Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008387.1 Hibiscus syriacus cultivar Beakdansim tig00111151_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: 2491990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:210224 original size:23 final size:22
Alignment explanation
Indices: 210161--210224 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
210151 TACTTTACAA
210161 CTACCTATTACATTATATAAACG
1 CTACCTATTACA-TATATAAACG
* * *
210184 ATACATATTACAATATATAAGCG
1 CTACCTATTAC-ATATATAAACG
210207 CTACCTATTACATCATAT
1 CTACCTATTACAT-ATAT
210225 TTTTACCTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 2 0.06
23 31 0.91
24 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (22 bp):
CTACCTATTACATATATAAACG
Found at i:210929 original size:229 final size:228
Alignment explanation
Indices: 210256--210964 Score: 1231
Period size: 228 Copynumber: 3.1 Consensus size: 228
210246 TGTCCATACT
*
210256 TTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGT
1 TTTTATAAAAAGGATAGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGT
*
210321 GTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTA
66 GTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTT
210386 TTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAA
131 TTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAA
*
210451 ATATGTTTTCCACAGTGAAATAAGTATGTACAC
196 ATATGTTTTCCACAGTGAAATAAGTATGAACAC
* * * *
210484 TTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCAAATTTTTTAATAGT
1 TTTTATAAAAAGGATAGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGT
*
210549 GTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACATAAAAAATTATTTGATTT
66 GTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTT
210614 TTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAA
131 TTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAA
* *
210679 ATATGTTTTCCACAGTGAAATAAATATAAACAC
196 ATATGTTTTCCACAGTGAAATAAGTATGAACAC
* *
210712 TTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAG
1 TTTTATAAAAAGGATAGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAG
* *
210777 TGTTTTATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACACAAAATTATTTGATT
65 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATT
* *
210842 GTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAATCAAAGATAATAGT
130 -TTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT
* *
210907 AAATATATTTT-CACAGTGAAATAAGTATGGACAC
194 AAATATGTTTTCCACAGTGAAATAAGTATGAACAC
210941 TTTTATAAAAAGGATAGATACTTT
1 TTTTATAAAAAGGATAGATACTTT
210965 ACAATATAAC
Statistics
Matches: 456, Mismatches: 23, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
228 269 0.59
229 115 0.25
230 72 0.16
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (228 bp):
TTTTATAAAAAGGATAGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGT
GTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTT
TTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAA
ATATGTTTTCCACAGTGAAATAAGTATGAACAC
Found at i:212853 original size:17 final size:18
Alignment explanation
Indices: 212833--212877 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 18
212823 AAAATGTAAT
212833 TTTAAATAAA-TTATTTA
1 TTTAAATAAATTTATTTA
212850 TTTATACGATAAATTTATTTA
1 TTTA-A--ATAAATTTATTTA
212871 TTTAAAT
1 TTTAAAT
212878 TTAATTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 4 0.17
18 3 0.12
20 6 0.25
21 11 0.46
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAAATAAATTTATTTA
Found at i:215750 original size:31 final size:31
Alignment explanation
Indices: 215709--215864 Score: 226
Period size: 31 Copynumber: 5.0 Consensus size: 31
215699 AGAGTCGAGG
** * *
215709 GTTTACCTATGTTCTTATGAACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
215740 GTTTAACTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
215771 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
215802 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
215833 GATTACCTA-GATTCTTCGGGATC-TATGGACT
1 GTTTACCTATG-TTCTTCGGGA-CATATGGACT
215864 G
1 G
215865 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
30 1 0.01
31 114 0.98
32 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:216684 original size:19 final size:20
Alignment explanation
Indices: 216646--216686 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
216636 GTACTATTTG
*
216646 TACAGTATTATTACTATTCA
1 TACAGTATTAATACTATTCA
*
216666 TACAGTA-TAATATTATTCA
1 TACAGTATTAATACTATTCA
216685 TA
1 TA
216687 AAAACGTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (20 bp):
TACAGTATTAATACTATTCA
Found at i:218118 original size:16 final size:16
Alignment explanation
Indices: 218097--218150 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
218087 TTACCCGACT
*
218097 TGTTTTCAACCTGACC
1 TGTTTTCAACCTGACA
218113 TGTTTTCAACCTGACA
1 TGTTTTCAACCTGACA
* *
218129 TGTTTTTAACATGACA
1 TGTTTTCAACCTGACA
218145 TGTTTT
1 TGTTTT
218151 TAACATGATC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.44
Consensus pattern (16 bp):
TGTTTTCAACCTGACA
Found at i:218151 original size:16 final size:16
Alignment explanation
Indices: 218097--218158 Score: 79
Period size: 16 Copynumber: 3.9 Consensus size: 16
218087 TTACCCGACT
* *
218097 TGTTTTCAACCTGACC
1 TGTTTTCAACATGACA
*
218113 TGTTTTCAACCTGACA
1 TGTTTTCAACATGACA
*
218129 TGTTTTTAACATGACA
1 TGTTTTCAACATGACA
*
218145 TGTTTTTAACATGA
1 TGTTTTCAACATGA
218159 TCTGATATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (16 bp):
TGTTTTCAACATGACA
Found at i:218401 original size:14 final size:14
Alignment explanation
Indices: 218379--218425 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
218369 TGCAAAGGAA
*
218379 AATTAATATAGTTT
1 AATTTATATAGTTT
218393 AATTTATATA----
1 AATTTATATAGTTT
218403 AA-TTATATAGTTT
1 AATTTATATAGTTT
218416 AATTTATATA
1 AATTTATATA
218426 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:218412 original size:23 final size:24
Alignment explanation
Indices: 218378--218427 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
218368 ATGCAAAGGA
218378 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
218402 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
218425 AAA
1 AAA
218428 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:218607 original size:14 final size:14
Alignment explanation
Indices: 218590--218643 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
218580 TCTATTTACA
*
218590 TTAGGGTTTATGGT
1 TTAGAGTTTATGGT
*
218604 TTAGTGTTTATGGT
1 TTAGAGTTTATGGT
* * *
218618 TTAAAATTTAGGGT
1 TTAGAGTTTATGGT
218632 TTAGAGTTTATG
1 TTAGAGTTTATG
218644 ATTAGAATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (14 bp):
TTAGAGTTTATGGT
Found at i:218661 original size:27 final size:28
Alignment explanation
Indices: 218603--218667 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
218593 GGGTTTATGG
* * *
218603 TTTAGTGTTTATGGTTTAAAATTTAGGG
1 TTTAGAGTTTATGGATTAAAATTTAGGA
*
218631 TTTAGAGTTTAT-GATTAGAATTTAGGA
1 TTTAGAGTTTATGGATTAAAATTTAGGA
*
218658 TTTAGGGTTT
1 TTTAGAGTTT
218668 TTATAATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (28 bp):
TTTAGAGTTTATGGATTAAAATTTAGGA
Found at i:218771 original size:17 final size:15
Alignment explanation
Indices: 218742--218791 Score: 82
Period size: 15 Copynumber: 3.2 Consensus size: 15
218732 TAATTTACTT
218742 TATATAGTTTATATA
1 TATATAGTTTATATA
218757 TATATATGTTATATATA
1 TATATA-GTT-TATATA
218774 TATATAGTTTATATA
1 TATATAGTTTATATA
218789 TAT
1 TAT
218792 TATACATGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.45
16 6 0.18
17 12 0.36
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:219190 original size:12 final size:12
Alignment explanation
Indices: 219173--219216 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
219163 AATTTTCACA
*
219173 CACGCACACGCG
1 CACGCACACACG
*
219185 CACGCACGCACG
1 CACGCACACACG
*
219197 CACGCACGCACG
1 CACGCACACACG
*
219209 CACTCACA
1 CACGCACA
219217 AAATTATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.27, C:0.50, G:0.20, T:0.02
Consensus pattern (12 bp):
CACGCACACACG
Found at i:219192 original size:4 final size:4
Alignment explanation
Indices: 219173--219211 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
219163 AATTTTCACA
* *
219173 CACG CACA CGCG CACG CACG CACG CACG CACG CACG CAC
1 CACG CACG CACG CACG CACG CACG CACG CACG CACG CAC
219212 TCACAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.51, G:0.23, T:0.00
Consensus pattern (4 bp):
CACG
Found at i:220085 original size:14 final size:14
Alignment explanation
Indices: 220068--220108 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
220058 ATGTGTATGG
*
220068 TTTAAAGTTTAGGA
1 TTTAAGGTTTAGGA
*
220082 TTTAAGGTTTATGA
1 TTTAAGGTTTAGGA
220096 TTTAAGGTTTAGG
1 TTTAAGGTTTAGG
220109 GTTTTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.46
Consensus pattern (14 bp):
TTTAAGGTTTAGGA
Found at i:220085 original size:28 final size:28
Alignment explanation
Indices: 220054--220108 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
220044 TACATTAGAG
* *
220054 TTTAATGTGTATGGTTTAAAGTTTAGGA
1 TTTAAGGTGTATGATTTAAAGTTTAGGA
* *
220082 TTTAAGGTTTATGATTTAAGGTTTAGG
1 TTTAAGGTGTATGATTTAAAGTTTAGG
220109 GTTTTTAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.47
Consensus pattern (28 bp):
TTTAAGGTGTATGATTTAAAGTTTAGGA
Found at i:220210 original size:511 final size:510
Alignment explanation
Indices: 219216--220189 Score: 1562
Period size: 511 Copynumber: 1.9 Consensus size: 510
219206 ACGCACTCAC
* *
219216 AAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCGC
1 AAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAATATGTCAC
*
219281 ATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTA
66 ATTGCATATTAAATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTA
219346 TTTTAGTTGCATGTTAGGTTAATTCACATTAATAACCCATTTATTTTGTTGTTATGAATAAATAA
131 TTTTAGTTGCATGTTAGGTTAATTCACATTAATAACCCATTTATTTTGTTGTTATGAATAAATAA
*
219411 TAATAAAACCCAAAAATAAGTCCATTTGCATTAGTGTTTGTCCATTTACATTAGTTTACATAGGC
196 TAATAAAACCCAAAAATAAGTCCATTTGCATTAGTGCTTGTCCATTTACATTAGTTTACATAGGC
* *
219476 CCAATACATAAGCTCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTACATTAA
261 CCAATACATAAGCCCACTCTTTTATTACAAACATATATGCATTAGTGCTAGTCCATTTACATTAA
* * * * *
219541 GGTTTATGGTTTAAAGTTTAGGGTGTATAGTTTATGTTTTAGGGTTTAGGGTTTCTGTAAACTAT
326 GGTGTATGGTTTAAAGTTTAGGATGTATAGTTTATGATTTAAGGTTTAGGGTTTCTATAAACTAT
* * * * * * *
219606 ATATTTTATTATTTTATATAGTTTATGCATAGTGTTTCTATTAACTATATAAGCAATTTACTTTA
391 ATACTTTATTACTTTATATAGTTTATACATAGTGTTTCCATTAACTATATAA-CAATATAATCTA
* *
219671 TATATATATACATGGTCTATACATACATATTATATAAAATTATTTAAAAAATCAAT
455 TAGATATATACATGATCTATACATACATATTATATAAAATTATTTAAAAAATCAAT
219727 AAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAATATGTCAC
1 AAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAATATGTCAC
*
219792 ATTGCATATTAAATGGTTCATAAATAGTAGTACATGTCATATTAATTTTATTTGCATAATTAGTA
66 ATTGCATATTAAATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTA
* *
219857 TTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAA
131 TTTTAGTTGCATGTTAGGTTAATTCACATTAATAACCCATTTATTTTGTTGTTATGAATAAATAA
*
219922 TAATAAAACCCAAAAATAAGTCCATTTGCATTAGTGCTTGTCCATTTACATTAGTTTACATATGC
196 TAATAAAACCCAAAAATAAGTCCATTTGCATTAGTGCTTGTCCATTTACATTAGTTTACATAGGC
* *
219987 CTAATACATAAGCCCACTCTTTTATTACAAACATATATGCATTAGTGCTAGTTCATTTACATTAG
261 CCAATACATAAGCCCACTCTTTTATTACAAACATATATGCATTAGTGCTAGTCCATTTACATTA-
* *
220052 AGTTTAATGTGTATGGTTTAAAGTTTAGGATTTA-AGGTTTATGATTTAAGGTTTAGGGTTTTTA
325 AG------GTGTATGGTTTAAAGTTTAGGATGTATA-GTTTATGATTTAAGGTTTAGGGTTTCT-
*
220116 ATAAACTATATACTTTATTACTTTATATAGTTTATACATAGTGTTTCCA-TAA-TATAT-A-TAT
382 ATAAACTATATACTTTATTACTTTATATAGTTTATACATAGTGTTTCCATTAACTATATAACAAT
220177 ATAATCTATAGAT
447 ATAATCTATAGAT
220190 TACTTATATT
Statistics
Matches: 426, Mismatches: 28, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
511 312 0.73
512 2 0.00
514 11 0.03
516 1 0.00
517 6 0.01
518 50 0.12
519 44 0.10
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (510 bp):
AAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAATATGTCAC
ATTGCATATTAAATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTA
TTTTAGTTGCATGTTAGGTTAATTCACATTAATAACCCATTTATTTTGTTGTTATGAATAAATAA
TAATAAAACCCAAAAATAAGTCCATTTGCATTAGTGCTTGTCCATTTACATTAGTTTACATAGGC
CCAATACATAAGCCCACTCTTTTATTACAAACATATATGCATTAGTGCTAGTCCATTTACATTAA
GGTGTATGGTTTAAAGTTTAGGATGTATAGTTTATGATTTAAGGTTTAGGGTTTCTATAAACTAT
ATACTTTATTACTTTATATAGTTTATACATAGTGTTTCCATTAACTATATAACAATATAATCTAT
AGATATATACATGATCTATACATACATATTATATAAAATTATTTAAAAAATCAAT
Found at i:220297 original size:4 final size:4
Alignment explanation
Indices: 220288--220441 Score: 308
Period size: 4 Copynumber: 38.5 Consensus size: 4
220278 GTACATATGA
220288 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
220336 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
220384 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
220432 ACAT ACAT AC
1 ACAT ACAT AC
220442 GTACGTACGT
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 150 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:220803 original size:2 final size:2
Alignment explanation
Indices: 220796--221003 Score: 90
Period size: 2 Copynumber: 109.0 Consensus size: 2
220786 ACTTTGAATA
*
220796 AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AA AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
220835 AGT TT AT AA ACT AT AT AT -T TT TT AT A- AT TT AT AC AT AT AT AGT
1 A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * * *
220878 TT AC AT AT AT AGT TT AT AT AA AT A- AT -T AT AT AT GCT -T AT A-
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
* *
220918 AT A- AT -T AT AT AT TT AT A- AT AT A- AT AT AGT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* *
220957 AT AT AT AT A- AT TT AT AT AT AA ACT -T AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
220997 -T AT AT AT
1 AT AT AT AT
221004 TTTTTAATTT
Statistics
Matches: 154, Mismatches: 28, Indels: 48
0.67 0.12 0.21
Matches are distributed among these distances:
1 17 0.11
2 131 0.85
3 6 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:220880 original size:15 final size:15
Alignment explanation
Indices: 220857--220895 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
220847 ATATATTTTT
*
220857 TATAATTTATACATA
1 TATAGTTTATACATA
220872 TATAG-TT-TACATA
1 TATAGTTTATACATA
220885 TATAGTTTATA
1 TATAGTTTATA
220896 TAAATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 11 0.52
14 4 0.19
15 6 0.29
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (15 bp):
TATAGTTTATACATA
Found at i:220882 original size:13 final size:13
Alignment explanation
Indices: 220866--220893 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
220856 TTATAATTTA
220866 TACATATATAGTT
1 TACATATATAGTT
220879 TACATATATAGTT
1 TACATATATAGTT
220892 TA
1 TA
220894 TATAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (13 bp):
TACATATATAGTT
Found at i:220920 original size:19 final size:17
Alignment explanation
Indices: 220898--221005 Score: 78
Period size: 17 Copynumber: 5.9 Consensus size: 17
220888 AGTTTATATA
220898 AATAATTATATATGCTTAT
1 AATAATTATATAT--TTAT
220917 AATAATTATATATTTAT
1 AATAATTATATATTTAT
*
220934 AAT-ATAATATAGTTTAT
1 AATAATTATATA-TTTAT
220951 ATATATATATATATAATTTAT
1 A-ATA-AT-TATAT-ATTTAT
*
220972 ATATAAACT-TATA-TTAT
1 A-AT-AATTATATATTTAT
220989 ATATATATTATATATTT
1 A-ATA-ATTATATATTT
221006 TTTAATTTTT
Statistics
Matches: 75, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
16 8 0.11
17 23 0.31
18 7 0.09
19 18 0.24
20 3 0.04
21 14 0.19
22 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
AATAATTATATATTTAT
Found at i:220933 original size:17 final size:18
Alignment explanation
Indices: 220793--221005 Score: 103
Period size: 16 Copynumber: 11.8 Consensus size: 18
220783 CTCACTTTGA
*
220793 ATAA-TATATATATATAT
1 ATAATTATATATTTATAT
220810 AT-A-TATATATATTA-AT
1 ATAATTATATAT-TTATAT
* *
220826 ATAAAT-TATAGTT-TAT
1 ATAATTATATATTTATAT
* *
220842 A-AACTATATATTT-TTT
1 ATAATTATATATTTATAT
* *
220858 ATAATTTATACATATATAGT
1 ATAA-TTATATATTTATA-T
*
220878 TTACA-TATATAGTTTATAT
1 ATA-ATTATATA-TTTATAT
220897 AAATAATTATATATGCTTATA-
1 --ATAATTATATAT--TTATAT
220918 ATAATTATATATTTATAAT
1 ATAATTATATATTTAT-AT
*
220937 ATAA-TATA-GTTTATAT
1 ATAATTATATATTTATAT
220953 ATATATATATATAATTTATAT
1 ATA-AT-TATAT-ATTTATAT
*
220974 ATAAACT-TATA-TTATAT
1 AT-AATTATATATTTATAT
220991 ATATATTATATATTT
1 ATA-ATTATATATTT
221006 TTTAATTTTT
Statistics
Matches: 152, Mismatches: 17, Indels: 52
0.69 0.08 0.24
Matches are distributed among these distances:
15 3 0.02
16 32 0.21
17 31 0.20
18 18 0.12
19 32 0.21
20 11 0.07
21 19 0.12
22 6 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
ATAATTATATATTTATAT
Found at i:220985 original size:56 final size:57
Alignment explanation
Indices: 220884--221002 Score: 131
Period size: 56 Copynumber: 2.1 Consensus size: 57
220874 TAGTTTACAT
*
220884 ATATAGTTTATATAAATAATTATATATGCTTATAATAATTATATATT-TATA-ATATA
1 ATATAGTTTATATAAATAATTATATAT-CTTATAATAACTATATATTATATATATATA
* *
220940 ATATAGTTTATATATAT-ATATATATAAT-TTATATATAAACT-TATATTATATATATATT
1 ATATAGTTTATATAAATAAT-TATAT-ATCTTATA-AT-AACTATATATTATATATATATA
220998 ATATA
1 ATATA
221003 TTTTTTAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
55 7 0.13
56 29 0.54
57 9 0.17
58 9 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.50
Consensus pattern (57 bp):
ATATAGTTTATATAAATAATTATATATCTTATAATAACTATATATTATATATATATA
Found at i:223325 original size:16 final size:16
Alignment explanation
Indices: 223304--223338 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
223294 ATAAGATCAG
*
223304 ATTCAAAAAAATGTGT
1 ATTCAAAAAAATATGT
223320 ATTCAAAAAAATATGT
1 ATTCAAAAAAATATGT
223336 ATT
1 ATT
223339 TTATTATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (16 bp):
ATTCAAAAAAATATGT
Found at i:223825 original size:22 final size:22
Alignment explanation
Indices: 223777--223825 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
223767 TCGTATATTT
*
223777 TTTTTTCTATTTTATGACACGA
1 TTTTTTCTATTTTATAACACGA
* *
223799 ATTTTTCTGTTTTCATAACAC-A
1 TTTTTTCTATTTT-ATAACACGA
223821 TTTTT
1 TTTTT
223826 CCTCAGTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.57
Consensus pattern (22 bp):
TTTTTTCTATTTTATAACACGA
Found at i:231767 original size:11 final size:11
Alignment explanation
Indices: 231751--231775 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
231741 ATATAAAAGA
231751 AAACTCGTCGG
1 AAACTCGTCGG
231762 AAACTCGTCGG
1 AAACTCGTCGG
231773 AAA
1 AAA
231776 TGTACGACGA
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:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (11 bp):
AAACTCGTCGG
Found at i:233611 original size:17 final size:17
Alignment explanation
Indices: 233589--233629 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
233579 ATGGTTTTCA
233589 GAACCGGCCCGGTTAAC
1 GAACCGGCCCGGTTAAC
233606 GAACCGGCCCGGTTAAC
1 GAACCGGCCCGGTTAAC
233623 GAACCGG
1 GAACCGG
233630 TCATGCTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.10
Consensus pattern (17 bp):
GAACCGGCCCGGTTAAC
Found at i:235579 original size:31 final size:29
Alignment explanation
Indices: 235516--235586 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
235506 ATTATATCGT
235516 TTATACCACTGAACTTTAAATTTTATCAA
1 TTATACCACTGAACTTTAAATTTTATCAA
* *
235545 TTATAGCACTGAACTTT-AATTTCCGTTTCAA
1 TTATACCACTGAACTTTAAATTT---TATCAA
235576 TTATACCACTG
1 TTATACCACTG
235587 GCCCTTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 5 0.14
29 16 0.44
31 15 0.42
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (29 bp):
TTATACCACTGAACTTTAAATTTTATCAA
Found at i:236438 original size:39 final size:38
Alignment explanation
Indices: 236353--236440 Score: 95
Period size: 39 Copynumber: 2.3 Consensus size: 38
236343 AACTAAATAT
* *** *
236353 GAAGACTCCACGATTGCATGGTGTCTTCATGAAAATGA
1 GAAGACCCCACGATTGCATGACATCTTCAAGAAAATGA
* *
236391 AAACGACCCCACGATTGCATGACATCTTCAAGCAAATGGA
1 GAA-GACCCCACGATTGCATGACATCTTCAAGAAAAT-GA
236431 GAAGACCCCA
1 GAAGACCCCA
236441 AAAGTGCACG
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
38 2 0.05
39 34 0.85
40 4 0.10
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.19
Consensus pattern (38 bp):
GAAGACCCCACGATTGCATGACATCTTCAAGAAAATGA
Found at i:239251 original size:29 final size:30
Alignment explanation
Indices: 239181--239239 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
239171 AATTTAAGGA
239181 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAC
239212 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
239240 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAC
Found at i:239354 original size:21 final size:21
Alignment explanation
Indices: 239329--239406 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
239319 TTCAAGATTG
* *
239329 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
239350 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
239368 CCC---GGGTACAGATA-CCC
1 CCCAGGGGGTACAGATACCCC
*
239385 CCCAGGTGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
239406 C
1 C
239407 TGCAGGTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
15 11 0.23
17 4 0.08
18 4 0.08
20 10 0.21
21 19 0.40
ACGTcount: A:0.23, C:0.36, G:0.27, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:239370 original size:20 final size:20
Alignment explanation
Indices: 239329--239406 Score: 85
Period size: 20 Copynumber: 4.1 Consensus size: 20
239319 TTCAAGATTG
* *
239329 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGA-TACCC
239350 CCCAGGGGGTACAGATA--C
1 CCCAGGGGGTACAGATACCC
239368 CCC---GGGTACAGATACCC
1 CCCAGGGGGTACAGATACCC
*
239385 CCCAGGTGGTACAGATACCC
1 CCCAGGGGGTACAGATACCC
239405 CC
1 CC
239407 TGCAGGTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
15 11 0.22
17 4 0.08
18 4 0.08
20 16 0.33
21 14 0.29
ACGTcount: A:0.23, C:0.36, G:0.27, T:0.14
Consensus pattern (20 bp):
CCCAGGGGGTACAGATACCC
Found at i:239376 original size:15 final size:15
Alignment explanation
Indices: 239356--239385 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
239346 CCCCCCCAGG
239356 GGGTACAGATACCCC
1 GGGTACAGATACCCC
239371 GGGTACAGATACCCC
1 GGGTACAGATACCCC
239386 CCAGGTGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:239482 original size:20 final size:21
Alignment explanation
Indices: 239444--239483 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
239434 GAATGTCCAG
239444 GGGGTACCGATTCCCCCCCAT
1 GGGGTACCGATTCCCCCCCAT
239465 GGGGTACCGATTCCCCCCC
1 GGGGTACCGATTCCCCCCC
239484 TGTTCAACAG
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:0.12, C:0.45, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGGTACCGATTCCCCCCCAT
Found at i:239545 original size:21 final size:21
Alignment explanation
Indices: 239519--239561 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
239509 ATTTGAATAT
* *
239519 TATGAAGGGGTATCGATTCCC
1 TATGAAGAGGTACCGATTCCC
239540 TATGAAGAGGTACCGATTCCC
1 TATGAAGAGGTACCGATTCCC
239561 T
1 T
239562 CTATTCTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
TATGAAGAGGTACCGATTCCC
Found at i:239627 original size:20 final size:22
Alignment explanation
Indices: 239589--239628 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
239579 TTTGAGTATA
239589 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
239611 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
239629 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:239882 original size:34 final size:32
Alignment explanation
Indices: 239843--239912 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
239833 TTTTGTAAAG
* *
239843 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
239877 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
239909 GGGA
1 GGGA
239913 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:240796 original size:19 final size:20
Alignment explanation
Indices: 240772--240819 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
240762 AATGATTTTC
*
240772 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
240791 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
240811 TTTTGAAAA
1 TTTTGAAAA
240820 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:241925 original size:22 final size:21
Alignment explanation
Indices: 241895--241942 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
241885 GTTTGGTTTG
241895 AAAAA-TTCAATTTCTTAATAA
1 AAAAATTTCAATTTCTTAA-AA
*
241916 AAAAATTTCAATTTCTTAAAG
1 AAAAATTTCAATTTCTTAAAA
241937 AAAAAT
1 AAAAAT
241943 GGGGAGCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAAATTTCAATTTCTTAAAA
Found at i:242171 original size:29 final size:30
Alignment explanation
Indices: 242100--242159 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
242090 CAATTTAAGG
242100 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
242131 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
242160 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:242274 original size:21 final size:21
Alignment explanation
Indices: 242249--242327 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
242239 TTCAAGATTG
* *
242249 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
242270 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
242288 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
* *
242306 CTCAGGGGGTATAGATACCCC
1 CCCAGGGGGTACAGATACCCC
242327 C
1 C
242328 TGCAGGTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
15 11 0.23
18 7 0.15
21 30 0.62
ACGTcount: A:0.23, C:0.34, G:0.28, T:0.15
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:242295 original size:36 final size:36
Alignment explanation
Indices: 242255--242326 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
242245 ATTGCCCAGG
* *
242255 GGGTATAGATTCCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
* *
242291 GGGTACAGATACCCCCTCAGGGGGTATAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
242327 CTGCAGGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.24, C:0.32, G:0.28, T:0.17
Consensus pattern (36 bp):
GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
Found at i:242296 original size:15 final size:15
Alignment explanation
Indices: 242276--242305 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
242266 CCCCCCCAGG
242276 GGGTACAGATACCCC
1 GGGTACAGATACCCC
242291 GGGTACAGATACCCC
1 GGGTACAGATACCCC
242306 CTCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:242465 original size:21 final size:21
Alignment explanation
Indices: 242439--242481 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
242429 ATTTGAATAT
* *
242439 TATGAAGGGGTATCGATTCCC
1 TATGAAGAGGTACCGATTCCC
242460 TATGAAGAGGTACCGATTCCC
1 TATGAAGAGGTACCGATTCCC
242481 T
1 T
242482 CTATTCTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
TATGAAGAGGTACCGATTCCC
Found at i:242802 original size:34 final size:32
Alignment explanation
Indices: 242763--242832 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
242753 TTTTGTAAAG
* *
242763 GGGAAAGGTTCTAGCTTAGCTCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
242797 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
242829 GGGA
1 GGGA
242833 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:245897 original size:16 final size:16
Alignment explanation
Indices: 245876--245916 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
245866 ATAGAAGATT
245876 AAAGAGAATGGGTTTC
1 AAAGAGAATGGGTTTC
245892 AAAGAGAATGGGTTTC
1 AAAGAGAATGGGTTTC
*
245908 AAAGTGAAT
1 AAAGAGAAT
245917 TTATGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.29, T:0.24
Consensus pattern (16 bp):
AAAGAGAATGGGTTTC
Found at i:246820 original size:21 final size:22
Alignment explanation
Indices: 246794--246839 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
246784 GTCGAGGGTT
*
246794 TCATAGGTCATTCGGGACA-AC
1 TCATAGGTCATTCAGGACATAC
*
246815 TCATAGGTCCTTCAGGACATAC
1 TCATAGGTCATTCAGGACATAC
246837 TCA
1 TCA
246840 CAAATCCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (22 bp):
TCATAGGTCATTCAGGACATAC
Found at i:247195 original size:24 final size:24
Alignment explanation
Indices: 247168--247241 Score: 130
Period size: 24 Copynumber: 3.1 Consensus size: 24
247158 AAGAACCAAT
247168 AATAGCAGAAATAGAAGTTGCAAG
1 AATAGCAGAAATAGAAGTTGCAAG
247192 AATAGCAGAAATAGAAGTTGCAAG
1 AATAGCAGAAATAGAAGTTGCAAG
* *
247216 AATAACAGAAATAGAAGTGGCAAG
1 AATAGCAGAAATAGAAGTTGCAAG
247240 AA
1 AA
247242 CAACAACACT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.53, C:0.08, G:0.24, T:0.15
Consensus pattern (24 bp):
AATAGCAGAAATAGAAGTTGCAAG
Found at i:247483 original size:21 final size:22
Alignment explanation
Indices: 247459--247504 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
247449 GTAGCAGTAA
*
247459 TGTAGCA-GGGTATCGGTTCCC
1 TGTAGCAGGGGAATCGGTTCCC
247480 TGTAGCAGGGGAATCGGTTCCC
1 TGTAGCAGGGGAATCGGTTCCC
247502 TGT
1 TGT
247505 CAATAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.15, C:0.22, G:0.35, T:0.28
Consensus pattern (22 bp):
TGTAGCAGGGGAATCGGTTCCC
Found at i:247912 original size:15 final size:14
Alignment explanation
Indices: 247887--247924 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
247877 ATTCGGTTAA
*
247887 AACCGAACTGAATT
1 AACCAAACTGAATT
247901 AACCATAACTGAATT
1 AACCA-AACTGAATT
247916 AACCAAACT
1 AACCAAACT
247925 TTTTTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.21
Consensus pattern (14 bp):
AACCAAACTGAATT
Found at i:248400 original size:186 final size:184
Alignment explanation
Indices: 248039--248427 Score: 640
Period size: 186 Copynumber: 2.1 Consensus size: 184
248029 TTTTCTAATT
* * *
248039 TATATAAAA-AT-TAAATGTTTTGTAATTAAAAAAGGTTTATAATTAATTTAAATAATATATAAT
1 TATATAAAATATATAAATATTTTGTAATTAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
248102 TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
66 TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
* *
248167 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTA
131 AGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
* *
248221 TATATAATATATATAAATATTTTTTAATTATAAAAACAGTTTACAATTAATTTAAATAATATATA
1 TATATAAAATATATAAATATTTTGTAATTA-AAAAA-AGTTTACAATTAATTTAAATAATATATA
* * *
248286 ATTATAAAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
64 ATTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
248351 TTAGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
129 TTAGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
*
248407 TATATAAAATATTTAAA-ATTT
1 TATATAAAATATATAAATATTT
248428 AAAATTTAAT
Statistics
Matches: 191, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
182 8 0.04
183 2 0.01
184 15 0.08
185 9 0.05
186 157 0.82
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (184 bp):
TATATAAAATATATAAATATTTTGTAATTAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
AGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:248754 original size:15 final size:15
Alignment explanation
Indices: 248731--248772 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
248721 TTGGCTACTT
*
248731 AGAGAAAATGAAGGA
1 AGAGGAAATGAAGGA
248746 AGAGGAAATG-AGGA
1 AGAGGAAATGAAGGA
* *
248760 GGATGAAATGAAG
1 AGAGGAAATGAAG
248773 AGAAAAAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.52, C:0.00, G:0.38, T:0.10
Consensus pattern (15 bp):
AGAGGAAATGAAGGA
Found at i:252461 original size:11 final size:11
Alignment explanation
Indices: 252447--252478 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
252437 CGAATAAAAA
*
252447 CTTTAAAATTT
1 CTTTAAAAATT
252458 CTTTAAAAATT
1 CTTTAAAAATT
252469 CTTTAAAAAT
1 CTTTAAAAAT
252479 ATTAATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (11 bp):
CTTTAAAAATT
Found at i:253772 original size:27 final size:29
Alignment explanation
Indices: 253742--253804 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
253732 AGCATGACTC
*
253742 AAATATCATA-A-A-CCATAATAATCATCA
1 AAATATCATAGATACCCATAA-AAGCATCA
* *
253769 AAATAGCATAGATACCCATAAAAGCATCC
1 AAATATCATAGATACCCATAAAAGCATCA
253798 AAATATC
1 AAATATC
253805 CAAAAGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 9 0.31
28 1 0.03
29 13 0.45
30 6 0.21
ACGTcount: A:0.52, C:0.21, G:0.05, T:0.22
Consensus pattern (29 bp):
AAATATCATAGATACCCATAAAAGCATCA
Found at i:259670 original size:21 final size:20
Alignment explanation
Indices: 259641--259679 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
259631 AAAATCATAC
*
259641 TTAACATTTATTTTTTTAATT
1 TTAACATTT-TTTTATTAATT
*
259662 TTAATATTTTTTTATTAA
1 TTAACATTTTTTTATTAA
259680 AAACTTAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TTAACATTTTTTTATTAATT
Found at i:265503 original size:2 final size:2
Alignment explanation
Indices: 265459--265489 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
265449 ATAATGTTCA
265459 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
265490 CTGAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:265967 original size:21 final size:20
Alignment explanation
Indices: 265941--266014 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
265931 AAGTTTCGGA
*
265941 TTTAGGGTTTATAATTTAAG
1 TTTAGGGTTTATAATTTGAG
* ***
265961 CTTTAGGTTTTAGGGTTTTGAG
1 -TTTAGGGTTTA-TAATTTGAG
*
265983 TTTAGTGTTTATAATTTGAGG
1 TTTAGGGTTTATAATTTGA-G
266004 TTTAGGGTTTA
1 TTTAGGGTTTA
266015 ATTTTTTTTA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 5 0.12
21 30 0.75
22 5 0.12
ACGTcount: A:0.22, C:0.01, G:0.26, T:0.51
Consensus pattern (20 bp):
TTTAGGGTTTATAATTTGAG
Found at i:269704 original size:13 final size:13
Alignment explanation
Indices: 269686--269719 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
269676 ACATATCATA
269686 TATAAAAACATTT
1 TATAAAAACATTT
269699 TAT-AAAACATTT
1 TATAAAAACATTT
*
269711 TACAAAAAC
1 TATAAAAAC
269720 CGGAGAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
TATAAAAACATTT
Found at i:270105 original size:53 final size:52
Alignment explanation
Indices: 270025--270184 Score: 171
Period size: 53 Copynumber: 3.1 Consensus size: 52
270015 ATGCAGACAA
*
270025 TGACTCTGCTAT-ACTAGTATCTGGTATCACACAACATCATATACTAGCCTCAC
1 TGACTCTGCTATGA-TAGTATCTGGTATCACACAACATCAGATACTAGCCT-AC
* * * * *
270078 TGACTCTGCTATGTTAGTATCTGGTATCACACAGCGTCAGATACTAACCGTAA
1 TGACTCTGCTATGATAGTATCTGGTATCACACAACATCAGATACTAGCC-TAC
** * * * *
270131 TGGGT-TACTATGATAGTACCTGATATCAAACAACATCAGATACTAGCCTAC
1 TGACTCTGCTATGATAGTATCTGGTATCACACAACATCAGATACTAGCCTAC
270182 TGA
1 TGA
270185 GAGGGGGTAC
Statistics
Matches: 87, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
51 4 0.05
52 35 0.40
53 47 0.54
54 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (52 bp):
TGACTCTGCTATGATAGTATCTGGTATCACACAACATCAGATACTAGCCTAC
Found at i:278245 original size:175 final size:175
Alignment explanation
Indices: 277927--278273 Score: 466
Period size: 175 Copynumber: 2.0 Consensus size: 175
277917 TCTAAATCTG
* * * *** * **
277927 TTGCATAGAGAATGAATCAAACTATACCTGAATCCAATCACGAATAACTTTGATAGCCTGTGATT
1 TTGCATAAAGAATGAATCAAACTAAACCTGAATCCAATCACGAAAAAAAATGAGAGCCTACGATT
* *
277992 TCAGTTCACTTTCCTAATCACCAAACAGTCCGATAAATCAGCATTTACGCCCCTCAAAAACCTTA
66 TCAGTTCACTTTCCCAATCACCAAACAGTCCGATAAATCAGCATTTAAGCCCCTCAAAAACCTTA
* *
278057 ATTCCAGTGCTTAAACTAACTAAACAAACACTTAGTTCCAATAAC
131 ATTCCAATGCTTAAACTAACTAAACAAACACTTAGCTCCAATAAC
* *
278102 TTGCATAAAGAATGAATCGAACTAAACCTGAATTCAATCACGAAAAAAAATGAGAGCCTACGATT
1 TTGCATAAAGAATGAATCAAACTAAACCTGAATCCAATCACGAAAAAAAATGAGAGCCTACGATT
* * *
278167 TCAGTTCACTTTCCCAATCACCAAACAG-CATGATAAATCAGCATTTAAGCTCCTTC-AAAAGCT
66 TCAGTTCACTTTCCCAATCACCAAACAGTC-CGATAAATCAGCATTTAAGC-CCCTCAAAAACCT
* *
278230 GT-ATTCCAATGCTTAAAGTAACTAAGCAAACACTTAGCTCCAAT
129 -TAATTCCAATGCTTAAACTAACTAAACAAACACTTAGCTCCAAT
278274 TACTGGCTAA
Statistics
Matches: 149, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
174 1 0.01
175 143 0.96
176 5 0.03
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (175 bp):
TTGCATAAAGAATGAATCAAACTAAACCTGAATCCAATCACGAAAAAAAATGAGAGCCTACGATT
TCAGTTCACTTTCCCAATCACCAAACAGTCCGATAAATCAGCATTTAAGCCCCTCAAAAACCTTA
ATTCCAATGCTTAAACTAACTAAACAAACACTTAGCTCCAATAAC
Found at i:278453 original size:2 final size:2
Alignment explanation
Indices: 278446--278482 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
278436 TCGCCTCTTT
278446 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 T
278483 TTAAGCTCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:278762 original size:24 final size:24
Alignment explanation
Indices: 278730--278777 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
278720 TTCAGGAAGA
278730 AAAAAAAAAGAATTAGGGTTTCTT
1 AAAAAAAAAGAATTAGGGTTTCTT
278754 AAAAAAAAAGAATTAGGGTTTCTT
1 AAAAAAAAAGAATTAGGGTTTCTT
278778 CCTTTAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.29
Consensus pattern (24 bp):
AAAAAAAAAGAATTAGGGTTTCTT
Found at i:279147 original size:4 final size:4
Alignment explanation
Indices: 279138--279165 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
279128 CCTATGGCAT
279138 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
279166 ATGTTCATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:279687 original size:15 final size:16
Alignment explanation
Indices: 279641--279690 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
279631 AAAAAATTAA
279641 AATTGAAAGTTAGAGT
1 AATTGAAAGTTAGAGT
*
279657 GATT-AAA-TTATGAGT
1 AATTGAAAGTTA-GAGT
279672 AATTGAAAGTTA-AGT
1 AATTGAAAGTTAGAGT
279687 AATT
1 AATT
279691 AAATTAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 3 0.10
15 17 0.59
16 6 0.21
17 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (16 bp):
AATTGAAAGTTAGAGT
Found at i:281560 original size:21 final size:21
Alignment explanation
Indices: 281536--281577 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
281526 TTGATGGTCA
281536 TTTCATTTTCATGAATACAAT
1 TTTCATTTTCATGAATACAAT
281557 TTTCATTTTCATGAATACAAT
1 TTTCATTTTCATGAATACAAT
281578 GGTCATGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (21 bp):
TTTCATTTTCATGAATACAAT
Found at i:281583 original size:21 final size:21
Alignment explanation
Indices: 281538--281583 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
281528 GATGGTCATT
**
281538 TCATTTTCATGAATACAATTT
1 TCATTTTCATGAATACAATGG
281559 TCATTTTCATGAATACAATGG
1 TCATTTTCATGAATACAATGG
281580 TCAT
1 TCAT
281584 GTTAAATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (21 bp):
TCATTTTCATGAATACAATGG
Found at i:283028 original size:33 final size:33
Alignment explanation
Indices: 282981--283051 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
282971 ACAAAGTTTA
* *
282981 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
**
283013 CGATAAATTCAAATACTTAAAAACTTTTAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
283046 CGATAA
1 CGATAA
283052 TTGAAACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 4 0.12
33 30 0.88
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:283072 original size:21 final size:21
Alignment explanation
Indices: 283048--283087 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
283038 TTTAAGTTCG
283048 ATAATTGAAACAAAATTTACA
1 ATAATTGAAACAAAATTTACA
* *
283069 ATAATTGAAATAAAGTTTA
1 ATAATTGAAACAAAATTTA
283088 AAAATAAACT
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:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
ATAATTGAAACAAAATTTACA
Found at i:284933 original size:177 final size:177
Alignment explanation
Indices: 284543--285234 Score: 1296
Period size: 177 Copynumber: 3.9 Consensus size: 177
284533 TTTTATGGTG
284543 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAATCATAAAATAAATCT
1 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAATCATAAAATAAATCT
284608 CGAGAAATCACTGAAGTCATTCAATAAATTTACCGACA-TTTTTTTCTCCTCCTACTTATGGAGA
66 CGAGAAATCACTGAAGTCATTCAATAAATTTACCGACATTTTTTTTCTCCTCCTACTTATGGAGA
*
284672 AAGTAATCTTTTTATTCTCTCTTTTGATTAATCTTAAAAGTAATCTT
131 AAGTAATCTTTTTATTCTCTCTTTTGATTAATCTTAGAAGTAATCTT
*
284719 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATTGATATAATCATAAAATAAATCT
1 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAATCATAAAATAAATCT
*
284784 AGAGAAATCACTGAAGTCATTCAATAAATTTACCGACATTTTTTTTCTCCTCCTACTTATGGAGA
66 CGAGAAATCACTGAAGTCATTCAATAAATTTACCGACATTTTTTTTCTCCTCCTACTTATGGAGA
* *
284849 ATGTAATCTTTGTATTCTCTCTTTTGATTAATCTTAGAAGTAATCTT
131 AAGTAATCTTTTTATTCTCTCTTTTGATTAATCTTAGAAGTAATCTT
284896 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAATCATAAAATAAATCT
1 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAATCATAAAATAAATCT
* *
284961 CGAGAAATCACTGAAGTCATTCAATAAATTCACCGACATTTTTTCTCTCCTCCTACTTATGGAGA
66 CGAGAAATCACTGAAGTCATTCAATAAATTTACCGACATTTTTTTTCTCCTCCTACTTATGGAGA
285026 AAGTAATCTTTTTATTCTCTCTTTTGATTAATCTTAGAAGTAATCTT
131 AAGTAATCTTTTTATTCTCTCTTTTGATTAATCTTAGAAGTAATCTT
*
285073 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAGTCATAAAATAAATCT
1 TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAATCATAAAATAAATCT
*
285138 CGAGAAATCACTGAAGTCACTCAATAAATTTACCGACATTTTTTTTCTCCTCCTACTTATGGAGA
66 CGAGAAATCACTGAAGTCATTCAATAAATTTACCGACATTTTTTTTCTCCTCCTACTTATGGAGA
285203 AAGTAATCTTTTTATTCTCTCTTTTGATTAAT
131 AAGTAATCTTTTTATTCTCTCTTTTGATTAAT
285235 ATGTCTACAA
Statistics
Matches: 500, Mismatches: 15, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
176 101 0.20
177 399 0.80
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (177 bp):
TTAGAGTAAAAATAATAATCTTAAAAGTATTTTTAATATGATCGATATAATCATAAAATAAATCT
CGAGAAATCACTGAAGTCATTCAATAAATTTACCGACATTTTTTTTCTCCTCCTACTTATGGAGA
AAGTAATCTTTTTATTCTCTCTTTTGATTAATCTTAGAAGTAATCTT
Found at i:287346 original size:18 final size:19
Alignment explanation
Indices: 287304--287351 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
287294 CGTCAAATTT
*
287304 TTAATAAAA-ATAAATAAA
1 TTAAAAAAATATAAATAAA
* *
287322 TTTAAAATATATAAAT-AA
1 TTAAAAAAATATAAATAAA
287340 TTAAAAAAATAT
1 TTAAAAAAATAT
287352 TTTTAAAACT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAAAAAATATAAATAAA
Found at i:294189 original size:14 final size:16
Alignment explanation
Indices: 294130--294191 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 16
294120 CAAAAACTTG
294130 ATTTGATTT-TTTTAT
1 ATTTGATTTATTTTAT
* *
294145 ATTT-ATTTAATTATAG
1 ATTTGATTT-ATTTTAT
*
294161 ATTATGCTTTATTTTAT
1 ATT-TGATTTATTTTAT
294178 ATTTG-TTT-TTTTAT
1 ATTTGATTTATTTTAT
294192 TTTATTTTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
14 10 0.26
15 7 0.18
16 9 0.24
17 9 0.24
18 3 0.08
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.68
Consensus pattern (16 bp):
ATTTGATTTATTTTAT
Found at i:294203 original size:41 final size:38
Alignment explanation
Indices: 294137--294226 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 38
294127 TTGATTTGAT
294137 TTTTTTATATTTATTTAATTATAGATTATGCTTTATTTTATA
1 TTTTTT-T-TTTATTTAATTATAGATTAT-CTTTATTTT-TA
* * *
294179 TTTGTTTTTTTATTTTATTTTAGATTATTTTTATTTTTA
1 TTT-TTTTTTTATTTAATTATAGATTATCTTTATTTTTA
294218 TTTTTTTTT
1 TTTTTTTTT
294227 AGTTTTAGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
38 6 0.14
39 5 0.11
40 8 0.18
41 18 0.41
42 4 0.09
43 3 0.07
ACGTcount: A:0.21, C:0.01, G:0.04, T:0.73
Consensus pattern (38 bp):
TTTTTTTTTTATTTAATTATAGATTATCTTTATTTTTA
Found at i:294215 original size:27 final size:27
Alignment explanation
Indices: 294177--294251 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
294167 CTTTATTTTA
294177 TATTTGTTTTTTTATTTTATTTTAG-AT
1 TATTT-TTTTTTTATTTTATTTTAGTAT
* *
294204 TATTTTTATTTTTATTTTTTTTTAGTTT
1 TATTTTT-TTTTTATTTTATTTTAGTAT
*
294232 TAGTTTTTGTTATTATTTTA
1 TA-TTTTT-TTTTTATTTTA
294252 AGTCTTGAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
27 21 0.52
28 3 0.08
29 14 0.35
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (27 bp):
TATTTTTTTTTTATTTTATTTTAGTAT
Found at i:294222 original size:7 final size:6
Alignment explanation
Indices: 294168--294250 Score: 52
Period size: 6 Copynumber: 14.3 Consensus size: 6
294158 TAGATTATGC
* *
294168 TTTATT TTATATT TGTT-TT TTTA-T TTTA-T TTTA-G ATTATT TTTATT
1 TTTATT TT-TATT T-TTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* * *
294214 TTTA-T TTT-TT TTTAGT TTTAGTT TTTGTT ATTATT TT
1 TTTATT TTTATT TTTATT TTTA-TT TTTATT TTTATT TT
294251 AAGTCTTGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
5 23 0.38
6 26 0.43
7 10 0.17
8 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:294225 original size:16 final size:17
Alignment explanation
Indices: 294185--294250 Score: 64
Period size: 16 Copynumber: 3.8 Consensus size: 17
294175 TATATTTGTT
294185 TTTTTATTTTA-TTTTAG
1 TTTTT-TTTTATTTTTAG
* *
294202 ATTATTTTTATTTTTA-
1 TTTTTTTTTATTTTTAG
*
294218 TTTTTTTTTAGTTTTAG
1 TTTTTTTTTATTTTTAG
294235 TTTTTGTTATTATTTT
1 TTTTT-TT-TTATTTT
294251 AAGTCTTGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 18 0.46
17 13 0.33
18 2 0.05
19 6 0.15
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTTTTTTTATTTTTAG
Found at i:298231 original size:15 final size:15
Alignment explanation
Indices: 298200--298237 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
298190 TTATTTTATA
298200 TTTTATTTTAGATTT
1 TTTTATTTTAGATTT
298215 TTTTAGTTTTAGATTT
1 TTTTA-TTTTAGATTT
*
298231 TGTTATT
1 TTTTATT
298238 ATTTTAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.71
Consensus pattern (15 bp):
TTTTATTTTAGATTT
Found at i:313297 original size:13 final size:13
Alignment explanation
Indices: 313279--313304 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
313269 TATATAAATA
313279 GGGTTATTTGCTC
1 GGGTTATTTGCTC
313292 GGGTTATTTGCTC
1 GGGTTATTTGCTC
313305 CAAAATGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (13 bp):
GGGTTATTTGCTC
Found at i:320617 original size:24 final size:24
Alignment explanation
Indices: 320590--320665 Score: 134
Period size: 24 Copynumber: 3.2 Consensus size: 24
320580 TTATCGACGG
*
320590 TGACTGTCACCAATGACCGAACGA
1 TGACTGTCACCGATGACCGAACGA
*
320614 TGACTGTCACTGATGACCGAACGA
1 TGACTGTCACCGATGACCGAACGA
320638 TGACTGTCACCGATGACCGAACGA
1 TGACTGTCACCGATGACCGAACGA
320662 TGAC
1 TGAC
320666 GGGGGATCGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.18
Consensus pattern (24 bp):
TGACTGTCACCGATGACCGAACGA
Found at i:320641 original size:11 final size:11
Alignment explanation
Indices: 320602--320665 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
320592 ACTGTCACCA
320602 ATGACCGAACG
1 ATGACCGAACG
* *
320613 ATGACTGTCACTG
1 ATGACCG-AAC-G
320626 ATGACCGAACG
1 ATGACCGAACG
* *
320637 ATGACTGTCACCG
1 ATGACCG--AACG
320650 ATGACCGAACG
1 ATGACCGAACG
320661 ATGAC
1 ATGAC
320666 GGGGGATCGA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
11 21 0.51
12 4 0.10
13 16 0.39
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (11 bp):
ATGACCGAACG
Found at i:322948 original size:16 final size:17
Alignment explanation
Indices: 322914--322957 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
322904 ATAATTTTTT
322914 TAAAATAAATATCATTAA
1 TAAAATAAATA-CATTAA
322932 TAAAATAAATA-ATTAA
1 TAAAATAAATACATTAA
*
322948 TAAAAAAAAT
1 TAAAATAAAT
322958 TTAAATATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 14 0.56
18 11 0.44
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAATAAATACATTAA
Found at i:323724 original size:2 final size:2
Alignment explanation
Indices: 323717--323743 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
323707 TTTTTCTGAC
323717 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
323744 AGTTAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:331936 original size:18 final size:18
Alignment explanation
Indices: 331913--331959 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
331903 ATGTAAAAAT
331913 GGTACTGATACCCAAAGG
1 GGTACTGATACCCAAAGG
331931 GGTACTGATACCCAAAGG
1 GGTACTGATACCCAAAGG
*
331949 GGTACCGATAC
1 GGTACTGATAC
331960 TACTTTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (18 bp):
GGTACTGATACCCAAAGG
Found at i:332139 original size:20 final size:21
Alignment explanation
Indices: 332103--332142 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
332093 GTAGAGAAAA
*
332103 CATCCCCAAATGGCTATAAAT
1 CATCCCCAAACGGCTATAAAT
332124 CATCCCC-AACGGCTATAAA
1 CATCCCCAAACGGCTATAAA
332143 CGACTACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.38, C:0.33, G:0.10, T:0.20
Consensus pattern (21 bp):
CATCCCCAAACGGCTATAAAT
Found at i:340801 original size:36 final size:36
Alignment explanation
Indices: 340730--340835 Score: 178
Period size: 36 Copynumber: 2.9 Consensus size: 36
340720 TCACCAATTT
*
340730 AGGTTTAATAAGAAATTTGAGTATTTTTTCTTATTAA
1 AGGTTTCATAAGAAATTTGAGTA-TTTTTCTTATTAA
340767 AGGTTTCATAAGAAATTTGAGTATTTTTCTTATTAA
1 AGGTTTCATAAGAAATTTGAGTATTTTTCTTATTAA
*
340803 AGGTTTCATAAGAAATTTGTGTA-TTTTCTTATT
1 AGGTTTCATAAGAAATTTGAGTATTTTTCTTATT
340836 GAAGATTAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 10 0.15
36 35 0.52
37 22 0.33
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (36 bp):
AGGTTTCATAAGAAATTTGAGTATTTTTCTTATTAA
Found at i:346988 original size:30 final size:32
Alignment explanation
Indices: 346923--346988 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
346913 AAGCCTATGA
*
346923 CTTAACCTTTTTATCCCAGGGAAGAAGAAAAG
1 CTTAACCTTTTTACCCCAGGGAAGAAGAAAAG
346955 CTTAACCTTTTT-CCCCA-GGAAG-AGAAAATG
1 CTTAACCTTTTTACCCCAGGGAAGAAGAAAA-G
346985 CTTA
1 CTTA
346989 CATAGGGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 6 0.19
30 10 0.31
31 4 0.12
32 12 0.38
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (32 bp):
CTTAACCTTTTTACCCCAGGGAAGAAGAAAAG
Found at i:347128 original size:33 final size:33
Alignment explanation
Indices: 347080--347145 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 33
347070 AGCCTATGAC
347080 TTAACCTTTTTTAT-CCCAGGGAAGAAGAAAAG
1 TTAACCTTTTTTATCCCCAGGGAAGAAGAAAAG
347112 TTAACCTTTTTTTATCCCCAGGGAAGAAGAAAAG
1 TTAACC-TTTTTTATCCCCAGGGAAGAAGAAAAG
347146 CTCAAAAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 6 0.19
33 8 0.25
34 18 0.56
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (33 bp):
TTAACCTTTTTTATCCCCAGGGAAGAAGAAAAG
Found at i:347154 original size:154 final size:150
Alignment explanation
Indices: 346842--347122 Score: 492
Period size: 154 Copynumber: 1.8 Consensus size: 150
346832 CTTACATAGG
346842 GAAAACAAAACCAAGGCAACATCACAGTGAGAGATAACATCCAAAGTAAAATACAAGTAACCCGT
1 GAAAACAAAACCAAGGCAACATCACAGTGAGAGATAACATCCAAAGTAAAATACAAGTAACCCGT
346907 GGTTATAAGCCTATGACTTAACCTTTTTATCCCAGGGAAGAAGAAAAGCTTAACCTTTTTCCCCA
66 GGTTATAAGCCTATGACTTAACCTTTTTATCCCAGGGAAGAAGAAAAGCTTAACCTTTTTCCCCA
346972 GGAAGAGAAAATGCTTACATA
131 GGAAGAGAAAATGCTTACA-A
346993 GGGAAAACAAAACCAAGGCAACAATCACAGTGAGAGATAACATCCAAAGTAAAATACAAGTAAAC
1 --GAAAACAAAACCAAGGCAAC-ATCACAGTGAGAGATAACATCCAAAGTAAAATACAAGT-AAC
347058 CCAGTGGTTATAAGCCTATGACTTAACCTTTTTTATCCCAGGGAAGAAGAAAAG-TTAACCTTTT
62 CC-GTGGTTATAAGCCTATGACTTAACC-TTTTTATCCCAGGGAAGAAGAAAAGCTTAACCTTTT
347122 T
125 T
347123 TTATCCCCAG
Statistics
Matches: 124, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
153 20 0.16
154 38 0.31
155 5 0.04
156 36 0.29
157 25 0.20
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.22
Consensus pattern (150 bp):
GAAAACAAAACCAAGGCAACATCACAGTGAGAGATAACATCCAAAGTAAAATACAAGTAACCCGT
GGTTATAAGCCTATGACTTAACCTTTTTATCCCAGGGAAGAAGAAAAGCTTAACCTTTTTCCCCA
GGAAGAGAAAATGCTTACAA
Found at i:347513 original size:20 final size:20
Alignment explanation
Indices: 347490--347541 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
347480 AACGCGATCC
347490 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
347510 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
347530 CCAAAATCGCAA
1 CCAGAATCGCAA
347542 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:347558 original size:21 final size:20
Alignment explanation
Indices: 347531--347629 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
347521 AATCAGTTTC
347531 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
347552 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
347573 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
347593 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
347614 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
347630 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:347658 original size:20 final size:20
Alignment explanation
Indices: 347596--347724 Score: 129
Period size: 20 Copynumber: 6.5 Consensus size: 20
347586 CGATTTTCCA
* ** *
347596 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
347616 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
347636 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
347656 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
347676 AAATCGCAA--CGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
347694 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
347714 ATATCGCAACG
1 AAATCGCAACG
347725 ATATTTCGTC
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
18 15 0.17
19 1 0.01
20 72 0.80
21 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:347698 original size:38 final size:38
Alignment explanation
Indices: 347616--347724 Score: 121
Period size: 38 Copynumber: 2.8 Consensus size: 38
347606 GCGAATATGA
* *
347616 AAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATC-CGTAAATCGCAA--CGTATCCGT
* **
347656 AAATCGCAACGTGTATCCGTAAATCGCAACGTATGGGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGTATCCGT
* *
347694 AAATCGCAATGCGTATCCGTATATCGCAACG
1 AAATCGCAACGCGTATCCGTAAATCGCAACG
347725 ATATTTCGTC
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
38 35 0.58
40 23 0.38
41 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (38 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGTATCCGT
Found at i:349264 original size:13 final size:13
Alignment explanation
Indices: 349246--349271 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
349236 TATTTTTATG
349246 TTTTTTTAAAATA
1 TTTTTTTAAAATA
349259 TTTTTTTAAAATA
1 TTTTTTTAAAATA
349272 ATTAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTTTAAAATA
Found at i:354182 original size:21 final size:22
Alignment explanation
Indices: 354126--354182 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
354116 AATAAATTAA
*
354126 TTTTTT-TTAAAAAAAAAATCT
1 TTTTTTATTAAAAATAAAATCT
* *
354147 TTTTTCATTAAAAATAATAT-T
1 TTTTTTATTAAAAATAAAATCT
354168 TTTTTTATTAAAAAT
1 TTTTTTATTAAAAAT
354183 TTTAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTTTATTAAAAATAAAATCT
Found at i:355881 original size:108 final size:108
Alignment explanation
Indices: 355712--355917 Score: 331
Period size: 108 Copynumber: 1.9 Consensus size: 108
355702 CTCTATTTAA
* * * * *
355712 GGGTCTGGTCTGGCTTAACTCTTGATATAGTCCCTTGGTTTCGAGTGGAAAGGAGCTCGATGCTC
1 GGGTCTGGCCTGGCTTAACTCTTGATATAGTCCCCTGGTTTCAAGTGGAAAGAAGCACGATGCTC
* * *
355777 TGTCTTGGTTTCGAGTCTTGCGGATGAAGAAATAGTTACTTAG
66 CGTCTTGGTTTCGAGTCATACGGATGAAGAAATAGTTACTTAG
355820 GGGTCTGGCCTGGCTTAACTCTTGATATAGTCCCCTGGTTTCAAGTGGAAAGAAGCACGATGCTC
1 GGGTCTGGCCTGGCTTAACTCTTGATATAGTCCCCTGGTTTCAAGTGGAAAGAAGCACGATGCTC
*
355885 CGTCTTGGTTTCGAGTCATATGGATGAAGAAAT
66 CGTCTTGGTTTCGAGTCATACGGATGAAGAAAT
355918 GACATTGGGA
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 89 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (108 bp):
GGGTCTGGCCTGGCTTAACTCTTGATATAGTCCCCTGGTTTCAAGTGGAAAGAAGCACGATGCTC
CGTCTTGGTTTCGAGTCATACGGATGAAGAAATAGTTACTTAG
Found at i:357362 original size:20 final size:19
Alignment explanation
Indices: 357328--357365 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
357318 TATTTTAATA
*
357328 TTTAAAAATATTATTATTT
1 TTTAAAAATAATATTATTT
357347 TTTAATAAATAATATTATT
1 TTTAA-AAATAATATTATT
357366 CATTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAAAATAATATTATTT
Found at i:360506 original size:23 final size:23
Alignment explanation
Indices: 360480--360523 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
360470 GTTAATTAGA
*
360480 AAATAGTTAAAATTA-TTATTTTT
1 AAATAG-TAAAATAATTTATTTTT
360503 AAATAGTAAAATAATTTATTT
1 AAATAGTAAAATAATTTATTT
360524 AATATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
AAATAGTAAAATAATTTATTTTT
Found at i:360535 original size:14 final size:15
Alignment explanation
Indices: 360516--360545 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
360506 TAGTAAAATA
360516 ATTTATTT-AATATT
1 ATTTATTTCAATATT
360530 ATTTATTTCAATATT
1 ATTTATTTCAATATT
360545 A
1 A
360546 ATATTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTATTTCAATATT
Found at i:365988 original size:2 final size:2
Alignment explanation
Indices: 365981--366013 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
365971 GATAAAAATA
365981 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
366014 CCCACGGACG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:367391 original size:14 final size:14
Alignment explanation
Indices: 367374--367403 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
367364 TATTTATTTA
*
367374 TTTTAAATATATAT
1 TTTTAAAAATATAT
367388 TTTTAAAAATATAT
1 TTTTAAAAATATAT
367402 TT
1 TT
367404 AAAGTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTAAAAATATAT
Found at i:368141 original size:18 final size:18
Alignment explanation
Indices: 368099--368151 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 18
368089 TAAAAAATGG
368099 GTGATCTTTTTTTTAGTA
1 GTGATCTTTTTTTTAGTA
368117 -TG-T-TTTTTATTT-GTA
1 GTGATCTTTTT-TTTAGTA
368132 GTGATCTTTTCTTTTTAGTA
1 GTGATC-TTT-TTTTTAGTA
368152 TGGTTTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
15 8 0.29
16 6 0.21
17 3 0.11
19 6 0.21
20 5 0.18
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.64
Consensus pattern (18 bp):
GTGATCTTTTTTTTAGTA
Found at i:368153 original size:35 final size:33
Alignment explanation
Indices: 368099--368167 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 33
368089 TAAAAAATGG
* *
368099 GTGATCTTTTTTTTAGTATGTTTTTTATTTGTA
1 GTGATCTTTTTTTTAGTATGGTTTTGATTTGTA
368132 GTGATCTTTTCTTTTTAGTATGGTTTTGATTTGTA
1 GTGATC-TTT-TTTTTAGTATGGTTTTGATTTGTA
368167 G
1 G
368168 CTTTGATGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 6 0.19
34 3 0.09
35 23 0.72
ACGTcount: A:0.14, C:0.04, G:0.19, T:0.62
Consensus pattern (33 bp):
GTGATCTTTTTTTTAGTATGGTTTTGATTTGTA
Found at i:375441 original size:154 final size:150
Alignment explanation
Indices: 375232--375514 Score: 392
Period size: 154 Copynumber: 1.9 Consensus size: 150
375222 CCTCATTTCA
* *
375232 TTATTTCTTCAATTTCCTTCATTTTAAGTCATTTTTACCAAATTTAAACCGCATGCTCCTAAACC
1 TTATTTCTTCAATTTCATTCATTTTAAGTCATTTTTACCAAATTTAAACCACATGCTCCTAAACC
* *
375297 TTAGTAGAATACATGTTTACTTTCAATTCCTCTTTTTGATAACAA-TTTTTATTTTTCAATTTAG
66 ATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGAT-ACAATTTTTTATTTTTCAATTTAG
375361 CCCTTCAATTTTTTAATCTCC
130 CCCTTCAATTTTTTAATCTCC
* *
375382 TTATTTCTTCAATTTATCATTTA-TTTAAGTCTATTTTTTTACCAAATTTGAGA-CACATGCTCC
1 TTATTTCTTCAA-TT-TCATTCATTTTAAGTC-A--TTTTTACCAAATTT-AAACCACATGCTCC
* *
375445 TAAACCATAGTAGAATACATGTGTGCTTTCAATTCCTCTTTTTTATACAATTTTTTTATTTTTCA
60 TAAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATACAA-TTTTTTATTTTTCA
*
375510 CTTTA
124 ATTTA
375515 ATCCTTGAAT
Statistics
Matches: 116, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
150 12 0.10
151 10 0.09
152 6 0.05
153 4 0.03
154 65 0.56
155 19 0.16
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (150 bp):
TTATTTCTTCAATTTCATTCATTTTAAGTCATTTTTACCAAATTTAAACCACATGCTCCTAAACC
ATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATACAATTTTTTATTTTTCAATTTAGC
CCTTCAATTTTTTAATCTCC
Found at i:375649 original size:117 final size:119
Alignment explanation
Indices: 375422--375657 Score: 343
Period size: 117 Copynumber: 2.0 Consensus size: 119
375412 CTATTTTTTT
** * *
375422 ACCAAATTTGAGACACATGCTCCTAAACCATAGTAGAATACATGTGTGCTTTCAATTCCTCTTTT
1 ACCAAATTTGAGACACAAACTCCTAAACCATAGTAGAATACA-GTGTACTTTCAATTCCTATTTT
* * * *
375487 TTATACAATTTTTTTATTTTTCACTTTAATCCTTGAATTTGTCATAATCTCCTTC
65 TGATACAAATTTTTTATTTTTCAATTTAATCCTTGAATTTGTCATAAGCTCCTTC
375542 ACCAAATTTGAG-C-CAAACTCCTAAACCATAGTAGAATACA-TGTACTTTCAATTCCTATTTTT
1 ACCAAATTTGAGACACAAACTCCTAAACCATAGTAGAATACAGTGTACTTTCAATTCCTATTTTT
* *
375604 GATAACAAATTTTTTATTTTTCAATTTAATCCTTTAATTTTTCATAAGCTCCTT
66 GAT-ACAAATTTTTTATTTTTCAATTTAATCCTTGAATTTGTCATAAGCTCCTT
375658 ATTCCTTCAA
Statistics
Matches: 105, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
116 22 0.21
117 45 0.43
118 25 0.24
119 1 0.01
120 12 0.11
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (119 bp):
ACCAAATTTGAGACACAAACTCCTAAACCATAGTAGAATACAGTGTACTTTCAATTCCTATTTTT
GATACAAATTTTTTATTTTTCAATTTAATCCTTGAATTTGTCATAAGCTCCTTC
Found at i:375948 original size:21 final size:20
Alignment explanation
Indices: 375918--375970 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
375908 TCTTTAAAAT
375918 ATAATATTATGAATATATTTG
1 ATAATATTAT-AATATATTTG
* *
375939 ATAATTTTATATTATATTTG
1 ATAATATTATAATATATTTG
375959 AT-ATATTA-AATA
1 ATAATATTATAATA
375971 ACATTATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 3 0.11
19 5 0.18
20 11 0.39
21 9 0.32
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (20 bp):
ATAATATTATAATATATTTG
Found at i:376678 original size:13 final size:13
Alignment explanation
Indices: 376660--376684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
376650 TCACCTTCTG
376660 TTTTTATTTTATT
1 TTTTTATTTTATT
376673 TTTTTATTTTAT
1 TTTTTATTTTAT
376685 ATTAAATAAT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:377449 original size:17 final size:17
Alignment explanation
Indices: 377416--377448 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
377406 TAAATTAGAG
*
377416 AAACTTATTTATTTTTT
1 AAACTAATTTATTTTTT
377433 AAACTAATTT-TTTTTT
1 AAACTAATTTATTTTTT
377449 TGTTCAAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
AAACTAATTTATTTTTT
Found at i:385455 original size:17 final size:17
Alignment explanation
Indices: 385421--385468 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
385411 ATCAAGAAAA
* *
385421 ATTATTATTTTAGAGAG
1 ATTATTAATTTATAGAG
*
385438 ATTATTAATTTATCGAG
1 ATTATTAATTTATAGAG
*
385455 AATATTAATTTATA
1 ATTATTAATTTATA
385469 AAGGTTCTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (17 bp):
ATTATTAATTTATAGAG
Found at i:387761 original size:21 final size:20
Alignment explanation
Indices: 387707--387750 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
387697 GGTATTTTAG
*
387707 TTTAAATAG-TTTTAAGTGT
1 TTTAATTAGTTTTTAAGTGT
*
387726 TTTAATTAGTATTTAAGATGT
1 TTTAATTAGTTTTTAAG-TGT
387747 TTTA
1 TTTA
387751 GCTTGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (20 bp):
TTTAATTAGTTTTTAAGTGT
Found at i:388279 original size:20 final size:20
Alignment explanation
Indices: 388250--388287 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
388240 TTTCAAAGGG
388250 ATGCACCGATGCAACAATCT
1 ATGCACCGATGCAACAATCT
* *
388270 ATGCATCGATGCACCAAT
1 ATGCACCGATGCAACAAT
388288 GAATAAATTG
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:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCAACAATCT
Found at i:388386 original size:46 final size:45
Alignment explanation
Indices: 388334--388438 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 45
388324 TGCACTATCC
* *
388334 ATGCATCGATGCACTCAGGGT-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAAGCTATTT-TG-AAACATCGAATGCATTTG
*
388380 ATGCATCGATGCACTCAAGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAAGCTATTTTGAAACATCGAATGCATTTG
*
388425 ATACATCGATGCAC
1 ATGCATCGATGCAC
388439 CCTTAGTGCA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
45 30 0.56
46 21 0.39
47 3 0.06
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (45 bp):
ATGCATCGATGCACTCAAGCTATTTTGAAACATCGAATGCATTTG
Found at i:389520 original size:19 final size:18
Alignment explanation
Indices: 389469--389517 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
389459 AATCTCTTTA
389469 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
* *
389488 TTTCTTTTATTTAATTCTT
1 ATT-TTTTATTTAATTATT
389507 ATTTTTTATTT
1 ATTTTTTATTT
389518 TAAAAACAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:389675 original size:23 final size:21
Alignment explanation
Indices: 389641--389683 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
389631 CTGGAATTTT
389641 ATGTTCTTTTAAAATCAAGAAAA
1 ATGTTCTTTT-AAATC-AGAAAA
389664 ATGTT-TTATTAAATCAGAAA
1 ATGTTCTT-TTAAATCAGAAA
389684 CACCACAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (21 bp):
ATGTTCTTTTAAATCAGAAAA
Found at i:390699 original size:2 final size:2
Alignment explanation
Indices: 390686--390737 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
390676 AATTTATAGT
390686 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
390729 TA TA T- TA TA
1 TA TA TA TA TA
390738 ATTAAATAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 45 0.94
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:392409 original size:20 final size:21
Alignment explanation
Indices: 392384--392476 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
392374 TTTTCCCAAT
*
392384 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
392404 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
392425 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
392445 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
392466 TCGCAATGCGA
1 TCGCAATGCGA
392477 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:392429 original size:41 final size:41
Alignment explanation
Indices: 392384--392476 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
392374 TTTTCCCAAT
392384 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
392425 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
392466 TCGCAATGCGA
1 TCGCAATGCGA
392477 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:392489 original size:41 final size:41
Alignment explanation
Indices: 392403--392537 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
392393 GAATAAGTAA
** *
392403 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
392444 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
392485 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
392526 TTCGCAACGCGA
1 ATCGCAACGCGA
392538 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:392490 original size:20 final size:20
Alignment explanation
Indices: 392465--392558 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
392455 AATTGGGAAA
*
392465 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
392485 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
392506 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
392526 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
392546 TTCGCAACGCGAT
1 ATCGCAACGCGAT
392559 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:393115 original size:19 final size:19
Alignment explanation
Indices: 393077--393143 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
393067 TTCGAGAATG
393077 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
393097 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
393116 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
393135 AAAATCGCA
1 AAAATCGCA
393144 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:393161 original size:19 final size:19
Alignment explanation
Indices: 393139--393270 Score: 148
Period size: 19 Copynumber: 7.1 Consensus size: 19
393129 GAAACCAAAA
*
393139 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
393158 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
393177 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
393196 TCGCGGTTGCGATTGTC---
1 TCGC-GTTGCGATTTTCATT
* **
393213 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
393230 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
393249 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
393269 TC
1 TC
393271 AACCAAAAGA
Statistics
Matches: 97, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
14 10 0.10
16 1 0.01
17 2 0.02
18 1 0.01
19 55 0.57
20 28 0.29
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Done.