Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001661.1 Hibiscus syriacus cultivar Beakdansim tig00003320_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: 46805
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:6234 original size:43 final size:43
Alignment explanation
Indices: 6187--6364 Score: 146
Period size: 43 Copynumber: 4.2 Consensus size: 43
6177 ATATACATAA
*
6187 TTTTTAGCAGTGTTTGTAAAAAAAACACCACTAAAGAAC-TGAC
1 TTTTT-GCAGTGTTTGTAACAAAAACACCACTAAAGAACGTGAC
** * *
6230 TTTTTGTGGGGTTTGTAACAAAAACATCACTAAAGAACGTGAC
1 TTTTTGCAGTGTTTGTAACAAAAACACCACTAAAGAACGTGAC
* ** * * * * *
6273 TTTTTGCGGCATTTATAACAAAAACGCCGCTAAAGAACTTAAC
1 TTTTTGCAGTGTTTGTAACAAAAACACCACTAAAGAACGTGAC
* * * * * *
6316 TTTTTGCAGCT-TTTGTAA-TAAAACGCCGCTAATGAACCTAAC
1 TTTTTGCAG-TGTTTGTAACAAAAACACCACTAAAGAACGTGAC
6358 TTTTTGC
1 TTTTTGC
6365 GTCATTTGTT
Statistics
Matches: 113, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
42 56 0.50
43 57 0.50
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (43 bp):
TTTTTGCAGTGTTTGTAACAAAAACACCACTAAAGAACGTGAC
Found at i:6244 original size:42 final size:43
Alignment explanation
Indices: 6198--6365 Score: 160
Period size: 42 Copynumber: 4.0 Consensus size: 43
6188 TTTTAGCAGT
* * *
6198 GTTTGTAAAAAAAACACCACTAAAGAAC-TGACTTTTTGTGGG
1 GTTTGTAACAAAAACACCACTAAAGAACGTGACTTTTTGCGGC
*
6240 GTTTGTAACAAAAACATCACTAAAGAACGTGACTTTTTGCGGC
1 GTTTGTAACAAAAACACCACTAAAGAACGTGACTTTTTGCGGC
* * * * * * *
6283 ATTTATAACAAAAACGCCGCTAAAGAACTTAACTTTTTGCAGC
1 GTTTGTAACAAAAACACCACTAAAGAACGTGACTTTTTGCGGC
* * * * * * *
6326 TTTTGTAA-TAAAACGCCGCTAATGAACCTAACTTTTTGCG
1 GTTTGTAACAAAAACACCACTAAAGAACGTGACTTTTTGCG
6366 TCATTTGTTG
Statistics
Matches: 107, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 54 0.50
43 53 0.50
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (43 bp):
GTTTGTAACAAAAACACCACTAAAGAACGTGACTTTTTGCGGC
Found at i:7065 original size:34 final size:34
Alignment explanation
Indices: 7008--7075 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
6998 TCCATTTCGA
*
7008 GATTACATCAATCCGGACGAAATTACTTCCAAGG
1 GATTACATCAATCCGGACAAAATTACTTCCAAGG
* * * *
7042 GATTACATCAATTCGGGCAAAATTTCTTCTAAGG
1 GATTACATCAATCCGGACAAAATTACTTCCAAGG
7076 TAGTGGCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (34 bp):
GATTACATCAATCCGGACAAAATTACTTCCAAGG
Found at i:8412 original size:30 final size:30
Alignment explanation
Indices: 8378--8439 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
8368 TAAAATATAA
* *
8378 AATTTA-TCAGTTTTTCGGATAATTTCATTT
1 AATTTATTCACTTTTT-GAATAATTTCATTT
*
8408 AATTTATTGACTTTTTGAATAATTTCATTT
1 AATTTATTCACTTTTTGAATAATTTCATTT
8438 AA
1 AA
8440 ATTTTAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (30 bp):
AATTTATTCACTTTTTGAATAATTTCATTT
Found at i:8640 original size:59 final size:59
Alignment explanation
Indices: 8529--8640 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 59
8519 ATACGAGATC
*
8529 ATCTTACGTAAATAGTTTTAGATACTTTGCAATAATTTGAAATATTTTTCAATTAGGCA
1 ATCTTACGTAAATAGTTTTAGATACTTTGCAATAATTTGAAATATTTCTCAATTAGGCA
* * *
8588 ATCTTACGTGAATAGTTTT-GTATACCTTTTCAATAATTTGAGATA-TTCTCAAT
1 ATCTTACGTAAATAGTTTTAG-ATA-CTTTGCAATAATTTGAAATATTTCTCAAT
8641 AATTTGAGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
58 1 0.02
59 28 0.60
60 18 0.38
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (59 bp):
ATCTTACGTAAATAGTTTTAGATACTTTGCAATAATTTGAAATATTTCTCAATTAGGCA
Found at i:8641 original size:19 final size:19
Alignment explanation
Indices: 8617--8653 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
8607 GTATACCTTT
8617 TCAATAATTTGAGATATTC
1 TCAATAATTTGAGATATTC
8636 TCAATAATTTGAGATATT
1 TCAATAATTTGAGATATT
8654 TTTTCGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (19 bp):
TCAATAATTTGAGATATTC
Found at i:9791 original size:25 final size:24
Alignment explanation
Indices: 9758--9817 Score: 102
Period size: 25 Copynumber: 2.5 Consensus size: 24
9748 TATTTGTAGT
9758 AGAAAAATAATATTTATTATAATG
1 AGAAAAATAATATTTATTATAATG
9782 ATGAAAAATAATATTTATTATAATG
1 A-GAAAAATAATATTTATTATAATG
*
9807 ACAAAAATAAT
1 AGAAAAATAAT
9818 GGCACCATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 10 0.29
25 24 0.71
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (24 bp):
AGAAAAATAATATTTATTATAATG
Found at i:13183 original size:64 final size:65
Alignment explanation
Indices: 13038--13191 Score: 174
Period size: 64 Copynumber: 2.4 Consensus size: 65
13028 AAGGTGTATT
* ** *
13038 GATGCACAGGTAGTGCATCGATGCA-CTCTTTTAAAATAAAAACATCGAATGCAATTAGTGCATC
1 GATGCACAAGTAGTGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCAATTAGTGCACC
* * * *
13102 GATGCATAAGGCA-TGCATCAATGCATC-CCATTAATAAT-AAAACATCGAATGCATTTTA-TGC
1 GATGCACAA-GTAGTGCATCGATGCATCTCCATTAA-AATAAAAACATCGAATGCA-ATTAGTGC
13163 ACC
63 ACC
13166 GATGCACAAGTAGTGCATCGATGCAT
1 GATGCACAAGTAGTGCATCGATGCAT
13192 ACCTTCATTA
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
63 2 0.03
64 63 0.85
65 9 0.12
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (65 bp):
GATGCACAAGTAGTGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCAATTAGTGCACC
Found at i:13608 original size:29 final size:29
Alignment explanation
Indices: 13566--13675 Score: 170
Period size: 29 Copynumber: 3.8 Consensus size: 29
13556 TATGTGATAT
13566 GAGAACATGACATGAGATACATGATCACAA
1 GAGAA-ATGACATGAGATACATGATCACAA
* *
13596 GAGAAATGACATGAGCTACACGATCACAA
1 GAGAAATGACATGAGATACATGATCACAA
13625 GAGAAATGACATGA-ACTACATGATCACAA
1 GAGAAATGACATGAGA-TACATGATCACAA
13654 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGATACATGA
13676 ACATATAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
28 7 0.09
29 62 0.84
30 5 0.07
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.16
Consensus pattern (29 bp):
GAGAAATGACATGAGATACATGATCACAA
Found at i:16765 original size:97 final size:100
Alignment explanation
Indices: 16651--16904 Score: 301
Period size: 101 Copynumber: 2.6 Consensus size: 100
16641 TTAAACAAAA
* *
16651 AATATGTTAATTCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAACAAAAAA-A-AA-
1 AATATGTAAAATCAAAATAAATAGTCTAA-TAATTTATATTTACAATAAAAACAAAAAATATAAT
**
16713 TTAAA-TAAACTTACCAAACCACTCAAATACATTTT
65 TTAAACTAAACTTACCAAACCACTCAAATACAACTT
*
16748 AATCTGTAAAATCAAAATAAATAGT-TCAATAATTTATA-TTACTCAATAAAAA-ATAAAAATAT
1 AATATGTAAAATCAAAATAAATAGTCT-AATAATTTATATTTA--CAATAAAAACA-AAAAATAT
* *
16810 AATTTAAACTACACTTACCAAACTACTCAAATACAACTT
62 AATTTAAACTAAACTTACCAAACCACTCAAATACAACTT
* *
16849 AATATGTAAAATCAAGATAAATAGTCTAATAA-TTATAATTTA-AATTAAAAGCAAAA
1 AATATGTAAAATCAAAATAAATAGTCTAATAATTTAT-ATTTACAA-TAAAAACAAAA
16905 TTTATACTAA
Statistics
Matches: 134, Mismatches: 10, Indels: 23
0.80 0.06 0.14
Matches are distributed among these distances:
95 3 0.02
96 11 0.08
97 38 0.28
98 1 0.01
99 4 0.03
100 17 0.13
101 56 0.42
102 4 0.03
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.31
Consensus pattern (100 bp):
AATATGTAAAATCAAAATAAATAGTCTAATAATTTATATTTACAATAAAAACAAAAAATATAATT
TAAACTAAACTTACCAAACCACTCAAATACAACTT
Found at i:17256 original size:11 final size:12
Alignment explanation
Indices: 17231--17260 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
17221 AATTAAAAAC
17231 AAAAATTACACT
1 AAAAATTACACT
17243 AAAAATTACA-T
1 AAAAATTACACT
17254 AAAAATT
1 AAAAATT
17261 TAAATTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAAATTACACT
Found at i:17297 original size:330 final size:316
Alignment explanation
Indices: 16662--17347 Score: 945
Period size: 330 Copynumber: 2.1 Consensus size: 316
16652 ATATGTTAAT
16662 TCAAAATAAATAGTCTAATTAATTTATATTTACAAT-AAAAACAAAAAAAAATTAAATAAACTTA
1 TCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAAACAAAAAAAAATTAAATAAACTTA
*
16726 CCAAACCACTCAAATACATTTTAATCTGTAAAATCAAAATAAATAGTTCAATAATTTATATTACT
66 CCAAACCACTCAAATACATTTTAATCTGTAAAATAAAAATAAATAGTTCAATAATTTATATTACT
* *
16791 CAATAAAAAATAAAAATATAATTTAAACTACACTTACCAAACTACTCAAATACAACTTAATATGT
131 CAATAAAAAATAAAAATATAATTTAAACTACACTTACCAAACTAATCAAATACAACTTAAAATGT
* * * *
16856 AAAATCAAGATAAATAGTCTAATAATTATAATTTAAATTAAAAGCAAAATTTATACTAAAAATTA
196 AAAATCAAAATAAATAGTCTAATAATTATAATTTAAATTAAAAACAAAAATTACACTAAAAATTA
* * * * *
16921 CATGAAAATTTAAATTTAACTTACCAAAGCACTCAAATACAATTTAATCTGTAAAA
261 CATAAAAATTTAAATTAAACTTACCAAACCACTCAAATACAATTTAATATATAAAA
*
16977 TCAAAATAAATAGTCTAATTAATTTATTTTTACAATAAAAACACAAAATAAAACAATAAATTTAA
1 TCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAA-AC-----AAAA-AA-AAA-TT-A
*** *
17042 AAGTAAACTTACCAAGGTACTCAAATACGA-TTTAATCTGTAAAATAAAAATAATTAG-TCTAAT
56 AA-TAAACTTACCAAACCACTCAAATAC-ATTTTAATCTGTAAAATAAAAATAAATAGTTC-AAT
** *
17105 AATTTATATTACTCAATAAAAAA-ACAAGGTAATAATTTAAACTACACTTA-CAAAGTTTTAATC
118 AATTTATATTACTCAATAAAAAATA-AAAAT-ATAATTTAAACTACACTTACCAAA---CTAATC
*
17168 AAATACAACTTAAAATGTAAAATTAAAATAAATAGTCTAATAATTATAATTTAAATTAAAAACAA
178 AAATACAACTTAAAATGTAAAATCAAAATAAATAGTCTAATAATTATAATTTAAATTAAAAACAA
17233 AAATTACACTAAAAATTACATAAAAATTTAAATTAAACTTACCAAACCACT-AGAATACAATTTA
243 AAATTACACTAAAAATTACATAAAAATTTAAATTAAACTTACCAAACCACTCA-AATACAATTTA
17297 ATATATAAAA
307 ATATATAAAA
*
17307 TCAAAATAAATAATCTAATTAATTTATATTT-CAAATAAAAA
1 TCAAAATAAATAGTCTAATTAATTTATATTTAC-AATAAAAA
17348 TTAAAAATGT
Statistics
Matches: 327, Mismatches: 23, Indels: 27
0.87 0.06 0.07
Matches are distributed among these distances:
315 35 0.11
316 4 0.01
317 2 0.01
322 4 0.01
323 2 0.01
324 3 0.01
325 2 0.01
326 6 0.02
327 80 0.24
328 20 0.06
329 2 0.01
330 167 0.51
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.31
Consensus pattern (316 bp):
TCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAAACAAAAAAAAATTAAATAAACTTA
CCAAACCACTCAAATACATTTTAATCTGTAAAATAAAAATAAATAGTTCAATAATTTATATTACT
CAATAAAAAATAAAAATATAATTTAAACTACACTTACCAAACTAATCAAATACAACTTAAAATGT
AAAATCAAAATAAATAGTCTAATAATTATAATTTAAATTAAAAACAAAAATTACACTAAAAATTA
CATAAAAATTTAAATTAAACTTACCAAACCACTCAAATACAATTTAATATATAAAA
Found at i:17823 original size:36 final size:38
Alignment explanation
Indices: 17729--17824 Score: 117
Period size: 38 Copynumber: 2.6 Consensus size: 38
17719 CGAAGTTTTT
17729 TTTTTTTCTGAAGATGCCAAGTAGTCTCAGAGTCTTCA
1 TTTTTTTCTGAAGATGCCAAGTAGTCTCAGAGTCTTCA
* * * *
17767 TTTTTTTCCGAAGACGCCAAGTAAT-TCTGGAGTCTT-A
1 TTTTTTTCTGAAGATGCCAAGTAGTCTC-AGAGTCTTCA
*
17804 -TTTTTTCTGAAGATACCAAGT
1 TTTTTTTCTGAAGATGCCAAGT
17825 GATCTTGGAG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
36 18 0.36
37 3 0.06
38 29 0.58
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (38 bp):
TTTTTTTCTGAAGATGCCAAGTAGTCTCAGAGTCTTCA
Found at i:34310 original size:23 final size:23
Alignment explanation
Indices: 34284--34332 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
34274 ATAAAGAACC
*
34284 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
34307 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
34330 AAA
1 AAA
34333 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:37793 original size:60 final size:59
Alignment explanation
Indices: 37658--37804 Score: 154
Period size: 60 Copynumber: 2.4 Consensus size: 59
37648 AATATAATGA
* *
37658 ATAGTCAGGTGACCATTTTGTAACTTTTAATAGTAAAGGGATTCAACAAAGTAACACTCT
1 ATAGTCAGG-GACCATTTTGTAACTTTTAATAGTAAAGAGATTCAACAAAGTAACACCCT
* * ** * **
37718 ATAGTCAAAGAACCATTTTGTAACTTTTAATAGTCGAGAGACTT-AATAAAGTAGTACCCT
1 ATAGTC-AGGGACCATTTTGTAACTTTTAATAGTAAAGAGA-TTCAACAAAGTAACACCCT
37778 ATAGTCGAGGGACCATTTGTGT-ACTTT
1 ATAGTC-AGGGACCATTT-TGTAACTTT
37805 ATCCTAATAA
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
60 65 0.90
61 7 0.10
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (59 bp):
ATAGTCAGGGACCATTTTGTAACTTTTAATAGTAAAGAGATTCAACAAAGTAACACCCT
Found at i:39383 original size:20 final size:21
Alignment explanation
Indices: 39332--39385 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
39322 CCCACCTTTA
39332 AAATTCGTCCATTTGAAATTT
1 AAATTCGTCCATTTGAAATTT
* * * *
39353 TAGTTCATCCATTT-TAATTT
1 AAATTCGTCCATTTGAAATTT
39373 AAATTCGTCCATT
1 AAATTCGTCCATT
39386 AACATAAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.46
Consensus pattern (21 bp):
AAATTCGTCCATTTGAAATTT
Found at i:43265 original size:19 final size:20
Alignment explanation
Indices: 43226--43276 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 20
43216 GAGCACCGAG
43226 AATGTCAGAGATGTAAACATTC
1 AATGTCA-AGATG-AAACATTC
43248 AATGTCAAGATG-AACATTC
1 AATGTCAAGATGAAACATTC
43267 AATGTCAAGA
1 AATGTCAAGA
43277 GATTGAGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 17 0.59
21 5 0.17
22 7 0.24
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (20 bp):
AATGTCAAGATGAAACATTC
Found at i:45737 original size:14 final size:14
Alignment explanation
Indices: 45718--45750 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
45708 TAGTGCATTA
45718 TATATATATATATG
1 TATATATATATATG
*
45732 TATATATGTATATG
1 TATATATATATATG
45746 TATAT
1 TATAT
45751 CGATTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (14 bp):
TATATATATATATG
Done.