Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009055.1 Hibiscus syriacus cultivar Beakdansim tig00112470_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: 451578
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:412254 original size:14 final size:14
Alignment explanation
Indices: 412231--412268 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
412221 TCTGTCTATA
*
412231 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
412244 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
412259 TGCAGGGATT
1 TGCAGGGATT
412269 ACTGCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:417225 original size:16 final size:16
Alignment explanation
Indices: 417204--417265 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
417194 TTGCTCGATT
* *
417204 GTTGCTCTTTAAGCTC
1 GTTGCTCGTTAAGCCC
*
417220 GTTGCTCGTTAATCCC
1 GTTGCTCGTTAAGCCC
417236 GTTGCTCGTTAAGCCC
1 GTTGCTCGTTAAGCCC
*
417252 GTTGCTCATTAAGC
1 GTTGCTCGTTAAGC
417266 TCACTGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.37
Consensus pattern (16 bp):
GTTGCTCGTTAAGCCC
Found at i:418330 original size:26 final size:25
Alignment explanation
Indices: 418271--418327 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
418261 TATGTTCTTT
* *
418271 TAATTAATTTATTTAAAAATATATA
1 TAATTAATTGATTTAAAAATATAAA
*
418296 TAATTAATTGATTTTAAAATACTAAA
1 TAATTAATTGATTTAAAAATA-TAAA
418322 T-ATTAA
1 TAATTAA
418328 ATTTAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
TAATTAATTGATTTAAAAATATAAA
Found at i:425041 original size:20 final size:20
Alignment explanation
Indices: 425016--425063 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
425006 AAAAGTGAAA
*
425016 TAAAATAATA-TATACAAATG
1 TAAAATAATAGCATACAAA-G
*
425036 TAAAATAATAGCGTACAAAG
1 TAAAATAATAGCATACAAAG
425056 TAAAATAA
1 TAAAATAA
425064 ATAAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.25
Consensus pattern (20 bp):
TAAAATAATAGCATACAAAG
Found at i:425235 original size:2 final size:2
Alignment explanation
Indices: 425223--425265 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
425213 ATACAAAATG
*
425223 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
425264 TA
1 TA
425266 ACATATAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:425273 original size:12 final size:14
Alignment explanation
Indices: 425223--425272 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
425213 ATACAAAATG
425223 TATACATATATATA
1 TATACATATATATA
*
425237 TATATATATATATA
1 TATACATATATATA
*
425251 TATATATATA-ATA
1 TATACATATATATA
425264 TA-ACATATA
1 TATACATATA
425273 AGTAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
12 6 0.18
13 5 0.15
14 23 0.68
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
TATACATATATATA
Found at i:425768 original size:20 final size:19
Alignment explanation
Indices: 425729--425769 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
425719 AGCGCCGCCT
*
425729 CGCCGCCGTCGTTGAACGG
1 CGCCGCCGTCGTTCAACGG
*
425748 CGCCGGCCGTCGTTCATCGG
1 CGCC-GCCGTCGTTCAACGG
425768 CG
1 CG
425770 ACGAACCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.07, C:0.39, G:0.37, T:0.17
Consensus pattern (19 bp):
CGCCGCCGTCGTTCAACGG
Found at i:427160 original size:105 final size:105
Alignment explanation
Indices: 426966--427741 Score: 1302
Period size: 105 Copynumber: 7.4 Consensus size: 105
426956 GTATTGTTCC
* * * *
426966 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGTTCTGGAACTGGA-AAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAATTTGAGAAA-TGTTTGTTGACA
* * *
427030 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
427072 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
427137 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
427177 GAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
427242 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
427282 GAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
427347 CAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
427387 GAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGAGACATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
427452 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
427492 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAGTTGAGAAATGGTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
427557 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
427597 GAGTCCAATATCCTTCGTTGTGAAGTTGAAACTGTCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
427662 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
427702 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
427742 GGTAAAACCT
Statistics
Matches: 636, Mismatches: 33, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
105 596 0.94
106 40 0.06
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:428572 original size:11 final size:11
Alignment explanation
Indices: 428553--428584 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
428543 CTAAACGTTC
*
428553 TTTTCTTTTCT
1 TTTTTTTTTCT
428564 TTTTTTTTTCT
1 TTTTTTTTTCT
428575 TTTTTTTTTC
1 TTTTTTTTTC
428585 AACTTAGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:428574 original size:16 final size:15
Alignment explanation
Indices: 428553--428583 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
428543 CTAAACGTTC
428553 TTTTCTTTTCTTTTTT
1 TTTTCTTTT-TTTTTT
428569 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
428584 CAACTTAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:439430 original size:2 final size:2
Alignment explanation
Indices: 439418--439458 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
439408 ATACAAAATG
*
439418 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
439459 ACATATAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:439464 original size:12 final size:13
Alignment explanation
Indices: 439418--439466 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
439408 ATACAAAATG
439418 TATACATAT-ATA
1 TATACATATAATA
*
439430 TATATATATATATA
1 TATACATATA-ATA
*
439444 TATATATATAATA
1 TATACATATAATA
439457 TA-ACATATAA
1 TATACATATAA
439467 GTAAAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 15 0.45
13 5 0.15
14 13 0.39
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (13 bp):
TATACATATAATA
Found at i:439959 original size:20 final size:19
Alignment explanation
Indices: 439920--439960 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
439910 AGCGCCGCCT
*
439920 CGCCGCCGTCGTTGAACGG
1 CGCCGCCGTCGTTCAACGG
*
439939 CGCCGGCCGTCGTTCATCGG
1 CGCC-GCCGTCGTTCAACGG
439959 CG
1 CG
439961 ACGAACCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.07, C:0.39, G:0.37, T:0.17
Consensus pattern (19 bp):
CGCCGCCGTCGTTCAACGG
Found at i:441093 original size:2 final size:2
Alignment explanation
Indices: 441086--441123 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
441076 TTCTTCTTCT
441086 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
441124 GTTTCACTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:441488 original size:21 final size:21
Alignment explanation
Indices: 441464--441503 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
441454 GATTAAATGA
441464 TAAA-AAAATATTATAATTTTT
1 TAAATAAAATATTA-AATTTTT
*
441485 TAAATAAAATTTTAAATTT
1 TAAATAAAATATTAAATTT
441504 AAATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAATAAAATATTAAATTTTT
Found at i:442184 original size:2 final size:2
Alignment explanation
Indices: 442179--442211 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
442169 TCTCTCTCTC
442179 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
442212 TCTTTCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:449964 original size:19 final size:18
Alignment explanation
Indices: 449931--449984 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
449921 AAGAAATAAT
449931 TTTTTATTAAAATTTTATA
1 TTTTTATT-AAATTTTATA
*
449950 TTCATTTA-TAAATTTAATA
1 TT--TTTATTAAATTTTATA
449969 TTTTTATTAAATTTTA
1 TTTTTATTAAATTTTA
449985 AAAAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 4 0.13
18 8 0.27
19 13 0.43
20 1 0.03
21 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTATTAAATTTTATA
Found at i:450373 original size:16 final size:16
Alignment explanation
Indices: 450352--450390 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
450342 GTAATTTCGG
*
450352 TTTGGTTCGGGTTAAT
1 TTTGGTTCGAGTTAAT
* *
450368 TTTGGTTCTAGTTGAT
1 TTTGGTTCGAGTTAAT
450384 TTTGGTT
1 TTTGGTT
450391 TCGCTGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.10, C:0.05, G:0.28, T:0.56
Consensus pattern (16 bp):
TTTGGTTCGAGTTAAT
Found at i:451096 original size:2 final size:2
Alignment explanation
Indices: 451089--451115 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
451079 AATAATAAGA
451089 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
451116 GGTGGTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.