Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003560.1 Hibiscus syriacus cultivar Beakdansim tig00007516_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: 69631
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:3258 original size:43 final size:43
Alignment explanation
Indices: 3197--3288 Score: 150
Period size: 43 Copynumber: 2.1 Consensus size: 43
3187 TACACCAATA
* *
3197 ACAGTACATAAAACTT-AAAAACATCCCTGCCATAAAAGCCTTT
1 ACAGTACATAAAACTTAAAAAAC-CCCCTGCCATAAAAGCCTTC
3240 ACAGTACATAAAACTTAAAAAACCCCCTGCCATAAAAGCCTTC
1 ACAGTACATAAAACTTAAAAAACCCCCTGCCATAAAAGCCTTC
3283 ACAGTA
1 ACAGTA
3289 GACCAGAGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 40 0.87
44 6 0.13
ACGTcount: A:0.45, C:0.27, G:0.08, T:0.21
Consensus pattern (43 bp):
ACAGTACATAAAACTTAAAAAACCCCCTGCCATAAAAGCCTTC
Found at i:7934 original size:31 final size:31
Alignment explanation
Indices: 7899--7968 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
7889 CTTTTAAAAC
* * *
7899 TTGCAATACAGTCTCCTAACATTTATTCTGT
1 TTGCAATACAGTCCCCCAACATTTATTCCGT
**
7930 TTGCAATATGGTCCCCCAACATTTATTCCGT
1 TTGCAATACAGTCCCCCAACATTTATTCCGT
*
7961 TTGAAATA
1 TTGCAATA
7969 TGGTCCCCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (31 bp):
TTGCAATACAGTCCCCCAACATTTATTCCGT
Found at i:7979 original size:30 final size:31
Alignment explanation
Indices: 7916--7976 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
7906 ACAGTCTCCT
* *
7916 AACATTTATTCTGTTTGCAATATGGTCCCCC
1 AACATTTATTCCGTTTGAAATATGGTCCCCC
7947 AACATTTATTCCGTTTGAAATATGGTCCCC
1 AACATTTATTCCGTTTGAAATATGGTCCCC
7977 AACTTAAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.38
Consensus pattern (31 bp):
AACATTTATTCCGTTTGAAATATGGTCCCCC
Found at i:13541 original size:29 final size:29
Alignment explanation
Indices: 13504--13573 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
13494 TTCAATATGT
13504 GTTGATAGATGTTA-ACT-TCCATTTTTTGA
1 GTTGATAGATGTTACA-TAT-CATTTTTTGA
*
13533 GTTGATAGATGTTACATATCATTTTTTGT
1 GTTGATAGATGTTACATATCATTTTTTGA
*
13562 GTTGATAAATGT
1 GTTGATAGATGT
13574 AAAGTGCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 35 0.95
30 2 0.05
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.49
Consensus pattern (29 bp):
GTTGATAGATGTTACATATCATTTTTTGA
Found at i:13701 original size:68 final size:70
Alignment explanation
Indices: 13591--13727 Score: 217
Period size: 68 Copynumber: 2.0 Consensus size: 70
13581 CATCTTTAGT
13591 GTCATTTTTTGTATATGACATAGTGACTTAGGCAATATGGTATGGTTGCCAAA-CATATACCAAT
1 GTCATTTTTTGTATATGACATAGTGACTTAGGCAATATGGTATGGTTGCCAAACCATATA-CAAT
13655 -ATATG
65 GATATG
* * *
13660 GTCATTTTTTGTATATG-CATAGTGGCTTAGTCAATATGGTATGGTTGTCAAACCATATACAATG
1 GTCATTTTTTGTATATGACATAGTGACTTAGGCAATATGGTATGGTTGCCAAACCATATACAATG
13724 ATAT
66 ATAT
13728 ATGGTAACAT
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
68 36 0.57
69 27 0.43
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (70 bp):
GTCATTTTTTGTATATGACATAGTGACTTAGGCAATATGGTATGGTTGCCAAACCATATACAATG
ATATG
Found at i:16541 original size:34 final size:35
Alignment explanation
Indices: 16503--16576 Score: 114
Period size: 34 Copynumber: 2.1 Consensus size: 35
16493 TTCATGCTCA
* *
16503 AAATTCCAAAGTAATTCAATTTCATTCTAAA-CTT
1 AAATTCCAAAATAATTCAATTACATTCTAAACCTT
*
16537 AAATTTCAAAATAATTCAATTACATTCTAAACCTT
1 AAATTCCAAAATAATTCAATTACATTCTAAACCTT
16572 AAATT
1 AAATT
16577 GAAGTATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
34 28 0.78
35 8 0.22
ACGTcount: A:0.45, C:0.16, G:0.01, T:0.38
Consensus pattern (35 bp):
AAATTCCAAAATAATTCAATTACATTCTAAACCTT
Found at i:16653 original size:35 final size:35
Alignment explanation
Indices: 16572--16684 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 35
16562 TCTAAACCTT
* *
16572 AAATTGAAGTATTTTAGAATTTGGGGGTTTAGAATT
1 AAATTGAATTATTTTAGAATTT-GGGGTTTAGAATA
* * * *
16608 TAATTAAATTATTTTAGAATTTAGGATTTAGAATA
1 AAATTGAATTATTTTAGAATTTGGGGTTTAGAATA
* * *
16643 AAATTGAATTACTTTAGGATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTAGAATTTGGGGTTTAGAATA
16678 AAATTGA
1 AAATTGA
16685 GGACTATTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
35 45 0.70
36 19 0.30
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTGGGGTTTAGAATA
Found at i:18139 original size:23 final size:21
Alignment explanation
Indices: 18113--18154 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
18103 TATAAAAAAT
18113 TATTTTTGATTAAATATTTTTGG
1 TATTTTT-ATTAAAT-TTTTTGG
*
18136 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
18155 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:19422 original size:2 final size:2
Alignment explanation
Indices: 19415--19442 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19405 AAGATGATTA
19415 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
19443 CTTTAAATAA
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:21817 original size:4 final size:4
Alignment explanation
Indices: 21808--21832 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
21798 AATTATAGAA
21808 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
21833 TTCCATGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:23711 original size:19 final size:18
Alignment explanation
Indices: 23665--23712 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
23655 TAATTTTTTG
*
23665 GTTATTAACTTTTTAAAA
1 GTTATTAAATTTTTAAAA
* *
23683 GTTATAAAATTTTGTTAAA
1 GTTATTAAATTTT-TAAAA
*
23702 TTTATTAAATT
1 GTTATTAAATT
23713 ATTATAAACT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (18 bp):
GTTATTAAATTTTTAAAA
Found at i:24051 original size:15 final size:15
Alignment explanation
Indices: 24027--24062 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
24017 ACACCATTAA
*
24027 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
24042 ATTAAATTATAAAAT
1 ATTAAATTATAAAAT
*
24057 ACTAAA
1 ATTAAA
24063 CATATGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:26341 original size:5 final size:5
Alignment explanation
Indices: 26331--26357 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
26321 ATTTATATAA
26331 AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AA
26358 AAATAATATT
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:37670 original size:16 final size:16
Alignment explanation
Indices: 37638--37671 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
37628 TCTGTAATAG
**
37638 TAATTTTGGATTGTTT
1 TAATTTTGGATAATTT
37654 TAATTTTGGATAATTT
1 TAATTTTGGATAATTT
37670 TA
1 TA
37672 GCTATACTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (16 bp):
TAATTTTGGATAATTT
Found at i:37844 original size:24 final size:23
Alignment explanation
Indices: 37825--37870 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
37815 TAAAGAAATT
37825 ACAAT-TTTTAAATTGTAAGAAA
1 ACAATATTTTAAATTGTAAGAAA
**
37847 AGGATATTTTAAATTGTAAGAAA
1 ACAATATTTTAAATTGTAAGAAA
37870 A
1 A
37871 GGGTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (23 bp):
ACAATATTTTAAATTGTAAGAAA
Found at i:37860 original size:23 final size:23
Alignment explanation
Indices: 37830--37882 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
37820 AAATTACAAT
37830 TTTTAAATTGTAAGAAAAGGATA
1 TTTTAAATTGTAAGAAAAGGATA
*
37853 TTTTAAATTGTAAGAAAAGGGTA
1 TTTTAAATTGTAAGAAAAGGATA
37876 TTTTAAA
1 TTTTAAA
37883 CCTCAACACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (23 bp):
TTTTAAATTGTAAGAAAAGGATA
Found at i:39793 original size:35 final size:35
Alignment explanation
Indices: 39754--39824 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
39744 TGGTGAAAGA
39754 AGGGATGACGGGTCAATAAAATGTCTTCTCCTAAC
1 AGGGATGACGGGTCAATAAAATGTCTTCTCCTAAC
39789 AGGGATGACGGGTCAATAAAATGTCTTCTCCTAAC
1 AGGGATGACGGGTCAATAAAATGTCTTCTCCTAAC
39824 A
1 A
39825 TTCTCATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (35 bp):
AGGGATGACGGGTCAATAAAATGTCTTCTCCTAAC
Found at i:46682 original size:39 final size:39
Alignment explanation
Indices: 46626--46712 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
46616 CATGGGAGGA
*
46626 GGTGGTGCTGGCACTCCACAAAGAGGTGGAGGTCGTGGG
1 GGTGGTCCTGGCACTCCACAAAGAGGTGGAGGTCGTGGG
* * *
46665 GGTGGTCCTGG-AGCTCCACGAATAGGTGGAGGTGGTGGG
1 GGTGGTCCTGGCA-CTCCACAAAGAGGTGGAGGTCGTGGG
46704 GGTGGTCCT
1 GGTGGTCCT
46713 CCATGTCGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 1 0.02
39 42 0.98
ACGTcount: A:0.15, C:0.17, G:0.47, T:0.21
Consensus pattern (39 bp):
GGTGGTCCTGGCACTCCACAAAGAGGTGGAGGTCGTGGG
Found at i:46878 original size:6 final size:6
Alignment explanation
Indices: 46867--46917 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
46857 CCTCGTAAAA
* * * * *
46867 GAGGTG GAGGTG GAGGTG GAGGTG GTGGTG GTGGTG GTGGAG GAGGAG
1 GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG
46915 GAG
1 GAG
46918 AAGCTCCGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.16, C:0.00, G:0.67, T:0.18
Consensus pattern (6 bp):
GAGGTG
Found at i:50350 original size:5 final size:5
Alignment explanation
Indices: 50336--50367 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
50326 ATTAGAAACC
50336 AAAAG AAAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG A
50368 GAAATTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:51521 original size:17 final size:16
Alignment explanation
Indices: 51487--51532 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
51477 AATAAATACC
*
51487 AATTGAATTAATATTT
1 AATTGAATTAATAATT
*
51503 AATTGATTTAAATAATT
1 AATTGAATT-AATAATT
*
51520 AATTAAATTAATA
1 AATTGAATTAATA
51533 GGGTAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
AATTGAATTAATAATT
Found at i:51783 original size:2 final size:2
Alignment explanation
Indices: 51776--51804 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
51766 ATTTTATGAT
51776 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 T
51805 GATTAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53634 original size:22 final size:22
Alignment explanation
Indices: 53609--53652 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
53599 AAAATTTACC
* *
53609 TAAAACATTATTATTTTCTAAT
1 TAAAACATAAATATTTTCTAAT
*
53631 TAAAACATAAATATTTTTTAAT
1 TAAAACATAAATATTTTCTAAT
53653 ATTTACGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAAACATAAATATTTTCTAAT
Found at i:54364 original size:24 final size:25
Alignment explanation
Indices: 54337--54402 Score: 89
Period size: 24 Copynumber: 2.6 Consensus size: 25
54327 CCGATATTTT
54337 ATTAAATAATAATTTTCTTGAT-TA
1 ATTAAATAATAATTTTCTTGATATA
* *
54361 ATTAAATAATATTTTTTTTGATAATA
1 ATTAAATAATAATTTTCTTGAT-ATA
*
54387 ATTAAATACTAATTTT
1 ATTAAATAATAATTTT
54403 ATTTGACGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
24 20 0.56
26 16 0.44
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (25 bp):
ATTAAATAATAATTTTCTTGATATA
Found at i:59123 original size:38 final size:37
Alignment explanation
Indices: 59049--59124 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 37
59039 GTTGGAAAAT
* *
59049 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* *
59086 ATTTATATAATTTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-A-TTTTCTTTAAAAAATTAAAAATCATAAA
59124 A
1 A
59125 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 8 0.24
38 7 0.21
39 18 0.55
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Done.