Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008288.1 Hibiscus syriacus cultivar Beakdansim tig00110951_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: 310337
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:207398 original size:30 final size:30
Alignment explanation
Indices: 207348--207404 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
207338 AGAACCACTA
* *
207348 TCCATATGTTTCAAACAATATAGGTAATTG
1 TCCATATGTTCCAAACAATATAAGTAATTG
* *
207378 TCCATATGTTCCGAAGAATATAAGTAA
1 TCCATATGTTCCAAACAATATAAGTAA
207405 CCCTCGACTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (30 bp):
TCCATATGTTCCAAACAATATAAGTAATTG
Found at i:208728 original size:20 final size:21
Alignment explanation
Indices: 208697--208736 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
208687 GAAAGTTTTC
*
208697 GTTGAGAGGGTATCGGTACCT
1 GTTGAGAGGGTATCGATACCT
208718 GTTGA-AGGGTATCGATACC
1 GTTGAGAGGGTATCGATACC
208737 CCTAACCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.23, C:0.15, G:0.35, T:0.28
Consensus pattern (21 bp):
GTTGAGAGGGTATCGATACCT
Found at i:210262 original size:679 final size:673
Alignment explanation
Indices: 208870--210222 Score: 2250
Period size: 679 Copynumber: 2.0 Consensus size: 673
208860 ATCTTTAACT
*
208870 TCAAAATCTAATACTCTACATAGAATTTAAGAATCACTCAAATTTCAACATGTTCTAAATCCTAT
1 TCAAAATCT-ATACTCTACAT---ATTAAAGAATCACTCAAATTTCAACATGTTCTAAATCCTAT
208935 TCTATCACTTCAATCCCTTAATTCGACCATTGACAAGTCAAATTTAACTTCAAATTCTTTTATCA
62 TCTATCACTTCAATCCCTTAATTCGACCATTGACAAGTCAAATTTAACTTCAAATTCTTTTATCA
209000 ATTCTTTCCAAAATTTCATTTAAAAACTCCAAATCTCTATCTCTCTTAACTCCTCATTCTTTGAT
127 ATTCTTTCCAAAATTTCATTTAAAAACTCCAAATCTCTATCTCTCTTAACTCCTCATTCTTTGAT
209065 TTTATTGTAACTTAAGCTTCCTTAAACTTATACATCAACTAAGGATCATAACCCAACTTTAATTT
192 TTTATTGTAACTTAAGCTTCCTTAAACTTATACATCAACTAAGGATCATAACCCAACTTTAATTT
209130 AGGAAATAATTAACCAACAGAAACTCACCTTTTATTTGGCTTCACGCAGAAGAAAAAAAAGAAGA
257 AGGAAATAATTAACCAACAGAAACTCACCTTTTATTTGGCTTCACGCA-AAGAAAAAAAAGAAGA
209195 AGAAGAGAGAAAATTCTGGAATCCTTCTCTTTTCTCTTCTATTCATCACGTGGGGATAATATAGT
321 AGAAGAGAGAAAATTCTGGAATCCTTCTCTTTTCTCTTCTATTCATCACGTGGGGATAATATAGT
209260 CCCTCTAAAAAAATCTTTCTATATAATGTCCATTTTGCTCTTCCACTCTTTTCATATTTACCAAT
386 CCCTCTAAAAAAATCTTTCTATATAATGTCCATTTTGCTCTTCCACTCTTTTCATATTTACCAAT
209325 CAATCCTCTTGAATAAAATTCTTATTAGATCCTTTAACTTTTAACTTGTTTCAAAATCGAGCCCA
451 CAATCCTCTTGAATAAAATTCTTATTAGATCCTTTAACTTTTAACTTGTTTCAAAATCGAGCCCA
*
209390 AAAGTTTCAAATTTTCAATTTAGTCATTGACCTTGATTTGGGATGTCACAAATCTCCCTCCTTTA
516 AAAGTTTCAAATTTTCAATTTAGTCATTGACCTTGATTTGGGATGTCACAAATCTCCCTCATTTA
209455 AAGAAAATTGTCTCGAATTTTCATGCACACCTTAATGAGAACATCTTCTAATGTTCTCATGTTGC
581 AAGAAAATTGTCTCGAATTTTCATGCACACCTTAATGAGAACATCTTCTAATGTTCTCATGTTGC
**
209520 TTTCTTTACTTATTATTCCATCTTTAAC
646 TTTCTTTACTTATTATTCCATCTGCAAC
*
209548 TTCAAAATCTAATACTCTACATAGAATTTAAGAATCATACTCAAATTTCAACATGTTCTAAATCC
1 -TCAAAATCT-ATACTCTACAT---ATTAAAGAATC--ACTCAAATTTCAACATGTTCTAAATCC
209613 TATTCTATTCACTTCACAT-CCTTAATTCGA-CATTGACAAGTCAAATTTAACTTCAAATTCTTT
59 TATTCTA-TCACTTCA-ATCCCTTAATTCGACCATTGACAAGTCAAATTTAACTTCAAATTC-TT
209676 TTATCAATTCTTTCCAAAA-TTCATTT-AAAACTCCAAATCTCTAATCTCTCTTAACTCCTTCA-
121 TTATCAATTCTTTCCAAAATTTCATTTAAAAACTCCAAATCTCT-ATCTCTCTTAACTCC-TCAT
209738 TCTTTGATTTTATTGTAACTTAAGCTTTCCTTAAAC-TATACATCAACTAAGGATCATAACCCAA
184 TCTTTGATTTTATTGTAACTTAAGC-TTCCTTAAACTTATACATCAACTAAGGATCATAACCCAA
209802 CTTTAAATTTAGGAAAT-A-TAACCAACAGAAAACTCACC-TTTATTTTGGCTTCACGC-AAGAA
248 CTTT-AATTTAGGAAATAATTAACCAACAG-AAACTCACCTTTTA-TTTGGCTTCACGCAAAGAA
*
209863 GAAAAAGAAGAAGAAGA-AGAAAACTTCTGGAATCCTTCTC-TTTCTCTTCTATTCATCCCACGT
310 AAAAAAGAAGAAGAAGAGAGAAAA-TTCTGGAATCCTTCTCTTTTCTCTTCTATTCAT--CACGT
209926 GGGGATAATATAGTCCCTCT-AAAAAATCTTTCTATATAATGTCCATTTTGC-CTTCCACTCTTT
372 GGGGATAATATAGTCCCTCTAAAAAAATCTTTCTATATAATGTCCATTTTGCTCTTCCACTCTTT
209989 TCATATTTACCAATCAATCCTCTTGAATAAAATTCTTAATTAGATCCTTTAACTTTTAACTTGTT
437 TCATATTTACCAATCAATCCTCTTGAATAAAATTCTT-ATTAGATCCTTTAACTTTTAACTTGTT
210054 TCAAAATCGAGCCCAAAAGTTTCAAAATTTTCAA-TTAGTCATTGACCTTGATTTGGGATGTCAC
501 TCAAAATCGAGCCCAAAAGTTTC-AAATTTTCAATTTAGTCATTGACCTTGATTTGGGATGTCAC
*
210118 AAATCTCCCCCTCATTTAAAGAAAATTGTCCTCGAATTTTCACTGCACACCTTAATGAGAATATC
565 AAATCT--CCCTCATTTAAAGAAAATTGT-CTCGAATTTTCA-TGCACACCTTAATGAGAACATC
210183 TTCTAATGTTCTCATGTTGCTTTCTTTACTTTATTTATTC
626 TTCTAATGTTCTCATGTTGCTTTCTTTAC-TTA-TTATTC
210223 GCAATTGCAA
Statistics
Matches: 649, Mismatches: 3, Indels: 38
0.94 0.00 0.06
Matches are distributed among these distances:
678 71 0.11
679 189 0.29
680 65 0.10
681 186 0.29
682 77 0.12
683 52 0.08
684 3 0.00
685 6 0.01
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.37
Consensus pattern (673 bp):
TCAAAATCTATACTCTACATATTAAAGAATCACTCAAATTTCAACATGTTCTAAATCCTATTCTA
TCACTTCAATCCCTTAATTCGACCATTGACAAGTCAAATTTAACTTCAAATTCTTTTATCAATTC
TTTCCAAAATTTCATTTAAAAACTCCAAATCTCTATCTCTCTTAACTCCTCATTCTTTGATTTTA
TTGTAACTTAAGCTTCCTTAAACTTATACATCAACTAAGGATCATAACCCAACTTTAATTTAGGA
AATAATTAACCAACAGAAACTCACCTTTTATTTGGCTTCACGCAAAGAAAAAAAAGAAGAAGAAG
AGAGAAAATTCTGGAATCCTTCTCTTTTCTCTTCTATTCATCACGTGGGGATAATATAGTCCCTC
TAAAAAAATCTTTCTATATAATGTCCATTTTGCTCTTCCACTCTTTTCATATTTACCAATCAATC
CTCTTGAATAAAATTCTTATTAGATCCTTTAACTTTTAACTTGTTTCAAAATCGAGCCCAAAAGT
TTCAAATTTTCAATTTAGTCATTGACCTTGATTTGGGATGTCACAAATCTCCCTCATTTAAAGAA
AATTGTCTCGAATTTTCATGCACACCTTAATGAGAACATCTTCTAATGTTCTCATGTTGCTTTCT
TTACTTATTATTCCATCTGCAAC
Found at i:212022 original size:24 final size:22
Alignment explanation
Indices: 211972--212023 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
211962 GGCATGTGAA
* *
211972 ATATGTCCCGAAGGACCTATGC
1 ATATGTCCCAAAGGACCTATCC
*
211994 GTATGTCCCAAAGGACCACTATCC
1 ATATGTCCCAAAGGA-C-CTATCC
212018 ATATGT
1 ATATGT
212024 TCTGAAGAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 13 0.54
23 1 0.04
24 10 0.42
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (22 bp):
ATATGTCCCAAAGGACCTATCC
Found at i:212051 original size:30 final size:30
Alignment explanation
Indices: 212015--212072 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
212005 AGGACCACTA
*
212015 TCCATATGTTCTGAAGAACATAAGTAACTG
1 TCCATATGTTCCGAAGAACATAAGTAACTG
*
212045 TCCATATGTTCCGAAGAACATAGGTAAC
1 TCCATATGTTCCGAAGAACATAAGTAAC
212073 CCTCAACTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (30 bp):
TCCATATGTTCCGAAGAACATAAGTAACTG
Found at i:214678 original size:16 final size:16
Alignment explanation
Indices: 214627--214678 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
214617 TGGTATTACC
214627 TGACATGTTTTCAACT
1 TGACATGTTTTCAACT
* * * * *
214643 TAACCTGTTATGAACC
1 TGACATGTTTTCAACT
*
214659 TGACTTGTTTTCAACT
1 TGACATGTTTTCAACT
214675 TGAC
1 TGAC
214679 CTATAAATGA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (16 bp):
TGACATGTTTTCAACT
Found at i:214694 original size:32 final size:32
Alignment explanation
Indices: 214624--214699 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
214614 AACTGGTATT
* * *
214624 ACCTGACATGTTTTCAACTTAACCTGTTATGA
1 ACCTGACTTGTTTTCAACTTAACCTATAATGA
*
214656 ACCTGACTTGTTTTCAACTTGACCTATAAATG-
1 ACCTGACTTGTTTTCAACTTAACCTAT-AATGA
*
214688 ATCTGACTTGTT
1 ACCTGACTTGTT
214700 ATTGACCTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
32 35 0.92
33 3 0.08
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (32 bp):
ACCTGACTTGTTTTCAACTTAACCTATAATGA
Found at i:216188 original size:21 final size:21
Alignment explanation
Indices: 216164--216311 Score: 60
Period size: 20 Copynumber: 7.2 Consensus size: 21
216154 TGCAACACAG
216164 TTTCCAAATTCGCAACGCGAA
1 TTTCCAAATTCGCAACGCGAA
* * *
216185 TTTCCCAAATTTGCAACTC-AG
1 TTT-CCAAATTCGCAACGCGAA
216206 TTTCTGC-AA-TCGCAACGCGAA
1 TTTC--CAAATTCGCAACGCGAA
** **
216227 TTT-C-TTTCTCGCAATACG-A
1 TTTCCAAAT-TCGCAACGCGAA
* *
216246 TTTCGAAATTCGCAACACGAAA
1 TTTCCAAATTCGCAACGCG-AA
* *
216268 TTT-CAAATTCACAACTCG-A
1 TTTCCAAATTCGCAACGCGAA
** * *
216287 TTTCTGAATTCGCAATGCAAA
1 TTTCCAAATTCGCAACGCGAA
216308 TTTC
1 TTTC
216312 TTTTTCACAA
Statistics
Matches: 92, Mismatches: 23, Indels: 24
0.66 0.17 0.17
Matches are distributed among these distances:
18 1 0.01
19 8 0.09
20 34 0.37
21 31 0.34
22 18 0.20
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (21 bp):
TTTCCAAATTCGCAACGCGAA
Found at i:216195 original size:22 final size:23
Alignment explanation
Indices: 216166--216231 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
216156 CAACACAGTT
216166 TCCAAATTCGCAACGCGAATTTC
1 TCCAAATTCGCAACGCGAATTTC
* * *
216189 -CCAAATTTGCAACTC-AGTTTC
1 TCCAAATTCGCAACGCGAATTTC
*
216210 TGC-AA-TCGCAACGCGAATTTC
1 TCCAAATTCGCAACGCGAATTTC
216231 T
1 T
216232 TTCTCGCAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
20 7 0.21
21 13 0.38
22 14 0.41
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (23 bp):
TCCAAATTCGCAACGCGAATTTC
Found at i:216207 original size:42 final size:42
Alignment explanation
Indices: 216149--216230 Score: 114
Period size: 42 Copynumber: 1.9 Consensus size: 42
216139 TGCGGACTCC
216149 AATTCTGCAACACAGTTTC-CAAATTCGCAACGCGAATTTCCCA
1 AATTCTGCAACACAGTTTCGC-AA-TCGCAACGCGAATTTCCCA
*
216192 AATT-TGCAACTCAGTTTCTGCAATCGCAACGCGAATTTC
1 AATTCTGCAACACAGTTTC-GCAATCGCAACGCGAATTTC
216231 TTTCTCGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
42 29 0.81
43 6 0.17
44 1 0.03
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (42 bp):
AATTCTGCAACACAGTTTCGCAATCGCAACGCGAATTTCCCA
Found at i:216258 original size:20 final size:20
Alignment explanation
Indices: 216235--216302 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
216225 AATTTCTTTC
216235 TCGCAATACGATTTCGAAAT
1 TCGCAATACGATTTCGAAAT
*
216255 TCGCAACACGAAATTTC-AAAT
1 TCGCAATACG--ATTTCGAAAT
*
216276 TCACAACT-CGATTTCTG-AAT
1 TCGCAA-TACGATTTC-GAAAT
216296 TCGCAAT
1 TCGCAAT
216303 GCAAATTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
19 6 0.15
20 17 0.44
21 11 0.28
22 5 0.13
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (20 bp):
TCGCAATACGATTTCGAAAT
Found at i:216291 original size:81 final size:81
Alignment explanation
Indices: 216164--216314 Score: 191
Period size: 81 Copynumber: 1.9 Consensus size: 81
216154 TGCAACACAG
* ** *
216164 TTTCCAAATTCGCAACGCGAATTTCCCAAATTTGCAACTCAGTTTCTGCAA-TCGCAACGCGAAT
1 TTTCCAAATTCGCAACACGAATTT-CCAAATTCACAACTCAGTTTCTG-AATTCGCAACGCAAAT
216228 TTCTTTCTCGCAATACGA
64 TTCTTTCTCGCAATACGA
* *
216246 TTTCGAAATTCGCAACACGAAATTT-CAAATTCACAACTC-GATTTCTGAATTCGCAATGCAAAT
1 TTTCCAAATTCGCAACACG-AATTTCCAAATTCACAACTCAG-TTTCTGAATTCGCAACGCAAAT
216309 TTCTTT
64 TTCTTT
216315 TTCACAACAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
80 3 0.05
81 35 0.58
82 17 0.28
83 5 0.08
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (81 bp):
TTTCCAAATTCGCAACACGAATTTCCAAATTCACAACTCAGTTTCTGAATTCGCAACGCAAATTT
CTTTCTCGCAATACGA
Found at i:216320 original size:40 final size:41
Alignment explanation
Indices: 216198--216322 Score: 107
Period size: 40 Copynumber: 3.1 Consensus size: 41
216188 CCCAAATTTG
* * * *
216198 CAACTC-AGTTTCTGCAA-TCGCAACGCGAATTTCTTTCTCG
1 CAACTCGA-TTTCTGAAATTCGCAACGCAAATTTCTTTTTCA
* ***
216238 CAA-TACGATTTC-GAAATTCGCAACACGAAATTTCAAATTCA
1 CAACT-CGATTTCTGAAATTCGCAACGC-AAATTTCTTTTTCA
*
216279 CAACTCGATTTCTG-AATTCGCAATGCAAATTTCTTTTTCA
1 CAACTCGATTTCTGAAATTCGCAACGCAAATTTCTTTTTCA
216319 CAAC
1 CAAC
216323 ACAAGTTTCC
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
39 4 0.06
40 31 0.47
41 29 0.44
42 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (41 bp):
CAACTCGATTTCTGAAATTCGCAACGCAAATTTCTTTTTCA
Found at i:216380 original size:21 final size:21
Alignment explanation
Indices: 216346--216411 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
216336 TCATAACAAG
* *
216346 ATTTTCTAAATCGCAACACGA
1 ATTTTCGAATTCGCAACACGA
* ** *
216367 ATTTTTGTTTTCGC-ACTCG-
1 ATTTTCGAATTCGCAACACGA
*
216386 ATTTTCGAATTCGCAACACAA
1 ATTTTCGAATTCGCAACACGA
216407 ATTTT
1 ATTTT
216412 AATTTCGCAG
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 11 0.34
20 7 0.22
21 14 0.44
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (21 bp):
ATTTTCGAATTCGCAACACGA
Found at i:216944 original size:21 final size:20
Alignment explanation
Indices: 216911--216991 Score: 92
Period size: 20 Copynumber: 4.0 Consensus size: 20
216901 TGCGATTGTT
*
216911 GCGAAAGTCAAATTCGCAAC
1 GCGAAAATCAAATTCGCAAC
216931 GCGAAAAATCAAATTCGCAAC
1 GCG-AAAATCAAATTCGCAAC
* *
216952 ACGAAAATCAAATTC-AACAC
1 GCGAAAATCAAATTCGCA-AC
* *
216972 GCGAAAATAAAAATCGCAAC
1 GCGAAAATCAAATTCGCAAC
216992 AGGAATTTGA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.02
20 31 0.61
21 19 0.37
ACGTcount: A:0.49, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GCGAAAATCAAATTCGCAAC
Found at i:216974 original size:41 final size:40
Alignment explanation
Indices: 216912--216992 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 40
216902 GCGATTGTTG
* * * *
216912 CGAAAGTCAAATTCGCAACGCGAAAAATCAAATTCGCAACA
1 CGAAAATCAAATTCACAACGCG-AAAATAAAAATCGCAACA
216953 CGAAAATCAAATTCA-ACACGCGAAAATAAAAATCGCAACA
1 CGAAAATCAAATTCACA-ACGCGAAAATAAAAATCGCAACA
216993 GGAATTTGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 17 0.49
41 18 0.51
ACGTcount: A:0.51, C:0.23, G:0.12, T:0.14
Consensus pattern (40 bp):
CGAAAATCAAATTCACAACGCGAAAATAAAAATCGCAACA
Found at i:218021 original size:21 final size:21
Alignment explanation
Indices: 217974--218037 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
217964 TCTTGAATAG
*
217974 TGGGAGGGGCCTC-TGAACAA
1 TGGGAGGGGCCTCTTGAACGA
*
217994 TGAGAGGGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
218015 TGGGAGGGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
218036 TG
1 TG
218038 ACAGGTGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 12 0.30
21 28 0.70
ACGTcount: A:0.22, C:0.19, G:0.41, T:0.19
Consensus pattern (21 bp):
TGGGAGGGGCCTCTTGAACGA
Found at i:218425 original size:42 final size:43
Alignment explanation
Indices: 218320--218427 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 43
218310 GAAACAATCT
* * * *
218320 CACGTAGAGCAGC-TACCTCATCACATAAAGTAGATATCTCAC
1 CACGTAAAGCACCATACCTCATCACATAAAATAGATACCTCAC
** * * *
218362 CACGTAAAGCACCAT-TGTCATCGCGTAAAATAGCTACCTCAC
1 CACGTAAAGCACCATACCTCATCACATAAAATAGATACCTCAC
*
218404 CACGTAAAG-ACCGTACCTCATCAC
1 CACGTAAAGCACCATACCTCATCAC
218428 GCCATGCACT
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
41 4 0.08
42 46 0.90
43 1 0.02
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.20
Consensus pattern (43 bp):
CACGTAAAGCACCATACCTCATCACATAAAATAGATACCTCAC
Found at i:218443 original size:63 final size:63
Alignment explanation
Indices: 218370--218491 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 63
218360 ACCACGTAAA
* * * *
218370 GCACCATTGTCATCGCGTAAAATAGCTACCTCACCACGTAAAG-ACCGTACCTCATCACGCCAT
1 GCACCATTGTCATCACGTAAAATACCGACCTCACCACGCAAAGCACCG-ACCTCATCACGCCAT
* * * * *
218433 GCACTATTGTCGTCACGTAAAGTACCGACCTCATCACGCAAAGCACTGACCTCATCACG
1 GCACCATTGTCATCACGTAAAATACCGACCTCACCACGCAAAGCACCGACCTCATCACG
218492 TAACTCCCCT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
63 46 0.94
64 3 0.06
ACGTcount: A:0.30, C:0.34, G:0.16, T:0.20
Consensus pattern (63 bp):
GCACCATTGTCATCACGTAAAATACCGACCTCACCACGCAAAGCACCGACCTCATCACGCCAT
Found at i:218469 original size:21 final size:21
Alignment explanation
Indices: 218445--218494 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
218435 ACTATTGTCG
*
218445 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
* *
218466 TCACGCAAAGCACTGACCTCA
1 TCACGTAAAGCACCGACCTCA
218487 TCACGTAA
1 TCACGTAA
218495 CTCCCCTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:218491 original size:42 final size:41
Alignment explanation
Indices: 218395--218494 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
218385 CGTAAAATAG
* * *
218395 CTACCTCACCACGTAAAGACCGTACCTCATCACGCCATGCA
1 CTACCTCATCACGTAAAGACCGTACCTCATCACGCAAAGCA
** *
218436 CTATTGTCGTCACGTAAAGTACCG-ACCTCATCACGCAAAGCA
1 CTA-CCTCATCACGTAAAG-ACCGTACCTCATCACGCAAAGCA
218478 CTGACCTCATCACGTAA
1 CT-ACCTCATCACGTAA
218495 CTCCCCTATC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
41 3 0.06
42 39 0.83
43 5 0.11
ACGTcount: A:0.30, C:0.36, G:0.14, T:0.20
Consensus pattern (41 bp):
CTACCTCATCACGTAAAGACCGTACCTCATCACGCAAAGCA
Found at i:220230 original size:19 final size:18
Alignment explanation
Indices: 220218--220256 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
220208 TTGCGTTGTG
220218 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCG-ATTT
220237 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCG-ATTT
220256 A
1 A
220257 AGTTTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.18, C:0.10, G:0.21, T:0.51
Consensus pattern (18 bp):
ATTTTCGTGTTGCGATTT
Found at i:222944 original size:233 final size:235
Alignment explanation
Indices: 222599--223067 Score: 844
Period size: 233 Copynumber: 2.0 Consensus size: 235
222589 AAATGTCAAA
222599 GGTTGAATATAAAATGCATGATCATGATTTTTGCATATGATGTTATCATGAGCATATATGATTTT
1 GGTTGAATATAAAATGCATGATCATGATTTTTGCATATGATGTTATCATGAGCATATATGATTTT
222664 TATCATGAATGATATTGCGGGTATGAACTGCCCAATTTTAAATGGTATTGATATAC-TTTCCATG
66 TATCATGAATGATATTGCGGGTATGAACTGCCCAATTTTAAATGGTATTGATATACTTTTCCATG
222728 GATGGATCAAATAAAATTGACTATATGCCCAAAGTATGTTATTGAGGTTCAGTGGTATTAATAGC
131 GA--GATCAAATAAAATTGACTATATGCCC-AAGTATGTTATTGAGGTTCAGTGGTATTAATAGC
222793 -TGACATAGAGTCTAGCAG-TACATATTAGGTAGAACTAGAGT
193 ATGACATAGAGTCTAGCAGCTACATATTAGGTAGAACTAGAGT
222834 GGTTGAATAT-AAATGCATTGATCACTGATTTTTGCATATGATGTTATCATGAGCATATATGA-T
1 GGTTGAATATAAAATGCA-TGATCA-TGATTTTTGCATATGATGTTATCATGAGCATATATGATT
222897 TTT-T-ATGAATGATATTGCGGGTATGAACTGCCCAATTTTAAATGGTATTGATATACTTTTCCA
64 TTTATCATGAATGATATTGCGGGTATGAACTGCCCAATTTTAAATGGTATTGATATACTTTTCCA
222960 TGGAGATCAAATAAAATTGACTATATGCCCAAGTATGTTATTGAGGTTCAGTGGTATTAATAGCA
129 TGGAGATCAAATAAAATTGACTATATGCCCAAGTATGTTATTGAGGTTCAGTGGTATTAATAGCA
223025 TGACATAGAGTCTAGCAGCTACATATTAGGTAGAACTAGAGT
194 TGACATAGAGTCTAGCAGCTACATATTAGGTAGAACTAGAGT
223067 G
1 G
223068 TCTAGAGAAG
Statistics
Matches: 229, Mismatches: 0, Indels: 12
0.95 0.00 0.05
Matches are distributed among these distances:
231 34 0.15
232 44 0.19
233 76 0.33
234 18 0.08
235 20 0.09
236 37 0.16
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.35
Consensus pattern (235 bp):
GGTTGAATATAAAATGCATGATCATGATTTTTGCATATGATGTTATCATGAGCATATATGATTTT
TATCATGAATGATATTGCGGGTATGAACTGCCCAATTTTAAATGGTATTGATATACTTTTCCATG
GAGATCAAATAAAATTGACTATATGCCCAAGTATGTTATTGAGGTTCAGTGGTATTAATAGCATG
ACATAGAGTCTAGCAGCTACATATTAGGTAGAACTAGAGT
Found at i:223370 original size:53 final size:53
Alignment explanation
Indices: 223290--223395 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
223280 ACATCAGTAT
223290 CGAGAGTATATTTCAATATCAGTAAGACATCCTATGATGGAATTTGATTTAGA
1 CGAGAGTATATTTCAATATCAGTAAGACATCCTATGATGGAATTTGATTTAGA
223343 CGAGAGTATATTTCAATATCAGTAAGACATCCTATGATGGAATTTGATTTAGA
1 CGAGAGTATATTTCAATATCAGTAAGACATCCTATGATGGAATTTGATTTAGA
223396 TAGTGGCATG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (53 bp):
CGAGAGTATATTTCAATATCAGTAAGACATCCTATGATGGAATTTGATTTAGA
Found at i:223667 original size:13 final size:13
Alignment explanation
Indices: 223634--223667 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
223624 CATTATTCAC
*
223634 TGTTCACGGGTAT
1 TGTTCACTGGTAT
*
223647 TGTTCACTGTTAT
1 TGTTCACTGGTAT
223660 TGTTCACT
1 TGTTCACT
223668 ATTTACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.47
Consensus pattern (13 bp):
TGTTCACTGGTAT
Found at i:232494 original size:20 final size:21
Alignment explanation
Indices: 232448--232508 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
232438 TCCCCTGTGG
*
232448 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TCAAA
232471 GGGGGAATCGATTCCCTC-AA
1 GGGGGAATCGATTCCCTCAAA
*
232491 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
232509 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 19 0.53
21 2 0.06
22 3 0.08
23 12 0.33
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTCAAA
Found at i:240640 original size:22 final size:21
Alignment explanation
Indices: 240612--240661 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
240602 ATAAACAACA
*
240612 TAAAATGATCAATAAAAAATTG
1 TAAAATG-TCAAGAAAAAATTG
* *
240634 TAAAATGTGAGGAAAAAATTG
1 TAAAATGTCAAGAAAAAATTG
240655 TAAAATG
1 TAAAATG
240662 GACTGAATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.56, C:0.02, G:0.16, T:0.26
Consensus pattern (21 bp):
TAAAATGTCAAGAAAAAATTG
Found at i:240719 original size:2 final size:2
Alignment explanation
Indices: 240708--242574 Score: 210
Period size: 2 Copynumber: 947.0 Consensus size: 2
240698 TTAAAACAAT
240708 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
240749 TA TA TA TA TA TA TA TA TA TA -A TGA -A TG T- TA TGA TA -A TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA T-A TA TA TA T-A
* * * * * * * *
240790 TG CA TG TA TA TA TA -A TG TA CA -A TA TA CT- TA TG CA TA GA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
*
240829 TA -A TA CA T- TA TA -A GTA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
240869 T- TA -A TA TA -A AA GTA TA TA CA TA GA -A GTA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * * * *
240909 CA CT- TA TT TA AA TA TA CA TA TA TA -A AA AA GTA TA -A GTA GA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * * * * *
240949 AA TA TA TA TA AA GTG TA AA CTA TA AA GTA TA AA TA TA T- TA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* * * * *
240991 AA TA TA TA TA TA AA CTA TA AA GTA TA TA TA CTT TA TA CTA -A AA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA -TA TA TA -TA TA TA
* *
241034 CTT TA TA TA TA T- TA TA TA T- TT TA TA T- TA TA TA CT- TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * *
241074 TA TA AA GTA TA -A T- TA TA AA GA T- TGA -A GTA TA TA -A GTA T-
1 TA TA TA -TA TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA -TA TA
* ** * **
241112 TA AA TA TA GG TA TA TA -A GTA T- TA AA TA TA GG TA TA TA -A GTA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
241153 T- TA AA TA TA AA GTA TA TA TA TA TA TA TA CT- TA TA TA CTT TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA
* *
241194 TA T- TA TA TA CT- TA TA TA CTT TA TA T- TA TA TGC T- TA TA TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA T-A TA TA TA TA
* * * *
241233 CTT TA GTA TT TA TA -A T- TA TA CTT TC TA TA TA TA TA TA -A TA
1 -TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * * *
241273 TA CT- TA TA CTT TA TA TG TA TA T- TT TA TA TA CTT TA TA TG TA
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * *
241314 TA TG TT TA TA TA CTT TA TA TA CA TA TA TA T- TT TA TA T- TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
241355 TA CT- TA TA TA CTT TA GTC TT TA TA -A T- TA TA CTT TA TA T- TA
1 TA -TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
241395 T- TA TA TA TG TA TA TA CTT TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
241436 TA TA GTA TA TA GTT TA TA TA TA TA CT- TA T- TA CTT TA TA TT TA
1 TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA
* * * * *
241478 AA CTA TA TA AA CTA TA TA -A TT TA TA CA TA GTA TA TA -A T- TT
1 TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
241518 TA TA GTT TA TA T- TA -A TA AA TA TA TA -A TT TA TA TA TA GTA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
241559 TA TA -A TT TA TA -A T- TA TA CA TA -A TA TA TA AA TA TA -A GT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * * *
241596 TG TA TA TA TT TA AA TA TA -A T- TCA TA TA TA -A TT TA CA -A GTA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA -TA
* * * *
241636 AA CTA TA TA -A TT TA TA T- TA -A TA AA CTA TA TA GTT TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * * *
241676 TA GT- TCA -A TA GT- TCA TA TA T- TA AA CTC TA TA GTT TA TA AA
1 TA -TA T-A TA TA -TA T-A TA TA TA TA TA -TA TA TA -TA TA TA TA
* * * * *
241716 TGG TA TA TA TA GTT TA TA CA TA -A TG TA TA TA TA GTT TA TA TA
1 T-A TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * *
241758 TA GTA TA TA -A TA TA TA TA TA TA TA TA AA CTT TA TA TG TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
241801 TA TA T- TT TA TA TA CT- TA AA TA T- TT TA TA T- TA TA TA CT- TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
241840 TA TA T- TT TA GTC TT TA TA -A T- TA TA CTT TA TA TT TA -A TA CT-
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA
* * * *
241880 TA TA TA CTT TA TA TGA TA TA TA TA TA TA CTT TA TA TT TA -A TT
1 TA TA TA -TA TA TA T-A TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
241922 TT TA T- TT TA TA T- TA TA TA GT- TA TA TA CTT TA TA T- TA TA TGC
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA T-A
* * * *
241963 T- TA TA T- TT TA GTC TT TA TA CT- TA TA CTT TA T- TA -A TA TA
1 TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
*
242001 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA CTT TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
242042 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
242084 TA TA TA TA CT- TA TA CTT TA TA T- TA T- TA TA CA TA TA T- TG TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
242124 TG TA TA TA CT- TA TA TA CTT TA TA TT TA AA CTG TA TA AA CTA TA
1 TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA
* * * *
242167 TA -A TT TA TA -A T- TA TA CA TA -A TA TA TA TA TA TA -A GA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
242204 TA TA TA TT TA AA TA TA -A T- TCA TA TA TA -A TT TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
* * * *
242244 CTA TA TA -A TT TA TA TA TA GT- TCA -A TA -A TC CA TA TA TA AA
1 -TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA
* * * * * *
242283 CTC TA TA GTT TA T- TCA TA GTA TA TA -A AA TT TT TA CA TA -A TA
1 -TA TA TA -TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
242324 TG TG TA TA T- TT TA TA TA TA GTA TA TA -A TA -A TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * * *
242364 AA CTA CA TA GTT TA TA TA TA TA TA TA TA TA CTT TA TA TA TA CA
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
242407 CTA TA TA -A TT TA TA TG TA -A TT TA TA T- TA -A TA AA CTA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
242447 GTT TA TA TA TA T- TA TA TA TA GTT TA TA TA TA GTA TA TA -A TA
1 -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA
* * * *
242488 -A TA TA AA TA TA AA CTA TA TA GTT TA TA TG TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * * *
242530 -A TT TA TA TA TA AA CTA TA T- TT TA TG CA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
242570 T- TA TA
1 TA TA TA
242575 ATTGTTTCAA
Statistics
Matches: 1307, Mismatches: 311, Indels: 494
0.62 0.15 0.23
Matches are distributed among these distances:
1 137 0.10
2 1059 0.81
3 111 0.08
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:240997 original size:13 final size:13
Alignment explanation
Indices: 240964--241009 Score: 53
Period size: 11 Copynumber: 3.7 Consensus size: 13
240954 ATATAAAGTG
*
240964 TAAACTATAAAGTA
1 TAAACTATATA-TA
240978 TAAA-TATAT-TA
1 TAAACTATATATA
240989 TAAA-TATATATA
1 TAAACTATATATA
241001 TAAACTATA
1 TAAACTATA
241010 AAGTATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 11 0.38
12 6 0.21
13 8 0.28
14 4 0.14
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (13 bp):
TAAACTATATATA
Found at i:241051 original size:7 final size:7
Alignment explanation
Indices: 241039--241074 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
241029 TAAAACTTTA
241039 TATATAT
1 TATATAT
241046 TATATAT
1 TATATAT
*
241053 TTTATAT
1 TATATAT
241060 TATATACT
1 TATATA-T
241068 TATATAT
1 TATATAT
241075 ATAAAGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (7 bp):
TATATAT
Found at i:241057 original size:31 final size:33
Alignment explanation
Indices: 241015--241077 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 33
241005 CTATAAAGTA
241015 TATATACTTTATACTA-AAACTT-TATATATAT
1 TATATACTTTATACTATAAACTTATATATATAT
* * *
241046 TATATATTTTATATTATATACTTATATATATA
1 TATATACTTTATACTATAAACTTATATATATA
241078 AAGTATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 14 0.52
32 5 0.19
33 8 0.30
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.52
Consensus pattern (33 bp):
TATATACTTTATACTATAAACTTATATATATAT
Found at i:241124 original size:21 final size:21
Alignment explanation
Indices: 241100--241170 Score: 124
Period size: 21 Copynumber: 3.3 Consensus size: 21
241090 AAAGATTGAA
241100 GTATATAAGTATTAAATATAG
1 GTATATAAGTATTAAATATAG
241121 GTATATAAGTATTAAATATAG
1 GTATATAAGTATTAAATATAG
*
241142 GTATATAAGTATTAAATATAAA
1 GTATATAAGTATTAAATAT-AG
241164 GTATATA
1 GTATATA
241171 TATATATATA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 40 0.83
22 8 0.17
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (21 bp):
GTATATAAGTATTAAATATAG
Found at i:241348 original size:132 final size:130
Alignment explanation
Indices: 241165--241455 Score: 357
Period size: 132 Copynumber: 2.3 Consensus size: 130
241155 AAATATAAAG
* * * *
241165 TATATATATAT-ATATACTTATATA-CTT-TATA--TTATATACTTATATACTTTATATTATATG
1 TATATATATATAATATA-GTATATAGTTTATATACTTTATATACATATATACTTTATATTATATA
*
241225 CTTATATACTTTAGTATTTATAATTATACTTTCTATATATATATAATATACT-TATACTTTATAT
65 CTTATATACTTTAGTATTTATAATTATACTTTATAT-TAT-TAT-ATAT-CTATATACTTTATAT
*
241289 GTATA
126 ATATA
* * *
241294 T-TTTATATACT-TTATATGTATAT-GTTTATATACTTTATATACATATATATTTTATATTATAT
1 TATATATATA-TAATATA-GTATATAGTTTATATACTTTATATACATATATACTTTATATTATAT
* *
241356 ACTTATATACTTTAGTCTTTATAATTATACTTTATATTATTATATATGTATATACTTTATATATA
64 ACTTATATACTTTAGTATTTATAATTATACTTTATATTATTATATATCTATATACTTTATATATA
241421 TA
129 TA
241423 TATATATATATAATATAGTATATAGTTTATATA
1 TATATATATATAATATAGTATATAGTTTATATA
241456 TATACTTATT
Statistics
Matches: 139, Mismatches: 14, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
128 8 0.06
129 41 0.29
130 27 0.19
131 3 0.02
132 60 0.43
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (130 bp):
TATATATATATAATATAGTATATAGTTTATATACTTTATATACATATATACTTTATATTATATAC
TTATATACTTTAGTATTTATAATTATACTTTATATTATTATATATCTATATACTTTATATATATA
Found at i:241407 original size:29 final size:27
Alignment explanation
Indices: 241258--241475 Score: 91
Period size: 27 Copynumber: 7.9 Consensus size: 27
241248 TTATACTTTC
241258 TATATATATATAATATAC-TTATACTTTAT
1 TATATAT-TATAATATACTTTATA--TTAT
* * *
241287 ATGTATATT-TTATATACTTTATA-T-G
1 -TATATATTATAATATACTTTATATTAT
* *
241312 TATATGTT-T-ATATACTTTATATACAT
1 TATATATTATAATATACTTTATAT-TAT
* *
241338 ATATATTTTATATTATATACTTATATACT-T
1 -TATATATTATA--ATATACTT-TATATTAT
*
241368 TAGTCT-TTATAATTATACTTTATATTAT
1 TA-TATATTATAA-TATACTTTATATTAT
*
241396 TATATA-TGT-ATATACTTTATATATAT
1 TATATATTATAATATACTTTATAT-TAT
* * *
241422 ATATATATATATAATATAGTATATAGT-T
1 -TATATAT-TATAATATACTTTATATTAT
*
241450 TATATA-TATACTTATTACTTTATATT
1 TATATATTATA-ATA-TACTTTATATT
241476 TAAACTATAT
Statistics
Matches: 145, Mismatches: 22, Indels: 45
0.68 0.10 0.21
Matches are distributed among these distances:
23 12 0.08
24 7 0.05
25 16 0.11
26 7 0.05
27 37 0.26
28 19 0.13
29 16 0.11
30 19 0.13
31 8 0.06
32 4 0.03
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (27 bp):
TATATATTATAATATACTTTATATTAT
Found at i:241457 original size:132 final size:131
Alignment explanation
Indices: 241196--241455 Score: 359
Period size: 132 Copynumber: 2.0 Consensus size: 131
241186 ATACTTTATA
* * *
241196 TTATATACTTATATACTTTATATTATATGCTTATATACTTTAGTATTTATAATTATACTTTCTAT
1 TTATATACATATATACTTTATATTATATACTTATATACTTTAGTATTTATAATTATACTTTATAT
* * *
241261 ATATATATAATATACTTATACTTTATATGTATATTTTATATACTTTATATGTATATGTTTATATA
66 ATATATATAATATAC-TATACTTTATATATATATTATATATACTATATATGTATATGTTTATATA
241326 CT
130 CT
* *
241328 TTATATACATATATATTTTATATTATATACTTATATACTTTAGTCTTTATAATTATACTTTATAT
1 TTATATACATATATACTTTATATTATATACTTATATACTTTAGTATTTATAATTATACTTTATAT
*
241393 -TAT-TATATATGTA-TATACTTTATATATATA-TATATATA-TATAATATAGTATATAGTTTAT
66 ATATATATA-ATATACTATACTTTATATATATATTATATATACTAT-ATAT-GTATAT-GTTTAT
241453 ATA
127 ATA
241456 TATACTTATT
Statistics
Matches: 115, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
127 2 0.02
128 11 0.10
129 22 0.19
130 13 0.11
131 7 0.06
132 60 0.52
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (131 bp):
TTATATACATATATACTTTATATTATATACTTATATACTTTAGTATTTATAATTATACTTTATAT
ATATATATAATATACTATACTTTATATATATATTATATATACTATATATGTATATGTTTATATAC
T
Found at i:241569 original size:11 final size:11
Alignment explanation
Indices: 241518--241629 Score: 58
Period size: 11 Copynumber: 10.8 Consensus size: 11
241508 TATATAATTT
*
241518 TATAGTTTATA
1 TATAATTTATA
**
241529 T-TAATAAATA
1 TATAATTTATA
241539 TATAATTTATA
1 TATAATTTATA
*
241550 TAT-A-GTATA
1 TATAATTTATA
241559 TATAATTTATA
1 TATAATTTATA
* **
241570 -ATTATACATA
1 TATAATTTATA
* *
241580 -AT-ATATAAA
1 TATAATTTATA
* *
241589 TATAAGTTGTA
1 TATAATTTATA
*
241600 TAT-ATTTAAA
1 TATAATTTATA
*
241610 TATAATTCATA
1 TATAATTTATA
241621 TATAATTTA
1 TATAATTTA
241630 CAAGTAAACT
Statistics
Matches: 73, Mismatches: 22, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
9 12 0.16
10 27 0.37
11 34 0.47
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (11 bp):
TATAATTTATA
Found at i:241575 original size:47 final size:47
Alignment explanation
Indices: 241413--241575 Score: 147
Period size: 47 Copynumber: 3.4 Consensus size: 47
241403 GTATATACTT
* * * *
241413 TATATAT-ATATATATATATA-TAATATAGTATATAGTTTATATATA-
1 TATATATAATTTATATTTATATTAATA-AATATATAATTTATATATAG
* * * *
241458 TACT-TATTACTTTATATTTAAACTATATAAACTATATAATTTATACATAG
1 TA-TATA-TAATTTATATTTATATTA-ATAAA-TATATAATTTATATATAG
*
241508 TATATA-ATTTTATAGTTTATATTAATAAATATATAATTTATATATAG
1 TATATATAATTTATA-TTTATATTAATAAATATATAATTTATATATAG
*
241555 TATATATAATTTATAATTATA
1 TATATATAATTTATATTTATA
241576 CATAATATAT
Statistics
Matches: 95, Mismatches: 13, Indels: 18
0.75 0.10 0.14
Matches are distributed among these distances:
45 4 0.04
46 2 0.02
47 37 0.39
48 22 0.23
49 26 0.27
50 4 0.04
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (47 bp):
TATATATAATTTATATTTATATTAATAAATATATAATTTATATATAG
Found at i:241580 original size:17 final size:17
Alignment explanation
Indices: 241540--241592 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
241530 TAATAAATAT
*
241540 ATAATTTATATATAGTATAT
1 ATAATTTATA-AT--TATAC
241560 ATAATTTATAATTATAC
1 ATAATTTATAATTATAC
* *
241577 ATAATATATAAATATA
1 ATAATTTATAATTATA
241593 AGTTGTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 18 0.60
19 2 0.07
20 10 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
ATAATTTATAATTATAC
Found at i:241622 original size:21 final size:22
Alignment explanation
Indices: 241576--241629 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
241566 TATAATTATA
*
241576 CATA-ATATATAAATATAAGTT
1 CATATATATTTAAATATAAGTT
*
241597 -GTATATATTTAAATATAA-TT
1 CATATATATTTAAATATAAGTT
241617 CATATATAATTTA
1 CATATAT-ATTTA
241630 CAAGTAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 4 0.15
21 18 0.67
22 5 0.19
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (22 bp):
CATATATATTTAAATATAAGTT
Found at i:241733 original size:11 final size:11
Alignment explanation
Indices: 241719--241804 Score: 68
Period size: 11 Copynumber: 7.7 Consensus size: 11
241709 TTATAAATGG
*
241719 TATATATAGTT
1 TATATATAGTA
* * *
241730 TATACATAATG
1 TATATATAGTA
*
241741 TATATATAGTT
1 TATATATAGTA
241752 TATATATAGTA
1 TATATATAGTA
241763 TATAATATA-TA
1 TAT-ATATAGTA
241774 TATATATA-TA
1 TATATATAGTA
* *
241784 AACTTTATATGTA
1 TA-TATATA-GTA
241797 TATATATA
1 TATATATA
241805 TTTTATATAC
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
10 8 0.13
11 39 0.65
12 10 0.17
13 3 0.05
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (11 bp):
TATATATAGTA
Found at i:242105 original size:82 final size:80
Alignment explanation
Indices: 241165--242139 Score: 321
Period size: 82 Copynumber: 11.9 Consensus size: 80
241155 AAATATAAAG
* * *
241165 TATATATATATATATACT-TATATACTTTATATTATATA-CT-TA-TATACTTTATATTATATGC
1 TATATATATATATATA-TATATATA-TATATATTATATATATATATTATACTTTATATTATAT-A
* *
241226 T-TATATACTTTAGTATTTA
63 TATATATA-TATA-TATATA
* * * *
241245 TAATTATACTTTCTATATATATATAATATACTTATACTTTATATGTATATTTTATATACTTTATA
1 T-A-TATA-TATATATATATATAT-ATATA--TATA--TTATATATATA-TAT-TATACTTTATA
* * * *
241310 TGTATATGTTTATATACTTTATATACA
56 T-TATATATATATATA-TATATATATA
* * *
241337 TATATAT-TTTATAT-TATATACT-TATATACTT-TAGTCTTTATAATTATACTTTATATTAT-T
1 TATATATATATATATATATATA-TATATATA-TTATA-TATATAT-ATTATACTTTATATTATAT
* *
241397 ATATATGTATATACTTTATA
62 ATATATATATATA-TATATA
*
241417 TATATATATATATATATA-ATATAGTATATAGTT-TATATATATACTTATTACTTTATATT-TAA
1 TATATATATATATATATATATATA-TATATA-TTATATATATATA-TTA-TACTTTATATTATAT
* *
241479 ACTATATAAACTATATA-ATT
62 A-TATATATA-TATATATATA
* * * *
241499 TATACATAGTATATA-AT-TTTATAGTTTATATTA-ATA-A-ATA-TATAATTTATA-TATAGTA
1 TATATATA-TATATATATATATATA-TATATATTATATATATATATTATACTTTATATTATA-TA
*
241557 TATATA-ATTTATA-AT-
63 TATATATATATATATATA
* * * * * *
241572 TATACATA-ATATATAAATATAAGTTGTATATATT-TAAATATA-ATTCATA-TATA-ATT-TAC
1 TATATATATATATATATATAT-A--TATATATATTATATATATATATT-ATACTTTATATTATAT
*
241631 A-AGTA-A-ACTATATA-ATT
62 ATA-TATATA-TATATATATA
* * * *
241648 TATAT-TA-ATAAACTATATAGTTTATATATAGTTCA-ATAGTTCATATATTAAACTCTATAGTT
1 TATATATATATATA-TATATA-TATATATATA-TT-ATATA--T-ATATATTATACTTTATA-TT
* * *
241710 -TATAAATGGTATATATAGTTTATA
58 ATATATAT-ATATATATA-TATATA
* * * * *
241734 CATAATGTATATATAGTTTATATATAGTATATAATATATATATATATATAAACTTTATATGTATA
1 TAT-ATATATATATA-TATATATATA-TATATATTATATATATATAT-TATACTTTATAT-TATA
*
241799 TATATAT-TTTATATACT-TA
61 TATATATATATATATA-TATA
* * * * *
241818 AATAT-TTTATAT-TATATACT-TATATATTTTAGTCTTTATA-ATTATACTTTATATT-TA-AT
1 TATATATATATATATATATA-TATATATATATTA-TATATATATATTATACTTTATATTATATAT
*
241877 ACT-TATATACTTTATATGA
64 A-TATATATA-TATATAT-A
* * * * *
241896 TATATATATATACTTTATATTTA-ATTTTTATTTTATATTATATAGTTATATACTTTATATTATA
1 TATATATATATA-TATATATATATATATATATTATATA-TATATA--T-TATACTTTATATTATA
* * * *
241960 TGCT-TATAT-TTTAGTCTTTA
61 T-ATATATATATATA-TATATA
*
241980 TACT-TATACTTTAT-TAATATATATATATATATATATATATATATATTATACTTTATATTATAT
1 TA-TATATA-TATATAT-ATATATATATATATAT-TATATATATATATTATACTTTATATTATAT
242043 ATATATATATATATATATA
62 ATATATATATATATATATA
* * * *
242062 TATATATATATATATATATATATATATATACTTATACTTTATATTATTATAC-ATATATTGTATG
1 TATATATATATATATATATATATATATATA-TTATA-TATATA-TATTATACTTTATATTATATA
242126 TATATACT-TATATA
63 TATATA-TATATATA
242140 CTTTATATTT
Statistics
Matches: 682, Mismatches: 104, Indels: 216
0.68 0.10 0.22
Matches are distributed among these distances:
71 5 0.01
72 1 0.00
73 10 0.01
74 18 0.03
75 33 0.05
76 40 0.06
77 15 0.02
78 20 0.03
79 27 0.04
80 53 0.08
81 60 0.09
82 137 0.20
83 50 0.07
84 49 0.07
85 42 0.06
86 28 0.04
87 22 0.03
88 16 0.02
89 16 0.02
90 5 0.01
91 1 0.00
92 18 0.03
93 16 0.02
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.51
Consensus pattern (80 bp):
TATATATATATATATATATATATATATATATTATATATATATATTATACTTTATATTATATATAT
ATATATATATATATA
Found at i:242231 original size:11 final size:11
Alignment explanation
Indices: 242215--242266 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
242205 ATATATTTAA
242215 ATATAATTCAT
1 ATATAATTCAT
*
242226 ATATAATTTAT
1 ATATAATTCAT
*
242237 ATATAA-AC-T
1 ATATAATTCAT
*
242246 ATATAATTTAT
1 ATATAATTCAT
*
242257 ATATAGTTCA
1 ATATAATTCA
242267 ATAATCCATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
9 7 0.22
11 25 0.78
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (11 bp):
ATATAATTCAT
Found at i:242349 original size:11 final size:10
Alignment explanation
Indices: 242335--242574 Score: 85
Period size: 11 Copynumber: 24.2 Consensus size: 10
242325 GTGTATATTT
242335 TATATATAGTA
1 TATATATA-TA
242346 TATA-ATA-A
1 TATATATATA
*
242354 TATAAATATA
1 TATATATATA
* * *
242364 AACTACATAGTT
1 TA-TATATA-TA
242376 TATATATATA
1 TATATATATA
*
242386 TATATATACTT
1 TATATATA-TA
*
242397 TATATATACA
1 TATATATATA
*
242407 CTATATA-ATT
1 -TATATATATA
*
242417 TATATGTA-A
1 TATATATATA
*
242426 TTTATAT-TA
1 TATATATATA
*
242435 -ATAAACTATA
1 TATATA-TATA
*
242445 TAGTTTATATA
1 TA-TATATATA
242456 TAT-TATATA
1 TATATATATA
*
242465 TAGTTTATATA
1 TA-TATATATA
242476 TAGTATATA-A
1 TA-TATATATA
*
242486 TA-ATATAAA
1 TATATATATA
*
242495 TATAAACTATA
1 TATATA-TATA
* *
242506 TAGTTTATATG
1 TA-TATATATA
242517 TATA-ATATA
1 TATATATATA
*
242526 TATA-ATTTA
1 TATATATATA
*
242535 TATATAAACTA
1 TATATATA-TA
* *
242546 TAT-TTTATG
1 TATATATATA
*
242555 CATA-ATATA
1 TATATATATA
242564 TATATAT-TA
1 TATATATATA
242573 TA
1 TA
242575 ATTGTTTCAA
Statistics
Matches: 170, Mismatches: 37, Indels: 46
0.67 0.15 0.18
Matches are distributed among these distances:
8 13 0.08
9 55 0.32
10 31 0.18
11 65 0.38
12 6 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (10 bp):
TATATATATA
Found at i:242384 original size:135 final size:134
Alignment explanation
Indices: 242245--242548 Score: 313
Period size: 135 Copynumber: 2.3 Consensus size: 134
242235 ATATATAAAC
* * *
242245 TATATAATTTATATATAGTTCAATA-ATCCA-TATATAAACTCTATA-GTTTATTCATAGTATAT
1 TATATAA-TTATATATACTT-AATATATACACTATAT-AA-TCTATATG-TAATTCATAGTA-AT
*
242307 AAA-AT-T-TTTACATAATATGTGTATAT-TTTATATATAGTATATAATAATATAAATATAAACT
60 AAACATATATTTACAT-ATAT-TATATATATTTATATATAGTATATAATAATATAAATATAAACT
242368 ACATAGTTTATA
123 ACATAGTTTATA
* * * *
242380 TATAT-A-TATATATACTTTATATATACACTATATAATTTATATGTAATTTATATTAATAAACTA
1 TATATAATTATATATACTTAATATATACACTATATAATCTATATGTAATTCATAGTAATAAAC-A
* *
242443 TATAGTTTATATATATTATATATAGTTTATATATAGTATATAATAATATAAATATAAACTATATA
65 TATA-TTTACATATATTATATATA-TTTATATATAGTATATAATAATATAAATATAAACTACATA
242508 GTTTATA
128 GTTTATA
* * * *
242515 TGTATAA-TATATATAATTTATATATAAACTATAT
1 TATATAATTATATATACTTAATATATACACTATAT
242549 TTTATGCATA
Statistics
Matches: 145, Mismatches: 13, Indels: 21
0.81 0.07 0.12
Matches are distributed among these distances:
130 5 0.03
131 17 0.12
132 19 0.13
133 12 0.08
134 5 0.03
135 61 0.42
136 26 0.18
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (134 bp):
TATATAATTATATATACTTAATATATACACTATATAATCTATATGTAATTCATAGTAATAAACAT
ATATTTACATATATTATATATATTTATATATAGTATATAATAATATAAATATAAACTACATAGTT
TATA
Found at i:242443 original size:33 final size:31
Alignment explanation
Indices: 242376--242529 Score: 107
Period size: 33 Copynumber: 4.8 Consensus size: 31
242366 CTACATAGTT
* * *
242376 TATATATATATATATATACTTTATATATACAC
1 TATATA-ATTTATATATAATTTATATATAAAC
*
242408 TATATAATTTATATGTAATTTATATTAATAAAC
1 TATATAATTTATATATAATTTATA-T-ATAAAC
* ***
242441 TATATAGTTTATATAT-A-TTATATATAGTT
1 TATATAATTTATATATAATTTATATATAAAC
* * *
242470 TATAT-ATAGTATATAATAATATAAATATAAAC
1 TATATAAT-TTATAT-ATAATTTATATATAAAC
* *
242502 TATATAGTTTATATGTATAATATATATA
1 TATATAATTTATA--TATAATTTATATA
242530 ATTTATATAT
Statistics
Matches: 94, Mismatches: 19, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
28 1 0.01
29 13 0.14
30 3 0.03
31 21 0.22
32 24 0.26
33 31 0.33
34 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.47
Consensus pattern (31 bp):
TATATAATTTATATATAATTTATATATAAAC
Found at i:242490 original size:53 final size:53
Alignment explanation
Indices: 242388--242548 Score: 127
Period size: 53 Copynumber: 3.1 Consensus size: 53
242378 TATATATATA
* * *
242388 TATATACTTTATATATACACTATATAATTTATATGTAATTTATATTAATAAAC
1 TATATACTTTATATATACACTATATAATTTATATATAATATATAATAATAAAC
* * * * *
242441 TATATAGTTTATATATATTA-TATATAGTTTATATATAGTATATAATAATATAAA
1 TATATACTTTATATATA-CACTATATAATTTATATATAATATATAATAATA-AAC
* * * * * *
242495 TATAAACTATATAGTTTATA-TGTATAA--TATATATAATTTAT-AT-ATAAAC
1 TATATACTTTATA-TATACACTATATAATTTATATATAATATATAATAATAAAC
242544 TATAT
1 TATAT
242549 TTTATGCATA
Statistics
Matches: 87, Mismatches: 18, Indels: 10
0.76 0.16 0.09
Matches are distributed among these distances:
49 6 0.07
50 3 0.03
51 2 0.02
52 12 0.14
53 41 0.47
54 20 0.23
55 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (53 bp):
TATATACTTTATATATACACTATATAATTTATATATAATATATAATAATAAAC
Found at i:242524 original size:9 final size:9
Alignment explanation
Indices: 242450--242576 Score: 61
Period size: 9 Copynumber: 14.1 Consensus size: 9
242440 CTATATAGTT
*
242450 TATATATAT
1 TATATATAA
*
242459 TATATATAG
1 TATATATAA
*
242468 TTTATAT-A
1 TATATATAA
242476 TAGTATATAA
1 TA-TATATAA
242486 TA-ATATAA
1 TATATATAA
242494 -ATATA-AA
1 TATATATAA
*
242501 CTATATAGTTTA
1 -TATATA--TAA
*
242513 TATGTATAA
1 TATATATAA
242522 TATATATAA
1 TATATATAA
242531 TTTATATATAA
1 --TATATATAA
**
242542 -ACTATATTT
1 TA-TATATAA
**
242551 TATGCATAA
1 TATATATAA
242560 TATATAT-A
1 TATATATAA
242568 TAT-TATAA
1 TATATATAA
242576 T
1 T
242577 TGTTTCAAAA
Statistics
Matches: 89, Mismatches: 16, Indels: 27
0.67 0.12 0.20
Matches are distributed among these distances:
7 6 0.07
8 17 0.19
9 47 0.53
10 4 0.04
11 14 0.16
12 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.47
Consensus pattern (9 bp):
TATATATAA
Found at i:246641 original size:17 final size:18
Alignment explanation
Indices: 246587--246641 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 18
246577 TCTGTTTTAA
** *
246587 TTTTATATTCTAAATTAT
1 TTTTATATTAAAAATAAT
246605 TTTTATATTAAAATAATAAT
1 TTTTATATT-AAA-AATAAT
246625 TTTTATATT-AAAATAAT
1 TTTTATATTAAAAATAAT
246642 AATAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.19
18 11 0.34
19 1 0.03
20 14 0.44
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTATATTAAAAATAAT
Found at i:246646 original size:23 final size:20
Alignment explanation
Indices: 246603--246644 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
246593 ATTCTAAATT
246603 ATTTTTATATTAAAATAATA
1 ATTTTTATATTAAAATAATA
246623 ATTTTTATATTAAAATAATA
1 ATTTTTATATTAAAATAATA
246643 AT
1 AT
246645 AAAAATACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTTATATTAAAATAATA
Found at i:253742 original size:20 final size:20
Alignment explanation
Indices: 253717--253761 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
253707 AATTTTTAGT
* *
253717 TTTGAAATTAATTTCGTATA
1 TTTGAAATTAATTTCATACA
253737 TTTGAAATTAATTTCATACA
1 TTTGAAATTAATTTCATACA
253757 TTTGA
1 TTTGA
253762 GTTAGAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.49
Consensus pattern (20 bp):
TTTGAAATTAATTTCATACA
Found at i:254947 original size:19 final size:20
Alignment explanation
Indices: 254905--254984 Score: 97
Period size: 20 Copynumber: 4.0 Consensus size: 20
254895 CCGTTAGTTA
254905 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
* * *
254925 GGGGGAATCTGTTCCCTCTG
1 GGGGGAATCGGTACCCCCTG
* *
254945 GGGTGAATCGGTACCCCTTGG
1 GGGGGAATCGGTACCCCCT-G
*
254966 GGGGGAATCTGTACCCCCT
1 GGGGGAATCGGTACCCCCT
254985 TTACATTCTG
Statistics
Matches: 48, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 31 0.65
21 17 0.35
ACGTcount: A:0.14, C:0.28, G:0.36, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:255045 original size:20 final size:20
Alignment explanation
Indices: 255020--255057 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
255010 AAACCTGCAT
255020 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
255040 GGGGAATCTGTACCCCCT
1 GGGGAATCTGTACCCCCT
255058 AGACAATCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.32, G:0.32, T:0.21
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:258067 original size:26 final size:26
Alignment explanation
Indices: 258025--258101 Score: 100
Period size: 26 Copynumber: 2.9 Consensus size: 26
258015 GTTTTAGGTT
* *
258025 AGGGATGCAAACATATAAAGTTTTAGA
1 AGGGAT-CAAACTTATAAAATTTTAGA
* **
258052 GGGGATGGAACTTATAAAATTTTAGA
1 AGGGATCAAACTTATAAAATTTTAGA
258078 AGGGATCAAACTTATAAAATTTTA
1 AGGGATCAAACTTATAAAATTTTA
258102 AGGAGGACGA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 37 0.88
27 5 0.12
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (26 bp):
AGGGATCAAACTTATAAAATTTTAGA
Found at i:259345 original size:22 final size:25
Alignment explanation
Indices: 259297--259348 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 25
259287 AAAAAAAATA
*
259297 AAATATATATTAAATTATTTATGTAT
1 AAATATATATTAAATTA-TTATATAT
259323 AAATAT-TATTAAA-TA-TATATAT
1 AAATATATATTAAATTATTATATAT
259345 AAAT
1 AAAT
259349 TACAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 10 0.40
24 2 0.08
25 7 0.28
26 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
AAATATATATTAAATTATTATATAT
Found at i:259350 original size:20 final size:20
Alignment explanation
Indices: 259297--259350 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
259287 AAAAAAAATA
259297 AAATATATAT-TAAATTATT
1 AAATATATATATAAATTATT
*
259316 ---TATGTATA-AATATTATT
1 AAATATATATATAA-ATTATT
259333 AAATATATATATAAATTA
1 AAATATATATATAAATTA
259351 CAAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 11
0.68 0.05 0.28
Matches are distributed among these distances:
16 8 0.30
17 6 0.22
20 11 0.41
21 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
AAATATATATATAAATTATT
Found at i:268518 original size:14 final size:14
Alignment explanation
Indices: 268485--268523 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
268475 ATGCTCTGAT
268485 AATTTATAAA-AAAA
1 AATTTA-AAATAAAA
268499 ATATTTAAAATAAAA
1 A-ATTTAAAATAAAA
268514 AATTTAAAAT
1 AATTTAAAAT
268524 TATGTGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTTAAAATAAAA
Found at i:273805 original size:29 final size:27
Alignment explanation
Indices: 273773--273826 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
273763 AGGTGATCCG
273773 TTAAAGACTAAATTAAAATGATATAAATA
1 TTAAAGAC-AAATTAAAAT-ATATAAATA
* *
273802 TTAAAGGCAATTTAAAATATATAAA
1 TTAAAGACAAATTAAAATATATAAA
273827 AGTACTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 9 0.39
29 7 0.30
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.31
Consensus pattern (27 bp):
TTAAAGACAAATTAAAATATATAAATA
Found at i:274730 original size:19 final size:19
Alignment explanation
Indices: 274706--274743 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
274696 AATATAAAAT
274706 GGAAAA-ATTACGAAATAAA
1 GGAAAACATT-CGAAATAAA
*
274725 GGAAAACATTCTAAATAAA
1 GGAAAACATTCGAAATAAA
274744 TAAGAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.61, C:0.08, G:0.13, T:0.18
Consensus pattern (19 bp):
GGAAAACATTCGAAATAAA
Found at i:275732 original size:24 final size:24
Alignment explanation
Indices: 275705--275751 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
275695 GGCCTGGCTT
*
275705 GGTGTTATAATAGGGTTTAGTTTG
1 GGTGTTAAAATAGGGTTTAGTTTG
*
275729 GGTGTTAAAATAGGGTTTTGTTT
1 GGTGTTAAAATAGGGTTTAGTTT
275752 AGGCCTAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (24 bp):
GGTGTTAAAATAGGGTTTAGTTTG
Found at i:276096 original size:95 final size:95
Alignment explanation
Indices: 275924--276604 Score: 768
Period size: 95 Copynumber: 7.2 Consensus size: 95
275914 TCAAGCTACG
* * * * * * * *
275924 AGTTCTTCTCATTATGAGCTCTCTACTGGAAATGCTAATCCCTTAAGTGAGGCGTAGCTGATTTG
1 AGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTCGTTGATTCG
* *
275989 AAATGTTGTGAATCGAGCAAAGGTTGAACA
66 AAAAGTCGTGAATCGAGCAAAGGTTGAACA
* * *
276019 AGTTCTTCTCATTATAAACTATCCATTGGAAATGTTAATCCCTCAAGTGAGGCATCGTTGATTCG
1 AGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTCGTTGATTCG
* * *
276084 AAAAGCCATGAATCAAGCAAAGGTTGAACA
66 AAAAGTCGTGAATCGAGCAAAGGTTGAACA
* * * * *
276114 TGTTATTCTTATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAATGAGGCGTCATTGATTC-
1 AGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTCGTTGATTCG
* * * *
276178 AAAATATTGTGAATTGATCAAAGGTTGAA-A
66 AAAA-GTCGTGAATCGAGCAAAGGTTGAACA
* * * * *
276208 A---CATTCTCATTATGAACTCTCAATTGGAAATGTTAATCCCTCAAGTAAGGTGTTGCTGATTC
1 AGTTC-TTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTCGTTGATTC
* * * *
276270 GAAATGTC-AGAATTGATCAAAGGTTGAACA
65 GAAAAGTCGTGAATCGAGCAAAGGTTGAACA
* * *
276300 AGTTCTTCTCATTATGAATTCTCCACTGGAAATGTTAATCCCTCAAGTGAGGCATCGTTGATTC-
1 AGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTCGTTGATTCG
* *
276364 AAAATGTCTTGAATCGAGCAAAGGTTAAACA
66 AAAA-GTCGTGAATCGAGCAAAGGTTGAACA
* * * * *
276395 AGTTCTTCTCATTTTGAACTCTCAATTGAAAATGTTAATCCCTCAAGTGAGGCGTCATTGATTAG
1 AGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTCGTTGATTCG
* * *
276460 AAATGTCGTGAATCGAGAAAAGGTTGAGCA
66 AAAAGTCGTGAATCGAGCAAAGGTTGAACA
* * * **
276490 TGTTCTTCTTATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCATCACTGATTC-
1 AGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTCGTTGATTCG
*
276554 AAAA-TACCGTGAATCAAGCAAAGGTTGAACA
66 AAAAGT--CGTGAATCGAGCAAAGGTTGAACA
*
276585 AGTTCTTCTCATTACGAACT
1 AGTTCTTCTCATTATGAACT
276605 TATTCTCCCT
Statistics
Matches: 488, Mismatches: 86, Indels: 24
0.82 0.14 0.04
Matches are distributed among these distances:
91 19 0.04
92 54 0.11
93 7 0.01
94 62 0.13
95 343 0.70
96 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (95 bp):
AGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTCGTTGATTCG
AAAAGTCGTGAATCGAGCAAAGGTTGAACA
Found at i:276433 original size:281 final size:281
Alignment explanation
Indices: 275929--276598 Score: 860
Period size: 281 Copynumber: 2.4 Consensus size: 281
275919 CTACGAGTTC
* * * * * *
275929 TTCTCATTATGAGCTCTCTACTGGAAATGCTAATCCCTTAAGTGAGGCGTAGCTGATTTGAAATG
1 TTCTCATTATGAACTCTCAATTGGAAATGTTAATCCCTCAAGTGAGGCGTAGCTGATTCGAAATG
* *
275994 TTGTGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTATAAACTATCCATTGGAAATGTTAATC
66 -TCTGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTATAAACTATCCACTGGAAATGTTAATC
* * *
276059 CCTCAAGTGAGGCATCGTTGATTCGAAAAGCCATGAATCAAGCAAAGGTTGAACATGTTATTCTT
130 CCTCAAGTGAGGCATCGTTGATTCGAAAAGCCATGAATCAAGCAAAGGTTAAACAAGTTATTCTC
* * *
276124 ATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAATGAGGCGTCATTGATTCA-AAATATTGT
195 ATTATGAACTCTCAATTGAAAATGTTAATCCCTCAAATGAGGCGTCATTGATT-AGAAATATCGT
* **
276188 GAATTGATCAAAGGTTGAAAACA
259 GAATCGAGAAAAGGTTGAAAACA
* * *
276211 TTCTCATTATGAACTCTCAATTGGAAATGTTAATCCCTCAAGTAAGGTGTTGCTGATTCGAAATG
1 TTCTCATTATGAACTCTCAATTGGAAATGTTAATCCCTCAAGTGAGGCGTAGCTGATTCGAAATG
* * * * * *
276276 TCAGAATTGATCAAAGGTTGAACAAGTTCTTCTCATTATGAATTCTCCACTGGAAATGTTAATCC
66 TCTGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTATAAACTATCCACTGGAAATGTTAATCC
* * * *
276341 CTCAAGTGAGGCATCGTTGATTC-AAAATGTCTTGAATCGAGCAAAGGTTAAACAAGTTCTTCTC
131 CTCAAGTGAGGCATCGTTGATTCGAAAA-GCCATGAATCAAGCAAAGGTTAAACAAGTTATTCTC
* * *
276405 ATTTTGAACTCTCAATTGAAAATGTTAATCCCTCAAGTGAGGCGTCATTGATTAGAAATGTCGTG
195 ATTATGAACTCTCAATTGAAAATGTTAATCCCTCAAATGAGGCGTCATTGATTAGAAATATCGTG
** **
276470 AATCGAGAAAAGGTTGAGCATG
260 AATCGAGAAAAGGTTGAAAACA
* * *
276492 TTCTTCTTATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCATCA-CTGATTCAA
1 TTC-TC--ATTATGAACTCTCAATTGGAAATGTTAATCCCTCAAGTGAGGCGT-AGCTGATTCGA
** *
276556 AATACCGTGAATCAAGCAAAGGTTGAACAAGTTCTTCTCATTA
62 AATGTC-TGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTA
276599 CGAACTTATT
Statistics
Matches: 332, Mismatches: 49, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
280 5 0.02
281 184 0.55
282 58 0.17
284 53 0.16
285 32 0.10
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (281 bp):
TTCTCATTATGAACTCTCAATTGGAAATGTTAATCCCTCAAGTGAGGCGTAGCTGATTCGAAATG
TCTGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTATAAACTATCCACTGGAAATGTTAATCC
CTCAAGTGAGGCATCGTTGATTCGAAAAGCCATGAATCAAGCAAAGGTTAAACAAGTTATTCTCA
TTATGAACTCTCAATTGAAAATGTTAATCCCTCAAATGAGGCGTCATTGATTAGAAATATCGTGA
ATCGAGAAAAGGTTGAAAACA
Found at i:278837 original size:21 final size:21
Alignment explanation
Indices: 278811--278868 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
278801 GTCGAGGGTT
278811 TTATGTGGTCATTCGGGACAA
1 TTATGTGGTCATTCGGGACAA
* *
278832 TTATGTAGTCCTTCGGGACAA
1 TTATGTGGTCATTCGGGACAA
*
278853 ATATGTGG-CACTTCGG
1 TTATGTGGTCA-TTCGG
278869 TGTAAACCTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (21 bp):
TTATGTGGTCATTCGGGACAA
Found at i:278886 original size:23 final size:23
Alignment explanation
Indices: 278854--278941 Score: 94
Period size: 23 Copynumber: 3.9 Consensus size: 23
278844 TCGGGACAAA
*
278854 TATGTGGCACTTCGGTGTAAACC
1 TATGTGGCACTTCGGTGCAAACC
* *
278877 TGTGTGGCACTTTGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
*
278900 TATGTGGTCA-TTCGG-G-ACAA-T
1 TATGTGG-CACTTCGGTGCA-AACC
278921 TATGTGGCACTTCGGTGCAAA
1 TATGTGGCACTTCGGTGCAAA
278942 TTACGAGATG
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
20 2 0.04
21 13 0.24
22 6 0.11
23 31 0.57
24 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAAACC
Found at i:285582 original size:21 final size:21
Alignment explanation
Indices: 285556--285611 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
285546 GTCGAGGGTT
*
285556 TTATGTGGTATTTCAGGACAA
1 TTATGTGGTACTTCAGGACAA
* * *
285577 TTATGTAGTCCTTCGGGACAA
1 TTATGTGGTACTTCAGGACAA
* *
285598 ATATGTGGCACTTC
1 TTATGTGGTACTTC
285612 GGTGCAAACC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (21 bp):
TTATGTGGTACTTCAGGACAA
Found at i:285632 original size:23 final size:23
Alignment explanation
Indices: 285599--285686 Score: 103
Period size: 23 Copynumber: 3.9 Consensus size: 23
285589 TCGGGACAAA
285599 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
*
285622 TATGTGACACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
* *
285645 TATGTAGTCA-TTCGG-G-ACAA-T
1 TATGT-GGCACTTCGGTGCA-AACC
285666 TATGTGGCACTTCGGTGCAAA
1 TATGTGGCACTTCGGTGCAAA
285687 TTACGAGTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.05
21 11 0.20
22 6 0.11
23 33 0.59
24 3 0.05
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAAACC
Found at i:288912 original size:2 final size:2
Alignment explanation
Indices: 288905--288934 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
288895 TTGATTTGTT
288905 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
288935 AAGATAATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:294279 original size:14 final size:14
Alignment explanation
Indices: 294260--294287 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
294250 GTTGTTTCAC
294260 AATGATGGTGTAGA
1 AATGATGGTGTAGA
294274 AATGATGGTGTAGA
1 AATGATGGTGTAGA
294288 TACTCAGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (14 bp):
AATGATGGTGTAGA
Found at i:297228 original size:20 final size:19
Alignment explanation
Indices: 297203--297241 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
297193 TTATATTGAC
297203 GACTTCAGATATAATATTTT
1 GACTTCAGATATAA-ATTTT
297223 GACTTCAGATATAAATTTT
1 GACTTCAGATATAAATTTT
297242 AAATGGGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (19 bp):
GACTTCAGATATAAATTTT
Found at i:298746 original size:20 final size:21
Alignment explanation
Indices: 298701--298747 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
298691 AAGCTGATAC
298701 CGATACTGAGCCCCTCAGTAT
1 CGATACTGAGCCCCTCAGTAT
* *
298722 CGATACTGA-CCCTTGAGTAT
1 CGATACTGAGCCCCTCAGTAT
*
298742 TGATAC
1 CGATAC
298748 CCATCCTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (21 bp):
CGATACTGAGCCCCTCAGTAT
Found at i:298765 original size:19 final size:20
Alignment explanation
Indices: 298717--298766 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
298707 TGAGCCCCTC
**
298717 AGTATCGATACTGACCCTTG
1 AGTATCGATACCCACCCTTG
* *
298737 AGTATTGATACCCATCCTTG
1 AGTATCGATACCCACCCTTG
298757 -GTATCGATAC
1 AGTATCGATAC
298767 TAAAAGTGTC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTATCGATACCCACCCTTG
Found at i:303288 original size:10 final size:10
Alignment explanation
Indices: 303273--303299 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
303263 ATTTAAATCA
303273 ACTAGCCGTT
1 ACTAGCCGTT
303283 ACTAGCCGTT
1 ACTAGCCGTT
303293 ACTAGCC
1 ACTAGCC
303300 TTTGGGCCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.26
Consensus pattern (10 bp):
ACTAGCCGTT
Found at i:307413 original size:49 final size:48
Alignment explanation
Indices: 307360--307454 Score: 127
Period size: 49 Copynumber: 2.0 Consensus size: 48
307350 AGTGCATTCG
* * * *
307360 TGCACTCCAGTATTAGTTCATTTGTTGCACTCTTATTTTAGTACCTTGT
1 TGCACTCCAGTAATAATGCATTTG-TGCACTCTTATATTAGTACCTTGT
* *
307409 TGCACTCCAGTAATAATGCATTTGTGCTCTCTTGTATTAGTACCTT
1 TGCACTCCAGTAATAATGCATTTGTGCACTCTTATATTAGTACCTT
307455 TGGGTACTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 19 0.47
49 21 0.52
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.44
Consensus pattern (48 bp):
TGCACTCCAGTAATAATGCATTTGTGCACTCTTATATTAGTACCTTGT
Found at i:310108 original size:19 final size:19
Alignment explanation
Indices: 310084--310122 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
310074 TTCTCAGTTG
310084 TTTTTTTTTTCTGTCTCTC
1 TTTTTTTTTTCTGTCTCTC
310103 TTTTTTTTTTCTGTCTCTC
1 TTTTTTTTTTCTGTCTCTC
310122 T
1 T
310123 GTCCGTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTTTTTTTCTGTCTCTC
Done.