Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006007.1 Hibiscus syriacus cultivar Beakdansim tig00014165_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: 75876
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:8447 original size:22 final size:21
Alignment explanation
Indices: 8421--8520 Score: 109
Period size: 19 Copynumber: 4.8 Consensus size: 21
8411 ATAGGGCATA
8421 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTT-AAG
*
8443 GGGAATCGAT-CCCCCTTAAA
1 GGGAATCGATACCCCCTTAAG
*
8463 GGG-ATCTGATTCCCCCTTTGAAG
1 GGGAATC-GATACCCCC-TT-AAG
*
8486 GGGAATCGATTCCCCC-T-AG
1 GGGAATCGATACCCCCTTAAG
8505 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
8521 CTGGGGTTCT
Statistics
Matches: 70, Mismatches: 3, Indels: 13
0.81 0.03 0.15
Matches are distributed among these distances:
19 20 0.29
20 8 0.11
21 13 0.19
22 12 0.17
23 14 0.20
24 3 0.04
ACGTcount: A:0.24, C:0.30, G:0.25, T:0.21
Consensus pattern (21 bp):
GGGAATCGATACCCCCTTAAG
Found at i:8522 original size:43 final size:43
Alignment explanation
Indices: 8420--8520 Score: 138
Period size: 42 Copynumber: 2.4 Consensus size: 43
8410 TATAGGGCAT
8420 AGGGAATCGATACCCCC-TTGAAGGGGAATCGATCCCCCTTAA
1 AGGGAATCGATACCCCCTTTGAAGGGGAATCGATCCCCCTTAA
*
8462 AGGG-ATCTGATTCCCCCTTTGAAGGGGAATCGATTCCCCC-T-A
1 AGGGAATC-GATACCCCCTTTGAAGGGGAATCGA-TCCCCCTTAA
*
8504 GGGGAATCGATACCCCC
1 AGGGAATCGATACCCCC
8521 CTGGGGTTCT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
41 3 0.06
42 24 0.46
43 19 0.37
44 6 0.12
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.21
Consensus pattern (43 bp):
AGGGAATCGATACCCCCTTTGAAGGGGAATCGATCCCCCTTAA
Found at i:18817 original size:30 final size:30
Alignment explanation
Indices: 18783--18862 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 30
18773 AAAAATATAT
18783 AACTTTTATAAATTACATTTTTGGTCC-CTA
1 AACTTTTATAAATTACATTTTT-GTCCACTA
* *
18813 AACTTTTATAAAGTT-TATACTTTGTCCACTA
1 AACTTTTATAAA-TTACAT-TTTTGTCCACTA
18844 AACTTTTA-AAATTAACATT
1 AACTTTTATAAATT-ACATT
18863 GTCACTAGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
29 2 0.05
30 21 0.51
31 18 0.44
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (30 bp):
AACTTTTATAAATTACATTTTTGTCCACTA
Found at i:23386 original size:17 final size:17
Alignment explanation
Indices: 23364--23403 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
23354 TTTGGTGGCC
23364 AAAGTAAAAAATTAGAA
1 AAAGTAAAAAATTAGAA
*
23381 AAAGTAAAAAATTAGGA
1 AAAGTAAAAAATTAGAA
23398 AAAGTA
1 AAAGTA
23404 TAGGGACCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (17 bp):
AAAGTAAAAAATTAGAA
Found at i:51055 original size:24 final size:24
Alignment explanation
Indices: 51027--51076 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
51017 TTCTTATTTG
51027 ATTTCATTAATTAT-TTACTTA-TCC
1 ATTTC-TT-ATTATATTACTTATTCC
*
51051 ATTTCTTATTCTATTACTTATTCC
1 ATTTCTTATTATATTACTTATTCC
51075 AT
1 AT
51077 CTATTTCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 4 0.17
23 9 0.39
24 10 0.43
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTCTTATTATATTACTTATTCC
Found at i:60881 original size:46 final size:45
Alignment explanation
Indices: 60778--60947 Score: 234
Period size: 45 Copynumber: 3.8 Consensus size: 45
60768 GTAAGCATGC
* *
60778 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGTA
*
60822 AAATAAGCTTACGAGCTTATGGAATTAAACGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA-TAAATGGTAAGTATTTTGGTA
* * * *
60868 AAATAGGCCTACGAGCTTATGGATTAAATGGTAAGTGTTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGTA
* * *
60913 AATTAAGCTTACGAGCATATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
60948 AGATTTTATC
Statistics
Matches: 110, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
44 24 0.22
45 49 0.45
46 37 0.34
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGTA
Found at i:60921 original size:91 final size:89
Alignment explanation
Indices: 60778--60947 Score: 232
Period size: 91 Copynumber: 1.9 Consensus size: 89
60768 GTAAGCATGC
* *
60778 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATAAGCCTACGAGCTTATGGAATAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCATATG
60843 GAATTAAACGGTAAGTATTTTGGTA
66 GAA-TAAACGGTAAGTATTTTGGTA
* * * * * *
60868 AAATAGGCCTACGAGCTTATGGATTAAATGGTAAGTGTTTTGGTAAATTAAGCTTACGAGCATAT
1 AAATAAGCCTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTAAAATAAGCTTACGAGCATAT
* *
60933 GGGATAAATGGTAAG
65 GGAATAAACGGTAAG
60948 AGATTTTATC
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
90 32 0.46
91 37 0.54
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (89 bp):
AAATAAGCCTACGAGCTTATGGAATAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCATATG
GAATAAACGGTAAGTATTTTGGTA
Found at i:67300 original size:21 final size:21
Alignment explanation
Indices: 67258--67301 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
67248 AATTATTTAG
* *
67258 TTGAATTACAACATGGATTAA
1 TTGAATTACAACAAGGACTAA
67279 TTGAATTA-AACAAGGACCTAA
1 TTGAATTACAACAAGGA-CTAA
67300 TT
1 TT
67302 AAAAAGAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (21 bp):
TTGAATTACAACAAGGACTAA
Found at i:67784 original size:24 final size:24
Alignment explanation
Indices: 67752--67806 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
67742 AGAGATTATG
67752 GTGATCATGTTGAGTTAAATTTAA
1 GTGATCATGTTGAGTTAAATTTAA
67776 GTGATCATGTTGAGTTAAATTTAA
1 GTGATCATGTTGAGTTAAATTTAA
67800 GTGATCA
1 GTGATCA
67807 AAAACCATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.40
Consensus pattern (24 bp):
GTGATCATGTTGAGTTAAATTTAA
Found at i:70829 original size:12 final size:12
Alignment explanation
Indices: 70812--70849 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
70802 TTCAAGAATA
70812 GGAGGAGGATTT
1 GGAGGAGGATTT
70824 GGAGGAGGATTT
1 GGAGGAGGATTT
*
70836 GGAGGTGGATTT
1 GGAGGAGGATTT
70848 GG
1 GG
70850 TTGATGGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.21, C:0.00, G:0.53, T:0.26
Consensus pattern (12 bp):
GGAGGAGGATTT
Found at i:71600 original size:20 final size:21
Alignment explanation
Indices: 71521--71601 Score: 76
Period size: 20 Copynumber: 3.9 Consensus size: 21
71511 CATAACCCCA
* *
71521 GGGGGTATCGATTCCC-CTAT
1 GGGGGAATCGATTCCCTCAAT
* *
71541 GGGGGAATCGGTTCCTCTTCAAA
1 GGGGGAATCGATTCC-C-TCAAT
*
71564 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGATTCCCTCAAT
*
71584 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
71602 TACACCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
20 30 0.59
21 3 0.06
22 1 0.02
23 17 0.33
ACGTcount: A:0.16, C:0.25, G:0.32, T:0.27
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTCAAT
Done.