Multiple sequence alignment - TraesCS4D01G087900

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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 TraesCS4D01G087900 chr4D 100.000 6019 0 0 1 6019 63048560 63042542 0.000000e+00 11116.0
1 TraesCS4D01G087900 chr4D 92.857 168 11 1 421 588 63047973 63047807 6.030000e-60 243.0
2 TraesCS4D01G087900 chr4D 92.857 168 11 1 588 754 63048140 63047973 6.030000e-60 243.0
3 TraesCS4D01G087900 chr4B 93.060 3487 138 35 121 3590 93413373 93409974 0.000000e+00 5003.0
4 TraesCS4D01G087900 chr4B 93.036 1996 73 23 4046 6019 93409227 93407276 0.000000e+00 2856.0
5 TraesCS4D01G087900 chr4B 97.256 328 9 0 3617 3944 93409678 93409351 1.900000e-154 556.0
6 TraesCS4D01G087900 chr4B 95.238 168 7 1 421 588 93412909 93412743 1.290000e-66 265.0
7 TraesCS4D01G087900 chr4B 91.071 168 12 3 588 754 93413074 93412909 2.180000e-54 224.0
8 TraesCS4D01G087900 chr4A 93.520 2145 84 20 421 2555 533257583 533259682 0.000000e+00 3140.0
9 TraesCS4D01G087900 chr4A 96.172 1515 37 6 3944 5451 533261152 533262652 0.000000e+00 2457.0
10 TraesCS4D01G087900 chr4A 89.264 1304 83 34 2659 3944 533259840 533261104 0.000000e+00 1580.0
11 TraesCS4D01G087900 chr4A 90.646 449 30 5 5581 6019 533262651 533263097 2.420000e-163 586.0
12 TraesCS4D01G087900 chr4A 96.763 278 4 1 1 273 533256719 533256996 5.500000e-125 459.0
13 TraesCS4D01G087900 chr4A 93.355 301 15 4 457 754 533256933 533257231 1.990000e-119 440.0
14 TraesCS4D01G087900 chr4A 95.736 258 8 2 421 676 533257063 533257319 4.340000e-111 412.0
15 TraesCS4D01G087900 chr4A 95.833 168 6 1 421 588 533257751 533257917 2.760000e-68 270.0
16 TraesCS4D01G087900 chr4A 92.571 175 11 1 582 754 533257577 533257751 3.600000e-62 250.0
17 TraesCS4D01G087900 chr4A 92.035 113 9 0 642 754 533256951 533257063 6.240000e-35 159.0
18 TraesCS4D01G087900 chr4A 96.703 91 2 1 421 511 533257231 533257320 3.760000e-32 150.0
19 TraesCS4D01G087900 chrUn 100.000 399 0 0 4609 5007 478813222 478812824 0.000000e+00 737.0
20 TraesCS4D01G087900 chr2D 81.436 738 127 7 4200 4935 394120045 394119316 4.020000e-166 595.0
21 TraesCS4D01G087900 chr2D 79.856 139 21 7 1340 1475 420312429 420312295 1.790000e-15 95.3
22 TraesCS4D01G087900 chr2B 80.629 795 133 15 4153 4935 465826788 465826003 4.020000e-166 595.0
23 TraesCS4D01G087900 chr2B 91.630 227 19 0 1267 1493 465829308 465829082 1.260000e-81 315.0
24 TraesCS4D01G087900 chr2A 80.350 743 129 12 4200 4935 532086892 532086160 1.140000e-151 547.0
25 TraesCS4D01G087900 chr2A 90.749 227 21 0 1267 1493 532089414 532089188 2.730000e-78 303.0
26 TraesCS4D01G087900 chr7D 83.750 80 8 3 5440 5514 141179751 141179672 3.010000e-08 71.3


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 TraesCS4D01G087900 chr4D 63042542 63048560 6018 True 3867.333333 11116 95.238000 1 6019 3 chr4D.!!$R1 6018
1 TraesCS4D01G087900 chr4B 93407276 93413373 6097 True 1780.800000 5003 93.932200 121 6019 5 chr4B.!!$R1 5898
2 TraesCS4D01G087900 chr4A 533256719 533263097 6378 False 900.272727 3140 93.872545 1 6019 11 chr4A.!!$F1 6018
3 TraesCS4D01G087900 chr2D 394119316 394120045 729 True 595.000000 595 81.436000 4200 4935 1 chr2D.!!$R1 735
4 TraesCS4D01G087900 chr2B 465826003 465829308 3305 True 455.000000 595 86.129500 1267 4935 2 chr2B.!!$R1 3668
5 TraesCS4D01G087900 chr2A 532086160 532089414 3254 True 425.000000 547 85.549500 1267 4935 2 chr2A.!!$R1 3668

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
462 637 1.133181 TGTGCCCTCCATGTGGAAGA 61.133 55.000 2.97 0.00 44.91 2.87 F
1513 2046 0.386113 GCCACCGTAAAACCAGCAAA 59.614 50.000 0.00 0.00 0.00 3.68 F
2408 3448 0.403271 ATCAACAGGGAGCAGTGCTT 59.597 50.000 20.80 0.00 39.88 3.91 F
2514 3641 0.668706 CTGTGGACTGAAGTCTGCCG 60.669 60.000 10.17 0.00 44.20 5.69 F
2515 3642 1.374758 GTGGACTGAAGTCTGCCGG 60.375 63.158 10.17 0.00 44.20 6.13 F
3504 5208 1.099295 ATGAGTGACATGCATGCCCG 61.099 55.000 26.53 8.67 37.87 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1574 2109 1.750780 GCACTAGCCTTTCCCTGCC 60.751 63.158 0.00 0.00 33.58 4.85 R
3428 5131 0.251916 CAGAATGGGCCTACGGTTCA 59.748 55.000 4.53 0.00 0.00 3.18 R
3487 5191 1.026182 TTCGGGCATGCATGTCACTC 61.026 55.000 30.90 14.11 33.08 3.51 R
3504 5208 1.286248 AGGTAGGTGGTGTCCCATTC 58.714 55.000 0.00 0.00 44.35 2.67 R
3858 5832 2.665000 CGAGGCCCTCATGTGTGT 59.335 61.111 12.13 0.00 0.00 3.72 R
5456 7524 0.457853 TGATCGCTTGCGTCTGTACC 60.458 55.000 14.70 0.00 0.00 3.34 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
50 51 5.239525 ACAAGTAAAAGAGAGTTGGTGCATC 59.760 40.000 0.00 0.00 32.49 3.91
283 290 4.081752 TCAAGCAGTGACAAACAAAATGGT 60.082 37.500 0.00 0.00 0.00 3.55
285 292 2.865551 GCAGTGACAAACAAAATGGTGG 59.134 45.455 0.00 0.00 0.00 4.61
359 366 5.590976 AAAGAAGACAGGGAGAAAAGGAT 57.409 39.130 0.00 0.00 0.00 3.24
360 367 4.566426 AGAAGACAGGGAGAAAAGGATG 57.434 45.455 0.00 0.00 0.00 3.51
361 368 4.171234 AGAAGACAGGGAGAAAAGGATGA 58.829 43.478 0.00 0.00 0.00 2.92
375 382 8.763984 AGAAAAGGATGAAGATGCTTATTCAT 57.236 30.769 19.02 19.02 46.21 2.57
445 620 8.082852 ACTCATAGCTCGTATCGAATTAAATGT 58.917 33.333 0.00 0.00 34.74 2.71
462 637 1.133181 TGTGCCCTCCATGTGGAAGA 61.133 55.000 2.97 0.00 44.91 2.87
580 1109 5.354513 TGATTATTCGCATTTTCACCGGTAA 59.645 36.000 6.87 0.00 0.00 2.85
621 1150 2.350772 CGAATTAAATGCGCCCTCCATC 60.351 50.000 4.18 0.00 0.00 3.51
622 1151 1.620822 ATTAAATGCGCCCTCCATCC 58.379 50.000 4.18 0.00 0.00 3.51
663 1192 9.571810 TTCCATTTCACATCAAATTCTTAATCG 57.428 29.630 0.00 0.00 0.00 3.34
664 1193 8.739039 TCCATTTCACATCAAATTCTTAATCGT 58.261 29.630 0.00 0.00 0.00 3.73
676 1205 4.092771 TCTTAATCGTGTTGTCTCCTCG 57.907 45.455 0.00 0.00 0.00 4.63
827 1356 4.935808 AGTTGCCTAGAATTTACCAAGACG 59.064 41.667 0.00 0.00 0.00 4.18
831 1360 4.680975 GCCTAGAATTTACCAAGACGCTCT 60.681 45.833 0.00 0.00 0.00 4.09
832 1361 5.420409 CCTAGAATTTACCAAGACGCTCTT 58.580 41.667 0.00 0.00 37.14 2.85
833 1362 6.570692 CCTAGAATTTACCAAGACGCTCTTA 58.429 40.000 0.00 0.00 33.78 2.10
834 1363 6.697892 CCTAGAATTTACCAAGACGCTCTTAG 59.302 42.308 0.00 0.00 33.78 2.18
835 1364 6.282199 AGAATTTACCAAGACGCTCTTAGA 57.718 37.500 0.87 0.00 33.78 2.10
836 1365 6.334202 AGAATTTACCAAGACGCTCTTAGAG 58.666 40.000 4.63 4.63 33.78 2.43
837 1366 4.451629 TTTACCAAGACGCTCTTAGAGG 57.548 45.455 11.54 3.97 33.78 3.69
1008 1537 6.473758 GGTAACTATAGGGGAAATGGATGTC 58.526 44.000 4.43 0.00 0.00 3.06
1175 1704 1.968493 GCATCCATCCATCCATGCTTT 59.032 47.619 0.00 0.00 38.89 3.51
1181 1710 3.449737 CCATCCATCCATGCTTTTGTCTT 59.550 43.478 0.00 0.00 0.00 3.01
1235 1764 4.276926 GTGCTCTGTTCTTGTCCTTTGAAT 59.723 41.667 0.00 0.00 0.00 2.57
1300 1829 1.331756 GCGTTTGAGATCATGGCGATT 59.668 47.619 0.00 0.00 33.17 3.34
1513 2046 0.386113 GCCACCGTAAAACCAGCAAA 59.614 50.000 0.00 0.00 0.00 3.68
1543 2076 9.764363 AAGGATCATTTCTTTTGTTTTTCTACC 57.236 29.630 0.00 0.00 0.00 3.18
1618 2153 7.184779 GTGCGACTTTAAAGTTTTAACTGACT 58.815 34.615 21.40 0.00 39.88 3.41
1826 2361 6.560711 CGAAAAGGAGGAAACTGAAAAGAAA 58.439 36.000 0.00 0.00 44.43 2.52
1827 2362 7.203218 CGAAAAGGAGGAAACTGAAAAGAAAT 58.797 34.615 0.00 0.00 44.43 2.17
1900 2529 3.198872 CGCCAGGTTTCTAAAGAGGATC 58.801 50.000 0.00 0.00 0.00 3.36
2408 3448 0.403271 ATCAACAGGGAGCAGTGCTT 59.597 50.000 20.80 0.00 39.88 3.91
2410 3450 1.160137 CAACAGGGAGCAGTGCTTAC 58.840 55.000 20.80 15.19 39.88 2.34
2411 3451 0.764890 AACAGGGAGCAGTGCTTACA 59.235 50.000 20.80 0.00 39.88 2.41
2423 3463 1.459592 GTGCTTACACAAGGTAGCGTG 59.540 52.381 6.30 6.30 46.61 5.34
2437 3562 1.947146 GCGTGGGGCGTTCAAAAAC 60.947 57.895 0.00 0.00 43.66 2.43
2452 3577 8.683774 GCGTTCAAAAACTAATTTAATCGAACA 58.316 29.630 0.00 0.00 31.88 3.18
2514 3641 0.668706 CTGTGGACTGAAGTCTGCCG 60.669 60.000 10.17 0.00 44.20 5.69
2515 3642 1.374758 GTGGACTGAAGTCTGCCGG 60.375 63.158 10.17 0.00 44.20 6.13
2516 3643 2.435059 GGACTGAAGTCTGCCGGC 60.435 66.667 22.73 22.73 44.20 6.13
2521 3650 2.436824 GAAGTCTGCCGGCCTTCC 60.437 66.667 26.77 9.31 30.67 3.46
2522 3651 3.249189 AAGTCTGCCGGCCTTCCA 61.249 61.111 26.77 2.93 0.00 3.53
2538 3667 4.096382 GCCTTCCACACAAATATCACGAAT 59.904 41.667 0.00 0.00 0.00 3.34
2719 3946 6.777580 TCATATTGGAATCCTCCTAAAAAGGC 59.222 38.462 0.00 0.00 42.94 4.35
2733 3960 9.500785 CTCCTAAAAAGGCAATATTTTCCAAAA 57.499 29.630 6.35 0.00 31.62 2.44
3013 4242 1.648720 CGCCGGCCAGTGATATTTG 59.351 57.895 23.46 0.00 0.00 2.32
3053 4282 3.999663 CCAAAAGGCACACAACAAAAAGA 59.000 39.130 0.00 0.00 0.00 2.52
3213 4900 8.559536 CCATAGCACACGAAACTCATATATTTT 58.440 33.333 0.00 0.00 0.00 1.82
3246 4933 5.120830 GGATCCATCCGAAGAAATTATCACG 59.879 44.000 6.95 0.00 37.19 4.35
3249 4936 6.110033 TCCATCCGAAGAAATTATCACGAAA 58.890 36.000 0.00 0.00 33.92 3.46
3481 5185 3.151554 TGCATCAATCATGGAGGTATGC 58.848 45.455 11.52 11.52 38.90 3.14
3482 5186 3.151554 GCATCAATCATGGAGGTATGCA 58.848 45.455 12.80 0.00 38.44 3.96
3487 5191 4.581409 TCAATCATGGAGGTATGCAACATG 59.419 41.667 0.00 0.00 40.06 3.21
3504 5208 1.099295 ATGAGTGACATGCATGCCCG 61.099 55.000 26.53 8.67 37.87 6.13
3593 5298 7.435068 TGTAAGTTACATTTTCTCCTTGAGC 57.565 36.000 11.75 0.00 32.89 4.26
3594 5299 7.224297 TGTAAGTTACATTTTCTCCTTGAGCT 58.776 34.615 11.75 0.00 32.89 4.09
3595 5300 6.809630 AAGTTACATTTTCTCCTTGAGCTC 57.190 37.500 6.82 6.82 0.00 4.09
3596 5301 5.869579 AGTTACATTTTCTCCTTGAGCTCA 58.130 37.500 13.74 13.74 0.00 4.26
3597 5302 6.479884 AGTTACATTTTCTCCTTGAGCTCAT 58.520 36.000 19.04 0.00 0.00 2.90
3598 5303 7.624549 AGTTACATTTTCTCCTTGAGCTCATA 58.375 34.615 19.04 7.79 0.00 2.15
3599 5304 8.270744 AGTTACATTTTCTCCTTGAGCTCATAT 58.729 33.333 19.04 0.00 0.00 1.78
3600 5305 6.939132 ACATTTTCTCCTTGAGCTCATATG 57.061 37.500 19.04 10.79 0.00 1.78
3601 5306 6.421485 ACATTTTCTCCTTGAGCTCATATGT 58.579 36.000 19.04 13.04 0.00 2.29
3602 5307 7.568349 ACATTTTCTCCTTGAGCTCATATGTA 58.432 34.615 19.04 0.25 0.00 2.29
3603 5308 8.216423 ACATTTTCTCCTTGAGCTCATATGTAT 58.784 33.333 19.04 1.59 0.00 2.29
3604 5309 9.716531 CATTTTCTCCTTGAGCTCATATGTATA 57.283 33.333 19.04 0.00 0.00 1.47
3605 5310 9.941325 ATTTTCTCCTTGAGCTCATATGTATAG 57.059 33.333 19.04 9.81 0.00 1.31
3606 5311 6.522625 TCTCCTTGAGCTCATATGTATAGC 57.477 41.667 19.04 6.75 36.48 2.97
3608 5313 7.406104 TCTCCTTGAGCTCATATGTATAGCTA 58.594 38.462 19.04 0.00 46.29 3.32
3609 5314 7.555914 TCTCCTTGAGCTCATATGTATAGCTAG 59.444 40.741 19.04 6.95 46.29 3.42
3610 5315 6.096141 TCCTTGAGCTCATATGTATAGCTAGC 59.904 42.308 19.04 6.62 46.29 3.42
3611 5316 6.096705 CCTTGAGCTCATATGTATAGCTAGCT 59.903 42.308 23.12 23.12 46.29 3.32
3612 5317 7.363705 CCTTGAGCTCATATGTATAGCTAGCTT 60.364 40.741 24.88 13.16 46.29 3.74
3613 5318 8.581253 TTGAGCTCATATGTATAGCTAGCTTA 57.419 34.615 24.88 9.19 46.29 3.09
3614 5319 8.219546 TGAGCTCATATGTATAGCTAGCTTAG 57.780 38.462 24.88 7.76 46.29 2.18
3658 5632 8.254508 CACCTCAAAGGCTAGGATAGTTATATC 58.745 40.741 8.80 0.00 41.93 1.63
3949 5976 4.945543 TGGTCAATGATGTTCTTCATGAGG 59.054 41.667 0.00 0.00 36.48 3.86
4042 6070 2.091885 TGAATGGATTACAGGCTTCCCC 60.092 50.000 0.63 0.00 0.00 4.81
5019 7068 0.033504 TGAGAAGGGTTCTGCGTGAC 59.966 55.000 0.00 0.00 40.87 3.67
5183 7236 9.847224 ATGTGGTTAGTTATTAATTAGTCCTGG 57.153 33.333 0.00 0.00 0.00 4.45
5184 7237 7.771826 TGTGGTTAGTTATTAATTAGTCCTGGC 59.228 37.037 0.00 0.00 0.00 4.85
5185 7238 6.987992 TGGTTAGTTATTAATTAGTCCTGGCG 59.012 38.462 0.00 0.00 0.00 5.69
5186 7239 6.426025 GGTTAGTTATTAATTAGTCCTGGCGG 59.574 42.308 0.00 0.00 0.00 6.13
5187 7240 4.969484 AGTTATTAATTAGTCCTGGCGGG 58.031 43.478 5.83 5.83 0.00 6.13
5188 7241 2.271944 ATTAATTAGTCCTGGCGGGC 57.728 50.000 7.74 2.78 34.14 6.13
5190 7243 2.091098 TAATTAGTCCTGGCGGGCTA 57.909 50.000 7.74 9.84 45.45 3.93
5192 7245 2.838225 TAGTCCTGGCGGGCTAGC 60.838 66.667 7.74 6.04 45.45 3.42
5270 7323 2.039348 GCAGTTGTGGGTAGGGAACTAA 59.961 50.000 0.00 0.00 46.54 2.24
5414 7473 1.802715 CGTGGTACGGTTACGCTGG 60.803 63.158 0.00 0.00 46.04 4.85
5417 7476 1.177895 TGGTACGGTTACGCTGGTCA 61.178 55.000 0.00 0.00 46.04 4.02
5472 7540 0.883153 TAAGGTACAGACGCAAGCGA 59.117 50.000 22.30 0.00 42.83 4.93
5483 7551 3.049912 GACGCAAGCGATCATACATACA 58.950 45.455 22.30 0.00 42.83 2.29
5484 7552 3.653344 ACGCAAGCGATCATACATACAT 58.347 40.909 22.30 0.00 42.83 2.29
5492 7564 7.163001 AGCGATCATACATACATGTACTCAT 57.837 36.000 7.96 0.00 45.11 2.90
5495 7567 7.629437 GCGATCATACATACATGTACTCATCCT 60.629 40.741 7.96 0.00 45.11 3.24
5519 7591 3.342909 TGCACACACGCATCTTGG 58.657 55.556 0.00 0.00 36.86 3.61
5523 7595 1.600636 ACACACGCATCTTGGTGGG 60.601 57.895 0.00 0.00 43.16 4.61
5527 7599 3.136123 CGCATCTTGGTGGGCTGG 61.136 66.667 0.00 0.00 0.00 4.85
5529 7601 2.043652 CATCTTGGTGGGCTGGGG 60.044 66.667 0.00 0.00 0.00 4.96
5534 7606 1.230149 TTGGTGGGCTGGGGATACT 60.230 57.895 0.00 0.00 0.00 2.12
5536 7608 0.693092 TGGTGGGCTGGGGATACTAC 60.693 60.000 0.00 0.00 0.00 2.73
5557 7629 5.048846 ACTGTCCACTTAACCATTCAACT 57.951 39.130 0.00 0.00 0.00 3.16
5559 7631 5.995897 ACTGTCCACTTAACCATTCAACTAC 59.004 40.000 0.00 0.00 0.00 2.73
5562 7634 6.183361 TGTCCACTTAACCATTCAACTACAGA 60.183 38.462 0.00 0.00 0.00 3.41
5623 7695 3.187227 CGCCCTCTCCGATTTCATTTATG 59.813 47.826 0.00 0.00 0.00 1.90
5735 7814 3.591789 ACATCCAGAGTATGCCATACCT 58.408 45.455 11.18 5.75 36.40 3.08
5806 7887 2.718062 TCATGCAAGATCCCCATACCAT 59.282 45.455 0.00 0.00 0.00 3.55
5821 7902 0.482446 ACCATGGAGGCCAGTTTGAA 59.518 50.000 21.47 0.00 43.14 2.69
5825 7906 3.420893 CATGGAGGCCAGTTTGAAACTA 58.579 45.455 10.63 0.00 40.46 2.24
5839 7920 6.768381 AGTTTGAAACTAGAACCTCTCCAAAG 59.232 38.462 9.13 0.00 40.69 2.77
5848 7929 0.111253 CCTCTCCAAAGCCAACCAGT 59.889 55.000 0.00 0.00 0.00 4.00
5849 7930 1.528129 CTCTCCAAAGCCAACCAGTC 58.472 55.000 0.00 0.00 0.00 3.51
5875 7956 5.391950 CCAAACATAATTGACCAGGAGAACG 60.392 44.000 0.00 0.00 31.84 3.95
5880 7961 6.098409 ACATAATTGACCAGGAGAACGACTAT 59.902 38.462 0.00 0.00 0.00 2.12
5885 7966 6.540438 TGACCAGGAGAACGACTATAAATT 57.460 37.500 0.00 0.00 0.00 1.82
5920 8001 1.879380 CGGCAAAGATCAACCAACAGA 59.121 47.619 0.00 0.00 0.00 3.41
5926 8007 4.778534 AAGATCAACCAACAGATGCAAG 57.221 40.909 0.00 0.00 0.00 4.01
5927 8008 4.025040 AGATCAACCAACAGATGCAAGA 57.975 40.909 0.00 0.00 0.00 3.02
5977 8058 0.991146 TTCAGCTAGCCACCAATCCA 59.009 50.000 12.13 0.00 0.00 3.41
5988 8069 3.259123 GCCACCAATCCAAAGAACTTCAT 59.741 43.478 0.00 0.00 0.00 2.57
6010 8091 1.852157 TCCACCCTTGTGATGCCCT 60.852 57.895 0.00 0.00 45.76 5.19
6013 8094 0.962356 CACCCTTGTGATGCCCTGTC 60.962 60.000 0.00 0.00 45.76 3.51
6014 8095 1.379916 CCCTTGTGATGCCCTGTCA 59.620 57.895 0.00 0.00 0.00 3.58
6015 8096 0.962356 CCCTTGTGATGCCCTGTCAC 60.962 60.000 0.00 0.00 44.77 3.67
6016 8097 0.037303 CCTTGTGATGCCCTGTCACT 59.963 55.000 7.65 0.00 44.80 3.41
6018 8099 1.808945 CTTGTGATGCCCTGTCACTTC 59.191 52.381 7.65 0.00 44.80 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.313317 ACTTGTAGTGGAGTTGTCGGA 58.687 47.619 0.00 0.00 0.00 4.55
16 17 7.210873 ACTCTCTTTTACTTGTAGTGGAGTTG 58.789 38.462 0.00 0.00 0.00 3.16
50 51 3.466836 TGTTGAGCTGTGACTTACAAGG 58.533 45.455 0.00 0.00 39.20 3.61
375 382 2.357465 CCCAAGGCCATTTCTGATGAGA 60.357 50.000 5.01 0.00 0.00 3.27
445 620 0.776810 TTTCTTCCACATGGAGGGCA 59.223 50.000 9.93 0.00 46.36 5.36
554 1083 4.911610 CCGGTGAAAATGCGAATAATCATC 59.088 41.667 0.00 0.00 0.00 2.92
652 1181 5.577164 CGAGGAGACAACACGATTAAGAATT 59.423 40.000 0.00 0.00 0.00 2.17
663 1192 0.315568 ACTGCTCGAGGAGACAACAC 59.684 55.000 36.65 7.43 36.93 3.32
664 1193 0.315251 CACTGCTCGAGGAGACAACA 59.685 55.000 36.65 13.15 36.93 3.33
676 1205 3.664107 TGATTGGTTACTGTCACTGCTC 58.336 45.455 0.00 0.00 0.00 4.26
714 1243 7.267811 GTGAAAATGCGAATAATCATCGATGAG 59.732 37.037 30.11 17.77 42.76 2.90
716 1245 6.303970 GGTGAAAATGCGAATAATCATCGATG 59.696 38.462 19.61 19.61 42.76 3.84
717 1246 6.373779 GGTGAAAATGCGAATAATCATCGAT 58.626 36.000 0.00 0.00 42.76 3.59
719 1248 4.608470 CGGTGAAAATGCGAATAATCATCG 59.392 41.667 8.98 8.98 42.99 3.84
731 1260 1.268352 TGTGCTTACCGGTGAAAATGC 59.732 47.619 19.93 11.66 0.00 3.56
831 1360 0.391228 TGTTGCGTGCTCACCTCTAA 59.609 50.000 0.00 0.00 0.00 2.10
832 1361 0.319555 GTGTTGCGTGCTCACCTCTA 60.320 55.000 8.66 0.00 0.00 2.43
833 1362 1.595382 GTGTTGCGTGCTCACCTCT 60.595 57.895 8.66 0.00 0.00 3.69
834 1363 2.607892 GGTGTTGCGTGCTCACCTC 61.608 63.158 22.45 6.79 45.46 3.85
835 1364 2.591715 GGTGTTGCGTGCTCACCT 60.592 61.111 22.45 0.00 45.46 4.00
837 1366 1.724582 AAAGGGTGTTGCGTGCTCAC 61.725 55.000 10.52 10.52 0.00 3.51
991 1520 3.318313 ACTCGACATCCATTTCCCCTAT 58.682 45.455 0.00 0.00 0.00 2.57
1008 1537 1.337817 CTTGTTGCCTCGACGACTCG 61.338 60.000 0.00 0.00 41.65 4.18
1131 1660 1.271054 CCTAGGACAAACACAGCAGCT 60.271 52.381 1.05 0.00 0.00 4.24
1175 1704 8.681486 TGATGAATCAAGAAGAAAGAAGACAA 57.319 30.769 0.00 0.00 33.08 3.18
1181 1710 9.676861 ACATACATGATGAATCAAGAAGAAAGA 57.323 29.630 0.00 0.00 40.69 2.52
1257 1786 1.577328 GATCCCTGCACCAACACGTG 61.577 60.000 15.48 15.48 36.80 4.49
1543 2076 2.817258 TCCCGTGCCTTTGATAGTTTTG 59.183 45.455 0.00 0.00 0.00 2.44
1574 2109 1.750780 GCACTAGCCTTTCCCTGCC 60.751 63.158 0.00 0.00 33.58 4.85
1618 2153 5.461737 GTCGCCACAATCTTTTCATTTTTCA 59.538 36.000 0.00 0.00 0.00 2.69
2408 3448 1.976898 CCCCACGCTACCTTGTGTA 59.023 57.895 0.00 0.00 34.28 2.90
2410 3450 2.746277 GCCCCACGCTACCTTGTG 60.746 66.667 0.00 0.00 35.87 3.33
2411 3451 4.388499 CGCCCCACGCTACCTTGT 62.388 66.667 0.00 0.00 34.21 3.16
2421 3461 3.653539 ATTAGTTTTTGAACGCCCCAC 57.346 42.857 0.00 0.00 0.00 4.61
2423 3463 6.034150 CGATTAAATTAGTTTTTGAACGCCCC 59.966 38.462 0.00 0.00 0.00 5.80
2476 3601 6.546772 TCCACAGTGTACGTCCACAATATATA 59.453 38.462 14.08 0.00 37.82 0.86
2514 3641 2.097466 CGTGATATTTGTGTGGAAGGCC 59.903 50.000 0.00 0.00 0.00 5.19
2515 3642 3.006940 TCGTGATATTTGTGTGGAAGGC 58.993 45.455 0.00 0.00 0.00 4.35
2516 3643 5.818136 ATTCGTGATATTTGTGTGGAAGG 57.182 39.130 0.00 0.00 0.00 3.46
2521 3650 7.803189 GGCCTATTTATTCGTGATATTTGTGTG 59.197 37.037 0.00 0.00 0.00 3.82
2522 3651 7.500892 TGGCCTATTTATTCGTGATATTTGTGT 59.499 33.333 3.32 0.00 0.00 3.72
2538 3667 3.198853 GGGGTGCAAAAATGGCCTATTTA 59.801 43.478 3.32 0.00 38.01 1.40
2628 3855 9.191995 GATTTGACGTGGTTAAAAATCTGATTT 57.808 29.630 9.76 9.76 35.39 2.17
2631 3858 7.504924 AGATTTGACGTGGTTAAAAATCTGA 57.495 32.000 0.00 0.00 42.84 3.27
2632 3859 8.574196 AAAGATTTGACGTGGTTAAAAATCTG 57.426 30.769 9.10 0.00 43.36 2.90
2635 3862 8.974408 GCTTAAAGATTTGACGTGGTTAAAAAT 58.026 29.630 0.00 0.00 0.00 1.82
2636 3863 7.166142 CGCTTAAAGATTTGACGTGGTTAAAAA 59.834 33.333 0.00 0.00 0.00 1.94
2637 3864 6.633634 CGCTTAAAGATTTGACGTGGTTAAAA 59.366 34.615 0.00 0.00 0.00 1.52
2638 3865 6.137415 CGCTTAAAGATTTGACGTGGTTAAA 58.863 36.000 0.00 0.00 0.00 1.52
2639 3866 5.681880 CGCTTAAAGATTTGACGTGGTTAA 58.318 37.500 0.00 0.00 0.00 2.01
2640 3867 4.377635 GCGCTTAAAGATTTGACGTGGTTA 60.378 41.667 0.00 0.00 0.00 2.85
2641 3868 3.608474 GCGCTTAAAGATTTGACGTGGTT 60.608 43.478 0.00 0.00 0.00 3.67
2642 3869 2.095919 GCGCTTAAAGATTTGACGTGGT 60.096 45.455 0.00 0.00 0.00 4.16
2646 3873 4.065423 TCTTGCGCTTAAAGATTTGACG 57.935 40.909 9.73 0.00 0.00 4.35
2648 3875 7.569226 GCAAATTTCTTGCGCTTAAAGATTTGA 60.569 33.333 24.57 6.60 36.57 2.69
2733 3960 9.610104 ACTTAATAAATCCCACTAAAACCCTTT 57.390 29.630 0.00 0.00 0.00 3.11
2735 3962 9.916360 CTACTTAATAAATCCCACTAAAACCCT 57.084 33.333 0.00 0.00 0.00 4.34
2846 4075 5.776358 TGCCTATTCACCCAAATATTTCCT 58.224 37.500 0.00 0.00 0.00 3.36
3013 4242 6.399639 TTTTGGGTCAAGGTTTTGTAGATC 57.600 37.500 0.00 0.00 35.73 2.75
3094 4325 8.094548 TGTAGCATATCTTACTGAACAACTTGT 58.905 33.333 0.00 0.00 0.00 3.16
3098 4329 9.708222 CAAATGTAGCATATCTTACTGAACAAC 57.292 33.333 0.00 0.00 0.00 3.32
3144 4375 4.435436 TGCGCGCCAGACTGGTAG 62.435 66.667 30.77 17.17 40.46 3.18
3165 4396 6.022315 TGGGATCTTGATTAACAACCCATTT 58.978 36.000 0.00 0.00 43.07 2.32
3281 4968 8.681806 TGTGACAAATATATTTACCACCACATG 58.318 33.333 24.36 10.35 33.84 3.21
3428 5131 0.251916 CAGAATGGGCCTACGGTTCA 59.748 55.000 4.53 0.00 0.00 3.18
3487 5191 1.026182 TTCGGGCATGCATGTCACTC 61.026 55.000 30.90 14.11 33.08 3.51
3504 5208 1.286248 AGGTAGGTGGTGTCCCATTC 58.714 55.000 0.00 0.00 44.35 2.67
3571 5276 7.450074 TGAGCTCAAGGAGAAAATGTAACTTA 58.550 34.615 15.67 0.00 0.00 2.24
3606 5311 6.932356 TTGATTTTCATGAGGCTAAGCTAG 57.068 37.500 0.00 0.00 0.00 3.42
3607 5312 7.176515 TGTTTTGATTTTCATGAGGCTAAGCTA 59.823 33.333 0.00 0.00 0.00 3.32
3608 5313 6.015180 TGTTTTGATTTTCATGAGGCTAAGCT 60.015 34.615 0.00 0.00 0.00 3.74
3609 5314 6.089954 GTGTTTTGATTTTCATGAGGCTAAGC 59.910 38.462 0.00 0.00 0.00 3.09
3610 5315 6.587608 GGTGTTTTGATTTTCATGAGGCTAAG 59.412 38.462 0.00 0.00 0.00 2.18
3611 5316 6.267471 AGGTGTTTTGATTTTCATGAGGCTAA 59.733 34.615 0.00 0.00 0.00 3.09
3612 5317 5.774690 AGGTGTTTTGATTTTCATGAGGCTA 59.225 36.000 0.00 0.00 0.00 3.93
3613 5318 4.590222 AGGTGTTTTGATTTTCATGAGGCT 59.410 37.500 0.00 0.00 0.00 4.58
3614 5319 4.886579 AGGTGTTTTGATTTTCATGAGGC 58.113 39.130 0.00 0.00 0.00 4.70
3615 5320 6.088016 TGAGGTGTTTTGATTTTCATGAGG 57.912 37.500 0.00 0.00 0.00 3.86
3858 5832 2.665000 CGAGGCCCTCATGTGTGT 59.335 61.111 12.13 0.00 0.00 3.72
3949 5976 4.913376 AGCGACATATTGCAAATGACTTC 58.087 39.130 20.96 11.60 37.75 3.01
4014 6042 7.064966 GGAAGCCTGTAATCCATTCAAAAATTG 59.935 37.037 0.00 0.00 33.30 2.32
5185 7238 2.203596 TACCTAGCCGGCTAGCCC 60.204 66.667 44.85 14.98 43.35 5.19
5186 7239 1.807495 CTGTACCTAGCCGGCTAGCC 61.807 65.000 44.85 34.82 43.35 3.93
5187 7240 1.108132 ACTGTACCTAGCCGGCTAGC 61.108 60.000 44.85 34.39 43.35 3.42
5188 7241 1.400737 AACTGTACCTAGCCGGCTAG 58.599 55.000 43.78 43.78 44.07 3.42
5189 7242 1.856629 AAACTGTACCTAGCCGGCTA 58.143 50.000 33.24 33.24 35.61 3.93
5190 7243 1.856629 TAAACTGTACCTAGCCGGCT 58.143 50.000 34.85 34.85 35.61 5.52
5191 7244 2.678471 TTAAACTGTACCTAGCCGGC 57.322 50.000 21.89 21.89 35.61 6.13
5192 7245 3.528532 CCTTTAAACTGTACCTAGCCGG 58.471 50.000 0.00 0.00 39.35 6.13
5193 7246 3.055602 ACCCTTTAAACTGTACCTAGCCG 60.056 47.826 0.00 0.00 0.00 5.52
5270 7323 2.237392 GCTACTTGATGTCTTGGTCCCT 59.763 50.000 0.00 0.00 0.00 4.20
5371 7430 3.877559 TCATGTGGCAGAGGATAACTTG 58.122 45.455 0.00 0.00 0.00 3.16
5414 7473 9.692749 TGTATCTCGGAACAATATTAATCTGAC 57.307 33.333 6.96 1.50 0.00 3.51
5456 7524 0.457853 TGATCGCTTGCGTCTGTACC 60.458 55.000 14.70 0.00 0.00 3.34
5462 7530 3.049912 TGTATGTATGATCGCTTGCGTC 58.950 45.455 14.70 11.62 0.00 5.19
5464 7532 3.429881 ACATGTATGTATGATCGCTTGCG 59.570 43.478 8.87 8.87 39.68 4.85
5465 7533 4.997905 ACATGTATGTATGATCGCTTGC 57.002 40.909 0.00 0.00 39.68 4.01
5483 7551 7.992608 TGTGTGCATTTATAAGGATGAGTACAT 59.007 33.333 0.00 0.00 39.67 2.29
5484 7552 7.279981 GTGTGTGCATTTATAAGGATGAGTACA 59.720 37.037 0.00 1.68 0.00 2.90
5492 7564 3.339141 TGCGTGTGTGCATTTATAAGGA 58.661 40.909 0.00 0.00 40.62 3.36
5514 7586 1.083895 TATCCCCAGCCCACCAAGA 59.916 57.895 0.00 0.00 0.00 3.02
5516 7588 0.045008 TAGTATCCCCAGCCCACCAA 59.955 55.000 0.00 0.00 0.00 3.67
5519 7591 0.759346 CAGTAGTATCCCCAGCCCAC 59.241 60.000 0.00 0.00 0.00 4.61
5523 7595 1.413077 GTGGACAGTAGTATCCCCAGC 59.587 57.143 0.00 0.00 33.69 4.85
5527 7599 4.713321 TGGTTAAGTGGACAGTAGTATCCC 59.287 45.833 0.00 0.00 33.69 3.85
5529 7601 7.553334 TGAATGGTTAAGTGGACAGTAGTATC 58.447 38.462 0.00 0.00 0.00 2.24
5534 7606 6.182507 AGTTGAATGGTTAAGTGGACAGTA 57.817 37.500 0.00 0.00 0.00 2.74
5536 7608 5.995282 TGTAGTTGAATGGTTAAGTGGACAG 59.005 40.000 0.00 0.00 0.00 3.51
5623 7695 6.281405 TCTATAAGCGAAGACCTTGATTTCC 58.719 40.000 0.00 0.00 0.00 3.13
5806 7887 2.708861 TCTAGTTTCAAACTGGCCTCCA 59.291 45.455 13.39 0.00 42.84 3.86
5821 7902 2.979678 TGGCTTTGGAGAGGTTCTAGTT 59.020 45.455 0.00 0.00 0.00 2.24
5825 7906 1.202940 GGTTGGCTTTGGAGAGGTTCT 60.203 52.381 0.00 0.00 0.00 3.01
5839 7920 1.620822 ATGTTTGGAGACTGGTTGGC 58.379 50.000 0.00 0.00 0.00 4.52
5848 7929 5.250543 TCTCCTGGTCAATTATGTTTGGAGA 59.749 40.000 0.00 0.00 43.33 3.71
5849 7930 5.500234 TCTCCTGGTCAATTATGTTTGGAG 58.500 41.667 0.00 0.00 39.69 3.86
5880 7961 6.174760 TGCCGCTAGACCTTTTTCTAATTTA 58.825 36.000 0.00 0.00 0.00 1.40
5885 7966 3.688694 TTGCCGCTAGACCTTTTTCTA 57.311 42.857 0.00 0.00 0.00 2.10
5926 8007 1.971695 CCCGTTGGGTTCTTGCCTC 60.972 63.158 0.00 0.00 38.25 4.70
5927 8008 2.115266 CCCGTTGGGTTCTTGCCT 59.885 61.111 0.00 0.00 38.25 4.75
5977 8058 2.519013 GGTGGAGGCATGAAGTTCTTT 58.481 47.619 4.17 0.00 0.00 2.52
5988 8069 1.379916 CATCACAAGGGTGGAGGCA 59.620 57.895 0.00 0.00 45.32 4.75


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

AutoCloner maintained by Alex Coulton.