Multiple sequence alignment - TraesCS7D01G478700

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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 TraesCS7D01G478700 chr7D 100.000 3437 0 0 1 3437 589392226 589388790 0.000000e+00 6348
1 TraesCS7D01G478700 chr7D 85.987 157 16 1 26 176 589448273 589448117 2.740000e-36 163
2 TraesCS7D01G478700 chr7A 94.192 2600 100 22 539 3123 680681141 680678578 0.000000e+00 3917
3 TraesCS7D01G478700 chr7A 92.913 254 9 2 26 270 680682813 680682560 9.070000e-96 361
4 TraesCS7D01G478700 chr7A 91.837 196 14 2 3116 3309 680677658 680677463 4.370000e-69 272
5 TraesCS7D01G478700 chr7A 82.857 210 25 7 301 505 680682559 680682356 9.800000e-41 178
6 TraesCS7D01G478700 chr7A 88.189 127 15 0 3311 3437 680665879 680665753 5.940000e-33 152
7 TraesCS7D01G478700 chr7B 92.644 2746 134 32 539 3271 663751605 663748915 0.000000e+00 3890
8 TraesCS7D01G478700 chr7B 93.491 1982 85 20 539 2511 663842874 663844820 0.000000e+00 2905
9 TraesCS7D01G478700 chr7B 88.723 736 66 11 2708 3437 663846247 663846971 0.000000e+00 883
10 TraesCS7D01G478700 chr7B 87.890 545 32 16 1 534 663752703 663752182 8.150000e-171 610
11 TraesCS7D01G478700 chr7B 93.625 251 9 2 26 270 663840320 663840569 5.420000e-98 368
12 TraesCS7D01G478700 chr7B 92.466 146 11 0 2578 2723 663844848 663844993 3.480000e-50 209
13 TraesCS7D01G478700 chr2B 82.353 1921 255 50 692 2556 138993599 138991707 0.000000e+00 1592
14 TraesCS7D01G478700 chr2B 82.328 1624 201 46 914 2479 12996047 12994452 0.000000e+00 1330
15 TraesCS7D01G478700 chr2B 80.226 1861 287 45 680 2476 12421990 12423833 0.000000e+00 1323
16 TraesCS7D01G478700 chr2B 81.907 1636 213 36 899 2479 11445348 11446955 0.000000e+00 1304
17 TraesCS7D01G478700 chr2D 81.927 1920 254 53 694 2556 85929888 85928005 0.000000e+00 1537
18 TraesCS7D01G478700 chr2D 81.494 1821 258 41 672 2433 19586685 19588485 0.000000e+00 1423
19 TraesCS7D01G478700 chr2D 80.960 1875 269 51 677 2479 8695334 8697192 0.000000e+00 1404
20 TraesCS7D01G478700 chr2D 82.540 1638 200 41 899 2479 9665345 9663737 0.000000e+00 1362
21 TraesCS7D01G478700 chr2D 80.258 1859 273 53 689 2476 9604432 9606267 0.000000e+00 1314
22 TraesCS7D01G478700 chr2D 81.102 1524 222 31 1000 2477 8670689 8672192 0.000000e+00 1158
23 TraesCS7D01G478700 chr2A 80.867 1453 238 18 1000 2414 7727400 7728850 0.000000e+00 1107
24 TraesCS7D01G478700 chr2A 82.143 504 66 13 2076 2568 86387306 86386816 8.880000e-111 411
25 TraesCS7D01G478700 chr2A 84.252 254 38 2 2232 2485 7513506 7513255 2.650000e-61 246
26 TraesCS7D01G478700 chrUn 83.061 1222 181 19 1280 2485 334662455 334663666 0.000000e+00 1086


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 TraesCS7D01G478700 chr7D 589388790 589392226 3436 True 6348.00 6348 100.00000 1 3437 1 chr7D.!!$R1 3436
1 TraesCS7D01G478700 chr7A 680677463 680682813 5350 True 1182.00 3917 90.44975 26 3309 4 chr7A.!!$R2 3283
2 TraesCS7D01G478700 chr7B 663748915 663752703 3788 True 2250.00 3890 90.26700 1 3271 2 chr7B.!!$R1 3270
3 TraesCS7D01G478700 chr7B 663840320 663846971 6651 False 1091.25 2905 92.07625 26 3437 4 chr7B.!!$F1 3411
4 TraesCS7D01G478700 chr2B 138991707 138993599 1892 True 1592.00 1592 82.35300 692 2556 1 chr2B.!!$R2 1864
5 TraesCS7D01G478700 chr2B 12994452 12996047 1595 True 1330.00 1330 82.32800 914 2479 1 chr2B.!!$R1 1565
6 TraesCS7D01G478700 chr2B 12421990 12423833 1843 False 1323.00 1323 80.22600 680 2476 1 chr2B.!!$F2 1796
7 TraesCS7D01G478700 chr2B 11445348 11446955 1607 False 1304.00 1304 81.90700 899 2479 1 chr2B.!!$F1 1580
8 TraesCS7D01G478700 chr2D 85928005 85929888 1883 True 1537.00 1537 81.92700 694 2556 1 chr2D.!!$R2 1862
9 TraesCS7D01G478700 chr2D 19586685 19588485 1800 False 1423.00 1423 81.49400 672 2433 1 chr2D.!!$F4 1761
10 TraesCS7D01G478700 chr2D 8695334 8697192 1858 False 1404.00 1404 80.96000 677 2479 1 chr2D.!!$F2 1802
11 TraesCS7D01G478700 chr2D 9663737 9665345 1608 True 1362.00 1362 82.54000 899 2479 1 chr2D.!!$R1 1580
12 TraesCS7D01G478700 chr2D 9604432 9606267 1835 False 1314.00 1314 80.25800 689 2476 1 chr2D.!!$F3 1787
13 TraesCS7D01G478700 chr2D 8670689 8672192 1503 False 1158.00 1158 81.10200 1000 2477 1 chr2D.!!$F1 1477
14 TraesCS7D01G478700 chr2A 7727400 7728850 1450 False 1107.00 1107 80.86700 1000 2414 1 chr2A.!!$F1 1414
15 TraesCS7D01G478700 chrUn 334662455 334663666 1211 False 1086.00 1086 83.06100 1280 2485 1 chrUn.!!$F1 1205

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
952 3630 0.033504 TTTGTCCAGACTCCGTGCTC 59.966 55.0 0.00 0.00 0.0 4.26 F
1440 4164 1.715019 TTGTTGTCCTCCTGGGTGGG 61.715 60.0 7.74 2.34 36.2 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 4749 1.961793 TTCAACAAGTGAACCTCGGG 58.038 50.0 0.0 0.0 41.47 5.14 R
3285 8259 0.548510 CCAATCTCCTCCTTCCCACC 59.451 60.0 0.0 0.0 0.00 4.61 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
114 124 1.160137 GGCACCAGAGTTGACATGAC 58.840 55.000 0.00 0.00 0.00 3.06
146 156 3.855950 CGAAGTTTAGTTAAGACGGCGAT 59.144 43.478 16.62 1.24 0.00 4.58
160 170 1.455786 CGGCGATAAATTGAGCTACCG 59.544 52.381 0.00 0.00 0.00 4.02
278 288 1.794714 AGAATATCCTGCCTCCGTGT 58.205 50.000 0.00 0.00 0.00 4.49
345 359 4.707030 TTCTTAATGAGCTTGCATGTGG 57.293 40.909 1.14 0.00 0.00 4.17
350 364 2.678934 AGCTTGCATGTGGGCCAG 60.679 61.111 6.40 0.00 0.00 4.85
353 367 1.039233 GCTTGCATGTGGGCCAGTAT 61.039 55.000 6.40 0.97 0.00 2.12
373 389 9.907229 CCAGTATGTCAGTCTAGTATATATCCA 57.093 37.037 0.00 0.00 0.00 3.41
378 394 9.815306 ATGTCAGTCTAGTATATATCCAAGTGT 57.185 33.333 0.00 0.00 0.00 3.55
391 407 5.746990 ATCCAAGTGTTACAACTCTAGCT 57.253 39.130 0.00 0.00 32.90 3.32
405 421 7.386851 ACAACTCTAGCTAGCTGATTTGTTAA 58.613 34.615 27.51 10.75 32.35 2.01
406 422 7.547370 ACAACTCTAGCTAGCTGATTTGTTAAG 59.453 37.037 27.51 17.35 32.35 1.85
411 427 9.502091 TCTAGCTAGCTGATTTGTTAAGAAAAA 57.498 29.630 27.68 0.00 0.00 1.94
412 428 9.548208 CTAGCTAGCTGATTTGTTAAGAAAAAC 57.452 33.333 27.68 1.12 0.00 2.43
413 429 8.171164 AGCTAGCTGATTTGTTAAGAAAAACT 57.829 30.769 18.57 0.93 0.00 2.66
414 430 9.284968 AGCTAGCTGATTTGTTAAGAAAAACTA 57.715 29.630 18.57 1.93 0.00 2.24
415 431 9.548208 GCTAGCTGATTTGTTAAGAAAAACTAG 57.452 33.333 7.70 10.70 0.00 2.57
416 432 9.548208 CTAGCTGATTTGTTAAGAAAAACTAGC 57.452 33.333 1.47 9.21 32.21 3.42
430 448 8.240883 AGAAAAACTAGCTAATTAGTCGTGTG 57.759 34.615 13.91 2.43 32.84 3.82
443 461 3.829948 AGTCGTGTGGTTTAGTCGTATG 58.170 45.455 0.00 0.00 0.00 2.39
449 467 4.624452 GTGTGGTTTAGTCGTATGAGTTCC 59.376 45.833 0.00 0.43 0.00 3.62
456 474 2.563179 AGTCGTATGAGTTCCAGTGCTT 59.437 45.455 0.00 0.00 0.00 3.91
462 480 5.505654 CGTATGAGTTCCAGTGCTTTTTGTT 60.506 40.000 0.00 0.00 0.00 2.83
469 487 6.756542 AGTTCCAGTGCTTTTTGTTTGTAATC 59.243 34.615 0.00 0.00 0.00 1.75
475 493 5.289917 GTGCTTTTTGTTTGTAATCGGTGTT 59.710 36.000 0.00 0.00 0.00 3.32
476 494 6.472808 GTGCTTTTTGTTTGTAATCGGTGTTA 59.527 34.615 0.00 0.00 0.00 2.41
478 496 6.693978 GCTTTTTGTTTGTAATCGGTGTTAGT 59.306 34.615 0.00 0.00 0.00 2.24
480 498 9.719279 CTTTTTGTTTGTAATCGGTGTTAGTTA 57.281 29.630 0.00 0.00 0.00 2.24
482 500 7.424227 TTGTTTGTAATCGGTGTTAGTTAGG 57.576 36.000 0.00 0.00 0.00 2.69
483 501 6.757237 TGTTTGTAATCGGTGTTAGTTAGGA 58.243 36.000 0.00 0.00 0.00 2.94
484 502 7.388437 TGTTTGTAATCGGTGTTAGTTAGGAT 58.612 34.615 0.00 0.00 0.00 3.24
485 503 7.332430 TGTTTGTAATCGGTGTTAGTTAGGATG 59.668 37.037 0.00 0.00 0.00 3.51
493 1952 5.699458 CGGTGTTAGTTAGGATGTCAAGTTT 59.301 40.000 0.00 0.00 0.00 2.66
496 1955 7.390718 GGTGTTAGTTAGGATGTCAAGTTTGAT 59.609 37.037 0.00 0.00 39.73 2.57
530 2002 7.510549 TTGTTTCCTCAATCTAAGGACAAAG 57.489 36.000 0.00 0.00 42.63 2.77
531 2003 6.601332 TGTTTCCTCAATCTAAGGACAAAGT 58.399 36.000 0.00 0.00 42.63 2.66
532 2004 7.741785 TGTTTCCTCAATCTAAGGACAAAGTA 58.258 34.615 0.00 0.00 42.63 2.24
533 2005 7.878127 TGTTTCCTCAATCTAAGGACAAAGTAG 59.122 37.037 0.00 0.00 42.63 2.57
534 2006 5.978814 TCCTCAATCTAAGGACAAAGTAGC 58.021 41.667 0.00 0.00 38.01 3.58
536 2008 6.213600 TCCTCAATCTAAGGACAAAGTAGCTT 59.786 38.462 0.00 0.00 38.01 3.74
537 2009 6.536941 CCTCAATCTAAGGACAAAGTAGCTTC 59.463 42.308 0.00 0.00 35.83 3.86
575 3232 6.404184 CCGGATGCTGTGTGAAATATAAAACA 60.404 38.462 0.00 0.00 0.00 2.83
577 3234 7.540400 CGGATGCTGTGTGAAATATAAAACAAA 59.460 33.333 0.00 0.00 0.00 2.83
596 3253 5.797051 ACAAATCCAATGGAAGACAAATGG 58.203 37.500 5.89 0.00 39.95 3.16
610 3267 9.136323 GGAAGACAAATGGAAGGATAATTACAT 57.864 33.333 0.00 0.00 35.12 2.29
625 3282 8.280497 GGATAATTACATCGTACATGTTTGTCC 58.720 37.037 2.30 14.39 37.28 4.02
627 3284 7.681939 AATTACATCGTACATGTTTGTCCTT 57.318 32.000 2.30 0.00 37.28 3.36
628 3285 8.780846 AATTACATCGTACATGTTTGTCCTTA 57.219 30.769 2.30 0.00 37.28 2.69
629 3286 7.821595 TTACATCGTACATGTTTGTCCTTAG 57.178 36.000 2.30 0.00 37.28 2.18
631 3288 6.640518 ACATCGTACATGTTTGTCCTTAGAT 58.359 36.000 2.30 0.00 37.28 1.98
632 3289 7.103641 ACATCGTACATGTTTGTCCTTAGATT 58.896 34.615 2.30 0.00 37.28 2.40
633 3290 6.961359 TCGTACATGTTTGTCCTTAGATTG 57.039 37.500 2.30 0.00 37.28 2.67
634 3291 6.693466 TCGTACATGTTTGTCCTTAGATTGA 58.307 36.000 2.30 0.00 37.28 2.57
635 3292 6.811665 TCGTACATGTTTGTCCTTAGATTGAG 59.188 38.462 2.30 0.00 37.28 3.02
637 3294 7.758076 CGTACATGTTTGTCCTTAGATTGAGTA 59.242 37.037 2.30 0.00 37.28 2.59
639 3296 8.553459 ACATGTTTGTCCTTAGATTGAGTAAG 57.447 34.615 0.00 0.00 0.00 2.34
640 3297 7.607991 ACATGTTTGTCCTTAGATTGAGTAAGG 59.392 37.037 0.00 2.94 45.61 2.69
642 3299 8.197592 TGTTTGTCCTTAGATTGAGTAAGGTA 57.802 34.615 8.41 0.00 44.84 3.08
643 3300 8.311836 TGTTTGTCCTTAGATTGAGTAAGGTAG 58.688 37.037 8.41 0.00 44.84 3.18
644 3301 6.466885 TGTCCTTAGATTGAGTAAGGTAGC 57.533 41.667 8.41 0.00 44.84 3.58
645 3302 5.955959 TGTCCTTAGATTGAGTAAGGTAGCA 59.044 40.000 8.41 4.84 44.84 3.49
646 3303 6.439375 TGTCCTTAGATTGAGTAAGGTAGCAA 59.561 38.462 8.41 0.00 44.84 3.91
647 3304 6.981559 GTCCTTAGATTGAGTAAGGTAGCAAG 59.018 42.308 8.41 0.00 44.84 4.01
648 3305 5.755861 CCTTAGATTGAGTAAGGTAGCAAGC 59.244 44.000 0.00 0.00 41.18 4.01
649 3306 6.407525 CCTTAGATTGAGTAAGGTAGCAAGCT 60.408 42.308 0.00 0.00 41.18 3.74
650 3307 7.201920 CCTTAGATTGAGTAAGGTAGCAAGCTA 60.202 40.741 0.00 0.00 41.18 3.32
651 3308 6.546428 AGATTGAGTAAGGTAGCAAGCTAA 57.454 37.500 2.92 0.00 35.49 3.09
652 3309 7.130681 AGATTGAGTAAGGTAGCAAGCTAAT 57.869 36.000 2.92 0.00 35.49 1.73
653 3310 8.251383 AGATTGAGTAAGGTAGCAAGCTAATA 57.749 34.615 2.92 0.00 35.49 0.98
654 3311 8.364142 AGATTGAGTAAGGTAGCAAGCTAATAG 58.636 37.037 2.92 0.00 35.49 1.73
655 3312 6.406692 TGAGTAAGGTAGCAAGCTAATAGG 57.593 41.667 2.92 0.00 31.75 2.57
656 3313 6.134055 TGAGTAAGGTAGCAAGCTAATAGGA 58.866 40.000 2.92 0.00 31.75 2.94
657 3314 6.782988 TGAGTAAGGTAGCAAGCTAATAGGAT 59.217 38.462 2.92 0.00 31.75 3.24
658 3315 6.998802 AGTAAGGTAGCAAGCTAATAGGATG 58.001 40.000 2.92 0.00 31.75 3.51
659 3316 6.782988 AGTAAGGTAGCAAGCTAATAGGATGA 59.217 38.462 2.92 0.00 31.75 2.92
660 3317 6.694445 AAGGTAGCAAGCTAATAGGATGAT 57.306 37.500 2.92 0.00 31.75 2.45
661 3318 6.047511 AGGTAGCAAGCTAATAGGATGATG 57.952 41.667 2.92 0.00 0.00 3.07
662 3319 5.545723 AGGTAGCAAGCTAATAGGATGATGT 59.454 40.000 2.92 0.00 0.00 3.06
663 3320 5.641209 GGTAGCAAGCTAATAGGATGATGTG 59.359 44.000 2.92 0.00 0.00 3.21
730 3391 1.522668 TTTCATGTTGCTCGGACAGG 58.477 50.000 0.00 0.00 0.00 4.00
745 3406 0.180406 ACAGGTGGCTTGTCGTTCTT 59.820 50.000 0.00 0.00 0.00 2.52
771 3434 2.457366 AGGTTAGGACTGCAACTTCG 57.543 50.000 0.00 0.00 0.00 3.79
911 3588 3.070018 ACTTCGCAAAGAATCTCTGTGG 58.930 45.455 0.00 0.00 38.34 4.17
919 3596 4.713792 AAGAATCTCTGTGGAACTTGGT 57.286 40.909 0.00 0.00 38.04 3.67
947 3625 3.045601 AGTCAATTTGTCCAGACTCCG 57.954 47.619 0.00 0.00 36.69 4.63
948 3626 2.368875 AGTCAATTTGTCCAGACTCCGT 59.631 45.455 0.00 0.00 36.69 4.69
949 3627 2.480419 GTCAATTTGTCCAGACTCCGTG 59.520 50.000 0.00 0.00 0.00 4.94
950 3628 1.197721 CAATTTGTCCAGACTCCGTGC 59.802 52.381 0.00 0.00 0.00 5.34
951 3629 0.687354 ATTTGTCCAGACTCCGTGCT 59.313 50.000 0.00 0.00 0.00 4.40
952 3630 0.033504 TTTGTCCAGACTCCGTGCTC 59.966 55.000 0.00 0.00 0.00 4.26
953 3631 1.816863 TTGTCCAGACTCCGTGCTCC 61.817 60.000 0.00 0.00 0.00 4.70
1345 4069 6.563381 GCGTTCTCGAACAAAAACTGAGAATA 60.563 38.462 10.10 0.00 44.66 1.75
1360 4084 4.858850 TGAGAATAATGACAAGGCCATGT 58.141 39.130 14.67 14.67 35.90 3.21
1440 4164 1.715019 TTGTTGTCCTCCTGGGTGGG 61.715 60.000 7.74 2.34 36.20 4.61
2002 4733 7.852263 AGTACAAATAGCAGATGAGTTTACCT 58.148 34.615 0.00 0.00 0.00 3.08
2018 4749 0.035056 ACCTGGGAGTTGCATAGTGC 60.035 55.000 0.00 0.00 45.29 4.40
2296 5048 2.544069 GCAGATCCTAGTGTTAGACCGC 60.544 54.545 0.00 0.00 0.00 5.68
2299 5051 3.767673 AGATCCTAGTGTTAGACCGCAAA 59.232 43.478 0.00 0.00 0.00 3.68
2310 5062 1.412710 AGACCGCAAAGAGACTTCACA 59.587 47.619 0.00 0.00 0.00 3.58
2532 5294 7.145323 GTGTTCATGTGGCTTTGTAGTTAAAT 58.855 34.615 0.00 0.00 0.00 1.40
2533 5295 8.293867 GTGTTCATGTGGCTTTGTAGTTAAATA 58.706 33.333 0.00 0.00 0.00 1.40
2678 5445 3.070476 TCATTTGATGTGGCAGTAGCA 57.930 42.857 0.00 0.00 44.61 3.49
2679 5446 3.623703 TCATTTGATGTGGCAGTAGCAT 58.376 40.909 0.00 0.00 44.61 3.79
2709 5476 3.488778 TCGGTAAGGTGGCTTGTTAAA 57.511 42.857 0.00 0.00 0.00 1.52
2754 6790 7.014711 ACGAGAAAGAGGTATACACATCATCAT 59.985 37.037 5.01 0.00 37.94 2.45
2886 6930 2.291465 CCATCCAATCAGTAACGCCATG 59.709 50.000 0.00 0.00 0.00 3.66
2902 6946 3.551454 CGCCATGCATAAAGGAAAGATGG 60.551 47.826 0.00 0.00 33.42 3.51
3014 7058 6.500041 ACGATTAGATCAAGAAGTCTGCTAC 58.500 40.000 0.00 0.00 0.00 3.58
3041 7085 5.067023 GCCAAGATCTACCCAAATCAGAAAG 59.933 44.000 0.00 0.00 0.00 2.62
3095 7139 3.930618 TCAAAACACGTGTGAATTCGAC 58.069 40.909 24.16 0.00 0.00 4.20
3101 7146 2.090041 CACGTGTGAATTCGACTTACGG 59.910 50.000 7.58 8.21 42.82 4.02
3108 7153 2.904697 ATTCGACTTACGGGGAATCC 57.095 50.000 0.00 0.00 42.82 3.01
3126 8100 1.961277 CGTTTTGGCGAGGTGCTCT 60.961 57.895 0.00 0.00 45.43 4.09
3183 8157 3.277211 TTGAAGTCCGCGACCTCCG 62.277 63.158 8.23 0.00 42.21 4.63
3309 8283 1.702401 GGAAGGAGGAGATTGGGGATC 59.298 57.143 0.00 0.00 34.83 3.36
3330 8304 2.521105 CCGGTAGGCACTGGTAATAC 57.479 55.000 0.00 0.00 45.06 1.89
3336 8310 1.211949 AGGCACTGGTAATACGGCATT 59.788 47.619 0.00 0.00 37.18 3.56
3340 8314 3.242739 GCACTGGTAATACGGCATTGAAG 60.243 47.826 0.00 0.00 0.00 3.02
3348 8322 0.671251 ACGGCATTGAAGCGGAAAAA 59.329 45.000 0.00 0.00 38.12 1.94
3355 8329 4.155280 GCATTGAAGCGGAAAAAGGTACTA 59.845 41.667 0.00 0.00 38.49 1.82
3375 8349 7.276658 GGTACTATGTCTCTTGTTTGACTCATG 59.723 40.741 0.00 0.00 34.57 3.07
3378 8352 4.769688 TGTCTCTTGTTTGACTCATGTGT 58.230 39.130 0.00 0.00 34.57 3.72
3385 8359 3.563808 TGTTTGACTCATGTGTTGGCTAC 59.436 43.478 1.31 0.00 0.00 3.58
3400 8374 3.086282 TGGCTACACTACGAGAATGTGA 58.914 45.455 0.00 0.00 35.83 3.58
3401 8375 3.699538 TGGCTACACTACGAGAATGTGAT 59.300 43.478 0.00 0.00 35.83 3.06
3433 8407 1.801178 CCCAGAGTTTTTCGAGTGCTC 59.199 52.381 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 156 3.431922 CGGAGTCGGTAGCTCAATTTA 57.568 47.619 0.00 0.00 34.83 1.40
160 170 5.725325 AAATTATAGTAGCCTCCGGAGTC 57.275 43.478 29.25 18.50 0.00 3.36
260 270 1.412710 TCACACGGAGGCAGGATATTC 59.587 52.381 0.00 0.00 0.00 1.75
345 359 8.754991 ATATATACTAGACTGACATACTGGCC 57.245 38.462 0.00 0.00 0.00 5.36
353 367 9.642343 AACACTTGGATATATACTAGACTGACA 57.358 33.333 12.69 0.00 0.00 3.58
373 389 5.477291 TCAGCTAGCTAGAGTTGTAACACTT 59.523 40.000 25.15 0.00 32.16 3.16
378 394 6.936279 ACAAATCAGCTAGCTAGAGTTGTAA 58.064 36.000 34.89 12.95 45.23 2.41
391 407 9.284968 AGCTAGTTTTTCTTAACAAATCAGCTA 57.715 29.630 0.00 0.00 0.00 3.32
405 421 7.331193 CCACACGACTAATTAGCTAGTTTTTCT 59.669 37.037 12.54 0.00 32.14 2.52
406 422 7.117379 ACCACACGACTAATTAGCTAGTTTTTC 59.883 37.037 12.54 3.64 32.14 2.29
411 427 5.656213 AACCACACGACTAATTAGCTAGT 57.344 39.130 12.54 7.24 34.76 2.57
412 428 7.256286 ACTAAACCACACGACTAATTAGCTAG 58.744 38.462 12.54 6.64 0.00 3.42
413 429 7.161773 ACTAAACCACACGACTAATTAGCTA 57.838 36.000 12.54 0.00 0.00 3.32
414 430 6.034161 ACTAAACCACACGACTAATTAGCT 57.966 37.500 12.54 0.00 0.00 3.32
415 431 5.004156 CGACTAAACCACACGACTAATTAGC 59.996 44.000 12.54 4.82 0.00 3.09
416 432 6.088824 ACGACTAAACCACACGACTAATTAG 58.911 40.000 11.05 11.05 0.00 1.73
425 443 3.829948 ACTCATACGACTAAACCACACG 58.170 45.455 0.00 0.00 0.00 4.49
426 444 4.624452 GGAACTCATACGACTAAACCACAC 59.376 45.833 0.00 0.00 0.00 3.82
430 448 4.863131 CACTGGAACTCATACGACTAAACC 59.137 45.833 0.00 0.00 0.00 3.27
443 461 4.494484 ACAAACAAAAAGCACTGGAACTC 58.506 39.130 0.00 0.00 0.00 3.01
449 467 5.040635 ACCGATTACAAACAAAAAGCACTG 58.959 37.500 0.00 0.00 0.00 3.66
456 474 8.344098 CCTAACTAACACCGATTACAAACAAAA 58.656 33.333 0.00 0.00 0.00 2.44
462 480 6.938507 ACATCCTAACTAACACCGATTACAA 58.061 36.000 0.00 0.00 0.00 2.41
469 487 4.817517 ACTTGACATCCTAACTAACACCG 58.182 43.478 0.00 0.00 0.00 4.94
476 494 9.965902 AATCTAATCAAACTTGACATCCTAACT 57.034 29.630 0.00 0.00 40.49 2.24
505 1964 7.725844 ACTTTGTCCTTAGATTGAGGAAACAAT 59.274 33.333 0.00 0.00 44.52 2.71
530 2002 3.181520 CGGTATTTGTGCACTGAAGCTAC 60.182 47.826 19.41 12.05 34.99 3.58
531 2003 3.000041 CGGTATTTGTGCACTGAAGCTA 59.000 45.455 19.41 1.16 34.99 3.32
532 2004 1.806542 CGGTATTTGTGCACTGAAGCT 59.193 47.619 19.41 2.08 34.99 3.74
533 2005 1.135689 CCGGTATTTGTGCACTGAAGC 60.136 52.381 19.41 9.43 0.00 3.86
534 2006 2.422597 TCCGGTATTTGTGCACTGAAG 58.577 47.619 19.41 3.07 0.00 3.02
536 2008 2.355197 CATCCGGTATTTGTGCACTGA 58.645 47.619 19.41 6.80 0.00 3.41
537 2009 1.202177 GCATCCGGTATTTGTGCACTG 60.202 52.381 19.41 4.70 35.93 3.66
575 3232 6.296030 CCTTCCATTTGTCTTCCATTGGATTT 60.296 38.462 6.15 0.00 36.29 2.17
577 3234 4.713321 CCTTCCATTTGTCTTCCATTGGAT 59.287 41.667 6.15 0.00 36.29 3.41
596 3253 9.864034 CAAACATGTACGATGTAATTATCCTTC 57.136 33.333 0.00 0.00 0.00 3.46
610 3267 6.693466 TCAATCTAAGGACAAACATGTACGA 58.307 36.000 0.00 0.00 0.00 3.43
625 3282 6.578023 AGCTTGCTACCTTACTCAATCTAAG 58.422 40.000 0.00 0.00 0.00 2.18
627 3284 7.655521 TTAGCTTGCTACCTTACTCAATCTA 57.344 36.000 1.37 0.00 0.00 1.98
628 3285 6.546428 TTAGCTTGCTACCTTACTCAATCT 57.454 37.500 1.37 0.00 0.00 2.40
629 3286 7.600752 CCTATTAGCTTGCTACCTTACTCAATC 59.399 40.741 1.37 0.00 0.00 2.67
631 3288 6.610020 TCCTATTAGCTTGCTACCTTACTCAA 59.390 38.462 1.37 0.00 0.00 3.02
632 3289 6.134055 TCCTATTAGCTTGCTACCTTACTCA 58.866 40.000 1.37 0.00 0.00 3.41
633 3290 6.651975 TCCTATTAGCTTGCTACCTTACTC 57.348 41.667 1.37 0.00 0.00 2.59
634 3291 6.782988 TCATCCTATTAGCTTGCTACCTTACT 59.217 38.462 1.37 0.00 0.00 2.24
635 3292 6.994221 TCATCCTATTAGCTTGCTACCTTAC 58.006 40.000 1.37 0.00 0.00 2.34
637 3294 6.043706 ACATCATCCTATTAGCTTGCTACCTT 59.956 38.462 1.37 0.00 0.00 3.50
639 3296 5.641209 CACATCATCCTATTAGCTTGCTACC 59.359 44.000 1.37 0.00 0.00 3.18
640 3297 6.146837 CACACATCATCCTATTAGCTTGCTAC 59.853 42.308 1.37 0.00 0.00 3.58
642 3299 5.061853 CACACATCATCCTATTAGCTTGCT 58.938 41.667 0.00 0.00 0.00 3.91
643 3300 5.059161 TCACACATCATCCTATTAGCTTGC 58.941 41.667 0.00 0.00 0.00 4.01
644 3301 6.017605 GGTTCACACATCATCCTATTAGCTTG 60.018 42.308 0.00 0.00 0.00 4.01
645 3302 6.058183 GGTTCACACATCATCCTATTAGCTT 58.942 40.000 0.00 0.00 0.00 3.74
646 3303 5.367937 AGGTTCACACATCATCCTATTAGCT 59.632 40.000 0.00 0.00 0.00 3.32
647 3304 5.615289 AGGTTCACACATCATCCTATTAGC 58.385 41.667 0.00 0.00 0.00 3.09
648 3305 7.015682 AGGTAGGTTCACACATCATCCTATTAG 59.984 40.741 0.00 0.00 31.61 1.73
649 3306 6.844388 AGGTAGGTTCACACATCATCCTATTA 59.156 38.462 0.00 0.00 31.61 0.98
650 3307 5.667626 AGGTAGGTTCACACATCATCCTATT 59.332 40.000 0.00 0.00 31.61 1.73
651 3308 5.219739 AGGTAGGTTCACACATCATCCTAT 58.780 41.667 0.00 0.00 31.61 2.57
652 3309 4.620723 AGGTAGGTTCACACATCATCCTA 58.379 43.478 0.00 0.00 0.00 2.94
653 3310 3.454858 AGGTAGGTTCACACATCATCCT 58.545 45.455 0.00 0.00 0.00 3.24
654 3311 3.914426 AGGTAGGTTCACACATCATCC 57.086 47.619 0.00 0.00 0.00 3.51
655 3312 5.599999 ACTAGGTAGGTTCACACATCATC 57.400 43.478 0.00 0.00 0.00 2.92
656 3313 6.195700 AGTACTAGGTAGGTTCACACATCAT 58.804 40.000 0.00 0.00 0.00 2.45
657 3314 5.577100 AGTACTAGGTAGGTTCACACATCA 58.423 41.667 0.00 0.00 0.00 3.07
658 3315 6.827762 AGTAGTACTAGGTAGGTTCACACATC 59.172 42.308 1.87 0.00 0.00 3.06
659 3316 6.602406 CAGTAGTACTAGGTAGGTTCACACAT 59.398 42.308 1.87 0.00 0.00 3.21
660 3317 5.942236 CAGTAGTACTAGGTAGGTTCACACA 59.058 44.000 1.87 0.00 0.00 3.72
661 3318 6.176183 TCAGTAGTACTAGGTAGGTTCACAC 58.824 44.000 1.87 0.00 0.00 3.82
662 3319 6.378661 TCAGTAGTACTAGGTAGGTTCACA 57.621 41.667 1.87 0.00 0.00 3.58
663 3320 7.108847 TCTTCAGTAGTACTAGGTAGGTTCAC 58.891 42.308 1.87 0.00 0.00 3.18
707 3367 4.155826 CCTGTCCGAGCAACATGAAAATAA 59.844 41.667 0.00 0.00 0.00 1.40
709 3369 2.489329 CCTGTCCGAGCAACATGAAAAT 59.511 45.455 0.00 0.00 0.00 1.82
730 3391 4.483476 AAACATAAGAACGACAAGCCAC 57.517 40.909 0.00 0.00 0.00 5.01
745 3406 6.368779 AGTTGCAGTCCTAACCTAAACATA 57.631 37.500 0.00 0.00 0.00 2.29
771 3434 2.497273 GCATAATGGCCCATGGAATACC 59.503 50.000 15.22 9.68 0.00 2.73
911 3588 4.803098 TTGACTAGCCTCTACCAAGTTC 57.197 45.455 0.00 0.00 0.00 3.01
919 3596 5.023452 TCTGGACAAATTGACTAGCCTCTA 58.977 41.667 0.00 0.00 0.00 2.43
947 3625 1.555075 TGGTTGGTCTCTATGGAGCAC 59.445 52.381 0.23 1.13 42.31 4.40
948 3626 1.833630 CTGGTTGGTCTCTATGGAGCA 59.166 52.381 0.23 0.00 41.16 4.26
949 3627 1.474143 GCTGGTTGGTCTCTATGGAGC 60.474 57.143 0.23 0.00 39.31 4.70
950 3628 1.833630 TGCTGGTTGGTCTCTATGGAG 59.166 52.381 0.00 0.00 40.73 3.86
951 3629 1.833630 CTGCTGGTTGGTCTCTATGGA 59.166 52.381 0.00 0.00 0.00 3.41
952 3630 1.745141 GCTGCTGGTTGGTCTCTATGG 60.745 57.143 0.00 0.00 0.00 2.74
953 3631 1.065926 TGCTGCTGGTTGGTCTCTATG 60.066 52.381 0.00 0.00 0.00 2.23
1015 3702 1.135689 CAATTCACCTGTAACCGCAGC 60.136 52.381 0.00 0.00 35.28 5.25
1020 3707 3.751518 ACTCACCAATTCACCTGTAACC 58.248 45.455 0.00 0.00 0.00 2.85
1360 4084 1.599606 GCTCCTTCTGACTCGAGGCA 61.600 60.000 22.21 22.21 0.00 4.75
1743 4474 5.297547 TCAGAAGCAAACTCAATAACGACT 58.702 37.500 0.00 0.00 0.00 4.18
2018 4749 1.961793 TTCAACAAGTGAACCTCGGG 58.038 50.000 0.00 0.00 41.47 5.14
2136 4867 4.339748 TGTTTGGATGCAAACCATAGCTA 58.660 39.130 31.87 14.59 39.15 3.32
2274 5026 2.688446 CGGTCTAACACTAGGATCTGCA 59.312 50.000 0.00 0.00 0.00 4.41
2296 5048 6.304356 TGCAATTAGTGTGAAGTCTCTTTG 57.696 37.500 0.00 0.00 0.00 2.77
2299 5051 4.940046 CCATGCAATTAGTGTGAAGTCTCT 59.060 41.667 0.00 0.00 0.00 3.10
2310 5062 7.014615 GGTATCCTTGATTTCCATGCAATTAGT 59.985 37.037 0.00 0.00 0.00 2.24
2532 5294 5.300792 TCAGCGGTATACATGAACACATCTA 59.699 40.000 5.01 0.00 0.00 1.98
2533 5295 4.099419 TCAGCGGTATACATGAACACATCT 59.901 41.667 5.01 0.00 0.00 2.90
2617 5381 4.716784 AGAGCAGGTGGATTGTTGTATCTA 59.283 41.667 0.00 0.00 0.00 1.98
2678 5445 3.606687 CACCTTACCGAAACCAGCTAAT 58.393 45.455 0.00 0.00 0.00 1.73
2679 5446 2.289819 CCACCTTACCGAAACCAGCTAA 60.290 50.000 0.00 0.00 0.00 3.09
2709 5476 5.124776 TCTCGTTGGTTCAATTTCTGTTTGT 59.875 36.000 0.00 0.00 0.00 2.83
2886 6930 4.275443 CAGAGCTCCATCTTTCCTTTATGC 59.725 45.833 10.93 0.00 0.00 3.14
2902 6946 2.052157 GTACAACACGTCACAGAGCTC 58.948 52.381 5.27 5.27 0.00 4.09
2979 7023 9.521841 TTCTTGATCTAATCGTATCCTGACTAT 57.478 33.333 0.00 0.00 0.00 2.12
3014 7058 0.742990 TTTGGGTAGATCTTGGCGCG 60.743 55.000 0.00 0.00 0.00 6.86
3101 7146 1.654023 CCTCGCCAAAACGGATTCCC 61.654 60.000 0.00 0.00 36.56 3.97
3108 7153 1.507141 AAGAGCACCTCGCCAAAACG 61.507 55.000 0.00 0.00 44.04 3.60
3183 8157 2.202703 CACCTAGTACGCGGCCAC 60.203 66.667 12.47 5.24 0.00 5.01
3192 8166 1.538512 GTATCGCCATCGCACCTAGTA 59.461 52.381 0.00 0.00 35.26 1.82
3277 8251 3.182263 CCTTCCCACCCCACCACA 61.182 66.667 0.00 0.00 0.00 4.17
3285 8259 0.548510 CCAATCTCCTCCTTCCCACC 59.451 60.000 0.00 0.00 0.00 4.61
3286 8260 0.548510 CCCAATCTCCTCCTTCCCAC 59.451 60.000 0.00 0.00 0.00 4.61
3289 8263 1.702401 GATCCCCAATCTCCTCCTTCC 59.298 57.143 0.00 0.00 0.00 3.46
3323 8297 1.263217 CCGCTTCAATGCCGTATTACC 59.737 52.381 0.00 0.00 0.00 2.85
3325 8299 2.605837 TCCGCTTCAATGCCGTATTA 57.394 45.000 0.00 0.00 0.00 0.98
3330 8304 1.339711 CTTTTTCCGCTTCAATGCCG 58.660 50.000 0.00 0.00 0.00 5.69
3336 8310 4.901868 ACATAGTACCTTTTTCCGCTTCA 58.098 39.130 0.00 0.00 0.00 3.02
3340 8314 4.756502 AGAGACATAGTACCTTTTTCCGC 58.243 43.478 0.00 0.00 0.00 5.54
3348 8322 6.493802 TGAGTCAAACAAGAGACATAGTACCT 59.506 38.462 0.00 0.00 37.23 3.08
3355 8329 5.371526 ACACATGAGTCAAACAAGAGACAT 58.628 37.500 0.00 0.00 37.23 3.06
3378 8352 3.508402 TCACATTCTCGTAGTGTAGCCAA 59.492 43.478 0.00 0.00 34.94 4.52
3385 8359 3.062639 GGCAACATCACATTCTCGTAGTG 59.937 47.826 0.00 0.00 34.67 2.74
3391 8365 3.064545 GCACTAGGCAACATCACATTCTC 59.935 47.826 0.00 0.00 43.97 2.87


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

AutoCloner maintained by Alex Coulton.