Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008161.1 Hibiscus syriacus cultivar Beakdansim tig00110730_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: 673301
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 4 of 4
Found at i:654695 original size:34 final size:34
Alignment explanation
Indices: 654639--654715 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 34
654629 TTATTTCATT
*
654639 AATTTGGTTGGATTTATTTTAATTTATTTT-GTTA
1 AATTT-GTTGGATTTATTTTAATGTATTTTGGTTA
654673 AATTTGTTGGACTTT-TTGTTAATGTATTTTGGTTA
1 AATTTGTTGGA-TTTATT-TTAATGTATTTTGGTTA
*
654708 ATTTTGTT
1 AATTTGTT
654716 TATTACCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 8 0.21
34 19 0.50
35 11 0.29
ACGTcount: A:0.21, C:0.01, G:0.17, T:0.61
Consensus pattern (34 bp):
AATTTGTTGGATTTATTTTAATGTATTTTGGTTA
Found at i:656522 original size:51 final size:51
Alignment explanation
Indices: 656403--656523 Score: 143
Period size: 51 Copynumber: 2.4 Consensus size: 51
656393 ACTTAACATG
* **
656403 TACTTACACCAATGTAAGTGAATAAAATAAAAAAGAATAGTAATTAACAAA
1 TACTTACACCAGTGTAAGTGAATAAAATAAAAAAGAATAACAATTAACAAA
* * * ** * *
656454 TACTTACATCGGTGTAAGTGAATAAAATAAGAAAGTGTAACATTTAACACA
1 TACTTACACCAGTGTAAGTGAATAAAATAAAAAAGAATAACAATTAACAAA
*
656505 TACTTACACCAGCGTAAGT
1 TACTTACACCAGTGTAAGT
656524 ATGTACATCT
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (51 bp):
TACTTACACCAGTGTAAGTGAATAAAATAAAAAAGAATAACAATTAACAAA
Found at i:656679 original size:38 final size:39
Alignment explanation
Indices: 656609--656687 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 39
656599 CAAATAAATA
***
656609 AAAAATATATATTAAGTTATTTGTATAAAAAATT-TATT
1 AAAAATATATATTAAGTTATAAATATAAAAAATTATATT
*
656647 AAAAATATATA-TAAGTTATAAATAATAGAAAATTATATT
1 AAAAATATATATTAAGTTATAAAT-ATAAAAAATTATATT
656686 AA
1 AA
656688 GTTATTTGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 9 0.26
38 20 0.57
39 6 0.17
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (39 bp):
AAAAATATATATTAAGTTATAAATATAAAAAATTATATT
Found at i:656997 original size:38 final size:38
Alignment explanation
Indices: 656911--656997 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 38
656901 GTAACATTAG
* **
656911 TATATTTTAAAATAATAAATGTTATTAATTATATTAGT
1 TATATTTTAAAATAATAAATGTTATTAATTATAATAAA
*
656949 TA-ATTATTAAAATAATATTATGTTA-T-ATTATCAATAAA
1 TATATT-TTAAAATAATA-AATGTTATTAATTAT-AATAAA
656987 TATATTTTAAA
1 TATATTTTAAA
656998 TATTTTACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
37 8 0.20
38 24 0.59
39 9 0.22
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.48
Consensus pattern (38 bp):
TATATTTTAAAATAATAAATGTTATTAATTATAATAAA
Found at i:657073 original size:26 final size:27
Alignment explanation
Indices: 657044--657111 Score: 68
Period size: 30 Copynumber: 2.4 Consensus size: 27
657034 ACAAATAATA
657044 TTATTTATTATAACAATCA-ATAAATT
1 TTATTTATTATAACAATCATATAAATT
* *
657070 TTATTTTATCAATATAATAATCATTTAAATT
1 TTA-TTTAT---TATAACAATCATATAAATT
657101 TTATTT-TTATA
1 TTATTTATTATA
657112 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
26 7 0.20
27 5 0.14
29 1 0.03
30 13 0.37
31 9 0.26
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (27 bp):
TTATTTATTATAACAATCATATAAATT
Found at i:660691 original size:38 final size:38
Alignment explanation
Indices: 660640--660723 Score: 168
Period size: 38 Copynumber: 2.2 Consensus size: 38
660630 AATTGAATTT
660640 TTCAAACTCATACTTCTCCCCTGTTATATAAAAAATAA
1 TTCAAACTCATACTTCTCCCCTGTTATATAAAAAATAA
660678 TTCAAACTCATACTTCTCCCCTGTTATATAAAAAATAA
1 TTCAAACTCATACTTCTCCCCTGTTATATAAAAAATAA
660716 TTCAAACT
1 TTCAAACT
660724 TTAAGTTTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (38 bp):
TTCAAACTCATACTTCTCCCCTGTTATATAAAAAATAA
Found at i:661729 original size:21 final size:19
Alignment explanation
Indices: 661680--661716 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
661670 TTGAAAGCTC
661680 AAAATTATT-TTTCAAAATA
1 AAAATT-TTCTTTCAAAATA
661699 AAAATTTTCTTTCAAAAT
1 AAAATTTTCTTTCAAAAT
661717 CAAATCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATTTTCTTTCAAAATA
Found at i:666774 original size:35 final size:35
Alignment explanation
Indices: 666735--666854 Score: 100
Period size: 35 Copynumber: 3.3 Consensus size: 35
666725 GTCTCCTTTC
*
666735 GTTCTACTTGAATTGAAAGTGCGATGCTTTCTTCT
1 GTTCTACTTGAATTGAAAGTGCGATGCTTACTTCT
** * *
666770 GTTCTACTTTAGAGGATAATTG-AAGTGTTATGCCTCCTT-T
1 GTTCTAC-TT----G--AATTGAAAGTGCGATGCTTACTTCT
*
666810 CGTTCTACTTGAATCGAAAGTGCGATGCTTACTTCT
1 -GTTCTACTTGAATTGAAAGTGCGATGCTTACTTCT
666846 GTTCTACTT
1 GTTCTACTT
666855 TATACGAGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 20
0.69 0.09 0.21
Matches are distributed among these distances:
34 4 0.06
35 29 0.44
36 4 0.06
40 4 0.06
41 20 0.30
42 5 0.08
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (35 bp):
GTTCTACTTGAATTGAAAGTGCGATGCTTACTTCT
Found at i:666822 original size:76 final size:77
Alignment explanation
Indices: 666708--666924 Score: 258
Period size: 76 Copynumber: 2.8 Consensus size: 77
666698 TCTGTCAACA
* ** * * *
666708 AGAATCAAAAGTCCTATGTCTCCTTTCGTTCTACTTGAATTGAAAGTGCGATGCTTTCTTCTGTT
1 AGAATCGAAAGTGTTATGCCTCCTTTCGTTCTACTTGAATCGAAAGTGCGATGCTTACTTCTGTT
*
666773 CTACTTTAGAGG
66 CTACTTTAGACG
* *
666785 ATAATTG-AAGTGTTATGCCTCCTTTCGTTCTACTTGAATCGAAAGTGCGATGCTTACTTCTGTT
1 AGAATCGAAAGTGTTATGCCTCCTTTCGTTCTACTTGAATCGAAAGTGCGATGCTTACTTCTGTT
*
666849 CTACTTTATACG
66 CTACTTTAGACG
* * * * * * * *
666861 AGAATCGAAAGTGTTATGCCT-CATTCTTTCAACTTGATTCAAAAGCGCGATGCTTCCTTTTGTT
1 AGAATCGAAAGTGTTATGCCTCCTTTCGTTCTACTTGAATCGAAAGTGCGATGCTTACTTCTGTT
666925 ATTCTTGTTC
Statistics
Matches: 119, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
76 102 0.86
77 17 0.14
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.39
Consensus pattern (77 bp):
AGAATCGAAAGTGTTATGCCTCCTTTCGTTCTACTTGAATCGAAAGTGCGATGCTTACTTCTGTT
CTACTTTAGACG
Found at i:667740 original size:21 final size:23
Alignment explanation
Indices: 667692--667741 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
667682 GATGAAGGAA
*
667692 AAACAATCGACTGAGAAGAAAAG
1 AAACAATCGAATGAGAAGAAAAG
* *
667715 CAACAATC-AATG-GAAGAAACG
1 AAACAATCGAATGAGAAGAAAAG
667736 AAACAA
1 AAACAA
667742 CATCAACGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 13 0.57
22 3 0.13
23 7 0.30
ACGTcount: A:0.58, C:0.16, G:0.18, T:0.08
Consensus pattern (23 bp):
AAACAATCGAATGAGAAGAAAAG
Found at i:672152 original size:24 final size:25
Alignment explanation
Indices: 672106--672152 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
672096 AGATAAATTT
**
672106 TAAAATTTAAAATAAGACGAACTTA
1 TAAAATTTAAAATAAGAAAAACTTA
*
672131 TAAAATTTTAAA-AAGAAAAACT
1 TAAAATTTAAAATAAGAAAAACT
672153 ATTATCAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (25 bp):
TAAAATTTAAAATAAGAAAAACTTA
Done.