Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014446.1 Kokia drynarioides strain JFW-HI SEQ_129485, 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: 684930
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 166 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:309042 original size:28 final size:28
Alignment explanation
Indices: 309005--309064 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
308995 TTATATTATA
* **
309005 ATAAAAAAAATCATACATTACATTAAAT
1 ATAAAAAAAAGCATACACCACATTAAAT
* *
309033 ATAAATAAAAGCATACGCCACATTAAAT
1 ATAAAAAAAAGCATACACCACATTAAAT
309061 ATAA
1 ATAA
309065 CCCTTATCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.25
Consensus pattern (28 bp):
ATAAAAAAAAGCATACACCACATTAAAT
Found at i:309447 original size:3 final size:3
Alignment explanation
Indices: 309439--309464 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
309429 GAGAATAACC
309439 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
309465 CGAGATATTT
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:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:321208 original size:24 final size:25
Alignment explanation
Indices: 321181--321232 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
321171 TTTTGAGCAA
321181 TTTAA-TTT-TTTTCTTTTATGTTTT
1 TTTAACTTTCTTTT-TTTTATGTTTT
* *
321205 TTTAACTTTCTTTTTTTTCTTTTTT
1 TTTAACTTTCTTTTTTTTATGTTTT
321230 TTT
1 TTT
321233 TTCCATTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.21
25 15 0.62
26 4 0.17
ACGTcount: A:0.10, C:0.08, G:0.02, T:0.81
Consensus pattern (25 bp):
TTTAACTTTCTTTTTTTTATGTTTT
Found at i:321758 original size:23 final size:24
Alignment explanation
Indices: 321725--321770 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
321715 TATAAAAAAG
321725 TAAAAAATAAAA-ATACTTTTTTA
1 TAAAAAATAAAATATACTTTTTTA
* *
321748 TAAAAATTAAAATATATTTTTTT
1 TAAAAAATAAAATATACTTTTTT
321771 CATTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAAAAATAAAATATACTTTTTTA
Found at i:321785 original size:30 final size:31
Alignment explanation
Indices: 321741--321806 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
321731 ATAAAAATAC
* *
321741 TTTTTTATAAAAATTAAAATATATTTTTTTCA
1 TTTTTTAT-AAAATTAAAATATATGTTTTTAA
**
321773 TTTTTTAT-AAATTTTAATATATGTTTTTAA
1 TTTTTTATAAAATTAAAATATATGTTTTTAA
321803 TTTT
1 TTTT
321807 CAAGTGATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 22 0.73
32 8 0.27
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (31 bp):
TTTTTTATAAAATTAAAATATATGTTTTTAA
Found at i:323572 original size:5 final size:5
Alignment explanation
Indices: 323562--323601 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
323552 AAGAGACCGC
323562 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
323602 CTCCCTCTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:323912 original size:4 final size:4
Alignment explanation
Indices: 323903--323929 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
323893 ATCCTAAGTG
323903 TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TAT
323930 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:326261 original size:26 final size:26
Alignment explanation
Indices: 326224--326274 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
326214 TACTGGAGTA
* *
326224 AAATCGTCAAAATTTTGTCGAGGGTT
1 AAATCGTCAAAATTTTATCAAGGGTT
*
326250 AAATCGTTAAAATTTTATCAAGGGT
1 AAATCGTCAAAATTTTATCAAGGGT
326275 AAAAATTGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (26 bp):
AAATCGTCAAAATTTTATCAAGGGTT
Found at i:333275 original size:25 final size:25
Alignment explanation
Indices: 333222--333337 Score: 81
Period size: 25 Copynumber: 4.6 Consensus size: 25
333212 CTTTGGATTC
* * * *
333222 TGGCTTGTAAGAGCATAATTATGTC
1 TGGCTCGTAAGAGCATAATTCTATT
*
333247 TGGCTCGTAAGAGCGTAATTCTATT
1 TGGCTCGTAAGAGCATAATTCTATT
** * * *
333272 TGGCTCAAAAGAGCGTAATTTCTGTA
1 TGGCTCGTAAGAGCATAA-TTCTATT
*
333298 TGGCTCG-AGAGAGCAAAATTCTATCT
1 TGGCTCGTA-AGAGCATAATTCTAT-T
* *
333324 GGGCTCGTGAGAGC
1 TGGCTCGTAAGAGC
333338 TAAACTCTGT
Statistics
Matches: 71, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
25 42 0.59
26 29 0.41
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (25 bp):
TGGCTCGTAAGAGCATAATTCTATT
Found at i:333301 original size:26 final size:25
Alignment explanation
Indices: 333255--333321 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
333245 TCTGGCTCGT
*
333255 AAGAGCGTAATTCTATTTGGCTCAA
1 AAGAGCGTAATTCTATATGGCTCAA
* *
333280 AAGAGCGTAATTTCTGTATGGCTCGA
1 AAGAGCGTAA-TTCTATATGGCTCAA
* **
333306 GAGAGCAAAATTCTAT
1 AAGAGCGTAATTCTAT
333322 CTGGGCTCGT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 15 0.44
26 19 0.56
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (25 bp):
AAGAGCGTAATTCTATATGGCTCAA
Found at i:333357 original size:26 final size:26
Alignment explanation
Indices: 333298--333357 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
333288 AATTTCTGTA
* *
333298 TGGCTCGAGAGAGCAAAATTCTATCT
1 TGGCTCGTGAGAGCAAAACTCTATCT
* * *
333324 GGGCTCGTGAGAGCTAAACTCTGTCT
1 TGGCTCGTGAGAGCAAAACTCTATCT
333350 TGGCTCGT
1 TGGCTCGT
333358 TTGAGATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (26 bp):
TGGCTCGTGAGAGCAAAACTCTATCT
Found at i:334608 original size:19 final size:19
Alignment explanation
Indices: 334561--334601 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
334551 TTTTATTCAT
*
334561 GTGATGTAGAATTGTTTAG
1 GTGATGTAGAATTATTTAG
334580 GTGATGTAGAATTATTTAG
1 GTGATGTAGAATTATTTAG
334599 GTG
1 GTG
334602 CTTTAGATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.32, T:0.41
Consensus pattern (19 bp):
GTGATGTAGAATTATTTAG
Found at i:336706 original size:10 final size:10
Alignment explanation
Indices: 336691--336717 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
336681 TGTATAAATC
336691 ATACTTTGTT
1 ATACTTTGTT
336701 ATACTTTGTT
1 ATACTTTGTT
336711 ATACTTT
1 ATACTTT
336718 CACTTATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.59
Consensus pattern (10 bp):
ATACTTTGTT
Found at i:336932 original size:20 final size:20
Alignment explanation
Indices: 336908--337011 Score: 95
Period size: 20 Copynumber: 5.2 Consensus size: 20
336898 AGAGTGCATT
336908 CAGGGGCATC-GAAGTGCAAA
1 CAGGGGCA-CAGAAGTGCAAA
* * *
336928 TAGGGGCATAGATGTTG-AAA
1 CAGGGGCACAGAAG-TGCAAA
* * * *
336948 TAGGGGCACTGAAATGAAAA
1 CAGGGGCACAGAAGTGCAAA
*
336968 CAGGGGCACAGATGTGCAAA
1 CAGGGGCACAGAAGTGCAAA
*
336988 CAGGGGCACAGATGTGCAAA
1 CAGGGGCACAGAAGTGCAAA
337008 CAGG
1 CAGG
337012 AACACCAAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.03
20 65 0.94
21 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.35, T:0.13
Consensus pattern (20 bp):
CAGGGGCACAGAAGTGCAAA
Found at i:337009 original size:40 final size:39
Alignment explanation
Indices: 336908--337011 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 39
336898 AGAGTGCATT
* *
336908 CAGGGGCATCGAAGTGCAAATAGGGGCATAGATGTTGAAA
1 CAGGGGCA-CGAAGTGCAAACAGGGGCACAGATGTTGAAA
* * *
336948 TAGGGGCACTGAAATGAAAACAGGGGCACAGATG-TGCAAA
1 CAGGGGCAC-GAAGTGCAAACAGGGGCACAGATGTTG-AAA
*
336988 CAGGGGCACAGATGTGCAAACAGG
1 CAGGGGCAC-GAAGTGCAAACAGG
337012 AACACCAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
39 3 0.06
40 49 0.94
ACGTcount: A:0.37, C:0.15, G:0.35, T:0.13
Consensus pattern (39 bp):
CAGGGGCACGAAGTGCAAACAGGGGCACAGATGTTGAAA
Found at i:342080 original size:20 final size:21
Alignment explanation
Indices: 342037--342088 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
342027 AAAAATAGAA
* *
342037 TTCTACTGATAGAACTGTGAG
1 TTCTACCGATAGAACTCTGAG
*
342058 TTCTACCGATA-AACTCTGGG
1 TTCTACCGATAGAACTCTGAG
*
342078 TTCTATCGATA
1 TTCTACCGATA
342089 CAATTCAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (21 bp):
TTCTACCGATAGAACTCTGAG
Found at i:348835 original size:20 final size:20
Alignment explanation
Indices: 348809--348896 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
348799 GCCATACCGG
*
348809 AGTGCAAAAAGGGGCACAGA
1 AGTGCAAACAGGGGCACAGA
*
348829 TGTGCAAACAGGGGCACTA-A
1 AGTGCAAACAGGGGCAC-AGA
348849 AGTGCAAACAGGGGCACAG-
1 AGTGCAAACAGGGGCACAGA
* *
348868 -GTGTAAATAGGGGCACCA-A
1 AGTGCAAACAGGGGCA-CAGA
348887 AGTGCAAACA
1 AGTGCAAACA
348897 TGCAAAGATG
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
18 13 0.23
19 3 0.05
20 39 0.70
21 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.32, T:0.10
Consensus pattern (20 bp):
AGTGCAAACAGGGGCACAGA
Found at i:348889 original size:38 final size:39
Alignment explanation
Indices: 348809--348896 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 39
348799 GCCATACCGG
* *
348809 AGTGCAAAAAGGGGCACAGATGTGCAAACAGGGGCACTAA
1 AGTGCAAACAGGGGCACAGA-GTGCAAACAGGGGCACCAA
* *
348849 AGTGCAAACAGGGGCACAG-GTGTAAATAGGGGCACCAA
1 AGTGCAAACAGGGGCACAGAGTGCAAACAGGGGCACCAA
348887 AGTGCAAACA
1 AGTGCAAACA
348897 TGCAAAGATG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 26 0.59
40 18 0.41
ACGTcount: A:0.40, C:0.18, G:0.32, T:0.10
Consensus pattern (39 bp):
AGTGCAAACAGGGGCACAGAGTGCAAACAGGGGCACCAA
Found at i:349096 original size:2 final size:2
Alignment explanation
Indices: 349089--349113 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
349079 ATCAAAGTAC
349089 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 T
349114 CAATTAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:349517 original size:12 final size:12
Alignment explanation
Indices: 349500--349528 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
349490 ATATATATTT
349500 TAACTTTAAAAA
1 TAACTTTAAAAA
349512 TAACTTTAAAAA
1 TAACTTTAAAAA
349524 TAACT
1 TAACT
349529 AAATAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (12 bp):
TAACTTTAAAAA
Found at i:351570 original size:16 final size:17
Alignment explanation
Indices: 351549--351586 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
351539 AATAAATAAA
351549 TAAAAGGA-TTAAATTT
1 TAAAAGGATTTAAATTT
* *
351565 TAAAAGTATTTAATTTT
1 TAAAAGGATTTAAATTT
351582 TAAAA
1 TAAAA
351587 AGAAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (17 bp):
TAAAAGGATTTAAATTT
Found at i:354035 original size:15 final size:14
Alignment explanation
Indices: 354016--354143 Score: 55
Period size: 14 Copynumber: 8.9 Consensus size: 14
354006 TAATTCATAT
354016 TTTAATAATAATTA
1 TTTAATAATAATTA
* *
354030 TATTAAGAAT-GTTA
1 T-TTAATAATAATTA
* *
354044 TTAAATTATATATTA
1 TTTAATAATA-ATTA
* * *
354059 TTTTATTAACATTTA
1 -TTTAATAATAATTA
354074 TTTAATAATAATTA
1 TTTAATAATAATTA
*
354088 TGTCAA-AATATGATTA
1 T-TTAATAATA--ATTA
* * * *
354104 TTTATTTATTATTT
1 TTTAATAATAATTA
*
354118 TTTATTAA-AATATA
1 TTTAATAATAAT-TA
354132 TTTAATAATAAT
1 TTTAATAATAAT
354144 ATTATTAAAA
Statistics
Matches: 80, Mismatches: 24, Indels: 19
0.65 0.20 0.15
Matches are distributed among these distances:
13 7 0.09
14 39 0.49
15 21 0.26
16 13 0.16
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (14 bp):
TTTAATAATAATTA
Found at i:354083 original size:58 final size:58
Alignment explanation
Indices: 354012--354154 Score: 168
Period size: 58 Copynumber: 2.5 Consensus size: 58
354002 TTTTTAATTC
* *
354012 ATAT-TTTAATAATAATTATATTAAGA-ATG-TTATTAAATTATATATTATTTTATTAAC
1 ATATATTTAATAATAATTATATTAAAATATGATTATTAAATTAT-TATT-TTTTATTAAA
* * * * *
354069 ATTTATTTAATAATAATTATGTCAAAATATGATTATTTATTTATTATTTTTTATTAAA
1 ATATATTTAATAATAATTATATTAAAATATGATTATTAAATTATTATTTTTTATTAAA
354127 ATATATTTAATAATAA-TATTATTAAAAT
1 ATATATTTAATAATAATTA-TATTAAAAT
354155 TTAATAACAA
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
57 5 0.07
58 50 0.69
59 7 0.10
60 10 0.14
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (58 bp):
ATATATTTAATAATAATTATATTAAAATATGATTATTAAATTATTATTTTTTATTAAA
Found at i:354303 original size:21 final size:21
Alignment explanation
Indices: 354277--354316 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
354267 TAAAAATGCT
* *
354277 ATTACAATTTTATTTCATTCC
1 ATTACAACTCTATTTCATTCC
354298 ATTACAACTCTATTTCATT
1 ATTACAACTCTATTTCATT
354317 ACATCCCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTACAACTCTATTTCATTCC
Found at i:354318 original size:16 final size:16
Alignment explanation
Indices: 354293--354335 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
354283 ATTTTATTTC
*
354293 ATTCCATTACAACTCT
1 ATTCCATTACAACCCT
* *
354309 ATTTCATTACATCCCT
1 ATTCCATTACAACCCT
354325 ATTCCATTACA
1 ATTCCATTACA
354336 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTCCATTACAACCCT
Found at i:354616 original size:13 final size:13
Alignment explanation
Indices: 354598--354622 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
354588 TTTCAAGATT
354598 TTTTTAATTAATG
1 TTTTTAATTAATG
354611 TTTTTAATTAAT
1 TTTTTAATTAAT
354623 AAATATATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:365007 original size:15 final size:15
Alignment explanation
Indices: 364987--365020 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
364977 GGGTTTGGAC
364987 TTGGTTCAATTGAGT
1 TTGGTTCAATTGAGT
*
365002 TTGGTTCAATTGGGT
1 TTGGTTCAATTGAGT
365017 TTGG
1 TTGG
365021 GCTTAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.06, G:0.32, T:0.47
Consensus pattern (15 bp):
TTGGTTCAATTGAGT
Found at i:371013 original size:3 final size:3
Alignment explanation
Indices: 371007--371038 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
370997 CCAAAATCAA
371007 AAT AAT AAT AAT AAT AAT AA- AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
371039 TAAGTTTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:371182 original size:39 final size:38
Alignment explanation
Indices: 371128--371203 Score: 125
Period size: 39 Copynumber: 2.0 Consensus size: 38
371118 TAAAACCCAG
371128 TGTGTCTCTAAAGTACATACAACCTAATATACTTATAAA
1 TGTGTCTCTAAAGTACATACAACCTAATATAC-TATAAA
* *
371167 TGTGTCTCTAAAGTACATATAACCTAATGTACTATAA
1 TGTGTCTCTAAAGTACATACAACCTAATATACTATAA
371204 CTCAACATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 5 0.14
39 30 0.86
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.34
Consensus pattern (38 bp):
TGTGTCTCTAAAGTACATACAACCTAATATACTATAAA
Found at i:397675 original size:30 final size:30
Alignment explanation
Indices: 397641--397860 Score: 200
Period size: 30 Copynumber: 7.4 Consensus size: 30
397631 ATTTGAGGTG
* * *
397641 AAAATGTAATTTTTGGAAACTTTAGGGGTC
1 AAAATGTGATTTTAGGAAAGTTTAGGGGTC
*
397671 AAAATGTAACTTTT-GGAAAG--T-GGGGTC
1 AAAATGTGA-TTTTAGGAAAGTTTAGGGGTC
* * * *
397698 AAAATATGATTTTGGGAAAGCTTGGGGGTC
1 AAAATGTGATTTTAGGAAAGTTTAGGGGTC
** *
397728 AAAATGTGATTTTAAGG-AAGTTTAACGGTT
1 AAAATGTGATTTT-AGGAAAGTTTAGGGGTC
* *
397758 AAAATGTGATTTTAGAAAAGTTTATGGGGTT
1 AAAATGTGATTTTAGGAAAGTTTA-GGGGTC
* *
397789 AAAATGTGATTTTGGGAAAGTTTA-GGGTT
1 AAAATGTGATTTTAGGAAAGTTTAGGGGTC
* **
397818 AAAATGTAATTTTAGGAAAGTTTATAGGTC
1 AAAATGTGATTTTAGGAAAGTTTAGGGGTC
*
397848 AAAATATGATTTT
1 AAAATGTGATTTT
397861 GAGAAAATTC
Statistics
Matches: 160, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.03
27 19 0.12
28 1 0.01
29 30 0.19
30 74 0.46
31 32 0.20
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAATGTGATTTTAGGAAAGTTTAGGGGTC
Found at i:397715 original size:27 final size:28
Alignment explanation
Indices: 397665--397740 Score: 93
Period size: 27 Copynumber: 2.7 Consensus size: 28
397655 GGAAACTTTA
*
397665 GGGGTCAAAATGTAACTTTTGGAAAG-T-
1 GGGGTCAAAATGTGA-TTTTGGAAAGCTG
*
397692 GGGGTCAAAATATGATTTTGGGAAAGCTTG
1 GGGGTCAAAATGTGATTTT-GGAAAGC-TG
397722 GGGGTCAAAATGTGATTTT
1 GGGGTCAAAATGTGATTTT
397741 AAGGAAGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.10
27 19 0.45
29 1 0.02
30 18 0.43
ACGTcount: A:0.30, C:0.07, G:0.32, T:0.32
Consensus pattern (28 bp):
GGGGTCAAAATGTGATTTTGGAAAGCTG
Found at i:397829 original size:29 final size:29
Alignment explanation
Indices: 397641--397911 Score: 174
Period size: 30 Copynumber: 9.2 Consensus size: 29
397631 ATTTGAGGTG
* * *
397641 AAAATGTAATTTTTGGAAACTTTAGGGGTC
1 AAAATGTGATTTTGGGAAAGTTTA-GGGTC
* *
397671 AAAATGTAACTTTT-GGAAAG--TGGGGTC
1 AAAATGTGA-TTTTGGGAAAGTTTAGGGTC
* **
397698 AAAATATGATTTTGGGAAAGCTTGGGGGTC
1 AAAATGTGATTTTGGGAAAG-TTTAGGGTC
* * *
397728 AAAATGTGATTTTAAGG-AAGTTTAACGGTT
1 AAAATGTGATTTT-GGGAAAGTTT-AGGGTC
* * *
397758 AAAATGTGATTTTAGAAAAGTTTATGGGGTT
1 AAAATGTGATTTTGGGAAAGTTTA--GGGTC
*
397789 AAAATGTGATTTTGGGAAAGTTTAGGGTT
1 AAAATGTGATTTTGGGAAAGTTTAGGGTC
* * *
397818 AAAATGTAATTTTAGGAAAGTTTATAGGTC
1 AAAATGTGATTTTGGGAAAGTTTA-GGGTC
* * * *
397848 AAAATATGATTTTGAGAAAATTCT-GGGTT
1 AAAATGTGATTTTGGGAAAGTT-TAGGGTC
* * * * *
397877 AAAATATAATTTTGGAAAATTTTATAGGTC
1 AAAATGTGATTTTGGGAAAGTTTA-GGGTC
397907 AAAAT
1 AAAAT
397912 ATGGTTTTTT
Statistics
Matches: 195, Mismatches: 32, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
26 4 0.02
27 18 0.09
28 2 0.01
29 53 0.27
30 85 0.44
31 33 0.17
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
AAAATGTGATTTTGGGAAAGTTTAGGGTC
Found at i:397881 original size:59 final size:59
Alignment explanation
Indices: 397724--397919 Score: 207
Period size: 59 Copynumber: 3.3 Consensus size: 59
397714 AAAGCTTGGG
* * * * * * * *
397724 GGTCAAAATGTGATTTTAAGGAAGTTTAACGGTTAAAATGTGATTTTAGAAAAGTTTATGG
1 GGTCAAAATATGATTTTGAGAAAATTT-AGGGTTAAAATGTAATTTTAGGAAAGTTTAT-A
* * * *
397785 GGTTAAAATGTGATTTTGGGAAAGTTTAGGGTTAAAATGTAATTTTAGGAAAGTTTATA
1 GGTCAAAATATGATTTTGAGAAAATTTAGGGTTAAAATGTAATTTTAGGAAAGTTTATA
* *
397844 GGTCAAAATATGATTTTGAGAAAATTCT-GGGTTAAAATATAATTTT-GGAAAATTTTATA
1 GGTCAAAATATGATTTTGAGAAAATT-TAGGGTTAAAATGTAATTTTAGG-AAAGTTTATA
*
397903 GGTCAAAATATGGTTTT
1 GGTCAAAATATGATTTT
397920 TTTGAAAGTT
Statistics
Matches: 118, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
58 2 0.02
59 64 0.54
60 29 0.25
61 23 0.19
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (59 bp):
GGTCAAAATATGATTTTGAGAAAATTTAGGGTTAAAATGTAATTTTAGGAAAGTTTATA
Found at i:402298 original size:43 final size:43
Alignment explanation
Indices: 402201--402509 Score: 374
Period size: 43 Copynumber: 7.2 Consensus size: 43
402191 TTATGAGGAA
* *
402201 AAACGCCGCTATAGAACATGGTCTTTAGCGGCGCTTAT-CCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * *
402243 AAACGCCGCTAAAGAACATGGCCTTTAGCAGTGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* *
402286 AAACACCGCTAAAGAACATGGTCTTTAGCGGCTC-TTTCTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTC-CCAC
* * * *
402329 CAACGCCGCTAAGGAACTTGGTCTTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * * *
402372 AGACGTCGCGAAAGAACATGGTCTTTAACGGTGC-TTTCCCAAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCC-AC
* *
402415 AAACGCTGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* *
402458 AAACGTCGCTAAAGAACATGGTCTTTAGTGGCG-TTTCTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTT-TCCCAC
*
402501 AAACTCCGC
1 AAACGCCGC
402510 GAAAATTAAT
Statistics
Matches: 223, Mismatches: 38, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
42 45 0.20
43 169 0.76
44 9 0.04
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
Found at i:405191 original size:19 final size:19
Alignment explanation
Indices: 405169--405210 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
405159 GTTATATAAG
*
405169 TTTT-AAATTTTAATAATTT
1 TTTTAAAATTTT-AGAATTT
405188 TTTTAAAATTTTAGAATTT
1 TTTTAAAATTTTAGAATTT
405207 TTTT
1 TTTT
405211 TAGTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTAAAATTTTAGAATTT
Found at i:405367 original size:41 final size:41
Alignment explanation
Indices: 405322--405541 Score: 316
Period size: 41 Copynumber: 5.4 Consensus size: 41
405312 CTATTGTTTA
* * * **
405322 ACCTTTAGCGGCGCTTGCCCAAAAACACCATTATTGCTCTG
1 ACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTG
* *
405363 ACCTTTAGCGACGCTTGCCCATAAGCGCTGCTATTGCTCTG
1 ACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTG
* * **
405404 ACTTTTAGTGGCGCTTGCCCATAAGTACCGCTATTGCTCTG
1 ACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTG
*
405445 ACCTTTAGCGGCGCTT-CCCATAAGCGCCGCTATTGCTTTG
1 ACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTG
*
405485 ACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTTTG
1 ACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTG
405526 ACCTTTAGCGGCGCTT
1 ACCTTTAGCGGCGCTT
405542 ATGGGAAAGC
Statistics
Matches: 160, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 37 0.23
41 123 0.77
ACGTcount: A:0.17, C:0.31, G:0.22, T:0.30
Consensus pattern (41 bp):
ACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTG
Found at i:405494 original size:24 final size:24
Alignment explanation
Indices: 405467--405540 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 24
405457 GCTTCCCATA
405467 AGCGCCGCTATTGCTTTGACCTTT
1 AGCGCCGCTATTGCTTTGACCTTT
* * *
405491 AGCG--GC----GC-TTGCCCATA
1 AGCGCCGCTATTGCTTTGACCTTT
405508 AGCGCCGCTATTGCTTTGACCTTT
1 AGCGCCGCTATTGCTTTGACCTTT
*
405532 AGCGGCGCT
1 AGCGCCGCT
405541 TATGGGAAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 14
0.63 0.12 0.25
Matches are distributed among these distances:
17 10 0.28
18 2 0.06
19 2 0.06
22 2 0.06
23 2 0.06
24 18 0.50
ACGTcount: A:0.14, C:0.31, G:0.26, T:0.30
Consensus pattern (24 bp):
AGCGCCGCTATTGCTTTGACCTTT
Found at i:405505 original size:81 final size:82
Alignment explanation
Indices: 405310--405541 Score: 333
Period size: 81 Copynumber: 2.9 Consensus size: 82
405300 GAAAAAACGT
* * * ** *
405310 CGCTATTG-TTTAACCTTTAGCGGCGCTTGCCCAAAAACACCATTATTGCTCTGACCTTTAGCGA
1 CGCTATTGCTTTGACCTTTAGCGGCGCTTGCCCATAAGCACCGCTATTGCTCTGACCTTTAGCGG
405374 CGCTTGCCCATAAGCGC
66 CGCTTGCCCATAAGCGC
* * * * *
405391 TGCTATTGCTCTGACTTTTAGTGGCGCTTGCCCATAAGTACCGCTATTGCTCTGACCTTTAGCGG
1 CGCTATTGCTTTGACCTTTAGCGGCGCTTGCCCATAAGCACCGCTATTGCTCTGACCTTTAGCGG
405456 CGCTT-CCCATAAGCGC
66 CGCTTGCCCATAAGCGC
* *
405472 CGCTATTGCTTTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTTTGACCTTTAGCGG
1 CGCTATTGCTTTGACCTTTAGCGGCGCTTGCCCATAAGCACCGCTATTGCTCTGACCTTTAGCGG
405537 CGCTT
66 CGCTT
405542 ATGGGAAAGC
Statistics
Matches: 132, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
81 81 0.61
82 51 0.39
ACGTcount: A:0.17, C:0.30, G:0.22, T:0.31
Consensus pattern (82 bp):
CGCTATTGCTTTGACCTTTAGCGGCGCTTGCCCATAAGCACCGCTATTGCTCTGACCTTTAGCGG
CGCTTGCCCATAAGCGC
Found at i:405557 original size:41 final size:40
Alignment explanation
Indices: 405322--405578 Score: 277
Period size: 41 Copynumber: 6.3 Consensus size: 40
405312 CTATTGTTTA
* * **
405322 ACCTTTAGCGGCGCTTGCCCAAAAACACCATTATTGCTCTG
1 ACCTTTAGCGGCGCTTG-CCATAAGCACCGCTATTGCTCTG
* * *
405363 ACCTTTAGCGACGCTTGCCCATAAGCGCTGCTATTGCTCTG
1 ACCTTTAGCGGCGCTTG-CCATAAGCACCGCTATTGCTCTG
* * *
405404 ACTTTTAGTGGCGCTTGCCCATAAGTACCGCTATTGCTCTG
1 ACCTTTAGCGGCGCTTG-CCATAAGCACCGCTATTGCTCTG
* * *
405445 ACCTTTAGCGGCGCTTCCCATAAGCGCCGCTATTGCTTTG
1 ACCTTTAGCGGCGCTTGCCATAAGCACCGCTATTGCTCTG
* *
405485 ACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTTTG
1 ACCTTTAGCGGCGCTTG-CCATAAGCACCGCTATTGCTCTG
**
405526 ACCTTTAGCGGCGCTTATGGGA-AAGCACCGCTATTGCTCT-
1 ACCTTTAGCGGCGC-T-TGCCATAAGCACCGCTATTGCTCTG
405566 ACCCTTT-GCGGCG
1 A-CCTTTAGCGGCG
405579 TTTATGTAAA
Statistics
Matches: 188, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
40 43 0.23
41 141 0.75
42 2 0.01
43 2 0.01
ACGTcount: A:0.18, C:0.31, G:0.23, T:0.29
Consensus pattern (40 bp):
ACCTTTAGCGGCGCTTGCCATAAGCACCGCTATTGCTCTG
Found at i:405600 original size:122 final size:122
Alignment explanation
Indices: 405322--405578 Score: 324
Period size: 122 Copynumber: 2.1 Consensus size: 122
405312 CTATTGTTTA
* * *
405322 ACCTTTAGCGGCGCTTGCCCAAAAACACCATTATTGCTCTGACCTTTAGCGACGCTTGCCCATAA
1 ACCTTTAGCGGCGCTT-CCCAAAAACGCCACTATTGCTTTGACCTTTAGCGACGCTTGCCCATAA
* * * *
405387 GCGCTGCTATTGCTCTGACTTTTAGTGGCGCTTGCCCATAAGTACCGCTATTGCTCTG
65 GCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCACCGCTATTGCTCTG
* * * *
405445 ACCTTTAGCGGCGCTTCCCATAAGCGCCGCTATTGCTTTGACCTTTAGCGGCGCTTGCCCATAAG
1 ACCTTTAGCGGCGCTTCCCAAAAACGCCACTATTGCTTTGACCTTTAGCGACGCTTGCCCATAAG
* **
405510 CGCCGCTATTGCTTTGACCTTTAGCGGCGCTTATG-GGA-AAGCACCGCTATTGCTCT-
66 CGCCGCTATTGCTCTGACCTTTAGCGGCGC-T-TGCCCATAAGCACCGCTATTGCTCTG
405566 ACCCTTT-GCGGCG
1 A-CCTTTAGCGGCG
405579 TTTATGTAAA
Statistics
Matches: 117, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
121 7 0.06
122 90 0.77
123 18 0.15
124 2 0.02
ACGTcount: A:0.18, C:0.31, G:0.23, T:0.29
Consensus pattern (122 bp):
ACCTTTAGCGGCGCTTCCCAAAAACGCCACTATTGCTTTGACCTTTAGCGACGCTTGCCCATAAG
CGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCACCGCTATTGCTCTG
Found at i:407102 original size:16 final size:16
Alignment explanation
Indices: 407081--407113 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
407071 TTAATCTAAC
407081 ACACTTATATCATAAT
1 ACACTTATATCATAAT
*
407097 ACACTTATGTCATAAT
1 ACACTTATATCATAAT
407113 A
1 A
407114 ATTAAACTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.36
Consensus pattern (16 bp):
ACACTTATATCATAAT
Found at i:409209 original size:19 final size:18
Alignment explanation
Indices: 409185--409220 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
409175 TTCCTTCTTT
409185 GAATATCCTTAAAAAATAC
1 GAATAT-CTTAAAAAATAC
*
409204 GAATATTTTAAAAAATA
1 GAATATCTTAAAAAATA
409221 TATACTAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.31
Consensus pattern (18 bp):
GAATATCTTAAAAAATAC
Found at i:412211 original size:2 final size:2
Alignment explanation
Indices: 412204--412239 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
412194 TTAATTGTTG
412204 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
412240 CGTTAATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:412381 original size:11 final size:11
Alignment explanation
Indices: 412365--412389 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
412355 CGTTTTTCAA
412365 AAATTCTAAAG
1 AAATTCTAAAG
412376 AAATTCTAAAG
1 AAATTCTAAAG
412387 AAA
1 AAA
412390 ACATATGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (11 bp):
AAATTCTAAAG
Found at i:417937 original size:2 final size:2
Alignment explanation
Indices: 417932--417967 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
417922 AGCGTGCGCG
*
417932 CA CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
417968 TATATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:418661 original size:34 final size:34
Alignment explanation
Indices: 418618--418686 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
418608 AGTGTGTTGT
418618 TAAAGTGTATACATCCACAGTCACAATATCACAA
1 TAAAGTGTATACATCCACAGTCACAATATCACAA
418652 TAAAGTGTATACATCCACAGTCACAATATCACAA
1 TAAAGTGTATACATCCACAGTCACAATATCACAA
418686 T
1 T
418687 CATTCATAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (34 bp):
TAAAGTGTATACATCCACAGTCACAATATCACAA
Found at i:421175 original size:14 final size:15
Alignment explanation
Indices: 421133--421177 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
421123 ACATAAGCAT
421133 AATGCAATATCACAC
1 AATGCAATATCACAC
*
421148 AATG-AA-CTCAACAC
1 AATGCAATATC-ACAC
421162 AA-GCAATATCACAC
1 AATGCAATATCACAC
421176 AA
1 AA
421178 AAGGATGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
13 3 0.12
14 16 0.64
15 6 0.24
ACGTcount: A:0.51, C:0.27, G:0.07, T:0.16
Consensus pattern (15 bp):
AATGCAATATCACAC
Found at i:423807 original size:29 final size:29
Alignment explanation
Indices: 423761--423882 Score: 181
Period size: 29 Copynumber: 4.2 Consensus size: 29
423751 AACTGCAACT
423761 ATTTTACAGTTTTGCCACTGGTTTTCTAG
1 ATTTTACAGTTTTGCCACTGGTTTTCTAG
* * *
423790 ATTTTACAGTTTTACCACTAGTTTTCCAG
1 ATTTTACAGTTTTGCCACTGGTTTTCTAG
* * *
423819 ATTTTACAATTTTGTCATTGGTTTTCTAG
1 ATTTTACAGTTTTGCCACTGGTTTTCTAG
*
423848 ATTTTTCAGTTTTGCCACTGGTTTTCTAG
1 ATTTTACAGTTTTGCCACTGGTTTTCTAG
423877 ATTTTA
1 ATTTTA
423883 TAAATTTGCC
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 79 1.00
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.51
Consensus pattern (29 bp):
ATTTTACAGTTTTGCCACTGGTTTTCTAG
Found at i:423810 original size:21 final size:21
Alignment explanation
Indices: 423786--423825 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
423776 CACTGGTTTT
423786 CTAGATTTTACAG-TTTTACCA
1 CTAG-TTTTACAGATTTTACCA
*
423807 CTAGTTTTCCAGATTTTAC
1 CTAGTTTTACAGATTTTAC
423826 AATTTTGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (21 bp):
CTAGTTTTACAGATTTTACCA
Found at i:423901 original size:29 final size:29
Alignment explanation
Indices: 423761--423902 Score: 149
Period size: 29 Copynumber: 4.9 Consensus size: 29
423751 AACTGCAACT
* *
423761 ATTTTACAGTTTTGCCACTGGTTTTCTAG
1 ATTTTACAATTTTGCCACTAGTTTTCTAG
* * *
423790 ATTTTACAGTTTTACCACTAGTTTTCCAG
1 ATTTTACAATTTTGCCACTAGTTTTCTAG
* * *
423819 ATTTTACAATTTTGTCATTGGTTTTCTAG
1 ATTTTACAATTTTGCCACTAGTTTTCTAG
* * *
423848 ATTTTTCAGTTTTGCCACTGGTTTTCTAG
1 ATTTTACAATTTTGCCACTAGTTTTCTAG
* * * *
423877 ATTTTATAAATTTGCCATTATTTTTC
1 ATTTTACAATTTTGCCACTAGTTTTC
423903 AAAAGAATTA
Statistics
Matches: 93, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 93 1.00
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.51
Consensus pattern (29 bp):
ATTTTACAATTTTGCCACTAGTTTTCTAG
Found at i:423902 original size:58 final size:58
Alignment explanation
Indices: 423761--423902 Score: 167
Period size: 58 Copynumber: 2.4 Consensus size: 58
423751 AACTGCAACT
** * *
423761 ATTTTACAGTTTTGCCACTGGTTTTCTAGATTTTACAGTTTTACCACTAGTTTTCCAG
1 ATTTTACAAATTTGCCATTAGTTTTCTAGATTTTACAGTTTTACCACTAGTTTTCCAG
* * * * * * *
423819 ATTTTACAATTTTGTCATTGGTTTTCTAGATTTTTCAGTTTTGCCACTGGTTTTCTAG
1 ATTTTACAAATTTGCCATTAGTTTTCTAGATTTTACAGTTTTACCACTAGTTTTCCAG
* *
423877 ATTTTATAAATTTGCCATTATTTTTC
1 ATTTTACAAATTTGCCATTAGTTTTC
423903 AAAAGAATTA
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 72 1.00
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.51
Consensus pattern (58 bp):
ATTTTACAAATTTGCCATTAGTTTTCTAGATTTTACAGTTTTACCACTAGTTTTCCAG
Found at i:424426 original size:45 final size:45
Alignment explanation
Indices: 424377--425210 Score: 1087
Period size: 45 Copynumber: 18.6 Consensus size: 45
424367 GCTATACGAC
* * *
424377 ATGGTAAATATTATTTGATTGACTATACTATACGGTATGCATGAT
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
* * *
424422 ATGGTAAATATTATTAT-ATTAAGTATTCTATACGATATGCATGAT
1 ATGGTAAATATTATT-TGATTGATTATGCTATACGATATGCATGAT
* * **
424467 ATGATAAATATTATTTGATTAATTATAATATACGATATGCATGAT
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
* *
424512 ATGGTAAA-AGTTATTTGATTGATTATGCTATACGAGATGTATGAT
1 ATGGTAAATA-TTATTTGATTGATTATGCTATACGATATGCATGAT
*
424557 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAC
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
* * *
424602 ATGATAAGTATTATTTGATTGATTATGCTATACGATATGTATGAT
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
* * * *
424647 ATGGTAAATATTATTTGATTGATTATGCTATATGGATTTGCTTGAC
1 ATGGTAAATATTATTTGATTGATTATGCTATA-CGATATGCATGAT
*
424693 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGTATGAT
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
** *
424738 AAAGTAAATATTATTTGATTGA-T-T--T-T--G-TATGCATGAC
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
* * *
424775 GTGGTAAATATTATTTGATTGATTATGTTATACGATATGTATGAT
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
* * **
424820 GTGGTAAATATTATTGGATTGATTATGCTATATAATATGCATGAT
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
* **
424865 ATGGTCAAA-ATTATTTAATTGATTATGCTATACGATATGCATGGC
1 ATGGT-AAATATTATTTGATTGATTATGCTATACGATATGCATGAT
* **
424910 ATGGTAAATATTTTTTGATTGATTATGCTATACGATATGCATGGC
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
* *
424955 ATGGTAAATATTATTTGATCGATTATGCTATACGATATGTATGAT
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
*
425000 ATGGTAAATATTATTGGATTGATTATGCTATACGATATGCATGAT
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
* *
425045 ATGGTAAATGTTATTTGATTGATTATGCTATACGATATGCATGAC
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
* * *
425090 ATTGTATATATTATTTGATTGATTGATTATGCTATACGATATGTATGAT
1 ATGGTAAATATTA--T--TTGATTGATTATGCTATACGATATGCATGAT
425139 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
* * *
425184 GTGGTAAATACTATTTGATTAATTATG
1 ATGGTAAATATTATTTGATTGATTATG
425211 ATATGGTAAA
Statistics
Matches: 692, Mismatches: 78, Indels: 38
0.86 0.10 0.05
Matches are distributed among these distances:
37 27 0.04
38 2 0.00
39 1 0.00
40 1 0.00
41 2 0.00
42 1 0.00
43 1 0.00
44 7 0.01
45 563 0.81
46 45 0.07
47 2 0.00
49 40 0.06
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (45 bp):
ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGAT
Found at i:424526 original size:135 final size:135
Alignment explanation
Indices: 424377--425373 Score: 1238
Period size: 135 Copynumber: 7.5 Consensus size: 135
424367 GCTATACGAC
* * *
424377 ATGGTAAATATTATTTGATTGACTATACTATACGGTATGCATGATATGGTAAATATTATTAT-AT
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTATT-TGAT
* * * * * **
424441 TAAGTATTCTATACGATATGCATGATATGATAAATATTATTTGATTAATTATAATATACGATATG
65 TGATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACGATATG
424506 CATGAT
130 CATGAT
* *
424512 ATGGTAAA-AGTTATTTGATTGATTATGCTATACGAGATGTATGATATGGTAAATATTATTTGAT
1 ATGGTAAATA-TTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTATTTGAT
* * *
424576 TGATTATGCTATACGATATGCATGACATGATAAGTATTATTTGATTGATTATGCTATACGATATG
65 TGATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACGATATG
*
424641 TATGAT
130 CATGAT
* * * *
424647 ATGGTAAATATTATTTGATTGATTATGCTATATGGATTTGCTTGACATGGTAAATATTATTTGAT
1 ATGGTAAATATTATTTGATTGATTATGCTATA-CGATATGCATGATATGGTAAATATTATTTGAT
* **
424712 TGATTATGCTATACGATATGTATGATAAAGTAAATATTATTTGATTGA-T-T--T-T--G-TATG
65 TGATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACGATATG
*
424769 CATGAC
130 CATGAT
* * * * *
424775 GTGGTAAATATTATTTGATTGATTATGTTATACGATATGTATGATGTGGTAAATATTATTGGATT
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATT
** *
424840 GATTATGCTATATAATATGCATGATATGGTCAAA-ATTATTTAATTGATTATGCTATACGATATG
66 GATTATGCTATACGATATGCATGATATGGT-AAATATTATTTGATTGATTATGCTATACGATATG
**
424904 CATGGC
130 CATGAT
* ** *
424910 ATGGTAAATATTTTTTGATTGATTATGCTATACGATATGCATGGCATGGTAAATATTATTTGATC
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATT
* *
424975 GATTATGCTATACGATATGTATGATATGGTAAATATTATTGGATTGATTATGCTATACGATATGC
66 GATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACGATATGC
425040 ATGAT
131 ATGAT
* * * *
425045 ATGGTAAATGTTATTTGATTGATTATGCTATACGATATGCATGACATTGTATATATTATTTGATT
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTA--T--TT
*
425110 GATTGATTATGCTATACGATATGTATGATATGGTAAATATTATTTGATTGATTATGCTATACGAT
62 GATTGATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACGAT
425175 ATGCATGAT
127 ATGCATGAT
* *
425184 GTGGTAAATACTA--T--TTG---A---T-TA--AT-T--ATGATATGGTAAATATTATTTGATT
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATT
* *
425233 AAGTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACGATATGC
66 GATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACGATATGC
425298 ATGAT
131 ATGAT
* ** ***
425303 GTGGTAAATATTATTTGATTGATTATATTATACGATATATGTGATATGGTAAATATTATTTGATT
1 ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATT
425368 GATTAT
66 GATTAT
425374 ACCATACAAC
Statistics
Matches: 748, Mismatches: 80, Indels: 68
0.83 0.09 0.08
Matches are distributed among these distances:
119 85 0.11
121 2 0.00
123 18 0.02
125 1 0.00
126 3 0.00
127 63 0.08
128 44 0.06
129 4 0.01
130 2 0.00
131 2 0.00
132 5 0.01
133 1 0.00
134 7 0.01
135 356 0.48
136 69 0.09
137 2 0.00
139 84 0.11
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (135 bp):
ATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATT
GATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACGATATGC
ATGAT
Found at i:425212 original size:29 final size:29
Alignment explanation
Indices: 425179--425239 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
425169 TACGATATGC
* *
425179 ATGATGTGGTAAATACTATTTGATTAATT
1 ATGATATGGTAAATACTATTTGATTAAGT
*
425208 ATGATATGGTAAATATTATTTGATTAAGT
1 ATGATATGGTAAATACTATTTGATTAAGT
425237 ATG
1 ATG
425240 CTATACGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.44
Consensus pattern (29 bp):
ATGATATGGTAAATACTATTTGATTAAGT
Found at i:425254 original size:74 final size:74
Alignment explanation
Indices: 425133--425284 Score: 259
Period size: 74 Copynumber: 2.1 Consensus size: 74
425123 ATACGATATG
* * *
425133 TATGATATGGTAAATATTATTTGATTGATTATGCTATACGATATGCATGATGTGGTAAATACTAT
1 TATGATATGGTAAATATTATTTGATTAAGTATGCTATACGATATGCATGATATGGTAAATACTAT
425198 TTGATTAAT
66 TTGATTAAT
*
425207 TATGATATGGTAAATATTATTTGATTAAGTATGCTATACGATATGCATGATATGGTAAATATTAT
1 TATGATATGGTAAATATTATTTGATTAAGTATGCTATACGATATGCATGATATGGTAAATACTAT
*
425272 TTGATTGAT
66 TTGATTAAT
425281 TATG
1 TATG
425285 CTATACGATA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (74 bp):
TATGATATGGTAAATATTATTTGATTAAGTATGCTATACGATATGCATGATATGGTAAATACTAT
TTGATTAAT
Found at i:425272 original size:45 final size:45
Alignment explanation
Indices: 425208--425373 Score: 260
Period size: 45 Copynumber: 3.7 Consensus size: 45
425198 TTGATTAATT
* *
425208 ATGATATGGTAAATATTATTTGATTAAGTATGCTATACGATATGC
1 ATGATATGGTAAATATTATTTGATTGATTATGCTATACGATATGC
425253 ATGATATGGTAAATATTATTTGATTGATTATGCTATACGATATGC
1 ATGATATGGTAAATATTATTTGATTGATTATGCTATACGATATGC
* ** **
425298 ATGATGTGGTAAATATTATTTGATTGATTATATTATACGATATAT
1 ATGATATGGTAAATATTATTTGATTGATTATGCTATACGATATGC
*
425343 GTGATATGGTAAATATTATTTGATTGATTAT
1 ATGATATGGTAAATATTATTTGATTGATTAT
425374 ACCATACAAC
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 112 1.00
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.44
Consensus pattern (45 bp):
ATGATATGGTAAATATTATTTGATTGATTATGCTATACGATATGC
Found at i:425312 original size:119 final size:119
Alignment explanation
Indices: 425108--425328 Score: 397
Period size: 119 Copynumber: 1.9 Consensus size: 119
425098 TATTATTTGA
* * *
425108 TTGATTGATTATGCTATACGATATGTATGATATGGTAAATATTATTTGATTGATTATGCTATACG
1 TTGATTAAGTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACG
425173 ATATGCATGATGTGGTAAATACTATTTGATTAATTATGATATGGTAAATATTAT
66 ATATGCATGATGTGGTAAATACTATTTGATTAATTATGATATGGTAAATATTAT
425227 TTGATTAAGTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACG
1 TTGATTAAGTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACG
* *
425292 ATATGCATGATGTGGTAAATATTATTTGATTGATTAT
66 ATATGCATGATGTGGTAAATACTATTTGATTAATTAT
425329 ATTATACGAT
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
119 97 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.43
Consensus pattern (119 bp):
TTGATTAAGTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATGCTATACG
ATATGCATGATGTGGTAAATACTATTTGATTAATTATGATATGGTAAATATTAT
Found at i:425337 original size:164 final size:166
Alignment explanation
Indices: 425040--425373 Score: 492
Period size: 164 Copynumber: 2.0 Consensus size: 166
425030 TACGATATGC
* * * * *
425040 ATGATATGGTAAATGTTATTTGATTGATTATGCTATACGATATGCATGACATTGTATATATTATT
1 ATGATATGGTAAATATTATTTGATTAAGTATGCTATACGATATGCATGACATGGTAAATATTA-T
* *
425105 TGATTGATTGATTATGCTATACGATATGTATGATATGGTAAATATTATTTGATTGATTATGCTAT
65 T-ATTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATACTAT
* *
425170 ACGATATGCATGATGTGGTAAATACTATTTGATTAATT
129 ACGATATACATGATATGGTAAATACTATTTGATTAATT
*
425208 ATGATATGGTAAATATTATTTGATTAAGTATGCTATACGATATGCATGATATGGTAAATATTA-T
1 ATGATATGGTAAATATTATTTGATTAAGTATGCTATACGATATGCATGACATGGTAAATATTATT
* *
425272 -TTGATTGATTATGCTATACGATATGCATGATGTGGTAAATATTATTTGATTGATTATATTATAC
66 ATTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATACTATAC
** * *
425336 GATATATGTGATATGGTAAATATTATTTGATTGATT
131 GATATACATGATATGGTAAATACTATTTGATTAATT
425372 AT
1 AT
425374 ACCATACAAC
Statistics
Matches: 150, Mismatches: 16, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
164 92 0.61
166 1 0.01
168 57 0.38
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (166 bp):
ATGATATGGTAAATATTATTTGATTAAGTATGCTATACGATATGCATGACATGGTAAATATTATT
ATTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTATTTGATTGATTATACTATAC
GATATACATGATATGGTAAATACTATTTGATTAATT
Found at i:425393 original size:45 final size:45
Alignment explanation
Indices: 425208--425394 Score: 248
Period size: 45 Copynumber: 4.2 Consensus size: 45
425198 TTGATTAATT
* * * *
425208 ATGATATGGTAAATATTATTTGATTAAGTATGCTATACGATATGC
1 ATGATATGGTAAATATTATTTGATTGATTATACTATACGATATAC
* *
425253 ATGATATGGTAAATATTATTTGATTGATTATGCTATACGATATGC
1 ATGATATGGTAAATATTATTTGATTGATTATACTATACGATATAC
* * *
425298 ATGATGTGGTAAATATTATTTGATTGATTATATTATACGATATAT
1 ATGATATGGTAAATATTATTTGATTGATTATACTATACGATATAC
* * * * *
425343 GTGATATGGTAAATATTATTTGATTGATTATACCATACAACACAC
1 ATGATATGGTAAATATTATTTGATTGATTATACTATACGATATAC
425388 ATGATAT
1 ATGATAT
425395 ACGTTTCGCT
Statistics
Matches: 126, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 126 1.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (45 bp):
ATGATATGGTAAATATTATTTGATTGATTATACTATACGATATAC
Found at i:425614 original size:36 final size:36
Alignment explanation
Indices: 425567--425637 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
425557 CGATATGCTT
* * * *
425567 GATATGATAAATGTTATTTGATTGATTATGCTATAC
1 GATATGATAAATATTATCTGATTAATTAAGCTATAC
*
425603 GATATGGTAAATATTATCTGATTAATTAAGCTATA
1 GATATGATAAATATTATCTGATTAATTAAGCTATA
425638 TGATGTGCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (36 bp):
GATATGATAAATATTATCTGATTAATTAAGCTATAC
Found at i:432624 original size:22 final size:21
Alignment explanation
Indices: 432582--432625 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
432572 TTTGAAAGAA
*
432582 AAATAATAATAACAATAAAAT
1 AAATAATAACAACAATAAAAT
432603 AAATAAATAACAA-AATATAAAT
1 AAAT-AATAACAACAATA-AAAT
432625 A
1 A
432626 GAAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATAATAACAACAATAAAAT
Found at i:432805 original size:14 final size:14
Alignment explanation
Indices: 432786--432812 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
432776 ATCATTACAT
432786 TTTGTTTTTTTCTA
1 TTTGTTTTTTTCTA
432800 TTTGTTTTTTTCT
1 TTTGTTTTTTTCT
432813 TCTTATCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.07, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTGTTTTTTTCTA
Found at i:434022 original size:13 final size:13
Alignment explanation
Indices: 434004--434032 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
433994 GAGACAAAGA
434004 ATTAGGGTTTTCC
1 ATTAGGGTTTTCC
434017 ATTAGGGTTTTCC
1 ATTAGGGTTTTCC
434030 ATT
1 ATT
434033 TTCAATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (13 bp):
ATTAGGGTTTTCC
Found at i:443954 original size:99 final size:98
Alignment explanation
Indices: 443722--444624 Score: 807
Period size: 99 Copynumber: 9.2 Consensus size: 98
443712 CGAGATTTGT
* * ** * * *
443722 CGTTGCGACCTCAATCCTTCCTATCATGT-TTCTAGGGTACAAGGTTTGCCGTTGCGGCCTCAAC
1 CGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTTGTCGTTGC-GCCTCAAC
* * * ** * **
443786 CTTTCCTCTTTATATTTTCATGATACTAGATCCAT
65 CTTTCC-CTTCATATCTTCATGGTACCGGATTCGC
* * * * * * ** * *
443821 CGTTGTGGTCTCGATCTTTCTCATCACGTC-TCTAAAATACCA-GGTTCGTCGTTGCGATCTCAA
1 CGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTA-CAGGGTTTGTCGTTGCG-CCTCAA
* *
443884 ACTTTCCCTTCATATCTTCATGGTATCGGATTCGC
64 CCTTTCCCTTCATATCTTCATGGTACCGGATTCGC
** * * * *
443919 CGTTGCAACCTCAATCCTTCTCATCACATCTTCTAAGGTACAAGGTTTATTGTTGCTGCCTCAAC
1 CGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTTGTCGTTGC-GCCTCAAC
* * **
443984 CTTTCCCTTTATATCTTCAT-GTACCAGATTTAC
65 CTTTCCCTTCATATCTTCATGGTACCGGATTCGC
* * *
444017 CGTTGCGGCATCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTTGTCGTTACGGCATCAAC
1 CGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTTGTCGTTGC-GCCTCAAC
* * *
444082 CTTTCCCTTTATATCTTCATGGTATCAGATTCGC
65 CTTTCCCTTCATATCTTCATGGTACCGGATTCGC
*** * * * * *
444116 AAATGCGGCCTCAAACCTTCCCATCACATCTTTTAAGGTACAAGGTTTG-CACTTGCGGCTTCAA
1 CGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTTGTC-GTTGC-GCCTCAA
* * * *
444180 CCTTTCCCTTTATATCTTTATGGTACCGAATTCAC
64 CCTTTCCCTTCATATCTTCATGGTACCGGATTCGC
* * * *
444215 TGTTGCGGCCTCAATCATTCCCATCACATCTTTTAAGGTATAGGGTTTGTCGTTGCGACCTC-AC
1 CGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTTGTCGTTGCG-CCTCAAC
*
444279 CTTTCCCTTCACATCTTCATGGTACCGGATTCGC
65 CTTTCCCTTCATATCTTCATGGTACCGGATTCGC
** *
444313 CGTTGCAACCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGATTT-TCCGTTATG-GCCTCA
1 CGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTTGT-CG-T-TGCGCCTCA
* *
444376 ACCTTTCCCTTCATATCTTTATGGTACCGGATTCGT
63 ACCTTTCCCTTCATATCTTCATGGTACCGGATTCGC
* * * * * * * * * *
444412 CATTACGACCTCAATCTTTCCCATCATATTTTTTAAGATACAGGGTTTGTCGTTACGGCCTCAAT
1 CGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTTGTCGTTGC-GCCTCAAC
* * *
444477 GTTTCCCTTCATATCTTCATGGTACCAGATTCAC
65 CTTTCCCTTCATATCTTCATGGTACCGGATTCGC
* * * * *
444511 TGTTACGGCCTCAATCCTTCCCATCACATCTTCTAAGGTATAGGGTTCGCCGTTGCGACCTCAAC
1 CGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTTGTCGTTGCG-CCTCAAC
* ** **
444576 CTTTCCCTTTATAT-TTCCATGGTACTAGATTCAT
65 CTTTCCCTTCATATCTT-CATGGTACCGGATTCGC
*
444610 CGTTGCGGCTTCAAT
1 CGTTGCGGCCTCAAT
444625 ATTTCTCAAC
Statistics
Matches: 654, Mismatches: 131, Indels: 38
0.79 0.16 0.05
Matches are distributed among these distances:
97 2 0.00
98 213 0.33
99 432 0.66
100 7 0.01
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.36
Consensus pattern (98 bp):
CGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTTGTCGTTGCGCCTCAACC
TTTCCCTTCATATCTTCATGGTACCGGATTCGC
Found at i:443981 original size:50 final size:50
Alignment explanation
Indices: 443918--444578 Score: 268
Period size: 50 Copynumber: 13.4 Consensus size: 50
443908 ATCGGATTCG
** *
443918 CCGTTGCAACCTCAATCCTTCTCATCACATCTTCTAAGGTACAAGGTTTA
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGTTTA
** * * * * * * *
443968 TTGTTGCTGCCTCAA-CCTTTCCCTTTATATCTTC--ATGTACCAGATTTA
1 CCGTTGCGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTACAAGGTTTA
* * *
444016 CCGTTGCGGCATCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTTG
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGTTTA
* * * * * * * * **
444066 TCGTTACGGCATCAA-CCTTTCCCTTTATATCTTC-ATGGTATC-AGATTCG
1 CCGTTGCGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTA-CAAGGTTTA
*** * * *
444115 CAAATGCGGCCTCAAACCTTCCCATCACATCTTTTAAGGTACAAGGTTTG
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGTTTA
* * * * * *
444165 CAC-TTGCGGCTTCAA-CCTTTCCCTTTATATCTT-TATGGTACCGAA--TTCA
1 C-CGTTGCGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTA-C-AAGGTTTA
* * * * * *
444214 CTGTTGCGGCCTCAATCATTCCCATCACATCTTTTAAGGTATAGGGTTTG
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGTTTA
* * * * * **
444264 TCGTTGCGACCTC-A-CCTTTCCCTTCACATCTTC-ATGGTAC-CGGATTCG
1 CCGTTGCGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTACAAGG-TTTA
** *
444312 CCGTTGCAACCTCAATCCTTCCCATCACATCTTCTAAGGTAC-AGGATTTT
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGG-TTTA
** * * * * *
444362 CCGTTATGGCCTCAA-CCTTTCCCTTCATATCTT-TATGGTAC-CGGATT-
1 CCGTTGCGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTACAAGGTTTA
* * * * * * * * * *
444409 CGTCATTACGACCTCAATCTTTCCCATCATATTTTTTAAGATACAGGGTTTG
1 C--CGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGTTTA
* * ** * * * * * *
444461 TCGTTACGGCCTCAATGTTTCCCTTCATATCTTC-ATGGTACCAGATTCA
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGTTTA
* * * * **
444510 CTGTTACGGCCTCAATCCTTCCCATCACATCTTCTAAGGTATAGGGTTCG
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGTTTA
*
444560 CCGTTGCGACCTCAA-CCTT
1 CCGTTGCGGCCTCAATCCTT
444579 TCCCTTTATA
Statistics
Matches: 450, Mismatches: 130, Indels: 63
0.70 0.20 0.10
Matches are distributed among these distances:
47 3 0.01
48 58 0.13
49 177 0.39
50 206 0.46
51 6 0.01
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (50 bp):
CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGTTTA
Found at i:444088 original size:197 final size:198
Alignment explanation
Indices: 443703--444629 Score: 985
Period size: 197 Copynumber: 4.7 Consensus size: 198
443693 CCCTAATCTT
* * * ** *
443703 TTCATGGT-TCGAGATTTGTCGTTGCGACCTCAATCCTTCCTATCATGT-TTCTAGGGTACAAGG
1 TTCATGGTATCG-GATTCGCCGTTGCGACCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGG
* * * * * *
443766 TTTGCCGTTGCGGCCTCAACCTTTCCTCTTTATATTTTCATGATACTAGATCCATCGTTGTGGTC
65 TTTGCCGTTGCGGCCTCAACCTTTCC-CTTTATATCTTCATGGTACCAGATTCATCGTTGCGGCC
* * * * * * ** *
443831 TCGATCTTTCTCATCACGTC-TCTAAAATACCA-GGTTCGTCGTTGCGATCTCAAACTTTCCCTT
129 TCAATCTTTCCCATCACATCTTCTAAGATA-CAGGGTTTGTCGTTACGGCCTCAACCTTTCCCTT
443894 CATATC
193 CATATC
* *
443900 TTCATGGTATCGGATTCGCCGTTGCAACCTCAATCCTTCTCATCACATCTTCTAAGGTACAAGGT
1 TTCATGGTATCGGATTCGCCGTTGCGACCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGT
*** * * * *
443965 TTATTGTTGCTGCCTCAACCTTTCCCTTTATATCTTCAT-GTACCAGATTTACCGTTGCGGCATC
66 TTGCCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATGGTACCAGATTCATCGTTGCGGCCTC
* * * *
444029 AATCCTTCCCATCACATCTTCTAAGGTACAGGGTTTGTCGTTACGGCATCAACCTTTCCCTTTAT
131 AATCTTTCCCATCACATCTTCTAAGATACAGGGTTTGTCGTTACGGCCTCAACCTTTCCCTTCAT
444094 ATC
196 ATC
* *** * * *
444097 TTCATGGTATCAGATTCGCAAATGCGGCCTCAAACCTTCCCATCACATCTTTTAAGGTACAAGGT
1 TTCATGGTATCGGATTCGCCGTTGCGACCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGT
* *
444162 TTGCAC-TTGCGGCTTCAACCTTTCCCTTTATATCTTTATGGTACC-GAATTCA-CTGTTGCGGC
66 TTGC-CGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATGGTACCAG-ATTCATC-GTTGCGGC
* * * * * *
444224 CTCAATCATTCCCATCACATCTTTTAAGGTATAGGGTTTGTCGTTGCGACCTC-ACCTTTCCCTT
128 CTCAATCTTTCCCATCACATCTTCTAAGATACAGGGTTTGTCGTTACGGCCTCAACCTTTCCCTT
*
444288 CACATC
193 CATATC
* *
444294 TTCATGGTACCGGATTCGCCGTTGCAACCTCAATCCTTCCCATCACATCTTCTAAGGTAC-AGGA
1 TTCATGGTATCGGATTCGCCGTTGCGACCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGG-
* ** * * * * * * *
444358 TTTTCCGTTATGGCCTCAACCTTTCCCTTCATATCTTTATGGTACCGGATTCGTCATTACGACCT
65 TTTGCCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATGGTACCAGATTCATCGTTGCGGCCT
* * * **
444423 CAATCTTTCCCATCATATTTTTTAAGATACAGGGTTTGTCGTTACGGCCTCAATGTTTCCCTTCA
130 CAATCTTTCCCATCACATCTTCTAAGATACAGGGTTTGTCGTTACGGCCTCAACCTTTCCCTTCA
444488 TATC
195 TATC
* * * * * * * *
444492 TTCATGGTACCAGATTCACTGTTACGGCCTCAATCCTTCCCATCACATCTTCTAAGGTATAGGGT
1 TTCATGGTATCGGATTCGCCGTTGCGACCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGT
* * * *
444557 TCGCCGTTGCGACCTCAACCTTTCCCTTTATAT-TTCCATGGTACTAGATTCATCGTTGCGGCTT
66 TTGCCGTTGCGGCCTCAACCTTTCCCTTTATATCTT-CATGGTACCAGATTCATCGTTGCGGCCT
*
444621 CAATATTTC
130 CAATCTTTC
444630 TCAACCTTGT
Statistics
Matches: 605, Mismatches: 110, Indels: 29
0.81 0.15 0.04
Matches are distributed among these distances:
196 37 0.06
197 339 0.56
198 227 0.38
199 2 0.00
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (198 bp):
TTCATGGTATCGGATTCGCCGTTGCGACCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGT
TTGCCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATGGTACCAGATTCATCGTTGCGGCCTC
AATCTTTCCCATCACATCTTCTAAGATACAGGGTTTGTCGTTACGGCCTCAACCTTTCCCTTCAT
ATC
Found at i:444318 original size:296 final size:297
Alignment explanation
Indices: 443879--444624 Score: 923
Period size: 296 Copynumber: 2.5 Consensus size: 297
443869 TCGTTGCGAT
* * * * ** *
443879 CTCAAACTTTCCCTTCATATCTTCATGGTATCGGATTCGCCGTTGCAACCTCAATCCTTCTCATC
1 CTCAAACTTTCCCTTCATATCTTCATGGTACCGAATTCACTGTTGCGGCCTCAATCCTTCCCATC
* * * *
443944 ACATCTTCTAAGGTACAAGGTTTATTGTTGCTG-CCTCAACCTTTCCCTTTATATCTTCAT-GTA
66 ACATCTTCTAAGGTATAGGGTTTGTCGTTGC-GACCTCAACCTTTCCCTTTATATCTTCATGGTA
* *
444007 CCAGATTTACCGTTGCGGCATCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTTGT-CGTT
130 CCAGATTCACCGTTGCGGCATCAATCCTTCCCATCACATCTTCTAAGGTACAGGATTT-TCCGTT
* * * *
444071 ACGGCATCAACCTTTCCCTTTATATCTTCATGGTATCAGATTCG-CAAATGCGGCCTCAAACCTT
194 ACGGCATCAACCTTTCCCTTCATATCTTCATGGTACCAGATTCGTC-AATACGACCTCAAACCTT
* *
444135 CCCATCACATCTTTTAAGGTACAAGGTTTG-CACTTGCGGC
258 CCCATCACATCTTTTAAGATACAAGGTTTGTC-CTTACGGC
* * * * *
444175 TTCAACCTTTCCCTTTATATCTTTATGGTACCGAATTCACTGTTGCGGCCTCAATCATTCCCATC
1 CTCAAACTTTCCCTTCATATCTTCATGGTACCGAATTCACTGTTGCGGCCTCAATCCTTCCCATC
* * *
444240 ACATCTTTTAAGGTATAGGGTTTGTCGTTGCGACCTC-ACCTTTCCCTTCACATCTTCATGGTAC
66 ACATCTTCTAAGGTATAGGGTTTGTCGTTGCGACCTCAACCTTTCCCTTTATATCTTCATGGTAC
* * ** * *
444304 CGGATTCGCCGTTGCAACCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGATTTTCCGTTAT
131 CAGATTCACCGTTGCGGCATCAATCCTTCCCATCACATCTTCTAAGGTACAGGATTTTCCGTTAC
* * * * * *
444369 GGCCTCAACCTTTCCCTTCATATCTTTATGGTACCGGATTCGTCATTACGACCTCAATCTTTCCC
196 GGCATCAACCTTTCCCTTCATATCTTCATGGTACCAGATTCGTCAATACGACCTCAAACCTTCCC
* * * *
444434 ATCATATTTTTTAAGATACAGGGTTTGTCGTTACGGC
261 ATCACATCTTTTAAGATACAAGGTTTGTCCTTACGGC
** *
444471 CTCAATGTTTCCCTTCATATCTTCATGGTACC-AGATTCACTGTTACGGCCTCAATCCTTCCCAT
1 CTCAAACTTTCCCTTCATATCTTCATGGTACCGA-ATTCACTGTTGCGGCCTCAATCCTTCCCAT
* *
444535 CACATCTTCTAAGGTATAGGGTTCGCCGTTGCGACCTCAACCTTTCCCTTTATAT-TTCCATGGT
65 CACATCTTCTAAGGTATAGGGTTTGTCGTTGCGACCTCAACCTTTCCCTTTATATCTT-CATGGT
* * *
444599 ACTAGATTCATCGTTGCGGCTTCAAT
129 ACCAGATTCACCGTTGCGGCATCAAT
444625 ATTTCTCAAC
Statistics
Matches: 380, Mismatches: 62, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
295 23 0.06
296 316 0.83
297 41 0.11
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.36
Consensus pattern (297 bp):
CTCAAACTTTCCCTTCATATCTTCATGGTACCGAATTCACTGTTGCGGCCTCAATCCTTCCCATC
ACATCTTCTAAGGTATAGGGTTTGTCGTTGCGACCTCAACCTTTCCCTTTATATCTTCATGGTAC
CAGATTCACCGTTGCGGCATCAATCCTTCCCATCACATCTTCTAAGGTACAGGATTTTCCGTTAC
GGCATCAACCTTTCCCTTCATATCTTCATGGTACCAGATTCGTCAATACGACCTCAAACCTTCCC
ATCACATCTTTTAAGATACAAGGTTTGTCCTTACGGC
Found at i:445681 original size:15 final size:15
Alignment explanation
Indices: 445643--445685 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
445633 TCGACCTCTC
445643 CTTTTTCTT-TTTTT
1 CTTTTTCTTCTTTTT
**
445657 AGTTTT-TTCTTTTT
1 CTTTTTCTTCTTTTT
445671 CTTTTTCTTCTTTTT
1 CTTTTTCTTCTTTTT
445686 GGGTGAAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 2 0.09
14 13 0.57
15 8 0.35
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (15 bp):
CTTTTTCTTCTTTTT
Found at i:445684 original size:22 final size:22
Alignment explanation
Indices: 445643--445685 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
445633 TCGACCTCTC
*
445643 CTTTTTCTTTTTTTAGTTTTTT
1 CTTTTTCTTTTTTTACTTTTTT
445665 CTTTTTCTTTTTCTT-CTTTTT
1 CTTTTTCTTTTT-TTACTTTTT
445686 GGGTGAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (22 bp):
CTTTTTCTTTTTTTACTTTTTT
Found at i:451990 original size:19 final size:20
Alignment explanation
Indices: 451953--451992 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
451943 GTTTTTGCTA
*
451953 TTTGTTTTTTTCTTCTTGTC
1 TTTGTTCTTTTCTTCTTGTC
451973 TTTGTTCTTTTC-TCTTGTC
1 TTTGTTCTTTTCTTCTTGTC
451992 T
1 T
451993 CTTGCAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.00, C:0.17, G:0.10, T:0.72
Consensus pattern (20 bp):
TTTGTTCTTTTCTTCTTGTC
Found at i:456645 original size:9 final size:10
Alignment explanation
Indices: 456629--456653 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
456619 CAAATATTTA
456629 AAATTTTTTT
1 AAATTTTTTT
456639 AAATTTTTTT
1 AAATTTTTTT
456649 AAATT
1 AAATT
456654 AATTAAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
AAATTTTTTT
Found at i:458574 original size:14 final size:15
Alignment explanation
Indices: 458544--458578 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
458534 TGCTTCTATA
458544 AATTGTTTCTGGGTT
1 AATTGTTTCTGGGTT
*
458559 AATTGTTT-TTGGTT
1 AATTGTTTCTGGGTT
458573 AATTGT
1 AATTGT
458579 CGTTTCAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.17, C:0.03, G:0.23, T:0.57
Consensus pattern (15 bp):
AATTGTTTCTGGGTT
Found at i:468037 original size:18 final size:16
Alignment explanation
Indices: 468014--468049 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
468004 CTTAGTAAAT
468014 ATTAAATTAGAGAATGAA
1 ATTAAATT-GA-AATGAA
468032 ATTAAATTGAAATGAA
1 ATTAAATTGAAATGAA
468048 AT
1 AT
468050 GGAATTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 2 0.11
18 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.31
Consensus pattern (16 bp):
ATTAAATTGAAATGAA
Found at i:468672 original size:52 final size:52
Alignment explanation
Indices: 468594--468826 Score: 371
Period size: 52 Copynumber: 4.5 Consensus size: 52
468584 GCAAAGGGTT
*
468594 CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTC
1 CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
*
468646 CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT-AAGTC
1 CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
* * *
468697 TGATGACTGTGTGTCACCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
1 CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
* * *
468749 CGATGACTATGTGTCATCGTGAGCATATGAATCATTGT-CGAATTATGAGGTC
1 CGATGACTATGTGTCATCGTGAGTATATGAATCCTT-TACGGATTATGAGGTC
468801 CGATGACTATGTGTCATCGTGAGTAT
1 CGATGACTATGTGTCATCGTGAGTAT
468827 CAAATGAGAA
Statistics
Matches: 166, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
51 47 0.28
52 118 0.71
53 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.34
Consensus pattern (52 bp):
CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
Found at i:468771 original size:26 final size:26
Alignment explanation
Indices: 468742--468823 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
468732 TTACGGATTA
468742 TGAGGTCCGATGACTATGTGTCATCG
1 TGAGGTCCGATGACTATGTGTCATCG
** * **
468768 TGA-G-CATATGAATCAT-TGTCGAATTA
1 TGAGGTCCGATGACT-ATGTGTC--ATCG
468794 TGAGGTCCGATGACTATGTGTCATCG
1 TGAGGTCCGATGACTATGTGTCATCG
468820 TGAG
1 TGAG
468824 TATCAAATGA
Statistics
Matches: 40, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
24 10 0.25
25 3 0.08
26 14 0.35
27 3 0.08
28 10 0.25
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (26 bp):
TGAGGTCCGATGACTATGTGTCATCG
Found at i:468777 original size:103 final size:104
Alignment explanation
Indices: 468594--468826 Score: 371
Period size: 103 Copynumber: 2.2 Consensus size: 104
468584 GCAAAGGGTT
468594 CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATGACTATGTG
1 CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATGACTATGTG
* * *
468659 TCATCGTGAGTATATGAATCCTT-TACGGATTAT-AAGTC
66 TCATCGTGAGCATATGAATCATTGT-CGAATTATGAAGTC
* * * *
468697 TGATGACTGTGTGTCACCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTG
1 CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATGACTATGTG
*
468762 TCATCGTGAGCATATGAATCATTGTCGAATTATGAGGTC
66 TCATCGTGAGCATATGAATCATTGTCGAATTATGAAGTC
468801 CGATGACTATGTGTCATCGTGAGTAT
1 CGATGACTATGTGTCATCGTGAGTAT
468827 CAAATGAGAA
Statistics
Matches: 117, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
103 89 0.76
104 28 0.24
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.34
Consensus pattern (104 bp):
CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATGACTATGTG
TCATCGTGAGCATATGAATCATTGTCGAATTATGAAGTC
Found at i:472911 original size:16 final size:16
Alignment explanation
Indices: 472890--472922 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
472880 TGATGATTTT
*
472890 AATGTTAAAGGACTAA
1 AATGTTAAAGGAATAA
472906 AATGTTAAAGGAATAA
1 AATGTTAAAGGAATAA
472922 A
1 A
472923 TTTGTAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (16 bp):
AATGTTAAAGGAATAA
Found at i:473992 original size:52 final size:52
Alignment explanation
Indices: 473909--474199 Score: 474
Period size: 52 Copynumber: 5.6 Consensus size: 52
473899 TAAATGTAAA
473909 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
473961 AGGTCCAATGACTATGTGTCATTGTGCGTATATGAATCCTTTACGGATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
474013 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
474065 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * *
474117 AGGTCTGATGATTATGTGTCATTGTGAGCATATGAATCCTTTTCGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
474169 AGGTCCAATGACTATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
474200 CAAATGAGAA
Statistics
Matches: 219, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 219 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:476989 original size:18 final size:17
Alignment explanation
Indices: 476938--476989 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 17
476928 AGCCAACCCG
* *
476938 TTTTAAATT-TATAATA
1 TTTTATATTATATAATT
* *
476954 TTTTATATTATGTTATT
1 TTTTATATTATATAATT
476971 TTTATATATTATATAATT
1 TTT-TATATTATATAATT
476989 T
1 T
476990 AGAACACATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 13 0.46
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTATATTATATAATT
Found at i:480318 original size:19 final size:19
Alignment explanation
Indices: 480294--480331 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
480284 TTCTTTTTGA
480294 TAAAAAAAAGTTACCCACT
1 TAAAAAAAAGTTACCCACT
* *
480313 TAAAAAAAATTTATCCACT
1 TAAAAAAAAGTTACCCACT
480332 ATGATAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (19 bp):
TAAAAAAAAGTTACCCACT
Found at i:480562 original size:22 final size:22
Alignment explanation
Indices: 480537--480581 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
480527 AGACGTGGAA
480537 AAATCTATTTATTTTATATTTC
1 AAATCTATTTATTTTATATTTC
480559 AAATCTATTTATTTTATATTTC
1 AAATCTATTTATTTTATATTTC
480581 A
1 A
480582 GTTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATCTATTTATTTTATATTTC
Found at i:481231 original size:52 final size:52
Alignment explanation
Indices: 481169--481272 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
481159 AAATGGAAGA
481169 ATGTGCATCGACTCGATACTGGCTGAGCCTTGTGATGTTCAAGTTCTTTACC
1 ATGTGCATCGACTCGATACTGGCTGAGCCTTGTGATGTTCAAGTTCTTTACC
481221 ATGTGCATCGACTCGATACTGGCTGAGCCTTGTGATGTTCAAGTTCTTTACC
1 ATGTGCATCGACTCGATACTGGCTGAGCCTTGTGATGTTCAAGTTCTTTACC
481273 GGTGTCCTCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (52 bp):
ATGTGCATCGACTCGATACTGGCTGAGCCTTGTGATGTTCAAGTTCTTTACC
Found at i:488991 original size:24 final size:24
Alignment explanation
Indices: 488964--489011 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
488954 CACAATTAAG
*
488964 AGTAAAATAGCTAAAATGAGGCTT
1 AGTAAAATAGCTAAAACGAGGCTT
488988 AGTAAAATAGCTAAAACGAGGCTT
1 AGTAAAATAGCTAAAACGAGGCTT
489012 TCGAGTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (24 bp):
AGTAAAATAGCTAAAACGAGGCTT
Found at i:495214 original size:681 final size:681
Alignment explanation
Indices: 493909--495270 Score: 2499
Period size: 681 Copynumber: 2.0 Consensus size: 681
493899 CAAAGATATC
* *
493909 TAATAAACCAATTGTTTTTACTGAATGGAGTAATCGAGTAGCTATTAATCCACCAGACAAGAACG
1 TAATAAACCAATTGTTTTTACTGAATGGAGTAATCGAGCAGCTATTAATCCACCACACAAGAACG
* *
493974 TACTAATTCCATATGTGGATCAATCATGAAGGCAGTTTTGAGAATGGATGATGGCAAAAAAACAC
66 TACTAATTCCATAAGTGGATCAATCATGAAGGCAGTTATGAGAATGGATGATGGCAAAAAAACAC
** * **
494039 AGTTGTTGTGAATAGATATGATCGATGAAAAGAGTTGGTGGTTATCAATGCAAGAAGAAAAGAAA
131 AACTGTCGTGAATAGATATGATCGATGAAAAGAGTTGGTGGTTATCAATAAAAGAAGAAAAGAAA
494104 AATTTAGAGAAGGAGATAAACGTCAAAGAGTAGCTTGGCACGACTGCTGCTGGACGAACACTAAT
196 AATTTAGAGAAGGAGATAAACGTCAAAGAGTAGCTTGGCACGACTGCTGCTGGACGAACACTAAT
*
494169 AGAACGAACTATTTGTGGCTATCGAAGTGTACACTAACACTCTTGTCAGACAATTTTGAAAGGTA
261 AGAACGAACTATTTGTGGCTACCGAAGTGTACACTAACACTCTTGTCAGACAATTTTGAAAGGTA
494234 TTAACACGTATTTTTATATTCATAAATACTAACATACTAACTCGGCAACATTTTTTTGTTTCAGG
326 TTAACACGTATTTTTATATTCATAAATACTAACATACTAACTCGGCAACATTTTTTTGTTTCAGG
*
494299 GTACTTTTCTCAGACTAACACGTTTGTTACGACACAGCCTCTCGATGTCATGACAAAGCAACCAA
391 GTACTTTTCTCAAACTAACACGTTTGTTACGACACAGCCTCTCGATGTCATGACAAAGCAACCAA
*
494364 ACTACTCCAAGAACGCTCAAGCATGCTATGATGTGACATACCCTTTATGTGTTGTGACAAAGGGG
456 ACTACTCCAAGAACGCTCAAGCATGCTATGATGTGACATACCCCTTATGTGTTGTGACAAAGGGG
494429 TCAGATTGCTGAAAATCCAAAACTGATAGGTTTGTTGCGAGATAGAAGATGCTATGTTGTGACAT
521 TCAGATTGCTGAAAATCCAAAACTGATAGGTTTGTTGCGAGATAGAAGATGCTATGTTGTGACAT
*
494494 AGGGGTTAGATTGTTGGAAATTCAAGATTGACAGGTTTGTCGTGACACAGGGTAAGCTACGTCGT
586 AGGGGTTAGATTGCTGGAAATTCAAGATTGACAGGTTTGTCGTGACACAGGGTAAGCTACGTCGT
*
494559 GACTAACATGGTATTGGAAGGTTGGTTGTGA
651 GACTAACATGGTACTGGAAGGTTGGTTGTGA
*
494590 TAATAAACCAATTGTTTTTACTGAATGGAGTAATCGAGCAGCTATTAATCCACCACACAAGAGCG
1 TAATAAACCAATTGTTTTTACTGAATGGAGTAATCGAGCAGCTATTAATCCACCACACAAGAACG
494655 TACTAATTCCATAAGTGGATCAATCATGAAGGCAGTTATGAGAATGGATGATGGCAAAAAAACAC
66 TACTAATTCCATAAGTGGATCAATCATGAAGGCAGTTATGAGAATGGATGATGGCAAAAAAACAC
*
494720 AACTGTCGTGAATAGATATGATCGATGAAAAGAGTTGGTGGTTATCAATAAAAGAAGAAAAGGAA
131 AACTGTCGTGAATAGATATGATCGATGAAAAGAGTTGGTGGTTATCAATAAAAGAAGAAAAGAAA
*
494785 AATTTAGAGAAGGAGATAAACGTCAAAGAGTAGCTTGGCACGACTGCTGCTGGACGAACACTGAT
196 AATTTAGAGAAGGAGATAAACGTCAAAGAGTAGCTTGGCACGACTGCTGCTGGACGAACACTAAT
* **
494850 AGAACGAACTATTTGTGGCTGCCGAAGTGTACACTAATGCTCTTGTCAGACAATTTTGAAAGGTA
261 AGAACGAACTATTTGTGGCTACCGAAGTGTACACTAACACTCTTGTCAGACAATTTTGAAAGGTA
*
494915 TTAACACGTATTTTTATATTCATAAATACTAACATACTAACTCGGTAACATTTTTTTGTTTCAGG
326 TTAACACGTATTTTTATATTCATAAATACTAACATACTAACTCGGCAACATTTTTTTGTTTCAGG
*
494980 GTACTTTTCTCAAACTAACACGTTTGTTGCGACACAGCCTCTCGATGTCATGACAAAGCAACCAA
391 GTACTTTTCTCAAACTAACACGTTTGTTACGACACAGCCTCTCGATGTCATGACAAAGCAACCAA
495045 ACTACTCCAAGAACGCTCAAGCATGCTATGATGTGACATACCCCTTATGTGTTGTGACAAAGGGG
456 ACTACTCCAAGAACGCTCAAGCATGCTATGATGTGACATACCCCTTATGTGTTGTGACAAAGGGG
*
495110 TCAGATTGCTGAAAATCCAAAACTGATAGGTTTGTTGCTAGATAGAAGATGCTATGTTGTGACAT
521 TCAGATTGCTGAAAATCCAAAACTGATAGGTTTGTTGCGAGATAGAAGATGCTATGTTGTGACAT
*
495175 AGGGGTTAGATTGCTGGAAATTCAAGATTGACGGGTTTGTCGTGACACAGGGTAAGCTACGTCGT
586 AGGGGTTAGATTGCTGGAAATTCAAGATTGACAGGTTTGTCGTGACACAGGGTAAGCTACGTCGT
*
495240 GACTAACATGGTACTGGGAGGTTGGTTGTGA
651 GACTAACATGGTACTGGAAGGTTGGTTGTGA
495271 CATACTTAGG
Statistics
Matches: 656, Mismatches: 25, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
681 656 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (681 bp):
TAATAAACCAATTGTTTTTACTGAATGGAGTAATCGAGCAGCTATTAATCCACCACACAAGAACG
TACTAATTCCATAAGTGGATCAATCATGAAGGCAGTTATGAGAATGGATGATGGCAAAAAAACAC
AACTGTCGTGAATAGATATGATCGATGAAAAGAGTTGGTGGTTATCAATAAAAGAAGAAAAGAAA
AATTTAGAGAAGGAGATAAACGTCAAAGAGTAGCTTGGCACGACTGCTGCTGGACGAACACTAAT
AGAACGAACTATTTGTGGCTACCGAAGTGTACACTAACACTCTTGTCAGACAATTTTGAAAGGTA
TTAACACGTATTTTTATATTCATAAATACTAACATACTAACTCGGCAACATTTTTTTGTTTCAGG
GTACTTTTCTCAAACTAACACGTTTGTTACGACACAGCCTCTCGATGTCATGACAAAGCAACCAA
ACTACTCCAAGAACGCTCAAGCATGCTATGATGTGACATACCCCTTATGTGTTGTGACAAAGGGG
TCAGATTGCTGAAAATCCAAAACTGATAGGTTTGTTGCGAGATAGAAGATGCTATGTTGTGACAT
AGGGGTTAGATTGCTGGAAATTCAAGATTGACAGGTTTGTCGTGACACAGGGTAAGCTACGTCGT
GACTAACATGGTACTGGAAGGTTGGTTGTGA
Found at i:504980 original size:17 final size:17
Alignment explanation
Indices: 504938--504988 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
504928 AATTATCCCG
*
504938 AAAATTACAAGCCTTAAA
1 AAAATTA-AAGTCTTAAA
504956 ATAAATTAAAGTCTTAAA
1 A-AAATTAAAGTCTTAAA
504974 AAAATTAAAGT-TTAA
1 AAAATTAAAGTCTTAA
504989 TCTTCATCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 4 0.13
17 10 0.32
18 11 0.35
19 6 0.19
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (17 bp):
AAAATTAAAGTCTTAAA
Found at i:510948 original size:26 final size:25
Alignment explanation
Indices: 510919--510976 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
510909 AAAAGTTTAG
* *
510919 CTCTTACAAGCCCAGGCAGAATATTA
1 CTCTTACAAG-CCAGACAGAATATCA
* *
510945 CTCTTACGAGCTAGACAGAATATCA
1 CTCTTACAAGCCAGACAGAATATCA
510970 CTCTTAC
1 CTCTTAC
510977 GAGTGAGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 19 0.68
26 9 0.32
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.26
Consensus pattern (25 bp):
CTCTTACAAGCCAGACAGAATATCA
Found at i:510966 original size:25 final size:25
Alignment explanation
Indices: 510935--511018 Score: 107
Period size: 25 Copynumber: 3.4 Consensus size: 25
510925 CAAGCCCAGG
510935 CAGAATATTACTCTTACGAGCTAGA
1 CAGAATATTACTCTTACGAGCTAGA
*
510960 CAGAATATCACTCTTACGAG-TGAGA
1 CAGAATATTACTCTTACGAGCT-AGA
* * *
510985 TAGAATATTGCTCTTATGAGCTAGA
1 CAGAATATTACTCTTACGAGCTAGA
*
511010 CAAAATATT
1 CAGAATATT
511019 TGCTCCATCG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
24 1 0.02
25 48 0.96
26 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (25 bp):
CAGAATATTACTCTTACGAGCTAGA
Found at i:528955 original size:132 final size:133
Alignment explanation
Indices: 528775--529186 Score: 634
Period size: 132 Copynumber: 3.1 Consensus size: 133
528765 TGTTACAGAT
* * * * *
528775 ACAGCTCATGTGAGCATTACTTGTTATATGGGTGTTGATCTTAGATGTCCTACCGATGGCTGAGG
1 ACAGCTCGTGTGAGCATTACATGTTATATGGGTGCTGGTCTTAGATGTCTTACCGATGGCTGAGG
* ** * *
528840 TCTTG-CATTGGTTGCGGATTCTCCACAGCTCGTGTAAGCAGCATCGTGTAGCC-CTACATCTTG
66 TCTCGACATTTATTGCGGATTCTCCACAGCTCGTGTAAGCAGCATCATGTAGCCTC-ACATCTCG
*
528903 ACCT
130 ACCC
*
528907 ACAACTCGTGTGAGCATTACATGTTATATGGGTGCTGGTCTTAGATGTCTTACCGATGGCTGAGG
1 ACAGCTCGTGTGAGCATTACATGTTATATGGGTGCTGGTCTTAGATGTCTTACCGATGGCTGAGG
* **
528972 T-TCGACATTTATTGCGGATTCTCCACAGCTCGTGTGAGCAATATCATGTAGCCTCACATCTCGA
66 TCTCGACATTTATTGCGGATTCTCCACAGCTCGTGTAAGCAGCATCATGTAGCCTCACATCTCGA
529036 CCC
131 CCC
529039 ACAGCTCGTGTGAGCATTACATGTTATATGGGTGCTGGTCTTAGATGTCTTACCGATGGCTGAGG
1 ACAGCTCGTGTGAGCATTACATGTTATATGGGTGCTGGTCTTAGATGTCTTACCGATGGCTGAGG
* *
529104 TC-CGACATTTATTGTGGATTCTCCACAGCTCGTGTAAGCAGCATCATATAGCCTCACATCTCGA
66 TCTCGACATTTATTGCGGATTCTCCACAGCTCGTGTAAGCAGCATCATGTAGCCTCACATCTCGA
529168 CCC
131 CCC
529171 ACAGCTCGTGTGAGCA
1 ACAGCTCGTGTGAGCA
529187 GACCCATTTC
Statistics
Matches: 256, Mismatches: 21, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
131 2 0.01
132 253 0.99
133 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (133 bp):
ACAGCTCGTGTGAGCATTACATGTTATATGGGTGCTGGTCTTAGATGTCTTACCGATGGCTGAGG
TCTCGACATTTATTGCGGATTCTCCACAGCTCGTGTAAGCAGCATCATGTAGCCTCACATCTCGA
CCC
Found at i:531898 original size:7 final size:7
Alignment explanation
Indices: 531886--531924 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
531876 GCAATTTTTC
531886 TTTCTCT
1 TTTCTCT
531893 TTTCTCT
1 TTTCTCT
531900 TTTCTCT
1 TTTCTCT
531907 TTT-TCT
1 TTTCTCT
531913 TTTCT-T
1 TTTCTCT
531919 TTTCTC
1 TTTCTC
531925 ATTTAACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTCTCT
Found at i:531913 original size:6 final size:6
Alignment explanation
Indices: 531880--531923 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
531870 TTTATAGCAA
*
531880 TTTTTC TTTCTC TTTTCTC TTTTCTC TTTTTC -TTTTC TTTTTC T
1 TTTTTC TTTTTC TTTT-TC TTTT-TC TTTTTC TTTTTC TTTTTC T
531924 CATTTAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.15
6 16 0.47
7 13 0.38
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:531913 original size:13 final size:13
Alignment explanation
Indices: 531880--531921 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
531870 TTTATAGCAA
531880 TTTTTC-TTTCTC
1 TTTTTCTTTTCTC
531892 TTTTCTCTTTTCTC
1 TTTT-TCTTTTCTC
531906 TTTTTCTTTTCT-
1 TTTTTCTTTTCTC
531918 TTTT
1 TTTT
531922 CTCATTTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.29
13 10 0.36
14 10 0.36
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTTCTC
Found at i:531936 original size:26 final size:26
Alignment explanation
Indices: 531881--531936 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
531871 TTATAGCAAT
* ** *
531881 TTTTCTTTCTCTTTTCTCTTTTCTCT
1 TTTTCTTTCTCTTTTCTCATTTAACA
531907 TTTTCTTT-TCTTTTTCTCATTTAACA
1 TTTTCTTTCTC-TTTTCTCATTTAACA
531933 TTTT
1 TTTT
531937 TTTACGTGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.71
Consensus pattern (26 bp):
TTTTCTTTCTCTTTTCTCATTTAACA
Found at i:540601 original size:20 final size:20
Alignment explanation
Indices: 540564--540601 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
540554 CTAAGATAGT
*
540564 TAAAATTGTCAATGCAATTA
1 TAAAATTGTAAATGCAATTA
540584 TAAAATT-TAAATGTCAAT
1 TAAAATTGTAAATG-CAAT
540602 ACAATTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (20 bp):
TAAAATTGTAAATGCAATTA
Found at i:547651 original size:118 final size:118
Alignment explanation
Indices: 547443--547682 Score: 444
Period size: 118 Copynumber: 2.0 Consensus size: 118
547433 ACATGATGGA
*
547443 GACACAACATTTCGAGATATTCACAAATAAAGGGAGAAGGACAACCACCATTAGAAGAAGAGTTT
1 GACACAACATTTCGAGATATTCACAAATAAAGGGAGAAGGACAACCACCATTAGAAGAAGAGCTT
* * *
547508 TCACGATGAATCGGGTAACTTCATTTCTTACTTTTTAGGGCCTACACATTGAG
66 TCACGATGAATCGGATAACCTCATTTCTTACTTTTTAAGGCCTACACATTGAG
547561 GACACAACATTTCGAGATATTCACAAATAAAGGGAGAAGGACAACCACCATTAGAAGAAGAGCTT
1 GACACAACATTTCGAGATATTCACAAATAAAGGGAGAAGGACAACCACCATTAGAAGAAGAGCTT
547626 TCACGATGAATCGGATAACCTCATTTCTTACTTTTTAAGGCCTACACATTGAG
66 TCACGATGAATCGGATAACCTCATTTCTTACTTTTTAAGGCCTACACATTGAG
547679 GACA
1 GACA
547683 ATGTGTTATC
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 118 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (118 bp):
GACACAACATTTCGAGATATTCACAAATAAAGGGAGAAGGACAACCACCATTAGAAGAAGAGCTT
TCACGATGAATCGGATAACCTCATTTCTTACTTTTTAAGGCCTACACATTGAG
Found at i:549280 original size:21 final size:21
Alignment explanation
Indices: 549256--549307 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
549246 TTGACTTCTT
*
549256 TGTCGTGACATACATTACTTA
1 TGTCGCGACATACATTACTTA
549277 TGTCGCGACATACATTACTTA
1 TGTCGCGACATACATTACTTA
549298 TGTCGCGACA
1 TGTCGCGACA
549308 ACACTTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (21 bp):
TGTCGCGACATACATTACTTA
Found at i:550433 original size:22 final size:22
Alignment explanation
Indices: 550408--550450 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
550398 TTTATGCCAA
*
550408 TTAAATGAATATAATTT-CATGT
1 TTAAATAAAT-TAATTTGCATGT
*
550430 TTAATTAAATTAATTTGCATG
1 TTAAATAAATTAATTTGCATG
550451 GTCCACTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (22 bp):
TTAAATAAATTAATTTGCATGT
Found at i:552541 original size:40 final size:40
Alignment explanation
Indices: 552497--552680 Score: 242
Period size: 40 Copynumber: 4.6 Consensus size: 40
552487 ACACCAACTT
* * * * *
552497 GTAGCTTGCTATGCCGTAGGTTGAGTCTTAACACTGGCTC
1 GTAGCCTGCTAAGCCGTAGCTTGAATCTTAACACCGGCTC
*
552537 GTAGCCTGCTAAGCCGTAGCTTGAATCCTAACACCGGCTC
1 GTAGCCTGCTAAGCCGTAGCTTGAATCTTAACACCGGCTC
* *
552577 ATAGCCTGCTAAGCCGTAGCTTGAATCTTAACACCGGCTT
1 GTAGCCTGCTAAGCCGTAGCTTGAATCTTAACACCGGCTC
* **
552617 GTAGCCTTCTAAGCCGTAGCTTGAATCTTAACACCAACTC
1 GTAGCCTGCTAAGCCGTAGCTTGAATCTTAACACCGGCTC
* * *
552657 GTAGCCGGCTAAGCTGAAGCTTGA
1 GTAGCCTGCTAAGCCGTAGCTTGA
552681 TATATCTCAT
Statistics
Matches: 126, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 126 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
GTAGCCTGCTAAGCCGTAGCTTGAATCTTAACACCGGCTC
Found at i:571622 original size:56 final size:56
Alignment explanation
Indices: 571530--571762 Score: 283
Period size: 56 Copynumber: 4.2 Consensus size: 56
571520 AATAGAGTGA
* * *
571530 TATTTTACACATGGCTCGAGTAGAGCGTTACTCTGAATCTTACTCGGGTAGAGCAT
1 TATTCTACATATGACTCGAGTAGAGCGTTACTCTGAATCTTACTCGGGTAGAGCAT
* * * * * * *
571586 TCTTCTGCTTATGACTCGGGTATAGCGTTACCCTGAATCTTACTCAGGTAGAGCAT
1 TATTCTACATATGACTCGAGTAGAGCGTTACTCTGAATCTTACTCGGGTAGAGCAT
* *
571642 TATTCTACATATGGCTC-AGGTAGACCGTTACTCTGAATCTTACTC-GGTAGAGCAT
1 TATTCTACATATGACTCGA-GTAGAGCGTTACTCTGAATCTTACTCGGGTAGAGCAT
* * * *
571697 TACTCTACATAT-AGCTCGAGTAAAGCGTTACTTTGAATCTTGCTCGGGTAGAGCAT
1 TATTCTACATATGA-CTCGAGTAGAGCGTTACTCTGAATCTTACTCGGGTAGAGCAT
571753 TATTCTACAT
1 TATTCTACAT
571763 CTTGCACGGG
Statistics
Matches: 148, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
55 46 0.31
56 102 0.69
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (56 bp):
TATTCTACATATGACTCGAGTAGAGCGTTACTCTGAATCTTACTCGGGTAGAGCAT
Found at i:571750 original size:111 final size:112
Alignment explanation
Indices: 571530--571762 Score: 312
Period size: 111 Copynumber: 2.1 Consensus size: 112
571520 AATAGAGTGA
* * * * *
571530 TATTTTACACATGGCTCGAGTAGAGCGTTACTCTGAATCTTACTCGGGTAGAGCATTCTTCTGCT
1 TATTCTACATATGGCTCGAGTAGACCGTTACTCTGAATCTTACTCGGGTAGAGCATTCTTCTACA
* *
571595 TATGACTCGGGTATAGCGTTACCCTGAATCTTACTCAGGTAGAGCAT
66 TATGACTCGAGTAAAGCGTTACCCTGAATCTTACTCAGGTAGAGCAT
571642 TATTCTACATATGGCTC-AGGTAGACCGTTACTCTGAATCTTACTC-GGTAGAGCATTAC-TCTA
1 TATTCTACATATGGCTCGA-GTAGACCGTTACTCTGAATCTTACTCGGGTAGAGCATT-CTTCTA
** * *
571704 CATAT-AGCTCGAGTAAAGCGTTACTTTGAATCTTGCTCGGGTAGAGCAT
64 CATATGA-CTCGAGTAAAGCGTTACCCTGAATCTTACTCAGGTAGAGCAT
571753 TATTCTACAT
1 TATTCTACAT
571763 CTTGCACGGG
Statistics
Matches: 107, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
110 1 0.01
111 65 0.61
112 41 0.38
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (112 bp):
TATTCTACATATGGCTCGAGTAGACCGTTACTCTGAATCTTACTCGGGTAGAGCATTCTTCTACA
TATGACTCGAGTAAAGCGTTACCCTGAATCTTACTCAGGTAGAGCAT
Found at i:571764 original size:28 final size:28
Alignment explanation
Indices: 571543--571788 Score: 146
Period size: 28 Copynumber: 8.8 Consensus size: 28
571533 TTTACACATG
* * *
571543 GCTCGAGTAGAGCGTTACTCTGAATCTT
1 GCTCGGGTAGAGCATTATTCTGAATCTT
* * *
571571 ACTCGGGTAGAGCATTCTTCTG-CT-TAT
1 GCTCGGGTAGAGCATTATTCTGAATCT-T
* * **
571598 GACTCGGGTATAGCGTTACCCTGAATCTT
1 G-CTCGGGTAGAGCATTATTCTGAATCTT
* * * *
571627 ACTCAGGTAGAGCATTATTCT-ACATATG
1 GCTCGGGTAGAGCATTATTCTGA-ATCTT
* * * *
571655 GCTCAGGTAGACCGTTACTCTGAATCTT
1 GCTCGGGTAGAGCATTATTCTGAATCTT
* * * *
571683 ACTC-GGTAGAGCATTACTCT-ACATATA
1 GCTCGGGTAGAGCATTATTCTGA-ATCTT
* * *
571710 GCTCGAGTAAAGCGTTACTT-TGAATCTT
1 GCTCGGGTAGAGCATTA-TTCTGAATCTT
571738 GCTCGGGTAGAGCATTATTCT-ACATCTT
1 GCTCGGGTAGAGCATTATTCTGA-ATCTT
* *
571766 GCACGGGTAAAGCATTATTCTGA
1 GCTCGGGTAGAGCATTATTCTGA
571789 TTTTGGCTTG
Statistics
Matches: 161, Mismatches: 44, Indels: 25
0.70 0.19 0.11
Matches are distributed among these distances:
26 2 0.01
27 26 0.16
28 126 0.78
29 6 0.04
30 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (28 bp):
GCTCGGGTAGAGCATTATTCTGAATCTT
Found at i:571776 original size:56 final size:56
Alignment explanation
Indices: 571543--571788 Score: 280
Period size: 56 Copynumber: 4.4 Consensus size: 56
571533 TTTACACATG
* * * * *
571543 GCTCGAGTAGAGCGTTACTCTGAATCTTACTCGGGTAGAGCATTCTTCTGCTTA-T
1 GCTCGGGTAAAGCGTTACTCTGAATCTTACTCGGGTAGAGCATTATTCTACATATT
* * * *
571598 GACTCGGGTATAGCGTTACCCTGAATCTTACTCAGGTAGAGCATTATTCTACATATG
1 G-CTCGGGTAAAGCGTTACTCTGAATCTTACTCGGGTAGAGCATTATTCTACATATT
* * * * *
571655 GCTCAGGTAGACCGTTACTCTGAATCTTACTC-GGTAGAGCATTACTCTACATATA
1 GCTCGGGTAAAGCGTTACTCTGAATCTTACTCGGGTAGAGCATTATTCTACATATT
* * * *
571710 GCTCGAGTAAAGCGTTACTTTGAATCTTGCTCGGGTAGAGCATTATTCTACATCTT
1 GCTCGGGTAAAGCGTTACTCTGAATCTTACTCGGGTAGAGCATTATTCTACATATT
* * *
571766 GCACGGGTAAAGCATTATTCTGA
1 GCTCGGGTAAAGCGTTACTCTGA
571789 TTTTGGCTTG
Statistics
Matches: 160, Mismatches: 28, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
55 48 0.30
56 111 0.69
57 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (56 bp):
GCTCGGGTAAAGCGTTACTCTGAATCTTACTCGGGTAGAGCATTATTCTACATATT
Found at i:571788 original size:111 final size:112
Alignment explanation
Indices: 571557--571788 Score: 281
Period size: 111 Copynumber: 2.1 Consensus size: 112
571547 GAGTAGAGCG
* * * *
571557 TTACTCTGAATCTTACTCGGGTAGAGCATTCTTCTGCTTATGACTCGGGTATAGCGTTACCCTGA
1 TTACTCTGAATCTTACTCGGGTAGAGCATTCTTCTACATATGACTCGAGTAAAGCGTTACCCTGA
* * *
571622 ATCTTACTCAGGTAGAGCATTATTCTACATATGGCTCAGGTAGACCG
66 ATCTTACTCAGGTAGAGCATTATTCTACATATGGCACAGGTAAACCA
**
571669 TTACTCTGAATCTTACTC-GGTAGAGCATTAC-TCTACATAT-AGCTCGAGTAAAGCGTTACTTT
1 TTACTCTGAATCTTACTCGGGTAGAGCATT-CTTCTACATATGA-CTCGAGTAAAGCGTTACCCT
* * * * * *
571731 GAATCTTGCTCGGGTAGAGCATTATTCTACATCTTGCACGGGTAAAGCA
64 GAATCTTACTCAGGTAGAGCATTATTCTACATATGGCACAGGTAAACCA
*
571780 TTATTCTGA
1 TTACTCTGA
571789 TTTTGGCTTG
Statistics
Matches: 102, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
110 1 0.01
111 82 0.80
112 19 0.19
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (112 bp):
TTACTCTGAATCTTACTCGGGTAGAGCATTCTTCTACATATGACTCGAGTAAAGCGTTACCCTGA
ATCTTACTCAGGTAGAGCATTATTCTACATATGGCACAGGTAAACCA
Found at i:571812 original size:28 final size:28
Alignment explanation
Indices: 571781--571896 Score: 124
Period size: 28 Copynumber: 4.1 Consensus size: 28
571771 GGTAAAGCAT
* * **
571781 TATTCTGATTTTGGCTTGGAAAGAATGG
1 TATTCTGATTCTGGCTTGAAAAGAGCGG
* *
571809 TATTCTGATTCTGGCTCGAAAAGAGCAG
1 TATTCTGATTCTGGCTTGAAAAGAGCGG
* * *
571837 TATTTTGATTTTGACTTGAAAAGAGCGG
1 TATTCTGATTCTGGCTTGAAAAGAGCGG
* * *
571865 TATTCTAATTCTGGCTCGAAAAGAGCGA
1 TATTCTGATTCTGGCTTGAAAAGAGCGG
571893 TATT
1 TATT
571897 TTGGTACTGG
Statistics
Matches: 71, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 71 1.00
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.35
Consensus pattern (28 bp):
TATTCTGATTCTGGCTTGAAAAGAGCGG
Found at i:571860 original size:56 final size:56
Alignment explanation
Indices: 571776--571899 Score: 169
Period size: 56 Copynumber: 2.2 Consensus size: 56
571766 GCACGGGTAA
* * * * * *
571776 AGCATTATTCTGATTTTGGCTTGGAAAGAATGGTATTCTGATTCTGGCTCGAAAAG
1 AGCAGTATTTTGATTTTGACTTGAAAAGAACGGTATTCTAATTCTGGCTCGAAAAG
*
571832 AGCAGTATTTTGATTTTGACTTGAAAAGAGCGGTATTCTAATTCTGGCTCGAAAAG
1 AGCAGTATTTTGATTTTGACTTGAAAAGAACGGTATTCTAATTCTGGCTCGAAAAG
571888 AGC-GATATTTTG
1 AGCAG-TATTTTG
571900 GTACTGGCTC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 1 0.02
56 59 0.98
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.35
Consensus pattern (56 bp):
AGCAGTATTTTGATTTTGACTTGAAAAGAACGGTATTCTAATTCTGGCTCGAAAAG
Found at i:571906 original size:28 final size:28
Alignment explanation
Indices: 571808--571940 Score: 135
Period size: 28 Copynumber: 4.8 Consensus size: 28
571798 GGAAAGAATG
*
571808 GTATTCTGATTCTGGCTCGAAAAGAGCA
1 GTATTTTGATTCTGGCTCGAAAAGAGCA
* * * *
571836 GTATTTTGATTTTGACTTGAAAAGAGCG
1 GTATTTTGATTCTGGCTCGAAAAGAGCA
* *
571864 GTATTCTAATTCTGGCTCGAAAAGAGC-
1 GTATTTTGATTCTGGCTCGAAAAGAGCA
* * *
571891 GATATTTTGGTACTGGCTCGAGAAGAGCA
1 G-TATTTTGATTCTGGCTCGAAAAGAGCA
*
571920 TTATTTT-ATTCTAGGCTCGAA
1 GTATTTTGATTCT-GGCTCGAA
571941 TGGGCAATGA
Statistics
Matches: 83, Mismatches: 19, Indels: 6
0.77 0.18 0.06
Matches are distributed among these distances:
27 4 0.05
28 79 0.95
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (28 bp):
GTATTTTGATTCTGGCTCGAAAAGAGCA
Found at i:574883 original size:21 final size:21
Alignment explanation
Indices: 574831--574884 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
574821 GGAGTTTTTA
*
574831 GTATCGGTAGAAGCATGACTT
1 GTATCGGTAGAAGCATCACTT
* *
574852 GTATTGATAGAAGCGA-CACTT
1 GTATCGGTAGAAGC-ATCACTT
574873 GTATCGGTAGAA
1 GTATCGGTAGAA
574885 TTCTGTACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (21 bp):
GTATCGGTAGAAGCATCACTT
Found at i:585783 original size:24 final size:26
Alignment explanation
Indices: 585729--585796 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 26
585719 CCCAAATTGT
*
585729 TGACCCAAACCATGAAGCCAAACCTA
1 TGACCCAAACCATAAAGCCAAACCTA
* *
585755 TGACCCAATCCA-AAAGCCTAA-CTA
1 TGACCCAAACCATAAAGCCAAACCTA
*
585779 TGACCCAAA-CATAGAGCC
1 TGACCCAAACCATAAAGCC
585797 CGTTCAATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.06
24 16 0.44
25 7 0.19
26 11 0.31
ACGTcount: A:0.41, C:0.34, G:0.12, T:0.13
Consensus pattern (26 bp):
TGACCCAAACCATAAAGCCAAACCTA
Found at i:585929 original size:13 final size:13
Alignment explanation
Indices: 585898--585935 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
585888 ATTAATCGAG
585898 CCATTGACTATTGA
1 CCATTGACT-TTGA
*
585912 TCATTGACTTTGA
1 CCATTGACTTTGA
585925 CCATTGACTTT
1 CCATTGACTTT
585936 TTTGAACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (13 bp):
CCATTGACTTTGA
Found at i:588026 original size:118 final size:118
Alignment explanation
Indices: 587887--588123 Score: 474
Period size: 118 Copynumber: 2.0 Consensus size: 118
587877 TTGAAAGAAT
587887 TTAAGGGTTTTTCACAACATCCTTTGAAAATAATAGGATTCTTCATTGATGATGAATGAACATTA
1 TTAAGGGTTTTTCACAACATCCTTTGAAAATAATAGGATTCTTCATTGATGATGAATGAACATTA
587952 GAACTTGACCTTTCTTTGTTTTCCAAACTAATTTCTTGGAACCACCTAAAGGC
66 GAACTTGACCTTTCTTTGTTTTCCAAACTAATTTCTTGGAACCACCTAAAGGC
588005 TTAAGGGTTTTTCACAACATCCTTTGAAAATAATAGGATTCTTCATTGATGATGAATGAACATTA
1 TTAAGGGTTTTTCACAACATCCTTTGAAAATAATAGGATTCTTCATTGATGATGAATGAACATTA
588070 GAACTTGACCTTTCTTTGTTTTCCAAACTAATTTCTTGGAACCACCTAAAGGC
66 GAACTTGACCTTTCTTTGTTTTCCAAACTAATTTCTTGGAACCACCTAAAGGC
588123 T
1 T
588124 GCTAATGCTT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 119 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (118 bp):
TTAAGGGTTTTTCACAACATCCTTTGAAAATAATAGGATTCTTCATTGATGATGAATGAACATTA
GAACTTGACCTTTCTTTGTTTTCCAAACTAATTTCTTGGAACCACCTAAAGGC
Found at i:589762 original size:14 final size:14
Alignment explanation
Indices: 589743--589787 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
589733 TTATAACAAG
589743 ATTTATTTTACTTT
1 ATTTATTTTACTTT
*
589757 ATTTATTTTATTTT
1 ATTTATTTTACTTT
*
589771 CATTCTATTTTAGTTT
1 -ATT-TATTTTACTTT
589787 A
1 A
589788 ACATTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 13 0.48
15 4 0.15
16 10 0.37
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (14 bp):
ATTTATTTTACTTT
Found at i:593196 original size:20 final size:20
Alignment explanation
Indices: 593168--593206 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
593158 TGTCTCAAGA
* *
593168 AATATATAAATAATAATAAT
1 AATAAATAAATAAAAATAAT
593188 AATAAATAAATAAAAATAA
1 AATAAATAAATAAAAATAA
593207 AGAAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AATAAATAAATAAAAATAAT
Found at i:596389 original size:28 final size:28
Alignment explanation
Indices: 596357--596421 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
596347 TTTTTTTGAC
596357 AATACAAGTTTTTTACTAAAAGATGAAG
1 AATACAAGTTTTTTACTAAAAGATGAAG
596385 AATACAAGTTTTTTACTAAAAGATGAAG
1 AATACAAGTTTTTTACTAAAAGATGAAG
596413 AATACAAGT
1 AATACAAGT
596422 GAACCCAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.31
Consensus pattern (28 bp):
AATACAAGTTTTTTACTAAAAGATGAAG
Found at i:602378 original size:16 final size:17
Alignment explanation
Indices: 602348--602388 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
602338 AATTTAGAAT
* *
602348 AAATTAAAATGAATTTA
1 AAATTTAAATGAATTAA
602365 AAATTTAAAT-AATTAA
1 AAATTTAAATGAATTAA
602381 AAATTTAA
1 AAATTTAA
602389 TATTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
AAATTTAAATGAATTAA
Found at i:602404 original size:24 final size:24
Alignment explanation
Indices: 602359--602424 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
602349 AATTAAAATG
** *
602359 AATTTAAAATT-TAAATAATTAAA
1 AATTTAAAATTATATTTATTTAAA
* *
602382 AATTTAATATTTTATTTATTTAAA
1 AATTTAAAATTATATTTATTTAAA
*
602406 ATTTTAAAATTATATTTAT
1 AATTTAAAATTATATTTAT
602425 AACTTTCATA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
23 10 0.29
24 25 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
AATTTAAAATTATATTTATTTAAA
Found at i:602959 original size:17 final size:17
Alignment explanation
Indices: 602929--602961 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
602919 TTAACTCAAT
602929 TTAATTAAAATAAAATA
1 TTAATTAAAATAAAATA
602946 TTAA-TAAAATTAAAAT
1 TTAATTAAAA-TAAAAT
602962 TAAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAATTAAAATAAAATA
Found at i:603212 original size:23 final size:23
Alignment explanation
Indices: 603186--603233 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
603176 TACTATTGAT
603186 TAAAAGAATAAATTTATTTAAAA
1 TAAAAGAATAAATTTATTTAAAA
* * *
603209 TAAATGTATAATTTTATTTAAAA
1 TAAAAGAATAAATTTATTTAAAA
603232 TA
1 TA
603234 TATTGTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
TAAAAGAATAAATTTATTTAAAA
Found at i:603290 original size:2 final size:2
Alignment explanation
Indices: 603283--603307 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
603273 CATAACATTA
603283 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 A
603308 ACTTGTAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:615050 original size:22 final size:21
Alignment explanation
Indices: 615011--615062 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
615001 TAATTCAATT
* *
615011 TTAATTTATATTGGTTTTTCAA
1 TTAATTTTTACTGGTTTTT-AA
*
615033 TTAATTTTTACTGTTTTTTAA
1 TTAATTTTTACTGGTTTTTAA
615054 -TAATTTTTA
1 TTAATTTTTA
615063 AAATAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 9 0.33
21 2 0.07
22 16 0.59
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (21 bp):
TTAATTTTTACTGGTTTTTAA
Found at i:615057 original size:20 final size:21
Alignment explanation
Indices: 615024--615062 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
615014 ATTTATATTG
615024 GTTTTTCAATTAATTTTTACT
1 GTTTTTCAATTAATTTTTACT
*
615045 GTTTTTTAA-TAATTTTTA
1 GTTTTTCAATTAATTTTTA
615063 AAATAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (21 bp):
GTTTTTCAATTAATTTTTACT
Found at i:618087 original size:80 final size:80
Alignment explanation
Indices: 617954--618117 Score: 292
Period size: 80 Copynumber: 2.0 Consensus size: 80
617944 GTGAGTTTGG
* *
617954 GAAAGCTTAGTGAATAAAGATGCATACAACACCATAAAACACATCAACGATTCTATAATAACTCG
1 GAAAGCTTAGTGAATAAAGATGCATACAACACCATAAAACACATCAACGATTCTATAACAACCCG
* *
618019 TTTTTCAGTGGTCTC
66 TTCTTCAGTGGTATC
618034 GAAAGCTTAGTGAATAAAGATGCATACAACACCATAAAACACATCAACGATTCTATAACAACCCG
1 GAAAGCTTAGTGAATAAAGATGCATACAACACCATAAAACACATCAACGATTCTATAACAACCCG
618099 TTCTTCAGTGGTATC
66 TTCTTCAGTGGTATC
618114 GAAA
1 GAAA
618118 ACGATGGTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (80 bp):
GAAAGCTTAGTGAATAAAGATGCATACAACACCATAAAACACATCAACGATTCTATAACAACCCG
TTCTTCAGTGGTATC
Done.