Multiple sequence alignment - TraesCS2A01G506700

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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 TraesCS2A01G506700 chr2A 100.000 7734 0 0 1 7734 734524258 734516525 0.000000e+00 14283.0
1 TraesCS2A01G506700 chr2A 98.462 2405 35 1 4322 6724 734535515 734533111 0.000000e+00 4235.0
2 TraesCS2A01G506700 chr2A 91.767 2247 102 42 4278 6493 10258580 10256386 0.000000e+00 3048.0
3 TraesCS2A01G506700 chr2A 98.185 1543 18 5 946 2484 734624574 734626110 0.000000e+00 2686.0
4 TraesCS2A01G506700 chr2A 98.756 1367 17 0 3037 4403 734536764 734535398 0.000000e+00 2431.0
5 TraesCS2A01G506700 chr2A 95.278 953 35 4 1 949 734623562 734624508 0.000000e+00 1502.0
6 TraesCS2A01G506700 chr2A 99.630 540 2 0 2499 3038 734626292 734626831 0.000000e+00 987.0
7 TraesCS2A01G506700 chr2A 90.476 63 6 0 2743 2805 30182025 30182087 4.970000e-12 84.2
8 TraesCS2A01G506700 chr6A 97.783 3699 52 11 3037 6722 23599541 23595860 0.000000e+00 6349.0
9 TraesCS2A01G506700 chr6A 96.900 2452 56 11 4286 6722 268197959 268200405 0.000000e+00 4089.0
10 TraesCS2A01G506700 chr6A 96.573 2451 57 10 4286 6724 23052499 23054934 0.000000e+00 4036.0
11 TraesCS2A01G506700 chr6A 95.347 1569 44 13 3037 4605 268196676 268198215 0.000000e+00 2466.0
12 TraesCS2A01G506700 chr6A 95.883 1506 34 12 3100 4605 23051278 23052755 0.000000e+00 2412.0
13 TraesCS2A01G506700 chr6A 94.819 1023 36 9 6720 7734 584504328 584503315 0.000000e+00 1580.0
14 TraesCS2A01G506700 chr6A 95.898 707 26 3 7030 7734 97612052 97611347 0.000000e+00 1142.0
15 TraesCS2A01G506700 chr6A 96.392 194 3 4 6720 6910 97613291 97613099 4.500000e-82 316.0
16 TraesCS2A01G506700 chr6A 96.373 193 4 3 6721 6910 97613819 97613627 1.620000e-81 315.0
17 TraesCS2A01G506700 chr6A 89.076 119 5 2 6913 7029 97613589 97613477 2.910000e-29 141.0
18 TraesCS2A01G506700 chr6A 92.079 101 2 1 6913 7013 97613061 97612967 3.760000e-28 137.0
19 TraesCS2A01G506700 chr7A 97.141 2448 58 7 4286 6722 130651510 130653956 0.000000e+00 4122.0
20 TraesCS2A01G506700 chr7A 97.790 1403 31 0 3037 4439 130650225 130651627 0.000000e+00 2420.0
21 TraesCS2A01G506700 chr7A 94.283 997 42 8 6746 7734 66752972 66753961 0.000000e+00 1511.0
22 TraesCS2A01G506700 chr7A 96.450 169 6 0 7444 7612 63875239 63875407 5.910000e-71 279.0
23 TraesCS2A01G506700 chr2B 92.137 2658 113 21 3832 6414 155882954 155885590 0.000000e+00 3663.0
24 TraesCS2A01G506700 chr2B 88.939 1546 101 36 782 2297 731339831 731341336 0.000000e+00 1844.0
25 TraesCS2A01G506700 chr2B 89.714 700 70 2 2 699 731313087 731313786 0.000000e+00 893.0
26 TraesCS2A01G506700 chr2B 89.971 339 34 0 6384 6722 155885524 155885862 9.210000e-119 438.0
27 TraesCS2A01G506700 chr2B 80.272 147 24 3 2342 2484 181060281 181060136 1.060000e-18 106.0
28 TraesCS2A01G506700 chr2B 78.689 122 21 4 2729 2850 609961483 609961599 8.320000e-10 76.8
29 TraesCS2A01G506700 chr2D 91.805 2294 114 37 772 3038 601201503 601203749 0.000000e+00 3127.0
30 TraesCS2A01G506700 chr2D 96.424 1622 49 6 3037 4649 339727478 339729099 0.000000e+00 2665.0
31 TraesCS2A01G506700 chr2D 87.952 332 39 1 1 331 601184781 601185112 2.620000e-104 390.0
32 TraesCS2A01G506700 chr2D 90.411 219 17 2 555 773 601188905 601189119 1.270000e-72 285.0
33 TraesCS2A01G506700 chr1D 92.916 2188 80 30 4286 6426 200756426 200754267 0.000000e+00 3112.0
34 TraesCS2A01G506700 chr1D 93.266 297 19 1 6429 6725 200754360 200754065 3.310000e-118 436.0
35 TraesCS2A01G506700 chr1D 78.543 508 70 17 6978 7475 120656980 120656502 1.630000e-76 298.0
36 TraesCS2A01G506700 chr1D 79.255 188 31 4 2347 2527 218666019 218666205 2.930000e-24 124.0
37 TraesCS2A01G506700 chr1D 79.255 188 31 4 2347 2527 234149388 234149574 2.930000e-24 124.0
38 TraesCS2A01G506700 chr1D 78.756 193 32 6 2342 2527 373485541 373485351 3.790000e-23 121.0
39 TraesCS2A01G506700 chr1D 83.333 120 17 3 2728 2847 365430056 365429940 2.950000e-19 108.0
40 TraesCS2A01G506700 chr6B 92.183 2162 98 32 4358 6493 481015811 481013695 0.000000e+00 2990.0
41 TraesCS2A01G506700 chr6B 85.285 333 30 5 6390 6722 481013847 481013534 7.480000e-85 326.0
42 TraesCS2A01G506700 chr6B 79.235 183 26 4 6541 6723 453527152 453527322 4.900000e-22 117.0
43 TraesCS2A01G506700 chr1A 96.279 1747 55 6 3037 4773 540659184 540660930 0.000000e+00 2857.0
44 TraesCS2A01G506700 chr1A 93.894 999 51 4 6738 7734 192592613 192591623 0.000000e+00 1498.0
45 TraesCS2A01G506700 chr1A 96.364 825 22 5 6913 7734 574821766 574822585 0.000000e+00 1351.0
46 TraesCS2A01G506700 chr1A 92.821 195 6 5 6728 6917 574820945 574821136 7.650000e-70 276.0
47 TraesCS2A01G506700 chr3A 96.226 1749 48 10 3037 4773 41415161 41413419 0.000000e+00 2848.0
48 TraesCS2A01G506700 chr3A 93.882 899 28 13 5518 6414 723559555 723560428 0.000000e+00 1330.0
49 TraesCS2A01G506700 chr3A 89.349 338 31 2 6387 6724 723560365 723560697 3.340000e-113 420.0
50 TraesCS2A01G506700 chr4A 96.105 1746 56 6 3037 4773 449968517 449966775 0.000000e+00 2837.0
51 TraesCS2A01G506700 chr4A 95.652 46 2 0 4394 4439 253994461 253994416 2.990000e-09 75.0
52 TraesCS2A01G506700 chr4A 77.311 119 18 6 2733 2848 433056911 433056799 2.330000e-05 62.1
53 TraesCS2A01G506700 chr5A 92.701 822 25 10 6913 7734 138078111 138077325 0.000000e+00 1153.0
54 TraesCS2A01G506700 chr5A 94.240 434 15 5 6973 7404 694498392 694497967 0.000000e+00 654.0
55 TraesCS2A01G506700 chr5A 96.373 193 4 3 6721 6910 138078342 138078150 1.620000e-81 315.0
56 TraesCS2A01G506700 chr5A 90.811 185 4 7 6721 6895 694498784 694498603 1.300000e-57 235.0
57 TraesCS2A01G506700 chr5A 83.088 136 22 1 2733 2868 539071652 539071786 1.050000e-23 122.0
58 TraesCS2A01G506700 chr3D 87.551 972 84 14 5757 6722 89282010 89282950 0.000000e+00 1090.0
59 TraesCS2A01G506700 chr3D 87.179 78 7 1 6328 6402 89282708 89282785 1.380000e-12 86.1
60 TraesCS2A01G506700 chr7D 87.853 354 42 1 6380 6732 196448123 196448476 1.550000e-111 414.0
61 TraesCS2A01G506700 chr7D 79.459 185 29 5 2350 2527 115977632 115977450 1.050000e-23 122.0
62 TraesCS2A01G506700 chr7D 78.919 185 31 4 2350 2527 617858903 617858720 1.360000e-22 119.0
63 TraesCS2A01G506700 chr7D 81.295 139 21 3 2350 2484 225707209 225707072 2.950000e-19 108.0
64 TraesCS2A01G506700 chr7D 84.127 63 10 0 2742 2804 602074390 602074452 2.330000e-05 62.1
65 TraesCS2A01G506700 chr1B 77.996 509 73 20 6988 7487 114875659 114875181 4.570000e-72 283.0
66 TraesCS2A01G506700 chr1B 82.569 109 14 4 2735 2842 312555262 312555366 2.970000e-14 91.6
67 TraesCS2A01G506700 chr5B 78.756 193 33 4 2342 2527 506578723 506578532 1.050000e-23 122.0
68 TraesCS2A01G506700 chr5B 92.500 40 3 0 2733 2772 391925184 391925145 3.010000e-04 58.4
69 TraesCS2A01G506700 chr4B 78.238 193 34 5 2342 2527 106355830 106356021 4.900000e-22 117.0
70 TraesCS2A01G506700 chr4B 80.303 132 22 2 6429 6557 434187764 434187634 6.390000e-16 97.1
71 TraesCS2A01G506700 chr7B 77.949 195 35 4 2342 2529 268063834 268063641 1.760000e-21 115.0
72 TraesCS2A01G506700 chr7B 80.556 72 14 0 2744 2815 57270391 57270320 1.000000e-03 56.5
73 TraesCS2A01G506700 chr6D 80.952 147 23 3 2342 2484 339854023 339853878 2.280000e-20 111.0
74 TraesCS2A01G506700 chr6D 80.808 99 18 1 2729 2826 403660713 403660811 8.320000e-10 76.8
75 TraesCS2A01G506700 chr6D 82.500 80 14 0 2733 2812 2900492 2900571 3.870000e-08 71.3
76 TraesCS2A01G506700 chr6D 83.117 77 13 0 2729 2805 445612613 445612689 3.870000e-08 71.3
77 TraesCS2A01G506700 chr3B 81.481 108 20 0 2729 2836 758458922 758459029 1.070000e-13 89.8
78 TraesCS2A01G506700 chr3B 87.500 72 9 0 2729 2800 238319934 238320005 4.970000e-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 TraesCS2A01G506700 chr2A 734516525 734524258 7733 True 14283.00 14283 100.000000 1 7734 1 chr2A.!!$R2 7733
1 TraesCS2A01G506700 chr2A 734533111 734536764 3653 True 3333.00 4235 98.609000 3037 6724 2 chr2A.!!$R3 3687
2 TraesCS2A01G506700 chr2A 10256386 10258580 2194 True 3048.00 3048 91.767000 4278 6493 1 chr2A.!!$R1 2215
3 TraesCS2A01G506700 chr2A 734623562 734626831 3269 False 1725.00 2686 97.697667 1 3038 3 chr2A.!!$F2 3037
4 TraesCS2A01G506700 chr6A 23595860 23599541 3681 True 6349.00 6349 97.783000 3037 6722 1 chr6A.!!$R1 3685
5 TraesCS2A01G506700 chr6A 268196676 268200405 3729 False 3277.50 4089 96.123500 3037 6722 2 chr6A.!!$F2 3685
6 TraesCS2A01G506700 chr6A 23051278 23054934 3656 False 3224.00 4036 96.228000 3100 6724 2 chr6A.!!$F1 3624
7 TraesCS2A01G506700 chr6A 584503315 584504328 1013 True 1580.00 1580 94.819000 6720 7734 1 chr6A.!!$R2 1014
8 TraesCS2A01G506700 chr6A 97611347 97613819 2472 True 410.20 1142 93.963600 6720 7734 5 chr6A.!!$R3 1014
9 TraesCS2A01G506700 chr7A 130650225 130653956 3731 False 3271.00 4122 97.465500 3037 6722 2 chr7A.!!$F3 3685
10 TraesCS2A01G506700 chr7A 66752972 66753961 989 False 1511.00 1511 94.283000 6746 7734 1 chr7A.!!$F2 988
11 TraesCS2A01G506700 chr2B 155882954 155885862 2908 False 2050.50 3663 91.054000 3832 6722 2 chr2B.!!$F4 2890
12 TraesCS2A01G506700 chr2B 731339831 731341336 1505 False 1844.00 1844 88.939000 782 2297 1 chr2B.!!$F3 1515
13 TraesCS2A01G506700 chr2B 731313087 731313786 699 False 893.00 893 89.714000 2 699 1 chr2B.!!$F2 697
14 TraesCS2A01G506700 chr2D 601201503 601203749 2246 False 3127.00 3127 91.805000 772 3038 1 chr2D.!!$F2 2266
15 TraesCS2A01G506700 chr2D 339727478 339729099 1621 False 2665.00 2665 96.424000 3037 4649 1 chr2D.!!$F1 1612
16 TraesCS2A01G506700 chr2D 601184781 601189119 4338 False 337.50 390 89.181500 1 773 2 chr2D.!!$F3 772
17 TraesCS2A01G506700 chr1D 200754065 200756426 2361 True 1774.00 3112 93.091000 4286 6725 2 chr1D.!!$R4 2439
18 TraesCS2A01G506700 chr6B 481013534 481015811 2277 True 1658.00 2990 88.734000 4358 6722 2 chr6B.!!$R1 2364
19 TraesCS2A01G506700 chr1A 540659184 540660930 1746 False 2857.00 2857 96.279000 3037 4773 1 chr1A.!!$F1 1736
20 TraesCS2A01G506700 chr1A 192591623 192592613 990 True 1498.00 1498 93.894000 6738 7734 1 chr1A.!!$R1 996
21 TraesCS2A01G506700 chr1A 574820945 574822585 1640 False 813.50 1351 94.592500 6728 7734 2 chr1A.!!$F2 1006
22 TraesCS2A01G506700 chr3A 41413419 41415161 1742 True 2848.00 2848 96.226000 3037 4773 1 chr3A.!!$R1 1736
23 TraesCS2A01G506700 chr3A 723559555 723560697 1142 False 875.00 1330 91.615500 5518 6724 2 chr3A.!!$F1 1206
24 TraesCS2A01G506700 chr4A 449966775 449968517 1742 True 2837.00 2837 96.105000 3037 4773 1 chr4A.!!$R3 1736
25 TraesCS2A01G506700 chr5A 138077325 138078342 1017 True 734.00 1153 94.537000 6721 7734 2 chr5A.!!$R1 1013
26 TraesCS2A01G506700 chr5A 694497967 694498784 817 True 444.50 654 92.525500 6721 7404 2 chr5A.!!$R2 683
27 TraesCS2A01G506700 chr3D 89282010 89282950 940 False 588.05 1090 87.365000 5757 6722 2 chr3D.!!$F1 965


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
160 162 0.036671 TAGCGACGACAGACCTCTGA 60.037 55.000 9.35 0.0 46.59 3.27 F
196 198 0.109342 CTGCTTGTTGTGTCCCTCCT 59.891 55.000 0.00 0.0 0.00 3.69 F
967 1057 0.266152 ACCACCAATCCCCAAAACCA 59.734 50.000 0.00 0.0 0.00 3.67 F
2300 2416 5.241403 TGGCTTCTTTATCCAAGACAAGA 57.759 39.130 0.00 0.0 41.56 3.02 F
2876 3166 5.104485 AGAGGGGAAAGAAAAGCACGTATAT 60.104 40.000 0.00 0.0 0.00 0.86 F
4019 4310 1.707989 TCAAGGGGATTGTGGCTGTTA 59.292 47.619 0.00 0.0 40.05 2.41 F
4354 4681 2.533916 TCTGCATCTCCTTGTGACTCT 58.466 47.619 0.00 0.0 0.00 3.24 F
4360 4687 2.603021 TCTCCTTGTGACTCTTGAGCT 58.397 47.619 0.00 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1574 1669 0.249911 GTCGTTTCTCACCTGCACCT 60.250 55.000 0.00 0.0 0.00 4.00 R
1575 1670 1.228657 GGTCGTTTCTCACCTGCACC 61.229 60.000 0.00 0.0 0.00 5.01 R
2490 2610 3.562609 GGTGGCCAAAATCAACCCTACTA 60.563 47.826 7.24 0.0 0.00 1.82 R
3936 4227 0.182775 GCCCCGATCAACCCTACATT 59.817 55.000 0.00 0.0 0.00 2.71 R
4230 4521 2.105477 ACAGACAAGCAGAGACATGGTT 59.895 45.455 0.00 0.0 41.37 3.67 R
5214 5674 4.005650 TCAAGTTGATGTTCAGATCCTGC 58.994 43.478 0.08 0.0 0.00 4.85 R
6621 9183 7.775053 ATTTGTTACAAACAGGTCACCATAT 57.225 32.000 13.01 0.0 43.27 1.78 R
6806 9692 4.995487 ACTGTGGTTCTAAGTTTCCGATTC 59.005 41.667 0.00 0.0 0.00 2.52 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
39 41 9.251440 ACTCCTGTCATTATATTATACGGCTTA 57.749 33.333 0.00 0.00 0.00 3.09
72 74 1.209128 GATAATGTGGCGGTGTCGAG 58.791 55.000 0.00 0.00 39.00 4.04
79 81 1.668151 GGCGGTGTCGAGCTTTCTT 60.668 57.895 0.00 0.00 39.00 2.52
142 144 0.390603 CCCTTCGTGGTCGTGCAATA 60.391 55.000 0.00 0.00 38.33 1.90
160 162 0.036671 TAGCGACGACAGACCTCTGA 60.037 55.000 9.35 0.00 46.59 3.27
196 198 0.109342 CTGCTTGTTGTGTCCCTCCT 59.891 55.000 0.00 0.00 0.00 3.69
200 202 2.027192 GCTTGTTGTGTCCCTCCTATGA 60.027 50.000 0.00 0.00 0.00 2.15
279 281 2.741878 CGGTGCGGTATCCTTTTGATCT 60.742 50.000 0.00 0.00 34.76 2.75
367 369 0.679505 GGAGCCCCCAACAAGTTTTC 59.320 55.000 0.00 0.00 34.14 2.29
568 573 5.375417 TGCTTGTAAGTGGTTGATCATTG 57.625 39.130 0.00 0.00 0.00 2.82
587 592 6.074648 TCATTGTAATTCTGTCTGGGGTTTT 58.925 36.000 0.00 0.00 0.00 2.43
652 657 5.775686 TCGGACGATGTCTTCTTCTAAAAA 58.224 37.500 0.00 0.00 32.47 1.94
653 658 6.395629 TCGGACGATGTCTTCTTCTAAAAAT 58.604 36.000 0.00 0.00 32.47 1.82
677 682 6.365970 AAGGACTCTGACAATACACATCTT 57.634 37.500 0.00 0.00 0.00 2.40
681 686 7.039011 AGGACTCTGACAATACACATCTTAACA 60.039 37.037 0.00 0.00 0.00 2.41
895 915 2.281070 CGCTGGGCAAGACACACT 60.281 61.111 0.00 0.00 0.00 3.55
916 936 6.183360 ACACTCATTAAACTGTGTGTCTTGTG 60.183 38.462 9.87 0.00 45.65 3.33
966 1056 1.429930 AACCACCAATCCCCAAAACC 58.570 50.000 0.00 0.00 0.00 3.27
967 1057 0.266152 ACCACCAATCCCCAAAACCA 59.734 50.000 0.00 0.00 0.00 3.67
1471 1565 6.360618 AGGATTTCAAGATGGTATTGGAGTC 58.639 40.000 0.00 0.00 0.00 3.36
2179 2291 6.014584 GGAATGGAAGACTATTTTGGTTTGGT 60.015 38.462 0.00 0.00 0.00 3.67
2300 2416 5.241403 TGGCTTCTTTATCCAAGACAAGA 57.759 39.130 0.00 0.00 41.56 3.02
2876 3166 5.104485 AGAGGGGAAAGAAAAGCACGTATAT 60.104 40.000 0.00 0.00 0.00 0.86
3936 4227 5.706833 TCAGCTCTTGCAATTGAAATCTGTA 59.293 36.000 10.34 1.73 42.74 2.74
4019 4310 1.707989 TCAAGGGGATTGTGGCTGTTA 59.292 47.619 0.00 0.00 40.05 2.41
4078 4369 4.847633 TGTTCTTCTTGCTTGAAACATCG 58.152 39.130 0.00 0.00 0.00 3.84
4242 4533 6.016777 AGAGCAAAGTAAAAACCATGTCTCTG 60.017 38.462 0.00 0.00 0.00 3.35
4339 4666 3.144657 TGAGCTTCTTCCAATTCTGCA 57.855 42.857 0.00 0.00 0.00 4.41
4340 4667 3.693807 TGAGCTTCTTCCAATTCTGCAT 58.306 40.909 0.00 0.00 0.00 3.96
4341 4668 3.693085 TGAGCTTCTTCCAATTCTGCATC 59.307 43.478 0.00 0.00 0.00 3.91
4342 4669 3.946558 GAGCTTCTTCCAATTCTGCATCT 59.053 43.478 0.00 0.00 0.00 2.90
4343 4670 3.946558 AGCTTCTTCCAATTCTGCATCTC 59.053 43.478 0.00 0.00 0.00 2.75
4344 4671 3.066481 GCTTCTTCCAATTCTGCATCTCC 59.934 47.826 0.00 0.00 0.00 3.71
4345 4672 4.525024 CTTCTTCCAATTCTGCATCTCCT 58.475 43.478 0.00 0.00 0.00 3.69
4346 4673 4.581309 TCTTCCAATTCTGCATCTCCTT 57.419 40.909 0.00 0.00 0.00 3.36
4347 4674 4.267536 TCTTCCAATTCTGCATCTCCTTG 58.732 43.478 0.00 0.00 0.00 3.61
4348 4675 3.726557 TCCAATTCTGCATCTCCTTGT 57.273 42.857 0.00 0.00 0.00 3.16
4349 4676 3.349927 TCCAATTCTGCATCTCCTTGTG 58.650 45.455 0.00 0.00 0.00 3.33
4350 4677 3.009363 TCCAATTCTGCATCTCCTTGTGA 59.991 43.478 0.00 0.00 0.00 3.58
4351 4678 3.128242 CCAATTCTGCATCTCCTTGTGAC 59.872 47.826 0.00 0.00 0.00 3.67
4352 4679 3.996921 ATTCTGCATCTCCTTGTGACT 57.003 42.857 0.00 0.00 0.00 3.41
4353 4680 3.325293 TTCTGCATCTCCTTGTGACTC 57.675 47.619 0.00 0.00 0.00 3.36
4354 4681 2.533916 TCTGCATCTCCTTGTGACTCT 58.466 47.619 0.00 0.00 0.00 3.24
4355 4682 2.902486 TCTGCATCTCCTTGTGACTCTT 59.098 45.455 0.00 0.00 0.00 2.85
4356 4683 3.001414 CTGCATCTCCTTGTGACTCTTG 58.999 50.000 0.00 0.00 0.00 3.02
4357 4684 2.634453 TGCATCTCCTTGTGACTCTTGA 59.366 45.455 0.00 0.00 0.00 3.02
4358 4685 3.260740 GCATCTCCTTGTGACTCTTGAG 58.739 50.000 0.00 0.00 0.00 3.02
4359 4686 3.260740 CATCTCCTTGTGACTCTTGAGC 58.739 50.000 0.00 0.00 0.00 4.26
4360 4687 2.603021 TCTCCTTGTGACTCTTGAGCT 58.397 47.619 0.00 0.00 0.00 4.09
4361 4688 2.968574 TCTCCTTGTGACTCTTGAGCTT 59.031 45.455 0.00 0.00 0.00 3.74
4362 4689 3.006323 TCTCCTTGTGACTCTTGAGCTTC 59.994 47.826 0.00 0.00 0.00 3.86
4363 4690 2.968574 TCCTTGTGACTCTTGAGCTTCT 59.031 45.455 0.00 0.00 0.00 2.85
4364 4691 3.389329 TCCTTGTGACTCTTGAGCTTCTT 59.611 43.478 0.00 0.00 0.00 2.52
6265 7842 4.742649 TCCAGGCGCTCGAGACCT 62.743 66.667 18.75 18.80 0.00 3.85
6454 9016 4.778415 CCACGGAGGAGCACGTCG 62.778 72.222 0.00 0.00 42.04 5.12
6621 9183 1.471684 GAAGGAAGAAGACGCGACCTA 59.528 52.381 15.93 0.00 0.00 3.08
6718 9596 0.471191 ACTTTTTCCGAACGGAGGGT 59.529 50.000 15.34 10.23 46.06 4.34
6806 9692 4.802039 ACGTACGCCAAATTATCTGTACTG 59.198 41.667 16.72 0.00 32.20 2.74
6826 9712 4.995487 ACTGAATCGGAAACTTAGAACCAC 59.005 41.667 0.00 0.00 0.00 4.16
6963 10624 0.517316 CAAACGACCAAGCTGTAGCC 59.483 55.000 0.00 0.00 43.38 3.93
6964 10625 0.107831 AAACGACCAAGCTGTAGCCA 59.892 50.000 0.00 0.00 43.38 4.75
6965 10626 0.107831 AACGACCAAGCTGTAGCCAA 59.892 50.000 0.00 0.00 43.38 4.52
6966 10627 0.107831 ACGACCAAGCTGTAGCCAAA 59.892 50.000 0.00 0.00 43.38 3.28
6967 10628 1.271379 ACGACCAAGCTGTAGCCAAAT 60.271 47.619 0.00 0.00 43.38 2.32
6968 10629 2.027561 ACGACCAAGCTGTAGCCAAATA 60.028 45.455 0.00 0.00 43.38 1.40
7004 10671 6.425721 TCAGAACTGAACACCGGTTATTAAAG 59.574 38.462 2.97 6.67 44.04 1.85
7163 12259 0.674269 TGCTGAATGATGCTGCACGA 60.674 50.000 3.57 0.00 35.68 4.35
7205 12301 4.832266 ACAATGTTAATTGGAGCCAAGTCA 59.168 37.500 5.38 0.00 46.34 3.41
7224 12320 6.683974 AGTCATTCATAAATTTGGACCTCG 57.316 37.500 0.00 0.00 0.00 4.63
7689 12786 0.788995 CAAGCAAGAGCACACGAGAG 59.211 55.000 0.00 0.00 45.49 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 34 1.275573 GACCCTGAAGAACTAAGCCGT 59.724 52.381 0.00 0.00 0.00 5.68
39 41 4.383118 CCACATTATCGACCCTGAAGAACT 60.383 45.833 0.00 0.00 0.00 3.01
72 74 2.422276 AATTGACACGGCAAGAAAGC 57.578 45.000 0.00 0.00 0.00 3.51
79 81 0.309302 CGAACCAAATTGACACGGCA 59.691 50.000 0.00 0.00 0.00 5.69
142 144 0.678366 ATCAGAGGTCTGTCGTCGCT 60.678 55.000 6.87 0.00 44.12 4.93
160 162 1.065854 GCAGACCACAGTTAGCTCCAT 60.066 52.381 0.00 0.00 0.00 3.41
196 198 1.148273 GGCAACCGGGAGCATCATA 59.852 57.895 19.97 0.00 36.25 2.15
200 202 3.965258 TGTGGCAACCGGGAGCAT 61.965 61.111 19.97 0.00 0.00 3.79
266 268 6.707608 CGACATCCATTCAGATCAAAAGGATA 59.292 38.462 13.88 0.00 36.00 2.59
279 281 1.667236 GGCACATCGACATCCATTCA 58.333 50.000 0.00 0.00 0.00 2.57
367 369 2.538437 CTAGCACTAGACAAGCAGCAG 58.462 52.381 0.00 0.00 35.21 4.24
497 499 2.540101 GTCAAACAACCTCAGACGACAG 59.460 50.000 0.00 0.00 0.00 3.51
542 547 4.696877 TGATCAACCACTTACAAGCATCAG 59.303 41.667 0.00 0.00 0.00 2.90
552 557 8.862325 ACAGAATTACAATGATCAACCACTTA 57.138 30.769 0.00 0.00 0.00 2.24
568 573 4.149598 ACCAAAACCCCAGACAGAATTAC 58.850 43.478 0.00 0.00 0.00 1.89
587 592 3.133362 CCTAGCCCGACTTACAATTACCA 59.867 47.826 0.00 0.00 0.00 3.25
624 629 1.022735 GAAGACATCGTCCGAGCCTA 58.977 55.000 0.00 0.00 32.18 3.93
652 657 7.667575 AGATGTGTATTGTCAGAGTCCTTAT 57.332 36.000 0.00 0.00 0.00 1.73
653 658 7.482169 AAGATGTGTATTGTCAGAGTCCTTA 57.518 36.000 0.00 0.00 0.00 2.69
670 675 8.327429 GTTGGTTGTTTTTCATGTTAAGATGTG 58.673 33.333 11.96 0.00 0.00 3.21
895 915 4.637977 TGCACAAGACACACAGTTTAATGA 59.362 37.500 0.00 0.00 0.00 2.57
1574 1669 0.249911 GTCGTTTCTCACCTGCACCT 60.250 55.000 0.00 0.00 0.00 4.00
1575 1670 1.228657 GGTCGTTTCTCACCTGCACC 61.229 60.000 0.00 0.00 0.00 5.01
1580 1675 2.317040 TCTTCAGGTCGTTTCTCACCT 58.683 47.619 0.00 0.00 44.42 4.00
2300 2416 4.640647 GCTAGGCTAAAAGCAAACATACCT 59.359 41.667 2.91 0.00 44.75 3.08
2490 2610 3.562609 GGTGGCCAAAATCAACCCTACTA 60.563 47.826 7.24 0.00 0.00 1.82
2876 3166 4.426416 CCGTCAAGATAATGTAACGGTCA 58.574 43.478 3.70 0.00 43.42 4.02
2993 3283 4.090761 AGTTTTGCTTGTCTGATCAGGA 57.909 40.909 22.42 7.05 0.00 3.86
3439 3729 2.827322 CCCTGCCATTCAAGACAAATGA 59.173 45.455 0.00 0.00 36.43 2.57
3936 4227 0.182775 GCCCCGATCAACCCTACATT 59.817 55.000 0.00 0.00 0.00 2.71
4019 4310 7.639113 AGAGAAAAGAACTAGATCTGTCGAT 57.361 36.000 5.18 0.00 0.00 3.59
4078 4369 3.435186 GCGGCAGGCCAAGAAGTC 61.435 66.667 5.01 0.00 35.37 3.01
4230 4521 2.105477 ACAGACAAGCAGAGACATGGTT 59.895 45.455 0.00 0.00 41.37 3.67
4339 4666 3.172339 AGCTCAAGAGTCACAAGGAGAT 58.828 45.455 0.00 0.00 0.00 2.75
4340 4667 2.603021 AGCTCAAGAGTCACAAGGAGA 58.397 47.619 0.00 0.00 0.00 3.71
4341 4668 3.006752 AGAAGCTCAAGAGTCACAAGGAG 59.993 47.826 0.00 0.00 0.00 3.69
4342 4669 2.968574 AGAAGCTCAAGAGTCACAAGGA 59.031 45.455 0.00 0.00 0.00 3.36
4343 4670 3.399440 AGAAGCTCAAGAGTCACAAGG 57.601 47.619 0.00 0.00 0.00 3.61
4344 4671 3.745458 GGAAGAAGCTCAAGAGTCACAAG 59.255 47.826 0.00 0.00 0.00 3.16
4345 4672 3.134623 TGGAAGAAGCTCAAGAGTCACAA 59.865 43.478 0.00 0.00 0.00 3.33
4346 4673 2.700371 TGGAAGAAGCTCAAGAGTCACA 59.300 45.455 0.00 0.00 0.00 3.58
4347 4674 3.393089 TGGAAGAAGCTCAAGAGTCAC 57.607 47.619 0.00 0.00 0.00 3.67
4348 4675 4.630644 ATTGGAAGAAGCTCAAGAGTCA 57.369 40.909 0.00 0.00 0.00 3.41
4349 4676 5.122082 CAGAATTGGAAGAAGCTCAAGAGTC 59.878 44.000 0.00 0.00 0.00 3.36
4350 4677 5.002516 CAGAATTGGAAGAAGCTCAAGAGT 58.997 41.667 0.00 0.00 0.00 3.24
4351 4678 4.142643 GCAGAATTGGAAGAAGCTCAAGAG 60.143 45.833 0.00 0.00 0.00 2.85
4352 4679 3.755378 GCAGAATTGGAAGAAGCTCAAGA 59.245 43.478 0.00 0.00 0.00 3.02
4353 4680 3.504906 TGCAGAATTGGAAGAAGCTCAAG 59.495 43.478 0.00 0.00 0.00 3.02
4354 4681 3.489355 TGCAGAATTGGAAGAAGCTCAA 58.511 40.909 0.00 0.00 0.00 3.02
4355 4682 3.144657 TGCAGAATTGGAAGAAGCTCA 57.855 42.857 0.00 0.00 0.00 4.26
4356 4683 3.946558 AGATGCAGAATTGGAAGAAGCTC 59.053 43.478 0.00 0.00 0.00 4.09
4357 4684 3.946558 GAGATGCAGAATTGGAAGAAGCT 59.053 43.478 0.00 0.00 0.00 3.74
4358 4685 3.066481 GGAGATGCAGAATTGGAAGAAGC 59.934 47.826 0.00 0.00 0.00 3.86
4359 4686 4.525024 AGGAGATGCAGAATTGGAAGAAG 58.475 43.478 0.00 0.00 0.00 2.85
4360 4687 4.581309 AGGAGATGCAGAATTGGAAGAA 57.419 40.909 0.00 0.00 0.00 2.52
4361 4688 4.263639 ACAAGGAGATGCAGAATTGGAAGA 60.264 41.667 0.00 0.00 0.00 2.87
4362 4689 4.015084 ACAAGGAGATGCAGAATTGGAAG 58.985 43.478 0.00 0.00 0.00 3.46
4363 4690 3.760151 CACAAGGAGATGCAGAATTGGAA 59.240 43.478 0.00 0.00 0.00 3.53
4364 4691 3.349927 CACAAGGAGATGCAGAATTGGA 58.650 45.455 0.00 0.00 0.00 3.53
5214 5674 4.005650 TCAAGTTGATGTTCAGATCCTGC 58.994 43.478 0.08 0.00 0.00 4.85
6621 9183 7.775053 ATTTGTTACAAACAGGTCACCATAT 57.225 32.000 13.01 0.00 43.27 1.78
6806 9692 4.995487 ACTGTGGTTCTAAGTTTCCGATTC 59.005 41.667 0.00 0.00 0.00 2.52
6826 9712 2.977914 AGGATGAAACGTGATGGACTG 58.022 47.619 0.00 0.00 0.00 3.51
6965 10626 9.647797 TGTTCAGTTCTGATACGTATTTGTATT 57.352 29.630 9.92 0.00 35.24 1.89
6966 10627 9.084164 GTGTTCAGTTCTGATACGTATTTGTAT 57.916 33.333 9.92 0.00 37.74 2.29
6967 10628 7.543172 GGTGTTCAGTTCTGATACGTATTTGTA 59.457 37.037 9.92 0.00 0.00 2.41
6968 10629 6.367969 GGTGTTCAGTTCTGATACGTATTTGT 59.632 38.462 9.92 0.00 0.00 2.83
7004 10671 6.318648 TGATATATTGGCCAGTGTTCTGTTTC 59.681 38.462 11.69 0.00 39.82 2.78
7163 12259 0.035317 TGGCTCTGCAGAATCGTTGT 59.965 50.000 18.85 0.00 0.00 3.32
7205 12301 3.636764 GCCCGAGGTCCAAATTTATGAAT 59.363 43.478 0.00 0.00 0.00 2.57
7224 12320 7.391148 TCTTATTTTTGTCTCATTGTAGCCC 57.609 36.000 0.00 0.00 0.00 5.19
7669 12766 0.104855 TCTCGTGTGCTCTTGCTTGT 59.895 50.000 0.00 0.00 40.48 3.16
7689 12786 4.467084 TGGGGCTCGCGTCCATTC 62.467 66.667 18.63 10.01 36.31 2.67



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

AutoCloner maintained by Alex Coulton.