Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004653.1 Hibiscus syriacus cultivar Beakdansim tig00010429_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: 85060
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1402 original size:17 final size:17
Alignment explanation
Indices: 1380--1412 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1370 CAGCACAATA
*
1380 TGAAATATTTTAAATTT
1 TGAAATATTTAAAATTT
1397 TGAAATATTTAAAATT
1 TGAAATATTTAAAATT
1413 ATGAGGTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
TGAAATATTTAAAATTT
Found at i:2472 original size:21 final size:21
Alignment explanation
Indices: 2448--2492 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2438 TTAGTAAAAA
**
2448 TTTATTTAAAATATTTTTATT
1 TTTATTTAAAATATTAATATT
2469 TTTATTTAAAATATTAATATT
1 TTTATTTAAAATATTAATATT
2490 TTT
1 TTT
2493 TAATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTATTTAAAATATTAATATT
Found at i:6099 original size:2 final size:2
Alignment explanation
Indices: 6092--6118 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6082 CAACAAACCC
6092 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
6119 GTGTGTGTGT
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:10296 original size:26 final size:27
Alignment explanation
Indices: 10238--10314 Score: 95
Period size: 26 Copynumber: 2.8 Consensus size: 27
10228 ATGCCATTAC
10238 TGTAATTTATAAAATATAAT-TTCTTTTTAT
1 TGTAATTTATAAAA-A-AATGTTC--TTTAT
*
10268 TGTAATTTA-CAAAAAATGTTCTTTAT
1 TGTAATTTATAAAAAAATGTTCTTTAT
10294 TGTAATTTATAAAAAAATGTT
1 TGTAATTTATAAAAAAATGTT
10315 GTCCTTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
26 14 0.33
27 13 0.30
28 4 0.09
29 3 0.07
30 9 0.21
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (27 bp):
TGTAATTTATAAAAAAATGTTCTTTAT
Found at i:10324 original size:30 final size:28
Alignment explanation
Indices: 10238--10333 Score: 90
Period size: 30 Copynumber: 3.4 Consensus size: 28
10228 ATGCCATTAC
*
10238 TGTAATTTATAAAATATAAT-TTCTTTTTAT
1 TGTAATTTATAAAA-A-AATGTT-TCTTTAT
*
10268 TGTAATTTA-CAAAAAATG-TTCTTTAT
1 TGTAATTTATAAAAAAATGTTTCTTTAT
10294 TGTAATTTATAAAAAAATGTTGTCCTTTAT
1 TGTAATTTATAAAAAAATGTT-T-CTTTAT
* *
10324 TATAAATTAT
1 TGTAATTTAT
10334 GGAAATTTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
26 15 0.27
27 12 0.21
28 2 0.04
29 4 0.07
30 23 0.41
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (28 bp):
TGTAATTTATAAAAAAATGTTTCTTTAT
Found at i:24679 original size:16 final size:17
Alignment explanation
Indices: 24658--24693 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
24648 ATTTATTATT
24658 AAATTCCTAATTTTT-A
1 AAATTCCTAATTTTTCA
*
24674 AAATTCCTTATTTTTCA
1 AAATTCCTAATTTTTCA
24691 AAA
1 AAA
24694 ATTTCTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCCTAATTTTTCA
Found at i:26189 original size:13 final size:13
Alignment explanation
Indices: 26171--26196 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26161 GGGTGCTAAC
26171 TGCTAAGGAATGT
1 TGCTAAGGAATGT
26184 TGCTAAGGAATGT
1 TGCTAAGGAATGT
26197 GTTGAAGCTT
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:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (13 bp):
TGCTAAGGAATGT
Found at i:28822 original size:22 final size:22
Alignment explanation
Indices: 28794--28845 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
28784 TGTGATAATT
*
28794 GAACCCAACCTGATATGAACCC
1 GAACCCAACATGATATGAACCC
*
28816 GAACCCAACATGATATGAACTC
1 GAACCCAACATGATATGAACCC
28838 GAACCCAA
1 GAACCCAA
28846 GATTAACTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.33, G:0.13, T:0.13
Consensus pattern (22 bp):
GAACCCAACATGATATGAACCC
Found at i:30643 original size:4 final size:4
Alignment explanation
Indices: 30634--30659 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
30624 TTATATTTTC
30634 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
30660 TTTAGTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:31503 original size:2 final size:2
Alignment explanation
Indices: 31498--31531 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
31488 TTTCTTTGAT
*
31498 TA TA TA TA TA TA TA CA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31532 TATTTTGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31584 original size:21 final size:21
Alignment explanation
Indices: 31542--31584 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
31532 TATTTTGATA
* *
31542 TTATGTTTTATATTTATAAAT
1 TTATGTTTGATATATATAAAT
* *
31563 TTATGTTTGGTATATATTAAT
1 TTATGTTTGATATATATAAAT
31584 T
1 T
31585 AATTCAAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.60
Consensus pattern (21 bp):
TTATGTTTGATATATATAAAT
Found at i:34672 original size:23 final size:22
Alignment explanation
Indices: 34594--34680 Score: 70
Period size: 23 Copynumber: 4.0 Consensus size: 22
34584 CAACTCGTAA
*
34594 TTTGCACCGAAGTGCCACATA-
1 TTTGAACCGAAGTGCCACATAG
* ** *
34615 ATTGTTCCAAAG-GACCACATAG
1 TTTGAACCGAAGTG-CCACATAG
*
34637 TTTGCACCGAAGTGCCACATAGG
1 TTTGAACCGAAGTGCCACATA-G
**
34660 TTTGAACTTAAGTGCCACATA
1 TTTGAACCGAAGTGCCACATA
34681 TTTATTTCGA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.02
21 15 0.29
22 15 0.29
23 20 0.39
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (22 bp):
TTTGAACCGAAGTGCCACATAG
Found at i:34901 original size:21 final size:21
Alignment explanation
Indices: 34857--34907 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
34847 CATAGAGTCT
***
34857 GTTCACATTCACTGATTTGGA
1 GTTCACATTCACTGATTCAAA
34878 GTTCACATTCACTGATTCAAA
1 GTTCACATTCACTGATTCAAA
34899 GTTCACATT
1 GTTCACATT
34908 TTCATATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (21 bp):
GTTCACATTCACTGATTCAAA
Found at i:35451 original size:20 final size:21
Alignment explanation
Indices: 35426--35483 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 21
35416 ATGTTTTAAG
*
35426 GGTATCGATACCATCCTT-CA
1 GGTATCGATACCACCCTTACA
*
35446 GGTATCGATACTACCCTTACA
1 GGTATCGATACCACCCTTACA
*
35467 -GTATCGATACTACCCTT
1 GGTATCGATACCACCCTT
35484 GCAAAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 33 0.94
21 2 0.06
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (21 bp):
GGTATCGATACCACCCTTACA
Found at i:40339 original size:2 final size:2
Alignment explanation
Indices: 40332--40357 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40322 ATCAACACAA
40332 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
40358 TAAAAAATGG
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:51412 original size:17 final size:17
Alignment explanation
Indices: 51390--51424 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
51380 AATTTCTAAT
*
51390 CATACCCGTGCCGGACA
1 CATACCCGTGCCCGACA
*
51407 CATACCTGTGCCCGACA
1 CATACCCGTGCCCGACA
51424 C
1 C
51425 TTGCACCCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.43, G:0.20, T:0.14
Consensus pattern (17 bp):
CATACCCGTGCCCGACA
Found at i:53093 original size:55 final size:55
Alignment explanation
Indices: 53005--53114 Score: 166
Period size: 55 Copynumber: 2.0 Consensus size: 55
52995 GAGAAATAGT
* * *
53005 ATTCTGCAGTCTATATGAATACATTCTCGTGAATTTCTTATTTCCGGCCGGTATC
1 ATTCTGCAGTCTATATGAATACATCCACATGAATTTCTTATTTCCGGCCGGTATC
* * *
53060 ATTCTGCAGTTTATATGAATACATCCACATGAATTTCTTATTTCTGGCTGGTATC
1 ATTCTGCAGTCTATATGAATACATCCACATGAATTTCTTATTTCCGGCCGGTATC
53115 TTGTATCCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (55 bp):
ATTCTGCAGTCTATATGAATACATCCACATGAATTTCTTATTTCCGGCCGGTATC
Found at i:54327 original size:49 final size:49
Alignment explanation
Indices: 54247--54347 Score: 139
Period size: 49 Copynumber: 2.1 Consensus size: 49
54237 AATTCCGGCA
* * * *
54247 TCCTGTACAGCAACTTTTAAGAATTCGGGCCAGATGTACGTTTTTCTTC
1 TCCTGTACAGCAACGTTTAAAAACTCAGGCCAGATGTACGTTTTTCTTC
* * *
54296 TCCTGTCCGGCAACGTTTAAAAACTCAGGCCAGGTGTACGTTTTTCTTC
1 TCCTGTACAGCAACGTTTAAAAACTCAGGCCAGATGTACGTTTTTCTTC
54345 TCC
1 TCC
54348 GATCGTCGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (49 bp):
TCCTGTACAGCAACGTTTAAAAACTCAGGCCAGATGTACGTTTTTCTTC
Found at i:57772 original size:2 final size:2
Alignment explanation
Indices: 57765--57807 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
57755 TTAACATCTC
57765 AT AT AT AT AT AT 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
57807 A
1 A
57808 AGTAATTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:67538 original size:24 final size:24
Alignment explanation
Indices: 67503--67568 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 24
67493 TGGCGGGAAG
*
67503 TTCGTTCATTTATGTTTATTTATA
1 TTCGTTCGTTTATGTTTATTTATA
** *
67527 TTCGTTCGTTTATGTTCGTTTATG
1 TTCGTTCGTTTATGTTTATTTATA
* *
67551 TGCTTTCGTTTATGTTTA
1 TTCGTTCGTTTATGTTTA
67569 GCCTAATATC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.14, C:0.11, G:0.15, T:0.61
Consensus pattern (24 bp):
TTCGTTCGTTTATGTTTATTTATA
Found at i:67749 original size:10 final size:10
Alignment explanation
Indices: 67734--67758 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
67724 AATATTTTCA
67734 TTTATGTTTG
1 TTTATGTTTG
67744 TTTATGTTTG
1 TTTATGTTTG
67754 TTTAT
1 TTTAT
67759 TGTGTTCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (10 bp):
TTTATGTTTG
Found at i:72624 original size:18 final size:18
Alignment explanation
Indices: 72600--72649 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
72590 TTGGTAATAA
72600 AATTAAAATAATAAAAGC
1 AATTAAAATAATAAAAGC
*
72618 GATT-AAATAAGTAAAAGC
1 AATTAAAATAA-TAAAAGC
*
72636 AATTAAAGTAATAA
1 AATTAAAATAATAA
72650 TAAGAAGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 6 0.22
18 16 0.59
19 5 0.19
ACGTcount: A:0.62, C:0.04, G:0.10, T:0.24
Consensus pattern (18 bp):
AATTAAAATAATAAAAGC
Found at i:84678 original size:26 final size:28
Alignment explanation
Indices: 84630--84681 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
84620 CATAAAATTA
84630 TGAAATTTTATAAGTTTAAATTCGTTCT
1 TGAAATTTTATAAGTTTAAATTCGTTCT
*
84658 TGAAA-TTT-TAAGTTTATATTCGTT
1 TGAAATTTTATAAGTTTAAATTCGTT
84682 TCCTTAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 15 0.65
27 3 0.13
28 5 0.22
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.52
Consensus pattern (28 bp):
TGAAATTTTATAAGTTTAAATTCGTTCT
Done.