Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008791.1 Hibiscus syriacus cultivar Beakdansim tig00111934_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: 42042
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:10481 original size:2 final size:2
Alignment explanation
Indices: 10474--10501 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10464 AGGATAAATT
10474 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10502 AATTTGGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11562 original size:15 final size:17
Alignment explanation
Indices: 11532--11563 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
11522 AAACATTATC
11532 TTATCTTTAGTTTATTA
1 TTATCTTTAGTTTATTA
11549 TTAT-TTTA-TTTATTA
1 TTATCTTTAGTTTATTA
11564 AACTACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (17 bp):
TTATCTTTAGTTTATTA
Found at i:12477 original size:28 final size:28
Alignment explanation
Indices: 12450--12504 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
12440 ATTAGTAATA
*
12450 ATTAATAATTTAAT-AATAATTTTAAAT
1 ATTAAGAATTTAATCAATAATTTTAAAT
* * *
12477 ATTAGGAATTTATTCAATTATTTTAAAT
1 ATTAAGAATTTAATCAATAATTTTAAAT
12505 TAGGACTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (28 bp):
ATTAAGAATTTAATCAATAATTTTAAAT
Found at i:13669 original size:23 final size:22
Alignment explanation
Indices: 13624--13670 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
13614 TAAGAAAATC
*
13624 TAATAATTTATATATATATAAA
1 TAATAATTTATATATATAGAAA
* *
13646 TAATATATTTATTTATTTAGAAA
1 TAATA-ATTTATATATATAGAAA
13669 TA
1 TA
13671 TCAGAAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TAATAATTTATATATATAGAAA
Found at i:15770 original size:14 final size:13
Alignment explanation
Indices: 15746--15778 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
15736 TAAAATTATT
15746 TATTAAATAATAA
1 TATTAAATAATAA
15759 TATTATAATAATAA
1 TATTA-AATAATAA
15773 TATTAA
1 TATTAA
15779 TAAAAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATTAAATAATAA
Found at i:23682 original size:22 final size:23
Alignment explanation
Indices: 23657--23699 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
23647 TTAAATGATT
23657 ATTTTAT-TTCTTATT-TTTTAGC
1 ATTTTATATTCTT-TTGTTTTAGC
23679 ATTTTATATTCTTTTGTTTTA
1 ATTTTATATTCTTTTGTTTTA
23700 ATTTTTGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (23 bp):
ATTTTATATTCTTTTGTTTTAGC
Found at i:24047 original size:2 final size:2
Alignment explanation
Indices: 24040--24064 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24030 AATGCTTCAA
24040 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
24065 CAAAATGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29969 original size:12 final size:12
Alignment explanation
Indices: 29945--30000 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
29935 TTTAAATAAA
29945 AAAAAT-ATGTTT
1 AAAAATAAT-TTT
29957 AAAAATAATTTT
1 AAAAATAATTTT
* **
29969 AAATTATTAAACTT
1 AAA--AATAATTTT
29983 AAAAATAATTTT
1 AAAAATAATTTT
29995 AAAAAT
1 AAAAAT
30001 GGTCCCTCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 24 0.69
13 2 0.06
14 9 0.26
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (12 bp):
AAAAATAATTTT
Found at i:30740 original size:16 final size:16
Alignment explanation
Indices: 30715--30757 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
30705 AACGTCTTTT
30715 AAAAACAATTTT-TAAG
1 AAAAA-AATTTTATAAG
30731 AAAAATAATTTTATAAG
1 AAAAA-AATTTTATAAG
*
30748 ACAAAAATTT
1 AAAAAAATTT
30758 GGTCTGCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAAAAATTTTATAAG
Found at i:32022 original size:28 final size:27
Alignment explanation
Indices: 31991--32045 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
31981 TTAAAATACT
*
31991 AAAAT-CAATAACAGAAAGTTAAAGGACC
1 AAAATCCAA-AACAGAAA-CTAAAGGACC
32019 AAAATGCCAAAACAGAAACTAAAGGAC
1 AAAAT-CCAAAACAGAAACTAAAGGAC
32046 TAAACAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 13 0.54
29 8 0.33
30 3 0.12
ACGTcount: A:0.58, C:0.16, G:0.15, T:0.11
Consensus pattern (27 bp):
AAAATCCAAAACAGAAACTAAAGGACC
Found at i:33447 original size:25 final size:25
Alignment explanation
Indices: 33409--33532 Score: 205
Period size: 25 Copynumber: 5.0 Consensus size: 25
33399 AGTTAGGGGA
* *
33409 TTAGGG-TTGAAACCCTAAATTGTT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
33433 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
33458 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
33483 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
33508 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
33533 GGGTTGGTTC
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
24 6 0.06
25 88 0.94
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:33669 original size:3 final size:3
Alignment explanation
Indices: 33661--33703 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
33651 ATATATAATT
*
33661 TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA -AA TTA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TA
33704 TAAAAAAGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.09
3 29 0.83
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:33702 original size:13 final size:13
Alignment explanation
Indices: 33661--33703 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
33651 ATATATAATT
33661 TAATAATAAT-AA
1 TAATAATAATAAA
*
33673 TAATAATAATAAT
1 TAATAATAATAAA
33686 TAATAA-AATTAAA
1 TAATAATAA-TAAA
33699 TAATA
1 TAATA
33704 TAAAAAAGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:33708 original size:15 final size:16
Alignment explanation
Indices: 33657--33708 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
33647 TGTAATATAT
*
33657 AATTTAATAATAATAA
1 AATTAAATAATAATAA
*
33673 TAATAATAATAATTAATAA
1 -AATTA-AATAA-TAATAA
33692 AATTAAATAAT-ATAA
1 AATTAAATAATAATAA
33707 AA
1 AA
33709 AAGACCCGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 6 0.20
16 1 0.03
17 8 0.27
18 9 0.30
19 6 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATTAAATAATAATAA
Found at i:33933 original size:43 final size:43
Alignment explanation
Indices: 33886--34170 Score: 136
Period size: 40 Copynumber: 6.4 Consensus size: 43
33876 AATGAAAAGG
33886 TCTGGTCGTCTAAGGGTGACACGGCTCCTACGTGATGAAGAAA
1 TCTGGTCGTCTAAGGGTGACACGGCTCCTACGTGATGAAGAAA
* * **
33929 TCT-G--GTC-AAGGGATGACACGGCTCATACGCGATGAAGAGT
1 TCTGGTCGTCTAAGGG-TGACACGGCTCCTACGTGATGAAGAAA
* * * * *
33969 TATGGTCATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGAAA
1 TCTGGTCGTC--T---AAGGGTG---ACACGGCTCCTACGTGATGAAGAAA
* * **
34020 TCT-G--GTC-AAGGGATGACACGGCTCATACGCGATGAAGAGT
1 TCTGGTCGTCTAAGGG-TGACACGGCTCCTACGTGATGAAGAAA
* * * *
34060 TCTGGTCATCTTTAAGAAGGGTGATAATTCGGTTCCTACGTGATGAGGAAA
1 TCTGGTCGTC--T---AAGGGTGA-CA--CGGCTCCTACGTGATGAAGAAA
* * ** * * *
34111 TCCGATTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAAG
1 TCTGGTCGTCTAAGGGTGACACGGCTCCTACGTGATGAAGAAA
34154 TCTGGTCGTCTAAGGGT
1 TCTGGTCGTCTAAGGGT
34171 AGATGACATG
Statistics
Matches: 174, Mismatches: 42, Indels: 52
0.65 0.16 0.19
Matches are distributed among these distances:
39 5 0.03
40 49 0.28
41 2 0.01
42 6 0.03
43 41 0.24
45 1 0.01
46 7 0.04
48 7 0.04
49 12 0.07
50 1 0.01
51 43 0.25
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (43 bp):
TCTGGTCGTCTAAGGGTGACACGGCTCCTACGTGATGAAGAAA
Found at i:34066 original size:91 final size:91
Alignment explanation
Indices: 33911--34112 Score: 377
Period size: 91 Copynumber: 2.2 Consensus size: 91
33901 GTGACACGGC
*
33911 TCCTACGTGATGAAGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTATGGTC
1 TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTATGGTC
33976 ATCTTTAAGAAGGGTGATAACTCGGT
66 ATCTTTAAGAAGGGTGATAACTCGGT
*
34002 TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTC
1 TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTATGGTC
*
34067 ATCTTTAAGAAGGGTGATAATTCGGT
66 ATCTTTAAGAAGGGTGATAACTCGGT
34093 TCCTACGTGATGAGGAAATC
1 TCCTACGTGATGAGGAAATC
34113 CGATTATCTA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 108 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (91 bp):
TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTATGGTC
ATCTTTAAGAAGGGTGATAACTCGGT
Found at i:34249 original size:141 final size:134
Alignment explanation
Indices: 34002--34302 Score: 343
Period size: 141 Copynumber: 2.2 Consensus size: 134
33992 ATAACTCGGT
* ** *
34002 TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTC
1 TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACACGATGAAGAACTCTGGCC
*
34067 ATCTTTAAGAAGGGTGATAATTCGGTTCCTACGTGATGAGGAAATCCGATTATCTAAGGTTGACA
66 ATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGAAATCCGATTATCTAAGGTTGACA
34132 CGGC
131 CGGC
* * * *
34136 TCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACATGATGAAGAAC
1 TCCTACGTGATGAGGAAATCT-G--GTC-AA-GG--GATGACACGGCTCATACACGATGAAGAAC
* *** * *
34201 TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAA
59 TCTGGCCATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGAAATCCGATTAT-CTAA
* *
34266 TGTTGACAC-TC
123 GGTTGACACGGC
* * *
34277 TCCTATGTGATAAGGAGATCTGGTCA
1 TCCTACGTGATGAGGAAATCTGGTCA
34303 GTTGATGTTG
Statistics
Matches: 138, Mismatches: 21, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
134 20 0.14
135 1 0.01
137 4 0.03
138 5 0.04
139 2 0.01
140 1 0.01
141 93 0.67
142 12 0.09
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (134 bp):
TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACACGATGAAGAACTCTGGCC
ATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGAAATCCGATTATCTAAGGTTGACA
CGGC
Found at i:35281 original size:7 final size:8
Alignment explanation
Indices: 35252--35288 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
35242 TCCTTTATTT
35252 ATTTTTTC
1 ATTTTTTC
*
35260 TTCTTTTTC
1 AT-TTTTTC
35269 ATTTTTTC
1 ATTTTTTC
35277 ATTTTTTC
1 ATTTTTTC
35285 ATTT
1 ATTT
35289 CCTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (8 bp):
ATTTTTTC
Done.