Multiple sequence alignment - TraesCS1B01G243800

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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 TraesCS1B01G243800 chr1B 100.000 5406 0 0 1 5406 432825828 432820423 0.000000e+00 9984.0
1 TraesCS1B01G243800 chr1A 93.111 4834 186 62 650 5406 403022775 403027538 0.000000e+00 6946.0
2 TraesCS1B01G243800 chr1A 81.947 637 70 27 1 608 403022010 403022630 1.050000e-136 497.0
3 TraesCS1B01G243800 chr1D 94.094 3437 126 34 2007 5406 319934999 319931603 0.000000e+00 5151.0
4 TraesCS1B01G243800 chr1D 91.014 1391 39 20 652 1980 319936363 319934997 0.000000e+00 1797.0
5 TraesCS1B01G243800 chr1D 83.279 610 47 25 5 570 319936982 319936384 1.340000e-140 510.0
6 TraesCS1B01G243800 chr1D 100.000 30 0 0 2076 2105 59876072 59876043 7.560000e-04 56.5
7 TraesCS1B01G243800 chr2A 89.189 296 32 0 5036 5331 621265133 621265428 2.380000e-98 370.0
8 TraesCS1B01G243800 chr2D 88.514 296 34 0 5036 5331 478118184 478118479 5.150000e-95 359.0
9 TraesCS1B01G243800 chr2B 88.514 296 34 0 5036 5331 560458458 560458753 5.150000e-95 359.0
10 TraesCS1B01G243800 chr3D 86.282 277 34 4 1362 1635 460497238 460497513 1.140000e-76 298.0
11 TraesCS1B01G243800 chr4A 85.921 277 39 0 1363 1639 114592044 114591768 4.090000e-76 296.0
12 TraesCS1B01G243800 chr3A 85.921 277 35 4 1362 1635 602917569 602917844 5.300000e-75 292.0
13 TraesCS1B01G243800 chr4D 85.305 279 40 1 1363 1640 350492633 350492911 2.460000e-73 287.0
14 TraesCS1B01G243800 chr4B 84.669 287 44 0 1357 1643 433641723 433642009 2.460000e-73 287.0
15 TraesCS1B01G243800 chr6A 100.000 28 0 0 2077 2104 469430128 469430101 1.000000e-02 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 TraesCS1B01G243800 chr1B 432820423 432825828 5405 True 9984.0 9984 100.000000 1 5406 1 chr1B.!!$R1 5405
1 TraesCS1B01G243800 chr1A 403022010 403027538 5528 False 3721.5 6946 87.529000 1 5406 2 chr1A.!!$F1 5405
2 TraesCS1B01G243800 chr1D 319931603 319936982 5379 True 2486.0 5151 89.462333 5 5406 3 chr1D.!!$R2 5401

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
644 804 0.173481 CGATCGGCACCTCTCAGAAA 59.827 55.000 7.38 0.0 0.00 2.52 F
1706 1928 1.144565 CTGGCTTCTCGTGATCGCTG 61.145 60.000 4.48 0.0 36.96 5.18 F
3337 3579 0.897621 GGGGCAAAACTATGCTTGCT 59.102 50.000 6.73 0.0 45.79 3.91 F
3979 4230 1.078918 CGATGGCAAGCAGACCAGA 60.079 57.895 0.00 0.0 39.88 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 2294 0.179702 TCATGTGATGCAGAGGCCTC 59.820 55.000 26.22 26.22 40.13 4.70 R
3543 3785 0.947244 CAACTCCTGACACCTGTTGC 59.053 55.000 0.00 0.00 32.99 4.17 R
4267 4518 0.255890 GCTCCTTGGCCTTGGTGATA 59.744 55.000 16.89 0.00 0.00 2.15 R
5003 5266 2.034879 ATCACCGCAAGCCTGAACG 61.035 57.895 0.00 0.00 0.00 3.95 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
23 24 2.997303 ACGTTTTTCAAACCAAGGTTGC 59.003 40.909 5.06 0.00 38.47 4.17
57 58 1.742411 CGCCACGAGGTTAACCATGAT 60.742 52.381 26.26 5.56 38.89 2.45
58 59 1.670811 GCCACGAGGTTAACCATGATG 59.329 52.381 26.26 16.94 38.89 3.07
60 61 3.808728 CCACGAGGTTAACCATGATGAT 58.191 45.455 26.26 3.55 38.89 2.45
64 65 3.496130 CGAGGTTAACCATGATGATCTGC 59.504 47.826 26.26 0.00 38.89 4.26
97 110 1.596260 ACGCGATTGAGCTCATTCATG 59.404 47.619 28.75 23.31 34.40 3.07
104 117 5.065090 CGATTGAGCTCATTCATGTGGTTAA 59.935 40.000 28.75 8.54 33.85 2.01
143 157 9.216148 TCTTAGTTAACCCCTACTATAAATGCA 57.784 33.333 0.88 0.00 0.00 3.96
212 231 8.825667 TGAATCAATTTGGTTTAAACTTAGGC 57.174 30.769 17.50 1.78 0.00 3.93
220 239 4.019501 TGGTTTAAACTTAGGCCCGATACA 60.020 41.667 17.50 0.26 0.00 2.29
224 243 1.300697 CTTAGGCCCGATACACGCC 60.301 63.158 0.00 0.00 43.35 5.68
260 279 9.013229 AGCATAAATTAAGACATCACAAACTCA 57.987 29.630 0.00 0.00 0.00 3.41
328 355 9.280174 TGATTCATTTTCGTCTAAACTTAGGTT 57.720 29.630 0.00 0.00 37.24 3.50
339 366 3.706600 AACTTAGGTTTGATACGCCCA 57.293 42.857 0.00 0.00 30.55 5.36
340 367 3.261981 ACTTAGGTTTGATACGCCCAG 57.738 47.619 0.00 0.00 0.00 4.45
341 368 2.835764 ACTTAGGTTTGATACGCCCAGA 59.164 45.455 0.00 0.00 0.00 3.86
351 378 4.377021 TGATACGCCCAGAATATGACAAC 58.623 43.478 0.00 0.00 0.00 3.32
356 383 4.462483 ACGCCCAGAATATGACAACAATTT 59.538 37.500 0.00 0.00 0.00 1.82
499 544 6.555463 TTAAAAACGGACCCTCTATGAGAT 57.445 37.500 0.00 0.00 0.00 2.75
501 546 3.314307 AACGGACCCTCTATGAGATCA 57.686 47.619 0.00 0.00 0.00 2.92
502 547 3.534357 ACGGACCCTCTATGAGATCAT 57.466 47.619 0.31 0.31 40.22 2.45
503 548 3.161067 ACGGACCCTCTATGAGATCATG 58.839 50.000 5.58 0.00 37.15 3.07
504 549 2.495270 CGGACCCTCTATGAGATCATGG 59.505 54.545 5.58 2.76 37.15 3.66
505 550 3.515562 GGACCCTCTATGAGATCATGGT 58.484 50.000 5.58 4.17 37.15 3.55
506 551 4.678256 GGACCCTCTATGAGATCATGGTA 58.322 47.826 5.58 0.00 37.15 3.25
523 568 6.539173 TCATGGTAATGGTATGGTGGTAATC 58.461 40.000 0.00 0.00 34.30 1.75
596 651 6.310711 CGGTGAAGTTCTATAGTGGTTTTCTC 59.689 42.308 4.17 0.84 0.00 2.87
597 652 7.159372 GGTGAAGTTCTATAGTGGTTTTCTCA 58.841 38.462 4.17 0.00 0.00 3.27
599 654 9.052759 GTGAAGTTCTATAGTGGTTTTCTCAAA 57.947 33.333 4.17 0.00 0.00 2.69
600 655 9.273016 TGAAGTTCTATAGTGGTTTTCTCAAAG 57.727 33.333 4.17 0.00 0.00 2.77
601 656 9.490379 GAAGTTCTATAGTGGTTTTCTCAAAGA 57.510 33.333 0.00 0.00 0.00 2.52
602 657 9.847224 AAGTTCTATAGTGGTTTTCTCAAAGAA 57.153 29.630 0.00 0.00 31.28 2.52
626 681 5.868043 AAAGGGTTATTTTCGTAGAACCG 57.132 39.130 0.00 0.00 45.90 4.44
628 683 5.349061 AGGGTTATTTTCGTAGAACCGAT 57.651 39.130 0.00 0.00 45.90 4.18
629 684 5.354767 AGGGTTATTTTCGTAGAACCGATC 58.645 41.667 0.00 0.00 45.90 3.69
630 685 4.207841 GGGTTATTTTCGTAGAACCGATCG 59.792 45.833 8.51 8.51 45.90 3.69
631 686 4.207841 GGTTATTTTCGTAGAACCGATCGG 59.792 45.833 32.20 32.20 45.90 4.18
632 687 1.632422 TTTTCGTAGAACCGATCGGC 58.368 50.000 33.62 18.52 45.90 5.54
634 689 0.179156 TTCGTAGAACCGATCGGCAC 60.179 55.000 33.62 25.48 45.90 5.01
635 690 1.588139 CGTAGAACCGATCGGCACC 60.588 63.158 33.62 21.47 39.32 5.01
636 691 1.814527 GTAGAACCGATCGGCACCT 59.185 57.895 33.62 26.60 39.32 4.00
638 798 0.395311 TAGAACCGATCGGCACCTCT 60.395 55.000 33.62 27.59 39.32 3.69
642 802 2.121538 CCGATCGGCACCTCTCAGA 61.122 63.158 23.37 0.00 0.00 3.27
643 803 1.667154 CCGATCGGCACCTCTCAGAA 61.667 60.000 23.37 0.00 0.00 3.02
644 804 0.173481 CGATCGGCACCTCTCAGAAA 59.827 55.000 7.38 0.00 0.00 2.52
705 865 3.432051 GACGGAGACCCTGGCGATG 62.432 68.421 0.00 0.00 0.00 3.84
709 869 2.039624 AGACCCTGGCGATGAGGT 59.960 61.111 0.00 0.00 34.57 3.85
710 870 2.187946 GACCCTGGCGATGAGGTG 59.812 66.667 0.00 0.00 31.10 4.00
711 871 2.284625 ACCCTGGCGATGAGGTGA 60.285 61.111 0.00 0.00 0.00 4.02
712 872 2.187946 CCCTGGCGATGAGGTGAC 59.812 66.667 0.00 0.00 0.00 3.67
713 873 2.659063 CCCTGGCGATGAGGTGACA 61.659 63.158 0.00 0.00 0.00 3.58
714 874 1.448540 CCTGGCGATGAGGTGACAC 60.449 63.158 0.00 0.00 0.00 3.67
715 875 1.807165 CTGGCGATGAGGTGACACG 60.807 63.158 0.00 0.00 0.00 4.49
716 876 3.188786 GGCGATGAGGTGACACGC 61.189 66.667 0.00 0.00 46.79 5.34
717 877 2.125912 GCGATGAGGTGACACGCT 60.126 61.111 0.00 0.00 44.67 5.07
758 918 2.340443 CCTAATCTCGCCGGCCTC 59.660 66.667 23.46 0.00 0.00 4.70
876 1061 1.148310 CCCGCAGCATAAATACCTCG 58.852 55.000 0.00 0.00 0.00 4.63
1081 1290 3.217743 CCGGCGAGTACTCCTCCC 61.218 72.222 17.23 13.29 36.82 4.30
1575 1793 2.959707 GGTCGACCAGATCTACCATCTT 59.040 50.000 29.75 0.00 41.82 2.40
1623 1841 1.713297 AGTACAACCCCGTCAAGACT 58.287 50.000 0.00 0.00 0.00 3.24
1636 1854 6.464465 CCCCGTCAAGACTATCATATCCTTTT 60.464 42.308 0.00 0.00 0.00 2.27
1706 1928 1.144565 CTGGCTTCTCGTGATCGCTG 61.145 60.000 4.48 0.00 36.96 5.18
1719 1941 4.970003 CGTGATCGCTGATTTTTATTTCCC 59.030 41.667 4.48 0.00 0.00 3.97
1733 1955 6.926630 TTTATTTCCCTGCATTTTACTGGT 57.073 33.333 0.00 0.00 0.00 4.00
1910 2132 2.926586 GCGGTGAATTTTGGAGCTTTCC 60.927 50.000 0.00 0.00 0.00 3.13
1948 2170 1.472376 GGAAGACCAGAGCTTGATCCG 60.472 57.143 0.00 0.00 35.97 4.18
1962 2184 2.173519 TGATCCGAGTTACCGTTTCCT 58.826 47.619 0.00 0.00 0.00 3.36
1967 2189 1.670967 CGAGTTACCGTTTCCTCCACC 60.671 57.143 0.00 0.00 0.00 4.61
1968 2190 1.345415 GAGTTACCGTTTCCTCCACCA 59.655 52.381 0.00 0.00 0.00 4.17
1969 2191 1.982958 AGTTACCGTTTCCTCCACCAT 59.017 47.619 0.00 0.00 0.00 3.55
1970 2192 2.081462 GTTACCGTTTCCTCCACCATG 58.919 52.381 0.00 0.00 0.00 3.66
2043 2265 6.001460 TCAATCAAACACTTGGGTTAGTAGG 58.999 40.000 0.00 0.00 33.01 3.18
2072 2294 4.272018 CCAATCTTGATAGGAGAACAAGCG 59.728 45.833 0.00 0.00 40.20 4.68
2107 2329 2.294979 CATGATGCACACAGCCATAGT 58.705 47.619 0.00 0.00 44.83 2.12
2148 2370 5.371526 TCAGATTTTCTAGATGTGGCATCC 58.628 41.667 5.59 0.00 0.00 3.51
2208 2435 2.294512 AGGAGAGAAAAAGGCAAAAGCG 59.705 45.455 0.00 0.00 0.00 4.68
2423 2650 9.747898 TTAGTCCAACAACCAAGTTATTATGAT 57.252 29.630 0.00 0.00 0.00 2.45
2424 2651 8.055279 AGTCCAACAACCAAGTTATTATGATG 57.945 34.615 0.00 0.00 0.00 3.07
2453 2680 1.339610 TGCGTGTTCCTTTGGAAATGG 59.660 47.619 0.12 0.00 43.86 3.16
2455 2682 2.607038 GCGTGTTCCTTTGGAAATGGTC 60.607 50.000 0.12 0.00 43.86 4.02
2456 2683 2.030274 CGTGTTCCTTTGGAAATGGTCC 60.030 50.000 0.12 0.00 43.86 4.46
2468 2701 3.370103 GGAAATGGTCCGTGTGATCCTTA 60.370 47.826 0.00 0.00 36.40 2.69
2651 2884 5.302059 CCATCGGTAAGAACTCTCCTCAATA 59.698 44.000 0.00 0.00 0.00 1.90
2751 2988 4.628333 GCTTATTGTTACACGAGGTTAGCA 59.372 41.667 0.00 0.00 0.00 3.49
2791 3028 5.303971 AGTTGGATCATGCATAGTAGAAGC 58.696 41.667 0.00 0.00 0.00 3.86
2869 3106 4.279922 TCTTCTGGACTCACGTTCATTACA 59.720 41.667 0.00 0.00 0.00 2.41
2941 3178 4.412858 TGGGGTTGTCCTAGTTTTACTCAA 59.587 41.667 0.00 0.00 35.33 3.02
2979 3216 7.962964 AGTAGTTTCGAGTGATTTTGATTGA 57.037 32.000 0.00 0.00 0.00 2.57
3003 3240 5.016245 AGGGGGTGGATTGAGAATAGAAAAA 59.984 40.000 0.00 0.00 0.00 1.94
3115 3355 4.723309 AGAAATGTTCTTGAGCTGAAGGT 58.277 39.130 13.24 0.00 36.36 3.50
3181 3421 3.542648 GGGTGTTGGAATCTTACTAGCC 58.457 50.000 0.00 0.00 0.00 3.93
3337 3579 0.897621 GGGGCAAAACTATGCTTGCT 59.102 50.000 6.73 0.00 45.79 3.91
3351 3593 2.694628 TGCTTGCTCTTGACCAAACATT 59.305 40.909 0.00 0.00 0.00 2.71
3435 3677 5.151632 GCTAGATAGCTACAGATAGTCGC 57.848 47.826 0.00 0.00 45.62 5.19
3447 3689 3.002042 CAGATAGTCGCTGCTCCATTTTG 59.998 47.826 0.00 0.00 0.00 2.44
3543 3785 7.272244 TGTGTATGTATGTATGTTTCTCTGGG 58.728 38.462 0.00 0.00 0.00 4.45
3646 3888 6.331369 CCTTGAGGTATTTTGTCATGTGTT 57.669 37.500 0.00 0.00 0.00 3.32
3647 3889 7.447374 CCTTGAGGTATTTTGTCATGTGTTA 57.553 36.000 0.00 0.00 0.00 2.41
3650 3897 9.988350 CTTGAGGTATTTTGTCATGTGTTATAC 57.012 33.333 0.00 0.00 0.00 1.47
3672 3919 6.764308 ACTATATTGTTGCAAGCACTGAAT 57.236 33.333 0.00 0.00 0.00 2.57
3687 3934 4.081531 GCACTGAATTTTCCATTCCATCCA 60.082 41.667 0.00 0.00 0.00 3.41
3691 3938 9.081204 CACTGAATTTTCCATTCCATCCATATA 57.919 33.333 0.00 0.00 0.00 0.86
3732 3979 6.362283 GTGTAGTGATTGGTGTATTTTGTTGC 59.638 38.462 0.00 0.00 0.00 4.17
3781 4028 2.702592 TCTTTAACACCTATGGCCCG 57.297 50.000 0.00 0.00 0.00 6.13
3841 4088 5.940192 TTGTTGCTCAGGTAAACATACAG 57.060 39.130 0.00 0.00 34.04 2.74
3842 4089 4.968259 TGTTGCTCAGGTAAACATACAGT 58.032 39.130 0.00 0.00 0.00 3.55
3843 4090 4.754618 TGTTGCTCAGGTAAACATACAGTG 59.245 41.667 0.00 0.00 0.00 3.66
3844 4091 3.334691 TGCTCAGGTAAACATACAGTGC 58.665 45.455 0.00 0.00 0.00 4.40
3845 4092 3.007940 TGCTCAGGTAAACATACAGTGCT 59.992 43.478 0.00 0.00 0.00 4.40
3846 4093 3.372206 GCTCAGGTAAACATACAGTGCTG 59.628 47.826 0.00 0.00 0.00 4.41
3847 4094 4.569943 CTCAGGTAAACATACAGTGCTGT 58.430 43.478 9.90 9.90 46.87 4.40
3868 4118 5.827666 TGTTGCTCTGCTAGTTTAAAAACC 58.172 37.500 2.02 0.00 39.71 3.27
3870 4120 3.058501 TGCTCTGCTAGTTTAAAAACCGC 60.059 43.478 2.02 6.31 39.71 5.68
3874 4124 4.577283 TCTGCTAGTTTAAAAACCGCAAGT 59.423 37.500 16.11 0.00 41.80 3.16
3889 4139 6.096673 ACCGCAAGTTTATTTTTCATTCCT 57.903 33.333 0.00 0.00 0.00 3.36
3890 4140 5.925969 ACCGCAAGTTTATTTTTCATTCCTG 59.074 36.000 0.00 0.00 0.00 3.86
3893 4143 7.359181 CCGCAAGTTTATTTTTCATTCCTGAAC 60.359 37.037 0.00 0.00 41.05 3.18
3909 4160 3.191371 CCTGAACTAACACCCAAATGCTC 59.809 47.826 0.00 0.00 0.00 4.26
3912 4163 5.815581 TGAACTAACACCCAAATGCTCTAT 58.184 37.500 0.00 0.00 0.00 1.98
3913 4164 5.647658 TGAACTAACACCCAAATGCTCTATG 59.352 40.000 0.00 0.00 0.00 2.23
3914 4165 5.179452 ACTAACACCCAAATGCTCTATGT 57.821 39.130 0.00 0.00 0.00 2.29
3916 4167 6.717289 ACTAACACCCAAATGCTCTATGTTA 58.283 36.000 0.00 0.00 31.63 2.41
3917 4168 7.172342 ACTAACACCCAAATGCTCTATGTTAA 58.828 34.615 0.00 0.00 32.38 2.01
3918 4169 7.834181 ACTAACACCCAAATGCTCTATGTTAAT 59.166 33.333 0.00 0.00 32.38 1.40
3919 4170 9.337396 CTAACACCCAAATGCTCTATGTTAATA 57.663 33.333 0.00 0.00 32.38 0.98
3920 4171 8.766994 AACACCCAAATGCTCTATGTTAATAT 57.233 30.769 0.00 0.00 0.00 1.28
3921 4172 9.860650 AACACCCAAATGCTCTATGTTAATATA 57.139 29.630 0.00 0.00 0.00 0.86
3922 4173 9.860650 ACACCCAAATGCTCTATGTTAATATAA 57.139 29.630 0.00 0.00 0.00 0.98
3979 4230 1.078918 CGATGGCAAGCAGACCAGA 60.079 57.895 0.00 0.00 39.88 3.86
4025 4276 5.277250 TGGTAGGTCATCTCTAACCATGAA 58.723 41.667 0.00 0.00 38.06 2.57
4026 4277 5.128827 TGGTAGGTCATCTCTAACCATGAAC 59.871 44.000 0.00 0.00 37.04 3.18
4027 4278 5.128827 GGTAGGTCATCTCTAACCATGAACA 59.871 44.000 0.00 0.00 38.94 3.18
4030 4281 6.725364 AGGTCATCTCTAACCATGAACAAAT 58.275 36.000 0.00 0.00 38.94 2.32
4031 4282 6.600822 AGGTCATCTCTAACCATGAACAAATG 59.399 38.462 0.00 0.00 38.94 2.32
4033 4284 7.121168 GGTCATCTCTAACCATGAACAAATGAA 59.879 37.037 0.00 0.00 36.81 2.57
4034 4285 8.680903 GTCATCTCTAACCATGAACAAATGAAT 58.319 33.333 0.00 0.00 30.76 2.57
4366 4617 3.264897 CGCAAGCGGATCTTCGGG 61.265 66.667 6.55 0.00 35.56 5.14
4473 4724 5.804639 TCTAGCTTGCTTCTTGGTTAATCA 58.195 37.500 0.00 0.00 0.00 2.57
4494 4746 0.467384 CCCACTGACAGAGCTATGGG 59.533 60.000 13.85 11.45 40.87 4.00
4596 4852 2.386501 CGTCTCAGCTATACGGACAC 57.613 55.000 6.74 0.00 33.13 3.67
4598 4854 2.539142 CGTCTCAGCTATACGGACACAC 60.539 54.545 6.74 0.00 33.13 3.82
4625 4881 8.051468 TCCCAGTTGGATTGTTGGATATATAA 57.949 34.615 0.00 0.00 38.61 0.98
4654 4915 9.917887 ATCTGGATCTTCTAATTCTTTGTTGAT 57.082 29.630 0.00 0.00 0.00 2.57
4655 4916 9.745018 TCTGGATCTTCTAATTCTTTGTTGATT 57.255 29.630 0.00 0.00 0.00 2.57
4656 4917 9.784680 CTGGATCTTCTAATTCTTTGTTGATTG 57.215 33.333 0.00 0.00 0.00 2.67
4657 4918 9.519191 TGGATCTTCTAATTCTTTGTTGATTGA 57.481 29.630 0.00 0.00 0.00 2.57
4709 4970 4.619973 TGTTGTTTCAGAAATGTGCATCC 58.380 39.130 0.00 0.00 0.00 3.51
4759 5020 7.504238 TCTCTCTCTAGAACACAAGAGAACTTT 59.496 37.037 12.45 0.00 45.69 2.66
4805 5066 1.078201 TACTGAGCATTCGTGCAGCG 61.078 55.000 3.03 0.00 43.01 5.18
5034 5297 2.482374 GTGATGGCTGCGCTTGTC 59.518 61.111 9.73 3.46 0.00 3.18
5194 5457 4.368543 GGGTCGGTCACGGTGTCC 62.369 72.222 13.47 13.47 41.39 4.02
5224 5487 1.316651 GCAGGATGAAGAAGGGCATC 58.683 55.000 0.00 0.00 39.69 3.91
5236 5499 2.501610 GGCATCCTGACCTCGGAC 59.498 66.667 0.00 0.00 32.41 4.79
5266 5529 1.153549 GACGTCCATGCTGGTCCTC 60.154 63.158 3.51 0.00 39.03 3.71
5329 5592 3.134442 AGATGAGCTTGTTCCTCCTGATC 59.866 47.826 0.00 0.00 0.00 2.92
5368 5631 0.807667 CCTTGAAGGCGGAGTCGATG 60.808 60.000 0.00 0.00 36.95 3.84
5380 5643 0.966920 AGTCGATGACGTCCTTGGTT 59.033 50.000 14.12 0.00 37.67 3.67
5383 5646 1.019278 CGATGACGTCCTTGGTTGGG 61.019 60.000 14.12 0.00 34.56 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.350192 GGCAACCTTGGTTTGAAAAACG 59.650 45.455 1.76 0.00 0.00 3.60
23 24 0.598680 GTGGCGAATCTCGAGATGGG 60.599 60.000 27.93 21.85 43.74 4.00
78 91 1.596260 ACATGAATGAGCTCAATCGCG 59.404 47.619 22.50 18.02 34.40 5.87
82 95 6.435277 ACTTTAACCACATGAATGAGCTCAAT 59.565 34.615 22.50 13.38 0.00 2.57
120 134 9.787435 CATTGCATTTATAGTAGGGGTTAACTA 57.213 33.333 5.42 0.00 32.98 2.24
143 157 9.822185 GAGATTGATTGGGTTTTATTAAGCATT 57.178 29.630 0.00 0.00 0.00 3.56
212 231 0.376852 CATGTTTGGCGTGTATCGGG 59.623 55.000 0.00 0.00 40.26 5.14
224 243 6.812656 TGTCTTAATTTATGCTGCCATGTTTG 59.187 34.615 0.00 0.00 32.85 2.93
293 320 9.914923 TTAGACGAAAATGAATCATTTATCGTG 57.085 29.630 34.61 21.78 45.28 4.35
313 340 5.005107 GGCGTATCAAACCTAAGTTTAGACG 59.995 44.000 10.69 10.69 44.47 4.18
328 355 4.681074 TGTCATATTCTGGGCGTATCAA 57.319 40.909 0.00 0.00 0.00 2.57
414 456 8.585018 AGGTCCAAGTTTATAGAACAAAAATGG 58.415 33.333 0.00 0.00 0.00 3.16
421 463 5.836024 ACCAGGTCCAAGTTTATAGAACA 57.164 39.130 0.00 0.00 0.00 3.18
422 464 5.809051 CGTACCAGGTCCAAGTTTATAGAAC 59.191 44.000 0.00 0.00 0.00 3.01
424 466 4.142093 GCGTACCAGGTCCAAGTTTATAGA 60.142 45.833 0.00 0.00 0.00 1.98
425 467 4.117685 GCGTACCAGGTCCAAGTTTATAG 58.882 47.826 0.00 0.00 0.00 1.31
426 468 3.118665 GGCGTACCAGGTCCAAGTTTATA 60.119 47.826 0.00 0.00 35.26 0.98
427 469 2.355412 GGCGTACCAGGTCCAAGTTTAT 60.355 50.000 0.00 0.00 35.26 1.40
499 544 5.977821 TTACCACCATACCATTACCATGA 57.022 39.130 0.00 0.00 31.07 3.07
501 546 6.562608 AGAGATTACCACCATACCATTACCAT 59.437 38.462 0.00 0.00 0.00 3.55
502 547 5.908831 AGAGATTACCACCATACCATTACCA 59.091 40.000 0.00 0.00 0.00 3.25
503 548 6.042781 TCAGAGATTACCACCATACCATTACC 59.957 42.308 0.00 0.00 0.00 2.85
504 549 7.062749 TCAGAGATTACCACCATACCATTAC 57.937 40.000 0.00 0.00 0.00 1.89
505 550 6.844388 ACTCAGAGATTACCACCATACCATTA 59.156 38.462 3.79 0.00 0.00 1.90
506 551 5.667626 ACTCAGAGATTACCACCATACCATT 59.332 40.000 3.79 0.00 0.00 3.16
567 622 4.285260 ACCACTATAGAACTTCACCGGTTT 59.715 41.667 2.97 0.00 0.00 3.27
568 623 3.836562 ACCACTATAGAACTTCACCGGTT 59.163 43.478 2.97 0.00 0.00 4.44
569 624 3.438183 ACCACTATAGAACTTCACCGGT 58.562 45.455 0.00 0.00 0.00 5.28
570 625 4.467198 AACCACTATAGAACTTCACCGG 57.533 45.455 6.78 0.00 0.00 5.28
571 626 6.164176 AGAAAACCACTATAGAACTTCACCG 58.836 40.000 6.78 0.00 0.00 4.94
572 627 7.159372 TGAGAAAACCACTATAGAACTTCACC 58.841 38.462 6.78 0.48 0.00 4.02
573 628 8.603242 TTGAGAAAACCACTATAGAACTTCAC 57.397 34.615 6.78 2.06 0.00 3.18
574 629 9.273016 CTTTGAGAAAACCACTATAGAACTTCA 57.727 33.333 6.78 0.00 0.00 3.02
602 657 6.486320 TCGGTTCTACGAAAATAACCCTTTTT 59.514 34.615 0.00 0.00 40.34 1.94
607 662 4.207841 CGATCGGTTCTACGAAAATAACCC 59.792 45.833 7.38 0.00 46.92 4.11
608 663 4.207841 CCGATCGGTTCTACGAAAATAACC 59.792 45.833 26.35 0.00 46.92 2.85
611 666 3.181488 TGCCGATCGGTTCTACGAAAATA 60.181 43.478 33.33 0.00 46.92 1.40
612 667 2.199236 GCCGATCGGTTCTACGAAAAT 58.801 47.619 33.33 0.00 46.92 1.82
615 670 0.179156 GTGCCGATCGGTTCTACGAA 60.179 55.000 33.33 8.19 46.92 3.85
617 672 1.588139 GGTGCCGATCGGTTCTACG 60.588 63.158 33.33 8.44 37.65 3.51
618 673 0.248949 GAGGTGCCGATCGGTTCTAC 60.249 60.000 33.33 24.61 37.65 2.59
619 674 0.395311 AGAGGTGCCGATCGGTTCTA 60.395 55.000 33.33 15.93 37.65 2.10
621 676 1.227002 GAGAGGTGCCGATCGGTTC 60.227 63.158 33.33 24.71 37.65 3.62
622 677 1.949847 CTGAGAGGTGCCGATCGGTT 61.950 60.000 33.33 17.64 37.65 4.44
623 678 2.362503 TGAGAGGTGCCGATCGGT 60.363 61.111 33.33 15.53 37.65 4.69
625 680 0.173481 TTTCTGAGAGGTGCCGATCG 59.827 55.000 8.51 8.51 0.00 3.69
626 681 2.386661 TTTTCTGAGAGGTGCCGATC 57.613 50.000 0.00 0.00 0.00 3.69
644 804 2.340337 CCGACCGGTTCTACGATTTTT 58.660 47.619 9.42 0.00 35.47 1.94
647 807 1.140375 GCCGACCGGTTCTACGATT 59.860 57.895 9.42 0.00 37.65 3.34
648 808 2.001361 CTGCCGACCGGTTCTACGAT 62.001 60.000 9.42 0.00 37.65 3.73
690 850 2.801631 CCTCATCGCCAGGGTCTCC 61.802 68.421 0.00 0.00 0.00 3.71
709 869 4.293648 CCGGGTGTGAGCGTGTCA 62.294 66.667 0.00 0.00 0.00 3.58
758 918 1.375013 CGTGGGTTTGACTACGGGG 60.375 63.158 0.00 0.00 33.27 5.73
813 982 4.143333 CGACCCGTTGGAGGCGAT 62.143 66.667 0.00 0.00 34.81 4.58
817 986 4.078516 GACCCGACCCGTTGGAGG 62.079 72.222 2.40 0.00 36.15 4.30
876 1061 1.594310 GTGTCAGAGGTGGGAGAGC 59.406 63.158 0.00 0.00 0.00 4.09
945 1130 1.154093 CGTGTAAGAGGAAGCGCGA 60.154 57.895 12.10 0.00 37.06 5.87
1636 1854 7.013655 AGCAGTTGAGCTTTGAATTAGAAGAAA 59.986 33.333 4.85 0.00 43.70 2.52
1706 1928 8.882736 CCAGTAAAATGCAGGGAAATAAAAATC 58.117 33.333 0.00 0.00 0.00 2.17
1719 1941 3.420893 TCTCCCAACCAGTAAAATGCAG 58.579 45.455 0.00 0.00 0.00 4.41
1733 1955 3.916359 TGTACCGCAAATATCTCCCAA 57.084 42.857 0.00 0.00 0.00 4.12
1894 2116 1.617740 CGCGGAAAGCTCCAAAATTC 58.382 50.000 0.00 0.00 42.58 2.17
1926 2148 2.158971 GGATCAAGCTCTGGTCTTCCTC 60.159 54.545 8.44 0.00 35.28 3.71
1948 2170 1.345415 TGGTGGAGGAAACGGTAACTC 59.655 52.381 0.00 0.00 0.00 3.01
1962 2184 7.432869 CAAAACAGAGTAATTTTCATGGTGGA 58.567 34.615 0.00 0.00 0.00 4.02
2011 2233 6.153680 ACCCAAGTGTTTGATTGAACTAAACA 59.846 34.615 5.14 5.14 40.73 2.83
2030 2252 2.771943 TGGCAGATCCTACTAACCCAAG 59.228 50.000 0.00 0.00 35.26 3.61
2043 2265 5.480642 TCTCCTATCAAGATTGGCAGATC 57.519 43.478 5.78 0.00 34.38 2.75
2072 2294 0.179702 TCATGTGATGCAGAGGCCTC 59.820 55.000 26.22 26.22 40.13 4.70
2347 2574 2.030805 GCAACAGGAAGGTCATGTGAAC 60.031 50.000 0.00 0.00 40.86 3.18
2453 2680 3.259902 GAAGGTTAAGGATCACACGGAC 58.740 50.000 0.00 0.00 0.00 4.79
2455 2682 2.094390 TCGAAGGTTAAGGATCACACGG 60.094 50.000 0.00 0.00 0.00 4.94
2456 2683 3.119602 TCTCGAAGGTTAAGGATCACACG 60.120 47.826 0.00 0.00 0.00 4.49
2468 2701 1.347707 TCTTGTGCCATCTCGAAGGTT 59.652 47.619 0.00 0.00 0.00 3.50
2574 2807 2.124768 TGCTGGAGGGGATCACCA 59.875 61.111 18.46 8.26 42.91 4.17
2651 2884 6.385467 ACTTAAGAATGAGCTGGAGGAGTATT 59.615 38.462 10.09 0.00 0.00 1.89
2791 3028 2.620112 CCACGCAAAGACTGGGCAG 61.620 63.158 0.00 0.00 41.66 4.85
2941 3178 7.047460 TCGAAACTACTTCCAAAACTACTCT 57.953 36.000 0.00 0.00 0.00 3.24
2979 3216 3.438131 TCTATTCTCAATCCACCCCCT 57.562 47.619 0.00 0.00 0.00 4.79
3003 3240 4.972751 ACCCAACTGGCAATATGTTTTT 57.027 36.364 0.00 0.00 37.83 1.94
3115 3355 7.844009 ACGAGGATTTCTGGTTATAACAGTAA 58.156 34.615 17.16 11.91 37.25 2.24
3337 3579 3.383185 GGTTGGTGAATGTTTGGTCAAGA 59.617 43.478 0.00 0.00 0.00 3.02
3351 3593 5.010933 TGTTTTAAGTGTCTTGGTTGGTGA 58.989 37.500 0.00 0.00 0.00 4.02
3386 3628 3.434940 AACTTCCCTCCTTTTATGCGT 57.565 42.857 0.00 0.00 0.00 5.24
3428 3670 2.991250 ACAAAATGGAGCAGCGACTAT 58.009 42.857 0.00 0.00 0.00 2.12
3435 3677 5.001237 TGCATTCATACAAAATGGAGCAG 57.999 39.130 0.00 0.00 35.19 4.24
3436 3678 5.601583 ATGCATTCATACAAAATGGAGCA 57.398 34.783 0.00 0.00 37.77 4.26
3447 3689 7.475015 ACAGTACATGACAAATGCATTCATAC 58.525 34.615 13.38 8.27 31.46 2.39
3543 3785 0.947244 CAACTCCTGACACCTGTTGC 59.053 55.000 0.00 0.00 32.99 4.17
3642 3884 8.612619 AGTGCTTGCAACAATATAGTATAACAC 58.387 33.333 0.00 0.00 0.00 3.32
3646 3888 8.956533 TTCAGTGCTTGCAACAATATAGTATA 57.043 30.769 0.00 0.00 0.00 1.47
3647 3889 7.864108 TTCAGTGCTTGCAACAATATAGTAT 57.136 32.000 0.00 0.00 0.00 2.12
3650 3897 8.470040 AAAATTCAGTGCTTGCAACAATATAG 57.530 30.769 0.00 0.00 0.00 1.31
3691 3938 9.959721 AATCACTACACATACAGACCTATTTTT 57.040 29.630 0.00 0.00 0.00 1.94
3732 3979 6.769822 AGCAATCCTAACCTGAATAGTGAATG 59.230 38.462 0.00 0.00 0.00 2.67
3781 4028 1.063006 ATCGTCAATGCACATGCGC 59.937 52.632 0.00 0.00 45.83 6.09
3841 4088 1.517242 AACTAGCAGAGCAACAGCAC 58.483 50.000 0.00 0.00 33.37 4.40
3842 4089 2.260844 AAACTAGCAGAGCAACAGCA 57.739 45.000 0.00 0.00 33.37 4.41
3843 4090 4.749245 TTTAAACTAGCAGAGCAACAGC 57.251 40.909 0.00 0.00 0.00 4.40
3844 4091 5.915196 GGTTTTTAAACTAGCAGAGCAACAG 59.085 40.000 5.43 0.00 38.89 3.16
3845 4092 5.504994 CGGTTTTTAAACTAGCAGAGCAACA 60.505 40.000 5.43 0.00 38.89 3.33
3846 4093 4.909880 CGGTTTTTAAACTAGCAGAGCAAC 59.090 41.667 5.43 0.00 38.89 4.17
3847 4094 4.555906 GCGGTTTTTAAACTAGCAGAGCAA 60.556 41.667 15.73 0.00 39.94 3.91
3868 4118 7.382218 AGTTCAGGAATGAAAAATAAACTTGCG 59.618 33.333 0.00 0.00 0.00 4.85
3874 4124 9.974980 GGTGTTAGTTCAGGAATGAAAAATAAA 57.025 29.630 0.00 0.00 0.00 1.40
3877 4127 6.553100 TGGGTGTTAGTTCAGGAATGAAAAAT 59.447 34.615 0.00 0.00 0.00 1.82
3878 4128 5.894393 TGGGTGTTAGTTCAGGAATGAAAAA 59.106 36.000 0.00 0.00 0.00 1.94
3883 4133 5.713025 CATTTGGGTGTTAGTTCAGGAATG 58.287 41.667 0.00 0.00 0.00 2.67
3884 4134 4.220602 GCATTTGGGTGTTAGTTCAGGAAT 59.779 41.667 0.00 0.00 0.00 3.01
3886 4136 3.153919 GCATTTGGGTGTTAGTTCAGGA 58.846 45.455 0.00 0.00 0.00 3.86
3887 4137 3.157087 AGCATTTGGGTGTTAGTTCAGG 58.843 45.455 0.00 0.00 0.00 3.86
3889 4139 4.098914 AGAGCATTTGGGTGTTAGTTCA 57.901 40.909 0.00 0.00 0.00 3.18
3890 4140 5.648092 ACATAGAGCATTTGGGTGTTAGTTC 59.352 40.000 0.00 0.00 0.00 3.01
3893 4143 7.624360 TTAACATAGAGCATTTGGGTGTTAG 57.376 36.000 0.00 0.00 33.67 2.34
3909 4160 5.586243 AGCGCCTGCCATTATATTAACATAG 59.414 40.000 2.29 0.00 44.31 2.23
3912 4163 3.750371 AGCGCCTGCCATTATATTAACA 58.250 40.909 2.29 0.00 44.31 2.41
3913 4164 5.163754 CCTTAGCGCCTGCCATTATATTAAC 60.164 44.000 2.29 0.00 44.31 2.01
3914 4165 4.941263 CCTTAGCGCCTGCCATTATATTAA 59.059 41.667 2.29 0.00 44.31 1.40
3916 4167 3.009033 TCCTTAGCGCCTGCCATTATATT 59.991 43.478 2.29 0.00 44.31 1.28
3917 4168 2.571653 TCCTTAGCGCCTGCCATTATAT 59.428 45.455 2.29 0.00 44.31 0.86
3918 4169 1.974957 TCCTTAGCGCCTGCCATTATA 59.025 47.619 2.29 0.00 44.31 0.98
3919 4170 0.764890 TCCTTAGCGCCTGCCATTAT 59.235 50.000 2.29 0.00 44.31 1.28
3920 4171 0.544223 TTCCTTAGCGCCTGCCATTA 59.456 50.000 2.29 0.00 44.31 1.90
3921 4172 0.749454 CTTCCTTAGCGCCTGCCATT 60.749 55.000 2.29 0.00 44.31 3.16
3922 4173 1.153086 CTTCCTTAGCGCCTGCCAT 60.153 57.895 2.29 0.00 44.31 4.40
3979 4230 7.145323 CCAAATCAGAAACGTATTGGAAACTT 58.855 34.615 0.00 0.00 39.69 2.66
4037 4288 8.696043 TTCCAGATAGCATTGCTACAATTTAT 57.304 30.769 20.17 4.05 44.24 1.40
4038 4289 8.570488 CATTCCAGATAGCATTGCTACAATTTA 58.430 33.333 20.17 6.22 44.24 1.40
4039 4290 7.431249 CATTCCAGATAGCATTGCTACAATTT 58.569 34.615 20.17 4.49 44.24 1.82
4040 4291 6.516194 GCATTCCAGATAGCATTGCTACAATT 60.516 38.462 20.17 4.88 44.24 2.32
4041 4292 5.048224 GCATTCCAGATAGCATTGCTACAAT 60.048 40.000 20.17 6.31 44.24 2.71
4042 4293 4.276678 GCATTCCAGATAGCATTGCTACAA 59.723 41.667 20.17 8.87 44.24 2.41
4043 4294 3.817084 GCATTCCAGATAGCATTGCTACA 59.183 43.478 20.17 1.72 44.24 2.74
4044 4295 3.120408 CGCATTCCAGATAGCATTGCTAC 60.120 47.826 20.17 13.68 44.24 3.58
4045 4296 3.069289 CGCATTCCAGATAGCATTGCTA 58.931 45.455 20.06 20.06 45.55 3.49
4046 4297 1.878088 CGCATTCCAGATAGCATTGCT 59.122 47.619 16.63 16.63 43.41 3.91
4267 4518 0.255890 GCTCCTTGGCCTTGGTGATA 59.744 55.000 16.89 0.00 0.00 2.15
4366 4617 2.967615 GCGGCGCTATCTTGGTCC 60.968 66.667 26.86 0.00 0.00 4.46
4473 4724 1.198713 CATAGCTCTGTCAGTGGGGT 58.801 55.000 0.00 0.71 0.00 4.95
4506 4758 7.606456 CCAAGGTATTTAGCAGTAAAACTCTCA 59.394 37.037 0.00 0.00 31.81 3.27
4577 4833 1.669265 TGTGTCCGTATAGCTGAGACG 59.331 52.381 0.00 2.95 42.49 4.18
4709 4970 0.392729 CTTCCTGAAGCAGCTGGGAG 60.393 60.000 17.12 0.00 0.00 4.30
4759 5020 7.224297 ACTGAATAAAGTTTTGCTCCACTCTA 58.776 34.615 0.00 0.00 0.00 2.43
4934 5197 4.043200 GCCTGTTTCCGGCAGCAC 62.043 66.667 0.00 0.00 46.77 4.40
5003 5266 2.034879 ATCACCGCAAGCCTGAACG 61.035 57.895 0.00 0.00 0.00 3.95
5034 5297 2.507102 ACATCGTCGCTTGGCTCG 60.507 61.111 0.00 0.00 0.00 5.03
5227 5490 2.574399 GACAGCCTGTCCGAGGTC 59.426 66.667 14.04 0.00 44.97 3.85
5329 5592 2.173382 CCCGTCAAGCGCGAAAAG 59.827 61.111 12.10 0.00 39.71 2.27
5368 5631 4.373771 GTCCCAACCAAGGACGTC 57.626 61.111 7.13 7.13 44.16 4.34
5380 5643 2.591915 GACCTGGAAGATCGTCCCA 58.408 57.895 22.87 13.11 36.80 4.37


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

AutoCloner maintained by Alex Coulton.