Multiple sequence alignment - TraesCS6D01G283400

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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 TraesCS6D01G283400 chr6D 100.000 3748 0 0 1 3748 390487439 390483692 0.000000e+00 6922.0
1 TraesCS6D01G283400 chr6D 91.464 2718 178 17 52 2734 390730525 390727827 0.000000e+00 3685.0
2 TraesCS6D01G283400 chr6D 93.702 2223 101 14 882 3082 390781349 390779144 0.000000e+00 3293.0
3 TraesCS6D01G283400 chr6D 94.379 676 26 2 3085 3748 390779075 390778400 0.000000e+00 1027.0
4 TraesCS6D01G283400 chr6D 88.576 604 26 18 3174 3746 390727027 390726436 0.000000e+00 693.0
5 TraesCS6D01G283400 chr6D 91.000 400 23 6 2745 3134 390727542 390727146 9.220000e-146 527.0
6 TraesCS6D01G283400 chr6D 91.860 172 14 0 52 223 390644126 390643955 1.350000e-59 241.0
7 TraesCS6D01G283400 chr6D 96.364 55 2 0 1 55 390644204 390644150 1.430000e-14 91.6
8 TraesCS6D01G283400 chr6A 92.451 2623 117 21 1102 3675 537020683 537018093 0.000000e+00 3672.0
9 TraesCS6D01G283400 chr6A 88.889 144 12 2 959 1101 537020866 537020726 1.380000e-39 174.0
10 TraesCS6D01G283400 chr6A 95.294 85 2 2 3663 3746 537005085 537005002 2.350000e-27 134.0
11 TraesCS6D01G283400 chr6B 92.526 2047 122 13 1102 3134 583723797 583725826 0.000000e+00 2904.0
12 TraesCS6D01G283400 chr6B 92.053 151 7 2 3601 3746 583728179 583728329 1.360000e-49 207.0
13 TraesCS6D01G283400 chr6B 92.414 145 8 2 3463 3605 583726546 583726689 1.760000e-48 204.0
14 TraesCS6D01G283400 chr6B 84.091 220 15 6 882 1101 583723552 583723751 1.060000e-45 195.0
15 TraesCS6D01G283400 chr6B 94.737 76 4 0 3171 3246 583725916 583725991 6.580000e-23 119.0
16 TraesCS6D01G283400 chr7B 74.938 1217 270 22 1463 2660 20721520 20720320 3.320000e-145 525.0
17 TraesCS6D01G283400 chr7B 84.910 391 57 2 435 824 141825970 141825581 9.760000e-106 394.0
18 TraesCS6D01G283400 chr7B 83.662 355 56 2 484 837 565202003 565202356 2.160000e-87 333.0
19 TraesCS6D01G283400 chr7A 74.447 1221 272 28 1463 2660 79334992 79333789 1.210000e-134 490.0
20 TraesCS6D01G283400 chr7A 81.558 385 70 1 452 835 653702759 653702375 2.170000e-82 316.0
21 TraesCS6D01G283400 chr7D 84.539 401 54 6 438 836 175946571 175946177 1.260000e-104 390.0
22 TraesCS6D01G283400 chr5B 84.127 378 45 3 460 836 526178556 526178193 5.960000e-93 351.0


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 TraesCS6D01G283400 chr6D 390483692 390487439 3747 True 6922.0 6922 100.000000 1 3748 1 chr6D.!!$R1 3747
1 TraesCS6D01G283400 chr6D 390778400 390781349 2949 True 2160.0 3293 94.040500 882 3748 2 chr6D.!!$R4 2866
2 TraesCS6D01G283400 chr6D 390726436 390730525 4089 True 1635.0 3685 90.346667 52 3746 3 chr6D.!!$R3 3694
3 TraesCS6D01G283400 chr6A 537018093 537020866 2773 True 1923.0 3672 90.670000 959 3675 2 chr6A.!!$R2 2716
4 TraesCS6D01G283400 chr6B 583723552 583728329 4777 False 725.8 2904 91.164200 882 3746 5 chr6B.!!$F1 2864
5 TraesCS6D01G283400 chr7B 20720320 20721520 1200 True 525.0 525 74.938000 1463 2660 1 chr7B.!!$R1 1197
6 TraesCS6D01G283400 chr7A 79333789 79334992 1203 True 490.0 490 74.447000 1463 2660 1 chr7A.!!$R1 1197

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
691 725 0.093365 GCGACGTTCGGCGAATAAAA 59.907 50.0 26.42 0.00 44.77 1.52 F
878 913 0.321298 AAATCTGACGTTCCACCGGG 60.321 55.0 6.32 0.00 0.00 5.73 F
2299 2403 1.176527 TATGCTGCAAGTTTGGAGGC 58.823 50.0 6.36 7.81 45.44 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2179 0.690762 TAGAAAGGTCCACCCACAGC 59.309 55.0 0.00 0.00 36.42 4.40 R
2578 2687 0.968405 GGCACAATTTCTTCCCTGCA 59.032 50.0 0.00 0.00 0.00 4.41 R
3156 3753 0.107066 AATGACGATGATGGCAGCCA 60.107 50.0 18.99 18.99 38.19 4.75 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
18 19 3.131326 TCTGGCGTATTCCGTGTTG 57.869 52.632 0.00 0.00 39.32 3.33
19 20 1.017177 TCTGGCGTATTCCGTGTTGC 61.017 55.000 0.00 0.00 39.32 4.17
20 21 2.291508 CTGGCGTATTCCGTGTTGCG 62.292 60.000 0.00 0.00 39.32 4.85
21 22 2.385091 GGCGTATTCCGTGTTGCGT 61.385 57.895 0.00 0.00 39.32 5.24
22 23 1.225637 GCGTATTCCGTGTTGCGTG 60.226 57.895 0.00 0.00 39.32 5.34
23 24 1.893168 GCGTATTCCGTGTTGCGTGT 61.893 55.000 0.00 0.00 39.32 4.49
24 25 0.179260 CGTATTCCGTGTTGCGTGTG 60.179 55.000 0.00 0.00 39.32 3.82
25 26 0.165079 GTATTCCGTGTTGCGTGTGG 59.835 55.000 0.00 0.00 39.32 4.17
26 27 1.570347 TATTCCGTGTTGCGTGTGGC 61.570 55.000 0.00 0.00 43.96 5.01
35 36 2.125753 GCGTGTGGCAGAGAGGAG 60.126 66.667 0.00 0.00 42.87 3.69
36 37 2.640302 GCGTGTGGCAGAGAGGAGA 61.640 63.158 0.00 0.00 42.87 3.71
37 38 1.510383 CGTGTGGCAGAGAGGAGAG 59.490 63.158 0.00 0.00 0.00 3.20
38 39 1.217779 GTGTGGCAGAGAGGAGAGC 59.782 63.158 0.00 0.00 0.00 4.09
39 40 1.228988 TGTGGCAGAGAGGAGAGCA 60.229 57.895 0.00 0.00 0.00 4.26
40 41 0.616964 TGTGGCAGAGAGGAGAGCAT 60.617 55.000 0.00 0.00 0.00 3.79
41 42 0.104671 GTGGCAGAGAGGAGAGCATC 59.895 60.000 0.00 0.00 0.00 3.91
42 43 0.325016 TGGCAGAGAGGAGAGCATCA 60.325 55.000 0.00 0.00 37.82 3.07
43 44 1.050204 GGCAGAGAGGAGAGCATCAT 58.950 55.000 0.00 0.00 37.82 2.45
44 45 2.246469 GGCAGAGAGGAGAGCATCATA 58.754 52.381 0.00 0.00 37.82 2.15
45 46 2.029110 GGCAGAGAGGAGAGCATCATAC 60.029 54.545 0.00 0.00 37.82 2.39
46 47 2.627221 GCAGAGAGGAGAGCATCATACA 59.373 50.000 0.00 0.00 37.82 2.29
47 48 3.552684 GCAGAGAGGAGAGCATCATACAC 60.553 52.174 0.00 0.00 37.82 2.90
48 49 3.635836 CAGAGAGGAGAGCATCATACACA 59.364 47.826 0.00 0.00 37.82 3.72
49 50 3.890756 AGAGAGGAGAGCATCATACACAG 59.109 47.826 0.00 0.00 37.82 3.66
50 51 2.964464 AGAGGAGAGCATCATACACAGG 59.036 50.000 0.00 0.00 37.82 4.00
56 57 3.771479 AGAGCATCATACACAGGTTCTGA 59.229 43.478 1.59 0.00 37.82 3.27
63 64 4.461431 TCATACACAGGTTCTGACGTATGT 59.539 41.667 23.86 13.24 43.27 2.29
116 117 7.440523 GGTCTTGCCGAAATATATCAAGAAT 57.559 36.000 12.80 0.00 42.95 2.40
118 119 9.167311 GGTCTTGCCGAAATATATCAAGAATAT 57.833 33.333 12.80 0.00 42.95 1.28
170 171 3.369385 GCTTAGCAATGCATGTGATGAC 58.631 45.455 8.35 0.00 0.00 3.06
177 178 2.573941 TGCATGTGATGACGAGAGAG 57.426 50.000 0.00 0.00 0.00 3.20
184 185 5.391312 TGTGATGACGAGAGAGAAATTGA 57.609 39.130 0.00 0.00 0.00 2.57
200 201 9.232473 AGAGAAATTGAAATTAGAGGTTGGTAC 57.768 33.333 0.00 0.00 0.00 3.34
278 297 5.734720 TCTAACAACCTAGCTGAAGAATGG 58.265 41.667 0.00 0.00 0.00 3.16
282 301 4.042187 ACAACCTAGCTGAAGAATGGAAGT 59.958 41.667 0.00 0.00 0.00 3.01
294 313 8.327941 TGAAGAATGGAAGTCTATTCAACAAG 57.672 34.615 16.74 0.00 42.57 3.16
323 342 5.525484 ACTAATCACTGGGTATCTACACCA 58.475 41.667 0.00 0.00 40.65 4.17
329 348 2.101582 CTGGGTATCTACACCAGTGAGC 59.898 54.545 4.48 0.00 45.21 4.26
330 349 2.108168 GGGTATCTACACCAGTGAGCA 58.892 52.381 4.48 0.00 40.65 4.26
331 350 2.159085 GGGTATCTACACCAGTGAGCAC 60.159 54.545 4.48 0.00 40.65 4.40
332 351 2.761208 GGTATCTACACCAGTGAGCACT 59.239 50.000 4.48 0.00 43.61 4.40
333 352 3.952323 GGTATCTACACCAGTGAGCACTA 59.048 47.826 4.48 0.00 40.20 2.74
334 353 4.401519 GGTATCTACACCAGTGAGCACTAA 59.598 45.833 4.48 0.00 40.20 2.24
349 369 2.744741 GCACTAAAGGAAGCCAGAAGAC 59.255 50.000 0.00 0.00 0.00 3.01
351 371 2.897969 ACTAAAGGAAGCCAGAAGACGA 59.102 45.455 0.00 0.00 0.00 4.20
384 418 2.550606 TCAATGCGAAACACCAAGGTAC 59.449 45.455 0.00 0.00 0.00 3.34
387 421 1.571215 GCGAAACACCAAGGTACGGG 61.571 60.000 0.00 0.00 0.00 5.28
399 433 4.791069 TACGGGAGGAGGGGGTGC 62.791 72.222 0.00 0.00 0.00 5.01
407 441 1.068352 AGGAGGGGGTGCTGTTCTTT 61.068 55.000 0.00 0.00 0.00 2.52
408 442 0.895559 GGAGGGGGTGCTGTTCTTTG 60.896 60.000 0.00 0.00 0.00 2.77
410 444 1.152830 GGGGGTGCTGTTCTTTGGA 59.847 57.895 0.00 0.00 0.00 3.53
442 476 0.313043 CATTCTTGGCCGGATCATGC 59.687 55.000 5.05 0.00 0.00 4.06
469 503 1.153489 CCCTCCACTCACGATGCAG 60.153 63.158 0.00 0.00 0.00 4.41
478 512 4.457496 ACGATGCAGAGGTGGCCG 62.457 66.667 0.00 0.00 0.00 6.13
493 527 2.959357 GCCGAGCTATTGGCGCATC 61.959 63.158 10.83 0.00 46.20 3.91
499 533 1.669115 CTATTGGCGCATCGGAGGG 60.669 63.158 10.83 0.00 0.00 4.30
508 542 0.972883 GCATCGGAGGGCTCTAATCT 59.027 55.000 0.00 0.00 0.00 2.40
534 568 3.664107 TCGAGAGCTACAAGTGCAAAAT 58.336 40.909 0.00 0.00 0.00 1.82
544 578 4.624015 ACAAGTGCAAAATGTGATCCTTG 58.376 39.130 0.00 0.00 35.51 3.61
553 587 7.282675 TGCAAAATGTGATCCTTGAAACAAATT 59.717 29.630 0.00 0.00 0.00 1.82
559 593 6.016024 TGTGATCCTTGAAACAAATTCTCAGG 60.016 38.462 0.00 0.00 39.09 3.86
591 625 8.025445 GTGAGTAAGATCAAGAATGTGCAAAAT 58.975 33.333 0.00 0.00 0.00 1.82
599 633 8.842358 ATCAAGAATGTGCAAAATGATTTCTT 57.158 26.923 0.00 0.00 33.50 2.52
603 637 9.545105 AAGAATGTGCAAAATGATTTCTTAACA 57.455 25.926 1.35 0.00 31.99 2.41
608 642 8.557864 TGTGCAAAATGATTTCTTAACAAATGG 58.442 29.630 0.00 0.00 0.00 3.16
619 653 9.965824 ATTTCTTAACAAATGGACAACTAGTTG 57.034 29.630 29.76 29.76 45.58 3.16
627 661 3.314693 TGGACAACTAGTTGAGGAGGTT 58.685 45.455 36.14 16.21 42.93 3.50
638 672 9.102453 ACTAGTTGAGGAGGTTAAAGATTTACT 57.898 33.333 0.00 0.00 0.00 2.24
642 676 6.947464 TGAGGAGGTTAAAGATTTACTGAGG 58.053 40.000 0.00 0.00 0.00 3.86
660 694 5.602978 ACTGAGGTCTTTTCAGGAGTTTAGA 59.397 40.000 7.13 0.00 44.96 2.10
661 695 6.099845 ACTGAGGTCTTTTCAGGAGTTTAGAA 59.900 38.462 7.13 0.00 44.96 2.10
663 697 7.162082 TGAGGTCTTTTCAGGAGTTTAGAATC 58.838 38.462 0.00 0.00 0.00 2.52
670 704 2.939103 CAGGAGTTTAGAATCGCTTGGG 59.061 50.000 0.00 0.00 0.00 4.12
682 716 3.411351 CTTGGGTGCGACGTTCGG 61.411 66.667 8.96 0.00 40.84 4.30
691 725 0.093365 GCGACGTTCGGCGAATAAAA 59.907 50.000 26.42 0.00 44.77 1.52
693 727 2.611070 CGACGTTCGGCGAATAAAATC 58.389 47.619 26.42 16.32 44.77 2.17
695 729 1.994779 ACGTTCGGCGAATAAAATCGT 59.005 42.857 26.42 24.03 44.49 3.73
697 731 3.611986 ACGTTCGGCGAATAAAATCGTAA 59.388 39.130 26.42 0.00 44.49 3.18
701 736 5.073192 TCGGCGAATAAAATCGTAATGTG 57.927 39.130 7.35 0.00 44.49 3.21
747 782 4.955811 TCTCTCTGTAAAACTTGGCTCA 57.044 40.909 0.00 0.00 0.00 4.26
764 799 5.263599 TGGCTCAATGTATCTTCCAAATGT 58.736 37.500 0.00 0.00 0.00 2.71
772 807 6.985188 TGTATCTTCCAAATGTGTTAGCTC 57.015 37.500 0.00 0.00 0.00 4.09
774 809 4.265904 TCTTCCAAATGTGTTAGCTCGA 57.734 40.909 0.00 0.00 0.00 4.04
785 820 3.552294 GTGTTAGCTCGAAGATTGCTACC 59.448 47.826 3.05 0.00 39.48 3.18
790 825 0.744874 TCGAAGATTGCTACCGAGGG 59.255 55.000 0.00 0.00 0.00 4.30
800 835 1.896465 GCTACCGAGGGAGCTATGAAT 59.104 52.381 18.73 0.00 35.73 2.57
813 848 9.920946 AGGGAGCTATGAATTTTGAATAAAGTA 57.079 29.630 0.00 0.00 0.00 2.24
827 862 9.615295 TTTGAATAAAGTAACAAGTATTTCCGC 57.385 29.630 0.00 0.00 0.00 5.54
829 864 9.656040 TGAATAAAGTAACAAGTATTTCCGCTA 57.344 29.630 0.00 0.00 0.00 4.26
857 892 2.095919 CGTTCGTTTTCCCATTCCTCAC 60.096 50.000 0.00 0.00 0.00 3.51
878 913 0.321298 AAATCTGACGTTCCACCGGG 60.321 55.000 6.32 0.00 0.00 5.73
895 930 4.500116 GTCGAGCCACCGCCTCTC 62.500 72.222 0.00 0.00 34.57 3.20
950 985 4.892934 GCCATTACCATATTCCACTTCCAA 59.107 41.667 0.00 0.00 0.00 3.53
1973 2074 2.278206 CGATGAGCTCCGTGACCG 60.278 66.667 12.15 1.90 0.00 4.79
2007 2108 4.870636 AGGCATATTTGTTTCCTGATCCA 58.129 39.130 0.00 0.00 0.00 3.41
2034 2135 2.162681 GGAAGCTACATTGTGGTGCTT 58.837 47.619 19.16 19.16 45.15 3.91
2299 2403 1.176527 TATGCTGCAAGTTTGGAGGC 58.823 50.000 6.36 7.81 45.44 4.70
2364 2471 7.671495 AATGGAAACCAGCAAAATATTTGTC 57.329 32.000 0.39 0.00 36.75 3.18
2578 2687 3.572255 TGTTCTAAATTTGGAAAGCGGCT 59.428 39.130 17.39 0.00 29.23 5.52
2826 3226 3.084039 CAAAGTTGGAGCTTAGATGGCA 58.916 45.455 0.00 0.00 0.00 4.92
2861 3261 4.734989 CCTTGTGGAAATGTTAACGCAACA 60.735 41.667 5.73 5.73 42.98 3.33
2889 3289 8.086522 TGTTGTACAAGGAAGATAGTTACTGAC 58.913 37.037 8.98 0.00 0.00 3.51
2900 3300 7.399245 AGATAGTTACTGACCAGAGAAGTTC 57.601 40.000 3.76 0.00 0.00 3.01
2968 3368 7.969387 TTTGTTCTTTCACTCAATTCTTTCG 57.031 32.000 0.00 0.00 0.00 3.46
3033 3443 8.924511 AATACCTTGTCATTATGAGTATTGGG 57.075 34.615 13.28 6.13 28.95 4.12
3054 3464 4.131596 GGCACACAAGTTTTCTACTGGTA 58.868 43.478 0.00 0.00 39.08 3.25
3127 3703 6.473758 AGCTCGTCTACCTTTTAGGATTTTT 58.526 36.000 0.00 0.00 37.67 1.94
3152 3749 6.817765 TTGGTTTCCATATCAGTTGAGTTC 57.182 37.500 0.00 0.00 31.53 3.01
3153 3750 4.935205 TGGTTTCCATATCAGTTGAGTTCG 59.065 41.667 0.00 0.00 0.00 3.95
3154 3751 4.935808 GGTTTCCATATCAGTTGAGTTCGT 59.064 41.667 0.00 0.00 0.00 3.85
3155 3752 6.103997 GGTTTCCATATCAGTTGAGTTCGTA 58.896 40.000 0.00 0.00 0.00 3.43
3156 3753 6.761714 GGTTTCCATATCAGTTGAGTTCGTAT 59.238 38.462 0.00 0.00 0.00 3.06
3157 3754 7.254455 GGTTTCCATATCAGTTGAGTTCGTATG 60.254 40.741 0.00 0.00 0.00 2.39
3158 3755 5.842907 TCCATATCAGTTGAGTTCGTATGG 58.157 41.667 10.45 10.45 38.80 2.74
3159 3756 4.449068 CCATATCAGTTGAGTTCGTATGGC 59.551 45.833 6.02 0.00 33.15 4.40
3160 3757 3.895232 ATCAGTTGAGTTCGTATGGCT 57.105 42.857 0.00 0.00 0.00 4.75
3161 3758 2.959516 TCAGTTGAGTTCGTATGGCTG 58.040 47.619 0.00 0.00 0.00 4.85
3162 3759 1.394917 CAGTTGAGTTCGTATGGCTGC 59.605 52.381 0.00 0.00 0.00 5.25
3163 3760 0.727398 GTTGAGTTCGTATGGCTGCC 59.273 55.000 12.87 12.87 0.00 4.85
3164 3761 0.323302 TTGAGTTCGTATGGCTGCCA 59.677 50.000 25.65 25.65 38.19 4.92
3165 3762 0.541392 TGAGTTCGTATGGCTGCCAT 59.459 50.000 34.21 34.21 46.99 4.40
3166 3763 1.221414 GAGTTCGTATGGCTGCCATC 58.779 55.000 35.64 24.41 40.74 3.51
3167 3764 0.541392 AGTTCGTATGGCTGCCATCA 59.459 50.000 35.64 18.97 40.74 3.07
3168 3765 1.141657 AGTTCGTATGGCTGCCATCAT 59.858 47.619 35.64 17.72 40.74 2.45
3169 3766 1.532868 GTTCGTATGGCTGCCATCATC 59.467 52.381 35.64 24.18 40.74 2.92
3170 3767 0.319813 TCGTATGGCTGCCATCATCG 60.320 55.000 35.64 32.03 40.74 3.84
3171 3768 0.601046 CGTATGGCTGCCATCATCGT 60.601 55.000 35.64 16.18 40.74 3.73
3172 3769 1.151668 GTATGGCTGCCATCATCGTC 58.848 55.000 35.64 16.57 40.74 4.20
3277 3880 8.691797 GTTCCCTGCCTTTTTGATATAAATGTA 58.308 33.333 0.00 0.00 0.00 2.29
3308 4307 4.024977 GCATTTCGCACAAAACATTCCTTT 60.025 37.500 0.00 0.00 41.79 3.11
3367 4367 6.614694 TTTAGGTATTGCAGAAGTGAGGTA 57.385 37.500 0.00 0.00 0.00 3.08
3369 4369 5.028549 AGGTATTGCAGAAGTGAGGTATG 57.971 43.478 0.00 0.00 0.00 2.39
3371 4371 4.811557 GGTATTGCAGAAGTGAGGTATGTC 59.188 45.833 0.00 0.00 0.00 3.06
3373 4373 4.350368 TTGCAGAAGTGAGGTATGTCAA 57.650 40.909 0.00 0.00 0.00 3.18
3374 4374 4.350368 TGCAGAAGTGAGGTATGTCAAA 57.650 40.909 0.00 0.00 0.00 2.69
3406 4422 7.814587 GGTTTTTGCTACAAGATCTGCTATTTT 59.185 33.333 0.00 0.00 0.00 1.82
3457 4473 6.345920 ACTGTCTTTCTCTGTTTACAAACG 57.654 37.500 0.74 0.00 41.74 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.125753 CTCCTCTCTGCCACACGC 60.126 66.667 0.00 0.00 38.31 5.34
19 20 1.510383 CTCTCCTCTCTGCCACACG 59.490 63.158 0.00 0.00 0.00 4.49
20 21 1.217779 GCTCTCCTCTCTGCCACAC 59.782 63.158 0.00 0.00 0.00 3.82
21 22 0.616964 ATGCTCTCCTCTCTGCCACA 60.617 55.000 0.00 0.00 0.00 4.17
22 23 0.104671 GATGCTCTCCTCTCTGCCAC 59.895 60.000 0.00 0.00 0.00 5.01
23 24 0.325016 TGATGCTCTCCTCTCTGCCA 60.325 55.000 0.00 0.00 0.00 4.92
24 25 1.050204 ATGATGCTCTCCTCTCTGCC 58.950 55.000 0.00 0.00 0.00 4.85
25 26 2.627221 TGTATGATGCTCTCCTCTCTGC 59.373 50.000 0.00 0.00 0.00 4.26
26 27 3.635836 TGTGTATGATGCTCTCCTCTCTG 59.364 47.826 0.00 0.00 0.00 3.35
27 28 3.890756 CTGTGTATGATGCTCTCCTCTCT 59.109 47.826 0.00 0.00 0.00 3.10
28 29 3.005684 CCTGTGTATGATGCTCTCCTCTC 59.994 52.174 0.00 0.00 0.00 3.20
29 30 2.964464 CCTGTGTATGATGCTCTCCTCT 59.036 50.000 0.00 0.00 0.00 3.69
30 31 2.697751 ACCTGTGTATGATGCTCTCCTC 59.302 50.000 0.00 0.00 0.00 3.71
31 32 2.756907 ACCTGTGTATGATGCTCTCCT 58.243 47.619 0.00 0.00 0.00 3.69
32 33 3.133721 AGAACCTGTGTATGATGCTCTCC 59.866 47.826 0.00 0.00 0.00 3.71
33 34 4.118410 CAGAACCTGTGTATGATGCTCTC 58.882 47.826 0.00 0.00 0.00 3.20
34 35 3.771479 TCAGAACCTGTGTATGATGCTCT 59.229 43.478 0.00 0.00 32.61 4.09
35 36 3.868077 GTCAGAACCTGTGTATGATGCTC 59.132 47.826 0.00 0.00 32.61 4.26
36 37 3.677148 CGTCAGAACCTGTGTATGATGCT 60.677 47.826 0.00 0.00 32.61 3.79
37 38 2.604914 CGTCAGAACCTGTGTATGATGC 59.395 50.000 0.00 0.00 32.61 3.91
38 39 3.849911 ACGTCAGAACCTGTGTATGATG 58.150 45.455 0.00 0.00 35.22 3.07
39 40 5.127194 ACATACGTCAGAACCTGTGTATGAT 59.873 40.000 27.53 18.05 44.34 2.45
40 41 4.461431 ACATACGTCAGAACCTGTGTATGA 59.539 41.667 27.53 7.10 44.34 2.15
41 42 4.744570 ACATACGTCAGAACCTGTGTATG 58.255 43.478 23.60 23.60 45.42 2.39
42 43 5.047590 TCAACATACGTCAGAACCTGTGTAT 60.048 40.000 0.00 0.00 35.92 2.29
43 44 4.278919 TCAACATACGTCAGAACCTGTGTA 59.721 41.667 0.00 0.00 32.61 2.90
44 45 3.069016 TCAACATACGTCAGAACCTGTGT 59.931 43.478 0.00 0.00 32.61 3.72
45 46 3.649073 TCAACATACGTCAGAACCTGTG 58.351 45.455 0.00 0.00 32.61 3.66
46 47 3.861131 GCTCAACATACGTCAGAACCTGT 60.861 47.826 0.00 0.00 32.61 4.00
47 48 2.668457 GCTCAACATACGTCAGAACCTG 59.332 50.000 0.00 0.00 0.00 4.00
48 49 2.671351 CGCTCAACATACGTCAGAACCT 60.671 50.000 0.00 0.00 0.00 3.50
49 50 1.654105 CGCTCAACATACGTCAGAACC 59.346 52.381 0.00 0.00 0.00 3.62
50 51 2.592194 TCGCTCAACATACGTCAGAAC 58.408 47.619 0.00 0.00 0.00 3.01
56 57 1.280982 CTGCATCGCTCAACATACGT 58.719 50.000 0.00 0.00 0.00 3.57
63 64 2.036571 CAGCCACTGCATCGCTCAA 61.037 57.895 0.00 0.00 41.13 3.02
111 112 4.349048 TGCACATAGCTCCTCCATATTCTT 59.651 41.667 0.00 0.00 45.94 2.52
116 117 2.303890 CCATGCACATAGCTCCTCCATA 59.696 50.000 0.00 0.00 45.94 2.74
118 119 0.471191 CCATGCACATAGCTCCTCCA 59.529 55.000 0.00 0.00 45.94 3.86
129 130 2.940971 GCCACTGTAGAATCCATGCACA 60.941 50.000 0.00 0.00 0.00 4.57
170 171 8.386606 CAACCTCTAATTTCAATTTCTCTCTCG 58.613 37.037 0.00 0.00 0.00 4.04
177 178 8.036273 TCGTACCAACCTCTAATTTCAATTTC 57.964 34.615 0.00 0.00 0.00 2.17
184 185 4.820894 AGCTCGTACCAACCTCTAATTT 57.179 40.909 0.00 0.00 0.00 1.82
214 215 3.433598 GGTCTCCCTTGCAGCATTACATA 60.434 47.826 0.00 0.00 0.00 2.29
216 217 1.340017 GGTCTCCCTTGCAGCATTACA 60.340 52.381 0.00 0.00 0.00 2.41
220 221 0.610232 GTTGGTCTCCCTTGCAGCAT 60.610 55.000 0.00 0.00 0.00 3.79
222 223 1.973812 GGTTGGTCTCCCTTGCAGC 60.974 63.158 0.00 0.00 0.00 5.25
246 247 5.988561 CAGCTAGGTTGTTAGATGGATTCTC 59.011 44.000 0.00 0.00 34.31 2.87
278 297 4.695928 GTCACCCCTTGTTGAATAGACTTC 59.304 45.833 0.00 0.00 0.00 3.01
282 301 6.214615 TGATTAGTCACCCCTTGTTGAATAGA 59.785 38.462 0.00 0.00 0.00 1.98
309 328 2.108168 GCTCACTGGTGTAGATACCCA 58.892 52.381 0.53 0.00 40.09 4.51
323 342 1.699634 TGGCTTCCTTTAGTGCTCACT 59.300 47.619 7.73 7.73 45.02 3.41
324 343 2.079925 CTGGCTTCCTTTAGTGCTCAC 58.920 52.381 0.00 0.00 0.00 3.51
325 344 1.977854 TCTGGCTTCCTTTAGTGCTCA 59.022 47.619 0.00 0.00 0.00 4.26
326 345 2.770164 TCTGGCTTCCTTTAGTGCTC 57.230 50.000 0.00 0.00 0.00 4.26
327 346 2.639839 TCTTCTGGCTTCCTTTAGTGCT 59.360 45.455 0.00 0.00 0.00 4.40
328 347 2.744741 GTCTTCTGGCTTCCTTTAGTGC 59.255 50.000 0.00 0.00 0.00 4.40
329 348 2.996621 CGTCTTCTGGCTTCCTTTAGTG 59.003 50.000 0.00 0.00 0.00 2.74
330 349 2.897969 TCGTCTTCTGGCTTCCTTTAGT 59.102 45.455 0.00 0.00 0.00 2.24
331 350 3.056465 AGTCGTCTTCTGGCTTCCTTTAG 60.056 47.826 0.00 0.00 0.00 1.85
332 351 2.897969 AGTCGTCTTCTGGCTTCCTTTA 59.102 45.455 0.00 0.00 0.00 1.85
333 352 1.694696 AGTCGTCTTCTGGCTTCCTTT 59.305 47.619 0.00 0.00 0.00 3.11
334 353 1.001406 CAGTCGTCTTCTGGCTTCCTT 59.999 52.381 0.00 0.00 0.00 3.36
349 369 2.159707 CGCATTGACTTTAACCCAGTCG 60.160 50.000 2.24 0.00 43.26 4.18
351 371 3.134574 TCGCATTGACTTTAACCCAGT 57.865 42.857 0.00 0.00 0.00 4.00
387 421 1.492993 AAGAACAGCACCCCCTCCTC 61.493 60.000 0.00 0.00 0.00 3.71
408 442 2.618312 GAATGCGCCATGGTTGCTCC 62.618 60.000 25.10 13.93 0.00 4.70
410 444 1.252904 AAGAATGCGCCATGGTTGCT 61.253 50.000 25.10 11.31 0.00 3.91
422 456 0.313043 CATGATCCGGCCAAGAATGC 59.687 55.000 2.24 0.00 0.00 3.56
463 497 2.202987 CTCGGCCACCTCTGCATC 60.203 66.667 2.24 0.00 0.00 3.91
469 503 1.227674 CCAATAGCTCGGCCACCTC 60.228 63.158 2.24 0.00 0.00 3.85
478 512 1.287730 CTCCGATGCGCCAATAGCTC 61.288 60.000 4.18 0.00 40.39 4.09
490 524 2.289320 CCAAGATTAGAGCCCTCCGATG 60.289 54.545 0.00 0.00 0.00 3.84
493 527 0.250081 GCCAAGATTAGAGCCCTCCG 60.250 60.000 0.00 0.00 0.00 4.63
494 528 1.071542 GAGCCAAGATTAGAGCCCTCC 59.928 57.143 0.00 0.00 0.00 4.30
499 533 3.011949 CTCTCGAGCCAAGATTAGAGC 57.988 52.381 7.81 0.00 0.00 4.09
528 562 6.601741 TTTGTTTCAAGGATCACATTTTGC 57.398 33.333 0.00 0.00 0.00 3.68
534 568 6.016024 CCTGAGAATTTGTTTCAAGGATCACA 60.016 38.462 0.00 0.00 40.43 3.58
544 578 2.162408 CCGCTCCCTGAGAATTTGTTTC 59.838 50.000 0.00 0.00 34.31 2.78
553 587 0.039180 TTACTCACCGCTCCCTGAGA 59.961 55.000 1.74 0.00 37.85 3.27
559 593 2.427453 TCTTGATCTTACTCACCGCTCC 59.573 50.000 0.00 0.00 0.00 4.70
591 625 9.349713 ACTAGTTGTCCATTTGTTAAGAAATCA 57.650 29.630 7.57 1.48 0.00 2.57
599 633 6.833041 TCCTCAACTAGTTGTCCATTTGTTA 58.167 36.000 29.83 10.12 41.16 2.41
603 637 4.351111 ACCTCCTCAACTAGTTGTCCATTT 59.649 41.667 29.83 12.82 41.16 2.32
607 641 5.479124 TTAACCTCCTCAACTAGTTGTCC 57.521 43.478 29.83 0.00 41.16 4.02
608 642 6.756221 TCTTTAACCTCCTCAACTAGTTGTC 58.244 40.000 29.83 0.00 41.16 3.18
613 647 9.372369 CAGTAAATCTTTAACCTCCTCAACTAG 57.628 37.037 0.00 0.00 0.00 2.57
616 650 7.334671 CCTCAGTAAATCTTTAACCTCCTCAAC 59.665 40.741 0.00 0.00 0.00 3.18
619 653 6.948589 ACCTCAGTAAATCTTTAACCTCCTC 58.051 40.000 0.00 0.00 0.00 3.71
627 661 8.656806 TCCTGAAAAGACCTCAGTAAATCTTTA 58.343 33.333 0.00 0.00 39.81 1.85
638 672 6.494666 TTCTAAACTCCTGAAAAGACCTCA 57.505 37.500 0.00 0.00 0.00 3.86
642 676 5.639931 AGCGATTCTAAACTCCTGAAAAGAC 59.360 40.000 0.00 0.00 0.00 3.01
670 704 1.676438 TTATTCGCCGAACGTCGCAC 61.676 55.000 0.00 0.00 44.19 5.34
682 716 8.816204 AGTTAACACATTACGATTTTATTCGC 57.184 30.769 8.61 0.00 42.82 4.70
691 725 9.498176 AACCTTTTCTAGTTAACACATTACGAT 57.502 29.630 8.61 0.00 0.00 3.73
693 727 8.553696 ACAACCTTTTCTAGTTAACACATTACG 58.446 33.333 8.61 0.00 0.00 3.18
729 764 5.695851 ACATTGAGCCAAGTTTTACAGAG 57.304 39.130 0.00 0.00 0.00 3.35
731 766 7.383102 AGATACATTGAGCCAAGTTTTACAG 57.617 36.000 0.00 0.00 0.00 2.74
739 774 5.902613 TTTGGAAGATACATTGAGCCAAG 57.097 39.130 0.00 0.00 35.59 3.61
747 782 7.201644 CGAGCTAACACATTTGGAAGATACATT 60.202 37.037 0.00 0.00 0.00 2.71
764 799 3.733988 CGGTAGCAATCTTCGAGCTAACA 60.734 47.826 16.16 0.00 46.25 2.41
772 807 0.744874 TCCCTCGGTAGCAATCTTCG 59.255 55.000 0.00 0.00 0.00 3.79
774 809 0.466124 GCTCCCTCGGTAGCAATCTT 59.534 55.000 0.00 0.00 38.63 2.40
785 820 7.496529 TTATTCAAAATTCATAGCTCCCTCG 57.503 36.000 0.00 0.00 0.00 4.63
848 883 5.362556 AACGTCAGATTTTGTGAGGAATG 57.637 39.130 0.00 0.00 34.58 2.67
857 892 1.196808 CCGGTGGAACGTCAGATTTTG 59.803 52.381 0.00 0.00 38.12 2.44
950 985 3.738703 ACTGGGGGATAGGGTACTCTTAT 59.261 47.826 0.00 0.00 0.00 1.73
2007 2108 3.569701 CCACAATGTAGCTTCCTGTTTGT 59.430 43.478 0.00 0.00 0.00 2.83
2078 2179 0.690762 TAGAAAGGTCCACCCACAGC 59.309 55.000 0.00 0.00 36.42 4.40
2243 2344 5.277683 GCCTGAACAATGTATATGTGCTCAG 60.278 44.000 0.00 1.64 36.27 3.35
2277 2381 3.018856 CCTCCAAACTTGCAGCATATCA 58.981 45.455 0.00 0.00 0.00 2.15
2364 2471 6.381481 TTTGCTGCCATGTCAATCTTATAG 57.619 37.500 0.00 0.00 0.00 1.31
2409 2516 0.978151 ACAACACATGGCCATGCAAT 59.022 45.000 39.74 25.01 42.39 3.56
2573 2682 1.598701 AATTTCTTCCCTGCAGCCGC 61.599 55.000 8.66 0.00 39.24 6.53
2578 2687 0.968405 GGCACAATTTCTTCCCTGCA 59.032 50.000 0.00 0.00 0.00 4.41
2861 3261 8.088981 CAGTAACTATCTTCCTTGTACAACACT 58.911 37.037 3.59 0.00 0.00 3.55
2889 3289 5.130145 ACCTGAATATCCTGAACTTCTCTGG 59.870 44.000 0.00 0.00 43.04 3.86
2900 3300 5.980116 CGTCTCAAAGTACCTGAATATCCTG 59.020 44.000 0.00 0.00 0.00 3.86
3027 3437 5.240623 CAGTAGAAAACTTGTGTGCCCAATA 59.759 40.000 0.00 0.00 35.76 1.90
3031 3441 2.293399 CCAGTAGAAAACTTGTGTGCCC 59.707 50.000 0.00 0.00 35.76 5.36
3033 3443 5.744666 TTACCAGTAGAAAACTTGTGTGC 57.255 39.130 0.00 0.00 35.03 4.57
3054 3464 4.803329 AGGATGTCCTTATTGGCTGATT 57.197 40.909 0.00 0.00 46.09 2.57
3127 3703 7.521423 CGAACTCAACTGATATGGAAACCAAAA 60.521 37.037 0.00 0.00 36.95 2.44
3152 3749 0.601046 ACGATGATGGCAGCCATACG 60.601 55.000 29.98 29.98 45.26 3.06
3153 3750 1.151668 GACGATGATGGCAGCCATAC 58.848 55.000 27.75 19.59 45.26 2.39
3154 3751 0.758123 TGACGATGATGGCAGCCATA 59.242 50.000 27.75 15.42 45.26 2.74
3156 3753 0.107066 AATGACGATGATGGCAGCCA 60.107 50.000 18.99 18.99 38.19 4.75
3157 3754 0.309922 CAATGACGATGATGGCAGCC 59.690 55.000 3.66 3.66 0.00 4.85
3158 3755 1.019673 ACAATGACGATGATGGCAGC 58.980 50.000 0.00 0.00 0.00 5.25
3159 3756 5.237996 AGAATAACAATGACGATGATGGCAG 59.762 40.000 0.00 0.00 0.00 4.85
3160 3757 5.125356 AGAATAACAATGACGATGATGGCA 58.875 37.500 0.00 0.00 0.00 4.92
3161 3758 5.679734 AGAATAACAATGACGATGATGGC 57.320 39.130 0.00 0.00 0.00 4.40
3162 3759 6.914215 CCAAAGAATAACAATGACGATGATGG 59.086 38.462 0.00 0.00 0.00 3.51
3163 3760 7.696755 TCCAAAGAATAACAATGACGATGATG 58.303 34.615 0.00 0.00 0.00 3.07
3164 3761 7.770433 TCTCCAAAGAATAACAATGACGATGAT 59.230 33.333 0.00 0.00 0.00 2.45
3165 3762 7.102993 TCTCCAAAGAATAACAATGACGATGA 58.897 34.615 0.00 0.00 0.00 2.92
3166 3763 7.307493 TCTCCAAAGAATAACAATGACGATG 57.693 36.000 0.00 0.00 0.00 3.84
3167 3764 7.012704 CCATCTCCAAAGAATAACAATGACGAT 59.987 37.037 0.00 0.00 34.49 3.73
3168 3765 6.316140 CCATCTCCAAAGAATAACAATGACGA 59.684 38.462 0.00 0.00 34.49 4.20
3169 3766 6.316140 TCCATCTCCAAAGAATAACAATGACG 59.684 38.462 0.00 0.00 34.49 4.35
3170 3767 7.630242 TCCATCTCCAAAGAATAACAATGAC 57.370 36.000 0.00 0.00 34.49 3.06
3171 3768 8.108999 TCTTCCATCTCCAAAGAATAACAATGA 58.891 33.333 0.00 0.00 34.49 2.57
3172 3769 8.284945 TCTTCCATCTCCAAAGAATAACAATG 57.715 34.615 0.00 0.00 34.49 2.82
3301 4300 7.628769 AAAAACAAAACATGCTGAAAGGAAT 57.371 28.000 0.00 0.00 38.32 3.01
3367 4367 9.606631 TTGTAGCAAAAACCTAAAATTTGACAT 57.393 25.926 0.00 0.00 36.41 3.06
3369 4369 9.308318 TCTTGTAGCAAAAACCTAAAATTTGAC 57.692 29.630 0.00 0.00 36.41 3.18
3373 4373 9.696917 CAGATCTTGTAGCAAAAACCTAAAATT 57.303 29.630 0.00 0.00 0.00 1.82
3374 4374 7.814587 GCAGATCTTGTAGCAAAAACCTAAAAT 59.185 33.333 0.00 0.00 0.00 1.82
3406 4422 7.170393 TCTTACTCTTCATTAGTGCAGCTTA 57.830 36.000 0.00 0.00 0.00 3.09
3457 4473 8.088981 ACCATATCTTTGAATCCGTACAGATAC 58.911 37.037 0.00 0.00 0.00 2.24
3706 6226 6.943146 TGCAACATACCACTTTACAATAGGAA 59.057 34.615 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.