Multiple sequence alignment - TraesCS7B01G433900

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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 TraesCS7B01G433900 chr7B 100.000 4664 0 0 1 4664 701207249 701202586 0.000000e+00 8613.0
1 TraesCS7B01G433900 chr7D 91.759 2718 130 37 2012 4664 611742443 611739755 0.000000e+00 3692.0
2 TraesCS7B01G433900 chr7D 88.796 2026 124 34 15 2015 611744552 611742605 0.000000e+00 2388.0
3 TraesCS7B01G433900 chr7D 82.258 434 44 10 1303 1736 129955206 129954806 1.240000e-90 344.0
4 TraesCS7B01G433900 chr7D 94.000 50 3 0 2012 2061 611742527 611742478 5.000000e-10 76.8
5 TraesCS7B01G433900 chr7A 92.091 1631 102 16 747 2364 701667919 701666303 0.000000e+00 2272.0
6 TraesCS7B01G433900 chr7A 96.143 1115 23 5 2366 3465 701666267 701665158 0.000000e+00 1803.0
7 TraesCS7B01G433900 chr7A 90.688 945 50 19 3464 4397 701665054 701664137 0.000000e+00 1223.0
8 TraesCS7B01G433900 chr7A 88.467 685 57 7 919 1601 162747452 162746788 0.000000e+00 808.0
9 TraesCS7B01G433900 chr7A 87.464 686 59 14 919 1601 14648146 14647485 0.000000e+00 765.0
10 TraesCS7B01G433900 chr7A 87.246 541 58 5 4 540 701673285 701672752 1.440000e-169 606.0
11 TraesCS7B01G433900 chr7A 91.416 233 11 4 4430 4662 701664151 701663928 1.260000e-80 311.0
12 TraesCS7B01G433900 chr7A 91.975 162 13 0 1538 1699 58682578 58682739 1.310000e-55 228.0
13 TraesCS7B01G433900 chr7A 96.610 59 0 1 650 706 701672309 701672251 3.840000e-16 97.1
14 TraesCS7B01G433900 chr2A 88.175 685 59 10 919 1601 776739251 776738587 0.000000e+00 797.0
15 TraesCS7B01G433900 chr2A 87.007 685 67 7 919 1601 272399632 272398968 0.000000e+00 752.0
16 TraesCS7B01G433900 chr2A 88.296 581 41 12 919 1497 549132189 549131634 0.000000e+00 671.0
17 TraesCS7B01G433900 chr2A 90.741 162 15 0 1538 1699 92990733 92990894 2.830000e-52 217.0
18 TraesCS7B01G433900 chr2A 91.195 159 14 0 1541 1699 549130084 549129926 2.830000e-52 217.0
19 TraesCS7B01G433900 chr5A 86.861 685 63 9 919 1601 233503271 233502612 0.000000e+00 741.0
20 TraesCS7B01G433900 chr3A 87.263 581 47 12 919 1497 114914863 114914308 5.090000e-179 638.0
21 TraesCS7B01G433900 chr3A 92.453 159 12 0 1541 1699 114912756 114912598 1.310000e-55 228.0
22 TraesCS7B01G433900 chr1A 86.747 581 50 11 919 1497 439587763 439588318 5.130000e-174 621.0
23 TraesCS7B01G433900 chr1A 93.082 159 11 0 1541 1699 264358612 264358454 2.810000e-57 233.0
24 TraesCS7B01G433900 chr1A 91.358 162 14 0 1538 1699 439589866 439590027 6.070000e-54 222.0
25 TraesCS7B01G433900 chr4A 91.358 162 14 0 1538 1699 130611900 130612061 6.070000e-54 222.0


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 TraesCS7B01G433900 chr7B 701202586 701207249 4663 True 8613.000000 8613 100.000000 1 4664 1 chr7B.!!$R1 4663
1 TraesCS7B01G433900 chr7D 611739755 611744552 4797 True 2052.266667 3692 91.518333 15 4664 3 chr7D.!!$R2 4649
2 TraesCS7B01G433900 chr7A 701663928 701667919 3991 True 1402.250000 2272 92.584500 747 4662 4 chr7A.!!$R3 3915
3 TraesCS7B01G433900 chr7A 162746788 162747452 664 True 808.000000 808 88.467000 919 1601 1 chr7A.!!$R2 682
4 TraesCS7B01G433900 chr7A 14647485 14648146 661 True 765.000000 765 87.464000 919 1601 1 chr7A.!!$R1 682
5 TraesCS7B01G433900 chr7A 701672251 701673285 1034 True 351.550000 606 91.928000 4 706 2 chr7A.!!$R4 702
6 TraesCS7B01G433900 chr2A 776738587 776739251 664 True 797.000000 797 88.175000 919 1601 1 chr2A.!!$R2 682
7 TraesCS7B01G433900 chr2A 272398968 272399632 664 True 752.000000 752 87.007000 919 1601 1 chr2A.!!$R1 682
8 TraesCS7B01G433900 chr2A 549129926 549132189 2263 True 444.000000 671 89.745500 919 1699 2 chr2A.!!$R3 780
9 TraesCS7B01G433900 chr5A 233502612 233503271 659 True 741.000000 741 86.861000 919 1601 1 chr5A.!!$R1 682
10 TraesCS7B01G433900 chr3A 114912598 114914863 2265 True 433.000000 638 89.858000 919 1699 2 chr3A.!!$R1 780
11 TraesCS7B01G433900 chr1A 439587763 439590027 2264 False 421.500000 621 89.052500 919 1699 2 chr1A.!!$F1 780

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
723 1097 0.037697 TACAGTCACACGCATCACCC 60.038 55.000 0.00 0.00 0.00 4.61 F
1352 1732 1.075536 GGTGGAATTTGTCTCTGGGGT 59.924 52.381 0.00 0.00 0.00 4.95 F
2420 4524 0.665369 GTTGGCAGCTCATGTGCAAC 60.665 55.000 20.92 12.49 43.12 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 3502 0.818296 TCTCTCTACAAGAAGCCGCC 59.182 55.0 0.00 0.0 32.23 6.13 R
2761 4871 0.659957 CAAGCAGCGAGGAAATAGGC 59.340 55.0 0.00 0.0 0.00 3.93 R
4119 6373 1.286248 AGAGGGCCAAATTCGTACCT 58.714 50.0 6.18 0.0 0.00 3.08 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
29 30 7.104290 TGTATCCAGATCGATAGTCGTAGAAT 58.896 38.462 0.00 0.00 41.35 2.40
69 70 3.545703 CCTTTGGCTTTCCGATCATAGT 58.454 45.455 0.00 0.00 34.14 2.12
79 80 4.655762 TCCGATCATAGTGTTTCTCCTG 57.344 45.455 0.00 0.00 0.00 3.86
82 83 4.806247 CCGATCATAGTGTTTCTCCTGTTC 59.194 45.833 0.00 0.00 0.00 3.18
98 99 3.199677 CTGTTCACCGTAAAACACCTCA 58.800 45.455 0.00 0.00 32.28 3.86
103 104 2.044758 ACCGTAAAACACCTCACTCCT 58.955 47.619 0.00 0.00 0.00 3.69
119 120 2.561037 CCTTGTGGGTTCCAACGCC 61.561 63.158 4.23 0.00 40.74 5.68
180 181 3.846588 ACCTTGAGTGATATGAACCTGGT 59.153 43.478 0.00 0.00 0.00 4.00
188 189 4.156008 GTGATATGAACCTGGTGACCAAAC 59.844 45.833 5.53 0.00 30.80 2.93
207 208 5.509501 CCAAACAGGCAGTGATTACAAACAT 60.510 40.000 0.00 0.00 0.00 2.71
218 219 7.275560 CAGTGATTACAAACATCGAGTACATCA 59.724 37.037 0.00 0.00 0.00 3.07
245 246 6.870965 CCCAAATTTGTTAAAATGATGGACGA 59.129 34.615 16.73 0.00 41.63 4.20
248 249 7.883229 AATTTGTTAAAATGATGGACGAACC 57.117 32.000 0.00 0.00 36.11 3.62
263 277 1.870580 CGAACCTGTTGTGGAGCGTTA 60.871 52.381 0.00 0.00 0.00 3.18
269 283 0.958382 GTTGTGGAGCGTTATGGCCA 60.958 55.000 8.56 8.56 0.00 5.36
317 335 1.651240 GAGGAATGTCGTCGGACGGA 61.651 60.000 28.07 16.56 46.49 4.69
335 353 2.662637 CGGAAACTCATTACGCACGTAA 59.337 45.455 16.99 16.99 38.80 3.18
383 401 0.835971 TTACCAGGCAGAGCAGGACA 60.836 55.000 6.71 0.00 0.00 4.02
421 439 0.250510 GAGCCCCGGATCCTCATTTC 60.251 60.000 10.75 0.00 0.00 2.17
442 460 4.555709 AGAACAACGGCGCCACCA 62.556 61.111 28.98 0.00 39.03 4.17
443 461 3.587933 GAACAACGGCGCCACCAA 61.588 61.111 28.98 0.00 39.03 3.67
444 462 3.536498 GAACAACGGCGCCACCAAG 62.536 63.158 28.98 12.44 39.03 3.61
445 463 4.868116 ACAACGGCGCCACCAAGT 62.868 61.111 28.98 13.21 39.03 3.16
446 464 3.591835 CAACGGCGCCACCAAGTT 61.592 61.111 28.98 18.85 39.03 2.66
447 465 3.591835 AACGGCGCCACCAAGTTG 61.592 61.111 28.98 9.93 39.03 3.16
458 476 2.727544 CAAGTTGCCAACACCCCG 59.272 61.111 10.69 0.00 0.00 5.73
461 479 0.106619 AAGTTGCCAACACCCCGTTA 60.107 50.000 10.69 0.00 35.52 3.18
471 490 1.214923 ACACCCCGTTACCCTGAAAAA 59.785 47.619 0.00 0.00 0.00 1.94
478 497 4.155280 CCCGTTACCCTGAAAAATGTACTG 59.845 45.833 0.00 0.00 0.00 2.74
479 498 4.155280 CCGTTACCCTGAAAAATGTACTGG 59.845 45.833 0.00 0.00 0.00 4.00
485 504 4.697352 CCCTGAAAAATGTACTGGACAGAG 59.303 45.833 6.29 0.00 42.79 3.35
495 514 2.329267 ACTGGACAGAGGATGTGTGAA 58.671 47.619 6.29 0.00 45.61 3.18
504 523 1.002624 GATGTGTGAAAGGGGCGGA 60.003 57.895 0.00 0.00 0.00 5.54
572 591 0.390735 GGATAAACACGAGGTGGCGT 60.391 55.000 0.42 0.00 46.88 5.68
645 1017 1.067250 GCAAAGCCGTTGGAAAGCA 59.933 52.632 0.35 0.00 37.73 3.91
706 1080 2.202531 GCTCGTTCCCGTCGGTAC 60.203 66.667 11.06 7.10 35.01 3.34
707 1081 2.981560 GCTCGTTCCCGTCGGTACA 61.982 63.158 11.06 0.00 35.01 2.90
708 1082 1.136147 CTCGTTCCCGTCGGTACAG 59.864 63.158 11.06 5.20 35.01 2.74
709 1083 1.580845 CTCGTTCCCGTCGGTACAGT 61.581 60.000 11.06 0.00 35.01 3.55
710 1084 1.154150 CGTTCCCGTCGGTACAGTC 60.154 63.158 11.06 0.00 30.03 3.51
711 1085 1.855213 CGTTCCCGTCGGTACAGTCA 61.855 60.000 11.06 0.00 30.03 3.41
712 1086 0.387750 GTTCCCGTCGGTACAGTCAC 60.388 60.000 11.06 0.00 30.03 3.67
713 1087 0.822944 TTCCCGTCGGTACAGTCACA 60.823 55.000 11.06 0.00 0.00 3.58
714 1088 1.080974 CCCGTCGGTACAGTCACAC 60.081 63.158 11.06 0.00 0.00 3.82
715 1089 1.441515 CCGTCGGTACAGTCACACG 60.442 63.158 2.08 0.00 0.00 4.49
716 1090 2.078914 CGTCGGTACAGTCACACGC 61.079 63.158 0.00 0.00 0.00 5.34
717 1091 1.008194 GTCGGTACAGTCACACGCA 60.008 57.895 0.00 0.00 0.00 5.24
718 1092 0.388134 GTCGGTACAGTCACACGCAT 60.388 55.000 0.00 0.00 0.00 4.73
719 1093 0.109458 TCGGTACAGTCACACGCATC 60.109 55.000 0.00 0.00 0.00 3.91
720 1094 0.388006 CGGTACAGTCACACGCATCA 60.388 55.000 0.00 0.00 0.00 3.07
721 1095 1.068474 GGTACAGTCACACGCATCAC 58.932 55.000 0.00 0.00 0.00 3.06
722 1096 1.068474 GTACAGTCACACGCATCACC 58.932 55.000 0.00 0.00 0.00 4.02
723 1097 0.037697 TACAGTCACACGCATCACCC 60.038 55.000 0.00 0.00 0.00 4.61
724 1098 2.048222 AGTCACACGCATCACCCG 60.048 61.111 0.00 0.00 0.00 5.28
725 1099 2.357034 GTCACACGCATCACCCGT 60.357 61.111 0.00 0.00 39.91 5.28
793 1167 2.510691 CCCGCGCGGTACATTCTT 60.511 61.111 43.12 0.00 0.00 2.52
894 1268 2.527951 CTTCCTCAGAAGCCCACGGG 62.528 65.000 0.00 0.00 42.97 5.28
935 1309 2.752238 AGCAGACGGAGGAGACGG 60.752 66.667 0.00 0.00 35.23 4.79
937 1311 3.141488 CAGACGGAGGAGACGGGG 61.141 72.222 0.00 0.00 35.23 5.73
938 1312 3.336568 AGACGGAGGAGACGGGGA 61.337 66.667 0.00 0.00 35.23 4.81
939 1313 2.829458 GACGGAGGAGACGGGGAG 60.829 72.222 0.00 0.00 35.23 4.30
943 1317 1.306970 GGAGGAGACGGGGAGAAGA 59.693 63.158 0.00 0.00 0.00 2.87
1191 1571 2.721167 TTGCAGATCCGTCGAGGGG 61.721 63.158 23.21 10.17 41.52 4.79
1330 1710 2.115291 GGCTCGAACCTGGCCAATC 61.115 63.158 7.01 4.73 44.69 2.67
1341 1721 2.181975 CTGGCCAATCTGGTGGAATTT 58.818 47.619 7.01 0.00 41.65 1.82
1352 1732 1.075536 GGTGGAATTTGTCTCTGGGGT 59.924 52.381 0.00 0.00 0.00 4.95
1354 1734 1.354368 TGGAATTTGTCTCTGGGGTCC 59.646 52.381 0.00 0.00 0.00 4.46
1438 1822 2.023741 CATGCATCGCCGTTGCTC 59.976 61.111 19.58 0.00 40.77 4.26
1439 1823 3.204827 ATGCATCGCCGTTGCTCC 61.205 61.111 19.58 0.00 40.77 4.70
1476 1864 4.337555 AGGCACATCACAATAGCTGATTTC 59.662 41.667 0.00 0.00 0.00 2.17
1499 1887 6.860080 TCATCCAGCTTCATCTTTGAAATTC 58.140 36.000 0.00 0.00 41.22 2.17
1539 3435 3.314080 TGCTGTGGCTACTGTTTGTTTAC 59.686 43.478 8.81 0.00 39.59 2.01
1573 3469 6.017440 TCCTTTTGTTCTGAGTATCAAAACCG 60.017 38.462 0.00 0.00 45.23 4.44
1602 3502 7.515215 CGACAGATGTAGGAACATGTTTATTCG 60.515 40.741 13.36 5.31 46.49 3.34
1604 3504 5.527582 AGATGTAGGAACATGTTTATTCGGC 59.472 40.000 13.36 0.00 46.49 5.54
1612 3512 1.816074 TGTTTATTCGGCGGCTTCTT 58.184 45.000 7.21 0.00 0.00 2.52
1773 3673 3.090952 TGAAAACGCACAAAGGAATGG 57.909 42.857 0.00 0.00 0.00 3.16
1804 3704 5.682943 TGACGTTTCTTTGGAAGTATTGG 57.317 39.130 0.00 0.00 32.61 3.16
1838 3738 6.805713 AGCATTTTTAGCATGTGTATAACCC 58.194 36.000 0.00 0.00 0.00 4.11
1953 3857 4.639310 ACTTCAGATCTTTGTCATGCATCC 59.361 41.667 0.00 0.00 0.00 3.51
2010 3914 4.009675 TCAATGTTTGTGGAGCTGATACC 58.990 43.478 0.00 0.00 0.00 2.73
2050 4119 2.958355 AGGTCCACCTGATGTTGTTTTG 59.042 45.455 0.00 0.00 46.55 2.44
2215 4285 5.777526 ACCATGCCCTTCCAAATTATTTT 57.222 34.783 0.00 0.00 0.00 1.82
2234 4304 4.844349 TTTGACTTCTCTTATGAGGGGG 57.156 45.455 5.84 0.40 40.58 5.40
2256 4326 8.121305 GGGGGAATTGCTTTTATTTGAATTTT 57.879 30.769 0.00 0.00 0.00 1.82
2257 4327 8.028354 GGGGGAATTGCTTTTATTTGAATTTTG 58.972 33.333 0.00 0.00 0.00 2.44
2296 4366 9.491675 TGTTCTTTCATGCATCATTGTTTTAAT 57.508 25.926 0.00 0.00 0.00 1.40
2357 4427 6.442513 AAAAGAAATAAGAGAATCCTGCGG 57.557 37.500 0.00 0.00 33.66 5.69
2358 4428 5.359194 AAGAAATAAGAGAATCCTGCGGA 57.641 39.130 0.00 0.00 33.66 5.54
2380 4484 7.576236 CGGAGAGTGCAATTATAGTTTATTGG 58.424 38.462 0.00 0.00 33.41 3.16
2420 4524 0.665369 GTTGGCAGCTCATGTGCAAC 60.665 55.000 20.92 12.49 43.12 4.17
2432 4536 2.162319 TGTGCAACGTTAGCAGATCA 57.838 45.000 20.60 14.39 43.63 2.92
2450 4554 6.206243 GCAGATCATCCTGTGCTTATTGTTAT 59.794 38.462 0.00 0.00 36.57 1.89
2632 4737 3.513912 TGTGATAGGTTCGAGTGGACATT 59.486 43.478 0.00 0.00 0.00 2.71
2647 4752 2.173569 GGACATTAGTGCCAGGAATCCT 59.826 50.000 0.00 0.00 0.00 3.24
2954 5064 3.780294 TGGAGAACATAGGTAAGTGGCAT 59.220 43.478 0.00 0.00 0.00 4.40
3127 5253 5.695363 TGTTGTGCATGTTCCATTTGTTATG 59.305 36.000 0.00 0.00 0.00 1.90
3230 5356 4.154015 TGTGCTGATTTGTATGTAGTGTGC 59.846 41.667 0.00 0.00 0.00 4.57
3287 5413 1.882623 AGTACTTGCCTTTTCAGCTGC 59.117 47.619 9.47 0.00 0.00 5.25
3298 5424 4.808364 CCTTTTCAGCTGCTCTATCTACAC 59.192 45.833 9.47 0.00 0.00 2.90
3381 5507 2.185004 ATGGTTTTGTAGCAGCGACT 57.815 45.000 7.22 0.00 37.73 4.18
3511 5743 4.884668 TTCTTCAACGATACTTCCTGGT 57.115 40.909 0.00 0.00 0.00 4.00
3536 5768 3.993736 TGATTTTCTGTCGATTTCGCTCA 59.006 39.130 0.00 0.00 39.60 4.26
3579 5811 7.609532 CCTGTCTGTTTTATTCTTGAAGATCCT 59.390 37.037 0.00 0.00 0.00 3.24
3648 5880 1.352352 TCCTTTTCTGGCTTGCTAGCT 59.648 47.619 19.45 0.00 46.90 3.32
3673 5905 4.506838 GCAAACAGCTAGATGTAGAACG 57.493 45.455 15.12 2.70 41.15 3.95
3681 5914 3.489398 GCTAGATGTAGAACGTGGGACAG 60.489 52.174 0.05 0.00 41.80 3.51
3722 5955 1.497278 CGACAAACATCCGTGCCAG 59.503 57.895 0.00 0.00 0.00 4.85
3736 5969 0.181114 TGCCAGACTGCTTCACACTT 59.819 50.000 0.00 0.00 0.00 3.16
3737 5970 0.871057 GCCAGACTGCTTCACACTTC 59.129 55.000 0.00 0.00 0.00 3.01
3933 6186 4.753107 CCATTTGAATATTGGATGCCTTGC 59.247 41.667 0.00 0.00 31.94 4.01
3952 6205 1.132643 GCTGAGTCGTTGACTATCGGT 59.867 52.381 0.00 0.00 43.53 4.69
4010 6264 3.950397 ACACCGCCAGAATATGAAAAGA 58.050 40.909 0.00 0.00 0.00 2.52
4015 6269 6.813152 CACCGCCAGAATATGAAAAGAAAAAT 59.187 34.615 0.00 0.00 0.00 1.82
4029 6283 9.981114 TGAAAAGAAAAATCAGATACCCTTTTC 57.019 29.630 20.13 20.13 43.78 2.29
4092 6346 3.301274 ACTCTTCTCCAGGGCTATGTAC 58.699 50.000 0.00 0.00 0.00 2.90
4093 6347 3.052490 ACTCTTCTCCAGGGCTATGTACT 60.052 47.826 0.00 0.00 0.00 2.73
4094 6348 3.964031 CTCTTCTCCAGGGCTATGTACTT 59.036 47.826 0.00 0.00 0.00 2.24
4095 6349 5.138758 TCTTCTCCAGGGCTATGTACTTA 57.861 43.478 0.00 0.00 0.00 2.24
4096 6350 5.141182 TCTTCTCCAGGGCTATGTACTTAG 58.859 45.833 10.67 10.67 0.00 2.18
4097 6351 4.537945 TCTCCAGGGCTATGTACTTAGT 57.462 45.455 15.13 0.00 0.00 2.24
4098 6352 4.471548 TCTCCAGGGCTATGTACTTAGTC 58.528 47.826 15.13 13.18 0.00 2.59
4100 6354 2.296471 CCAGGGCTATGTACTTAGTCGG 59.704 54.545 15.13 8.26 0.00 4.79
4119 6373 5.104374 GTCGGTTCCTGATAACATTTCGTA 58.896 41.667 0.00 0.00 0.00 3.43
4169 6423 3.551046 GGATGATACTAGCTGTGTGGTCG 60.551 52.174 0.00 0.00 0.00 4.79
4190 6444 3.193691 CGGTCAGACAAAGTAGAGTCCAT 59.806 47.826 2.17 0.00 35.38 3.41
4221 6475 6.569226 GCCTTGTCAATATGTTATGGATCTGC 60.569 42.308 0.00 0.00 0.00 4.26
4283 6537 6.999871 TGATGATGCATTCCAGAAGCTATTAA 59.000 34.615 0.00 0.00 0.00 1.40
4304 6558 8.801882 ATTAATTTTAGTTCGGGAAGATGACA 57.198 30.769 0.00 0.00 0.00 3.58
4310 6564 0.895530 TCGGGAAGATGACAGTGTCC 59.104 55.000 20.43 6.13 0.00 4.02
4344 6598 1.648467 GATTGCGCCTCACCTTGGTC 61.648 60.000 4.18 0.00 0.00 4.02
4345 6599 2.129555 ATTGCGCCTCACCTTGGTCT 62.130 55.000 4.18 0.00 0.00 3.85
4360 6614 1.071699 TGGTCTGTTCTTAGTGCACCC 59.928 52.381 14.63 3.74 0.00 4.61
4361 6615 1.348036 GGTCTGTTCTTAGTGCACCCT 59.652 52.381 14.63 0.00 0.00 4.34
4362 6616 2.565834 GGTCTGTTCTTAGTGCACCCTA 59.434 50.000 14.63 0.00 0.00 3.53
4363 6617 3.368531 GGTCTGTTCTTAGTGCACCCTAG 60.369 52.174 14.63 8.65 0.00 3.02
4402 6656 6.319658 AGCATGATATGGAACCTGTTACAAAG 59.680 38.462 0.00 0.00 36.91 2.77
4404 6658 4.947388 TGATATGGAACCTGTTACAAAGGC 59.053 41.667 0.00 0.00 36.91 4.35
4416 6670 1.369209 CAAAGGCGCACAAGTGACG 60.369 57.895 10.83 8.31 38.67 4.35
4425 6679 2.662791 CGCACAAGTGACGAGAAATTGG 60.663 50.000 4.04 0.00 33.99 3.16
4487 6741 7.313646 CGAAAGTGACTAGAAACTGATTCCTA 58.686 38.462 0.00 0.00 38.94 2.94
4488 6742 7.486551 CGAAAGTGACTAGAAACTGATTCCTAG 59.513 40.741 0.00 0.00 38.94 3.02
4489 6743 7.784470 AAGTGACTAGAAACTGATTCCTAGT 57.216 36.000 0.00 0.00 38.94 2.57
4490 6744 8.880991 AAGTGACTAGAAACTGATTCCTAGTA 57.119 34.615 0.00 0.00 38.94 1.82
4540 6794 8.537728 AATCATAAGAGAGACTTCTGATGACT 57.462 34.615 12.97 4.55 44.22 3.41
4571 6825 0.986527 ACATGTGTGCATCTCTCCCA 59.013 50.000 0.00 0.00 31.99 4.37
4572 6826 1.065636 ACATGTGTGCATCTCTCCCAG 60.066 52.381 0.00 0.00 31.99 4.45
4573 6827 1.208776 CATGTGTGCATCTCTCCCAGA 59.791 52.381 0.00 0.00 31.99 3.86
4574 6828 0.900421 TGTGTGCATCTCTCCCAGAG 59.100 55.000 0.00 0.00 43.64 3.35
4607 6862 1.145571 TAAAGGTTGGTCTGCCACCT 58.854 50.000 3.71 0.00 46.98 4.00
4611 6866 1.529244 GTTGGTCTGCCACCTGCTT 60.529 57.895 3.71 0.00 46.98 3.91
4629 6884 2.035066 GCTTCATTGGATATGTGCACCC 59.965 50.000 15.69 8.74 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.171213 ACGACTATCGATCTGGATACATACA 58.829 40.000 0.00 0.00 45.53 2.29
1 2 6.665474 ACGACTATCGATCTGGATACATAC 57.335 41.667 0.00 0.00 45.53 2.39
2 3 7.779073 TCTACGACTATCGATCTGGATACATA 58.221 38.462 0.00 0.00 45.53 2.29
6 7 7.104290 ACATTCTACGACTATCGATCTGGATA 58.896 38.462 0.00 0.00 43.74 2.59
22 23 7.485277 GGAGGATGACGAATTATACATTCTACG 59.515 40.741 0.00 0.00 29.97 3.51
29 30 6.288294 CAAAGGGAGGATGACGAATTATACA 58.712 40.000 0.00 0.00 0.00 2.29
69 70 3.823281 TTACGGTGAACAGGAGAAACA 57.177 42.857 0.00 0.00 0.00 2.83
79 80 3.200483 AGTGAGGTGTTTTACGGTGAAC 58.800 45.455 0.00 0.00 0.00 3.18
82 83 2.140717 GGAGTGAGGTGTTTTACGGTG 58.859 52.381 0.00 0.00 0.00 4.94
98 99 0.179029 CGTTGGAACCCACAAGGAGT 60.179 55.000 0.00 0.00 39.89 3.85
103 104 2.321263 TACGGCGTTGGAACCCACAA 62.321 55.000 21.24 0.00 30.78 3.33
180 181 2.363306 AATCACTGCCTGTTTGGTCA 57.637 45.000 0.00 0.00 38.35 4.02
188 189 3.684305 TCGATGTTTGTAATCACTGCCTG 59.316 43.478 0.00 0.00 0.00 4.85
207 208 3.992943 AATTTGGGGTGATGTACTCGA 57.007 42.857 0.00 0.00 0.00 4.04
218 219 6.939730 GTCCATCATTTTAACAAATTTGGGGT 59.060 34.615 21.74 9.40 35.51 4.95
245 246 2.151202 CATAACGCTCCACAACAGGTT 58.849 47.619 0.00 0.00 0.00 3.50
248 249 0.447801 GCCATAACGCTCCACAACAG 59.552 55.000 0.00 0.00 0.00 3.16
263 277 2.828549 GCGGTTCCGAATGGCCAT 60.829 61.111 14.09 14.09 34.14 4.40
269 283 0.608640 AGTCTCTTGCGGTTCCGAAT 59.391 50.000 15.69 0.00 0.00 3.34
317 335 3.367025 GCTCTTACGTGCGTAATGAGTTT 59.633 43.478 25.49 0.78 39.49 2.66
387 405 1.817099 GCTCGCTGGTGCTGCTAAT 60.817 57.895 0.00 0.00 36.97 1.73
389 407 4.457496 GGCTCGCTGGTGCTGCTA 62.457 66.667 0.00 0.00 36.84 3.49
401 419 2.044806 AAATGAGGATCCGGGGCTCG 62.045 60.000 5.98 0.00 38.88 5.03
411 429 3.684788 CGTTGTTCTTCCGAAATGAGGAT 59.315 43.478 0.00 0.00 37.65 3.24
421 439 4.084888 GGCGCCGTTGTTCTTCCG 62.085 66.667 12.58 0.00 0.00 4.30
442 460 0.106619 TAACGGGGTGTTGGCAACTT 60.107 50.000 28.71 16.73 42.01 2.66
443 461 0.820482 GTAACGGGGTGTTGGCAACT 60.820 55.000 28.71 11.13 42.01 3.16
444 462 1.655885 GTAACGGGGTGTTGGCAAC 59.344 57.895 23.12 23.12 42.01 4.17
445 463 1.528776 GGTAACGGGGTGTTGGCAA 60.529 57.895 0.00 0.00 42.01 4.52
446 464 2.113562 GGTAACGGGGTGTTGGCA 59.886 61.111 0.00 0.00 42.01 4.92
447 465 2.674033 GGGTAACGGGGTGTTGGC 60.674 66.667 0.00 0.00 42.01 4.52
448 466 1.302993 CAGGGTAACGGGGTGTTGG 60.303 63.158 0.00 0.00 42.01 3.77
449 467 0.108963 TTCAGGGTAACGGGGTGTTG 59.891 55.000 0.00 0.00 42.01 3.33
458 476 5.766174 TGTCCAGTACATTTTTCAGGGTAAC 59.234 40.000 0.00 0.00 31.43 2.50
461 479 4.104102 TCTGTCCAGTACATTTTTCAGGGT 59.896 41.667 0.00 0.00 37.50 4.34
471 490 3.196469 CACACATCCTCTGTCCAGTACAT 59.804 47.826 0.00 0.00 37.50 2.29
478 497 2.616510 CCCTTTCACACATCCTCTGTCC 60.617 54.545 0.00 0.00 35.29 4.02
479 498 2.616510 CCCCTTTCACACATCCTCTGTC 60.617 54.545 0.00 0.00 35.29 3.51
485 504 2.046285 CCGCCCCTTTCACACATCC 61.046 63.158 0.00 0.00 0.00 3.51
504 523 2.514592 CATCGCTCCAATGCCCGT 60.515 61.111 0.00 0.00 0.00 5.28
508 527 0.462581 TCACTCCATCGCTCCAATGC 60.463 55.000 0.00 0.00 0.00 3.56
510 529 0.467384 CCTCACTCCATCGCTCCAAT 59.533 55.000 0.00 0.00 0.00 3.16
544 563 4.493049 TGTTTATCCCCCGCCGGC 62.493 66.667 19.07 19.07 0.00 6.13
706 1080 2.382746 CGGGTGATGCGTGTGACTG 61.383 63.158 0.00 0.00 0.00 3.51
707 1081 2.048222 CGGGTGATGCGTGTGACT 60.048 61.111 0.00 0.00 0.00 3.41
708 1082 2.357034 ACGGGTGATGCGTGTGAC 60.357 61.111 0.00 0.00 0.00 3.67
709 1083 2.356913 CACGGGTGATGCGTGTGA 60.357 61.111 0.00 0.00 32.39 3.58
710 1084 4.088762 GCACGGGTGATGCGTGTG 62.089 66.667 0.00 0.00 36.20 3.82
782 1156 0.808755 GCCCACCAAAGAATGTACCG 59.191 55.000 0.00 0.00 0.00 4.02
787 1161 2.350458 CCCGGCCCACCAAAGAATG 61.350 63.158 0.00 0.00 34.57 2.67
894 1268 3.219928 TCCTCCGGATGCTCTCGC 61.220 66.667 3.57 0.00 0.00 5.03
906 1280 3.695606 TCTGCTGTGCCGTCCTCC 61.696 66.667 0.00 0.00 0.00 4.30
907 1281 2.433318 GTCTGCTGTGCCGTCCTC 60.433 66.667 0.00 0.00 0.00 3.71
908 1282 4.363990 CGTCTGCTGTGCCGTCCT 62.364 66.667 0.00 0.00 0.00 3.85
935 1309 1.134175 CACGAGAGCTTCTCTTCTCCC 59.866 57.143 10.25 0.00 41.35 4.30
937 1311 1.472480 AGCACGAGAGCTTCTCTTCTC 59.528 52.381 10.25 1.02 43.70 2.87
938 1312 1.472480 GAGCACGAGAGCTTCTCTTCT 59.528 52.381 10.25 5.54 46.75 2.85
939 1313 1.793714 CGAGCACGAGAGCTTCTCTTC 60.794 57.143 0.00 0.00 46.75 2.87
943 1317 2.180518 GCGAGCACGAGAGCTTCT 59.819 61.111 8.01 0.00 46.75 2.85
1173 1553 2.721167 CCCCTCGACGGATCTGCAA 61.721 63.158 0.00 0.00 33.16 4.08
1330 1710 2.440409 CCCAGAGACAAATTCCACCAG 58.560 52.381 0.00 0.00 0.00 4.00
1341 1721 0.040646 ATGTACGGACCCCAGAGACA 59.959 55.000 0.00 0.00 0.00 3.41
1352 1732 4.805231 CACGCGCCCATGTACGGA 62.805 66.667 5.73 0.00 0.00 4.69
1354 1734 2.584970 ATCACGCGCCCATGTACG 60.585 61.111 5.73 0.54 0.00 3.67
1438 1822 2.832931 GCCTGTAGCATGCTATCGG 58.167 57.895 29.17 28.38 42.97 4.18
1476 1864 5.742453 CGAATTTCAAAGATGAAGCTGGATG 59.258 40.000 0.00 0.00 45.82 3.51
1499 1887 3.777925 CAACTCCAACGCGGCTCG 61.778 66.667 12.47 0.00 45.38 5.03
1539 3435 3.057104 TCAGAACAAAAGGATGCAGCATG 60.057 43.478 14.22 0.46 40.87 4.06
1573 3469 4.938080 ACATGTTCCTACATCTGTCGATC 58.062 43.478 0.00 0.00 43.07 3.69
1602 3502 0.818296 TCTCTCTACAAGAAGCCGCC 59.182 55.000 0.00 0.00 32.23 6.13
1604 3504 1.407258 CCCTCTCTCTACAAGAAGCCG 59.593 57.143 0.00 0.00 32.23 5.52
1612 3512 3.024547 CGTCAATTCCCCTCTCTCTACA 58.975 50.000 0.00 0.00 0.00 2.74
1750 3650 4.260172 CCATTCCTTTGTGCGTTTTCAAAC 60.260 41.667 0.00 0.00 35.59 2.93
1773 3673 2.907910 AAGAAACGTCATGCAGCATC 57.092 45.000 4.38 0.00 0.00 3.91
1804 3704 7.430502 CACATGCTAAAAATGCTCTTACTAAGC 59.569 37.037 0.00 0.00 40.26 3.09
1838 3738 1.234615 ACACGGCACCAAAATCCGAG 61.235 55.000 6.91 1.39 45.53 4.63
1953 3857 4.060900 TCTAAGTGCACTTCAAGAAGCAG 58.939 43.478 34.29 22.49 41.99 4.24
2010 3914 3.700038 ACCTCACGGGAGAACATTAGTAG 59.300 47.826 18.51 0.00 44.26 2.57
2050 4119 3.873361 TGCAGCTATAAGCACAACAGATC 59.127 43.478 1.22 0.00 45.56 2.75
2256 4326 8.239314 GCATGAAAGAACAGACTAAATTGATCA 58.761 33.333 0.00 0.00 0.00 2.92
2257 4327 8.239314 TGCATGAAAGAACAGACTAAATTGATC 58.761 33.333 0.00 0.00 0.00 2.92
2296 4366 9.753674 AAAGTATCCTCAGAAAAATGGACAATA 57.246 29.630 0.00 0.00 0.00 1.90
2352 4422 3.722147 ACTATAATTGCACTCTCCGCAG 58.278 45.455 0.00 0.00 41.18 5.18
2357 4427 8.451908 ACCCAATAAACTATAATTGCACTCTC 57.548 34.615 0.00 0.00 32.79 3.20
2358 4428 8.823220 AACCCAATAAACTATAATTGCACTCT 57.177 30.769 0.00 0.00 32.79 3.24
2380 4484 7.460296 CCAACAGTGAAACATTTTTACAAACC 58.540 34.615 0.00 0.00 41.43 3.27
2388 4492 3.118665 AGCTGCCAACAGTGAAACATTTT 60.119 39.130 0.00 0.00 46.30 1.82
2420 4524 1.863454 GCACAGGATGATCTGCTAACG 59.137 52.381 0.00 0.00 39.69 3.18
2432 4536 5.653255 AGGGATAACAATAAGCACAGGAT 57.347 39.130 0.00 0.00 0.00 3.24
2450 4554 5.309806 GGCTTAAGGATATTAGGTCAAGGGA 59.690 44.000 4.29 0.00 0.00 4.20
2647 4752 0.901114 ATGCTGCTTGAATGTGCCCA 60.901 50.000 0.00 0.00 0.00 5.36
2761 4871 0.659957 CAAGCAGCGAGGAAATAGGC 59.340 55.000 0.00 0.00 0.00 3.93
3127 5253 2.206576 ACTCTGAATGGGCTCAAACC 57.793 50.000 0.00 0.00 0.00 3.27
3263 5389 2.605580 GCTGAAAAGGCAAGTACTGTGC 60.606 50.000 16.84 16.84 41.45 4.57
3272 5398 2.566833 TAGAGCAGCTGAAAAGGCAA 57.433 45.000 20.43 0.00 0.00 4.52
3287 5413 6.420306 CAGCAAGCAATGTAGTGTAGATAGAG 59.580 42.308 0.00 0.00 0.00 2.43
3298 5424 7.756722 AAAAGTATTTAGCAGCAAGCAATGTAG 59.243 33.333 0.00 0.00 42.00 2.74
3326 5452 2.159448 CGAAACAAACAGCCTGACACAA 60.159 45.455 0.00 0.00 0.00 3.33
3327 5453 1.400142 CGAAACAAACAGCCTGACACA 59.600 47.619 0.00 0.00 0.00 3.72
3377 5503 6.311445 ACAAACAGCTATGATTGTAAGAGTCG 59.689 38.462 2.52 0.00 46.83 4.18
3484 5715 8.141909 CCAGGAAGTATCGTTGAAGAATATACA 58.858 37.037 0.00 0.00 0.00 2.29
3485 5716 8.142551 ACCAGGAAGTATCGTTGAAGAATATAC 58.857 37.037 0.00 0.00 0.00 1.47
3491 5723 5.988310 TTACCAGGAAGTATCGTTGAAGA 57.012 39.130 0.00 0.00 0.00 2.87
3511 5743 6.312672 TGAGCGAAATCGACAGAAAATCATTA 59.687 34.615 7.06 0.00 43.02 1.90
3536 5768 5.600484 CAGACAGGAAGTGAGGAAGGTATAT 59.400 44.000 0.00 0.00 0.00 0.86
3579 5811 4.223700 TCTTGAGCTTGCTTTATCTCCTCA 59.776 41.667 0.00 0.00 0.00 3.86
3673 5905 3.270877 CTTAAGCCACATACTGTCCCAC 58.729 50.000 0.00 0.00 0.00 4.61
3681 5914 6.018262 TCGCATCATAAACTTAAGCCACATAC 60.018 38.462 1.29 0.00 0.00 2.39
3722 5955 1.808945 CCATGGAAGTGTGAAGCAGTC 59.191 52.381 5.56 0.00 0.00 3.51
3736 5969 2.692368 GTCCCAGCCTCCCATGGA 60.692 66.667 15.22 0.00 39.02 3.41
3737 5970 2.563013 CTTGTCCCAGCCTCCCATGG 62.563 65.000 4.14 4.14 36.27 3.66
3825 6074 1.480545 GCCAGGTGTTTCACAAGGTTT 59.519 47.619 2.41 0.00 35.86 3.27
3830 6079 1.748493 GTTCAGCCAGGTGTTTCACAA 59.252 47.619 2.41 0.00 35.86 3.33
3832 6081 1.680338 AGTTCAGCCAGGTGTTTCAC 58.320 50.000 0.00 0.00 0.00 3.18
3873 6122 4.698780 ACACTGTACTTGACGTGAGCTATA 59.301 41.667 0.00 0.00 36.61 1.31
3874 6123 3.506455 ACACTGTACTTGACGTGAGCTAT 59.494 43.478 0.00 0.00 36.61 2.97
3886 6135 6.093082 GGTTAACAAGTTGACACACTGTACTT 59.907 38.462 10.54 0.00 31.56 2.24
3933 6186 3.869832 TCTACCGATAGTCAACGACTCAG 59.130 47.826 0.00 0.00 42.40 3.35
3952 6205 2.961741 GGTCAGCATCAGGATGTCTCTA 59.038 50.000 10.69 0.00 40.80 2.43
4010 6264 6.093082 CGTACCGAAAAGGGTATCTGATTTTT 59.907 38.462 0.00 0.00 44.02 1.94
4015 6269 3.091545 ACGTACCGAAAAGGGTATCTGA 58.908 45.455 0.00 0.00 44.02 3.27
4024 6278 5.396484 TCAGTTCAGATACGTACCGAAAAG 58.604 41.667 0.00 0.00 0.00 2.27
4026 6280 5.571784 ATCAGTTCAGATACGTACCGAAA 57.428 39.130 0.00 0.00 0.00 3.46
4036 6290 5.047021 GCCTGCCATAGTATCAGTTCAGATA 60.047 44.000 0.00 0.00 0.00 1.98
4092 6346 6.019801 CGAAATGTTATCAGGAACCGACTAAG 60.020 42.308 0.00 0.00 0.00 2.18
4093 6347 5.808540 CGAAATGTTATCAGGAACCGACTAA 59.191 40.000 0.00 0.00 0.00 2.24
4094 6348 5.105635 ACGAAATGTTATCAGGAACCGACTA 60.106 40.000 0.00 0.00 0.00 2.59
4095 6349 4.181578 CGAAATGTTATCAGGAACCGACT 58.818 43.478 0.00 0.00 0.00 4.18
4096 6350 3.930848 ACGAAATGTTATCAGGAACCGAC 59.069 43.478 0.00 0.00 0.00 4.79
4097 6351 4.196626 ACGAAATGTTATCAGGAACCGA 57.803 40.909 0.00 0.00 0.00 4.69
4098 6352 4.506654 CCTACGAAATGTTATCAGGAACCG 59.493 45.833 0.00 0.00 0.00 4.44
4100 6354 7.460751 GTACCTACGAAATGTTATCAGGAAC 57.539 40.000 0.00 0.00 0.00 3.62
4119 6373 1.286248 AGAGGGCCAAATTCGTACCT 58.714 50.000 6.18 0.00 0.00 3.08
4132 6386 6.479884 AGTATCATCCATAAATGAAGAGGGC 58.520 40.000 0.00 0.00 39.04 5.19
4169 6423 4.810191 ATGGACTCTACTTTGTCTGACC 57.190 45.455 5.17 0.00 34.01 4.02
4190 6444 6.942005 CCATAACATATTGACAAGGCTGGATA 59.058 38.462 0.00 0.00 0.00 2.59
4283 6537 5.643777 CACTGTCATCTTCCCGAACTAAAAT 59.356 40.000 0.00 0.00 0.00 1.82
4310 6564 1.522355 AATCATGTCCTGCGAGCGG 60.522 57.895 0.00 0.00 0.00 5.52
4344 6598 2.234908 AGCTAGGGTGCACTAAGAACAG 59.765 50.000 17.98 5.88 34.99 3.16
4345 6599 2.257207 AGCTAGGGTGCACTAAGAACA 58.743 47.619 17.98 0.00 34.99 3.18
4360 6614 5.536260 TCATGCTATCAAACTGCTAGCTAG 58.464 41.667 16.84 16.84 41.29 3.42
4361 6615 5.535753 TCATGCTATCAAACTGCTAGCTA 57.464 39.130 17.23 1.31 41.29 3.32
4362 6616 4.412796 TCATGCTATCAAACTGCTAGCT 57.587 40.909 17.23 0.00 41.29 3.32
4363 6617 6.183360 CCATATCATGCTATCAAACTGCTAGC 60.183 42.308 8.10 8.10 41.14 3.42
4402 6656 1.495584 TTTCTCGTCACTTGTGCGCC 61.496 55.000 4.18 0.00 0.00 6.53
4404 6658 2.563976 CAATTTCTCGTCACTTGTGCG 58.436 47.619 9.89 9.89 0.00 5.34
4416 6670 6.842676 AGGTTCCATATCCTACCAATTTCTC 58.157 40.000 0.00 0.00 33.02 2.87
4425 6679 7.817418 TTGCAAAATAGGTTCCATATCCTAC 57.183 36.000 0.00 0.00 38.84 3.18
4487 6741 9.322773 GACAAAAGGTTTTACAGAACTACTACT 57.677 33.333 0.00 0.00 0.00 2.57
4488 6742 9.322773 AGACAAAAGGTTTTACAGAACTACTAC 57.677 33.333 0.00 0.00 0.00 2.73
4490 6744 9.895138 TTAGACAAAAGGTTTTACAGAACTACT 57.105 29.630 0.00 0.00 0.00 2.57
4540 6794 6.658816 AGATGCACACATGTCCTAAAATTACA 59.341 34.615 0.00 0.00 36.35 2.41
4571 6825 7.124147 CCAACCTTTATTCTTCTCTCTCTCTCT 59.876 40.741 0.00 0.00 0.00 3.10
4572 6826 7.093509 ACCAACCTTTATTCTTCTCTCTCTCTC 60.094 40.741 0.00 0.00 0.00 3.20
4573 6827 6.728632 ACCAACCTTTATTCTTCTCTCTCTCT 59.271 38.462 0.00 0.00 0.00 3.10
4574 6828 6.941857 ACCAACCTTTATTCTTCTCTCTCTC 58.058 40.000 0.00 0.00 0.00 3.20
4575 6829 6.728632 AGACCAACCTTTATTCTTCTCTCTCT 59.271 38.462 0.00 0.00 0.00 3.10
4576 6830 6.816140 CAGACCAACCTTTATTCTTCTCTCTC 59.184 42.308 0.00 0.00 0.00 3.20
4607 6862 2.689471 GGTGCACATATCCAATGAAGCA 59.311 45.455 20.43 6.02 33.78 3.91
4611 6866 1.852309 AGGGGTGCACATATCCAATGA 59.148 47.619 20.43 0.00 0.00 2.57
4629 6884 5.166398 GTCATTTTCAGCATCCAGAAAAGG 58.834 41.667 0.00 0.00 44.18 3.11


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

AutoCloner maintained by Alex Coulton.