Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004560.1 Hibiscus syriacus cultivar Beakdansim tig00010136_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: 80755
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:2397 original size:59 final size:59
Alignment explanation
Indices: 2276--2388 Score: 181
Period size: 59 Copynumber: 1.9 Consensus size: 59
2266 TCAGGATTGT
* **
2276 ACTAAAGGATAAATAGTGCATATGGTGGGCACGACCTTATGTGTCATATTCGGGACTAC
1 ACTAAAGGATAAATAGTGCATATCGTGGGCACGACCTTATGTGTCATATTCAAGACTAC
* *
2335 ACTAAAGTATAACTAGTGCATATCGTGGGCACGACCTTATGTGTCATATTCAAG
1 ACTAAAGGATAAATAGTGCATATCGTGGGCACGACCTTATGTGTCATATTCAAG
2389 TTAGCACTAC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (59 bp):
ACTAAAGGATAAATAGTGCATATCGTGGGCACGACCTTATGTGTCATATTCAAGACTAC
Found at i:2851 original size:14 final size:13
Alignment explanation
Indices: 2832--2866 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2822 TCGAATACCT
2832 AAAAATACATTTTA
1 AAAAATA-ATTTTA
2846 AAAAATAATTTTA
1 AAAAATAATTTTA
*
2859 AAAGATAA
1 AAAAATAA
2867 AAAAGGATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (13 bp):
AAAAATAATTTTA
Found at i:5641 original size:135 final size:135
Alignment explanation
Indices: 4974--5624 Score: 740
Period size: 135 Copynumber: 4.8 Consensus size: 135
4964 TCAAATTAGA
* * * * * **
4974 AATCTGCTCCACTATTTTTTAGGGGAGATCAGACTCGAG--AAATTTTGATCCACTTTGCTGCTC
1 AATCTGCTCCGCTACTCTTTAAGGGAGATCAGACTCGAGAAAAAATTTGATCCACTTCACTGCTC
* * * * * * * *
5037 TTCAAGGAAGGTTAAATCGGA-TTCAATTTGCTTCACTACT-TTTCAAGACAACCAAATCTAAAA
66 TTCAGGGAAGATTGAATCGAACTT-GATTTGCTTCACTGCTCTTT-AGGAAAACCAAATCTAAAA
5100 GAAGAAG
129 GAAGAAG
* * * * **
5107 TATCTGCTCCACTACTCTTTAAGGGAGATCAAACTCGAG-AAAACTTTGATCCACTTCACTATTC
1 AATCTGCTCCGCTACTCTTTAAGGGAGATCAGACTCGAGAAAAAATTTGATCCACTTCACTGCTC
* * * * * *** * *
5171 TTCAGGGAAGATTAAATC-ATAATCGATTTACTTCAGTGCTCCCCAGGAAGACCAAATCTAAAAA
66 TTCAGGGAAGATTGAATCGA-ACTTGATTTGCTTCACTGCTCTTTAGGAAAACCAAATCTAAAAG
5235 AAGAAG
130 AAGAAG
* * * *
5241 AATTTGCTCCTCTACTCTTTATGTGAGATCAGACTCGAGAAAAAATTTGATCCACTTCACTGCTC
1 AATCTGCTCCGCTACTCTTTAAGGGAGATCAGACTCGAGAAAAAATTTGATCCACTTCACTGCTC
* * *
5306 TTCAGGAAAGATTGAATCGAACTTGACTTGCTTCACTGCTCTTTAGGAAAACCAAATCTGAAAGA
66 TTCAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGCTCTTTAGGAAAACCAAATCTAAAAGA
5371 AGAAG
131 AGAAG
* * * **
5376 AATCTTCTCCGCTACTGTTTAAGGGAGATCAGACTTGAGAAAAAATTTGATCCACTTCACTATTC
1 AATCTGCTCCGCTACTCTTTAAGGGAGATCAGACTCGAGAAAAAATTTGATCCACTTCACTGCTC
** * *
5441 TTCAGACAAGATTGAATCGAACTTGATTTGCTTCACTTCTATTTAGGAAAACCAAATCTAAAAGA
66 TTCAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGCTCTTTAGGAAAACCAAATCTAAAAGA
5506 AGAAG
131 AGAAG
* * * * **
5511 AATATGCTCTGCTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTTGATCCACTTCGTTGCTC
1 AATCTGCTCCGCTACTCTTTAAGGGAGATCAGACTCGAGAAAAAATTTGATCCACTTCACTGCTC
5576 TTCAGGGAAGATTGAATCGAACTTGATTTGCTT-AGCTGCTCTTTAGGAA
66 TTCAGGGAAGATTGAATCGAACTTGATTTGCTTCA-CTGCTCTTTAGGAA
5625 GACAAAATAT
Statistics
Matches: 434, Mismatches: 77, Indels: 12
0.83 0.15 0.02
Matches are distributed among these distances:
133 34 0.08
134 104 0.24
135 295 0.68
136 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (135 bp):
AATCTGCTCCGCTACTCTTTAAGGGAGATCAGACTCGAGAAAAAATTTGATCCACTTCACTGCTC
TTCAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGCTCTTTAGGAAAACCAAATCTAAAAGA
AGAAG
Found at i:6864 original size:12 final size:12
Alignment explanation
Indices: 6831--6864 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6821 TTTATTTATT
*
6831 TTTTCTTTTCCC
1 TTTTCTTTTTCC
*
6843 TTTTCCTTTTCC
1 TTTTCTTTTTCC
6855 TTTTCTTTTT
1 TTTTCTTTTT
6865 TTCCTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTCTTTTTCC
Found at i:6865 original size:19 final size:17
Alignment explanation
Indices: 6843--6896 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 17
6833 TTCTTTTCCC
6843 TTTTCCTTTTCCTTTTCTTT
1 TTTTCCTTTT--TTTTC-TT
6863 TTTTCCTTTTTTTGTCTT
1 TTTTCCTTTTTTT-TCTT
6881 TTTT--TTTTTTTT-TT
1 TTTTCCTTTTTTTTCTT
6895 TT
1 TT
6897 CTTTTTTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 4 0.12
15 1 0.03
16 7 0.21
18 9 0.27
19 2 0.06
20 10 0.30
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (17 bp):
TTTTCCTTTTTTTTCTT
Found at i:6882 original size:30 final size:29
Alignment explanation
Indices: 6848--6904 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
6838 TTCCCTTTTC
6848 CTTTTCCTTTTCTTTTTTTCCTTTTTTTGT
1 CTTTT-CTTTTCTTTTTTTCCTTTTTTTGT
* * *
6878 CTTTTTTTTTTTTTTTTTTCTTTTTTT
1 CTTTTCTTTTCTTTTTTTCCTTTTTTT
6905 AGGAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (29 bp):
CTTTTCTTTTCTTTTTTTCCTTTTTTTGT
Found at i:6899 original size:19 final size:19
Alignment explanation
Indices: 6843--6904 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
6833 TTCTTTTCCC
*
6843 TTTTCCTTTTCCTTTTCTTT
1 TTTTCCTTTT-TTTTTCTTT
*
6863 TTTTCCTTTTTTTGTCTTT
1 TTTTCCTTTTTTTTTCTTT
**
6882 TTTTTTTTTTTTTTTCTTT
1 TTTTCCTTTTTTTTTCTTT
6901 TTTT
1 TTTT
6905 AGGAAAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 27 0.73
20 10 0.27
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.84
Consensus pattern (19 bp):
TTTTCCTTTTTTTTTCTTT
Found at i:22488 original size:14 final size:13
Alignment explanation
Indices: 22471--22550 Score: 54
Period size: 13 Copynumber: 5.8 Consensus size: 13
22461 TTTATTTTTC
22471 TTTTCTTTTTCCCTT
1 TTTTCTTTTT-CC-T
*
22486 TTTCTCTTTTTTCTT
1 TTT-TC-TTTTTCCT
*
22501 TTTTCTTTTTTCT
1 TTTTCTTTTTCCT
* *
22514 TTTTTTGTTTTATCT
1 TTTTCT-TTTT-CCT
*
22529 CTTT-TTTTTCCT
1 TTTTCTTTTTCCT
22541 TTTTCTTTTT
1 TTTTCTTTTT
22551 TCAGGCAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
12 5 0.09
13 20 0.38
14 7 0.13
15 13 0.25
16 3 0.06
17 5 0.09
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTTCCT
Found at i:22495 original size:16 final size:16
Alignment explanation
Indices: 22474--22512 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
22464 ATTTTTCTTT
22474 TCTTTTTCCCTTTTTC
1 TCTTTTTCCCTTTTTC
* *
22490 TCTTTTTTCTTTTTTC
1 TCTTTTTCCCTTTTTC
22506 T-TTTTTC
1 TCTTTTTC
22513 TTTTTTTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTTTTTCCCTTTTTC
Found at i:22517 original size:7 final size:7
Alignment explanation
Indices: 22471--22552 Score: 78
Period size: 7 Copynumber: 11.7 Consensus size: 7
22461 TTTATTTTTC
22471 TTTTCTT
1 TTTTCTT
*
22478 TTTCCCTT
1 TTT-TCTT
22486 TTTCTCTT
1 TTT-TCTT
22494 TTTTCTT
1 TTTTCTT
22501 TTTTCTT
1 TTTTCTT
22508 TTTTCTT
1 TTTTCTT
*
22515 TTTT-TG
1 TTTTCTT
* *
22521 TTTTATC
1 TTTTCTT
*
22528 TCTT-TT
1 TTTTCTT
*
22534 TTTTCCT
1 TTTTCTT
22541 TTTTCTT
1 TTTTCTT
22548 TTTTC
1 TTTTC
22553 AGGCAAAATA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
6 9 0.14
7 41 0.65
8 13 0.21
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.79
Consensus pattern (7 bp):
TTTTCTT
Found at i:40057 original size:292 final size:292
Alignment explanation
Indices: 39533--40118 Score: 1048
Period size: 292 Copynumber: 2.0 Consensus size: 292
39523 AAGTTTGGAG
39533 ATTTCTTCAAAACCAAAACTCCCTTGCTTTTAATGTCTTCAAAGAAAAGTATTTTCCTAACTCTT
1 ATTTCTTCAAAACCAAAACTCCCTTGCTTTTAATGTCTTCAAAGAAAAGTATTTTCCTAACTCTT
39598 CCTTTTTTGATGCCAAACTAGGAGATAGAGCCCCTACGCCTGGTCTAGTCTCTTCAAAGCAAAAG
66 CCTTTTTTGATGCCAAACTAGGAGATAGAGCCCCTACGCCTGGTCTAGTCTCTTCAAAGCAAAAG
*
39663 AATATTAAAAGATGACTTCTTCTGGATGATTGGTTTTGAGGGAGAAGCTATAATGTTCTTGTACA
131 AATATTAAAAGATGACTTCTTCTGGATGATTGGTTTTGAGGGAGAAGCTAAAATGTTCTTGTACA
39728 AGTGGGGGTGCCTACCCAATCAATTGGACTTTCTCTTATCATCATAACTTGGATTGTCTTTTAAA
196 AGTGGGGGTGCCTACCCAATCAATTGGACTTTCTCTTATCATCATAACTTGGATTGTCTTTTAAA
39793 TGTGTTAACTTTATAATTCCAAATGCCCCAAT
261 TGTGTTAACTTTATAATTCCAAATGCCCCAAT
** * **
39825 ATTTCTTCATGACCATAACTCCCTTGCTTTTAATGTCTTCAAATCAAAGTATTTTCCTAACTCTT
1 ATTTCTTCAAAACCAAAACTCCCTTGCTTTTAATGTCTTCAAAGAAAAGTATTTTCCTAACTCTT
39890 -CTTTTCTTGATGCCAAACTAGGAGATAGAGCCCCTACGCCTGGTCTAGTCTCTTCAAAGCAAAA
66 CCTTTT-TTGATGCCAAACTAGGAGATAGAGCCCCTACGCCTGGTCTAGTCTCTTCAAAGCAAAA
* * *
39954 TAATATTGAAAGATGACTTCTTCTGGATGATTGGTTTTGAGGGAGAATCTAAAATGTTCTTGTAC
130 GAATATTAAAAGATGACTTCTTCTGGATGATTGGTTTTGAGGGAGAAGCTAAAATGTTCTTGTAC
* *
40019 AAGTGGGGGTGCCTCCCCGATCAATTGGACTTTCTCTTATCATCATAACTTGGATTGTCTTTTAA
195 AAGTGGGGGTGCCTACCCAATCAATTGGACTTTCTCTTATCATCATAACTTGGATTGTCTTTTAA
*
40084 TTGTGTTAACTTTATAATTCCAAATGCCCCAAT
260 ATGTGTTAACTTTATAATTCCAAATGCCCCAAT
40117 AT
1 AT
40119 GGGATGAAGT
Statistics
Matches: 281, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
291 5 0.02
292 276 0.98
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (292 bp):
ATTTCTTCAAAACCAAAACTCCCTTGCTTTTAATGTCTTCAAAGAAAAGTATTTTCCTAACTCTT
CCTTTTTTGATGCCAAACTAGGAGATAGAGCCCCTACGCCTGGTCTAGTCTCTTCAAAGCAAAAG
AATATTAAAAGATGACTTCTTCTGGATGATTGGTTTTGAGGGAGAAGCTAAAATGTTCTTGTACA
AGTGGGGGTGCCTACCCAATCAATTGGACTTTCTCTTATCATCATAACTTGGATTGTCTTTTAAA
TGTGTTAACTTTATAATTCCAAATGCCCCAAT
Found at i:51315 original size:12 final size:12
Alignment explanation
Indices: 51298--51322 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51288 TACCTAAACA
51298 TAAAGAAAATAT
1 TAAAGAAAATAT
51310 TAAAGAAAATAT
1 TAAAGAAAATAT
51322 T
1 T
51323 CACCAAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (12 bp):
TAAAGAAAATAT
Found at i:55165 original size:2 final size:2
Alignment explanation
Indices: 55158--55230 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
55148 ATGTTGTATG
55158 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
55200 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 T
55231 TAAAATCAAG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:69219 original size:21 final size:21
Alignment explanation
Indices: 69193--69232 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
69183 CAGAACCCCA
*
69193 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
69214 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
69233 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:76896 original size:28 final size:27
Alignment explanation
Indices: 76864--76919 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 27
76854 ACATTCTAGA
76864 TCAGACGACTTGCAGAGTATGTCTTGAG
1 TCAGACGACTTGCAGAGTATG-CTTGAG
76892 TCAGACGACTTGCAGAGTATGCTTGAG
1 TCAGACGACTTGCAGAGTATGCTTGAG
76919 T
1 T
76920 ATTTGTAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (27 bp):
TCAGACGACTTGCAGAGTATGCTTGAG
Done.