Multiple sequence alignment - TraesCS1B01G066900

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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 TraesCS1B01G066900 chr1B 100.000 3749 0 0 1 3749 51104503 51108251 0.000000e+00 6924.0
1 TraesCS1B01G066900 chr1B 91.166 1381 88 19 2397 3749 51140916 51142290 0.000000e+00 1844.0
2 TraesCS1B01G066900 chr1B 92.556 900 48 10 2173 3056 51113048 51113944 0.000000e+00 1273.0
3 TraesCS1B01G066900 chr1B 95.231 713 21 7 3048 3749 51135342 51136052 0.000000e+00 1116.0
4 TraesCS1B01G066900 chr1B 85.714 70 4 4 2173 2238 51140848 51140915 6.720000e-08 69.4
5 TraesCS1B01G066900 chr1A 87.571 3516 253 81 351 3749 32259538 32262986 0.000000e+00 3903.0
6 TraesCS1B01G066900 chr1A 88.889 324 29 5 3432 3749 32306159 32306481 3.510000e-105 392.0
7 TraesCS1B01G066900 chr1A 88.580 324 25 6 1 315 32259220 32259540 2.110000e-102 383.0
8 TraesCS1B01G066900 chr1A 84.080 402 32 16 2909 3295 32272180 32272564 3.560000e-95 359.0
9 TraesCS1B01G066900 chr1A 85.667 300 37 4 3286 3580 32272734 32273032 1.010000e-80 311.0
10 TraesCS1B01G066900 chr1D 88.693 2326 156 59 351 2630 33638003 33640267 0.000000e+00 2739.0
11 TraesCS1B01G066900 chr1D 85.701 1084 93 21 2711 3749 33640366 33641432 0.000000e+00 1086.0
12 TraesCS1B01G066900 chr1D 89.035 228 18 4 93 315 33637780 33638005 3.690000e-70 276.0
13 TraesCS1B01G066900 chr6D 79.129 781 115 37 2008 2758 3726998 3727760 2.600000e-136 496.0
14 TraesCS1B01G066900 chr6D 80.851 564 85 20 2004 2556 3740063 3740614 4.480000e-114 422.0
15 TraesCS1B01G066900 chr6D 80.565 566 85 23 2006 2558 4721460 4720907 2.690000e-111 412.0
16 TraesCS1B01G066900 chr6D 79.549 577 78 30 2010 2556 3763844 3764410 3.540000e-100 375.0
17 TraesCS1B01G066900 chr6D 78.438 640 88 39 2006 2622 3714102 3714714 4.570000e-99 372.0
18 TraesCS1B01G066900 chr6D 83.476 351 42 12 1658 1997 3739612 3739957 2.810000e-81 313.0
19 TraesCS1B01G066900 chr6D 82.659 346 39 15 1665 2002 3713605 3713937 1.700000e-73 287.0
20 TraesCS1B01G066900 chr6D 81.534 352 52 11 1658 2002 4721956 4721611 1.030000e-70 278.0
21 TraesCS1B01G066900 chr6D 84.103 195 17 7 714 903 3725744 3725929 3.850000e-40 176.0
22 TraesCS1B01G066900 chr6D 78.414 227 39 8 447 669 3756642 3756862 5.050000e-29 139.0
23 TraesCS1B01G066900 chr6D 74.667 300 44 17 2475 2758 3766658 3766941 1.840000e-18 104.0
24 TraesCS1B01G066900 chr6B 81.368 585 72 29 2004 2563 9080357 9080929 3.440000e-120 442.0
25 TraesCS1B01G066900 chr6B 81.317 562 78 23 2006 2558 9035581 9036124 7.440000e-117 431.0
26 TraesCS1B01G066900 chr6B 82.162 370 47 14 1645 2002 9079894 9080256 2.190000e-77 300.0
27 TraesCS1B01G066900 chr6B 80.833 360 56 11 1650 2002 9035078 9035431 1.720000e-68 270.0
28 TraesCS1B01G066900 chr6B 81.143 350 44 12 1665 2002 9058855 9059194 1.030000e-65 261.0
29 TraesCS1B01G066900 chr6B 80.000 145 22 7 529 667 9057623 9057766 2.380000e-17 100.0
30 TraesCS1B01G066900 chr6A 80.944 572 79 24 2004 2558 3747022 3746464 3.460000e-115 425.0
31 TraesCS1B01G066900 chr6A 80.247 567 87 23 2006 2558 3772962 3772407 1.620000e-108 403.0
32 TraesCS1B01G066900 chr6A 84.078 358 37 12 1658 2002 3747473 3747123 1.000000e-85 327.0
33 TraesCS1B01G066900 chr6A 80.940 383 71 2 1791 2172 601472861 601473242 6.090000e-78 302.0
34 TraesCS1B01G066900 chr6A 82.369 363 41 13 1653 2002 3773465 3773113 1.020000e-75 294.0
35 TraesCS1B01G066900 chrUn 78.750 640 86 39 2006 2622 306429316 306429928 2.110000e-102 383.0
36 TraesCS1B01G066900 chrUn 82.421 347 39 16 1665 2002 306428817 306429150 2.200000e-72 283.0
37 TraesCS1B01G066900 chr5D 84.568 162 25 0 3264 3425 221596883 221596722 1.080000e-35 161.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G066900 chr1B 51104503 51108251 3748 False 6924.0 6924 100.000000 1 3749 1 chr1B.!!$F1 3748
1 TraesCS1B01G066900 chr1B 51113048 51113944 896 False 1273.0 1273 92.556000 2173 3056 1 chr1B.!!$F2 883
2 TraesCS1B01G066900 chr1B 51135342 51136052 710 False 1116.0 1116 95.231000 3048 3749 1 chr1B.!!$F3 701
3 TraesCS1B01G066900 chr1B 51140848 51142290 1442 False 956.7 1844 88.440000 2173 3749 2 chr1B.!!$F4 1576
4 TraesCS1B01G066900 chr1A 32259220 32262986 3766 False 2143.0 3903 88.075500 1 3749 2 chr1A.!!$F2 3748
5 TraesCS1B01G066900 chr1A 32272180 32273032 852 False 335.0 359 84.873500 2909 3580 2 chr1A.!!$F3 671
6 TraesCS1B01G066900 chr1D 33637780 33641432 3652 False 1367.0 2739 87.809667 93 3749 3 chr1D.!!$F1 3656
7 TraesCS1B01G066900 chr6D 3739612 3740614 1002 False 367.5 422 82.163500 1658 2556 2 chr6D.!!$F4 898
8 TraesCS1B01G066900 chr6D 4720907 4721956 1049 True 345.0 412 81.049500 1658 2558 2 chr6D.!!$R1 900
9 TraesCS1B01G066900 chr6D 3725744 3727760 2016 False 336.0 496 81.616000 714 2758 2 chr6D.!!$F3 2044
10 TraesCS1B01G066900 chr6D 3713605 3714714 1109 False 329.5 372 80.548500 1665 2622 2 chr6D.!!$F2 957
11 TraesCS1B01G066900 chr6D 3763844 3766941 3097 False 239.5 375 77.108000 2010 2758 2 chr6D.!!$F5 748
12 TraesCS1B01G066900 chr6B 9079894 9080929 1035 False 371.0 442 81.765000 1645 2563 2 chr6B.!!$F3 918
13 TraesCS1B01G066900 chr6B 9035078 9036124 1046 False 350.5 431 81.075000 1650 2558 2 chr6B.!!$F1 908
14 TraesCS1B01G066900 chr6A 3746464 3747473 1009 True 376.0 425 82.511000 1658 2558 2 chr6A.!!$R1 900
15 TraesCS1B01G066900 chr6A 3772407 3773465 1058 True 348.5 403 81.308000 1653 2558 2 chr6A.!!$R2 905
16 TraesCS1B01G066900 chrUn 306428817 306429928 1111 False 333.0 383 80.585500 1665 2622 2 chrUn.!!$F1 957

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
339 346 0.039527 CACGCTAAACTGTTTGGGGC 60.040 55.0 25.9 19.38 37.54 5.80 F
968 1059 0.041238 TCTCCTCATCAACCCGACCT 59.959 55.0 0.0 0.00 0.00 3.85 F
2304 2769 0.341609 CCCTTCTCCCTCTCCCTCTT 59.658 60.0 0.0 0.00 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 1443 0.746659 GGGGCCTGCAACAATATGTC 59.253 55.000 0.84 0.0 0.0 3.06 R
2451 2952 0.743097 GAATGTTGGGGAGCTGCATC 59.257 55.000 7.79 0.0 0.0 3.91 R
3581 5867 1.584495 GTGGGGAAAATGCACGGAC 59.416 57.895 0.00 0.0 0.0 4.79 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
23 24 4.562082 TGCAGCATTGAATCAGGAAAAAG 58.438 39.130 0.00 0.00 0.00 2.27
30 32 3.968265 TGAATCAGGAAAAAGGGCTAGG 58.032 45.455 0.00 0.00 0.00 3.02
31 33 3.591527 TGAATCAGGAAAAAGGGCTAGGA 59.408 43.478 0.00 0.00 0.00 2.94
57 59 2.127708 AGCCCTCTTCCATCCGTAAAT 58.872 47.619 0.00 0.00 0.00 1.40
64 66 5.509840 CCTCTTCCATCCGTAAATACAGGAG 60.510 48.000 9.06 0.00 34.29 3.69
87 89 2.575993 CTGGCAGAGTCGTCCAGG 59.424 66.667 19.82 7.08 42.70 4.45
106 108 4.580580 CCAGGAACCAGGATTATTTGCTAC 59.419 45.833 0.00 0.00 0.00 3.58
251 253 2.237751 ACTGACGTGTGCGCACTTC 61.238 57.895 37.59 29.11 43.16 3.01
253 255 4.059459 GACGTGTGCGCACTTCGG 62.059 66.667 38.28 28.27 43.16 4.30
257 259 4.908687 TGTGCGCACTTCGGCACT 62.909 61.111 37.59 0.00 41.93 4.40
259 261 3.648982 TGCGCACTTCGGCACTTG 61.649 61.111 5.66 0.00 38.94 3.16
261 263 2.314647 GCGCACTTCGGCACTTGTA 61.315 57.895 0.30 0.00 38.94 2.41
262 264 1.837538 GCGCACTTCGGCACTTGTAA 61.838 55.000 0.30 0.00 38.94 2.41
263 265 0.110823 CGCACTTCGGCACTTGTAAC 60.111 55.000 0.00 0.00 33.78 2.50
264 266 0.110823 GCACTTCGGCACTTGTAACG 60.111 55.000 0.00 0.00 0.00 3.18
265 267 0.511221 CACTTCGGCACTTGTAACGG 59.489 55.000 0.00 0.00 0.00 4.44
292 299 1.135575 AGCTGGTACTTACGTACGTGC 60.136 52.381 30.25 21.01 45.52 5.34
311 318 1.633852 CTGTTTCTCAGCTGCCGCTC 61.634 60.000 9.47 0.00 45.15 5.03
312 319 2.433145 TTTCTCAGCTGCCGCTCG 60.433 61.111 9.47 0.00 45.15 5.03
313 320 3.226429 TTTCTCAGCTGCCGCTCGT 62.226 57.895 9.47 0.00 45.15 4.18
314 321 3.921767 TTCTCAGCTGCCGCTCGTG 62.922 63.158 9.47 0.00 45.15 4.35
330 337 2.914379 GTGCCTGACACGCTAAACT 58.086 52.632 0.00 0.00 40.07 2.66
331 338 0.512952 GTGCCTGACACGCTAAACTG 59.487 55.000 0.00 0.00 40.07 3.16
332 339 0.105964 TGCCTGACACGCTAAACTGT 59.894 50.000 0.00 0.00 0.00 3.55
333 340 1.226746 GCCTGACACGCTAAACTGTT 58.773 50.000 0.00 0.00 0.00 3.16
334 341 1.602377 GCCTGACACGCTAAACTGTTT 59.398 47.619 10.98 10.98 0.00 2.83
335 342 2.602217 GCCTGACACGCTAAACTGTTTG 60.602 50.000 15.69 7.10 0.00 2.93
336 343 2.032030 CCTGACACGCTAAACTGTTTGG 60.032 50.000 15.69 13.65 0.00 3.28
337 344 1.944024 TGACACGCTAAACTGTTTGGG 59.056 47.619 15.69 14.53 0.00 4.12
338 345 1.265905 GACACGCTAAACTGTTTGGGG 59.734 52.381 24.87 24.87 39.43 4.96
339 346 0.039527 CACGCTAAACTGTTTGGGGC 60.040 55.000 25.90 19.38 37.54 5.80
340 347 1.176619 ACGCTAAACTGTTTGGGGCC 61.177 55.000 25.90 0.00 37.54 5.80
341 348 1.175983 CGCTAAACTGTTTGGGGCCA 61.176 55.000 17.88 0.00 0.00 5.36
342 349 1.266178 GCTAAACTGTTTGGGGCCAT 58.734 50.000 15.69 0.00 0.00 4.40
343 350 2.452505 GCTAAACTGTTTGGGGCCATA 58.547 47.619 15.69 0.00 0.00 2.74
344 351 3.031013 GCTAAACTGTTTGGGGCCATAT 58.969 45.455 15.69 0.00 0.00 1.78
345 352 3.450817 GCTAAACTGTTTGGGGCCATATT 59.549 43.478 15.69 0.00 0.00 1.28
346 353 4.441495 GCTAAACTGTTTGGGGCCATATTC 60.441 45.833 15.69 0.00 0.00 1.75
347 354 2.159179 ACTGTTTGGGGCCATATTCC 57.841 50.000 4.39 0.00 0.00 3.01
348 355 1.360852 ACTGTTTGGGGCCATATTCCA 59.639 47.619 4.39 0.00 0.00 3.53
349 356 2.023113 ACTGTTTGGGGCCATATTCCAT 60.023 45.455 4.39 0.00 0.00 3.41
350 357 2.366266 CTGTTTGGGGCCATATTCCATG 59.634 50.000 4.39 0.00 0.00 3.66
351 358 2.292785 TGTTTGGGGCCATATTCCATGT 60.293 45.455 4.39 0.00 0.00 3.21
356 363 2.158534 GGGGCCATATTCCATGTGTGTA 60.159 50.000 4.39 0.00 0.00 2.90
357 364 2.884639 GGGCCATATTCCATGTGTGTAC 59.115 50.000 4.39 0.00 0.00 2.90
361 368 3.248363 CCATATTCCATGTGTGTACGCAG 59.752 47.826 9.91 0.00 39.97 5.18
363 370 0.953471 TTCCATGTGTGTACGCAGCC 60.953 55.000 9.91 0.00 39.97 4.85
390 398 2.468532 CGCAAGTAACCGCGTGAC 59.531 61.111 4.92 0.00 46.23 3.67
391 399 2.304401 CGCAAGTAACCGCGTGACA 61.304 57.895 4.92 0.00 46.23 3.58
395 403 1.191647 CAAGTAACCGCGTGACAACTC 59.808 52.381 4.92 0.00 0.00 3.01
409 417 6.624423 GCGTGACAACTCATAACTCCTAACTA 60.624 42.308 0.00 0.00 0.00 2.24
410 418 6.967767 CGTGACAACTCATAACTCCTAACTAG 59.032 42.308 0.00 0.00 0.00 2.57
411 419 6.752815 GTGACAACTCATAACTCCTAACTAGC 59.247 42.308 0.00 0.00 0.00 3.42
412 420 6.663953 TGACAACTCATAACTCCTAACTAGCT 59.336 38.462 0.00 0.00 0.00 3.32
414 422 8.228035 ACAACTCATAACTCCTAACTAGCTAG 57.772 38.462 19.44 19.44 0.00 3.42
460 480 1.209019 AGACGCATCTGATCCTTTGCT 59.791 47.619 8.60 0.00 32.29 3.91
471 491 0.110295 TCCTTTGCTGCTTAGTGGCA 59.890 50.000 0.00 0.00 40.15 4.92
481 501 4.487714 TGCTTAGTGGCAGCTATAACTT 57.512 40.909 0.00 0.00 38.19 2.66
482 502 5.607939 TGCTTAGTGGCAGCTATAACTTA 57.392 39.130 0.00 0.00 38.19 2.24
483 503 6.174720 TGCTTAGTGGCAGCTATAACTTAT 57.825 37.500 0.00 0.00 38.19 1.73
485 505 7.732025 TGCTTAGTGGCAGCTATAACTTATTA 58.268 34.615 0.00 0.00 38.19 0.98
486 506 7.872993 TGCTTAGTGGCAGCTATAACTTATTAG 59.127 37.037 0.00 0.00 38.19 1.73
488 508 5.552178 AGTGGCAGCTATAACTTATTAGCC 58.448 41.667 0.00 0.00 39.95 3.93
491 511 4.246458 GCAGCTATAACTTATTAGCCGCT 58.754 43.478 0.00 0.00 36.39 5.52
492 512 5.408356 GCAGCTATAACTTATTAGCCGCTA 58.592 41.667 0.00 0.00 36.39 4.26
493 513 5.288952 GCAGCTATAACTTATTAGCCGCTAC 59.711 44.000 0.00 0.00 36.39 3.58
494 514 6.387465 CAGCTATAACTTATTAGCCGCTACA 58.613 40.000 0.00 0.00 36.29 2.74
495 515 6.528423 CAGCTATAACTTATTAGCCGCTACAG 59.472 42.308 0.00 0.00 36.29 2.74
496 516 5.805994 GCTATAACTTATTAGCCGCTACAGG 59.194 44.000 0.00 0.00 0.00 4.00
498 518 2.395619 ACTTATTAGCCGCTACAGGGT 58.604 47.619 0.00 0.00 45.09 4.34
499 519 3.569491 ACTTATTAGCCGCTACAGGGTA 58.431 45.455 0.00 0.00 42.68 3.69
501 521 0.672342 ATTAGCCGCTACAGGGTACG 59.328 55.000 0.00 0.00 43.14 3.67
504 528 3.145551 CCGCTACAGGGTACGGCT 61.146 66.667 0.00 0.00 39.08 5.52
524 548 1.424638 AAGCTGGCCATACGTAGGAT 58.575 50.000 5.51 0.00 0.00 3.24
606 632 3.576648 GAGAGGAAAAGTGTACCGACAG 58.423 50.000 0.00 0.00 35.82 3.51
628 654 1.135199 GGGAGCTTTGTGTCATGCATG 60.135 52.381 21.07 21.07 0.00 4.06
669 696 1.454847 TTAATGCGGTCCCATGGCC 60.455 57.895 6.09 1.64 0.00 5.36
745 772 4.588528 AGGAATAGTTTGTGTGTGCCAATT 59.411 37.500 0.00 0.00 0.00 2.32
771 804 2.246397 CGCGATAAGGCATGTGCG 59.754 61.111 0.00 0.00 43.26 5.34
788 821 1.671054 CGCCTTTTCTTGCCTCCGA 60.671 57.895 0.00 0.00 0.00 4.55
789 822 1.639298 CGCCTTTTCTTGCCTCCGAG 61.639 60.000 0.00 0.00 0.00 4.63
790 823 1.927608 GCCTTTTCTTGCCTCCGAGC 61.928 60.000 0.00 0.00 0.00 5.03
791 824 0.322008 CCTTTTCTTGCCTCCGAGCT 60.322 55.000 0.00 0.00 0.00 4.09
793 826 1.466558 CTTTTCTTGCCTCCGAGCTTC 59.533 52.381 0.00 0.00 0.00 3.86
795 828 1.194781 TTCTTGCCTCCGAGCTTCCT 61.195 55.000 0.00 0.00 0.00 3.36
824 857 6.426646 AGCACTATATAAACCCTTCTGAGG 57.573 41.667 0.00 0.00 43.15 3.86
962 1053 3.118482 TCTCATTGCTCTCCTCATCAACC 60.118 47.826 0.00 0.00 0.00 3.77
968 1059 0.041238 TCTCCTCATCAACCCGACCT 59.959 55.000 0.00 0.00 0.00 3.85
994 1085 9.959721 TTCTCAAATTCATAGCTAGTTAAGGTT 57.040 29.630 0.00 0.00 37.13 3.50
1016 1107 1.751927 CAATGGGTGGCCTCTCTGC 60.752 63.158 3.32 0.00 0.00 4.26
1048 1139 1.602771 GCCTTTACCTTCGGCCTCT 59.397 57.895 0.00 0.00 37.86 3.69
1059 1150 4.105377 ACCTTCGGCCTCTTAGGTATACTA 59.895 45.833 11.79 0.00 39.17 1.82
1095 1186 8.972127 GTCTACCTCAATATATAGATGCTTCCA 58.028 37.037 0.00 0.00 0.00 3.53
1206 1297 5.003804 AGTGGATTCTTGTGTCAACATACC 58.996 41.667 0.00 0.00 35.83 2.73
1222 1314 2.124320 CCCATGGGGCGTTACCTG 60.124 66.667 24.53 0.00 35.35 4.00
1291 1404 6.091305 GCATGCCAAAAGTAAAAGATTTCTCC 59.909 38.462 6.36 0.00 0.00 3.71
1296 1409 7.382488 GCCAAAAGTAAAAGATTTCTCCTGTTC 59.618 37.037 0.00 0.00 0.00 3.18
1324 1437 4.982241 AGTGATCCTTCCTCTTTTGTCA 57.018 40.909 0.00 0.00 0.00 3.58
1328 1441 1.766496 TCCTTCCTCTTTTGTCACCGT 59.234 47.619 0.00 0.00 0.00 4.83
1329 1442 2.967201 TCCTTCCTCTTTTGTCACCGTA 59.033 45.455 0.00 0.00 0.00 4.02
1330 1443 3.006537 TCCTTCCTCTTTTGTCACCGTAG 59.993 47.826 0.00 0.00 0.00 3.51
1365 1479 2.103410 CCCCCGCCGTTAATTTCTG 58.897 57.895 0.00 0.00 0.00 3.02
1450 1572 2.166664 TGGTGACGGAAAACAAAAAGGG 59.833 45.455 0.00 0.00 0.00 3.95
1457 1579 5.795972 ACGGAAAACAAAAAGGGAGAAAAA 58.204 33.333 0.00 0.00 0.00 1.94
1471 1593 5.244851 AGGGAGAAAAAGGAAAGAAAGATGC 59.755 40.000 0.00 0.00 0.00 3.91
1498 1620 8.506196 AACTAAAGGGCTCCAATACATATAGA 57.494 34.615 0.00 0.00 0.00 1.98
1499 1621 8.140112 ACTAAAGGGCTCCAATACATATAGAG 57.860 38.462 0.00 0.00 0.00 2.43
1500 1622 7.735321 ACTAAAGGGCTCCAATACATATAGAGT 59.265 37.037 0.00 0.00 0.00 3.24
1501 1623 9.256228 CTAAAGGGCTCCAATACATATAGAGTA 57.744 37.037 0.00 0.00 0.00 2.59
1503 1625 5.659079 AGGGCTCCAATACATATAGAGTAGC 59.341 44.000 0.00 0.00 0.00 3.58
1584 1708 2.621668 GGCTAACTGGGGATTGAAAGCT 60.622 50.000 0.00 0.00 0.00 3.74
1637 1762 5.107453 GCTGGATAACTGTCGTATGTAATGC 60.107 44.000 0.00 0.00 0.00 3.56
1717 1847 2.272471 GCCCCACTGTAAGCCTCC 59.728 66.667 0.00 0.00 37.60 4.30
1745 1935 5.468409 GTGTTTCTCTCTCTAGCTTTGCTTT 59.532 40.000 0.00 0.00 40.44 3.51
1747 1937 6.017605 TGTTTCTCTCTCTAGCTTTGCTTTTG 60.018 38.462 0.00 0.00 40.44 2.44
1829 2033 4.615223 CGGATCTACAAGAACAAGTCGACA 60.615 45.833 19.50 0.00 0.00 4.35
1973 2177 2.619177 CGAGACCATCTACATCGTCCTT 59.381 50.000 0.00 0.00 0.00 3.36
2184 2559 3.636231 TGAGCACCCCAACTCCCG 61.636 66.667 0.00 0.00 31.65 5.14
2304 2769 0.341609 CCCTTCTCCCTCTCCCTCTT 59.658 60.000 0.00 0.00 0.00 2.85
2390 2860 4.031201 CCGTAAGCAACACAAACAAAACAG 59.969 41.667 0.00 0.00 0.00 3.16
2451 2952 2.556189 TGATCCGTTGGTGTTGATTTGG 59.444 45.455 0.00 0.00 0.00 3.28
2523 3024 0.952280 TCTACGCCCTCTATCGCAAG 59.048 55.000 0.00 0.00 0.00 4.01
2613 3120 2.653967 GCACGTCGTCAACATCGCA 61.654 57.895 0.00 0.00 0.00 5.10
2624 3131 0.602638 AACATCGCAAAGCTCGGACA 60.603 50.000 0.00 0.00 0.00 4.02
2628 3144 3.793144 GCAAAGCTCGGACAGGCG 61.793 66.667 0.00 0.00 0.00 5.52
3187 5270 8.944138 TCTATATGGGATTGTTGATAAGGACAA 58.056 33.333 0.00 0.00 0.00 3.18
3309 5582 3.660111 GTGTGGCGTGGTGGCTTC 61.660 66.667 0.00 0.00 45.14 3.86
3662 5951 3.306364 CCCTATAGCGGTGAAGATTCCTG 60.306 52.174 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.520874 GCTGATAATCCTAGCCCTTTTTCC 59.479 45.833 0.00 0.00 0.00 3.13
30 32 3.618507 CGGATGGAAGAGGGCTGATAATC 60.619 52.174 0.00 0.00 0.00 1.75
31 33 2.304180 CGGATGGAAGAGGGCTGATAAT 59.696 50.000 0.00 0.00 0.00 1.28
40 42 4.344102 TCCTGTATTTACGGATGGAAGAGG 59.656 45.833 0.00 0.00 34.49 3.69
64 66 4.154347 CGACTCTGCCAGGCTCCC 62.154 72.222 14.15 0.00 0.00 4.30
87 89 4.035208 CGTGGTAGCAAATAATCCTGGTTC 59.965 45.833 0.00 0.00 0.00 3.62
106 108 0.320247 ACTCAGCTTGCTTCTCGTGG 60.320 55.000 0.00 0.00 0.00 4.94
221 223 1.597854 CGTCAGTGCCCTTTGCTCA 60.598 57.895 0.00 0.00 42.00 4.26
251 253 3.784412 CGCCCGTTACAAGTGCCG 61.784 66.667 0.00 0.00 0.00 5.69
253 255 0.945265 TGTACGCCCGTTACAAGTGC 60.945 55.000 0.00 0.00 0.00 4.40
254 256 1.065358 CTGTACGCCCGTTACAAGTG 58.935 55.000 0.00 0.00 0.00 3.16
257 259 0.668096 CAGCTGTACGCCCGTTACAA 60.668 55.000 5.25 0.00 40.39 2.41
259 261 1.808390 CCAGCTGTACGCCCGTTAC 60.808 63.158 13.81 0.00 40.39 2.50
261 263 2.277591 TACCAGCTGTACGCCCGTT 61.278 57.895 13.81 0.00 40.39 4.44
262 264 2.677524 TACCAGCTGTACGCCCGT 60.678 61.111 13.81 3.81 40.39 5.28
263 265 2.202703 GTACCAGCTGTACGCCCG 60.203 66.667 13.81 0.00 40.44 6.13
312 319 0.512952 CAGTTTAGCGTGTCAGGCAC 59.487 55.000 19.02 8.98 44.36 5.01
313 320 0.105964 ACAGTTTAGCGTGTCAGGCA 59.894 50.000 19.02 3.30 0.00 4.75
314 321 1.226746 AACAGTTTAGCGTGTCAGGC 58.773 50.000 9.52 9.52 0.00 4.85
315 322 2.032030 CCAAACAGTTTAGCGTGTCAGG 60.032 50.000 0.00 0.00 0.00 3.86
316 323 2.032030 CCCAAACAGTTTAGCGTGTCAG 60.032 50.000 0.00 0.00 0.00 3.51
317 324 1.944024 CCCAAACAGTTTAGCGTGTCA 59.056 47.619 0.00 0.00 0.00 3.58
318 325 1.265905 CCCCAAACAGTTTAGCGTGTC 59.734 52.381 0.00 0.00 0.00 3.67
319 326 1.314730 CCCCAAACAGTTTAGCGTGT 58.685 50.000 0.00 0.00 0.00 4.49
320 327 0.039527 GCCCCAAACAGTTTAGCGTG 60.040 55.000 0.00 0.00 0.00 5.34
321 328 1.176619 GGCCCCAAACAGTTTAGCGT 61.177 55.000 0.00 0.00 0.00 5.07
322 329 1.175983 TGGCCCCAAACAGTTTAGCG 61.176 55.000 0.00 0.00 0.00 4.26
323 330 1.266178 ATGGCCCCAAACAGTTTAGC 58.734 50.000 0.00 2.50 0.00 3.09
324 331 4.099419 GGAATATGGCCCCAAACAGTTTAG 59.901 45.833 0.00 0.00 0.00 1.85
325 332 4.027437 GGAATATGGCCCCAAACAGTTTA 58.973 43.478 0.00 0.00 0.00 2.01
326 333 2.837591 GGAATATGGCCCCAAACAGTTT 59.162 45.455 0.00 0.00 0.00 2.66
327 334 2.225496 TGGAATATGGCCCCAAACAGTT 60.225 45.455 0.00 0.00 0.00 3.16
328 335 1.360852 TGGAATATGGCCCCAAACAGT 59.639 47.619 0.00 0.00 0.00 3.55
329 336 2.157640 TGGAATATGGCCCCAAACAG 57.842 50.000 0.00 0.00 0.00 3.16
330 337 2.292785 ACATGGAATATGGCCCCAAACA 60.293 45.455 0.00 0.00 33.15 2.83
331 338 2.102925 CACATGGAATATGGCCCCAAAC 59.897 50.000 0.00 0.00 33.15 2.93
332 339 2.292785 ACACATGGAATATGGCCCCAAA 60.293 45.455 0.00 0.00 33.15 3.28
333 340 1.290431 ACACATGGAATATGGCCCCAA 59.710 47.619 0.00 0.00 33.15 4.12
334 341 0.932955 ACACATGGAATATGGCCCCA 59.067 50.000 0.00 0.00 0.00 4.96
335 342 1.331214 CACACATGGAATATGGCCCC 58.669 55.000 0.00 0.00 0.00 5.80
336 343 2.071778 ACACACATGGAATATGGCCC 57.928 50.000 0.00 0.00 0.00 5.80
337 344 2.548057 CGTACACACATGGAATATGGCC 59.452 50.000 0.00 0.00 0.00 5.36
338 345 2.032030 GCGTACACACATGGAATATGGC 60.032 50.000 0.00 0.00 0.00 4.40
339 346 3.202097 TGCGTACACACATGGAATATGG 58.798 45.455 0.00 0.00 0.00 2.74
340 347 3.303329 GCTGCGTACACACATGGAATATG 60.303 47.826 0.00 0.00 0.00 1.78
341 348 2.872245 GCTGCGTACACACATGGAATAT 59.128 45.455 0.00 0.00 0.00 1.28
342 349 2.276201 GCTGCGTACACACATGGAATA 58.724 47.619 0.00 0.00 0.00 1.75
343 350 1.086696 GCTGCGTACACACATGGAAT 58.913 50.000 0.00 0.00 0.00 3.01
344 351 0.953471 GGCTGCGTACACACATGGAA 60.953 55.000 0.00 0.00 0.00 3.53
345 352 1.375396 GGCTGCGTACACACATGGA 60.375 57.895 0.00 0.00 0.00 3.41
346 353 2.739704 CGGCTGCGTACACACATGG 61.740 63.158 0.00 0.00 0.00 3.66
347 354 2.027073 ACGGCTGCGTACACACATG 61.027 57.895 0.00 0.00 0.00 3.21
348 355 2.027073 CACGGCTGCGTACACACAT 61.027 57.895 0.00 0.00 0.00 3.21
349 356 2.660224 CACGGCTGCGTACACACA 60.660 61.111 0.00 0.00 0.00 3.72
350 357 4.072088 GCACGGCTGCGTACACAC 62.072 66.667 0.00 0.00 32.44 3.82
363 370 0.991770 GTTACTTGCGCTGTTGCACG 60.992 55.000 9.73 0.00 46.25 5.34
389 397 8.053963 TCTAGCTAGTTAGGAGTTATGAGTTGT 58.946 37.037 20.10 0.00 0.00 3.32
390 398 8.453238 TCTAGCTAGTTAGGAGTTATGAGTTG 57.547 38.462 20.10 0.00 0.00 3.16
391 399 8.276477 ACTCTAGCTAGTTAGGAGTTATGAGTT 58.724 37.037 20.10 0.00 0.00 3.01
395 403 7.502895 TCCAACTCTAGCTAGTTAGGAGTTATG 59.497 40.741 20.10 14.66 37.61 1.90
409 417 1.896465 GACCAGTGTCCAACTCTAGCT 59.104 52.381 0.00 0.00 36.83 3.32
410 418 1.896465 AGACCAGTGTCCAACTCTAGC 59.104 52.381 0.00 0.00 42.81 3.42
411 419 3.157881 TGAGACCAGTGTCCAACTCTAG 58.842 50.000 0.00 0.00 42.81 2.43
412 420 3.157881 CTGAGACCAGTGTCCAACTCTA 58.842 50.000 0.00 0.00 42.81 2.43
414 422 2.447244 CTGAGACCAGTGTCCAACTC 57.553 55.000 0.00 0.00 42.81 3.01
441 457 1.329906 CAGCAAAGGATCAGATGCGTC 59.670 52.381 0.00 0.00 43.39 5.19
448 464 2.681848 CCACTAAGCAGCAAAGGATCAG 59.318 50.000 0.00 0.00 0.00 2.90
460 480 4.487714 AAGTTATAGCTGCCACTAAGCA 57.512 40.909 0.00 0.00 43.37 3.91
471 491 6.350277 CCTGTAGCGGCTAATAAGTTATAGCT 60.350 42.308 11.98 14.27 35.97 3.32
474 494 5.776716 ACCCTGTAGCGGCTAATAAGTTATA 59.223 40.000 11.98 0.00 0.00 0.98
475 495 4.591924 ACCCTGTAGCGGCTAATAAGTTAT 59.408 41.667 11.98 0.00 0.00 1.89
476 496 3.962718 ACCCTGTAGCGGCTAATAAGTTA 59.037 43.478 11.98 0.00 0.00 2.24
477 497 2.770232 ACCCTGTAGCGGCTAATAAGTT 59.230 45.455 11.98 0.00 0.00 2.66
478 498 2.395619 ACCCTGTAGCGGCTAATAAGT 58.604 47.619 11.98 4.85 0.00 2.24
479 499 3.611057 CGTACCCTGTAGCGGCTAATAAG 60.611 52.174 11.98 9.58 0.00 1.73
481 501 1.881973 CGTACCCTGTAGCGGCTAATA 59.118 52.381 11.98 3.24 0.00 0.98
482 502 0.672342 CGTACCCTGTAGCGGCTAAT 59.328 55.000 11.98 0.00 0.00 1.73
483 503 1.386525 CCGTACCCTGTAGCGGCTAA 61.387 60.000 11.98 1.78 37.69 3.09
485 505 3.145551 CCGTACCCTGTAGCGGCT 61.146 66.667 7.98 7.98 37.69 5.52
488 508 0.030369 CTTAGCCGTACCCTGTAGCG 59.970 60.000 0.00 0.00 0.00 4.26
491 511 1.108776 CAGCTTAGCCGTACCCTGTA 58.891 55.000 0.00 0.00 0.00 2.74
492 512 1.614241 CCAGCTTAGCCGTACCCTGT 61.614 60.000 0.00 0.00 0.00 4.00
493 513 1.144057 CCAGCTTAGCCGTACCCTG 59.856 63.158 0.00 0.00 0.00 4.45
494 514 2.732619 GCCAGCTTAGCCGTACCCT 61.733 63.158 0.00 0.00 0.00 4.34
495 515 2.203029 GCCAGCTTAGCCGTACCC 60.203 66.667 0.00 0.00 0.00 3.69
496 516 2.203029 GGCCAGCTTAGCCGTACC 60.203 66.667 8.74 0.00 41.41 3.34
504 528 2.076207 TCCTACGTATGGCCAGCTTA 57.924 50.000 13.05 3.87 0.00 3.09
514 538 8.964772 ACACTTCAAGTTAACTATCCTACGTAT 58.035 33.333 8.92 0.00 0.00 3.06
544 568 5.654650 TGCGTGGAATTATTAGGGAAATTGT 59.345 36.000 0.00 0.00 0.00 2.71
606 632 0.807496 GCATGACACAAAGCTCCCTC 59.193 55.000 0.00 0.00 0.00 4.30
628 654 6.690194 ACAAAGGACAAGATAATCATCAGC 57.310 37.500 0.00 0.00 33.21 4.26
669 696 1.247567 GCATGGATAATCCCAACCCG 58.752 55.000 0.00 0.00 40.04 5.28
670 697 2.380064 TGCATGGATAATCCCAACCC 57.620 50.000 0.00 0.00 40.04 4.11
710 737 7.830697 ACACAAACTATTCCTGATCAATCATCA 59.169 33.333 0.00 0.00 39.39 3.07
711 738 8.127327 CACACAAACTATTCCTGATCAATCATC 58.873 37.037 0.00 0.00 36.02 2.92
745 772 0.457853 GCCTTATCGCGTGTGACTCA 60.458 55.000 5.77 0.00 0.00 3.41
771 804 1.927608 GCTCGGAGGCAAGAAAAGGC 61.928 60.000 7.20 0.00 0.00 4.35
788 821 7.857404 TTATATAGTGCTAGGAAAGGAAGCT 57.143 36.000 0.00 0.00 37.16 3.74
789 822 7.388224 GGTTTATATAGTGCTAGGAAAGGAAGC 59.612 40.741 0.00 0.00 36.77 3.86
790 823 7.878644 GGGTTTATATAGTGCTAGGAAAGGAAG 59.121 40.741 0.00 0.00 0.00 3.46
791 824 7.571357 AGGGTTTATATAGTGCTAGGAAAGGAA 59.429 37.037 0.00 0.00 0.00 3.36
793 826 7.317722 AGGGTTTATATAGTGCTAGGAAAGG 57.682 40.000 0.00 0.00 0.00 3.11
795 828 8.429641 CAGAAGGGTTTATATAGTGCTAGGAAA 58.570 37.037 0.00 0.00 0.00 3.13
854 887 0.249114 GCCAGCTTACTACTCGAGGC 60.249 60.000 18.41 9.21 0.00 4.70
962 1053 4.446371 AGCTATGAATTTGAGAAGGTCGG 58.554 43.478 0.00 0.00 0.00 4.79
968 1059 9.959721 AACCTTAACTAGCTATGAATTTGAGAA 57.040 29.630 0.00 0.00 0.00 2.87
994 1085 0.899717 GAGAGGCCACCCATTGCAAA 60.900 55.000 5.01 0.00 0.00 3.68
1107 1198 8.766476 TGGGCAATGAGATTAAAAATATGGAAA 58.234 29.630 0.00 0.00 0.00 3.13
1146 1237 7.092716 GCAAACCATATTGAACAAAGATGAGT 58.907 34.615 11.67 7.28 31.84 3.41
1147 1238 6.532657 GGCAAACCATATTGAACAAAGATGAG 59.467 38.462 11.67 6.87 35.26 2.90
1182 1273 5.106555 GGTATGTTGACACAAGAATCCACTG 60.107 44.000 0.00 0.00 36.16 3.66
1206 1297 2.828549 GCAGGTAACGCCCCATGG 60.829 66.667 4.14 4.14 46.39 3.66
1222 1314 3.861840 TGCTCAGAATACTACCACAAGC 58.138 45.455 0.00 0.00 0.00 4.01
1291 1404 1.743958 AGGATCACTACGTCGGAACAG 59.256 52.381 0.00 0.00 0.00 3.16
1296 1409 1.334243 GAGGAAGGATCACTACGTCGG 59.666 57.143 0.00 0.00 0.00 4.79
1324 1437 3.531538 CCTGCAACAATATGTCTACGGT 58.468 45.455 0.00 0.00 0.00 4.83
1328 1441 2.422803 GGGGCCTGCAACAATATGTCTA 60.423 50.000 0.84 0.00 0.00 2.59
1329 1442 1.686115 GGGGCCTGCAACAATATGTCT 60.686 52.381 0.84 0.00 0.00 3.41
1330 1443 0.746659 GGGGCCTGCAACAATATGTC 59.253 55.000 0.84 0.00 0.00 3.06
1438 1560 8.160765 TCTTTCCTTTTTCTCCCTTTTTGTTTT 58.839 29.630 0.00 0.00 0.00 2.43
1450 1572 7.708322 AGTTTGCATCTTTCTTTCCTTTTTCTC 59.292 33.333 0.00 0.00 0.00 2.87
1457 1579 6.015095 CCCTTTAGTTTGCATCTTTCTTTCCT 60.015 38.462 0.00 0.00 0.00 3.36
1471 1593 7.823745 ATATGTATTGGAGCCCTTTAGTTTG 57.176 36.000 0.00 0.00 0.00 2.93
1498 1620 5.109903 CGCTACACCATAAGAAAAGCTACT 58.890 41.667 0.00 0.00 0.00 2.57
1499 1621 4.868734 ACGCTACACCATAAGAAAAGCTAC 59.131 41.667 0.00 0.00 0.00 3.58
1500 1622 4.868171 CACGCTACACCATAAGAAAAGCTA 59.132 41.667 0.00 0.00 0.00 3.32
1501 1623 3.684788 CACGCTACACCATAAGAAAAGCT 59.315 43.478 0.00 0.00 0.00 3.74
1503 1625 4.451096 ACACACGCTACACCATAAGAAAAG 59.549 41.667 0.00 0.00 0.00 2.27
1584 1708 2.158769 AGGAGATATGGATGTTGCGCAA 60.159 45.455 21.02 21.02 0.00 4.85
1717 1847 5.554822 AAGCTAGAGAGAGAAACACGTAG 57.445 43.478 0.00 0.00 0.00 3.51
1745 1935 3.071457 TCAGATGAGAGACCAACAAGCAA 59.929 43.478 0.00 0.00 0.00 3.91
1747 1937 2.999355 GTCAGATGAGAGACCAACAAGC 59.001 50.000 0.00 0.00 0.00 4.01
1748 1938 4.244066 CAGTCAGATGAGAGACCAACAAG 58.756 47.826 0.00 0.00 35.38 3.16
1750 1940 2.028658 GCAGTCAGATGAGAGACCAACA 60.029 50.000 0.00 0.00 35.38 3.33
1751 1941 2.615869 GCAGTCAGATGAGAGACCAAC 58.384 52.381 0.00 0.00 35.38 3.77
1753 1943 0.813821 CGCAGTCAGATGAGAGACCA 59.186 55.000 0.00 0.00 35.38 4.02
1754 1944 0.814457 ACGCAGTCAGATGAGAGACC 59.186 55.000 0.00 0.00 29.74 3.85
1755 1945 1.906757 CACGCAGTCAGATGAGAGAC 58.093 55.000 0.00 0.00 41.61 3.36
1829 2033 2.526873 ACCGACTGGAAGCCCTGT 60.527 61.111 0.00 0.00 45.76 4.00
2184 2559 3.125146 TCAAGATAAATGCAGACACACGC 59.875 43.478 0.00 0.00 0.00 5.34
2390 2860 4.621886 AGCGTCGAAAGTAGAGTGAAAATC 59.378 41.667 0.00 0.00 0.00 2.17
2451 2952 0.743097 GAATGTTGGGGAGCTGCATC 59.257 55.000 7.79 0.00 0.00 3.91
2613 3120 3.591254 GACCGCCTGTCCGAGCTTT 62.591 63.158 0.00 0.00 38.09 3.51
2982 3665 8.762426 GCTGGTTCTTTATAATAAGACCGTTAG 58.238 37.037 0.00 0.00 34.04 2.34
3187 5270 5.421277 TCCACGAAATAATAATGTCACGGT 58.579 37.500 0.00 0.00 0.00 4.83
3225 5319 7.736447 AGTTAGATCCGGAATCATCAATTTC 57.264 36.000 9.01 0.00 36.79 2.17
3309 5582 6.345723 GGCAAAAACATACATCAAACAACTCG 60.346 38.462 0.00 0.00 0.00 4.18
3389 5662 3.372440 AAGAGCTTGAAATCCCCGATT 57.628 42.857 0.00 0.00 33.25 3.34
3581 5867 1.584495 GTGGGGAAAATGCACGGAC 59.416 57.895 0.00 0.00 0.00 4.79
3662 5951 7.463383 CGATTGTTATTGAAGCACTGAGTCTAC 60.463 40.741 0.00 0.00 0.00 2.59
3703 6001 3.837213 TTGCTCATGCTTTGCTAAGTC 57.163 42.857 9.64 3.09 40.48 3.01
3704 6002 3.508793 ACATTGCTCATGCTTTGCTAAGT 59.491 39.130 9.64 0.00 40.48 2.24


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

AutoCloner maintained by Alex Coulton.