Multiple sequence alignment - TraesCS4B01G231000

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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 TraesCS4B01G231000 chr4B 100.000 2579 0 0 1 2579 482779973 482777395 0.000000e+00 4763
1 TraesCS4B01G231000 chr4D 95.344 988 41 3 929 1912 393122815 393121829 0.000000e+00 1565
2 TraesCS4B01G231000 chr4D 89.776 939 51 19 1 901 393123825 393122894 0.000000e+00 1160
3 TraesCS4B01G231000 chr4D 94.273 454 25 1 2029 2481 393116526 393116073 0.000000e+00 693
4 TraesCS4B01G231000 chr4D 90.517 116 11 0 1912 2027 393121769 393121654 1.240000e-33 154
5 TraesCS4B01G231000 chr4A 94.646 990 47 4 929 1912 74577123 74576134 0.000000e+00 1530
6 TraesCS4B01G231000 chr4A 89.328 937 63 19 1 906 74578127 74577197 0.000000e+00 1142
7 TraesCS4B01G231000 chr4A 91.434 572 46 2 1912 2481 74576074 74575504 0.000000e+00 782


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 TraesCS4B01G231000 chr4B 482777395 482779973 2578 True 4763.000000 4763 100.000000 1 2579 1 chr4B.!!$R1 2578
1 TraesCS4B01G231000 chr4D 393121654 393123825 2171 True 959.666667 1565 91.879000 1 2027 3 chr4D.!!$R2 2026
2 TraesCS4B01G231000 chr4A 74575504 74578127 2623 True 1151.333333 1530 91.802667 1 2481 3 chr4A.!!$R1 2480

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
560 576 0.592754 CGATCGCCTCTCCTCGTTTC 60.593 60.0 0.26 0.0 0.0 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2539 2695 0.034896 TCCACTTCGGGCTTCAGAAC 59.965 55.0 0.0 0.0 34.36 3.01 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
112 113 3.954981 ACCCCCAGCTGTACCCCT 61.955 66.667 13.81 0.00 0.00 4.79
198 199 3.131223 ACTGCTACGTCATGAAGCTGTAT 59.869 43.478 21.84 5.67 43.73 2.29
210 211 0.760567 AGCTGTATCCGGATGGCAGA 60.761 55.000 35.06 15.36 34.14 4.26
246 247 3.426568 GTCAGCTGCAAGGCGGTC 61.427 66.667 9.47 0.00 37.24 4.79
261 262 4.452733 GTCGCGGGCTGCTACCTT 62.453 66.667 17.54 0.00 43.27 3.50
271 272 0.886043 CTGCTACCTTGTGTGCAGCA 60.886 55.000 0.00 0.00 40.03 4.41
283 284 4.527157 GCAGCAATGGAGACGCGC 62.527 66.667 5.73 0.00 0.00 6.86
369 370 2.746277 GAATTCCAGCGGTGCGGT 60.746 61.111 9.63 0.00 38.40 5.68
419 435 3.056107 GTCTAGCCACGGCCATATGATTA 60.056 47.826 2.24 0.00 43.17 1.75
420 436 2.949177 AGCCACGGCCATATGATTAA 57.051 45.000 2.24 0.00 43.17 1.40
421 437 3.439857 AGCCACGGCCATATGATTAAT 57.560 42.857 2.24 0.00 43.17 1.40
422 438 3.766545 AGCCACGGCCATATGATTAATT 58.233 40.909 2.24 0.00 43.17 1.40
429 445 5.048991 ACGGCCATATGATTAATTCGGTTTC 60.049 40.000 2.24 0.00 0.00 2.78
461 477 6.509656 TCTATCGGCTTAAGCGAGATTTAAA 58.490 36.000 29.41 17.35 43.26 1.52
463 479 3.619929 TCGGCTTAAGCGAGATTTAAACC 59.380 43.478 20.80 1.92 43.26 3.27
465 481 4.094442 CGGCTTAAGCGAGATTTAAACCTT 59.906 41.667 20.80 0.00 43.26 3.50
466 482 5.391629 CGGCTTAAGCGAGATTTAAACCTTT 60.392 40.000 20.80 0.00 43.26 3.11
476 492 7.519970 GCGAGATTTAAACCTTTCAGTTTCTCA 60.520 37.037 8.19 0.00 40.38 3.27
492 508 1.613925 TCTCACGGGACAGACAAGAAG 59.386 52.381 0.00 0.00 0.00 2.85
514 530 8.164058 GAAGAATTCTTCCATCCCAATCTTAG 57.836 38.462 30.16 0.00 44.93 2.18
560 576 0.592754 CGATCGCCTCTCCTCGTTTC 60.593 60.000 0.26 0.00 0.00 2.78
585 601 1.197721 CAGAAAGCAACTCGGCGATTT 59.802 47.619 11.27 8.70 39.27 2.17
591 616 2.124122 GCAACTCGGCGATTTGTTTTT 58.876 42.857 31.39 7.79 0.00 1.94
593 618 2.699251 ACTCGGCGATTTGTTTTTCC 57.301 45.000 11.27 0.00 0.00 3.13
605 630 6.457663 CGATTTGTTTTTCCGATATGGCTGTA 60.458 38.462 0.00 0.00 37.80 2.74
623 648 4.318831 GCTGTAGCACACACTGTTTAAGTC 60.319 45.833 0.00 0.00 37.84 3.01
668 701 2.754552 GCTAAGGTGACCATGCATGAAA 59.245 45.455 28.31 9.90 0.00 2.69
701 734 3.904136 ACTGCTTGGAATTTTCTCACG 57.096 42.857 0.00 0.00 0.00 4.35
702 735 3.476552 ACTGCTTGGAATTTTCTCACGA 58.523 40.909 0.00 0.00 0.00 4.35
715 748 0.673956 CTCACGAGTCTCCTGGTCGA 60.674 60.000 10.88 0.00 37.16 4.20
731 764 2.294791 GGTCGATCGATTCAGATCCACT 59.705 50.000 22.50 0.00 42.94 4.00
732 765 3.243569 GGTCGATCGATTCAGATCCACTT 60.244 47.826 22.50 0.00 42.94 3.16
767 800 1.173913 ATTTCGCCAAGCTGTAACCC 58.826 50.000 0.00 0.00 0.00 4.11
768 801 1.231958 TTTCGCCAAGCTGTAACCCG 61.232 55.000 0.00 0.00 0.00 5.28
781 814 2.548904 TGTAACCCGAACACCATTTTCG 59.451 45.455 0.00 0.00 44.40 3.46
790 823 1.732259 ACACCATTTTCGCGAGATGAC 59.268 47.619 26.45 0.00 41.60 3.06
799 832 4.895224 TTCGCGAGATGACAGTACTTAT 57.105 40.909 9.59 0.00 41.60 1.73
800 833 4.469625 TCGCGAGATGACAGTACTTATC 57.530 45.455 3.71 0.00 33.31 1.75
801 834 3.250280 TCGCGAGATGACAGTACTTATCC 59.750 47.826 3.71 0.00 33.31 2.59
803 836 4.497507 CGCGAGATGACAGTACTTATCCAA 60.498 45.833 0.00 0.00 0.00 3.53
804 837 5.348986 GCGAGATGACAGTACTTATCCAAA 58.651 41.667 0.00 0.00 0.00 3.28
805 838 5.810587 GCGAGATGACAGTACTTATCCAAAA 59.189 40.000 0.00 0.00 0.00 2.44
807 840 7.011482 GCGAGATGACAGTACTTATCCAAAAAT 59.989 37.037 0.00 0.00 0.00 1.82
808 841 8.331022 CGAGATGACAGTACTTATCCAAAAATG 58.669 37.037 0.00 0.00 0.00 2.32
809 842 7.989826 AGATGACAGTACTTATCCAAAAATGC 58.010 34.615 0.00 0.00 0.00 3.56
836 871 1.135139 TCATCTGCTGTCTCTTACCGC 59.865 52.381 0.00 0.00 38.68 5.68
871 906 3.132863 CAAATTCTTGGGCTGCTGC 57.867 52.632 7.10 7.10 38.76 5.25
886 923 2.877168 CTGCTGCACACTTTTTCTCTCT 59.123 45.455 0.00 0.00 0.00 3.10
902 939 5.291905 TCTCTCTTTTTCTTCTTTCCCGT 57.708 39.130 0.00 0.00 0.00 5.28
906 943 4.070009 TCTTTTTCTTCTTTCCCGTAGCC 58.930 43.478 0.00 0.00 0.00 3.93
907 944 2.088950 TTTCTTCTTTCCCGTAGCCG 57.911 50.000 0.00 0.00 0.00 5.52
908 945 0.971386 TTCTTCTTTCCCGTAGCCGT 59.029 50.000 0.00 0.00 0.00 5.68
911 948 3.554934 TCTTCTTTCCCGTAGCCGTATA 58.445 45.455 0.00 0.00 0.00 1.47
913 950 5.316167 TCTTCTTTCCCGTAGCCGTATATA 58.684 41.667 0.00 0.00 0.00 0.86
914 951 5.182001 TCTTCTTTCCCGTAGCCGTATATAC 59.818 44.000 2.53 2.53 0.00 1.47
915 952 4.397420 TCTTTCCCGTAGCCGTATATACA 58.603 43.478 13.22 0.00 0.00 2.29
916 953 4.216257 TCTTTCCCGTAGCCGTATATACAC 59.784 45.833 13.22 4.45 0.00 2.90
918 955 2.813754 TCCCGTAGCCGTATATACACAC 59.186 50.000 13.22 1.72 0.00 3.82
919 956 2.553602 CCCGTAGCCGTATATACACACA 59.446 50.000 13.22 0.00 0.00 3.72
920 957 3.558505 CCGTAGCCGTATATACACACAC 58.441 50.000 13.22 4.59 0.00 3.82
921 958 3.558505 CGTAGCCGTATATACACACACC 58.441 50.000 13.22 0.00 0.00 4.16
923 960 4.497842 CGTAGCCGTATATACACACACCAA 60.498 45.833 13.22 0.00 0.00 3.67
924 961 4.475051 AGCCGTATATACACACACCAAA 57.525 40.909 13.22 0.00 0.00 3.28
925 962 4.439057 AGCCGTATATACACACACCAAAG 58.561 43.478 13.22 0.00 0.00 2.77
926 963 3.001939 GCCGTATATACACACACCAAAGC 59.998 47.826 13.22 0.00 0.00 3.51
927 964 3.244345 CCGTATATACACACACCAAAGCG 59.756 47.826 13.22 0.00 0.00 4.68
951 1039 1.134699 GCTCGATCACATCACTCCCAA 60.135 52.381 0.00 0.00 0.00 4.12
978 1066 2.945984 CAACGCACGCACCATCTT 59.054 55.556 0.00 0.00 0.00 2.40
1213 1301 4.394712 GGGACTGGTGCCACCTCG 62.395 72.222 16.23 8.74 41.16 4.63
1632 1720 4.383602 GCGTGTCGGCGTGCAAAT 62.384 61.111 6.85 0.00 0.00 2.32
1665 1753 2.512485 TGCAAGCCAAATGTTGACAG 57.488 45.000 0.00 0.00 0.00 3.51
1671 1760 5.585390 CAAGCCAAATGTTGACAGGATATC 58.415 41.667 0.00 0.00 0.00 1.63
1673 1762 4.885907 AGCCAAATGTTGACAGGATATCAG 59.114 41.667 4.83 0.00 0.00 2.90
1835 1929 0.460722 TTCCCTCGACGAACAACACA 59.539 50.000 0.00 0.00 0.00 3.72
1964 2118 1.004918 CCTCCGACTCGCCTTTGTT 60.005 57.895 0.00 0.00 0.00 2.83
1992 2146 3.450115 CTCCTCGTCACCGGTCCC 61.450 72.222 2.59 0.00 33.95 4.46
2004 2158 3.003763 GGTCCCGGCTCAGTCCTT 61.004 66.667 0.00 0.00 0.00 3.36
2031 2185 3.006859 GGCCTTGCACTACTGGAATTTTT 59.993 43.478 0.00 0.00 0.00 1.94
2032 2186 4.237724 GCCTTGCACTACTGGAATTTTTC 58.762 43.478 0.00 0.00 0.00 2.29
2045 2199 6.267471 ACTGGAATTTTTCAATTAGGCACTCA 59.733 34.615 0.00 0.00 41.75 3.41
2070 2224 0.517316 GCATTTGTCGAGTCCCACAC 59.483 55.000 0.00 0.00 0.00 3.82
2089 2243 3.103911 CGGTGAACACGACTCGGC 61.104 66.667 2.98 0.00 0.00 5.54
2125 2279 4.029043 GCAAAACTGACTTTGTCGAGTTC 58.971 43.478 12.29 0.00 38.35 3.01
2134 2288 5.642063 TGACTTTGTCGAGTTCTTTTTCACT 59.358 36.000 0.00 0.00 34.95 3.41
2147 2301 1.581934 TTTCACTGGCACTCGACAAG 58.418 50.000 0.00 0.00 0.00 3.16
2155 2309 1.673033 GGCACTCGACAAGCACATACT 60.673 52.381 2.02 0.00 0.00 2.12
2157 2311 3.448686 GCACTCGACAAGCACATACTAT 58.551 45.455 0.00 0.00 0.00 2.12
2158 2312 3.865745 GCACTCGACAAGCACATACTATT 59.134 43.478 0.00 0.00 0.00 1.73
2159 2313 4.330074 GCACTCGACAAGCACATACTATTT 59.670 41.667 0.00 0.00 0.00 1.40
2194 2350 4.487948 CGTGTATAGGGAACTCGACAAAA 58.512 43.478 0.00 0.00 43.67 2.44
2195 2351 4.925054 CGTGTATAGGGAACTCGACAAAAA 59.075 41.667 0.00 0.00 43.67 1.94
2228 2384 2.353269 CAGAACGGCGCATTAATGGTAA 59.647 45.455 17.02 0.00 0.00 2.85
2289 2445 1.277495 GCACTCGGCAATGCAACAAC 61.277 55.000 7.79 0.00 43.97 3.32
2359 2515 3.692576 CGAAACTCGACAATACCTCGAT 58.307 45.455 0.00 0.00 43.74 3.59
2363 2519 2.358267 ACTCGACAATACCTCGATGGAC 59.642 50.000 7.76 0.00 39.36 4.02
2391 2547 5.110814 AGTGCCACATAGCATAACCTTTA 57.889 39.130 0.00 0.00 46.24 1.85
2408 2564 5.488341 ACCTTTATCGAGTGTTGCTTGTAT 58.512 37.500 0.00 0.00 0.00 2.29
2410 2566 5.351465 CCTTTATCGAGTGTTGCTTGTATGT 59.649 40.000 0.00 0.00 0.00 2.29
2417 2573 3.251729 AGTGTTGCTTGTATGTTGCTCAG 59.748 43.478 0.00 0.00 0.00 3.35
2481 2637 6.639279 GGCAGTCTTTATCGAGTTTCTATCTC 59.361 42.308 0.00 0.00 0.00 2.75
2482 2638 6.639279 GCAGTCTTTATCGAGTTTCTATCTCC 59.361 42.308 0.00 0.00 0.00 3.71
2483 2639 6.853872 CAGTCTTTATCGAGTTTCTATCTCCG 59.146 42.308 0.00 0.00 0.00 4.63
2484 2640 5.626132 GTCTTTATCGAGTTTCTATCTCCGC 59.374 44.000 0.00 0.00 0.00 5.54
2485 2641 5.531659 TCTTTATCGAGTTTCTATCTCCGCT 59.468 40.000 0.00 0.00 0.00 5.52
2486 2642 6.709397 TCTTTATCGAGTTTCTATCTCCGCTA 59.291 38.462 0.00 0.00 0.00 4.26
2487 2643 6.483385 TTATCGAGTTTCTATCTCCGCTAG 57.517 41.667 0.00 0.00 0.00 3.42
2488 2644 2.548904 TCGAGTTTCTATCTCCGCTAGC 59.451 50.000 4.06 4.06 0.00 3.42
2489 2645 2.663334 CGAGTTTCTATCTCCGCTAGCG 60.663 54.545 29.93 29.93 39.44 4.26
2490 2646 2.291190 GAGTTTCTATCTCCGCTAGCGT 59.709 50.000 33.18 18.76 37.81 5.07
2491 2647 2.291190 AGTTTCTATCTCCGCTAGCGTC 59.709 50.000 33.18 11.34 37.81 5.19
2492 2648 0.866427 TTCTATCTCCGCTAGCGTCG 59.134 55.000 33.18 23.33 37.81 5.12
2493 2649 0.033090 TCTATCTCCGCTAGCGTCGA 59.967 55.000 33.18 27.24 37.81 4.20
2494 2650 0.440758 CTATCTCCGCTAGCGTCGAG 59.559 60.000 33.18 29.97 37.81 4.04
2495 2651 0.033090 TATCTCCGCTAGCGTCGAGA 59.967 55.000 33.42 33.42 39.60 4.04
2496 2652 1.225376 ATCTCCGCTAGCGTCGAGAG 61.225 60.000 33.84 30.11 39.03 3.20
2497 2653 2.887889 CTCCGCTAGCGTCGAGAGG 61.888 68.421 33.18 17.46 37.81 3.69
2498 2654 3.203412 CCGCTAGCGTCGAGAGGT 61.203 66.667 33.18 0.00 37.81 3.85
2499 2655 2.325166 CGCTAGCGTCGAGAGGTC 59.675 66.667 28.66 0.00 34.35 3.85
2500 2656 2.174969 CGCTAGCGTCGAGAGGTCT 61.175 63.158 28.66 0.00 34.35 3.85
2501 2657 0.875040 CGCTAGCGTCGAGAGGTCTA 60.875 60.000 28.66 0.00 34.35 2.59
2502 2658 1.297664 GCTAGCGTCGAGAGGTCTAA 58.702 55.000 0.00 0.00 0.00 2.10
2503 2659 1.003652 GCTAGCGTCGAGAGGTCTAAC 60.004 57.143 0.00 0.00 0.00 2.34
2504 2660 1.598601 CTAGCGTCGAGAGGTCTAACC 59.401 57.143 0.00 0.00 38.99 2.85
2505 2661 1.031029 AGCGTCGAGAGGTCTAACCC 61.031 60.000 0.00 0.00 39.75 4.11
2506 2662 1.310933 GCGTCGAGAGGTCTAACCCA 61.311 60.000 0.00 0.00 39.75 4.51
2507 2663 0.733729 CGTCGAGAGGTCTAACCCAG 59.266 60.000 0.00 0.00 39.75 4.45
2508 2664 1.678123 CGTCGAGAGGTCTAACCCAGA 60.678 57.143 0.00 0.00 39.75 3.86
2509 2665 2.018515 GTCGAGAGGTCTAACCCAGAG 58.981 57.143 0.00 0.00 39.75 3.35
2510 2666 1.634459 TCGAGAGGTCTAACCCAGAGT 59.366 52.381 0.00 0.00 39.75 3.24
2511 2667 2.842496 TCGAGAGGTCTAACCCAGAGTA 59.158 50.000 0.00 0.00 39.75 2.59
2512 2668 3.458857 TCGAGAGGTCTAACCCAGAGTAT 59.541 47.826 0.00 0.00 39.75 2.12
2513 2669 3.816523 CGAGAGGTCTAACCCAGAGTATC 59.183 52.174 0.00 0.00 39.75 2.24
2514 2670 4.445162 CGAGAGGTCTAACCCAGAGTATCT 60.445 50.000 0.00 0.00 41.15 1.98
2515 2671 5.221682 CGAGAGGTCTAACCCAGAGTATCTA 60.222 48.000 0.00 0.00 41.76 1.98
2516 2672 6.521084 CGAGAGGTCTAACCCAGAGTATCTAT 60.521 46.154 0.00 0.00 41.76 1.98
2517 2673 6.548321 AGAGGTCTAACCCAGAGTATCTATG 58.452 44.000 0.00 0.00 41.76 2.23
2518 2674 6.103501 AGAGGTCTAACCCAGAGTATCTATGT 59.896 42.308 0.00 0.00 41.76 2.29
2519 2675 6.684538 AGGTCTAACCCAGAGTATCTATGTT 58.315 40.000 0.00 0.00 41.76 2.71
2520 2676 7.133483 AGGTCTAACCCAGAGTATCTATGTTT 58.867 38.462 0.00 0.00 41.76 2.83
2521 2677 7.070074 AGGTCTAACCCAGAGTATCTATGTTTG 59.930 40.741 0.00 0.00 41.76 2.93
2529 2685 5.874892 GAGTATCTATGTTTGCTGACGAC 57.125 43.478 0.00 0.00 0.00 4.34
2530 2686 4.352039 AGTATCTATGTTTGCTGACGACG 58.648 43.478 0.00 0.00 0.00 5.12
2531 2687 1.346365 TCTATGTTTGCTGACGACGC 58.654 50.000 0.00 0.00 0.00 5.19
2532 2688 0.370273 CTATGTTTGCTGACGACGCC 59.630 55.000 0.00 0.00 0.00 5.68
2533 2689 1.348538 TATGTTTGCTGACGACGCCG 61.349 55.000 0.00 0.00 42.50 6.46
2543 2699 2.202440 CGACGCCGTGATCGTTCT 60.202 61.111 0.00 0.00 40.59 3.01
2544 2700 2.497092 CGACGCCGTGATCGTTCTG 61.497 63.158 0.00 0.00 40.59 3.02
2545 2701 1.154093 GACGCCGTGATCGTTCTGA 60.154 57.895 0.00 0.00 40.59 3.27
2546 2702 0.731514 GACGCCGTGATCGTTCTGAA 60.732 55.000 0.00 0.00 40.59 3.02
2547 2703 0.732880 ACGCCGTGATCGTTCTGAAG 60.733 55.000 0.00 0.00 36.72 3.02
2548 2704 1.710339 GCCGTGATCGTTCTGAAGC 59.290 57.895 0.00 0.00 35.01 3.86
2549 2705 1.696832 GCCGTGATCGTTCTGAAGCC 61.697 60.000 0.00 0.00 35.01 4.35
2550 2706 1.084370 CCGTGATCGTTCTGAAGCCC 61.084 60.000 0.00 0.00 35.01 5.19
2551 2707 1.413767 CGTGATCGTTCTGAAGCCCG 61.414 60.000 0.00 0.00 0.00 6.13
2552 2708 0.108804 GTGATCGTTCTGAAGCCCGA 60.109 55.000 4.42 4.42 0.00 5.14
2553 2709 0.606096 TGATCGTTCTGAAGCCCGAA 59.394 50.000 5.82 0.00 32.53 4.30
2554 2710 1.281899 GATCGTTCTGAAGCCCGAAG 58.718 55.000 5.82 0.00 32.53 3.79
2555 2711 0.608640 ATCGTTCTGAAGCCCGAAGT 59.391 50.000 5.82 0.00 32.53 3.01
2556 2712 0.319555 TCGTTCTGAAGCCCGAAGTG 60.320 55.000 0.00 0.00 0.00 3.16
2557 2713 1.291877 CGTTCTGAAGCCCGAAGTGG 61.292 60.000 0.00 0.00 37.55 4.00
2558 2714 0.034896 GTTCTGAAGCCCGAAGTGGA 59.965 55.000 0.00 0.00 42.00 4.02
2559 2715 0.762418 TTCTGAAGCCCGAAGTGGAA 59.238 50.000 0.00 0.00 42.00 3.53
2560 2716 0.321671 TCTGAAGCCCGAAGTGGAAG 59.678 55.000 0.00 0.00 42.00 3.46
2561 2717 0.321671 CTGAAGCCCGAAGTGGAAGA 59.678 55.000 0.00 0.00 42.00 2.87
2562 2718 0.034896 TGAAGCCCGAAGTGGAAGAC 59.965 55.000 0.00 0.00 42.00 3.01
2563 2719 0.673956 GAAGCCCGAAGTGGAAGACC 60.674 60.000 0.00 0.00 42.00 3.85
2564 2720 1.128188 AAGCCCGAAGTGGAAGACCT 61.128 55.000 0.00 0.00 42.00 3.85
2565 2721 1.079057 GCCCGAAGTGGAAGACCTC 60.079 63.158 0.00 0.00 42.00 3.85
2566 2722 1.215647 CCCGAAGTGGAAGACCTCG 59.784 63.158 0.00 0.00 42.00 4.63
2567 2723 1.446272 CCGAAGTGGAAGACCTCGC 60.446 63.158 0.00 0.00 42.00 5.03
2568 2724 1.587054 CGAAGTGGAAGACCTCGCT 59.413 57.895 0.00 0.00 37.04 4.93
2569 2725 0.809385 CGAAGTGGAAGACCTCGCTA 59.191 55.000 0.00 0.00 37.04 4.26
2570 2726 1.467713 CGAAGTGGAAGACCTCGCTAC 60.468 57.143 0.00 0.00 37.04 3.58
2571 2727 1.819903 GAAGTGGAAGACCTCGCTACT 59.180 52.381 0.00 0.00 37.04 2.57
2572 2728 1.926108 AGTGGAAGACCTCGCTACTT 58.074 50.000 0.00 0.00 37.04 2.24
2573 2729 1.546476 AGTGGAAGACCTCGCTACTTG 59.454 52.381 0.00 0.00 37.04 3.16
2574 2730 0.246635 TGGAAGACCTCGCTACTTGC 59.753 55.000 0.00 0.00 37.04 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 0.802607 CGTGCTCTTCCTACCTTCGC 60.803 60.000 0.00 0.00 0.00 4.70
166 167 2.488820 GTAGCAGTCGTCGGGGTC 59.511 66.667 0.00 0.00 0.00 4.46
169 170 2.099831 GACGTAGCAGTCGTCGGG 59.900 66.667 11.20 0.00 45.64 5.14
198 199 2.366837 ACCCATCTGCCATCCGGA 60.367 61.111 6.61 6.61 0.00 5.14
210 211 1.153249 CGCCACGGTTATGACCCAT 60.153 57.895 0.22 0.00 43.42 4.00
261 262 1.229975 CGTCTCCATTGCTGCACACA 61.230 55.000 0.00 0.00 0.00 3.72
271 272 4.760047 AAGCGGCGCGTCTCCATT 62.760 61.111 27.59 10.58 0.00 3.16
343 344 3.264897 CTGGAATTCGGAGGCGCG 61.265 66.667 0.00 0.00 0.00 6.86
419 435 5.006358 CGATAGAAACCATCGAAACCGAATT 59.994 40.000 0.00 0.00 46.39 2.17
420 436 4.506654 CGATAGAAACCATCGAAACCGAAT 59.493 41.667 0.00 0.00 46.39 3.34
421 437 3.861113 CGATAGAAACCATCGAAACCGAA 59.139 43.478 0.00 0.00 46.39 4.30
422 438 3.441163 CGATAGAAACCATCGAAACCGA 58.559 45.455 0.00 0.00 46.39 4.69
429 445 3.184581 GCTTAAGCCGATAGAAACCATCG 59.815 47.826 17.00 0.00 43.80 3.84
461 477 1.766496 TCCCGTGAGAAACTGAAAGGT 59.234 47.619 0.00 0.00 39.30 3.50
463 479 2.802816 CTGTCCCGTGAGAAACTGAAAG 59.197 50.000 0.00 0.00 42.29 2.62
465 481 2.036387 TCTGTCCCGTGAGAAACTGAA 58.964 47.619 0.00 0.00 0.00 3.02
466 482 1.340248 GTCTGTCCCGTGAGAAACTGA 59.660 52.381 0.00 0.00 0.00 3.41
476 492 3.325135 AGAATTCTTCTTGTCTGTCCCGT 59.675 43.478 0.88 0.00 36.36 5.28
492 508 7.888250 AACTAAGATTGGGATGGAAGAATTC 57.112 36.000 0.00 0.00 46.67 2.17
505 521 6.986817 ACGGACTCATGATTAACTAAGATTGG 59.013 38.462 0.00 0.00 0.00 3.16
508 524 6.098409 ACCACGGACTCATGATTAACTAAGAT 59.902 38.462 0.00 0.00 0.00 2.40
510 526 5.661458 ACCACGGACTCATGATTAACTAAG 58.339 41.667 0.00 0.00 0.00 2.18
511 527 5.670792 ACCACGGACTCATGATTAACTAA 57.329 39.130 0.00 0.00 0.00 2.24
514 530 4.454504 ACAAACCACGGACTCATGATTAAC 59.545 41.667 0.00 0.00 0.00 2.01
560 576 1.205064 CGAGTTGCTTTCTGCCACG 59.795 57.895 0.00 0.00 41.58 4.94
585 601 3.625764 GCTACAGCCATATCGGAAAAACA 59.374 43.478 0.00 0.00 36.56 2.83
591 616 1.068588 GTGTGCTACAGCCATATCGGA 59.931 52.381 0.00 0.00 41.18 4.55
593 618 1.860950 GTGTGTGCTACAGCCATATCG 59.139 52.381 0.00 0.00 40.69 2.92
605 630 3.275617 TGGACTTAAACAGTGTGTGCT 57.724 42.857 0.00 0.00 35.01 4.40
668 701 2.124860 GCAGTAAACCGGCCCGAT 60.125 61.111 3.71 0.00 0.00 4.18
701 734 1.600023 ATCGATCGACCAGGAGACTC 58.400 55.000 22.06 0.00 40.21 3.36
702 735 1.950909 GAATCGATCGACCAGGAGACT 59.049 52.381 22.06 0.00 46.44 3.24
715 748 4.836825 ACAACAAGTGGATCTGAATCGAT 58.163 39.130 0.00 0.00 32.24 3.59
731 764 4.804108 CGAAATTGGCTGGAATACAACAA 58.196 39.130 0.00 0.00 32.70 2.83
732 765 3.366883 GCGAAATTGGCTGGAATACAACA 60.367 43.478 0.00 0.00 0.00 3.33
768 801 2.415168 TCATCTCGCGAAAATGGTGTTC 59.585 45.455 23.39 0.00 0.00 3.18
781 814 4.569761 TGGATAAGTACTGTCATCTCGC 57.430 45.455 0.00 0.00 0.00 5.03
804 837 7.122353 AGAGACAGCAGATGATTAAAAGCATTT 59.878 33.333 0.00 0.00 42.41 2.32
805 838 6.602406 AGAGACAGCAGATGATTAAAAGCATT 59.398 34.615 0.00 0.00 34.76 3.56
807 840 5.494724 AGAGACAGCAGATGATTAAAAGCA 58.505 37.500 0.00 0.00 0.00 3.91
808 841 6.434018 AAGAGACAGCAGATGATTAAAAGC 57.566 37.500 0.00 0.00 0.00 3.51
809 842 7.254252 CGGTAAGAGACAGCAGATGATTAAAAG 60.254 40.741 0.00 0.00 0.00 2.27
836 871 1.579964 TTGGCTGCATGTGCTTCTCG 61.580 55.000 6.55 0.00 42.66 4.04
871 906 9.631452 AAAGAAGAAAAAGAGAGAAAAAGTGTG 57.369 29.630 0.00 0.00 0.00 3.82
886 923 2.809696 CGGCTACGGGAAAGAAGAAAAA 59.190 45.455 0.00 0.00 36.18 1.94
902 939 5.593968 CTTTGGTGTGTGTATATACGGCTA 58.406 41.667 8.33 0.00 0.00 3.93
906 943 3.302221 GCGCTTTGGTGTGTGTATATACG 60.302 47.826 0.00 0.00 0.00 3.06
907 944 3.001939 GGCGCTTTGGTGTGTGTATATAC 59.998 47.826 7.64 5.89 0.00 1.47
908 945 3.199677 GGCGCTTTGGTGTGTGTATATA 58.800 45.455 7.64 0.00 0.00 0.86
911 948 1.573829 CGGCGCTTTGGTGTGTGTAT 61.574 55.000 7.64 0.00 0.00 2.29
913 950 3.582120 CGGCGCTTTGGTGTGTGT 61.582 61.111 7.64 0.00 0.00 3.72
914 951 4.326766 CCGGCGCTTTGGTGTGTG 62.327 66.667 7.64 0.00 0.00 3.82
926 963 3.032609 GATGTGATCGAGCCGGCG 61.033 66.667 23.20 8.11 0.00 6.46
927 964 2.106938 TGATGTGATCGAGCCGGC 59.893 61.111 21.89 21.89 0.00 6.13
978 1066 1.372997 GTGCAAGACCGAGAGCGAA 60.373 57.895 0.00 0.00 40.82 4.70
1093 1181 4.406173 CGCCACAGACGAGTCGCT 62.406 66.667 13.59 8.07 34.09 4.93
1104 1192 3.690280 TCGATGGACTGCGCCACA 61.690 61.111 4.18 0.00 41.56 4.17
1213 1301 2.126189 GTCGGGGTCGTAGCACAC 60.126 66.667 0.00 0.00 37.69 3.82
1665 1753 2.061773 CACAACCGATCGCTGATATCC 58.938 52.381 18.81 0.00 0.00 2.59
1671 1760 3.243101 ACTCTATACACAACCGATCGCTG 60.243 47.826 10.32 11.57 0.00 5.18
1673 1762 3.351020 ACTCTATACACAACCGATCGC 57.649 47.619 10.32 0.00 0.00 4.58
1714 1803 0.544697 TCAAACGATAGGGGCCCTTC 59.455 55.000 33.98 24.71 43.77 3.46
1739 1829 0.317436 TGCACAAATCGACGCAAACC 60.317 50.000 0.00 0.00 0.00 3.27
1835 1929 5.469084 GGACAAGACGGTGTTAGAAGAAATT 59.531 40.000 0.00 0.00 0.00 1.82
1964 2118 3.636231 CGAGGAGGGGTGTTGCCA 61.636 66.667 0.00 0.00 39.65 4.92
1989 2143 3.706373 GCAAGGACTGAGCCGGGA 61.706 66.667 2.18 0.00 0.00 5.14
1992 2146 2.037136 CCAAGCAAGGACTGAGCCG 61.037 63.158 0.00 0.00 0.00 5.52
2004 2158 0.890542 CAGTAGTGCAAGGCCAAGCA 60.891 55.000 17.04 17.04 38.65 3.91
2031 2185 2.489329 GCTTTGCTGAGTGCCTAATTGA 59.511 45.455 0.00 0.00 42.00 2.57
2032 2186 2.229543 TGCTTTGCTGAGTGCCTAATTG 59.770 45.455 0.00 0.00 42.00 2.32
2045 2199 1.537202 GGACTCGACAAATGCTTTGCT 59.463 47.619 8.09 0.00 44.39 3.91
2070 2224 1.442184 CCGAGTCGTGTTCACCGAG 60.442 63.158 12.31 0.00 34.56 4.63
2096 2250 2.584492 AAGTCAGTTTTGCCAACAGC 57.416 45.000 0.00 0.00 44.14 4.40
2109 2263 5.960105 GTGAAAAAGAACTCGACAAAGTCAG 59.040 40.000 0.00 0.00 32.09 3.51
2125 2279 1.939934 TGTCGAGTGCCAGTGAAAAAG 59.060 47.619 0.00 0.00 0.00 2.27
2134 2288 0.320050 TATGTGCTTGTCGAGTGCCA 59.680 50.000 0.00 0.00 0.00 4.92
2158 2312 4.696402 CCTATACACGGTACTTGGCAAAAA 59.304 41.667 0.00 0.00 0.00 1.94
2159 2313 4.255301 CCTATACACGGTACTTGGCAAAA 58.745 43.478 0.00 0.00 0.00 2.44
2194 2350 3.638484 GCCGTTCTGTTTGCACTATTTT 58.362 40.909 0.00 0.00 0.00 1.82
2195 2351 2.350388 CGCCGTTCTGTTTGCACTATTT 60.350 45.455 0.00 0.00 0.00 1.40
2198 2354 1.837538 GCGCCGTTCTGTTTGCACTA 61.838 55.000 0.00 0.00 0.00 2.74
2231 2387 0.667993 AAAGACGTGTTGCCATGTGG 59.332 50.000 0.00 0.00 40.91 4.17
2267 2423 2.551006 TTGCATTGCCGAGTGCGTT 61.551 52.632 6.12 0.00 45.60 4.84
2269 2425 2.502510 GTTGCATTGCCGAGTGCG 60.503 61.111 6.12 0.00 45.60 5.34
2276 2432 1.522258 CTCGTTTGTTGTTGCATTGCC 59.478 47.619 6.12 0.00 0.00 4.52
2289 2445 1.172180 ATGTGCCACACCCTCGTTTG 61.172 55.000 0.00 0.00 32.73 2.93
2322 2478 0.611200 TTCGCCTGGGAAGAAATCGA 59.389 50.000 0.00 0.00 0.00 3.59
2324 2480 2.420372 GAGTTTCGCCTGGGAAGAAATC 59.580 50.000 11.56 8.20 36.45 2.17
2325 2481 2.437413 GAGTTTCGCCTGGGAAGAAAT 58.563 47.619 11.56 4.56 36.45 2.17
2328 2484 1.183030 TCGAGTTTCGCCTGGGAAGA 61.183 55.000 0.00 0.00 40.21 2.87
2356 2512 1.519455 GGCACTCCTTCGTCCATCG 60.519 63.158 0.00 0.00 41.41 3.84
2359 2515 1.480212 ATGTGGCACTCCTTCGTCCA 61.480 55.000 19.83 0.00 0.00 4.02
2363 2519 0.108186 TGCTATGTGGCACTCCTTCG 60.108 55.000 19.83 2.71 37.29 3.79
2366 2522 2.158755 GGTTATGCTATGTGGCACTCCT 60.159 50.000 19.83 6.19 45.36 3.69
2391 2547 3.120199 GCAACATACAAGCAACACTCGAT 60.120 43.478 0.00 0.00 0.00 3.59
2417 2573 1.079503 CTCCTGGAGTAAGCGTTTGC 58.920 55.000 15.76 0.00 43.24 3.68
2481 2637 3.170810 GACCTCTCGACGCTAGCGG 62.171 68.421 37.66 22.77 44.69 5.52
2482 2638 0.875040 TAGACCTCTCGACGCTAGCG 60.875 60.000 34.27 34.27 46.03 4.26
2483 2639 1.003652 GTTAGACCTCTCGACGCTAGC 60.004 57.143 4.06 4.06 0.00 3.42
2484 2640 1.598601 GGTTAGACCTCTCGACGCTAG 59.401 57.143 0.00 0.00 34.73 3.42
2485 2641 1.661341 GGTTAGACCTCTCGACGCTA 58.339 55.000 0.00 0.00 34.73 4.26
2486 2642 1.031029 GGGTTAGACCTCTCGACGCT 61.031 60.000 0.00 0.00 38.64 5.07
2487 2643 1.310933 TGGGTTAGACCTCTCGACGC 61.311 60.000 0.00 0.00 38.64 5.19
2488 2644 0.733729 CTGGGTTAGACCTCTCGACG 59.266 60.000 0.00 0.00 38.64 5.12
2489 2645 2.018515 CTCTGGGTTAGACCTCTCGAC 58.981 57.143 0.00 0.00 38.64 4.20
2490 2646 1.634459 ACTCTGGGTTAGACCTCTCGA 59.366 52.381 0.00 0.00 38.64 4.04
2491 2647 2.131776 ACTCTGGGTTAGACCTCTCG 57.868 55.000 0.00 0.00 38.64 4.04
2492 2648 5.056553 AGATACTCTGGGTTAGACCTCTC 57.943 47.826 0.00 0.00 38.64 3.20
2493 2649 6.103501 ACATAGATACTCTGGGTTAGACCTCT 59.896 42.308 0.00 0.00 38.64 3.69
2494 2650 6.308566 ACATAGATACTCTGGGTTAGACCTC 58.691 44.000 0.00 0.00 38.64 3.85
2495 2651 6.282568 ACATAGATACTCTGGGTTAGACCT 57.717 41.667 0.00 0.00 38.64 3.85
2496 2652 6.980416 AACATAGATACTCTGGGTTAGACC 57.020 41.667 0.00 0.00 37.60 3.85
2497 2653 6.702282 GCAAACATAGATACTCTGGGTTAGAC 59.298 42.308 0.00 0.00 0.00 2.59
2498 2654 6.611642 AGCAAACATAGATACTCTGGGTTAGA 59.388 38.462 0.00 0.00 0.00 2.10
2499 2655 6.703607 CAGCAAACATAGATACTCTGGGTTAG 59.296 42.308 0.00 0.00 0.00 2.34
2500 2656 6.382859 TCAGCAAACATAGATACTCTGGGTTA 59.617 38.462 0.00 0.00 0.00 2.85
2501 2657 5.189736 TCAGCAAACATAGATACTCTGGGTT 59.810 40.000 0.00 0.00 0.00 4.11
2502 2658 4.716784 TCAGCAAACATAGATACTCTGGGT 59.283 41.667 0.00 0.00 0.00 4.51
2503 2659 5.053145 GTCAGCAAACATAGATACTCTGGG 58.947 45.833 0.00 0.00 0.00 4.45
2504 2660 4.742167 CGTCAGCAAACATAGATACTCTGG 59.258 45.833 0.00 0.00 0.00 3.86
2505 2661 5.457148 GTCGTCAGCAAACATAGATACTCTG 59.543 44.000 0.00 0.00 0.00 3.35
2506 2662 5.583495 GTCGTCAGCAAACATAGATACTCT 58.417 41.667 0.00 0.00 0.00 3.24
2507 2663 4.438145 CGTCGTCAGCAAACATAGATACTC 59.562 45.833 0.00 0.00 0.00 2.59
2508 2664 4.352039 CGTCGTCAGCAAACATAGATACT 58.648 43.478 0.00 0.00 0.00 2.12
2509 2665 3.061139 GCGTCGTCAGCAAACATAGATAC 60.061 47.826 0.00 0.00 34.19 2.24
2510 2666 3.113322 GCGTCGTCAGCAAACATAGATA 58.887 45.455 0.00 0.00 34.19 1.98
2511 2667 1.927174 GCGTCGTCAGCAAACATAGAT 59.073 47.619 0.00 0.00 34.19 1.98
2512 2668 1.346365 GCGTCGTCAGCAAACATAGA 58.654 50.000 0.00 0.00 34.19 1.98
2513 2669 0.370273 GGCGTCGTCAGCAAACATAG 59.630 55.000 0.00 0.00 36.08 2.23
2514 2670 1.348538 CGGCGTCGTCAGCAAACATA 61.349 55.000 0.00 0.00 36.08 2.29
2515 2671 2.667318 CGGCGTCGTCAGCAAACAT 61.667 57.895 0.00 0.00 36.08 2.71
2516 2672 3.334751 CGGCGTCGTCAGCAAACA 61.335 61.111 0.00 0.00 36.08 2.83
2526 2682 2.202440 AGAACGATCACGGCGTCG 60.202 61.111 10.85 14.37 41.75 5.12
2527 2683 0.731514 TTCAGAACGATCACGGCGTC 60.732 55.000 10.85 0.00 41.75 5.19
2528 2684 0.732880 CTTCAGAACGATCACGGCGT 60.733 55.000 6.77 6.77 44.94 5.68
2529 2685 1.991430 CTTCAGAACGATCACGGCG 59.009 57.895 4.80 4.80 44.46 6.46
2530 2686 1.696832 GGCTTCAGAACGATCACGGC 61.697 60.000 0.00 0.00 44.46 5.68
2531 2687 1.084370 GGGCTTCAGAACGATCACGG 61.084 60.000 0.00 0.00 44.46 4.94
2532 2688 1.413767 CGGGCTTCAGAACGATCACG 61.414 60.000 0.00 0.00 45.75 4.35
2533 2689 0.108804 TCGGGCTTCAGAACGATCAC 60.109 55.000 0.00 0.00 0.00 3.06
2534 2690 0.606096 TTCGGGCTTCAGAACGATCA 59.394 50.000 0.00 0.00 35.10 2.92
2535 2691 1.281899 CTTCGGGCTTCAGAACGATC 58.718 55.000 0.00 0.00 35.10 3.69
2536 2692 0.608640 ACTTCGGGCTTCAGAACGAT 59.391 50.000 0.00 0.00 35.10 3.73
2537 2693 0.319555 CACTTCGGGCTTCAGAACGA 60.320 55.000 0.00 0.00 0.00 3.85
2538 2694 1.291877 CCACTTCGGGCTTCAGAACG 61.292 60.000 0.00 0.00 0.00 3.95
2539 2695 0.034896 TCCACTTCGGGCTTCAGAAC 59.965 55.000 0.00 0.00 34.36 3.01
2540 2696 0.762418 TTCCACTTCGGGCTTCAGAA 59.238 50.000 0.00 0.00 34.36 3.02
2541 2697 0.321671 CTTCCACTTCGGGCTTCAGA 59.678 55.000 0.00 0.00 34.36 3.27
2542 2698 0.321671 TCTTCCACTTCGGGCTTCAG 59.678 55.000 0.00 0.00 34.36 3.02
2543 2699 0.034896 GTCTTCCACTTCGGGCTTCA 59.965 55.000 0.00 0.00 34.36 3.02
2544 2700 0.673956 GGTCTTCCACTTCGGGCTTC 60.674 60.000 0.00 0.00 34.36 3.86
2545 2701 1.128188 AGGTCTTCCACTTCGGGCTT 61.128 55.000 0.00 0.00 35.89 4.35
2546 2702 1.536662 AGGTCTTCCACTTCGGGCT 60.537 57.895 0.00 0.00 35.89 5.19
2547 2703 1.079057 GAGGTCTTCCACTTCGGGC 60.079 63.158 0.00 0.00 35.89 6.13
2551 2707 1.819903 AGTAGCGAGGTCTTCCACTTC 59.180 52.381 0.00 0.00 35.89 3.01
2552 2708 1.926108 AGTAGCGAGGTCTTCCACTT 58.074 50.000 0.00 0.00 35.89 3.16
2553 2709 1.546476 CAAGTAGCGAGGTCTTCCACT 59.454 52.381 0.00 0.00 35.89 4.00
2554 2710 1.997669 CAAGTAGCGAGGTCTTCCAC 58.002 55.000 0.00 0.00 35.89 4.02
2555 2711 0.246635 GCAAGTAGCGAGGTCTTCCA 59.753 55.000 0.00 0.00 35.89 3.53
2556 2712 3.052181 GCAAGTAGCGAGGTCTTCC 57.948 57.895 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.