Multiple sequence alignment - TraesCS3D01G506400

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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 TraesCS3D01G506400 chr3D 100.000 3522 0 0 1 3522 593243406 593246927 0.000000e+00 6505.0
1 TraesCS3D01G506400 chr3D 86.882 1456 144 23 1023 2453 593078319 593079752 0.000000e+00 1587.0
2 TraesCS3D01G506400 chr3D 93.160 921 59 2 1062 1981 593261462 593260545 0.000000e+00 1349.0
3 TraesCS3D01G506400 chr3D 81.013 395 32 26 676 1058 593265219 593264856 1.250000e-69 274.0
4 TraesCS3D01G506400 chr3D 79.769 173 30 4 2666 2836 593235181 593235012 1.720000e-23 121.0
5 TraesCS3D01G506400 chr3A 91.599 2690 159 24 754 3400 724519087 724521752 0.000000e+00 3653.0
6 TraesCS3D01G506400 chr3A 88.355 1331 103 26 676 1981 724525678 724524375 0.000000e+00 1552.0
7 TraesCS3D01G506400 chr3A 85.597 1458 160 28 1024 2453 724305348 724306783 0.000000e+00 1483.0
8 TraesCS3D01G506400 chr3B 94.046 2066 100 9 574 2623 795913309 795915367 0.000000e+00 3112.0
9 TraesCS3D01G506400 chr3B 90.357 1234 77 22 773 1981 795920409 795919193 0.000000e+00 1581.0
10 TraesCS3D01G506400 chr3B 84.901 1159 132 12 1307 2453 795280864 795281991 0.000000e+00 1131.0
11 TraesCS3D01G506400 chr3B 91.667 600 39 9 2806 3400 795915414 795916007 0.000000e+00 821.0
12 TraesCS3D01G506400 chr3B 84.758 269 22 6 1024 1274 795280605 795280872 5.840000e-63 252.0
13 TraesCS3D01G506400 chr6D 96.239 585 9 5 1 572 215532950 215532366 0.000000e+00 946.0
14 TraesCS3D01G506400 chr6D 80.337 178 28 6 2665 2836 383743397 383743573 1.030000e-25 128.0
15 TraesCS3D01G506400 chr5D 95.197 583 15 6 1 572 305196021 305195441 0.000000e+00 909.0
16 TraesCS3D01G506400 chr5D 77.419 186 28 10 2662 2834 410248486 410248670 8.050000e-17 99.0
17 TraesCS3D01G506400 chr7D 94.889 587 18 4 1 575 573900990 573900404 0.000000e+00 907.0
18 TraesCS3D01G506400 chr7D 94.549 587 17 6 1 572 102992572 102993158 0.000000e+00 893.0
19 TraesCS3D01G506400 chr7D 95.455 132 5 1 3392 3522 65054694 65054563 3.560000e-50 209.0
20 TraesCS3D01G506400 chrUn 94.965 576 14 5 9 572 266168514 266169086 0.000000e+00 889.0
21 TraesCS3D01G506400 chrUn 95.113 573 13 5 12 572 344074007 344073438 0.000000e+00 889.0
22 TraesCS3D01G506400 chr2D 94.764 573 15 5 12 572 15231411 15230842 0.000000e+00 878.0
23 TraesCS3D01G506400 chr2D 94.415 573 17 5 12 572 15267122 15266553 0.000000e+00 867.0
24 TraesCS3D01G506400 chr2D 94.241 573 18 5 12 572 15252647 15252078 0.000000e+00 861.0
25 TraesCS3D01G506400 chr2D 96.094 128 4 1 3396 3522 57381654 57381527 1.280000e-49 207.0
26 TraesCS3D01G506400 chr2D 96.748 123 4 0 3400 3522 426116675 426116553 4.610000e-49 206.0
27 TraesCS3D01G506400 chr2D 93.333 135 7 2 3388 3522 257766806 257766674 7.710000e-47 198.0
28 TraesCS3D01G506400 chr2D 90.972 144 11 1 3381 3522 192659937 192659794 3.590000e-45 193.0
29 TraesCS3D01G506400 chr2D 83.529 170 25 2 2665 2831 590938003 590937834 4.710000e-34 156.0
30 TraesCS3D01G506400 chr2D 81.081 185 20 8 2667 2838 82141163 82141345 2.210000e-27 134.0
31 TraesCS3D01G506400 chr2D 76.536 179 33 8 2662 2833 498332234 498332410 4.840000e-14 89.8
32 TraesCS3D01G506400 chr4D 96.748 123 4 0 3400 3522 103806504 103806382 4.610000e-49 206.0
33 TraesCS3D01G506400 chr4D 95.276 127 4 2 3396 3522 143070254 143070130 2.140000e-47 200.0
34 TraesCS3D01G506400 chr1D 94.074 135 6 2 3389 3522 375569381 375569514 1.660000e-48 204.0
35 TraesCS3D01G506400 chr1D 90.476 147 9 3 3376 3522 335229044 335228903 4.640000e-44 189.0
36 TraesCS3D01G506400 chr4B 82.353 187 17 8 2666 2840 27243824 27243642 7.880000e-32 148.0
37 TraesCS3D01G506400 chr5B 79.330 179 24 6 2665 2831 677735429 677735606 2.870000e-21 113.0
38 TraesCS3D01G506400 chr1B 89.773 88 7 2 2750 2836 553893104 553893190 1.030000e-20 111.0
39 TraesCS3D01G506400 chr1B 93.103 58 4 0 2664 2721 539480255 539480198 6.260000e-13 86.1
40 TraesCS3D01G506400 chr7B 88.636 88 7 3 2748 2833 77429533 77429447 1.730000e-18 104.0
41 TraesCS3D01G506400 chr7B 82.979 94 14 2 2655 2746 423165558 423165465 2.250000e-12 84.2


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 TraesCS3D01G506400 chr3D 593243406 593246927 3521 False 6505.0 6505 100.0000 1 3522 1 chr3D.!!$F2 3521
1 TraesCS3D01G506400 chr3D 593078319 593079752 1433 False 1587.0 1587 86.8820 1023 2453 1 chr3D.!!$F1 1430
2 TraesCS3D01G506400 chr3D 593260545 593265219 4674 True 811.5 1349 87.0865 676 1981 2 chr3D.!!$R2 1305
3 TraesCS3D01G506400 chr3A 724519087 724521752 2665 False 3653.0 3653 91.5990 754 3400 1 chr3A.!!$F2 2646
4 TraesCS3D01G506400 chr3A 724524375 724525678 1303 True 1552.0 1552 88.3550 676 1981 1 chr3A.!!$R1 1305
5 TraesCS3D01G506400 chr3A 724305348 724306783 1435 False 1483.0 1483 85.5970 1024 2453 1 chr3A.!!$F1 1429
6 TraesCS3D01G506400 chr3B 795913309 795916007 2698 False 1966.5 3112 92.8565 574 3400 2 chr3B.!!$F2 2826
7 TraesCS3D01G506400 chr3B 795919193 795920409 1216 True 1581.0 1581 90.3570 773 1981 1 chr3B.!!$R1 1208
8 TraesCS3D01G506400 chr3B 795280605 795281991 1386 False 691.5 1131 84.8295 1024 2453 2 chr3B.!!$F1 1429
9 TraesCS3D01G506400 chr6D 215532366 215532950 584 True 946.0 946 96.2390 1 572 1 chr6D.!!$R1 571
10 TraesCS3D01G506400 chr5D 305195441 305196021 580 True 909.0 909 95.1970 1 572 1 chr5D.!!$R1 571
11 TraesCS3D01G506400 chr7D 573900404 573900990 586 True 907.0 907 94.8890 1 575 1 chr7D.!!$R2 574
12 TraesCS3D01G506400 chr7D 102992572 102993158 586 False 893.0 893 94.5490 1 572 1 chr7D.!!$F1 571
13 TraesCS3D01G506400 chrUn 266168514 266169086 572 False 889.0 889 94.9650 9 572 1 chrUn.!!$F1 563
14 TraesCS3D01G506400 chrUn 344073438 344074007 569 True 889.0 889 95.1130 12 572 1 chrUn.!!$R1 560
15 TraesCS3D01G506400 chr2D 15230842 15231411 569 True 878.0 878 94.7640 12 572 1 chr2D.!!$R1 560
16 TraesCS3D01G506400 chr2D 15266553 15267122 569 True 867.0 867 94.4150 12 572 1 chr2D.!!$R3 560
17 TraesCS3D01G506400 chr2D 15252078 15252647 569 True 861.0 861 94.2410 12 572 1 chr2D.!!$R2 560

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
145 155 0.319469 CCCATTCACGGTGCCAAAAC 60.319 55.0 2.51 0.0 0.00 2.43 F
908 963 0.749454 GGCTGGACACCACCATCATC 60.749 60.0 0.00 0.0 39.34 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 5385 1.670730 CATGTACTGCACCGTGCCA 60.671 57.895 20.67 11.43 44.23 4.92 R
2618 6130 1.927174 CTAATCACAAGGAAGTCGCCG 59.073 52.381 0.00 0.00 0.00 6.46 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
28 29 0.746563 AACTTCACCACCACCACACG 60.747 55.000 0.00 0.00 0.00 4.49
145 155 0.319469 CCCATTCACGGTGCCAAAAC 60.319 55.000 2.51 0.00 0.00 2.43
154 164 0.806492 GGTGCCAAAACCGCGAAAAA 60.806 50.000 8.23 0.00 0.00 1.94
584 602 5.986004 AAAAATTAGCGAGATTAGACCGG 57.014 39.130 0.00 0.00 0.00 5.28
585 603 2.726832 ATTAGCGAGATTAGACCGGC 57.273 50.000 0.00 0.00 0.00 6.13
601 619 1.067213 CCGGCCCAATTTGACGAAAAT 60.067 47.619 0.00 0.00 40.32 1.82
604 622 3.733684 CGGCCCAATTTGACGAAAATAGG 60.734 47.826 0.00 1.62 37.51 2.57
612 630 5.907866 TTTGACGAAAATAGGGGGATTTC 57.092 39.130 0.00 0.00 0.00 2.17
614 632 5.961398 TGACGAAAATAGGGGGATTTCTA 57.039 39.130 0.00 0.00 32.28 2.10
626 644 1.145803 GATTTCTATGTACCGCCCGC 58.854 55.000 0.00 0.00 0.00 6.13
637 655 3.294493 CGCCCGCCCCATATTTGG 61.294 66.667 0.00 0.00 43.23 3.28
650 668 1.164411 TATTTGGCACTGCAGTTCCG 58.836 50.000 27.08 13.93 33.92 4.30
686 704 2.454336 TCCGGGAGCTAGAAGAATGA 57.546 50.000 0.00 0.00 0.00 2.57
736 774 1.580704 ACGAGCGCGAAAATTAGTACG 59.419 47.619 19.05 1.93 41.64 3.67
740 778 2.854185 AGCGCGAAAATTAGTACGTACC 59.146 45.455 21.80 4.08 0.00 3.34
770 813 3.248363 CCACATACCAGATATGCACAACG 59.752 47.826 0.00 0.00 44.12 4.10
847 891 4.980805 TGAACCGACGGCAGTGGC 62.981 66.667 15.39 6.62 40.13 5.01
908 963 0.749454 GGCTGGACACCACCATCATC 60.749 60.000 0.00 0.00 39.34 2.92
1483 4976 4.452733 GTTCTGAGGTCGGGCCCG 62.453 72.222 39.13 39.13 38.26 6.13
1569 5063 1.135527 CGACGGAAACCTGGTGCTATA 59.864 52.381 0.00 0.00 0.00 1.31
1789 5283 3.137459 CTCGGCCTCAGCGAGACT 61.137 66.667 0.00 0.00 40.08 3.24
1794 5288 2.653115 CCTCAGCGAGACTGCACA 59.347 61.111 7.07 0.00 46.76 4.57
2327 5830 1.034292 GTTCTACTACGGCCCGGACT 61.034 60.000 8.57 0.00 0.00 3.85
2481 5985 7.096189 CCTGAACACTATACGCACATAATACAC 60.096 40.741 0.00 0.00 0.00 2.90
2618 6130 1.542915 AGCACCTCATGACAAATGCAC 59.457 47.619 14.69 0.00 35.51 4.57
2628 6140 1.154225 CAAATGCACGGCGACTTCC 60.154 57.895 16.62 0.00 0.00 3.46
2629 6141 1.302511 AAATGCACGGCGACTTCCT 60.303 52.632 16.62 0.00 0.00 3.36
2651 6164 3.485394 TGTGATTAGCTTGTGCCAAAGA 58.515 40.909 0.00 0.00 40.80 2.52
2653 6166 2.489329 TGATTAGCTTGTGCCAAAGAGC 59.511 45.455 0.00 0.00 40.80 4.09
2660 6173 4.706476 AGCTTGTGCCAAAGAGCAATAATA 59.294 37.500 0.00 0.00 46.19 0.98
2683 6196 9.593134 AATATCTACAGTTTTGCTAAGTCTCAG 57.407 33.333 0.00 0.00 0.00 3.35
2689 6202 4.038162 AGTTTTGCTAAGTCTCAGTCGACT 59.962 41.667 13.58 13.58 45.73 4.18
2706 6219 8.470941 CAGTCGACTGATACTTCGTGAAGTCA 62.471 46.154 36.73 10.47 45.86 3.41
2715 6228 4.079665 CTTCGTGAAGTCACAGTCGATA 57.920 45.455 11.77 0.00 46.75 2.92
2721 6234 6.019237 TCGTGAAGTCACAGTCGATACTATAC 60.019 42.308 11.77 0.00 46.75 1.47
2836 6357 1.348064 CTGAGACCTAACCACACCCA 58.652 55.000 0.00 0.00 0.00 4.51
2837 6358 1.909302 CTGAGACCTAACCACACCCAT 59.091 52.381 0.00 0.00 0.00 4.00
2838 6359 1.906574 TGAGACCTAACCACACCCATC 59.093 52.381 0.00 0.00 0.00 3.51
2919 6440 5.071653 TGTGGCTCCTATGCATATAGAAACA 59.928 40.000 16.54 15.18 38.88 2.83
2933 6454 8.924691 GCATATAGAAACAGAGCTTCATAGAAG 58.075 37.037 2.48 2.48 0.00 2.85
2976 6501 3.979101 AAAAACATAACTGGCCATGGG 57.021 42.857 15.13 0.00 0.00 4.00
2997 6522 9.656040 CATGGGAATGAATACAATGAAGAAAAA 57.344 29.630 0.00 0.00 0.00 1.94
3114 6641 9.773328 ATGTGAACATATCTTTTTGAATACACG 57.227 29.630 0.00 0.00 34.26 4.49
3136 6663 7.168972 ACACGAACATTATTTTTCAACACATGG 59.831 33.333 0.00 0.00 0.00 3.66
3197 6725 6.916360 ACAGAACATTTTCCCAACATACAT 57.084 33.333 0.00 0.00 31.28 2.29
3200 6728 8.522830 ACAGAACATTTTCCCAACATACATAAG 58.477 33.333 0.00 0.00 31.28 1.73
3294 6822 7.867445 AGGTAACAATGTTTTATTTTCAGCG 57.133 32.000 3.17 0.00 41.41 5.18
3384 6914 2.715880 TGATATGCAAATCCCAGGCCTA 59.284 45.455 3.98 0.00 0.00 3.93
3394 6924 0.854218 CCCAGGCCTAGTCTAGAGGA 59.146 60.000 3.98 0.00 35.99 3.71
3398 6928 0.178955 GGCCTAGTCTAGAGGACCCC 60.179 65.000 8.56 0.00 45.54 4.95
3399 6929 0.854908 GCCTAGTCTAGAGGACCCCT 59.145 60.000 8.56 0.00 45.54 4.79
3400 6930 1.218450 GCCTAGTCTAGAGGACCCCTT 59.782 57.143 8.56 0.00 45.54 3.95
3401 6931 2.952116 CCTAGTCTAGAGGACCCCTTG 58.048 57.143 8.56 0.00 45.54 3.61
3402 6932 2.514582 CCTAGTCTAGAGGACCCCTTGA 59.485 54.545 8.56 0.00 45.54 3.02
3403 6933 2.838637 AGTCTAGAGGACCCCTTGAG 57.161 55.000 0.00 0.00 45.54 3.02
3404 6934 1.289530 AGTCTAGAGGACCCCTTGAGG 59.710 57.143 0.00 0.00 45.54 3.86
3414 6944 4.896979 CCTTGAGGGAGTCCTGGA 57.103 61.111 9.58 0.00 45.05 3.86
3415 6945 2.291856 CCTTGAGGGAGTCCTGGAC 58.708 63.158 19.20 19.20 45.05 4.02
3416 6946 0.252467 CCTTGAGGGAGTCCTGGACT 60.252 60.000 28.70 28.70 46.42 3.85
3417 6947 1.007238 CCTTGAGGGAGTCCTGGACTA 59.993 57.143 28.41 10.70 43.53 2.59
3418 6948 2.559931 CCTTGAGGGAGTCCTGGACTAA 60.560 54.545 28.41 17.32 43.53 2.24
3419 6949 2.534042 TGAGGGAGTCCTGGACTAAG 57.466 55.000 28.41 0.00 43.53 2.18
3420 6950 1.007238 TGAGGGAGTCCTGGACTAAGG 59.993 57.143 28.41 0.00 43.53 2.69
3421 6951 0.340208 AGGGAGTCCTGGACTAAGGG 59.660 60.000 28.41 0.00 43.53 3.95
3422 6952 0.691413 GGGAGTCCTGGACTAAGGGG 60.691 65.000 28.41 0.00 43.53 4.79
3423 6953 0.042881 GGAGTCCTGGACTAAGGGGT 59.957 60.000 28.41 5.74 43.53 4.95
3424 6954 1.487300 GAGTCCTGGACTAAGGGGTC 58.513 60.000 28.41 11.40 43.53 4.46
3430 6960 3.951765 GACTAAGGGGTCCTCGGG 58.048 66.667 0.00 0.00 30.89 5.14
3431 6961 2.365237 ACTAAGGGGTCCTCGGGC 60.365 66.667 0.00 0.00 30.89 6.13
3432 6962 3.537874 CTAAGGGGTCCTCGGGCG 61.538 72.222 0.00 0.00 30.89 6.13
3433 6963 4.387343 TAAGGGGTCCTCGGGCGT 62.387 66.667 0.00 0.00 30.89 5.68
3447 6977 2.588034 GCGTCCGGCCTGTTATCC 60.588 66.667 0.00 0.00 34.80 2.59
3448 6978 2.897207 CGTCCGGCCTGTTATCCA 59.103 61.111 0.00 0.00 0.00 3.41
3449 6979 1.445942 CGTCCGGCCTGTTATCCAT 59.554 57.895 0.00 0.00 0.00 3.41
3450 6980 0.179056 CGTCCGGCCTGTTATCCATT 60.179 55.000 0.00 0.00 0.00 3.16
3451 6981 1.308998 GTCCGGCCTGTTATCCATTG 58.691 55.000 0.00 0.00 0.00 2.82
3452 6982 0.182537 TCCGGCCTGTTATCCATTGG 59.817 55.000 0.00 0.00 0.00 3.16
3453 6983 0.823356 CCGGCCTGTTATCCATTGGG 60.823 60.000 0.00 0.00 0.00 4.12
3454 6984 1.455383 CGGCCTGTTATCCATTGGGC 61.455 60.000 0.00 0.00 39.56 5.36
3455 6985 2.429927 GCCTGTTATCCATTGGGCC 58.570 57.895 2.09 0.00 34.19 5.80
3456 6986 1.455383 GCCTGTTATCCATTGGGCCG 61.455 60.000 2.09 0.00 34.19 6.13
3457 6987 0.823356 CCTGTTATCCATTGGGCCGG 60.823 60.000 2.09 0.00 0.00 6.13
3458 6988 0.182537 CTGTTATCCATTGGGCCGGA 59.817 55.000 5.05 0.00 35.27 5.14
3459 6989 0.106918 TGTTATCCATTGGGCCGGAC 60.107 55.000 5.05 0.00 33.05 4.79
3460 6990 0.182775 GTTATCCATTGGGCCGGACT 59.817 55.000 7.57 0.00 33.05 3.85
3461 6991 0.182537 TTATCCATTGGGCCGGACTG 59.817 55.000 7.57 0.00 33.05 3.51
3462 6992 0.692756 TATCCATTGGGCCGGACTGA 60.693 55.000 7.57 0.00 33.05 3.41
3463 6993 1.570857 ATCCATTGGGCCGGACTGAA 61.571 55.000 7.57 0.00 33.05 3.02
3464 6994 1.750399 CCATTGGGCCGGACTGAAG 60.750 63.158 7.57 0.00 0.00 3.02
3465 6995 1.750399 CATTGGGCCGGACTGAAGG 60.750 63.158 7.57 0.00 0.00 3.46
3466 6996 2.983879 ATTGGGCCGGACTGAAGGG 61.984 63.158 7.57 0.00 0.00 3.95
3470 7000 3.706373 GCCGGACTGAAGGGCTGA 61.706 66.667 5.05 0.00 43.52 4.26
3471 7001 2.581354 CCGGACTGAAGGGCTGAG 59.419 66.667 0.00 0.00 0.00 3.35
3472 7002 1.984570 CCGGACTGAAGGGCTGAGA 60.985 63.158 0.00 0.00 0.00 3.27
3473 7003 1.544825 CCGGACTGAAGGGCTGAGAA 61.545 60.000 0.00 0.00 0.00 2.87
3474 7004 0.108424 CGGACTGAAGGGCTGAGAAG 60.108 60.000 0.00 0.00 0.00 2.85
3475 7005 1.270907 GGACTGAAGGGCTGAGAAGA 58.729 55.000 0.00 0.00 0.00 2.87
3476 7006 1.066502 GGACTGAAGGGCTGAGAAGAC 60.067 57.143 0.00 0.00 0.00 3.01
3477 7007 1.620819 GACTGAAGGGCTGAGAAGACA 59.379 52.381 0.00 0.00 0.00 3.41
3478 7008 2.235898 GACTGAAGGGCTGAGAAGACAT 59.764 50.000 0.00 0.00 0.00 3.06
3479 7009 2.027377 ACTGAAGGGCTGAGAAGACATG 60.027 50.000 0.00 0.00 0.00 3.21
3480 7010 2.235650 CTGAAGGGCTGAGAAGACATGA 59.764 50.000 0.00 0.00 0.00 3.07
3481 7011 2.639347 TGAAGGGCTGAGAAGACATGAA 59.361 45.455 0.00 0.00 0.00 2.57
3482 7012 3.269178 GAAGGGCTGAGAAGACATGAAG 58.731 50.000 0.00 0.00 0.00 3.02
3483 7013 1.558756 AGGGCTGAGAAGACATGAAGG 59.441 52.381 0.00 0.00 0.00 3.46
3484 7014 1.377536 GGCTGAGAAGACATGAAGGC 58.622 55.000 0.00 0.00 0.00 4.35
3485 7015 1.377536 GCTGAGAAGACATGAAGGCC 58.622 55.000 0.00 0.00 0.00 5.19
3486 7016 1.649664 CTGAGAAGACATGAAGGCCG 58.350 55.000 0.00 0.00 0.00 6.13
3487 7017 1.205655 CTGAGAAGACATGAAGGCCGA 59.794 52.381 0.00 0.00 0.00 5.54
3488 7018 1.623311 TGAGAAGACATGAAGGCCGAA 59.377 47.619 0.00 0.00 0.00 4.30
3489 7019 2.275318 GAGAAGACATGAAGGCCGAAG 58.725 52.381 0.00 0.00 0.00 3.79
3490 7020 1.902508 AGAAGACATGAAGGCCGAAGA 59.097 47.619 0.00 0.00 0.00 2.87
3491 7021 2.003301 GAAGACATGAAGGCCGAAGAC 58.997 52.381 0.00 0.00 0.00 3.01
3492 7022 1.270907 AGACATGAAGGCCGAAGACT 58.729 50.000 0.00 0.00 0.00 3.24
3493 7023 1.066573 AGACATGAAGGCCGAAGACTG 60.067 52.381 0.00 0.00 0.00 3.51
3494 7024 0.687354 ACATGAAGGCCGAAGACTGT 59.313 50.000 0.00 0.00 0.00 3.55
3495 7025 1.899814 ACATGAAGGCCGAAGACTGTA 59.100 47.619 0.00 0.00 0.00 2.74
3496 7026 2.271800 CATGAAGGCCGAAGACTGTAC 58.728 52.381 0.00 0.00 0.00 2.90
3497 7027 0.242825 TGAAGGCCGAAGACTGTACG 59.757 55.000 0.00 0.00 0.00 3.67
3498 7028 1.077089 GAAGGCCGAAGACTGTACGC 61.077 60.000 0.00 0.00 0.00 4.42
3499 7029 2.814183 AAGGCCGAAGACTGTACGCG 62.814 60.000 3.53 3.53 0.00 6.01
3500 7030 2.126580 GCCGAAGACTGTACGCGT 60.127 61.111 19.17 19.17 0.00 6.01
3501 7031 2.434134 GCCGAAGACTGTACGCGTG 61.434 63.158 24.59 7.93 0.00 5.34
3502 7032 1.081641 CCGAAGACTGTACGCGTGT 60.082 57.895 24.59 11.86 0.00 4.49
3503 7033 1.063951 CCGAAGACTGTACGCGTGTC 61.064 60.000 24.59 20.51 0.00 3.67
3504 7034 1.063951 CGAAGACTGTACGCGTGTCC 61.064 60.000 24.59 10.30 0.00 4.02
3505 7035 1.063951 GAAGACTGTACGCGTGTCCG 61.064 60.000 24.59 13.45 37.07 4.79
3506 7036 2.467946 AAGACTGTACGCGTGTCCGG 62.468 60.000 24.59 16.53 33.68 5.14
3507 7037 2.969806 GACTGTACGCGTGTCCGGA 61.970 63.158 24.59 0.00 33.68 5.14
3508 7038 2.262471 GACTGTACGCGTGTCCGGAT 62.262 60.000 24.59 0.00 33.68 4.18
3509 7039 1.153901 CTGTACGCGTGTCCGGATT 60.154 57.895 24.59 0.00 33.68 3.01
3510 7040 1.410737 CTGTACGCGTGTCCGGATTG 61.411 60.000 24.59 1.10 33.68 2.67
3511 7041 2.162754 GTACGCGTGTCCGGATTGG 61.163 63.158 24.59 0.01 40.09 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.600470 GGTGGTGAAGTTGGGGCC 60.600 66.667 0.00 0.00 0.00 5.80
145 155 2.050477 AATGAGCAAGTTTTTCGCGG 57.950 45.000 6.13 0.00 0.00 6.46
154 164 7.285401 CCCATTTATACACCTAAATGAGCAAGT 59.715 37.037 14.87 0.00 45.59 3.16
572 590 2.618709 CAAATTGGGCCGGTCTAATCTC 59.381 50.000 18.69 0.00 0.00 2.75
575 593 2.375146 GTCAAATTGGGCCGGTCTAAT 58.625 47.619 12.45 12.45 0.00 1.73
576 594 1.828979 GTCAAATTGGGCCGGTCTAA 58.171 50.000 7.51 7.51 0.00 2.10
577 595 0.391927 CGTCAAATTGGGCCGGTCTA 60.392 55.000 5.77 0.00 0.00 2.59
578 596 1.674322 CGTCAAATTGGGCCGGTCT 60.674 57.895 5.77 0.00 0.00 3.85
579 597 1.238625 TTCGTCAAATTGGGCCGGTC 61.239 55.000 1.90 0.00 0.00 4.79
580 598 0.824182 TTTCGTCAAATTGGGCCGGT 60.824 50.000 1.90 0.00 0.00 5.28
581 599 0.315568 TTTTCGTCAAATTGGGCCGG 59.684 50.000 0.00 0.00 0.00 6.13
582 600 2.362169 ATTTTCGTCAAATTGGGCCG 57.638 45.000 0.00 0.00 30.09 6.13
583 601 3.780902 CCTATTTTCGTCAAATTGGGCC 58.219 45.455 0.00 0.00 41.57 5.80
601 619 2.901839 GCGGTACATAGAAATCCCCCTA 59.098 50.000 0.00 0.00 0.00 3.53
604 622 1.271217 GGGCGGTACATAGAAATCCCC 60.271 57.143 0.00 0.00 0.00 4.81
612 630 4.309950 GGGGCGGGCGGTACATAG 62.310 72.222 0.00 0.00 0.00 2.23
637 655 4.030452 GTGGCGGAACTGCAGTGC 62.030 66.667 22.49 19.82 36.28 4.40
671 689 3.536570 GTTGGGTCATTCTTCTAGCTCC 58.463 50.000 0.00 0.00 0.00 4.70
686 704 5.541101 TGCTCGTAGTATATATTGGTTGGGT 59.459 40.000 0.00 0.00 0.00 4.51
701 719 1.669211 GCTCGTTTCCTTGCTCGTAGT 60.669 52.381 0.00 0.00 0.00 2.73
702 720 0.992802 GCTCGTTTCCTTGCTCGTAG 59.007 55.000 0.00 0.00 0.00 3.51
736 774 3.488363 TGGTATGTGGTTTGGTTGGTAC 58.512 45.455 0.00 0.00 0.00 3.34
740 778 5.450412 GCATATCTGGTATGTGGTTTGGTTG 60.450 44.000 9.52 0.00 41.86 3.77
806 850 2.278923 TTCTGCGCGTCGTCAACA 60.279 55.556 8.43 0.00 0.00 3.33
908 963 1.271840 TGGATGGGGAAGACGGAAGG 61.272 60.000 0.00 0.00 0.00 3.46
1306 4799 1.739562 GAGCAGGAACTCCGTGCAG 60.740 63.158 17.10 0.00 40.34 4.41
1729 5223 3.838795 GCGTTGACGTAGGCGCTG 61.839 66.667 18.48 0.00 45.48 5.18
1891 5385 1.670730 CATGTACTGCACCGTGCCA 60.671 57.895 20.67 11.43 44.23 4.92
2089 5589 3.003763 GGCCTCCGGAAGTCCACT 61.004 66.667 5.23 0.00 35.14 4.00
2198 5701 2.726691 CGTTGAAGTAGGCCGTGCG 61.727 63.158 0.00 0.00 0.00 5.34
2481 5985 4.392047 TCAAGGACAATGCCATATGCTAG 58.608 43.478 0.00 0.00 42.00 3.42
2575 6087 6.707440 TCAATGTAGAGAGAATGGAGAGAC 57.293 41.667 0.00 0.00 0.00 3.36
2618 6130 1.927174 CTAATCACAAGGAAGTCGCCG 59.073 52.381 0.00 0.00 0.00 6.46
2660 6173 6.998802 ACTGAGACTTAGCAAAACTGTAGAT 58.001 36.000 0.00 0.00 0.00 1.98
2682 6195 4.343811 CTTCACGAAGTATCAGTCGACT 57.656 45.455 13.58 13.58 41.61 4.18
2700 6213 5.333952 CGGGTATAGTATCGACTGTGACTTC 60.334 48.000 0.00 0.00 36.28 3.01
2704 6217 3.811497 CACGGGTATAGTATCGACTGTGA 59.189 47.826 12.05 0.00 36.28 3.58
2706 6219 4.063689 CTCACGGGTATAGTATCGACTGT 58.936 47.826 0.00 0.00 36.28 3.55
2715 6228 6.776116 TCAATGTAAGATCTCACGGGTATAGT 59.224 38.462 0.00 0.00 0.00 2.12
2721 6234 4.655762 TCTCAATGTAAGATCTCACGGG 57.344 45.455 0.00 0.00 0.00 5.28
2784 6305 7.410174 AGATTTAACCAAGTCCCAATCATGTA 58.590 34.615 0.00 0.00 0.00 2.29
2794 6315 4.626172 GTCGACTGAGATTTAACCAAGTCC 59.374 45.833 8.70 0.00 0.00 3.85
2919 6440 1.480137 AGCGCACTTCTATGAAGCTCT 59.520 47.619 11.47 0.00 32.08 4.09
2933 6454 1.438651 TAGTTCCAATGTGAGCGCAC 58.561 50.000 14.25 14.25 45.35 5.34
2958 6483 2.917713 TCCCATGGCCAGTTATGTTT 57.082 45.000 13.05 0.00 0.00 2.83
2959 6484 2.917713 TTCCCATGGCCAGTTATGTT 57.082 45.000 13.05 0.00 0.00 2.71
2960 6485 2.244510 TCATTCCCATGGCCAGTTATGT 59.755 45.455 13.05 0.00 0.00 2.29
3112 6639 7.429633 TCCATGTGTTGAAAAATAATGTTCGT 58.570 30.769 0.00 0.00 0.00 3.85
3231 6759 9.400638 TCCAAATTAAAATTGTCGTGTAACATC 57.599 29.630 4.31 0.00 35.74 3.06
3285 6813 7.094377 ACACATGTTACCTTAATCGCTGAAAAT 60.094 33.333 0.00 0.00 0.00 1.82
3294 6822 9.005777 TCAGGTTTAACACATGTTACCTTAATC 57.994 33.333 14.08 3.66 41.68 1.75
3384 6914 1.289530 CCTCAAGGGGTCCTCTAGACT 59.710 57.143 0.00 0.00 45.54 3.24
3398 6928 2.534042 TAGTCCAGGACTCCCTCAAG 57.466 55.000 26.42 0.00 42.40 3.02
3399 6929 2.559931 CCTTAGTCCAGGACTCCCTCAA 60.560 54.545 26.42 13.05 42.40 3.02
3400 6930 1.007238 CCTTAGTCCAGGACTCCCTCA 59.993 57.143 26.42 5.02 42.40 3.86
3401 6931 1.689892 CCCTTAGTCCAGGACTCCCTC 60.690 61.905 26.42 0.00 42.40 4.30
3402 6932 0.340208 CCCTTAGTCCAGGACTCCCT 59.660 60.000 26.42 4.72 42.40 4.20
3403 6933 0.691413 CCCCTTAGTCCAGGACTCCC 60.691 65.000 26.42 0.00 42.40 4.30
3404 6934 0.042881 ACCCCTTAGTCCAGGACTCC 59.957 60.000 26.42 0.00 42.40 3.85
3405 6935 1.487300 GACCCCTTAGTCCAGGACTC 58.513 60.000 26.42 6.18 42.40 3.36
3406 6936 3.713867 GACCCCTTAGTCCAGGACT 57.286 57.895 25.92 25.92 45.54 3.85
3413 6943 2.433146 GCCCGAGGACCCCTTAGTC 61.433 68.421 0.00 0.00 31.76 2.59
3414 6944 2.365237 GCCCGAGGACCCCTTAGT 60.365 66.667 0.00 0.00 31.76 2.24
3415 6945 3.537874 CGCCCGAGGACCCCTTAG 61.538 72.222 0.00 0.00 31.76 2.18
3416 6946 4.387343 ACGCCCGAGGACCCCTTA 62.387 66.667 0.00 0.00 31.76 2.69
3430 6960 2.588034 GGATAACAGGCCGGACGC 60.588 66.667 10.86 0.00 0.00 5.19
3431 6961 0.179056 AATGGATAACAGGCCGGACG 60.179 55.000 10.86 0.24 0.00 4.79
3432 6962 1.308998 CAATGGATAACAGGCCGGAC 58.691 55.000 10.86 0.00 0.00 4.79
3433 6963 0.182537 CCAATGGATAACAGGCCGGA 59.817 55.000 10.86 0.00 0.00 5.14
3434 6964 0.823356 CCCAATGGATAACAGGCCGG 60.823 60.000 0.00 0.00 0.00 6.13
3435 6965 1.455383 GCCCAATGGATAACAGGCCG 61.455 60.000 0.00 0.00 33.13 6.13
3436 6966 1.115326 GGCCCAATGGATAACAGGCC 61.115 60.000 0.00 1.48 46.84 5.19
3437 6967 1.455383 CGGCCCAATGGATAACAGGC 61.455 60.000 0.00 0.00 37.25 4.85
3438 6968 0.823356 CCGGCCCAATGGATAACAGG 60.823 60.000 0.00 0.00 0.00 4.00
3439 6969 0.182537 TCCGGCCCAATGGATAACAG 59.817 55.000 0.00 0.00 0.00 3.16
3440 6970 0.106918 GTCCGGCCCAATGGATAACA 60.107 55.000 0.00 0.00 36.48 2.41
3441 6971 0.182775 AGTCCGGCCCAATGGATAAC 59.817 55.000 0.00 0.00 36.48 1.89
3442 6972 0.182537 CAGTCCGGCCCAATGGATAA 59.817 55.000 0.00 0.00 36.48 1.75
3443 6973 0.692756 TCAGTCCGGCCCAATGGATA 60.693 55.000 0.00 0.00 36.48 2.59
3444 6974 1.570857 TTCAGTCCGGCCCAATGGAT 61.571 55.000 0.00 0.00 36.48 3.41
3445 6975 2.196997 CTTCAGTCCGGCCCAATGGA 62.197 60.000 0.00 0.00 0.00 3.41
3446 6976 1.750399 CTTCAGTCCGGCCCAATGG 60.750 63.158 0.00 0.00 0.00 3.16
3447 6977 1.750399 CCTTCAGTCCGGCCCAATG 60.750 63.158 0.00 0.00 0.00 2.82
3448 6978 2.677228 CCTTCAGTCCGGCCCAAT 59.323 61.111 0.00 0.00 0.00 3.16
3449 6979 3.646715 CCCTTCAGTCCGGCCCAA 61.647 66.667 0.00 0.00 0.00 4.12
3452 6982 4.785453 CAGCCCTTCAGTCCGGCC 62.785 72.222 0.00 0.00 44.13 6.13
3453 6983 3.672295 CTCAGCCCTTCAGTCCGGC 62.672 68.421 0.00 0.00 43.35 6.13
3454 6984 1.544825 TTCTCAGCCCTTCAGTCCGG 61.545 60.000 0.00 0.00 0.00 5.14
3455 6985 0.108424 CTTCTCAGCCCTTCAGTCCG 60.108 60.000 0.00 0.00 0.00 4.79
3456 6986 1.066502 GTCTTCTCAGCCCTTCAGTCC 60.067 57.143 0.00 0.00 0.00 3.85
3457 6987 1.620819 TGTCTTCTCAGCCCTTCAGTC 59.379 52.381 0.00 0.00 0.00 3.51
3458 6988 1.722034 TGTCTTCTCAGCCCTTCAGT 58.278 50.000 0.00 0.00 0.00 3.41
3459 6989 2.235650 TCATGTCTTCTCAGCCCTTCAG 59.764 50.000 0.00 0.00 0.00 3.02
3460 6990 2.259917 TCATGTCTTCTCAGCCCTTCA 58.740 47.619 0.00 0.00 0.00 3.02
3461 6991 3.269178 CTTCATGTCTTCTCAGCCCTTC 58.731 50.000 0.00 0.00 0.00 3.46
3462 6992 2.026449 CCTTCATGTCTTCTCAGCCCTT 60.026 50.000 0.00 0.00 0.00 3.95
3463 6993 1.558756 CCTTCATGTCTTCTCAGCCCT 59.441 52.381 0.00 0.00 0.00 5.19
3464 6994 2.016096 GCCTTCATGTCTTCTCAGCCC 61.016 57.143 0.00 0.00 0.00 5.19
3465 6995 1.377536 GCCTTCATGTCTTCTCAGCC 58.622 55.000 0.00 0.00 0.00 4.85
3466 6996 1.377536 GGCCTTCATGTCTTCTCAGC 58.622 55.000 0.00 0.00 0.00 4.26
3467 6997 1.205655 TCGGCCTTCATGTCTTCTCAG 59.794 52.381 0.00 0.00 0.00 3.35
3468 6998 1.266178 TCGGCCTTCATGTCTTCTCA 58.734 50.000 0.00 0.00 0.00 3.27
3469 6999 2.093973 TCTTCGGCCTTCATGTCTTCTC 60.094 50.000 0.00 0.00 0.00 2.87
3470 7000 1.902508 TCTTCGGCCTTCATGTCTTCT 59.097 47.619 0.00 0.00 0.00 2.85
3471 7001 2.003301 GTCTTCGGCCTTCATGTCTTC 58.997 52.381 0.00 0.00 0.00 2.87
3472 7002 1.625818 AGTCTTCGGCCTTCATGTCTT 59.374 47.619 0.00 0.00 0.00 3.01
3473 7003 1.066573 CAGTCTTCGGCCTTCATGTCT 60.067 52.381 0.00 0.00 0.00 3.41
3474 7004 1.338200 ACAGTCTTCGGCCTTCATGTC 60.338 52.381 0.00 0.00 0.00 3.06
3475 7005 0.687354 ACAGTCTTCGGCCTTCATGT 59.313 50.000 0.00 0.00 0.00 3.21
3476 7006 2.271800 GTACAGTCTTCGGCCTTCATG 58.728 52.381 0.00 0.00 0.00 3.07
3477 7007 1.135083 CGTACAGTCTTCGGCCTTCAT 60.135 52.381 0.00 0.00 0.00 2.57
3478 7008 0.242825 CGTACAGTCTTCGGCCTTCA 59.757 55.000 0.00 0.00 0.00 3.02
3479 7009 1.077089 GCGTACAGTCTTCGGCCTTC 61.077 60.000 0.00 0.00 0.00 3.46
3480 7010 1.080025 GCGTACAGTCTTCGGCCTT 60.080 57.895 0.00 0.00 0.00 4.35
3481 7011 2.572284 GCGTACAGTCTTCGGCCT 59.428 61.111 0.00 0.00 0.00 5.19
3482 7012 2.879462 CGCGTACAGTCTTCGGCC 60.879 66.667 0.00 0.00 0.00 6.13
3483 7013 2.126580 ACGCGTACAGTCTTCGGC 60.127 61.111 11.67 0.00 0.00 5.54
3484 7014 1.063951 GACACGCGTACAGTCTTCGG 61.064 60.000 13.44 0.00 0.00 4.30
3485 7015 1.063951 GGACACGCGTACAGTCTTCG 61.064 60.000 22.51 6.97 32.98 3.79
3486 7016 1.063951 CGGACACGCGTACAGTCTTC 61.064 60.000 22.51 10.10 32.98 2.87
3487 7017 1.081641 CGGACACGCGTACAGTCTT 60.082 57.895 22.51 0.00 32.98 3.01
3488 7018 2.559840 CGGACACGCGTACAGTCT 59.440 61.111 22.51 0.00 32.98 3.24
3489 7019 2.262471 ATCCGGACACGCGTACAGTC 62.262 60.000 13.44 15.85 39.22 3.51
3490 7020 1.870055 AATCCGGACACGCGTACAGT 61.870 55.000 13.44 5.76 39.22 3.55
3491 7021 1.153901 AATCCGGACACGCGTACAG 60.154 57.895 13.44 10.09 39.22 2.74
3492 7022 1.444724 CAATCCGGACACGCGTACA 60.445 57.895 13.44 0.00 39.22 2.90
3493 7023 2.162754 CCAATCCGGACACGCGTAC 61.163 63.158 13.44 9.46 39.22 3.67
3494 7024 2.182284 CCAATCCGGACACGCGTA 59.818 61.111 13.44 0.00 39.22 4.42
3495 7025 3.687102 TCCAATCCGGACACGCGT 61.687 61.111 6.12 5.58 39.64 6.01


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

AutoCloner maintained by Alex Coulton.