Multiple sequence alignment - TraesCS7A01G239500

Loading Multiple Alignment...

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 TraesCS7A01G239500 chr7A 100.000 2600 0 0 1 2600 214300750 214303349 0.000000e+00 4802
1 TraesCS7A01G239500 chr7A 80.000 310 54 7 1180 1485 670536908 670537213 3.370000e-54 222
2 TraesCS7A01G239500 chr7A 88.043 184 15 4 2415 2598 494786824 494787000 7.290000e-51 211
3 TraesCS7A01G239500 chr7B 90.924 1796 81 47 622 2349 165098210 165099991 0.000000e+00 2338
4 TraesCS7A01G239500 chr7B 85.048 622 89 2 4 624 639365904 639365286 4.720000e-177 630
5 TraesCS7A01G239500 chr7D 93.917 1463 44 21 622 2058 200764656 200766099 0.000000e+00 2167
6 TraesCS7A01G239500 chr7D 86.538 624 80 2 2 624 62679926 62679306 0.000000e+00 684
7 TraesCS7A01G239500 chr7D 84.901 404 26 14 2043 2422 200766125 200766517 2.440000e-100 375
8 TraesCS7A01G239500 chr7D 81.613 310 49 7 1180 1485 578465376 578465681 1.540000e-62 250
9 TraesCS7A01G239500 chr6D 88.978 626 63 4 1 624 472019688 472020309 0.000000e+00 769
10 TraesCS7A01G239500 chr6D 88.387 620 66 4 1 618 471969508 471970123 0.000000e+00 741
11 TraesCS7A01G239500 chr6D 88.764 178 11 5 2410 2587 431160836 431160668 2.620000e-50 209
12 TraesCS7A01G239500 chr6D 87.568 185 15 4 2417 2600 93646390 93646213 9.430000e-50 207
13 TraesCS7A01G239500 chr1A 86.304 606 79 2 1 605 550450452 550451054 0.000000e+00 656
14 TraesCS7A01G239500 chr5D 89.313 524 36 13 1008 1530 369427841 369428345 7.850000e-180 640
15 TraesCS7A01G239500 chr3A 85.233 623 87 3 2 623 435812529 435811911 1.010000e-178 636
16 TraesCS7A01G239500 chr2B 85.072 623 87 4 4 624 506169984 506170602 4.720000e-177 630
17 TraesCS7A01G239500 chr2B 84.270 623 92 4 4 624 43639987 43639369 1.030000e-168 603
18 TraesCS7A01G239500 chr5A 88.931 524 38 13 1008 1530 471946517 471947021 1.700000e-176 628
19 TraesCS7A01G239500 chr5A 90.286 175 12 1 2416 2590 558675492 558675661 9.360000e-55 224
20 TraesCS7A01G239500 chr5A 90.116 172 11 2 2421 2591 320214405 320214239 4.360000e-53 219
21 TraesCS7A01G239500 chr5B 88.550 524 40 13 1008 1530 438557155 438557659 3.680000e-173 617
22 TraesCS7A01G239500 chr5B 88.525 183 16 4 2416 2594 136413791 136413610 1.570000e-52 217
23 TraesCS7A01G239500 chr4B 85.284 598 79 6 4 599 338432503 338433093 2.210000e-170 608
24 TraesCS7A01G239500 chr4A 82.991 341 43 12 1181 1509 83572035 83571698 7.040000e-76 294
25 TraesCS7A01G239500 chr2A 90.173 173 8 4 2416 2587 696850881 696850717 1.570000e-52 217
26 TraesCS7A01G239500 chr6B 88.764 178 11 5 2410 2587 650598708 650598540 2.620000e-50 209
27 TraesCS7A01G239500 chr4D 88.333 180 12 4 2409 2587 26204839 26205010 9.430000e-50 207
28 TraesCS7A01G239500 chr3D 80.319 188 29 7 1181 1364 55156659 55156842 4.510000e-28 135


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 TraesCS7A01G239500 chr7A 214300750 214303349 2599 False 4802 4802 100.000 1 2600 1 chr7A.!!$F1 2599
1 TraesCS7A01G239500 chr7B 165098210 165099991 1781 False 2338 2338 90.924 622 2349 1 chr7B.!!$F1 1727
2 TraesCS7A01G239500 chr7B 639365286 639365904 618 True 630 630 85.048 4 624 1 chr7B.!!$R1 620
3 TraesCS7A01G239500 chr7D 200764656 200766517 1861 False 1271 2167 89.409 622 2422 2 chr7D.!!$F2 1800
4 TraesCS7A01G239500 chr7D 62679306 62679926 620 True 684 684 86.538 2 624 1 chr7D.!!$R1 622
5 TraesCS7A01G239500 chr6D 472019688 472020309 621 False 769 769 88.978 1 624 1 chr6D.!!$F2 623
6 TraesCS7A01G239500 chr6D 471969508 471970123 615 False 741 741 88.387 1 618 1 chr6D.!!$F1 617
7 TraesCS7A01G239500 chr1A 550450452 550451054 602 False 656 656 86.304 1 605 1 chr1A.!!$F1 604
8 TraesCS7A01G239500 chr5D 369427841 369428345 504 False 640 640 89.313 1008 1530 1 chr5D.!!$F1 522
9 TraesCS7A01G239500 chr3A 435811911 435812529 618 True 636 636 85.233 2 623 1 chr3A.!!$R1 621
10 TraesCS7A01G239500 chr2B 506169984 506170602 618 False 630 630 85.072 4 624 1 chr2B.!!$F1 620
11 TraesCS7A01G239500 chr2B 43639369 43639987 618 True 603 603 84.270 4 624 1 chr2B.!!$R1 620
12 TraesCS7A01G239500 chr5A 471946517 471947021 504 False 628 628 88.931 1008 1530 1 chr5A.!!$F1 522
13 TraesCS7A01G239500 chr5B 438557155 438557659 504 False 617 617 88.550 1008 1530 1 chr5B.!!$F1 522
14 TraesCS7A01G239500 chr4B 338432503 338433093 590 False 608 608 85.284 4 599 1 chr4B.!!$F1 595

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
672 675 0.968901 ACCCGAACGCATCTAGGTGA 60.969 55.0 7.33 0.0 32.71 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 1796 2.427453 GCCTCGATCAGAAGAACCTACA 59.573 50.0 0.0 0.0 0.0 2.74 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
64 65 3.256383 GTGGCCATAAAAACCCGTAAACT 59.744 43.478 9.72 0.00 0.00 2.66
75 76 4.490899 ACCCGTAAACTGCCAATATACA 57.509 40.909 0.00 0.00 0.00 2.29
76 77 5.043737 ACCCGTAAACTGCCAATATACAT 57.956 39.130 0.00 0.00 0.00 2.29
77 78 5.442391 ACCCGTAAACTGCCAATATACATT 58.558 37.500 0.00 0.00 0.00 2.71
175 176 3.525800 AAAACAAGACTAGGCCACCAT 57.474 42.857 5.01 0.00 0.00 3.55
205 206 5.163374 CCATCACTCTCCACTACAATCATCA 60.163 44.000 0.00 0.00 0.00 3.07
207 208 5.724328 TCACTCTCCACTACAATCATCAAC 58.276 41.667 0.00 0.00 0.00 3.18
261 262 6.183360 CGGCCTTACATTTATTCAAGTGTGAT 60.183 38.462 0.00 0.00 35.58 3.06
279 280 8.097078 AGTGTGATTCAGAGAGAAAAATCAAG 57.903 34.615 0.00 0.00 39.20 3.02
283 284 8.782144 GTGATTCAGAGAGAAAAATCAAGTCTT 58.218 33.333 0.00 0.00 39.20 3.01
285 286 9.218440 GATTCAGAGAGAAAAATCAAGTCTTCT 57.782 33.333 0.00 0.00 40.22 2.85
289 290 8.834465 CAGAGAGAAAAATCAAGTCTTCTTTGA 58.166 33.333 0.00 0.00 0.00 2.69
299 300 2.838202 AGTCTTCTTTGATCCGCCCTTA 59.162 45.455 0.00 0.00 0.00 2.69
312 313 1.550976 CGCCCTTAGAGTTCCAAGAGT 59.449 52.381 0.00 0.00 0.00 3.24
378 379 1.227383 GATCCTCATTTGGCCCGGT 59.773 57.895 0.00 0.00 0.00 5.28
464 465 5.091261 TGTAAGCATCTTCCTCCTCTTTC 57.909 43.478 0.00 0.00 0.00 2.62
467 468 2.430332 AGCATCTTCCTCCTCTTTCTCG 59.570 50.000 0.00 0.00 0.00 4.04
565 566 5.426689 ACACTCATCTCACCATACAACAT 57.573 39.130 0.00 0.00 0.00 2.71
575 577 6.376299 TCTCACCATACAACATACGTTCTAGT 59.624 38.462 0.00 0.00 31.13 2.57
577 579 7.380536 TCACCATACAACATACGTTCTAGTTT 58.619 34.615 0.00 0.00 31.13 2.66
601 603 7.976135 TTCCATCTCTCTCTCAAAAGAAAAG 57.024 36.000 0.00 0.00 0.00 2.27
660 663 6.505044 AATTACCAACATTTAGACCCGAAC 57.495 37.500 0.00 0.00 0.00 3.95
662 665 1.129811 CCAACATTTAGACCCGAACGC 59.870 52.381 0.00 0.00 0.00 4.84
672 675 0.968901 ACCCGAACGCATCTAGGTGA 60.969 55.000 7.33 0.00 32.71 4.02
708 711 2.010145 AGTCAGCGTTAATGCGATGT 57.990 45.000 13.84 4.38 46.62 3.06
714 717 2.482336 AGCGTTAATGCGATGTTTGACA 59.518 40.909 13.84 0.00 40.67 3.58
729 732 7.065803 CGATGTTTGACACCAGATATTTAACCT 59.934 37.037 0.00 0.00 0.00 3.50
732 735 7.504238 TGTTTGACACCAGATATTTAACCTTGT 59.496 33.333 0.00 0.00 0.00 3.16
736 739 7.822334 TGACACCAGATATTTAACCTTGTACTG 59.178 37.037 0.00 0.00 0.00 2.74
739 756 7.010183 CACCAGATATTTAACCTTGTACTGACG 59.990 40.741 0.00 0.00 0.00 4.35
762 779 1.615424 GGCCCCTACCACTCCTTGA 60.615 63.158 0.00 0.00 0.00 3.02
772 789 6.350445 CCCTACCACTCCTTGAAAATGAAATG 60.350 42.308 0.00 0.00 0.00 2.32
774 791 4.248058 CCACTCCTTGAAAATGAAATGGC 58.752 43.478 0.00 0.00 0.00 4.40
775 792 3.922240 CACTCCTTGAAAATGAAATGGCG 59.078 43.478 0.00 0.00 0.00 5.69
776 793 3.826157 ACTCCTTGAAAATGAAATGGCGA 59.174 39.130 0.00 0.00 0.00 5.54
777 794 4.082571 ACTCCTTGAAAATGAAATGGCGAG 60.083 41.667 0.00 0.00 0.00 5.03
778 795 2.925563 CCTTGAAAATGAAATGGCGAGC 59.074 45.455 0.00 0.00 0.00 5.03
779 796 2.652941 TGAAAATGAAATGGCGAGCC 57.347 45.000 7.26 7.26 0.00 4.70
810 827 3.261216 CACGCAGACACGCACACA 61.261 61.111 0.00 0.00 36.19 3.72
815 832 3.261951 AGACACGCACACACACGC 61.262 61.111 0.00 0.00 0.00 5.34
816 833 3.559344 GACACGCACACACACGCA 61.559 61.111 0.00 0.00 0.00 5.24
818 835 4.918060 CACGCACACACACGCACG 62.918 66.667 0.00 0.00 0.00 5.34
869 886 6.318900 CCGGAAAGCAAACTCTAATAAATCCT 59.681 38.462 0.00 0.00 0.00 3.24
887 904 3.849951 CCACCCCCGGATCGACAG 61.850 72.222 0.73 0.00 0.00 3.51
888 905 4.530857 CACCCCCGGATCGACAGC 62.531 72.222 0.73 0.00 0.00 4.40
891 908 3.917760 CCCCGGATCGACAGCCTC 61.918 72.222 0.73 0.00 0.00 4.70
971 999 1.308746 TCTCTTCCCCCAATCCCCC 60.309 63.158 0.00 0.00 0.00 5.40
972 1000 2.694616 TCTTCCCCCAATCCCCCG 60.695 66.667 0.00 0.00 0.00 5.73
973 1001 4.522975 CTTCCCCCAATCCCCCGC 62.523 72.222 0.00 0.00 0.00 6.13
1006 1034 1.216990 AACCCTAGCTGGAATGGAGG 58.783 55.000 0.00 0.00 38.35 4.30
1623 1657 1.927174 CTGCAGTATGTTACAGCGGAC 59.073 52.381 5.25 0.00 46.69 4.79
1748 1784 8.523658 CCTCTATGTTATAAGTGATTCGATCCA 58.476 37.037 0.00 0.00 0.00 3.41
1760 1796 3.887621 TTCGATCCAAGAAGAATCGGT 57.112 42.857 4.39 0.00 35.68 4.69
1761 1797 3.165058 TCGATCCAAGAAGAATCGGTG 57.835 47.619 4.39 0.00 35.68 4.94
1884 1920 6.365789 CGTAATTTGCAGTGAAATGGTTTGAT 59.634 34.615 0.00 0.00 0.00 2.57
1887 1923 4.933505 TGCAGTGAAATGGTTTGATTGA 57.066 36.364 0.00 0.00 0.00 2.57
1985 2021 3.373130 GGGCCAAGTGTTCGTATAACTTC 59.627 47.826 4.39 0.00 31.88 3.01
2066 2143 5.882557 AGATACATGCTTCTTTGGTAAGTGG 59.117 40.000 0.00 0.00 32.98 4.00
2088 2165 0.322648 ACTACCAAGGGCGTAACACC 59.677 55.000 0.00 0.00 0.00 4.16
2094 2171 2.736579 AAGGGCGTAACACCGTTCCC 62.737 60.000 0.00 0.00 29.49 3.97
2174 2255 6.017440 CGTAGGGACTGAAATTGAAGTTTTGA 60.017 38.462 0.00 0.00 41.52 2.69
2210 2292 7.550551 TGATTCTTGTTGTTATTTGCAAAACCA 59.449 29.630 17.19 10.07 0.00 3.67
2269 2351 6.544928 AACTCCTGACATTTTCTTTGGTTT 57.455 33.333 0.00 0.00 0.00 3.27
2273 2355 7.123547 ACTCCTGACATTTTCTTTGGTTTAACA 59.876 33.333 0.00 0.00 0.00 2.41
2304 2386 7.929941 ACATTCCTTTATTCTCTTTGAGGTC 57.070 36.000 0.00 0.00 0.00 3.85
2308 2391 7.808279 TCCTTTATTCTCTTTGAGGTCCTAA 57.192 36.000 0.00 0.00 0.00 2.69
2422 2528 7.751047 TTGCGTGTTCATTCTCTTATACTAC 57.249 36.000 0.00 0.00 0.00 2.73
2423 2529 7.096884 TGCGTGTTCATTCTCTTATACTACT 57.903 36.000 0.00 0.00 0.00 2.57
2424 2530 7.194278 TGCGTGTTCATTCTCTTATACTACTC 58.806 38.462 0.00 0.00 0.00 2.59
2425 2531 6.637658 GCGTGTTCATTCTCTTATACTACTCC 59.362 42.308 0.00 0.00 0.00 3.85
2426 2532 7.468906 GCGTGTTCATTCTCTTATACTACTCCT 60.469 40.741 0.00 0.00 0.00 3.69
2427 2533 8.407064 CGTGTTCATTCTCTTATACTACTCCTT 58.593 37.037 0.00 0.00 0.00 3.36
2430 2536 9.453325 GTTCATTCTCTTATACTACTCCTTTCG 57.547 37.037 0.00 0.00 0.00 3.46
2431 2537 8.749026 TCATTCTCTTATACTACTCCTTTCGT 57.251 34.615 0.00 0.00 0.00 3.85
2432 2538 9.186837 TCATTCTCTTATACTACTCCTTTCGTT 57.813 33.333 0.00 0.00 0.00 3.85
2433 2539 9.804758 CATTCTCTTATACTACTCCTTTCGTTT 57.195 33.333 0.00 0.00 0.00 3.60
2435 2541 8.804912 TCTCTTATACTACTCCTTTCGTTTCT 57.195 34.615 0.00 0.00 0.00 2.52
2436 2542 9.896645 TCTCTTATACTACTCCTTTCGTTTCTA 57.103 33.333 0.00 0.00 0.00 2.10
2478 2584 8.814235 AGAGTTTTCAATACGAATTACATACGG 58.186 33.333 0.00 0.00 32.32 4.02
2479 2585 8.706492 AGTTTTCAATACGAATTACATACGGA 57.294 30.769 0.00 0.00 32.32 4.69
2480 2586 9.321562 AGTTTTCAATACGAATTACATACGGAT 57.678 29.630 0.00 0.00 32.32 4.18
2481 2587 9.365311 GTTTTCAATACGAATTACATACGGATG 57.635 33.333 5.94 5.94 34.64 3.51
2482 2588 8.651391 TTTCAATACGAATTACATACGGATGT 57.349 30.769 19.12 19.12 40.52 3.06
2483 2589 9.747293 TTTCAATACGAATTACATACGGATGTA 57.253 29.630 16.71 16.71 45.01 2.29
2484 2590 9.917129 TTCAATACGAATTACATACGGATGTAT 57.083 29.630 20.99 7.47 45.77 2.29
2489 2595 8.332996 ACGAATTACATACGGATGTATAGAGT 57.667 34.615 20.99 15.28 45.77 3.24
2490 2596 9.440773 ACGAATTACATACGGATGTATAGAGTA 57.559 33.333 20.99 5.70 45.77 2.59
2520 2626 9.725019 ACATATTTTGAAGTGTAGATTCACTCA 57.275 29.630 0.00 0.00 46.25 3.41
2525 2631 9.734620 TTTTGAAGTGTAGATTCACTCATTTTG 57.265 29.630 0.00 0.00 46.25 2.44
2526 2632 6.902341 TGAAGTGTAGATTCACTCATTTTGC 58.098 36.000 0.00 0.00 46.25 3.68
2527 2633 6.712095 TGAAGTGTAGATTCACTCATTTTGCT 59.288 34.615 0.00 0.00 46.25 3.91
2528 2634 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2529 2635 6.471146 AGTGTAGATTCACTCATTTTGCTCT 58.529 36.000 0.00 0.00 44.07 4.09
2530 2636 6.370994 AGTGTAGATTCACTCATTTTGCTCTG 59.629 38.462 0.00 0.00 44.07 3.35
2531 2637 6.148480 GTGTAGATTCACTCATTTTGCTCTGT 59.852 38.462 0.00 0.00 35.68 3.41
2532 2638 7.331934 GTGTAGATTCACTCATTTTGCTCTGTA 59.668 37.037 0.00 0.00 35.68 2.74
2533 2639 8.043113 TGTAGATTCACTCATTTTGCTCTGTAT 58.957 33.333 0.00 0.00 0.00 2.29
2534 2640 7.317842 AGATTCACTCATTTTGCTCTGTATG 57.682 36.000 0.00 0.00 0.00 2.39
2535 2641 6.883217 AGATTCACTCATTTTGCTCTGTATGT 59.117 34.615 0.00 0.00 0.00 2.29
2536 2642 8.043113 AGATTCACTCATTTTGCTCTGTATGTA 58.957 33.333 0.00 0.00 0.00 2.29
2537 2643 7.601073 TTCACTCATTTTGCTCTGTATGTAG 57.399 36.000 0.00 0.00 0.00 2.74
2538 2644 6.701340 TCACTCATTTTGCTCTGTATGTAGT 58.299 36.000 0.00 0.00 0.00 2.73
2539 2645 6.813649 TCACTCATTTTGCTCTGTATGTAGTC 59.186 38.462 0.00 0.00 0.00 2.59
2540 2646 6.815641 CACTCATTTTGCTCTGTATGTAGTCT 59.184 38.462 0.00 0.00 0.00 3.24
2541 2647 7.976175 CACTCATTTTGCTCTGTATGTAGTCTA 59.024 37.037 0.00 0.00 0.00 2.59
2542 2648 8.700051 ACTCATTTTGCTCTGTATGTAGTCTAT 58.300 33.333 0.00 0.00 0.00 1.98
2547 2653 9.764363 TTTTGCTCTGTATGTAGTCTATATTGG 57.236 33.333 0.00 0.00 0.00 3.16
2548 2654 8.706322 TTGCTCTGTATGTAGTCTATATTGGA 57.294 34.615 0.00 0.00 0.00 3.53
2549 2655 8.706322 TGCTCTGTATGTAGTCTATATTGGAA 57.294 34.615 0.00 0.00 0.00 3.53
2550 2656 9.314133 TGCTCTGTATGTAGTCTATATTGGAAT 57.686 33.333 0.00 0.00 0.00 3.01
2551 2657 9.796120 GCTCTGTATGTAGTCTATATTGGAATC 57.204 37.037 0.00 0.00 0.00 2.52
2582 2688 9.868160 AAAAGACTTATATTTAGGAATGGAGGG 57.132 33.333 0.00 0.00 0.00 4.30
2583 2689 8.814448 AAGACTTATATTTAGGAATGGAGGGA 57.186 34.615 0.00 0.00 0.00 4.20
2584 2690 8.442660 AGACTTATATTTAGGAATGGAGGGAG 57.557 38.462 0.00 0.00 0.00 4.30
2585 2691 8.019652 AGACTTATATTTAGGAATGGAGGGAGT 58.980 37.037 0.00 0.00 0.00 3.85
2586 2692 9.322769 GACTTATATTTAGGAATGGAGGGAGTA 57.677 37.037 0.00 0.00 0.00 2.59
2587 2693 9.860393 ACTTATATTTAGGAATGGAGGGAGTAT 57.140 33.333 0.00 0.00 0.00 2.12
2592 2698 7.947782 TTTAGGAATGGAGGGAGTATTATGT 57.052 36.000 0.00 0.00 0.00 2.29
2593 2699 7.947782 TTAGGAATGGAGGGAGTATTATGTT 57.052 36.000 0.00 0.00 0.00 2.71
2594 2700 6.192970 AGGAATGGAGGGAGTATTATGTTG 57.807 41.667 0.00 0.00 0.00 3.33
2595 2701 5.073691 AGGAATGGAGGGAGTATTATGTTGG 59.926 44.000 0.00 0.00 0.00 3.77
2596 2702 5.316987 GAATGGAGGGAGTATTATGTTGGG 58.683 45.833 0.00 0.00 0.00 4.12
2597 2703 2.441750 TGGAGGGAGTATTATGTTGGGC 59.558 50.000 0.00 0.00 0.00 5.36
2598 2704 2.711547 GGAGGGAGTATTATGTTGGGCT 59.288 50.000 0.00 0.00 0.00 5.19
2599 2705 3.244596 GGAGGGAGTATTATGTTGGGCTC 60.245 52.174 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.296715 CCACCCGGTTTGGAGAGAG 59.703 63.158 13.13 0.0 42.00 3.20
30 31 3.961414 GGCCACCCGGTTTGGAGA 61.961 66.667 21.00 0.0 42.00 3.71
175 176 0.970937 GTGGAGAGTGATGGTCGGGA 60.971 60.000 0.00 0.0 0.00 5.14
205 206 5.235616 TGCGTCGTTTTCTATCTTTTGAGTT 59.764 36.000 0.00 0.0 0.00 3.01
207 208 5.264060 TGCGTCGTTTTCTATCTTTTGAG 57.736 39.130 0.00 0.0 0.00 3.02
218 219 3.569957 GATGAGCTGCGTCGTTTTC 57.430 52.632 0.00 0.0 0.00 2.29
261 262 8.970859 AAGAAGACTTGATTTTTCTCTCTGAA 57.029 30.769 0.00 0.0 34.80 3.02
279 280 2.115343 AAGGGCGGATCAAAGAAGAC 57.885 50.000 0.00 0.0 0.00 3.01
283 284 2.467880 ACTCTAAGGGCGGATCAAAGA 58.532 47.619 0.00 0.0 0.00 2.52
285 286 2.093128 GGAACTCTAAGGGCGGATCAAA 60.093 50.000 0.00 0.0 0.00 2.69
289 290 1.486726 CTTGGAACTCTAAGGGCGGAT 59.513 52.381 0.00 0.0 31.74 4.18
299 300 3.718815 GTTCGTGAACTCTTGGAACTCT 58.281 45.455 5.51 0.0 38.25 3.24
323 324 1.760875 GGTATGCTCTCCCCCACGA 60.761 63.158 0.00 0.0 0.00 4.35
402 403 1.543208 GGTTGGAGATGATGGCGCATA 60.543 52.381 10.83 0.0 0.00 3.14
449 450 3.129638 CGAACGAGAAAGAGGAGGAAGAT 59.870 47.826 0.00 0.0 0.00 2.40
452 453 1.067776 GCGAACGAGAAAGAGGAGGAA 60.068 52.381 0.00 0.0 0.00 3.36
464 465 5.051907 GGTTATTACACATGTAGCGAACGAG 60.052 44.000 0.00 0.0 0.00 4.18
467 468 4.271776 GGGGTTATTACACATGTAGCGAAC 59.728 45.833 0.00 0.0 0.00 3.95
565 566 6.885376 AGAGAGAGATGGAAAACTAGAACGTA 59.115 38.462 0.00 0.0 0.00 3.57
575 577 8.752005 TTTTCTTTTGAGAGAGAGATGGAAAA 57.248 30.769 0.00 0.0 0.00 2.29
577 579 7.512992 ACTTTTCTTTTGAGAGAGAGATGGAA 58.487 34.615 0.00 0.0 0.00 3.53
662 665 0.593518 CAGCGAGCGTCACCTAGATG 60.594 60.000 0.00 0.0 36.29 2.90
672 675 0.811915 ACTAAGATGACAGCGAGCGT 59.188 50.000 0.00 0.0 0.00 5.07
708 711 9.005777 GTACAAGGTTAAATATCTGGTGTCAAA 57.994 33.333 0.00 0.0 0.00 2.69
714 717 7.039882 CGTCAGTACAAGGTTAAATATCTGGT 58.960 38.462 0.00 0.0 0.00 4.00
729 732 2.356553 GCCGTGGCGTCAGTACAA 60.357 61.111 0.00 0.0 0.00 2.41
754 771 3.826157 TCGCCATTTCATTTTCAAGGAGT 59.174 39.130 0.00 0.0 0.00 3.85
762 779 0.887933 ACGGCTCGCCATTTCATTTT 59.112 45.000 8.87 0.0 35.37 1.82
818 835 2.409152 CTCGAGATTAAGACGAGGCC 57.591 55.000 6.58 0.0 46.10 5.19
819 836 5.759963 TTAATCTCGAGATTAAGACGAGGC 58.240 41.667 38.60 0.0 46.28 4.70
869 886 4.385740 TGTCGATCCGGGGGTGGA 62.386 66.667 0.00 0.0 43.58 4.02
971 999 3.075005 TTTCGGGGAGGAGGAGCG 61.075 66.667 0.00 0.0 0.00 5.03
972 1000 2.585153 GTTTCGGGGAGGAGGAGC 59.415 66.667 0.00 0.0 0.00 4.70
973 1001 2.368011 GGGTTTCGGGGAGGAGGAG 61.368 68.421 0.00 0.0 0.00 3.69
1006 1034 1.682344 GAGGGGTGGTGGATTTGGC 60.682 63.158 0.00 0.0 0.00 4.52
1623 1657 6.965500 CAGCACAATCTTAGATGCAACTTAAG 59.035 38.462 0.30 0.0 40.63 1.85
1748 1784 5.485209 AAGAACCTACACCGATTCTTCTT 57.515 39.130 0.00 0.0 36.86 2.52
1758 1794 3.181485 CCTCGATCAGAAGAACCTACACC 60.181 52.174 0.00 0.0 0.00 4.16
1760 1796 2.427453 GCCTCGATCAGAAGAACCTACA 59.573 50.000 0.00 0.0 0.00 2.74
1761 1797 2.427453 TGCCTCGATCAGAAGAACCTAC 59.573 50.000 0.00 0.0 0.00 3.18
1894 1930 7.208064 ACAACAGGGTAATAGTTACATGGAT 57.792 36.000 0.00 0.0 37.88 3.41
1908 1944 7.558444 CCTAAATGCCTAAAATACAACAGGGTA 59.442 37.037 0.00 0.0 0.00 3.69
1913 1949 7.093992 GCAACCTAAATGCCTAAAATACAACA 58.906 34.615 0.00 0.0 37.85 3.33
1985 2021 8.810427 CCAATTAAACATGCACATAAAAGCTAG 58.190 33.333 0.00 0.0 0.00 3.42
2033 2069 9.064706 CCAAAGAAGCATGTATCTGAATTATCT 57.935 33.333 3.58 0.0 0.00 1.98
2066 2143 3.451526 GTGTTACGCCCTTGGTAGTATC 58.548 50.000 0.00 0.0 0.00 2.24
2088 2165 8.889717 ACTAAATTTTACATCATACAGGGAACG 58.110 33.333 0.00 0.0 0.00 3.95
2193 2275 7.097192 TGTGTTACTGGTTTTGCAAATAACAA 58.903 30.769 25.53 17.3 34.01 2.83
2210 2292 4.975147 TCCCCATTCCTATGATGTGTTACT 59.025 41.667 0.00 0.0 33.37 2.24
2282 2364 7.277405 AGGACCTCAAAGAGAATAAAGGAAT 57.723 36.000 0.00 0.0 0.00 3.01
2285 2367 9.114952 GAATTAGGACCTCAAAGAGAATAAAGG 57.885 37.037 0.00 0.0 0.00 3.11
2304 2386 3.445096 CCAAAGTGCCTTGAGGAATTAGG 59.555 47.826 0.06 0.0 37.39 2.69
2308 2391 2.683211 ACCAAAGTGCCTTGAGGAAT 57.317 45.000 0.06 0.0 37.39 3.01
2316 2399 4.112634 TCCATCTTTAACCAAAGTGCCT 57.887 40.909 0.00 0.0 41.66 4.75
2376 2482 7.915397 CGCAAAGCTATTTGGTATCTAAAACAT 59.085 33.333 0.52 0.0 44.97 2.71
2384 2490 4.616181 ACACGCAAAGCTATTTGGTATC 57.384 40.909 0.52 0.0 44.97 2.24
2393 2499 3.664107 AGAGAATGAACACGCAAAGCTA 58.336 40.909 0.00 0.0 0.00 3.32
2452 2558 8.814235 CCGTATGTAATTCGTATTGAAAACTCT 58.186 33.333 0.00 0.0 40.71 3.24
2453 2559 8.810427 TCCGTATGTAATTCGTATTGAAAACTC 58.190 33.333 0.00 0.0 40.71 3.01
2454 2560 8.706492 TCCGTATGTAATTCGTATTGAAAACT 57.294 30.769 0.00 0.0 40.71 2.66
2455 2561 9.365311 CATCCGTATGTAATTCGTATTGAAAAC 57.635 33.333 0.00 0.0 40.71 2.43
2456 2562 9.100554 ACATCCGTATGTAATTCGTATTGAAAA 57.899 29.630 0.00 0.0 44.66 2.29
2457 2563 8.651391 ACATCCGTATGTAATTCGTATTGAAA 57.349 30.769 0.00 0.0 44.66 2.69
2506 2612 6.148480 ACAGAGCAAAATGAGTGAATCTACAC 59.852 38.462 0.00 0.0 40.60 2.90
2507 2613 6.233434 ACAGAGCAAAATGAGTGAATCTACA 58.767 36.000 0.00 0.0 0.00 2.74
2508 2614 6.734104 ACAGAGCAAAATGAGTGAATCTAC 57.266 37.500 0.00 0.0 0.00 2.59
2509 2615 8.043113 ACATACAGAGCAAAATGAGTGAATCTA 58.957 33.333 0.00 0.0 0.00 1.98
2510 2616 6.883217 ACATACAGAGCAAAATGAGTGAATCT 59.117 34.615 0.00 0.0 0.00 2.40
2511 2617 7.081526 ACATACAGAGCAAAATGAGTGAATC 57.918 36.000 0.00 0.0 0.00 2.52
2512 2618 7.826252 ACTACATACAGAGCAAAATGAGTGAAT 59.174 33.333 0.00 0.0 0.00 2.57
2513 2619 7.161404 ACTACATACAGAGCAAAATGAGTGAA 58.839 34.615 0.00 0.0 0.00 3.18
2514 2620 6.701340 ACTACATACAGAGCAAAATGAGTGA 58.299 36.000 0.00 0.0 0.00 3.41
2515 2621 6.815641 AGACTACATACAGAGCAAAATGAGTG 59.184 38.462 0.00 0.0 0.00 3.51
2516 2622 6.940739 AGACTACATACAGAGCAAAATGAGT 58.059 36.000 0.00 0.0 0.00 3.41
2521 2627 9.764363 CCAATATAGACTACATACAGAGCAAAA 57.236 33.333 0.00 0.0 0.00 2.44
2522 2628 9.143155 TCCAATATAGACTACATACAGAGCAAA 57.857 33.333 0.00 0.0 0.00 3.68
2523 2629 8.706322 TCCAATATAGACTACATACAGAGCAA 57.294 34.615 0.00 0.0 0.00 3.91
2524 2630 8.706322 TTCCAATATAGACTACATACAGAGCA 57.294 34.615 0.00 0.0 0.00 4.26
2525 2631 9.796120 GATTCCAATATAGACTACATACAGAGC 57.204 37.037 0.00 0.0 0.00 4.09
2556 2662 9.868160 CCCTCCATTCCTAAATATAAGTCTTTT 57.132 33.333 0.00 0.0 0.00 2.27
2557 2663 9.237706 TCCCTCCATTCCTAAATATAAGTCTTT 57.762 33.333 0.00 0.0 0.00 2.52
2558 2664 8.814448 TCCCTCCATTCCTAAATATAAGTCTT 57.186 34.615 0.00 0.0 0.00 3.01
2559 2665 8.019652 ACTCCCTCCATTCCTAAATATAAGTCT 58.980 37.037 0.00 0.0 0.00 3.24
2560 2666 8.208575 ACTCCCTCCATTCCTAAATATAAGTC 57.791 38.462 0.00 0.0 0.00 3.01
2561 2667 9.860393 ATACTCCCTCCATTCCTAAATATAAGT 57.140 33.333 0.00 0.0 0.00 2.24
2566 2672 9.629649 ACATAATACTCCCTCCATTCCTAAATA 57.370 33.333 0.00 0.0 0.00 1.40
2567 2673 8.525729 ACATAATACTCCCTCCATTCCTAAAT 57.474 34.615 0.00 0.0 0.00 1.40
2568 2674 7.947782 ACATAATACTCCCTCCATTCCTAAA 57.052 36.000 0.00 0.0 0.00 1.85
2569 2675 7.202186 CCAACATAATACTCCCTCCATTCCTAA 60.202 40.741 0.00 0.0 0.00 2.69
2570 2676 6.272324 CCAACATAATACTCCCTCCATTCCTA 59.728 42.308 0.00 0.0 0.00 2.94
2571 2677 5.073691 CCAACATAATACTCCCTCCATTCCT 59.926 44.000 0.00 0.0 0.00 3.36
2572 2678 5.316987 CCAACATAATACTCCCTCCATTCC 58.683 45.833 0.00 0.0 0.00 3.01
2573 2679 5.316987 CCCAACATAATACTCCCTCCATTC 58.683 45.833 0.00 0.0 0.00 2.67
2574 2680 4.447762 GCCCAACATAATACTCCCTCCATT 60.448 45.833 0.00 0.0 0.00 3.16
2575 2681 3.074538 GCCCAACATAATACTCCCTCCAT 59.925 47.826 0.00 0.0 0.00 3.41
2576 2682 2.441750 GCCCAACATAATACTCCCTCCA 59.558 50.000 0.00 0.0 0.00 3.86
2577 2683 2.711547 AGCCCAACATAATACTCCCTCC 59.288 50.000 0.00 0.0 0.00 4.30
2578 2684 4.009370 GAGCCCAACATAATACTCCCTC 57.991 50.000 0.00 0.0 0.00 4.30


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

AutoCloner maintained by Alex Coulton.