Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009600.1 Hibiscus syriacus cultivar Beakdansim tig00116980_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: 308658
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:254575 original size:13 final size:13
Alignment explanation
Indices: 254539--254586 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
254529 ATCAAAGCAA
*
254539 AAAGAGAAAAAAGC
1 AAAG-GAAAAAAAC
*
254553 AAAGAGAAAATAA-
1 AAAG-GAAAAAAAC
254566 AAAGGAAAAAAAC
1 AAAGGAAAAAAAC
254579 AAAGGAAA
1 AAAGGAAA
254587 TTTGAAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 7 0.23
13 12 0.40
14 11 0.37
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (13 bp):
AAAGGAAAAAAAC
Found at i:255682 original size:32 final size:31
Alignment explanation
Indices: 255641--255735 Score: 118
Period size: 32 Copynumber: 2.9 Consensus size: 31
255631 TGAAGGCATC
*
255641 TTTGAAGATTCAACATCAAATGCTGGGGCATTT
1 TTTG-AGATTCAACATCAAAT-TTGGGGCATTT
* *
255674 TTTGAGATTTAACATCAAAATTTAGGGCATTT
1 TTTGAGATTCAACATC-AAATTTGGGGCATTT
*
255706 TTTGAGATTCAACATCGAATATTGGGGCAT
1 TTTGAGATTCAACATCAAAT-TTGGGGCAT
255736 CTTTGGGAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
31 3 0.06
32 43 0.80
33 8 0.15
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.36
Consensus pattern (31 bp):
TTTGAGATTCAACATCAAATTTGGGGCATTT
Found at i:256738 original size:376 final size:376
Alignment explanation
Indices: 256045--256796 Score: 1468
Period size: 376 Copynumber: 2.0 Consensus size: 376
256035 ATTCAGAGTC
* *
256045 AATTTCAACTTCACAGCAAAGGATATTAAACTCAAAGCGACACAATTTTCTCGAGAGTAGATTTC
1 AATTTCAACTTCACAGCAAAGGATATTAAACTCAAAGCAACACAATTTGCTCGAGAGTAGATTTC
*
256110 AACTTCACGACGAAGAATATCTAGCTTGAAGTCAAACTTCACAATAAAGGGGTCATCTACGGTTT
66 AACTTCACGACGAAGAATATCTAGCTTGAAGTCAAACTTCACAATAAAGGGGTCATCCACGGTTT
*
256175 CAACTTCACAACGAATGGAATTGTGTCCACCCGCAACATACAATACTTGGATTTCAAATTCACGA
131 CAACTTCACAACGAATGGAATTGTGTCCACCCACAACATACAATACTTGGATTTCAAATTCACGA
256240 CGAAGGATATTCAAGTCAAGGCTCAACTTTACGACGAAGGGGCCATCCACGATTTCAACTCCACA
196 CGAAGGATATTCAAGTCAAGGCTCAACTTTACGACGAAGGGGCCATCCACGATTTCAACTCCACA
256305 ACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACAACGGAGGATATCGTTCTATTTT
261 ACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACAACGGAGGATATCGTTCTATTTT
256370 GAGGCTCAACTTCACGACGAATGGGATTCCCAGTTTCAGAGCCAATTTCAA
326 GAGGCTCAACTTCACGACGAATGGGATTCCCAGTTTCAGAGCCAATTTCAA
256421 AATTTCAACTTCACAGCAAAGGATATTAAACTCAAAGCAACACAATTTGCTCGAGAGTAGATTTC
1 AATTTCAACTTCACAGCAAAGGATATTAAACTCAAAGCAACACAATTTGCTCGAGAGTAGATTTC
256486 AACTTCACGACGAAGAATATCTAGCTTGAAGTCAAACTTCACAATAAAGGGGTCATCCACGGTTT
66 AACTTCACGACGAAGAATATCTAGCTTGAAGTCAAACTTCACAATAAAGGGGTCATCCACGGTTT
256551 CAACTTCACAACGAATGGAATTGTGTCCACCCACAACATACAATACTTGGATTTCAAATTCACGA
131 CAACTTCACAACGAATGGAATTGTGTCCACCCACAACATACAATACTTGGATTTCAAATTCACGA
256616 CGAAGGATATTCAAGTCAAGGCTCAACTTTACGACGAAGGGGCCATCCACGATTTCAACTCCACA
196 CGAAGGATATTCAAGTCAAGGCTCAACTTTACGACGAAGGGGCCATCCACGATTTCAACTCCACA
256681 ACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACAACGGAGGATATCGTTCTATTTT
261 ACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACAACGGAGGATATCGTTCTATTTT
256746 GAGGCTCAACTTCACGACGAATGGGATTCCCAGTTTCAGAGCCAATTTCAA
326 GAGGCTCAACTTCACGACGAATGGGATTCCCAGTTTCAGAGCCAATTTCAA
256797 CTTCACATCG
Statistics
Matches: 372, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
376 372 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (376 bp):
AATTTCAACTTCACAGCAAAGGATATTAAACTCAAAGCAACACAATTTGCTCGAGAGTAGATTTC
AACTTCACGACGAAGAATATCTAGCTTGAAGTCAAACTTCACAATAAAGGGGTCATCCACGGTTT
CAACTTCACAACGAATGGAATTGTGTCCACCCACAACATACAATACTTGGATTTCAAATTCACGA
CGAAGGATATTCAAGTCAAGGCTCAACTTTACGACGAAGGGGCCATCCACGATTTCAACTCCACA
ACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACAACGGAGGATATCGTTCTATTTT
GAGGCTCAACTTCACGACGAATGGGATTCCCAGTTTCAGAGCCAATTTCAA
Found at i:257376 original size:37 final size:37
Alignment explanation
Indices: 257326--257398 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
257316 TTTCCAAGTT
257326 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATA
257363 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
257399 CTTTGAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATA
Found at i:257499 original size:32 final size:34
Alignment explanation
Indices: 257436--257527 Score: 91
Period size: 36 Copynumber: 2.7 Consensus size: 34
257426 TTTCGTCTCC
* *
257436 CTTGAGACAGTTTCTTTT-AGAACTAA-GTTTT-T
1 CTTGAGACAATTTCTTTTGA-AACAAATGTTTTCT
* *
257468 CTTGAGACATTTTCTTTTGAAACAAATTTTTTCCCT
1 CTTGAGACAATTTCTTTTGAAACAAATGTTTT--CT
*
257504 CTTGAGACAATTTCTCTTGAAACA
1 CTTGAGACAATTTCTTTTGAAACA
257528 CAAAAAAACC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
32 22 0.44
33 5 0.10
36 23 0.46
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.43
Consensus pattern (34 bp):
CTTGAGACAATTTCTTTTGAAACAAATGTTTTCT
Found at i:257574 original size:40 final size:39
Alignment explanation
Indices: 257525--257601 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
257515 TTCTCTTGAA
*
257525 ACACA-AAAAAACCCTCGAAATTGTTTCTCTTGAAACAC
1 ACACACAAAAAACCCTCGAAAATGTTTCTCTTGAAACAC
* *
257563 ACACACAAAAAACCTTTGAAAATGTTTCTCTTGAAACAC
1 ACACACAAAAAACCCTCGAAAATGTTTCTCTTGAAACAC
257602 CAAACCCTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 5 0.14
39 30 0.86
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.25
Consensus pattern (39 bp):
ACACACAAAAAACCCTCGAAAATGTTTCTCTTGAAACAC
Found at i:259165 original size:72 final size:70
Alignment explanation
Indices: 259020--259165 Score: 186
Period size: 70 Copynumber: 2.1 Consensus size: 70
259010 TTCCCTCCGA
* * * *
259020 AGAGGACCCCATGTAGAATCAGTACGATATATAATCTCATACAGAATCGGATAGAGATTATGCCC
1 AGAGGACCCCATCTAGAATCAGAACGAGATATAATCTCATACAGAATCGAATAGAGATTATGCCC
259085 TTCAT
66 TTCAT
* * * *
259090 AGAGGATCCCATCTAGAATCAGAACGGAGATATAAT-TCCATGCAGAATCAGAATGGTGATTATG
1 AGAGGACCCCATCTAGAATCAGAAC-GAGATATAATCT-CATACAGAATC-GAATAGAGATTATG
259154 CCCTTCAT
63 CCCTTCAT
259162 AGAG
1 AGAG
259166 TGCAATGCCC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
70 23 0.35
71 19 0.29
72 23 0.35
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (70 bp):
AGAGGACCCCATCTAGAATCAGAACGAGATATAATCTCATACAGAATCGAATAGAGATTATGCCC
TTCAT
Found at i:277525 original size:80 final size:79
Alignment explanation
Indices: 277398--277544 Score: 204
Period size: 80 Copynumber: 1.8 Consensus size: 79
277388 TGAAAAAAAC
* * * * * *
277398 AAAATAAATACACAAATCAAGTTATATTTATAAATAGATATTGTCTTATACTCACTCTATATTAA
1 AAAATAAATACACAAATCAAGTGATATCTATAAACAAATATTATCTTATACTCAC-CTAGATTAA
277463 TAATAATAAAAAGAT
65 TAATAATAAAAAGAT
** *
277478 AAAATAAATACATGAATTAAGTGATATCTATAAACAAATATTATCTTATACTCACCTAGATTAAT
1 AAAATAAATACACAAATCAAGTGATATCTATAAACAAATATTATCTTATACTCACCTAGATTAAT
277543 AA
66 AA
277545 AAAAATTAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
79 11 0.19
80 47 0.81
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (79 bp):
AAAATAAATACACAAATCAAGTGATATCTATAAACAAATATTATCTTATACTCACCTAGATTAAT
AATAATAAAAAGAT
Found at i:278180 original size:20 final size:19
Alignment explanation
Indices: 278155--278198 Score: 79
Period size: 20 Copynumber: 2.3 Consensus size: 19
278145 TTTATCCATA
278155 TATTATAATATAATTATATT
1 TATTATAATATAATTATA-T
278175 TATTATAATATAATTATAT
1 TATTATAATATAATTATAT
278194 TATTA
1 TATTA
278199 ATATATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTATAATATAATTATAT
Found at i:296478 original size:21 final size:21
Alignment explanation
Indices: 296437--296478 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
296427 TTCTGGGCTG
* *
296437 GGGGAATCGGTACCCATTCAA
1 GGGGAATCGATACCCACTCAA
*
296458 GGGGAATCGATACCCCCTCAA
1 GGGGAATCGATACCCACTCAA
296479 CGAATATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGGAATCGATACCCACTCAA
Found at i:296530 original size:20 final size:20
Alignment explanation
Indices: 296505--296542 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
296495 GAATGCTAGA
*
296505 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
296525 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
296543 TAAAAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:298890 original size:24 final size:24
Alignment explanation
Indices: 298863--298928 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
298853 AGCTCATATA
298863 AATTTGCACCGTAGTGCCACGTAG
1 AATTTGCACCGTAGTGCCACGTAG
* *
298887 AATTTGCACCGAAGTGCCGCGTAG
1 AATTTGCACCGTAGTGCCACGTAG
*
298911 AA-ATGCACCGTAGTGCCA
1 AATTTGCACCGTAGTGCCA
298929 TATAATATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 13 0.35
24 24 0.65
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.21
Consensus pattern (24 bp):
AATTTGCACCGTAGTGCCACGTAG
Found at i:299078 original size:24 final size:24
Alignment explanation
Indices: 299042--299109 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
299032 ATACATATAC
299042 GTCCCGAAGGACCACGTAGAATTT
1 GTCCCGAAGGACCACGTAGAATTT
*
299066 GTCCCGAATGACCACGTAGAATTT
1 GTCCCGAAGGACCACGTAGAATTT
*
299090 GTCCCGAAGGACCGCGTAGA
1 GTCCCGAAGGACCACGTAGA
299110 CCCTCGACTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.19
Consensus pattern (24 bp):
GTCCCGAAGGACCACGTAGAATTT
Done.