Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 29
Found at i:6138533 original size:38 final size:38
Alignment explanation
Indices: 6138482--6138556 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
6138472 CAAATTACTC
*
6138482 ATGTTTTAATCACTCTAATTTATTTTATTAATAATTTT
1 ATGTTCTAATCACTCTAATTTATTTTATTAATAATTTT
6138520 ATGTTCTAATCACTCTAATTTATTTTATTAATAATTT
1 ATGTTCTAATCACTCTAATTTATTTTATTAATAATTT
6138557 GTGTGACATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.56
Consensus pattern (38 bp):
ATGTTCTAATCACTCTAATTTATTTTATTAATAATTTT
Found at i:6138551 original size:22 final size:22
Alignment explanation
Indices: 6138487--6138551 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 22
6138477 TACTCATGTT
6138487 TTAATCACTCTAATTTATTTTA
1 TTAATCACTCTAATTTATTTTA
* *
6138509 TTAAT-A----ATTTTATGTT-
1 TTAATCACTCTAATTTATTTTA
*
6138525 CTAATCACTCTAATTTATTTTA
1 TTAATCACTCTAATTTATTTTA
6138547 TTAAT
1 TTAAT
6138552 AATTTGTGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 12
0.63 0.12 0.24
Matches are distributed among these distances:
16 4 0.13
17 9 0.29
21 9 0.29
22 9 0.29
ACGTcount: A:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (22 bp):
TTAATCACTCTAATTTATTTTA
Found at i:6138875 original size:16 final size:17
Alignment explanation
Indices: 6138835--6138878 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
6138825 CCACTCCCTT
*
6138835 AAATCCCTAAATCTTTA
1 AAATCCCTAAATCATTA
*
6138852 AAAT-CCTAAA-CATTC
1 AAATCCCTAAATCATTA
6138867 AAATCCCTAAAT
1 AAATCCCTAAAT
6138879 AATTCCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 7 0.30
16 12 0.52
17 4 0.17
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATCCCTAAATCATTA
Found at i:6139076 original size:22 final size:23
Alignment explanation
Indices: 6139050--6139103 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
6139040 TTTATTTTTC
6139050 TTTTAAATGTTTTTAAAAT-AAAA
1 TTTTAAAT-TTTTTAAAATAAAAA
* *
6139073 -TTTATATTTTTTTAAATAAAAA
1 TTTTAAATTTTTTAAAATAAAAA
6139095 TTTTAAATT
1 TTTTAAATT
6139104 ATTGAAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 9 0.35
22 10 0.38
23 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTAAATTTTTTAAAATAAAAA
Found at i:6139813 original size:2 final size:2
Alignment explanation
Indices: 6139806--6139833 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6139796 ATTAAAAATA
6139806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6139834 TATCATATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6140166 original size:23 final size:23
Alignment explanation
Indices: 6140140--6140187 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
6140130 ATAAAGTACA
* *
6140140 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAAGTAGCGCTTAT
**
6140163 ATAATGTAATAAGTAGCGCTTAT
1 ATAACATAATAAGTAGCGCTTAT
6140186 AT
1 AT
6140188 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAAGTAGCGCTTAT
Found at i:6140640 original size:23 final size:23
Alignment explanation
Indices: 6140614--6140676 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
6140604 ATATAACCAC
6140614 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
6140637 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
6140660 TACCTATTACATCATAT
1 TACCTATTACATTATAT
6140677 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:6140858 original size:29 final size:29
Alignment explanation
Indices: 6140822--6140886 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
6140812 TCATTTGCAC
*
6140822 AAAA-ATTATTT-G-ATTTTTGATATTTTAT
1 AAAATATTATTTAGAATTTTT-A-ATTTAAT
6140850 AAAATATTATTTAGAATTTTTAATTTAAT
1 AAAATATTATTTAGAATTTTTAATTTAAT
6140879 AATAATAT
1 AA-AATAT
6140887 ATCGTAACGT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 4 0.12
29 15 0.47
30 7 0.22
31 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTAGAATTTTTAATTTAAT
Found at i:6141051 original size:426 final size:430
Alignment explanation
Indices: 6140254--6141305 Score: 1893
Period size: 426 Copynumber: 2.5 Consensus size: 430
6140244 TATTACATTA
* *
6140254 TATTATATTGAAAATATCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
6140319 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
* *
6140384 ATTTGCACAAAAAAATATTTAATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
6140449 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
196 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
*
6140514 TTAAAATTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGAACATTT
261 TTAAAATTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGAACACTT
6140579 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
326 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
*
6140644 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 TACATTATATAAGCGCTACCTATTACATCATATGTTTACC
6140684 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
6140749 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
6140814 ATTTGCAC-AAAAATTATTTGA-TTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
6140877 ATAAT-A-ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
196 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
*
6140940 TTAAAACTT-ACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
261 TTAAAA-TTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGAACACT
*
6141004 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
325 TTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
6141069 TTACATTATATAAGCGCTACCTATTACATCATATGTTTACC
390 TTACATTATATAAGCGCTACCTATTACATCATATGTTTACC
*
6141110 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAA
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTT-AAAGTTATGTAA
* *
6141175 TTTATGTTTCAA-TTTTTTTAATAGTGTTTTATGTTTTCCACATACAATATTAATTTAATAATTT
65 TTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTT
* * * *
6141239 CATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTATAA-TTTAAATT
130 CATTTGCACAAAAAATTATTTGATT-TTTTGATATTTTATAAAATATTATTTAGAATTTTTAATT
6141303 TAA
194 TAA
6141306 CAACATTAAC
Statistics
Matches: 602, Mismatches: 15, Indels: 12
0.96 0.02 0.02
Matches are distributed among these distances:
426 329 0.55
427 40 0.07
428 58 0.10
429 39 0.06
430 136 0.23
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (430 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
TTAAAATTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGAACACTT
TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
TACATTATATAAGCGCTACCTATTACATCATATGTTTACC
Found at i:6141066 original size:23 final size:23
Alignment explanation
Indices: 6141040--6141102 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
6141030 ATATAACCAC
6141040 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
6141063 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
6141086 TACCTATTACATCATAT
1 TACCTATTACATTATAT
6141103 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:6142023 original size:199 final size:199
Alignment explanation
Indices: 6141664--6142833 Score: 2150
Period size: 199 Copynumber: 5.9 Consensus size: 199
6141654 TTTAAATTAG
*
6141664 TATCGACACAAACTAAA--ACGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
1 TATCGACACAAACTAAATTA-GTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAA
6141727 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
* *
6141792 TCGACACTTTTTATATATGGATCGTCACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
6141857 -AAAA
195 AAAAA
*
6141861 TAATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACAGGTAA
1 T-ATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAA
6141926 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
6141991 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC
6142056 AAAAA
195 AAAAA
6142061 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
* *
6142126 CTTGTACTGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGATTCGATGATTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
6142191 CGATACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
6142256 AAAA
196 AAAA
6142260 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
6142325 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
6142390 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGAAACT
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
6142455 AAAA
196 AAAA
6142459 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
* *
6142524 CTTGTACTGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGATTCGATGA-TTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
6142588 CGATACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
6142653 AAAA
196 AAAA
6142657 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
* *
6142722 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
6142787 TTGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
6142834 GGCCATATTG
Statistics
Matches: 944, Mismatches: 23, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
197 1 0.00
198 201 0.21
199 684 0.72
200 58 0.06
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (199 bp):
TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
AAAA
Found at i:6142998 original size:19 final size:19
Alignment explanation
Indices: 6142952--6143000 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
6142942 TTATATTCAC
*
6142952 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
6142971 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
6142990 ATACAAAATTA
1 ATACAAAATTA
6143001 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:6144823 original size:33 final size:33
Alignment explanation
Indices: 6144786--6144851 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
6144776 CATCTTAATA
*
6144786 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
6144819 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
6144852 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:6144910 original size:21 final size:21
Alignment explanation
Indices: 6144885--6144928 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
6144875 CCCCTTATGC
6144885 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
6144906 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
6144927 CT
1 CT
6144929 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:6147154 original size:17 final size:18
Alignment explanation
Indices: 6147132--6147174 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
6147122 ATATATCCGG
6147132 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
6147149 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
6147169 TATCAT
1 TATCAT
6147175 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:6147192 original size:20 final size:19
Alignment explanation
Indices: 6147137--6147183 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
6147127 TCCGGTATCA
6147137 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
6147156 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
6147177 TTTTACC
1 TTTTACC
6147184 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:6147344 original size:20 final size:19
Alignment explanation
Indices: 6147317--6147377 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 19
6147307 TCCGGTAACG
6147317 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
6147336 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
*
6147357 TTTTACCTGG-TATATCATT
1 TTTTACC-GGTTTTATCATT
6147376 TT
1 TT
6147378 AATATTTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
19 5 0.13
20 28 0.74
21 5 0.13
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.56
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:6147806 original size:227 final size:227
Alignment explanation
Indices: 6147412--6147899 Score: 890
Period size: 227 Copynumber: 2.1 Consensus size: 227
6147402 ACTTTTATTC
6147412 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
6147477 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
66 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
*
6147542 TATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAATC-AAG
131 TATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
*
6147606 ATAATAATAAATATGTTTTCCACAGTG-AATAA
196 ATAATAATAAATATATTTT-CACAGTGAAATAA
*
6147638 GTATGGACACTTTTATAAAAATGATATATATTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TT
*
6147703 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACACAAAA
65 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
6147768 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
130 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
6147833 GATAATAATAAATATATTTTCACAGTGAAATAA
195 GATAATAATAAATATATTTTCACAGTGAAATAA
* *
6147866 GTATGGACACTTTTATAAAAAGGATAGATACTTT
1 GTATGGACACTTTTATAAAAATGATATATACTTT
6147900 ACAATATAAC
Statistics
Matches: 252, Mismatches: 7, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
226 61 0.24
227 134 0.53
228 57 0.23
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (227 bp):
GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
TATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
ATAATAATAAATATATTTTCACAGTGAAATAA
Found at i:6155166 original size:45 final size:46
Alignment explanation
Indices: 6155092--6155184 Score: 179
Period size: 45 Copynumber: 2.0 Consensus size: 46
6155082 AGGTTTTTAA
6155092 TAACATGTAGAACAAAAGAAGACATATCATATACCATATCGGAGAC
1 TAACATGTAGAACAAAAGAAGACATATCATATACCATATCGGAGAC
6155138 TAACATGTAGAAC-AAAGAAGACATATCATATACCATATCGGAGAC
1 TAACATGTAGAACAAAAGAAGACATATCATATACCATATCGGAGAC
6155183 TA
1 TA
6155185 TCTTTGAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 34 0.72
46 13 0.28
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.20
Consensus pattern (46 bp):
TAACATGTAGAACAAAAGAAGACATATCATATACCATATCGGAGAC
Found at i:6161156 original size:21 final size:22
Alignment explanation
Indices: 6161132--6161176 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
6161122 AAGTACATAT
6161132 TTAAATTATTGATGTTGTT-TA
1 TTAAATTATTGATGTTGTTATA
6161153 TTAAATTATTGATGTTGTTATA
1 TTAAATTATTGATGTTGTTATA
6161175 TT
1 TT
6161177 TGATTGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (22 bp):
TTAAATTATTGATGTTGTTATA
Found at i:6162790 original size:14 final size:14
Alignment explanation
Indices: 6162771--6162807 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
6162761 AATTTTTGAG
6162771 ATAGTTAAATTCGA
1 ATAGTTAAATTCGA
6162785 ATAGTTAAATTCGA
1 ATAGTTAAATTCGA
*
6162799 ATGGTTAAA
1 ATAGTTAAA
6162808 GATATTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.35
Consensus pattern (14 bp):
ATAGTTAAATTCGA
Found at i:6166707 original size:17 final size:18
Alignment explanation
Indices: 6166661--6166725 Score: 87
Period size: 18 Copynumber: 3.7 Consensus size: 18
6166651 GTAGAATTTA
*
6166661 TCCCGTAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
6166679 TCCCGAAGGACCACTGTG
1 TCCCGAAGGACCACTATG
*
6166697 TCCCG-AGGACCATTATG
1 TCCCGAAGGACCACTATG
*
6166714 CCCCGAAGGACC
1 TCCCGAAGGACC
6166726 GCGTAGACCC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
17 14 0.34
18 27 0.66
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:6181582 original size:16 final size:16
Alignment explanation
Indices: 6181561--6181593 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6181551 GTAGCAACAA
6181561 CACAAGCACCAAGTGT
1 CACAAGCACCAAGTGT
6181577 CACAAGCACCAAGTGT
1 CACAAGCACCAAGTGT
6181593 C
1 C
6181594 CGACTCCCAG
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:0.36, C:0.33, G:0.18, T:0.12
Consensus pattern (16 bp):
CACAAGCACCAAGTGT
Found at i:6189488 original size:41 final size:41
Alignment explanation
Indices: 6189442--6189521 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
6189432 AAGTTTCCAT
* *
6189442 ATAACTGATTTTAGTCGGTTGAAATCCCTTGTAGAATCTCC
1 ATAACTAATTTTAGTCGGTTGAAATCCCATGTAGAATCTCC
*
6189483 ATAACTAATTTTAGTCGGTTTAAATCCCATGTAGAATCT
1 ATAACTAATTTTAGTCGGTTGAAATCCCATGTAGAATCT
6189522 TAATCACTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (41 bp):
ATAACTAATTTTAGTCGGTTGAAATCCCATGTAGAATCTCC
Found at i:6196096 original size:16 final size:17
Alignment explanation
Indices: 6196075--6196111 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
6196065 AAATTTTTTT
6196075 ATTTTAT-TTTATC-TTA
1 ATTTTATATTT-TCATTA
6196091 ATTTTATATTTTCATTA
1 ATTTTATATTTTCATTA
6196108 ATTT
1 ATTT
6196112 AAATAAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTATATTTTCATTA
Found at i:6200617 original size:12 final size:12
Alignment explanation
Indices: 6200600--6200624 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6200590 GATCCTTGTA
6200600 GGAGGAATCTAT
1 GGAGGAATCTAT
6200612 GGAGGAATCTAT
1 GGAGGAATCTAT
6200624 G
1 G
6200625 ATAAGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.36, T:0.24
Consensus pattern (12 bp):
GGAGGAATCTAT
Found at i:6201180 original size:21 final size:22
Alignment explanation
Indices: 6201154--6201196 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6201144 TCTCATATTG
*
6201154 ACAATTT-GAAGATGCTTTGGT
1 ACAATTTCGAAAATGCTTTGGT
6201175 ACAATTTCGAAAATGCTTTGGT
1 ACAATTTCGAAAATGCTTTGGT
6201197 TCCTGTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (22 bp):
ACAATTTCGAAAATGCTTTGGT
Found at i:6205568 original size:2 final size:2
Alignment explanation
Indices: 6205561--6205595 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6205551 AAAAATTGAT
*
6205561 TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6205596 GGTTAGGACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6213534 original size:5 final size:5
Alignment explanation
Indices: 6213526--6213560 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
6213516 TATAGAATTA
*
6213526 TTAAT TTAAA TTAAT TTAAAT TTAAT TTAAT TTAA
1 TTAAT TTAAT TTAAT TT-AAT TTAAT TTAAT TTAA
6213561 ATAGTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
TTAAT
Found at i:6213547 original size:16 final size:16
Alignment explanation
Indices: 6213528--6213562 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
6213518 TAGAATTATT
6213528 AATTTAAATTAATTTA
1 AATTTAAATTAATTTA
*
6213544 AATTTAATTTAATTTA
1 AATTTAAATTAATTTA
6213560 AAT
1 AAT
6213563 AGTATATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTAAATTAATTTA
Done.