Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004540.1 Hibiscus syriacus cultivar Beakdansim tig00010050_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: 429677
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:216485 original size:28 final size:29
Alignment explanation
Indices: 216423--216490 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 29
216413 ATAAGATAGA
* *
216423 AATTAAAAATCAATTTAATATTTTTATATT
1 AATT-AAAATAAATTTAATATTATTATATT
* *
216453 -TTTAAAATAAATTTTATATTATTA-ATT
1 AATTAAAATAAATTTAATATTATTATATT
216480 AATTAATAATA
1 AATTAA-AATA
216491 TTTATTTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
27 3 0.10
28 22 0.71
29 6 0.19
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (29 bp):
AATTAAAATAAATTTAATATTATTATATT
Found at i:216524 original size:2 final size:2
Alignment explanation
Indices: 216517--216561 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
216507 AGTGTAAGTT
216517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
216559 TA T
1 TA T
216562 TGTAATAGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:216823 original size:24 final size:24
Alignment explanation
Indices: 216791--216853 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
216781 CATTTAAATG
*
216791 ATAAACGAACACAAATGAACGAAC
1 ATAAACGAACACAAATAAACGAAC
* **
216815 ATAAACGAACAGATGTAAACGAAC
1 ATAAACGAACACAAATAAACGAAC
* *
216839 GTACACGAACACAAA
1 ATAAACGAACACAAA
216854 CGAGTGAATG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.56, C:0.21, G:0.14, T:0.10
Consensus pattern (24 bp):
ATAAACGAACACAAATAAACGAAC
Found at i:218826 original size:13 final size:13
Alignment explanation
Indices: 218804--218838 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
218794 GAGTTTTTAA
218804 AAAAATAAAAAGGC
1 AAAAA-AAAAAGGC
218818 -AAAAAAAAAGGC
1 AAAAAAAAAAGGC
218830 AAAAAAAAA
1 AAAAAAAAA
218839 GAAGAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAAGGC
Found at i:218833 original size:11 final size:12
Alignment explanation
Indices: 218805--218839 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
218795 AGTTTTTAAA
218805 AAAATAAAAAGGC
1 AAAA-AAAAAGGC
218818 AAAAAAAAAGGC
1 AAAAAAAAAGGC
218830 AAAAAAAAAG
1 AAAAAAAAAG
218840 AAGAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.77, C:0.06, G:0.14, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAGGC
Found at i:219719 original size:3 final size:3
Alignment explanation
Indices: 219711--219758 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
219701 CCCGACCTTC
219711 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
219759 TACATCTACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:223317 original size:22 final size:26
Alignment explanation
Indices: 223290--223336 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
223280 TTTCATCCTA
223290 TTTTTTA-A-AATTTTAT-TATTCAT
1 TTTTTTACATAATTTTATATATTCAT
223313 TTTTTTACATAATTTTATATATTC
1 TTTTTTACATAATTTTATATATTC
223337 CTTTACATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 1 0.05
25 8 0.38
26 5 0.24
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTTTTACATAATTTTATATATTCAT
Found at i:225207 original size:17 final size:16
Alignment explanation
Indices: 225181--225212 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
225171 TTAATTGAAA
225181 AATTGATATTAATCTG
1 AATTGATATTAATCTG
225197 AATTAGATATTAATCT
1 AATT-GATATTAATCT
225213 ACTTTATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (16 bp):
AATTGATATTAATCTG
Found at i:226167 original size:17 final size:17
Alignment explanation
Indices: 226145--226177 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
226135 AATTATCAAA
226145 AAAAT-CTATAATCTCTT
1 AAAATCCTA-AATCTCTT
226162 AAAATCCTAAATCTCT
1 AAAATCCTAAATCTCT
226178 AACTCGCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATCCTAAATCTCTT
Found at i:228206 original size:24 final size:22
Alignment explanation
Indices: 228162--228208 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
228152 AGTAATATCT
**
228162 TAATAATAAAATGATTGGAATC
1 TAATAATAAAATGATAAGAATC
228184 TAATAATAAAGATTGATAAGAATC
1 TAATAATAAA-A-TGATAAGAATC
228208 T
1 T
228209 TAATTACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 1 0.05
24 10 0.48
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.32
Consensus pattern (22 bp):
TAATAATAAAATGATAAGAATC
Found at i:229744 original size:21 final size:21
Alignment explanation
Indices: 229720--229774 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
229710 TCGTTAGAAC
* *
229720 TCTACCTAAAATGTTATTTTT
1 TCTATCTAAAATGTTAATTTT
**
229741 TCTATCGGAAATGTTAATTTT
1 TCTATCTAAAATGTTAATTTT
*
229762 GCTATCTAAAATG
1 TCTATCTAAAATG
229775 AATATTTCTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (21 bp):
TCTATCTAAAATGTTAATTTT
Found at i:231246 original size:2 final size:2
Alignment explanation
Indices: 231239--231264 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
231229 CTTGCTGGCA
231239 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
231265 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:233105 original size:20 final size:20
Alignment explanation
Indices: 233080--233127 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
233070 TAATTCGGTT
*
233080 AATTAACTAATTTCAAACCA
1 AATTAACCAATTTCAAACCA
*
233100 AATTAACCGATTTCAAACCA
1 AATTAACCAATTTCAAACCA
233120 AATTAACC
1 AATTAACC
233128 GTTAACCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (20 bp):
AATTAACCAATTTCAAACCA
Found at i:233128 original size:20 final size:20
Alignment explanation
Indices: 233089--233128 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
233079 TAATTAACTA
233089 ATTTCAAACCAAATTAACCG
1 ATTTCAAACCAAATTAACCG
233109 ATTTCAAACCAAATTAACCG
1 ATTTCAAACCAAATTAACCG
233129 TTAACCGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (20 bp):
ATTTCAAACCAAATTAACCG
Found at i:234164 original size:13 final size:13
Alignment explanation
Indices: 234132--234169 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
234122 AAATTATAAC
*
234132 TAATAATATT-AA
1 TAATTATATTAAA
*
234144 TTATTATATTAAA
1 TAATTATATTAAA
234157 TAATTATATTAAA
1 TAATTATATTAAA
234170 AATATTTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATTATATTAAA
Found at i:234267 original size:23 final size:24
Alignment explanation
Indices: 234223--234269 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
234213 ATACATTGAC
*
234223 AAATTATATAAATACAATAACATT
1 AAATTATATAAATACAAAAACATT
234247 AAATTAT-TAGAA-ACAAAAACATT
1 AAATTATATA-AATACAAAAACATT
234270 CATTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (24 bp):
AAATTATATAAATACAAAAACATT
Found at i:237155 original size:8 final size:8
Alignment explanation
Indices: 237142--237182 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
237132 CTCATTTTCA
237142 GAGAATTT
1 GAGAATTT
237150 GAGAATTT
1 GAGAATTT
*
237158 -AGAGTTT
1 GAGAATTT
*
237165 GGGAATTT
1 GAGAATTT
237173 GAGAATTT
1 GAGAATTT
237181 GA
1 GA
237183 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:237538 original size:128 final size:128
Alignment explanation
Indices: 237303--238115 Score: 1356
Period size: 128 Copynumber: 6.3 Consensus size: 128
237293 ATTATTTTGT
* *
237303 TTATCATTGCCCTATTATGTCACTCATGTCCCTCAGGGACACTATTTATATCAGTACCTATTATT
1 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATT
* * * *
237368 TCTCAAGGGACTTGAAGGCGCGTTGCCGGGGGCACGCATTCCATTATTTTGTCAGAGAATATG
66 TCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
* * *
237431 TTATCATTGCCTTATTATGTCACTTATGTCTCTCGGGGACACTATTCATATCAGTACCTATTATT
1 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATT
* * * *
237496 TCTCAGGGTACTTGAAGACGCGTTCCCGGGGGCGCGTCTTCCATTATTTTATCAGAGAATATG
66 TCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
*
237559 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATTAGTACCTATTATT
1 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATT
* * * *
237624 TCTCAAGGGACTTGAAGGCTCGTTCTCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATG
66 TCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
* * *
237687 TTATCATTGCTCTATTATGCCACTCATGTCCCTCGTGGACACTATTCATATCAGTACCTATTATT
1 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATT
*
237752 TCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATG
66 TCTCAGGGGACTTGAAGGCGCGTTCCC-GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
* *
237816 TTATCATCGCCCTATTATGTCACTCATGTCCCTCAGGGACACTATTCATATCAGTACCTATTATT
1 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATT
*
237881 TCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATG
66 TCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
*
237944 TTATCATTGCCCTATTATGTCACTCATATCCCTCGGGGACACTATTCATATCAGTACCTATTATT
1 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATT
** *
238009 TCTCAGGGGACTTGAAAACGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
66 TCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
238072 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTA
1 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTA
238116 GATAAATTGA
Statistics
Matches: 637, Mismatches: 47, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
128 514 0.81
129 123 0.19
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (128 bp):
TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATT
TCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
Found at i:238012 original size:385 final size:383
Alignment explanation
Indices: 237303--238115 Score: 1347
Period size: 385 Copynumber: 2.1 Consensus size: 383
237293 ATTATTTTGT
*
237303 TTATCATTGCCCTATTATGTCACTCATGTCCCTCAGGGACACTATTTATATCAGTACCTATTATT
1 TTATCATTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTATTCATATCAGTACCTATTATT
*
237368 TCTCAAGGGACTTGAAGGCGCGTTGCCGGGGGCACGCATTCCATTATTTTGTCAGAGAATATGTT
65 TCTCAAGGGACTTGAAGGCGCGTTCCCGGGGGCACGCATTCCATTATTTTGTCAGAGAATATGTT
* * * * *
237433 ATCATTGCCTTATTATGTCACTTATGTCTCTCGGGGACACTATTCATATCAGTACCTATTATTTC
130 ATCATCGCCCTATTATGTCACTCATGTCCCTCAGGGACACTATTCATATCAGTACCTATTATTTC
* *
237498 TCAGGGTACTTGAAGACGCGTTCCCGGGGGCGCGTCTTCCATTATTTTATCAGAGAATATGTTAT
195 TCAGGGGACTTGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTAT
* *
237563 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATTAGTACCTATTATTTCTC
260 CATTGCCCTATTATGTCACTCATATCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTC
** * * * *
237628 AAGGGACTTGAAGGCTCGTTCTCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATG
325 AAGGGACTTGAAAACGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
* *
237687 TTATCATTGCTCTATTATGCCACTCATGTCCCTCGTGGACACTATTCATATCAGTACCTATTATT
1 TTATCATTGCCCTATTATGTCACTCATGTCCCTCG-GGACACTATTCATATCAGTACCTATTATT
* ** *
237752 TCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGT
65 TCTCAAGGGACTTGAAGGCGCGTTCCC-GGGGGCACGCATTCCATTATTTTGTCAGAGAATATGT
237817 TATCATCGCCCTATTATGTCACTCATGTCCCTCAGGGACACTATTCATATCAGTACCTATTATTT
129 TATCATCGCCCTATTATGTCACTCATGTCCCTCAGGGACACTATTCATATCAGTACCTATTATTT
* * *
237882 CTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTA
194 CTCAGGGGACTTGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTA
237947 TCATTGCCCTATTATGTCACTCATATCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCT
259 TCATTGCCCTATTATGTCACTCATATCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCT
*
238012 CAGGGGACTTGAAAACGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
324 CAAGGGACTTGAAAACGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
238072 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTA
1 TTATCATTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTA
238116 GATAAATTGA
Statistics
Matches: 397, Mismatches: 29, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
383 1 0.00
384 85 0.21
385 310 0.78
386 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (383 bp):
TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTATTCATATCAGTACCTATTATTT
CTCAAGGGACTTGAAGGCGCGTTCCCGGGGGCACGCATTCCATTATTTTGTCAGAGAATATGTTA
TCATCGCCCTATTATGTCACTCATGTCCCTCAGGGACACTATTCATATCAGTACCTATTATTTCT
CAGGGGACTTGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATC
ATTGCCCTATTATGTCACTCATATCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCA
AGGGACTTGAAAACGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
Found at i:238511 original size:34 final size:34
Alignment explanation
Indices: 238406--238513 Score: 153
Period size: 34 Copynumber: 3.1 Consensus size: 34
238396 TAAGTTGAAA
*
238406 TTTAATGTTAAATTTCGAATACTATAATTTATATT
1 TTTAAT-TTAAATTTCGAATAATATAATTTATATT
* * *
238441 TTAAATTTAAATTTCGAATAATATTATTTTTATT
1 TTTAATTTAAATTTCGAATAATATAATTTATATT
* *
238475 TTTATTTTAAATTTCGAATAATATAATTTGTATT
1 TTTAATTTAAATTTCGAATAATATAATTTATATT
238509 TTTAA
1 TTTAA
238514 AACATTTATC
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
34 59 0.92
35 5 0.08
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.55
Consensus pattern (34 bp):
TTTAATTTAAATTTCGAATAATATAATTTATATT
Found at i:239083 original size:21 final size:21
Alignment explanation
Indices: 239033--239104 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
239023 TATGGTATAA
*
239033 AACCCTGCGGGCTAGGCATG-
1 AACCCTGCGGGCTAGGAATGT
*
239053 AA-CCTGGCGGGCTAGAAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
239074 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
239095 AACCCTGCGG
1 AACCCTGCGG
239105 AGATGGCATA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
19 3 0.07
20 14 0.31
21 25 0.56
22 3 0.07
ACGTcount: A:0.22, C:0.28, G:0.33, T:0.17
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:240937 original size:49 final size:48
Alignment explanation
Indices: 240842--240942 Score: 109
Period size: 48 Copynumber: 2.1 Consensus size: 48
240832 ATTAGCACAC
* *
240842 AAAAATTAATATTCTAAATAAATAATAATTATATAAATATATTTTAATA
1 AAAAAATAATATTCTAAATAAATAATAATAATATAAATATATTTTAA-A
* * *
240891 AAAAAATAATATT-TACATAAATATTAATAA-ATATAATA-ATTATTTAA
1 AAAAAATAATATTCTAAATAAATAATAATAATATA-AATATATT-TTAAA
240938 AAAAA
1 AAAAA
240943 TACTAACATA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
47 12 0.27
48 21 0.47
49 12 0.27
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (48 bp):
AAAAAATAATATTCTAAATAAATAATAATAATATAAATATATTTTAAA
Found at i:243381 original size:14 final size:14
Alignment explanation
Indices: 243362--243428 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
243352 TTTTATTATA
243362 TTTAAAAATATATT
1 TTTAAAAATATATT
243376 TTTAAAAATTTATAATT
1 TTTAAAAA--TAT-ATT
* * *
243393 ATCAATAATATATT
1 TTTAAAAATATATT
* *
243407 TTTAATAATATAAT
1 TTTAAAAATATATT
243421 TTTAAAAA
1 TTTAAAAA
243429 AATCTAAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
14 29 0.67
15 3 0.07
16 3 0.07
17 8 0.19
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTAAAAATATATT
Found at i:247960 original size:31 final size:29
Alignment explanation
Indices: 247925--247983 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 29
247915 AAACTACACA
247925 TTTAGTACCTAAACTATCAATTTTGTTTCAT
1 TTTAGTACCTAAACTATC--TTTTGTTTCAT
*
247956 TTTAGTACCTAAACTTTCTTTTGTTTCA
1 TTTAGTACCTAAACTATCTTTTGTTTCA
247984 AAATCATACC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.37
31 17 0.63
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.51
Consensus pattern (29 bp):
TTTAGTACCTAAACTATCTTTTGTTTCAT
Found at i:250160 original size:31 final size:31
Alignment explanation
Indices: 250088--250160 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
250078 TACAAGGACC
** *
250088 AAATAGC-AAAAACATTAACTTAAAGGATCA
1 AAATAGCAAAAAACAAGAACTTAAAGGATAA
* *
250118 AAA-CGAAAAAAAACAAGAACTTAAAGGATAA
1 AAATAG-CAAAAAACAAGAACTTAAAGGATAA
250149 AAATAGCAAAAA
1 AAATAGCAAAAA
250161 TAGAAAGTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
29 1 0.03
30 3 0.09
31 28 0.85
32 1 0.03
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.14
Consensus pattern (31 bp):
AAATAGCAAAAAACAAGAACTTAAAGGATAA
Found at i:251905 original size:17 final size:18
Alignment explanation
Indices: 251875--251910 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
251865 TCATATGCGA
251875 TGAAGAGTTCGAGTCATT
1 TGAAGAGTTCGAGTCATT
251893 TGAAGAG-TCGAGTCATT
1 TGAAGAGTTCGAGTCATT
251910 T
1 T
251911 AAAGGGTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (18 bp):
TGAAGAGTTCGAGTCATT
Found at i:252219 original size:123 final size:125
Alignment explanation
Indices: 252050--252361 Score: 427
Period size: 125 Copynumber: 2.5 Consensus size: 125
252040 GCACACTACT
** * *
252050 ACATAATGGGAGATATGGTCATGTGATGACACTGCTCATCTGTTCATGAGTCTTAGCCATCTAAG
1 ACATAATAAGAGATCTGGTCATGTGATGACACTGCTCATCTGTTCATGAGTCTTGGCCATCTAAG
* * * *
252115 GGTGATAACACA-TT-CACTCTGATGGGGACGGCTGGTTAT-TGAGTTGACACATCTCCTT
66 GGTGATAACACAGTTCCACTCTAATGGGGACAGCTGGTTATCTGAGCTGACACATCTCC-C
* *
252173 A-ATAATGAAGAGATCTGGTCAGGTGATGACACTGCTCATCTGTTCATGATTCTTGGCCATCTAA
1 ACATAAT-AAGAGATCTGGTCATGTGATGACACTGCTCATCTGTTCATGAGTCTTGGCCATCTAA
* *
252237 GGGTGATAACACAGTTCCACTCTAATGTGGACAGTTGGTTATCTGAGCTGACACATCTCCC
65 GGGTGATAACACAGTTCCACTCTAATGGGGACAGCTGGTTATCTGAGCTGACACATCTCCC
** *
252298 ACATAATAAG-GAATCTAATCATGTGATGACACTGCTCATATGTTCATGAGTCTTGGCCATCTAA
1 ACATAATAAGAG-ATCTGGTCATGTGATGACACTGCTCATCTGTTCATGAGTCTTGGCCATCTAA
252362 AGGATTGGTT
Statistics
Matches: 166, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
122 5 0.03
123 65 0.39
124 3 0.02
125 72 0.43
126 21 0.13
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.30
Consensus pattern (125 bp):
ACATAATAAGAGATCTGGTCATGTGATGACACTGCTCATCTGTTCATGAGTCTTGGCCATCTAAG
GGTGATAACACAGTTCCACTCTAATGGGGACAGCTGGTTATCTGAGCTGACACATCTCCC
Found at i:258297 original size:27 final size:28
Alignment explanation
Indices: 258258--258318 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
258248 AAAATAGAAA
* * *
258258 AAAAACATGACTTAATGGATC-AAATGGC
1 AAAAACATAACTTAAAGGA-CAAAATAGC
258286 AAAAA-ATAACTTAAAGGACAAAATAGC
1 AAAAACATAACTTAAAGGACAAAATAGC
258313 AAAAAC
1 AAAAAC
258319 TGAAAGTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.04
27 22 0.79
28 5 0.18
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.16
Consensus pattern (28 bp):
AAAAACATAACTTAAAGGACAAAATAGC
Found at i:259844 original size:9 final size:9
Alignment explanation
Indices: 259802--259843 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
259792 AGAATTAGTA
*
259802 AATAATAAT
1 AATATTAAT
259811 AATATTAAT
1 AATATTAAT
259820 AATATTAAT
1 AATATTAAT
* *
259829 ACTATTTAT
1 AATATTAAT
259838 AATATT
1 AATATT
259844 TTTTTAGCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (9 bp):
AATATTAAT
Found at i:262331 original size:25 final size:27
Alignment explanation
Indices: 262288--262338 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
262278 TCATTACCTT
262288 TAATGCTATTTTAGAAT-AAATTTTTG
1 TAATGCTATTTTAGAATAAAATTTTTG
262314 TAATGCTA-TTTAGAATAAAATTTTT
1 TAATGCTATTTTAGAATAAAATTTTT
262339 CTTTTATTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (27 bp):
TAATGCTATTTTAGAATAAAATTTTTG
Found at i:262774 original size:51 final size:51
Alignment explanation
Indices: 262704--262804 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
262694 TAAGGAATGT
*
262704 TGTTAAGCAAAAGTCAATGTGATCACCAAAATCAAGTTATACTGTTAAGGC
1 TGTTAAGCAAAAGTCAATGTGATCACCAAAATCAAGTTATAATGTTAAGGC
*
262755 TGTTAAGTAAAAGTCAATGTGATCACCAAAATCAAGTTATAATGTTAAGG
1 TGTTAAGCAAAAGTCAATGTGATCACCAAAATCAAGTTATAATGTTAAGG
262805 TTGGTCCAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (51 bp):
TGTTAAGCAAAAGTCAATGTGATCACCAAAATCAAGTTATAATGTTAAGGC
Found at i:264611 original size:2 final size:2
Alignment explanation
Indices: 264604--264658 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
264594 TCAACTCGAC
264604 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
264646 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
264659 GGGATAAGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:266058 original size:12 final size:12
Alignment explanation
Indices: 266025--266051 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
266015 TTCCATAACA
266025 AAATCAGTGTTG
1 AAATCAGTGTTG
266037 AAATCAGTGTTG
1 AAATCAGTGTTG
266049 AAA
1 AAA
266052 CAAGTGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (12 bp):
AAATCAGTGTTG
Found at i:266783 original size:2 final size:2
Alignment explanation
Indices: 266776--266814 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
266766 AAATAACATA
266776 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
266815 ATTTAATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:269048 original size:99 final size:99
Alignment explanation
Indices: 268930--269128 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
268920 TGTGTTCGAG
268930 ACTCTTTATCTATATGCTGAAAAGATAAGCTAAATACACCCGGAAATAACACATTAGATACGAGT
1 ACTCTTTATCTATATGCTGAAAAGATAAGCTAAATACACCCGGAAATAACACATTAGATACGAGT
268995 TAACTGTTTTTAACGGTAAGAATAATCACTACGA
66 TAACTGTTTTTAACGGTAAGAATAATCACTACGA
269029 ACTCTTTATCTATATGCTGAAAAGATAAGCTAAATACACCCGGAAATAACACATTAGATACGAGT
1 ACTCTTTATCTATATGCTGAAAAGATAAGCTAAATACACCCGGAAATAACACATTAGATACGAGT
269094 TAACTGTTTTTAACGGTAAGAATAATCACTACGA
66 TAACTGTTTTTAACGGTAAGAATAATCACTACGA
269128 A
1 A
269129 GTTACATTGA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (99 bp):
ACTCTTTATCTATATGCTGAAAAGATAAGCTAAATACACCCGGAAATAACACATTAGATACGAGT
TAACTGTTTTTAACGGTAAGAATAATCACTACGA
Found at i:274479 original size:32 final size:32
Alignment explanation
Indices: 274438--274501 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
274428 GAAAGGCCGT
274438 TGATGAATCGGATTAATGGCGGTCACTACCAC
1 TGATGAATCGGATTAATGGCGGTCACTACCAC
*
274470 TGATGAATCGGATTAATGGTGGTCACTACCAC
1 TGATGAATCGGATTAATGGCGGTCACTACCAC
274502 AACCATGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (32 bp):
TGATGAATCGGATTAATGGCGGTCACTACCAC
Found at i:277281 original size:27 final size:28
Alignment explanation
Indices: 277220--277295 Score: 136
Period size: 27 Copynumber: 2.8 Consensus size: 28
277210 CTTAACCTAC
277220 TTTTACTTTCTCTTTATCATTATTTTAG
1 TTTTACTTTCTCTTTATCATTATTTTAG
*
277248 TTTTACTTTTTCTTTATCATTA-TTTAG
1 TTTTACTTTCTCTTTATCATTATTTTAG
277275 TTTTACTTTCTCTTTATCATT
1 TTTTACTTTCTCTTTATCATT
277296 TATATATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 25 0.54
28 21 0.46
ACGTcount: A:0.17, C:0.14, G:0.03, T:0.66
Consensus pattern (28 bp):
TTTTACTTTCTCTTTATCATTATTTTAG
Found at i:278108 original size:30 final size:30
Alignment explanation
Indices: 278065--278123 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
278055 GTTTGAGGGC
*
278065 AAAAATCGTGAGATAATGGTG-TGGAGAAA
1 AAAAATCCTGAGATAATGGTGTTGGAGAAA
*
278094 AAAAATTCCTGAGATAATGTTGTTGGAGAA
1 AAAAA-TCCTGAGATAATGGTGTTGGAGAA
278124 TTATTTGCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.19
30 14 0.54
31 7 0.27
ACGTcount: A:0.42, C:0.05, G:0.27, T:0.25
Consensus pattern (30 bp):
AAAAATCCTGAGATAATGGTGTTGGAGAAA
Found at i:278941 original size:7 final size:7
Alignment explanation
Indices: 278929--278958 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
278919 TGATTTTGTG
278929 AACCTTA
1 AACCTTA
278936 AACCTTA
1 AACCTTA
*
278943 AACCCTA
1 AACCTTA
278950 AACCTTA
1 AACCTTA
278957 AA
1 AA
278959 AATATTTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (7 bp):
AACCTTA
Found at i:278995 original size:7 final size:7
Alignment explanation
Indices: 278979--279008 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
278969 TTGTTGCTAA
278979 AAACCCT
1 AAACCCT
*
278986 AAACCTT
1 AAACCCT
278993 AAACCCT
1 AAACCCT
279000 AAACCCT
1 AAACCCT
279007 AA
1 AA
279009 CCATTCTCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:279274 original size:14 final size:14
Alignment explanation
Indices: 279252--279302 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
279242 TTATTGTTGA
* *
279252 AAACTCTAAACGCT
1 AAACCCTAAACACT
**
279266 AAACCCTAAATTCT
1 AAACCCTAAACACT
279280 AAACCCTAAACACT
1 AAACCCTAAACACT
*
279294 AAATCCTAA
1 AAACCCTAA
279303 CCATTATCCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (14 bp):
AAACCCTAAACACT
Found at i:279282 original size:21 final size:21
Alignment explanation
Indices: 279256--279302 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
279246 TGTTGAAAAC
* *
279256 TCTAAACGCTAAACCCTAAAT
1 TCTAAACCCTAAACACTAAAT
279277 TCTAAACCCTAAACACTAAAT
1 TCTAAACCCTAAACACTAAAT
*
279298 CCTAA
1 TCTAA
279303 CCATTATCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (21 bp):
TCTAAACCCTAAACACTAAAT
Found at i:279517 original size:296 final size:288
Alignment explanation
Indices: 278979--279694 Score: 994
Period size: 296 Copynumber: 2.5 Consensus size: 288
278969 TTGTTGCTAA
* * *
278979 AAACCCTAAACCTTAAACCCTAAACCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAAA
1 AAACCCTAAACCCTAAACACTAAATCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAAA
* *
279044 C-AATATGTAACCACTATCATGGTAGATATCACCATCCTCTACCCCCTTCATTGCCCTCAACATA
66 CAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCTTTCATTGCCCTCAACATA
* * * *
279108 TCATGAATTTATAAAGGTTTTCAGCAATAATCAAAATATTTTAGGGTTTAAGGTTCCAAAATAAA
131 CCATGAACTTATAAAGGTTTTCAGCAACAACCAAAATATTTTAGGGTTTAAGGTTCCAAAATAAA
* * *
279173 TATACAATAAATAATATGAGGAACTATTGATTTTGTGAACCCTAAACCCTAAACCCTAAAATATT
196 TATACAACAAATAATATCAGGAACTATTGA-TTT-TG----C-AAACCTTAAACCCTAAAATATT
* * * *
279238 TT-GCTTATTGTTGAAAACTCT-AAACGCTAAACCCT
254 TTAG-TTATTATTAAAAACCCTAAAAC-CTAAAACCT
** * *
279273 AAATTCTAAACCCTAAACACTAAATCCTAACCATTATCCCTCCAATCAATGTCTTCTTATAAAAA
1 AAACCCTAAACCCTAAACACTAAATCCTAACCATTCTCCCTCCAATCAATTTCTTCTTAT-AAAA
* *
279338 ACAAATTTGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCTTTCATTACCCTCAACAT
65 ACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCTTTCATTGCCCTCAACAT
*
279403 ACCATGAACTTATAAAGGTTTTCAGCAACAACCAAAATATTTTAGGGTTT-AGGCTTCCAAAATC
130 ACCATGAACTTATAAAGGTTTTCAGCAACAACCAAAATATTTTAGGGTTTAAGG-TTCCAAAATA
* *
279467 AATATACAACAAATAATATCAGTAATTATTGATTTTGCAAACCTTAAACCCTAAAATATTTTAGT
194 AATATACAACAAATAATATCAGGAACTATTGATTTTGCAAACCTTAAACCCTAAAATATTTTAGT
* **
279532 TGTTATTAAAAACCCTAAAACCTAAAATTT
259 TATTATTAAAAACCCTAAAACCTAAAACCT
* * *
279562 AAACCCTAAAACCTAAA-ATTTAAAT-CTAAACATTCTCCCTCCAATCAATTTCTTCTTATAAAA
1 AAACCCTAAACCCTAAACA-CTAAATCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAA
*
279625 ACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACTCCTTTCATTGCCCTCAACAT
65 ACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCTTTCATTGCCCTCAACAT
279690 ACCAT
130 ACCAT
279695 TGCCCTATCT
Statistics
Matches: 378, Mismatches: 38, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
287 71 0.19
288 32 0.08
289 61 0.16
290 6 0.02
294 55 0.15
295 12 0.03
296 141 0.37
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (288 bp):
AAACCCTAAACCCTAAACACTAAATCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAAA
CAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCTTTCATTGCCCTCAACATA
CCATGAACTTATAAAGGTTTTCAGCAACAACCAAAATATTTTAGGGTTTAAGGTTCCAAAATAAA
TATACAACAAATAATATCAGGAACTATTGATTTTGCAAACCTTAAACCCTAAAATATTTTAGTTA
TTATTAAAAACCCTAAAACCTAAAACCT
Found at i:279566 original size:21 final size:21
Alignment explanation
Indices: 279541--279585 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
279531 TTGTTATTAA
279541 AAACCCTAAAACCTAAAATTT
1 AAACCCTAAAACCTAAAATTT
279562 AAACCCTAAAACCTAAAATTT
1 AAACCCTAAAACCTAAAATTT
279583 AAA
1 AAA
279586 TCTAAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (21 bp):
AAACCCTAAAACCTAAAATTT
Found at i:279894 original size:22 final size:21
Alignment explanation
Indices: 279872--279912 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
279862 CTATTTTTTA
279872 AATCA-TTAGATAATAAAAATT
1 AATCATTTA-ATAATAAAAATT
279893 AATCATTTAATAATAAAAAT
1 AATCATTTAATAATAAAAAT
279913 AATATTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
AATCATTTAATAATAAAAATT
Found at i:279896 original size:21 final size:19
Alignment explanation
Indices: 279872--279924 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 19
279862 CTATTTTTTA
279872 AATCATTAGATAATAAAAATT
1 AATCATTA-ATAATAAAAA-T
279893 AATCATTTAATAATAAAAAT
1 AATCA-TTAATAATAAAAAT
279913 AAT-ATTATATAA
1 AATCATTA-ATAA
279925 AACAAATCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.10
19 5 0.17
20 4 0.13
21 15 0.50
22 3 0.10
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (19 bp):
AATCATTAATAATAAAAAT
Found at i:280336 original size:29 final size:30
Alignment explanation
Indices: 280279--280336 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
280269 CAGCAAATAA
*
280279 TTCTCCAACAACATTATCTCAATAATTTTT
1 TTCTCCAACAACATTATCTCAAGAATTTTT
* *
280309 TTCTCC-ACACCATTATCTCACG-ATTTTT
1 TTCTCCAACAACATTATCTCAAGAATTTTT
280337 GCCATTGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.24
29 13 0.52
30 6 0.24
ACGTcount: A:0.28, C:0.28, G:0.02, T:0.43
Consensus pattern (30 bp):
TTCTCCAACAACATTATCTCAAGAATTTTT
Found at i:280446 original size:16 final size:16
Alignment explanation
Indices: 280422--280470 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
280412 GATATCTTAA
280422 ATTTCAAATATAAAAAT
1 ATTT-AAATATAAAAAT
280439 ATTTAAATATTGAAAAA-
1 ATTTAAATA-T-AAAAAT
280456 A-TTAAATATAAAAAT
1 ATTTAAATATAAAAAT
280471 TAAATTACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 5 0.17
15 1 0.03
16 12 0.41
17 6 0.21
18 5 0.17
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
ATTTAAATATAAAAAT
Found at i:280470 original size:13 final size:13
Alignment explanation
Indices: 280452--280492 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
280442 TAAATATTGA
*
280452 AAAAATTAAATAT
1 AAAAATTAAATAC
280465 AAAAATTAAATTAC
1 AAAAATTAAA-TAC
*
280479 AAAAAATAAATAC
1 AAAAATTAAATAC
280492 A
1 A
280493 TATTAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATTAAATAC
Found at i:280482 original size:14 final size:14
Alignment explanation
Indices: 280452--280489 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
280442 TAAATATTGA
*
280452 AAAAATTAAA-TAT
1 AAAAATTAAATTAC
280465 AAAAATTAAATTAC
1 AAAAATTAAATTAC
*
280479 AAAAAATAAAT
1 AAAAATTAAAT
280490 ACATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATTAAATTAC
Found at i:281020 original size:42 final size:41
Alignment explanation
Indices: 280941--281097 Score: 142
Period size: 42 Copynumber: 3.7 Consensus size: 41
280931 AAGATTATAA
* * *
280941 TATTTTATTAAAAT-ATAAAAT-TATTATAAACTATATTAGT
1 TATTTTATTAAAATAAAAAAATATATTATTAA-TATATTAAT
280981 TATTTTA-TAAAATAAAAATAATATATTATTAATTATATTAAT
1 TATTTTATTAAAATAAAAA-AATATATTATTAA-TATATTAAT
* *
281023 TA-CTTATTAAAATATTAAAAAATATTATTATTAAAATATTAAAAT
1 TATTTTATTAAAATA--AAAAAATA-TATTATTAATATATT--AAT
* *
281068 TATATTATTAAAATAAAAATATTATATTAT
1 TATTTTATTAAAATAAAAA-AATATATTAT
281098 ATTTTAAGGA
Statistics
Matches: 98, Mismatches: 8, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
39 6 0.06
40 10 0.10
41 6 0.06
42 25 0.26
43 9 0.09
44 23 0.23
45 8 0.08
46 11 0.11
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (41 bp):
TATTTTATTAAAATAAAAAAATATATTATTAATATATTAAT
Found at i:281053 original size:24 final size:23
Alignment explanation
Indices: 281021--281096 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 23
281011 AATTATATTA
281021 ATTACTTATTAAAATATTAAAAAAT
1 ATTA-TTATTAAAATATT-AAAAAT
*
281046 ATTATTATTAAAATATTAAAATT
1 ATTATTATTAAAATATTAAAAAT
281069 A-TATTATT-AAA-A-TAAAAAT
1 ATTATTATTAAAATATTAAAAAT
281088 ATTA-TATTA
1 ATTATTATTA
281097 TATTTTAAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
19 11 0.23
20 3 0.06
21 3 0.06
22 7 0.15
23 6 0.13
24 13 0.28
25 4 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTATTATTAAAATATTAAAAAT
Found at i:281069 original size:14 final size:14
Alignment explanation
Indices: 281041--281091 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
281031 AAAATATTAA
**
281041 AAAATATTATTATT
1 AAAATATTAAAATT
281055 AAAATATTAAAATT
1 AAAATATTAAAATT
* * *
281069 ATATTATTAAAATA
1 AAAATATTAAAATT
281083 AAAATATTA
1 AAAATATTA
281092 TATTATATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATATTAAAATT
Found at i:281073 original size:22 final size:22
Alignment explanation
Indices: 281002--281097 Score: 92
Period size: 22 Copynumber: 4.4 Consensus size: 22
280992 ATAAAAATAA
*
281002 TATATTATTAATTATATT--AAT
1 TATATTATTAA-AATATTAAAAT
* *
281023 TA-CTTATTAAAATATTAAAAAA
1 TATATTATTAAAATATT-AAAAT
281045 TATTATTATTAAAATATTAAAAT
1 TA-TATTATTAAAATATTAAAAT
*
281068 TATATTATTAAAATA-AAAATAT
1 TATATTATTAAAATATTAAA-AT
281090 TATATTAT
1 TATATTAT
281098 ATTTTAAGGA
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
19 5 0.08
20 7 0.11
21 5 0.08
22 27 0.43
23 6 0.10
24 13 0.21
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (22 bp):
TATATTATTAAAATATTAAAAT
Found at i:281217 original size:22 final size:22
Alignment explanation
Indices: 281189--281265 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
281179 TAATTTATTA
*
281189 TATATTATAAAAATAAAAATAT
1 TATATTATATAAATAAAAATAT
* * *
281211 TATATTATATATATTATAAT-T
1 TATATTATATAAATAAAAATAT
*
281232 ATATAATTATATCAATAAAAATAT
1 -TAT-ATTATATAAATAAAAATAT
*
281256 AATATTATAT
1 TATATTATAT
281266 TAAAAAAGTA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
21 1 0.02
22 26 0.60
23 15 0.35
24 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (22 bp):
TATATTATATAAATAAAAATAT
Found at i:281226 original size:14 final size:14
Alignment explanation
Indices: 281207--281243 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
281197 AAAAATAAAA
281207 ATATTATATTATAT
1 ATATTATATTATAT
281221 ATATTATAATTATAT
1 ATATTAT-ATTATAT
281236 A-ATTATAT
1 ATATTATAT
281244 CAATAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 12 0.55
15 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATATTATATTATAT
Found at i:281334 original size:30 final size:28
Alignment explanation
Indices: 281292--281364 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 28
281282 AATATAATTG
281292 AATAATTAATATTTTTATTAAAATGATAGTAA
1 AATAA-TAATATTTTTATT-AAAT-ATA-TAA
* **
281324 AATCAT-ATATTAATATTAAATATATAA
1 AATAATAATATTTTTATTAAATATATAA
281351 AATAATAATATTTT
1 AATAATAATATTTT
281365 GAGTGTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
27 8 0.24
28 8 0.24
29 4 0.12
30 9 0.26
31 1 0.03
32 4 0.12
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (28 bp):
AATAATAATATTTTTATTAAATATATAA
Found at i:281754 original size:2 final size:2
Alignment explanation
Indices: 281747--281810 Score: 105
Period size: 2 Copynumber: 33.0 Consensus size: 2
281737 GATGATATGA
281747 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
*
281789 AT AT AT AT A- AT GT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
281811 TTTAAAAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:282118 original size:27 final size:27
Alignment explanation
Indices: 282049--282127 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 27
282039 GATTATCTTA
282049 AATATATATATTTTAGTAATTTAATTTTT
1 AATATATAT-TTTTA-TAATTTAATTTTT
* *
282078 AAT-TTTAATATTTTATAA-TTATTTTTT
1 AATATAT-AT-TTTTATAATTTAATTTTT
*
282105 AATATACTATTTTTATATTTTAA
1 AATATA-TATTTTTATAATTTAA
282128 CTTTAAGACA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 18 0.44
28 11 0.27
29 12 0.29
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (27 bp):
AATATATATTTTTATAATTTAATTTTT
Found at i:283120 original size:31 final size:31
Alignment explanation
Indices: 283085--283159 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
283075 AAGTTAAATG
*
283085 TTTTATTAAAATACAAATATCACT-TTAAACA
1 TTTTATTAAAGTACAAATATCA-TATTAAACA
*
283116 TTTTA--AAAGTATAAATATCATATTAAACA
1 TTTTATTAAAGTACAAATATCATATTAAACA
283145 TATTT-TTAAAGTACA
1 T-TTTATTAAAGTACA
283160 TGTACCACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
28 1 0.03
29 21 0.57
30 3 0.08
31 12 0.32
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (31 bp):
TTTTATTAAAGTACAAATATCATATTAAACA
Found at i:284122 original size:105 final size:105
Alignment explanation
Indices: 283940--284144 Score: 356
Period size: 105 Copynumber: 2.0 Consensus size: 105
283930 TAACTCGCTA
* * * *
283940 AAAAATTTGTTGAAAAATATTATATTATAAATCTAATGTTGTTGTTTTCTACCGGTCGGTTTACC
1 AAAAATTCGTTGAAAAATATTATATTACAAATCTAACGTTGTTGTTTTCTACCGGTCGATTTACC
*
284005 ATCGTCTAATAATCACCCAACAATCGTTTAACAGTGGGTG
66 ATCGTCTAATAATCACCCAACAATCGTTCAACAGTGGGTG
*
284045 AAAAATTCGTTGAAAAATATTATATTACAAATCTAACGTTGTTGTTTTCTATCGGTCGATTTACC
1 AAAAATTCGTTGAAAAATATTATATTACAAATCTAACGTTGTTGTTTTCTACCGGTCGATTTACC
284110 ATCGTCTAATAATCACCCAACAATCGTTCAACAGT
66 ATCGTCTAATAATCACCCAACAATCGTTCAACAGT
284145 CGAACGTCTA
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 94 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (105 bp):
AAAAATTCGTTGAAAAATATTATATTACAAATCTAACGTTGTTGTTTTCTACCGGTCGATTTACC
ATCGTCTAATAATCACCCAACAATCGTTCAACAGTGGGTG
Found at i:285168 original size:64 final size:64
Alignment explanation
Indices: 285095--285315 Score: 231
Period size: 64 Copynumber: 3.5 Consensus size: 64
285085 TGTTTGATTG
* * **
285095 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTC
1 TGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
285158 A
64 A
* * **
285159 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
* ** * *
285223 TGCATCGATGCATAAGG-AGTGCATCGATGCATCTCAGCAATAATACAACATCGAAT---ATTTA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
*
285284 TGCACCGATGCATCA-GTAGTGCATCGATGCAT
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCAT
285316 ACCTTCATTA
Statistics
Matches: 135, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
60 1 0.01
61 31 0.23
64 95 0.70
65 8 0.06
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:285967 original size:31 final size:31
Alignment explanation
Indices: 285929--286053 Score: 225
Period size: 31 Copynumber: 4.0 Consensus size: 31
285919 AAGGGTCGAG
285929 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
285960 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
285991 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
286022 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
286053 G
1 G
286054 GTCCTTCGGG
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
31 91 0.99
32 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:287050 original size:80 final size:80
Alignment explanation
Indices: 286958--287120 Score: 308
Period size: 80 Copynumber: 2.0 Consensus size: 80
286948 ATCATATGCA
*
286958 CACGTGATATGTGATAGAAGAAATGATATGAGAGTTTTTAAAGTGAAATACAAGATGATAGACCT
1 CACGTGATATGTGATAGAAGAAATGATATGAGAGTTTTTAAAGTGAAATACAAGACGATAGACCT
287023 GAAGATAATAGCATT
66 GAAGATAATAGCATT
287038 CACGTGATATGTGATAGAAGAAATGATATGAGAGTTTTTAAAGTGAAATACAAGACGATAGACCT
1 CACGTGATATGTGATAGAAGAAATGATATGAGAGTTTTTAAAGTGAAATACAAGACGATAGACCT
*
287103 GAAGGTAATAGCATT
66 GAAGATAATAGCATT
287118 CAC
1 CAC
287121 CTGCCCTGGC
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (80 bp):
CACGTGATATGTGATAGAAGAAATGATATGAGAGTTTTTAAAGTGAAATACAAGACGATAGACCT
GAAGATAATAGCATT
Found at i:288893 original size:3 final size:3
Alignment explanation
Indices: 288885--288910 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
288875 AGATAGATTC
288885 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
288911 ATGTAGAGAA
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:289517 original size:64 final size:63
Alignment explanation
Indices: 289444--289667 Score: 252
Period size: 64 Copynumber: 3.5 Consensus size: 63
289434 TGTTTGATTG
** *
289444 TGCACCGATGCATTGGTAGTGCATCGATGCACTCTTTTAA-AATAAAGACATCGAATGCAATTCA
1 TGCACCGATGCATAAGTAGTGCATCGATGCA-TCTATTAATAATAAA-ACATCGAATGCAATTCA
* * * **
289508 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCACCGATGCATAAGTAGTGCATCGATGCAT-CTATTAATAATAAAACATCGAATGCAATTCA
* * ** * * * *
289572 TGCATCGATGCATAAGGAGTGCATCGATGCATCTCAGCAATAATACAACATCGAATACATTTTA
1 TGCACCGATGCATAAGTAGTGCATCGATGCATCT-ATTAATAATAAAACATCGAATGCAATTCA
*
289636 TGCACCGATGCATCAGTAGTGCATCGATGCAT
1 TGCACCGATGCATAAGTAGTGCATCGATGCAT
289668 ACCTTCATTA
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
63 2 0.01
64 129 0.95
65 5 0.04
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCACCGATGCATAAGTAGTGCATCGATGCATCTATTAATAATAAAACATCGAATGCAATTCA
Found at i:297522 original size:15 final size:15
Alignment explanation
Indices: 297502--297534 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
297492 TTAGCTGGGT
*
297502 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
297517 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
297532 GGG
1 GGG
297535 TAATGTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.15, G:0.70, T:0.09
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:300713 original size:15 final size:17
Alignment explanation
Indices: 300690--300723 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
300680 TAAAGGTCTT
300690 AAATAAATAATAAA-TA
1 AAATAAATAATAAACTA
300706 AAAT-AATAATAAACTA
1 AAATAAATAATAAACTA
300722 AA
1 AA
300724 CATATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAATAATAAACTA
Found at i:303239 original size:30 final size:30
Alignment explanation
Indices: 303203--303268 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
303193 GCTTAATCCC
* *
303203 TTAAATGTCTAT-CTTTGCTATTTTAGTACA
1 TTAAATGTATATAATTTG-TATTTTAGTACA
* *
303233 TTAAATGTATGTAATTTGTATTTTAGTTCA
1 TTAAATGTATATAATTTGTATTTTAGTACA
303263 TTAAAT
1 TTAAAT
303269 TTCAGTTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.52
Consensus pattern (30 bp):
TTAAATGTATATAATTTGTATTTTAGTACA
Found at i:306744 original size:12 final size:12
Alignment explanation
Indices: 306717--306772 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
306707 CAAAGAGAAA
*
306717 AAAAAAG-AAAC
1 AAAAAAGCAAAG
306728 AAAAAAGCAAAGG
1 AAAAAAGCAAA-G
*
306741 AAAAGAAG-AAAA
1 AAAA-AAGCAAAG
306753 ATAAAAAGCAAAG
1 A-AAAAAGCAAAG
306766 AAAAAAG
1 AAAAAAG
306773 AACAAGATGC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 7 0.19
12 13 0.35
13 14 0.38
14 3 0.08
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAAAAGCAAAG
Found at i:306758 original size:26 final size:23
Alignment explanation
Indices: 306717--306774 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 23
306707 CAAAGAGAAA
*
306717 AAAAAAGAAACAAAAAAGCAAAGG
1 AAAAAAGAAAAAAAAAAGCAAA-G
306741 AAAAGAAGAAAAATAAAAAGCAAAG
1 AAAA-AAGAAAAA-AAAAAGCAAAG
306766 AAAAAAGAA
1 AAAAAAGAA
306775 CAAGATGCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 9 0.29
25 12 0.39
26 10 0.32
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.02
Consensus pattern (23 bp):
AAAAAAGAAAAAAAAAAGCAAAG
Found at i:306772 original size:27 final size:26
Alignment explanation
Indices: 306712--306774 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
306702 CAGAACAAAG
* *
306712 AGAAAAAAAAAGAAACAAAAAAGCAA
1 AGAAAAAAGAAGAAAAAAAAAAGCAA
*
306738 AG-GAAAAGAAGAAAAATAAAAAGCAA
1 AGAAAAAAGAAGAAAAA-AAAAAGCAA
306764 AGAAAAAAGAA
1 AGAAAAAAGAA
306775 CAAGATGCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 11 0.35
26 13 0.42
27 7 0.23
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.02
Consensus pattern (26 bp):
AGAAAAAAGAAGAAAAAAAAAAGCAA
Found at i:307884 original size:32 final size:32
Alignment explanation
Indices: 307802--307895 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 32
307792 AAGCAATGAG
* * **
307802 GAATAATGGGGCATCTTTAAAGATTCAACAAT
1 GAATATTGGGGCATATTTGGAGATTCAACAAT
* * * *
307834 AAATGTTGGGGCATATTTGGAGATTCAATATT
1 GAATATTGGGGCATATTTGGAGATTCAACAAT
*
307866 GAATATTGGGGCATATTTGGGGATTCAACA
1 GAATATTGGGGCATATTTGGAGATTCAACA
307896 TCCTGATACA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (32 bp):
GAATATTGGGGCATATTTGGAGATTCAACAAT
Found at i:308369 original size:43 final size:43
Alignment explanation
Indices: 308306--308429 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 43
308296 ACGAAGGGGC
* * *
308306 CATCCACGATTTTAACTCCACGACGGAGGATATCGTACCAACG
1 CATCCACGATTTCAATTCCACGACGGAGGATATCGTACCAACA
* * * *
308349 GATCCACGATTTCAATTCCACGACAGAGGATATCGTGCCTACA
1 CATCCACGATTTCAATTCCACGACGGAGGATATCGTACCAACA
* *
308392 CATCCACGGTTTCAACTT-CACGACGAAGGGA-ATCGTAC
1 CATCCACGATTTCAA-TTCCACGACGGA-GGATATCGTAC
308430 ACACAAGCAA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 62 0.93
44 5 0.07
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (43 bp):
CATCCACGATTTCAATTCCACGACGGAGGATATCGTACCAACA
Found at i:308675 original size:335 final size:335
Alignment explanation
Indices: 308099--309013 Score: 1336
Period size: 335 Copynumber: 2.7 Consensus size: 335
308089 CTTGATTCAA
* *
308099 AAGCAGCATCCATCTCTAGACTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGA
1 AAGCAGCATCCATCTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAAGA
* * * * * *
308164 GTGTCTGTCAATAAACTTTTCAGCTTCATAGCCAATTTCAACTTCACGACGAAGGATATTGGACT
66 GTGTTTGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTTCATGGCGAAGGATATTGGACT
* * *
308229 CGAAACAACACAAGCTTGGATTTCAACTTCACAACGAAGGATATTCAAGTCAAGGCTTAACTTCA
131 CGAAACAGCACAAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCA
* * *
308294 CGACGAAGGGGCCATCCACGATTTTAACTCCACGACGGAGGATATCGTACCAACGGATCCACGAT
196 CGACGAATGGGTCATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACGGATCCACGAT
* * *
308359 TTCAA-TTCC-ACGACAGAGGATATCGTGCCTACACATCCACGGTTTCAACTTCACGACGAAGGG
261 TTCAACTTCCTA--ACAGAGGATATAGTGCCCACACATCCACGGTTTCAACTTCACGACGAAGGA
308422 AATCGTACACAC
324 AATCGTACACAC
* *
308434 AAGCAACATCCATGTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAAGA
1 AAGCAGCATCCATCTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAAGA
*
308499 GTGTTTGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTTCATGGCAAAGGATATTGGACT
66 GTGTTTGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTTCATGGCGAAGGATATTGGACT
*
308564 CGAAACAGCACAAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGATCAACTTCA
131 CGAAACAGCACAAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCA
* * * * *
308629 CGACGAATGGTTCAT-CAGCAATTTCAACTCCACGACGGAGGATATCGTACCCATGGATCCGCGA
196 CGACGAATGGGTCATCCA-CGATTTCAACTCCACGACGGAGGATATCGTACCAACGGATCCACGA
*
308693 TTTCAACTTCCTAACAGAGGATATATTGCCCACACATCCACGGTTTCAACTTCACGACGAAGGAA
260 TTTCAACTTCCTAACAGAGGATATAGTGCCCACACATCCACGGTTTCAACTTCACGACGAAGGAA
308758 ATCGTACACAC
325 ATCGTACACAC
* * * * *
308769 AAGCAGCATCCATCTCT-GTTTGGATTTTAACTTCATGACGAATGATATCCAACTCAAAGAATGA
1 AAGCAGCATCCATCTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAAGA
* * *
308833 GTGTTTGTCAATAAACTTTCTAGTTTCAGAGTCAATTTCAACTTCATGGCGAAGGATATTGGCCT
66 GTGTTTGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTTCATGGCGAAGGATATTGGACT
* * * *
308898 CGAAACAGCGCAACTTACATTGGATTTCAACTTCACGACGAAGGATATACAATTCCAAGGCTCAA
131 CGAAACAGCACAA---GC-TTGGATTTCAACTTCACGACGAAGGATATTCAAGT-CAAGGCTCAA
* * *
308963 CTTCACAACGAATGGGTCATCCACGA-TTCTAACTTCACGACGAAGGATATC
191 CTTCACGACGAATGGGTCATCCACGATTTC-AACTCCACGACGGAGGATATC
309014 CTGTCCATCA
Statistics
Matches: 522, Mismatches: 48, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
334 117 0.22
335 313 0.60
336 4 0.01
337 2 0.00
338 36 0.07
339 48 0.09
340 2 0.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (335 bp):
AAGCAGCATCCATCTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAAGA
GTGTTTGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTTCATGGCGAAGGATATTGGACT
CGAAACAGCACAAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCA
CGACGAATGGGTCATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACGGATCCACGAT
TTCAACTTCCTAACAGAGGATATAGTGCCCACACATCCACGGTTTCAACTTCACGACGAAGGAAA
TCGTACACAC
Found at i:309313 original size:35 final size:36
Alignment explanation
Indices: 309254--309358 Score: 117
Period size: 35 Copynumber: 3.0 Consensus size: 36
309244 CGTTGAATCT
* * *
309254 GTTTCCC-CGAAATAAATTTCGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
309289 GTTT-TCTTGAAACAAATTTTGTCTCTTTTGAGGA-A
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGA-GACA
* *
309324 GTTTCCCTTGAAACATATTTTGTCTCACTTGAGAC
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC
309359 CATTTCTCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
34 1 0.02
35 31 0.54
36 25 0.44
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:309370 original size:36 final size:36
Alignment explanation
Indices: 309262--309370 Score: 125
Period size: 36 Copynumber: 3.1 Consensus size: 36
309252 CTGTTTCCCC
* *
309262 GAAATAAATTTCGTCTCTCTTGAGACAGTTT-TCTT
1 GAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* *
309297 GAAACAAATTTTGTCTCTTTTGAGGA-AGTTTCCCTT
1 GAAACAAATTTTGTCTCTCTTGA-GACAGTTTCTCTT
* *
309333 GAAACATATTTTGTCTCACTTGAGACCA-TTTCTCTT
1 GAAACAAATTTTGTCTCTCTTGAGA-CAGTTTCTCTT
309369 GA
1 GA
309371 CCAGGTCTCT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
35 27 0.44
36 34 0.55
37 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (36 bp):
GAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:309604 original size:131 final size:130
Alignment explanation
Indices: 309370--309805 Score: 523
Period size: 131 Copynumber: 3.3 Consensus size: 130
309360 ATTTCTCTTG
* *
309370 ACCAGGTCTCTTCATCACGTAGGAGCCGTGCCAACCTTAGATAATCAGTCGTCCTCATCACGTAG
1 ACCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCTTAGATAATCAGTCGTCCTCATCACGTAG
* * * * * *
309435 GAATCGTGTTATCATCCCTAATGATGGCCTGCCATCCTCATCACGTAGGAACTGTGTCATCATTT
66 GAACCGTGTTATCATCCCTAAAGATGACATGCCATCCTCATCACGTAGGAACCGTGTCATCA-TC
309500 A
130 A
* ** * *
309501 ACCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCTTAGATAAACAACCGTCCTCATTACGTAA
1 ACCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCTTAGATAATCAGTCGTCCTCATCACGTAG
** * *
309566 GAACCGTGTTATCATCCCTAAAGATGACATATCATCCTCATCACGTATGAACCGTGTCATCCCAC
66 GAACCGTGTTATCATCCCTAAAGATGACATGCCATCCTCATCACGTAGGAACCGTGTCAT--CAT
*
309631 CG
129 CA
* *** ** *
309633 ACCAGATCTCCACATCACGTAGGAGTTATGTTAATCTTAGATAATCAGTCGTCCTCATCACGTAG
1 ACCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCTTAGATAATCAGTCGTCCTCATCACGTAG
* * * *
309698 GAACCATGTTATCATCCCTAAAGATGGCCA-GCCGTCCTCATCACGTAGGAACCGTGTCATCCCT
66 GAACCGTGTTATCATCCCTAAAGAT-GACATGCCATCCTCATCACGTAGGAACCGTGTCAT-CAT
309762 CA
129 CA
* * *
309764 ACCTGATTTCCTCATCACGTAGGAGCCGTGTCAACCCTTAGA
1 ACCAGATCTCCTCATCACGTAGGAGCCGTGCCAA-CCTTAGA
309806 CGACCACAAG
Statistics
Matches: 254, Mismatches: 47, Indels: 7
0.82 0.15 0.02
Matches are distributed among these distances:
131 140 0.55
132 109 0.43
133 5 0.02
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (130 bp):
ACCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCTTAGATAATCAGTCGTCCTCATCACGTAG
GAACCGTGTTATCATCCCTAAAGATGACATGCCATCCTCATCACGTAGGAACCGTGTCATCATCA
Found at i:311113 original size:30 final size:30
Alignment explanation
Indices: 311077--311133 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
311067 GTTTTTGTCA
311077 TTTAGTC-TCTTAAATTTTGATTTTTATTCT
1 TTTAGTCAT-TTAAATTTTGATTTTTATTCT
* *
311107 TTTAGTCATTTAAGTTTTTATTTTTAT
1 TTTAGTCATTTAAATTTTGATTTTTAT
311134 AGCTTAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.65
Consensus pattern (30 bp):
TTTAGTCATTTAAATTTTGATTTTTATTCT
Found at i:311677 original size:15 final size:16
Alignment explanation
Indices: 311642--311678 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
311632 GCATACTAGC
*
311642 TTTTGTCTTAAAAATA
1 TTTTTTCTTAAAAATA
*
311658 TTTTTTCTTAAAATTA
1 TTTTTTCTTAAAAATA
311674 TTTTT
1 TTTTT
311679 AAAGATGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTTTTCTTAAAAATA
Found at i:312818 original size:21 final size:21
Alignment explanation
Indices: 312767--312819 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
312757 ATTATTACTA
312767 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
312788 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
312809 TCGCAATGCGA
1 TCGCAATGCGA
312820 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:312852 original size:21 final size:21
Alignment explanation
Indices: 312809--312922 Score: 92
Period size: 21 Copynumber: 5.5 Consensus size: 21
312799 TTTTCCCAAT
* *
312809 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTAGAAAA
*
312829 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
* **
312850 TCGCAATGCG-ATACT-GACTA
1 TCGCAATGCGAAT-TTAGAAAA
* * *
312870 TCGCAACGCG-ATAATACAAAA
1 TCGCAATGCGAAT-TTAGAAAA
*
312891 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
312912 TCGCAATGCGA
1 TCGCAATGCGA
312923 TATTGACTAT
Statistics
Matches: 75, Mismatches: 15, Indels: 7
0.77 0.15 0.07
Matches are distributed among these distances:
20 30 0.40
21 43 0.57
22 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTTAGAAAA
Found at i:312860 original size:62 final size:60
Alignment explanation
Indices: 312809--312950 Score: 187
Period size: 62 Copynumber: 2.3 Consensus size: 60
312799 TTTTCCCAAT
* * *
312809 TCGCAATGCGAATAAGT-AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTA
1 TCGCAACGCG-ATAA-TAAAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTCACAA
* * *
312870 TCGCAACGCGATAATACAAAATCGCAATGCGAATTTGGAAAATCGCAATGCGATATTGACTA
1 TCGCAACGCGATAAT--AAAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTCACAA
312932 TCGCAACGCGATAATAAAA
1 TCGCAACGCGATAATAAAA
312951 AATCGCAACG
Statistics
Matches: 76, Mismatches: 2, Indels: 7
0.89 0.02 0.08
Matches are distributed among these distances:
59 1 0.01
60 8 0.11
61 9 0.12
62 58 0.76
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (60 bp):
TCGCAACGCGATAATAAAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTCACAA
Found at i:312936 original size:20 final size:20
Alignment explanation
Indices: 312849--313020 Score: 116
Period size: 20 Copynumber: 8.4 Consensus size: 20
312839 AATTTGGAAA
* *
312849 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATATTGACT
* *
312869 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATATTGAC--T
* **
312890 ATCGCAATGCGA-ATTTGGAAA
1 ATCGCAACGCGATA-TT-GACT
*
312911 ATCGCAATGCGATATTGACT
1 ATCGCAACGCGATATTGACT
** **
312931 ATCGCAACGCGATAATAAAAA
1 ATCGCAACGCGAT-ATTGACT
*
312952 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATATTGACT
* *
312972 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATATTGACT
*
312992 TTCGCAACGCGAT-TCTGACT
1 ATCGCAACGCGATAT-TGACT
*
313012 TTCGCAACG
1 ATCGCAACG
313021 AGATTCTGAC
Statistics
Matches: 124, Mismatches: 20, Indels: 16
0.77 0.12 0.10
Matches are distributed among these distances:
19 2 0.02
20 77 0.62
21 43 0.35
22 1 0.01
23 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATATTGACT
Found at i:312953 original size:62 final size:62
Alignment explanation
Indices: 312826--313004 Score: 254
Period size: 62 Copynumber: 2.9 Consensus size: 62
312816 GCGAATAAGT
*
312826 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
1 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAAA
*
312888 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATATTGACTATCGCAACGCGATAATAAA
1 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAAA
* * *** * *
312950 AAATCGCAACGCG-ATACT-GACTTTCGCAACGCGATACTGACTTTCGCAACGCGAT
1 AAATCGCAATGCGAAT-TTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGAT
313005 TCTGACTTTC
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
61 33 0.31
62 73 0.69
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (62 bp):
AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAAA
Found at i:312957 original size:21 final size:21
Alignment explanation
Indices: 312845--312965 Score: 95
Period size: 21 Copynumber: 5.9 Consensus size: 21
312835 TGCGAATTTG
* *
312845 GAAAATCGCAATGCGATACT-
1 GAAAATCGCAACGCGATAATA
**
312865 GACTATCGCAACGCGATAATA
1 GAAAATCGCAACGCGATAATA
* * * *
312886 CAAAATCGCAATGCGA-ATTTG
1 GAAAATCGCAACGCGATA-ATA
* *
312907 GAAAATCGCAATGCGAT-ATT
1 GAAAATCGCAACGCGATAATA
**
312927 GACTATCGCAACGCGATAATA
1 GAAAATCGCAACGCGATAATA
*
312948 AAAAATCGCAACGCGATA
1 GAAAATCGCAACGCGATA
312966 CTGACTTTCG
Statistics
Matches: 77, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
20 32 0.42
21 45 0.58
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (21 bp):
GAAAATCGCAACGCGATAATA
Found at i:312984 original size:41 final size:40
Alignment explanation
Indices: 312908--313020 Score: 136
Period size: 41 Copynumber: 2.8 Consensus size: 40
312898 GCGAATTTGG
* * *
312908 AAAATCGCAATGCGATATTGACTATCGCAACGCGATAATAA
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-A
* *
312949 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTG
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATA
*** *
312989 ACTTTCGCAACGCGATTCTGACTTTCGCAACG
1 AAAATCGCAACGCGATACTGACTTTCGCAACG
313021 AGATTCTGAC
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
40 28 0.44
41 35 0.56
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (40 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATA
Found at i:313036 original size:20 final size:20
Alignment explanation
Indices: 312912--313030 Score: 130
Period size: 20 Copynumber: 5.9 Consensus size: 20
312902 ATTTGGAAAA
* * *
312912 TCGCAATGCGATATTGACTA
1 TCGCAACGCGATACTGACTT
* * ***
312932 TCGCAACGCGATAATAAAAAA
1 TCGCAACGCGATACT-GACTT
312953 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
312973 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
312993 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
* *
313013 TCGCAACGAGATTCTGAC
1 TCGCAACGCGATACTGAC
313031 AATCGCTACG
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 70 0.81
21 16 0.19
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:313041 original size:20 final size:20
Alignment explanation
Indices: 312951--313044 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
312941 GATAATAAAA
* *
312951 AATCGCAACGCGATACTGAC
1 AATCGCAACGAGATTCTGAC
** * *
312971 TTTCGCAACGCGATACTGAC
1 AATCGCAACGAGATTCTGAC
** *
312991 TTTCGCAACGCGATTCTGAC
1 AATCGCAACGAGATTCTGAC
**
313011 TTTCGCAACGAGATTCTGAC
1 AATCGCAACGAGATTCTGAC
*
313031 AATCGCTACGAGAT
1 AATCGCAACGAGAT
313045 AATACAGAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (20 bp):
AATCGCAACGAGATTCTGAC
Found at i:313814 original size:24 final size:24
Alignment explanation
Indices: 313787--313840 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
313777 GTATTCGAAA
*
313787 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
313811 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
313835 TTTGAT
1 TTTGAT
313841 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:314032 original size:12 final size:12
Alignment explanation
Indices: 314015--314039 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
314005 ATATAATCCT
314015 GAAGAAGAAAAA
1 GAAGAAGAAAAA
314027 GAAGAAGAAAAA
1 GAAGAAGAAAAA
314039 G
1 G
314040 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:316371 original size:20 final size:19
Alignment explanation
Indices: 316343--316397 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
316333 CAATCATCTT
*
316343 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
316363 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
316382 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
316398 AGAGAATCGC
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:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:316412 original size:33 final size:33
Alignment explanation
Indices: 316370--316456 Score: 138
Period size: 33 Copynumber: 2.6 Consensus size: 33
316360 GGAAATGACT
316370 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
316403 ATCGCAATGCGAAATGAAAATCGTAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
316436 ATCACAAAGCGAAATGAAAAT
1 ATCGCAATGCGAAATGAAAAT
316457 TGTAACGCGA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:316485 original size:19 final size:19
Alignment explanation
Indices: 316463--316504 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
316453 AAATTGTAAC
316463 GCGAATTTAGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
* *
316482 GCGATTTTCGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
316501 GCGA
1 GCGA
316505 TTCGCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.12, C:0.19, G:0.29, T:0.40
Consensus pattern (19 bp):
GCGAATTTAGTTTCGCGTT
Found at i:316664 original size:14 final size:14
Alignment explanation
Indices: 316645--316681 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
316635 CATCAATTAA
316645 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
316659 ACAAATCATCTTTT
1 ACAAATCAACTTTT
316673 ACAAATCAA
1 ACAAATCAA
316682 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:318058 original size:21 final size:20
Alignment explanation
Indices: 318034--318094 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
318024 GTGAATCAGG
*
318034 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGG-C
* * **
318055 CTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGC
318076 CTCTTGAACGGTGGGAGGG
1 CTCTTGAACGGTGGGAGGG
318095 GACTCTCGAG
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.20, C:0.20, G:0.38, T:0.23
Consensus pattern (20 bp):
CTCTTGAACGGTGGGAGGGC
Found at i:318119 original size:42 final size:41
Alignment explanation
Indices: 318034--318156 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
318024 GTGAATCAGG
* * * *
318034 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
318076 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
318118 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
318157 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:318706 original size:94 final size:94
Alignment explanation
Indices: 318545--318849 Score: 512
Period size: 94 Copynumber: 3.3 Consensus size: 94
318535 GAATAGTTTC
* *
318545 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAATAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
318610 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
*
318639 AATTGGCAGCAACCGAATAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACAAACTTC
1 AATTGGCAGCAACCGAATAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
318704 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
*
318733 AATTGACAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTT
1 AATTGGCAGCAACCGAATAAATTTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTT
*
318797 CACAGTGTT----AATAAACAGTTTAGCAG
65 CACAGTGTTAAAGAATACACAGTTTAGCAG
*
318823 TATTGGCAGCAACCGAATAAATTTACT
1 AATTGGCAGCAACCGAATAAATTTACT
318850 AAGCAATCTA
Statistics
Matches: 201, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
90 40 0.20
93 19 0.09
94 142 0.71
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (94 bp):
AATTGGCAGCAACCGAATAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
ACAGTGTTAAAGAATACACAGTTTAGCAG
Found at i:320580 original size:14 final size:14
Alignment explanation
Indices: 320561--320616 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
320551 GGAAATGACT
320561 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
320575 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
320594 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
320608 ATCGCAACG
1 ATCGCAACG
320617 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:320598 original size:19 final size:19
Alignment explanation
Indices: 320532--320657 Score: 110
Period size: 19 Copynumber: 7.1 Consensus size: 19
320522 TCTTTTGGTT
*
320532 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAATGC
**
320551 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAATGC
*
320569 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
320585 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
* *
320602 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAATGC
*
320618 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAATGC
320637 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
320656 GA
1 GA
320658 TTTTGGTTTC
Statistics
Matches: 86, Mismatches: 10, Indels: 21
0.74 0.09 0.18
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 3 0.03
18 3 0.03
19 41 0.48
20 14 0.16
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:320598 original size:33 final size:33
Alignment explanation
Indices: 320540--320638 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
320530 TTGAAATGAA
**
320540 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
*
320574 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
320607 AATCGCAACGCGAAATGAAAATCGCAATGAGA
1 AATCGCAACGCGAAATGAAAATCGCAACGAGA
320639 AATGAAAATC
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 50 0.83
34 10 0.17
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:320688 original size:14 final size:14
Alignment explanation
Indices: 320669--320705 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
320659 TTTGGTTTCG
320669 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
320683 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
320697 CGTTGCGAT
1 CGTTGCGAT
320706 AGTCATTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:321283 original size:20 final size:20
Alignment explanation
Indices: 321258--321309 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
321248 GCTATGTAAA
321258 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
*
321278 TCGCATTGTGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
*
321298 TTGCATTGCGAT
1 TCGCATTGCGAT
321310 TTACGTATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAGAT
Found at i:321323 original size:20 final size:20
Alignment explanation
Indices: 321300--321389 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
321290 AGTCAGATTT
321300 GCATTGCGATTTACGTATTC
1 GCATTGCGATTTACGTATTC
* *
321320 GCATTGCGATTTTCCTAATTC
1 GCATTGCGATTTACGT-ATTC
* *
321341 GCATTGCGATTTACTTAATC
1 GCATTGCGATTTACGTATTC
*
321361 GCGTTGCGATTTACGTATTC
1 GCATTGCGATTTACGTATTC
321381 GCATTGCGA
1 GCATTGCGA
321390 ATTATGAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
20 42 0.70
21 18 0.30
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (20 bp):
GCATTGCGATTTACGTATTC
Found at i:321350 original size:41 final size:40
Alignment explanation
Indices: 321300--321389 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 40
321290 AGTCAGATTT
* *
321300 GCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTC
1 GCATTGCGATTTACGTAATCGCATTGCGATTTACCT-ATTC
* * *
321341 GCATTGCGATTTACTTAATCGCGTTGCGATTTACGTATTC
1 GCATTGCGATTTACGTAATCGCATTGCGATTTACCTATTC
321381 GCATTGCGA
1 GCATTGCGA
321390 ATTATGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 13 0.30
41 31 0.70
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (40 bp):
GCATTGCGATTTACGTAATCGCATTGCGATTTACCTATTC
Found at i:321402 original size:41 final size:41
Alignment explanation
Indices: 321318--321527 Score: 144
Period size: 41 Copynumber: 5.1 Consensus size: 41
321308 ATTTACGTAT
* * * *
321318 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACT--TAA
1 TCGCATTGCGATTTACGT-ATTCGCATTGCGAATTA-TGAAAA
*
321359 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTATGAAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGAATTATGAAAA
** * * * *
321400 TCGCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCATTGCGATTTACGT-ATTCGCATTGCGAATTATGAAAA
* * * * *
321441 TTGCATTGCGATAGT-CAGTA-TCGCATTGC-AATTTTCCAAAT
1 TCGCATTGCGAT-TTAC-GTATTCGCATTGCGAATTAT-GAAAA
* * **
321482 TCGCATTGCGATTTACTTATTCGTATTGCGAATTGGGAAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGAATTATGAAAA
321523 TCGCA
1 TCGCA
321528 ACGTAAAATT
Statistics
Matches: 130, Mismatches: 29, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
39 1 0.01
40 28 0.22
41 92 0.71
42 6 0.05
43 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGAATTATGAAAA
Found at i:321410 original size:21 final size:21
Alignment explanation
Indices: 321386--321441 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
321376 TATTCGCATT
*
321386 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
321407 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
321427 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
321442 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:321422 original size:61 final size:61
Alignment explanation
Indices: 321303--321423 Score: 138
Period size: 61 Copynumber: 2.0 Consensus size: 61
321293 CAGATTTGCA
* * * ** * *
321303 TTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACTTAATCGCG
1 TTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATACTAAATCGCG
*
321364 TTGCGATTTACGTATTCGCATTGCGAATTAT-GAAAATCGCAACGCGA-ATACGTAAATCGC
1 TTGCGATTTACGTATTCGCATTGCG-ATTATCCAAAATCGCAACGCGATATAC-TAAATCGC
321424 AATGCGAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 3 0.06
61 43 0.86
62 4 0.08
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (61 bp):
TTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATACTAAATCGCG
Found at i:321450 original size:21 final size:21
Alignment explanation
Indices: 321379--321451 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
321369 ATTTACGTAT
* *
321379 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
321400 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
321420 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
321441 TTGCATTGCGA
1 TCGCAATGCGA
321452 TAGTCAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:329469 original size:20 final size:21
Alignment explanation
Indices: 329444--329495 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
329434 TTTTCCCAAT
*
329444 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
329464 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
329485 TCGCAATGCGA
1 TCGCAATGCGA
329496 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:329509 original size:20 final size:20
Alignment explanation
Indices: 329484--329597 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
329474 AATTGGGAAA
*
329484 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
329504 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
329524 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
329545 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
329565 TTCGCAACGTGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
329585 TTCGCAACGCGAT
1 ATCGCAACGCGAT
329598 TTACATAGCG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:329528 original size:61 final size:61
Alignment explanation
Indices: 329481--329597 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
329471 GCGAATTGGG
* * * * *
329481 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
329542 AAAATCGCAACGAGATACTGACTTTCGCAACGTGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
329598 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:330176 original size:19 final size:19
Alignment explanation
Indices: 330152--330195 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
330142 GCAACAAGAG
*
330152 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
330171 AATCGC-ACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
330189 AATCGCA
1 AATCGCA
330196 TTGCGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:330213 original size:19 final size:19
Alignment explanation
Indices: 330191--330336 Score: 96
Period size: 19 Copynumber: 8.1 Consensus size: 19
330181 GAAACCAAAA
*
330191 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
330210 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
330229 TCGGGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
330243 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
330262 TTGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
330276 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
330295 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
330315 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
330335 TC
1 TC
330337 AACCAAAAGA
Statistics
Matches: 97, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
14 17 0.18
16 4 0.04
17 5 0.05
19 39 0.40
20 31 0.32
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:330261 original size:33 final size:33
Alignment explanation
Indices: 330224--330311 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
330214 GTTGCGATTT
*
330224 TCATTTCGGGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
330257 TCATTTTGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
330290 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
330312 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 36 0.72
34 14 0.28
ACGTcount: A:0.11, C:0.25, G:0.24, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:330313 original size:20 final size:20
Alignment explanation
Indices: 330279--330336 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
330269 GCGATTCTCT
**
330279 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
330299 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
330319 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
330337 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:332510 original size:21 final size:21
Alignment explanation
Indices: 332486--332636 Score: 58
Period size: 21 Copynumber: 7.2 Consensus size: 21
332476 TCATTCCTCG
332486 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** *
332507 AGAGGCCACTGTCATCC-CTCA
1 AGAGTCCCCTCCCA-CCGTTCA
* * * *
332528 AGAGTCCACTCCTATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
* ** *
332549 AGAGGCCCCTATCATTCC--TCG
1 AGAGTCCCCTCCCA--CCGTTCA
332570 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
332591 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
332612 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
332633 AGAG
1 AGAG
332637 CCCGATTCAC
Statistics
Matches: 86, Mismatches: 37, Indels: 15
0.62 0.27 0.11
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 78 0.91
22 3 0.03
23 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:332510 original size:42 final size:42
Alignment explanation
Indices: 332439--332636 Score: 202
Period size: 42 Copynumber: 4.7 Consensus size: 42
332429 GCCTGCCATC
* * * * * *
332439 CCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATT
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATT
* *
332481 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATC
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATT
* * * * * *
332523 CCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATT
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATT
*
332565 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCA-T
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATT
* * *
332606 CGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
332637 CCCGATTCAC
Statistics
Matches: 128, Mismatches: 26, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
41 4 0.03
42 122 0.95
43 2 0.02
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (42 bp):
CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATT
Found at i:332615 original size:84 final size:84
Alignment explanation
Indices: 332435--332606 Score: 344
Period size: 84 Copynumber: 2.0 Consensus size: 84
332425 ACTCGCCTGC
332435 CATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCA
1 CATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCA
332500 CCGTTCAAGAGGCCACTGT
66 CCGTTCAAGAGGCCACTGT
332519 CATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCA
1 CATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCA
332584 CCGTTCAAGAGGCCACTGT
66 CCGTTCAAGAGGCCACTGT
332603 CATC
1 CATC
332607 GTTGAAGAGG
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (84 bp):
CATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCA
CCGTTCAAGAGGCCACTGT
Found at i:332636 original size:84 final size:84
Alignment explanation
Indices: 332435--332636 Score: 289
Period size: 84 Copynumber: 2.4 Consensus size: 84
332425 ACTCGCCTGC
* * * *
332435 CATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCA
1 CATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCA
332500 CCGTTCAAGAGGCCACTGT
66 CCGTTCAAGAGGCCACTGT
* * * *
332519 CATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCA
1 CATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCA
332584 CCGTTCAAGAGGCCACTGT
66 CCGTTCAAGAGGCCACTGT
** *
332603 CATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
332637 CCCGATTCAC
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
84 106 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.22
Consensus pattern (84 bp):
CATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCA
CCGTTCAAGAGGCCACTGT
Done.