Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007032.1 Hibiscus syriacus cultivar Beakdansim tig00018205_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: 83163
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1872 original size:23 final size:23
Alignment explanation
Indices: 1842--1887 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1832 GATTATTGGG
1842 GGGTGAGTCACCATTGACGAGTC
1 GGGTGAGTCACCATTGACGAGTC
* * *
1865 GGGTGAGTTATCATTGATGAGTC
1 GGGTGAGTCACCATTGACGAGTC
1888 TTTCTTATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.15, G:0.35, T:0.28
Consensus pattern (23 bp):
GGGTGAGTCACCATTGACGAGTC
Found at i:11004 original size:75 final size:75
Alignment explanation
Indices: 10881--11089 Score: 267
Period size: 75 Copynumber: 2.8 Consensus size: 75
10871 AACAATCGGC
* * * * **
10881 CTTTCCGTCCCGTAAATGAACAAGCTGCGTCTCATGGTCATCTTCCTCGGCTCCCTTTTAGTGGA
1 CTTTCTGTCCCATAAACGAACAAGCTGCGTCTCATGGTCATCTTCCTCGGCTCCCTTTCACCGGA
*
10946 CGAAATA-AAT
66 C-AAAAACAAT
* * * *
10956 CTTTCTGTCCCTTGAACGAACAAGCTGTGTCTCATGGTCATCTTCCTCGGCTCCCTTTCACCGGT
1 CTTTCTGTCCCATAAACGAACAAGCTGCGTCTCATGGTCATCTTCCTCGGCTCCCTTTCACCGGA
11021 CAAAAACAAT
66 CAAAAACAAT
* ** *
11031 CTTTCTGTCCCATAAATGAACAAGCTGCAACTCATGGTCATCTTCCTCAGCTCCCTTTC
1 CTTTCTGTCCCATAAACGAACAAGCTGCGTCTCATGGTCATCTTCCTCGGCTCCCTTTC
11090 GCCAATAGAT
Statistics
Matches: 116, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
74 4 0.03
75 112 0.97
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (75 bp):
CTTTCTGTCCCATAAACGAACAAGCTGCGTCTCATGGTCATCTTCCTCGGCTCCCTTTCACCGGA
CAAAAACAAT
Found at i:29158 original size:17 final size:17
Alignment explanation
Indices: 29133--29166 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29123 TCTTTATTTG
*
29133 TTTCGTTCCCCCCTTTT
1 TTTCCTTCCCCCCTTTT
*
29150 TTTCCTTCCCCTCTTTT
1 TTTCCTTCCCCCCTTTT
29167 GTGTGTGTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.41, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTCCTTCCCCCCTTTT
Found at i:29458 original size:24 final size:25
Alignment explanation
Indices: 29431--29481 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
29421 TGTTATTGTT
*
29431 ATTTCAATAAAATATATA-TTTT-AA
1 ATTTAAATAAAA-ATATACTTTTGAA
29455 ATTTAAATAAAAATATACTTTTGAA
1 ATTTAAATAAAAATATACTTTTGAA
29480 AT
1 AT
29482 ATAGAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 15 0.62
25 4 0.17
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTTAAATAAAAATATACTTTTGAA
Found at i:39703 original size:29 final size:29
Alignment explanation
Indices: 39671--39730 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
39661 CAAAAAAGTT
*
39671 TAAGTTGCAAATC-ACAAACCAAACTCAAG
1 TAAGTTGCAAACCGA-AAACCAAACTCAAG
*
39700 TAAGTTGCAAACCGAAAACCAAATTCAAG
1 TAAGTTGCAAACCGAAAACCAAACTCAAG
39729 TA
1 TA
39731 CTTAATTGCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.48, C:0.22, G:0.12, T:0.18
Consensus pattern (29 bp):
TAAGTTGCAAACCGAAAACCAAACTCAAG
Found at i:46990 original size:37 final size:37
Alignment explanation
Indices: 46949--47023 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 37
46939 GTTGGAAAAT
*
46949 ATTTATAT-ATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATAATTTTCTTTAAAAAATTTAAAAT-ATAAA
* *
46986 ATTTATATAATTTTTTTTACAAAATTTAAAATATAAA
1 ATTTATATAATTTTCTTTAAAAAATTTAAAATATAAA
47023 A
1 A
47024 AGTTTAATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 14 0.41
38 20 0.59
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (37 bp):
ATTTATATAATTTTCTTTAAAAAATTTAAAATATAAA
Found at i:51340 original size:16 final size:16
Alignment explanation
Indices: 51319--51351 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
51309 TCCAATTAAC
*
51319 ACATTCAGAGAGTACT
1 ACATTCAGAAAGTACT
51335 ACATTCAGAAAGTACT
1 ACATTCAGAAAGTACT
51351 A
1 A
51352 ACATGTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (16 bp):
ACATTCAGAAAGTACT
Found at i:53567 original size:27 final size:27
Alignment explanation
Indices: 53535--53597 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
53525 AATATTATCT
53535 AATACAAATTAGTTAACTAATATATTA
1 AATACAAATTAGTTAACTAATATATTA
*
53562 AATACAAAATAGTTAACTAATATATTA
1 AATACAAATTAGTTAACTAATATATTA
*
53589 AATATAAAT
1 AATACAAAT
53598 ATTTTTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (27 bp):
AATACAAATTAGTTAACTAATATATTA
Found at i:57340 original size:2 final size:2
Alignment explanation
Indices: 57335--57370 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
57325 ATTTTAATAG
57335 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
57371 CAAGACAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62824 original size:86 final size:87
Alignment explanation
Indices: 62722--62894 Score: 276
Period size: 86 Copynumber: 2.0 Consensus size: 87
62712 CGCGGTTTGG
* ** ** *
62722 GGATGAAAATGAAATGTTTAAAAGTTTGAGGATTAATTTAGAATGATAGTCATTATTTAAGGGTG
1 GGATGAAAATGAAATGTTTAAAAATTTGAGGATTAATTTAGAATGATAACCACAATTTAAAGGTG
*
62787 AAATTGAAAT-TTTAAAAAATT
66 AAATTAAAATATTTAAAAAATT
62808 GGATGAAAATGAAATGTTTAAAAATTTGAGGATTAATTTAGAATGATAACCACAATTTAAAGGTG
1 GGATGAAAATGAAATGTTTAAAAATTTGAGGATTAATTTAGAATGATAACCACAATTTAAAGGTG
62873 AAATTAAAATATTTAAAAAATT
66 AAATTAAAATATTTAAAAAATT
62895 ATAGACTAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 68 0.86
87 11 0.14
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.34
Consensus pattern (87 bp):
GGATGAAAATGAAATGTTTAAAAATTTGAGGATTAATTTAGAATGATAACCACAATTTAAAGGTG
AAATTAAAATATTTAAAAAATT
Found at i:62923 original size:15 final size:16
Alignment explanation
Indices: 62903--62937 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
62893 TTATAGACTA
62903 ATTTAAAATA-AAATT
1 ATTTAAAATATAAATT
*
62918 ATTTAAAATATATATT
1 ATTTAAAATATAAATT
62934 ATTT
1 ATTT
62938 TATAACCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTAAAATATAAATT
Found at i:63340 original size:20 final size:20
Alignment explanation
Indices: 63317--63382 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
63307 GAACTCTAAC
63317 TTCGCAACTCAGTTTACAAA
1 TTCGCAACTCAGTTTACAAA
*
63337 TTCGCAACTCAATTTACAAA
1 TTCGCAACTCAGTTTACAAA
* *
63357 TTCGTAACTCAGTTTCCAAA
1 TTCGCAACTCAGTTTACAAA
63377 TTCGCA
1 TTCGCA
63383 CTGTGGTAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.32
Consensus pattern (20 bp):
TTCGCAACTCAGTTTACAAA
Found at i:66308 original size:68 final size:68
Alignment explanation
Indices: 66199--66327 Score: 231
Period size: 68 Copynumber: 1.9 Consensus size: 68
66189 AACACATATG
* *
66199 CCCAAAGAGTTCCACACGACACCGTTTGATTTGTGTGGCTTTAGGGATCGCAATAAATTGGGTCC
1 CCCAAAGAGCTCCACACGACACCGTTTGATTTGTGTGGCTTTAGGGACCGCAATAAATTGGGTCC
66264 AAA
66 AAA
*
66267 CCCAAAGAGCTCCACACGATACCGTTTGATTTGTGTGGCTTTAGGGACCGCAATAAATTGG
1 CCCAAAGAGCTCCACACGACACCGTTTGATTTGTGTGGCTTTAGGGACCGCAATAAATTGG
66328 AGTGGACCCA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.26
Consensus pattern (68 bp):
CCCAAAGAGCTCCACACGACACCGTTTGATTTGTGTGGCTTTAGGGACCGCAATAAATTGGGTCC
AAA
Found at i:75537 original size:18 final size:19
Alignment explanation
Indices: 75504--75547 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
75494 GCAAGATTCT
* *
75504 CAATTTTACAAGGTGG-GC
1 CAATTTTACAACGTGGACC
*
75522 CAATTTTACACCGTGGACC
1 CAATTTTACAACGTGGACC
75541 CAATTTT
1 CAATTTT
75548 GGGCGAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (19 bp):
CAATTTTACAACGTGGACC
Found at i:81020 original size:26 final size:27
Alignment explanation
Indices: 80980--81030 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
80970 AGGTAATATT
80980 TTTTTCAAAAATATATAAA-ATTTATAA
1 TTTTTCAAAAATATA-AAATATTTATAA
*
81007 TTTTT-AAAATTATAAAATATTTAT
1 TTTTTCAAAAATATAAAATATTTAT
81031 TATTATCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 14 0.64
27 5 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTTTCAAAAATATAAAATATTTATAA
Found at i:81177 original size:344 final size:341
Alignment explanation
Indices: 80551--81370 Score: 1285
Period size: 344 Copynumber: 2.4 Consensus size: 341
80541 AAAAATATTA
*
80551 AATAATAATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATA-TTTTTTATATTCTT
1 AATAATAATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTATATTTTT
*
80615 AAACAATTAATTTTAAAAGGCAATAATTTTTTTTAAAATATATGAAATTTATAAGTTTTT-AAAT
66 AAACAATTAATTTTAAAAGG-AAT-ATTTTTTTCAAAATATATGAAATTTATAA-TTTTTAAAAT
80679 TAT-AAAA--TA-T-TTATCATCATCATCATCATTTTGTAAAAGAAATATTAATTATAAAACTTT
128 TATAAAAATTTATTATTATCATCATCATCATCATTTTGTAAAAGAAATATTAATTATAAAACTTT
** * *
80739 TATAAAATTATTCATATTGTAAAATACTTGTCTTCAAAGTTTTTATATACTAGATTATATGTATT
193 TATAAAATTATTCATATTGTAAAATACTTACCCTCAAAGTTTTTATATACTAGATTATACGTATT
* ** *
80804 GTGTAATTTTAATGCAAAAATTTAAATAATTTTATTAAAAATGAATAAACATTATTATCTGTTGT
258 GTGTAATTTTAATACAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAACTGTTGT
*
80869 TAAAAATTAAAAATTAATG
323 TAAAAAATAAAAATTAATG
80888 AATAATAATTCATTTGATAT-CTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTATATTTT
1 AATAATAATTCATTTGAT-TCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTATATTTT
*
80952 TAAACAATTAATTTTAAAAGGTAATATTTTTTTCAAAAATATATAAAATTTATAATTTTTAAAAT
65 TAAACAATTAATTTTAAAAGG-AATATTTTTTTC-AAAATATATGAAATTTATAATTTTTAAAAT
* *
81017 TATAAAATATTTATTATTATCATCATCATCATCATTTTGTAAAAGAAATATTAGTTATAAAATTT
128 TATAAAA-ATTTATTATTATCATCATCATCATCATTTTGTAAAAGAAATATTAATTATAAAACTT
* *
81082 TTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTTCTATACTAGATTATACGTAT
192 TTATAAAATTATTCATATTGTAAAATACTTACCCTCAAAGTTTTTATATACTAGATTATACGTAT
*
81147 TGTGTAATTTTAATACAAAAATCAAAATAATTTTATTAAAAATGAATAAATATTATTAACTGTTG
257 TGTGTAATTTTAATACAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAACTGTTG
81212 TTAAAAAATAAAAATTAATG
322 TTAAAAAATAAAAATTAATG
* *
81232 AATAATAATTCATTTAATTCCTTAATTGTAATTAAAAGTTTATTTTAATATTTTTTTATATTTTT
1 AATAATAATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTATATTTTT
81297 AAACAATTAATTTTAAAA--AA-A-----TTCAAAATATATGAAATTTATAATTTTTAAAATTAT
66 AAACAATTAATTTTAAAAGGAATATTTTTTTCAAAATATATGAAATTTATAATTTTTAAAATTAT
81354 AAAAAATTTATTATTAT
131 -AAAAATTTATTATTAT
81371 AAAAAATAAA
Statistics
Matches: 450, Mismatches: 21, Indels: 27
0.90 0.04 0.05
Matches are distributed among these distances:
334 44 0.10
335 7 0.02
337 61 0.14
338 63 0.14
339 3 0.01
340 2 0.00
341 2 0.00
342 2 0.00
343 2 0.00
344 264 0.59
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (341 bp):
AATAATAATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTATATTTTT
AAACAATTAATTTTAAAAGGAATATTTTTTTCAAAATATATGAAATTTATAATTTTTAAAATTAT
AAAAATTTATTATTATCATCATCATCATCATTTTGTAAAAGAAATATTAATTATAAAACTTTTAT
AAAATTATTCATATTGTAAAATACTTACCCTCAAAGTTTTTATATACTAGATTATACGTATTGTG
TAATTTTAATACAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTTAA
AAAATAAAAATTAATG
Done.