Multiple sequence alignment - TraesCS5A01G257000

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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 TraesCS5A01G257000 chr5A 100.000 5769 0 0 1 5769 472348557 472342789 0.000000e+00 10654.0
1 TraesCS5A01G257000 chr5D 94.652 4600 172 17 487 5027 369875890 369871306 0.000000e+00 7064.0
2 TraesCS5A01G257000 chr5D 82.588 626 75 13 4911 5536 369871358 369870767 6.620000e-144 521.0
3 TraesCS5A01G257000 chr5D 86.761 355 30 5 1 339 369876996 369876643 4.220000e-101 379.0
4 TraesCS5A01G257000 chr5D 81.527 406 68 5 5164 5564 505371964 505371561 1.550000e-85 327.0
5 TraesCS5A01G257000 chr5D 95.082 61 3 0 475 535 416198973 416199033 4.760000e-16 97.1
6 TraesCS5A01G257000 chr5B 93.596 4294 203 25 620 4853 439234413 439230132 0.000000e+00 6340.0
7 TraesCS5A01G257000 chr5B 82.476 953 107 35 4839 5769 439229117 439228203 0.000000e+00 780.0
8 TraesCS5A01G257000 chr5B 85.500 600 68 16 1 591 439235001 439234412 4.940000e-170 608.0
9 TraesCS5A01G257000 chr6A 82.576 396 61 5 5175 5565 199806240 199805848 5.540000e-90 342.0
10 TraesCS5A01G257000 chr6A 81.527 406 70 3 5164 5565 54372403 54372807 4.310000e-86 329.0
11 TraesCS5A01G257000 chr6A 80.941 404 68 5 5169 5565 540151355 540151756 1.560000e-80 311.0
12 TraesCS5A01G257000 chr3B 81.454 399 59 12 5177 5567 775364180 775363789 4.340000e-81 313.0
13 TraesCS5A01G257000 chr3B 81.203 399 61 10 5174 5564 582468543 582468935 5.610000e-80 309.0
14 TraesCS5A01G257000 chr7D 81.013 395 69 4 5174 5563 406805657 406806050 5.610000e-80 309.0
15 TraesCS5A01G257000 chr4D 80.392 408 72 5 5177 5581 6227015 6226613 2.610000e-78 303.0
16 TraesCS5A01G257000 chr6D 81.281 203 33 5 349 549 418463713 418463514 5.980000e-35 159.0
17 TraesCS5A01G257000 chr2D 100.000 28 0 0 683 710 17076568 17076595 1.000000e-02 52.8


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 TraesCS5A01G257000 chr5A 472342789 472348557 5768 True 10654.000000 10654 100.000000 1 5769 1 chr5A.!!$R1 5768
1 TraesCS5A01G257000 chr5D 369870767 369876996 6229 True 2654.666667 7064 88.000333 1 5536 3 chr5D.!!$R2 5535
2 TraesCS5A01G257000 chr5B 439228203 439235001 6798 True 2576.000000 6340 87.190667 1 5769 3 chr5B.!!$R1 5768

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
72 73 0.601311 GTCAAGCTCAGTGAACGCCT 60.601 55.000 0.96 0.0 0.00 5.52 F
176 179 0.810648 GGATTGCGTTCATGCCAAGA 59.189 50.000 0.00 0.0 0.00 3.02 F
582 1217 0.978907 TCTAAAAGGTGGACCCGACC 59.021 55.000 0.00 0.0 38.74 4.79 F
774 1417 1.000163 CGGTGCTCGATAGGCAGTAAT 60.000 52.381 0.00 0.0 41.68 1.89 F
2674 3354 0.398948 CCCATATGCTTGGCCCCTTT 60.399 55.000 0.00 0.0 35.29 3.11 F
4205 4930 0.399091 TGGAGAAGATGGAGGCCGAT 60.399 55.000 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 2122 1.141881 CAAGATCCGGGTCCAGACG 59.858 63.158 12.23 0.0 0.00 4.18 R
1962 2637 2.042686 TGCTCCCTTCATGAAATCCG 57.957 50.000 9.88 0.0 0.00 4.18 R
2569 3247 3.646554 CGAAGCAGCAGCAACAGA 58.353 55.556 3.17 0.0 45.49 3.41 R
2695 3375 3.181445 TGTGCACAACTAGGAACCTCATT 60.181 43.478 19.28 0.0 0.00 2.57 R
4560 5285 0.835941 AGGCTCATCCGCAGAGAAAT 59.164 50.000 0.00 0.0 40.77 2.17 R
5180 6992 0.036732 ACACGTCCACCAATGATGCT 59.963 50.000 0.00 0.0 0.00 3.79 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
64 65 1.920835 GGAGGGGGTCAAGCTCAGT 60.921 63.158 0.00 0.00 0.00 3.41
72 73 0.601311 GTCAAGCTCAGTGAACGCCT 60.601 55.000 0.96 0.00 0.00 5.52
87 88 2.464459 GCCTGTCATGGTAGTGCGC 61.464 63.158 0.00 0.00 0.00 6.09
110 113 3.155167 GCCCCGACAGGAGGTAGG 61.155 72.222 0.00 0.00 41.56 3.18
120 123 3.235200 ACAGGAGGTAGGCATGAGATAC 58.765 50.000 0.00 0.00 0.00 2.24
127 130 4.894114 AGGTAGGCATGAGATACGTAGTTT 59.106 41.667 0.08 0.00 37.78 2.66
149 152 6.683974 TTGTTGGAGAAGAAGAGAAACAAG 57.316 37.500 0.00 0.00 32.72 3.16
169 172 2.503356 AGAGAGAAGGGATTGCGTTCAT 59.497 45.455 12.21 1.68 0.00 2.57
176 179 0.810648 GGATTGCGTTCATGCCAAGA 59.189 50.000 0.00 0.00 0.00 3.02
186 191 4.681744 GTTCATGCCAAGAAAACAAGTGA 58.318 39.130 0.00 0.00 0.00 3.41
198 203 3.281727 AACAAGTGAAGGAGAGCAACA 57.718 42.857 0.00 0.00 0.00 3.33
200 205 1.876156 CAAGTGAAGGAGAGCAACACC 59.124 52.381 0.00 0.00 32.76 4.16
262 283 4.845580 CTGCGCGATCTTGCCCCT 62.846 66.667 12.10 0.00 0.00 4.79
296 317 2.202610 CGCGATCGGCAAGAGACA 60.203 61.111 18.30 0.00 43.84 3.41
335 356 5.168569 TGCAGAACGTTTACCTTCATCTAG 58.831 41.667 0.46 0.00 0.00 2.43
369 725 4.445453 AGCGAACATCATTTGATAGCAGA 58.555 39.130 0.00 0.00 32.63 4.26
397 753 1.438651 TGAGGAAAGATCAAACGGCG 58.561 50.000 4.80 4.80 0.00 6.46
399 755 1.393883 GAGGAAAGATCAAACGGCGAC 59.606 52.381 16.62 0.00 0.00 5.19
406 762 2.223377 AGATCAAACGGCGACAGTTTTC 59.777 45.455 16.62 5.68 39.50 2.29
418 774 5.456173 GGCGACAGTTTTCAAACGAAAATTA 59.544 36.000 3.89 0.00 42.66 1.40
420 776 6.195798 GCGACAGTTTTCAAACGAAAATTACT 59.804 34.615 3.89 0.00 42.66 2.24
427 783 9.002080 GTTTTCAAACGAAAATTACTTTCTCGA 57.998 29.630 13.09 0.00 42.66 4.04
436 792 8.443937 CGAAAATTACTTTCTCGAGGAAGAAAT 58.556 33.333 35.05 18.35 42.68 2.17
454 810 5.178797 AGAAATTACCATGTCGTCTGAAGG 58.821 41.667 0.00 0.00 0.00 3.46
484 1117 1.605712 CCCTCGTCACTTCCTCACAAC 60.606 57.143 0.00 0.00 0.00 3.32
518 1151 3.487376 CGAAATCGTTTGCATATGCCACT 60.487 43.478 24.54 5.87 35.83 4.00
523 1156 2.679837 CGTTTGCATATGCCACTCTCTT 59.320 45.455 24.54 0.00 41.18 2.85
547 1181 2.325761 CGAACGTTCACCAGGTAAGAG 58.674 52.381 26.71 3.27 0.00 2.85
554 1188 4.031611 GTTCACCAGGTAAGAGGGTCTAT 58.968 47.826 0.00 0.00 31.03 1.98
582 1217 0.978907 TCTAAAAGGTGGACCCGACC 59.021 55.000 0.00 0.00 38.74 4.79
605 1240 7.341805 ACCTTATAAAACTCTGCATGATCTGT 58.658 34.615 0.00 0.00 0.00 3.41
606 1241 7.281774 ACCTTATAAAACTCTGCATGATCTGTG 59.718 37.037 0.00 0.00 0.00 3.66
607 1242 7.281774 CCTTATAAAACTCTGCATGATCTGTGT 59.718 37.037 0.00 0.00 0.00 3.72
608 1243 6.674694 ATAAAACTCTGCATGATCTGTGTC 57.325 37.500 0.00 0.00 0.00 3.67
634 1269 5.749109 GTCTGGTAGAATGATGTAGAAACCG 59.251 44.000 0.00 0.00 0.00 4.44
693 1336 4.883300 CGTCTAGCCGTCGCCGTC 62.883 72.222 0.00 0.00 34.57 4.79
694 1337 4.883300 GTCTAGCCGTCGCCGTCG 62.883 72.222 0.00 0.00 34.57 5.12
725 1368 3.972276 CCTAGCTCGCGCCTCCTC 61.972 72.222 0.00 0.00 36.60 3.71
770 1413 1.299468 GACGGTGCTCGATAGGCAG 60.299 63.158 0.00 0.00 41.68 4.85
774 1417 1.000163 CGGTGCTCGATAGGCAGTAAT 60.000 52.381 0.00 0.00 41.68 1.89
775 1418 2.408050 GGTGCTCGATAGGCAGTAATG 58.592 52.381 0.00 0.00 41.68 1.90
776 1419 2.035961 GGTGCTCGATAGGCAGTAATGA 59.964 50.000 0.00 0.00 41.68 2.57
777 1420 3.492656 GGTGCTCGATAGGCAGTAATGAA 60.493 47.826 0.00 0.00 41.68 2.57
778 1421 4.310769 GTGCTCGATAGGCAGTAATGAAT 58.689 43.478 0.00 0.00 41.68 2.57
807 1450 6.978659 TCTTGGTAGATTGCGTAATCAAGTAG 59.021 38.462 25.11 15.53 44.14 2.57
957 1605 1.286260 GGTCCGAGATCGAATCCCG 59.714 63.158 3.31 0.00 43.02 5.14
963 1611 1.402984 CGAGATCGAATCCCGGGAATC 60.403 57.143 30.84 28.29 43.02 2.52
1221 1872 2.799916 GAGCACCACGACGACGAC 60.800 66.667 15.32 0.00 42.66 4.34
1284 1947 2.584694 GCTGCTAGCGCTGAGGTC 60.585 66.667 22.90 4.71 37.28 3.85
1371 2034 2.913060 GCGGCCGAGGAGGATAGT 60.913 66.667 33.48 0.00 45.00 2.12
1962 2637 4.261741 GGTGATTTGTATGCCCATGATCAC 60.262 45.833 0.00 8.94 40.49 3.06
2112 2787 7.713704 ATAATCCCCCTTCAGTTTATTCTCT 57.286 36.000 0.00 0.00 0.00 3.10
2118 2793 8.228905 TCCCCCTTCAGTTTATTCTCTTAAAAA 58.771 33.333 0.00 0.00 0.00 1.94
2159 2834 6.903883 TTGATGAGCTAACGAGTTTATTCC 57.096 37.500 0.00 0.00 0.00 3.01
2168 2843 8.421784 AGCTAACGAGTTTATTCCATTAGATCA 58.578 33.333 0.00 0.00 0.00 2.92
2367 3042 8.677300 TGGAAATAACTGAAAGCTTGATGTATC 58.323 33.333 0.00 0.00 37.60 2.24
2502 3180 5.505654 CCAAGTGTTGTGGATTCAGTAACAC 60.506 44.000 19.57 19.57 44.18 3.32
2569 3247 5.254032 AGGGAAAAGTGGTCATTCTCCTAAT 59.746 40.000 0.00 0.00 0.00 1.73
2674 3354 0.398948 CCCATATGCTTGGCCCCTTT 60.399 55.000 0.00 0.00 35.29 3.11
2695 3375 2.104622 TGATGCAGTGACTTCTTGTCCA 59.895 45.455 0.00 0.00 44.75 4.02
2737 3443 0.681175 AGTCACCTTTTGGCCATTGC 59.319 50.000 6.09 0.00 45.59 3.56
2817 3524 9.489084 AGTTGAATTTAATTTGTTAAGCCTTCC 57.511 29.630 0.00 0.00 0.00 3.46
2819 3526 7.093992 TGAATTTAATTTGTTAAGCCTTCCCG 58.906 34.615 0.00 0.00 0.00 5.14
2872 3580 2.123982 CCCTCATGGAAGCCTGGC 60.124 66.667 11.65 11.65 35.39 4.85
2886 3594 1.202580 GCCTGGCGATAGTGAGTCATT 60.203 52.381 1.35 0.00 39.35 2.57
2922 3630 6.774656 AGTTGAAATGGAAGAGAAGTTGATGT 59.225 34.615 0.00 0.00 0.00 3.06
3085 3797 1.575244 TAGCAGACATGATTGCGAGC 58.425 50.000 16.45 4.43 44.80 5.03
3140 3852 3.170672 AGGGTGTCAGCTGTGGCA 61.171 61.111 14.67 8.83 41.70 4.92
3151 3863 2.488937 CAGCTGTGGCATGAATACACAA 59.511 45.455 5.25 0.00 43.67 3.33
3155 3867 4.229096 CTGTGGCATGAATACACAACAAC 58.771 43.478 0.00 0.00 43.67 3.32
3276 3991 2.969821 TGGCAAACCTGGTGTAGAAT 57.030 45.000 0.00 0.00 36.63 2.40
3294 4009 7.485913 GTGTAGAATTTGGCTCACATTATGTTG 59.514 37.037 0.00 0.00 0.00 3.33
3440 4155 8.846943 TGTTTAACACATCAGACTATCAACAT 57.153 30.769 0.00 0.00 0.00 2.71
3516 4231 6.509418 TTAATTACTGCCATTGTGGACTTC 57.491 37.500 0.00 0.00 40.96 3.01
3657 4375 1.722011 ATTTTGTACTCCGCAGTCCG 58.278 50.000 0.00 0.00 33.62 4.79
3806 4527 0.451383 TGTTGCCGTATCATTGCAGC 59.549 50.000 0.00 0.00 36.21 5.25
3852 4573 4.549458 ACATGAAACCATCTTTTGCTTCG 58.451 39.130 0.00 0.00 0.00 3.79
3958 4683 5.455392 CAGTGACAATTCCACAGACAATTC 58.545 41.667 9.41 0.00 37.01 2.17
4205 4930 0.399091 TGGAGAAGATGGAGGCCGAT 60.399 55.000 0.00 0.00 0.00 4.18
4400 5125 1.797635 GAGTCACAGTGCAAAGAGCTC 59.202 52.381 5.27 5.27 45.94 4.09
4403 5128 1.413812 TCACAGTGCAAAGAGCTCTCA 59.586 47.619 18.55 8.22 44.72 3.27
4560 5285 8.197592 TGTACCTACTTGATGAGGTTAGAAAA 57.802 34.615 0.00 0.00 43.87 2.29
4587 5312 0.175760 GCGGATGAGCCTCTGTGTAA 59.824 55.000 0.00 0.00 0.00 2.41
4598 5323 6.595326 TGAGCCTCTGTGTAAACATTATTGAG 59.405 38.462 0.00 0.00 0.00 3.02
4813 5539 2.727123 TCTTCCCTGTTGCTGTTTGA 57.273 45.000 0.00 0.00 0.00 2.69
4816 5542 4.724399 TCTTCCCTGTTGCTGTTTGAATA 58.276 39.130 0.00 0.00 0.00 1.75
4869 6624 2.094286 TGCAATTTTTCTGGGGCATACG 60.094 45.455 0.00 0.00 0.00 3.06
4880 6635 2.237643 TGGGGCATACGTACTGAACATT 59.762 45.455 0.00 0.00 0.00 2.71
4897 6652 5.047306 TGAACATTACTGTCTCGTGGAGAAT 60.047 40.000 0.00 0.00 40.59 2.40
4946 6701 5.119743 CAGCTAAAGTCTACGTTTGGTAACC 59.880 44.000 0.00 0.00 0.00 2.85
4958 6713 4.031652 CGTTTGGTAACCGGTAAGTAATCG 59.968 45.833 8.00 8.86 0.00 3.34
4997 6752 2.185004 TCAGTTGGCAGCTAAAGTCC 57.815 50.000 2.72 0.00 0.00 3.85
5003 6758 1.019805 GGCAGCTAAAGTCCACGTCC 61.020 60.000 0.00 0.00 0.00 4.79
5004 6759 0.037232 GCAGCTAAAGTCCACGTCCT 60.037 55.000 0.00 0.00 0.00 3.85
5093 6905 2.548787 CGTTGCGACGCATGTCAA 59.451 55.556 25.09 5.00 45.80 3.18
5098 6910 1.154244 GCGACGCATGTCAATTGCA 60.154 52.632 16.42 2.71 45.80 4.08
5104 6916 3.761657 ACGCATGTCAATTGCATGTAAG 58.238 40.909 27.97 23.42 43.93 2.34
5155 6967 0.175760 GGCTTCTCTACCGTGCATGA 59.824 55.000 7.72 0.00 0.00 3.07
5166 6978 3.084039 ACCGTGCATGAATTCATTGTCT 58.916 40.909 18.41 0.00 33.61 3.41
5167 6979 3.127548 ACCGTGCATGAATTCATTGTCTC 59.872 43.478 18.41 10.14 33.61 3.36
5172 6984 4.877251 TGCATGAATTCATTGTCTCGATGA 59.123 37.500 18.41 0.00 33.61 2.92
5180 6992 5.835113 TCATTGTCTCGATGATGTGTCTA 57.165 39.130 0.00 0.00 30.18 2.59
5181 6993 5.825507 TCATTGTCTCGATGATGTGTCTAG 58.174 41.667 0.00 0.00 30.18 2.43
5182 6994 3.699779 TGTCTCGATGATGTGTCTAGC 57.300 47.619 0.00 0.00 0.00 3.42
5193 7005 2.989909 TGTGTCTAGCATCATTGGTGG 58.010 47.619 0.00 0.00 34.79 4.61
5194 7006 2.571202 TGTGTCTAGCATCATTGGTGGA 59.429 45.455 0.00 0.00 38.35 4.02
5202 7014 0.322456 ATCATTGGTGGACGTGTGGG 60.322 55.000 0.00 0.00 0.00 4.61
5204 7016 2.457323 ATTGGTGGACGTGTGGGGT 61.457 57.895 0.00 0.00 0.00 4.95
5212 7024 0.463116 GACGTGTGGGGTTGTGTCTT 60.463 55.000 0.00 0.00 0.00 3.01
5229 7041 2.097036 TCTTCGGCGGATCTGTTCTTA 58.903 47.619 7.21 0.00 0.00 2.10
5282 7097 8.564574 GTCTACATTCATGTGTTTTTAGGTTGA 58.435 33.333 2.50 0.00 41.89 3.18
5289 7104 9.528018 TTCATGTGTTTTTAGGTTGAATTCTTC 57.472 29.630 7.05 0.00 0.00 2.87
5290 7105 8.912988 TCATGTGTTTTTAGGTTGAATTCTTCT 58.087 29.630 7.05 4.29 0.00 2.85
5330 7145 4.680237 CGGCGGTTGCTGGTCTGA 62.680 66.667 0.00 0.00 44.10 3.27
5345 7160 2.035961 GGTCTGATGCGCTGGTTCTATA 59.964 50.000 9.73 0.00 0.00 1.31
5349 7164 1.618837 GATGCGCTGGTTCTATAGGGA 59.381 52.381 9.73 0.00 0.00 4.20
5357 7172 4.101119 GCTGGTTCTATAGGGACTTAGCAA 59.899 45.833 19.13 0.00 41.75 3.91
5363 7178 6.726490 TCTATAGGGACTTAGCAAAACGAT 57.274 37.500 0.00 0.00 41.75 3.73
5367 7182 5.784578 AGGGACTTAGCAAAACGATTTTT 57.215 34.783 0.00 0.00 31.37 1.94
5372 7187 6.074516 GGACTTAGCAAAACGATTTTTCAACC 60.075 38.462 0.00 0.00 32.27 3.77
5395 7210 8.836268 ACCGTCTACTACAATAAATTTTGTCA 57.164 30.769 0.00 0.00 40.25 3.58
5421 7236 1.153086 GCGAGGGAGGTGCATTGAT 60.153 57.895 0.00 0.00 0.00 2.57
5423 7238 0.816825 CGAGGGAGGTGCATTGATGG 60.817 60.000 0.00 0.00 0.00 3.51
5446 7261 1.845809 CGCGCCTTCAACTTGCTTCT 61.846 55.000 0.00 0.00 0.00 2.85
5447 7262 0.312102 GCGCCTTCAACTTGCTTCTT 59.688 50.000 0.00 0.00 0.00 2.52
5461 7276 3.202906 TGCTTCTTTGCTTGTAGTCGTT 58.797 40.909 0.00 0.00 0.00 3.85
5479 7294 1.476845 TTGCTAGGTGGTCTGCGGAA 61.477 55.000 0.00 0.00 0.00 4.30
5480 7295 1.264749 TGCTAGGTGGTCTGCGGAAT 61.265 55.000 0.00 0.00 0.00 3.01
5482 7297 1.138266 GCTAGGTGGTCTGCGGAATTA 59.862 52.381 0.00 0.00 0.00 1.40
5495 7310 7.432252 GGTCTGCGGAATTAGATGTAATTTTTG 59.568 37.037 9.06 4.33 38.70 2.44
5536 7351 5.121105 TGTACTGCCATGATTGAAGATGAG 58.879 41.667 0.00 0.00 0.00 2.90
5538 7353 4.597004 ACTGCCATGATTGAAGATGAGTT 58.403 39.130 0.00 0.00 0.00 3.01
5541 7356 6.094603 ACTGCCATGATTGAAGATGAGTTAAC 59.905 38.462 0.00 0.00 0.00 2.01
5542 7357 5.357878 TGCCATGATTGAAGATGAGTTAACC 59.642 40.000 0.88 0.00 0.00 2.85
5552 7367 7.992008 TGAAGATGAGTTAACCGAAAGTTTTT 58.008 30.769 0.88 0.00 40.05 1.94
5586 7407 9.586435 AAAATCTCGTTTCAAATGTTTTCTTCT 57.414 25.926 0.00 0.00 0.00 2.85
5641 7464 8.725212 CTTTGAAGCAAGACAGATTCTAAAAG 57.275 34.615 0.00 0.00 35.10 2.27
5642 7465 6.808008 TGAAGCAAGACAGATTCTAAAAGG 57.192 37.500 0.00 0.00 35.10 3.11
5643 7466 6.299141 TGAAGCAAGACAGATTCTAAAAGGT 58.701 36.000 0.00 0.00 35.10 3.50
5644 7467 6.428159 TGAAGCAAGACAGATTCTAAAAGGTC 59.572 38.462 0.00 0.00 35.10 3.85
5645 7468 5.869579 AGCAAGACAGATTCTAAAAGGTCA 58.130 37.500 4.50 0.00 32.51 4.02
5649 7472 7.592903 GCAAGACAGATTCTAAAAGGTCAAAAG 59.407 37.037 4.50 0.00 32.51 2.27
5651 7474 9.579932 AAGACAGATTCTAAAAGGTCAAAAGAT 57.420 29.630 4.50 0.00 32.51 2.40
5663 7487 8.465273 AAAGGTCAAAAGATAAAAGTAGCACT 57.535 30.769 0.00 0.00 0.00 4.40
5668 7492 8.940952 GTCAAAAGATAAAAGTAGCACTGATCT 58.059 33.333 0.00 0.00 29.45 2.75
5679 7503 1.881973 GCACTGATCTCAAAGCAACCA 59.118 47.619 0.00 0.00 0.00 3.67
5681 7505 2.880268 CACTGATCTCAAAGCAACCACA 59.120 45.455 0.00 0.00 0.00 4.17
5686 7510 0.588252 CTCAAAGCAACCACAGACGG 59.412 55.000 0.00 0.00 0.00 4.79
5701 7525 0.102481 GACGGTGGATCTACGCACAT 59.898 55.000 2.84 0.00 0.00 3.21
5717 7541 1.599071 CACATGATATCCCGTGCACAC 59.401 52.381 18.64 0.00 0.00 3.82
5727 7551 1.269448 CCCGTGCACACTAAAATTGCT 59.731 47.619 18.64 0.00 37.16 3.91
5741 7574 8.190784 CACTAAAATTGCTTTTCTACTATGGGG 58.809 37.037 0.00 0.00 36.09 4.96
5744 7577 7.790782 AAATTGCTTTTCTACTATGGGGAAA 57.209 32.000 0.00 0.00 0.00 3.13
5760 7593 9.804977 CTATGGGGAAAAGAGAGATAAAATCAT 57.195 33.333 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.036010 CGATGTTGCTCTCCCACCTT 60.036 55.000 0.00 0.00 0.00 3.50
64 65 0.973632 ACTACCATGACAGGCGTTCA 59.026 50.000 0.00 0.00 0.00 3.18
72 73 2.125713 CCGCGCACTACCATGACA 60.126 61.111 8.75 0.00 0.00 3.58
110 113 4.868171 TCCAACAAACTACGTATCTCATGC 59.132 41.667 0.00 0.00 0.00 4.06
120 123 5.529791 TCTCTTCTTCTCCAACAAACTACG 58.470 41.667 0.00 0.00 0.00 3.51
127 130 5.989477 TCTTGTTTCTCTTCTTCTCCAACA 58.011 37.500 0.00 0.00 0.00 3.33
149 152 2.386661 TGAACGCAATCCCTTCTCTC 57.613 50.000 0.00 0.00 0.00 3.20
169 172 3.360867 TCCTTCACTTGTTTTCTTGGCA 58.639 40.909 0.00 0.00 0.00 4.92
176 179 4.016444 TGTTGCTCTCCTTCACTTGTTTT 58.984 39.130 0.00 0.00 0.00 2.43
186 191 1.622811 CTCTCAGGTGTTGCTCTCCTT 59.377 52.381 1.51 0.00 37.88 3.36
198 203 1.826024 CCGCCTTATGCTCTCAGGT 59.174 57.895 0.00 0.00 38.05 4.00
200 205 1.953138 CGCCGCCTTATGCTCTCAG 60.953 63.158 0.00 0.00 38.05 3.35
340 361 2.642139 AATGATGTTCGCTTGCCAAG 57.358 45.000 0.00 0.00 0.00 3.61
369 725 8.893727 CCGTTTGATCTTTCCTCATAACTAAAT 58.106 33.333 0.00 0.00 0.00 1.40
377 733 2.009774 CGCCGTTTGATCTTTCCTCAT 58.990 47.619 0.00 0.00 0.00 2.90
418 774 6.110411 TGGTAATTTCTTCCTCGAGAAAGT 57.890 37.500 15.71 8.46 45.73 2.66
420 776 6.472887 ACATGGTAATTTCTTCCTCGAGAAA 58.527 36.000 15.71 7.03 46.36 2.52
427 783 5.046591 TCAGACGACATGGTAATTTCTTCCT 60.047 40.000 0.00 0.00 0.00 3.36
436 792 4.610605 TTTCCTTCAGACGACATGGTAA 57.389 40.909 0.00 0.00 0.00 2.85
454 810 1.002624 TGACGAGGGGTGGCATTTC 60.003 57.895 0.00 0.00 0.00 2.17
506 1139 2.646930 CCAAAGAGAGTGGCATATGCA 58.353 47.619 28.07 12.31 44.36 3.96
518 1151 1.214367 GTGAACGTTCGCCAAAGAGA 58.786 50.000 27.45 2.88 0.00 3.10
562 1196 1.066358 GGTCGGGTCCACCTTTTAGAG 60.066 57.143 0.00 0.00 36.97 2.43
576 1211 3.869065 TGCAGAGTTTTATAAGGTCGGG 58.131 45.455 0.00 0.00 0.00 5.14
582 1217 8.206325 ACACAGATCATGCAGAGTTTTATAAG 57.794 34.615 0.00 0.00 0.00 1.73
587 1222 4.454847 CAGACACAGATCATGCAGAGTTTT 59.545 41.667 0.00 0.00 0.00 2.43
605 1240 6.187682 TCTACATCATTCTACCAGACAGACA 58.812 40.000 0.00 0.00 0.00 3.41
606 1241 6.701145 TCTACATCATTCTACCAGACAGAC 57.299 41.667 0.00 0.00 0.00 3.51
607 1242 7.363880 GGTTTCTACATCATTCTACCAGACAGA 60.364 40.741 0.00 0.00 0.00 3.41
608 1243 6.758886 GGTTTCTACATCATTCTACCAGACAG 59.241 42.308 0.00 0.00 0.00 3.51
634 1269 2.158769 TGGTGTATGTCATGGCCTCATC 60.159 50.000 3.32 0.00 0.00 2.92
666 1303 1.664965 GGCTAGACGGCTAATGCGG 60.665 63.158 0.00 0.00 43.85 5.69
731 1374 3.151958 ATCGGGACAATCGAGCGGG 62.152 63.158 0.00 0.00 40.09 6.13
734 1377 1.661821 CGGATCGGGACAATCGAGC 60.662 63.158 0.00 0.00 41.56 5.03
770 1413 7.800380 CGCAATCTACCAAGATCAATTCATTAC 59.200 37.037 0.00 0.00 41.81 1.89
774 1417 5.185454 ACGCAATCTACCAAGATCAATTCA 58.815 37.500 0.00 0.00 41.81 2.57
775 1418 5.741388 ACGCAATCTACCAAGATCAATTC 57.259 39.130 0.00 0.00 41.81 2.17
776 1419 7.498900 TGATTACGCAATCTACCAAGATCAATT 59.501 33.333 9.69 0.00 41.81 2.32
777 1420 6.992123 TGATTACGCAATCTACCAAGATCAAT 59.008 34.615 9.69 0.00 41.81 2.57
778 1421 6.345298 TGATTACGCAATCTACCAAGATCAA 58.655 36.000 9.69 0.00 41.81 2.57
807 1450 4.057432 GCTTCTATGATGCCTGTCTTCTC 58.943 47.826 0.00 0.00 0.00 2.87
963 1611 2.294078 GGGGCTATGAGGATCGGGG 61.294 68.421 0.00 0.00 38.61 5.73
1447 2122 1.141881 CAAGATCCGGGTCCAGACG 59.858 63.158 12.23 0.00 0.00 4.18
1716 2391 4.117661 GAGCGCGAGTTCTCCGGT 62.118 66.667 12.10 12.35 38.41 5.28
1878 2553 3.118261 CCTTATAGAAACCTCCAGCTGCA 60.118 47.826 8.66 0.00 0.00 4.41
1962 2637 2.042686 TGCTCCCTTCATGAAATCCG 57.957 50.000 9.88 0.00 0.00 4.18
2145 2820 9.042008 GCTTGATCTAATGGAATAAACTCGTTA 57.958 33.333 0.00 0.00 0.00 3.18
2159 2834 5.633830 ACAAACACCTGCTTGATCTAATG 57.366 39.130 0.00 0.00 0.00 1.90
2168 2843 6.320164 TGTCAAATAGTAACAAACACCTGCTT 59.680 34.615 0.00 0.00 0.00 3.91
2215 2890 7.296098 TCTAAGGTCTAAGATGGTAAGTAGGG 58.704 42.308 0.00 0.00 0.00 3.53
2367 3042 8.224389 TGTCCCATTTATTGTTGATCACTATG 57.776 34.615 0.00 0.00 0.00 2.23
2502 3180 3.795561 ACGCTTTCTTCAGAATTGACG 57.204 42.857 0.00 0.00 33.54 4.35
2569 3247 3.646554 CGAAGCAGCAGCAACAGA 58.353 55.556 3.17 0.00 45.49 3.41
2695 3375 3.181445 TGTGCACAACTAGGAACCTCATT 60.181 43.478 19.28 0.00 0.00 2.57
2816 3523 2.547642 GCATTCAGATTCTCCTCTCGGG 60.548 54.545 0.00 0.00 0.00 5.14
2817 3524 2.364970 AGCATTCAGATTCTCCTCTCGG 59.635 50.000 0.00 0.00 0.00 4.63
2819 3526 4.669206 TCAGCATTCAGATTCTCCTCTC 57.331 45.455 0.00 0.00 0.00 3.20
2872 3580 8.634475 TCTGTTAATGAAATGACTCACTATCG 57.366 34.615 0.00 0.00 0.00 2.92
2886 3594 8.690203 TCTTCCATTTCAACTCTGTTAATGAA 57.310 30.769 0.00 0.00 32.34 2.57
2922 3630 8.239038 TGTTGATGAAACATGGGTTACTAAAA 57.761 30.769 0.00 0.00 43.96 1.52
3085 3797 6.344500 AGCATTGATGTGTCCTAACTTCTAG 58.656 40.000 0.00 0.00 0.00 2.43
3140 3852 2.227865 GCCACCGTTGTTGTGTATTCAT 59.772 45.455 0.00 0.00 31.71 2.57
3151 3863 2.030562 CTCTTCCGCCACCGTTGT 59.969 61.111 0.00 0.00 0.00 3.32
3155 3867 3.031417 ATTCCCTCTTCCGCCACCG 62.031 63.158 0.00 0.00 0.00 4.94
3276 3991 3.772387 TCCCAACATAATGTGAGCCAAA 58.228 40.909 0.00 0.00 0.00 3.28
3294 4009 3.444034 GGACTGTTTTAGCAGGATTTCCC 59.556 47.826 0.00 0.00 40.59 3.97
3338 4053 2.756840 ACACCTCGCCTTAAACCTAC 57.243 50.000 0.00 0.00 0.00 3.18
3440 4155 7.815840 TCAACTCATCAAATCACCACTTAAA 57.184 32.000 0.00 0.00 0.00 1.52
3601 4319 3.445008 AGGAGATGAAGCAGACCACTTA 58.555 45.455 0.00 0.00 0.00 2.24
3639 4357 0.947180 GCGGACTGCGGAGTACAAAA 60.947 55.000 20.15 0.00 31.52 2.44
3657 4375 7.334671 ACTGAAACTACTAGGAAATAAGCTTGC 59.665 37.037 9.86 0.00 0.00 4.01
3806 4527 6.639671 TTTCAACAAAACATTTTCGTCCAG 57.360 33.333 0.00 0.00 0.00 3.86
3958 4683 3.379372 ACTGCTCCATTCATTTTCATCGG 59.621 43.478 0.00 0.00 0.00 4.18
4082 4807 8.988064 TGAGTGTATCAAGTTCAAGTATTCTC 57.012 34.615 0.00 0.00 34.02 2.87
4133 4858 7.071321 AGGGAAAGTAGCTTGCTATTGTATAGT 59.929 37.037 5.59 0.00 0.00 2.12
4269 4994 3.679502 GTCTTCTGAGCTTCTTGAAGAGC 59.320 47.826 13.87 8.07 43.42 4.09
4400 5125 1.001406 AGGACCTCTGAAGCGTTTGAG 59.999 52.381 0.00 0.00 0.00 3.02
4403 5128 3.614399 CAGGACCTCTGAAGCGTTT 57.386 52.632 0.00 0.00 46.18 3.60
4463 5188 1.532868 CACAGCAGCACTAACTGAACC 59.467 52.381 0.00 0.00 40.25 3.62
4560 5285 0.835941 AGGCTCATCCGCAGAGAAAT 59.164 50.000 0.00 0.00 40.77 2.17
4598 5323 9.478768 GCCTAATAGATTACAGGAAGTAACTTC 57.521 37.037 0.00 0.00 44.95 3.01
4869 6624 4.857588 CCACGAGACAGTAATGTTCAGTAC 59.142 45.833 0.00 2.76 0.00 2.73
4880 6635 6.827251 ACAGTTATATTCTCCACGAGACAGTA 59.173 38.462 0.00 0.00 38.51 2.74
4897 6652 8.531146 TGTCAACTGAATCATGAGACAGTTATA 58.469 33.333 31.18 24.17 46.94 0.98
4921 6676 4.332428 ACCAAACGTAGACTTTAGCTGT 57.668 40.909 0.00 0.00 0.00 4.40
4997 6752 8.703336 CATCAATATGATTACTTACAGGACGTG 58.297 37.037 0.00 0.00 34.28 4.49
5077 6889 0.976963 CAATTGACATGCGTCGCAAC 59.023 50.000 25.66 18.00 45.80 4.17
5155 6967 6.111382 AGACACATCATCGAGACAATGAATT 58.889 36.000 0.00 0.00 36.75 2.17
5172 6984 3.200605 TCCACCAATGATGCTAGACACAT 59.799 43.478 0.00 0.00 0.00 3.21
5180 6992 0.036732 ACACGTCCACCAATGATGCT 59.963 50.000 0.00 0.00 0.00 3.79
5181 6993 0.168788 CACACGTCCACCAATGATGC 59.831 55.000 0.00 0.00 0.00 3.91
5182 6994 0.804364 CCACACGTCCACCAATGATG 59.196 55.000 0.00 0.00 0.00 3.07
5193 7005 0.463116 AAGACACAACCCCACACGTC 60.463 55.000 0.00 0.00 0.00 4.34
5194 7006 0.463116 GAAGACACAACCCCACACGT 60.463 55.000 0.00 0.00 0.00 4.49
5202 7014 1.359459 GATCCGCCGAAGACACAACC 61.359 60.000 0.00 0.00 0.00 3.77
5204 7016 0.389817 CAGATCCGCCGAAGACACAA 60.390 55.000 0.00 0.00 0.00 3.33
5212 7024 2.429250 TCATTAAGAACAGATCCGCCGA 59.571 45.455 0.00 0.00 0.00 5.54
5229 7041 3.624777 ACCAGATCCGAGCAAATTCATT 58.375 40.909 0.00 0.00 0.00 2.57
5289 7104 8.446273 CCGCCAATGAAAAATAGTATAGATCAG 58.554 37.037 0.00 0.00 0.00 2.90
5290 7105 7.094805 GCCGCCAATGAAAAATAGTATAGATCA 60.095 37.037 0.00 0.00 0.00 2.92
5297 7112 2.356382 CCGCCGCCAATGAAAAATAGTA 59.644 45.455 0.00 0.00 0.00 1.82
5298 7113 1.134175 CCGCCGCCAATGAAAAATAGT 59.866 47.619 0.00 0.00 0.00 2.12
5302 7117 0.598680 CAACCGCCGCCAATGAAAAA 60.599 50.000 0.00 0.00 0.00 1.94
5304 7119 2.647875 CAACCGCCGCCAATGAAA 59.352 55.556 0.00 0.00 0.00 2.69
5325 7140 2.231215 ATAGAACCAGCGCATCAGAC 57.769 50.000 11.47 0.00 0.00 3.51
5330 7145 1.344763 GTCCCTATAGAACCAGCGCAT 59.655 52.381 11.47 0.00 0.00 4.73
5345 7160 5.300792 TGAAAAATCGTTTTGCTAAGTCCCT 59.699 36.000 0.00 0.00 37.07 4.20
5349 7164 5.457473 CGGTTGAAAAATCGTTTTGCTAAGT 59.543 36.000 0.00 0.00 37.07 2.24
5357 7172 5.996669 AGTAGACGGTTGAAAAATCGTTT 57.003 34.783 0.00 0.00 37.92 3.60
5367 7182 9.275398 ACAAAATTTATTGTAGTAGACGGTTGA 57.725 29.630 0.00 0.00 41.56 3.18
5372 7187 7.903431 GCCTGACAAAATTTATTGTAGTAGACG 59.097 37.037 0.00 0.00 43.31 4.18
5387 7202 2.040544 CGCCGGAGCCTGACAAAAT 61.041 57.895 5.05 0.00 34.57 1.82
5436 7251 4.260784 CGACTACAAGCAAAGAAGCAAGTT 60.261 41.667 0.00 0.00 36.85 2.66
5437 7252 3.248602 CGACTACAAGCAAAGAAGCAAGT 59.751 43.478 0.00 0.00 36.85 3.16
5446 7261 3.064207 CCTAGCAACGACTACAAGCAAA 58.936 45.455 0.00 0.00 0.00 3.68
5447 7262 2.036733 ACCTAGCAACGACTACAAGCAA 59.963 45.455 0.00 0.00 0.00 3.91
5461 7276 1.264749 ATTCCGCAGACCACCTAGCA 61.265 55.000 0.00 0.00 0.00 3.49
5495 7310 8.062448 GGCAGTACAACGAATATCAGAAATAAC 58.938 37.037 0.00 0.00 0.00 1.89
5517 7332 6.459298 GGTTAACTCATCTTCAATCATGGCAG 60.459 42.308 5.42 0.00 0.00 4.85
5637 7460 8.914011 AGTGCTACTTTTATCTTTTGACCTTTT 58.086 29.630 0.00 0.00 0.00 2.27
5638 7461 8.352942 CAGTGCTACTTTTATCTTTTGACCTTT 58.647 33.333 0.00 0.00 0.00 3.11
5641 7464 7.435068 TCAGTGCTACTTTTATCTTTTGACC 57.565 36.000 0.00 0.00 0.00 4.02
5642 7465 8.940952 AGATCAGTGCTACTTTTATCTTTTGAC 58.059 33.333 0.00 0.00 0.00 3.18
5643 7466 9.155975 GAGATCAGTGCTACTTTTATCTTTTGA 57.844 33.333 0.00 0.00 0.00 2.69
5644 7467 8.939929 TGAGATCAGTGCTACTTTTATCTTTTG 58.060 33.333 0.00 0.00 0.00 2.44
5645 7468 9.507329 TTGAGATCAGTGCTACTTTTATCTTTT 57.493 29.630 0.00 0.00 0.00 2.27
5649 7472 7.065085 TGCTTTGAGATCAGTGCTACTTTTATC 59.935 37.037 0.00 0.00 0.00 1.75
5651 7474 6.230472 TGCTTTGAGATCAGTGCTACTTTTA 58.770 36.000 0.00 0.00 0.00 1.52
5655 7479 3.969287 TGCTTTGAGATCAGTGCTACT 57.031 42.857 0.00 0.00 0.00 2.57
5663 7487 3.141398 GTCTGTGGTTGCTTTGAGATCA 58.859 45.455 0.00 0.00 0.00 2.92
5668 7492 0.107410 ACCGTCTGTGGTTGCTTTGA 60.107 50.000 0.00 0.00 39.99 2.69
5679 7503 0.963856 TGCGTAGATCCACCGTCTGT 60.964 55.000 0.00 0.00 0.00 3.41
5681 7505 0.963856 TGTGCGTAGATCCACCGTCT 60.964 55.000 0.00 0.00 0.00 4.18
5686 7510 4.177026 GGATATCATGTGCGTAGATCCAC 58.823 47.826 4.83 0.00 33.12 4.02
5692 7516 2.328473 CACGGGATATCATGTGCGTAG 58.672 52.381 12.02 0.00 0.00 3.51
5695 7519 1.862123 GCACGGGATATCATGTGCG 59.138 57.895 25.94 7.38 46.80 5.34
5701 7525 3.897141 TTTAGTGTGCACGGGATATCA 57.103 42.857 13.13 0.00 36.20 2.15
5715 7539 8.190784 CCCCATAGTAGAAAAGCAATTTTAGTG 58.809 37.037 0.00 0.00 0.00 2.74
5717 7541 8.519799 TCCCCATAGTAGAAAAGCAATTTTAG 57.480 34.615 0.00 0.00 0.00 1.85
5727 7551 7.808279 TCTCTCTTTTCCCCATAGTAGAAAA 57.192 36.000 0.00 0.00 37.20 2.29


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

AutoCloner maintained by Alex Coulton.