Multiple sequence alignment - TraesCS6A01G394700

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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 TraesCS6A01G394700 chr6A 100.000 2998 0 0 1 2998 608072356 608075353 0.000000e+00 5537.0
1 TraesCS6A01G394700 chr6B 90.292 1576 90 26 1432 2998 703147050 703148571 0.000000e+00 2004.0
2 TraesCS6A01G394700 chr6B 84.091 528 31 27 669 1170 703146032 703146532 7.570000e-126 460.0
3 TraesCS6A01G394700 chr6B 85.976 164 12 6 520 676 702956388 702956547 6.650000e-37 165.0
4 TraesCS6A01G394700 chr6D 89.354 1456 72 25 1 1433 461386221 461387616 0.000000e+00 1753.0
5 TraesCS6A01G394700 chr6D 90.859 1280 65 19 1414 2684 461387637 461388873 0.000000e+00 1668.0
6 TraesCS6A01G394700 chr2D 84.954 545 71 7 1460 1999 207251558 207251020 2.630000e-150 542.0
7 TraesCS6A01G394700 chr2D 96.850 127 4 0 993 1119 207251760 207251634 2.340000e-51 213.0
8 TraesCS6A01G394700 chr2B 81.851 551 64 12 1460 1999 260638978 260639503 5.940000e-117 431.0
9 TraesCS6A01G394700 chr2B 94.488 127 7 0 993 1119 260638792 260638918 2.360000e-46 196.0
10 TraesCS6A01G394700 chr2A 81.096 529 61 17 1460 1979 257854046 257854544 1.300000e-103 387.0
11 TraesCS6A01G394700 chr2A 95.082 122 6 0 998 1119 257853859 257853980 3.050000e-45 193.0
12 TraesCS6A01G394700 chr5B 80.000 250 36 6 284 530 605167753 605167515 3.970000e-39 172.0
13 TraesCS6A01G394700 chr5B 80.620 129 16 9 2707 2828 462886294 462886420 1.140000e-14 91.6
14 TraesCS6A01G394700 chr3D 79.339 242 41 6 271 506 26300225 26299987 8.600000e-36 161.0
15 TraesCS6A01G394700 chr7D 81.313 198 34 3 271 468 628522859 628523053 1.110000e-34 158.0
16 TraesCS6A01G394700 chr7D 75.355 211 42 9 299 506 53633009 53633212 3.180000e-15 93.5
17 TraesCS6A01G394700 chr5D 79.512 205 35 6 305 507 465200226 465200027 4.030000e-29 139.0
18 TraesCS6A01G394700 chr3A 77.489 231 43 8 280 506 63129230 63129005 2.430000e-26 130.0
19 TraesCS6A01G394700 chr3B 83.582 67 9 2 271 337 43925486 43925422 8.970000e-06 62.1
20 TraesCS6A01G394700 chr3B 83.582 67 9 2 271 337 44031300 44031236 8.970000e-06 62.1


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 TraesCS6A01G394700 chr6A 608072356 608075353 2997 False 5537.0 5537 100.0000 1 2998 1 chr6A.!!$F1 2997
1 TraesCS6A01G394700 chr6B 703146032 703148571 2539 False 1232.0 2004 87.1915 669 2998 2 chr6B.!!$F2 2329
2 TraesCS6A01G394700 chr6D 461386221 461388873 2652 False 1710.5 1753 90.1065 1 2684 2 chr6D.!!$F1 2683
3 TraesCS6A01G394700 chr2D 207251020 207251760 740 True 377.5 542 90.9020 993 1999 2 chr2D.!!$R1 1006
4 TraesCS6A01G394700 chr2B 260638792 260639503 711 False 313.5 431 88.1695 993 1999 2 chr2B.!!$F1 1006
5 TraesCS6A01G394700 chr2A 257853859 257854544 685 False 290.0 387 88.0890 998 1979 2 chr2A.!!$F1 981

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
570 590 0.109964 GATCGAGATCGCCGAGAAGG 60.11 60.0 16.04 0.0 39.55 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2198 2708 0.32336 ATGCCTTGCGTAACACCCAT 60.323 50.0 0.0 0.0 0.0 4.0 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
102 104 8.877808 AGAAGAAAACAATGAAAATGGAGAAC 57.122 30.769 0.00 0.00 0.00 3.01
104 106 9.317936 GAAGAAAACAATGAAAATGGAGAACTT 57.682 29.630 0.00 0.00 0.00 2.66
143 145 8.837389 AGTAGAAGTTGTCAAATTTTGGTAGTC 58.163 33.333 9.18 1.20 0.00 2.59
164 166 4.929808 GTCCGGTGACATATATGATGAACC 59.070 45.833 19.63 16.77 41.37 3.62
168 170 5.491982 GGTGACATATATGATGAACCCCTC 58.508 45.833 19.63 3.77 0.00 4.30
187 189 4.282957 CCCTCTATGCTATGTGTGTGATCT 59.717 45.833 0.00 0.00 0.00 2.75
192 194 9.171877 CTCTATGCTATGTGTGTGATCTAGATA 57.828 37.037 4.89 0.00 0.00 1.98
238 240 8.151141 ACATTGCACAACAATCTATAGATCTG 57.849 34.615 15.62 16.31 46.28 2.90
240 242 8.496751 CATTGCACAACAATCTATAGATCTGAG 58.503 37.037 15.62 12.22 46.28 3.35
244 246 7.545265 GCACAACAATCTATAGATCTGAGGATC 59.455 40.741 15.62 0.00 46.33 3.36
255 257 5.075858 GATCTGAGGATCTGCTTATGAGG 57.924 47.826 0.00 0.00 43.55 3.86
264 266 2.426024 TCTGCTTATGAGGTACACGGAC 59.574 50.000 0.00 0.00 0.00 4.79
280 282 3.934068 ACGGACGTGAATAAATGAACCT 58.066 40.909 0.00 0.00 0.00 3.50
325 338 0.733909 GGCAAGCGAACCATCTTTGC 60.734 55.000 0.00 0.00 40.32 3.68
389 402 7.678947 TTTTTGAACAAAAATTGCCTTCTCA 57.321 28.000 17.66 0.00 43.08 3.27
407 420 4.012374 TCTCAGGAAGAAAATGCCATGTC 58.988 43.478 0.00 0.00 0.00 3.06
409 422 4.410099 TCAGGAAGAAAATGCCATGTCTT 58.590 39.130 4.09 4.09 33.07 3.01
410 423 4.460382 TCAGGAAGAAAATGCCATGTCTTC 59.540 41.667 17.24 17.24 43.40 2.87
412 425 4.461781 AGGAAGAAAATGCCATGTCTTCTG 59.538 41.667 21.57 0.00 43.56 3.02
413 426 4.460382 GGAAGAAAATGCCATGTCTTCTGA 59.540 41.667 21.57 0.00 43.56 3.27
414 427 5.047802 GGAAGAAAATGCCATGTCTTCTGAA 60.048 40.000 21.57 0.00 43.56 3.02
415 428 6.409524 AAGAAAATGCCATGTCTTCTGAAA 57.590 33.333 0.00 0.00 0.00 2.69
416 429 6.409524 AGAAAATGCCATGTCTTCTGAAAA 57.590 33.333 0.00 0.00 0.00 2.29
417 430 6.819284 AGAAAATGCCATGTCTTCTGAAAAA 58.181 32.000 0.00 0.00 0.00 1.94
439 452 2.360475 GCCACTGCTCCCCACTTC 60.360 66.667 0.00 0.00 33.53 3.01
440 453 3.160585 CCACTGCTCCCCACTTCA 58.839 61.111 0.00 0.00 0.00 3.02
453 466 5.640147 TCCCCACTTCATCACAACTAAAAT 58.360 37.500 0.00 0.00 0.00 1.82
459 473 7.756722 CCACTTCATCACAACTAAAATTCCATC 59.243 37.037 0.00 0.00 0.00 3.51
479 493 0.452784 GAATCGTTCGCTTGTGCCAC 60.453 55.000 0.00 0.00 35.36 5.01
480 494 1.852067 AATCGTTCGCTTGTGCCACC 61.852 55.000 0.00 0.00 35.36 4.61
484 504 3.842925 TTCGCTTGTGCCACCTCCC 62.843 63.158 0.00 0.00 35.36 4.30
493 513 3.411517 CCACCTCCCCTGGCGAAT 61.412 66.667 0.00 0.00 0.00 3.34
498 518 1.299648 CTCCCCTGGCGAATGTTCA 59.700 57.895 0.00 0.00 0.00 3.18
505 525 2.552599 TGGCGAATGTTCACCAGTTA 57.447 45.000 0.00 0.00 34.66 2.24
506 526 2.852449 TGGCGAATGTTCACCAGTTAA 58.148 42.857 0.00 0.00 34.66 2.01
507 527 3.417101 TGGCGAATGTTCACCAGTTAAT 58.583 40.909 0.00 0.00 34.66 1.40
508 528 3.823873 TGGCGAATGTTCACCAGTTAATT 59.176 39.130 0.00 0.00 34.66 1.40
528 548 2.907458 AGGAGGGTCCCAAATGAAAG 57.093 50.000 11.55 0.00 37.19 2.62
531 551 2.447443 GAGGGTCCCAAATGAAAGGTC 58.553 52.381 11.55 0.00 0.00 3.85
537 557 1.547372 CCCAAATGAAAGGTCCAGCTG 59.453 52.381 6.78 6.78 0.00 4.24
549 569 2.558359 GGTCCAGCTGTTAATTTGCAGT 59.442 45.455 13.81 0.00 35.33 4.40
550 570 3.366374 GGTCCAGCTGTTAATTTGCAGTC 60.366 47.826 13.81 0.00 35.33 3.51
551 571 2.483877 TCCAGCTGTTAATTTGCAGTCG 59.516 45.455 13.81 0.00 35.33 4.18
552 572 2.483877 CCAGCTGTTAATTTGCAGTCGA 59.516 45.455 13.81 0.00 35.33 4.20
570 590 0.109964 GATCGAGATCGCCGAGAAGG 60.110 60.000 16.04 0.00 39.55 3.46
579 599 1.375908 GCCGAGAAGGACATGTGCA 60.376 57.895 20.21 0.00 45.00 4.57
587 607 0.677731 AGGACATGTGCAATGACCCG 60.678 55.000 20.21 0.00 35.06 5.28
661 681 3.850122 TCACAGATGTCACGACCTTAG 57.150 47.619 0.00 0.00 0.00 2.18
686 706 2.639065 GTTTGTGACAAGTCAGTCCCA 58.361 47.619 2.62 0.00 40.75 4.37
727 752 2.612212 CCACGACCTTAAATGGAATCGG 59.388 50.000 0.00 0.00 33.80 4.18
756 782 5.991933 TGAGCAGTTCAGAAATAGAGAGT 57.008 39.130 0.00 0.00 0.00 3.24
969 1009 1.202698 GGACCGGGATCCATCTTCTTG 60.203 57.143 15.23 0.00 38.77 3.02
970 1010 1.486726 GACCGGGATCCATCTTCTTGT 59.513 52.381 15.23 0.00 0.00 3.16
991 1031 3.292492 TGTTGGTAGCTCCTCGATCTA 57.708 47.619 0.00 0.00 37.07 1.98
1143 1187 1.181786 CTTCTTCTCGTCCAGCCTCT 58.818 55.000 0.00 0.00 0.00 3.69
1226 1288 7.437267 GCTACATCTAAAATTCATGCATGCTTT 59.563 33.333 22.25 20.11 0.00 3.51
1227 1289 7.766219 ACATCTAAAATTCATGCATGCTTTC 57.234 32.000 22.25 0.00 0.00 2.62
1228 1290 7.553334 ACATCTAAAATTCATGCATGCTTTCT 58.447 30.769 22.25 14.57 0.00 2.52
1229 1291 8.038944 ACATCTAAAATTCATGCATGCTTTCTT 58.961 29.630 22.25 12.65 0.00 2.52
1230 1292 8.879759 CATCTAAAATTCATGCATGCTTTCTTT 58.120 29.630 22.25 16.45 0.00 2.52
1261 1323 4.037446 TCTTGTTTCTTCAATTTCACCCGG 59.963 41.667 0.00 0.00 0.00 5.73
1262 1324 3.292460 TGTTTCTTCAATTTCACCCGGT 58.708 40.909 0.00 0.00 0.00 5.28
1263 1325 4.462133 TGTTTCTTCAATTTCACCCGGTA 58.538 39.130 0.00 0.00 0.00 4.02
1264 1326 4.517453 TGTTTCTTCAATTTCACCCGGTAG 59.483 41.667 0.00 0.00 0.00 3.18
1294 1356 3.200483 CACCAAGCAGATGATCGATTCA 58.800 45.455 0.00 0.00 39.12 2.57
1309 1371 1.674962 GATTCAGATCTGCTTGGTGCC 59.325 52.381 18.36 0.00 42.00 5.01
1313 1375 1.378250 GATCTGCTTGGTGCCAGCT 60.378 57.895 11.72 0.00 42.00 4.24
1314 1376 0.107508 GATCTGCTTGGTGCCAGCTA 60.108 55.000 11.72 0.00 42.00 3.32
1324 1386 0.390472 GTGCCAGCTATATCCGAGGC 60.390 60.000 0.64 0.64 42.32 4.70
1341 1403 0.169009 GGCGGATGAAACAAGCAGAC 59.831 55.000 0.00 0.00 0.00 3.51
1382 1448 7.927092 TGCTTGTTTCTTCAATTTCATTCATGA 59.073 29.630 0.00 0.00 34.44 3.07
1412 1478 8.105097 TCGATTCAGATCAACAATTAAAACCA 57.895 30.769 0.00 0.00 32.33 3.67
1425 1531 7.740805 ACAATTAAAACCACTCTCTCTCTCTT 58.259 34.615 0.00 0.00 0.00 2.85
1443 1924 4.836736 TCTCTTTCTCTCTTTTTACCCGGA 59.163 41.667 0.73 0.00 0.00 5.14
1444 1925 5.484290 TCTCTTTCTCTCTTTTTACCCGGAT 59.516 40.000 0.73 0.00 0.00 4.18
1594 2075 2.939103 GTTTGATCAACATCTCCCTCCG 59.061 50.000 7.89 0.00 35.18 4.63
1643 2130 8.126074 CGCCAATATACTCTACTCTGATGATAC 58.874 40.741 0.00 0.00 0.00 2.24
1668 2158 8.928448 ACAACATTTCATATCTCTTAGCTCCTA 58.072 33.333 0.00 0.00 0.00 2.94
1868 2370 0.323908 AGGAGAACAGCTACTCGGCT 60.324 55.000 0.00 0.00 44.10 5.52
2007 2509 1.259316 GTCGCGGTGATTTGATTTGC 58.741 50.000 6.13 0.00 0.00 3.68
2008 2510 0.877743 TCGCGGTGATTTGATTTGCA 59.122 45.000 6.13 0.00 0.00 4.08
2009 2511 1.135717 TCGCGGTGATTTGATTTGCAG 60.136 47.619 6.13 0.00 0.00 4.41
2050 2558 5.446143 TGCCTTTTGTGATCGTAATGTTT 57.554 34.783 0.00 0.00 0.00 2.83
2051 2559 5.218885 TGCCTTTTGTGATCGTAATGTTTG 58.781 37.500 0.00 0.00 0.00 2.93
2052 2560 5.219633 GCCTTTTGTGATCGTAATGTTTGT 58.780 37.500 0.00 0.00 0.00 2.83
2094 2602 9.322776 GCTATGAAAATAATTAAGCGATGTCTG 57.677 33.333 0.00 0.00 0.00 3.51
2142 2652 5.192927 TGTAATGATTTGTGGATCTCACCC 58.807 41.667 10.60 0.00 45.48 4.61
2146 2656 0.323629 TTTGTGGATCTCACCCGGAC 59.676 55.000 0.73 0.00 45.48 4.79
2231 2741 5.221441 ACGCAAGGCATGTGATAGACTTATA 60.221 40.000 10.57 0.00 42.32 0.98
2285 2795 4.339247 GGTTCTGCATATGTTGTATGGCTT 59.661 41.667 4.29 0.00 0.00 4.35
2353 2864 2.497273 AGCCACTCCATGTTAATTTGCC 59.503 45.455 0.00 0.00 0.00 4.52
2356 2867 4.685924 CCACTCCATGTTAATTTGCCATC 58.314 43.478 0.00 0.00 0.00 3.51
2357 2868 4.353737 CACTCCATGTTAATTTGCCATCG 58.646 43.478 0.00 0.00 0.00 3.84
2358 2869 4.096231 CACTCCATGTTAATTTGCCATCGA 59.904 41.667 0.00 0.00 0.00 3.59
2359 2870 4.889409 ACTCCATGTTAATTTGCCATCGAT 59.111 37.500 0.00 0.00 0.00 3.59
2360 2871 5.009010 ACTCCATGTTAATTTGCCATCGATC 59.991 40.000 0.00 0.00 0.00 3.69
2361 2872 4.886489 TCCATGTTAATTTGCCATCGATCA 59.114 37.500 0.00 0.00 0.00 2.92
2362 2873 5.535783 TCCATGTTAATTTGCCATCGATCAT 59.464 36.000 0.00 0.00 0.00 2.45
2363 2874 6.714356 TCCATGTTAATTTGCCATCGATCATA 59.286 34.615 0.00 0.00 0.00 2.15
2364 2875 7.394077 TCCATGTTAATTTGCCATCGATCATAT 59.606 33.333 0.00 0.00 0.00 1.78
2365 2876 8.030692 CCATGTTAATTTGCCATCGATCATATT 58.969 33.333 0.00 1.73 0.00 1.28
2366 2877 8.856247 CATGTTAATTTGCCATCGATCATATTG 58.144 33.333 0.00 0.00 0.00 1.90
2367 2878 7.939782 TGTTAATTTGCCATCGATCATATTGT 58.060 30.769 0.00 0.00 0.00 2.71
2368 2879 8.075574 TGTTAATTTGCCATCGATCATATTGTC 58.924 33.333 0.00 0.00 0.00 3.18
2369 2880 6.638096 AATTTGCCATCGATCATATTGTCA 57.362 33.333 0.00 0.00 0.00 3.58
2370 2881 6.638096 ATTTGCCATCGATCATATTGTCAA 57.362 33.333 0.00 0.00 0.00 3.18
2371 2882 5.422666 TTGCCATCGATCATATTGTCAAC 57.577 39.130 0.00 0.00 0.00 3.18
2372 2883 4.450053 TGCCATCGATCATATTGTCAACA 58.550 39.130 0.00 0.00 0.00 3.33
2373 2884 4.273235 TGCCATCGATCATATTGTCAACAC 59.727 41.667 0.00 0.00 0.00 3.32
2374 2885 4.273235 GCCATCGATCATATTGTCAACACA 59.727 41.667 0.00 0.00 0.00 3.72
2375 2886 5.741425 CCATCGATCATATTGTCAACACAC 58.259 41.667 0.00 0.00 29.76 3.82
2376 2887 5.294060 CCATCGATCATATTGTCAACACACA 59.706 40.000 0.00 0.00 29.76 3.72
2377 2888 6.017687 CCATCGATCATATTGTCAACACACAT 60.018 38.462 0.00 0.00 29.76 3.21
2378 2889 6.983474 TCGATCATATTGTCAACACACATT 57.017 33.333 0.00 0.00 29.76 2.71
2379 2890 7.376435 TCGATCATATTGTCAACACACATTT 57.624 32.000 0.00 0.00 29.76 2.32
2380 2891 8.485976 TCGATCATATTGTCAACACACATTTA 57.514 30.769 0.00 0.00 29.76 1.40
2381 2892 8.940952 TCGATCATATTGTCAACACACATTTAA 58.059 29.630 0.00 0.00 29.76 1.52
2382 2893 9.720667 CGATCATATTGTCAACACACATTTAAT 57.279 29.630 0.00 0.00 29.76 1.40
2414 2925 6.743575 ATTTTGACCTTACAGAGTATGCAC 57.256 37.500 0.00 0.00 0.00 4.57
2416 2927 2.194271 GACCTTACAGAGTATGCACGC 58.806 52.381 0.00 0.00 0.00 5.34
2426 2937 2.355756 GAGTATGCACGCCATGTCAAAT 59.644 45.455 0.00 0.00 35.34 2.32
2427 2938 2.754552 AGTATGCACGCCATGTCAAATT 59.245 40.909 0.00 0.00 35.34 1.82
2428 2939 2.747396 ATGCACGCCATGTCAAATTT 57.253 40.000 0.00 0.00 31.48 1.82
2429 2940 2.063156 TGCACGCCATGTCAAATTTC 57.937 45.000 0.00 0.00 0.00 2.17
2430 2941 1.339291 TGCACGCCATGTCAAATTTCA 59.661 42.857 0.00 0.00 0.00 2.69
2431 2942 1.987770 GCACGCCATGTCAAATTTCAG 59.012 47.619 0.00 0.00 0.00 3.02
2432 2943 1.987770 CACGCCATGTCAAATTTCAGC 59.012 47.619 0.00 0.00 0.00 4.26
2466 2977 6.575244 AACATCACCCTGAACCTTGATATA 57.425 37.500 0.00 0.00 0.00 0.86
2538 3049 3.808174 CGTTTTCTTTCTTCCCGAGAACT 59.192 43.478 0.00 0.00 43.90 3.01
2549 3060 2.027469 TCCCGAGAACTAAAGAAAGGCC 60.027 50.000 0.00 0.00 0.00 5.19
2554 3065 2.654896 AGAACTAAAGAAAGGCCCCCAT 59.345 45.455 0.00 0.00 0.00 4.00
2567 3078 0.823356 CCCCCATGCGATTAGGGTTG 60.823 60.000 0.00 0.00 41.16 3.77
2575 3093 1.526225 GATTAGGGTTGCCTCGCCC 60.526 63.158 0.00 0.00 45.16 6.13
2576 3094 2.960359 GATTAGGGTTGCCTCGCCCC 62.960 65.000 0.00 0.00 45.95 5.80
2581 3099 4.021925 GTTGCCTCGCCCCTCACT 62.022 66.667 0.00 0.00 0.00 3.41
2608 3126 1.445716 CCGCCGATCTACCTCGTCTT 61.446 60.000 0.00 0.00 36.93 3.01
2609 3127 0.317103 CGCCGATCTACCTCGTCTTG 60.317 60.000 0.00 0.00 36.93 3.02
2657 3175 1.342975 TGGATCTCGACCCTTGATGGA 60.343 52.381 0.00 0.00 38.35 3.41
2703 3221 7.729124 ATAGTGGTTGTTTAGCCTACTTAGA 57.271 36.000 0.00 0.00 0.00 2.10
2706 3224 6.042897 AGTGGTTGTTTAGCCTACTTAGAGTT 59.957 38.462 0.00 0.00 0.00 3.01
2708 3226 7.874528 GTGGTTGTTTAGCCTACTTAGAGTTTA 59.125 37.037 0.00 0.00 0.00 2.01
2729 3247 0.177604 ATCCTGCTCAAGAAGGCGAG 59.822 55.000 0.00 0.00 40.90 5.03
2753 3271 2.612972 GGCAACGACTTCTTGAGGATGA 60.613 50.000 0.00 0.00 0.00 2.92
2784 3302 4.609018 CCGCATAGCCCTGTCCCG 62.609 72.222 0.00 0.00 0.00 5.14
2808 3326 2.105128 CCTCTCGCATCGTGGGAC 59.895 66.667 1.66 0.00 34.23 4.46
2809 3327 2.278206 CTCTCGCATCGTGGGACG 60.278 66.667 0.00 0.00 44.19 4.79
2849 3367 2.429236 CGGATCTCGCGGGATTCG 60.429 66.667 33.25 33.25 38.18 3.34
2854 3372 3.884350 CTCGCGGGATTCGGTCGA 61.884 66.667 0.00 0.00 39.69 4.20
2891 3409 4.828939 TGGATTTGCATGGATCCAGTATTC 59.171 41.667 21.33 11.34 45.14 1.75
2989 3507 4.202192 TGTGTAACATCCAAATGCAGCAAA 60.202 37.500 0.00 0.00 45.67 3.68
2992 3510 1.693062 ACATCCAAATGCAGCAAACCA 59.307 42.857 0.00 0.00 36.26 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 6.482973 TCATTGTTTTCTTCTTTTCCATTGGC 59.517 34.615 0.00 0.00 0.00 4.52
104 106 8.794553 TGACAACTTCTACTAAACCAACAAAAA 58.205 29.630 0.00 0.00 0.00 1.94
125 127 4.036971 CACCGGACTACCAAAATTTGACAA 59.963 41.667 9.46 0.00 35.59 3.18
128 130 3.816523 GTCACCGGACTACCAAAATTTGA 59.183 43.478 9.46 0.00 40.99 2.69
143 145 4.253685 GGGTTCATCATATATGTCACCGG 58.746 47.826 12.42 0.00 0.00 5.28
164 166 4.282957 AGATCACACACATAGCATAGAGGG 59.717 45.833 0.00 0.00 0.00 4.30
238 240 4.557695 CGTGTACCTCATAAGCAGATCCTC 60.558 50.000 0.00 0.00 0.00 3.71
240 242 3.553096 CCGTGTACCTCATAAGCAGATCC 60.553 52.174 0.00 0.00 0.00 3.36
244 246 2.794981 CGTCCGTGTACCTCATAAGCAG 60.795 54.545 0.00 0.00 0.00 4.24
252 254 3.492421 TTATTCACGTCCGTGTACCTC 57.508 47.619 18.23 0.00 45.55 3.85
255 257 5.445010 GGTTCATTTATTCACGTCCGTGTAC 60.445 44.000 18.23 0.00 45.55 2.90
264 266 2.675844 TCGCCAGGTTCATTTATTCACG 59.324 45.455 0.00 0.00 0.00 4.35
270 272 2.172851 ACGTTCGCCAGGTTCATTTA 57.827 45.000 0.00 0.00 0.00 1.40
302 315 2.676471 ATGGTTCGCTTGCCACCC 60.676 61.111 6.26 0.00 37.62 4.61
325 338 7.254852 TCTTGTTTTACAACTAAAACTGCCAG 58.745 34.615 14.18 0.00 46.58 4.85
357 370 9.597999 GGCAATTTTTGTTCAAAAACTGATATC 57.402 29.630 25.52 13.57 37.90 1.63
358 371 9.341078 AGGCAATTTTTGTTCAAAAACTGATAT 57.659 25.926 25.52 13.34 37.90 1.63
359 372 8.729805 AGGCAATTTTTGTTCAAAAACTGATA 57.270 26.923 25.52 7.86 37.90 2.15
360 373 7.628769 AGGCAATTTTTGTTCAAAAACTGAT 57.371 28.000 25.52 15.31 37.90 2.90
361 374 7.390162 AGAAGGCAATTTTTGTTCAAAAACTGA 59.610 29.630 25.52 8.70 37.90 3.41
370 383 5.200368 TCCTGAGAAGGCAATTTTTGTTC 57.800 39.130 0.00 0.00 0.00 3.18
389 402 4.461781 CAGAAGACATGGCATTTTCTTCCT 59.538 41.667 28.81 19.73 43.36 3.36
422 435 2.360475 GAAGTGGGGAGCAGTGGC 60.360 66.667 0.00 0.00 41.61 5.01
423 436 0.393537 GATGAAGTGGGGAGCAGTGG 60.394 60.000 0.00 0.00 0.00 4.00
424 437 0.325933 TGATGAAGTGGGGAGCAGTG 59.674 55.000 0.00 0.00 0.00 3.66
425 438 0.326264 GTGATGAAGTGGGGAGCAGT 59.674 55.000 0.00 0.00 0.00 4.40
426 439 0.325933 TGTGATGAAGTGGGGAGCAG 59.674 55.000 0.00 0.00 0.00 4.24
427 440 0.770499 TTGTGATGAAGTGGGGAGCA 59.230 50.000 0.00 0.00 0.00 4.26
428 441 1.168714 GTTGTGATGAAGTGGGGAGC 58.831 55.000 0.00 0.00 0.00 4.70
439 452 7.374228 CGATTCGATGGAATTTTAGTTGTGATG 59.626 37.037 4.32 0.00 42.86 3.07
440 453 7.065803 ACGATTCGATGGAATTTTAGTTGTGAT 59.934 33.333 13.95 0.00 42.86 3.06
470 484 2.034687 CAGGGGAGGTGGCACAAG 59.965 66.667 20.82 0.00 44.16 3.16
471 485 3.579302 CCAGGGGAGGTGGCACAA 61.579 66.667 20.82 0.00 44.16 3.33
479 493 1.452108 GAACATTCGCCAGGGGAGG 60.452 63.158 6.28 6.06 0.00 4.30
480 494 1.026718 GTGAACATTCGCCAGGGGAG 61.027 60.000 6.28 0.00 0.00 4.30
493 513 4.600111 ACCCTCCTAATTAACTGGTGAACA 59.400 41.667 0.00 0.00 0.00 3.18
498 518 3.120898 GGGACCCTCCTAATTAACTGGT 58.879 50.000 2.09 0.00 36.57 4.00
505 525 4.965283 TTCATTTGGGACCCTCCTAATT 57.035 40.909 13.00 0.00 36.86 1.40
506 526 4.326132 CCTTTCATTTGGGACCCTCCTAAT 60.326 45.833 13.00 3.70 36.86 1.73
507 527 3.011257 CCTTTCATTTGGGACCCTCCTAA 59.989 47.826 13.00 1.31 35.05 2.69
508 528 2.580783 CCTTTCATTTGGGACCCTCCTA 59.419 50.000 13.00 0.00 36.57 2.94
528 548 2.558359 ACTGCAAATTAACAGCTGGACC 59.442 45.455 19.93 0.00 37.42 4.46
531 551 2.483877 TCGACTGCAAATTAACAGCTGG 59.516 45.455 19.93 0.00 37.42 4.85
537 557 5.643339 ATCTCGATCGACTGCAAATTAAC 57.357 39.130 15.15 0.00 0.00 2.01
551 571 0.109964 CCTTCTCGGCGATCTCGATC 60.110 60.000 11.27 0.00 43.02 3.69
552 572 0.535328 TCCTTCTCGGCGATCTCGAT 60.535 55.000 11.27 0.00 43.02 3.59
570 590 1.656818 CCCGGGTCATTGCACATGTC 61.657 60.000 14.18 0.00 0.00 3.06
661 681 4.331962 GACTGACTTGTCACAAACGAAAC 58.668 43.478 0.00 0.00 36.97 2.78
686 706 1.537202 GGTGCGTTTTCTTCAGCTGAT 59.463 47.619 19.04 0.00 0.00 2.90
727 752 7.212976 TCTATTTCTGAACTGCTCATATCCAC 58.787 38.462 0.00 0.00 32.14 4.02
756 782 2.203408 TCCAACAACGCATGCCCA 60.203 55.556 13.15 0.00 0.00 5.36
923 958 3.549221 GGAGAAGAAGATGGATCGTCGTC 60.549 52.174 9.37 9.37 41.33 4.20
924 959 2.359531 GGAGAAGAAGATGGATCGTCGT 59.640 50.000 0.00 0.00 39.73 4.34
925 960 2.287909 GGGAGAAGAAGATGGATCGTCG 60.288 54.545 0.00 0.00 39.73 5.12
926 961 2.036604 GGGGAGAAGAAGATGGATCGTC 59.963 54.545 0.00 0.00 35.87 4.20
927 962 2.043227 GGGGAGAAGAAGATGGATCGT 58.957 52.381 0.00 0.00 0.00 3.73
928 963 1.346068 GGGGGAGAAGAAGATGGATCG 59.654 57.143 0.00 0.00 0.00 3.69
969 1009 2.166664 AGATCGAGGAGCTACCAACAAC 59.833 50.000 0.00 0.00 42.04 3.32
970 1010 2.457598 AGATCGAGGAGCTACCAACAA 58.542 47.619 0.00 0.00 42.04 2.83
991 1031 1.302033 GGCGCTCCATGGATCGATT 60.302 57.895 35.46 0.00 36.04 3.34
1233 1295 9.710900 GGGTGAAATTGAAGAAACAAGATTAAT 57.289 29.630 0.00 0.00 33.22 1.40
1234 1296 7.865385 CGGGTGAAATTGAAGAAACAAGATTAA 59.135 33.333 0.00 0.00 33.22 1.40
1241 1303 3.292460 ACCGGGTGAAATTGAAGAAACA 58.708 40.909 6.32 0.00 0.00 2.83
1261 1323 3.319405 TCTGCTTGGTGCTAGCTATCTAC 59.681 47.826 17.23 4.85 43.37 2.59
1262 1324 3.566351 TCTGCTTGGTGCTAGCTATCTA 58.434 45.455 17.23 1.81 43.37 1.98
1263 1325 2.392662 TCTGCTTGGTGCTAGCTATCT 58.607 47.619 17.23 0.00 43.37 1.98
1264 1326 2.898729 TCTGCTTGGTGCTAGCTATC 57.101 50.000 17.23 6.44 43.37 2.08
1324 1386 1.428448 TCGTCTGCTTGTTTCATCCG 58.572 50.000 0.00 0.00 0.00 4.18
1412 1478 7.839680 AAAAAGAGAGAAAGAGAGAGAGAGT 57.160 36.000 0.00 0.00 0.00 3.24
1425 1531 6.540083 AGAAAATCCGGGTAAAAAGAGAGAA 58.460 36.000 0.00 0.00 0.00 2.87
1594 2075 5.617751 CGGTGAGTTTGTGAAATCCTGATTC 60.618 44.000 0.00 0.00 0.00 2.52
1643 2130 9.770097 TTAGGAGCTAAGAGATATGAAATGTTG 57.230 33.333 0.00 0.00 0.00 3.33
1688 2178 6.149474 AGACTTCCTGTGACGGAAATAAAATG 59.851 38.462 9.46 1.15 42.20 2.32
1857 2359 2.888863 GCTGTCAGCCGAGTAGCT 59.111 61.111 14.27 0.00 46.45 3.32
2007 2509 1.150081 CAATAGCTGGCCTCCCCTG 59.850 63.158 3.32 0.00 35.75 4.45
2008 2510 2.761465 GCAATAGCTGGCCTCCCCT 61.761 63.158 3.32 0.00 37.91 4.79
2009 2511 2.203408 GCAATAGCTGGCCTCCCC 60.203 66.667 3.32 0.00 37.91 4.81
2094 2602 5.124936 GTGGGTGTTATGTAAAGAATGGGAC 59.875 44.000 0.00 0.00 0.00 4.46
2142 2652 2.404265 TATTATACACGCACCGTCCG 57.596 50.000 0.00 0.00 38.32 4.79
2146 2656 3.313690 TGCTCATATTATACACGCACCG 58.686 45.455 0.00 0.00 0.00 4.94
2154 2664 6.700081 TCACCAAGACGTTGCTCATATTATAC 59.300 38.462 0.00 0.00 31.64 1.47
2198 2708 0.323360 ATGCCTTGCGTAACACCCAT 60.323 50.000 0.00 0.00 0.00 4.00
2205 2715 3.118775 AGTCTATCACATGCCTTGCGTAA 60.119 43.478 0.00 0.00 0.00 3.18
2210 2720 8.580720 AGTAGTATAAGTCTATCACATGCCTTG 58.419 37.037 0.00 0.00 0.00 3.61
2231 2741 1.064685 GCAAGCATTACCCCCAGTAGT 60.065 52.381 0.00 0.00 30.92 2.73
2334 2845 4.685924 GATGGCAAATTAACATGGAGTGG 58.314 43.478 0.00 0.00 0.00 4.00
2353 2864 6.348621 TGTGTGTTGACAATATGATCGATG 57.651 37.500 0.54 0.00 32.49 3.84
2356 2867 9.720667 ATTAAATGTGTGTTGACAATATGATCG 57.279 29.630 0.00 0.00 32.49 3.69
2388 2899 8.893727 GTGCATACTCTGTAAGGTCAAAATTAT 58.106 33.333 0.00 0.00 0.00 1.28
2404 2915 0.536724 TGACATGGCGTGCATACTCT 59.463 50.000 6.62 0.00 0.00 3.24
2411 2922 1.987770 CTGAAATTTGACATGGCGTGC 59.012 47.619 6.62 0.27 0.00 5.34
2414 2925 2.642139 AGCTGAAATTTGACATGGCG 57.358 45.000 0.00 0.00 0.00 5.69
2416 2927 4.753107 AGCAAAAGCTGAAATTTGACATGG 59.247 37.500 11.84 0.00 38.50 3.66
2426 2937 6.208644 GTGATGTTTAGAGCAAAAGCTGAAA 58.791 36.000 0.00 0.00 0.00 2.69
2427 2938 5.278463 GGTGATGTTTAGAGCAAAAGCTGAA 60.278 40.000 0.00 0.00 0.00 3.02
2428 2939 4.216257 GGTGATGTTTAGAGCAAAAGCTGA 59.784 41.667 0.00 0.00 0.00 4.26
2429 2940 4.479619 GGTGATGTTTAGAGCAAAAGCTG 58.520 43.478 0.00 0.00 0.00 4.24
2430 2941 3.507622 GGGTGATGTTTAGAGCAAAAGCT 59.492 43.478 0.00 0.00 0.00 3.74
2431 2942 3.507622 AGGGTGATGTTTAGAGCAAAAGC 59.492 43.478 0.00 0.00 0.00 3.51
2432 2943 4.761739 TCAGGGTGATGTTTAGAGCAAAAG 59.238 41.667 0.00 0.00 0.00 2.27
2441 2952 4.715534 TCAAGGTTCAGGGTGATGTTTA 57.284 40.909 0.00 0.00 0.00 2.01
2472 2983 7.067859 TGTTAGCGGTAACATACTAGTCTCATT 59.932 37.037 30.59 0.00 42.99 2.57
2526 3037 3.685272 GCCTTTCTTTAGTTCTCGGGAAG 59.315 47.826 0.00 0.00 31.46 3.46
2538 3049 0.682855 CGCATGGGGGCCTTTCTTTA 60.683 55.000 0.84 0.00 0.00 1.85
2549 3060 1.455383 GCAACCCTAATCGCATGGGG 61.455 60.000 10.21 5.41 44.97 4.96
2554 3065 1.153449 CGAGGCAACCCTAATCGCA 60.153 57.895 0.00 0.00 43.12 5.10
2636 3154 1.202580 CCATCAAGGGTCGAGATCCAC 60.203 57.143 5.08 0.00 32.73 4.02
2703 3221 5.372373 GCCTTCTTGAGCAGGATATAAACT 58.628 41.667 0.64 0.00 29.45 2.66
2706 3224 3.641436 TCGCCTTCTTGAGCAGGATATAA 59.359 43.478 0.64 0.00 29.45 0.98
2708 3226 2.036992 CTCGCCTTCTTGAGCAGGATAT 59.963 50.000 0.64 0.00 29.45 1.63
2729 3247 1.901650 CTCAAGAAGTCGTTGCCGCC 61.902 60.000 0.00 0.00 0.00 6.13
2735 3253 6.595716 CCTTATTTCATCCTCAAGAAGTCGTT 59.404 38.462 0.00 0.00 0.00 3.85
2748 3266 3.477530 CGGGGAGAACCTTATTTCATCC 58.522 50.000 0.00 0.00 40.03 3.51
2753 3271 3.747708 GCTATGCGGGGAGAACCTTATTT 60.748 47.826 0.00 0.00 40.03 1.40
2808 3326 2.587753 ACACAACTCCACACGCCG 60.588 61.111 0.00 0.00 0.00 6.46
2809 3327 1.222115 GAGACACAACTCCACACGCC 61.222 60.000 0.00 0.00 0.00 5.68
2832 3350 2.429236 CGAATCCCGCGAGATCCG 60.429 66.667 8.23 0.00 42.21 4.18
2849 3367 2.864343 CCACCGAAGAATAACATCGACC 59.136 50.000 0.00 0.00 41.35 4.79
2854 3372 4.704540 TGCAAATCCACCGAAGAATAACAT 59.295 37.500 0.00 0.00 0.00 2.71
2891 3409 2.139811 GCATGAGCGCAAACGAACG 61.140 57.895 11.47 0.00 43.93 3.95


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

AutoCloner maintained by Alex Coulton.