Multiple sequence alignment - TraesCS6B01G339900

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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 TraesCS6B01G339900 chr6B 100.000 3356 0 0 1 3356 599400640 599397285 0.000000e+00 6198.0
1 TraesCS6B01G339900 chr6B 78.947 114 17 6 3110 3219 404456998 404457108 1.670000e-08 71.3
2 TraesCS6B01G339900 chr6D 90.247 892 57 15 1603 2489 400463172 400462306 0.000000e+00 1138.0
3 TraesCS6B01G339900 chr6D 90.803 772 61 4 820 1584 400471084 400470316 0.000000e+00 1024.0
4 TraesCS6B01G339900 chr6D 89.434 795 64 14 2520 3307 400448902 400448121 0.000000e+00 985.0
5 TraesCS6B01G339900 chr6D 94.105 458 20 4 1 451 400538677 400538220 0.000000e+00 689.0
6 TraesCS6B01G339900 chr6D 94.152 171 8 2 658 828 400537403 400537235 3.320000e-65 259.0
7 TraesCS6B01G339900 chr6D 96.040 101 4 0 481 581 400537725 400537625 7.450000e-37 165.0
8 TraesCS6B01G339900 chr6D 82.667 150 21 3 3086 3230 419761217 419761068 9.770000e-26 128.0
9 TraesCS6B01G339900 chr6D 78.992 119 20 4 3103 3218 263475890 263476006 3.590000e-10 76.8
10 TraesCS6B01G339900 chr5B 84.576 979 121 14 1474 2443 451632077 451631120 0.000000e+00 944.0
11 TraesCS6B01G339900 chr5B 84.576 979 121 14 1474 2443 452233167 452232210 0.000000e+00 944.0
12 TraesCS6B01G339900 chr5B 84.458 978 118 18 1474 2440 452633295 452634249 0.000000e+00 933.0
13 TraesCS6B01G339900 chr5B 90.485 515 49 0 961 1475 451632683 451632169 0.000000e+00 680.0
14 TraesCS6B01G339900 chr5B 90.485 515 49 0 961 1475 452233773 452233259 0.000000e+00 680.0
15 TraesCS6B01G339900 chr5B 90.485 515 49 0 961 1475 452632689 452633203 0.000000e+00 680.0
16 TraesCS6B01G339900 chr5B 84.543 427 39 13 2026 2443 452232149 452231741 6.750000e-107 398.0
17 TraesCS6B01G339900 chr5D 84.372 979 123 14 1474 2443 378474743 378473786 0.000000e+00 933.0
18 TraesCS6B01G339900 chr5D 90.485 515 49 0 961 1475 378475349 378474835 0.000000e+00 680.0
19 TraesCS6B01G339900 chr5D 89.709 515 52 1 961 1475 378613780 378614293 0.000000e+00 656.0
20 TraesCS6B01G339900 chr6A 93.762 513 26 4 2799 3310 546473475 546472968 0.000000e+00 765.0
21 TraesCS6B01G339900 chr6A 94.792 480 18 4 1 476 546478004 546477528 0.000000e+00 741.0
22 TraesCS6B01G339900 chr6A 91.604 536 34 5 1880 2415 546476772 546476248 0.000000e+00 730.0
23 TraesCS6B01G339900 chr6A 94.568 405 20 2 862 1264 546477176 546476772 2.840000e-175 625.0
24 TraesCS6B01G339900 chr6A 86.782 348 26 5 2408 2740 546473814 546473472 1.470000e-98 370.0
25 TraesCS6B01G339900 chr6A 98.507 67 1 0 724 790 546477261 546477195 5.880000e-23 119.0
26 TraesCS6B01G339900 chr3D 87.755 147 16 2 3086 3230 81373656 81373510 1.600000e-38 171.0
27 TraesCS6B01G339900 chr2B 89.231 130 10 3 3086 3212 296022977 296022849 3.470000e-35 159.0
28 TraesCS6B01G339900 chr2B 100.000 28 0 0 3049 3076 750221967 750221940 6.000000e-03 52.8
29 TraesCS6B01G339900 chr4D 84.247 146 21 2 3087 3230 507123202 507123057 1.260000e-29 141.0
30 TraesCS6B01G339900 chr7B 82.993 147 22 3 3086 3230 602639051 602638906 2.720000e-26 130.0
31 TraesCS6B01G339900 chr5A 83.221 149 18 4 3086 3230 444879930 444879785 2.720000e-26 130.0
32 TraesCS6B01G339900 chr1D 83.108 148 20 4 3086 3230 316879549 316879404 2.720000e-26 130.0
33 TraesCS6B01G339900 chr4A 79.444 180 35 2 1029 1207 598607914 598608092 3.520000e-25 126.0
34 TraesCS6B01G339900 chr4A 92.647 68 4 1 562 629 624117292 624117358 2.760000e-16 97.1
35 TraesCS6B01G339900 chr4A 100.000 28 0 0 3049 3076 722974421 722974448 6.000000e-03 52.8
36 TraesCS6B01G339900 chr4B 82.090 134 22 2 1075 1207 8416306 8416174 2.740000e-21 113.0
37 TraesCS6B01G339900 chr4B 92.593 54 4 0 553 606 97390261 97390208 9.980000e-11 78.7
38 TraesCS6B01G339900 chr2A 100.000 45 0 0 562 606 95825291 95825247 2.150000e-12 84.2
39 TraesCS6B01G339900 chr2A 95.556 45 2 0 562 606 193730670 193730626 4.640000e-09 73.1
40 TraesCS6B01G339900 chr7D 89.394 66 5 1 562 625 518568922 518568857 7.720000e-12 82.4
41 TraesCS6B01G339900 chr7D 91.379 58 5 0 549 606 135974668 135974725 2.780000e-11 80.5
42 TraesCS6B01G339900 chr7D 86.486 74 5 1 562 630 225203083 225203156 3.590000e-10 76.8
43 TraesCS6B01G339900 chr1A 86.567 67 4 1 562 623 77272792 77272726 6.010000e-08 69.4
44 TraesCS6B01G339900 chr1A 100.000 28 0 0 2443 2470 375014501 375014528 6.000000e-03 52.8
45 TraesCS6B01G339900 chr1B 84.000 75 5 4 562 629 551725765 551725839 7.770000e-07 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G339900 chr6B 599397285 599400640 3355 True 6198.000000 6198 100.000000 1 3356 1 chr6B.!!$R1 3355
1 TraesCS6B01G339900 chr6D 400462306 400463172 866 True 1138.000000 1138 90.247000 1603 2489 1 chr6D.!!$R2 886
2 TraesCS6B01G339900 chr6D 400470316 400471084 768 True 1024.000000 1024 90.803000 820 1584 1 chr6D.!!$R3 764
3 TraesCS6B01G339900 chr6D 400448121 400448902 781 True 985.000000 985 89.434000 2520 3307 1 chr6D.!!$R1 787
4 TraesCS6B01G339900 chr6D 400537235 400538677 1442 True 371.000000 689 94.765667 1 828 3 chr6D.!!$R5 827
5 TraesCS6B01G339900 chr5B 451631120 451632683 1563 True 812.000000 944 87.530500 961 2443 2 chr5B.!!$R1 1482
6 TraesCS6B01G339900 chr5B 452632689 452634249 1560 False 806.500000 933 87.471500 961 2440 2 chr5B.!!$F1 1479
7 TraesCS6B01G339900 chr5B 452231741 452233773 2032 True 674.000000 944 86.534667 961 2443 3 chr5B.!!$R2 1482
8 TraesCS6B01G339900 chr5D 378473786 378475349 1563 True 806.500000 933 87.428500 961 2443 2 chr5D.!!$R1 1482
9 TraesCS6B01G339900 chr5D 378613780 378614293 513 False 656.000000 656 89.709000 961 1475 1 chr5D.!!$F1 514
10 TraesCS6B01G339900 chr6A 546472968 546478004 5036 True 558.333333 765 93.335833 1 3310 6 chr6A.!!$R1 3309

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
367 368 0.968405 AAATTGCGACCATGTTGGCT 59.032 45.0 0.00 0.0 42.67 4.75 F
1621 2375 0.173708 CCTGTACCACTCGGAGAAGC 59.826 60.0 12.86 0.0 34.09 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 2395 0.474184 CATCCCCCGATACTTTGGCT 59.526 55.000 0.00 0.00 0.00 4.75 R
3322 7019 1.075698 GGATAGTCCTCATCCTCCGGA 59.924 57.143 2.93 2.93 39.17 5.14 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
88 89 4.693532 TCCGCTGTGGACAACATC 57.306 55.556 5.70 0.00 43.74 3.06
232 233 2.103263 CCAGTACCTTGATAGGCAGTCC 59.897 54.545 0.00 0.00 46.22 3.85
355 356 4.795278 GTCTAGGCTTTGATGAAAATTGCG 59.205 41.667 0.00 0.00 0.00 4.85
357 358 3.578688 AGGCTTTGATGAAAATTGCGAC 58.421 40.909 0.00 0.00 0.00 5.19
367 368 0.968405 AAATTGCGACCATGTTGGCT 59.032 45.000 0.00 0.00 42.67 4.75
390 394 3.447742 CACTTTGCCTTTTGTTGGACTC 58.552 45.455 0.00 0.00 0.00 3.36
409 413 3.265791 CTCGGTGGAGATTCTTTTGAGG 58.734 50.000 0.00 0.00 43.27 3.86
435 443 7.605410 AATGGTAAAGACGTTATTTCATCGT 57.395 32.000 3.29 0.00 40.49 3.73
479 957 4.978083 ATCAGCTGGTCAATGTGAAATC 57.022 40.909 15.13 0.00 0.00 2.17
505 983 9.559958 CTTTAAGAAATTTGATACACTGCGATT 57.440 29.630 0.00 0.00 0.00 3.34
517 995 1.197721 ACTGCGATTCCTTTTTCTGCG 59.802 47.619 0.00 0.00 0.00 5.18
581 1062 3.331294 TCCTCCTTCCGTCCCAAAATAAA 59.669 43.478 0.00 0.00 0.00 1.40
582 1063 4.017867 TCCTCCTTCCGTCCCAAAATAAAT 60.018 41.667 0.00 0.00 0.00 1.40
584 1065 4.668636 TCCTTCCGTCCCAAAATAAATGT 58.331 39.130 0.00 0.00 0.00 2.71
585 1066 4.703093 TCCTTCCGTCCCAAAATAAATGTC 59.297 41.667 0.00 0.00 0.00 3.06
587 1068 5.163652 CCTTCCGTCCCAAAATAAATGTCTC 60.164 44.000 0.00 0.00 0.00 3.36
588 1069 4.912586 TCCGTCCCAAAATAAATGTCTCA 58.087 39.130 0.00 0.00 0.00 3.27
589 1070 5.317808 TCCGTCCCAAAATAAATGTCTCAA 58.682 37.500 0.00 0.00 0.00 3.02
590 1071 5.182380 TCCGTCCCAAAATAAATGTCTCAAC 59.818 40.000 0.00 0.00 0.00 3.18
625 1277 3.739401 ACTTATTTTGGGACTGAGGGG 57.261 47.619 0.00 0.00 0.00 4.79
653 1305 1.856920 ACCACCAGGGAAGGAAAAAGA 59.143 47.619 8.22 0.00 41.15 2.52
790 1442 6.681368 GCAATGACTGGATTTAATCTTGGTCC 60.681 42.308 4.87 0.00 0.00 4.46
812 1464 5.771165 TCCTTTTCCTTTACCAAAAGCGTAT 59.229 36.000 0.00 0.00 40.73 3.06
815 1467 8.083462 CCTTTTCCTTTACCAAAAGCGTATAAA 58.917 33.333 0.00 0.00 40.73 1.40
817 1469 9.984190 TTTTCCTTTACCAAAAGCGTATAAAAT 57.016 25.926 0.00 0.00 40.73 1.82
920 1572 5.888982 ATAGAACCATAAACACCGGATCT 57.111 39.130 9.46 0.00 36.14 2.75
968 1625 3.569200 GACCCAGGGCCAAGACCAC 62.569 68.421 4.91 0.00 29.21 4.16
1005 1663 0.174389 TCTCAAGCTGAGCGATGGAC 59.826 55.000 12.16 0.00 43.95 4.02
1324 1982 0.794473 GTTCCATCCCGTGACGAAAC 59.206 55.000 6.54 0.00 0.00 2.78
1379 2037 3.798511 CGGGGAGGGGAAGAAGGC 61.799 72.222 0.00 0.00 0.00 4.35
1420 2081 4.733725 TCCCTAACCCTGGCCGCT 62.734 66.667 0.00 0.00 0.00 5.52
1458 2119 3.432051 CTCGGCTACCCTCTTGCGG 62.432 68.421 0.00 0.00 0.00 5.69
1519 2273 2.615465 CCCCATGGAGCCAACCAGA 61.615 63.158 15.22 0.00 43.49 3.86
1521 2275 0.967380 CCCATGGAGCCAACCAGAAC 60.967 60.000 15.22 0.00 43.49 3.01
1528 2282 2.604174 GCCAACCAGAACGACCACG 61.604 63.158 0.00 0.00 45.75 4.94
1545 2299 3.260483 GACTGCGAGGCATGCGAG 61.260 66.667 12.44 6.46 38.13 5.03
1551 2305 2.094659 CGAGGCATGCGAGTTCGTT 61.095 57.895 12.44 0.00 42.22 3.85
1556 2310 0.921347 GCATGCGAGTTCGTTATCGT 59.079 50.000 0.00 0.00 40.97 3.73
1590 2344 2.375766 GCGCGTGAGAAGGACACAG 61.376 63.158 8.43 0.00 38.04 3.66
1593 2347 1.560860 GCGTGAGAAGGACACAGCAC 61.561 60.000 0.00 0.00 38.04 4.40
1621 2375 0.173708 CCTGTACCACTCGGAGAAGC 59.826 60.000 12.86 0.00 34.09 3.86
1641 2395 1.203441 AGGCCTGGAGCATCAAGACA 61.203 55.000 3.11 0.00 38.98 3.41
1652 2406 3.944015 AGCATCAAGACAGCCAAAGTATC 59.056 43.478 0.00 0.00 0.00 2.24
1665 2419 1.472662 AAGTATCGGGGGATGCTCCG 61.473 60.000 21.18 21.18 46.89 4.63
1677 2431 1.933853 GATGCTCCGTACAATCACCAC 59.066 52.381 0.00 0.00 0.00 4.16
1695 2449 1.608590 CACTGGACGGACAAAGCAATT 59.391 47.619 0.00 0.00 0.00 2.32
1785 2539 4.083862 GCCGAGACCCCCACACTC 62.084 72.222 0.00 0.00 0.00 3.51
1842 2599 2.346365 GGAGTTGGGACCGGTGAC 59.654 66.667 14.63 4.66 0.00 3.67
1886 2643 1.024271 ATTGCCGATGGTTTCATCCG 58.976 50.000 0.00 0.00 45.20 4.18
2079 3305 0.813184 AGATTTCCATGTTGCTGCCG 59.187 50.000 0.00 0.00 0.00 5.69
2112 3338 0.681733 ATGAGGGTAGCACCATAGCG 59.318 55.000 7.49 0.00 41.02 4.26
2136 3362 2.281070 AGACTGCACGTTGGCCTG 60.281 61.111 3.32 0.00 0.00 4.85
2315 3547 2.731027 GCCAGGCGTTTATTGCAAGTAC 60.731 50.000 4.94 1.82 0.00 2.73
2326 3558 7.547227 GTTTATTGCAAGTACCATCTCCAAAT 58.453 34.615 4.94 0.00 0.00 2.32
2327 3559 8.682710 GTTTATTGCAAGTACCATCTCCAAATA 58.317 33.333 4.94 0.00 0.00 1.40
2370 3602 4.746611 GGTAATTGATTATGCTTTGCTGCC 59.253 41.667 0.00 0.00 0.00 4.85
2375 3607 1.530876 TTATGCTTTGCTGCCGCCAA 61.531 50.000 0.00 0.00 34.43 4.52
2376 3608 1.321805 TATGCTTTGCTGCCGCCAAT 61.322 50.000 0.00 0.00 34.43 3.16
2377 3609 1.321805 ATGCTTTGCTGCCGCCAATA 61.322 50.000 0.00 0.00 34.43 1.90
2378 3610 1.321805 TGCTTTGCTGCCGCCAATAT 61.322 50.000 0.00 0.00 34.43 1.28
2384 3616 4.497473 TTGCTGCCGCCAATATTATTAC 57.503 40.909 0.00 0.00 34.43 1.89
2391 3623 6.734137 TGCCGCCAATATTATTACTTTCAAG 58.266 36.000 0.00 0.00 0.00 3.02
2392 3624 5.629435 GCCGCCAATATTATTACTTTCAAGC 59.371 40.000 0.00 0.00 0.00 4.01
2405 3637 5.613358 ACTTTCAAGCATCCTTTTACTCG 57.387 39.130 0.00 0.00 0.00 4.18
2406 3638 4.455877 ACTTTCAAGCATCCTTTTACTCGG 59.544 41.667 0.00 0.00 0.00 4.63
2429 6102 8.713971 TCGGTATATTATTTGCCATGGATATCT 58.286 33.333 18.40 0.00 0.00 1.98
2455 6128 0.966875 TTCGGATTGCCATGCTTGCT 60.967 50.000 0.00 0.00 0.00 3.91
2456 6129 0.107263 TCGGATTGCCATGCTTGCTA 60.107 50.000 0.00 0.00 0.00 3.49
2462 6135 4.142182 GGATTGCCATGCTTGCTAACTAAA 60.142 41.667 0.00 0.00 0.00 1.85
2489 6177 2.861935 CACCTCGTGTCAACTAACGTTT 59.138 45.455 5.91 0.00 40.61 3.60
2498 6186 1.405821 CAACTAACGTTTGGGTTGCCA 59.594 47.619 20.09 0.00 33.86 4.92
2500 6188 3.143211 ACTAACGTTTGGGTTGCCATA 57.857 42.857 5.91 0.00 0.00 2.74
2514 6202 7.129425 TGGGTTGCCATACTTAAAATCCTAAT 58.871 34.615 0.00 0.00 0.00 1.73
2518 6206 9.869757 GTTGCCATACTTAAAATCCTAATGTTT 57.130 29.630 0.00 0.00 0.00 2.83
2625 6314 2.086869 CATGGGCATCAGAAACGTTCT 58.913 47.619 0.00 0.00 41.70 3.01
2640 6329 7.875971 AGAAACGTTCTGATGCTATTTTTCTT 58.124 30.769 0.00 0.00 38.91 2.52
2641 6330 8.352942 AGAAACGTTCTGATGCTATTTTTCTTT 58.647 29.630 0.00 0.00 38.91 2.52
2642 6331 7.858052 AACGTTCTGATGCTATTTTTCTTTG 57.142 32.000 0.00 0.00 0.00 2.77
2643 6332 6.381801 ACGTTCTGATGCTATTTTTCTTTGG 58.618 36.000 0.00 0.00 0.00 3.28
2644 6333 5.801947 CGTTCTGATGCTATTTTTCTTTGGG 59.198 40.000 0.00 0.00 0.00 4.12
2645 6334 6.349280 CGTTCTGATGCTATTTTTCTTTGGGA 60.349 38.462 0.00 0.00 0.00 4.37
2646 6335 6.515272 TCTGATGCTATTTTTCTTTGGGAC 57.485 37.500 0.00 0.00 0.00 4.46
2717 6406 6.019748 AGTATAGGGATGAGGGTGAACTATG 58.980 44.000 0.00 0.00 0.00 2.23
2770 6459 5.757320 GTGAGGATACCAGTCATCTCAAATG 59.243 44.000 0.00 0.00 30.66 2.32
2772 6461 4.723789 AGGATACCAGTCATCTCAAATGGT 59.276 41.667 0.70 0.70 45.87 3.55
2778 6467 3.822735 CAGTCATCTCAAATGGTGTTGGT 59.177 43.478 0.00 0.00 0.00 3.67
2814 6504 1.066143 CCCCGATACTTCACACAGCTT 60.066 52.381 0.00 0.00 0.00 3.74
2885 6578 5.651139 ACATGTATGGCTATACCTACTACCG 59.349 44.000 16.65 0.00 38.71 4.02
2970 6664 6.698008 TTTTCGTCCATCATGATAATTGCT 57.302 33.333 8.15 0.00 0.00 3.91
2971 6665 7.800155 TTTTCGTCCATCATGATAATTGCTA 57.200 32.000 8.15 0.00 0.00 3.49
3008 6702 1.959710 TACCCACTATTGCCACCTGA 58.040 50.000 0.00 0.00 0.00 3.86
3014 6708 4.385199 CCCACTATTGCCACCTGAAAGATA 60.385 45.833 0.00 0.00 34.07 1.98
3033 6727 9.717942 GAAAGATATACTACCTCCGTCTAAGTA 57.282 37.037 0.00 0.00 0.00 2.24
3045 6739 3.127203 CCGTCTAAGTATATCAGCCCTCG 59.873 52.174 0.00 0.00 0.00 4.63
3145 6842 9.640974 TTTCTAACGATATTATTTTTGCTACGC 57.359 29.630 0.00 0.00 0.00 4.42
3147 6844 8.270799 TCTAACGATATTATTTTTGCTACGCAC 58.729 33.333 0.00 0.00 38.71 5.34
3148 6845 6.352682 ACGATATTATTTTTGCTACGCACA 57.647 33.333 0.00 0.00 38.71 4.57
3310 7007 0.736325 GACGAATCCGCCGGATATGG 60.736 60.000 20.72 13.65 42.27 2.74
3311 7008 1.292223 CGAATCCGCCGGATATGGT 59.708 57.895 20.72 2.84 42.27 3.55
3312 7009 0.528924 CGAATCCGCCGGATATGGTA 59.471 55.000 20.72 0.00 42.27 3.25
3313 7010 1.136305 CGAATCCGCCGGATATGGTAT 59.864 52.381 20.72 1.52 42.27 2.73
3314 7011 2.798499 CGAATCCGCCGGATATGGTATC 60.798 54.545 20.72 11.01 42.27 2.24
3315 7012 0.744874 ATCCGCCGGATATGGTATCG 59.255 55.000 18.86 0.00 41.16 2.92
3316 7013 0.322726 TCCGCCGGATATGGTATCGA 60.323 55.000 5.05 0.00 0.00 3.59
3317 7014 0.744874 CCGCCGGATATGGTATCGAT 59.255 55.000 5.05 2.16 0.00 3.59
3318 7015 1.951602 CCGCCGGATATGGTATCGATA 59.048 52.381 5.05 0.00 0.00 2.92
3319 7016 2.359848 CCGCCGGATATGGTATCGATAA 59.640 50.000 5.05 0.00 0.00 1.75
3320 7017 3.005472 CCGCCGGATATGGTATCGATAAT 59.995 47.826 5.05 0.60 0.00 1.28
3321 7018 4.216902 CCGCCGGATATGGTATCGATAATA 59.783 45.833 5.05 3.04 0.00 0.98
3322 7019 5.105877 CCGCCGGATATGGTATCGATAATAT 60.106 44.000 5.05 7.91 0.00 1.28
3323 7020 6.028368 CGCCGGATATGGTATCGATAATATC 58.972 44.000 19.91 19.91 33.23 1.63
3324 7021 6.331061 GCCGGATATGGTATCGATAATATCC 58.669 44.000 28.14 28.14 43.94 2.59
3327 7024 7.698506 GGATATGGTATCGATAATATCCGGA 57.301 40.000 26.11 6.61 40.52 5.14
3328 7025 7.763356 GGATATGGTATCGATAATATCCGGAG 58.237 42.308 26.11 0.00 40.52 4.63
3343 7040 1.169577 CGGAGGATGAGGACTATCCG 58.830 60.000 0.00 0.00 46.93 4.18
3344 7041 1.551452 GGAGGATGAGGACTATCCGG 58.449 60.000 0.00 0.00 46.93 5.14
3345 7042 1.203075 GGAGGATGAGGACTATCCGGT 60.203 57.143 0.00 0.00 46.93 5.28
3346 7043 2.041350 GGAGGATGAGGACTATCCGGTA 59.959 54.545 0.00 0.00 46.93 4.02
3347 7044 3.309265 GGAGGATGAGGACTATCCGGTAT 60.309 52.174 0.00 0.00 46.93 2.73
3348 7045 4.345854 GAGGATGAGGACTATCCGGTATT 58.654 47.826 0.00 0.00 46.93 1.89
3349 7046 4.753186 AGGATGAGGACTATCCGGTATTT 58.247 43.478 0.00 0.00 46.93 1.40
3350 7047 5.155905 AGGATGAGGACTATCCGGTATTTT 58.844 41.667 0.00 0.00 46.93 1.82
3351 7048 5.607171 AGGATGAGGACTATCCGGTATTTTT 59.393 40.000 0.00 0.00 46.93 1.94
3352 7049 5.701290 GGATGAGGACTATCCGGTATTTTTG 59.299 44.000 0.00 0.00 42.75 2.44
3353 7050 4.448210 TGAGGACTATCCGGTATTTTTGC 58.552 43.478 0.00 0.00 42.75 3.68
3354 7051 4.163458 TGAGGACTATCCGGTATTTTTGCT 59.837 41.667 0.00 0.00 42.75 3.91
3355 7052 5.364446 TGAGGACTATCCGGTATTTTTGCTA 59.636 40.000 0.00 0.00 42.75 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.904800 TCCTTTGAATCCGCATCTACA 57.095 42.857 0.00 0.00 0.00 2.74
88 89 3.743899 GCTTCTTCCTTATCTGCTCCAGG 60.744 52.174 0.00 0.00 31.51 4.45
232 233 4.748892 TGTAATCGGCTCTCTTCAAGAAG 58.251 43.478 3.43 3.43 39.71 2.85
355 356 0.675633 AAAGTGCAGCCAACATGGTC 59.324 50.000 0.00 0.00 40.46 4.02
357 358 0.947180 GCAAAGTGCAGCCAACATGG 60.947 55.000 0.00 0.00 44.26 3.66
390 394 3.059352 ACCTCAAAAGAATCTCCACCG 57.941 47.619 0.00 0.00 0.00 4.94
409 413 8.598075 ACGATGAAATAACGTCTTTACCATTAC 58.402 33.333 0.00 0.00 35.33 1.89
435 443 8.271458 TGATTGTATAATAAGAGGACAAGGCAA 58.729 33.333 0.00 0.00 33.80 4.52
479 957 9.559958 AATCGCAGTGTATCAAATTTCTTAAAG 57.440 29.630 0.00 0.00 0.00 1.85
505 983 0.951558 GCCTTCACGCAGAAAAAGGA 59.048 50.000 4.23 0.00 40.63 3.36
517 995 5.186996 TCACTTTGATTTGAAGCCTTCAC 57.813 39.130 6.65 0.00 39.87 3.18
560 1041 3.359695 TTATTTTGGGACGGAAGGAGG 57.640 47.619 0.00 0.00 0.00 4.30
582 1063 9.880157 AAGTAAAGTTAGTACAAAGTTGAGACA 57.120 29.630 0.00 0.00 0.00 3.41
615 1267 0.323957 GTGTTGTACCCCCTCAGTCC 59.676 60.000 0.00 0.00 0.00 3.85
637 1289 5.018809 TGAATGATCTTTTTCCTTCCCTGG 58.981 41.667 0.00 0.00 0.00 4.45
638 1290 6.210185 ACTTGAATGATCTTTTTCCTTCCCTG 59.790 38.462 0.00 0.00 0.00 4.45
641 1293 7.392953 AGAGACTTGAATGATCTTTTTCCTTCC 59.607 37.037 0.00 0.00 0.00 3.46
653 1305 3.618351 CAGCCCAAGAGACTTGAATGAT 58.382 45.455 12.25 0.00 0.00 2.45
703 1355 8.859517 ATATACGAGCTTCTACTCTTTTGTTC 57.140 34.615 0.00 0.00 34.35 3.18
705 1357 9.088512 CAAATATACGAGCTTCTACTCTTTTGT 57.911 33.333 0.00 0.00 34.35 2.83
712 1364 6.481434 AACCCAAATATACGAGCTTCTACT 57.519 37.500 0.00 0.00 0.00 2.57
790 1442 9.465985 TTTTATACGCTTTTGGTAAAGGAAAAG 57.534 29.630 0.00 0.00 40.90 2.27
812 1464 8.858094 ACCGAACCCAATTGTACTTTTATTTTA 58.142 29.630 4.43 0.00 0.00 1.52
815 1467 6.904463 ACCGAACCCAATTGTACTTTTATT 57.096 33.333 4.43 0.00 0.00 1.40
817 1469 6.073331 CGTAACCGAACCCAATTGTACTTTTA 60.073 38.462 4.43 0.00 35.63 1.52
818 1470 5.277925 CGTAACCGAACCCAATTGTACTTTT 60.278 40.000 4.43 0.00 35.63 2.27
825 1477 1.810959 TCCGTAACCGAACCCAATTG 58.189 50.000 0.00 0.00 35.63 2.32
829 1481 0.455410 CGTATCCGTAACCGAACCCA 59.545 55.000 0.00 0.00 35.63 4.51
830 1482 0.738389 TCGTATCCGTAACCGAACCC 59.262 55.000 0.00 0.00 35.63 4.11
920 1572 5.411669 TGCGCTGATCGATATAAGTAGAGAA 59.588 40.000 9.73 0.00 41.67 2.87
968 1625 4.147449 TGGATGCCTCCACGCTCG 62.147 66.667 6.63 0.00 46.95 5.03
1125 1783 3.003173 CTGCCCTTGAGGTCGGGA 61.003 66.667 0.00 0.00 43.44 5.14
1351 2009 4.112341 CTCCCCGTCGGTGTCGTC 62.112 72.222 11.06 0.00 37.69 4.20
1362 2020 3.798511 GCCTTCTTCCCCTCCCCG 61.799 72.222 0.00 0.00 0.00 5.73
1519 2273 2.050351 CTCGCAGTCGTGGTCGTT 60.050 61.111 0.00 0.00 38.33 3.85
1528 2282 3.260483 CTCGCATGCCTCGCAGTC 61.260 66.667 13.15 0.00 43.65 3.51
1545 2299 1.782285 GCTTTGCGACGATAACGAAC 58.218 50.000 0.00 0.00 42.66 3.95
1578 2332 1.011451 GCTCGTGCTGTGTCCTTCTC 61.011 60.000 1.41 0.00 36.03 2.87
1590 2344 1.807573 GTACAGGCAGAGCTCGTGC 60.808 63.158 22.40 22.40 40.42 5.34
1593 2347 1.153745 GTGGTACAGGCAGAGCTCG 60.154 63.158 8.37 4.60 41.80 5.03
1621 2375 0.747283 GTCTTGATGCTCCAGGCCTG 60.747 60.000 26.87 26.87 40.92 4.85
1641 2395 0.474184 CATCCCCCGATACTTTGGCT 59.526 55.000 0.00 0.00 0.00 4.75
1665 2419 1.274167 TCCGTCCAGTGGTGATTGTAC 59.726 52.381 9.54 0.00 0.00 2.90
1677 2431 1.666888 GCAATTGCTTTGTCCGTCCAG 60.667 52.381 23.21 0.00 37.65 3.86
1695 2449 1.614711 GTCATCCCCTCCAATGGCA 59.385 57.895 0.00 0.00 0.00 4.92
1818 2572 1.460699 GGTCCCAACTCCCTTGCTT 59.539 57.895 0.00 0.00 0.00 3.91
1842 2599 4.113815 TCCCGGCTGCATCTTGGG 62.114 66.667 10.91 10.91 41.43 4.12
1886 2643 0.813210 GATCTGCAGCTGGGTGTAGC 60.813 60.000 17.12 0.00 44.01 3.58
2026 2783 4.767255 GAGGAGGCCCGTGTGCTG 62.767 72.222 0.00 0.00 37.58 4.41
2079 3305 1.134965 CCCTCATCGACCACAAGACTC 60.135 57.143 0.00 0.00 0.00 3.36
2112 3338 0.778815 CAACGTGCAGTCTCTCGAAC 59.221 55.000 0.00 0.00 0.00 3.95
2153 3379 7.222031 CGAGGAAATAAACAATGTCGTCATCTA 59.778 37.037 0.00 0.00 36.79 1.98
2315 3547 8.295288 GCAACTTTGAGATATATTTGGAGATGG 58.705 37.037 0.00 0.00 0.00 3.51
2326 3558 4.721776 ACCCTGGAGCAACTTTGAGATATA 59.278 41.667 0.00 0.00 0.00 0.86
2327 3559 3.525199 ACCCTGGAGCAACTTTGAGATAT 59.475 43.478 0.00 0.00 0.00 1.63
2370 3602 7.538678 GGATGCTTGAAAGTAATAATATTGGCG 59.461 37.037 0.00 0.00 0.00 5.69
2384 3616 4.455877 ACCGAGTAAAAGGATGCTTGAAAG 59.544 41.667 0.00 0.00 0.00 2.62
2405 3637 9.851686 TCAGATATCCATGGCAAATAATATACC 57.148 33.333 6.96 0.00 0.00 2.73
2418 6091 5.308014 TCCGAATGTTTCAGATATCCATGG 58.692 41.667 4.97 4.97 0.00 3.66
2429 6102 2.417107 GCATGGCAATCCGAATGTTTCA 60.417 45.455 0.00 0.00 34.14 2.69
2455 6128 3.181463 ACACGAGGTGGCAAGTTTAGTTA 60.181 43.478 0.00 0.00 37.94 2.24
2456 6129 2.218603 CACGAGGTGGCAAGTTTAGTT 58.781 47.619 0.00 0.00 0.00 2.24
2621 6310 6.808704 GTCCCAAAGAAAAATAGCATCAGAAC 59.191 38.462 0.00 0.00 0.00 3.01
2625 6314 5.007034 TCGTCCCAAAGAAAAATAGCATCA 58.993 37.500 0.00 0.00 0.00 3.07
2644 6333 7.962964 TGATCTGGTAAATTTGGATATCGTC 57.037 36.000 0.00 0.00 0.00 4.20
2645 6334 8.786898 CATTGATCTGGTAAATTTGGATATCGT 58.213 33.333 0.00 0.00 0.00 3.73
2646 6335 7.752239 GCATTGATCTGGTAAATTTGGATATCG 59.248 37.037 0.00 0.00 0.00 2.92
2661 6350 4.159693 CCCAATGGATATGCATTGATCTGG 59.840 45.833 37.24 28.46 40.22 3.86
2686 6375 3.381908 CCCTCATCCCTATACTACGATGC 59.618 52.174 0.00 0.00 33.62 3.91
2770 6459 5.581085 GTCATGAGTAGTATCAACCAACACC 59.419 44.000 0.00 0.00 31.76 4.16
2772 6461 5.338056 GGGTCATGAGTAGTATCAACCAACA 60.338 44.000 0.00 0.00 33.49 3.33
2778 6467 3.905968 TCGGGGTCATGAGTAGTATCAA 58.094 45.455 0.00 0.00 31.76 2.57
2814 6504 2.571653 CTCACCAGGGACTTCCACAATA 59.428 50.000 0.00 0.00 34.60 1.90
2825 6515 3.459828 TCATTTATGACCTCACCAGGGA 58.540 45.455 0.00 0.00 45.53 4.20
2950 6644 7.160726 TCATTAGCAATTATCATGATGGACGA 58.839 34.615 18.72 0.00 0.00 4.20
2970 6664 9.816787 AGTGGGTAATTTCCTTTAACTTCATTA 57.183 29.630 0.73 0.00 0.00 1.90
2971 6665 8.721133 AGTGGGTAATTTCCTTTAACTTCATT 57.279 30.769 0.73 0.00 0.00 2.57
3014 6708 7.769970 GCTGATATACTTAGACGGAGGTAGTAT 59.230 40.741 0.00 0.00 0.00 2.12
3033 6727 5.299279 CCAAAAATACAACGAGGGCTGATAT 59.701 40.000 0.00 0.00 0.00 1.63
3037 6731 2.556622 ACCAAAAATACAACGAGGGCTG 59.443 45.455 0.00 0.00 0.00 4.85
3310 7007 6.072397 CCTCATCCTCCGGATATTATCGATAC 60.072 46.154 3.57 0.00 40.98 2.24
3311 7008 6.004574 CCTCATCCTCCGGATATTATCGATA 58.995 44.000 3.57 0.00 40.98 2.92
3312 7009 4.830046 CCTCATCCTCCGGATATTATCGAT 59.170 45.833 3.57 2.16 40.98 3.59
3313 7010 4.079958 TCCTCATCCTCCGGATATTATCGA 60.080 45.833 3.57 0.00 40.98 3.59
3314 7011 4.036971 GTCCTCATCCTCCGGATATTATCG 59.963 50.000 3.57 0.00 40.98 2.92
3315 7012 5.205056 AGTCCTCATCCTCCGGATATTATC 58.795 45.833 3.57 0.00 40.98 1.75
3316 7013 5.213868 AGTCCTCATCCTCCGGATATTAT 57.786 43.478 3.57 0.00 40.98 1.28
3317 7014 4.676799 AGTCCTCATCCTCCGGATATTA 57.323 45.455 3.57 0.00 40.98 0.98
3318 7015 3.551635 AGTCCTCATCCTCCGGATATT 57.448 47.619 3.57 0.00 40.98 1.28
3319 7016 4.386986 GGATAGTCCTCATCCTCCGGATAT 60.387 50.000 3.57 0.00 39.17 1.63
3320 7017 3.053544 GGATAGTCCTCATCCTCCGGATA 60.054 52.174 3.57 0.00 39.17 2.59
3321 7018 2.291930 GGATAGTCCTCATCCTCCGGAT 60.292 54.545 3.57 0.00 39.17 4.18
3322 7019 1.075698 GGATAGTCCTCATCCTCCGGA 59.924 57.143 2.93 2.93 39.17 5.14
3323 7020 1.551452 GGATAGTCCTCATCCTCCGG 58.449 60.000 0.00 0.00 39.17 5.14
3324 7021 1.169577 CGGATAGTCCTCATCCTCCG 58.830 60.000 0.00 0.00 39.96 4.63
3325 7022 1.203075 ACCGGATAGTCCTCATCCTCC 60.203 57.143 9.46 0.00 39.96 4.30
3326 7023 2.296073 ACCGGATAGTCCTCATCCTC 57.704 55.000 9.46 0.00 39.96 3.71
3327 7024 4.405756 AATACCGGATAGTCCTCATCCT 57.594 45.455 9.46 0.00 39.96 3.24
3328 7025 5.485209 AAAATACCGGATAGTCCTCATCC 57.515 43.478 9.46 0.00 38.92 3.51
3329 7026 5.179555 GCAAAAATACCGGATAGTCCTCATC 59.820 44.000 9.46 0.00 33.30 2.92
3330 7027 5.063880 GCAAAAATACCGGATAGTCCTCAT 58.936 41.667 9.46 0.00 33.30 2.90
3331 7028 4.163458 AGCAAAAATACCGGATAGTCCTCA 59.837 41.667 9.46 0.00 33.30 3.86
3332 7029 4.704965 AGCAAAAATACCGGATAGTCCTC 58.295 43.478 9.46 0.00 33.30 3.71
3333 7030 4.772886 AGCAAAAATACCGGATAGTCCT 57.227 40.909 9.46 0.00 33.30 3.85


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

AutoCloner maintained by Alex Coulton.