Multiple sequence alignment - TraesCS7D01G134300

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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 TraesCS7D01G134300 chr7D 100.000 6492 0 0 1 6492 85907931 85914422 0.000000e+00 11989.0
1 TraesCS7D01G134300 chr7D 96.053 76 3 0 274 349 41157603 41157528 2.460000e-24 124.0
2 TraesCS7D01G134300 chr7D 100.000 52 0 0 5961 6012 85913844 85913895 5.360000e-16 97.1
3 TraesCS7D01G134300 chr7D 100.000 52 0 0 5914 5965 85913891 85913942 5.360000e-16 97.1
4 TraesCS7D01G134300 chr7A 97.346 5200 97 18 750 5926 87304929 87310110 0.000000e+00 8800.0
5 TraesCS7D01G134300 chr7A 95.455 462 16 3 1 459 87304293 87304752 0.000000e+00 732.0
6 TraesCS7D01G134300 chr7A 91.841 527 37 2 5968 6489 87324430 87324955 0.000000e+00 730.0
7 TraesCS7D01G134300 chr7A 90.256 195 16 1 537 728 87304747 87304941 1.080000e-62 252.0
8 TraesCS7D01G134300 chr7A 93.519 108 3 2 441 545 44739955 44739849 2.420000e-34 158.0
9 TraesCS7D01G134300 chr7A 97.917 48 1 0 302 349 40549782 40549735 4.170000e-12 84.2
10 TraesCS7D01G134300 chr7B 96.389 4486 120 21 1503 5965 35081949 35086415 0.000000e+00 7348.0
11 TraesCS7D01G134300 chr7B 95.776 876 28 5 540 1410 35081071 35081942 0.000000e+00 1404.0
12 TraesCS7D01G134300 chr7B 93.258 534 30 2 5961 6489 35086364 35086896 0.000000e+00 782.0
13 TraesCS7D01G134300 chr7B 91.892 370 12 2 106 460 35080705 35081071 9.720000e-138 501.0
14 TraesCS7D01G134300 chr7B 88.182 110 9 3 1 108 35079278 35079385 1.900000e-25 128.0
15 TraesCS7D01G134300 chr3D 94.565 184 10 0 2262 2445 193390462 193390279 1.070000e-72 285.0
16 TraesCS7D01G134300 chr3D 96.970 99 2 1 449 546 427057379 427057281 1.450000e-36 165.0
17 TraesCS7D01G134300 chr3D 79.191 173 19 9 177 349 422748719 422748564 3.200000e-18 104.0
18 TraesCS7D01G134300 chrUn 93.443 183 12 0 2262 2444 189405809 189405627 8.290000e-69 272.0
19 TraesCS7D01G134300 chrUn 93.443 183 12 0 2262 2444 251410745 251410927 8.290000e-69 272.0
20 TraesCS7D01G134300 chrUn 93.443 183 12 0 2262 2444 405354558 405354376 8.290000e-69 272.0
21 TraesCS7D01G134300 chrUn 93.443 183 12 0 2262 2444 452187712 452187894 8.290000e-69 272.0
22 TraesCS7D01G134300 chr6D 93.443 183 12 0 2262 2444 124530848 124530666 8.290000e-69 272.0
23 TraesCS7D01G134300 chr6D 96.907 97 3 0 447 543 221219306 221219402 5.210000e-36 163.0
24 TraesCS7D01G134300 chr1D 93.443 183 12 0 2262 2444 141318408 141318590 8.290000e-69 272.0
25 TraesCS7D01G134300 chr4A 97.917 96 2 0 449 544 603462440 603462345 4.030000e-37 167.0
26 TraesCS7D01G134300 chr4A 94.737 76 4 0 274 349 647198759 647198834 1.140000e-22 119.0
27 TraesCS7D01G134300 chr6A 96.907 97 3 0 447 543 262052040 262052136 5.210000e-36 163.0
28 TraesCS7D01G134300 chr6A 96.000 100 4 0 446 545 563127899 563127998 5.210000e-36 163.0
29 TraesCS7D01G134300 chr5D 95.098 102 3 2 450 551 7421551 7421452 6.740000e-35 159.0
30 TraesCS7D01G134300 chr1B 95.960 99 3 1 443 541 654313672 654313575 6.740000e-35 159.0
31 TraesCS7D01G134300 chr1A 93.269 104 7 0 456 559 327008707 327008604 3.130000e-33 154.0
32 TraesCS7D01G134300 chr1A 91.228 57 4 1 280 336 335027575 335027520 6.980000e-10 76.8


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 TraesCS7D01G134300 chr7D 85907931 85914422 6491 False 4061.066667 11989 100.000000 1 6492 3 chr7D.!!$F1 6491
1 TraesCS7D01G134300 chr7A 87304293 87310110 5817 False 3261.333333 8800 94.352333 1 5926 3 chr7A.!!$F2 5925
2 TraesCS7D01G134300 chr7A 87324430 87324955 525 False 730.000000 730 91.841000 5968 6489 1 chr7A.!!$F1 521
3 TraesCS7D01G134300 chr7B 35079278 35086896 7618 False 2032.600000 7348 93.099400 1 6489 5 chr7B.!!$F1 6488

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
192 1515 0.607489 AGTTGCCGCTGATTCTGCTT 60.607 50.000 12.85 0.0 0.00 3.91 F
732 2077 1.405105 TGTGGTTTGCAACTGAGAAGC 59.595 47.619 0.00 0.0 0.00 3.86 F
733 2078 1.405105 GTGGTTTGCAACTGAGAAGCA 59.595 47.619 0.00 0.0 36.32 3.91 F
1748 3129 1.216444 GATGCTCACTGACAGCCGA 59.784 57.895 1.25 0.0 35.89 5.54 F
2122 3504 5.136828 TGTGCCTAGTTTCTCATTTCCAAA 58.863 37.500 0.00 0.0 0.00 3.28 F
3116 4503 4.399303 AGCTATACAGGCAACCATTTGAAC 59.601 41.667 0.00 0.0 34.24 3.18 F
4092 5479 9.790389 CTAACTTTTATACCAGACACTACAGAG 57.210 37.037 0.00 0.0 0.00 3.35 F
4531 5918 1.511887 CGAGCGTGCAATTTTCCCG 60.512 57.895 0.00 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1112 2491 0.172803 CAGGAGCTGCCAAAGATTGC 59.827 55.000 0.00 0.00 40.02 3.56 R
1546 2927 2.956333 GCAGAACAAACCAAAGGTAGGT 59.044 45.455 0.00 0.00 42.34 3.08 R
2122 3504 4.080695 TGAGGAGCTCAAAGTTCTGCATAT 60.081 41.667 17.19 0.00 37.57 1.78 R
2589 3976 4.207165 TCAGGTATTGAGCCATTTAAGCC 58.793 43.478 0.00 0.00 0.00 4.35 R
3321 4708 9.944376 AGCAGAAATAGAACTACAGAAACAATA 57.056 29.630 0.00 0.00 0.00 1.90 R
4531 5918 0.174617 CAGCTCCTTCGAGGAAGTCC 59.825 60.000 0.00 0.00 45.28 3.85 R
5052 6440 1.226717 CGACGGGTAAGCTCAGCTC 60.227 63.158 0.00 0.00 38.25 4.09 R
6366 7776 0.040058 TTGATGTTGGCTGCCCTCAT 59.960 50.000 17.53 19.15 32.30 2.90 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
120 1443 1.270094 CGTGGAGCTGTGGTTTAGTGA 60.270 52.381 0.00 0.00 0.00 3.41
142 1465 2.048603 GCGGCTGGGCTTCATCTTT 61.049 57.895 0.00 0.00 0.00 2.52
192 1515 0.607489 AGTTGCCGCTGATTCTGCTT 60.607 50.000 12.85 0.00 0.00 3.91
463 1804 8.667592 ACTGAAGTTCTTAATAAGTACTCCCT 57.332 34.615 11.74 0.00 38.05 4.20
464 1805 8.751242 ACTGAAGTTCTTAATAAGTACTCCCTC 58.249 37.037 11.74 7.56 38.05 4.30
466 1807 6.712179 AGTTCTTAATAAGTACTCCCTCCG 57.288 41.667 6.49 0.00 34.53 4.63
467 1808 6.193504 AGTTCTTAATAAGTACTCCCTCCGT 58.806 40.000 6.49 0.00 34.53 4.69
468 1809 7.349598 AGTTCTTAATAAGTACTCCCTCCGTA 58.650 38.462 6.49 0.00 34.53 4.02
469 1810 7.836183 AGTTCTTAATAAGTACTCCCTCCGTAA 59.164 37.037 6.49 0.00 34.53 3.18
470 1811 8.470002 GTTCTTAATAAGTACTCCCTCCGTAAA 58.530 37.037 0.00 0.00 0.00 2.01
471 1812 8.000780 TCTTAATAAGTACTCCCTCCGTAAAC 57.999 38.462 0.00 0.00 0.00 2.01
472 1813 7.836183 TCTTAATAAGTACTCCCTCCGTAAACT 59.164 37.037 0.00 0.00 0.00 2.66
473 1814 9.125026 CTTAATAAGTACTCCCTCCGTAAACTA 57.875 37.037 0.00 0.00 0.00 2.24
474 1815 7.961326 AATAAGTACTCCCTCCGTAAACTAA 57.039 36.000 0.00 0.00 0.00 2.24
475 1816 8.544687 AATAAGTACTCCCTCCGTAAACTAAT 57.455 34.615 0.00 0.00 0.00 1.73
476 1817 9.646522 AATAAGTACTCCCTCCGTAAACTAATA 57.353 33.333 0.00 0.00 0.00 0.98
477 1818 9.819754 ATAAGTACTCCCTCCGTAAACTAATAT 57.180 33.333 0.00 0.00 0.00 1.28
479 1820 9.646522 AAGTACTCCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
480 1821 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
481 1822 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
482 1823 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
483 1824 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
484 1825 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
485 1826 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
486 1827 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
487 1828 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
488 1829 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
489 1830 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
490 1831 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
504 1845 9.570488 AAGAGCGTTTAGAATACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
505 1846 8.954350 AGAGCGTTTAGAATACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
506 1847 9.733219 GAGCGTTTAGAATACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
507 1848 9.733219 AGCGTTTAGAATACTAAAGTAGTGATC 57.267 33.333 0.00 0.00 45.42 2.92
508 1849 9.733219 GCGTTTAGAATACTAAAGTAGTGATCT 57.267 33.333 0.00 4.67 45.42 2.75
537 1878 8.777578 TGCTCTTATATTAGTTTACAGAGGGA 57.222 34.615 0.00 0.00 0.00 4.20
538 1879 8.861086 TGCTCTTATATTAGTTTACAGAGGGAG 58.139 37.037 0.00 0.00 0.00 4.30
539 1880 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
546 1887 5.893897 AGTTTACAGAGGGAGTACTAACG 57.106 43.478 0.00 0.00 0.00 3.18
641 1986 8.734386 GCTCAAGTTTTCTCCCCATAATATATG 58.266 37.037 0.00 0.00 0.00 1.78
714 2059 7.497249 GGCATTTAGAATCAGTTATCTCACTGT 59.503 37.037 0.97 0.00 44.10 3.55
715 2060 8.333908 GCATTTAGAATCAGTTATCTCACTGTG 58.666 37.037 0.17 0.17 44.10 3.66
718 2063 6.365970 AGAATCAGTTATCTCACTGTGGTT 57.634 37.500 8.11 0.00 44.10 3.67
719 2064 6.773638 AGAATCAGTTATCTCACTGTGGTTT 58.226 36.000 8.11 0.00 44.10 3.27
720 2065 6.652481 AGAATCAGTTATCTCACTGTGGTTTG 59.348 38.462 8.11 0.00 44.10 2.93
721 2066 4.065088 TCAGTTATCTCACTGTGGTTTGC 58.935 43.478 8.11 0.00 44.10 3.68
722 2067 3.814842 CAGTTATCTCACTGTGGTTTGCA 59.185 43.478 8.11 0.00 39.59 4.08
723 2068 4.275689 CAGTTATCTCACTGTGGTTTGCAA 59.724 41.667 8.11 0.00 39.59 4.08
724 2069 4.275936 AGTTATCTCACTGTGGTTTGCAAC 59.724 41.667 8.11 5.59 0.00 4.17
725 2070 2.418368 TCTCACTGTGGTTTGCAACT 57.582 45.000 8.11 0.00 0.00 3.16
726 2071 2.016318 TCTCACTGTGGTTTGCAACTG 58.984 47.619 8.11 0.00 0.00 3.16
727 2072 2.016318 CTCACTGTGGTTTGCAACTGA 58.984 47.619 8.11 0.00 0.00 3.41
728 2073 2.016318 TCACTGTGGTTTGCAACTGAG 58.984 47.619 8.11 0.00 0.00 3.35
729 2074 2.016318 CACTGTGGTTTGCAACTGAGA 58.984 47.619 0.00 0.00 0.00 3.27
730 2075 2.423185 CACTGTGGTTTGCAACTGAGAA 59.577 45.455 0.00 0.00 0.00 2.87
731 2076 2.684881 ACTGTGGTTTGCAACTGAGAAG 59.315 45.455 0.00 0.00 0.00 2.85
732 2077 1.405105 TGTGGTTTGCAACTGAGAAGC 59.595 47.619 0.00 0.00 0.00 3.86
733 2078 1.405105 GTGGTTTGCAACTGAGAAGCA 59.595 47.619 0.00 0.00 36.32 3.91
734 2079 2.098614 TGGTTTGCAACTGAGAAGCAA 58.901 42.857 0.00 11.05 45.53 3.91
735 2080 2.694628 TGGTTTGCAACTGAGAAGCAAT 59.305 40.909 14.60 0.00 46.32 3.56
736 2081 3.243501 TGGTTTGCAACTGAGAAGCAATC 60.244 43.478 14.60 13.52 46.32 2.67
737 2082 3.243501 GGTTTGCAACTGAGAAGCAATCA 60.244 43.478 14.60 1.84 46.32 2.57
738 2083 4.362279 GTTTGCAACTGAGAAGCAATCAA 58.638 39.130 14.60 1.26 46.32 2.57
739 2084 3.909776 TGCAACTGAGAAGCAATCAAG 57.090 42.857 1.52 0.00 34.97 3.02
740 2085 3.479489 TGCAACTGAGAAGCAATCAAGA 58.521 40.909 1.52 0.00 34.97 3.02
741 2086 4.077108 TGCAACTGAGAAGCAATCAAGAT 58.923 39.130 1.52 0.00 34.97 2.40
742 2087 4.082949 TGCAACTGAGAAGCAATCAAGATG 60.083 41.667 1.52 0.00 34.97 2.90
743 2088 4.155462 GCAACTGAGAAGCAATCAAGATGA 59.845 41.667 0.00 0.00 0.00 2.92
744 2089 5.163642 GCAACTGAGAAGCAATCAAGATGAT 60.164 40.000 0.00 0.00 39.09 2.45
917 2296 1.554160 CCTCTGCTGGTCTTCTCATGT 59.446 52.381 0.00 0.00 0.00 3.21
1035 2414 2.093658 TCGAGCAGTGTTTCTATTCCCC 60.094 50.000 0.00 0.00 0.00 4.81
1112 2491 4.099419 GGATTAGTTTTATTGGGGTGCCTG 59.901 45.833 0.00 0.00 0.00 4.85
1363 2743 5.818678 TTGCCATAGTAATCCTACGGAAT 57.181 39.130 0.00 0.00 30.18 3.01
1364 2744 5.147330 TGCCATAGTAATCCTACGGAATG 57.853 43.478 0.00 0.00 30.18 2.67
1397 2777 8.877864 TGTAATTGGGGCATAAAAGGATATAG 57.122 34.615 0.00 0.00 0.00 1.31
1483 2863 5.594926 AGAAAATTTGCAGTTCTGTTCCAG 58.405 37.500 0.00 0.00 30.48 3.86
1485 2865 4.574599 AATTTGCAGTTCTGTTCCAGAC 57.425 40.909 1.78 0.00 40.46 3.51
1562 2943 3.945640 AGTGACCTACCTTTGGTTTGT 57.054 42.857 0.00 0.00 38.03 2.83
1689 3070 8.079203 TCGTAATACTGCAAACAAAATGACATT 58.921 29.630 0.00 0.00 0.00 2.71
1748 3129 1.216444 GATGCTCACTGACAGCCGA 59.784 57.895 1.25 0.00 35.89 5.54
1919 3300 7.351414 TGAACATAGTGAAGTGAAATCTTCG 57.649 36.000 0.00 0.00 44.53 3.79
2122 3504 5.136828 TGTGCCTAGTTTCTCATTTCCAAA 58.863 37.500 0.00 0.00 0.00 3.28
2382 3769 9.243637 CATTTTGTTCTCGTTTCCAAATTTCTA 57.756 29.630 0.00 0.00 0.00 2.10
2817 4204 4.868171 CCTTTTCATGCTGACAAATCCATG 59.132 41.667 0.00 0.00 37.11 3.66
3116 4503 4.399303 AGCTATACAGGCAACCATTTGAAC 59.601 41.667 0.00 0.00 34.24 3.18
4092 5479 9.790389 CTAACTTTTATACCAGACACTACAGAG 57.210 37.037 0.00 0.00 0.00 3.35
4531 5918 1.511887 CGAGCGTGCAATTTTCCCG 60.512 57.895 0.00 0.00 0.00 5.14
4749 6137 7.334421 GTGCTTAGAATGGAAGATGTTTAGACA 59.666 37.037 0.00 0.00 40.71 3.41
4766 6154 3.206150 AGACATCCCGTATGAACAATGC 58.794 45.455 2.30 0.00 39.07 3.56
5052 6440 4.767255 GTGGGAGGAGTGGCAGCG 62.767 72.222 0.00 0.00 0.00 5.18
5095 6483 3.941483 AGCAGTACGAAAATAAGCAGCAT 59.059 39.130 0.00 0.00 0.00 3.79
5152 6540 2.586258 TCTATGAAGCCGTTGAGCTC 57.414 50.000 6.82 6.82 44.11 4.09
5285 6695 3.612955 GCTATCTATCTGGTTGCGAGACC 60.613 52.174 1.04 1.04 40.23 3.85
5396 6806 9.264719 CTCAGACATTATTAACATCTGTATGCA 57.735 33.333 14.14 0.00 38.35 3.96
5705 7115 2.420687 GCAATGTGTTTCCCCCACAAAA 60.421 45.455 0.00 0.00 45.20 2.44
5934 7344 2.576191 TCCAGTGAGGACCCATAAAAGG 59.424 50.000 0.00 0.00 43.07 3.11
5935 7345 2.308866 CCAGTGAGGACCCATAAAAGGT 59.691 50.000 0.00 0.00 41.22 3.50
5944 7354 4.993705 ACCCATAAAAGGTCAAGACTGA 57.006 40.909 0.00 0.00 28.99 3.41
5945 7355 4.911390 ACCCATAAAAGGTCAAGACTGAG 58.089 43.478 0.00 0.00 28.99 3.35
5946 7356 4.597507 ACCCATAAAAGGTCAAGACTGAGA 59.402 41.667 0.00 0.00 28.99 3.27
5947 7357 5.073144 ACCCATAAAAGGTCAAGACTGAGAA 59.927 40.000 0.00 0.00 28.99 2.87
5948 7358 6.003950 CCCATAAAAGGTCAAGACTGAGAAA 58.996 40.000 0.00 0.00 30.14 2.52
5949 7359 6.150140 CCCATAAAAGGTCAAGACTGAGAAAG 59.850 42.308 0.00 0.00 30.14 2.62
5950 7360 6.936900 CCATAAAAGGTCAAGACTGAGAAAGA 59.063 38.462 0.00 0.00 30.14 2.52
5951 7361 7.095017 CCATAAAAGGTCAAGACTGAGAAAGAC 60.095 40.741 0.00 0.00 30.14 3.01
5952 7362 5.359194 AAAGGTCAAGACTGAGAAAGACA 57.641 39.130 0.00 0.00 30.14 3.41
5953 7363 5.559148 AAGGTCAAGACTGAGAAAGACAT 57.441 39.130 0.00 0.00 30.14 3.06
5954 7364 5.559148 AGGTCAAGACTGAGAAAGACATT 57.441 39.130 0.00 0.00 30.14 2.71
5955 7365 5.934781 AGGTCAAGACTGAGAAAGACATTT 58.065 37.500 0.00 0.00 30.14 2.32
5956 7366 6.360618 AGGTCAAGACTGAGAAAGACATTTT 58.639 36.000 0.00 0.00 30.14 1.82
5957 7367 6.484977 AGGTCAAGACTGAGAAAGACATTTTC 59.515 38.462 0.00 0.00 30.14 2.29
5958 7368 6.260936 GGTCAAGACTGAGAAAGACATTTTCA 59.739 38.462 0.00 0.00 30.14 2.69
5959 7369 7.128976 GTCAAGACTGAGAAAGACATTTTCAC 58.871 38.462 2.88 0.00 30.14 3.18
5960 7370 7.011857 GTCAAGACTGAGAAAGACATTTTCACT 59.988 37.037 2.88 0.00 30.14 3.41
5961 7371 7.225538 TCAAGACTGAGAAAGACATTTTCACTC 59.774 37.037 2.88 0.00 0.00 3.51
5962 7372 5.994668 AGACTGAGAAAGACATTTTCACTCC 59.005 40.000 2.88 0.00 0.00 3.85
5963 7373 5.684704 ACTGAGAAAGACATTTTCACTCCA 58.315 37.500 2.88 0.00 0.00 3.86
5964 7374 5.762218 ACTGAGAAAGACATTTTCACTCCAG 59.238 40.000 2.88 0.00 0.00 3.86
5978 7388 2.915869 ACTCCAGTGAGGACCCATAAA 58.084 47.619 0.00 0.00 43.07 1.40
6008 7418 7.225538 TCAAGACTGAGAAAGACATTTTCACTC 59.774 37.037 2.88 0.00 0.00 3.51
6037 7447 3.538379 CTGTGGTGCAGCTGACATA 57.462 52.632 20.43 10.10 38.52 2.29
6111 7521 5.494724 AGCATCAAGATTTTGCTGACTAGA 58.505 37.500 4.16 0.00 44.63 2.43
6123 7533 5.426689 TGCTGACTAGACATGAATTTCCT 57.573 39.130 0.00 0.00 0.00 3.36
6134 7544 5.203528 ACATGAATTTCCTGAGTTATGGGG 58.796 41.667 0.00 0.00 0.00 4.96
6140 7550 5.888982 TTTCCTGAGTTATGGGGATACTC 57.111 43.478 0.00 0.00 38.96 2.59
6162 7572 6.322201 ACTCATCTGTTTTGGTCAGTTTTCAT 59.678 34.615 0.00 0.00 34.86 2.57
6164 7574 5.261209 TCTGTTTTGGTCAGTTTTCATGG 57.739 39.130 0.00 0.00 34.86 3.66
6251 7661 4.038402 CAGTTCCCAGTTTTTGCAAGAGAT 59.962 41.667 0.00 0.00 0.00 2.75
6359 7769 5.585047 AGTTGCCGTATCTGGAATAGTTTTC 59.415 40.000 0.00 0.00 0.00 2.29
6366 7776 4.280436 TCTGGAATAGTTTTCGAGCCAA 57.720 40.909 1.32 0.00 0.00 4.52
6429 7839 4.413087 CAAGAATCATGTCTGCAGAAAGC 58.587 43.478 20.19 6.95 45.96 3.51
6478 7893 1.063972 GCAACGTTCTGCAGCACAA 59.936 52.632 16.75 0.00 42.17 3.33
6484 7899 2.068519 CGTTCTGCAGCACAACTATGA 58.931 47.619 16.75 0.00 0.00 2.15
6489 7904 6.611381 GTTCTGCAGCACAACTATGATAAAA 58.389 36.000 11.86 0.00 0.00 1.52
6490 7905 7.253422 GTTCTGCAGCACAACTATGATAAAAT 58.747 34.615 11.86 0.00 0.00 1.82
6491 7906 6.788243 TCTGCAGCACAACTATGATAAAATG 58.212 36.000 9.47 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 1465 3.150949 CACCTCAGCACCAGGACA 58.849 61.111 0.00 0.00 34.75 4.02
192 1515 4.104102 ACAACACCTCCACTTTCTCCAATA 59.896 41.667 0.00 0.00 0.00 1.90
364 1705 0.757561 GGAGGAGAGGAGTACCCAGC 60.758 65.000 3.60 0.00 37.41 4.85
421 1762 8.715191 AACTTCAGTATCAAGATTCATGACTC 57.285 34.615 4.94 4.94 0.00 3.36
460 1801 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
462 1803 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
463 1804 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
464 1805 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
478 1819 9.570488 CACTACTTTAGTATTCTAAACGCTCTT 57.430 33.333 0.76 0.00 40.05 2.85
479 1820 8.954350 TCACTACTTTAGTATTCTAAACGCTCT 58.046 33.333 0.76 0.00 40.05 4.09
480 1821 9.733219 ATCACTACTTTAGTATTCTAAACGCTC 57.267 33.333 0.76 0.00 40.05 5.03
481 1822 9.733219 GATCACTACTTTAGTATTCTAAACGCT 57.267 33.333 0.76 0.00 40.05 5.07
482 1823 9.733219 AGATCACTACTTTAGTATTCTAAACGC 57.267 33.333 0.76 0.00 40.05 4.84
511 1852 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
512 1853 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
513 1854 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
520 1861 9.113838 CGTTAGTACTCCCTCTGTAAACTAATA 57.886 37.037 0.00 0.00 0.00 0.98
521 1862 7.831193 TCGTTAGTACTCCCTCTGTAAACTAAT 59.169 37.037 0.00 0.00 0.00 1.73
522 1863 7.168219 TCGTTAGTACTCCCTCTGTAAACTAA 58.832 38.462 0.00 0.00 0.00 2.24
523 1864 6.711277 TCGTTAGTACTCCCTCTGTAAACTA 58.289 40.000 0.00 0.00 0.00 2.24
524 1865 5.564550 TCGTTAGTACTCCCTCTGTAAACT 58.435 41.667 0.00 0.00 0.00 2.66
525 1866 5.414144 ACTCGTTAGTACTCCCTCTGTAAAC 59.586 44.000 0.00 0.00 32.84 2.01
526 1867 5.564550 ACTCGTTAGTACTCCCTCTGTAAA 58.435 41.667 0.00 0.00 32.84 2.01
527 1868 5.171339 ACTCGTTAGTACTCCCTCTGTAA 57.829 43.478 0.00 0.00 32.84 2.41
528 1869 4.833478 ACTCGTTAGTACTCCCTCTGTA 57.167 45.455 0.00 0.00 32.84 2.74
529 1870 3.717452 ACTCGTTAGTACTCCCTCTGT 57.283 47.619 0.00 0.00 32.84 3.41
530 1871 3.757493 ACAACTCGTTAGTACTCCCTCTG 59.243 47.826 0.00 0.00 33.75 3.35
531 1872 3.757493 CACAACTCGTTAGTACTCCCTCT 59.243 47.826 0.00 0.00 33.75 3.69
532 1873 3.755378 TCACAACTCGTTAGTACTCCCTC 59.245 47.826 0.00 0.00 33.75 4.30
533 1874 3.759581 TCACAACTCGTTAGTACTCCCT 58.240 45.455 0.00 0.00 33.75 4.20
534 1875 4.510038 TTCACAACTCGTTAGTACTCCC 57.490 45.455 0.00 0.00 33.75 4.30
535 1876 6.128634 CCAAATTCACAACTCGTTAGTACTCC 60.129 42.308 0.00 0.00 33.75 3.85
536 1877 6.128634 CCCAAATTCACAACTCGTTAGTACTC 60.129 42.308 0.00 0.00 33.75 2.59
537 1878 5.699458 CCCAAATTCACAACTCGTTAGTACT 59.301 40.000 0.00 0.00 33.75 2.73
538 1879 5.106830 CCCCAAATTCACAACTCGTTAGTAC 60.107 44.000 0.00 0.00 33.75 2.73
539 1880 4.998672 CCCCAAATTCACAACTCGTTAGTA 59.001 41.667 0.00 0.00 33.75 1.82
540 1881 3.818773 CCCCAAATTCACAACTCGTTAGT 59.181 43.478 0.00 0.00 37.65 2.24
541 1882 4.069304 TCCCCAAATTCACAACTCGTTAG 58.931 43.478 0.00 0.00 0.00 2.34
542 1883 4.069304 CTCCCCAAATTCACAACTCGTTA 58.931 43.478 0.00 0.00 0.00 3.18
543 1884 2.884639 CTCCCCAAATTCACAACTCGTT 59.115 45.455 0.00 0.00 0.00 3.85
544 1885 2.504367 CTCCCCAAATTCACAACTCGT 58.496 47.619 0.00 0.00 0.00 4.18
545 1886 1.812571 CCTCCCCAAATTCACAACTCG 59.187 52.381 0.00 0.00 0.00 4.18
546 1887 2.876581 ACCTCCCCAAATTCACAACTC 58.123 47.619 0.00 0.00 0.00 3.01
719 2064 3.479489 TCTTGATTGCTTCTCAGTTGCA 58.521 40.909 0.00 0.00 34.69 4.08
720 2065 4.155462 TCATCTTGATTGCTTCTCAGTTGC 59.845 41.667 0.00 0.00 0.00 4.17
721 2066 5.874895 TCATCTTGATTGCTTCTCAGTTG 57.125 39.130 0.00 0.00 0.00 3.16
734 2079 7.834881 ATTGCAACCTATCAATCATCTTGAT 57.165 32.000 0.00 5.83 39.09 2.57
735 2080 7.339976 TCAATTGCAACCTATCAATCATCTTGA 59.660 33.333 0.00 0.00 32.27 3.02
736 2081 7.485810 TCAATTGCAACCTATCAATCATCTTG 58.514 34.615 0.00 0.00 32.27 3.02
737 2082 7.649533 TCAATTGCAACCTATCAATCATCTT 57.350 32.000 0.00 0.00 32.27 2.40
738 2083 7.417116 GGTTCAATTGCAACCTATCAATCATCT 60.417 37.037 22.31 0.00 40.33 2.90
739 2084 6.698766 GGTTCAATTGCAACCTATCAATCATC 59.301 38.462 22.31 3.04 40.33 2.92
740 2085 6.407299 GGGTTCAATTGCAACCTATCAATCAT 60.407 38.462 25.61 0.00 42.73 2.45
741 2086 5.105392 GGGTTCAATTGCAACCTATCAATCA 60.105 40.000 25.61 0.00 42.73 2.57
742 2087 5.105392 TGGGTTCAATTGCAACCTATCAATC 60.105 40.000 25.61 15.07 42.73 2.67
743 2088 4.776837 TGGGTTCAATTGCAACCTATCAAT 59.223 37.500 25.61 0.00 42.73 2.57
744 2089 4.155709 TGGGTTCAATTGCAACCTATCAA 58.844 39.130 25.61 3.25 42.73 2.57
745 2090 3.772387 TGGGTTCAATTGCAACCTATCA 58.228 40.909 25.61 17.95 42.73 2.15
746 2091 4.799564 TTGGGTTCAATTGCAACCTATC 57.200 40.909 25.61 16.43 42.73 2.08
917 2296 7.710044 TGCATTACTGAAAAGAAAAATGAAGCA 59.290 29.630 0.00 0.00 0.00 3.91
1112 2491 0.172803 CAGGAGCTGCCAAAGATTGC 59.827 55.000 0.00 0.00 40.02 3.56
1166 2545 6.209192 TGTCTGATGTGGCAAAGATGTTTATT 59.791 34.615 0.00 0.00 0.00 1.40
1172 2551 4.713824 AATGTCTGATGTGGCAAAGATG 57.286 40.909 0.00 0.00 0.00 2.90
1363 2743 1.626686 CCCCAATTACAACACCAGCA 58.373 50.000 0.00 0.00 0.00 4.41
1364 2744 0.246360 GCCCCAATTACAACACCAGC 59.754 55.000 0.00 0.00 0.00 4.85
1397 2777 6.618287 TGGTGCATTAGTTTCTGTATATGC 57.382 37.500 0.00 0.00 38.97 3.14
1431 2811 4.860802 TGAAGGTGTGGTTGATATCCAT 57.139 40.909 0.00 0.00 37.30 3.41
1483 2863 5.507077 TGCTTTTACAGTTTCATGTTCGTC 58.493 37.500 0.00 0.00 34.56 4.20
1485 2865 6.991485 AATGCTTTTACAGTTTCATGTTCG 57.009 33.333 0.00 0.00 34.56 3.95
1546 2927 2.956333 GCAGAACAAACCAAAGGTAGGT 59.044 45.455 0.00 0.00 42.34 3.08
1562 2943 5.129320 TCTGGATAGCTTAACTGATGCAGAA 59.871 40.000 12.17 0.00 41.84 3.02
1992 3373 7.067615 TGCTGTTGAAGTAAAACCATTGTTCTA 59.932 33.333 0.00 0.00 32.15 2.10
2122 3504 4.080695 TGAGGAGCTCAAAGTTCTGCATAT 60.081 41.667 17.19 0.00 37.57 1.78
2589 3976 4.207165 TCAGGTATTGAGCCATTTAAGCC 58.793 43.478 0.00 0.00 0.00 4.35
2817 4204 5.938125 TGACTTTCACTATTAGGCAGGTTTC 59.062 40.000 0.00 0.00 0.00 2.78
3321 4708 9.944376 AGCAGAAATAGAACTACAGAAACAATA 57.056 29.630 0.00 0.00 0.00 1.90
4212 5599 1.992667 GTGCGATCGTCATTCTTGTCA 59.007 47.619 17.81 0.00 0.00 3.58
4501 5888 1.301716 ACGCTCGCCTGTCACAATT 60.302 52.632 0.00 0.00 0.00 2.32
4531 5918 0.174617 CAGCTCCTTCGAGGAAGTCC 59.825 60.000 0.00 0.00 45.28 3.85
4749 6137 1.494721 AGGGCATTGTTCATACGGGAT 59.505 47.619 0.00 0.00 0.00 3.85
4766 6154 4.871933 ATTTTACTGGAAAGTGCAAGGG 57.128 40.909 0.00 0.00 0.00 3.95
4885 6273 1.512926 CACAGCCTATATTGCGGTCC 58.487 55.000 0.83 0.00 34.90 4.46
5052 6440 1.226717 CGACGGGTAAGCTCAGCTC 60.227 63.158 0.00 0.00 38.25 4.09
5513 6923 1.271597 GGATAGGCTGGCCCTTACATG 60.272 57.143 8.11 0.00 43.06 3.21
5571 6981 5.422666 TTCAAGATATTACATGCCAAGCG 57.577 39.130 0.00 0.00 0.00 4.68
5705 7115 5.583457 CGAGTTACCCTTACAATTTCGGATT 59.417 40.000 0.00 0.00 0.00 3.01
5926 7336 7.442364 TGTCTTTCTCAGTCTTGACCTTTTATG 59.558 37.037 0.00 0.00 0.00 1.90
5927 7337 7.509546 TGTCTTTCTCAGTCTTGACCTTTTAT 58.490 34.615 0.00 0.00 0.00 1.40
5928 7338 6.884832 TGTCTTTCTCAGTCTTGACCTTTTA 58.115 36.000 0.00 0.00 0.00 1.52
5929 7339 5.745227 TGTCTTTCTCAGTCTTGACCTTTT 58.255 37.500 0.00 0.00 0.00 2.27
5930 7340 5.359194 TGTCTTTCTCAGTCTTGACCTTT 57.641 39.130 0.00 0.00 0.00 3.11
5931 7341 5.559148 ATGTCTTTCTCAGTCTTGACCTT 57.441 39.130 0.00 0.00 0.00 3.50
5932 7342 5.559148 AATGTCTTTCTCAGTCTTGACCT 57.441 39.130 0.00 0.00 0.00 3.85
5933 7343 6.260936 TGAAAATGTCTTTCTCAGTCTTGACC 59.739 38.462 0.00 0.00 0.00 4.02
5934 7344 7.011857 AGTGAAAATGTCTTTCTCAGTCTTGAC 59.988 37.037 0.00 0.00 0.00 3.18
5935 7345 7.050377 AGTGAAAATGTCTTTCTCAGTCTTGA 58.950 34.615 0.00 0.00 0.00 3.02
5936 7346 7.256756 AGTGAAAATGTCTTTCTCAGTCTTG 57.743 36.000 0.00 0.00 0.00 3.02
5937 7347 6.484977 GGAGTGAAAATGTCTTTCTCAGTCTT 59.515 38.462 8.67 0.00 35.28 3.01
5938 7348 5.994668 GGAGTGAAAATGTCTTTCTCAGTCT 59.005 40.000 8.67 0.00 35.28 3.24
5939 7349 5.760253 TGGAGTGAAAATGTCTTTCTCAGTC 59.240 40.000 2.40 2.40 34.83 3.51
5940 7350 5.684704 TGGAGTGAAAATGTCTTTCTCAGT 58.315 37.500 0.00 0.00 0.00 3.41
5941 7351 5.762218 ACTGGAGTGAAAATGTCTTTCTCAG 59.238 40.000 0.00 0.00 0.00 3.35
5942 7352 5.684704 ACTGGAGTGAAAATGTCTTTCTCA 58.315 37.500 0.00 0.00 0.00 3.27
5960 7370 2.576191 CCTTTTATGGGTCCTCACTGGA 59.424 50.000 0.00 0.00 43.86 3.86
5961 7371 2.308866 ACCTTTTATGGGTCCTCACTGG 59.691 50.000 0.00 0.00 30.15 4.00
5962 7372 3.610911 GACCTTTTATGGGTCCTCACTG 58.389 50.000 1.80 0.00 45.31 3.66
5978 7388 5.559148 ATGTCTTTCTCAGTCTTGACCTT 57.441 39.130 0.00 0.00 0.00 3.50
6008 7418 1.735360 CACCACAGTTGTTGGCTGG 59.265 57.895 0.00 0.00 38.22 4.85
6048 7458 2.096442 GTGGCGCCTACACGGTTAC 61.096 63.158 29.70 10.25 34.25 2.50
6111 7521 5.044179 TCCCCATAACTCAGGAAATTCATGT 60.044 40.000 7.53 0.00 29.15 3.21
6123 7533 5.467738 ACAGATGAGTATCCCCATAACTCA 58.532 41.667 6.84 6.84 40.98 3.41
6134 7544 7.440523 AAACTGACCAAAACAGATGAGTATC 57.559 36.000 0.00 0.00 38.55 2.24
6140 7550 5.693104 CCATGAAAACTGACCAAAACAGATG 59.307 40.000 0.00 0.00 38.55 2.90
6141 7551 5.363580 ACCATGAAAACTGACCAAAACAGAT 59.636 36.000 0.00 0.00 38.55 2.90
6228 7638 3.381272 TCTCTTGCAAAAACTGGGAACTG 59.619 43.478 0.00 0.00 0.00 3.16
6251 7661 5.415701 GTCAAGCTGGTTGGATATCAGAAAA 59.584 40.000 18.41 0.00 36.71 2.29
6366 7776 0.040058 TTGATGTTGGCTGCCCTCAT 59.960 50.000 17.53 19.15 32.30 2.90
6449 7859 4.414852 GCAGAACGTTGCACATCATATTT 58.585 39.130 5.00 0.00 43.53 1.40


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

AutoCloner maintained by Alex Coulton.