Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007643.1 Hibiscus syriacus cultivar Beakdansim tig00024392_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: 10939
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.28
Found at i:782 original size:328 final size:326
Alignment explanation
Indices: 66--740 Score: 1207
Period size: 325 Copynumber: 2.1 Consensus size: 326
56 ATGTAGGTAC
66 TTGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGACTCGGCGGAGCTTTCTTAGCCGAGAAACG
1 TTGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGACTCGGCGGAGCTTTCTTAGCCGAGAAACG
131 GTC-AAAAACTCCAGTTTTTTGACCGTTCGCGAAAGTTCACCGACCGCGCGTTTTTCGCCGATCC
66 GTCAAAAAACTCCAGTTTTTTGACCGTTCGCGAAAGTTCACCGACCGCGCGTTTTTCGCCGATCC
195 AGCGGACCAGCGGACTCGCAGAGCTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAAGG
131 AGCGGACCAGCGGACTCGCAGAGCTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAAGG
* *
260 GACTTGCCGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCATTCTTC
196 GACTTGCCGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCATGCTAC
*
325 CCCTGTCGATTTTCTCGATTTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCTTACATA
261 CCCTGTCGATTTTCTCGATTATGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCTTACATA
390 G
326 G
*
391 TTGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGGCTCGGCGGAGCTTTCTTAGCCGAGAAACG
1 TTGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGACTCGGCGGAGCTTTCTTAGCCGAGAAACG
*
456 GTCAAAAAAC-CC-TTTTTTTGACCGTTTCGCGAAAGTTCACCGACCGCGCGTTTTTTCGCCGAT
66 GTCAAAAAACTCCAGTTTTTTGACCG-TTCGCGAAAGTTCACCGACCGCGCG-TTTTTCGCCGAT
519 CCAGCGGACCAGCGGACTCGCAGAGCTTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCA
129 CCAGCGGACCAGCGGACTCGCAGAGC-TTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCA
584 AGGGGACTTGCCCGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAA-TTCACTCCAT
193 A-GGGACTTG-CCGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCAT
*
648 GGTACCCCTGTCGATTTTTCTCGATTATGGAGGAG-AAAAAAATTTCGAGCTGAGTGTCGGATCT
256 GCTACCCCTGTCGA-TTTTCTCGATTATGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCT
712 TACATAG
320 TACATAG
719 TTGGAGGCGTAGAATCGATTCC
1 TTGGAGGCGTAGAATCGATTCC
741 GCACGGTCTT
Statistics
Matches: 337, Mismatches: 6, Indels: 11
0.95 0.02 0.03
Matches are distributed among these distances:
324 11 0.03
325 94 0.28
326 44 0.13
327 39 0.12
328 87 0.26
329 62 0.18
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.26
Consensus pattern (326 bp):
TTGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGACTCGGCGGAGCTTTCTTAGCCGAGAAACG
GTCAAAAAACTCCAGTTTTTTGACCGTTCGCGAAAGTTCACCGACCGCGCGTTTTTCGCCGATCC
AGCGGACCAGCGGACTCGCAGAGCTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAAGG
GACTTGCCGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCATGCTAC
CCCTGTCGATTTTCTCGATTATGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCTTACATA
G
Found at i:1510 original size:320 final size:311
Alignment explanation
Indices: 938--1526 Score: 685
Period size: 320 Copynumber: 1.9 Consensus size: 311
928 GGTTTTTGCC
* *
938 CGATGGGCGAACTTTCGATTTCGACCCGAAAAATTTAGTCCATGTAACCCATGTCAGTTTTTCTC
1 CGATCGGCGAACTATCGATTTCGACCCGAAAAATTTAGTCCATGT-ACCCATGTCAGTTTTTCTC
* ** * *
1003 CAGTTTGGACTGAGAAAAAACGTTTGAAATTTCAGTTGCATCCTACGTAGTTGGAGGCGTAGAAT
65 CAGTTTGGACTGAAAAAAAAAATTCGAAATTTCAGTTGCATCCTACGCAGTTGGAGGCGTAGAAT
*
1068 CGATTCCGCACGGTCCCGACTCTCTGCGAGACTTCCTGAGCCGAGAAACAGTCAAAAACGAGCAT
130 CGATTCCGCACGGTCCCGACGCTCTGCGAGACTTCCTGAGCCGAGAAACAGTCAAAAACGAGCAT
* * * * *
1133 TTCTGAACACTTTTTGACTCTTTCTCCGTACGTTTTTCAGCAGATAGCTCTAAGCGAGGGACTCG
195 TTCTGAACAATTTTTGACTCTTTCTCAGTACGTTTTTCAGCAGACAGCCCGAAGCGAGGGACTCG
1198 CGGAGCTTTCGGACTCAGCGTCAATTCCAAGCGGCCTAACTTGCTTTCGGCT
260 CGGAGCTTTCGGACTCAGCGTCAATTCCAAGCGGCCTAACTTGCTTTCGGCT
* * * *
1250 CGATCGGCGAACTATCGATTTTTGACGCTAAAAGTTTAGTCCATGT-CCC-TGTC-GATTTTTCT
1 CGATCGGCGAACTATCGA-TTTCGACCCGAAAAATTTAGTCCATGTACCCATGTCAG-TTTTTCT
* *
1312 CGA-TTTGGGACTGAAAAAAAAAATTCGAGATTTCAGTCT-CATCCTACGCAG-T-GAGGCGTAG
64 CCAGTTT-GGACTGAAAAAAAAAATTCGAAATTTCAGT-TGCATCCTACGCAGTTGGAGGCGTAG
** * * *
1373 AATCGATTCCGCACGGTCTTGGCGCTCTGCGAGGCTTCCTTAGCCGAAAAAACAGTCAAAAACAG
127 AATCGATTCCGCACGGTCCCGACGCTCTGCGAGACTTCCTGAGCCG-------AG----AAACA-
* * *
1438 GTCAAAAACGAGCTTTTCTGACCAATTTTTGACTCTTTGGCT-AG-AGCG-TTTTCAGCGGACAG
180 GTCAAAAACGAGCATTTCTGAACAATTTTTGACTCTTT--CTCAGTA-CGTTTTTCAGCAGACAG
1500 CCCGAAGCGAGGGACTCGCGGAGCTTT
242 CCCGAAGCGAGGGACTCGCGGAGCTTT
1527 TCAGACTGGA
Statistics
Matches: 231, Mismatches: 27, Indels: 30
0.80 0.09 0.10
Matches are distributed among these distances:
308 49 0.21
309 5 0.02
310 49 0.21
311 4 0.02
312 16 0.07
313 23 0.10
315 2 0.01
319 5 0.02
320 73 0.32
321 3 0.01
322 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (311 bp):
CGATCGGCGAACTATCGATTTCGACCCGAAAAATTTAGTCCATGTACCCATGTCAGTTTTTCTCC
AGTTTGGACTGAAAAAAAAAATTCGAAATTTCAGTTGCATCCTACGCAGTTGGAGGCGTAGAATC
GATTCCGCACGGTCCCGACGCTCTGCGAGACTTCCTGAGCCGAGAAACAGTCAAAAACGAGCATT
TCTGAACAATTTTTGACTCTTTCTCAGTACGTTTTTCAGCAGACAGCCCGAAGCGAGGGACTCGC
GGAGCTTTCGGACTCAGCGTCAATTCCAAGCGGCCTAACTTGCTTTCGGCT
Found at i:3035 original size:328 final size:330
Alignment explanation
Indices: 2558--3489 Score: 1042
Period size: 327 Copynumber: 2.8 Consensus size: 330
2548 GATCTTACAT
** * * * *
2558 AGTTGGAGGCGTAGAATCGATTCCGCACGGTCTTGACTCTCGGCG-GAGCTTTCTTAGCCTAGAA
1 AGTTGGAGGCGTAGAATCGATTCCGCACGGTCCCGACGCTCTGCGAGA-CTTCCTGAGCC--G--
* * * * * *
2622 ACAGTCAGAAACTGGTCGAAAACGAGCATTTCCGACCACTTTTTGACTCTTTTTCTGGAGCATTT
61 A-AG--A-AAACAGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTC-AGAGCGTTT
* *
2687 TCAGCAGATAGCTGTAAGCGAGGGACTTGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAG
121 TCAGCAGATAGCTCTAAGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAG
* * * *
2752 TCTATTCAAAGCGAGCTTACTTGGTTTTGGCCTGATGGGCGAACTTTCGATTTCGACCCGAAAAA
186 TCAATTCCAAGCGAGCTTACTTGGTTTCGGCCTGATCGGCGAACTTTCGATTTCGACCCGAAAAA
**
2817 TTTAGTCCATGTAACCCATGTCAATTTTTCTCCAGTTT-GGACTGAGAAAAAACGTTT-GAAATT
251 TTTAGTCCATGTAACCCATGTCAATTTTTCTCCA-TTTGGGACTGA-AAAAAAAATTTCGAAATT
*
2880 TCAGT-TGCATCCTACGT
314 TCAGTCT-CATCCTACGC
*
2897 AGTTGGAGGCGTAGAATCGATTCCGCACGGTCCCGACTCTCTGCGAGACTTCCTGAGCCG-AG-A
1 AGTTGGAGGCGTAGAATCGATTCCGCACGGTCCCGACGCTCTGCGAGACTTCCTGAGCCGAAGAA
* *
2960 AACA-GTCAAAAACGAGCATTTCTGAACACTTTTTGACTCTTTCTCCGTAGCGTTTTCAGCAGAT
66 AACAGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCAG-AGCGTTTTCAGCAGAT
*
3024 AGCTCTAAGCGAGGGACTCGCGGAGC-TTTCGGACTCGAAAATCGCACTCAGCGGGTCAATTCCA
130 AGCTCTAAGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCCA
* * * * * * *
3088 AGCG-GCCTAACTTGCTTTCGG-CTCGATCGGCGAACTATCGATTTTGACGCTAAAAGTTTAGTC
195 AGCGAG-CTTACTTGGTTTCGGCCT-GATCGGCGAACTTTCGATTTCGACCCGAAAAATTTAGTC
* * * *
3151 CATGTAACCCCTGTCGATTTTTCTCGATTTGGGACTGAAAAAAAAATTTCGAGATTTCAGTCTCA
258 CATGTAACCCATGTCAATTTTTCTCCATTTGGGACTGAAAAAAAAATTTCGAAATTTCAGTCTCA
3216 TCCTACGC
323 TCCTACGC
** * * *
3224 AGTTGGAGGCGTAGAATCGATTCCGCACGGTCTTGGCGCTCTGCGAGGCTTCCTTAGCCGAAAAA
1 AGTTGGAGGCGTAGAATCGATTCCGCACGGTCCCGACGCTCTGCGAGACTTCCTGAGCCG----A
* *
3289 CAGTCAAAAACAGGTCAAAAACGAGCTTTTCTGACCAATTTTTGACTCTTTGGCT-AGAGCGTTT
62 -AG---AAAACAGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTT--CTCAGAGCGTTT
* * * * * * * * *
3353 TCAGCGGACAGCCCGAAGCGAGGGACTCGCGGAGCTTTTCAGACTGGAGAATCGCACTTAGCGTG
121 TCAGCAGATAGCTCTAAGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAG
* * *
3418 TCAATTCCAAGCGAGCTTCCTCGGTTTCAGCCTGATCGGCGAACTTTCGATTTCGACCCCG-AAA
186 TCAATTCCAAGCGAGCTTACTTGGTTTCGGCCTGATCGGCGAACTTTCGATTTCGA-CCCGAAAA
3482 ATTTAGTC
250 ATTTAGTC
3490 GATTAAAGAA
Statistics
Matches: 507, Mismatches: 62, Indels: 48
0.82 0.10 0.08
Matches are distributed among these distances:
326 15 0.03
327 189 0.37
328 77 0.15
329 4 0.01
333 4 0.01
337 6 0.01
338 73 0.14
339 130 0.26
340 9 0.02
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (330 bp):
AGTTGGAGGCGTAGAATCGATTCCGCACGGTCCCGACGCTCTGCGAGACTTCCTGAGCCGAAGAA
AACAGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCAGAGCGTTTTCAGCAGATA
GCTCTAAGCGAGGGACTCGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGCGAGTCAATTCCAA
GCGAGCTTACTTGGTTTCGGCCTGATCGGCGAACTTTCGATTTCGACCCGAAAAATTTAGTCCAT
GTAACCCATGTCAATTTTTCTCCATTTGGGACTGAAAAAAAAATTTCGAAATTTCAGTCTCATCC
TACGC
Found at i:8904 original size:197 final size:197
Alignment explanation
Indices: 8548--8910 Score: 426
Period size: 197 Copynumber: 1.8 Consensus size: 197
8538 GAAACTGGTC
* * **
8548 AAAAACGAGCATTTCTGACTCCTTTTTGAATCTTTCTCTGGAGCGTTTTCAGCGGATAGCTTTAA
1 AAAAACGAGCATTTCTGACTCCTTTTTGAACCTTTCTCTGGAGCGTTTTCAGCAGATAGCTCGAA
* * * * **
8613 GCGAGGGAGTCGCGAACCTTTACCGACTCGAAAATCGCACTCGGCGGGTCAATTCCAAGTTACCT
66 GCAAGGGACTCACGAACCTTTACCGACTCGAAAATCGCACTCAGCGGGTCAATTCCAAGGGACCT
** * * * ** *
8678 TACTTGGTGCCGGTCCGATTGGCGAACTTTTGATTTTGTCAAGCCGAGAACCAGTCAAAAACAGG
131 TACCCGGTGCCAGCCCGATCGAAGAACTTTCGATTTTGTCAAGCCGAGAACCAGTCAAAAACAGG
8743 GG
196 GG
*
8745 AAAAACGAGCATTTCTGAC-CACTTTTTGACCCTTTCTCTGGAGCGTTTTCAGCAGATAGCTCGA
1 AAAAACGAGCATTTCTGACTC-CTTTTTGAACCTTTCTCTGGAGCGTTTTCAGCAGATAGCTCGA
* * * * * *
8809 AGCAAGGGACTTACGGAGCTATT-CCGACTGGAAAATTGCACTCAGCGGGTCATTTCCAAGGGGA
65 AGCAAGGGACTCACGAACCT-TTACCGACTCGAAAATCGCACTCAGCGGGTCAATTCCAA-GGGA
* **
8873 -CTTGCCCGGTTTCAGCCCGATCGAAGAACTTTCGATTT
128 CCTTACCCGGTGCCAGCCCGATCGAAGAACTTTCGATTT
8911 CGACCCCGAA
Statistics
Matches: 135, Mismatches: 28, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
196 1 0.01
197 130 0.96
198 4 0.03
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (197 bp):
AAAAACGAGCATTTCTGACTCCTTTTTGAACCTTTCTCTGGAGCGTTTTCAGCAGATAGCTCGAA
GCAAGGGACTCACGAACCTTTACCGACTCGAAAATCGCACTCAGCGGGTCAATTCCAAGGGACCT
TACCCGGTGCCAGCCCGATCGAAGAACTTTCGATTTTGTCAAGCCGAGAACCAGTCAAAAACAGG
GG
Found at i:10490 original size:332 final size:332
Alignment explanation
Indices: 9884--10544 Score: 1225
Period size: 332 Copynumber: 2.0 Consensus size: 332
9874 GCTTTCCGAT
*
9884 TGGTCCCGAGGCTCGACGGAGCTTTCTTAGCCGAGAAACGGTCAAAAACTCCAGTGTTTTTGATC
1 TGGTCCCGAGGCTCGACGGAGCTTTCTTAGCCGAGAAACGGTCAAAAACTCCAGTGTTTTTGACC
*
9949 GTTTCGCGAAAGTTCACCGACCTCGCGCTTTTCGCCGATCCAGCGGACCAGCGGACTCGCAGAGC
66 GTTTCGCGAAAGTTCACCGACCGCGCGCTTTTCGCCGATCCAGCGGACCAGCGGACTCGCAGAGC
10014 TTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAAGGGGACTTGCCCGGTTTCAGCCCGA
131 TTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAAGGGGACTTGCCCGGTTTCAGCCCGA
*
10079 TCGGAGAACTTTCGATTTCGACCCCGAAATTTCACTCCATGGTACCCCTGTCGATTAATCTCGAT
196 TCGGAGAACTTTCGATTTCGACCCCGAAATTTCACTCCATGCTACCCCTGTCGATTAATCTCGAT
10144 TTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCTTACATAGTTGGAGGCGTAGAATCGA
261 TTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCTTACATAGTTGGAGGCGTAGAATCGA
10209 TTCCCCG
326 TTCCCCG
*
10216 TGGTCCCGAGGCTCGGCGGAGCTTTCTTAGCCGAGAAACGGTCAAAAACTCCAGTGTTTTTGACC
1 TGGTCCCGAGGCTCGACGGAGCTTTCTTAGCCGAGAAACGGTCAAAAACTCCAGTGTTTTTGACC
*
10281 GTTTCGCGAAAGTTCACCGACCGCGCGTTTTTCGCCGATCCAGCGGACCAGCGGACTCGCAGAGC
66 GTTTCGCGAAAGTTCACCGACCGCGCGCTTTTCGCCGATCCAGCGGACCAGCGGACTCGCAGAGC
10346 TTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAAGGGGACTTGCCCGGTTTCAGCCCGA
131 TTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAAGGGGACTTGCCCGGTTTCAGCCCGA
* * * *
10411 TCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCATTCT-CACCCTGTCGATTTATCTTGA
196 TCGGAGAACTTTCGATTTCGACCCCGAAATTTCACTCCATGCTAC-CCCTGTCGATTAATCTCGA
10475 TTTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCTTACATAGTTGGAGGCGTAGAATCG
260 TTTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCTTACATAGTTGGAGGCGTAGAATCG
10540 ATTCC
325 ATTCC
10545 GCACGGTCTT
Statistics
Matches: 319, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
331 1 0.00
332 318 1.00
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (332 bp):
TGGTCCCGAGGCTCGACGGAGCTTTCTTAGCCGAGAAACGGTCAAAAACTCCAGTGTTTTTGACC
GTTTCGCGAAAGTTCACCGACCGCGCGCTTTTCGCCGATCCAGCGGACCAGCGGACTCGCAGAGC
TTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAAGGGGACTTGCCCGGTTTCAGCCCGA
TCGGAGAACTTTCGATTTCGACCCCGAAATTTCACTCCATGCTACCCCTGTCGATTAATCTCGAT
TTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCTTACATAGTTGGAGGCGTAGAATCGA
TTCCCCG
Done.