Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004869.1 Hibiscus syriacus cultivar Beakdansim tig00010977_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: 69318
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:453 original size:18 final size:20
Alignment explanation
Indices: 426--468 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
416 TATCTTTTAT
426 TTATTCATTTCATT-CT-TA
1 TTATTCATTTCATTACTATA
*
444 TTATTTATTTCATTACTATA
1 TTATTCATTTCATTACTATA
464 TTATT
1 TTATT
469 ACCCTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.59
19 2 0.09
20 7 0.32
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTCATTTCATTACTATA
Found at i:8219 original size:72 final size:71
Alignment explanation
Indices: 8102--8237 Score: 175
Period size: 72 Copynumber: 1.9 Consensus size: 71
8092 TAAATTCATC
* * * ** *
8102 CATTCATGCACATTCATGCAAGAAGCCAAATAGTCATGTTCACACAAGG-GGGAAGAATTTCAGC
1 CATTCATGAACATTCATCCAAGAAGACAAATAAACAAGTTCACACAAGGTGGGAAGAA-TTCAGC
8166 AAGGATA
65 AAGGATA
* *
8173 CATTCATGAACATTCATCCATAGAAGACAAATAAACAAGTTTACACAAGGTGGGATGAATTCAGC
1 CATTCATGAACATTCATCCA-AGAAGACAAATAAACAAGTTCACACAAGGTGGGAAGAATTCAGC
8238 CAAATGATGT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
71 18 0.33
72 30 0.55
73 7 0.13
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (71 bp):
CATTCATGAACATTCATCCAAGAAGACAAATAAACAAGTTCACACAAGGTGGGAAGAATTCAGCA
AGGATA
Found at i:22968 original size:36 final size:36
Alignment explanation
Indices: 22927--23058 Score: 183
Period size: 36 Copynumber: 3.7 Consensus size: 36
22917 ATTTATAAGT
* * *
22927 TGGTGATAATATGGGCGTGATAATGGTGGTGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
** *
22963 TGGTGACGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
* *
22999 TGGTGATAATAAAGGTGTGATAATGGTGATGGACTA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
*
23035 TGGTGATGATATAGGCGTGATAAT
1 TGGTGATAATATAGGCGTGATAAT
23059 AAAGGTGGAA
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 82 1.00
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
Found at i:23074 original size:72 final size:72
Alignment explanation
Indices: 22927--23075 Score: 199
Period size: 72 Copynumber: 2.1 Consensus size: 72
22917 ATTTATAAGT
** * **
22927 TGGTGATAATATGGGCGTGATAATGGTGGTGGAATATGGTGACGATATAGGCGTGATAATGGAGA
1 TGGTGATAATAAAGGCGTGATAATGGTGATGGAATATGGTGACGATATAGGCGTGATAATAAAGA
**
22992 TGGACTA
66 TGGAAGA
* * * *
22999 TGGTGATAATAAAGGTGTGATAATGGTGATGGACTATGGTGATGATATAGGCGTGATAATAAAGG
1 TGGTGATAATAAAGGCGTGATAATGGTGATGGAATATGGTGACGATATAGGCGTGATAATAAAGA
23064 TGGAAGA
66 TGGAAGA
23071 TGGTG
1 TGGTG
23076 TTGGACAGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.31, C:0.04, G:0.37, T:0.28
Consensus pattern (72 bp):
TGGTGATAATAAAGGCGTGATAATGGTGATGGAATATGGTGACGATATAGGCGTGATAATAAAGA
TGGAAGA
Found at i:27610 original size:33 final size:33
Alignment explanation
Indices: 27568--27636 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
27558 GTTGATGAAT
*
27568 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
27601 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
27634 GAA
1 GAA
27637 CATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:27678 original size:36 final size:36
Alignment explanation
Indices: 27607--27719 Score: 167
Period size: 36 Copynumber: 3.2 Consensus size: 36
27597 AATGGAAGGA
* *
27607 TGATGTTATTGGCGTGAT-ATGGTGATGGAAC-ATGG
1 TGATGATATAGGCGTGATAATGGTGATGG-ACTATGG
27642 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
* *
27678 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
27714 TGATGA
1 TGATGA
27720 AAATAGTATC
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
35 18 0.25
36 54 0.75
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:32134 original size:33 final size:33
Alignment explanation
Indices: 32092--32160 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
32082 GTTGATGAAT
*
32092 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
32125 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
32158 GAA
1 GAA
32161 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:32165 original size:13 final size:12
Alignment explanation
Indices: 32146--32242 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
32136 TTATTGGCGT
32146 GATATGGTGATG
1 GATATGGTGATG
32158 GAATATGGTGAT-
1 G-ATATGGTGATG
*
32170 GATATAGG-CAT-
1 GATAT-GGTGATG
32181 GATAATGGTGATG
1 GAT-ATGGTGATG
32194 GACTATGGTGAT-
1 GA-TATGGTGATG
*
32206 GATATAGGCG-T-
1 GATAT-GGTGATG
*
32217 GATAATGGAGATG
1 GAT-ATGGTGATG
32230 GATTATGGTGATG
1 GA-TATGGTGATG
32243 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:32194 original size:36 final size:36
Alignment explanation
Indices: 32131--32243 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
32121 AATGGAAGGA
* *
32131 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
32166 TGATGATATAGGCATGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
32202 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
32238 TGATGA
1 TGATGA
32244 AAATAGTATC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 15 0.21
36 55 0.79
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:35012 original size:36 final size:36
Alignment explanation
Indices: 34961--35090 Score: 197
Period size: 36 Copynumber: 3.6 Consensus size: 36
34951 TTATAAGTTT
* * * *
34961 GTGATAATATGGGCGTGATAATGGTGGTGGAATATG
1 GTGATGATATAGGCGTGATAATGGTGATGGACTATG
* *
34997 GTGACGATATAGGCGTGATAATGGAGATGGACTATG
1 GTGATGATATAGGCGTGATAATGGTGATGGACTATG
*
35033 GTGATGATAAAGGCGTGATAATGGTGATGGACTATG
1 GTGATGATATAGGCGTGATAATGGTGATGGACTATG
35069 GTGATGATATAGGCGTGATAAT
1 GTGATGATATAGGCGTGATAAT
35091 AAAGGTGGAA
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 84 1.00
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.28
Consensus pattern (36 bp):
GTGATGATATAGGCGTGATAATGGTGATGGACTATG
Found at i:35106 original size:72 final size:72
Alignment explanation
Indices: 34972--35107 Score: 200
Period size: 72 Copynumber: 1.9 Consensus size: 72
34962 TGATAATATG
* ** **
34972 GGCGTGATAATGGTGGTGGAATATGGTGACGATATAGGCGTGATAATGGAGATGGACTATGGTGA
1 GGCGTGATAATGGTGATGGAATATGGTGACGATATAGGCGTGATAATAAAGATGGAAGATGGTGA
35037 TGATAAA
66 TGATAAA
* * *
35044 GGCGTGATAATGGTGATGGACTATGGTGATGATATAGGCGTGATAATAAAGGTGGAAGATGGTG
1 GGCGTGATAATGGTGATGGAATATGGTGACGATATAGGCGTGATAATAAAGATGGAAGATGGTG
35108 TTGGACAGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.30, C:0.05, G:0.38, T:0.26
Consensus pattern (72 bp):
GGCGTGATAATGGTGATGGAATATGGTGACGATATAGGCGTGATAATAAAGATGGAAGATGGTGA
TGATAAA
Found at i:37732 original size:24 final size:25
Alignment explanation
Indices: 37705--37754 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
37695 GTATTTGCAA
*
37705 TTTTGCTTC-ACTTTTTCTTTGCTT
1 TTTTGATTCTACTTTTTCTTTGCTT
* *
37729 TTTTGATTCTTCTTTTTCTTTTCTT
1 TTTTGATTCTACTTTTTCTTTGCTT
37754 T
1 T
37755 CTTTTGCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.04, C:0.18, G:0.06, T:0.72
Consensus pattern (25 bp):
TTTTGATTCTACTTTTTCTTTGCTT
Found at i:38208 original size:33 final size:33
Alignment explanation
Indices: 38166--38234 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
38156 GTTGATGAAT
*
38166 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
38199 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
38232 GAA
1 GAA
38235 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:38239 original size:13 final size:12
Alignment explanation
Indices: 38220--38280 Score: 65
Period size: 13 Copynumber: 5.0 Consensus size: 12
38210 TTATTGGCGT
38220 GATATGGTGATG
1 GATATGGTGATG
38232 GAATATGGTGAT-
1 G-ATATGGTGATG
38244 GATATAGGTG-T-
1 GATAT-GGTGATG
38255 GATAATGGTGATG
1 GAT-ATGGTGATG
38268 GACTATGGTGATG
1 GA-TATGGTGATG
38281 AAAATAGTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
11 12 0.28
12 9 0.21
13 21 0.49
14 1 0.02
ACGTcount: A:0.28, C:0.02, G:0.38, T:0.33
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:38667 original size:19 final size:20
Alignment explanation
Indices: 38620--38670 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
38610 GAAATCCCTT
**
38620 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
38640 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
38659 TGAAGATACATG
1 TGAAAATACATG
38671 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:40179 original size:23 final size:23
Alignment explanation
Indices: 40134--40179 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40124 TTATACCTAT
*
40134 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
40157 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
40180 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:43457 original size:11 final size:12
Alignment explanation
Indices: 43428--43462 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
43418 TTTGGTGATG
43428 GAAACAAGATAA
1 GAAACAAGATAA
*
43440 GAAACAAGATTA
1 GAAACAAGATAA
43452 -AAACAAGATAA
1 GAAACAAGATAA
43463 ATAAAAGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.66, C:0.09, G:0.14, T:0.11
Consensus pattern (12 bp):
GAAACAAGATAA
Found at i:56306 original size:11 final size:12
Alignment explanation
Indices: 56278--56310 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
56268 TTGGTGATGT
56278 AAACAAGATAAG
1 AAACAAGATAAG
*
56290 AAACAAGATTA-
1 AAACAAGATAAG
56301 AAACAAGATA
1 AAACAAGATA
56311 GATAAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.67, C:0.09, G:0.12, T:0.12
Consensus pattern (12 bp):
AAACAAGATAAG
Found at i:67610 original size:35 final size:35
Alignment explanation
Indices: 67557--67666 Score: 123
Period size: 35 Copynumber: 3.2 Consensus size: 35
67547 TAAGATACTA
** *
67557 CCTA-AACATCACTGTCTTCCATCACCATTTCATG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* *
67591 CCTATAACATCACCATCTTCCATTACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * * * *
67626 CCTATATCCTTACCATCTTCTATCATCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
67661 CCTATA
1 CCTATA
67667 TAACCACCAA
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
34 4 0.06
35 59 0.94
ACGTcount: A:0.26, C:0.35, G:0.05, T:0.34
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:67849 original size:16 final size:15
Alignment explanation
Indices: 67812--67850 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
67802 TCTTTGATAA
67812 CATTTCTTTCCATTT
1 CATTTCTTTCCATTT
*
67827 CAATTCTTTCCATTTT
1 CATTTCTTTCCA-TTT
67843 CATTTCTT
1 CATTTCTT
67851 AATTATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (15 bp):
CATTTCTTTCCATTT
Found at i:68353 original size:26 final size:26
Alignment explanation
Indices: 68317--68383 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
68307 ATCTTTTTCT
*
68317 TAACCTTTTCTATCCTACCCCTATCA
1 TAACCATTTCTATCCTACCCCTATCA
68343 TAACCATTTCTATCCTACCCCTATCA
1 TAACCATTTCTATCCTACCCCTATCA
68369 TAACCATTTCTATCC
1 TAACCATTTCTATCC
68384 CTAACCATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.25, C:0.37, G:0.00, T:0.37
Consensus pattern (26 bp):
TAACCATTTCTATCCTACCCCTATCA
Done.