Multiple sequence alignment - TraesCS6D01G071300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G071300 chr6D 100.000 3866 0 0 1 3866 36107118 36103253 0.000000e+00 7140.0
1 TraesCS6D01G071300 chr6D 88.945 1375 126 16 2149 3512 36073835 36072476 0.000000e+00 1674.0
2 TraesCS6D01G071300 chr6D 80.357 1736 250 50 924 2633 35667612 35665942 0.000000e+00 1232.0
3 TraesCS6D01G071300 chr6D 84.041 589 81 12 1049 1635 35717983 35717406 4.360000e-154 555.0
4 TraesCS6D01G071300 chr6D 82.183 623 94 15 2435 3056 35716006 35715400 1.590000e-143 520.0
5 TraesCS6D01G071300 chr6D 79.278 748 110 28 1699 2433 35641434 35640719 7.510000e-132 481.0
6 TraesCS6D01G071300 chr6D 78.996 757 117 26 1668 2413 35717403 35716678 2.700000e-131 479.0
7 TraesCS6D01G071300 chr6D 80.383 627 93 21 2475 3091 36083438 36082832 2.120000e-122 449.0
8 TraesCS6D01G071300 chr6D 83.376 391 51 13 1021 1407 36090455 36090075 2.210000e-92 350.0
9 TraesCS6D01G071300 chr6D 85.933 327 35 8 3187 3506 36082838 36082516 4.780000e-89 339.0
10 TraesCS6D01G071300 chr6D 86.139 303 33 8 1020 1319 36074171 36073875 6.230000e-83 318.0
11 TraesCS6D01G071300 chr6D 79.464 112 19 3 3083 3190 179322 179211 4.140000e-10 76.8
12 TraesCS6D01G071300 chr6D 97.222 36 1 0 2191 2226 36073769 36073734 1.160000e-05 62.1
13 TraesCS6D01G071300 chr6A 93.292 3056 125 23 1 3012 39879032 39876013 0.000000e+00 4434.0
14 TraesCS6D01G071300 chr6A 94.373 782 32 10 3082 3860 39875995 39875223 0.000000e+00 1190.0
15 TraesCS6D01G071300 chr6A 81.260 619 99 13 1021 1635 39670758 39670153 5.810000e-133 484.0
16 TraesCS6D01G071300 chr6A 80.707 622 102 13 1020 1635 39628970 39628361 5.850000e-128 468.0
17 TraesCS6D01G071300 chr6A 80.625 160 29 2 3243 3401 41578932 41578774 5.250000e-24 122.0
18 TraesCS6D01G071300 chr6A 81.395 86 12 4 3079 3161 53144347 53144431 2.490000e-07 67.6
19 TraesCS6D01G071300 chr6B 79.670 1997 299 54 1020 2982 75268452 75266529 0.000000e+00 1339.0
20 TraesCS6D01G071300 chr6B 80.559 1538 227 48 1020 2535 75514582 75513095 0.000000e+00 1118.0
21 TraesCS6D01G071300 chr6B 81.176 1275 200 21 1019 2288 75510363 75509124 0.000000e+00 989.0
22 TraesCS6D01G071300 chr6B 83.411 645 91 12 996 1635 75423508 75422875 5.570000e-163 584.0
23 TraesCS6D01G071300 chr6B 81.350 622 92 17 1020 1635 75526308 75525705 5.810000e-133 484.0
24 TraesCS6D01G071300 chr6B 78.117 754 129 20 1668 2413 75422872 75422147 2.740000e-121 446.0
25 TraesCS6D01G071300 chr6B 79.773 618 96 20 2439 3056 75421459 75420871 4.620000e-114 422.0
26 TraesCS6D01G071300 chr6B 79.735 528 80 15 2504 3029 75524587 75524085 1.320000e-94 357.0
27 TraesCS6D01G071300 chr6B 77.561 615 97 29 1035 1642 75990605 75990025 2.230000e-87 333.0
28 TraesCS6D01G071300 chr6B 80.233 172 24 9 2185 2350 51560351 51560518 1.890000e-23 121.0
29 TraesCS6D01G071300 chr6B 90.667 75 7 0 3579 3653 20106380 20106306 2.460000e-17 100.0
30 TraesCS6D01G071300 chr1D 82.683 589 81 14 1022 1609 37880025 37880593 1.600000e-138 503.0
31 TraesCS6D01G071300 chr1D 84.962 266 34 1 1700 1965 37880648 37880907 8.240000e-67 265.0
32 TraesCS6D01G071300 chr1D 86.301 146 10 10 3186 3327 37883662 37883801 2.410000e-32 150.0
33 TraesCS6D01G071300 chr1D 90.789 76 7 0 3579 3654 66541224 66541299 6.830000e-18 102.0
34 TraesCS6D01G071300 chr1D 81.250 96 13 5 3106 3197 100459072 100458978 5.360000e-09 73.1
35 TraesCS6D01G071300 chr1B 81.188 606 98 11 2434 3029 57617228 57617827 1.260000e-129 473.0
36 TraesCS6D01G071300 chr1B 83.388 307 45 1 1668 1974 57615789 57616089 2.940000e-71 279.0
37 TraesCS6D01G071300 chr1B 84.746 118 11 7 3085 3198 301273394 301273508 1.140000e-20 111.0
38 TraesCS6D01G071300 chr1B 84.956 113 12 4 3082 3190 469612821 469612932 4.080000e-20 110.0
39 TraesCS6D01G071300 chr1B 90.667 75 7 0 3579 3653 145313571 145313645 2.460000e-17 100.0
40 TraesCS6D01G071300 chr1B 90.667 75 7 0 3579 3653 318701914 318701988 2.460000e-17 100.0
41 TraesCS6D01G071300 chr1A 85.714 315 37 6 1000 1310 36785354 36785664 3.720000e-85 326.0
42 TraesCS6D01G071300 chr1A 85.547 256 29 3 1700 1953 36789469 36789718 1.070000e-65 261.0
43 TraesCS6D01G071300 chr1A 83.636 220 35 1 2762 2981 36791302 36791520 5.060000e-49 206.0
44 TraesCS6D01G071300 chr1A 80.297 269 40 8 1351 1609 36789149 36789414 1.420000e-44 191.0
45 TraesCS6D01G071300 chr1A 90.789 76 7 0 3579 3654 549569326 549569401 6.830000e-18 102.0
46 TraesCS6D01G071300 chr1A 90.667 75 7 0 3579 3653 534582504 534582430 2.460000e-17 100.0
47 TraesCS6D01G071300 chr2D 85.345 116 14 3 3086 3198 392161776 392161661 2.440000e-22 117.0
48 TraesCS6D01G071300 chr2D 93.750 48 3 0 347 394 551836121 551836074 5.360000e-09 73.1
49 TraesCS6D01G071300 chr5A 89.333 75 8 0 3579 3653 559911341 559911267 1.140000e-15 95.3
50 TraesCS6D01G071300 chr4B 82.569 109 17 2 3547 3653 83161573 83161681 1.140000e-15 95.3
51 TraesCS6D01G071300 chr7B 89.394 66 5 2 3098 3161 719651888 719651953 8.900000e-12 82.4
52 TraesCS6D01G071300 chr7D 94.000 50 3 0 347 396 104964100 104964051 4.140000e-10 76.8
53 TraesCS6D01G071300 chr3D 95.349 43 2 0 352 394 427302584 427302626 6.930000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G071300 chr6D 36103253 36107118 3865 True 7140.0 7140 100.000000 1 3866 1 chr6D.!!$R5 3865
1 TraesCS6D01G071300 chr6D 35665942 35667612 1670 True 1232.0 1232 80.357000 924 2633 1 chr6D.!!$R3 1709
2 TraesCS6D01G071300 chr6D 36072476 36074171 1695 True 684.7 1674 90.768667 1020 3512 3 chr6D.!!$R7 2492
3 TraesCS6D01G071300 chr6D 35715400 35717983 2583 True 518.0 555 81.740000 1049 3056 3 chr6D.!!$R6 2007
4 TraesCS6D01G071300 chr6D 35640719 35641434 715 True 481.0 481 79.278000 1699 2433 1 chr6D.!!$R2 734
5 TraesCS6D01G071300 chr6D 36082516 36083438 922 True 394.0 449 83.158000 2475 3506 2 chr6D.!!$R8 1031
6 TraesCS6D01G071300 chr6A 39875223 39879032 3809 True 2812.0 4434 93.832500 1 3860 2 chr6A.!!$R4 3859
7 TraesCS6D01G071300 chr6A 39670153 39670758 605 True 484.0 484 81.260000 1021 1635 1 chr6A.!!$R2 614
8 TraesCS6D01G071300 chr6A 39628361 39628970 609 True 468.0 468 80.707000 1020 1635 1 chr6A.!!$R1 615
9 TraesCS6D01G071300 chr6B 75266529 75268452 1923 True 1339.0 1339 79.670000 1020 2982 1 chr6B.!!$R2 1962
10 TraesCS6D01G071300 chr6B 75509124 75514582 5458 True 1053.5 1118 80.867500 1019 2535 2 chr6B.!!$R5 1516
11 TraesCS6D01G071300 chr6B 75420871 75423508 2637 True 484.0 584 80.433667 996 3056 3 chr6B.!!$R4 2060
12 TraesCS6D01G071300 chr6B 75524085 75526308 2223 True 420.5 484 80.542500 1020 3029 2 chr6B.!!$R6 2009
13 TraesCS6D01G071300 chr6B 75990025 75990605 580 True 333.0 333 77.561000 1035 1642 1 chr6B.!!$R3 607
14 TraesCS6D01G071300 chr1D 37880025 37883801 3776 False 306.0 503 84.648667 1022 3327 3 chr1D.!!$F2 2305
15 TraesCS6D01G071300 chr1B 57615789 57617827 2038 False 376.0 473 82.288000 1668 3029 2 chr1B.!!$F5 1361
16 TraesCS6D01G071300 chr1A 36785354 36791520 6166 False 246.0 326 83.798500 1000 2981 4 chr1A.!!$F2 1981

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
175 176 0.034767 CACATCTCACCCATGCCTGT 60.035 55.0 0.00 0.00 0.00 4.00 F
288 289 0.318784 GGTACTCCGATGCGACATCC 60.319 60.0 12.27 0.75 0.00 3.51 F
1335 1388 0.108804 ACGACCGCATCTGGTACTTG 60.109 55.0 0.00 0.00 44.01 3.16 F
1422 4950 0.666577 GGGACACCTTCAACGTCGAG 60.667 60.0 0.00 0.00 0.00 4.04 F
2117 5812 0.908198 ATCCAGCTTGAGTCCCTGAC 59.092 55.0 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1331 1384 0.259938 GGATCCCAAGGGCATCAAGT 59.740 55.0 0.00 0.00 34.68 3.16 R
1657 5194 0.610785 TTGGTGGGAAATTCGCCCTC 60.611 55.0 15.24 12.05 46.19 4.30 R
2171 5872 0.755686 ACTACCTCCTGCAGCATAGC 59.244 55.0 8.66 0.00 0.00 2.97 R
2381 6135 0.888736 TCACAGGAAATGCCACCACG 60.889 55.0 0.00 0.00 40.02 4.94 R
3565 11463 0.040425 CGGCGGGTCTTTTTGAACTG 60.040 55.0 0.00 0.00 41.62 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.737793 GGATGATTTTCCACTCGCGTT 59.262 47.619 5.77 0.00 35.72 4.84
143 144 2.187946 CGCAAGCTCGATCCCCTT 59.812 61.111 0.00 0.00 0.00 3.95
144 145 1.450312 CGCAAGCTCGATCCCCTTT 60.450 57.895 0.00 0.00 0.00 3.11
145 146 1.026718 CGCAAGCTCGATCCCCTTTT 61.027 55.000 0.00 0.00 0.00 2.27
146 147 0.735471 GCAAGCTCGATCCCCTTTTC 59.265 55.000 0.00 0.00 0.00 2.29
147 148 1.680249 GCAAGCTCGATCCCCTTTTCT 60.680 52.381 0.00 0.00 0.00 2.52
148 149 2.284190 CAAGCTCGATCCCCTTTTCTC 58.716 52.381 0.00 0.00 0.00 2.87
149 150 0.461961 AGCTCGATCCCCTTTTCTCG 59.538 55.000 0.00 0.00 0.00 4.04
150 151 0.175989 GCTCGATCCCCTTTTCTCGT 59.824 55.000 0.00 0.00 33.10 4.18
151 152 1.803252 GCTCGATCCCCTTTTCTCGTC 60.803 57.143 0.00 0.00 33.10 4.20
154 155 1.205055 GATCCCCTTTTCTCGTCCCT 58.795 55.000 0.00 0.00 0.00 4.20
164 165 0.611896 TCTCGTCCCTGCACATCTCA 60.612 55.000 0.00 0.00 0.00 3.27
175 176 0.034767 CACATCTCACCCATGCCTGT 60.035 55.000 0.00 0.00 0.00 4.00
182 183 0.538057 CACCCATGCCTGTTGTGTCT 60.538 55.000 0.00 0.00 0.00 3.41
183 184 1.064003 ACCCATGCCTGTTGTGTCTA 58.936 50.000 0.00 0.00 0.00 2.59
190 191 1.453155 CCTGTTGTGTCTACCATGGC 58.547 55.000 13.04 0.00 0.00 4.40
197 198 0.620030 TGTCTACCATGGCTGCACAT 59.380 50.000 13.04 0.00 0.00 3.21
256 257 4.993945 GCGTGCTGCGACACAACG 62.994 66.667 9.30 3.90 44.77 4.10
257 258 4.354212 CGTGCTGCGACACAACGG 62.354 66.667 9.30 0.00 44.77 4.44
265 266 1.828331 GCGACACAACGGTCCTTGAC 61.828 60.000 7.74 0.00 34.24 3.18
272 273 1.067425 CAACGGTCCTTGACATCGGTA 60.067 52.381 0.00 0.00 33.68 4.02
288 289 0.318784 GGTACTCCGATGCGACATCC 60.319 60.000 12.27 0.75 0.00 3.51
312 313 1.717937 GGCTGCTATGCAACACTCG 59.282 57.895 0.00 0.00 38.41 4.18
317 318 0.371645 GCTATGCAACACTCGTGAGC 59.628 55.000 3.74 7.96 36.35 4.26
337 338 3.689002 TTGCACTGCCACACGACCA 62.689 57.895 0.00 0.00 0.00 4.02
517 518 2.782222 TACTGCGGCCACGGATCTC 61.782 63.158 6.59 0.00 40.49 2.75
527 528 4.812476 CGGATCTCGTTGGCGGCA 62.812 66.667 7.97 7.97 38.89 5.69
543 544 2.398429 CAGAGCTGCGATGCAACG 59.602 61.111 12.54 12.54 38.41 4.10
556 557 1.234615 TGCAACGCCTAAGGTCTTGC 61.235 55.000 7.94 7.94 38.16 4.01
559 560 0.396811 AACGCCTAAGGTCTTGCTGT 59.603 50.000 0.00 0.00 0.00 4.40
571 572 2.994387 CTTGCTGTGTGGCGGAGTGA 62.994 60.000 0.00 0.00 34.52 3.41
595 596 0.978667 TACAAGCTGGGGCGGTGATA 60.979 55.000 0.00 0.00 44.37 2.15
600 601 1.172812 GCTGGGGCGGTGATATTTCC 61.173 60.000 0.00 0.00 0.00 3.13
602 603 0.626382 TGGGGCGGTGATATTTCCAA 59.374 50.000 0.00 0.00 0.00 3.53
668 669 3.594134 AGAACAAAGCAAGAGGAGATCG 58.406 45.455 0.00 0.00 0.00 3.69
705 706 3.743521 TGACTCATCCAACAACCAAGAG 58.256 45.455 0.00 0.00 0.00 2.85
715 716 4.322049 CCAACAACCAAGAGAGACGTATCT 60.322 45.833 13.49 13.49 38.15 1.98
729 730 2.873133 GTATCTGACGGTTCCTGGAG 57.127 55.000 0.00 0.00 0.00 3.86
735 753 1.974957 TGACGGTTCCTGGAGAAATCA 59.025 47.619 0.00 0.00 35.85 2.57
790 808 7.440523 AAAGGACACTATTTGTTAGCTTCAG 57.559 36.000 0.00 0.00 39.17 3.02
909 927 1.921049 TCTCTCCCGAAGTAGGAAGGA 59.079 52.381 0.00 0.00 31.49 3.36
913 931 4.875389 TCTCCCGAAGTAGGAAGGATTTA 58.125 43.478 0.00 0.00 31.49 1.40
988 1021 3.365265 GTGGGTTGCCGCTTCCAG 61.365 66.667 6.71 0.00 0.00 3.86
1331 1384 1.985447 GACGACGACCGCATCTGGTA 61.985 60.000 0.00 0.00 44.01 3.25
1335 1388 0.108804 ACGACCGCATCTGGTACTTG 60.109 55.000 0.00 0.00 44.01 3.16
1408 4936 1.770110 AAGCTCCTGGTGTGGGACA 60.770 57.895 0.00 0.00 0.00 4.02
1422 4950 0.666577 GGGACACCTTCAACGTCGAG 60.667 60.000 0.00 0.00 0.00 4.04
1510 5047 2.046314 CCGCCGGAGACAACCAAT 60.046 61.111 5.05 0.00 0.00 3.16
1653 5190 5.364157 ACCCAAGGCTTCTAGTTCTACTATG 59.636 44.000 0.00 0.00 29.08 2.23
1654 5191 5.221541 CCCAAGGCTTCTAGTTCTACTATGG 60.222 48.000 0.00 0.00 29.08 2.74
1655 5192 5.221541 CCAAGGCTTCTAGTTCTACTATGGG 60.222 48.000 0.00 0.00 29.08 4.00
1656 5193 3.898741 AGGCTTCTAGTTCTACTATGGGC 59.101 47.826 0.00 0.00 29.08 5.36
1657 5194 3.305471 GGCTTCTAGTTCTACTATGGGCG 60.305 52.174 0.00 0.00 29.08 6.13
1658 5195 3.568853 GCTTCTAGTTCTACTATGGGCGA 59.431 47.826 0.00 0.00 29.08 5.54
1822 5359 1.153168 GCTGTGATACCGGTGCCAT 60.153 57.895 19.93 1.66 0.00 4.40
2116 5811 1.198713 GATCCAGCTTGAGTCCCTGA 58.801 55.000 0.00 0.00 0.00 3.86
2117 5812 0.908198 ATCCAGCTTGAGTCCCTGAC 59.092 55.000 0.00 0.00 0.00 3.51
2171 5872 4.094294 TCGCTATTTTCCATTCGAAAGTGG 59.906 41.667 10.95 10.95 41.47 4.00
2381 6135 2.412847 CGTCCTCTTTTCGGATGTTTGC 60.413 50.000 0.00 0.00 33.75 3.68
2549 10342 2.270352 TTGAGTGTGCGGGATTCTTT 57.730 45.000 0.00 0.00 0.00 2.52
3036 10923 4.892934 GGTATCTCTATGGCTAGGGATCTG 59.107 50.000 8.90 0.00 40.54 2.90
3044 10931 2.292521 TGGCTAGGGATCTGTGAAGTCT 60.293 50.000 0.00 0.00 0.00 3.24
3052 10939 3.256879 GGATCTGTGAAGTCTGAGTGTGA 59.743 47.826 0.00 0.00 0.00 3.58
3053 10940 4.081752 GGATCTGTGAAGTCTGAGTGTGAT 60.082 45.833 0.00 0.00 0.00 3.06
3054 10941 4.944619 TCTGTGAAGTCTGAGTGTGATT 57.055 40.909 0.00 0.00 0.00 2.57
3055 10942 5.282055 TCTGTGAAGTCTGAGTGTGATTT 57.718 39.130 0.00 0.00 0.00 2.17
3058 10945 4.811024 TGTGAAGTCTGAGTGTGATTTGTC 59.189 41.667 0.00 0.00 0.00 3.18
3133 11020 3.881089 TCGCTCAAACGGATGTATCTAGA 59.119 43.478 0.00 0.00 0.00 2.43
3134 11021 3.975670 CGCTCAAACGGATGTATCTAGAC 59.024 47.826 0.00 0.00 0.00 2.59
3135 11022 3.975670 GCTCAAACGGATGTATCTAGACG 59.024 47.826 0.00 0.00 0.00 4.18
3137 11024 5.571784 TCAAACGGATGTATCTAGACGTT 57.428 39.130 9.89 9.89 45.05 3.99
3138 11025 5.337554 TCAAACGGATGTATCTAGACGTTG 58.662 41.667 14.81 10.34 42.75 4.10
3321 11214 3.057315 AGTGCTCGCTTGCAATTATTGTT 60.057 39.130 0.00 0.00 45.12 2.83
3391 11284 5.703130 GCCTTTCTTTGTCACTCTAACTCAT 59.297 40.000 0.00 0.00 0.00 2.90
3456 11353 3.795623 TCTAGAGTAATGGACCGTTGC 57.204 47.619 9.34 7.83 0.00 4.17
3476 11373 2.159099 GCATGACCGAAGAGTCCACATA 60.159 50.000 0.00 0.00 35.83 2.29
3565 11463 4.432712 AGTGCCAAAAACATCAAAGTGTC 58.567 39.130 0.00 0.00 0.00 3.67
3584 11484 0.040425 CAGTTCAAAAAGACCCGCCG 60.040 55.000 0.00 0.00 0.00 6.46
3615 11515 1.153958 CGACGGTAGTTTCGGGGAC 60.154 63.158 0.00 0.00 0.00 4.46
3622 11522 2.174360 GTAGTTTCGGGGACTACACCT 58.826 52.381 14.69 0.00 45.52 4.00
3639 11539 0.179100 CCTAGTGGGTGCACTCATCG 60.179 60.000 24.85 13.78 36.68 3.84
3648 12404 2.436646 CACTCATCGTGCCCCCAC 60.437 66.667 0.00 0.00 36.72 4.61
3683 12439 2.655952 AAAAACCGTTGGCACTCGCG 62.656 55.000 0.00 0.00 39.92 5.87
3751 12507 0.036388 GTCTTTGACATCGCCCTCCA 60.036 55.000 0.00 0.00 32.09 3.86
3772 12528 3.179265 CGCGCACGAGTAGTTGGG 61.179 66.667 8.75 0.00 43.93 4.12
3860 12616 2.602257 GCAGGTTGTTGCCTTTTCTT 57.398 45.000 0.00 0.00 38.13 2.52
3861 12617 2.905075 GCAGGTTGTTGCCTTTTCTTT 58.095 42.857 0.00 0.00 38.13 2.52
3862 12618 3.270027 GCAGGTTGTTGCCTTTTCTTTT 58.730 40.909 0.00 0.00 38.13 2.27
3863 12619 3.309682 GCAGGTTGTTGCCTTTTCTTTTC 59.690 43.478 0.00 0.00 38.13 2.29
3864 12620 4.758688 CAGGTTGTTGCCTTTTCTTTTCT 58.241 39.130 0.00 0.00 36.58 2.52
3865 12621 5.681179 GCAGGTTGTTGCCTTTTCTTTTCTA 60.681 40.000 0.00 0.00 38.13 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.209898 CGTCCGTAGCACGTGGTTA 59.790 57.895 26.96 9.09 36.66 2.85
92 93 1.132500 GATAAGGCTAGCAGGTGGGT 58.868 55.000 18.24 0.00 0.00 4.51
136 137 0.912486 CAGGGACGAGAAAAGGGGAT 59.088 55.000 0.00 0.00 0.00 3.85
137 138 1.838073 GCAGGGACGAGAAAAGGGGA 61.838 60.000 0.00 0.00 0.00 4.81
138 139 1.377333 GCAGGGACGAGAAAAGGGG 60.377 63.158 0.00 0.00 0.00 4.79
139 140 0.955919 GTGCAGGGACGAGAAAAGGG 60.956 60.000 0.00 0.00 0.00 3.95
140 141 0.250295 TGTGCAGGGACGAGAAAAGG 60.250 55.000 0.00 0.00 0.00 3.11
141 142 1.734465 GATGTGCAGGGACGAGAAAAG 59.266 52.381 0.00 0.00 0.00 2.27
142 143 1.347707 AGATGTGCAGGGACGAGAAAA 59.652 47.619 0.00 0.00 0.00 2.29
143 144 0.976641 AGATGTGCAGGGACGAGAAA 59.023 50.000 0.00 0.00 0.00 2.52
144 145 0.532573 GAGATGTGCAGGGACGAGAA 59.467 55.000 0.00 0.00 0.00 2.87
145 146 0.611896 TGAGATGTGCAGGGACGAGA 60.612 55.000 0.00 0.00 0.00 4.04
146 147 0.459237 GTGAGATGTGCAGGGACGAG 60.459 60.000 0.00 0.00 0.00 4.18
147 148 1.591703 GTGAGATGTGCAGGGACGA 59.408 57.895 0.00 0.00 0.00 4.20
148 149 1.448540 GGTGAGATGTGCAGGGACG 60.449 63.158 0.00 0.00 0.00 4.79
149 150 1.078143 GGGTGAGATGTGCAGGGAC 60.078 63.158 0.00 0.00 0.00 4.46
150 151 0.915872 ATGGGTGAGATGTGCAGGGA 60.916 55.000 0.00 0.00 0.00 4.20
151 152 0.750546 CATGGGTGAGATGTGCAGGG 60.751 60.000 0.00 0.00 0.00 4.45
154 155 1.378911 GGCATGGGTGAGATGTGCA 60.379 57.895 0.00 0.00 37.53 4.57
164 165 1.064003 TAGACACAACAGGCATGGGT 58.936 50.000 2.31 0.00 37.06 4.51
175 176 0.399833 TGCAGCCATGGTAGACACAA 59.600 50.000 14.67 0.00 0.00 3.33
182 183 3.923013 GCATGTGCAGCCATGGTA 58.077 55.556 14.67 0.00 42.01 3.25
183 184 2.036731 AGCATGTGCAGCCATGGT 59.963 55.556 14.67 17.75 45.88 3.55
190 191 0.251354 AGTAGGTGGAGCATGTGCAG 59.749 55.000 7.83 0.00 45.16 4.41
256 257 1.136500 GGAGTACCGATGTCAAGGACC 59.864 57.143 4.89 0.00 0.00 4.46
257 258 2.580966 GGAGTACCGATGTCAAGGAC 57.419 55.000 4.89 0.00 0.00 3.85
272 273 2.797278 GGGGATGTCGCATCGGAGT 61.797 63.158 11.83 0.00 0.00 3.85
286 287 3.536917 CATAGCAGCCGTCGGGGA 61.537 66.667 14.38 0.00 38.47 4.81
288 289 4.529219 TGCATAGCAGCCGTCGGG 62.529 66.667 14.38 0.00 33.32 5.14
312 313 3.279116 TGGCAGTGCAACGCTCAC 61.279 61.111 18.61 0.00 45.86 3.51
317 318 3.268603 TCGTGTGGCAGTGCAACG 61.269 61.111 23.40 23.40 45.86 4.10
337 338 2.993264 GCACCAGCAGCCACCAAT 60.993 61.111 0.00 0.00 41.58 3.16
380 381 0.460109 ACATCGCGAAGTGCTGCATA 60.460 50.000 17.16 0.00 37.71 3.14
396 397 3.744719 CCTGCAGCAGCGCAACAT 61.745 61.111 17.81 0.00 46.23 2.71
418 419 1.756375 GCTACATTGCAGCTCCGTCG 61.756 60.000 1.43 0.00 36.07 5.12
479 480 2.676121 TTGGGGGTTGCATCGCAG 60.676 61.111 13.17 0.00 40.61 5.18
543 544 1.160137 CACACAGCAAGACCTTAGGC 58.840 55.000 0.00 0.00 0.00 3.93
546 547 0.602638 CGCCACACAGCAAGACCTTA 60.603 55.000 0.00 0.00 0.00 2.69
556 557 1.956170 GTGTCACTCCGCCACACAG 60.956 63.158 0.00 0.00 40.22 3.66
559 560 1.532078 TAGGTGTCACTCCGCCACA 60.532 57.895 2.35 0.00 37.47 4.17
571 572 2.757077 GCCCCAGCTTGTAGGTGT 59.243 61.111 5.31 0.00 41.84 4.16
595 596 0.442310 CATGCGTCGTCGTTGGAAAT 59.558 50.000 3.66 0.00 39.49 2.17
600 601 1.121850 CAATGCATGCGTCGTCGTTG 61.122 55.000 13.95 2.52 39.49 4.10
602 603 2.778026 CAATGCATGCGTCGTCGT 59.222 55.556 13.95 0.00 39.49 4.34
645 646 3.409026 TCTCCTCTTGCTTTGTTCTCC 57.591 47.619 0.00 0.00 0.00 3.71
668 669 1.377202 TCAACAAGATGCCGCTCCC 60.377 57.895 0.00 0.00 0.00 4.30
715 716 1.974957 TGATTTCTCCAGGAACCGTCA 59.025 47.619 0.00 0.00 33.13 4.35
724 725 1.094073 CAGCCGGCTGATTTCTCCAG 61.094 60.000 46.72 19.48 46.30 3.86
735 753 2.107141 GCTACGAATCAGCCGGCT 59.893 61.111 27.08 27.08 32.68 5.52
769 787 6.398918 TCTCTGAAGCTAACAAATAGTGTCC 58.601 40.000 0.00 0.00 40.60 4.02
773 791 7.934120 ACTGTTTCTCTGAAGCTAACAAATAGT 59.066 33.333 0.00 0.00 33.87 2.12
774 792 8.316640 ACTGTTTCTCTGAAGCTAACAAATAG 57.683 34.615 0.00 0.00 31.07 1.73
776 794 7.573968 AACTGTTTCTCTGAAGCTAACAAAT 57.426 32.000 0.00 0.00 31.07 2.32
790 808 6.659776 ACGCAGAATTTTCTAACTGTTTCTC 58.340 36.000 0.00 0.00 35.34 2.87
829 847 3.985019 ACACGGTCTCTCTCTCTCTAA 57.015 47.619 0.00 0.00 0.00 2.10
831 849 4.652421 AGTATACACGGTCTCTCTCTCTCT 59.348 45.833 5.50 0.00 0.00 3.10
832 850 4.748102 CAGTATACACGGTCTCTCTCTCTC 59.252 50.000 5.50 0.00 0.00 3.20
833 851 4.162698 ACAGTATACACGGTCTCTCTCTCT 59.837 45.833 5.50 0.00 0.00 3.10
845 863 6.814644 TCCCTCAAATACAAACAGTATACACG 59.185 38.462 5.50 0.00 42.56 4.49
847 865 7.913789 ACTCCCTCAAATACAAACAGTATACA 58.086 34.615 5.50 0.00 42.56 2.29
909 927 1.628340 GCCCAAAGCCCAAAGGTAAAT 59.372 47.619 0.00 0.00 34.35 1.40
913 931 1.074547 AAGCCCAAAGCCCAAAGGT 60.075 52.632 0.00 0.00 45.47 3.50
988 1021 1.271054 ACAGCTCATGTGGGAAGTGTC 60.271 52.381 0.00 0.00 41.91 3.67
1331 1384 0.259938 GGATCCCAAGGGCATCAAGT 59.740 55.000 0.00 0.00 34.68 3.16
1335 1388 2.113986 CGGGATCCCAAGGGCATC 59.886 66.667 30.42 4.84 35.37 3.91
1408 4936 1.664965 GCTGCTCGACGTTGAAGGT 60.665 57.895 6.99 0.00 0.00 3.50
1505 5042 2.632537 AGACCACCTGGAAGTATTGGT 58.367 47.619 0.00 1.72 40.99 3.67
1510 5047 2.112279 ACCAAGACCACCTGGAAGTA 57.888 50.000 0.00 0.00 38.94 2.24
1653 5190 3.209812 GGAAATTCGCCCTCGCCC 61.210 66.667 0.00 0.00 35.26 6.13
1654 5191 3.209812 GGGAAATTCGCCCTCGCC 61.210 66.667 8.69 0.00 42.56 5.54
1655 5192 2.437716 TGGGAAATTCGCCCTCGC 60.438 61.111 15.24 1.83 46.19 5.03
1656 5193 2.112815 GGTGGGAAATTCGCCCTCG 61.113 63.158 15.24 0.00 46.19 4.63
1657 5194 0.610785 TTGGTGGGAAATTCGCCCTC 60.611 55.000 15.24 12.05 46.19 4.30
1658 5195 0.611896 CTTGGTGGGAAATTCGCCCT 60.612 55.000 15.24 0.00 46.19 5.19
2034 5729 6.368779 TTGTACTCAGCAAACCCTAGTATT 57.631 37.500 0.00 0.00 0.00 1.89
2116 5811 5.165676 GGTTTTGGAAACTTTCTTGAACGT 58.834 37.500 1.57 0.00 0.00 3.99
2117 5812 4.565166 GGGTTTTGGAAACTTTCTTGAACG 59.435 41.667 1.57 0.00 0.00 3.95
2171 5872 0.755686 ACTACCTCCTGCAGCATAGC 59.244 55.000 8.66 0.00 0.00 2.97
2381 6135 0.888736 TCACAGGAAATGCCACCACG 60.889 55.000 0.00 0.00 40.02 4.94
2515 8629 5.390991 GCACACTCAAACTATTAGCTGAACC 60.391 44.000 0.00 0.00 0.00 3.62
2642 10488 2.296190 GGAAAACAGCTCGGGTTTGATT 59.704 45.455 1.77 0.00 38.40 2.57
2689 10535 2.744202 GGGCGCATCGATGAGATATTTT 59.256 45.455 29.98 0.00 37.52 1.82
2874 10759 7.631007 ACATCACAATAGCATATCCATCTGAT 58.369 34.615 0.00 0.00 37.49 2.90
3036 10923 4.811024 TGACAAATCACACTCAGACTTCAC 59.189 41.667 0.00 0.00 0.00 3.18
3044 10931 7.509141 ACATACAAATGACAAATCACACTCA 57.491 32.000 0.00 0.00 37.79 3.41
3052 10939 5.779771 AGGGGACAACATACAAATGACAAAT 59.220 36.000 0.00 0.00 36.54 2.32
3053 10940 5.144100 AGGGGACAACATACAAATGACAAA 58.856 37.500 0.00 0.00 36.54 2.83
3054 10941 4.735369 AGGGGACAACATACAAATGACAA 58.265 39.130 0.00 0.00 36.54 3.18
3055 10942 4.042809 AGAGGGGACAACATACAAATGACA 59.957 41.667 0.00 0.00 36.54 3.58
3058 10945 5.354234 GTGTAGAGGGGACAACATACAAATG 59.646 44.000 0.00 0.00 39.17 2.32
3134 11021 3.002042 ACGGATGTATCTAGACGTCAACG 59.998 47.826 19.50 5.37 46.33 4.10
3135 11022 4.548991 ACGGATGTATCTAGACGTCAAC 57.451 45.455 19.50 8.05 37.13 3.18
3137 11024 4.637091 TCAAACGGATGTATCTAGACGTCA 59.363 41.667 19.50 2.84 37.13 4.35
3138 11025 5.165911 TCAAACGGATGTATCTAGACGTC 57.834 43.478 7.70 7.70 35.04 4.34
3321 11214 5.968676 ACCACCTACAAGGCTAATATTGA 57.031 39.130 0.00 0.00 39.63 2.57
3456 11353 2.680312 ATGTGGACTCTTCGGTCATG 57.320 50.000 0.00 0.00 37.91 3.07
3476 11373 8.608185 AATGGTATTGGATAAAACCTTGATGT 57.392 30.769 0.00 0.00 32.99 3.06
3565 11463 0.040425 CGGCGGGTCTTTTTGAACTG 60.040 55.000 0.00 0.00 41.62 3.16
3639 11539 4.035102 GTCCTCCTGTGGGGGCAC 62.035 72.222 0.00 0.00 35.33 5.01
3683 12439 0.680921 TAGCATTTGTGCTCTGGGGC 60.681 55.000 6.15 0.00 45.00 5.80
3704 12460 0.745468 GTCGGCGGGAGTCTTAGAAT 59.255 55.000 7.21 0.00 0.00 2.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.