Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006282.1 Hibiscus syriacus cultivar Beakdansim tig00014995_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: 45033
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1512 original size:20 final size:19
Alignment explanation
Indices: 1487--1525 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
1477 GAGTTTGTTT
1487 TCATTTTCA-ATTTTGAAACA
1 TCATTTT-ATATTTT-AAACA
1507 TCATTTTATATTTTAAACA
1 TCATTTTATATTTTAAACA
1526 ATTTCTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.49
Consensus pattern (19 bp):
TCATTTTATATTTTAAACA
Found at i:5286 original size:21 final size:21
Alignment explanation
Indices: 5262--5312 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
5252 ACTATATATT
5262 GATACCCTTTCAATATGTATA
1 GATACCCTTTCAATATGTATA
* * *
5283 GATACCTCTTTGAATGTGTATC
1 GATACC-CTTTCAATATGTATA
5305 GATACCCT
1 GATACCCT
5313 CTTTGAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (21 bp):
GATACCCTTTCAATATGTATA
Found at i:5302 original size:22 final size:22
Alignment explanation
Indices: 5262--5333 Score: 101
Period size: 23 Copynumber: 3.3 Consensus size: 22
5252 ACTATATATT
* * *
5262 GATACC-CTTTCAATATGTATA
1 GATACCTCTTTGAATGTGTATC
5283 GATACCTCTTTGAATGTGTATC
1 GATACCTCTTTGAATGTGTATC
5305 GATACCCTCTTTGAATGTGTATC
1 GATA-CCTCTTTGAATGTGTATC
5328 GATACC
1 GATACC
5334 CCTATAAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.13
22 18 0.39
23 22 0.48
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (22 bp):
GATACCTCTTTGAATGTGTATC
Found at i:5786 original size:18 final size:19
Alignment explanation
Indices: 5759--5797 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
5749 ATATTTATGA
5759 TTTTTTTAA-T-TGTTGTT
1 TTTTTTTAATTATGTTGTT
5776 TTTTATTTAATTATGTTGTT
1 TTTT-TTTAATTATGTTGTT
5796 TT
1 TT
5798 CATGAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 5 0.26
19 1 0.05
20 9 0.47
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.74
Consensus pattern (19 bp):
TTTTTTTAATTATGTTGTT
Found at i:7968 original size:54 final size:54
Alignment explanation
Indices: 7886--8006 Score: 188
Period size: 54 Copynumber: 2.2 Consensus size: 54
7876 CTCATAGGGT
7886 GTACCGATACCCCTATGCCAATTTTGGCTCCAAGAAAAACAAAATGCCAAATGG
1 GTACCGATACCCCTATGCCAATTTTGGCTCCAAGAAAAACAAAATGCCAAATGG
* * * * * *
7940 GTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAATAGAATGTCGATTGG
1 GTACCGATACCCCTATGCCAATTTTGGCTCCAAGAAAAACAAAATGCCAAATGG
7994 GTACCGATACCCC
1 GTACCGATACCCC
8007 CTTAGAGGTA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (54 bp):
GTACCGATACCCCTATGCCAATTTTGGCTCCAAGAAAAACAAAATGCCAAATGG
Found at i:14825 original size:64 final size:65
Alignment explanation
Indices: 14757--14895 Score: 181
Period size: 64 Copynumber: 2.2 Consensus size: 65
14747 GAACACTTGA
* * *
14757 TGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGAG
1 TGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAG
***** **
14821 TGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAG
1 TGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAG
14886 TGCATCGATG
1 TGCATCGATG
14896 TATGGATAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
64 40 0.62
65 24 0.38
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (65 bp):
TGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAG
Found at i:14909 original size:65 final size:65
Alignment explanation
Indices: 14776--14935 Score: 223
Period size: 65 Copynumber: 2.5 Consensus size: 65
14766 GCACCAAGTG
* * **
14776 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGAGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGATAA
* ** *
14840 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGTATGGATAA
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGATAA
* *
14905 TGCATCGGTGCATGGAATGCATTCGATGTTT
1 TGCATCGATGCATGAAATGCATTCGATGTTT
14936 CAATTAATTC
Statistics
Matches: 84, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
64 27 0.32
65 57 0.68
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (65 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGATAA
Found at i:14910 original size:19 final size:17
Alignment explanation
Indices: 14886--14933 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
14876 ATATTCAGAG
14886 TGCATCGATGTATGGATAA
1 TGCATCGATGTATGG--AA
* *
14905 TGCATCGGTGCATGGAA
1 TGCATCGATGTATGGAA
14922 TGCATTCGATGT
1 TGCA-TCGATGT
14934 TTCAATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 6 0.25
18 5 0.21
19 13 0.54
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (17 bp):
TGCATCGATGTATGGAA
Found at i:14955 original size:65 final size:63
Alignment explanation
Indices: 14776--14982 Score: 211
Period size: 65 Copynumber: 3.2 Consensus size: 63
14766 GCACCAAGTG
* * **
14776 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGC-CTGAGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAT-TCACT-AGTGCATCGATGCATGGATAA
* * *
14840 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGTATGGATA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTG-AAA-ATTCACTAGTGCATCGATGCATGGATA
14904 A
63 A
* * * * * *
14905 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATTCACTAGTGCATCGATGCATGGATAA
*
14970 TGCATCGGTGCAT
1 TGCATCGATGCAT
14983 CACCTCAAAT
Statistics
Matches: 120, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
63 2 0.02
64 35 0.29
65 77 0.64
66 4 0.03
67 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (63 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCACTAGTGCATCGATGCATGGATAA
Found at i:23376 original size:18 final size:17
Alignment explanation
Indices: 23349--23383 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
23339 GCACCAAGTG
23349 TGCATCGATGTATGAAA
1 TGCATCGATGTATGAAA
*
23366 TGCATTCGATGTTTGAAA
1 TGCA-TCGATGTATGAAA
23384 ATAGCCTGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (17 bp):
TGCATCGATGTATGAAA
Found at i:23398 original size:64 final size:65
Alignment explanation
Indices: 23330--23468 Score: 172
Period size: 64 Copynumber: 2.2 Consensus size: 65
23320 GAACACTTGA
* * * *
23330 TGCATCGGTGCACCAAGTGTGCATCGATGTATGAAATGCATTCGATG-TTTGAAAATAGCCTGAG
1 TGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAG
***** **
23394 TGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAG
1 TGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAG
23459 TGCATCGATG
1 TGCATCGATG
23469 TATGGAGAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
64 39 0.62
65 24 0.38
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (65 bp):
TGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAG
Found at i:23482 original size:65 final size:65
Alignment explanation
Indices: 23349--23508 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 65
23339 GCACCAAGTG
* * ****
23349 TGCATCGATGTATGAAATGCATTCGATG-TTTGAAAATAGCCTGAGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
* ** *
23413 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGTATGGAGAA
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
* *
23478 TGCATCGGTGCATGGAATGCATTCGATGTTT
1 TGCATCGATGCATGAAATGCATTCGATGTTT
23509 CAATTAATTC
Statistics
Matches: 82, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
64 26 0.32
65 56 0.68
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (65 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
Found at i:23483 original size:19 final size:17
Alignment explanation
Indices: 23459--23506 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
23449 ATATTCAGAG
23459 TGCATCGATGTATGGAGAA
1 TGCATCGATGTAT-G-GAA
* *
23478 TGCATCGGTGCATGGAA
1 TGCATCGATGTATGGAA
23495 TGCATTCGATGT
1 TGCA-TCGATGT
23507 TTCAATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 7 0.29
18 6 0.25
19 11 0.46
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.29
Consensus pattern (17 bp):
TGCATCGATGTATGGAA
Found at i:32560 original size:29 final size:29
Alignment explanation
Indices: 32518--32575 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
32508 AAGCTACAAC
32518 CCTATTGTCAATCATCCCTCGCAATTCGT
1 CCTATTGTCAATCATCCCTCGCAATTCGT
32547 CCTATTGTCAATCATCCCTCGCAATTCGT
1 CCTATTGTCAATCATCCCTCGCAATTCGT
32576 AATTTGAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.34, G:0.10, T:0.34
Consensus pattern (29 bp):
CCTATTGTCAATCATCCCTCGCAATTCGT
Found at i:34117 original size:17 final size:15
Alignment explanation
Indices: 34076--34116 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
34066 TAAGAATTTT
34076 TATTTAAAAAATATA
1 TATTTAAAAAATATA
34091 TATTTAAAAAATATA
1 TATTTAAAAAATATA
34106 TATTTAAAAAA
1 TATTTAAAAAA
34117 ACCTTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATTTAAAAAATATA
Found at i:34163 original size:28 final size:27
Alignment explanation
Indices: 34107--34167 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
34097 AAAAATATAT
* * **
34107 ATTTAAAAAAACCTTAAATTTTTTCAA
1 ATTTAAAAAAACCTAAAACTTTTAAAA
34134 ATCTTAAAAAAACCTAAAACTTTTAAAA
1 AT-TTAAAAAAACCTAAAACTTTTAAAA
34162 ATTTAA
1 ATTTAA
34168 TTTTAATCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 6 0.21
28 23 0.79
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (27 bp):
ATTTAAAAAAACCTAAAACTTTTAAAA
Found at i:41839 original size:20 final size:21
Alignment explanation
Indices: 41816--41895 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
41806 TTGGTGCAGA
*
41816 GGGAATCGATTCCCCCCTGA-
1 GGGAACCGATTCCCCCCTGAG
*
41836 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-CTG-AG
**
41859 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCTGAG
* *
41880 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
41896 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
20 15 0.30
21 18 0.36
22 1 0.02
23 16 0.32
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCTGAG
Found at i:41866 original size:23 final size:20
Alignment explanation
Indices: 41814--41875 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
41804 TTTTGGTGCA
*
41814 GAGGGAATCGATTCCCCCCT
1 GAGGGAACCGATTCCCCCCT
*
41834 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-CT
41855 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
41876 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 17 0.47
21 2 0.06
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCCT
Found at i:41883 original size:21 final size:20
Alignment explanation
Indices: 41816--41895 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 20
41806 TTGGTGCAGA
* *
41816 GGGAATCGATTCCCCCC-TG
1 GGGAACCGATTCCCCCCAAG
*
41835 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAACCGATTCCCCC---CAAG
41859 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCA-AG
* *
41880 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
41896 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 16 0.33
21 16 0.33
23 16 0.33
24 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCAAG
Done.