Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008236.1 Hibiscus syriacus cultivar Beakdansim tig00110882_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: 1100419
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1093700 original size:83 final size:83
Alignment explanation
Indices: 1093531--1093701 Score: 211
Period size: 83 Copynumber: 2.0 Consensus size: 83
1093521 TTTTGAAAAA
* * **
1093531 ATATATATTATATAGTTTTTAAAAATATTTTTGAAAATTATATATTGTATAGTTTTTAAAACATT
1 ATATATATTATATAGTTTTTAAAAATATTTTTGAAAAATATATAATACATAGTTTTTAAAACATT
* *
1093596 TTAGAATATATATAATAT
66 TTAGAAAACATATAATAT
*
1093614 ATATATATATATATAGTTTTT-AAAATCA-TTTTGAAAAATATATAATACATAGTTTTTTGAAAT
1 ATATATAT-TATATAGTTTTTAAAAAT-ATTTTTGAAAAATATATAATACATAG-TTTTT-AAAA
* *
1093677 CATTTTTGAAAACATATATTAT
62 CATTTTAGAAAACATATAATAT
1093699 ATA
1 ATA
1093702 GTTTTGAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
83 33 0.44
84 18 0.24
85 24 0.32
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (83 bp):
ATATATATTATATAGTTTTTAAAAATATTTTTGAAAAATATATAATACATAGTTTTTAAAACATT
TTAGAAAACATATAATAT
Found at i:1093829 original size:73 final size:73
Alignment explanation
Indices: 1093617--1093853 Score: 250
Period size: 73 Copynumber: 3.2 Consensus size: 73
1093607 ATAATATATA
* * * *
1093617 TATATATATATAGTTTTTAAAATCATTTTG-AAAA-ATATATAATACATAGTTTTTTGAAATCAT
1 TATATATATATAGTTTTGAAAA-CATTTTGAAAAATATATATAATATATA-ATTTTT-AAAACAT
*
1093680 TTTTGAAAACA
63 TTTTGAAAACT
* ** *
1093691 TATAT-TATATAGTTTTGAAAATATTTTTTAAAATATATATAATATATAGTTTTTGAAAACATTT
1 TATATATATATAGTTTTGAAAACATTTTGAAAAATATATATAATATATAATTTTT-AAAACATTT
1093755 TTGAAAACT
65 TTGAAAACT
* * * **
1093764 TATATAT-TATAGTTTTGAAAACATTTTCGAAAACATTTATATATTTTATAATTTTT-AAATGTT
1 TATATATATATAGTTTTGAAAACATTTT-GAAAA-ATATATATAATATATAATTTTTAAAACATT
1093827 TTTGAAAACT
64 TTTGAAAACT
1093837 TATATATAATATAGTTT
1 TATATAT-ATATAGTTT
1093854 ATATAATATT
Statistics
Matches: 140, Mismatches: 16, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
72 5 0.04
73 87 0.62
74 22 0.16
75 26 0.19
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (73 bp):
TATATATATATAGTTTTGAAAACATTTTGAAAAATATATATAATATATAATTTTTAAAACATTTT
TGAAAACT
Found at i:1095147 original size:15 final size:15
Alignment explanation
Indices: 1095123--1095192 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
1095113 TTAAAAAAAC
*
1095123 TTTTCATTTTTCATT
1 TTTTCTTTTTTCATT
1095138 TTTTCTTTTTTCATT
1 TTTTCTTTTTTCATT
* *
1095153 TCTT-TTTATT--TT
1 TTTTCTTTTTTCATT
*
1095165 TTTTCATTTTTTCCTT
1 TTTTC-TTTTTTCATT
*
1095181 TTATTATTTTTT
1 TT-TTCTTTTTT
1095193 TTCCTTTTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
12 5 0.11
14 10 0.23
15 17 0.39
16 10 0.23
17 2 0.05
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTTTCATT
Found at i:1095154 original size:20 final size:20
Alignment explanation
Indices: 1095131--1095173 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1095121 ACTTTTCATT
1095131 TTTCATTTTT-TCTTTTTTCA
1 TTTC-TTTTTATCTTTTTTCA
*
1095151 TTTCTTTTTATTTTTTTTCA
1 TTTCTTTTTATCTTTTTTCA
1095171 TTT
1 TTT
1095174 TTTCCTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTCTTTTTATCTTTTTTCA
Found at i:1095167 original size:26 final size:25
Alignment explanation
Indices: 1095136--1095202 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
1095126 TCATTTTTCA
* *
1095136 TTTTTTCTTTTTTCATTTCTTTTTATT
1 TTTTTTCTTTTTTC-CTT-TTATTATT
1095163 TTTTTTCATTTTTTCCTTTTATTATT
1 TTTTTTC-TTTTTTCCTTTTATTATT
*
1095189 TTTTTTCCTTTTTC
1 TTTTTTCTTTTTTC
1095203 TTCTCCTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 6 0.17
26 14 0.39
27 9 0.25
28 7 0.19
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTTTCTTTTTTCCTTTTATTATT
Found at i:1095174 original size:10 final size:10
Alignment explanation
Indices: 1095143--1095176 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1095133 TCATTTTTTC
1095143 TTTTTTCATT
1 TTTTTTCATT
1095153 TCTTTTT-ATT
1 T-TTTTTCATT
1095163 TTTTTTCATT
1 TTTTTTCATT
1095173 TTTT
1 TTTT
1095177 CCTTTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 5 0.23
10 12 0.55
11 5 0.23
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:1095201 original size:35 final size:35
Alignment explanation
Indices: 1095129--1095201 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
1095119 AAACTTTTCA
*
1095129 TTTTTCATTTTTTCTTTTTTCATTTCTTTTTATTT
1 TTTTTCATTTTTTCTTTTTTCATTTCTTTTTACTT
*
1095164 TTTTTCATTTTTTCCTTTTATT-ATTT-TTTTTCCTT
1 TTTTTCATTTTTT-CTTTT-TTCATTTCTTTTTACTT
1095199 TTT
1 TTT
1095202 CTTCTCCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 23 0.68
36 9 0.26
37 2 0.06
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.79
Consensus pattern (35 bp):
TTTTTCATTTTTTCTTTTTTCATTTCTTTTTACTT
Found at i:1095251 original size:10 final size:10
Alignment explanation
Indices: 1095234--1095284 Score: 75
Period size: 10 Copynumber: 5.1 Consensus size: 10
1095224 TTATTTGGTG
*
1095234 TATATATGTA
1 TATATATATA
* *
1095244 TGTATATGTA
1 TATATATATA
1095254 TATATATATA
1 TATATATATA
1095264 TATATATATA
1 TATATATATA
1095274 TATATATATA
1 TATATATATA
1095284 T
1 T
1095285 TATTTTACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (10 bp):
TATATATATA
Found at i:1095253 original size:6 final size:6
Alignment explanation
Indices: 1095234--1095284 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
1095224 TTATTTGGTG
* * *
1095234 TATATA TGTATG TATATG TATATA TATATA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
1095282 TAT
1 TAT
1095285 TATTTTACTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (6 bp):
TATATA
Found at i:1095259 original size:4 final size:4
Alignment explanation
Indices: 1095234--1095284 Score: 75
Period size: 4 Copynumber: 12.8 Consensus size: 4
1095224 TTATTTGGTG
* * *
1095234 TATA TATG TATG TATA TGTA TATA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
1095282 TAT
1 TAT
1095285 TATTTTACTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:1096335 original size:21 final size:21
Alignment explanation
Indices: 1096311--1096350 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1096301 ATCGTCAAAG
* *
1096311 TGTACTAACATGTCATCATAA
1 TGTAATAACATATCATCATAA
*
1096332 TGTAATGACATATCATCAT
1 TGTAATAACATATCATCAT
1096351 TGGAAAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (21 bp):
TGTAATAACATATCATCATAA
Found at i:1099889 original size:2 final size:2
Alignment explanation
Indices: 1099882--1099922 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
1099872 TTCATATACT
*
1099882 TA TA TA TA TA TA TA TA TA TA TA TA GA T- 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 TA
1099922 T
1 T
1099923 TTAATCATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Done.