Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004847.1 Hibiscus syriacus cultivar Beakdansim tig00010928_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: 91221
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4311 original size:23 final size:22
Alignment explanation
Indices: 4253--4310 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
4243 TGTTTTCATA
*
4253 AAAAAAAC-CTAAAAGTATTTC
1 AAAAAATCTCTAAAAGTATTTC
4274 AAAAAATCTCTAAAAGTATTTC
1 AAAAAATCTCTAAAAGTATTTC
4296 GAAAAAATCT-TAAAA
1 -AAAAAATCTCTAAAA
4311 AAACGTCAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 7 0.21
22 18 0.53
23 9 0.26
ACGTcount: A:0.57, C:0.12, G:0.05, T:0.26
Consensus pattern (22 bp):
AAAAAATCTCTAAAAGTATTTC
Found at i:8329 original size:17 final size:17
Alignment explanation
Indices: 8307--8340 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
8297 CGTGCACACA
8307 AATCAAAAATTTAAATG
1 AATCAAAAATTTAAATG
8324 AATCAAAAATTTAAATG
1 AATCAAAAATTTAAATG
8341 TTAGATTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
AATCAAAAATTTAAATG
Found at i:9705 original size:7 final size:7
Alignment explanation
Indices: 9693--9726 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
9683 TGTTTGTTTT
9693 GGTTTAG
1 GGTTTAG
9700 GGTTTAG
1 GGTTTAG
9707 GGTTTAG
1 GGTTTAG
9714 GGTTTAG
1 GGTTTAG
9721 GGTTTA
1 GGTTTA
9727 TATAAATCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:13906 original size:22 final size:22
Alignment explanation
Indices: 13865--13906 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
13855 AAGACTAAAT
*
13865 AAATTTTATATTTTATATTTCA
1 AAATTTTATAATTTATATTTCA
13887 AAATTTTATCAATTTA-ATTT
1 AAATTTTAT-AATTTATATTT
13907 TTATTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (22 bp):
AAATTTTATAATTTATATTTCA
Found at i:14771 original size:60 final size:60
Alignment explanation
Indices: 14602--14771 Score: 184
Period size: 60 Copynumber: 2.9 Consensus size: 60
14592 TTGGATGAAA
* * * * *
14602 TTTG-GGATGAAATTGGAAGATTCAAAAGTCTAATGACTAATTTAGAAA-AAGGGTCATAT
1 TTTGAGGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTA-AAATGAGAGTCATAT
* * * * * * *
14661 TTTAAGGATGGAATTAGAATGTTCAAAAGTTTAAGGACTGATTTAGAATGAGAGTCATGT
1 TTTGAGGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAT
*
14721 TTTGAGGATGAAATTGGAATATTCAAAAGTTTGAGGA-TCAATTTAAAATGA
1 TTTGAGGATGAAATTGGAATATTCAAAAGTTTAAGGACT-AATTTAAAATGA
14772 AGATTATAGT
Statistics
Matches: 89, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
59 6 0.07
60 83 0.93
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.32
Consensus pattern (60 bp):
TTTGAGGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAT
Found at i:17428 original size:43 final size:44
Alignment explanation
Indices: 17367--17452 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
17357 TACATCCATA
*
17367 ATTTATTTTTTTATCAAATAAAATAA-AATTTATCTTTTTTATAT
1 ATTTATTTTTTTATCAAATAAAATAATAA-TAATCTTTTTTATAT
*
17411 ATTTA-TTTTTTATCAAATAAAATAATAATAATTTTTTTTATA
1 ATTTATTTTTTTATCAAATAAAATAATAATAATCTTTTTTATA
17453 ATATCTCTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
43 32 0.82
44 7 0.18
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (44 bp):
ATTTATTTTTTTATCAAATAAAATAATAATAATCTTTTTTATAT
Found at i:25012 original size:2 final size:2
Alignment explanation
Indices: 25005--25032 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24995 ATAAATCATA
25005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25033 TTGAATATTC
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):
AT
Found at i:25189 original size:2 final size:2
Alignment explanation
Indices: 25182--25209 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25172 AATATTATCA
25182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25210 TAATTAATTT
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):
AT
Found at i:28729 original size:17 final size:17
Alignment explanation
Indices: 28707--28750 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
28697 ATGTAAAAAT
28707 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
28724 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
28741 AAATATTTAA
1 AAATATTTAA
28751 TCAAGTGGGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:33260 original size:18 final size:18
Alignment explanation
Indices: 33233--33276 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
33223 CAGTTTATAA
*
33233 TGTTGCTGTTGTTGCTGC
1 TGTTGCTGTTGATGCTGC
*
33251 TGTTGTTGTTGATGCTGC
1 TGTTGCTGTTGATGCTGC
*
33269 TGCTGCTG
1 TGTTGCTG
33277 CTGCTGCAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.02, C:0.16, G:0.34, T:0.48
Consensus pattern (18 bp):
TGTTGCTGTTGATGCTGC
Found at i:36362 original size:30 final size:29
Alignment explanation
Indices: 36316--36373 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 29
36306 CATGATTTTA
36316 AGAAAAAAATAAAATTT-AATATTAAAAT
1 AGAAAAAAATAAAATTTAAATATTAAAAT
36344 AGAACAAAAATAATAATTTAAATATTAAAA
1 AGAA-AAAAATAA-AATTTAAATATTAAAA
36374 ATATAGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 8 0.30
30 5 0.19
31 10 0.37
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (29 bp):
AGAAAAAAATAAAATTTAAATATTAAAAT
Found at i:39039 original size:2 final size:2
Alignment explanation
Indices: 39028--39082 Score: 59
Period size: 2 Copynumber: 30.5 Consensus size: 2
39018 GAATCCGAAA
*
39028 AT AT -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39064 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
39083 ATCGGGACGG
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
1 6 0.13
2 40 0.87
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41602 original size:17 final size:18
Alignment explanation
Indices: 41582--41615 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41572 AAGAAAATAT
41582 AATAA-ATAAGTAAAAAC
1 AATAACATAAGTAAAAAC
41599 AATAACATAAGTAAAAA
1 AATAACATAAGTAAAAA
41616 TAAATTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (18 bp):
AATAACATAAGTAAAAAC
Found at i:43218 original size:3 final size:3
Alignment explanation
Indices: 43210--43263 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
43200 TATGTAAAAT
* *
43210 TAA TAA TAA TAA TAA TAA TAGT TAA TAA TAA TTAA TAA TAA -AA AAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA -TAA TAA TAA TAA TAA
43256 TAA -AA TAA
1 TAA TAA TAA
43264 AAGACCCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
2 4 0.09
3 35 0.80
4 5 0.11
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:43250 original size:10 final size:10
Alignment explanation
Indices: 43207--43250 Score: 61
Period size: 10 Copynumber: 4.2 Consensus size: 10
43197 TAATATGTAA
43207 AATTAATAAT
1 AATTAATAAT
43217 AATAATAATAAT
1 AAT--TAATAAT
*
43229 AGTTAATAAT
1 AATTAATAAT
43239 AATTAATAAT
1 AATTAATAAT
43249 AA
1 AA
43251 AAAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 21 0.70
12 9 0.30
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
AATTAATAAT
Found at i:43473 original size:43 final size:40
Alignment explanation
Indices: 43419--43522 Score: 118
Period size: 40 Copynumber: 2.5 Consensus size: 40
43409 GACGACACTG
* *
43419 CTCATACGTGATGAAGAGTTCGGGTCGTCTAAGGGTGACACGG
1 CTCATACGTGATGAAGAGTTCGGGTCG---AAGGATGACACGA
* * ** *
43462 TTCATACGTGATGAGGAAATCTGGTCGAAGGATGACACGA
1 CTCATACGTGATGAAGAGTTCGGGTCGAAGGATGACACGA
43502 CTCATACGTGATGAAGAGTTC
1 CTCATACGTGATGAAGAGTTC
43523 TTGGCCATCT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
40 28 0.56
43 22 0.44
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (40 bp):
CTCATACGTGATGAAGAGTTCGGGTCGAAGGATGACACGA
Found at i:43734 original size:130 final size:134
Alignment explanation
Indices: 43446--43754 Score: 373
Period size: 135 Copynumber: 2.3 Consensus size: 134
43436 GTTCGGGTCG
** *
43446 TCTAAGGGTGACACGGTTCATACGTGATGAGGAAATCTGGTC-GAAGGATGACACGACTCATACG
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAAATCTGGTCAGAAGGATGACACGACTCATACG
* *
43510 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGTGTGATAACTCGGTTCCTACGCGATGAGGACGGC
66 TGATGAAGAGTTCTTGGCCATCTTTA-GAAG-GTGATAACTCAGTTCCTACGCAATGAGGACGGC
43575 TGGTTA
129 TGGTTA
* * * *
43581 TCTAAGGGTGACACGACTCCTACGTGATGAGGATATCTAGTCAG-GGGATGACACTG-CTCCTAC
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAAATCTGGTCAGAAGGATGACAC-GACTCATAC
* *
43644 GTGATGAAGAGTTCTTGGCCAT-TTTA-TA-GTGATAACAT-AGTTCCTACGTAATGAGGACGGC
65 GTGATGAAGAGTTCTTGGCCATCTTTAGAAGGTGATAAC-TCAGTTCCTACGCAATGAGGACGGC
43705 TGGTTA
129 TGGTTA
* * ** *
43711 TCTAATGTTGACGTTG-CTCCTACGTGATGAGGAGATCTGGTCAG
1 TCTAAGGGTGAC-ACGACTCCTACGTGATGAGGAAATCTGGTCAG
43755 CTGATGTTGA
Statistics
Matches: 153, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
130 70 0.46
131 2 0.01
132 1 0.01
134 4 0.03
135 74 0.48
136 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (134 bp):
TCTAAGGGTGACACGACTCCTACGTGATGAGGAAATCTGGTCAGAAGGATGACACGACTCATACG
TGATGAAGAGTTCTTGGCCATCTTTAGAAGGTGATAACTCAGTTCCTACGCAATGAGGACGGCTG
GTTA
Found at i:44740 original size:23 final size:23
Alignment explanation
Indices: 44695--44756 Score: 90
Period size: 23 Copynumber: 2.6 Consensus size: 23
44685 TTGAACCCTC
44695 CTTTATTTATTTTTTCTTCTTTCTT
1 CTTT-TTTA-TTTTTCTTCTTTCTT
44720 CTTTTTTCATTTTTCTT-TTTCTT
1 CTTTTTT-ATTTTTCTTCTTTCTT
44743 CTTTTTTATTTTTC
1 CTTTTTTATTTTTC
44757 CATCATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.19
23 13 0.36
24 11 0.31
25 5 0.14
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (23 bp):
CTTTTTTATTTTTCTTCTTTCTT
Found at i:56617 original size:17 final size:18
Alignment explanation
Indices: 56597--56630 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
56587 AAGAAAATAT
56597 AATAA-ATAAGTAAAAAC
1 AATAACATAAGTAAAAAC
56614 AATAACATAAGTAAAAA
1 AATAACATAAGTAAAAA
56631 TAAATTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (18 bp):
AATAACATAAGTAAAAAC
Found at i:58233 original size:3 final size:3
Alignment explanation
Indices: 58225--58268 Score: 61
Period size: 3 Copynumber: 14.0 Consensus size: 3
58215 TATGTAAAAT
*
58225 TAA TAA TAA TAA TAA TAA TAGT TAA TAA TAA TTAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA -TAA TAA TAA TAA
58269 AAAAATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 32 0.86
4 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:58265 original size:10 final size:10
Alignment explanation
Indices: 58222--58266 Score: 63
Period size: 10 Copynumber: 4.3 Consensus size: 10
58212 TAATATGTAA
58222 AATTAATAAT
1 AATTAATAAT
58232 AATAATAATAAT
1 AAT--TAATAAT
*
58244 AGTTAATAAT
1 AATTAATAAT
58254 AATTAATAAT
1 AATTAATAAT
58264 AAT
1 AAT
58267 AAAAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 22 0.71
12 9 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
AATTAATAAT
Found at i:58268 original size:13 final size:12
Alignment explanation
Indices: 58225--58268 Score: 61
Period size: 13 Copynumber: 3.5 Consensus size: 12
58215 TATGTAAAAT
58225 TAATAATAATAA
1 TAATAATAATAA
*
58237 TAATAATAGTTAA
1 TAATAATA-ATAA
58250 TAATAATTAATAA
1 TAATAA-TAATAA
58263 TAATAA
1 TAATAA
58269 AAAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 8 0.29
13 18 0.64
14 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (12 bp):
TAATAATAATAA
Found at i:64859 original size:17 final size:20
Alignment explanation
Indices: 64823--64861 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
64813 TTTGAATTAT
64823 ATTATTTATATATCTTTTAA
1 ATTATTTATATATCTTTTAA
64843 ATTA-TTAT-TAT-TTTTAA
1 ATTATTTATATATCTTTTAA
64860 AT
1 AT
64862 AAGGGAGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 3 0.16
19 4 0.21
20 4 0.21
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTATTTATATATCTTTTAA
Found at i:66188 original size:14 final size:14
Alignment explanation
Indices: 66163--66198 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
66153 TAAAATATAG
66163 TATTTCTAAAAAATT
1 TATTT-TAAAAAATT
66178 TATTTT-AAAAATT
1 TATTTTAAAAAATT
66191 TATTTTAA
1 TATTTTAA
66199 TCACATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 13 0.65
14 2 0.10
15 5 0.25
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTTTAAAAAATT
Found at i:67501 original size:22 final size:22
Alignment explanation
Indices: 67475--67524 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
67465 ACTCACTCAT
*
67475 TGGCGAAAGACGATATCAATGG
1 TGGCGAAAGACGATACCAATGG
67497 TGGCGAAAGACGATACCAATGG
1 TGGCGAAAGACGATACCAATGG
*
67519 CGGCGA
1 TGGCGA
67525 TGATAATGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.34, C:0.18, G:0.34, T:0.14
Consensus pattern (22 bp):
TGGCGAAAGACGATACCAATGG
Found at i:87165 original size:15 final size:15
Alignment explanation
Indices: 87130--87168 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
87120 CAAAATTTAT
87130 AAAAAATTAAAGAAA
1 AAAAAATTAAAGAAA
** *
87145 TTAAAATTAAATAAA
1 AAAAAATTAAAGAAA
87160 AAAAAATTA
1 AAAAAATTA
87169 CTATATGATG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAAAATTAAAGAAA
Done.