Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005082.1 Hibiscus syriacus cultivar Beakdansim tig00011413_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: 29551
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:312 original size:19 final size:19
Alignment explanation
Indices: 274--313 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
264 CTGCAAAACG
* **
274 AAGCATCAACACACCGAAA
1 AAGCATCAAAACACAAAAA
293 AAGCATCAAAACACAAAAA
1 AAGCATCAAAACACAAAAA
312 AA
1 AA
314 AACAAGCATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.25, G:0.07, T:0.05
Consensus pattern (19 bp):
AAGCATCAAAACACAAAAA
Found at i:1690 original size:32 final size:31
Alignment explanation
Indices: 1652--1736 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
1642 AAAAAGTTCG
* *
1652 GGGCCACGGGGCCTACCTAAGAACACATCTTA
1 GGGCCACAGGGCCTACCTAAGAACA-ATCTCA
* *
1684 GGGCCACAGGGCCTACCCAAGAATAATCTCA
1 GGGCCACAGGGCCTACCTAAGAACAATCTCA
* *
1715 GGGCCGCAGAGCCTACCTAAGA
1 GGGCCACAGGGCCTACCTAAGA
1737 GTCACATTAG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 24 0.52
32 22 0.48
ACGTcount: A:0.29, C:0.32, G:0.26, T:0.13
Consensus pattern (31 bp):
GGGCCACAGGGCCTACCTAAGAACAATCTCA
Found at i:12483 original size:10 final size:10
Alignment explanation
Indices: 12464--12727 Score: 174
Period size: 8 Copynumber: 29.9 Consensus size: 10
12454 CGAGACCTTT
12464 TATA-ATATA
1 TATATATATA
12473 TATATATATA
1 TATATATATA
*
12483 T-TATTTAGTA
1 TATATATA-TA
*
12493 TA-ATGTATA
1 TATATATATA
12502 T-TATATAGTA
1 TATATATA-TA
12512 TAT-TATATA
1 TATATATATA
*
12521 -AGATA-ATA
1 TATATATATA
12529 T-TATATAGTA
1 TATATATA-TA
*
12539 TATTTATATA
1 TATATATATA
12549 T-TATAT-TA
1 TATATATATA
12557 TATAGTATAT-
1 TATA-TATATA
12567 TAT-TATATA
1 TATATATATA
12576 T-TATAT-TA
1 TATATATATA
*
12584 TATTTATAT-
1 TATATATATA
12593 TATAT-TATA
1 TATATATATA
12602 T-TATAT-TA
1 TATATATATA
12610 TAT-TATATA
1 TATATATATA
12619 TATAT-TATA
1 TATATATATA
12628 T-TATAT-TA
1 TATATATATA
12636 TAT-TATATA
1 TATATATATA
12645 TAT-TATAT-
1 TATATATATA
12653 TATAT-TATA
1 TATATATATA
12662 T-TATAT-TA
1 TATATATATA
12670 TAT-TATAT-
1 TATATATATA
12678 TATAT-TATA
1 TATATATATA
12687 T-TATAT-TA
1 TATATATATA
12695 TAT-TATAT-
1 TATATATATA
12703 TATAT-TATA
1 TATATATATA
12712 T-TATAT-TA
1 TATATATATA
12720 TAT-TATAT
1 TATATATAT
12728 TACATTACAT
Statistics
Matches: 205, Mismatches: 9, Indels: 82
0.69 0.03 0.28
Matches are distributed among these distances:
8 85 0.41
9 79 0.39
10 34 0.17
11 7 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
TATATATATA
Found at i:12519 original size:5 final size:5
Alignment explanation
Indices: 12463--12817 Score: 357
Period size: 5 Copynumber: 70.2 Consensus size: 5
12453 TCGAGACCTT
*
12463 TTATA ATATA -TATA TATATA TTAT- TTAGTA -TA-A TGTATA TTATA
1 TTATA TTATA TTATA T-TATA TTATA TTA-TA TTATA T-TATA TTATA
* * *
12507 TAGTATA TTATA TAAGA TAATA TTATA TAGTATA TT-TA -TATA TTATA
1 T--TATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA
12554 TTATA TAGTATA TTAT- TATATA TTATA TTATA TTTATA TTATA TTATA
1 TTATA T--TATA TTATA T-TATA TTATA TTATA -TTATA TTATA TTATA
12602 TTATA TTATA TTATA TATATA TTATA TTATA TTATA TTATA -TATA TTATA
1 TTATA TTATA TTATA T-TATA TTATA TTATA TTATA TTATA TTATA TTATA
12652 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * * *
12702 TTATA TTATA TTATA TTATA TTATA TTACA TTACA TTACA TTACA TTACA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * * * * * * * *
12752 TTACA TTACA TTACA TTACA TTACA TTACA TTACA TTACA TTACA TTACA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* *
12802 TTACA TTACA TTATA T
1 TTATA TTATA TTATA T
12818 ATTCAAGTAA
Statistics
Matches: 323, Mismatches: 7, Indels: 40
0.87 0.02 0.11
Matches are distributed among these distances:
3 2 0.01
4 16 0.05
5 272 0.84
6 18 0.06
7 15 0.05
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (5 bp):
TTATA
Found at i:16228 original size:16 final size:16
Alignment explanation
Indices: 16140--16239 Score: 53
Period size: 16 Copynumber: 6.2 Consensus size: 16
16130 GTTTGAACCA
*
16140 AAAATAATCCGAATCG
1 AAAACAATCCGAATCG
* *
16156 AAAGCAA-CTCGAA-CAA
1 AAAACAATC-CGAATC-G
** *
16172 AAAACAATCATAACCG
1 AAAACAATCCGAATCG
* *
16188 AAAATAAACCGAATC-
1 AAAACAATCCGAATCG
*
16203 AAAATTAATCCGAATCG
1 AAAA-CAATCCGAATCG
* *
16220 AAAACAATCTGAACCG
1 AAAACAATCCGAATCG
16236 AAAA
1 AAAA
16240 TAACCTGAAC
Statistics
Matches: 62, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
15 6 0.10
16 50 0.81
17 6 0.10
ACGTcount: A:0.55, C:0.21, G:0.10, T:0.14
Consensus pattern (16 bp):
AAAACAATCCGAATCG
Found at i:16535 original size:36 final size:33
Alignment explanation
Indices: 16451--16541 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
16441 AATAGTTAAT
* * *
16451 TACCACCTTTGATAATAGTTTAGTAACCATCAG
1 TACCACATTTGATAATAATTTAATAACCATCAG
16484 TACCACATTTGATAATAATTTAATAACCA-CTAG
1 TACCACATTTGATAATAATTTAATAACCATC-AG
*
16517 TACCACGTTTGATAATAATTTAATA
1 TACCACATTTGATAATAATTTAATA
16542 GTTTATTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 1 0.02
33 52 0.98
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (33 bp):
TACCACATTTGATAATAATTTAATAACCATCAG
Found at i:16821 original size:17 final size:17
Alignment explanation
Indices: 16778--16822 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
16768 ATTTTTTTAC
*
16778 GAACACAAAATAACATG
1 GAACACAAATTAACATG
16795 GAACACAAATTAACAT-
1 GAACACAAATTAACATG
16811 GAGACACAAATT
1 GA-ACACAAATT
16823 TTAAATAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 2 0.08
17 24 0.92
ACGTcount: A:0.56, C:0.18, G:0.11, T:0.16
Consensus pattern (17 bp):
GAACACAAATTAACATG
Found at i:16934 original size:20 final size:19
Alignment explanation
Indices: 16899--16940 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
16889 ACAAAGTTAA
16899 AAATTTTAATAAAAATATT
1 AAATTTTAATAAAAATATT
*
16918 AAATTTATAATACAAATATT
1 AAATTT-TAATAAAAATATT
16938 AAA
1 AAA
16941 AATTTACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTTTAATAAAAATATT
Found at i:18372 original size:18 final size:19
Alignment explanation
Indices: 18335--18372 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
18325 CACGGAATGT
*
18335 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GAGAATAA
18355 AAGATTACCA-GAGAATAA
1 AAGATTACCAGGAGAATAA
18373 GATTACTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.11, G:0.21, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGAGAATAA
Found at i:18544 original size:15 final size:15
Alignment explanation
Indices: 18526--18556 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18516 AAATTCTAAA
18526 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
18541 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
18556 T
1 T
18557 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:23723 original size:10 final size:10
Alignment explanation
Indices: 23701--23733 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
23691 ATGCTTCATT
23701 TATTTGTTA-G
1 TATTT-TTATG
23711 TATTTTTATG
1 TATTTTTATG
23721 TATTTTTATG
1 TATTTTTATG
23731 TAT
1 TAT
23734 CTCGCTCGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 3 0.14
10 19 0.86
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (10 bp):
TATTTTTATG
Found at i:23951 original size:22 final size:22
Alignment explanation
Indices: 23923--23967 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
23913 CTTCAATTTT
23923 CTACTCGAATTTGCAAGTTCCA
1 CTACTCGAATTTGCAAGTTCCA
23945 CTACTCGAATTTGCAAGTTCCA
1 CTACTCGAATTTGCAAGTTCCA
23967 C
1 C
23968 ATTTAAGACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (22 bp):
CTACTCGAATTTGCAAGTTCCA
Found at i:24113 original size:15 final size:17
Alignment explanation
Indices: 24083--24114 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
24073 ACACCGATTA
24083 ATTTTTATCTTTAAAAT
1 ATTTTTATCTTTAAAAT
24100 ATTTTT-TC-TTAAAAT
1 ATTTTTATCTTTAAAAT
24115 TACTTTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTTATCTTTAAAAT
Done.