Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004836.1 Hibiscus syriacus cultivar Beakdansim tig00010896_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: 63090
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3774 original size:17 final size:17
Alignment explanation
Indices: 3752--3797 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
3742 ATCCTTTTGC
3752 ATTTTATTTTTTAGAAT
1 ATTTTATTTTTTAGAAT
* *
3769 ATTTTATTCTCT--AAT
1 ATTTTATTTTTTAGAAT
3784 ATTTTATTTTTTAG
1 ATTTTATTTTTTAG
3798 TTAAAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
15 13 0.57
17 10 0.43
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (17 bp):
ATTTTATTTTTTAGAAT
Found at i:9037 original size:22 final size:20
Alignment explanation
Indices: 9012--9051 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9002 CTTTTTTTTC
9012 AATTATTCATTTATTGTGTATG
1 AATTA-TCATTT-TTGTGTATG
*
9034 AATTATGATTTTTGTGTA
1 AATTATCATTTTTGTGTA
9052 AATACAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 5 0.29
22 5 0.29
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.55
Consensus pattern (20 bp):
AATTATCATTTTTGTGTATG
Found at i:19800 original size:37 final size:36
Alignment explanation
Indices: 19754--19840 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 36
19744 TGGCAACCAA
19754 CTTTGAAAAAATGATTTTCAAAGTTTAGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTAGTAAATGTTT
* * *
19791 CTTTGAAAAATAATTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGA-TTTTCAAAGTTTAGTAAATGTTT
*
19828 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
19841 AATGGAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
35 1 0.02
36 17 0.39
37 26 0.59
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTAGTAAATGTTT
Found at i:20737 original size:30 final size:30
Alignment explanation
Indices: 20701--20770 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 30
20691 TGGTAGCTTA
* *
20701 GATGCAGATGCACAA-ACTGTCTGTATGTTT
1 GATGCAGATGCACAACA-TGTCCGCATGTTT
20731 GATGCAGATGCACAACATGTCCGCATGTTT
1 GATGCAGATGCACAACATGTCCGCATGTTT
20761 GATGCAGATG
1 GATGCAGATG
20771 GTGGGGAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 36 0.97
31 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (30 bp):
GATGCAGATGCACAACATGTCCGCATGTTT
Found at i:26090 original size:6 final size:6
Alignment explanation
Indices: 26079--26151 Score: 128
Period size: 6 Copynumber: 12.2 Consensus size: 6
26069 TCGGCTCGGC
* *
26079 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
26127 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
26152 AATACGTGTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.32
Consensus pattern (6 bp):
TCGTGG
Found at i:26454 original size:22 final size:22
Alignment explanation
Indices: 26429--26483 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
26419 TCAGGAGTTA
* *
26429 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
26451 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
26473 CGGGAGTTATA
1 CAGGAGTTATA
26484 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:32034 original size:5 final size:5
Alignment explanation
Indices: 32015--32058 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
32005 GTCCGTCCGT
* * *
32015 CTCGT CTCGT CTCGG CTCGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
32059 TGGTCGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.02, C:0.41, G:0.34, T:0.23
Consensus pattern (5 bp):
CTCGG
Found at i:32067 original size:6 final size:6
Alignment explanation
Indices: 32056--32122 Score: 116
Period size: 6 Copynumber: 11.2 Consensus size: 6
32046 TCGGCTCGGC
* *
32056 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
32104 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
32123 AATACGTGTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:32425 original size:22 final size:22
Alignment explanation
Indices: 32400--32454 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
32390 TCAGGAGTTA
* *
32400 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
32422 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
32444 CGGGAGTTATA
1 CAGGAGTTATA
32455 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:40121 original size:22 final size:20
Alignment explanation
Indices: 40096--40148 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
40086 CATAATTATT
40096 TAAAAAAATTAAATAAAAATA
1 TAAAAAAATTAAAT-AAAATA
* *
40117 CTAAAAATATTTAATAAAATA
1 -TAAAAAAATTAAATAAAATA
*
40138 AAAAAAAATTA
1 TAAAAAAATTA
40149 GGTTGAACCG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 8 0.31
21 6 0.23
22 12 0.46
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAAAAATTAAATAAAATA
Found at i:44202 original size:45 final size:43
Alignment explanation
Indices: 44148--44480 Score: 294
Period size: 45 Copynumber: 7.4 Consensus size: 43
44138 GTATCAGAAA
* *
44148 ATGATACTGTTTTGGAAGAAAAGAGTGTTGATCTTGGATCAAGCG
1 ATGATACTGTTTTGGAAGAAAAGAG-GTTGATCTTGCATCAA-TG
* * *
44193 ATGACACTGTTTTGGAAGAAAAGAGAATTGATCTTGCATCCAA-A
1 ATGATACTGTTTTGGAAGAAAAGAG-GTTGATCTTGCAT-CAATG
* * * * *
44237 AGCGATACAGTTTTGGATGAAAAGAGGACTGATCTTGCATTGAATG
1 A-TGATACTGTTTTGGAAGAAAAGAGG-TTGATCTTGCA-TCAATG
* * * *
44283 ATGTTACCGTTTTGGAAGAAAAGAGAATTGATCTTGCATCCGAA-A
1 ATGATACTGTTTTGGAAGAAAAGAG-GTTGATCTTGCAT-C-AATG
* * * *
44328 ATGACACTGTTTTGGATGAAAAGAGGATTGGTCTTGGATCAAGTG
1 ATGATACTGTTTTGGAAGAAAAGAGG-TTGATCTTGCATCAA-TG
* *
44373 ATGATACTGTTTTGGAAGAAAAGAGAATTGATCTTGCATCCGAA-A
1 ATGATACTGTTTTGGAAGAAAAGAG-GTTGATCTTGCAT-C-AATG
* *
44418 ATGATACAGTTTTGGATGAAAAGAGGATTGATCTTGCATCAAATG
1 ATGATACTGTTTTGGAAGAAAAGAGG-TTGATCTTGCATC-AATG
44463 ATGATACTGTTTTGGAAG
1 ATGATACTGTTTTGGAAG
44481 GATATAGCAC
Statistics
Matches: 230, Mismatches: 42, Indels: 32
0.76 0.14 0.11
Matches are distributed among these distances:
43 2 0.01
44 6 0.03
45 212 0.92
46 8 0.03
47 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.30
Consensus pattern (43 bp):
ATGATACTGTTTTGGAAGAAAAGAGGTTGATCTTGCATCAATG
Found at i:44270 original size:90 final size:90
Alignment explanation
Indices: 44112--44480 Score: 494
Period size: 90 Copynumber: 4.1 Consensus size: 90
44102 GATAAGGTTA
* * * * * * *
44112 TTTTGGAAGGAAAGA-AGATTAATATTGTATCAGAAAATGATACTGTTTTGGAAGAAAAGAGTG-
1 TTTTGGAAGAAAAGAGA-ATTGATCTTGCATCCGAAAATGATACAGTTTTGGATGAAAAGAG-GA
* * *
44175 TTGATCTTGGATCAAGCGATGACACTG
64 TTGATCTTGCATCAAGTGATGATACTG
* *
44202 TTTTGGAAGAAAAGAGAATTGATCTTGCATCC-AAAAGCGATACAGTTTTGGATGAAAAGAGGAC
1 TTTTGGAAGAAAAGAGAATTGATCTTGCATCCGAAAA-TGATACAGTTTTGGATGAAAAGAGGAT
* * *
44266 TGATCTTGCATTGAA-TGATGTTACCG
65 TGATCTTGCA-TCAAGTGATGATACTG
* *
44292 TTTTGGAAGAAAAGAGAATTGATCTTGCATCCGAAAATGACACTGTTTTGGATGAAAAGAGGATT
1 TTTTGGAAGAAAAGAGAATTGATCTTGCATCCGAAAATGATACAGTTTTGGATGAAAAGAGGATT
* *
44357 GGTCTTGGATCAAGTGATGATACTG
66 GATCTTGCATCAAGTGATGATACTG
44382 TTTTGGAAGAAAAGAGAATTGATCTTGCATCCGAAAATGATACAGTTTTGGATGAAAAGAGGATT
1 TTTTGGAAGAAAAGAGAATTGATCTTGCATCCGAAAATGATACAGTTTTGGATGAAAAGAGGATT
*
44447 GATCTTGCATCAAATGATGATACTG
66 GATCTTGCATCAAGTGATGATACTG
44472 TTTTGGAAG
1 TTTTGGAAG
44481 GATATAGCAC
Statistics
Matches: 244, Mismatches: 29, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
89 8 0.03
90 228 0.93
91 8 0.03
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (90 bp):
TTTTGGAAGAAAAGAGAATTGATCTTGCATCCGAAAATGATACAGTTTTGGATGAAAAGAGGATT
GATCTTGCATCAAGTGATGATACTG
Found at i:44363 original size:135 final size:133
Alignment explanation
Indices: 44144--44480 Score: 381
Period size: 135 Copynumber: 2.5 Consensus size: 133
44134 TATTGTATCA
* ** * *
44144 GAAAATGATACTGTTTTGGAAGAAAAGAGTGTTGATCTTGGATCAAGCGATGACACTGTTTTGGA
1 GAAAATGATACAGTTTTGGAAGAAAAGAGAATTGATCTTGCATCAA--AATGACACTGTTTTGGA
* *
44209 AGAAAAGAGAATTGATCTTGCATCCAAAAG-CGATACAGTTTTGGATGAAAAGAGGACTGATCTT
64 AGAAAAGAGAATTGATCTTGCAT-CAAAAGACGATACAGTTTTGGAAGAAAAGAGAACTGATCTT
*
44273 GCAT-T
128 GCATCC
* * *
44278 GAATGATGTTACCGTTTTGGAAGAAAAGAGAATTGATCTTGCATCCGAAAATGACACTGTTTTGG
1 GAA-AATGATACAGTTTTGGAAGAAAAGAGAATTGATCTTGCAT-C-AAAATGACACTGTTTTGG
* * * * ** * * *
44343 ATGAAAAGAGGATTGGTCTTGGATCAAGTGATGATACTGTTTTGGAAGAAAAGAGAATTGATCTT
63 AAGAAAAGAGAATTGATCTTGCATCAAAAGACGATACAGTTTTGGAAGAAAAGAGAACTGATCTT
44408 GCATCC
128 GCATCC
* * *
44414 GAAAATGATACAGTTTTGGATGAAAAGAGGATTGATCTTGCATCAAATGATGATACTGTTTTGGA
1 GAAAATGATACAGTTTTGGAAGAAAAGAGAATTGATCTTGCATCAAA--ATGACACTGTTTTGGA
44479 AG
64 AG
44481 GATATAGCAC
Statistics
Matches: 170, Mismatches: 26, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
133 3 0.02
134 8 0.05
135 153 0.90
136 4 0.02
137 2 0.01
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (133 bp):
GAAAATGATACAGTTTTGGAAGAAAAGAGAATTGATCTTGCATCAAAATGACACTGTTTTGGAAG
AAAAGAGAATTGATCTTGCATCAAAAGACGATACAGTTTTGGAAGAAAAGAGAACTGATCTTGCA
TCC
Found at i:44426 original size:180 final size:180
Alignment explanation
Indices: 44112--44480 Score: 546
Period size: 180 Copynumber: 2.0 Consensus size: 180
44102 GATAAGGTTA
* * *
44112 TTTTGGAAGGAAAGAAGATTAATATTGTATCAGAAAATGATACTGTTTTGGAAGAAAAGAGTGTT
1 TTTTGGAAGAAAAGAAGATTAATATTGCATCAGAAAATGACACTGTTTTGGAAGAAAAGAGTGTT
44177 GATCTTGGATCAAGCGATGACACTGTTTTGGAAGAAAAGAGAATTGATCTTGCATCCAAAAGCGA
66 GATCTTGGATCAAGCGATGACACTGTTTTGGAAGAAAAGAGAATTGATCTTGCATCCAAAAGCGA
** *
44242 TACAGTTTTGGATGAAAAGAGGACTGATCTTGCATTGAATGATGTTACCG
131 TACAGTTTTGGATGAAAAGAGGACTGATCTTGCATCAAATGATGATACCG
* * * *
44292 TTTTGGAAGAAAAG-AGAATTGATCTTGCATCCGAAAATGACACTGTTTTGGATGAAAAGAG-GA
1 TTTTGGAAGAAAAGAAG-ATTAATATTGCATCAGAAAATGACACTGTTTTGGAAGAAAAGAGTG-
* * *
44355 TTGGTCTTGGATCAAGTGATGATACTGTTTTGGAAGAAAAGAGAATTGATCTTGCATCCGAAAA-
64 TTGATCTTGGATCAAGCGATGACACTGTTTTGGAAGAAAAGAGAATTGATCTTGCATCC-AAAAG
* * *
44419 TGATACAGTTTTGGATGAAAAGAGGATTGATCTTGCATCAAATGATGATACTG
128 CGATACAGTTTTGGATGAAAAGAGGACTGATCTTGCATCAAATGATGATACCG
44472 TTTTGGAAG
1 TTTTGGAAG
44481 GATATAGCAC
Statistics
Matches: 170, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
179 3 0.02
180 163 0.96
181 4 0.02
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (180 bp):
TTTTGGAAGAAAAGAAGATTAATATTGCATCAGAAAATGACACTGTTTTGGAAGAAAAGAGTGTT
GATCTTGGATCAAGCGATGACACTGTTTTGGAAGAAAAGAGAATTGATCTTGCATCCAAAAGCGA
TACAGTTTTGGATGAAAAGAGGACTGATCTTGCATCAAATGATGATACCG
Found at i:53871 original size:36 final size:36
Alignment explanation
Indices: 53830--53902 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
53820 TTGCTCATGA
53830 TTGTTCCCTCCTGATGCTTAACCATGGGAATGGACC
1 TTGTTCCCTCCTGATGCTTAACCATGGGAATGGACC
53866 TTGTTCCCTCCTGATGCTTAACCATGGGAATGGACC
1 TTGTTCCCTCCTGATGCTTAACCATGGGAATGGACC
53902 T
1 T
53903 CCTTTTAGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32
Consensus pattern (36 bp):
TTGTTCCCTCCTGATGCTTAACCATGGGAATGGACC
Done.