Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002118.1 Hibiscus syriacus cultivar Beakdansim tig00004343_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: 68793
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:130 original size:35 final size:35
Alignment explanation
Indices: 91--167 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
81 GTTGGGCATA
* * *
91 TAATTGAAGTATTTTGGAATTTGA-GATTTAGAATG
1 TAATTAAAATATTTTGG-ATTTGAGGATTTAAAATG
* *
126 TAATTAAAATATTTTGGATTTTAGGGTTTAAAATG
1 TAATTAAAATATTTTGGATTTGAGGATTTAAAATG
161 TAATTAA
1 TAATTAA
168 TGACTGTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
34 5 0.14
35 31 0.86
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (35 bp):
TAATTAAAATATTTTGGATTTGAGGATTTAAAATG
Found at i:4390 original size:8 final size:8
Alignment explanation
Indices: 4377--4402 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
4367 GGTAAACATA
4377 TTCTTCTG
1 TTCTTCTG
4385 TTCTTCTG
1 TTCTTCTG
4393 TTCTTCTG
1 TTCTTCTG
4401 TT
1 TT
4403 GGCTTTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.12, T:0.65
Consensus pattern (8 bp):
TTCTTCTG
Found at i:22197 original size:16 final size:17
Alignment explanation
Indices: 22162--22203 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
22152 TATACTGCAG
*
22162 ATCATCGATTCAACCCC
1 ATCATCAATTCAACCCC
22179 ATCATCAATTCAA-CCC
1 ATCATCAATTCAACCCC
22195 ATCATCAAT
1 ATCATCAAT
22204 GGCCTGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (17 bp):
ATCATCAATTCAACCCC
Found at i:28107 original size:250 final size:247
Alignment explanation
Indices: 27669--28164 Score: 710
Period size: 253 Copynumber: 2.0 Consensus size: 247
27659 TTTTTTTATT
* * *
27669 TCGGGTCGGGTTTCTAATTCTTATATTCGGATCGGGTCGAGTGAAACTTTATTTTGGTCGTGTCG
1 TCGGGTCGGATTTCTAATTCATATATTCGGATCGGGTCGAGTGAAACTTTATTTTGGTCGGGTCG
* *
27734 GTTTTTTTAAGTATGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCTGACCCG
66 GTTTTTTTAAGTATGATATTCGGGT---GTCGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCG
* *
27799 AAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAAT
128 AAAAAATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCCTC--TATAT-AT
* *
27864 TTTTTTCAATTAAGTCACTATTTTTATTAAATAAAAATAATTTTATTATTATTTCGGG
190 TTTTTCCAATTAAATCACTATTTTTATTAAATAAAAATAATTTTATTATTATTTCGGG
* * * *
27922 TCGGGTCGGATTTCTAATTCATATATTGGGGTCGGGTCGGGTGAAATTTTATTTTGGTCGGGTCG
1 TCGGGTCGGATTTCTAATTCATATATTCGGATCGGGTCGAGTGAAACTTTATTTTGGTCGGGTCG
* *
27987 GATTTTTTTTAAGTGTGATATTCGGGT-T-GGGTTCGAGTTTAGGGTGAAAAATACCCGACCC-A
66 G--TTTTTTTAAGTATGATATTCGGGTGTCGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCGA
* *
28049 AAAAATATATAATTTTACCTTATATATTTTAGAAATAATTACAATAATATCTCTCTATATATTTT
129 AAAAATATATAATTTTACCTTATATA-TTTAGAAATAATTACAATAATACCCCTCTATATATTTT
* * *
28114 TTCCAATTAAATCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTT
193 TTCCAATTAAATCACTATTTTTATTAAATAAAAATAATTTTATTATTATTT
28165 TAGGTCAAAT
Statistics
Matches: 220, Mismatches: 20, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
247 51 0.23
248 5 0.02
249 26 0.12
250 55 0.25
251 1 0.00
253 59 0.27
255 23 0.10
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (247 bp):
TCGGGTCGGATTTCTAATTCATATATTCGGATCGGGTCGAGTGAAACTTTATTTTGGTCGGGTCG
GTTTTTTTAAGTATGATATTCGGGTGTCGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCGAAA
AAATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCCTCTATATATTTTTTC
CAATTAAATCACTATTTTTATTAAATAAAAATAATTTTATTATTATTTCGGG
Found at i:35229 original size:77 final size:77
Alignment explanation
Indices: 35095--35658 Score: 479
Period size: 77 Copynumber: 7.4 Consensus size: 77
35085 ATTCCACATT
* * * * * *
35095 GCAACTTACTTTCTTAGT-AAACCATAATATTATTGTGCGCAA-TCCTTTTAATTAATAAAAATA
1 GCAACCTA-TTTCTTAGTGAAA-CATGACATTCTTGGGCGCAACTCATTTT-ATTAATAAAAATA
*
35158 TTAATATT-TCATATC
63 TTAACATTCT-ATATC
* * * * *
35173 GCAACCTATTTGTTAGTCAAACATGGCATTCTTGGGTGTAAC-CTATTTTATTAATAAAAATATT
1 GCAACCTATTTCTTAGTGAAACATGACATTCTTGGGCGCAACTC-ATTTTATTAATAAAAATATT
* *
35237 AAAATTCCATATC
65 AACATTCTATATC
* * * *
35250 GCAACATATTTCTTAGTGAACCATGACATT-AT--CCGCAACTCATTTTATT-A-AAAAATATTA
1 GCAACCTATTTCTTAGTGAAACATGACATTCTTGGGCGCAACTCATTTTATTAATAAAAATATTA
*
35310 ACATTCTAGATC
66 ACATTCTATATC
* * * *
35322 GCAACCTATTTTTTAGT-AAATCATGACAATCTTGGGCGCAACTCATTTTATAAATAAAAACATT
1 GCAACCTATTTCTTAGTGAAA-CATGACATTCTTGGGCGCAACTCATTTTATTAATAAAAATATT
35386 AACATTCTATATC
65 AACATTCTATATC
* * * * * * * * *
35399 ACAATCTATTTCTTAGTGAATCATTACATTGTTGGACGTAACCCATTTCATTAATAAAAAATATT
1 GCAACCTATTTCTTAGTGAAACATGACATTCTTGGGCGCAACTCATTTTATTAAT-AAAAATATT
* * *
35464 AACATTCCAGATA
65 AACATTCTATATC
* * * * * * * * **
35477 TCATCCTATCTCTTAGTGAACCATGCCATGCTTAGGCGCAACTCATTTAATT-A-CCAAATATTA
1 GCAACCTATTTCTTAGTGAAACATGACATTCTTGGGCGCAACTCATTTTATTAATAAAAATATTA
* *
35540 ACATCCTAGATC
66 ACATTCTATATC
* * * * *
35552 ACAACTTATTTCTTAGT-AAACCATGACATTTTTTGGCGCAACCCATTTTATTAATAAAAATATT
1 GCAACCTATTTCTTAGTGAAA-CATGACATTCTTGGGCGCAACTCATTTTATTAATAAAAATATT
35616 AACATTCTATATC
65 AACATTCTATATC
* *
35629 ACAACCTATTTCTTAGTGAACCATGACATT
1 GCAACCTATTTCTTAGTGAAACATGACATT
35659 TTTAGACACA
Statistics
Matches: 384, Mismatches: 85, Indels: 35
0.76 0.17 0.07
Matches are distributed among these distances:
71 2 0.01
72 42 0.11
73 2 0.01
74 14 0.04
75 71 0.18
76 3 0.01
77 176 0.46
78 74 0.19
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (77 bp):
GCAACCTATTTCTTAGTGAAACATGACATTCTTGGGCGCAACTCATTTTATTAATAAAAATATTA
ACATTCTATATC
Found at i:35355 original size:149 final size:149
Alignment explanation
Indices: 35151--35656 Score: 368
Period size: 149 Copynumber: 3.3 Consensus size: 149
35141 TTTAATTAAT
* * * * * *
35151 AAAAATATTAATATTTCATATCGCAACCTATTTGTTAGTCAAACATGGCATTCTTGGGTGTAAC-
1 AAAAATATTAACATTTCAGATCGCAACCTATTTGTTAGTCAAACATGACAATCTTGGGCGCAACT
* * *
35215 CTATTTTATTAATAAAAATATTAAAATTCCATATCGCAA-CATATTTCTTAGTGAACCATGACAT
66 C-ATTTTATAAATAAAAACATTAAAATTCCATATCACAATC-TATTTCTTAGTGAACCATGACAT
35279 TATCCGCAACTCATTTTATTA
129 TATCCGCAACTCATTTTATTA
*
35300 AAAAATATTAACA-TTCTAGATCGCAACCTATTTTTTAGT-AAATCATGACAATCTTGGGCGCAA
1 AAAAATATTAACATTTC-AGATCGCAACCTATTTGTTAGTCAAA-CATGACAATCTTGGGCGCAA
* * * *
35363 CTCATTTTATAAATAAAAACATTAACATTCTATATCACAATCTATTTCTTAGTGAATCATTACAT
64 CTCATTTTATAAATAAAAACATTAAAATTCCATATCACAATCTATTTCTTAGTGAACCATGACAT
* * * * *
35428 TGTTGGACGTAACCCATTTCATTAATA
129 T-AT--CCGCAACTCA-TT--TTATTA
* ** * * * * * * *
35455 AAAAATATTAACATTCCAGATATCATCCTATCTCTTAGTGAACCATG-CCATGCTTAGGCGCAAC
1 AAAAATATTAACATTTCAGATCGCAACCTATTTGTTAGTCAAACATGACAAT-CTTGGGCGCAAC
* * * * * *
35519 TCA--TT-TAATTACCAAATATTAACA-TCCTAGATCACAA-CTTATTTCTTAGTAAACCATGAC
65 TCATTTTATAAATA-AAAACATTAAAATTCC-ATATCACAATC-TATTTCTTAGTGAACCATGAC
* * *
35579 ATTTTTTGGCGCAACCCATTTTATTAA
127 A--TTAT-CCGCAACTCATTTTATT-A
* * * * *
35606 TAAAAATATTAACA-TTCTATATCACAACCTATTTCTTAGTGAACCATGACA
1 -AAAAATATTAACATTTC-AGATCGCAACCTATTTGTTAGTCAAACATGACA
35657 TTTTTAGACA
Statistics
Matches: 289, Mismatches: 46, Indels: 40
0.77 0.12 0.11
Matches are distributed among these distances:
148 6 0.02
149 103 0.36
150 7 0.02
151 3 0.01
152 55 0.19
153 51 0.18
154 5 0.02
155 55 0.19
156 4 0.01
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.36
Consensus pattern (149 bp):
AAAAATATTAACATTTCAGATCGCAACCTATTTGTTAGTCAAACATGACAATCTTGGGCGCAACT
CATTTTATAAATAAAAACATTAAAATTCCATATCACAATCTATTTCTTAGTGAACCATGACATTA
TCCGCAACTCATTTTATTA
Found at i:35551 original size:230 final size:226
Alignment explanation
Indices: 35104--35658 Score: 646
Period size: 230 Copynumber: 2.4 Consensus size: 226
35094 TGCAACTTAC
* * * * * * *
35104 TTTCTTAGTAAACCATAATATTATTGTGCGCAA-TCCTTTTAATTAATAAAAATATTAATATT-T
1 TTTCTTAGTAAACCATGACAATCTTGGGCGCAACTCATTTT-ATTAATAAAAATATTAACATTCT
* * * * ** * *
35167 CATATCGCAACCTATTTGTTAGTCAAACATGGCATTCTTGGGTGTAACCTATTTTATTAATAAAA
65 -ATATCACAACCTATTTCTTAGTGAAACATGACATTCTTGGACGTAACCCATTTCATTAATAAAA
* * * * *
35232 ATATTAAAATTCCATATCGCAACATATTTCTTAGTGAACCATGACATTATCCGCAACTCATTTTA
129 ATATTAAAATTCCAGATAGCAACATATCTCTTAGTGAACCATGACATTAGCCGCAACTCATTTAA
* *
35297 TTAAAAAATATTAACATTCTAGATCGCAACCTA
194 TTAAAAAATATTAACATCCTAGATCACAACCTA
* * * *
35330 TTTTTTAGTAAATCATGACAATCTTGGGCGCAACTCATTTTATAAATAAAAACATTAACATTCTA
1 TTTCTTAGTAAACCATGACAATCTTGGGCGCAACTCATTTTATTAATAAAAATATTAACATTCTA
* * * *
35395 TATCACAATCTATTTCTTAGTGAATCATTACATTGTTGGACGTAACCCATTTCATTAATAAAAAA
66 TATCACAACCTATTTCTTAGTGAAACATGACATTCTTGGACGTAACCCATTTCATTAAT-AAAAA
* * * * * *
35460 TATTAACATTCCAGATATCATCCTATCTCTTAGTGAACCATGCCATGCTTAGGCGCAACTCATTT
130 TATTAAAATTCCAGATAGCAACATATCTCTTAGTGAACCATGACA---TTAGCCGCAACTCATTT
** *
35525 AATTACCAAATATTAACATCCTAGATCACAACTTA
192 AATTAAAAAATATTAACATCCTAGATCACAACCTA
* * * *
35560 TTTCTTAGTAAACCATGACATTTTTTGGCGCAACCCATTTTATTAATAAAAATATTAACATTCTA
1 TTTCTTAGTAAACCATGACAATCTTGGGCGCAACTCATTTTATTAATAAAAATATTAACATTCTA
*
35625 TATCACAACCTATTTCTTAGTGAACCATGACATT
66 TATCACAACCTATTTCTTAGTGAAACATGACATT
35659 TTTAGACACA
Statistics
Matches: 273, Mismatches: 50, Indels: 8
0.82 0.15 0.02
Matches are distributed among these distances:
226 92 0.34
227 49 0.18
230 132 0.48
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.37
Consensus pattern (226 bp):
TTTCTTAGTAAACCATGACAATCTTGGGCGCAACTCATTTTATTAATAAAAATATTAACATTCTA
TATCACAACCTATTTCTTAGTGAAACATGACATTCTTGGACGTAACCCATTTCATTAATAAAAAT
ATTAAAATTCCAGATAGCAACATATCTCTTAGTGAACCATGACATTAGCCGCAACTCATTTAATT
AAAAAATATTAACATCCTAGATCACAACCTA
Found at i:44721 original size:14 final size:15
Alignment explanation
Indices: 44684--44720 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
44674 TTTTAAAAAA
44684 ATTAAAAATTTAGAT
1 ATTAAAAATTTAGAT
44699 ATTAAAAATTTAGAT
1 ATTAAAAATTTAGAT
44714 ATTAAAA
1 ATTAAAA
44721 TATGCCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
ATTAAAAATTTAGAT
Found at i:46178 original size:64 final size:64
Alignment explanation
Indices: 46046--46178 Score: 140
Period size: 64 Copynumber: 2.1 Consensus size: 64
46036 TCAGACTATT
* * * * * * * ** *
46046 AATTAGTATTCGGATAAAATCAGAAACAATCAATTAATACCGTCTTAAATAAAATTTGATTGTT
1 AATTAGTATCCGGATAAAATAAAAAACAATCAATTAACACCGTATTAAATAAAATATAATCATG
* * * *
46110 AATTAGTATCCGGATAAAATAAAAAATAATCAATTAACACTGTATTATATAGAATATAATCATG
1 AATTAGTATCCGGATAAAATAAAAAACAATCAATTAACACCGTATTAAATAAAATATAATCATG
46174 AATTA
1 AATTA
46179 CAAGTCATAC
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (64 bp):
AATTAGTATCCGGATAAAATAAAAAACAATCAATTAACACCGTATTAAATAAAATATAATCATG
Found at i:53758 original size:68 final size:68
Alignment explanation
Indices: 53649--53784 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
53639 CCTGGCTGGC
53649 CTGCCTCCGACTCATCCATGTATAATAATTGCGTAATTATTTCAAAACGAATGAATCCGATACAT
1 CTGCCTCCGACTCATCCATGTATAATAATTGCGTAATTATTTCAAAACGAATGAATCCGATACAT
53714 ATT
66 ATT
53717 CTGCCTCCGACTCATCCATGTATAATAATTGCGTAATTATTTCAAAACGAATGAATCCGATACAT
1 CTGCCTCCGACTCATCCATGTATAATAATTGCGTAATTATTTCAAAACGAATGAATCCGATACAT
53782 ATT
66 ATT
53785 ATAGGTGTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (68 bp):
CTGCCTCCGACTCATCCATGTATAATAATTGCGTAATTATTTCAAAACGAATGAATCCGATACAT
ATT
Found at i:63426 original size:29 final size:27
Alignment explanation
Indices: 63371--63427 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
63361 AACTAATACT
* **
63371 AAAAAAAGTTAAAATAATTATTTTATA
1 AAAAAAAATTAAAATAATTATGATATA
63398 AAAAAAAATTAAAAATGAATTATGATATA
1 AAAAAAAATT-AAAAT-AATTATGATATA
63427 A
1 A
63428 TATACTTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.36
28 5 0.20
29 11 0.44
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (27 bp):
AAAAAAAATTAAAATAATTATGATATA
Found at i:64408 original size:37 final size:37
Alignment explanation
Indices: 64358--64432 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
64348 GACGACATGA
*
64358 ACCACCCCTATAATATAACTCTCTAATGTCCAATCTG
1 ACCACCCCTATAATAGAACTCTCTAATGTCCAATCTG
*
64395 ACCACCCCTATAATAGAACTCTGTAATGTCCAATCTG
1 ACCACCCCTATAATAGAACTCTCTAATGTCCAATCTG
64432 A
1 A
64433 ACTAATCGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.28
Consensus pattern (37 bp):
ACCACCCCTATAATAGAACTCTCTAATGTCCAATCTG
Found at i:65358 original size:24 final size:24
Alignment explanation
Indices: 65331--65380 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
65321 TGACAGTACC
65331 CCTCCCCTTAATTAAAATCCCTAA
1 CCTCCCCTTAATTAAAATCCCTAA
* *
65355 CCTCCCTTTAATTGAAATCCCTAA
1 CCTCCCCTTAATTAAAATCCCTAA
65379 CC
1 CC
65381 CTATTTCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.38, G:0.02, T:0.30
Consensus pattern (24 bp):
CCTCCCCTTAATTAAAATCCCTAA
Found at i:68214 original size:23 final size:24
Alignment explanation
Indices: 68188--68236 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
68178 TGGCAGTACC
68188 CCTC-CCTTAATTAAAATCCCTAA
1 CCTCTCCTTAATTAAAATCCCTAA
* *
68211 CCTCTCTTTAATTGAAATCCCTAA
1 CCTCTCCTTAATTAAAATCCCTAA
68235 CC
1 CC
68237 CTATTTCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.31, C:0.35, G:0.02, T:0.33
Consensus pattern (24 bp):
CCTCTCCTTAATTAAAATCCCTAA
Done.