Multiple sequence alignment - TraesCS3B01G126400

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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 TraesCS3B01G126400 chr3B 100.000 4617 0 0 1 4617 103026548 103031164 0.000000e+00 8527.0
1 TraesCS3B01G126400 chr3B 100.000 310 0 0 5015 5324 103031562 103031871 1.660000e-159 573.0
2 TraesCS3B01G126400 chr3B 85.243 515 69 6 1 510 61647275 61647787 1.700000e-144 523.0
3 TraesCS3B01G126400 chr3D 94.240 4549 178 41 96 4610 63405217 63409715 0.000000e+00 6872.0
4 TraesCS3B01G126400 chr3D 92.490 253 15 2 5015 5267 63409738 63409986 5.070000e-95 359.0
5 TraesCS3B01G126400 chr3D 84.861 251 27 7 3300 3548 66166429 66166670 5.330000e-60 243.0
6 TraesCS3B01G126400 chr3D 84.462 251 29 8 3300 3548 66234069 66234311 6.890000e-59 239.0
7 TraesCS3B01G126400 chr3D 84.462 251 29 8 3300 3548 66268373 66268615 6.890000e-59 239.0
8 TraesCS3B01G126400 chr3D 84.462 251 27 8 3300 3548 66270202 66270442 2.480000e-58 237.0
9 TraesCS3B01G126400 chr3D 84.064 251 30 8 3300 3548 66204660 66204902 3.210000e-57 233.0
10 TraesCS3B01G126400 chr3D 83.267 251 32 8 3300 3548 66164392 66164634 6.940000e-54 222.0
11 TraesCS3B01G126400 chr3D 81.863 204 18 8 5136 5324 373599710 373599511 2.570000e-33 154.0
12 TraesCS3B01G126400 chr3A 92.958 4587 212 49 92 4610 72487443 72491986 0.000000e+00 6578.0
13 TraesCS3B01G126400 chr3A 82.659 519 75 7 1 505 50000905 50001422 3.780000e-121 446.0
14 TraesCS3B01G126400 chr3A 88.321 274 21 5 5057 5324 72492226 72492494 8.600000e-83 318.0
15 TraesCS3B01G126400 chr5D 85.277 523 62 5 1 510 391194684 391195204 4.720000e-145 525.0
16 TraesCS3B01G126400 chr5D 83.000 200 19 9 5136 5324 495365821 495366016 3.300000e-37 167.0
17 TraesCS3B01G126400 chr5D 81.463 205 17 9 5136 5324 256182577 256182776 1.190000e-31 148.0
18 TraesCS3B01G126400 chr7B 85.156 512 67 7 1 510 577670618 577670114 2.840000e-142 516.0
19 TraesCS3B01G126400 chr1A 84.069 521 72 6 1 510 267790980 267790460 4.790000e-135 492.0
20 TraesCS3B01G126400 chr4D 83.366 511 78 3 1 510 478023212 478022708 2.900000e-127 466.0
21 TraesCS3B01G126400 chr4D 82.885 520 78 8 1 510 68065626 68065108 1.750000e-124 457.0
22 TraesCS3B01G126400 chr2D 83.022 536 68 13 1 518 645835375 645834845 1.040000e-126 464.0
23 TraesCS3B01G126400 chr2D 81.863 204 18 8 5136 5324 617044754 617044953 2.570000e-33 154.0
24 TraesCS3B01G126400 chr5B 83.074 514 82 5 1 511 300099414 300098903 3.760000e-126 462.0
25 TraesCS3B01G126400 chr5B 79.791 287 37 10 3262 3543 6523722 6523452 7.040000e-44 189.0
26 TraesCS3B01G126400 chr7A 84.368 467 67 6 1 463 68780701 68781165 2.260000e-123 453.0
27 TraesCS3B01G126400 chr7A 91.304 69 6 0 5063 5131 336662265 336662333 1.580000e-15 95.3
28 TraesCS3B01G126400 chr2A 90.608 181 15 2 2345 2524 755067164 755066985 6.890000e-59 239.0
29 TraesCS3B01G126400 chrUn 82.439 205 17 9 5136 5324 161260 161059 1.530000e-35 161.0
30 TraesCS3B01G126400 chr1D 82.439 205 17 9 5136 5324 18760994 18760793 1.530000e-35 161.0
31 TraesCS3B01G126400 chr1D 81.863 204 17 8 5136 5324 102156353 102156551 2.570000e-33 154.0
32 TraesCS3B01G126400 chr6A 92.727 110 7 1 2345 2453 8971047 8971156 1.980000e-34 158.0


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 TraesCS3B01G126400 chr3B 103026548 103031871 5323 False 4550.0 8527 100.0000 1 5324 2 chr3B.!!$F2 5323
1 TraesCS3B01G126400 chr3B 61647275 61647787 512 False 523.0 523 85.2430 1 510 1 chr3B.!!$F1 509
2 TraesCS3B01G126400 chr3D 63405217 63409986 4769 False 3615.5 6872 93.3650 96 5267 2 chr3D.!!$F3 5171
3 TraesCS3B01G126400 chr3D 66268373 66270442 2069 False 238.0 239 84.4620 3300 3548 2 chr3D.!!$F5 248
4 TraesCS3B01G126400 chr3D 66164392 66166670 2278 False 232.5 243 84.0640 3300 3548 2 chr3D.!!$F4 248
5 TraesCS3B01G126400 chr3A 72487443 72492494 5051 False 3448.0 6578 90.6395 92 5324 2 chr3A.!!$F2 5232
6 TraesCS3B01G126400 chr3A 50000905 50001422 517 False 446.0 446 82.6590 1 505 1 chr3A.!!$F1 504
7 TraesCS3B01G126400 chr5D 391194684 391195204 520 False 525.0 525 85.2770 1 510 1 chr5D.!!$F2 509
8 TraesCS3B01G126400 chr7B 577670114 577670618 504 True 516.0 516 85.1560 1 510 1 chr7B.!!$R1 509
9 TraesCS3B01G126400 chr1A 267790460 267790980 520 True 492.0 492 84.0690 1 510 1 chr1A.!!$R1 509
10 TraesCS3B01G126400 chr4D 478022708 478023212 504 True 466.0 466 83.3660 1 510 1 chr4D.!!$R2 509
11 TraesCS3B01G126400 chr4D 68065108 68065626 518 True 457.0 457 82.8850 1 510 1 chr4D.!!$R1 509
12 TraesCS3B01G126400 chr2D 645834845 645835375 530 True 464.0 464 83.0220 1 518 1 chr2D.!!$R1 517
13 TraesCS3B01G126400 chr5B 300098903 300099414 511 True 462.0 462 83.0740 1 511 1 chr5B.!!$R2 510

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
362 369 0.248702 GCGGCGTTGTTTTTGGAGAA 60.249 50.0 9.37 0.0 0.00 2.87 F
1256 1331 0.319728 GTGCTCCTCTTGCTGTCTCA 59.680 55.0 0.00 0.0 0.00 3.27 F
2110 2208 0.036022 AGGACTTCTGGAGTTGCTGC 59.964 55.0 0.00 0.0 39.19 5.25 F
2647 2757 0.187361 TTGGAACTTCAAGGGGTGGG 59.813 55.0 0.00 0.0 0.00 4.61 F
2889 2999 0.768622 TCGGTGTCCCAAAGACCATT 59.231 50.0 0.00 0.0 45.68 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1935 0.172578 CAGATTACCTGCGACGGTCA 59.827 55.000 9.1 0.0 38.49 4.02 R
2599 2709 0.176680 CCCCTCTCTTGTGGATGTCG 59.823 60.000 0.0 0.0 0.00 4.35 R
3904 6063 0.032952 GGGTGCAGTAGACGTTGTCA 59.967 55.000 0.0 0.0 34.60 3.58 R
4116 6275 1.412710 ACGACCTTGTTCTGCTTCTCA 59.587 47.619 0.0 0.0 0.00 3.27 R
4405 6564 4.601084 AGTCTCTACTACAAGGCAAGCTA 58.399 43.478 0.0 0.0 32.84 3.32 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
29 31 4.282703 GGTGTAGACAACTTGGAGAAGGTA 59.717 45.833 0.00 0.00 32.95 3.08
32 34 7.310237 GGTGTAGACAACTTGGAGAAGGTAATA 60.310 40.741 0.00 0.00 32.95 0.98
49 51 5.964477 AGGTAATAGTGGTTGAGAATGGAGA 59.036 40.000 0.00 0.00 0.00 3.71
78 80 1.948145 GACGAATAGAGCCTTCGAGGA 59.052 52.381 11.87 0.00 46.36 3.71
155 160 2.238521 GGCAACACTGGAGGAATTCAA 58.761 47.619 7.93 0.00 0.00 2.69
204 209 3.424703 CCATGACTTTCAGGGTGACAAT 58.575 45.455 0.00 0.00 42.90 2.71
234 240 1.337167 GGCCTTCATTGGTTGTGCTTC 60.337 52.381 0.00 0.00 0.00 3.86
344 351 4.503741 TGTGCACTATTTCTTTCTTGGC 57.496 40.909 19.41 0.00 0.00 4.52
352 359 1.098712 TTCTTTCTTGGCGGCGTTGT 61.099 50.000 9.37 0.00 0.00 3.32
362 369 0.248702 GCGGCGTTGTTTTTGGAGAA 60.249 50.000 9.37 0.00 0.00 2.87
379 388 6.702716 TGGAGAACTTTTATGTTTTTCGGT 57.297 33.333 0.00 0.00 0.00 4.69
405 415 6.321435 TGTTGTATTTGGTGGTGATTTGTGTA 59.679 34.615 0.00 0.00 0.00 2.90
513 560 4.764172 ACATCTTGTAGGTGCAGAGATTC 58.236 43.478 0.00 0.00 0.00 2.52
518 565 0.824109 TAGGTGCAGAGATTCGGTGG 59.176 55.000 0.00 0.00 0.00 4.61
570 634 2.742774 AGCAAAGTGGCGATGTTTTTC 58.257 42.857 0.00 0.00 39.27 2.29
583 647 6.419413 GGCGATGTTTTTCAGTCAAACAAATA 59.581 34.615 2.56 0.00 45.02 1.40
584 648 7.273659 GCGATGTTTTTCAGTCAAACAAATAC 58.726 34.615 2.56 0.00 45.02 1.89
585 649 7.167468 GCGATGTTTTTCAGTCAAACAAATACT 59.833 33.333 2.56 0.00 45.02 2.12
604 672 7.631717 AATACTACCAGAAAAGGAGCAAATC 57.368 36.000 0.00 0.00 0.00 2.17
626 694 1.480545 CCCGTGATATATCCCATCGCA 59.519 52.381 10.25 0.00 33.44 5.10
638 706 2.101415 TCCCATCGCATACTGACAAGAG 59.899 50.000 0.00 0.00 0.00 2.85
746 814 2.033194 CCGCGAAGTTTCCCACCTC 61.033 63.158 8.23 0.00 0.00 3.85
757 825 4.825679 CCACCTCCCCCTCCCCTC 62.826 77.778 0.00 0.00 0.00 4.30
945 1013 2.303022 AGCTCCCTCGTGATCTCAAAAA 59.697 45.455 0.00 0.00 0.00 1.94
947 1015 3.003480 CTCCCTCGTGATCTCAAAAACC 58.997 50.000 0.00 0.00 0.00 3.27
948 1016 2.370519 TCCCTCGTGATCTCAAAAACCA 59.629 45.455 0.00 0.00 0.00 3.67
950 1018 3.375299 CCCTCGTGATCTCAAAAACCATC 59.625 47.826 0.00 0.00 0.00 3.51
1256 1331 0.319728 GTGCTCCTCTTGCTGTCTCA 59.680 55.000 0.00 0.00 0.00 3.27
1269 1344 1.872679 GTCTCACGTTCCGATCGCC 60.873 63.158 10.32 0.00 0.00 5.54
1279 1355 2.279120 CGATCGCCTGGTGCTCTC 60.279 66.667 0.26 2.69 38.05 3.20
1285 1361 2.575993 CCTGGTGCTCTCGTCTGG 59.424 66.667 0.00 0.00 0.00 3.86
1327 1403 2.977178 CTCGGAGCTGCCAAGTCT 59.023 61.111 0.00 0.00 35.94 3.24
1329 1405 1.603236 CTCGGAGCTGCCAAGTCTCT 61.603 60.000 0.00 0.00 35.94 3.10
1346 1422 3.792185 CTATGCTTTCCCGGCCCCC 62.792 68.421 0.00 0.00 0.00 5.40
1375 1451 0.462759 GCCCTTCTGTGGATTCTCCG 60.463 60.000 0.00 0.00 40.17 4.63
1461 1543 4.634199 CTGCTCCAACAATTTTGGAACAT 58.366 39.130 17.89 0.00 46.85 2.71
1467 1549 5.245075 TCCAACAATTTTGGAACATAGGGAC 59.755 40.000 15.44 0.00 44.90 4.46
1478 1560 5.542251 TGGAACATAGGGACATCAATCGATA 59.458 40.000 0.00 0.00 0.00 2.92
1501 1591 0.859232 CGATCCCCGAAAACATAGCG 59.141 55.000 0.00 0.00 41.76 4.26
1502 1592 1.537348 CGATCCCCGAAAACATAGCGA 60.537 52.381 0.00 0.00 41.76 4.93
1506 1596 3.349022 TCCCCGAAAACATAGCGATTTT 58.651 40.909 0.00 0.00 0.00 1.82
1507 1597 3.127895 TCCCCGAAAACATAGCGATTTTG 59.872 43.478 0.00 0.00 0.00 2.44
1508 1598 3.434637 CCCGAAAACATAGCGATTTTGG 58.565 45.455 0.00 0.00 39.55 3.28
1509 1599 3.127895 CCCGAAAACATAGCGATTTTGGA 59.872 43.478 5.51 0.00 41.43 3.53
1510 1600 4.380023 CCCGAAAACATAGCGATTTTGGAA 60.380 41.667 5.51 0.00 41.43 3.53
1512 1602 5.150683 CGAAAACATAGCGATTTTGGAACA 58.849 37.500 0.00 0.00 0.00 3.18
1513 1603 5.799936 CGAAAACATAGCGATTTTGGAACAT 59.200 36.000 0.00 0.00 39.30 2.71
1514 1604 6.964370 CGAAAACATAGCGATTTTGGAACATA 59.036 34.615 0.00 0.00 39.30 2.29
1649 1739 3.063725 CCTACTCGGTCGTCAAGTAAGAG 59.936 52.174 0.00 0.00 0.00 2.85
1835 1933 6.759497 ATACTTTTGGTCTAACAGAATGCC 57.241 37.500 0.00 0.00 42.53 4.40
1836 1934 4.469657 ACTTTTGGTCTAACAGAATGCCA 58.530 39.130 0.00 0.00 42.53 4.92
1837 1935 5.079643 ACTTTTGGTCTAACAGAATGCCAT 58.920 37.500 0.00 0.00 42.53 4.40
1838 1936 5.047802 ACTTTTGGTCTAACAGAATGCCATG 60.048 40.000 0.00 0.00 42.53 3.66
1839 1937 3.998913 TGGTCTAACAGAATGCCATGA 57.001 42.857 0.00 0.00 42.53 3.07
1840 1938 3.609853 TGGTCTAACAGAATGCCATGAC 58.390 45.455 0.00 0.00 42.53 3.06
1841 1939 2.945668 GGTCTAACAGAATGCCATGACC 59.054 50.000 0.00 0.00 42.53 4.02
1842 1940 2.609459 GTCTAACAGAATGCCATGACCG 59.391 50.000 0.00 0.00 42.53 4.79
1843 1941 2.236146 TCTAACAGAATGCCATGACCGT 59.764 45.455 0.00 0.00 42.53 4.83
1844 1942 1.453155 AACAGAATGCCATGACCGTC 58.547 50.000 0.00 0.00 42.53 4.79
1845 1943 0.740868 ACAGAATGCCATGACCGTCG 60.741 55.000 0.00 0.00 42.53 5.12
1846 1944 1.815421 AGAATGCCATGACCGTCGC 60.815 57.895 0.00 0.00 0.00 5.19
1851 1949 2.889617 CCATGACCGTCGCAGGTA 59.110 61.111 0.00 0.00 46.09 3.08
1857 1955 0.527817 GACCGTCGCAGGTAATCTGG 60.528 60.000 1.60 0.00 46.09 3.86
1869 1967 2.237392 GGTAATCTGGTGAGGCTGACTT 59.763 50.000 3.64 0.00 0.00 3.01
1876 1974 0.954452 GTGAGGCTGACTTTTGTGGG 59.046 55.000 0.00 0.00 0.00 4.61
1878 1976 1.239347 GAGGCTGACTTTTGTGGGTC 58.761 55.000 0.00 0.00 0.00 4.46
1880 1978 0.534203 GGCTGACTTTTGTGGGTCGA 60.534 55.000 0.00 0.00 35.45 4.20
1970 2068 1.153881 GTACTTCCAGCCCGACGAC 60.154 63.158 0.00 0.00 0.00 4.34
2072 2170 1.000506 GACATGTACGGTGTCACCAGT 59.999 52.381 21.91 20.18 44.13 4.00
2075 2173 0.825410 TGTACGGTGTCACCAGTGTT 59.175 50.000 21.91 2.95 38.47 3.32
2099 2197 2.292521 TGGCATAGAGGTGAGGACTTCT 60.293 50.000 0.00 0.00 41.26 2.85
2105 2203 2.158234 AGAGGTGAGGACTTCTGGAGTT 60.158 50.000 0.00 0.00 37.16 3.01
2106 2204 1.974236 AGGTGAGGACTTCTGGAGTTG 59.026 52.381 0.00 0.00 39.19 3.16
2107 2205 1.609320 GGTGAGGACTTCTGGAGTTGC 60.609 57.143 0.00 0.00 39.19 4.17
2108 2206 1.346068 GTGAGGACTTCTGGAGTTGCT 59.654 52.381 0.00 0.00 39.19 3.91
2109 2207 1.345741 TGAGGACTTCTGGAGTTGCTG 59.654 52.381 0.00 0.00 39.19 4.41
2110 2208 0.036022 AGGACTTCTGGAGTTGCTGC 59.964 55.000 0.00 0.00 39.19 5.25
2122 2220 3.366719 GAGTTGCTGCTCTTGTTTGTTC 58.633 45.455 0.00 0.00 32.99 3.18
2124 2222 3.065925 AGTTGCTGCTCTTGTTTGTTCTC 59.934 43.478 0.00 0.00 0.00 2.87
2128 2226 3.611057 GCTGCTCTTGTTTGTTCTCCATG 60.611 47.826 0.00 0.00 0.00 3.66
2170 2271 7.876068 TCCGGTTAGTATTTTAGGATTAGCATG 59.124 37.037 0.00 0.00 0.00 4.06
2199 2300 3.317149 TGTTACGATGCTAACGAGGCTAT 59.683 43.478 0.00 0.00 30.33 2.97
2206 2307 6.073765 ACGATGCTAACGAGGCTATTTAATTG 60.074 38.462 0.00 0.00 34.70 2.32
2253 2355 6.365520 AGGAAGGTGTGATTTAGAACAAACT 58.634 36.000 0.00 0.00 0.00 2.66
2318 2427 5.419542 TCAGCTGTCACCTAATAACATGAC 58.580 41.667 14.67 0.00 41.51 3.06
2346 2455 5.565439 GCAATGTTGATAAGCCTGAAACTGT 60.565 40.000 0.00 0.00 0.00 3.55
2492 2602 5.933790 TGCTATTTGTCAACCGTTATGTTC 58.066 37.500 0.00 0.00 0.00 3.18
2494 2604 5.793457 GCTATTTGTCAACCGTTATGTTCAC 59.207 40.000 0.00 0.00 0.00 3.18
2599 2709 4.037923 ACATTGACACCCAAATCAGTGAAC 59.962 41.667 0.00 0.00 38.43 3.18
2647 2757 0.187361 TTGGAACTTCAAGGGGTGGG 59.813 55.000 0.00 0.00 0.00 4.61
2788 2898 2.373169 ACTGCAGGAAGGTCTCAATCAA 59.627 45.455 19.93 0.00 0.00 2.57
2812 2922 5.101648 TGCTCAATTCCATGTCTCACATA 57.898 39.130 0.00 0.00 36.53 2.29
2889 2999 0.768622 TCGGTGTCCCAAAGACCATT 59.231 50.000 0.00 0.00 45.68 3.16
2964 3074 6.119536 ACAAGAGTGATTGTTTTCCACACTA 58.880 36.000 0.00 0.00 40.47 2.74
2991 3101 6.814043 TGTGATTTTGATGTTGAATTGTCCA 58.186 32.000 0.00 0.00 0.00 4.02
3101 3211 1.133790 GCAGAGAATGGCATTGGTGTC 59.866 52.381 19.07 8.69 0.00 3.67
3130 3240 3.053896 GGGCCGCAACAGTGGTAC 61.054 66.667 0.00 0.00 35.33 3.34
3162 3272 3.666883 TGTTACAAACTTGCAGTCACG 57.333 42.857 0.00 0.00 0.00 4.35
3164 3274 3.437395 TGTTACAAACTTGCAGTCACGTT 59.563 39.130 0.00 0.00 36.40 3.99
3167 3277 3.498082 ACAAACTTGCAGTCACGTTTTC 58.502 40.909 0.00 0.00 41.04 2.29
3350 5507 4.669318 ACATAACAGTAATGTCGAGTCGG 58.331 43.478 13.54 0.00 32.02 4.79
3467 5625 0.895530 TCGAGAAACGGCTCAAGGAT 59.104 50.000 0.00 0.00 42.82 3.24
3617 5775 4.163078 TCCCAGAAGATCAAGGTCAGATTC 59.837 45.833 0.00 0.00 0.00 2.52
3701 5859 8.327941 TGGCTCATTCAAGTATATTAGCATTC 57.672 34.615 0.00 0.00 0.00 2.67
3862 6021 6.901300 ACTTCCCCATAACTCTCAAGTACATA 59.099 38.462 0.00 0.00 33.48 2.29
3904 6063 2.342648 GTCCGGTCAAACGCCTCT 59.657 61.111 0.00 0.00 0.00 3.69
4045 6204 2.498167 ACAGCAGGAAACAGTGATCAC 58.502 47.619 18.47 18.47 0.00 3.06
4046 6205 2.158769 ACAGCAGGAAACAGTGATCACA 60.159 45.455 27.02 0.00 0.00 3.58
4060 6219 3.931468 GTGATCACACCTGAGATCTGTTG 59.069 47.826 21.07 0.00 40.98 3.33
4116 6275 2.574006 TTTGGCTGCAGAGAATCACT 57.426 45.000 20.43 0.00 37.82 3.41
4227 6386 2.263077 GTCGAGAACATGAAGCACGAT 58.737 47.619 0.00 0.00 0.00 3.73
4233 6392 1.350193 ACATGAAGCACGATGACGAC 58.650 50.000 0.00 0.00 42.66 4.34
4515 6674 9.176181 GTAGAAGCTCGATTTTGTAGATTAGAG 57.824 37.037 0.00 0.00 0.00 2.43
4595 6754 9.342308 TCATCTGAATCCTGGTTTATTATTCAC 57.658 33.333 2.99 0.00 34.01 3.18
5060 7219 4.540359 TGCAATGAAGCAAGCCTTTTAT 57.460 36.364 0.00 0.00 42.46 1.40
5068 7227 2.678336 AGCAAGCCTTTTATAGACGTGC 59.322 45.455 0.00 0.00 0.00 5.34
5070 7229 3.065371 GCAAGCCTTTTATAGACGTGCAT 59.935 43.478 0.00 0.00 0.00 3.96
5198 7357 0.605319 GACGACATTGGTGGAAGGCA 60.605 55.000 0.00 0.00 0.00 4.75
5239 7399 9.486497 TTGATGCTTACTTTCAAATGCATTTTA 57.514 25.926 21.95 11.99 40.58 1.52
5255 7415 9.709495 AATGCATTTTAAAGCTCTGATTTTGTA 57.291 25.926 5.99 0.00 0.00 2.41
5269 7429 6.016693 TCTGATTTTGTATTTTCTTGCCACGA 60.017 34.615 0.00 0.00 0.00 4.35
5270 7430 5.918011 TGATTTTGTATTTTCTTGCCACGAC 59.082 36.000 0.00 0.00 0.00 4.34
5276 7436 3.414549 TTTTCTTGCCACGACTTTCAC 57.585 42.857 0.00 0.00 0.00 3.18
5320 7485 4.533225 TTTGCATGCACAACAAACATTC 57.467 36.364 22.58 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 31 6.962182 TGATTCTCCATTCTCAACCACTATT 58.038 36.000 0.00 0.00 0.00 1.73
32 34 4.288105 ACTGATTCTCCATTCTCAACCACT 59.712 41.667 0.00 0.00 0.00 4.00
49 51 6.472686 AAGGCTCTATTCGTCTAACTGATT 57.527 37.500 0.00 0.00 0.00 2.57
78 80 1.734655 ACACCTGGTTGACTCCATCT 58.265 50.000 0.00 0.00 36.84 2.90
155 160 0.609131 CCGAGGAGCACCACCAAAAT 60.609 55.000 2.07 0.00 38.94 1.82
234 240 2.074547 CCTTCAGCAAGGCAATTGTG 57.925 50.000 7.40 0.00 43.14 3.33
344 351 1.064952 AGTTCTCCAAAAACAACGCCG 59.935 47.619 0.00 0.00 0.00 6.46
352 359 8.874816 CCGAAAAACATAAAAGTTCTCCAAAAA 58.125 29.630 0.00 0.00 0.00 1.94
362 369 9.589111 AATACAACAACCGAAAAACATAAAAGT 57.411 25.926 0.00 0.00 0.00 2.66
379 388 6.045318 CACAAATCACCACCAAATACAACAA 58.955 36.000 0.00 0.00 0.00 2.83
405 415 0.175302 CGACTTCTCTCAGCAGCCAT 59.825 55.000 0.00 0.00 0.00 4.40
469 516 1.671979 CAACGACATCCAGGATGCAT 58.328 50.000 27.17 10.71 43.15 3.96
545 609 1.680735 ACATCGCCACTTTGCTTGAAA 59.319 42.857 0.00 0.00 0.00 2.69
570 634 8.076178 CCTTTTCTGGTAGTATTTGTTTGACTG 58.924 37.037 0.00 0.00 0.00 3.51
583 647 4.336280 GGATTTGCTCCTTTTCTGGTAGT 58.664 43.478 0.00 0.00 41.29 2.73
584 648 3.696548 GGGATTTGCTCCTTTTCTGGTAG 59.303 47.826 0.00 0.00 44.28 3.18
585 649 3.563479 GGGGATTTGCTCCTTTTCTGGTA 60.563 47.826 0.00 0.00 44.28 3.25
604 672 1.412710 CGATGGGATATATCACGGGGG 59.587 57.143 14.60 0.00 31.21 5.40
626 694 1.486211 CCGGGTCCTCTTGTCAGTAT 58.514 55.000 0.00 0.00 0.00 2.12
638 706 2.814913 AAGAAATGTCGCCCGGGTCC 62.815 60.000 24.63 10.88 0.00 4.46
746 814 4.179599 GAGAGGGAGGGGAGGGGG 62.180 77.778 0.00 0.00 0.00 5.40
867 935 1.073199 CTTGGTGTGTGGGGAGGAC 59.927 63.158 0.00 0.00 0.00 3.85
956 1027 0.034896 GCACGAGGTGGAAAGAGGAA 59.965 55.000 0.00 0.00 33.64 3.36
957 1028 0.832135 AGCACGAGGTGGAAAGAGGA 60.832 55.000 0.00 0.00 33.64 3.71
1269 1344 0.668706 CAACCAGACGAGAGCACCAG 60.669 60.000 0.00 0.00 0.00 4.00
1279 1355 1.076332 GACGGGAAATCAACCAGACG 58.924 55.000 0.00 0.00 0.00 4.18
1285 1361 2.782615 CCGCGACGGGAAATCAAC 59.217 61.111 8.23 0.00 44.15 3.18
1327 1403 2.752807 GGGGCCGGGAAAGCATAGA 61.753 63.158 2.18 0.00 0.00 1.98
1329 1405 3.816090 GGGGGCCGGGAAAGCATA 61.816 66.667 2.18 0.00 0.00 3.14
1354 1430 1.078143 AGAATCCACAGAAGGGCGC 60.078 57.895 0.00 0.00 0.00 6.53
1491 1573 6.751888 GCTATGTTCCAAAATCGCTATGTTTT 59.248 34.615 0.00 0.00 0.00 2.43
1495 1585 4.211164 TCGCTATGTTCCAAAATCGCTATG 59.789 41.667 0.00 0.00 0.00 2.23
1498 1588 2.627945 TCGCTATGTTCCAAAATCGCT 58.372 42.857 0.00 0.00 0.00 4.93
1499 1589 3.609103 ATCGCTATGTTCCAAAATCGC 57.391 42.857 0.00 0.00 0.00 4.58
1501 1591 7.447430 CAAACAAATCGCTATGTTCCAAAATC 58.553 34.615 0.00 0.00 38.75 2.17
1502 1592 6.128580 GCAAACAAATCGCTATGTTCCAAAAT 60.129 34.615 0.00 0.00 38.75 1.82
1506 1596 3.254411 TGCAAACAAATCGCTATGTTCCA 59.746 39.130 0.00 0.00 38.75 3.53
1507 1597 3.832276 TGCAAACAAATCGCTATGTTCC 58.168 40.909 0.00 0.00 38.75 3.62
1508 1598 4.722194 TCTGCAAACAAATCGCTATGTTC 58.278 39.130 0.00 0.00 38.75 3.18
1509 1599 4.764679 TCTGCAAACAAATCGCTATGTT 57.235 36.364 0.00 0.00 41.31 2.71
1510 1600 4.970662 ATCTGCAAACAAATCGCTATGT 57.029 36.364 0.00 0.00 0.00 2.29
1512 1602 6.094048 ACTGTAATCTGCAAACAAATCGCTAT 59.906 34.615 0.00 0.00 0.00 2.97
1513 1603 5.411361 ACTGTAATCTGCAAACAAATCGCTA 59.589 36.000 0.00 0.00 0.00 4.26
1514 1604 4.216257 ACTGTAATCTGCAAACAAATCGCT 59.784 37.500 0.00 0.00 0.00 4.93
1649 1739 1.257743 GGCAAAGAAAGGAGGGGAAC 58.742 55.000 0.00 0.00 0.00 3.62
1822 1920 2.236146 ACGGTCATGGCATTCTGTTAGA 59.764 45.455 0.00 0.00 0.00 2.10
1824 1922 2.627945 GACGGTCATGGCATTCTGTTA 58.372 47.619 12.97 0.00 0.00 2.41
1835 1933 1.202417 AGATTACCTGCGACGGTCATG 60.202 52.381 9.10 0.00 38.49 3.07
1836 1934 1.112113 AGATTACCTGCGACGGTCAT 58.888 50.000 9.10 0.00 38.49 3.06
1837 1935 0.172578 CAGATTACCTGCGACGGTCA 59.827 55.000 9.10 0.00 38.49 4.02
1838 1936 0.527817 CCAGATTACCTGCGACGGTC 60.528 60.000 0.00 0.00 41.57 4.79
1839 1937 1.255667 ACCAGATTACCTGCGACGGT 61.256 55.000 0.00 1.62 41.57 4.83
1840 1938 0.806102 CACCAGATTACCTGCGACGG 60.806 60.000 0.00 0.00 41.57 4.79
1841 1939 0.172578 TCACCAGATTACCTGCGACG 59.827 55.000 0.00 0.00 41.57 5.12
1842 1940 1.471676 CCTCACCAGATTACCTGCGAC 60.472 57.143 0.00 0.00 41.57 5.19
1843 1941 0.824109 CCTCACCAGATTACCTGCGA 59.176 55.000 0.00 0.00 41.57 5.10
1844 1942 0.811616 GCCTCACCAGATTACCTGCG 60.812 60.000 0.00 0.00 41.57 5.18
1845 1943 0.543749 AGCCTCACCAGATTACCTGC 59.456 55.000 0.00 0.00 41.57 4.85
1846 1944 1.833630 TCAGCCTCACCAGATTACCTG 59.166 52.381 0.00 0.00 42.55 4.00
1851 1949 3.152341 CAAAAGTCAGCCTCACCAGATT 58.848 45.455 0.00 0.00 0.00 2.40
1857 1955 0.954452 CCCACAAAAGTCAGCCTCAC 59.046 55.000 0.00 0.00 0.00 3.51
1869 1967 2.198827 ATCTGCAATCGACCCACAAA 57.801 45.000 0.00 0.00 0.00 2.83
1876 1974 3.155998 CGAACAACAATCTGCAATCGAC 58.844 45.455 0.00 0.00 0.00 4.20
1878 1976 3.187478 ACGAACAACAATCTGCAATCG 57.813 42.857 0.00 0.00 35.36 3.34
1880 1978 5.940192 TCTTACGAACAACAATCTGCAAT 57.060 34.783 0.00 0.00 0.00 3.56
2036 2134 1.592131 GTCGTACAACCCGCACACA 60.592 57.895 0.00 0.00 0.00 3.72
2072 2170 2.290260 CCTCACCTCTATGCCAACAACA 60.290 50.000 0.00 0.00 0.00 3.33
2075 2173 1.555075 GTCCTCACCTCTATGCCAACA 59.445 52.381 0.00 0.00 0.00 3.33
2099 2197 1.677576 CAAACAAGAGCAGCAACTCCA 59.322 47.619 0.00 0.00 37.39 3.86
2105 2203 1.949525 GGAGAACAAACAAGAGCAGCA 59.050 47.619 0.00 0.00 0.00 4.41
2106 2204 1.949525 TGGAGAACAAACAAGAGCAGC 59.050 47.619 0.00 0.00 0.00 5.25
2107 2205 3.567164 ACATGGAGAACAAACAAGAGCAG 59.433 43.478 0.00 0.00 0.00 4.24
2108 2206 3.316029 CACATGGAGAACAAACAAGAGCA 59.684 43.478 0.00 0.00 0.00 4.26
2109 2207 3.316308 ACACATGGAGAACAAACAAGAGC 59.684 43.478 0.00 0.00 0.00 4.09
2110 2208 6.618287 TTACACATGGAGAACAAACAAGAG 57.382 37.500 0.00 0.00 0.00 2.85
2122 2220 6.498304 GGAGCATTGTAATTTACACATGGAG 58.502 40.000 20.67 0.00 38.63 3.86
2124 2222 5.273170 CGGAGCATTGTAATTTACACATGG 58.727 41.667 20.67 10.27 38.63 3.66
2128 2226 4.957759 ACCGGAGCATTGTAATTTACAC 57.042 40.909 9.46 0.00 38.63 2.90
2170 2271 3.723835 CGTTAGCATCGTAACAAAGCACC 60.724 47.826 0.00 0.00 33.20 5.01
2199 2300 9.462174 CAGTCAAAATCAGTTACTGCAATTAAA 57.538 29.630 7.61 0.00 32.02 1.52
2253 2355 4.133820 CGTCAATATTGTATTCCCAGGCA 58.866 43.478 14.97 0.00 0.00 4.75
2318 2427 1.402968 AGGCTTATCAACATTGCAGCG 59.597 47.619 0.00 0.00 0.00 5.18
2492 2602 6.389906 AGGTTCAGAAAACAAAAACAGAGTG 58.610 36.000 0.00 0.00 0.00 3.51
2494 2604 9.586435 AATTAGGTTCAGAAAACAAAAACAGAG 57.414 29.630 0.00 0.00 0.00 3.35
2599 2709 0.176680 CCCCTCTCTTGTGGATGTCG 59.823 60.000 0.00 0.00 0.00 4.35
2647 2757 2.477375 CACAATTTTGGCAGTGTCATGC 59.523 45.455 0.00 0.00 45.74 4.06
2788 2898 4.338012 TGTGAGACATGGAATTGAGCATT 58.662 39.130 0.00 0.00 0.00 3.56
2812 2922 8.232913 TCCTGAAATTAAGTTTAAGCAGTTGT 57.767 30.769 0.00 0.00 28.17 3.32
2889 2999 5.338056 GGGGAGTACCGCAATATCATTATCA 60.338 44.000 0.00 0.00 46.50 2.15
2964 3074 7.439056 GGACAATTCAACATCAAAATCACAACT 59.561 33.333 0.00 0.00 0.00 3.16
2975 3085 3.569277 CCTGTGTGGACAATTCAACATCA 59.431 43.478 0.00 0.00 38.02 3.07
2991 3101 6.275335 CAAAAGATTTGTCAATCACCTGTGT 58.725 36.000 0.00 0.00 41.37 3.72
3050 3160 2.153645 TCAACATGAGCAGCGTTGATT 58.846 42.857 2.38 0.00 42.95 2.57
3101 3211 2.823829 GCGGCCCATTAGCTTCACG 61.824 63.158 0.00 0.00 0.00 4.35
3130 3240 5.986004 AGTTTGTAACAAGGAAAGAGACG 57.014 39.130 0.00 0.00 0.00 4.18
3162 3272 4.094442 CAGGAGCGGGTATTACTTGAAAAC 59.906 45.833 0.00 0.00 0.00 2.43
3164 3274 3.869065 CAGGAGCGGGTATTACTTGAAA 58.131 45.455 0.00 0.00 0.00 2.69
3167 3277 1.134521 TGCAGGAGCGGGTATTACTTG 60.135 52.381 0.00 0.00 46.23 3.16
3229 3340 7.572523 TGAACCCTGCATCAATAGAATTTAG 57.427 36.000 0.00 0.00 0.00 1.85
3236 3347 2.225019 GCGATGAACCCTGCATCAATAG 59.775 50.000 0.00 0.00 41.66 1.73
3350 5507 2.287248 GCAAAGCAAAGTGGTCAGTCTC 60.287 50.000 0.00 0.00 0.00 3.36
3467 5625 4.473196 ACCACAATGACCATATGACCACTA 59.527 41.667 3.65 0.00 0.00 2.74
3617 5775 2.628178 GGAAAGGAAAGTTTGGACCAGG 59.372 50.000 0.00 0.00 0.00 4.45
3701 5859 7.130917 GCTTGTTGCTAATTCTATCATGACTG 58.869 38.462 0.00 0.00 38.95 3.51
3862 6021 1.613925 CGGATCATGTATGTCGGGTCT 59.386 52.381 0.00 0.00 0.00 3.85
3904 6063 0.032952 GGGTGCAGTAGACGTTGTCA 59.967 55.000 0.00 0.00 34.60 3.58
4045 6204 3.594134 GAGTTCCAACAGATCTCAGGTG 58.406 50.000 0.00 0.00 39.97 4.00
4046 6205 2.569404 GGAGTTCCAACAGATCTCAGGT 59.431 50.000 0.00 0.00 41.38 4.00
4060 6219 5.529060 CAGCATAAGGTTTGATAGGAGTTCC 59.471 44.000 0.00 0.00 0.00 3.62
4116 6275 1.412710 ACGACCTTGTTCTGCTTCTCA 59.587 47.619 0.00 0.00 0.00 3.27
4405 6564 4.601084 AGTCTCTACTACAAGGCAAGCTA 58.399 43.478 0.00 0.00 32.84 3.32
4515 6674 4.723248 CTCGAACCCAAAACTTAGCATTC 58.277 43.478 0.00 0.00 0.00 2.67
5060 7219 4.021807 TCAGGTGTAGAAAATGCACGTCTA 60.022 41.667 0.00 0.00 44.74 2.59
5068 7227 6.293298 GCATATGAGCTCAGGTGTAGAAAATG 60.293 42.308 22.96 12.03 0.00 2.32
5070 7229 5.104776 AGCATATGAGCTCAGGTGTAGAAAA 60.105 40.000 22.96 0.00 42.18 2.29
5131 7290 8.163516 GCACAACAAACATTTTTAAAGTACGTT 58.836 29.630 0.00 0.00 0.00 3.99
5132 7291 7.328737 TGCACAACAAACATTTTTAAAGTACGT 59.671 29.630 0.00 0.00 0.00 3.57
5133 7292 7.667283 TGCACAACAAACATTTTTAAAGTACG 58.333 30.769 0.00 0.00 0.00 3.67
5134 7293 9.419737 CATGCACAACAAACATTTTTAAAGTAC 57.580 29.630 0.00 0.00 0.00 2.73
5181 7340 0.452987 CATGCCTTCCACCAATGTCG 59.547 55.000 0.00 0.00 0.00 4.35
5182 7341 0.819582 CCATGCCTTCCACCAATGTC 59.180 55.000 0.00 0.00 0.00 3.06
5183 7342 0.114954 ACCATGCCTTCCACCAATGT 59.885 50.000 0.00 0.00 0.00 2.71
5239 7399 7.386025 GGCAAGAAAATACAAAATCAGAGCTTT 59.614 33.333 0.00 0.00 0.00 3.51
5255 7415 3.243401 GGTGAAAGTCGTGGCAAGAAAAT 60.243 43.478 4.28 0.00 0.00 1.82
5276 7436 7.837202 AAATTGCATTATGAAGTCACATTGG 57.163 32.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.