Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001403.1 Hibiscus syriacus cultivar Beakdansim tig00002739_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: 59558
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1102 original size:7 final size:7
Alignment explanation
Indices: 1090--1115 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1080 GATGTCTTCA
1090 ATTATAC
1 ATTATAC
1097 ATTATAC
1 ATTATAC
1104 ATTATAC
1 ATTATAC
1111 ATTAT
1 ATTAT
1116 TTTTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (7 bp):
ATTATAC
Found at i:2522 original size:305 final size:304
Alignment explanation
Indices: 1913--2526 Score: 969
Period size: 305 Copynumber: 2.0 Consensus size: 304
1903 AGTCAAATCA
*
1913 ATGATGAAGAGAGTTTCCTTCACCCCCAAGCTCATATGCAAAAAAAAAAGGAGAAAAGGGGGAAC
1 ATGATGAAGAGAGATTCCTTCACCCCCAAGCTCATATGCAAAAAAAAAAGGAGAAAAGGGGGAAC
*
1978 TAAAAAAAATCTTTTCAACAACTGTAAATCAAGCAACATAGCAACCTAAAAAAGAAACAAATAGA
66 CAAAAAAAATCTTTTCAACAACTGTAAATCAAGCAACATAGCAACCTAAAAAAGAAACAAATAGA
* *
2043 GAATACCTATATACAAAAAAGAAACTGAGAGCCTTTGAAGAAAACAAGAAAAAAAGGAAAAGAGA
131 GAATACCCATATACAAAAAAGAAACTGAGAGCCTTTGAAGAAAACAAGAAAAAAAGAAAAAGAGA
* *
2108 AAGAAGAAATCTTACCCTCTTGGTGGAAGCACTCTCCTTCTACATCAGAGCTAGGTCCTTCGACC
196 AAGAAGAAATCTTACCCTATTGGTGGAAGCACTCTCCTTCTACATCAGAGCTAGGTCATTCGACC
*
2173 GAAGCTAATTTTCAAACCCTTCATTTAGATCATTTAGAGGATGGT
261 GAAGCTAA-TTTAAAACCCTTCATTTAGATCATTTAGAGGATGGT
*
2218 ATGATGAAGATAGATTCCTTCACCCCCAAGCTCATATGCAAAAAAAAAAAAAGGAG-AAA-GGGG
1 ATGATGAAGAGAGATTCCTTCACCCCCAAGCTCATATGC---AAAAAAAAAAGGAGAAAAGGGGG
2281 AACCAAAAAAAATCTTTTCAACAACTGTAAATC-AGCAACA-A-CAACCTAAAAAA-AAACAAAT
63 AACCAAAAAAAATCTTTTCAACAACTGTAAATCAAGCAACATAGCAACCTAAAAAAGAAACAAAT
2342 AGAGAATACCCATATACAAAAAA-AAACTGAGAGCCTTTGAAGAAAAACAAG-AAAAAAGAAACA
128 AGAGAATACCCATATACAAAAAAGAAACTGAGAGCCTTTGAAG-AAAACAAGAAAAAAAGAAA-A
2405 AGAGAAAGAAGAAATCTTACCC-ATTGGTGGAAGCACTCTCCTTCTACATCAGAGCTAGAGGTCA
191 AGAGAAAGAAGAAATCTTACCCTATTGGTGGAAGCACTCTCCTTCTACATCAGAGCT--AGGTCA
*
2469 TTCGACGACGAAGGTAA-TTAAAACCCTTCATTTGAGATCCATTTAGAGGATGGT
254 TTCGAC--CGAAGCTAATTTAAAACCCTTCATTT-AGAT-CATTTAGAGGATGGT
2523 ATGA
1 ATGA
2527 GTATAGGTCA
Statistics
Matches: 289, Mismatches: 9, Indels: 22
0.90 0.03 0.07
Matches are distributed among these distances:
301 61 0.21
302 61 0.21
303 38 0.13
304 5 0.02
305 71 0.25
306 36 0.12
307 3 0.01
308 14 0.05
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (304 bp):
ATGATGAAGAGAGATTCCTTCACCCCCAAGCTCATATGCAAAAAAAAAAGGAGAAAAGGGGGAAC
CAAAAAAAATCTTTTCAACAACTGTAAATCAAGCAACATAGCAACCTAAAAAAGAAACAAATAGA
GAATACCCATATACAAAAAAGAAACTGAGAGCCTTTGAAGAAAACAAGAAAAAAAGAAAAAGAGA
AAGAAGAAATCTTACCCTATTGGTGGAAGCACTCTCCTTCTACATCAGAGCTAGGTCATTCGACC
GAAGCTAATTTAAAACCCTTCATTTAGATCATTTAGAGGATGGT
Found at i:4105 original size:9 final size:10
Alignment explanation
Indices: 4081--4113 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
4071 TTTTTTTAAA
4081 AAAATTTTAAT
1 AAAATTTT-AT
4092 AAAATTTT-T
1 AAAATTTTAT
4101 AAAATTTTAT
1 AAAATTTTAT
4111 AAA
1 AAA
4114 GACAACACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 4 0.19
11 8 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
AAAATTTTAT
Found at i:4692 original size:27 final size:27
Alignment explanation
Indices: 4630--4699 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
4620 TATTTTTTTA
* *
4630 TTAATAATCTATTTTGCCTCTTAAAAT
1 TTAATAATTTATTTTTCCTCTTAAAAT
*
4657 TTTATAATTTATTTTTCC-CTTAAAAT
1 TTAATAATTTATTTTTCCTCTTAAAAT
* *
4683 CTTAAGAATTAATTTTT
1 -TTAATAATTTATTTTT
4700 TAATATAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
26 8 0.22
27 28 0.78
ACGTcount: A:0.33, C:0.11, G:0.03, T:0.53
Consensus pattern (27 bp):
TTAATAATTTATTTTTCCTCTTAAAAT
Found at i:7490 original size:24 final size:24
Alignment explanation
Indices: 7458--7504 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
7448 TTGCCTTATT
7458 TTTAAAGTGATAGCAATATTAGTG
1 TTTAAAGTGATAGCAATATTAGTG
7482 TTTAAAGTGATAGCAATATTAGT
1 TTTAAAGTGATAGCAATATTAGT
7505 ATTTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.38
Consensus pattern (24 bp):
TTTAAAGTGATAGCAATATTAGTG
Found at i:14216 original size:20 final size:20
Alignment explanation
Indices: 14193--14243 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
14183 CTATCCTGTG
14193 AGTATCGATACCGGCCTTTC
1 AGTATCGATACCGGCCTTTC
14213 AGTATCGATACCGGCCTTTC
1 AGTATCGATACCGGCCTTTC
14233 AGTATCGATAC
1 AGTATCGATAC
14244 TCCTCGCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (20 bp):
AGTATCGATACCGGCCTTTC
Found at i:30369 original size:22 final size:22
Alignment explanation
Indices: 30341--30400 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
30331 CAATCTCATC
30341 TGAGTCATTCAAGCCATTAAGT
1 TGAGTCATTCAAGCCATTAAGT
*
30363 TGAGTCATTCAAACCATTAAGT
1 TGAGTCATTCAAGCCATTAAGT
*
30385 CGAGTCATTCAAGCCA
1 TGAGTCATTCAAGCCA
30401 CCGTTTGAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (22 bp):
TGAGTCATTCAAGCCATTAAGT
Found at i:40874 original size:97 final size:97
Alignment explanation
Indices: 40699--40896 Score: 288
Period size: 97 Copynumber: 2.0 Consensus size: 97
40689 GCGAAGTAAC
* * * * *
40699 CAAAATCATACCTGGATTACCTGGCTGATGAAGATAATAAGGATTGCATCATTATCAAATTAATT
1 CAAAATAATACCTGGATTACCAGACTGATGAAGATAATAAAGATTGCATCATTATCAAATTAATC
* *
40764 ACTAGGATCACCCATGATGAATACCAAGAGAA
66 ACTACGATAACCCATGATGAATACCAAGAGAA
* * * *
40796 CAAAATAATTCCTGGATTATCAGACTGATGAAGATAGTAAAGATTGTATCATTATCAAATTAATC
1 CAAAATAATACCTGGATTACCAGACTGATGAAGATAATAAAGATTGCATCATTATCAAATTAATC
*
40861 ATTACGATAACCCATGATGAATACCAAGAGAA
66 ACTACGATAACCCATGATGAATACCAAGAGAA
40893 CAAA
1 CAAA
40897 GAAACAAGGA
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 89 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.26
Consensus pattern (97 bp):
CAAAATAATACCTGGATTACCAGACTGATGAAGATAATAAAGATTGCATCATTATCAAATTAATC
ACTACGATAACCCATGATGAATACCAAGAGAA
Found at i:41571 original size:205 final size:206
Alignment explanation
Indices: 41211--41586 Score: 533
Period size: 205 Copynumber: 1.8 Consensus size: 206
41201 CACTTACAGA
* * *
41211 GGAATATAAACAATAGAGATGCTGGCGTAATGGTAAAACAAATAATCGATGAATTAGACCGATTT
1 GGAATATAAACAATAGAGATGCTGACGTAATGGTAAAACAAATAATCGATGAATAAAACCGATTT
* * * *
41276 AATTATTTTTATTATTAAATTAATTTTTTAATATGAAATGAGTATAAAATAATATTTATTCAAAT
66 AATTATCTTTATTAATAAATTAATTTTTAAATATGAAA-GAATATAAAATAATATTTATTCAAAT
* * * *
41341 AATTATTAATCAGTCGATAATTAACGTTTGAAAACGTTTACTGAAGTATGCTTGAACCTAAAATC
130 AATTATTAATCACTCAACAATTAACGTTTAAAAACGTTTACTGAAGTATGCTTGAACCTAAAATC
41406 TTTGGAGATGAC
195 TTTGGAGATGAC
** * * *
41418 GGAATATAGTCAATAGAGATGCTGATGTAATGGTAAAACAAA-AGTCGATGAATAAAACTGATTT
1 GGAATATAAACAATAGAGATGCTGACGTAATGGTAAAACAAATAATCGATGAATAAAACCGATTT
* *
41482 AATTGAATCTTTATTAATAATTTAATTTTTAAATAT-AAA-AATATAAAATAATATTTGTTCAAA
66 AATT--ATCTTTATTAATAAATTAATTTTTAAATATGAAAGAATATAAAATAATATTTATTCAAA
*
41545 TAATTATTAATCACTCAACCATTAACGTTTAAAAACGTTTAC
129 TAATTATTAATCACTCAACAATTAACGTTTAAAAACGTTTAC
41587 GTTTACTGAA
Statistics
Matches: 148, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
205 59 0.40
206 22 0.15
207 41 0.28
208 26 0.18
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (206 bp):
GGAATATAAACAATAGAGATGCTGACGTAATGGTAAAACAAATAATCGATGAATAAAACCGATTT
AATTATCTTTATTAATAAATTAATTTTTAAATATGAAAGAATATAAAATAATATTTATTCAAATA
ATTATTAATCACTCAACAATTAACGTTTAAAAACGTTTACTGAAGTATGCTTGAACCTAAAATCT
TTGGAGATGAC
Found at i:43890 original size:21 final size:21
Alignment explanation
Indices: 43852--43892 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43842 TTAAAAGTGT
*
43852 TTAATGTGATGATTTATGATG
1 TTAATGTGATGATCTATGATG
43873 TTAATGTGAT-AGTCTATGAT
1 TTAATGTGATGA-TCTATGAT
43893 AATGACATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.46
Consensus pattern (21 bp):
TTAATGTGATGATCTATGATG
Found at i:56959 original size:77 final size:78
Alignment explanation
Indices: 56869--57021 Score: 190
Period size: 77 Copynumber: 2.0 Consensus size: 78
56859 TTCGAATTAA
*
56869 AAAAACTTATTTAATTAATT-C-AACTTAAATAT-ACATT-AAAGACTTATAATCAGAATTACA-
1 AAAAACTTATTTAATT-ATTCCGAA-TTAAATATCA-ATTAAAAGACTTATAATCAAAATTACAT
56929 ATCTTTAATGTTTATTT
63 AT-TTTAATGTTTATTT
* * *
56946 AAAATCTTATTTAATTATTCCGAATTAAATATCAATTAAAAGAGTTGTAATCAAAATTACATTAT
1 AAAAACTTATTTAATTATTCCGAATTAAATATCAATTAAAAGACTTATAATCAAAATTACA-TAT
57011 TTTAATGTTTA
65 TTTAATGTTTA
57022 CTACTATATT
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
76 3 0.05
77 27 0.41
78 23 0.35
79 11 0.17
80 2 0.03
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (78 bp):
AAAAACTTATTTAATTATTCCGAATTAAATATCAATTAAAAGACTTATAATCAAAATTACATATT
TTAATGTTTATTT
Found at i:58233 original size:3 final size:3
Alignment explanation
Indices: 58225--58262 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
58215 GTTTTATTTT
*
58225 TTA TTA TTA TTA TCA TTA TTA TTTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T
58263 ATTTTGTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:58243 original size:22 final size:22
Alignment explanation
Indices: 58218--58267 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
58208 ATACACCGTT
58218 TTATTTTTTATTATTATTATCA
1 TTATTTTTTATTATTATTATCA
* *
58240 TTATTATTTATTATTATTATTA
1 TTATTTTTTATTATTATTATCA
58262 -TATTTT
1 TTATTTT
58268 GTTTGCAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATTTTTTATTATTATTATCA
Found at i:58252 original size:19 final size:18
Alignment explanation
Indices: 58228--58266 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
58218 TTATTTTTTA
58228 TTATTATTATCATTATTAT
1 TTATTATTATCATTA-TAT
*
58247 TTATTATTATTATTATAT
1 TTATTATTATCATTATAT
58265 TT
1 TT
58267 TGTTTGCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTATTATCATTATAT
Found at i:59488 original size:22 final size:22
Alignment explanation
Indices: 59463--59512 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
59453 TAAAAAGTTA
59463 AAAAATAAAATGAATA-ATTAAT
1 AAAAATAAAA-GAATATATTAAT
* * *
59485 AAAAAGAAAAGATTATATTTAT
1 AAAAATAAAAGAATATATTAAT
59507 AAAAAT
1 AAAAAT
59513 TAGGGGGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (22 bp):
AAAAATAAAAGAATATATTAAT
Done.