Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001869.1 Hibiscus syriacus cultivar Beakdansim tig00003786_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: 52154
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:348 original size:12 final size:13
Alignment explanation
Indices: 331--363 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
321 TTAGAAATAT
331 TTAAGATT-AAGA
1 TTAAGATTCAAGA
343 TTAAGATTCAAGA
1 TTAAGATTCAAGA
356 TTCAAGAT
1 TT-AAGAT
364 AGTAGATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 6 0.32
14 5 0.26
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (13 bp):
TTAAGATTCAAGA
Found at i:552 original size:3 final size:3
Alignment explanation
Indices: 546--570 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
536 GGTGACGACA
546 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
571 GATATTGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:3660 original size:21 final size:21
Alignment explanation
Indices: 3618--3660 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3608 TTTCTGAGTT
* * *
3618 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
3639 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
3660 A
1 A
3661 CGGATATGAA
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:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:3715 original size:66 final size:69
Alignment explanation
Indices: 3640--3791 Score: 238
Period size: 66 Copynumber: 2.2 Consensus size: 69
3630 ACCCATTCAA
* *
3640 GGGGAACCGATACCCCCTCAACGGATATGAATTTCCAGAATACTAGAGGGGAATCGAT-CCCCC-
1 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCCA
3703 A-GG
66 AGGG
* *
3706 GGGGAACCGATACCCCCTCAACGGATATGAAATTCTAGAATGCTAGAGGGGAACCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCCA
3771 AGGG
66 AGGG
*
3775 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
3792 ATGAGAAAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
66 54 0.69
67 5 0.06
68 1 0.01
69 18 0.23
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCCA
AGGG
Found at i:4444 original size:23 final size:23
Alignment explanation
Indices: 4400--4444 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4390 ATTATTATAT
*
4400 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
4423 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
4445 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:10493 original size:21 final size:21
Alignment explanation
Indices: 10451--10493 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
10441 TTTCTGAGTT
* * *
10451 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
10472 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
10493 A
1 A
10494 CGGATATGAA
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:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:10554 original size:67 final size:68
Alignment explanation
Indices: 10473--10623 Score: 250
Period size: 67 Copynumber: 2.2 Consensus size: 68
10463 ACCCATTCAA
* * *
10473 GGGGAACCGATACCCCCTCAACGGATATGAATTTCCAGAATACTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCAA
10538 -GG
66 GGG
*
10540 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCAA
1 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCAA
10605 GGG
66 GGG
*
10608 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
10624 ATGAGAAAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
67 61 0.78
68 17 0.22
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCAA
GGG
Found at i:11371 original size:149 final size:149
Alignment explanation
Indices: 11101--11404 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
11091 GGGTAGAGGG
11101 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
11166 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
*
11231 TATGGCATTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
11250 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
11315 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
11380 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
11399 TCTACG
1 TCTACG
11405 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:11427 original size:23 final size:23
Alignment explanation
Indices: 11383--11427 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11373 ATTATTATAT
*
11383 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
11406 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
11428 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:20612 original size:2 final size:2
Alignment explanation
Indices: 20605--20629 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20595 CAGCACTGCC
20605 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 T
20630 TCATATAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41476 original size:65 final size:65
Alignment explanation
Indices: 41266--41458 Score: 323
Period size: 65 Copynumber: 3.0 Consensus size: 65
41256 AAGCAGCTAT
41266 TTTTTTATTAAAAATAAAATATATCTAAATCAGAACGAATGTTTATGCTCATAATTGTAAATTTA
1 TTTTTTATTAAAAATAAAATATATCTAAATCAGAACGAATGTTTATGCTCATAATTGTAAATTTA
41331 TTTTTTATTAAAAATAAAATATATCTAAATCAGAACGAATGTTTATGCTCATAATTGTAAATTTA
1 TTTTTTATTAAAAATAAAATATATCTAAATCAGAACGAATGTTTATGCTCATAATTGTAAATTTA
* * * * * * *
41396 TTTTTTATTAAAAATAATATATATATAAATTAGAACGAATATTTACGATCATCATTGTAAATT
1 TTTTTTATTAAAAATAAAATATATCTAAATCAGAACGAATGTTTATGCTCATAATTGTAAATT
41459 AAATACATAA
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 121 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (65 bp):
TTTTTTATTAAAAATAAAATATATCTAAATCAGAACGAATGTTTATGCTCATAATTGTAAATTTA
Found at i:41879 original size:23 final size:23
Alignment explanation
Indices: 41827--41891 Score: 84
Period size: 22 Copynumber: 2.9 Consensus size: 23
41817 CAAACGACTG
41827 AAATGTACCATAAA---AGCAGAA
1 AAATGTACCATAAAGGTAG-AGAA
41848 AAATCGTACCATAAAGGTAGAGAA
1 AAAT-GTACCATAAAGGTAGAGAA
41872 AAATGTACCAT-AAGGTAGAG
1 AAATGTACCATAAAGGTAGAG
41892 TTATTAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.10
22 19 0.47
23 7 0.17
24 8 0.20
25 2 0.05
ACGTcount: A:0.51, C:0.12, G:0.20, T:0.17
Consensus pattern (23 bp):
AAATGTACCATAAAGGTAGAGAA
Found at i:41908 original size:7 final size:7
Alignment explanation
Indices: 41896--41946 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
41886 GTAGAGTTAT
41896 TAAAAAA
1 TAAAAAA
41903 TAAAAAA
1 TAAAAAA
* *
41910 TTAAAGA
1 TAAAAAA
*
41917 TAAACAA
1 TAAAAAA
41924 TAATAAAA
1 TAA-AAAA
41932 T-AAAAA
1 TAAAAAA
*
41938 CAAAAAA
1 TAAAAAA
41945 TA
1 TA
41947 CCGACGGTCG
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
6 4 0.12
7 26 0.76
8 4 0.12
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (7 bp):
TAAAAAA
Found at i:41920 original size:21 final size:21
Alignment explanation
Indices: 41896--41946 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
41886 GTAGAGTTAT
*
41896 TAAAAAATAA-AAAATTAAAGA
1 TAAAAAATAATAAAA-TAAAAA
*
41917 TAAACAATAATAAAATAAAAA
1 TAAAAAATAATAAAATAAAAA
*
41938 CAAAAAATA
1 TAAAAAATA
41947 CCGACGGTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (21 bp):
TAAAAAATAATAAAATAAAAA
Found at i:43467 original size:31 final size:30
Alignment explanation
Indices: 43428--43575 Score: 102
Period size: 31 Copynumber: 4.8 Consensus size: 30
43418 GTAAATATTC
*
43428 AAATATTATATAATAATCATTAAAATTTTT
1 AAATATTATAAAATAATCATTAAAATTTTT
* * * * *
43458 AAATAATTATTAATTGATTATT-AAATTTATC
1 AAAT-ATTATAAAATAATCATTAAAATTT-TT
* * *
43489 AAACTATTATAAAATAGTCATTGAACTTTTT
1 AAA-TATTATAAAATAATCATTAAAATTTTT
* * *
43520 AAATAATTATAAAATACTCATT-AAATTGATC
1 AAAT-ATTATAAAATAATCATTAAAATT-TTT
**
43551 AAATTATTATAAAATGGTCATTAAA
1 AAA-TATTATAAAATAATCATTAAA
43576 CTTATCAAAA
Statistics
Matches: 91, Mismatches: 19, Indels: 14
0.73 0.15 0.11
Matches are distributed among these distances:
30 15 0.16
31 67 0.74
32 9 0.10
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (30 bp):
AAATATTATAAAATAATCATTAAAATTTTT
Found at i:43519 original size:62 final size:61
Alignment explanation
Indices: 43426--43578 Score: 191
Period size: 62 Copynumber: 2.5 Consensus size: 61
43416 AAGTAAATAT
* * * * * * *
43426 TCAAATATTATATAATAATCATTAAAATTTTTAAATAATTATTAATTGA-TTATTAAATTTA
1 TCAAATATTATAAAATAGTCATTAAACTTTTTAAATAATTATAAAAT-ACTCATTAAATTGA
*
43487 TCAAACTATTATAAAATAGTCATTGAACTTTTTAAATAATTATAAAATACTCATTAAATTGA
1 TCAAA-TATTATAAAATAGTCATTAAACTTTTTAAATAATTATAAAATACTCATTAAATTGA
*
43549 TCAAATTATTATAAAATGGTCATTAAACTT
1 TCAAA-TATTATAAAATAGTCATTAAACTT
43579 ATCAAAATTT
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
61 6 0.08
62 73 0.92
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (61 bp):
TCAAATATTATAAAATAGTCATTAAACTTTTTAAATAATTATAAAATACTCATTAAATTGA
Found at i:43583 original size:31 final size:31
Alignment explanation
Indices: 43477--43593 Score: 128
Period size: 31 Copynumber: 3.7 Consensus size: 31
43467 TTAATTGATT
* *
43477 ATTAAATTTATCAAACTATTATAAAATAGTC
1 ATTAAACTTATCAAATTATTATAAAATAGTC
* * * * *
43508 ATTGAACTTTTTAAATAATTATAAAATACTC
1 ATTAAACTTATCAAATTATTATAAAATAGTC
*
43539 ATTAAA-TTGATCAAATTATTATAAAATGGTC
1 ATTAAACTT-ATCAAATTATTATAAAATAGTC
43570 ATTAAACTTATCAAAATTTATTAT
1 ATTAAACTTATC-AAA-TTATTAT
43594 TATTTATAAT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
30 2 0.03
31 55 0.80
32 5 0.07
33 7 0.10
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (31 bp):
ATTAAACTTATCAAATTATTATAAAATAGTC
Found at i:44813 original size:2 final size:2
Alignment explanation
Indices: 44808--44835 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44798 CCCCATCTTA
44808 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
44836 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:44840 original size:2 final size:2
Alignment explanation
Indices: 44835--44879 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
44825 TCTCTCTCTC
44835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44877 TA T
1 TA T
44880 GGGATAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.