Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009610.1 Hibiscus syriacus cultivar Beakdansim tig00116996_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3811333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 18
Found at i:501165 original size:13 final size:14
Alignment explanation
Indices: 501134--501186 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 14
501124 ATATGTATAT
501134 ATATAAATATAGGA
1 ATATAAATATAGGA
501148 TATATAAATATAGG-
1 -ATATAAATATAGGA
*
501162 ATATAAA-ATAGATA
1 ATATAAATATAG-GA
*
501176 ATATAAGTATA
1 ATATAAATATA
501187 TATATATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 4 0.12
13 7 0.21
14 6 0.18
15 16 0.48
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (14 bp):
ATATAAATATAGGA
Found at i:501172 original size:27 final size:28
Alignment explanation
Indices: 501134--501186 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
501124 ATATGTATAT
501134 ATATAAATATAGGAT-ATATAAATATAGG
1 ATATAAATATA-GATAATATAAATATAGG
*
501162 ATATAAA-ATAGATAATATAAGTATA
1 ATATAAATATAGATAATATAAATATA
501187 TATATATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 13 0.57
28 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (28 bp):
ATATAAATATAGATAATATAAATATAGG
Found at i:501276 original size:26 final size:26
Alignment explanation
Indices: 501246--501295 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
501236 AACGTGATAT
** *
501246 ACATATATATTTATATAAATAAAATA
1 ACATATATAAATAAATAAATAAAATA
*
501272 ACATATGTAAATAAATAAATAAAA
1 ACATATATAAATAAATAAATAAAA
501296 ATTAAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (26 bp):
ACATATATAAATAAATAAATAAAATA
Found at i:503047 original size:106 final size:106
Alignment explanation
Indices: 502912--503487 Score: 813
Period size: 106 Copynumber: 5.4 Consensus size: 106
502902 TGCTGACAGT
502912 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAG
1 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAG
*
502977 -TAAGAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
66 TTGA-AATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * *
503018 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACGATATCCTCCG-TCGT
1 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT--C-CAATATCCTTCGCT-GT
* * *** * * *
503082 GGAGTTGAAA-TCGCGGGAGAAACT-GAAAAGTTGTTTATTGACAAC
62 GAAGTTGAAATTGGC-TCTGAAATTGGGAAA-TTGTTTGTTGACAAC
* *
503127 CAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAG
1 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAG
503192 TTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
66 TTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * * *
503233 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGAAGTCCAATATCCTTCGTTGTGAA
1 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG-AGTCCAATATCCTTCGCTGTGAA
*
503297 GTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAAC
65 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * * *
503339 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
1 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAG
*
503404 TTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAC
66 TTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
503444 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
1 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
503488 GATATCCTCC
Statistics
Matches: 421, Mismatches: 37, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
105 53 0.13
106 268 0.64
107 10 0.02
108 9 0.02
109 79 0.19
110 2 0.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (106 bp):
CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAG
TTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
Found at i:505007 original size:21 final size:21
Alignment explanation
Indices: 504981--505025 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
504971 GATTTCTGGG
* *
504981 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
505002 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
505023 CAA
1 CAA
505026 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:518002 original size:19 final size:18
Alignment explanation
Indices: 517960--518002 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
517950 GTATTAGATG
*
517960 GAAAAATGAAAAAAGAAA
1 GAAAAAGGAAAAAAGAAA
*
517978 GTAAAAAGGAATAAAATAAA
1 G-AAAAAGGAA-AAAAGAAA
517998 GAAAA
1 GAAAA
518003 TAAACATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 12 0.57
20 8 0.38
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.09
Consensus pattern (18 bp):
GAAAAAGGAAAAAAGAAA
Found at i:518341 original size:15 final size:15
Alignment explanation
Indices: 518321--518360 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
518311 ATATATGTAT
518321 ATATATAAATATAGG
1 ATATATAAATATAGG
518336 ATATATAAATATAGG
1 ATATATAAATATAGG
518351 ATATA-AAATA
1 ATATATAAATA
518361 GATAATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (15 bp):
ATATATAAATATAGG
Found at i:518354 original size:13 final size:14
Alignment explanation
Indices: 518323--518375 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 14
518313 ATATGTATAT
518323 ATATAAATATAGGA
1 ATATAAATATAGGA
518337 TATATAAATATAGG-
1 -ATATAAATATAGGA
*
518351 ATATAAA-ATAGATA
1 ATATAAATATAG-GA
*
518365 ATATAAGTATA
1 ATATAAATATA
518376 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 4 0.12
13 7 0.21
14 6 0.18
15 16 0.48
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (14 bp):
ATATAAATATAGGA
Found at i:518361 original size:27 final size:28
Alignment explanation
Indices: 518323--518375 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
518313 ATATGTATAT
518323 ATATAAATATAGGAT-ATATAAATATAGG
1 ATATAAATATA-GATAATATAAATATAGG
*
518351 ATATAAA-ATAGATAATATAAGTATA
1 ATATAAATATAGATAATATAAATATA
518376 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 13 0.57
28 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (28 bp):
ATATAAATATAGATAATATAAATATAGG
Found at i:518467 original size:26 final size:26
Alignment explanation
Indices: 518437--518486 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
518427 AACGTGATAT
** *
518437 ACATATATATTTATATAAATAAAATA
1 ACATATATAAATAAATAAATAAAATA
*
518463 ACATATGTAAATAAATAAATAAAA
1 ACATATATAAATAAATAAATAAAA
518487 ATTAAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (26 bp):
ACATATATAAATAAATAAATAAAATA
Found at i:520431 original size:32 final size:32
Alignment explanation
Indices: 520385--520456 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
520375 CATACATTTT
* *
520385 AGACATTGCCACATTAATGATATTATTACACC
1 AGACTTTGCCACATTAATGATATTATCACACC
*
520417 AGACTTTGCCACATTACTGATATTATCACACC
1 AGACTTTGCCACATTAATGATATTATCACACC
520449 AGACTTTG
1 AGACTTTG
520457 GGTGTCTTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (32 bp):
AGACTTTGCCACATTAATGATATTATCACACC
Found at i:523217 original size:13 final size:13
Alignment explanation
Indices: 523199--523238 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
523189 CCTTCTATAC
*
523199 AAGAGAGAGAAAA
1 AAGAGAAAGAAAA
523212 AAGAGAAAGAAAA
1 AAGAGAAAGAAAA
**
523225 AATTGAAAGAAAA
1 AAGAGAAAGAAAA
523238 A
1 A
523239 GAAAACCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (13 bp):
AAGAGAAAGAAAA
Found at i:530567 original size:15 final size:15
Alignment explanation
Indices: 530547--530577 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
530537 AAACAAAGTC
530547 ATTTGTACTAACTTG
1 ATTTGTACTAACTTG
530562 ATTTGTACTAACTTG
1 ATTTGTACTAACTTG
530577 A
1 A
530578 ACTCGTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (15 bp):
ATTTGTACTAACTTG
Found at i:532487 original size:26 final size:28
Alignment explanation
Indices: 532457--532509 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
532447 ATTAAAATTT
*
532457 TTAATATTATATA-AATTATTT-TCATA
1 TTAATATTATATAGAATAATTTGTCATA
*
532483 TTAATTTTATATAGAATAATTTGTCAT
1 TTAATATTATATAGAATAATTTGTCAT
532510 CGAATGCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 7 0.30
28 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (28 bp):
TTAATATTATATAGAATAATTTGTCATA
Found at i:536541 original size:17 final size:18
Alignment explanation
Indices: 536509--536542 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
536499 TCTTCAGGTT
536509 ATTTTCATTCTTCTTAAA
1 ATTTTCATTCTTCTTAAA
*
536527 ATTTTCGTT-TTCTTAA
1 ATTTTCATTCTTCTTAA
536543 TAAAATGCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.15, G:0.03, T:0.59
Consensus pattern (18 bp):
ATTTTCATTCTTCTTAAA
Found at i:542637 original size:15 final size:16
Alignment explanation
Indices: 542617--542650 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
542607 AGCCACTCGA
542617 TTATTAA-TAAATTTT
1 TTATTAATTAAATTTT
*
542632 TTATTAATTATATTTT
1 TTATTAATTAAATTTT
542648 TTA
1 TTA
542651 AAAAAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTAATTAAATTTT
Found at i:542662 original size:37 final size:37
Alignment explanation
Indices: 542621--542702 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
542611 ACTCGATTAT
* *
542621 TAATAAATTTTTTATTAATTATATTTTTTAAAAAAGA
1 TAATAAATTTTTAATCAATTATATTTTTTAAAAAAGA
* *
542658 TAATAAGTTTTTAATCAATTATATTTTTTTAAAAAGA
1 TAATAAATTTTTAATCAATTATATTTTTTAAAAAAGA
*
542695 AAATAAAT
1 TAATAAAT
542703 CTATCACTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TAATAAATTTTTAATCAATTATATTTTTTAAAAAAGA
Found at i:544719 original size:20 final size:20
Alignment explanation
Indices: 544694--544786 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
544684 TTTTCCCAAT
544694 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
544714 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
544734 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* * *
544755 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
544776 TCGCAATGCGA
1 TCGCAATGCGA
544787 TACTGACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.46
21 32 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:544736 original size:41 final size:41
Alignment explanation
Indices: 544691--544786 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
544681 CGATTTTCCC
*
544691 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
544732 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
*
544773 AAATCGCAATGCGA
1 AATTCGCAATGCGA
544787 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
Found at i:544799 original size:41 final size:41
Alignment explanation
Indices: 544713--544847 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
544703 GAATAAGTAA
* * * *
544713 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
544754 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
544795 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
544836 TTCGCAACGCGA
1 ATCGCAACGCGA
544848 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:544800 original size:20 final size:20
Alignment explanation
Indices: 544775--544869 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
544765 AATTGAGAAA
*
544775 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
544795 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
544816 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
544836 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
544856 TTCGCAACGCGATA
1 ATCGCAACGCGATA
544870 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:545085 original size:22 final size:22
Alignment explanation
Indices: 545057--545100 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
545047 CACTCTCTCA
545057 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
545079 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
545101 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:545388 original size:20 final size:20
Alignment explanation
Indices: 545363--545400 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
545353 CGATTCTCTC
545363 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
545383 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
545401 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:546741 original size:18 final size:18
Alignment explanation
Indices: 546720--546764 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
546710 TCCACTTCAG
*
546720 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
546738 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
546756 GAGCCATCA
1 GAGCCATCA
546765 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:547290 original size:19 final size:20
Alignment explanation
Indices: 547236--547302 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
547226 TAGTTTACTT
* *
547236 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
547256 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
547276 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
547295 TCGCAACG
1 TCGCAACG
547303 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:547310 original size:14 final size:14
Alignment explanation
Indices: 547291--547348 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
547281 ATGCGAAATG
547291 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
547305 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
547321 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
547337 AAAATCGCAACG
1 AAAATCGCAACG
547349 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:547333 original size:32 final size:33
Alignment explanation
Indices: 547275--547365 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
547265 GGAAATGGCT
*
547275 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
547308 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
547340 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
547366 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:547359 original size:19 final size:19
Alignment explanation
Indices: 547236--547370 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
547226 TAGTTTACTT
* **
547236 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
547256 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
547276 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
547295 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
547309 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
547327 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
547341 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
547360 TCGCAATGCGA
1 TCGCAACGCGA
547371 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:547416 original size:32 final size:32
Alignment explanation
Indices: 547377--547487 Score: 204
Period size: 32 Copynumber: 3.4 Consensus size: 32
547367 GCGATTTGTG
547377 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
547409 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
547441 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
*
547474 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
547488 AGCCATTTCC
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 59 0.77
33 18 0.23
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:547486 original size:19 final size:18
Alignment explanation
Indices: 547377--547528 Score: 121
Period size: 14 Copynumber: 8.9 Consensus size: 18
547367 GCGATTTGTG
547377 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
547393 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
547409 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
547425 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
547441 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
547457 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
* **
547474 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGAT-TTCA
*
547493 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGAT-TTCA
547513 TTTCGCGTTGCGATTT
1 TTTCGCGTTGCGATTT
547529 TAAGTTTCGT
Statistics
Matches: 109, Mismatches: 12, Indels: 28
0.73 0.08 0.19
Matches are distributed among these distances:
14 30 0.28
15 3 0.03
16 10 0.09
17 2 0.02
18 24 0.22
19 23 0.21
20 17 0.16
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.44
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:547506 original size:20 final size:19
Alignment explanation
Indices: 547472--547526 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
547462 TTGCGATTTT
*
547472 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
547491 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
547511 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
547527 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:549413 original size:14 final size:14
Alignment explanation
Indices: 549394--549429 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
549384 ATTGTTTAAT
549394 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
549408 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
549422 TGATTTGT
1 TGATTTGT
549430 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:549568 original size:19 final size:19
Alignment explanation
Indices: 549546--549613 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
549536 ATCGCAACGA
549546 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
549565 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
549584 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
549598 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
549614 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:549657 original size:20 final size:20
Alignment explanation
Indices: 549632--549688 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
549622 TCGCATTGCG
*
549632 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
549652 ATTTTCGCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
*
549672 ATTTTCGCATTGCGATA
1 ATTTTCGCGTTGCGATA
549689 GTCAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:550074 original size:14 final size:14
Alignment explanation
Indices: 550055--550090 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
550045 ATTGTTTAAT
550055 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
550069 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
550083 TGATTTGT
1 TGATTTGT
550091 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:550664 original size:14 final size:14
Alignment explanation
Indices: 550645--550680 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
550635 ATTGTTTAAT
550645 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
550659 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
550673 TGATTTGT
1 TGATTTGT
550681 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:550706 original size:590 final size:590
Alignment explanation
Indices: 549652--551056 Score: 2749
Period size: 590 Copynumber: 2.4 Consensus size: 590
549642 TGCGATAACC
*
549652 ATTTTCGCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
549717 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
549782 AAGTGCACACAT-AAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
549846 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
549911 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
549976 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
550041 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
550106 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
456 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
550171 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCAATTTTCGTTTCGCA
521 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCAATTTTCGTTTCGCA
550236 TTGCG
586 TTGCG
550241 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
550306 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
550371 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
* *
550436 ATGTTTGGTTAAGTACCTAGAATTTAATAATTTGTTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
550501 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
550566 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
550631 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
550696 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
456 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
*
550761 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
521 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCAATTTTCGTTTCGCA
550826 TTGCG
586 TTGCG
550831 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
*
550896 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGTCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
550961 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
*
551026 ATATTTGGTTAAGTACCTAGAATTCAATAAT
196 ATGTTTGGTTAAGTACCTAGAATTCAATAAT
551057 AATTGTTAAA
Statistics
Matches: 808, Mismatches: 7, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
589 141 0.17
590 667 0.83
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (590 bp):
ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCAATTTTCGTTTCGCA
TTGCG
Found at i:551980 original size:24 final size:24
Alignment explanation
Indices: 551924--551982 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
551914 AGTCAGTATT
* *
551924 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
551948 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
551972 CGAATTTTGAT
1 CGAAATTTGAT
551983 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:552174 original size:12 final size:12
Alignment explanation
Indices: 552157--552181 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
552147 ATATAATCCT
552157 GAAGAAGAAAAA
1 GAAGAAGAAAAA
552169 GAAGAAGAAAAA
1 GAAGAAGAAAAA
552181 G
1 G
552182 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:554500 original size:19 final size:19
Alignment explanation
Indices: 554478--554575 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
554468 GGAAATTACT
554478 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
554497 ATCGTAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
554511 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
554530 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
554544 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
554563 ATCGCAACGCGAA
1 ATCGCAATGCGAA
554576 TTTAATTTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 18 0.30
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.50
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:554520 original size:33 final size:33
Alignment explanation
Indices: 554478--554571 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
554468 GGAAATTACT
*
554478 ATCGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
554511 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
554544 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
554572 CGAATTTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:554593 original size:19 final size:20
Alignment explanation
Indices: 554571--554613 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
554561 AAATCGCAAC
554571 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
554590 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
554610 GCGA
1 GCGA
554614 TTCTCTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:554773 original size:14 final size:14
Alignment explanation
Indices: 554754--554790 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
554744 CATCAATTAA
554754 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
554768 ACAAATCACCTTTT
1 ACAAATCAACTTTT
554782 ACAAATCAA
1 ACAAATCAA
554791 TTAAACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:556214 original size:21 final size:21
Alignment explanation
Indices: 556148--556214 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
556138 GTGAATCGGG
*
556148 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
556168 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
556190 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
556211 CTCT
1 CTCT
556215 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:556233 original size:42 final size:41
Alignment explanation
Indices: 556148--556270 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
556138 GTGAATCGGG
* * * * *
556148 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
556190 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
556232 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
556271 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:558352 original size:33 final size:33
Alignment explanation
Indices: 558295--558429 Score: 144
Period size: 33 Copynumber: 3.9 Consensus size: 33
558285 ATGAGATAAT
* *
558295 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
558329 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
558362 GAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA--CG--A
* **
558399 TGAAAATCGCAACGCGAAATGAAAATCGCAA
1 -GAGAATCGCAACGCGAAATGACTATCGCAA
558430 TGCGATTTTG
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
33 44 0.49
34 13 0.15
35 2 0.02
37 1 0.01
38 29 0.33
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:558387 original size:19 final size:19
Alignment explanation
Indices: 558365--558434 Score: 131
Period size: 19 Copynumber: 3.7 Consensus size: 19
558355 GCGACGAGAG
558365 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
558384 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
558403 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
558422 AATCGCAATGCGA
1 AATCGCAACGCGA
558435 TTTTGGTTTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:558463 original size:19 final size:19
Alignment explanation
Indices: 558430--558496 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
558420 AAAATCGCAA
**
558430 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
558449 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
** *
558468 TGCGATAGTTATTTCCGCTT
1 TGCGATTTTTATTT-CGCGT
558488 TGCGATTTT
1 TGCGATTTT
558497 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:559110 original size:20 final size:20
Alignment explanation
Indices: 559017--559110 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
559007 CGCTAAGTAA
* *
559017 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
559037 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
559057 ATCTCTTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
559078 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
559098 ATCGCATTGCGAT
1 ATCGCATTGCGAT
559111 TTTCCCAATT
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
20 46 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:559129 original size:41 final size:41
Alignment explanation
Indices: 559038--559172 Score: 121
Period size: 41 Copynumber: 3.3 Consensus size: 41
559028 AAAGTCAGTA
* * * ** *
559038 TCGCGTTGCGAAAGTAAGTATCTCTTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
559078 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
559120 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
*
559161 TTGCGTTGCGAT
1 TCGCGTTGCGAT
559173 TTACTTATTC
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 3 0.04
41 72 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:559143 original size:20 final size:20
Alignment explanation
Indices: 559099--559191 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
559089 ATAGTCAGTA
* **
559099 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
559120 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
559140 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
* *
559161 TTGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
559181 TCGCATTGCGA
1 TCGCATTGCGA
559192 ATTAGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:559173 original size:41 final size:41
Alignment explanation
Indices: 559099--559194 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
559089 ATAGTCAGTA
*
559099 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
*
559140 TCGCATTGCGAATTTCCCAATTTGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
559181 TCGCATTGCGAATT
1 TCGCATTGCGAATT
559195 AGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:562794 original size:56 final size:56
Alignment explanation
Indices: 562708--562820 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
562698 AATTTTCCAT
562708 GACTTCTACTTTCTATACGTTTCTGTCATTGGAAATTATGAAGGCTTAGAACTAGG
1 GACTTCTACTTTCTATACGTTTCTGTCATTGGAAATTATGAAGGCTTAGAACTAGG
562764 GACTTCTACTTTCTATACGTTTCTGTCATTGGAAATTATGAAGGCTTAGAACTAGG
1 GACTTCTACTTTCTATACGTTTCTGTCATTGGAAATTATGAAGGCTTAGAACTAGG
562820 G
1 G
562821 TAGCAGAGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (56 bp):
GACTTCTACTTTCTATACGTTTCTGTCATTGGAAATTATGAAGGCTTAGAACTAGG
Found at i:563062 original size:2 final size:2
Alignment explanation
Indices: 563055--563087 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
563045 TACAACTATT
563055 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
563088 GCATTGTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:570888 original size:8 final size:8
Alignment explanation
Indices: 570859--570897 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
570849 GGTAATTTGG
*
570859 ATATATAT
1 ATATAAAT
*
570867 ATATATAT
1 ATATAAAT
570875 ATATAAAT
1 ATATAAAT
570883 ATATAAAT
1 ATATAAAT
*
570891 AAATAAA
1 ATATAAA
570898 ACAGGACATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAAAT
Found at i:570892 original size:12 final size:12
Alignment explanation
Indices: 570859--570895 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
570849 GGTAATTTGG
*
570859 ATATATATATAT
1 ATATATATAAAT
570871 ATATATATAAAT
1 ATATATATAAAT
*
570883 ATATAAATAAAT
1 ATATATATAAAT
570895 A
1 A
570896 AAACAGGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATAAAT
Found at i:573363 original size:20 final size:23
Alignment explanation
Indices: 573347--573391 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
573337 ATATAAATTT
573347 ACTTTTAAAATTATAAATTTATTG
1 ACTTTTAAAATTATAAA-TTATTG
573371 ACTTTTAAAATTAT-AATTATT
1 ACTTTTAAAATTATAAATTATT
573392 CATTTGATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.24
23 2 0.10
24 14 0.67
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
ACTTTTAAAATTATAAATTATTG
Found at i:574751 original size:23 final size:23
Alignment explanation
Indices: 574718--574840 Score: 104
Period size: 23 Copynumber: 5.3 Consensus size: 23
574708 CACTATTTCT
574718 GAACATATAAACGAACATGTTCAC
1 GAACAT-TAAACGAACATGTTCAC
* *
574742 GAACGTTAAACAAACATGTT-AGC
1 GAACATTAAACGAACATGTTCA-C
** * ***
574765 GAATGTTAAACAAACATGTTTGT
1 GAACATTAAACGAACATGTTCAC
* * *
574788 GAACATATGAACGAACATGTCCGC
1 GAACAT-TAAACGAACATGTTCAC
*
574812 GAACATTAAACGAAAATGTTCAC
1 GAACATTAAACGAACATGTTCAC
574835 GAACAT
1 GAACAT
574841 CTTCAGAAAT
Statistics
Matches: 80, Mismatches: 16, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
22 1 0.01
23 56 0.70
24 23 0.29
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (23 bp):
GAACATTAAACGAACATGTTCAC
Found at i:574839 original size:47 final size:46
Alignment explanation
Indices: 574718--574840 Score: 113
Period size: 47 Copynumber: 2.6 Consensus size: 46
574708 CACTATTTCT
* * *
574718 GAACATATAAACGAACATGTTCACGAACGTTAAACAAACATGTTAGC
1 GAACAT-TAAACGAAAATGTTCACGAACATTAAACAAACATGTCAGC
** *** * * *
574765 GAATGTTAAAC-AAACATGTTTGTGAACATATGAACGAACATGTCCGC
1 GAACATTAAACGAAA-ATGTTCACGAACAT-TAAACAAACATGTCAGC
574812 GAACATTAAACGAAAATGTTCACGAACAT
1 GAACATTAAACGAAAATGTTCACGAACAT
574841 CTTCAGAAAT
Statistics
Matches: 57, Mismatches: 16, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
45 2 0.04
46 15 0.26
47 37 0.65
48 3 0.05
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (46 bp):
GAACATTAAACGAAAATGTTCACGAACATTAAACAAACATGTCAGC
Found at i:586489 original size:20 final size:21
Alignment explanation
Indices: 586464--586507 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
586454 TATTTTTTAA
586464 TATTTTT-TTTATTAAAAGTT
1 TATTTTTATTTATTAAAAGTT
* *
586484 TATTTTTATTTTTTAAAATTT
1 TATTTTTATTTATTAAAAGTT
586505 TAT
1 TAT
586508 AAATTCATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
TATTTTTATTTATTAAAAGTT
Found at i:587093 original size:8 final size:8
Alignment explanation
Indices: 587080--587106 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
587070 GTTTTTAAGT
587080 AATTTTAA
1 AATTTTAA
587088 AATTTTAA
1 AATTTTAA
587096 AATTTTAA
1 AATTTTAA
587104 AAT
1 AAT
587107 AAATAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:587866 original size:16 final size:16
Alignment explanation
Indices: 587828--587866 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
587818 TTCAAGATAA
*
587828 TTTATATTTTCGTTTT
1 TTTATATTTTCCTTTT
* *
587844 ATAATATTTTCCTTTT
1 TTTATATTTTCCTTTT
587860 TTTATAT
1 TTTATAT
587867 AAAATTCTGA
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTATATTTTCCTTTT
Found at i:587962 original size:7 final size:7
Alignment explanation
Indices: 587950--587996 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
587940 AATATTTTAT
587950 TATATTA
1 TATATTA
587957 TATATTA
1 TATATTA
*
587964 TTTATTA
1 TATATTA
*
587971 TTTATTA
1 TATATTA
587978 T-TATTA
1 TATATTA
587984 T-TATTAA
1 TATATT-A
587991 TATATT
1 TATATT
587997 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
6 10 0.27
7 23 0.62
8 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TATATTA
Found at i:587965 original size:3 final size:3
Alignment explanation
Indices: 587942--588010 Score: 65
Period size: 3 Copynumber: 23.3 Consensus size: 3
587932 TCTACAAAAA
587942 TAT T-T TAT TA- TAT TAT ATAT TATT TAT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TA-T TAT TAT TAT TAT TAT
* *
587988 TAA TA- TAT TTT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
588011 TTTGCAGGCC
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
2 8 0.14
3 39 0.70
4 9 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:587969 original size:19 final size:18
Alignment explanation
Indices: 587945--588002 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 18
587935 ACAAAAATAT
587945 TTTATTATATTATATATTA
1 TTTATTAT-TTATATATTA
587964 TTTATTATTTAT-TATTA
1 TTTATTATTTATATATTA
*
587981 -TTATTATTAATATATT-
1 TTTATTATTTATATATTA
587997 TTTATT
1 TTTATT
588003 TTATTATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
16 10 0.28
17 14 0.39
18 4 0.11
19 8 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTATTTATATATTA
Found at i:587971 original size:14 final size:13
Alignment explanation
Indices: 587945--588011 Score: 70
Period size: 14 Copynumber: 5.2 Consensus size: 13
587935 ACAAAAATAT
587945 TTTATTA-TATTA
1 TTTATTATTATTA
*
587957 TATATTATTTATTA
1 TTTATTA-TTATTA
587971 TTTATTATTATTA
1 TTTATTATTATTA
587984 -TTATTAATATATT-
1 TTTATT-AT-TATTA
587997 TTTATT-TTATTA
1 TTTATTATTATTA
588009 TTT
1 TTT
588012 TTGCAGGCCC
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
11 4 0.09
12 15 0.32
13 8 0.17
14 20 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:588006 original size:19 final size:18
Alignment explanation
Indices: 587942--588009 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 18
587932 TCTACAAAAA
587942 TATTTTATTATATTATATAT
1 TATTTTATTATA-TAT-TAT
*
587962 TA-TTTATTATTTATTAT
1 TATTTTATTATATATTAT
*
587979 TATTATTATTAATATATTTT
1 TATT-TTATT-ATATATTAT
587999 TATTTTATTAT
1 TATTTTATTAT
588010 TTTTGCAGGC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
17 5 0.12
18 6 0.14
19 18 0.43
20 13 0.31
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTTATTATATATTAT
Found at i:589584 original size:17 final size:18
Alignment explanation
Indices: 589553--589593 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
589543 TTTAGGCCTG
*
589553 GCCTGTGCCTGTTTAAAA
1 GCCTGTGCCTATTTAAAA
589571 GCCTG-GCCTATTTAAAA
1 GCCTGTGCCTATTTAAAA
589588 GCCTGT
1 GCCTGT
589594 TTAAAAGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (18 bp):
GCCTGTGCCTATTTAAAA
Found at i:589591 original size:12 final size:12
Alignment explanation
Indices: 589576--589609 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
589566 TAAAAGCCTG
*
589576 GCCTATTTAAAA
1 GCCTGTTTAAAA
589588 GCCTGTTTAAAA
1 GCCTGTTTAAAA
589600 GCCTGTTTAA
1 GCCTGTTTAA
589610 CAATAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (12 bp):
GCCTGTTTAAAA
Found at i:590864 original size:60 final size:60
Alignment explanation
Indices: 590767--590917 Score: 212
Period size: 60 Copynumber: 2.5 Consensus size: 60
590757 TAATCATAAA
* * * * *
590767 TTACAAAATGATCTTCCGACTATAAGACGTCATTTTATTAAATTCATCTACTATTGAAAG
1 TTACAAAATGATCTTCCGACTATAAGACGTTACTTTATTAAATCCATCGACTATTAAAAG
* *
590827 TTACAAAATGATCTTCCGACTATAAGACGTTACTTTATTAAGTCCTTCGACTATTAAAAG
1 TTACAAAATGATCTTCCGACTATAAGACGTTACTTTATTAAATCCATCGACTATTAAAAG
* * *
590887 TTACAAAATGATCATCCAACTATAGGACGTT
1 TTACAAAATGATCTTCCGACTATAAGACGTT
590918 TGTTGAGTAA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 81 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (60 bp):
TTACAAAATGATCTTCCGACTATAAGACGTTACTTTATTAAATCCATCGACTATTAAAAG
Found at i:613123 original size:17 final size:18
Alignment explanation
Indices: 613101--613135 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
613091 CTCATATGGG
*
613101 ATAAAATCTTTTT-AATA
1 ATAAAATATTTTTGAATA
613118 ATAAAATATTTTTGAATA
1 ATAAAATATTTTTGAATA
613136 TACTCAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (18 bp):
ATAAAATATTTTTGAATA
Found at i:614083 original size:2 final size:2
Alignment explanation
Indices: 614076--614158 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
614066 AGAGCAGGAA
614076 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
614118 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
614159 TCGAATGAAC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:614685 original size:16 final size:15
Alignment explanation
Indices: 614641--614686 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
614631 ATAAGGTAAT
* *
614641 TTTATTATAATATTT
1 TTTATTATATTATTA
614656 TTTATTATACTTATTA
1 TTTATTATA-TTATTA
614672 TTTATTATGATTATT
1 TTTATTAT-ATTATT
614687 TAAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 9 0.33
16 17 0.63
17 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTATTATATTATTA
Found at i:615428 original size:136 final size:136
Alignment explanation
Indices: 615184--615459 Score: 545
Period size: 136 Copynumber: 2.0 Consensus size: 136
615174 CAATGATGAT
615184 GTTGAAATGATGGCTGATTCTCAAAGTAATTATTCAGACACCGATATTGAGATGTATGCAAAGTT
1 GTTGAAATGATGGCTGATTCTCAAAGTAATTATTCAGACACCGATATTGAGATGTATGCAAAGTT
615249 TGCTCAAGTGTGTGCTGTTCGGGGTCAGTCATTAAGCTCCCACTATGGGTTGGCTGAACAAGTTG
66 TGCTCAAGTGTGTGCTGTTCGGGGTCAGTCATTAAGCTCCCACTATGGGTTGGCTGAACAAGTTG
615314 ATCAAA
131 ATCAAA
615320 GTTGAAATGATGGCTGATTCTCAAAGTAATTATTCAGACACCGATATTGAGATGTATGCAAAGTT
1 GTTGAAATGATGGCTGATTCTCAAAGTAATTATTCAGACACCGATATTGAGATGTATGCAAAGTT
615385 TGCTCAAGTGTGTGCTGTTCGGGGTCAGTCATTAAGCTCCCACTATGGGTTGGCTGAACAAGTTG
66 TGCTCAAGTGTGTGCTGTTCGGGGTCAGTCATTAAGCTCCCACTATGGGTTGGCTGAACAAGTTG
615450 ATCAAA
131 ATCAAA
615456 -TTGA
1 GTTGA
615460 CAGCCCGACT
Statistics
Matches: 140, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
135 4 0.03
136 136 0.97
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (136 bp):
GTTGAAATGATGGCTGATTCTCAAAGTAATTATTCAGACACCGATATTGAGATGTATGCAAAGTT
TGCTCAAGTGTGTGCTGTTCGGGGTCAGTCATTAAGCTCCCACTATGGGTTGGCTGAACAAGTTG
ATCAAA
Found at i:616452 original size:50 final size:51
Alignment explanation
Indices: 616377--616477 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 51
616367 AGCCATCATG
616377 CCCATGGTAAAAGCAAGCTCTCATATAGCTGTTGCTGTGTTGA-TTCAGTT
1 CCCATGGTAAAAGCAAGCTCTCATATAGCTGTTGCTGTGTTGATTTCAGTT
616427 CCCATGGTAAAAGCAAGCTCTCATATAGCTGTTGCTGTGTTGATTTCAGTT
1 CCCATGGTAAAAGCAAGCTCTCATATAGCTGTTGCTGTGTTGATTTCAGTT
616478 ATACAATCGC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 43 0.86
51 7 0.14
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (51 bp):
CCCATGGTAAAAGCAAGCTCTCATATAGCTGTTGCTGTGTTGATTTCAGTT
Found at i:618327 original size:35 final size:34
Alignment explanation
Indices: 618242--618328 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
618232 AATATAATTT
*
618242 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
*
618276 TAAATGATAA-ACAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACA-AAATTACAATAA--G-TATTAAATGG
618314 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
618329 ACCAAAATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 4 0.09
38 11 0.24
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:618361 original size:34 final size:33
Alignment explanation
Indices: 618323--618406 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 33
618313 GTAATAAACA
*
618323 AAATTAACCAAAATACATTAACAA-AAAGTCCAA-C
1 AAATTAA-CAAAATAAATTAA-AATAAA-TCCAACC
618357 AAATTTAACAAAATAAATTAAAATAAATCCAACC
1 AAA-TTAACAAAATAAATTAAAATAAATCCAACC
**
618391 AAATTAATGAAATAAA
1 AAATTAACAAAATAAA
618407 GTAAGTATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 18 0.41
34 22 0.50
35 4 0.09
ACGTcount: A:0.62, C:0.14, G:0.02, T:0.21
Consensus pattern (33 bp):
AAATTAACAAAATAAATTAAAATAAATCCAACC
Found at i:618406 original size:33 final size:34
Alignment explanation
Indices: 618319--618395 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 34
618309 AATGGTAATA
* *
618319 AACAAAATTAACCAAAATACATTAACAAAAAGTCC
1 AACAAATTTAA-CAAAATAAATTAACAAAAAGTCC
618354 AACAAATTTAACAAAATAAATTAA-AATAAA-TCC
1 AACAAATTTAACAAAATAAATTAACAA-AAAGTCC
618387 AACCAAATT
1 AA-CAAATT
618396 AATGAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 7 0.18
34 21 0.55
35 10 0.26
ACGTcount: A:0.61, C:0.17, G:0.01, T:0.21
Consensus pattern (34 bp):
AACAAATTTAACAAAATAAATTAACAAAAAGTCC
Found at i:620689 original size:16 final size:18
Alignment explanation
Indices: 620654--620708 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
620644 TATATCTACA
* *
620654 AAAATAATTAATTAAA-T
1 AAAATACTTAAATAAATT
620671 AAAATA-TTAAA-AAATT
1 AAAATACTTAAATAAATT
620687 -AAATACTTAAATAAATT
1 AAAATACTTAAATAAATT
620704 GAAAA
1 -AAAA
620709 CAAAATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
15 8 0.25
16 10 0.31
17 11 0.34
19 3 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAATACTTAAATAAATT
Found at i:622694 original size:20 final size:20
Alignment explanation
Indices: 622666--622920 Score: 131
Period size: 20 Copynumber: 12.7 Consensus size: 20
622656 GATTTTCCAG
*
622666 AATCTCAACGCGAATATGAA
1 AATCGCAACGCGAATATGAA
*
622686 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAATATGA-A
* * *
622706 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATATGAA
* *
622726 TATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATATG-AA
* *
622747 AATCGCAACGCGTATCT-ATA
1 AATCGCAACGCGAATATGA-A
* * *
622767 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATATGAA
* ** * *
622787 AATCGCAACACTTATTTGTA
1 AATCGCAACGCGAATATGAA
* * *
622807 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATATGAA
* *
622827 AATCGCAACGAGAATATGTA
1 AATCGCAACGCGAATATGAA
* * * ** *
622847 AATCGTAATGCGTATCCGTA
1 AATCGCAACGCGAATATGAA
*
622867 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATATG-AA
* ** *
622888 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATATGAA
622908 AATCGCAACGCGA
1 AATCGCAACGCGA
622921 TTTTTAAAGC
Statistics
Matches: 178, Mismatches: 47, Indels: 20
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.01
20 146 0.82
21 30 0.17
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGAATATGAA
Found at i:622715 original size:40 final size:39
Alignment explanation
Indices: 622666--622920 Score: 149
Period size: 40 Copynumber: 6.3 Consensus size: 39
622656 GATTTTCCAG
* *
622666 AATCTCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGAATATGAAAATCGCAACGCGAAC-TGTA
* * ** *
622706 AATCGCAACGCGATTCTGACTATCGCAACGACAATAC-GTAA
1 AATCGCAACGCGAATATGAAAATCGCAACG-CGA-ACTGT-A
* * *
622747 AATCGCAACGCGTATCT-ATAAATCGCAACGAGAA-TACGTA
1 AATCGCAACGCGAATATGA-AAATCGCAACGCGAACT--GTA
* ** * * *
622787 AATCGCAACACTTATTTGTAAATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACTGTA
* * * * * *
622827 AATCGCAACGAGAATATGTAAATCGTAATGCGTATCCGTA
1 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACTGTA
* * *
622867 AATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACG-CGAATATG-AAAATCGCAACGCG-AACTGTA
622908 AATCGCAACGCGA
1 AATCGCAACGCGA
622921 TTTTTAAAGC
Statistics
Matches: 170, Mismatches: 32, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
39 1 0.01
40 106 0.62
41 60 0.35
42 3 0.02
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (39 bp):
AATCGCAACGCGAATATGAAAATCGCAACGCGAACTGTA
Found at i:622758 original size:41 final size:39
Alignment explanation
Indices: 622704--622795 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 39
622694 CGCGAACATA
622704 TAAATCGCAACGCG-ATTCTGACT-ATCGCAACGACAATACG
1 TAAATCGCAACGCGTA-TCT-A-TAATCGCAACGACAATACG
*
622744 TAAAATCGCAACGCGTATCTATAAATCGCAACGAGAATACG
1 T-AAATCGCAACGCGTATCTAT-AATCGCAACGACAATACG
622785 TAAATCGCAAC
1 TAAATCGCAAC
622796 ACTTATTTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
39 1 0.02
40 12 0.26
41 33 0.70
42 1 0.02
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (39 bp):
TAAATCGCAACGCGTATCTATAATCGCAACGACAATACG
Found at i:622868 original size:60 final size:60
Alignment explanation
Indices: 622746--622916 Score: 193
Period size: 60 Copynumber: 2.8 Consensus size: 60
622736 ACAATACGTA
* **
622746 AAATCGCAACGCGTATCTATAAATCGCAACGAGAATACGTAAATCGCAACACTTATTTGT
1 AAATCGCAACGCGTATCTATAAATCGCAACGAGAATACGTAAATCGCAACACGTATCCGT
* * * **
622806 AAATCGCAACGCGTATCTGTAAATCGCAACGAGAATATGTAAATCGTAATGCGTATCCGT
1 AAATCGCAACGCGTATCTATAAATCGCAACGAGAATACGTAAATCGCAACACGTATCCGT
* * * *
622866 AAATCGCAACGAC-AATACGTA-AAATCGCAACGCGTATCCGTAAATCGCAAC
1 AAATCGCAACG-CGTAT-C-TATAAATCGCAACGAGAATACGTAAATCGCAAC
622917 GCGATTTTTA
Statistics
Matches: 92, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
60 65 0.71
61 26 0.28
62 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (60 bp):
AAATCGCAACGCGTATCTATAAATCGCAACGAGAATACGTAAATCGCAACACGTATCCGT
Found at i:623222 original size:20 final size:20
Alignment explanation
Indices: 623197--623234 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
623187 GCGATTTTCC
623197 TAAATCACAACGCGATTACG
1 TAAATCACAACGCGATTACG
* *
623217 TAAATCGCAATGCGATTA
1 TAAATCACAACGCGATTA
623235 TTCGTATTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (20 bp):
TAAATCACAACGCGATTACG
Found at i:623278 original size:20 final size:20
Alignment explanation
Indices: 623236--623274 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
623226 ATGCGATTAT
623236 TCGTATTGCGATTTACGTAA
1 TCGTATTGCGATTTACGTAA
623256 TCGTATTGCGATTTA-GTAA
1 TCGTATTGCGATTTACGTAA
623275 ATCGCAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (20 bp):
TCGTATTGCGATTTACGTAA
Found at i:624197 original size:24 final size:24
Alignment explanation
Indices: 624139--624185 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
624129 AGTCAGTATT
*
624139 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
624163 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
624186 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:626744 original size:14 final size:14
Alignment explanation
Indices: 626725--626761 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
626715 CATCAATTAA
626725 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
626739 ACAAATCATCTTTT
1 ACAAATCAACTTTT
626753 ACAAATCAA
1 ACAAATCAA
626762 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:628706 original size:19 final size:19
Alignment explanation
Indices: 628679--628762 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
628669 GCAACGAGAG
*
628679 AATCACAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
628698 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
628717 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
628731 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
628750 AATCGCAACGCGA
1 AATCGCAACGCGA
628763 TTATAGTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 40 0.71
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:628727 original size:52 final size:50
Alignment explanation
Indices: 628650--628762 Score: 190
Period size: 52 Copynumber: 2.2 Consensus size: 50
628640 AAAATGACTT
628650 TCGCAACGCGAAATGAATCGCAACGAGAGAATCACAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAATCGCAACGAGAGAATCACAACGCGAAATGAAAA
* *
628700 TCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATG--AATCGCAACGAGAGAATCACAACGCGAAATGAAAA
628752 TCGCAACGCGA
1 TCGCAACGCGA
628763 TTATAGTTTC
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
50 15 0.25
52 44 0.75
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (50 bp):
TCGCAACGCGAAATGAATCGCAACGAGAGAATCACAACGCGAAATGAAAA
Found at i:628781 original size:19 final size:19
Alignment explanation
Indices: 628759--628802 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
628749 AAATCGCAAC
628759 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
* *
628778 GCGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
628797 GCGATT
1 GCGATT
628803 TTGTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.30, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTCGCGTT
Found at i:628803 original size:19 final size:18
Alignment explanation
Indices: 628768--628835 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 18
628758 CGCGATTATA
628768 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
628786 GGTTTCGCGTTGCGATTTT
1 -GTTTCGCGTTGCGATTTT
628805 G--T--CGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
*
628819 CATTTCGCGTTGCGATT
1 -GTTTCGCGTTGCGATT
628836 CTCTCGTTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
14 12 0.28
16 1 0.02
17 1 0.02
18 1 0.02
19 28 0.65
ACGTcount: A:0.07, C:0.18, G:0.28, T:0.47
Consensus pattern (18 bp):
GTTTCGCGTTGCGATTTT
Found at i:628816 original size:33 final size:33
Alignment explanation
Indices: 628774--628898 Score: 182
Period size: 33 Copynumber: 3.8 Consensus size: 33
628764 TATAGTTTCG
** * *
628774 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
628807 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
628840 CGTTGTGATTTTCATTTCTCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
628873 CGTTGCGA--TTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
628899 AGTCATTTTT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
31 17 0.20
33 67 0.80
ACGTcount: A:0.09, C:0.21, G:0.24, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:628849 original size:14 final size:14
Alignment explanation
Indices: 628826--628883 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
628816 TTTCATTTCG
628826 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
628840 CGTTGTGATTTTCATTTCT
1 CGTTGCGA--TTC---TCT
628859 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
628873 CGTTGCGATTC
1 CGTTGCGATTC
628884 ATTTCGCGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.57
16 3 0.08
17 3 0.08
19 10 0.27
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:629132 original size:94 final size:94
Alignment explanation
Indices: 628986--629365 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
628976 ATGGATTGCA
* * *
628986 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
629050 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
629079 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
629144 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
629173 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATATACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
* *
629238 TTAGCAGAATTGGCAGCAACTGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
629267 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACCGTGTTAAAGAATAAACAA
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAA
* *
629331 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
629361 TTACT
1 TTACT
629366 AAGCAATCTA
Statistics
Matches: 272, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
93 23 0.08
94 249 0.92
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:631181 original size:20 final size:20
Alignment explanation
Indices: 631135--631203 Score: 86
Period size: 20 Copynumber: 3.4 Consensus size: 20
631125 TTGGTTTCGC
631135 GTTGCGATAGTCATTTCTC-T
1 GTTGCGATAGTCATTT-TCAT
631155 CGTTGCGATAGTCATTTTCAT
1 -GTTGCGATAGTCATTTTCAT
* **
631176 GTTGCGCTTTTCATTTTCAT
1 GTTGCGATAGTCATTTTCAT
631196 GTTGCGAT
1 GTTGCGAT
631204 TTTAAGTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 26 0.60
21 17 0.40
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCAT
Found at i:631830 original size:20 final size:20
Alignment explanation
Indices: 631805--631971 Score: 156
Period size: 20 Copynumber: 8.2 Consensus size: 20
631795 GATTTTTGTC
*
631805 GCGATTTACGGATACGCATT
1 GCGATTTACGGATACGCGTT
* * *
631825 GCGATTTACGTATTCTCGTT
1 GCGATTTACGGATACGCGTT
*
631845 GCGATTTACAGATACGCGTT
1 GCGATTTACGGATACGCGTT
* * *
631865 GCGATTTACGTATTCTCGTT
1 GCGATTTACGGATACGCGTT
*
631885 GCAATTTACGGATACGCGTT
1 GCGATTTACGGATACGCGTT
* * *
631905 GTGATTTTACGTAT-TGTCGTT
1 GCGA-TTTACGGATACG-CGTT
* *
631926 GCGATTTACGGATACACATT
1 GCGATTTACGGATACGCGTT
* *
631946 GCGATTTTACGGATACTCATT
1 GCGA-TTTACGGATACGCGTT
631967 GCGAT
1 GCGAT
631972 AGTCAGAATC
Statistics
Matches: 117, Mismatches: 26, Indels: 8
0.77 0.17 0.05
Matches are distributed among these distances:
20 83 0.71
21 34 0.29
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.37
Consensus pattern (20 bp):
GCGATTTACGGATACGCGTT
Found at i:631926 original size:41 final size:40
Alignment explanation
Indices: 631766--631971 Score: 233
Period size: 40 Copynumber: 5.2 Consensus size: 40
631756 TTAAAAATCG
* *
631766 CGTTGCGATTTATGGATACG--TTGCG-TTT-CG-ATTTT
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
* *
631801 TGTCGCGATTTACGGATACGCATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
* *
631841 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
* * * *
631881 CGTTGCAATTTACGGATACGCGTTGTGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
* * *
631922 CGTTGCGATTTACGGATACACATTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
*
631963 CATTGCGAT
1 CGTTGCGAT
631972 AGTCAGAATC
Statistics
Matches: 145, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
35 17 0.12
37 5 0.03
38 3 0.02
39 2 0.01
40 65 0.45
41 53 0.37
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
Found at i:632131 original size:20 final size:19
Alignment explanation
Indices: 632082--632135 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
632072 ATTCTTCATA
632082 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
632101 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
632122 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
632136 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:636651 original size:23 final size:23
Alignment explanation
Indices: 636620--636666 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
636610 TCAAGTAGTT
*
636620 TGGAGAATGTTGAACCAGCCAAG
1 TGGAAAATGTTGAACCAGCCAAG
* *
636643 TGGAAAATGTTGAACGAGTCAAG
1 TGGAAAATGTTGAACCAGCCAAG
636666 T
1 T
636667 TTTGAAGCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (23 bp):
TGGAAAATGTTGAACCAGCCAAG
Found at i:638702 original size:33 final size:33
Alignment explanation
Indices: 638664--638736 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
638654 TTTTTTTTAG
638664 AAAAAGAAAAGGAAGGTGAGTAAGTAGAACGAA
1 AAAAAGAAAAGGAAGGTGAGTAAGTAGAACGAA
*
638697 AAAAAGAAAAGGAAGGTGAGTAAGTAGAATGAA
1 AAAAAGAAAAGGAAGGTGAGTAAGTAGAACGAA
*
638730 AGAAAGA
1 AAAAAGA
638737 GTAACACTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.59, C:0.01, G:0.30, T:0.10
Consensus pattern (33 bp):
AAAAAGAAAAGGAAGGTGAGTAAGTAGAACGAA
Found at i:638916 original size:23 final size:23
Alignment explanation
Indices: 638886--638932 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
638876 TCAAGTAGTT
638886 TGGAGAATGTTGAACCAGCCAAG
1 TGGAGAATGTTGAACCAGCCAAG
* *
638909 TGGAGAATGTTGAACGAGTCAAG
1 TGGAGAATGTTGAACCAGCCAAG
638932 T
1 T
638933 TTTGAAGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (23 bp):
TGGAGAATGTTGAACCAGCCAAG
Found at i:645975 original size:195 final size:196
Alignment explanation
Indices: 645643--646033 Score: 775
Period size: 195 Copynumber: 2.0 Consensus size: 196
645633 TAACTGAAAC
645643 GGAGAATCATAAGACGTAGTAGAACTAGAAAATGATAATTTAGGGCTATTTCCCATATGACAAGC
1 GGAGAATCATAAGACGTAGTAGAACTAGAAAATGATAATTTAGGGCTATTTCCCATATGACAAGC
645708 AACACAAACTTTATTAACATCTTTTAAAATTTTTACATCAATTATATTGCATACATTTTATAAAG
66 AACACAAACTTTATTAACATCTTTTAAAATTTTTACATCAATTATATTGCATACATTTTATAAAG
645773 TTACGGGAGCA-GATGCCTCATCCTACGATGCCATAGCTCATACAGATCATCCGAGCTCACCGAG
131 TTACGGGAGCAGGATGCCTCATCCTACGATGCCATAGCTCATACAGATCATCCGAGCTCACCGAG
645837 A
196 A
645838 GGAGAATCATAAGACGTAGTAGAACTAGAAAATGATAATTTAGGGCTATTTCCCATATGACAAGC
1 GGAGAATCATAAGACGTAGTAGAACTAGAAAATGATAATTTAGGGCTATTTCCCATATGACAAGC
645903 AACACAAACTTTATTAACATCTTTTAAAATTTTTACATCAATTATATTGCATACATTTTATAAAG
66 AACACAAACTTTATTAACATCTTTTAAAATTTTTACATCAATTATATTGCATACATTTTATAAAG
645968 TTACGGGAGCAGGATGCCTCATCCTACGATGCCATAGCTCATACAGATCATCCGAGCTCACCGAG
131 TTACGGGAGCAGGATGCCTCATCCTACGATGCCATAGCTCATACAGATCATCCGAGCTCACCGAG
646033 A
196 A
646034 CCAATACTTC
Statistics
Matches: 195, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
195 141 0.72
196 54 0.28
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (196 bp):
GGAGAATCATAAGACGTAGTAGAACTAGAAAATGATAATTTAGGGCTATTTCCCATATGACAAGC
AACACAAACTTTATTAACATCTTTTAAAATTTTTACATCAATTATATTGCATACATTTTATAAAG
TTACGGGAGCAGGATGCCTCATCCTACGATGCCATAGCTCATACAGATCATCCGAGCTCACCGAG
A
Found at i:651353 original size:4 final size:4
Alignment explanation
Indices: 651344--651390 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
651334 CTTTATAGAG
* * *
651344 ATGT ATGT ATGT ATTT ATGC ATGT ATGT ATGT ATAT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
651391 GAATCTGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:652378 original size:22 final size:22
Alignment explanation
Indices: 652326--652379 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
652316 AGTGTGTTCG
652326 GTTTATTTATATTTATGAACAA
1 GTTTATTTATATTTATGAACAA
** * *
652348 GTTCGTTTATGTTTATGAATAA
1 GTTTATTTATATTTATGAACAA
652370 GTTTATTTAT
1 GTTTATTTAT
652380 TGACTCATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.54
Consensus pattern (22 bp):
GTTTATTTATATTTATGAACAA
Found at i:657416 original size:37 final size:38
Alignment explanation
Indices: 657366--657446 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 38
657356 AATCACACAA
657366 ATTTTATTTATATGAATTATC-AAA-AATAAAAAAATAT
1 ATTTTATTTATATGAATTATCAAAAGAAT-AAAAAATAT
657403 ATTTTATTTATATGAATTATCAAAAGAATAAAAAATAT
1 ATTTTATTTATATGAATTATCAAAAGAATAAAAAATAT
657441 ATTTTA
1 ATTTTA
657447 GAAAATTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
37 21 0.50
38 18 0.43
39 3 0.07
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (38 bp):
ATTTTATTTATATGAATTATCAAAAGAATAAAAAATAT
Found at i:658334 original size:44 final size:45
Alignment explanation
Indices: 658273--658394 Score: 174
Period size: 45 Copynumber: 2.7 Consensus size: 45
658263 CCGATAAAGA
* *
658273 GCTACCTAAAACATTATTTGTTCTACCGGAATGATAATATTGGGC
1 GCTACCTAAAACATTATTTTTTCTACCGGAATGATAATATTGGAC
* *
658318 GCTACCT-AAACATTATTTTTTCTAACGGAAATGTTAATATTGGAC
1 GCTACCTAAAACATTATTTTTTCTACCGG-AATGATAATATTGGAC
*
658363 GCTACATAAAACATTATTTTTTTCTACCGGAA
1 GCTACCTAAAACATTA-TTTTTTCTACCGGAA
658395 ATTAGCTAGC
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 19 0.28
45 27 0.40
46 10 0.15
47 12 0.18
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (45 bp):
GCTACCTAAAACATTATTTTTTCTACCGGAATGATAATATTGGAC
Found at i:666270 original size:21 final size:21
Alignment explanation
Indices: 666244--666283 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
666234 GTCACCATCA
666244 AATTATATAGAAAATTAATCG
1 AATTATATAGAAAATTAATCG
666265 AATTATATAGAAAATTAAT
1 AATTATATAGAAAATTAAT
666284 AGAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (21 bp):
AATTATATAGAAAATTAATCG
Found at i:666290 original size:12 final size:12
Alignment explanation
Indices: 666243--666289 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
666233 TGTCACCATC
666243 AAATTATATAGA
1 AAATTATATAGA
*
666255 AAATTA-ATCG-
1 AAATTATATAGA
666265 -AATTATATAGA
1 AAATTATATAGA
666276 AAATTA-ATAGA
1 AAATTATATAGA
666287 AAA
1 AAA
666290 AGAAGCAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
11 11 0.37
12 11 0.37
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (12 bp):
AAATTATATAGA
Found at i:666553 original size:21 final size:21
Alignment explanation
Indices: 666527--666569 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
666517 ATTTTCGTAT
666527 CCACCACCTACCCACTATCTA
1 CCACCACCTACCCACTATCTA
666548 CCACCACCTACCCACTATCTA
1 CCACCACCTACCCACTATCTA
666569 C
1 C
666570 AATGAGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.53, G:0.00, T:0.19
Consensus pattern (21 bp):
CCACCACCTACCCACTATCTA
Found at i:666795 original size:30 final size:31
Alignment explanation
Indices: 666756--666815 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
666746 TTCATGTAAT
666756 AAAATGTTTATACCCTAACATTTAGTTAAAC
1 AAAATGTTTATACCCTAACATTTAGTTAAAC
*
666787 AAAA-GTTTATACCCTAACATTTGGTTAAA
1 AAAATGTTTATACCCTAACATTTAGTTAAA
666816 TTATAAGTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (31 bp):
AAAATGTTTATACCCTAACATTTAGTTAAAC
Found at i:672371 original size:11 final size:12
Alignment explanation
Indices: 672352--672376 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
672342 TGTAATTGAG
672352 TGAAAAAAATTA
1 TGAAAAAAATTA
672364 TGAAAAAAATTA
1 TGAAAAAAATTA
672376 T
1 T
672377 ATAAGGTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (12 bp):
TGAAAAAAATTA
Found at i:673690 original size:38 final size:38
Alignment explanation
Indices: 673637--673732 Score: 156
Period size: 38 Copynumber: 2.5 Consensus size: 38
673627 TTCGAGATAT
*
673637 ATGATAGGTCCTTCGGGACACAGATGACATCATTAGGG
1 ATGATAGGTCATTCGGGACACAGATGACATCATTAGGG
* *
673675 ATGATAGGTCATTCGGGACACAGATGACATCCTTTGGG
1 ATGATAGGTCATTCGGGACACAGATGACATCATTAGGG
*
673713 ATGATAGGTCTTTCGGGACA
1 ATGATAGGTCATTCGGGACA
673733 TAAATTTCAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (38 bp):
ATGATAGGTCATTCGGGACACAGATGACATCATTAGGG
Found at i:674025 original size:18 final size:18
Alignment explanation
Indices: 673986--674026 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
673976 AATGTATTAC
*
673986 ATGATAATGATAGAGATT
1 ATGATAATGATAGAGATA
**
674004 ATGATAATGATATTGATA
1 ATGATAATGATAGAGATA
674022 ATGAT
1 ATGAT
674027 GGTATTTGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.37
Consensus pattern (18 bp):
ATGATAATGATAGAGATA
Found at i:676276 original size:53 final size:53
Alignment explanation
Indices: 676210--676315 Score: 176
Period size: 53 Copynumber: 2.0 Consensus size: 53
676200 AAATCGCATG
* *
676210 AATAGTCAGATGACTAAATTCGTAGTTTACGCATTAAAGATCGAACAAAAACC
1 AATAGTCAAATGACTAAATTCGTAGTTTACGCATTAAAGATCAAACAAAAACC
* *
676263 AATAGTTAAATGACTAAATTCGTAGTTTACGCATTAAATATCAAACAAAAACC
1 AATAGTCAAATGACTAAATTCGTAGTTTACGCATTAAAGATCAAACAAAAACC
676316 TATTATGGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.26
Consensus pattern (53 bp):
AATAGTCAAATGACTAAATTCGTAGTTTACGCATTAAAGATCAAACAAAAACC
Found at i:676397 original size:14 final size:14
Alignment explanation
Indices: 676368--676406 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
676358 TCATAAATAG
*
676368 AATTATAAATATTTT
1 AATTATATA-ATTTT
676383 AATTATATAATTTT
1 AATTATATAATTTT
*
676397 AATTAAATAA
1 AATTATATAA
676407 AACCATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTATATAATTTT
Found at i:683208 original size:31 final size:31
Alignment explanation
Indices: 683166--683228 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
683156 ATATTTATGC
* * * *
683166 AAGATGGTTTTATTACAAGTAATATCTTATT
1 AAGATGATTTTATGAAAAATAATATCTTATT
*
683197 AAGATGATTTTATGAAAAATAATATTTTATT
1 AAGATGATTTTATGAAAAATAATATCTTATT
683228 A
1 A
683229 GAGAATATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.44
Consensus pattern (31 bp):
AAGATGATTTTATGAAAAATAATATCTTATT
Found at i:686820 original size:55 final size:55
Alignment explanation
Indices: 686712--686820 Score: 125
Period size: 55 Copynumber: 2.0 Consensus size: 55
686702 CAAAGAGTTA
* **
686712 ACCTAAGAGAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTTGGGGCCT
1 ACCTAAGAGAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCT
**
686767 ACCTAAGA-ACACATCTTAGGGCC-GCAGAGCCTACCGGAGA-ATGATCTCAGGGCC
1 ACCTAAGAGA-ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCC
686821 GTAGAGCCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
54 3 0.07
55 43 0.93
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (55 bp):
ACCTAAGAGAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCT
Found at i:689044 original size:5 final size:5
Alignment explanation
Indices: 689034--689058 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
689024 CACCGGTCAA
689034 CGGGT CGGGT CGGGT CGGGT CGGGT
1 CGGGT CGGGT CGGGT CGGGT CGGGT
689059 TGTGACCGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (5 bp):
CGGGT
Found at i:693453 original size:10 final size:11
Alignment explanation
Indices: 693433--693460 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
693423 ACAACATGTA
693433 TTTCTTTTTTT
1 TTTCTTTTTTT
693444 TTTCTTTTTTT
1 TTTCTTTTTTT
693455 TTTCTT
1 TTTCTT
693461 ACATTGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:695496 original size:2 final size:2
Alignment explanation
Indices: 695491--695548 Score: 52
Period size: 2 Copynumber: 30.5 Consensus size: 2
695481 AAATTAAAAA
* * *
695491 AT AT AT A- AT AT AT AT AT A- AT AT AA AT TT AT AT AT AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
695532 AT -T AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
695549 ATTATTATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
1 4 0.09
2 40 0.89
3 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.