Multiple sequence alignment - TraesCS1A01G221300

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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 TraesCS1A01G221300 chr1A 100.000 3800 0 0 1 3800 390103120 390099321 0.000000e+00 7018.0
1 TraesCS1A01G221300 chr1A 81.452 124 15 6 493 615 534927750 534927866 1.120000e-15 95.3
2 TraesCS1A01G221300 chr1D 95.119 1598 59 2 880 2458 310254316 310252719 0.000000e+00 2501.0
3 TraesCS1A01G221300 chr1D 95.404 1349 54 6 2459 3800 310252668 310251321 0.000000e+00 2141.0
4 TraesCS1A01G221300 chr1D 92.445 728 51 4 1 725 310255515 310254789 0.000000e+00 1037.0
5 TraesCS1A01G221300 chr1B 94.336 1642 68 6 842 2458 420369498 420367857 0.000000e+00 2494.0
6 TraesCS1A01G221300 chr1B 94.244 1355 62 7 2459 3800 420367805 420366454 0.000000e+00 2056.0
7 TraesCS1A01G221300 chr5D 73.433 1276 259 52 998 2251 432781795 432783012 4.570000e-109 405.0
8 TraesCS1A01G221300 chr5D 69.786 1026 239 50 1251 2240 432983442 432984432 1.120000e-20 111.0
9 TraesCS1A01G221300 chr5D 89.744 78 7 1 493 569 532009435 532009358 8.690000e-17 99.0
10 TraesCS1A01G221300 chr5D 94.444 54 3 0 2187 2240 433011772 433011825 2.430000e-12 84.2
11 TraesCS1A01G221300 chrUn 72.827 1277 261 59 998 2249 63282944 63281729 1.300000e-94 357.0
12 TraesCS1A01G221300 chrUn 72.827 1277 261 59 998 2249 327299180 327297965 1.300000e-94 357.0
13 TraesCS1A01G221300 chr5B 71.115 1229 279 54 1050 2240 526269632 526270822 2.280000e-57 233.0
14 TraesCS1A01G221300 chr5A 86.875 160 21 0 1056 1215 547406430 547406271 3.020000e-41 180.0
15 TraesCS1A01G221300 chr5A 89.744 78 7 1 493 569 634088770 634088847 8.690000e-17 99.0
16 TraesCS1A01G221300 chr5A 98.148 54 1 0 2187 2240 547597072 547597125 1.120000e-15 95.3
17 TraesCS1A01G221300 chr3A 83.871 124 12 3 493 615 589179643 589179759 1.120000e-20 111.0
18 TraesCS1A01G221300 chr3A 97.059 34 1 0 3427 3460 724803114 724803081 1.470000e-04 58.4
19 TraesCS1A01G221300 chr2A 83.065 124 13 3 493 615 539305224 539305108 5.190000e-19 106.0
20 TraesCS1A01G221300 chr7D 90.909 77 6 1 493 568 91043636 91043712 6.720000e-18 102.0
21 TraesCS1A01G221300 chr6B 89.744 78 7 1 493 569 581872273 581872350 8.690000e-17 99.0
22 TraesCS1A01G221300 chr6B 100.000 29 0 0 3427 3455 525111022 525110994 2.000000e-03 54.7
23 TraesCS1A01G221300 chr7A 77.083 192 29 9 494 682 42435155 42434976 3.120000e-16 97.1
24 TraesCS1A01G221300 chr3B 100.000 30 0 0 3427 3456 814509240 814509269 5.300000e-04 56.5


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 TraesCS1A01G221300 chr1A 390099321 390103120 3799 True 7018 7018 100.000000 1 3800 1 chr1A.!!$R1 3799
1 TraesCS1A01G221300 chr1D 310251321 310255515 4194 True 1893 2501 94.322667 1 3800 3 chr1D.!!$R1 3799
2 TraesCS1A01G221300 chr1B 420366454 420369498 3044 True 2275 2494 94.290000 842 3800 2 chr1B.!!$R1 2958
3 TraesCS1A01G221300 chr5D 432781795 432783012 1217 False 405 405 73.433000 998 2251 1 chr5D.!!$F1 1253
4 TraesCS1A01G221300 chrUn 63281729 63282944 1215 True 357 357 72.827000 998 2249 1 chrUn.!!$R1 1251
5 TraesCS1A01G221300 chrUn 327297965 327299180 1215 True 357 357 72.827000 998 2249 1 chrUn.!!$R2 1251
6 TraesCS1A01G221300 chr5B 526269632 526270822 1190 False 233 233 71.115000 1050 2240 1 chr5B.!!$F1 1190

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
391 394 0.173708 GACTGCCTTGTACTCCCTCG 59.826 60.0 0.00 0.0 0.00 4.63 F
614 618 0.239879 AAACGCACATCGCCGAAAAT 59.760 45.0 0.00 0.0 43.23 1.82 F
744 748 0.249398 ACCCCCTTTCGAGATTGACG 59.751 55.0 0.00 0.0 0.00 4.35 F
1113 1447 0.330532 TCCTCCATCTCCCCTCCCTA 60.331 60.0 0.00 0.0 0.00 3.53 F
1761 2110 0.962356 ATTGGAAGCGCAAGACCCAG 60.962 55.0 11.47 0.0 43.02 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 2153 0.807275 GGCTGCGGCAAATCCATTTC 60.807 55.000 21.31 0.00 40.87 2.17 R
2252 2613 1.062886 TCCAGGGACCAGATGTAGGAG 60.063 57.143 0.00 0.00 0.00 3.69 R
2518 2949 1.199327 GCACTTTACCGGAAAGAAGCC 59.801 52.381 24.21 12.89 46.57 4.35 R
2520 2951 3.399330 TCTGCACTTTACCGGAAAGAAG 58.601 45.455 24.21 18.70 46.57 2.85 R
3178 3615 0.395862 TCGGTCTCTTGGGAGCTAGG 60.396 60.000 0.00 0.00 39.31 3.02 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
34 35 1.263356 TAACAACCTCCCAGACCGAG 58.737 55.000 0.00 0.00 0.00 4.63
44 45 1.626686 CCAGACCGAGGCTATGATCT 58.373 55.000 0.00 0.00 0.00 2.75
48 49 3.823873 CAGACCGAGGCTATGATCTAAGT 59.176 47.826 0.00 0.00 0.00 2.24
75 76 0.246635 GGACAAGCGCTCACTTCCTA 59.753 55.000 12.06 0.00 0.00 2.94
90 91 2.642254 CCTACGGGCGTGAGGAACA 61.642 63.158 0.00 0.00 31.45 3.18
100 101 4.000988 GGCGTGAGGAACATTTTCTTCTA 58.999 43.478 5.46 0.00 38.40 2.10
104 105 6.359883 GCGTGAGGAACATTTTCTTCTAAAAC 59.640 38.462 5.46 0.00 38.40 2.43
162 163 5.894393 TGATGGTTTAAAACTCAACCCTGAA 59.106 36.000 4.60 0.00 41.73 3.02
173 174 0.385390 AACCCTGAACTGCAAAAGCG 59.615 50.000 0.00 0.00 0.00 4.68
183 184 2.819608 ACTGCAAAAGCGGTGAACATAT 59.180 40.909 0.45 0.00 0.00 1.78
187 188 3.670203 CAAAAGCGGTGAACATATCGTC 58.330 45.455 0.00 0.00 0.00 4.20
202 203 5.291128 ACATATCGTCGTCTCAATTTTGACC 59.709 40.000 0.00 0.00 32.90 4.02
261 263 2.270986 GCCAACTCAACAGCCCCAG 61.271 63.158 0.00 0.00 0.00 4.45
351 354 1.737793 GGAAGTGTTGTTCCATAGCCG 59.262 52.381 0.00 0.00 44.89 5.52
391 394 0.173708 GACTGCCTTGTACTCCCTCG 59.826 60.000 0.00 0.00 0.00 4.63
398 401 2.830321 CCTTGTACTCCCTCGGTTAACT 59.170 50.000 5.42 0.00 0.00 2.24
429 432 5.783111 AGCTTTGTGTCAAGTCAAACTTTT 58.217 33.333 0.00 0.00 36.03 2.27
458 461 2.726821 ACGATTCATGGGCAGTTCATT 58.273 42.857 0.00 0.00 0.00 2.57
479 482 2.185608 GAGAAGAGCTCCCGCCAC 59.814 66.667 10.93 0.00 37.69 5.01
521 525 2.606155 CTTCGAGAGACTGAGCCGGC 62.606 65.000 21.89 21.89 41.84 6.13
531 535 4.067896 AGACTGAGCCGGCATATTATTTG 58.932 43.478 31.54 9.91 0.00 2.32
540 544 5.048782 GCCGGCATATTATTTGAGATTGACA 60.049 40.000 24.80 0.00 0.00 3.58
577 581 3.121944 GTCTCGTAGTCGACAACTAACGA 59.878 47.826 19.50 20.23 42.11 3.85
578 582 3.740832 TCTCGTAGTCGACAACTAACGAA 59.259 43.478 19.50 11.42 42.11 3.85
593 597 0.531311 ACGAAAACGTCTCCACCCAC 60.531 55.000 0.00 0.00 0.00 4.61
598 602 2.538512 AACGTCTCCACCCACTAAAC 57.461 50.000 0.00 0.00 0.00 2.01
606 610 0.442310 CACCCACTAAACGCACATCG 59.558 55.000 0.00 0.00 45.38 3.84
609 613 1.058748 CACTAAACGCACATCGCCG 59.941 57.895 0.00 0.00 43.23 6.46
610 614 1.080366 ACTAAACGCACATCGCCGA 60.080 52.632 0.00 0.00 43.23 5.54
614 618 0.239879 AAACGCACATCGCCGAAAAT 59.760 45.000 0.00 0.00 43.23 1.82
629 633 5.293569 CGCCGAAAATATCAGGACTTAAACT 59.706 40.000 0.00 0.00 0.00 2.66
642 646 3.933332 GACTTAAACTCTGATGAACGGGG 59.067 47.826 0.00 0.00 0.00 5.73
643 647 3.581332 ACTTAAACTCTGATGAACGGGGA 59.419 43.478 0.00 0.00 0.00 4.81
644 648 4.225267 ACTTAAACTCTGATGAACGGGGAT 59.775 41.667 0.00 0.00 0.00 3.85
645 649 5.424252 ACTTAAACTCTGATGAACGGGGATA 59.576 40.000 0.00 0.00 0.00 2.59
646 650 3.821421 AACTCTGATGAACGGGGATAC 57.179 47.619 0.00 0.00 0.00 2.24
666 670 2.290323 ACCACTGTCTTGCTAACCATCC 60.290 50.000 0.00 0.00 0.00 3.51
672 676 2.488153 GTCTTGCTAACCATCCAACCAC 59.512 50.000 0.00 0.00 0.00 4.16
675 679 0.802494 GCTAACCATCCAACCACACG 59.198 55.000 0.00 0.00 0.00 4.49
678 682 2.642154 AACCATCCAACCACACGTTA 57.358 45.000 0.00 0.00 31.77 3.18
691 695 8.344098 CCAACCACACGTTAGTTAGAAATTAAA 58.656 33.333 0.00 0.00 31.77 1.52
725 729 7.862372 GCACACTCTATTTTTCACTTTGATCAA 59.138 33.333 3.38 3.38 0.00 2.57
726 730 9.173939 CACACTCTATTTTTCACTTTGATCAAC 57.826 33.333 7.89 0.00 0.00 3.18
727 731 8.352942 ACACTCTATTTTTCACTTTGATCAACC 58.647 33.333 7.89 0.00 0.00 3.77
728 732 7.809806 CACTCTATTTTTCACTTTGATCAACCC 59.190 37.037 7.89 0.00 0.00 4.11
729 733 7.039714 ACTCTATTTTTCACTTTGATCAACCCC 60.040 37.037 7.89 0.00 0.00 4.95
730 734 4.681074 TTTTTCACTTTGATCAACCCCC 57.319 40.909 7.89 0.00 0.00 5.40
731 735 3.611025 TTTCACTTTGATCAACCCCCT 57.389 42.857 7.89 0.00 0.00 4.79
732 736 3.611025 TTCACTTTGATCAACCCCCTT 57.389 42.857 7.89 0.00 0.00 3.95
733 737 3.611025 TCACTTTGATCAACCCCCTTT 57.389 42.857 7.89 0.00 0.00 3.11
734 738 3.496331 TCACTTTGATCAACCCCCTTTC 58.504 45.455 7.89 0.00 0.00 2.62
735 739 2.228822 CACTTTGATCAACCCCCTTTCG 59.771 50.000 7.89 0.00 0.00 3.46
736 740 2.107552 ACTTTGATCAACCCCCTTTCGA 59.892 45.455 7.89 0.00 0.00 3.71
737 741 2.489938 TTGATCAACCCCCTTTCGAG 57.510 50.000 3.38 0.00 0.00 4.04
738 742 1.651737 TGATCAACCCCCTTTCGAGA 58.348 50.000 0.00 0.00 0.00 4.04
739 743 2.196595 TGATCAACCCCCTTTCGAGAT 58.803 47.619 0.00 0.00 0.00 2.75
740 744 2.576191 TGATCAACCCCCTTTCGAGATT 59.424 45.455 0.00 0.00 0.00 2.40
741 745 2.489938 TCAACCCCCTTTCGAGATTG 57.510 50.000 0.00 0.00 0.00 2.67
742 746 1.982226 TCAACCCCCTTTCGAGATTGA 59.018 47.619 0.00 0.00 0.00 2.57
743 747 2.084546 CAACCCCCTTTCGAGATTGAC 58.915 52.381 0.00 0.00 0.00 3.18
744 748 0.249398 ACCCCCTTTCGAGATTGACG 59.751 55.000 0.00 0.00 0.00 4.35
745 749 0.462047 CCCCCTTTCGAGATTGACGG 60.462 60.000 0.00 0.00 0.00 4.79
746 750 0.462047 CCCCTTTCGAGATTGACGGG 60.462 60.000 0.00 0.00 0.00 5.28
747 751 0.249398 CCCTTTCGAGATTGACGGGT 59.751 55.000 0.00 0.00 0.00 5.28
748 752 1.479323 CCCTTTCGAGATTGACGGGTA 59.521 52.381 0.00 0.00 0.00 3.69
749 753 2.481449 CCCTTTCGAGATTGACGGGTAG 60.481 54.545 0.00 0.00 0.00 3.18
750 754 2.481449 CCTTTCGAGATTGACGGGTAGG 60.481 54.545 0.00 0.00 0.00 3.18
751 755 1.108776 TTCGAGATTGACGGGTAGGG 58.891 55.000 0.00 0.00 0.00 3.53
772 1078 1.076549 GGGGCCACTGACCATTGAA 59.923 57.895 4.39 0.00 0.00 2.69
777 1083 2.288395 GGCCACTGACCATTGAAACAAG 60.288 50.000 0.00 0.00 0.00 3.16
779 1085 3.181476 GCCACTGACCATTGAAACAAGTT 60.181 43.478 0.00 0.00 0.00 2.66
781 1087 5.451242 GCCACTGACCATTGAAACAAGTTTA 60.451 40.000 0.00 0.00 32.11 2.01
782 1088 6.568869 CCACTGACCATTGAAACAAGTTTAA 58.431 36.000 0.00 0.00 32.11 1.52
784 1090 7.416213 CCACTGACCATTGAAACAAGTTTAAGA 60.416 37.037 0.00 0.00 32.11 2.10
798 1104 8.871686 ACAAGTTTAAGACAAATCATCAAACC 57.128 30.769 0.00 0.00 0.00 3.27
800 1106 7.839680 AGTTTAAGACAAATCATCAAACCCT 57.160 32.000 0.00 0.00 0.00 4.34
802 1108 8.704668 AGTTTAAGACAAATCATCAAACCCTTT 58.295 29.630 0.00 0.00 0.00 3.11
809 1115 9.271828 GACAAATCATCAAACCCTTTGTAAAAT 57.728 29.630 0.00 0.00 39.43 1.82
813 1119 7.353414 TCATCAAACCCTTTGTAAAATGTGA 57.647 32.000 0.00 0.00 41.36 3.58
814 1120 7.206687 TCATCAAACCCTTTGTAAAATGTGAC 58.793 34.615 0.00 0.00 41.36 3.67
831 1137 4.450976 TGTGACAAATCATCTAATCCCCG 58.549 43.478 0.00 0.00 37.14 5.73
832 1138 3.815401 GTGACAAATCATCTAATCCCCGG 59.185 47.826 0.00 0.00 37.14 5.73
834 1140 2.783510 ACAAATCATCTAATCCCCGGGT 59.216 45.455 21.85 2.88 0.00 5.28
835 1141 3.977999 ACAAATCATCTAATCCCCGGGTA 59.022 43.478 21.85 2.85 0.00 3.69
836 1142 4.601857 ACAAATCATCTAATCCCCGGGTAT 59.398 41.667 21.85 6.12 0.00 2.73
837 1143 5.074515 ACAAATCATCTAATCCCCGGGTATT 59.925 40.000 21.85 18.91 0.00 1.89
838 1144 5.437191 AATCATCTAATCCCCGGGTATTC 57.563 43.478 21.85 0.00 0.00 1.75
839 1145 2.829720 TCATCTAATCCCCGGGTATTCG 59.170 50.000 21.85 12.12 0.00 3.34
840 1146 0.971386 TCTAATCCCCGGGTATTCGC 59.029 55.000 21.85 0.00 0.00 4.70
863 1171 8.122952 TCGCTAGTTATACTTTTCCGTAGTAAC 58.877 37.037 0.00 0.00 32.28 2.50
875 1183 1.924524 CGTAGTAACATTCGGCCACTG 59.075 52.381 2.24 0.00 0.00 3.66
1113 1447 0.330532 TCCTCCATCTCCCCTCCCTA 60.331 60.000 0.00 0.00 0.00 3.53
1519 1853 2.725008 GCTCCCTCGAGATCCACG 59.275 66.667 15.71 3.92 38.52 4.94
1761 2110 0.962356 ATTGGAAGCGCAAGACCCAG 60.962 55.000 11.47 0.00 43.02 4.45
1804 2153 1.150827 TGCGACATTGCAGTTCTCTG 58.849 50.000 0.00 0.00 40.62 3.35
1955 2304 1.667154 TTCTGGAGAGCCGACGATGG 61.667 60.000 0.00 0.00 36.79 3.51
2024 2385 1.068588 TGAGTTCACCGAGTGTTCAGG 59.931 52.381 4.33 0.00 34.79 3.86
2050 2411 2.613026 TCATGTCGTGGTGAACAGTT 57.387 45.000 0.00 0.00 0.00 3.16
2252 2613 2.087646 GGTGAGCCTGAACTTGAATCC 58.912 52.381 0.00 0.00 0.00 3.01
2319 2696 5.278957 GGTGCCTATTGTTGTGAAAATCTGT 60.279 40.000 0.00 0.00 0.00 3.41
2324 2701 7.429340 GCCTATTGTTGTGAAAATCTGTTATCG 59.571 37.037 0.00 0.00 0.00 2.92
2325 2702 8.664798 CCTATTGTTGTGAAAATCTGTTATCGA 58.335 33.333 0.00 0.00 0.00 3.59
2342 2719 6.871492 TGTTATCGACTCTTCACATTTTGCTA 59.129 34.615 0.00 0.00 0.00 3.49
2346 2723 6.831769 TCGACTCTTCACATTTTGCTATTTC 58.168 36.000 0.00 0.00 0.00 2.17
2347 2724 6.426633 TCGACTCTTCACATTTTGCTATTTCA 59.573 34.615 0.00 0.00 0.00 2.69
2353 2730 5.702865 TCACATTTTGCTATTTCAGTCAGC 58.297 37.500 0.00 0.00 35.82 4.26
2357 2734 4.754372 TTTGCTATTTCAGTCAGCTGTG 57.246 40.909 14.67 5.73 43.05 3.66
2372 2752 4.887071 TCAGCTGTGGTTGATTTTGTTACT 59.113 37.500 14.67 0.00 0.00 2.24
2391 2771 8.089625 TGTTACTGAGGGATGAATTGATTCTA 57.910 34.615 5.42 0.00 37.67 2.10
2431 2811 4.729227 TGTCTGGTTTGCGTATCTCATA 57.271 40.909 0.00 0.00 0.00 2.15
2454 2834 4.697352 AGTACATGAGTTCAATTGCAGACC 59.303 41.667 0.00 0.00 0.00 3.85
2515 2946 5.345702 CCACATTGACAATATTTGAGGCTG 58.654 41.667 0.00 0.00 0.00 4.85
2518 2949 5.359009 ACATTGACAATATTTGAGGCTGGAG 59.641 40.000 0.00 0.00 0.00 3.86
2520 2951 2.620585 GACAATATTTGAGGCTGGAGGC 59.379 50.000 0.00 0.00 41.43 4.70
2529 2960 1.746991 GGCTGGAGGCTTCTTTCCG 60.747 63.158 0.00 0.00 41.46 4.30
2621 3053 5.225642 CGACTGTGTGACATATCATGCTAT 58.774 41.667 0.00 0.00 37.14 2.97
2651 3083 4.142403 TGCCTCTGTGCATGCTAAATAAAC 60.142 41.667 20.33 7.20 36.04 2.01
2652 3084 4.096984 GCCTCTGTGCATGCTAAATAAACT 59.903 41.667 20.33 0.00 0.00 2.66
2878 3315 3.706086 GGTTAGTGATGATGGGGCAAAAT 59.294 43.478 0.00 0.00 0.00 1.82
2880 3317 5.338300 GGTTAGTGATGATGGGGCAAAATTT 60.338 40.000 0.00 0.00 0.00 1.82
2972 3409 0.750249 TTGACAACTGCGAGGAGTCA 59.250 50.000 0.00 0.00 37.43 3.41
3020 3457 6.348950 CGATAGCTACAGGGAATAGACAGAAG 60.349 46.154 0.00 0.00 0.00 2.85
3178 3615 2.900122 TGAGCTTTTATTCAGCGTGC 57.100 45.000 0.00 0.00 42.55 5.34
3257 3694 7.607607 TGTATTGCTGTCTATGATTGAGTTTGT 59.392 33.333 0.00 0.00 0.00 2.83
3263 3700 7.566760 TGTCTATGATTGAGTTTGTTGTTGT 57.433 32.000 0.00 0.00 0.00 3.32
3383 3820 8.465999 CCTATCATACTGTGGATCTCTATTGTC 58.534 40.741 0.00 0.00 0.00 3.18
3408 3845 6.801575 TCCAAAAGAAAATCACAACCTACAC 58.198 36.000 0.00 0.00 0.00 2.90
3420 3857 1.125633 ACCTACACACTCCCAACGTT 58.874 50.000 0.00 0.00 0.00 3.99
3447 3884 6.238484 GGAAATACATCCATTTCTCCGACAAG 60.238 42.308 8.11 0.00 42.22 3.16
3448 3885 2.359900 ACATCCATTTCTCCGACAAGC 58.640 47.619 0.00 0.00 0.00 4.01
3457 3895 1.369091 CTCCGACAAGCATTTCCGGG 61.369 60.000 0.00 0.00 40.48 5.73
3460 3898 2.282180 ACAAGCATTTCCGGGCGT 60.282 55.556 0.00 0.00 34.54 5.68
3461 3899 1.862602 GACAAGCATTTCCGGGCGTT 61.863 55.000 0.00 0.00 34.54 4.84
3592 4031 2.026636 TCCACAGGCAGTATTTACACCC 60.027 50.000 0.00 0.00 0.00 4.61
3594 4033 3.009723 CACAGGCAGTATTTACACCCAG 58.990 50.000 0.00 0.00 0.00 4.45
3612 4054 6.775629 ACACCCAGTACATTAAGTTCACAAAT 59.224 34.615 0.00 0.00 0.00 2.32
3658 4100 5.009854 ACCACAAAACATTCTGTTCTTGG 57.990 39.130 13.91 12.36 40.14 3.61
3740 4182 8.613060 AAGCAACACATATGATACATAGGAAG 57.387 34.615 10.38 5.27 0.00 3.46
3741 4183 6.652481 AGCAACACATATGATACATAGGAAGC 59.348 38.462 10.38 7.70 0.00 3.86
3742 4184 6.427853 GCAACACATATGATACATAGGAAGCA 59.572 38.462 10.38 0.00 0.00 3.91
3744 4186 9.006839 CAACACATATGATACATAGGAAGCAAT 57.993 33.333 10.38 0.00 0.00 3.56
3784 4230 7.539712 AGTGAATTAATCATAACACTCACCG 57.460 36.000 8.37 0.00 40.97 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.823570 TCCGATAGCTACTTAGATCATAGCC 59.176 44.000 0.00 1.34 41.91 3.93
44 45 2.287427 GCGCTTGTCCGATAGCTACTTA 60.287 50.000 0.00 0.00 35.25 2.24
48 49 0.311165 GAGCGCTTGTCCGATAGCTA 59.689 55.000 13.26 0.00 34.85 3.32
75 76 0.536460 AAAATGTTCCTCACGCCCGT 60.536 50.000 0.00 0.00 0.00 5.28
100 101 8.885722 TGTTGTACTATGAACTTTTCTCGTTTT 58.114 29.630 0.00 0.00 0.00 2.43
104 105 7.639162 AGTGTTGTACTATGAACTTTTCTCG 57.361 36.000 0.00 0.00 38.04 4.04
117 118 5.900425 TCACGTTGGTTTAGTGTTGTACTA 58.100 37.500 0.00 0.00 40.89 1.82
173 174 3.416119 TGAGACGACGATATGTTCACC 57.584 47.619 0.00 0.00 0.00 4.02
183 184 2.224090 TGGGTCAAAATTGAGACGACGA 60.224 45.455 0.00 0.00 37.98 4.20
187 188 3.138304 TGACTGGGTCAAAATTGAGACG 58.862 45.455 0.00 0.00 39.78 4.18
202 203 8.141268 AGTAATGTGGTAAAAACAATTGACTGG 58.859 33.333 13.59 0.00 0.00 4.00
252 254 0.409484 AATTAGTTGGCTGGGGCTGT 59.591 50.000 0.00 0.00 38.73 4.40
321 324 5.105513 TGGAACAACACTTCCTTTCCTTTTC 60.106 40.000 0.00 0.00 40.56 2.29
391 394 7.041644 TGACACAAAGCTTATACACAGTTAACC 60.042 37.037 0.00 0.00 0.00 2.85
398 401 6.052360 TGACTTGACACAAAGCTTATACACA 58.948 36.000 0.00 0.00 0.00 3.72
429 432 7.164230 ACTGCCCATGAATCGTAAATTTTAA 57.836 32.000 0.00 0.00 0.00 1.52
458 461 3.292656 CGGGAGCTCTTCTCTGCA 58.707 61.111 14.64 0.00 41.60 4.41
490 493 1.680735 CTCTCGAAGGTGCTCATAGCT 59.319 52.381 0.00 0.00 42.97 3.32
491 494 1.678627 TCTCTCGAAGGTGCTCATAGC 59.321 52.381 0.00 0.00 42.82 2.97
492 495 2.948979 AGTCTCTCGAAGGTGCTCATAG 59.051 50.000 0.00 0.00 0.00 2.23
501 505 1.431440 CGGCTCAGTCTCTCGAAGG 59.569 63.158 0.00 0.00 0.00 3.46
531 535 8.206325 ACACATATGATGACTTTGTCAATCTC 57.794 34.615 10.38 0.00 45.96 2.75
540 544 7.101652 ACTACGAGACACATATGATGACTTT 57.898 36.000 10.38 4.55 0.00 2.66
577 581 3.208594 GTTTAGTGGGTGGAGACGTTTT 58.791 45.455 0.00 0.00 0.00 2.43
578 582 2.804212 CGTTTAGTGGGTGGAGACGTTT 60.804 50.000 0.00 0.00 0.00 3.60
606 610 6.539103 AGAGTTTAAGTCCTGATATTTTCGGC 59.461 38.462 0.00 0.00 0.00 5.54
614 618 7.258441 CGTTCATCAGAGTTTAAGTCCTGATA 58.742 38.462 12.27 1.04 42.51 2.15
629 633 1.760613 GTGGTATCCCCGTTCATCAGA 59.239 52.381 0.00 0.00 35.15 3.27
642 646 4.202245 TGGTTAGCAAGACAGTGGTATC 57.798 45.455 0.00 0.00 31.88 2.24
643 647 4.384208 GGATGGTTAGCAAGACAGTGGTAT 60.384 45.833 0.00 0.00 31.88 2.73
644 648 3.055385 GGATGGTTAGCAAGACAGTGGTA 60.055 47.826 0.00 0.00 0.00 3.25
645 649 2.290323 GGATGGTTAGCAAGACAGTGGT 60.290 50.000 0.00 0.00 0.00 4.16
646 650 2.290260 TGGATGGTTAGCAAGACAGTGG 60.290 50.000 0.00 0.00 0.00 4.00
666 670 9.887406 ATTTAATTTCTAACTAACGTGTGGTTG 57.113 29.630 10.09 0.00 39.75 3.77
678 682 9.821662 GTGTGCGTTAAGATTTAATTTCTAACT 57.178 29.630 0.00 0.00 0.00 2.24
691 695 7.387948 AGTGAAAAATAGAGTGTGCGTTAAGAT 59.612 33.333 0.00 0.00 0.00 2.40
703 707 7.039714 GGGGTTGATCAAAGTGAAAAATAGAGT 60.040 37.037 10.35 0.00 0.00 3.24
706 710 6.211384 AGGGGGTTGATCAAAGTGAAAAATAG 59.789 38.462 10.35 0.00 0.00 1.73
725 729 0.249398 CGTCAATCTCGAAAGGGGGT 59.751 55.000 0.00 0.00 0.00 4.95
726 730 0.462047 CCGTCAATCTCGAAAGGGGG 60.462 60.000 0.00 0.00 0.00 5.40
727 731 0.462047 CCCGTCAATCTCGAAAGGGG 60.462 60.000 0.00 0.00 33.61 4.79
728 732 0.249398 ACCCGTCAATCTCGAAAGGG 59.751 55.000 3.79 3.79 39.67 3.95
729 733 2.481449 CCTACCCGTCAATCTCGAAAGG 60.481 54.545 0.00 0.00 0.00 3.11
730 734 2.481449 CCCTACCCGTCAATCTCGAAAG 60.481 54.545 0.00 0.00 0.00 2.62
731 735 1.479323 CCCTACCCGTCAATCTCGAAA 59.521 52.381 0.00 0.00 0.00 3.46
732 736 1.108776 CCCTACCCGTCAATCTCGAA 58.891 55.000 0.00 0.00 0.00 3.71
733 737 1.389609 GCCCTACCCGTCAATCTCGA 61.390 60.000 0.00 0.00 0.00 4.04
734 738 1.067582 GCCCTACCCGTCAATCTCG 59.932 63.158 0.00 0.00 0.00 4.04
735 739 1.446366 GGCCCTACCCGTCAATCTC 59.554 63.158 0.00 0.00 0.00 2.75
736 740 2.432300 CGGCCCTACCCGTCAATCT 61.432 63.158 0.00 0.00 43.24 2.40
737 741 2.108362 CGGCCCTACCCGTCAATC 59.892 66.667 0.00 0.00 43.24 2.67
738 742 3.476419 CCGGCCCTACCCGTCAAT 61.476 66.667 0.00 0.00 46.71 2.57
772 1078 9.313118 GGTTTGATGATTTGTCTTAAACTTGTT 57.687 29.630 0.00 0.00 0.00 2.83
777 1083 8.764287 CAAAGGGTTTGATGATTTGTCTTAAAC 58.236 33.333 0.00 0.00 43.26 2.01
779 1085 8.017418 ACAAAGGGTTTGATGATTTGTCTTAA 57.983 30.769 6.40 0.00 43.26 1.85
781 1087 6.484364 ACAAAGGGTTTGATGATTTGTCTT 57.516 33.333 6.40 0.00 43.26 3.01
782 1088 7.595819 TTACAAAGGGTTTGATGATTTGTCT 57.404 32.000 6.40 0.00 41.70 3.41
784 1090 9.054922 CATTTTACAAAGGGTTTGATGATTTGT 57.945 29.630 6.40 6.80 44.05 2.83
809 1115 4.450976 CGGGGATTAGATGATTTGTCACA 58.549 43.478 0.00 0.00 0.00 3.58
813 1119 2.783510 ACCCGGGGATTAGATGATTTGT 59.216 45.455 27.92 0.00 0.00 2.83
814 1120 3.508845 ACCCGGGGATTAGATGATTTG 57.491 47.619 27.92 0.00 0.00 2.32
826 1132 0.397535 AACTAGCGAATACCCGGGGA 60.398 55.000 27.92 19.95 0.00 4.81
831 1137 6.364435 CGGAAAAGTATAACTAGCGAATACCC 59.636 42.308 0.00 0.00 0.00 3.69
832 1138 6.920210 ACGGAAAAGTATAACTAGCGAATACC 59.080 38.462 0.00 0.00 0.00 2.73
834 1140 8.840321 ACTACGGAAAAGTATAACTAGCGAATA 58.160 33.333 0.00 0.00 0.00 1.75
835 1141 7.710896 ACTACGGAAAAGTATAACTAGCGAAT 58.289 34.615 0.00 0.00 0.00 3.34
836 1142 7.088589 ACTACGGAAAAGTATAACTAGCGAA 57.911 36.000 0.00 0.00 0.00 4.70
837 1143 6.683974 ACTACGGAAAAGTATAACTAGCGA 57.316 37.500 0.00 0.00 0.00 4.93
838 1144 7.910162 TGTTACTACGGAAAAGTATAACTAGCG 59.090 37.037 0.00 0.00 30.74 4.26
839 1145 9.741647 ATGTTACTACGGAAAAGTATAACTAGC 57.258 33.333 0.00 0.00 30.74 3.42
875 1183 0.741915 CAGGAGTTCTCTAGGCCGAC 59.258 60.000 0.00 0.00 0.00 4.79
881 1189 1.202245 GCAGACGCAGGAGTTCTCTAG 60.202 57.143 0.00 0.00 38.36 2.43
882 1190 0.811915 GCAGACGCAGGAGTTCTCTA 59.188 55.000 0.00 0.00 38.36 2.43
938 1269 1.310904 TTTCGGAAGGAAACGGTTGG 58.689 50.000 0.00 0.00 39.67 3.77
1188 1522 3.467226 TGGAGCGACCGGAATCCC 61.467 66.667 9.46 2.82 42.61 3.85
1344 1678 2.210341 GAGAGGGGTCGTCGTTGTCC 62.210 65.000 0.00 0.00 0.00 4.02
1804 2153 0.807275 GGCTGCGGCAAATCCATTTC 60.807 55.000 21.31 0.00 40.87 2.17
1955 2304 1.293924 CATCCATCTCTTGACACCGC 58.706 55.000 0.00 0.00 0.00 5.68
2024 2385 3.510388 TCACCACGACATGATCTTCTC 57.490 47.619 0.00 0.00 0.00 2.87
2050 2411 2.933878 AAGCCGTCGACAACTGCCAA 62.934 55.000 17.16 0.00 38.76 4.52
2252 2613 1.062886 TCCAGGGACCAGATGTAGGAG 60.063 57.143 0.00 0.00 0.00 3.69
2295 2672 5.163513 CAGATTTTCACAACAATAGGCACC 58.836 41.667 0.00 0.00 0.00 5.01
2319 2696 8.492673 AATAGCAAAATGTGAAGAGTCGATAA 57.507 30.769 0.00 0.00 0.00 1.75
2324 2701 7.588512 ACTGAAATAGCAAAATGTGAAGAGTC 58.411 34.615 0.00 0.00 0.00 3.36
2325 2702 7.229306 TGACTGAAATAGCAAAATGTGAAGAGT 59.771 33.333 0.00 0.00 0.00 3.24
2347 2724 3.290710 ACAAAATCAACCACAGCTGACT 58.709 40.909 23.35 0.00 0.00 3.41
2353 2730 5.278463 CCCTCAGTAACAAAATCAACCACAG 60.278 44.000 0.00 0.00 0.00 3.66
2357 2734 5.710099 TCATCCCTCAGTAACAAAATCAACC 59.290 40.000 0.00 0.00 0.00 3.77
2372 2752 7.443302 AGACTTAGAATCAATTCATCCCTCA 57.557 36.000 5.59 0.00 39.23 3.86
2391 2771 9.869667 ACCAGACATGTTACTATATCTAGACTT 57.130 33.333 0.00 0.00 0.00 3.01
2431 2811 4.697352 GGTCTGCAATTGAACTCATGTACT 59.303 41.667 10.34 0.00 0.00 2.73
2454 2834 9.136323 TGTGTGCTATCATATATCCTACCTATG 57.864 37.037 0.00 0.00 0.00 2.23
2515 2946 2.290134 ACTTTACCGGAAAGAAGCCTCC 60.290 50.000 24.21 0.00 46.57 4.30
2518 2949 1.199327 GCACTTTACCGGAAAGAAGCC 59.801 52.381 24.21 12.89 46.57 4.35
2520 2951 3.399330 TCTGCACTTTACCGGAAAGAAG 58.601 45.455 24.21 18.70 46.57 2.85
2674 3106 8.133754 TGTATATACAAATTGTGCGAGGTTAC 57.866 34.615 13.24 2.51 32.40 2.50
2878 3315 4.307032 AAAAGGCCTCTATCTCTGCAAA 57.693 40.909 5.23 0.00 0.00 3.68
2880 3317 4.471386 AGTAAAAAGGCCTCTATCTCTGCA 59.529 41.667 5.23 0.00 0.00 4.41
2883 3320 6.154706 TCGAAAGTAAAAAGGCCTCTATCTCT 59.845 38.462 5.23 0.00 0.00 3.10
2972 3409 5.394663 CGAAGAACACCTATCCTCAAGATGT 60.395 44.000 0.00 0.00 36.33 3.06
3020 3457 3.468770 ACATTGATCATCAGCTCTCTGC 58.531 45.455 0.00 0.00 40.13 4.26
3178 3615 0.395862 TCGGTCTCTTGGGAGCTAGG 60.396 60.000 0.00 0.00 39.31 3.02
3257 3694 6.371548 GCTGTAAGATGGATCAAGTACAACAA 59.628 38.462 0.00 0.00 34.07 2.83
3263 3700 5.939764 AGTGCTGTAAGATGGATCAAGTA 57.060 39.130 0.00 0.00 34.07 2.24
3383 3820 6.918022 GTGTAGGTTGTGATTTTCTTTTGGAG 59.082 38.462 0.00 0.00 0.00 3.86
3420 3857 5.588648 GTCGGAGAAATGGATGTATTTCCAA 59.411 40.000 7.41 0.00 44.27 3.53
3447 3884 4.128388 CCCAACGCCCGGAAATGC 62.128 66.667 0.73 0.00 0.00 3.56
3448 3885 2.360600 TCCCAACGCCCGGAAATG 60.361 61.111 0.73 0.00 0.00 2.32
3457 3895 2.000447 GTTGTGATCTACTCCCAACGC 59.000 52.381 0.00 0.00 0.00 4.84
3460 3898 4.020218 CCTTCTGTTGTGATCTACTCCCAA 60.020 45.833 0.00 0.00 0.00 4.12
3461 3899 3.515502 CCTTCTGTTGTGATCTACTCCCA 59.484 47.826 0.00 0.00 0.00 4.37
3678 4120 8.043113 TGTTATGTGCAGTCTTCTCATAGAATT 58.957 33.333 0.00 0.00 33.13 2.17


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

AutoCloner maintained by Alex Coulton.