Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004908.1 Hibiscus syriacus cultivar Beakdansim tig00011042_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: 53411
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:11079 original size:5 final size:5
Alignment explanation
Indices: 11066--11098 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
11056 AAGGAAAAAG
*
11066 AAACG AAACA AAACA AAACA AAACA AAACA AAA
1 AAACA AAACA AAACA AAACA AAACA AAACA AAA
11099 AGGTCCTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.79, C:0.18, G:0.03, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:18695 original size:3 final size:3
Alignment explanation
Indices: 18687--18722 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
18677 TAAGTAATAT
18687 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18723 AAGTTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:21148 original size:63 final size:63
Alignment explanation
Indices: 21049--21177 Score: 249
Period size: 63 Copynumber: 2.0 Consensus size: 63
21039 ATGAGCCGCC
*
21049 ACTAAGTAGATTCCCTATGCAATGTAGAATATTTCACCTTTGTCTAAGGGACTTTTGGGTTCT
1 ACTAAGTAGATTCCCCATGCAATGTAGAATATTTCACCTTTGTCTAAGGGACTTTTGGGTTCT
21112 ACTAAGTAGATTCCCCATGCAATGTAGAATATTTCACCTTTGTCTAAGGGACTTTTGGGTTCT
1 ACTAAGTAGATTCCCCATGCAATGTAGAATATTTCACCTTTGTCTAAGGGACTTTTGGGTTCT
21175 ACT
1 ACT
21178 TTGGACGTCG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (63 bp):
ACTAAGTAGATTCCCCATGCAATGTAGAATATTTCACCTTTGTCTAAGGGACTTTTGGGTTCT
Found at i:22338 original size:71 final size:71
Alignment explanation
Indices: 22217--22417 Score: 359
Period size: 71 Copynumber: 2.8 Consensus size: 71
22207 CATTCATTCA
* * * *
22217 TTCATTTACACTAACATTCCCCTTGCAACCTTCATCTTCAAACCTCCTTCAAAACTCAAATTGAA
1 TTCATTTACACTAACATTCCCCCTGCAATCTTCAACTTCAAACCTTCTTCAAAACTCAAATTGAA
22282 CTAATG
66 CTAATG
22288 TTCATTTACACTAACATTCCCCCTGCAATCTTCAACTTCAAACCTTCTTCAAAACTCAAATTGAA
1 TTCATTTACACTAACATTCCCCCTGCAATCTTCAACTTCAAACCTTCTTCAAAACTCAAATTGAA
22353 CTAATG
66 CTAATG
22359 TTCATTTACACTAACATTCCCCCTGCAATCTTCAACTTCAAACCTTCTTC-AAACTCAAA
1 TTCATTTACACTAACATTCCCCCTGCAATCTTCAACTTCAAACCTTCTTCAAAACTCAAA
22418 CTGATCTGCT
Statistics
Matches: 126, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 9 0.07
71 117 0.93
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.32
Consensus pattern (71 bp):
TTCATTTACACTAACATTCCCCCTGCAATCTTCAACTTCAAACCTTCTTCAAAACTCAAATTGAA
CTAATG
Found at i:30920 original size:16 final size:16
Alignment explanation
Indices: 30865--30920 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
30855 AAATAATTAT
30865 AAAATCAACAA-AATAA
1 AAAAT-AACAATAATAA
* *
30881 ATAAATAACAATATTAT
1 A-AAATAACAATAATAA
*
30898 AATATAACAATAATAA
1 AAAATAACAATAATAA
30914 AAAATAA
1 AAAATAA
30921 ATTCACTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 24 0.75
17 8 0.25
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAACAATAATAA
Found at i:32464 original size:24 final size:24
Alignment explanation
Indices: 32437--32484 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
32427 TTTTTACTAC
32437 TAAATAATTATTAGTAATAATTAT
1 TAAATAATTATTAGTAATAATTAT
* * * *
32461 TAAATCATTGTTTGTAATTATTAT
1 TAAATAATTATTAGTAATAATTAT
32485 AATTTCATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (24 bp):
TAAATAATTATTAGTAATAATTAT
Found at i:32775 original size:25 final size:28
Alignment explanation
Indices: 32714--32775 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 28
32704 AAGTTTGCAT
32714 TGAAGACGCCTAGATATCTAACATAGCAAA
1 TGAAGACGCCTAGATATC--ACATAGCAAA
32744 TGAAGACGCCTAGATATC-CA-AG-AAA
1 TGAAGACGCCTAGATATCACATAGCAAA
32769 TGAAGAC
1 TGAAGAC
32776 TAAGTTGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 10 0.31
26 2 0.06
27 2 0.06
30 18 0.56
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (28 bp):
TGAAGACGCCTAGATATCACATAGCAAA
Found at i:35253 original size:2 final size:2
Alignment explanation
Indices: 35237--35275 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
35227 CTATTACAAG
* * *
35237 TA TA TA CA TA GA TA TA TA TA TA TA TA TA TA CA 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
35276 TAAAATATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:35887 original size:63 final size:63
Alignment explanation
Indices: 35781--35906 Score: 198
Period size: 63 Copynumber: 2.0 Consensus size: 63
35771 AAGGGAATTA
*
35781 AACCGATTTGGGGACCAAATTAAACGTTTTTTAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAACGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
* * * * *
35844 AACCGGTTTGGGGACCAAATTGAATGTTTTTCAGAACATAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAACGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
35907 CTTTTAACAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (63 bp):
AACCGATTTGGGGACCAAATTAAACGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
Found at i:37446 original size:105 final size:105
Alignment explanation
Indices: 37164--38007 Score: 1553
Period size: 105 Copynumber: 8.0 Consensus size: 105
37154 GTTGTGAAGT
* * **
37164 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
*
37229 CTGGAGTCCAATATCCTTCGTTGTGACGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
37270 TGAAATTGAGAAGTTGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 TGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
37335 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
37376 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
37441 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
37481 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
37546 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
37586 TGAAATTGAGAAATGTTCGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
37651 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
37691 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
37756 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
37796 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
37861 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
37901 TGAAATTGAGAAATGTTCGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
37966 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
38006 TG
1 TG
38008 GGTAAAACCT
Statistics
Matches: 719, Mismatches: 18, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
105 609 0.85
106 110 0.15
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:50027 original size:61 final size:63
Alignment explanation
Indices: 49923--50046 Score: 189
Period size: 61 Copynumber: 2.0 Consensus size: 63
49913 AAGGGAATTA
*
49923 AACCGATTTGGGGACCAAATTAAACGTTTTTTAAAACAGAGGGAGCC-AAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAACGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
* * * *
49985 AACCG-TTTGGGGACCAAATTGAATGTTTTTCAGAACATAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAACGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
50047 TTTTAACAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 36 0.64
62 20 0.36
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (63 bp):
AACCGATTTGGGGACCAAATTAAACGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
Found at i:52912 original size:21 final size:21
Alignment explanation
Indices: 52886--52958 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 21
52876 GTTTCTAGAT
52886 TCGCAACGCGATAATACATAA
1 TCGCAACGCGATAATACATAA
**
52907 TCGCAACGCGATTCTA-ACT-A
1 TCGCAACGCGATAATACA-TAA
*
52927 TCGCAACGCGATAAT-CAAAA
1 TCGCAACGCGATAATACATAA
*
52947 TCGCAATGCGAT
1 TCGCAACGCGAT
52959 TTTCAAAGCG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (21 bp):
TCGCAACGCGATAATACATAA
Found at i:53127 original size:22 final size:22
Alignment explanation
Indices: 53102--53174 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
53092 TCTACGCGAC
53102 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
53124 ATCCGTCCCTATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* * *
53146 ATCCGTCCCCATCTCGGGCAAA
1 ATCCGTCCCCATCTCCGACGAA
53168 ATCCGTC
1 ATCCGTC
53175 TATCTCCATC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Done.