Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001880.1 Hibiscus syriacus cultivar Beakdansim tig00003817_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: 64335
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:370 original size:35 final size:35
Alignment explanation
Indices: 328--396 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
318 TGACACTAAC
328 TTTGAAAAATATTTTTC-AAGTTTGATAAATGTTTA
1 TTTGAAAAATATTTTTCAAAGTTTGATAAA-GTTTA
* *
363 TTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
1 TTTGAAAAATATTTTTCAAAGTTTGATAAAGTTT
397 GGTAGATGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.48
Consensus pattern (35 bp):
TTTGAAAAATATTTTTCAAAGTTTGATAAAGTTTA
Found at i:4886 original size:40 final size:39
Alignment explanation
Indices: 4841--4952 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 39
4831 TGGCAACCAA
4841 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTTTTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATG-TTTTTT
* *
4881 TTTTGAAAAATATTTTTCAAAGTTTGGTAAATG---TTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTTTTT
* *
4917 CTTTGAAAAATGTTTTACAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
4953 GTTGAAAATA
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
36 32 0.51
40 31 0.49
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.49
Consensus pattern (39 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTTTTT
Found at i:8225 original size:26 final size:26
Alignment explanation
Indices: 8191--8245 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
8181 AATAATATTA
8191 TTTATATGCTGACAATCATTCTTAAT
1 TTTATATGCTGACAATCATTCTTAAT
*
8217 TTTATATGCTGACAATTATTCTTAAT
1 TTTATATGCTGACAATCATTCTTAAT
8243 TTT
1 TTT
8246 TTAAACTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.13, G:0.07, T:0.51
Consensus pattern (26 bp):
TTTATATGCTGACAATCATTCTTAAT
Found at i:8883 original size:2 final size:2
Alignment explanation
Indices: 8876--8907 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8866 GTTACTAAAA
8876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8908 TATTTTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9981 original size:60 final size:60
Alignment explanation
Indices: 9847--9988 Score: 169
Period size: 60 Copynumber: 2.4 Consensus size: 60
9837 ATATCCTCAG
* * * * * *
9847 ACTATGACTCTCATTTTAAATTGGTCCTTAAACTTTTAAATATTCTAATTTCATTCATAA
1 ACTATGACTCTCATTTTAAATTAGTCATTAAACTTTGAAAAATTCTAATTTCATACACAA
* *
9907 ACTATGACTATCATTTTAAATTAGTCATTAAACGTTTGAAAAATTC-AATTTCATACCCAA
1 ACTATGACTCTCATTTTAAATTAGTCATTAAAC-TTTGAAAAATTCTAATTTCATACACAA
* * *
9967 ACTATGTCCCTCATTCTAAATT
1 ACTATGACTCTCATTTTAAATT
9989 GATCCCCAAA
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
60 59 0.86
61 10 0.14
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (60 bp):
ACTATGACTCTCATTTTAAATTAGTCATTAAACTTTGAAAAATTCTAATTTCATACACAA
Found at i:21860 original size:51 final size:51
Alignment explanation
Indices: 21801--21901 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
21791 TCAGGGGGAG
* *
21801 AGTTACAAGGAATTTCAGCCTGTTCAAACCGATATTTCTTTATAGCCTATT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCTATT
*
21852 AGTTACAAGGAATTTCAACCTGTTCAAATCGATATTTCTTTACAGCCTAT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCTAT
21902 CATTTTCTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (51 bp):
AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCTATT
Found at i:24133 original size:16 final size:16
Alignment explanation
Indices: 24112--24142 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
24102 TAACAGACTT
24112 GTCTGTTTTCTACACA
1 GTCTGTTTTCTACACA
24128 GTCTGTTTTCTACAC
1 GTCTGTTTTCTACAC
24143 TTTCATCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.26, G:0.13, T:0.45
Consensus pattern (16 bp):
GTCTGTTTTCTACACA
Found at i:41536 original size:16 final size:16
Alignment explanation
Indices: 41502--41544 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
41492 GAGTGGAAAC
* * *
41502 AAAATTGGAAAGTTTG
1 AAAATTAGAAAGATAG
41518 AAAATTAGAAAGATAG
1 AAAATTAGAAAGATAG
*
41534 AAAACTAGAAA
1 AAAATTAGAAA
41545 AAAATATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.58, C:0.02, G:0.19, T:0.21
Consensus pattern (16 bp):
AAAATTAGAAAGATAG
Found at i:45384 original size:22 final size:22
Alignment explanation
Indices: 45354--45404 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
45344 CTATATTTCC
* * *
45354 CATCT-AAAATCACTTGATCTA
1 CATCTCAAAATAACATGAACTA
45375 CATCTCAAAATAACATGAACTA
1 CATCTCAAAATAACATGAACTA
*
45397 CTTCTCAA
1 CATCTCAA
45405 TGTTGCTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.41, C:0.25, G:0.04, T:0.29
Consensus pattern (22 bp):
CATCTCAAAATAACATGAACTA
Found at i:47979 original size:2 final size:2
Alignment explanation
Indices: 47972--47998 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47962 AAATAGAAAA
47972 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
47999 AGCCTAAAAA
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
Found at i:52311 original size:12 final size:12
Alignment explanation
Indices: 52294--52358 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 12
52284 ATTATTTAAA
52294 AGGTATTGGGCC
1 AGGTATTGGGCC
*
52306 AGGTATTGGGTC
1 AGGTATTGGGCC
* *
52318 GGGTATTGGGTC
1 AGGTATTGGGCC
*
52330 -GGTATTGGGCT
1 AGGTATTGGGCC
* *
52341 AGGAATCGGGCC
1 AGGTATTGGGCC
*
52353 GGGTAT
1 AGGTAT
52359 ATATATATAT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
11 9 0.21
12 34 0.79
ACGTcount: A:0.15, C:0.12, G:0.45, T:0.28
Consensus pattern (12 bp):
AGGTATTGGGCC
Found at i:52335 original size:11 final size:12
Alignment explanation
Indices: 52294--52338 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
52284 ATTATTTAAA
*
52294 AGGTATTGGGCC
1 AGGTATTGGGTC
52306 AGGTATTGGGTC
1 AGGTATTGGGTC
*
52318 GGGTATTGGGTC
1 AGGTATTGGGTC
52330 -GGTATTGGG
1 AGGTATTGGG
52339 CTAGGAATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.29
12 22 0.71
ACGTcount: A:0.13, C:0.09, G:0.47, T:0.31
Consensus pattern (12 bp):
AGGTATTGGGTC
Found at i:52426 original size:24 final size:25
Alignment explanation
Indices: 52361--52426 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 25
52351 CCGGGTATAT
52361 ATATATATATATATATATTTAAATTAA
1 ATATATAT-TATAT-TATTTAAATTAA
*
52388 ATATATATT-TTTTATTTAAATTAA
1 ATATATATTATATTATTTAAATTAA
52412 AT-T-TATTAATATTAT
1 ATATATATT-ATATTAT
52427 ATATATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
22 4 0.11
23 1 0.03
24 19 0.54
25 2 0.06
26 1 0.03
27 8 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATATATTATATTATTTAAATTAA
Found at i:52598 original size:12 final size:13
Alignment explanation
Indices: 52583--52611 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
52573 TTTATCAGGT
52583 CGGGT-ATCGGGG
1 CGGGTAATCGGGG
52595 CGGGTAATCGGGG
1 CGGGTAATCGGGG
52608 CGGG
1 CGGG
52612 GATTACCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.10, C:0.17, G:0.59, T:0.14
Consensus pattern (13 bp):
CGGGTAATCGGGG
Found at i:56170 original size:2 final size:2
Alignment explanation
Indices: 56163--56192 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
56153 AAACTAGGGG
56163 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56193 TATCATGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57178 original size:32 final size:32
Alignment explanation
Indices: 57109--57198 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 32
57099 GACGTGATAC
* * * * *
57109 ATGTTATGTCATTTAAAGTGATGACATGTTAT
1 ATGTCATGTCACTTAAAATGATGATATGTCAT
*
57141 ATGTCATGTCACTTAAAATGATGATGTGTCAT
1 ATGTCATGTCACTTAAAATGATGATATGTCAT
* ** *
57173 GTGTCACATCAC-CAAAATGATGATAT
1 ATGTCATGTCACTTAAAATGATGATAT
57199 CACGCGTGTA
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
31 12 0.26
32 35 0.74
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
ATGTCATGTCACTTAAAATGATGATATGTCAT
Found at i:57871 original size:14 final size:15
Alignment explanation
Indices: 57847--57893 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
57837 AGTTTAAGAA
57847 TTTAA-ATTTTAGAT
1 TTTAATATTTTAGAT
57861 TTTAATA-TTTAGA-
1 TTTAATATTTTAGAT
*
57874 TTTAATATTTTAAAT
1 TTTAATATTTTAGAT
57889 TTTAA
1 TTTAA
57894 GATTCAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 7 0.24
14 16 0.55
15 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (15 bp):
TTTAATATTTTAGAT
Done.