Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000500.1 Hibiscus syriacus cultivar Beakdansim tig00000952_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: 83126
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:752 original size:21 final size:21
Alignment explanation
Indices: 726--777 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
716 TGGAGCGTGG
726 GGGAATC-AGTACCCCCTCATA
1 GGGAATCGA-TACCCCCTCATA
*
747 GGGAATCGATTCCCCCTCATA
1 GGGAATCGATACCCCCTCATA
768 GGGAATCGAT
1 GGGAATCGAT
778 TCCCTAATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (21 bp):
GGGAATCGATACCCCCTCATA
Found at i:778 original size:21 final size:21
Alignment explanation
Indices: 737--781 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
727 GGAATCAGTA
737 CCCCCTCATAGGGAATCGATT
1 CCCCCTCATAGGGAATCGATT
758 CCCCCTCATAGGGAATCGATT
1 CCCCCTCATAGGGAATCGATT
779 CCC
1 CCC
782 TAATGTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.22
Consensus pattern (21 bp):
CCCCCTCATAGGGAATCGATT
Found at i:2827 original size:23 final size:22
Alignment explanation
Indices: 2796--2881 Score: 113
Period size: 23 Copynumber: 3.9 Consensus size: 22
2786 ACACAAAGTG
2796 CCATAGTACACAAATGT-CTCTT
1 CCATAGTACACAAA-GTACTCTT
* *
2818 GTCATAGTACACAAAGTACTATT
1 -CCATAGTACACAAAGTACTCTT
2841 CCA-AGTACACAAAGTACTCTT
1 CCATAGTACACAAAGTACTCTT
2862 ACCATAGTACACAAAGTACT
1 -CCATAGTACACAAAGTACT
2882 ACTACAAGTA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
21 17 0.30
22 7 0.12
23 32 0.57
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.27
Consensus pattern (22 bp):
CCATAGTACACAAAGTACTCTT
Found at i:2849 original size:21 final size:21
Alignment explanation
Indices: 2823--2897 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
2813 CTCTTGTCAT
2823 AGTACACAAAGTACTATTCCA
1 AGTACACAAAGTACTATTCCA
*
2844 AGTACACAAAGTACTCTTACCA
1 AGTACACAAAGTACTATT-CCA
* *
2866 TAGTACACAAAGTACTACTACA
1 -AGTACACAAAGTACTATTCCA
*
2888 AGTAGACAAA
1 AGTACACAAA
2898 ATATTCTTGC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 26 0.55
22 5 0.11
23 16 0.34
ACGTcount: A:0.45, C:0.23, G:0.11, T:0.21
Consensus pattern (21 bp):
AGTACACAAAGTACTATTCCA
Found at i:2852 original size:44 final size:44
Alignment explanation
Indices: 2800--2897 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
2790 AAAGTGCCAT
** * *
2800 AGTACACAAATGT-CTCTTGTCATAGTACACAAAGTACTATTCCA
1 AGTACACAAA-GTACTCTTACCATAGTACACAAAGTACTACTACA
2844 AGTACACAAAGTACTCTTACCATAGTACACAAAGTACTACTACA
1 AGTACACAAAGTACTCTTACCATAGTACACAAAGTACTACTACA
*
2888 AGTAGACAAA
1 AGTACACAAA
2898 ATATTCTTGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 2 0.04
44 46 0.96
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.24
Consensus pattern (44 bp):
AGTACACAAAGTACTCTTACCATAGTACACAAAGTACTACTACA
Found at i:5907 original size:28 final size:27
Alignment explanation
Indices: 5868--5925 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 27
5858 AATTCAATCG
5868 ATATTAGCCGAACTATCTCTTTTATGT
1 ATATTAGCCGAACTATCTCTTTTATGT
5895 ATATGTAGCCGAACTATCTCTTTTATGT
1 ATAT-TAGCCGAACTATCTCTTTTATGT
5923 ATA
1 ATA
5926 ACTCATCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 4 0.13
28 26 0.87
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (27 bp):
ATATTAGCCGAACTATCTCTTTTATGT
Found at i:9305 original size:32 final size:32
Alignment explanation
Indices: 9269--9330 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
9259 AATAATATAG
9269 TTTATAAAACACTCTTCAAATACATACATACA
1 TTTATAAAACACTCTTCAAATACATACATACA
* *
9301 TTTATAAATCATTCTTCAAATACATACATA
1 TTTATAAAACACTCTTCAAATACATACATA
9331 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTATAAAACACTCTTCAAATACATACATACA
Found at i:9951 original size:23 final size:22
Alignment explanation
Indices: 9894--10021 Score: 115
Period size: 21 Copynumber: 5.9 Consensus size: 22
9884 ACACAAAGTG
9894 CCATAGTACACAAAGTACTACT
1 CCATAGTACACAAAGTACTACT
*
9916 ACA-AGTACACAAAGTACT-CTT
1 CCATAGTACACAAAGTACTAC-T
*
9937 GCCATAATACACAAAGTACTACT
1 -CCATAGTACACAAAGTACTACT
*
9960 CCA-AGTACACAAA-TA-AATCTT
1 CCATAGTACACAAAGTACTA-C-T
*
9981 ACCATAGTACACAAAGTAATACT
1 -CCATAGTACACAAAGTACTACT
* *
10004 CCA-AGTAGACAAAATACT
1 CCATAGTACACAAAGTACT
10022 CTTACAAAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
19 1 0.01
20 4 0.05
21 38 0.44
22 13 0.15
23 26 0.30
24 4 0.05
25 1 0.01
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (22 bp):
CCATAGTACACAAAGTACTACT
Found at i:10025 original size:44 final size:44
Alignment explanation
Indices: 9894--10026 Score: 187
Period size: 44 Copynumber: 3.0 Consensus size: 44
9884 ACACAAAGTG
* * *
9894 CCATAGTACACAAAGTACTACTACAAGTACACAAAGTACTCTTG
1 CCATAGTACACAAAGTACTACTCCAAGTACACAAAATACTCTTA
* *
9938 CCATAATACACAAAGTACTACTCCAAGTACAC-AAATAAATCTTA
1 CCATAGTACACAAAGTACTACTCCAAGTACACAAAAT-ACTCTTA
* *
9982 CCATAGTACACAAAGTAATACTCCAAGTAGACAAAATACTCTTA
1 CCATAGTACACAAAGTACTACTCCAAGTACACAAAATACTCTTA
10026 C
1 C
10027 AAAAATGCAA
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
43 3 0.04
44 71 0.91
45 4 0.05
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.23
Consensus pattern (44 bp):
CCATAGTACACAAAGTACTACTCCAAGTACACAAAATACTCTTA
Found at i:11063 original size:12 final size:11
Alignment explanation
Indices: 11035--11065 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
11025 AAGCCATGGT
*
11035 AATTTTTCTAC
1 AATTTTTCCAC
11046 AATTTTTCCAC
1 AATTTTTCCAC
11057 AATTTTTCC
1 AATTTTTCC
11066 TACCCTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTTTTCCAC
Found at i:21480 original size:28 final size:28
Alignment explanation
Indices: 21440--21496 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
21430 ATAAATGTTA
21440 GGGAATATACTAACATTTGGTATGATAT
1 GGGAATATACTAACATTTGGTATGATAT
21468 GGGAATATACTAACATTTGGTATGATAT
1 GGGAATATACTAACATTTGGTATGATAT
21496 G
1 G
21497 TGTCTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (28 bp):
GGGAATATACTAACATTTGGTATGATAT
Found at i:21757 original size:54 final size:54
Alignment explanation
Indices: 21688--22246 Score: 714
Period size: 54 Copynumber: 10.4 Consensus size: 54
21678 TATGTATTGC
* *
21688 AATTTCTGTGTTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATG
1 AATTTCTGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATG
*
21742 AATTTCTGTATTGGCACT-TGTGTGCAACCTAAGAAATTCAAAATAAGTTTATG
1 AATTTCTGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATG
* *
21795 AATTTCCT-TATTGGCACTATGTGAGCAACCTAAGAAATTCATATTAAGTTTATG
1 AATTT-CTGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATG
** * * * *
21849 AATTTCCATATTGGCACTATGTGTACAACCTAATAAATTCATATTAAGTTAATG
1 AATTTCTGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATG
* *
21903 AATTT-TCGTATTGGCACTATGTATGCAACCTAAGAAATTCATAATAAGTTTATA
1 AATTTCT-GTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATG
*
21957 AATTTCTGTTTTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATG
1 AATTTCTGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATG
* **
22011 AATTT-TCGTATTGGAACTATGTGTGCAAGATAAGAAATTCATAATAAGTTTATG
1 AATTTCT-GTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATG
** * * *
22065 AATTTCCATTTTGGCACTATGTGTGCAACCTAAGAAATTAATAATGAGTTTATG
1 AATTTCTGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATG
* * * *
22119 AATTT-TCGTATTGGCACTATGTCTGCAACTTAATAAATTCATAATGAGTTTATG
1 AATTTCT-GTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATG
* * * * * * *
22173 AATTTCTGTATTGGCACTAAGTGTGTAACCCCACGTAATTCATAATGAGTTTGTG
1 AATTTCTGTATTGGCACTATGTGTGCAA-CCTAAGAAATTCATAATAAGTTTATG
* * *
22228 AATTACTTTATTGGGACTA
1 AATTTCTGTATTGGCACTA
22247 CAAGTGCAAA
Statistics
Matches: 442, Mismatches: 53, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
53 50 0.11
54 354 0.80
55 38 0.09
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (54 bp):
AATTTCTGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATG
Found at i:40828 original size:54 final size:54
Alignment explanation
Indices: 40722--41180 Score: 631
Period size: 54 Copynumber: 8.5 Consensus size: 54
40712 TGTATTGCAA
*
40722 TTTCTGTATTGGCACTATGTGTGCAACCTAA-AAATTCATAATAAATTTATGAAT
1 TTTC-GTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT
* * *
40776 TTTCGTATTGACACTATGTGTTCAAACTAAGAAATTCATAATAAGTTTATGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT
* *
40830 TTAT-GTATTGGCACTATGTGTTCAACCTAAGAAATTCATAAGAAGTTTATGAAT
1 TT-TCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT
* *
40884 TTCCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAA-
1 TTTCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT
* *
40937 TTTCTGTATTGGCACCATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATGAAT
1 TTTC-GTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT
* *
40992 TTAT-GTATTGACACTATATGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT
1 TT-TCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT
* * *
41046 TTTCGTATTGGCACTATATGTGCAACCTAAGAAATTCATAATGAGGTTATGAA-
1 TTTCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT
* * * * *
41099 TTTCTATATTGGCACTGTGTGTGCAACTTAAGAAATTCGTAATGAGTTTATGAAT
1 TTTC-GTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT
* * *
41154 TTTCATGTTGGCACTAAGTGTGCAACC
1 TTTCGTATTGGCACTATGTGTGCAACC
41181 CCACATAATT
Statistics
Matches: 364, Mismatches: 32, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
53 31 0.09
54 325 0.89
55 7 0.02
56 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (54 bp):
TTTCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT
Found at i:44714 original size:20 final size:20
Alignment explanation
Indices: 44691--44744 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
44681 ATGTTATTAT
*
44691 AATATTGATACTATATGAAC
1 AATACTGATACTATATGAAC
44711 AATACTGATACTATATGAAC
1 AATACTGATACTATATGAAC
44731 AATACTGATACTAT
1 AATACTGATACTAT
44745 TCATGTGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.33
Consensus pattern (20 bp):
AATACTGATACTATATGAAC
Found at i:47604 original size:2 final size:2
Alignment explanation
Indices: 47587--47621 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
47577 TCATAATAAC
*
47587 TA TA GA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47622 ACTATCTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:49497 original size:21 final size:22
Alignment explanation
Indices: 49473--49520 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
49463 TCAAAAAAAC
* *
49473 AAAAGAAAACAAAAAAA-GGCA
1 AAAAAAAAACAAAAAAATGCCA
49494 AAAAAAAAACAAAAAAATGCCA
1 AAAAAAAAACAAAAAAATGCCA
49516 AAAAA
1 AAAAA
49521 GCCAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.79, C:0.10, G:0.08, T:0.02
Consensus pattern (22 bp):
AAAAAAAAACAAAAAAATGCCA
Found at i:49519 original size:31 final size:31
Alignment explanation
Indices: 49465--49527 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
49455 TTTTTTTTTC
*
49465 AAAAAAACAAAAGAAAACAAAAAAAGGCAAA
1 AAAAAAACAAAAGAAAACAAAAAAAGCCAAA
* *
49496 AAAAAAACAAAA-AAATGCCAAAAAAGCCAAA
1 AAAAAAACAAAAGAAA-ACAAAAAAAGCCAAA
49527 A
1 A
49528 TTTCAAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.78, C:0.13, G:0.08, T:0.02
Consensus pattern (31 bp):
AAAAAAACAAAAGAAAACAAAAAAAGCCAAA
Found at i:64775 original size:35 final size:34
Alignment explanation
Indices: 64735--64802 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 34
64725 TTATAAATAT
64735 ATAAAAAGTATTATATATATTAAATTAATTTTTAA
1 ATAAAAAGTATTATATATATT-AATTAATTTTTAA
* * *
64770 ATAAAAATTATTATGTATATTAATTTATTTTTA
1 ATAAAAAGTATTATATATATTAATTAATTTTTA
64803 GTTACATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 11 0.37
35 19 0.63
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (34 bp):
ATAAAAAGTATTATATATATTAATTAATTTTTAA
Found at i:65033 original size:2 final size:2
Alignment explanation
Indices: 65026--65054 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
65016 AATTTCAAAT
65026 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
65055 GCACTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78824 original size:29 final size:28
Alignment explanation
Indices: 78746--78824 Score: 70
Period size: 29 Copynumber: 2.8 Consensus size: 28
78736 GAAAATATAT
* * *
78746 AACTTTAAAA-TTACATTTTTAGTCTCA
1 AACTTTAAAATTTACATTTTGACTATCA
* * *
78773 AACTTTTTAAAATTTATACTTTGACTATTA
1 AAC--TTTAAAATTTACATTTTGACTATCA
78803 AACTTTCAAAATTTACATTTTG
1 AACTTT-AAAATTTACATTTTG
78825 GTCACTACTA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
27 3 0.08
28 3 0.08
29 20 0.50
30 14 0.35
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.47
Consensus pattern (28 bp):
AACTTTAAAATTTACATTTTGACTATCA
Done.