Multiple sequence alignment - TraesCS3D01G533200

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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 TraesCS3D01G533200 chr3D 100.000 4260 0 0 1 4260 608949895 608954154 0.000000e+00 7867.0
1 TraesCS3D01G533200 chr3D 92.622 1613 54 17 1 1587 608980277 608981850 0.000000e+00 2259.0
2 TraesCS3D01G533200 chr3D 86.929 1247 154 6 2110 3355 609286678 609285440 0.000000e+00 1391.0
3 TraesCS3D01G533200 chr3D 96.269 804 9 5 1612 2415 608981844 608982626 0.000000e+00 1299.0
4 TraesCS3D01G533200 chr3D 89.159 535 49 5 959 1487 609004575 609005106 0.000000e+00 658.0
5 TraesCS3D01G533200 chr3D 80.282 497 46 17 3398 3872 608993753 608994219 1.140000e-85 327.0
6 TraesCS3D01G533200 chr3D 75.957 470 91 20 28 485 553334217 553333758 5.540000e-54 222.0
7 TraesCS3D01G533200 chr3D 80.727 275 49 3 3 277 93478257 93478527 1.200000e-50 211.0
8 TraesCS3D01G533200 chr3D 90.728 151 11 3 1743 1892 548565163 548565311 9.340000e-47 198.0
9 TraesCS3D01G533200 chr3D 87.349 166 15 4 1731 1892 83698786 83698623 7.270000e-43 185.0
10 TraesCS3D01G533200 chr3B 92.833 1507 97 7 1890 3393 819650969 819652467 0.000000e+00 2174.0
11 TraesCS3D01G533200 chr3B 92.800 1500 101 4 1894 3393 819382075 819383567 0.000000e+00 2165.0
12 TraesCS3D01G533200 chr3B 88.405 1768 142 29 2 1731 819380339 819382081 0.000000e+00 2071.0
13 TraesCS3D01G533200 chr3B 89.267 1677 134 17 1 1638 819649024 819650693 0.000000e+00 2058.0
14 TraesCS3D01G533200 chr3B 92.135 1424 102 6 1975 3393 819522959 819524377 0.000000e+00 2001.0
15 TraesCS3D01G533200 chr3B 92.335 1396 103 4 1999 3393 819299949 819301341 0.000000e+00 1982.0
16 TraesCS3D01G533200 chr3B 88.854 1597 130 22 1 1558 819521374 819522961 0.000000e+00 1919.0
17 TraesCS3D01G533200 chr3B 95.205 584 27 1 920 1502 819298075 819298658 0.000000e+00 922.0
18 TraesCS3D01G533200 chr3B 87.782 532 61 3 959 1487 819740033 819740563 1.680000e-173 619.0
19 TraesCS3D01G533200 chr3B 87.786 393 37 4 3879 4260 819306436 819306828 2.340000e-122 449.0
20 TraesCS3D01G533200 chr3B 82.281 491 63 15 3402 3872 819305916 819306402 1.840000e-108 403.0
21 TraesCS3D01G533200 chr3B 84.536 388 43 10 3881 4260 819559466 819559844 6.730000e-98 368.0
22 TraesCS3D01G533200 chr3B 84.184 392 41 10 3881 4260 819659220 819659602 1.130000e-95 361.0
23 TraesCS3D01G533200 chr3B 86.347 271 31 5 3402 3671 819656940 819657205 1.500000e-74 291.0
24 TraesCS3D01G533200 chr3B 88.152 211 11 4 1495 1691 819299541 819299751 5.510000e-59 239.0
25 TraesCS3D01G533200 chr3B 84.746 236 33 3 3404 3638 819558770 819559003 2.560000e-57 233.0
26 TraesCS3D01G533200 chr3B 91.304 115 3 4 1624 1731 819650865 819650979 2.650000e-32 150.0
27 TraesCS3D01G533200 chr3A 86.925 1522 127 24 1 1491 742331269 742332749 0.000000e+00 1642.0
28 TraesCS3D01G533200 chr3A 91.093 1089 94 2 2305 3393 742313762 742314847 0.000000e+00 1471.0
29 TraesCS3D01G533200 chr3A 86.626 1144 148 2 2110 3253 742872387 742871249 0.000000e+00 1260.0
30 TraesCS3D01G533200 chr3A 92.832 851 53 4 2549 3393 742333342 742334190 0.000000e+00 1227.0
31 TraesCS3D01G533200 chr3A 94.148 581 31 1 1990 2567 742332750 742333330 0.000000e+00 881.0
32 TraesCS3D01G533200 chr3A 88.540 637 49 14 608 1239 742277384 742278001 0.000000e+00 750.0
33 TraesCS3D01G533200 chr3A 95.561 428 18 1 1890 2317 742298637 742299063 0.000000e+00 684.0
34 TraesCS3D01G533200 chr3A 90.656 503 36 7 1230 1731 742298155 742298647 0.000000e+00 658.0
35 TraesCS3D01G533200 chr3A 88.722 532 51 6 959 1487 742355389 742355914 3.590000e-180 641.0
36 TraesCS3D01G533200 chr3A 88.220 382 36 6 3887 4260 742318453 742318833 8.400000e-122 448.0
37 TraesCS3D01G533200 chr3A 80.885 497 59 15 3402 3877 742317929 742318410 4.050000e-95 359.0
38 TraesCS3D01G533200 chr3A 88.772 285 24 4 3948 4224 742338599 742338883 4.080000e-90 342.0
39 TraesCS3D01G533200 chr3A 80.974 431 29 18 3402 3802 742338192 742338599 4.170000e-75 292.0
40 TraesCS3D01G533200 chr2D 86.865 1142 138 8 2110 3249 623438591 623439722 0.000000e+00 1267.0
41 TraesCS3D01G533200 chr2D 80.727 275 50 3 13 286 606149685 606149957 1.200000e-50 211.0
42 TraesCS3D01G533200 chr2D 79.725 291 54 5 4 292 483146124 483146411 5.580000e-49 206.0
43 TraesCS3D01G533200 chrUn 100.000 352 0 0 1 352 480923364 480923013 0.000000e+00 651.0
44 TraesCS3D01G533200 chr5D 76.285 506 96 22 3 495 457669348 457668854 9.150000e-62 248.0
45 TraesCS3D01G533200 chr5D 78.799 283 59 1 4 286 486903752 486904033 5.620000e-44 189.0
46 TraesCS3D01G533200 chr2B 92.593 162 11 1 1732 1892 131150574 131150413 9.210000e-57 231.0
47 TraesCS3D01G533200 chr6B 90.854 164 15 0 1732 1895 262582337 262582174 1.990000e-53 220.0
48 TraesCS3D01G533200 chr1D 81.139 281 47 5 5 284 290704439 290704714 1.990000e-53 220.0
49 TraesCS3D01G533200 chr6D 91.391 151 11 2 1743 1892 4031320 4031469 5.580000e-49 206.0
50 TraesCS3D01G533200 chr4A 74.850 501 102 11 3 487 160247306 160247798 5.580000e-49 206.0
51 TraesCS3D01G533200 chr6A 88.344 163 17 2 1730 1892 46872634 46872474 1.210000e-45 195.0
52 TraesCS3D01G533200 chr6A 89.404 151 14 2 1743 1892 44841349 44841498 5.620000e-44 189.0
53 TraesCS3D01G533200 chr2A 88.272 162 14 5 1733 1892 772746387 772746229 5.620000e-44 189.0
54 TraesCS3D01G533200 chr1B 89.583 48 5 0 383 430 403974991 403975038 1.280000e-05 62.1


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 TraesCS3D01G533200 chr3D 608949895 608954154 4259 False 7867.000000 7867 100.000000 1 4260 1 chr3D.!!$F3 4259
1 TraesCS3D01G533200 chr3D 608980277 608982626 2349 False 1779.000000 2259 94.445500 1 2415 2 chr3D.!!$F6 2414
2 TraesCS3D01G533200 chr3D 609285440 609286678 1238 True 1391.000000 1391 86.929000 2110 3355 1 chr3D.!!$R3 1245
3 TraesCS3D01G533200 chr3D 609004575 609005106 531 False 658.000000 658 89.159000 959 1487 1 chr3D.!!$F5 528
4 TraesCS3D01G533200 chr3B 819380339 819383567 3228 False 2118.000000 2165 90.602500 2 3393 2 chr3B.!!$F4 3391
5 TraesCS3D01G533200 chr3B 819521374 819524377 3003 False 1960.000000 2001 90.494500 1 3393 2 chr3B.!!$F5 3392
6 TraesCS3D01G533200 chr3B 819649024 819652467 3443 False 1460.666667 2174 91.134667 1 3393 3 chr3B.!!$F7 3392
7 TraesCS3D01G533200 chr3B 819298075 819301341 3266 False 1047.666667 1982 91.897333 920 3393 3 chr3B.!!$F2 2473
8 TraesCS3D01G533200 chr3B 819740033 819740563 530 False 619.000000 619 87.782000 959 1487 1 chr3B.!!$F1 528
9 TraesCS3D01G533200 chr3B 819305916 819306828 912 False 426.000000 449 85.033500 3402 4260 2 chr3B.!!$F3 858
10 TraesCS3D01G533200 chr3B 819656940 819659602 2662 False 326.000000 361 85.265500 3402 4260 2 chr3B.!!$F8 858
11 TraesCS3D01G533200 chr3B 819558770 819559844 1074 False 300.500000 368 84.641000 3404 4260 2 chr3B.!!$F6 856
12 TraesCS3D01G533200 chr3A 742871249 742872387 1138 True 1260.000000 1260 86.626000 2110 3253 1 chr3A.!!$R1 1143
13 TraesCS3D01G533200 chr3A 742331269 742334190 2921 False 1250.000000 1642 91.301667 1 3393 3 chr3A.!!$F5 3392
14 TraesCS3D01G533200 chr3A 742313762 742318833 5071 False 759.333333 1471 86.732667 2305 4260 3 chr3A.!!$F4 1955
15 TraesCS3D01G533200 chr3A 742277384 742278001 617 False 750.000000 750 88.540000 608 1239 1 chr3A.!!$F1 631
16 TraesCS3D01G533200 chr3A 742298155 742299063 908 False 671.000000 684 93.108500 1230 2317 2 chr3A.!!$F3 1087
17 TraesCS3D01G533200 chr3A 742355389 742355914 525 False 641.000000 641 88.722000 959 1487 1 chr3A.!!$F2 528
18 TraesCS3D01G533200 chr3A 742338192 742338883 691 False 317.000000 342 84.873000 3402 4224 2 chr3A.!!$F6 822
19 TraesCS3D01G533200 chr2D 623438591 623439722 1131 False 1267.000000 1267 86.865000 2110 3249 1 chr2D.!!$F3 1139

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
815 874 0.613260 CCACACCTAGCTAGCCAACA 59.387 55.0 15.74 0.0 0.00 3.33 F
1305 1376 0.388649 AGGTGATGAAGACGCACGAC 60.389 55.0 0.00 0.0 33.48 4.34 F
1828 3062 0.248289 GCCCGCTTTAGCCCGATATA 59.752 55.0 0.00 0.0 37.91 0.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1780 3014 0.178068 AGACGACCATTTAGCGGCAT 59.822 50.0 1.45 0.00 35.0 4.40 R
3177 4541 0.534652 GCCTTCCTCCTGCATGCTAG 60.535 60.0 20.33 13.98 0.0 3.42 R
3640 8249 0.387622 ACGACGTACCATCACAACCG 60.388 55.0 0.00 0.00 0.0 4.44 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
583 637 5.523188 TGGTTGTGTGCTTCATTGAAAATTC 59.477 36.000 0.01 0.00 0.00 2.17
584 638 5.523188 GGTTGTGTGCTTCATTGAAAATTCA 59.477 36.000 0.01 0.00 34.92 2.57
696 754 5.074115 ACCGAAATACAAAACCATCCAGAA 58.926 37.500 0.00 0.00 0.00 3.02
720 778 0.615261 AGGAGACGGGAAAGGGAGAC 60.615 60.000 0.00 0.00 0.00 3.36
815 874 0.613260 CCACACCTAGCTAGCCAACA 59.387 55.000 15.74 0.00 0.00 3.33
835 894 6.207417 CCAACATCTCAGAAAACAGTACCATT 59.793 38.462 0.00 0.00 0.00 3.16
851 910 5.780793 AGTACCATTAGAGAACAGGTTCACT 59.219 40.000 14.79 14.79 41.92 3.41
856 915 1.546476 AGAGAACAGGTTCACTAGCGG 59.454 52.381 14.06 0.00 41.84 5.52
881 940 2.822707 AAGTCTCTAAGGGGACGCTA 57.177 50.000 0.00 0.00 37.52 4.26
895 954 1.132640 CGCTAACGCAGGAGCAAAC 59.867 57.895 2.14 0.00 40.05 2.93
928 990 4.799586 GCAAAAGGAGTTTAAAAGGCCTCC 60.800 45.833 5.23 12.53 43.14 4.30
1091 1162 0.603569 GTCTCCCTCGTGCTCTTGAA 59.396 55.000 0.00 0.00 0.00 2.69
1305 1376 0.388649 AGGTGATGAAGACGCACGAC 60.389 55.000 0.00 0.00 33.48 4.34
1316 1387 2.807045 GCACGACGAGGACTGCTG 60.807 66.667 0.00 0.00 0.00 4.41
1317 1388 2.807045 CACGACGAGGACTGCTGC 60.807 66.667 0.00 0.00 0.00 5.25
1318 1389 3.295273 ACGACGAGGACTGCTGCA 61.295 61.111 0.00 0.88 0.00 4.41
1319 1390 2.807045 CGACGAGGACTGCTGCAC 60.807 66.667 0.00 0.00 0.00 4.57
1320 1391 2.433318 GACGAGGACTGCTGCACC 60.433 66.667 0.00 0.00 0.00 5.01
1321 1392 3.941657 GACGAGGACTGCTGCACCC 62.942 68.421 0.00 2.99 0.00 4.61
1323 1394 4.767255 GAGGACTGCTGCACCCGG 62.767 72.222 0.00 0.00 0.00 5.73
1390 1481 2.104729 GGTTCGCGCCATACGGTA 59.895 61.111 0.00 0.00 43.93 4.02
1583 2584 9.213799 GAATTATCTCCACTCCAACATATTCTC 57.786 37.037 0.00 0.00 0.00 2.87
1584 2585 5.559148 ATCTCCACTCCAACATATTCTCC 57.441 43.478 0.00 0.00 0.00 3.71
1585 2586 4.624913 TCTCCACTCCAACATATTCTCCT 58.375 43.478 0.00 0.00 0.00 3.69
1586 2587 4.406972 TCTCCACTCCAACATATTCTCCTG 59.593 45.833 0.00 0.00 0.00 3.86
1587 2588 3.118261 TCCACTCCAACATATTCTCCTGC 60.118 47.826 0.00 0.00 0.00 4.85
1588 2589 3.370846 CCACTCCAACATATTCTCCTGCA 60.371 47.826 0.00 0.00 0.00 4.41
1589 2590 4.264253 CACTCCAACATATTCTCCTGCAA 58.736 43.478 0.00 0.00 0.00 4.08
1590 2591 4.701651 CACTCCAACATATTCTCCTGCAAA 59.298 41.667 0.00 0.00 0.00 3.68
1591 2592 5.183713 CACTCCAACATATTCTCCTGCAAAA 59.816 40.000 0.00 0.00 0.00 2.44
1592 2593 5.774690 ACTCCAACATATTCTCCTGCAAAAA 59.225 36.000 0.00 0.00 0.00 1.94
1716 2950 7.298854 CAAAACACGGTAAAAACCAACAAAAT 58.701 30.769 0.00 0.00 0.00 1.82
1780 3014 3.494398 CCGCTATAGCCTTTTTAGCAGGA 60.494 47.826 19.00 0.00 38.58 3.86
1797 3031 0.814010 GGATGCCGCTAAATGGTCGT 60.814 55.000 0.00 0.00 0.00 4.34
1811 3045 5.813080 AATGGTCGTCTTTACAAATAGCC 57.187 39.130 0.00 0.00 0.00 3.93
1812 3046 3.602483 TGGTCGTCTTTACAAATAGCCC 58.398 45.455 0.00 0.00 0.00 5.19
1813 3047 2.606272 GGTCGTCTTTACAAATAGCCCG 59.394 50.000 0.00 0.00 0.00 6.13
1814 3048 2.030091 GTCGTCTTTACAAATAGCCCGC 59.970 50.000 0.00 0.00 0.00 6.13
1815 3049 2.093869 TCGTCTTTACAAATAGCCCGCT 60.094 45.455 0.00 0.00 0.00 5.52
1816 3050 2.676342 CGTCTTTACAAATAGCCCGCTT 59.324 45.455 0.00 0.00 0.00 4.68
1817 3051 3.126343 CGTCTTTACAAATAGCCCGCTTT 59.874 43.478 0.00 0.00 0.00 3.51
1818 3052 4.330620 CGTCTTTACAAATAGCCCGCTTTA 59.669 41.667 0.00 0.00 0.00 1.85
1819 3053 5.501897 CGTCTTTACAAATAGCCCGCTTTAG 60.502 44.000 0.00 0.00 0.00 1.85
1820 3054 4.334481 TCTTTACAAATAGCCCGCTTTAGC 59.666 41.667 0.00 0.00 37.78 3.09
1821 3055 1.389555 ACAAATAGCCCGCTTTAGCC 58.610 50.000 0.00 0.00 37.91 3.93
1822 3056 0.668535 CAAATAGCCCGCTTTAGCCC 59.331 55.000 0.00 0.00 37.91 5.19
1823 3057 0.818040 AAATAGCCCGCTTTAGCCCG 60.818 55.000 0.00 0.00 37.91 6.13
1824 3058 1.692173 AATAGCCCGCTTTAGCCCGA 61.692 55.000 0.00 0.00 37.91 5.14
1825 3059 1.481056 ATAGCCCGCTTTAGCCCGAT 61.481 55.000 0.00 0.00 37.91 4.18
1826 3060 0.828762 TAGCCCGCTTTAGCCCGATA 60.829 55.000 0.00 0.00 37.91 2.92
1827 3061 1.003718 GCCCGCTTTAGCCCGATAT 60.004 57.895 0.00 0.00 37.91 1.63
1828 3062 0.248289 GCCCGCTTTAGCCCGATATA 59.752 55.000 0.00 0.00 37.91 0.86
1829 3063 1.739371 GCCCGCTTTAGCCCGATATAG 60.739 57.143 0.00 0.00 37.91 1.31
1830 3064 1.641577 CCGCTTTAGCCCGATATAGC 58.358 55.000 0.00 0.00 37.91 2.97
1831 3065 1.204941 CCGCTTTAGCCCGATATAGCT 59.795 52.381 0.00 0.00 43.20 3.32
2635 3995 4.955811 ACTAACTGACATCACTCACCAA 57.044 40.909 0.00 0.00 0.00 3.67
2701 4065 1.069090 GGCGACGATTCTATGGGCA 59.931 57.895 0.00 0.00 0.00 5.36
2770 4134 2.532715 ATCAGGGCTGTGGTGGGT 60.533 61.111 0.00 0.00 0.00 4.51
2812 4176 1.681793 GACGATCTGGCCAAGCTAGTA 59.318 52.381 7.01 0.00 38.31 1.82
2830 4194 5.773680 GCTAGTATACCTCAAGATGGTGGTA 59.226 44.000 0.00 0.00 38.42 3.25
3070 4434 2.534903 GCTAACTCCATTCGGCGCC 61.535 63.158 19.07 19.07 0.00 6.53
3393 4757 5.067023 ACGTACTACCAGTCTATTACCTTGC 59.933 44.000 0.00 0.00 0.00 4.01
3396 4760 6.561519 ACTACCAGTCTATTACCTTGCAAT 57.438 37.500 0.00 0.00 0.00 3.56
3399 4763 6.561519 ACCAGTCTATTACCTTGCAATACT 57.438 37.500 0.00 0.00 0.00 2.12
3400 4764 6.349300 ACCAGTCTATTACCTTGCAATACTG 58.651 40.000 0.00 4.35 0.00 2.74
3469 7906 2.611292 GCATGATCCTAGTGCACTTGAC 59.389 50.000 27.06 16.69 38.68 3.18
3497 7937 6.375455 TCTTGGATGCCTAAAGATTTCAGTTC 59.625 38.462 0.00 0.00 0.00 3.01
3501 7941 7.233348 TGGATGCCTAAAGATTTCAGTTCTTTT 59.767 33.333 4.22 0.00 42.08 2.27
3502 7942 8.739972 GGATGCCTAAAGATTTCAGTTCTTTTA 58.260 33.333 4.22 0.00 42.08 1.52
3578 8018 0.035458 GGCTCATCCCTGGATTACCG 59.965 60.000 0.00 0.00 39.42 4.02
3611 8051 4.645863 TGGGGCTATAGTACGTATCTGA 57.354 45.455 0.00 0.00 0.00 3.27
3640 8249 5.766174 TCCCCATTATTAAAACGGAGTATGC 59.234 40.000 0.00 0.00 45.00 3.14
3666 9830 3.247442 GTGATGGTACGTCGTGATTTGA 58.753 45.455 8.47 0.00 0.00 2.69
3674 9838 4.141855 ACGTCGTGATTTGATTTGGTTC 57.858 40.909 0.00 0.00 0.00 3.62
3684 9848 5.998454 TTTGATTTGGTTCCGTACGTTTA 57.002 34.783 15.21 0.00 0.00 2.01
3700 9864 7.149524 CCGTACGTTTATTTGTTTTCACGTTAC 60.150 37.037 15.21 0.00 34.39 2.50
3704 9870 9.209297 ACGTTTATTTGTTTTCACGTTACTTAC 57.791 29.630 0.00 0.00 0.00 2.34
3724 9890 8.311395 ACTTACAGAGTATCATTCTTGGATGA 57.689 34.615 0.00 0.00 40.11 2.92
3728 9894 6.838090 ACAGAGTATCATTCTTGGATGAGAGA 59.162 38.462 0.00 0.00 39.26 3.10
3872 10063 0.967662 TTACCATCGACCGTTGGACA 59.032 50.000 21.91 9.48 38.13 4.02
3885 10109 2.430921 GGACAGGACGACGTGCAG 60.431 66.667 21.84 16.06 35.62 4.41
3915 10347 4.511826 AGTTTGAGCTAAAGGTCGAAGTTG 59.488 41.667 11.25 0.00 43.37 3.16
3990 10431 6.971184 GCTATTTTGTTCTCATCCAGAATGTG 59.029 38.462 0.00 0.00 43.33 3.21
3993 10434 6.713762 TTTGTTCTCATCCAGAATGTGTTT 57.286 33.333 0.00 0.00 43.33 2.83
4027 10469 1.293924 GATGTTCACGCTCTGGATGG 58.706 55.000 0.00 0.00 0.00 3.51
4032 10476 2.104859 CACGCTCTGGATGGTGCAG 61.105 63.158 0.00 0.00 37.15 4.41
4063 10507 4.495422 GGTGTACAAAGACTCATCGATGT 58.505 43.478 24.09 6.77 34.31 3.06
4109 10557 2.084610 TGATTCAAGCTGACACGGAG 57.915 50.000 0.00 0.00 0.00 4.63
4204 10659 0.885879 TGTCTAACGCGACAGATGGT 59.114 50.000 15.93 0.00 38.89 3.55
4206 10661 0.885879 TCTAACGCGACAGATGGTGT 59.114 50.000 15.93 0.00 44.49 4.16
4215 10670 2.159184 CGACAGATGGTGTAGCAGACAT 60.159 50.000 0.00 0.00 40.56 3.06
4238 10693 3.248495 TGAATTAATGGACGCGGTACA 57.752 42.857 12.47 6.58 0.00 2.90
4250 10705 0.243636 GCGGTACAAATTTGCAGGCT 59.756 50.000 18.12 0.78 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
495 524 0.817229 GCTGGAGGGCTCATGCTTAC 60.817 60.000 0.00 0.00 39.59 2.34
672 728 5.806818 TCTGGATGGTTTTGTATTTCGGTA 58.193 37.500 0.00 0.00 0.00 4.02
675 733 9.632807 TTAAATTCTGGATGGTTTTGTATTTCG 57.367 29.630 0.00 0.00 0.00 3.46
696 754 3.187112 TCCCTTTCCCGTCTCCTTAAAT 58.813 45.455 0.00 0.00 0.00 1.40
727 785 1.706287 GGTTCTCCGCCGATGCTTTC 61.706 60.000 0.00 0.00 34.43 2.62
742 800 1.516423 GAGCTCCTACGGTGGGTTC 59.484 63.158 10.54 3.86 0.00 3.62
751 809 3.138798 TCGTGGGCGAGCTCCTAC 61.139 66.667 8.47 2.77 42.81 3.18
797 856 2.169352 AGATGTTGGCTAGCTAGGTGTG 59.831 50.000 22.10 0.00 0.00 3.82
815 874 8.367660 TCTCTAATGGTACTGTTTTCTGAGAT 57.632 34.615 0.00 0.00 0.00 2.75
835 894 2.753452 CCGCTAGTGAACCTGTTCTCTA 59.247 50.000 16.55 16.55 41.75 2.43
851 910 3.321111 CCTTAGAGACTTATTGCCCGCTA 59.679 47.826 0.00 0.00 0.00 4.26
856 915 3.492829 CGTCCCCTTAGAGACTTATTGCC 60.493 52.174 2.01 0.00 0.00 4.52
881 940 1.806542 CTATGTGTTTGCTCCTGCGTT 59.193 47.619 0.00 0.00 43.34 4.84
895 954 2.440409 ACTCCTTTTGCTGCCTATGTG 58.560 47.619 0.00 0.00 0.00 3.21
928 990 5.237815 TCTTGTACATGTGTTAGAGCCTTG 58.762 41.667 9.11 0.00 0.00 3.61
1091 1162 2.038295 CCTTTGTTGCTCAGTCTCCTCT 59.962 50.000 0.00 0.00 0.00 3.69
1306 1377 4.767255 CCGGGTGCAGCAGTCCTC 62.767 72.222 19.06 0.00 0.00 3.71
1592 2593 3.552068 GGGAGCACATTAACTGCGTTTTT 60.552 43.478 0.00 0.00 39.79 1.94
1593 2594 2.030274 GGGAGCACATTAACTGCGTTTT 60.030 45.455 0.00 0.00 39.79 2.43
1594 2595 1.539827 GGGAGCACATTAACTGCGTTT 59.460 47.619 0.00 0.00 39.79 3.60
1595 2596 1.165270 GGGAGCACATTAACTGCGTT 58.835 50.000 2.14 0.02 39.79 4.84
1596 2597 0.676782 GGGGAGCACATTAACTGCGT 60.677 55.000 2.14 0.00 39.79 5.24
1597 2598 0.392998 AGGGGAGCACATTAACTGCG 60.393 55.000 2.14 0.00 39.79 5.18
1598 2599 1.098050 CAGGGGAGCACATTAACTGC 58.902 55.000 0.00 0.00 34.63 4.40
1599 2600 2.496899 ACAGGGGAGCACATTAACTG 57.503 50.000 0.00 0.00 0.00 3.16
1600 2601 4.862641 AATACAGGGGAGCACATTAACT 57.137 40.909 0.00 0.00 0.00 2.24
1601 2602 4.440112 GCAAATACAGGGGAGCACATTAAC 60.440 45.833 0.00 0.00 0.00 2.01
1602 2603 3.699038 GCAAATACAGGGGAGCACATTAA 59.301 43.478 0.00 0.00 0.00 1.40
1603 2604 3.287222 GCAAATACAGGGGAGCACATTA 58.713 45.455 0.00 0.00 0.00 1.90
1604 2605 2.102578 GCAAATACAGGGGAGCACATT 58.897 47.619 0.00 0.00 0.00 2.71
1605 2606 1.005805 TGCAAATACAGGGGAGCACAT 59.994 47.619 0.00 0.00 0.00 3.21
1606 2607 0.403655 TGCAAATACAGGGGAGCACA 59.596 50.000 0.00 0.00 0.00 4.57
1607 2608 1.767759 ATGCAAATACAGGGGAGCAC 58.232 50.000 0.00 0.00 34.54 4.40
1608 2609 2.101783 CAATGCAAATACAGGGGAGCA 58.898 47.619 0.00 0.00 36.34 4.26
1609 2610 2.102578 ACAATGCAAATACAGGGGAGC 58.897 47.619 0.00 0.00 0.00 4.70
1610 2611 3.091545 ACACAATGCAAATACAGGGGAG 58.908 45.455 0.00 0.00 0.00 4.30
1611 2612 3.168035 ACACAATGCAAATACAGGGGA 57.832 42.857 0.00 0.00 0.00 4.81
1612 2613 5.596836 AATACACAATGCAAATACAGGGG 57.403 39.130 0.00 0.00 0.00 4.79
1613 2614 6.866480 AGAAATACACAATGCAAATACAGGG 58.134 36.000 0.00 0.00 0.00 4.45
1716 2950 6.783708 AAAACTATGGTGTTTTCAGACCAA 57.216 33.333 0.00 0.00 43.95 3.67
1773 3007 1.543208 CCATTTAGCGGCATCCTGCTA 60.543 52.381 1.45 0.00 44.28 3.49
1780 3014 0.178068 AGACGACCATTTAGCGGCAT 59.822 50.000 1.45 0.00 35.00 4.40
1797 3031 4.334481 GCTAAAGCGGGCTATTTGTAAAGA 59.666 41.667 0.00 0.00 0.00 2.52
1811 3045 1.204941 AGCTATATCGGGCTAAAGCGG 59.795 52.381 0.00 0.00 43.26 5.52
1812 3046 2.531206 GAGCTATATCGGGCTAAAGCG 58.469 52.381 0.00 0.00 43.26 4.68
1813 3047 2.735762 CGGAGCTATATCGGGCTAAAGC 60.736 54.545 0.00 0.00 39.05 3.51
1814 3048 3.152261 CGGAGCTATATCGGGCTAAAG 57.848 52.381 0.00 0.00 39.05 1.85
1952 3186 4.067972 TGTGTGGGTCTTGTTCTTCTAC 57.932 45.455 0.00 0.00 0.00 2.59
2571 3922 7.493645 TCAATCAAGACATGACATGATGTAGAC 59.506 37.037 22.19 4.53 41.93 2.59
2606 3959 6.870439 TGAGTGATGTCAGTTAGTTGATCTTG 59.130 38.462 0.00 0.00 0.00 3.02
2609 3962 5.578727 GGTGAGTGATGTCAGTTAGTTGATC 59.421 44.000 0.00 0.00 0.00 2.92
2610 3963 5.012046 TGGTGAGTGATGTCAGTTAGTTGAT 59.988 40.000 0.00 0.00 0.00 2.57
2611 3964 4.343814 TGGTGAGTGATGTCAGTTAGTTGA 59.656 41.667 0.00 0.00 0.00 3.18
2680 4044 0.663568 CCCATAGAATCGTCGCCGTC 60.664 60.000 0.00 0.00 35.01 4.79
2701 4065 3.329889 TGGGTCAGCTCCGCCATT 61.330 61.111 0.00 0.00 0.00 3.16
2718 4082 3.283751 CTCTCCAGTAGTCGTGGATTCT 58.716 50.000 0.00 0.00 43.33 2.40
2770 4134 1.974875 TCGCACCCTCTCGTTGCTA 60.975 57.895 0.00 0.00 0.00 3.49
2812 4176 5.036916 TCCTTTACCACCATCTTGAGGTAT 58.963 41.667 0.00 0.00 37.23 2.73
2842 4206 2.942796 CGCTGGTGGGTGCAGTCTA 61.943 63.158 0.00 0.00 0.00 2.59
2843 4207 4.320456 CGCTGGTGGGTGCAGTCT 62.320 66.667 0.00 0.00 0.00 3.24
2845 4209 4.626081 GTCGCTGGTGGGTGCAGT 62.626 66.667 0.00 0.00 0.00 4.40
3018 4382 2.035321 CCCTTGAAGTCTATCTCGCTCC 59.965 54.545 0.00 0.00 0.00 4.70
3177 4541 0.534652 GCCTTCCTCCTGCATGCTAG 60.535 60.000 20.33 13.98 0.00 3.42
3365 4729 6.989169 AGGTAATAGACTGGTAGTACGTACAG 59.011 42.308 26.55 17.16 32.62 2.74
3370 4734 5.066893 TGCAAGGTAATAGACTGGTAGTACG 59.933 44.000 0.00 0.00 0.00 3.67
3393 4757 5.691754 GCTTGTGAAGAAAAACCCAGTATTG 59.308 40.000 0.00 0.00 0.00 1.90
3396 4760 4.532834 AGCTTGTGAAGAAAAACCCAGTA 58.467 39.130 0.00 0.00 0.00 2.74
3399 4763 2.693074 GGAGCTTGTGAAGAAAAACCCA 59.307 45.455 0.00 0.00 0.00 4.51
3400 4764 2.959030 AGGAGCTTGTGAAGAAAAACCC 59.041 45.455 0.00 0.00 0.00 4.11
3469 7906 5.595542 TGAAATCTTTAGGCATCCAAGATGG 59.404 40.000 6.51 0.00 37.34 3.51
3534 7974 6.402550 CCAACCTCATCTACTTTCAATGAACG 60.403 42.308 0.00 0.00 0.00 3.95
3578 8018 2.273588 TAGCCCCAATTACCCGCACC 62.274 60.000 0.00 0.00 0.00 5.01
3587 8027 6.014647 TCAGATACGTACTATAGCCCCAATT 58.985 40.000 0.00 0.00 0.00 2.32
3611 8051 6.157471 ACTCCGTTTTAATAATGGGGACTAGT 59.843 38.462 12.65 0.00 0.00 2.57
3640 8249 0.387622 ACGACGTACCATCACAACCG 60.388 55.000 0.00 0.00 0.00 4.44
3644 8253 2.990514 CAAATCACGACGTACCATCACA 59.009 45.455 0.00 0.00 0.00 3.58
3666 9830 6.316440 ACAAATAAACGTACGGAACCAAAT 57.684 33.333 21.06 0.23 0.00 2.32
3674 9838 5.196825 ACGTGAAAACAAATAAACGTACGG 58.803 37.500 21.06 1.80 41.94 4.02
3684 9848 8.205131 ACTCTGTAAGTAACGTGAAAACAAAT 57.795 30.769 0.00 0.00 36.07 2.32
3700 9864 8.637099 TCTCATCCAAGAATGATACTCTGTAAG 58.363 37.037 0.00 0.00 35.21 2.34
3704 9870 7.287512 TCTCTCATCCAAGAATGATACTCTG 57.712 40.000 0.00 0.00 35.21 3.35
3724 9890 9.790344 CACCTATCCAAAAAGATGATATTCTCT 57.210 33.333 0.00 0.00 0.00 3.10
3788 9973 8.030913 ACCCTTTATAAATAACGTGATCCTCT 57.969 34.615 0.00 0.00 0.00 3.69
3838 10023 9.893305 GGTCGATGGTAATTTCCTTAATTAATG 57.107 33.333 2.53 0.00 39.70 1.90
3847 10032 3.267483 CAACGGTCGATGGTAATTTCCT 58.733 45.455 2.53 0.00 0.00 3.36
3863 10048 2.430244 CGTCGTCCTGTCCAACGG 60.430 66.667 0.00 0.00 39.31 4.44
3872 10063 1.080705 GCTAACTGCACGTCGTCCT 60.081 57.895 0.00 0.00 42.31 3.85
3909 10341 2.640316 ACCACTGGTCTTCCAACTTC 57.360 50.000 0.00 0.00 43.81 3.01
3990 10431 7.115378 GTGAACATCATGATTTGTCCTTCAAAC 59.885 37.037 5.16 0.00 46.77 2.93
3993 10434 5.106594 CGTGAACATCATGATTTGTCCTTCA 60.107 40.000 5.16 2.10 35.46 3.02
4027 10469 1.433053 TACACCGTGTTGCACTGCAC 61.433 55.000 9.98 0.03 38.71 4.57
4032 10476 1.666700 TCTTTGTACACCGTGTTGCAC 59.333 47.619 9.98 2.74 0.00 4.57
4063 10507 0.605319 GTGGGCCGTTCATTGACTGA 60.605 55.000 0.00 0.00 0.00 3.41
4109 10557 0.438830 GTCGTCACCGAAAGTGCATC 59.561 55.000 0.00 0.00 46.26 3.91
4153 10601 2.268298 CCATCCTTTGGTACGAAGTCG 58.732 52.381 0.00 0.00 40.99 4.18
4204 10659 9.056005 GTCCATTAATTCATAATGTCTGCTACA 57.944 33.333 7.26 0.00 46.32 2.74
4206 10661 7.095229 GCGTCCATTAATTCATAATGTCTGCTA 60.095 37.037 7.26 0.00 46.32 3.49
4215 10670 5.358090 TGTACCGCGTCCATTAATTCATAA 58.642 37.500 4.92 0.00 0.00 1.90
4227 10682 0.238817 TGCAAATTTGTACCGCGTCC 59.761 50.000 19.03 0.40 0.00 4.79
4238 10693 0.686789 GGAACCCAGCCTGCAAATTT 59.313 50.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.