Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005476.1 Hibiscus syriacus cultivar Beakdansim tig00012561_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: 65958
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:11006 original size:45 final size:45
Alignment explanation
Indices: 10946--11135 Score: 274
Period size: 45 Copynumber: 4.2 Consensus size: 45
10936 ACTGGTGGTA
* * * * * * *
10946 GTGGGGGTGGGGACTTGTATTTATAATGGTGCTTGGGCGGTGATG
1 GTGGCGGTGGAGACTTGTACTTGTGAGGGTGCTTGGGTGGTGATG
*
10991 GTGGAGGTGGAGACTTGTACTTGT-ATGGGTGCTTGGGTGGTGATG
1 GTGGCGGTGGAGACTTGTACTTGTGA-GGGTGCTTGGGTGGTGATG
*
11036 GTGGTGGTGGAGACTTGTACTTGTGAGGGTGCTTGGGTGGTGATG
1 GTGGCGGTGGAGACTTGTACTTGTGAGGGTGCTTGGGTGGTGATG
11081 GTGGCGGTGGAGACTTGTACTTGTGAGGGTGCTTGGGTGGTGATG
1 GTGGCGGTGGAGACTTGTACTTGTGAGGGTGCTTGGGTGGTGATG
*
11126 ATGGCGGTGG
1 GTGGCGGTGG
11136 GGGAGACTTA
Statistics
Matches: 134, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
44 1 0.01
45 132 0.99
46 1 0.01
ACGTcount: A:0.12, C:0.07, G:0.48, T:0.32
Consensus pattern (45 bp):
GTGGCGGTGGAGACTTGTACTTGTGAGGGTGCTTGGGTGGTGATG
Found at i:11361 original size:27 final size:27
Alignment explanation
Indices: 11323--11377 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
11313 TGATAATGAC
11323 CTGGTGGAGGAGGTGGAGACTTATAAA
1 CTGGTGGAGGAGGTGGAGACTTATAAA
11350 CTGGTGGAGGAGGTGGAGACTTATAAA
1 CTGGTGGAGGAGGTGGAGACTTATAAA
11377 C
1 C
11378 AGGAGTTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.09, G:0.40, T:0.22
Consensus pattern (27 bp):
CTGGTGGAGGAGGTGGAGACTTATAAA
Found at i:15766 original size:21 final size:22
Alignment explanation
Indices: 15745--15786 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
15735 TAGATTGCTC
15745 AGAGGGAATCGATTCCCCCTCA
1 AGAGGGAATCGATTCCCCCTCA
* *
15767 AGGGGGTATCGATTCCCCCT
1 AGAGGGAATCGATTCCCCCT
15787 GAATGGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.31, G:0.26, T:0.21
Consensus pattern (22 bp):
AGAGGGAATCGATTCCCCCTCA
Found at i:15858 original size:21 final size:21
Alignment explanation
Indices: 15827--15880 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
15817 CTCGGAGGGA
*
15827 ACCGATCCCCCCCAAGGAGGT
1 ACCGATTCCCCCCAAGGAGGT
* *
15848 ATCGATTCCCCCCAAGGGGGT
1 ACCGATTCCCCCCAAGGAGGT
15869 ACCGATTCCCCC
1 ACCGATTCCCCC
15881 TGTTTAACAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.43, G:0.22, T:0.15
Consensus pattern (21 bp):
ACCGATTCCCCCCAAGGAGGT
Found at i:25404 original size:14 final size:16
Alignment explanation
Indices: 25373--25404 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25363 CAAGCTAACT
25373 AAGATTGGATTGCTTG
1 AAGATTGGATTGCTTG
25389 AAGATTGG-TT-CTTG
1 AAGATTGGATTGCTTG
25403 AA
1 AA
25405 AAGAAGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 2 0.12
16 8 0.50
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.38
Consensus pattern (16 bp):
AAGATTGGATTGCTTG
Found at i:29691 original size:29 final size:29
Alignment explanation
Indices: 29648--29730 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
29638 CTCACCTAAC
29648 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
29678 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
29707 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
29731 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:34458 original size:29 final size:29
Alignment explanation
Indices: 34415--34497 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
34405 CTCACCTAAC
34415 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
34445 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
34474 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
34498 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:36021 original size:26 final size:26
Alignment explanation
Indices: 35952--36029 Score: 70
Period size: 30 Copynumber: 2.8 Consensus size: 26
35942 TGAATATAAC
35952 AAATAAATATAATAATAAT-AATAATTA
1 AAATAAA-ATAAT-ATAATAAATAATTA
* *
35979 ATATTAATTATTAAATATAATAAATAATTA
1 A-AATAA--AAT-AATATAATAAATAATTA
36009 AAATAAAATAATAT-ATAAATA
1 AAATAAAATAATATAATAAATA
36030 TAGTAATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
25 7 0.17
26 5 0.12
27 3 0.07
28 4 0.10
29 10 0.24
30 13 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
AAATAAAATAATATAATAAATAATTA
Found at i:48764 original size:14 final size:14
Alignment explanation
Indices: 48745--48773 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
48735 TACTTGATCT
48745 AATTATTATTAAAA
1 AATTATTATTAAAA
48759 AATTATTATTAAAA
1 AATTATTATTAAAA
48773 A
1 A
48774 TAAGATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTATTATTAAAA
Found at i:56767 original size:2 final size:2
Alignment explanation
Indices: 56760--56788 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
56750 AGAAAGTAAG
56760 AT 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 AT A
56789 CATACGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57238 original size:43 final size:43
Alignment explanation
Indices: 57177--57262 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
57167 TTAAATATTA
57177 ATGACAAGTGGCTTAATTAAATGTATTTAAATAGTTGAGTGGC
1 ATGACAAGTGGCTTAATTAAATGTATTTAAATAGTTGAGTGGC
57220 ATGACAAGTGGCTTAATTAAATGTATTTAAATAGTTGAGTGGC
1 ATGACAAGTGGCTTAATTAAATGTATTTAAATAGTTGAGTGGC
57263 CTGAATGACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (43 bp):
ATGACAAGTGGCTTAATTAAATGTATTTAAATAGTTGAGTGGC
Done.