Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001408.1 Hibiscus syriacus cultivar Beakdansim tig00002745_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: 73804
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:6519 original size:185 final size:182
Alignment explanation
Indices: 6286--6671 Score: 537
Period size: 185 Copynumber: 2.1 Consensus size: 182
6276 TTTTATAATT
* * * *
6286 TATATAAAAATTAAATGTTTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATA-AAT
1 TATATAAATATTTAATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
6350 TATAAAATAAAAATTTCAGATAAAGTTTTTTAATTAATTAATATTGATATAGGTTTTAAAA-TTA
66 TATAAAATAAAAATTTCAGAT-AAGTTTTTTAATTAATTAATATTGATATAGG-TTTAAAAGTTA
* ** **
6414 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGACTTAGCCCATATGTTA
129 TTAGATCTT-AATTATT-ATTGAATTTTAAATGGTTTGGACCGAGCCCATATGTTA
6470 TATATAATATATTTAATATTTTTTAATT-AAAAAAACAGTTTACAATTAATTTAAATAATATATA
1 TATATAA-ATATTTAATATTTTTTAATTCAAAAAAA-AGTTTACAATTAATTTAAATAATATATA
* * * *
6534 ATTATAAAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
64 ATTATAAAATAAAAATTTCAGATAAGTTTTTTAATTAATTAATATTGATATAGGTTTAAAAGTTA
* * * *
6599 TTATATCTTAATTATTATTGAATTTTAAATGTTTTGGGCCGAGTCCATATGTTA
129 TTAGATCTTAATTATTATTGAATTTTAAATGGTTTGGACCGAGCCCATATGTTA
6653 TATAT-AATATTTAATATTT
1 TATATAAATATTTAATATTT
6672 AAAATTTAAT
Statistics
Matches: 181, Mismatches: 17, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
181 13 0.07
182 1 0.01
183 36 0.20
184 28 0.15
185 81 0.45
186 22 0.12
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (182 bp):
TATATAAATATTTAATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAATTTCAGATAAGTTTTTTAATTAATTAATATTGATATAGGTTTAAAAGTTATT
AGATCTTAATTATTATTGAATTTTAAATGGTTTGGACCGAGCCCATATGTTA
Found at i:20802 original size:27 final size:28
Alignment explanation
Indices: 20772--20851 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 28
20762 GTTAAAAAAT
*
20772 TTAGTTTTTGTTTCATTTTAGTACCC-A
1 TTAGTTTTTGTTTCATTTCAGTACCCTA
* * *
20799 TTAGTATTTGTTTCATTTGAGTACCCCTG
1 TTAGTTTTTGTTTCATTTCAGTA-CCCTA
20828 TTAGTTTTTGTTTCATTTCAGTAC
1 TTAGTTTTTGTTTCATTTCAGTAC
20852 TATGTTCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 21 0.46
28 4 0.09
29 21 0.46
ACGTcount: A:0.17, C:0.15, G:0.14, T:0.54
Consensus pattern (28 bp):
TTAGTTTTTGTTTCATTTCAGTACCCTA
Found at i:20841 original size:29 final size:28
Alignment explanation
Indices: 20772--20851 Score: 108
Period size: 29 Copynumber: 2.9 Consensus size: 28
20762 GTTAAAAAAT
*
20772 TTAGTTTTTGTTTCATTTTAGTA-CCCA
1 TTAGTTTTTGTTTCATTTCAGTACCCCA
* * *
20799 TTAGTATTTGTTTCATTTGAGTACCCCTG
1 TTAGTTTTTGTTTCATTTCAGTACCCC-A
20828 TTAGTTTTTGTTTCATTTCAGTAC
1 TTAGTTTTTGTTTCATTTCAGTAC
20852 TATGTTCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 21 0.46
28 3 0.07
29 22 0.48
ACGTcount: A:0.17, C:0.15, G:0.14, T:0.54
Consensus pattern (28 bp):
TTAGTTTTTGTTTCATTTCAGTACCCCA
Found at i:25929 original size:87 final size:84
Alignment explanation
Indices: 25783--25955 Score: 247
Period size: 87 Copynumber: 2.0 Consensus size: 84
25773 GGCGGCATCA
* *
25783 TCAATGATTAAGCTTGGGATTTCAGCACACGGCAAGGAATTTTCAATGTTTAAGCTTGGGACTTC
1 TCAATGATTAAGCTTGGGATTTCAGCACACGGCAAGGAACTTTCAATGTTGAAGCTTGGGA-TT-
* *
25848 ATCAGCACCCGGCGAGGAACTT
64 -TCAGCACACAGCGAGGAACTT
* * * *
25870 TCAATGTTTAAGCTTGGGATTTCATCACACGGCAAGGGACTTTCGATGTTGAAGCTTGGGATTTC
1 TCAATGATTAAGCTTGGGATTTCAGCACACGGCAAGGAACTTTCAATGTTGAAGCTTGGGATTTC
25935 AGCACACAGCGAGGAACTT
66 AGCACACAGCGAGGAACTT
25954 TC
1 TC
25956 GTCTTCACCA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
84 21 0.27
86 2 0.03
87 55 0.71
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (84 bp):
TCAATGATTAAGCTTGGGATTTCAGCACACGGCAAGGAACTTTCAATGTTGAAGCTTGGGATTTC
AGCACACAGCGAGGAACTT
Found at i:25956 original size:42 final size:42
Alignment explanation
Indices: 25783--25955 Score: 229
Period size: 42 Copynumber: 4.0 Consensus size: 42
25773 GGCGGCATCA
* *
25783 TCAATGATTAAGCTTGGGATTTCAGCACACGGCAAGGAATTT
1 TCAATGTTTAAGCTTGGGATTTCAGCACACGGCAAGGAACTT
* *
25825 TCAATGTTTAAGCTTGGGACTTCATCAGCACCCGGCGAGGAACTT
1 TCAATGTTTAAGCTTGGGA-TT--TCAGCACACGGCAAGGAACTT
* *
25870 TCAATGTTTAAGCTTGGGATTTCATCACACGGCAAGGGACTT
1 TCAATGTTTAAGCTTGGGATTTCAGCACACGGCAAGGAACTT
* * * *
25912 TCGATGTTGAAGCTTGGGATTTCAGCACACAGCGAGGAACTT
1 TCAATGTTTAAGCTTGGGATTTCAGCACACGGCAAGGAACTT
25954 TC
1 TC
25956 GTCTTCACCA
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
42 73 0.64
43 2 0.02
44 2 0.02
45 37 0.32
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (42 bp):
TCAATGTTTAAGCTTGGGATTTCAGCACACGGCAAGGAACTT
Found at i:30701 original size:16 final size:16
Alignment explanation
Indices: 30677--30707 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30667 TATAAGATCA
30677 TTTAAAAAAATGAGTC
1 TTTAAAAAAATGAGTC
*
30693 TTTAGAAAAATGAGT
1 TTTAAAAAAATGAGT
30708 TGTACGAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.16, T:0.32
Consensus pattern (16 bp):
TTTAAAAAAATGAGTC
Found at i:31877 original size:30 final size:30
Alignment explanation
Indices: 31819--31879 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
31809 AACTGAATTT
*
31819 ATTCGGTTCAGTTAATACTTTAAAAAAAAA
1 ATTCGGTTCAGTTAATACATTAAAAAAAAA
* *
31849 ATTCGGTTCGGTTAA-CCATTAAAGAAAAAA
1 ATTCGGTTCAGTTAATACATTAAA-AAAAAA
31879 A
1 A
31880 AGTTCGATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (30 bp):
ATTCGGTTCAGTTAATACATTAAAAAAAAA
Found at i:42157 original size:58 final size:58
Alignment explanation
Indices: 42062--42237 Score: 201
Period size: 58 Copynumber: 3.0 Consensus size: 58
42052 GCATCATTCG
* * *
42062 TCCCTAAACTATGATTCTCATTTTAAATTAATACTTAAACTTTTGAATATTCCAATTTCA
1 TCCCTAAACTATGA--CTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCA
* * *
42122 T-CCTCAAACTATGACTCATTCTAAACTAGTCCTTAAACTTTTGAATATTCTAATTTTA
1 TCCCT-AAACTATGACTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCA
* * ** *
42180 TCCCTAAACTATGACACTCTTTCTAAATTGGTCCCCAAACTTTTGAATATTTCAATTT
1 TCCCTAAACTATG--ACTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCCAATTT
42238 TATTCCCAAA
Statistics
Matches: 99, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
58 47 0.47
59 6 0.06
60 46 0.46
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.41
Consensus pattern (58 bp):
TCCCTAAACTATGACTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCA
Found at i:42187 original size:29 final size:29
Alignment explanation
Indices: 42097--42189 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
42087 AATTAATACT
* *
42097 TAAACTTTTGAATATTCCAATTTCAT-CC
1 TAAACTTTTGAATATTCTAATTTTATCCC
* * ** *
42125 TCAAAC-TATGACTCATTCTAA-ACTAGTCCT
1 T-AAACTTTTGAAT-ATTCTAATTTTA-TCCC
42155 TAAACTTTTGAATATTCTAATTTTATCCC
1 TAAACTTTTGAATATTCTAATTTTATCCC
42184 TAAACT
1 TAAACT
42190 ATGACACTCT
Statistics
Matches: 47, Mismatches: 12, Indels: 11
0.67 0.17 0.16
Matches are distributed among these distances:
28 7 0.15
29 31 0.66
30 9 0.19
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (29 bp):
TAAACTTTTGAATATTCTAATTTTATCCC
Found at i:42229 original size:60 final size:58
Alignment explanation
Indices: 42098--42240 Score: 173
Period size: 60 Copynumber: 2.4 Consensus size: 58
42088 ATTAATACTT
* * **
42098 AAACTTTTGAATATTCCAATTTCATCCTCAAACTATGACTCATTCTAAACTAGTCCTT
1 AAACTTTTGAATATTCTAATTTTATCCTCAAACTATGACTCATTCTAAACTAGTCCCC
* * *
42156 AAACTTTTGAATATTCTAATTTTATCC-CTAAACTATGACACTCTTTCTAAATTGGTCCCC
1 AAACTTTTGAATATTCTAATTTTATCCTC-AAACTATG--ACTCATTCTAAACTAGTCCCC
42216 AAACTTTTGAATATT-TCAATTTTAT
1 AAACTTTTGAATATTCT-AATTTTAT
42241 TCCCAAATTC
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
57 1 0.01
58 33 0.45
59 1 0.01
60 39 0.53
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (58 bp):
AAACTTTTGAATATTCTAATTTTATCCTCAAACTATGACTCATTCTAAACTAGTCCCC
Found at i:42463 original size:60 final size:60
Alignment explanation
Indices: 42370--42560 Score: 154
Period size: 60 Copynumber: 3.2 Consensus size: 60
42360 ATATACATAC
* * * *
42370 AGTTT-GGGATAAAATCAGAATTTTCAAAAAGTTTGGGGACTAATTTAGAATGAATGTCAT
1 AGTTTGGGGATGAAATTAAAATATTC-AAAAGTTTGGGGACTAATTTAGAATGAATGTCAT
* * * * * * *
42430 AGTTTGGGGATGAAATTGAAATGTTCAAAAGTTTGAGAACTAATTCAGAATG-ATAATAAT
1 AGTTTGGGGATGAAATTAAAATATTCAAAAGTTTGGGGACTAATTTAGAATGAAT-GTCAT
* * * * * * *
42490 AGTTTAGAGATGAAATTAAAATATTTAAAAATTTAGGGA-TCAATTTAAAATGAAGGTCAT
1 AGTTTGGGGATGAAATTAAAATATTCAAAAGTTTGGGGACT-AATTTAGAATGAATGTCAT
* *
42550 ACTTTGAGGAT
1 AGTTTGGGGAT
42561 ATTTGGTGCA
Statistics
Matches: 99, Mismatches: 28, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
59 3 0.03
60 80 0.81
61 16 0.16
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.33
Consensus pattern (60 bp):
AGTTTGGGGATGAAATTAAAATATTCAAAAGTTTGGGGACTAATTTAGAATGAATGTCAT
Found at i:55127 original size:25 final size:28
Alignment explanation
Indices: 55078--55133 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 28
55068 GACATGTGAT
*
55078 ATATCATCATTATGTAATATAATATGTC
1 ATATCATCATTATGTAATATAATATGAC
*
55106 ATATCATCATT-T-TAA-ATGATATGAC
1 ATATCATCATTATGTAATATAATATGAC
55131 ATA
1 ATA
55134 ATATATTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 11 0.42
26 3 0.12
27 1 0.04
28 11 0.42
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (28 bp):
ATATCATCATTATGTAATATAATATGAC
Found at i:55170 original size:30 final size:30
Alignment explanation
Indices: 55106--55196 Score: 83
Period size: 30 Copynumber: 2.9 Consensus size: 30
55096 ATAATATGTC
* *
55106 ATATCATCATTTTAAATGATATGACATAAT
1 ATATTATCATTTTAAATGACATGACATAAT
* *
55136 ATATTATCGTTTTAAATGACGTGACATATAAT
1 ATATTATCATTTTAAATGACATGAC--ATAAT
* * * *
55168 ATTTTATCACTTCATATGACATAGACATA
1 ATATTATCATTTTAAATGACAT-GACATA
55197 TCACATCATT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
30 21 0.44
31 3 0.06
32 21 0.44
33 3 0.06
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (30 bp):
ATATTATCATTTTAAATGACATGACATAAT
Found at i:64119 original size:2 final size:2
Alignment explanation
Indices: 64112--64140 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
64102 AAATACATAC
64112 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64141 GGGTAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64130 original size:13 final size:13
Alignment explanation
Indices: 64112--64137 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64102 AAATACATAC
64112 ATATATATATATA
1 ATATATATATATA
64125 ATATATATATATA
1 ATATATATATATA
64138 TATGGGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Done.