Multiple sequence alignment - TraesCS6D01G348900

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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 TraesCS6D01G348900 chr6D 100.000 2881 0 0 1 2881 446881212 446884092 0.000000e+00 5321.0
1 TraesCS6D01G348900 chr6D 82.308 910 85 27 1733 2601 446727415 446726541 0.000000e+00 719.0
2 TraesCS6D01G348900 chr6D 83.650 685 69 25 963 1629 446728193 446727534 3.180000e-169 604.0
3 TraesCS6D01G348900 chr6D 77.756 998 122 45 1109 2052 446934808 446935759 3.290000e-144 521.0
4 TraesCS6D01G348900 chr6D 80.909 550 65 16 1039 1587 446814736 446815246 5.780000e-107 398.0
5 TraesCS6D01G348900 chr6D 80.990 505 65 18 1092 1572 446902004 446902501 3.510000e-99 372.0
6 TraesCS6D01G348900 chr6D 100.000 29 0 0 1086 1114 446728102 446728074 1.000000e-03 54.7
7 TraesCS6D01G348900 chr6B 84.000 1625 145 44 785 2381 676036128 676037665 0.000000e+00 1454.0
8 TraesCS6D01G348900 chr6B 86.131 1370 106 38 785 2136 676047050 676048353 0.000000e+00 1400.0
9 TraesCS6D01G348900 chr6B 80.556 864 66 30 785 1629 675702818 675702038 3.220000e-159 571.0
10 TraesCS6D01G348900 chr6B 84.423 520 36 18 1733 2242 675701908 675701424 1.210000e-128 470.0
11 TraesCS6D01G348900 chr6B 90.000 370 24 7 1777 2143 675672785 675672426 1.560000e-127 466.0
12 TraesCS6D01G348900 chr6B 92.355 327 18 5 52 376 676046295 676046616 2.620000e-125 459.0
13 TraesCS6D01G348900 chr6B 75.706 992 133 56 1109 2052 676123577 676124508 5.780000e-107 398.0
14 TraesCS6D01G348900 chr6B 85.117 383 45 11 395 773 676046691 676047065 5.830000e-102 381.0
15 TraesCS6D01G348900 chr6B 90.650 246 16 5 2131 2370 675672392 675672148 1.290000e-83 320.0
16 TraesCS6D01G348900 chr6B 89.272 261 21 3 2628 2881 676048847 676049107 1.290000e-83 320.0
17 TraesCS6D01G348900 chr6B 89.020 255 27 1 2628 2881 675700975 675700721 5.990000e-82 315.0
18 TraesCS6D01G348900 chr6B 83.600 250 22 14 1792 2040 676536710 676536479 1.740000e-52 217.0
19 TraesCS6D01G348900 chr6B 84.416 231 16 9 2628 2858 676038017 676038227 2.910000e-50 209.0
20 TraesCS6D01G348900 chr6B 83.412 211 26 6 1848 2055 677087419 677087215 1.360000e-43 187.0
21 TraesCS6D01G348900 chr6B 89.189 148 11 4 2456 2602 675701247 675701104 2.280000e-41 180.0
22 TraesCS6D01G348900 chr6B 83.500 200 24 5 47 246 676035854 676036044 8.200000e-41 178.0
23 TraesCS6D01G348900 chr6B 79.787 282 28 16 2250 2507 676048347 676048623 8.200000e-41 178.0
24 TraesCS6D01G348900 chr6B 96.491 57 0 1 719 773 676036087 676036143 3.060000e-15 93.5
25 TraesCS6D01G348900 chr6B 94.118 34 2 0 1592 1625 677128960 677128927 5.000000e-03 52.8
26 TraesCS6D01G348900 chr6A 89.512 820 52 16 818 1628 593732570 593733364 0.000000e+00 1007.0
27 TraesCS6D01G348900 chr6A 83.244 931 65 25 1733 2627 593733458 593734333 0.000000e+00 771.0
28 TraesCS6D01G348900 chr6A 81.752 822 76 40 1733 2524 593561698 593560921 1.130000e-173 619.0
29 TraesCS6D01G348900 chr6A 85.911 582 41 12 1056 1629 593562365 593561817 1.490000e-162 582.0
30 TraesCS6D01G348900 chr6A 80.109 548 74 18 1095 1619 593777173 593777708 2.710000e-100 375.0
31 TraesCS6D01G348900 chr6A 79.927 548 76 16 1039 1585 593700118 593700632 3.510000e-99 372.0
32 TraesCS6D01G348900 chr6A 81.352 488 61 10 1100 1587 593682458 593682915 1.260000e-98 370.0
33 TraesCS6D01G348900 chr6A 90.038 261 19 1 2628 2881 593734404 593734664 5.950000e-87 331.0
34 TraesCS6D01G348900 chr6A 87.013 154 16 2 93 246 593732032 593732181 1.370000e-38 171.0
35 TraesCS6D01G348900 chr6A 79.060 234 37 9 1163 1395 594365815 594366037 1.790000e-32 150.0
36 TraesCS6D01G348900 chr6A 89.109 101 11 0 2781 2881 593560129 593560029 3.010000e-25 126.0
37 TraesCS6D01G348900 chr6A 85.714 98 8 5 1829 1924 593575780 593575873 6.570000e-17 99.0
38 TraesCS6D01G348900 chr6A 88.158 76 8 1 2152 2227 594320763 594320837 3.950000e-14 89.8
39 TraesCS6D01G348900 chr6A 100.000 31 0 0 105 135 593776668 593776698 1.110000e-04 58.4
40 TraesCS6D01G348900 chr7B 84.043 376 50 8 292 659 716701424 716701051 1.270000e-93 353.0
41 TraesCS6D01G348900 chr7B 84.043 376 49 9 292 659 716975795 716976167 4.570000e-93 351.0
42 TraesCS6D01G348900 chr3A 82.933 375 48 12 292 659 675122405 675122040 9.960000e-85 324.0
43 TraesCS6D01G348900 chr3A 98.182 55 1 0 1 55 696281656 696281602 2.360000e-16 97.1
44 TraesCS6D01G348900 chr2B 81.233 373 61 9 292 660 391525902 391525535 2.810000e-75 292.0
45 TraesCS6D01G348900 chrUn 78.131 503 76 19 1091 1587 81268072 81268546 3.630000e-74 289.0
46 TraesCS6D01G348900 chrUn 78.248 331 53 14 257 583 143849830 143849515 8.150000e-46 195.0
47 TraesCS6D01G348900 chr1A 81.470 313 42 11 308 615 34987346 34987647 2.870000e-60 243.0
48 TraesCS6D01G348900 chr5A 80.805 323 48 12 300 615 536276279 536275964 1.030000e-59 241.0
49 TraesCS6D01G348900 chr5A 76.676 373 76 10 300 664 10801551 10801182 2.260000e-46 196.0
50 TraesCS6D01G348900 chr7A 86.061 165 20 3 292 454 715685975 715685812 1.060000e-39 174.0
51 TraesCS6D01G348900 chr1D 78.832 137 24 5 528 661 27782796 27782930 1.420000e-13 87.9


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 TraesCS6D01G348900 chr6D 446881212 446884092 2880 False 5321.000000 5321 100.000000 1 2881 1 chr6D.!!$F2 2880
1 TraesCS6D01G348900 chr6D 446934808 446935759 951 False 521.000000 521 77.756000 1109 2052 1 chr6D.!!$F4 943
2 TraesCS6D01G348900 chr6D 446726541 446728193 1652 True 459.233333 719 88.652667 963 2601 3 chr6D.!!$R1 1638
3 TraesCS6D01G348900 chr6D 446814736 446815246 510 False 398.000000 398 80.909000 1039 1587 1 chr6D.!!$F1 548
4 TraesCS6D01G348900 chr6B 676046295 676049107 2812 False 547.600000 1400 86.532400 52 2881 5 chr6B.!!$F3 2829
5 TraesCS6D01G348900 chr6B 676035854 676038227 2373 False 483.625000 1454 87.101750 47 2858 4 chr6B.!!$F2 2811
6 TraesCS6D01G348900 chr6B 676123577 676124508 931 False 398.000000 398 75.706000 1109 2052 1 chr6B.!!$F1 943
7 TraesCS6D01G348900 chr6B 675672148 675672785 637 True 393.000000 466 90.325000 1777 2370 2 chr6B.!!$R4 593
8 TraesCS6D01G348900 chr6B 675700721 675702818 2097 True 384.000000 571 85.797000 785 2881 4 chr6B.!!$R5 2096
9 TraesCS6D01G348900 chr6A 593732032 593734664 2632 False 570.000000 1007 87.451750 93 2881 4 chr6A.!!$F6 2788
10 TraesCS6D01G348900 chr6A 593560029 593562365 2336 True 442.333333 619 85.590667 1056 2881 3 chr6A.!!$R1 1825
11 TraesCS6D01G348900 chr6A 593700118 593700632 514 False 372.000000 372 79.927000 1039 1585 1 chr6A.!!$F3 546
12 TraesCS6D01G348900 chr6A 593776668 593777708 1040 False 216.700000 375 90.054500 105 1619 2 chr6A.!!$F7 1514

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
650 750 0.036010 ATCAACCAGGCTCCGAAGTG 60.036 55.0 0.00 0.0 0.0 3.16 F
1619 2181 1.078709 AATCAACGTCGACATGCCAG 58.921 50.0 17.16 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 2298 0.321996 GAGGACGAGCCCACTTTCTT 59.678 55.0 0.00 0.0 37.37 2.52 R
2699 3987 1.006832 AATCGCAGTACGTTGCCATC 58.993 50.0 6.64 0.0 44.19 3.51 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
23 24 5.161358 TGATTTATCGTGCATAGATCGTCC 58.839 41.667 10.35 2.32 33.13 4.79
24 25 3.570926 TTATCGTGCATAGATCGTCCC 57.429 47.619 10.35 0.00 0.00 4.46
25 26 1.621992 ATCGTGCATAGATCGTCCCT 58.378 50.000 0.00 0.00 0.00 4.20
26 27 1.399714 TCGTGCATAGATCGTCCCTT 58.600 50.000 0.00 0.00 0.00 3.95
27 28 1.754803 TCGTGCATAGATCGTCCCTTT 59.245 47.619 0.00 0.00 0.00 3.11
28 29 2.953648 TCGTGCATAGATCGTCCCTTTA 59.046 45.455 0.00 0.00 0.00 1.85
29 30 3.572682 TCGTGCATAGATCGTCCCTTTAT 59.427 43.478 0.00 0.00 0.00 1.40
30 31 3.675225 CGTGCATAGATCGTCCCTTTATG 59.325 47.826 0.00 0.00 0.00 1.90
31 32 4.632153 GTGCATAGATCGTCCCTTTATGT 58.368 43.478 0.00 0.00 0.00 2.29
32 33 4.686554 GTGCATAGATCGTCCCTTTATGTC 59.313 45.833 0.00 0.00 0.00 3.06
33 34 3.921021 GCATAGATCGTCCCTTTATGTCG 59.079 47.826 0.00 0.00 0.00 4.35
34 35 4.558898 GCATAGATCGTCCCTTTATGTCGT 60.559 45.833 0.00 0.00 0.00 4.34
35 36 3.438297 AGATCGTCCCTTTATGTCGTG 57.562 47.619 0.00 0.00 0.00 4.35
36 37 1.859080 GATCGTCCCTTTATGTCGTGC 59.141 52.381 0.00 0.00 0.00 5.34
37 38 0.604073 TCGTCCCTTTATGTCGTGCA 59.396 50.000 0.00 0.00 0.00 4.57
38 39 1.206132 TCGTCCCTTTATGTCGTGCAT 59.794 47.619 0.00 1.49 41.42 3.96
39 40 1.327460 CGTCCCTTTATGTCGTGCATG 59.673 52.381 0.00 0.00 38.47 4.06
40 41 1.670811 GTCCCTTTATGTCGTGCATGG 59.329 52.381 5.98 0.00 38.47 3.66
41 42 1.557371 TCCCTTTATGTCGTGCATGGA 59.443 47.619 5.98 0.00 38.47 3.41
42 43 1.942657 CCCTTTATGTCGTGCATGGAG 59.057 52.381 5.98 0.00 38.47 3.86
43 44 1.331756 CCTTTATGTCGTGCATGGAGC 59.668 52.381 5.98 0.00 45.96 4.70
151 152 1.205064 GATTCGGATCGGCATTGCG 59.795 57.895 1.91 0.00 0.00 4.85
175 176 0.580104 AGTCCGAACACGCTTTTTCG 59.420 50.000 4.64 4.64 43.40 3.46
190 196 5.277154 CGCTTTTTCGGAAGAGAAACTTACA 60.277 40.000 0.00 0.00 39.01 2.41
216 222 0.393132 TGCTGTTCACACGGAAACCA 60.393 50.000 0.00 0.00 37.23 3.67
303 346 8.890718 GGTGTTTCTACCTTCTATATGGAAAAC 58.109 37.037 2.92 4.36 37.74 2.43
376 419 8.573035 TGAAATAAACCTGACCTTTCATTGTAC 58.427 33.333 0.00 0.00 32.52 2.90
377 420 8.472007 AAATAAACCTGACCTTTCATTGTACA 57.528 30.769 0.00 0.00 0.00 2.90
378 421 8.650143 AATAAACCTGACCTTTCATTGTACAT 57.350 30.769 0.00 0.00 0.00 2.29
379 422 5.964958 AACCTGACCTTTCATTGTACATG 57.035 39.130 0.00 0.00 0.00 3.21
381 424 4.761739 ACCTGACCTTTCATTGTACATGTG 59.238 41.667 9.11 0.00 0.00 3.21
382 425 5.003160 CCTGACCTTTCATTGTACATGTGA 58.997 41.667 9.11 1.61 0.00 3.58
384 427 5.863965 TGACCTTTCATTGTACATGTGAGA 58.136 37.500 9.11 0.00 0.00 3.27
385 428 6.295249 TGACCTTTCATTGTACATGTGAGAA 58.705 36.000 9.11 2.64 0.00 2.87
386 429 6.770303 TGACCTTTCATTGTACATGTGAGAAA 59.230 34.615 9.11 9.99 0.00 2.52
387 430 7.284261 TGACCTTTCATTGTACATGTGAGAAAA 59.716 33.333 9.11 1.24 0.00 2.29
388 431 8.181904 ACCTTTCATTGTACATGTGAGAAAAT 57.818 30.769 9.11 0.00 0.00 1.82
389 432 8.641541 ACCTTTCATTGTACATGTGAGAAAATT 58.358 29.630 9.11 0.00 0.00 1.82
390 433 9.480053 CCTTTCATTGTACATGTGAGAAAATTT 57.520 29.630 9.11 0.00 0.00 1.82
394 437 9.462174 TCATTGTACATGTGAGAAAATTTTCAC 57.538 29.630 28.00 23.04 43.07 3.18
469 567 8.893727 GCTAAAATTGTGTGAATAGTGACCTAT 58.106 33.333 0.00 0.00 35.33 2.57
499 597 6.640499 GCAAATAAATTTTGTCCTTTTTGCCC 59.360 34.615 0.00 0.00 40.90 5.36
501 599 7.509141 AATAAATTTTGTCCTTTTTGCCCTG 57.491 32.000 0.00 0.00 0.00 4.45
506 604 2.306847 TGTCCTTTTTGCCCTGAAGTC 58.693 47.619 0.00 0.00 0.00 3.01
516 614 0.944386 CCCTGAAGTCAACGTTGGTG 59.056 55.000 27.02 3.66 0.00 4.17
641 741 4.408182 ACAGAGTGTATATCAACCAGGC 57.592 45.455 0.00 0.00 0.00 4.85
643 743 4.100189 ACAGAGTGTATATCAACCAGGCTC 59.900 45.833 0.00 0.00 0.00 4.70
650 750 0.036010 ATCAACCAGGCTCCGAAGTG 60.036 55.000 0.00 0.00 0.00 3.16
658 758 1.209747 AGGCTCCGAAGTGTATTTCCC 59.790 52.381 0.00 0.00 0.00 3.97
659 759 1.287425 GCTCCGAAGTGTATTTCCCG 58.713 55.000 0.00 0.00 0.00 5.14
660 760 1.405121 GCTCCGAAGTGTATTTCCCGT 60.405 52.381 0.00 0.00 0.00 5.28
661 761 2.268298 CTCCGAAGTGTATTTCCCGTG 58.732 52.381 0.00 0.00 0.00 4.94
685 786 3.241701 GCGAGATGCTACTAATCAGAGC 58.758 50.000 0.00 0.00 41.73 4.09
692 793 2.804933 GCTACTAATCAGAGCACTGGGC 60.805 54.545 11.42 0.00 43.60 5.36
752 855 4.574599 AGAAATTGACCAGCACTTTGAC 57.425 40.909 0.00 0.00 30.53 3.18
756 859 2.121291 TGACCAGCACTTTGACACAA 57.879 45.000 0.00 0.00 0.00 3.33
757 860 2.441410 TGACCAGCACTTTGACACAAA 58.559 42.857 0.00 0.00 0.00 2.83
758 861 2.822561 TGACCAGCACTTTGACACAAAA 59.177 40.909 0.00 0.00 0.00 2.44
759 862 3.446873 TGACCAGCACTTTGACACAAAAT 59.553 39.130 0.00 0.00 0.00 1.82
761 864 5.301551 TGACCAGCACTTTGACACAAAATAT 59.698 36.000 0.00 0.00 0.00 1.28
763 866 6.215845 ACCAGCACTTTGACACAAAATATTC 58.784 36.000 0.00 0.00 0.00 1.75
764 867 6.183360 ACCAGCACTTTGACACAAAATATTCA 60.183 34.615 0.00 0.00 0.00 2.57
765 868 6.700960 CCAGCACTTTGACACAAAATATTCAA 59.299 34.615 0.00 0.00 0.00 2.69
766 869 7.224362 CCAGCACTTTGACACAAAATATTCAAA 59.776 33.333 0.00 0.00 36.70 2.69
772 875 8.715191 TTTGACACAAAATATTCAAAGCAAGT 57.285 26.923 0.00 0.00 33.96 3.16
773 876 9.809096 TTTGACACAAAATATTCAAAGCAAGTA 57.191 25.926 0.00 0.00 33.96 2.24
774 877 9.979578 TTGACACAAAATATTCAAAGCAAGTAT 57.020 25.926 0.00 0.00 0.00 2.12
775 878 9.979578 TGACACAAAATATTCAAAGCAAGTATT 57.020 25.926 0.00 0.00 0.00 1.89
812 915 1.826385 AGCAAGTTGGCATGAGTACC 58.174 50.000 4.75 0.00 35.83 3.34
838 1214 2.492025 AGAATATTGGGGAGCTGACCA 58.508 47.619 0.00 0.00 34.29 4.02
1274 1742 3.692406 GTCTTCCTCCACCGGCGT 61.692 66.667 6.01 0.00 0.00 5.68
1329 1842 4.972733 TCGACGAACCACCCGGGA 62.973 66.667 32.02 0.00 41.15 5.14
1619 2181 1.078709 AATCAACGTCGACATGCCAG 58.921 50.000 17.16 0.00 0.00 4.85
1638 2204 5.044558 GCCAGAGCAAGATAGTTGTAGTAC 58.955 45.833 0.00 0.00 39.53 2.73
1645 2211 9.881529 GAGCAAGATAGTTGTAGTACATAGTAC 57.118 37.037 3.28 0.00 33.69 2.73
1708 2278 2.928116 CGATTCCGGACTGGTCTTTTAC 59.072 50.000 1.83 0.00 39.52 2.01
1736 2360 2.480419 CGTAGGTGCAGAAAGAAAGTGG 59.520 50.000 0.00 0.00 0.00 4.00
1752 2376 3.071206 GGGCTCGTCCTCTGCTCA 61.071 66.667 0.00 0.00 34.39 4.26
1754 2378 2.347322 GGCTCGTCCTCTGCTCACT 61.347 63.158 0.00 0.00 0.00 3.41
1797 2452 7.121315 GCCCTTGGTTTTGGATATATATGAGTC 59.879 40.741 0.00 0.00 0.00 3.36
1814 2469 3.876914 TGAGTCACAAATTGGAGACACAC 59.123 43.478 18.25 11.63 42.67 3.82
1833 2488 5.122869 ACACACACATGCATCTAAATCTGAC 59.877 40.000 0.00 0.00 0.00 3.51
2056 2723 2.893398 GAACGGATCAGGCGAGGT 59.107 61.111 0.00 0.00 0.00 3.85
2059 2726 2.105128 CGGATCAGGCGAGGTGAC 59.895 66.667 0.00 0.00 0.00 3.67
2064 2731 1.471829 ATCAGGCGAGGTGACACACA 61.472 55.000 8.08 0.00 35.86 3.72
2149 2867 8.499967 GTGAGATTTTTCTTCTTCCTAGTTGTC 58.500 37.037 0.00 0.00 0.00 3.18
2220 2941 0.663153 AACTCCTGAACTTGCGCAAC 59.337 50.000 21.02 10.74 0.00 4.17
2251 2992 2.202987 GCTCGCACAGCTGGCTAT 60.203 61.111 19.93 0.00 45.83 2.97
2297 3068 1.243342 TGGCCGGAAATGAGTTGCTG 61.243 55.000 5.05 0.00 0.00 4.41
2299 3070 0.960364 GCCGGAAATGAGTTGCTGGA 60.960 55.000 5.05 0.00 0.00 3.86
2401 3203 0.809636 CATTGTACCGGCGCAGATCA 60.810 55.000 10.83 2.34 0.00 2.92
2420 3222 2.560981 TCATCTGTTCAGAACCGCTGTA 59.439 45.455 10.93 0.00 45.14 2.74
2493 3346 2.512692 TCAAGTGGGGTTGATGATGG 57.487 50.000 0.00 0.00 31.31 3.51
2505 3358 6.126409 GGGTTGATGATGGTGGAATAAAGTA 58.874 40.000 0.00 0.00 0.00 2.24
2507 3360 6.238374 GGTTGATGATGGTGGAATAAAGTACG 60.238 42.308 0.00 0.00 0.00 3.67
2508 3361 5.984725 TGATGATGGTGGAATAAAGTACGT 58.015 37.500 0.00 0.00 0.00 3.57
2509 3362 7.114866 TGATGATGGTGGAATAAAGTACGTA 57.885 36.000 0.00 0.00 0.00 3.57
2510 3363 6.982141 TGATGATGGTGGAATAAAGTACGTAC 59.018 38.462 18.10 18.10 0.00 3.67
2512 3365 7.643569 TGATGGTGGAATAAAGTACGTACTA 57.356 36.000 27.59 14.35 34.99 1.82
2513 3366 7.709947 TGATGGTGGAATAAAGTACGTACTAG 58.290 38.462 27.59 0.00 34.99 2.57
2527 3406 8.550710 AGTACGTACTAGATGAATATCTGACC 57.449 38.462 26.36 0.00 43.41 4.02
2602 3772 2.283780 CTGAAATGTCAGCGTCGCCG 62.284 60.000 14.86 3.21 44.74 6.46
2645 3927 1.281925 ATCACCCGGGCTGGAAGATT 61.282 55.000 24.08 0.00 42.00 2.40
2699 3987 4.776322 TGACCGGGCAGGCAATCG 62.776 66.667 5.41 0.00 46.52 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.563184 GGGACGATCTATGCACGATAAATC 59.437 45.833 0.24 0.33 0.00 2.17
2 3 4.220821 AGGGACGATCTATGCACGATAAAT 59.779 41.667 0.24 0.00 0.00 1.40
3 4 3.572682 AGGGACGATCTATGCACGATAAA 59.427 43.478 0.24 0.00 0.00 1.40
4 5 3.154710 AGGGACGATCTATGCACGATAA 58.845 45.455 0.24 0.00 0.00 1.75
5 6 2.791655 AGGGACGATCTATGCACGATA 58.208 47.619 0.24 0.00 0.00 2.92
6 7 1.621992 AGGGACGATCTATGCACGAT 58.378 50.000 0.24 0.24 0.00 3.73
7 8 1.399714 AAGGGACGATCTATGCACGA 58.600 50.000 0.24 0.00 0.00 4.35
8 9 2.225068 AAAGGGACGATCTATGCACG 57.775 50.000 0.00 0.00 0.00 5.34
10 11 4.558697 CGACATAAAGGGACGATCTATGCA 60.559 45.833 0.00 0.00 0.00 3.96
11 12 3.921021 CGACATAAAGGGACGATCTATGC 59.079 47.826 0.00 0.00 0.00 3.14
12 13 4.917998 CACGACATAAAGGGACGATCTATG 59.082 45.833 0.00 0.00 0.00 2.23
13 14 4.558898 GCACGACATAAAGGGACGATCTAT 60.559 45.833 0.00 0.00 0.00 1.98
14 15 3.243301 GCACGACATAAAGGGACGATCTA 60.243 47.826 0.00 0.00 0.00 1.98
15 16 2.481449 GCACGACATAAAGGGACGATCT 60.481 50.000 0.00 0.00 0.00 2.75
16 17 1.859080 GCACGACATAAAGGGACGATC 59.141 52.381 0.00 0.00 0.00 3.69
17 18 1.206132 TGCACGACATAAAGGGACGAT 59.794 47.619 0.00 0.00 0.00 3.73
18 19 0.604073 TGCACGACATAAAGGGACGA 59.396 50.000 0.00 0.00 0.00 4.20
19 20 1.327460 CATGCACGACATAAAGGGACG 59.673 52.381 0.00 0.00 36.64 4.79
20 21 1.670811 CCATGCACGACATAAAGGGAC 59.329 52.381 0.00 0.00 36.64 4.46
21 22 1.557371 TCCATGCACGACATAAAGGGA 59.443 47.619 0.00 0.00 36.64 4.20
22 23 1.942657 CTCCATGCACGACATAAAGGG 59.057 52.381 0.00 0.00 36.64 3.95
23 24 1.331756 GCTCCATGCACGACATAAAGG 59.668 52.381 0.00 0.00 42.31 3.11
24 25 2.744787 GCTCCATGCACGACATAAAG 57.255 50.000 0.00 0.00 42.31 1.85
35 36 0.730494 GCAACGAAACTGCTCCATGC 60.730 55.000 0.00 0.00 43.25 4.06
36 37 3.389741 GCAACGAAACTGCTCCATG 57.610 52.632 0.00 0.00 36.84 3.66
50 51 2.809601 ATGTCGCCGTCGAGCAAC 60.810 61.111 0.00 0.00 46.46 4.17
57 58 1.501741 ACATTTGCATGTCGCCGTC 59.498 52.632 0.00 0.00 39.69 4.79
151 152 3.723348 GCGTGTTCGGACTTGGGC 61.723 66.667 0.00 0.00 37.56 5.36
175 176 5.106908 GCACTGATGTGTAAGTTTCTCTTCC 60.107 44.000 0.00 0.00 45.44 3.46
242 283 2.019249 TCGTGTCCCTCGGTATACTTG 58.981 52.381 2.25 0.00 0.00 3.16
250 291 1.300388 AAACGTTCGTGTCCCTCGG 60.300 57.895 0.00 0.00 0.00 4.63
262 305 1.842052 ACACCAAGGAACCAAACGTT 58.158 45.000 0.00 0.00 37.41 3.99
361 404 5.863965 TCTCACATGTACAATGAAAGGTCA 58.136 37.500 12.71 0.00 38.41 4.02
381 424 9.554724 GGGTTTTCTTTTTGTGAAAATTTTCTC 57.445 29.630 26.73 23.67 42.76 2.87
382 425 8.519526 GGGGTTTTCTTTTTGTGAAAATTTTCT 58.480 29.630 26.73 0.00 42.76 2.52
384 427 7.607250 GGGGGTTTTCTTTTTGTGAAAATTTT 58.393 30.769 2.28 2.28 42.76 1.82
385 428 7.164230 GGGGGTTTTCTTTTTGTGAAAATTT 57.836 32.000 5.20 0.00 42.76 1.82
386 429 6.767524 GGGGGTTTTCTTTTTGTGAAAATT 57.232 33.333 5.20 0.00 42.76 1.82
451 549 6.323739 TGCTATCATAGGTCACTATTCACACA 59.676 38.462 0.00 0.00 37.82 3.72
482 580 4.164030 ACTTCAGGGCAAAAAGGACAAAAT 59.836 37.500 0.00 0.00 0.00 1.82
490 588 2.099098 ACGTTGACTTCAGGGCAAAAAG 59.901 45.455 0.00 0.00 45.57 2.27
499 597 3.757745 AAACACCAACGTTGACTTCAG 57.242 42.857 29.35 13.61 0.00 3.02
539 637 4.795970 ACTTGACTTTCGTTTGCACTAG 57.204 40.909 0.00 0.00 0.00 2.57
540 638 5.554822 AAACTTGACTTTCGTTTGCACTA 57.445 34.783 0.00 0.00 30.39 2.74
613 712 8.306313 TGGTTGATATACACTCTGTATCAGTT 57.694 34.615 0.00 0.00 42.16 3.16
614 713 7.014711 CCTGGTTGATATACACTCTGTATCAGT 59.985 40.741 0.00 0.00 42.16 3.41
617 716 6.015010 AGCCTGGTTGATATACACTCTGTATC 60.015 42.308 0.00 0.00 42.16 2.24
624 723 2.365617 CGGAGCCTGGTTGATATACACT 59.634 50.000 0.00 0.00 0.00 3.55
636 736 2.280628 GAAATACACTTCGGAGCCTGG 58.719 52.381 0.00 0.00 0.00 4.45
641 741 2.268298 CACGGGAAATACACTTCGGAG 58.732 52.381 0.00 0.00 0.00 4.63
643 743 2.088950 ACACGGGAAATACACTTCGG 57.911 50.000 0.00 0.00 0.00 4.30
685 786 0.904649 TAGATGGACACAGCCCAGTG 59.095 55.000 0.51 0.51 44.93 3.66
776 879 9.474920 CCAACTTGCTTTGAATATTAGACAAAA 57.525 29.630 0.00 0.00 34.03 2.44
777 880 7.598493 GCCAACTTGCTTTGAATATTAGACAAA 59.402 33.333 0.00 0.00 33.49 2.83
778 881 7.090173 GCCAACTTGCTTTGAATATTAGACAA 58.910 34.615 0.00 0.00 0.00 3.18
779 882 6.208402 TGCCAACTTGCTTTGAATATTAGACA 59.792 34.615 0.00 0.00 0.00 3.41
780 883 6.620678 TGCCAACTTGCTTTGAATATTAGAC 58.379 36.000 0.00 0.00 0.00 2.59
781 884 6.832520 TGCCAACTTGCTTTGAATATTAGA 57.167 33.333 0.00 0.00 0.00 2.10
782 885 7.259882 TCATGCCAACTTGCTTTGAATATTAG 58.740 34.615 0.00 0.00 0.00 1.73
783 886 7.093814 ACTCATGCCAACTTGCTTTGAATATTA 60.094 33.333 0.00 0.00 0.00 0.98
812 915 4.101585 TCAGCTCCCCAATATTCTACTGTG 59.898 45.833 0.00 0.00 0.00 3.66
838 1214 2.978156 TTCAGGATTCAAGGCAGGTT 57.022 45.000 0.00 0.00 0.00 3.50
1233 1701 2.104859 CGAGACGCTGACGGACCTA 61.105 63.158 0.00 0.00 46.04 3.08
1235 1703 3.664223 GACGAGACGCTGACGGACC 62.664 68.421 0.00 0.00 46.04 4.46
1299 1806 2.447887 CGTCGAGGAGCACATGCAC 61.448 63.158 6.64 0.00 45.16 4.57
1619 2181 9.881529 GTACTATGTACTACAACTATCTTGCTC 57.118 37.037 0.00 0.00 0.00 4.26
1631 2194 8.050930 TCCACAAGATCAGTACTATGTACTACA 58.949 37.037 9.65 0.00 0.00 2.74
1638 2204 8.628630 TCTATCTCCACAAGATCAGTACTATG 57.371 38.462 0.00 0.00 43.90 2.23
1645 2211 5.010516 ACCGATTCTATCTCCACAAGATCAG 59.989 44.000 0.00 0.00 43.90 2.90
1653 2219 1.344763 CCCCACCGATTCTATCTCCAC 59.655 57.143 0.00 0.00 0.00 4.02
1720 2290 1.268079 GAGCCCACTTTCTTTCTGCAC 59.732 52.381 0.00 0.00 0.00 4.57
1727 2298 0.321996 GAGGACGAGCCCACTTTCTT 59.678 55.000 0.00 0.00 37.37 2.52
1731 2302 2.948720 GCAGAGGACGAGCCCACTT 61.949 63.158 0.00 0.00 37.37 3.16
1736 2360 2.183046 GTGAGCAGAGGACGAGCC 59.817 66.667 0.00 0.00 0.00 4.70
1752 2376 0.578211 CGTTCGTTTTACACCGCAGT 59.422 50.000 0.00 0.00 0.00 4.40
1754 2378 1.276250 GCGTTCGTTTTACACCGCA 59.724 52.632 0.00 0.00 40.72 5.69
1797 2452 4.292599 CATGTGTGTGTCTCCAATTTGTG 58.707 43.478 0.00 0.00 0.00 3.33
1814 2469 6.263344 CAAAGGTCAGATTTAGATGCATGTG 58.737 40.000 2.46 0.00 0.00 3.21
1873 2529 3.486841 CAGAAAGTTGTTCGGCAAACATG 59.513 43.478 4.92 0.00 46.94 3.21
1874 2530 3.705604 CAGAAAGTTGTTCGGCAAACAT 58.294 40.909 4.92 0.00 46.94 2.71
2123 2794 8.384607 ACAACTAGGAAGAAGAAAAATCTCAC 57.615 34.615 0.00 0.00 0.00 3.51
2149 2867 4.260212 CCGTCGAGCCAACAGTAAAATATG 60.260 45.833 0.00 0.00 0.00 1.78
2220 2941 1.442526 GCGAGCCCACCATCATCTTG 61.443 60.000 0.00 0.00 0.00 3.02
2251 2992 9.396022 AGAAACAGAACTGATTAAACAAGAAGA 57.604 29.630 8.87 0.00 0.00 2.87
2297 3068 5.767816 AACTGATAAGTTTTGGTGTGTCC 57.232 39.130 0.00 0.00 0.00 4.02
2299 3070 5.127031 AGCAAACTGATAAGTTTTGGTGTGT 59.873 36.000 5.36 0.00 39.68 3.72
2308 3079 6.112058 GGAGATGAGAGCAAACTGATAAGTT 58.888 40.000 0.00 0.00 0.00 2.66
2401 3203 3.055819 ACATACAGCGGTTCTGAACAGAT 60.056 43.478 22.00 14.47 45.72 2.90
2420 3222 4.705507 CAGTGTACCTACAGTCCTACACAT 59.294 45.833 13.83 2.34 40.91 3.21
2493 3346 9.962783 ATTCATCTAGTACGTACTTTATTCCAC 57.037 33.333 31.58 1.22 37.73 4.02
2505 3358 6.999272 ACTGGTCAGATATTCATCTAGTACGT 59.001 38.462 4.84 0.00 39.62 3.57
2507 3360 8.085296 CCAACTGGTCAGATATTCATCTAGTAC 58.915 40.741 4.84 0.00 39.62 2.73
2508 3361 8.183104 CCAACTGGTCAGATATTCATCTAGTA 57.817 38.462 4.84 0.00 39.62 1.82
2509 3362 7.060383 CCAACTGGTCAGATATTCATCTAGT 57.940 40.000 4.84 0.00 39.62 2.57
2645 3927 1.675310 CAGATTCCGTGGCAGGCAA 60.675 57.895 0.00 0.00 0.00 4.52
2699 3987 1.006832 AATCGCAGTACGTTGCCATC 58.993 50.000 6.64 0.00 44.19 3.51
2705 3993 2.478894 CACTGGAAAATCGCAGTACGTT 59.521 45.455 0.00 0.00 44.19 3.99
2739 4034 2.593725 CCTATCGGTCGCCCTCGA 60.594 66.667 0.00 0.00 43.28 4.04
2849 4325 6.549242 TCCATGGATGATTAAGCTGATTCAT 58.451 36.000 11.44 8.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.