Multiple sequence alignment - TraesCS5A01G086100

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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 TraesCS5A01G086100 chr5A 100.000 5641 0 0 1 5641 114702411 114708051 0.000000e+00 10418.0
1 TraesCS5A01G086100 chr5D 93.750 4160 154 49 708 4793 111950560 111954687 0.000000e+00 6144.0
2 TraesCS5A01G086100 chr5D 89.382 857 49 5 4792 5641 111954739 111955560 0.000000e+00 1040.0
3 TraesCS5A01G086100 chr5D 87.955 714 62 10 1 712 111949828 111950519 0.000000e+00 821.0
4 TraesCS5A01G086100 chr5B 94.380 2669 91 23 2148 4793 121001887 121004519 0.000000e+00 4043.0
5 TraesCS5A01G086100 chr5B 91.834 1298 46 28 838 2095 121000614 121001891 0.000000e+00 1755.0
6 TraesCS5A01G086100 chr5B 90.160 813 31 17 4875 5641 121004681 121005490 0.000000e+00 1013.0
7 TraesCS5A01G086100 chr5B 88.005 767 77 10 1 765 120997721 120998474 0.000000e+00 893.0
8 TraesCS5A01G086100 chr5B 96.907 97 3 0 4792 4888 121004571 121004667 4.520000e-36 163.0
9 TraesCS5A01G086100 chr5B 100.000 57 0 0 757 813 120999025 120999081 7.730000e-19 106.0
10 TraesCS5A01G086100 chr6D 87.868 577 61 6 2018 2591 447742462 447743032 0.000000e+00 669.0
11 TraesCS5A01G086100 chr7D 88.628 554 52 6 2020 2572 63618724 63619267 0.000000e+00 664.0
12 TraesCS5A01G086100 chr7D 90.064 312 29 1 2022 2333 63635205 63635514 2.450000e-108 403.0
13 TraesCS5A01G086100 chr7D 95.833 48 2 0 1566 1613 532252974 532253021 1.680000e-10 78.7
14 TraesCS5A01G086100 chr7A 87.565 579 62 6 2020 2592 66457252 66457826 0.000000e+00 662.0
15 TraesCS5A01G086100 chr7A 88.000 75 9 0 4837 4911 539512653 539512579 7.780000e-14 89.8
16 TraesCS5A01G086100 chr6B 86.689 586 56 8 2021 2591 676813526 676812948 1.030000e-176 630.0
17 TraesCS5A01G086100 chr6B 88.397 474 44 4 2018 2489 678218613 678219077 1.370000e-155 560.0
18 TraesCS5A01G086100 chr6A 88.713 505 51 4 2018 2520 594341422 594341922 3.740000e-171 612.0
19 TraesCS5A01G086100 chr6A 95.745 47 2 0 1570 1616 255186874 255186920 6.060000e-10 76.8
20 TraesCS5A01G086100 chr7B 90.698 172 14 2 2423 2592 4142481 4142652 1.580000e-55 228.0
21 TraesCS5A01G086100 chr2D 79.487 234 32 11 4905 5137 27783509 27783727 9.790000e-33 152.0
22 TraesCS5A01G086100 chr2D 91.667 60 2 2 1567 1624 99733141 99733199 4.680000e-11 80.5
23 TraesCS5A01G086100 chr1D 95.833 48 2 0 1571 1618 50709176 50709223 1.680000e-10 78.7
24 TraesCS5A01G086100 chr3D 95.652 46 2 0 1570 1615 307935898 307935853 2.180000e-09 75.0
25 TraesCS5A01G086100 chr3A 92.308 52 4 0 1563 1614 38541520 38541571 2.180000e-09 75.0
26 TraesCS5A01G086100 chr1A 93.750 48 3 0 1567 1614 181775586 181775633 7.840000e-09 73.1
27 TraesCS5A01G086100 chr3B 85.294 68 6 4 4841 4905 16211378 16211444 3.650000e-07 67.6


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 TraesCS5A01G086100 chr5A 114702411 114708051 5640 False 10418.000000 10418 100.000000 1 5641 1 chr5A.!!$F1 5640
1 TraesCS5A01G086100 chr5D 111949828 111955560 5732 False 2668.333333 6144 90.362333 1 5641 3 chr5D.!!$F1 5640
2 TraesCS5A01G086100 chr5B 120997721 121005490 7769 False 1328.833333 4043 93.547667 1 5641 6 chr5B.!!$F1 5640
3 TraesCS5A01G086100 chr6D 447742462 447743032 570 False 669.000000 669 87.868000 2018 2591 1 chr6D.!!$F1 573
4 TraesCS5A01G086100 chr7D 63618724 63619267 543 False 664.000000 664 88.628000 2020 2572 1 chr7D.!!$F1 552
5 TraesCS5A01G086100 chr7A 66457252 66457826 574 False 662.000000 662 87.565000 2020 2592 1 chr7A.!!$F1 572
6 TraesCS5A01G086100 chr6B 676812948 676813526 578 True 630.000000 630 86.689000 2021 2591 1 chr6B.!!$R1 570
7 TraesCS5A01G086100 chr6A 594341422 594341922 500 False 612.000000 612 88.713000 2018 2520 1 chr6A.!!$F2 502

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
425 429 0.321298 TAAGGCAACAGAAGTCGGGC 60.321 55.000 0.00 0.00 41.41 6.13 F
1072 3192 0.901580 CCTGGCTTGGGCACATTCTT 60.902 55.000 0.00 0.00 40.87 2.52 F
1343 3485 0.325390 CCCTACCTTTCTCTCCCCGT 60.325 60.000 0.00 0.00 0.00 5.28 F
1357 3499 0.460284 CCCCGTGTTCATCTCGAAGG 60.460 60.000 0.00 0.00 33.09 3.46 F
1373 3515 0.743345 AAGGATACGTCGGCTTTGGC 60.743 55.000 0.00 0.00 46.39 4.52 F
1437 3579 0.944999 TGGGAGGGAAGCTAGATCCT 59.055 55.000 13.02 1.77 37.14 3.24 F
1477 3619 1.004277 GTGCCCTCCATCTGTTTGGTA 59.996 52.381 0.00 0.00 38.01 3.25 F
1886 4051 1.032014 CCTAATTCATTGTGGCCCGG 58.968 55.000 0.00 0.00 0.00 5.73 F
1941 4106 1.202302 CGCGAGAGAGGCTTATTGTCA 60.202 52.381 0.00 0.00 0.00 3.58 F
2095 4264 1.556911 CAATGGTACTGAGGCCAGAGT 59.443 52.381 5.01 8.89 43.02 3.24 F
2450 4637 1.747206 GCATGATGTACCGGCTTCCTT 60.747 52.381 0.00 0.00 0.00 3.36 F
2462 4649 3.610911 CGGCTTCCTTGGACTAATTTCT 58.389 45.455 0.00 0.00 0.00 2.52 F
4454 6672 1.576356 GCCTCTGGCGATTTAGTCTG 58.424 55.000 0.00 0.00 39.62 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1334 3476 0.101399 CGAGATGAACACGGGGAGAG 59.899 60.000 0.0 0.00 0.00 3.20 R
2742 4939 0.110644 GAACGCTGAAGGCAAGAACG 60.111 55.000 0.0 0.00 41.91 3.95 R
2859 5056 4.486125 AGGGACAAACAACATTTTTGCT 57.514 36.364 0.0 0.00 37.45 3.91 R
2868 5065 4.817464 TGTACACATGTAGGGACAAACAAC 59.183 41.667 0.0 0.00 39.59 3.32 R
3371 5584 4.864247 GTCGCAACAATATCCAAGCATTTT 59.136 37.500 0.0 0.00 0.00 1.82 R
3419 5632 8.610035 GGAGTTAAGGAAATTATACAAACCTCG 58.390 37.037 0.0 0.00 0.00 4.63 R
3552 5766 4.708726 ACCTTCAGCAGTAAAATCATGC 57.291 40.909 0.0 0.00 40.29 4.06 R
3701 5916 8.167392 TCCCCATTTTAGAGATAACTGAAACAA 58.833 33.333 0.0 0.00 30.52 2.83 R
4080 6298 5.391449 GGAAACTAAAAATCGAAGGACAGC 58.609 41.667 0.0 0.00 0.00 4.40 R
4246 6464 4.350368 TGATGGTGAGCAGTCAAACTAA 57.650 40.909 0.0 0.00 33.27 2.24 R
4257 6475 0.179089 AGCGTGAGATGATGGTGAGC 60.179 55.000 0.0 0.00 0.00 4.26 R
4570 6789 1.457346 AGCCCAAAATCAGAAGCGAG 58.543 50.000 0.0 0.00 0.00 5.03 R
5507 7854 1.618447 TAGGGTGGAGCTTTCCCCC 60.618 63.158 15.2 12.23 41.95 5.40 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
26 27 9.439500 TTTGCTTGTACGTACCTTATTCTTAAT 57.561 29.630 22.43 0.00 0.00 1.40
30 31 7.775397 TGTACGTACCTTATTCTTAATTGGC 57.225 36.000 22.43 0.00 0.00 4.52
31 32 6.762661 TGTACGTACCTTATTCTTAATTGGCC 59.237 38.462 22.43 0.00 0.00 5.36
62 63 5.614324 TTTTGAGAGAGTTCTTCACTGGA 57.386 39.130 0.00 0.00 35.01 3.86
71 72 1.649321 TCTTCACTGGAGTGCTGGAT 58.351 50.000 1.63 0.00 45.25 3.41
79 80 2.437281 CTGGAGTGCTGGATGATTACCT 59.563 50.000 0.00 0.00 0.00 3.08
168 171 0.401738 AGTGCCAAGCTACATGTGGT 59.598 50.000 9.11 1.20 34.71 4.16
172 175 1.611673 GCCAAGCTACATGTGGTGACT 60.612 52.381 9.11 0.00 34.71 3.41
174 177 2.289631 CCAAGCTACATGTGGTGACTCA 60.290 50.000 9.11 0.00 38.36 3.41
182 185 2.462456 TGTGGTGACTCAGATCAAGC 57.538 50.000 0.00 0.00 0.00 4.01
205 208 5.867716 GCGAATGAGAAAACTCTAGGTTACA 59.132 40.000 0.00 0.00 37.12 2.41
212 215 5.544562 AGAAAACTCTAGGTTACAAGCCTCT 59.455 40.000 0.00 0.00 37.12 3.69
213 216 4.810191 AACTCTAGGTTACAAGCCTCTG 57.190 45.455 0.00 0.00 37.54 3.35
251 255 4.803613 CCACAAAACAAAAGAACCAGCTAC 59.196 41.667 0.00 0.00 0.00 3.58
254 258 6.912591 CACAAAACAAAAGAACCAGCTACTAG 59.087 38.462 0.00 0.00 0.00 2.57
312 316 4.654262 TGGAGACAAAGAGACCTACAAAGT 59.346 41.667 0.00 0.00 37.44 2.66
313 317 5.130477 TGGAGACAAAGAGACCTACAAAGTT 59.870 40.000 0.00 0.00 37.44 2.66
317 321 6.098409 AGACAAAGAGACCTACAAAGTTCTGA 59.902 38.462 0.00 0.00 0.00 3.27
322 326 7.540474 AGAGACCTACAAAGTTCTGATGTTA 57.460 36.000 0.00 0.00 0.00 2.41
339 343 9.612066 TCTGATGTTATACATGATAGTTTTGCA 57.388 29.630 0.00 0.00 39.27 4.08
349 353 7.605449 ACATGATAGTTTTGCAGTAAAATGCT 58.395 30.769 0.00 0.00 46.63 3.79
414 418 1.663695 TATCGGCAAGCTAAGGCAAC 58.336 50.000 12.19 0.00 41.70 4.17
420 424 1.882623 GCAAGCTAAGGCAACAGAAGT 59.117 47.619 0.00 0.00 41.70 3.01
425 429 0.321298 TAAGGCAACAGAAGTCGGGC 60.321 55.000 0.00 0.00 41.41 6.13
452 456 4.138487 ACCTCTGGGAATACAATCGAAC 57.862 45.455 0.00 0.00 36.25 3.95
466 470 4.103153 ACAATCGAACATGACCCTGGATAT 59.897 41.667 0.00 0.00 0.00 1.63
491 496 4.217767 GCATATCCTGGTCACGACATACTA 59.782 45.833 0.00 0.00 0.00 1.82
537 542 1.676678 CGGGACACTCCACCATCGAT 61.677 60.000 0.00 0.00 38.64 3.59
585 590 1.226547 GCTTCCACTCTCGAGAGCG 60.227 63.158 36.50 28.91 45.79 5.03
604 609 3.315796 CGAGCACGTTCAACCGTT 58.684 55.556 0.00 0.00 39.45 4.44
652 657 2.274437 GTGATGCATTCGAGCTCAGAA 58.726 47.619 15.40 17.37 34.99 3.02
705 710 5.831997 AGTGGACTTTGAAAAATTCCTTCG 58.168 37.500 9.63 0.00 0.00 3.79
744 795 2.613977 CGCCTTTGAGATAGCCCATAGG 60.614 54.545 0.00 0.00 35.49 2.57
818 2007 4.350368 TGCCGAATATCCATTGCTTAGA 57.650 40.909 0.00 0.00 0.00 2.10
822 2011 4.629200 CCGAATATCCATTGCTTAGAGCTC 59.371 45.833 5.27 5.27 42.97 4.09
863 2981 2.737252 GGTGTTCTGACAACGGAAGATC 59.263 50.000 0.00 0.00 41.33 2.75
1047 3167 0.957888 GTTGCCCAGCTTCTCCTCAC 60.958 60.000 0.00 0.00 0.00 3.51
1072 3192 0.901580 CCTGGCTTGGGCACATTCTT 60.902 55.000 0.00 0.00 40.87 2.52
1082 3202 1.134250 GGCACATTCTTCTCCTCCTCC 60.134 57.143 0.00 0.00 0.00 4.30
1083 3203 1.836802 GCACATTCTTCTCCTCCTCCT 59.163 52.381 0.00 0.00 0.00 3.69
1084 3204 2.158971 GCACATTCTTCTCCTCCTCCTC 60.159 54.545 0.00 0.00 0.00 3.71
1085 3205 2.433970 CACATTCTTCTCCTCCTCCTCC 59.566 54.545 0.00 0.00 0.00 4.30
1086 3206 2.317594 ACATTCTTCTCCTCCTCCTCCT 59.682 50.000 0.00 0.00 0.00 3.69
1087 3207 2.838637 TTCTTCTCCTCCTCCTCCTC 57.161 55.000 0.00 0.00 0.00 3.71
1293 3435 3.622455 CGCCTTCCTCCAAGAAAGGTAAT 60.622 47.826 2.64 0.00 35.29 1.89
1333 3475 1.274242 CCTCCCCTACACCCTACCTTT 60.274 57.143 0.00 0.00 0.00 3.11
1334 3476 2.117051 CTCCCCTACACCCTACCTTTC 58.883 57.143 0.00 0.00 0.00 2.62
1337 3479 2.292984 CCCCTACACCCTACCTTTCTCT 60.293 54.545 0.00 0.00 0.00 3.10
1340 3482 1.954035 ACACCCTACCTTTCTCTCCC 58.046 55.000 0.00 0.00 0.00 4.30
1341 3483 1.205055 CACCCTACCTTTCTCTCCCC 58.795 60.000 0.00 0.00 0.00 4.81
1343 3485 0.325390 CCCTACCTTTCTCTCCCCGT 60.325 60.000 0.00 0.00 0.00 5.28
1344 3486 0.824759 CCTACCTTTCTCTCCCCGTG 59.175 60.000 0.00 0.00 0.00 4.94
1346 3488 1.900486 CTACCTTTCTCTCCCCGTGTT 59.100 52.381 0.00 0.00 0.00 3.32
1349 3491 1.279271 CCTTTCTCTCCCCGTGTTCAT 59.721 52.381 0.00 0.00 0.00 2.57
1351 3493 1.938585 TTCTCTCCCCGTGTTCATCT 58.061 50.000 0.00 0.00 0.00 2.90
1357 3499 0.460284 CCCCGTGTTCATCTCGAAGG 60.460 60.000 0.00 0.00 33.09 3.46
1359 3501 1.137086 CCCGTGTTCATCTCGAAGGAT 59.863 52.381 0.00 0.00 33.09 3.24
1360 3502 2.361119 CCCGTGTTCATCTCGAAGGATA 59.639 50.000 0.00 0.00 33.09 2.59
1361 3503 3.372954 CCGTGTTCATCTCGAAGGATAC 58.627 50.000 0.00 0.00 33.09 2.24
1373 3515 0.743345 AAGGATACGTCGGCTTTGGC 60.743 55.000 0.00 0.00 46.39 4.52
1437 3579 0.944999 TGGGAGGGAAGCTAGATCCT 59.055 55.000 13.02 1.77 37.14 3.24
1467 3609 3.451556 CTCGCGATGTGCCCTCCAT 62.452 63.158 10.36 0.00 42.08 3.41
1477 3619 1.004277 GTGCCCTCCATCTGTTTGGTA 59.996 52.381 0.00 0.00 38.01 3.25
1478 3620 1.707989 TGCCCTCCATCTGTTTGGTAA 59.292 47.619 0.00 0.00 38.01 2.85
1534 3676 3.194755 TCTTGATCCGGAAATCGTCTCAA 59.805 43.478 9.01 11.31 36.57 3.02
1560 3702 4.798288 CGATTCGCGTCCTTACCA 57.202 55.556 5.77 0.00 34.64 3.25
1561 3703 3.267900 CGATTCGCGTCCTTACCAT 57.732 52.632 5.77 0.00 34.64 3.55
1566 3728 1.216977 CGCGTCCTTACCATCACCA 59.783 57.895 0.00 0.00 0.00 4.17
1671 3835 4.069312 TGTTAGATCCTTGTAGGGGTCA 57.931 45.455 0.00 0.00 38.88 4.02
1830 3995 2.477825 CCTACTTGTGGATGAGCATCG 58.522 52.381 4.54 0.00 38.61 3.84
1861 4026 4.184079 AGTCCAAACTATACACCGTGTC 57.816 45.455 7.63 0.00 32.59 3.67
1879 4044 4.625742 CGTGTCGAACTCCTAATTCATTGT 59.374 41.667 0.00 0.00 0.00 2.71
1883 4048 3.065371 CGAACTCCTAATTCATTGTGGCC 59.935 47.826 0.00 0.00 0.00 5.36
1884 4049 3.018423 ACTCCTAATTCATTGTGGCCC 57.982 47.619 0.00 0.00 0.00 5.80
1885 4050 1.949525 CTCCTAATTCATTGTGGCCCG 59.050 52.381 0.00 0.00 0.00 6.13
1886 4051 1.032014 CCTAATTCATTGTGGCCCGG 58.968 55.000 0.00 0.00 0.00 5.73
1941 4106 1.202302 CGCGAGAGAGGCTTATTGTCA 60.202 52.381 0.00 0.00 0.00 3.58
1995 4160 8.501580 CATGTCGAATGAACTGCTTATTATGAT 58.498 33.333 0.00 0.00 0.00 2.45
2095 4264 1.556911 CAATGGTACTGAGGCCAGAGT 59.443 52.381 5.01 8.89 43.02 3.24
2096 4265 1.958288 ATGGTACTGAGGCCAGAGTT 58.042 50.000 5.01 0.00 43.02 3.01
2336 4519 7.559533 TCTGCAGGCTTTTAAACAATCCATATA 59.440 33.333 15.13 0.00 0.00 0.86
2436 4623 7.157347 CACATGTACTATACTTCCAGCATGAT 58.843 38.462 0.00 0.00 39.69 2.45
2450 4637 1.747206 GCATGATGTACCGGCTTCCTT 60.747 52.381 0.00 0.00 0.00 3.36
2462 4649 3.610911 CGGCTTCCTTGGACTAATTTCT 58.389 45.455 0.00 0.00 0.00 2.52
2499 4686 8.463607 CCATGTACACCGTACATGTATATGATA 58.536 37.037 30.66 6.01 46.75 2.15
2626 4817 4.385825 ACAGTTCCTGCAAATAAAGTCGA 58.614 39.130 0.00 0.00 34.37 4.20
2633 4824 4.438744 CCTGCAAATAAAGTCGATGTTCCC 60.439 45.833 0.00 0.00 0.00 3.97
2677 4868 7.043565 GCCATTCCATAATGACTGATTTTGTT 58.956 34.615 0.00 0.00 44.50 2.83
2808 5005 4.863491 ACTGATTTTGTGCATCACAGTTC 58.137 39.130 0.00 0.81 45.39 3.01
2819 5016 6.986231 TGTGCATCACAGTTCGATATTTATCT 59.014 34.615 0.00 0.00 39.62 1.98
2868 5065 4.121317 TCCAGCAAGTTTCAGCAAAAATG 58.879 39.130 0.00 0.00 0.00 2.32
3250 5458 6.243900 ACATGGAGTCAACTCTTGATCATTT 58.756 36.000 9.85 0.00 42.47 2.32
3464 5678 4.065789 CTCCGCTCCTTTTTCAGTTTACT 58.934 43.478 0.00 0.00 0.00 2.24
3588 5802 6.765403 TGCTGAAGGTTGTAGTTACATTACT 58.235 36.000 0.00 0.00 35.89 2.24
3737 5952 7.690454 TCTCTAAAATGGGGAATACAGATCA 57.310 36.000 0.00 0.00 0.00 2.92
4246 6464 4.255510 ACTCAGGTAAAATGGCCATGAT 57.744 40.909 21.63 13.92 0.00 2.45
4257 6475 5.587388 AATGGCCATGATTAGTTTGACTG 57.413 39.130 21.63 0.00 0.00 3.51
4297 6515 6.816640 ACGCTCAGTATTGCTAAACTCAATTA 59.183 34.615 0.00 0.00 35.87 1.40
4454 6672 1.576356 GCCTCTGGCGATTTAGTCTG 58.424 55.000 0.00 0.00 39.62 3.51
4521 6739 4.508971 GCGTGACAGAAATGTATCAATCG 58.491 43.478 0.00 0.00 0.00 3.34
4532 6750 8.892723 AGAAATGTATCAATCGCATTCAGTTTA 58.107 29.630 0.00 0.00 32.38 2.01
4533 6751 9.669353 GAAATGTATCAATCGCATTCAGTTTAT 57.331 29.630 0.00 0.00 32.38 1.40
4534 6752 9.454585 AAATGTATCAATCGCATTCAGTTTATG 57.545 29.630 0.00 0.00 32.38 1.90
4536 6754 6.542005 TGTATCAATCGCATTCAGTTTATGGT 59.458 34.615 0.00 0.00 0.00 3.55
4537 6755 7.713073 TGTATCAATCGCATTCAGTTTATGGTA 59.287 33.333 0.00 0.00 0.00 3.25
4552 6771 9.449719 CAGTTTATGGTATTGGAACTCTAAACT 57.550 33.333 0.00 0.00 37.20 2.66
4580 6799 3.081804 TGTAGATGACACTCGCTTCTGA 58.918 45.455 0.00 0.00 31.20 3.27
4590 6809 2.027192 ACTCGCTTCTGATTTTGGGCTA 60.027 45.455 0.00 0.00 0.00 3.93
4628 6847 4.135966 CGCTTGATGAAACAAAATTTGCG 58.864 39.130 5.52 0.00 34.89 4.85
4709 6928 0.392729 AAGATGAGCTGCTCCAGTGC 60.393 55.000 25.61 10.87 33.43 4.40
4712 6931 2.033141 GAGCTGCTCCAGTGCCAA 59.967 61.111 18.80 0.00 33.43 4.52
4927 7227 4.553330 TTCTTGGACCCTGATAAGTGTC 57.447 45.455 0.00 0.00 0.00 3.67
4928 7228 2.496070 TCTTGGACCCTGATAAGTGTCG 59.504 50.000 0.00 0.00 0.00 4.35
4985 7299 8.825667 ACGTTTTTAATGGCAAGTTTAATGAT 57.174 26.923 0.00 0.00 0.00 2.45
5010 7324 3.412386 AGGATAGCAACTTTCGTGCTTT 58.588 40.909 3.99 0.00 39.79 3.51
5011 7325 4.575885 AGGATAGCAACTTTCGTGCTTTA 58.424 39.130 3.99 0.00 39.79 1.85
5012 7326 4.631813 AGGATAGCAACTTTCGTGCTTTAG 59.368 41.667 3.99 0.00 39.79 1.85
5038 7352 9.516314 GTAGTTTATTTTTGACAGAAACTTGCT 57.484 29.630 3.88 0.00 40.08 3.91
5103 7440 1.529152 GAAAAACGTTGGGGCCGGAT 61.529 55.000 5.05 0.00 0.00 4.18
5201 7538 3.056678 TGAACATGGCATGGATTTGTCAC 60.057 43.478 29.49 9.05 33.31 3.67
5317 7658 8.194769 TGTAGCGAAATCCTTTTTCTTTTCTTT 58.805 29.630 0.00 0.00 0.00 2.52
5362 7703 2.304092 TGCATCAAGAGGCCATTGATC 58.696 47.619 25.41 20.62 43.74 2.92
5385 7726 1.797025 CTCCTTCCTTTCGGTCACAC 58.203 55.000 0.00 0.00 0.00 3.82
5386 7727 1.344763 CTCCTTCCTTTCGGTCACACT 59.655 52.381 0.00 0.00 0.00 3.55
5428 7775 5.073311 TCCCTATCACACGAAAGAAGAAG 57.927 43.478 0.00 0.00 0.00 2.85
5504 7851 1.876156 CGCCCTGATCAATTTCTAGGC 59.124 52.381 0.00 0.20 33.66 3.93
5507 7854 3.397482 CCCTGATCAATTTCTAGGCGAG 58.603 50.000 0.00 0.00 0.00 5.03
5548 7895 3.059800 GTCGTGCTGTTAAGAACTCAACC 60.060 47.826 0.00 0.00 28.30 3.77
5550 7897 3.560068 CGTGCTGTTAAGAACTCAACCTT 59.440 43.478 0.00 0.00 28.30 3.50
5551 7898 4.748102 CGTGCTGTTAAGAACTCAACCTTA 59.252 41.667 0.00 0.00 28.30 2.69
5598 7945 2.661399 GCTCTGAGCAGCACCTGA 59.339 61.111 24.02 0.00 41.89 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 117 8.862085 TCCATTATGTATCCGTACAAACATCTA 58.138 33.333 0.00 0.00 43.60 1.98
168 171 3.445096 TCTCATTCGCTTGATCTGAGTCA 59.555 43.478 5.96 0.00 35.16 3.41
172 175 5.240891 AGTTTTCTCATTCGCTTGATCTGA 58.759 37.500 0.00 0.00 0.00 3.27
174 177 5.793026 GAGTTTTCTCATTCGCTTGATCT 57.207 39.130 0.00 0.00 45.53 2.75
205 208 2.614057 CGAAAGTCAAACACAGAGGCTT 59.386 45.455 0.00 0.00 0.00 4.35
212 215 0.736053 GTGGGCGAAAGTCAAACACA 59.264 50.000 0.00 0.00 37.54 3.72
213 216 0.736053 TGTGGGCGAAAGTCAAACAC 59.264 50.000 0.00 0.00 37.54 3.32
290 294 5.216614 ACTTTGTAGGTCTCTTTGTCTCC 57.783 43.478 0.00 0.00 0.00 3.71
294 298 6.235231 TCAGAACTTTGTAGGTCTCTTTGT 57.765 37.500 0.00 0.00 45.46 2.83
313 317 9.612066 TGCAAAACTATCATGTATAACATCAGA 57.388 29.630 0.00 0.00 36.53 3.27
322 326 9.520204 GCATTTTACTGCAAAACTATCATGTAT 57.480 29.630 0.00 0.00 41.87 2.29
339 343 8.644374 TTCCAAGGTTGTTATAGCATTTTACT 57.356 30.769 0.00 0.00 0.00 2.24
342 346 7.872483 CACTTTCCAAGGTTGTTATAGCATTTT 59.128 33.333 0.00 0.00 0.00 1.82
349 353 8.934023 ATCTTTCACTTTCCAAGGTTGTTATA 57.066 30.769 0.00 0.00 0.00 0.98
414 418 0.391263 GGTTACAGGCCCGACTTCTG 60.391 60.000 0.00 0.00 34.91 3.02
420 424 1.987855 CCAGAGGTTACAGGCCCGA 60.988 63.158 0.00 0.00 0.00 5.14
425 429 4.837093 TTGTATTCCCAGAGGTTACAGG 57.163 45.455 0.00 0.00 35.61 4.00
466 470 1.552792 TGTCGTGACCAGGATATGCAA 59.447 47.619 0.00 0.00 0.00 4.08
491 496 1.209747 GAATTCTAGGGAAGCGGGTGT 59.790 52.381 0.00 0.00 34.70 4.16
537 542 3.181469 GGTAGGCCACGTGAAGATCAATA 60.181 47.826 19.30 0.00 34.09 1.90
623 628 3.544684 TCGAATGCATCACAAAGGCTAT 58.455 40.909 0.00 0.00 0.00 2.97
652 657 1.835531 CCTGTTCGGGGTAGGTACATT 59.164 52.381 0.00 0.00 0.00 2.71
744 795 6.538742 TCATCAAGCTTGTTGTTACCTATAGC 59.461 38.462 28.17 0.00 31.53 2.97
745 796 8.492673 TTCATCAAGCTTGTTGTTACCTATAG 57.507 34.615 28.17 7.38 31.53 1.31
746 797 8.492673 CTTCATCAAGCTTGTTGTTACCTATA 57.507 34.615 28.17 10.90 31.53 1.31
747 798 7.383102 CTTCATCAAGCTTGTTGTTACCTAT 57.617 36.000 28.17 10.61 31.53 2.57
748 799 6.801539 CTTCATCAAGCTTGTTGTTACCTA 57.198 37.500 28.17 12.08 31.53 3.08
749 800 5.695851 CTTCATCAAGCTTGTTGTTACCT 57.304 39.130 28.17 5.07 31.53 3.08
818 2007 0.678048 GGCATCAAAAGACCCGAGCT 60.678 55.000 0.00 0.00 0.00 4.09
822 2011 2.358898 CCTAATGGCATCAAAAGACCCG 59.641 50.000 0.00 0.00 0.00 5.28
1072 3192 0.996762 GGAGGAGGAGGAGGAGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
1082 3202 2.370189 GAGAGAGAGAGAGGAGGAGGAG 59.630 59.091 0.00 0.00 0.00 3.69
1083 3203 2.022035 AGAGAGAGAGAGAGGAGGAGGA 60.022 54.545 0.00 0.00 0.00 3.71
1084 3204 2.370189 GAGAGAGAGAGAGAGGAGGAGG 59.630 59.091 0.00 0.00 0.00 4.30
1085 3205 3.312890 AGAGAGAGAGAGAGAGGAGGAG 58.687 54.545 0.00 0.00 0.00 3.69
1086 3206 3.051803 AGAGAGAGAGAGAGAGAGGAGGA 60.052 52.174 0.00 0.00 0.00 3.71
1087 3207 3.312890 AGAGAGAGAGAGAGAGAGGAGG 58.687 54.545 0.00 0.00 0.00 4.30
1333 3475 1.475403 GAGATGAACACGGGGAGAGA 58.525 55.000 0.00 0.00 0.00 3.10
1334 3476 0.101399 CGAGATGAACACGGGGAGAG 59.899 60.000 0.00 0.00 0.00 3.20
1337 3479 0.530744 CTTCGAGATGAACACGGGGA 59.469 55.000 0.00 0.00 33.71 4.81
1340 3482 2.586258 ATCCTTCGAGATGAACACGG 57.414 50.000 0.00 0.00 33.71 4.94
1341 3483 3.036633 CGTATCCTTCGAGATGAACACG 58.963 50.000 0.00 0.00 31.87 4.49
1343 3485 3.242641 CGACGTATCCTTCGAGATGAACA 60.243 47.826 0.00 0.00 37.43 3.18
1344 3486 3.289911 CGACGTATCCTTCGAGATGAAC 58.710 50.000 0.00 0.00 37.43 3.18
1346 3488 1.871676 CCGACGTATCCTTCGAGATGA 59.128 52.381 0.00 0.00 37.43 2.92
1349 3491 0.463295 AGCCGACGTATCCTTCGAGA 60.463 55.000 0.00 0.00 37.43 4.04
1351 3493 0.813184 AAAGCCGACGTATCCTTCGA 59.187 50.000 0.00 0.00 37.43 3.71
1357 3499 1.356527 AACGCCAAAGCCGACGTATC 61.357 55.000 0.00 0.00 37.87 2.24
1359 3501 2.023223 GAACGCCAAAGCCGACGTA 61.023 57.895 0.00 0.00 37.87 3.57
1360 3502 3.343421 GAACGCCAAAGCCGACGT 61.343 61.111 0.00 0.00 41.16 4.34
1361 3503 3.011760 GAGAACGCCAAAGCCGACG 62.012 63.158 0.00 0.00 34.57 5.12
1373 3515 3.467119 CGGAACACCGCGAGAACG 61.467 66.667 8.23 0.00 40.29 3.95
1467 3609 3.078837 GCTCCCGAATTTACCAAACAGA 58.921 45.455 0.00 0.00 0.00 3.41
1477 3619 1.000896 CCACCCAGCTCCCGAATTT 60.001 57.895 0.00 0.00 0.00 1.82
1478 3620 2.677228 CCACCCAGCTCCCGAATT 59.323 61.111 0.00 0.00 0.00 2.17
1512 3654 2.758423 TGAGACGATTTCCGGATCAAGA 59.242 45.455 4.15 0.00 43.93 3.02
1534 3676 2.807895 CGCGAATCGTCCCACGTT 60.808 61.111 0.00 0.00 43.14 3.99
1553 3695 3.454447 TGGAGTACATGGTGATGGTAAGG 59.546 47.826 0.00 0.00 33.39 2.69
1554 3696 4.753516 TGGAGTACATGGTGATGGTAAG 57.246 45.455 0.00 0.00 33.39 2.34
1557 3699 2.439507 GGATGGAGTACATGGTGATGGT 59.560 50.000 0.00 0.00 40.72 3.55
1558 3700 2.548707 CGGATGGAGTACATGGTGATGG 60.549 54.545 0.00 0.00 40.72 3.51
1559 3701 2.103094 ACGGATGGAGTACATGGTGATG 59.897 50.000 0.00 0.00 40.72 3.07
1560 3702 2.365617 GACGGATGGAGTACATGGTGAT 59.634 50.000 0.00 0.00 40.72 3.06
1561 3703 1.754803 GACGGATGGAGTACATGGTGA 59.245 52.381 0.00 0.00 40.72 4.02
1566 3728 2.103153 ATGGGACGGATGGAGTACAT 57.897 50.000 0.00 0.00 44.18 2.29
1609 3773 9.405587 GCTGAGATAGATCAAAAGTACTCATAC 57.594 37.037 0.00 0.00 33.71 2.39
1619 3783 5.587844 GGAGCTTTGCTGAGATAGATCAAAA 59.412 40.000 0.00 0.00 39.88 2.44
1856 4021 4.625742 ACAATGAATTAGGAGTTCGACACG 59.374 41.667 0.00 0.00 0.00 4.49
1861 4026 3.065371 GGCCACAATGAATTAGGAGTTCG 59.935 47.826 0.00 0.00 0.00 3.95
1941 4106 4.080582 TGAACCGTATCCCATGATTGAGTT 60.081 41.667 0.00 0.00 32.18 3.01
1995 4160 6.481976 ACGAATTTGGTCGAATATGCAAGATA 59.518 34.615 1.02 0.00 43.86 1.98
2336 4519 3.099141 CCAGGTTGTCCATAATTTGGCT 58.901 45.455 2.75 0.00 46.01 4.75
2421 4608 3.244215 CCGGTACATCATGCTGGAAGTAT 60.244 47.826 1.02 0.00 41.98 2.12
2436 4623 0.834687 AGTCCAAGGAAGCCGGTACA 60.835 55.000 1.90 0.00 0.00 2.90
2499 4686 7.040409 GGAAAGTGTAGATGTGGAATTGAAAGT 60.040 37.037 0.00 0.00 0.00 2.66
2626 4817 7.506938 CAGGTTCAAATATAATGGAGGGAACAT 59.493 37.037 0.00 0.00 36.13 2.71
2633 4824 6.906157 ATGGCAGGTTCAAATATAATGGAG 57.094 37.500 0.00 0.00 0.00 3.86
2731 4922 5.761234 TGAAGGCAAGAACGTACATACTTTT 59.239 36.000 0.00 0.00 0.00 2.27
2732 4923 5.302360 TGAAGGCAAGAACGTACATACTTT 58.698 37.500 0.00 0.00 0.00 2.66
2733 4924 4.890088 TGAAGGCAAGAACGTACATACTT 58.110 39.130 0.00 0.00 0.00 2.24
2734 4925 4.495422 CTGAAGGCAAGAACGTACATACT 58.505 43.478 0.00 0.00 0.00 2.12
2735 4926 3.062234 GCTGAAGGCAAGAACGTACATAC 59.938 47.826 0.00 0.00 41.35 2.39
2736 4927 3.259064 GCTGAAGGCAAGAACGTACATA 58.741 45.455 0.00 0.00 41.35 2.29
2742 4939 0.110644 GAACGCTGAAGGCAAGAACG 60.111 55.000 0.00 0.00 41.91 3.95
2859 5056 4.486125 AGGGACAAACAACATTTTTGCT 57.514 36.364 0.00 0.00 37.45 3.91
2868 5065 4.817464 TGTACACATGTAGGGACAAACAAC 59.183 41.667 0.00 0.00 39.59 3.32
3338 5551 7.189512 CAGGAATTTTCGCCTGTAATAAGAAG 58.810 38.462 0.00 0.00 45.21 2.85
3371 5584 4.864247 GTCGCAACAATATCCAAGCATTTT 59.136 37.500 0.00 0.00 0.00 1.82
3419 5632 8.610035 GGAGTTAAGGAAATTATACAAACCTCG 58.390 37.037 0.00 0.00 0.00 4.63
3552 5766 4.708726 ACCTTCAGCAGTAAAATCATGC 57.291 40.909 0.00 0.00 40.29 4.06
3701 5916 8.167392 TCCCCATTTTAGAGATAACTGAAACAA 58.833 33.333 0.00 0.00 30.52 2.83
4080 6298 5.391449 GGAAACTAAAAATCGAAGGACAGC 58.609 41.667 0.00 0.00 0.00 4.40
4246 6464 4.350368 TGATGGTGAGCAGTCAAACTAA 57.650 40.909 0.00 0.00 33.27 2.24
4257 6475 0.179089 AGCGTGAGATGATGGTGAGC 60.179 55.000 0.00 0.00 0.00 4.26
4297 6515 4.082787 CCGAGCAATTGTAACCTGACAAAT 60.083 41.667 7.40 0.00 42.39 2.32
4454 6672 1.986378 GAGCACACACACTATGACGAC 59.014 52.381 0.00 0.00 0.00 4.34
4521 6739 7.067494 AGAGTTCCAATACCATAAACTGAATGC 59.933 37.037 0.00 0.00 30.68 3.56
4532 6750 6.655003 CACACAGTTTAGAGTTCCAATACCAT 59.345 38.462 0.00 0.00 0.00 3.55
4533 6751 5.995282 CACACAGTTTAGAGTTCCAATACCA 59.005 40.000 0.00 0.00 0.00 3.25
4534 6752 5.411669 CCACACAGTTTAGAGTTCCAATACC 59.588 44.000 0.00 0.00 0.00 2.73
4536 6754 5.995282 CACCACACAGTTTAGAGTTCCAATA 59.005 40.000 0.00 0.00 0.00 1.90
4537 6755 4.821805 CACCACACAGTTTAGAGTTCCAAT 59.178 41.667 0.00 0.00 0.00 3.16
4570 6789 1.457346 AGCCCAAAATCAGAAGCGAG 58.543 50.000 0.00 0.00 0.00 5.03
4580 6799 6.664428 AAACAAGTACATGTAGCCCAAAAT 57.336 33.333 5.62 0.00 32.02 1.82
4590 6809 4.062293 TCAAGCGCTAAACAAGTACATGT 58.938 39.130 12.05 2.69 34.24 3.21
4645 6864 5.649782 ACATGCCAGAAAAGAAGGTAATG 57.350 39.130 0.00 0.00 0.00 1.90
4864 7137 7.203910 ACAACTTGATTTGCCATAAAAACGTA 58.796 30.769 0.00 0.00 0.00 3.57
4927 7227 0.933097 GTGCTCATACCTGACATGCG 59.067 55.000 0.00 0.00 0.00 4.73
4928 7228 2.028420 TGTGCTCATACCTGACATGC 57.972 50.000 0.00 0.00 0.00 4.06
4968 7282 4.440525 CCTCGCATCATTAAACTTGCCATT 60.441 41.667 0.00 0.00 0.00 3.16
4985 7299 1.067142 ACGAAAGTTGCTATCCTCGCA 60.067 47.619 0.00 0.00 46.40 5.10
5011 7325 9.516314 GCAAGTTTCTGTCAAAAATAAACTACT 57.484 29.630 0.00 0.00 38.95 2.57
5012 7326 9.516314 AGCAAGTTTCTGTCAAAAATAAACTAC 57.484 29.630 0.00 0.00 38.95 2.73
5038 7352 1.066303 GGCAAATTCCAACGACACACA 59.934 47.619 0.00 0.00 0.00 3.72
5103 7440 2.112928 ACATCAGGTGCGTGGCAA 59.887 55.556 0.00 0.00 41.47 4.52
5201 7538 5.007724 GGATGGCAATTTTCTCTAGTAACCG 59.992 44.000 0.00 0.00 0.00 4.44
5248 7586 9.202273 GTGACCATAGCAAATTGAATGTTTTTA 57.798 29.630 0.00 0.00 0.00 1.52
5317 7658 4.220724 AGCAGAATAATAGTACCCCACGA 58.779 43.478 0.00 0.00 0.00 4.35
5385 7726 3.919216 AGTCCTGAAACTCGTCATCAAG 58.081 45.455 0.00 0.00 0.00 3.02
5386 7727 3.306088 GGAGTCCTGAAACTCGTCATCAA 60.306 47.826 0.41 0.00 45.45 2.57
5428 7775 7.115378 GTCAGAAAAATGTGGTTTCATGTCATC 59.885 37.037 0.00 0.00 37.43 2.92
5478 7825 4.802051 TTGATCAGGGCGGGCTGC 62.802 66.667 10.59 10.59 45.38 5.25
5504 7851 2.269241 GTGGAGCTTTCCCCCTCG 59.731 66.667 0.00 0.00 0.00 4.63
5507 7854 1.618447 TAGGGTGGAGCTTTCCCCC 60.618 63.158 15.20 12.23 41.95 5.40
5598 7945 2.420967 GGTGTGTGTTTCTACTGGGTGT 60.421 50.000 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.