Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005431.1 Hibiscus syriacus cultivar Beakdansim tig00012452_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: 72597
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3108 original size:15 final size:17
Alignment explanation
Indices: 3083--3121 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3073 TTACATTAAC
*
3083 TAAAATACTATTAGAT-
1 TAAAATACTATTAAATA
3099 TAAAAT-CTATTAAATA
1 TAAAATACTATTAAATA
3115 TAAAATA
1 TAAAATA
3122 ATTTTACAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (17 bp):
TAAAATACTATTAAATA
Found at i:9888 original size:59 final size:60
Alignment explanation
Indices: 9774--9910 Score: 172
Period size: 59 Copynumber: 2.3 Consensus size: 60
9764 GAACATATAA
* * *
9774 ATAATCAGATGA-CAATTTTGTAACTTTTAATAGTAATAATACTCAATAAATAAACATCTT
1 ATAATCGGATGATC-ATTTTATAACTTTTAATAGTAATAATACTCAATAAATAAACATCCT
* *
9834 ATAATCGGATGATCATTTTATAA-TTTTTATAGTCA-AATAACTCAATAAATAAACATCCT
1 ATAATCGGATGATCATTTTATAACTTTTAATAGTAATAAT-ACTCAATAAATAAACATCCT
* *
9893 ATAATCGAAAGATCATTT
1 ATAATCGGATGATCATTT
9911 ATATTCTTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
58 3 0.04
59 45 0.66
60 19 0.28
61 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.36
Consensus pattern (60 bp):
ATAATCGGATGATCATTTTATAACTTTTAATAGTAATAATACTCAATAAATAAACATCCT
Found at i:13551 original size:40 final size:40
Alignment explanation
Indices: 13495--13580 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
13485 AATTCTATCC
*
13495 TATTAAGAGATAAGAGTTATAGAATATTTAAACTACTTAAT
1 TATT-AGAGATAAGAGTTATAGAATATCTAAACTACTTAAT
* *
13536 TATTAGAGATAAGAGTTATAGGATATCTAAACTACTTAGT
1 TATTAGAGATAAGAGTTATAGAATATCTAAACTACTTAAT
13576 TATTA
1 TATTA
13581 ATAGTAAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 38 0.90
41 4 0.10
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (40 bp):
TATTAGAGATAAGAGTTATAGAATATCTAAACTACTTAAT
Found at i:37850 original size:43 final size:43
Alignment explanation
Indices: 37817--38064 Score: 247
Period size: 43 Copynumber: 5.8 Consensus size: 43
37807 TCAATTCTAT
* *
37817 TTTCTACCTTTACAATTGAGGTCCAT-ATTTTTTTAATCCCACC
1 TTTCTACCTTTATAATTGAGGTCCATAATTTTTTTAATCTCA-C
* * * * *
37860 TTT-TAACTTTATAATTTAGGCCCTTAATTTTTTCAATCTCAC
1 TTTCTACCTTTATAATTGAGGTCCATAATTTTTTTAATCTCAC
*
37902 TTTCTACCTTTATAATTGAGACG-CC-TAATTTTTTTAATCTCAT
1 TTTCTACCTTTATAATTGAG--GTCCATAATTTTTTTAATCTCAC
** *
37945 TTTCTAGTTTTATAATTGAGGTTCATAATTTTTTTAATCTCAC
1 TTTCTACCTTTATAATTGAGGTCCATAATTTTTTTAATCTCAC
* *
37988 TTTCTACCTTTATAATTGATG-CCACTAATTTTTTTAA-ATCAC
1 TTTCTACCTTTATAATTGAGGTCCA-TAATTTTTTTAATCTCAC
* * * ** *
38030 TTTTTGCCTTTATAAGTGAGCACCCTAATTTTTTT
1 TTTCTACCTTTATAATTGAGGTCCATAATTTTTTT
38065 TAATTCCATA
Statistics
Matches: 171, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
41 1 0.01
42 54 0.32
43 113 0.66
44 2 0.01
45 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (43 bp):
TTTCTACCTTTATAATTGAGGTCCATAATTTTTTTAATCTCAC
Found at i:37949 original size:128 final size:128
Alignment explanation
Indices: 37802--38070 Score: 323
Period size: 128 Copynumber: 2.1 Consensus size: 128
37792 AGTCCTAACC
*
37802 TTTTTTCAATTCTATTTTCTACCTTTACAATTGAGGTCCAT-ATTTTTTTAATCCCACCTTT-TA
1 TTTTTTTAATTCTATTTTCTACCTTTACAATTGAGGTCCATAATTTTTTTAATCCCA-CTTTCTA
* * *
37865 ACTTTATAATTTAGGCC-CTTAATTTTTTCAATCTCACTTTCTACCTTTATAATTGAG-ACGCCT
65 ACTTTATAATTGAGGCCAC-TAATTTTTTCAA-ATCACTTTCTACCTTTATAAGTGAGCAC-CCT
37928 AA
127 AA
** * * *
37930 TTTTTTTAA-TCTCATTTTCTAGTTTTATAATTGAGGTTCATAATTTTTTTAATCTCACTTTCTA
1 TTTTTTTAATTCT-ATTTTCTACCTTTACAATTGAGGTCCATAATTTTTTTAATCCCACTTTCTA
* * * * *
37994 CCTTTATAATTGATGCCACTAATTTTTTTAAATCACTTTTTGCCTTTATAAGTGAGCACCCTAA
65 ACTTTATAATTGAGGCCACTAATTTTTTCAAATCACTTTCTACCTTTATAAGTGAGCACCCTAA
38058 TTTTTTTTAATTC
1 -TTTTTTTAATTC
38071 CATAAAAATC
Statistics
Matches: 120, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
127 3 0.03
128 62 0.52
129 52 0.43
130 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (128 bp):
TTTTTTTAATTCTATTTTCTACCTTTACAATTGAGGTCCATAATTTTTTTAATCCCACTTTCTAA
CTTTATAATTGAGGCCACTAATTTTTTCAAATCACTTTCTACCTTTATAAGTGAGCACCCTAA
Found at i:40673 original size:32 final size:32
Alignment explanation
Indices: 40636--40709 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
40626 TATATTCAAT
* * * *
40636 TGATGATGTGATATGTGTCACATCATTCAAAG
1 TGATGATGTGATATATATAACATCATTCAAAA
*
40668 TGATGATGTGATATATATAACATCATTTAAAA
1 TGATGATGTGATATATATAACATCATTCAAAA
40700 TGATGATGTG
1 TGATGATGTG
40710 GTAACAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.36
Consensus pattern (32 bp):
TGATGATGTGATATATATAACATCATTCAAAA
Found at i:41522 original size:31 final size:31
Alignment explanation
Indices: 41487--41573 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 31
41477 TCGAAAATCG
41487 ATTGATCCGACCCG-AAACCAACCAA-TCTGAT
1 ATTGA-CCGACCCGAAAACCAACCAATTC-GAT
* *
41518 ATTGACCTGACCCGAAAATCAACCTATTCGAT
1 ATTGACC-GACCCGAAAACCAACCAATTCGAT
**
41550 ATTGACCCGACTTGAAAACCAACC
1 ATTGA-CCGACCCGAAAACCAACC
41574 CAACCCGACT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
30 2 0.04
31 11 0.23
32 30 0.64
33 4 0.09
ACGTcount: A:0.36, C:0.31, G:0.13, T:0.21
Consensus pattern (31 bp):
ATTGACCGACCCGAAAACCAACCAATTCGAT
Found at i:64953 original size:30 final size:29
Alignment explanation
Indices: 64918--65069 Score: 182
Period size: 30 Copynumber: 5.1 Consensus size: 29
64908 AATCCATTGG
*
64918 TAATTGAAGGACTAGCTGAAGATAAATCTT
1 TAATTGAAGGAC-AGCTGAAGATAAATCCT
* *
64948 TAATTGAAGGACACGATGAAGATAAATCCA
1 TAATTGAAGGACA-GCTGAAGATAAATCCT
64978 TAATTGAAGGACAAGAC-GAAGATAAATCCT
1 TAATTGAAGGAC-AG-CTGAAGATAAATCCT
* *
65008 TAACTGAAGGGCACGCTGAAGATAAATCCT
1 TAATTGAAGGACA-GCTGAAGATAAATCCT
65038 TAATTGAAGGACA-CATTGAAGATAAATCCT
1 TAATTGAAGGACAGC--TGAAGATAAATCCT
65068 TA
1 TA
65070 GTATCAACTA
Statistics
Matches: 106, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
28 1 0.01
29 3 0.03
30 101 0.95
31 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.24
Consensus pattern (29 bp):
TAATTGAAGGACAGCTGAAGATAAATCCT
Done.