Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002439.1 Hibiscus syriacus cultivar Beakdansim tig00004995_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: 99971
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:8421 original size:33 final size:33
Alignment explanation
Indices: 8347--8423 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
8337 TCATAACCAA
* *
8347 AATGAGGGCAGACTTAGCTATGTGTAGAAAGTT
1 AATGAGGGTAGACTTAGCTATGCGTAGAAAGTT
*
8380 AATGAGGGTAGACTTTGCTATGCGTAGAAAGTT
1 AATGAGGGTAGACTTAGCTATGCGTAGAAAGTT
8413 AATGAGGGTAG
1 AATGAGGGTAG
8424 TACAAATTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.27
Consensus pattern (33 bp):
AATGAGGGTAGACTTAGCTATGCGTAGAAAGTT
Found at i:10452 original size:24 final size:24
Alignment explanation
Indices: 10425--10487 Score: 90
Period size: 26 Copynumber: 2.5 Consensus size: 24
10415 AAATTGAACG
*
10425 ACCGGTTTTTTTACCGGATTAAAA
1 ACCGGTTTTTTTACCGGATAAAAA
*
10449 ACCGGTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTT--TACCGGATAAAAA
10475 ACCGGTTTTTTTA
1 ACCGGTTTTTTTA
10488 AAAAACCGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.35
26 22 0.65
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (24 bp):
ACCGGTTTTTTTACCGGATAAAAA
Found at i:10491 original size:17 final size:17
Alignment explanation
Indices: 10469--10541 Score: 92
Period size: 17 Copynumber: 4.0 Consensus size: 17
10459 TCAAACCGGA
10469 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
10486 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
10503 ATCCAAAAAAATCCGGTTTTTT
1 -T---AAAAAA-CCGGTTTTTT
*
10525 TTAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
10542 GCAAACCAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
17 27 0.54
18 6 0.12
21 7 0.14
22 10 0.20
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (17 bp):
TAAAAAACCGGTTTTTT
Found at i:22240 original size:2 final size:2
Alignment explanation
Indices: 22233--22311 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
22223 ATCAATTAAT
22233 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
22275 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22312 TATGAAAAAG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27084 original size:21 final size:21
Alignment explanation
Indices: 27060--27105 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
27050 GTATGTAACA
27060 GTGAAGACAGTACTTTGGTAT
1 GTGAAGACAGTACTTTGGTAT
27081 GTGAAGACAGTACTTTGGTAT
1 GTGAAGACAGTACTTTGGTAT
27102 GTGA
1 GTGA
27106 GAAGTCTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.09, G:0.30, T:0.33
Consensus pattern (21 bp):
GTGAAGACAGTACTTTGGTAT
Found at i:30450 original size:2 final size:2
Alignment explanation
Indices: 30443--30470 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30433 GAAAAGTTAA
30443 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
30471 TATGATTTAT
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:33617 original size:32 final size:33
Alignment explanation
Indices: 33570--33635 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
33560 TTATTTCAAC
33570 TTTAAGAATAAAATAATTTATTT-GAATATTAT
1 TTTAAGAATAAAATAATTTATTTGGAATATTAT
**
33602 TTTAAGAATGGAATAATTTATTTGGAATATTAT
1 TTTAAGAATAAAATAATTTATTTGGAATATTAT
33635 T
1 T
33636 GGAATAGGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 21 0.68
33 10 0.32
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (33 bp):
TTTAAGAATAAAATAATTTATTTGGAATATTAT
Found at i:36107 original size:23 final size:23
Alignment explanation
Indices: 36079--36124 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
36069 TTTTGCTCGA
*
36079 CTCGTTAAGTTCGATGCTCGTTG
1 CTCGTTAAGCTCGATGCTCGTTG
36102 CTCGTTAAGCTCGATGCTCGTTG
1 CTCGTTAAGCTCGATGCTCGTTG
36125 TTCGCCTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.24, G:0.26, T:0.37
Consensus pattern (23 bp):
CTCGTTAAGCTCGATGCTCGTTG
Found at i:36113 original size:16 final size:16
Alignment explanation
Indices: 36094--36183 Score: 54
Period size: 16 Copynumber: 5.2 Consensus size: 16
36084 TAAGTTCGAT
36094 GCTCGTTGCTCGTTAA
1 GCTCGTTGCTCGTTAA
* **
36110 GCTCGATGCTCGTTGTTC
1 GCTCGTTGCTCG-T-TAA
* *
36128 GCCTTGTTACTCGTTAA
1 G-CTCGTTGCTCGTTAA
* **
36145 GCTCGATGCTCGTTGCTT
1 GCTCGTTGCTCGTT--AA
36163 GTCTCGTTGCTCGTTAA
1 G-CTCGTTGCTCGTTAA
36180 GCTC
1 GCTC
36184 ACTGAAATTT
Statistics
Matches: 52, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
16 24 0.46
17 4 0.08
18 4 0.08
19 20 0.38
ACGTcount: A:0.10, C:0.27, G:0.24, T:0.39
Consensus pattern (16 bp):
GCTCGTTGCTCGTTAA
Found at i:36147 original size:35 final size:35
Alignment explanation
Indices: 36095--36183 Score: 126
Period size: 35 Copynumber: 2.5 Consensus size: 35
36085 AAGTTCGATG
*
36095 CTCGTTGCTCGTTAAGCTCGATGCTCGTTG-TTCGC
1 CTCGTTACTCGTTAAGCTCGATGCTCGTTGCTT-GC
* *
36130 CTTGTTACTCGTTAAGCTCGATGCTCGTTGCTTGT
1 CTCGTTACTCGTTAAGCTCGATGCTCGTTGCTTGC
*
36165 CTCGTTGCTCGTTAAGCTC
1 CTCGTTACTCGTTAAGCTC
36184 ACTGAAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 46 0.96
36 2 0.04
ACGTcount: A:0.10, C:0.27, G:0.24, T:0.39
Consensus pattern (35 bp):
CTCGTTACTCGTTAAGCTCGATGCTCGTTGCTTGC
Found at i:43903 original size:21 final size:21
Alignment explanation
Indices: 43879--43918 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43869 ATATCTTTTA
*
43879 TATTAATTACATTTATATATC
1 TATTAATAACATTTATATATC
*
43900 TATTAATAACATTTGTATA
1 TATTAATAACATTTATATA
43919 GATTTATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (21 bp):
TATTAATAACATTTATATATC
Found at i:44674 original size:25 final size:28
Alignment explanation
Indices: 44636--44701 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 28
44626 TTGTTTTTTT
*
44636 ATTTTCTTCATTTTTTTAAAAAA-T-AAA
1 ATTTTC-TAATTTTTTTAAAAAATTCAAA
44663 ATTTT-TAA--TTTTTAAAAAATTCAAA
1 ATTTTCTAATTTTTTTAAAAAATTCAAA
*
44688 ATTTTCTTATTTTT
1 ATTTTCTAATTTTT
44702 CATAAAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
23 11 0.34
24 1 0.03
25 10 0.31
26 2 0.06
27 5 0.16
28 3 0.09
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTTCTAATTTTTTTAAAAAATTCAAA
Found at i:44677 original size:23 final size:26
Alignment explanation
Indices: 44648--44701 Score: 78
Period size: 23 Copynumber: 2.2 Consensus size: 26
44638 TTTCTTCATT
44648 TTTTTAAAAAA-T-AAAATTTT-TAA
1 TTTTTAAAAAATTCAAAATTTTCTAA
*
44671 TTTTTAAAAAATTCAAAATTTTCTTA
1 TTTTTAAAAAATTCAAAATTTTCTAA
44697 TTTTT
1 TTTTT
44702 CATAAAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 8 0.30
26 7 0.26
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTTAAAAAATTCAAAATTTTCTAA
Found at i:51400 original size:16 final size:16
Alignment explanation
Indices: 51379--51424 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 16
51369 TTTATCAAAT
51379 TATGTGTATGCATATA
1 TATGTGTATGCATATA
51395 TATGTGTGTATGCATATA
1 TA--TGTGTATGCATATA
*
51413 TATGTGTGTGCA
1 TATGTGTATGCA
51425 GTCATTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 11 0.41
18 16 0.59
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (16 bp):
TATGTGTATGCATATA
Found at i:51404 original size:18 final size:18
Alignment explanation
Indices: 51381--51421 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
51371 TATCAAATTA
51381 TGTGTATGCATATATATG
1 TGTGTATGCATATATATG
51399 TGTGTATGCATATATATG
1 TGTGTATGCATATATATG
51417 TGTGT
1 TGTGT
51422 GCAGTCATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.46
Consensus pattern (18 bp):
TGTGTATGCATATATATG
Found at i:58863 original size:37 final size:37
Alignment explanation
Indices: 58783--58863 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 37
58773 AATAAGTTAA
*
58783 AAAATATTTATATATTTTTTTAAAAAAAATTAAATTCAT
1 AAAA-ATTTATATATTTTTTT-AAAAAAATTAAAATCAT
*
58822 -AAAATTTATATAATTTTTTT-ACAAAATTAAAAAT-AT
1 AAAAATTTATAT-ATTTTTTTAAAAAAATT-AAAATCAT
58858 AAAAAT
1 AAAAAT
58864 GTCTAATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
36 9 0.24
37 17 0.46
38 11 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (37 bp):
AAAAATTTATATATTTTTTTAAAAAAATTAAAATCAT
Found at i:66469 original size:26 final size:26
Alignment explanation
Indices: 66431--66537 Score: 169
Period size: 26 Copynumber: 4.1 Consensus size: 26
66421 GATATCCTTG
*
66431 TTTCTACACTATCTTGTGAGTTCATC
1 TTTCTACCCTATCTTGTGAGTTCATC
*
66457 TTTCTACCTTATCTTGTGAGTTCATC
1 TTTCTACCCTATCTTGTGAGTTCATC
*
66483 TTTCTACCCTATCTTGTGAGTTTATC
1 TTTCTACCCTATCTTGTGAGTTCATC
* *
66509 TTTCTACCCTATCCTGTGAGTTTATC
1 TTTCTACCCTATCTTGTGAGTTCATC
66535 TTT
1 TTT
66538 TTAACAGGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.16, C:0.23, G:0.11, T:0.50
Consensus pattern (26 bp):
TTTCTACCCTATCTTGTGAGTTCATC
Found at i:75630 original size:39 final size:39
Alignment explanation
Indices: 75558--75650 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
75548 TCAATTTATA
* * *
75558 TCTAACATTCTAAATTCATGATTTGTCAAATTA-TTT-C
1 TCTAACATTCTAAATCCATAATTTCTCAAATTATTTTAC
*
75595 GTCCTAACATTCTAAATCC-TAAATTTCTCAGATTATTTTAC
1 -T-CTAACATTCTAAATCCAT-AATTTCTCAAATTATTTTAC
75636 TCTAACATTCTAAAT
1 TCTAACATTCTAAAT
75651 TATTCTTTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
38 2 0.04
39 40 0.85
40 4 0.09
41 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.43
Consensus pattern (39 bp):
TCTAACATTCTAAATCCATAATTTCTCAAATTATTTTAC
Found at i:75789 original size:2 final size:2
Alignment explanation
Indices: 75784--75813 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
75774 TTTGATTTTT
75784 TA 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 TA
75814 ATTTGAATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:85153 original size:25 final size:25
Alignment explanation
Indices: 85108--85155 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
85098 TCAGAAAAAT
*
85108 ATAAAAATATTTTTAATTATAAACA
1 ATAAAAATATTTATAATTATAAACA
*
85133 ATAAATAATATTTATCA-TATAAA
1 ATAAA-AATATTTATAATTATAAA
85156 TATTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
ATAAAAATATTTATAATTATAAACA
Found at i:92425 original size:20 final size:21
Alignment explanation
Indices: 92402--92480 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 21
92392 TTGGTGTAGA
92402 GGGAATCGATACCCCCATGA-
1 GGGAATCGATACCCCCATGAG
* * **
92422 GGGAACCGATTCCCCTTTGAAG
1 GGGAATCGATACCCCCATG-AG
* *
92444 GGGAATCGATTCCCCCCA-CAG
1 GGGAATCGA-TACCCCCATGAG
92465 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
92481 CTGTGGTTCT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 21 0.46
21 12 0.26
22 8 0.17
23 5 0.11
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAATCGATACCCCCATGAG
Found at i:92468 original size:21 final size:21
Alignment explanation
Indices: 92442--92481 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
92432 TCCCCTTTGA
*
92442 AGGGGAATCGATTCCCCCCAC
1 AGGGGAATCGATACCCCCCAC
92463 AGGGGAATCGATACCCCCC
1 AGGGGAATCGATACCCCCC
92482 TGTGGTTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
AGGGGAATCGATACCCCCCAC
Found at i:99419 original size:37 final size:36
Alignment explanation
Indices: 99347--99420 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
99337 GTTCGAAAAT
* *
99347 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
*
99383 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTGAAAATCATAAA
99420 A
1 A
99421 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 8 0.24
37 15 0.45
38 10 0.30
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Done.