Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006992.1 Hibiscus syriacus cultivar Beakdansim tig00018030_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: 58118
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:344 original size:175 final size:177
Alignment explanation
Indices: 1--418 Score: 632
Period size: 175 Copynumber: 2.4 Consensus size: 177
* * **
1 ATGTATTGATCCATAACAATA-AACATGTCAAAA-ATGACAAAACCGGTCTATAAATGACAAAAC
1 ATGTATCGATCCATAACAATATAACAGGT-AAAATATGACAAAACCGGTCTCGAAATGACAAAAC
* ** *
64 AGGTAAAGCGCTACCGGATGTTGATAGTGTCGATACTTTATTATAGGTATCGACACTTTTGGAAT
65 CGGTAAAAAGCTACCGGATGTTGATAGTGTCGATACTTTACTATA-G-ATCGACACTTTTGGAAT
* * *
129 TTAAAAGAGAATAAGTTATAGCGCTAATAAAGTGTCGATACTTTATAAAA
128 TTAAAAGAAAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAA
179 ATGTATCGATCCATAACAATATAACAGGTAAAATATGAC-AAACCGGTCTCGAAATGACAAAACC
1 ATGTATCGATCCATAACAATATAACAGGTAAAATATGACAAAACCGGTCTCGAAATGACAAAACC
*
243 GGTAAAAAGGTACCGGATTGTTGATAGTGTCGATACTTTACTATA-ATCGACAC-TTTGGAATTT
66 GGTAAAAAGCTACCGGA-TGTTGATAGTGTCGATACTTTACTATAGATCGACACTTTTGGAATTT
306 AAAAGAAAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAA
130 AAAAGAAAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAA
* *
354 ATGTATCGATCCATAACAATAT-ACAGGTAAAATATGACAAAATCGATCTCGAAATGACAAAACC
1 ATGTATCGATCCATAACAATATAACAGGTAAAATATGACAAAACCGGTCTCGAAATGACAAAACC
418 G
66 G
419 ATAGTAAAAA
Statistics
Matches: 222, Mismatches: 14, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
174 16 0.07
175 101 0.45
176 8 0.04
178 60 0.27
179 37 0.17
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (177 bp):
ATGTATCGATCCATAACAATATAACAGGTAAAATATGACAAAACCGGTCTCGAAATGACAAAACC
GGTAAAAAGCTACCGGATGTTGATAGTGTCGATACTTTACTATAGATCGACACTTTTGGAATTTA
AAAGAAAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAA
Found at i:3603 original size:60 final size:59
Alignment explanation
Indices: 3471--3609 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 59
3461 TAAATATTTT
*** * **
3471 AATTTCATCCCTAAACTATGAATATCATTCTAAATTAGTCTTTACACTTTTGAACATTTG
1 AATTTCATCCC-AAACTATGAATATCATTCTAAATTAGTCCCCAAACTTTTGAACATTCC
* *
3531 AATTTCATTCCCAAACTATGACCT-TCATTCTAAATTAGTCCCCAAACATTTTTAACATTCC
1 AATTTCA-TCCCAAACTATGA-ATATCATTCTAAATTAGTCCCCAAAC-TTTTGAACATTCC
*
3592 AATTTTATCCCAAACTAT
1 AATTTCATCCCAAACTAT
3610 ACGTATATAC
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
60 46 0.69
61 21 0.31
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (59 bp):
AATTTCATCCCAAACTATGAATATCATTCTAAATTAGTCCCCAAACTTTTGAACATTCC
Found at i:4676 original size:13 final size:13
Alignment explanation
Indices: 4658--4683 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4648 TTGAGTCATA
4658 TACAAATAATATT
1 TACAAATAATATT
4671 TACAAATAATATT
1 TACAAATAATATT
4684 ATAGTCCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TACAAATAATATT
Found at i:7280 original size:19 final size:19
Alignment explanation
Indices: 7256--7301 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
7246 TTTTGTGTAC
7256 CGATGCACATACCATGCAT
1 CGATGCACATACCATGCAT
7275 CGATGCACATACCATGCAT
1 CGATGCACATACCATGCAT
7294 CGATGCAC
1 CGATGCAC
7302 TCCTGGCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (19 bp):
CGATGCACATACCATGCAT
Found at i:13148 original size:44 final size:44
Alignment explanation
Indices: 13066--13168 Score: 163
Period size: 44 Copynumber: 2.4 Consensus size: 44
13056 TTGTGCAAAG
13066 TGCATCGATACACTA-GAAAGTGTACCGATACATCCCTTGAATA
1 TGCATCGATACACTATGAAAGTGTACCGATACATCCCTTGAATA
* * * *
13109 TGCATCGATACACTATGAAGGTGTACCGATGCATTCCTTGAATG
1 TGCATCGATACACTATGAAAGTGTACCGATACATCCCTTGAATA
13153 TGCATCGATACACTAT
1 TGCATCGATACACTAT
13169 ACAATGTATC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
43 15 0.27
44 40 0.73
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (44 bp):
TGCATCGATACACTATGAAAGTGTACCGATACATCCCTTGAATA
Found at i:15729 original size:19 final size:19
Alignment explanation
Indices: 15705--15750 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
15695 TTTTGTGTAC
15705 CGATGCACATACCATGCAT
1 CGATGCACATACCATGCAT
15724 CGATGCACATACCATGCAT
1 CGATGCACATACCATGCAT
15743 CGATGCAC
1 CGATGCAC
15751 TCATGGCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (19 bp):
CGATGCACATACCATGCAT
Found at i:18058 original size:20 final size:20
Alignment explanation
Indices: 18033--18072 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18023 TATCCGCCTG
18033 CATCCTTTTGTACCCGTCCA
1 CATCCTTTTGTACCCGTCCA
18053 CATCCTTTTGTACCCGTCCA
1 CATCCTTTTGTACCCGTCCA
18073 TACTTGTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.40, G:0.10, T:0.35
Consensus pattern (20 bp):
CATCCTTTTGTACCCGTCCA
Found at i:18416 original size:33 final size:33
Alignment explanation
Indices: 18379--18442 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
18369 TCTTCCATCC
18379 TTACTTAAGGTTATGTATTATGTGACTGATTCT
1 TTACTTAAGGTTATGTATTATGTGACTGATTCT
* *
18412 TTACTTGAGGTTATGTATTATGTGATTGATT
1 TTACTTAAGGTTATGTATTATGTGACTGATT
18443 ATTTTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.06, G:0.20, T:0.50
Consensus pattern (33 bp):
TTACTTAAGGTTATGTATTATGTGACTGATTCT
Found at i:25591 original size:21 final size:21
Alignment explanation
Indices: 25546--25593 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
25536 TTTATCCGGA
*
25546 AAAAAATCCGATCTAGGGTTT
1 AAAAAATCCGATCTAGGATTT
*
25567 -AAAAATCCGGTCT-GAGATTT
1 AAAAAATCCGATCTAG-GATTT
25587 AAAAAAT
1 AAAAAAT
25594 TGGATGACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 16 0.70
21 6 0.26
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (21 bp):
AAAAAATCCGATCTAGGATTT
Found at i:30553 original size:36 final size:36
Alignment explanation
Indices: 30503--30611 Score: 139
Period size: 36 Copynumber: 3.1 Consensus size: 36
30493 GAAGGTGAAT
* *
30503 AAGAAGAACAAAAGGAAGCATCGGCACTTTCGATTC
1 AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTC
*
30539 AAGAAGAACGAAAGGAAGCATCAGCACTTTTGATTC
1 AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTC
* ** * *
30575 AAG-TGAACGGGAGGAAGCATAAGCACTTTCTATTC
1 AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTC
30610 AA
1 AA
30612 TTGTTCATCT
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
35 28 0.44
36 36 0.56
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (36 bp):
AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTC
Found at i:31534 original size:2 final size:2
Alignment explanation
Indices: 31527--31553 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31517 CATTTTATGT
31527 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
31554 TGTCAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45227 original size:112 final size:111
Alignment explanation
Indices: 44993--45270 Score: 439
Period size: 112 Copynumber: 2.5 Consensus size: 111
44983 ACAAATAAAA
* *
44993 AAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAATTGTATC
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAATGTATC
* *
45058 GATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTAT
66 GATCCATAACAATAAAACAGGTAAAAAAATGACAAAACCGATCTAT
* *
45104 AAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATATTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAT-AAAATGTAT
* *
45169 CGATCTATAACAATAAAACAGGTAAAAAAATGACAAAACTGATCTAT
65 CGATCCATAACAATAAAACAGGTAAAAAAATGACAAAACCGATCTAT
* * * *
45216 AAATTACAAAACAGATAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAT
45271 TATAAGTATC
Statistics
Matches: 152, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
111 52 0.34
112 100 0.66
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (111 bp):
AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAATGTATC
GATCCATAACAATAAAACAGGTAAAAAAATGACAAAACCGATCTAT
Found at i:45446 original size:181 final size:182
Alignment explanation
Indices: 45141--45592 Score: 721
Period size: 181 Copynumber: 2.5 Consensus size: 182
45131 AGATATATTG
* * *
45141 AAAGTGTCGATATTTTATAAAAATGTATCGATCTATAACAATAAAACAGGTAAAAAAATGACAAA
1 AAAGTGTCGATATTTTAT-AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
45206 A-CTGATCTATAAATTACAAAA-CAGATAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTT
65 ATC-GATCTAGAAATGACAAAACCAGATAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTT
* *
45269 ATTATAAGTATCGACACTTTTAGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
129 ATTATAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
45323 AAAGTGTCGATATTTTATAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA
1 AAAGTGTCGATATTTTATAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA
* * *
45388 TCGGTCTCGAAATGATAAAACCAG-TAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 TCGATCTAGAAATGACAAAACCAGATAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
* *
45452 TATAAGTATCGACACTTTTGGAATTTAAAATAAAAGAAGTTATAGCGCCAAT
131 TATAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
* *
45504 AAAGTGTCGATACTTTATAAAATTGTATCGATCCATAATAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATATTTTATAAAA-TGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
45569 ATCGATCTAGAAATGACAAAACCA
65 ATCGATCTAGAAATGACAAAACCA
45593 ATAGTAAAAA
Statistics
Matches: 249, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
181 165 0.66
182 84 0.34
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (182 bp):
AAAGTGTCGATATTTTATAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA
TCGATCTAGAAATGACAAAACCAGATAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
Found at i:47909 original size:12 final size:13
Alignment explanation
Indices: 47892--47920 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
47882 GTGTTATTAG
47892 TATTTTA-TTATT
1 TATTTTATTTATT
47904 TATTTTATTTATT
1 TATTTTATTTATT
47917 TATT
1 TATT
47921 ATATATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTATTTATT
Found at i:47977 original size:2 final size:2
Alignment explanation
Indices: 47967--48008 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
47957 TTACAAGTTA
* *
47967 AT AT TT AT AT AA AT 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 AT AT AT AT AT AT AT
48009 GTTTTTATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.