Multiple sequence alignment - TraesCS7D01G037400

Loading Multiple Alignment...

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 TraesCS7D01G037400 chr7D 100.000 2776 0 0 1 2776 18925453 18928228 0.000000e+00 5127.0
1 TraesCS7D01G037400 chr7D 77.014 509 71 28 1128 1623 18879145 18878670 1.650000e-62 250.0
2 TraesCS7D01G037400 chr7D 88.514 148 11 2 1555 1699 18878600 18878456 1.020000e-39 174.0
3 TraesCS7D01G037400 chr7D 77.917 240 31 18 795 1027 18879559 18879335 2.240000e-26 130.0
4 TraesCS7D01G037400 chr7D 84.956 113 12 2 873 985 18842400 18842293 2.920000e-20 110.0
5 TraesCS7D01G037400 chr7A 85.129 1587 102 56 1109 2610 19418006 19419543 0.000000e+00 1500.0
6 TraesCS7D01G037400 chr7A 82.787 488 40 20 1287 1737 19372139 19372619 2.000000e-106 396.0
7 TraesCS7D01G037400 chr7A 80.769 338 42 14 1 337 19370057 19370372 2.760000e-60 243.0
8 TraesCS7D01G037400 chr7A 76.402 517 70 30 1128 1625 19252304 19251821 5.980000e-57 231.0
9 TraesCS7D01G037400 chr7A 86.139 202 13 5 1367 1565 19215801 19215612 1.300000e-48 204.0
10 TraesCS7D01G037400 chr7A 76.886 411 56 21 711 1105 19417542 19417929 2.180000e-46 196.0
11 TraesCS7D01G037400 chr7A 90.541 148 11 1 1555 1699 19251741 19251594 2.820000e-45 193.0
12 TraesCS7D01G037400 chr7A 87.209 172 18 4 2528 2697 19373510 19373679 2.820000e-45 193.0
13 TraesCS7D01G037400 chr7A 89.189 148 13 1 1555 1699 19215493 19215346 6.110000e-42 182.0
14 TraesCS7D01G037400 chr7A 90.647 139 8 3 1610 1745 19235615 19235479 2.200000e-41 180.0
15 TraesCS7D01G037400 chr7A 91.057 123 10 1 985 1107 19371754 19371875 6.150000e-37 165.0
16 TraesCS7D01G037400 chr7A 84.516 155 16 5 268 422 19374811 19374957 2.230000e-31 147.0
17 TraesCS7D01G037400 chr7A 76.630 184 18 16 2595 2776 19420269 19420429 8.240000e-11 78.7
18 TraesCS7D01G037400 chr4A 85.736 673 52 17 1096 1735 713829977 713830638 0.000000e+00 671.0
19 TraesCS7D01G037400 chr4A 80.670 657 70 25 1109 1741 713399167 713399790 9.060000e-125 457.0
20 TraesCS7D01G037400 chr4A 84.767 407 35 17 2384 2776 713832968 713833361 1.560000e-102 383.0
21 TraesCS7D01G037400 chr4A 91.102 236 18 1 1851 2083 713370657 713370892 1.600000e-82 316.0
22 TraesCS7D01G037400 chr4A 79.245 424 39 21 1306 1699 713140343 713140747 1.650000e-62 250.0
23 TraesCS7D01G037400 chr4A 76.448 518 64 35 1125 1623 713120068 713120546 7.730000e-56 228.0
24 TraesCS7D01G037400 chr4A 89.362 188 8 8 1998 2181 713831979 713832158 2.780000e-55 226.0
25 TraesCS7D01G037400 chr4A 88.462 182 12 2 1527 1699 713120576 713120757 7.790000e-51 211.0
26 TraesCS7D01G037400 chr4A 77.297 370 43 19 750 1107 713829590 713829930 2.200000e-41 180.0
27 TraesCS7D01G037400 chr4A 80.788 203 17 12 1104 1285 713367673 713367874 3.730000e-29 139.0
28 TraesCS7D01G037400 chr4A 89.815 108 11 0 1350 1457 713826888 713826995 3.730000e-29 139.0
29 TraesCS7D01G037400 chr4A 79.186 221 25 16 873 1084 713119775 713119983 1.730000e-27 134.0


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 TraesCS7D01G037400 chr7D 18925453 18928228 2775 False 5127.000000 5127 100.000000 1 2776 1 chr7D.!!$F1 2775
1 TraesCS7D01G037400 chr7A 19417542 19420429 2887 False 591.566667 1500 79.548333 711 2776 3 chr7A.!!$F2 2065
2 TraesCS7D01G037400 chr7A 19370057 19374957 4900 False 228.800000 396 85.267600 1 2697 5 chr7A.!!$F1 2696
3 TraesCS7D01G037400 chr7A 19251594 19252304 710 True 212.000000 231 83.471500 1128 1699 2 chr7A.!!$R3 571
4 TraesCS7D01G037400 chr4A 713399167 713399790 623 False 457.000000 457 80.670000 1109 1741 1 chr4A.!!$F2 632
5 TraesCS7D01G037400 chr4A 713826888 713833361 6473 False 319.800000 671 85.395400 750 2776 5 chr4A.!!$F5 2026
6 TraesCS7D01G037400 chr4A 713367673 713370892 3219 False 227.500000 316 85.945000 1104 2083 2 chr4A.!!$F4 979

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
898 2860 0.392336 GACCCTCTGCTCTGCCTATG 59.608 60.0 0.0 0.0 0.0 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 8585 0.388659 ACTGCAGAGCGATGATCCTC 59.611 55.0 23.35 3.62 0.0 3.71 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
67 68 6.856938 GGTAGTAAGAGTAGTATGTTCATGCG 59.143 42.308 0.00 0.00 0.00 4.73
70 71 4.737855 AGAGTAGTATGTTCATGCGGTT 57.262 40.909 0.00 0.00 0.00 4.44
82 83 6.450545 TGTTCATGCGGTTTTGAAATTATGA 58.549 32.000 0.00 0.00 33.90 2.15
83 84 6.364706 TGTTCATGCGGTTTTGAAATTATGAC 59.635 34.615 0.00 0.00 33.90 3.06
97 98 8.934023 TGAAATTATGACTAAAAGTTGGAGGT 57.066 30.769 0.00 0.00 0.00 3.85
119 120 6.442564 AGGTACAACTGATGTAGGGATGTAAA 59.557 38.462 0.00 0.00 45.00 2.01
122 123 6.122277 ACAACTGATGTAGGGATGTAAATGG 58.878 40.000 0.00 0.00 41.63 3.16
135 136 6.105333 GGATGTAAATGGCAAATAAACAGCA 58.895 36.000 0.00 0.00 0.00 4.41
138 139 4.348863 AAATGGCAAATAAACAGCACCA 57.651 36.364 0.00 0.00 0.00 4.17
140 141 2.315176 TGGCAAATAAACAGCACCAGT 58.685 42.857 0.00 0.00 0.00 4.00
144 145 4.485163 GCAAATAAACAGCACCAGTAAGG 58.515 43.478 0.00 0.00 45.67 2.69
147 148 0.478507 AAACAGCACCAGTAAGGCCT 59.521 50.000 0.00 0.00 43.14 5.19
148 149 1.358152 AACAGCACCAGTAAGGCCTA 58.642 50.000 5.16 0.00 43.14 3.93
157 158 5.758784 GCACCAGTAAGGCCTATTTAGTTAG 59.241 44.000 5.16 0.00 43.14 2.34
159 160 7.336396 CACCAGTAAGGCCTATTTAGTTAGTT 58.664 38.462 5.16 0.00 43.14 2.24
160 161 7.827729 CACCAGTAAGGCCTATTTAGTTAGTTT 59.172 37.037 5.16 0.00 43.14 2.66
162 163 9.895138 CCAGTAAGGCCTATTTAGTTAGTTTTA 57.105 33.333 5.16 0.00 0.00 1.52
169 170 8.209584 GGCCTATTTAGTTAGTTTTACCTAGCT 58.790 37.037 0.00 0.00 33.67 3.32
187 188 8.045720 ACCTAGCTCTATATTTCATTTTCCCA 57.954 34.615 0.00 0.00 0.00 4.37
188 189 8.160106 ACCTAGCTCTATATTTCATTTTCCCAG 58.840 37.037 0.00 0.00 0.00 4.45
190 191 9.213799 CTAGCTCTATATTTCATTTTCCCAGAC 57.786 37.037 0.00 0.00 0.00 3.51
191 192 7.577303 AGCTCTATATTTCATTTTCCCAGACA 58.423 34.615 0.00 0.00 0.00 3.41
193 194 9.507329 GCTCTATATTTCATTTTCCCAGACATA 57.493 33.333 0.00 0.00 0.00 2.29
282 283 6.299141 TCCCTAAGCTGATGATTTGGAATAC 58.701 40.000 0.00 0.00 36.78 1.89
284 285 5.474876 CCTAAGCTGATGATTTGGAATACCC 59.525 44.000 0.00 0.00 36.78 3.69
299 300 6.285224 TGGAATACCCTTGATGTGTATTACG 58.715 40.000 0.00 0.00 38.21 3.18
312 313 6.216801 TGTGTATTACGTATCTTTGCTCCT 57.783 37.500 0.00 0.00 0.00 3.69
316 317 5.762825 ATTACGTATCTTTGCTCCTCGTA 57.237 39.130 0.00 0.00 0.00 3.43
321 322 5.472478 ACGTATCTTTGCTCCTCGTATATGA 59.528 40.000 0.00 0.00 0.00 2.15
352 353 3.145212 TCGATAGAATGTGTCGTGGTG 57.855 47.619 0.00 0.00 46.15 4.17
356 1172 2.910688 AGAATGTGTCGTGGTGAAGT 57.089 45.000 0.00 0.00 0.00 3.01
382 1198 7.214467 ACCAATAAAAATGGATAGTATGCCG 57.786 36.000 0.00 0.00 40.56 5.69
383 1199 6.092748 CCAATAAAAATGGATAGTATGCCGC 58.907 40.000 0.00 0.00 40.56 6.53
405 1224 8.638565 GCCGCTAAAATTATAGTTGCAAATATG 58.361 33.333 25.41 10.74 0.00 1.78
421 1240 8.449251 TGCAAATATGTTGAATATGCTACTGA 57.551 30.769 0.00 0.00 33.66 3.41
423 1242 9.390795 GCAAATATGTTGAATATGCTACTGAAG 57.609 33.333 0.00 0.00 0.00 3.02
445 1284 9.833813 TGAAGCTTCATTATGGTGGAACACGTA 62.834 40.741 25.16 0.00 46.58 3.57
474 1313 8.892723 TCTGATTTTAAGTTGGTATATGTGCTG 58.107 33.333 0.00 0.00 0.00 4.41
475 1314 8.574251 TGATTTTAAGTTGGTATATGTGCTGT 57.426 30.769 0.00 0.00 0.00 4.40
476 1315 8.673711 TGATTTTAAGTTGGTATATGTGCTGTC 58.326 33.333 0.00 0.00 0.00 3.51
477 1316 7.987750 TTTTAAGTTGGTATATGTGCTGTCA 57.012 32.000 0.00 0.00 0.00 3.58
481 1320 7.466746 AAGTTGGTATATGTGCTGTCATTTT 57.533 32.000 0.00 0.00 0.00 1.82
483 1322 7.538575 AGTTGGTATATGTGCTGTCATTTTTC 58.461 34.615 0.00 0.00 0.00 2.29
486 1325 6.883756 TGGTATATGTGCTGTCATTTTTCAGA 59.116 34.615 0.00 0.00 34.02 3.27
487 1326 7.392953 TGGTATATGTGCTGTCATTTTTCAGAA 59.607 33.333 0.00 0.00 34.02 3.02
488 1327 8.408601 GGTATATGTGCTGTCATTTTTCAGAAT 58.591 33.333 0.00 0.00 34.02 2.40
489 1328 9.793252 GTATATGTGCTGTCATTTTTCAGAATT 57.207 29.630 0.00 0.00 34.02 2.17
531 1370 4.365514 TCAGCAGGTTTCAATGAGGTTA 57.634 40.909 0.00 0.00 0.00 2.85
532 1371 4.922206 TCAGCAGGTTTCAATGAGGTTAT 58.078 39.130 0.00 0.00 0.00 1.89
563 1406 6.791303 TCCGTTTTAGAATATTTGGTGCATC 58.209 36.000 0.00 0.00 0.00 3.91
565 1408 6.457663 CCGTTTTAGAATATTTGGTGCATCGA 60.458 38.462 0.00 0.00 0.00 3.59
722 1579 2.877043 ACCAAGTGAGCAGCAAAAAG 57.123 45.000 0.00 0.00 0.00 2.27
729 1586 5.789643 AGTGAGCAGCAAAAAGGAAAATA 57.210 34.783 0.00 0.00 0.00 1.40
734 1591 5.247862 AGCAGCAAAAAGGAAAATATTGGG 58.752 37.500 0.00 0.00 0.00 4.12
779 2733 3.627577 TGCTGGAATAAAAGCGGAGATTC 59.372 43.478 0.00 0.00 42.54 2.52
812 2766 3.419759 CCGACGAAAAGGGCGGTG 61.420 66.667 0.00 0.00 37.22 4.94
819 2773 4.684134 AAAGGGCGGTGGCATGCT 62.684 61.111 18.92 0.00 42.47 3.79
857 2811 3.406361 GTGCGTGCGTGTCTCCTG 61.406 66.667 0.00 0.00 0.00 3.86
860 2814 2.807045 CGTGCGTGTCTCCTGCTC 60.807 66.667 0.00 0.00 0.00 4.26
862 2816 2.601666 TGCGTGTCTCCTGCTCCT 60.602 61.111 0.00 0.00 0.00 3.69
895 2857 3.073735 CGACCCTCTGCTCTGCCT 61.074 66.667 0.00 0.00 0.00 4.75
896 2858 1.754621 CGACCCTCTGCTCTGCCTA 60.755 63.158 0.00 0.00 0.00 3.93
897 2859 1.112315 CGACCCTCTGCTCTGCCTAT 61.112 60.000 0.00 0.00 0.00 2.57
898 2860 0.392336 GACCCTCTGCTCTGCCTATG 59.608 60.000 0.00 0.00 0.00 2.23
900 2862 1.409251 CCCTCTGCTCTGCCTATGCT 61.409 60.000 0.00 0.00 38.71 3.79
901 2863 0.469070 CCTCTGCTCTGCCTATGCTT 59.531 55.000 0.00 0.00 38.71 3.91
944 2906 3.799755 GTGTCGCCACGCCATTCC 61.800 66.667 0.00 0.00 0.00 3.01
945 2907 4.015406 TGTCGCCACGCCATTCCT 62.015 61.111 0.00 0.00 0.00 3.36
946 2908 3.195698 GTCGCCACGCCATTCCTC 61.196 66.667 0.00 0.00 0.00 3.71
947 2909 4.812476 TCGCCACGCCATTCCTCG 62.812 66.667 0.00 0.00 0.00 4.63
953 2915 4.880537 CGCCATTCCTCGCGCTCT 62.881 66.667 5.56 0.00 42.17 4.09
954 2916 2.964389 GCCATTCCTCGCGCTCTC 60.964 66.667 5.56 0.00 0.00 3.20
955 2917 2.811101 CCATTCCTCGCGCTCTCT 59.189 61.111 5.56 0.00 0.00 3.10
956 2918 1.142748 CCATTCCTCGCGCTCTCTT 59.857 57.895 5.56 0.00 0.00 2.85
965 2927 1.216710 GCGCTCTCTTGCCACTAGT 59.783 57.895 0.00 0.00 0.00 2.57
1047 3009 1.958288 TCAGGGAAGGGAGGAAGAAG 58.042 55.000 0.00 0.00 0.00 2.85
1069 3038 1.594310 GTCTCAGGCTCAGACCACC 59.406 63.158 7.38 0.00 35.19 4.61
1110 3212 1.548269 GTACTGCTCCTGCTCTGAAGT 59.452 52.381 0.00 0.00 40.48 3.01
1123 3232 2.479656 CTCTGAAGTTGCTCTGCTGTTC 59.520 50.000 0.00 0.00 0.00 3.18
1224 3350 0.961753 GCAGGTAACCAGCTTTGCTT 59.038 50.000 0.00 0.00 36.40 3.91
1232 3370 0.528249 CCAGCTTTGCTTTGCGTTGT 60.528 50.000 0.00 0.00 36.40 3.32
1242 3380 2.479560 GCTTTGCGTTGTCACCTTCTTT 60.480 45.455 0.00 0.00 0.00 2.52
1265 3415 0.613260 TGGCCGTCTTGAACTAGCAT 59.387 50.000 0.00 0.00 0.00 3.79
1269 3419 2.094417 GCCGTCTTGAACTAGCATTCAC 59.906 50.000 0.00 0.00 38.31 3.18
1278 3428 2.636830 ACTAGCATTCACTCATGGCAC 58.363 47.619 0.00 0.00 0.00 5.01
1286 3436 0.107993 CACTCATGGCACCATCGACT 60.108 55.000 0.00 0.00 33.90 4.18
1294 3461 1.079503 GCACCATCGACTCTGTTTCC 58.920 55.000 0.00 0.00 0.00 3.13
1296 3463 0.389948 ACCATCGACTCTGTTTCCGC 60.390 55.000 0.00 0.00 0.00 5.54
1299 3466 0.603569 ATCGACTCTGTTTCCGCAGT 59.396 50.000 0.00 0.00 37.70 4.40
1300 3467 1.241165 TCGACTCTGTTTCCGCAGTA 58.759 50.000 0.00 0.00 37.70 2.74
1307 3477 1.745489 GTTTCCGCAGTAGGGCCAG 60.745 63.158 6.18 0.00 0.00 4.85
1433 3612 3.062466 CGTCGAGGTGCTCCAGGA 61.062 66.667 7.70 0.57 35.89 3.86
1474 3656 3.503363 GCACCGTGCTGCCAGATC 61.503 66.667 16.51 0.00 40.96 2.75
1539 3736 2.363975 GGTGCCCGACCAGGATACA 61.364 63.158 0.00 0.00 45.34 2.29
1685 4041 2.501610 GGAGGACATGGAGGACGC 59.498 66.667 0.00 0.00 0.00 5.19
1686 4042 2.501610 GAGGACATGGAGGACGCC 59.498 66.667 0.00 0.00 0.00 5.68
1764 4201 9.857957 GTTAGCTATCCATGGTAGAATTAGTAC 57.142 37.037 19.53 0.00 0.00 2.73
1767 4204 9.469097 AGCTATCCATGGTAGAATTAGTACTAG 57.531 37.037 19.53 0.00 0.00 2.57
1768 4205 8.192110 GCTATCCATGGTAGAATTAGTACTAGC 58.808 40.741 19.53 5.28 37.54 3.42
1800 5322 1.810455 TCCCATGGATGCATCTCTCA 58.190 50.000 25.28 15.62 0.00 3.27
1805 5327 3.215151 CATGGATGCATCTCTCAAAGCT 58.785 45.455 25.28 0.00 0.00 3.74
1823 5348 7.816640 TCAAAGCTTGTAGTAATAAAAGGCTG 58.183 34.615 0.00 0.00 0.00 4.85
1902 7940 7.402071 CCAGCTTATGTCCCCCTATTATACTTA 59.598 40.741 0.00 0.00 0.00 2.24
2009 8068 6.280643 TGTATGCAATTATAGTCGAGCACTT 58.719 36.000 0.00 0.00 36.43 3.16
2017 8076 6.505044 TTATAGTCGAGCACTTAACACTGA 57.495 37.500 0.00 0.00 36.43 3.41
2084 8164 7.659390 TGGGCGAAAAATTCAAAGAAATTGTAT 59.341 29.630 0.00 0.00 40.11 2.29
2153 8234 0.459489 TCAAAACTGCTGCAACACCC 59.541 50.000 3.02 0.00 0.00 4.61
2185 8279 4.617253 ACACATAGAATTAGCGGCCATA 57.383 40.909 2.24 0.00 0.00 2.74
2194 8288 5.362430 AGAATTAGCGGCCATATTCCAAAAA 59.638 36.000 2.24 0.00 0.00 1.94
2195 8289 4.647424 TTAGCGGCCATATTCCAAAAAG 57.353 40.909 2.24 0.00 0.00 2.27
2337 8585 0.518636 CACCTTCAGCGAACACCATG 59.481 55.000 0.00 0.00 0.00 3.66
2354 8602 2.508361 TGAGGATCATCGCTCTGCA 58.492 52.632 2.49 0.00 42.56 4.41
2374 8924 4.087892 GGCCTGCCGAGCTCTCAA 62.088 66.667 12.85 0.00 0.00 3.02
2483 9225 8.498054 TGCTAGATTTCAATAGAAGTTGGAAG 57.502 34.615 0.00 0.00 34.71 3.46
2501 9243 3.181500 GGAAGAAGTGAAGCGTTTTGTGT 60.181 43.478 0.00 0.00 0.00 3.72
2581 9337 2.398588 TCTGTAATGCCTAGGACCCAG 58.601 52.381 14.75 10.15 0.00 4.45
2613 9369 5.360591 ACAATTCATTATCAGACGGGACTC 58.639 41.667 0.00 0.00 0.00 3.36
2617 10114 5.677319 TCATTATCAGACGGGACTCTTTT 57.323 39.130 0.00 0.00 0.00 2.27
2619 10116 2.770164 ATCAGACGGGACTCTTTTGG 57.230 50.000 0.00 0.00 0.00 3.28
2620 10117 1.712056 TCAGACGGGACTCTTTTGGA 58.288 50.000 0.00 0.00 0.00 3.53
2621 10118 1.618837 TCAGACGGGACTCTTTTGGAG 59.381 52.381 0.00 0.00 46.87 3.86
2622 10119 1.618837 CAGACGGGACTCTTTTGGAGA 59.381 52.381 0.00 0.00 44.45 3.71
2623 10120 2.234908 CAGACGGGACTCTTTTGGAGAT 59.765 50.000 0.00 0.00 44.45 2.75
2635 10132 7.911651 ACTCTTTTGGAGATAGACATTCAGAA 58.088 34.615 0.00 0.00 44.45 3.02
2639 10136 6.932356 TTGGAGATAGACATTCAGAATTGC 57.068 37.500 0.00 0.00 0.00 3.56
2665 10162 7.879160 CCAAAATTTGAAGAAATCAGGATTGGA 59.121 33.333 7.37 0.00 39.33 3.53
2684 10208 2.412847 GGAATGTTCGAAGGAAAGCACG 60.413 50.000 0.00 0.00 33.05 5.34
2685 10209 1.156736 ATGTTCGAAGGAAAGCACGG 58.843 50.000 0.00 0.00 33.05 4.94
2715 10239 9.059260 TGGAACACTAAAATTCAAACCTAGTAC 57.941 33.333 0.00 0.00 0.00 2.73
2716 10240 8.225777 GGAACACTAAAATTCAAACCTAGTACG 58.774 37.037 0.00 0.00 0.00 3.67
2717 10241 7.662604 ACACTAAAATTCAAACCTAGTACGG 57.337 36.000 0.00 0.00 0.00 4.02
2718 10242 6.148315 ACACTAAAATTCAAACCTAGTACGGC 59.852 38.462 0.00 0.00 0.00 5.68
2719 10243 6.148150 CACTAAAATTCAAACCTAGTACGGCA 59.852 38.462 0.00 0.00 0.00 5.69
2720 10244 5.366829 AAAATTCAAACCTAGTACGGCAC 57.633 39.130 0.00 0.00 0.00 5.01
2721 10245 3.975168 ATTCAAACCTAGTACGGCACT 57.025 42.857 0.00 0.00 41.62 4.40
2722 10246 3.308438 TTCAAACCTAGTACGGCACTC 57.692 47.619 0.00 0.00 38.80 3.51
2723 10247 2.241160 TCAAACCTAGTACGGCACTCA 58.759 47.619 0.00 0.00 38.80 3.41
2724 10248 2.629137 TCAAACCTAGTACGGCACTCAA 59.371 45.455 0.00 0.00 38.80 3.02
2725 10249 3.069872 TCAAACCTAGTACGGCACTCAAA 59.930 43.478 0.00 0.00 38.80 2.69
2726 10250 3.975168 AACCTAGTACGGCACTCAAAT 57.025 42.857 0.00 0.00 38.80 2.32
2727 10251 3.521947 ACCTAGTACGGCACTCAAATC 57.478 47.619 0.00 0.00 38.80 2.17
2728 10252 2.829720 ACCTAGTACGGCACTCAAATCA 59.170 45.455 0.00 0.00 38.80 2.57
2729 10253 3.259876 ACCTAGTACGGCACTCAAATCAA 59.740 43.478 0.00 0.00 38.80 2.57
2730 10254 3.617263 CCTAGTACGGCACTCAAATCAAC 59.383 47.826 0.00 0.00 38.80 3.18
2731 10255 3.120321 AGTACGGCACTCAAATCAACA 57.880 42.857 0.00 0.00 28.33 3.33
2732 10256 3.472652 AGTACGGCACTCAAATCAACAA 58.527 40.909 0.00 0.00 28.33 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.899278 ACTACCCCAACCAAAGAAATATGT 58.101 37.500 0.00 0.00 0.00 2.29
25 26 7.832187 TCTTACTACCCCAACCAAAGAAATATG 59.168 37.037 0.00 0.00 0.00 1.78
36 37 5.896106 ACATACTACTCTTACTACCCCAACC 59.104 44.000 0.00 0.00 0.00 3.77
97 98 7.279615 CCATTTACATCCCTACATCAGTTGTA 58.720 38.462 0.00 0.00 39.87 2.41
119 120 2.899256 ACTGGTGCTGTTTATTTGCCAT 59.101 40.909 0.00 0.00 0.00 4.40
122 123 4.485163 CCTTACTGGTGCTGTTTATTTGC 58.515 43.478 0.00 0.00 0.00 3.68
135 136 7.506361 AACTAACTAAATAGGCCTTACTGGT 57.494 36.000 12.58 2.15 38.35 4.00
138 139 9.896645 GGTAAAACTAACTAAATAGGCCTTACT 57.103 33.333 12.58 0.00 0.00 2.24
144 145 9.258826 GAGCTAGGTAAAACTAACTAAATAGGC 57.741 37.037 0.00 0.00 0.00 3.93
162 163 8.045720 TGGGAAAATGAAATATAGAGCTAGGT 57.954 34.615 0.00 0.00 0.00 3.08
163 164 8.378565 TCTGGGAAAATGAAATATAGAGCTAGG 58.621 37.037 0.00 0.00 0.00 3.02
166 167 7.577303 TGTCTGGGAAAATGAAATATAGAGCT 58.423 34.615 0.00 0.00 0.00 4.09
184 185 9.927668 ACAATTCAATAAAGTTTTATGTCTGGG 57.072 29.630 0.00 0.00 33.85 4.45
233 234 7.027874 TGTAAACAGGGTTCTGAATAATCCT 57.972 36.000 0.00 0.00 40.80 3.24
240 241 3.655777 AGGGATGTAAACAGGGTTCTGAA 59.344 43.478 0.00 0.00 43.49 3.02
243 244 4.324331 GCTTAGGGATGTAAACAGGGTTCT 60.324 45.833 0.00 0.00 0.00 3.01
282 283 7.518370 GCAAAGATACGTAATACACATCAAGGG 60.518 40.741 0.00 0.00 0.00 3.95
284 285 8.131455 AGCAAAGATACGTAATACACATCAAG 57.869 34.615 0.00 0.00 0.00 3.02
299 300 8.029522 TGAATCATATACGAGGAGCAAAGATAC 58.970 37.037 0.00 0.00 0.00 2.24
338 339 3.185797 GGTTACTTCACCACGACACATTC 59.814 47.826 0.00 0.00 36.73 2.67
342 343 2.228138 TGGTTACTTCACCACGACAC 57.772 50.000 0.00 0.00 42.27 3.67
348 349 7.841282 TCCATTTTTATTGGTTACTTCACCA 57.159 32.000 0.00 0.00 45.68 4.17
356 1172 8.788806 CGGCATACTATCCATTTTTATTGGTTA 58.211 33.333 0.00 0.00 35.64 2.85
361 1177 8.630054 TTAGCGGCATACTATCCATTTTTATT 57.370 30.769 1.45 0.00 0.00 1.40
415 1234 5.674525 TCCACCATAATGAAGCTTCAGTAG 58.325 41.667 32.43 24.54 40.50 2.57
421 1240 3.440173 CGTGTTCCACCATAATGAAGCTT 59.560 43.478 0.00 0.00 0.00 3.74
423 1242 2.747446 ACGTGTTCCACCATAATGAAGC 59.253 45.455 0.00 0.00 0.00 3.86
427 1246 3.255725 ACGTACGTGTTCCACCATAATG 58.744 45.455 22.14 0.00 0.00 1.90
428 1247 3.194116 AGACGTACGTGTTCCACCATAAT 59.806 43.478 28.16 0.00 0.00 1.28
430 1249 2.095110 CAGACGTACGTGTTCCACCATA 60.095 50.000 28.16 0.00 0.00 2.74
431 1250 0.963962 AGACGTACGTGTTCCACCAT 59.036 50.000 28.16 0.00 0.00 3.55
433 1252 0.311790 TCAGACGTACGTGTTCCACC 59.688 55.000 28.16 9.39 0.00 4.61
445 1284 8.879759 CACATATACCAACTTAAAATCAGACGT 58.120 33.333 0.00 0.00 0.00 4.34
447 1286 8.893727 AGCACATATACCAACTTAAAATCAGAC 58.106 33.333 0.00 0.00 0.00 3.51
502 1341 7.048629 TCATTGAAACCTGCTGATAAAAACA 57.951 32.000 0.00 0.00 0.00 2.83
508 1347 4.574674 ACCTCATTGAAACCTGCTGATA 57.425 40.909 0.00 0.00 0.00 2.15
531 1370 9.338622 CCAAATATTCTAAAACGGAGGAAGTAT 57.661 33.333 0.00 0.00 0.00 2.12
532 1371 8.323567 ACCAAATATTCTAAAACGGAGGAAGTA 58.676 33.333 0.00 0.00 0.00 2.24
709 1566 5.933463 CCAATATTTTCCTTTTTGCTGCTCA 59.067 36.000 0.00 0.00 0.00 4.26
734 1591 4.887748 TCGATGCTTTCTCAGGGATATTC 58.112 43.478 0.00 0.00 0.00 1.75
779 2733 1.205064 CGGACAAAGACAAGCGCAG 59.795 57.895 11.47 3.78 0.00 5.18
784 2738 3.303132 CCTTTTCGTCGGACAAAGACAAG 60.303 47.826 17.69 11.00 38.46 3.16
785 2739 2.610374 CCTTTTCGTCGGACAAAGACAA 59.390 45.455 17.69 3.69 38.46 3.18
843 2797 2.807045 GAGCAGGAGACACGCACG 60.807 66.667 0.00 0.00 33.79 5.34
844 2798 2.433318 GGAGCAGGAGACACGCAC 60.433 66.667 0.00 0.00 33.79 5.34
846 2800 2.183046 GAGGAGCAGGAGACACGC 59.817 66.667 0.00 0.00 0.00 5.34
848 2802 1.594310 GGTGAGGAGCAGGAGACAC 59.406 63.158 0.00 0.00 0.00 3.67
849 2803 1.979155 CGGTGAGGAGCAGGAGACA 60.979 63.158 0.00 0.00 0.00 3.41
850 2804 2.888863 CGGTGAGGAGCAGGAGAC 59.111 66.667 0.00 0.00 0.00 3.36
851 2805 3.071206 GCGGTGAGGAGCAGGAGA 61.071 66.667 0.00 0.00 0.00 3.71
857 2811 1.596477 GATGGATGCGGTGAGGAGC 60.596 63.158 0.00 0.00 0.00 4.70
858 2812 0.531532 GTGATGGATGCGGTGAGGAG 60.532 60.000 0.00 0.00 0.00 3.69
860 2814 1.524621 GGTGATGGATGCGGTGAGG 60.525 63.158 0.00 0.00 0.00 3.86
862 2816 2.186644 CGGTGATGGATGCGGTGA 59.813 61.111 0.00 0.00 0.00 4.02
895 2857 2.677836 GCCATTGACGAGACAAAGCATA 59.322 45.455 0.00 0.00 35.05 3.14
896 2858 1.470098 GCCATTGACGAGACAAAGCAT 59.530 47.619 0.00 0.00 35.05 3.79
897 2859 0.874390 GCCATTGACGAGACAAAGCA 59.126 50.000 0.00 0.00 35.05 3.91
898 2860 0.179215 CGCCATTGACGAGACAAAGC 60.179 55.000 0.00 0.35 33.44 3.51
900 2862 1.573829 GGCGCCATTGACGAGACAAA 61.574 55.000 24.80 0.00 33.44 2.83
901 2863 2.032634 GGCGCCATTGACGAGACAA 61.033 57.895 24.80 0.00 0.00 3.18
937 2899 2.914777 AAGAGAGCGCGAGGAATGGC 62.915 60.000 12.10 0.00 0.00 4.40
938 2900 1.142748 AAGAGAGCGCGAGGAATGG 59.857 57.895 12.10 0.00 0.00 3.16
939 2901 1.760268 GCAAGAGAGCGCGAGGAATG 61.760 60.000 12.10 1.63 0.00 2.67
940 2902 1.520342 GCAAGAGAGCGCGAGGAAT 60.520 57.895 12.10 0.00 0.00 3.01
941 2903 2.125912 GCAAGAGAGCGCGAGGAA 60.126 61.111 12.10 0.00 0.00 3.36
942 2904 4.135153 GGCAAGAGAGCGCGAGGA 62.135 66.667 12.10 0.00 34.64 3.71
943 2905 4.441695 TGGCAAGAGAGCGCGAGG 62.442 66.667 12.10 0.00 34.64 4.63
944 2906 2.271607 TAGTGGCAAGAGAGCGCGAG 62.272 60.000 12.10 0.00 34.64 5.03
945 2907 2.271607 CTAGTGGCAAGAGAGCGCGA 62.272 60.000 12.10 0.00 34.64 5.87
946 2908 1.875813 CTAGTGGCAAGAGAGCGCG 60.876 63.158 0.00 0.00 34.64 6.86
947 2909 0.804156 GACTAGTGGCAAGAGAGCGC 60.804 60.000 0.00 0.00 34.64 5.92
948 2910 0.524392 CGACTAGTGGCAAGAGAGCG 60.524 60.000 0.00 3.95 34.64 5.03
949 2911 0.528470 ACGACTAGTGGCAAGAGAGC 59.472 55.000 0.00 0.00 0.00 4.09
950 2912 1.133407 GGACGACTAGTGGCAAGAGAG 59.867 57.143 0.00 1.12 0.00 3.20
951 2913 1.174783 GGACGACTAGTGGCAAGAGA 58.825 55.000 0.00 0.00 0.00 3.10
952 2914 0.173708 GGGACGACTAGTGGCAAGAG 59.826 60.000 0.00 0.00 0.00 2.85
953 2915 2.273908 GGGACGACTAGTGGCAAGA 58.726 57.895 0.00 0.00 0.00 3.02
954 2916 4.913126 GGGACGACTAGTGGCAAG 57.087 61.111 0.00 0.00 0.00 4.01
1026 2988 2.668850 TCTTCCTCCCTTCCCTGAAT 57.331 50.000 0.00 0.00 0.00 2.57
1047 3009 1.509004 GTCTGAGCCTGAGACCGAC 59.491 63.158 0.00 0.00 34.84 4.79
1075 3049 4.177026 AGCAGTACGAGTTTGAGCTTATG 58.823 43.478 0.00 0.00 0.00 1.90
1110 3212 2.669569 GCCGGAACAGCAGAGCAA 60.670 61.111 5.05 0.00 0.00 3.91
1224 3350 3.859411 AAAAAGAAGGTGACAACGCAA 57.141 38.095 0.00 0.00 0.00 4.85
1242 3380 2.292292 GCTAGTTCAAGACGGCCAAAAA 59.708 45.455 2.24 0.00 0.00 1.94
1247 3385 1.666189 GAATGCTAGTTCAAGACGGCC 59.334 52.381 0.00 0.00 33.25 6.13
1252 3390 5.181009 CCATGAGTGAATGCTAGTTCAAGA 58.819 41.667 0.00 0.00 39.61 3.02
1255 3405 3.273434 GCCATGAGTGAATGCTAGTTCA 58.727 45.455 0.00 0.00 35.84 3.18
1262 3412 1.066605 GATGGTGCCATGAGTGAATGC 59.933 52.381 8.64 0.00 36.70 3.56
1265 3415 0.612744 TCGATGGTGCCATGAGTGAA 59.387 50.000 8.64 0.00 36.70 3.18
1269 3419 0.463204 AGAGTCGATGGTGCCATGAG 59.537 55.000 8.64 2.99 36.70 2.90
1278 3428 0.389817 TGCGGAAACAGAGTCGATGG 60.390 55.000 0.00 0.00 0.00 3.51
1286 3436 1.295423 GCCCTACTGCGGAAACAGA 59.705 57.895 0.00 0.00 40.25 3.41
1294 3461 2.125106 GTTCCTGGCCCTACTGCG 60.125 66.667 0.00 0.00 0.00 5.18
1296 3463 1.201429 AGTGGTTCCTGGCCCTACTG 61.201 60.000 0.00 0.00 0.00 2.74
1299 3466 1.615424 GGAGTGGTTCCTGGCCCTA 60.615 63.158 0.00 0.00 43.16 3.53
1300 3467 2.936032 GGAGTGGTTCCTGGCCCT 60.936 66.667 0.00 0.00 43.16 5.19
1334 3510 0.105039 GTCCCTGCGGTATTCCTCAG 59.895 60.000 1.54 1.54 43.79 3.35
1400 3579 1.495584 GACGTTCTTGCGGTTCAGCA 61.496 55.000 0.00 0.00 46.54 4.41
1433 3612 3.432588 CGACGTGCTCCTCCTCGT 61.433 66.667 0.00 0.00 39.21 4.18
1457 3639 3.503363 GATCTGGCAGCACGGTGC 61.503 66.667 25.00 25.00 45.46 5.01
1536 3733 1.303888 AGGGACGAAGACGCCTGTA 60.304 57.895 0.00 0.00 43.96 2.74
1539 3736 4.070552 GCAGGGACGAAGACGCCT 62.071 66.667 0.00 0.00 43.96 5.52
1764 4201 7.911651 TCCATGGGATTTATTCTTCTAGCTAG 58.088 38.462 15.01 15.01 0.00 3.42
1766 4203 6.770286 TCCATGGGATTTATTCTTCTAGCT 57.230 37.500 13.02 0.00 0.00 3.32
1767 4204 6.127786 GCATCCATGGGATTTATTCTTCTAGC 60.128 42.308 13.02 0.00 39.79 3.42
1768 4205 6.944290 TGCATCCATGGGATTTATTCTTCTAG 59.056 38.462 13.02 0.00 39.79 2.43
1800 5322 7.360946 CGACAGCCTTTTATTACTACAAGCTTT 60.361 37.037 0.00 0.00 0.00 3.51
1805 5327 5.797051 ACCGACAGCCTTTTATTACTACAA 58.203 37.500 0.00 0.00 0.00 2.41
1823 5348 1.661112 GATTAGCAGCAGTGAACCGAC 59.339 52.381 0.00 0.00 0.00 4.79
2009 8068 7.416817 CACTGTGTTCATCAATTTCAGTGTTA 58.583 34.615 12.33 0.00 43.17 2.41
2017 8076 4.473444 AGTCCCACTGTGTTCATCAATTT 58.527 39.130 7.08 0.00 0.00 1.82
2084 8164 4.287067 GTGAATTGCCTCCTCTATCCCATA 59.713 45.833 0.00 0.00 0.00 2.74
2168 8262 5.435686 TGGAATATGGCCGCTAATTCTAT 57.564 39.130 14.87 0.00 0.00 1.98
2208 8401 6.567602 AGGATTGCTAGACCTGTTAATTCT 57.432 37.500 0.00 0.00 32.39 2.40
2219 8412 8.512956 TCGAGTATTATGTTAGGATTGCTAGAC 58.487 37.037 0.00 0.00 0.00 2.59
2337 8585 0.388659 ACTGCAGAGCGATGATCCTC 59.611 55.000 23.35 3.62 0.00 3.71
2374 8924 4.020218 AGCCTGTGACATACTGTACATTGT 60.020 41.667 0.00 0.69 0.00 2.71
2448 9190 8.704668 TCTATTGAAATCTAGCATAAGGTCACA 58.295 33.333 0.00 0.00 0.00 3.58
2483 9225 3.098636 GACACACAAAACGCTTCACTTC 58.901 45.455 0.00 0.00 0.00 3.01
2613 9369 7.914346 GCAATTCTGAATGTCTATCTCCAAAAG 59.086 37.037 3.22 0.00 0.00 2.27
2617 10114 5.104402 TGGCAATTCTGAATGTCTATCTCCA 60.104 40.000 3.22 1.03 0.00 3.86
2619 10116 6.932356 TTGGCAATTCTGAATGTCTATCTC 57.068 37.500 3.22 0.00 0.00 2.75
2620 10117 7.707624 TTTTGGCAATTCTGAATGTCTATCT 57.292 32.000 0.00 0.00 0.00 1.98
2621 10118 8.937634 AATTTTGGCAATTCTGAATGTCTATC 57.062 30.769 0.00 0.00 0.00 2.08
2622 10119 9.158233 CAAATTTTGGCAATTCTGAATGTCTAT 57.842 29.630 0.00 0.00 0.00 1.98
2623 10120 8.366401 TCAAATTTTGGCAATTCTGAATGTCTA 58.634 29.630 0.00 0.00 0.00 2.59
2635 10132 7.225725 TCCTGATTTCTTCAAATTTTGGCAAT 58.774 30.769 0.00 3.34 31.94 3.56
2639 10136 7.879160 TCCAATCCTGATTTCTTCAAATTTTGG 59.121 33.333 9.18 0.00 31.94 3.28
2665 10162 1.535462 CCGTGCTTTCCTTCGAACATT 59.465 47.619 0.00 0.00 0.00 2.71
2684 10208 6.649141 GGTTTGAATTTTAGTGTTCCATTCCC 59.351 38.462 0.00 0.00 0.00 3.97
2685 10209 7.441836 AGGTTTGAATTTTAGTGTTCCATTCC 58.558 34.615 0.00 0.00 0.00 3.01
2697 10221 6.232692 AGTGCCGTACTAGGTTTGAATTTTA 58.767 36.000 0.00 0.00 38.04 1.52
2702 10226 2.629137 TGAGTGCCGTACTAGGTTTGAA 59.371 45.455 0.00 0.00 40.53 2.69
2709 10233 4.242475 TGTTGATTTGAGTGCCGTACTAG 58.758 43.478 0.00 0.00 40.53 2.57
2711 10235 3.120321 TGTTGATTTGAGTGCCGTACT 57.880 42.857 0.00 0.00 44.02 2.73
2712 10236 3.889196 TTGTTGATTTGAGTGCCGTAC 57.111 42.857 0.00 0.00 0.00 3.67
2713 10237 4.068599 TGATTGTTGATTTGAGTGCCGTA 58.931 39.130 0.00 0.00 0.00 4.02
2714 10238 2.884012 TGATTGTTGATTTGAGTGCCGT 59.116 40.909 0.00 0.00 0.00 5.68
2715 10239 3.557577 TGATTGTTGATTTGAGTGCCG 57.442 42.857 0.00 0.00 0.00 5.69
2716 10240 6.424509 TGATTTTGATTGTTGATTTGAGTGCC 59.575 34.615 0.00 0.00 0.00 5.01
2717 10241 7.410800 TGATTTTGATTGTTGATTTGAGTGC 57.589 32.000 0.00 0.00 0.00 4.40
2718 10242 7.170151 TGCTGATTTTGATTGTTGATTTGAGTG 59.830 33.333 0.00 0.00 0.00 3.51
2719 10243 7.211573 TGCTGATTTTGATTGTTGATTTGAGT 58.788 30.769 0.00 0.00 0.00 3.41
2720 10244 7.646446 TGCTGATTTTGATTGTTGATTTGAG 57.354 32.000 0.00 0.00 0.00 3.02
2721 10245 8.499967 CATTGCTGATTTTGATTGTTGATTTGA 58.500 29.630 0.00 0.00 0.00 2.69
2722 10246 8.286800 ACATTGCTGATTTTGATTGTTGATTTG 58.713 29.630 0.00 0.00 0.00 2.32
2723 10247 8.286800 CACATTGCTGATTTTGATTGTTGATTT 58.713 29.630 0.00 0.00 0.00 2.17
2724 10248 7.442969 ACACATTGCTGATTTTGATTGTTGATT 59.557 29.630 0.00 0.00 0.00 2.57
2725 10249 6.932400 ACACATTGCTGATTTTGATTGTTGAT 59.068 30.769 0.00 0.00 0.00 2.57
2726 10250 6.282167 ACACATTGCTGATTTTGATTGTTGA 58.718 32.000 0.00 0.00 0.00 3.18
2727 10251 6.533819 ACACATTGCTGATTTTGATTGTTG 57.466 33.333 0.00 0.00 0.00 3.33
2728 10252 6.366877 GCTACACATTGCTGATTTTGATTGTT 59.633 34.615 0.00 0.00 0.00 2.83
2729 10253 5.865552 GCTACACATTGCTGATTTTGATTGT 59.134 36.000 0.00 0.00 0.00 2.71
2730 10254 5.865013 TGCTACACATTGCTGATTTTGATTG 59.135 36.000 0.00 0.00 0.00 2.67
2731 10255 5.865552 GTGCTACACATTGCTGATTTTGATT 59.134 36.000 0.00 0.00 34.08 2.57
2732 10256 5.047872 TGTGCTACACATTGCTGATTTTGAT 60.048 36.000 0.00 0.00 39.62 2.57


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

AutoCloner maintained by Alex Coulton.