Multiple sequence alignment - TraesCS4D01G028100

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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 TraesCS4D01G028100 chr4D 100.000 4423 0 0 1 4423 12525369 12529791 0.000000e+00 8168.0
1 TraesCS4D01G028100 chr4D 94.334 1712 79 5 2003 3711 12535562 12537258 0.000000e+00 2608.0
2 TraesCS4D01G028100 chr4D 85.120 457 52 7 3978 4421 12537339 12537792 1.880000e-123 453.0
3 TraesCS4D01G028100 chr4B 89.859 3757 199 59 740 4423 22877512 22881159 0.000000e+00 4660.0
4 TraesCS4D01G028100 chr4B 84.211 456 56 7 3978 4420 22892409 22892861 3.160000e-116 429.0
5 TraesCS4D01G028100 chr4B 82.430 461 57 15 206 657 22876858 22877303 8.980000e-102 381.0
6 TraesCS4D01G028100 chr4B 85.271 129 11 6 1484 1611 22878501 22878622 4.640000e-25 126.0
7 TraesCS4D01G028100 chr4B 89.831 59 4 2 1357 1415 135817032 135816976 1.710000e-09 75.0
8 TraesCS4D01G028100 chr4B 100.000 29 0 0 1 29 484576279 484576307 2.000000e-03 54.7
9 TraesCS4D01G028100 chr4A 93.403 2577 113 24 1368 3933 590105079 590102549 0.000000e+00 3764.0
10 TraesCS4D01G028100 chr4A 83.745 1335 90 48 1 1258 590106480 590105196 0.000000e+00 1146.0
11 TraesCS4D01G028100 chr4A 86.364 66 3 5 1357 1419 405575806 405575744 2.860000e-07 67.6
12 TraesCS4D01G028100 chr4A 100.000 29 0 0 1 29 25567216 25567188 2.000000e-03 54.7
13 TraesCS4D01G028100 chrUn 93.144 1692 93 11 2003 3684 354805316 354803638 0.000000e+00 2460.0
14 TraesCS4D01G028100 chrUn 94.286 35 2 0 486 520 338584404 338584370 2.000000e-03 54.7
15 TraesCS4D01G028100 chrUn 96.875 32 1 0 486 517 370097326 370097357 2.000000e-03 54.7
16 TraesCS4D01G028100 chrUn 96.875 32 1 0 486 517 371345838 371345869 2.000000e-03 54.7
17 TraesCS4D01G028100 chrUn 94.286 35 2 0 486 520 436309692 436309658 2.000000e-03 54.7
18 TraesCS4D01G028100 chr2B 87.603 121 15 0 3861 3981 24208255 24208375 1.660000e-29 141.0
19 TraesCS4D01G028100 chr2B 89.655 58 4 2 1357 1414 166470850 166470905 6.140000e-09 73.1
20 TraesCS4D01G028100 chr5B 86.777 121 15 1 3859 3979 689263875 689263994 2.780000e-27 134.0
21 TraesCS4D01G028100 chr3D 87.826 115 13 1 3867 3981 89960921 89960808 2.780000e-27 134.0
22 TraesCS4D01G028100 chr6B 84.328 134 17 3 3852 3982 306798722 306798854 1.290000e-25 128.0
23 TraesCS4D01G028100 chr6D 85.714 119 17 0 3861 3979 384221045 384220927 4.640000e-25 126.0
24 TraesCS4D01G028100 chr6D 92.308 52 2 2 1357 1408 365846932 365846883 6.140000e-09 73.1
25 TraesCS4D01G028100 chr3B 85.833 120 16 1 3861 3980 88422029 88422147 4.640000e-25 126.0
26 TraesCS4D01G028100 chr3B 100.000 29 0 0 1 29 494814232 494814260 2.000000e-03 54.7
27 TraesCS4D01G028100 chr3B 90.000 40 4 0 2 41 650077509 650077470 8.000000e-03 52.8
28 TraesCS4D01G028100 chr5A 85.124 121 16 2 3861 3980 355470714 355470595 6.010000e-24 122.0
29 TraesCS4D01G028100 chr5A 92.308 52 2 2 1357 1408 174593682 174593731 6.140000e-09 73.1
30 TraesCS4D01G028100 chr5A 100.000 29 0 0 1 29 588102412 588102384 2.000000e-03 54.7
31 TraesCS4D01G028100 chr7D 89.655 58 4 2 1357 1414 265703393 265703338 6.140000e-09 73.1
32 TraesCS4D01G028100 chr7A 89.655 58 4 2 1357 1414 290922173 290922118 6.140000e-09 73.1
33 TraesCS4D01G028100 chr1B 92.308 52 2 2 1357 1408 487409011 487408962 6.140000e-09 73.1
34 TraesCS4D01G028100 chr1B 100.000 29 0 0 1 29 218945724 218945696 2.000000e-03 54.7
35 TraesCS4D01G028100 chr1B 94.286 35 2 0 486 520 677778557 677778523 2.000000e-03 54.7
36 TraesCS4D01G028100 chr1B 94.286 35 2 0 486 520 677822602 677822568 2.000000e-03 54.7
37 TraesCS4D01G028100 chr1B 94.286 35 2 0 486 520 677868945 677868911 2.000000e-03 54.7
38 TraesCS4D01G028100 chr2D 90.476 42 2 2 1 41 95177398 95177438 2.000000e-03 54.7
39 TraesCS4D01G028100 chr5D 100.000 28 0 0 2 29 243473217 243473244 8.000000e-03 52.8


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 TraesCS4D01G028100 chr4D 12525369 12529791 4422 False 8168.000000 8168 100.000000 1 4423 1 chr4D.!!$F1 4422
1 TraesCS4D01G028100 chr4D 12535562 12537792 2230 False 1530.500000 2608 89.727000 2003 4421 2 chr4D.!!$F2 2418
2 TraesCS4D01G028100 chr4B 22876858 22881159 4301 False 1722.333333 4660 85.853333 206 4423 3 chr4B.!!$F3 4217
3 TraesCS4D01G028100 chr4A 590102549 590106480 3931 True 2455.000000 3764 88.574000 1 3933 2 chr4A.!!$R3 3932
4 TraesCS4D01G028100 chrUn 354803638 354805316 1678 True 2460.000000 2460 93.144000 2003 3684 1 chrUn.!!$R2 1681

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
530 537 0.384309 GGACGTGTCACACTCTCACA 59.616 55.0 6.33 0.00 31.34 3.58 F
560 567 0.462581 CACCATCACCACCATCGAGG 60.463 60.0 0.00 0.00 45.67 4.63 F
1675 1927 0.529773 TTTATCTACTGGGCGCGCAG 60.530 55.0 42.14 42.14 0.00 5.18 F
1696 1948 0.321653 AGTGCTAAGAAACCGCCAGG 60.322 55.0 0.00 0.00 45.13 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 1931 0.321298 GACCTGGCGGTTTCTTAGCA 60.321 55.000 0.0 0.0 45.73 3.49 R
1680 1932 1.359459 CGACCTGGCGGTTTCTTAGC 61.359 60.000 0.0 0.0 45.73 3.09 R
2708 2982 0.248825 CTCATCAAGTCGAGAGGCGG 60.249 60.000 0.0 0.0 43.49 6.13 R
3590 3869 2.158827 ACAACACAGTACATCAGCACCA 60.159 45.455 0.0 0.0 0.00 4.17 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 30 3.237746 TGTTGATGGCTTTGATTTCCCA 58.762 40.909 0.00 0.00 0.00 4.37
33 34 3.839490 TGATGGCTTTGATTTCCCATGTT 59.161 39.130 0.00 0.00 38.15 2.71
60 61 0.533755 GAATGGTCCCGGCAGATCAG 60.534 60.000 0.00 0.00 28.35 2.90
65 66 1.758514 TCCCGGCAGATCAGTCCTC 60.759 63.158 0.00 0.00 0.00 3.71
72 73 1.756430 CAGATCAGTCCTCCGTGAGA 58.244 55.000 0.00 0.00 0.00 3.27
73 74 2.305928 CAGATCAGTCCTCCGTGAGAT 58.694 52.381 0.00 0.00 0.00 2.75
88 89 4.452455 CCGTGAGATAGAAGTGCTTTGTTT 59.548 41.667 0.00 0.00 0.00 2.83
90 91 6.074005 CGTGAGATAGAAGTGCTTTGTTTTC 58.926 40.000 0.00 0.00 0.00 2.29
100 101 2.223711 TGCTTTGTTTTCTTTCCGCCTC 60.224 45.455 0.00 0.00 0.00 4.70
107 108 2.010145 TTCTTTCCGCCTCGAAGATG 57.990 50.000 0.00 0.00 33.89 2.90
114 115 2.202932 CCTCGAAGATGGTGGCGG 60.203 66.667 0.00 0.00 33.89 6.13
119 120 0.878416 CGAAGATGGTGGCGGAAAAA 59.122 50.000 0.00 0.00 0.00 1.94
120 121 1.401018 CGAAGATGGTGGCGGAAAAAC 60.401 52.381 0.00 0.00 0.00 2.43
126 127 1.249407 GGTGGCGGAAAAACCATGTA 58.751 50.000 0.00 0.00 38.46 2.29
132 133 5.575218 GTGGCGGAAAAACCATGTAAATTAG 59.425 40.000 0.00 0.00 38.46 1.73
138 139 7.555965 GGAAAAACCATGTAAATTAGAGGCAT 58.444 34.615 0.00 0.00 38.79 4.40
140 141 9.736023 GAAAAACCATGTAAATTAGAGGCATAG 57.264 33.333 0.00 0.00 0.00 2.23
161 162 8.573885 GCATAGGTTTTAGGGTAAAATATGACC 58.426 37.037 12.66 4.20 39.56 4.02
164 165 7.123383 AGGTTTTAGGGTAAAATATGACCAGG 58.877 38.462 4.57 0.00 39.56 4.45
165 166 6.322969 GGTTTTAGGGTAAAATATGACCAGGG 59.677 42.308 0.00 0.00 39.56 4.45
168 169 2.177016 GGGTAAAATATGACCAGGGGCT 59.823 50.000 0.00 0.00 37.47 5.19
171 172 1.607225 AAATATGACCAGGGGCTCCA 58.393 50.000 4.79 0.00 34.83 3.86
184 185 1.521616 GCTCCAGAGAGAGGCAAGG 59.478 63.158 0.00 0.00 43.39 3.61
240 241 2.436115 GGGTCAGGCCGTGTAAGC 60.436 66.667 0.00 0.00 38.44 3.09
294 295 1.277580 CCCTGGCTCTCTTCCCATGT 61.278 60.000 0.00 0.00 0.00 3.21
343 349 6.235664 ACTTTTCCAAGCTCCGAATAACTAA 58.764 36.000 0.00 0.00 32.57 2.24
354 360 7.769044 AGCTCCGAATAACTAATTTCTTTGCTA 59.231 33.333 0.00 0.00 0.00 3.49
356 362 7.902032 TCCGAATAACTAATTTCTTTGCTACG 58.098 34.615 0.00 0.00 0.00 3.51
399 405 7.654022 TTTTTGTAGTTTTCTGACAATCCCT 57.346 32.000 0.00 0.00 33.33 4.20
400 406 6.633500 TTTGTAGTTTTCTGACAATCCCTG 57.367 37.500 0.00 0.00 33.33 4.45
402 408 3.515602 AGTTTTCTGACAATCCCTGCT 57.484 42.857 0.00 0.00 0.00 4.24
404 410 4.985538 AGTTTTCTGACAATCCCTGCTTA 58.014 39.130 0.00 0.00 0.00 3.09
452 459 9.911788 AGACAAAGATATAAGAATGGTGTGATT 57.088 29.630 0.00 0.00 0.00 2.57
463 470 7.303634 AGAATGGTGTGATTATCGTGTAAAC 57.696 36.000 0.00 0.00 0.00 2.01
468 475 7.548967 TGGTGTGATTATCGTGTAAACTATGA 58.451 34.615 0.00 0.00 0.00 2.15
469 476 7.704899 TGGTGTGATTATCGTGTAAACTATGAG 59.295 37.037 0.00 0.00 0.00 2.90
516 523 8.561738 AAGAAATAGTGATGTAAAATGGACGT 57.438 30.769 0.00 0.00 0.00 4.34
517 524 7.974675 AGAAATAGTGATGTAAAATGGACGTG 58.025 34.615 0.00 0.00 0.00 4.49
525 532 3.805422 TGTAAAATGGACGTGTCACACTC 59.195 43.478 6.33 2.73 31.34 3.51
526 533 2.910688 AAATGGACGTGTCACACTCT 57.089 45.000 6.33 0.00 31.34 3.24
528 535 1.328279 ATGGACGTGTCACACTCTCA 58.672 50.000 6.33 1.50 31.34 3.27
530 537 0.384309 GGACGTGTCACACTCTCACA 59.616 55.000 6.33 0.00 31.34 3.58
534 541 1.588404 CGTGTCACACTCTCACAACAC 59.412 52.381 6.33 0.00 34.98 3.32
560 567 0.462581 CACCATCACCACCATCGAGG 60.463 60.000 0.00 0.00 45.67 4.63
632 643 2.284190 GATGTTGCCTCTCACCTTAGC 58.716 52.381 0.00 0.00 0.00 3.09
646 658 2.040412 ACCTTAGCTAAACAAGGCAGCT 59.960 45.455 12.14 0.55 44.39 4.24
647 659 2.680339 CCTTAGCTAAACAAGGCAGCTC 59.320 50.000 7.74 0.00 44.32 4.09
775 913 3.892588 TCCATGGTTTCCCTTTGTGTAAC 59.107 43.478 12.58 0.00 37.35 2.50
781 919 4.756135 GGTTTCCCTTTGTGTAACGTGATA 59.244 41.667 0.00 0.00 42.39 2.15
810 948 1.679944 CGACTTGATCCATGGTTGCCT 60.680 52.381 12.58 0.00 0.00 4.75
978 1151 1.332997 GCCAAGATCCAAGAAGCATCG 59.667 52.381 0.00 0.00 0.00 3.84
1105 1296 0.824109 CAAGGTACTCAGATCCGCCA 59.176 55.000 0.00 0.00 38.49 5.69
1112 1303 1.075301 TCAGATCCGCCATCTCCCA 60.075 57.895 0.00 0.00 40.20 4.37
1270 1471 2.203153 GGTTCCGCTGGTGTGTGT 60.203 61.111 0.00 0.00 0.00 3.72
1271 1472 2.542907 GGTTCCGCTGGTGTGTGTG 61.543 63.158 0.00 0.00 0.00 3.82
1324 1529 5.867903 TTGTTGGGTTCTGAAAATGATGT 57.132 34.783 0.00 0.00 0.00 3.06
1326 1531 3.940209 TGGGTTCTGAAAATGATGTGC 57.060 42.857 0.00 0.00 0.00 4.57
1410 1647 6.934083 TGAAAGGCTTTGTTTTTCTTGTTCTT 59.066 30.769 18.79 0.00 33.21 2.52
1414 1651 6.710295 AGGCTTTGTTTTTCTTGTTCTTGTTT 59.290 30.769 0.00 0.00 0.00 2.83
1415 1652 6.796552 GGCTTTGTTTTTCTTGTTCTTGTTTG 59.203 34.615 0.00 0.00 0.00 2.93
1416 1653 6.796552 GCTTTGTTTTTCTTGTTCTTGTTTGG 59.203 34.615 0.00 0.00 0.00 3.28
1417 1654 7.519809 GCTTTGTTTTTCTTGTTCTTGTTTGGT 60.520 33.333 0.00 0.00 0.00 3.67
1418 1655 6.777526 TGTTTTTCTTGTTCTTGTTTGGTG 57.222 33.333 0.00 0.00 0.00 4.17
1470 1720 4.004982 GCTGATGAAACCCATTTGCATTT 58.995 39.130 0.00 0.00 35.17 2.32
1480 1730 8.694975 AAACCCATTTGCATTTTAAAACAAAC 57.305 26.923 15.14 2.83 35.06 2.93
1493 1743 4.670896 AAAACAAACTGAATGGTCTGGG 57.329 40.909 0.00 0.00 0.00 4.45
1520 1770 8.994429 AACTTATAAGCTGATGAATAGATCGG 57.006 34.615 12.54 0.00 32.57 4.18
1552 1804 3.808834 AAAGACGAATTTCCCCTTCCT 57.191 42.857 0.00 0.00 0.00 3.36
1554 1806 3.808834 AGACGAATTTCCCCTTCCTTT 57.191 42.857 0.00 0.00 0.00 3.11
1555 1807 3.421844 AGACGAATTTCCCCTTCCTTTG 58.578 45.455 0.00 0.00 0.00 2.77
1565 1817 1.228124 CTTCCTTTGCCGTGGGACA 60.228 57.895 0.00 0.00 0.00 4.02
1577 1829 3.004944 GCCGTGGGACAGAATTTTACAAA 59.995 43.478 0.00 0.00 41.80 2.83
1578 1830 4.794169 CCGTGGGACAGAATTTTACAAAG 58.206 43.478 0.00 0.00 41.80 2.77
1579 1831 4.226761 CGTGGGACAGAATTTTACAAAGC 58.773 43.478 0.00 0.00 41.80 3.51
1621 1873 7.882791 ACTATTGTTCCTGTATGATGTGTTCAA 59.117 33.333 0.00 0.00 38.03 2.69
1628 1880 8.837788 TCCTGTATGATGTGTTCAATATGATC 57.162 34.615 0.00 0.00 38.03 2.92
1631 1883 9.410556 CTGTATGATGTGTTCAATATGATCGTA 57.589 33.333 0.00 0.00 38.03 3.43
1668 1920 7.336679 TGATGTGTTCACATTTTATCTACTGGG 59.663 37.037 17.64 0.00 0.00 4.45
1675 1927 0.529773 TTTATCTACTGGGCGCGCAG 60.530 55.000 42.14 42.14 0.00 5.18
1692 1944 2.882742 CAGAAGTGCTAAGAAACCGC 57.117 50.000 0.00 0.00 0.00 5.68
1693 1945 1.464997 CAGAAGTGCTAAGAAACCGCC 59.535 52.381 0.00 0.00 0.00 6.13
1694 1946 1.071699 AGAAGTGCTAAGAAACCGCCA 59.928 47.619 0.00 0.00 0.00 5.69
1695 1947 1.464997 GAAGTGCTAAGAAACCGCCAG 59.535 52.381 0.00 0.00 0.00 4.85
1696 1948 0.321653 AGTGCTAAGAAACCGCCAGG 60.322 55.000 0.00 0.00 45.13 4.45
1755 2021 5.559770 TGGATAACTGACAAGCTGATGAAA 58.440 37.500 0.00 0.00 0.00 2.69
1764 2030 5.106948 TGACAAGCTGATGAAAAGATCGAAC 60.107 40.000 0.00 0.00 0.00 3.95
1817 2083 2.747446 CCCGTGGGACAGAATTTTACTG 59.253 50.000 0.00 0.00 41.80 2.74
1878 2144 5.123186 TCGATGTGTTCACATTTTATCCACC 59.877 40.000 17.64 3.49 0.00 4.61
1879 2145 5.106357 CGATGTGTTCACATTTTATCCACCA 60.106 40.000 17.64 0.00 0.00 4.17
1904 2170 2.357517 AGAAACCACCAGCTCGCG 60.358 61.111 0.00 0.00 0.00 5.87
1972 2238 2.609459 GGCAATCAAGACATCCACTACG 59.391 50.000 0.00 0.00 0.00 3.51
1979 2245 7.772332 ATCAAGACATCCACTACGATTTTAC 57.228 36.000 0.00 0.00 0.00 2.01
1986 2252 6.869913 ACATCCACTACGATTTTACGAGAAAA 59.130 34.615 0.00 0.00 37.03 2.29
1987 2253 7.385752 ACATCCACTACGATTTTACGAGAAAAA 59.614 33.333 0.00 0.00 37.03 1.94
2029 2295 3.388024 TGAGTAACTGTGCACTTTCTCCT 59.612 43.478 19.41 6.79 0.00 3.69
2036 2302 4.276926 ACTGTGCACTTTCTCCTGAATTTC 59.723 41.667 19.41 0.00 31.56 2.17
2074 2340 8.388853 GCTAAGTTTTCCTTATAACACTGTAGC 58.611 37.037 0.00 0.00 35.14 3.58
2113 2386 5.531634 TGTTGACAATTTCAAGAAGATGGC 58.468 37.500 0.00 0.00 45.23 4.40
2188 2461 5.527951 ACAAGAACATGAAAAATGCATTGCA 59.472 32.000 13.82 14.72 44.86 4.08
2229 2502 3.140325 TCCCATTCCAAGTGTCAAGTC 57.860 47.619 0.00 0.00 0.00 3.01
2233 2506 0.468226 TTCCAAGTGTCAAGTCGCCT 59.532 50.000 0.00 0.00 0.00 5.52
2234 2507 1.334160 TCCAAGTGTCAAGTCGCCTA 58.666 50.000 0.00 0.00 0.00 3.93
2235 2508 1.272490 TCCAAGTGTCAAGTCGCCTAG 59.728 52.381 0.00 0.00 0.00 3.02
2334 2607 9.556030 CTAAAGTGCTTATTAGTGGCTTAAAAC 57.444 33.333 0.00 0.00 0.00 2.43
2335 2608 7.519032 AAGTGCTTATTAGTGGCTTAAAACA 57.481 32.000 0.00 0.00 0.00 2.83
2346 2619 3.243941 TGGCTTAAAACAGCTCGTCACTA 60.244 43.478 0.00 0.00 39.97 2.74
2347 2620 3.368236 GGCTTAAAACAGCTCGTCACTAG 59.632 47.826 0.00 0.00 39.97 2.57
2370 2643 6.798766 AGGATTTCTCCATCTTCCTCTTTTT 58.201 36.000 0.00 0.00 44.79 1.94
2554 2828 6.317391 AGAGCATTAACAGGAGAAATACTTGC 59.683 38.462 0.00 0.00 0.00 4.01
2712 2986 6.679327 AGAAACTGTAAAAAGATATCCGCC 57.321 37.500 0.00 0.00 0.00 6.13
2981 3258 1.401552 TCTTGAAGCACAACACTGCAC 59.598 47.619 0.00 0.00 39.86 4.57
3011 3288 7.279536 GCATCTGAACTCATGATTCAAAGACTA 59.720 37.037 16.29 4.83 35.70 2.59
3032 3309 7.229506 AGACTAGCTAAATGCAGTTCTTGTTTT 59.770 33.333 1.02 0.00 45.94 2.43
3039 3316 3.772932 TGCAGTTCTTGTTTTGCTGAAG 58.227 40.909 0.00 0.00 37.45 3.02
3058 3335 5.063204 TGAAGGAGTTATGTGTTTGTGAGG 58.937 41.667 0.00 0.00 0.00 3.86
3087 3364 8.677148 AAACATGCATCCTATTAGTATCGTTT 57.323 30.769 0.00 0.00 0.00 3.60
3094 3371 8.230486 GCATCCTATTAGTATCGTTTTCAATGG 58.770 37.037 0.00 0.00 0.00 3.16
3112 3389 3.134574 TGGTTAGGCTTGTAACACAGG 57.865 47.619 0.00 0.00 35.00 4.00
3263 3540 5.273944 GTCAAGTTTGGTGTCATCTTCAAC 58.726 41.667 0.00 0.00 0.00 3.18
3590 3869 3.197265 GCTTGCATGGTTGTTGAAACTT 58.803 40.909 1.34 0.00 0.00 2.66
3673 3952 5.178797 GCCACTGTGTTATTGAGAGTGTAT 58.821 41.667 7.08 0.00 33.60 2.29
3995 4275 4.261656 GGGAGTATTAGTCATGACTCGTGG 60.262 50.000 31.09 0.00 42.54 4.94
4097 4387 4.646492 GGCAAAGGATAATCAGTTCATGGT 59.354 41.667 0.00 0.00 0.00 3.55
4146 4436 0.611200 TGATCCACGACGTTGGGATT 59.389 50.000 17.98 3.84 41.39 3.01
4174 4464 3.010138 TCCGACCTTTTGAGGGATTCATT 59.990 43.478 0.00 0.00 35.27 2.57
4272 4563 9.997172 TGATCATGTCTGGTTCTACCTATATAT 57.003 33.333 0.00 0.00 39.58 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.081531 TGGGAAATCAAAGCCATCAACATC 60.082 41.667 0.00 0.00 0.00 3.06
9 10 3.959535 TGGGAAATCAAAGCCATCAAC 57.040 42.857 0.00 0.00 0.00 3.18
29 30 0.546598 GACCATTCCCCTCCGAACAT 59.453 55.000 0.00 0.00 0.00 2.71
60 61 2.223618 GCACTTCTATCTCACGGAGGAC 60.224 54.545 1.76 0.00 0.00 3.85
65 66 3.589988 ACAAAGCACTTCTATCTCACGG 58.410 45.455 0.00 0.00 0.00 4.94
72 73 6.438763 CGGAAAGAAAACAAAGCACTTCTAT 58.561 36.000 0.00 0.00 0.00 1.98
73 74 5.732247 GCGGAAAGAAAACAAAGCACTTCTA 60.732 40.000 0.00 0.00 0.00 2.10
88 89 1.405526 CCATCTTCGAGGCGGAAAGAA 60.406 52.381 0.00 0.00 0.00 2.52
90 91 0.108138 ACCATCTTCGAGGCGGAAAG 60.108 55.000 9.36 0.00 0.00 2.62
100 101 0.878416 TTTTTCCGCCACCATCTTCG 59.122 50.000 0.00 0.00 0.00 3.79
107 108 1.249407 TACATGGTTTTTCCGCCACC 58.751 50.000 0.00 0.00 37.62 4.61
114 115 9.736023 CTATGCCTCTAATTTACATGGTTTTTC 57.264 33.333 0.00 0.00 0.00 2.29
119 120 6.515512 ACCTATGCCTCTAATTTACATGGT 57.484 37.500 0.00 0.00 0.00 3.55
120 121 7.823745 AAACCTATGCCTCTAATTTACATGG 57.176 36.000 0.00 0.00 0.00 3.66
126 127 6.981737 ACCCTAAAACCTATGCCTCTAATTT 58.018 36.000 0.00 0.00 0.00 1.82
132 133 8.793592 CATATTTTACCCTAAAACCTATGCCTC 58.206 37.037 0.00 0.00 40.12 4.70
138 139 8.276477 CCTGGTCATATTTTACCCTAAAACCTA 58.724 37.037 0.00 0.00 40.12 3.08
140 141 6.322969 CCCTGGTCATATTTTACCCTAAAACC 59.677 42.308 0.00 0.00 40.12 3.27
161 162 1.761667 CCTCTCTCTGGAGCCCCTG 60.762 68.421 0.00 0.00 39.31 4.45
164 165 1.970352 CTTGCCTCTCTCTGGAGCCC 61.970 65.000 0.00 0.00 39.31 5.19
165 166 1.521616 CTTGCCTCTCTCTGGAGCC 59.478 63.158 0.00 0.00 39.31 4.70
168 169 0.906756 CACCCTTGCCTCTCTCTGGA 60.907 60.000 0.00 0.00 0.00 3.86
171 172 3.397906 GCACCCTTGCCTCTCTCT 58.602 61.111 0.00 0.00 43.66 3.10
223 224 2.436115 GCTTACACGGCCTGACCC 60.436 66.667 0.00 0.00 33.26 4.46
231 232 1.748879 CATGTGGGGGCTTACACGG 60.749 63.158 0.00 0.00 40.39 4.94
240 241 4.447342 GGGAGGTGCATGTGGGGG 62.447 72.222 0.00 0.00 0.00 5.40
316 317 6.371825 AGTTATTCGGAGCTTGGAAAAGTTAG 59.628 38.462 4.74 0.00 0.00 2.34
318 319 5.070685 AGTTATTCGGAGCTTGGAAAAGTT 58.929 37.500 4.74 0.00 0.00 2.66
319 320 4.652822 AGTTATTCGGAGCTTGGAAAAGT 58.347 39.130 4.74 2.56 0.00 2.66
320 321 6.737254 TTAGTTATTCGGAGCTTGGAAAAG 57.263 37.500 4.74 0.00 0.00 2.27
379 385 4.072131 GCAGGGATTGTCAGAAAACTACA 58.928 43.478 0.00 0.00 0.00 2.74
383 389 4.762251 ACTAAGCAGGGATTGTCAGAAAAC 59.238 41.667 0.00 0.00 0.00 2.43
452 459 9.157104 TCAAAATTGCTCATAGTTTACACGATA 57.843 29.630 0.00 0.00 0.00 2.92
455 462 8.500837 TTTCAAAATTGCTCATAGTTTACACG 57.499 30.769 0.00 0.00 0.00 4.49
463 470 9.414295 TCACAAGATTTTCAAAATTGCTCATAG 57.586 29.630 0.00 0.00 0.00 2.23
468 475 9.985730 TCTTATCACAAGATTTTCAAAATTGCT 57.014 25.926 0.00 0.00 35.67 3.91
516 523 2.233676 ACAGTGTTGTGAGAGTGTGACA 59.766 45.455 0.00 0.00 35.83 3.58
517 524 2.860735 GACAGTGTTGTGAGAGTGTGAC 59.139 50.000 0.00 0.00 37.76 3.67
525 532 1.138859 TGGTGGAGACAGTGTTGTGAG 59.861 52.381 0.00 0.00 44.46 3.51
526 533 1.199615 TGGTGGAGACAGTGTTGTGA 58.800 50.000 0.00 0.00 44.46 3.58
528 535 1.768275 TGATGGTGGAGACAGTGTTGT 59.232 47.619 0.00 0.00 44.46 3.32
530 537 1.072331 GGTGATGGTGGAGACAGTGTT 59.928 52.381 0.00 0.00 44.46 3.32
534 541 0.036010 GGTGGTGATGGTGGAGACAG 60.036 60.000 0.00 0.00 44.46 3.51
609 618 0.976641 AGGTGAGAGGCAACATCGAA 59.023 50.000 0.00 0.00 36.36 3.71
613 624 1.912043 AGCTAAGGTGAGAGGCAACAT 59.088 47.619 0.00 0.00 36.36 2.71
614 625 1.352083 AGCTAAGGTGAGAGGCAACA 58.648 50.000 0.00 0.00 36.36 3.33
621 632 3.326588 TGCCTTGTTTAGCTAAGGTGAGA 59.673 43.478 13.35 0.00 44.21 3.27
632 643 1.996191 GTCTCGAGCTGCCTTGTTTAG 59.004 52.381 7.81 0.00 0.00 1.85
646 658 3.243101 GCAGATGGATAAACTCGTCTCGA 60.243 47.826 0.00 0.00 0.00 4.04
647 659 3.046390 GCAGATGGATAAACTCGTCTCG 58.954 50.000 0.00 0.00 0.00 4.04
775 913 3.122780 TCAAGTCGCACACAAATATCACG 59.877 43.478 0.00 0.00 0.00 4.35
781 919 2.503331 TGGATCAAGTCGCACACAAAT 58.497 42.857 0.00 0.00 0.00 2.32
810 948 2.443952 ATGGACGGGCGAGATGGA 60.444 61.111 0.00 0.00 0.00 3.41
932 1102 2.745968 GGGATGCTTGTTAATGGGGAA 58.254 47.619 0.00 0.00 0.00 3.97
940 1110 2.822255 GCGGCGGGATGCTTGTTA 60.822 61.111 9.78 0.00 45.43 2.41
978 1151 0.453449 CGCCGCTTCTTTCTTTCTGC 60.453 55.000 0.00 0.00 0.00 4.26
1105 1296 2.579201 CAGAACGCGGTGGGAGAT 59.421 61.111 12.47 0.00 0.00 2.75
1164 1359 4.705519 CGCCAAACCGCCTGCTTG 62.706 66.667 0.00 0.00 0.00 4.01
1215 1416 0.825425 TCCAGCAAAACGGGCAATGA 60.825 50.000 0.00 0.00 32.86 2.57
1302 1503 5.599732 CACATCATTTTCAGAACCCAACAA 58.400 37.500 0.00 0.00 0.00 2.83
1303 1504 4.501229 GCACATCATTTTCAGAACCCAACA 60.501 41.667 0.00 0.00 0.00 3.33
1304 1505 3.989817 GCACATCATTTTCAGAACCCAAC 59.010 43.478 0.00 0.00 0.00 3.77
1305 1506 3.305267 CGCACATCATTTTCAGAACCCAA 60.305 43.478 0.00 0.00 0.00 4.12
1326 1531 1.306148 AATCATGGATCTGCACTGCG 58.694 50.000 0.00 0.00 0.00 5.18
1415 1652 1.153745 CTGCGCTACTGGTCTCACC 60.154 63.158 9.73 0.00 39.22 4.02
1416 1653 1.153745 CCTGCGCTACTGGTCTCAC 60.154 63.158 9.73 0.00 32.81 3.51
1417 1654 2.351244 CCCTGCGCTACTGGTCTCA 61.351 63.158 9.73 0.00 35.64 3.27
1418 1655 2.496817 CCCTGCGCTACTGGTCTC 59.503 66.667 9.73 0.00 35.64 3.36
1470 1720 5.659079 ACCCAGACCATTCAGTTTGTTTTAA 59.341 36.000 0.00 0.00 0.00 1.52
1480 1730 6.483640 GCTTATAAGTTACCCAGACCATTCAG 59.516 42.308 13.91 0.00 0.00 3.02
1534 1784 3.421844 CAAAGGAAGGGGAAATTCGTCT 58.578 45.455 0.00 0.00 0.00 4.18
1552 1804 1.698506 AAATTCTGTCCCACGGCAAA 58.301 45.000 0.00 0.00 0.00 3.68
1554 1806 2.156098 GTAAAATTCTGTCCCACGGCA 58.844 47.619 0.00 0.00 0.00 5.69
1555 1807 2.156098 TGTAAAATTCTGTCCCACGGC 58.844 47.619 0.00 0.00 0.00 5.68
1604 1856 7.386025 ACGATCATATTGAACACATCATACAGG 59.614 37.037 0.00 0.00 38.03 4.00
1628 1880 7.222611 TGTGAACACATCATCATACTGAATACG 59.777 37.037 3.39 0.00 40.97 3.06
1662 1914 3.691342 ACTTCTGCGCGCCCAGTA 61.691 61.111 30.77 13.13 34.47 2.74
1675 1927 1.464997 CTGGCGGTTTCTTAGCACTTC 59.535 52.381 0.00 0.00 0.00 3.01
1676 1928 1.523758 CTGGCGGTTTCTTAGCACTT 58.476 50.000 0.00 0.00 0.00 3.16
1677 1929 0.321653 CCTGGCGGTTTCTTAGCACT 60.322 55.000 0.00 0.00 0.00 4.40
1678 1930 0.605589 ACCTGGCGGTTTCTTAGCAC 60.606 55.000 0.00 0.00 42.13 4.40
1679 1931 0.321298 GACCTGGCGGTTTCTTAGCA 60.321 55.000 0.00 0.00 45.73 3.49
1680 1932 1.359459 CGACCTGGCGGTTTCTTAGC 61.359 60.000 0.00 0.00 45.73 3.09
1681 1933 1.359459 GCGACCTGGCGGTTTCTTAG 61.359 60.000 11.41 0.00 45.73 2.18
1682 1934 1.375013 GCGACCTGGCGGTTTCTTA 60.375 57.895 11.41 0.00 45.73 2.10
1683 1935 2.668550 GCGACCTGGCGGTTTCTT 60.669 61.111 11.41 0.00 45.73 2.52
1684 1936 4.699522 GGCGACCTGGCGGTTTCT 62.700 66.667 11.41 0.00 45.73 2.52
1755 2021 4.941873 GTCCTATGGTTTTGGTTCGATCTT 59.058 41.667 0.00 0.00 0.00 2.40
1764 2030 4.142249 GGGAAATTCGTCCTATGGTTTTGG 60.142 45.833 0.00 0.00 37.85 3.28
1878 2144 2.551270 GTGGTTTCTGCGCGTCTG 59.449 61.111 8.43 4.48 0.00 3.51
1879 2145 2.665185 GGTGGTTTCTGCGCGTCT 60.665 61.111 8.43 0.00 0.00 4.18
1912 2178 2.320745 TGCATATCAGACTGCAGTGG 57.679 50.000 27.27 16.41 43.11 4.00
1928 2194 2.279743 GGCATCCATCCCCTTGCA 59.720 61.111 0.00 0.00 36.82 4.08
2009 2275 3.388024 TCAGGAGAAAGTGCACAGTTACT 59.612 43.478 21.04 10.40 0.00 2.24
2029 2295 2.566010 GCGGCTTGCGGAAATTCA 59.434 55.556 4.36 0.00 0.00 2.57
2074 2340 9.467258 AATTGTCAACATTCAGATAAAACTGTG 57.533 29.630 0.00 0.00 38.79 3.66
2188 2461 4.156008 GGAATGCAAAACTCATTAGACGGT 59.844 41.667 0.00 0.00 34.59 4.83
2229 2502 7.145985 ACAACATGACATAATACTACTAGGCG 58.854 38.462 0.00 0.00 0.00 5.52
2233 2506 9.363401 AGCCTACAACATGACATAATACTACTA 57.637 33.333 0.00 0.00 0.00 1.82
2234 2507 8.251383 AGCCTACAACATGACATAATACTACT 57.749 34.615 0.00 0.00 0.00 2.57
2235 2508 8.888579 AAGCCTACAACATGACATAATACTAC 57.111 34.615 0.00 0.00 0.00 2.73
2334 2607 3.490078 GGAGAAATCCTAGTGACGAGCTG 60.490 52.174 0.00 0.00 0.00 4.24
2335 2608 2.691011 GGAGAAATCCTAGTGACGAGCT 59.309 50.000 0.00 0.00 0.00 4.09
2346 2619 6.400096 AAAAGAGGAAGATGGAGAAATCCT 57.600 37.500 0.00 0.00 43.07 3.24
2370 2643 8.736244 GGGAGTACTTAATTTAGCATTTGTCAA 58.264 33.333 0.00 0.00 0.00 3.18
2554 2828 5.047847 CCATTTTGGCATTGCTCTGATTAG 58.952 41.667 8.82 0.00 0.00 1.73
2708 2982 0.248825 CTCATCAAGTCGAGAGGCGG 60.249 60.000 0.00 0.00 43.49 6.13
2712 2986 2.361757 AGCCATCTCATCAAGTCGAGAG 59.638 50.000 0.00 0.00 41.39 3.20
2821 3095 9.140286 GTCAAAATTTATGAAGAGTTAAAGGCC 57.860 33.333 0.00 0.00 0.00 5.19
2981 3258 2.704464 TCATGAGTTCAGATGCCTGG 57.296 50.000 0.00 0.00 40.76 4.45
2988 3265 6.815641 GCTAGTCTTTGAATCATGAGTTCAGA 59.184 38.462 15.46 12.33 36.96 3.27
3011 3288 4.746611 GCAAAACAAGAACTGCATTTAGCT 59.253 37.500 0.00 0.00 45.94 3.32
3032 3309 4.275689 CACAAACACATAACTCCTTCAGCA 59.724 41.667 0.00 0.00 0.00 4.41
3039 3316 8.448615 GTTTATACCTCACAAACACATAACTCC 58.551 37.037 0.00 0.00 33.39 3.85
3087 3364 5.133941 TGTGTTACAAGCCTAACCATTGAA 58.866 37.500 0.00 0.00 0.00 2.69
3094 3371 4.386711 AGTTCCTGTGTTACAAGCCTAAC 58.613 43.478 0.00 0.00 0.00 2.34
3097 3374 3.577805 AAGTTCCTGTGTTACAAGCCT 57.422 42.857 0.00 0.00 0.00 4.58
3263 3540 3.474904 TTTGCGCATCGGTCGTCG 61.475 61.111 12.75 0.00 40.90 5.12
3590 3869 2.158827 ACAACACAGTACATCAGCACCA 60.159 45.455 0.00 0.00 0.00 4.17
3673 3952 4.979943 TTGTCAGACAAGCAATGTGAAA 57.020 36.364 12.24 0.00 44.12 2.69
3995 4275 3.318313 TCTTCCCAATGTCTCCTATCCC 58.682 50.000 0.00 0.00 0.00 3.85
4128 4418 1.396996 CAAATCCCAACGTCGTGGATC 59.603 52.381 15.44 0.00 41.65 3.36
4164 4454 3.643320 TGATCACGAGCTAATGAATCCCT 59.357 43.478 3.63 0.00 0.00 4.20
4165 4455 3.995199 TGATCACGAGCTAATGAATCCC 58.005 45.455 3.63 0.00 0.00 3.85
4174 4464 4.870426 GGTCAAATTCTTGATCACGAGCTA 59.130 41.667 0.00 0.00 43.39 3.32
4279 4570 9.551734 CAGAGATTCCAATGTATCACAGATTAA 57.448 33.333 0.00 0.00 0.00 1.40
4280 4571 8.708378 ACAGAGATTCCAATGTATCACAGATTA 58.292 33.333 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.