Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006850.1 Hibiscus syriacus cultivar Beakdansim tig00017420_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: 61000
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:13739 original size:6 final size:6
Alignment explanation
Indices: 13730--13754 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13720 TTTTTCAACA
13730 AGCAAT AGCAAT AGCAAT AGCAAT A
1 AGCAAT AGCAAT AGCAAT AGCAAT A
13755 TCATCTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AGCAAT
Found at i:16509 original size:3 final size:3
Alignment explanation
Indices: 16493--16527 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
16483 CAGAAGCTTA
16493 TCT TCTT TCTT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TC-T TC-T TCT TCT TCT TCT TCT TCT TCT TCT
16528 CGTGGCTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 24 0.77
4 7 0.23
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:17270 original size:2 final size:2
Alignment explanation
Indices: 17263--17293 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17253 ATACTGATAG
17263 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 T
17294 GATTGTGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20038 original size:20 final size:22
Alignment explanation
Indices: 20013--20069 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
20003 ATTTAAAGTA
20013 GGTATCGGTACACTCT-A-TAG
1 GGTATCGGTACACTCTCACTAG
* * *
20033 GGTATCGATACATCCCTCACTGG
1 GGTATCGGTACA-CTCTCACTAG
20056 GGTATCGGTACACT
1 GGTATCGGTACACT
20070 GCCTGTGTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 11 0.38
21 3 0.10
22 2 0.07
23 13 0.45
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (22 bp):
GGTATCGGTACACTCTCACTAG
Found at i:22333 original size:64 final size:64
Alignment explanation
Indices: 22265--22485 Score: 259
Period size: 64 Copynumber: 3.5 Consensus size: 64
22255 TTGAAGGTGT
** **
22265 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTTGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTTGTG
22328 C
64 C
** *
22329 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGC
* * * * * *
22393 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTATGC
1 ATCGATGCATAA-GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGC
* *
22457 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
22486 ACCTTCATTA
Statistics
Matches: 134, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
63 2 0.01
64 125 0.93
65 7 0.05
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGC
Found at i:23462 original size:103 final size:103
Alignment explanation
Indices: 23237--23454 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
23227 GTCGATGGTC
*
23237 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
* *
23302 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
23340 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
*
23405 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
23443 TATGTGGTCCTT
1 TATGTGGTCCTT
23455 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:23538 original size:23 final size:23
Alignment explanation
Indices: 23478--23538 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
23468 TATGGAACTA
*
23478 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTCTATGCGGCACTC
* * *
23501 CGGTGTAATTCTATGTGGCACTT
1 CGGTGCAATTCTATGCGGCACTC
*
23524 CGGTGCAATTATATG
1 CGGTGCAATTCTATG
23539 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (23 bp):
CGGTGCAATTCTATGCGGCACTC
Found at i:28342 original size:64 final size:64
Alignment explanation
Indices: 28273--28481 Score: 253
Period size: 64 Copynumber: 3.3 Consensus size: 64
28263 CGATGTATTG
**
28273 GTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTTGTGCATCGATGCATA
1 GTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTTGTGCATCGATGCATA
28336 A
64 A
** *
28337 GTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTAGTGCATCGATGCATAA
1 GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGCATCGATGCATAA
* * * * * * * *
28401 GGCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTATGCACCGATGCATCA
1 -GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGCATCGATGCATAA
28465 GTAGTGCATCGATGCAT
1 GTAGTGCATCGATGCAT
28482 ACATTCATTA
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
63 2 0.02
64 115 0.93
65 7 0.06
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (64 bp):
GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGCATCGATGCATAA
Found at i:29459 original size:103 final size:103
Alignment explanation
Indices: 29234--29451 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
29224 GTCGATGGTC
*
29234 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
* *
29299 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
29337 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
*
29402 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
29440 TATGTGGTCCTT
1 TATGTGGTCCTT
29452 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:29501 original size:23 final size:23
Alignment explanation
Indices: 29468--29530 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
29458 ATTATTATAT
29468 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGTAATTCTACGC
* * *
29491 GGCACTCCGGTGTAATTCTATGT
1 GGCACTACGGTGTAATTCTACGC
* *
29514 GGCACTTCGGTGCAATT
1 GGCACTACGGTGTAATT
29531 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.30
Consensus pattern (23 bp):
GGCACTACGGTGTAATTCTACGC
Found at i:29535 original size:23 final size:23
Alignment explanation
Indices: 29458--29535 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
29448 CCTTATGGAC
*
29458 ATTATTATATGGCACTACGGTGTA
1 ATTA-TATGTGGCACTACGGTGTA
* * * *
29482 ATTCTACGCGGCACTCCGGTGTA
1 ATTATATGTGGCACTACGGTGTA
* * *
29505 ATTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGTA
29528 ATTATATG
1 ATTATATG
29536 AGCTGTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGTA
Found at i:32415 original size:23 final size:23
Alignment explanation
Indices: 32380--32424 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
32370 TAAACATGTA
32380 CACATATCATCATTATT-CTATT
1 CACATATCATCATTATTACTATT
*
32402 CACATTATTATCATTATTACTAT
1 CACA-TATCATCATTATTACTAT
32425 CATTAATCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (23 bp):
CACATATCATCATTATTACTATT
Found at i:39066 original size:82 final size:82
Alignment explanation
Indices: 38980--39152 Score: 220
Period size: 82 Copynumber: 2.1 Consensus size: 82
38970 GTGTTTATTG
* ** * * *
38980 AAAAAAGTCACTATAGATGAACTTATTGTGGCGTTTGTATAAAAACGCCGCCAAAGTGCTACTTT
1 AAAAAAGCCACTATAGATGAACTTATTACGGCATTTGTATAAAAACGCCGCCAAAGTACTACTCT
*
39045 GTTGCGTCGTTTGTCAA
66 GTTGCGGCGTTTGTCAA
* * * *
39062 AAAAATGCCACTATAGATGGACTTATTACGGCATTTGTATAAAAACGCCTCTAAAGTACTACTCT
1 AAAAAAGCCACTATAGATGAACTTATTACGGCATTTGTATAAAAACGCCGCCAAAGTACTACTCT
* *
39127 GTTGTGGCGTTTGTCGA
66 GTTGCGGCGTTTGTCAA
*
39144 AGAAAAGCC
1 AAAAAAGCC
39153 GCTAACATTA
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (82 bp):
AAAAAAGCCACTATAGATGAACTTATTACGGCATTTGTATAAAAACGCCGCCAAAGTACTACTCT
GTTGCGGCGTTTGTCAA
Found at i:39140 original size:41 final size:40
Alignment explanation
Indices: 39000--39140 Score: 97
Period size: 41 Copynumber: 3.5 Consensus size: 40
38990 CTATAGATGA
* * * * *
39000 ACTTATTGTGGCGTTTGTATAAAAACGCCGCCAAAGTGCT
1 ACTTGTTGCGGCGTTTGTATAAAAACGCCACTAAAGTACT
* * * *
39040 ACTTTGTTGCGTCGTTTGTCAAAAAAATGCCACTATAG-A-T
1 AC-TTGTTGCGGCGTTTGT-ATAAAAACGCCACTAAAGTACT
* * * *
39080 GGACTTATTACGGCATTTGTATAAAAACGCCTCTAAAGTACT
1 --ACTTGTTGCGGCGTTTGTATAAAAACGCCACTAAAGTACT
*
39122 ACTCTGTTGTGGCGTTTGT
1 ACT-TGTTGCGGCGTTTGT
39141 CGAAGAAAAG
Statistics
Matches: 73, Mismatches: 21, Indels: 13
0.68 0.20 0.12
Matches are distributed among these distances:
40 20 0.27
41 37 0.51
42 16 0.22
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (40 bp):
ACTTGTTGCGGCGTTTGTATAAAAACGCCACTAAAGTACT
Found at i:49286 original size:15 final size:15
Alignment explanation
Indices: 49266--49332 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
49256 AATGGATTTG
49266 TAATTTTTTAATACT
1 TAATTTTTTAATACT
*
49281 TAATTTTATTTAAGACT
1 TAA-TTT-TTTAATACT
* * * *
49298 TTACTTTTTAGTATT
1 TAATTTTTTAATACT
* *
49313 TAGTATTTTAATACT
1 TAATTTTTTAATACT
49328 TAATT
1 TAATT
49333 ATTATAAATT
Statistics
Matches: 36, Mismatches: 14, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
15 21 0.58
16 5 0.14
17 10 0.28
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.58
Consensus pattern (15 bp):
TAATTTTTTAATACT
Found at i:54981 original size:16 final size:16
Alignment explanation
Indices: 54957--54990 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
54947 TATCCCCGAC
*
54957 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
54973 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
54989 CG
1 CG
54991 TGGATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:59478 original size:18 final size:18
Alignment explanation
Indices: 59455--59490 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
59445 TTTTTTTTTA
59455 ATATGGTCAATATAGCTT
1 ATATGGTCAATATAGCTT
59473 ATATGGTCAATATAGCTT
1 ATATGGTCAATATAGCTT
59491 TATAGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (18 bp):
ATATGGTCAATATAGCTT
Done.