Multiple sequence alignment - TraesCS7D01G540700

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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 TraesCS7D01G540700 chr7D 100.000 4764 0 0 1 4764 630531005 630526242 0.000000e+00 8798
1 TraesCS7D01G540700 chr7D 82.891 339 50 4 4426 4764 630504293 630504623 1.000000e-76 298
2 TraesCS7D01G540700 chr7D 80.351 285 46 7 4426 4708 630523088 630523364 1.740000e-49 207
3 TraesCS7D01G540700 chr7D 88.235 136 16 0 3118 3253 630527810 630527675 3.810000e-36 163
4 TraesCS7D01G540700 chr7D 88.235 136 16 0 3196 3331 630527888 630527753 3.810000e-36 163
5 TraesCS7D01G540700 chr7B 92.469 4289 235 51 519 4764 733526977 733531220 0.000000e+00 6050
6 TraesCS7D01G540700 chr7B 84.333 517 59 15 1 505 733526415 733526921 1.990000e-133 486
7 TraesCS7D01G540700 chr7B 84.071 339 46 5 4426 4764 733310148 733310478 2.140000e-83 320
8 TraesCS7D01G540700 chr7B 81.232 341 50 10 4426 4764 733082503 733082831 3.660000e-66 263
9 TraesCS7D01G540700 chr7B 87.234 141 18 0 3118 3258 733529653 733529793 1.370000e-35 161
10 TraesCS7D01G540700 chr7A 89.426 3168 192 52 247 3331 726485889 726482782 0.000000e+00 3862
11 TraesCS7D01G540700 chr7A 94.944 1167 51 4 3118 4283 726482917 726481758 0.000000e+00 1821
12 TraesCS7D01G540700 chr7A 89.960 249 22 3 1 249 726486371 726486126 7.690000e-83 318
13 TraesCS7D01G540700 chr7A 82.849 344 53 4 4426 4764 726468601 726468943 2.150000e-78 303
14 TraesCS7D01G540700 chr7A 81.091 275 43 6 4426 4698 726476229 726476496 1.340000e-50 211
15 TraesCS7D01G540700 chr7A 93.651 126 6 1 4444 4569 726479580 726479457 2.260000e-43 187
16 TraesCS7D01G540700 chr7A 90.141 142 12 2 3191 3331 726483000 726482860 2.930000e-42 183
17 TraesCS7D01G540700 chr7A 87.234 141 18 0 3118 3258 726482839 726482699 1.370000e-35 161
18 TraesCS7D01G540700 chr7A 81.757 148 20 4 4284 4427 726479775 726479631 3.010000e-22 117
19 TraesCS7D01G540700 chr6B 84.118 340 51 3 4426 4763 662030610 662030272 4.600000e-85 326
20 TraesCS7D01G540700 chr6B 76.371 237 40 10 4535 4764 145055340 145055113 3.900000e-21 113
21 TraesCS7D01G540700 chr1D 74.709 344 68 11 4426 4764 473407182 473407511 8.320000e-28 135


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 TraesCS7D01G540700 chr7D 630526242 630531005 4763 True 3041.333333 8798 92.156667 1 4764 3 chr7D.!!$R1 4763
1 TraesCS7D01G540700 chr7B 733526415 733531220 4805 False 2232.333333 6050 88.012000 1 4764 3 chr7B.!!$F3 4763
2 TraesCS7D01G540700 chr7A 726479457 726486371 6914 True 949.857143 3862 89.587571 1 4569 7 chr7A.!!$R1 4568

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
280 524 0.036199 CCACGGGGAAATTCGGTACA 60.036 55.0 0.00 0.0 35.59 2.90 F
791 1089 0.179248 CGCTCGTTTCGCCTCTTTTC 60.179 55.0 0.00 0.0 0.00 2.29 F
793 1091 0.179248 CTCGTTTCGCCTCTTTTCGC 60.179 55.0 0.00 0.0 0.00 4.70 F
795 1093 0.451135 CGTTTCGCCTCTTTTCGCTG 60.451 55.0 0.00 0.0 0.00 5.18 F
796 1094 0.726118 GTTTCGCCTCTTTTCGCTGC 60.726 55.0 0.00 0.0 0.00 5.25 F
2608 2971 0.671781 ATCCATATCCTCGCAAGCGC 60.672 55.0 9.97 0.0 39.59 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1115 1432 0.468648 CTGGACGGTAAATCCCTCCC 59.531 60.000 0.00 0.00 39.59 4.30 R
1897 2254 0.469917 AACATCCACCGATAGCCCTG 59.530 55.000 0.00 0.00 0.00 4.45 R
1940 2297 0.543277 TGACAGGATGCTCACCCATC 59.457 55.000 0.00 0.00 42.53 3.51 R
2587 2950 0.801251 GCTTGCGAGGATATGGATGC 59.199 55.000 2.37 0.00 0.00 3.91 R
2722 3085 1.203052 CCAAAAGCATCCGACTGCATT 59.797 47.619 11.04 3.43 44.77 3.56 R
3925 4368 0.954449 CTGTGCCCTGCTCTTCACAG 60.954 60.000 12.63 12.63 46.68 3.66 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
30 31 8.423906 TTGGCCTTATCTAAAATTTACCAACA 57.576 30.769 3.32 0.00 0.00 3.33
47 48 6.220726 ACCAACATTGCTACAATTTATCCC 57.779 37.500 0.00 0.00 0.00 3.85
48 49 5.163561 ACCAACATTGCTACAATTTATCCCG 60.164 40.000 0.00 0.00 0.00 5.14
67 68 3.244249 CCCGGAAATATCTCCAGAGGTTC 60.244 52.174 0.73 0.00 34.91 3.62
97 98 2.208431 CTCTCATGTTCGAATGGCTCC 58.792 52.381 0.00 0.00 0.00 4.70
117 118 2.029470 CCAGATATTCGTGGCTCTCCTC 60.029 54.545 0.00 0.00 0.00 3.71
127 128 3.144193 CTCTCCTCCGCCTCGCTT 61.144 66.667 0.00 0.00 0.00 4.68
209 213 1.349259 CGCGTACCACAGTAACAGCC 61.349 60.000 0.00 0.00 0.00 4.85
232 236 2.437200 AATGCAACAACAATGTCCCG 57.563 45.000 0.00 0.00 39.40 5.14
243 247 4.664150 ACAATGTCCCGTCAAACAAATT 57.336 36.364 0.00 0.00 0.00 1.82
249 253 7.639113 ATGTCCCGTCAAACAAATTATGTAT 57.361 32.000 0.00 0.00 42.99 2.29
280 524 0.036199 CCACGGGGAAATTCGGTACA 60.036 55.000 0.00 0.00 35.59 2.90
281 527 1.407712 CCACGGGGAAATTCGGTACAT 60.408 52.381 0.00 0.00 35.59 2.29
296 542 3.933955 CGGTACATTATTCCAAACCGTCA 59.066 43.478 3.65 0.00 43.62 4.35
304 550 9.179909 ACATTATTCCAAACCGTCATACAAATA 57.820 29.630 0.00 0.00 0.00 1.40
314 560 6.049149 ACCGTCATACAAATAATGTCAGGAG 58.951 40.000 0.00 0.00 42.70 3.69
318 564 8.830580 CGTCATACAAATAATGTCAGGAGAATT 58.169 33.333 0.00 0.00 42.70 2.17
336 583 9.319143 AGGAGAATTAGATAGAAAAATCACACG 57.681 33.333 0.00 0.00 0.00 4.49
354 601 0.228742 CGCAAATCGTACCGAATCCG 59.771 55.000 0.00 0.00 39.99 4.18
355 602 1.283736 GCAAATCGTACCGAATCCGT 58.716 50.000 0.00 0.00 39.99 4.69
356 603 1.662122 GCAAATCGTACCGAATCCGTT 59.338 47.619 0.00 0.00 39.99 4.44
358 605 3.306703 GCAAATCGTACCGAATCCGTTTA 59.693 43.478 0.00 0.00 39.99 2.01
359 606 4.549489 GCAAATCGTACCGAATCCGTTTAG 60.549 45.833 0.00 0.00 39.99 1.85
360 607 4.637483 AATCGTACCGAATCCGTTTAGA 57.363 40.909 0.00 0.00 39.99 2.10
361 608 4.843220 ATCGTACCGAATCCGTTTAGAT 57.157 40.909 0.00 0.00 39.99 1.98
362 609 4.637483 TCGTACCGAATCCGTTTAGATT 57.363 40.909 0.00 0.00 39.19 2.40
363 610 4.997565 TCGTACCGAATCCGTTTAGATTT 58.002 39.130 0.00 0.00 36.60 2.17
365 612 5.971202 TCGTACCGAATCCGTTTAGATTTAC 59.029 40.000 0.00 0.00 36.60 2.01
366 613 5.108630 CGTACCGAATCCGTTTAGATTTACG 60.109 44.000 0.00 0.00 36.60 3.18
368 615 5.039333 ACCGAATCCGTTTAGATTTACGAG 58.961 41.667 0.00 0.00 40.03 4.18
670 964 1.082206 CCACCCCACCTTCCTCCTA 59.918 63.158 0.00 0.00 0.00 2.94
678 972 0.259356 ACCTTCCTCCTACTCCTCCG 59.741 60.000 0.00 0.00 0.00 4.63
687 984 3.657038 TACTCCTCCGCCTCCGCTT 62.657 63.158 0.00 0.00 0.00 4.68
688 985 4.214327 CTCCTCCGCCTCCGCTTC 62.214 72.222 0.00 0.00 0.00 3.86
791 1089 0.179248 CGCTCGTTTCGCCTCTTTTC 60.179 55.000 0.00 0.00 0.00 2.29
792 1090 0.179248 GCTCGTTTCGCCTCTTTTCG 60.179 55.000 0.00 0.00 0.00 3.46
793 1091 0.179248 CTCGTTTCGCCTCTTTTCGC 60.179 55.000 0.00 0.00 0.00 4.70
794 1092 0.599204 TCGTTTCGCCTCTTTTCGCT 60.599 50.000 0.00 0.00 0.00 4.93
795 1093 0.451135 CGTTTCGCCTCTTTTCGCTG 60.451 55.000 0.00 0.00 0.00 5.18
796 1094 0.726118 GTTTCGCCTCTTTTCGCTGC 60.726 55.000 0.00 0.00 0.00 5.25
797 1095 2.170260 TTTCGCCTCTTTTCGCTGCG 62.170 55.000 17.25 17.25 46.09 5.18
798 1096 3.414700 CGCCTCTTTTCGCTGCGT 61.415 61.111 22.48 0.00 40.33 5.24
799 1097 2.476499 GCCTCTTTTCGCTGCGTC 59.524 61.111 22.48 0.00 0.00 5.19
800 1098 2.029844 GCCTCTTTTCGCTGCGTCT 61.030 57.895 22.48 0.00 0.00 4.18
801 1099 1.784062 CCTCTTTTCGCTGCGTCTG 59.216 57.895 22.48 10.76 0.00 3.51
802 1100 0.946221 CCTCTTTTCGCTGCGTCTGT 60.946 55.000 22.48 0.00 0.00 3.41
803 1101 0.861837 CTCTTTTCGCTGCGTCTGTT 59.138 50.000 22.48 0.00 0.00 3.16
804 1102 1.261619 CTCTTTTCGCTGCGTCTGTTT 59.738 47.619 22.48 0.00 0.00 2.83
805 1103 1.260561 TCTTTTCGCTGCGTCTGTTTC 59.739 47.619 22.48 0.00 0.00 2.78
1094 1408 4.552608 GCTTGCTGCGAATTTTTACTTC 57.447 40.909 0.00 0.00 0.00 3.01
1146 1463 3.320673 ACCGTCCAGATTTCTGTTCTC 57.679 47.619 6.81 0.00 42.27 2.87
1344 1691 4.040584 ACCGGAATATCTTTAGAGGCTTCC 59.959 45.833 9.46 7.30 31.70 3.46
1365 1712 2.364970 CAGAACTAGAGATGGGCAGGAG 59.635 54.545 0.00 0.00 0.00 3.69
1366 1713 1.691434 GAACTAGAGATGGGCAGGAGG 59.309 57.143 0.00 0.00 0.00 4.30
1367 1714 0.937441 ACTAGAGATGGGCAGGAGGA 59.063 55.000 0.00 0.00 0.00 3.71
1368 1715 1.337118 CTAGAGATGGGCAGGAGGAC 58.663 60.000 0.00 0.00 0.00 3.85
1372 1719 0.842030 AGATGGGCAGGAGGACACAA 60.842 55.000 0.00 0.00 0.00 3.33
1374 1721 1.136329 ATGGGCAGGAGGACACAACT 61.136 55.000 0.00 0.00 0.00 3.16
1375 1722 1.003233 GGGCAGGAGGACACAACTC 60.003 63.158 0.00 0.00 0.00 3.01
1386 1733 2.241176 GGACACAACTCCCATCCCATAA 59.759 50.000 0.00 0.00 0.00 1.90
1389 1736 5.398581 GGACACAACTCCCATCCCATAATTA 60.399 44.000 0.00 0.00 0.00 1.40
1390 1737 6.279813 ACACAACTCCCATCCCATAATTAT 57.720 37.500 0.00 0.00 0.00 1.28
1391 1738 6.682537 ACACAACTCCCATCCCATAATTATT 58.317 36.000 0.00 0.00 0.00 1.40
1409 1756 9.930158 ATAATTATTTTAGAGCCACCTACCAAA 57.070 29.630 0.00 0.00 0.00 3.28
1410 1757 7.640597 ATTATTTTAGAGCCACCTACCAAAC 57.359 36.000 0.00 0.00 0.00 2.93
1411 1758 4.440826 TTTTAGAGCCACCTACCAAACA 57.559 40.909 0.00 0.00 0.00 2.83
1422 1769 2.086869 CTACCAAACACATGCCAGGAG 58.913 52.381 0.00 0.00 0.00 3.69
1449 1796 4.344679 TGAGTGCCAAATCCAGAAACAATT 59.655 37.500 0.00 0.00 0.00 2.32
1540 1891 4.395542 ACTGCTAGTAGTTACCAGTCTTCG 59.604 45.833 7.78 0.00 31.61 3.79
1552 1903 5.296813 ACCAGTCTTCGTTTAATTCATGC 57.703 39.130 0.00 0.00 0.00 4.06
1679 2036 8.514594 TGTTGATCCTGTTTAATCAGAAACATC 58.485 33.333 13.98 9.92 45.67 3.06
1687 2044 9.817365 CTGTTTAATCAGAAACATCTGTAGTTG 57.183 33.333 7.65 0.00 45.67 3.16
1703 2060 6.538742 TCTGTAGTTGTAGCTCAAATTATGCC 59.461 38.462 0.00 0.00 37.81 4.40
1756 2113 4.009675 TGGACACTATTTTGGCTTGCTAG 58.990 43.478 0.00 0.00 0.00 3.42
1757 2114 3.378427 GGACACTATTTTGGCTTGCTAGG 59.622 47.826 0.00 0.00 0.00 3.02
1772 2129 5.684030 GCTTGCTAGGTAATTACTGCTGGTA 60.684 44.000 15.05 4.15 0.00 3.25
1774 2131 6.494666 TGCTAGGTAATTACTGCTGGTATT 57.505 37.500 15.05 0.00 0.00 1.89
1795 2152 0.961019 GGAACTGTTTGCAGCCATGA 59.039 50.000 0.00 0.00 46.30 3.07
1831 2188 1.661341 GGCTGGCTGAAGTACTGATG 58.339 55.000 0.00 0.00 0.00 3.07
1940 2297 2.761465 GGAGCCCAATGAGGAGGGG 61.761 68.421 0.00 0.00 45.58 4.79
1977 2334 4.585879 TGTCAAGGTAGCCATTTCTTACC 58.414 43.478 0.00 0.00 0.00 2.85
2036 2394 4.037565 TCCCATCGGCGTATCATATATCAC 59.962 45.833 6.85 0.00 0.00 3.06
2044 2402 2.672961 ATCATATATCACCGCCGTGG 57.327 50.000 5.34 0.00 46.41 4.94
2059 2417 2.213499 CCGTGGTGCCTAATGATCTTC 58.787 52.381 0.00 0.00 0.00 2.87
2067 2425 3.198068 GCCTAATGATCTTCGTCTTGCA 58.802 45.455 0.00 0.00 0.00 4.08
2087 2445 3.416156 CATTGATTAGCCTAGGAAGCCC 58.584 50.000 14.75 0.00 0.00 5.19
2195 2553 2.866460 GCGTCAGATACAAGGTGTGTGT 60.866 50.000 0.00 0.00 41.89 3.72
2204 2562 1.334869 CAAGGTGTGTGTCAGCCTTTC 59.665 52.381 0.00 0.00 44.62 2.62
2221 2579 6.144724 CAGCCTTTCTAAGTATAACGCATCTC 59.855 42.308 0.00 0.00 0.00 2.75
2223 2581 5.117287 CCTTTCTAAGTATAACGCATCTCGC 59.883 44.000 0.00 0.00 43.23 5.03
2228 2586 7.535997 TCTAAGTATAACGCATCTCGCATTAT 58.464 34.615 0.00 0.00 42.60 1.28
2385 2743 7.713507 TGTAGTTATGATACATTTGGCCTGTAC 59.286 37.037 3.32 0.84 32.24 2.90
2425 2783 9.594038 CAGCGGTTTATGTTATATGTTTGTATC 57.406 33.333 0.00 0.00 0.00 2.24
2484 2846 7.489113 GCTAATTTGAACCATTTGAATGTCGAT 59.511 33.333 3.30 0.00 34.60 3.59
2486 2848 5.956068 TTGAACCATTTGAATGTCGATCA 57.044 34.783 3.30 0.00 34.60 2.92
2510 2873 1.243342 TTCTCATGCGGGGTTGCTTG 61.243 55.000 0.00 0.00 40.33 4.01
2587 2950 0.961753 GGCCAAAGAGGAAACCACTG 59.038 55.000 0.00 0.00 41.22 3.66
2608 2971 0.671781 ATCCATATCCTCGCAAGCGC 60.672 55.000 9.97 0.00 39.59 5.92
2626 2989 2.753966 CGCGAACTCCTGCAATGGG 61.754 63.158 0.00 0.00 0.00 4.00
2633 2996 2.216750 CTCCTGCAATGGGGCAAACG 62.217 60.000 0.00 0.00 44.40 3.60
2644 3007 1.300853 GGCAAACGCAGCAAATGGT 60.301 52.632 0.00 0.00 0.00 3.55
2714 3077 2.567497 GGTTCTCCCGTGTCGGTGA 61.567 63.158 7.40 2.85 46.80 4.02
2722 3085 0.102300 CCGTGTCGGTGATATCTGCA 59.898 55.000 3.98 0.00 42.73 4.41
2774 3137 0.670546 AAACCCGTCATCTCGCAGTG 60.671 55.000 0.00 0.00 0.00 3.66
2805 3168 5.473162 CAGAGTCGTCAGATGAGGAGAATAT 59.527 44.000 5.52 0.00 39.29 1.28
2910 3273 1.808945 GTTAGCTGCACTGCTGAACAT 59.191 47.619 10.53 0.00 43.87 2.71
2927 3290 6.459298 GCTGAACATCCTTATTGAATGACCAG 60.459 42.308 0.00 0.00 0.00 4.00
2952 3316 4.756642 TGAACTTATTGGACTGCTCTTGTG 59.243 41.667 0.00 0.00 0.00 3.33
3061 3425 0.178533 TGTTTGGGAAGACGGTCGTT 59.821 50.000 1.89 0.00 0.00 3.85
3116 3480 0.112995 AGGCTCAGGGCATGAAAACA 59.887 50.000 2.54 0.00 44.01 2.83
3125 3489 2.352127 GGGCATGAAAACAGAGAGCAAC 60.352 50.000 0.00 0.00 0.00 4.17
3131 3495 2.557920 AAACAGAGAGCAACCCTCAG 57.442 50.000 0.00 0.00 43.31 3.35
3133 3497 1.265236 ACAGAGAGCAACCCTCAGAG 58.735 55.000 0.00 0.00 43.31 3.35
3701 4143 0.863538 CGTGAGAGTGAAGCCGATCG 60.864 60.000 8.51 8.51 0.00 3.69
3733 4175 3.647771 GAGCCGGTGAGGGGGTTT 61.648 66.667 1.90 0.00 41.48 3.27
3847 4289 3.433031 CCACATATTCCTTTGCTCCGGTA 60.433 47.826 0.00 0.00 0.00 4.02
3918 4361 2.747507 AATGCGCGTTGTTTCCTGCC 62.748 55.000 15.39 0.00 0.00 4.85
3957 4400 0.609131 GGCACAGGTGGTTGCTGTAT 60.609 55.000 1.10 0.00 0.00 2.29
4009 4453 2.092538 AGGGATGCCAATTCTCTGTCTG 60.093 50.000 5.86 0.00 0.00 3.51
4231 4675 5.200368 ACATGGAAGGAAACATTGTTCAC 57.800 39.130 1.83 0.00 0.00 3.18
4289 6717 5.287226 CCATGGCTGCTAAATTCAATTCTC 58.713 41.667 0.00 0.00 0.00 2.87
4298 6726 6.032717 GCTAAATTCAATTCTCTCAAGTGGC 58.967 40.000 0.00 0.00 0.00 5.01
4310 6738 8.806429 TTCTCTCAAGTGGCAAATTATGAATA 57.194 30.769 0.00 0.00 0.00 1.75
4314 6742 9.806203 TCTCAAGTGGCAAATTATGAATATTTG 57.194 29.630 0.00 0.00 38.07 2.32
4322 6750 9.585099 GGCAAATTATGAATATTTGTCTGAACA 57.415 29.630 0.00 0.00 37.06 3.18
4420 6864 1.037579 GTGCTGGGAATTGTAGGGGC 61.038 60.000 0.00 0.00 0.00 5.80
4561 7037 5.698089 TGTATCAAGAAGCAGAGAGTTGTTG 59.302 40.000 0.00 0.00 0.00 3.33
4572 7048 7.217200 AGCAGAGAGTTGTTGTAATGAACTTA 58.783 34.615 0.00 0.00 30.01 2.24
4617 7093 8.796475 AGCTTGTTGATGTTAATGTTCACTATT 58.204 29.630 0.00 0.00 0.00 1.73
4653 7129 4.141321 ACATTGTCAGGCTCATGATATGGT 60.141 41.667 0.00 0.01 32.62 3.55
4674 7150 7.618019 TGGTGCTTGACCTTATAATATCTCT 57.382 36.000 0.00 0.00 46.32 3.10
4677 7153 9.810545 GGTGCTTGACCTTATAATATCTCTATC 57.189 37.037 0.00 0.00 42.25 2.08
4706 7182 7.551585 TGAAGAGAATTTTGCCACAGTTTTAA 58.448 30.769 0.00 0.00 0.00 1.52
4712 7188 3.423996 TTGCCACAGTTTTAAACCGTC 57.576 42.857 4.01 0.00 0.00 4.79
4726 7202 1.813513 ACCGTCTCTGCAATCCTTTG 58.186 50.000 0.00 0.00 35.85 2.77
4746 7222 1.880027 GCCAAACAAGAACCATCGACT 59.120 47.619 0.00 0.00 0.00 4.18
4748 7224 3.403038 CCAAACAAGAACCATCGACTCT 58.597 45.455 0.00 0.00 0.00 3.24
4749 7225 3.433615 CCAAACAAGAACCATCGACTCTC 59.566 47.826 0.00 0.00 0.00 3.20
4750 7226 2.638556 ACAAGAACCATCGACTCTCG 57.361 50.000 0.00 0.00 42.10 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 6.976934 ATTTCCGGGATAAATTGTAGCAAT 57.023 33.333 0.00 0.00 0.00 3.56
47 48 3.643763 CGAACCTCTGGAGATATTTCCG 58.356 50.000 7.73 3.38 40.27 4.30
48 49 3.070302 AGCGAACCTCTGGAGATATTTCC 59.930 47.826 5.31 5.31 37.77 3.13
67 68 2.108566 CATGAGAGGCCAGGAGCG 59.891 66.667 5.01 0.00 45.17 5.03
97 98 2.029470 GGAGGAGAGCCACGAATATCTG 60.029 54.545 0.00 0.00 36.29 2.90
126 127 1.157751 AAGTGGAGACGGAGGGGAA 59.842 57.895 0.00 0.00 0.00 3.97
127 128 1.609501 CAAGTGGAGACGGAGGGGA 60.610 63.158 0.00 0.00 0.00 4.81
182 186 5.062433 TGTTACTGTGGTACGCGAAATAATG 59.938 40.000 15.93 0.00 45.01 1.90
189 193 0.387622 GCTGTTACTGTGGTACGCGA 60.388 55.000 15.93 0.00 45.01 5.87
209 213 4.236935 GGGACATTGTTGTTGCATTACAG 58.763 43.478 0.00 0.00 35.79 2.74
243 247 6.285224 CCCGTGGTTTATTGTCTCATACATA 58.715 40.000 0.00 0.00 38.10 2.29
249 253 1.979308 TCCCCGTGGTTTATTGTCTCA 59.021 47.619 0.00 0.00 0.00 3.27
263 506 2.793288 AATGTACCGAATTTCCCCGT 57.207 45.000 0.00 0.00 0.00 5.28
264 507 4.214758 GGAATAATGTACCGAATTTCCCCG 59.785 45.833 0.00 0.00 0.00 5.73
314 560 9.554724 TTTGCGTGTGATTTTTCTATCTAATTC 57.445 29.630 0.00 0.00 0.00 2.17
318 564 7.398746 CGATTTGCGTGTGATTTTTCTATCTA 58.601 34.615 0.00 0.00 34.64 1.98
346 593 5.276270 TCTCGTAAATCTAAACGGATTCGG 58.724 41.667 0.00 0.00 41.39 4.30
349 596 8.767478 TTCTTTCTCGTAAATCTAAACGGATT 57.233 30.769 0.00 0.00 39.52 3.01
413 663 7.704578 ACAAGTGTATTCTCTTACTAGCTCA 57.295 36.000 0.00 0.00 0.00 4.26
426 676 9.811995 TGTCCAAGTGTATATACAAGTGTATTC 57.188 33.333 17.07 2.78 41.18 1.75
678 972 3.855853 GGAGGAGGAAGCGGAGGC 61.856 72.222 0.00 0.00 40.37 4.70
687 984 4.144727 GAGGCGGAGGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
791 1089 3.777925 CCCGAAACAGACGCAGCG 61.778 66.667 14.82 14.82 0.00 5.18
792 1090 2.665185 ACCCGAAACAGACGCAGC 60.665 61.111 0.00 0.00 0.00 5.25
793 1091 2.372690 CGACCCGAAACAGACGCAG 61.373 63.158 0.00 0.00 0.00 5.18
794 1092 2.355363 CGACCCGAAACAGACGCA 60.355 61.111 0.00 0.00 0.00 5.24
795 1093 3.110178 CCGACCCGAAACAGACGC 61.110 66.667 0.00 0.00 0.00 5.19
796 1094 0.877213 AAACCGACCCGAAACAGACG 60.877 55.000 0.00 0.00 0.00 4.18
797 1095 0.863799 GAAACCGACCCGAAACAGAC 59.136 55.000 0.00 0.00 0.00 3.51
798 1096 0.754472 AGAAACCGACCCGAAACAGA 59.246 50.000 0.00 0.00 0.00 3.41
799 1097 1.589803 AAGAAACCGACCCGAAACAG 58.410 50.000 0.00 0.00 0.00 3.16
800 1098 1.671845 CAAAGAAACCGACCCGAAACA 59.328 47.619 0.00 0.00 0.00 2.83
801 1099 1.002142 CCAAAGAAACCGACCCGAAAC 60.002 52.381 0.00 0.00 0.00 2.78
802 1100 1.310904 CCAAAGAAACCGACCCGAAA 58.689 50.000 0.00 0.00 0.00 3.46
803 1101 0.535553 CCCAAAGAAACCGACCCGAA 60.536 55.000 0.00 0.00 0.00 4.30
804 1102 1.071814 CCCAAAGAAACCGACCCGA 59.928 57.895 0.00 0.00 0.00 5.14
805 1103 1.228033 ACCCAAAGAAACCGACCCG 60.228 57.895 0.00 0.00 0.00 5.28
1062 1376 2.740055 AGCAAGCGAGAACAGCCG 60.740 61.111 0.00 0.00 34.64 5.52
1075 1389 3.560503 CGGAAGTAAAAATTCGCAGCAA 58.439 40.909 0.00 0.00 0.00 3.91
1115 1432 0.468648 CTGGACGGTAAATCCCTCCC 59.531 60.000 0.00 0.00 39.59 4.30
1344 1691 2.364970 CTCCTGCCCATCTCTAGTTCTG 59.635 54.545 0.00 0.00 0.00 3.02
1365 1712 0.625849 ATGGGATGGGAGTTGTGTCC 59.374 55.000 0.00 0.00 35.64 4.02
1366 1713 3.644966 TTATGGGATGGGAGTTGTGTC 57.355 47.619 0.00 0.00 0.00 3.67
1367 1714 4.608170 AATTATGGGATGGGAGTTGTGT 57.392 40.909 0.00 0.00 0.00 3.72
1368 1715 7.601705 AAATAATTATGGGATGGGAGTTGTG 57.398 36.000 0.00 0.00 0.00 3.33
1372 1719 7.890655 GCTCTAAAATAATTATGGGATGGGAGT 59.109 37.037 0.00 0.00 0.00 3.85
1374 1721 7.182060 GGCTCTAAAATAATTATGGGATGGGA 58.818 38.462 0.00 0.00 0.00 4.37
1375 1722 6.953520 TGGCTCTAAAATAATTATGGGATGGG 59.046 38.462 0.00 0.00 0.00 4.00
1376 1723 7.093771 GGTGGCTCTAAAATAATTATGGGATGG 60.094 40.741 0.00 0.00 0.00 3.51
1377 1724 7.671398 AGGTGGCTCTAAAATAATTATGGGATG 59.329 37.037 0.00 0.00 0.00 3.51
1378 1725 7.769652 AGGTGGCTCTAAAATAATTATGGGAT 58.230 34.615 0.00 0.00 0.00 3.85
1386 1733 7.122204 GTGTTTGGTAGGTGGCTCTAAAATAAT 59.878 37.037 0.00 0.00 0.00 1.28
1389 1736 4.765339 GTGTTTGGTAGGTGGCTCTAAAAT 59.235 41.667 0.00 0.00 0.00 1.82
1390 1737 4.139038 GTGTTTGGTAGGTGGCTCTAAAA 58.861 43.478 0.00 0.00 0.00 1.52
1391 1738 3.136809 TGTGTTTGGTAGGTGGCTCTAAA 59.863 43.478 0.00 0.00 0.00 1.85
1426 1773 2.942804 TGTTTCTGGATTTGGCACTCA 58.057 42.857 0.00 0.00 0.00 3.41
1427 1774 4.525912 ATTGTTTCTGGATTTGGCACTC 57.474 40.909 0.00 0.00 0.00 3.51
1430 1777 4.952071 TCAATTGTTTCTGGATTTGGCA 57.048 36.364 5.13 0.00 0.00 4.92
1431 1778 4.632688 CCATCAATTGTTTCTGGATTTGGC 59.367 41.667 5.13 0.00 0.00 4.52
1531 1882 5.295431 TGCATGAATTAAACGAAGACTGG 57.705 39.130 0.00 0.00 0.00 4.00
1540 1891 5.931146 TCAACCAACCATGCATGAATTAAAC 59.069 36.000 28.31 0.00 0.00 2.01
1607 1958 8.603304 ACTGGTAAAAATCTACTATCAACCACT 58.397 33.333 0.00 0.00 31.53 4.00
1608 1959 8.788325 ACTGGTAAAAATCTACTATCAACCAC 57.212 34.615 0.00 0.00 31.53 4.16
1609 1960 9.880157 GTACTGGTAAAAATCTACTATCAACCA 57.120 33.333 0.00 0.00 33.65 3.67
1679 2036 6.510157 CGGCATAATTTGAGCTACAACTACAG 60.510 42.308 0.00 0.00 38.29 2.74
1687 2044 3.691049 TTGCGGCATAATTTGAGCTAC 57.309 42.857 2.28 0.00 33.43 3.58
1703 2060 0.808755 GGGGGTAACTGAACATTGCG 59.191 55.000 0.00 0.00 0.00 4.85
1756 2113 6.602009 AGTTCCAAATACCAGCAGTAATTACC 59.398 38.462 12.05 0.00 33.70 2.85
1757 2114 7.120726 ACAGTTCCAAATACCAGCAGTAATTAC 59.879 37.037 7.57 7.57 33.70 1.89
1772 2129 1.761784 TGGCTGCAAACAGTTCCAAAT 59.238 42.857 0.50 0.00 46.30 2.32
1774 2131 1.068895 CATGGCTGCAAACAGTTCCAA 59.931 47.619 0.50 0.00 46.30 3.53
1795 2152 1.972795 AGCCCAAAACACATTGCTGAT 59.027 42.857 0.00 0.00 0.00 2.90
1831 2188 4.498177 GGAGGCAAGAACAGAAGAAACAAC 60.498 45.833 0.00 0.00 0.00 3.32
1897 2254 0.469917 AACATCCACCGATAGCCCTG 59.530 55.000 0.00 0.00 0.00 4.45
1940 2297 0.543277 TGACAGGATGCTCACCCATC 59.457 55.000 0.00 0.00 42.53 3.51
2044 2402 3.001736 GCAAGACGAAGATCATTAGGCAC 59.998 47.826 0.00 0.00 0.00 5.01
2059 2417 3.496130 CCTAGGCTAATCAATGCAAGACG 59.504 47.826 0.00 0.00 0.00 4.18
2067 2425 3.331120 AGGGCTTCCTAGGCTAATCAAT 58.669 45.455 2.96 0.00 45.78 2.57
2087 2445 0.917259 GCTGCTTCGTGATCGTGTAG 59.083 55.000 0.00 0.00 38.33 2.74
2195 2553 5.333299 TGCGTTATACTTAGAAAGGCTGA 57.667 39.130 0.00 0.00 35.59 4.26
2425 2783 9.874215 CAATTCTGCTTCTACATTACATGTATG 57.126 33.333 6.36 9.60 44.11 2.39
2433 2791 4.640201 GCCACCAATTCTGCTTCTACATTA 59.360 41.667 0.00 0.00 0.00 1.90
2434 2792 3.445096 GCCACCAATTCTGCTTCTACATT 59.555 43.478 0.00 0.00 0.00 2.71
2435 2793 3.019564 GCCACCAATTCTGCTTCTACAT 58.980 45.455 0.00 0.00 0.00 2.29
2486 2848 1.545582 CAACCCCGCATGAGAAAACAT 59.454 47.619 0.00 0.00 0.00 2.71
2587 2950 0.801251 GCTTGCGAGGATATGGATGC 59.199 55.000 2.37 0.00 0.00 3.91
2608 2971 2.753966 CCCATTGCAGGAGTTCGCG 61.754 63.158 0.00 0.00 0.00 5.87
2626 2989 1.284297 GACCATTTGCTGCGTTTGCC 61.284 55.000 0.00 0.00 41.78 4.52
2644 3007 4.529897 ACATATGAGCAAGCTTGGATTGA 58.470 39.130 27.10 0.00 0.00 2.57
2722 3085 1.203052 CCAAAAGCATCCGACTGCATT 59.797 47.619 11.04 3.43 44.77 3.56
2774 3137 2.680352 TGACGACTCTGGGGAGGC 60.680 66.667 0.00 0.00 43.91 4.70
2805 3168 2.621055 CCGTTCACCATTGGAAGAACAA 59.379 45.455 28.22 7.30 39.34 2.83
2910 3273 6.542821 AGTTCAACTGGTCATTCAATAAGGA 58.457 36.000 0.00 0.00 0.00 3.36
2927 3290 5.239525 ACAAGAGCAGTCCAATAAGTTCAAC 59.760 40.000 0.00 0.00 0.00 3.18
3046 3410 0.819582 GGATAACGACCGTCTTCCCA 59.180 55.000 10.71 0.00 0.00 4.37
3061 3425 2.116238 CTTTTCCTCGGGTCTGGGATA 58.884 52.381 0.00 0.00 0.00 2.59
3116 3480 1.555967 GACTCTGAGGGTTGCTCTCT 58.444 55.000 9.85 0.00 32.78 3.10
3125 3489 3.196685 CCTTTGTTAGAGGACTCTGAGGG 59.803 52.174 11.95 2.35 40.71 4.30
3131 3495 5.639931 GTGATGTTCCTTTGTTAGAGGACTC 59.360 44.000 0.00 0.00 42.82 3.36
3133 3497 5.305585 TGTGATGTTCCTTTGTTAGAGGAC 58.694 41.667 0.00 0.00 42.82 3.85
3175 3539 6.381498 TCTCCCTTTGTATGTGTTGGAATA 57.619 37.500 0.00 0.00 0.00 1.75
3499 3941 3.677148 CGCTCTCATCAGTAGCTTTTCCA 60.677 47.826 0.00 0.00 34.03 3.53
3701 4143 1.882167 GCTCATCTCCGCTGCTGAC 60.882 63.158 0.00 0.00 0.00 3.51
3733 4175 1.996898 CTACATCTTTTGTACGGCGCA 59.003 47.619 10.83 0.00 39.87 6.09
3918 4361 3.123620 GCTCTTCACAGGGCGCAG 61.124 66.667 10.83 0.00 36.54 5.18
3925 4368 0.954449 CTGTGCCCTGCTCTTCACAG 60.954 60.000 12.63 12.63 46.68 3.66
3929 4372 1.673665 CACCTGTGCCCTGCTCTTC 60.674 63.158 0.00 0.00 0.00 2.87
3931 4374 3.644606 CCACCTGTGCCCTGCTCT 61.645 66.667 0.00 0.00 0.00 4.09
3957 4400 3.263170 TCCTGCTTTTATCCTACAGCACA 59.737 43.478 0.00 0.00 37.35 4.57
4009 4453 6.437928 TGCTTTTACATCAACAACATGAGAC 58.562 36.000 0.00 0.00 31.76 3.36
4245 4689 2.036346 GCAGGAAACTTCAAAGGCATGT 59.964 45.455 0.00 0.00 40.21 3.21
4289 6717 9.590451 ACAAATATTCATAATTTGCCACTTGAG 57.410 29.630 8.13 0.00 38.46 3.02
4310 6738 4.202182 AGCAACTGCATTGTTCAGACAAAT 60.202 37.500 4.22 0.00 42.94 2.32
4314 6742 2.291465 TCAGCAACTGCATTGTTCAGAC 59.709 45.455 4.22 0.00 45.16 3.51
4322 6750 2.629137 TGGAATGTTCAGCAACTGCATT 59.371 40.909 4.22 0.00 45.16 3.56
4323 6751 2.241160 TGGAATGTTCAGCAACTGCAT 58.759 42.857 4.22 0.00 45.16 3.96
4420 6864 6.084326 AGTACAACAAACAAGCCTTTATGG 57.916 37.500 0.00 0.00 39.35 2.74
4472 6948 3.751175 TCCATTTCGGTTCTTCACATGAC 59.249 43.478 0.00 0.00 35.57 3.06
4583 7059 6.839124 TTAACATCAACAAGCTGGATCAAT 57.161 33.333 0.00 0.00 0.00 2.57
4617 7093 9.638239 GAGCCTGACAATGTTTTTAAAATCATA 57.362 29.630 19.77 7.93 30.42 2.15
4628 7104 5.301045 CCATATCATGAGCCTGACAATGTTT 59.699 40.000 0.09 0.00 0.00 2.83
4674 7150 6.885918 TGTGGCAAAATTCTCTTCATCTGATA 59.114 34.615 0.00 0.00 0.00 2.15
4677 7153 5.048224 ACTGTGGCAAAATTCTCTTCATCTG 60.048 40.000 0.00 0.00 0.00 2.90
4685 7161 6.292114 CGGTTTAAAACTGTGGCAAAATTCTC 60.292 38.462 1.03 0.00 33.03 2.87
4706 7182 2.154462 CAAAGGATTGCAGAGACGGTT 58.846 47.619 0.00 0.00 0.00 4.44
4726 7202 1.880027 AGTCGATGGTTCTTGTTTGGC 59.120 47.619 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.