Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015131.1 Kokia drynarioides strain JFW-HI SEQ_130175, 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: 745397
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 719 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:570527 original size:157 final size:156
Alignment explanation
Indices: 570237--570846 Score: 509
Period size: 157 Copynumber: 3.9 Consensus size: 156
570227 TTACCTTAAG
* * * *
570237 TAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGGGGCAGATCGAAACAATCCAA
1 TAGAGGGCAGATTGAAG-CCATCCAATCTCTTACCCTGACCAT-GGGCAGATTGAAGCAATCCAA
** * * * * ** * *
570302 TCTTTTACCCCGACCATG-GGGCAAATTGAAG-TAATTCAGATCTTTTACCCTAACTAGAGAGAA
64 TCTTTTACCCTAACTA-GAGGGCAGATTGAAGATCATTC-GATCTCTTACCCCGACCAGAGGGAA
** * * *
570365 GATTGAATTAATCTAATATTTTACCCCAAT
127 GATTGAAGCAACCCAATATTTTACCCCAAC
570395 TAGAGGGCAGATTGAAGCCATCCAATCTCTTACCCTGACCATGGTGCAGATTGAAGCAATCCAAT
1 TAGAGGGCAGATTGAAGCCATCCAATCTCTTACCCTGACCATGG-GCAGATTGAAGCAATCCAAT
* *
570460 CTTTTACCCTAACTAGAGGGCAGATTAAAGATCATTCGATCTCTTACCCCGACCATAGGGCAA-A
65 CTTTTACCCTAACTAGAGGGCAGATTGAAGATCATTCGATCTCTTACCCCGACCAGAGGG-AAGA
* * *
570524 TTGAAGCAACCCAATCTTTTACTCTAAC
129 TTGAAGCAACCCAATATTTTACCCCAAC
* ** ** *
570552 TAGAAGGCAGATTGAAGTTATTTAATCTCTTA-CCTCGACCATAGGGCAGATTGAAGTAATCCAA
1 TAGAGGGCAGATTGAAGCCATCCAATCTCTTACCCT-GACCAT-GGGCAGATTGAAGCAATCCAA
* * * *
570616 TCTTTTACCTTAACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCAGAGGGTAGA
64 TCTTTTACCCTAACTAGAGGGCAGATTGAAGATCATTCGATCTCTTACCCCGACCAGAGGGAAGA
* * * * *
570681 TTAAAGACCATCCGATCTCTTT-CCCCAAC
129 TTGAAG-CAACCCAATAT-TTTACCCCAAC
* * ** * *
570710 CATG-GGGCAGATTGAAGACCATCCAATCTTTTACCCCAACCAGAGGGCAGATTGAAGACCATCC
1 TA-GAGGGCAGATTGAAG-CCATCCAATCTCTTACCCTGACCA-TGGGCAGATTGAAG-CAATCC
* * * * * * ** *
570774 GATCTCTTACTCC-AACCATG-GGGTAGATTGAAG-TAATTCAGATCTTTTACCCTAACCAGAAG
62 AATCTTTTAC-CCTAACTA-GAGGGCAGATTGAAGATCATTC-GATCTCTTACCCCGACCAGAGG
*
570836 GCAGATTGAAG
124 GAAGATTGAAG
570847 TAATACAGAT
Statistics
Matches: 367, Mismatches: 68, Indels: 32
0.79 0.15 0.07
Matches are distributed among these distances:
156 7 0.02
157 215 0.59
158 52 0.14
159 34 0.09
160 57 0.16
161 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (156 bp):
TAGAGGGCAGATTGAAGCCATCCAATCTCTTACCCTGACCATGGGCAGATTGAAGCAATCCAATC
TTTTACCCTAACTAGAGGGCAGATTGAAGATCATTCGATCTCTTACCCCGACCAGAGGGAAGATT
GAAGCAACCCAATATTTTACCCCAAC
Found at i:570818 original size:40 final size:40
Alignment explanation
Indices: 570238--570864 Score: 309
Period size: 40 Copynumber: 15.8 Consensus size: 40
570228 TACCTTAAGT
* * *
570238 AGAGGGCAGATTGAAGACCATCCA-ATCTCTTACCCCGATC
1 AGAGGGCAGATTGAAGA-CATTCAGATCTCTTACCCCAACC
* * * *
570278 ATG-GGGCAGATCGAA-ACAATCCA-ATCTTTTACCCCGACC
1 A-GAGGGCAGATTGAAGAC-ATTCAGATCTCTTACCCCAACC
* * * *
570317 ATG-GGGCAAATTGAAGTA-ATTCAGATCTTTTACCCTAACT
1 A-GAGGGCAGATTGAAG-ACATTCAGATCTCTTACCCCAACC
* * * * * **
570357 AGAGAGAAGATTGAATTA-A-TCTA-ATATTTTACCCCAATT
1 AGAGGGCAGATTGAA-GACATTC-AGATCTCTTACCCCAACC
* * **
570396 AGAGGGCAGATTGAAGCCATCCA-ATCTCTTACCCTGACC
1 AGAGGGCAGATTGAAGACATTCAGATCTCTTACCCCAACC
* * * * *
570435 ATG-GTGCAGATTGAAG-CAATCCA-ATCTTTTACCCTAACT
1 A-GAGGGCAGATTGAAGAC-ATTCAGATCTCTTACCCCAACC
* *
570474 AGAGGGCAGATTAAAGATCATTC-GATCTCTTACCCCGACC
1 AGAGGGCAGATTGAAGA-CATTCAGATCTCTTACCCCAACC
* * ** * * * *
570514 ATAGGGCAAATTGAAG-CAACCCA-ATCTTTTACTCTAACT
1 AGAGGGCAGATTGAAGAC-ATTCAGATCTCTTACCCCAACC
* ** * * *
570553 AGAAGGCAGATTGAAGTTATTTA-ATCTCTTACCTCGACC
1 AGAGGGCAGATTGAAGACATTCAGATCTCTTACCCCAACC
* * * ** *
570592 ATAGGGCAGATTGAAGTA-ATCCA-ATCTTTTACCTTAACT
1 AGAGGGCAGATTGAAG-ACATTCAGATCTCTTACCCCAACC
* *
570631 AGAGGGCAGATTGAAGACCA-TCCGATCTCTTACCCCGACC
1 AGAGGGCAGATTGAAGA-CATTCAGATCTCTTACCCCAACC
* * * *
570671 AGAGGGTAGATTAAAGACCA-TCCGATCTCTTTCCCCAACC
1 AGAGGGCAGATTGAAGA-CATTCAGATCTCTTACCCCAACC
* *
570711 ATG-GGGCAGATTGAAGACCATCCA-ATCTTTTACCCCAACC
1 A-GAGGGCAGATTGAAGA-CATTCAGATCTCTTACCCCAACC
* *
570751 AGAGGGCAGATTGAAGACCA-TCCGATCTCTTACTCCAACC
1 AGAGGGCAGATTGAAGA-CATTCAGATCTCTTACCCCAACC
* * *
570791 ATG-GGGTAGATTGAAGTA-ATTCAGATCTTTTACCCTAACC
1 A-GAGGGCAGATTGAAG-ACATTCAGATCTCTTACCCCAACC
* *
570831 AGAAGGCAGATTGAAGTA-ATACAGATCTCTTACC
1 AGAGGGCAGATTGAAG-ACATTCAGATCTCTTACC
570865 TCGATCATGA
Statistics
Matches: 455, Mismatches: 101, Indels: 62
0.74 0.16 0.10
Matches are distributed among these distances:
38 5 0.01
39 208 0.46
40 235 0.52
41 7 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (40 bp):
AGAGGGCAGATTGAAGACATTCAGATCTCTTACCCCAACC
Found at i:570843 original size:80 final size:80
Alignment explanation
Indices: 570241--570846 Score: 327
Period size: 79 Copynumber: 7.7 Consensus size: 80
570231 CTTAAGTAGA
* * * * * *
570241 GGGCAGATTGAAGACCATCCA-ATCTCTTACCCCGATCATG-GGGCAGATCGAA-ACAATCCAAT
1 GGGCAGATTGAAGA-CATCCAGATCTTTTACCCCAACCA-GAGGGCAGATTGAAGACCATCCGAT
* *
570303 CTTTTACCCCGACCATG
64 CTCTTACCCCAACCATG
* * * * * * * **
570320 GGGCAAATTGAAGTA-ATTCAGATCTTTTACCCTAACTAGAGAGAAGATTGAATTA--ATCTAAT
1 GGGCAGATTGAAG-ACATCCAGATCTTTTACCCCAACCAGAGGGCAGATTGAA-GACCATCCGAT
* * **
570382 ATTTTACCCCAATTA-G
64 CTCTTACCCCAACCATG
* * ** * * *
570398 AGGGCAGATTGAAGCCATCCA-ATCTCTTACCCTGACCATG-GTGCAGATTGAAG-CAATCCAAT
1 -GGGCAGATTGAAGACATCCAGATCTTTTACCCCAACCA-GAGGGCAGATTGAAGACCATCCGAT
* * *
570460 CTTTTACCCTAACTA-G
64 CTCTTACCCCAACCATG
* * * * * * * * *
570476 AGGGCAGATTAAAGATCATTC-GATCTCTTACCCCGACCATAGGGCAAATTGAAG-CAACCCAAT
1 -GGGCAGATTGAAGA-CATCCAGATCTTTTACCCCAACCAGAGGGCAGATTGAAGACCATCCGAT
* * * *
570539 CTTTTACTCTAACTA-G
64 CTCTTACCCCAACCATG
* ** ** * * * * *
570555 AAGGCAGATTGAAGTTATTTA-ATCTCTTACCTCGACCATAGGGCAGATTGAAGTA--ATCCAAT
1 -GGGCAGATTGAAGACATCCAGATCTTTTACCCCAACCAGAGGGCAGATTGAAG-ACCATCCGAT
* ** *
570617 CTTTTACCTTAACTA-G
64 CTCTTACCCCAACCATG
* * * *
570633 AGGGCAGATTGAAGACCATCC-GATCTCTTACCCCGACCAGAGGGTAGATTAAAGACCATCCGAT
1 -GGGCAGATTGAAGA-CATCCAGATCTTTTACCCCAACCAGAGGGCAGATTGAAGACCATCCGAT
*
570697 CTCTTTCCCCAACCATG
64 CTCTTACCCCAACCATG
570714 GGGCAGATTGAAGACCATCCA-ATCTTTTACCCCAACCAGAGGGCAGATTGAAGACCATCCGATC
1 GGGCAGATTGAAGA-CATCCAGATCTTTTACCCCAACCAGAGGGCAGATTGAAGACCATCCGATC
*
570778 TCTTACTCCAACCATG
65 TCTTACCCCAACCATG
* * * *
570794 GGGTAGATTGAAGTA-ATTCAGATCTTTTACCCTAACCAGAAGGCAGATTGAAG
1 GGGCAGATTGAAG-ACATCCAGATCTTTTACCCCAACCAGAGGGCAGATTGAAG
570847 TAATACAGAT
Statistics
Matches: 431, Mismatches: 72, Indels: 47
0.78 0.13 0.09
Matches are distributed among these distances:
78 129 0.30
79 167 0.39
80 132 0.31
81 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (80 bp):
GGGCAGATTGAAGACATCCAGATCTTTTACCCCAACCAGAGGGCAGATTGAAGACCATCCGATCT
CTTACCCCAACCATG
Found at i:570882 original size:40 final size:40
Alignment explanation
Indices: 570774--570882 Score: 116
Period size: 40 Copynumber: 2.7 Consensus size: 40
570764 AAGACCATCC
* *
570774 GATCTCTTACTCC-AACCATGGGGTAGATTGAAGTAATTCA
1 GATCTCTTAC-CCTAACCATGAGGTAGATTGAAGTAATACA
* *
570814 GATCTTTTACCCTAACCA-GAAGGCAGATTGAAGTAATACA
1 GATCTCTTACCCTAACCATG-AGGTAGATTGAAGTAATACA
* *
570854 GATCTCTTA-CCTCGATCATGAGGTAGATT
1 GATCTCTTACCCT-AACCATGAGGTAGATT
570883 TAAACCATCA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
39 6 0.11
40 50 0.88
41 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (40 bp):
GATCTCTTACCCTAACCATGAGGTAGATTGAAGTAATACA
Found at i:570970 original size:39 final size:40
Alignment explanation
Indices: 570924--571036 Score: 115
Period size: 40 Copynumber: 2.9 Consensus size: 40
570914 TTACCCCGAT
* * *
570924 ATGAGGCAAATTGAAGCAATCCAATCTTTTACCCT-AACT
1 ATGAGGCAGATTAAAGCAATCCAATCTTTTACCCTCAACC
* **
570963 A-GAAGGCAGATTAAAGACCATCTGATCTTTTA-CCTCAACC
1 ATG-AGGCAGATTAAAG-CAATCCAATCTTTTACCCTCAACC
* *
571003 ATGGGGCAGATTAAAGCAATTCAATCTTTTACCC
1 ATGAGGCAGATTAAAGCAATCCAATCTTTTACCC
571037 CTAAAGCTAT
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
38 1 0.02
39 26 0.45
40 30 0.52
41 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (40 bp):
ATGAGGCAGATTAAAGCAATCCAATCTTTTACCCTCAACC
Found at i:571014 original size:132 final size:134
Alignment explanation
Indices: 570757--571014 Score: 317
Period size: 132 Copynumber: 1.9 Consensus size: 134
570747 AACCAGAGGG
* * * * * * *
570757 CAGATTGAAGACCATCCGATCTCTTACTCCAACCATGGGGTAGATTGAAGTAATTCAGATCTTTT
1 CAGATTGAAGACCATCCAATCTCTTACCCCAACCATGAGGCAAATTGAAGCAATCCAGATCTTTT
* * * *
570822 ACCCTAACCAGAAGGCAGATTGAAGTAATACAGATCTCTTACCTCGATCATGAGGTAGATTTAAA
66 ACCCTAACCAGAAGGCAGATTAAAGTAATACAGATCTCTTACCTCAACCATGAGGCAGATTTAAA
570887 CCAT
131 CCAT
* *
570891 CAGATTGAAGACCATCCAATCTCTTACCCCGA-TATGAGGCAAATTGAAGCAATCCA-ATCTTTT
1 CAGATTGAAGACCATCCAATCTCTTACCCCAACCATGAGGCAAATTGAAGCAATCCAGATCTTTT
* * * *
570954 ACCCTAACTAGAAGGCAGATTAAAG-ACCAT-CTGATCTTTTACCTCAACCATGGGGCAGATT
66 ACCCTAACCAGAAGGCAGATTAAAGTA--ATACAGATCTCTTACCTCAACCATGAGGCAGATT
571015 AAAGCAATTC
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
131 1 0.01
132 55 0.52
133 20 0.19
134 29 0.28
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (134 bp):
CAGATTGAAGACCATCCAATCTCTTACCCCAACCATGAGGCAAATTGAAGCAATCCAGATCTTTT
ACCCTAACCAGAAGGCAGATTAAAGTAATACAGATCTCTTACCTCAACCATGAGGCAGATTTAAA
CCAT
Found at i:573173 original size:18 final size:17
Alignment explanation
Indices: 573142--573176 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
573132 GATTTAGGGT
573142 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
573159 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
573177 AGATCTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:574315 original size:3 final size:3
Alignment explanation
Indices: 574307--574345 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
574297 ATGAGGAAGT
*
574307 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
574346 GAATTACAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:575375 original size:13 final size:15
Alignment explanation
Indices: 575349--575380 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
575339 TTTTTTTCTC
575349 AAAAACTCCTATAAA
1 AAAAACTCCTATAAA
575364 AAAAACT-C-ATAAA
1 AAAAACTCCTATAAA
575377 AAAA
1 AAAA
575381 CAAATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 1 0.06
15 7 0.41
ACGTcount: A:0.69, C:0.16, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAACTCCTATAAA
Found at i:581405 original size:31 final size:31
Alignment explanation
Indices: 581369--581464 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
581359 ATTAAAAGCA
* *
581369 AAATAAAATAGCTTTTTATAGTTGGTGTTAT
1 AAATAAGATAGCTTCTTATAGTTGGTGTTAT
581400 AAATAAGATAGCTTCTTATAGTTGGTGTTAT
1 AAATAAGATAGCTTCTTATAGTTGGTGTTAT
581431 AAATAAGATAGCTTCTTATAGTTGGTGTTAT
1 AAATAAGATAGCTTCTTATAGTTGGTGTTAT
581462 AAA
1 AAA
581465 CATGACTAAC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (31 bp):
AAATAAGATAGCTTCTTATAGTTGGTGTTAT
Found at i:582327 original size:41 final size:41
Alignment explanation
Indices: 582267--582378 Score: 127
Period size: 41 Copynumber: 2.7 Consensus size: 41
582257 AAATAAGTGT
* * *
582267 CGCTAATGTTCTGATCTTTAGTGGCACTT-ACACAAAAGCGC
1 CGCTATTGCTCTGACCTTTAGTGGCACTTGA-ACAAAAGCGC
* * *
582308 CGCTATTGGTCTGACCTTTAGTGGCGCTTGAACAAAAGCGT
1 CGCTATTGCTCTGACCTTTAGTGGCACTTGAACAAAAGCGC
* * *
582349 CGTTATTGCTCTGACCTTTAGCGGCGCTTG
1 CGCTATTGCTCTGACCTTTAGTGGCACTTG
582379 CTATAACCTG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 61 0.98
42 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (41 bp):
CGCTATTGCTCTGACCTTTAGTGGCACTTGAACAAAAGCGC
Found at i:582459 original size:41 final size:41
Alignment explanation
Indices: 582398--582505 Score: 144
Period size: 41 Copynumber: 2.6 Consensus size: 41
582388 GTAGCGGTGT
* * *
582398 TTTCGCAGAAGCACCACTATTGCTCTGACCTTTACCGGCGC
1 TTTCCCAGAAGCGCCGCTATTGCTCTGACCTTTACCGGCGC
* * *
582439 TTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGTGC
1 TTTCCCAGAAGCGCCGCTATTGCTCTGACCTTTACCGGCGC
* *
582480 TTTCGCAGAAGTGCCGCTATTGCTCT
1 TTTCCCAGAAGCGCCGCTATTGCTCT
582506 ATCTTTTACG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.17, C:0.31, G:0.21, T:0.31
Consensus pattern (41 bp):
TTTCCCAGAAGCGCCGCTATTGCTCTGACCTTTACCGGCGC
Found at i:592288 original size:150 final size:150
Alignment explanation
Indices: 592017--592317 Score: 575
Period size: 150 Copynumber: 2.0 Consensus size: 150
592007 TTTGATCCAA
592017 ACCATTCCCTCCATTTGAAATGTCCGCTTTTAAGCTATGGAGACTCTTATTGTGCTCATCAGCCC
1 ACCATTCCCTCCATTTGAAATGTCCGCTTTTAAGCTATGGAGACTCTTATTGTGCTCATCAGCCC
592082 CAGAAAGTAGTGCCCTCCCTCCGAAACTATGCGTATCACCATTAACTTTGGAAGCACTTGAAGTC
66 CAGAAAGTAGTGCCCTCCCTCCGAAACTATGCGTATCACCATTAACTTTGGAAGCACTTGAAGTC
592147 TGTCTATCAGACTCCACCCT
131 TGTCTATCAGACTCCACCCT
592167 ACCATTCCCTCCATTTGAAATGTCCGCTTTTAAGCTATGGAGACTCTTATTGTGCTCATCAGCCC
1 ACCATTCCCTCCATTTGAAATGTCCGCTTTTAAGCTATGGAGACTCTTATTGTGCTCATCAGCCC
* *
592232 CAGAAAGTAGTGCCCTCCCTCTGAAACTATGCGTATCACCATTACCTTTGGAAGCACTTGAAGTC
66 CAGAAAGTAGTGCCCTCCCTCCGAAACTATGCGTATCACCATTAACTTTGGAAGCACTTGAAGTC
*
592297 TGTCTGTCAGACTCCACCCT
131 TGTCTATCAGACTCCACCCT
592317 A
1 A
592318 GAAACAGTTT
Statistics
Matches: 148, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 148 1.00
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (150 bp):
ACCATTCCCTCCATTTGAAATGTCCGCTTTTAAGCTATGGAGACTCTTATTGTGCTCATCAGCCC
CAGAAAGTAGTGCCCTCCCTCCGAAACTATGCGTATCACCATTAACTTTGGAAGCACTTGAAGTC
TGTCTATCAGACTCCACCCT
Found at i:595059 original size:122 final size:122
Alignment explanation
Indices: 594874--595116 Score: 459
Period size: 122 Copynumber: 2.0 Consensus size: 122
594864 TCCCATCATT
594874 CTCTCAGGATTTAATTATGTCACACAATGAACATCACAAGTGAATAAATCCATAAACGGATTTAG
1 CTCTCAGGATTTAATTATGTCACACAATGAACATCACAAGTGAATAAATCCATAAACGGATTTAG
594939 GATTTATTCTACTTGGGTATTGTATGATGTATTGTCAGTTCAGTCAGTACACTTATC
66 GATTTATTCTACTTGGGTATTGTATGATGTATTGTCAGTTCAGTCAGTACACTTATC
* *
594996 CTCTTAGGATTTAATTATGTCACACAATGAACATCACAAGTGAATAAATCCATAAACGTATTTAG
1 CTCTCAGGATTTAATTATGTCACACAATGAACATCACAAGTGAATAAATCCATAAACGGATTTAG
*
595061 GATTTATTCTACTTGGGTATTGTATGATGTATTGTCAGTTCAGTCAGTACATTTAT
66 GATTTATTCTACTTGGGTATTGTATGATGTATTGTCAGTTCAGTCAGTACACTTAT
595117 GTCTCTATCT
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 118 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (122 bp):
CTCTCAGGATTTAATTATGTCACACAATGAACATCACAAGTGAATAAATCCATAAACGGATTTAG
GATTTATTCTACTTGGGTATTGTATGATGTATTGTCAGTTCAGTCAGTACACTTATC
Found at i:595277 original size:71 final size:71
Alignment explanation
Indices: 595161--595304 Score: 270
Period size: 71 Copynumber: 2.0 Consensus size: 71
595151 TCAAAACAAA
* *
595161 ATATCTCTCCAATTGGACTTGATAGACGACATATTAGTCTTTCAATTGGTTTGTTCATTTTTTAT
1 ATATCTCTCCAATTGGACTTGATAGACGACATATTAGTCTTTCAATTGGTTTGTTCATTTCTGAT
595226 TAGATT
66 TAGATT
595232 ATATCTCTCCAATTGGACTTGATAGACGACATATTAGTCTTTCAATTGGTTTGTTCATTTCTGAT
1 ATATCTCTCCAATTGGACTTGATAGACGACATATTAGTCTTTCAATTGGTTTGTTCATTTCTGAT
595297 TAGATT
66 TAGATT
595303 AT
1 AT
595305 TTACTAATAT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.45
Consensus pattern (71 bp):
ATATCTCTCCAATTGGACTTGATAGACGACATATTAGTCTTTCAATTGGTTTGTTCATTTCTGAT
TAGATT
Found at i:596424 original size:59 final size:59
Alignment explanation
Indices: 596332--596449 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
596322 TTCTTTAATT
596332 TTTGGTTGGGAATTGGATAAGGAACGATAGATAATGAATAGCCAAGTGATAGAATTAAG
1 TTTGGTTGGGAATTGGATAAGGAACGATAGATAATGAATAGCCAAGTGATAGAATTAAG
596391 TTTGGTTGGGAATTGGATAAGGAACGATAGATAATGAATAGCCAAGTGATAGAATTAAG
1 TTTGGTTGGGAATTGGATAAGGAACGATAGATAATGAATAGCCAAGTGATAGAATTAAG
596450 CTTGAATTAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.27
Consensus pattern (59 bp):
TTTGGTTGGGAATTGGATAAGGAACGATAGATAATGAATAGCCAAGTGATAGAATTAAG
Found at i:617214 original size:25 final size:25
Alignment explanation
Indices: 617185--617232 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
617175 TTACCATAAC
617185 TATCACATAGTAATCACAACACTAT
1 TATCACATAGTAATCACAACACTAT
617210 TATCACATAGTAATCACAACACT
1 TATCACATAGTAATCACAACACT
617233 GTTCTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.25, G:0.04, T:0.27
Consensus pattern (25 bp):
TATCACATAGTAATCACAACACTAT
Found at i:620070 original size:26 final size:26
Alignment explanation
Indices: 620023--620076 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
620013 TTTCTCAAAA
*
620023 AAGTCAACGTTCAATTGCCAACGGTC
1 AAGTCAACGTTCAATGGCCAACGGTC
*
620049 AAGTCAACGATT-AATGGTCAACGGTC
1 AAGTCAACG-TTCAATGGCCAACGGTC
620075 AA
1 AA
620077 TGGGTTAACG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (26 bp):
AAGTCAACGTTCAATGGCCAACGGTC
Found at i:620078 original size:14 final size:14
Alignment explanation
Indices: 620025--620079 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
620015 TCTCAAAAAA
* *
620025 GTCAACGTTCAATT
1 GTCAACGGTCAATG
*
620039 GCCAACGGTCAA--
1 GTCAACGGTCAATG
* *
620051 GTCAACGATTAATG
1 GTCAACGGTCAATG
620065 GTCAACGGTCAATG
1 GTCAACGGTCAATG
620079 G
1 G
620080 GTTAACGATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
12 9 0.28
14 23 0.72
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (14 bp):
GTCAACGGTCAATG
Found at i:628585 original size:16 final size:16
Alignment explanation
Indices: 628564--628604 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
628554 AGTTCAAAGC
628564 AAATAAATTATTAAAA
1 AAATAAATTATTAAAA
* *
628580 AAATAAAATATTATAA
1 AAATAAATTATTAAAA
*
628596 AAATCAATT
1 AAATAAATT
628605 CAATTGACAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAAATTATTAAAA
Found at i:630954 original size:25 final size:25
Alignment explanation
Indices: 630920--630970 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
630910 ATATTGTTTT
* *
630920 ATTTTATTATTTAATAATTTTATAC
1 ATTTTATTATTAAAAAATTTTATAC
*
630945 ATTTTTTTATTAAAAAATTTTATAC
1 ATTTTATTATTAAAAAATTTTATAC
630970 A
1 A
630971 ATCATCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTTATTATTAAAAAATTTTATAC
Found at i:635290 original size:17 final size:17
Alignment explanation
Indices: 635270--635362 Score: 57
Period size: 17 Copynumber: 5.5 Consensus size: 17
635260 ACTATTATTC
635270 TAATATAAATATTAAAA
1 TAATATAAATATTAAAA
* * **
635287 TAATATTAATATGATTA
1 TAATATAAATATTAAAA
**
635304 T-ATATAAA-ATTTCAA
1 TAATATAAATATTAAAA
*
635319 TAAATAAAAAATATATAAAA
1 T-AAT-ATAAATAT-TAAAA
* *
635339 TTAT-TAAGTATTAAAA
1 TAATATAAATATTAAAA
635355 TAATATAA
1 TAATATAA
635363 TATGAATATT
Statistics
Matches: 54, Mismatches: 16, Indels: 12
0.66 0.20 0.15
Matches are distributed among these distances:
15 4 0.07
16 14 0.26
17 24 0.44
18 4 0.07
19 4 0.07
20 4 0.07
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (17 bp):
TAATATAAATATTAAAA
Found at i:641520 original size:7 final size:7
Alignment explanation
Indices: 641508--641538 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
641498 CCAGTATCCT
641508 TCCTACA
1 TCCTACA
641515 TCCTACA
1 TCCTACA
641522 TCCTACA
1 TCCTACA
641529 TCCTACA
1 TCCTACA
641536 TCC
1 TCC
641539 ATGGTCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.29
Consensus pattern (7 bp):
TCCTACA
Found at i:647222 original size:10 final size:10
Alignment explanation
Indices: 647207--647266 Score: 67
Period size: 10 Copynumber: 6.5 Consensus size: 10
647197 TTCATGCAAT
*
647207 TTTTTTAAAA
1 TTTTTTATAA
647217 TTTTTTATAA
1 TTTTTTATAA
647227 --TTTTATAA
1 TTTTTTATAA
647235 TTTTTT-TAA
1 TTTTTTATAA
647244 -TTTTT-TAA
1 TTTTTTATAA
*
647252 TCTTTTATAA
1 TTTTTTATAA
647262 TTTTT
1 TTTTT
647267 AAATTATTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
8 16 0.37
9 7 0.16
10 20 0.47
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:647236 original size:18 final size:18
Alignment explanation
Indices: 647209--647265 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
647199 CATGCAATTT
*
647209 TTTTAAAATTTTTTATAA
1 TTTTATAATTTTTTATAA
647227 TTTTATAATTTTTT-TAA
1 TTTTATAATTTTTTATAA
* *
647244 TTTTTTAATCTTTTATAA
1 TTTTATAATTTTTTATAA
647262 TTTT
1 TTTT
647266 TAAATTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
17 15 0.43
18 20 0.57
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTATAATTTTTTATAA
Found at i:647238 original size:27 final size:27
Alignment explanation
Indices: 647208--647269 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
647198 TCATGCAATT
647208 TTTTTAAAATTTTTT-ATAATTTTATAA
1 TTTTTAAAATTTTTTAAT-ATTTTATAA
** *
647235 TTTTTTTAATTTTTTAATCTTTTATAA
1 TTTTTAAAATTTTTTAATATTTTATAA
647262 TTTTTAAA
1 TTTTTAAA
647270 TTATTTGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTTTAAAATTTTTTAATATTTTATAA
Found at i:647266 original size:17 final size:16
Alignment explanation
Indices: 647218--647268 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 16
647208 TTTTTAAAAT
647218 TTTTTATAATTTTATAA
1 TTTTTATAATTTT-TAA
*
647235 TTTTTTTAATTTTTTAA
1 TTTTTATAA-TTTTTAA
647252 TCTTTTATAATTTTTAA
1 T-TTTTATAATTTTTAA
647269 ATTATTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 19 0.63
18 11 0.37
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTATAATTTTTAA
Found at i:647581 original size:2 final size:2
Alignment explanation
Indices: 647574--647604 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
647564 ATATTCATAA
647574 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
647605 GTACATAAAA
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:647782 original size:45 final size:45
Alignment explanation
Indices: 647732--647821 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
647722 TCCGATTGTT
647732 TTTGAAAAGTTAATGATAAAATTTAACTCTTATTAGAAGGTTGAA
1 TTTGAAAAGTTAATGATAAAATTTAACTCTTATTAGAAGGTTGAA
647777 TTTGAAAAGTTAATGATAAAATTTAACTCTTATTAGAAGGTTGAA
1 TTTGAAAAGTTAATGATAAAATTTAACTCTTATTAGAAGGTTGAA
647822 GGTTAAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (45 bp):
TTTGAAAAGTTAATGATAAAATTTAACTCTTATTAGAAGGTTGAA
Found at i:689811 original size:29 final size:32
Alignment explanation
Indices: 689759--689818 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 32
689749 TAGGCCCGAA
689759 TATATTATGTTATAAAAATTAATTATATTAAT
1 TATATTATGTTATAAAAATTAATTATATTAAT
* *
689791 TATA-TATGTTA-AATAA-TAATTATGTTAA
1 TATATTATGTTATAAAAATTAATTATATTAA
689819 ATAAAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.42
30 4 0.15
31 7 0.27
32 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (32 bp):
TATATTATGTTATAAAAATTAATTATATTAAT
Found at i:689816 original size:16 final size:16
Alignment explanation
Indices: 689757--689826 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
689747 GCTAGGCCCG
*
689757 AATATATTATGTTATAAA
1 AATA-ATTATGTTA-AAT
*
689775 AATTAATTATATT-AAT
1 AA-TAATTATGTTAAAT
*
689791 TAT-A-TATGTTAAAT
1 AATAATTATGTTAAAT
689805 AATAATTATGTTAAAT
1 AATAATTATGTTAAAT
689821 AA-AATT
1 AATAATT
689827 TGGCTGAGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
13 5 0.12
14 6 0.14
15 6 0.14
16 15 0.35
18 9 0.21
19 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
AATAATTATGTTAAAT
Found at i:691513 original size:31 final size:31
Alignment explanation
Indices: 691475--691533 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
691465 TAAACTTTAT
691475 GCATTAGGGGATAGT-TCCAGTTATGCATTCA
1 GCATTAGGGGATAGTAT-CAGTTATGCATTCA
691506 GCATTAGGGGATAGTATCAGTTATGCAT
1 GCATTAGGGGATAGTATCAGTTATGCAT
691534 CTAGATTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (31 bp):
GCATTAGGGGATAGTATCAGTTATGCATTCA
Found at i:695934 original size:62 final size:61
Alignment explanation
Indices: 695796--695935 Score: 140
Period size: 62 Copynumber: 2.2 Consensus size: 61
695786 TGTCAAATTT
* ** *
695796 AAAAAATTAGGGGAAGCTAACTAAAATTTTCTAAAAACTTAAAGAGAAGAATAAAATTTTCT
1 AAAAAATTAGGGG-GGCTAACTAAAATTTTCTAAAAACTTAAAGAGAAGAATAAAATTCCCA
* * * * *
695858 AAAAATTCTGGGGGGGCTAATTAAAATTTTCTAAAAATTTCAAG-GAA-AAGTAAAATTCCCCAA
1 AAAAAAT-TAGGGGGGCTAACTAAAATTTTCTAAAAACTTAAAGAGAAGAA-TAAAATT-CCC-A
695921 AAAAAATTAGGGGGG
1 AAAAAATTAGGGGGG
695936 GCCTTAAGCC
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
60 2 0.03
61 10 0.16
62 40 0.63
63 11 0.17
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (61 bp):
AAAAAATTAGGGGGGCTAACTAAAATTTTCTAAAAACTTAAAGAGAAGAATAAAATTCCCA
Found at i:696440 original size:17 final size:17
Alignment explanation
Indices: 696418--696451 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
696408 CTAATATCCT
696418 TGGTCTATCTCCATGGG
1 TGGTCTATCTCCATGGG
696435 TGGTCTATCTCCATGGG
1 TGGTCTATCTCCATGGG
696452 CATGCGAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.29, T:0.35
Consensus pattern (17 bp):
TGGTCTATCTCCATGGG
Found at i:696506 original size:16 final size:16
Alignment explanation
Indices: 696487--696519 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
696477 GGACGTGGAG
696487 GATAAGGATTCGAGAA
1 GATAAGGATTCGAGAA
696503 GATAAGGATTCGAGAA
1 GATAAGGATTCGAGAA
696519 G
1 G
696520 CCTAGATCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.33, T:0.18
Consensus pattern (16 bp):
GATAAGGATTCGAGAA
Found at i:696749 original size:111 final size:111
Alignment explanation
Indices: 696555--696777 Score: 430
Period size: 111 Copynumber: 2.0 Consensus size: 111
696545 TAGCATTTCA
696555 TGTTTGGAGTATTGCACGTAATCCAGAATCCTCAGAATTAGCATCTTCACATGAGGATGTTAACC
1 TGTTTGGAGTATTGCACGTAATCCAGAATCCTCAGAATTAGCATCTTCACATGAGGATGTTAACC
696620 TGTTTCGTTGGGTTTGGCAAACCTTTATTTCCAGAAGGTGCTTTTG
66 TGTTTCGTTGGGTTTGGCAAACCTTTATTTCCAGAAGGTGCTTTTG
696666 TGTTTGGAGTGA-TGCACGTAATCCAGAATCCTCAGAATTAGCATCTTCACATGAGGATGTTAAC
1 TGTTTGGAGT-ATTGCACGTAATCCAGAATCCTCAGAATTAGCATCTTCACATGAGGATGTTAAC
696730 CTGTTTCGTTGGGTTTGGCAAACCTTTATTTCCAGAAGGTGCTTTTG
65 CTGTTTCGTTGGGTTTGGCAAACCTTTATTTCCAGAAGGTGCTTTTG
696777 T
1 T
696778 ATGACTAACA
Statistics
Matches: 111, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
111 110 0.99
112 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (111 bp):
TGTTTGGAGTATTGCACGTAATCCAGAATCCTCAGAATTAGCATCTTCACATGAGGATGTTAACC
TGTTTCGTTGGGTTTGGCAAACCTTTATTTCCAGAAGGTGCTTTTG
Found at i:702450 original size:28 final size:25
Alignment explanation
Indices: 702386--702450 Score: 60
Period size: 26 Copynumber: 2.4 Consensus size: 25
702376 TAAAGTGCTA
* *
702386 TAAAATTAAATATATTTGATTCTTT
1 TAAAATTATATATATTTAATTCTTT
702411 TCATAAA-TATATATATTTAACTTCAATTT
1 T-A-AAATTATATATATTTAA-TTC--TTT
702440 TAAAATTATAT
1 TAAAATTATAT
702451 TTAATTTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
25 1 0.03
26 12 0.38
27 9 0.28
28 6 0.19
29 4 0.12
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (25 bp):
TAAAATTATATATATTTAATTCTTT
Found at i:707903 original size:29 final size:29
Alignment explanation
Indices: 707861--707929 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
707851 CAACGTCAGT
707861 TTGTGTGAGCAACCCTAATCACTGT-AAGC
1 TTGTGTGAGCAACCCTAATCACTGTCAA-C
* *
707890 TTGTGTGAGTAACCCTAGTCACTGTCAAC
1 TTGTGTGAGCAACCCTAATCACTGTCAAC
707919 TTGTGTGAGCA
1 TTGTGTGAGCA
707930 CTATAGTCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 34 0.94
30 2 0.06
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (29 bp):
TTGTGTGAGCAACCCTAATCACTGTCAAC
Found at i:717718 original size:17 final size:17
Alignment explanation
Indices: 717696--717734 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
717686 CTCCACCTTG
* *
717696 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
717713 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
717730 ACAAG
1 ACAAG
717735 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:722059 original size:16 final size:17
Alignment explanation
Indices: 722029--722061 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
722019 ATGGATAAGT
722029 CAAAAGCAAGTGAGAAA
1 CAAAAGCAAGTGAGAAA
*
722046 CAAAGGCAAG-GAGAAA
1 CAAAAGCAAGTGAGAAA
722062 TTTGCTTTAG
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:0.58, C:0.12, G:0.27, T:0.03
Consensus pattern (17 bp):
CAAAAGCAAGTGAGAAA
Found at i:723741 original size:17 final size:16
Alignment explanation
Indices: 723715--723749 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
723705 ATTAAATTAA
*
723715 TTTTAATTAATTAATT
1 TTTTAATTAAATAATT
723731 TTTTCAATTAAATAATT
1 TTTT-AATTAAATAATT
723748 TT
1 TT
723750 CACAATCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTAATTAAATAATT
Found at i:729568 original size:20 final size:19
Alignment explanation
Indices: 729519--729574 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
729509 AATTTTTATT
*
729519 TTTAAAATATTTTGACATAA
1 TTTAAAATATTTTTA-ATAA
**
729539 TTTTTAATATTTTTAATAA
1 TTTAAAATATTTTTAATAA
729558 TTTAAATATATTTTTAA
1 TTTAAA-ATATTTTTAA
729575 GATTTTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTAAAATATTTTTAATAA
Found at i:730113 original size:18 final size:18
Alignment explanation
Indices: 730075--730112 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
730065 TATTTGTTTG
730075 TTTGTTTATTATTTATAT
1 TTTGTTTATTATTTATAT
730093 TTTGTTTAATT-TTTA-AT
1 TTTGTTT-ATTATTTATAT
730110 TTT
1 TTT
730113 TCAATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 11 0.58
19 3 0.16
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTGTTTATTATTTATAT
Found at i:730960 original size:13 final size:15
Alignment explanation
Indices: 730941--730977 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
730931 ATGTCCACAT
730941 CTATTTTAAA-AA-A
1 CTATTTTAAAGAATA
*
730954 TTATTTTAAAGAATA
1 CTATTTTAAAGAATA
730969 CTATTTTAA
1 CTATTTTAA
730978 TTTCTTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 9 0.45
14 2 0.10
15 9 0.45
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (15 bp):
CTATTTTAAAGAATA
Found at i:734094 original size:21 final size:21
Alignment explanation
Indices: 734056--734097 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
734046 AAATAACTAA
* **
734056 CTAAATTATATAGTATTTATT
1 CTAAATTACATAAAATTTATT
734077 CTAAATTACATAAAATTTATT
1 CTAAATTACATAAAATTTATT
734098 ATTAATCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (21 bp):
CTAAATTACATAAAATTTATT
Done.