Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003890.1 Hibiscus syriacus cultivar Beakdansim tig00008403_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: 83555
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2305 original size:30 final size:30
Alignment explanation
Indices: 2247--2359 Score: 110
Period size: 30 Copynumber: 3.9 Consensus size: 30
2237 TTTAAAATTT
*
2247 ATTTAAGATCG-A-TAAA-TAATTTG-AATA
1 ATTTAAAATCGAATTAAACTAA-TTGAAATA
* *
2274 ATTTAAAATGGAATTAAACATACTT-AAATA
1 ATTTAAAATCGAATTAAAC-TAATTGAAATA
* *
2304 ATTTAAAATCGAGTCAAACTAATTGAAATA
1 ATTTAAAATCGAATTAAACTAATTGAAATA
* *
2334 TTTTAAAATCGAATTAAATTAATTGA
1 ATTTAAAATCGAATTAAACTAATTGA
2360 GAGTGAATTA
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
27 9 0.13
28 1 0.01
29 8 0.12
30 49 0.71
31 2 0.03
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (30 bp):
ATTTAAAATCGAATTAAACTAATTGAAATA
Found at i:2722 original size:26 final size:27
Alignment explanation
Indices: 2663--2722 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
2653 TTATTTTTAA
* *
2663 ATATATAATAATATGATCTAACAATTTT
1 ATATA-AAAAATATGATCTAACAATTTG
2691 AT-TAAAAAATATGAT-TAA-AATATTG
1 ATATAAAAAATATGATCTAACAAT-TTG
2716 ATATAAA
1 ATATAAA
2723 CTGAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
24 3 0.11
25 7 0.25
26 14 0.50
27 2 0.07
28 2 0.07
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.38
Consensus pattern (27 bp):
ATATAAAAAATATGATCTAACAATTTG
Found at i:10068 original size:14 final size:14
Alignment explanation
Indices: 10049--10077 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10039 CTAGGTTGAA
10049 GTTATTAAAAGATT
1 GTTATTAAAAGATT
10063 GTTATTAAAAGATT
1 GTTATTAAAAGATT
10077 G
1 G
10078 CCATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (14 bp):
GTTATTAAAAGATT
Found at i:11255 original size:42 final size:42
Alignment explanation
Indices: 11194--11275 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
11184 ATATTCTTTG
*
11194 CCTAGCTCAAATACTGAATGTAGCAACAAACAAAAAGCTCTT
1 CCTAGCTCAAATACAGAATGTAGCAACAAACAAAAAGCTCTT
11236 CCTAGCTCAAATACAGAATGTAGCAACAAACAAAAAGCTC
1 CCTAGCTCAAATACAGAATGTAGCAACAAACAAAAAGCTC
11276 CAGAAACCCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.18
Consensus pattern (42 bp):
CCTAGCTCAAATACAGAATGTAGCAACAAACAAAAAGCTCTT
Found at i:11697 original size:122 final size:122
Alignment explanation
Indices: 11473--11703 Score: 295
Period size: 122 Copynumber: 1.9 Consensus size: 122
11463 CCGGAGAGTA
**
11473 TGTTACATCAACGGTCACAGTTGGAACAGCAATCCCATGTTACAATTAGCATCTAGTTCATCAAT
1 TGTTACATCAACGGTCACAGTTGGAACAGCAATCCCATGTTACAATTAGCATCTAACTCATCAAT
*** *
11538 GCCTATTCTAAGCTAACACATCGATTACAAGTGTATACAAGCATTGGGGGGGGGGGG
66 GCCTATTCTAAGCTAACACAAAAATTACAAGTATATACAAGCATTGGGGGGGGGGGG
* * * * **
11595 TGTTACATTAACGGTTACAGTTGGATCAGCAA-CCCTATGTTACAATTTGCATCTAACTCATCTG
1 TGTTACATCAACGGTCACAGTTGGAACAGCAATCCC-ATGTTACAATTAGCATCTAACTCATCAA
* * *
11659 TGCCTATTCTATGCTAACATAAAAATTACGCA-TATATACAAGCAT
65 TGCCTATTCTAAGCTAACACAAAAATTAC-AAGTATATACAAGCAT
11704 GTACAAGTGC
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
121 3 0.03
122 88 0.96
123 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (122 bp):
TGTTACATCAACGGTCACAGTTGGAACAGCAATCCCATGTTACAATTAGCATCTAACTCATCAAT
GCCTATTCTAAGCTAACACAAAAATTACAAGTATATACAAGCATTGGGGGGGGGGGG
Found at i:12568 original size:2 final size:2
Alignment explanation
Indices: 12561--12585 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12551 AAAGATAACA
12561 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
12586 TGGGAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16802 original size:22 final size:22
Alignment explanation
Indices: 16757--16822 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
16747 AAATTACATG
* *
16757 AATATCAAATT-TATAAA-AAA
1 AATATAAAATTATAAAAATAAA
16777 AATA-AAAAGTTATAAAAATAAA
1 AATATAAAA-TTATAAAAATAAA
* *
16799 AATATCATATTATAAAAATAAA
1 AATATAAAATTATAAAAATAAA
16821 AA
1 AA
16823 GAATATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 3 0.08
20 6 0.16
21 5 0.13
22 22 0.58
23 2 0.05
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (22 bp):
AATATAAAATTATAAAAATAAA
Found at i:17548 original size:14 final size:15
Alignment explanation
Indices: 17519--17552 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
17509 ATTTGGGGTT
*
17519 ATTTTTTAGATTTTA
1 ATTTTTTAGATATTA
17534 ATTTTTTA-ATATTA
1 ATTTTTTAGATATTA
17548 ATTTT
1 ATTTT
17553 ATGTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
ATTTTTTAGATATTA
Found at i:23488 original size:60 final size:60
Alignment explanation
Indices: 23326--23490 Score: 174
Period size: 60 Copynumber: 2.8 Consensus size: 60
23316 TAAAAATTGT
* * * *
23326 AATATTCAAAAGTTTGGGGATCAATTTAGAA-AAAAGTCACAGTTTAGGGATCAAATTAG
1 AATATTCAAAAGTTTAGGGACCAATTTAGAATAAAAGTCATAGTTTAGGAATCAAATTAG
* ** * * * *
23385 AATGTTCAAAAGAATAGGGACTAAGTTAGAATGAAAGTCATAGTTT-GAGAATGAAATTAG
1 AATATTCAAAAGTTTAGGGACCAATTTAGAATAAAAGTCATAGTTTAG-GAATCAAATTAG
* *
23445 AATATTCAAAAGTTTAAGGACCAATTTAAAATAAAAG-CTATAGTTT
1 AATATTCAAAAGTTTAGGGACCAATTTAGAATAAAAGTC-ATAGTTT
23491 TGGGACTTAT
Statistics
Matches: 84, Mismatches: 19, Indels: 5
0.78 0.18 0.05
Matches are distributed among these distances:
59 26 0.31
60 58 0.69
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (60 bp):
AATATTCAAAAGTTTAGGGACCAATTTAGAATAAAAGTCATAGTTTAGGAATCAAATTAG
Found at i:37850 original size:37 final size:40
Alignment explanation
Indices: 37800--37883 Score: 129
Period size: 37 Copynumber: 2.2 Consensus size: 40
37790 CCTTTGTTCA
*
37800 GTTGATGTTATTGCAGAAAAAAC-T-CATACTCTACAA-T
1 GTTGATGTTATTGCAGAAAAAACTTAAATACTCTACAATT
*
37837 GTTGATGTTATTGCAGAAAAAGCTTAAATACTCTACAATT
1 GTTGATGTTATTGCAGAAAAAACTTAAATACTCTACAATT
37877 GTTGATG
1 GTTGATG
37884 CTCAAACTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
37 22 0.52
38 1 0.02
39 11 0.26
40 8 0.19
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (40 bp):
GTTGATGTTATTGCAGAAAAAACTTAAATACTCTACAATT
Found at i:44345 original size:113 final size:112
Alignment explanation
Indices: 44105--44310 Score: 319
Period size: 113 Copynumber: 1.8 Consensus size: 112
44095 TTATTTATTT
* *
44105 TAGTAACTTGGACACCCTTGCTAAATGGTTGTATATTTAAACCTTAGATTTTCAACAAGAACCAA
1 TAGTAACTTGGACACCCTCGCTAAATGGTAGTATATTTAAACCTTAGATTTTCAACAAGAACCAA
* *
44170 AAAGACGAAAACACCCTTGCTAAGTATGTATATCATATCAGCCACTAA
66 AAAGACGAAAACACCCTTGCTAAG-ATGAAGATCATATCAGCCACTAA
* *
44218 TAGTAACTTAGACACCCTCGCTAAATGGTAGTATATTTAAACCCTT-GATTTTCAACAATAACCA
1 TAGTAACTTGGACACCCTCGCTAAATGGTAGTATATTTAAA-CCTTAGATTTTCAACAAGAACCA
44282 AAAAGACGAAAACACCCTTG-TAA-ATGAAG
65 AAAAGACGAAAACACCCTTGCTAAGATGAAG
44311 GTGTTTTCAG
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
110 4 0.05
112 3 0.03
113 75 0.87
114 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.27
Consensus pattern (112 bp):
TAGTAACTTGGACACCCTCGCTAAATGGTAGTATATTTAAACCTTAGATTTTCAACAAGAACCAA
AAAGACGAAAACACCCTTGCTAAGATGAAGATCATATCAGCCACTAA
Found at i:45237 original size:18 final size:18
Alignment explanation
Indices: 45214--45259 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
45204 TTTAGGTTAA
45214 GGAGAATCCTTCACTTTG
1 GGAGAATCCTTCACTTTG
*
45232 GGAGAATCATTCACTTTG
1 GGAGAATCCTTCACTTTG
*
45250 GGAGAGTCCT
1 GGAGAATCCT
45260 ATATCTGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (18 bp):
GGAGAATCCTTCACTTTG
Found at i:61984 original size:3 final size:3
Alignment explanation
Indices: 61976--62004 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
61966 TCAGATGTGG
61976 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
62005 ATATCGGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:73736 original size:68 final size:67
Alignment explanation
Indices: 73558--73761 Score: 263
Period size: 68 Copynumber: 3.0 Consensus size: 67
73548 AATTTTGAAA
* *
73558 AAATAATAATCGAATGACTAAAACATAAATTAAATAATATATAAGTGACCAAATAGATAGTTTAC
1 AAATAATAATCG-ATGACTAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
*
73623 CAT
65 CCT
* * * *
73626 AAATAAAAAT-GTAT-A-TATGAA-TTATATTAGATAATATATAAGTGACCAAATAGGTAGTTTA
1 AAATAATAATCG-ATGACTA-AAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTA
73687 CCCT
64 CCCT
* *
73691 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATACGTAGTTTAC
1 AAATAATAATCGA-TGACTAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
73756 CCT
65 CCT
73759 AAA
1 AAA
73762 AAAATCCCTA
Statistics
Matches: 116, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
65 51 0.44
66 5 0.04
67 6 0.05
68 54 0.47
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (67 bp):
AAATAATAATCGATGACTAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACC
CT
Done.