTTATAAACTCAAATTGAAAAAATTTCGTGTCAACT
66 AATTCAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACT
*
403057 ATTTTATAAACTGAACTG
131 ACTTTATAAACTGAACTG
* *
403075 AATTAGAATCAAATAATATTATACTATGATAAATATTTATAATTAAATTTAGACAGAAACTCAAA
1 AATTAGAATCAAATAATATTATACTATGATAAATATTTATAATTAAATTAAAACAGAAACTCAAA
* *
403140 AATTCAATTCAATTCAACTTGATTTAAATTTTATGAATTCAAATCGAAAAAATTTCGAGTCAACT
66 AATTCAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACT
403205 ACTTTATAAACTGAA
131 ACTTTATAAACTGAA
403220 TTGAGTATTT
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
148 133 1.00
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (148 bp):
AATTAGAATCAAATAATATTATACTATGATAAATATTTATAATTAAATTAAAACAGAAACTCAAA
AATTCAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACT
ACTTTATAAACTGAACTG
Found at i:403394 original size:34 final size:34
Alignment explanation
Indices: 403355--403429 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
403345 GAATTGATTA
*
403355 TGAATTTGGGGTCGAAT-ATGTAATTGAAGTATTT
1 TGAATTTGAGGT-GAATAATGTAATTGAAGTATTT
**
403389 TGAATTTGAGGTTTATAATGTAATTGAAGTATTT
1 TGAATTTGAGGTGAATAATGTAATTGAAGTATTT
*
403423 TGGATTT
1 TGAATTT
403430 TAGGGTTTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
33 2 0.06
34 34 0.94
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.45
Consensus pattern (34 bp):
TGAATTTGAGGTGAATAATGTAATTGAAGTATTT
Found at i:403444 original size:35 final size:34
Alignment explanation
Indices: 403372--403448 Score: 118
Period size: 34 Copynumber: 2.2 Consensus size: 34
403362 GGGGTCGAAT
*
403372 ATGTAATTGAAGTATTTTGAATTTGAGGTTTATA
1 ATGTAATTGAAGTATTTTGAATTTGAGGTTTAGA
* *
403406 ATGTAATTGAAGTATTTTGGATTTTAGGGTTTAGA
1 ATGTAATTGAAGTATTTTGAATTTGA-GGTTTAGA
403441 ATGTAATT
1 ATGTAATT
403449 AATGACTATG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 24 0.62
35 15 0.38
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (34 bp):
ATGTAATTGAAGTATTTTGAATTTGAGGTTTAGA
Found at i:405132 original size:30 final size:29
Alignment explanation
Indices: 405041--405142 Score: 88
Period size: 30 Copynumber: 3.6 Consensus size: 29
405031 TAAGGAAATA
* *
405041 TTCGTGTTTGTTTATTTATTTTAAAAGATG
1 TTCGTGTTCGTTTATTTATTTT-TAAGATG
* * * *
405071 TTCATGTTCGTTTA--AATTATT-A-ATA
1 TTCGTGTTCGTTTATTTATTTTTAAGATG
405096 TT-GTGTTCGTTTATTTATTTTTGAAGATG
1 TTCGTGTTCGTTTATTTATTTTT-AAGATG
*
405125 TTCGTGTTCGTTTGTTTA
1 TTCGTGTTCGTTTATTTA
405143 GCATTCGTGA
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
24 10 0.18
25 4 0.07
26 6 0.11
28 5 0.09
29 4 0.07
30 26 0.47
ACGTcount: A:0.21, C:0.06, G:0.17, T:0.57
Consensus pattern (29 bp):
TTCGTGTTCGTTTATTTATTTTTAAGATG
Found at i:405441 original size:38 final size:38
Alignment explanation
Indices: 405390--405466 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
405380 CAAAAGTAGC
* *
405390 TTGTTCATGAACATAAACGAGCGAGTCAATAAACGAGT
1 TTGTTCATGAACATAAACGAACAAGTCAATAAACGAGT
* * *
405428 TTGTTCATGAACATGAATGAACAAGTTAATAAACGAGT
1 TTGTTCATGAACATAAACGAACAAGTCAATAAACGAGT
405466 T
1 T
405467 CATAAATGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (38 bp):
TTGTTCATGAACATAAACGAACAAGTCAATAAACGAGT
Found at i:415512 original size:185 final size:185
Alignment explanation
Indices: 415183--415571 Score: 649
Period size: 185 Copynumber: 2.1 Consensus size: 185
415173 ATTTCGAATT
* * * *
415183 TATATAA-AAATTAAATA-TTTTTAATTCAAAAAAATAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
415246 ATTATAAAATAAAAATTTTATATAAAATTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
66 ATTATAAAATAAAAATTTTATATAAAATTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
* *
415311 TAGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGACTTAGCCCATATGTTA
131 TAGATCTTAAATTATTAATTAGGTTTTAAATGGTTTGGACTAAGCCCATATGTTA
415366 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
** *
415431 ATTATAAAATAAAAATTTTATATAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 ATTATAAAATAAAAATTTTATATAAAATTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
*
415496 T-GAATCTTAAATTATTAATTAGGTTTTAAATGGTTTGGGCTAAGCCCATATGTTA
131 TAG-ATCTTAAATTATTAATTAGGTTTTAAATGGTTTGGACTAAGCCCATATGTTA
*
415551 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
415572 AAAATTTAAT
Statistics
Matches: 192, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
183 7 0.04
184 9 0.05
185 176 0.92
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTTTATATAAAATTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
TAGATCTTAAATTATTAATTAGGTTTTAAATGGTTTGGACTAAGCCCATATGTTA
Found at i:421549 original size:12 final size:12
Alignment explanation
Indices: 421526--421563 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
421516 GTCAGATTTC
421526 CTTTCT-TT-TA
1 CTTTCTCTTCTA
421536 CTTTCTCTTCTA
1 CTTTCTCTTCTA
421548 CTTTCTCTTCTA
1 CTTTCTCTTCTA
421560 CTTT
1 CTTT
421564 TAGTTGCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 6 0.23
11 2 0.08
12 18 0.69
ACGTcount: A:0.08, C:0.29, G:0.00, T:0.63
Consensus pattern (12 bp):
CTTTCTCTTCTA
Found at i:422561 original size:21 final size:21
Alignment explanation
Indices: 422536--422575 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
422526 GTTAATTAGT
422536 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
422557 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
422576 CATATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:422633 original size:41 final size:40
Alignment explanation
Indices: 422585--422686 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 40
422575 TCATATAAAA
*
422585 ATAAAAAATTATTTAATTAGTATGTT-T-GATAGTTATAT
1 ATAAAAAAATATTTAATTAGTATGTTATCGATAGTTATAT
* * * *
422623 ATTAATAAAAATAATTAGTTAGTTTGTTAGTCGTTAGTTATAT
1 A-TAA-AAAAATATTTAATTAGTATGTTA-TCGATAGTTATAT
*
422666 ATAAAAAAATATGTAATTAGT
1 ATAAAAAAATATTTAATTAGT
422687 TTGTGTTAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
38 1 0.02
39 3 0.06
40 18 0.35
41 14 0.27
42 4 0.08
43 11 0.22
ACGTcount: A:0.43, C:0.01, G:0.12, T:0.44
Consensus pattern (40 bp):
ATAAAAAAATATTTAATTAGTATGTTATCGATAGTTATAT
Found at i:422802 original size:30 final size:30
Alignment explanation
Indices: 422762--422858 Score: 124
Period size: 30 Copynumber: 3.2 Consensus size: 30
422752 AATTATTTTT
*
422762 TTAGTATTAAATTATAATTAAA-AATCGTTTA
1 TTAGT-TTAAATTAT-ATTAAAGAATAGTTTA
* *
422793 TTAGTTTAAATTGTATTAAAGTATAGTTTA
1 TTAGTTTAAATTATATTAAAGAATAGTTTA
* *
422823 TTAGTTGAAGTTATATTAAAGAATAGTTTA
1 TTAGTTTAAATTATATTAAAGAATAGTTTA
422853 TTAGTT
1 TTAGTT
422859 GTTTAAGGGA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
29 6 0.10
30 47 0.81
31 5 0.09
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.47
Consensus pattern (30 bp):
TTAGTTTAAATTATATTAAAGAATAGTTTA
Found at i:423488 original size:20 final size:20
Alignment explanation
Indices: 423459--423514 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
423449 TTTCAAAGTG
*
423459 ATGCACCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
423479 ATGCATCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
*
423499 TTGCATCGATGCACCA
1 ATGCATCGATGCACCA
423515 TGGAATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.36, G:0.16, T:0.20
Consensus pattern (20 bp):
ATGCATCGATGCACCAATCC
Found at i:423557 original size:45 final size:45
Alignment explanation
Indices: 423500--423647 Score: 149
Period size: 45 Copynumber: 3.3 Consensus size: 45
423490 CACCAATCCT
423500 TGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATTTCA
1 TGCATCGATGCACTCA-GGAATAAA-TGAAACATCGAATGCATTTCA
** ** *
423545 TGCATCGATGCACTCAGGGTTTTATGAAACATCGAATGCATTTGA
1 TGCATCGATGCACTCAGGAATAAATGAAACATCGAATGCATTTCA
* *** * *
423590 TGCATCGATGCACTCA-GACTTTTTCAAAGCATCGAATGCATTTTA
1 TGCATCGATGCACTCAGGAATAAATGAAA-CATCGAATGCATTTCA
423635 TGCATCGATGCAC
1 TGCATCGATGCAC
423648 ACTTAGTGCA
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
44 10 0.11
45 78 0.87
46 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (45 bp):
TGCATCGATGCACTCAGGAATAAATGAAACATCGAATGCATTTCA
Found at i:425003 original size:11 final size:11
Alignment explanation
Indices: 424983--425096 Score: 102
Period size: 11 Copynumber: 10.2 Consensus size: 11
424973 AATTTTGATT
*
424983 ATTATCAAATC
1 ATTATTAAATC
*
424994 ATTACTAAATC
1 ATTATTAAATC
*
425005 ATTGTTAAATC
1 ATTATTAAATC
* *
425016 ATTATTATCATT
1 ATTATTA-AATC
*
425028 ATTATCAAATC
1 ATTATTAAATC
*
425039 ATTACTAAATC
1 ATTATTAAATC
*
425050 ATTGTTAAATC
1 ATTATTAAATC
* *
425061 ATTATTATCATT
1 ATTATTA-AATC
*
425073 ATTATCAAATC
1 ATTATTAAATC
*
425084 ATTACTAAATC
1 ATTATTAAATC
425095 AT
1 AT
425097 CAAATCATTA
Statistics
Matches: 79, Mismatches: 22, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
11 63 0.80
12 16 0.20
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (11 bp):
ATTATTAAATC
Found at i:425027 original size:9 final size:9
Alignment explanation
Indices: 425013--425079 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
425003 TCATTGTTAA
425013 ATCATTATT
1 ATCATTATT
425022 ATCATTATT
1 ATCATTATT
425031 ATCA--A--
1 ATCATTATT
*
425036 ATCATTACTAA
1 ATCATTA-T-T
*
425047 ATCATTGTT
1 ATCATTATT
425056 AAATCATTATT
1 --ATCATTATT
425067 ATCATTATT
1 ATCATTATT
425076 ATCA
1 ATCA
425080 AATCATTACT
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
5 4 0.09
7 2 0.04
9 26 0.55
10 1 0.02
11 14 0.30
ACGTcount: A:0.39, C:0.13, G:0.01, T:0.46
Consensus pattern (9 bp):
ATCATTATT
Found at i:425041 original size:14 final size:14
Alignment explanation
Indices: 425022--425136 Score: 54
Period size: 14 Copynumber: 8.5 Consensus size: 14
425012 AATCATTATT
425022 ATCATTATTATCAA
1 ATCATTATTATCAA
*
425036 ATCATTA--CT-AA
1 ATCATTATTATCAA
*
425047 ATCATT-GT-T-AA
1 ATCATTATTATCAA
425058 ATCATTATTATC--
1 ATCATTATTATCAA
425070 ---ATTATTATCAA
1 ATCATTATTATCAA
425081 ATCATTACTAAATCATCAA
1 ATCATTA-T---T-ATCAA
* *
425100 ATCATTAAATATTAAA
1 ATCATT-ATTA-TCAA
425116 ATCATTATTATCAA
1 ATCATTATTATCAA
425130 ATCATTA
1 ATCATTA
425137 CTAAATCATA
Statistics
Matches: 78, Mismatches: 6, Indels: 34
0.66 0.05 0.29
Matches are distributed among these distances:
9 9 0.12
11 17 0.22
12 2 0.03
13 1 0.01
14 21 0.27
15 5 0.06
16 10 0.13
18 1 0.01
19 11 0.14
20 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.41
Consensus pattern (14 bp):
ATCATTATTATCAA
Found at i:425044 original size:45 final size:45
Alignment explanation
Indices: 424980--425145 Score: 253
Period size: 45 Copynumber: 3.6 Consensus size: 45
424970 GGGAATTTTG
424980 ATTATTATCAAATCATTACTAAATCATTGTTAAATCATTATTATC
1 ATTATTATCAAATCATTACTAAATCATTGTTAAATCATTATTATC
425025 ATTATTATCAAATCATTACTAAATCATTGTTAAATCATTATTATC
1 ATTATTATCAAATCATTACTAAATCATTGTTAAATCATTATTATC
* **
425070 ATTATTATCAAATCATTACTAAATCATCAAATCATTAAAT-ATTAAAATC
1 ATTATTATCAAATCATTACTAAATCAT----T-GTTAAATCATTATTATC
425119 ATTATTATCAAATCATTACTAAATCAT
1 ATTATTATCAAATCATTACTAAATCAT
425146 ATAATTATTA
Statistics
Matches: 113, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
45 72 0.64
49 35 0.31
50 6 0.05
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.42
Consensus pattern (45 bp):
ATTATTATCAAATCATTACTAAATCATTGTTAAATCATTATTATC
Found at i:425108 original size:16 final size:15
Alignment explanation
Indices: 425075--425136 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 15
425065 TTATCATTAT
425075 TATCAAATCATTACTAAA
1 TATCAAATCA-T--TAAA
425093 TCATCAAATCATTAAA
1 T-ATCAAATCATTAAA
* *
425109 TATTAAAATCATT-AT
1 TA-TCAAATCATTAAA
425124 TATCAAATCATTA
1 TATCAAATCATTA
425137 CTAAATCATA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.24
15 4 0.11
16 14 0.37
18 2 0.05
19 9 0.24
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (15 bp):
TATCAAATCATTAAA
Found at i:425400 original size:11 final size:12
Alignment explanation
Indices: 425386--425435 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 12
425376 ATTATTAATG
425386 ATTA-AATCATT
1 ATTACAATCATT
425397 ATTACAATTTCATT
1 ATTACAA--TCATT
425411 ATTACTAATCATT
1 ATTAC-AATCATT
*
425424 ATT-TAATCATT
1 ATTACAATCATT
425435 A
1 A
425436 ATATCAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 12 0.35
12 2 0.06
13 8 0.24
14 10 0.29
15 2 0.06
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTACAATCATT
Found at i:425505 original size:40 final size:38
Alignment explanation
Indices: 425451--425562 Score: 106
Period size: 40 Copynumber: 3.0 Consensus size: 38
425441 AAATTCTTAA
425451 ATATTAATAATAAATCATTATTAATAATCATTACTAAATG
1 ATATTAATAATAAATCATTA--AATAATCATTACTAAATG
* * * * *
425491 ATATTATTAGTAAATCATTAAATAATTATTACTAAGTC
1 ATATTAATAATAAATCATTAAATAATCATTACTAAATG
* *
425529 AT-TAAATACA-AAATCATT-AA-AATCATTATTAAAT
1 ATATTAATA-ATAAATCATTAAATAATCATTACTAAAT
425563 CATTAGTACA
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
35 11 0.18
36 2 0.03
37 12 0.20
38 17 0.28
40 18 0.30
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (38 bp):
ATATTAATAATAAATCATTAAATAATCATTACTAAATG
Found at i:425519 original size:22 final size:22
Alignment explanation
Indices: 425493--425536 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
425483 ACTAAATGAT
*
425493 ATTATTAGTAAATCATTAAATA
1 ATTATTACTAAATCATTAAATA
*
425515 ATTATTACTAAGTCATTAAATA
1 ATTATTACTAAATCATTAAATA
425537 CAAAATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (22 bp):
ATTATTACTAAATCATTAAATA
Found at i:428815 original size:19 final size:19
Alignment explanation
Indices: 428787--428849 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
428777 ATATAAATTA
*
428787 AACAAAATATTTTTTAAAC
1 AACAATATATTTTTTAAAC
428806 AACAATATATATTTTTAAAC
1 AACAATATAT-TTTTTAAAC
* *
428826 -AGAATAT-TTTTTAAAAC
1 AACAATATATTTTTTAAAC
*
428843 AAGAATA
1 AACAATA
428850 AATTAAACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
17 8 0.21
18 7 0.18
19 15 0.38
20 9 0.23
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.37
Consensus pattern (19 bp):
AACAATATATTTTTTAAAC
Found at i:428822 original size:20 final size:19
Alignment explanation
Indices: 428787--428826 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
428777 ATATAAATTA
428787 AACAAAATATTTTTTAAAC
1 AACAAAATATTTTTTAAAC
*
428806 AACAATATATATTTTTAAAC
1 AACAAAATAT-TTTTTAAAC
428826 A
1 A
428827 GAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (19 bp):
AACAAAATATTTTTTAAAC
Found at i:428826 original size:17 final size:15
Alignment explanation
Indices: 428784--428840 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 15
428774 CTAATATAAA
428784 TTAAACAAAATATTTT
1 TTAAAC-AAATATTTT
428800 TTAAACAACAATATATATTT
1 TT--A-AACAA-ATAT-TTT
428820 TTAAACAGAATATTTT
1 TTAAACA-AATATTTT
428836 TTAAA
1 TTAAA
428841 ACAAGAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
16 10 0.29
17 8 0.23
18 5 0.14
19 7 0.20
20 5 0.14
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (15 bp):
TTAAACAAATATTTT
Found at i:428842 original size:17 final size:17
Alignment explanation
Indices: 428786--428849 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
428776 AATATAAATT
*
428786 AAACAAAATATTTTTTAA
1 AAACAGAATATTTTTT-A
428804 ACAACA-ATATATATTTTT-
1 A-AACAGA-ATAT-TTTTTA
428822 AAACAGAATATTTTTTA
1 AAACAGAATATTTTTTA
428839 AAACAAGAATA
1 AAAC-AGAATA
428850 AATTAAACTA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
16 5 0.12
17 12 0.30
18 10 0.25
19 8 0.20
20 5 0.12
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (17 bp):
AAACAGAATATTTTTTA
Found at i:429753 original size:46 final size:53
Alignment explanation
Indices: 429678--429782 Score: 134
Period size: 51 Copynumber: 2.1 Consensus size: 53
429668 GTTTAATCAC
*
429678 ACTAAGAAACAACTAATTAAATAA-TTTTTTA-A-CATAT-A-ATATAACTTAA
1 ACTAAGAAAC-ACTAATTAAATAATTTTTTTATATAATATAATATATAACTTAA
*
429727 ACTAAGAAAC-C-AATTAACTAATTTTTTTATATAATATAATATATAACTTAA
1 ACTAAGAAACACTAATTAAATAATTTTTTTATATAATATAATATATAACTTAA
429778 ACTAA
1 ACTAA
429783 TAATTTAAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
46 9 0.18
47 8 0.16
48 1 0.02
49 14 0.29
50 1 0.02
51 16 0.33
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.36
Consensus pattern (53 bp):
ACTAAGAAACACTAATTAAATAATTTTTTTATATAATATAATATATAACTTAA
Found at i:429947 original size:20 final size:19
Alignment explanation
Indices: 429917--429956 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
429907 CTTTTCTGCC
*
429917 TTTCTTCTGCTTCCTTTCT
1 TTTCTTCTGCTTCCGTTCT
429936 TTTCTCTCTGCTTCCGTTCT
1 TTTCT-TCTGCTTCCGTTCT
429956 T
1 T
429957 GCTTTGTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.00, C:0.33, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTCTTCTGCTTCCGTTCT
Found at i:430236 original size:29 final size:30
Alignment explanation
Indices: 430204--430274 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 30
430194 CGCTGGGACT
* *
430204 GCATGGCAACCTCCGACCGTGCA-TGGGGG
1 GCATGGCGACCTCCGACCGTGCATTGGCGG
*
430233 GCATGGCGACCTCCGACCGTGCATTGGCGT
1 GCATGGCGACCTCCGACCGTGCATTGGCGG
430263 GCATGGCGACCT
1 GCATGGCGACCT
430275 TCAACAGTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 22 0.58
30 16 0.42
ACGTcount: A:0.15, C:0.32, G:0.35, T:0.17
Consensus pattern (30 bp):
GCATGGCGACCTCCGACCGTGCATTGGCGG
Found at i:431940 original size:63 final size:63
Alignment explanation
Indices: 431841--431962 Score: 235
Period size: 63 Copynumber: 1.9 Consensus size: 63
431831 ATCAACATCA
*
431841 AACGGGTGAGGGGAATTGCCCTGAGGCAGCTATCTTTGAGGAAAAAGAACTTGGTGTGCAGTC
1 AACGGGTGAGGGGAATTGCACTGAGGCAGCTATCTTTGAGGAAAAAGAACTTGGTGTGCAGTC
431904 AACGGGTGAGGGGAATTGCACTGAGGCAGCTATCTTTGAGGAAAAAGAACTTGGTGTGC
1 AACGGGTGAGGGGAATTGCACTGAGGCAGCTATCTTTGAGGAAAAAGAACTTGGTGTGC
431963 TGTGTGTAAC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.28, C:0.15, G:0.35, T:0.22
Consensus pattern (63 bp):
AACGGGTGAGGGGAATTGCACTGAGGCAGCTATCTTTGAGGAAAAAGAACTTGGTGTGCAGTC
Found at i:432452 original size:2 final size:2
Alignment explanation
Indices: 432439--432498 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
432429 CATATTCATC
* *
432439 TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA GA 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
432481 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
432499 ATCCACGCAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:432835 original size:28 final size:28
Alignment explanation
Indices: 432802--432858 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
432792 CCTAAATTAA
432802 TTTGATGTCATTGCTTACATCAATTAGT
1 TTTGATGTCATTGCTTACATCAATTAGT
432830 TTTGATGTCATTGCTTACATCAATTAGT
1 TTTGATGTCATTGCTTACATCAATTAGT
432858 T
1 T
432859 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (28 bp):
TTTGATGTCATTGCTTACATCAATTAGT
Found at i:436338 original size:29 final size:29
Alignment explanation
Indices: 436304--436362 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
436294 CCTAAATTAA
436304 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
436333 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
436362 T
1 T
436363 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:436717 original size:29 final size:30
Alignment explanation
Indices: 436675--436771 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
436665 CCCGAAGGAC
*
436675 CTATCCAGAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
* *
436704 CTATCCAGAGGTCATAAAGAACCTCGATAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
* * * *
436734 CTGTCCATAGGTCCCAAAGAACCTAGGTAAA
1 CTATCCAGAGGTCACAAAGAACCTCGGT-AA
436765 CTATCCA
1 CTATCCA
436772 TATGTTCTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 18 0.32
30 30 0.54
31 8 0.14
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.19
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGTAA
Found at i:436786 original size:31 final size:31
Alignment explanation
Indices: 436751--436859 Score: 114
Period size: 31 Copynumber: 3.5 Consensus size: 31
436741 TAGGTCCCAA
* * *
436751 AGAACCTAGGTAAACTATCCATATGTTCTTT
1 AGAACATAGGTAAACTGTCCATATGTTCTCT
* * *
436782 AGAACATAGGTATACTGTCCATATG-CCTCG
1 AGAACATAGGTAAACTGTCCATATGTTCTCT
*
436812 AAAGACATAGGTAAAACTGTCCATATGTTC-CGT
1 AGA-ACATAGGT-AAACTGTCCATATGTTCTC-T
436845 AGAACATAGGTAAAC
1 AGAACATAGGTAAAC
436860 CCTCGACTCT
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
30 4 0.06
31 34 0.54
32 22 0.35
33 3 0.05
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (31 bp):
AGAACATAGGTAAACTGTCCATATGTTCTCT
Found at i:437668 original size:16 final size:16
Alignment explanation
Indices: 437647--437677 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
437637 TATTTTAGGG
437647 TATGCATCGATGCACT
1 TATGCATCGATGCACT
437663 TATGCATCGATGCAC
1 TATGCATCGATGCAC
437678 CAATCGCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (16 bp):
TATGCATCGATGCACT
Found at i:437688 original size:60 final size:61
Alignment explanation
Indices: 437581--437741 Score: 184
Period size: 60 Copynumber: 2.6 Consensus size: 61
437571 GCATCCCTAG
* * **
437581 ATGGGTGCATCGATGCACTATCTATGCATCGATGCATAAATCTCATTCGATGTTTGTATTTT-
1 ATGGGTGCATCGATGCAC--TCTATGCATCGATGCACAAATCGCATTCGATGTTTCCATTTTA
*
437643 A-GGGTATGCATCGATGCACT-TATGCATCGATGCACCAATCGCATTCGATGTTTCCATTTTA
1 ATGGG--TGCATCGATGCACTCTATGCATCGATGCACAAATCGCATTCGATGTTTCCATTTTA
* *
437704 ATGGGTGCATCGATGCACTCCCTGTGCATCGATACACA
1 ATGGGTGCATCGATGCACT--CTATGCATCGATGCACA
437742 CTGAACAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
60 49 0.58
61 5 0.06
62 4 0.05
63 26 0.31
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (61 bp):
ATGGGTGCATCGATGCACTCTATGCATCGATGCACAAATCGCATTCGATGTTTCCATTTTA
Found at i:439812 original size:19 final size:20
Alignment explanation
Indices: 439783--439820 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
439773 AGAAATTTGT
439783 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
439803 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
439821 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:439873 original size:63 final size:63
Alignment explanation
Indices: 439788--439946 Score: 212
Period size: 63 Copynumber: 2.5 Consensus size: 63
439778 TTTGTTGAAG
* * * * *
439788 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATAAGGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCA
** **
439851 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCATAAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
*
439914 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCATAAGGAGTGCATCGATGCAT
439947 GCCTCCATTA
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
63 81 0.95
64 4 0.05
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCATAAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:441278 original size:21 final size:17
Alignment explanation
Indices: 441234--441269 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
441224 CTTAAGGAAT
441234 GATATGTGGTCCTTCGG
1 GATATGTGGTCCTTCGG
441251 GATATGTGGTCCTTCGG
1 GATATGTGGTCCTTCGG
441268 GA
1 GA
441270 CATATATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.14, C:0.17, G:0.36, T:0.33
Consensus pattern (17 bp):
GATATGTGGTCCTTCGG
Found at i:441350 original size:119 final size:120
Alignment explanation
Indices: 441136--441484 Score: 604
Period size: 118 Copynumber: 3.0 Consensus size: 120
441126 AGTCGAGGTC
441136 TATGTGGTCCTTC-GGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGT--GACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
441198 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGA
441253 TATGTGGTCCTTCGGGACATATATGTA-TCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
441317 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGA
* * *
441372 CAT-TGGGTCCTTTGGGAC--ATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATA
1 TATGT-GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
*
441434 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTT
65 CTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTT
441485 ATGGACATTA
Statistics
Matches: 223, Mismatches: 4, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
117 46 0.21
118 99 0.44
119 78 0.35
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (120 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGA
Found at i:441568 original size:23 final size:23
Alignment explanation
Indices: 441500--441560 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
441490 CATTATTATA
*
441500 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
441523 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
441546 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
441561 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:446906 original size:203 final size:201
Alignment explanation
Indices: 446541--446945 Score: 776
Period size: 203 Copynumber: 2.0 Consensus size: 201
446531 TAACTGATAC
446541 TTCGACATATGATTGCTGTGAATGCTTGTTATTTTGCAAGTTGTGAAAACAAAAAAAAGTGAATT
1 TTCGACATATGATTGCTGTGAATGCTTGTTATTTTGCAAGTTGTGAAAACAAAAAAAAGTGAATT
446606 TGTTCTTGTATCTTTCAGTGTGATGACTGGTTTGCTTAACCTTGTGACCCTAACTTTCTACTTCG
66 TGTTCTTGTATCTTTCAGTGTGATGACTGGTTTGCTTAACCTTGTGACCCTAACTTTCTACTTCG
446671 ACACGGCAATTACTGCCGGAGTTCGAACGAATTTCGGTATCTATTTTCTGTTTTACTTTCATGGA
131 ACACGGCAATTACTGCCGGAGTTCGAACGAATTTCGGTATCTATTTTCTGTTTTACTTTCATGGA
446736 TGACAA
196 TGACAA
446742 TTCGACATATGATTGCTGTGAATGCTTGTTTATTTTGCAAGTTGTGAAAACAAAAAAAAGTGAAT
1 TTCGACATATGATTGCTGTGAATGCTTG-TTATTTTGCAAGTTGTGAAAACAAAAAAAAGTGAAT
446807 TTGTTCTTGTATCTTTTCAGTGTGATGACTGGTTTGCTTAACCTTGTGACCCTAACATTTCTACT
65 TTGTTCTTGTATC-TTTCAGTGTGATGACTGGTTTGCTTAACCTTGTGACCCTAAC-TTTCTACT
446872 TCGACACGGCAATTACTGCCGGAGTTCG-ACGAATTTCGGTATCTATTTTCTGTTTTACTTTCAT
128 TCGACACGGCAATTACTGCCGGAGTTCGAACGAATTTCGGTATCTATTTTCTGTTTTACTTTCAT
446936 GGATGACAA
193 GGATGACAA
446945 T
1 T
446946 CTCTTTTCTA
Statistics
Matches: 201, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
201 28 0.14
202 49 0.24
203 88 0.44
204 36 0.18
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (201 bp):
TTCGACATATGATTGCTGTGAATGCTTGTTATTTTGCAAGTTGTGAAAACAAAAAAAAGTGAATT
TGTTCTTGTATCTTTCAGTGTGATGACTGGTTTGCTTAACCTTGTGACCCTAACTTTCTACTTCG
ACACGGCAATTACTGCCGGAGTTCGAACGAATTTCGGTATCTATTTTCTGTTTTACTTTCATGGA
TGACAA
Found at i:451436 original size:29 final size:30
Alignment explanation
Indices: 451375--451447 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 30
451365 GAAAATCAAA
* *
451375 TTAAATGGAGACGGGAAAAAATTGTTTAAG
1 TTAAATGGGGACGGGAAAAAATCGTTTAAG
* *
451405 TTAAACGGGGACGGG-AAAAATCGTTTATG
1 TTAAATGGGGACGGGAAAAAATCGTTTAAG
451434 TTAAATGGGGACGG
1 TTAAATGGGGACGG
451448 AGACGGGGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
29 25 0.66
30 13 0.34
ACGTcount: A:0.37, C:0.07, G:0.32, T:0.25
Consensus pattern (30 bp):
TTAAATGGGGACGGGAAAAAATCGTTTAAG
Found at i:451569 original size:38 final size:38
Alignment explanation
Indices: 451525--451709 Score: 153
Period size: 38 Copynumber: 4.9 Consensus size: 38
451515 TTTATTATAT
451525 ATATATATATAATATTAATAAATTTAATTTAAATTAAC
1 ATATATATATAATATTAATAAATTTAATTTAAATTAAC
* *
451563 ATATATATATAATATTTATATATTTAATTTAAA-TAACC
1 ATATATATATAATATTAATAAATTTAATTTAAATTAA-C
** ** ****** ** **
451601 CGAT-TACCT-GGCCCGATAAATATTAA-AAATAATTATT
1 ATATATATATAATATTAATAAAT-TTAATTTA-AATTAAC
451638 ATATATATATAATATTAATAAATTTAATTTAAATTAAC
1 ATATATATATAATATTAATAAATTTAATTTAAATTAAC
* *
451676 ATATATATATAATATTTATATATTTAATTTAAAT
1 ATATATATATAATATTAATAAATTTAATTTAAAT
451710 ATATATACCC
Statistics
Matches: 107, Mismatches: 33, Indels: 14
0.69 0.21 0.09
Matches are distributed among these distances:
36 6 0.06
37 14 0.13
38 80 0.75
39 7 0.07
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (38 bp):
ATATATATATAATATTAATAAATTTAATTTAAATTAAC
Found at i:451683 original size:113 final size:117
Alignment explanation
Indices: 451483--451710 Score: 410
Period size: 113 Copynumber: 2.0 Consensus size: 117
451473 AATCTCTGTT
*
451483 CCGATTACCCGGCCCGATAAATATTAAAATAATTTATTATATATATATATATAATATTAATAAAT
1 CCGATTACCCGGCCCGATAAATATTAAAATAATTAATTATATATATATATATAATATTAATAAAT
451548 TTAATTTAAATTAACATATATATATAATATTTATATATTTAATTTAAATAAC
66 TTAATTTAAATTAACATATATATATAATATTTATATATTTAATTTAAATAAC
*
451600 CCGATTACCTGGCCCGATAAATATT-AAA-AA-TAATTAT-TATATATATATAATATTAATAAAT
1 CCGATTACCCGGCCCGATAAATATTAAAATAATTAATTATATATATATATATAATATTAATAAAT
451661 TTAATTTAAATTAACATATATATATAATATTTATATATTTAATTTAAATA
66 TTAATTTAAATTAACATATATATATAATATTTATATATTTAATTTAAATA
451711 TATATACCCG
Statistics
Matches: 109, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
113 74 0.68
114 6 0.06
115 2 0.02
116 3 0.03
117 24 0.22
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (117 bp):
CCGATTACCCGGCCCGATAAATATTAAAATAATTAATTATATATATATATATAATATTAATAAAT
TTAATTTAAATTAACATATATATATAATATTTATATATTTAATTTAAATAAC
Found at i:451954 original size:2 final size:2
Alignment explanation
Indices: 451947--451974 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
451937 TGACGGTTTA
451947 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
451975 TTGTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:453846 original size:25 final size:25
Alignment explanation
Indices: 453818--453881 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
453808 AATATTTTAT
453818 ATATAATTA-ATATAAAAAATATAAA
1 ATAT-ATTATATATAAAAAATATAAA
**
453843 ATAT-TATATATATAATTAATATAAA
1 ATATAT-TATATATAAAAAATATAAA
*
453868 AAATATTATATATA
1 ATATATTATATATA
453882 TATATATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 1 0.03
24 2 0.06
25 29 0.88
26 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATATATTATATATAAAAAATATAAA
Found at i:453846 original size:34 final size:34
Alignment explanation
Indices: 453806--453891 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 34
453796 CCCGAATCCG
*
453806 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
453840 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
* *
453874 TATATATATATATATATA
1 AAAATAT-TATATATATA
453892 TATATATATC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 38 0.79
35 10 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:453852 original size:2 final size:2
Alignment explanation
Indices: 453843--453900 Score: 56
Period size: 2 Copynumber: 32.0 Consensus size: 2
453833 AAAATATAAA
* *
453843 AT AT -T AT AT AT AT A- AT -T A- AT AT A- AA AA AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
453879 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
453901 CGAGGCGGGA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
1 6 0.12
2 43 0.88
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:455645 original size:21 final size:21
Alignment explanation
Indices: 455611--455652 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
455601 ATGTAATCAA
*
455611 AATTTATATTCTTTTGTTATGT
1 AATTTATACTC-TTTGTTATGT
455633 AATTT-TACTCTTTGTTATGT
1 AATTTATACTCTTTGTTATGT
455653 GGTTTAGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 4 0.21
22 5 0.26
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (21 bp):
AATTTATACTCTTTGTTATGT
Found at i:457507 original size:14 final size:14
Alignment explanation
Indices: 457488--457516 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
457478 TGAATCTATA
457488 AAAAAAATTAAATT
1 AAAAAAATTAAATT
457502 AAAAAAATTAAATT
1 AAAAAAATTAAATT
457516 A
1 A
457517 TATATTGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAAAATTAAATT
Found at i:457622 original size:14 final size:15
Alignment explanation
Indices: 457603--457633 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
457593 TAAAAATCTA
457603 TAAAAAAA-TTAAAT
1 TAAAAAAATTTAAAT
457617 TAAAAAAATTTAAAT
1 TAAAAAAATTTAAAT
457632 TA
1 TA
457634 TATTGAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAAAAATTTAAAT
Found at i:457624 original size:15 final size:15
Alignment explanation
Indices: 457604--457633 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
457594 AAAAATCTAT
457604 AAAAAAATTAAATTA
1 AAAAAAATTAAATTA
*
457619 AAAAAATTTAAATTA
1 AAAAAAATTAAATTA
457634 TATTGAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAAAATTAAATTA
Found at i:457650 original size:115 final size:120
Alignment explanation
Indices: 457480--457716 Score: 423
Period size: 117 Copynumber: 2.0 Consensus size: 120
457470 TGAATGTTTG
457480 AATCTATAAAAAAAATTAAATTAAAAAAATTAAATTATATATTGAACATCACAATTTGC-AAAAA
1 AATCTATAAAAAAAATTAAATTAAAAAAATTAAATTATATATTGAACATCACAATTTGCAAAAAA
457544 ACCAAATCCG-TTGAAATTTTAGATATCTAAAATTTGAGTGCCCTAAG-AATAAA
66 ACCAAATCCGTTTGAAATTTTAGATATCTAAAATTTGAGTGCCCTAAGAAATAAA
457597 AATCTAT-AAAAAAATTAAATTAAAAAAATTTAAA-T-TATATTGAACATCACAATTTGCAAAAA
1 AATCTATAAAAAAAATTAAATTAAAAAAA-TTAAATTATATATTGAACATCACAATTTGCAAAAA
457659 AACCAAATCCGTTTGAAATTTTAGATATCTAAAATTTGAGTGCCCTAAGAAATAAA
65 AACCAAATCCGTTTGAAATTTTAGATATCTAAAATTTGAGTGCCCTAAGAAATAAA
457715 AA
1 AA
457717 AAAACATTTC
Statistics
Matches: 116, Mismatches: 0, Indels: 7
0.94 0.00 0.06
Matches are distributed among these distances:
115 22 0.19
116 37 0.32
117 49 0.42
118 8 0.07
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (120 bp):
AATCTATAAAAAAAATTAAATTAAAAAAATTAAATTATATATTGAACATCACAATTTGCAAAAAA
ACCAAATCCGTTTGAAATTTTAGATATCTAAAATTTGAGTGCCCTAAGAAATAAA
Found at i:458615 original size:11 final size:11
Alignment explanation
Indices: 458594--458650 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
458584 ATAATTATAT
*
458594 TTTAAAAAATA
1 TTTATAAAATA
*
458605 TTTTTAAAATA
1 TTTATAAAATA
*
458616 TATATAAAATA
1 TTTATAAAATA
* *
458627 TATAAAAAATA
1 TTTATAAAATA
*
458638 TTTTTAAAATA
1 TTTATAAAATA
458649 TT
1 TT
458651 GTGTCATTAG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 38 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TTTATAAAATA
Found at i:462480 original size:87 final size:87
Alignment explanation
Indices: 462332--462506 Score: 278
Period size: 87 Copynumber: 2.0 Consensus size: 87
462322 TTTCTCATTC
* *
462332 TACAATCGTTTAAATTAATTAGAGTGAATCTTAAAGAAGCATAACTTTAGATAATTGCTTACAAC
1 TACAATCGTTTAAATTAATTAGAGTCAATCTTAAAGAAGCATAACTTTAAATAATTGCTTACAAC
*
462397 ATTTATTTAATGTTAAGAGATT
66 ATTTATTTAATGTTAAAAGATT
* * * * *
462419 TACAATCTTTTAAATTAATTAGAGTCAATCTTTAGGAAGCATAACTTTAAATAATTTCTTACAAT
1 TACAATCGTTTAAATTAATTAGAGTCAATCTTAAAGAAGCATAACTTTAAATAATTGCTTACAAC
462484 ATTTATTTAATGTTAAAAGATT
66 ATTTATTTAATGTTAAAAGATT
462506 T
1 T
462507 TGTATTTGTC
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (87 bp):
TACAATCGTTTAAATTAATTAGAGTCAATCTTAAAGAAGCATAACTTTAAATAATTGCTTACAAC
ATTTATTTAATGTTAAAAGATT
Found at i:464280 original size:16 final size:17
Alignment explanation
Indices: 464253--464287 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
464243 TAATTAAGTA
464253 AAAAATACATTTATTTT
1 AAAAATACATTTATTTT
464270 AAAAATA-ATTTATTTT
1 AAAAATACATTTATTTT
464286 AA
1 AA
464288 GGATTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
AAAAATACATTTATTTT
Found at i:467047 original size:19 final size:20
Alignment explanation
Indices: 467020--467069 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
467010 GCTCACTAAC
*
467020 TATTAATTATTA-ATAAAAA
1 TATTTATTATTAGATAAAAA
*
467039 TATTTATTATTAGATAAATA
1 TATTTATTATTAGATAAAAA
467059 TATTTAATTAT
1 TATTT-ATTAT
467070 CACATCAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 11 0.41
20 11 0.41
21 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TATTTATTATTAGATAAAAA
Found at i:467079 original size:21 final size:20
Alignment explanation
Indices: 467032--467083 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
467022 TTAATTATTA
* * *
467032 ATAAAAATATTTATTATTAG
1 ATAAATATATTTATTATCAC
467052 ATAAATATATTTAATTATCAC
1 ATAAATATATTT-ATTATCAC
*
467073 ATCAATA-ATTT
1 ATAAATATATTT
467084 TTAACAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (20 bp):
ATAAATATATTTATTATCAC
Found at i:469168 original size:36 final size:38
Alignment explanation
Indices: 469117--469194 Score: 99
Period size: 36 Copynumber: 2.1 Consensus size: 38
469107 TTTTACTAAA
* *
469117 TATTATTTATCTATATTTA-TCTGTTTGATTTATTTTAT
1 TATTATTTATCTATATTAATTCTGTTTCATTT-TTTTAT
*
469155 TATTA-TTAT-TATATTAATTCTTTTTCATTTTTTTAT
1 TATTATTTATCTATATTAATTCTGTTTCATTTTTTTAT
469191 TATT
1 TATT
469195 TTCCCCTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 17 0.47
37 14 0.39
38 5 0.14
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (38 bp):
TATTATTTATCTATATTAATTCTGTTTCATTTTTTTAT
Found at i:473467 original size:95 final size:95
Alignment explanation
Indices: 473303--473484 Score: 287
Period size: 95 Copynumber: 1.9 Consensus size: 95
473293 ATCTTATTTA
* * *
473303 TATACAATACAACTTGAGTTGTCACTCTAAAGTAATTGGTTAAACGCCCCGACTTTATGGATAAT
1 TATACAATACAACTTGAGTTGTCACTCTAAAGCAATTGGTTAAACACCCCGACTTTATGGATAAG
*
473368 ATTCAGCTAGCCTGATAAAGGTGACTATAC
66 ATTCAGCTAACCTGATAAAGGTGACTATAC
*
473398 TATACAATA-AAGCTTGAGTTGTTC-CTCTAAGGCAATTGGTTAAACACCCCGACTTTATGGATA
1 TATACAATACAA-CTTGAGTTG-TCACTCTAAAGCAATTGGTTAAACACCCCGACTTTATGGATA
473461 AGATTCAGCTAACCTGATAAAGGT
64 AGATTCAGCTAACCTGATAAAGGT
473485 ATTTACATAT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
94 2 0.03
95 76 0.95
96 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (95 bp):
TATACAATACAACTTGAGTTGTCACTCTAAAGCAATTGGTTAAACACCCCGACTTTATGGATAAG
ATTCAGCTAACCTGATAAAGGTGACTATAC
Done.