Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000035.1 Hibiscus syriacus cultivar Beakdansim tig00000056_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: 91659
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:9787 original size:34 final size:32
Alignment explanation
Indices: 9725--9795 Score: 97
Period size: 34 Copynumber: 2.2 Consensus size: 32
9715 ACCTTACAAC
* *
9725 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
9757 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
9791 TCCCT
1 TCCCT
9796 TTACAAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:10100 original size:21 final size:21
Alignment explanation
Indices: 10074--10115 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
10064 CCAGAATGGG
*
10074 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
10095 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
10116 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:10247 original size:15 final size:15
Alignment explanation
Indices: 10227--10288 Score: 70
Period size: 15 Copynumber: 4.0 Consensus size: 15
10217 AAACCATGCA
10227 GGGGAATCTATACCC
1 GGGGAATCTATACCC
*
10242 GGGGAATCAATACCC
1 GGGGAATCTATACCC
* *
10257 TTGGGGAATCTGTTCCC
1 --GGGGAATCTATACCC
*
10274 GGGGAATCGATACCC
1 GGGGAATCTATACCC
10289 CCTGGGGGGG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
15 26 0.68
17 12 0.32
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (15 bp):
GGGGAATCTATACCC
Found at i:10263 original size:32 final size:32
Alignment explanation
Indices: 10227--10288 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
10217 AAACCATGCA
10227 GGGGAATCTATACCCGGGGAATCAATACCCTT
1 GGGGAATCTATACCCGGGGAATCAATACCCTT
* * *
10259 GGGGAATCTGTTCCCGGGGAATCGATACCC
1 GGGGAATCTATACCCGGGGAATCAATACCC
10289 CCTGGGGGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (32 bp):
GGGGAATCTATACCCGGGGAATCAATACCCTT
Found at i:10298 original size:21 final size:21
Alignment explanation
Indices: 10274--10314 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
10264 ATCTGTTCCC
10274 GGGGAATC-GATACCCCCTGGG
1 GGGGAATCTG-TACCCCCTGGG
10295 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
10315 ACAATCTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.17, C:0.29, G:0.37, T:0.17
Consensus pattern (21 bp):
GGGGAATCTGTACCCCCTGGG
Found at i:13315 original size:34 final size:32
Alignment explanation
Indices: 13262--13331 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
13252 CCTTACAAAC
* *
13262 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
*
13294 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
13328 TCCC
1 TCCC
13332 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:13637 original size:21 final size:21
Alignment explanation
Indices: 13611--13651 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
13601 CAGAATGGGG
*
13611 GGAATCGGTACCCCTTCATAT
1 GGAATCGATACCCCTTCATAT
13632 GGAATCGATACCCCTTCATA
1 GGAATCGATACCCCTTCATA
13652 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (21 bp):
GGAATCGATACCCCTTCATAT
Found at i:13803 original size:33 final size:35
Alignment explanation
Indices: 13763--13841 Score: 117
Period size: 33 Copynumber: 2.3 Consensus size: 35
13753 CAAACCATGC
13763 AGGGGGAATCTGTACCCGGGGAATCAATACC-CCT
1 AGGGGGAATCTGTACCCGGGGAATCAATACCTCCT
** *
13797 -GGGGGAATCTGTTTCCGGGGAATCGATACCTCCT
1 AGGGGGAATCTGTACCCGGGGAATCAATACCTCCT
13831 AGGGGGAATCT
1 AGGGGGAATCT
13842 ATTCCCCCTG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
33 27 0.68
34 3 0.08
35 10 0.25
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.22
Consensus pattern (35 bp):
AGGGGGAATCTGTACCCGGGGAATCAATACCTCCT
Found at i:13871 original size:20 final size:20
Alignment explanation
Indices: 13813--13872 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
13803 ATCTGTTTCC
* *
13813 GGGGAATC-GATACCTCCTAG
1 GGGGAATCTG-TACCCCCTGG
* *
13833 GGGGAATCTATTCCCCCTGG
1 GGGGAATCTGTACCCCCTGG
13853 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
13873 ACAATCTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.18, C:0.28, G:0.32, T:0.22
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:14670 original size:21 final size:20
Alignment explanation
Indices: 14647--14685 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
14637 GAACCCCCCG
*
14647 GGGGGGTATCGATTCCCCTA
1 GGGGGGAATCGATTCCCCTA
*
14667 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
14686 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.26, G:0.38, T:0.23
Consensus pattern (20 bp):
GGGGGGAATCGATTCCCCTA
Found at i:25454 original size:60 final size:60
Alignment explanation
Indices: 25379--25496 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 60
25369 CTAAATTAGA
*
25379 TCTTCTGTTCCCAGTATCCACTTCTCCCTCCAACGAACCATCATCAGGCTCCTTCCTATT
1 TCTTCTGTTCCCAGTATCCACTTCTCCCTCCAACCAACCATCATCAGGCTCCTTCCTATT
* * * * *
25439 TCTTCTGTTCTCAGTATCCGCTTCTCCCTCCAACCCACCTTCATCGGGCTCCTTCCTA
1 TCTTCTGTTCCCAGTATCCACTTCTCCCTCCAACCAACCATCATCAGGCTCCTTCCTA
25497 GTCTTTGAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.15, C:0.42, G:0.09, T:0.34
Consensus pattern (60 bp):
TCTTCTGTTCCCAGTATCCACTTCTCCCTCCAACCAACCATCATCAGGCTCCTTCCTATT
Found at i:43632 original size:84 final size:84
Alignment explanation
Indices: 43491--43662 Score: 317
Period size: 84 Copynumber: 2.0 Consensus size: 84
43481 TATTTTTGTT
* *
43491 TAAATGTATGACACGTTTTATTTTAGGAGATAACAACTTATTTGATAGATATATAAAATATTTAA
1 TAAATGTATGACACGTTTTATTTCAGGAGATAACAAATTATTTGATAGATATATAAAATATTTAA
*
43556 TGTGAAATGTATCTTTTAA
66 TGTGAAATATATCTTTTAA
43575 TAAATGTATGACACGTTTTATTTCAGGAGATAACAAATTATTTGATAGATATATAAAATATTTAA
1 TAAATGTATGACACGTTTTATTTCAGGAGATAACAAATTATTTGATAGATATATAAAATATTTAA
43640 TGTGAAATATATCTTTTAA
66 TGTGAAATATATCTTTTAA
43659 TAAA
1 TAAA
43663 ATATTTAATA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (84 bp):
TAAATGTATGACACGTTTTATTTCAGGAGATAACAAATTATTTGATAGATATATAAAATATTTAA
TGTGAAATATATCTTTTAA
Found at i:54437 original size:24 final size:25
Alignment explanation
Indices: 54399--54446 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
54389 AAATTATACA
54399 TTTAATACTTAAATTA-TTATTTTAT
1 TTTAATACTTAAATTACTT-TTTTAT
*
54424 TTTAATA-TTTAATTACTTTTTTA
1 TTTAATACTTAAATTACTTTTTTA
54447 GGTATCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTAATACTTAAATTACTTTTTTAT
Found at i:56903 original size:51 final size:51
Alignment explanation
Indices: 56829--56925 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 51
56819 TATGATGAAT
*
56829 TTTTAGTGGAGTAGTGGATGATTTGTTAAATGGATAGTGGGTTAGGTTTTA
1 TTTTAGTGGAGTAGTGGAGGATTTGTTAAATGGATAGTGGGTTAGGTTTTA
* * * **
56880 TTTTAGTGGATTAGTTGAGGATTTGTTTAATGTTTAGTGGGTTAGG
1 TTTTAGTGGAGTAGTGGAGGATTTGTTAAATGGATAGTGGGTTAGG
56926 GAAGGTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (51 bp):
TTTTAGTGGAGTAGTGGAGGATTTGTTAAATGGATAGTGGGTTAGGTTTTA
Found at i:61519 original size:15 final size:15
Alignment explanation
Indices: 61496--61525 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61486 TGCATTTTAC
*
61496 AGGATGAGGAAGAAG
1 AGGAGGAGGAAGAAG
61511 AGGAGGAGGAAGAAG
1 AGGAGGAGGAAGAAG
61526 TTAAATTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (15 bp):
AGGAGGAGGAAGAAG
Found at i:70073 original size:78 final size:78
Alignment explanation
Indices: 69979--70134 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
69969 GGGGGGTTGT
*
69979 TAGATGGGTTGCAAGGACAGCTAATATGGATGCTGATGCTTTAGCAAAGGCTGGTATAAGCTGAA
1 TAGATGGGCTGCAAGGACAGCTAATATGGATGCTGATGCTTTAGCAAAGGCTGGTATAAGCTGAA
70044 TTTTATGTTATAA
66 TTTTATGTTATAA
70057 TAGATGGGCTGCAAGGACAGCTAATATGGATGCTGATGCTTTAGCAAAGGCTGGTATAAGCTGAA
1 TAGATGGGCTGCAAGGACAGCTAATATGGATGCTGATGCTTTAGCAAAGGCTGGTATAAGCTGAA
70122 TTTTATGTTATAA
66 TTTTATGTTATAA
70135 GCGCGGTTTG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (78 bp):
TAGATGGGCTGCAAGGACAGCTAATATGGATGCTGATGCTTTAGCAAAGGCTGGTATAAGCTGAA
TTTTATGTTATAA
Found at i:81701 original size:90 final size:89
Alignment explanation
Indices: 81583--81757 Score: 287
Period size: 90 Copynumber: 2.0 Consensus size: 89
81573 TCTCGAATAT
* * * * *
81583 TTAATTTCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCCTGATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAG
81648 GGTAACTTGGATATAAAAGGATTA
66 GGTAACTTGGATATAAAAGGATTA
81672 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
*
81737 GGGTAACTTGGCTATAAAAGG
65 GGGTAACTTGGATATAAAAGG
81758 GTGTGTTACA
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 7 0.09
90 72 0.91
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAG
GGTAACTTGGATATAAAAGGATTA
Found at i:86440 original size:16 final size:16
Alignment explanation
Indices: 86419--86453 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
86409 CTCTGACTAG
86419 TGTCTACTCCCTTCGT
1 TGTCTACTCCCTTCGT
86435 TGTCTACTCCCTTCGT
1 TGTCTACTCCCTTCGT
86451 TGT
1 TGT
86454 TCATTGGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.06, C:0.34, G:0.14, T:0.46
Consensus pattern (16 bp):
TGTCTACTCCCTTCGT
Done.