Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002589.1 Hibiscus syriacus cultivar Beakdansim tig00005242_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: 34964
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:91 original size:3 final size:3
Alignment explanation
Indices: 85--127 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
75 TTCTTCTTAT
85 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
128 GTTCGTGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5431 original size:59 final size:60
Alignment explanation
Indices: 5317--5467 Score: 205
Period size: 59 Copynumber: 2.5 Consensus size: 60
5307 TAATCGGATG
* *
5317 ACCATTTTGTAACTTTTAATAGTTGGGAGACTCAACAAAATAATATCCTATAGTCAAAGA
1 ACCATTTTGTAACTTTTAATAGTTGAGAGACTCAACAAAATAATATCATATAGTCAAAGA
* * *
5377 ACCATTTTGTAACTTTTAATAGTTTAG-GACTCAACAAAATAATTTCATATAGTCAAAGG
1 ACCATTTTGTAACTTTTAATAGTTGAGAGACTCAACAAAATAATATCATATAGTCAAAGA
** * * *
5436 ATGATTCTATAACTTTTAATAGTTAAGAGACT
1 ACCATTTTGTAACTTTTAATAGTTGAGAGACT
5468 TGATAAAGCA
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 51 0.64
60 29 0.36
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (60 bp):
ACCATTTTGTAACTTTTAATAGTTGAGAGACTCAACAAAATAATATCATATAGTCAAAGA
Found at i:10984 original size:24 final size:24
Alignment explanation
Indices: 10957--11035 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
10947 AACTTCAAAC
10957 ATTTTTCAAAATTCTTTCATAAAA
1 ATTTTTCAAAATTCTTTCATAAAA
** *
10981 ATTTTTCAATTTTTTTTCAT----
1 ATTTTTCAAAATTCTTTCATAAAA
11001 -TTTTT-AAAATTCTTTCATAAAA
1 ATTTTTCAAAATTCTTTCATAAAA
11023 CA-TTTTCAAAATT
1 -ATTTTTCAAAATT
11036 TCATCATCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
18 10 0.24
19 5 0.12
23 4 0.10
24 23 0.55
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTTTCAAAATTCTTTCATAAAA
Found at i:11882 original size:201 final size:202
Alignment explanation
Indices: 11516--11911 Score: 533
Period size: 201 Copynumber: 2.0 Consensus size: 202
11506 CAGTGTTGTC
* * * * * *
11516 TTCAGATACGACTAGACGTCCTCATCATGTAGGAAAAAATGTCGTCCACTTACTAGACCTCCTCA
1 TTCAAATACGACTAGACATACTCATCAAGTAGG-AAAAATGTCATCCACTAACTAGACCTCCTCA
* * * * * * ** *
11581 ACATGAAGGAGCAATGTCATCAGAAATGACCAGATTCTCCTCATTACGTAGGAGTCGTGTCGTTT
65 ACATGAAGGAGCAATGTCATAAAAAATGACAAGATTCTCCTAATCACGTAAGAACCGTGTCGTAT
* * *
11646 CCAACATCAAATTGTCTCTAAGCAATCAGATTTCCTCAACAAGAAGGAACAATGTTGTCGTCAGA
130 CCAAAATCAAATTGTCTATAAGCAATCAGATTTCCTCAACAAGAAGGAACAAGGTTGTCGTCAGA
11711 CGTAATCT
195 CGTAATCT
* *
11719 TTCAAATACGACTAGACATACTTATCAAGTAGG-AAAATGTCATCCACTAACTAGACCTCCTTAA
1 TTCAAATACGACTAGACATACTCATCAAGTAGGAAAAATGTCATCCACTAACTAGACCTCCTCAA
*
11783 TATGAAGGAGCAATGTCATAAAAAATGACAAGATTCTCCTAATCACGTAAGAACCGTGTCGTATC
66 CATGAAGGAGCAATGTCATAAAAAATGACAAGATTCTCCTAATCACGTAAGAACCGTGTCGTATC
* * * ** *
11848 CAAAATCAAATTGTCTATAGGCAATTATATTTCCTCAACATTAAGGAACAAGGTTGTCTTCAGA
131 CAAAATCAAATTGTCTATAAGCAATCAGATTTCCTCAACAAGAAGGAACAAGGTTGTCGTCAGA
11912 TGCATAGTCA
Statistics
Matches: 166, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
201 138 0.83
203 28 0.17
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (202 bp):
TTCAAATACGACTAGACATACTCATCAAGTAGGAAAAATGTCATCCACTAACTAGACCTCCTCAA
CATGAAGGAGCAATGTCATAAAAAATGACAAGATTCTCCTAATCACGTAAGAACCGTGTCGTATC
CAAAATCAAATTGTCTATAAGCAATCAGATTTCCTCAACAAGAAGGAACAAGGTTGTCGTCAGAC
GTAATCT
Found at i:12488 original size:3 final size:3
Alignment explanation
Indices: 12480--12546 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
12470 TGGATTTTAG
* * * * * * * *
12480 TTA TTA TTA TTA TTA TTA TTA TCA TCA TCA TCA TCA TTA TAA TAA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12528 TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA T-TA TTA
12547 AATACTAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (3 bp):
TTA
Found at i:12848 original size:14 final size:13
Alignment explanation
Indices: 12822--12846 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12812 CAAAATAATG
12822 AAAAAAATAAAAT
1 AAAAAAATAAAAT
12835 AAAAAAATAAAA
1 AAAAAAATAAAA
12847 ATCAAACTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:14096 original size:16 final size:17
Alignment explanation
Indices: 14031--14096 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 17
14021 TTAAATAATT
*
14031 TTTTAAATATATTA-TA
1 TTTTATATATATTATTA
*
14047 TTTTA-ATATATTTTTA
1 TTTTATATATATTATTA
* *
14063 TTTTTTACTAGATATATTA
1 TTTTATA-TATAT-TATTA
14082 TTTTATATA-ATTATT
1 TTTTATATATATTATT
14097 TTAATAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 7 0.17
16 15 0.37
17 3 0.07
18 6 0.15
19 10 0.24
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTTATATATATTATTA
Found at i:14180 original size:14 final size:12
Alignment explanation
Indices: 14116--14196 Score: 60
Period size: 13 Copynumber: 6.4 Consensus size: 12
14106 AATGTTCATT
14116 TTTATTTATTTTA
1 TTTA-TTATTTTA
*
14129 TGTA-TATATTTA
1 TTTATTAT-TTTA
14141 TTTATTATTTTAA
1 TTTATTATTTT-A
*
14154 ATTATTATTTTTA
1 TTTATTA-TTTTA
14167 TTTATCTATGTTTA
1 TTTAT-TAT-TTTA
14181 GTTT-TTA-TTTA
1 -TTTATTATTTTA
14192 TTTAT
1 TTTAT
14197 CATGATTGGT
Statistics
Matches: 56, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
10 3 0.05
11 8 0.14
12 10 0.18
13 21 0.38
14 11 0.20
15 3 0.05
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.69
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:20999 original size:17 final size:17
Alignment explanation
Indices: 20974--21007 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20964 CCGGTTTCGG
20974 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
* *
20991 TTTTTAAAAATCCGGTT
1 TTTTAAAAAAACCGGTT
21008 ATAAAAAACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:21103 original size:32 final size:33
Alignment explanation
Indices: 21067--21175 Score: 170
Period size: 33 Copynumber: 3.4 Consensus size: 33
21057 ACAAAGTTTA
*
21067 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
*
21099 CGATAAATTAAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
*
21132 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
21164 CGAT-AATTGAAA
1 CGATAAATTGAAA
21176 CAAAGTTTAC
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 7 0.10
32 14 0.19
33 51 0.71
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (33 bp):
CGATAAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:21188 original size:21 final size:21
Alignment explanation
Indices: 21164--21205 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21154 ACTTCAAGTT
*
21164 CGATAATTGAAACAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
*
21185 CGATAATTAAAATAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
21206 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTAAAACAAAGTTTA
Found at i:23508 original size:12 final size:12
Alignment explanation
Indices: 23491--23536 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
23481 TTCGGATAAA
23491 AACCGGTTTTTT
1 AACCGGTTTTTT
23503 AACCGGTTTTTTT
1 AACCGG-TTTTTT
23516 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
23530 ATCCGGT
1 AACCGGT
23537 AAAAAACCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:23521 original size:15 final size:14
Alignment explanation
Indices: 23490--23529 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
23480 TTTCGGATAA
23490 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
23503 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
23516 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
23530 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:32949 original size:45 final size:45
Alignment explanation
Indices: 32893--33001 Score: 130
Period size: 46 Copynumber: 2.4 Consensus size: 45
32883 TGCACCAATC
* *
32893 CATGCATCGATGCACCATGAATTAAATTG-AACATCGAATGCATTT
1 CATGCATCGATGCACCAGGAATTAAA-TGAAAAATCGAATGCATTT
* * **
32938 CATGCATCGATGCACTGAGGATTTTTATGAAAAATCGAATGCATTT
1 CATGCATCGATGCAC-CAGGAATTAAATGAAAAATCGAATGCATTT
*
32984 GATGCATCGATGCACCAG
1 CATGCATCGATGCACCAG
33002 CCATGCATCG
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
45 19 0.35
46 35 0.65
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (45 bp):
CATGCATCGATGCACCAGGAATTAAATGAAAAATCGAATGCATTT
Found at i:34726 original size:18 final size:18
Alignment explanation
Indices: 34703--34739 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
34693 TTTTTCTCGA
34703 AAAATGTCACTTTAGAGC
1 AAAATGTCACTTTAGAGC
34721 AAAATGTCACTTTAGAGC
1 AAAATGTCACTTTAGAGC
34739 A
1 A
34740 TGTTTCGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (18 bp):
AAAATGTCACTTTAGAGC
Done.