Multiple sequence alignment - TraesCS7B01G058500

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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 TraesCS7B01G058500 chr7B 100.000 3638 0 0 1 3638 61080173 61076536 0.000000e+00 6719.0
1 TraesCS7B01G058500 chr7B 90.044 683 61 5 2957 3637 4492310 4492987 0.000000e+00 878.0
2 TraesCS7B01G058500 chr7A 91.584 2923 139 54 5 2866 107795230 107792354 0.000000e+00 3936.0
3 TraesCS7B01G058500 chr7D 94.348 2247 86 18 539 2771 102902742 102900523 0.000000e+00 3408.0
4 TraesCS7B01G058500 chr7D 88.107 412 20 11 91 489 102903145 102902750 2.560000e-126 462.0
5 TraesCS7B01G058500 chr7D 83.721 86 14 0 5 90 102903422 102903337 8.370000e-12 82.4
6 TraesCS7B01G058500 chr5B 88.619 1608 138 36 997 2587 616439743 616438164 0.000000e+00 1914.0
7 TraesCS7B01G058500 chr5D 88.195 1618 145 25 997 2586 497493230 497491631 0.000000e+00 1888.0
8 TraesCS7B01G058500 chr5A 87.916 1622 151 24 997 2600 621540391 621538797 0.000000e+00 1868.0
9 TraesCS7B01G058500 chr6B 89.296 682 69 4 2959 3637 289525293 289524613 0.000000e+00 852.0
10 TraesCS7B01G058500 chr1B 87.844 691 76 7 2952 3637 291472101 291471414 0.000000e+00 804.0
11 TraesCS7B01G058500 chrUn 85.714 672 92 4 2968 3637 213167060 213166391 0.000000e+00 706.0
12 TraesCS7B01G058500 chrUn 85.565 672 93 4 2968 3637 213179684 213179015 0.000000e+00 701.0
13 TraesCS7B01G058500 chr1A 85.714 672 92 4 2968 3637 6813086 6813755 0.000000e+00 706.0
14 TraesCS7B01G058500 chr1A 85.714 672 92 4 2968 3637 6831858 6832527 0.000000e+00 706.0
15 TraesCS7B01G058500 chr1A 85.714 672 92 4 2968 3637 6846641 6847310 0.000000e+00 706.0
16 TraesCS7B01G058500 chr1A 85.544 671 93 4 2968 3636 6800017 6800685 0.000000e+00 699.0
17 TraesCS7B01G058500 chr1A 71.523 1359 314 59 1215 2529 580988492 580989821 7.640000e-77 298.0
18 TraesCS7B01G058500 chr2D 73.452 1292 273 52 1214 2461 147968257 147966992 4.340000e-114 422.0
19 TraesCS7B01G058500 chr2A 72.847 1289 286 46 1214 2461 154413987 154415252 2.050000e-102 383.0
20 TraesCS7B01G058500 chr1D 71.196 1354 327 52 1215 2529 483972824 483974153 7.690000e-72 281.0


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 TraesCS7B01G058500 chr7B 61076536 61080173 3637 True 6719.000000 6719 100.000000 1 3638 1 chr7B.!!$R1 3637
1 TraesCS7B01G058500 chr7B 4492310 4492987 677 False 878.000000 878 90.044000 2957 3637 1 chr7B.!!$F1 680
2 TraesCS7B01G058500 chr7A 107792354 107795230 2876 True 3936.000000 3936 91.584000 5 2866 1 chr7A.!!$R1 2861
3 TraesCS7B01G058500 chr7D 102900523 102903422 2899 True 1317.466667 3408 88.725333 5 2771 3 chr7D.!!$R1 2766
4 TraesCS7B01G058500 chr5B 616438164 616439743 1579 True 1914.000000 1914 88.619000 997 2587 1 chr5B.!!$R1 1590
5 TraesCS7B01G058500 chr5D 497491631 497493230 1599 True 1888.000000 1888 88.195000 997 2586 1 chr5D.!!$R1 1589
6 TraesCS7B01G058500 chr5A 621538797 621540391 1594 True 1868.000000 1868 87.916000 997 2600 1 chr5A.!!$R1 1603
7 TraesCS7B01G058500 chr6B 289524613 289525293 680 True 852.000000 852 89.296000 2959 3637 1 chr6B.!!$R1 678
8 TraesCS7B01G058500 chr1B 291471414 291472101 687 True 804.000000 804 87.844000 2952 3637 1 chr1B.!!$R1 685
9 TraesCS7B01G058500 chrUn 213166391 213167060 669 True 706.000000 706 85.714000 2968 3637 1 chrUn.!!$R1 669
10 TraesCS7B01G058500 chrUn 213179015 213179684 669 True 701.000000 701 85.565000 2968 3637 1 chrUn.!!$R2 669
11 TraesCS7B01G058500 chr1A 6813086 6813755 669 False 706.000000 706 85.714000 2968 3637 1 chr1A.!!$F2 669
12 TraesCS7B01G058500 chr1A 6831858 6832527 669 False 706.000000 706 85.714000 2968 3637 1 chr1A.!!$F3 669
13 TraesCS7B01G058500 chr1A 6846641 6847310 669 False 706.000000 706 85.714000 2968 3637 1 chr1A.!!$F4 669
14 TraesCS7B01G058500 chr1A 6800017 6800685 668 False 699.000000 699 85.544000 2968 3636 1 chr1A.!!$F1 668
15 TraesCS7B01G058500 chr1A 580988492 580989821 1329 False 298.000000 298 71.523000 1215 2529 1 chr1A.!!$F5 1314
16 TraesCS7B01G058500 chr2D 147966992 147968257 1265 True 422.000000 422 73.452000 1214 2461 1 chr2D.!!$R1 1247
17 TraesCS7B01G058500 chr2A 154413987 154415252 1265 False 383.000000 383 72.847000 1214 2461 1 chr2A.!!$F1 1247
18 TraesCS7B01G058500 chr1D 483972824 483974153 1329 False 281.000000 281 71.196000 1215 2529 1 chr1D.!!$F1 1314

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
322 517 0.103572 ACACTCGTTGGCTGTACGTT 59.896 50.0 0.0 0.0 39.84 3.99 F
462 670 0.108186 CACTAATGCTCGCTGTCCCA 60.108 55.0 0.0 0.0 0.00 4.37 F
1593 1854 0.321122 GCTTCGGCATCCTCATAGGG 60.321 60.0 0.0 0.0 41.33 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 2027 0.927537 CGTCGTGTTGCAGACTTTCA 59.072 50.0 2.77 0.0 35.38 2.69 R
1947 2232 2.611473 CGTCAGATGCTGGAAGAAGTGT 60.611 50.0 0.00 0.0 34.07 3.55 R
3451 3753 0.667993 CACCGCACAACAATGTTCCT 59.332 50.0 0.00 0.0 37.82 3.36 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
31 34 9.271921 AGAAGATTTAAAATCTTAAGGCCCATT 57.728 29.630 0.00 0.00 38.38 3.16
64 67 9.173021 CACCCATGTTCAGAATACAAAACTATA 57.827 33.333 0.00 0.00 0.00 1.31
69 72 8.821147 TGTTCAGAATACAAAACTATACACGT 57.179 30.769 0.00 0.00 0.00 4.49
72 75 8.915871 TCAGAATACAAAACTATACACGTACC 57.084 34.615 0.00 0.00 0.00 3.34
81 84 9.793252 CAAAACTATACACGTACCACTAACTAT 57.207 33.333 0.00 0.00 0.00 2.12
87 90 6.519679 ACACGTACCACTAACTATTGATCA 57.480 37.500 0.00 0.00 0.00 2.92
125 320 7.197071 TGTATTACAAAACAGTCGATTTGCT 57.803 32.000 8.72 1.15 38.18 3.91
126 321 7.644490 TGTATTACAAAACAGTCGATTTGCTT 58.356 30.769 8.72 0.00 38.18 3.91
127 322 6.991485 ATTACAAAACAGTCGATTTGCTTG 57.009 33.333 8.72 9.98 38.18 4.01
128 323 4.370364 ACAAAACAGTCGATTTGCTTGT 57.630 36.364 8.72 10.47 38.18 3.16
129 324 4.351192 ACAAAACAGTCGATTTGCTTGTC 58.649 39.130 8.72 0.00 38.18 3.18
130 325 3.626028 AAACAGTCGATTTGCTTGTCC 57.374 42.857 0.00 0.00 0.00 4.02
131 326 1.523758 ACAGTCGATTTGCTTGTCCC 58.476 50.000 0.00 0.00 0.00 4.46
154 349 3.279853 TCGATCGCTCTCATCTGAATG 57.720 47.619 11.09 0.00 0.00 2.67
262 457 1.359848 CCACTGTGCTATCGTCCAAC 58.640 55.000 1.29 0.00 0.00 3.77
287 482 3.567397 AGCGTCCAAGATATACCTCACT 58.433 45.455 0.00 0.00 0.00 3.41
315 510 0.393077 AGCTGTTACACTCGTTGGCT 59.607 50.000 0.00 0.00 0.00 4.75
316 511 0.512952 GCTGTTACACTCGTTGGCTG 59.487 55.000 0.00 0.00 0.00 4.85
317 512 1.865865 CTGTTACACTCGTTGGCTGT 58.134 50.000 0.00 0.00 0.00 4.40
318 513 2.864882 GCTGTTACACTCGTTGGCTGTA 60.865 50.000 0.00 0.00 0.00 2.74
319 514 2.729882 CTGTTACACTCGTTGGCTGTAC 59.270 50.000 0.00 0.00 0.00 2.90
320 515 1.717645 GTTACACTCGTTGGCTGTACG 59.282 52.381 0.00 0.00 40.23 3.67
321 516 0.953727 TACACTCGTTGGCTGTACGT 59.046 50.000 0.00 0.00 39.84 3.57
322 517 0.103572 ACACTCGTTGGCTGTACGTT 59.896 50.000 0.00 0.00 39.84 3.99
323 518 0.506932 CACTCGTTGGCTGTACGTTG 59.493 55.000 0.00 0.00 39.84 4.10
383 580 6.291849 CGCACTAGTATTTCTCCAAATCTTCG 60.292 42.308 0.00 0.00 33.95 3.79
395 592 3.674753 CCAAATCTTCGTGAACAAATGCC 59.325 43.478 0.00 0.00 0.00 4.40
399 596 0.309302 TTCGTGAACAAATGCCGTGG 59.691 50.000 0.00 0.00 0.00 4.94
426 627 1.204146 GCCCCTCTTGGTGATGTAGA 58.796 55.000 0.00 0.00 0.00 2.59
427 628 1.771255 GCCCCTCTTGGTGATGTAGAT 59.229 52.381 0.00 0.00 0.00 1.98
428 629 2.173569 GCCCCTCTTGGTGATGTAGATT 59.826 50.000 0.00 0.00 0.00 2.40
429 630 3.745797 GCCCCTCTTGGTGATGTAGATTC 60.746 52.174 0.00 0.00 0.00 2.52
462 670 0.108186 CACTAATGCTCGCTGTCCCA 60.108 55.000 0.00 0.00 0.00 4.37
492 704 3.831715 AGGCGTAATCTTTCTTGCAAC 57.168 42.857 0.00 0.00 0.00 4.17
495 707 3.426292 GGCGTAATCTTTCTTGCAACCTC 60.426 47.826 0.00 0.00 0.00 3.85
563 775 3.929955 TTGACATCTCCATATGGCACA 57.070 42.857 17.58 3.24 44.60 4.57
568 780 8.801891 TTGACATCTCCATATGGCACAGTCAG 62.802 46.154 25.10 15.02 44.60 3.51
646 866 1.298993 CATCACCACTGCAGCCTCT 59.701 57.895 15.27 0.00 0.00 3.69
657 877 1.242076 GCAGCCTCTCAAACACATGT 58.758 50.000 0.00 0.00 0.00 3.21
750 974 3.632145 TCTTGTTCACTCTTTTCTTGGGC 59.368 43.478 0.00 0.00 0.00 5.36
751 975 1.946768 TGTTCACTCTTTTCTTGGGCG 59.053 47.619 0.00 0.00 0.00 6.13
752 976 1.947456 GTTCACTCTTTTCTTGGGCGT 59.053 47.619 0.00 0.00 0.00 5.68
753 977 1.593196 TCACTCTTTTCTTGGGCGTG 58.407 50.000 0.00 0.00 0.00 5.34
757 981 3.192954 CTTTTCTTGGGCGTGCGCA 62.193 57.895 18.36 5.66 44.11 6.09
758 982 2.476534 CTTTTCTTGGGCGTGCGCAT 62.477 55.000 15.91 0.00 44.11 4.73
759 983 2.470801 TTTTCTTGGGCGTGCGCATC 62.471 55.000 15.91 8.93 44.11 3.91
760 984 4.695993 TCTTGGGCGTGCGCATCA 62.696 61.111 15.91 7.52 44.11 3.07
761 985 3.736100 CTTGGGCGTGCGCATCAA 61.736 61.111 15.91 14.87 44.11 2.57
762 986 3.266230 CTTGGGCGTGCGCATCAAA 62.266 57.895 15.91 5.67 44.11 2.69
763 987 3.550339 TTGGGCGTGCGCATCAAAC 62.550 57.895 15.91 4.08 44.11 2.93
764 988 3.737172 GGGCGTGCGCATCAAACT 61.737 61.111 15.91 0.00 44.11 2.66
765 989 2.502510 GGCGTGCGCATCAAACTG 60.503 61.111 15.91 0.00 44.11 3.16
766 990 2.555782 GCGTGCGCATCAAACTGA 59.444 55.556 15.91 0.00 41.49 3.41
876 1100 4.868900 GGCGTGCTTATGCGTGCG 62.869 66.667 9.68 8.50 43.34 5.34
920 1144 8.068380 GGCTCGTGATTGATTATTAAACTAACC 58.932 37.037 0.00 0.00 0.00 2.85
940 1167 4.003648 ACCAGCTAGTAGTTCATGTTTGC 58.996 43.478 0.00 0.00 0.00 3.68
995 1223 4.029809 GACCACGGTGGGGAAGGG 62.030 72.222 29.44 4.48 43.37 3.95
1054 1285 4.431524 ATGGGGGCGGGAGGAAGA 62.432 66.667 0.00 0.00 0.00 2.87
1055 1286 3.962530 ATGGGGGCGGGAGGAAGAA 62.963 63.158 0.00 0.00 0.00 2.52
1059 1290 3.387947 GGCGGGAGGAAGAACGGA 61.388 66.667 0.00 0.00 0.00 4.69
1095 1326 2.507944 GCCTGCTCCATCATCGGT 59.492 61.111 0.00 0.00 0.00 4.69
1134 1369 1.741770 GGGCTACGGTGAGCACAAG 60.742 63.158 8.27 0.00 45.76 3.16
1147 1382 1.284198 AGCACAAGGGAGCATCATCTT 59.716 47.619 0.00 0.00 36.25 2.40
1150 1385 3.349927 CACAAGGGAGCATCATCTTCAA 58.650 45.455 0.00 0.00 36.25 2.69
1195 1450 0.937304 CGATGGAGCGTGTTAATGGG 59.063 55.000 0.00 0.00 0.00 4.00
1407 1668 4.161295 TGCATCTTCCTCGCCGGG 62.161 66.667 2.18 0.00 0.00 5.73
1503 1764 3.401411 GCTCTCATGATCGCGCCG 61.401 66.667 0.00 0.00 0.00 6.46
1593 1854 0.321122 GCTTCGGCATCCTCATAGGG 60.321 60.000 0.00 0.00 41.33 3.53
1740 2001 4.147449 CTCGTCATGCAGGGCCGA 62.147 66.667 12.16 12.16 0.00 5.54
1766 2027 2.048127 GGCGCTCGTTGTTCTCCT 60.048 61.111 7.64 0.00 0.00 3.69
1783 2044 1.138069 TCCTGAAAGTCTGCAACACGA 59.862 47.619 0.00 0.00 0.00 4.35
2691 2978 1.128692 GTGTTTGACGCTATCTGTGCC 59.871 52.381 0.00 0.00 0.00 5.01
2738 3025 4.042062 ACATGAACTGTTCAGGAGATGGAA 59.958 41.667 33.62 7.18 43.68 3.53
2749 3036 5.634118 TCAGGAGATGGAAAAGTGAATTGT 58.366 37.500 0.00 0.00 0.00 2.71
2785 3075 4.954092 AGCTTTTATAGTGCTGCACTTC 57.046 40.909 36.80 17.88 42.59 3.01
2796 3086 1.880646 GCTGCACTTCGGAGGGTTTAA 60.881 52.381 0.00 0.00 32.67 1.52
2803 3097 4.700213 CACTTCGGAGGGTTTAAACATGAT 59.300 41.667 19.57 2.45 0.00 2.45
2804 3098 5.183140 CACTTCGGAGGGTTTAAACATGATT 59.817 40.000 19.57 0.00 0.00 2.57
2866 3162 3.990469 CCCTGACTTATCCAAATCGATCG 59.010 47.826 9.36 9.36 0.00 3.69
2867 3163 4.501571 CCCTGACTTATCCAAATCGATCGT 60.502 45.833 15.94 0.00 0.00 3.73
2868 3164 5.050490 CCTGACTTATCCAAATCGATCGTT 58.950 41.667 15.94 3.47 0.00 3.85
2869 3165 6.213677 CCTGACTTATCCAAATCGATCGTTA 58.786 40.000 15.94 0.00 0.00 3.18
2870 3166 6.700081 CCTGACTTATCCAAATCGATCGTTAA 59.300 38.462 15.94 0.00 0.00 2.01
2871 3167 7.306632 CCTGACTTATCCAAATCGATCGTTAAC 60.307 40.741 15.94 0.00 0.00 2.01
2872 3168 7.262772 TGACTTATCCAAATCGATCGTTAACT 58.737 34.615 15.94 0.00 0.00 2.24
2873 3169 7.762615 TGACTTATCCAAATCGATCGTTAACTT 59.237 33.333 15.94 0.00 0.00 2.66
2874 3170 8.488651 ACTTATCCAAATCGATCGTTAACTTT 57.511 30.769 15.94 5.89 0.00 2.66
2875 3171 8.388103 ACTTATCCAAATCGATCGTTAACTTTG 58.612 33.333 15.94 15.81 0.00 2.77
2876 3172 6.978343 ATCCAAATCGATCGTTAACTTTGA 57.022 33.333 15.94 7.32 0.00 2.69
2877 3173 6.403333 TCCAAATCGATCGTTAACTTTGAG 57.597 37.500 15.94 11.29 0.00 3.02
2878 3174 6.160684 TCCAAATCGATCGTTAACTTTGAGA 58.839 36.000 15.94 12.87 0.00 3.27
2879 3175 6.647481 TCCAAATCGATCGTTAACTTTGAGAA 59.353 34.615 15.94 5.63 0.00 2.87
2880 3176 6.955963 CCAAATCGATCGTTAACTTTGAGAAG 59.044 38.462 15.94 3.32 38.87 2.85
2881 3177 7.148639 CCAAATCGATCGTTAACTTTGAGAAGA 60.149 37.037 15.94 5.06 36.69 2.87
2882 3178 7.513190 AATCGATCGTTAACTTTGAGAAGAG 57.487 36.000 15.94 0.00 36.69 2.85
2883 3179 4.857588 TCGATCGTTAACTTTGAGAAGAGC 59.142 41.667 15.94 0.00 36.69 4.09
2884 3180 4.621460 CGATCGTTAACTTTGAGAAGAGCA 59.379 41.667 7.03 0.00 36.69 4.26
2885 3181 5.289675 CGATCGTTAACTTTGAGAAGAGCAT 59.710 40.000 7.03 0.00 36.69 3.79
2886 3182 6.183360 CGATCGTTAACTTTGAGAAGAGCATT 60.183 38.462 7.03 0.00 36.69 3.56
2887 3183 6.861065 TCGTTAACTTTGAGAAGAGCATTT 57.139 33.333 3.71 0.00 36.69 2.32
2888 3184 6.658831 TCGTTAACTTTGAGAAGAGCATTTG 58.341 36.000 3.71 0.00 36.69 2.32
2889 3185 6.481976 TCGTTAACTTTGAGAAGAGCATTTGA 59.518 34.615 3.71 0.00 36.69 2.69
2890 3186 7.011950 TCGTTAACTTTGAGAAGAGCATTTGAA 59.988 33.333 3.71 0.00 36.69 2.69
2891 3187 7.112148 CGTTAACTTTGAGAAGAGCATTTGAAC 59.888 37.037 3.71 0.00 36.69 3.18
2892 3188 6.705863 AACTTTGAGAAGAGCATTTGAACT 57.294 33.333 0.00 0.00 36.69 3.01
2893 3189 6.069684 ACTTTGAGAAGAGCATTTGAACTG 57.930 37.500 0.00 0.00 36.69 3.16
2894 3190 5.591877 ACTTTGAGAAGAGCATTTGAACTGT 59.408 36.000 0.00 0.00 36.69 3.55
2895 3191 5.428496 TTGAGAAGAGCATTTGAACTGTG 57.572 39.130 0.00 0.00 0.00 3.66
2896 3192 4.454678 TGAGAAGAGCATTTGAACTGTGT 58.545 39.130 0.00 0.00 0.00 3.72
2897 3193 4.883585 TGAGAAGAGCATTTGAACTGTGTT 59.116 37.500 0.00 0.00 0.00 3.32
2898 3194 6.054941 TGAGAAGAGCATTTGAACTGTGTTA 58.945 36.000 0.00 0.00 0.00 2.41
2899 3195 6.712095 TGAGAAGAGCATTTGAACTGTGTTAT 59.288 34.615 0.00 0.00 0.00 1.89
2900 3196 7.877612 TGAGAAGAGCATTTGAACTGTGTTATA 59.122 33.333 0.00 0.00 0.00 0.98
2901 3197 8.034058 AGAAGAGCATTTGAACTGTGTTATAC 57.966 34.615 0.00 0.00 0.00 1.47
2902 3198 7.880195 AGAAGAGCATTTGAACTGTGTTATACT 59.120 33.333 0.00 0.00 0.00 2.12
2903 3199 9.151471 GAAGAGCATTTGAACTGTGTTATACTA 57.849 33.333 0.00 0.00 0.00 1.82
2904 3200 9.672673 AAGAGCATTTGAACTGTGTTATACTAT 57.327 29.630 0.00 0.00 0.00 2.12
2905 3201 9.319143 AGAGCATTTGAACTGTGTTATACTATC 57.681 33.333 0.00 0.00 0.00 2.08
2906 3202 8.438676 AGCATTTGAACTGTGTTATACTATCC 57.561 34.615 0.00 0.00 0.00 2.59
2907 3203 8.267894 AGCATTTGAACTGTGTTATACTATCCT 58.732 33.333 0.00 0.00 0.00 3.24
2908 3204 9.542462 GCATTTGAACTGTGTTATACTATCCTA 57.458 33.333 0.00 0.00 0.00 2.94
2928 3224 7.179076 TCCTATTTGGAAGTACTACAAGTCC 57.821 40.000 10.25 7.38 42.94 3.85
2929 3225 6.958192 TCCTATTTGGAAGTACTACAAGTCCT 59.042 38.462 11.04 0.00 42.94 3.85
2930 3226 8.117956 TCCTATTTGGAAGTACTACAAGTCCTA 58.882 37.037 11.04 2.09 42.94 2.94
2931 3227 8.755977 CCTATTTGGAAGTACTACAAGTCCTAA 58.244 37.037 11.04 10.00 38.35 2.69
2936 3232 8.890410 TGGAAGTACTACAAGTCCTAAATAGT 57.110 34.615 11.04 0.00 0.00 2.12
2937 3233 9.979897 TGGAAGTACTACAAGTCCTAAATAGTA 57.020 33.333 11.04 0.00 0.00 1.82
2950 3246 9.884814 AGTCCTAAATAGTATAATCTCCACTGT 57.115 33.333 0.00 0.00 0.00 3.55
3006 3302 1.361204 TGGAGCCCTCTTGTTGATCA 58.639 50.000 0.00 0.00 0.00 2.92
3024 3320 5.323581 TGATCATGGACTTTGGTCAAATGA 58.676 37.500 12.61 12.61 43.99 2.57
3066 3362 7.398829 TGGTTTTCTAGCCAATGATTACTACA 58.601 34.615 0.00 0.00 0.00 2.74
3120 3417 9.657419 AAAACTGATTTTCTTGACTTGATTGTT 57.343 25.926 0.00 0.00 32.29 2.83
3123 3420 7.026631 TGATTTTCTTGACTTGATTGTTCGT 57.973 32.000 0.00 0.00 0.00 3.85
3230 3529 9.246423 CACGTGTTCGAATTAAACATAAGTAAG 57.754 33.333 7.58 0.83 38.75 2.34
3248 3548 1.392589 AGCATTAAATGGCCGGTCAG 58.607 50.000 16.89 0.00 0.00 3.51
3249 3549 1.102978 GCATTAAATGGCCGGTCAGT 58.897 50.000 16.89 9.89 0.00 3.41
3324 3626 1.488705 CCTCCCAACCACCTAGCACA 61.489 60.000 0.00 0.00 0.00 4.57
3347 3649 0.460311 CCCTAGGTGTCACCATCGTC 59.540 60.000 24.02 0.00 41.95 4.20
3348 3650 1.182667 CCTAGGTGTCACCATCGTCA 58.817 55.000 24.02 1.15 41.95 4.35
3381 3683 1.136500 GTAAGGTCTACGAAGGCTGGG 59.864 57.143 0.00 0.00 0.00 4.45
3451 3753 1.985159 CCTACAGCCTATGCCCCATTA 59.015 52.381 0.00 0.00 38.69 1.90
3469 3771 2.264005 TAGGAACATTGTTGTGCGGT 57.736 45.000 6.80 0.00 35.83 5.68
3592 3894 2.755876 TCCGCGTGCTCCTCAGAT 60.756 61.111 4.92 0.00 0.00 2.90
3618 3920 3.160585 CTGTCCCCAGTGCTCCAA 58.839 61.111 0.00 0.00 33.80 3.53
3637 3939 0.338120 AGTAGGCCTCCTCTTGCTCT 59.662 55.000 9.68 0.00 34.61 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.936329 TGGGCCTTAAGATTTTAAATCTTCTAT 57.064 29.630 29.12 13.64 39.01 1.98
64 67 6.519679 TGATCAATAGTTAGTGGTACGTGT 57.480 37.500 0.00 0.00 0.00 4.49
72 75 5.008019 GGCACCACATGATCAATAGTTAGTG 59.992 44.000 0.00 9.90 0.00 2.74
81 84 1.992538 TGTTGGCACCACATGATCAA 58.007 45.000 0.00 0.00 0.00 2.57
87 90 4.339748 TGTAATACATGTTGGCACCACAT 58.660 39.130 2.30 0.00 0.00 3.21
125 320 1.153901 GAGCGATCGAACGGGACAA 60.154 57.895 21.57 0.00 0.00 3.18
126 321 1.989966 GAGAGCGATCGAACGGGACA 61.990 60.000 21.57 0.00 0.00 4.02
127 322 1.298488 GAGAGCGATCGAACGGGAC 60.298 63.158 21.57 0.00 0.00 4.46
128 323 1.101635 ATGAGAGCGATCGAACGGGA 61.102 55.000 21.57 0.00 0.00 5.14
129 324 0.661780 GATGAGAGCGATCGAACGGG 60.662 60.000 21.57 0.00 0.00 5.28
130 325 0.309302 AGATGAGAGCGATCGAACGG 59.691 55.000 21.57 0.00 0.00 4.44
131 326 1.003438 TCAGATGAGAGCGATCGAACG 60.003 52.381 21.57 11.09 0.00 3.95
154 349 5.237048 TCCTTTCTTTATTTTGCATGTGGC 58.763 37.500 0.00 0.00 45.13 5.01
166 361 7.762159 TGTTTTCGTTTTTGCTCCTTTCTTTAT 59.238 29.630 0.00 0.00 0.00 1.40
167 362 7.091443 TGTTTTCGTTTTTGCTCCTTTCTTTA 58.909 30.769 0.00 0.00 0.00 1.85
171 366 5.347635 ACTTGTTTTCGTTTTTGCTCCTTTC 59.652 36.000 0.00 0.00 0.00 2.62
262 457 3.978687 AGGTATATCTTGGACGCTTTCG 58.021 45.455 0.00 0.00 42.43 3.46
287 482 4.617808 GAGTGTAACAGCTCAGTCGATA 57.382 45.455 0.00 0.00 41.43 2.92
315 510 2.006169 CATGCATACAGCCAACGTACA 58.994 47.619 0.00 0.00 44.83 2.90
316 511 1.330521 CCATGCATACAGCCAACGTAC 59.669 52.381 0.00 0.00 44.83 3.67
317 512 1.662517 CCATGCATACAGCCAACGTA 58.337 50.000 0.00 0.00 44.83 3.57
318 513 1.656818 GCCATGCATACAGCCAACGT 61.657 55.000 0.00 0.00 44.83 3.99
319 514 1.064621 GCCATGCATACAGCCAACG 59.935 57.895 0.00 0.00 44.83 4.10
320 515 0.179129 GTGCCATGCATACAGCCAAC 60.179 55.000 0.00 0.00 41.91 3.77
321 516 1.321805 GGTGCCATGCATACAGCCAA 61.322 55.000 16.38 0.00 41.91 4.52
322 517 1.753848 GGTGCCATGCATACAGCCA 60.754 57.895 16.38 1.06 41.91 4.75
323 518 0.179020 TAGGTGCCATGCATACAGCC 60.179 55.000 21.12 15.29 41.91 4.85
383 580 2.030363 TGAATCCACGGCATTTGTTCAC 60.030 45.455 0.00 0.00 0.00 3.18
395 592 1.526917 GAGGGGCCATGAATCCACG 60.527 63.158 4.39 0.00 0.00 4.94
399 596 0.259938 ACCAAGAGGGGCCATGAATC 59.740 55.000 4.39 0.00 42.91 2.52
426 627 6.459066 CATTAGTGTGGATGGATACGAGAAT 58.541 40.000 0.00 0.00 42.51 2.40
427 628 5.739070 GCATTAGTGTGGATGGATACGAGAA 60.739 44.000 0.00 0.00 42.51 2.87
428 629 4.262036 GCATTAGTGTGGATGGATACGAGA 60.262 45.833 0.00 0.00 42.51 4.04
429 630 3.990469 GCATTAGTGTGGATGGATACGAG 59.010 47.826 0.00 0.00 42.51 4.18
462 670 1.751924 AGATTACGCCTTCGCTTCTCT 59.248 47.619 0.00 0.00 39.84 3.10
563 775 2.105477 ACACTTGCAGATGGAACTGACT 59.895 45.455 0.00 0.00 39.94 3.41
594 806 0.329931 ACCACCACCACTGTTGACAA 59.670 50.000 0.00 0.00 0.00 3.18
646 866 1.675483 GAGTGGTGCACATGTGTTTGA 59.325 47.619 26.01 6.68 36.74 2.69
750 974 1.393196 TGTATCAGTTTGATGCGCACG 59.607 47.619 14.90 0.00 41.50 5.34
751 975 2.416547 ACTGTATCAGTTTGATGCGCAC 59.583 45.455 14.90 7.75 42.59 5.34
752 976 2.416202 CACTGTATCAGTTTGATGCGCA 59.584 45.455 14.96 14.96 42.59 6.09
753 977 2.223112 CCACTGTATCAGTTTGATGCGC 60.223 50.000 0.00 0.00 42.59 6.09
757 981 3.002791 CACGCCACTGTATCAGTTTGAT 58.997 45.455 0.00 0.00 42.59 2.57
758 982 2.412870 CACGCCACTGTATCAGTTTGA 58.587 47.619 0.00 0.00 42.59 2.69
759 983 1.135972 GCACGCCACTGTATCAGTTTG 60.136 52.381 0.00 0.00 42.59 2.93
760 984 1.156736 GCACGCCACTGTATCAGTTT 58.843 50.000 0.00 0.00 42.59 2.66
761 985 1.014044 CGCACGCCACTGTATCAGTT 61.014 55.000 0.00 0.00 42.59 3.16
762 986 1.446099 CGCACGCCACTGTATCAGT 60.446 57.895 0.00 0.00 46.51 3.41
763 987 2.802667 GCGCACGCCACTGTATCAG 61.803 63.158 0.30 0.00 34.64 2.90
764 988 2.813474 GCGCACGCCACTGTATCA 60.813 61.111 0.30 0.00 34.56 2.15
765 989 2.173669 ATGCGCACGCCACTGTATC 61.174 57.895 14.90 0.00 41.09 2.24
766 990 2.125147 ATGCGCACGCCACTGTAT 60.125 55.556 14.90 0.00 41.09 2.29
876 1100 1.512926 CCTGTGGCTTATGCGTATCC 58.487 55.000 0.00 0.00 40.82 2.59
894 1118 8.068380 GGTTAGTTTAATAATCAATCACGAGCC 58.932 37.037 0.00 0.00 0.00 4.70
920 1144 4.256920 AGGCAAACATGAACTACTAGCTG 58.743 43.478 0.00 0.00 0.00 4.24
933 1157 2.636893 AGTCAGAGTCAGAGGCAAACAT 59.363 45.455 0.00 0.00 0.00 2.71
940 1167 2.789213 TCTGTCAGTCAGAGTCAGAGG 58.211 52.381 0.00 0.00 46.77 3.69
966 1193 1.000771 CGTGGTCTCCTCCTCCTCA 60.001 63.158 0.00 0.00 0.00 3.86
995 1223 3.174265 CCTCCTCCCCCATGGCTC 61.174 72.222 6.09 0.00 0.00 4.70
1054 1285 0.939419 GCGTACTTGTTGGTTCCGTT 59.061 50.000 0.00 0.00 0.00 4.44
1055 1286 1.216941 CGCGTACTTGTTGGTTCCGT 61.217 55.000 0.00 0.00 0.00 4.69
1059 1290 1.161563 CCACCGCGTACTTGTTGGTT 61.162 55.000 4.92 0.00 0.00 3.67
1095 1326 4.635699 CATGAGGATGGAGATGATGGAA 57.364 45.455 0.00 0.00 0.00 3.53
1134 1369 1.213926 AGGGTTGAAGATGATGCTCCC 59.786 52.381 0.00 0.00 0.00 4.30
1147 1382 2.234661 CACATGCAGAGTAGAGGGTTGA 59.765 50.000 0.00 0.00 0.00 3.18
1150 1385 2.238084 TCACATGCAGAGTAGAGGGT 57.762 50.000 0.00 0.00 0.00 4.34
1195 1450 2.713154 GTCCACAACGCCACACAC 59.287 61.111 0.00 0.00 0.00 3.82
1503 1764 1.298190 GATCTCGACGGCGTACACC 60.298 63.158 14.74 0.00 38.98 4.16
1593 1854 1.274447 AGGAAGTAGTTGGCCACGTAC 59.726 52.381 3.88 10.51 0.00 3.67
1766 2027 0.927537 CGTCGTGTTGCAGACTTTCA 59.072 50.000 2.77 0.00 35.38 2.69
1947 2232 2.611473 CGTCAGATGCTGGAAGAAGTGT 60.611 50.000 0.00 0.00 34.07 3.55
2709 2996 4.494484 TCCTGAACAGTTCATGTCATACG 58.506 43.478 16.53 2.49 43.00 3.06
2738 3025 7.687941 AAATCATACGAGGACAATTCACTTT 57.312 32.000 0.00 0.00 0.00 2.66
2785 3075 6.319399 GTTACAATCATGTTTAAACCCTCCG 58.681 40.000 15.59 3.08 41.05 4.63
2796 3086 7.338710 ACATACTGCTAGGTTACAATCATGTT 58.661 34.615 0.00 0.00 41.05 2.71
2803 3097 8.790718 GCTACTATACATACTGCTAGGTTACAA 58.209 37.037 0.00 0.00 0.00 2.41
2804 3098 8.162085 AGCTACTATACATACTGCTAGGTTACA 58.838 37.037 0.00 0.00 0.00 2.41
2866 3162 8.131731 AGTTCAAATGCTCTTCTCAAAGTTAAC 58.868 33.333 0.00 0.00 33.95 2.01
2867 3163 8.131100 CAGTTCAAATGCTCTTCTCAAAGTTAA 58.869 33.333 0.00 0.00 33.95 2.01
2868 3164 7.283127 ACAGTTCAAATGCTCTTCTCAAAGTTA 59.717 33.333 0.00 0.00 33.95 2.24
2869 3165 6.096001 ACAGTTCAAATGCTCTTCTCAAAGTT 59.904 34.615 0.00 0.00 33.95 2.66
2870 3166 5.591877 ACAGTTCAAATGCTCTTCTCAAAGT 59.408 36.000 0.00 0.00 33.95 2.66
2871 3167 5.913514 CACAGTTCAAATGCTCTTCTCAAAG 59.086 40.000 0.00 0.00 0.00 2.77
2872 3168 5.357878 ACACAGTTCAAATGCTCTTCTCAAA 59.642 36.000 0.00 0.00 0.00 2.69
2873 3169 4.883585 ACACAGTTCAAATGCTCTTCTCAA 59.116 37.500 0.00 0.00 0.00 3.02
2874 3170 4.454678 ACACAGTTCAAATGCTCTTCTCA 58.545 39.130 0.00 0.00 0.00 3.27
2875 3171 5.429957 AACACAGTTCAAATGCTCTTCTC 57.570 39.130 0.00 0.00 0.00 2.87
2876 3172 7.880195 AGTATAACACAGTTCAAATGCTCTTCT 59.120 33.333 0.00 0.00 0.00 2.85
2877 3173 8.034058 AGTATAACACAGTTCAAATGCTCTTC 57.966 34.615 0.00 0.00 0.00 2.87
2878 3174 7.986085 AGTATAACACAGTTCAAATGCTCTT 57.014 32.000 0.00 0.00 0.00 2.85
2879 3175 9.319143 GATAGTATAACACAGTTCAAATGCTCT 57.681 33.333 0.00 0.00 0.00 4.09
2880 3176 8.552034 GGATAGTATAACACAGTTCAAATGCTC 58.448 37.037 0.00 0.00 0.00 4.26
2881 3177 8.267894 AGGATAGTATAACACAGTTCAAATGCT 58.732 33.333 0.00 0.00 0.00 3.79
2882 3178 8.438676 AGGATAGTATAACACAGTTCAAATGC 57.561 34.615 0.00 0.00 0.00 3.56
2904 3200 6.958192 AGGACTTGTAGTACTTCCAAATAGGA 59.042 38.462 12.10 0.00 35.35 2.94
2905 3201 7.184067 AGGACTTGTAGTACTTCCAAATAGG 57.816 40.000 12.10 3.07 35.35 2.57
2910 3206 9.317827 ACTATTTAGGACTTGTAGTACTTCCAA 57.682 33.333 12.10 9.58 35.35 3.53
2911 3207 8.890410 ACTATTTAGGACTTGTAGTACTTCCA 57.110 34.615 12.10 2.58 35.35 3.53
2924 3220 9.884814 ACAGTGGAGATTATACTATTTAGGACT 57.115 33.333 0.00 0.00 0.00 3.85
2939 3235 9.606631 GTAGAGATTTGATTTACAGTGGAGATT 57.393 33.333 0.00 0.00 0.00 2.40
2940 3236 8.762645 TGTAGAGATTTGATTTACAGTGGAGAT 58.237 33.333 0.00 0.00 0.00 2.75
2941 3237 8.134202 TGTAGAGATTTGATTTACAGTGGAGA 57.866 34.615 0.00 0.00 0.00 3.71
2942 3238 8.777865 TTGTAGAGATTTGATTTACAGTGGAG 57.222 34.615 0.00 0.00 0.00 3.86
2943 3239 9.739276 AATTGTAGAGATTTGATTTACAGTGGA 57.261 29.630 0.00 0.00 0.00 4.02
2953 3249 9.771534 GGAGCTTAGTAATTGTAGAGATTTGAT 57.228 33.333 0.00 0.00 0.00 2.57
2954 3250 8.204836 GGGAGCTTAGTAATTGTAGAGATTTGA 58.795 37.037 0.00 0.00 0.00 2.69
2955 3251 7.987458 TGGGAGCTTAGTAATTGTAGAGATTTG 59.013 37.037 0.00 0.00 0.00 2.32
3006 3302 4.463891 GTCCATCATTTGACCAAAGTCCAT 59.536 41.667 1.57 0.00 42.81 3.41
3024 3320 1.077265 CAGCTTTGGTGGGGTCCAT 59.923 57.895 0.00 0.00 37.33 3.41
3066 3362 5.364778 TCGCTTGTACTAATACATTGCCAT 58.635 37.500 0.00 0.00 41.02 4.40
3188 3486 9.121517 TCGAACACGTGTTTTTAAAATTGTTTA 57.878 25.926 32.71 4.59 38.56 2.01
3206 3505 7.953173 TGCTTACTTATGTTTAATTCGAACACG 59.047 33.333 0.00 0.00 39.57 4.49
3230 3529 1.065551 GACTGACCGGCCATTTAATGC 59.934 52.381 0.00 0.00 0.00 3.56
3248 3548 1.443702 GTGGATTTTTGCCGGCGAC 60.444 57.895 23.90 7.80 0.00 5.19
3249 3549 1.175983 AAGTGGATTTTTGCCGGCGA 61.176 50.000 23.90 19.26 0.00 5.54
3324 3626 2.785743 TGGTGACACCTAGGGCAAT 58.214 52.632 24.81 0.00 39.58 3.56
3451 3753 0.667993 CACCGCACAACAATGTTCCT 59.332 50.000 0.00 0.00 37.82 3.36
3577 3879 4.624293 CTATCTGAGGAGCACGCG 57.376 61.111 3.53 3.53 0.00 6.01
3592 3894 2.866378 TGGGGACAGCTCCACCTA 59.134 61.111 5.59 0.00 40.67 3.08
3618 3920 0.338120 AGAGCAAGAGGAGGCCTACT 59.662 55.000 20.68 20.68 31.76 2.57


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

AutoCloner maintained by Alex Coulton.