Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000658.1 Hibiscus syriacus cultivar Beakdansim tig00001280_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: 243114
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:210311 original size:3 final size:3
Alignment explanation
Indices: 210305--210377 Score: 128
Period size: 3 Copynumber: 24.0 Consensus size: 3
210295 TTATTTAAAT
*
210305 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
210353 TTA TTA TTA TTA TATA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA
210378 AATAAATATA
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 64 0.96
4 3 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:211715 original size:20 final size:21
Alignment explanation
Indices: 211669--211715 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
211659 CTGCTTTTAA
211669 ATATATTGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
211690 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
211709 ATATATT
1 ATATATT
211716 TAAATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:211793 original size:23 final size:24
Alignment explanation
Indices: 211759--211803 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
211749 TATATATGAT
211759 AAATAATAA-TTT-ATATTTTTTA
1 AAATAATAATTTTAATATTTTTTA
*
211781 AAATAAATTATTTTAATATTTTT
1 AAAT-AATAATTTTAATATTTTT
211804 CAATATCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 4 0.21
24 3 0.16
25 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
AAATAATAATTTTAATATTTTTTA
Found at i:216891 original size:13 final size:14
Alignment explanation
Indices: 216869--216905 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
216859 GTCAAAGAAA
216869 GTCAACGGTCAACG
1 GTCAACGGTCAACG
216883 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
216896 GTCAACGGTC
1 GTCAACGGTC
216906 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:216917 original size:17 final size:17
Alignment explanation
Indices: 216895--216952 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
216885 CACGGTCAAC
216895 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
216912 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
216929 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
216946 GGTCAAC
1 GGTCAAC
216953 CCGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:216922 original size:7 final size:7
Alignment explanation
Indices: 216869--216905 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
216859 GTCAAAGAAA
216869 GTCAACG
1 GTCAACG
216876 GTCAACG
1 GTCAACG
216883 GTC-ACG
1 GTCAACG
216889 GTCAACG
1 GTCAACG
216896 GTCAACG
1 GTCAACG
216903 GTC
1 GTC
216906 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:216970 original size:19 final size:19
Alignment explanation
Indices: 216946--217034 Score: 135
Period size: 19 Copynumber: 4.7 Consensus size: 19
216936 AGTCGGGTCG
*
216946 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
216965 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
216984 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
217003 GGTCAAACCGGTTCAAAAC
1 GGTCAAACCGGTTCAGACC
217022 GGTCAAACCGGTT
1 GGTCAAACCGGTT
217035 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
18 1 0.02
19 64 0.98
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:216976 original size:9 final size:9
Alignment explanation
Indices: 216946--217033 Score: 95
Period size: 9 Copynumber: 9.3 Consensus size: 9
216936 AGTCGGGTCG
*
216946 GGTCAACCC
1 GGTCAAACC
*
216955 GGTTCAGACC
1 GG-TCAAACC
216965 GGTCAAACC
1 GGTCAAACC
*
216974 GGTTCAGACC
1 GG-TCAAACC
216984 GGTCAAACC
1 GGTCAAACC
*
216993 GGTTCGAACC
1 GG-TCAAACC
217003 GGTCAAACC
1 GGTCAAACC
*
217012 GGTTCAAAAC
1 GG-TCAAACC
217022 GGTCAAACC
1 GGTCAAACC
217031 GGT
1 GGT
217034 TTTCCAGCAG
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
9 35 0.53
10 31 0.47
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:223347 original size:65 final size:65
Alignment explanation
Indices: 223243--223372 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
223233 CCCAAAAGTA
223243 TTTTCCATATAGCTTACTTTATGCACATAGCAAAAAGAAAGCCGACTTAAGGATAGGCTATGAAG
1 TTTTCCATATAGCTTACTTTATGCACATAGCAAAAAGAAAGCCGACTTAAGGATAGGCTATGAAG
223308 TTTTCCATATAGCTTACTTTATGCACATAGCAAAAAGAAAGCCGACTTAAGGATAGGCTATGAAG
1 TTTTCCATATAGCTTACTTTATGCACATAGCAAAAAGAAAGCCGACTTAAGGATAGGCTATGAAG
223373 CTTGTATCCT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (65 bp):
TTTTCCATATAGCTTACTTTATGCACATAGCAAAAAGAAAGCCGACTTAAGGATAGGCTATGAAG
Found at i:224276 original size:13 final size:14
Alignment explanation
Indices: 224254--224290 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
224244 GTCAAAGAAA
224254 GTCAACGGTCAACG
1 GTCAACGGTCAACG
224268 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
224281 GTCAACGGTC
1 GTCAACGGTC
224291 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:224302 original size:17 final size:17
Alignment explanation
Indices: 224280--224337 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
224270 CACGGTCAAC
224280 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
224297 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
224314 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
224331 GGTCAAC
1 GGTCAAC
224338 CCGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:224307 original size:7 final size:7
Alignment explanation
Indices: 224254--224290 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
224244 GTCAAAGAAA
224254 GTCAACG
1 GTCAACG
224261 GTCAACG
1 GTCAACG
224268 GTC-ACG
1 GTCAACG
224274 GTCAACG
1 GTCAACG
224281 GTCAACG
1 GTCAACG
224288 GTC
1 GTC
224291 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:224355 original size:19 final size:19
Alignment explanation
Indices: 224331--224419 Score: 135
Period size: 19 Copynumber: 4.7 Consensus size: 19
224321 AGTCGGGTCG
*
224331 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
224350 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
224369 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
224388 GGTCAAACCGGTTCAAAAC
1 GGTCAAACCGGTTCAGACC
224407 GGTCAAACCGGTT
1 GGTCAAACCGGTT
224420 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
18 1 0.02
19 64 0.98
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:224361 original size:9 final size:9
Alignment explanation
Indices: 224331--224418 Score: 95
Period size: 9 Copynumber: 9.3 Consensus size: 9
224321 AGTCGGGTCG
*
224331 GGTCAACCC
1 GGTCAAACC
*
224340 GGTTCAGACC
1 GG-TCAAACC
224350 GGTCAAACC
1 GGTCAAACC
*
224359 GGTTCAGACC
1 GG-TCAAACC
224369 GGTCAAACC
1 GGTCAAACC
*
224378 GGTTCGAACC
1 GG-TCAAACC
224388 GGTCAAACC
1 GGTCAAACC
*
224397 GGTTCAAAAC
1 GG-TCAAACC
224407 GGTCAAACC
1 GGTCAAACC
224416 GGT
1 GGT
224419 TTTCCAGCAG
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
9 35 0.53
10 31 0.47
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:229232 original size:3 final size:3
Alignment explanation
Indices: 229224--229260 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
229214 AGCAAGTGAA
229224 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
229261 GTTTTTCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:230159 original size:16 final size:17
Alignment explanation
Indices: 230133--230164 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
230123 TAGATTTATT
230133 AAAAATAAAAAATAAGA
1 AAAAATAAAAAATAAGA
230150 AAAAAT-AAAAATAAG
1 AAAAATAAAAAATAAG
230165 CTATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAATAAAAAATAAGA
Found at i:232187 original size:24 final size:23
Alignment explanation
Indices: 232149--232240 Score: 91
Period size: 23 Copynumber: 4.0 Consensus size: 23
232139 CACCACAGCT
232149 CGTA-AATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
232171 CGTAGAATTTGTC-CCGAAG-GACCG
1 CGTAGAA-TTG-CACCGAAGTG-CCA
*
232195 CGTAGAATTGCATCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
232218 CGTAGAAATGCATCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
232241 TATAAGATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
22 5 0.08
23 34 0.58
24 19 0.32
25 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:232383 original size:23 final size:23
Alignment explanation
Indices: 232352--232395 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
232342 ATAATACATA
*
232352 TGTCTCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
*
232375 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
232396 CCCTCGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:238568 original size:23 final size:23
Alignment explanation
Indices: 238542--238617 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
238532 AACTCGTATA
238542 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
238565 AATTTGTC-CCGAAG-GACGCGTAG
1 AA-TTG-CACCGAAGTGCCACGTAG
* * *
238588 AATTACACTGAAGTGCCATGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
238611 AAATGCA
1 AATTGCA
238618 TCATAGTGCC
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
21 1 0.03
22 7 0.17
23 22 0.55
24 9 0.22
25 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:238774 original size:18 final size:18
Alignment explanation
Indices: 238751--238787 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
238741 AAGGACCACC
238751 TCTTTAGAAAATGTGCAA
1 TCTTTAGAAAATGTGCAA
238769 TCTTTAGAAAATGTGCAA
1 TCTTTAGAAAATGTGCAA
238787 T
1 T
238788 AATCAGTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (18 bp):
TCTTTAGAAAATGTGCAA
Found at i:241212 original size:29 final size:29
Alignment explanation
Indices: 241142--241212 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
241132 ATTGGAGTTT
* **
241142 AATTTTTTTAATTAATTGCTTAACTTTCA
1 AATTTTTTTATTTAATCACTTAACTTTCA
** *
241171 AATTTCCTAATTTAATCACTCTAACTTTC-
1 AATTTTTTTATTTAATCACT-TAACTTTCA
241200 AATTTTTTTATTT
1 AATTTTTTTATTT
241213 TAATATATCA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.30, C:0.14, G:0.01, T:0.55
Consensus pattern (29 bp):
AATTTTTTTATTTAATCACTTAACTTTCA
Done.