Multiple sequence alignment - TraesCS5A01G419400

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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 TraesCS5A01G419400 chr5A 100.000 2480 0 0 1 2480 606768195 606770674 0.000000e+00 4580.0
1 TraesCS5A01G419400 chr5A 96.126 826 28 4 845 1667 606699936 606700760 0.000000e+00 1345.0
2 TraesCS5A01G419400 chr5A 90.476 777 55 15 79 846 606699118 606699884 0.000000e+00 1007.0
3 TraesCS5A01G419400 chr5A 92.833 586 39 3 1148 1730 606579144 606579729 0.000000e+00 846.0
4 TraesCS5A01G419400 chr5A 87.568 555 49 10 79 619 606560447 606560995 2.090000e-175 625.0
5 TraesCS5A01G419400 chr5A 84.715 543 70 6 964 1499 606783388 606783924 4.700000e-147 531.0
6 TraesCS5A01G419400 chr5A 91.909 309 23 2 845 1152 606561467 606561774 4.900000e-117 431.0
7 TraesCS5A01G419400 chr5A 74.121 398 64 25 995 1374 606531680 606532056 7.200000e-26 128.0
8 TraesCS5A01G419400 chr5A 92.771 83 6 0 2 84 473248598 473248516 1.200000e-23 121.0
9 TraesCS5A01G419400 chr5A 89.655 58 6 0 2406 2463 397142715 397142772 9.510000e-10 75.0
10 TraesCS5A01G419400 chr5B 88.413 1519 123 28 846 2334 596982274 596983769 0.000000e+00 1781.0
11 TraesCS5A01G419400 chr5B 90.736 788 43 16 79 846 596981444 596982221 0.000000e+00 1024.0
12 TraesCS5A01G419400 chr5B 84.981 526 68 8 984 1499 597080197 597080721 7.860000e-145 523.0
13 TraesCS5A01G419400 chr5D 93.675 838 40 5 845 1679 485928512 485929339 0.000000e+00 1242.0
14 TraesCS5A01G419400 chr5D 90.278 864 52 16 845 1691 485605435 485606283 0.000000e+00 1101.0
15 TraesCS5A01G419400 chr5D 87.563 796 53 18 80 850 485604614 485605388 0.000000e+00 880.0
16 TraesCS5A01G419400 chr5D 91.000 500 26 6 82 566 485919784 485920279 0.000000e+00 656.0
17 TraesCS5A01G419400 chr5D 88.309 556 48 7 79 620 485767502 485768054 0.000000e+00 651.0
18 TraesCS5A01G419400 chr5D 90.543 497 34 6 1203 1691 485768804 485769295 0.000000e+00 645.0
19 TraesCS5A01G419400 chr5D 84.615 546 70 7 964 1497 486015740 486016283 4.700000e-147 531.0
20 TraesCS5A01G419400 chr5D 83.549 541 53 20 845 1380 485768514 485769023 8.030000e-130 473.0
21 TraesCS5A01G419400 chr5D 89.189 296 15 12 562 846 485928171 485928460 1.090000e-93 353.0
22 TraesCS5A01G419400 chr5D 76.110 653 119 26 1783 2404 560378355 560377709 8.620000e-80 307.0
23 TraesCS5A01G419400 chr5D 92.553 188 9 3 663 846 485768276 485768462 5.260000e-67 265.0
24 TraesCS5A01G419400 chr6A 78.233 634 102 27 1783 2397 2959092 2958476 8.380000e-100 374.0
25 TraesCS5A01G419400 chr6A 77.287 656 103 31 1783 2404 32664220 32663577 6.570000e-91 344.0
26 TraesCS5A01G419400 chr4D 78.019 646 106 28 1785 2404 487799806 487799171 8.380000e-100 374.0
27 TraesCS5A01G419400 chr4B 77.948 653 104 29 1783 2404 623427952 623427309 3.010000e-99 372.0
28 TraesCS5A01G419400 chr6D 77.610 661 96 34 1785 2404 30278606 30279255 1.090000e-93 353.0
29 TraesCS5A01G419400 chr6D 89.873 79 3 4 4 82 361412254 361412181 2.030000e-16 97.1
30 TraesCS5A01G419400 chr7D 77.015 670 98 36 1785 2404 41697394 41696731 1.420000e-87 333.0
31 TraesCS5A01G419400 chr7D 83.754 357 47 9 2026 2373 625530181 625529827 6.610000e-86 327.0
32 TraesCS5A01G419400 chr3A 76.555 627 100 32 1785 2373 443197882 443197265 1.440000e-77 300.0
33 TraesCS5A01G419400 chr3A 91.250 80 2 1 4 83 737821707 737821781 1.210000e-18 104.0
34 TraesCS5A01G419400 chr3A 90.625 64 4 2 2405 2466 61303069 61303132 1.580000e-12 84.2
35 TraesCS5A01G419400 chr3D 73.507 653 114 34 1783 2399 605410505 605411134 2.520000e-45 193.0
36 TraesCS5A01G419400 chr3D 72.783 654 117 35 1783 2399 606470532 606471161 5.490000e-37 165.0
37 TraesCS5A01G419400 chr3D 86.441 59 7 1 2406 2463 48814749 48814807 2.060000e-06 63.9
38 TraesCS5A01G419400 chr4A 90.476 84 3 1 4 87 600683411 600683333 3.370000e-19 106.0
39 TraesCS5A01G419400 chr7B 91.250 80 1 6 4 83 544471126 544471053 1.210000e-18 104.0
40 TraesCS5A01G419400 chr7B 90.000 80 3 1 4 83 461248072 461247998 5.640000e-17 99.0
41 TraesCS5A01G419400 chr7B 88.095 84 4 3 1 83 149964610 149964532 7.300000e-16 95.3
42 TraesCS5A01G419400 chr1B 91.250 80 2 1 4 83 593010701 593010775 1.210000e-18 104.0
43 TraesCS5A01G419400 chr6B 90.000 80 3 1 4 83 46090969 46090895 5.640000e-17 99.0
44 TraesCS5A01G419400 chr2B 84.932 73 10 1 2408 2479 163544767 163544839 3.420000e-09 73.1
45 TraesCS5A01G419400 chr3B 94.595 37 1 1 2427 2463 136955926 136955961 3.450000e-04 56.5
46 TraesCS5A01G419400 chr2D 90.244 41 4 0 2425 2465 606408471 606408511 1.000000e-03 54.7


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 TraesCS5A01G419400 chr5A 606768195 606770674 2479 False 4580.0 4580 100.0000 1 2480 1 chr5A.!!$F4 2479
1 TraesCS5A01G419400 chr5A 606699118 606700760 1642 False 1176.0 1345 93.3010 79 1667 2 chr5A.!!$F7 1588
2 TraesCS5A01G419400 chr5A 606579144 606579729 585 False 846.0 846 92.8330 1148 1730 1 chr5A.!!$F3 582
3 TraesCS5A01G419400 chr5A 606783388 606783924 536 False 531.0 531 84.7150 964 1499 1 chr5A.!!$F5 535
4 TraesCS5A01G419400 chr5A 606560447 606561774 1327 False 528.0 625 89.7385 79 1152 2 chr5A.!!$F6 1073
5 TraesCS5A01G419400 chr5B 596981444 596983769 2325 False 1402.5 1781 89.5745 79 2334 2 chr5B.!!$F2 2255
6 TraesCS5A01G419400 chr5B 597080197 597080721 524 False 523.0 523 84.9810 984 1499 1 chr5B.!!$F1 515
7 TraesCS5A01G419400 chr5D 485604614 485606283 1669 False 990.5 1101 88.9205 80 1691 2 chr5D.!!$F3 1611
8 TraesCS5A01G419400 chr5D 485928171 485929339 1168 False 797.5 1242 91.4320 562 1679 2 chr5D.!!$F5 1117
9 TraesCS5A01G419400 chr5D 486015740 486016283 543 False 531.0 531 84.6150 964 1497 1 chr5D.!!$F2 533
10 TraesCS5A01G419400 chr5D 485767502 485769295 1793 False 508.5 651 88.7385 79 1691 4 chr5D.!!$F4 1612
11 TraesCS5A01G419400 chr5D 560377709 560378355 646 True 307.0 307 76.1100 1783 2404 1 chr5D.!!$R1 621
12 TraesCS5A01G419400 chr6A 2958476 2959092 616 True 374.0 374 78.2330 1783 2397 1 chr6A.!!$R1 614
13 TraesCS5A01G419400 chr6A 32663577 32664220 643 True 344.0 344 77.2870 1783 2404 1 chr6A.!!$R2 621
14 TraesCS5A01G419400 chr4D 487799171 487799806 635 True 374.0 374 78.0190 1785 2404 1 chr4D.!!$R1 619
15 TraesCS5A01G419400 chr4B 623427309 623427952 643 True 372.0 372 77.9480 1783 2404 1 chr4B.!!$R1 621
16 TraesCS5A01G419400 chr6D 30278606 30279255 649 False 353.0 353 77.6100 1785 2404 1 chr6D.!!$F1 619
17 TraesCS5A01G419400 chr7D 41696731 41697394 663 True 333.0 333 77.0150 1785 2404 1 chr7D.!!$R1 619
18 TraesCS5A01G419400 chr3A 443197265 443197882 617 True 300.0 300 76.5550 1785 2373 1 chr3A.!!$R1 588

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
52 53 0.106868 TCCCAGATGCAATGCAGAGG 60.107 55.0 14.98 14.42 43.65 3.69 F
258 261 0.677288 TCGTTGAGATTGTCACGGGT 59.323 50.0 0.00 0.00 33.71 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1431 1967 0.443869 GCATAGGCACGTTGACAGTG 59.556 55.000 0.0 0.0 42.15 3.66 R
1747 2312 1.275856 TGCATGTTTGGAGGCAATTCC 59.724 47.619 0.0 0.0 37.77 3.01 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
28 29 9.467258 AAGAATAATCAATAAAATGACCGCATG 57.533 29.630 0.00 0.00 34.26 4.06
29 30 7.596248 AGAATAATCAATAAAATGACCGCATGC 59.404 33.333 7.91 7.91 34.26 4.06
30 31 4.652421 ATCAATAAAATGACCGCATGCA 57.348 36.364 19.57 0.00 34.26 3.96
31 32 4.652421 TCAATAAAATGACCGCATGCAT 57.348 36.364 19.57 4.56 34.26 3.96
32 33 4.609947 TCAATAAAATGACCGCATGCATC 58.390 39.130 19.57 14.88 34.26 3.91
33 34 4.338964 TCAATAAAATGACCGCATGCATCT 59.661 37.500 19.57 0.00 34.26 2.90
34 35 2.857592 AAAATGACCGCATGCATCTC 57.142 45.000 19.57 8.81 34.26 2.75
35 36 1.027357 AAATGACCGCATGCATCTCC 58.973 50.000 19.57 2.12 34.26 3.71
36 37 0.820891 AATGACCGCATGCATCTCCC 60.821 55.000 19.57 0.65 34.26 4.30
37 38 1.986632 ATGACCGCATGCATCTCCCA 61.987 55.000 19.57 6.58 32.31 4.37
38 39 1.890979 GACCGCATGCATCTCCCAG 60.891 63.158 19.57 0.00 0.00 4.45
39 40 2.315781 GACCGCATGCATCTCCCAGA 62.316 60.000 19.57 0.00 0.00 3.86
40 41 1.072678 CCGCATGCATCTCCCAGAT 59.927 57.895 19.57 0.00 34.74 2.90
48 49 1.687563 CATCTCCCAGATGCAATGCA 58.312 50.000 11.44 11.44 44.69 3.96
49 50 1.609072 CATCTCCCAGATGCAATGCAG 59.391 52.381 14.98 0.00 44.69 4.41
50 51 0.913924 TCTCCCAGATGCAATGCAGA 59.086 50.000 14.98 3.94 43.65 4.26
51 52 1.134189 TCTCCCAGATGCAATGCAGAG 60.134 52.381 14.98 13.95 43.65 3.35
52 53 0.106868 TCCCAGATGCAATGCAGAGG 60.107 55.000 14.98 14.42 43.65 3.69
53 54 1.734137 CCAGATGCAATGCAGAGGC 59.266 57.895 14.98 3.12 43.65 4.70
54 55 1.734137 CAGATGCAATGCAGAGGCC 59.266 57.895 14.98 0.00 43.65 5.19
55 56 1.822613 AGATGCAATGCAGAGGCCG 60.823 57.895 14.98 0.00 43.65 6.13
56 57 2.831742 ATGCAATGCAGAGGCCGG 60.832 61.111 14.98 0.00 43.65 6.13
57 58 3.348554 ATGCAATGCAGAGGCCGGA 62.349 57.895 14.98 0.00 43.65 5.14
58 59 3.207669 GCAATGCAGAGGCCGGAG 61.208 66.667 5.05 0.00 40.13 4.63
240 243 3.496331 TCCCTTTGTTCCCACTCAAATC 58.504 45.455 0.00 0.00 33.93 2.17
258 261 0.677288 TCGTTGAGATTGTCACGGGT 59.323 50.000 0.00 0.00 33.71 5.28
335 338 6.866770 TGACTTAAGTAGTTGAACGGATGAAG 59.133 38.462 8.42 0.00 37.17 3.02
353 356 5.084818 TGAAGATGCAGGAATAAGAACGA 57.915 39.130 0.00 0.00 0.00 3.85
420 424 0.794473 CCAAGTCGGCGTAAAAGACC 59.206 55.000 6.85 0.00 35.65 3.85
427 431 1.070175 CGGCGTAAAAGACCACACAAG 60.070 52.381 0.00 0.00 0.00 3.16
448 452 2.582052 CAACCCACTCTAAAAGGCACA 58.418 47.619 0.00 0.00 0.00 4.57
455 459 3.624861 CACTCTAAAAGGCACATGCTAGG 59.375 47.826 3.48 0.00 41.70 3.02
460 464 4.953940 AAAAGGCACATGCTAGGAAAAA 57.046 36.364 3.48 0.00 41.70 1.94
488 508 9.871238 ATATTACCGAGCACCAAGTAATTATAG 57.129 33.333 0.00 0.00 36.88 1.31
489 509 5.609533 ACCGAGCACCAAGTAATTATAGT 57.390 39.130 0.00 0.00 0.00 2.12
490 510 6.720112 ACCGAGCACCAAGTAATTATAGTA 57.280 37.500 0.00 0.00 0.00 1.82
512 532 5.446143 AACACGAATGCCACTGAAATTTA 57.554 34.783 0.00 0.00 0.00 1.40
575 603 7.465353 TTGACTATTCAAAATCAATCAGGCA 57.535 32.000 0.00 0.00 38.87 4.75
673 894 7.319052 TCCCCTGTGTTTGAAATAGTACTTA 57.681 36.000 0.00 0.00 0.00 2.24
1023 1551 0.895530 CCTCCACCACGAGCTTCTTA 59.104 55.000 0.00 0.00 0.00 2.10
1227 1757 2.290287 ACCTATGCCGACTGTGCCA 61.290 57.895 0.00 0.00 0.00 4.92
1228 1764 1.815421 CCTATGCCGACTGTGCCAC 60.815 63.158 0.00 0.00 0.00 5.01
1392 1928 1.152881 GATGCCCGCCATTCCTTCT 60.153 57.895 0.00 0.00 33.29 2.85
1410 1946 2.316108 TCTATGCCCAAGATGACGCTA 58.684 47.619 0.00 0.00 0.00 4.26
1431 1967 1.003233 GCCGATGCCTTCTATCCCC 60.003 63.158 0.00 0.00 0.00 4.81
1746 2311 0.370273 GCTTCTTGCGGTATGTCACG 59.630 55.000 0.00 0.00 0.00 4.35
1747 2312 0.999406 CTTCTTGCGGTATGTCACGG 59.001 55.000 0.00 0.00 0.00 4.94
1755 2320 1.021968 GGTATGTCACGGGAATTGCC 58.978 55.000 5.80 5.80 0.00 4.52
1770 2335 2.237393 TTGCCTCCAAACATGCAAAC 57.763 45.000 0.00 0.00 40.46 2.93
1771 2336 0.392336 TGCCTCCAAACATGCAAACC 59.608 50.000 0.00 0.00 0.00 3.27
1772 2337 0.667184 GCCTCCAAACATGCAAACCG 60.667 55.000 0.00 0.00 0.00 4.44
1773 2338 0.958091 CCTCCAAACATGCAAACCGA 59.042 50.000 0.00 0.00 0.00 4.69
1774 2339 1.335872 CCTCCAAACATGCAAACCGAC 60.336 52.381 0.00 0.00 0.00 4.79
1836 2409 1.345715 GGCCTGCCCATGTAGTAGGT 61.346 60.000 15.48 0.00 39.16 3.08
1878 2455 8.525290 TCTATTCATGTGTGAGAAGATGTAGA 57.475 34.615 0.00 0.00 35.39 2.59
2295 2931 9.015577 TCATAAAACGTTCACTCATTCAAAAAC 57.984 29.630 0.00 0.00 0.00 2.43
2370 3014 6.940831 AAATTGTTCCACCAATTTCCAAAG 57.059 33.333 6.15 0.00 46.73 2.77
2385 3031 8.550376 CAATTTCCAAAGAATGTTTGTCGATTT 58.450 29.630 2.22 0.00 0.00 2.17
2388 3034 9.587772 TTTCCAAAGAATGTTTGTCGATTTTAA 57.412 25.926 2.22 0.00 0.00 1.52
2404 3050 7.216693 GTCGATTTTAAAAATGTTCGCGGATTA 59.783 33.333 6.13 0.00 0.00 1.75
2405 3051 7.427030 TCGATTTTAAAAATGTTCGCGGATTAG 59.573 33.333 6.13 0.00 0.00 1.73
2406 3052 7.427030 CGATTTTAAAAATGTTCGCGGATTAGA 59.573 33.333 6.13 0.00 0.00 2.10
2407 3053 7.784790 TTTTAAAAATGTTCGCGGATTAGAC 57.215 32.000 6.13 0.00 0.00 2.59
2408 3054 6.730960 TTAAAAATGTTCGCGGATTAGACT 57.269 33.333 6.13 0.00 0.00 3.24
2409 3055 4.859629 AAAATGTTCGCGGATTAGACTC 57.140 40.909 6.13 0.00 0.00 3.36
2410 3056 2.510768 ATGTTCGCGGATTAGACTCC 57.489 50.000 6.13 0.00 0.00 3.85
2411 3057 0.458669 TGTTCGCGGATTAGACTCCC 59.541 55.000 6.13 0.00 31.04 4.30
2412 3058 0.594284 GTTCGCGGATTAGACTCCCG 60.594 60.000 6.13 0.00 45.51 5.14
2415 3061 3.428797 CGGATTAGACTCCCGCGA 58.571 61.111 8.23 0.00 36.62 5.87
2416 3062 1.731700 CGGATTAGACTCCCGCGAA 59.268 57.895 8.23 0.00 36.62 4.70
2417 3063 0.317938 CGGATTAGACTCCCGCGAAG 60.318 60.000 8.23 7.39 36.62 3.79
2430 3076 4.043168 CGAAGCCCTCACGTTTGT 57.957 55.556 0.00 0.00 0.00 2.83
2431 3077 2.317230 CGAAGCCCTCACGTTTGTT 58.683 52.632 0.00 0.00 0.00 2.83
2432 3078 0.661020 CGAAGCCCTCACGTTTGTTT 59.339 50.000 0.00 0.00 0.00 2.83
2433 3079 1.333791 CGAAGCCCTCACGTTTGTTTC 60.334 52.381 0.00 0.00 0.00 2.78
2434 3080 1.001706 GAAGCCCTCACGTTTGTTTCC 60.002 52.381 0.00 0.00 0.00 3.13
2435 3081 1.164041 AGCCCTCACGTTTGTTTCCG 61.164 55.000 0.00 0.00 0.00 4.30
2436 3082 1.946267 CCCTCACGTTTGTTTCCGG 59.054 57.895 0.00 0.00 0.00 5.14
2437 3083 0.816421 CCCTCACGTTTGTTTCCGGT 60.816 55.000 0.00 0.00 0.00 5.28
2438 3084 1.018910 CCTCACGTTTGTTTCCGGTT 58.981 50.000 0.00 0.00 0.00 4.44
2439 3085 1.402613 CCTCACGTTTGTTTCCGGTTT 59.597 47.619 0.00 0.00 0.00 3.27
2440 3086 2.446282 CTCACGTTTGTTTCCGGTTTG 58.554 47.619 0.00 0.00 0.00 2.93
2441 3087 0.917939 CACGTTTGTTTCCGGTTTGC 59.082 50.000 0.00 0.00 0.00 3.68
2442 3088 0.523757 ACGTTTGTTTCCGGTTTGCG 60.524 50.000 0.00 1.17 0.00 4.85
2443 3089 1.203600 CGTTTGTTTCCGGTTTGCGG 61.204 55.000 0.00 0.00 0.00 5.69
2444 3090 0.872451 GTTTGTTTCCGGTTTGCGGG 60.872 55.000 0.00 0.00 36.54 6.13
2445 3091 1.035932 TTTGTTTCCGGTTTGCGGGA 61.036 50.000 0.00 0.00 41.55 5.14
2446 3092 1.448922 TTGTTTCCGGTTTGCGGGAG 61.449 55.000 0.00 0.00 43.57 4.30
2447 3093 1.598685 GTTTCCGGTTTGCGGGAGA 60.599 57.895 0.00 0.00 43.57 3.71
2448 3094 1.148723 TTTCCGGTTTGCGGGAGAA 59.851 52.632 0.00 0.00 43.57 2.87
2449 3095 0.465824 TTTCCGGTTTGCGGGAGAAA 60.466 50.000 0.00 0.00 43.57 2.52
2450 3096 0.250989 TTCCGGTTTGCGGGAGAAAT 60.251 50.000 0.00 0.00 43.57 2.17
2451 3097 0.675522 TCCGGTTTGCGGGAGAAATC 60.676 55.000 0.00 0.00 38.90 2.17
2452 3098 1.423845 CGGTTTGCGGGAGAAATCG 59.576 57.895 0.00 0.00 31.17 3.34
2457 3103 3.262686 GCGGGAGAAATCGCGTCC 61.263 66.667 5.77 4.85 45.79 4.79
2458 3104 2.183300 CGGGAGAAATCGCGTCCA 59.817 61.111 13.89 0.00 40.45 4.02
2459 3105 1.878522 CGGGAGAAATCGCGTCCAG 60.879 63.158 13.89 6.73 40.45 3.86
2460 3106 1.515954 GGGAGAAATCGCGTCCAGA 59.484 57.895 13.89 0.00 31.31 3.86
2461 3107 0.806492 GGGAGAAATCGCGTCCAGAC 60.806 60.000 13.89 0.63 31.31 3.51
2462 3108 0.806492 GGAGAAATCGCGTCCAGACC 60.806 60.000 5.77 0.99 0.00 3.85
2463 3109 0.108804 GAGAAATCGCGTCCAGACCA 60.109 55.000 5.77 0.00 0.00 4.02
2464 3110 0.389948 AGAAATCGCGTCCAGACCAC 60.390 55.000 5.77 0.00 0.00 4.16
2465 3111 1.683790 GAAATCGCGTCCAGACCACG 61.684 60.000 5.77 2.39 40.35 4.94
2470 3116 2.959372 CGTCCAGACCACGCTGTA 59.041 61.111 0.00 0.00 34.06 2.74
2471 3117 1.287815 CGTCCAGACCACGCTGTAA 59.712 57.895 0.00 0.00 34.06 2.41
2472 3118 0.319211 CGTCCAGACCACGCTGTAAA 60.319 55.000 0.00 0.00 34.06 2.01
2473 3119 1.145803 GTCCAGACCACGCTGTAAAC 58.854 55.000 0.00 0.00 34.06 2.01
2474 3120 0.034337 TCCAGACCACGCTGTAAACC 59.966 55.000 0.00 0.00 34.06 3.27
2475 3121 0.250124 CCAGACCACGCTGTAAACCA 60.250 55.000 0.00 0.00 34.06 3.67
2476 3122 1.588674 CAGACCACGCTGTAAACCAA 58.411 50.000 0.00 0.00 0.00 3.67
2477 3123 2.151202 CAGACCACGCTGTAAACCAAT 58.849 47.619 0.00 0.00 0.00 3.16
2478 3124 3.331150 CAGACCACGCTGTAAACCAATA 58.669 45.455 0.00 0.00 0.00 1.90
2479 3125 3.124636 CAGACCACGCTGTAAACCAATAC 59.875 47.826 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.381948 TGCATGCGGTCATTTTATTGATTATTC 59.618 33.333 14.09 0.00 0.00 1.75
6 7 6.747125 TGCATGCGGTCATTTTATTGATTAT 58.253 32.000 14.09 0.00 0.00 1.28
7 8 6.141560 TGCATGCGGTCATTTTATTGATTA 57.858 33.333 14.09 0.00 0.00 1.75
8 9 5.008619 TGCATGCGGTCATTTTATTGATT 57.991 34.783 14.09 0.00 0.00 2.57
9 10 4.652421 TGCATGCGGTCATTTTATTGAT 57.348 36.364 14.09 0.00 0.00 2.57
10 11 4.338964 AGATGCATGCGGTCATTTTATTGA 59.661 37.500 20.70 0.00 0.00 2.57
11 12 4.613944 AGATGCATGCGGTCATTTTATTG 58.386 39.130 20.70 0.00 0.00 1.90
12 13 4.261741 GGAGATGCATGCGGTCATTTTATT 60.262 41.667 20.70 2.87 0.00 1.40
13 14 3.254166 GGAGATGCATGCGGTCATTTTAT 59.746 43.478 20.70 3.70 0.00 1.40
14 15 2.618241 GGAGATGCATGCGGTCATTTTA 59.382 45.455 20.70 0.00 0.00 1.52
15 16 1.406539 GGAGATGCATGCGGTCATTTT 59.593 47.619 20.70 4.40 0.00 1.82
16 17 1.027357 GGAGATGCATGCGGTCATTT 58.973 50.000 20.70 2.56 0.00 2.32
17 18 0.820891 GGGAGATGCATGCGGTCATT 60.821 55.000 20.70 5.31 0.00 2.57
18 19 1.228063 GGGAGATGCATGCGGTCAT 60.228 57.895 20.70 6.79 0.00 3.06
19 20 2.190313 GGGAGATGCATGCGGTCA 59.810 61.111 20.70 1.95 0.00 4.02
20 21 1.890979 CTGGGAGATGCATGCGGTC 60.891 63.158 14.09 13.66 0.00 4.79
21 22 1.703014 ATCTGGGAGATGCATGCGGT 61.703 55.000 14.09 3.84 32.80 5.68
22 23 1.072678 ATCTGGGAGATGCATGCGG 59.927 57.895 14.09 0.00 32.80 5.69
23 24 2.244946 CATCTGGGAGATGCATGCG 58.755 57.895 14.09 0.00 44.69 4.73
30 31 1.493446 TCTGCATTGCATCTGGGAGAT 59.507 47.619 12.53 0.00 38.13 2.75
31 32 0.913924 TCTGCATTGCATCTGGGAGA 59.086 50.000 12.53 0.92 38.13 3.71
32 33 1.309950 CTCTGCATTGCATCTGGGAG 58.690 55.000 12.53 10.77 38.13 4.30
33 34 0.106868 CCTCTGCATTGCATCTGGGA 60.107 55.000 12.53 4.61 38.13 4.37
34 35 1.735376 GCCTCTGCATTGCATCTGGG 61.735 60.000 12.53 12.24 38.13 4.45
35 36 1.734137 GCCTCTGCATTGCATCTGG 59.266 57.895 12.53 14.60 38.13 3.86
36 37 1.734137 GGCCTCTGCATTGCATCTG 59.266 57.895 12.53 0.55 38.13 2.90
37 38 1.822613 CGGCCTCTGCATTGCATCT 60.823 57.895 12.53 0.00 38.13 2.90
38 39 2.719979 CGGCCTCTGCATTGCATC 59.280 61.111 12.53 2.14 38.13 3.91
39 40 2.831742 CCGGCCTCTGCATTGCAT 60.832 61.111 12.53 0.00 38.13 3.96
40 41 3.982316 CTCCGGCCTCTGCATTGCA 62.982 63.158 11.50 11.50 40.13 4.08
41 42 3.207669 CTCCGGCCTCTGCATTGC 61.208 66.667 0.00 0.46 40.13 3.56
42 43 2.515523 CCTCCGGCCTCTGCATTG 60.516 66.667 0.00 0.00 40.13 2.82
43 44 3.011517 ACCTCCGGCCTCTGCATT 61.012 61.111 0.00 0.00 40.13 3.56
44 45 3.474570 GACCTCCGGCCTCTGCAT 61.475 66.667 0.00 0.00 40.13 3.96
46 47 2.932130 GAATGACCTCCGGCCTCTGC 62.932 65.000 0.00 0.00 0.00 4.26
47 48 1.144936 GAATGACCTCCGGCCTCTG 59.855 63.158 0.00 0.00 0.00 3.35
48 49 1.002274 AGAATGACCTCCGGCCTCT 59.998 57.895 0.00 0.00 0.00 3.69
49 50 1.443828 GAGAATGACCTCCGGCCTC 59.556 63.158 0.00 0.00 0.00 4.70
50 51 2.066999 GGAGAATGACCTCCGGCCT 61.067 63.158 0.00 0.00 42.80 5.19
51 52 2.506472 GGAGAATGACCTCCGGCC 59.494 66.667 0.00 0.00 42.80 6.13
88 89 2.440627 TGCTCAGCCATCCAACATATCT 59.559 45.455 0.00 0.00 0.00 1.98
240 243 0.790207 CACCCGTGACAATCTCAACG 59.210 55.000 0.00 0.00 0.00 4.10
247 250 1.519408 GTGTAAGCACCCGTGACAAT 58.481 50.000 0.00 0.00 39.61 2.71
335 338 5.938322 TGTTTTCGTTCTTATTCCTGCATC 58.062 37.500 0.00 0.00 0.00 3.91
420 424 2.254546 TAGAGTGGGTTGCTTGTGTG 57.745 50.000 0.00 0.00 0.00 3.82
427 431 1.269723 GTGCCTTTTAGAGTGGGTTGC 59.730 52.381 0.00 0.00 0.00 4.17
460 464 7.875327 AATTACTTGGTGCTCGGTAATATTT 57.125 32.000 0.00 0.00 34.90 1.40
463 467 8.863086 ACTATAATTACTTGGTGCTCGGTAATA 58.137 33.333 0.00 0.00 34.90 0.98
488 508 3.889196 TTTCAGTGGCATTCGTGTTAC 57.111 42.857 0.00 0.00 0.00 2.50
489 509 5.446143 AAATTTCAGTGGCATTCGTGTTA 57.554 34.783 0.00 0.00 0.00 2.41
490 510 4.320608 AAATTTCAGTGGCATTCGTGTT 57.679 36.364 0.00 0.00 0.00 3.32
512 532 7.207383 TCAGATATTCGGTGAACATCGTTAAT 58.793 34.615 7.33 4.01 31.59 1.40
575 603 0.109723 TAAGAAAGGGCGTGGCAACT 59.890 50.000 0.00 0.00 37.61 3.16
673 894 6.387465 TCGTCACTCTTTCTTCACGATAAAT 58.613 36.000 0.00 0.00 31.65 1.40
1119 1649 1.450312 GAGGCCAGGGACATCAACG 60.450 63.158 5.01 0.00 0.00 4.10
1121 1651 2.308722 GGGAGGCCAGGGACATCAA 61.309 63.158 5.01 0.00 0.00 2.57
1392 1928 1.070134 GGTAGCGTCATCTTGGGCATA 59.930 52.381 0.00 0.00 0.00 3.14
1410 1946 1.367840 GATAGAAGGCATCGGCGGT 59.632 57.895 7.21 0.00 42.47 5.68
1431 1967 0.443869 GCATAGGCACGTTGACAGTG 59.556 55.000 0.00 0.00 42.15 3.66
1511 2047 4.338539 AGCGTGTGACCGTCGACC 62.339 66.667 10.58 0.00 0.00 4.79
1710 2270 6.681368 GCAAGAAGCAATATCCCTTTAGTTGG 60.681 42.308 0.00 0.00 44.79 3.77
1711 2271 6.268566 GCAAGAAGCAATATCCCTTTAGTTG 58.731 40.000 0.00 0.00 44.79 3.16
1712 2272 5.066505 CGCAAGAAGCAATATCCCTTTAGTT 59.933 40.000 0.00 0.00 46.13 2.24
1713 2273 4.576463 CGCAAGAAGCAATATCCCTTTAGT 59.424 41.667 0.00 0.00 46.13 2.24
1714 2274 4.023707 CCGCAAGAAGCAATATCCCTTTAG 60.024 45.833 0.00 0.00 46.13 1.85
1746 2311 1.405933 GCATGTTTGGAGGCAATTCCC 60.406 52.381 0.00 0.00 36.35 3.97
1747 2312 1.275856 TGCATGTTTGGAGGCAATTCC 59.724 47.619 0.00 0.00 37.77 3.01
1755 2320 1.335872 GGTCGGTTTGCATGTTTGGAG 60.336 52.381 0.00 0.00 0.00 3.86
1836 2409 7.250032 TGAATAGAGCGTAGTATAGGAGGTA 57.750 40.000 0.00 0.00 0.00 3.08
1878 2455 3.966543 CTGGACCAAACGGGGGCT 61.967 66.667 0.00 0.00 42.91 5.19
2267 2900 8.555166 TTTGAATGAGTGAACGTTTTATGAAC 57.445 30.769 0.46 0.00 0.00 3.18
2385 3031 6.183360 GGAGTCTAATCCGCGAACATTTTTAA 60.183 38.462 8.23 0.00 0.00 1.52
2388 3034 3.621715 GGAGTCTAATCCGCGAACATTTT 59.378 43.478 8.23 0.00 0.00 1.82
2405 3051 4.516195 GAGGGCTTCGCGGGAGTC 62.516 72.222 6.13 6.35 0.00 3.36
2407 3053 4.821589 GTGAGGGCTTCGCGGGAG 62.822 72.222 6.13 6.12 0.00 4.30
2412 3058 1.782028 AACAAACGTGAGGGCTTCGC 61.782 55.000 0.00 0.00 0.00 4.70
2413 3059 0.661020 AAACAAACGTGAGGGCTTCG 59.339 50.000 0.00 0.00 0.00 3.79
2414 3060 1.001706 GGAAACAAACGTGAGGGCTTC 60.002 52.381 0.00 0.00 0.00 3.86
2415 3061 1.029681 GGAAACAAACGTGAGGGCTT 58.970 50.000 0.00 0.00 0.00 4.35
2416 3062 1.164041 CGGAAACAAACGTGAGGGCT 61.164 55.000 0.00 0.00 0.00 5.19
2417 3063 1.281656 CGGAAACAAACGTGAGGGC 59.718 57.895 0.00 0.00 0.00 5.19
2418 3064 0.816421 ACCGGAAACAAACGTGAGGG 60.816 55.000 9.46 0.00 0.00 4.30
2419 3065 1.018910 AACCGGAAACAAACGTGAGG 58.981 50.000 9.46 0.00 0.00 3.86
2420 3066 2.446282 CAAACCGGAAACAAACGTGAG 58.554 47.619 9.46 0.00 0.00 3.51
2421 3067 1.467713 GCAAACCGGAAACAAACGTGA 60.468 47.619 9.46 0.00 0.00 4.35
2422 3068 0.917939 GCAAACCGGAAACAAACGTG 59.082 50.000 9.46 0.00 0.00 4.49
2423 3069 0.523757 CGCAAACCGGAAACAAACGT 60.524 50.000 9.46 0.00 0.00 3.99
2424 3070 2.200039 CGCAAACCGGAAACAAACG 58.800 52.632 9.46 0.00 0.00 3.60
2434 3080 1.423845 CGATTTCTCCCGCAAACCG 59.576 57.895 0.00 0.00 0.00 4.44
2441 3087 1.878522 CTGGACGCGATTTCTCCCG 60.879 63.158 15.93 0.57 0.00 5.14
2442 3088 0.806492 GTCTGGACGCGATTTCTCCC 60.806 60.000 15.93 2.39 0.00 4.30
2443 3089 0.806492 GGTCTGGACGCGATTTCTCC 60.806 60.000 15.93 9.86 0.00 3.71
2444 3090 0.108804 TGGTCTGGACGCGATTTCTC 60.109 55.000 15.93 0.00 0.00 2.87
2445 3091 0.389948 GTGGTCTGGACGCGATTTCT 60.390 55.000 15.93 0.00 0.00 2.52
2446 3092 1.683790 CGTGGTCTGGACGCGATTTC 61.684 60.000 15.93 0.00 34.15 2.17
2447 3093 1.736645 CGTGGTCTGGACGCGATTT 60.737 57.895 15.93 0.00 34.15 2.17
2448 3094 2.126071 CGTGGTCTGGACGCGATT 60.126 61.111 15.93 0.00 34.15 3.34
2453 3099 0.319211 TTTACAGCGTGGTCTGGACG 60.319 55.000 0.00 0.00 38.36 4.79
2454 3100 1.145803 GTTTACAGCGTGGTCTGGAC 58.854 55.000 0.00 0.00 38.36 4.02
2455 3101 0.034337 GGTTTACAGCGTGGTCTGGA 59.966 55.000 0.00 0.00 38.36 3.86
2456 3102 0.250124 TGGTTTACAGCGTGGTCTGG 60.250 55.000 0.00 0.00 38.36 3.86
2457 3103 1.588674 TTGGTTTACAGCGTGGTCTG 58.411 50.000 0.00 0.00 39.86 3.51
2458 3104 2.561478 ATTGGTTTACAGCGTGGTCT 57.439 45.000 0.00 0.00 0.00 3.85
2459 3105 3.734776 GTATTGGTTTACAGCGTGGTC 57.265 47.619 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.