Multiple sequence alignment - TraesCS3A01G018300

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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 TraesCS3A01G018300 chr3A 100.000 3612 0 0 1 3612 11460161 11456550 0.000000e+00 6671.0
1 TraesCS3A01G018300 chr3A 92.391 2221 130 18 1001 3203 10825771 10823572 0.000000e+00 3129.0
2 TraesCS3A01G018300 chr3A 98.900 1000 11 0 1 1000 40447247 40448246 0.000000e+00 1786.0
3 TraesCS3A01G018300 chr3A 83.473 1791 236 34 1001 2752 11410733 11408964 0.000000e+00 1613.0
4 TraesCS3A01G018300 chr3A 85.167 1254 171 8 1557 2799 11001149 10999900 0.000000e+00 1271.0
5 TraesCS3A01G018300 chr3A 85.091 1100 147 10 1659 2752 10952686 10951598 0.000000e+00 1107.0
6 TraesCS3A01G018300 chr3A 93.522 247 16 0 3062 3308 10823618 10823372 5.700000e-98 368.0
7 TraesCS3A01G018300 chr3A 95.261 211 5 2 3405 3611 10823330 10823121 2.690000e-86 329.0
8 TraesCS3A01G018300 chr3A 81.739 230 24 4 1001 1212 11001713 11001484 3.710000e-40 176.0
9 TraesCS3A01G018300 chr3A 88.406 138 15 1 3067 3203 10823661 10823524 8.020000e-37 165.0
10 TraesCS3A01G018300 chr3A 91.837 98 5 3 3059 3156 10823571 10823477 2.260000e-27 134.0
11 TraesCS3A01G018300 chr5A 99.800 999 2 0 1 999 687742741 687743739 0.000000e+00 1834.0
12 TraesCS3A01G018300 chr5A 98.899 999 9 1 1 999 687733224 687732228 0.000000e+00 1783.0
13 TraesCS3A01G018300 chr3B 99.000 1000 10 0 1 1000 793276016 793275017 0.000000e+00 1792.0
14 TraesCS3A01G018300 chr3B 86.561 1012 77 32 1 999 799581425 799580460 0.000000e+00 1061.0
15 TraesCS3A01G018300 chr3B 80.745 1127 196 15 1659 2779 28363690 28364801 0.000000e+00 859.0
16 TraesCS3A01G018300 chr3B 98.319 476 7 1 524 999 737880217 737879743 0.000000e+00 833.0
17 TraesCS3A01G018300 chr3B 96.429 56 2 0 641 696 793275481 793275426 3.840000e-15 93.5
18 TraesCS3A01G018300 chrUn 84.148 1842 233 32 1001 2802 214330144 214328322 0.000000e+00 1729.0
19 TraesCS3A01G018300 chrUn 100.000 873 0 0 1 873 371198697 371199569 0.000000e+00 1613.0
20 TraesCS3A01G018300 chrUn 82.033 1820 268 40 1003 2801 34656173 34657954 0.000000e+00 1495.0
21 TraesCS3A01G018300 chrUn 85.749 1249 161 12 1540 2782 35316301 35317538 0.000000e+00 1304.0
22 TraesCS3A01G018300 chrUn 84.783 1150 163 7 1637 2782 39602720 39603861 0.000000e+00 1144.0
23 TraesCS3A01G018300 chrUn 95.582 249 11 0 1 249 91408362 91408114 2.020000e-107 399.0
24 TraesCS3A01G018300 chrUn 89.474 304 25 6 1001 1302 35315795 35316093 9.470000e-101 377.0
25 TraesCS3A01G018300 chrUn 86.829 205 27 0 1003 1207 222090566 222090362 2.810000e-56 230.0
26 TraesCS3A01G018300 chrUn 83.099 213 16 7 1001 1194 36343832 36344043 3.710000e-40 176.0
27 TraesCS3A01G018300 chrUn 82.870 216 17 7 1001 1197 214891173 214890959 3.710000e-40 176.0
28 TraesCS3A01G018300 chr4A 99.395 661 4 0 1 661 646322917 646322257 0.000000e+00 1199.0
29 TraesCS3A01G018300 chr4A 99.309 434 2 1 571 1004 646322382 646321950 0.000000e+00 784.0
30 TraesCS3A01G018300 chr4A 91.141 587 28 12 1 579 708296022 708296592 0.000000e+00 774.0
31 TraesCS3A01G018300 chr4A 87.838 370 26 12 641 999 708296549 708296910 2.010000e-112 416.0
32 TraesCS3A01G018300 chr4B 99.092 661 6 0 1 661 631190450 631189790 0.000000e+00 1188.0
33 TraesCS3A01G018300 chr4B 98.840 431 4 1 569 999 631189917 631189488 0.000000e+00 767.0
34 TraesCS3A01G018300 chr3D 85.143 1151 158 8 1637 2783 4985067 4983926 0.000000e+00 1166.0
35 TraesCS3A01G018300 chr3D 83.544 237 21 4 1001 1219 5007727 5007491 4.730000e-49 206.0
36 TraesCS3A01G018300 chr3D 77.686 121 23 3 1001 1119 28331164 28331282 1.800000e-08 71.3
37 TraesCS3A01G018300 chr5B 79.359 1061 193 14 1645 2693 687165327 687166373 0.000000e+00 723.0
38 TraesCS3A01G018300 chr5B 98.239 284 5 0 201 484 534682345 534682628 6.960000e-137 497.0
39 TraesCS3A01G018300 chr2B 99.077 325 3 0 675 999 56907350 56907674 5.200000e-163 584.0


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 TraesCS3A01G018300 chr3A 11456550 11460161 3611 True 6671.00 6671 100.0000 1 3612 1 chr3A.!!$R3 3611
1 TraesCS3A01G018300 chr3A 40447247 40448246 999 False 1786.00 1786 98.9000 1 1000 1 chr3A.!!$F1 999
2 TraesCS3A01G018300 chr3A 11408964 11410733 1769 True 1613.00 1613 83.4730 1001 2752 1 chr3A.!!$R2 1751
3 TraesCS3A01G018300 chr3A 10951598 10952686 1088 True 1107.00 1107 85.0910 1659 2752 1 chr3A.!!$R1 1093
4 TraesCS3A01G018300 chr3A 10823121 10825771 2650 True 825.00 3129 92.2834 1001 3611 5 chr3A.!!$R4 2610
5 TraesCS3A01G018300 chr3A 10999900 11001713 1813 True 723.50 1271 83.4530 1001 2799 2 chr3A.!!$R5 1798
6 TraesCS3A01G018300 chr5A 687742741 687743739 998 False 1834.00 1834 99.8000 1 999 1 chr5A.!!$F1 998
7 TraesCS3A01G018300 chr5A 687732228 687733224 996 True 1783.00 1783 98.8990 1 999 1 chr5A.!!$R1 998
8 TraesCS3A01G018300 chr3B 799580460 799581425 965 True 1061.00 1061 86.5610 1 999 1 chr3B.!!$R2 998
9 TraesCS3A01G018300 chr3B 793275017 793276016 999 True 942.75 1792 97.7145 1 1000 2 chr3B.!!$R3 999
10 TraesCS3A01G018300 chr3B 28363690 28364801 1111 False 859.00 859 80.7450 1659 2779 1 chr3B.!!$F1 1120
11 TraesCS3A01G018300 chrUn 214328322 214330144 1822 True 1729.00 1729 84.1480 1001 2802 1 chrUn.!!$R2 1801
12 TraesCS3A01G018300 chrUn 371198697 371199569 872 False 1613.00 1613 100.0000 1 873 1 chrUn.!!$F4 872
13 TraesCS3A01G018300 chrUn 34656173 34657954 1781 False 1495.00 1495 82.0330 1003 2801 1 chrUn.!!$F1 1798
14 TraesCS3A01G018300 chrUn 39602720 39603861 1141 False 1144.00 1144 84.7830 1637 2782 1 chrUn.!!$F3 1145
15 TraesCS3A01G018300 chrUn 35315795 35317538 1743 False 840.50 1304 87.6115 1001 2782 2 chrUn.!!$F5 1781
16 TraesCS3A01G018300 chr4A 646321950 646322917 967 True 991.50 1199 99.3520 1 1004 2 chr4A.!!$R1 1003
17 TraesCS3A01G018300 chr4A 708296022 708296910 888 False 595.00 774 89.4895 1 999 2 chr4A.!!$F1 998
18 TraesCS3A01G018300 chr4B 631189488 631190450 962 True 977.50 1188 98.9660 1 999 2 chr4B.!!$R1 998
19 TraesCS3A01G018300 chr3D 4983926 4985067 1141 True 1166.00 1166 85.1430 1637 2783 1 chr3D.!!$R1 1146
20 TraesCS3A01G018300 chr5B 687165327 687166373 1046 False 723.00 723 79.3590 1645 2693 1 chr5B.!!$F2 1048

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
902 933 0.541863 CGGTCTGTATTTCTGGGCCT 59.458 55.0 4.53 0.0 0.0 5.19 F
1519 1629 2.519377 TATGTTGAATACGAGCGGGG 57.481 50.0 0.00 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1736 1852 0.693049 AGGAACTTCCCGACTGCATT 59.307 50.0 4.01 0.0 37.19 3.56 R
3040 3174 0.041312 CGGCCGGCGATGATTTTTAG 60.041 55.0 22.54 0.0 0.00 1.85 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
902 933 0.541863 CGGTCTGTATTTCTGGGCCT 59.458 55.000 4.53 0.00 0.00 5.19
1060 1091 7.181143 ACTTATGTTTACGTGTTAACTGGTG 57.819 36.000 7.22 0.00 0.00 4.17
1064 1095 5.358090 TGTTTACGTGTTAACTGGTGATGA 58.642 37.500 7.22 0.00 0.00 2.92
1207 1256 5.183904 AGTGGATTTGCTGTTATGTTTCCTC 59.816 40.000 0.00 0.00 0.00 3.71
1278 1343 4.800993 CGGTGAGTTACAGATCTTGACATC 59.199 45.833 0.00 0.00 0.00 3.06
1311 1414 6.531948 TGTTGTTTTATTTGTTGCCTGTGTAC 59.468 34.615 0.00 0.00 0.00 2.90
1449 1559 3.091545 TGGATTGTGGGAATTCTTCTGC 58.908 45.455 5.23 0.00 0.00 4.26
1507 1617 8.106462 TGTGACTGGATTTCCTTATTATGTTGA 58.894 33.333 0.00 0.00 36.82 3.18
1519 1629 2.519377 TATGTTGAATACGAGCGGGG 57.481 50.000 0.00 0.00 0.00 5.73
1736 1852 9.753674 AGTATTGGAAAACAAGGATCAGAATTA 57.246 29.630 0.00 0.00 43.48 1.40
1903 2019 0.724549 GCAATGTTCATGTCGCGGTA 59.275 50.000 6.13 0.00 0.00 4.02
1975 2091 3.242011 AGTTTCAACCATTGGCAGGATT 58.758 40.909 1.54 0.00 0.00 3.01
2242 2358 4.388485 ACAATTTCATCCCAAAAGTTGCC 58.612 39.130 0.00 0.00 0.00 4.52
2299 2415 1.227409 TTTTGTGCCGTCGAGAGCA 60.227 52.632 5.22 5.22 36.44 4.26
2442 2560 0.249322 AACGCCGATCCGAATACAGG 60.249 55.000 0.00 0.00 0.00 4.00
2534 2655 6.817140 TGAGATATATGCTCATGTTGATGCTC 59.183 38.462 9.48 0.00 37.46 4.26
2624 2749 0.598680 ACGATGAGCGAGGCAATAGC 60.599 55.000 0.00 0.00 44.57 2.97
2802 2930 4.707030 TGCAGAAAATGATGCACTTAGG 57.293 40.909 0.00 0.00 46.97 2.69
2822 2950 5.294734 AGGTGGTGCATTTTTCTTGAAAT 57.705 34.783 0.00 0.00 0.00 2.17
2828 2956 6.149142 TGGTGCATTTTTCTTGAAATAATGGC 59.851 34.615 19.61 15.53 0.00 4.40
2839 2967 7.874940 TCTTGAAATAATGGCTGTACATATGC 58.125 34.615 1.58 0.00 0.00 3.14
2840 2968 7.501892 TCTTGAAATAATGGCTGTACATATGCA 59.498 33.333 1.58 0.00 0.00 3.96
2841 2969 7.764141 TGAAATAATGGCTGTACATATGCAT 57.236 32.000 3.79 3.79 0.00 3.96
2842 2970 7.595604 TGAAATAATGGCTGTACATATGCATG 58.404 34.615 10.16 0.00 38.21 4.06
2854 2982 7.053498 TGTACATATGCATGGTTGTATCAAGT 58.947 34.615 10.16 0.00 36.39 3.16
2883 3011 5.138276 ACTATCTGCTGTATTTCCGGAGTA 58.862 41.667 3.34 0.00 0.00 2.59
2903 3031 7.490000 GGAGTAGTGTGTACATGTAATAGCTT 58.510 38.462 7.25 0.00 0.00 3.74
2957 3091 7.996098 TGTCATCTTATTCATGCATGATGAT 57.004 32.000 29.13 21.92 40.92 2.45
2958 3092 9.681062 ATGTCATCTTATTCATGCATGATGATA 57.319 29.630 29.13 23.96 40.92 2.15
2959 3093 9.681062 TGTCATCTTATTCATGCATGATGATAT 57.319 29.630 29.13 20.91 40.92 1.63
2994 3128 1.602888 CTGCTCCTGGTGCTGCTTT 60.603 57.895 20.19 0.00 0.00 3.51
2995 3129 1.863662 CTGCTCCTGGTGCTGCTTTG 61.864 60.000 20.19 2.30 0.00 2.77
2997 3131 1.954528 CTCCTGGTGCTGCTTTGTG 59.045 57.895 0.00 0.00 0.00 3.33
2998 3132 0.820891 CTCCTGGTGCTGCTTTGTGT 60.821 55.000 0.00 0.00 0.00 3.72
2999 3133 0.395586 TCCTGGTGCTGCTTTGTGTT 60.396 50.000 0.00 0.00 0.00 3.32
3001 3135 1.134729 CCTGGTGCTGCTTTGTGTTTT 60.135 47.619 0.00 0.00 0.00 2.43
3004 3138 2.195922 GGTGCTGCTTTGTGTTTTCTG 58.804 47.619 0.00 0.00 0.00 3.02
3005 3139 2.417243 GGTGCTGCTTTGTGTTTTCTGT 60.417 45.455 0.00 0.00 0.00 3.41
3006 3140 3.253230 GTGCTGCTTTGTGTTTTCTGTT 58.747 40.909 0.00 0.00 0.00 3.16
3007 3141 4.420168 GTGCTGCTTTGTGTTTTCTGTTA 58.580 39.130 0.00 0.00 0.00 2.41
3008 3142 5.043248 GTGCTGCTTTGTGTTTTCTGTTAT 58.957 37.500 0.00 0.00 0.00 1.89
3009 3143 5.042593 TGCTGCTTTGTGTTTTCTGTTATG 58.957 37.500 0.00 0.00 0.00 1.90
3010 3144 4.084900 GCTGCTTTGTGTTTTCTGTTATGC 60.085 41.667 0.00 0.00 0.00 3.14
3011 3145 5.261209 TGCTTTGTGTTTTCTGTTATGCT 57.739 34.783 0.00 0.00 0.00 3.79
3012 3146 5.280945 TGCTTTGTGTTTTCTGTTATGCTC 58.719 37.500 0.00 0.00 0.00 4.26
3014 3148 5.748152 GCTTTGTGTTTTCTGTTATGCTCAA 59.252 36.000 0.00 0.00 0.00 3.02
3017 3151 7.928908 TTGTGTTTTCTGTTATGCTCAAATC 57.071 32.000 0.00 0.00 0.00 2.17
3018 3152 7.275888 TGTGTTTTCTGTTATGCTCAAATCT 57.724 32.000 0.00 0.00 0.00 2.40
3019 3153 7.715657 TGTGTTTTCTGTTATGCTCAAATCTT 58.284 30.769 0.00 0.00 0.00 2.40
3020 3154 8.196771 TGTGTTTTCTGTTATGCTCAAATCTTT 58.803 29.630 0.00 0.00 0.00 2.52
3021 3155 8.482429 GTGTTTTCTGTTATGCTCAAATCTTTG 58.518 33.333 0.00 0.00 39.48 2.77
3022 3156 8.196771 TGTTTTCTGTTATGCTCAAATCTTTGT 58.803 29.630 2.82 0.00 39.18 2.83
3023 3157 8.482429 GTTTTCTGTTATGCTCAAATCTTTGTG 58.518 33.333 2.82 2.07 39.18 3.33
3024 3158 6.882610 TCTGTTATGCTCAAATCTTTGTGT 57.117 33.333 2.82 0.00 39.18 3.72
3025 3159 7.275888 TCTGTTATGCTCAAATCTTTGTGTT 57.724 32.000 2.82 0.00 39.18 3.32
3026 3160 7.715657 TCTGTTATGCTCAAATCTTTGTGTTT 58.284 30.769 2.82 0.00 39.18 2.83
3027 3161 7.862372 TCTGTTATGCTCAAATCTTTGTGTTTC 59.138 33.333 2.82 0.00 39.18 2.78
3028 3162 6.922957 TGTTATGCTCAAATCTTTGTGTTTCC 59.077 34.615 2.82 0.00 39.18 3.13
3029 3163 4.320608 TGCTCAAATCTTTGTGTTTCCC 57.679 40.909 2.82 0.00 39.18 3.97
3030 3164 3.703556 TGCTCAAATCTTTGTGTTTCCCA 59.296 39.130 2.82 0.00 39.18 4.37
3031 3165 4.344679 TGCTCAAATCTTTGTGTTTCCCAT 59.655 37.500 2.82 0.00 39.18 4.00
3032 3166 5.538053 TGCTCAAATCTTTGTGTTTCCCATA 59.462 36.000 2.82 0.00 39.18 2.74
3033 3167 6.211184 TGCTCAAATCTTTGTGTTTCCCATAT 59.789 34.615 2.82 0.00 39.18 1.78
3034 3168 7.395772 TGCTCAAATCTTTGTGTTTCCCATATA 59.604 33.333 2.82 0.00 39.18 0.86
3035 3169 8.416329 GCTCAAATCTTTGTGTTTCCCATATAT 58.584 33.333 2.82 0.00 39.18 0.86
3038 3172 9.236691 CAAATCTTTGTGTTTCCCATATATTCG 57.763 33.333 0.00 0.00 33.59 3.34
3039 3173 6.371809 TCTTTGTGTTTCCCATATATTCGC 57.628 37.500 0.00 0.00 0.00 4.70
3040 3174 5.298276 TCTTTGTGTTTCCCATATATTCGCC 59.702 40.000 0.00 0.00 0.00 5.54
3044 3178 6.358178 TGTGTTTCCCATATATTCGCCTAAA 58.642 36.000 0.00 0.00 0.00 1.85
3053 3187 6.907212 CCATATATTCGCCTAAAAATCATCGC 59.093 38.462 0.00 0.00 0.00 4.58
3059 3193 0.041312 CTAAAAATCATCGCCGGCCG 60.041 55.000 23.46 21.04 38.61 6.13
3069 3222 2.812499 GCCGGCCGAGACATTAGA 59.188 61.111 30.73 0.00 0.00 2.10
3088 3241 9.273016 ACATTAGAACTTAATAATCATCACCGG 57.727 33.333 0.00 0.00 0.00 5.28
3090 3243 5.930135 AGAACTTAATAATCATCACCGGCT 58.070 37.500 0.00 0.00 0.00 5.52
3213 3462 8.390854 AGATATTAAACTAATAATCGACCGCG 57.609 34.615 0.00 0.00 34.59 6.46
3262 3511 8.789825 ATCAGTATAAATCTTCATGATCAGCC 57.210 34.615 0.09 0.00 33.57 4.85
3308 3557 2.922758 GCGATTCCTACCTGCTATCGTG 60.923 54.545 0.00 0.00 40.00 4.35
3309 3558 2.678324 GATTCCTACCTGCTATCGTGC 58.322 52.381 0.00 0.00 0.00 5.34
3310 3559 1.480789 TTCCTACCTGCTATCGTGCA 58.519 50.000 0.00 0.00 41.05 4.57
3311 3560 1.480789 TCCTACCTGCTATCGTGCAA 58.519 50.000 0.00 0.00 42.83 4.08
3312 3561 2.039418 TCCTACCTGCTATCGTGCAAT 58.961 47.619 0.00 0.00 42.83 3.56
3332 3595 2.813908 GCGCGGTAGGTGACTTGG 60.814 66.667 8.83 0.00 43.67 3.61
3333 3596 2.654877 CGCGGTAGGTGACTTGGT 59.345 61.111 0.00 0.00 43.67 3.67
3335 3598 1.289109 CGCGGTAGGTGACTTGGTTG 61.289 60.000 0.00 0.00 43.67 3.77
3336 3599 0.250166 GCGGTAGGTGACTTGGTTGT 60.250 55.000 0.00 0.00 43.67 3.32
3337 3600 1.812708 GCGGTAGGTGACTTGGTTGTT 60.813 52.381 0.00 0.00 43.67 2.83
3338 3601 2.567985 CGGTAGGTGACTTGGTTGTTT 58.432 47.619 0.00 0.00 43.67 2.83
3339 3602 2.946990 CGGTAGGTGACTTGGTTGTTTT 59.053 45.455 0.00 0.00 43.67 2.43
3340 3603 3.242936 CGGTAGGTGACTTGGTTGTTTTG 60.243 47.826 0.00 0.00 43.67 2.44
3341 3604 3.949113 GGTAGGTGACTTGGTTGTTTTGA 59.051 43.478 0.00 0.00 43.67 2.69
3342 3605 4.583073 GGTAGGTGACTTGGTTGTTTTGAT 59.417 41.667 0.00 0.00 43.67 2.57
3343 3606 4.918810 AGGTGACTTGGTTGTTTTGATC 57.081 40.909 0.00 0.00 37.44 2.92
3344 3607 4.536765 AGGTGACTTGGTTGTTTTGATCT 58.463 39.130 0.00 0.00 37.44 2.75
3345 3608 4.580580 AGGTGACTTGGTTGTTTTGATCTC 59.419 41.667 0.00 0.00 37.44 2.75
3346 3609 4.261614 GGTGACTTGGTTGTTTTGATCTCC 60.262 45.833 0.00 0.00 0.00 3.71
3347 3610 4.580580 GTGACTTGGTTGTTTTGATCTCCT 59.419 41.667 0.00 0.00 0.00 3.69
3348 3611 5.763204 GTGACTTGGTTGTTTTGATCTCCTA 59.237 40.000 0.00 0.00 0.00 2.94
3349 3612 6.262273 GTGACTTGGTTGTTTTGATCTCCTAA 59.738 38.462 0.00 0.00 0.00 2.69
3350 3613 6.831353 TGACTTGGTTGTTTTGATCTCCTAAA 59.169 34.615 0.00 0.00 0.00 1.85
3351 3614 7.505585 TGACTTGGTTGTTTTGATCTCCTAAAT 59.494 33.333 0.00 0.00 0.00 1.40
3352 3615 8.934023 ACTTGGTTGTTTTGATCTCCTAAATA 57.066 30.769 0.00 0.00 0.00 1.40
3353 3616 9.362151 ACTTGGTTGTTTTGATCTCCTAAATAA 57.638 29.630 0.00 0.00 0.00 1.40
3355 3618 9.974980 TTGGTTGTTTTGATCTCCTAAATAAAC 57.025 29.630 0.00 0.00 32.27 2.01
3356 3619 9.362151 TGGTTGTTTTGATCTCCTAAATAAACT 57.638 29.630 0.00 0.00 32.63 2.66
3376 3639 5.408880 ACTAGTTAGTTTTGAGGAGCTCC 57.591 43.478 26.22 26.22 31.13 4.70
3377 3640 4.838986 ACTAGTTAGTTTTGAGGAGCTCCA 59.161 41.667 33.90 12.52 33.38 3.86
3378 3641 4.706842 AGTTAGTTTTGAGGAGCTCCAA 57.293 40.909 33.90 19.31 38.89 3.53
3379 3642 4.390264 AGTTAGTTTTGAGGAGCTCCAAC 58.610 43.478 33.90 26.54 38.89 3.77
3380 3643 4.103311 AGTTAGTTTTGAGGAGCTCCAACT 59.897 41.667 33.90 31.01 37.07 3.16
3381 3644 3.133141 AGTTTTGAGGAGCTCCAACTC 57.867 47.619 33.90 22.64 38.89 3.01
3382 3645 2.708325 AGTTTTGAGGAGCTCCAACTCT 59.292 45.455 33.90 19.56 38.89 3.24
3383 3646 3.137360 AGTTTTGAGGAGCTCCAACTCTT 59.863 43.478 33.90 12.93 38.89 2.85
3384 3647 2.847327 TTGAGGAGCTCCAACTCTTG 57.153 50.000 33.90 0.00 38.89 3.02
3385 3648 1.722034 TGAGGAGCTCCAACTCTTGT 58.278 50.000 33.90 11.28 38.89 3.16
3386 3649 1.620819 TGAGGAGCTCCAACTCTTGTC 59.379 52.381 33.90 19.77 38.89 3.18
3387 3650 1.899142 GAGGAGCTCCAACTCTTGTCT 59.101 52.381 33.90 9.66 38.89 3.41
3388 3651 2.301583 GAGGAGCTCCAACTCTTGTCTT 59.698 50.000 33.90 9.08 38.89 3.01
3389 3652 3.511477 AGGAGCTCCAACTCTTGTCTTA 58.489 45.455 33.90 0.00 38.89 2.10
3390 3653 3.259625 AGGAGCTCCAACTCTTGTCTTAC 59.740 47.826 33.90 1.29 38.89 2.34
3391 3654 3.006967 GGAGCTCCAACTCTTGTCTTACA 59.993 47.826 28.43 0.00 36.87 2.41
3392 3655 4.503296 GGAGCTCCAACTCTTGTCTTACAA 60.503 45.833 28.43 0.00 36.87 2.41
3393 3656 6.308908 GGAGCTCCAACTCTTGTCTTACAAG 61.309 48.000 28.43 12.53 44.97 3.16
3394 3657 8.634750 GGAGCTCCAACTCTTGTCTTACAAGT 62.635 46.154 28.43 0.00 44.49 3.16
3402 3665 3.857157 TTGTCTTACAAGTCTGGCCTT 57.143 42.857 3.32 0.00 32.34 4.35
3403 3666 3.126001 TGTCTTACAAGTCTGGCCTTG 57.874 47.619 3.32 1.98 45.83 3.61
3455 3718 9.337396 ACAGTCTTGTCTTACACAAATTATTGA 57.663 29.630 0.00 0.00 44.71 2.57
3491 3754 1.202604 ACTTGGTGGGTTACTGTCACG 60.203 52.381 0.00 0.00 32.65 4.35
3494 3757 1.695242 TGGTGGGTTACTGTCACGAAT 59.305 47.619 0.00 0.00 32.65 3.34
3496 3759 3.324268 TGGTGGGTTACTGTCACGAATAA 59.676 43.478 0.00 0.00 32.65 1.40
3611 3878 1.950909 CGGCCGGCCAATAGATTAAAA 59.049 47.619 42.78 0.00 35.37 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
902 933 0.766131 TAGAAAAACAGGACGGGCCA 59.234 50.000 4.39 0.00 40.02 5.36
1064 1095 7.816995 GCTCGAGATACTCCATTGAATTAGATT 59.183 37.037 18.75 0.00 0.00 2.40
1207 1256 2.351835 CGCCCACCGTAGAATATCTGAG 60.352 54.545 0.00 0.00 0.00 3.35
1278 1343 6.468484 CAACAAATAAAACAACAGTGTGCAG 58.532 36.000 0.00 0.00 38.27 4.41
1311 1414 0.320374 TCGAACAAGGTAGCCAGGTG 59.680 55.000 0.00 0.00 0.00 4.00
1417 1527 3.269118 TCCCACAATCCAATCCTTGATGA 59.731 43.478 0.00 0.00 0.00 2.92
1449 1559 2.093764 AGTCTGCGAAATCTCCCTCAAG 60.094 50.000 0.00 0.00 0.00 3.02
1519 1629 5.475719 TCCACATAGTAATTAGTATGGCGC 58.524 41.667 30.54 0.00 41.63 6.53
1736 1852 0.693049 AGGAACTTCCCGACTGCATT 59.307 50.000 4.01 0.00 37.19 3.56
1903 2019 3.767673 TGGAGTTACCGTCTAGCATCTTT 59.232 43.478 0.00 0.00 42.61 2.52
2299 2415 3.463329 TGTACCCTATAGTTCCCCGTAGT 59.537 47.826 0.00 0.00 0.00 2.73
2442 2560 5.470437 GGGTAGTATGCTTGGCTAGAATTTC 59.530 44.000 0.00 0.00 0.00 2.17
2534 2655 2.169978 TCCTCTCCAACTCATGCATCTG 59.830 50.000 0.00 0.00 0.00 2.90
2802 2930 7.520686 CCATTATTTCAAGAAAAATGCACCAC 58.479 34.615 16.34 0.00 33.12 4.16
2822 2950 4.984295 ACCATGCATATGTACAGCCATTA 58.016 39.130 0.00 0.00 32.21 1.90
2828 2956 7.227314 ACTTGATACAACCATGCATATGTACAG 59.773 37.037 16.75 15.01 31.65 2.74
2841 2969 9.599866 CAGATAGTTTCATACTTGATACAACCA 57.400 33.333 0.00 0.00 36.58 3.67
2842 2970 8.552034 GCAGATAGTTTCATACTTGATACAACC 58.448 37.037 0.00 0.00 36.58 3.77
2854 2982 6.929049 CCGGAAATACAGCAGATAGTTTCATA 59.071 38.462 0.00 0.00 0.00 2.15
2883 3011 4.566759 CGCAAGCTATTACATGTACACACT 59.433 41.667 4.68 0.00 0.00 3.55
2957 3091 5.673337 GCAGGAGCGAAATTTCATGTATA 57.327 39.130 17.99 0.00 0.00 1.47
2958 3092 4.558538 GCAGGAGCGAAATTTCATGTAT 57.441 40.909 17.99 0.00 0.00 2.29
2960 3094 2.927553 GCAGGAGCGAAATTTCATGT 57.072 45.000 17.99 1.53 0.00 3.21
2994 3128 7.275888 AGATTTGAGCATAACAGAAAACACA 57.724 32.000 0.00 0.00 0.00 3.72
2995 3129 8.482429 CAAAGATTTGAGCATAACAGAAAACAC 58.518 33.333 0.00 0.00 40.55 3.32
2997 3131 8.482429 CACAAAGATTTGAGCATAACAGAAAAC 58.518 33.333 12.07 0.00 40.55 2.43
2998 3132 8.196771 ACACAAAGATTTGAGCATAACAGAAAA 58.803 29.630 12.07 0.00 40.55 2.29
2999 3133 7.715657 ACACAAAGATTTGAGCATAACAGAAA 58.284 30.769 12.07 0.00 40.55 2.52
3001 3135 6.882610 ACACAAAGATTTGAGCATAACAGA 57.117 33.333 12.07 0.00 40.55 3.41
3004 3138 6.366061 GGGAAACACAAAGATTTGAGCATAAC 59.634 38.462 12.07 0.00 40.55 1.89
3005 3139 6.041409 TGGGAAACACAAAGATTTGAGCATAA 59.959 34.615 12.07 0.00 40.55 1.90
3006 3140 5.538053 TGGGAAACACAAAGATTTGAGCATA 59.462 36.000 12.07 0.00 40.55 3.14
3007 3141 4.344679 TGGGAAACACAAAGATTTGAGCAT 59.655 37.500 12.07 0.00 40.55 3.79
3008 3142 3.703556 TGGGAAACACAAAGATTTGAGCA 59.296 39.130 12.07 0.00 40.55 4.26
3009 3143 4.320608 TGGGAAACACAAAGATTTGAGC 57.679 40.909 12.07 0.00 40.55 4.26
3012 3146 9.236691 CGAATATATGGGAAACACAAAGATTTG 57.763 33.333 3.79 3.79 43.62 2.32
3014 3148 7.425606 GCGAATATATGGGAAACACAAAGATT 58.574 34.615 0.00 0.00 0.00 2.40
3017 3151 5.299279 AGGCGAATATATGGGAAACACAAAG 59.701 40.000 0.00 0.00 0.00 2.77
3018 3152 5.197451 AGGCGAATATATGGGAAACACAAA 58.803 37.500 0.00 0.00 0.00 2.83
3019 3153 4.787551 AGGCGAATATATGGGAAACACAA 58.212 39.130 0.00 0.00 0.00 3.33
3020 3154 4.431416 AGGCGAATATATGGGAAACACA 57.569 40.909 0.00 0.00 0.00 3.72
3021 3155 6.870971 TTTAGGCGAATATATGGGAAACAC 57.129 37.500 0.00 0.00 0.00 3.32
3022 3156 7.883391 TTTTTAGGCGAATATATGGGAAACA 57.117 32.000 0.00 0.00 0.00 2.83
3023 3157 8.573035 TGATTTTTAGGCGAATATATGGGAAAC 58.427 33.333 0.00 0.00 0.00 2.78
3024 3158 8.698973 TGATTTTTAGGCGAATATATGGGAAA 57.301 30.769 0.00 0.00 0.00 3.13
3025 3159 8.877864 ATGATTTTTAGGCGAATATATGGGAA 57.122 30.769 0.00 0.00 0.00 3.97
3026 3160 7.279981 CGATGATTTTTAGGCGAATATATGGGA 59.720 37.037 0.00 0.00 0.00 4.37
3027 3161 7.409697 CGATGATTTTTAGGCGAATATATGGG 58.590 38.462 0.00 0.00 0.00 4.00
3028 3162 6.907212 GCGATGATTTTTAGGCGAATATATGG 59.093 38.462 0.00 0.00 0.00 2.74
3029 3163 6.907212 GGCGATGATTTTTAGGCGAATATATG 59.093 38.462 0.00 0.00 0.00 1.78
3030 3164 7.016361 GGCGATGATTTTTAGGCGAATATAT 57.984 36.000 0.00 0.00 0.00 0.86
3031 3165 6.417191 GGCGATGATTTTTAGGCGAATATA 57.583 37.500 0.00 0.00 0.00 0.86
3032 3166 5.296813 GGCGATGATTTTTAGGCGAATAT 57.703 39.130 0.00 0.00 0.00 1.28
3033 3167 4.742438 GGCGATGATTTTTAGGCGAATA 57.258 40.909 0.00 0.00 0.00 1.75
3034 3168 3.626028 GGCGATGATTTTTAGGCGAAT 57.374 42.857 0.00 0.00 0.00 3.34
3037 3171 3.437845 CGGCGATGATTTTTAGGCG 57.562 52.632 0.00 0.00 43.73 5.52
3038 3172 0.317854 GCCGGCGATGATTTTTAGGC 60.318 55.000 12.58 0.00 36.32 3.93
3039 3173 0.310854 GGCCGGCGATGATTTTTAGG 59.689 55.000 22.54 0.00 0.00 2.69
3040 3174 0.041312 CGGCCGGCGATGATTTTTAG 60.041 55.000 22.54 0.00 0.00 1.85
3044 3178 2.588877 CTCGGCCGGCGATGATTT 60.589 61.111 27.83 0.00 0.00 2.17
3053 3187 0.460311 AGTTCTAATGTCTCGGCCGG 59.540 55.000 27.83 16.54 0.00 6.13
3069 3222 5.680619 TCAGCCGGTGATGATTATTAAGTT 58.319 37.500 1.90 0.00 30.48 2.66
3083 3236 3.074412 AGTTTTAATGTCTCAGCCGGTG 58.926 45.455 1.90 0.00 0.00 4.94
3088 3241 7.290857 TGTCGATTAGTTTTAATGTCTCAGC 57.709 36.000 0.00 0.00 29.67 4.26
3126 3327 4.508128 GTCTCGGCCGGCGATGAA 62.508 66.667 27.83 2.05 0.00 2.57
3164 3413 2.290641 GCCGGCGATGATTATCAAGTTT 59.709 45.455 12.58 0.00 32.67 2.66
3165 3414 1.873591 GCCGGCGATGATTATCAAGTT 59.126 47.619 12.58 0.00 32.67 2.66
3170 3419 1.078759 CTCGGCCGGCGATGATTATC 61.079 60.000 27.83 1.28 0.00 1.75
3213 3462 3.268023 AGTCAAGGCATTAGCTGTACC 57.732 47.619 0.00 0.00 41.70 3.34
3275 3524 1.478510 AGGAATCGCTGGTGTAGACAG 59.521 52.381 0.00 0.00 38.95 3.51
3309 3558 3.261951 CACCTACCGCGCCGATTG 61.262 66.667 0.00 0.00 0.00 2.67
3310 3559 3.454573 TCACCTACCGCGCCGATT 61.455 61.111 0.00 0.00 0.00 3.34
3311 3560 4.203076 GTCACCTACCGCGCCGAT 62.203 66.667 0.00 0.00 0.00 4.18
3351 3614 7.015877 TGGAGCTCCTCAAAACTAACTAGTTTA 59.984 37.037 32.28 3.03 44.40 2.01
3352 3615 6.183361 TGGAGCTCCTCAAAACTAACTAGTTT 60.183 38.462 32.28 8.71 45.64 2.66
3353 3616 5.307196 TGGAGCTCCTCAAAACTAACTAGTT 59.693 40.000 32.28 13.68 41.53 2.24
3354 3617 4.838986 TGGAGCTCCTCAAAACTAACTAGT 59.161 41.667 32.28 0.00 35.93 2.57
3355 3618 5.407407 TGGAGCTCCTCAAAACTAACTAG 57.593 43.478 32.28 0.00 36.82 2.57
3356 3619 5.307196 AGTTGGAGCTCCTCAAAACTAACTA 59.693 40.000 32.28 5.35 37.25 2.24
3357 3620 4.103311 AGTTGGAGCTCCTCAAAACTAACT 59.897 41.667 32.28 25.19 37.25 2.24
3358 3621 4.390264 AGTTGGAGCTCCTCAAAACTAAC 58.610 43.478 32.28 23.53 37.25 2.34
3359 3622 4.348168 AGAGTTGGAGCTCCTCAAAACTAA 59.652 41.667 32.28 13.69 38.29 2.24
3360 3623 3.904339 AGAGTTGGAGCTCCTCAAAACTA 59.096 43.478 32.28 7.74 38.29 2.24
3361 3624 2.708325 AGAGTTGGAGCTCCTCAAAACT 59.292 45.455 32.28 29.63 39.73 2.66
3362 3625 3.133141 AGAGTTGGAGCTCCTCAAAAC 57.867 47.619 32.28 25.88 36.20 2.43
3363 3626 3.117888 ACAAGAGTTGGAGCTCCTCAAAA 60.118 43.478 32.28 16.32 36.20 2.44
3364 3627 2.439507 ACAAGAGTTGGAGCTCCTCAAA 59.560 45.455 32.28 16.70 36.20 2.69
3365 3628 2.037772 GACAAGAGTTGGAGCTCCTCAA 59.962 50.000 32.28 17.46 36.20 3.02
3366 3629 1.620819 GACAAGAGTTGGAGCTCCTCA 59.379 52.381 32.28 17.14 36.20 3.86
3367 3630 1.899142 AGACAAGAGTTGGAGCTCCTC 59.101 52.381 32.28 23.74 36.20 3.71
3368 3631 2.022718 AGACAAGAGTTGGAGCTCCT 57.977 50.000 32.28 13.87 36.20 3.69
3369 3632 2.849294 AAGACAAGAGTTGGAGCTCC 57.151 50.000 26.78 26.78 36.20 4.70
3370 3633 4.258702 TGTAAGACAAGAGTTGGAGCTC 57.741 45.455 4.71 4.71 35.82 4.09
3371 3634 4.689612 TTGTAAGACAAGAGTTGGAGCT 57.310 40.909 0.00 0.00 32.34 4.09
3382 3645 3.476552 CAAGGCCAGACTTGTAAGACAA 58.523 45.455 5.01 0.00 42.18 3.18
3383 3646 3.126001 CAAGGCCAGACTTGTAAGACA 57.874 47.619 5.01 0.00 42.18 3.41
3391 3654 1.780503 AAGCAAACAAGGCCAGACTT 58.219 45.000 5.01 0.00 0.00 3.01
3392 3655 2.623416 GTTAAGCAAACAAGGCCAGACT 59.377 45.455 5.01 0.00 38.05 3.24
3393 3656 2.360801 TGTTAAGCAAACAAGGCCAGAC 59.639 45.455 5.01 0.00 45.11 3.51
3394 3657 2.660572 TGTTAAGCAAACAAGGCCAGA 58.339 42.857 5.01 0.00 45.11 3.86
3402 3665 2.941453 TTGGCGTTGTTAAGCAAACA 57.059 40.000 0.88 0.88 46.41 2.83
3403 3666 3.440228 TCTTTGGCGTTGTTAAGCAAAC 58.560 40.909 0.00 0.00 39.03 2.93
3420 3683 6.480320 GTGTAAGACAAGACTGTGACATCTTT 59.520 38.462 2.66 0.00 35.30 2.52
3455 3718 5.361285 CCACCAAGTCTAGCTAGTCTACAAT 59.639 44.000 18.93 2.97 0.00 2.71
3456 3719 4.705507 CCACCAAGTCTAGCTAGTCTACAA 59.294 45.833 18.93 0.00 0.00 2.41
3494 3757 8.564574 CCGATAATGGCTAAGCTAATTGTTTTA 58.435 33.333 0.00 0.00 0.00 1.52
3496 3759 6.770785 TCCGATAATGGCTAAGCTAATTGTTT 59.229 34.615 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.