Multiple sequence alignment - TraesCS4A01G378100

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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 TraesCS4A01G378100 chr4A 100.000 3581 0 0 1 3581 655261655 655258075 0.000000e+00 6613.0
1 TraesCS4A01G378100 chr7D 90.966 2557 149 31 320 2856 44300957 44298463 0.000000e+00 3367.0
2 TraesCS4A01G378100 chr7D 79.497 795 94 43 2823 3581 44298465 44297704 5.340000e-138 501.0
3 TraesCS4A01G378100 chr7D 93.921 329 9 5 1 326 44301305 44300985 1.490000e-133 486.0
4 TraesCS4A01G378100 chr7A 92.612 758 40 10 2101 2856 46721381 46720638 0.000000e+00 1075.0
5 TraesCS4A01G378100 chr7A 89.045 712 44 11 973 1674 46722724 46722037 0.000000e+00 852.0
6 TraesCS4A01G378100 chr7A 78.176 669 84 34 1459 2099 46722051 46721417 1.570000e-98 370.0
7 TraesCS4A01G378100 chr7A 94.828 232 11 1 715 945 46723254 46723023 9.450000e-96 361.0
8 TraesCS4A01G378100 chr7A 75.354 495 79 29 326 805 46723729 46723263 7.840000e-47 198.0
9 TraesCS4A01G378100 chr7A 91.176 102 9 0 2994 3095 46720399 46720298 4.820000e-29 139.0
10 TraesCS4A01G378100 chr7A 88.421 95 5 4 2823 2911 46720640 46720546 3.780000e-20 110.0
11 TraesCS4A01G378100 chr6B 100.000 28 0 0 3282 3309 535624724 535624697 6.000000e-03 52.8
12 TraesCS4A01G378100 chr5D 100.000 28 0 0 3282 3309 333078311 333078338 6.000000e-03 52.8
13 TraesCS4A01G378100 chr4B 100.000 28 0 0 3282 3309 88841085 88841058 6.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G378100 chr4A 655258075 655261655 3580 True 6613.000000 6613 100.000000 1 3581 1 chr4A.!!$R1 3580
1 TraesCS4A01G378100 chr7D 44297704 44301305 3601 True 1451.333333 3367 88.128000 1 3581 3 chr7D.!!$R1 3580
2 TraesCS4A01G378100 chr7A 46720298 46723729 3431 True 443.571429 1075 87.087429 326 3095 7 chr7A.!!$R1 2769

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
168 169 1.002468 ACTGCAGTGTTCACGCAATTC 60.002 47.619 20.97 0.82 34.75 2.17 F
1525 1945 0.878416 GATTTGCTTGGTGTGGCGTA 59.122 50.000 0.00 0.00 0.00 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 2298 0.179009 TGCAAGCAGAAGTCAAGGCT 60.179 50.0 0.00 0.00 38.45 4.58 R
2721 3398 0.040157 GTGAACAATGAAGCGCTGCA 60.040 50.0 23.07 23.07 0.00 4.41 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
70 71 2.162208 GCTGAACCATCATTTGAGCGAA 59.838 45.455 0.00 0.00 34.37 4.70
72 73 3.145286 TGAACCATCATTTGAGCGAACA 58.855 40.909 0.00 0.00 0.00 3.18
168 169 1.002468 ACTGCAGTGTTCACGCAATTC 60.002 47.619 20.97 0.82 34.75 2.17
224 225 4.898320 TCATGTGTGACTCAACTTGCTAT 58.102 39.130 0.00 0.00 0.00 2.97
226 227 5.764686 TCATGTGTGACTCAACTTGCTATTT 59.235 36.000 0.00 0.00 0.00 1.40
227 228 5.422666 TGTGTGACTCAACTTGCTATTTG 57.577 39.130 0.00 0.00 0.00 2.32
228 229 4.222114 GTGTGACTCAACTTGCTATTTGC 58.778 43.478 0.00 0.00 43.25 3.68
247 251 1.068954 GCTACAGTTGCAGGCAAGAAC 60.069 52.381 6.99 0.00 36.52 3.01
259 263 2.108952 AGGCAAGAACTTTGGGATCACT 59.891 45.455 0.00 0.00 0.00 3.41
275 279 3.243359 TCACTCTCCCAAAAGGCAATT 57.757 42.857 0.00 0.00 34.51 2.32
276 280 3.575805 TCACTCTCCCAAAAGGCAATTT 58.424 40.909 0.00 0.00 34.51 1.82
277 281 3.321682 TCACTCTCCCAAAAGGCAATTTG 59.678 43.478 8.34 8.34 39.47 2.32
303 307 5.357742 TGTGAACTCTGCCATGTATGTAT 57.642 39.130 0.00 0.00 0.00 2.29
304 308 5.118286 TGTGAACTCTGCCATGTATGTATG 58.882 41.667 0.00 0.00 0.00 2.39
305 309 5.118990 GTGAACTCTGCCATGTATGTATGT 58.881 41.667 0.00 0.00 0.00 2.29
306 310 6.127196 TGTGAACTCTGCCATGTATGTATGTA 60.127 38.462 0.00 0.00 0.00 2.29
307 311 6.201044 GTGAACTCTGCCATGTATGTATGTAC 59.799 42.308 0.00 0.00 0.00 2.90
364 402 2.034179 TCAGGAATGGACAGCGTATACG 59.966 50.000 20.87 20.87 43.27 3.06
385 423 2.228822 GGTTTAGAACACTCGGACGGTA 59.771 50.000 0.00 0.00 0.00 4.02
445 483 6.964370 GCATCGTGCATTGTAAACTGTAATAA 59.036 34.615 0.00 0.00 44.26 1.40
478 518 6.115446 TGAGAAGCAAGTCCATTGTAATAGG 58.885 40.000 0.00 0.00 41.29 2.57
485 525 4.755411 AGTCCATTGTAATAGGTGTCGTG 58.245 43.478 0.00 0.00 0.00 4.35
498 538 1.654105 GTGTCGTGCTCGTATGAAAGG 59.346 52.381 8.17 0.00 38.33 3.11
578 618 3.869912 GCCTGAGATTCTTGGCACTTACA 60.870 47.826 20.02 0.00 44.34 2.41
670 712 8.689061 CATCTTCAATGGGAAATCAATGAGTTA 58.311 33.333 0.00 0.00 34.44 2.24
675 724 7.124599 TCAATGGGAAATCAATGAGTTATTGCT 59.875 33.333 10.68 0.00 44.69 3.91
678 727 7.771183 TGGGAAATCAATGAGTTATTGCTAAC 58.229 34.615 0.00 0.00 44.69 2.34
728 865 4.338879 AGAATGAACTCTGATTGTTGGGG 58.661 43.478 0.00 0.00 0.00 4.96
986 1396 4.825679 CTCCCCACCCCTCCCCTC 62.826 77.778 0.00 0.00 0.00 4.30
1305 1715 1.687660 TGCGTCAAGGTAGTACCAACA 59.312 47.619 21.49 6.93 41.95 3.33
1310 1720 2.565834 TCAAGGTAGTACCAACAGAGCC 59.434 50.000 21.49 0.00 41.95 4.70
1311 1721 2.567615 CAAGGTAGTACCAACAGAGCCT 59.432 50.000 21.49 0.00 41.95 4.58
1313 1723 2.832733 AGGTAGTACCAACAGAGCCTTC 59.167 50.000 21.49 0.00 41.95 3.46
1315 1725 2.031495 AGTACCAACAGAGCCTTCCT 57.969 50.000 0.00 0.00 0.00 3.36
1317 1727 1.066071 GTACCAACAGAGCCTTCCTCC 60.066 57.143 0.00 0.00 41.74 4.30
1318 1728 1.301293 CCAACAGAGCCTTCCTCCC 59.699 63.158 0.00 0.00 41.74 4.30
1319 1729 1.078848 CAACAGAGCCTTCCTCCCG 60.079 63.158 0.00 0.00 41.74 5.14
1320 1730 2.960688 AACAGAGCCTTCCTCCCGC 61.961 63.158 0.00 0.00 41.74 6.13
1321 1731 4.168291 CAGAGCCTTCCTCCCGCC 62.168 72.222 0.00 0.00 41.74 6.13
1340 1750 2.352805 CCTTCCGCCAGCTCCTTT 59.647 61.111 0.00 0.00 0.00 3.11
1366 1776 7.538334 TCTTGATAATGTTCATTTTTGTCGCTG 59.462 33.333 3.36 0.00 0.00 5.18
1461 1881 6.183359 GCAGTGATTGAATGAACGAATGTTTC 60.183 38.462 0.00 0.00 38.78 2.78
1489 1909 3.655276 GCATGGATAGAATGCTTTGGG 57.345 47.619 0.00 0.00 45.62 4.12
1491 1911 2.071778 TGGATAGAATGCTTTGGGCC 57.928 50.000 0.00 0.00 40.92 5.80
1493 1913 1.959282 GGATAGAATGCTTTGGGCCTG 59.041 52.381 4.53 0.00 40.92 4.85
1516 1936 2.754946 AACATGCCTGATTTGCTTGG 57.245 45.000 0.00 0.00 37.98 3.61
1525 1945 0.878416 GATTTGCTTGGTGTGGCGTA 59.122 50.000 0.00 0.00 0.00 4.42
1559 1979 2.289547 TCAGGCGTGTTTGTTTAGAAGC 59.710 45.455 6.26 0.00 0.00 3.86
1625 2246 7.043656 GCGTTTCTGCCCATTATAAAAATGTAC 60.044 37.037 0.00 0.00 0.00 2.90
1677 2298 7.342026 TGAGTAATTTCTGAGCTACCATGACTA 59.658 37.037 0.00 0.00 0.00 2.59
1680 2301 2.311463 TCTGAGCTACCATGACTAGCC 58.689 52.381 15.18 9.67 37.88 3.93
1702 2323 2.642427 TGACTTCTGCTTGCACTTCAA 58.358 42.857 0.00 0.00 0.00 2.69
1704 2325 2.615912 GACTTCTGCTTGCACTTCAACT 59.384 45.455 0.00 0.00 0.00 3.16
1821 2442 1.134175 CCGGATGTTGGCAACCAATAC 59.866 52.381 26.31 14.36 45.80 1.89
1837 2458 6.976934 ACCAATACAGGTGATTGACTTTTT 57.023 33.333 0.00 0.00 41.30 1.94
1875 2496 4.508461 TTTCCGTCAGTAAATCGACTCA 57.492 40.909 0.00 0.00 0.00 3.41
1879 2500 5.100259 TCCGTCAGTAAATCGACTCATTTC 58.900 41.667 0.00 0.00 0.00 2.17
1888 2509 3.251479 TCGACTCATTTCAGGATGTGG 57.749 47.619 0.00 0.00 37.40 4.17
1902 2523 4.334759 CAGGATGTGGTGATCATCTGTTTC 59.665 45.833 7.64 0.00 40.76 2.78
1924 2565 5.919755 TCCATACGCTACATTTTCATGGTA 58.080 37.500 0.00 0.00 34.27 3.25
2140 2815 3.932545 TCCGTCATTTTCACAAATGGG 57.067 42.857 7.63 3.22 46.57 4.00
2152 2827 2.680370 AAATGGGACCCTCGAGGCC 61.680 63.158 26.87 21.61 40.58 5.19
2185 2860 4.216472 GCTCTTACCAAAGAAAGGGAACAG 59.784 45.833 0.00 0.00 41.19 3.16
2245 2920 1.032014 CACTGGGGGCATTTTATCCG 58.968 55.000 0.00 0.00 0.00 4.18
2298 2973 9.118300 GTCATTCATTATTCTTCCTTGTGAGAT 57.882 33.333 0.00 0.00 0.00 2.75
2333 3008 8.491152 CAAATGGCGTTCTAGTAGAATAATGAG 58.509 37.037 15.53 5.34 36.50 2.90
2516 3191 1.301293 GCCCTCCAAAGACCCAGAG 59.699 63.158 0.00 0.00 0.00 3.35
2538 3213 5.679601 AGGAAGATAAGCTCCAAGATTGAC 58.320 41.667 0.00 0.00 0.00 3.18
2616 3291 2.901192 TCCCGGTTCTCATCAAACTGTA 59.099 45.455 0.00 0.00 32.23 2.74
2617 3292 3.325425 TCCCGGTTCTCATCAAACTGTAA 59.675 43.478 0.00 0.00 32.23 2.41
2628 3303 9.076781 TCTCATCAAACTGTAAAATCCATCAAA 57.923 29.630 0.00 0.00 0.00 2.69
2674 3350 1.203052 AGTTCTGCATGATTTTGCCGG 59.797 47.619 0.00 0.00 42.06 6.13
2693 3370 3.370061 CCGGAAAGTTTCGTAGGAATGTC 59.630 47.826 14.53 0.00 30.88 3.06
2701 3378 2.447443 TCGTAGGAATGTCTCAGCAGT 58.553 47.619 0.00 0.00 0.00 4.40
2714 3391 4.594367 GCAGTCTGCTGACAGGAG 57.406 61.111 23.61 17.32 45.28 3.69
2715 3392 1.741032 GCAGTCTGCTGACAGGAGC 60.741 63.158 23.61 17.18 45.28 4.70
2716 3393 1.079266 CAGTCTGCTGACAGGAGCC 60.079 63.158 23.61 8.06 45.28 4.70
2717 3394 1.534959 AGTCTGCTGACAGGAGCCA 60.535 57.895 23.61 0.05 45.20 4.75
2718 3395 1.079266 GTCTGCTGACAGGAGCCAG 60.079 63.158 18.49 9.86 44.59 4.85
2719 3396 1.228988 TCTGCTGACAGGAGCCAGA 60.229 57.895 18.49 11.94 44.59 3.86
2720 3397 1.079266 CTGCTGACAGGAGCCAGAC 60.079 63.158 11.33 0.00 40.48 3.51
2721 3398 1.534959 TGCTGACAGGAGCCAGACT 60.535 57.895 4.26 0.00 38.28 3.24
2759 3436 2.813754 CACTTGGTCACGGTGATTCATT 59.186 45.455 14.78 4.21 33.32 2.57
2793 3470 5.718724 AGATAGCATCAATCATCTGTCGA 57.281 39.130 0.00 0.00 0.00 4.20
2819 3496 1.944709 AGTTTTTCTCCGTCCGTTTGG 59.055 47.619 0.00 0.00 0.00 3.28
2821 3498 2.871633 GTTTTTCTCCGTCCGTTTGGTA 59.128 45.455 0.00 0.00 36.30 3.25
2825 3502 2.726821 TCTCCGTCCGTTTGGTATACT 58.273 47.619 2.25 0.00 36.30 2.12
2831 3508 3.550275 CGTCCGTTTGGTATACTCATGTG 59.450 47.826 2.25 0.00 36.30 3.21
2837 3514 6.984474 CCGTTTGGTATACTCATGTGTATCTT 59.016 38.462 20.62 4.59 35.14 2.40
2838 3515 7.042725 CCGTTTGGTATACTCATGTGTATCTTG 60.043 40.741 20.62 7.91 35.14 3.02
2895 3607 6.727824 AGATGTAACTTTTGGTCGATTCAG 57.272 37.500 0.00 0.00 0.00 3.02
2906 3619 5.107109 TGGTCGATTCAGTTGTGAAAATG 57.893 39.130 0.00 0.00 45.88 2.32
2916 3713 7.060600 TCAGTTGTGAAAATGTATAGAAGCG 57.939 36.000 0.00 0.00 0.00 4.68
2933 3730 4.819630 AGAAGCGTTCTTATTCACAAACCA 59.180 37.500 0.00 0.00 36.36 3.67
2934 3731 5.473504 AGAAGCGTTCTTATTCACAAACCAT 59.526 36.000 0.00 0.00 36.36 3.55
2935 3732 5.705609 AGCGTTCTTATTCACAAACCATT 57.294 34.783 0.00 0.00 0.00 3.16
2936 3733 6.084326 AGCGTTCTTATTCACAAACCATTT 57.916 33.333 0.00 0.00 0.00 2.32
2938 3735 7.653647 AGCGTTCTTATTCACAAACCATTTTA 58.346 30.769 0.00 0.00 0.00 1.52
2939 3736 8.303876 AGCGTTCTTATTCACAAACCATTTTAT 58.696 29.630 0.00 0.00 0.00 1.40
2948 3745 9.775854 ATTCACAAACCATTTTATTCACAATCA 57.224 25.926 0.00 0.00 0.00 2.57
2949 3746 9.775854 TTCACAAACCATTTTATTCACAATCAT 57.224 25.926 0.00 0.00 0.00 2.45
2950 3747 9.205719 TCACAAACCATTTTATTCACAATCATG 57.794 29.630 0.00 0.00 0.00 3.07
2968 3765 9.128404 ACAATCATGTGTATAGAAGCATCAATT 57.872 29.630 0.00 0.00 38.69 2.32
2970 3767 8.913487 ATCATGTGTATAGAAGCATCAATTCA 57.087 30.769 0.00 0.00 0.00 2.57
2971 3768 8.913487 TCATGTGTATAGAAGCATCAATTCAT 57.087 30.769 0.00 0.00 0.00 2.57
2972 3769 8.996271 TCATGTGTATAGAAGCATCAATTCATC 58.004 33.333 0.00 0.00 0.00 2.92
2973 3770 8.780249 CATGTGTATAGAAGCATCAATTCATCA 58.220 33.333 0.00 0.00 0.00 3.07
2974 3771 8.374327 TGTGTATAGAAGCATCAATTCATCAG 57.626 34.615 0.00 0.00 0.00 2.90
2975 3772 7.989170 TGTGTATAGAAGCATCAATTCATCAGT 59.011 33.333 0.00 0.00 0.00 3.41
2976 3773 8.834465 GTGTATAGAAGCATCAATTCATCAGTT 58.166 33.333 0.00 0.00 0.00 3.16
2977 3774 9.049523 TGTATAGAAGCATCAATTCATCAGTTC 57.950 33.333 0.00 0.00 0.00 3.01
2978 3775 9.049523 GTATAGAAGCATCAATTCATCAGTTCA 57.950 33.333 0.00 0.00 0.00 3.18
2979 3776 8.693120 ATAGAAGCATCAATTCATCAGTTCAT 57.307 30.769 0.00 0.00 0.00 2.57
2980 3777 7.028926 AGAAGCATCAATTCATCAGTTCATC 57.971 36.000 0.00 0.00 0.00 2.92
2981 3778 6.602009 AGAAGCATCAATTCATCAGTTCATCA 59.398 34.615 0.00 0.00 0.00 3.07
2982 3779 6.769134 AGCATCAATTCATCAGTTCATCAA 57.231 33.333 0.00 0.00 0.00 2.57
2983 3780 7.348080 AGCATCAATTCATCAGTTCATCAAT 57.652 32.000 0.00 0.00 0.00 2.57
2984 3781 7.426410 AGCATCAATTCATCAGTTCATCAATC 58.574 34.615 0.00 0.00 0.00 2.67
2985 3782 7.068226 AGCATCAATTCATCAGTTCATCAATCA 59.932 33.333 0.00 0.00 0.00 2.57
2986 3783 7.867909 GCATCAATTCATCAGTTCATCAATCAT 59.132 33.333 0.00 0.00 0.00 2.45
2987 3784 9.399403 CATCAATTCATCAGTTCATCAATCATC 57.601 33.333 0.00 0.00 0.00 2.92
2988 3785 8.747538 TCAATTCATCAGTTCATCAATCATCT 57.252 30.769 0.00 0.00 0.00 2.90
2989 3786 8.621286 TCAATTCATCAGTTCATCAATCATCTG 58.379 33.333 0.00 0.00 0.00 2.90
2990 3787 8.406297 CAATTCATCAGTTCATCAATCATCTGT 58.594 33.333 0.00 0.00 0.00 3.41
2991 3788 7.933215 TTCATCAGTTCATCAATCATCTGTT 57.067 32.000 0.00 0.00 0.00 3.16
2992 3789 9.623000 ATTCATCAGTTCATCAATCATCTGTTA 57.377 29.630 0.00 0.00 0.00 2.41
3062 3859 3.031736 GGAGATAACACTACTGCTCCCA 58.968 50.000 0.00 0.00 36.73 4.37
3074 3871 1.136695 CTGCTCCCAACAAAGTTGCAA 59.863 47.619 0.00 0.00 0.00 4.08
3083 3880 4.810491 CCAACAAAGTTGCAATAAAGCAGT 59.190 37.500 0.59 0.00 46.54 4.40
3134 3951 6.991531 TGCATAATAATTCTCATTTTTGCCCC 59.008 34.615 0.00 0.00 0.00 5.80
3147 3964 3.386932 TTTGCCCCTGCTGATTATTCT 57.613 42.857 0.00 0.00 38.71 2.40
3148 3965 2.353357 TGCCCCTGCTGATTATTCTG 57.647 50.000 0.00 0.00 38.71 3.02
3173 3991 9.508642 TGTTGAGGTTCCTTTTGTTTTAAAAAT 57.491 25.926 1.31 0.00 0.00 1.82
3194 4012 2.296073 TAAACGGCATCCCTGGTTTT 57.704 45.000 0.00 0.00 0.00 2.43
3195 4013 0.678950 AAACGGCATCCCTGGTTTTG 59.321 50.000 0.00 0.00 0.00 2.44
3196 4014 1.815817 AACGGCATCCCTGGTTTTGC 61.816 55.000 4.66 4.66 0.00 3.68
3216 4035 1.746787 CGCTACCCCCACAAATAAACC 59.253 52.381 0.00 0.00 0.00 3.27
3221 4040 2.249139 CCCCCACAAATAAACCCGAAA 58.751 47.619 0.00 0.00 0.00 3.46
3222 4041 2.633481 CCCCCACAAATAAACCCGAAAA 59.367 45.455 0.00 0.00 0.00 2.29
3234 4053 8.821147 AATAAACCCGAAAAGGAACAAAATAC 57.179 30.769 0.00 0.00 45.00 1.89
3241 4060 5.912955 CGAAAAGGAACAAAATACTGGTGTC 59.087 40.000 0.00 0.00 0.00 3.67
3271 4090 2.629017 AATGGCCAAAGGAGTCCATT 57.371 45.000 10.96 2.08 42.61 3.16
3278 4097 3.259123 GCCAAAGGAGTCCATTTCACAAT 59.741 43.478 12.86 0.00 0.00 2.71
3282 4101 7.147915 GCCAAAGGAGTCCATTTCACAATAATA 60.148 37.037 12.86 0.00 0.00 0.98
3293 4112 9.144747 CCATTTCACAATAATATACTCTCTCCG 57.855 37.037 0.00 0.00 0.00 4.63
3294 4113 8.651588 CATTTCACAATAATATACTCTCTCCGC 58.348 37.037 0.00 0.00 0.00 5.54
3298 4117 2.696526 AATATACTCTCTCCGCCCCA 57.303 50.000 0.00 0.00 0.00 4.96
3299 4118 2.696526 ATATACTCTCTCCGCCCCAA 57.303 50.000 0.00 0.00 0.00 4.12
3310 4129 2.560981 CTCCGCCCCAAAAATAAGTGTT 59.439 45.455 0.00 0.00 0.00 3.32
3320 4139 8.947115 CCCCAAAAATAAGTGTTGTTGTTTTAA 58.053 29.630 0.00 0.00 31.71 1.52
3358 4181 8.699283 ATAACTAGAACAACGACACTTATTCC 57.301 34.615 0.00 0.00 0.00 3.01
3360 4183 4.247267 AGAACAACGACACTTATTCCGA 57.753 40.909 0.00 0.00 0.00 4.55
3384 4215 6.268566 AGACGGACGGACTACATATTTAAAC 58.731 40.000 0.00 0.00 0.00 2.01
3389 4220 6.764560 GGACGGACTACATATTTAAACACCAT 59.235 38.462 0.00 0.00 0.00 3.55
3407 4238 9.877178 AAACACCATATTTCTACAACACAAAAA 57.123 25.926 0.00 0.00 0.00 1.94
3500 4331 9.964303 TCATAACAATATATTTTCACACATGGC 57.036 29.630 0.00 0.00 0.00 4.40
3501 4332 8.904712 CATAACAATATATTTTCACACATGGCG 58.095 33.333 0.00 0.00 0.00 5.69
3502 4333 6.449635 ACAATATATTTTCACACATGGCGT 57.550 33.333 0.00 0.00 0.00 5.68
3503 4334 7.561021 ACAATATATTTTCACACATGGCGTA 57.439 32.000 0.00 0.00 0.00 4.42
3504 4335 7.414436 ACAATATATTTTCACACATGGCGTAC 58.586 34.615 0.00 0.00 0.00 3.67
3505 4336 7.066404 ACAATATATTTTCACACATGGCGTACA 59.934 33.333 0.00 0.00 0.00 2.90
3506 4337 5.888691 ATATTTTCACACATGGCGTACAA 57.111 34.783 0.00 0.00 0.00 2.41
3507 4338 4.782019 ATTTTCACACATGGCGTACAAT 57.218 36.364 0.00 0.00 0.00 2.71
3508 4339 5.888691 ATTTTCACACATGGCGTACAATA 57.111 34.783 0.00 0.00 0.00 1.90
3509 4340 5.690997 TTTTCACACATGGCGTACAATAA 57.309 34.783 0.00 0.00 0.00 1.40
3510 4341 4.671880 TTCACACATGGCGTACAATAAC 57.328 40.909 0.00 0.00 0.00 1.89
3511 4342 3.665190 TCACACATGGCGTACAATAACA 58.335 40.909 0.00 0.00 0.00 2.41
3516 4347 5.688176 ACACATGGCGTACAATAACAAAAAC 59.312 36.000 0.00 0.00 0.00 2.43
3517 4348 5.687730 CACATGGCGTACAATAACAAAAACA 59.312 36.000 0.00 0.00 0.00 2.83
3565 4398 3.941704 TTTGGGCCAGGATTTTGTTTT 57.058 38.095 6.23 0.00 0.00 2.43
3571 4404 3.250762 GGCCAGGATTTTGTTTTCTTTGC 59.749 43.478 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 0.820891 CTGAAGCAGGGCAACACTGT 60.821 55.000 0.00 0.00 37.25 3.55
72 73 4.488790 CTGAAGCAGGGCAACACT 57.511 55.556 0.00 0.00 39.74 3.55
168 169 9.601971 CAATCCAAGACAAAAATTTATTTGCAG 57.398 29.630 3.08 0.00 42.68 4.41
174 175 9.492973 CTTCCACAATCCAAGACAAAAATTTAT 57.507 29.630 0.00 0.00 0.00 1.40
179 180 4.714308 ACCTTCCACAATCCAAGACAAAAA 59.286 37.500 0.00 0.00 0.00 1.94
224 225 1.337703 CTTGCCTGCAACTGTAGCAAA 59.662 47.619 0.00 0.00 42.17 3.68
226 227 0.108396 TCTTGCCTGCAACTGTAGCA 59.892 50.000 0.00 0.00 40.19 3.49
227 228 1.068954 GTTCTTGCCTGCAACTGTAGC 60.069 52.381 0.00 0.00 0.00 3.58
228 229 2.498167 AGTTCTTGCCTGCAACTGTAG 58.502 47.619 0.00 0.00 0.00 2.74
259 263 2.837532 GCAAATTGCCTTTTGGGAGA 57.162 45.000 6.72 0.00 42.25 3.71
275 279 0.106769 TGGCAGAGTTCACAAGGCAA 60.107 50.000 0.00 0.00 0.00 4.52
276 280 0.111061 ATGGCAGAGTTCACAAGGCA 59.889 50.000 0.00 0.00 39.14 4.75
277 281 0.524862 CATGGCAGAGTTCACAAGGC 59.475 55.000 0.00 0.00 0.00 4.35
364 402 1.000171 ACCGTCCGAGTGTTCTAAACC 60.000 52.381 0.00 0.00 0.00 3.27
385 423 2.288702 TGTGCACAAACAGTTTTGCAGT 60.289 40.909 24.29 8.06 45.32 4.40
478 518 1.654105 CCTTTCATACGAGCACGACAC 59.346 52.381 11.40 0.00 42.66 3.67
485 525 3.385577 GTCCAGATCCTTTCATACGAGC 58.614 50.000 0.00 0.00 0.00 5.03
498 538 1.078759 CACGCCACTTCGTCCAGATC 61.079 60.000 0.00 0.00 41.21 2.75
514 554 1.135689 GCATAACTGTTCTTGGCCACG 60.136 52.381 3.88 2.81 0.00 4.94
578 618 1.899814 TCCCGACAGTTTGCATCTACT 59.100 47.619 0.00 0.00 0.00 2.57
699 748 7.199541 ACAATCAGAGTTCATTCTCAAACAG 57.800 36.000 0.00 0.00 36.97 3.16
701 750 6.860023 CCAACAATCAGAGTTCATTCTCAAAC 59.140 38.462 0.00 0.00 36.97 2.93
743 880 4.016444 TGATTTTGGGCCTCAGAATGTAC 58.984 43.478 4.53 0.00 37.40 2.90
751 889 4.440145 GCCTGATTTTGGGCCTCA 57.560 55.556 4.53 0.00 42.30 3.86
815 954 3.423154 GTTGGTCGCTTCGCCCAG 61.423 66.667 0.00 0.00 0.00 4.45
826 965 2.125766 GAGGAGTGTGGGGGTTGGTC 62.126 65.000 0.00 0.00 0.00 4.02
945 1089 2.955402 CGGAGATCGGGATCGGAC 59.045 66.667 3.19 0.43 42.48 4.79
986 1396 4.873129 CCATCTCGTCGGCGTGGG 62.873 72.222 10.18 0.13 39.49 4.61
1029 1439 4.918201 AGCGCGCATAGGAAGGCC 62.918 66.667 35.10 0.00 0.00 5.19
1310 1720 3.798511 GAAGGGGGCGGGAGGAAG 61.799 72.222 0.00 0.00 0.00 3.46
1340 1750 7.538334 CAGCGACAAAAATGAACATTATCAAGA 59.462 33.333 0.37 0.00 32.06 3.02
1406 1826 2.270275 TGCGCGGATAAAATGGTTTG 57.730 45.000 8.83 0.00 0.00 2.93
1419 1839 1.132640 GCTAGTTTCACTTGCGCGG 59.867 57.895 8.83 0.00 37.24 6.46
1491 1911 3.119245 AGCAAATCAGGCATGTTAAGCAG 60.119 43.478 0.00 0.00 0.00 4.24
1493 1913 3.515330 AGCAAATCAGGCATGTTAAGC 57.485 42.857 0.00 0.00 0.00 3.09
1516 1936 0.179189 GCTTCAAGCATACGCCACAC 60.179 55.000 3.89 0.00 41.89 3.82
1539 1959 2.032799 TGCTTCTAAACAAACACGCCTG 59.967 45.455 0.00 0.00 0.00 4.85
1540 1960 2.294074 TGCTTCTAAACAAACACGCCT 58.706 42.857 0.00 0.00 0.00 5.52
1559 1979 3.405823 AGACCAAAACATGCCCAATTG 57.594 42.857 0.00 0.00 0.00 2.32
1677 2298 0.179009 TGCAAGCAGAAGTCAAGGCT 60.179 50.000 0.00 0.00 38.45 4.58
1680 2301 2.615447 TGAAGTGCAAGCAGAAGTCAAG 59.385 45.455 0.00 0.00 0.00 3.02
1702 2323 4.202264 GGGATCATATTCGACCTGAACAGT 60.202 45.833 0.00 0.00 40.00 3.55
1704 2325 3.071023 GGGGATCATATTCGACCTGAACA 59.929 47.826 0.00 0.00 40.00 3.18
1837 2458 9.204570 CTGACGGAAAATAAGTCTAGAGAAAAA 57.795 33.333 0.00 0.00 36.01 1.94
1838 2459 8.365647 ACTGACGGAAAATAAGTCTAGAGAAAA 58.634 33.333 0.00 0.00 36.01 2.29
1852 2473 5.475719 TGAGTCGATTTACTGACGGAAAAT 58.524 37.500 0.00 0.00 40.05 1.82
1875 2496 5.131067 CAGATGATCACCACATCCTGAAAT 58.869 41.667 0.00 0.00 43.30 2.17
1879 2500 3.555527 ACAGATGATCACCACATCCTG 57.444 47.619 0.00 0.12 43.30 3.86
1902 2523 6.801539 ATACCATGAAAATGTAGCGTATGG 57.198 37.500 0.00 0.00 39.49 2.74
1924 2565 6.513806 TGCGATAATGCCATATGCTAAAAT 57.486 33.333 0.00 0.00 42.00 1.82
1941 2582 3.932545 AATGTTGGCTTTGTTGCGATA 57.067 38.095 0.00 0.00 0.00 2.92
1942 2583 2.818130 AATGTTGGCTTTGTTGCGAT 57.182 40.000 0.00 0.00 0.00 4.58
2023 2664 3.873952 GAGGATAGTGAGGCAAATGTGTC 59.126 47.826 0.00 0.00 0.00 3.67
2114 2789 6.128035 CCATTTGTGAAAATGACGGATCTGTA 60.128 38.462 7.30 0.00 41.44 2.74
2140 2815 1.144936 CAATCTGGCCTCGAGGGTC 59.855 63.158 32.06 16.64 40.85 4.46
2152 2827 2.408271 TGGTAAGAGCAGCCAATCTG 57.592 50.000 0.00 0.00 45.62 2.90
2245 2920 1.271597 ACCTGATGTTCTGGTTCAGCC 60.272 52.381 0.69 0.00 44.87 4.85
2298 2973 0.317799 AACGCCATTTGCATTGCAGA 59.682 45.000 11.76 7.97 40.61 4.26
2326 3001 8.861086 ACGACATACATAAAGAGGACTCATTAT 58.139 33.333 1.75 3.30 34.85 1.28
2333 3008 4.267928 GTGCACGACATACATAAAGAGGAC 59.732 45.833 0.00 0.00 0.00 3.85
2516 3191 4.509600 CGTCAATCTTGGAGCTTATCTTCC 59.490 45.833 0.00 0.00 0.00 3.46
2556 3231 3.536917 TCGCGTAGGATGGGCCAG 61.537 66.667 13.78 0.00 40.02 4.85
2616 3291 9.962809 ATGTTGGATTACAATTTGATGGATTTT 57.037 25.926 2.79 0.00 41.95 1.82
2628 3303 9.739276 TCTCTTGTTTCTATGTTGGATTACAAT 57.261 29.630 0.00 0.00 41.95 2.71
2674 3350 5.163943 GCTGAGACATTCCTACGAAACTTTC 60.164 44.000 0.00 0.00 0.00 2.62
2701 3378 1.228988 TCTGGCTCCTGTCAGCAGA 60.229 57.895 0.00 0.00 44.96 4.26
2712 3389 4.756458 AGCGCTGCAGTCTGGCTC 62.756 66.667 10.39 0.00 34.04 4.70
2713 3390 4.326507 AAGCGCTGCAGTCTGGCT 62.327 61.111 12.58 15.59 35.01 4.75
2714 3391 3.797546 GAAGCGCTGCAGTCTGGC 61.798 66.667 12.58 13.59 0.00 4.85
2715 3392 1.303799 AATGAAGCGCTGCAGTCTGG 61.304 55.000 25.01 3.76 0.00 3.86
2716 3393 0.179197 CAATGAAGCGCTGCAGTCTG 60.179 55.000 25.01 16.39 0.00 3.51
2717 3394 0.604780 ACAATGAAGCGCTGCAGTCT 60.605 50.000 25.01 5.90 0.00 3.24
2718 3395 0.239347 AACAATGAAGCGCTGCAGTC 59.761 50.000 25.01 12.24 0.00 3.51
2719 3396 0.239347 GAACAATGAAGCGCTGCAGT 59.761 50.000 25.01 19.80 0.00 4.40
2720 3397 0.239082 TGAACAATGAAGCGCTGCAG 59.761 50.000 25.01 13.77 0.00 4.41
2721 3398 0.040157 GTGAACAATGAAGCGCTGCA 60.040 50.000 23.07 23.07 0.00 4.41
2728 3405 3.303990 CCGTGACCAAGTGAACAATGAAG 60.304 47.826 0.00 0.00 0.00 3.02
2819 3496 7.653713 CCCAGAACAAGATACACATGAGTATAC 59.346 40.741 14.72 9.31 34.95 1.47
2821 3498 6.586344 CCCAGAACAAGATACACATGAGTAT 58.414 40.000 14.66 14.66 37.40 2.12
2825 3502 3.264193 AGCCCAGAACAAGATACACATGA 59.736 43.478 0.00 0.00 0.00 3.07
2831 3508 2.421424 CAGCAAGCCCAGAACAAGATAC 59.579 50.000 0.00 0.00 0.00 2.24
2837 3514 1.228245 GTCCAGCAAGCCCAGAACA 60.228 57.895 0.00 0.00 0.00 3.18
2838 3515 0.610232 ATGTCCAGCAAGCCCAGAAC 60.610 55.000 0.00 0.00 0.00 3.01
2895 3607 7.519002 AGAACGCTTCTATACATTTTCACAAC 58.481 34.615 0.00 0.00 38.49 3.32
2906 3619 8.114905 GGTTTGTGAATAAGAACGCTTCTATAC 58.885 37.037 1.53 0.00 39.61 1.47
2943 3740 9.608617 GAATTGATGCTTCTATACACATGATTG 57.391 33.333 0.00 0.00 0.00 2.67
2944 3741 9.346005 TGAATTGATGCTTCTATACACATGATT 57.654 29.630 0.00 0.00 0.00 2.57
2945 3742 8.913487 TGAATTGATGCTTCTATACACATGAT 57.087 30.769 0.00 0.00 0.00 2.45
2946 3743 8.913487 ATGAATTGATGCTTCTATACACATGA 57.087 30.769 0.00 0.00 0.00 3.07
2947 3744 8.780249 TGATGAATTGATGCTTCTATACACATG 58.220 33.333 0.88 0.00 0.00 3.21
2948 3745 8.913487 TGATGAATTGATGCTTCTATACACAT 57.087 30.769 0.88 6.21 0.00 3.21
2949 3746 7.989170 ACTGATGAATTGATGCTTCTATACACA 59.011 33.333 0.88 2.27 0.00 3.72
2950 3747 8.375608 ACTGATGAATTGATGCTTCTATACAC 57.624 34.615 0.88 0.00 0.00 2.90
2952 3749 9.049523 TGAACTGATGAATTGATGCTTCTATAC 57.950 33.333 0.88 0.00 0.00 1.47
2953 3750 9.788889 ATGAACTGATGAATTGATGCTTCTATA 57.211 29.630 0.88 0.00 0.00 1.31
2954 3751 8.693120 ATGAACTGATGAATTGATGCTTCTAT 57.307 30.769 0.88 0.00 0.00 1.98
2955 3752 7.771826 TGATGAACTGATGAATTGATGCTTCTA 59.228 33.333 0.88 0.00 0.00 2.10
2956 3753 6.602009 TGATGAACTGATGAATTGATGCTTCT 59.398 34.615 0.88 0.00 0.00 2.85
2957 3754 6.792326 TGATGAACTGATGAATTGATGCTTC 58.208 36.000 0.00 0.00 0.00 3.86
2958 3755 6.769134 TGATGAACTGATGAATTGATGCTT 57.231 33.333 0.00 0.00 0.00 3.91
2961 3758 9.399403 GATGATTGATGAACTGATGAATTGATG 57.601 33.333 0.00 0.00 0.00 3.07
2964 3761 8.406297 ACAGATGATTGATGAACTGATGAATTG 58.594 33.333 0.00 0.00 0.00 2.32
2965 3762 8.521170 ACAGATGATTGATGAACTGATGAATT 57.479 30.769 0.00 0.00 0.00 2.17
2966 3763 8.521170 AACAGATGATTGATGAACTGATGAAT 57.479 30.769 0.00 0.00 0.00 2.57
2968 3765 7.713942 CCTAACAGATGATTGATGAACTGATGA 59.286 37.037 0.00 0.00 0.00 2.92
2970 3767 6.996879 CCCTAACAGATGATTGATGAACTGAT 59.003 38.462 0.00 0.00 0.00 2.90
2971 3768 6.156775 TCCCTAACAGATGATTGATGAACTGA 59.843 38.462 0.00 0.00 0.00 3.41
2972 3769 6.351711 TCCCTAACAGATGATTGATGAACTG 58.648 40.000 0.00 0.00 0.00 3.16
2973 3770 6.566079 TCCCTAACAGATGATTGATGAACT 57.434 37.500 0.00 0.00 0.00 3.01
2974 3771 7.814264 ATTCCCTAACAGATGATTGATGAAC 57.186 36.000 0.00 0.00 0.00 3.18
2975 3772 8.054572 TCAATTCCCTAACAGATGATTGATGAA 58.945 33.333 0.00 0.00 0.00 2.57
2976 3773 7.576403 TCAATTCCCTAACAGATGATTGATGA 58.424 34.615 0.00 0.00 0.00 2.92
2977 3774 7.812690 TCAATTCCCTAACAGATGATTGATG 57.187 36.000 0.00 0.00 0.00 3.07
2978 3775 8.857098 CATTCAATTCCCTAACAGATGATTGAT 58.143 33.333 0.00 0.00 0.00 2.57
2979 3776 7.286087 CCATTCAATTCCCTAACAGATGATTGA 59.714 37.037 0.00 0.00 0.00 2.57
2980 3777 7.286087 TCCATTCAATTCCCTAACAGATGATTG 59.714 37.037 0.00 0.00 0.00 2.67
2981 3778 7.356680 TCCATTCAATTCCCTAACAGATGATT 58.643 34.615 0.00 0.00 0.00 2.57
2982 3779 6.914665 TCCATTCAATTCCCTAACAGATGAT 58.085 36.000 0.00 0.00 0.00 2.45
2983 3780 6.325993 TCCATTCAATTCCCTAACAGATGA 57.674 37.500 0.00 0.00 0.00 2.92
2984 3781 7.592885 ATTCCATTCAATTCCCTAACAGATG 57.407 36.000 0.00 0.00 0.00 2.90
2985 3782 8.063770 AGAATTCCATTCAATTCCCTAACAGAT 58.936 33.333 0.65 0.00 41.82 2.90
2986 3783 7.413446 AGAATTCCATTCAATTCCCTAACAGA 58.587 34.615 0.65 0.00 41.82 3.41
2987 3784 7.651027 AGAATTCCATTCAATTCCCTAACAG 57.349 36.000 0.65 0.00 41.82 3.16
2988 3785 7.454380 ACAAGAATTCCATTCAATTCCCTAACA 59.546 33.333 0.65 0.00 41.82 2.41
2989 3786 7.840931 ACAAGAATTCCATTCAATTCCCTAAC 58.159 34.615 0.65 0.00 41.82 2.34
2990 3787 9.540538 TTACAAGAATTCCATTCAATTCCCTAA 57.459 29.630 0.65 0.00 41.82 2.69
2991 3788 9.540538 TTTACAAGAATTCCATTCAATTCCCTA 57.459 29.630 0.65 0.00 41.82 3.53
2992 3789 8.434589 TTTACAAGAATTCCATTCAATTCCCT 57.565 30.769 0.65 0.00 41.82 4.20
3033 3830 6.607600 AGCAGTAGTGTTATCTCCATCTGTAA 59.392 38.462 0.00 0.00 0.00 2.41
3056 3853 2.531522 ATTGCAACTTTGTTGGGAGC 57.468 45.000 0.00 0.00 0.00 4.70
3062 3859 7.432869 TGATACTGCTTTATTGCAACTTTGTT 58.567 30.769 0.00 0.00 42.83 2.83
3096 3893 8.136800 AGAATTATTATGCATTGCAAACGATCA 58.863 29.630 16.46 0.00 43.62 2.92
3100 3897 7.682593 TGAGAATTATTATGCATTGCAAACG 57.317 32.000 16.46 0.00 43.62 3.60
3134 3951 5.065731 GGAACCTCAACAGAATAATCAGCAG 59.934 44.000 0.00 0.00 0.00 4.24
3147 3964 8.904099 TTTTTAAAACAAAAGGAACCTCAACA 57.096 26.923 0.00 0.00 0.00 3.33
3173 3991 2.296073 AACCAGGGATGCCGTTTAAA 57.704 45.000 0.00 0.00 0.00 1.52
3179 3997 2.573340 GCAAAACCAGGGATGCCG 59.427 61.111 0.00 0.00 32.73 5.69
3194 4012 0.328592 TTATTTGTGGGGGTAGCGCA 59.671 50.000 11.47 0.00 0.00 6.09
3195 4013 1.133598 GTTTATTTGTGGGGGTAGCGC 59.866 52.381 0.00 0.00 0.00 5.92
3196 4014 1.746787 GGTTTATTTGTGGGGGTAGCG 59.253 52.381 0.00 0.00 0.00 4.26
3216 4035 5.219633 CACCAGTATTTTGTTCCTTTTCGG 58.780 41.667 0.00 0.00 0.00 4.30
3221 4040 5.531287 GTGAGACACCAGTATTTTGTTCCTT 59.469 40.000 0.00 0.00 0.00 3.36
3222 4041 5.063880 GTGAGACACCAGTATTTTGTTCCT 58.936 41.667 0.00 0.00 0.00 3.36
3249 4068 2.688477 TGGACTCCTTTGGCCATTTTT 58.312 42.857 6.09 0.00 0.00 1.94
3250 4069 2.397044 TGGACTCCTTTGGCCATTTT 57.603 45.000 6.09 0.00 0.00 1.82
3271 4090 6.295123 GGGCGGAGAGAGTATATTATTGTGAA 60.295 42.308 0.00 0.00 0.00 3.18
3278 4097 3.820195 TGGGGCGGAGAGAGTATATTA 57.180 47.619 0.00 0.00 0.00 0.98
3282 4101 1.580059 TTTTGGGGCGGAGAGAGTAT 58.420 50.000 0.00 0.00 0.00 2.12
3284 4103 0.698818 ATTTTTGGGGCGGAGAGAGT 59.301 50.000 0.00 0.00 0.00 3.24
3285 4104 2.710096 TATTTTTGGGGCGGAGAGAG 57.290 50.000 0.00 0.00 0.00 3.20
3293 4112 4.447290 ACAACAACACTTATTTTTGGGGC 58.553 39.130 0.00 0.00 0.00 5.80
3294 4113 6.993786 AAACAACAACACTTATTTTTGGGG 57.006 33.333 0.00 0.00 0.00 4.96
3333 4152 7.487189 CGGAATAAGTGTCGTTGTTCTAGTTAT 59.513 37.037 0.00 0.00 30.52 1.89
3340 4163 4.089636 GTCTCGGAATAAGTGTCGTTGTTC 59.910 45.833 0.00 0.00 0.00 3.18
3358 4181 1.575244 TATGTAGTCCGTCCGTCTCG 58.425 55.000 0.00 0.00 0.00 4.04
3360 4183 6.127647 TGTTTAAATATGTAGTCCGTCCGTCT 60.128 38.462 0.00 0.00 0.00 4.18
3483 4314 6.986904 TTGTACGCCATGTGTGAAAATATA 57.013 33.333 0.00 0.00 0.00 0.86
3496 4327 7.772332 TTTTGTTTTTGTTATTGTACGCCAT 57.228 28.000 0.00 0.00 0.00 4.40
3497 4328 7.772332 ATTTTGTTTTTGTTATTGTACGCCA 57.228 28.000 0.00 0.00 0.00 5.69
3498 4329 8.753175 TGTATTTTGTTTTTGTTATTGTACGCC 58.247 29.630 0.00 0.00 0.00 5.68
3516 4347 8.929827 TGGCTCATTTTCATGTATGTATTTTG 57.070 30.769 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.