Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007233.1 Hibiscus syriacus cultivar Beakdansim tig00019144_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: 59148
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3497 original size:14 final size:14
Alignment explanation
Indices: 3474--3503 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3464 TGTTATTATT
*
3474 TATTATATAATATG
1 TATTAAATAATATG
3488 TATTAAATAATATG
1 TATTAAATAATATG
3502 TA
1 TA
3504 AATATTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
TATTAAATAATATG
Found at i:4982 original size:22 final size:21
Alignment explanation
Indices: 4957--4997 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
4947 AAATAAATAA
4957 ATAACAATAG-TTTTGTATTTGT
1 ATAACAA-AGCTTTTG-ATTTGT
4979 ATAACAAAGCTTTTGATTT
1 ATAACAAAGCTTTTGATTT
4998 TATGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.46
Consensus pattern (21 bp):
ATAACAAAGCTTTTGATTTGT
Found at i:5260 original size:21 final size:21
Alignment explanation
Indices: 5201--5247 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 21
5191 GGAGGGCAAC
5201 TAAAAAATAAAAATGAGTAAATTA
1 TAAAAAATAAAAAT---TAAATTA
5225 TAAAAAATAAAAATTAAA-TA
1 TAAAAAATAAAAATTAAATTA
5245 TAA
1 TAA
5248 TAATATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.22
21 4 0.17
24 14 0.61
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (21 bp):
TAAAAAATAAAAATTAAATTA
Found at i:8084 original size:25 final size:22
Alignment explanation
Indices: 8047--8112 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 22
8037 ATGACTTTTT
8047 AAATT-AATA-ATTTAAATAAA
1 AAATTAAATATATTTAAATAAA
*
8067 AAATTATAATTTATATTTAAATTAA
1 AAATTA-AA--TATATTTAAATAAA
* *
8092 TAATTAAATATATTTATATAA
1 AAATTAAATATATTTAAATAA
8113 TTATTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 5 0.14
22 13 0.35
24 4 0.11
25 15 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATTAAATATATTTAAATAAA
Found at i:8094 original size:19 final size:19
Alignment explanation
Indices: 8044--8100 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
8034 TATATGACTT
8044 TTTAAATTAATAATTTAAA
1 TTTAAATTAATAATTTAAA
** *
8063 TAAAAAATT-ATAATTTATA
1 T-TTAAATTAATAATTTAAA
8082 TTTAAATTAATAA-TTAAA
1 TTTAAATTAATAATTTAAA
8100 T
1 T
8101 ATATTTATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 10 0.33
19 15 0.50
20 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTAAATTAATAATTTAAA
Found at i:8098 original size:12 final size:12
Alignment explanation
Indices: 8045--8100 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 12
8035 ATATGACTTT
8045 TTAAATTAATAA
1 TTAAATTAATAA
* *
8057 TTTAAATAAAAAA
1 -TTAAATTAATAA
* *
8070 TTATAATTTATAT
1 TTA-AATTAATAA
8083 TTAAATTAATAA
1 TTAAATTAATAA
8095 TTAAAT
1 TTAAAT
8101 ATATTTATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
12 16 0.47
13 18 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TTAAATTAATAA
Found at i:8914 original size:19 final size:19
Alignment explanation
Indices: 8882--8927 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
8872 CGACCCGATC
8882 AAATAAAA-AATTTATTTT
1 AAATAAAATAATTTATTTT
8900 AAATAAAATAATTTATTTT
1 AAATAAAATAATTTATTTT
8919 AAATAAAAT
1 AAATAAAAT
8928 CAAAGTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATAAAATAATTTATTTT
Found at i:9620 original size:3 final size:3
Alignment explanation
Indices: 9612--9663 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
9602 GTTTCCATGC
9612 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9660 ATA A
1 ATA A
9664 AATTGAGAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10164 original size:23 final size:22
Alignment explanation
Indices: 10138--10209 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 22
10128 TACTTGCTCT
10138 AAATTTCAATAATTTATGAATTC
1 AAATTT-AATAATTTATGAATTC
10161 AAATGTT-A-AATTT-T-AA--C
1 AAAT-TTAATAATTTATGAATTC
10178 AAATTTAAATAATTTATGAATTC
1 AAATTT-AATAATTTATGAATTC
10201 AAATGTTAA
1 AAAT-TTAA
10210 ATTTTAACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 18
0.69 0.00 0.31
Matches are distributed among these distances:
16 2 0.05
17 5 0.12
18 1 0.03
19 7 0.17
20 2 0.05
21 7 0.17
22 1 0.03
23 11 0.28
24 4 0.10
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (22 bp):
AAATTTAATAATTTATGAATTC
Found at i:10193 original size:40 final size:40
Alignment explanation
Indices: 10138--10228 Score: 173
Period size: 40 Copynumber: 2.3 Consensus size: 40
10128 TACTTGCTCT
*
10138 AAATTTCAATAATTTATGAATTCAAATGTTAAATTTTAAC
1 AAATTTAAATAATTTATGAATTCAAATGTTAAATTTTAAC
10178 AAATTTAAATAATTTATGAATTCAAATGTTAAATTTTAAC
1 AAATTTAAATAATTTATGAATTCAAATGTTAAATTTTAAC
10218 AAATTTAAATA
1 AAATTTAAATA
10229 TAAAAGGAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.42
Consensus pattern (40 bp):
AAATTTAAATAATTTATGAATTCAAATGTTAAATTTTAAC
Found at i:10220 original size:17 final size:16
Alignment explanation
Indices: 10160--10227 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 16
10150 TTTATGAATT
10160 CAAATGTTAAATTTTAA
1 CAAAT-TTAAATTTTAA
10177 CAAATTTAAATAATTTATGAA
1 CAAATTT--A-AATTT-T-AA
10198 TTCAAATGTTAAATTTTAA
1 --CAAAT-TTAAATTTTAA
10217 CAAATTTAAAT
1 CAAATTTAAAT
10228 ATAAAAGGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 17
0.72 0.00 0.28
Matches are distributed among these distances:
16 8 0.19
17 10 0.23
18 1 0.02
19 7 0.16
20 2 0.05
21 7 0.16
22 1 0.02
23 5 0.12
24 2 0.05
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (16 bp):
CAAATTTAAATTTTAA
Found at i:19519 original size:2 final size:2
Alignment explanation
Indices: 19506--19541 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
19496 GATGTAGACG
*
19506 AT AT AC 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
19542 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20095 original size:41 final size:41
Alignment explanation
Indices: 20033--20114 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
20023 TCGGCCTAAT
20033 TTAAATATAATAAGAAGATTTCATTTGACTTGAAACCCGAC
1 TTAAATATAATAAGAAGATTTCATTTGACTTGAAACCCGAC
* *
20074 TTAACTATAATAAGAAGATTTCATTTGACTTGAAGCCCGAC
1 TTAAATATAATAAGAAGATTTCATTTGACTTGAAACCCGAC
20115 CTAATTTGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (41 bp):
TTAAATATAATAAGAAGATTTCATTTGACTTGAAACCCGAC
Found at i:20188 original size:24 final size:25
Alignment explanation
Indices: 20124--20193 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
20114 CCTAATTTGT
*
20124 AAGTTAAAAATTTGAATCCAACTTCG
1 AAGTT-AAAATTTGCATCCAACTTCG
20150 AAGTTAAAATTTGCATCCAACTTCG
1 AAGTTAAAATTTGCATCCAACTTCG
20175 AAGTT-AAATTTGCATCCAA
1 AAGTTAAAATTTGCATCCAA
20194 TTTGACACAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
24 14 0.33
25 24 0.56
26 5 0.12
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (25 bp):
AAGTTAAAATTTGCATCCAACTTCG
Found at i:24075 original size:21 final size:21
Alignment explanation
Indices: 24048--24119 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
24038 ATGCAATACT
24048 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * * *
24069 ATTGCAATGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
24090 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
24111 ATCGCAACG
1 ATCGCAACG
24120 CGAACTTCGA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
19 9 0.23
21 21 0.54
23 9 0.23
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:24092 original size:42 final size:42
Alignment explanation
Indices: 24045--24138 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 42
24035 CAAATGCAAT
* *
24045 ACTATCGCAACGAATTTGGAATAAATTGCAATGCGAACTTCG
1 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG
24087 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG
24129 ACTATCGCAA
1 ACTATCGCAA
24139 TGCGAATATG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.23
Consensus pattern (42 bp):
ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG
Found at i:24135 original size:21 final size:21
Alignment explanation
Indices: 24072--24144 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
24062 GGAATAAATT
24072 GCAATGCGAACTTCGACTATC
1 GCAATGCGAACTTCGACTATC
* * *
24093 GCAA--CGAATTTGGAATAAATC
1 GCAATGCGAACTTCGACT--ATC
*
24114 GCAACGCGAACTTCGACTATC
1 GCAATGCGAACTTCGACTATC
24135 GCAATGCGAA
1 GCAATGCGAA
24145 TATGTAAATC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
19 9 0.22
21 23 0.56
23 9 0.22
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (21 bp):
GCAATGCGAACTTCGACTATC
Found at i:24231 original size:69 final size:71
Alignment explanation
Indices: 24098--24236 Score: 198
Period size: 69 Copynumber: 2.0 Consensus size: 71
24088 CTATCGCAAC
*
24098 GAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCGTTGCG
1 GAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCATTGCG
24163 ATAGTT
66 ATAGTT
*
24169 GAATTTGG-A-AAATCGCAACGCGAACTTCGACTATCGCATTGCG-AT-T-TACATATTCGCATT
1 GAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTA-A-A-TCGCATT
24229 GCGATAGT
63 GCGATAGT
24237 CGAAGTTCGC
Statistics
Matches: 63, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
66 2 0.03
67 2 0.03
68 3 0.05
69 47 0.75
70 1 0.02
71 8 0.13
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (71 bp):
GAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCATTGCG
ATAGTT
Found at i:25774 original size:16 final size:19
Alignment explanation
Indices: 25726--25775 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
25716 GTTATAATGT
*
25726 AATTTCCCTCCTCCCACTC
1 AATTTCTCTCCTCCCACTC
25745 AATTTCTCTCCTCCCACTC
1 AATTTCTCTCCTCCCACTC
25764 AATTTCTCTCCT
1 AATTTCTCTCCT
25776 ACAAAGCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.16, C:0.46, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTTCTCTCCTCCCACTC
Found at i:27714 original size:20 final size:20
Alignment explanation
Indices: 27691--27767 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
27681 ATTCGCGTTG
27691 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* * *
27711 CATTTCGCGTTGCGGTAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** *
27732 AAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTC
27752 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
27768 AGTCTACAGT
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 30 0.68
21 14 0.32
ACGTcount: A:0.14, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:28566 original size:42 final size:42
Alignment explanation
Indices: 28519--28653 Score: 177
Period size: 41 Copynumber: 3.3 Consensus size: 42
28509 ACAACGAATT
* * * *
28519 TGGAAAATCGCAACGACAACTGT-AGACTATCGCACCGCGAAA
1 TGGAAAATCGCAACG-CGATTTTCAGACTATCGCAACGCGAAA
*
28561 TGGAAAAGCGCAACGCGATTTTCAG-CTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAGACTATCGCAACGCGAAA
* *
28602 TGGAAAATCGTAACGCGATTTTCA-ACTATCACAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAGACTATCGCAACGCGAAA
28643 TGGAAAATCGC
1 TGGAAAATCGC
28654 GATCGCAACG
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
41 66 0.80
42 16 0.20
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (42 bp):
TGGAAAATCGCAACGCGATTTTCAGACTATCGCAACGCGAAA
Found at i:47685 original size:53 final size:53
Alignment explanation
Indices: 47605--47712 Score: 173
Period size: 53 Copynumber: 2.0 Consensus size: 53
47595 TATTCTCGTA
*
47605 CGCTGTTGGTAGATGCAATGCTTATTAG-TACTTAATATTAGCTTACAATTAAC
1 CGCTGTTGGTAGATGCAATGCTTATTAGCT-CTTAACATTAGCTTACAATTAAC
* *
47658 CGCTGTTGGTAGGTGCAATGTTTATTAGCTCTTAACATTAGCTTACAATTAAC
1 CGCTGTTGGTAGATGCAATGCTTATTAGCTCTTAACATTAGCTTACAATTAAC
47711 CG
1 CG
47713 AACAGTTATG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 50 0.98
54 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (53 bp):
CGCTGTTGGTAGATGCAATGCTTATTAGCTCTTAACATTAGCTTACAATTAAC
Found at i:51572 original size:28 final size:28
Alignment explanation
Indices: 51517--51572 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
51507 AAAATTTAAC
*
51517 TTTTGAAAAATTAATAAAAGACACTTTT
1 TTTTGAAAAATTAATAAAAGAAACTTTT
*
51545 TTTTGAAAAGTTAATAAAAGAAA-TTTT
1 TTTTGAAAAATTAATAAAAGAAACTTTT
51572 T
1 T
51573 AATGGGAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (28 bp):
TTTTGAAAAATTAATAAAAGAAACTTTT
Done.