Multiple sequence alignment - TraesCS4D01G082600

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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 TraesCS4D01G082600 chr4D 100.000 6344 0 0 1 6344 56031159 56024816 0.000000e+00 11716.0
1 TraesCS4D01G082600 chr4A 94.005 2719 138 17 1 2699 540605549 540602836 0.000000e+00 4095.0
2 TraesCS4D01G082600 chr4A 90.204 2154 130 25 4014 6146 540601604 540599511 0.000000e+00 2734.0
3 TraesCS4D01G082600 chr4A 94.529 658 30 3 2841 3495 540602836 540602182 0.000000e+00 1011.0
4 TraesCS4D01G082600 chr4A 94.326 282 9 1 3724 4005 540601944 540601670 5.880000e-115 425.0
5 TraesCS4D01G082600 chr4A 92.818 181 8 1 3525 3700 540602109 540601929 2.270000e-64 257.0
6 TraesCS4D01G082600 chr4A 85.612 139 8 5 6217 6343 540599515 540599377 1.110000e-27 135.0
7 TraesCS4D01G082600 chr4B 91.361 2373 153 22 4007 6343 83054276 83051920 0.000000e+00 3199.0
8 TraesCS4D01G082600 chr4B 95.391 1866 79 4 1 1859 83059853 83057988 0.000000e+00 2963.0
9 TraesCS4D01G082600 chr4B 90.747 2183 133 31 1858 4011 83056468 83054326 0.000000e+00 2848.0
10 TraesCS4D01G082600 chr4B 100.000 31 0 0 3670 3700 83054627 83054597 2.470000e-04 58.4


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 TraesCS4D01G082600 chr4D 56024816 56031159 6343 True 11716.000000 11716 100.000000 1 6344 1 chr4D.!!$R1 6343
1 TraesCS4D01G082600 chr4A 540599377 540605549 6172 True 1442.833333 4095 91.915667 1 6343 6 chr4A.!!$R1 6342
2 TraesCS4D01G082600 chr4B 83051920 83059853 7933 True 2267.100000 3199 94.374750 1 6343 4 chr4B.!!$R1 6342

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
550 554 0.259356 TCGACCAGGGTTTTTGGGTT 59.741 50.000 0.0 0.00 40.11 4.11 F
2334 3872 1.000274 CGGGCACGACTGATGATGATA 60.000 52.381 0.0 0.00 44.60 2.15 F
2359 3897 0.459585 GTTGCTACCGCGGATGAAGA 60.460 55.000 35.9 10.08 39.65 2.87 F
2573 4114 0.596083 CGTATCGCCCTCAGCAAGAG 60.596 60.000 0.0 0.00 44.04 2.85 F
4316 5974 0.036164 TCACGAAACCCCATCACCAG 59.964 55.000 0.0 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2359 3897 0.032416 ACTCCCGGCACCAGTAGTAT 60.032 55.000 0.00 0.0 0.00 2.12 R
3826 5420 0.449388 GCATTGCCTCAGGAACTTCG 59.551 55.000 0.00 0.0 34.60 3.79 R
4170 5828 1.673665 GCTCAACAGCAGGTGGAGG 60.674 63.158 13.08 0.0 46.14 4.30 R
4372 6031 0.325272 TTATTGCACCACCTGCCGTA 59.675 50.000 0.00 0.0 46.51 4.02 R
6307 8014 0.108520 GCCAACACAAGGGATGCATG 60.109 55.000 2.46 0.0 0.00 4.06 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
113 115 1.333619 TGAAAGTGCACTTTTCCGCTC 59.666 47.619 37.78 26.76 45.37 5.03
129 131 1.131883 CGCTCAAAATTCTCCTGCCTG 59.868 52.381 0.00 0.00 0.00 4.85
146 148 5.415701 CCTGCCTGTGTTTGTCTACAATTAT 59.584 40.000 0.00 0.00 35.55 1.28
268 270 4.261825 GCGTTGACTGATAAGAGGAGCTAT 60.262 45.833 0.00 0.00 0.00 2.97
299 301 8.901472 AGATGTGGAGCTAGGATTACATAATA 57.099 34.615 0.00 0.00 0.00 0.98
327 329 3.047877 CCACGACCGAACAAGGGC 61.048 66.667 0.00 0.00 35.43 5.19
445 448 1.289160 TTCTAGCATTGGGTCAGGCT 58.711 50.000 0.00 0.00 40.26 4.58
509 513 2.254546 TGTCTTTCGGACTGCACAAT 57.745 45.000 0.00 0.00 44.74 2.71
516 520 1.236616 CGGACTGCACAATGAGGCAA 61.237 55.000 5.94 0.00 39.93 4.52
550 554 0.259356 TCGACCAGGGTTTTTGGGTT 59.741 50.000 0.00 0.00 40.11 4.11
562 566 2.132089 TTTGGGTTGGACTAGGGCCG 62.132 60.000 0.00 0.00 0.00 6.13
583 587 1.871039 GGTTGCGTATGTTGTGACACT 59.129 47.619 7.20 0.00 38.91 3.55
624 629 2.325583 TGCCAAGCTATTACCCGAAG 57.674 50.000 0.00 0.00 0.00 3.79
703 708 3.197265 CGGGGCATTGATTTTGATTTCC 58.803 45.455 0.00 0.00 0.00 3.13
967 972 3.244976 CACAATGGATGAAACGGCTTTC 58.755 45.455 0.00 3.44 36.97 2.62
1020 1025 3.181476 GCCTTTAAATACCGACGGTCCTA 60.181 47.826 25.58 6.62 37.09 2.94
1212 1217 5.638596 TCTACAATGTCTAAAGTCGAGCA 57.361 39.130 0.00 0.00 0.00 4.26
1347 1352 7.857456 TGGTAGTGTTGTGGTTGATTCTATAT 58.143 34.615 0.00 0.00 0.00 0.86
1615 1624 6.865411 TCCAATGGATGTTTAATGACATGTG 58.135 36.000 1.15 0.00 40.21 3.21
1673 1682 6.110411 AGTTATTGGTTTCTCTCCTTCGAA 57.890 37.500 0.00 0.00 0.00 3.71
1678 1687 2.299297 GGTTTCTCTCCTTCGAACCAGA 59.701 50.000 0.00 0.00 0.00 3.86
1680 1689 2.287977 TCTCTCCTTCGAACCAGACA 57.712 50.000 0.00 0.00 0.00 3.41
1974 3506 8.134895 TGGAACTGAACTTTACTTTTAAGCATG 58.865 33.333 0.00 0.00 0.00 4.06
2257 3795 1.943693 CACAAAACGGCCAAGTGCG 60.944 57.895 2.24 0.00 42.61 5.34
2258 3796 3.029735 CAAAACGGCCAAGTGCGC 61.030 61.111 2.24 0.00 42.61 6.09
2285 3823 2.971598 CGACCCCAGCATCCCAACT 61.972 63.158 0.00 0.00 0.00 3.16
2305 3843 6.128336 CCAACTGATGACAAAGACTTCATCTC 60.128 42.308 14.01 5.02 45.71 2.75
2312 3850 4.573900 ACAAAGACTTCATCTCGAGCAAT 58.426 39.130 7.81 0.00 36.27 3.56
2323 3861 2.514013 CGAGCAATACGGGCACGAC 61.514 63.158 19.19 0.00 45.96 4.34
2324 3862 1.153628 GAGCAATACGGGCACGACT 60.154 57.895 19.19 3.46 44.60 4.18
2334 3872 1.000274 CGGGCACGACTGATGATGATA 60.000 52.381 0.00 0.00 44.60 2.15
2359 3897 0.459585 GTTGCTACCGCGGATGAAGA 60.460 55.000 35.90 10.08 39.65 2.87
2362 3900 1.000607 TGCTACCGCGGATGAAGATAC 60.001 52.381 35.90 10.44 39.65 2.24
2436 3974 3.954904 TCACCAAATTCGGGAACTTGAAA 59.045 39.130 4.34 0.00 29.87 2.69
2573 4114 0.596083 CGTATCGCCCTCAGCAAGAG 60.596 60.000 0.00 0.00 44.04 2.85
2657 4198 5.536260 GGTACGGACCAGTCTTATTTATCC 58.464 45.833 13.46 0.00 46.12 2.59
2686 4228 7.809331 TGATGTTTACACAAGATTTGATCAAGC 59.191 33.333 8.41 5.33 36.16 4.01
2726 4268 8.894409 TTAAACGAGAAATGATGTATGCTTTG 57.106 30.769 0.00 0.00 0.00 2.77
2727 4269 6.741992 AACGAGAAATGATGTATGCTTTGA 57.258 33.333 0.00 0.00 0.00 2.69
2738 4280 7.307694 TGATGTATGCTTTGAGTTTTGACATC 58.692 34.615 0.00 0.00 40.53 3.06
2806 4348 8.943002 AGTTGGACTATATTCCTTTTGTTTACG 58.057 33.333 10.24 0.00 36.51 3.18
2807 4349 8.724229 GTTGGACTATATTCCTTTTGTTTACGT 58.276 33.333 10.24 0.00 36.51 3.57
2808 4350 9.941325 TTGGACTATATTCCTTTTGTTTACGTA 57.059 29.630 10.24 0.00 36.51 3.57
2809 4351 9.369904 TGGACTATATTCCTTTTGTTTACGTAC 57.630 33.333 10.24 0.00 36.51 3.67
2810 4352 9.591792 GGACTATATTCCTTTTGTTTACGTACT 57.408 33.333 0.00 0.00 32.24 2.73
2815 4357 7.895975 ATTCCTTTTGTTTACGTACTACTCC 57.104 36.000 0.00 0.00 0.00 3.85
2816 4358 5.460646 TCCTTTTGTTTACGTACTACTCCG 58.539 41.667 0.00 0.00 0.00 4.63
2817 4359 5.009610 TCCTTTTGTTTACGTACTACTCCGT 59.990 40.000 0.00 0.00 40.87 4.69
2818 4360 6.205853 TCCTTTTGTTTACGTACTACTCCGTA 59.794 38.462 0.00 0.00 38.43 4.02
2819 4361 6.305638 CCTTTTGTTTACGTACTACTCCGTAC 59.694 42.308 0.00 0.00 39.08 3.67
2820 4362 6.554334 TTTGTTTACGTACTACTCCGTACT 57.446 37.500 0.00 0.00 39.08 2.73
2821 4363 6.554334 TTGTTTACGTACTACTCCGTACTT 57.446 37.500 0.00 0.00 39.08 2.24
2822 4364 6.554334 TGTTTACGTACTACTCCGTACTTT 57.446 37.500 0.00 0.00 39.08 2.66
2846 4391 7.230849 TGTTTAGCACCTCAATCATGAAATT 57.769 32.000 0.00 0.00 34.49 1.82
3223 4768 2.825387 GGCTGCGCATCATCCACA 60.825 61.111 12.24 0.00 31.37 4.17
3225 4770 2.713770 CTGCGCATCATCCACAGC 59.286 61.111 12.24 0.00 0.00 4.40
3227 4772 3.945434 GCGCATCATCCACAGCCG 61.945 66.667 0.30 0.00 0.00 5.52
3496 5041 5.670792 TCATGGACGAGGTAACATAACTT 57.329 39.130 0.00 0.00 41.41 2.66
3497 5042 5.416083 TCATGGACGAGGTAACATAACTTG 58.584 41.667 0.00 0.00 41.41 3.16
3498 5043 4.877378 TGGACGAGGTAACATAACTTGT 57.123 40.909 0.00 0.00 42.76 3.16
3571 5159 1.032014 GGCAGAACTGTTGGCTTGAA 58.968 50.000 0.00 0.00 38.03 2.69
3577 5165 3.192633 AGAACTGTTGGCTTGAAACGTTT 59.807 39.130 14.57 14.57 30.28 3.60
3608 5196 2.250939 TCAAGTGTTTCCGCCAGCG 61.251 57.895 4.75 4.75 39.44 5.18
3687 5279 8.696374 TGCAAAATAGCTCTCATACTAGTAGTT 58.304 33.333 8.40 0.00 34.99 2.24
3688 5280 8.973378 GCAAAATAGCTCTCATACTAGTAGTTG 58.027 37.037 8.40 7.07 0.00 3.16
3689 5281 9.469807 CAAAATAGCTCTCATACTAGTAGTTGG 57.530 37.037 8.40 1.42 0.00 3.77
3692 5284 9.863650 AATAGCTCTCATACTAGTAGTTGGTTA 57.136 33.333 8.40 0.00 0.00 2.85
3698 5290 9.529823 TCTCATACTAGTAGTTGGTTATATGGG 57.470 37.037 8.40 4.45 0.00 4.00
3700 5292 9.305555 TCATACTAGTAGTTGGTTATATGGGTC 57.694 37.037 8.40 0.00 0.00 4.46
3703 5295 8.247666 ACTAGTAGTTGGTTATATGGGTCTTC 57.752 38.462 0.00 0.00 0.00 2.87
3704 5296 6.496144 AGTAGTTGGTTATATGGGTCTTCC 57.504 41.667 0.00 0.00 0.00 3.46
3716 5308 2.281539 GGTCTTCCCCCTTTTCGAAA 57.718 50.000 6.47 6.47 0.00 3.46
3718 5310 2.960384 GGTCTTCCCCCTTTTCGAAAAA 59.040 45.455 22.67 6.34 0.00 1.94
3826 5420 1.210155 GGGTGTCGAGTTGCAATGC 59.790 57.895 0.59 0.00 0.00 3.56
3834 5428 1.725931 CGAGTTGCAATGCGAAGTTCC 60.726 52.381 15.98 0.00 0.00 3.62
4011 5605 3.056107 TGGCTACTGCAAGGTAACTAGTG 60.056 47.826 0.00 0.00 44.27 2.74
4012 5606 3.056035 GGCTACTGCAAGGTAACTAGTGT 60.056 47.826 0.00 0.00 44.27 3.55
4034 5692 9.388506 AGTGTGAATTCTCATAATTTCTACTGG 57.611 33.333 12.95 0.00 33.05 4.00
4089 5747 8.762481 AATGGATATATCATATGCATTGTGCT 57.238 30.769 19.06 0.00 45.31 4.40
4146 5804 0.736636 TGATCGTGAACGCGGAGTAT 59.263 50.000 12.47 0.00 39.60 2.12
4183 5841 3.699894 CGCTCCTCCACCTGCTGT 61.700 66.667 0.00 0.00 0.00 4.40
4212 5870 2.967076 CACACCTTCAGCGCACGT 60.967 61.111 11.47 0.00 0.00 4.49
4316 5974 0.036164 TCACGAAACCCCATCACCAG 59.964 55.000 0.00 0.00 0.00 4.00
4318 5976 0.768622 ACGAAACCCCATCACCAGAA 59.231 50.000 0.00 0.00 0.00 3.02
4333 5991 4.913355 TCACCAGAACATCCACCCATATAT 59.087 41.667 0.00 0.00 0.00 0.86
4361 6020 1.952296 GGTCCAGATGGTCATGCAATC 59.048 52.381 0.00 0.00 36.34 2.67
4372 6031 4.283978 TGGTCATGCAATCCTGAAACATTT 59.716 37.500 0.00 0.00 0.00 2.32
4450 6109 2.292292 GAGGATGACGGAGAGCTTCTAC 59.708 54.545 0.00 0.00 0.00 2.59
4538 6215 4.648626 AGCTGGCCATGCACGTGT 62.649 61.111 23.46 0.00 0.00 4.49
4546 6223 1.577328 CCATGCACGTGTTGACTCCC 61.577 60.000 18.38 0.00 0.00 4.30
4653 6330 0.098200 TTCGACTACATCTGCGACGG 59.902 55.000 0.00 0.00 31.91 4.79
4823 6507 0.390603 TACTTCGGTCCGCATTGTGG 60.391 55.000 10.10 10.10 33.99 4.17
4828 6512 1.669760 GGTCCGCATTGTGGTCGAA 60.670 57.895 15.63 0.00 34.40 3.71
4857 6549 3.137544 TGGATATCTAACGGTTGGCCATT 59.862 43.478 6.09 0.00 34.09 3.16
5104 6797 1.000396 GCTTGATGCCAACCCCTCT 60.000 57.895 0.00 0.00 35.15 3.69
5106 6799 0.682209 CTTGATGCCAACCCCTCTGG 60.682 60.000 0.00 0.00 41.37 3.86
5119 6812 1.219124 CTCTGGTGTCGACCCCATG 59.781 63.158 20.48 13.91 42.34 3.66
5247 6940 3.136763 CCGGTTCCATCATGAAGATCAG 58.863 50.000 0.00 0.40 33.72 2.90
5250 6943 2.883386 GTTCCATCATGAAGATCAGGGC 59.117 50.000 0.00 0.00 33.72 5.19
5254 6947 1.210538 TCATGAAGATCAGGGCTGCT 58.789 50.000 0.00 0.00 0.00 4.24
5255 6948 1.140452 TCATGAAGATCAGGGCTGCTC 59.860 52.381 0.00 0.00 0.00 4.26
5303 6996 1.261619 GATGCGCCTTCTACCATTTCG 59.738 52.381 4.18 0.00 0.00 3.46
5304 6997 0.036765 TGCGCCTTCTACCATTTCGT 60.037 50.000 4.18 0.00 0.00 3.85
5305 6998 1.205179 TGCGCCTTCTACCATTTCGTA 59.795 47.619 4.18 0.00 0.00 3.43
5360 7053 8.697507 AGACTGAGAATAAATTTGTGGACTTT 57.302 30.769 0.00 0.00 0.00 2.66
5507 7200 4.744570 TCGTTAACAAAATGCCAACAACA 58.255 34.783 6.39 0.00 0.00 3.33
5610 7303 6.070995 TCCTAAAAGTATTCGAGGTGTGTCAT 60.071 38.462 0.00 0.00 0.00 3.06
5678 7371 2.044806 AAACTGTCCACTGCGAGCCT 62.045 55.000 0.00 0.00 0.00 4.58
5754 7447 1.352114 CGGTTTTGGCAGCAATGATG 58.648 50.000 0.00 0.00 0.00 3.07
5765 7458 3.583054 CAATGATGCCACCCAGAGT 57.417 52.632 0.00 0.00 0.00 3.24
5788 7481 8.664669 AGTTGTTGGGAATATTTCATTTACCT 57.335 30.769 0.00 0.00 0.00 3.08
5790 7483 8.527810 GTTGTTGGGAATATTTCATTTACCTCA 58.472 33.333 0.00 0.00 0.00 3.86
5824 7517 7.757242 ATAAGATAACCTTTGTTCCTCCTCT 57.243 36.000 0.00 0.00 36.34 3.69
5827 7520 6.503944 AGATAACCTTTGTTCCTCCTCTAGA 58.496 40.000 0.00 0.00 35.87 2.43
5851 7544 5.779771 ACCATCTCTTCTCAACTCTTCTCTT 59.220 40.000 0.00 0.00 0.00 2.85
5860 7553 3.326006 TCAACTCTTCTCTTGCATCCACT 59.674 43.478 0.00 0.00 0.00 4.00
5876 7569 6.003950 GCATCCACTATGGCCTCTAAAAATA 58.996 40.000 3.32 0.00 37.47 1.40
5955 7648 7.064609 CACGACAACAATAAGGTCTACATCAAT 59.935 37.037 0.00 0.00 0.00 2.57
6075 7769 7.785033 AGAACCACACAAAAGAAAGATCAAAT 58.215 30.769 0.00 0.00 0.00 2.32
6084 7778 9.545105 ACAAAAGAAAGATCAAATATGTGCAAA 57.455 25.926 0.00 0.00 0.00 3.68
6099 7793 9.499479 AATATGTGCAAATAAACCAACATCAAA 57.501 25.926 0.00 0.00 0.00 2.69
6119 7813 2.532843 AGGCTTCATGCATGAGGTTTT 58.467 42.857 31.90 18.83 45.15 2.43
6134 7828 5.555966 TGAGGTTTTGCTACACACATCATA 58.444 37.500 0.00 0.00 0.00 2.15
6141 7835 7.776933 TTTGCTACACACATCATATCTTCTC 57.223 36.000 0.00 0.00 0.00 2.87
6146 7840 7.175816 GCTACACACATCATATCTTCTCTCCTA 59.824 40.741 0.00 0.00 0.00 2.94
6150 7844 7.396907 CACACATCATATCTTCTCTCCTATCCT 59.603 40.741 0.00 0.00 0.00 3.24
6151 7845 7.615365 ACACATCATATCTTCTCTCCTATCCTC 59.385 40.741 0.00 0.00 0.00 3.71
6153 7847 8.401105 ACATCATATCTTCTCTCCTATCCTCTT 58.599 37.037 0.00 0.00 0.00 2.85
6155 7849 7.109501 TCATATCTTCTCTCCTATCCTCTTCG 58.890 42.308 0.00 0.00 0.00 3.79
6163 7857 4.038522 TCTCCTATCCTCTTCGAAATGCAG 59.961 45.833 0.00 0.00 0.00 4.41
6175 7869 3.502211 TCGAAATGCAGAACTTTCTTCCC 59.498 43.478 8.45 0.00 34.74 3.97
6180 7874 4.222124 TGCAGAACTTTCTTCCCCTATC 57.778 45.455 0.00 0.00 34.74 2.08
6187 7881 6.892456 AGAACTTTCTTCCCCTATCCAAAATC 59.108 38.462 0.00 0.00 32.55 2.17
6200 7894 7.315890 CCTATCCAAAATCCACAACTTTCTTC 58.684 38.462 0.00 0.00 0.00 2.87
6202 7896 4.959210 TCCAAAATCCACAACTTTCTTCCA 59.041 37.500 0.00 0.00 0.00 3.53
6203 7897 5.602145 TCCAAAATCCACAACTTTCTTCCAT 59.398 36.000 0.00 0.00 0.00 3.41
6204 7898 5.697633 CCAAAATCCACAACTTTCTTCCATG 59.302 40.000 0.00 0.00 0.00 3.66
6205 7899 6.282930 CAAAATCCACAACTTTCTTCCATGT 58.717 36.000 0.00 0.00 0.00 3.21
6206 7900 5.712152 AATCCACAACTTTCTTCCATGTC 57.288 39.130 0.00 0.00 0.00 3.06
6208 7902 3.117701 TCCACAACTTTCTTCCATGTCCA 60.118 43.478 0.00 0.00 0.00 4.02
6211 7905 5.284079 CACAACTTTCTTCCATGTCCAAAG 58.716 41.667 0.00 0.00 0.00 2.77
6225 7920 1.490490 TCCAAAGTGCACACCTTCTCT 59.510 47.619 21.04 0.00 0.00 3.10
6287 7994 0.250553 TTTGCTGGTGGAACTACCCG 60.251 55.000 4.98 0.13 40.09 5.28
6297 8004 0.679960 GAACTACCCGCAATGGCCTT 60.680 55.000 3.32 0.00 36.38 4.35
6324 8031 0.108520 GCCATGCATCCCTTGTGTTG 60.109 55.000 0.00 0.00 0.00 3.33
6333 8040 2.392662 TCCCTTGTGTTGGCAATGAAA 58.607 42.857 1.92 0.00 0.00 2.69
6343 8050 4.642437 TGTTGGCAATGAAACTACACTCAA 59.358 37.500 1.92 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 115 4.053295 CAAACACAGGCAGGAGAATTTTG 58.947 43.478 0.00 0.00 0.00 2.44
268 270 2.514160 TCCTAGCTCCACATCTACCTCA 59.486 50.000 0.00 0.00 0.00 3.86
383 385 4.160626 AGTCATAGTTGTAGGACTGAAGGC 59.839 45.833 0.00 0.00 46.18 4.35
463 466 2.229543 GTCGGGGCGGTCTTTAAATTTT 59.770 45.455 0.00 0.00 0.00 1.82
509 513 1.774217 AGGTTGGGTCCTTGCCTCA 60.774 57.895 0.00 0.00 33.52 3.86
516 520 1.155390 TCGAGTCAGGTTGGGTCCT 59.845 57.895 0.00 0.00 38.51 3.85
550 554 3.006728 CAACCCGGCCCTAGTCCA 61.007 66.667 0.00 0.00 0.00 4.02
562 566 1.069500 GTGTCACAACATACGCAACCC 60.069 52.381 0.00 0.00 37.81 4.11
583 587 7.987458 TGGCAACCATATTCTTGTTAAACAAAA 59.013 29.630 0.00 0.00 37.69 2.44
624 629 5.077134 ACCAAAGGCAAGAATATTGAAGC 57.923 39.130 0.00 0.00 0.00 3.86
682 687 3.197265 GGAAATCAAAATCAATGCCCCG 58.803 45.455 0.00 0.00 0.00 5.73
971 976 3.636381 GACCGACGGAAATGTCTATACC 58.364 50.000 23.38 0.00 36.71 2.73
1020 1025 0.969149 TCTCGTGGTGCAGATCAACT 59.031 50.000 0.00 0.00 32.28 3.16
1103 1108 0.321671 CGGGCAGTTCTTCTCCTTGA 59.678 55.000 0.00 0.00 0.00 3.02
1186 1191 6.635239 GCTCGACTTTAGACATTGTAGATCTC 59.365 42.308 0.00 0.00 0.00 2.75
1212 1217 3.966665 ACCAATTGTGTCAAAGAACCCAT 59.033 39.130 4.43 0.00 0.00 4.00
1347 1352 5.372373 TGGACACAACAACACAATCAGATA 58.628 37.500 0.00 0.00 0.00 1.98
1615 1624 8.613482 GCCTCTAAACCTTATAGATGAAAACAC 58.387 37.037 0.00 0.00 0.00 3.32
1678 1687 7.676043 ATGTGGCTACAGAGGATACTATATTGT 59.324 37.037 9.38 0.00 43.46 2.71
1680 1689 8.671987 AATGTGGCTACAGAGGATACTATATT 57.328 34.615 9.38 0.00 43.46 1.28
1779 1788 6.223120 AGTGGAAAGTTTACAAATGGAATGC 58.777 36.000 0.95 0.00 0.00 3.56
1963 3495 9.533253 CCCAAATAATTCTACCATGCTTAAAAG 57.467 33.333 0.00 0.00 0.00 2.27
1974 3506 8.691797 TGCATAAACTTCCCAAATAATTCTACC 58.308 33.333 0.00 0.00 0.00 3.18
2176 3710 5.689383 AGCATGTCAAAAACATTACGACT 57.311 34.783 0.00 0.00 46.73 4.18
2305 3843 2.202690 TCGTGCCCGTATTGCTCG 60.203 61.111 0.00 0.00 44.45 5.03
2312 3850 0.102300 CATCATCAGTCGTGCCCGTA 59.898 55.000 0.00 0.00 35.01 4.02
2323 3861 7.359849 CGGTAGCAACATCTTTATCATCATCAG 60.360 40.741 0.00 0.00 0.00 2.90
2324 3862 6.424812 CGGTAGCAACATCTTTATCATCATCA 59.575 38.462 0.00 0.00 0.00 3.07
2334 3872 0.036765 TCCGCGGTAGCAACATCTTT 60.037 50.000 27.15 0.00 45.49 2.52
2359 3897 0.032416 ACTCCCGGCACCAGTAGTAT 60.032 55.000 0.00 0.00 0.00 2.12
2362 3900 2.579201 CACTCCCGGCACCAGTAG 59.421 66.667 0.00 0.00 0.00 2.57
2414 3952 3.216187 TCAAGTTCCCGAATTTGGTGA 57.784 42.857 10.97 4.59 38.20 4.02
2416 3954 3.243267 CGTTTCAAGTTCCCGAATTTGGT 60.243 43.478 10.97 0.00 38.20 3.67
2573 4114 1.649271 AAGAGGATCCATGCCCACCC 61.649 60.000 15.82 0.00 33.66 4.61
2654 4195 8.805175 TCAAATCTTGTGTAAACATCAATGGAT 58.195 29.630 0.00 0.00 0.00 3.41
2657 4198 9.628746 TGATCAAATCTTGTGTAAACATCAATG 57.371 29.630 0.00 0.00 0.00 2.82
2714 4256 7.533426 AGATGTCAAAACTCAAAGCATACATC 58.467 34.615 0.00 0.00 40.45 3.06
2810 4352 4.281688 AGGTGCTAAACAAAGTACGGAGTA 59.718 41.667 0.00 0.00 45.11 2.59
2812 4354 3.660865 AGGTGCTAAACAAAGTACGGAG 58.339 45.455 0.00 0.00 33.37 4.63
2813 4355 3.069872 TGAGGTGCTAAACAAAGTACGGA 59.930 43.478 0.00 0.00 33.37 4.69
2814 4356 3.395639 TGAGGTGCTAAACAAAGTACGG 58.604 45.455 0.00 0.00 33.37 4.02
2815 4357 5.178623 TGATTGAGGTGCTAAACAAAGTACG 59.821 40.000 0.00 0.00 33.37 3.67
2816 4358 6.554334 TGATTGAGGTGCTAAACAAAGTAC 57.446 37.500 0.00 0.00 0.00 2.73
2817 4359 6.939730 TCATGATTGAGGTGCTAAACAAAGTA 59.060 34.615 0.00 0.00 0.00 2.24
2818 4360 5.769662 TCATGATTGAGGTGCTAAACAAAGT 59.230 36.000 0.00 0.00 0.00 2.66
2819 4361 6.258230 TCATGATTGAGGTGCTAAACAAAG 57.742 37.500 0.00 0.00 0.00 2.77
2820 4362 6.647334 TTCATGATTGAGGTGCTAAACAAA 57.353 33.333 0.00 0.00 32.27 2.83
2821 4363 6.647334 TTTCATGATTGAGGTGCTAAACAA 57.353 33.333 0.00 0.00 32.27 2.83
2822 4364 6.839124 ATTTCATGATTGAGGTGCTAAACA 57.161 33.333 0.00 0.00 32.27 2.83
2846 4391 5.586243 GCTCATTCTGGTTCTGCATTTAGTA 59.414 40.000 0.00 0.00 0.00 1.82
2903 4448 5.524284 TCGATTCTCTTCTGCTAGCATAAC 58.476 41.667 19.72 3.52 0.00 1.89
3169 4714 2.591753 ATGGTGTCCGCCATGAGG 59.408 61.111 11.44 0.00 46.63 3.86
3379 4924 1.144276 GGGAAGCTCGAGTAAGCCC 59.856 63.158 15.13 15.38 43.56 5.19
3496 5041 7.327975 AGAAGTCATATGTGAAATTACGGACA 58.672 34.615 1.90 0.00 35.80 4.02
3497 5042 7.042658 GGAGAAGTCATATGTGAAATTACGGAC 60.043 40.741 1.90 0.00 35.80 4.79
3498 5043 6.984474 GGAGAAGTCATATGTGAAATTACGGA 59.016 38.462 1.90 0.00 35.80 4.69
3608 5196 0.461339 ATACAACCGTGGCCGATGTC 60.461 55.000 0.00 0.00 36.09 3.06
3697 5289 2.281539 TTTCGAAAAGGGGGAAGACC 57.718 50.000 8.44 0.00 39.11 3.85
3718 5310 5.105917 CGCAACCCATATAACCAACTCTTTT 60.106 40.000 0.00 0.00 0.00 2.27
3720 5312 3.945285 CGCAACCCATATAACCAACTCTT 59.055 43.478 0.00 0.00 0.00 2.85
3721 5313 3.054655 ACGCAACCCATATAACCAACTCT 60.055 43.478 0.00 0.00 0.00 3.24
3722 5314 3.275999 ACGCAACCCATATAACCAACTC 58.724 45.455 0.00 0.00 0.00 3.01
3766 5360 2.067013 CTGCATTCATCTGCGATCGAT 58.933 47.619 21.57 0.00 45.30 3.59
3826 5420 0.449388 GCATTGCCTCAGGAACTTCG 59.551 55.000 0.00 0.00 34.60 3.79
4011 5605 8.213518 TGCCAGTAGAAATTATGAGAATTCAC 57.786 34.615 8.44 1.50 35.83 3.18
4012 5606 8.985315 ATGCCAGTAGAAATTATGAGAATTCA 57.015 30.769 8.44 0.00 37.81 2.57
4034 5692 6.498304 ACTATAGTTGTTTGCAGCAATATGC 58.502 36.000 9.12 0.56 46.68 3.14
4080 5738 6.824305 AGGGATTATACATAAGCACAATGC 57.176 37.500 2.62 0.00 45.46 3.56
4089 5747 5.121611 CGAATGCGCAAGGGATTATACATAA 59.878 40.000 17.11 0.00 36.75 1.90
4095 5753 1.967319 ACGAATGCGCAAGGGATTAT 58.033 45.000 17.11 0.00 42.48 1.28
4165 5823 4.463879 CAGCAGGTGGAGGAGCGG 62.464 72.222 0.00 0.00 0.00 5.52
4169 5827 2.061220 CTCAACAGCAGGTGGAGGA 58.939 57.895 4.26 0.00 42.91 3.71
4170 5828 1.673665 GCTCAACAGCAGGTGGAGG 60.674 63.158 13.08 0.00 46.14 4.30
4183 5841 1.708993 AAGGTGTGCCCTGAGCTCAA 61.709 55.000 18.85 0.00 45.47 3.02
4316 5974 6.931281 CGATCCATATATATGGGTGGATGTTC 59.069 42.308 32.33 16.35 46.88 3.18
4318 5976 5.307976 CCGATCCATATATATGGGTGGATGT 59.692 44.000 32.33 15.29 46.88 3.06
4337 5995 1.875576 GCATGACCATCTGGACCGATC 60.876 57.143 2.55 0.00 38.94 3.69
4341 5999 1.952296 GATTGCATGACCATCTGGACC 59.048 52.381 2.55 0.00 38.94 4.46
4361 6020 2.095263 CACCTGCCGTAAATGTTTCAGG 60.095 50.000 4.69 4.69 44.80 3.86
4372 6031 0.325272 TTATTGCACCACCTGCCGTA 59.675 50.000 0.00 0.00 46.51 4.02
4405 6064 2.032681 AGCTCCAGGGCGTTGTTC 59.967 61.111 0.00 0.00 37.29 3.18
4538 6215 2.922503 TGCAGCGAGGGGAGTCAA 60.923 61.111 0.00 0.00 0.00 3.18
4751 6431 3.842925 TTGCAGTGGGGCGAAGGAC 62.843 63.158 0.00 0.00 36.28 3.85
4767 6447 3.444742 TGAAGCTAGGATGCAAACCATTG 59.555 43.478 14.25 6.13 39.65 2.82
4823 6507 5.175126 CGTTAGATATCCACATTGGTTCGAC 59.825 44.000 0.00 0.00 39.03 4.20
4828 6512 5.123227 CAACCGTTAGATATCCACATTGGT 58.877 41.667 0.00 0.00 39.03 3.67
4857 6549 1.068610 CCTGCGGCAATTCGAAGAAAA 60.069 47.619 3.44 0.00 45.90 2.29
4878 6571 0.456312 GCTTCTACCACGACCACGAG 60.456 60.000 0.00 0.00 42.66 4.18
5106 6799 2.267961 GGTCCATGGGGTCGACAC 59.732 66.667 18.91 14.85 34.93 3.67
5107 6800 2.203862 TGGTCCATGGGGTCGACA 60.204 61.111 18.91 0.00 34.93 4.35
5119 6812 3.775654 CGGCTCCTCTGGTGGTCC 61.776 72.222 0.00 0.00 0.00 4.46
5247 6940 3.650298 TTGGCATGGAGAGCAGCCC 62.650 63.158 0.00 0.00 46.45 5.19
5250 6943 0.464013 CCTCTTGGCATGGAGAGCAG 60.464 60.000 16.25 0.00 38.43 4.24
5254 6947 1.965414 TAACCCTCTTGGCATGGAGA 58.035 50.000 16.25 3.75 37.83 3.71
5255 6948 2.173356 TCATAACCCTCTTGGCATGGAG 59.827 50.000 9.97 9.97 37.83 3.86
5387 7080 8.757164 CAGTTCAATGTCTACAATGTACTGTA 57.243 34.615 20.83 0.00 43.76 2.74
5388 7081 7.658179 CAGTTCAATGTCTACAATGTACTGT 57.342 36.000 20.83 0.00 43.76 3.55
5390 7083 6.147821 GTGCAGTTCAATGTCTACAATGTACT 59.852 38.462 5.03 5.03 37.71 2.73
5391 7084 6.307155 GTGCAGTTCAATGTCTACAATGTAC 58.693 40.000 0.00 1.05 30.32 2.90
5490 7183 3.936564 AGTGTGTTGTTGGCATTTTGTT 58.063 36.364 0.00 0.00 0.00 2.83
5507 7200 7.143514 ACAACAAAAATGCAATGAAAAGTGT 57.856 28.000 0.00 0.00 0.00 3.55
5578 7271 7.816031 CACCTCGAATACTTTTAGGACTTACAA 59.184 37.037 0.00 0.00 0.00 2.41
5579 7272 7.039504 ACACCTCGAATACTTTTAGGACTTACA 60.040 37.037 0.00 0.00 0.00 2.41
5610 7303 8.380099 TGCATTTTAGAACTTTTAGGACCTAGA 58.620 33.333 0.48 0.00 0.00 2.43
5678 7371 3.153919 GGACTTGGTCAGCCACAATTAA 58.846 45.455 0.14 0.00 46.01 1.40
5754 7447 3.763671 CCAACAACTCTGGGTGGC 58.236 61.111 0.00 0.00 0.00 5.01
5765 7458 8.657387 TGAGGTAAATGAAATATTCCCAACAA 57.343 30.769 0.00 0.00 0.00 2.83
5788 7481 8.902806 CAAAGGTTATCTTATAGTGCCAAATGA 58.097 33.333 0.00 0.00 34.78 2.57
5790 7483 8.823220 ACAAAGGTTATCTTATAGTGCCAAAT 57.177 30.769 0.00 0.00 34.78 2.32
5793 7486 6.826741 GGAACAAAGGTTATCTTATAGTGCCA 59.173 38.462 0.00 0.00 37.36 4.92
5824 7517 6.489603 AGAAGAGTTGAGAAGAGATGGTCTA 58.510 40.000 0.00 0.00 32.65 2.59
5827 7520 5.332743 AGAGAAGAGTTGAGAAGAGATGGT 58.667 41.667 0.00 0.00 0.00 3.55
5851 7544 2.101640 TAGAGGCCATAGTGGATGCA 57.898 50.000 5.01 0.00 40.96 3.96
5876 7569 8.905850 TGCATCTATTTGTTGTGAACATATCAT 58.094 29.630 0.00 0.00 41.79 2.45
5955 7648 7.971201 AGACCTTATTGCTCTCAATGATCATA 58.029 34.615 9.04 0.00 42.50 2.15
5986 7679 9.803315 TGTTAGAAACTAGTGTATGATCATGAC 57.197 33.333 18.72 13.90 0.00 3.06
6075 7769 7.601886 CCTTTGATGTTGGTTTATTTGCACATA 59.398 33.333 0.00 0.00 0.00 2.29
6084 7778 6.400568 CATGAAGCCTTTGATGTTGGTTTAT 58.599 36.000 0.00 0.00 0.00 1.40
6099 7793 2.226962 AAACCTCATGCATGAAGCCT 57.773 45.000 28.39 12.02 44.83 4.58
6119 7813 6.239148 GGAGAGAAGATATGATGTGTGTAGCA 60.239 42.308 0.00 0.00 0.00 3.49
6134 7828 5.576563 TCGAAGAGGATAGGAGAGAAGAT 57.423 43.478 0.00 0.00 0.00 2.40
6141 7835 4.038522 TCTGCATTTCGAAGAGGATAGGAG 59.961 45.833 0.00 0.00 38.43 3.69
6146 7840 4.213564 AGTTCTGCATTTCGAAGAGGAT 57.786 40.909 0.00 0.00 38.43 3.24
6150 7844 5.049405 GGAAGAAAGTTCTGCATTTCGAAGA 60.049 40.000 0.00 0.00 39.78 2.87
6151 7845 5.149977 GGAAGAAAGTTCTGCATTTCGAAG 58.850 41.667 0.00 0.00 39.78 3.79
6153 7847 3.502211 GGGAAGAAAGTTCTGCATTTCGA 59.498 43.478 1.48 0.00 39.78 3.71
6155 7849 3.829026 AGGGGAAGAAAGTTCTGCATTTC 59.171 43.478 1.48 2.86 37.65 2.17
6163 7857 6.096987 GGATTTTGGATAGGGGAAGAAAGTTC 59.903 42.308 0.00 0.00 0.00 3.01
6175 7869 6.840780 AGAAAGTTGTGGATTTTGGATAGG 57.159 37.500 0.00 0.00 0.00 2.57
6180 7874 5.275067 TGGAAGAAAGTTGTGGATTTTGG 57.725 39.130 0.00 0.00 0.00 3.28
6187 7881 3.221771 TGGACATGGAAGAAAGTTGTGG 58.778 45.455 0.00 0.00 0.00 4.17
6203 7897 1.064758 AGAAGGTGTGCACTTTGGACA 60.065 47.619 19.41 0.00 46.44 4.02
6204 7898 1.604278 GAGAAGGTGTGCACTTTGGAC 59.396 52.381 19.41 7.07 39.30 4.02
6205 7899 1.490490 AGAGAAGGTGTGCACTTTGGA 59.510 47.619 19.41 0.00 30.37 3.53
6206 7900 1.972872 AGAGAAGGTGTGCACTTTGG 58.027 50.000 19.41 0.00 30.37 3.28
6208 7902 2.945668 GACAAGAGAAGGTGTGCACTTT 59.054 45.455 19.41 9.83 33.06 2.66
6211 7905 1.230324 GGACAAGAGAAGGTGTGCAC 58.770 55.000 10.75 10.75 36.24 4.57
6254 7949 2.401351 CAGCAAAGAAGAAGGCAAAGC 58.599 47.619 0.00 0.00 0.00 3.51
6287 7994 2.263540 CACAGCCAAGGCCATTGC 59.736 61.111 5.01 0.00 43.17 3.56
6307 8014 0.108520 GCCAACACAAGGGATGCATG 60.109 55.000 2.46 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.