Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008960.1 Hibiscus syriacus cultivar Beakdansim tig00112294_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: 362692
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:343685 original size:21 final size:21
Alignment explanation
Indices: 343642--343686 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
343632 ACGAGGATTG
** *
343642 ATCCTCCTTTACGAGGGACCA
1 ATCCTCCTTTACGAAAGAACA
*
343663 ATCCTCCTTTAGGAAAGAACA
1 ATCCTCCTTTACGAAAGAACA
343684 ATC
1 ATC
343687 TTAAAGGGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (21 bp):
ATCCTCCTTTACGAAAGAACA
Found at i:344720 original size:81 final size:83
Alignment explanation
Indices: 344606--344769 Score: 215
Period size: 81 Copynumber: 2.0 Consensus size: 83
344596 CAAACGCCAC
* * * *
344606 AAAATAGTAACTTTAGCGGCATTTTTATACAAACGCTGCAATAGGGTTAACTTATACAGGTGTTT
1 AAAATAGTAACTTTAGCGGCAGTTTTATACAAACGCCGCAATAGGATTAACCTATACAGGTGTTT
344671 TTCAATAAACACCGCAAT
66 TTCAATAAACACCGCAAT
* * * ** *
344689 AAAATAG-AACTTTAGCGGC-GTTTTATACAAACGCCGTAATAGTATTTACCTATAGTGGTTTTT
1 AAAATAGTAACTTTAGCGGCAGTTTTATACAAACGCCGCAATAGGATTAACCTATACAGGTGTTT
*
344752 TTCAATAAACGCCGCAAT
66 TTCAATAAACACCGCAAT
344770 TGCTTGAATT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
81 51 0.73
82 12 0.17
83 7 0.10
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (83 bp):
AAAATAGTAACTTTAGCGGCAGTTTTATACAAACGCCGCAATAGGATTAACCTATACAGGTGTTT
TTCAATAAACACCGCAAT
Found at i:347397 original size:3 final size:3
Alignment explanation
Indices: 347389--347435 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
347379 TAATGGTGAT
347389 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
347436 TTCTGATGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:348517 original size:43 final size:43
Alignment explanation
Indices: 348451--348669 Score: 144
Period size: 43 Copynumber: 5.1 Consensus size: 43
348441 ATGCTAATTA
* * * *
348451 GCGGCGTTTGTATCAAAATATGCCGTTATAGATATAACTTTTT
1 GCGGCGTTTGTATAAAAAAATGCCGCTATAGATATAACCTTTT
* *
348494 GCGGCGTTTGTATAAAAAAATGCCGCTATAGATTTGACCTTTT
1 GCGGCGTTTGTATAAAAAAATGCCGCTATAGATATAACCTTTT
** ** * * * * *
348537 GCGGTTTTTGTAT-TTAAAACGTCGCTATAGATCTGATCTTTT
1 GCGGCGTTTGTATAAAAAAATGCCGCTATAGATATAACCTTTT
* * * * *
348579 GCGGTGTTTGT-TCCAAAAACAT--CGCTATAGGTCTGACCTTTT
1 GCGGCGTTTGTAT--AAAAAAATGCCGCTATAGATATAACCTTTT
* * * *
348621 GCGGTGTTTGTATCCAAAAACAT--CGCTATAGATTTGACCTTTT
1 GCGGCGTTTGTAT--AAAAAAATGCCGCTATAGATATAACCTTTT
348664 GCGGCG
1 GCGGCG
348670 CTATAGATCT
Statistics
Matches: 148, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
41 1 0.01
42 62 0.42
43 82 0.55
44 3 0.02
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.37
Consensus pattern (43 bp):
GCGGCGTTTGTATAAAAAAATGCCGCTATAGATATAACCTTTT
Found at i:348578 original size:42 final size:43
Alignment explanation
Indices: 348490--348667 Score: 220
Period size: 42 Copynumber: 4.2 Consensus size: 43
348480 AGATATAACT
* * *
348490 TTTTGCGGCGTTTGTAT--AAAAAAATGCCGCTATAGATTTGACC
1 TTTTGCGGTGTTTGTATCCAAAAACAT--CGCTATAGATCTGACC
* ** * *
348533 TTTTGCGGTTTTTGTAT-TTAAAACGTCGCTATAGATCTGATC
1 TTTTGCGGTGTTTGTATCCAAAAACATCGCTATAGATCTGACC
*
348575 TTTTGCGGTGTTTGT-TCCAAAAACATCGCTATAGGTCTGACC
1 TTTTGCGGTGTTTGTATCCAAAAACATCGCTATAGATCTGACC
*
348617 TTTTGCGGTGTTTGTATCCAAAAACATCGCTATAGATTTGACC
1 TTTTGCGGTGTTTGTATCCAAAAACATCGCTATAGATCTGACC
348660 TTTTGCGG
1 TTTTGCGG
348668 CGCTATAGAT
Statistics
Matches: 117, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.01
42 63 0.54
43 48 0.41
44 5 0.04
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (43 bp):
TTTTGCGGTGTTTGTATCCAAAAACATCGCTATAGATCTGACC
Found at i:348671 original size:24 final size:25
Alignment explanation
Indices: 348644--348694 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
348634 CCAAAAACAT
*
348644 CGCTATAGAT-TTGACCTTTTGCGG
1 CGCTATAGATCTTGACCTTTAGCGG
348668 CGCTATAGATCTTGACCTTTAGCGG
1 CGCTATAGATCTTGACCTTTAGCGG
348693 CG
1 CG
348695 TTTGTATCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (25 bp):
CGCTATAGATCTTGACCTTTAGCGG
Found at i:348731 original size:68 final size:67
Alignment explanation
Indices: 348601--348736 Score: 173
Period size: 68 Copynumber: 2.0 Consensus size: 67
348591 CCAAAAACAT
* * * * * *
348601 CGCTATAGGTCTGACCTTTTGCGGTGTTTGTATCCAAAAACATCGCTATAGATTTGACCTTTTGC
1 CGCTATAGATCTGACCTTTAGCGGCGTTTGTATCCAAAAACATCGCTATAAATCTAACCTTTTGC
348666 GG
66 GG
** * *
348668 CGCTATAGATCTTGACCTTTAGCGGCGTTTGTATCCAAAAATGTCGGTATAAATCTAATCTTTTG
1 CGCTATAGATC-TGACCTTTAGCGGCGTTTGTATCCAAAAACATCGCTATAAATCTAACCTTTTG
348733 CGG
65 CGG
348736 C
1 C
348737 TTTGTTTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
67 10 0.17
68 48 0.83
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (67 bp):
CGCTATAGATCTGACCTTTAGCGGCGTTTGTATCCAAAAACATCGCTATAAATCTAACCTTTTGC
GG
Found at i:350383 original size:51 final size:50
Alignment explanation
Indices: 350328--350439 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 50
350318 CTTGCCCCGT
** * *
350328 GCTATATGCTGATTTGGCGTCACAT-TGAGTATAGCGCGCCTCCTGTACTGC
1 GCTATA-GCTGACATGGC-TCACATGTGAGTATAGCGCGCCCCCTGTACCGC
* * *
350379 GCTATACGCTGACATGGCTTACATGTGGGTATAGCGCGCCCCCTGTTCCGC
1 GCTATA-GCTGACATGGCTCACATGTGAGTATAGCGCGCCCCCTGTACCGC
350430 GCTATAGCTG
1 GCTATAGCTG
350440 TTTATCTGAC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
50 9 0.17
51 43 0.83
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.29
Consensus pattern (50 bp):
GCTATAGCTGACATGGCTCACATGTGAGTATAGCGCGCCCCCTGTACCGC
Found at i:356241 original size:11 final size:12
Alignment explanation
Indices: 356225--356254 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
356215 AAGTATAATA
356225 AACAAAA-TTAT
1 AACAAAATTTAT
356236 AACAAAATTTAT
1 AACAAAATTTAT
356248 AACAAAA
1 AACAAAA
356255 AATCGCACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (12 bp):
AACAAAATTTAT
Found at i:357479 original size:39 final size:39
Alignment explanation
Indices: 357436--357519 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
357426 AACGGTGAAG
*
357436 TAGGGAGTG-AGATGCGA-AGGAGAAATGAAAAAGGGGAAT
1 TAGGGAGTGAAG-GGCGAGAGGA-AAATGAAAAAGGGGAAT
* * **
357475 TAGGGATTGAAGGGCGAGAGGAAAATGAGATTGGGGAAT
1 TAGGGAGTGAAGGGCGAGAGGAAAATGAAAAAGGGGAAT
357514 TAGGGA
1 TAGGGA
357520 TTATGGCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 32 0.84
40 6 0.16
ACGTcount: A:0.39, C:0.02, G:0.43, T:0.15
Consensus pattern (39 bp):
TAGGGAGTGAAGGGCGAGAGGAAAATGAAAAAGGGGAAT
Found at i:362622 original size:39 final size:39
Alignment explanation
Indices: 362579--362662 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
362569 AACGGTGAAG
*
362579 TAGGGAGTG-AGATGCGA-AGGAGAAATGAAAAAGGGGAAT
1 TAGGGAGTGAAG-GGCGAGAGGA-AAATGAAAAAGGGGAAT
* * **
362618 TAGGGATTGAAGGGCGAGAGGAAAATGAGATTGGGGAAT
1 TAGGGAGTGAAGGGCGAGAGGAAAATGAAAAAGGGGAAT
362657 TAGGGA
1 TAGGGA
362663 TTATGGCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 32 0.84
40 6 0.16
ACGTcount: A:0.39, C:0.02, G:0.43, T:0.15
Consensus pattern (39 bp):
TAGGGAGTGAAGGGCGAGAGGAAAATGAAAAAGGGGAAT
Done.