Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007555.1 Hibiscus syriacus cultivar Beakdansim tig00021219_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: 41689
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Found at i:2205 original size:25 final size:25
Alignment explanation
Indices: 2177--2263 Score: 90
Period size: 25 Copynumber: 3.5 Consensus size: 25
2167 TAAGAATATA
*
2177 TTAATTTAAATTATATTATATATTC
1 TTAAATTAAATTATATTATATATTC
*
2202 TTAAATTAAATTAT-TCTA-ATATTA
1 TTAAATTAAATTATAT-TATATATTC
* * *
2226 TTAAAATATTATTATATAAT-TATTC
1 TTAAATTA-AATTATATTATATATTC
2251 TTAAATTAAATTA
1 TTAAATTAAATTA
2264 ATTTATTCTC
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
24 17 0.34
25 32 0.64
26 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAAATTAAATTATATTATATATTC
Found at i:2242 original size:19 final size:19
Alignment explanation
Indices: 2205--2247 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
2195 TATATTCTTA
* *
2205 AATTAAATTATTCTAATAT
1 AATTAAAATATTATAATAT
* *
2224 TATTAAAATATTATTATAT
1 AATTAAAATATTATAATAT
2243 AATTA
1 AATTA
2248 TTCTTAAATT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTAAAATATTATAATAT
Found at i:3410 original size:21 final size:23
Alignment explanation
Indices: 3376--3419 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
3366 ATTTCCAATC
*
3376 ATATTCTATAAAATTATATTAAT
1 ATATTCTATAAAATTAAATTAAT
3399 ATATTCT-T-AAATTAAATTAAT
1 ATATTCTATAAAATTAAATTAAT
3420 TTAGACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 1 0.05
23 7 0.35
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTCTATAAAATTAAATTAAT
Found at i:3567 original size:22 final size:21
Alignment explanation
Indices: 3542--3609 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
3532 TTTATTCTTA
3542 AATTAATTTAAATTAT-ATATAT
1 AATT-ATTTAAATTATAATAT-T
* *
3564 AATTTATTAAAATCATAATATT
1 AA-TTATTTAAATTATAATATT
3586 AA-TATTTAAATTATAA-ATT
1 AATTATTTAAATTATAATATT
3605 -ATTAT
1 AATTAT
3610 ATATTTGGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
18 1 0.03
19 6 0.15
20 12 0.31
22 14 0.36
23 6 0.15
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTATTTAAATTATAATATT
Found at i:23148 original size:2 final size:2
Alignment explanation
Indices: 23141--23169 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23131 ATCATTTTAA
23141 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23170 AAGTGTATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27236 original size:32 final size:32
Alignment explanation
Indices: 27199--27433 Score: 303
Period size: 32 Copynumber: 7.3 Consensus size: 32
27189 CACGTTACTC
*
27199 ACATAGGTAATTCTGTTCATATGTCCCGAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
* * * *
27231 ACATAGGTAATACCGTCAATATGTCCCAAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
* * *
27263 ACATAGGTAATTTTGTCCATATGTCTCAAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
* *
27295 ACATAGGTAATACTATCCATATGTCCCGAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
* * *
27327 ACGTATGTAATT-TCATCCATATGTCCCGAAAG
1 ACATAGGTAATTCT-GTCCATATGTCCCGAAAG
27359 ACATAGGTAATAT-TGTCCATATGTCCCGAAAG
1 ACATAGGTAAT-TCTGTCCATATGTCCCGAAAG
* *
27391 ACATAGGTAATTCTGTCTATATGTCCTGAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
27423 ACATAGGTAAT
1 ACATAGGTAAT
27434 ACTTGACTCT
Statistics
Matches: 177, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
31 2 0.01
32 173 0.98
33 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (32 bp):
ACATAGGTAATTCTGTCCATATGTCCCGAAAG
Found at i:27284 original size:64 final size:64
Alignment explanation
Indices: 27199--27436 Score: 334
Period size: 64 Copynumber: 3.7 Consensus size: 64
27189 CACGTTACTC
* * * *
27199 ACATAGGTAATTCTGTTCATATGTCCCGAAAGACATAGGTAATACCGTCAATATGTCCCAAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCCGAAAG
* * * *
27263 ACATAGGTAATTTTGTCCATATGTCTCAAAAGACATAGGTAATACTATCCATATGTCCCGAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCCGAAAG
* * * *
27327 ACGTATGTAATT-TCATCCATATGTCCCGAAAGACATAGGTAATATTGTCCATATGTCCCGAAAG
1 ACATAGGTAATTCT-GTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCCGAAAG
* *
27391 ACATAGGTAATTCTGTCTATATGTCCTGAAAGACATAGGTAATACT
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATACT
27437 TGACTCTTGG
Statistics
Matches: 151, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
63 1 0.01
64 149 0.99
65 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (64 bp):
ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCCGAAAG
Found at i:27363 original size:96 final size:96
Alignment explanation
Indices: 27199--27435 Score: 339
Period size: 96 Copynumber: 2.5 Consensus size: 96
27189 CACGTTACTC
* *
27199 ACATAGGTAATTCTGTTCATATGTCCCGAAAGACATAGGTAATACCGTCAATATGTCCCAAAAGA
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATACCATCAATATGTCCCAAAAGA
* *
27264 CATAGGTAATTTTGTCCATATGTCTCAAAAG
66 CATAGGTAATATTGTCCATATGTCCCAAAAG
* * * * ** * *
27295 ACATAGGTAATACTATCCATATGTCCCGAAAGACGTATGTAATTTCATCCATATGTCCCGAAAGA
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATACCATCAATATGTCCCAAAAGA
*
27360 CATAGGTAATATTGTCCATATGTCCCGAAAG
66 CATAGGTAATATTGTCCATATGTCCCAAAAG
* *
27391 ACATAGGTAATTCTGTCTATATGTCCTGAAAGACATAGGTAATAC
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATAC
27436 TTGACTCTTG
Statistics
Matches: 120, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 120 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (96 bp):
ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATACCATCAATATGTCCCAAAAGA
CATAGGTAATATTGTCCATATGTCCCAAAAG
Found at i:35314 original size:14 final size:16
Alignment explanation
Indices: 35287--35325 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
35277 ATAGATAGTT
* *
35287 GATTTTAAAAAAATTA
1 GATTTTAAAAATATCA
35303 GATTTTAAAAATATCA
1 GATTTTAAAAATATCA
35319 GATTTTA
1 GATTTTA
35326 TTTATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (16 bp):
GATTTTAAAAATATCA
Found at i:38344 original size:21 final size:19
Alignment explanation
Indices: 38292--38340 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
38282 AAATACTAAT
38292 ATTTAAATTATA-ATTTTA
1 ATTTAAATTATATATTTTA
*
38310 A-TTATATTAATATATTCTTA
1 ATTTAAATT-ATATATT-TTA
38330 ATTTAAATTAT
1 ATTTAAATTAT
38341 TATAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 6 0.24
18 4 0.16
19 3 0.12
20 6 0.24
21 6 0.24
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTAAATTATATATTTTA
Found at i:38351 original size:26 final size:25
Alignment explanation
Indices: 38298--38359 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
38288 TAATATTTAA
* *
38298 ATTATAATTTTAATTATATTAATAT
1 ATTATAATTTAAATTATATAAATAT
*
38323 ATTCTTAATTTAAATTATTATAAAT-T
1 ATT-ATAATTTAAATTA-TATAAATAT
38349 ATTATAATTTA
1 ATTATAATTTA
38360 TTTGAAATCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 10 0.32
26 15 0.48
27 6 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTATAATTTAAATTATATAAATAT
Found at i:40669 original size:13 final size:13
Alignment explanation
Indices: 40651--40675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40641 TAATATTAAT
40651 ATTTAAATTATAA
1 ATTTAAATTATAA
40664 ATTTAAATTATA
1 ATTTAAATTATA
40676 TTAATATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTAAATTATAA
Found at i:41225 original size:15 final size:16
Alignment explanation
Indices: 41201--41230 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41191 CTTTTCTCTC
41201 TTTTTCCTATGGAAAA
1 TTTTTCCTATGGAAAA
41217 TTTTT-CTATGGAAA
1 TTTTTCCTATGGAAA
41231 TTGTAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (16 bp):
TTTTTCCTATGGAAAA
Done.