Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008310.1 Hibiscus syriacus cultivar Beakdansim tig00111000_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: 3887810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 15
Found at i:3847299 original size:8 final size:8
Alignment explanation
Indices: 3847286--3847320 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
3847276 CTTCTTCTTC
3847286 TTTTTGTT
1 TTTTTGTT
3847294 TTTTTGTT
1 TTTTTGTT
3847302 TTTTTG-T
1 TTTTTGTT
3847309 TTTTTGTT
1 TTTTTGTT
3847317 TTTT
1 TTTT
3847321 GTGGAAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTTGTT
Found at i:3847303 original size:7 final size:7
Alignment explanation
Indices: 3847286--3847322 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
3847276 CTTCTTCTTC
3847286 TTTTTGTT
1 TTTTTG-T
3847294 TTTTTGTT
1 TTTTTG-T
3847302 TTTTTGT
1 TTTTTGT
3847309 TTTTTGT
1 TTTTTGT
3847316 TTTTTGT
1 TTTTTGT
3847323 GGAAAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (7 bp):
TTTTTGT
Found at i:3847311 original size:15 final size:16
Alignment explanation
Indices: 3847286--3847320 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
3847276 CTTCTTCTTC
3847286 TTTTTGTTTTTTTGTT
1 TTTTTGTTTTTTTGTT
3847302 TTTTTG-TTTTTTGTT
1 TTTTTGTTTTTTTGTT
3847317 TTTT
1 TTTT
3847321 GTGGAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (16 bp):
TTTTTGTTTTTTTGTT
Found at i:3848130 original size:14 final size:15
Alignment explanation
Indices: 3848105--3848146 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
3848095 AATTAAATTA
3848105 AAAAT-AAAATAAAT
1 AAAATGAAAATAAAT
**
3848119 GGAATG-AAATAAAT
1 AAAATGAAAATAAAT
3848133 AAAATGAAAATAAA
1 AAAATGAAAATAAA
3848147 ACAAAATGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (15 bp):
AAAATGAAAATAAAT
Found at i:3856165 original size:18 final size:17
Alignment explanation
Indices: 3856144--3856187 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
3856134 AAGTTATTTT
3856144 TTAAATAAAAGATAAGAA
1 TTAAATAAAAGA-AAGAA
*
3856162 TTAAATAAAAGAAATAA
1 TTAAATAAAAGAAAGAA
*
3856179 ATAAATAAA
1 TTAAATAAA
3856188 TAAAATAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
TTAAATAAAAGAAAGAA
Found at i:3856854 original size:32 final size:32
Alignment explanation
Indices: 3856813--3856874 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
3856803 TTTAAACTAA
3856813 AATACCTAAAA-TAAATATAAAATA-TAAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAAT
*
3856844 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAA
3856875 CCTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 14 0.52
33 9 0.33
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (32 bp):
AATACCTAAAACTAAATTAAAATACTAAAAAT
Found at i:3858541 original size:18 final size:17
Alignment explanation
Indices: 3858520--3858563 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
3858510 AAGTTATTTT
3858520 TTAAATAAAAGATAAGAA
1 TTAAATAAAAGA-AAGAA
*
3858538 TTAAATAAAAGAAATAA
1 TTAAATAAAAGAAAGAA
*
3858555 ATAAATAAA
1 TTAAATAAA
3858564 TAATAGAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
TTAAATAAAAGAAAGAA
Found at i:3859228 original size:32 final size:32
Alignment explanation
Indices: 3859187--3859248 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
3859177 TTTAAACTAA
3859187 AATACCTAAAA-TAAATATAAAATA-TAAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAAT
*
3859218 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAA
3859249 CCTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 14 0.52
33 9 0.33
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (32 bp):
AATACCTAAAACTAAATTAAAATACTAAAAAT
Found at i:3863159 original size:3 final size:3
Alignment explanation
Indices: 3863151--3863204 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
3863141 ATATGTTTTG
3863151 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT T-T T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
3863195 TAT TGAT TAT
1 TAT T-AT TAT
3863205 GCCTCACTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.08
3 38 0.79
4 6 0.12
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:3869155 original size:3 final size:3
Alignment explanation
Indices: 3869147--3869246 Score: 191
Period size: 3 Copynumber: 33.0 Consensus size: 3
3869137 TTTGATATGA
3869147 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3869195 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
3869241 TAT TAT
1 TAT TAT
3869247 GTCTCACTAA
Statistics
Matches: 96, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 93 0.97
4 3 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3870162 original size:32 final size:32
Alignment explanation
Indices: 3870116--3870213 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 32
3870106 ATAATACAAG
* *
3870116 AATAATATTGGTACTACAACAGTATTGGTACTA-
1 AATAGTATTGGTACT--AACAGTATTGCTACTAC
* *
3870149 GA-AGTATTGGTACTAATAGTATTGCTACTAC
1 AATAGTATTGGTACTAACAGTATTGCTACTAC
* *
3870180 AATAGTATTGGTACTAACAGTATCGATACTAC
1 AATAGTATTGGTACTAACAGTATTGCTACTAC
3870212 AA
1 AA
3870214 AAACAATATC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
30 14 0.25
31 1 0.02
32 39 0.71
33 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (32 bp):
AATAGTATTGGTACTAACAGTATTGCTACTAC
Found at i:3870210 original size:47 final size:47
Alignment explanation
Indices: 3870116--3870210 Score: 129
Period size: 47 Copynumber: 2.0 Consensus size: 47
3870106 ATAATACAAG
* * *
3870116 AATAATATTGGTACTACAACAGTATTGGTACTAGAAGTATTGGTACT
1 AATAATATTGCTACTACAACAGTATTGGTACTAGAAGTATCGATACT
* *
3870163 AATAGTATTGCTACTACAATAGTATTGGTACTA-ACAGTATCGATACT
1 AATAATATTGCTACTACAACAGTATTGGTACTAGA-AGTATCGATACT
3870210 A
1 A
3870211 CAAAAACAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
46 1 0.02
47 41 0.98
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.34
Consensus pattern (47 bp):
AATAATATTGCTACTACAACAGTATTGGTACTAGAAGTATCGATACT
Found at i:3877430 original size:18 final size:18
Alignment explanation
Indices: 3877407--3877447 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
3877397 AACTTAAACA
3877407 AATTAATAATGAAAAATT
1 AATTAATAATGAAAAATT
**
3877425 AATTAATAATTTAAAATT
1 AATTAATAATGAAAAATT
3877443 AATTA
1 AATTA
3877448 TATTCGTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AATTAATAATGAAAAATT
Found at i:3881188 original size:20 final size:20
Alignment explanation
Indices: 3881163--3881212 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3881153 AGTGAACTTG
*
3881163 GTATCGATGCCAC-CCTATGA
1 GTATCGATGCCACACCTA-CA
* *
3881183 GTATCGATACCTCACCTACA
1 GTATCGATGCCACACCTACA
3881203 GTATCGATGC
1 GTATCGATGC
3881213 TTATTTCATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (20 bp):
GTATCGATGCCACACCTACA
Found at i:3884272 original size:116 final size:115
Alignment explanation
Indices: 3883936--3884391 Score: 459
Period size: 116 Copynumber: 3.9 Consensus size: 115
3883926 TTTTAAAGGA
* * * * *
3883936 TCAAATTCATCACATAAGGAGTTCGATCAACATTTTCAACGGAGAGTTCATAATGAGAAGAACTC
1 TCAAATCCATCATAGAAGGAGGTGGATCAACATTTTCAA-GG-GAGTTCATAATGAGAAGAACTC
* * * *
3884001 ATCCACGGATGAAGAAGAAGTTCACAATAAGAAGAACTTGTTCAACATTTTGC
64 ATCCACGGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAAC-CTTTAC
* ** ** * *
3884054 TCAAATCTATCA-AGAATAAGAAGGATCAACATTTTC-ATGGAGTTCATAATGAGAAAAACTCAT
1 TCAAATCCATCATAGAAGGAGGTGGATCAACATTTTCAAGGGAGTTCATAATGAGAAGAACTCAT
*
3884117 CCACAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTATAC
66 CCACGGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTT-TAC
* * * * * *
3884168 TCAAATCCATCATATAAGGAGGTGGTTCAACATTTTCAAGGGAATTTATAATAAGAAGAACAT-G
1 TCAAATCCATCATAGAAGGAGGTGGATCAACATTTTCAAGGGAGTTCATAATGAGAAGAAC-TCA
* * * * *
3884232 TCTACGGAGGGAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTAGA
65 TCCACGGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTA-C
* * ** ***
3884284 TCAACTCCATCATAGAAAGAGGTGGATCAACATTATAAATATAAAGTTCATAATGAGAAGAACTC
1 TCAAATCCATCATAGAAGGAGGTGGATCAACATT-TTCA-AGGGAGTTCATAATGAGAAGAACTC
* ** * *
3884349 ACCCAAAGAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTC
64 ATCCACGGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
3884392 GACATTTTGC
Statistics
Matches: 276, Mismatches: 54, Indels: 16
0.80 0.16 0.05
Matches are distributed among these distances:
113 2 0.01
114 77 0.28
115 21 0.08
116 92 0.33
117 22 0.08
118 62 0.22
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.25
Consensus pattern (115 bp):
TCAAATCCATCATAGAAGGAGGTGGATCAACATTTTCAAGGGAGTTCATAATGAGAAGAACTCAT
CCACGGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTAC
Done.