Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004113.1 Hibiscus syriacus cultivar Beakdansim tig00009000_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: 39180
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Found at i:7449 original size:2 final size:2
Alignment explanation
Indices: 7442--7524 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
7432 TGGTGATCCC
7442 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
7484 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
7525 CACTATTATA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8824 original size:138 final size:137
Alignment explanation
Indices: 8508--8964 Score: 612
Period size: 138 Copynumber: 3.3 Consensus size: 137
8498 TTCGTTCACT
* *
8508 GTATTGAACAGATGAATGACTTGACTCCTGGATTGTCTCAAGACCTAGATGATGTGAGCCACCAT
1 GTATTGAACAGATGAATGACTTGACTCCTGGATTGTCTCAAGATCAAGATGATGTGAGCCACCAT
* * * * * * * *
8573 TCTACCCACGATTCATCTAAAAAGATCTGGAAAAACAATGATGTTGGATTTGCAAAG-TGCAAAT
66 TCTACTCACGAGTCATCTCAAAAGATCTGCAAAGACAATGATGATGGAGTTGCAAAGATG-AATT
*
8637 TATTTACG
130 TGTTTACG
* * * *
8645 GTATTGAACAGATGAATGACTTCACTCCTGGATTGTCTCAAGATCGAGATTATGTGAACCACCAT
1 GTATTGAACAGATGAATGACTTGACTCCTGGATTGTCTCAAGATCAAGATGATGTGAGCCACCAT
* * * * *
8710 TCTACTCAAGAGTCATCTC-AAAGAACCTGCAAAGACAATGATGACGGGGTGGCAAAGACTGAAT
66 TCTACTCACGAGTCATCTCAAAAG-ATCTGCAAAGACAATGATGATGGAGTTGCAAAGA-TGAAT
8774 TTGTTTACG
129 TTGTTTACG
* * *
8783 GTATTGAACAAATGAATGACTTGACTCCTGGATTGTCTCAAGATCAAGATGATGTTAGCCACAAT
1 GTATTGAACAGATGAATGACTTGACTCCTGGATTGTCTCAAGATCAAGATGATGTGAGCCACCAT
* * *
8848 TCTACTCACGAGTCATCTCAAAATATTTGCAAAGACAATGATGGTGGAGTTGCAAAGATTGAATT
66 TCTACTCACGAGTCATCTCAAAAGATCTGCAAAGACAATGATGATGGAGTTGCAAAGA-TGAATT
*
8913 TGTCTACG
130 TGTTTACG
*
8921 GTATTGAACAGATGAATGACTTGACTCCTGGATTGTCTCTAGAT
1 GTATTGAACAGATGAATGACTTGACTCCTGGATTGTCTCAAGAT
8965 GAGTCATCTC
Statistics
Matches: 278, Mismatches: 38, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
136 4 0.01
137 100 0.36
138 169 0.61
139 5 0.02
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (137 bp):
GTATTGAACAGATGAATGACTTGACTCCTGGATTGTCTCAAGATCAAGATGATGTGAGCCACCAT
TCTACTCACGAGTCATCTCAAAAGATCTGCAAAGACAATGATGATGGAGTTGCAAAGATGAATTT
GTTTACG
Found at i:11936 original size:23 final size:23
Alignment explanation
Indices: 11918--11970 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
11908 AATGCACCAA
11918 AGTGCCACGTAGAATTGCACCGT
1 AGTGCCACGTAGAATTGCACCGT
**
11941 AGTGCCGTGTAGAATTGCACCGT
1 AGTGCCACGTAGAATTGCACCGT
11964 AGTGCCA
1 AGTGCCA
11971 TATAAGATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (23 bp):
AGTGCCACGTAGAATTGCACCGT
Found at i:12217 original size:21 final size:21
Alignment explanation
Indices: 12193--12248 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
12183 CATTCACATA
12193 TACACATAGTCTCATAGTTCT
1 TACACATAGTCTCATAGTTCT
12214 TACACATAGTCTCATAGTTCT
1 TACACATAGTCTCATAGTTCT
*
12235 TTCACATAG-CTCAT
1 TACACATAGTCTCAT
12249 TGTCATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 5 0.15
21 29 0.85
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.38
Consensus pattern (21 bp):
TACACATAGTCTCATAGTTCT
Found at i:13614 original size:24 final size:24
Alignment explanation
Indices: 13582--13662 Score: 153
Period size: 24 Copynumber: 3.4 Consensus size: 24
13572 TACACAATGT
13582 ATCGATGCATCCCTTAACGTGTGC
1 ATCGATGCATCCCTTAACGTGTGC
13606 ATCGATGCATCCCTTAACGTGTGC
1 ATCGATGCATCCCTTAACGTGTGC
*
13630 ATCGATGCATCCTTTAACGTGTGC
1 ATCGATGCATCCCTTAACGTGTGC
13654 ATCGATGCA
1 ATCGATGCA
13663 CTATCTATGC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (24 bp):
ATCGATGCATCCCTTAACGTGTGC
Found at i:18165 original size:16 final size:16
Alignment explanation
Indices: 18144--18183 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
18134 CTTTTCATTT
18144 CTTTATTCCATTATTC
1 CTTTATTCCATTATTC
*
18160 CTTTATTCCATTGTTC
1 CTTTATTCCATTATTC
18176 CTTTATTC
1 CTTTATTC
18184 ATTCCAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.15, C:0.25, G:0.03, T:0.57
Consensus pattern (16 bp):
CTTTATTCCATTATTC
Found at i:19827 original size:23 final size:24
Alignment explanation
Indices: 19785--19837 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
19775 CCACTAGGGG
*
19785 CTATGAAATTTGTCCTGAAGGACCA
1 CTATGAAA-TTGTCCCGAAGGACCA
19810 CTATGAAA-TGTCCCGAAGGACCA
1 CTATGAAATTGTCCCGAAGGACCA
19833 CTATG
1 CTATG
19838 TCCCGAAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 19 0.70
25 8 0.30
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (24 bp):
CTATGAAATTGTCCCGAAGGACCA
Found at i:21946 original size:2 final size:2
Alignment explanation
Indices: 21939--22014 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
21929 TTCATATTAC
21939 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
21981 AT AT AT 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 AT AT AT
22015 TACATATGTT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22183 original size:23 final size:23
Alignment explanation
Indices: 22130--22186 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
22120 CTCGTATAAA
*
22130 TGCACCGAAGTACCACGTAGAAT
1 TGCACCGTAGTACCACGTAGAAT
* *
22153 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTACCACGTAGAAT
22176 TGCACCGTAGT
1 TGCACCGTAGT
22187 TCCATATAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGTAGTACCACGTAGAAT
Found at i:22896 original size:22 final size:21
Alignment explanation
Indices: 22845--22897 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
22835 TGTACTCCTT
22845 TTCCTATAATTGATACATTAA
1 TTCCTATAATTGATACATTAA
* * **
22866 TGTCATATAATTTATATTTCTAA
1 T-TCCTATAATTGATACAT-TAA
22889 TTCCTATAA
1 TTCCTATAA
22898 CATCCTCACA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.04
22 20 0.80
23 4 0.16
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (21 bp):
TTCCTATAATTGATACATTAA
Found at i:23729 original size:22 final size:22
Alignment explanation
Indices: 23704--23752 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
23694 AAAGAAATGT
*
23704 TATTTTCATCTTTTAATG-AGG
1 TATTTTCATCTCTTAATGAAGG
23725 CTATTTTCATCTCTTAATGAAGG
1 -TATTTTCATCTCTTAATGAAGG
23748 TATTT
1 TATTT
23753 ATCGATGCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.51
Consensus pattern (22 bp):
TATTTTCATCTCTTAATGAAGG
Found at i:23808 original size:24 final size:24
Alignment explanation
Indices: 23781--23949 Score: 295
Period size: 24 Copynumber: 7.0 Consensus size: 24
23771 GTATCGATTT
*
23781 ATCCCTTAAGGTGTGCATCGATGC
1 ATCCCTTAACGTGTGCATCGATGC
23805 ATCCCTTAACGTGTGCATCGATGC
1 ATCCCTTAACGTGTGCATCGATGC
*
23829 ATCCCTTAACGTGTACATCGATGC
1 ATCCCTTAACGTGTGCATCGATGC
*
23853 ATCCCTTAACGTGTGCATCAATGC
1 ATCCCTTAACGTGTGCATCGATGC
23877 ATCCCTTAACGTGTGCATC-ATTGC
1 ATCCCTTAACGTGTGCATCGA-TGC
23901 ATCCCTTAACGTGTGCATCGATGC
1 ATCCCTTAACGTGTGCATCGATGC
23925 ATCCCTTAACGTGTGCATCGATGC
1 ATCCCTTAACGTGTGCATCGATGC
23949 A
1 A
23950 CTATCTATGC
Statistics
Matches: 139, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
23 1 0.01
24 137 0.99
25 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (24 bp):
ATCCCTTAACGTGTGCATCGATGC
Found at i:31198 original size:21 final size:21
Alignment explanation
Indices: 31174--31219 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
31164 AATCAATTTT
*
31174 TCAAAAGCATGCACCGATGCA
1 TCAAAACCATGCACCGATGCA
* *
31195 TCAATACCATGCATCGATGCA
1 TCAAAACCATGCACCGATGCA
31216 TCAA
1 TCAA
31220 TGAATAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (21 bp):
TCAAAACCATGCACCGATGCA
Found at i:31220 original size:21 final size:21
Alignment explanation
Indices: 31181--31220 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31171 TTTTCAAAAG
31181 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
31202 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
31221 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:31270 original size:19 final size:19
Alignment explanation
Indices: 31246--31284 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
31236 TCGAATGCAT
31246 TTCATGCACCGATGCACTC
1 TTCATGCACCGATGCACTC
*
31265 TTCATGCATCGATGCACTC
1 TTCATGCACCGATGCACTC
31284 T
1 T
31285 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (19 bp):
TTCATGCACCGATGCACTC
Found at i:31308 original size:64 final size:65
Alignment explanation
Indices: 31202--31410 Score: 223
Period size: 64 Copynumber: 3.2 Consensus size: 65
31192 GCATCAATAC
* * * *
31202 CATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGCATTTCATGCACCGATGCACTCT
1 CATGCATCGATGCACTC-ATGATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCT
31266 T
65 T
* ****
31267 CATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTTGATGCATCGATGCACAAGC
1 CATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTT
* * *
31331 CATGCATCGATGCAC-CAGGCTATTT--TTCAAACATCGAATGCACTTCATGCATCGATGCACTC
1 CATGCATCGATGCACTCATG--ATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACTC
31393 TT
64 TT
*
31395 -AGTGCACCGATGCACT
1 CA-TGCATCGATGCACT
31411 AGGAGTCCAA
Statistics
Matches: 120, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
63 2 0.02
64 98 0.82
65 14 0.12
66 6 0.05
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (65 bp):
CATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTT
Found at i:31390 original size:17 final size:19
Alignment explanation
Indices: 31362--31410 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
31352 ATTTTTCAAA
31362 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
31380 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
31399 CACCGATGCACT
1 CATCGATGCACT
31411 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Done.