Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005227.1 Hibiscus syriacus cultivar Beakdansim tig00011836_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: 73895
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:13525 original size:17 final size:17
Alignment explanation
Indices: 13484--13528 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
13474 ATTTATGCAT
13484 CTAGTTCATTGAATAAA
1 CTAGTTCATTGAATAAA
* *
13501 CTTAGTTCATTGATTACA
1 C-TAGTTCATTGAATAAA
13519 CTAGTTCATT
1 CTAGTTCATT
13529 CAACAACCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (17 bp):
CTAGTTCATTGAATAAA
Found at i:15199 original size:62 final size:63
Alignment explanation
Indices: 15075--15201 Score: 152
Period size: 62 Copynumber: 2.0 Consensus size: 63
15065 AAGAGGGGAG
* * **
15075 AAAAAAGAATAGAAAAAAATAAATAAAATAAATATATATATATATATATAAAAGTATTTAAAT
1 AAAAAAGAATAGAAAAAAATAAATAAAATAAAAAGATATATATATATATAAAAGTACATAAAT
* * *
15138 AAAAAAGAA-AGGAAAAAAT-AATAATGATAAAAAGATATATATATATATATATA-TACATAAAT
1 AAAAAAGAATAGAAAAAAATAAATAA-AATAAAAAGATATATATATATATA-AAAGTACATAAAT
15200 AA
1 AA
15202 CACACTAACA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
61 5 0.09
62 39 0.71
63 11 0.20
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (63 bp):
AAAAAAGAATAGAAAAAAATAAATAAAATAAAAAGATATATATATATATAAAAGTACATAAAT
Found at i:15256 original size:21 final size:21
Alignment explanation
Indices: 15211--15272 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 21
15201 ACACACTAAC
*
15211 AAAAATAACAATAATAATAATAAT
1 AAAAAT-A-AATAAT-ATAAAAAT
15235 AACAAA-AAATAATATAAAAAT
1 AA-AAATAAATAATATAAAAAT
*
15256 AAAAATAAAAAATATAA
1 AAAAATAAATAATATAA
15273 TTAAATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 3 0.09
21 19 0.56
22 6 0.18
23 1 0.03
24 2 0.06
25 3 0.09
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAAATAAATAATATAAAAAT
Found at i:15256 original size:24 final size:24
Alignment explanation
Indices: 15224--15269 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
15214 AATAACAATA
* *
15224 ATAATAATAATAACAAAAAATAAT
1 ATAAAAATAAAAACAAAAAATAAT
*
15248 ATAAAAATAAAAATAAAAAATA
1 ATAAAAATAAAAACAAAAAATA
15270 TAATTAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (24 bp):
ATAAAAATAAAAACAAAAAATAAT
Found at i:17990 original size:7 final size:7
Alignment explanation
Indices: 17975--18033 Score: 57
Period size: 7 Copynumber: 8.3 Consensus size: 7
17965 CTTGAACCCA
*
17975 TCTTATT
1 TCTTTTT
17982 TCTTTTT
1 TCTTTTT
17989 TCTTTTT
1 TCTTTTT
17996 TCTTTCTCT
1 TCTTT-T-T
*
18005 TCTTTGT
1 TCTTTTT
18012 TCTTTTT
1 TCTTTTT
* *
18019 T-TCTCT
1 TCTTTTT
18025 TCTTTTT
1 TCTTTTT
18032 TC
1 TC
18034 CAATTTAGGG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
6 4 0.10
7 31 0.74
8 1 0.02
9 6 0.14
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (7 bp):
TCTTTTT
Found at i:18007 original size:23 final size:20
Alignment explanation
Indices: 17981--18033 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
17971 CCCATCTTAT
17981 TTCTTTTTTCTTTTTTCTTTCTC
1 TTCTTTTTTC--TTTT-TTTCTC
*
18004 TTCTTTGTTCTTTTTTTCTC
1 TTCTTTTTTCTTTTTTTCTC
18024 TTCTTTTTTC
1 TTCTTTTTTC
18034 CAATTTAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 15 0.54
21 4 0.14
23 9 0.32
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (20 bp):
TTCTTTTTTCTTTTTTTCTC
Found at i:24828 original size:12 final size:13
Alignment explanation
Indices: 24803--24831 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
24793 TGAAAAATAT
24803 AAAAATAAACATG
1 AAAAATAAACATG
24816 AAAAATAAA-ATG
1 AAAAATAAACATG
24828 AAAA
1 AAAA
24832 GTATGAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAATAAACATG
Found at i:28485 original size:30 final size:30
Alignment explanation
Indices: 28449--28506 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
28439 TAACAATAAT
*
28449 AATAATAATAATAAAT-AAGAAAAAAGAAAA
1 AATAAT-ATAAAAAATAAAGAAAAAAGAAAA
*
28479 AATAATATAAAAAATAAATAAAAAAGAA
1 AATAATATAAAAAATAAAGAAAAAAGAA
28507 TATAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (30 bp):
AATAATATAAAAAATAAAGAAAAAAGAAAA
Found at i:28492 original size:12 final size:12
Alignment explanation
Indices: 28475--28511 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
28465 AAGAAAAAAG
28475 AAAAAATAATAT
1 AAAAAATAATAT
28487 AAAAAATAA-AT
1 AAAAAATAATAT
*
28498 AAAAAAGAATAT
1 AAAAAATAATAT
28510 AA
1 AA
28512 TTAAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (12 bp):
AAAAAATAATAT
Found at i:35720 original size:32 final size:32
Alignment explanation
Indices: 35683--35760 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 32
35673 CGTCTATGTT
*
35683 CGTTCGTTTATGTTTTTTTACGTTTGATAATC
1 CGTTCGTTTATGTTTGTTTACGTTTGATAATC
* *
35715 CGTTCG-TTACTGTTTGTTTATGTTTGATAATT
1 CGTTCGTTTA-TGTTTGTTTACGTTTGATAATC
35747 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
35761 CGTACGTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 3 0.07
32 35 0.85
33 3 0.07
ACGTcount: A:0.14, C:0.12, G:0.18, T:0.56
Consensus pattern (32 bp):
CGTTCGTTTATGTTTGTTTACGTTTGATAATC
Found at i:37596 original size:13 final size:13
Alignment explanation
Indices: 37578--37616 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
37568 ACAGATGCGC
37578 ATATGAAGACTGT
1 ATATGAAGACTGT
37591 ATATGAAGACTGT
1 ATATGAAGACTGT
37604 ATATGAAGACTGT
1 ATATGAAGACTGT
37617 TCAACTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
ATATGAAGACTGT
Found at i:38150 original size:15 final size:15
Alignment explanation
Indices: 38130--38178 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
38120 TTTTATATGG
*
38130 AAATGTTCTATGTGA
1 AAATGTTCTAAGTGA
*
38145 AAATGTGCTAAGTGA
1 AAATGTTCTAAGTGA
*
38160 AAATAG-TCTACGTGA
1 AAAT-GTTCTAAGTGA
38175 AAAT
1 AAAT
38179 ACCCTATGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 28 0.97
16 1 0.03
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (15 bp):
AAATGTTCTAAGTGA
Found at i:44184 original size:18 final size:17
Alignment explanation
Indices: 44140--44207 Score: 109
Period size: 17 Copynumber: 3.9 Consensus size: 17
44130 ACATTGTTTA
44140 TAACTTAAAAATACTTT
1 TAACTTAAAAATACTTT
44157 TAACTTAAAAATACTTT
1 TAACTTAAAAATACTTT
*
44174 TAACTTAAAAATAGTTT
1 TAACTTAAAAATACTTT
*
44191 TAACTCCAAAAATACTT
1 TAACT-TAAAAATACTT
44208 AAAAATACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
17 38 0.81
18 9 0.19
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.38
Consensus pattern (17 bp):
TAACTTAAAAATACTTT
Found at i:45149 original size:39 final size:39
Alignment explanation
Indices: 45049--45151 Score: 113
Period size: 39 Copynumber: 2.6 Consensus size: 39
45039 ATTATCAAAT
*
45049 TATTTCACTTTAACATTCTAAATTACTAATATCTTAAAA
1 TATTTCACATTAACATTCTAAATTACTAATATCTTAAAA
* * * *
45088 T-TTTCCACCA-TAATATTTTAAATT-CTTAATTTCTTAAAC
1 TATTT-CA-CATTAACATTCTAAATTAC-TAATATCTTAAAA
45127 TATTTCACATTAACATTCTAAATTA
1 TATTTCACATTAACATTCTAAATTA
45152 TTCTTTAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
38 6 0.12
39 41 0.80
40 4 0.08
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.46
Consensus pattern (39 bp):
TATTTCACATTAACATTCTAAATTACTAATATCTTAAAA
Found at i:49189 original size:46 final size:46
Alignment explanation
Indices: 49118--49211 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
49108 CTTTACACCC
* *
49118 CCGGAGTAATCAACTACGATTGACAGAGACTGATCTTTGTTTCGGT
1 CCGGAGTAATCAACTACGATCGACAGAGACTGATCTTTGTTTCAGT
* * *
49164 CCGGAGTAGTCGACTATGATCGACAGAGACTGATCTTTGTTTCAGT
1 CCGGAGTAATCAACTACGATCGACAGAGACTGATCTTTGTTTCAGT
49210 CC
1 CC
49212 AGCTGCTTCG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (46 bp):
CCGGAGTAATCAACTACGATCGACAGAGACTGATCTTTGTTTCAGT
Found at i:55347 original size:21 final size:21
Alignment explanation
Indices: 55323--55369 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
55313 AATTTCACAA
55323 GAAAAGCTAGTTACATCCCAG
1 GAAAAGCTAGTTACATCCCAG
* *
55344 GAAAAGCTGGTTGCATCCCAG
1 GAAAAGCTAGTTACATCCCAG
*
55365 AAAAA
1 GAAAA
55370 ATTCCAAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (21 bp):
GAAAAGCTAGTTACATCCCAG
Found at i:57462 original size:23 final size:23
Alignment explanation
Indices: 57432--57477 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
57422 CCCATGTCTC
57432 CAGTCATGACCAAATAATAAAAA
1 CAGTCATGACCAAATAATAAAAA
57455 CAGTCATGACCAAATAATAAAAA
1 CAGTCATGACCAAATAATAAAAA
57478 AATGCATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.17, G:0.09, T:0.17
Consensus pattern (23 bp):
CAGTCATGACCAAATAATAAAAA
Found at i:62021 original size:27 final size:27
Alignment explanation
Indices: 61980--62053 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
61970 CTAGTATGCG
* *
61980 CTGACTAAATTTTCTAGAAAACTGTTA
1 CTGACTAGATCTTCTAGAAAACTGTTA
62007 CTGACTAGATCTTCTAGAAAACTGTTA
1 CTGACTAGATCTTCTAGAAAACTGTTA
* *
62034 CTGACTGGACCTTCTAGAAA
1 CTGACTAGATCTTCTAGAAA
62054 CTTCCACGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (27 bp):
CTGACTAGATCTTCTAGAAAACTGTTA
Found at i:67778 original size:40 final size:40
Alignment explanation
Indices: 67716--67799 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
67706 TTGGGAAATA
*
67716 AATTGAAATTGAAGATGACAACTTGTGATTTTGATGTGTT
1 AATTAAAATTGAAGATGACAACTTGTGATTTTGATGTGTT
*
67756 AATTAAAATTGAAGATGGCAACTTGTGATTTTGATGTGTT
1 AATTAAAATTGAAGATGACAACTTGTGATTTTGATGTGTT
67796 AATT
1 AATT
67800 GAGGAATGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.40
Consensus pattern (40 bp):
AATTAAAATTGAAGATGACAACTTGTGATTTTGATGTGTT
Found at i:68354 original size:11 final size:11
Alignment explanation
Indices: 68335--68372 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
68325 AACACATCTT
68335 CATTCAGAAAA
1 CATTCAGAAAA
*
68346 CATTTAGAAAA
1 CATTCAGAAAA
68357 CATTCA-AAAA
1 CATTCAGAAAA
68367 TCATTC
1 -CATTC
68373 TTCTTCTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 4 0.17
11 20 0.83
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.26
Consensus pattern (11 bp):
CATTCAGAAAA
Found at i:68439 original size:29 final size:30
Alignment explanation
Indices: 68402--68459 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
68392 TAATAAAAGC
68402 TTTTCTTTTC-TTTTTCAAAGTTATTCTTTG
1 TTTTCTTTTCTTTTTTCAAAGTT-TTCTTTG
*
68432 TTTT-TTTTCTTTTTTCTAAGTTTTCTTT
1 TTTTCTTTTCTTTTTTCAAAGTTTTCTTT
68460 TAAGCCGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.72
Consensus pattern (30 bp):
TTTTCTTTTCTTTTTTCAAAGTTTTCTTTG
Found at i:71006 original size:15 final size:15
Alignment explanation
Indices: 70983--71012 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
70973 ATTCAATTTA
*
70983 TTTATTATATATAAT
1 TTTACTATATATAAT
70998 TTTACTATATATAAT
1 TTTACTATATATAAT
71013 AAACATAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTACTATATATAAT
Found at i:72301 original size:16 final size:16
Alignment explanation
Indices: 72276--72306 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
72266 CCCATATCCT
72276 TAAATAATATTACACA
1 TAAATAATATTACACA
*
72292 TAAATGATATTACAC
1 TAAATAATATTACAC
72307 CCACAAGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (16 bp):
TAAATAATATTACACA
Done.