Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008867.1 Hibiscus syriacus cultivar Beakdansim tig00112101_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: 75041
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:8067 original size:79 final size:81
Alignment explanation
Indices: 7981--8184 Score: 279
Period size: 83 Copynumber: 2.5 Consensus size: 81
7971 GAGTTTCTTA
*
7981 AACAAACGCCGCGATAGAGTAGTACTTTACTGCGTTTTTATACAAA-TGCC-AAATAGGGATCGT
1 AACAAACGCCGCGATAGAGTAGTACTTTACTGCGTTTTTATACAAACT-CCTAAATAGGGATCAT
*
8044 TTATAGTGG-TTTTTCT
65 TTATAGTGGATTTTTCC
* * *
8060 AATAAACGCCGCGATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTCCTCAATAGGGATCAT
1 AACAAACGCCGCGATAGAGTAGTACTTTA-CTGCGTTTTTATACAAACTCCTAAATAGGGATCAT
*
8125 TTATATTGGCATTTTTCC
65 TTATAGTGG-ATTTTTCC
* * *
8143 AACAAATGTCGCGATAGAGTAGTACTTTAATGCGTTTTTATA
1 AACAAACGCCGCGATAGAGTAGTACTTTACTGCGTTTTTATA
8185 TAACACGTAA
Statistics
Matches: 109, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
79 28 0.26
80 18 0.17
81 20 0.18
82 11 0.10
83 32 0.29
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (81 bp):
AACAAACGCCGCGATAGAGTAGTACTTTACTGCGTTTTTATACAAACTCCTAAATAGGGATCATT
TATAGTGGATTTTTCC
Found at i:9938 original size:22 final size:22
Alignment explanation
Indices: 9913--9967 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
9903 TTTGTAAAGC
9913 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
9935 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
9957 CTTCTTGATCC
1 CTTCTTGATCC
9968 GTCTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (22 bp):
CTTCTTGATCCTTGAATGTTTA
Found at i:27168 original size:83 final size:83
Alignment explanation
Indices: 27069--27282 Score: 252
Period size: 83 Copynumber: 2.6 Consensus size: 83
27059 ATGTTTCTTA
*
27069 AACAAACGCCGCGATAGAGTAGTACTTTAACTGCGTTTTTATACAAA-TGCCAAAATAGGGATCG
1 AACAAACGCCGCGATAGAGTAGTACTTTAACTGCGTTTTTATACAAACT-CCAAAATAGGGATCA
* * *
27133 TTTATGGTGGTACTTTTCT
65 TTTATAGTGGCACTTTTCC
* * * * **
27152 AATAAACGCCGTGATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTCCTCAATAGGGATCAT
1 AACAAACGCCGCGATAGAGTAGTACTTTAACTGCGTTTTTATACAAACTCCAAAATAGGGATCAT
* *
27217 TTATATTGGCATTTTTCC
66 TTATAGTGGCACTTTTCC
* * * *
27235 AACAAATGTCGCGATAGAGTAGTACTTTAA-TGGTGTTTTTATATAAAC
1 AACAAACGCCGCGATAGAGTAGTACTTTAACT-GCGTTTTTATACAAAC
27283 ACCGTAATAG
Statistics
Matches: 109, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
83 108 0.99
84 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (83 bp):
AACAAACGCCGCGATAGAGTAGTACTTTAACTGCGTTTTTATACAAACTCCAAAATAGGGATCAT
TTATAGTGGCACTTTTCC
Found at i:27625 original size:38 final size:40
Alignment explanation
Indices: 27534--27639 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 40
27524 CTTGTCTTTT
*
27534 GTGGCGCTTTTAAACAAACGCCGCAATAAATCAGTGCAGTA
1 GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAG-A
* *
27575 GTGGCGTTTTTAAACAAACGCCGCAATAAGTTAGTG-A-A
1 GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGA
*
27613 GTGGTGTTTTTAAATACAAACGCCGCA
1 GTGGCGTTTTT-AA-ACAAACGCCGCA
27640 TGTTTTGGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
38 11 0.19
39 2 0.03
40 13 0.22
41 33 0.56
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (40 bp):
GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGA
Found at i:29090 original size:22 final size:22
Alignment explanation
Indices: 29065--29119 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
29055 TTTGTAAAGC
29065 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
29087 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
29109 CTTCTTGATCC
1 CTTCTTGATCC
29120 GTCTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (22 bp):
CTTCTTGATCCTTGAATGTTTA
Found at i:31896 original size:62 final size:62
Alignment explanation
Indices: 31799--31924 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
31789 ACCCGTTTTT
31799 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
31861 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
31923 AT
1 AT
31925 GATACGTAAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (62 bp):
ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
Found at i:46375 original size:83 final size:83
Alignment explanation
Indices: 46285--46498 Score: 252
Period size: 83 Copynumber: 2.6 Consensus size: 83
46275 GTGTTTCTTA
*
46285 AACAAACGCCGCGATAGAGTAGTACTTTAACTGCGTTTTTATACAAA-TGCCAAAATAGGGATCG
1 AACAAACGCCGCGATAGAGTAGTACTTTAACTGCGTTTTTATACAAACT-CCAAAATAGGGATCA
* * *
46349 TTTATGGTGGTACTTTTCT
65 TTTATAGTGGCACTTTTCC
* * * * **
46368 AATAAACGCCGTGATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTCCTCAATAGGGATCAT
1 AACAAACGCCGCGATAGAGTAGTACTTTAACTGCGTTTTTATACAAACTCCAAAATAGGGATCAT
* *
46433 TTATATTGGCATTTTTCC
66 TTATAGTGGCACTTTTCC
* * * *
46451 AACAAATGTCGCGATAGAGTAGTACTTTAA-TGGTGTTTTTATATAAAC
1 AACAAACGCCGCGATAGAGTAGTACTTTAACT-GCGTTTTTATACAAAC
46499 ACCGTAATAG
Statistics
Matches: 109, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
83 108 0.99
84 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (83 bp):
AACAAACGCCGCGATAGAGTAGTACTTTAACTGCGTTTTTATACAAACTCCAAAATAGGGATCAT
TTATAGTGGCACTTTTCC
Found at i:46841 original size:38 final size:40
Alignment explanation
Indices: 46750--46855 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 40
46740 CTTGTCTTTT
*
46750 GTGGCGCTTTTAAACAAACGCCGCAATAAATCAGTGCAGTA
1 GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAG-A
* *
46791 GTGGCGTTTTTAAACAAACGCCGCAATAAGTTAGTG-A-A
1 GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGA
*
46829 GTGGTGTTTTTAAATACAAACGCCGCA
1 GTGGCGTTTTT-AA-ACAAACGCCGCA
46856 TGTTTTGGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
38 11 0.19
39 2 0.03
40 13 0.22
41 33 0.56
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (40 bp):
GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGA
Found at i:48303 original size:22 final size:22
Alignment explanation
Indices: 48278--48332 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
48268 TTTGTAAAGC
48278 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
48300 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
48322 CTTCTTGATCC
1 CTTCTTGATCC
48333 GTCTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (22 bp):
CTTCTTGATCCTTGAATGTTTA
Found at i:51104 original size:62 final size:62
Alignment explanation
Indices: 51007--51132 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
50997 ACCCGTTTTT
51007 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
51069 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
51131 AT
1 AT
51133 GATACGTAAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (62 bp):
ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
Found at i:65553 original size:14 final size:15
Alignment explanation
Indices: 65483--65567 Score: 64
Period size: 15 Copynumber: 5.5 Consensus size: 15
65473 GGCAGTAATG
*
65483 TTTATTTATTTATTTA
1 TTTATTTGTTT-TTTA
*
65499 TTTATTTGAATTTATGTA
1 TTTATTTG--TTT-TTTA
* * * *
65517 TTCATTTATTTCTAA
1 TTTATTTGTTTTTTA
65532 TTTATTTG-TTTTTA
1 TTTATTTGTTTTTTA
*
65546 TTTGTTTGTTTTTTA
1 TTTATTTGTTTTTTA
65561 TTTATTT
1 TTTATTT
65568 ATTTATTCCA
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
14 11 0.21
15 19 0.36
16 10 0.19
18 13 0.25
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.72
Consensus pattern (15 bp):
TTTATTTGTTTTTTA
Found at i:65594 original size:4 final size:4
Alignment explanation
Indices: 65483--65574 Score: 75
Period size: 4 Copynumber: 23.5 Consensus size: 4
65473 GGCAGTAATG
* * * *
65483 TTTA TTTA TTTA TTTA TTTA TTTGAA TTTA TGTA TTCA TTTA TTT- CTAA
1 TTTA TTTA TTTA TTTA TTTA TTT--A TTTA TTTA TTTA TTTA TTTA TTTA
* * *
65532 TTTA TTT- GTT- TTTA TTTG TTTG TTT- TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
65575 CCACTCAAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
3 8 0.11
4 60 0.83
6 4 0.06
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:71739 original size:82 final size:82
Alignment explanation
Indices: 71517--71741 Score: 249
Period size: 83 Copynumber: 2.7 Consensus size: 82
71507 GTGTTTCTTA
* ** * *
71517 AACAAACGCCGCGATAGAGTAGTACTTTAGCT-GCGTTTTTATACAAATGCCAAAATAGGGATCG
1 AACAAACGCCGCGATAGAGTAGTACTTTA-ATGGCGTTTTTATACAAACACC-TAATAGGGATCA
* * *
71581 TTTATGGTGGTATTTTTCT
64 TTTATAGTGGCATTTTTCC
* * *
71600 AATAAACGCCGTGATAGAGTAGTACTTT-ATCGGCGTTTTTATACAAACTCCTCAATAGGGATCA
1 AACAAACGCCGCGATAGAGTAGTACTTTAAT-GGCGTTTTTATACAAACACCT-AATAGGGATCA
*
71664 TTTATATTGGCA-TTTTCC
64 TTTATAGTGGCATTTTTCC
* * *
71682 AACAAATGTCGCGATAGAGTAGTACTTTAATGGCGTTTTTATATAAACACCGTAATAGGG
1 AACAAACGCCGCGATAGAGTAGTACTTTAATGGCGTTTTTATACAAACACC-TAATAGGG
71742 TTCTTTAGCA
Statistics
Matches: 120, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
81 1 0.01
82 54 0.45
83 65 0.54
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (82 bp):
AACAAACGCCGCGATAGAGTAGTACTTTAATGGCGTTTTTATACAAACACCTAATAGGGATCATT
TATAGTGGCATTTTTCC
Found at i:72078 original size:40 final size:40
Alignment explanation
Indices: 71982--72086 Score: 126
Period size: 40 Copynumber: 2.6 Consensus size: 40
71972 ACTTGTCTTT
*
71982 GTGGCGCTTTTAAACAAACGCCGCAATAAATCAGTGCAGTA
1 GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAG-A
* *
72023 GTGGCGTTTTT-AACAAACGCCGCAATAAGTTAGTG-A-A
1 GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGA
*
72060 GTGGTGTTTTTAAAAACAAACGCCGCA
1 GTGGCGTTTTT--AAACAAACGCCGCA
72087 TGTTTTGGAT
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
37 11 0.19
39 1 0.02
40 35 0.61
41 10 0.18
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (40 bp):
GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGA
Found at i:73510 original size:22 final size:22
Alignment explanation
Indices: 73485--73539 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
73475 TTTGTAAAGC
73485 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
73507 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
73529 CTTCTTGATCC
1 CTTCTTGATCC
73540 GTCTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (22 bp):
CTTCTTGATCCTTGAATGTTTA
Done.