Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008898.1 Hibiscus syriacus cultivar Beakdansim tig00112170_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: 53127
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1016 original size:21 final size:21
Alignment explanation
Indices: 992--1048 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
982 AAGGGTTAAG
*
992 ACCTTTTGATGAAAGGACTTA
1 ACCTTTTGATTAAAGGACTTA
1013 ACCTTTTGATTAAAGGACTTA
1 ACCTTTTGATTAAAGGACTTA
*
1034 TCCTTTTGATTAAAG
1 ACCTTTTGATTAAAG
1049 AATCTAATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (21 bp):
ACCTTTTGATTAAAGGACTTA
Found at i:1060 original size:21 final size:21
Alignment explanation
Indices: 993--1061 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
983 AGGGTTAAGA
* *
993 CCTTTTGATGAAAGGACTTAA-
1 CCTTTTGATTAAAGAAC-TAAT
* *
1014 CCTTTTGATTAAAGGACTTAT
1 CCTTTTGATTAAAGAACTAAT
1035 CCTTTTGATTAAAGAATCTAAT
1 CCTTTTGATTAAAGAA-CTAAT
1057 -CTTTT
1 CCTTTT
1062 CATGAAGAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.05
21 36 0.86
22 4 0.10
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (21 bp):
CCTTTTGATTAAAGAACTAAT
Found at i:2877 original size:7 final size:7
Alignment explanation
Indices: 2865--2895 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2855 GTCAAAGAAA
2865 GTCAACG
1 GTCAACG
2872 GTCAACG
1 GTCAACG
2879 GTCAACG
1 GTCAACG
*
2886 GTTAACG
1 GTCAACG
2893 GTC
1 GTC
2896 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:2911 original size:17 final size:17
Alignment explanation
Indices: 2889--2922 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2879 GTCAACGGTT
2889 AACGGTCGGGTCGGGTC
1 AACGGTCGGGTCGGGTC
*
2906 AACGGTTGGGTCGGGTC
1 AACGGTCGGGTCGGGTC
2923 GGGTCAACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.21, G:0.47, T:0.21
Consensus pattern (17 bp):
AACGGTCGGGTCGGGTC
Found at i:2920 original size:22 final size:22
Alignment explanation
Indices: 2878--2939 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
2868 AACGGTCAAC
*
2878 GGTCAACGGTTAACGGTCGGGTCG
1 GGTCAACGGTT--GGGTCGGGTCG
2902 GGTCAACGGTTGGGTCGGGTCG
1 GGTCAACGGTTGGGTCGGGTCG
* *
2924 GGTCAACAGTCGGGTC
1 GGTCAACGGTTGGGTC
2940 AGACCGGTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 24 0.69
24 11 0.31
ACGTcount: A:0.15, C:0.21, G:0.44, T:0.21
Consensus pattern (22 bp):
GGTCAACGGTTGGGTCGGGTCG
Found at i:2954 original size:9 final size:9
Alignment explanation
Indices: 2936--3051 Score: 65
Period size: 9 Copynumber: 12.3 Consensus size: 9
2926 TCAACAGTCG
*
2936 GGTCAGACC
1 GGTCAAACC
2945 GGTCAAACC
1 GGTCAAACC
* *
2954 GGTTTAGA--
1 GG-TCAAACC
2962 GGTCAAACC
1 GGTCAAACC
*
2971 GGTTCAGACC
1 GG-TCAAACC
2981 GGTCAAACC
1 GGTCAAACC
*
2990 GGTTCGAACC
1 GG-TCAAACC
*
3000 GGTTGAAACC
1 GG-TCAAACC
3010 GGTCAAACC
1 GGTCAAACC
*
3019 AGTCAGAACC
1 GGTCA-AACC
* *
3029 TGTTGAAAACC
1 -GGT-CAAACC
*
3040 GGTTAAACC
1 GGTCAAACC
3049 GGT
1 GGT
3052 TTCCAGCAGC
Statistics
Matches: 82, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
7 3 0.04
8 2 0.02
9 38 0.46
10 33 0.40
11 5 0.06
12 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2986 original size:19 final size:19
Alignment explanation
Indices: 2938--3052 Score: 94
Period size: 19 Copynumber: 6.1 Consensus size: 19
2928 AACAGTCGGG
2938 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
2957 TTAGA--GGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
2974 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
2993 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
* * *
3012 TCAAACCAGTCAGAACCTGT
1 TCAGACCGGTCA-AACCGGT
* * *
3032 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
3052 T
1 T
3053 TCCAGCAGCC
Statistics
Matches: 77, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
17 16 0.21
18 3 0.04
19 34 0.44
20 16 0.21
21 8 0.10
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:3009 original size:10 final size:10
Alignment explanation
Indices: 2964--3052 Score: 78
Period size: 10 Copynumber: 9.1 Consensus size: 10
2954 GGTTTAGAGG
2964 TCAAACCGGT
1 TCAAACCGGT
*
2974 TCAGACCGG-
1 TCAAACCGGT
2983 TCAAACCGGT
1 TCAAACCGGT
*
2993 TCGAACCGGT
1 TCAAACCGGT
*
3003 TGAAACCGG-
1 TCAAACCGGT
*
3012 TCAAACCAG-
1 TCAAACCGGT
*
3021 TCAGAACCTGT
1 TCA-AACCGGT
*
3032 TGAAAACCGGT
1 T-CAAACCGGT
3043 T-AAACCGGT
1 TCAAACCGGT
3052 T
1 T
3053 TCCAGCAGCC
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
9 27 0.42
10 29 0.45
11 8 0.12
12 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:3027 original size:29 final size:29
Alignment explanation
Indices: 2963--3048 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
2953 CGGTTTAGAG
* * *
2963 GTCA-AACCGGTTCAGACCGGTCAAACCG
1 GTCAGAACCGGTTGAAACCGGTCAAACCA
2991 GTTC-GAACCGGTTGAAACCGGTCAAACCA
1 G-TCAGAACCGGTTGAAACCGGTCAAACCA
* *
3020 GTCAGAACCTGTTGAAAACCGGTTAAACC
1 GTCAGAACCGGTTG-AAACCGGTCAAACC
3049 GGTTTCCAGC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 3 0.06
29 33 0.67
30 13 0.27
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.17
Consensus pattern (29 bp):
GTCAGAACCGGTTGAAACCGGTCAAACCA
Found at i:8586 original size:21 final size:21
Alignment explanation
Indices: 8549--8604 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
8539 AAGGGTTAAG
*
8549 ACCTTTTGA-TGAAGGACTTA
1 ACCTTTTGATTAAAGGACTTA
8569 ACCTTTTGATTAAAGGACTTA
1 ACCTTTTGATTAAAGGACTTA
*
8590 TCCTTTTGATTAAAG
1 ACCTTTTGATTAAAG
8605 AATCTAATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 9 0.27
21 24 0.73
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (21 bp):
ACCTTTTGATTAAAGGACTTA
Found at i:8616 original size:21 final size:21
Alignment explanation
Indices: 8570--8617 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
8560 AAGGACTTAA
* *
8570 CCTTTTGATTAAAGGACTTAT
1 CCTTTTGATTAAAGAACTAAT
8591 CCTTTTGATTAAAGAATCTAAT
1 CCTTTTGATTAAAGAA-CTAAT
8613 -CTTTT
1 CCTTTT
8618 CATGAAGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (21 bp):
CCTTTTGATTAAAGAACTAAT
Found at i:13118 original size:44 final size:44
Alignment explanation
Indices: 13070--13183 Score: 138
Period size: 45 Copynumber: 2.5 Consensus size: 44
13060 GTGTAGAGAT
* *
13070 GTATTAAATTTTAAAGAAAATGTTGAGATTCGAACCCACACTAG
1 GTATTAAATTTTAAAGAAAACGTCGAGATTCGAACCCACACTAG
* * * *
13114 GTATTATAGTTTTAAAGCAAACGTCGAGATTTGAACCCACGCTAG
1 GTATTA-AATTTTAAAGAAAACGTCGAGATTCGAACCCACACTAG
* *
13159 GTATTACATTTTAAAGGACAACGTC
1 GTATTAAATTTTAAA-GAAAACGTC
13184 AAATTCACTA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
44 13 0.22
45 45 0.78
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (44 bp):
GTATTAAATTTTAAAGAAAACGTCGAGATTCGAACCCACACTAG
Found at i:16488 original size:97 final size:100
Alignment explanation
Indices: 16315--16509 Score: 344
Period size: 97 Copynumber: 2.0 Consensus size: 100
16305 CTTGTGGGGG
16315 TGTACTTTGTTAATTCTTAAATACAAGGTACCCTTTTTCAACACAAAAAAAAGGTAAGTGGACTA
1 TGTACTTTGTTAATTCTTAAATACAAGGTACCCTTTTTCAACACAAAAAAAAGGTAAGTGGACTA
*
16380 TGATATTGATTTCTTTTATATTTTAATTGGATTTTC
66 TGATATTGATTTC-TTTATATTTAAATTGGATTTTC
16416 TGTACTTTGTTAATTCTTAAATACAAGGTA-CCTTTTTC-A-AC-AAAAAAAGGTAAGTGGACTA
1 TGTACTTTGTTAATTCTTAAATACAAGGTACCCTTTTTCAACACAAAAAAAAGGTAAGTGGACTA
16477 TGATATTGATTTCTTTATATTTAAATTGGATTT
66 TGATATTGATTTCTTTATATTTAAATTGGATTT
16510 GCCAAAGGAA
Statistics
Matches: 93, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
96 19 0.20
97 33 0.35
98 2 0.02
99 1 0.01
100 8 0.09
101 30 0.32
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (100 bp):
TGTACTTTGTTAATTCTTAAATACAAGGTACCCTTTTTCAACACAAAAAAAAGGTAAGTGGACTA
TGATATTGATTTCTTTATATTTAAATTGGATTTTC
Found at i:16707 original size:43 final size:43
Alignment explanation
Indices: 16646--16731 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
16636 AATCACGACC
16646 AATTTTCTGTTTGAGAGTGTGTATCAATATTGAGGATGAAGGT
1 AATTTTCTGTTTGAGAGTGTGTATCAATATTGAGGATGAAGGT
16689 AATTTTCTGTTTGAGAGTGTGTATCAATATTGAGGATGAAGGT
1 AATTTTCTGTTTGAGAGTGTGTATCAATATTGAGGATGAAGGT
16732 TAAAAGTATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.40
Consensus pattern (43 bp):
AATTTTCTGTTTGAGAGTGTGTATCAATATTGAGGATGAAGGT
Found at i:21450 original size:28 final size:30
Alignment explanation
Indices: 21405--21462 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
21395 GTAAAGTCCA
** *
21405 AAAATTTTAAGATTAAAAT-ATATATATTT
1 AAAATTTTAAGACAAAAATAAAATATATTT
21434 AAAA-TTTAAGACAAAAATAAAATATATTT
1 AAAATTTTAAGACAAAAATAAAATATATTT
21463 TTAAGTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTTTAAGACAAAAATAAAATATATTT
Found at i:21471 original size:29 final size:28
Alignment explanation
Indices: 21449--21587 Score: 109
Period size: 28 Copynumber: 4.8 Consensus size: 28
21439 TTAAGACAAA
21449 AATAAAATATATTTTTAAGTTAAATAAG
1 AATAAAATATATTTTTAAGTTAAATAAG
* *
21477 AATAAAATGTATTTTTAAGTTCATATAAG
1 AATAAAATATATTTTTAAGTT-AAATAAG
** * * *
21506 AATAAAATATAAAAATTTAAATAAAATAAT
1 AATAAAATAT--ATTTTTAAGTTAAATAAG
* * ** *
21536 AATAAATTAAATTAAATAAGTTAAGATAAA
1 AATAAAATATATT-TTTAAGTTAA-ATAAG
*
21566 AATGAAATAT-TTTTTAAGTTAA
1 AATAAAATATATTTTTAAGTTAA
21588 GATGCGAATT
Statistics
Matches: 83, Mismatches: 23, Indels: 10
0.72 0.20 0.09
Matches are distributed among these distances:
28 29 0.35
29 23 0.28
30 24 0.29
31 7 0.08
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (28 bp):
AATAAAATATATTTTTAAGTTAAATAAG
Found at i:21489 original size:28 final size:29
Alignment explanation
Indices: 21449--21516 Score: 111
Period size: 28 Copynumber: 2.4 Consensus size: 29
21439 TTAAGACAAA
21449 AATAAAATATATTTTTAAGTT-AAATAAG
1 AATAAAATATATTTTTAAGTTCAAATAAG
* *
21477 AATAAAATGTATTTTTAAGTTCATATAAG
1 AATAAAATATATTTTTAAGTTCAAATAAG
21506 AATAAAATATA
1 AATAAAATATA
21517 AAAATTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
28 20 0.56
29 16 0.44
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.38
Consensus pattern (29 bp):
AATAAAATATATTTTTAAGTTCAAATAAG
Found at i:21545 original size:20 final size:20
Alignment explanation
Indices: 21506--21554 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
21496 TTCATATAAG
21506 AATAAAAT-ATAAAAATTTA
1 AATAAAATAATAAAAATTTA
21525 AATAAAATAATAATAAA-TTA
1 AATAAAATAATAA-AAATTTA
*
21545 AATTAAATAA
1 AATAAAATAA
21555 GTTAAGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 8 0.30
20 16 0.59
21 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAAAATAATAAAAATTTA
Found at i:21661 original size:2 final size:2
Alignment explanation
Indices: 21656--21681 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21646 ACTAAAATAC
21656 TA 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
21682 CCATATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44963 original size:2 final size:2
Alignment explanation
Indices: 44956--44984 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44946 ATTAAATGGA
44956 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44985 ACATTAAAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51628 original size:34 final size:34
Alignment explanation
Indices: 51587--51658 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
51577 TTATTTTCTT
*
51587 AAAATCATCTAAAAGAACTAACT-ACTTAATAATA
1 AAAATCATCGAAAAGAACT-ACTCACTTAATAATA
* *
51621 AAAATCATCGAAGAGAACTAGTCACTTAATAATA
1 AAAATCATCGAAAAGAACTACTCACTTAATAATA
51655 AAAA
1 AAAA
51659 ACTCAATACA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 2 0.06
34 32 0.94
ACGTcount: A:0.56, C:0.14, G:0.07, T:0.24
Consensus pattern (34 bp):
AAAATCATCGAAAAGAACTACTCACTTAATAATA
Done.