Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000505.1 Hibiscus syriacus cultivar Beakdansim tig00000962_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: 56286
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:1642 original size:136 final size:136
Alignment explanation
Indices: 1375--2141 Score: 828
Period size: 136 Copynumber: 5.7 Consensus size: 136
1365 CAACTGGTGT
* *
1375 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTGAAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * * * * * * * *
1440 CCTTC--GAT---GA--TGTGGTTATCTGAGGATGACTCAGCTTATACGTGATGAGTAGTTCTGG
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGACAC-GCTTCTTCATGATGAGGAATTCTGA
1498 TCAGTGG
130 TCAGTGG
* *
1505 ATGACATTGTTTCTTCGTGATGAGGACGT-TACCCATCTTTAAAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * * * * *
1569 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGTTGACACGACTCCTACGTGATGAGGAGTTCTGG
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGACACG-CTTCTTCATGATGAGGAATTCTGA
1634 TCAGTGG
130 TCAGTGG
* * * * *
1641 ATGACTTTGTTCATTCGTGATGAGGATGTCTAACCATCTTTAAAGATA-TTGAGATAACACGATT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * * * ** * * * *
1705 CTTTAGTGATGAAGACGTCTGGCTATCTAAGGATGATGCTGCTCCTTTATCATAAGGAATTCTGA
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGACAC-GCTTCTTCATGATGAGGAATTCTGA
*
1770 TCAATGG
130 TCAGTGG
* ***
1777 ATGACATTGTTCCTTCGTGATGA-GATGTCTAGCCATCTTTAAAGATATTTGAGATAACACAACT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * *
1841 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGATGCTTCTTCATGATGAGGAATTCTGA
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGA-CACGCTTCTTCATGATGAGGAATTCTGA
*
1906 TCAATGG
130 TCAGTGG
* * * * **
1913 ATGACATTGTTCATTCGTG-T--TGA-GTCCAACCATCTTTAAAGATA-TTGAGATAACAAAGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACGGTT
* *** * *
1973 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGTTGCTGCTTCTTC-TGATGAGGATTTCTAA
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGACAC-GCTTCTTCATGATGAGGAATTCTGA
*
2037 TCGGTGG
130 TCAGTGG
* * * *
2044 ATGATATTGTTCCTTCATGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACATGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACGGTT
*
2109 CTTTCGTGATGAGGACGTCTGGTTATCTAAGGA
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGA
2142 CGATGTTTCC
Statistics
Matches: 544, Mismatches: 74, Indels: 32
0.84 0.11 0.05
Matches are distributed among these distances:
129 37 0.07
130 28 0.05
131 38 0.07
132 57 0.10
133 19 0.03
134 6 0.01
135 43 0.08
136 298 0.55
137 18 0.03
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (136 bp):
ATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACGGTT
CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGACACGCTTCTTCATGATGAGGAATTCTGAT
CAGTGG
Found at i:2117 original size:268 final size:273
Alignment explanation
Indices: 1498--2146 Score: 857
Period size: 268 Copynumber: 2.4 Consensus size: 273
1488 GTAGTTCTGG
* *
1498 TCAGTGGATGACATTGTTTCTTCGTGATGAGGACGT-TACCCATCTTTAAAGATATTTGAGATAA
1 TCAGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAA
* * *
1562 CACGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGTTGA-CACGACTCCTACGTGATGAGG
66 CACGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGACGACTCCTACATGATGAGG
* * * * *
1626 AGTTCTGGTCAGTGGATGACTTTGTTCATTCGTGATGAGGATGTCTAACCATCTTTAAAGATATT
131 AATTCTGATCAATGGATGACATTGTTCATTCGTGAT-AGGATGTCCAACCATCTTTAAAGATATT
* * *
1691 GAGATAACACGATTCTTTAGTGATGAAGACGTCTGGCTATCTAAGGATGATGCTGCTCCTTTATC
195 GAGATAACAAGATTCCTTAGTGATGAAGACATCTGGCTATCTAAGGATGATGCTGCTCCTTTATC
*
1756 ATAAGGAATTCTGA
260 ATAAGGAATTCTAA
* *
1770 TCAATGGATGACATTGTTCCTTCGTGATGA-GATGTCTAGCCATCTTTAAAGATATTTGAGATAA
1 TCAGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAA
*** * * * *
1834 CACAACTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGATG-CTTCTTCATGATGAGG
66 CACGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGACGACTCCTACATGATGAGG
*
1898 AATTCTGATCAATGGATGACATTGTTCATTCGTG-T-TGA-GTCCAACCATCTTTAAAGATATTG
131 AATTCTGATCAATGGATGACATTGTTCATTCGTGATAGGATGTCCAACCATCTTTAAAGATATTG
* * * * * * *
1960 AGATAACAA-AGTTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGTTGCTGCTTC-TTCTG
196 AGATAACAAGA-TTCCTTAGTGATGAAGACATCTGGCTATCTAAGGATGATGCTGCTCCTTTATC
* *
2023 ATGAGGATTTCTAA
260 ATAAGGAATTCTAA
* * * *
2037 TCGGTGGATGATATTGTTCCTTCATGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAA
1 TCAGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAA
* * *
2102 CATGGTTCTTTCGTGATGAGGACGTCTGGTTATCTAAGGACGATG
66 CACGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATG
2147 TTTCCTAATT
Statistics
Matches: 327, Mismatches: 46, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
267 41 0.13
268 141 0.43
269 2 0.01
271 5 0.02
272 136 0.42
273 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (273 bp):
TCAGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAA
CACGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGACGACTCCTACATGATGAGG
AATTCTGATCAATGGATGACATTGTTCATTCGTGATAGGATGTCCAACCATCTTTAAAGATATTG
AGATAACAAGATTCCTTAGTGATGAAGACATCTGGCTATCTAAGGATGATGCTGCTCCTTTATCA
TAAGGAATTCTAA
Found at i:8200 original size:24 final size:24
Alignment explanation
Indices: 8156--8205 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
8146 ATAAAGAACC
*
8156 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
8180 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
8204 AA
1 AA
8206 TCAACCACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:17227 original size:24 final size:24
Alignment explanation
Indices: 17183--17232 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
17173 ATAAAGAACC
*
17183 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
17207 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
17231 AA
1 AA
17233 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:22141 original size:31 final size:31
Alignment explanation
Indices: 22103--22198 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 31
22093 GAACCTCAAC
*
22103 AACTATCCATAGGTCCCAAAGAACCTAGGTA
1 AACTATCCATAGGTCCCAAAGAACATAGGTA
* ** *
22134 AACTATCCATATGTCCCGTAGAACATATGTA
1 AACTATCCATAGGTCCCAAAGAACATAGGTA
* ** *
22165 AACTGTCCATATATCCTGAAAG-ACATAGGTA
1 AACTATCCATAGGTCC-CAAAGAACATAGGTA
22196 AAC
1 AAC
22199 CCTCGACTCT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 51 0.96
32 2 0.04
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.24
Consensus pattern (31 bp):
AACTATCCATAGGTCCCAAAGAACATAGGTA
Found at i:27351 original size:31 final size:31
Alignment explanation
Indices: 27313--27408 Score: 113
Period size: 31 Copynumber: 3.1 Consensus size: 31
27303 GAACCTCGAC
* *
27313 AACTATCCATAGGTCCCAAAGAACCTAGGTA
1 AACTATCCATATGTCCCAAAGAACATAGGTA
* **
27344 AACTATCCATATATCCCGTAGAACATAGGTA
1 AACTATCCATATGTCCCAAAGAACATAGGTA
* *
27375 AACTGTTCATATGTCCCGAAAG-ACATAGGTA
1 AACTATCCATATGTCCC-AAAGAACATAGGTA
27406 AAC
1 AAC
27409 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 52 0.96
32 2 0.04
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (31 bp):
AACTATCCATATGTCCCAAAGAACATAGGTA
Found at i:28198 original size:24 final size:24
Alignment explanation
Indices: 28171--28231 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
28161 TGCACTCTTT
* *
28171 AGTGTATCGATGCATCCCTTAACG
1 AGTGCATCGATGCATCCATTAACG
28195 AGTGCATCGATGCATCCATTAACG
1 AGTGCATCGATGCATCCATTAACG
28219 AGTGCATCGATGC
1 AGTGCATCGATGC
28232 TCTATCTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (24 bp):
AGTGCATCGATGCATCCATTAACG
Found at i:45330 original size:61 final size:63
Alignment explanation
Indices: 45241--45361 Score: 158
Period size: 61 Copynumber: 2.0 Consensus size: 63
45231 CCTCGGCAAC
*
45241 TGTCCATAGGTCCCGAAGAACCTAGGTAA-ATTCTCCATATATTCT-TAGAACATAGGTATAT
1 TGTCCATAGGTCCCGAAGAACATAGGTAATATTCTCCATATATTCTGTAGAACATAGGTATAT
* * * * *
45302 TGTCCATATGTCTCGAA-AGACATAGGTAATTTTGTCCATATGTTCTGTAGAACATAGGTA
1 TGTCCATAGGTCCCGAAGA-ACATAGGTAATATTCTCCATATATTCTGTAGAACATAGGTA
45362 AACCATCGAC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
60 1 0.02
61 24 0.47
62 13 0.25
63 13 0.25
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (63 bp):
TGTCCATAGGTCCCGAAGAACATAGGTAATATTCTCCATATATTCTGTAGAACATAGGTATAT
Found at i:45357 original size:32 final size:32
Alignment explanation
Indices: 45257--45362 Score: 114
Period size: 32 Copynumber: 3.4 Consensus size: 32
45247 TAGGTCCCGA
* * *
45257 AGAACCTAGGTAA-ATTCTCCATATATTCT-T
1 AGAACATAGGTAATATTGTCCATATGTTCTGT
45287 AGAACATAGGT-ATATTGTCCATATG-TCTCG-
1 AGAACATAGGTAATATTGTCCATATGTTCT-GT
* *
45317 AAAGACATAGGTAATTTTGTCCATATGTTCTGT
1 AGA-ACATAGGTAATATTGTCCATATGTTCTGT
45350 AGAACATAGGTAA
1 AGAACATAGGTAA
45363 ACCATCGACT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
29 4 0.06
30 22 0.35
31 8 0.13
32 24 0.38
33 5 0.08
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (32 bp):
AGAACATAGGTAATATTGTCCATATGTTCTGT
Found at i:46018 original size:15 final size:15
Alignment explanation
Indices: 45994--46032 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
45984 ATGGACACTG
*
45994 AACATATATCATATA
1 AACATGTATCATATA
46009 AACATGTATCATATA
1 AACATGTATCATATA
46024 AACATGTAT
1 AACATGTAT
46033 TCACACATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (15 bp):
AACATGTATCATATA
Found at i:46249 original size:19 final size:19
Alignment explanation
Indices: 46225--46261 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
46215 TTATGATTTT
46225 CTTATGCATCGATGCACTC
1 CTTATGCATCGATGCACTC
46244 CTTATGCATCGATGCACT
1 CTTATGCATCGATGCACT
46262 AATTGCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (19 bp):
CTTATGCATCGATGCACTC
Found at i:50900 original size:3 final size:3
Alignment explanation
Indices: 50892--50938 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
50882 ATTTATTTTG
50892 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
50939 TGATAGTCTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:51605 original size:18 final size:18
Alignment explanation
Indices: 51582--51617 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
51572 GAGGGATTAT
*
51582 TAGTGGTCCTTCGGGACA
1 TAGTGGTCCTACGGGACA
51600 TAGTGGTCCTACGGGACA
1 TAGTGGTCCTACGGGACA
51618 AATTCTACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.25
Consensus pattern (18 bp):
TAGTGGTCCTACGGGACA
Found at i:51736 original size:2 final size:2
Alignment explanation
Indices: 51731--51758 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
51721 TAAAAAAGAA
51731 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51759 TACATGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54981 original size:29 final size:29
Alignment explanation
Indices: 54948--55006 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
54938 AAGATTAATC
54948 GTGCCAAAGCTCTTGAAAGAGCTTAGAAT
1 GTGCCAAAGCTCTTGAAAGAGCTTAGAAT
54977 GTGCCAAAGCTCTTGAAAGAGCTTAGAAT
1 GTGCCAAAGCTCTTGAAAGAGCTTAGAAT
55006 G
1 G
55007 AGAGATTCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (29 bp):
GTGCCAAAGCTCTTGAAAGAGCTTAGAAT
Done.