Multiple sequence alignment - TraesCS6D01G026000

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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 TraesCS6D01G026000 chr6D 100.000 2668 0 0 1 2668 9914571 9917238 0.000000e+00 4927
1 TraesCS6D01G026000 chr6D 99.107 560 5 0 2109 2668 9929343 9929902 0.000000e+00 1007
2 TraesCS6D01G026000 chr6D 77.528 1246 236 24 380 1590 9858635 9857399 0.000000e+00 710
3 TraesCS6D01G026000 chr6D 81.057 227 33 6 1 225 10315643 10315425 3.530000e-39 172
4 TraesCS6D01G026000 chr6D 79.825 228 38 5 1 227 9851022 9850802 2.750000e-35 159
5 TraesCS6D01G026000 chr6B 83.873 1761 219 37 377 2108 18166927 18168651 0.000000e+00 1618
6 TraesCS6D01G026000 chr6B 84.530 1170 158 20 377 1535 18268353 18269510 0.000000e+00 1136
7 TraesCS6D01G026000 chr6B 80.914 1116 127 49 684 1737 18431284 18432375 0.000000e+00 802
8 TraesCS6D01G026000 chr6B 88.110 471 28 13 1639 2108 18269538 18269981 3.910000e-148 534
9 TraesCS6D01G026000 chr6B 78.774 848 133 35 857 1674 18633202 18634032 2.350000e-145 525
10 TraesCS6D01G026000 chr6B 84.824 369 42 7 3 367 18268015 18268373 2.530000e-95 359
11 TraesCS6D01G026000 chr6B 90.323 186 17 1 1751 1936 18210791 18210975 2.650000e-60 243
12 TraesCS6D01G026000 chr6B 79.736 227 36 5 1 225 18847816 18847598 3.560000e-34 156
13 TraesCS6D01G026000 chr6B 83.636 165 15 4 1840 2004 18210615 18210767 7.700000e-31 145
14 TraesCS6D01G026000 chr6A 80.391 1790 232 59 377 2108 11499103 11500831 0.000000e+00 1251
15 TraesCS6D01G026000 chr6A 76.849 1244 244 25 383 1590 11007139 11005904 0.000000e+00 662
16 TraesCS6D01G026000 chr6A 85.873 361 41 4 9 367 11476678 11477030 2.510000e-100 375
17 TraesCS6D01G026000 chr6A 84.239 368 48 5 2 367 11498764 11499123 1.520000e-92 350
18 TraesCS6D01G026000 chr5D 98.393 560 9 0 2109 2668 507502869 507502310 0.000000e+00 985
19 TraesCS6D01G026000 chr5D 98.039 561 10 1 2109 2668 507490225 507489665 0.000000e+00 974
20 TraesCS6D01G026000 chr7D 98.217 561 9 1 2109 2668 600255693 600255133 0.000000e+00 979
21 TraesCS6D01G026000 chr7D 97.683 561 11 2 2109 2668 182239535 182238976 0.000000e+00 963
22 TraesCS6D01G026000 chr7D 97.504 561 12 2 2109 2668 182226880 182226321 0.000000e+00 957
23 TraesCS6D01G026000 chr1D 97.865 562 11 1 2108 2668 229385560 229384999 0.000000e+00 970
24 TraesCS6D01G026000 chr1D 97.861 561 11 1 2109 2668 229372780 229372220 0.000000e+00 968
25 TraesCS6D01G026000 chr2D 97.500 560 12 2 2109 2667 75951005 75951563 0.000000e+00 955
26 TraesCS6D01G026000 chrUn 82.250 569 74 20 1133 1674 240894476 240895044 1.450000e-127 466
27 TraesCS6D01G026000 chrUn 82.168 572 75 20 1133 1677 268929424 268928853 1.450000e-127 466
28 TraesCS6D01G026000 chrUn 87.738 367 35 6 3 367 240893362 240893720 1.140000e-113 420
29 TraesCS6D01G026000 chrUn 88.089 361 33 6 9 367 268930532 268930180 1.140000e-113 420


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 TraesCS6D01G026000 chr6D 9914571 9917238 2667 False 4927.000000 4927 100.000000 1 2668 1 chr6D.!!$F1 2667
1 TraesCS6D01G026000 chr6D 9929343 9929902 559 False 1007.000000 1007 99.107000 2109 2668 1 chr6D.!!$F2 559
2 TraesCS6D01G026000 chr6D 9857399 9858635 1236 True 710.000000 710 77.528000 380 1590 1 chr6D.!!$R2 1210
3 TraesCS6D01G026000 chr6B 18166927 18168651 1724 False 1618.000000 1618 83.873000 377 2108 1 chr6B.!!$F1 1731
4 TraesCS6D01G026000 chr6B 18431284 18432375 1091 False 802.000000 802 80.914000 684 1737 1 chr6B.!!$F2 1053
5 TraesCS6D01G026000 chr6B 18268015 18269981 1966 False 676.333333 1136 85.821333 3 2108 3 chr6B.!!$F5 2105
6 TraesCS6D01G026000 chr6B 18633202 18634032 830 False 525.000000 525 78.774000 857 1674 1 chr6B.!!$F3 817
7 TraesCS6D01G026000 chr6A 11498764 11500831 2067 False 800.500000 1251 82.315000 2 2108 2 chr6A.!!$F2 2106
8 TraesCS6D01G026000 chr6A 11005904 11007139 1235 True 662.000000 662 76.849000 383 1590 1 chr6A.!!$R1 1207
9 TraesCS6D01G026000 chr5D 507502310 507502869 559 True 985.000000 985 98.393000 2109 2668 1 chr5D.!!$R2 559
10 TraesCS6D01G026000 chr5D 507489665 507490225 560 True 974.000000 974 98.039000 2109 2668 1 chr5D.!!$R1 559
11 TraesCS6D01G026000 chr7D 600255133 600255693 560 True 979.000000 979 98.217000 2109 2668 1 chr7D.!!$R3 559
12 TraesCS6D01G026000 chr7D 182238976 182239535 559 True 963.000000 963 97.683000 2109 2668 1 chr7D.!!$R2 559
13 TraesCS6D01G026000 chr7D 182226321 182226880 559 True 957.000000 957 97.504000 2109 2668 1 chr7D.!!$R1 559
14 TraesCS6D01G026000 chr1D 229384999 229385560 561 True 970.000000 970 97.865000 2108 2668 1 chr1D.!!$R2 560
15 TraesCS6D01G026000 chr1D 229372220 229372780 560 True 968.000000 968 97.861000 2109 2668 1 chr1D.!!$R1 559
16 TraesCS6D01G026000 chr2D 75951005 75951563 558 False 955.000000 955 97.500000 2109 2667 1 chr2D.!!$F1 558
17 TraesCS6D01G026000 chrUn 240893362 240895044 1682 False 443.000000 466 84.994000 3 1674 2 chrUn.!!$F1 1671
18 TraesCS6D01G026000 chrUn 268928853 268930532 1679 True 443.000000 466 85.128500 9 1677 2 chrUn.!!$R1 1668

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
450 451 0.032017 GGCTCCTTAGGTCCCTCTCA 60.032 60.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 1907 0.964358 AAGCAGGGCAAGCATCACTC 60.964 55.0 3.26 0.0 0.0 3.51 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
73 74 7.943079 TGCAAAGAATTGGAGAATCTATTCA 57.057 32.000 5.55 0.00 38.04 2.57
75 76 8.627403 TGCAAAGAATTGGAGAATCTATTCATC 58.373 33.333 5.55 0.95 38.04 2.92
91 92 8.948631 TCTATTCATCAAAGGATAGTTGTCAC 57.051 34.615 0.00 0.00 30.87 3.67
92 93 8.762645 TCTATTCATCAAAGGATAGTTGTCACT 58.237 33.333 0.00 0.00 36.99 3.41
94 95 8.641498 ATTCATCAAAGGATAGTTGTCACTTT 57.359 30.769 0.00 0.00 34.06 2.66
96 97 9.567776 TTCATCAAAGGATAGTTGTCACTTTTA 57.432 29.630 0.00 0.00 34.06 1.52
98 99 7.979444 TCAAAGGATAGTTGTCACTTTTAGG 57.021 36.000 0.00 0.00 34.06 2.69
101 102 3.945921 GGATAGTTGTCACTTTTAGGGGC 59.054 47.826 0.00 0.00 34.06 5.80
102 103 4.324331 GGATAGTTGTCACTTTTAGGGGCT 60.324 45.833 0.00 0.00 34.06 5.19
103 104 2.863809 AGTTGTCACTTTTAGGGGCTG 58.136 47.619 0.00 0.00 0.00 4.85
104 105 1.269723 GTTGTCACTTTTAGGGGCTGC 59.730 52.381 0.00 0.00 0.00 5.25
105 106 0.251165 TGTCACTTTTAGGGGCTGCC 60.251 55.000 11.05 11.05 0.00 4.85
106 107 0.038310 GTCACTTTTAGGGGCTGCCT 59.962 55.000 19.68 1.54 0.00 4.75
186 187 1.918262 TCACTCCCCAAGCAGATCATT 59.082 47.619 0.00 0.00 0.00 2.57
259 260 1.141053 AGGAAGAGTTGCCGAAAGTGT 59.859 47.619 0.00 0.00 0.00 3.55
261 262 3.135994 GGAAGAGTTGCCGAAAGTGTTA 58.864 45.455 0.00 0.00 0.00 2.41
284 285 6.395426 ACACATTGACACAACATCTTCATT 57.605 33.333 0.00 0.00 0.00 2.57
308 309 1.686110 CAGCTTACGGAGGGGAGGT 60.686 63.158 0.00 0.00 0.00 3.85
313 314 0.032813 TTACGGAGGGGAGGTACCAG 60.033 60.000 15.94 0.00 41.20 4.00
340 341 5.046735 GTGCATCCACATACTGATCTATCCT 60.047 44.000 0.00 0.00 41.67 3.24
346 347 5.279708 CCACATACTGATCTATCCTTCCACC 60.280 48.000 0.00 0.00 0.00 4.61
347 348 4.524714 ACATACTGATCTATCCTTCCACCG 59.475 45.833 0.00 0.00 0.00 4.94
348 349 2.320781 ACTGATCTATCCTTCCACCGG 58.679 52.381 0.00 0.00 0.00 5.28
349 350 1.620819 CTGATCTATCCTTCCACCGGG 59.379 57.143 6.32 0.00 0.00 5.73
350 351 1.219469 TGATCTATCCTTCCACCGGGA 59.781 52.381 6.32 0.00 43.03 5.14
351 352 1.896465 GATCTATCCTTCCACCGGGAG 59.104 57.143 6.32 0.00 46.01 4.30
352 353 0.931468 TCTATCCTTCCACCGGGAGA 59.069 55.000 6.32 0.00 46.01 3.71
353 354 1.289830 TCTATCCTTCCACCGGGAGAA 59.710 52.381 6.32 7.38 46.01 2.87
354 355 2.116238 CTATCCTTCCACCGGGAGAAA 58.884 52.381 6.32 0.00 46.01 2.52
355 356 0.912486 ATCCTTCCACCGGGAGAAAG 59.088 55.000 6.32 1.92 46.01 2.62
356 357 1.198759 TCCTTCCACCGGGAGAAAGG 61.199 60.000 16.71 16.71 46.01 3.11
357 358 1.198759 CCTTCCACCGGGAGAAAGGA 61.199 60.000 17.52 7.43 46.01 3.36
358 359 0.250513 CTTCCACCGGGAGAAAGGAG 59.749 60.000 6.32 0.00 46.01 3.69
359 360 0.178915 TTCCACCGGGAGAAAGGAGA 60.179 55.000 6.32 0.00 46.01 3.71
360 361 0.178915 TCCACCGGGAGAAAGGAGAA 60.179 55.000 6.32 0.00 38.64 2.87
361 362 0.690762 CCACCGGGAGAAAGGAGAAA 59.309 55.000 6.32 0.00 35.59 2.52
362 363 1.282157 CCACCGGGAGAAAGGAGAAAT 59.718 52.381 6.32 0.00 35.59 2.17
363 364 2.359900 CACCGGGAGAAAGGAGAAATG 58.640 52.381 6.32 0.00 0.00 2.32
364 365 1.985895 ACCGGGAGAAAGGAGAAATGT 59.014 47.619 6.32 0.00 0.00 2.71
365 366 2.375509 ACCGGGAGAAAGGAGAAATGTT 59.624 45.455 6.32 0.00 0.00 2.71
366 367 3.181433 ACCGGGAGAAAGGAGAAATGTTT 60.181 43.478 6.32 0.00 0.00 2.83
367 368 3.440522 CCGGGAGAAAGGAGAAATGTTTC 59.559 47.826 0.00 0.00 37.45 2.78
369 370 4.762251 CGGGAGAAAGGAGAAATGTTTCTT 59.238 41.667 9.20 0.00 46.84 2.52
370 371 5.241728 CGGGAGAAAGGAGAAATGTTTCTTT 59.758 40.000 9.20 0.88 46.84 2.52
371 372 6.239036 CGGGAGAAAGGAGAAATGTTTCTTTT 60.239 38.462 9.20 7.05 46.84 2.27
372 373 6.925718 GGGAGAAAGGAGAAATGTTTCTTTTG 59.074 38.462 9.20 0.00 46.84 2.44
373 374 7.201911 GGGAGAAAGGAGAAATGTTTCTTTTGA 60.202 37.037 9.20 0.00 46.84 2.69
374 375 8.197439 GGAGAAAGGAGAAATGTTTCTTTTGAA 58.803 33.333 9.20 0.00 46.84 2.69
375 376 9.242477 GAGAAAGGAGAAATGTTTCTTTTGAAG 57.758 33.333 9.20 0.00 46.84 3.02
396 397 5.444663 AGCACCAGAAAGAAGAAATGTTC 57.555 39.130 0.00 0.00 0.00 3.18
409 410 2.999185 AATGTTCAAGGGTGGATGGT 57.001 45.000 0.00 0.00 0.00 3.55
450 451 0.032017 GGCTCCTTAGGTCCCTCTCA 60.032 60.000 0.00 0.00 0.00 3.27
505 506 9.860898 TCATACATATTGATATCTGTACTGCAC 57.139 33.333 3.98 0.00 29.40 4.57
516 523 0.804989 GTACTGCACCTGATGTTGGC 59.195 55.000 0.00 0.00 0.00 4.52
519 526 4.120331 GCACCTGATGTTGGCGGC 62.120 66.667 0.00 0.00 0.00 6.53
532 539 2.747460 GCGGCAGCAACATCCAGA 60.747 61.111 3.18 0.00 44.35 3.86
540 547 2.486982 CAGCAACATCCAGAGAACAAGG 59.513 50.000 0.00 0.00 0.00 3.61
554 561 5.598830 AGAGAACAAGGAGTGACAAACTAGA 59.401 40.000 0.00 0.00 40.07 2.43
572 579 3.641434 AGAGCAAGTCCAACAGCATAT 57.359 42.857 0.00 0.00 0.00 1.78
609 616 3.129638 ACTCGAAGTACAGAGATGCCTTC 59.870 47.826 16.45 0.00 37.87 3.46
617 624 0.473326 AGAGATGCCTTCAGGGATGC 59.527 55.000 4.29 0.00 46.79 3.91
670 677 1.009829 CGTGCTAGAGAAATGGTGGC 58.990 55.000 0.00 0.00 0.00 5.01
671 678 1.675714 CGTGCTAGAGAAATGGTGGCA 60.676 52.381 0.00 0.00 0.00 4.92
672 679 2.648059 GTGCTAGAGAAATGGTGGCAT 58.352 47.619 0.00 0.00 0.00 4.40
673 680 2.357009 GTGCTAGAGAAATGGTGGCATG 59.643 50.000 0.00 0.00 0.00 4.06
690 703 5.196695 TGGCATGCCAACTATACATGTTTA 58.803 37.500 36.95 7.62 44.12 2.01
707 720 7.491682 ACATGTTTAATAAAGGTGATGATGCC 58.508 34.615 0.00 0.00 0.00 4.40
711 724 0.465460 TAAAGGTGATGATGCCCGGC 60.465 55.000 1.04 1.04 0.00 6.13
740 753 1.134461 CAGACTCTTGGAGGATGCTGG 60.134 57.143 0.00 0.00 33.35 4.85
753 787 1.069358 GATGCTGGAGGTGCTAGTACC 59.931 57.143 21.41 21.41 41.17 3.34
800 834 1.463444 GTGTGACTTGGTTACATCGCC 59.537 52.381 0.00 0.00 34.74 5.54
830 864 7.704899 CGTGTATGATAACTTGTCCATCACTAA 59.295 37.037 0.00 0.00 31.83 2.24
846 880 2.563179 CACTAATATCCCTGGACCTCCG 59.437 54.545 0.00 0.00 39.43 4.63
849 883 0.178891 ATATCCCTGGACCTCCGCAT 60.179 55.000 0.00 0.00 39.43 4.73
937 989 2.766828 ACTGTTCCCTATGGCACTAGTC 59.233 50.000 0.00 0.00 0.00 2.59
940 992 1.414158 TCCCTATGGCACTAGTCTGC 58.586 55.000 0.00 0.00 36.33 4.26
949 1013 1.344458 CACTAGTCTGCACAGCTTCG 58.656 55.000 0.00 0.00 0.00 3.79
996 1060 3.386078 CCAAGCTCCTCTCTGCACTATAA 59.614 47.826 0.00 0.00 0.00 0.98
1000 1064 4.898265 AGCTCCTCTCTGCACTATAAATCA 59.102 41.667 0.00 0.00 0.00 2.57
1001 1065 5.543405 AGCTCCTCTCTGCACTATAAATCAT 59.457 40.000 0.00 0.00 0.00 2.45
1025 1089 4.033932 GGACAAACCAGTTGAAAAATGTGC 59.966 41.667 0.00 0.00 40.94 4.57
1039 1103 3.874392 AATGTGCCTTCATTAACCTGC 57.126 42.857 0.00 0.00 36.44 4.85
1053 1117 3.433306 AACCTGCTGTTATTGCACCTA 57.567 42.857 0.00 0.00 34.69 3.08
1083 1147 1.086067 CCAGGCTCGTACATGTGCTG 61.086 60.000 9.11 4.06 0.00 4.41
1114 1205 3.932545 TGTGGGACAAATACACATTGC 57.067 42.857 0.00 0.00 44.16 3.56
1117 1208 2.230992 TGGGACAAATACACATTGCAGC 59.769 45.455 0.00 0.00 31.92 5.25
1122 1213 2.036958 AATACACATTGCAGCGGCTA 57.963 45.000 10.92 2.18 41.91 3.93
1124 1215 0.461870 TACACATTGCAGCGGCTAGG 60.462 55.000 10.92 6.91 41.91 3.02
1141 1259 1.333177 AGGGACCATCGAGATAGTGC 58.667 55.000 0.00 0.00 0.00 4.40
1215 1342 8.688747 AGCAGGATAAAATTCTAGAATTCCTG 57.311 34.615 35.01 35.01 45.73 3.86
1282 1409 0.249120 CTGTGGGCGTAGGATGTTCA 59.751 55.000 0.00 0.00 0.00 3.18
1283 1410 0.908910 TGTGGGCGTAGGATGTTCAT 59.091 50.000 0.00 0.00 0.00 2.57
1306 1433 2.160417 CCAAAACTCGAGACCATCAAGC 59.840 50.000 21.68 0.00 0.00 4.01
1341 1468 1.901085 CCTTAGGCGTCTTCCTGCT 59.099 57.895 0.00 0.00 37.01 4.24
1423 1550 2.221299 TGGGACGGGTTGGAGAAGG 61.221 63.158 0.00 0.00 0.00 3.46
1424 1551 2.669240 GGACGGGTTGGAGAAGGG 59.331 66.667 0.00 0.00 0.00 3.95
1429 1556 2.359975 GGTTGGAGAAGGGCCACG 60.360 66.667 6.18 0.00 34.56 4.94
1465 1593 0.882927 GCCAAGCCACTCGTTGTACA 60.883 55.000 0.00 0.00 0.00 2.90
1530 1663 7.470702 GCTTCACATCTAGCTAGTTCCATCTTA 60.471 40.741 20.10 0.00 34.57 2.10
1531 1664 8.484214 TTCACATCTAGCTAGTTCCATCTTAT 57.516 34.615 20.10 0.48 0.00 1.73
1532 1665 7.890515 TCACATCTAGCTAGTTCCATCTTATG 58.109 38.462 20.10 14.41 0.00 1.90
1534 1667 8.797438 CACATCTAGCTAGTTCCATCTTATGTA 58.203 37.037 20.10 0.00 0.00 2.29
1538 1686 7.999545 TCTAGCTAGTTCCATCTTATGTACACT 59.000 37.037 20.10 0.00 0.00 3.55
1630 1804 6.823497 AGTACTGTAAATAGTGTGTGGTTGT 58.177 36.000 0.00 0.00 32.19 3.32
1631 1805 7.954835 AGTACTGTAAATAGTGTGTGGTTGTA 58.045 34.615 0.00 0.00 32.19 2.41
1632 1806 8.423349 AGTACTGTAAATAGTGTGTGGTTGTAA 58.577 33.333 0.00 0.00 32.19 2.41
1634 1808 9.044150 TACTGTAAATAGTGTGTGGTTGTAAAC 57.956 33.333 0.00 0.00 37.87 2.01
1691 1866 3.534554 CATCACTTCCGTGGATTGATCA 58.465 45.455 9.49 0.00 41.53 2.92
1694 1869 2.615447 CACTTCCGTGGATTGATCATGG 59.385 50.000 0.00 0.00 41.41 3.66
1706 1881 2.527497 TGATCATGGGCTTCTTGCAAA 58.473 42.857 0.00 0.00 45.15 3.68
1732 1907 0.179001 TGCATGATCCTGAGGCATGG 60.179 55.000 17.20 3.79 39.71 3.66
1737 1952 1.126488 GATCCTGAGGCATGGAGTGA 58.874 55.000 0.00 0.00 35.63 3.41
1771 1986 4.743348 GCTTCCCATTTGATTGGTTTGTGT 60.743 41.667 0.00 0.00 34.77 3.72
1828 2043 1.669760 CGGTGCGGCTTCCAGTTTA 60.670 57.895 0.00 0.00 0.00 2.01
1829 2044 1.024579 CGGTGCGGCTTCCAGTTTAT 61.025 55.000 0.00 0.00 0.00 1.40
1830 2045 1.173913 GGTGCGGCTTCCAGTTTATT 58.826 50.000 0.00 0.00 0.00 1.40
1831 2046 1.544246 GGTGCGGCTTCCAGTTTATTT 59.456 47.619 0.00 0.00 0.00 1.40
1832 2047 2.029380 GGTGCGGCTTCCAGTTTATTTT 60.029 45.455 0.00 0.00 0.00 1.82
1833 2048 2.986479 GTGCGGCTTCCAGTTTATTTTG 59.014 45.455 0.00 0.00 0.00 2.44
1834 2049 2.887783 TGCGGCTTCCAGTTTATTTTGA 59.112 40.909 0.00 0.00 0.00 2.69
1835 2050 3.509575 TGCGGCTTCCAGTTTATTTTGAT 59.490 39.130 0.00 0.00 0.00 2.57
1836 2051 4.021544 TGCGGCTTCCAGTTTATTTTGATT 60.022 37.500 0.00 0.00 0.00 2.57
1837 2052 4.327087 GCGGCTTCCAGTTTATTTTGATTG 59.673 41.667 0.00 0.00 0.00 2.67
1838 2053 4.864247 CGGCTTCCAGTTTATTTTGATTGG 59.136 41.667 0.00 0.00 0.00 3.16
1839 2054 5.566627 CGGCTTCCAGTTTATTTTGATTGGT 60.567 40.000 0.00 0.00 0.00 3.67
1842 2057 7.307930 GGCTTCCAGTTTATTTTGATTGGTTTG 60.308 37.037 0.00 0.00 0.00 2.93
1847 2062 9.065798 CCAGTTTATTTTGATTGGTTTGGATTT 57.934 29.630 0.00 0.00 0.00 2.17
1872 2098 3.866703 TGGTTTGGTGTGATCAACCTA 57.133 42.857 20.58 14.11 0.00 3.08
1873 2099 4.171878 TGGTTTGGTGTGATCAACCTAA 57.828 40.909 20.58 17.65 0.00 2.69
1938 2164 1.674980 GCTTCTGCAGCTTGAGCCT 60.675 57.895 9.47 0.00 46.27 4.58
2232 2458 0.529992 CGGCGAATCTTACCCAGGTC 60.530 60.000 0.00 0.00 0.00 3.85
2632 2859 1.336125 GTCGGCGGCTACTTACTGTAT 59.664 52.381 3.23 0.00 0.00 2.29
2643 2870 1.096967 TTACTGTATCCGCGCCTCGA 61.097 55.000 0.00 0.00 41.67 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.399934 CCATCACATCCATCAACAATGACA 59.600 41.667 0.00 0.00 38.69 3.58
5 6 3.454719 ACCCATCACATCCATCAACAA 57.545 42.857 0.00 0.00 0.00 2.83
7 8 5.913137 TTTAACCCATCACATCCATCAAC 57.087 39.130 0.00 0.00 0.00 3.18
66 67 8.762645 AGTGACAACTATCCTTTGATGAATAGA 58.237 33.333 0.00 0.00 33.79 1.98
73 74 7.611855 CCCTAAAAGTGACAACTATCCTTTGAT 59.388 37.037 0.00 0.00 34.77 2.57
75 76 6.151144 CCCCTAAAAGTGACAACTATCCTTTG 59.849 42.308 0.00 0.00 34.77 2.77
83 84 2.863809 CAGCCCCTAAAAGTGACAACT 58.136 47.619 0.00 0.00 38.71 3.16
84 85 1.269723 GCAGCCCCTAAAAGTGACAAC 59.730 52.381 0.00 0.00 0.00 3.32
88 89 1.559682 CTAGGCAGCCCCTAAAAGTGA 59.440 52.381 8.22 0.00 45.50 3.41
89 90 2.019156 GCTAGGCAGCCCCTAAAAGTG 61.019 57.143 8.22 0.00 45.50 3.16
90 91 0.256177 GCTAGGCAGCCCCTAAAAGT 59.744 55.000 8.22 0.00 45.50 2.66
91 92 3.102090 GCTAGGCAGCCCCTAAAAG 57.898 57.895 8.22 0.00 45.50 2.27
101 102 0.685785 TGAGAGGTCCAGCTAGGCAG 60.686 60.000 0.00 0.00 37.29 4.85
102 103 0.685785 CTGAGAGGTCCAGCTAGGCA 60.686 60.000 0.00 0.00 37.29 4.75
103 104 1.398958 CCTGAGAGGTCCAGCTAGGC 61.399 65.000 0.00 0.00 37.29 3.93
104 105 1.398958 GCCTGAGAGGTCCAGCTAGG 61.399 65.000 0.00 0.00 37.80 3.02
105 106 0.685785 TGCCTGAGAGGTCCAGCTAG 60.686 60.000 0.00 0.00 37.80 3.42
106 107 0.972983 GTGCCTGAGAGGTCCAGCTA 60.973 60.000 0.00 0.00 37.80 3.32
114 115 0.972134 TCACTCTTGTGCCTGAGAGG 59.028 55.000 10.77 0.00 42.88 3.69
186 187 1.812525 CTTCTCGCAGCCTAGCAGA 59.187 57.895 0.00 0.00 0.00 4.26
259 260 6.934048 TGAAGATGTTGTGTCAATGTGTAA 57.066 33.333 0.00 0.00 0.00 2.41
261 262 6.395426 AATGAAGATGTTGTGTCAATGTGT 57.605 33.333 0.00 0.00 0.00 3.72
308 309 2.877097 ATGTGGATGCACAACTGGTA 57.123 45.000 24.45 0.00 38.69 3.25
313 314 4.194640 AGATCAGTATGTGGATGCACAAC 58.805 43.478 24.45 20.62 38.69 3.32
328 329 2.320781 CCGGTGGAAGGATAGATCAGT 58.679 52.381 0.00 0.00 0.00 3.41
329 330 1.620819 CCCGGTGGAAGGATAGATCAG 59.379 57.143 0.00 0.00 0.00 2.90
340 341 0.178915 TCTCCTTTCTCCCGGTGGAA 60.179 55.000 0.00 0.95 41.17 3.53
346 347 4.327680 AGAAACATTTCTCCTTTCTCCCG 58.672 43.478 0.87 0.00 43.72 5.14
347 348 6.656632 AAAGAAACATTTCTCCTTTCTCCC 57.343 37.500 7.32 0.00 46.22 4.30
348 349 7.716612 TCAAAAGAAACATTTCTCCTTTCTCC 58.283 34.615 7.32 0.00 46.22 3.71
349 350 9.242477 CTTCAAAAGAAACATTTCTCCTTTCTC 57.758 33.333 7.32 0.00 46.22 2.87
350 351 7.708322 GCTTCAAAAGAAACATTTCTCCTTTCT 59.292 33.333 7.32 0.00 46.22 2.52
351 352 7.492344 TGCTTCAAAAGAAACATTTCTCCTTTC 59.508 33.333 7.32 0.00 46.22 2.62
352 353 7.278646 GTGCTTCAAAAGAAACATTTCTCCTTT 59.721 33.333 7.32 3.35 46.22 3.11
353 354 6.758416 GTGCTTCAAAAGAAACATTTCTCCTT 59.242 34.615 7.32 2.39 46.22 3.36
354 355 6.276091 GTGCTTCAAAAGAAACATTTCTCCT 58.724 36.000 7.32 0.00 46.22 3.69
355 356 5.463392 GGTGCTTCAAAAGAAACATTTCTCC 59.537 40.000 7.32 0.00 46.22 3.71
356 357 6.042143 TGGTGCTTCAAAAGAAACATTTCTC 58.958 36.000 7.32 0.00 46.22 2.87
358 359 6.042143 TCTGGTGCTTCAAAAGAAACATTTC 58.958 36.000 0.00 0.00 31.95 2.17
359 360 5.976458 TCTGGTGCTTCAAAAGAAACATTT 58.024 33.333 0.00 0.00 31.95 2.32
360 361 5.596836 TCTGGTGCTTCAAAAGAAACATT 57.403 34.783 0.00 0.00 31.95 2.71
361 362 5.596836 TTCTGGTGCTTCAAAAGAAACAT 57.403 34.783 0.00 0.00 31.95 2.71
362 363 5.184864 TCTTTCTGGTGCTTCAAAAGAAACA 59.815 36.000 0.00 0.00 34.10 2.83
363 364 5.650543 TCTTTCTGGTGCTTCAAAAGAAAC 58.349 37.500 0.00 0.00 34.10 2.78
364 365 5.913137 TCTTTCTGGTGCTTCAAAAGAAA 57.087 34.783 0.00 0.00 34.10 2.52
365 366 5.652014 TCTTCTTTCTGGTGCTTCAAAAGAA 59.348 36.000 17.26 17.26 41.27 2.52
366 367 5.192927 TCTTCTTTCTGGTGCTTCAAAAGA 58.807 37.500 0.00 0.00 34.94 2.52
367 368 5.505173 TCTTCTTTCTGGTGCTTCAAAAG 57.495 39.130 0.00 0.00 0.00 2.27
368 369 5.913137 TTCTTCTTTCTGGTGCTTCAAAA 57.087 34.783 0.00 0.00 0.00 2.44
369 370 5.913137 TTTCTTCTTTCTGGTGCTTCAAA 57.087 34.783 0.00 0.00 0.00 2.69
370 371 5.360714 ACATTTCTTCTTTCTGGTGCTTCAA 59.639 36.000 0.00 0.00 0.00 2.69
371 372 4.889409 ACATTTCTTCTTTCTGGTGCTTCA 59.111 37.500 0.00 0.00 0.00 3.02
372 373 5.444663 ACATTTCTTCTTTCTGGTGCTTC 57.555 39.130 0.00 0.00 0.00 3.86
373 374 5.360714 TGAACATTTCTTCTTTCTGGTGCTT 59.639 36.000 0.00 0.00 0.00 3.91
374 375 4.889409 TGAACATTTCTTCTTTCTGGTGCT 59.111 37.500 0.00 0.00 0.00 4.40
375 376 5.186996 TGAACATTTCTTCTTTCTGGTGC 57.813 39.130 0.00 0.00 0.00 5.01
378 379 5.302823 ACCCTTGAACATTTCTTCTTTCTGG 59.697 40.000 0.00 0.00 0.00 3.86
396 397 1.826720 CAAATCCACCATCCACCCTTG 59.173 52.381 0.00 0.00 0.00 3.61
409 410 3.421919 TGCATCTGTGAGACAAATCCA 57.578 42.857 0.00 0.00 0.00 3.41
479 480 9.860898 GTGCAGTACAGATATCAATATGTATGA 57.139 33.333 5.32 0.00 40.78 2.15
505 506 3.818787 GCTGCCGCCAACATCAGG 61.819 66.667 0.00 0.00 0.00 3.86
516 523 0.674581 TTCTCTGGATGTTGCTGCCG 60.675 55.000 0.00 0.00 0.00 5.69
519 526 2.486982 CCTTGTTCTCTGGATGTTGCTG 59.513 50.000 0.00 0.00 0.00 4.41
532 539 5.740513 GCTCTAGTTTGTCACTCCTTGTTCT 60.741 44.000 0.00 0.00 36.88 3.01
540 547 3.991121 GGACTTGCTCTAGTTTGTCACTC 59.009 47.826 0.00 0.00 36.88 3.51
554 561 4.848357 ACTTATATGCTGTTGGACTTGCT 58.152 39.130 0.00 0.00 0.00 3.91
572 579 7.094248 TGTACTTCGAGTGCATTAAGGTACTTA 60.094 37.037 12.12 1.83 40.74 2.24
617 624 1.303888 ATCACTGCTGCAACTGGGG 60.304 57.895 3.02 0.00 0.00 4.96
652 659 2.113860 TGCCACCATTTCTCTAGCAC 57.886 50.000 0.00 0.00 0.00 4.40
653 660 2.646930 CATGCCACCATTTCTCTAGCA 58.353 47.619 0.00 0.00 0.00 3.49
655 662 1.952296 GGCATGCCACCATTTCTCTAG 59.048 52.381 32.08 0.00 35.81 2.43
658 665 2.582272 TGGCATGCCACCATTTCTC 58.418 52.632 35.59 5.78 41.89 2.87
672 679 9.469097 ACCTTTATTAAACATGTATAGTTGGCA 57.531 29.630 0.00 0.00 0.00 4.92
673 680 9.730420 CACCTTTATTAAACATGTATAGTTGGC 57.270 33.333 0.00 0.00 0.00 4.52
690 703 2.586425 CCGGGCATCATCACCTTTATT 58.414 47.619 0.00 0.00 0.00 1.40
711 724 0.607489 CCAAGAGTCTGTTGCCCTGG 60.607 60.000 4.18 0.00 0.00 4.45
740 753 1.187087 AGCACTGGTACTAGCACCTC 58.813 55.000 13.44 0.83 39.50 3.85
780 814 1.463444 GGCGATGTAACCAAGTCACAC 59.537 52.381 0.00 0.00 0.00 3.82
800 834 3.000078 GGACAAGTTATCATACACGTGCG 60.000 47.826 17.22 4.51 0.00 5.34
830 864 0.178891 ATGCGGAGGTCCAGGGATAT 60.179 55.000 0.00 0.00 35.14 1.63
846 880 2.842496 TCTATCCCATCCTGATCCATGC 59.158 50.000 0.00 0.00 0.00 4.06
849 883 3.931241 AGTCTATCCCATCCTGATCCA 57.069 47.619 0.00 0.00 0.00 3.41
925 962 1.134699 GCTGTGCAGACTAGTGCCATA 60.135 52.381 0.00 0.00 43.28 2.74
937 989 1.370900 GCCAAACGAAGCTGTGCAG 60.371 57.895 0.00 0.00 0.00 4.41
949 1013 2.159198 CCCATAATGTCTGCAGCCAAAC 60.159 50.000 9.47 2.12 0.00 2.93
996 1060 5.867903 TTTCAACTGGTTTGTCCATGATT 57.132 34.783 0.00 0.00 46.12 2.57
1000 1064 5.816777 CACATTTTTCAACTGGTTTGTCCAT 59.183 36.000 0.00 0.00 46.12 3.41
1001 1065 5.174395 CACATTTTTCAACTGGTTTGTCCA 58.826 37.500 0.00 0.00 45.01 4.02
1025 1089 5.105797 TGCAATAACAGCAGGTTAATGAAGG 60.106 40.000 16.16 2.37 42.82 3.46
1039 1103 3.935203 CAGTGGTCTAGGTGCAATAACAG 59.065 47.826 0.00 0.00 0.00 3.16
1083 1147 2.763215 TCCCACATGGACAAGGGC 59.237 61.111 0.00 0.00 41.22 5.19
1114 1205 2.423446 GATGGTCCCTAGCCGCTG 59.577 66.667 2.16 0.00 0.00 5.18
1117 1208 0.896019 ATCTCGATGGTCCCTAGCCG 60.896 60.000 0.00 0.00 0.00 5.52
1122 1213 1.333177 GCACTATCTCGATGGTCCCT 58.667 55.000 0.00 0.00 29.60 4.20
1124 1215 1.683917 AGTGCACTATCTCGATGGTCC 59.316 52.381 20.16 0.00 29.60 4.46
1141 1259 2.734723 CCTGACGTCACCGCAGTG 60.735 66.667 15.76 2.67 46.00 3.66
1215 1342 1.202698 AGGTGGATGCGCCTTAGATTC 60.203 52.381 14.41 0.00 37.63 2.52
1282 1409 2.290260 TGATGGTCTCGAGTTTTGGCAT 60.290 45.455 13.13 0.00 0.00 4.40
1283 1410 1.071542 TGATGGTCTCGAGTTTTGGCA 59.928 47.619 13.13 2.66 0.00 4.92
1306 1433 4.486503 GCTCCAGCAGCCCCTGAG 62.487 72.222 2.97 0.00 43.17 3.35
1341 1468 1.885388 CTTGGTGTTGCGTCCGACA 60.885 57.895 0.00 0.00 32.93 4.35
1371 1498 0.976641 ACCATTCCTTCTCGCAGTCA 59.023 50.000 0.00 0.00 0.00 3.41
1423 1550 4.097361 GAGGGAAGGGTCGTGGCC 62.097 72.222 0.00 0.00 0.00 5.36
1424 1551 1.684734 TAGAGGGAAGGGTCGTGGC 60.685 63.158 0.00 0.00 0.00 5.01
1491 1622 2.316108 TGTGAAGCTCACCTGAGTACA 58.684 47.619 11.99 2.95 46.40 2.90
1530 1663 7.841956 AGTAAGCTAATTCACAGAGTGTACAT 58.158 34.615 0.00 0.00 34.79 2.29
1531 1664 7.176865 AGAGTAAGCTAATTCACAGAGTGTACA 59.823 37.037 0.00 0.00 34.79 2.90
1532 1665 7.540299 AGAGTAAGCTAATTCACAGAGTGTAC 58.460 38.462 0.00 0.00 34.79 2.90
1534 1667 6.597832 AGAGTAAGCTAATTCACAGAGTGT 57.402 37.500 0.00 0.00 34.79 3.55
1538 1686 9.371136 CAACATAAGAGTAAGCTAATTCACAGA 57.629 33.333 0.00 0.00 0.00 3.41
1602 1766 7.553334 ACCACACACTATTTACAGTACTATGG 58.447 38.462 0.00 0.00 0.00 2.74
1616 1788 6.877322 GGTATGAGTTTACAACCACACACTAT 59.123 38.462 0.00 0.00 0.00 2.12
1706 1881 3.687125 CCTCAGGATCATGCATATTGCT 58.313 45.455 1.57 0.00 45.31 3.91
1732 1907 0.964358 AAGCAGGGCAAGCATCACTC 60.964 55.000 3.26 0.00 0.00 3.51
1737 1952 2.363406 GGGAAGCAGGGCAAGCAT 60.363 61.111 3.26 0.00 0.00 3.79
1771 1986 6.351711 AGCATATGTTATGCAGAGAGAACAA 58.648 36.000 18.70 0.00 46.77 2.83
1811 2026 1.173913 AATAAACTGGAAGCCGCACC 58.826 50.000 0.00 0.00 37.60 5.01
1828 2043 8.578151 CCAAATCAAATCCAAACCAATCAAAAT 58.422 29.630 0.00 0.00 0.00 1.82
1829 2044 7.559170 ACCAAATCAAATCCAAACCAATCAAAA 59.441 29.630 0.00 0.00 0.00 2.44
1830 2045 7.059156 ACCAAATCAAATCCAAACCAATCAAA 58.941 30.769 0.00 0.00 0.00 2.69
1831 2046 6.599445 ACCAAATCAAATCCAAACCAATCAA 58.401 32.000 0.00 0.00 0.00 2.57
1832 2047 6.185114 ACCAAATCAAATCCAAACCAATCA 57.815 33.333 0.00 0.00 0.00 2.57
1833 2048 7.361894 CAAACCAAATCAAATCCAAACCAATC 58.638 34.615 0.00 0.00 0.00 2.67
1834 2049 6.264970 CCAAACCAAATCAAATCCAAACCAAT 59.735 34.615 0.00 0.00 0.00 3.16
1835 2050 5.591877 CCAAACCAAATCAAATCCAAACCAA 59.408 36.000 0.00 0.00 0.00 3.67
1836 2051 5.128919 CCAAACCAAATCAAATCCAAACCA 58.871 37.500 0.00 0.00 0.00 3.67
1837 2052 5.008514 CACCAAACCAAATCAAATCCAAACC 59.991 40.000 0.00 0.00 0.00 3.27
1838 2053 5.588246 ACACCAAACCAAATCAAATCCAAAC 59.412 36.000 0.00 0.00 0.00 2.93
1839 2054 5.587844 CACACCAAACCAAATCAAATCCAAA 59.412 36.000 0.00 0.00 0.00 3.28
1842 2057 4.954875 TCACACCAAACCAAATCAAATCC 58.045 39.130 0.00 0.00 0.00 3.01
1847 2062 4.202202 GGTTGATCACACCAAACCAAATCA 60.202 41.667 17.20 0.00 0.00 2.57
1938 2164 1.875514 GCAACAACATGAGCACTCAGA 59.124 47.619 0.00 0.00 43.61 3.27
2632 2859 2.279451 CATCATTCGAGGCGCGGA 60.279 61.111 11.46 1.07 41.33 5.54
2643 2870 2.636830 CTCGACAAAGCCCTCATCATT 58.363 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.