Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007817.1 Hibiscus syriacus cultivar Beakdansim tig00110152_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: 465523
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:417769 original size:23 final size:23
Alignment explanation
Indices: 417736--417814 Score: 104
Period size: 23 Copynumber: 3.4 Consensus size: 23
417726 TTCAGGATAT
*
417736 TTCTATATGGTCCTTCGGGACAA
1 TTCTATGTGGTCCTTCGGGACAA
* *
417759 TTATATGTGGTCATTCGGGACAA
1 TTCTATGTGGTCCTTCGGGACAA
* *
417782 TTCTACGCGGTCCTTCGGGACAA
1 TTCTATGTGGTCCTTCGGGACAA
*
417805 ATCTATGTGG
1 TTCTATGTGG
417815 CACTTTGGTG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAA
Found at i:417838 original size:24 final size:24
Alignment explanation
Indices: 417772--417861 Score: 80
Period size: 24 Copynumber: 3.8 Consensus size: 24
417762 TATGTGGTCA
* *
417772 TTCGG-GACAATTCTACGCGGTC-C
1 TTCGGTGAAAATTCTACGTGG-CAC
*
417795 TTCGG-GACAAA-TCTATGTGGCAC
1 TTCGGTGA-AAATTCTACGTGGCAC
* * *
417818 TTTGGTGCATATTCTACGTGGCAC
1 TTCGGTGAAAATTCTACGTGGCAC
417842 TTCGGTGAAAATTCTACGTG
1 TTCGGTGAAAATTCTACGTG
417862 ACAGTTTCGA
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
22 1 0.02
23 21 0.40
24 31 0.58
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (24 bp):
TTCGGTGAAAATTCTACGTGGCAC
Found at i:424693 original size:23 final size:23
Alignment explanation
Indices: 424663--424733 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
424653 GGTTCCTAGC
424663 GGTCCTTTAGGACAATTCTATGT
1 GGTCCTTTAGGACAATTCTATGT
* *
424686 GGTCCTTTGGGACAATTCTATGC
1 GGTCCTTTAGGACAATTCTATGT
*
424709 GGTCCTTTAGGAAAAATT-TATGT
1 GGTCCTTTAGG-ACAATTCTATGT
424732 GG
1 GG
424734 CACTTCGGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 37 0.88
24 5 0.12
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (23 bp):
GGTCCTTTAGGACAATTCTATGT
Found at i:424778 original size:24 final size:23
Alignment explanation
Indices: 424721--424778 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
424711 TCCTTTAGGA
*
424721 AAAATTTATGTGGCACTTCGGTG
1 AAAATTTACGTGGCACTTCGGTG
* *
424744 CATATTCTACGTGGCACTTCGGTG
1 AAAATT-TACGTGGCACTTCGGTG
424768 AAAATTATACG
1 AAAATT-TACG
424779 CTGCAATTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (23 bp):
AAAATTTACGTGGCACTTCGGTG
Found at i:425785 original size:9 final size:9
Alignment explanation
Indices: 425771--425796 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
425761 GGTTTGATTC
425771 TATTTTATG
1 TATTTTATG
425780 TATTTTATG
1 TATTTTATG
425789 TATTTTAT
1 TATTTTAT
425797 ACATTAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (9 bp):
TATTTTATG
Found at i:426864 original size:132 final size:131
Alignment explanation
Indices: 426710--427029 Score: 480
Period size: 132 Copynumber: 2.4 Consensus size: 131
426700 TTGATATTGA
* * * *
426710 AAATAGTAATATCTTTTCATTTCGGTTGGAGTAATAAATGGCTGCTTTAAGGTATGAGAGGTCAT
1 AAATAGTAATATATTTTCATTTCGGTTGGAGTAATAAATGACTGCTTTAAGGCATGAGACGTCAT
* * * *
426775 TTATTCTCGATTGAAAATCATTAGATATTTTTGTTTTTCTCTCGAATCAATATTGATTTTTAAGA
66 TTATTATCGATTGAAAATCATTAGATATTATCG-TTTTCTCTCGAATCAATATTGATTTGTAAGA
426840 CG
130 CG
* *
426842 AAATGGTAATATATTTTCATTTCGGTTGGAGTAATAAATGACTGCTTTAAGGCATGAGACGTTAT
1 AAATAGTAATATATTTTCATTTCGGTTGGAGTAATAAATGACTGCTTTAAGGCATGAGACGTCAT
* *
426907 TTATTATCGATTGAAAATCATTAGATATTATCGTTTTCTCTCGAATCATTATTGATTTGTAAGGC
66 TTATTATCGATTGAAAATCATTAGATATTATCGTTTTCTCTCGAATCAATATTGATTTGTAAGAC
426972 G
131 G
* * *
426973 AAATAGTGATATATCCTT-ATTTCGGTTGGAGTAATAAATGACTACTTTAAGGCATGA
1 AAATAGTAATATAT-TTTCATTTCGGTTGGAGTAATAAATGACTGCTTTAAGGCATGA
427030 AATAATTAGA
Statistics
Matches: 171, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
131 80 0.47
132 91 0.53
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (131 bp):
AAATAGTAATATATTTTCATTTCGGTTGGAGTAATAAATGACTGCTTTAAGGCATGAGACGTCAT
TTATTATCGATTGAAAATCATTAGATATTATCGTTTTCTCTCGAATCAATATTGATTTGTAAGAC
G
Found at i:427194 original size:35 final size:35
Alignment explanation
Indices: 427148--427215 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
427138 AGTAAGAATC
* *
427148 AAATGCTTTAAGGTATGAGATGTTGATTCTTCTCG
1 AAATGCTTTAAGGTATGAGAGGTTGATTATTCTCG
427183 AAATGCTTTAAGGTATGAGAGGTTGATTATTCT
1 AAATGCTTTAAGGTATGAGAGGTTGATTATTCT
427216 ATGAAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.40
Consensus pattern (35 bp):
AAATGCTTTAAGGTATGAGAGGTTGATTATTCTCG
Found at i:431115 original size:12 final size:12
Alignment explanation
Indices: 431071--431122 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
431061 TATAGCTTTT
*
431071 TTATTTTACTTTT
1 TTATTTTA-TTTG
*
431084 TTACTTT-TTTG
1 TTATTTTATTTG
431095 TATAGTTTTATTTG
1 T-TA-TTTTATTTG
431109 TTATTTTATTTG
1 TTATTTTATTTG
431121 TT
1 TT
431123 TTCCTTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
11 4 0.12
12 13 0.39
13 11 0.33
14 5 0.15
ACGTcount: A:0.15, C:0.04, G:0.08, T:0.73
Consensus pattern (12 bp):
TTATTTTATTTG
Found at i:435939 original size:15 final size:14
Alignment explanation
Indices: 435915--435962 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
435905 ATGCAAAAAT
435915 AAATAAAAAAATTG
1 AAATAAAAAAATTG
435929 AAATAAAAAAATTG
1 AAATAAAAAAATTG
*
435943 AAATAAATAAAAATG
1 AAATAAA-AAAATTG
435958 AAATA
1 AAATA
435963 TGGGTTGCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (14 bp):
AAATAAAAAAATTG
Found at i:438040 original size:17 final size:19
Alignment explanation
Indices: 437999--438046 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
437989 TGACGAACAA
437999 TATCGATACTGATGCAAGTGG
1 TATCGATACTGATG--AGTGG
438020 TATCGATACTGATG-G-GG
1 TATCGATACTGATGAGTGG
438037 TATCGATACT
1 TATCGATACT
438047 ACAAAGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 12 0.44
18 1 0.04
21 14 0.52
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (19 bp):
TATCGATACTGATGAGTGG
Found at i:441180 original size:20 final size:20
Alignment explanation
Indices: 441151--441189 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
441141 AGAGCTCATA
*
441151 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
441171 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
441190 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:442604 original size:20 final size:22
Alignment explanation
Indices: 442576--442615 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
442566 ATATTACCAT
442576 CATTCCA-TTT-CCACAACATC
1 CATTCCATTTTGCCACAACATC
*
442596 CATTTCATTTTGCCACAACA
1 CATTCCATTTTGCCACAACA
442616 CTCTCATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 3 0.18
22 8 0.47
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.33
Consensus pattern (22 bp):
CATTCCATTTTGCCACAACATC
Found at i:445306 original size:16 final size:15
Alignment explanation
Indices: 445287--445326 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 15
445277 AAAAAACTTA
445287 AAAGAAAATAACAAAG
1 AAAGAAAATAA-AAAG
445303 AAAGAAATATAAAAAG
1 AAAGAAA-ATAAAAAG
445319 AAAGAAAA
1 AAAGAAAA
445327 GAAAGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.04
16 18 0.78
17 4 0.17
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.07
Consensus pattern (15 bp):
AAAGAAAATAAAAAG
Found at i:461478 original size:26 final size:26
Alignment explanation
Indices: 461444--461497 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
461434 CTTCCCTTAA
461444 AGTCATTCTTTCTCTCTTCTTTAGGT
1 AGTCATTCTTTCTCTCTTCTTTAGGT
461470 AGTCATTCTTTCTCTCTTCTTTAGGT
1 AGTCATTCTTTCTCTCTTCTTTAGGT
461496 AG
1 AG
461498 GATTAGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.13, C:0.22, G:0.13, T:0.52
Consensus pattern (26 bp):
AGTCATTCTTTCTCTCTTCTTTAGGT
Found at i:463461 original size:21 final size:20
Alignment explanation
Indices: 463428--463467 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
463418 ATAATTATTT
463428 AAAAAATTAAATAAAAATAC
1 AAAAAATTAAATAAAAATAC
*
463448 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
463468 ATTTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAAATTAAATAAAAATAC
Done.