Multiple sequence alignment - TraesCS6A01G300500

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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 TraesCS6A01G300500 chr6A 100.000 3625 0 0 873 4497 533404235 533400611 0.000000e+00 6695
1 TraesCS6A01G300500 chr6A 100.000 589 0 0 1 589 533405107 533404519 0.000000e+00 1088
2 TraesCS6A01G300500 chr6A 88.333 120 12 2 4088 4206 411770406 411770288 4.690000e-30 143
3 TraesCS6A01G300500 chr6A 85.593 118 15 2 4088 4204 523947678 523947562 6.110000e-24 122
4 TraesCS6A01G300500 chr6B 92.621 2995 153 33 878 3856 579536081 579533139 0.000000e+00 4244
5 TraesCS6A01G300500 chr6B 86.545 602 51 14 2 587 579536794 579536207 1.760000e-178 636
6 TraesCS6A01G300500 chr6D 94.921 2402 86 12 1487 3856 388121978 388119581 0.000000e+00 3727
7 TraesCS6A01G300500 chr6D 87.936 688 35 25 878 1543 388122678 388122017 0.000000e+00 767
8 TraesCS6A01G300500 chr6D 88.816 456 22 12 4059 4497 388119386 388118943 2.380000e-147 532
9 TraesCS6A01G300500 chr6D 90.000 350 30 5 2 347 388123912 388123564 8.870000e-122 448
10 TraesCS6A01G300500 chr6D 89.677 310 27 5 2 307 388123350 388123042 1.520000e-104 390
11 TraesCS6A01G300500 chr6D 95.213 188 6 3 3874 4059 388119604 388119418 1.220000e-75 294
12 TraesCS6A01G300500 chr6D 86.441 118 14 2 4088 4204 381997538 381997422 1.310000e-25 128
13 TraesCS6A01G300500 chr5B 88.333 120 12 2 4088 4206 278229910 278229792 4.690000e-30 143
14 TraesCS6A01G300500 chr3A 86.719 128 12 4 4083 4206 208033827 208033701 2.180000e-28 137
15 TraesCS6A01G300500 chr4A 87.603 121 10 5 4088 4206 48887311 48887428 7.850000e-28 135
16 TraesCS6A01G300500 chr4D 85.950 121 14 3 4089 4207 500822302 500822421 4.720000e-25 126
17 TraesCS6A01G300500 chr2A 82.114 123 18 4 4086 4206 763426799 763426679 7.960000e-18 102


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 TraesCS6A01G300500 chr6A 533400611 533405107 4496 True 3891.500000 6695 100.000000 1 4497 2 chr6A.!!$R3 4496
1 TraesCS6A01G300500 chr6B 579533139 579536794 3655 True 2440.000000 4244 89.583000 2 3856 2 chr6B.!!$R1 3854
2 TraesCS6A01G300500 chr6D 388118943 388123912 4969 True 1026.333333 3727 91.093833 2 4497 6 chr6D.!!$R2 4495

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
950 1475 0.537653 CTTCCTCGGTTCCTCTTCCC 59.462 60.000 0.0 0.0 0.00 3.97 F
1143 1673 0.036306 AGGAATGACGGGCGTTTCTT 59.964 50.000 0.0 0.0 25.92 2.52 F
1287 1830 0.401738 ATCTTGTGGGTCTGGGTGTG 59.598 55.000 0.0 0.0 0.00 3.82 F
1875 2515 1.076632 TTTTCCCGCCACACCTTGT 60.077 52.632 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 2920 1.197036 CGAGCGCTAACTGGATATCGA 59.803 52.381 11.50 0.00 0.00 3.59 R
3025 3694 0.098200 GCGCCACCGGAAAAGTAATC 59.902 55.000 9.46 0.00 34.32 1.75 R
3084 3753 5.537674 AGTTGTTTGCTTCAATCTCCTTCAT 59.462 36.000 0.00 0.00 0.00 2.57 R
3684 4359 1.063174 GCCTCAAGTTAGCGCAATGAG 59.937 52.381 11.47 14.62 37.77 2.90 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
25 26 7.378181 ACATGGGTTGTTTGATTTGTAAGATC 58.622 34.615 0.00 0.00 33.74 2.75
63 72 7.496920 TGTCTATGATGATTCCTTTTGCACTAG 59.503 37.037 0.00 0.00 0.00 2.57
70 79 6.913170 TGATTCCTTTTGCACTAGATTTCAC 58.087 36.000 0.00 0.00 0.00 3.18
75 84 6.205464 TCCTTTTGCACTAGATTTCACAGAAG 59.795 38.462 0.00 0.00 0.00 2.85
83 93 7.061557 GCACTAGATTTCACAGAAGAAAATTGC 59.938 37.037 0.00 0.00 40.54 3.56
131 141 3.418047 CTTTTCCCGAGGTACAACCAAT 58.582 45.455 0.00 0.00 41.95 3.16
137 147 3.054948 CCCGAGGTACAACCAATTTAGGA 60.055 47.826 0.00 0.00 41.95 2.94
248 261 6.014840 GCCATAAGATGTTGGAATGGATGAAT 60.015 38.462 6.98 0.00 39.60 2.57
297 312 6.602179 TGAATTCTGTCTTTGCAATCTTACG 58.398 36.000 7.05 0.00 0.00 3.18
308 323 5.119931 TGCAATCTTACGAAACAAATGCT 57.880 34.783 0.00 0.00 32.74 3.79
317 332 3.250744 CGAAACAAATGCTCCTCGTAGA 58.749 45.455 0.00 0.00 0.00 2.59
393 814 1.853963 AAGGGCACGAGATAGACACT 58.146 50.000 0.00 0.00 0.00 3.55
419 840 4.082895 CCAGTGCCAGATTTCTCTTTTCTG 60.083 45.833 0.00 0.00 37.27 3.02
445 866 6.037786 TCTGGAGTTGTCTGGTACATTTAG 57.962 41.667 0.00 0.00 38.10 1.85
545 1069 6.950041 AGTAATTATAGGTGCACCGGATACTA 59.050 38.462 29.68 15.97 42.08 1.82
548 1072 6.675413 TTATAGGTGCACCGGATACTATTT 57.325 37.500 29.68 11.09 42.08 1.40
552 1076 3.537580 GTGCACCGGATACTATTTCCAA 58.462 45.455 9.46 0.00 32.45 3.53
950 1475 0.537653 CTTCCTCGGTTCCTCTTCCC 59.462 60.000 0.00 0.00 0.00 3.97
954 1479 0.966370 CTCGGTTCCTCTTCCCGTCT 60.966 60.000 0.00 0.00 42.30 4.18
955 1480 0.541296 TCGGTTCCTCTTCCCGTCTT 60.541 55.000 0.00 0.00 42.30 3.01
963 1488 1.218316 CTTCCCGTCTTCCTTCCCG 59.782 63.158 0.00 0.00 0.00 5.14
976 1501 2.873557 CTTCCCGGACCCCTAGAGCA 62.874 65.000 0.73 0.00 0.00 4.26
979 1504 1.559065 CCCGGACCCCTAGAGCAAAA 61.559 60.000 0.73 0.00 0.00 2.44
1012 1542 4.175489 CGGAGATGGCGACGACGT 62.175 66.667 9.33 0.00 41.98 4.34
1064 1594 2.070039 TTCGCCGGATCTTCCCCAT 61.070 57.895 5.05 0.00 31.13 4.00
1065 1595 0.761323 TTCGCCGGATCTTCCCCATA 60.761 55.000 5.05 0.00 31.13 2.74
1068 1598 1.271379 CGCCGGATCTTCCCCATAAAT 60.271 52.381 5.05 0.00 31.13 1.40
1069 1599 2.814097 CGCCGGATCTTCCCCATAAATT 60.814 50.000 5.05 0.00 31.13 1.82
1070 1600 2.820197 GCCGGATCTTCCCCATAAATTC 59.180 50.000 5.05 0.00 31.13 2.17
1073 1603 3.074538 CGGATCTTCCCCATAAATTCCCT 59.925 47.826 0.00 0.00 31.13 4.20
1075 1605 5.080337 GGATCTTCCCCATAAATTCCCTTC 58.920 45.833 0.00 0.00 0.00 3.46
1076 1606 4.536295 TCTTCCCCATAAATTCCCTTCC 57.464 45.455 0.00 0.00 0.00 3.46
1077 1607 4.126823 TCTTCCCCATAAATTCCCTTCCT 58.873 43.478 0.00 0.00 0.00 3.36
1078 1608 3.971468 TCCCCATAAATTCCCTTCCTG 57.029 47.619 0.00 0.00 0.00 3.86
1079 1609 2.091333 TCCCCATAAATTCCCTTCCTGC 60.091 50.000 0.00 0.00 0.00 4.85
1080 1610 2.091111 CCCCATAAATTCCCTTCCTGCT 60.091 50.000 0.00 0.00 0.00 4.24
1081 1611 3.225940 CCCATAAATTCCCTTCCTGCTC 58.774 50.000 0.00 0.00 0.00 4.26
1082 1612 3.225940 CCATAAATTCCCTTCCTGCTCC 58.774 50.000 0.00 0.00 0.00 4.70
1083 1613 3.117360 CCATAAATTCCCTTCCTGCTCCT 60.117 47.826 0.00 0.00 0.00 3.69
1084 1614 4.540715 CATAAATTCCCTTCCTGCTCCTT 58.459 43.478 0.00 0.00 0.00 3.36
1085 1615 3.549898 AAATTCCCTTCCTGCTCCTTT 57.450 42.857 0.00 0.00 0.00 3.11
1086 1616 2.816777 ATTCCCTTCCTGCTCCTTTC 57.183 50.000 0.00 0.00 0.00 2.62
1087 1617 1.444933 TTCCCTTCCTGCTCCTTTCA 58.555 50.000 0.00 0.00 0.00 2.69
1088 1618 1.444933 TCCCTTCCTGCTCCTTTCAA 58.555 50.000 0.00 0.00 0.00 2.69
1089 1619 1.352352 TCCCTTCCTGCTCCTTTCAAG 59.648 52.381 0.00 0.00 0.00 3.02
1143 1673 0.036306 AGGAATGACGGGCGTTTCTT 59.964 50.000 0.00 0.00 25.92 2.52
1144 1674 0.446616 GGAATGACGGGCGTTTCTTC 59.553 55.000 0.00 0.00 0.00 2.87
1174 1704 1.267574 ATTGCAGAAGGGAGAGGCGA 61.268 55.000 0.00 0.00 0.00 5.54
1215 1745 3.061848 CGGGCCAAGGTTCGCAAT 61.062 61.111 4.39 0.00 0.00 3.56
1286 1829 0.693049 GATCTTGTGGGTCTGGGTGT 59.307 55.000 0.00 0.00 0.00 4.16
1287 1830 0.401738 ATCTTGTGGGTCTGGGTGTG 59.598 55.000 0.00 0.00 0.00 3.82
1288 1831 1.898574 CTTGTGGGTCTGGGTGTGC 60.899 63.158 0.00 0.00 0.00 4.57
1325 1871 2.668550 GGGCAACGTGACCCAGAC 60.669 66.667 18.91 0.00 40.64 3.51
1480 2030 5.824429 TGCTATCAAATTGCTGCTTCATAC 58.176 37.500 0.00 0.00 32.18 2.39
1481 2031 5.591472 TGCTATCAAATTGCTGCTTCATACT 59.409 36.000 0.00 0.00 32.18 2.12
1482 2032 6.095860 TGCTATCAAATTGCTGCTTCATACTT 59.904 34.615 0.00 0.00 32.18 2.24
1484 2034 8.131100 GCTATCAAATTGCTGCTTCATACTTTA 58.869 33.333 0.00 0.00 0.00 1.85
1485 2035 9.443283 CTATCAAATTGCTGCTTCATACTTTAC 57.557 33.333 0.00 0.00 0.00 2.01
1558 2197 2.368655 AAAAGGATGTGAATTGCGGC 57.631 45.000 0.00 0.00 0.00 6.53
1573 2212 5.852282 ATTGCGGCTATTAGAACCAAATT 57.148 34.783 0.00 0.00 0.00 1.82
1622 2261 3.189618 TGATGTCTATGCAAGAGCCAG 57.810 47.619 0.00 0.00 41.13 4.85
1648 2287 1.280421 GGCAGTCCCTTCTTGATGTCT 59.720 52.381 0.00 0.00 0.00 3.41
1652 2291 4.701765 CAGTCCCTTCTTGATGTCTATGG 58.298 47.826 0.00 0.00 0.00 2.74
1745 2384 3.828451 AGGAATGGTGTCTGTTCAAATGG 59.172 43.478 0.00 0.00 0.00 3.16
1752 2391 4.156739 GGTGTCTGTTCAAATGGGAAGATC 59.843 45.833 0.00 0.00 0.00 2.75
1756 2395 5.649395 GTCTGTTCAAATGGGAAGATCATCA 59.351 40.000 0.00 0.00 0.00 3.07
1757 2396 6.320672 GTCTGTTCAAATGGGAAGATCATCAT 59.679 38.462 0.00 0.00 0.00 2.45
1761 2400 6.720112 TCAAATGGGAAGATCATCATTTCC 57.280 37.500 0.00 1.38 37.62 3.13
1768 2407 4.586421 GGAAGATCATCATTTCCCCCTTTC 59.414 45.833 0.00 0.00 35.43 2.62
1801 2440 8.083462 CAGTACACACTGTTTTTCTTATGCTA 57.917 34.615 0.00 0.00 46.03 3.49
1818 2457 8.385491 TCTTATGCTATTATCATGTGTTCCCAT 58.615 33.333 0.00 0.00 0.00 4.00
1829 2469 5.830457 TCATGTGTTCCCATTAAACAACTCA 59.170 36.000 0.00 0.00 38.29 3.41
1860 2500 9.634163 GGATGTTGATATTCCTTTTTACGTTTT 57.366 29.630 0.00 0.00 0.00 2.43
1866 2506 1.608109 TCCTTTTTACGTTTTCCCGCC 59.392 47.619 0.00 0.00 0.00 6.13
1875 2515 1.076632 TTTTCCCGCCACACCTTGT 60.077 52.632 0.00 0.00 0.00 3.16
1890 2530 6.408548 CCACACCTTGTCTCCTTCACATATAT 60.409 42.308 0.00 0.00 0.00 0.86
1898 2538 8.262601 TGTCTCCTTCACATATATACCATTGT 57.737 34.615 0.00 0.00 0.00 2.71
1976 2622 2.743636 TAACTGTCGAGCTTCCTTGG 57.256 50.000 0.00 0.00 0.00 3.61
2093 2739 3.317993 GCTTGGTTTTTCTGCTGGTAAGA 59.682 43.478 0.00 0.00 0.00 2.10
2231 2877 4.938226 GCCAATTTAGCTGAGAACTAGTGT 59.062 41.667 0.00 0.00 0.00 3.55
2320 2966 7.549134 GCCTGGGAATTAGAAACAATTTTTAGG 59.451 37.037 0.00 0.00 31.45 2.69
2490 3159 5.564048 ACTGTAAAAACAACTTGGCGTAA 57.436 34.783 0.00 0.00 0.00 3.18
2757 3426 4.517285 GTTTGACTGCAGGGAAGATGATA 58.483 43.478 19.93 0.00 0.00 2.15
2769 3438 9.842775 GCAGGGAAGATGATATATTATGAATCA 57.157 33.333 0.00 0.00 34.35 2.57
2804 3473 2.027561 GCCTATACATATTGGGCCGTGA 60.028 50.000 0.00 0.00 37.12 4.35
3025 3694 7.667635 TCTCTACACTGATCAATACCAGGATAG 59.332 40.741 0.00 0.00 34.85 2.08
3084 3753 2.501723 GACAGCACCTATCTGGAAAGGA 59.498 50.000 0.00 0.00 39.71 3.36
3179 3850 2.673368 GACTTACAACTGATCTTGCGGG 59.327 50.000 0.00 0.00 0.00 6.13
3555 4226 9.046296 AGTGATACTTGATGTTCGAATATTTCC 57.954 33.333 8.90 0.00 0.00 3.13
3569 4240 5.470098 CGAATATTTCCATTCCCTTCGACAT 59.530 40.000 0.00 0.00 36.93 3.06
3684 4359 9.353999 AGTACACATTTTTGTTCTCTTGTTTTC 57.646 29.630 0.00 0.00 0.00 2.29
3759 4434 3.334604 CCCAATCTGGCTAGCCCA 58.665 61.111 30.81 17.87 42.79 5.36
3821 4496 2.616524 ACTGTAGCCCCTGACTTGTAA 58.383 47.619 0.00 0.00 0.00 2.41
3856 4531 6.589523 CAGAGATCTCGTTCTGTTTTCATCTT 59.410 38.462 16.97 0.00 36.82 2.40
3857 4532 7.117523 CAGAGATCTCGTTCTGTTTTCATCTTT 59.882 37.037 16.97 0.00 36.82 2.52
3860 4535 7.659390 AGATCTCGTTCTGTTTTCATCTTTTCT 59.341 33.333 0.00 0.00 0.00 2.52
3861 4536 7.178712 TCTCGTTCTGTTTTCATCTTTTCTC 57.821 36.000 0.00 0.00 0.00 2.87
3862 4537 6.986817 TCTCGTTCTGTTTTCATCTTTTCTCT 59.013 34.615 0.00 0.00 0.00 3.10
3863 4538 7.495934 TCTCGTTCTGTTTTCATCTTTTCTCTT 59.504 33.333 0.00 0.00 0.00 2.85
3864 4539 7.985476 TCGTTCTGTTTTCATCTTTTCTCTTT 58.015 30.769 0.00 0.00 0.00 2.52
3865 4540 8.122952 TCGTTCTGTTTTCATCTTTTCTCTTTC 58.877 33.333 0.00 0.00 0.00 2.62
3866 4541 8.125448 CGTTCTGTTTTCATCTTTTCTCTTTCT 58.875 33.333 0.00 0.00 0.00 2.52
3867 4542 9.794685 GTTCTGTTTTCATCTTTTCTCTTTCTT 57.205 29.630 0.00 0.00 0.00 2.52
3896 4571 6.718454 AGAATCTCGTTCTGTTTTCATCTG 57.282 37.500 0.00 0.00 45.38 2.90
3897 4572 6.459066 AGAATCTCGTTCTGTTTTCATCTGA 58.541 36.000 0.00 0.00 45.38 3.27
3898 4573 7.102346 AGAATCTCGTTCTGTTTTCATCTGAT 58.898 34.615 0.00 0.00 45.38 2.90
3899 4574 6.900568 ATCTCGTTCTGTTTTCATCTGATC 57.099 37.500 0.00 0.00 0.00 2.92
3900 4575 5.783111 TCTCGTTCTGTTTTCATCTGATCA 58.217 37.500 0.00 0.00 0.00 2.92
3901 4576 5.866092 TCTCGTTCTGTTTTCATCTGATCAG 59.134 40.000 17.07 17.07 0.00 2.90
3937 4612 3.760151 TGTACCGTACATACTCTGTTGCT 59.240 43.478 7.32 0.00 39.39 3.91
3939 4614 5.415389 TGTACCGTACATACTCTGTTGCTAA 59.585 40.000 7.32 0.00 39.39 3.09
3965 4640 2.974489 CTTGCAACAGCAGGGCGAG 61.974 63.158 0.00 0.00 39.82 5.03
3979 4654 1.402984 GGGCGAGTGTTGTCTAGACTG 60.403 57.143 23.01 6.14 28.97 3.51
4039 4714 9.914834 AAAATACTAGGCCTAATTATGTTGACA 57.085 29.630 14.85 0.00 0.00 3.58
4064 4739 7.596749 AAAAATCATAGTTACTCCTGACACG 57.403 36.000 0.00 0.00 0.00 4.49
4065 4740 6.525578 AAATCATAGTTACTCCTGACACGA 57.474 37.500 0.00 0.00 0.00 4.35
4066 4741 5.759506 ATCATAGTTACTCCTGACACGAG 57.240 43.478 0.00 0.45 0.00 4.18
4067 4742 3.377485 TCATAGTTACTCCTGACACGAGC 59.623 47.826 1.79 0.00 0.00 5.03
4077 4784 2.022129 GACACGAGCAGTTCACCGG 61.022 63.158 0.00 0.00 0.00 5.28
4104 4811 4.456662 AGATATACTCCCTCCGTTCACT 57.543 45.455 0.00 0.00 0.00 3.41
4115 4822 8.337739 ACTCCCTCCGTTCACTAATATAGATAT 58.662 37.037 0.00 0.00 0.00 1.63
4156 4863 5.424757 TGGACTAAATACGGACTGAAATGG 58.575 41.667 0.00 0.00 0.00 3.16
4159 4866 6.407299 GGACTAAATACGGACTGAAATGGGTA 60.407 42.308 0.00 0.00 0.00 3.69
4163 4870 3.495434 ACGGACTGAAATGGGTAAACA 57.505 42.857 0.00 0.00 0.00 2.83
4170 4877 5.901552 ACTGAAATGGGTAAACAAACACAG 58.098 37.500 0.00 0.00 35.92 3.66
4176 4883 8.481974 AAATGGGTAAACAAACACAGTAAAAC 57.518 30.769 0.00 0.00 35.92 2.43
4183 4890 6.724694 AACAAACACAGTAAAACGTGTCTA 57.275 33.333 0.00 0.00 45.37 2.59
4186 4893 8.597662 ACAAACACAGTAAAACGTGTCTATAT 57.402 30.769 0.00 0.00 45.37 0.86
4188 4895 9.947897 CAAACACAGTAAAACGTGTCTATATAC 57.052 33.333 0.00 0.00 45.37 1.47
4189 4896 9.695526 AAACACAGTAAAACGTGTCTATATACA 57.304 29.630 0.00 0.00 45.37 2.29
4190 4897 9.865321 AACACAGTAAAACGTGTCTATATACAT 57.135 29.630 0.00 0.00 45.37 2.29
4191 4898 9.512435 ACACAGTAAAACGTGTCTATATACATC 57.488 33.333 0.00 0.00 42.61 3.06
4192 4899 9.731819 CACAGTAAAACGTGTCTATATACATCT 57.268 33.333 0.00 0.00 0.00 2.90
4193 4900 9.731819 ACAGTAAAACGTGTCTATATACATCTG 57.268 33.333 0.00 0.00 0.00 2.90
4194 4901 9.946165 CAGTAAAACGTGTCTATATACATCTGA 57.054 33.333 0.00 0.00 0.00 3.27
4241 4959 5.427157 TGGAGGCAGTATTTCATAAGGTACA 59.573 40.000 0.00 0.00 0.00 2.90
4295 5013 6.214615 TGTGAAGGGATTACTATCCTTTGTGA 59.785 38.462 6.30 0.00 46.83 3.58
4358 5077 4.081254 ACGTAGGTTTAGATCCCTGGAAAC 60.081 45.833 0.00 0.00 32.08 2.78
4375 5094 3.756434 GGAAACGAAAATGGTGATCAGGA 59.244 43.478 0.00 0.00 0.00 3.86
4376 5095 4.217550 GGAAACGAAAATGGTGATCAGGAA 59.782 41.667 0.00 0.00 0.00 3.36
4377 5096 5.278758 GGAAACGAAAATGGTGATCAGGAAA 60.279 40.000 0.00 0.00 0.00 3.13
4378 5097 4.766404 ACGAAAATGGTGATCAGGAAAC 57.234 40.909 0.00 0.00 0.00 2.78
4379 5098 3.506067 ACGAAAATGGTGATCAGGAAACC 59.494 43.478 0.00 0.00 34.38 3.27
4380 5099 3.426159 CGAAAATGGTGATCAGGAAACCG 60.426 47.826 0.00 0.00 36.73 4.44
4381 5100 2.879103 AATGGTGATCAGGAAACCGT 57.121 45.000 0.00 0.00 36.73 4.83
4382 5101 2.113860 ATGGTGATCAGGAAACCGTG 57.886 50.000 0.00 0.00 36.73 4.94
4383 5102 0.762418 TGGTGATCAGGAAACCGTGT 59.238 50.000 0.00 0.00 36.73 4.49
4384 5103 1.142060 TGGTGATCAGGAAACCGTGTT 59.858 47.619 0.00 0.00 36.73 3.32
4400 5119 2.864343 CGTGTTCTCGGAATGGGTATTC 59.136 50.000 0.00 0.00 41.59 1.75
4488 5210 3.691575 TGCGGAGGATAGGAGAGATTAG 58.308 50.000 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.723298 TCTTACAAATCAAACAACCCATGT 57.277 33.333 0.00 0.00 46.82 3.21
56 65 7.750229 ATTTTCTTCTGTGAAATCTAGTGCA 57.250 32.000 0.00 0.00 36.07 4.57
63 72 5.406477 GTGGGCAATTTTCTTCTGTGAAATC 59.594 40.000 0.00 0.00 36.07 2.17
70 79 4.589216 TTGAGTGGGCAATTTTCTTCTG 57.411 40.909 0.00 0.00 0.00 3.02
75 84 4.692228 TGAAGTTTGAGTGGGCAATTTTC 58.308 39.130 0.00 0.00 0.00 2.29
83 93 3.563808 TCGTTCAATGAAGTTTGAGTGGG 59.436 43.478 0.00 0.00 36.97 4.61
188 200 5.688176 TGCATGATTACAAATCGCATGAATG 59.312 36.000 0.00 0.00 38.82 2.67
248 261 7.531857 TCTGCACTAAATTTTATTGGAACCA 57.468 32.000 0.00 0.00 0.00 3.67
297 312 4.495422 TCTCTACGAGGAGCATTTGTTTC 58.505 43.478 0.00 0.00 33.70 2.78
308 323 7.235935 TCCTTACAATTTTTCTCTACGAGGA 57.764 36.000 0.00 0.00 0.00 3.71
317 332 9.190317 GGAGGTTATGATCCTTACAATTTTTCT 57.810 33.333 0.00 0.00 35.20 2.52
393 814 5.441718 AAAGAGAAATCTGGCACTGGATA 57.558 39.130 0.00 0.00 0.00 2.59
403 824 7.228308 ACTCCAGAAACAGAAAAGAGAAATCTG 59.772 37.037 0.00 0.00 44.77 2.90
419 840 4.067972 TGTACCAGACAACTCCAGAAAC 57.932 45.455 0.00 0.00 34.15 2.78
445 866 6.384224 TCTGCATCACACAAGATTTCAAATC 58.616 36.000 1.42 1.42 0.00 2.17
455 949 5.296035 ACATCATGTATCTGCATCACACAAG 59.704 40.000 0.00 0.00 0.00 3.16
463 957 4.132336 GGACACACATCATGTATCTGCAT 58.868 43.478 0.00 0.00 40.64 3.96
875 1400 0.314302 CTAATCTACACGGGCCGAGG 59.686 60.000 35.78 25.51 0.00 4.63
876 1401 1.030457 ACTAATCTACACGGGCCGAG 58.970 55.000 35.78 28.52 0.00 4.63
909 1434 8.864087 GGAAGAAGAAGCATATTGGGATTTAAT 58.136 33.333 0.00 0.00 0.00 1.40
910 1435 8.061304 AGGAAGAAGAAGCATATTGGGATTTAA 58.939 33.333 0.00 0.00 0.00 1.52
921 1446 3.118738 GGAACCGAGGAAGAAGAAGCATA 60.119 47.826 0.00 0.00 0.00 3.14
963 1488 1.955683 GCCTTTTTGCTCTAGGGGTCC 60.956 57.143 0.00 0.00 0.00 4.46
1012 1542 2.444696 CCCCCACATGCCCTTCAA 59.555 61.111 0.00 0.00 0.00 2.69
1064 1594 4.044065 TGAAAGGAGCAGGAAGGGAATTTA 59.956 41.667 0.00 0.00 0.00 1.40
1065 1595 3.181418 TGAAAGGAGCAGGAAGGGAATTT 60.181 43.478 0.00 0.00 0.00 1.82
1068 1598 1.444933 TGAAAGGAGCAGGAAGGGAA 58.555 50.000 0.00 0.00 0.00 3.97
1069 1599 1.352352 CTTGAAAGGAGCAGGAAGGGA 59.648 52.381 0.00 0.00 0.00 4.20
1070 1600 1.831580 CTTGAAAGGAGCAGGAAGGG 58.168 55.000 0.00 0.00 0.00 3.95
1082 1612 3.329225 AGGAGGAAAGGAGACCTTGAAAG 59.671 47.826 3.73 0.00 43.92 2.62
1083 1613 3.327439 AGGAGGAAAGGAGACCTTGAAA 58.673 45.455 3.73 0.00 43.92 2.69
1084 1614 2.991580 AGGAGGAAAGGAGACCTTGAA 58.008 47.619 3.73 0.00 43.92 2.69
1085 1615 2.723530 AGGAGGAAAGGAGACCTTGA 57.276 50.000 3.73 0.00 43.92 3.02
1086 1616 2.909662 AGAAGGAGGAAAGGAGACCTTG 59.090 50.000 0.00 0.00 43.92 3.61
1088 1618 2.827755 GAGAAGGAGGAAAGGAGACCT 58.172 52.381 0.00 0.00 39.41 3.85
1089 1619 1.478916 CGAGAAGGAGGAAAGGAGACC 59.521 57.143 0.00 0.00 0.00 3.85
1090 1620 1.478916 CCGAGAAGGAGGAAAGGAGAC 59.521 57.143 0.00 0.00 45.00 3.36
1174 1704 3.474570 GACCTCCAGCTCCCGCAT 61.475 66.667 0.00 0.00 39.10 4.73
1476 2026 9.669353 GGATTCATAGCACAATTGTAAAGTATG 57.331 33.333 11.53 14.36 0.00 2.39
1480 2030 7.765307 AGTGGATTCATAGCACAATTGTAAAG 58.235 34.615 11.53 0.00 0.00 1.85
1481 2031 7.701539 AGTGGATTCATAGCACAATTGTAAA 57.298 32.000 11.53 0.00 0.00 2.01
1482 2032 7.701539 AAGTGGATTCATAGCACAATTGTAA 57.298 32.000 11.53 0.89 0.00 2.41
1484 2034 7.176515 TGTTAAGTGGATTCATAGCACAATTGT 59.823 33.333 4.92 4.92 0.00 2.71
1485 2035 7.537715 TGTTAAGTGGATTCATAGCACAATTG 58.462 34.615 3.24 3.24 0.00 2.32
1558 2197 8.723942 ACAGTGCTCTAATTTGGTTCTAATAG 57.276 34.615 0.00 0.00 0.00 1.73
1573 2212 1.813178 CTCGGAACAGACAGTGCTCTA 59.187 52.381 0.00 0.00 0.00 2.43
1648 2287 4.017126 TCTTCGAAGAGAGAACTGCCATA 58.983 43.478 23.74 0.00 38.43 2.74
1652 2291 6.952935 TTATTTCTTCGAAGAGAGAACTGC 57.047 37.500 25.73 0.00 38.43 4.40
1707 2346 2.638154 CTCGGAGGATACGCGGTC 59.362 66.667 12.47 8.27 46.39 4.79
1712 2351 1.000163 CACCATTCCTCGGAGGATACG 60.000 57.143 26.54 17.75 45.34 3.06
1715 2354 1.123928 GACACCATTCCTCGGAGGAT 58.876 55.000 26.54 11.32 45.34 3.24
1745 2384 3.891805 AGGGGGAAATGATGATCTTCC 57.108 47.619 6.17 5.20 38.33 3.46
1752 2391 5.302823 GGTTATGAGAAAGGGGGAAATGATG 59.697 44.000 0.00 0.00 0.00 3.07
1756 2395 4.294970 ACTGGTTATGAGAAAGGGGGAAAT 59.705 41.667 0.00 0.00 0.00 2.17
1757 2396 3.660669 ACTGGTTATGAGAAAGGGGGAAA 59.339 43.478 0.00 0.00 0.00 3.13
1761 2400 4.019681 TGTGTACTGGTTATGAGAAAGGGG 60.020 45.833 0.00 0.00 0.00 4.79
1815 2454 7.161773 ACATCCTTCATGAGTTGTTTAATGG 57.838 36.000 0.00 0.00 36.21 3.16
1818 2457 7.815840 TCAACATCCTTCATGAGTTGTTTAA 57.184 32.000 18.76 3.42 40.19 1.52
1860 2500 2.847234 AGACAAGGTGTGGCGGGA 60.847 61.111 0.00 0.00 41.91 5.14
1866 2506 2.620251 TGTGAAGGAGACAAGGTGTG 57.380 50.000 0.00 0.00 0.00 3.82
1875 2515 8.713971 ACAACAATGGTATATATGTGAAGGAGA 58.286 33.333 0.00 0.00 0.00 3.71
1890 2530 7.883391 TTCCAGAAACTAAACAACAATGGTA 57.117 32.000 0.00 0.00 0.00 3.25
1976 2622 4.202284 TGTGGTACCAACAGTAAACCTCTC 60.202 45.833 18.31 0.00 29.59 3.20
2018 2664 7.655328 CCCAACAATTTTATGTACTGCAAAAGA 59.345 33.333 0.00 0.00 32.02 2.52
2019 2665 7.095271 CCCCAACAATTTTATGTACTGCAAAAG 60.095 37.037 0.00 0.00 32.02 2.27
2093 2739 1.838077 GGCCAGTACCAGGTTCATAGT 59.162 52.381 0.00 0.00 0.00 2.12
2274 2920 1.197036 CGAGCGCTAACTGGATATCGA 59.803 52.381 11.50 0.00 0.00 3.59
2275 2921 1.607713 CGAGCGCTAACTGGATATCG 58.392 55.000 11.50 1.03 0.00 2.92
2320 2966 5.514279 ACTAGTACATATCGTTAACGTGCC 58.486 41.667 25.98 12.10 40.80 5.01
2432 3101 7.913297 GTGTACTTAAATGAACAAAACTGAGCA 59.087 33.333 0.00 0.00 0.00 4.26
2462 3131 6.474102 CGCCAAGTTGTTTTTACAGTAAACAT 59.526 34.615 5.16 0.00 42.95 2.71
2463 3132 5.800941 CGCCAAGTTGTTTTTACAGTAAACA 59.199 36.000 5.16 1.50 42.09 2.83
2490 3159 4.833478 ACAGACTACATGCTTCCTCAAT 57.167 40.909 0.00 0.00 0.00 2.57
2700 3369 7.201714 GGAATATTGCTCCATCAGATTAGCATC 60.202 40.741 15.11 10.71 43.94 3.91
2769 3438 4.717877 TGTATAGGCTAGTTGCATGCAAT 58.282 39.130 33.94 23.73 45.15 3.56
2804 3473 1.298014 CGCTCAAAGGGCTCCTCTT 59.702 57.895 0.00 0.00 30.89 2.85
2885 3554 6.102897 AGCTAGTACACTTGACACAGATTT 57.897 37.500 0.00 0.00 0.00 2.17
3025 3694 0.098200 GCGCCACCGGAAAAGTAATC 59.902 55.000 9.46 0.00 34.32 1.75
3084 3753 5.537674 AGTTGTTTGCTTCAATCTCCTTCAT 59.462 36.000 0.00 0.00 0.00 2.57
3555 4226 2.228582 TGCAACAATGTCGAAGGGAATG 59.771 45.455 0.00 0.00 0.00 2.67
3569 4240 7.763528 AGAATATCAAAAGTGTGTTTGCAACAA 59.236 29.630 0.00 0.00 44.16 2.83
3684 4359 1.063174 GCCTCAAGTTAGCGCAATGAG 59.937 52.381 11.47 14.62 37.77 2.90
3752 4427 4.248859 CGATTGGATCTACAATGGGCTAG 58.751 47.826 2.36 0.00 40.92 3.42
3759 4434 7.445121 TGATTTCTAGCGATTGGATCTACAAT 58.555 34.615 0.00 0.00 43.36 2.71
3821 4496 2.305928 CGAGATCTCTGACCCAGTGAT 58.694 52.381 20.26 10.23 44.12 3.06
3867 4542 7.757526 TGAAAACAGAACGAGATTCTCAAAAA 58.242 30.769 13.88 0.00 44.99 1.94
3868 4543 7.315247 TGAAAACAGAACGAGATTCTCAAAA 57.685 32.000 13.88 0.00 44.99 2.44
3869 4544 6.918892 TGAAAACAGAACGAGATTCTCAAA 57.081 33.333 13.88 0.00 44.99 2.69
3870 4545 6.931281 AGATGAAAACAGAACGAGATTCTCAA 59.069 34.615 13.88 0.00 44.99 3.02
3871 4546 6.367149 CAGATGAAAACAGAACGAGATTCTCA 59.633 38.462 13.88 0.00 44.99 3.27
3872 4547 6.587990 TCAGATGAAAACAGAACGAGATTCTC 59.412 38.462 3.43 3.43 44.99 2.87
3874 4549 6.712241 TCAGATGAAAACAGAACGAGATTC 57.288 37.500 0.00 0.00 37.62 2.52
3875 4550 6.875726 TGATCAGATGAAAACAGAACGAGATT 59.124 34.615 0.00 0.00 0.00 2.40
3876 4551 6.401394 TGATCAGATGAAAACAGAACGAGAT 58.599 36.000 0.00 0.00 0.00 2.75
3877 4552 5.783111 TGATCAGATGAAAACAGAACGAGA 58.217 37.500 0.00 0.00 0.00 4.04
3878 4553 5.866092 TCTGATCAGATGAAAACAGAACGAG 59.134 40.000 21.67 0.00 33.53 4.18
3879 4554 5.783111 TCTGATCAGATGAAAACAGAACGA 58.217 37.500 21.67 0.00 33.53 3.85
3880 4555 6.471976 TTCTGATCAGATGAAAACAGAACG 57.528 37.500 25.64 0.00 37.59 3.95
3937 4612 3.369546 GCTGTTGCAAGAAAAGGCTTA 57.630 42.857 0.00 0.00 39.41 3.09
3939 4614 3.974222 GCTGTTGCAAGAAAAGGCT 57.026 47.368 0.00 0.00 39.41 4.58
3965 4640 3.057174 CCCAGTCTCAGTCTAGACAACAC 60.057 52.174 24.44 14.26 46.89 3.32
3979 4654 0.689080 TGATGGAGAGGCCCAGTCTC 60.689 60.000 11.24 11.24 39.97 3.36
4059 4734 2.022129 CCGGTGAACTGCTCGTGTC 61.022 63.158 0.00 0.00 0.00 3.67
4061 4736 2.029073 ACCGGTGAACTGCTCGTG 59.971 61.111 6.12 0.00 0.00 4.35
4062 4737 1.457823 TACACCGGTGAACTGCTCGT 61.458 55.000 40.21 17.29 0.00 4.18
4064 4739 1.798813 CTTTACACCGGTGAACTGCTC 59.201 52.381 40.21 0.00 0.00 4.26
4065 4740 1.414919 TCTTTACACCGGTGAACTGCT 59.585 47.619 40.21 19.60 0.00 4.24
4066 4741 1.873698 TCTTTACACCGGTGAACTGC 58.126 50.000 40.21 0.00 0.00 4.40
4067 4742 6.570692 AGTATATCTTTACACCGGTGAACTG 58.429 40.000 40.21 24.63 0.00 3.16
4077 4784 6.040166 TGAACGGAGGGAGTATATCTTTACAC 59.960 42.308 0.00 0.00 0.00 2.90
4145 4852 5.163499 TGTGTTTGTTTACCCATTTCAGTCC 60.163 40.000 0.00 0.00 0.00 3.85
4156 4863 6.085573 ACACGTTTTACTGTGTTTGTTTACC 58.914 36.000 0.00 0.00 46.61 2.85
4204 4911 7.902920 ATACTGCCTCCATTCACAAATTATT 57.097 32.000 0.00 0.00 0.00 1.40
4205 4912 7.902920 AATACTGCCTCCATTCACAAATTAT 57.097 32.000 0.00 0.00 0.00 1.28
4241 4959 5.221342 GGAACAGTGAGCAGCTATGTAGTAT 60.221 44.000 0.00 0.00 0.00 2.12
4334 5052 3.716431 TCCAGGGATCTAAACCTACGTT 58.284 45.455 0.00 0.00 34.71 3.99
4358 5077 3.426159 CGGTTTCCTGATCACCATTTTCG 60.426 47.826 0.00 0.00 0.00 3.46
4379 5098 2.596904 ATACCCATTCCGAGAACACG 57.403 50.000 0.00 0.00 0.00 4.49
4380 5099 3.869065 TGAATACCCATTCCGAGAACAC 58.131 45.455 0.00 0.00 39.97 3.32
4381 5100 3.681594 GCTGAATACCCATTCCGAGAACA 60.682 47.826 0.00 0.00 39.97 3.18
4382 5101 2.872858 GCTGAATACCCATTCCGAGAAC 59.127 50.000 0.00 0.00 39.97 3.01
4383 5102 2.503765 TGCTGAATACCCATTCCGAGAA 59.496 45.455 0.00 0.00 39.97 2.87
4384 5103 2.115427 TGCTGAATACCCATTCCGAGA 58.885 47.619 0.00 0.00 39.97 4.04


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

AutoCloner maintained by Alex Coulton.