Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004420.1 Hibiscus syriacus cultivar Beakdansim tig00009692_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: 36990
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:27 original size:18 final size:18
Alignment explanation
Indices: 4--44 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1 CTT
4 ATTTTTATTGAATAAATA
1 ATTTTTATTGAATAAATA
* *
22 ATTTTTTTTTAATAAATA
1 ATTTTTATTGAATAAATA
*
40 GTTTT
1 ATTTT
45 ATTTCGTGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
ATTTTTATTGAATAAATA
Found at i:692 original size:13 final size:15
Alignment explanation
Indices: 673--708 Score: 58
Period size: 13 Copynumber: 2.5 Consensus size: 15
663 AATTTTAATC
673 AAAATATTAATT-TT
1 AAAATATTAATTATT
687 -AAATATTAATTATT
1 AAAATATTAATTATT
701 AAAATATT
1 AAAATATT
709 TAAAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.55
14 2 0.10
15 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATATTAATTATT
Found at i:737 original size:19 final size:19
Alignment explanation
Indices: 715--759 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
705 TATTTAAAAT
715 ATATTA-ATTAAATTTTATA
1 ATATTATATTAAATTTT-TA
* *
734 ATATAATATTATATTTTTA
1 ATATTATATTAAATTTTTA
753 ATATTAT
1 ATATTAT
760 TATATTATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTATATTAAATTTTTA
Found at i:763 original size:30 final size:30
Alignment explanation
Indices: 641--768 Score: 75
Period size: 30 Copynumber: 4.1 Consensus size: 30
631 TTTGTGTATC
* *
641 TAATATTAATATATTTTAATATAATTTTAATCA
1 TAATATT-ATAT-TTTTAATATTATTATAAT-A
* *
674 AAATATTA-ATTTTAAATATTAATTATTAAAATA
1 TAATATTATATTTTTAATATT-ATTA-T--AATA
* *
707 TTTAA-AATATATTAATTAA-ATT-TTATAATA
1 --TAATATTATATT-TTTAATATTATTATAATA
*
737 TAATATTATATTTTTAATATTATTATATTA
1 TAATATTATATTTTTAATATTATTATAATA
767 TA
1 TA
769 CTCAATTATA
Statistics
Matches: 73, Mismatches: 11, Indels: 25
0.67 0.10 0.23
Matches are distributed among these distances:
28 7 0.10
29 10 0.14
30 21 0.29
31 5 0.07
32 3 0.04
33 10 0.14
34 6 0.08
35 8 0.11
36 3 0.04
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.52
Consensus pattern (30 bp):
TAATATTATATTTTTAATATTATTATAATA
Found at i:768 original size:22 final size:22
Alignment explanation
Indices: 676--766 Score: 68
Period size: 22 Copynumber: 4.3 Consensus size: 22
666 TTTAATCAAA
*
676 ATATT-AATTTTAAATATTAATT
1 ATATTAAATTTTTAATATT-ATT
* * *
698 AT-TAAAATATTTAAAATATATT
1 ATATTAAATTTTTAATAT-TATT
720 A-ATTAAATTTTATAATA-TA--
1 ATATTAAATTTT-TAATATTATT
*
739 ATATTATATTTTTAATATTATT
1 ATATTAAATTTTTAATATTATT
761 ATATTA
1 ATATTA
767 TACTCAATTA
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
19 6 0.11
20 11 0.21
21 3 0.06
22 28 0.53
23 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTAAATTTTTAATATTATT
Found at i:3436 original size:22 final size:24
Alignment explanation
Indices: 3397--3460 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
3387 ATTATCCAAA
* *
3397 AATAATAATCTAATAATATTTTAA-T
1 AATAAT-ATTTAA-AATATATTAATT
3422 AA-AATATTTAAAATATATTAATT
1 AATAATATTTAAAATATATTAATT
*
3445 AATAATTTTTAAAATA
1 AATAATATTTAAAATA
3461 GAGTAGAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 9 0.26
23 8 0.24
24 15 0.44
25 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
AATAATATTTAAAATATATTAATT
Found at i:3961 original size:13 final size:15
Alignment explanation
Indices: 3938--3969 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3928 CATTTTACAG
3938 AAAATATTTTTCAA-
1 AAAATATTTTTCAAT
3952 AAAATA-TTTTCAAT
1 AAAATATTTTTCAAT
3966 AAAA
1 AAAA
3970 CAAATAGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATATTTTTCAAT
Found at i:4312 original size:46 final size:46
Alignment explanation
Indices: 4240--4398 Score: 187
Period size: 46 Copynumber: 3.5 Consensus size: 46
4230 ATATTGGATC
* * * * *
4240 GTTGGTTTCAGTTCGGGTCAAGCTTTAGATTTTCGAGTCAATTCGG
1 GTTGGTTTCGGTTTGGATCAACCTTTAGATTTTCGAGTTAATTCGG
* *
4286 GTTGGTTTCGGTTTGGATCAACCTTTAGATTTACGGGTTAATTCGG
1 GTTGGTTTCGGTTTGGATCAACCTTTAGATTTTCGAGTTAATTCGG
* * * *
4332 GTTGGTTTTGGTTTAGATCAACCTTTAGATTTTTGAGTTAATTCGA
1 GTTGGTTTCGGTTTGGATCAACCTTTAGATTTTCGAGTTAATTCGG
*
4378 GTT-GTTTCTGTTTAGG-TCAAC
1 GTTGGTTTCGGTTT-GGATCAAC
4399 AATCTTCACT
Statistics
Matches: 96, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
45 13 0.14
46 83 0.86
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.43
Consensus pattern (46 bp):
GTTGGTTTCGGTTTGGATCAACCTTTAGATTTTCGAGTTAATTCGG
Found at i:11721 original size:67 final size:66
Alignment explanation
Indices: 11644--11771 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 66
11634 AATAAAAAAA
* * * *
11644 ATATTATGAAAAGCAAGGTCATTAATGAATATCTGAATAAATTCTGAAGTAATCAATTAATAAGA
1 ATATTATGAAAAACAAAGTCATTAATGAATATCTAAAT-AATTCGGAAGTAATCAATTAATAAGA
11709 AT
65 AT
* * * *
11711 ATATTCTGAAAAATAAAGTCGTTAATGAGTATCTAAATAATTCGGAAGTAATCAATTAATA
1 ATATTATGAAAAACAAAGTCATTAATGAATATCTAAATAATTCGGAAGTAATCAATTAATA
11772 TCGCATTTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
66 22 0.42
67 31 0.58
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (66 bp):
ATATTATGAAAAACAAAGTCATTAATGAATATCTAAATAATTCGGAAGTAATCAATTAATAAGAA
T
Found at i:21952 original size:20 final size:20
Alignment explanation
Indices: 21929--21967 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21919 TACTTTTCTG
21929 GAAATTAATGTTAGAATGTT
1 GAAATTAATGTTAGAATGTT
*
21949 GAAATTGATGTTAGAATGT
1 GAAATTAATGTTAGAATGT
21968 GAGATAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (20 bp):
GAAATTAATGTTAGAATGTT
Found at i:22595 original size:22 final size:21
Alignment explanation
Indices: 22538--22614 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
22528 AGAATGCTCG
*
22538 GATGATACCGATACCCCC-CA
1 GATGGTACCGATACCCCCTCA
*
22558 GA--GTATCGATACCCCCATGCA
1 GATGGTACCGATACCCCC-T-CA
*
22579 -ATGGTACCGATAGCCCCTCA
1 GATGGTACCGATACCCCCTCA
*
22599 GGTGGTACCGATACCC
1 GATGGTACCGATACCC
22615 TAAGGCATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
18 12 0.27
20 5 0.11
21 16 0.36
22 12 0.27
ACGTcount: A:0.26, C:0.35, G:0.21, T:0.18
Consensus pattern (21 bp):
GATGGTACCGATACCCCCTCA
Found at i:24542 original size:21 final size:21
Alignment explanation
Indices: 24518--24557 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
24508 GAGAAATTGT
24518 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
24539 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
24558 AAACAATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:28411 original size:23 final size:23
Alignment explanation
Indices: 28381--28461 Score: 105
Period size: 23 Copynumber: 3.6 Consensus size: 23
28371 CCCTAAGTCT
28381 GGTATCGATACCCCCTTTGAATA
1 GGTATCGATACCCCCTTTGAATA
28404 GGTATCGATA-CCCC--TGCAATA
1 GGTATCGATACCCCCTTTG-AATA
** *
28425 GGTATCGATACCATCTTTGAATG
1 GGTATCGATACCCCCTTTGAATA
28448 GGTATCGATACCCC
1 GGTATCGATACCCC
28462 TTGATGGTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.04
21 14 0.29
22 6 0.12
23 25 0.51
24 2 0.04
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (23 bp):
GGTATCGATACCCCCTTTGAATA
Found at i:28426 original size:21 final size:20
Alignment explanation
Indices: 28356--28479 Score: 92
Period size: 21 Copynumber: 5.8 Consensus size: 20
28346 ATTTTTGTGC
28356 ATAGAGTATCGATACCCCT-A
1 ATAG-GTATCGATACCCCTGA
*
28376 AGTCTGGTATCGATACCCCCTTTGA
1 A-T-AGGTATCGATA-CCCC--TGA
28401 ATAGGTATCGATACCCCTGCA
1 ATAGGTATCGATACCCCTG-A
*
28422 ATAGGTATCGATACCATCTTTGA
1 ATAGGTATCGATACC--C-CTGA
*
28445 ATGGGTATCGATACCCCTTG-
1 ATAGGTATCGATACCCC-TGA
*
28465 AT-GGTATTGATACCC
1 ATAGGTATCGATACCC
28480 TCCACGGGGT
Statistics
Matches: 87, Mismatches: 6, Indels: 23
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.14
20 5 0.06
21 29 0.33
22 9 0.10
23 26 0.30
24 4 0.05
25 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (20 bp):
ATAGGTATCGATACCCCTGA
Found at i:28429 original size:44 final size:44
Alignment explanation
Indices: 28356--28462 Score: 137
Period size: 44 Copynumber: 2.4 Consensus size: 44
28346 ATTTTTGTGC
* *
28356 ATAGAGTATCGATACCCCTAAGTCTGGTATCGATACCCCCTTTGA
1 ATAG-GTATCGATACCCCTAAGTCAGGTATCGATACCACCTTTGA
*
28401 ATAGGTATCGATACCCCTGCAA-T-AGGTATCGATACCATCTTTGA
1 ATAGGTATCGATACCCCT--AAGTCAGGTATCGATACCACCTTTGA
*
28445 ATGGGTATCGATACCCCT
1 ATAGGTATCGATACCCCT
28463 TGATGGTATT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
44 49 0.88
45 5 0.09
46 2 0.04
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
ATAGGTATCGATACCCCTAAGTCAGGTATCGATACCACCTTTGA
Found at i:32962 original size:28 final size:29
Alignment explanation
Indices: 32893--32951 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
32883 ACAATTAAGG
32893 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
32924 CAAAATGTTTTTGGACTT-ATTGAATTTA
1 CAAAATGTTTTTGGACTTAATTGAATTTA
32952 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (29 bp):
CAAAATGTTTTTGGACTTAATTGAATTTA
Found at i:33058 original size:13 final size:13
Alignment explanation
Indices: 33040--33064 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33030 AGTTCATCTA
33040 TGCATCCCTGCAG
1 TGCATCCCTGCAG
33053 TGCATCCCTGCA
1 TGCATCCCTGCA
33065 CCTGCACTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.20, T:0.24
Consensus pattern (13 bp):
TGCATCCCTGCAG
Found at i:33086 original size:22 final size:23
Alignment explanation
Indices: 33051--33093 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
33041 GCATCCCTGC
*
33051 AGTGCATCCCTGCACC-TGCACT
1 AGTGCATCCATGCACCATGCACT
*
33073 AGTGCATCGATGCACCATGCA
1 AGTGCATCCATGCACCATGCA
33094 GTGCATCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (23 bp):
AGTGCATCCATGCACCATGCACT
Found at i:33169 original size:21 final size:21
Alignment explanation
Indices: 33125--33198 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
33115 GAATGCATTA
* **
33125 GTGCATCGATGCA-TCATTCT
1 GTGCATCGATGCATTAAGGCT
33145 GTGCATCGATGCATTAAGGCT
1 GTGCATCGATGCATTAAGGCT
*
33166 GTGCATCGATGCATCAAGG-T
1 GTGCATCGATGCATTAAGGCT
33186 -TGCATCGATGCAT
1 GTGCATCGATGCAT
33199 CCTGTTGTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
19 13 0.27
20 14 0.29
21 22 0.45
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.30
Consensus pattern (21 bp):
GTGCATCGATGCATTAAGGCT
Found at i:34281 original size:18 final size:19
Alignment explanation
Indices: 34258--34331 Score: 53
Period size: 19 Copynumber: 3.9 Consensus size: 19
34248 TATGCATTGG
* *
34258 GCTATGGATTTGAAA-TAA
1 GCTATGAATCTGAAAGTAA
34276 GCTATGAATCTGAAAGTAA
1 GCTATGAATCTGAAAGTAA
* * * *
34295 GTTCTGAATCAGAAAATGAA
1 GCTATGAATCTGAAAGT-AA
* *
34315 -TTATGAATATGAAAGTA
1 GCTATGAATCTGAAAGTA
34332 CTTTTATGTA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
18 14 0.32
19 28 0.64
20 2 0.05
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (19 bp):
GCTATGAATCTGAAAGTAA
Found at i:34302 original size:19 final size:18
Alignment explanation
Indices: 34278--34331 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
34268 TGAAATAAGC
34278 TATGAATCTGAAAGTAAGT
1 TATGAATCTGAAAGTAA-T
* * *
34297 TCTGAATCAGAAAATGAAT
1 TATGAATCTGAAAGT-AAT
*
34316 TATGAATATGAAAGTA
1 TATGAATCTGAAAGTA
34332 CTTTTATGTA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
18 1 0.04
19 24 0.89
20 2 0.07
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.30
Consensus pattern (18 bp):
TATGAATCTGAAAGTAAT
Found at i:35426 original size:40 final size:40
Alignment explanation
Indices: 35298--35428 Score: 115
Period size: 41 Copynumber: 3.2 Consensus size: 40
35288 CGATTTTTTT
* * * * * *
35298 AAAACGCCACTATATTACAATTTTGTGACGGCGGTT-TTTA
1 AAAACGCCACTAAAGTACAAGTTTGTCACGGC-GTTCGTGA
* * *
35338 AGAAACACCACTAAAGTACTAGTTTGTCACGGCGTTTGTGA
1 A-AAACGCCACTAAAGTACAAGTTTGTCACGGCGTTCGTGA
35379 AATAACGCCACTAAAGTACAAG-TTGT-AGCGGCGTTCGTGGA
1 AA-AACGCCACTAAAGTACAAGTTTGTCA-CGGCGTTCGT-GA
35420 AAAACGCCA
1 AAAACGCCA
35429 TTAATGTTAT
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
39 1 0.01
40 25 0.33
41 49 0.65
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (40 bp):
AAAACGCCACTAAAGTACAAGTTTGTCACGGCGTTCGTGA
Done.