Multiple sequence alignment - TraesCS7B01G407400

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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 TraesCS7B01G407400 chr7B 100.000 3260 0 0 1 3260 676423131 676426390 0.000000e+00 6021.0
1 TraesCS7B01G407400 chr7B 77.910 1426 231 50 1016 2382 676211018 676209618 0.000000e+00 811.0
2 TraesCS7B01G407400 chr7B 77.906 1299 219 45 1026 2266 676534931 676533643 0.000000e+00 747.0
3 TraesCS7B01G407400 chr7B 77.884 1153 206 37 1151 2267 676993485 676994624 0.000000e+00 671.0
4 TraesCS7B01G407400 chr7B 90.909 44 4 0 453 496 676423543 676423586 3.510000e-05 60.2
5 TraesCS7B01G407400 chr7B 90.909 44 4 0 413 456 676423583 676423626 3.510000e-05 60.2
6 TraesCS7B01G407400 chr7D 90.319 2975 236 24 294 3259 597655032 597652101 0.000000e+00 3851.0
7 TraesCS7B01G407400 chr7D 78.473 1310 201 54 1026 2266 597570225 597568928 0.000000e+00 782.0
8 TraesCS7B01G407400 chr7D 79.735 1130 180 32 1287 2384 597965471 597966583 0.000000e+00 773.0
9 TraesCS7B01G407400 chr7D 77.975 1294 220 39 1026 2266 597546405 597545124 0.000000e+00 750.0
10 TraesCS7B01G407400 chr7A 81.780 2124 273 69 324 2366 690399102 690401192 0.000000e+00 1674.0
11 TraesCS7B01G407400 chr7A 93.611 1080 58 7 1560 2636 690412962 690414033 0.000000e+00 1602.0
12 TraesCS7B01G407400 chr7A 91.500 800 59 7 739 1530 690412168 690412966 0.000000e+00 1092.0
13 TraesCS7B01G407400 chr7A 92.450 596 42 3 2666 3260 690414034 690414627 0.000000e+00 848.0
14 TraesCS7B01G407400 chr7A 78.033 1434 223 52 1023 2384 690195776 690194363 0.000000e+00 819.0
15 TraesCS7B01G407400 chr7A 78.034 1302 213 43 1023 2266 690517294 690518580 0.000000e+00 752.0
16 TraesCS7B01G407400 chr7A 77.675 972 187 22 1287 2247 690425715 690426667 1.700000e-157 566.0
17 TraesCS7B01G407400 chr7A 87.576 491 44 10 222 710 690411709 690412184 1.320000e-153 553.0
18 TraesCS7B01G407400 chr7A 91.026 234 19 2 1 234 690411298 690411529 6.790000e-82 315.0
19 TraesCS7B01G407400 chr7A 76.505 515 69 29 1023 1488 690438769 690439280 1.960000e-57 233.0
20 TraesCS7B01G407400 chr1D 76.792 823 159 25 2451 3259 258959975 258959171 1.800000e-117 433.0
21 TraesCS7B01G407400 chr1D 75.152 821 138 44 2467 3259 394807473 394808255 3.140000e-85 326.0
22 TraesCS7B01G407400 chr2B 75.601 832 161 27 2451 3257 208618004 208617190 1.100000e-99 374.0
23 TraesCS7B01G407400 chr2B 77.660 188 31 5 2919 3106 493503365 493503189 1.600000e-18 104.0
24 TraesCS7B01G407400 chr2A 75.402 809 149 33 2473 3259 140368497 140367717 2.410000e-91 346.0
25 TraesCS7B01G407400 chr5B 78.198 555 106 13 2611 3158 381386870 381387416 1.120000e-89 340.0
26 TraesCS7B01G407400 chr5B 78.643 501 87 16 2617 3106 633834855 633834364 6.790000e-82 315.0
27 TraesCS7B01G407400 chr5B 77.500 280 44 12 2451 2716 81771697 81771423 2.030000e-32 150.0
28 TraesCS7B01G407400 chr2D 76.888 662 110 30 2451 3103 610271074 610271701 5.210000e-88 335.0
29 TraesCS7B01G407400 chr2D 76.737 662 111 30 2451 3103 610265485 610266112 2.420000e-86 329.0
30 TraesCS7B01G407400 chr2D 75.982 662 140 18 2609 3260 562910598 562909946 1.130000e-84 324.0
31 TraesCS7B01G407400 chr1A 77.080 589 103 26 2451 3021 85821098 85821672 8.780000e-81 311.0
32 TraesCS7B01G407400 chr3A 74.419 688 123 32 2451 3103 113975097 113975766 2.510000e-61 246.0
33 TraesCS7B01G407400 chr3A 90.323 62 6 0 1637 1698 438637779 438637840 7.500000e-12 82.4
34 TraesCS7B01G407400 chr3B 73.715 506 105 26 2609 3103 544538300 544537812 4.320000e-39 172.0
35 TraesCS7B01G407400 chr3D 94.340 53 3 0 1646 1698 326233117 326233065 7.500000e-12 82.4


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 TraesCS7B01G407400 chr7B 676423131 676426390 3259 False 2047.133333 6021 93.939333 1 3260 3 chr7B.!!$F2 3259
1 TraesCS7B01G407400 chr7B 676209618 676211018 1400 True 811.000000 811 77.910000 1016 2382 1 chr7B.!!$R1 1366
2 TraesCS7B01G407400 chr7B 676533643 676534931 1288 True 747.000000 747 77.906000 1026 2266 1 chr7B.!!$R2 1240
3 TraesCS7B01G407400 chr7B 676993485 676994624 1139 False 671.000000 671 77.884000 1151 2267 1 chr7B.!!$F1 1116
4 TraesCS7B01G407400 chr7D 597652101 597655032 2931 True 3851.000000 3851 90.319000 294 3259 1 chr7D.!!$R3 2965
5 TraesCS7B01G407400 chr7D 597568928 597570225 1297 True 782.000000 782 78.473000 1026 2266 1 chr7D.!!$R2 1240
6 TraesCS7B01G407400 chr7D 597965471 597966583 1112 False 773.000000 773 79.735000 1287 2384 1 chr7D.!!$F1 1097
7 TraesCS7B01G407400 chr7D 597545124 597546405 1281 True 750.000000 750 77.975000 1026 2266 1 chr7D.!!$R1 1240
8 TraesCS7B01G407400 chr7A 690399102 690401192 2090 False 1674.000000 1674 81.780000 324 2366 1 chr7A.!!$F1 2042
9 TraesCS7B01G407400 chr7A 690411298 690414627 3329 False 882.000000 1602 91.232600 1 3260 5 chr7A.!!$F5 3259
10 TraesCS7B01G407400 chr7A 690194363 690195776 1413 True 819.000000 819 78.033000 1023 2384 1 chr7A.!!$R1 1361
11 TraesCS7B01G407400 chr7A 690517294 690518580 1286 False 752.000000 752 78.034000 1023 2266 1 chr7A.!!$F4 1243
12 TraesCS7B01G407400 chr7A 690425715 690426667 952 False 566.000000 566 77.675000 1287 2247 1 chr7A.!!$F2 960
13 TraesCS7B01G407400 chr7A 690438769 690439280 511 False 233.000000 233 76.505000 1023 1488 1 chr7A.!!$F3 465
14 TraesCS7B01G407400 chr1D 258959171 258959975 804 True 433.000000 433 76.792000 2451 3259 1 chr1D.!!$R1 808
15 TraesCS7B01G407400 chr1D 394807473 394808255 782 False 326.000000 326 75.152000 2467 3259 1 chr1D.!!$F1 792
16 TraesCS7B01G407400 chr2B 208617190 208618004 814 True 374.000000 374 75.601000 2451 3257 1 chr2B.!!$R1 806
17 TraesCS7B01G407400 chr2A 140367717 140368497 780 True 346.000000 346 75.402000 2473 3259 1 chr2A.!!$R1 786
18 TraesCS7B01G407400 chr5B 381386870 381387416 546 False 340.000000 340 78.198000 2611 3158 1 chr5B.!!$F1 547
19 TraesCS7B01G407400 chr2D 610271074 610271701 627 False 335.000000 335 76.888000 2451 3103 1 chr2D.!!$F2 652
20 TraesCS7B01G407400 chr2D 610265485 610266112 627 False 329.000000 329 76.737000 2451 3103 1 chr2D.!!$F1 652
21 TraesCS7B01G407400 chr2D 562909946 562910598 652 True 324.000000 324 75.982000 2609 3260 1 chr2D.!!$R1 651
22 TraesCS7B01G407400 chr1A 85821098 85821672 574 False 311.000000 311 77.080000 2451 3021 1 chr1A.!!$F1 570
23 TraesCS7B01G407400 chr3A 113975097 113975766 669 False 246.000000 246 74.419000 2451 3103 1 chr3A.!!$F1 652

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
725 944 1.216678 TCCAGGGAAATGTTGTGGTGT 59.783 47.619 0.00 0.0 0.00 4.16 F
1474 1844 0.391793 GGAGCTCGGTTCCTTCAAGG 60.392 60.000 7.83 0.0 36.46 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 2022 1.001378 GACGTTTGGTTGCAGCTGATT 60.001 47.619 20.43 0.0 0.0 2.57 R
2823 3285 0.248621 GCAAGTGTTGTCTGGTGTGC 60.249 55.000 0.00 0.0 0.0 4.57 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 4.034394 TGATGATTTCGCTGACAAGTATGC 59.966 41.667 0.00 0.00 0.00 3.14
31 32 2.349886 GCTGACAAGTATGCGAAGGAAG 59.650 50.000 0.00 0.00 0.00 3.46
32 33 3.849911 CTGACAAGTATGCGAAGGAAGA 58.150 45.455 0.00 0.00 0.00 2.87
127 128 3.005367 ACATTGTTGGCCTTCTAAAACGG 59.995 43.478 3.32 0.00 0.00 4.44
128 129 2.351706 TGTTGGCCTTCTAAAACGGT 57.648 45.000 3.32 0.00 0.00 4.83
141 142 6.778834 TCTAAAACGGTGTCCTATCACATA 57.221 37.500 0.00 0.00 39.76 2.29
151 152 6.550108 GGTGTCCTATCACATACCTCTAGAAA 59.450 42.308 0.00 0.00 39.76 2.52
158 159 9.650539 CTATCACATACCTCTAGAAATCCATTG 57.349 37.037 0.00 0.00 0.00 2.82
206 207 1.550072 TCTCGATCATCAAGTGTGGCA 59.450 47.619 0.00 0.00 0.00 4.92
214 215 6.238566 CGATCATCAAGTGTGGCATATCTTTT 60.239 38.462 0.00 0.00 0.00 2.27
277 469 4.337274 TGCATGTCATCAATTCATCCACTC 59.663 41.667 0.00 0.00 0.00 3.51
280 472 6.430308 GCATGTCATCAATTCATCCACTCTAT 59.570 38.462 0.00 0.00 0.00 1.98
286 478 9.828039 TCATCAATTCATCCACTCTATATATGC 57.172 33.333 0.00 0.00 0.00 3.14
287 479 9.609346 CATCAATTCATCCACTCTATATATGCA 57.391 33.333 0.00 0.00 0.00 3.96
346 539 8.532408 TTTGTCGTTGTAAGTTTTTAATCGAC 57.468 30.769 0.00 0.00 38.01 4.20
347 540 7.231705 TGTCGTTGTAAGTTTTTAATCGACA 57.768 32.000 11.44 11.44 40.94 4.35
531 741 4.864806 TCAGTTAATCTTGATGTCAGCGTC 59.135 41.667 0.00 0.00 0.00 5.19
534 744 5.877012 AGTTAATCTTGATGTCAGCGTCATT 59.123 36.000 0.00 0.00 40.03 2.57
535 745 4.611310 AATCTTGATGTCAGCGTCATTG 57.389 40.909 0.00 0.00 40.03 2.82
545 755 6.312399 TGTCAGCGTCATTGAAAAACTTAT 57.688 33.333 0.00 0.00 0.00 1.73
550 760 7.174253 TCAGCGTCATTGAAAAACTTATAAGGT 59.826 33.333 16.73 7.38 0.00 3.50
557 767 9.191995 CATTGAAAAACTTATAAGGTCAACACC 57.808 33.333 16.73 0.00 44.19 4.16
568 778 2.754472 GGTCAACACCTTTTGAATGCC 58.246 47.619 0.00 0.00 40.00 4.40
576 786 3.192422 CACCTTTTGAATGCCGACCATAA 59.808 43.478 0.00 0.00 32.67 1.90
588 798 3.213506 CCGACCATAAATCATGCTTGGA 58.786 45.455 0.00 0.00 32.84 3.53
591 801 4.096231 CGACCATAAATCATGCTTGGACAA 59.904 41.667 0.00 0.00 32.84 3.18
592 802 5.329035 ACCATAAATCATGCTTGGACAAC 57.671 39.130 0.00 0.00 32.84 3.32
597 807 1.241165 TCATGCTTGGACAACTGCAG 58.759 50.000 13.48 13.48 38.87 4.41
644 854 6.335777 CCTTCAAGGCCAAATCTTATCTTTG 58.664 40.000 5.01 0.00 34.17 2.77
652 862 9.205513 AGGCCAAATCTTATCTTTGACAAATAT 57.794 29.630 5.01 2.62 35.99 1.28
697 916 3.834489 ATTTTGTCACAATGCCCACAA 57.166 38.095 0.00 0.00 0.00 3.33
698 917 3.616956 TTTTGTCACAATGCCCACAAA 57.383 38.095 0.00 2.14 37.04 2.83
699 918 3.834489 TTTGTCACAATGCCCACAAAT 57.166 38.095 0.00 0.00 34.56 2.32
700 919 3.834489 TTGTCACAATGCCCACAAATT 57.166 38.095 0.00 0.00 0.00 1.82
701 920 3.834489 TGTCACAATGCCCACAAATTT 57.166 38.095 0.00 0.00 0.00 1.82
702 921 4.944619 TGTCACAATGCCCACAAATTTA 57.055 36.364 0.00 0.00 0.00 1.40
703 922 5.282055 TGTCACAATGCCCACAAATTTAA 57.718 34.783 0.00 0.00 0.00 1.52
704 923 5.862845 TGTCACAATGCCCACAAATTTAAT 58.137 33.333 0.00 0.00 0.00 1.40
705 924 6.294473 TGTCACAATGCCCACAAATTTAATT 58.706 32.000 0.00 0.00 0.00 1.40
706 925 6.426328 TGTCACAATGCCCACAAATTTAATTC 59.574 34.615 0.00 0.00 0.00 2.17
707 926 5.936956 TCACAATGCCCACAAATTTAATTCC 59.063 36.000 0.00 0.00 0.00 3.01
708 927 5.704515 CACAATGCCCACAAATTTAATTCCA 59.295 36.000 0.00 0.00 0.00 3.53
709 928 5.939296 ACAATGCCCACAAATTTAATTCCAG 59.061 36.000 0.00 0.00 0.00 3.86
710 929 4.550076 TGCCCACAAATTTAATTCCAGG 57.450 40.909 0.00 0.00 0.00 4.45
711 930 3.262915 TGCCCACAAATTTAATTCCAGGG 59.737 43.478 13.47 13.47 36.85 4.45
712 931 3.517500 GCCCACAAATTTAATTCCAGGGA 59.482 43.478 18.89 0.00 35.81 4.20
713 932 4.019771 GCCCACAAATTTAATTCCAGGGAA 60.020 41.667 18.89 2.75 35.81 3.97
714 933 5.513962 GCCCACAAATTTAATTCCAGGGAAA 60.514 40.000 18.89 0.00 37.69 3.13
715 934 6.720309 CCCACAAATTTAATTCCAGGGAAAT 58.280 36.000 4.63 0.00 37.69 2.17
716 935 6.598850 CCCACAAATTTAATTCCAGGGAAATG 59.401 38.462 4.63 0.00 37.69 2.32
717 936 7.167535 CCACAAATTTAATTCCAGGGAAATGT 58.832 34.615 4.63 0.00 37.69 2.71
718 937 7.665145 CCACAAATTTAATTCCAGGGAAATGTT 59.335 33.333 4.63 0.00 37.69 2.71
719 938 8.505625 CACAAATTTAATTCCAGGGAAATGTTG 58.494 33.333 4.63 6.75 37.69 3.33
720 939 8.217111 ACAAATTTAATTCCAGGGAAATGTTGT 58.783 29.630 4.63 7.28 37.69 3.32
721 940 8.505625 CAAATTTAATTCCAGGGAAATGTTGTG 58.494 33.333 4.63 0.00 37.69 3.33
722 941 5.736951 TTAATTCCAGGGAAATGTTGTGG 57.263 39.130 4.63 0.00 37.69 4.17
723 942 2.765689 TTCCAGGGAAATGTTGTGGT 57.234 45.000 0.00 0.00 0.00 4.16
724 943 1.993956 TCCAGGGAAATGTTGTGGTG 58.006 50.000 0.00 0.00 0.00 4.17
725 944 1.216678 TCCAGGGAAATGTTGTGGTGT 59.783 47.619 0.00 0.00 0.00 4.16
726 945 2.443632 TCCAGGGAAATGTTGTGGTGTA 59.556 45.455 0.00 0.00 0.00 2.90
727 946 2.819608 CCAGGGAAATGTTGTGGTGTAG 59.180 50.000 0.00 0.00 0.00 2.74
728 947 3.486383 CAGGGAAATGTTGTGGTGTAGT 58.514 45.455 0.00 0.00 0.00 2.73
729 948 4.505918 CCAGGGAAATGTTGTGGTGTAGTA 60.506 45.833 0.00 0.00 0.00 1.82
730 949 5.067273 CAGGGAAATGTTGTGGTGTAGTAA 58.933 41.667 0.00 0.00 0.00 2.24
731 950 5.181245 CAGGGAAATGTTGTGGTGTAGTAAG 59.819 44.000 0.00 0.00 0.00 2.34
732 951 5.072600 AGGGAAATGTTGTGGTGTAGTAAGA 59.927 40.000 0.00 0.00 0.00 2.10
733 952 5.944007 GGGAAATGTTGTGGTGTAGTAAGAT 59.056 40.000 0.00 0.00 0.00 2.40
734 953 7.037873 AGGGAAATGTTGTGGTGTAGTAAGATA 60.038 37.037 0.00 0.00 0.00 1.98
735 954 7.608761 GGGAAATGTTGTGGTGTAGTAAGATAA 59.391 37.037 0.00 0.00 0.00 1.75
736 955 8.448615 GGAAATGTTGTGGTGTAGTAAGATAAC 58.551 37.037 0.00 0.00 0.00 1.89
737 956 8.911918 AAATGTTGTGGTGTAGTAAGATAACA 57.088 30.769 0.00 0.00 0.00 2.41
738 957 7.900782 ATGTTGTGGTGTAGTAAGATAACAC 57.099 36.000 0.00 0.00 42.17 3.32
739 958 6.818233 TGTTGTGGTGTAGTAAGATAACACA 58.182 36.000 7.10 0.00 44.18 3.72
740 959 6.702723 TGTTGTGGTGTAGTAAGATAACACAC 59.297 38.462 7.10 0.00 44.18 3.82
758 1028 6.843069 ACACACCAATTTAATTGCAGAAAC 57.157 33.333 11.82 0.00 38.92 2.78
963 1255 7.148507 CCAAAAGTAGATCTGCAACACTTCTAG 60.149 40.741 13.64 4.66 0.00 2.43
967 1259 5.070770 AGATCTGCAACACTTCTAGTCTG 57.929 43.478 0.00 0.00 0.00 3.51
1012 1319 4.606255 TTTTCTCTAAAATGGGGAGTCCCT 59.394 41.667 27.69 10.20 40.50 4.20
1013 1320 5.281037 TTTTCTCTAAAATGGGGAGTCCCTC 60.281 44.000 27.69 17.70 40.50 4.30
1050 1360 2.974489 CTTTGCCGTCCTGCTGCTG 61.974 63.158 0.00 0.00 0.00 4.41
1130 1440 2.107041 ATCGACACGGGCAACTTCCA 62.107 55.000 0.00 0.00 0.00 3.53
1132 1442 2.203294 ACACGGGCAACTTCCACC 60.203 61.111 0.00 0.00 0.00 4.61
1280 1635 6.426633 TCACTCGTGCTTGATTTCTGAATTTA 59.573 34.615 0.00 0.00 0.00 1.40
1317 1684 4.666253 TTGGGGCTGCCACTGCTC 62.666 66.667 23.45 1.76 38.71 4.26
1326 1693 2.737180 CCACTGCTCACACCGAGT 59.263 61.111 0.00 0.00 44.33 4.18
1474 1844 0.391793 GGAGCTCGGTTCCTTCAAGG 60.392 60.000 7.83 0.00 36.46 3.61
1530 1901 8.273557 GGTACGTACTCATGCAACAAAATATAG 58.726 37.037 24.07 0.00 0.00 1.31
1600 2002 4.754114 CCTGCATTAGTCAGCTAATTCCTC 59.246 45.833 0.00 0.00 43.31 3.71
1613 2019 5.827797 AGCTAATTCCTCTTTTTGTGTGTGA 59.172 36.000 0.00 0.00 0.00 3.58
1614 2020 6.491403 AGCTAATTCCTCTTTTTGTGTGTGAT 59.509 34.615 0.00 0.00 0.00 3.06
1615 2021 7.014615 AGCTAATTCCTCTTTTTGTGTGTGATT 59.985 33.333 0.00 0.00 0.00 2.57
1616 2022 8.296713 GCTAATTCCTCTTTTTGTGTGTGATTA 58.703 33.333 0.00 0.00 0.00 1.75
1914 2326 1.614317 GGCTGCCTCAAGTGGTACAAT 60.614 52.381 12.43 0.00 44.16 2.71
2268 2680 2.749621 CCACGCTTGCTAGGAGAATTTT 59.250 45.455 0.00 0.00 0.00 1.82
2312 2727 3.689347 TGCTGCAACCAAGATCTGTTAT 58.311 40.909 0.00 0.00 0.00 1.89
2562 2982 1.125851 CATATACGCGCGCTCGTTG 59.874 57.895 31.39 19.12 43.15 4.10
2590 3010 2.507944 GCCTCACCTCGGCATGAT 59.492 61.111 0.00 0.00 46.77 2.45
2761 3216 3.578716 TCCCGTCTCTTTGTTTCATCTCT 59.421 43.478 0.00 0.00 0.00 3.10
2763 3218 4.322349 CCCGTCTCTTTGTTTCATCTCTCT 60.322 45.833 0.00 0.00 0.00 3.10
2767 3222 6.422100 CGTCTCTTTGTTTCATCTCTCTTCAA 59.578 38.462 0.00 0.00 0.00 2.69
2823 3285 0.738389 GTCGCTCCTCTCCAGAGAAG 59.262 60.000 5.08 0.00 44.74 2.85
2861 3324 0.673644 CATCACACCACCGAGTTCCC 60.674 60.000 0.00 0.00 0.00 3.97
2903 3366 3.574354 ATCTTCTCCATCCCAGCTTTC 57.426 47.619 0.00 0.00 0.00 2.62
2981 3444 1.000955 GTACGGGAGAATGGCGATGAT 59.999 52.381 0.00 0.00 0.00 2.45
3036 3503 5.255397 ACTCTTCATAATGGGTGGAACAA 57.745 39.130 0.00 0.00 44.16 2.83
3045 3512 2.181521 GGTGGAACAAACGCCGACA 61.182 57.895 0.00 0.00 44.16 4.35
3046 3513 1.512156 GGTGGAACAAACGCCGACAT 61.512 55.000 0.00 0.00 44.16 3.06
3121 3591 3.276091 TGACAACGCCAACGCCAG 61.276 61.111 0.00 0.00 45.53 4.85
3188 3659 6.395426 TTGTTTGAGATCATGCTGAGTTTT 57.605 33.333 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.010145 TCCTTCGCATACTTGTCAGC 57.990 50.000 0.00 0.00 0.00 4.26
23 24 5.793030 ATATGGGTAAGACTCTTCCTTCG 57.207 43.478 0.00 0.00 0.00 3.79
24 25 7.713073 CAGAAATATGGGTAAGACTCTTCCTTC 59.287 40.741 0.00 0.00 0.00 3.46
26 27 6.903534 TCAGAAATATGGGTAAGACTCTTCCT 59.096 38.462 0.00 0.00 0.00 3.36
27 28 7.125792 TCAGAAATATGGGTAAGACTCTTCC 57.874 40.000 0.00 0.00 0.00 3.46
87 88 3.742433 TGTGGCGAACATGGAAAATTT 57.258 38.095 0.00 0.00 32.36 1.82
127 128 7.584122 TTTCTAGAGGTATGTGATAGGACAC 57.416 40.000 0.00 0.00 40.68 3.67
128 129 7.451877 GGATTTCTAGAGGTATGTGATAGGACA 59.548 40.741 0.00 0.00 0.00 4.02
141 142 7.937700 TTAGATCCAATGGATTTCTAGAGGT 57.062 36.000 16.90 0.00 43.27 3.85
151 152 5.044328 CCCCATCTGATTAGATCCAATGGAT 60.044 44.000 15.71 15.71 46.28 3.41
189 190 4.313282 AGATATGCCACACTTGATGATCG 58.687 43.478 0.00 0.00 0.00 3.69
255 447 4.579340 AGAGTGGATGAATTGATGACATGC 59.421 41.667 0.00 0.00 34.02 4.06
256 448 7.981102 ATAGAGTGGATGAATTGATGACATG 57.019 36.000 0.00 0.00 0.00 3.21
286 478 7.120726 ACAAGATGACCATATATCATGCATGTG 59.879 37.037 25.43 15.73 36.92 3.21
287 479 7.173032 ACAAGATGACCATATATCATGCATGT 58.827 34.615 25.43 15.34 36.92 3.21
341 534 7.157347 AGTTAATGCTGATGTCATATGTCGAT 58.843 34.615 1.90 0.00 0.00 3.59
498 708 9.471702 ACATCAAGATTAACTGAGGAAATCATT 57.528 29.630 10.38 2.05 37.28 2.57
499 709 9.118300 GACATCAAGATTAACTGAGGAAATCAT 57.882 33.333 10.38 0.00 37.28 2.45
500 710 8.102676 TGACATCAAGATTAACTGAGGAAATCA 58.897 33.333 10.38 0.00 33.06 2.57
501 711 8.498054 TGACATCAAGATTAACTGAGGAAATC 57.502 34.615 3.52 2.02 0.00 2.17
531 741 9.191995 GGTGTTGACCTTATAAGTTTTTCAATG 57.808 33.333 11.50 0.00 39.47 2.82
550 760 2.034053 GTCGGCATTCAAAAGGTGTTGA 59.966 45.455 0.00 0.00 35.72 3.18
557 767 5.649557 TGATTTATGGTCGGCATTCAAAAG 58.350 37.500 0.00 0.00 0.00 2.27
568 778 3.627123 TGTCCAAGCATGATTTATGGTCG 59.373 43.478 0.00 0.00 46.27 4.79
576 786 2.230508 CTGCAGTTGTCCAAGCATGATT 59.769 45.455 5.25 0.00 36.28 2.57
624 834 6.271488 TGTCAAAGATAAGATTTGGCCTTG 57.729 37.500 3.32 0.00 40.67 3.61
627 837 9.822185 AATATTTGTCAAAGATAAGATTTGGCC 57.178 29.630 5.88 0.00 40.67 5.36
665 875 9.229784 GCATTGTGACAAAATATCTATCACTTG 57.770 33.333 0.62 0.00 40.28 3.16
697 916 7.167535 CCACAACATTTCCCTGGAATTAAATT 58.832 34.615 0.00 0.00 33.79 1.82
698 917 6.272090 ACCACAACATTTCCCTGGAATTAAAT 59.728 34.615 0.00 0.00 33.79 1.40
699 918 5.604650 ACCACAACATTTCCCTGGAATTAAA 59.395 36.000 0.00 0.00 33.79 1.52
700 919 5.011533 CACCACAACATTTCCCTGGAATTAA 59.988 40.000 0.00 0.00 33.79 1.40
701 920 4.526262 CACCACAACATTTCCCTGGAATTA 59.474 41.667 0.00 0.00 33.79 1.40
702 921 3.324556 CACCACAACATTTCCCTGGAATT 59.675 43.478 0.00 0.00 33.79 2.17
703 922 2.899256 CACCACAACATTTCCCTGGAAT 59.101 45.455 0.00 0.00 33.79 3.01
704 923 2.315176 CACCACAACATTTCCCTGGAA 58.685 47.619 0.00 0.00 0.00 3.53
705 924 1.216678 ACACCACAACATTTCCCTGGA 59.783 47.619 0.00 0.00 0.00 3.86
706 925 1.703411 ACACCACAACATTTCCCTGG 58.297 50.000 0.00 0.00 0.00 4.45
707 926 3.486383 ACTACACCACAACATTTCCCTG 58.514 45.455 0.00 0.00 0.00 4.45
708 927 3.876309 ACTACACCACAACATTTCCCT 57.124 42.857 0.00 0.00 0.00 4.20
709 928 5.310451 TCTTACTACACCACAACATTTCCC 58.690 41.667 0.00 0.00 0.00 3.97
710 929 8.448615 GTTATCTTACTACACCACAACATTTCC 58.551 37.037 0.00 0.00 0.00 3.13
711 930 8.995220 TGTTATCTTACTACACCACAACATTTC 58.005 33.333 0.00 0.00 0.00 2.17
712 931 8.780249 GTGTTATCTTACTACACCACAACATTT 58.220 33.333 0.00 0.00 36.93 2.32
713 932 7.934665 TGTGTTATCTTACTACACCACAACATT 59.065 33.333 0.00 0.00 41.03 2.71
714 933 7.386848 GTGTGTTATCTTACTACACCACAACAT 59.613 37.037 0.00 0.00 41.03 2.71
715 934 6.702723 GTGTGTTATCTTACTACACCACAACA 59.297 38.462 0.00 0.00 41.03 3.33
716 935 7.113704 GTGTGTTATCTTACTACACCACAAC 57.886 40.000 0.00 0.00 41.03 3.32
726 945 9.855021 GCAATTAAATTGGTGTGTTATCTTACT 57.145 29.630 0.00 0.00 40.57 2.24
727 946 9.632807 TGCAATTAAATTGGTGTGTTATCTTAC 57.367 29.630 0.00 0.00 40.57 2.34
728 947 9.853555 CTGCAATTAAATTGGTGTGTTATCTTA 57.146 29.630 0.00 0.00 40.57 2.10
729 948 8.584157 TCTGCAATTAAATTGGTGTGTTATCTT 58.416 29.630 0.00 0.00 40.57 2.40
730 949 8.121305 TCTGCAATTAAATTGGTGTGTTATCT 57.879 30.769 0.00 0.00 40.57 1.98
731 950 8.755696 TTCTGCAATTAAATTGGTGTGTTATC 57.244 30.769 0.00 0.00 40.57 1.75
732 951 8.987890 GTTTCTGCAATTAAATTGGTGTGTTAT 58.012 29.630 0.00 0.00 40.57 1.89
733 952 7.981789 TGTTTCTGCAATTAAATTGGTGTGTTA 59.018 29.630 0.00 0.00 40.57 2.41
734 953 6.820656 TGTTTCTGCAATTAAATTGGTGTGTT 59.179 30.769 0.00 0.00 40.57 3.32
735 954 6.257630 GTGTTTCTGCAATTAAATTGGTGTGT 59.742 34.615 0.00 0.00 40.57 3.72
736 955 6.479660 AGTGTTTCTGCAATTAAATTGGTGTG 59.520 34.615 0.00 0.00 40.57 3.82
737 956 6.479660 CAGTGTTTCTGCAATTAAATTGGTGT 59.520 34.615 0.00 0.00 40.57 4.16
738 957 6.879962 CAGTGTTTCTGCAATTAAATTGGTG 58.120 36.000 0.00 0.00 40.57 4.17
860 1151 5.009854 TGAGCGTGTATCAAGATGAATCA 57.990 39.130 0.00 0.00 0.00 2.57
864 1155 3.521560 GGTTGAGCGTGTATCAAGATGA 58.478 45.455 0.00 0.00 37.35 2.92
1009 1316 1.284841 AAGAGGAGGGCCAATGAGGG 61.285 60.000 6.18 0.00 38.09 4.30
1012 1319 0.846427 ACCAAGAGGAGGGCCAATGA 60.846 55.000 6.18 0.00 38.69 2.57
1013 1320 0.394899 GACCAAGAGGAGGGCCAATG 60.395 60.000 6.18 0.00 38.69 2.82
1014 1321 0.551131 AGACCAAGAGGAGGGCCAAT 60.551 55.000 6.18 0.00 38.69 3.16
1050 1360 0.739561 ACGACCCTAGATCAGCGTTC 59.260 55.000 0.00 0.00 0.00 3.95
1130 1440 1.983224 CTCCACATCGAACCTGGGT 59.017 57.895 0.00 0.00 0.00 4.51
1132 1442 1.450312 GGCTCCACATCGAACCTGG 60.450 63.158 0.00 0.00 0.00 4.45
1280 1635 2.537560 GCTTGCGCTGACACACACT 61.538 57.895 9.73 0.00 0.00 3.55
1305 1672 3.360340 GGTGTGAGCAGTGGCAGC 61.360 66.667 0.00 0.00 44.61 5.25
1326 1693 2.683933 GTCTTCTCCTCGGGCCCA 60.684 66.667 24.92 8.28 0.00 5.36
1355 1722 3.047877 CGAAGTTGGCACCGGTCC 61.048 66.667 2.59 10.36 0.00 4.46
1474 1844 2.202743 TATCCGTGCGAGCACTGC 60.203 61.111 23.39 0.00 44.16 4.40
1600 2002 6.129009 GCAGCTGATTAATCACACACAAAAAG 60.129 38.462 20.43 2.27 32.50 2.27
1613 2019 3.255642 ACGTTTGGTTGCAGCTGATTAAT 59.744 39.130 20.43 0.00 0.00 1.40
1614 2020 2.621055 ACGTTTGGTTGCAGCTGATTAA 59.379 40.909 20.43 6.13 0.00 1.40
1615 2021 2.225491 GACGTTTGGTTGCAGCTGATTA 59.775 45.455 20.43 0.00 0.00 1.75
1616 2022 1.001378 GACGTTTGGTTGCAGCTGATT 60.001 47.619 20.43 0.00 0.00 2.57
1843 2255 2.375174 TCTTGTGCCCACTCAGGTAAAT 59.625 45.455 0.00 0.00 34.66 1.40
1914 2326 1.334160 TGTGCTTCTGGGAGAACGTA 58.666 50.000 0.00 0.00 29.89 3.57
2268 2680 6.511767 GCAACATTTCTTCAAGTCTCGAAAGA 60.512 38.462 0.00 0.00 39.12 2.52
2312 2727 3.658757 AAAATTCCAAAAGCTAGCGCA 57.341 38.095 11.47 0.00 39.10 6.09
2761 3216 2.555123 GGCGAACTGGCATTGAAGA 58.445 52.632 0.00 0.00 44.08 2.87
2823 3285 0.248621 GCAAGTGTTGTCTGGTGTGC 60.249 55.000 0.00 0.00 0.00 4.57
2877 3340 3.135530 GCTGGGATGGAGAAGATTGTAGT 59.864 47.826 0.00 0.00 0.00 2.73
2981 3444 2.875672 GCAGAGCACTACCCACAAATGA 60.876 50.000 0.00 0.00 0.00 2.57
3036 3503 0.953960 GGGAAGTGAATGTCGGCGTT 60.954 55.000 6.85 0.00 0.00 4.84
3045 3512 1.214589 CGTCGTCGGGGAAGTGAAT 59.785 57.895 0.00 0.00 0.00 2.57
3046 3513 1.898094 TCGTCGTCGGGGAAGTGAA 60.898 57.895 1.55 0.00 37.69 3.18
3121 3591 3.652539 ATGGCAGTTGCATTGGCGC 62.653 57.895 16.83 0.00 45.35 6.53
3188 3659 9.755804 CATATCTAGAACAGATGCTAGAACAAA 57.244 33.333 0.00 0.00 44.33 2.83


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

AutoCloner maintained by Alex Coulton.