Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005022.1 Hibiscus syriacus cultivar Beakdansim tig00011272_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: 66024
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2910 original size:16 final size:16
Alignment explanation
Indices: 2885--2931 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
2875 GGCATGCCTG
2885 GAAG-TGATTTAAGTT
1 GAAGTTGATTTAAGTT
2900 GAAGTTGATTTAAGTT
1 GAAGTTGATTTAAGTT
* * *
2916 AAAGTTAACTTAAGTT
1 GAAGTTGATTTAAGTT
2932 ATGATACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 4 0.14
16 24 0.86
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.40
Consensus pattern (16 bp):
GAAGTTGATTTAAGTT
Found at i:37738 original size:28 final size:28
Alignment explanation
Indices: 37688--37752 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
37678 CACTCTACTA
* *
37688 TCCAAGAACGAGTGAAGATAGTTTGATG
1 TCCAAGAATGAGTGAAGACAGTTTGATG
** * *
37716 TCCAAGAATGAGTGGGGACAGTTTGTTT
1 TCCAAGAATGAGTGAAGACAGTTTGATG
37744 TCCAAGAAT
1 TCCAAGAAT
37753 AAGTACTCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (28 bp):
TCCAAGAATGAGTGAAGACAGTTTGATG
Found at i:37929 original size:48 final size:47
Alignment explanation
Indices: 37885--38000 Score: 160
Period size: 47 Copynumber: 2.5 Consensus size: 47
37875 GTAATTTTTT
* *
37885 TCTTAATGGGACCTTTGGATATGAACTTCGATTGATTTTCAATTTGA
1 TCTTAATGGGACCTTTGGATATGAACTTAGATTGATTATCAATTTGA
* * ** *
37932 TCTTAATTGGACTTTTGGATATGAAGGTAGATTGATTAGCAATTTGA
1 TCTTAATGGGACCTTTGGATATGAACTTAGATTGATTATCAATTTGA
*
37979 TCTTAATGTGACCTTTGGATAT
1 TCTTAATGGGACCTTTGGATAT
38001 AAAAGAGTAC
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (47 bp):
TCTTAATGGGACCTTTGGATATGAACTTAGATTGATTATCAATTTGA
Found at i:39125 original size:21 final size:20
Alignment explanation
Indices: 39092--39160 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
39082 CATAAAAATA
*
39092 ATCGATCCATTTGAAAAAGG
1 ATCGATCCTTTTGAAAAAGG
*
39112 ATCGATCCCTTTTGTAAAAGG
1 ATCGAT-CCTTTTGAAAAAGG
*
39133 ATTC-ATCCTTTTGAAAAGGG
1 A-TCGATCCTTTTGAAAAAGG
*
39153 ATCCATCC
1 ATCGATCC
39161 CTTCATTGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
19 2 0.05
20 23 0.55
21 15 0.36
22 2 0.05
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (20 bp):
ATCGATCCTTTTGAAAAAGG
Found at i:45804 original size:16 final size:16
Alignment explanation
Indices: 45783--45823 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
45773 ATATATAGAT
45783 TTTAGGTTCGGATTGC
1 TTTAGGTTCGGATTGC
45799 TTTAGGTTCGGATTGC
1 TTTAGGTTCGGATTGC
*
45815 TTTCGGTTC
1 TTTAGGTTC
45824 AGATAAACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.10, C:0.15, G:0.29, T:0.46
Consensus pattern (16 bp):
TTTAGGTTCGGATTGC
Found at i:45909 original size:33 final size:33
Alignment explanation
Indices: 45867--45931 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
45857 TTAAATTTGG
* *
45867 TTTGGGTTGCTATTGGTTCGATTTATTTTTCGA
1 TTTGGGTTGCTATCGGTTCGAGTTATTTTTCGA
45900 TTTGGGTTGCTATCGGTTCGAGTTATTTTTCG
1 TTTGGGTTGCTATCGGTTCGAGTTATTTTTCG
45932 GTTCGAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.11, C:0.11, G:0.26, T:0.52
Consensus pattern (33 bp):
TTTGGGTTGCTATCGGTTCGAGTTATTTTTCGA
Found at i:45948 original size:16 final size:17
Alignment explanation
Indices: 45912--45952 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
45902 TGGGTTGCTA
* *
45912 TCGGTTCGAGTTATTTT
1 TCGGTTCGAATTATCTT
45929 TCGGTTCGAATTA-CTT
1 TCGGTTCGAATTATCTT
45945 TCGGTTCG
1 TCGGTTCG
45953 GGTTGCTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.12, C:0.17, G:0.24, T:0.46
Consensus pattern (17 bp):
TCGGTTCGAATTATCTT
Found at i:45961 original size:16 final size:16
Alignment explanation
Indices: 45903--45987 Score: 62
Period size: 16 Copynumber: 5.2 Consensus size: 16
45893 TTTTCGATTT
*
45903 GGGTTGCTATCGGTTC
1 GGGTTGCTTTCGGTTC
* **
45919 GAGTTATTTTTCGGTTC
1 GGGTT-GCTTTCGGTTC
** *
45936 GAATTACTTTCGGTTC
1 GGGTTGCTTTCGGTTC
* *
45952 GGGTTGCTTTCAGTTT
1 GGGTTGCTTTCGGTTC
* *
45968 AGGTTGCTTTCGGTTT
1 GGGTTGCTTTCGGTTC
45984 GGGT
1 GGGT
45988 CAAACTTGAT
Statistics
Matches: 53, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
16 41 0.77
17 12 0.23
ACGTcount: A:0.09, C:0.14, G:0.31, T:0.46
Consensus pattern (16 bp):
GGGTTGCTTTCGGTTC
Found at i:48982 original size:96 final size:91
Alignment explanation
Indices: 48818--49001 Score: 314
Period size: 96 Copynumber: 2.0 Consensus size: 91
48808 GTTTCTTAAC
*
48818 TATTAAAATTACAAAATGATTTTCCGATATATTACTATTTTTTGAGTCCTTTAGCTATTAAAAGT
1 TATTAAAATTACAAAATGATTCTCCGATATATTACTATTTTTTGAGTCCTTTAGCTATTAAAAGT
48883 TACAAAATGGTCAATAGGCTACAGTT
66 TACAAAATGGTCAATAGGCTACAGTT
48909 TATTAAAAATTACAAAATGATTCTCCGACTATATATTACTATTTTTTTGAGTCCTTTAGCTATTA
1 TATT-AAAATTACAAAATGATTCTCCG---ATATATTACTA-TTTTTTGAGTCCTTTAGCTATTA
48974 AAAGTTACAAAATGGTCAATAGGCTACA
61 AAAGTTACAAAATGGTCAATAGGCTACA
49002 AATATATTCT
Statistics
Matches: 87, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
91 4 0.05
92 21 0.24
95 11 0.13
96 51 0.59
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (91 bp):
TATTAAAATTACAAAATGATTCTCCGATATATTACTATTTTTTGAGTCCTTTAGCTATTAAAAGT
TACAAAATGGTCAATAGGCTACAGTT
Found at i:50631 original size:22 final size:23
Alignment explanation
Indices: 50598--50644 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
50588 GATTTGTAAA
50598 TATTATGAATTT-TCAATAT-ATT
1 TATTATGAATTTGT-AATATAATT
50620 TATTGATG-ATTTGTAATATAATT
1 TATT-ATGAATTTGTAATATAATT
50643 TA
1 TA
50645 ATATAAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (23 bp):
TATTATGAATTTGTAATATAATT
Found at i:51557 original size:3 final size:3
Alignment explanation
Indices: 51549--51573 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
51539 TTTTGAAATT
51549 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
51574 CTGGAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:56376 original size:2 final size:2
Alignment explanation
Indices: 56369--56393 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56359 ATTTAAAATT
56369 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 T
56394 TAAAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58479 original size:21 final size:20
Alignment explanation
Indices: 58432--58489 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 20
58422 ATTTAAAAAT
* * *
58432 AATTAAAAATTCAAACATTA
1 AATTAAGAATTAAAAAATTA
*
58452 AAATAAGAATTAAAAAATTTA
1 AATTAAGAATTAAAAAA-TTA
58473 AATTAAGAATTAAAAAA
1 AATTAAGAATTAAAAAA
58490 ACATATTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
AATTAAGAATTAAAAAATTA
Found at i:60067 original size:40 final size:40
Alignment explanation
Indices: 60012--60092 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
60002 GAGAAAGAGT
*
60012 ACACCATATTTTAATATACATGACATTATGCCTTATTATA
1 ACACCATATTTTAATATACATGACATGATGCCTTATTATA
60052 ACACCATATTTTAATATACATGACATGATGCCTTATTATA
1 ACACCATATTTTAATATACATGACATGATGCCTTATTATA
60092 A
1 A
60093 AACTTTTCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (40 bp):
ACACCATATTTTAATATACATGACATGATGCCTTATTATA
Found at i:62906 original size:21 final size:21
Alignment explanation
Indices: 62880--62935 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
62870 ATAAGAACAA
62880 TATCGATACTGATGCAATTAG
1 TATCGATACTGATGCAATTAG
* *
62901 TATCGATATTGATACAATTAG
1 TATCGATACTGATGCAATTAG
62922 TATCGATACTGATG
1 TATCGATACTGATG
62936 TGGGTATCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (21 bp):
TATCGATACTGATGCAATTAG
Found at i:63610 original size:47 final size:48
Alignment explanation
Indices: 63557--63649 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
63547 AGAGGTGCAC
*
63557 TTCGGCATAAAA-GTGCCACAAATGAAAGTTAAATGCATAACGGTGTA
1 TTCGGCATAAAAGGTGCCACAAATGAAAGTGAAATGCATAACGGTGTA
* *
63604 TTCGGCATAAAAGGTGCCACTAATGAAGGTGAAATGCATAACGGTG
1 TTCGGCATAAAAGGTGCCACAAATGAAAGTGAAATGCATAACGGTG
63650 CATTTTCGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 12 0.29
48 30 0.71
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (48 bp):
TTCGGCATAAAAGGTGCCACAAATGAAAGTGAAATGCATAACGGTGTA
Done.