Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009026.1 Hibiscus syriacus cultivar Beakdansim tig00112423_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: 71164
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:2428 original size:15 final size:16
Alignment explanation
Indices: 2400--2431 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2390 AAAATCTTTC
2400 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
2416 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
2431 T
1 T
2432 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:3206 original size:16 final size:16
Alignment explanation
Indices: 3182--3213 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3172 TATCGCCGAC
*
3182 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
3198 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
3214 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:3635 original size:13 final size:13
Alignment explanation
Indices: 3611--3656 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
3601 AAAAAATTAC
3611 AGCAGCCCCCCCTT
1 AGCAG-CCCCCCTT
3625 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
3638 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
3651 AGCAGC
1 AGCAGC
3657 ACAGTGACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 27 0.84
14 5 0.16
ACGTcount: A:0.17, C:0.52, G:0.17, T:0.13
Consensus pattern (13 bp):
AGCAGCCCCCCTT
Found at i:5227 original size:2 final size:2
Alignment explanation
Indices: 5220--5254 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5210 TCTTAGATTG
5220 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5255 CACCATTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22481 original size:33 final size:33
Alignment explanation
Indices: 22444--22509 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
22434 CATCTTAATA
*
22444 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
22477 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
22510 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:24642 original size:24 final size:24
Alignment explanation
Indices: 24605--24657 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
24595 CCGTTCTATC
24605 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
24629 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
24653 TATTT
1 TATTT
24658 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:24993 original size:20 final size:20
Alignment explanation
Indices: 24967--25012 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
24957 CACTTTTAAA
24967 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
24986 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
25007 TTTACC
1 TTTACC
25013 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:26090 original size:22 final size:23
Alignment explanation
Indices: 26059--26103 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
26049 CAATATATTC
*
26059 TTTTATTG-AATTTGATTTAATTT
1 TTTTATTGAAATTT-AATTAATTT
26082 TTTTA-TGAAATTTAATTAATTT
1 TTTTATTGAAATTTAATTAATTT
26104 AGATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (23 bp):
TTTTATTGAAATTTAATTAATTT
Found at i:29149 original size:2 final size:2
Alignment explanation
Indices: 29142--29180 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29132 TTAAATTGCT
29142 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29181 GTAACACCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29861 original size:31 final size:31
Alignment explanation
Indices: 29823--30009 Score: 304
Period size: 31 Copynumber: 6.0 Consensus size: 31
29813 CCCGAAGGAC
* *
29823 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* * *
29854 CAGTCCATATATCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
29885 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
29916 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
29947 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
29978 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
30009 C
1 C
30010 CCTCGACCCT
Statistics
Matches: 145, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
31 145 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:30213 original size:23 final size:24
Alignment explanation
Indices: 30187--30233 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
30177 ATATACTTGT
*
30187 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
30210 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
30234 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:30896 original size:21 final size:21
Alignment explanation
Indices: 30866--30910 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
30856 ATTCTGTCGT
* *
30866 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
30887 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
30908 TTG
1 TTG
30911 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:34008 original size:31 final size:31
Alignment explanation
Indices: 33970--34156 Score: 313
Period size: 31 Copynumber: 6.0 Consensus size: 31
33960 CCCGAAGGAC
* *
33970 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
34001 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
34032 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
34063 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
34094 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
34125 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
34156 C
1 C
34157 CCTCGACCCT
Statistics
Matches: 147, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
31 146 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:35043 original size:21 final size:21
Alignment explanation
Indices: 35013--35057 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35003 ATTCTGTCGT
* *
35013 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
35034 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
35055 TTG
1 TTG
35058 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:36125 original size:2 final size:2
Alignment explanation
Indices: 36109--36143 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
36099 ATATTTTTGT
36109 TA TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36144 GATGTGAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46102 original size:13 final size:13
Alignment explanation
Indices: 46078--46123 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
46068 AAAAAATTAC
46078 AGCAGCCCCCCCTT
1 AGCAG-CCCCCCTT
46092 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
46105 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
46118 AGCAGC
1 AGCAGC
46124 ACAGTGACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 27 0.84
14 5 0.16
ACGTcount: A:0.17, C:0.52, G:0.17, T:0.13
Consensus pattern (13 bp):
AGCAGCCCCCCTT
Found at i:47693 original size:2 final size:2
Alignment explanation
Indices: 47686--47724 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
47676 TCTTAGATTG
47686 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47725 CACCATTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65058 original size:43 final size:43
Alignment explanation
Indices: 64997--65082 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
64987 GCAACCAAGC
64997 GAACTTTATAAAGCTCAATTTAACCAGAAGATGCCACCCAGTT
1 GAACTTTATAAAGCTCAATTTAACCAGAAGATGCCACCCAGTT
*
65040 GAACTTTATAACA-CTCAATTTCACCAGAAGATGCCACCCAGTT
1 GAACTTTATAA-AGCTCAATTTAACCAGAAGATGCCACCCAGTT
65083 TCCTCCACTG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
43 40 0.98
44 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (43 bp):
GAACTTTATAAAGCTCAATTTAACCAGAAGATGCCACCCAGTT
Found at i:67359 original size:41 final size:41
Alignment explanation
Indices: 67282--67361 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
67272 TATGAATTCA
* * * *
67282 TACCAAGCTCTAGGTATCAGTCGGAATGGATACTATCAGAT
1 TACCAACCTCTAGGCATCAGTAGGAATAGATACTATCAGAT
* * *
67323 TACCAACCTCTAGGCATCTGTATGAATAGATCCTATCAG
1 TACCAACCTCTAGGCATCAGTAGGAATAGATACTATCAG
67362 TATCTGGATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (41 bp):
TACCAACCTCTAGGCATCAGTAGGAATAGATACTATCAGAT
Done.