Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009173.1 Hibiscus syriacus cultivar Beakdansim tig00112731_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: 46312
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:5831 original size:8 final size:8
Alignment explanation
Indices: 5820--5853 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
5810 CATATTTATA
5820 TATTTAAT
1 TATTTAAT
*
5828 TATTCAAT
1 TATTTAAT
*
5836 TATTTAAC
1 TATTTAAT
5844 TATTTAAT
1 TATTTAAT
5852 TA
1 TA
5854 CTATCCGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (8 bp):
TATTTAAT
Found at i:6203 original size:54 final size:54
Alignment explanation
Indices: 6114--6251 Score: 190
Period size: 54 Copynumber: 2.6 Consensus size: 54
6104 ATATTCGGAA
* * *
6114 AACGAGCTCGCTCCCTCATT-TTAGGGAGTATAGAACTCGAACAATTTTCTG-C
1 AACGAGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
* *
6166 GAACGAGTTCACTCCCTCTTTCTTCGGGAGTATAGAACTCGAACAATCTTCTGTC
1 -AACGAGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
* *
6221 AACGGGTTCGTTCCCTCTTTCTTAGGGAGTA
1 AACGAGTTCGCTCCCTCTTTCTTAGGGAGTA
6252 GGGACTTGAA
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
53 17 0.23
54 56 0.76
55 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.31
Consensus pattern (54 bp):
AACGAGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
Found at i:6536 original size:53 final size:54
Alignment explanation
Indices: 6177--6752 Score: 608
Period size: 53 Copynumber: 10.8 Consensus size: 54
6167 AACGAGTTCA
* * * *
6177 CTCCCTCTTTCTTC-GGGAGTAT-AGAACTCGAACAATCTTCTGTCAA-CGGGTTCG
1 CTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTC-ATCAATCGTG-TCG
* * * ** * *
6231 TTCCCTCTTTCTT-AGGGAGTA-GGGACTTGAAGAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTC-G
* * * * *
6284 CTCCCTATTTCCTCAGAGAGTATAAGACCCAAACAATCTTCAACAAATCTTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATC-AATCGTGTC-G
* *
6340 CT-CCTATTTCTTCAGAGAGTATAAGACCCAAACAATC-T--TC-ATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTC-G
* *
6390 CTCCCCA-TTCTTTCAGAGAGTATAAGACTTGAACAATCTTCATCAATCGTGTCG
1 CTCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCG
**
6444 CTCCCTATTTCCGCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCG
* * * *
6498 CTCCCTATTT-TGCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTCTGCT
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGT-CG
* *
6552 CTCCCTATTTCTTCAGAGAGTACAAGACTCG-A-AATCTTCATCCATCGTGT-G
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCG
* * * *
6603 CTCCATATTTCTGCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTC-G
* * * *
6658 CTCCCTATTTTTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCT
1 CTCCCTA-TTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCG
*
6713 CTCCCT-TTTCTTCAGAGAGTATAAGACTCGATCAATCTTC
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
6753 GATTATCGTT
Statistics
Matches: 448, Mismatches: 53, Indels: 43
0.82 0.10 0.08
Matches are distributed among these distances:
50 14 0.03
51 55 0.12
52 9 0.02
53 127 0.28
54 99 0.22
55 90 0.20
56 54 0.12
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (54 bp):
CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCG
Found at i:6751 original size:215 final size:214
Alignment explanation
Indices: 6254--6752 Score: 645
Period size: 213 Copynumber: 2.3 Consensus size: 214
6244 AGGGAGTAGG
* * * * *
6254 GACTTGAAGAATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACCCAAACA
1 GACTCGAACAATCTTCATCAATCGTGTCT-CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACA
* *
6319 ATCTTCAACAAATCTTGTCTGCTCCTATTTCTTCAGAGAGTATAAGACCCAAACAATCTTCATCG
65 ATCTTCAACAAATCTTGTCTGCTCCTATTTCTTCAGAGAGTACAAGACCCAAACAATCTTCATCA
* * * *
6384 TGTCTGCTCCCCATTCTTTCAGAGAGTATAAGACTTGAACAATCTTCATCAATCGTGTCGCTCCC
130 TGTCTGCTCCACATTCTTGCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCGCTCCC
6449 TATTTCCGCAGAGAGTATAA
195 TATTTCCGCAGAGAGTATAA
* *
6469 GACTCGAACAATCTTCATCAATCGTGTCGCTCCCTATTT-TGCAGAGAGTATAAGACTCGAACAA
1 GACTCGAACAATCTTCATCAATCGTGTCTCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* *
6533 TCTTCAAC-AATC--GTCTGCTCTCCCTATTTCTTCAGAGAGTACAAGACTC-GA-AATCTTCAT
66 TCTTCAACAAATCTTGTCTG--CT-CCTATTTCTTCAGAGAGTACAAGACCCAAACAATCTTCAT
* * *
6593 CCATCGTGTGCTCCATATT-TCTGCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCT
128 -CAT-GTCTGCTCCACATTCT-TGCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTC-
***
6657 GCTCCCTATTTTTTTCAGAGAGTATAA
189 GCTCCCTA-TTTCCGCAGAGAGTATAA
* * *
6684 GACTCGAACAATCTTCAACAATCGCGTCTCTCCCT-TTTCTTCAGAGAGTATAAGACTCGATCAA
1 GACTCGAACAATCTTCATCAATCGTGTCTCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
6748 TCTTC
66 TCTTC
6753 GATTATCGTT
Statistics
Matches: 249, Mismatches: 26, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
210 5 0.02
211 9 0.04
212 10 0.04
213 103 0.41
214 21 0.08
215 101 0.41
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (214 bp):
GACTCGAACAATCTTCATCAATCGTGTCTCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
TCTTCAACAAATCTTGTCTGCTCCTATTTCTTCAGAGAGTACAAGACCCAAACAATCTTCATCAT
GTCTGCTCCACATTCTTGCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCGCTCCCT
ATTTCCGCAGAGAGTATAA
Found at i:7759 original size:15 final size:14
Alignment explanation
Indices: 7739--7794 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
7729 GAACCCTTCC
*
7739 TTTTTTCCATTTTTT
1 TTTTTTTCA-TTTTT
*
7754 TTTTTTTTATTTTT
1 TTTTTTTCATTTTT
*
7768 TTTTTTTTATTTTT
1 TTTTTTTCATTTTT
*
7782 TCTTTTTCATTTT
1 TTTTTTTCATTTT
7795 CACTCATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
14 30 0.81
15 7 0.19
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTTCATTTTT
Found at i:7806 original size:1 final size:1
Alignment explanation
Indices: 7748--7788 Score: 55
Period size: 1 Copynumber: 41.0 Consensus size: 1
7738 CTTTTTTCCA
* * *
7748 TTTTTTTTTTTTTTATTTTTTTTTTTTTATTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
7789 CATTTTCACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.05, C:0.02, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:25488 original size:13 final size:13
Alignment explanation
Indices: 25472--25510 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
25462 GTCATAAATC
*
25472 TATGAAGCGCATT
1 TATGACGCGCATT
* *
25485 TATGACTCACATT
1 TATGACGCGCATT
25498 TATGACGCGCATT
1 TATGACGCGCATT
25511 GAGCATCATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:25674 original size:2 final size:2
Alignment explanation
Indices: 25667--25699 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
25657 TTTCATAAAT
25667 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 T
25700 TGTAGATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33174 original size:19 final size:19
Alignment explanation
Indices: 33152--33204 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
33142 TTTCTATCAC
33152 ATTTTTCTTTTAAATTAAT
1 ATTTTTCTTTTAAATTAAT
* * *
33171 ATTTTTAGTTTT-ATTTTAT
1 ATTTTT-CTTTTAAATTAAT
*
33190 ATTTTTCTTTCAAAT
1 ATTTTTCTTTTAAAT
33205 AATTTAAGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
18 3 0.12
19 19 0.73
20 4 0.15
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTTTCTTTTAAATTAAT
Found at i:35118 original size:21 final size:21
Alignment explanation
Indices: 35092--35134 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
35082 AATCCTTATC
35092 AGTTTAAATTCAAGTAAAATT
1 AGTTTAAATTCAAGTAAAATT
35113 AGTTTAAATTCAAGTAAAATT
1 AGTTTAAATTCAAGTAAAATT
35134 A
1 A
35135 AACTTTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (21 bp):
AGTTTAAATTCAAGTAAAATT
Done.