Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002290.1 Hibiscus syriacus cultivar Beakdansim tig00004657_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: 39603
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:2374 original size:6 final size:5
Alignment explanation
Indices: 2318--2372 Score: 65
Period size: 5 Copynumber: 10.8 Consensus size: 5
2308 GTCCGTCCGT
* * * *
2318 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTCGTG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG-G
2369 CTCG
1 CTCG
2373 TGGTCGTGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
5 41 0.89
6 5 0.11
ACGTcount: A:0.05, C:0.40, G:0.36, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:2379 original size:6 final size:6
Alignment explanation
Indices: 2364--2423 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
2354 TCGGCTCGGC
* * *
2364 TCGTGC TCGTGG TCGTGG TCG-GG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
2411 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
2424 AATACGTGTC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
5 5 0.10
6 46 0.90
ACGTcount: A:0.03, C:0.18, G:0.48, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:8247 original size:6 final size:6
Alignment explanation
Indices: 8236--8298 Score: 71
Period size: 6 Copynumber: 11.2 Consensus size: 6
8226 TCGGCTCGGC
* * *
8236 TCGTGG TCGTGG TCGT-G TCGAGG TCGAGG TCGAGG TCGTGG TC---G
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
8280 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
8299 AATACGTGTC
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
3 3 0.06
5 4 0.08
6 44 0.86
ACGTcount: A:0.05, C:0.17, G:0.48, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:8287 original size:15 final size:15
Alignment explanation
Indices: 8264--8295 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
8254 CGAGGTCGAG
8264 GTCGAGGTCGTGGTC
1 GTCGAGGTCGTGGTC
*
8279 GTCGTGGTCGTGGTC
1 GTCGAGGTCGTGGTC
8294 GT
1 GT
8296 GGTAATACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.03, C:0.19, G:0.47, T:0.31
Consensus pattern (15 bp):
GTCGAGGTCGTGGTC
Found at i:14144 original size:5 final size:5
Alignment explanation
Indices: 14130--14178 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
14120 GTCCGTCCGT
* * * *
14130 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
14179 TGGTCGTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.06, C:0.41, G:0.37, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:14187 original size:6 final size:6
Alignment explanation
Indices: 14176--14236 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
14166 TCGGCTCGGC
* * *
14176 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
14224 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
14237 AATACGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.05, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:19999 original size:21 final size:19
Alignment explanation
Indices: 19959--20001 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
19949 AAATTGTAAC
**
19959 AAAATAAAAATATAGGATT
1 AAAATAAAAATATAAAATT
19978 AAAATGAAAAATATATAAATT
1 AAAAT-AAAAATATA-AAATT
19999 AAA
1 AAA
20002 GGCCCTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 9 0.45
21 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (19 bp):
AAAATAAAAATATAAAATT
Found at i:25892 original size:3 final size:3
Alignment explanation
Indices: 25884--25933 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
25874 TTCAGACCTG
25884 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25931 TAA
1 TAA
25934 CAACAACAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:26749 original size:218 final size:217
Alignment explanation
Indices: 26386--27216 Score: 1315
Period size: 218 Copynumber: 3.8 Consensus size: 217
26376 AGGTCTTATG
* * * *
26386 AATCAAGAAACCCCCAAAGGCTTAGTTTCTTAATTATCAAGAAACCCCTTTGTTAGGCTTAGCTT
1 AATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAA-CCCTTTGTTAGGCTTAGCTT
* * *
26451 CCTTTAACAACTCTTTTGAGATAATTAGGAAACCCCAGAAGGCTTAATTTCTAAAATCTCATTTG
65 CCTTTAACATCTCTTTTGAGATAATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTG
**
26516 AAAACAT-TCTGCACTGAAGGTCTTATGGATGACTTGAAGGCTTTATCATCTAGCTCGAAAAGCT
130 AAAACATCT-TGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTAGCTCGAAAAGCT
*
26580 TAGAGATGACCCGAAGGATTTAAA
194 TACAGATGACCCGAAGGATTTAAA
*
26604 AATCAAGAAACCCTCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCTCTTTGTTAGGCTTAGCTT
1 AATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACC-CTTTGTTAGGCTTAGCTT
*
26669 CCTTTAACATCTCTTTTGAGATATTTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTG
65 CCTTTAACATCTCTTTTGAGATAATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTG
* * *
26734 AAAACATCTTGCACTGAAGGTCTTACGGATGACCCTAAGGCTTTATCATCTAGCTCAAAAAGCTT
130 AAAACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTAGCTCGAAAAGCTT
*
26799 ACAGATGACCGGAAGGATTTAAA
195 ACAGATGACCCGAAGGATTTAAA
* *
26822 AATCAAGAAACCACCGAAGACTTAGTTTCTTAGTTGTCAAGGAACCCTTTGTTAGGCTTAGCTTC
1 AATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCTTTGTTAGGCTTAGCTTC
* * * *
26887 CTTTAACATCTCTGTTGAGATATTTAAGAAACCCTCGAAGGCTTAGTTTCTAAAATCTCATTTGA
66 CTTTAACATCTCTTTTGAGATAATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGA
* * *
26952 AAACATC-TGAACTAAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTAGCTCGAAATGCTTA
131 AAACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTAGCTCGAAAAGCTTA
*
27016 CAGATAACCCGAAGGATTTAAA
196 CAGATGACCCGAAGGATTTAAA
*
27038 AATCAAGAAACCCCCGAAGGCTTAGTTTATTAGTTGTCAAGGAATCCCTTTGTTAGGCTTAGCTT
1 AATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAA-CCCTTTGTTAGGCTTAGCTT
* * *
27103 CCTTTAACAGCTCTTTTGAGATAATTAGGAAACCCCTGAAGGCTTAGTTTCTAAATTCTCATTTG
65 CCTTTAACATCTCTTTTGAGATAATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTG
* * *
27168 AAAACATCCTGCATTGAAGGTCTTATGGATGAACCGAAGGCTTTATCAT
130 AAAACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCAT
27217 ATAGGGAAAT
Statistics
Matches: 565, Mismatches: 44, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
216 112 0.20
217 176 0.31
218 276 0.49
219 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (217 bp):
AATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCTTTGTTAGGCTTAGCTTC
CTTTAACATCTCTTTTGAGATAATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGA
AAACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTAGCTCGAAAAGCTTA
CAGATGACCCGAAGGATTTAAA
Found at i:27949 original size:22 final size:22
Alignment explanation
Indices: 27882--27973 Score: 78
Period size: 22 Copynumber: 4.1 Consensus size: 22
27872 GTAGAAATCC
* * *
27882 AATAAAGCTTTCATCTTTGAAA
1 AATAAATCTATCATCTTTGAAG
* * * *
27904 AAGAGAATCTGTTATCTTTAAAG
1 AATA-AATCTATCATCTTTGAAG
*
27927 AGA-AAATCTATCATTTTTGAAG
1 A-ATAAATCTATCATCTTTGAAG
*
27949 AATGAATCTATCATCTTTGAAG
1 AATAAATCTATCATCTTTGAAG
27971 AAT
1 AAT
27974 GTATCTAGAT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
21 1 0.02
22 38 0.69
23 15 0.27
24 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (22 bp):
AATAAATCTATCATCTTTGAAG
Found at i:27974 original size:22 final size:22
Alignment explanation
Indices: 27931--27980 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
27921 TTAAAGAGAA
*
27931 AATCTATCATTTTTGAAGAATG
1 AATCTATCATCTTTGAAGAATG
27953 AATCTATCATCTTTGAAGAATG
1 AATCTATCATCTTTGAAGAATG
*
27975 TATCTA
1 AATCTA
27981 GATATGCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAATG
Found at i:32626 original size:42 final size:42
Alignment explanation
Indices: 32567--32650 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
32557 TTAATTTTTT
* * * *
32567 CATTTGCTCTTTTGAATCATCTTGGAA-TTTTTTCGCTTGATC
1 CATTTGCTCATTTGAATCACCCTGGAACTTTTTT-ACTTGATC
*
32609 CATTTGTTCATTTGAATCACCCTGGAACTTTTTTACTTGATC
1 CATTTGCTCATTTGAATCACCCTGGAACTTTTTTACTTGATC
32651 AATCATCTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 30 0.83
43 6 0.17
ACGTcount: A:0.19, C:0.20, G:0.13, T:0.48
Consensus pattern (42 bp):
CATTTGCTCATTTGAATCACCCTGGAACTTTTTTACTTGATC
Found at i:32967 original size:21 final size:21
Alignment explanation
Indices: 32927--32972 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
32917 ATGTGGATGT
* *
32927 AAAATGAAAATGCAAATATGC
1 AAAATGAAAATACAAATATGA
**
32948 AAAATGAAAATACATGTATGA
1 AAAATGAAAATACAAATATGA
32969 AAAA
1 AAAA
32973 GGTGTTACTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.61, C:0.07, G:0.13, T:0.20
Consensus pattern (21 bp):
AAAATGAAAATACAAATATGA
Found at i:33580 original size:36 final size:36
Alignment explanation
Indices: 33540--33611 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
33530 CCTTATCGTT
*
33540 GAATACTTTTGGTATCAATCTAATAGGATCTTTGTG
1 GAATACTTTTGGTATCAATCTAACAGGATCTTTGTG
*
33576 GAATACTTTTGGTATCAATTTAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATCTAACAGGATCTTTGTG
33612 TGCATAGCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATCTAACAGGATCTTTGTG
Found at i:36686 original size:3 final size:3
Alignment explanation
Indices: 36667--36746 Score: 76
Period size: 3 Copynumber: 27.0 Consensus size: 3
36657 TTCAGGCCTG
* * *
36667 TAA TAA T-A TAA TTA TAA TAA TAA TAA TATT TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
* *
36712 CAA TAA TAA T-A TTA TAA TAA TAA TAAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
36747 AATGTGCAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
2 6 0.10
3 53 0.84
4 4 0.06
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:36702 original size:19 final size:20
Alignment explanation
Indices: 36667--36736 Score: 79
Period size: 19 Copynumber: 3.4 Consensus size: 20
36657 TTCAGGCCTG
36667 TAATAATATAATTATAATAA
1 TAATAATATAATTATAATAA
*
36687 TAATAATAT-TTTATAATAA
1 TAATAATATAATTATAATAA
* *
36706 TAATAACAATAATAATATTATAA
1 TAATAA-TATAAT--TATAATAA
36729 TAATAATA
1 TAATAATA
36737 AATAAAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
19 15 0.37
20 11 0.27
21 1 0.02
22 1 0.02
23 13 0.32
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (20 bp):
TAATAATATAATTATAATAA
Done.