Multiple sequence alignment - TraesCS5A01G200900

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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 TraesCS5A01G200900 chr5A 100.000 7225 0 0 1 7225 406831444 406838668 0.000000e+00 13343.0
1 TraesCS5A01G200900 chr5A 83.780 635 96 6 1 630 299252080 299252712 4.830000e-166 595.0
2 TraesCS5A01G200900 chr5B 96.362 3051 85 11 3318 6347 359473647 359476692 0.000000e+00 4996.0
3 TraesCS5A01G200900 chr5B 93.178 2492 138 20 844 3318 359470963 359473439 0.000000e+00 3631.0
4 TraesCS5A01G200900 chr5B 84.578 830 89 15 6418 7220 508150993 508151810 0.000000e+00 787.0
5 TraesCS5A01G200900 chr5B 93.775 498 30 1 1 497 359468584 359469081 0.000000e+00 747.0
6 TraesCS5A01G200900 chr5B 87.520 633 75 4 1 630 77650200 77650831 0.000000e+00 728.0
7 TraesCS5A01G200900 chr5B 79.310 638 127 4 1 633 206503252 206502615 6.650000e-120 442.0
8 TraesCS5A01G200900 chr5B 85.948 306 42 1 1 305 142715396 142715091 6.990000e-85 326.0
9 TraesCS5A01G200900 chr5B 92.593 108 8 0 488 595 359470268 359470375 9.700000e-34 156.0
10 TraesCS5A01G200900 chr5B 95.918 49 2 0 6382 6430 359476686 359476734 6.010000e-11 80.5
11 TraesCS5A01G200900 chr5D 95.331 3127 93 17 3319 6430 313091770 313094858 0.000000e+00 4916.0
12 TraesCS5A01G200900 chr5D 92.489 2716 135 25 626 3318 313088637 313091306 0.000000e+00 3821.0
13 TraesCS5A01G200900 chr5D 86.957 828 64 16 6428 7217 539037300 539036479 0.000000e+00 891.0
14 TraesCS5A01G200900 chr7D 89.268 820 67 6 6419 7225 553821925 553822736 0.000000e+00 1007.0
15 TraesCS5A01G200900 chr7D 84.337 830 65 28 6423 7225 79977677 79976886 0.000000e+00 752.0
16 TraesCS5A01G200900 chr7D 83.196 851 77 37 6423 7225 90255707 90254875 0.000000e+00 719.0
17 TraesCS5A01G200900 chr7D 90.741 54 4 1 631 684 518715223 518715275 3.620000e-08 71.3
18 TraesCS5A01G200900 chr6D 88.228 824 67 14 6421 7225 132055943 132055131 0.000000e+00 957.0
19 TraesCS5A01G200900 chr6D 85.714 602 85 1 1 601 107953230 107953831 1.020000e-177 634.0
20 TraesCS5A01G200900 chrUn 87.838 814 62 12 6423 7208 265237712 265238516 0.000000e+00 920.0
21 TraesCS5A01G200900 chr3D 86.232 828 76 12 6421 7220 577413104 577412287 0.000000e+00 863.0
22 TraesCS5A01G200900 chr3D 85.018 841 68 26 6425 7225 549376580 549377402 0.000000e+00 802.0
23 TraesCS5A01G200900 chr3D 87.460 630 52 4 6621 7225 143236026 143236653 0.000000e+00 701.0
24 TraesCS5A01G200900 chr3D 87.708 301 24 3 6938 7225 606302784 606302484 8.980000e-89 339.0
25 TraesCS5A01G200900 chr1B 85.316 824 73 19 6427 7217 512774062 512773254 0.000000e+00 808.0
26 TraesCS5A01G200900 chr1B 90.971 587 50 2 38 621 484364439 484365025 0.000000e+00 787.0
27 TraesCS5A01G200900 chr1B 87.333 600 51 9 6651 7225 550979760 550980359 0.000000e+00 664.0
28 TraesCS5A01G200900 chr1B 90.196 51 4 1 579 629 289733353 289733402 1.680000e-06 65.8
29 TraesCS5A01G200900 chr1A 84.964 838 79 22 6427 7225 503545849 503546678 0.000000e+00 806.0
30 TraesCS5A01G200900 chr1A 85.227 528 61 9 6425 6942 85900932 85900412 1.790000e-145 527.0
31 TraesCS5A01G200900 chr2D 85.949 790 54 13 6465 7225 606662550 606663311 0.000000e+00 791.0
32 TraesCS5A01G200900 chr3A 76.698 1369 287 25 1701 3046 19772345 19773704 0.000000e+00 732.0
33 TraesCS5A01G200900 chr3A 85.782 633 87 3 1 630 476347780 476348412 0.000000e+00 667.0
34 TraesCS5A01G200900 chr1D 74.902 1530 345 32 1701 3206 415970706 415972220 0.000000e+00 662.0
35 TraesCS5A01G200900 chr4B 81.213 841 89 31 6413 7225 362136774 362137573 1.330000e-171 614.0
36 TraesCS5A01G200900 chr4B 73.486 1569 361 43 1701 3235 604884390 604882843 6.380000e-150 542.0
37 TraesCS5A01G200900 chr3B 85.077 583 84 2 1 582 262709914 262709334 6.240000e-165 592.0
38 TraesCS5A01G200900 chr2A 86.974 499 53 7 6425 6919 80890927 80891417 1.060000e-152 551.0
39 TraesCS5A01G200900 chr6A 90.659 182 16 1 7045 7225 93267853 93267672 2.600000e-59 241.0
40 TraesCS5A01G200900 chr6A 96.154 52 1 1 633 684 53088475 53088425 4.640000e-12 84.2
41 TraesCS5A01G200900 chr6B 89.394 66 6 1 632 696 506834351 506834416 1.670000e-11 82.4
42 TraesCS5A01G200900 chr6B 86.885 61 3 4 573 630 233406107 233406165 6.050000e-06 63.9
43 TraesCS5A01G200900 chr7A 91.071 56 2 3 633 687 127044405 127044352 1.010000e-08 73.1
44 TraesCS5A01G200900 chr4A 89.655 58 4 2 633 689 628000638 628000582 1.010000e-08 73.1
45 TraesCS5A01G200900 chr4D 89.474 57 4 2 573 629 174160180 174160234 3.620000e-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 TraesCS5A01G200900 chr5A 406831444 406838668 7224 False 13343.0 13343 100.0000 1 7225 1 chr5A.!!$F2 7224
1 TraesCS5A01G200900 chr5A 299252080 299252712 632 False 595.0 595 83.7800 1 630 1 chr5A.!!$F1 629
2 TraesCS5A01G200900 chr5B 359468584 359476734 8150 False 1922.1 4996 94.3652 1 6430 5 chr5B.!!$F3 6429
3 TraesCS5A01G200900 chr5B 508150993 508151810 817 False 787.0 787 84.5780 6418 7220 1 chr5B.!!$F2 802
4 TraesCS5A01G200900 chr5B 77650200 77650831 631 False 728.0 728 87.5200 1 630 1 chr5B.!!$F1 629
5 TraesCS5A01G200900 chr5B 206502615 206503252 637 True 442.0 442 79.3100 1 633 1 chr5B.!!$R2 632
6 TraesCS5A01G200900 chr5D 313088637 313094858 6221 False 4368.5 4916 93.9100 626 6430 2 chr5D.!!$F1 5804
7 TraesCS5A01G200900 chr5D 539036479 539037300 821 True 891.0 891 86.9570 6428 7217 1 chr5D.!!$R1 789
8 TraesCS5A01G200900 chr7D 553821925 553822736 811 False 1007.0 1007 89.2680 6419 7225 1 chr7D.!!$F2 806
9 TraesCS5A01G200900 chr7D 79976886 79977677 791 True 752.0 752 84.3370 6423 7225 1 chr7D.!!$R1 802
10 TraesCS5A01G200900 chr7D 90254875 90255707 832 True 719.0 719 83.1960 6423 7225 1 chr7D.!!$R2 802
11 TraesCS5A01G200900 chr6D 132055131 132055943 812 True 957.0 957 88.2280 6421 7225 1 chr6D.!!$R1 804
12 TraesCS5A01G200900 chr6D 107953230 107953831 601 False 634.0 634 85.7140 1 601 1 chr6D.!!$F1 600
13 TraesCS5A01G200900 chrUn 265237712 265238516 804 False 920.0 920 87.8380 6423 7208 1 chrUn.!!$F1 785
14 TraesCS5A01G200900 chr3D 577412287 577413104 817 True 863.0 863 86.2320 6421 7220 1 chr3D.!!$R1 799
15 TraesCS5A01G200900 chr3D 549376580 549377402 822 False 802.0 802 85.0180 6425 7225 1 chr3D.!!$F2 800
16 TraesCS5A01G200900 chr3D 143236026 143236653 627 False 701.0 701 87.4600 6621 7225 1 chr3D.!!$F1 604
17 TraesCS5A01G200900 chr1B 512773254 512774062 808 True 808.0 808 85.3160 6427 7217 1 chr1B.!!$R1 790
18 TraesCS5A01G200900 chr1B 484364439 484365025 586 False 787.0 787 90.9710 38 621 1 chr1B.!!$F2 583
19 TraesCS5A01G200900 chr1B 550979760 550980359 599 False 664.0 664 87.3330 6651 7225 1 chr1B.!!$F3 574
20 TraesCS5A01G200900 chr1A 503545849 503546678 829 False 806.0 806 84.9640 6427 7225 1 chr1A.!!$F1 798
21 TraesCS5A01G200900 chr1A 85900412 85900932 520 True 527.0 527 85.2270 6425 6942 1 chr1A.!!$R1 517
22 TraesCS5A01G200900 chr2D 606662550 606663311 761 False 791.0 791 85.9490 6465 7225 1 chr2D.!!$F1 760
23 TraesCS5A01G200900 chr3A 19772345 19773704 1359 False 732.0 732 76.6980 1701 3046 1 chr3A.!!$F1 1345
24 TraesCS5A01G200900 chr3A 476347780 476348412 632 False 667.0 667 85.7820 1 630 1 chr3A.!!$F2 629
25 TraesCS5A01G200900 chr1D 415970706 415972220 1514 False 662.0 662 74.9020 1701 3206 1 chr1D.!!$F1 1505
26 TraesCS5A01G200900 chr4B 362136774 362137573 799 False 614.0 614 81.2130 6413 7225 1 chr4B.!!$F1 812
27 TraesCS5A01G200900 chr4B 604882843 604884390 1547 True 542.0 542 73.4860 1701 3235 1 chr4B.!!$R1 1534
28 TraesCS5A01G200900 chr3B 262709334 262709914 580 True 592.0 592 85.0770 1 582 1 chr3B.!!$R1 581

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
356 361 0.103390 TCTGCACGTCCGTCTTTTGA 59.897 50.0 0.00 0.00 0.00 2.69 F
439 444 0.716108 GCGGCCGATCTAATTCATCG 59.284 55.0 33.48 11.18 42.36 3.84 F
1346 2889 0.734253 CGCTACTGGTCTCTGCACAC 60.734 60.0 0.00 0.00 0.00 3.82 F
2834 4405 0.456995 GCGTCTACAGCTCAGTCACC 60.457 60.0 0.00 0.00 0.00 4.02 F
4724 6787 0.608856 TCCACATGCTGCGGTTTGAT 60.609 50.0 0.00 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 3499 0.930310 CCATGTCGCGTAGGTCATTG 59.070 55.000 5.77 0.0 0.00 2.82 R
2333 3900 1.600916 GAGGCAGCGGTTTTGGACT 60.601 57.895 0.00 0.0 0.00 3.85 R
3024 4595 0.179051 GGGGCAGCTGAAGATGAGAG 60.179 60.000 20.43 0.0 32.25 3.20 R
4767 6830 0.458543 TCATCAGAACCTTCGAGCGC 60.459 55.000 0.00 0.0 0.00 5.92 R
6453 8533 0.248458 ATTTTTAGCAATCGCGCCGG 60.248 50.000 0.00 0.0 45.49 6.13 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
94 95 4.219919 TCAATACAGGGTATGGACATCGA 58.780 43.478 0.00 0.00 0.00 3.59
97 98 5.825593 ATACAGGGTATGGACATCGAATT 57.174 39.130 0.00 0.00 0.00 2.17
99 100 3.199946 ACAGGGTATGGACATCGAATTGT 59.800 43.478 0.00 0.00 0.00 2.71
259 264 1.539065 CCTAGCATTGCTACCGACCAG 60.539 57.143 14.33 4.94 40.44 4.00
305 310 0.607762 TGGCTGCCAGAAAACGCATA 60.608 50.000 19.30 0.00 33.78 3.14
352 357 1.007271 CACTCTGCACGTCCGTCTT 60.007 57.895 0.00 0.00 0.00 3.01
356 361 0.103390 TCTGCACGTCCGTCTTTTGA 59.897 50.000 0.00 0.00 0.00 2.69
439 444 0.716108 GCGGCCGATCTAATTCATCG 59.284 55.000 33.48 11.18 42.36 3.84
464 469 4.393155 ACGCTCTTGGCATCGGCA 62.393 61.111 0.00 0.00 43.71 5.69
499 1700 8.174085 AGGAGAGCAATATGGTATAGAGTAGTT 58.826 37.037 0.00 0.00 0.00 2.24
566 1770 4.024725 GGCGGTGCATATCGTTTGTATTTA 60.025 41.667 0.00 0.00 31.62 1.40
610 1814 7.652105 TCTTCTATAAAGCTAAGGTACGCAATG 59.348 37.037 0.00 0.00 0.00 2.82
658 1862 4.664150 TTGAAACGGAGGCAAAAGATTT 57.336 36.364 0.00 0.00 0.00 2.17
660 1864 2.438868 AACGGAGGCAAAAGATTTGC 57.561 45.000 17.18 17.18 44.22 3.68
761 1965 8.649841 ACAATCATTTCGCTAATTTTGAACATG 58.350 29.630 0.00 0.00 0.00 3.21
813 2018 8.041143 TGTATTTTTAGCATACATAGGGAGGT 57.959 34.615 0.00 0.00 33.11 3.85
814 2019 8.499406 TGTATTTTTAGCATACATAGGGAGGTT 58.501 33.333 0.00 0.00 33.11 3.50
815 2020 9.350951 GTATTTTTAGCATACATAGGGAGGTTT 57.649 33.333 0.00 0.00 0.00 3.27
816 2021 8.838649 ATTTTTAGCATACATAGGGAGGTTTT 57.161 30.769 0.00 0.00 0.00 2.43
919 2462 7.736880 CGTAAAAATTCGAATTCGTGAACTGTA 59.263 33.333 25.93 9.92 40.80 2.74
932 2475 4.379603 CGTGAACTGTAGTGAACCTCCTAG 60.380 50.000 0.00 0.00 0.00 3.02
933 2476 4.082136 GTGAACTGTAGTGAACCTCCTAGG 60.082 50.000 0.82 0.82 42.49 3.02
1346 2889 0.734253 CGCTACTGGTCTCTGCACAC 60.734 60.000 0.00 0.00 0.00 3.82
1443 2988 4.341520 GGTAGATCGAACCTCCTATGTGTT 59.658 45.833 11.78 0.00 33.97 3.32
1449 2994 4.935205 TCGAACCTCCTATGTGTTTTCATG 59.065 41.667 0.00 0.00 0.00 3.07
1475 3020 4.214119 CAGTTGCCGTATAGGGATGATTTG 59.786 45.833 15.70 2.02 41.19 2.32
1479 3024 2.618045 CCGTATAGGGATGATTTGGCCC 60.618 54.545 5.49 0.00 42.37 5.80
1486 3031 0.819666 GATGATTTGGCCCGGTCTCC 60.820 60.000 0.00 0.00 0.00 3.71
1495 3040 1.295423 CCCGGTCTCCGTTCATGTT 59.705 57.895 0.00 0.00 46.80 2.71
1531 3076 6.536582 GCAGTCTGAGCTTGTAATATTCTTCA 59.463 38.462 3.32 0.00 0.00 3.02
1532 3077 7.254387 GCAGTCTGAGCTTGTAATATTCTTCAG 60.254 40.741 3.32 0.00 0.00 3.02
1533 3078 7.763528 CAGTCTGAGCTTGTAATATTCTTCAGT 59.236 37.037 0.00 0.00 0.00 3.41
1561 3108 5.673514 TGTTAAATAACCTATCGGTCCACC 58.326 41.667 1.13 0.00 44.73 4.61
1858 3405 1.420138 CTGAGTTGGGTGTGGTTAGGT 59.580 52.381 0.00 0.00 0.00 3.08
1872 3419 4.080751 GTGGTTAGGTGCCTAAAGGACATA 60.081 45.833 11.83 0.00 39.82 2.29
1950 3499 0.966875 TGCCCATGCATGTTCAGGAC 60.967 55.000 24.58 14.15 44.23 3.85
2062 3611 2.757868 CTCTCAATGGACGACTTCCTCT 59.242 50.000 0.00 0.00 46.10 3.69
2071 3620 0.735471 CGACTTCCTCTCGCTCATCA 59.265 55.000 0.00 0.00 0.00 3.07
2203 3758 1.545706 GCTCCCTCCGTTGGTTCTCT 61.546 60.000 0.00 0.00 0.00 3.10
2212 3767 1.872952 CGTTGGTTCTCTGTGCAATCA 59.127 47.619 0.00 0.00 0.00 2.57
2233 3788 3.121030 CCCTGCGTCGCTCCTTTG 61.121 66.667 19.50 1.86 0.00 2.77
2234 3789 3.121030 CCTGCGTCGCTCCTTTGG 61.121 66.667 19.50 7.10 0.00 3.28
2236 3791 2.357034 TGCGTCGCTCCTTTGGAC 60.357 61.111 19.50 0.00 0.00 4.02
2237 3792 3.119096 GCGTCGCTCCTTTGGACC 61.119 66.667 10.68 0.00 0.00 4.46
2239 3794 3.119096 GTCGCTCCTTTGGACCGC 61.119 66.667 0.00 0.00 31.59 5.68
2240 3795 4.735132 TCGCTCCTTTGGACCGCG 62.735 66.667 12.14 12.14 44.22 6.46
2242 3797 3.119096 GCTCCTTTGGACCGCGTC 61.119 66.667 4.92 2.44 0.00 5.19
2243 3798 2.809601 CTCCTTTGGACCGCGTCG 60.810 66.667 4.92 0.00 32.65 5.12
2295 3862 0.833834 CTGGGATAGGATGGTCCGCT 60.834 60.000 0.00 0.00 42.75 5.52
2381 3948 1.405463 CTGCTACATCGCCTACACTCA 59.595 52.381 0.00 0.00 0.00 3.41
2483 4050 2.284995 GGCCCTCACTGGTCCTCT 60.285 66.667 0.00 0.00 0.00 3.69
2562 4129 4.680237 CCACCGCGTTCTGGCTGA 62.680 66.667 4.92 0.00 0.00 4.26
2572 4139 2.731691 TTCTGGCTGAACTCGTGGCC 62.732 60.000 2.37 0.00 44.31 5.36
2664 4234 1.091771 CCGTCATCGCATTTGGCTCT 61.092 55.000 0.00 0.00 41.67 4.09
2673 4243 1.382522 CATTTGGCTCTATGGCGTGT 58.617 50.000 0.00 0.00 45.14 4.49
2828 4399 4.129737 GCCGGCGTCTACAGCTCA 62.130 66.667 12.58 0.00 34.52 4.26
2834 4405 0.456995 GCGTCTACAGCTCAGTCACC 60.457 60.000 0.00 0.00 0.00 4.02
2971 4542 3.798380 CGGAAGCACATCATCGCA 58.202 55.556 0.00 0.00 0.00 5.10
3024 4595 2.725008 CCTCGAGACGGCTGATCC 59.275 66.667 15.71 0.00 0.00 3.36
3044 4615 0.619832 TCTCATCTTCAGCTGCCCCT 60.620 55.000 9.47 0.00 0.00 4.79
3085 4656 5.163754 GGGAATTTGTAGGTCTGAATCAACG 60.164 44.000 0.00 0.00 0.00 4.10
3107 4678 1.480212 ATGTTGCCTCCGTCAGGTCA 61.480 55.000 0.00 0.00 45.61 4.02
3196 4773 2.650196 GCAATTGTGGAAGCGCCA 59.350 55.556 2.29 0.00 46.96 5.69
3235 4812 3.469970 TGTGCCGCCATCGATCCT 61.470 61.111 0.00 0.00 38.10 3.24
3239 4816 3.606662 CCGCCATCGATCCTCCGT 61.607 66.667 0.00 0.00 38.10 4.69
3282 4859 3.314331 CCGTGCTGTGGAGGGTCT 61.314 66.667 0.00 0.00 0.00 3.85
3365 5406 8.629158 TGTCTTTGCAAAATTACTGACATAGTT 58.371 29.630 19.79 0.00 40.89 2.24
3398 5439 9.400638 CAAAATTACCGACAACAATTTAGCTAA 57.599 29.630 0.86 0.86 32.89 3.09
3444 5485 1.075659 GCCCCTTCTCCAGTTTGCT 59.924 57.895 0.00 0.00 0.00 3.91
3608 5650 6.593770 CAGCTTGTATACCACATGTTCTTACA 59.406 38.462 0.00 0.00 36.90 2.41
3609 5651 7.280876 CAGCTTGTATACCACATGTTCTTACAT 59.719 37.037 0.00 0.00 45.81 2.29
3717 5759 2.834549 TCTTCCTCCACAGAAGATGGTC 59.165 50.000 0.00 0.00 43.65 4.02
3752 5794 4.385358 TGCTGCGAGAACAGATAACATA 57.615 40.909 0.00 0.00 40.25 2.29
3925 5967 7.097192 CAGTACTTGATAGCTTGGTAAACTCA 58.903 38.462 0.00 0.00 0.00 3.41
3943 5985 9.387123 GTAAACTCATCACATCTTCTTGTTTTC 57.613 33.333 0.00 0.00 0.00 2.29
3966 6008 6.066032 TCCGTATGGATAACATGAGACTACA 58.934 40.000 0.00 0.00 40.17 2.74
4055 6097 6.007703 CCAATTTACACTTTGGGTCTAAGGA 58.992 40.000 0.00 0.00 38.98 3.36
4077 6119 6.940867 AGGACTTAACTAAACATGGGTCTTTC 59.059 38.462 0.00 0.00 0.00 2.62
4136 6178 8.706492 AATAAAACATATTCTGGCACAACATG 57.294 30.769 0.00 0.00 38.70 3.21
4453 6516 4.964593 AGAATTTTGTGCTTTCCTGCAAT 58.035 34.783 0.00 0.00 45.12 3.56
4563 6626 3.756933 ACATTTGCATTTCTGTTGGCT 57.243 38.095 0.00 0.00 0.00 4.75
4724 6787 0.608856 TCCACATGCTGCGGTTTGAT 60.609 50.000 0.00 0.00 0.00 2.57
4821 6884 1.270305 CGGGTTCTGAGAGTGCTGAAA 60.270 52.381 0.00 0.00 0.00 2.69
4880 6943 2.373169 TCAAGATGGAGCAGTCAAGGTT 59.627 45.455 0.00 0.00 0.00 3.50
5116 7179 9.785982 AATAAGCTAATATTCTTCCTCTTGGAC 57.214 33.333 0.00 0.00 43.06 4.02
5134 7197 5.426689 TGGACAGATTTCTCACTATTGCT 57.573 39.130 0.00 0.00 0.00 3.91
5428 7492 2.213499 GGAGAGTTGGTATTCCATGCG 58.787 52.381 0.00 0.00 43.91 4.73
5430 7494 3.270877 GAGAGTTGGTATTCCATGCGTT 58.729 45.455 0.00 0.00 43.91 4.84
5825 7903 7.912773 GTCTAAACCCTACGTTAAGATACTCAC 59.087 40.741 0.00 0.00 33.05 3.51
5844 7922 0.580578 CGCTCCTTTGCATCATCTCG 59.419 55.000 0.00 0.00 0.00 4.04
5885 7963 2.011122 TCTACCTATACCTGCAGGCC 57.989 55.000 33.06 0.00 39.32 5.19
5906 7984 2.026445 TTTGCTGCTTGCGCTGTG 59.974 55.556 9.73 0.00 46.63 3.66
5985 8063 7.233553 TGACTAGCCTATATACAGATGCAAACT 59.766 37.037 0.00 0.00 0.00 2.66
6086 8164 4.640364 TCATGTCATGCAGTGTTACTTCA 58.360 39.130 8.03 0.00 0.00 3.02
6279 8359 6.726490 AACAAGGAGTTACTCACAGTCTTA 57.274 37.500 14.72 0.00 39.09 2.10
6391 8471 4.717233 TCATTTGCAGTTGTTCAAGTGT 57.283 36.364 17.81 0.46 33.45 3.55
6545 8636 1.444553 CGGCCGCCGCAAAATAAAA 60.445 52.632 20.79 0.00 41.17 1.52
6665 8786 1.615883 CGTCACATAGCCTGCTCCTAT 59.384 52.381 0.00 0.00 0.00 2.57
6767 8909 3.279183 CGACTCGGACTCTGCCTT 58.721 61.111 0.00 0.00 0.00 4.35
6877 9020 1.077716 AATTTAGCGCCCGCCTTCT 60.078 52.632 2.29 0.00 43.17 2.85
6878 9021 0.179468 AATTTAGCGCCCGCCTTCTA 59.821 50.000 2.29 0.00 43.17 2.10
7011 9205 0.614697 TGGCTTCCTCGTCCATCTCA 60.615 55.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 3.259374 AGTCCATGTCTCTGTCGACAATT 59.741 43.478 20.49 0.00 46.00 2.32
97 98 1.541588 CAGTCCATGTCTCTGTCGACA 59.458 52.381 18.88 18.88 46.82 4.35
99 100 0.528017 GCAGTCCATGTCTCTGTCGA 59.472 55.000 9.57 0.00 0.00 4.20
259 264 2.094649 CAGTCTCCTAACGTGTCTTCCC 60.095 54.545 0.00 0.00 0.00 3.97
305 310 2.510382 TCCTCTCCGGTATCTCTTGTCT 59.490 50.000 0.00 0.00 0.00 3.41
352 357 5.020132 TCCTCTGTTTCCAAAGGTTTCAAA 58.980 37.500 0.00 0.00 0.00 2.69
356 361 3.380320 CGTTCCTCTGTTTCCAAAGGTTT 59.620 43.478 0.00 0.00 0.00 3.27
439 444 2.970576 GCCAAGAGCGTGATCTCTC 58.029 57.895 0.00 0.00 42.25 3.20
454 459 1.078214 CTTCCTCTTGCCGATGCCA 60.078 57.895 0.00 0.00 36.33 4.92
464 469 4.347583 CCATATTGCTCTCCTCTTCCTCTT 59.652 45.833 0.00 0.00 0.00 2.85
499 1700 0.762842 ACCACTCCACACACTAGGCA 60.763 55.000 0.00 0.00 0.00 4.75
538 1739 2.870341 CGATATGCACCGCCACACG 61.870 63.158 0.00 0.00 43.15 4.49
583 1787 7.104043 TGCGTACCTTAGCTTTATAGAAGAA 57.896 36.000 0.00 0.00 0.00 2.52
658 1862 9.784531 CCTCTTCTTATTTAATGAGATAAGGCA 57.215 33.333 11.89 0.00 36.79 4.75
791 1996 8.838649 AAAACCTCCCTATGTATGCTAAAAAT 57.161 30.769 0.00 0.00 0.00 1.82
818 2023 4.854173 TCCCTATGTATGCAGCTTCAAAA 58.146 39.130 0.00 0.00 0.00 2.44
819 2024 4.080356 ACTCCCTATGTATGCAGCTTCAAA 60.080 41.667 0.00 0.00 0.00 2.69
820 2025 3.455910 ACTCCCTATGTATGCAGCTTCAA 59.544 43.478 0.00 0.00 0.00 2.69
821 2026 3.041211 ACTCCCTATGTATGCAGCTTCA 58.959 45.455 0.00 0.00 0.00 3.02
823 2028 4.901849 TCTAACTCCCTATGTATGCAGCTT 59.098 41.667 0.00 0.00 0.00 3.74
824 2029 4.483950 TCTAACTCCCTATGTATGCAGCT 58.516 43.478 0.00 0.00 0.00 4.24
827 2032 9.725019 CATTATTTCTAACTCCCTATGTATGCA 57.275 33.333 0.00 0.00 0.00 3.96
932 2475 2.324860 GACATTTTGGCTTACGCAACC 58.675 47.619 0.00 0.00 38.10 3.77
933 2476 1.976045 CGACATTTTGGCTTACGCAAC 59.024 47.619 0.00 0.00 38.10 4.17
935 2478 1.463056 CTCGACATTTTGGCTTACGCA 59.537 47.619 0.00 0.00 38.10 5.24
940 2483 3.003689 CAGTTCACTCGACATTTTGGCTT 59.996 43.478 0.00 0.00 0.00 4.35
1321 2864 2.361357 AGACCAGTAGCGGCGAGT 60.361 61.111 12.98 0.00 0.00 4.18
1331 2874 1.070445 GCAGTGTGCAGAGACCAGT 59.930 57.895 0.00 0.00 44.26 4.00
1417 2960 4.960469 ACATAGGAGGTTCGATCTACCAAA 59.040 41.667 14.21 0.00 38.16 3.28
1443 2988 5.113383 CCTATACGGCAACTGTACATGAAA 58.887 41.667 0.00 0.00 0.00 2.69
1449 2994 3.319972 TCATCCCTATACGGCAACTGTAC 59.680 47.826 0.00 0.00 0.00 2.90
1486 3031 3.612423 TGCTCGATCACTTAACATGAACG 59.388 43.478 0.00 7.82 41.96 3.95
1495 3040 2.098280 GCTCAGACTGCTCGATCACTTA 59.902 50.000 0.00 0.00 0.00 2.24
1561 3108 1.878102 CGTGTTTCCAAGAGACAGGGG 60.878 57.143 1.30 0.00 31.82 4.79
1680 3227 4.469945 GGGGCATCCACAGCTACTTATATA 59.530 45.833 0.00 0.00 35.00 0.86
1858 3405 3.452990 TCGTCCAATATGTCCTTTAGGCA 59.547 43.478 0.00 0.00 34.44 4.75
1872 3419 2.540145 GACCGCAAAGTCGTCCAAT 58.460 52.632 0.00 0.00 0.00 3.16
1894 3441 4.161001 GTGAAAATTGATGATCAGCCCCTT 59.839 41.667 8.78 0.00 0.00 3.95
1895 3442 3.703052 GTGAAAATTGATGATCAGCCCCT 59.297 43.478 8.78 0.00 0.00 4.79
1950 3499 0.930310 CCATGTCGCGTAGGTCATTG 59.070 55.000 5.77 0.00 0.00 2.82
2071 3620 2.829458 GGAGAGGTAGCGCTCGGT 60.829 66.667 16.34 0.00 31.95 4.69
2195 3750 1.872952 CGTTGATTGCACAGAGAACCA 59.127 47.619 0.00 0.00 0.00 3.67
2203 3758 2.918345 GCAGGGCGTTGATTGCACA 61.918 57.895 0.00 0.00 38.54 4.57
2242 3797 4.796231 CTCCCGACGCCTTGTCCG 62.796 72.222 0.00 0.00 45.23 4.79
2286 3853 2.370445 CCTCCTTGGAGCGGACCAT 61.370 63.158 11.01 0.00 39.82 3.55
2295 3862 3.009115 CCCGCCTTCCTCCTTGGA 61.009 66.667 0.00 0.00 44.51 3.53
2333 3900 1.600916 GAGGCAGCGGTTTTGGACT 60.601 57.895 0.00 0.00 0.00 3.85
2500 4067 1.476891 GGAAGATCGCTCTGTACACCA 59.523 52.381 0.00 0.00 0.00 4.17
2643 4210 2.406616 GCCAAATGCGATGACGGGT 61.407 57.895 0.00 0.00 40.15 5.28
2673 4243 2.022934 GTGGTTCAAACGGGGTACAAA 58.977 47.619 0.00 0.00 0.00 2.83
2794 4364 3.753434 CCGAGGAGAGCAGTGCGT 61.753 66.667 10.00 0.20 0.00 5.24
2834 4405 3.663176 CACCTGCACGCCACCAAG 61.663 66.667 0.00 0.00 0.00 3.61
3024 4595 0.179051 GGGGCAGCTGAAGATGAGAG 60.179 60.000 20.43 0.00 32.25 3.20
3044 4615 0.882927 CCCAGAACCGACGAGCAAAA 60.883 55.000 0.00 0.00 0.00 2.44
3085 4656 1.450312 CTGACGGAGGCAACATCCC 60.450 63.158 0.00 0.00 41.41 3.85
3107 4678 1.915769 GGGAGACAGCAGGTGGAGT 60.916 63.158 4.26 0.00 0.00 3.85
3235 4812 0.319900 GCAGAGTTTCAGCAGACGGA 60.320 55.000 0.00 0.00 0.00 4.69
3281 4858 1.143620 GAGAGCTACAGGCAGCCAG 59.856 63.158 15.80 8.60 42.84 4.85
3282 4859 1.194121 TTGAGAGCTACAGGCAGCCA 61.194 55.000 15.80 0.00 42.84 4.75
3365 5406 7.789273 TTGTTGTCGGTAATTTTGTAGAAGA 57.211 32.000 0.00 0.00 0.00 2.87
3381 5422 9.941991 CAATTTCATTTAGCTAAATTGTTGTCG 57.058 29.630 25.71 14.46 41.97 4.35
3416 5457 2.158325 TGGAGAAGGGGCACAAGAAAAT 60.158 45.455 0.00 0.00 0.00 1.82
3444 5485 4.617253 ACAGTACATTAGCACCAGACAA 57.383 40.909 0.00 0.00 0.00 3.18
3608 5650 3.242284 CCGCAACAATTACATCGTTCGAT 60.242 43.478 1.68 1.68 0.00 3.59
3609 5651 2.092995 CCGCAACAATTACATCGTTCGA 59.907 45.455 0.00 0.00 0.00 3.71
3717 5759 3.567530 TCGCAGCAATGTTTTCAGAATG 58.432 40.909 0.00 0.00 37.54 2.67
3752 5794 5.445964 ACATTAGGACAGAAAACCAACACT 58.554 37.500 0.00 0.00 0.00 3.55
3914 5956 6.998074 ACAAGAAGATGTGATGAGTTTACCAA 59.002 34.615 0.00 0.00 30.82 3.67
3925 5967 6.094048 CCATACGGAAAACAAGAAGATGTGAT 59.906 38.462 0.00 0.00 32.81 3.06
3943 5985 6.327279 TGTAGTCTCATGTTATCCATACGG 57.673 41.667 0.00 0.00 30.71 4.02
3955 5997 9.404348 GTAGAATGTGACATATGTAGTCTCATG 57.596 37.037 8.71 0.00 44.66 3.07
4055 6097 6.293698 ACGAAAGACCCATGTTTAGTTAAGT 58.706 36.000 0.00 0.00 0.00 2.24
4326 6368 2.287188 CCAAAGATGTCTGCACACACAC 60.287 50.000 0.00 0.00 34.48 3.82
4453 6516 8.923270 ACCATTCAAAATACTTTCTTCTCCAAA 58.077 29.630 0.00 0.00 0.00 3.28
4536 6599 7.566709 CCAACAGAAATGCAAATGTAGAAAAC 58.433 34.615 0.00 0.00 0.00 2.43
4724 6787 3.399330 CGCCCTTGAAAGTAACTTCTCA 58.601 45.455 0.00 0.00 0.00 3.27
4767 6830 0.458543 TCATCAGAACCTTCGAGCGC 60.459 55.000 0.00 0.00 0.00 5.92
4991 7054 1.825191 CAGCACACCACCAGCAGTT 60.825 57.895 0.00 0.00 0.00 3.16
5116 7179 4.521146 ACCCAGCAATAGTGAGAAATCTG 58.479 43.478 0.00 0.00 0.00 2.90
5134 7197 2.335316 AACTGCGACTAACAAACCCA 57.665 45.000 0.00 0.00 0.00 4.51
5373 7437 0.567968 CTGAATTAGCAGCGTCGACG 59.432 55.000 32.57 32.57 43.27 5.12
5428 7492 1.529865 GCTCTCACGGTGGTACAAAAC 59.470 52.381 8.50 0.00 44.16 2.43
5430 7494 1.000506 GAGCTCTCACGGTGGTACAAA 59.999 52.381 6.43 0.00 44.16 2.83
5791 7856 5.934402 ACGTAGGGTTTAGACTTCATCAT 57.066 39.130 0.00 0.00 0.00 2.45
5792 7857 5.733620 AACGTAGGGTTTAGACTTCATCA 57.266 39.130 0.00 0.00 34.41 3.07
5793 7858 7.542025 TCTTAACGTAGGGTTTAGACTTCATC 58.458 38.462 0.00 0.00 38.86 2.92
5825 7903 0.580578 CGAGATGATGCAAAGGAGCG 59.419 55.000 0.00 0.00 37.31 5.03
5844 7922 6.716438 AGAAGCGTTAAAAAGAACTTCTGAC 58.284 36.000 0.00 0.00 28.23 3.51
5906 7984 0.389025 CCACCCTGTGCAAAAAGTCC 59.611 55.000 0.00 0.00 31.34 3.85
5985 8063 1.539157 ACTGCTCTCACGAGATCACA 58.461 50.000 0.00 0.00 39.74 3.58
6373 8453 7.816995 AGAAAATTACACTTGAACAACTGCAAA 59.183 29.630 0.00 0.00 0.00 3.68
6391 8471 9.130661 TGTGGTCAGATTGAGAAAAGAAAATTA 57.869 29.630 0.00 0.00 0.00 1.40
6453 8533 0.248458 ATTTTTAGCAATCGCGCCGG 60.248 50.000 0.00 0.00 45.49 6.13
6460 8540 7.044052 GGCGTTGTATTCTGATTTTTAGCAATC 60.044 37.037 0.00 0.00 34.23 2.67
6461 8541 6.751888 GGCGTTGTATTCTGATTTTTAGCAAT 59.248 34.615 0.00 0.00 0.00 3.56
6462 8542 6.090129 GGCGTTGTATTCTGATTTTTAGCAA 58.910 36.000 0.00 0.00 0.00 3.91
6463 8543 5.636837 GGCGTTGTATTCTGATTTTTAGCA 58.363 37.500 0.00 0.00 0.00 3.49
6642 8762 0.249238 GAGCAGGCTATGTGACGGAG 60.249 60.000 0.00 0.00 0.00 4.63
6644 8764 1.227380 GGAGCAGGCTATGTGACGG 60.227 63.158 0.00 0.00 0.00 4.79
6739 8881 4.692129 CGAGTCGGAGAATGACGG 57.308 61.111 4.10 0.00 39.69 4.79
6767 8909 0.970937 GTCGGAGGAGGACATCACCA 60.971 60.000 0.00 0.00 34.56 4.17
6877 9020 3.044809 GCGAGGACAAGCGAACATA 57.955 52.632 0.00 0.00 0.00 2.29
6878 9021 3.876300 GCGAGGACAAGCGAACAT 58.124 55.556 0.00 0.00 0.00 2.71
6986 9180 1.511305 GACGAGGAAGCCATGACGA 59.489 57.895 0.00 0.00 0.00 4.20
7110 9320 0.323629 TCCCGTTGGGACATGAACTC 59.676 55.000 0.00 0.00 46.17 3.01


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

AutoCloner maintained by Alex Coulton.