Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009202.1 Hibiscus syriacus cultivar Beakdansim tig00112787_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: 39662
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Found at i:1858 original size:32 final size:33
Alignment explanation
Indices: 1798--1862 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1788 AATTCTTATA
* * *
1798 ATATGATATTATATTCTTTAATATTATAATGAT
1 ATATAATATTATATTATTTAATAATATAATGAT
1831 ATATAATATTAT-TTATTTAATAATATAATGAT
1 ATATAATATTATATTATTTAATAATATAATGAT
1863 TTTTCAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (33 bp):
ATATAATATTATATTATTTAATAATATAATGAT
Found at i:4989 original size:26 final size:26
Alignment explanation
Indices: 4935--5000 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
4925 CTCATAATTC
*
4935 TTATAATTGATAT-TATATTCTTTAATA
1 TTATAA-TGATATATATATACTTT-ATA
4962 TTATAATGATATATATTATACTTT-TA
1 TTATAATGATATATA-TATACTTTATA
* *
4988 TTTTAATAATATA
1 TTATAATGATATA
5001 ATTTTTCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 19 0.56
27 8 0.24
28 7 0.21
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (26 bp):
TTATAATGATATATATATACTTTATA
Found at i:17307 original size:2 final size:2
Alignment explanation
Indices: 17302--17331 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17292 AGAAAAAATA
*
17302 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17332 CAAGAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17787 original size:15 final size:16
Alignment explanation
Indices: 17740--17791 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
17730 TTTACTCATA
* *
17740 ATTATAATAATATGAT
1 ATTATAATCATATAAT
* *
17756 ATTATATTC-TTTAAT
1 ATTATAATCATATAAT
17771 ATTATAATCATAT-AT
1 ATTATAATCATATAAT
17786 ATTATA
1 ATTATA
17792 CTTTTATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 20 0.69
16 9 0.31
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (16 bp):
ATTATAATCATATAAT
Found at i:17799 original size:26 final size:28
Alignment explanation
Indices: 17740--17812 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 28
17730 TTTACTCATA
17740 ATTATAATAATATGATATTATATTCTTTAAT
1 ATTATAATAATAT-ATATTATA-TCTTT-AT
*
17771 ATTATAATCATATATATTATA-CTTT-T
1 ATTATAATAATATATATTATATCTTTAT
*
17797 ATTTTAATAATATATA
1 ATTATAATAATATATA
17813 ATGATTTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
26 15 0.38
28 4 0.10
30 8 0.21
31 12 0.31
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (28 bp):
ATTATAATAATATATATTATATCTTTAT
Found at i:18685 original size:24 final size:24
Alignment explanation
Indices: 18658--18730 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
18648 GTAAACGGAG
18658 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
* * *
18682 ATATCAGATATCATAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTC
* * *
18706 AGATCAGAAGTCAGAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
18730 A
1 A
18731 GGTAATGTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.21
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:18731 original size:12 final size:12
Alignment explanation
Indices: 18662--18731 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
18652 ACGGAGATAT
* *
18662 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
18674 CAGAATTCATAT
1 CAGAATTCAGAA
*
18686 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
18698 CAGAATCCAGAT
1 CAGAATTCAGAA
*
18710 CAGAAGTCAGAA
1 CAGAATTCAGAA
18722 CAGAATTCAG
1 CAGAATTCAG
18732 GTAATGTATC
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:23387 original size:24 final size:24
Alignment explanation
Indices: 23360--23432 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
23350 GTAAACGGAG
*
23360 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
23384 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
23408 AGATCAGAAATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
23432 A
1 A
23433 GGTAATGTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:23391 original size:12 final size:12
Alignment explanation
Indices: 23364--23433 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
23354 ACGGAGATAT
* *
23364 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
23376 CAGAATTCATAT
1 CAGAATTCAGAA
23388 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
23400 CAGAATCCAGAT
1 CAGAATTCAGAA
*
23412 CAGAAATCAGAA
1 CAGAATTCAGAA
23424 CAGAATTCAG
1 CAGAATTCAG
23434 GTAATGTATC
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:23444 original size:48 final size:47
Alignment explanation
Indices: 23362--23470 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 47
23352 AAACGGAGAT
* * *
23362 ATCAGAAATCAAAACAGAATTCATATCAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCA
* * *
23409 GATCAGAAATCAGAACAGAATTCAGGTAATG-TATCATAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGATAA-GATATCAGAACAGAATCCA
23457 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
23471 TAAAATATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 1 0.02
48 51 0.96
49 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.20
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCA
Found at i:23468 original size:24 final size:24
Alignment explanation
Indices: 23363--23470 Score: 105
Period size: 24 Copynumber: 4.5 Consensus size: 24
23353 AACGGAGATA
*
23363 TCAGAAATCAAAACAGAATTCATA-
1 TCAGAAATCAGAACAGAATTCA-AG
* *
23387 TCAGATATCAGAACAGAA-TCCAG
1 TCAGAAATCAGAACAGAATTCAAG
*
23410 ATCAGAAATCAGAACAGAATTCAGG
1 -TCAGAAATCAGAACAGAATTCAAG
* * *
23435 TAATG-TATCATAACAGAATTCAAG
1 TCA-GAAATCAGAACAGAATTCAAG
23459 TCAGAAATCAGA
1 TCAGAAATCAGA
23471 TAAAATATTT
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
22 1 0.02
23 3 0.05
24 58 0.88
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:25936 original size:8 final size:8
Alignment explanation
Indices: 25896--25942 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
25886 TCAAAGTTTT
25896 GGTCAACAG
1 GGTCAAC-G
25905 TGGTCAACG
1 -GGTCAACG
25914 CCGGTCAAC-
1 --GGTCAACG
25923 GGTCAACG
1 GGTCAACG
25931 GGTCAACG
1 GGTCAACG
25939 GGTC
1 GGTC
25943 GGGAAAATGG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 12 0.35
9 1 0.03
10 14 0.41
ACGTcount: A:0.23, C:0.28, G:0.34, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:25936 original size:15 final size:16
Alignment explanation
Indices: 25906--25939 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
25896 GGTCAACAGT
25906 GGTCAACGCCGGTCAAC
1 GGTCAACG-CGGTCAAC
25923 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
25938 GG
1 GG
25940 GTCGGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.29, G:0.35, T:0.12
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:30814 original size:2 final size:2
Alignment explanation
Indices: 30807--30842 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
30797 TTTCTTGGAA
30807 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
30843 TTTTTATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35727 original size:29 final size:29
Alignment explanation
Indices: 35656--35728 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
35646 CTCATAATTC
*
35656 TAATAATATGATATTATAATCTTTAATATT
1 TAATAATAT-ATAATATAATCTTTAATATT
* * * *
35686 AAATGATATATAATATTATACTTTTAT-TT
1 TAATAATATATAATATAAT-CTTTAATATT
35715 TAATAATATATAAT
1 TAATAATATATAAT
35729 GATTTTTCAG
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (29 bp):
TAATAATATATAATATAATCTTTAATATT
Found at i:36381 original size:140 final size:141
Alignment explanation
Indices: 36129--36410 Score: 521
Period size: 140 Copynumber: 2.0 Consensus size: 141
36119 CCTATGATAG
36129 CTACATTAACACTTTGAACTTCCATCTCCACATTTAGAATCACCTTGTAAGTATCGAGCAATGGG
1 CTACATTAACACTTTGAACTTCCATCTCCACATTTAGAATCACCTTGTAAGTATCGAGCAATGGG
*
36194 ACATGATAATTATATTTTATTTAAGGGCTAAATTGTGAGTAAAAATGGTTTAGAGACTAAAAATA
66 ACATGATAATTATATTTTATTTAAGGGCTAAATTGTGAGCAAAAATGGTTTAGAGACTAAAAATA
36259 T-TTTTTTTGA
131 TATTTTTTTGA
* *
36269 CTACATTAACACTTTGAACTTCCATCTCCACATTTAGGATCACCTTGTAAGTATCGAGCAATGGT
1 CTACATTAACACTTTGAACTTCCATCTCCACATTTAGAATCACCTTGTAAGTATCGAGCAATGGG
36334 ACATGATAATTATATTTTATTTAAGGGCTAAATTGTGAGCAAAAATGGTTTAGAGACTAAAAATA
66 ACATGATAATTATATTTTATTTAAGGGCTAAATTGTGAGCAAAAATGGTTTAGAGACTAAAAATA
36399 TAATTTTTTTGA
131 T-ATTTTTTTGA
36411 ATTGTTAGAG
Statistics
Matches: 137, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
140 128 0.93
142 9 0.07
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (141 bp):
CTACATTAACACTTTGAACTTCCATCTCCACATTTAGAATCACCTTGTAAGTATCGAGCAATGGG
ACATGATAATTATATTTTATTTAAGGGCTAAATTGTGAGCAAAAATGGTTTAGAGACTAAAAATA
TATTTTTTTGA
Done.