Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003822.1 Hibiscus syriacus cultivar Beakdansim tig00008196_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: 68110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1001 original size:150 final size:149
Alignment explanation
Indices: 824--1101 Score: 481
Period size: 150 Copynumber: 1.9 Consensus size: 149
814 CCCCCCCCCC
824 CCCCGCCGAGAGGATCCCCTTCCCCCTTTTGATGGGTTCTCCC-A-AATAATAAAATGTTGCTGA
1 CCCCGCCGAGAGGATCCCCTTCCCCCTTTTGATGGGTTCTCCCAATAATAATAAAATG-TG-TGA
*
887 TCTCTTTTGCTTACTATTTTGGTTTTACTGGAACAAGGATGGCATGGTAGCAGGGAGATCTTACT
64 TCTC-TTTGCTTACTATTTAGGTTTTACTGGAACAAGGATGGCATGGTAGCAGGGAGATC-TACT
952 GGCTCTTACAATTTTTTTCTTCT
127 GGCTCTTACAATTTTTTTCTTCT
975 CCCC-CCGAGAGGATCCCCTTCCCCCTTTTGATGGGTTCTCCCAAATAATAATAAAATGTGTGAT
1 CCCCGCCGAGAGGATCCCCTTCCCCCTTTTGATGGGTTCTCCC-AATAATAATAAAATGTGTGAT
1039 CTCTTTGCTTACTATTTAGGTTTTACTGGAACAAGGATGGCATGGTAGCAGGGAGATCTACTG
65 CTCTTTGCTTACTATTTAGGTTTTACTGGAACAAGGATGGCATGGTAGCAGGGAGATCTACTG
1102 ATGGCAGCAA
Statistics
Matches: 123, Mismatches: 1, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
149 5 0.04
150 92 0.75
151 11 0.09
152 3 0.02
153 12 0.10
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (149 bp):
CCCCGCCGAGAGGATCCCCTTCCCCCTTTTGATGGGTTCTCCCAATAATAATAAAATGTGTGATC
TCTTTGCTTACTATTTAGGTTTTACTGGAACAAGGATGGCATGGTAGCAGGGAGATCTACTGGCT
CTTACAATTTTTTTCTTCT
Found at i:3227 original size:3 final size:3
Alignment explanation
Indices: 3207--3251 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
3197 TTATTGTATC
* * *
3207 ATA ATA AGA ATA ACA ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3252 GAGATATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:3460 original size:2 final size:2
Alignment explanation
Indices: 3455--3526 Score: 126
Period size: 2 Copynumber: 36.0 Consensus size: 2
3445 GTGTGTGTGT
**
3455 TA TA TA TA TA GG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3497 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3527 CCTAAAAATA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5443 original size:3 final size:3
Alignment explanation
Indices: 5437--5513 Score: 90
Period size: 3 Copynumber: 27.0 Consensus size: 3
5427 TATAATAATA
* *
5437 ATT ATT ATT ATT A-T ATT ATT A-A ATT ATT ATT ATT A-T ATT ATT A-A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
5481 ATT ATT ATT ATT ATT AAT ATT AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5514 TTACAGTTAC
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
2 6 0.10
3 56 0.90
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:5464 original size:22 final size:22
Alignment explanation
Indices: 5436--5513 Score: 129
Period size: 22 Copynumber: 3.5 Consensus size: 22
5426 TTATAATAAT
5436 AATTATTATTATTATATTATTA
1 AATTATTATTATTATATTATTA
5458 AATTATTATTATTATATTATTA
1 AATTATTATTATTATATTATTA
*
5480 AATTATTATTATTATTAATATTA
1 AATTATTATTATTA-TATTATTA
5503 ATATTATTATT
1 A-ATTATTATT
5514 TTACAGTTAC
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
22 36 0.68
23 8 0.15
24 9 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
AATTATTATTATTATATTATTA
Found at i:5705 original size:19 final size:19
Alignment explanation
Indices: 5681--5719 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5671 ACAGCCCTCT
*
5681 ATCCCACCGACGCCGAGCC
1 ATCCCACCAACGCCGAGCC
5700 ATCCCACCAACGCCGAGCC
1 ATCCCACCAACGCCGAGCC
5719 A
1 A
5720 CTGAATGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.51, G:0.18, T:0.05
Consensus pattern (19 bp):
ATCCCACCAACGCCGAGCC
Found at i:7030 original size:2 final size:2
Alignment explanation
Indices: 7023--7048 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7013 TTTTATATTC
7023 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
7049 TACAAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10234 original size:2 final size:2
Alignment explanation
Indices: 10224--10259 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
10214 CAACAAAAAA
10224 AT AT A- AT 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 AT AT AT AT A
10260 CAATAAAGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12197 original size:18 final size:18
Alignment explanation
Indices: 12109--12189 Score: 119
Period size: 18 Copynumber: 4.5 Consensus size: 18
12099 TTCAGTTTTA
*
12109 AACCTAAAATATGGTTAT
1 AACCTAAAATATGGTTAC
12127 AACCTAAAATATGGTTAC
1 AACCTAAAATATGGTTAC
*
12145 AACCTAAAAACAT-GTTAC
1 AACCT-AAAATATGGTTAC
*
12163 AACCCAAAATATGGTTAC
1 AACCTAAAATATGGTTAC
12181 AACCTAAAA
1 AACCTAAAA
12190 ATAAGTTAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
17 6 0.11
18 44 0.79
19 6 0.11
ACGTcount: A:0.48, C:0.19, G:0.09, T:0.25
Consensus pattern (18 bp):
AACCTAAAATATGGTTAC
Found at i:24019 original size:65 final size:64
Alignment explanation
Indices: 23943--24078 Score: 184
Period size: 65 Copynumber: 2.1 Consensus size: 64
23933 ACACTAATTA
* * *
23943 TATTTGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGTCTGTGAATCGGTACATAAAAT
1 TATTCGATGTTTCAATAA-AGCCAAGAGTGCATCGATGCATGG-CTGTGAATCGGTACACAAAAT
24007 G
64 G
** *
24008 TATTCGATGTTTCAATAAATTCAAGAGTGCATCGATGCATGGCTGTGCATCGGTACACAAAATG
1 TATTCGATGTTTCAATAAAGCCAAGAGTGCATCGATGCATGGCTGTGAATCGGTACACAAAATG
*
24072 AATTCGA
1 TATTCGA
24079 AATAGGGTGT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
64 26 0.41
65 35 0.56
66 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (64 bp):
TATTCGATGTTTCAATAAAGCCAAGAGTGCATCGATGCATGGCTGTGAATCGGTACACAAAATG
Found at i:27083 original size:20 final size:22
Alignment explanation
Indices: 27049--27088 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
27039 AACTTTCTAA
27049 AAAAAGGATCAAT-CCTTTTGC
1 AAAAAGGATCAATCCCTTTTGC
*
27070 AAAAAGGAT-TATCCCTTTT
1 AAAAAGGATCAATCCCTTTT
27089 ACGAAAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (22 bp):
AAAAAGGATCAATCCCTTTTGC
Found at i:34993 original size:3 final size:3
Alignment explanation
Indices: 34985--35015 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
34975 CATGACATGT
34985 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
35016 AACCCTATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:38129 original size:32 final size:31
Alignment explanation
Indices: 38085--38169 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
38075 AGAAAGTTCG
* *
38085 GGGCCACGGGGCCTACCTAAGAACACATCTTA
1 GGGCCACAGGGCCTACCTAAGAACA-ATCTCA
** *
38117 GGGCCACAGGGCCTACCCGAGAATAATCTCA
1 GGGCCACAGGGCCTACCTAAGAACAATCTCA
* *
38148 GGGCCGCAGAGCCTACCTAAGA
1 GGGCCACAGGGCCTACCTAAGA
38170 GTCACATTAG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 23 0.52
32 21 0.48
ACGTcount: A:0.28, C:0.32, G:0.27, T:0.13
Consensus pattern (31 bp):
GGGCCACAGGGCCTACCTAAGAACAATCTCA
Found at i:49229 original size:13 final size:13
Alignment explanation
Indices: 49211--49235 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49201 GTTACTGAGA
49211 TTAAGACAATAAG
1 TTAAGACAATAAG
49224 TTAAGACAATAA
1 TTAAGACAATAA
49236 AATAAGGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
TTAAGACAATAAG
Found at i:55586 original size:12 final size:11
Alignment explanation
Indices: 55552--55590 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
55542 TGTGTGTGCC
55552 TTTTTCTTTTA
1 TTTTTCTTTTA
55563 TTTCTT-TTTTA
1 TTT-TTCTTTTA
55574 TTTTTCCTTTTA
1 TTTTT-CTTTTA
55586 TTTTT
1 TTTTT
55591 GATGAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 11 0.44
12 12 0.48
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTTTTA
Found at i:59215 original size:17 final size:18
Alignment explanation
Indices: 59191--59232 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
59181 ACGGGTCGGG
*
59191 TCGGGTTGGGTCAACGGT
1 TCGGGTTGAGTCAACGGT
*
59209 T-GGGTTGAGTGAACGGT
1 TCGGGTTGAGTCAACGGT
59226 TCGGGTT
1 TCGGGTT
59233 TTGGGCCGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.12, C:0.12, G:0.45, T:0.31
Consensus pattern (18 bp):
TCGGGTTGAGTCAACGGT
Found at i:59598 original size:19 final size:19
Alignment explanation
Indices: 59574--59642 Score: 120
Period size: 19 Copynumber: 3.6 Consensus size: 19
59564 GTAACTAATC
*
59574 GTTAACAGCCTTAACTGCT
1 GTTAACAGCCTTAACTACT
59593 GTTAACAGCCTTAACTACT
1 GTTAACAGCCTTAACTACT
59612 GTTAACAGCCTTAACTACT
1 GTTAACAGCCTTAACTACT
*
59631 GTTAACAACCTT
1 GTTAACAGCCTT
59643 CTAGACCCTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (19 bp):
GTTAACAGCCTTAACTACT
Found at i:59617 original size:38 final size:39
Alignment explanation
Indices: 59565--59642 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 39
59555 ACAGACTCTG
* *
59565 TAACTAATCGTTAACAGCCTTAACTGCTGTTAACAGCCT
1 TAACTAATCGTTAACAGCCTTAACTACTGTTAACAACCT
*
59604 TAACTACT-GTTAACAGCCTTAACTACTGTTAACAACCT
1 TAACTAATCGTTAACAGCCTTAACTACTGTTAACAACCT
59642 T
1 T
59643 CTAGACCCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 29 0.81
39 7 0.19
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (39 bp):
TAACTAATCGTTAACAGCCTTAACTACTGTTAACAACCT
Found at i:63138 original size:12 final size:12
Alignment explanation
Indices: 63121--63145 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
63111 AGATACCATA
63121 AGTTGTATTTAT
1 AGTTGTATTTAT
63133 AGTTGTATTTAT
1 AGTTGTATTTAT
63145 A
1 A
63146 ATTTGATGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (12 bp):
AGTTGTATTTAT
Done.