Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000936.1 Hibiscus syriacus cultivar Beakdansim tig00001871_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: 107503
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:6642 original size:23 final size:23
Alignment explanation
Indices: 6593--6644 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
6583 TTTTAAAAAA
*
6593 AATAAAAAATAAGTATTAAAATG
1 AATAAAAAATAAATATTAAAATG
6616 AATAAAAAATGATAATATT-AAAT-
1 AATAAAAAAT-A-AATATTAAAATG
6639 AATAAA
1 AATAAA
6645 CTAAAGGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 16 0.62
24 5 0.19
25 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (23 bp):
AATAAAAAATAAATATTAAAATG
Found at i:6654 original size:25 final size:26
Alignment explanation
Indices: 6601--6655 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
6591 AAAATAAAAA
*
6601 ATAAGTATTAAAATGAATAAAAAATG
1 ATAAGTATTAAAATGAATAAAAAAGG
6627 ATAA-TATT-AAAT-AATAAACTAAAGG
1 ATAAGTATTAAAATGAATAAA--AAAGG
6652 ATAA
1 ATAA
6656 ATGATCCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 6 0.23
24 4 0.15
25 12 0.46
26 4 0.15
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.27
Consensus pattern (26 bp):
ATAAGTATTAAAATGAATAAAAAAGG
Found at i:11110 original size:2 final size:2
Alignment explanation
Indices: 11103--11172 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
11093 GGGTGAGCGC
11103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11145 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11173 TATTAAAATT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11442 original size:28 final size:26
Alignment explanation
Indices: 11395--11451 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 26
11385 TATAAATATT
11395 TATATTATTTTATGAATATTTTTAGATA
1 TATATTATTTTATGAATA-TTTTAGA-A
*
11423 TATATTATTTT-TAGATTATTTTAGAA
1 TATATTATTTTAT-GAATATTTTAGAA
11449 TAT
1 TAT
11452 TTTCAAGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
27 8 0.30
28 15 0.56
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (26 bp):
TATATTATTTTATGAATATTTTAGAA
Found at i:12364 original size:2 final size:2
Alignment explanation
Indices: 12359--12386 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12349 ATTTAATTTA
12359 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12387 GTTTGATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16467 original size:35 final size:35
Alignment explanation
Indices: 16416--16527 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 35
16406 AAAACATTCC
*
16416 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
16451 TCAATTTCATTATAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * * *
16486 TCAATTACATTCTAAAACCCAAATTCTAAAATATT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
16521 TCAATTT
1 TCAATTT
16528 AAGGAGGAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:17629 original size:35 final size:34
Alignment explanation
Indices: 17580--17692 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
17570 ATAAAAAACA
* *
17580 GAAATTGAAGTATTTTAGAATTTGGATTTTAGAAT
1 GAAATTGAATTATTTTAGAATTTGG-GTTTAGAAT
*
17615 GTAATTGAATTATTTTAGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTAGAATTT-GGGTTTAGAAT
* *
17650 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTAGAATTTG-GGTTTAGAAT
17685 GAAATTGA
1 GAAATTGA
17693 GGATTGTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.96
36 2 0.03
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTAGAATTTGGGTTTAGAAT
Found at i:29619 original size:74 final size:74
Alignment explanation
Indices: 29491--29669 Score: 247
Period size: 74 Copynumber: 2.4 Consensus size: 74
29481 ATAGGGAGGC
* * *
29491 ACCGATACCCCTCATAGGGTGTACCGATACTCCTATGTCAATTTTGGCTTCGAGAAAAACAGAAT
1 ACCGATACCCCTCATA-GG-GTACTGATACCCCTATGTCAATTTTGGCTCCGAGAAAAACAGAAT
*
29556 GCCAAATGGGT
64 GCCAAATGGAT
29567 ACCGATACCCCTCATAGGGTACTGATACCCCTATGTCAATTTTGG-TACCGAGAAAAACAGAATG
1 ACCGATACCCCTCATAGGGTACTGATACCCCTATGTCAATTTTGGCT-CCGAGAAAAACAGAATG
*
29631 CCCAATGGAT
65 CCAAATGGAT
*
29641 ACCGATACCCC-C-TAGAGGTATTGATACCC
1 ACCGATACCCCTCATAG-GGTACTGATACCC
29670 TTAGTCATTT
Statistics
Matches: 95, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
72 3 0.03
73 14 0.15
74 60 0.63
75 2 0.02
76 16 0.17
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (74 bp):
ACCGATACCCCTCATAGGGTACTGATACCCCTATGTCAATTTTGGCTCCGAGAAAAACAGAATGC
CAAATGGAT
Found at i:40243 original size:21 final size:21
Alignment explanation
Indices: 40219--40269 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
40209 ATGTAATTTT
40219 TAATATAATAATATAATAAAA
1 TAATATAATAATATAATAAAA
* ** *
40240 TAATGTAATTTTTTAATAAAA
1 TAATATAATAATATAATAAAA
*
40261 TAAAATAAT
1 TAATATAAT
40270 GATGGAACCC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TAATATAATAATATAATAAAA
Found at i:45210 original size:20 final size:19
Alignment explanation
Indices: 45185--45239 Score: 87
Period size: 18 Copynumber: 2.9 Consensus size: 19
45175 CACGGGATGT
45185 AAGATTACCAGTGGGAATAA
1 AAGATTACCA-TGGGAATAA
45205 AAGATTACCAT-GGAATAA
1 AAGATTACCATGGGAATAA
45223 AAGATTACC-TGGGAATA
1 AAGATTACCATGGGAATA
45240 GAATTACTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.03
18 22 0.65
19 1 0.03
20 10 0.29
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (19 bp):
AAGATTACCATGGGAATAA
Found at i:47133 original size:2 final size:2
Alignment explanation
Indices: 47128--47159 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47118 AACACACAAC
47128 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47160 TCCACATGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55648 original size:21 final size:21
Alignment explanation
Indices: 55624--55663 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55614 TATTTACGGA
*
55624 GTTGACATGGAGGTCCACATT
1 GTTGACATGGAAGTCCACATT
*
55645 GTTGATATGGAAGTCCACA
1 GTTGACATGGAAGTCCACA
55664 GTGGTTTATA
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:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
GTTGACATGGAAGTCCACATT
Found at i:63896 original size:37 final size:33
Alignment explanation
Indices: 63825--63896 Score: 81
Period size: 37 Copynumber: 2.1 Consensus size: 33
63815 CAAATTATAA
**
63825 AATATTTATATTTTCTTTAAAAATTAAATTTAT
1 AATATTTATATTTTCTTTAAAAATTAAAAATAT
*
63858 AATATTTATATAATTTGTTTTACAAAATTAAAAATAT
1 AATATTTATAT--TTT-CTTTA-AAAATTAAAAATAT
63895 AA
1 AA
63897 AAATGTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 11 0.34
35 3 0.09
36 4 0.12
37 14 0.44
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (33 bp):
AATATTTATATTTTCTTTAAAAATTAAAAATAT
Found at i:71567 original size:16 final size:17
Alignment explanation
Indices: 71531--71577 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
71521 ATTTAGTTTC
*
71531 GATTATAAAATATTATT
1 GATTATTAAATATTATT
71548 --TTATTAAATATT-TT
1 GATTATTAAATATTATT
*
71562 GATTATTAAAAATTAT
1 GATTATTAAATATTAT
71578 AAATTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 11 0.44
17 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
GATTATTAAATATTATT
Found at i:75191 original size:18 final size:18
Alignment explanation
Indices: 75168--75202 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
75158 ATTTTTATTG
75168 AATAAAAATAATATTTTT
1 AATAAAAATAATATTTTT
* *
75186 AATAAATATATTATTTT
1 AATAAAAATAATATTTT
75203 AGGTCGGATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAAAAATAATATTTTT
Found at i:88158 original size:28 final size:28
Alignment explanation
Indices: 88092--88199 Score: 200
Period size: 28 Copynumber: 3.9 Consensus size: 28
88082 TAGAGCTTTA
88092 TGAAGTTTAATGATGTATAATTATTA-T
1 TGAAGTTTAATGATGTATAATTATTATT
88119 TGAAGTTTAATGATGTATAATTATTATT
1 TGAAGTTTAATGATGTATAATTATTATT
88147 TGAAGTTTAATGATGTATAATTATTATT
1 TGAAGTTTAATGATGTATAATTATTATT
*
88175 TGAAGTTTAATGATGTATAACTATT
1 TGAAGTTTAATGATGTATAATTATT
88200 CTACTATATC
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
27 26 0.33
28 53 0.67
ACGTcount: A:0.36, C:0.01, G:0.15, T:0.48
Consensus pattern (28 bp):
TGAAGTTTAATGATGTATAATTATTATT
Found at i:95067 original size:16 final size:14
Alignment explanation
Indices: 95032--95078 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
95022 TTGAAAGTTA
95032 AAGTAATTAAA-TT
1 AAGTAATTAAATTT
95045 AGGAGTAATTTAAAATTT
1 A--AGTAA-TT-AAATTT
95063 AAGTAATTAAATTT
1 AAGTAATTAAATTT
95077 AA
1 AA
95079 AAAATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.03
14 8 0.28
15 7 0.24
16 7 0.24
17 3 0.10
18 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (14 bp):
AAGTAATTAAATTT
Found at i:96629 original size:18 final size:18
Alignment explanation
Indices: 96606--96642 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
96596 AATTAATATA
*
96606 TATTTTTATTGAT-AATT
1 TATTTTTATTCATAAATT
96623 TATTTTTATTCATAAATT
1 TATTTTTATTCATAAATT
96641 TA
1 TA
96643 AAAATGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TATTTTTATTCATAAATT
Found at i:98546 original size:60 final size:59
Alignment explanation
Indices: 98479--98612 Score: 162
Period size: 60 Copynumber: 2.3 Consensus size: 59
98469 AGAGTGACGG
* *
98479 TTTTGTAACTTTTAACACTCAACAG-ACTCAACAAAACAACTCCCAATAGTTGAAATATCA
1 TTTTGTAACTTTTAACACTCAA-AGCACTCAACAAAACAACT-CCAATAGTCGAAATATAA
** * * * * *
98539 TTTTGTAACTTTTAGTAGTCAATGCACTCAGCAAAGCAACTCCTATAGTCGAAATATAA
1 TTTTGTAACTTTTAACACTCAAAGCACTCAACAAAACAACTCCAATAGTCGAAATATAA
98598 TTTTGTAACTTTTAA
1 TTTTGTAACTTTTAA
98613 TAGCTCGATG
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 30 0.48
60 33 0.52
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (59 bp):
TTTTGTAACTTTTAACACTCAAAGCACTCAACAAAACAACTCCAATAGTCGAAATATAA
Found at i:99261 original size:46 final size:46
Alignment explanation
Indices: 99165--99279 Score: 135
Period size: 46 Copynumber: 2.5 Consensus size: 46
99155 ATGTAAGTAC
* * *
99165 GTGTTAAGTGTTACATTTTTTTATTTTATTTACTTACACTTAAGTAT
1 GTGTTAAGTGTTACATTTTTTTATTTCACTTAC-TACACTTAACTAT
*
99212 GTGTTAAGTGTTACATTTTTTTA-TTCACTTAC-ACAGGTATAACTAT
1 GTGTTAAGTGTTACATTTTTTTATTTCACTTACTACA-CT-TAACTAT
* *
99258 GTGTTAAGTGCTATATTTTTTT
1 GTGTTAAGTGTTACATTTTTTT
99280 GTAGTATGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
44 3 0.05
45 1 0.02
46 33 0.55
47 23 0.38
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (46 bp):
GTGTTAAGTGTTACATTTTTTTATTTCACTTACTACACTTAACTAT
Found at i:103278 original size:35 final size:33
Alignment explanation
Indices: 103195--103279 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
103185 AATAATTTTA
*
103195 AATACAACAAACTTACAATAAGTATTAAATGAT
1 AATACAACAAAATTACAATAAGTATTAAATGAT
* * *
103228 AACTGATAACGAAATTACAATAACTGATATTAAATGGT
1 AA-T-ACAACAAAATTACAATAA--G-TATTAAATGAT
103266 AATA-AACAAAATTA
1 AATACAACAAAATTA
103280 ATTAAATACA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 2 0.05
38 12 0.29
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.27
Consensus pattern (33 bp):
AATACAACAAAATTACAATAAGTATTAAATGAT
Done.