Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009509.1 Hibiscus syriacus cultivar Beakdansim tig00115291_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: 36199
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Found at i:1161 original size:20 final size:21
Alignment explanation
Indices: 1125--1166 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
1115 TATAAAATAT
*
1125 TATAAATATAGTTTTA-TAAA
1 TATAAATATAGTATTATTAAA
1145 TATAAATATAAG-ATTATTAAA
1 TATAAATAT-AGTATTATTAAA
1166 T
1 T
1167 TTTATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
TATAAATATAGTATTATTAAA
Found at i:1408 original size:26 final size:30
Alignment explanation
Indices: 1379--1445 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
1369 ATTGAAAATC
1379 ATTATATTATTA-AA-A-TAAAG-TATAAT
1 ATTATATTATTATAATATTAAAGATATAAT
*
1405 ATTATATCATTATAATATTAAAGAATATAAT
1 ATTATATTATTATAATATTAAAG-ATATAAT
*
1436 ATCATATTAT
1 ATTATATTAT
1446 AGAATTATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 11 0.33
27 2 0.06
28 1 0.03
29 5 0.15
31 14 0.42
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (30 bp):
ATTATATTATTATAATATTAAAGATATAAT
Found at i:1851 original size:2 final size:2
Alignment explanation
Indices: 1844--1892 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
1834 TTAATTCTTG
*
1844 AT AT AT AT -T AT AT AT AG AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1884 AT AT AT AT A
1 AT AT AT AT A
1893 AAATATTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1902 original size:23 final size:23
Alignment explanation
Indices: 1848--1917 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
1838 TTCTTGATAT
* *
1848 ATATTA-TATATAGATATATATAT
1 ATATTATTATATAAATATATA-AA
*
1871 ATATATATTATATATATATATAAA
1 ATAT-TATTATATAAATATATAAA
*
1895 ATATTATTTTATAAATA-ATAAA
1 ATATTATTATATAAATATATAAA
1917 A
1 A
1918 GTCCTCAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 6 0.15
23 15 0.37
24 7 0.17
25 13 0.32
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (23 bp):
ATATTATTATATAAATATATAAA
Found at i:4596 original size:25 final size:25
Alignment explanation
Indices: 4550--4597 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
4540 ATAAAAGTAC
*
4550 AATATTATATATCATTATAATTAAG
1 AATATTATATATCATTAGAATTAAG
*
4575 AATATTATCATATTA-TAGAATTA
1 AATATTAT-ATATCATTAGAATTA
4598 TGAGTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (25 bp):
AATATTATATATCATTAGAATTAAG
Found at i:11366 original size:2 final size:2
Alignment explanation
Indices: 11359--11387 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11349 TTTAATTCTT
11359 TA 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 TA T
11388 TATTTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23924 original size:12 final size:12
Alignment explanation
Indices: 23903--23967 Score: 62
Period size: 12 Copynumber: 5.4 Consensus size: 12
23893 ATGACTTGAA
23903 TTCTGTTCTGAT
1 TTCTGTTCTGAT
*
23915 TTCTGATCTGGA-
1 TTCTGTTCT-GAT
23927 TTCTGTTCTGAT
1 TTCTGTTCTGAT
* *
23939 ATT-TTTTCTGAA
1 -TTCTGTTCTGAT
*
23951 TTCTGTTTTGAT
1 TTCTGTTCTGAT
23963 TTCTG
1 TTCTG
23968 ATATCTCCGT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 4 0.10
12 34 0.81
13 4 0.10
ACGTcount: A:0.12, C:0.14, G:0.17, T:0.57
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:23929 original size:24 final size:24
Alignment explanation
Indices: 23899--23969 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
23889 ACACATGACT
23899 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATTTCTGATC
* **
23923 TGGATTCTGTTCTGATATT-TTTTC
1 TGAATTCTGTTCTGAT-TTCTGATC
*
23947 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATTTCTGAT
23970 ATCTCCGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 2 0.05
24 34 0.89
25 2 0.05
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.55
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATC
Found at i:25839 original size:37 final size:37
Alignment explanation
Indices: 25763--25839 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
25753 AAATTCGTTA
**
25763 TATAATATTAAAATAAAAGTATAATATTATATATCAT
1 TATAATATTAAAATAAAAGTATAATATTATATAGAAT
* *
25800 TATAATATTAAAGAATATAA-TATCATATTAT-TAGAAT
1 TATAATATT-AA-AATAAAAGTATAATATTATATAGAAT
25837 TAT
1 TAT
25840 GAGTAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
37 16 0.47
38 12 0.35
39 6 0.18
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.42
Consensus pattern (37 bp):
TATAATATTAAAATAAAAGTATAATATTATATAGAAT
Found at i:29479 original size:2 final size:2
Alignment explanation
Indices: 29474--29512 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29464 AAAAATATCT
29474 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
29513 TTCCAAGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30649 original size:16 final size:16
Alignment explanation
Indices: 30616--30650 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30606 CTTTTAATAA
* *
30616 ATTATAATAATTTTTT
1 ATTATAATAATATATT
30632 ATTATAATAATATATT
1 ATTATAATAATATATT
30648 ATT
1 ATT
30651 GATTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTATAATAATATATT
Found at i:30695 original size:26 final size:26
Alignment explanation
Indices: 30666--30733 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 26
30656 TTTTTATTAC
*
30666 TATTGAAAATAATAATATTTTTAAAA
1 TATTGAAAATAATAATATTATTAAAA
*
30692 TATT-AAAA-ACT-ATATTATTAAAA
1 TATTGAAAATAATAATATTATTAAAA
*
30715 TA-AGAATAATATATAATAT
1 TATTGAA-AATA-ATAATAT
30734 AGTAAGGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
23 15 0.45
24 4 0.12
25 5 0.15
26 5 0.15
27 4 0.12
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (26 bp):
TATTGAAAATAATAATATTATTAAAA
Found at i:31346 original size:18 final size:18
Alignment explanation
Indices: 31320--31358 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
31310 ATATATATAT
* *
31320 TATTTTTTTTCTAAAAAA
1 TATTATTTTTATAAAAAA
*
31338 TATTATTTTTATAAATAA
1 TATTATTTTTATAAAAAA
31356 TAT
1 TAT
31359 AAAAGTCCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTATTTTTATAAAAAA
Found at i:34418 original size:13 final size:13
Alignment explanation
Indices: 34389--34456 Score: 85
Period size: 13 Copynumber: 5.7 Consensus size: 13
34379 ATCAACGGTC
34389 AACGGGTCGGGT-
1 AACGGGTCGGGTA
34401 --CGGGTCGGGTA
1 AACGGGTCGGGTA
*
34412 AATGGGTCGGGT-
1 AACGGGTCGGGTA
34424 --CGGGTCGGGTA
1 AACGGGTCGGGTA
34435 AACGGGTCGGGTA
1 AACGGGTCGGGTA
34448 AACGGGTCG
1 AACGGGTCG
34457 TGACCGGTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
10 19 0.40
13 29 0.60
ACGTcount: A:0.16, C:0.16, G:0.50, T:0.18
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:34422 original size:23 final size:23
Alignment explanation
Indices: 34389--34446 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
34379 ATCAACGGTC
34389 AACGGGTCGGGTCGGGTCGGGTA
1 AACGGGTCGGGTCGGGTCGGGTA
*
34412 AATGGGTCGGGTCGGGTCGGGTA
1 AACGGGTCGGGTCGGGTCGGGTA
34435 AACGGGTCGGGT
1 AACGGGTCGGGT
34447 AAACGGGTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.14, C:0.16, G:0.52, T:0.19
Consensus pattern (23 bp):
AACGGGTCGGGTCGGGTCGGGTA
Found at i:34446 original size:5 final size:5
Alignment explanation
Indices: 34391--34433 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
34381 CAACGGTCAA
*
34391 CGGGT CGGGT CGGGT CGGGT AAATGGGT CGGGT CGGGT CGGGT
1 CGGGT CGGGT CGGGT CGGGT ---CGGGT CGGGT CGGGT CGGGT
34434 AAACGGGTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 29 0.88
8 4 0.12
ACGTcount: A:0.07, C:0.16, G:0.56, T:0.21
Consensus pattern (5 bp):
CGGGT
Found at i:35603 original size:24 final size:24
Alignment explanation
Indices: 35569--35641 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
35559 ATACATTACC
*
35569 TGAATTTTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
* *
35593 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
*
35617 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
35641 T
1 T
35642 CTCTGTTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:35609 original size:48 final size:48
Alignment explanation
Indices: 35535--35641 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 48
35525 ATGTTATCTA
* * *
35535 ATTTCTGACT-TGAATTCTGTTATGATA-CATTACCTGAATTTTGTTCTG
1 ATTTCTGA-TATGAATTCTGTTATGATATC-TGACATGAATTCTGTTCTG
* * * *
35583 ATTTCTGATATGGATTCTGTTCTGATATCTGATATGAATTCTGTTTTG
1 ATTTCTGATATGAATTCTGTTATGATATCTGACATGAATTCTGTTCTG
35631 ATTTCTGATAT
1 ATTTCTGATAT
35642 CTCTGTTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 1 0.02
48 48 0.96
49 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (48 bp):
ATTTCTGATATGAATTCTGTTATGATATCTGACATGAATTCTGTTCTG
Done.