Multiple sequence alignment - TraesCS3B01G194700

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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 TraesCS3B01G194700 chr3B 100.000 2927 0 0 1 2927 215384200 215387126 0.000000e+00 5406.0
1 TraesCS3B01G194700 chr3B 94.575 2175 79 18 759 2927 221979723 221981864 0.000000e+00 3326.0
2 TraesCS3B01G194700 chr3B 96.956 1708 41 5 759 2461 221912243 221913944 0.000000e+00 2856.0
3 TraesCS3B01G194700 chr3B 93.750 1312 60 9 793 2098 215310364 215311659 0.000000e+00 1949.0
4 TraesCS3B01G194700 chr3B 91.119 1126 59 13 810 1934 221457693 221458778 0.000000e+00 1487.0
5 TraesCS3B01G194700 chr3B 91.340 1097 80 7 795 1888 215104599 215105683 0.000000e+00 1485.0
6 TraesCS3B01G194700 chr3B 95.044 565 27 1 1 565 215308725 215309288 0.000000e+00 887.0
7 TraesCS3B01G194700 chr3B 94.523 566 27 4 1 565 221979143 221979705 0.000000e+00 870.0
8 TraesCS3B01G194700 chr3B 92.794 569 35 4 1 564 221456900 221457467 0.000000e+00 819.0
9 TraesCS3B01G194700 chr3B 96.421 475 13 2 1924 2394 221466768 221467242 0.000000e+00 780.0
10 TraesCS3B01G194700 chr3B 94.816 463 24 0 103 565 221748577 221749039 0.000000e+00 723.0
11 TraesCS3B01G194700 chr3B 95.272 423 20 0 2505 2927 221467241 221467663 0.000000e+00 671.0
12 TraesCS3B01G194700 chr3B 92.441 463 33 2 2464 2924 221913916 221914378 0.000000e+00 660.0
13 TraesCS3B01G194700 chr3B 95.262 401 13 5 167 565 221911829 221912225 5.320000e-177 630.0
14 TraesCS3B01G194700 chr3B 92.326 417 26 2 155 565 215571445 215571861 3.250000e-164 588.0
15 TraesCS3B01G194700 chr3B 92.857 168 9 2 1965 2130 221750207 221750373 1.050000e-59 241.0
16 TraesCS3B01G194700 chr3B 95.035 141 6 1 2095 2234 215314370 215314510 1.370000e-53 220.0
17 TraesCS3B01G194700 chr3B 90.184 163 14 2 1969 2130 215114890 215115051 8.220000e-51 211.0
18 TraesCS3B01G194700 chr3B 96.117 103 4 0 1 103 221748066 221748168 5.020000e-38 169.0
19 TraesCS3B01G194700 chr3B 93.333 90 6 0 2838 2927 221752847 221752936 1.830000e-27 134.0
20 TraesCS3B01G194700 chr3B 83.607 122 11 4 2274 2387 203346827 203346947 3.990000e-19 106.0
21 TraesCS3B01G194700 chr3B 83.607 122 11 4 2274 2387 203553951 203554071 3.990000e-19 106.0
22 TraesCS3B01G194700 chr3B 98.276 58 1 0 2836 2893 203554326 203554383 5.160000e-18 102.0
23 TraesCS3B01G194700 chr3B 92.754 69 5 0 580 648 710918920 710918852 1.860000e-17 100.0
24 TraesCS3B01G194700 chr3B 92.593 54 4 0 595 648 202694428 202694375 8.700000e-11 78.7
25 TraesCS3B01G194700 chr3A 88.846 1291 90 27 873 2130 166923328 166924597 0.000000e+00 1537.0
26 TraesCS3B01G194700 chr3A 88.490 1086 91 18 908 1969 159831904 159832979 0.000000e+00 1282.0
27 TraesCS3B01G194700 chr3A 81.416 339 39 11 2589 2927 166924833 166925147 3.740000e-64 255.0
28 TraesCS3B01G194700 chr3A 87.597 129 15 1 2021 2149 177889141 177889268 6.540000e-32 148.0
29 TraesCS3B01G194700 chr3A 89.744 117 8 4 2274 2387 159833074 159833189 2.350000e-31 147.0
30 TraesCS3B01G194700 chr3A 98.039 51 1 0 1965 2015 159833004 159833054 4.020000e-14 89.8
31 TraesCS3B01G194700 chr3D 92.864 1023 64 5 873 1886 149204949 149205971 0.000000e+00 1476.0
32 TraesCS3B01G194700 chr3D 92.669 1023 66 5 873 1886 147336153 147335131 0.000000e+00 1465.0
33 TraesCS3B01G194700 chr3D 92.593 1026 64 8 873 1886 149544110 149545135 0.000000e+00 1463.0
34 TraesCS3B01G194700 chr3D 90.323 310 21 6 96 397 149204435 149204743 5.880000e-107 398.0
35 TraesCS3B01G194700 chr3D 90.323 310 21 6 96 397 149543592 149543900 5.880000e-107 398.0
36 TraesCS3B01G194700 chr3D 84.713 314 32 10 1969 2270 149206090 149206399 1.710000e-77 300.0
37 TraesCS3B01G194700 chr3D 84.112 321 34 12 1969 2276 147334720 147334404 7.930000e-76 294.0
38 TraesCS3B01G194700 chr3D 80.495 323 35 17 2589 2911 149545623 149545917 3.800000e-54 222.0
39 TraesCS3B01G194700 chr3D 90.303 165 15 1 96 259 147336710 147336546 6.350000e-52 215.0
40 TraesCS3B01G194700 chr3D 88.415 164 8 8 242 397 147336523 147336363 1.380000e-43 187.0
41 TraesCS3B01G194700 chr3D 96.053 76 3 0 2836 2911 141412094 141412169 1.100000e-24 124.0
42 TraesCS3B01G194700 chr3D 90.805 87 6 2 566 651 441197835 441197920 6.630000e-22 115.0
43 TraesCS3B01G194700 chr3D 91.667 84 6 1 566 648 498485587 498485504 6.630000e-22 115.0
44 TraesCS3B01G194700 chr3D 90.123 81 7 1 2309 2388 147334643 147334563 1.430000e-18 104.0
45 TraesCS3B01G194700 chr3D 90.123 81 7 1 2309 2388 149206167 149206247 1.430000e-18 104.0
46 TraesCS3B01G194700 chr3D 86.207 87 12 0 665 751 441197901 441197987 8.640000e-16 95.3
47 TraesCS3B01G194700 chr3D 98.039 51 1 0 1965 2015 141411677 141411727 4.020000e-14 89.8
48 TraesCS3B01G194700 chr3D 90.625 64 4 1 2086 2147 149768809 149768746 1.870000e-12 84.2
49 TraesCS3B01G194700 chr6A 87.805 123 11 4 2277 2396 146440536 146440415 1.090000e-29 141.0
50 TraesCS3B01G194700 chr6A 96.774 62 2 0 2836 2897 146438854 146438793 1.430000e-18 104.0
51 TraesCS3B01G194700 chr6A 96.078 51 2 0 1965 2015 146440609 146440559 1.870000e-12 84.2
52 TraesCS3B01G194700 chr2B 93.548 93 6 0 665 757 97439907 97439999 3.930000e-29 139.0
53 TraesCS3B01G194700 chr2B 93.548 93 6 0 665 757 654785126 654785218 3.930000e-29 139.0
54 TraesCS3B01G194700 chr2B 91.398 93 8 0 665 757 108548561 108548653 8.510000e-26 128.0
55 TraesCS3B01G194700 chr2B 84.946 93 11 2 665 754 636487088 636487180 1.120000e-14 91.6
56 TraesCS3B01G194700 chr5B 92.473 93 6 1 665 756 21188596 21188504 6.580000e-27 132.0
57 TraesCS3B01G194700 chr5B 95.833 48 2 0 601 648 468797685 468797732 8.700000e-11 78.7
58 TraesCS3B01G194700 chr7B 91.209 91 8 0 666 756 733198447 733198357 1.100000e-24 124.0
59 TraesCS3B01G194700 chr7B 91.463 82 5 2 565 646 703287069 703287148 8.570000e-21 111.0
60 TraesCS3B01G194700 chr7B 89.286 84 8 1 566 648 733198515 733198432 1.430000e-18 104.0
61 TraesCS3B01G194700 chr4B 90.323 93 8 1 665 756 639236046 639236138 1.420000e-23 121.0
62 TraesCS3B01G194700 chr4B 90.217 92 8 1 665 755 580942503 580942594 5.120000e-23 119.0
63 TraesCS3B01G194700 chr4B 90.805 87 8 0 563 649 580942434 580942520 1.840000e-22 117.0
64 TraesCS3B01G194700 chr4B 88.506 87 8 2 562 646 22260605 22260691 1.430000e-18 104.0
65 TraesCS3B01G194700 chr4B 93.617 47 3 0 2412 2458 185238766 185238720 1.460000e-08 71.3
66 TraesCS3B01G194700 chr6D 85.567 97 11 3 73 167 446286949 446287044 6.680000e-17 99.0
67 TraesCS3B01G194700 chr6D 85.333 75 4 5 2389 2458 434443376 434443304 1.460000e-08 71.3
68 TraesCS3B01G194700 chr1D 86.957 69 6 2 2393 2458 415405142 415405074 1.130000e-09 75.0
69 TraesCS3B01G194700 chr2A 95.122 41 2 0 2418 2458 538394488 538394528 6.770000e-07 65.8
70 TraesCS3B01G194700 chr5D 79.048 105 12 4 2418 2516 382500541 382500441 2.440000e-06 63.9


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 TraesCS3B01G194700 chr3B 215384200 215387126 2926 False 5406.000000 5406 100.000000 1 2927 1 chr3B.!!$F4 2926
1 TraesCS3B01G194700 chr3B 221979143 221981864 2721 False 2098.000000 3326 94.549000 1 2927 2 chr3B.!!$F12 2926
2 TraesCS3B01G194700 chr3B 215104599 215105683 1084 False 1485.000000 1485 91.340000 795 1888 1 chr3B.!!$F2 1093
3 TraesCS3B01G194700 chr3B 221911829 221914378 2549 False 1382.000000 2856 94.886333 167 2924 3 chr3B.!!$F11 2757
4 TraesCS3B01G194700 chr3B 221456900 221458778 1878 False 1153.000000 1487 91.956500 1 1934 2 chr3B.!!$F8 1933
5 TraesCS3B01G194700 chr3B 215308725 215314510 5785 False 1018.666667 1949 94.609667 1 2234 3 chr3B.!!$F7 2233
6 TraesCS3B01G194700 chr3B 221466768 221467663 895 False 725.500000 780 95.846500 1924 2927 2 chr3B.!!$F9 1003
7 TraesCS3B01G194700 chr3B 221748066 221752936 4870 False 316.750000 723 94.280750 1 2927 4 chr3B.!!$F10 2926
8 TraesCS3B01G194700 chr3A 166923328 166925147 1819 False 896.000000 1537 85.131000 873 2927 2 chr3A.!!$F3 2054
9 TraesCS3B01G194700 chr3A 159831904 159833189 1285 False 506.266667 1282 92.091000 908 2387 3 chr3A.!!$F2 1479
10 TraesCS3B01G194700 chr3D 149543592 149545917 2325 False 694.333333 1463 87.803667 96 2911 3 chr3D.!!$F3 2815
11 TraesCS3B01G194700 chr3D 149204435 149206399 1964 False 569.500000 1476 89.505750 96 2388 4 chr3D.!!$F2 2292
12 TraesCS3B01G194700 chr3D 147334404 147336710 2306 True 453.000000 1465 89.124400 96 2388 5 chr3D.!!$R3 2292

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
602 1073 0.036875 GGCACTAGCACCCAAGACTT 59.963 55.0 0.0 0.0 44.61 3.01 F
678 1149 0.171231 GCGGCAGGAACCAGAAATTC 59.829 55.0 0.0 0.0 0.00 2.17 F
1014 2744 0.234106 CGAACATGGCAGCGATCATC 59.766 55.0 0.0 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1403 3133 0.677731 CTTGATGCCCTTGAAGCGGA 60.678 55.000 4.22 0.0 0.0 5.54 R
1807 3566 1.737236 GTTGATTATGTGTGGCTGCGA 59.263 47.619 0.00 0.0 0.0 5.10 R
2756 7684 0.798776 CTGACGAATGTGCCTTGGAC 59.201 55.000 0.00 0.0 0.0 4.02 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
262 720 2.172717 GGAGAATGCCTAGGTTTAGCCA 59.827 50.000 11.31 0.00 40.61 4.75
488 959 3.418619 CGTGAGAATGAAAAACTGTTGCG 59.581 43.478 0.00 0.00 0.00 4.85
591 1062 5.535753 AAATAAAATCCATGGGCACTAGC 57.464 39.130 13.02 0.00 41.10 3.42
592 1063 2.530460 AAAATCCATGGGCACTAGCA 57.470 45.000 13.02 0.00 44.61 3.49
594 1065 0.106519 AATCCATGGGCACTAGCACC 60.107 55.000 13.02 0.00 46.13 5.01
595 1066 1.999634 ATCCATGGGCACTAGCACCC 62.000 60.000 13.02 12.83 46.13 4.61
599 1070 3.077907 GGGCACTAGCACCCAAGA 58.922 61.111 14.48 0.00 46.22 3.02
600 1071 1.377333 GGGCACTAGCACCCAAGAC 60.377 63.158 14.48 0.00 46.22 3.01
601 1072 1.679898 GGCACTAGCACCCAAGACT 59.320 57.895 0.00 0.00 44.61 3.24
602 1073 0.036875 GGCACTAGCACCCAAGACTT 59.963 55.000 0.00 0.00 44.61 3.01
603 1074 1.278127 GGCACTAGCACCCAAGACTTA 59.722 52.381 0.00 0.00 44.61 2.24
604 1075 2.622436 GCACTAGCACCCAAGACTTAG 58.378 52.381 0.00 0.00 41.58 2.18
605 1076 2.028020 GCACTAGCACCCAAGACTTAGT 60.028 50.000 0.00 0.00 41.58 2.24
606 1077 3.557264 GCACTAGCACCCAAGACTTAGTT 60.557 47.826 0.00 0.00 41.58 2.24
607 1078 4.642429 CACTAGCACCCAAGACTTAGTTT 58.358 43.478 0.00 0.00 0.00 2.66
608 1079 5.063880 CACTAGCACCCAAGACTTAGTTTT 58.936 41.667 0.00 0.00 0.00 2.43
609 1080 6.228258 CACTAGCACCCAAGACTTAGTTTTA 58.772 40.000 0.00 0.00 0.00 1.52
610 1081 6.879458 CACTAGCACCCAAGACTTAGTTTTAT 59.121 38.462 0.00 0.00 0.00 1.40
611 1082 8.038944 CACTAGCACCCAAGACTTAGTTTTATA 58.961 37.037 0.00 0.00 0.00 0.98
612 1083 8.258708 ACTAGCACCCAAGACTTAGTTTTATAG 58.741 37.037 0.00 0.00 0.00 1.31
613 1084 7.253905 AGCACCCAAGACTTAGTTTTATAGA 57.746 36.000 0.00 0.00 0.00 1.98
614 1085 7.686434 AGCACCCAAGACTTAGTTTTATAGAA 58.314 34.615 0.00 0.00 0.00 2.10
615 1086 7.824779 AGCACCCAAGACTTAGTTTTATAGAAG 59.175 37.037 0.00 0.00 0.00 2.85
616 1087 7.822822 GCACCCAAGACTTAGTTTTATAGAAGA 59.177 37.037 0.00 0.00 0.00 2.87
617 1088 9.720769 CACCCAAGACTTAGTTTTATAGAAGAA 57.279 33.333 0.00 0.00 0.00 2.52
618 1089 9.945904 ACCCAAGACTTAGTTTTATAGAAGAAG 57.054 33.333 0.00 0.00 0.00 2.85
619 1090 8.884726 CCCAAGACTTAGTTTTATAGAAGAAGC 58.115 37.037 0.00 0.00 0.00 3.86
620 1091 8.884726 CCAAGACTTAGTTTTATAGAAGAAGCC 58.115 37.037 0.00 0.00 0.00 4.35
621 1092 8.884726 CAAGACTTAGTTTTATAGAAGAAGCCC 58.115 37.037 0.00 0.00 0.00 5.19
622 1093 8.147244 AGACTTAGTTTTATAGAAGAAGCCCA 57.853 34.615 0.00 0.00 0.00 5.36
623 1094 8.041919 AGACTTAGTTTTATAGAAGAAGCCCAC 58.958 37.037 0.00 0.00 0.00 4.61
624 1095 7.110810 ACTTAGTTTTATAGAAGAAGCCCACC 58.889 38.462 0.00 0.00 0.00 4.61
625 1096 4.856509 AGTTTTATAGAAGAAGCCCACCC 58.143 43.478 0.00 0.00 0.00 4.61
626 1097 3.553828 TTTATAGAAGAAGCCCACCCG 57.446 47.619 0.00 0.00 0.00 5.28
627 1098 1.420430 TATAGAAGAAGCCCACCCGG 58.580 55.000 0.00 0.00 0.00 5.73
651 1122 5.316770 GTGAAGAACCAGAAATTCGATTCG 58.683 41.667 0.00 0.00 34.46 3.34
652 1123 5.120208 GTGAAGAACCAGAAATTCGATTCGA 59.880 40.000 4.29 4.29 34.46 3.71
660 1131 4.609995 TTCGATTCGAACCCTGGC 57.390 55.556 17.08 0.00 41.05 4.85
661 1132 1.447140 TTCGATTCGAACCCTGGCG 60.447 57.895 17.08 0.00 41.05 5.69
662 1133 2.845752 TTCGATTCGAACCCTGGCGG 62.846 60.000 17.08 0.00 41.05 6.13
663 1134 3.202706 GATTCGAACCCTGGCGGC 61.203 66.667 0.00 0.00 33.26 6.53
664 1135 3.969250 GATTCGAACCCTGGCGGCA 62.969 63.158 12.58 12.58 33.26 5.69
665 1136 3.976701 ATTCGAACCCTGGCGGCAG 62.977 63.158 30.63 30.63 33.26 4.85
674 1145 3.565214 TGGCGGCAGGAACCAGAA 61.565 61.111 7.97 0.00 0.00 3.02
675 1146 2.282180 GGCGGCAGGAACCAGAAA 60.282 61.111 3.07 0.00 0.00 2.52
676 1147 1.678970 GGCGGCAGGAACCAGAAAT 60.679 57.895 3.07 0.00 0.00 2.17
677 1148 1.250840 GGCGGCAGGAACCAGAAATT 61.251 55.000 3.07 0.00 0.00 1.82
678 1149 0.171231 GCGGCAGGAACCAGAAATTC 59.829 55.000 0.00 0.00 0.00 2.17
679 1150 0.447801 CGGCAGGAACCAGAAATTCG 59.552 55.000 0.00 0.00 0.00 3.34
680 1151 1.821216 GGCAGGAACCAGAAATTCGA 58.179 50.000 0.00 0.00 0.00 3.71
681 1152 1.468914 GGCAGGAACCAGAAATTCGAC 59.531 52.381 0.00 0.00 0.00 4.20
682 1153 1.468914 GCAGGAACCAGAAATTCGACC 59.531 52.381 0.00 0.00 0.00 4.79
683 1154 2.084546 CAGGAACCAGAAATTCGACCC 58.915 52.381 0.00 0.00 0.00 4.46
684 1155 1.985895 AGGAACCAGAAATTCGACCCT 59.014 47.619 0.00 0.00 0.00 4.34
685 1156 2.084546 GGAACCAGAAATTCGACCCTG 58.915 52.381 0.00 0.00 0.00 4.45
686 1157 2.290071 GGAACCAGAAATTCGACCCTGA 60.290 50.000 0.00 0.00 0.00 3.86
687 1158 2.474410 ACCAGAAATTCGACCCTGAC 57.526 50.000 0.00 0.00 0.00 3.51
688 1159 1.697432 ACCAGAAATTCGACCCTGACA 59.303 47.619 0.00 0.00 0.00 3.58
689 1160 2.289694 ACCAGAAATTCGACCCTGACAG 60.290 50.000 0.00 0.00 0.00 3.51
690 1161 2.350522 CAGAAATTCGACCCTGACAGG 58.649 52.381 15.15 15.15 34.30 4.00
691 1162 2.028112 CAGAAATTCGACCCTGACAGGA 60.028 50.000 23.77 2.29 37.67 3.86
692 1163 2.840651 AGAAATTCGACCCTGACAGGAT 59.159 45.455 23.77 5.21 37.67 3.24
693 1164 3.264450 AGAAATTCGACCCTGACAGGATT 59.736 43.478 23.77 11.02 37.67 3.01
694 1165 2.990066 ATTCGACCCTGACAGGATTC 57.010 50.000 23.77 16.52 37.67 2.52
695 1166 1.639722 TTCGACCCTGACAGGATTCA 58.360 50.000 23.77 7.00 37.67 2.57
696 1167 1.639722 TCGACCCTGACAGGATTCAA 58.360 50.000 23.77 1.20 37.67 2.69
697 1168 1.974957 TCGACCCTGACAGGATTCAAA 59.025 47.619 23.77 6.99 37.67 2.69
698 1169 2.076863 CGACCCTGACAGGATTCAAAC 58.923 52.381 23.77 5.03 37.67 2.93
699 1170 2.437413 GACCCTGACAGGATTCAAACC 58.563 52.381 23.77 0.00 37.67 3.27
700 1171 1.075536 ACCCTGACAGGATTCAAACCC 59.924 52.381 23.77 0.00 37.67 4.11
701 1172 1.355720 CCCTGACAGGATTCAAACCCT 59.644 52.381 23.77 0.00 37.67 4.34
705 1176 2.583472 CAGGATTCAAACCCTGGCC 58.417 57.895 0.00 0.00 44.68 5.36
706 1177 1.000896 AGGATTCAAACCCTGGCCG 60.001 57.895 0.00 0.00 0.00 6.13
707 1178 2.710902 GGATTCAAACCCTGGCCGC 61.711 63.158 0.00 0.00 0.00 6.53
708 1179 1.976474 GATTCAAACCCTGGCCGCA 60.976 57.895 0.00 0.00 0.00 5.69
709 1180 1.937546 GATTCAAACCCTGGCCGCAG 61.938 60.000 0.00 0.00 0.00 5.18
734 1205 4.601794 CAGTGCCCACCCTTGCCA 62.602 66.667 0.00 0.00 0.00 4.92
735 1206 4.603535 AGTGCCCACCCTTGCCAC 62.604 66.667 0.00 0.00 0.00 5.01
736 1207 4.603535 GTGCCCACCCTTGCCACT 62.604 66.667 0.00 0.00 0.00 4.00
737 1208 2.856494 TGCCCACCCTTGCCACTA 60.856 61.111 0.00 0.00 0.00 2.74
738 1209 2.044946 GCCCACCCTTGCCACTAG 60.045 66.667 0.00 0.00 0.00 2.57
739 1210 2.677228 CCCACCCTTGCCACTAGG 59.323 66.667 0.00 0.00 38.23 3.02
769 1240 2.771089 AGTTCTCAAGAAATCGCAGCA 58.229 42.857 0.00 0.00 35.58 4.41
1014 2744 0.234106 CGAACATGGCAGCGATCATC 59.766 55.000 0.00 0.00 0.00 2.92
1084 2814 3.612371 GACTTCGAGGCGACGTGCT 62.612 63.158 3.70 0.00 45.43 4.40
1207 2937 2.306847 GTCCAAAACATCACCCTGTGT 58.693 47.619 0.00 0.00 34.79 3.72
1420 3150 0.960364 GTTCCGCTTCAAGGGCATCA 60.960 55.000 0.00 0.00 0.00 3.07
1433 3163 1.092345 GGCATCAAGAAGCCCTCGTC 61.092 60.000 5.04 0.00 45.18 4.20
1437 3167 1.056660 TCAAGAAGCCCTCGTCCTTT 58.943 50.000 0.00 0.00 0.00 3.11
1807 3566 4.326507 AGCAGAAGCAGCAGCCGT 62.327 61.111 0.00 0.00 45.49 5.68
1925 3864 0.108186 CAGTCTGGATGCGGCAACTA 60.108 55.000 6.82 0.42 0.00 2.24
2234 7081 7.223971 CACAAATGCCTCATCATATTGGAAAAG 59.776 37.037 0.00 0.00 0.00 2.27
2290 7140 7.563924 ACAAATGCCTCAACTATACTCCTAGTA 59.436 37.037 0.00 0.00 34.82 1.82
2405 7258 6.894103 TCTTTTAAATACTACTCCCTCCGTCT 59.106 38.462 0.00 0.00 0.00 4.18
2409 7262 5.579753 AATACTACTCCCTCCGTCTCATA 57.420 43.478 0.00 0.00 0.00 2.15
2412 7265 4.208746 ACTACTCCCTCCGTCTCATAAAG 58.791 47.826 0.00 0.00 0.00 1.85
2413 7266 3.383698 ACTCCCTCCGTCTCATAAAGA 57.616 47.619 0.00 0.00 0.00 2.52
2428 7293 6.926826 TCTCATAAAGACGCTTTTTGACACTA 59.073 34.615 15.66 5.58 0.00 2.74
2436 7301 5.835257 ACGCTTTTTGACACTAGTGTAGTA 58.165 37.500 27.98 14.71 45.05 1.82
2624 7549 2.824936 ACGAATGCCACAATTCCAATCA 59.175 40.909 0.00 0.00 33.74 2.57
2711 7636 2.588877 GGCATCCATCACGTCGGG 60.589 66.667 0.00 0.00 0.00 5.14
2798 7727 2.616842 ACCGAACAAGACAATGTTGACC 59.383 45.455 0.00 0.00 43.31 4.02
2834 7763 4.202253 GCCGCATATCACCATCATATAGGA 60.202 45.833 0.00 0.00 0.00 2.94
2893 9887 7.049799 ACTGTAGATTTCTGAGATAAGAGCC 57.950 40.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
262 720 1.938577 GCATGATGACTGATGTCGCTT 59.061 47.619 0.00 0.00 45.70 4.68
464 931 4.672413 GCAACAGTTTTTCATTCTCACGAG 59.328 41.667 0.00 0.00 0.00 4.18
567 1038 6.070309 TGCTAGTGCCCATGGATTTTATTTTT 60.070 34.615 15.22 0.00 38.71 1.94
568 1039 5.424895 TGCTAGTGCCCATGGATTTTATTTT 59.575 36.000 15.22 0.00 38.71 1.82
569 1040 4.961730 TGCTAGTGCCCATGGATTTTATTT 59.038 37.500 15.22 0.00 38.71 1.40
570 1041 4.342092 GTGCTAGTGCCCATGGATTTTATT 59.658 41.667 15.22 0.00 38.71 1.40
571 1042 3.891366 GTGCTAGTGCCCATGGATTTTAT 59.109 43.478 15.22 0.00 38.71 1.40
573 1044 2.102578 GTGCTAGTGCCCATGGATTTT 58.897 47.619 15.22 0.00 38.71 1.82
575 1046 0.106519 GGTGCTAGTGCCCATGGATT 60.107 55.000 15.22 0.00 38.71 3.01
576 1047 1.533711 GGTGCTAGTGCCCATGGAT 59.466 57.895 15.22 0.00 38.71 3.41
577 1048 2.679342 GGGTGCTAGTGCCCATGGA 61.679 63.158 15.22 0.00 44.23 3.41
578 1049 2.124151 GGGTGCTAGTGCCCATGG 60.124 66.667 15.91 4.14 44.23 3.66
582 1053 1.377333 GTCTTGGGTGCTAGTGCCC 60.377 63.158 14.48 14.48 45.04 5.36
583 1054 0.036875 AAGTCTTGGGTGCTAGTGCC 59.963 55.000 0.00 0.00 38.71 5.01
584 1055 2.028020 ACTAAGTCTTGGGTGCTAGTGC 60.028 50.000 0.64 0.00 40.20 4.40
585 1056 3.963428 ACTAAGTCTTGGGTGCTAGTG 57.037 47.619 0.64 0.00 0.00 2.74
586 1057 4.976540 AAACTAAGTCTTGGGTGCTAGT 57.023 40.909 0.64 0.00 0.00 2.57
587 1058 8.475639 TCTATAAAACTAAGTCTTGGGTGCTAG 58.524 37.037 0.64 0.00 0.00 3.42
588 1059 8.370266 TCTATAAAACTAAGTCTTGGGTGCTA 57.630 34.615 0.64 0.00 0.00 3.49
589 1060 7.253905 TCTATAAAACTAAGTCTTGGGTGCT 57.746 36.000 0.64 0.00 0.00 4.40
590 1061 7.822822 TCTTCTATAAAACTAAGTCTTGGGTGC 59.177 37.037 0.64 0.00 0.00 5.01
591 1062 9.720769 TTCTTCTATAAAACTAAGTCTTGGGTG 57.279 33.333 0.64 0.00 0.00 4.61
592 1063 9.945904 CTTCTTCTATAAAACTAAGTCTTGGGT 57.054 33.333 0.64 0.00 0.00 4.51
593 1064 8.884726 GCTTCTTCTATAAAACTAAGTCTTGGG 58.115 37.037 0.64 0.00 0.00 4.12
594 1065 8.884726 GGCTTCTTCTATAAAACTAAGTCTTGG 58.115 37.037 0.00 0.00 0.00 3.61
595 1066 8.884726 GGGCTTCTTCTATAAAACTAAGTCTTG 58.115 37.037 0.00 0.00 0.00 3.02
596 1067 8.603304 TGGGCTTCTTCTATAAAACTAAGTCTT 58.397 33.333 0.00 0.00 0.00 3.01
597 1068 8.041919 GTGGGCTTCTTCTATAAAACTAAGTCT 58.958 37.037 0.00 0.00 0.00 3.24
598 1069 7.280428 GGTGGGCTTCTTCTATAAAACTAAGTC 59.720 40.741 0.00 0.00 0.00 3.01
599 1070 7.110810 GGTGGGCTTCTTCTATAAAACTAAGT 58.889 38.462 0.00 0.00 0.00 2.24
600 1071 6.542735 GGGTGGGCTTCTTCTATAAAACTAAG 59.457 42.308 0.00 0.00 0.00 2.18
601 1072 6.420638 GGGTGGGCTTCTTCTATAAAACTAA 58.579 40.000 0.00 0.00 0.00 2.24
602 1073 5.395990 CGGGTGGGCTTCTTCTATAAAACTA 60.396 44.000 0.00 0.00 0.00 2.24
603 1074 4.625564 CGGGTGGGCTTCTTCTATAAAACT 60.626 45.833 0.00 0.00 0.00 2.66
604 1075 3.626217 CGGGTGGGCTTCTTCTATAAAAC 59.374 47.826 0.00 0.00 0.00 2.43
605 1076 3.371166 CCGGGTGGGCTTCTTCTATAAAA 60.371 47.826 0.00 0.00 0.00 1.52
606 1077 2.171870 CCGGGTGGGCTTCTTCTATAAA 59.828 50.000 0.00 0.00 0.00 1.40
607 1078 1.766496 CCGGGTGGGCTTCTTCTATAA 59.234 52.381 0.00 0.00 0.00 0.98
608 1079 1.420430 CCGGGTGGGCTTCTTCTATA 58.580 55.000 0.00 0.00 0.00 1.31
609 1080 2.221918 CCGGGTGGGCTTCTTCTAT 58.778 57.895 0.00 0.00 0.00 1.98
610 1081 3.721868 CCGGGTGGGCTTCTTCTA 58.278 61.111 0.00 0.00 0.00 2.10
620 1091 2.033602 GGTTCTTCACCCGGGTGG 59.966 66.667 45.13 32.89 45.43 4.61
621 1092 1.302511 CTGGTTCTTCACCCGGGTG 60.303 63.158 42.62 42.62 46.68 4.61
622 1093 1.057851 TTCTGGTTCTTCACCCGGGT 61.058 55.000 24.16 24.16 46.68 5.28
623 1094 0.109723 TTTCTGGTTCTTCACCCGGG 59.890 55.000 22.25 22.25 46.68 5.73
624 1095 2.200373 ATTTCTGGTTCTTCACCCGG 57.800 50.000 0.00 0.00 46.68 5.73
625 1096 2.159627 CGAATTTCTGGTTCTTCACCCG 59.840 50.000 0.00 0.00 46.68 5.28
626 1097 3.408634 TCGAATTTCTGGTTCTTCACCC 58.591 45.455 0.00 0.00 46.68 4.61
627 1098 7.775105 TCGAATCGAATTTCTGGTTCTTCACC 61.775 42.308 1.57 0.00 38.45 4.02
628 1099 5.120208 TCGAATCGAATTTCTGGTTCTTCAC 59.880 40.000 1.57 0.00 31.06 3.18
629 1100 5.234752 TCGAATCGAATTTCTGGTTCTTCA 58.765 37.500 1.57 0.00 31.06 3.02
630 1101 5.779806 TCGAATCGAATTTCTGGTTCTTC 57.220 39.130 1.57 0.00 31.06 2.87
643 1114 1.447140 CGCCAGGGTTCGAATCGAA 60.447 57.895 14.59 14.59 43.75 3.71
644 1115 2.183300 CGCCAGGGTTCGAATCGA 59.817 61.111 0.00 0.00 0.00 3.59
645 1116 2.890474 CCGCCAGGGTTCGAATCG 60.890 66.667 0.00 0.00 0.00 3.34
646 1117 3.202706 GCCGCCAGGGTTCGAATC 61.203 66.667 0.00 0.00 38.44 2.52
647 1118 3.976701 CTGCCGCCAGGGTTCGAAT 62.977 63.158 0.00 0.00 38.44 3.34
648 1119 4.697756 CTGCCGCCAGGGTTCGAA 62.698 66.667 0.00 0.00 38.44 3.71
657 1128 2.424842 ATTTCTGGTTCCTGCCGCCA 62.425 55.000 0.00 0.00 0.00 5.69
658 1129 1.250840 AATTTCTGGTTCCTGCCGCC 61.251 55.000 0.00 0.00 0.00 6.13
659 1130 0.171231 GAATTTCTGGTTCCTGCCGC 59.829 55.000 0.00 0.00 0.00 6.53
660 1131 0.447801 CGAATTTCTGGTTCCTGCCG 59.552 55.000 0.00 0.00 0.00 5.69
661 1132 1.468914 GTCGAATTTCTGGTTCCTGCC 59.531 52.381 0.00 0.00 0.00 4.85
662 1133 1.468914 GGTCGAATTTCTGGTTCCTGC 59.531 52.381 0.00 0.00 0.00 4.85
663 1134 2.084546 GGGTCGAATTTCTGGTTCCTG 58.915 52.381 0.00 0.00 0.00 3.86
664 1135 1.985895 AGGGTCGAATTTCTGGTTCCT 59.014 47.619 0.00 0.00 0.00 3.36
665 1136 2.084546 CAGGGTCGAATTTCTGGTTCC 58.915 52.381 0.00 0.00 0.00 3.62
666 1137 2.742589 GTCAGGGTCGAATTTCTGGTTC 59.257 50.000 0.00 0.00 0.00 3.62
667 1138 2.105821 TGTCAGGGTCGAATTTCTGGTT 59.894 45.455 0.00 0.00 0.00 3.67
668 1139 1.697432 TGTCAGGGTCGAATTTCTGGT 59.303 47.619 0.00 0.00 0.00 4.00
669 1140 2.350522 CTGTCAGGGTCGAATTTCTGG 58.649 52.381 0.00 0.00 0.00 3.86
670 1141 2.028112 TCCTGTCAGGGTCGAATTTCTG 60.028 50.000 19.11 0.00 35.59 3.02
671 1142 2.257207 TCCTGTCAGGGTCGAATTTCT 58.743 47.619 19.11 0.00 35.59 2.52
672 1143 2.762535 TCCTGTCAGGGTCGAATTTC 57.237 50.000 19.11 0.00 35.59 2.17
673 1144 3.009033 TGAATCCTGTCAGGGTCGAATTT 59.991 43.478 19.11 0.00 35.59 1.82
674 1145 2.571653 TGAATCCTGTCAGGGTCGAATT 59.428 45.455 19.11 10.43 35.59 2.17
675 1146 2.187958 TGAATCCTGTCAGGGTCGAAT 58.812 47.619 19.11 1.51 35.59 3.34
676 1147 1.639722 TGAATCCTGTCAGGGTCGAA 58.360 50.000 19.11 0.00 35.59 3.71
677 1148 1.639722 TTGAATCCTGTCAGGGTCGA 58.360 50.000 19.11 13.03 35.59 4.20
678 1149 2.076863 GTTTGAATCCTGTCAGGGTCG 58.923 52.381 19.11 0.00 35.59 4.79
679 1150 2.437413 GGTTTGAATCCTGTCAGGGTC 58.563 52.381 19.11 15.98 35.59 4.46
680 1151 1.075536 GGGTTTGAATCCTGTCAGGGT 59.924 52.381 19.11 9.30 35.59 4.34
681 1152 1.355720 AGGGTTTGAATCCTGTCAGGG 59.644 52.381 19.11 0.53 38.36 4.45
682 1153 2.887151 AGGGTTTGAATCCTGTCAGG 57.113 50.000 13.21 13.21 38.36 3.86
688 1159 1.000896 CGGCCAGGGTTTGAATCCT 60.001 57.895 2.24 0.00 41.23 3.24
689 1160 2.710902 GCGGCCAGGGTTTGAATCC 61.711 63.158 2.24 0.00 0.00 3.01
690 1161 1.937546 CTGCGGCCAGGGTTTGAATC 61.938 60.000 2.24 0.00 35.38 2.52
691 1162 1.978617 CTGCGGCCAGGGTTTGAAT 60.979 57.895 2.24 0.00 35.38 2.57
692 1163 2.597217 CTGCGGCCAGGGTTTGAA 60.597 61.111 2.24 0.00 35.38 2.69
717 1188 4.601794 TGGCAAGGGTGGGCACTG 62.602 66.667 0.00 0.00 35.74 3.66
720 1191 2.856494 TAGTGGCAAGGGTGGGCA 60.856 61.111 0.00 0.00 38.62 5.36
721 1192 2.044946 CTAGTGGCAAGGGTGGGC 60.045 66.667 0.00 0.00 0.00 5.36
722 1193 2.677228 CCTAGTGGCAAGGGTGGG 59.323 66.667 0.00 0.00 0.00 4.61
738 1209 4.322801 TTTCTTGAGAACTAGGCTGTAGCC 60.323 45.833 15.02 15.02 46.88 3.93
739 1210 4.457834 TTCTTGAGAACTAGGCTGTAGC 57.542 45.455 0.00 0.00 41.14 3.58
740 1211 5.746245 CGATTTCTTGAGAACTAGGCTGTAG 59.254 44.000 0.00 0.00 33.13 2.74
741 1212 5.651530 CGATTTCTTGAGAACTAGGCTGTA 58.348 41.667 0.00 0.00 33.13 2.74
742 1213 4.499183 CGATTTCTTGAGAACTAGGCTGT 58.501 43.478 0.00 0.00 33.13 4.40
743 1214 3.308323 GCGATTTCTTGAGAACTAGGCTG 59.692 47.826 0.00 0.00 33.13 4.85
744 1215 3.055819 TGCGATTTCTTGAGAACTAGGCT 60.056 43.478 0.00 0.00 33.13 4.58
745 1216 3.262420 TGCGATTTCTTGAGAACTAGGC 58.738 45.455 0.00 0.00 33.13 3.93
746 1217 3.308323 GCTGCGATTTCTTGAGAACTAGG 59.692 47.826 0.00 0.00 33.13 3.02
747 1218 3.928992 TGCTGCGATTTCTTGAGAACTAG 59.071 43.478 0.00 0.00 33.13 2.57
748 1219 3.925379 TGCTGCGATTTCTTGAGAACTA 58.075 40.909 0.00 0.00 33.13 2.24
749 1220 2.771089 TGCTGCGATTTCTTGAGAACT 58.229 42.857 0.00 0.00 33.13 3.01
750 1221 3.754188 ATGCTGCGATTTCTTGAGAAC 57.246 42.857 0.00 0.00 33.13 3.01
751 1222 4.478699 CAAATGCTGCGATTTCTTGAGAA 58.521 39.130 6.96 0.00 0.00 2.87
752 1223 3.119743 CCAAATGCTGCGATTTCTTGAGA 60.120 43.478 6.96 0.00 0.00 3.27
753 1224 3.176708 CCAAATGCTGCGATTTCTTGAG 58.823 45.455 6.96 0.00 0.00 3.02
754 1225 2.557924 ACCAAATGCTGCGATTTCTTGA 59.442 40.909 6.96 0.00 0.00 3.02
755 1226 2.950433 ACCAAATGCTGCGATTTCTTG 58.050 42.857 6.96 0.00 0.00 3.02
756 1227 3.665745 AACCAAATGCTGCGATTTCTT 57.334 38.095 6.96 1.62 0.00 2.52
757 1228 3.243839 ACAAACCAAATGCTGCGATTTCT 60.244 39.130 6.96 0.00 0.00 2.52
967 2684 2.464459 GCGCAAACTCGAGATGGGG 61.464 63.158 27.39 20.40 0.00 4.96
968 2685 2.802667 CGCGCAAACTCGAGATGGG 61.803 63.158 21.68 23.59 0.00 4.00
969 2686 2.697425 CGCGCAAACTCGAGATGG 59.303 61.111 21.68 5.97 0.00 3.51
970 2687 2.020559 GCGCGCAAACTCGAGATG 59.979 61.111 29.10 17.91 0.00 2.90
1065 2795 2.504244 CACGTCGCCTCGAAGTCC 60.504 66.667 4.94 0.00 44.06 3.85
1084 2814 2.501223 AAGATCCGCGCGTCTTGGAA 62.501 55.000 28.13 7.68 34.97 3.53
1403 3133 0.677731 CTTGATGCCCTTGAAGCGGA 60.678 55.000 4.22 0.00 0.00 5.54
1420 3150 1.056660 TCAAAGGACGAGGGCTTCTT 58.943 50.000 0.00 0.00 0.00 2.52
1587 3317 1.744368 CCGCATGAGCTCAGCAAGT 60.744 57.895 26.77 9.42 39.10 3.16
1609 3339 2.355108 CGGTGATGTTGATCTTGACCCT 60.355 50.000 0.00 0.00 0.00 4.34
1724 3471 4.074526 GAGGCGACTGCTGCTGGA 62.075 66.667 0.00 0.00 44.43 3.86
1730 3477 4.731612 CTGTGCGAGGCGACTGCT 62.732 66.667 0.00 0.00 44.43 4.24
1807 3566 1.737236 GTTGATTATGTGTGGCTGCGA 59.263 47.619 0.00 0.00 0.00 5.10
2257 7107 4.734398 AGTTGAGGCATTTGTGTTCAAA 57.266 36.364 0.00 0.00 45.71 2.69
2382 7234 6.664816 TGAGACGGAGGGAGTAGTATTTAAAA 59.335 38.462 0.00 0.00 0.00 1.52
2386 7238 4.246712 TGAGACGGAGGGAGTAGTATTT 57.753 45.455 0.00 0.00 0.00 1.40
2405 7258 6.704493 ACTAGTGTCAAAAAGCGTCTTTATGA 59.296 34.615 0.00 0.91 0.00 2.15
2409 7262 4.634443 ACACTAGTGTCAAAAAGCGTCTTT 59.366 37.500 22.95 0.00 40.24 2.52
2412 7265 4.743644 ACTACACTAGTGTCAAAAAGCGTC 59.256 41.667 31.11 0.00 43.74 5.19
2413 7266 4.690122 ACTACACTAGTGTCAAAAAGCGT 58.310 39.130 31.11 13.23 43.74 5.07
2456 7321 8.486210 TAAGATGCCTTTTGACACTAGTCATAT 58.514 33.333 0.00 0.00 42.48 1.78
2457 7322 7.847096 TAAGATGCCTTTTGACACTAGTCATA 58.153 34.615 0.00 0.00 42.48 2.15
2458 7323 6.711277 TAAGATGCCTTTTGACACTAGTCAT 58.289 36.000 0.00 0.00 42.48 3.06
2459 7324 6.109156 TAAGATGCCTTTTGACACTAGTCA 57.891 37.500 0.00 0.00 41.91 3.41
2460 7325 8.894768 ATATAAGATGCCTTTTGACACTAGTC 57.105 34.615 0.00 0.00 38.24 2.59
2474 7339 9.862371 CCTCCGTATCATATAATATAAGATGCC 57.138 37.037 7.93 0.01 0.00 4.40
2475 7340 9.862371 CCCTCCGTATCATATAATATAAGATGC 57.138 37.037 7.93 6.06 0.00 3.91
2492 7357 9.683870 CTTCTATTATTACTACTCCCTCCGTAT 57.316 37.037 0.00 0.00 0.00 3.06
2493 7358 8.884323 TCTTCTATTATTACTACTCCCTCCGTA 58.116 37.037 0.00 0.00 0.00 4.02
2608 7504 4.316645 CATTGTTGATTGGAATTGTGGCA 58.683 39.130 0.00 0.00 0.00 4.92
2624 7549 2.542824 CGACTTTCCCGTTTGCATTGTT 60.543 45.455 0.00 0.00 0.00 2.83
2711 7636 1.734117 GTTGCCGCCATGTCTTTGC 60.734 57.895 0.00 0.00 0.00 3.68
2756 7684 0.798776 CTGACGAATGTGCCTTGGAC 59.201 55.000 0.00 0.00 0.00 4.02
2798 7727 1.940883 ATGCGGCAAGATGGCAAGTG 61.941 55.000 6.82 0.00 43.94 3.16
2893 9887 6.203145 TGTGTTGGAGCAAATGATTTGAATTG 59.797 34.615 21.14 0.00 43.26 2.32


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

AutoCloner maintained by Alex Coulton.