Multiple sequence alignment - TraesCS7B01G337600

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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 TraesCS7B01G337600 chr7B 100.000 5384 0 0 1 5384 592365588 592360205 0.000000e+00 9943.0
1 TraesCS7B01G337600 chr7A 94.351 4355 177 29 1040 5384 633040301 633036006 0.000000e+00 6634.0
2 TraesCS7B01G337600 chr7A 94.711 2666 99 26 1040 3698 632590898 632588268 0.000000e+00 4104.0
3 TraesCS7B01G337600 chr7A 95.087 2239 75 9 3164 5384 632971777 632969556 0.000000e+00 3494.0
4 TraesCS7B01G337600 chr7A 95.175 2176 79 8 3218 5384 632909170 632907012 0.000000e+00 3413.0
5 TraesCS7B01G337600 chr7A 94.014 2105 87 20 1040 3143 632911562 632909496 0.000000e+00 3153.0
6 TraesCS7B01G337600 chr7A 93.887 2094 89 20 1040 3132 632974014 632971959 0.000000e+00 3121.0
7 TraesCS7B01G337600 chr7A 93.818 1294 54 9 3706 4995 632588145 632586874 0.000000e+00 1923.0
8 TraesCS7B01G337600 chr7A 93.792 1047 42 8 4342 5384 632712321 632711294 0.000000e+00 1552.0
9 TraesCS7B01G337600 chr7A 93.505 1047 46 7 4342 5384 633096635 633095607 0.000000e+00 1537.0
10 TraesCS7B01G337600 chr7A 87.310 985 116 4 3569 4544 630389933 630390917 0.000000e+00 1118.0
11 TraesCS7B01G337600 chr7A 86.328 1024 107 24 2166 3167 631964009 631962997 0.000000e+00 1085.0
12 TraesCS7B01G337600 chr7A 86.771 960 97 19 2163 3103 630388346 630389294 0.000000e+00 1042.0
13 TraesCS7B01G337600 chr7A 87.840 773 89 4 3760 4528 631961088 631960317 0.000000e+00 902.0
14 TraesCS7B01G337600 chr7A 85.360 806 99 11 3772 4574 630035649 630036438 0.000000e+00 817.0
15 TraesCS7B01G337600 chr7A 84.981 526 66 5 2727 3247 630034536 630035053 6.180000e-144 521.0
16 TraesCS7B01G337600 chr7A 91.343 335 26 2 3197 3531 630389605 630389936 6.360000e-124 455.0
17 TraesCS7B01G337600 chr7A 96.567 233 4 3 5033 5265 632586875 632586647 3.040000e-102 383.0
18 TraesCS7B01G337600 chr7A 84.225 355 37 14 3339 3680 630035292 630035640 1.450000e-85 327.0
19 TraesCS7B01G337600 chr7A 81.892 370 48 14 1040 1398 630032736 630033097 1.470000e-75 294.0
20 TraesCS7B01G337600 chr7A 80.978 368 58 7 1626 1984 630387922 630388286 1.140000e-71 281.0
21 TraesCS7B01G337600 chr7A 81.096 365 49 15 1711 2068 630033382 630033733 1.910000e-69 274.0
22 TraesCS7B01G337600 chr7A 100.000 72 0 0 5313 5384 632586633 632586562 3.380000e-27 134.0
23 TraesCS7B01G337600 chr7D 93.399 2227 100 14 3170 5384 548805740 548803549 0.000000e+00 3254.0
24 TraesCS7B01G337600 chr7D 92.308 1378 68 13 706 2065 548808026 548806669 0.000000e+00 1923.0
25 TraesCS7B01G337600 chr7D 88.623 1336 113 24 2212 3524 548132996 548131677 0.000000e+00 1589.0
26 TraesCS7B01G337600 chr7D 95.905 928 27 6 2173 3094 548806668 548805746 0.000000e+00 1493.0
27 TraesCS7B01G337600 chr7D 80.583 1133 148 32 2163 3247 546752677 546753785 0.000000e+00 808.0
28 TraesCS7B01G337600 chr7D 85.200 750 103 5 3772 4518 546754399 546755143 0.000000e+00 763.0
29 TraesCS7B01G337600 chr7D 89.397 547 34 11 2 545 115100797 115100272 0.000000e+00 667.0
30 TraesCS7B01G337600 chr7D 83.790 438 49 16 3257 3680 546753961 546754390 3.910000e-106 396.0
31 TraesCS7B01G337600 chr7D 90.459 283 15 3 4290 4572 548129988 548129718 3.960000e-96 363.0
32 TraesCS7B01G337600 chr7D 84.146 328 39 4 1071 1398 546751694 546752008 6.770000e-79 305.0
33 TraesCS7B01G337600 chr7D 89.262 149 9 4 3567 3708 548131675 548131527 4.280000e-41 180.0
34 TraesCS7B01G337600 chr7D 98.077 52 0 1 584 634 548808226 548808175 7.430000e-14 89.8
35 TraesCS7B01G337600 chr7D 100.000 47 0 0 650 696 548808119 548808073 2.670000e-13 87.9
36 TraesCS7B01G337600 chr1B 93.773 546 27 2 1 545 675360741 675361280 0.000000e+00 813.0
37 TraesCS7B01G337600 chr1B 92.405 553 33 4 1 551 517492810 517492265 0.000000e+00 780.0
38 TraesCS7B01G337600 chr1B 92.182 550 28 9 2 545 658389191 658389731 0.000000e+00 763.0
39 TraesCS7B01G337600 chr3B 93.407 546 29 2 1 545 764720293 764720832 0.000000e+00 802.0
40 TraesCS7B01G337600 chr2B 91.606 548 36 5 1 545 229534358 229534898 0.000000e+00 749.0
41 TraesCS7B01G337600 chr2B 91.728 544 35 5 2 543 729777727 729777192 0.000000e+00 747.0
42 TraesCS7B01G337600 chr2B 91.026 78 7 0 557 634 765786426 765786349 7.380000e-19 106.0
43 TraesCS7B01G337600 chr6D 89.416 548 30 4 2 546 472511484 472510962 0.000000e+00 665.0
44 TraesCS7B01G337600 chr6D 88.848 547 37 11 2 545 51499989 51499464 0.000000e+00 651.0
45 TraesCS7B01G337600 chr1D 89.174 545 33 11 2 545 475527777 475528296 0.000000e+00 656.0
46 TraesCS7B01G337600 chr1D 82.650 317 48 4 4664 4976 445557864 445558177 1.910000e-69 274.0
47 TraesCS7B01G337600 chr5B 91.572 439 26 3 1 434 599310287 599309855 3.590000e-166 595.0
48 TraesCS7B01G337600 chr5B 86.667 90 10 1 3676 3765 49558758 49558845 1.230000e-16 99.0
49 TraesCS7B01G337600 chr1A 82.561 367 51 8 4668 5031 500838150 500837794 1.460000e-80 311.0
50 TraesCS7B01G337600 chr1A 81.395 172 16 7 544 703 531691350 531691183 5.660000e-25 126.0
51 TraesCS7B01G337600 chr2A 83.534 249 35 4 4668 4915 764900881 764901124 1.510000e-55 228.0
52 TraesCS7B01G337600 chr2D 94.872 78 4 0 557 634 624018741 624018664 7.320000e-24 122.0
53 TraesCS7B01G337600 chrUn 88.506 87 8 1 3679 3765 84439838 84439922 2.650000e-18 104.0
54 TraesCS7B01G337600 chr4D 88.506 87 8 1 3679 3765 432765544 432765460 2.650000e-18 104.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G337600 chr7B 592360205 592365588 5383 True 9943.000000 9943 100.00000 1 5384 1 chr7B.!!$R1 5383
1 TraesCS7B01G337600 chr7A 633036006 633040301 4295 True 6634.000000 6634 94.35100 1040 5384 1 chr7A.!!$R2 4344
2 TraesCS7B01G337600 chr7A 632969556 632974014 4458 True 3307.500000 3494 94.48700 1040 5384 2 chr7A.!!$R7 4344
3 TraesCS7B01G337600 chr7A 632907012 632911562 4550 True 3283.000000 3413 94.59450 1040 5384 2 chr7A.!!$R6 4344
4 TraesCS7B01G337600 chr7A 632586562 632590898 4336 True 1636.000000 4104 96.27400 1040 5384 4 chr7A.!!$R5 4344
5 TraesCS7B01G337600 chr7A 632711294 632712321 1027 True 1552.000000 1552 93.79200 4342 5384 1 chr7A.!!$R1 1042
6 TraesCS7B01G337600 chr7A 633095607 633096635 1028 True 1537.000000 1537 93.50500 4342 5384 1 chr7A.!!$R3 1042
7 TraesCS7B01G337600 chr7A 631960317 631964009 3692 True 993.500000 1085 87.08400 2166 4528 2 chr7A.!!$R4 2362
8 TraesCS7B01G337600 chr7A 630387922 630390917 2995 False 724.000000 1118 86.60050 1626 4544 4 chr7A.!!$F2 2918
9 TraesCS7B01G337600 chr7A 630032736 630036438 3702 False 446.600000 817 83.51080 1040 4574 5 chr7A.!!$F1 3534
10 TraesCS7B01G337600 chr7D 548803549 548808226 4677 True 1369.540000 3254 95.93780 584 5384 5 chr7D.!!$R3 4800
11 TraesCS7B01G337600 chr7D 548129718 548132996 3278 True 710.666667 1589 89.44800 2212 4572 3 chr7D.!!$R2 2360
12 TraesCS7B01G337600 chr7D 115100272 115100797 525 True 667.000000 667 89.39700 2 545 1 chr7D.!!$R1 543
13 TraesCS7B01G337600 chr7D 546751694 546755143 3449 False 568.000000 808 83.42975 1071 4518 4 chr7D.!!$F1 3447
14 TraesCS7B01G337600 chr1B 675360741 675361280 539 False 813.000000 813 93.77300 1 545 1 chr1B.!!$F2 544
15 TraesCS7B01G337600 chr1B 517492265 517492810 545 True 780.000000 780 92.40500 1 551 1 chr1B.!!$R1 550
16 TraesCS7B01G337600 chr1B 658389191 658389731 540 False 763.000000 763 92.18200 2 545 1 chr1B.!!$F1 543
17 TraesCS7B01G337600 chr3B 764720293 764720832 539 False 802.000000 802 93.40700 1 545 1 chr3B.!!$F1 544
18 TraesCS7B01G337600 chr2B 229534358 229534898 540 False 749.000000 749 91.60600 1 545 1 chr2B.!!$F1 544
19 TraesCS7B01G337600 chr2B 729777192 729777727 535 True 747.000000 747 91.72800 2 543 1 chr2B.!!$R1 541
20 TraesCS7B01G337600 chr6D 472510962 472511484 522 True 665.000000 665 89.41600 2 546 1 chr6D.!!$R2 544
21 TraesCS7B01G337600 chr6D 51499464 51499989 525 True 651.000000 651 88.84800 2 545 1 chr6D.!!$R1 543
22 TraesCS7B01G337600 chr1D 475527777 475528296 519 False 656.000000 656 89.17400 2 545 1 chr1D.!!$F2 543

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
939 1041 0.179215 CTCATGACGAACTTTGCGCC 60.179 55.0 4.18 0.0 0.00 6.53 F
1497 1628 0.120377 ATAAGACAGGGGGTGTGGGA 59.880 55.0 0.00 0.0 40.56 4.37 F
2662 2960 0.248539 CCTCTAGTGACGCGCTTACC 60.249 60.0 5.73 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2753 3249 0.460109 CGGATGTCGCAATCTGTGGA 60.460 55.0 0.00 0.0 0.0 4.02 R
3294 5428 1.253100 AATGGTGGCCTAAACAACGG 58.747 50.0 3.32 0.0 0.0 4.44 R
4428 8079 0.394899 GTCTTGGCCCATTCCTCAGG 60.395 60.0 0.00 0.0 0.0 3.86 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
202 212 2.912956 AGAGGAGAGTGAGAGTGAGAGT 59.087 50.000 0.00 0.00 0.00 3.24
203 213 3.009723 GAGGAGAGTGAGAGTGAGAGTG 58.990 54.545 0.00 0.00 0.00 3.51
204 214 2.642311 AGGAGAGTGAGAGTGAGAGTGA 59.358 50.000 0.00 0.00 0.00 3.41
205 215 3.009723 GGAGAGTGAGAGTGAGAGTGAG 58.990 54.545 0.00 0.00 0.00 3.51
286 305 3.348151 TGCCGACAGAGAGAGAAGT 57.652 52.632 0.00 0.00 0.00 3.01
382 401 2.280797 GCTGACGTGGCCTGACAA 60.281 61.111 3.32 0.00 0.00 3.18
475 495 6.488683 CCAACAAGAAAAGTGGTAGGTATCAA 59.511 38.462 0.00 0.00 0.00 2.57
546 567 6.260271 GTGGTAGTTTTATGCTATTCACTCCC 59.740 42.308 0.00 0.00 0.00 4.30
551 572 8.056407 AGTTTTATGCTATTCACTCCCTTTTC 57.944 34.615 0.00 0.00 0.00 2.29
552 573 7.669722 AGTTTTATGCTATTCACTCCCTTTTCA 59.330 33.333 0.00 0.00 0.00 2.69
553 574 8.303876 GTTTTATGCTATTCACTCCCTTTTCAA 58.696 33.333 0.00 0.00 0.00 2.69
554 575 8.415950 TTTATGCTATTCACTCCCTTTTCAAA 57.584 30.769 0.00 0.00 0.00 2.69
555 576 8.593945 TTATGCTATTCACTCCCTTTTCAAAT 57.406 30.769 0.00 0.00 0.00 2.32
556 577 6.271488 TGCTATTCACTCCCTTTTCAAATG 57.729 37.500 0.00 0.00 0.00 2.32
557 578 6.009589 TGCTATTCACTCCCTTTTCAAATGA 58.990 36.000 0.00 0.00 0.00 2.57
558 579 6.151648 TGCTATTCACTCCCTTTTCAAATGAG 59.848 38.462 0.00 0.00 0.00 2.90
559 580 6.375455 GCTATTCACTCCCTTTTCAAATGAGA 59.625 38.462 0.00 0.00 0.00 3.27
560 581 6.581171 ATTCACTCCCTTTTCAAATGAGAC 57.419 37.500 0.00 0.00 0.00 3.36
561 582 4.065088 TCACTCCCTTTTCAAATGAGACG 58.935 43.478 0.00 0.00 0.00 4.18
562 583 4.065088 CACTCCCTTTTCAAATGAGACGA 58.935 43.478 0.00 0.00 0.00 4.20
563 584 4.153117 CACTCCCTTTTCAAATGAGACGAG 59.847 45.833 0.00 0.00 0.00 4.18
564 585 4.040461 ACTCCCTTTTCAAATGAGACGAGA 59.960 41.667 0.00 0.00 0.00 4.04
565 586 4.569943 TCCCTTTTCAAATGAGACGAGAG 58.430 43.478 0.00 0.00 0.00 3.20
566 587 3.126000 CCCTTTTCAAATGAGACGAGAGC 59.874 47.826 0.00 0.00 0.00 4.09
567 588 3.999663 CCTTTTCAAATGAGACGAGAGCT 59.000 43.478 0.00 0.00 0.00 4.09
568 589 4.092675 CCTTTTCAAATGAGACGAGAGCTC 59.907 45.833 5.27 5.27 35.67 4.09
569 590 3.942130 TTCAAATGAGACGAGAGCTCA 57.058 42.857 17.77 0.00 44.19 4.26
570 591 3.500558 TCAAATGAGACGAGAGCTCAG 57.499 47.619 17.77 12.04 43.64 3.35
571 592 2.165234 TCAAATGAGACGAGAGCTCAGG 59.835 50.000 17.77 9.54 43.64 3.86
572 593 0.459489 AATGAGACGAGAGCTCAGGC 59.541 55.000 17.77 11.88 43.64 4.85
573 594 1.723608 ATGAGACGAGAGCTCAGGCG 61.724 60.000 17.77 17.98 43.64 5.52
574 595 2.045829 AGACGAGAGCTCAGGCGA 60.046 61.111 24.04 0.00 44.37 5.54
575 596 2.047151 GAGACGAGAGCTCAGGCGAG 62.047 65.000 24.04 8.94 44.37 5.03
583 604 4.746361 CTCAGGCGAGCGATGAAT 57.254 55.556 0.00 0.00 31.00 2.57
584 605 2.515376 CTCAGGCGAGCGATGAATC 58.485 57.895 0.00 0.00 31.00 2.52
723 821 3.058501 CCTACGTTCCGACTTTTGCAATT 60.059 43.478 0.00 0.00 0.00 2.32
730 828 2.910482 CCGACTTTTGCAATTGATCACG 59.090 45.455 10.34 4.94 0.00 4.35
748 846 1.874345 CGCCACAAGTACGGAGGACT 61.874 60.000 7.93 0.00 0.00 3.85
816 917 0.519077 AGGTAACGACGACGACCTTC 59.481 55.000 15.32 0.00 41.68 3.46
850 951 4.662961 CGTGTGGGCTGCTGTCGA 62.663 66.667 0.00 0.00 0.00 4.20
851 952 3.044305 GTGTGGGCTGCTGTCGAC 61.044 66.667 9.11 9.11 0.00 4.20
852 953 4.662961 TGTGGGCTGCTGTCGACG 62.663 66.667 11.62 7.05 28.80 5.12
853 954 4.664677 GTGGGCTGCTGTCGACGT 62.665 66.667 11.62 0.00 0.00 4.34
854 955 2.986979 TGGGCTGCTGTCGACGTA 60.987 61.111 11.62 4.64 0.00 3.57
855 956 2.202623 GGGCTGCTGTCGACGTAG 60.203 66.667 11.62 14.70 0.00 3.51
856 957 2.202623 GGCTGCTGTCGACGTAGG 60.203 66.667 20.16 9.71 0.00 3.18
857 958 2.202623 GCTGCTGTCGACGTAGGG 60.203 66.667 20.16 8.58 0.00 3.53
876 977 1.235281 GCTTGAAGACGGGGTGGAAC 61.235 60.000 0.00 0.00 0.00 3.62
912 1014 1.074951 GTTGGGAACTGGGAGTGGG 59.925 63.158 0.00 0.00 0.00 4.61
920 1022 1.303643 CTGGGAGTGGGCAAGTTCC 60.304 63.158 0.00 0.00 0.00 3.62
936 1038 2.808543 AGTTCCTCATGACGAACTTTGC 59.191 45.455 25.43 8.41 44.90 3.68
939 1041 0.179215 CTCATGACGAACTTTGCGCC 60.179 55.000 4.18 0.00 0.00 6.53
1035 1141 2.727798 CTGCAAAAGCGAAAACCTGATG 59.272 45.455 0.00 0.00 0.00 3.07
1111 1217 2.270874 GATGCCAATCCCCCGTCAGT 62.271 60.000 0.00 0.00 0.00 3.41
1115 1221 0.887933 CCAATCCCCCGTCAGTTTTG 59.112 55.000 0.00 0.00 0.00 2.44
1123 1229 0.878523 CCGTCAGTTTTGCCGTCTCA 60.879 55.000 0.00 0.00 0.00 3.27
1199 1305 0.745128 TCGCGACCTCTCCTCTCTTC 60.745 60.000 3.71 0.00 0.00 2.87
1267 1373 1.767681 GAGCCTTCCCTCTCATGATGT 59.232 52.381 0.00 0.00 0.00 3.06
1277 1383 4.387598 CCTCTCATGATGTTTCCAGATCC 58.612 47.826 0.00 0.00 0.00 3.36
1289 1395 3.148279 AGATCCGCCTGTCCGTCC 61.148 66.667 0.00 0.00 0.00 4.79
1309 1419 2.268298 CTGTTTCCCGGTATGTTCTCG 58.732 52.381 0.00 0.00 0.00 4.04
1316 1426 2.287668 CCCGGTATGTTCTCGTCATCTC 60.288 54.545 0.00 0.00 0.00 2.75
1352 1462 4.793028 GCGCCTTTAGTTTCTTTTCTTGCT 60.793 41.667 0.00 0.00 0.00 3.91
1353 1463 5.562113 GCGCCTTTAGTTTCTTTTCTTGCTA 60.562 40.000 0.00 0.00 0.00 3.49
1354 1464 6.435428 CGCCTTTAGTTTCTTTTCTTGCTAA 58.565 36.000 0.00 0.00 0.00 3.09
1355 1465 7.084486 CGCCTTTAGTTTCTTTTCTTGCTAAT 58.916 34.615 0.00 0.00 0.00 1.73
1356 1466 8.234546 CGCCTTTAGTTTCTTTTCTTGCTAATA 58.765 33.333 0.00 0.00 0.00 0.98
1497 1628 0.120377 ATAAGACAGGGGGTGTGGGA 59.880 55.000 0.00 0.00 40.56 4.37
1505 1636 3.053077 CAGGGGGTGTGGGATCTTATAA 58.947 50.000 0.00 0.00 0.00 0.98
1506 1637 3.073062 CAGGGGGTGTGGGATCTTATAAG 59.927 52.174 6.11 6.11 0.00 1.73
1509 1640 4.286291 GGGGGTGTGGGATCTTATAAGTAG 59.714 50.000 12.19 0.00 0.00 2.57
1511 1642 5.368816 GGGGTGTGGGATCTTATAAGTAGTT 59.631 44.000 12.19 0.00 0.00 2.24
1512 1643 6.556116 GGGGTGTGGGATCTTATAAGTAGTTA 59.444 42.308 12.19 0.00 0.00 2.24
1513 1644 7.071572 GGGGTGTGGGATCTTATAAGTAGTTAA 59.928 40.741 12.19 0.00 0.00 2.01
1584 1720 2.163211 GGGTGCTCAGATTTGCTCTTTC 59.837 50.000 0.00 0.00 29.16 2.62
1650 1876 1.270550 GTGGGACAACCTTGCAAGATG 59.729 52.381 28.05 24.91 44.16 2.90
1656 1882 4.232221 GACAACCTTGCAAGATGTGAATG 58.768 43.478 30.24 17.97 0.00 2.67
1719 1945 5.132502 ACATCTCTGGTTGTGATGAAAACA 58.867 37.500 12.62 0.00 44.80 2.83
1766 2001 1.605710 GCATTGGTAGCAAGCGATGAT 59.394 47.619 13.51 0.00 44.53 2.45
1869 2116 7.548196 TCGTGGAAAAGGATGTATAATGTTC 57.452 36.000 0.00 0.00 0.00 3.18
1983 2230 4.564782 TCTCTGTTGAAATCATCTGGCT 57.435 40.909 0.00 0.00 0.00 4.75
1984 2231 4.914983 TCTCTGTTGAAATCATCTGGCTT 58.085 39.130 0.00 0.00 0.00 4.35
2069 2319 5.423015 TGCATTTGTTAGGTTTTGCAAAGA 58.577 33.333 12.41 1.08 37.17 2.52
2070 2320 5.293079 TGCATTTGTTAGGTTTTGCAAAGAC 59.707 36.000 12.41 12.77 37.17 3.01
2142 2392 4.865228 TCCACCAACCCACCCCCA 62.865 66.667 0.00 0.00 0.00 4.96
2143 2393 4.299796 CCACCAACCCACCCCCAG 62.300 72.222 0.00 0.00 0.00 4.45
2144 2394 3.507713 CACCAACCCACCCCCAGT 61.508 66.667 0.00 0.00 0.00 4.00
2145 2395 2.702253 ACCAACCCACCCCCAGTT 60.702 61.111 0.00 0.00 0.00 3.16
2146 2396 2.117423 CCAACCCACCCCCAGTTC 59.883 66.667 0.00 0.00 0.00 3.01
2180 2431 7.710475 CACATGACTGGTTTTTATCCTTTTTGT 59.290 33.333 0.00 0.00 0.00 2.83
2206 2460 4.328983 GTCACCATGTACCGTACAGAAATG 59.671 45.833 16.25 9.63 42.77 2.32
2441 2720 7.881232 TGTTTTAGTAATTCTTGGGGTAGACAG 59.119 37.037 0.00 0.00 0.00 3.51
2636 2934 1.389555 GGAAACTTCCAATAGGGCCG 58.610 55.000 0.00 0.00 46.76 6.13
2654 2952 1.065701 CCGTGGAATCCTCTAGTGACG 59.934 57.143 0.00 0.00 0.00 4.35
2662 2960 0.248539 CCTCTAGTGACGCGCTTACC 60.249 60.000 5.73 0.00 0.00 2.85
2675 2973 2.222953 GCGCTTACCTTTTGTATGACGG 60.223 50.000 0.00 0.00 31.37 4.79
2680 2978 5.050295 GCTTACCTTTTGTATGACGGCTATC 60.050 44.000 0.00 0.00 0.00 2.08
2753 3249 1.195115 TGAAGCTCGGCTACCAGATT 58.805 50.000 0.00 0.00 38.25 2.40
2831 3327 8.424731 GCGTGTTACAAATTTTCTCATTAAAGG 58.575 33.333 0.00 0.00 0.00 3.11
2903 3425 2.420642 CAGTGCGGGATTATCTGGATG 58.579 52.381 0.00 0.00 0.00 3.51
3069 3595 7.616935 CCCTTGAAGCATTCCATATGGTATAAT 59.383 37.037 21.28 11.06 46.93 1.28
3332 5471 9.179909 CCACCATTACACCAAGTTTATATTGTA 57.820 33.333 0.00 0.00 0.00 2.41
3473 5612 8.635328 AGCATGAATCATTGCATCACTATTAAA 58.365 29.630 15.95 0.00 0.00 1.52
3598 5747 4.863131 GTGTACACTATGTAACCAGTCAGC 59.137 45.833 18.92 0.00 34.21 4.26
3743 7295 8.346476 TCAATTTGAATTACCAAAACGTCTTG 57.654 30.769 0.00 0.00 39.20 3.02
3851 7490 2.191375 CATCGACATGGCTGGCCT 59.809 61.111 13.05 0.00 36.94 5.19
3970 7609 3.822167 TGGTGTAACAGACATAGACGACA 59.178 43.478 0.00 0.00 41.14 4.35
4007 7649 2.279659 GTGCATTGAAAAATCGCATCCG 59.720 45.455 0.00 0.00 34.66 4.18
4056 7698 1.918868 TAGCACGTGTCGATGACGCT 61.919 55.000 18.38 6.95 40.44 5.07
4124 7766 0.790866 GATCTGCGCTTGCGTTGTTC 60.791 55.000 16.38 9.80 43.34 3.18
4128 7770 0.871722 TGCGCTTGCGTTGTTCTATT 59.128 45.000 16.38 0.00 43.34 1.73
4134 7785 0.878416 TGCGTTGTTCTATTGGTGGC 59.122 50.000 0.00 0.00 0.00 5.01
4144 7795 6.408035 TGTTCTATTGGTGGCTATAACGAAA 58.592 36.000 0.00 0.00 0.00 3.46
4223 7874 0.179045 GCTGTAGCGGATGGTTCCAT 60.179 55.000 3.80 3.80 42.74 3.41
4251 7902 0.843309 TGAAGTTCAAGGTGGCCTCA 59.157 50.000 3.32 0.00 30.89 3.86
4428 8079 6.806120 ATAAAGTTTGTCGAAAAGTTGTGC 57.194 33.333 11.38 0.00 0.00 4.57
4579 8240 2.158638 TGGGGTACACTGGTTTTGGTAC 60.159 50.000 0.00 0.00 36.30 3.34
4586 8247 2.803956 CACTGGTTTTGGTACCTGTACG 59.196 50.000 14.36 0.00 45.25 3.67
4665 8326 1.975660 AAAACGGCTCCAGCAACTTA 58.024 45.000 0.03 0.00 44.36 2.24
4672 8333 3.920412 CGGCTCCAGCAACTTAATTTTTC 59.080 43.478 0.03 0.00 44.36 2.29
4723 8384 6.578944 AGTTCACAAAACTGGGAAAATAACC 58.421 36.000 0.00 0.00 32.46 2.85
4729 8390 6.183360 ACAAAACTGGGAAAATAACCGTGATT 60.183 34.615 0.00 0.00 0.00 2.57
4794 8455 6.372937 AGAATCAGAAAGCTTGGCTAGTAAAC 59.627 38.462 0.00 0.00 38.25 2.01
4814 8475 1.139853 CGGGCTTCTCTATTCAAGGCT 59.860 52.381 5.36 0.00 43.14 4.58
4873 8535 8.822805 TGGTTGTCCTTAACTTAATCTCAGTAT 58.177 33.333 0.00 0.00 34.23 2.12
4983 8645 5.248020 AGAAGATCATCCGCCAAAGATAGAT 59.752 40.000 0.00 0.00 0.00 1.98
5065 8727 5.820423 CGTACATGATCCCAAGTAATTTCCA 59.180 40.000 0.00 0.00 29.58 3.53
5066 8728 6.017934 CGTACATGATCCCAAGTAATTTCCAG 60.018 42.308 0.00 0.00 29.58 3.86
5168 8830 1.581447 CCTCTTCGGCCAAAACAGC 59.419 57.895 2.24 0.00 0.00 4.40
5265 8927 1.725641 TGACTGCGGCACATTAGAAG 58.274 50.000 0.00 0.00 0.00 2.85
5266 8928 1.001974 TGACTGCGGCACATTAGAAGT 59.998 47.619 0.00 0.00 0.00 3.01
5267 8929 2.076863 GACTGCGGCACATTAGAAGTT 58.923 47.619 0.00 0.00 0.00 2.66
5268 8930 2.484264 GACTGCGGCACATTAGAAGTTT 59.516 45.455 0.00 0.00 0.00 2.66
5269 8931 3.670625 ACTGCGGCACATTAGAAGTTTA 58.329 40.909 0.00 0.00 0.00 2.01
5270 8932 3.684788 ACTGCGGCACATTAGAAGTTTAG 59.315 43.478 0.00 0.00 0.00 1.85
5271 8933 3.932710 CTGCGGCACATTAGAAGTTTAGA 59.067 43.478 0.00 0.00 0.00 2.10
5272 8934 4.320023 TGCGGCACATTAGAAGTTTAGAA 58.680 39.130 0.00 0.00 0.00 2.10
5273 8935 4.153475 TGCGGCACATTAGAAGTTTAGAAC 59.847 41.667 0.00 0.00 0.00 3.01
5274 8936 4.392138 GCGGCACATTAGAAGTTTAGAACT 59.608 41.667 0.00 0.00 45.46 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 212 0.455005 CGCACTCATCTCTGCTCTCA 59.545 55.000 0.00 0.00 0.00 3.27
203 213 0.248990 CCGCACTCATCTCTGCTCTC 60.249 60.000 0.00 0.00 0.00 3.20
204 214 1.674764 CCCGCACTCATCTCTGCTCT 61.675 60.000 0.00 0.00 0.00 4.09
205 215 1.227205 CCCGCACTCATCTCTGCTC 60.227 63.158 0.00 0.00 0.00 4.26
364 383 2.994387 CTTGTCAGGCCACGTCAGCA 62.994 60.000 5.01 0.00 0.00 4.41
455 475 7.458397 TGTGATTGATACCTACCACTTTTCTT 58.542 34.615 0.00 0.00 0.00 2.52
516 537 9.908152 GTGAATAGCATAAAACTACCACTTTTT 57.092 29.630 0.00 0.00 0.00 1.94
546 567 4.687948 TGAGCTCTCGTCTCATTTGAAAAG 59.312 41.667 16.19 0.00 35.81 2.27
551 572 2.538437 CCTGAGCTCTCGTCTCATTTG 58.462 52.381 16.19 0.00 39.56 2.32
552 573 1.134848 GCCTGAGCTCTCGTCTCATTT 60.135 52.381 16.19 0.00 39.56 2.32
553 574 0.459489 GCCTGAGCTCTCGTCTCATT 59.541 55.000 16.19 0.00 39.56 2.57
554 575 1.723608 CGCCTGAGCTCTCGTCTCAT 61.724 60.000 16.19 0.00 39.56 2.90
555 576 2.402572 CGCCTGAGCTCTCGTCTCA 61.403 63.158 16.19 0.00 38.16 3.27
556 577 2.047151 CTCGCCTGAGCTCTCGTCTC 62.047 65.000 16.19 0.00 34.96 3.36
557 578 2.045829 TCGCCTGAGCTCTCGTCT 60.046 61.111 16.19 0.00 36.60 4.18
558 579 2.407210 CTCGCCTGAGCTCTCGTC 59.593 66.667 16.19 0.71 34.96 4.20
566 587 1.274126 CGATTCATCGCTCGCCTGAG 61.274 60.000 0.00 0.00 43.84 3.35
567 588 1.299392 CGATTCATCGCTCGCCTGA 60.299 57.895 0.00 0.00 43.84 3.86
568 589 3.228624 CGATTCATCGCTCGCCTG 58.771 61.111 0.00 0.00 43.84 4.85
577 598 0.532862 ACGGCACCCATCGATTCATC 60.533 55.000 0.00 0.00 0.00 2.92
578 599 0.532862 GACGGCACCCATCGATTCAT 60.533 55.000 0.00 0.00 0.00 2.57
579 600 1.153449 GACGGCACCCATCGATTCA 60.153 57.895 0.00 0.00 0.00 2.57
580 601 1.887707 GGACGGCACCCATCGATTC 60.888 63.158 0.00 0.00 0.00 2.52
581 602 2.189521 GGACGGCACCCATCGATT 59.810 61.111 0.00 0.00 0.00 3.34
582 603 2.764128 AGGACGGCACCCATCGAT 60.764 61.111 0.00 0.00 0.00 3.59
583 604 3.770040 CAGGACGGCACCCATCGA 61.770 66.667 0.00 0.00 0.00 3.59
584 605 3.605749 AACAGGACGGCACCCATCG 62.606 63.158 0.00 0.00 0.00 3.84
585 606 2.040544 CAACAGGACGGCACCCATC 61.041 63.158 0.00 0.00 0.00 3.51
586 607 2.034066 CAACAGGACGGCACCCAT 59.966 61.111 0.00 0.00 0.00 4.00
587 608 4.263572 CCAACAGGACGGCACCCA 62.264 66.667 0.00 0.00 0.00 4.51
723 821 0.389296 CCGTACTTGTGGCGTGATCA 60.389 55.000 0.00 0.00 0.00 2.92
730 828 0.320697 AAGTCCTCCGTACTTGTGGC 59.679 55.000 0.00 0.00 35.87 5.01
845 946 0.242825 CTTCAAGCCCTACGTCGACA 59.757 55.000 17.16 0.00 0.00 4.35
847 948 0.524862 GTCTTCAAGCCCTACGTCGA 59.475 55.000 0.00 0.00 0.00 4.20
848 949 0.797249 CGTCTTCAAGCCCTACGTCG 60.797 60.000 0.00 0.00 0.00 5.12
849 950 0.458025 CCGTCTTCAAGCCCTACGTC 60.458 60.000 0.00 0.00 31.87 4.34
850 951 1.590147 CCGTCTTCAAGCCCTACGT 59.410 57.895 0.00 0.00 31.87 3.57
851 952 1.153628 CCCGTCTTCAAGCCCTACG 60.154 63.158 0.00 0.00 0.00 3.51
852 953 1.221021 CCCCGTCTTCAAGCCCTAC 59.779 63.158 0.00 0.00 0.00 3.18
853 954 1.229400 ACCCCGTCTTCAAGCCCTA 60.229 57.895 0.00 0.00 0.00 3.53
854 955 2.529389 ACCCCGTCTTCAAGCCCT 60.529 61.111 0.00 0.00 0.00 5.19
855 956 2.359975 CACCCCGTCTTCAAGCCC 60.360 66.667 0.00 0.00 0.00 5.19
856 957 2.359975 CCACCCCGTCTTCAAGCC 60.360 66.667 0.00 0.00 0.00 4.35
857 958 1.072505 TTCCACCCCGTCTTCAAGC 59.927 57.895 0.00 0.00 0.00 4.01
876 977 3.740128 CTTCATCGGTGAGGGCGGG 62.740 68.421 0.00 0.00 35.39 6.13
912 1014 2.882742 GTTCGTCATGAGGAACTTGC 57.117 50.000 36.55 21.03 46.66 4.01
920 1022 0.179215 GGCGCAAAGTTCGTCATGAG 60.179 55.000 10.83 0.00 0.00 2.90
939 1041 0.531532 CACGCCTTCAGCCTAGATGG 60.532 60.000 0.00 0.00 38.78 3.51
977 1083 3.927163 AACCTAACGCGGACGCTGG 62.927 63.158 12.47 12.80 45.53 4.85
989 1095 1.378531 GCGCACCATGATGAACCTAA 58.621 50.000 0.30 0.00 0.00 2.69
1016 1122 2.982470 CTCATCAGGTTTTCGCTTTTGC 59.018 45.455 0.00 0.00 43.23 3.68
1035 1141 1.208293 GTGTGGAGAATGGGGAGTCTC 59.792 57.143 0.00 0.00 39.70 3.36
1111 1217 4.294523 CCGGATGAGACGGCAAAA 57.705 55.556 0.00 0.00 45.34 2.44
1251 1357 4.080695 TCTGGAAACATCATGAGAGGGAAG 60.081 45.833 0.09 0.00 41.51 3.46
1267 1373 1.602237 GGACAGGCGGATCTGGAAA 59.398 57.895 3.14 0.00 38.98 3.13
1277 1383 2.027625 GAAACAGGACGGACAGGCG 61.028 63.158 0.00 0.00 0.00 5.52
1289 1395 2.268298 CGAGAACATACCGGGAAACAG 58.732 52.381 6.32 0.00 0.00 3.16
1309 1419 3.305094 CGCAAAATTTGGCATGAGATGAC 59.695 43.478 17.60 0.00 39.32 3.06
1316 1426 1.158434 AAGGCGCAAAATTTGGCATG 58.842 45.000 17.60 3.39 0.00 4.06
1356 1466 8.160106 GGTCAGAATCCAGATCCAAAACTATAT 58.840 37.037 0.00 0.00 0.00 0.86
1449 1580 6.263516 ACAGAAATCAACACATGAAGGATG 57.736 37.500 0.00 0.00 42.54 3.51
1483 1614 0.120377 TAAGATCCCACACCCCCTGT 59.880 55.000 0.00 0.00 0.00 4.00
1505 1636 9.421399 CCCTTTTATTTCATGGGATTAACTACT 57.579 33.333 0.00 0.00 40.23 2.57
1506 1637 8.638873 CCCCTTTTATTTCATGGGATTAACTAC 58.361 37.037 0.00 0.00 40.23 2.73
1509 1640 7.669089 TCCCCTTTTATTTCATGGGATTAAC 57.331 36.000 0.00 0.00 40.23 2.01
1511 1642 6.613679 GGTTCCCCTTTTATTTCATGGGATTA 59.386 38.462 0.00 0.00 41.50 1.75
1512 1643 5.428457 GGTTCCCCTTTTATTTCATGGGATT 59.572 40.000 0.00 0.00 41.50 3.01
1513 1644 4.968719 GGTTCCCCTTTTATTTCATGGGAT 59.031 41.667 0.00 0.00 41.50 3.85
1519 1652 6.324254 TCTTTTTCGGTTCCCCTTTTATTTCA 59.676 34.615 0.00 0.00 0.00 2.69
1584 1720 7.313951 GTGGAAATCTATCACCAAAGAGAAG 57.686 40.000 0.00 0.00 34.11 2.85
1650 1876 1.593196 TTGCCGGCTATAGCATTCAC 58.407 50.000 29.70 10.61 44.36 3.18
1656 1882 1.593196 TCATGTTTGCCGGCTATAGC 58.407 50.000 29.70 16.78 41.14 2.97
1719 1945 4.566488 CCTTCTATTGGTTGCACTCCTTCT 60.566 45.833 8.33 0.00 0.00 2.85
1766 2001 8.597167 CCCAGGTCAAGTATATCATATTCTTCA 58.403 37.037 0.00 0.00 0.00 3.02
1869 2116 4.966965 ACTTACTCTCACTACGGTCATG 57.033 45.455 0.00 0.00 0.00 3.07
2044 2294 5.731599 TTGCAAAACCTAACAAATGCAAG 57.268 34.783 6.87 0.00 45.61 4.01
2069 2319 3.260205 TCTGAAGAATTTCCTCCCCTGT 58.740 45.455 0.00 0.00 32.09 4.00
2070 2320 4.516652 ATCTGAAGAATTTCCTCCCCTG 57.483 45.455 0.00 0.00 32.09 4.45
2142 2392 0.949105 GTCATGTGGCGAACCGAACT 60.949 55.000 0.00 0.00 39.70 3.01
2143 2393 0.949105 AGTCATGTGGCGAACCGAAC 60.949 55.000 0.00 0.00 39.70 3.95
2144 2394 0.948623 CAGTCATGTGGCGAACCGAA 60.949 55.000 0.00 0.00 39.70 4.30
2145 2395 1.374125 CAGTCATGTGGCGAACCGA 60.374 57.895 0.00 0.00 39.70 4.69
2146 2396 2.390599 CCAGTCATGTGGCGAACCG 61.391 63.158 0.00 0.00 39.70 4.44
2206 2460 8.003784 GTGCTAAAAATGCAAGTTTATGAACAC 58.996 33.333 2.93 2.29 42.41 3.32
2361 2639 9.698309 TCTATTGTTTCACTTTCTAGAAGTCTG 57.302 33.333 5.12 2.95 0.00 3.51
2441 2720 7.966339 ACCCCCTAAACTTATTTATTGGTTC 57.034 36.000 0.00 0.00 28.45 3.62
2636 2934 1.534175 CGCGTCACTAGAGGATTCCAC 60.534 57.143 5.29 0.00 0.00 4.02
2654 2952 2.222953 CCGTCATACAAAAGGTAAGCGC 60.223 50.000 0.00 0.00 35.14 5.92
2662 2960 6.967199 GGAAAAAGATAGCCGTCATACAAAAG 59.033 38.462 0.00 0.00 0.00 2.27
2675 2973 8.303876 TGGAAAACAATACAGGAAAAAGATAGC 58.696 33.333 0.00 0.00 0.00 2.97
2680 2978 9.757227 TGTAATGGAAAACAATACAGGAAAAAG 57.243 29.630 0.00 0.00 39.81 2.27
2753 3249 0.460109 CGGATGTCGCAATCTGTGGA 60.460 55.000 0.00 0.00 0.00 4.02
2796 3292 4.852609 ATTTGTAACACGCGATTAGGTC 57.147 40.909 15.93 0.30 0.00 3.85
2831 3327 2.543777 TCCACAGTAAGTTCAGCCAC 57.456 50.000 0.00 0.00 0.00 5.01
2903 3425 6.810888 ATTGACAACATAATTACGCAATGC 57.189 33.333 0.00 0.00 0.00 3.56
3294 5428 1.253100 AATGGTGGCCTAAACAACGG 58.747 50.000 3.32 0.00 0.00 4.44
3295 5429 2.814919 TGTAATGGTGGCCTAAACAACG 59.185 45.455 3.32 0.00 0.00 4.10
3296 5430 3.057104 GGTGTAATGGTGGCCTAAACAAC 60.057 47.826 3.32 0.00 0.00 3.32
3498 5637 7.473735 TCCCAATTTTTACATAAGCATGTCA 57.526 32.000 0.00 0.00 44.42 3.58
3598 5747 5.105635 ACCAACATCTTTGCCACATATCAAG 60.106 40.000 0.00 0.00 0.00 3.02
3730 7282 5.508200 TTCTAAATGCAAGACGTTTTGGT 57.492 34.783 19.20 0.00 38.46 3.67
3851 7490 6.710744 GGAAATCAAATCTATCCCTCGCTTAA 59.289 38.462 0.00 0.00 0.00 1.85
3970 7609 1.339644 GCACAATTCCATGGGCCCAT 61.340 55.000 32.75 32.75 44.07 4.00
4056 7698 4.438608 GCAACTTCAATATTCGCCATGACA 60.439 41.667 0.00 0.00 0.00 3.58
4124 7766 7.730364 ATTCTTTCGTTATAGCCACCAATAG 57.270 36.000 0.00 0.00 0.00 1.73
4144 7795 3.356529 ACCATTGAAGAGCCGAATTCT 57.643 42.857 3.52 0.00 0.00 2.40
4223 7874 4.159506 CCACCTTGAACTTCAAAACCAGAA 59.840 41.667 5.72 0.00 35.73 3.02
4251 7902 2.679716 GCTGAACCAGATGGCCCT 59.320 61.111 0.00 0.00 39.32 5.19
4428 8079 0.394899 GTCTTGGCCCATTCCTCAGG 60.395 60.000 0.00 0.00 0.00 3.86
4579 8240 2.722629 CACGAACAACACTACGTACAGG 59.277 50.000 0.00 0.00 37.22 4.00
4586 8247 2.470821 ACTGAGCACGAACAACACTAC 58.529 47.619 0.00 0.00 0.00 2.73
4665 8326 7.446931 ACAAAGTTTGGTGGTTCTTGAAAAATT 59.553 29.630 19.45 0.00 34.12 1.82
4672 8333 7.038659 TGAATAACAAAGTTTGGTGGTTCTTG 58.961 34.615 22.97 0.43 31.62 3.02
4723 8384 1.138859 TGGGACAGCCTCATAATCACG 59.861 52.381 0.00 0.00 0.00 4.35
4794 8455 1.139853 AGCCTTGAATAGAGAAGCCCG 59.860 52.381 0.00 0.00 0.00 6.13
4814 8475 5.946972 TGTAGTTTTTGTTTCTGAGGGTCAA 59.053 36.000 0.00 0.00 0.00 3.18
4873 8535 5.046663 TGCACTGGTACTCATTGTCTGATTA 60.047 40.000 0.00 0.00 32.10 1.75
4882 8544 0.035056 GGGCTGCACTGGTACTCATT 60.035 55.000 0.50 0.00 0.00 2.57
4887 8549 0.609131 AACATGGGCTGCACTGGTAC 60.609 55.000 2.50 0.00 0.00 3.34
4983 8645 0.178068 GGTATCGCTTGCAGGGAAGA 59.822 55.000 4.63 0.00 40.66 2.87
5065 8727 3.181467 GCTGTATGCATGGACTCTTCTCT 60.181 47.826 10.16 0.00 42.31 3.10
5066 8728 3.129871 GCTGTATGCATGGACTCTTCTC 58.870 50.000 10.16 0.00 42.31 2.87
5168 8830 2.287769 CAACTTTTGGTTTTGGGGCAG 58.712 47.619 0.00 0.00 35.74 4.85
5265 8927 5.467063 CAGTGGAAGGAACTGAGTTCTAAAC 59.533 44.000 23.06 14.46 46.55 2.01
5266 8928 5.365605 TCAGTGGAAGGAACTGAGTTCTAAA 59.634 40.000 23.06 4.36 46.96 1.85
5267 8929 4.899457 TCAGTGGAAGGAACTGAGTTCTAA 59.101 41.667 23.06 4.04 46.96 2.10
5268 8930 4.480115 TCAGTGGAAGGAACTGAGTTCTA 58.520 43.478 23.06 4.42 46.96 2.10
5269 8931 3.309296 TCAGTGGAAGGAACTGAGTTCT 58.691 45.455 23.06 6.05 46.96 3.01
5270 8932 3.753294 TCAGTGGAAGGAACTGAGTTC 57.247 47.619 16.70 16.70 46.96 3.01


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

AutoCloner maintained by Alex Coulton.