Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003112.1 Hibiscus syriacus cultivar Beakdansim tig00006507_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: 642031
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:623971 original size:3 final size:3
Alignment explanation
Indices: 623965--624003 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
623955 TACTATTAAA
*
623965 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA
624004 CTTAATCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:624065 original size:33 final size:33
Alignment explanation
Indices: 624013--624099 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
624003 ACTTAATCTA
* ** **
624013 AAAAACCCACTACCTATTAAATAATCATTCACT
1 AAAAACTCACTACCTATTAAATAAAAACCCACT
* *
624046 AAAAACTCAATACCCATTAAATAAAAACCCACT
1 AAAAACTCACTACCTATTAAATAAAAACCCACT
624079 AAAAACTCACTACCTATTAAA
1 AAAAACTCACTACCTATTAAA
624100 CAAAGAAAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (33 bp):
AAAAACTCACTACCTATTAAATAAAAACCCACT
Found at i:627180 original size:18 final size:18
Alignment explanation
Indices: 627157--627192 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
627147 ATATTTTCTT
627157 TATTAATGAGCAGTATTA
1 TATTAATGAGCAGTATTA
627175 TATTAATGAGCAGTATTA
1 TATTAATGAGCAGTATTA
627193 ATACATCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (18 bp):
TATTAATGAGCAGTATTA
Found at i:627260 original size:18 final size:18
Alignment explanation
Indices: 627237--627272 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
627227 CCCCACTGAC
*
627237 TATTAATGAGCAGTATTA
1 TATTAATGAGAAGTATTA
627255 TATTAATGAGAAGTATTA
1 TATTAATGAGAAGTATTA
627273 ATACAACTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.39
Consensus pattern (18 bp):
TATTAATGAGAAGTATTA
Found at i:627714 original size:20 final size:20
Alignment explanation
Indices: 627677--627715 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
627667 TAAATTTATT
*
627677 AAATTGAATTAAATTATAAA
1 AAATTGAATAAAATTATAAA
627697 AAATT-AATAAAATATATAA
1 AAATTGAATAAAAT-TATAA
627716 TTATTTAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAATTGAATAAAATTATAAA
Found at i:628144 original size:19 final size:19
Alignment explanation
Indices: 628122--628163 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
628112 CACGGGTAAC
*
628122 CCGCGAAACCTG-TAATAAT
1 CCGCGAAACCCGCT-ATAAT
628141 CCGCGAAACCCGCTATAAT
1 CCGCGAAACCCGCTATAAT
628160 CCGC
1 CCGC
628164 AATAGTCCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.31, C:0.36, G:0.17, T:0.17
Consensus pattern (19 bp):
CCGCGAAACCCGCTATAAT
Found at i:628179 original size:19 final size:19
Alignment explanation
Indices: 628157--628196 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
628147 AACCCGCTAT
628157 AATCCGCAATAGTCCGTTA
1 AATCCGCAATAGTCCGTTA
628176 AATCCGCAATAGTCCGTTA
1 AATCCGCAATAGTCCGTTA
628195 AA
1 AA
628197 ACTCGCGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (19 bp):
AATCCGCAATAGTCCGTTA
Found at i:631477 original size:51 final size:52
Alignment explanation
Indices: 631378--631481 Score: 151
Period size: 52 Copynumber: 2.0 Consensus size: 52
631368 TACCAATGAG
* *
631378 ATCACTTAGTGGGTTCAAAAAGATTATTTTTCTTTCATCAAAATGATGGGAT
1 ATCACTTAGTGGGTTCAAAAAGATTAATTTTCTTCCATCAAAATGATGGGAT
631430 ATCACTT-GATGGGTT-AAAAAGTATTAATTTTCTTCCATC-AAATGATGGGAT
1 ATCACTTAG-TGGGTTCAAAAAG-ATTAATTTTCTTCCATCAAAATGATGGGAT
631481 A
1 A
631482 ATATAAAACT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
51 20 0.42
52 28 0.58
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.38
Consensus pattern (52 bp):
ATCACTTAGTGGGTTCAAAAAGATTAATTTTCTTCCATCAAAATGATGGGAT
Found at i:632810 original size:24 final size:24
Alignment explanation
Indices: 632778--632833 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
632768 CCTAAATCTA
*
632778 TGTAAAATTAAAAGAATTTTACAT
1 TGTATAATTAAAAGAATTTTACAT
632802 TGTATAATTAAAAGAATTTTACAT
1 TGTATAATTAAAAGAATTTTACAT
632826 TGTATAAT
1 TGTATAAT
632834 AAGATCTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (24 bp):
TGTATAATTAAAAGAATTTTACAT
Found at i:634027 original size:56 final size:59
Alignment explanation
Indices: 633906--634028 Score: 155
Period size: 56 Copynumber: 2.1 Consensus size: 59
633896 AACCAATAAG
* *
633906 TCAAGTTCAAGTACCTAATTGGACTAAAATAAACTTTAGGTACCAAATTGAGCCTTAAAA
1 TCAAGTTCAAATACCTAATTGGACT-AAATAAACTTTAAGTACCAAATTGAGCCTTAAAA
* * *
633966 ACAAGTTCAAATACCTAATTGGA-T-AA-AAAGTTTAAGTACCAAATTGTA-CTTTAAAA
1 TCAAGTTCAAATACCTAATTGGACTAAATAAACTTTAAGTACCAAATTG-AGCCTTAAAA
634022 TCAAGTT
1 TCAAGTT
634029 GGTTACCTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
56 31 0.55
57 3 0.05
59 1 0.02
60 21 0.38
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (59 bp):
TCAAGTTCAAATACCTAATTGGACTAAATAAACTTTAAGTACCAAATTGAGCCTTAAAA
Found at i:635994 original size:3 final size:3
Alignment explanation
Indices: 635979--636043 Score: 91
Period size: 3 Copynumber: 22.7 Consensus size: 3
635969 AGTTAAAAAA
*
635979 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
636024 TAT TAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
636044 AGTGTGTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 5 0.09
3 51 0.91
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Done.