Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004446.1 Hibiscus syriacus cultivar Beakdansim tig00009760_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: 30437
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2072 original size:24 final size:24
Alignment explanation
Indices: 2045--2095 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2035 ATATATCAAA
*
2045 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAAACAGAATTCAGGTCAAGT
* * *
2069 ATCATATCAGAATTCATGTCAAGT
1 ATCAAAACAGAATTCAGGTCAAGT
2093 ATC
1 ATC
2096 GGATTAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGGTCAAGT
Found at i:2113 original size:24 final size:24
Alignment explanation
Indices: 2059--2137 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 24
2049 AAACATAATT
* * *
2059 CAGGTCAAGTATCATATCAGAATT
1 CAGGTCAAGTATCAGATCAAAATC
* * *
2083 CATGTCAAGTATCGGATTAAAATC
1 CAGGTCAAGTATCAGATCAAAATC
*
2107 CAGGTCAAGTATCAGATCATAATC
1 CAGGTCAAGTATCAGATCAAAATC
*
2131 CATGTCA
1 CAGGTCA
2138 GGAATCACAA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAAAATC
Found at i:14430 original size:19 final size:19
Alignment explanation
Indices: 14406--14442 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
14396 CTATTAAAAT
14406 TTATAAAATAATATTTTGA
1 TTATAAAATAATATTTTGA
* *
14425 TTATAATATATTATTTTG
1 TTATAAAATAATATTTTG
14443 TTGAATATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTATAAAATAATATTTTGA
Found at i:15670 original size:37 final size:37
Alignment explanation
Indices: 15620--15694 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
15610 AACGGTCGTT
15620 GGGAATGTCGTGAATCGAGGCGTGAATATTCACTGTG
1 GGGAATGTCGTGAATCGAGGCGTGAATATTCACTGTG
15657 GGGAATGTCGTGAATCGAGGCGTGAATATTCACTGTG
1 GGGAATGTCGTGAATCGAGGCGTGAATATTCACTGTG
15694 G
1 G
15695 AGGCAACTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.13, G:0.36, T:0.27
Consensus pattern (37 bp):
GGGAATGTCGTGAATCGAGGCGTGAATATTCACTGTG
Found at i:21230 original size:3 final size:3
Alignment explanation
Indices: 21222--21269 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
21212 CTACAAAATG
* * * * *
21222 TAA TAA TAA TAA TAA TTA TTA TTA TTA TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21270 CGGGTCTCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:21636 original size:36 final size:35
Alignment explanation
Indices: 21581--22160 Score: 143
Period size: 36 Copynumber: 17.6 Consensus size: 35
21571 GGATAATTGT
* **
21581 TTTCAAGATAAACTGTCTCAAGGGAGACAAAATTTG
1 TTTCAAGAGAAACAATCTCAA-GGAGACAAAATTTG
**
21617 TTTCAAGAGAAACAATCTCAA--AG----GTTTATG
1 TTTCAAGAGAAACAATCTCAAGGAGACAAAATT-TG
* *
21647 TTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTG
1 TTTCAAGAGAAACAATCTCAAG-GAGACAAAATTTG
**
21683 TTTCAAGAGAAACAATCTCAA--AG----GTTTATG
1 TTTCAAGAGAAACAATCTCAAGGAGACAAAATT-TG
* *
21713 TTTCAAGAGAAA-ATGTCTCAAGAGATACAAAATTTG
1 TTTCAAGAGAAACA-ATCTCAAG-GAGACAAAATTTG
* ** **
21749 TTTTAAGAGAAATGATCTCAA--AG----GTTTATG
1 TTTCAAGAGAAACAATCTCAAGGAGACAAAATT-TG
*** *
21779 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTG
1 TTTCAAGAGAAACAATCTCAAG-GAGACAAAATTTG
* *
21815 TTTCAAGAGAAACAATTTCAA--AG-----TTTATG
1 TTTCAAGAGAAACAATCTCAAGGAGACAAAATT-TG
*** * * *
21844 TTTCAAGAGAAATTGTCTCAAGCAAGGCAAAACTTG
1 TTTCAAGAGAAACAATCTCAAG-GAGACAAAATTTG
* * *
21880 TTTCAAAAGAAATAATCTCAA--AG-----TTTATG
1 TTTCAAGAGAAACAATCTCAAGGAGACAAAATT-TG
* *
21909 TTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTG
1 TTTCAAGAGAAACAATCTCAAG-GAGACAAAATTTG
*
21945 TTTCAAGAGAAACAATCTCAA--AG-----TTTATG
1 TTTCAAGAGAAACAATCTCAAGGAGACAAAATT-TG
** * * *
21974 TTTCAAGAGAAACTTTCTCAAGCTAGTCAAAACTTG
1 TTTCAAGAGAAACAATCTCAAG-GAGACAAAATTTG
* *
22010 TTTCAAGAGAAAGAATCTCAA--AG-----TTTATG
1 TTTCAAGAGAAACAATCTCAAGGAGACAAAATT-TG
** *
22039 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTG
1 TTTCAAGAGAAACAATCTCAAG-GAGACAAAATTTG
* * **
22075 TTTAAAAAGAAACAATCTCAA--AG----TTTTATG
1 TTTCAAGAGAAACAATCTCAAGGAGACAAAATT-TG
* ** * *
22105 TTTTAAGAGAAACTGTTTCAAGCGAGAC-AAACTTG
1 TTTCAAGAGAAACAATCTCAAG-GAGACAAAATTTG
22140 TTTCAAGAGAAACAATCTCAA
1 TTTCAAGAGAAACAATCTCAA
22161 AGGTTTATCA
Statistics
Matches: 388, Mismatches: 87, Indels: 139
0.63 0.14 0.23
Matches are distributed among these distances:
28 4 0.01
29 87 0.22
30 80 0.21
32 8 0.02
33 22 0.06
35 19 0.05
36 160 0.41
37 8 0.02
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (35 bp):
TTTCAAGAGAAACAATCTCAAGGAGACAAAATTTG
Found at i:21687 original size:66 final size:66
Alignment explanation
Indices: 21581--22168 Score: 880
Period size: 65 Copynumber: 9.0 Consensus size: 66
21571 GGATAATTGT
* * *
21581 TTTCAAGATAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
21646 G
66 G
*
21647 TTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
21712 G
66 G
* * * * * **
21713 TTTCAAGAGAAAATGTCTCAAGAGATACAAAATTTGTTTTAAGAGAAATGATCTCAAAGGTTTAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
21778 G
66 G
* * *
21779 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATTTCAAA-GTTTAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
21843 G
66 G
* * * * *
21844 TTTCAAGAGAAATTGTCTCAAGCAAGGCAAAACTTGTTTCAAAAGAAATAATCTCAAA-GTTTAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
21908 G
66 G
*
21909 TTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAA-GTTTAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
21973 G
66 G
* * * *
21974 TTTCAAGAGAAACTTTCTCAAGCTAGTCAAAACTTGTTTCAAGAGAAAGAATCTCAAA-GTTTAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
22038 G
66 G
* * *
22039 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTGTTTAAAAAGAAACAATCTCAAAGTTTTAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
22104 G
66 G
* *
22105 TTTTAAGAGAAACTGTTTCAAGCGAGAC-AAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
22169 CAATTTTGTT
Statistics
Matches: 474, Mismatches: 47, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
65 271 0.57
66 203 0.43
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (66 bp):
TTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
G
Found at i:21864 original size:29 final size:29
Alignment explanation
Indices: 21813--22051 Score: 127
Period size: 29 Copynumber: 7.5 Consensus size: 29
21803 AGACAAAACT
*
21813 TGTTTCAAGAGAAACAATTTCAAAGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGTTTA
*** ***
21842 TGTTTCAAGAGAAATTGTCTCAAGCAAGGCAAAA
1 TGTTTCAAGAGAAACAATCTC-A--AA-G-TTTA
* *
21876 CTTGTTTCAAAAGAAATAATCTCAAAGTTTA
1 --TGTTTCAAGAGAAACAATCTCAAAGTTTA
* ***
21907 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAA
1 TGTTTCAAGAGAAACAATCTCAA---AG--TTTA
21941 CTTGTTTCAAGAGAAACAATCTCAAAGTTTA
1 --TGTTTCAAGAGAAACAATCTCAAAGTTTA
** **
21972 TGTTTCAAGAGAAACTTTCTCAAGCTAGTCAAAA
1 TGTTTCAAGAGAAACAATCTCAA---AGT--TTA
*
22006 CTTGTTTCAAGAGAAAGAATCTCAAAGTTTA
1 --TGTTTCAAGAGAAACAATCTCAAAGTTTA
22037 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
22052 TGTCTCAAGC
Statistics
Matches: 156, Mismatches: 33, Indels: 42
0.68 0.14 0.18
Matches are distributed among these distances:
29 72 0.46
30 1 0.01
31 3 0.02
32 8 0.05
33 8 0.05
34 3 0.02
35 1 0.01
36 60 0.38
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (29 bp):
TGTTTCAAGAGAAACAATCTCAAAGTTTA
Found at i:22154 original size:20 final size:19
Alignment explanation
Indices: 22114--22154 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
22104 GTTTTAAGAG
* *
22114 AAACTGTTTCAAGCGAGAC
1 AAACTGTTTCAAGAGAAAC
22133 AAACTTGTTTCAAGAGAAAC
1 AAAC-TGTTTCAAGAGAAAC
22153 AA
1 AA
22155 TCTCAAAGGT
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:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (19 bp):
AAACTGTTTCAAGAGAAAC
Found at i:29727 original size:3 final size:3
Alignment explanation
Indices: 29719--29760 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
29709 CTACAAAATG
29719 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29761 ACCCGACAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:30115 original size:36 final size:36
Alignment explanation
Indices: 30068--30195 Score: 135
Period size: 36 Copynumber: 3.7 Consensus size: 36
30058 TCTTTAGGAT
* *
30068 AATTTGTTTCAAGATAAACTATCTCAAGCGAGACAA
1 AATTTGTTTCAAGAGAAACAATCTCAAGCGAGACAA
*
30104 AATTTGTTTCAAGGGAAACAATCTCAA---AG----
1 AATTTGTTTCAAGAGAAACAATCTCAAGCGAGACAA
** *
30133 GTTTATGTTTCAAGAGAAACTATCTCAAGCGAGACAA
1 AATT-TGTTTCAAGAGAAACAATCTCAAGCGAGACAA
*
30170 AACTTGTTTCAAGAGAAACAATCTCA
1 AATTTGTTTCAAGAGAAACAATCTCA
30196 TAGGTTTGTT
Statistics
Matches: 73, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
29 2 0.03
30 21 0.29
33 4 0.05
36 45 0.62
37 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (36 bp):
AATTTGTTTCAAGAGAAACAATCTCAAGCGAGACAA
Found at i:30178 original size:66 final size:66
Alignment explanation
Indices: 30072--30417 Score: 444
Period size: 66 Copynumber: 5.4 Consensus size: 66
30062 TAGGATAATT
* * *
30072 TGTTTCAAGATAAACTATCTCAAGCGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTT
30137 A
66 A
*
30138 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCATAGG-TT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTT
30202 -
66 A
* * * * * *
30202 TG-TTCAAGAGAAAATGTCTCAAGAGAGA-TAAA-TTTTTTCAAGAGAAACGATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTT
30264 A
66 A
* * * * *
30265 TG-TTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATTTCAAAGTTTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTT
30329 A
66 A
* * * *
30330 TGTTTCAAGAGAAATTGTCTCAAGC-AGGCAAAACTTGTTTCAA-AGAAATAATCTCAAA-GTTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTT
30392 A
66 A
30393 TGTTTC-A-AGAAACTATCTCAAGCGA
1 TGTTTCAAGAGAAACTATCTCAAGCGA
30418 TAACAGCTAT
Statistics
Matches: 250, Mismatches: 24, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
61 38 0.15
62 7 0.03
63 60 0.24
64 18 0.07
65 48 0.19
66 79 0.32
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTT
A
Done.