Multiple sequence alignment - TraesCS1D01G403100

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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 TraesCS1D01G403100 chr1D 100.000 3731 0 0 1 3731 467847504 467851234 0.000000e+00 6890.0
1 TraesCS1D01G403100 chr1D 84.239 920 121 8 1000 1895 467863404 467862485 0.000000e+00 874.0
2 TraesCS1D01G403100 chr1D 79.536 733 135 10 2081 2807 467862212 467861489 3.320000e-140 508.0
3 TraesCS1D01G403100 chr1D 100.000 36 0 0 552 587 467847972 467848007 2.400000e-07 67.6
4 TraesCS1D01G403100 chr1D 100.000 36 0 0 469 504 467848055 467848090 2.400000e-07 67.6
5 TraesCS1D01G403100 chr1D 100.000 28 0 0 204 231 467847734 467847707 7.000000e-03 52.8
6 TraesCS1D01G403100 chr1A 94.192 1670 56 23 259 1912 560836726 560838370 0.000000e+00 2508.0
7 TraesCS1D01G403100 chr1A 93.551 1132 53 12 2015 3138 560838459 560839578 0.000000e+00 1668.0
8 TraesCS1D01G403100 chr1A 85.081 925 114 9 994 1907 560840385 560841296 0.000000e+00 922.0
9 TraesCS1D01G403100 chr1A 85.173 897 109 12 1022 1894 560881599 560880703 0.000000e+00 898.0
10 TraesCS1D01G403100 chr1A 82.256 727 125 4 2081 2806 560841477 560842200 3.160000e-175 625.0
11 TraesCS1D01G403100 chr1A 93.333 150 9 1 47 195 560836477 560836626 1.740000e-53 220.0
12 TraesCS1D01G403100 chr1A 88.000 75 9 0 513 587 560836877 560836951 5.130000e-14 89.8
13 TraesCS1D01G403100 chr1A 97.872 47 1 0 1 47 560836406 560836452 8.590000e-12 82.4
14 TraesCS1D01G403100 chr1A 100.000 37 0 0 468 504 560836998 560837034 6.690000e-08 69.4
15 TraesCS1D01G403100 chr1B 94.633 1118 56 2 2049 3166 645887920 645889033 0.000000e+00 1729.0
16 TraesCS1D01G403100 chr1B 90.523 1108 88 9 2015 3115 645906321 645905224 0.000000e+00 1448.0
17 TraesCS1D01G403100 chr1B 94.697 924 47 1 991 1912 645886694 645887617 0.000000e+00 1434.0
18 TraesCS1D01G403100 chr1B 87.457 1164 87 31 528 1673 645913639 645912517 0.000000e+00 1286.0
19 TraesCS1D01G403100 chr1B 91.146 881 63 9 1033 1911 645904362 645903495 0.000000e+00 1181.0
20 TraesCS1D01G403100 chr1B 85.094 852 102 5 1062 1903 645896411 645895575 0.000000e+00 846.0
21 TraesCS1D01G403100 chr1B 95.208 480 20 3 3165 3642 645889062 645889540 0.000000e+00 756.0
22 TraesCS1D01G403100 chr1B 90.000 460 44 2 2072 2530 645902047 645901589 8.920000e-166 593.0
23 TraesCS1D01G403100 chr1B 85.833 600 26 23 332 915 645886100 645886656 1.930000e-162 582.0
24 TraesCS1D01G403100 chr1B 80.874 732 124 13 2079 2802 645895366 645894643 2.520000e-156 562.0
25 TraesCS1D01G403100 chr1B 90.544 349 23 3 2563 2911 645901595 645901257 1.580000e-123 453.0
26 TraesCS1D01G403100 chr1B 86.008 243 15 3 1671 1911 645906626 645906401 3.720000e-60 243.0
27 TraesCS1D01G403100 chr1B 89.205 176 14 4 47 217 645885883 645886058 8.120000e-52 215.0
28 TraesCS1D01G403100 chr1B 92.857 70 5 0 357 426 645913739 645913670 6.590000e-18 102.0
29 TraesCS1D01G403100 chr1B 100.000 38 0 0 468 505 645913614 645913577 1.860000e-08 71.3
30 TraesCS1D01G403100 chr1B 100.000 37 0 0 468 504 645886285 645886321 6.690000e-08 69.4
31 TraesCS1D01G403100 chr5D 80.831 626 96 17 1100 1712 478689648 478689034 1.570000e-128 470.0


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 TraesCS1D01G403100 chr1D 467847504 467851234 3730 False 2341.733333 6890 100.000000 1 3731 3 chr1D.!!$F1 3730
1 TraesCS1D01G403100 chr1D 467861489 467863404 1915 True 691.000000 874 81.887500 1000 2807 2 chr1D.!!$R2 1807
2 TraesCS1D01G403100 chr1A 560880703 560881599 896 True 898.000000 898 85.173000 1022 1894 1 chr1A.!!$R1 872
3 TraesCS1D01G403100 chr1A 560836406 560842200 5794 False 773.075000 2508 91.785625 1 3138 8 chr1A.!!$F1 3137
4 TraesCS1D01G403100 chr1B 645885883 645889540 3657 False 797.566667 1729 93.262667 47 3642 6 chr1B.!!$F1 3595
5 TraesCS1D01G403100 chr1B 645901257 645906626 5369 True 783.600000 1448 89.644200 1033 3115 5 chr1B.!!$R2 2082
6 TraesCS1D01G403100 chr1B 645894643 645896411 1768 True 704.000000 846 82.984000 1062 2802 2 chr1B.!!$R1 1740
7 TraesCS1D01G403100 chr1B 645912517 645913739 1222 True 486.433333 1286 93.438000 357 1673 3 chr1B.!!$R3 1316
8 TraesCS1D01G403100 chr5D 478689034 478689648 614 True 470.000000 470 80.831000 1100 1712 1 chr5D.!!$R1 612

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
314 409 0.306533 GCTCGTGTTCGCCTTTTCAA 59.693 50.0 0.0 0.0 36.96 2.69 F
432 527 0.527565 AATGGTGGTGCGATTTCTGC 59.472 50.0 0.0 0.0 0.00 4.26 F
445 540 1.243342 TTTCTGCGGTGATGCCAAGG 61.243 55.0 0.0 0.0 36.97 3.61 F
2239 5057 0.036388 CCATGCTAGTGGAACCGTGT 60.036 55.0 0.0 0.0 42.02 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 4918 0.249073 CGGCAGAGAATACGTCCTGG 60.249 60.000 0.00 0.00 0.00 4.45 R
2115 4933 1.315981 TTGTTGTTTCACTGCCGGCA 61.316 50.000 30.59 30.59 0.00 5.69 R
2271 5089 1.880340 CTCTCGGATGACCAAGCGC 60.880 63.158 0.00 0.00 35.59 5.92 R
3457 6370 0.607217 TGGGCATGTGCTCTGTCTTG 60.607 55.000 6.41 0.00 43.37 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 151 5.508200 TGAACATAACGGCATTTTATCCC 57.492 39.130 0.00 0.00 0.00 3.85
129 155 5.656480 ACATAACGGCATTTTATCCCAAAC 58.344 37.500 0.00 0.00 0.00 2.93
158 187 4.599047 TTTTGGCCCAACTCAAATACAG 57.401 40.909 0.00 0.00 33.58 2.74
191 220 2.126031 GACAGAGGGGTTCGTCGC 60.126 66.667 0.00 0.00 33.41 5.19
217 248 0.383860 GGTTTTCCAGCGAACGAACG 60.384 55.000 0.00 0.00 40.31 3.95
219 250 1.008329 TTTTCCAGCGAACGAACGTT 58.992 45.000 12.30 12.30 41.54 3.99
248 279 2.837291 GTTGTTGCACCCCTGGCA 60.837 61.111 0.00 0.00 40.00 4.92
253 284 3.256082 TGCACCCCTGGCAAACTA 58.744 55.556 0.00 0.00 38.54 2.24
255 286 0.825840 TGCACCCCTGGCAAACTAAC 60.826 55.000 0.00 0.00 38.54 2.34
256 287 1.862602 GCACCCCTGGCAAACTAACG 61.863 60.000 0.00 0.00 0.00 3.18
257 288 0.536460 CACCCCTGGCAAACTAACGT 60.536 55.000 0.00 0.00 0.00 3.99
259 290 1.271001 ACCCCTGGCAAACTAACGTAC 60.271 52.381 0.00 0.00 0.00 3.67
260 291 1.073177 CCCTGGCAAACTAACGTACG 58.927 55.000 15.01 15.01 0.00 3.67
262 293 1.458064 CCTGGCAAACTAACGTACGTG 59.542 52.381 23.57 13.07 0.00 4.49
274 369 2.976729 ACGTACGTGACAAATTTGTGC 58.023 42.857 27.85 17.97 42.43 4.57
307 402 3.554692 CGATGGCTCGTGTTCGCC 61.555 66.667 0.00 0.00 46.46 5.54
310 405 1.298859 GATGGCTCGTGTTCGCCTTT 61.299 55.000 0.00 0.00 46.42 3.11
312 407 1.206831 GGCTCGTGTTCGCCTTTTC 59.793 57.895 0.00 0.00 42.98 2.29
313 408 1.503818 GGCTCGTGTTCGCCTTTTCA 61.504 55.000 0.00 0.00 42.98 2.69
314 409 0.306533 GCTCGTGTTCGCCTTTTCAA 59.693 50.000 0.00 0.00 36.96 2.69
315 410 1.268335 GCTCGTGTTCGCCTTTTCAAA 60.268 47.619 0.00 0.00 36.96 2.69
317 412 3.430931 CTCGTGTTCGCCTTTTCAAAAA 58.569 40.909 0.00 0.00 36.96 1.94
345 440 2.620585 ACAAAAACAGAGGAGCAGCTTC 59.379 45.455 0.00 0.00 0.00 3.86
346 441 2.883386 CAAAAACAGAGGAGCAGCTTCT 59.117 45.455 1.44 1.44 32.37 2.85
347 442 4.067896 CAAAAACAGAGGAGCAGCTTCTA 58.932 43.478 2.00 0.00 30.81 2.10
348 443 3.608316 AAACAGAGGAGCAGCTTCTAG 57.392 47.619 2.00 1.84 30.81 2.43
402 497 1.346395 TCCTTGGAGCTTCGCTTTGTA 59.654 47.619 0.00 0.00 39.88 2.41
426 521 0.881118 GTCAACAATGGTGGTGCGAT 59.119 50.000 0.00 0.00 42.67 4.58
427 522 1.269448 GTCAACAATGGTGGTGCGATT 59.731 47.619 0.00 0.00 42.67 3.34
428 523 1.959985 TCAACAATGGTGGTGCGATTT 59.040 42.857 0.00 0.00 42.67 2.17
430 525 1.909700 ACAATGGTGGTGCGATTTCT 58.090 45.000 0.00 0.00 0.00 2.52
431 526 1.541147 ACAATGGTGGTGCGATTTCTG 59.459 47.619 0.00 0.00 0.00 3.02
432 527 0.527565 AATGGTGGTGCGATTTCTGC 59.472 50.000 0.00 0.00 0.00 4.26
435 530 2.031919 TGGTGCGATTTCTGCGGT 59.968 55.556 0.00 0.00 34.24 5.68
440 535 1.297893 GCGATTTCTGCGGTGATGC 60.298 57.895 0.00 0.00 0.00 3.91
445 540 1.243342 TTTCTGCGGTGATGCCAAGG 61.243 55.000 0.00 0.00 36.97 3.61
448 543 1.369091 CTGCGGTGATGCCAAGGTAC 61.369 60.000 0.00 0.00 36.97 3.34
462 557 2.770164 AGGTACTTGGCTACTTGCTG 57.230 50.000 0.00 0.00 37.29 4.41
550 648 1.334869 GCTGCGGGAAGATATTTGGTG 59.665 52.381 0.00 0.00 0.00 4.17
713 824 5.221641 ACCTTCAGTGTACAAGTCAAGCATA 60.222 40.000 0.00 0.00 0.00 3.14
714 825 5.349817 CCTTCAGTGTACAAGTCAAGCATAG 59.650 44.000 0.00 0.00 0.00 2.23
715 826 4.245660 TCAGTGTACAAGTCAAGCATAGC 58.754 43.478 0.00 0.00 0.00 2.97
716 827 3.996363 CAGTGTACAAGTCAAGCATAGCA 59.004 43.478 0.00 0.00 0.00 3.49
905 1026 3.632145 TCAGTTGAGATCGGATTCATCGA 59.368 43.478 0.00 0.00 41.04 3.59
906 1027 3.733224 CAGTTGAGATCGGATTCATCGAC 59.267 47.826 0.00 9.47 39.55 4.20
972 1093 4.434520 GTGACACTACATTCCTTAGCTCC 58.565 47.826 0.00 0.00 0.00 4.70
1032 1153 4.148825 ATCACGGTCTGCCTCGCC 62.149 66.667 0.00 0.00 0.00 5.54
1036 1157 4.554363 CGGTCTGCCTCGCCGTAG 62.554 72.222 0.00 0.00 40.53 3.51
1383 2636 3.818787 GTCTTCGCGCCCTACGGA 61.819 66.667 0.00 0.00 43.93 4.69
1386 2639 3.060020 CTTCGCGCCCTACGGAGAA 62.060 63.158 0.00 0.00 38.47 2.87
1482 2735 3.827898 GAGGAGGAGGTCGCCACG 61.828 72.222 0.00 0.00 37.84 4.94
1775 3040 1.305718 AGGAGCACCTGGAGAGGAC 60.306 63.158 0.22 0.00 45.92 3.85
1913 3200 8.639761 GGTAAGTACTATTCTCTTTGCATAGGA 58.360 37.037 4.23 0.00 0.00 2.94
1917 3204 8.527810 AGTACTATTCTCTTTGCATAGGATAGC 58.472 37.037 14.89 5.10 0.00 2.97
1923 3210 6.759272 TCTCTTTGCATAGGATAGCGTTATT 58.241 36.000 4.23 0.00 0.00 1.40
1924 3211 7.217200 TCTCTTTGCATAGGATAGCGTTATTT 58.783 34.615 4.23 0.00 0.00 1.40
1926 3213 8.220755 TCTTTGCATAGGATAGCGTTATTTTT 57.779 30.769 4.23 0.00 0.00 1.94
1927 3214 8.128582 TCTTTGCATAGGATAGCGTTATTTTTG 58.871 33.333 4.23 0.00 0.00 2.44
1929 3216 7.328277 TGCATAGGATAGCGTTATTTTTGTT 57.672 32.000 0.00 0.00 0.00 2.83
1930 3217 7.192913 TGCATAGGATAGCGTTATTTTTGTTG 58.807 34.615 0.00 0.00 0.00 3.33
1932 3219 7.468084 GCATAGGATAGCGTTATTTTTGTTGGA 60.468 37.037 0.00 0.00 0.00 3.53
1933 3220 6.190954 AGGATAGCGTTATTTTTGTTGGAC 57.809 37.500 0.00 0.00 0.00 4.02
1935 3222 3.276882 AGCGTTATTTTTGTTGGACCG 57.723 42.857 0.00 0.00 0.00 4.79
1936 3223 1.717113 GCGTTATTTTTGTTGGACCGC 59.283 47.619 0.00 0.00 0.00 5.68
1937 3224 2.321263 CGTTATTTTTGTTGGACCGCC 58.679 47.619 0.00 0.00 0.00 6.13
1938 3225 2.030628 CGTTATTTTTGTTGGACCGCCT 60.031 45.455 0.00 0.00 34.31 5.52
1941 3228 5.530712 GTTATTTTTGTTGGACCGCCTTAA 58.469 37.500 0.00 0.00 34.31 1.85
1952 3239 2.745281 GACCGCCTTAATTACTTGCACA 59.255 45.455 0.00 0.00 0.00 4.57
1953 3240 3.352648 ACCGCCTTAATTACTTGCACAT 58.647 40.909 0.00 0.00 0.00 3.21
1954 3241 3.761752 ACCGCCTTAATTACTTGCACATT 59.238 39.130 0.00 0.00 0.00 2.71
1955 3242 4.142469 ACCGCCTTAATTACTTGCACATTC 60.142 41.667 0.00 0.00 0.00 2.67
1956 3243 4.351192 CGCCTTAATTACTTGCACATTCC 58.649 43.478 0.00 0.00 0.00 3.01
1957 3244 4.351192 GCCTTAATTACTTGCACATTCCG 58.649 43.478 0.00 0.00 0.00 4.30
2012 4398 9.461312 AATCTCCATAATTAAGTTAACACTGCA 57.539 29.630 8.61 0.00 31.60 4.41
2013 4399 8.856153 TCTCCATAATTAAGTTAACACTGCAA 57.144 30.769 8.61 0.00 31.60 4.08
2026 4415 7.968405 AGTTAACACTGCAAAAGTTAAAGTGAG 59.032 33.333 15.41 0.00 40.54 3.51
2037 4426 8.559536 CAAAAGTTAAAGTGAGCAGAGTTATCA 58.440 33.333 0.00 0.00 0.00 2.15
2045 4626 7.602517 AGTGAGCAGAGTTATCATAAAACAC 57.397 36.000 0.00 0.00 0.00 3.32
2046 4627 7.161404 AGTGAGCAGAGTTATCATAAAACACA 58.839 34.615 0.00 0.00 0.00 3.72
2115 4933 6.070995 TGTTTTATGTCCAGGACGTATTCTCT 60.071 38.462 20.46 0.00 34.57 3.10
2118 4936 1.112113 TCCAGGACGTATTCTCTGCC 58.888 55.000 0.00 0.00 0.00 4.85
2239 5057 0.036388 CCATGCTAGTGGAACCGTGT 60.036 55.000 0.00 0.00 42.02 4.49
2271 5089 1.000283 CTAAGCGAGCTCCCATACCTG 60.000 57.143 8.47 0.00 0.00 4.00
2815 5638 9.394477 AGAAAATAAATTGCAAAGTTCTACGAC 57.606 29.630 1.71 0.00 34.98 4.34
3007 5835 8.997621 ACTCTACAGCGAAAATTATAGAAACA 57.002 30.769 0.00 0.00 0.00 2.83
3242 6113 2.439507 GTCATCATATATGGCCCCCGAT 59.560 50.000 12.78 0.00 0.00 4.18
3385 6298 5.902613 TGATCATCCCATGAAAAGTTCAC 57.097 39.130 0.00 0.00 43.48 3.18
3402 6315 9.747293 AAAAGTTCACAACTACTCTAGTTAGTC 57.253 33.333 7.10 0.00 46.66 2.59
3420 6333 6.812160 AGTTAGTCTAAAGTTTAGGTGATGCG 59.188 38.462 20.04 0.00 0.00 4.73
3432 6345 8.150945 AGTTTAGGTGATGCGTTATATCTGATT 58.849 33.333 0.00 0.00 0.00 2.57
3457 6370 5.771153 AAGGAGCTAACGGTAGATAGTTC 57.229 43.478 12.83 0.00 34.07 3.01
3530 6443 1.204231 GAGGTTGAACGACTCCTACCC 59.796 57.143 0.00 0.00 31.21 3.69
3532 6445 0.108945 GTTGAACGACTCCTACCCGG 60.109 60.000 0.00 0.00 0.00 5.73
3533 6446 1.880819 TTGAACGACTCCTACCCGGC 61.881 60.000 0.00 0.00 0.00 6.13
3624 7580 2.681848 GTGGAAACATGCAGAGGATGAG 59.318 50.000 5.50 0.00 46.14 2.90
3632 7588 1.489230 TGCAGAGGATGAGCATGATGT 59.511 47.619 0.00 0.00 32.55 3.06
3636 7592 3.810386 CAGAGGATGAGCATGATGTTGAG 59.190 47.826 0.00 0.00 0.00 3.02
3638 7594 2.172930 AGGATGAGCATGATGTTGAGCT 59.827 45.455 0.00 0.00 40.60 4.09
3639 7595 2.290916 GGATGAGCATGATGTTGAGCTG 59.709 50.000 0.00 0.00 37.48 4.24
3640 7596 1.092348 TGAGCATGATGTTGAGCTGC 58.908 50.000 0.00 0.00 37.48 5.25
3641 7597 1.092348 GAGCATGATGTTGAGCTGCA 58.908 50.000 1.02 0.00 37.48 4.41
3651 7607 2.582728 TTGAGCTGCAACCAAACAAG 57.417 45.000 1.02 0.00 0.00 3.16
3652 7608 1.761449 TGAGCTGCAACCAAACAAGA 58.239 45.000 1.02 0.00 0.00 3.02
3653 7609 2.309613 TGAGCTGCAACCAAACAAGAT 58.690 42.857 1.02 0.00 0.00 2.40
3654 7610 2.294233 TGAGCTGCAACCAAACAAGATC 59.706 45.455 1.02 0.00 0.00 2.75
3655 7611 2.555757 GAGCTGCAACCAAACAAGATCT 59.444 45.455 1.02 0.00 0.00 2.75
3656 7612 2.555757 AGCTGCAACCAAACAAGATCTC 59.444 45.455 1.02 0.00 0.00 2.75
3657 7613 2.294233 GCTGCAACCAAACAAGATCTCA 59.706 45.455 0.00 0.00 0.00 3.27
3660 7616 5.627499 TGCAACCAAACAAGATCTCATAC 57.373 39.130 0.00 0.00 0.00 2.39
3661 7617 5.069318 TGCAACCAAACAAGATCTCATACA 58.931 37.500 0.00 0.00 0.00 2.29
3663 7619 5.182001 GCAACCAAACAAGATCTCATACACT 59.818 40.000 0.00 0.00 0.00 3.55
3664 7620 6.371548 GCAACCAAACAAGATCTCATACACTA 59.628 38.462 0.00 0.00 0.00 2.74
3665 7621 7.066284 GCAACCAAACAAGATCTCATACACTAT 59.934 37.037 0.00 0.00 0.00 2.12
3666 7622 8.950210 CAACCAAACAAGATCTCATACACTATT 58.050 33.333 0.00 0.00 0.00 1.73
3667 7623 8.723942 ACCAAACAAGATCTCATACACTATTC 57.276 34.615 0.00 0.00 0.00 1.75
3668 7624 8.543774 ACCAAACAAGATCTCATACACTATTCT 58.456 33.333 0.00 0.00 0.00 2.40
3678 7634 8.693120 TCTCATACACTATTCTAGTTACCTGG 57.307 38.462 0.00 0.00 36.76 4.45
3679 7635 8.280084 TCTCATACACTATTCTAGTTACCTGGT 58.720 37.037 4.05 4.05 36.76 4.00
3681 7637 5.831702 ACACTATTCTAGTTACCTGGTCG 57.168 43.478 0.63 0.00 36.76 4.79
3682 7638 5.503927 ACACTATTCTAGTTACCTGGTCGA 58.496 41.667 0.63 0.00 36.76 4.20
3683 7639 5.948162 ACACTATTCTAGTTACCTGGTCGAA 59.052 40.000 0.63 0.40 36.76 3.71
3684 7640 6.095160 ACACTATTCTAGTTACCTGGTCGAAG 59.905 42.308 0.63 0.00 36.76 3.79
3685 7641 5.593502 ACTATTCTAGTTACCTGGTCGAAGG 59.406 44.000 0.63 1.40 38.46 3.46
3686 7642 8.763599 CACTATTCTAGTTACCTGGTCGAAGGT 61.764 44.444 13.23 13.23 44.51 3.50
3694 7650 2.893637 CCTGGTCGAAGGTGTCATAAG 58.106 52.381 0.00 0.00 32.17 1.73
3695 7651 2.271800 CTGGTCGAAGGTGTCATAAGC 58.728 52.381 0.00 0.00 0.00 3.09
3697 7653 2.301870 TGGTCGAAGGTGTCATAAGCTT 59.698 45.455 3.48 3.48 40.47 3.74
3700 7656 4.184629 GTCGAAGGTGTCATAAGCTTGAT 58.815 43.478 9.86 0.00 37.98 2.57
3701 7657 4.631813 GTCGAAGGTGTCATAAGCTTGATT 59.368 41.667 9.86 0.00 37.98 2.57
3702 7658 5.122396 GTCGAAGGTGTCATAAGCTTGATTT 59.878 40.000 9.86 0.00 37.98 2.17
3703 7659 5.122239 TCGAAGGTGTCATAAGCTTGATTTG 59.878 40.000 9.86 1.79 37.98 2.32
3704 7660 5.106555 CGAAGGTGTCATAAGCTTGATTTGT 60.107 40.000 9.86 0.00 37.98 2.83
3706 7662 7.360861 CGAAGGTGTCATAAGCTTGATTTGTTA 60.361 37.037 9.86 0.00 37.98 2.41
3707 7663 7.944729 AGGTGTCATAAGCTTGATTTGTTAT 57.055 32.000 9.86 0.00 0.00 1.89
3708 7664 8.353423 AGGTGTCATAAGCTTGATTTGTTATT 57.647 30.769 9.86 0.00 0.00 1.40
3709 7665 8.462016 AGGTGTCATAAGCTTGATTTGTTATTC 58.538 33.333 9.86 0.00 0.00 1.75
3711 7667 9.846248 GTGTCATAAGCTTGATTTGTTATTCTT 57.154 29.630 9.86 0.00 0.00 2.52
3719 7675 9.635520 AGCTTGATTTGTTATTCTTTCTTCATG 57.364 29.630 0.00 0.00 0.00 3.07
3723 7679 8.306038 TGATTTGTTATTCTTTCTTCATGTGGG 58.694 33.333 0.00 0.00 0.00 4.61
3724 7680 5.643379 TGTTATTCTTTCTTCATGTGGGC 57.357 39.130 0.00 0.00 0.00 5.36
3725 7681 5.324409 TGTTATTCTTTCTTCATGTGGGCT 58.676 37.500 0.00 0.00 0.00 5.19
3728 7684 4.853924 TTCTTTCTTCATGTGGGCTTTC 57.146 40.909 0.00 0.00 0.00 2.62
3729 7685 2.813754 TCTTTCTTCATGTGGGCTTTCG 59.186 45.455 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 182 4.986659 GTCTGTACGACAAAACACCTGTAT 59.013 41.667 11.36 0.00 42.37 2.29
154 183 4.362279 GTCTGTACGACAAAACACCTGTA 58.638 43.478 11.36 0.00 42.37 2.74
191 220 2.361230 GCTGGAAAACCCCTCCCG 60.361 66.667 0.00 0.00 31.32 5.14
198 227 0.383860 CGTTCGTTCGCTGGAAAACC 60.384 55.000 0.00 0.00 33.05 3.27
217 248 0.935196 AACAACTCCAGCGAACGAAC 59.065 50.000 0.00 0.00 0.00 3.95
219 250 1.495584 GCAACAACTCCAGCGAACGA 61.496 55.000 0.00 0.00 0.00 3.85
248 279 6.683708 CACAAATTTGTCACGTACGTTAGTTT 59.316 34.615 20.23 10.94 39.91 2.66
250 281 5.730269 CACAAATTTGTCACGTACGTTAGT 58.270 37.500 20.23 0.13 39.91 2.24
253 284 3.356145 GCACAAATTTGTCACGTACGTT 58.644 40.909 20.23 0.00 39.91 3.99
255 286 2.303537 GGCACAAATTTGTCACGTACG 58.696 47.619 20.85 15.01 39.91 3.67
256 287 2.286536 ACGGCACAAATTTGTCACGTAC 60.287 45.455 31.88 15.62 43.85 3.67
257 288 1.941294 ACGGCACAAATTTGTCACGTA 59.059 42.857 31.88 0.00 43.85 3.57
259 290 1.394697 GACGGCACAAATTTGTCACG 58.605 50.000 28.57 28.57 39.91 4.35
260 291 1.066303 TGGACGGCACAAATTTGTCAC 59.934 47.619 20.85 15.24 39.91 3.67
262 293 2.030363 TGATGGACGGCACAAATTTGTC 60.030 45.455 20.85 14.74 39.91 3.18
314 409 7.012799 TGCTCCTCTGTTTTTGTTTTTGTTTTT 59.987 29.630 0.00 0.00 0.00 1.94
315 410 6.484977 TGCTCCTCTGTTTTTGTTTTTGTTTT 59.515 30.769 0.00 0.00 0.00 2.43
317 412 5.546526 TGCTCCTCTGTTTTTGTTTTTGTT 58.453 33.333 0.00 0.00 0.00 2.83
319 414 4.033243 GCTGCTCCTCTGTTTTTGTTTTTG 59.967 41.667 0.00 0.00 0.00 2.44
325 420 2.883386 AGAAGCTGCTCCTCTGTTTTTG 59.117 45.455 1.00 0.00 0.00 2.44
326 421 3.220674 AGAAGCTGCTCCTCTGTTTTT 57.779 42.857 1.00 0.00 0.00 1.94
330 425 0.823460 GCTAGAAGCTGCTCCTCTGT 59.177 55.000 12.88 0.00 38.45 3.41
345 440 4.219944 TGTGGTCTGGTACAAAGTAGCTAG 59.780 45.833 0.00 4.45 38.70 3.42
346 441 4.021719 GTGTGGTCTGGTACAAAGTAGCTA 60.022 45.833 7.73 0.00 38.70 3.32
347 442 2.969950 TGTGGTCTGGTACAAAGTAGCT 59.030 45.455 7.73 0.00 38.70 3.32
348 443 3.064931 GTGTGGTCTGGTACAAAGTAGC 58.935 50.000 0.00 0.00 38.70 3.58
402 497 0.472471 ACCACCATTGTTGACCGAGT 59.528 50.000 0.00 0.00 0.00 4.18
426 521 1.243342 CCTTGGCATCACCGCAGAAA 61.243 55.000 0.00 0.00 43.94 2.52
427 522 1.675310 CCTTGGCATCACCGCAGAA 60.675 57.895 0.00 0.00 43.94 3.02
428 523 1.549243 TACCTTGGCATCACCGCAGA 61.549 55.000 0.00 0.00 43.94 4.26
430 525 1.376683 GTACCTTGGCATCACCGCA 60.377 57.895 0.00 0.00 43.94 5.69
431 526 0.676782 AAGTACCTTGGCATCACCGC 60.677 55.000 0.00 0.00 43.94 5.68
432 527 1.086696 CAAGTACCTTGGCATCACCG 58.913 55.000 0.00 0.00 43.94 4.94
452 547 0.731417 CCAGATGCACAGCAAGTAGC 59.269 55.000 0.00 0.00 43.62 3.58
453 548 2.005451 GACCAGATGCACAGCAAGTAG 58.995 52.381 0.00 0.00 43.62 2.57
454 549 1.347378 TGACCAGATGCACAGCAAGTA 59.653 47.619 0.00 0.00 43.62 2.24
455 550 0.109153 TGACCAGATGCACAGCAAGT 59.891 50.000 0.00 0.00 43.62 3.16
457 552 0.607217 CCTGACCAGATGCACAGCAA 60.607 55.000 0.00 0.00 43.62 3.91
458 553 1.002990 CCTGACCAGATGCACAGCA 60.003 57.895 0.00 0.00 44.86 4.41
460 555 0.322648 TCACCTGACCAGATGCACAG 59.677 55.000 0.00 0.00 0.00 3.66
461 556 0.322648 CTCACCTGACCAGATGCACA 59.677 55.000 0.00 0.00 0.00 4.57
462 557 0.392193 CCTCACCTGACCAGATGCAC 60.392 60.000 0.00 0.00 0.00 4.57
550 648 4.008933 ACGCCTCACCTGACCAGC 62.009 66.667 0.00 0.00 0.00 4.85
713 824 1.819928 TTTCCACGTACATGCATGCT 58.180 45.000 26.53 15.56 0.00 3.79
714 825 2.849880 ATTTCCACGTACATGCATGC 57.150 45.000 26.53 11.82 0.00 4.06
715 826 4.262743 CGAAAATTTCCACGTACATGCATG 59.737 41.667 25.09 25.09 0.00 4.06
716 827 4.411327 CGAAAATTTCCACGTACATGCAT 58.589 39.130 0.00 0.00 0.00 3.96
905 1026 2.710377 TGCAAGTTGTGAGTTGTGAGT 58.290 42.857 4.48 0.00 38.27 3.41
906 1027 3.763097 TTGCAAGTTGTGAGTTGTGAG 57.237 42.857 4.48 0.00 38.27 3.51
1032 1153 1.734359 GCAGCGAAACGAGAGCTACG 61.734 60.000 10.54 10.54 39.48 3.51
1033 1154 0.456995 AGCAGCGAAACGAGAGCTAC 60.457 55.000 0.00 0.00 39.48 3.58
1034 1155 0.179161 GAGCAGCGAAACGAGAGCTA 60.179 55.000 0.00 0.00 39.48 3.32
1036 1157 1.080995 ATGAGCAGCGAAACGAGAGC 61.081 55.000 0.00 0.00 0.00 4.09
1383 2636 1.144936 GAGCTGGCGCCAGTATTCT 59.855 57.895 46.58 37.17 45.24 2.40
1386 2639 4.227134 CGGAGCTGGCGCCAGTAT 62.227 66.667 46.58 37.81 45.24 2.12
1545 2798 3.060000 TCCGTCACGAGCGTGGAT 61.060 61.111 21.14 0.00 45.43 3.41
1581 2834 2.586079 CTGCACCGGTCGCCTATG 60.586 66.667 21.23 4.31 0.00 2.23
1913 3200 4.673320 GCGGTCCAACAAAAATAACGCTAT 60.673 41.667 0.00 0.00 41.10 2.97
1914 3201 3.365164 GCGGTCCAACAAAAATAACGCTA 60.365 43.478 0.00 0.00 41.10 4.26
1917 3204 2.030628 AGGCGGTCCAACAAAAATAACG 60.031 45.455 0.00 0.00 33.74 3.18
1923 3210 4.828387 AGTAATTAAGGCGGTCCAACAAAA 59.172 37.500 0.00 0.00 33.74 2.44
1924 3211 4.400120 AGTAATTAAGGCGGTCCAACAAA 58.600 39.130 0.00 0.00 33.74 2.83
1926 3213 3.706600 AGTAATTAAGGCGGTCCAACA 57.293 42.857 0.00 0.00 33.74 3.33
1927 3214 3.427098 GCAAGTAATTAAGGCGGTCCAAC 60.427 47.826 0.00 0.00 33.74 3.77
1929 3216 2.290387 TGCAAGTAATTAAGGCGGTCCA 60.290 45.455 0.00 0.00 33.74 4.02
1930 3217 2.096980 GTGCAAGTAATTAAGGCGGTCC 59.903 50.000 0.00 0.00 0.00 4.46
1932 3219 2.785562 TGTGCAAGTAATTAAGGCGGT 58.214 42.857 0.00 0.00 0.00 5.68
1933 3220 4.351192 GAATGTGCAAGTAATTAAGGCGG 58.649 43.478 0.00 0.00 0.00 6.13
1935 3222 4.095782 TCGGAATGTGCAAGTAATTAAGGC 59.904 41.667 0.00 0.00 0.00 4.35
1936 3223 5.811399 TCGGAATGTGCAAGTAATTAAGG 57.189 39.130 0.00 0.00 0.00 2.69
1937 3224 9.950680 ATAAATCGGAATGTGCAAGTAATTAAG 57.049 29.630 0.00 0.00 0.00 1.85
1986 4362 9.461312 TGCAGTGTTAACTTAATTATGGAGATT 57.539 29.630 7.22 0.00 32.98 2.40
1989 4365 9.906660 TTTTGCAGTGTTAACTTAATTATGGAG 57.093 29.630 7.22 0.00 32.98 3.86
1990 4366 9.906660 CTTTTGCAGTGTTAACTTAATTATGGA 57.093 29.630 7.22 0.00 32.98 3.41
1991 4367 9.691362 ACTTTTGCAGTGTTAACTTAATTATGG 57.309 29.630 7.22 0.00 32.98 2.74
2002 4388 6.750039 GCTCACTTTAACTTTTGCAGTGTTAA 59.250 34.615 13.33 13.33 36.91 2.01
2012 4398 8.677148 TGATAACTCTGCTCACTTTAACTTTT 57.323 30.769 0.00 0.00 0.00 2.27
2013 4399 8.854614 ATGATAACTCTGCTCACTTTAACTTT 57.145 30.769 0.00 0.00 0.00 2.66
2026 4415 6.554419 TGCATGTGTTTTATGATAACTCTGC 58.446 36.000 0.00 0.00 31.56 4.26
2100 4918 0.249073 CGGCAGAGAATACGTCCTGG 60.249 60.000 0.00 0.00 0.00 4.45
2115 4933 1.315981 TTGTTGTTTCACTGCCGGCA 61.316 50.000 30.59 30.59 0.00 5.69
2118 4936 2.598907 CGTAGTTGTTGTTTCACTGCCG 60.599 50.000 0.00 0.00 0.00 5.69
2239 5057 4.143333 GCTTAGGGCGTGCTCGGA 62.143 66.667 10.52 0.00 37.56 4.55
2271 5089 1.880340 CTCTCGGATGACCAAGCGC 60.880 63.158 0.00 0.00 35.59 5.92
2679 5501 2.345244 CGCAACAGGAGCTGGTCT 59.655 61.111 6.83 0.00 35.51 3.85
2776 5599 9.301153 GCAATTTATTTTCTATGTGGGTACAAG 57.699 33.333 0.00 0.00 40.84 3.16
2918 5741 9.619316 TGTATCAATTGAAATAAAACGTCCAAG 57.381 29.630 13.09 0.00 0.00 3.61
3160 5988 9.712305 TTCATGGACAAAAGAAGTTAAAACAAA 57.288 25.926 0.00 0.00 0.00 2.83
3242 6113 1.269448 GCTTTTGGATCGGCAACTTCA 59.731 47.619 0.00 0.00 0.00 3.02
3402 6315 9.477484 AGATATAACGCATCACCTAAACTTTAG 57.523 33.333 1.95 1.95 0.00 1.85
3420 6333 8.704234 CGTTAGCTCCTTTCAATCAGATATAAC 58.296 37.037 0.00 0.00 0.00 1.89
3432 6345 5.198965 ACTATCTACCGTTAGCTCCTTTCA 58.801 41.667 0.00 0.00 0.00 2.69
3457 6370 0.607217 TGGGCATGTGCTCTGTCTTG 60.607 55.000 6.41 0.00 43.37 3.02
3530 6443 1.153549 GTAGACCTTCAGCTGGCCG 60.154 63.158 15.13 3.53 0.00 6.13
3532 6445 2.409948 AATGTAGACCTTCAGCTGGC 57.590 50.000 15.13 0.00 0.00 4.85
3533 6446 4.080863 AGGTTAATGTAGACCTTCAGCTGG 60.081 45.833 15.13 0.00 43.64 4.85
3562 6475 4.728882 GCTGTGTCAATCGATGGATTTGAC 60.729 45.833 17.80 17.80 40.90 3.18
3632 7588 2.098614 TCTTGTTTGGTTGCAGCTCAA 58.901 42.857 0.00 0.45 0.00 3.02
3636 7592 2.294233 TGAGATCTTGTTTGGTTGCAGC 59.706 45.455 0.00 0.00 0.00 5.25
3638 7594 5.048782 GTGTATGAGATCTTGTTTGGTTGCA 60.049 40.000 0.00 0.00 0.00 4.08
3639 7595 5.182001 AGTGTATGAGATCTTGTTTGGTTGC 59.818 40.000 0.00 0.00 0.00 4.17
3640 7596 6.808008 AGTGTATGAGATCTTGTTTGGTTG 57.192 37.500 0.00 0.00 0.00 3.77
3641 7597 9.167311 GAATAGTGTATGAGATCTTGTTTGGTT 57.833 33.333 0.00 0.00 0.00 3.67
3643 7599 8.954950 AGAATAGTGTATGAGATCTTGTTTGG 57.045 34.615 0.00 0.00 0.00 3.28
3670 7626 1.342174 TGACACCTTCGACCAGGTAAC 59.658 52.381 8.48 6.69 46.27 2.50
3671 7627 1.707106 TGACACCTTCGACCAGGTAA 58.293 50.000 8.48 0.00 46.27 2.85
3672 7628 1.933021 ATGACACCTTCGACCAGGTA 58.067 50.000 8.48 0.00 46.27 3.08
3674 7630 2.893637 CTTATGACACCTTCGACCAGG 58.106 52.381 1.40 1.40 40.23 4.45
3675 7631 2.093973 AGCTTATGACACCTTCGACCAG 60.094 50.000 0.00 0.00 0.00 4.00
3676 7632 1.899814 AGCTTATGACACCTTCGACCA 59.100 47.619 0.00 0.00 0.00 4.02
3677 7633 2.673368 CAAGCTTATGACACCTTCGACC 59.327 50.000 0.00 0.00 0.00 4.79
3678 7634 3.585862 TCAAGCTTATGACACCTTCGAC 58.414 45.455 0.00 0.00 0.00 4.20
3679 7635 3.953712 TCAAGCTTATGACACCTTCGA 57.046 42.857 0.00 0.00 0.00 3.71
3681 7637 6.259550 ACAAATCAAGCTTATGACACCTTC 57.740 37.500 0.00 0.00 30.82 3.46
3682 7638 6.655078 AACAAATCAAGCTTATGACACCTT 57.345 33.333 0.00 0.00 30.82 3.50
3683 7639 7.944729 ATAACAAATCAAGCTTATGACACCT 57.055 32.000 0.00 0.00 30.82 4.00
3684 7640 8.462016 AGAATAACAAATCAAGCTTATGACACC 58.538 33.333 0.00 0.00 30.82 4.16
3685 7641 9.846248 AAGAATAACAAATCAAGCTTATGACAC 57.154 29.630 0.00 0.00 30.82 3.67
3694 7650 9.415544 ACATGAAGAAAGAATAACAAATCAAGC 57.584 29.630 0.00 0.00 0.00 4.01
3697 7653 8.306038 CCCACATGAAGAAAGAATAACAAATCA 58.694 33.333 0.00 0.00 0.00 2.57
3700 7656 6.267471 AGCCCACATGAAGAAAGAATAACAAA 59.733 34.615 0.00 0.00 0.00 2.83
3701 7657 5.774690 AGCCCACATGAAGAAAGAATAACAA 59.225 36.000 0.00 0.00 0.00 2.83
3702 7658 5.324409 AGCCCACATGAAGAAAGAATAACA 58.676 37.500 0.00 0.00 0.00 2.41
3703 7659 5.904362 AGCCCACATGAAGAAAGAATAAC 57.096 39.130 0.00 0.00 0.00 1.89
3704 7660 6.349280 CGAAAGCCCACATGAAGAAAGAATAA 60.349 38.462 0.00 0.00 0.00 1.40
3706 7662 4.082571 CGAAAGCCCACATGAAGAAAGAAT 60.083 41.667 0.00 0.00 0.00 2.40
3707 7663 3.253188 CGAAAGCCCACATGAAGAAAGAA 59.747 43.478 0.00 0.00 0.00 2.52
3708 7664 2.813754 CGAAAGCCCACATGAAGAAAGA 59.186 45.455 0.00 0.00 0.00 2.52
3709 7665 2.095059 CCGAAAGCCCACATGAAGAAAG 60.095 50.000 0.00 0.00 0.00 2.62
3711 7667 1.533625 CCGAAAGCCCACATGAAGAA 58.466 50.000 0.00 0.00 0.00 2.52
3712 7668 3.248043 CCGAAAGCCCACATGAAGA 57.752 52.632 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.