Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001990.1 Hibiscus syriacus cultivar Beakdansim tig00004068_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: 42502
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:2518 original size:20 final size:21
Alignment explanation
Indices: 2493--2541 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
2483 TCCGGTAACG
2493 TTTGTTACCGGTTTTATCAT-
1 TTTGTTACCGGTTTTATCATA
2513 TTTGTTACCGGTTTTATCATA
1 TTTGTTACCGGTTTTATCATA
2534 TTT-TTACC
1 TTTGTTACC
2542 TGATATATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.16, C:0.16, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTGTTACCGGTTTTATCATA
Found at i:2974 original size:221 final size:222
Alignment explanation
Indices: 2592--3060 Score: 822
Period size: 221 Copynumber: 2.1 Consensus size: 222
2582 TTATACATTG
2592 ACTTTTATAAAAATGATATATACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTAATAGT
1 ACTTTTATAAAAATGATATATACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTAATAGT
2657 GTTTCATGTTTTCCACCTACAATATTAATTTAATAATTCATTTACACAAAAAATTATTTGATTAT
66 GTTTCATGTTTTCCACCTACAATATTAATTTAATAATTCATTTACACAAAAAATTATTTGATTAT
2722 TTGATATTTTAAAATATTATTTAGAATTTAAA-TTAACAATATTAACCAAAGATAATAATAAATA
131 TTGATATTTTAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATA
*
2786 T-TTTCCACAGTGAAATAAGTATGGAC
196 TATTTCCACAGTGAAATAAGTATGAAC
2812 ACTTTTATAAAAATGATATATACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAG
1 ACTTTTATAAAAATGATATATACTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTAATAG
*
2877 TGTTTCATGTTTTCCACCTACAA-ATTAATTTAATAATTTCATTTACACACAAAATTATTTGATT
65 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAA-TTCATTTACACAAAAAATTATTTGATT
*
2941 TTTTGATA-TTTATAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAA
129 ATTTGATATTTTA-AAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAA
*
3005 ATATATTTTCACAGTGAAATAAGTATGAAC
193 ATATATTTCCACAGTGAAATAAGTATGAAC
* *
3035 ACTTTTATAAAAAGGATAGATA-TTTT
1 ACTTTTATAAAAATGATATATACTTTT
3061 ACAATATAAC
Statistics
Matches: 238, Mismatches: 6, Indels: 8
0.94 0.02 0.03
Matches are distributed among these distances:
220 70 0.29
221 88 0.37
222 37 0.16
223 43 0.18
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.44
Consensus pattern (222 bp):
ACTTTTATAAAAATGATATATACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTAATAGT
GTTTCATGTTTTCCACCTACAATATTAATTTAATAATTCATTTACACAAAAAATTATTTGATTAT
TTGATATTTTAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATA
TATTTCCACAGTGAAATAAGTATGAAC
Found at i:5261 original size:3 final size:3
Alignment explanation
Indices: 5253--5313 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
5243 TTTTTATCCA
*
5253 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5300 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
5314 AATATATATT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 1 0.02
3 54 0.98
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5828 original size:24 final size:24
Alignment explanation
Indices: 5779--5829 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
5769 AGAACGAGAC
*
5779 AGAGAGACAAAAAAAAAAGAATAG
1 AGAGAGACAAAAAAAAAAGAACAG
*
5803 AGAGAGACATAGAAAAAAA-AACAG
1 AGAGAGACA-AAAAAAAAAGAACAG
5827 AGA
1 AGA
5830 AAATACAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.69, C:0.06, G:0.22, T:0.04
Consensus pattern (24 bp):
AGAGAGACAAAAAAAAAAGAACAG
Found at i:6649 original size:19 final size:18
Alignment explanation
Indices: 6610--6661 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 18
6600 TGAATTAGAT
* *
6610 TTTAATTTATT-TTTTCG
1 TTTATTTTATTGTTTTCA
6627 TTTATTTTATATGTTTTCA
1 TTTATTTTAT-TGTTTTCA
6646 TTTATTTTATTGTTTT
1 TTTATTTTATTGTTTT
6662 TAAATATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 9 0.29
18 7 0.23
19 15 0.48
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.73
Consensus pattern (18 bp):
TTTATTTTATTGTTTTCA
Found at i:6729 original size:13 final size:13
Alignment explanation
Indices: 6701--6735 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
6691 TTTTATTATA
6701 TTATTAAATA-TT
1 TTATTAAATATTT
6713 TTATTAAATATTT
1 TTATTAAATATTT
6726 TTA-TAAATAT
1 TTATTAAATAT
6736 ATAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTAAATATTT
Found at i:7485 original size:13 final size:15
Alignment explanation
Indices: 7454--7490 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
7444 TTATATGTTT
7454 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
7469 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
7482 TA-TTTATTT
1 TATTTTATTT
7491 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:19367 original size:84 final size:83
Alignment explanation
Indices: 19224--19405 Score: 303
Period size: 84 Copynumber: 2.2 Consensus size: 83
19214 ATATCTTAGT
19224 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* *
19289 TGATCTGATTTGG-CAGAA
66 TAATCTG-GTTGGACAGAA
19307 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
19372 CTAATCTGGTTGGACAGAA
65 CTAATCTGGTTGGACAGAA
*
19391 CCAATCGTTGGAATT
1 CCAATCATT-GAATT
19406 AAAAGATGAA
Statistics
Matches: 93, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
83 34 0.37
84 54 0.58
85 5 0.05
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (83 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TAATCTGGTTGGACAGAA
Found at i:20313 original size:113 final size:113
Alignment explanation
Indices: 20115--20781 Score: 1149
Period size: 113 Copynumber: 5.9 Consensus size: 113
20105 TCAAATCCAC
* *
20115 TTGATGGATCATTCATTGCCAGA-TAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCA-ACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
20179 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
20228 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
20293 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
20341 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
20406 AGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* *
20454 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
20519 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
*
20567 TTGATGGATCAACATTGCCAGAGAAATTTCATGAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCAACATTGCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * * *
20632 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCAC
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* *** *
20681 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
20746 AGTTCATAATGAGAAGAGCTTGTTCAAC-CTTTGTTT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
20782 GATACTATCA
Statistics
Matches: 530, Mismatches: 22, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
112 17 0.03
113 411 0.78
114 102 0.19
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (113 bp):
TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
Found at i:21103 original size:3 final size:3
Alignment explanation
Indices: 21095--21165 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
21085 TTTTTATCCA
*
21095 TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
21143 TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
21166 AATATATATT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:21663 original size:24 final size:25
Alignment explanation
Indices: 21631--21682 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
21621 AGAACGAGAC
*
21631 AGAGAGACA-A-AAAAAAAAGAATAG
1 AGAGAGACATAGAAAAAAAA-AACAG
21655 AGAGAGACATAGAAAAAAAAAACAG
1 AGAGAGACATAGAAAAAAAAAACAG
21680 AGA
1 AGA
21683 AAATACAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 8 0.32
26 8 0.32
ACGTcount: A:0.69, C:0.06, G:0.21, T:0.04
Consensus pattern (25 bp):
AGAGAGACATAGAAAAAAAAAACAG
Found at i:22510 original size:19 final size:18
Alignment explanation
Indices: 22474--22522 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
22464 TAGATTTTTA
*
22474 ATTTTATT-TTTTCGTTT
1 ATTTTATTGTTTTCATTT
22491 ATTTTATATGTTTTCATTT
1 ATTTTAT-TGTTTTCATTT
22510 ATTTTATTGTTTT
1 ATTTTATTGTTTT
22523 TAAATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (18 bp):
ATTTTATTGTTTTCATTT
Found at i:22590 original size:13 final size:13
Alignment explanation
Indices: 22562--22596 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
22552 TTTTATTATA
22562 TTATTAAATA-TT
1 TTATTAAATATTT
22574 TTATTAAATATTT
1 TTATTAAATATTT
22587 TTA-TAAATAT
1 TTATTAAATAT
22597 ATAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTAAATATTT
Found at i:23874 original size:24 final size:24
Alignment explanation
Indices: 23833--23919 Score: 140
Period size: 24 Copynumber: 3.7 Consensus size: 24
23823 TATTCGTTTA
* *
23833 TTTAT-TGTTCACGAACATGTTCG
1 TTTATATGTTCACGAACATATTTG
*
23856 TTTATATGTCCACGAACATATTTG
1 TTTATATGTTCACGAACATATTTG
23880 TTTATATGTTCACGAACATATTTG
1 TTTATATGTTCACGAACATATTTG
23904 TTTATATGTTCACGAA
1 TTTATATGTTCACGAA
23920 TGTGTTCATT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 5 0.08
24 54 0.92
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (24 bp):
TTTATATGTTCACGAACATATTTG
Found at i:23931 original size:24 final size:24
Alignment explanation
Indices: 23823--23919 Score: 131
Period size: 24 Copynumber: 3.9 Consensus size: 24
23813 AAAGTGTTCG
23823 TATTCGTTTATTTATTGTTCACGAACA
1 TATTCGTTTA--TA-TGTTCACGAACA
* *
23850 TGTTCGTTTATATGTCCACGAACA
1 TATTCGTTTATATGTTCACGAACA
*
23874 TATTTGTTTATATGTTCACGAACA
1 TATTCGTTTATATGTTCACGAACA
*
23898 TATTTGTTTATATGTTCACGAA
1 TATTCGTTTATATGTTCACGAA
23920 TGTGTTCATT
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
24 54 0.83
25 2 0.03
27 9 0.14
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.45
Consensus pattern (24 bp):
TATTCGTTTATATGTTCACGAACA
Found at i:24217 original size:24 final size:24
Alignment explanation
Indices: 24190--24237 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
24180 GAACGAGTTG
24190 ATAAACAAACTCATAAACAAGCTT
1 ATAAACAAACTCATAAACAAGCTT
** * *
24214 ATAAATGAGCTCATAAACGAGCTT
1 ATAAACAAACTCATAAACAAGCTT
24238 GTACGTGAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (24 bp):
ATAAACAAACTCATAAACAAGCTT
Found at i:24253 original size:22 final size:22
Alignment explanation
Indices: 24225--24277 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
24215 TAAATGAGCT
24225 CATAAACGAGCTTGTACGTGAA
1 CATAAACGAGCTTGTACGTGAA
24247 CATAAACGAGCTTGTACGTGAA
1 CATAAACGAGCTTGTACGTGAA
24269 CATAAACGA
1 CATAAACGA
24278 ACCAAATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (22 bp):
CATAAACGAGCTTGTACGTGAA
Found at i:26078 original size:20 final size:22
Alignment explanation
Indices: 26027--26080 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
26017 TACTCAGACA
* *
26027 AGTATCGATATCCCAGATCAGG
1 AGTATCGATACCCCAGACCAGG
*
26049 AGTATTGATACCCCA-ACCAGG
1 AGTATCGATACCCCAGACCAGG
26070 -GTATCGATACC
1 AGTATCGATACC
26081 AACTCTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.36
21 5 0.18
22 13 0.46
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (22 bp):
AGTATCGATACCCCAGACCAGG
Found at i:26400 original size:20 final size:22
Alignment explanation
Indices: 26348--26402 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
26338 CAGGACACCC
*
26348 AAGTATCGATACCCTAGATTAG
1 AAGTATCGATACCCCAGATTAG
*
26370 AAGTATTGATACCCCA-ATTAG
1 AAGTATCGATACCCCAGATTAG
*
26391 -GGTATCGATACC
1 AAGTATCGATACC
26403 AACTCTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 10 0.34
21 5 0.17
22 14 0.48
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (22 bp):
AAGTATCGATACCCCAGATTAG
Found at i:32277 original size:2 final size:2
Alignment explanation
Indices: 32270--32316 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
32260 ATTTCAAAAC
32270 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
32312 TA TA T
1 TA TA T
32317 CGATAATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.