Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008083.1 Hibiscus syriacus cultivar Beakdansim tig00110586_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: 73570
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:15421 original size:14 final size:14
Alignment explanation
Indices: 15398--15437 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
15388 AAAAAAAGTT
*
15398 TCTTTGTTTCTTCA
1 TCTTTCTTTCTTCA
15412 TCTTTCTTTCTTCA
1 TCTTTCTTTCTTCA
15426 T-TTCTCTTTCTT
1 TCTT-TCTTTCTT
15438 TCTTGTTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 2 0.08
14 22 0.92
ACGTcount: A:0.05, C:0.25, G:0.03, T:0.68
Consensus pattern (14 bp):
TCTTTCTTTCTTCA
Found at i:23662 original size:24 final size:24
Alignment explanation
Indices: 23629--23689 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
23619 TCAACTTCCT
23629 GTATAAAATCAAAATGGAGTCCAA
1 GTATAAAATCAAAATGGAGTCCAA
* *
23653 GTATATAATCAATATGGAGTCCAA
1 GTATAAAATCAAAATGGAGTCCAA
23677 GTATAAAATCAAA
1 GTATAAAATCAAA
23690 TTAAAACAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (24 bp):
GTATAAAATCAAAATGGAGTCCAA
Found at i:29074 original size:25 final size:25
Alignment explanation
Indices: 29040--29098 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
29030 TACTTTAAAC
29040 CGAGTGCCCGAATTGTCTTCAATTT
1 CGAGTGCCCGAATTGTCTTCAATTT
29065 CGAGTGCCCGAATTGTCTTCAATTT
1 CGAGTGCCCGAATTGTCTTCAATTT
*
29090 CGACTGCCC
1 CGAGTGCCC
29099 CATGAGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.32
Consensus pattern (25 bp):
CGAGTGCCCGAATTGTCTTCAATTT
Found at i:44621 original size:14 final size:15
Alignment explanation
Indices: 44598--44632 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
44588 TTTCTATTAT
*
44598 TTTTAATTCATAAA-
1 TTTTATTTCATAAAG
44612 TTTTATTTCATAAAG
1 TTTTATTTCATAAAG
44627 TTTTAT
1 TTTTAT
44633 CACAAATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (15 bp):
TTTTATTTCATAAAG
Found at i:45124 original size:61 final size:58
Alignment explanation
Indices: 44952--45125 Score: 158
Period size: 57 Copynumber: 3.0 Consensus size: 58
44942 AATATATGCG
* * *
44952 TATTTATAGGTACCAAGAAATG-AGAAATGTAAATA-TTAGACCGATATAAGTATGTATT
1 TATTTATAGGTACCAA-AAATGAAGAAATATAAATACTTACA-CGATATAAATATGTATT
* * * * *
45010 TATTTATAAGTA-CAAAAAT-AAGAAATATACATGCTTACACTAATGTAAATATGTATT
1 TATTTATAGGTACCAAAAATGAAGAAATATAAATACTTACAC-GATATAAATATGTATT
* * * *
45067 TATTTATAGGTACCCGAAAAATGAAAAAATATATATACTTATATCGATATAATTATGTA
1 TATTTATAGGTA-CC-AAAAATGAAGAAATATAAATACTTACA-CGATATAAATATGTA
45126 CAAAATAATG
Statistics
Matches: 92, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
56 15 0.16
57 31 0.34
58 11 0.12
59 1 0.01
60 6 0.07
61 27 0.29
62 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.34
Consensus pattern (58 bp):
TATTTATAGGTACCAAAAATGAAGAAATATAAATACTTACACGATATAAATATGTATT
Found at i:46138 original size:40 final size:40
Alignment explanation
Indices: 46062--46141 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
46052 TTACCTAAGT
*
46062 TACAAAAAATTATGATTCTGCATATCATATGTGTGATTAA
1 TACAAAAAATTATGATTCTGCATATCATATGCGTGATTAA
46102 TACAAAAAATTATGATTCTGCATATCATATGCGTGATTAA
1 TACAAAAAATTATGATTCTGCATATCATATGCGTGATTAA
46142 CCCTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (40 bp):
TACAAAAAATTATGATTCTGCATATCATATGCGTGATTAA
Found at i:48551 original size:39 final size:39
Alignment explanation
Indices: 48428--48540 Score: 147
Period size: 39 Copynumber: 2.9 Consensus size: 39
48418 CCTGTACACC
* * * *
48428 AGTAAGGGCTTACCATGTACACAAAGTAGTGGAGCCTGT
1 AGTAAGGTCTTATCATGTGCACAAAGTAGAGGAGCCTGT
* *
48467 AGTAAGGTCTTATCATGTGCACAAAGTAGAGTAGCCTAT
1 AGTAAGGTCTTATCATGTGCACAAAGTAGAGGAGCCTGT
*
48506 AGTAAGGTCTTAT-ATGATGCGCAAAGTAGAGGAGC
1 AGTAAGGTCTTATCATG-TGCACAAAGTAGAGGAGC
48541 ATGCGGTAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
38 3 0.05
39 62 0.95
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (39 bp):
AGTAAGGTCTTATCATGTGCACAAAGTAGAGGAGCCTGT
Found at i:55235 original size:15 final size:15
Alignment explanation
Indices: 55217--55249 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
55207 TCTTTCAATT
55217 TATGTTATACACAAA
1 TATGTTATACACAAA
55232 TATGTTATACACAAA
1 TATGTTATACACAAA
55247 TAT
1 TAT
55250 ATAACTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (15 bp):
TATGTTATACACAAA
Found at i:64410 original size:3 final size:3
Alignment explanation
Indices: 64397--64430 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
64387 GTCGCTTCAC
*
64397 TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
64431 ACAAGGACGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:65450 original size:31 final size:31
Alignment explanation
Indices: 65394--65468 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 31
65384 TGGGGCTTGC
65394 GAGCCTACCCAAGAAAATTCTCAGGGCCACGGA
1 GAGCCTACCCAAGAAAATTCTCAGGG-C-CGGA
*
65427 G-GCCTACCCAAGAAAA-TCTCAGGGCCGTA
1 GAGCCTACCCAAGAAAATTCTCAGGGCCGGA
65456 GAGCCTACCCAAG
1 GAGCCTACCCAAG
65469 CGCAGTCTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 4 0.10
30 12 0.30
31 8 0.20
32 15 0.38
33 1 0.03
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (31 bp):
GAGCCTACCCAAGAAAATTCTCAGGGCCGGA
Found at i:66590 original size:27 final size:27
Alignment explanation
Indices: 66533--66590 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
66523 ACTTTAAGCC
* * *
66533 ATTTTACACTTTAAGGGTATTTTGGTC
1 ATTTTACACTTTAAGGGCATTTTGATA
*
66560 ATTTTACACTTTAGGGGCATTATT-ATA
1 ATTTTACACTTTAAGGGCATT-TTGATA
66587 ATTT
1 ATTT
66591 ATCCATGGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (27 bp):
ATTTTACACTTTAAGGGCATTTTGATA
Found at i:68591 original size:24 final size:24
Alignment explanation
Indices: 68564--68636 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
68554 CAGAAATTAG
*
68564 AACAAAATTCAGATCATATATCAT
1 AACAAAATTCAGATCAGATATCAT
* * *
68588 AACAGAATTCATATTAGATATCAT
1 AACAAAATTCAGATCAGATATCAT
* * * * *
68612 AATAGAATCCGGATCAGAAATCAT
1 AACAAAATTCAGATCAGATATCAT
68636 A
1 A
68637 TAAAATATTC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (24 bp):
AACAAAATTCAGATCAGATATCAT
Found at i:70746 original size:24 final size:24
Alignment explanation
Indices: 70700--70746 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
70690 ATAAGATATC
* *
70700 ATAATAGAATCTGGATCAGAAATA
1 ATAATAGAATCTGGATAAAAAATA
70724 ATAATAGAAATC-GGATAAAAAAT
1 ATAATAG-AATCTGGATAAAAAAT
70747 TCATGTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.55, C:0.06, G:0.15, T:0.23
Consensus pattern (24 bp):
ATAATAGAATCTGGATAAAAAATA
Found at i:71553 original size:27 final size:27
Alignment explanation
Indices: 71496--71553 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
71486 ACTTTAAGCT
* *
71496 ATTTTACACTTTAGGGGTATTTTGGTC
1 ATTTTACACTTTAGGGGCATTTTGGTA
71523 ATTTTACACTTTAGGGGCATTATT-GTA
1 ATTTTACACTTTAGGGGCATT-TTGGTA
71550 ATTT
1 ATTT
71554 ATGCATGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.22, C:0.10, G:0.19, T:0.48
Consensus pattern (27 bp):
ATTTTACACTTTAGGGGCATTTTGGTA
Done.