Multiple sequence alignment - TraesCS7A01G256200

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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 TraesCS7A01G256200 chr7A 100.000 3919 0 0 1 3919 244606045 244602127 0.000000e+00 7238.0
1 TraesCS7A01G256200 chr7B 86.681 3679 225 107 3 3543 203030783 203027232 0.000000e+00 3834.0
2 TraesCS7A01G256200 chr7B 91.163 215 10 6 3618 3832 203026741 203026536 2.310000e-72 283.0
3 TraesCS7A01G256200 chr7B 87.838 74 6 2 3543 3613 203027208 203027135 2.510000e-12 84.2
4 TraesCS7A01G256200 chr7D 90.377 1964 108 31 8 1936 232410481 232408564 0.000000e+00 2505.0
5 TraesCS7A01G256200 chr7D 90.661 1724 73 34 1946 3613 232408513 232406822 0.000000e+00 2211.0
6 TraesCS7A01G256200 chr7D 89.700 233 13 8 3618 3849 232406408 232406186 1.780000e-73 287.0


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 TraesCS7A01G256200 chr7A 244602127 244606045 3918 True 7238.000000 7238 100.000000 1 3919 1 chr7A.!!$R1 3918
1 TraesCS7A01G256200 chr7B 203026536 203030783 4247 True 1400.400000 3834 88.560667 3 3832 3 chr7B.!!$R1 3829
2 TraesCS7A01G256200 chr7D 232406186 232410481 4295 True 1667.666667 2505 90.246000 8 3849 3 chr7D.!!$R1 3841

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
169 170 0.170339 CAGCGTAGTCACCATCGTCA 59.830 55.0 0.0 0.0 0.00 4.35 F
1696 1751 0.108756 GAGCGGGTACAGTCCTGAAC 60.109 60.0 0.4 0.0 36.02 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1753 0.250381 GGAGAGGCAGCATGATCAGG 60.25 60.0 2.22 2.22 39.69 3.86 R
3153 3331 0.319900 ATCTGCACCGTGTCTCACAC 60.32 55.0 0.00 0.00 45.26 3.82 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
58 59 2.112297 TCCACCAAGGGAACACGC 59.888 61.111 0.00 0.00 38.24 5.34
88 89 4.810730 GCAGCAAGCAACAACACA 57.189 50.000 0.00 0.00 44.79 3.72
90 91 0.646895 GCAGCAAGCAACAACACAAC 59.353 50.000 0.00 0.00 44.79 3.32
94 95 1.202132 GCAAGCAACAACACAACGAGA 60.202 47.619 0.00 0.00 0.00 4.04
95 96 2.730715 GCAAGCAACAACACAACGAGAA 60.731 45.455 0.00 0.00 0.00 2.87
96 97 3.497118 CAAGCAACAACACAACGAGAAA 58.503 40.909 0.00 0.00 0.00 2.52
99 100 2.159435 GCAACAACACAACGAGAAAGGT 60.159 45.455 0.00 0.00 0.00 3.50
100 101 3.680789 CAACAACACAACGAGAAAGGTC 58.319 45.455 0.00 0.00 0.00 3.85
142 143 1.043116 TCGGCATCGGATGAGGACTT 61.043 55.000 21.69 0.00 29.58 3.01
169 170 0.170339 CAGCGTAGTCACCATCGTCA 59.830 55.000 0.00 0.00 0.00 4.35
176 177 2.261361 CACCATCGTCACCGCTCA 59.739 61.111 0.00 0.00 0.00 4.26
179 180 2.880879 CATCGTCACCGCTCACCG 60.881 66.667 0.00 0.00 0.00 4.94
214 215 5.804692 ACAACTGTTTGACGAAATGTACA 57.195 34.783 0.00 0.00 36.48 2.90
215 216 5.565695 ACAACTGTTTGACGAAATGTACAC 58.434 37.500 0.00 0.00 36.48 2.90
216 217 5.122554 ACAACTGTTTGACGAAATGTACACA 59.877 36.000 0.00 0.00 36.48 3.72
217 218 6.183360 ACAACTGTTTGACGAAATGTACACAT 60.183 34.615 0.00 0.00 35.88 3.21
226 227 5.527951 ACGAAATGTACACATGCAAATGTT 58.472 33.333 11.08 0.00 36.56 2.71
241 242 5.457148 TGCAAATGTTAGTTTTACTGCGTTG 59.543 36.000 0.00 0.00 0.00 4.10
254 256 3.596214 ACTGCGTTGAGTTTAGGGTATG 58.404 45.455 0.00 0.00 0.00 2.39
269 271 5.175388 AGGGTATGGGTTAGAAAAGACAC 57.825 43.478 0.00 0.00 0.00 3.67
305 307 9.771534 GAGCAAATGTACTCCTCTAAAGAATAT 57.228 33.333 0.00 0.00 0.00 1.28
447 449 2.890945 GGCACTGGTTGTTCCTTGTAAT 59.109 45.455 0.00 0.00 37.07 1.89
496 498 6.314896 GTGGACACAAAATTTGAAATTCCACA 59.685 34.615 27.27 7.66 41.97 4.17
507 509 4.222336 TGAAATTCCACATGTTTCCCACT 58.778 39.130 0.00 0.00 32.33 4.00
508 510 5.389520 TGAAATTCCACATGTTTCCCACTA 58.610 37.500 0.00 0.00 32.33 2.74
530 532 2.877043 AATCCAGCGAAAATCCATGC 57.123 45.000 0.00 0.00 0.00 4.06
591 594 2.749044 CCCTCCGTCGACCGAGAA 60.749 66.667 28.33 3.20 39.56 2.87
592 595 2.484203 CCTCCGTCGACCGAGAAC 59.516 66.667 28.33 0.00 39.56 3.01
664 667 2.588034 GGTCATTACGGAGCCGGC 60.588 66.667 21.89 21.89 44.69 6.13
665 668 2.960129 GTCATTACGGAGCCGGCG 60.960 66.667 23.20 9.91 44.69 6.46
666 669 4.215742 TCATTACGGAGCCGGCGG 62.216 66.667 24.35 24.35 44.69 6.13
667 670 4.215742 CATTACGGAGCCGGCGGA 62.216 66.667 33.44 6.97 44.69 5.54
804 807 2.843545 GCCACTTTGACCCTCCCA 59.156 61.111 0.00 0.00 0.00 4.37
805 808 1.152830 GCCACTTTGACCCTCCCAA 59.847 57.895 0.00 0.00 0.00 4.12
806 809 0.251787 GCCACTTTGACCCTCCCAAT 60.252 55.000 0.00 0.00 0.00 3.16
807 810 1.827245 GCCACTTTGACCCTCCCAATT 60.827 52.381 0.00 0.00 0.00 2.32
808 811 1.895131 CCACTTTGACCCTCCCAATTG 59.105 52.381 0.00 0.00 0.00 2.32
852 866 4.803908 CCTTCGCCCCCAAGCCTC 62.804 72.222 0.00 0.00 0.00 4.70
853 867 4.803908 CTTCGCCCCCAAGCCTCC 62.804 72.222 0.00 0.00 0.00 4.30
880 894 1.589399 CCTCCTCCTCCTCCACCTCT 61.589 65.000 0.00 0.00 0.00 3.69
908 922 0.318784 CTCCTATAAGTGCCGCGTCC 60.319 60.000 4.92 0.00 0.00 4.79
926 940 1.395826 CCCCGGCTTCTCTCGATTCT 61.396 60.000 0.00 0.00 0.00 2.40
1182 1203 3.257933 CTGTCCAGCTTCAACGGC 58.742 61.111 0.00 0.00 0.00 5.68
1192 1213 2.175184 CTTCAACGGCCAGCACTTCG 62.175 60.000 2.24 0.00 0.00 3.79
1260 1299 4.131088 GAGGCGTCCTCCGTGTCC 62.131 72.222 13.12 0.00 44.36 4.02
1451 1503 2.118683 CGTCAATTGTGTTGTGCCTTG 58.881 47.619 5.13 0.00 0.00 3.61
1580 1632 4.847444 GGCGAGCAGAGGAAGGGC 62.847 72.222 0.00 0.00 0.00 5.19
1582 1634 4.521062 CGAGCAGAGGAAGGGCGG 62.521 72.222 0.00 0.00 0.00 6.13
1673 1728 1.670406 CACTGACAGCCACAGCCTC 60.670 63.158 1.25 0.00 41.25 4.70
1696 1751 0.108756 GAGCGGGTACAGTCCTGAAC 60.109 60.000 0.40 0.00 36.02 3.18
1697 1752 0.542232 AGCGGGTACAGTCCTGAACT 60.542 55.000 0.40 0.00 39.44 3.01
1698 1753 0.108756 GCGGGTACAGTCCTGAACTC 60.109 60.000 0.40 0.00 35.45 3.01
1699 1754 0.531200 CGGGTACAGTCCTGAACTCC 59.469 60.000 0.40 0.00 35.45 3.85
1712 1767 1.307097 GAACTCCTGATCATGCTGCC 58.693 55.000 0.00 0.00 0.00 4.85
1715 1770 0.759959 CTCCTGATCATGCTGCCTCT 59.240 55.000 0.00 0.00 0.00 3.69
1716 1771 0.757512 TCCTGATCATGCTGCCTCTC 59.242 55.000 0.00 0.00 0.00 3.20
1717 1772 0.250381 CCTGATCATGCTGCCTCTCC 60.250 60.000 0.00 0.00 0.00 3.71
1718 1773 0.759959 CTGATCATGCTGCCTCTCCT 59.240 55.000 0.00 0.00 0.00 3.69
1735 1790 3.639094 TCTCCTTCCTTCTAGTAGCATGC 59.361 47.826 10.51 10.51 0.00 4.06
1755 1810 1.403679 CTGTTGCTTCGGTTTGTCCAA 59.596 47.619 0.00 0.00 35.57 3.53
1760 1815 1.814248 GCTTCGGTTTGTCCAACTCCT 60.814 52.381 0.00 0.00 35.46 3.69
1763 1818 0.949105 CGGTTTGTCCAACTCCTCCG 60.949 60.000 0.00 0.00 35.46 4.63
1784 1839 0.958876 AACGGAATTCCCTTGGACGC 60.959 55.000 19.01 0.00 0.00 5.19
1803 1858 2.968737 TCACAGGTGAGGAGAGAGC 58.031 57.895 0.00 0.00 34.14 4.09
1826 1881 1.382522 TCAGCCAGCGGATGAAATTC 58.617 50.000 12.09 0.00 45.57 2.17
1900 1976 9.730705 AGTTCACAATGATAAATCAGAAAGAGA 57.269 29.630 0.00 0.00 40.64 3.10
1930 2006 7.634671 AACAAGCACATGATAATCTTGATGA 57.365 32.000 0.00 0.00 37.96 2.92
1937 2013 8.965172 GCACATGATAATCTTGATGAACATTTC 58.035 33.333 0.00 0.00 0.00 2.17
1978 2096 6.827727 AGACAGTCTTTGTGTACAAGGTTAT 58.172 36.000 0.00 0.00 41.05 1.89
2003 2121 5.687770 ATTAAACTGGCCAAATTTTGTGC 57.312 34.783 17.43 10.27 0.00 4.57
2102 2220 1.597461 GTAAGAAGAGCGTGGGCCT 59.403 57.895 4.53 0.00 41.24 5.19
2154 2298 3.261897 TGATCAACTCCTCCTCTGTTTCC 59.738 47.826 0.00 0.00 0.00 3.13
2185 2329 1.591059 CCTCTCCATGAAGCTCGCG 60.591 63.158 0.00 0.00 0.00 5.87
2261 2405 0.895559 CTCAAAACCCACCCCTGCTC 60.896 60.000 0.00 0.00 0.00 4.26
2316 2460 3.325716 TGGTTACTTACTCACCTTGTCCC 59.674 47.826 0.00 0.00 0.00 4.46
2581 2725 0.881118 TGCCTTCAGAATTTCGTGGC 59.119 50.000 13.86 13.86 39.33 5.01
2583 2727 1.131315 GCCTTCAGAATTTCGTGGCTC 59.869 52.381 13.62 0.00 36.32 4.70
2639 2786 9.047947 AGACCTTATCCTGATACAGTTTAGTTT 57.952 33.333 0.00 0.00 0.00 2.66
2640 2787 9.668497 GACCTTATCCTGATACAGTTTAGTTTT 57.332 33.333 0.00 0.00 0.00 2.43
2641 2788 9.449719 ACCTTATCCTGATACAGTTTAGTTTTG 57.550 33.333 0.00 0.00 0.00 2.44
2642 2789 9.449719 CCTTATCCTGATACAGTTTAGTTTTGT 57.550 33.333 0.00 0.00 0.00 2.83
2644 2791 9.787435 TTATCCTGATACAGTTTAGTTTTGTGT 57.213 29.630 0.00 0.00 0.00 3.72
2652 2799 4.495472 CAGTTTAGTTTTGTGTTGCGTCTG 59.505 41.667 0.00 0.00 0.00 3.51
2677 2824 2.682269 GCAGAGGAATTTCTGGGAGGAC 60.682 54.545 8.80 0.00 43.80 3.85
2705 2852 2.290367 CAGAGCGTTTTTCATGTGGACA 59.710 45.455 0.00 0.00 0.00 4.02
2706 2853 2.290641 AGAGCGTTTTTCATGTGGACAC 59.709 45.455 0.00 0.00 0.00 3.67
2707 2854 1.336755 AGCGTTTTTCATGTGGACACC 59.663 47.619 0.00 0.00 0.00 4.16
2737 2884 1.740285 CCAGGATAACGGGGTCTCG 59.260 63.158 0.00 0.00 0.00 4.04
2776 2923 2.629639 AGTTAAAAGCCCGCGATTTG 57.370 45.000 8.23 0.00 0.00 2.32
2808 2955 0.660595 GTCGCTACCGTCGATGATGG 60.661 60.000 6.11 3.52 43.80 3.51
2826 2973 1.352156 GGCATCGTCACTGAACGGAC 61.352 60.000 7.31 0.00 42.80 4.79
2881 3039 2.925162 AATGGAGTTCTAGCCGGCGC 62.925 60.000 23.20 10.25 0.00 6.53
2941 3110 2.611518 AGAATCAAGAAGACGGAAGCG 58.388 47.619 0.00 0.00 0.00 4.68
2959 3128 0.384309 CGGTGGCGAGTGAAGCTATA 59.616 55.000 0.00 0.00 34.52 1.31
3009 3178 8.156165 TCTCTGTAATTAGGCTCTACTACTACC 58.844 40.741 0.00 0.00 0.00 3.18
3089 3267 2.154854 TATCGCTGGCACTGATTAGC 57.845 50.000 2.41 0.00 0.00 3.09
3093 3271 2.037641 TCGCTGGCACTGATTAGCATAT 59.962 45.455 0.00 0.00 35.98 1.78
3094 3272 2.414481 CGCTGGCACTGATTAGCATATC 59.586 50.000 0.00 0.00 35.98 1.63
3096 3274 3.683822 GCTGGCACTGATTAGCATATCTC 59.316 47.826 0.00 0.00 36.24 2.75
3097 3275 4.801914 GCTGGCACTGATTAGCATATCTCA 60.802 45.833 0.00 0.00 36.24 3.27
3098 3276 5.489249 CTGGCACTGATTAGCATATCTCAT 58.511 41.667 0.00 0.00 0.00 2.90
3099 3277 5.485620 TGGCACTGATTAGCATATCTCATC 58.514 41.667 0.00 0.00 0.00 2.92
3100 3278 4.565962 GGCACTGATTAGCATATCTCATCG 59.434 45.833 0.00 0.00 29.90 3.84
3101 3279 5.405797 GCACTGATTAGCATATCTCATCGA 58.594 41.667 0.00 0.00 29.90 3.59
3102 3280 6.041511 GCACTGATTAGCATATCTCATCGAT 58.958 40.000 0.00 0.00 36.11 3.59
3103 3281 7.199078 GCACTGATTAGCATATCTCATCGATA 58.801 38.462 0.00 0.00 38.88 2.92
3105 3283 9.747293 CACTGATTAGCATATCTCATCGATATT 57.253 33.333 0.00 0.00 41.47 1.28
3153 3331 3.182372 CGATCAGTTACAGTGTGTGTGTG 59.818 47.826 5.88 0.00 40.69 3.82
3175 3354 2.159240 TGTGAGACACGGTGCAGATATC 60.159 50.000 8.30 0.00 37.14 1.63
3213 3392 1.941668 GCCGATCCTAATACTGCTGCC 60.942 57.143 0.00 0.00 0.00 4.85
3226 3405 2.501316 ACTGCTGCCCTTCAAAGTTTTT 59.499 40.909 0.00 0.00 0.00 1.94
3228 3407 4.344968 ACTGCTGCCCTTCAAAGTTTTTAT 59.655 37.500 0.00 0.00 0.00 1.40
3244 3423 7.251704 AGTTTTTATTATCTGTGGCGATGAG 57.748 36.000 0.00 0.00 0.00 2.90
3304 3498 1.227002 CTCTCCGCCTTAAGCCGTC 60.227 63.158 5.03 0.00 38.78 4.79
3442 3637 2.105766 TCGCTTTTAGTCCCCTCTACC 58.894 52.381 0.00 0.00 0.00 3.18
3540 3735 5.584253 TCTTCAGCTCTGTATACTTCACC 57.416 43.478 4.17 0.00 0.00 4.02
3573 3792 2.806745 CGTGCCCAGTTTCTTCAGAGAA 60.807 50.000 0.00 0.00 40.07 2.87
3609 3834 0.454285 CATGCGGGCGTTACAGTTTG 60.454 55.000 0.00 0.00 0.00 2.93
3613 3838 1.153353 CGGGCGTTACAGTTTGACAT 58.847 50.000 0.00 0.00 0.00 3.06
3615 3840 1.401018 GGGCGTTACAGTTTGACATGC 60.401 52.381 0.00 0.00 0.00 4.06
3716 4357 1.893062 GTGCCTGCCCATTTCTTCC 59.107 57.895 0.00 0.00 0.00 3.46
3832 4474 2.069273 CCGTGCTCTGTTTCTAGGTTG 58.931 52.381 0.00 0.00 0.00 3.77
3840 4482 3.807622 TCTGTTTCTAGGTTGCGTCTTTG 59.192 43.478 0.00 0.00 0.00 2.77
3841 4483 2.289547 TGTTTCTAGGTTGCGTCTTTGC 59.710 45.455 0.00 0.00 0.00 3.68
3842 4484 2.543777 TTCTAGGTTGCGTCTTTGCT 57.456 45.000 0.00 0.00 35.36 3.91
3846 4488 0.179018 AGGTTGCGTCTTTGCTCCTT 60.179 50.000 0.00 0.00 36.86 3.36
3847 4489 0.238553 GGTTGCGTCTTTGCTCCTTC 59.761 55.000 0.00 0.00 35.36 3.46
3848 4490 1.230324 GTTGCGTCTTTGCTCCTTCT 58.770 50.000 0.00 0.00 35.36 2.85
3849 4491 1.069636 GTTGCGTCTTTGCTCCTTCTG 60.070 52.381 0.00 0.00 35.36 3.02
3850 4492 0.603707 TGCGTCTTTGCTCCTTCTGG 60.604 55.000 0.00 0.00 35.36 3.86
3851 4493 0.603975 GCGTCTTTGCTCCTTCTGGT 60.604 55.000 0.00 0.00 34.23 4.00
3852 4494 1.151668 CGTCTTTGCTCCTTCTGGTG 58.848 55.000 0.00 0.00 34.23 4.17
3853 4495 1.270305 CGTCTTTGCTCCTTCTGGTGA 60.270 52.381 0.00 0.00 34.23 4.02
3854 4496 2.613977 CGTCTTTGCTCCTTCTGGTGAT 60.614 50.000 0.00 0.00 34.23 3.06
3855 4497 3.006247 GTCTTTGCTCCTTCTGGTGATC 58.994 50.000 0.00 0.00 34.23 2.92
3856 4498 2.909006 TCTTTGCTCCTTCTGGTGATCT 59.091 45.455 0.00 0.00 34.23 2.75
3857 4499 4.081420 GTCTTTGCTCCTTCTGGTGATCTA 60.081 45.833 0.00 0.00 34.23 1.98
3858 4500 4.532126 TCTTTGCTCCTTCTGGTGATCTAA 59.468 41.667 0.00 0.00 34.23 2.10
3859 4501 3.895232 TGCTCCTTCTGGTGATCTAAC 57.105 47.619 0.00 0.00 34.23 2.34
3860 4502 3.173151 TGCTCCTTCTGGTGATCTAACA 58.827 45.455 0.00 0.00 34.23 2.41
3861 4503 3.196469 TGCTCCTTCTGGTGATCTAACAG 59.804 47.826 4.40 4.40 34.23 3.16
3862 4504 3.791245 CTCCTTCTGGTGATCTAACAGC 58.209 50.000 5.59 0.00 38.53 4.40
3863 4505 3.173151 TCCTTCTGGTGATCTAACAGCA 58.827 45.455 5.59 0.00 44.20 4.41
3867 4509 2.099141 TGGTGATCTAACAGCAGCAC 57.901 50.000 0.00 0.00 42.11 4.40
3868 4510 1.625315 TGGTGATCTAACAGCAGCACT 59.375 47.619 0.00 0.00 42.11 4.40
3882 4524 3.273919 CAGCACTGCTTTTAACCACTC 57.726 47.619 0.00 0.00 36.40 3.51
3883 4525 1.873591 AGCACTGCTTTTAACCACTCG 59.126 47.619 0.00 0.00 33.89 4.18
3884 4526 1.602377 GCACTGCTTTTAACCACTCGT 59.398 47.619 0.00 0.00 0.00 4.18
3885 4527 2.803956 GCACTGCTTTTAACCACTCGTA 59.196 45.455 0.00 0.00 0.00 3.43
3886 4528 3.120649 GCACTGCTTTTAACCACTCGTAG 60.121 47.826 0.00 0.00 0.00 3.51
3887 4529 4.304110 CACTGCTTTTAACCACTCGTAGA 58.696 43.478 0.00 0.00 0.00 2.59
3888 4530 4.929808 CACTGCTTTTAACCACTCGTAGAT 59.070 41.667 0.00 0.00 33.89 1.98
3889 4531 5.408604 CACTGCTTTTAACCACTCGTAGATT 59.591 40.000 0.00 0.00 33.89 2.40
3890 4532 6.588756 CACTGCTTTTAACCACTCGTAGATTA 59.411 38.462 0.00 0.00 33.89 1.75
3891 4533 6.812160 ACTGCTTTTAACCACTCGTAGATTAG 59.188 38.462 0.00 0.00 33.89 1.73
3892 4534 6.694447 TGCTTTTAACCACTCGTAGATTAGT 58.306 36.000 0.00 0.00 33.89 2.24
3893 4535 6.588756 TGCTTTTAACCACTCGTAGATTAGTG 59.411 38.462 0.00 0.00 42.25 2.74
3894 4536 6.455246 GCTTTTAACCACTCGTAGATTAGTGC 60.455 42.308 0.00 0.00 41.45 4.40
3895 4537 5.909621 TTAACCACTCGTAGATTAGTGCT 57.090 39.130 0.00 0.00 41.45 4.40
3896 4538 7.395190 TTTAACCACTCGTAGATTAGTGCTA 57.605 36.000 0.00 0.00 41.45 3.49
3897 4539 5.909621 AACCACTCGTAGATTAGTGCTAA 57.090 39.130 0.00 0.00 41.45 3.09
3898 4540 5.909621 ACCACTCGTAGATTAGTGCTAAA 57.090 39.130 0.00 0.00 41.45 1.85
3899 4541 6.276832 ACCACTCGTAGATTAGTGCTAAAA 57.723 37.500 0.00 0.00 41.45 1.52
3900 4542 6.694447 ACCACTCGTAGATTAGTGCTAAAAA 58.306 36.000 0.00 0.00 41.45 1.94
3901 4543 6.589139 ACCACTCGTAGATTAGTGCTAAAAAC 59.411 38.462 0.00 0.00 41.45 2.43
3902 4544 6.237490 CCACTCGTAGATTAGTGCTAAAAACG 60.237 42.308 13.19 13.19 41.45 3.60
3903 4545 5.287992 ACTCGTAGATTAGTGCTAAAAACGC 59.712 40.000 13.95 0.00 33.89 4.84
3904 4546 5.162794 TCGTAGATTAGTGCTAAAAACGCA 58.837 37.500 13.95 0.00 33.02 5.24
3905 4547 5.808540 TCGTAGATTAGTGCTAAAAACGCAT 59.191 36.000 13.95 0.00 39.89 4.73
3906 4548 6.311935 TCGTAGATTAGTGCTAAAAACGCATT 59.688 34.615 13.95 0.00 39.89 3.56
3907 4549 6.959311 CGTAGATTAGTGCTAAAAACGCATTT 59.041 34.615 9.45 0.00 39.89 2.32
3908 4550 8.111836 CGTAGATTAGTGCTAAAAACGCATTTA 58.888 33.333 9.45 0.00 39.89 1.40
3909 4551 9.207042 GTAGATTAGTGCTAAAAACGCATTTAC 57.793 33.333 0.00 0.00 39.89 2.01
3910 4552 7.812648 AGATTAGTGCTAAAAACGCATTTACA 58.187 30.769 0.00 0.00 39.89 2.41
3911 4553 8.458843 AGATTAGTGCTAAAAACGCATTTACAT 58.541 29.630 0.00 0.00 39.89 2.29
3912 4554 8.980143 ATTAGTGCTAAAAACGCATTTACATT 57.020 26.923 0.00 0.00 39.89 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 1.213094 CGCACGTGACCTTTCTCGTT 61.213 55.000 22.23 0.00 46.96 3.85
90 91 0.732880 ATCGCACGTGACCTTTCTCG 60.733 55.000 22.23 10.73 43.01 4.04
94 95 1.999735 CACATATCGCACGTGACCTTT 59.000 47.619 22.23 0.77 32.23 3.11
95 96 1.640428 CACATATCGCACGTGACCTT 58.360 50.000 22.23 2.71 32.23 3.50
96 97 0.806102 GCACATATCGCACGTGACCT 60.806 55.000 22.23 4.48 32.23 3.85
99 100 0.248866 ATCGCACATATCGCACGTGA 60.249 50.000 22.23 0.00 32.23 4.35
100 101 0.111574 CATCGCACATATCGCACGTG 60.112 55.000 12.28 12.28 0.00 4.49
129 130 1.819288 GAGTCACAAGTCCTCATCCGA 59.181 52.381 0.00 0.00 0.00 4.55
142 143 3.030415 TGACTACGCTGGAGTCACA 57.970 52.632 16.44 0.32 46.49 3.58
176 177 1.937899 GTTGTTATATGCCTTCGCGGT 59.062 47.619 6.13 0.00 38.08 5.68
179 180 4.616181 AACAGTTGTTATATGCCTTCGC 57.384 40.909 0.00 0.00 36.32 4.70
188 189 9.043079 TGTACATTTCGTCAAACAGTTGTTATA 57.957 29.630 0.00 0.00 37.25 0.98
213 214 6.398830 CGCAGTAAAACTAACATTTGCATGTG 60.399 38.462 0.00 0.00 43.34 3.21
214 215 5.629020 CGCAGTAAAACTAACATTTGCATGT 59.371 36.000 0.00 0.00 46.34 3.21
215 216 5.629020 ACGCAGTAAAACTAACATTTGCATG 59.371 36.000 0.00 0.00 41.94 4.06
216 217 5.768317 ACGCAGTAAAACTAACATTTGCAT 58.232 33.333 0.00 0.00 41.94 3.96
217 218 5.176407 ACGCAGTAAAACTAACATTTGCA 57.824 34.783 0.00 0.00 41.94 4.08
226 227 5.697633 CCCTAAACTCAACGCAGTAAAACTA 59.302 40.000 0.00 0.00 45.00 2.24
241 242 7.551974 GTCTTTTCTAACCCATACCCTAAACTC 59.448 40.741 0.00 0.00 0.00 3.01
305 307 2.381911 AGAGGAGTATAAACCGCCGAA 58.618 47.619 0.00 0.00 0.00 4.30
406 408 7.750458 CAGTGCCAAGTAGTATTACATTTTGTG 59.250 37.037 0.00 0.00 31.96 3.33
414 416 5.243207 ACAACCAGTGCCAAGTAGTATTAC 58.757 41.667 0.00 0.00 0.00 1.89
420 422 1.880027 GGAACAACCAGTGCCAAGTAG 59.120 52.381 0.00 0.00 46.38 2.57
421 423 1.975660 GGAACAACCAGTGCCAAGTA 58.024 50.000 0.00 0.00 46.38 2.24
422 424 2.807247 GGAACAACCAGTGCCAAGT 58.193 52.632 0.00 0.00 46.38 3.16
447 449 3.261580 CCGTCATGTGATGCAGAGTAAA 58.738 45.455 0.00 0.00 0.00 2.01
496 498 4.273318 GCTGGATTTCTAGTGGGAAACAT 58.727 43.478 0.00 0.00 37.91 2.71
507 509 4.036734 GCATGGATTTTCGCTGGATTTCTA 59.963 41.667 0.00 0.00 0.00 2.10
508 510 3.181483 GCATGGATTTTCGCTGGATTTCT 60.181 43.478 0.00 0.00 0.00 2.52
587 590 1.063469 CTCGCTCTCCTTCTCGTTCTC 59.937 57.143 0.00 0.00 0.00 2.87
588 591 1.091537 CTCGCTCTCCTTCTCGTTCT 58.908 55.000 0.00 0.00 0.00 3.01
589 592 1.088306 TCTCGCTCTCCTTCTCGTTC 58.912 55.000 0.00 0.00 0.00 3.95
590 593 0.806241 GTCTCGCTCTCCTTCTCGTT 59.194 55.000 0.00 0.00 0.00 3.85
591 594 1.027792 GGTCTCGCTCTCCTTCTCGT 61.028 60.000 0.00 0.00 0.00 4.18
592 595 1.725066 GGTCTCGCTCTCCTTCTCG 59.275 63.158 0.00 0.00 0.00 4.04
664 667 1.672854 TAAGCTCATCACCCCGTCCG 61.673 60.000 0.00 0.00 0.00 4.79
665 668 0.539986 TTAAGCTCATCACCCCGTCC 59.460 55.000 0.00 0.00 0.00 4.79
666 669 2.396590 TTTAAGCTCATCACCCCGTC 57.603 50.000 0.00 0.00 0.00 4.79
667 670 2.871096 TTTTAAGCTCATCACCCCGT 57.129 45.000 0.00 0.00 0.00 5.28
804 807 1.075748 GGATGCTGGAGGGGCAATT 60.076 57.895 0.00 0.00 43.14 2.32
805 808 1.661990 ATGGATGCTGGAGGGGCAAT 61.662 55.000 0.00 0.00 43.14 3.56
806 809 1.877672 AATGGATGCTGGAGGGGCAA 61.878 55.000 0.00 0.00 43.14 4.52
807 810 2.288642 GAATGGATGCTGGAGGGGCA 62.289 60.000 0.00 0.00 44.05 5.36
808 811 1.530183 GAATGGATGCTGGAGGGGC 60.530 63.158 0.00 0.00 0.00 5.80
851 865 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
852 866 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
853 867 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
854 868 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
855 869 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
856 870 1.292941 TGGAGGAGGAGGAGGAGGAG 61.293 65.000 0.00 0.00 0.00 3.69
880 894 3.494398 GGCACTTATAGGAGAATGGCGAA 60.494 47.826 0.00 0.00 0.00 4.70
926 940 1.442520 CGTCGTTCCTTTACGCGGA 60.443 57.895 12.47 0.00 41.16 5.54
957 971 4.741781 CAAGAACCGCCGCGCAAG 62.742 66.667 8.75 0.00 43.44 4.01
1122 1143 3.423154 GGGTCGCCGCAGAACTTG 61.423 66.667 0.00 0.00 0.00 3.16
1251 1290 4.436998 GCAGGGTCGGACACGGAG 62.437 72.222 14.83 5.52 41.39 4.63
1451 1503 3.672295 CTTCTGCTCCCCGACCTGC 62.672 68.421 0.00 0.00 0.00 4.85
1580 1632 2.418083 GGCATTCTTCCCCTTGCCG 61.418 63.158 0.00 0.00 44.58 5.69
1581 1633 3.621225 GGCATTCTTCCCCTTGCC 58.379 61.111 0.00 0.00 46.94 4.52
1582 1634 0.533951 CTTGGCATTCTTCCCCTTGC 59.466 55.000 0.00 0.00 0.00 4.01
1696 1751 0.759959 AGAGGCAGCATGATCAGGAG 59.240 55.000 12.39 3.66 39.69 3.69
1697 1752 0.757512 GAGAGGCAGCATGATCAGGA 59.242 55.000 12.39 0.00 39.69 3.86
1698 1753 0.250381 GGAGAGGCAGCATGATCAGG 60.250 60.000 2.22 2.22 39.69 3.86
1699 1754 0.759959 AGGAGAGGCAGCATGATCAG 59.240 55.000 0.09 0.00 39.69 2.90
1712 1767 4.261994 GCATGCTACTAGAAGGAAGGAGAG 60.262 50.000 11.37 0.00 0.00 3.20
1715 1770 3.386078 CAGCATGCTACTAGAAGGAAGGA 59.614 47.826 22.19 0.00 0.00 3.36
1716 1771 3.133721 ACAGCATGCTACTAGAAGGAAGG 59.866 47.826 22.19 5.55 42.53 3.46
1717 1772 4.399004 ACAGCATGCTACTAGAAGGAAG 57.601 45.455 22.19 5.77 42.53 3.46
1718 1773 4.507710 CAACAGCATGCTACTAGAAGGAA 58.492 43.478 22.19 0.00 42.53 3.36
1735 1790 1.021202 TGGACAAACCGAAGCAACAG 58.979 50.000 0.00 0.00 42.61 3.16
1760 1815 5.492804 GTCCAAGGGAATTCCGTTACGGA 62.493 52.174 27.35 25.79 43.86 4.69
1763 1818 2.004733 CGTCCAAGGGAATTCCGTTAC 58.995 52.381 27.35 21.86 41.68 2.50
1774 1829 2.046892 CCTGTGAGCGTCCAAGGG 60.047 66.667 0.00 0.00 0.00 3.95
1796 1851 1.363443 CTGGCTGATCCGCTCTCTC 59.637 63.158 9.11 0.00 37.80 3.20
1803 1858 2.649245 TTCATCCGCTGGCTGATCCG 62.649 60.000 0.00 0.00 37.80 4.18
1826 1881 1.608717 CTGGAACGAGGTCCTGGAGG 61.609 65.000 8.06 0.00 38.62 4.30
1874 1929 9.730705 TCTCTTTCTGATTTATCATTGTGAACT 57.269 29.630 0.00 0.00 36.02 3.01
1875 1930 9.985318 CTCTCTTTCTGATTTATCATTGTGAAC 57.015 33.333 0.00 0.00 36.02 3.18
1951 2069 5.104900 ACCTTGTACACAAAGACTGTCTTCT 60.105 40.000 22.24 10.64 35.27 2.85
1978 2096 6.238593 GCACAAAATTTGGCCAGTTTAATTGA 60.239 34.615 12.73 0.00 34.12 2.57
1987 2105 0.860533 CACGCACAAAATTTGGCCAG 59.139 50.000 5.11 0.00 34.12 4.85
2102 2220 1.368345 CGCATCGGATGGTTTCAGCA 61.368 55.000 18.96 0.00 0.00 4.41
2154 2298 1.270305 TGGAGAGGAACTGAAGCAACG 60.270 52.381 0.00 0.00 41.55 4.10
2224 2368 1.082496 GCTCACGTCTTTGTGCAGC 60.082 57.895 0.00 0.00 39.73 5.25
2261 2405 0.234106 GCGCGATGGTGATGATGAAG 59.766 55.000 12.10 0.00 0.00 3.02
2316 2460 1.854743 CCGTACATCTGCATTCGACAG 59.145 52.381 0.00 0.00 36.44 3.51
2556 2700 4.855388 CACGAAATTCTGAAGGCAAGAATG 59.145 41.667 9.84 2.88 33.19 2.67
2581 2725 3.065015 GTCAAGCGACGCGAAGAG 58.935 61.111 15.93 1.28 31.07 2.85
2612 2756 9.710818 AACTAAACTGTATCAGGATAAGGTCTA 57.289 33.333 1.90 0.00 35.51 2.59
2635 2782 2.080693 TGACAGACGCAACACAAAACT 58.919 42.857 0.00 0.00 0.00 2.66
2639 2786 0.742635 TGCTGACAGACGCAACACAA 60.743 50.000 6.65 0.00 32.40 3.33
2640 2787 1.153469 TGCTGACAGACGCAACACA 60.153 52.632 6.65 0.00 32.40 3.72
2641 2788 3.717899 TGCTGACAGACGCAACAC 58.282 55.556 6.65 0.00 32.40 3.32
2652 2799 2.026822 TCCCAGAAATTCCTCTGCTGAC 60.027 50.000 2.12 0.00 41.36 3.51
2665 2812 1.486211 GGAGATCGTCCTCCCAGAAA 58.514 55.000 12.70 0.00 45.44 2.52
2677 2824 2.337583 TGAAAAACGCTCTGGAGATCG 58.662 47.619 1.35 0.00 39.31 3.69
2737 2884 2.125350 CCGTGGAAGCTCTCTGCC 60.125 66.667 0.00 0.00 44.23 4.85
2808 2955 0.388649 AGTCCGTTCAGTGACGATGC 60.389 55.000 14.17 6.24 45.47 3.91
2902 3061 3.959293 TCTTCCTATGTACAGACCGTCA 58.041 45.455 0.33 0.00 0.00 4.35
2906 3065 7.113658 TCTTGATTCTTCCTATGTACAGACC 57.886 40.000 0.33 0.00 0.00 3.85
2941 3110 1.870167 GCTATAGCTTCACTCGCCACC 60.870 57.143 17.75 0.00 38.21 4.61
3009 3178 2.544267 GACACAAGAAACTCGTCCCTTG 59.456 50.000 0.00 0.00 41.12 3.61
3108 3286 9.871238 ATCGTTCCGCTATATTAATAATCACTT 57.129 29.630 0.00 0.00 0.00 3.16
3110 3288 9.297586 TGATCGTTCCGCTATATTAATAATCAC 57.702 33.333 0.00 0.00 0.00 3.06
3111 3289 9.516314 CTGATCGTTCCGCTATATTAATAATCA 57.484 33.333 0.00 0.10 0.00 2.57
3112 3290 9.517609 ACTGATCGTTCCGCTATATTAATAATC 57.482 33.333 0.00 0.00 0.00 1.75
3113 3291 9.871238 AACTGATCGTTCCGCTATATTAATAAT 57.129 29.630 0.00 0.00 0.00 1.28
3115 3293 9.778993 GTAACTGATCGTTCCGCTATATTAATA 57.221 33.333 0.00 0.00 37.05 0.98
3153 3331 0.319900 ATCTGCACCGTGTCTCACAC 60.320 55.000 0.00 0.00 45.26 3.82
3196 3375 3.071602 TGAAGGGCAGCAGTATTAGGATC 59.928 47.826 0.00 0.00 0.00 3.36
3213 3392 7.273381 CGCCACAGATAATAAAAACTTTGAAGG 59.727 37.037 0.00 0.00 0.00 3.46
3226 3405 4.262463 GGGTTCTCATCGCCACAGATAATA 60.262 45.833 0.00 0.00 0.00 0.98
3228 3407 2.158957 GGGTTCTCATCGCCACAGATAA 60.159 50.000 0.00 0.00 0.00 1.75
3244 3423 2.884894 CAGTATACTGACGGGGGTTC 57.115 55.000 25.83 0.00 46.59 3.62
3304 3498 2.554775 CAGCAGAGCACGCAACAG 59.445 61.111 0.00 0.00 0.00 3.16
3396 3590 2.040544 CCTACCCAGCTTTGGTGCG 61.041 63.158 13.81 5.85 36.57 5.34
3406 3600 0.457337 GCGACGTGTAACCTACCCAG 60.457 60.000 0.00 0.00 0.00 4.45
3442 3637 0.941542 GAGAGGAGACGAGACGGATG 59.058 60.000 0.00 0.00 0.00 3.51
3609 3834 3.545481 CGACAGCGACCGCATGTC 61.545 66.667 23.68 23.68 44.88 3.06
3661 4302 2.594119 CTTTGGCTCGCTGCATGCTC 62.594 60.000 20.33 9.76 45.15 4.26
3662 4303 2.674033 TTTGGCTCGCTGCATGCT 60.674 55.556 20.33 0.00 45.15 3.79
3716 4357 1.596477 GCAGCGCCATAAGAGAGGG 60.596 63.158 2.29 0.00 0.00 4.30
3806 4448 0.601311 GAAACAGAGCACGGCACTCT 60.601 55.000 0.00 0.00 45.39 3.24
3807 4449 0.601311 AGAAACAGAGCACGGCACTC 60.601 55.000 0.00 0.00 0.00 3.51
3832 4474 0.603975 ACCAGAAGGAGCAAAGACGC 60.604 55.000 0.00 0.00 38.69 5.19
3840 4482 3.791245 CTGTTAGATCACCAGAAGGAGC 58.209 50.000 0.00 0.00 38.69 4.70
3841 4483 3.196469 TGCTGTTAGATCACCAGAAGGAG 59.804 47.826 9.65 0.00 38.69 3.69
3842 4484 3.173151 TGCTGTTAGATCACCAGAAGGA 58.827 45.455 9.65 0.00 38.69 3.36
3846 4488 1.901833 TGCTGCTGTTAGATCACCAGA 59.098 47.619 0.00 0.00 0.00 3.86
3847 4489 2.005451 GTGCTGCTGTTAGATCACCAG 58.995 52.381 0.00 0.00 0.00 4.00
3848 4490 1.625315 AGTGCTGCTGTTAGATCACCA 59.375 47.619 0.00 0.00 0.00 4.17
3849 4491 2.005451 CAGTGCTGCTGTTAGATCACC 58.995 52.381 0.00 0.00 40.27 4.02
3862 4504 2.349817 CGAGTGGTTAAAAGCAGTGCTG 60.350 50.000 20.55 0.00 39.93 4.41
3863 4505 1.873591 CGAGTGGTTAAAAGCAGTGCT 59.126 47.619 13.14 13.14 39.93 4.40
3864 4506 1.602377 ACGAGTGGTTAAAAGCAGTGC 59.398 47.619 7.13 7.13 39.93 4.40
3865 4507 4.304110 TCTACGAGTGGTTAAAAGCAGTG 58.696 43.478 6.95 3.24 39.93 3.66
3866 4508 4.595762 TCTACGAGTGGTTAAAAGCAGT 57.404 40.909 2.02 2.02 42.30 4.40
3867 4509 6.812160 ACTAATCTACGAGTGGTTAAAAGCAG 59.188 38.462 0.00 0.00 37.04 4.24
3868 4510 6.588756 CACTAATCTACGAGTGGTTAAAAGCA 59.411 38.462 0.00 0.00 39.55 3.91
3869 4511 6.455246 GCACTAATCTACGAGTGGTTAAAAGC 60.455 42.308 4.36 0.00 42.77 3.51
3870 4512 6.990546 GCACTAATCTACGAGTGGTTAAAAG 58.009 40.000 4.36 0.00 42.77 2.27
3871 4513 6.956299 GCACTAATCTACGAGTGGTTAAAA 57.044 37.500 4.36 0.00 42.77 1.52
3877 4519 6.237490 CGTTTTTAGCACTAATCTACGAGTGG 60.237 42.308 11.08 0.00 42.77 4.00
3878 4520 6.683883 CGTTTTTAGCACTAATCTACGAGTG 58.316 40.000 11.08 0.00 44.88 3.51
3879 4521 5.287992 GCGTTTTTAGCACTAATCTACGAGT 59.712 40.000 16.70 0.00 31.38 4.18
3880 4522 5.287752 TGCGTTTTTAGCACTAATCTACGAG 59.712 40.000 16.70 0.00 40.01 4.18
3881 4523 5.162794 TGCGTTTTTAGCACTAATCTACGA 58.837 37.500 16.70 6.02 40.01 3.43
3882 4524 5.444586 TGCGTTTTTAGCACTAATCTACG 57.555 39.130 11.74 11.74 40.01 3.51


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

AutoCloner maintained by Alex Coulton.