Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009608.1 Hibiscus syriacus cultivar Beakdansim tig00116994_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: 1053610
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1032271 original size:19 final size:20
Alignment explanation
Indices: 1032247--1032290 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1032237 AAGTGGCCCG
*
1032247 ATTTC-ACATTCTAACATCA
1 ATTTCAACACTCTAACATCA
*
1032266 ATTTCAACACTCTAACATTA
1 ATTTCAACACTCTAACATCA
1032286 ATTTC
1 ATTTC
1032291 CAATATAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTTCAACACTCTAACATCA
Found at i:1033865 original size:16 final size:16
Alignment explanation
Indices: 1033840--1033878 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
1033830 AAGAAAACAA
*
1033840 AAAGAAAATTTG-GAG
1 AAAGAAAAATTGAGAG
1033855 AAAGAAAAATTGAGAG
1 AAAGAAAAATTGAGAG
1033871 AAAGAAAA
1 AAAGAAAA
1033879 GAGGAGTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.13
Consensus pattern (16 bp):
AAAGAAAAATTGAGAG
Found at i:1036104 original size:36 final size:35
Alignment explanation
Indices: 1036059--1036129 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
1036049 TGGCAACTAA
1036059 CTTTGAAAAATGTTTTTCAAAGTTTAGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTAGTAAA-GTTT
*
1036095 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTAGTAAAGTTT
1036130 GGAAATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (35 bp):
CTTTGAAAAATGTTTTTCAAAGTTTAGTAAAGTTT
Found at i:1036921 original size:16 final size:16
Alignment explanation
Indices: 1036898--1036934 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1036888 GAAAAAAATG
*
1036898 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
1036913 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
1036929 AGAAAA
1 AGAAAA
1036935 GAGGATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:1037183 original size:2 final size:2
Alignment explanation
Indices: 1037176--1037201 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1037166 TAAATATAAC
1037176 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
1037202 TATGATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1038501 original size:17 final size:17
Alignment explanation
Indices: 1038479--1038514 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1038469 CCTTATGTGC
1038479 TAGCTTCAATCATATGT
1 TAGCTTCAATCATATGT
1038496 TAGCTTCAATCATATGT
1 TAGCTTCAATCATATGT
1038513 TA
1 TA
1038515 AAATTGCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.42
Consensus pattern (17 bp):
TAGCTTCAATCATATGT
Found at i:1039041 original size:16 final size:16
Alignment explanation
Indices: 1039018--1039054 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1039008 GAAAAAAATG
*
1039018 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
1039033 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
1039049 AGAAAA
1 AGAAAA
1039055 GAGGATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:1040452 original size:17 final size:17
Alignment explanation
Indices: 1040430--1040465 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1040420 CCTTATGTGC
1040430 TAGCTTCAATCATATGT
1 TAGCTTCAATCATATGT
1040447 TAGCTTCAATCATATGT
1 TAGCTTCAATCATATGT
1040464 TA
1 TA
1040466 AAATTGCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.42
Consensus pattern (17 bp):
TAGCTTCAATCATATGT
Found at i:1042532 original size:20 final size:20
Alignment explanation
Indices: 1042496--1042543 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1042486 CAAAGTGACC
*
1042496 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
1042515 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
1042535 TAATTTCAA
1 CAATTTCAA
1042544 GCATAGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:1044130 original size:16 final size:16
Alignment explanation
Indices: 1044107--1044143 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1044097 GAAAAAAATG
*
1044107 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
1044122 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
1044138 AGAAAA
1 AGAAAA
1044144 GAGGATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:1047889 original size:20 final size:20
Alignment explanation
Indices: 1047853--1047900 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1047843 CAAAGTGACC
*
1047853 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
1047872 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
1047892 TAATTTCAA
1 CAATTTCAA
1047901 GCATAGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:1049475 original size:16 final size:16
Alignment explanation
Indices: 1049452--1049488 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1049442 AAAAAAAATG
*
1049452 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
1049467 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
1049483 AGAAAA
1 AGAAAA
1049489 GAGGATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:1053196 original size:20 final size:20
Alignment explanation
Indices: 1053160--1053207 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1053150 CGAAGTGACC
*
1053160 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
1053179 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
1053199 TAATTTCAA
1 CAATTTCAA
1053208 GCATAGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Done.