Multiple sequence alignment - TraesCS2B01G131900

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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 TraesCS2B01G131900 chr2B 100.000 4021 0 0 1 4021 98360637 98364657 0.000000e+00 7426.0
1 TraesCS2B01G131900 chr2D 89.605 3088 202 51 654 3660 62956354 62959403 0.000000e+00 3814.0
2 TraesCS2B01G131900 chr2D 92.357 314 15 5 3709 4021 62959422 62959727 4.770000e-119 438.0
3 TraesCS2B01G131900 chr2D 91.954 261 11 7 1 257 62955171 62955425 1.370000e-94 357.0
4 TraesCS2B01G131900 chr2A 91.631 2545 129 31 814 3318 63824449 63826949 0.000000e+00 3443.0
5 TraesCS2B01G131900 chr2A 88.034 468 20 9 1 433 63823620 63824086 4.610000e-144 521.0
6 TraesCS2B01G131900 chr7B 93.447 763 38 8 1590 2348 391659908 391659154 0.000000e+00 1122.0
7 TraesCS2B01G131900 chr7B 87.111 225 18 9 1288 1507 391660168 391659950 1.120000e-60 244.0
8 TraesCS2B01G131900 chr5A 83.537 164 24 3 1336 1499 5348024 5347864 2.500000e-32 150.0
9 TraesCS2B01G131900 chr3A 82.955 176 21 5 2347 2514 354931400 354931574 2.500000e-32 150.0
10 TraesCS2B01G131900 chr4A 92.105 38 3 0 556 593 468255371 468255334 2.000000e-03 54.7


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 TraesCS2B01G131900 chr2B 98360637 98364657 4020 False 7426.000000 7426 100.000000 1 4021 1 chr2B.!!$F1 4020
1 TraesCS2B01G131900 chr2D 62955171 62959727 4556 False 1536.333333 3814 91.305333 1 4021 3 chr2D.!!$F1 4020
2 TraesCS2B01G131900 chr2A 63823620 63826949 3329 False 1982.000000 3443 89.832500 1 3318 2 chr2A.!!$F1 3317
3 TraesCS2B01G131900 chr7B 391659154 391660168 1014 True 683.000000 1122 90.279000 1288 2348 2 chr7B.!!$R1 1060

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
494 971 0.520404 AGTACAGCGTAGACACACCG 59.480 55.0 0.00 0.0 0.00 4.94 F
638 1149 0.538287 GGTTCCTGATGGGCTATGGC 60.538 60.0 0.00 0.0 37.82 4.40 F
2289 2971 0.313043 AGTGAATGTGCTGCAACTGC 59.687 50.0 2.77 0.0 42.50 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2288 2970 0.039708 GCAGAACTCAGTTGCCTTGC 60.040 55.0 0.00 0.0 31.79 4.01 R
2531 3225 0.523072 CATGAGCCTTGGTGAAACGG 59.477 55.0 0.00 0.0 38.12 4.44 R
3959 4702 0.039764 TCTCCACCGTGTGATCTCCT 59.960 55.0 5.71 0.0 35.23 3.69 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
64 65 5.452078 TTCTTTTGTGGAGAAATCGCATT 57.548 34.783 0.00 0.00 30.60 3.56
148 154 1.987770 CTCCAAATCAAACGCATGTGC 59.012 47.619 6.08 0.00 37.78 4.57
184 191 9.403110 CTTTTGAGATACCTGAAACAGATTTTG 57.597 33.333 0.00 0.00 32.44 2.44
193 200 7.820648 ACCTGAAACAGATTTTGTCATGTATC 58.179 34.615 0.00 0.00 39.73 2.24
293 728 2.291540 ACCCCTCATGGTATGTTTGGTG 60.292 50.000 0.00 0.00 36.67 4.17
318 756 2.637382 CCCAAGTTTGCCCTACCAAAAT 59.363 45.455 0.00 0.00 36.55 1.82
356 794 8.729805 AAATTTCAGTCAAGGTTTTATTTGCA 57.270 26.923 0.00 0.00 0.00 4.08
413 856 3.706594 AGAGAGAACTGGAGTGAACACAA 59.293 43.478 7.68 0.00 0.00 3.33
427 870 7.273381 GGAGTGAACACAATTACATTAACATGC 59.727 37.037 7.68 0.00 33.05 4.06
432 875 7.887996 ACACAATTACATTAACATGCCAAAG 57.112 32.000 0.00 0.00 33.05 2.77
434 877 6.313411 CACAATTACATTAACATGCCAAAGGG 59.687 38.462 0.00 0.00 33.05 3.95
448 911 1.727880 CAAAGGGCATGCATCAAAACG 59.272 47.619 21.36 0.00 0.00 3.60
466 929 8.703604 TCAAAACGAAGTCCATATTCTCTTAG 57.296 34.615 0.00 0.00 45.00 2.18
469 932 9.720769 AAAACGAAGTCCATATTCTCTTAGAAA 57.279 29.630 0.00 0.00 45.00 2.52
473 936 9.413048 CGAAGTCCATATTCTCTTAGAAATACC 57.587 37.037 0.00 0.00 37.82 2.73
494 971 0.520404 AGTACAGCGTAGACACACCG 59.480 55.000 0.00 0.00 0.00 4.94
497 974 1.284715 CAGCGTAGACACACCGACA 59.715 57.895 0.00 0.00 0.00 4.35
502 979 1.534385 CGTAGACACACCGACAACACA 60.534 52.381 0.00 0.00 0.00 3.72
539 1034 8.099364 TGGAGTTACAAAGAAGATTGATCAAC 57.901 34.615 11.07 5.15 34.38 3.18
551 1060 5.702865 AGATTGATCAACCATTGTTTGTCG 58.297 37.500 11.07 0.00 30.42 4.35
620 1130 6.595682 AGATGATGTCCAACCTAGTATTTGG 58.404 40.000 8.18 8.18 43.29 3.28
628 1138 5.491078 TCCAACCTAGTATTTGGTTCCTGAT 59.509 40.000 12.43 0.00 43.88 2.90
638 1149 0.538287 GGTTCCTGATGGGCTATGGC 60.538 60.000 0.00 0.00 37.82 4.40
667 1216 6.010219 ACAACCCTGCTAACATGTTAATTCT 58.990 36.000 18.55 0.00 0.00 2.40
672 1221 7.232534 ACCCTGCTAACATGTTAATTCTCAAAA 59.767 33.333 18.55 0.00 0.00 2.44
719 1286 8.746052 TTATCGAAGTCCATATTTTGGTCAAT 57.254 30.769 0.00 0.00 46.52 2.57
721 1288 6.176896 TCGAAGTCCATATTTTGGTCAATGA 58.823 36.000 0.00 0.00 46.52 2.57
728 1295 8.469200 GTCCATATTTTGGTCAATGATCTGAAA 58.531 33.333 0.00 0.00 46.52 2.69
729 1296 8.469200 TCCATATTTTGGTCAATGATCTGAAAC 58.531 33.333 0.00 0.00 46.52 2.78
733 1300 8.597662 ATTTTGGTCAATGATCTGAAACTTTG 57.402 30.769 0.00 0.00 0.00 2.77
769 1337 4.816925 GGCAGTCTGAACTTTCAACTAAGT 59.183 41.667 3.32 0.00 39.97 2.24
770 1338 5.277538 GGCAGTCTGAACTTTCAACTAAGTG 60.278 44.000 3.32 0.00 38.33 3.16
771 1339 5.523916 GCAGTCTGAACTTTCAACTAAGTGA 59.476 40.000 3.32 0.00 38.33 3.41
772 1340 6.037172 GCAGTCTGAACTTTCAACTAAGTGAA 59.963 38.462 3.32 0.00 38.33 3.18
773 1341 7.625553 CAGTCTGAACTTTCAACTAAGTGAAG 58.374 38.462 0.00 0.00 38.69 3.02
774 1342 7.492669 CAGTCTGAACTTTCAACTAAGTGAAGA 59.507 37.037 0.00 0.00 38.69 2.87
775 1343 8.041323 AGTCTGAACTTTCAACTAAGTGAAGAA 58.959 33.333 0.00 0.00 38.69 2.52
776 1344 8.117370 GTCTGAACTTTCAACTAAGTGAAGAAC 58.883 37.037 0.00 0.00 38.69 3.01
777 1345 7.000575 TGAACTTTCAACTAAGTGAAGAACG 57.999 36.000 0.00 0.00 38.69 3.95
778 1346 5.986004 ACTTTCAACTAAGTGAAGAACGG 57.014 39.130 0.00 0.00 38.69 4.44
779 1347 5.425630 ACTTTCAACTAAGTGAAGAACGGT 58.574 37.500 0.00 0.00 38.69 4.83
780 1348 5.293569 ACTTTCAACTAAGTGAAGAACGGTG 59.706 40.000 0.00 0.00 38.69 4.94
781 1349 4.395959 TCAACTAAGTGAAGAACGGTGT 57.604 40.909 0.00 0.00 0.00 4.16
782 1350 4.761975 TCAACTAAGTGAAGAACGGTGTT 58.238 39.130 0.00 0.00 0.00 3.32
783 1351 5.904941 TCAACTAAGTGAAGAACGGTGTTA 58.095 37.500 0.00 0.00 0.00 2.41
784 1352 6.339730 TCAACTAAGTGAAGAACGGTGTTAA 58.660 36.000 0.00 0.00 0.00 2.01
785 1353 6.817641 TCAACTAAGTGAAGAACGGTGTTAAA 59.182 34.615 0.00 0.00 0.00 1.52
786 1354 7.333921 TCAACTAAGTGAAGAACGGTGTTAAAA 59.666 33.333 0.00 0.00 0.00 1.52
787 1355 7.614124 ACTAAGTGAAGAACGGTGTTAAAAA 57.386 32.000 0.00 0.00 0.00 1.94
934 1573 2.679336 CCTATAAACCCCCAAAACGACG 59.321 50.000 0.00 0.00 0.00 5.12
1017 1656 1.146263 CATGGTAAGTCCCCTCCGC 59.854 63.158 0.00 0.00 34.77 5.54
1019 1658 3.477346 GGTAAGTCCCCTCCGCCC 61.477 72.222 0.00 0.00 0.00 6.13
1020 1659 3.477346 GTAAGTCCCCTCCGCCCC 61.477 72.222 0.00 0.00 0.00 5.80
1107 1772 1.209747 GCTCTACGATGTTTTCCCCCT 59.790 52.381 0.00 0.00 0.00 4.79
1127 1792 3.577667 CTGAATTTTGCGCTGATTTCCA 58.422 40.909 9.73 1.25 0.00 3.53
1140 1805 1.429148 ATTTCCACCGCGCTCGATTC 61.429 55.000 5.56 0.00 38.10 2.52
1302 1969 0.539051 CTGATGCGACCCCTCTTTCT 59.461 55.000 0.00 0.00 0.00 2.52
1457 2127 6.855914 CGTAAGTGCTTTGTGTAATGTTTCAT 59.144 34.615 0.00 0.00 0.00 2.57
1458 2128 7.378461 CGTAAGTGCTTTGTGTAATGTTTCATT 59.622 33.333 0.80 0.80 0.00 2.57
1459 2129 7.698836 AAGTGCTTTGTGTAATGTTTCATTC 57.301 32.000 0.00 0.00 0.00 2.67
1460 2130 6.804677 AGTGCTTTGTGTAATGTTTCATTCA 58.195 32.000 0.00 0.00 0.00 2.57
1503 2174 1.537202 CAGTTGGTGCTTGCCTAGAAC 59.463 52.381 0.00 0.00 0.00 3.01
1504 2175 1.421646 AGTTGGTGCTTGCCTAGAACT 59.578 47.619 0.00 0.00 32.40 3.01
1505 2176 2.637872 AGTTGGTGCTTGCCTAGAACTA 59.362 45.455 0.00 0.00 32.40 2.24
1506 2177 3.003480 GTTGGTGCTTGCCTAGAACTAG 58.997 50.000 0.00 2.23 32.40 2.57
1537 2208 2.871022 AGAGATGATGATTGTTCGCTGC 59.129 45.455 0.00 0.00 0.00 5.25
1548 2219 1.375396 TTCGCTGCCGCAGTTGTAT 60.375 52.632 21.29 0.00 35.30 2.29
1562 2236 7.201617 GCCGCAGTTGTATAACTTTTTAGAGAT 60.202 37.037 1.55 0.00 44.57 2.75
1570 2244 7.773690 TGTATAACTTTTTAGAGATGAAGGGGC 59.226 37.037 0.00 0.00 0.00 5.80
1578 2252 1.075748 GATGAAGGGGCCAGGCAAT 60.076 57.895 15.19 0.00 0.00 3.56
1670 2345 1.783711 CTCGTGATGTAGAATCAGCGC 59.216 52.381 0.00 0.00 0.00 5.92
1844 2523 2.002586 CAAGGTACATGCTCTGTTCCG 58.997 52.381 9.01 0.00 46.84 4.30
1881 2560 3.980775 CACAAACCTTTCTTATTGCACCG 59.019 43.478 0.00 0.00 0.00 4.94
2030 2710 1.812571 CTTCAAATCAGTGGGTTCCCG 59.187 52.381 3.27 0.00 0.00 5.14
2046 2727 1.689813 TCCCGCTCGGCTAAATATTGA 59.310 47.619 2.18 0.00 0.00 2.57
2048 2729 1.455786 CCGCTCGGCTAAATATTGACG 59.544 52.381 0.00 0.00 0.00 4.35
2158 2839 4.155709 TGAGATCTATCAGGCAACCTAGG 58.844 47.826 7.41 7.41 29.64 3.02
2200 2882 7.119553 TGCATATGTCGTGCATTTCATATACAT 59.880 33.333 15.08 0.00 46.76 2.29
2288 2970 2.787601 AAGTGAATGTGCTGCAACTG 57.212 45.000 2.77 0.00 0.00 3.16
2289 2971 0.313043 AGTGAATGTGCTGCAACTGC 59.687 50.000 2.77 0.00 42.50 4.40
2340 3033 6.588373 TGTTTTTGGTCTGAAGTTGCTTTTAC 59.412 34.615 0.00 0.00 0.00 2.01
2360 3053 3.009723 ACCAGCATTCGGTGAACAATAG 58.990 45.455 0.00 0.00 43.56 1.73
2396 3090 8.584157 CATATACTATTTCTTCTCCACTGAGCT 58.416 37.037 0.00 0.00 38.58 4.09
2398 3092 2.847327 TTTCTTCTCCACTGAGCTGG 57.153 50.000 0.00 0.00 38.58 4.85
2531 3225 0.755698 TCATCCGGCCTACTGGTCTC 60.756 60.000 0.00 0.00 43.58 3.36
2615 3309 3.786516 TCGGTGAAGAAAAACCCAAAC 57.213 42.857 0.00 0.00 32.44 2.93
2636 3330 3.056749 ACGGTCCAATGTACACTTCTCTC 60.057 47.826 0.00 0.00 0.00 3.20
2673 3367 4.280929 GGGGAACAATTATTGAGGTATGCC 59.719 45.833 12.28 6.68 0.00 4.40
2705 3399 7.806180 ACCTTATCTCCACTGCAATAGTATTT 58.194 34.615 0.00 0.00 37.60 1.40
2728 3422 7.454553 TTGTAGCTAATATACTTTTCCCCCA 57.545 36.000 0.00 0.00 0.00 4.96
2789 3490 6.024552 TGATTTATTTTCCTGTTGGTGCTC 57.975 37.500 0.00 0.00 34.23 4.26
2805 3506 8.028354 TGTTGGTGCTCACAATAATAAATCTTG 58.972 33.333 2.21 0.00 0.00 3.02
2996 3697 1.895707 CCCGGAGAATGATGGCTGC 60.896 63.158 0.73 0.00 0.00 5.25
3071 3772 2.395360 TGCGCTGTTTGTATCCGGC 61.395 57.895 9.73 0.00 0.00 6.13
3169 3870 2.289756 GGTGGAACAGTCTTCTTCCCTC 60.290 54.545 4.28 0.00 41.80 4.30
3171 3872 2.368875 TGGAACAGTCTTCTTCCCTCAC 59.631 50.000 4.28 0.00 32.76 3.51
3172 3873 2.635427 GGAACAGTCTTCTTCCCTCACT 59.365 50.000 0.00 0.00 0.00 3.41
3243 3948 4.894784 TGGAAGTACCACATGTCTTTCTC 58.105 43.478 0.00 0.00 44.64 2.87
3256 3961 6.769822 ACATGTCTTTCTCCCATGTTCATATC 59.230 38.462 0.00 0.00 45.01 1.63
3292 3997 3.467803 CCTTATTCTGACGGTTCATCCC 58.532 50.000 0.00 0.00 0.00 3.85
3318 4023 7.315142 CCAGTAACACAAAAATATCATGCTGT 58.685 34.615 0.00 0.00 0.00 4.40
3336 4045 3.502211 GCTGTAGGTATTTGTTGTGTGCT 59.498 43.478 0.00 0.00 0.00 4.40
3338 4047 3.252215 TGTAGGTATTTGTTGTGTGCTGC 59.748 43.478 0.00 0.00 0.00 5.25
3354 4071 1.731160 GCTGCGATCCATGCTTATCTC 59.269 52.381 0.00 0.00 0.00 2.75
3370 4088 1.956869 TCTCTGGATCACCCACATGT 58.043 50.000 0.00 0.00 40.82 3.21
3397 4132 9.432077 GCAACAGTATTTTGTTTTACAATTTGG 57.568 29.630 0.78 0.00 39.17 3.28
3408 4143 8.994170 TTGTTTTACAATTTGGGCTATAAAAGC 58.006 29.630 0.78 0.00 40.97 3.51
3446 4181 7.948357 ACATAAAAGTAACCCTTCTTTTGGAC 58.052 34.615 11.48 0.00 41.77 4.02
3505 4240 9.860898 AATAATGCAAAGTATCTTCAAAGAACC 57.139 29.630 0.00 0.00 38.77 3.62
3528 4263 8.503428 ACCTTCTTCACTCAAGATATATCCAT 57.497 34.615 9.18 0.00 41.02 3.41
3530 4265 9.790344 CCTTCTTCACTCAAGATATATCCATTT 57.210 33.333 9.18 0.00 41.02 2.32
3555 4290 8.574251 TTACAAGCTAAATCTTTGCCATAAGA 57.426 30.769 0.00 0.00 38.43 2.10
3556 4291 7.651027 ACAAGCTAAATCTTTGCCATAAGAT 57.349 32.000 0.00 0.00 44.62 2.40
3559 4294 8.623903 CAAGCTAAATCTTTGCCATAAGATGTA 58.376 33.333 6.59 5.32 42.53 2.29
3561 4296 7.446625 AGCTAAATCTTTGCCATAAGATGTAGG 59.553 37.037 20.75 10.67 44.99 3.18
3598 4336 8.531982 TCTTGATATATAGGCACATACTTCACC 58.468 37.037 0.00 0.00 0.00 4.02
3599 4337 6.863275 TGATATATAGGCACATACTTCACCG 58.137 40.000 0.00 0.00 0.00 4.94
3626 4368 6.582437 AAAATTTGCACTTGGTACTTTTCG 57.418 33.333 0.00 0.00 0.00 3.46
3654 4396 5.523188 ACAATGTAAAGTTGCCACAAACATG 59.477 36.000 0.00 0.00 32.21 3.21
3664 4406 1.481772 CCACAAACATGGCCTAATGGG 59.518 52.381 3.32 0.00 38.36 4.00
3676 4418 3.094484 CCTAATGGGCAGGGTTTTGTA 57.906 47.619 0.00 0.00 0.00 2.41
3677 4419 2.758423 CCTAATGGGCAGGGTTTTGTAC 59.242 50.000 0.00 0.00 0.00 2.90
3678 4420 2.390225 AATGGGCAGGGTTTTGTACA 57.610 45.000 0.00 0.00 0.00 2.90
3679 4421 1.627864 ATGGGCAGGGTTTTGTACAC 58.372 50.000 0.00 0.00 0.00 2.90
3680 4422 0.468400 TGGGCAGGGTTTTGTACACC 60.468 55.000 0.00 0.00 0.00 4.16
3681 4423 1.520600 GGGCAGGGTTTTGTACACCG 61.521 60.000 0.00 0.00 34.79 4.94
3682 4424 0.820482 GGCAGGGTTTTGTACACCGT 60.820 55.000 0.00 0.00 34.79 4.83
3684 4426 1.670791 CAGGGTTTTGTACACCGTGT 58.329 50.000 9.58 9.58 42.72 4.49
3685 4427 2.836262 CAGGGTTTTGTACACCGTGTA 58.164 47.619 7.32 7.32 42.72 2.90
3686 4428 3.404899 CAGGGTTTTGTACACCGTGTAT 58.595 45.455 14.37 0.00 42.72 2.29
3687 4429 3.187637 CAGGGTTTTGTACACCGTGTATG 59.812 47.826 14.37 2.92 42.72 2.39
3688 4430 2.095617 GGGTTTTGTACACCGTGTATGC 60.096 50.000 14.37 3.78 35.05 3.14
3689 4431 2.095617 GGTTTTGTACACCGTGTATGCC 60.096 50.000 14.37 8.78 35.05 4.40
3690 4432 1.810959 TTTGTACACCGTGTATGCCC 58.189 50.000 14.37 2.76 35.05 5.36
3691 4433 0.978151 TTGTACACCGTGTATGCCCT 59.022 50.000 14.37 0.00 35.05 5.19
3692 4434 1.849977 TGTACACCGTGTATGCCCTA 58.150 50.000 14.37 0.00 35.05 3.53
3693 4435 1.752498 TGTACACCGTGTATGCCCTAG 59.248 52.381 14.37 0.00 35.05 3.02
3694 4436 1.068127 GTACACCGTGTATGCCCTAGG 59.932 57.143 14.37 0.06 35.05 3.02
3695 4437 0.324923 ACACCGTGTATGCCCTAGGA 60.325 55.000 11.48 0.00 0.00 2.94
3696 4438 0.104304 CACCGTGTATGCCCTAGGAC 59.896 60.000 11.48 0.00 0.00 3.85
3697 4439 0.324923 ACCGTGTATGCCCTAGGACA 60.325 55.000 11.48 4.87 0.00 4.02
3698 4440 0.828022 CCGTGTATGCCCTAGGACAA 59.172 55.000 11.48 0.00 0.00 3.18
3699 4441 1.472728 CCGTGTATGCCCTAGGACAAC 60.473 57.143 11.48 6.88 0.00 3.32
3700 4442 1.206132 CGTGTATGCCCTAGGACAACA 59.794 52.381 11.48 9.46 0.00 3.33
3701 4443 2.354303 CGTGTATGCCCTAGGACAACAA 60.354 50.000 11.48 0.00 0.00 2.83
3702 4444 3.681593 GTGTATGCCCTAGGACAACAAA 58.318 45.455 11.48 0.00 0.00 2.83
3703 4445 4.076394 GTGTATGCCCTAGGACAACAAAA 58.924 43.478 11.48 0.00 0.00 2.44
3704 4446 4.156008 GTGTATGCCCTAGGACAACAAAAG 59.844 45.833 11.48 0.00 0.00 2.27
3705 4447 2.286365 TGCCCTAGGACAACAAAAGG 57.714 50.000 11.48 0.00 0.00 3.11
3706 4448 1.497286 TGCCCTAGGACAACAAAAGGT 59.503 47.619 11.48 0.00 0.00 3.50
3707 4449 2.712087 TGCCCTAGGACAACAAAAGGTA 59.288 45.455 11.48 0.00 0.00 3.08
3730 4472 4.307032 AACTGGTTCCACTGAATGCTAT 57.693 40.909 0.00 0.00 31.98 2.97
3751 4493 8.952278 TGCTATAACCAAAATATTTTCTGTCGT 58.048 29.630 10.53 6.49 0.00 4.34
3766 4508 9.831737 ATTTTCTGTCGTTCTTTATCAAAGATG 57.168 29.630 2.40 0.04 46.15 2.90
3773 4516 6.371271 TCGTTCTTTATCAAAGATGACATGCA 59.629 34.615 2.40 0.00 46.15 3.96
3781 4524 1.867166 AGATGACATGCATGCGAGAG 58.133 50.000 26.53 1.91 37.34 3.20
3782 4525 0.866427 GATGACATGCATGCGAGAGG 59.134 55.000 26.53 1.10 37.34 3.69
3796 4539 2.882324 CGAGAGGTAAACTGCTTCCTC 58.118 52.381 0.00 0.00 44.61 3.71
3802 4545 3.193056 AGGTAAACTGCTTCCTCGAGTAC 59.807 47.826 12.31 3.73 0.00 2.73
3917 4660 6.515531 GCTTTCTTGGATCTTGAACACATCAA 60.516 38.462 0.00 0.00 45.71 2.57
3918 4661 7.528996 TTTCTTGGATCTTGAACACATCAAT 57.471 32.000 0.00 0.00 46.62 2.57
3919 4662 6.748333 TCTTGGATCTTGAACACATCAATC 57.252 37.500 0.00 0.00 46.62 2.67
3920 4663 6.240145 TCTTGGATCTTGAACACATCAATCA 58.760 36.000 0.00 0.00 46.62 2.57
3921 4664 5.885230 TGGATCTTGAACACATCAATCAC 57.115 39.130 0.00 0.00 46.62 3.06
3922 4665 4.392754 TGGATCTTGAACACATCAATCACG 59.607 41.667 0.00 0.00 46.62 4.35
3923 4666 4.393062 GGATCTTGAACACATCAATCACGT 59.607 41.667 0.00 0.00 46.62 4.49
3924 4667 5.580691 GGATCTTGAACACATCAATCACGTA 59.419 40.000 0.00 0.00 46.62 3.57
3958 4701 1.593196 TTCGTGTTTGCTTCCCAGAG 58.407 50.000 0.00 0.00 0.00 3.35
3959 4702 0.756294 TCGTGTTTGCTTCCCAGAGA 59.244 50.000 0.00 0.00 0.00 3.10
3960 4703 1.151668 CGTGTTTGCTTCCCAGAGAG 58.848 55.000 0.00 0.00 0.00 3.20
3993 4736 7.093201 ACACGGTGGAGAAAATTAATAGTCCTA 60.093 37.037 13.48 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 8.929260 AATCTGAATGAACATATATTCTGGCA 57.071 30.769 0.00 0.00 35.02 4.92
148 154 1.928868 ATCTCAAAAGGCACAAGGGG 58.071 50.000 0.00 0.00 0.00 4.79
276 711 2.164219 GCACCACCAAACATACCATGAG 59.836 50.000 0.00 0.00 0.00 2.90
318 756 7.004555 TGACTGAAATTTAGGCTAGACAGAA 57.995 36.000 0.00 0.00 0.00 3.02
387 826 5.866633 GTGTTCACTCCAGTTCTCTCTTATG 59.133 44.000 0.00 0.00 0.00 1.90
396 837 6.560253 ATGTAATTGTGTTCACTCCAGTTC 57.440 37.500 4.59 0.00 0.00 3.01
427 870 2.078392 GTTTTGATGCATGCCCTTTGG 58.922 47.619 16.68 0.00 0.00 3.28
432 875 1.067635 ACTTCGTTTTGATGCATGCCC 60.068 47.619 16.68 7.77 0.00 5.36
434 877 2.253603 GGACTTCGTTTTGATGCATGC 58.746 47.619 11.82 11.82 0.00 4.06
438 901 6.037610 AGAGAATATGGACTTCGTTTTGATGC 59.962 38.462 0.00 0.00 0.00 3.91
466 929 5.287992 GTGTCTACGCTGTACTTGGTATTTC 59.712 44.000 0.00 0.00 0.00 2.17
469 932 3.760151 TGTGTCTACGCTGTACTTGGTAT 59.240 43.478 0.00 0.00 0.00 2.73
473 936 2.325761 GGTGTGTCTACGCTGTACTTG 58.674 52.381 0.00 0.00 37.47 3.16
476 939 0.518636 TCGGTGTGTCTACGCTGTAC 59.481 55.000 0.00 0.00 42.85 2.90
494 971 4.035017 CCAATGAGAACGTTTGTGTTGTC 58.965 43.478 0.46 0.00 41.20 3.18
497 974 3.945285 ACTCCAATGAGAACGTTTGTGTT 59.055 39.130 0.46 0.00 41.42 3.32
502 979 6.540914 TCTTTGTAACTCCAATGAGAACGTTT 59.459 34.615 0.46 0.00 41.42 3.60
539 1034 4.235939 TGTTTCCATCGACAAACAATGG 57.764 40.909 13.89 4.93 39.10 3.16
555 1064 4.037923 TCTTTCAGTGGAAGGCAATGTTTC 59.962 41.667 11.39 0.00 33.82 2.78
562 1071 4.949856 GGATTATTCTTTCAGTGGAAGGCA 59.050 41.667 11.39 0.00 33.82 4.75
592 1102 8.727100 AATACTAGGTTGGACATCATCTATGA 57.273 34.615 0.00 0.00 41.70 2.15
620 1130 0.475906 AGCCATAGCCCATCAGGAAC 59.524 55.000 0.00 0.00 41.25 3.62
628 1138 1.340600 GGTTGTTGTAGCCATAGCCCA 60.341 52.381 0.00 0.00 41.25 5.36
638 1149 4.072131 ACATGTTAGCAGGGTTGTTGTAG 58.928 43.478 0.00 0.00 0.00 2.74
713 1262 6.974965 AGTTCAAAGTTTCAGATCATTGACC 58.025 36.000 0.00 0.00 0.00 4.02
787 1355 3.128349 TCACGCTCTTCGCTTAGTTTTT 58.872 40.909 0.00 0.00 43.23 1.94
788 1356 2.750948 TCACGCTCTTCGCTTAGTTTT 58.249 42.857 0.00 0.00 43.23 2.43
789 1357 2.433868 TCACGCTCTTCGCTTAGTTT 57.566 45.000 0.00 0.00 43.23 2.66
790 1358 2.094700 TGATCACGCTCTTCGCTTAGTT 60.095 45.455 0.00 0.00 43.23 2.24
791 1359 1.472878 TGATCACGCTCTTCGCTTAGT 59.527 47.619 0.00 0.00 43.23 2.24
792 1360 2.194800 TGATCACGCTCTTCGCTTAG 57.805 50.000 0.00 0.00 43.23 2.18
793 1361 2.647529 TTGATCACGCTCTTCGCTTA 57.352 45.000 0.00 0.00 43.23 3.09
847 1485 2.583593 GTTAGGAGGCTCGCGCAG 60.584 66.667 8.75 5.26 38.10 5.18
934 1573 1.406205 CGGAAAGGAAGGAGAAGAGGC 60.406 57.143 0.00 0.00 0.00 4.70
1107 1772 3.316283 GTGGAAATCAGCGCAAAATTCA 58.684 40.909 11.47 0.00 0.00 2.57
1302 1969 4.574421 CGCACAGAAACATACATGGGATAA 59.426 41.667 0.00 0.00 0.00 1.75
1457 2127 2.854963 ACAGCAAGCAGTCATTCTGAA 58.145 42.857 0.00 0.00 46.27 3.02
1458 2128 2.551032 CAACAGCAAGCAGTCATTCTGA 59.449 45.455 0.00 0.00 46.27 3.27
1459 2129 2.921069 GCAACAGCAAGCAGTCATTCTG 60.921 50.000 0.00 0.00 46.12 3.02
1460 2130 1.268899 GCAACAGCAAGCAGTCATTCT 59.731 47.619 0.00 0.00 0.00 2.40
1503 2174 6.373005 TCATCATCTCTCCTAGAGTCCTAG 57.627 45.833 3.98 0.00 42.83 3.02
1504 2175 6.968400 ATCATCATCTCTCCTAGAGTCCTA 57.032 41.667 3.98 0.00 42.83 2.94
1505 2176 5.865977 ATCATCATCTCTCCTAGAGTCCT 57.134 43.478 3.98 0.00 42.83 3.85
1506 2177 5.774690 ACAATCATCATCTCTCCTAGAGTCC 59.225 44.000 3.98 0.00 42.83 3.85
1507 2178 6.899393 ACAATCATCATCTCTCCTAGAGTC 57.101 41.667 3.98 0.00 42.83 3.36
1508 2179 6.016360 CGAACAATCATCATCTCTCCTAGAGT 60.016 42.308 3.98 0.00 42.83 3.24
1509 2180 6.380995 CGAACAATCATCATCTCTCCTAGAG 58.619 44.000 0.00 0.00 43.64 2.43
1510 2181 5.278709 GCGAACAATCATCATCTCTCCTAGA 60.279 44.000 0.00 0.00 39.02 2.43
1519 2190 1.333524 CGGCAGCGAACAATCATCATC 60.334 52.381 0.00 0.00 0.00 2.92
1537 2208 7.591006 TCTCTAAAAAGTTATACAACTGCGG 57.409 36.000 0.00 0.00 44.41 5.69
1548 2219 5.014755 TGGCCCCTTCATCTCTAAAAAGTTA 59.985 40.000 0.00 0.00 0.00 2.24
1562 2236 0.324275 GTTATTGCCTGGCCCCTTCA 60.324 55.000 17.53 0.00 0.00 3.02
1570 2244 1.376609 GACAGCGGGTTATTGCCTGG 61.377 60.000 0.00 0.00 35.47 4.45
1670 2345 3.970721 TGCAACCGCAGTCAGATG 58.029 55.556 0.00 0.00 45.36 2.90
1687 2362 1.705186 ACACTTGTGAGTAAGGCCCAT 59.295 47.619 7.83 0.00 33.90 4.00
1881 2560 4.205792 GCAATTGACGATAAATCAGCAAGC 59.794 41.667 10.34 0.00 0.00 4.01
2030 2710 1.136611 CGCGTCAATATTTAGCCGAGC 60.137 52.381 0.00 0.00 0.00 5.03
2046 2727 0.950555 TGCAAGAAGATGAAGCGCGT 60.951 50.000 8.43 0.00 0.00 6.01
2048 2729 0.098376 CCTGCAAGAAGATGAAGCGC 59.902 55.000 0.00 0.00 34.07 5.92
2146 2827 3.418684 AACTGTAACCTAGGTTGCCTG 57.581 47.619 33.19 26.73 39.42 4.85
2158 2839 8.785101 CGACATATGCAAATTACAAACTGTAAC 58.215 33.333 1.58 0.00 44.54 2.50
2200 2882 9.421806 CAAGGAATTACAAACTTATGCAATTCA 57.578 29.630 12.50 0.00 41.62 2.57
2288 2970 0.039708 GCAGAACTCAGTTGCCTTGC 60.040 55.000 0.00 0.00 31.79 4.01
2289 2971 1.602311 AGCAGAACTCAGTTGCCTTG 58.398 50.000 0.00 0.00 38.58 3.61
2300 2982 7.502561 AGACCAAAAACATAAGTTAGCAGAACT 59.497 33.333 0.00 0.00 36.84 3.01
2301 2983 7.591426 CAGACCAAAAACATAAGTTAGCAGAAC 59.409 37.037 0.00 0.00 36.84 3.01
2340 3033 2.223340 GCTATTGTTCACCGAATGCTGG 60.223 50.000 0.00 0.00 0.00 4.85
2531 3225 0.523072 CATGAGCCTTGGTGAAACGG 59.477 55.000 0.00 0.00 38.12 4.44
2615 3309 3.512680 GAGAGAAGTGTACATTGGACCG 58.487 50.000 0.00 0.00 0.00 4.79
2636 3330 0.533491 TTCCCCTCGTCATAACACCG 59.467 55.000 0.00 0.00 0.00 4.94
2673 3367 3.119708 GCAGTGGAGATAAGGTTTGCTTG 60.120 47.826 0.00 0.00 0.00 4.01
2705 3399 7.454553 TTGGGGGAAAAGTATATTAGCTACA 57.545 36.000 0.00 0.00 0.00 2.74
2728 3422 7.578310 AGCATCATTACTGTAAGCATTGATT 57.422 32.000 10.24 0.00 37.60 2.57
2789 3490 9.123902 TCACCTGGATCAAGATTTATTATTGTG 57.876 33.333 0.00 0.00 0.00 3.33
2805 3506 5.491982 AGTTCACTAACATTCACCTGGATC 58.508 41.667 0.00 0.00 38.12 3.36
2996 3697 1.736126 ACGAGCAAGACAGCATTGATG 59.264 47.619 0.00 0.00 36.85 3.07
3071 3772 3.574614 CGACAAAATTGCCCTTGTTAGG 58.425 45.455 0.00 0.00 41.60 2.69
3169 3870 4.521130 TCTTACAGCAGGTTACAGAGTG 57.479 45.455 0.00 0.00 0.00 3.51
3171 3872 5.126222 TCAGATCTTACAGCAGGTTACAGAG 59.874 44.000 0.00 0.00 0.00 3.35
3172 3873 5.016831 TCAGATCTTACAGCAGGTTACAGA 58.983 41.667 0.00 0.00 0.00 3.41
3241 3946 4.025730 CGAAACGTGATATGAACATGGGAG 60.026 45.833 0.00 0.00 0.00 4.30
3243 3948 3.002246 CCGAAACGTGATATGAACATGGG 59.998 47.826 0.00 0.00 0.00 4.00
3256 3961 0.945813 TAAGGCAAACCCGAAACGTG 59.054 50.000 0.00 0.00 39.21 4.49
3292 3997 6.753279 CAGCATGATATTTTTGTGTTACTGGG 59.247 38.462 0.00 0.00 39.69 4.45
3318 4023 2.482336 CGCAGCACACAACAAATACCTA 59.518 45.455 0.00 0.00 0.00 3.08
3328 4037 1.925415 GCATGGATCGCAGCACACAA 61.925 55.000 0.00 0.00 0.00 3.33
3336 4045 2.289257 CCAGAGATAAGCATGGATCGCA 60.289 50.000 0.00 0.00 34.60 5.10
3338 4047 3.949842 TCCAGAGATAAGCATGGATCG 57.050 47.619 0.00 0.00 36.92 3.69
3370 4088 9.979270 CAAATTGTAAAACAAAATACTGTTGCA 57.021 25.926 0.00 0.00 41.96 4.08
3383 4101 8.541133 GCTTTTATAGCCCAAATTGTAAAACA 57.459 30.769 0.00 0.00 44.48 2.83
3422 4157 7.014808 TGGTCCAAAAGAAGGGTTACTTTTATG 59.985 37.037 0.00 0.00 42.08 1.90
3431 4166 3.897505 CAAGATGGTCCAAAAGAAGGGTT 59.102 43.478 0.00 0.00 0.00 4.11
3432 4167 3.117131 ACAAGATGGTCCAAAAGAAGGGT 60.117 43.478 0.00 0.00 0.00 4.34
3433 4168 3.500343 ACAAGATGGTCCAAAAGAAGGG 58.500 45.455 0.00 0.00 0.00 3.95
3528 4263 9.638239 CTTATGGCAAAGATTTAGCTTGTAAAA 57.362 29.630 0.00 0.00 0.00 1.52
3530 4265 8.574251 TCTTATGGCAAAGATTTAGCTTGTAA 57.426 30.769 0.00 0.00 30.54 2.41
3559 4294 9.965902 CCTATATATCAAGAAGTAATTTGGCCT 57.034 33.333 3.32 0.00 0.00 5.19
3561 4296 9.231297 TGCCTATATATCAAGAAGTAATTTGGC 57.769 33.333 0.00 0.00 0.00 4.52
3607 4345 4.156190 TGAACGAAAAGTACCAAGTGCAAA 59.844 37.500 0.00 0.00 0.00 3.68
3609 4347 3.064271 GTGAACGAAAAGTACCAAGTGCA 59.936 43.478 0.00 0.00 0.00 4.57
3614 4352 5.821516 ACATTGTGAACGAAAAGTACCAA 57.178 34.783 0.00 0.00 0.00 3.67
3615 4353 6.922247 TTACATTGTGAACGAAAAGTACCA 57.078 33.333 0.00 0.00 0.00 3.25
3616 4354 7.412063 ACTTTACATTGTGAACGAAAAGTACC 58.588 34.615 10.07 0.00 34.79 3.34
3617 4355 8.730427 CAACTTTACATTGTGAACGAAAAGTAC 58.270 33.333 11.53 0.00 35.32 2.73
3619 4357 6.252655 GCAACTTTACATTGTGAACGAAAAGT 59.747 34.615 0.00 3.67 37.30 2.66
3626 4368 4.677584 TGTGGCAACTTTACATTGTGAAC 58.322 39.130 0.00 0.00 37.61 3.18
3657 4399 3.192633 GTGTACAAAACCCTGCCCATTAG 59.807 47.826 0.00 0.00 0.00 1.73
3658 4400 3.158676 GTGTACAAAACCCTGCCCATTA 58.841 45.455 0.00 0.00 0.00 1.90
3659 4401 1.967779 GTGTACAAAACCCTGCCCATT 59.032 47.619 0.00 0.00 0.00 3.16
3662 4404 1.520600 CGGTGTACAAAACCCTGCCC 61.521 60.000 0.00 0.00 33.88 5.36
3664 4406 0.309612 CACGGTGTACAAAACCCTGC 59.690 55.000 0.00 0.00 33.88 4.85
3667 4409 2.095617 GCATACACGGTGTACAAAACCC 60.096 50.000 22.22 0.00 35.42 4.11
3670 4412 2.152830 GGGCATACACGGTGTACAAAA 58.847 47.619 22.22 3.04 35.42 2.44
3671 4413 1.348366 AGGGCATACACGGTGTACAAA 59.652 47.619 22.22 3.43 35.42 2.83
3673 4415 1.752498 CTAGGGCATACACGGTGTACA 59.248 52.381 22.22 4.60 35.42 2.90
3674 4416 1.068127 CCTAGGGCATACACGGTGTAC 59.932 57.143 22.22 11.15 35.42 2.90
3676 4418 0.324923 TCCTAGGGCATACACGGTGT 60.325 55.000 18.89 18.89 0.00 4.16
3677 4419 0.104304 GTCCTAGGGCATACACGGTG 59.896 60.000 9.01 6.58 0.00 4.94
3678 4420 0.324923 TGTCCTAGGGCATACACGGT 60.325 55.000 13.40 0.00 0.00 4.83
3679 4421 0.828022 TTGTCCTAGGGCATACACGG 59.172 55.000 18.79 0.00 0.00 4.94
3680 4422 1.206132 TGTTGTCCTAGGGCATACACG 59.794 52.381 18.79 0.00 0.00 4.49
3681 4423 3.343941 TTGTTGTCCTAGGGCATACAC 57.656 47.619 18.79 13.39 0.00 2.90
3682 4424 4.331968 CTTTTGTTGTCCTAGGGCATACA 58.668 43.478 18.79 19.90 0.00 2.29
3683 4425 3.694566 CCTTTTGTTGTCCTAGGGCATAC 59.305 47.826 18.79 17.63 0.00 2.39
3684 4426 3.332485 ACCTTTTGTTGTCCTAGGGCATA 59.668 43.478 18.79 6.84 0.00 3.14
3685 4427 2.110011 ACCTTTTGTTGTCCTAGGGCAT 59.890 45.455 18.79 0.00 0.00 4.40
3686 4428 1.497286 ACCTTTTGTTGTCCTAGGGCA 59.503 47.619 13.40 13.40 0.00 5.36
3687 4429 2.287977 ACCTTTTGTTGTCCTAGGGC 57.712 50.000 6.37 6.37 0.00 5.19
3688 4430 5.831525 AGTTTTACCTTTTGTTGTCCTAGGG 59.168 40.000 9.46 0.00 0.00 3.53
3689 4431 6.238925 CCAGTTTTACCTTTTGTTGTCCTAGG 60.239 42.308 0.82 0.82 0.00 3.02
3690 4432 6.320418 ACCAGTTTTACCTTTTGTTGTCCTAG 59.680 38.462 0.00 0.00 0.00 3.02
3691 4433 6.189133 ACCAGTTTTACCTTTTGTTGTCCTA 58.811 36.000 0.00 0.00 0.00 2.94
3692 4434 5.020795 ACCAGTTTTACCTTTTGTTGTCCT 58.979 37.500 0.00 0.00 0.00 3.85
3693 4435 5.333299 ACCAGTTTTACCTTTTGTTGTCC 57.667 39.130 0.00 0.00 0.00 4.02
3694 4436 5.808540 GGAACCAGTTTTACCTTTTGTTGTC 59.191 40.000 0.00 0.00 0.00 3.18
3695 4437 5.246429 TGGAACCAGTTTTACCTTTTGTTGT 59.754 36.000 0.00 0.00 0.00 3.32
3696 4438 5.579119 GTGGAACCAGTTTTACCTTTTGTTG 59.421 40.000 0.00 0.00 0.00 3.33
3697 4439 5.482526 AGTGGAACCAGTTTTACCTTTTGTT 59.517 36.000 0.00 0.00 37.80 2.83
3698 4440 5.020795 AGTGGAACCAGTTTTACCTTTTGT 58.979 37.500 0.00 0.00 37.80 2.83
3699 4441 5.126384 TCAGTGGAACCAGTTTTACCTTTTG 59.874 40.000 0.00 0.00 37.80 2.44
3700 4442 5.265989 TCAGTGGAACCAGTTTTACCTTTT 58.734 37.500 0.00 0.00 37.80 2.27
3701 4443 4.862371 TCAGTGGAACCAGTTTTACCTTT 58.138 39.130 0.00 0.00 37.80 3.11
3702 4444 4.513406 TCAGTGGAACCAGTTTTACCTT 57.487 40.909 0.00 0.00 37.80 3.50
3703 4445 4.513406 TTCAGTGGAACCAGTTTTACCT 57.487 40.909 0.00 0.00 37.80 3.08
3704 4446 4.558697 GCATTCAGTGGAACCAGTTTTACC 60.559 45.833 0.00 0.00 37.80 2.85
3705 4447 4.278419 AGCATTCAGTGGAACCAGTTTTAC 59.722 41.667 0.00 0.00 37.80 2.01
3706 4448 4.469657 AGCATTCAGTGGAACCAGTTTTA 58.530 39.130 0.00 0.00 37.80 1.52
3707 4449 3.299503 AGCATTCAGTGGAACCAGTTTT 58.700 40.909 0.00 0.00 37.80 2.43
3764 4506 0.179702 ACCTCTCGCATGCATGTCAT 59.820 50.000 26.79 4.47 35.31 3.06
3766 4508 1.939974 TTACCTCTCGCATGCATGTC 58.060 50.000 26.79 17.75 0.00 3.06
3773 4516 2.622436 GAAGCAGTTTACCTCTCGCAT 58.378 47.619 0.00 0.00 0.00 4.73
3781 4524 2.745515 ACTCGAGGAAGCAGTTTACC 57.254 50.000 18.41 0.00 0.00 2.85
3782 4525 4.170292 TGTACTCGAGGAAGCAGTTTAC 57.830 45.455 18.41 7.20 0.00 2.01
3836 4579 7.596749 AGTTCAGGTGTTTATTTACGAGATG 57.403 36.000 0.00 0.00 0.00 2.90
3941 4684 1.151668 CTCTCTGGGAAGCAAACACG 58.848 55.000 0.00 0.00 0.00 4.49
3958 4701 0.457851 CTCCACCGTGTGATCTCCTC 59.542 60.000 5.71 0.00 35.23 3.71
3959 4702 0.039764 TCTCCACCGTGTGATCTCCT 59.960 55.000 5.71 0.00 35.23 3.69
3960 4703 0.895530 TTCTCCACCGTGTGATCTCC 59.104 55.000 5.71 0.00 35.23 3.71


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

AutoCloner maintained by Alex Coulton.