Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005145.1 Hibiscus syriacus cultivar Beakdansim tig00011587_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: 52801
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:1360 original size:117 final size:116
Alignment explanation
Indices: 1154--1378 Score: 432
Period size: 117 Copynumber: 1.9 Consensus size: 116
1144 GTCTTAAAAT
1154 GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
1 GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
*
1219 CTTGGCGCCAACTTGAAGCAAGATGATGGTTTGGCCGAATGGAGGGTTCAAC
66 CTTGGCACCAACTTGAAGCAAGATGATGGTTT-GCCGAATGGAGGGTTCAAC
1271 GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
1 GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
1336 CTTGGCACCAACTTGAAGCAAGATGATGGTTTGCCGAATGGAG
66 CTTGGCACCAACTTGAAGCAAGATGATGGTTTGCCGAATGGAG
1379 AGAACCCTCT
Statistics
Matches: 107, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
116 11 0.10
117 96 0.90
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.28
Consensus pattern (116 bp):
GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
CTTGGCACCAACTTGAAGCAAGATGATGGTTTGCCGAATGGAGGGTTCAAC
Found at i:22072 original size:36 final size:33
Alignment explanation
Indices: 21999--22072 Score: 78
Period size: 36 Copynumber: 2.2 Consensus size: 33
21989 TATCTTCACT
* * *
21999 TTCTTATTATTTCATTTCCTTTTCTTTCATCTT
1 TTCTTATTATTTCATATCCTTTTCTTCCATCTC
22032 TTCTTATTTCATTATCATATCCTTTTCTTACCAT-TC
1 TTCTTA-TT-ATT-TCATATCCTTTTCTT-CCATCTC
22068 TTCTT
1 TTCTT
22073 TCCTACCCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 6 0.18
34 2 0.06
35 3 0.09
36 20 0.59
37 3 0.09
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (33 bp):
TTCTTATTATTTCATATCCTTTTCTTCCATCTC
Found at i:30250 original size:20 final size:19
Alignment explanation
Indices: 30227--30272 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 19
30217 AAATTTTGGC
30227 TTTTTTGGCTCTTTTTTTGTTT
1 TTTTTTGGC-C-TTTTTTG-TT
*
30249 TTTTTTTGCCTTTTTTGTT
1 TTTTTTGGCCTTTTTTGTT
30268 TTTTT
1 TTTTT
30273 GTGTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 7 0.30
21 1 0.04
22 8 0.35
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (19 bp):
TTTTTTGGCCTTTTTTGTT
Found at i:30251 original size:21 final size:20
Alignment explanation
Indices: 30227--30272 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
30217 AAATTTTGGC
30227 TTTTTTGGCTCTTTTTTTGTTT
1 TTTTTTGGC-C-TTTTTTGTTT
*
30249 TTTTTTTGCCTTTTTTGTTT
1 TTTTTTGGCCTTTTTTGTTT
30269 TTTT
1 TTTT
30273 GTGTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.61
21 1 0.04
22 8 0.35
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (20 bp):
TTTTTTGGCCTTTTTTGTTT
Found at i:33323 original size:22 final size:21
Alignment explanation
Indices: 33288--33329 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
33278 AGCCTTTTTC
*
33288 TTCTAAATATCTTTATCTCAAG
1 TTCTAAATAACTTTA-CTCAAG
*
33310 TTCTAAGTAACTTTACTCAA
1 TTCTAAATAACTTTACTCAA
33330 ATCTGTACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (21 bp):
TTCTAAATAACTTTACTCAAG
Found at i:33627 original size:11 final size:11
Alignment explanation
Indices: 33611--33635 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33601 TTTTTATTCT
33611 TTCACTTGCAC
1 TTCACTTGCAC
33622 TTCACTTGCAC
1 TTCACTTGCAC
33633 TTC
1 TTC
33636 TTTTTGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:36890 original size:19 final size:20
Alignment explanation
Indices: 36868--36924 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
36858 AATTGGAGTG
36868 CAAAAAGAAAAGAAAA-AGA
1 CAAAAAGAAAAGAAAACAGA
*
36887 CAAAAAGAAGAAAAAAATCAGA
1 CAAAAAGAA-AAGAAAA-CAGA
36909 -AAAGAAGAAAAGAAAA
1 CAAA-AAGAAAAGAAAA
36925 GAAATTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 9 0.28
20 6 0.19
21 9 0.28
22 8 0.25
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (20 bp):
CAAAAAGAAAAGAAAACAGA
Found at i:43100 original size:19 final size:20
Alignment explanation
Indices: 43076--43114 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
43066 TATAATATGC
*
43076 ATATTCTTA-TTACTTTATA
1 ATATTCATACTTACTTTATA
*
43095 ATATTCATACTTAGTTTATA
1 ATATTCATACTTACTTTATA
43115 TTATGCTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.54
Consensus pattern (20 bp):
ATATTCATACTTACTTTATA
Found at i:43927 original size:19 final size:20
Alignment explanation
Indices: 43903--43945 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
43893 GAGCATTATC
*
43903 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
43922 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
43942 TTCA
1 TTCA
43946 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:46143 original size:5 final size:5
Alignment explanation
Indices: 46135--46163 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
46125 AAGAGAAGAA
46135 AAAAG AAAAG AAAAG AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
46164 TTGAAAGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:50836 original size:64 final size:65
Alignment explanation
Indices: 50735--50864 Score: 199
Period size: 64 Copynumber: 2.0 Consensus size: 65
50725 TATACTAGCC
*
50735 CCATGTGCCTTGCATGAGGAACATTTAGGGGCCAAGATGAAGAGTTCTCTCCCTATTCGG-CAAG
1 CCATGTGCCTTGCATGAGGAACATTTAGGGGCCAAGATGAAGAGCTCTCTCCCTATTCGGCCAAG
* *** *
50799 CCATGTGCCTTGCATGTGGTTTATTTAGGTGCCAAGATGAAGAGCTCTCTCCCTATTCGGCCAAG
1 CCATGTGCCTTGCATGAGGAACATTTAGGGGCCAAGATGAAGAGCTCTCTCCCTATTCGGCCAAG
50864 C
1 C
50865 ACCATTTCCC
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
64 54 0.92
65 5 0.08
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (65 bp):
CCATGTGCCTTGCATGAGGAACATTTAGGGGCCAAGATGAAGAGCTCTCTCCCTATTCGGCCAAG
Done.