Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007706.1 Hibiscus syriacus cultivar Beakdansim tig00109921_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: 338066
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:275742 original size:3 final size:3
Alignment explanation
Indices: 275736--275774 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
275726 TTAAAATTAA
*
275736 ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
275775 TCAATAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:281940 original size:22 final size:22
Alignment explanation
Indices: 281901--281967 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
281891 CGTATAAATG
281901 CACCGAAGTGCCCCGTAGAATTA
1 CACCGAAGTG-CCCGTAGAATTA
*
281924 CACCGAAGTGCCCGTAGAATTG
1 CACCGAAGTGCCCGTAGAATTA
281946 CACCGAAGTGCCCGTAGAATTA
1 CACCGAAGTGCCCGTAGAATTA
281968 TGTCCATAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
22 32 0.76
23 10 0.24
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.18
Consensus pattern (22 bp):
CACCGAAGTGCCCGTAGAATTA
Found at i:282225 original size:30 final size:31
Alignment explanation
Indices: 282184--282243 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
282174 TAGACATAGT
*
282184 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
282214 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
282244 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:282300 original size:29 final size:29
Alignment explanation
Indices: 282258--282329 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
282248 TTTTCTGCAT
**
282258 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
282287 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
282316 ATTCATGTCATGTA
1 ATTCATGTCATGTA
282330 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:282746 original size:66 final size:64
Alignment explanation
Indices: 282632--282801 Score: 205
Period size: 66 Copynumber: 2.6 Consensus size: 64
282622 TTTTTCTCAT
* * * *
282632 GGGGGAATCGGTTCCCCCTGGGGGTATCGATTCCTCTCAAGCAATCTGGAATTTCATATACGATG
1 GGGGGTATCGGTTCCCCCT-GGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACGATG
282697 A
64 A
* * * *
282698 GGGGGTATCGGTTCCCCCCTGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCATTTCGTTGA
1 GGGGGTATCGGTT-CCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATGA
*
282763 GGGGGTATCGGTTCCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCTG---GGGTACCGATTCCCCT
282802 AACCCAGAAA
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 6 0.07
65 19 0.21
66 44 0.48
67 22 0.24
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.29
Consensus pattern (64 bp):
GGGGGTATCGGTTCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATGA
Found at i:283282 original size:21 final size:22
Alignment explanation
Indices: 283253--283294 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
283243 AGCCACACGT
283253 TGAGAGAAGGAAG-AGAAGAAAA
1 TGAGAGAA-GAAGAAGAAGAAAA
283275 TGAG-GAAGAAGAAGAAGAAA
1 TGAGAGAAGAAGAAGAAGAAA
283295 TGGGAGGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.36, T:0.05
Consensus pattern (22 bp):
TGAGAGAAGAAGAAGAAGAAAA
Found at i:288855 original size:23 final size:23
Alignment explanation
Indices: 288829--288880 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
288819 CACCACAGCT
*
288829 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
*
288852 CGTAGAATTGCACCGAAGTG-CC
1 CGTAGAAATGCACCGAAGTGCCC
288874 CGTAGAA
1 CGTAGAA
288881 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:288878 original size:22 final size:23
Alignment explanation
Indices: 288837--288882 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
288827 CTCGTATAAA
288837 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
288860 TGCACCGAAGTG-CCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
288882 T
1 T
288883 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:289218 original size:29 final size:29
Alignment explanation
Indices: 289176--289247 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
289166 TTTTCTGCAT
**
289176 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
289205 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
289234 ATTCATGTCATGTA
1 ATTCATGTCATGTA
289248 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:289685 original size:67 final size:68
Alignment explanation
Indices: 289550--289700 Score: 216
Period size: 68 Copynumber: 2.2 Consensus size: 68
289540 TTTTTCTCAT
* * * *
289550 GGGGGAATCGGTT-CCCCCCTGGGGGTATCGATTCCTCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
289614 TGA
66 TGA
* * * *
289617 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
289681 TGA
66 TGA
289684 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
289701 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
67 35 0.47
68 40 0.53
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.28
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
TGA
Found at i:289712 original size:67 final size:67
Alignment explanation
Indices: 289550--289722 Score: 215
Period size: 67 Copynumber: 2.6 Consensus size: 67
289540 TTTTTCTCAT
* * * *
289550 GGGGGAATCGGTTCCCCCCTGGGGGTATCGATTCCTCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
289615 GA
66 GA
* * * *
289617 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGT
1 GGGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
289681 TGA
65 TGA
* *
289684 GGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
289723 AACCCAGAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
65 6 0.06
67 47 0.51
68 40 0.43
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:298974 original size:16 final size:15
Alignment explanation
Indices: 298953--298992 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
298943 TTTAAAAAAT
298953 ATATTTTATTTTAATA
1 ATATTTTATTTTAA-A
298969 ATATTTATATTTTAAA
1 ATATTT-TATTTTAAA
*
298985 ATAATTTA
1 ATATTTTA
298993 AAAATAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 12 0.55
17 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATTTTATTTTAAA
Found at i:298981 original size:17 final size:16
Alignment explanation
Indices: 298953--298992 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
298943 TTTAAAAAAT
298953 ATATTT-TATTTTAATA
1 ATATTTATATTTTAA-A
298969 ATATTTATATTTTAAA
1 ATATTTATATTTTAAA
298985 ATAATTTA
1 AT-ATTTA
298993 AAAATAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATTTATATTTTAAA
Found at i:309681 original size:2 final size:2
Alignment explanation
Indices: 309674--309722 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
309664 ATATTATTAT
309674 TA TA TA TA TA TA 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
309716 TA TA TA T
1 TA TA TA T
309723 CACCTAGCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:311648 original size:17 final size:16
Alignment explanation
Indices: 311622--311653 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
311612 TTGCCCGCTG
311622 GCCGCTGCCGCCGCCC
1 GCCGCTGCCGCCGCCC
311638 GCCGTCTGCCGCCGCC
1 GCCG-CTGCCGCCGCC
311654 GTCAGCCGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.59, G:0.31, T:0.09
Consensus pattern (16 bp):
GCCGCTGCCGCCGCCC
Found at i:311651 original size:20 final size:20
Alignment explanation
Indices: 311623--311670 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
311613 TGCCCGCTGG
* *
311623 CCGCTGCCGCCGCCCGCCGT
1 CCGCCGCCGCCGCCAGCCGT
* *
311643 CTGCCGCCGCCGTCAGCCGT
1 CCGCCGCCGCCGCCAGCCGT
311663 CCGCCGCC
1 CCGCCGCC
311671 ACACTCTGAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.02, C:0.58, G:0.29, T:0.10
Consensus pattern (20 bp):
CCGCCGCCGCCGCCAGCCGT
Found at i:319947 original size:75 final size:77
Alignment explanation
Indices: 319739--319948 Score: 291
Period size: 75 Copynumber: 2.8 Consensus size: 77
319729 CAAAGCAAAA
* * * **
319739 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGA-TCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
319804 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
* *
319817 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATT-CCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
319881 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * *
319892 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCT
319949 TATACAACGG
Statistics
Matches: 118, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
74 12 0.10
75 46 0.39
76 14 0.12
77 23 0.19
78 23 0.19
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:325727 original size:21 final size:21
Alignment explanation
Indices: 325701--325763 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
325691 TTTTGGTGCA
*
325701 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
325722 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
325743 GAATGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
325764 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:328502 original size:76 final size:77
Alignment explanation
Indices: 328335--328545 Score: 300
Period size: 76 Copynumber: 2.8 Consensus size: 77
328325 CAAAGCCAAA
* * * **
328335 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
328400 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
*
328413 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
328478 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * * *
328489 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
328546 TGTACAACAG
Statistics
Matches: 121, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
75 19 0.16
76 40 0.33
77 37 0.31
78 25 0.21
ACGTcount: A:0.24, C:0.33, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:329838 original size:92 final size:93
Alignment explanation
Indices: 329652--329839 Score: 238
Period size: 92 Copynumber: 2.0 Consensus size: 93
329642 ACAAAAATGT
* *
329652 GCTTAATGAGGTTTACTTAATAAATACTTTTATTCAAAACATCCATTACTGACACGAAATCGGCA
1 GCTTAATGAGCTTTACTTAATAAATAC-TTTATTCAAAACATCCATTACTGACACGAAATCAGCA
* *
329717 TTTACTTGCACAGGAAGGTTCACCCATCG
65 TTTACTTGAACAGGAAGGTTCACCAATCG
* * * *
329746 GCTTAATGAGCTTTTCTTGATAAATAC-TTCTTCAAAACATCCATTACTGACCCGAAATCAGC-T
1 GCTTAATGAGCTTTACTTAATAAATACTTTATTCAAAACATCCATTACTGACACGAAATCAGCAT
* *
329809 CTTACTTGAACCGG-AGGATTCGCCAATCG
66 -TTACTTGAACAGGAAGG-TTCACCAATCG
329838 GC
1 GC
329840 AGGCCATGTC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
91 4 0.05
92 54 0.66
94 24 0.29
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Consensus pattern (93 bp):
GCTTAATGAGCTTTACTTAATAAATACTTTATTCAAAACATCCATTACTGACACGAAATCAGCAT
TTACTTGAACAGGAAGGTTCACCAATCG
Done.