Multiple sequence alignment - TraesCS5D01G414700

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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 TraesCS5D01G414700 chr5D 100.000 4271 0 0 1 4271 477028452 477032722 0.000000e+00 7888.0
1 TraesCS5D01G414700 chr5A 92.666 3777 189 47 21 3732 596461883 596465636 0.000000e+00 5360.0
2 TraesCS5D01G414700 chr5A 81.900 558 39 27 3725 4255 596479001 596479523 8.540000e-112 414.0
3 TraesCS5D01G414700 chr5A 91.667 240 17 2 375 612 22993862 22993624 3.180000e-86 329.0
4 TraesCS5D01G414700 chr5A 90.717 237 19 2 375 609 457834978 457835213 3.210000e-81 313.0
5 TraesCS5D01G414700 chr5B 89.666 3319 205 64 593 3856 584853048 584856283 0.000000e+00 4102.0
6 TraesCS5D01G414700 chr5B 88.793 348 24 7 3923 4263 584859250 584859589 3.070000e-111 412.0
7 TraesCS5D01G414700 chr5B 89.498 219 15 5 596 806 584852653 584852871 1.960000e-68 270.0
8 TraesCS5D01G414700 chr7B 92.405 237 15 2 375 609 41198836 41199071 6.840000e-88 335.0
9 TraesCS5D01G414700 chr3B 91.561 237 16 3 375 609 28079251 28079485 1.480000e-84 324.0
10 TraesCS5D01G414700 chr3A 90.833 240 19 2 375 612 715693491 715693253 6.890000e-83 318.0
11 TraesCS5D01G414700 chr7A 90.000 240 21 2 375 612 473949824 473949586 1.490000e-79 307.0
12 TraesCS5D01G414700 chr7A 90.278 144 11 2 468 609 665439974 665440116 7.290000e-43 185.0
13 TraesCS5D01G414700 chr1A 92.391 92 6 1 518 609 466349645 466349735 3.470000e-26 130.0
14 TraesCS5D01G414700 chr1A 100.000 31 0 0 468 498 466349614 466349644 1.660000e-04 58.4


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 TraesCS5D01G414700 chr5D 477028452 477032722 4270 False 7888.000000 7888 100.000 1 4271 1 chr5D.!!$F1 4270
1 TraesCS5D01G414700 chr5A 596461883 596465636 3753 False 5360.000000 5360 92.666 21 3732 1 chr5A.!!$F2 3711
2 TraesCS5D01G414700 chr5A 596479001 596479523 522 False 414.000000 414 81.900 3725 4255 1 chr5A.!!$F3 530
3 TraesCS5D01G414700 chr5B 584852653 584859589 6936 False 1594.666667 4102 89.319 593 4263 3 chr5B.!!$F1 3670

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
124 135 0.164647 CTGCTCTCGTTTTTCTGCGG 59.835 55.0 0.00 0.00 0.00 5.69 F
977 1418 0.177604 CTTCTGCAGCTACCTCCAGG 59.822 60.0 9.47 0.00 42.17 4.45 F
1008 1458 0.461548 TCCTACGAAGCATGGCAGAG 59.538 55.0 0.00 0.00 0.00 3.35 F
2204 2673 0.609151 TGCACATTGGCCATTCCTTG 59.391 50.0 6.09 2.26 35.26 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1392 1845 0.403271 CCCCATCCTTGCCATAGAGG 59.597 60.0 0.00 0.00 41.84 3.69 R
2736 3209 0.321996 GAACCGGTTCCTTGAGCTCT 59.678 55.0 33.02 0.63 33.64 4.09 R
2925 3398 0.449388 CAATCGCCACAAAGAGCCTC 59.551 55.0 0.00 0.00 0.00 4.70 R
3308 3781 0.029834 TCTACTTACGAATCGGCGCC 59.970 55.0 19.07 19.07 33.86 6.53 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
21 22 3.839432 GGACGGAGCGAAGGGAGG 61.839 72.222 0.00 0.00 0.00 4.30
23 24 3.358076 GACGGAGCGAAGGGAGGTG 62.358 68.421 0.00 0.00 0.00 4.00
24 25 4.148825 CGGAGCGAAGGGAGGTGG 62.149 72.222 0.00 0.00 0.00 4.61
25 26 3.787001 GGAGCGAAGGGAGGTGGG 61.787 72.222 0.00 0.00 0.00 4.61
28 29 4.785453 GCGAAGGGAGGTGGGCTG 62.785 72.222 0.00 0.00 0.00 4.85
29 30 4.101448 CGAAGGGAGGTGGGCTGG 62.101 72.222 0.00 0.00 0.00 4.85
30 31 3.732849 GAAGGGAGGTGGGCTGGG 61.733 72.222 0.00 0.00 0.00 4.45
38 39 4.426313 GTGGGCTGGGCAGGGTAC 62.426 72.222 0.00 0.00 0.00 3.34
75 76 2.563050 TTCGCTCGGTGCCTCTGATG 62.563 60.000 0.00 0.00 38.78 3.07
82 93 0.835941 GGTGCCTCTGATGGTCTGAT 59.164 55.000 0.00 0.00 0.00 2.90
85 96 1.483827 TGCCTCTGATGGTCTGATGTC 59.516 52.381 0.00 0.00 0.00 3.06
86 97 1.202627 GCCTCTGATGGTCTGATGTCC 60.203 57.143 0.00 0.00 0.00 4.02
92 103 0.835941 ATGGTCTGATGTCCTGAGGC 59.164 55.000 0.00 0.00 0.00 4.70
93 104 0.252421 TGGTCTGATGTCCTGAGGCT 60.252 55.000 0.00 0.00 0.00 4.58
102 113 1.913262 TCCTGAGGCTTTGAGGCGA 60.913 57.895 0.00 0.00 46.58 5.54
117 128 0.667792 GGCGACTCTGCTCTCGTTTT 60.668 55.000 0.00 0.00 34.52 2.43
118 129 1.140816 GCGACTCTGCTCTCGTTTTT 58.859 50.000 0.00 0.00 32.30 1.94
121 132 2.406691 CGACTCTGCTCTCGTTTTTCTG 59.593 50.000 0.00 0.00 0.00 3.02
122 133 2.139118 ACTCTGCTCTCGTTTTTCTGC 58.861 47.619 0.00 0.00 0.00 4.26
124 135 0.164647 CTGCTCTCGTTTTTCTGCGG 59.835 55.000 0.00 0.00 0.00 5.69
125 136 0.249699 TGCTCTCGTTTTTCTGCGGA 60.250 50.000 0.00 0.00 0.00 5.54
224 247 2.675317 GCAGGAGAGGTATGTGTCACAC 60.675 54.545 8.08 0.00 34.56 3.82
228 251 3.511934 GGAGAGGTATGTGTCACACTCTT 59.488 47.826 19.92 9.03 35.61 2.85
238 261 1.540267 GTCACACTCTTACGCTCCTCA 59.460 52.381 0.00 0.00 0.00 3.86
260 283 2.153366 ATTTTCCTTTTGCTGCGTGG 57.847 45.000 0.00 0.00 0.00 4.94
285 308 0.322456 TGGCTGAAATTGGTCTCCCG 60.322 55.000 0.00 0.00 0.00 5.14
376 399 1.738099 GATTGAGCGTCCGTGCAGT 60.738 57.895 0.00 0.00 37.31 4.40
402 425 5.473504 TGCCTCTAGAAATGTTTGGAGTTTC 59.526 40.000 0.00 0.00 33.24 2.78
421 444 0.807667 CTCTGGTAGTCCATGCGTGC 60.808 60.000 0.00 0.00 43.43 5.34
424 447 0.391130 TGGTAGTCCATGCGTGCTTC 60.391 55.000 0.00 0.00 39.03 3.86
425 448 0.391130 GGTAGTCCATGCGTGCTTCA 60.391 55.000 0.00 0.00 0.00 3.02
499 522 2.599082 GAGCTCGGTCTGAATTTGTACG 59.401 50.000 0.00 0.00 0.00 3.67
500 523 2.029290 AGCTCGGTCTGAATTTGTACGT 60.029 45.455 0.00 0.00 0.00 3.57
501 524 2.735134 GCTCGGTCTGAATTTGTACGTT 59.265 45.455 0.00 0.00 0.00 3.99
504 527 3.985279 TCGGTCTGAATTTGTACGTTCTG 59.015 43.478 0.00 6.54 0.00 3.02
505 528 3.985279 CGGTCTGAATTTGTACGTTCTGA 59.015 43.478 0.00 9.43 32.28 3.27
506 529 4.446385 CGGTCTGAATTTGTACGTTCTGAA 59.554 41.667 0.00 0.00 35.18 3.02
511 536 7.742089 GTCTGAATTTGTACGTTCTGAAATGAG 59.258 37.037 0.00 0.00 35.18 2.90
530 555 5.590530 TGAGAAAACAGAGAGATCTAGGC 57.409 43.478 0.00 0.00 0.00 3.93
531 556 4.097135 TGAGAAAACAGAGAGATCTAGGCG 59.903 45.833 0.00 0.00 0.00 5.52
567 592 2.376808 GAGCTGTACTCACACTGCAT 57.623 50.000 0.00 0.00 45.49 3.96
571 596 5.193663 AGCTGTACTCACACTGCATATAG 57.806 43.478 7.67 0.00 43.54 1.31
587 612 8.774890 CTGCATATAGAGAAGATGCTGTAAAT 57.225 34.615 7.52 0.00 45.04 1.40
599 624 4.829064 TGCTGTAAATTGTCTTGGTGAC 57.171 40.909 0.00 0.00 45.54 3.67
621 646 4.142381 ACTTTGTTCCAGTTTGCTCAAGAC 60.142 41.667 0.00 0.00 0.00 3.01
646 671 3.073062 AGCAACCATGTAGTCAGGTTCTT 59.927 43.478 0.00 0.00 43.43 2.52
653 678 6.659242 ACCATGTAGTCAGGTTCTTTAAATGG 59.341 38.462 0.00 0.00 36.57 3.16
665 690 9.102453 AGGTTCTTTAAATGGTTAGACTCTAGT 57.898 33.333 0.00 0.00 0.00 2.57
677 710 2.894126 AGACTCTAGTGTTGGTCTGGTG 59.106 50.000 0.00 0.00 37.60 4.17
687 720 3.886505 TGTTGGTCTGGTGGTTTGATTAC 59.113 43.478 0.00 0.00 0.00 1.89
691 724 3.435671 GGTCTGGTGGTTTGATTACGAAG 59.564 47.826 0.00 0.00 0.00 3.79
773 806 6.951643 AGTTTGTACCACTTTCGTAATGAAC 58.048 36.000 0.00 0.00 35.97 3.18
806 839 3.838317 ACTATGAACTTGGAGGTGCACTA 59.162 43.478 17.98 0.00 0.00 2.74
808 841 3.126001 TGAACTTGGAGGTGCACTAAG 57.874 47.619 17.98 16.97 33.26 2.18
809 842 2.703536 TGAACTTGGAGGTGCACTAAGA 59.296 45.455 17.98 0.00 31.87 2.10
811 844 2.330216 ACTTGGAGGTGCACTAAGAGT 58.670 47.619 17.98 11.51 31.87 3.24
813 846 0.976641 TGGAGGTGCACTAAGAGTGG 59.023 55.000 17.98 0.00 46.01 4.00
820 864 3.244112 GGTGCACTAAGAGTGGTACTGTT 60.244 47.826 17.98 0.00 46.01 3.16
824 868 4.928020 GCACTAAGAGTGGTACTGTTAACC 59.072 45.833 8.61 0.00 46.01 2.85
825 869 5.510179 GCACTAAGAGTGGTACTGTTAACCA 60.510 44.000 8.61 0.00 46.01 3.67
876 1317 9.046296 TCTTCTTTCTTACTTACAGAGCAAAAG 57.954 33.333 0.00 0.00 0.00 2.27
976 1417 0.461693 GCTTCTGCAGCTACCTCCAG 60.462 60.000 9.47 0.00 46.27 3.86
977 1418 0.177604 CTTCTGCAGCTACCTCCAGG 59.822 60.000 9.47 0.00 42.17 4.45
1008 1458 0.461548 TCCTACGAAGCATGGCAGAG 59.538 55.000 0.00 0.00 0.00 3.35
1074 1524 2.350895 CCGATTGCTGTCACCCCA 59.649 61.111 0.00 0.00 0.00 4.96
1141 1591 2.031120 TGAAGAACCAAAACCAGCAGG 58.969 47.619 0.00 0.00 42.21 4.85
1189 1639 2.124942 CCTCAAAGGCCTCCTCGC 60.125 66.667 5.23 0.00 30.89 5.03
1270 1720 4.272991 CCAGAGCTAATTCAGATGAGCAAC 59.727 45.833 0.00 0.00 41.58 4.17
1308 1761 1.508667 ATGCCACCTCCAATCCACCA 61.509 55.000 0.00 0.00 0.00 4.17
1392 1845 5.132897 AGATGAGTGACTTGAGAGTTGTC 57.867 43.478 0.00 0.00 35.88 3.18
1395 1848 3.319405 TGAGTGACTTGAGAGTTGTCCTC 59.681 47.826 0.00 0.00 40.80 3.71
1479 1932 6.054860 AGCACCTTCTTTTCTGATAAGCTA 57.945 37.500 3.34 0.00 0.00 3.32
1480 1933 6.112058 AGCACCTTCTTTTCTGATAAGCTAG 58.888 40.000 3.34 3.86 0.00 3.42
1500 1953 1.612726 GCAAGGCAATCTCCAGTGTCT 60.613 52.381 0.00 0.00 0.00 3.41
1611 2064 1.375551 AGAAAAGTGTTCCACGCGTT 58.624 45.000 10.22 0.00 39.64 4.84
1617 2070 1.066093 TGTTCCACGCGTTCTTCGA 59.934 52.632 10.22 0.00 42.86 3.71
1633 2086 6.145696 CGTTCTTCGAATCTTGAAGGTTTACT 59.854 38.462 0.00 0.00 42.43 2.24
1649 2102 4.748600 GGTTTACTCAACGTTAACTCTGCT 59.251 41.667 0.00 0.00 35.90 4.24
1659 2112 5.123936 ACGTTAACTCTGCTTCTCCTTTTT 58.876 37.500 3.71 0.00 0.00 1.94
1787 2240 3.004734 ACATGTGCTGGTGCTTTAAGTTC 59.995 43.478 0.00 0.00 40.48 3.01
1789 2242 3.287222 TGTGCTGGTGCTTTAAGTTCTT 58.713 40.909 0.00 0.00 40.48 2.52
2032 2493 4.955925 TGCGTGTTGTTATATCAAAGGG 57.044 40.909 0.00 0.00 0.00 3.95
2038 2500 7.009174 GCGTGTTGTTATATCAAAGGGATTTTG 59.991 37.037 0.00 0.00 46.09 2.44
2040 2502 7.816995 GTGTTGTTATATCAAAGGGATTTTGCA 59.183 33.333 0.00 0.00 44.69 4.08
2135 2597 3.804601 TGCATCTTGCTTGCATGTG 57.195 47.368 8.07 7.27 44.73 3.21
2204 2673 0.609151 TGCACATTGGCCATTCCTTG 59.391 50.000 6.09 2.26 35.26 3.61
2442 2915 1.895798 TCTGTTCGGCATCTTCAGACT 59.104 47.619 0.00 0.00 31.51 3.24
2603 3076 2.369860 TGCTCAAGCTTCTCAAGGAGAA 59.630 45.455 12.13 8.27 44.68 2.87
2606 3079 4.384056 CTCAAGCTTCTCAAGGAGAACAA 58.616 43.478 0.00 0.00 42.78 2.83
2736 3209 4.282957 AGTGATTTCTCTGAGCAGTCTTCA 59.717 41.667 0.00 0.00 0.00 3.02
2742 3215 2.159338 CTCTGAGCAGTCTTCAGAGCTC 60.159 54.545 15.47 5.27 46.98 4.09
2802 3275 5.221661 GGATAATCTCCTGTGGTTAACCGAT 60.222 44.000 19.65 11.67 41.29 4.18
2815 3288 1.111277 AACCGATATTTTGGCTGGCC 58.889 50.000 4.43 4.43 0.00 5.36
3159 3632 0.974383 TCGGGAGTTTCCTCAAGGTC 59.026 55.000 0.00 0.00 39.64 3.85
3243 3716 0.242825 CTTACGTCGAACAGCAGGGA 59.757 55.000 0.00 0.00 0.00 4.20
3284 3757 2.415010 CTGAGATCTCCGGTGGCG 59.585 66.667 20.03 0.00 0.00 5.69
3285 3758 3.144120 CTGAGATCTCCGGTGGCGG 62.144 68.421 20.03 0.00 0.00 6.13
3286 3759 4.593864 GAGATCTCCGGTGGCGGC 62.594 72.222 12.00 0.00 0.00 6.53
3308 3781 4.671569 GCAGGGAGGCTATCGCGG 62.672 72.222 6.13 0.00 45.29 6.46
3309 3782 3.996124 CAGGGAGGCTATCGCGGG 61.996 72.222 6.13 0.00 45.29 6.13
3339 3812 4.659088 TCGTAAGTAGAACATCGCTGAAG 58.341 43.478 0.00 0.00 39.48 3.02
3343 3816 5.392767 AAGTAGAACATCGCTGAAGAAGA 57.607 39.130 0.00 0.00 0.00 2.87
3344 3817 5.590530 AGTAGAACATCGCTGAAGAAGAT 57.409 39.130 0.00 0.00 0.00 2.40
3347 3820 7.548097 AGTAGAACATCGCTGAAGAAGATTTA 58.452 34.615 0.00 0.00 0.00 1.40
3348 3821 6.900568 AGAACATCGCTGAAGAAGATTTAG 57.099 37.500 0.00 0.00 0.00 1.85
3349 3822 6.402222 AGAACATCGCTGAAGAAGATTTAGT 58.598 36.000 0.00 0.00 0.00 2.24
3350 3823 6.533367 AGAACATCGCTGAAGAAGATTTAGTC 59.467 38.462 0.00 0.00 0.00 2.59
3375 3850 6.655078 ATAAGTTGATTTGTGTGAGGCTTT 57.345 33.333 0.00 0.00 0.00 3.51
3376 3851 4.311816 AGTTGATTTGTGTGAGGCTTTG 57.688 40.909 0.00 0.00 0.00 2.77
3377 3852 3.953612 AGTTGATTTGTGTGAGGCTTTGA 59.046 39.130 0.00 0.00 0.00 2.69
3378 3853 4.037208 AGTTGATTTGTGTGAGGCTTTGAG 59.963 41.667 0.00 0.00 0.00 3.02
3427 3902 1.721926 CTTCTTCGGTTCTTCGCTGAC 59.278 52.381 0.00 0.00 0.00 3.51
3439 3914 0.596600 TCGCTGACACGTGAAGTTCC 60.597 55.000 25.01 5.90 0.00 3.62
3452 3927 2.095461 GAAGTTCCCTGAATTCTGGCC 58.905 52.381 22.52 13.51 34.08 5.36
3492 3967 1.076332 GTGCTGCTTACTTACCACGG 58.924 55.000 0.00 0.00 0.00 4.94
3541 4017 2.953466 ACTACGACATTGTGCGGTAT 57.047 45.000 0.00 0.00 0.00 2.73
3597 4073 3.293311 ACTGAATGCTTGTGATGCAAC 57.707 42.857 0.00 0.00 44.01 4.17
3669 4146 3.102972 TCTGAGATTTGGGAGAGTGAGG 58.897 50.000 0.00 0.00 0.00 3.86
3670 4147 3.102972 CTGAGATTTGGGAGAGTGAGGA 58.897 50.000 0.00 0.00 0.00 3.71
3671 4148 3.102972 TGAGATTTGGGAGAGTGAGGAG 58.897 50.000 0.00 0.00 0.00 3.69
3674 4151 4.027437 AGATTTGGGAGAGTGAGGAGTAC 58.973 47.826 0.00 0.00 0.00 2.73
3694 4171 4.228912 ACTTTGAATCTTGCTTCAACGG 57.771 40.909 7.32 3.57 43.03 4.44
3728 4216 6.061022 TGGGATTCTACAAATGTTGAGCTA 57.939 37.500 0.00 0.00 31.97 3.32
3734 4222 2.162681 ACAAATGTTGAGCTACCTGCC 58.837 47.619 0.00 0.00 44.23 4.85
3754 4242 3.796717 GCCAAGGCAGCGTTATTTAATTC 59.203 43.478 6.14 0.00 41.49 2.17
3760 4248 4.672409 GCAGCGTTATTTAATTCTGCCTT 58.328 39.130 12.10 0.00 37.39 4.35
3761 4249 4.735338 GCAGCGTTATTTAATTCTGCCTTC 59.265 41.667 12.10 0.00 37.39 3.46
3762 4250 5.273944 CAGCGTTATTTAATTCTGCCTTCC 58.726 41.667 0.00 0.00 0.00 3.46
3763 4251 4.947388 AGCGTTATTTAATTCTGCCTTCCA 59.053 37.500 0.00 0.00 0.00 3.53
3764 4252 5.066505 AGCGTTATTTAATTCTGCCTTCCAG 59.933 40.000 0.00 0.00 43.17 3.86
3765 4253 5.273944 CGTTATTTAATTCTGCCTTCCAGC 58.726 41.667 0.00 0.00 41.50 4.85
3808 4296 4.276926 CCTCTTCCTGTTTCAAACTTCAGG 59.723 45.833 1.10 0.31 46.00 3.86
3843 4332 3.664025 GCGAAATCTGTCGGTTTTCTTTG 59.336 43.478 11.63 1.09 41.40 2.77
3885 4393 3.511540 TGGATAATCTGGGATGCTCGTAG 59.488 47.826 0.00 0.00 0.00 3.51
3921 4429 3.570125 TGCGATGATTACCTCCTCTAGTG 59.430 47.826 0.00 0.00 0.00 2.74
3938 7336 7.451877 TCCTCTAGTGTAGAACTCATGAAAGTT 59.548 37.037 0.00 0.00 42.10 2.66
3941 7339 8.082852 TCTAGTGTAGAACTCATGAAAGTTGAC 58.917 37.037 5.16 4.45 39.55 3.18
3944 7342 2.808543 AGAACTCATGAAAGTTGACGCC 59.191 45.455 5.16 0.00 39.55 5.68
4043 7444 3.138728 GCCCCCTGATGGTGATCCC 62.139 68.421 0.00 0.00 0.00 3.85
4045 7446 1.386485 CCCCTGATGGTGATCCCCT 60.386 63.158 0.00 0.00 0.00 4.79
4061 7462 1.668294 CCTCAGCGGGCGATCTAAT 59.332 57.895 0.00 0.00 0.00 1.73
4062 7463 0.389166 CCTCAGCGGGCGATCTAATC 60.389 60.000 0.00 0.00 0.00 1.75
4063 7464 0.600557 CTCAGCGGGCGATCTAATCT 59.399 55.000 0.00 0.00 0.00 2.40
4064 7465 1.813178 CTCAGCGGGCGATCTAATCTA 59.187 52.381 0.00 0.00 0.00 1.98
4065 7466 2.229062 CTCAGCGGGCGATCTAATCTAA 59.771 50.000 0.00 0.00 0.00 2.10
4142 7544 1.000993 TCCTCAGACCTCCTCCTGC 59.999 63.158 0.00 0.00 0.00 4.85
4241 7649 2.030371 TGAGCAGCAATTTGTGGTTGA 58.970 42.857 0.00 0.00 35.13 3.18
4263 7671 3.266510 TGATCAGTAGGGTCAACATGC 57.733 47.619 0.00 0.00 0.00 4.06
4264 7672 2.205074 GATCAGTAGGGTCAACATGCG 58.795 52.381 0.00 0.00 0.00 4.73
4265 7673 0.249120 TCAGTAGGGTCAACATGCGG 59.751 55.000 0.00 0.00 0.00 5.69
4266 7674 0.036388 CAGTAGGGTCAACATGCGGT 60.036 55.000 0.00 0.00 0.00 5.68
4267 7675 0.690762 AGTAGGGTCAACATGCGGTT 59.309 50.000 0.00 0.00 41.47 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.068691 CCTTCGCTCCGTCCCTCA 61.069 66.667 0.00 0.00 0.00 3.86
2 3 4.377760 TCCCTTCGCTCCGTCCCT 62.378 66.667 0.00 0.00 0.00 4.20
5 6 3.069318 ACCTCCCTTCGCTCCGTC 61.069 66.667 0.00 0.00 0.00 4.79
6 7 3.382832 CACCTCCCTTCGCTCCGT 61.383 66.667 0.00 0.00 0.00 4.69
7 8 4.148825 CCACCTCCCTTCGCTCCG 62.149 72.222 0.00 0.00 0.00 4.63
11 12 4.785453 CAGCCCACCTCCCTTCGC 62.785 72.222 0.00 0.00 0.00 4.70
12 13 4.101448 CCAGCCCACCTCCCTTCG 62.101 72.222 0.00 0.00 0.00 3.79
21 22 4.426313 GTACCCTGCCCAGCCCAC 62.426 72.222 0.00 0.00 0.00 4.61
47 48 2.278857 CCGAGCGAATCACCGGAG 60.279 66.667 9.46 0.00 44.29 4.63
48 49 3.066190 ACCGAGCGAATCACCGGA 61.066 61.111 9.46 0.00 44.29 5.14
75 76 0.908198 AAGCCTCAGGACATCAGACC 59.092 55.000 0.00 0.00 0.00 3.85
82 93 1.376466 GCCTCAAAGCCTCAGGACA 59.624 57.895 0.00 0.00 0.00 4.02
85 96 1.743252 GTCGCCTCAAAGCCTCAGG 60.743 63.158 0.00 0.00 0.00 3.86
86 97 0.739112 GAGTCGCCTCAAAGCCTCAG 60.739 60.000 0.00 0.00 37.67 3.35
92 103 0.246086 AGAGCAGAGTCGCCTCAAAG 59.754 55.000 13.31 0.00 40.40 2.77
93 104 0.244994 GAGAGCAGAGTCGCCTCAAA 59.755 55.000 13.31 0.00 40.40 2.69
102 113 2.139118 GCAGAAAAACGAGAGCAGAGT 58.861 47.619 0.00 0.00 0.00 3.24
111 122 1.841663 GCAGCTCCGCAGAAAAACGA 61.842 55.000 0.00 0.00 0.00 3.85
112 123 1.441016 GCAGCTCCGCAGAAAAACG 60.441 57.895 0.00 0.00 0.00 3.60
117 128 0.321919 AAATCAGCAGCTCCGCAGAA 60.322 50.000 0.00 0.00 30.68 3.02
118 129 1.022982 CAAATCAGCAGCTCCGCAGA 61.023 55.000 0.00 0.00 0.00 4.26
121 132 2.042831 ACCAAATCAGCAGCTCCGC 61.043 57.895 0.00 0.00 0.00 5.54
122 133 1.651240 CCACCAAATCAGCAGCTCCG 61.651 60.000 0.00 0.00 0.00 4.63
124 135 1.093159 CTCCACCAAATCAGCAGCTC 58.907 55.000 0.00 0.00 0.00 4.09
125 136 0.323178 CCTCCACCAAATCAGCAGCT 60.323 55.000 0.00 0.00 0.00 4.24
127 138 2.426024 CAATCCTCCACCAAATCAGCAG 59.574 50.000 0.00 0.00 0.00 4.24
129 140 1.753073 CCAATCCTCCACCAAATCAGC 59.247 52.381 0.00 0.00 0.00 4.26
173 195 3.121030 CAGCGCAAACCCTCCTCG 61.121 66.667 11.47 0.00 0.00 4.63
181 204 2.504681 CAATCCGGCAGCGCAAAC 60.505 61.111 11.47 0.00 0.00 2.93
186 209 2.587194 CTCTCCAATCCGGCAGCG 60.587 66.667 0.00 0.00 33.14 5.18
188 211 1.523258 CTGCTCTCCAATCCGGCAG 60.523 63.158 0.00 0.00 43.03 4.85
224 247 6.284459 AGGAAAATAATGAGGAGCGTAAGAG 58.716 40.000 0.00 0.00 43.02 2.85
228 251 6.404293 GCAAAAGGAAAATAATGAGGAGCGTA 60.404 38.462 0.00 0.00 0.00 4.42
238 261 4.244862 CCACGCAGCAAAAGGAAAATAAT 58.755 39.130 0.00 0.00 0.00 1.28
260 283 3.421844 AGACCAATTTCAGCCAGGTTAC 58.578 45.455 0.00 0.00 31.57 2.50
376 399 4.287067 ACTCCAAACATTTCTAGAGGCAGA 59.713 41.667 0.00 0.00 0.00 4.26
380 403 7.118971 CAGAGAAACTCCAAACATTTCTAGAGG 59.881 40.741 0.00 0.00 41.58 3.69
421 444 6.869315 ATGCTCTGAAGATTCATGATGAAG 57.131 37.500 13.79 0.00 40.05 3.02
424 447 5.687730 GCAAATGCTCTGAAGATTCATGATG 59.312 40.000 0.00 0.00 35.82 3.07
425 448 5.833082 GCAAATGCTCTGAAGATTCATGAT 58.167 37.500 0.00 0.00 35.82 2.45
482 505 3.985279 CAGAACGTACAAATTCAGACCGA 59.015 43.478 0.00 0.00 0.00 4.69
499 522 7.721286 TCTCTCTGTTTTCTCATTTCAGAAC 57.279 36.000 0.00 0.00 35.26 3.01
500 523 8.373981 AGATCTCTCTGTTTTCTCATTTCAGAA 58.626 33.333 0.00 0.00 35.26 3.02
501 524 7.905265 AGATCTCTCTGTTTTCTCATTTCAGA 58.095 34.615 0.00 0.00 34.62 3.27
504 527 7.224557 GCCTAGATCTCTCTGTTTTCTCATTTC 59.775 40.741 0.00 0.00 32.66 2.17
505 528 7.047271 GCCTAGATCTCTCTGTTTTCTCATTT 58.953 38.462 0.00 0.00 32.66 2.32
506 529 6.581712 GCCTAGATCTCTCTGTTTTCTCATT 58.418 40.000 0.00 0.00 32.66 2.57
511 536 3.131400 ACCGCCTAGATCTCTCTGTTTTC 59.869 47.826 0.00 0.00 32.66 2.29
530 555 3.381908 AGCTCCTAGTTCATAGTTCACCG 59.618 47.826 0.00 0.00 0.00 4.94
531 556 4.160626 ACAGCTCCTAGTTCATAGTTCACC 59.839 45.833 0.00 0.00 0.00 4.02
571 596 6.150140 ACCAAGACAATTTACAGCATCTTCTC 59.850 38.462 0.00 0.00 0.00 2.87
587 612 3.691575 TGGAACAAAGTCACCAAGACAA 58.308 40.909 0.00 0.00 43.18 3.18
599 624 4.096984 AGTCTTGAGCAAACTGGAACAAAG 59.903 41.667 0.00 0.00 38.70 2.77
621 646 2.027745 ACCTGACTACATGGTTGCTCAG 60.028 50.000 0.00 0.00 0.00 3.35
646 671 7.970102 ACCAACACTAGAGTCTAACCATTTAA 58.030 34.615 0.64 0.00 0.00 1.52
653 678 4.523558 ACCAGACCAACACTAGAGTCTAAC 59.476 45.833 0.64 0.00 37.48 2.34
665 690 2.746279 ATCAAACCACCAGACCAACA 57.254 45.000 0.00 0.00 0.00 3.33
677 710 4.668431 GCTCGGAAACTTCGTAATCAAACC 60.668 45.833 0.00 0.00 0.00 3.27
687 720 1.606606 GCAAATGCTCGGAAACTTCG 58.393 50.000 0.00 0.00 38.21 3.79
773 806 5.991606 TCCAAGTTCATAGTTCACACTCTTG 59.008 40.000 0.00 0.00 32.97 3.02
812 845 4.473477 AGAGCAGATGGTTAACAGTACC 57.527 45.455 8.10 0.00 36.17 3.34
813 846 7.097834 AGTAAAGAGCAGATGGTTAACAGTAC 58.902 38.462 8.10 0.00 0.00 2.73
820 864 7.004555 TCAAGAAGTAAAGAGCAGATGGTTA 57.995 36.000 0.00 0.00 0.00 2.85
884 1325 8.806429 TGATGAACTGAAGCTGGAATTAATAA 57.194 30.769 0.00 0.00 0.00 1.40
890 1331 4.019501 AGACTGATGAACTGAAGCTGGAAT 60.020 41.667 0.00 0.00 0.00 3.01
976 1417 2.037144 TCGTAGGAAGCTTATGACCCC 58.963 52.381 0.00 0.00 0.00 4.95
977 1418 3.718815 CTTCGTAGGAAGCTTATGACCC 58.281 50.000 11.93 0.00 42.90 4.46
1074 1524 1.073897 GCAGCACCAGAACCCTTCT 59.926 57.895 0.00 0.00 41.70 2.85
1110 1560 2.838736 TGGTTCTTCACTGTCTTCTGC 58.161 47.619 0.00 0.00 0.00 4.26
1141 1591 3.288484 GCCCACTTTAGGCCTTGC 58.712 61.111 12.58 0.00 45.16 4.01
1161 1611 1.301293 CTTTGAGGCAGGAGGGGAC 59.699 63.158 0.00 0.00 0.00 4.46
1173 1623 1.153469 GAGCGAGGAGGCCTTTGAG 60.153 63.158 6.77 0.06 31.76 3.02
1189 1639 1.112315 ATAGTCAGCGCCCTCTGGAG 61.112 60.000 2.29 0.00 34.91 3.86
1202 1652 1.761198 TCCTCTCCGACGAGATAGTCA 59.239 52.381 0.00 0.00 44.25 3.41
1227 1677 1.541588 GACCTTGTTGGAGTGGAATGC 59.458 52.381 0.00 0.00 39.71 3.56
1308 1761 2.262915 CTCTCGCTCGCCACCTTT 59.737 61.111 0.00 0.00 0.00 3.11
1392 1845 0.403271 CCCCATCCTTGCCATAGAGG 59.597 60.000 0.00 0.00 41.84 3.69
1395 1848 1.696063 CAACCCCATCCTTGCCATAG 58.304 55.000 0.00 0.00 0.00 2.23
1468 1921 3.912496 TTGCCTTGCTAGCTTATCAGA 57.088 42.857 17.23 0.00 0.00 3.27
1479 1932 0.403271 ACACTGGAGATTGCCTTGCT 59.597 50.000 0.00 0.00 0.00 3.91
1480 1933 0.807496 GACACTGGAGATTGCCTTGC 59.193 55.000 0.00 0.00 0.00 4.01
1500 1953 4.162131 TCACAATCAGGCACTTCTATGCTA 59.838 41.667 0.00 0.00 45.38 3.49
1611 2064 6.755206 TGAGTAAACCTTCAAGATTCGAAGA 58.245 36.000 3.35 0.00 42.05 2.87
1617 2070 6.937436 AACGTTGAGTAAACCTTCAAGATT 57.063 33.333 0.00 0.00 35.13 2.40
1633 2086 3.321111 AGGAGAAGCAGAGTTAACGTTGA 59.679 43.478 11.99 0.00 0.00 3.18
1793 2246 3.954904 TGCACTAACTTAAAGCACCCAAA 59.045 39.130 0.00 0.00 0.00 3.28
1795 2248 3.216187 TGCACTAACTTAAAGCACCCA 57.784 42.857 0.00 0.00 0.00 4.51
1796 2249 4.783764 ATTGCACTAACTTAAAGCACCC 57.216 40.909 0.00 0.00 34.56 4.61
1845 2299 6.574350 TCAAAGCATTTCGGTTAAGGAAAAA 58.426 32.000 5.90 0.00 35.03 1.94
1854 2308 6.817765 TCTAGATTTCAAAGCATTTCGGTT 57.182 33.333 0.00 0.00 35.03 4.44
2135 2597 0.379669 CTCAATCTGCACCAATCGGC 59.620 55.000 0.00 0.00 34.57 5.54
2235 2704 6.773976 TTTGTTCTGAAGATTCCAAGTTGT 57.226 33.333 1.45 0.00 0.00 3.32
2315 2788 5.360714 CCCAATAATTCTGCAACCTGTACAT 59.639 40.000 0.00 0.00 0.00 2.29
2442 2915 0.899720 GGGTGACACCGTAATCCTCA 59.100 55.000 18.40 0.00 39.83 3.86
2603 3076 2.124193 TGGCACAGCTGCTGTTGT 60.124 55.556 31.20 9.96 42.59 3.32
2736 3209 0.321996 GAACCGGTTCCTTGAGCTCT 59.678 55.000 33.02 0.63 33.64 4.09
2742 3215 2.540145 CCGAAGAACCGGTTCCTTG 58.460 57.895 37.53 29.46 44.23 3.61
2802 3275 1.110442 CATTCCGGCCAGCCAAAATA 58.890 50.000 9.78 0.00 35.37 1.40
2823 3296 0.524862 AGCCTGCAAATTCTTCTGCG 59.475 50.000 0.00 0.00 41.63 5.18
2865 3338 1.377994 CTTGGAGTGAAGCCCAGCT 59.622 57.895 0.00 0.00 42.56 4.24
2925 3398 0.449388 CAATCGCCACAAAGAGCCTC 59.551 55.000 0.00 0.00 0.00 4.70
3147 3620 2.549349 GCTGTTACCGACCTTGAGGAAA 60.549 50.000 3.59 0.00 38.94 3.13
3159 3632 2.033448 TTGGGGCAGCTGTTACCG 59.967 61.111 16.64 0.00 0.00 4.02
3286 3759 1.596477 GATAGCCTCCCTGCGCAAG 60.596 63.158 13.05 4.91 36.02 4.01
3308 3781 0.029834 TCTACTTACGAATCGGCGCC 59.970 55.000 19.07 19.07 33.86 6.53
3309 3782 1.516042 GTTCTACTTACGAATCGGCGC 59.484 52.381 7.80 0.00 33.86 6.53
3315 3788 5.244785 TCAGCGATGTTCTACTTACGAAT 57.755 39.130 0.00 0.00 0.00 3.34
3347 3820 6.595716 GCCTCACACAAATCAACTTATAGACT 59.404 38.462 0.00 0.00 0.00 3.24
3348 3821 6.595716 AGCCTCACACAAATCAACTTATAGAC 59.404 38.462 0.00 0.00 0.00 2.59
3349 3822 6.711277 AGCCTCACACAAATCAACTTATAGA 58.289 36.000 0.00 0.00 0.00 1.98
3350 3823 6.992063 AGCCTCACACAAATCAACTTATAG 57.008 37.500 0.00 0.00 0.00 1.31
3375 3850 2.416202 CACAGCGCACAAACATATCTCA 59.584 45.455 11.47 0.00 0.00 3.27
3376 3851 2.789092 GCACAGCGCACAAACATATCTC 60.789 50.000 11.47 0.00 41.79 2.75
3377 3852 1.131126 GCACAGCGCACAAACATATCT 59.869 47.619 11.47 0.00 41.79 1.98
3378 3853 1.131126 AGCACAGCGCACAAACATATC 59.869 47.619 11.47 0.00 46.13 1.63
3427 3902 3.187227 CAGAATTCAGGGAACTTCACGTG 59.813 47.826 9.94 9.94 40.21 4.49
3439 3914 0.830648 TCGGTAGGCCAGAATTCAGG 59.169 55.000 12.38 12.38 34.09 3.86
3452 3927 4.564372 CACATCAGACAAGACATTCGGTAG 59.436 45.833 0.00 0.00 0.00 3.18
3492 3967 3.737266 CACAATGCAACAAACTGATGTCC 59.263 43.478 0.00 0.00 31.81 4.02
3541 4017 3.687212 CCGCAATAATACAGTGTCACCAA 59.313 43.478 0.00 0.00 0.00 3.67
3597 4073 7.502226 TCCTACATCCCAGCAAAATATTTACAG 59.498 37.037 0.01 0.00 0.00 2.74
3728 4216 2.484287 ATAACGCTGCCTTGGCAGGT 62.484 55.000 34.06 27.37 43.18 4.00
3734 4222 4.500477 GCAGAATTAAATAACGCTGCCTTG 59.500 41.667 13.79 0.00 38.60 3.61
3749 4237 1.915489 TGGAGCTGGAAGGCAGAATTA 59.085 47.619 0.00 0.00 34.17 1.40
3754 4242 2.271497 CCTGGAGCTGGAAGGCAG 59.729 66.667 0.00 0.00 34.17 4.85
3760 4248 1.305633 CCTCTGACCTGGAGCTGGA 60.306 63.158 0.00 0.00 0.00 3.86
3761 4249 1.305633 TCCTCTGACCTGGAGCTGG 60.306 63.158 0.00 0.00 0.00 4.85
3762 4250 1.896694 GTCCTCTGACCTGGAGCTG 59.103 63.158 0.00 0.00 35.34 4.24
3763 4251 4.451544 GTCCTCTGACCTGGAGCT 57.548 61.111 0.00 0.00 35.34 4.09
3808 4296 0.523072 ATTTCGCTGACATGTGCCAC 59.477 50.000 1.15 0.00 0.00 5.01
3843 4332 4.464244 TCCATAGGATCGACAGGATTCATC 59.536 45.833 0.00 0.00 34.82 2.92
3885 4393 2.224079 TCATCGCAGAAGACTTTTGCAC 59.776 45.455 25.28 3.10 43.58 4.57
3921 4429 4.143094 GGCGTCAACTTTCATGAGTTCTAC 60.143 45.833 0.00 0.00 37.76 2.59
4043 7444 0.389166 GATTAGATCGCCCGCTGAGG 60.389 60.000 0.00 0.00 40.63 3.86
4045 7446 1.905637 TAGATTAGATCGCCCGCTGA 58.094 50.000 0.00 0.00 0.00 4.26
4061 7462 2.445274 GGCGGGGGCTAGGTTAGA 60.445 66.667 0.00 0.00 0.00 2.10
4062 7463 2.446036 AGGCGGGGGCTAGGTTAG 60.446 66.667 0.00 0.00 36.44 2.34
4063 7464 2.445274 GAGGCGGGGGCTAGGTTA 60.445 66.667 0.00 0.00 38.98 2.85
4064 7465 4.416601 AGAGGCGGGGGCTAGGTT 62.417 66.667 0.00 0.00 38.98 3.50
4065 7466 4.862823 GAGAGGCGGGGGCTAGGT 62.863 72.222 0.00 0.00 38.98 3.08
4107 7508 1.737008 GAGGGCGTTCGAGGTGTTC 60.737 63.158 0.00 0.00 0.00 3.18
4119 7520 3.151022 GGAGGTCTGAGGAGGGCG 61.151 72.222 0.00 0.00 0.00 6.13
4142 7544 0.256752 TCCAGATCATTGTGGGCAGG 59.743 55.000 0.00 0.00 36.91 4.85
4167 7569 3.989167 GCCGTGCCGTTACAACATATATA 59.011 43.478 0.00 0.00 0.00 0.86
4168 7570 2.803956 GCCGTGCCGTTACAACATATAT 59.196 45.455 0.00 0.00 0.00 0.86
4169 7571 2.159071 AGCCGTGCCGTTACAACATATA 60.159 45.455 0.00 0.00 0.00 0.86
4170 7572 1.011333 GCCGTGCCGTTACAACATAT 58.989 50.000 0.00 0.00 0.00 1.78
4174 7576 1.081094 AATAGCCGTGCCGTTACAAC 58.919 50.000 0.00 0.00 0.00 3.32
4218 7623 1.755959 ACCACAAATTGCTGCTCACAA 59.244 42.857 0.00 0.00 0.00 3.33
4241 7649 4.202441 GCATGTTGACCCTACTGATCATT 58.798 43.478 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.