Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004003.1 Hibiscus syriacus cultivar Beakdansim tig00008726_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: 39305
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:9724 original size:14 final size:14
Alignment explanation
Indices: 9705--9755 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
9695 CATAGATTCT
9705 ACCTTTTTCTACAA
1 ACCTTTTTCTACAA
* *
9719 ACCTTTTT-TAGATTCG
1 ACCTTTTTCTACA---A
9735 ACCTTTTTCTACAA
1 ACCTTTTTCTACAA
9749 ACCTTTT
1 ACCTTTT
9756 CAAAATTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 3 0.10
14 15 0.52
16 8 0.28
17 3 0.10
ACGTcount: A:0.24, C:0.25, G:0.04, T:0.47
Consensus pattern (14 bp):
ACCTTTTTCTACAA
Found at i:9733 original size:30 final size:30
Alignment explanation
Indices: 9697--9755 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
9687 AAGAAAATCA
*
9697 TAGATTCTACCTTTTTCTACAAACCTTTTT
1 TAGATTCGACCTTTTTCTACAAACCTTTTT
9727 TAGATTCGACCTTTTTCTACAAACCTTTT
1 TAGATTCGACCTTTTTCTACAAACCTTTT
9756 CAAAATTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.47
Consensus pattern (30 bp):
TAGATTCGACCTTTTTCTACAAACCTTTTT
Found at i:28537 original size:20 final size:21
Alignment explanation
Indices: 28504--28542 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28494 TCAAATTCAC
28504 TTTTTAAAAGACTTTGAATTA
1 TTTTTAAAAGACTTTGAATTA
*
28525 TTTTTGAAA-ACTTTGAAT
1 TTTTTAAAAGACTTTGAAT
28543 AAATTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (21 bp):
TTTTTAAAAGACTTTGAATTA
Found at i:30279 original size:18 final size:18
Alignment explanation
Indices: 30256--30291 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
30246 GTTGTTTTTT
*
30256 TAAAAGATAAGAATTAAA
1 TAAAAGAAAAGAATTAAA
*
30274 TAAAAGAAAATAATTAAA
1 TAAAAGAAAAGAATTAAA
30292 CAAATAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (18 bp):
TAAAAGAAAAGAATTAAA
Found at i:30939 original size:20 final size:20
Alignment explanation
Indices: 30916--30953 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30906 AAATAAAAAT
30916 AAAAC-AAAGAAAAACTTTGA
1 AAAACAAAAG-AAAACTTTGA
*
30936 AAAAGAAAAGAAAACTTT
1 AAAACAAAAGAAAACTTT
30954 TATTAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.66, C:0.08, G:0.11, T:0.16
Consensus pattern (20 bp):
AAAACAAAAGAAAACTTTGA
Found at i:33669 original size:22 final size:22
Alignment explanation
Indices: 33628--33669 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
33618 AAAACGAAAC
*
33628 ATAAAAAAATAAAGTGAAATGT
1 ATAAAAAAATAAAATGAAATGT
* *
33650 ATAAAAATATAAAATTAAAT
1 ATAAAAAAATAAAATGAAAT
33670 ACACTATACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (22 bp):
ATAAAAAAATAAAATGAAATGT
Found at i:35775 original size:94 final size:96
Alignment explanation
Indices: 35596--35779 Score: 268
Period size: 95 Copynumber: 1.9 Consensus size: 96
35586 CCCCTCCCCC
*
35596 CTCTCTCTCTCTTACAGTTCGTTAGTAATTTAGGGAGGCCTCCTCGCCCACATAGAGTACCCGAA
1 CTCTCTCTCTCTTACAGTTCGTTAGTAATTTAAGGAGGCCTCCTCGCCCACATAGAGTACCCGAA
35661 AAAATATTTTCACGTGTAGAGTATCCTCTCT
66 AAAATATTTTCACGTGTAGAGTATCCTCTCT
* * * * *
35692 CTCTCTTTCTCTTACAGTTCGTT-GTAATTTAAGGAGGCTTCCTTG-CC-CATATAGTAGCCGAA
1 CTCTCTCTCTCTTACAGTTCGTTAGTAATTTAAGGAGGCCTCCTCGCCCACATAGAGTACCCGAA
35754 AAATATATTTTTC-CGTGTAGAGTATC
66 AAA-ATA-TTTTCACGTGTAGAGTATC
35780 ATTGTATTAT
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
93 16 0.20
94 18 0.22
95 24 0.30
96 22 0.28
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (96 bp):
CTCTCTCTCTCTTACAGTTCGTTAGTAATTTAAGGAGGCCTCCTCGCCCACATAGAGTACCCGAA
AAAATATTTTCACGTGTAGAGTATCCTCTCT
Found at i:37782 original size:16 final size:16
Alignment explanation
Indices: 37761--37801 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
37751 TTTTATATCA
37761 CAAGTCATATTCAAAG
1 CAAGTCATATTCAAAG
37777 CAAGTCATATTCAAAG
1 CAAGTCATATTCAAAG
37793 CAAGTCATA
1 CAAGTCATA
37802 ACATATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (16 bp):
CAAGTCATATTCAAAG
Done.