Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006692.1 Hibiscus syriacus cultivar Beakdansim tig00016648_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: 75327
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:12396 original size:28 final size:26
Alignment explanation
Indices: 12353--12438 Score: 102
Period size: 28 Copynumber: 3.1 Consensus size: 26
12343 ACGTGGTGCA
12353 TTTAAGTCTTTTAGGTACATAACTTT
1 TTTAAGTCTTTTAGGTACATAACTTT
12379 TTTATAGTCTTTTTAGGTACATAACTTT
1 TTTA-AGTC-TTTTAGGTACATAACTTT
*
12407 TTTAATGGTTCATTTAGGTATC-TAACTTT
1 TTTAA--G-TCTTTTAGGTA-CATAACTTT
12436 TTT
1 TTT
12439 TGTTGCAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
26 4 0.08
27 5 0.09
28 22 0.42
29 19 0.36
30 3 0.06
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.53
Consensus pattern (26 bp):
TTTAAGTCTTTTAGGTACATAACTTT
Found at i:12422 original size:29 final size:28
Alignment explanation
Indices: 12353--12438 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 28
12343 ACGTGGTGCA
12353 TTTA-AGTCT-TTTAGGTACATAACTTT
1 TTTATAGTCTATTTAGGTACATAACTTT
*
12379 TTTATAGTCTTTTTAGGTACATAACTTT
1 TTTATAGTCTATTTAGGTACATAACTTT
*
12407 TTTAATGGT-TCATTTAGGTATC-TAACTTT
1 TTT-ATAGTCT-ATTTAGGTA-CATAACTTT
12436 TTT
1 TTT
12439 TGTTGCAATT
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
26 4 0.08
27 5 0.09
28 21 0.40
29 22 0.42
30 1 0.02
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.53
Consensus pattern (28 bp):
TTTATAGTCTATTTAGGTACATAACTTT
Found at i:12491 original size:31 final size:31
Alignment explanation
Indices: 12454--12527 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
12444 CAATTAGCTC
* *
12454 TATCCAACTTTTATTTTTTGGTGCATTTAAG
1 TATCCAACTTTTATTTTTTGGTGCAATTAAA
* *
12485 TATCCAAATTTCATTTTTTGGTGCAATTAAA
1 TATCCAACTTTTATTTTTTGGTGCAATTAAA
12516 TA-CTCAACTTTT
1 TATC-CAACTTTT
12528 TCTAAAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (31 bp):
TATCCAACTTTTATTTTTTGGTGCAATTAAA
Found at i:23198 original size:25 final size:23
Alignment explanation
Indices: 23154--23215 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
23144 GGGAAAAATA
*
23154 AAATAA-ATAAAATAAATAAGTAAG
1 AAATAAGA-AAAAAAAAT-AGTAAG
23178 --ATAAGAAAAAAAAATAGTAAG
1 AAATAAGAAAAAAAAATAGTAAG
*
23199 AAATAAGACAAAAAAAT
1 AAATAAGAAAAAAAAAT
23216 GGGCCCTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 6 0.18
22 12 0.36
23 15 0.45
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.16
Consensus pattern (23 bp):
AAATAAGAAAAAAAAATAGTAAG
Found at i:23316 original size:21 final size:21
Alignment explanation
Indices: 23290--23355 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
23280 TTTTTTTTTT
*
23290 TAAATAATAATATAATAATAA
1 TAAATAATAATATAAAAATAA
* * * *
23311 TGAATAAAAAAACAAAAATAA
1 TAAATAATAATATAAAAATAA
* *
23332 TAAAAAATAATATAAATAT-A
1 TAAATAATAATATAAAAATAA
23352 TAAA
1 TAAA
23356 GTTATAAGAT
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
20 5 0.15
21 29 0.85
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAATAATAATATAAAAATAA
Found at i:23567 original size:18 final size:19
Alignment explanation
Indices: 23537--23573 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
23527 ATATATATAT
23537 ATATATAATAAT-AATAAA
1 ATATATAATAATAAATAAA
23555 ATATAGTAA-AATAAATAAA
1 ATATA-TAATAATAAATAAA
23574 TGAAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
ATATATAATAATAAATAAA
Found at i:23623 original size:46 final size:45
Alignment explanation
Indices: 23568--23660 Score: 109
Period size: 46 Copynumber: 2.0 Consensus size: 45
23558 TAGTAAAATA
* * * *
23568 AATAAATGAA-AAT-AATTTAATATATATATATACACATATAATAAT
1 AATAAATGAATAATAAAATAAATAAATAAATAT-C-CATATAATAAT
23613 AATAACATGAATAATAAAATAAATAAATAAATATCCATATAATAAT
1 AATAA-ATGAATAATAAAATAAATAAATAAATATCCATATAATAAT
23659 AA
1 AA
23661 AAGGACTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
45 5 0.12
46 18 0.44
47 4 0.10
48 14 0.34
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.31
Consensus pattern (45 bp):
AATAAATGAATAATAAAATAAATAAATAAATATCCATATAATAAT
Found at i:23645 original size:64 final size:63
Alignment explanation
Indices: 23522--23643 Score: 181
Period size: 64 Copynumber: 1.9 Consensus size: 63
23512 AATATTAAAG
* * *
23522 AATATATATATATATATATATAATAATAATAAAATATAGTAAAATAAATAAATGAAAATAATTT
1 AATATATATATATACACATATAATAATAATAAAATATAATAAAATAAATAAAT-AAAATAATTT
*
23586 AATATATATATATACACATATAATAATAATAACATGAATAATAAAATAAATAAATAAA
1 AATATATATATATACACATATAATAATAATAAAAT--ATAATAAAATAAATAAATAAA
23644 TATCCATATA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 32 0.62
65 3 0.06
66 17 0.33
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (63 bp):
AATATATATATATACACATATAATAATAATAAAATATAATAAAATAAATAAATAAAATAATTT
Found at i:24076 original size:37 final size:37
Alignment explanation
Indices: 23994--24095 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
23984 GTGCTTGTGG
* * * * * *
23994 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* * *
24031 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
24068 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
24096 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:25545 original size:3 final size:3
Alignment explanation
Indices: 25537--25571 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
25527 AATTAATCAG
*
25537 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
25572 GATGATGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:26977 original size:19 final size:19
Alignment explanation
Indices: 26953--26994 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
26943 ATACGGATTC
*
26953 CATTCCTATAAGAATCCCA
1 CATTCCCATAAGAATCCCA
**
26972 CATTCCCATGGGAATCCCA
1 CATTCCCATAAGAATCCCA
26991 CATT
1 CATT
26995 TCCGAACCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.33, G:0.10, T:0.26
Consensus pattern (19 bp):
CATTCCCATAAGAATCCCA
Found at i:43406 original size:225 final size:226
Alignment explanation
Indices: 42968--43429 Score: 818
Period size: 225 Copynumber: 2.0 Consensus size: 226
42958 CGATTCAGAG
*
42968 ACTCCATCTTCGGAGTTAATAGCGGAAACGGGATCACCCTCAACAACATCCCTTGAATTTTGTTC
1 ACTCCATCTTCGGAGTTAATAGCGGAAACGGGATCACCCCCAACAACATCCCTTGAATTTTGTTC
43033 ATCAACAGGGCTCTCCCCATGACACAATTCAACTGGCTCCTCCTCCTCCTGATCCCCAGTTCCGA
66 ATCAACAGGGCTCTCCCCATGACACAATTCAACTGG--CCTCCTCCTCCTGATCCCCAGTTCCGA
*
43098 TGCTATATTCATCTTCAACTAAATAGGATTCGGATTTCACTTCTTCACCCTCTTCACCAATGCAA
129 TGCTATATTCATCTTCAACTAAATAGGATTCGGATTTCACTTCTCCACCCTCTTCACCAATGCAA
43163 TTGTCGTTTTTCTCGCTATTCGAATCCTCTGGA
194 TTGTCGTTTTTCTCGCTATTCGAATCCTCTGGA
*
43196 ACTCCATCTTCTGAGTTAATAGCGGAAACGGGATCACCCCCAACAACATCCCTTGAATTTTGTTC
1 ACTCCATCTTCGGAGTTAATAGCGGAAACGGGATCACCCCCAACAACATCCCTTGAATTTTGTTC
* * * *
43261 ATCAATAGGGCTCTCCCCGTGACACAATTCAATTGG-CTCCTCCTCGTGATCCCCAGTTCCGATG
66 ATCAACAGGGCTCTCCCCATGACACAATTCAACTGGCCTCCTCCTCCTGATCCCCAGTTCCGATG
*
43325 CTATATTCATCTTCAACTAAATAGGATTCGGATTTCACTTCTCCATCCTCTTCACCAATGCAATT
131 CTATATTCATCTTCAACTAAATAGGATTCGGATTTCACTTCTCCACCCTCTTCACCAATGCAATT
*
43390 GTCGTTTTTCTCGCTATTCGACTCCTCTGGA
196 GTCGTTTTTCTCGCTATTCGAATCCTCTGGA
43421 ACTCCATCT
1 ACTCCATCT
43430 ATGACGTCGT
Statistics
Matches: 225, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
225 129 0.57
228 96 0.43
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.32
Consensus pattern (226 bp):
ACTCCATCTTCGGAGTTAATAGCGGAAACGGGATCACCCCCAACAACATCCCTTGAATTTTGTTC
ATCAACAGGGCTCTCCCCATGACACAATTCAACTGGCCTCCTCCTCCTGATCCCCAGTTCCGATG
CTATATTCATCTTCAACTAAATAGGATTCGGATTTCACTTCTCCACCCTCTTCACCAATGCAATT
GTCGTTTTTCTCGCTATTCGAATCCTCTGGA
Found at i:45971 original size:21 final size:20
Alignment explanation
Indices: 45937--45983 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
45927 TCAATGTTTC
45937 TAAAAATTCATTTTTTCCAA
1 TAAAAATTCATTTTTTCCAA
45957 TAAAAATTCATTTTTTCCAA
1 TAAAAATTCATTTTTTCCAA
*
45977 TACAAAT
1 TAAAAAT
45984 ATATATCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAAAATTCATTTTTTCCAA
Found at i:47453 original size:2 final size:2
Alignment explanation
Indices: 47446--47485 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
47436 AGATTCGAAC
47446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47486 TTGAACGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54156 original size:3 final size:3
Alignment explanation
Indices: 54148--54179 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
54138 TTCGCATGAC
54148 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54180 AAGCCTTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:65141 original size:3 final size:3
Alignment explanation
Indices: 65133--65160 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
65123 TCAAACACTT
65133 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
65161 GGTTTGGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:66640 original size:17 final size:17
Alignment explanation
Indices: 66610--66651 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
66600 GGTAGTAAAA
*
66610 TATTATTTATAATAATTAC
1 TATT-TTTAAAATAA-TAC
66629 -ATTTTTAAAATAATAC
1 TATTTTTAAAATAATAC
66645 TATTTTT
1 TATTTTT
66652 TCATCCCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 15 0.71
18 3 0.14
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTTTAAAATAATAC
Found at i:71593 original size:13 final size:13
Alignment explanation
Indices: 71575--71600 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
71565 CAGCAGCAGA
71575 AAATCACTTTTCG
1 AAATCACTTTTCG
71588 AAATCACTTTTCG
1 AAATCACTTTTCG
71601 CCATTGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
AAATCACTTTTCG
Done.