Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005708.1 Hibiscus syriacus cultivar Beakdansim tig00013345_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: 80394
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3287 original size:18 final size:18
Alignment explanation
Indices: 3237--3287 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
3227 ATTCTTCATA
*
3237 ATTTTGATAATATTAATT
1 ATTTTTATAATATTAATT
3255 ATTTTATATAA-ATTAATT
1 ATTTT-TATAATATTAATT
3273 -TCTTTTATAATATTA
1 AT-TTTTATAATATTA
3288 TTTTATTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 6 0.21
18 19 0.66
19 4 0.14
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
ATTTTTATAATATTAATT
Found at i:6909 original size:33 final size:33
Alignment explanation
Indices: 6867--6947 Score: 155
Period size: 32 Copynumber: 2.5 Consensus size: 33
6857 CCATAATTGT
6867 GACCACTTGATGTGATTTTTTTTTTTGATAAAA
1 GACCACTTGATGTGATTTTTTTTTTTGATAAAA
6900 GACCACTTGATGTGA-TTTTTTTTTTGATAAAA
1 GACCACTTGATGTGATTTTTTTTTTTGATAAAA
6932 GACCACTTGATGTGAT
1 GACCACTTGATGTGAT
6948 GAACAAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
32 32 0.68
33 15 0.32
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.44
Consensus pattern (33 bp):
GACCACTTGATGTGATTTTTTTTTTTGATAAAA
Found at i:8026 original size:16 final size:17
Alignment explanation
Indices: 7997--8036 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
7987 CCCCCTCATT
7997 AAAAAAATGAGGAAAAAG
1 AAAAAAAT-AGGAAAAAG
*
8015 AAAAAAAT-GGAAACAG
1 AAAAAAATAGGAAAAAG
8031 AAAAAA
1 AAAAAA
8037 CACTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
18 8 0.38
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (17 bp):
AAAAAAATAGGAAAAAG
Found at i:11506 original size:12 final size:12
Alignment explanation
Indices: 11489--11524 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
11479 CACTAAATAC
11489 GCAAAACAAAGT
1 GCAAAACAAAGT
11501 GCAAAACAAAGT
1 GCAAAACAAAGT
* *
11513 ACAAATCAAAGT
1 GCAAAACAAAGT
11525 TCGCCCCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.58, C:0.17, G:0.14, T:0.11
Consensus pattern (12 bp):
GCAAAACAAAGT
Found at i:12988 original size:18 final size:18
Alignment explanation
Indices: 12965--13000 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12955 ACTGAATATT
*
12965 TGTCCCAAATGACCACTA
1 TGTCCCAAAGGACCACTA
*
12983 TGTCCCGAAGGACCACTA
1 TGTCCCAAAGGACCACTA
13001 ATAATTCCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:15559 original size:22 final size:22
Alignment explanation
Indices: 15506--15559 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
15496 TCGGGTTGAG
*
15506 TCTCGGGTGAAAGATTTATTGT
1 TCTCGGGTGGAAGATTTATTGT
*
15528 TCTCTGGTGGAAGATTCT-TTGT
1 TCTCGGGTGGAAGATT-TATTGT
15550 TCTCGGGTGG
1 TCTCGGGTGG
15560 GGTCGGGTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.15, C:0.13, G:0.31, T:0.41
Consensus pattern (22 bp):
TCTCGGGTGGAAGATTTATTGT
Found at i:26987 original size:21 final size:21
Alignment explanation
Indices: 26962--27013 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
26952 TATTTTAGGA
26962 TTTAAGTTTATAATTCAAAGG
1 TTTAAGTTTATAATTCAAAGG
* * *
26983 TTTAAGTTTATAATTTAGAGT
1 TTTAAGTTTATAATTCAAAGG
27004 TTTAAGTTTA
1 TTTAAGTTTA
27014 GAGTAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (21 bp):
TTTAAGTTTATAATTCAAAGG
Found at i:27013 original size:14 final size:15
Alignment explanation
Indices: 26982--27017 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
26972 TAATTCAAAG
26982 GTTTA-AGTTTATAA
1 GTTTAGAGTTTATAA
26996 -TTTAGAGTTT-TAA
1 GTTTAGAGTTTATAA
27009 GTTTAGAGT
1 GTTTAGAGT
27018 AAATATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (15 bp):
GTTTAGAGTTTATAA
Found at i:37497 original size:37 final size:36
Alignment explanation
Indices: 37452--37524 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 36
37442 AAAATCTACC
37452 AAACTTTACCAAACTTTG-AAAAACATTTTTTCAAAG
1 AAACTTTACCAAACTTTGAAAAAACATTTTTT-AAAG
37488 AAACATTTACCAAACTTTGAAAAAACATTTTTTAAAG
1 AAAC-TTTACCAAACTTTGAAAAAACATTTTTTAAAG
37525 TTGATTGCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
36 4 0.11
37 18 0.51
38 13 0.37
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (36 bp):
AAACTTTACCAAACTTTGAAAAAACATTTTTTAAAG
Found at i:46587 original size:30 final size:30
Alignment explanation
Indices: 46513--46587 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
46503 GAAAATCGAA
* *
46513 TTAAACAGGGACGGAGAAAAATCGTTTATG
1 TTAAACGGGGACGGGGAAAAATCGTTTATG
46543 TTAAACGGGGACGGGGAAAAATCGTTTATG
1 TTAAACGGGGACGGGGAAAAATCGTTTATG
46573 TTAAACGGGGACGGG
1 TTAAACGGGGACGGG
46588 TTTAGTAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.35, C:0.11, G:0.33, T:0.21
Consensus pattern (30 bp):
TTAAACGGGGACGGGGAAAAATCGTTTATG
Found at i:46862 original size:25 final size:24
Alignment explanation
Indices: 46825--46878 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
46815 TTTAAATCCC
* *
46825 TACGGTTTTTTAAGCGGGGACGGG
1 TACGGTTTTTTAAACAGGGACGGG
46849 TACGCGTTTTTTAAACAGGGACGGG
1 TACG-GTTTTTTAAACAGGGACGGG
*
46874 GACGG
1 TACGG
46879 GGGACCAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.20, C:0.15, G:0.39, T:0.26
Consensus pattern (24 bp):
TACGGTTTTTTAAACAGGGACGGG
Found at i:47864 original size:17 final size:18
Alignment explanation
Indices: 47817--47864 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
47807 AAGTTGTAAG
*
47817 CTTTGCCTTTTTTGTGTT
1 CTTTGCTTTTTTTGTGTT
47835 CTTTGCTTTTTTTGTGTT
1 CTTTGCTTTTTTTGTGTT
47853 CTTTG-TTTTTTT
1 CTTTGCTTTTTTT
47865 CATTTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 7 0.24
18 22 0.76
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.73
Consensus pattern (18 bp):
CTTTGCTTTTTTTGTGTT
Found at i:51506 original size:88 final size:89
Alignment explanation
Indices: 51348--51509 Score: 238
Period size: 88 Copynumber: 1.8 Consensus size: 89
51338 ATGATCTTTC
* * * *
51348 TAAGTTTTCGTAACGCTTGTATGTTTCTATGATCTTTTTAAGAAGTGAATTAGGATTATATGATG
1 TAAGTTGTCGTAACGCTCGTATGTTTCTATGATCTTTATAAGAAGTGAATTAGGATAATATGATG
51413 ATCTTTCTAAGTTTTTGTAACACT
66 ATCTTTCTAAGTTTTTGTAACACT
* *
51437 TAAGTTGTCGTAACGCTCGTGTGCTTT-TATGATC-TTATCAGAAGTGAATTAGGATAATATGAT
1 TAAGTTGTCGTAACGCTCGTATG-TTTCTATGATCTTTATAAGAAGTGAATTAGGATAATATGAT
*
51500 GTTCTTTCTA
65 GATCTTTCTA
51510 TGTTGTGGTA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
88 35 0.54
89 27 0.42
90 3 0.05
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.44
Consensus pattern (89 bp):
TAAGTTGTCGTAACGCTCGTATGTTTCTATGATCTTTATAAGAAGTGAATTAGGATAATATGATG
ATCTTTCTAAGTTTTTGTAACACT
Found at i:51558 original size:71 final size:71
Alignment explanation
Indices: 51440--51729 Score: 234
Period size: 71 Copynumber: 4.2 Consensus size: 71
51430 TAACACTTAA
* * * * * * *
51440 GTTGTCGTAACGCTCGTGTGCTTTTATGATCTTATCAGAAGTGAATTAGGATAATATGATGTTCT
1 GTTGTCGTAACCCTCATGCGATTTGATGATCTTTTAAGAAGTGAATTAGGATAATATGATGTTCT
51505 TTCTAT
66 TTCTAT
* ** * * * * * * *
51511 GTTGTGGTAATGCTTATGCGATTTGATGATCTTTTAAGAAGTAAATTAGGATCATACGGTGATCC
1 GTTGTCGTAACCCTCATGCGATTTGATGATCTTTTAAGAAGTGAATTAGGATAATATGATGTTCT
51576 TTCTAT
66 TTCTAT
* *** * *
51582 GTTGTCGTAACCCTCCTGTTCTTTTATGATCTTTTAAGAAGTGAATTAGGATATTAT-AT-TAAT
1 GTTGTCGTAACCCTCATGCGATTTGATGATCTTTTAAGAAGTGAATTAGGATAATATGATGT--T
51645 CTTTCTAT
64 CTTTCTAT
* * * * * *
51653 GTTGTCGTAACACTCGTGC--TTTTATGATCTTTT-A-AA-TGAATTAGGATCATATAATGATCT
1 GTTGTCGTAACCCTCATGCGATTTGATGATCTTTTAAGAAGTGAATTAGGATAATATGATGTTCT
* *
51713 TTTTAA
66 TTCTAT
51719 GTTGTCGTAAC
1 GTTGTCGTAAC
51730 GAACGCCTGT
Statistics
Matches: 176, Mismatches: 39, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
66 32 0.18
67 4 0.02
68 1 0.01
69 14 0.08
70 1 0.01
71 124 0.70
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.43
Consensus pattern (71 bp):
GTTGTCGTAACCCTCATGCGATTTGATGATCTTTTAAGAAGTGAATTAGGATAATATGATGTTCT
TTCTAT
Found at i:55404 original size:15 final size:15
Alignment explanation
Indices: 55384--55422 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
55374 TTAAATCCAG
*
55384 TTTTGGTTCTAGTTA
1 TTTTGGTTCTAGATA
*
55399 TTTTGGTTCTGGATA
1 TTTTGGTTCTAGATA
55414 TTTTCGGTT
1 TTTT-GGTT
55423 TGGGTTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.10, C:0.08, G:0.23, T:0.59
Consensus pattern (15 bp):
TTTTGGTTCTAGATA
Found at i:56066 original size:2 final size:2
Alignment explanation
Indices: 56061--56107 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
56051 CACACACATT
56061 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
56103 TA TA T
1 TA TA T
56108 CATTTAAACA
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
Found at i:57911 original size:12 final size:12
Alignment explanation
Indices: 57894--57918 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57884 TTGAGACTTT
57894 AAACCGAACCGA
1 AAACCGAACCGA
57906 AAACCGAACCGA
1 AAACCGAACCGA
57918 A
1 A
57919 TAATATCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACCGAACCGA
Found at i:57931 original size:20 final size:20
Alignment explanation
Indices: 57906--57956 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
57896 ACCGAACCGA
57906 AAACCGAACCGAATAATATC
1 AAACCGAACCGAATAATATC
* *
57926 AAACCGAACTGAATAATGTC
1 AAACCGAACCGAATAATATC
57946 AAACCGAACCG
1 AAACCGAACCG
57957 TTTTACTCGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.25, G:0.14, T:0.14
Consensus pattern (20 bp):
AAACCGAACCGAATAATATC
Found at i:66213 original size:140 final size:140
Alignment explanation
Indices: 65961--66213 Score: 488
Period size: 140 Copynumber: 1.8 Consensus size: 140
65951 AAAAAGGATT
65961 TGGTTAAACCAATGAATCACAGAATAACCCGAACCCTCAGAGCTACCCAAATACATGTAAAGCAA
1 TGGTTAAACCAATGAATCACAGAATAACCCGAACCCTCAGAGCTACCCAAATACATGTAAAGCAA
*
66026 CAAACAGGAAATACCCACAAAGGAGAAAAGAAAGGATTTGTGGTAATCGTTGAAGAAGAGCCTGG
66 CAAACAGGAAATACCCACAAAGGAGAAAAGAAAGGAATTGTGGTAATCGTTGAAGAAGAGCCTGG
66091 TTTGAAGATC
131 TTTGAAGATC
*
66101 TGGTTAAACCAATGAATCCCAGAATAACCCGAACCCTCAGAGCTACCCAAATACATGTAAAGCAA
1 TGGTTAAACCAATGAATCACAGAATAACCCGAACCCTCAGAGCTACCCAAATACATGTAAAGCAA
66166 CAAACAGGAAATACCCACAAAGGAGAAAAGAAAGGAATTGTGGTAATC
66 CAAACAGGAAATACCCACAAAGGAGAAAAGAAAGGAATTGTGGTAATC
66214 ATTGTGGTAA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 111 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (140 bp):
TGGTTAAACCAATGAATCACAGAATAACCCGAACCCTCAGAGCTACCCAAATACATGTAAAGCAA
CAAACAGGAAATACCCACAAAGGAGAAAAGAAAGGAATTGTGGTAATCGTTGAAGAAGAGCCTGG
TTTGAAGATC
Found at i:68285 original size:7 final size:8
Alignment explanation
Indices: 68261--68292 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
68251 TTGATTTTGA
68261 TATTTTTAT
1 TATTTTT-T
68270 TATTTTTT
1 TATTTTTT
68278 TATTTTTT
1 TATTTTTT
68286 TATTTTT
1 TATTTTT
68293 AATAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
TATTTTTT
Found at i:68839 original size:12 final size:12
Alignment explanation
Indices: 68822--68847 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
68812 ACTTCAGCTT
68822 TTATAAAATTTG
1 TTATAAAATTTG
68834 TTATAAAATTTG
1 TTATAAAATTTG
68846 TT
1 TT
68848 TAATCAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (12 bp):
TTATAAAATTTG
Found at i:79701 original size:23 final size:24
Alignment explanation
Indices: 79670--79714 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
79660 GATAACGTAT
* *
79670 ATTTTATCATATATA-TATTTTTA
1 ATTTAATCATACATATTATTTTTA
79693 ATTTAATCATACATATTATTTT
1 ATTTAATCATACATATTATTTT
79715 GAGGAATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTAATCATACATATTATTTTTA
Found at i:79985 original size:36 final size:34
Alignment explanation
Indices: 79929--79997 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 34
79919 AATTGAACGT
79929 TAAATTTTGAACAGAATACTAAAATCAAACAAAC
1 TAAATTTTGAACAGAATACTAAAATCAAACAAAC
* * *
79963 TAAAGTTTTTAACAAGAGTACTAAAATGAAACAAA
1 TAAA-TTTTGAAC-AGAATACTAAAATCAAACAAA
79998 AAATTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 4 0.13
35 7 0.23
36 19 0.63
ACGTcount: A:0.55, C:0.12, G:0.09, T:0.25
Consensus pattern (34 bp):
TAAATTTTGAACAGAATACTAAAATCAAACAAAC
Done.