Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003535.1 Hibiscus syriacus cultivar Beakdansim tig00007461_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: 61046
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:11095 original size:18 final size:18
Alignment explanation
Indices: 11069--11114 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
11059 TTCACGAAAT
* *
11069 ATAAAATTATCGGTGGGA
1 ATAAGATTACCGGTGGGA
*
11087 ATAAGATTACCGGTTGGA
1 ATAAGATTACCGGTGGGA
11105 ATAAGATTAC
1 ATAAGATTAC
11115 TGGGAATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (18 bp):
ATAAGATTACCGGTGGGA
Found at i:11340 original size:36 final size:37
Alignment explanation
Indices: 11267--11340 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
11257 TACTATAATT
**
11267 AATTTATATATTTTCTTTAAAAAAATTAAATTCATAA
1 AATTTATATATTTTCTTTAAAAAAATTAAAAACATAA
* *
11304 AATTTATATAATTTT-TTT-ACAAAATTAAAAAGATAA
1 AATTTATAT-ATTTTCTTTAAAAAAATTAAAAACATAA
11340 A
1 A
11341 TATGTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 15 0.47
37 12 0.38
38 5 0.16
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (37 bp):
AATTTATATATTTTCTTTAAAAAAATTAAAAACATAA
Found at i:12383 original size:14 final size:14
Alignment explanation
Indices: 12366--12393 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12356 ATCATAACAA
12366 AATTATATAACTAT
1 AATTATATAACTAT
12380 AATTATATAACTAT
1 AATTATATAACTAT
12394 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:17439 original size:16 final size:16
Alignment explanation
Indices: 17418--17456 Score: 55
Period size: 14 Copynumber: 2.5 Consensus size: 16
17408 ATGCAAGGTA
17418 TATAAATATTAATAAT
1 TATAAATATTAATAAT
17434 TAT-AA-ATTAATAAT
1 TATAAATATTAATAAT
17448 TATAGAATA
1 TATA-AATA
17457 AAAATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 12 0.60
15 2 0.10
16 5 0.25
17 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
TATAAATATTAATAAT
Found at i:18204 original size:60 final size:60
Alignment explanation
Indices: 18140--18252 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
18130 TTTAAGGATG
* *
18140 AAATTGAAATATTAAAAAGTTTA-AGAACTAATTTAGAATAATAA-TCATAGTTTGAGAATA
1 AAATTAAAATATTAAAAAGTTTAGAG-ACTAATTTAAAATAA-AAGTCATAGTTTGAGAATA
* *
18200 AAATTAAAATATTCAAAAGTTTAGAGATTAATTTAAAATAAAAGTCATAGTTT
1 AAATTAAAATATTAAAAAGTTTAGAGACTAATTTAAAATAAAAGTCATAGTTT
18253 AAGGACGTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
59 2 0.04
60 43 0.91
61 2 0.04
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.35
Consensus pattern (60 bp):
AAATTAAAATATTAAAAAGTTTAGAGACTAATTTAAAATAAAAGTCATAGTTTGAGAATA
Found at i:26540 original size:18 final size:18
Alignment explanation
Indices: 26517--26551 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26507 ATATTTATTA
26517 ATATTTCTAATAATATAT
1 ATATTTCTAATAATATAT
* *
26535 ATATTTTTAATATTATA
1 ATATTTCTAATAATATA
26552 ATAAAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTTCTAATAATATAT
Found at i:26759 original size:23 final size:23
Alignment explanation
Indices: 26733--26777 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
26723 AATAATATTT
26733 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
26756 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
26778 ATATAACACT
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:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:26909 original size:91 final size:89
Alignment explanation
Indices: 26746--26915 Score: 195
Period size: 91 Copynumber: 1.9 Consensus size: 89
26736 TAAAGATATT
* * * * * *
26746 TAAAATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAACA
1 TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAACA
26811 TAATTTAAAATATTTTTATTTCAA
66 TAATTTAAAATATTTTTATTTCAA
*
26835 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATAATA-TTTAAT-AATAAAT
1 TAAAATATA-CAA-ATTAATATTTTTA-AAATAAAA-TATAAAAATAATACTTTAATAAATAAAT
* *
26898 AA-ATTATTT-TAATATTTT
62 AACATAATTTAAAATATTTT
26916 AAAAATAATT
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
89 17 0.25
90 8 0.12
91 21 0.31
92 12 0.18
93 10 0.15
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.45
Consensus pattern (89 bp):
TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAACA
TAATTTAAAATATTTTTATTTCAA
Found at i:26910 original size:27 final size:26
Alignment explanation
Indices: 26880--26956 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
26870 ATTATAAAAA
26880 TAATATTTAATAATAAATAAATTATTT
1 TAATATTT-ATAATAAATAAATTATTT
*
26907 TAATATTT-TAA-AAAT-AATTATAT
1 TAATATTTATAATAAATAAATTATTT
*
26930 TAAGT-TTTATGATAAATAATATTATTT
1 TAA-TATTTATAATAAATAA-ATTATTT
26957 ATTGTATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
23 13 0.31
24 7 0.17
25 7 0.17
26 1 0.02
27 14 0.33
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (26 bp):
TAATATTTATAATAAATAAATTATTT
Found at i:26932 original size:23 final size:26
Alignment explanation
Indices: 26880--26954 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 26
26870 ATTATAAAAA
*
26880 TAATATTTAATAATAAATAAATTATTT
1 TAATATTT-ATAATAAATAAATTATAT
26907 TAATATTT-TAA-AAAT-AATTATAT
1 TAATATTTATAATAAATAAATTATAT
*
26930 TAAGT-TTTATGATAAATAATATTAT
1 TAA-TATTTATAATAAATAA-ATTAT
26955 TTATTGTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 13 0.32
24 7 0.17
25 7 0.17
26 1 0.02
27 13 0.32
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (26 bp):
TAATATTTATAATAAATAAATTATAT
Found at i:27097 original size:14 final size:14
Alignment explanation
Indices: 27069--27111 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
27059 AAATGTAATT
27069 CATTTTCCTGGAAAA
1 CATTTTCC-GGAAAA
27084 CATTTTCCGGAAAA
1 CATTTTCCGGAAAA
* *
27098 TATTTTCCAGAAAA
1 CATTTTCCGGAAAA
27112 TATAATTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (14 bp):
CATTTTCCGGAAAA
Found at i:32865 original size:23 final size:21
Alignment explanation
Indices: 32832--32916 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 21
32822 TCAAACGATC
*
32832 GAAAACATGTCATAAAGACATAA
1 GAAAACGTGTCATAAAG--ATAA
*
32855 GAAAATGTGTCATAAAGATAGA
1 GAAAACGTGTCATAAAGATA-A
*
32877 GAAAAACGTATCATAAATGTATAA
1 G-AAAACGTGTCATAAA-G-ATAA
32901 GAAAACGTGTCATAAA
1 GAAAACGTGTCATAAA
32917 AAAAGAGTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
21 3 0.06
22 2 0.04
23 42 0.79
24 3 0.06
25 3 0.06
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.21
Consensus pattern (21 bp):
GAAAACGTGTCATAAAGATAA
Found at i:38291 original size:20 final size:21
Alignment explanation
Indices: 38252--38291 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
38242 TTTTCAATCT
* *
38252 TTTCAACACATTTTGTGAAAG
1 TTTCAAAACATTTTGAGAAAG
38273 TTTCAAAAC-TTTTGAGAAA
1 TTTCAAAACATTTTGAGAAA
38292 CTTCGAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (21 bp):
TTTCAAAACATTTTGAGAAAG
Found at i:38552 original size:14 final size:14
Alignment explanation
Indices: 38536--38568 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
38526 AATTAATATA
38536 ATATAAT-ATAAAT
1 ATATAATGATAAAT
38549 A-ATAATGATAAAT
1 ATATAATGATAAAT
38562 ATATAAT
1 ATATAAT
38569 CACATAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 8 0.44
14 5 0.28
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
ATATAATGATAAAT
Found at i:41449 original size:20 final size:20
Alignment explanation
Indices: 41421--41541 Score: 118
Period size: 20 Copynumber: 5.9 Consensus size: 20
41411 TAGTTGAAAA
*
41421 TCGCTTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
41441 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
41461 TCGTGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
41482 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* *
41502 TCGCGTTGCGATAGTCTACATT
1 TCGCGTTGCGAT--TTTCCATT
41524 T-GTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
41542 AATTCGTTGC
Statistics
Matches: 80, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
20 49 0.61
21 15 0.19
22 16 0.20
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:41499 original size:61 final size:61
Alignment explanation
Indices: 41399--41513 Score: 203
Period size: 61 Copynumber: 1.9 Consensus size: 61
41389 CTATCGCAAA
*
41399 TTCGCGTTGCAATAGTTGAAAATCGCTTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCAATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAT
* *
41460 TTCGTGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
1 TTCGCGTTGCAATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
41514 AGTCTACATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (61 bp):
TTCGCGTTGCAATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAT
Found at i:41530 original size:22 final size:22
Alignment explanation
Indices: 41505--41619 Score: 121
Period size: 22 Copynumber: 5.4 Consensus size: 22
41495 TTCCATTTCG
*
41505 CGTTGCGATAGTCTACATTTGT
1 CGTTGCGATAGTCTACAATTGT
* * *
41527 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAATTGT
*
41546 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAATTGT
* * *
41568 TGTTGCGATAGTTTACAAAT-T
1 CGTTGCGATAGTCTACAATTGT
*
41589 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAATTGT
41611 CGTTGCGAT
1 CGTTGCGAT
41620 TTTCCAAATT
Statistics
Matches: 73, Mismatches: 16, Indels: 8
0.75 0.16 0.08
Matches are distributed among these distances:
19 10 0.14
20 5 0.07
21 22 0.30
22 36 0.49
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAATTGT
Found at i:41554 original size:61 final size:61
Alignment explanation
Indices: 41399--41535 Score: 177
Period size: 61 Copynumber: 2.2 Consensus size: 61
41389 CTATCGCAAA
* * * * * *
41399 TTCGCGTTGCAATAGTTGAAAATCGCTTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAT
1 TTCGTGTTGCGATAGTTCAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTCTACAT
*
41460 TTCGTGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAT
1 TTCGTGTTGCGATAGTTCAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT--TCTACAT
41523 TT-GTCGTTGCGAT
1 TTCGT-GTTGCGAT
41536 TTTCCAAATT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
61 51 0.75
62 2 0.03
63 15 0.22
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.40
Consensus pattern (61 bp):
TTCGTGTTGCGATAGTTCAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTCTACAT
Found at i:41601 original size:43 final size:41
Alignment explanation
Indices: 41485--41637 Score: 227
Period size: 41 Copynumber: 3.7 Consensus size: 41
41475 TTGAAAATCG
* *
41485 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACATTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
41527 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
* *
41568 TGTTGCGATAGTTTACAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGAT--TTTCCAAATTCGTTGCGATAGTCTACAGTTGT
41611 CGTTGCGATTTTCCAAATTCGTTGCGA
1 CGTTGCGATTTTCCAAATTCGTTGCGA
41638 AAATTCGTTG
Statistics
Matches: 102, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
41 46 0.45
42 14 0.14
43 42 0.41
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:42768 original size:21 final size:20
Alignment explanation
Indices: 42739--42802 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
42729 AATATCACAA
42739 CGAATTTGGAAAATCGCAACG
1 CGAA-TTGGAAAATCGCAACG
** *
42760 AC-AACTTGGACTATCACAACG
1 -CGAA-TTGGAAAATCGCAACG
*
42781 CGAAATGGAAAATCGCAACG
1 CGAATTGGAAAATCGCAACG
42801 CG
1 CG
42803 GTTTTCAACT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 15 0.45
21 17 0.52
22 1 0.03
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (20 bp):
CGAATTGGAAAATCGCAACG
Found at i:42799 original size:20 final size:21
Alignment explanation
Indices: 42745--42802 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
42735 ACAACGAATT
*
42745 TGGAAAATCGCAACGAC-AACT
1 TGGAAAATCGCAACG-CGAACA
** *
42766 TGGACTATCACAACGCGAA-A
1 TGGAAAATCGCAACGCGAACA
42786 TGGAAAATCGCAACGCG
1 TGGAAAATCGCAACGCG
42803 GTTTTCAACT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (21 bp):
TGGAAAATCGCAACGCGAACA
Found at i:49266 original size:24 final size:23
Alignment explanation
Indices: 49239--49284 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
49229 AACCAAATAT
* *
49239 TAATAATTATTTATATAATTTATC
1 TAATAATTAATTA-ATAAATTATC
*
49263 TAATATTTAATTAATAAATTAT
1 TAATAATTAATTAATAAATTAT
49285 TTTTATTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATAATTAATTAATAAATTATC
Done.