Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000157.1 Hibiscus syriacus cultivar Beakdansim tig00000279_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: 101067
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:554 original size:41 final size:42
Alignment explanation
Indices: 499--591 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 42
489 ATATTAATCG
499 AATTAATTTTAAATTAATCAAATCAATAAATCATATTTCATT
1 AATTAATTTTAAATTAATCAAATCAATAAATCATATTTCATT
541 AATT-ATTTTAAATTAATCAAATCAATAAATCATATTT-ATT
1 AATTAATTTTAAATTAATCAAATCAATAAATCATATTTCATT
**
581 GTTTAATTTTA
1 AATTAATTTTA
592 TTTAAAATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
40 5 0.10
41 39 0.81
42 4 0.08
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (42 bp):
AATTAATTTTAAATTAATCAAATCAATAAATCATATTTCATT
Found at i:6478 original size:12 final size:12
Alignment explanation
Indices: 6457--6490 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6447 TACGTACTTA
*
6457 TATATGTGTATG
1 TATATATGTATG
*
6469 TATGTATGTATG
1 TATATATGTATG
6481 TATATATGTA
1 TATATATGTA
6491 CCTTCTTAGC
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:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (12 bp):
TATATATGTATG
Found at i:11134 original size:5 final size:5
Alignment explanation
Indices: 11124--11150 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
11114 CTCCACCCGT
11124 GACCC GACCC GACCC GACCC GACCC GA
1 GACCC GACCC GACCC GACCC GACCC GA
11151 ATATATGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.56, G:0.22, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:15822 original size:271 final size:271
Alignment explanation
Indices: 15295--15838 Score: 768
Period size: 271 Copynumber: 2.0 Consensus size: 271
15285 TATAAATAAA
* * *
15295 TTAAGTAATCAATTATGTTATAAAATCATAAGTTATTAGAAGTATCATGTAAATAAATGTGTAGT
1 TTAAGTAACCAATTATGTTATAAAATCATAAGGTATTAGAAGTATCATGTAAATAAAAGTGTAGT
* * *
15360 ACTATTAAAGTTGCATTTATAATTTGATGAGAGACAGAGTTATAAGTACAAACAGTAACTGATTC
66 ACTATTAAAGTTGCATTTATAATTTGATGAGAGACAGAGTTATAAATACAAACAATAACTGATTA
* * * *
15425 GATAAGCTATATAAAGGGGTTATGGTCCTCAAGAAATAGATATCTCATATTTTCTCTTATCCTCA
131 AATAAGCTATATAAAGAGGTTATGGTCCCCAAGAAATAGATATATCATATTTTCTCTTATCCTCA
* * ** * **
15490 TCAGAGAGTTTATACTCAAGGGAATTCTATCTTATTGGAAGATCACAACCGGAAGACAATCTTCA
196 TAAGAGAGTTTATACTCAAGAGAATTCTATCTTATTAAAAGACCACAACCAAAAGACAATCTTCA
*
15555 AGATCTCAACC
261 AAATCTCAACC
* *
15566 TTAAGTGACCAATTATGTTATAAAGTCATAAGGTATTAGAAGTATCATAG-AAATAAAAGTGTAG
1 TTAAGTAACCAATTATGTTATAAAATCATAAGGTATTAGAAGTATCAT-GTAAATAAAAGTGTAG
* * * ** *
15630 ATACTATTAAAGTTGTATTTATAATTTGATTAGGGGTAGAGTTATAAATACAGACAATAACTGAT
65 -TACTATTAAAGTTGCATTTATAATTTGATGAGAGACAGAGTTATAAATACAAACAATAACTGAT
* **
15695 TAAATCAGCTATATAAAGAGGTTATGGTCCCCAAGAAATAGATATATTGTATTTTCTCTTATCC-
129 TAAATAAGCTATATAAAGAGGTTATGGTCCCCAAGAAATAGATATATCATATTTTCTCTTATCCT
* * *
15759 CGTAAGAGAGTTTATACTCAAGAGAATTCTATCTTCTTAAAAGACCACAACCAAAATACAATCTT
194 CATAAGAGAGTTTATACTCAAGAGAATTCTATCTTATTAAAAGACCACAACCAAAAGACAATCTT
15824 CAAAATCTCAACC
259 CAAAATCTCAACC
15837 TT
1 TT
15839 CTAGGTAATC
Statistics
Matches: 239, Mismatches: 32, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
271 126 0.53
272 113 0.47
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (271 bp):
TTAAGTAACCAATTATGTTATAAAATCATAAGGTATTAGAAGTATCATGTAAATAAAAGTGTAGT
ACTATTAAAGTTGCATTTATAATTTGATGAGAGACAGAGTTATAAATACAAACAATAACTGATTA
AATAAGCTATATAAAGAGGTTATGGTCCCCAAGAAATAGATATATCATATTTTCTCTTATCCTCA
TAAGAGAGTTTATACTCAAGAGAATTCTATCTTATTAAAAGACCACAACCAAAAGACAATCTTCA
AAATCTCAACC
Found at i:16992 original size:44 final size:44
Alignment explanation
Indices: 16942--17031 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
16932 TACTTTGACC
16942 TTTACTTTTAGTTAAATGTTGTTTGTTTTGAATTCAATCTATCT
1 TTTACTTTTAGTTAAATGTTGTTTGTTTTGAATTCAATCTATCT
*
16986 TTTACTTTTAGTTAAATGTTGTTTGTTTTGAATTCAATCTGTCT
1 TTTACTTTTAGTTAAATGTTGTTTGTTTTGAATTCAATCTATCT
17030 TT
1 TT
17032 AGTAATTTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (44 bp):
TTTACTTTTAGTTAAATGTTGTTTGTTTTGAATTCAATCTATCT
Found at i:17585 original size:2 final size:2
Alignment explanation
Indices: 17578--17605 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17568 TGTTAATGTA
17578 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
17606 TCAATTCGGT
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:20914 original size:30 final size:30
Alignment explanation
Indices: 20878--20955 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
20868 TTAATCAAAA
20878 TAAGTACCTAAAGTATTTA-TCTTTGTCATC
1 TAAGTACCTAAAGTATTTACT-TTTGTCATC
* * * *
20908 TAAGTACATAAAGTAATCACTTTTTTCATC
1 TAAGTACCTAAAGTATTTACTTTTGTCATC
**
20938 TGGGTACCTAAAGTATTT
1 TAAGTACCTAAAGTATTT
20956 TTAATTAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 37 0.97
31 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (30 bp):
TAAGTACCTAAAGTATTTACTTTTGTCATC
Found at i:23121 original size:42 final size:41
Alignment explanation
Indices: 23031--23121 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 41
23021 TTATTTTTAT
* * *
23031 ATTATTAAAATATGTTATTTAATTATTGAAAAAATATAAATT
1 ATTA-TAAAATATATTATTTAATTAGTGAAAAAATATAAATG
*
23073 ACTATAAAATATATTATTTTAATT-GT-AAAAATATAATAAATG
1 ATTATAAAATATATTA-TTTAATTAGTGAAAAA-AT-ATAAATG
23115 ATTATAA
1 ATTATAA
23122 GCATGTTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
40 5 0.12
41 14 0.34
42 22 0.54
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (41 bp):
ATTATAAAATATATTATTTAATTAGTGAAAAAATATAAATG
Found at i:29406 original size:6 final size:6
Alignment explanation
Indices: 29395--29423 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
29385 AATACTCAAA
29395 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
29424 ACACCGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:34832 original size:12 final size:12
Alignment explanation
Indices: 34798--34835 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
34788 ATTAGGATAA
* *
34798 TATTGTTATTGT
1 TATTATTATTTT
34810 TATTATTATTTT
1 TATTATTATTTT
34822 TATTATTATTTT
1 TATTATTATTTT
34834 TA
1 TA
34836 AGCATTAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (12 bp):
TATTATTATTTT
Found at i:40815 original size:16 final size:16
Alignment explanation
Indices: 40794--40827 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
40784 ATAAGAAAAC
40794 TTCATTTT-CTTTTCAT
1 TTCATTTTCCTTTT-AT
40810 TTCATTTTCCTTTTAT
1 TTCATTTTCCTTTTAT
40826 TT
1 TT
40828 AAGTTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (16 bp):
TTCATTTTCCTTTTAT
Found at i:47857 original size:21 final size:21
Alignment explanation
Indices: 47832--47878 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
47822 TCATCAATTA
* *
47832 AAAGTCAATGAACACTT-TTGT
1 AAAGTCAATCAAC-CTTATTGC
47853 AAAGTCAATCAACCTTATTGC
1 AAAGTCAATCAACCTTATTGC
47874 AAAGT
1 AAAGT
47879 TATAGCTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (21 bp):
AAAGTCAATCAACCTTATTGC
Found at i:59735 original size:33 final size:33
Alignment explanation
Indices: 59685--59758 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
59675 AGAGAAAGCT
* *
59685 TAAGAACACTTTAGTAAATCATGTCTGGCAGAA
1 TAAGCACACTTTAGTAAATCATGTCTGACAGAA
*
59718 TAAGCACACTTTGGTAAATCATGTCTGACAGAA
1 TAAGCACACTTTAGTAAATCATGTCTGACAGAA
*
59751 TACGCACA
1 TAAGCACA
59759 ACATTCTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (33 bp):
TAAGCACACTTTAGTAAATCATGTCTGACAGAA
Found at i:67078 original size:16 final size:17
Alignment explanation
Indices: 67044--67082 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
67034 TAATATTCAA
*
67044 AAAATATTGAAATAAAT
1 AAAATATTGAAAAAAAT
67061 AAAATATT-AAAAAAAT
1 AAAATATTGAAAAAAAT
67077 AAAATA
1 AAAATA
67083 ATTTAATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAATATTGAAAAAAAT
Found at i:67989 original size:3 final size:3
Alignment explanation
Indices: 67981--68023 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
67971 CCATGCTCTT
*
67981 TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
68024 ATGGATAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:69564 original size:23 final size:23
Alignment explanation
Indices: 69523--69598 Score: 98
Period size: 23 Copynumber: 3.3 Consensus size: 23
69513 AGAATAATTA
69523 TGTCTTTGTGACATGTTTATCTC
1 TGTCTTTGTGACATGTTTATCTC
* * * *
69546 TGTCTTTATGATATATTTATCTA
1 TGTCTTTGTGACATGTTTATCTC
* *
69569 TGTCTTTGTGACACGTTTTTCTC
1 TGTCTTTGTGACATGTTTATCTC
69592 TGTCTTT
1 TGTCTTT
69599 TGGTAGTTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.55
Consensus pattern (23 bp):
TGTCTTTGTGACATGTTTATCTC
Found at i:72316 original size:6 final size:6
Alignment explanation
Indices: 72278--72330 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
72268 GTTTAGTATT
* * * * *
72278 TAATATA TAATAA TTATTA TTATAA TGACAA TAATAA TAATAA TAATAA
1 TAATA-A TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA
72327 TAAT
1 TAAT
72331 TAAAACCCAG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
6 34 0.87
7 5 0.13
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (6 bp):
TAATAA
Found at i:72319 original size:9 final size:9
Alignment explanation
Indices: 72278--72330 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
72268 GTTTAGTATT
72278 TAATATATAA
1 TAATA-ATAA
* *
72288 TAATTATTA
1 TAATAATAA
* *
72297 TTATAATGA
1 TAATAATAA
*
72306 CAATAATAA
1 TAATAATAA
72315 TAATAATAA
1 TAATAATAA
72324 TAATAAT
1 TAATAAT
72331 TAAAACCCAG
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
9 30 0.88
10 4 0.12
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (9 bp):
TAATAATAA
Found at i:73142 original size:11 final size:11
Alignment explanation
Indices: 73126--73150 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
73116 ACCAACATGC
73126 TAAAAAGTAAA
1 TAAAAAGTAAA
73137 TAAAAAGTAAA
1 TAAAAAGTAAA
73148 TAA
1 TAA
73151 TTTTAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (11 bp):
TAAAAAGTAAA
Found at i:77319 original size:14 final size:14
Alignment explanation
Indices: 77300--77329 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
77290 ATTGAAAGGA
77300 AGAGCAATTGATAG
1 AGAGCAATTGATAG
*
77314 AGAGCATTTGATAG
1 AGAGCAATTGATAG
77328 AG
1 AG
77330 GGGAGCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (14 bp):
AGAGCAATTGATAG
Found at i:84040 original size:22 final size:22
Alignment explanation
Indices: 83958--84032 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
83948 GGGTAAACGC
* * *
83958 GGTCCTTCGGGACATATACAGA
1 GGTCATTCGGGACAAATACATA
83980 GGTCATTCGGGACAAATACATA
1 GGTCATTCGGGACAAATACATA
* *
84002 GGTCCTTTGGGACAAATACATA
1 GGTCATTCGGGACAAATACATA
84024 GGTCATTCG
1 GGTCATTCG
84033 AGATAAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTCATTCGGGACAAATACATA
Found at i:84670 original size:21 final size:21
Alignment explanation
Indices: 84644--84684 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
84634 ATGAAATTAC
*
84644 TGTAGCAGTGCATCAGTACAT
1 TGTAGCAGTGCATCAATACAT
84665 TGTAGCAGTGCATCAATACA
1 TGTAGCAGTGCATCAATACA
84685 CATTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (21 bp):
TGTAGCAGTGCATCAATACAT
Found at i:87948 original size:4 final size:4
Alignment explanation
Indices: 87939--87987 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
87929 TACACTGTAA
87939 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
87987 T
1 T
87988 TCCTCCTCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:93783 original size:33 final size:30
Alignment explanation
Indices: 93714--93773 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
93704 ATTATTTATG
93714 TGATAATTTTTTTAATAATGAAATGATATT
1 TGATAATTTTTTTAATAATGAAATGATATT
93744 TGATAATTTTTTTAATAATGAAATGATATT
1 TGATAATTTTTTTAATAATGAAATGATATT
93774 ATTTTATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (30 bp):
TGATAATTTTTTTAATAATGAAATGATATT
Done.