Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002004.1 Hibiscus syriacus cultivar Beakdansim tig00004099_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: 56212
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6616 original size:20 final size:20
Alignment explanation
Indices: 6591--6649 Score: 55
Period size: 23 Copynumber: 2.8 Consensus size: 20
6581 ATGACGGTAA
*
6591 ATTTTTGTTTTATTATTGTT
1 ATTTTTGTTTTACTATTGTT
*
6611 ATTTTTAAGGTATTACTATTGTT
1 ATTTTT---GTTTTACTATTGTT
* *
6634 ATTTCTGTTTTTCTAT
1 ATTTTTGTTTTACTAT
6650 ACATTTCATG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 14 0.45
23 17 0.55
ACGTcount: A:0.19, C:0.05, G:0.10, T:0.66
Consensus pattern (20 bp):
ATTTTTGTTTTACTATTGTT
Found at i:19361 original size:24 final size:24
Alignment explanation
Indices: 19325--19387 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
19315 TGATACCTCT
* *
19325 AAATTTGTATATTTTTATATTATTA
1 AAATTTGTATATTTATATACT-TTA
*
19350 AAATTT-TGTATTTATATACTTTA
1 AAATTTGTATATTTATATACTTTA
*
19373 AAATTTCTA-ATTTAT
1 AAATTTGTATATTTAT
19388 TCGTCTACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 15 0.45
24 12 0.36
25 6 0.18
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (24 bp):
AAATTTGTATATTTATATACTTTA
Found at i:20655 original size:77 final size:77
Alignment explanation
Indices: 20528--20679 Score: 243
Period size: 77 Copynumber: 2.0 Consensus size: 77
20518 AACGTTTTGA
* * * *
20528 ACTAAAATGCCTTTAATTTTTTTTTCTAAAAATATCCTTATTTTGTCATTGAACAATAAAAATTT
1 ACTAAAATCCCTTAAATTTTTTTTTCTAAAAATATACTTATTTTGTCATTGAACAATAAAAATTA
20593 TATGAATGTTGG
66 TATGAATGTTGG
*
20605 ACTAAAATACCCTTAAATTTTTTTTTC-AAAAATATACTTATTTTGTCATTGAATAATAAAAATT
1 ACTAAAAT-CCCTTAAATTTTTTTTTCTAAAAATATACTTATTTTGTCATTGAACAATAAAAATT
20669 ATATGAATGTT
65 ATATGAATGTT
20680 AAATTATAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
77 53 0.77
78 16 0.23
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (77 bp):
ACTAAAATCCCTTAAATTTTTTTTTCTAAAAATATACTTATTTTGTCATTGAACAATAAAAATTA
TATGAATGTTGG
Found at i:38012 original size:21 final size:20
Alignment explanation
Indices: 37986--38258 Score: 191
Period size: 21 Copynumber: 13.2 Consensus size: 20
37976 GTTTCCAGAT
37986 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAA-TTGGACTA
* *
38007 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAAT-TGGACTA
*
38027 TCGCAATGCGATAGTCGG-CTA
1 TCGCAATGCGA-A-TTGGACTA
* *
38048 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAAT-TGGACTA
* *
38068 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGA-ATTGGACTA
*
38089 TCGCAATGTGAACTTGGACTA
1 TCGCAATGCGAA-TTGGACTA
*
38110 TCGCAATGTGAACTTGGACTA
1 TCGCAATGCGAA-TTGGACTA
*
38131 TCGCAATGCGATAGTCGG-CTA
1 TCGCAATGCGA-A-TTGGACTA
*
38152 TCGCAATGCGATAGTCGG-CTA
1 TCGCAATGCGA-A-TTGGACTA
*
38173 TCGCAATGCGATAGTCGG-CTA
1 TCGCAATGCGA-A-TTGGACTA
* * *
38194 TCGCAATACGAATATGTA-AA
1 TCGCAATGCGAAT-TGGACTA
* *
38214 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGA-ATTGGACTA
38235 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAA-TTGGACTA
38256 TCG
1 TCG
38259 TATTGCGATT
Statistics
Matches: 208, Mismatches: 29, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.01
20 46 0.22
21 155 0.75
22 5 0.02
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGAATTGGACTA
Found at i:38031 original size:20 final size:20
Alignment explanation
Indices: 38006--38078 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
37996 AACTTGGACT
38006 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
***
38026 ATCGCAATGCG-ATAGTCGGCT
1 ATCGCAATGCGAATA-T-GTAA
38047 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
38067 ATCGCAATGCGA
1 ATCGCAATGCGA
38079 TAGTCGACTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 25 0.57
21 13 0.30
22 3 0.07
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:38031 original size:41 final size:42
Alignment explanation
Indices: 37986--38183 Score: 194
Period size: 41 Copynumber: 4.8 Consensus size: 42
37976 GTTTCCAGAT
37986 TCGCAATGCGA-ACTTGGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGATACTTGGACTATCGCAATGCGAATATGTAAA
* *
38027 TCGCAATGCGATAGTCGG-CTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGATACTTGGACTATCGCAATGCGAATATGTAAA
* * * * *
38068 TCGCAATGCGATA-GTCGACTATCGCAATGTGAACT-TGGACTA
1 TCGCAATGCGATACTTGGACTATCGCAATGCGAA-TATGTA-AA
* ***
38110 TCGCAATGTGA-ACTTGGACTATCGCAATGCG-ATAGTCGGCTA
1 TCGCAATGCGATACTTGGACTATCGCAATGCGAATA-T-GTAAA
* *
38152 TCGCAATGCGATAGTCGG-CTATCGCAATGCGA
1 TCGCAATGCGATACTTGGACTATCGCAATGCGA
38184 TAGTCGGCTA
Statistics
Matches: 131, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
40 2 0.02
41 66 0.50
42 57 0.44
43 6 0.05
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (42 bp):
TCGCAATGCGATACTTGGACTATCGCAATGCGAATATGTAAA
Found at i:39032 original size:21 final size:22
Alignment explanation
Indices: 39007--39130 Score: 127
Period size: 21 Copynumber: 5.8 Consensus size: 22
38997 ATTTTGGACT
39007 ATCGCAA-CGAACTTGGAATAA
1 ATCGCAACCGAACTTGGAATAA
* *
39028 ATCGCAACGCGAACTTCG-AT-T
1 ATCGCAAC-CGAACTTGGAATAA
*
39049 ATCGCAA-CGAATTTGGAATAA
1 ATCGCAACCGAACTTGGAATAA
* *
39070 ATCGCAACGCGAACTTCGACT--
1 ATCGCAAC-CGAACTTGGAATAA
39091 ATCGCAA-CGAACTTGGAATAA
1 ATCGCAACCGAACTTGGAATAA
39112 ATCGCAACGCGAACTTGGA
1 ATCGCAAC-CGAACTTGGA
39131 CTATCGCAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
19 17 0.20
20 2 0.02
21 35 0.42
22 2 0.02
23 27 0.33
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (22 bp):
ATCGCAACCGAACTTGGAATAA
Found at i:39065 original size:42 final size:42
Alignment explanation
Indices: 39003--39139 Score: 247
Period size: 42 Copynumber: 3.3 Consensus size: 42
38993 TGCGATTTTG
39003 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
39045 GATTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
39087 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
39129 GACTATCGCAA
1 GACTATCGCAA
39140 TGCAAATATG
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:39136 original size:21 final size:19
Alignment explanation
Indices: 39000--39139 Score: 109
Period size: 21 Copynumber: 6.7 Consensus size: 19
38990 CGTTGCGATT
*
39000 TTGGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
39019 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* * *
39042 TTCGATTATCGCAACGAAT
1 TTGGAATATCGCAACGAAC
39061 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* *
39084 TTCGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
39103 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
*
39126 TTGGACTATCGCAA
1 TTGGAATATCGCAA
39140 TGCAAATATG
Statistics
Matches: 97, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
19 25 0.26
21 42 0.43
23 30 0.31
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (19 bp):
TTGGAATATCGCAACGAAC
Found at i:41351 original size:27 final size:27
Alignment explanation
Indices: 41320--41392 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
41310 GGTTTTTTGA
*
41320 CCGGATTAAAAACTGGTTTGAAAAAAG
1 CCGGATAAAAAACTGGTTTGAAAAAAG
*
41347 CCGGATAAAAAACTGGTTTGAAAAAAT
1 CCGGATAAAAAACTGGTTTGAAAAAAG
*
41374 CCGGATAAAAAACCGGTTT
1 CCGGATAAAAAACTGGTTT
41393 TTTATTCGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.22
Consensus pattern (27 bp):
CCGGATAAAAAACTGGTTTGAAAAAAG
Found at i:41370 original size:14 final size:14
Alignment explanation
Indices: 41327--41372 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
41317 TGACCGGATT
41327 AAAAACTGGTTTGA
1 AAAAACTGGTTTGA
* *
41341 AAAAAGCCGG-AT-A
1 AAAAA-CTGGTTTGA
41354 AAAAACTGGTTTGA
1 AAAAACTGGTTTGA
41368 AAAAA
1 AAAAA
41373 TCCGGATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
12 3 0.12
13 7 0.28
14 12 0.48
15 3 0.12
ACGTcount: A:0.52, C:0.09, G:0.20, T:0.20
Consensus pattern (14 bp):
AAAAACTGGTTTGA
Found at i:45021 original size:9 final size:9
Alignment explanation
Indices: 45004--45034 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
44994 AAATAAACAA
45004 TATTTTTAT
1 TATTTTTAT
*
45013 TATTATTAT
1 TATTTTTAT
45022 TATTTTTAT
1 TATTTTTAT
45031 TATT
1 TATT
45035 CATTGTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TATTTTTAT
Found at i:47810 original size:20 final size:20
Alignment explanation
Indices: 47772--47811 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
47762 TCTTAAAAAC
*
47772 TATATAAATTTTTTTAATTT
1 TATATAAATTTTTTAAATTT
47792 TATATACAA-TTTTTAAATTT
1 TATATA-AATTTTTTAAATTT
47812 ATCGGATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATAAATTTTTTAAATTT
Done.