Multiple sequence alignment - TraesCS6D01G061100

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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 TraesCS6D01G061100 chr6D 100.000 4363 0 0 1 4363 28659393 28655031 0.000000e+00 8058.0
1 TraesCS6D01G061100 chr6D 78.752 513 76 19 283 770 409844387 409843883 3.280000e-81 313.0
2 TraesCS6D01G061100 chr6D 80.412 97 18 1 2692 2787 27861522 27861618 6.050000e-09 73.1
3 TraesCS6D01G061100 chr6A 95.512 3610 101 21 774 4363 34028895 34032463 0.000000e+00 5712.0
4 TraesCS6D01G061100 chr6A 83.208 1197 172 15 1020 2210 45066280 45065107 0.000000e+00 1070.0
5 TraesCS6D01G061100 chr6A 78.030 1188 217 26 1053 2224 47488159 47487000 0.000000e+00 708.0
6 TraesCS6D01G061100 chr6A 80.537 745 124 12 1107 1836 47471754 47471016 1.770000e-153 553.0
7 TraesCS6D01G061100 chr6A 83.698 411 65 2 1946 2356 47470129 47469721 1.900000e-103 387.0
8 TraesCS6D01G061100 chr6A 80.384 469 43 23 2249 2710 45065106 45064680 1.180000e-80 311.0
9 TraesCS6D01G061100 chr6A 89.873 158 11 3 21 174 45341798 45341642 9.570000e-47 198.0
10 TraesCS6D01G061100 chr6A 92.857 112 8 0 74 185 34014702 34014813 3.490000e-36 163.0
11 TraesCS6D01G061100 chr6A 84.000 125 14 5 2802 2921 46715134 46715011 9.920000e-22 115.0
12 TraesCS6D01G061100 chr6A 90.667 75 4 2 2835 2909 34011252 34011181 3.590000e-16 97.1
13 TraesCS6D01G061100 chr6A 82.474 97 16 1 2692 2787 29968230 29968134 2.800000e-12 84.2
14 TraesCS6D01G061100 chr6A 90.476 63 5 1 3 64 45341864 45341802 1.010000e-11 82.4
15 TraesCS6D01G061100 chr6A 81.633 98 17 1 2692 2788 29887258 29887161 3.620000e-11 80.5
16 TraesCS6D01G061100 chr6B 91.769 3025 198 27 1 3017 62124579 62127560 0.000000e+00 4159.0
17 TraesCS6D01G061100 chr6B 84.540 1947 227 36 1049 2979 77764787 77762899 0.000000e+00 1860.0
18 TraesCS6D01G061100 chr6B 79.744 1328 228 23 1039 2352 82004592 82005892 0.000000e+00 924.0
19 TraesCS6D01G061100 chr6B 86.785 734 60 15 3015 3738 62127627 62128333 0.000000e+00 784.0
20 TraesCS6D01G061100 chr6B 78.238 1305 215 33 1087 2356 82165952 82167222 0.000000e+00 773.0
21 TraesCS6D01G061100 chr6B 78.512 1196 213 26 1039 2218 82156662 82157829 0.000000e+00 745.0
22 TraesCS6D01G061100 chr6B 83.926 815 80 24 3015 3814 77762802 77762024 0.000000e+00 732.0
23 TraesCS6D01G061100 chr6B 76.190 1344 257 40 1056 2383 82427475 82426179 0.000000e+00 651.0
24 TraesCS6D01G061100 chr6B 93.812 404 25 0 1 404 62112974 62113377 3.730000e-170 608.0
25 TraesCS6D01G061100 chr6B 70.539 1317 318 51 1094 2384 51559016 51560288 7.350000e-53 219.0
26 TraesCS6D01G061100 chr6B 75.592 422 92 8 1966 2383 77392347 77392761 9.570000e-47 198.0
27 TraesCS6D01G061100 chr6B 78.438 320 52 10 3088 3405 82008392 82008696 4.450000e-45 193.0
28 TraesCS6D01G061100 chr6B 78.193 321 43 14 3088 3405 82161872 82162168 3.470000e-41 180.0
29 TraesCS6D01G061100 chr6B 78.868 265 48 7 2692 2954 62109354 62109612 5.800000e-39 172.0
30 TraesCS6D01G061100 chr6B 79.293 198 30 7 2747 2936 79848674 79848868 1.270000e-25 128.0
31 TraesCS6D01G061100 chr6B 90.667 75 4 2 2835 2909 62121009 62120938 3.590000e-16 97.1
32 TraesCS6D01G061100 chrUn 83.905 1982 233 43 1046 3014 112648916 112650824 0.000000e+00 1814.0
33 TraesCS6D01G061100 chrUn 78.851 1305 207 37 1087 2356 26970953 26969683 0.000000e+00 817.0
34 TraesCS6D01G061100 chrUn 85.073 824 84 17 3015 3824 112650894 112651692 0.000000e+00 804.0
35 TraesCS6D01G061100 chrUn 74.837 1379 248 66 1040 2384 112677008 112678321 2.310000e-147 532.0
36 TraesCS6D01G061100 chrUn 79.151 777 144 12 1039 1801 27073072 27073844 5.000000e-144 521.0
37 TraesCS6D01G061100 chrUn 83.023 483 77 4 1874 2356 27073884 27074361 2.410000e-117 433.0
38 TraesCS6D01G061100 chrUn 88.701 177 14 4 3 174 112600872 112601047 1.230000e-50 211.0
39 TraesCS6D01G061100 chr7D 91.250 400 24 6 3828 4218 625342773 625343170 6.420000e-148 534.0
40 TraesCS6D01G061100 chr7D 89.487 409 39 4 3820 4226 607048870 607049276 8.370000e-142 514.0
41 TraesCS6D01G061100 chr7D 92.550 349 22 4 3828 4174 538352158 538352504 8.430000e-137 497.0
42 TraesCS6D01G061100 chr7D 86.288 299 28 4 217 515 24157800 24157515 3.280000e-81 313.0
43 TraesCS6D01G061100 chr3B 93.182 352 19 5 3828 4179 42739187 42738841 3.010000e-141 512.0
44 TraesCS6D01G061100 chr3B 92.264 349 19 7 3828 4174 815467255 815466913 5.070000e-134 488.0
45 TraesCS6D01G061100 chr3B 79.010 505 77 17 283 764 377708801 377709299 7.040000e-83 318.0
46 TraesCS6D01G061100 chr1D 89.877 405 24 5 3828 4218 469388237 469388638 5.040000e-139 505.0
47 TraesCS6D01G061100 chr3A 89.848 394 32 8 3828 4218 20245227 20245615 2.340000e-137 499.0
48 TraesCS6D01G061100 chr7A 92.264 349 23 4 3826 4174 26466038 26465694 3.920000e-135 492.0
49 TraesCS6D01G061100 chr2B 87.750 400 36 7 3828 4218 165094057 165094452 5.140000e-124 455.0
50 TraesCS6D01G061100 chr2B 83.234 501 61 8 217 697 744061116 744060619 5.180000e-119 438.0
51 TraesCS6D01G061100 chr4D 83.768 499 59 9 219 698 12501218 12500723 1.850000e-123 453.0
52 TraesCS6D01G061100 chr4D 76.420 352 57 16 2580 2924 5545686 5545354 2.700000e-37 167.0
53 TraesCS6D01G061100 chr2A 88.630 343 30 7 3827 4165 779202060 779202397 4.060000e-110 409.0
54 TraesCS6D01G061100 chr2A 78.627 510 84 11 283 770 45159867 45159361 9.110000e-82 315.0
55 TraesCS6D01G061100 chr1A 82.164 499 65 12 217 694 518724893 518725388 1.460000e-109 407.0
56 TraesCS6D01G061100 chr1A 81.727 498 66 12 219 697 541324201 541323710 4.090000e-105 392.0
57 TraesCS6D01G061100 chr1A 81.222 442 55 18 283 700 567458530 567458093 9.040000e-87 331.0
58 TraesCS6D01G061100 chr7B 81.727 498 60 17 219 697 660234760 660235245 1.900000e-103 387.0
59 TraesCS6D01G061100 chr7B 79.208 505 76 17 283 764 684104109 684103611 1.510000e-84 324.0
60 TraesCS6D01G061100 chr5B 79.920 503 75 14 283 764 697441875 697441378 3.230000e-91 346.0
61 TraesCS6D01G061100 chr5B 79.874 477 70 16 309 764 698476909 698477380 4.210000e-85 326.0
62 TraesCS6D01G061100 chr5B 78.193 509 74 17 284 764 27441956 27442455 1.530000e-74 291.0
63 TraesCS6D01G061100 chr5D 79.523 503 75 19 283 763 125782750 125783246 2.510000e-87 333.0
64 TraesCS6D01G061100 chr4B 94.286 35 2 0 4184 4218 561895842 561895876 2.000000e-03 54.7


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 TraesCS6D01G061100 chr6D 28655031 28659393 4362 True 8058.0 8058 100.0000 1 4363 1 chr6D.!!$R1 4362
1 TraesCS6D01G061100 chr6D 409843883 409844387 504 True 313.0 313 78.7520 283 770 1 chr6D.!!$R2 487
2 TraesCS6D01G061100 chr6A 34028895 34032463 3568 False 5712.0 5712 95.5120 774 4363 1 chr6A.!!$F2 3589
3 TraesCS6D01G061100 chr6A 47487000 47488159 1159 True 708.0 708 78.0300 1053 2224 1 chr6A.!!$R5 1171
4 TraesCS6D01G061100 chr6A 45064680 45066280 1600 True 690.5 1070 81.7960 1020 2710 2 chr6A.!!$R6 1690
5 TraesCS6D01G061100 chr6A 47469721 47471754 2033 True 470.0 553 82.1175 1107 2356 2 chr6A.!!$R8 1249
6 TraesCS6D01G061100 chr6B 62124579 62128333 3754 False 2471.5 4159 89.2770 1 3738 2 chr6B.!!$F6 3737
7 TraesCS6D01G061100 chr6B 77762024 77764787 2763 True 1296.0 1860 84.2330 1049 3814 2 chr6B.!!$R3 2765
8 TraesCS6D01G061100 chr6B 82156662 82157829 1167 False 745.0 745 78.5120 1039 2218 1 chr6B.!!$F4 1179
9 TraesCS6D01G061100 chr6B 82426179 82427475 1296 True 651.0 651 76.1900 1056 2383 1 chr6B.!!$R2 1327
10 TraesCS6D01G061100 chr6B 82004592 82008696 4104 False 558.5 924 79.0910 1039 3405 2 chr6B.!!$F7 2366
11 TraesCS6D01G061100 chr6B 82161872 82167222 5350 False 476.5 773 78.2155 1087 3405 2 chr6B.!!$F8 2318
12 TraesCS6D01G061100 chr6B 62109354 62113377 4023 False 390.0 608 86.3400 1 2954 2 chr6B.!!$F5 2953
13 TraesCS6D01G061100 chr6B 51559016 51560288 1272 False 219.0 219 70.5390 1094 2384 1 chr6B.!!$F1 1290
14 TraesCS6D01G061100 chrUn 112648916 112651692 2776 False 1309.0 1814 84.4890 1046 3824 2 chrUn.!!$F4 2778
15 TraesCS6D01G061100 chrUn 26969683 26970953 1270 True 817.0 817 78.8510 1087 2356 1 chrUn.!!$R1 1269
16 TraesCS6D01G061100 chrUn 112677008 112678321 1313 False 532.0 532 74.8370 1040 2384 1 chrUn.!!$F2 1344
17 TraesCS6D01G061100 chrUn 27073072 27074361 1289 False 477.0 521 81.0870 1039 2356 2 chrUn.!!$F3 1317
18 TraesCS6D01G061100 chr2A 45159361 45159867 506 True 315.0 315 78.6270 283 770 1 chr2A.!!$R1 487

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
602 603 0.319813 TGTGCAGTCTCGGATGTGTG 60.320 55.000 0.0 0.0 0.0 3.82 F
1014 1034 0.693049 ACCCGCACCATCTTCTCTTT 59.307 50.000 0.0 0.0 0.0 2.52 F
1015 1035 1.339151 ACCCGCACCATCTTCTCTTTC 60.339 52.381 0.0 0.0 0.0 2.62 F
1018 1038 1.404181 CGCACCATCTTCTCTTTCGGA 60.404 52.381 0.0 0.0 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 5957 0.899720 TGAAGAGGCCGATAACCGTT 59.100 50.000 0.00 0.00 36.31 4.44 R
2147 6007 1.154197 GGTCGTAGTGTTGGAAAGCC 58.846 55.000 0.00 0.00 0.00 4.35 R
2998 8630 1.412710 TCCACTCGCAACAGACTCTTT 59.587 47.619 0.00 0.00 0.00 2.52 R
3455 9543 4.966965 AAAGATTCAAGATGCAGCTCAG 57.033 40.909 4.22 0.73 0.00 3.35 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
26 27 7.933577 AGAAGGAATTATCAATTGATGACGCTA 59.066 33.333 27.59 6.71 41.93 4.26
47 48 7.010552 ACGCTATGATTAAGTAAAACTGAGCAG 59.989 37.037 0.00 0.00 0.00 4.24
80 81 8.455682 GGTTTTATTATTCTTCGGATGTTCACA 58.544 33.333 0.00 0.00 0.00 3.58
118 119 6.250819 GGTGAACACAAACGATTATCATCAG 58.749 40.000 7.25 0.00 0.00 2.90
147 148 5.255207 TCTTTTCTTTGGGAGGGGATTATCA 59.745 40.000 0.00 0.00 0.00 2.15
150 151 5.749422 TCTTTGGGAGGGGATTATCAATT 57.251 39.130 0.00 0.00 0.00 2.32
201 202 3.612247 ATCAGCCACACTCCACCGC 62.612 63.158 0.00 0.00 0.00 5.68
209 210 1.450312 CACTCCACCGCCATCTTCC 60.450 63.158 0.00 0.00 0.00 3.46
233 234 0.738762 CTGAGTGTGGCTGATGTCGG 60.739 60.000 0.00 0.00 0.00 4.79
262 263 4.760047 CTGGCTTGGGGTCGACGG 62.760 72.222 9.92 0.00 0.00 4.79
278 279 1.404035 GACGGTGGTTTTTGTGCTCTT 59.596 47.619 0.00 0.00 0.00 2.85
282 283 3.428862 CGGTGGTTTTTGTGCTCTTCTTT 60.429 43.478 0.00 0.00 0.00 2.52
283 284 3.865164 GGTGGTTTTTGTGCTCTTCTTTG 59.135 43.478 0.00 0.00 0.00 2.77
399 400 1.468565 CCTCGCGTGTCCTTTCGAATA 60.469 52.381 5.77 0.00 0.00 1.75
445 446 0.953727 TGTTGTGCAGTCTTGGATGC 59.046 50.000 0.00 0.00 42.86 3.91
518 519 1.491670 CGATGCCCTTCGACTATGTG 58.508 55.000 0.00 0.00 41.62 3.21
558 559 2.787473 TGATCCTTCGAATGTGCCTT 57.213 45.000 0.00 0.00 0.00 4.35
602 603 0.319813 TGTGCAGTCTCGGATGTGTG 60.320 55.000 0.00 0.00 0.00 3.82
620 621 4.024387 TGTGTGAAGCCTTTCAATTACGTC 60.024 41.667 0.00 0.00 44.49 4.34
623 624 4.092968 GTGAAGCCTTTCAATTACGTCGAT 59.907 41.667 0.00 0.00 44.49 3.59
679 680 1.735018 TGCCGTTCGATTACATTGGTG 59.265 47.619 0.00 0.00 0.00 4.17
685 686 3.066291 TCGATTACATTGGTGGTGCTT 57.934 42.857 0.00 0.00 0.00 3.91
705 706 4.566759 GCTTTTTGTTGTGTTTCCCTCTTC 59.433 41.667 0.00 0.00 0.00 2.87
709 710 3.349022 TGTTGTGTTTCCCTCTTCGTTT 58.651 40.909 0.00 0.00 0.00 3.60
889 893 5.181690 TGTGGTGTCTGCAATAAAACTTC 57.818 39.130 0.00 0.00 0.00 3.01
964 981 2.234300 GGTTCTCACCACGTTCTGAA 57.766 50.000 0.00 0.00 43.61 3.02
965 982 1.865340 GGTTCTCACCACGTTCTGAAC 59.135 52.381 10.48 10.48 43.61 3.18
966 983 2.483188 GGTTCTCACCACGTTCTGAACT 60.483 50.000 17.60 3.25 43.61 3.01
967 984 3.195661 GTTCTCACCACGTTCTGAACTT 58.804 45.455 17.60 6.34 33.31 2.66
969 986 2.693591 TCTCACCACGTTCTGAACTTCT 59.306 45.455 17.60 0.00 0.00 2.85
970 987 2.797156 CTCACCACGTTCTGAACTTCTG 59.203 50.000 17.60 9.96 0.00 3.02
971 988 2.429250 TCACCACGTTCTGAACTTCTGA 59.571 45.455 17.60 8.82 0.00 3.27
1010 1030 1.003355 CACACCCGCACCATCTTCT 60.003 57.895 0.00 0.00 0.00 2.85
1011 1031 1.021390 CACACCCGCACCATCTTCTC 61.021 60.000 0.00 0.00 0.00 2.87
1012 1032 1.194781 ACACCCGCACCATCTTCTCT 61.195 55.000 0.00 0.00 0.00 3.10
1014 1034 0.693049 ACCCGCACCATCTTCTCTTT 59.307 50.000 0.00 0.00 0.00 2.52
1015 1035 1.339151 ACCCGCACCATCTTCTCTTTC 60.339 52.381 0.00 0.00 0.00 2.62
1018 1038 1.404181 CGCACCATCTTCTCTTTCGGA 60.404 52.381 0.00 0.00 0.00 4.55
1368 4373 1.450312 CTTCCCCTTTCAGCGCGAT 60.450 57.895 12.10 0.00 0.00 4.58
1419 4430 1.972660 GCCATGGCCTCCTACTCGTT 61.973 60.000 27.24 0.00 34.56 3.85
1462 4475 3.876589 CTTGTGTGGGACCCCGTCG 62.877 68.421 8.45 0.00 39.42 5.12
1939 5778 1.670406 CACTCAGACTGCTGTGCCC 60.670 63.158 0.00 0.00 42.84 5.36
2097 5957 4.926244 ACAATAATGTGTTGTTGTTGCGA 58.074 34.783 0.00 0.00 44.15 5.10
2147 6007 5.595885 TCTTGAGTCACTGAAGTTCAAGAG 58.404 41.667 16.62 0.00 45.09 2.85
2279 6175 7.752239 GTCGATAATTGGCTGATGAAATTATGG 59.248 37.037 4.97 4.51 36.88 2.74
2322 6218 6.735130 AGCCAACAATTTTAAGTAGTGTCAC 58.265 36.000 0.00 0.00 0.00 3.67
2323 6219 6.320164 AGCCAACAATTTTAAGTAGTGTCACA 59.680 34.615 5.62 0.00 0.00 3.58
2572 6741 5.984233 TGTGGCGATGTTCTTATGTTATC 57.016 39.130 0.00 0.00 0.00 1.75
2998 8630 9.168451 TGTTCACAGTTAATCTTAACACTTCAA 57.832 29.630 13.65 0.17 44.14 2.69
3455 9543 0.755686 CCTGGTCACCTCCTATGCTC 59.244 60.000 0.00 0.00 0.00 4.26
3500 9588 1.667724 CGATGCACTGTTTCCTCATCC 59.332 52.381 0.00 0.00 32.23 3.51
3501 9589 2.679059 CGATGCACTGTTTCCTCATCCT 60.679 50.000 0.00 0.00 32.23 3.24
3502 9590 2.957402 TGCACTGTTTCCTCATCCTT 57.043 45.000 0.00 0.00 0.00 3.36
3503 9591 3.228188 TGCACTGTTTCCTCATCCTTT 57.772 42.857 0.00 0.00 0.00 3.11
3504 9592 3.149196 TGCACTGTTTCCTCATCCTTTC 58.851 45.455 0.00 0.00 0.00 2.62
3505 9593 2.489722 GCACTGTTTCCTCATCCTTTCC 59.510 50.000 0.00 0.00 0.00 3.13
3506 9594 3.812167 GCACTGTTTCCTCATCCTTTCCT 60.812 47.826 0.00 0.00 0.00 3.36
3507 9595 4.006319 CACTGTTTCCTCATCCTTTCCTC 58.994 47.826 0.00 0.00 0.00 3.71
3508 9596 3.652869 ACTGTTTCCTCATCCTTTCCTCA 59.347 43.478 0.00 0.00 0.00 3.86
3509 9597 4.290722 ACTGTTTCCTCATCCTTTCCTCAT 59.709 41.667 0.00 0.00 0.00 2.90
3510 9598 4.848357 TGTTTCCTCATCCTTTCCTCATC 58.152 43.478 0.00 0.00 0.00 2.92
3548 9636 1.657822 GTTCTCTTCCATTCGCCTCC 58.342 55.000 0.00 0.00 0.00 4.30
3549 9637 1.066143 GTTCTCTTCCATTCGCCTCCA 60.066 52.381 0.00 0.00 0.00 3.86
3550 9638 0.537188 TCTCTTCCATTCGCCTCCAC 59.463 55.000 0.00 0.00 0.00 4.02
3551 9639 0.462759 CTCTTCCATTCGCCTCCACC 60.463 60.000 0.00 0.00 0.00 4.61
3552 9640 1.452108 CTTCCATTCGCCTCCACCC 60.452 63.158 0.00 0.00 0.00 4.61
3553 9641 2.196997 CTTCCATTCGCCTCCACCCA 62.197 60.000 0.00 0.00 0.00 4.51
3554 9642 2.438434 CCATTCGCCTCCACCCAC 60.438 66.667 0.00 0.00 0.00 4.61
3555 9643 2.438434 CATTCGCCTCCACCCACC 60.438 66.667 0.00 0.00 0.00 4.61
3556 9644 3.728373 ATTCGCCTCCACCCACCC 61.728 66.667 0.00 0.00 0.00 4.61
3612 9708 1.362932 ACCCCTCTCTACTGGATGTGT 59.637 52.381 0.00 0.00 0.00 3.72
3625 9721 2.224281 TGGATGTGTTCTTTCACTCGCT 60.224 45.455 0.00 0.00 38.90 4.93
3627 9723 3.120511 GGATGTGTTCTTTCACTCGCTTC 60.121 47.826 0.00 0.00 38.90 3.86
3629 9725 2.210116 GTGTTCTTTCACTCGCTTCCA 58.790 47.619 0.00 0.00 35.68 3.53
3835 9977 3.510360 AGTAGCAAATGTACGAGTGAGGT 59.490 43.478 0.00 0.00 0.00 3.85
3842 9984 2.206750 TGTACGAGTGAGGTGTTTTGC 58.793 47.619 0.00 0.00 0.00 3.68
3865 10007 0.545171 CCAGGATCATCTGCACCTGT 59.455 55.000 15.41 0.00 45.65 4.00
3889 10032 8.939929 TGTGCTCAATACAAAAATCAAAACAAA 58.060 25.926 0.00 0.00 0.00 2.83
4061 10204 7.864108 TCATATACTGTTCTGACCCAATTTG 57.136 36.000 0.00 0.00 0.00 2.32
4069 10212 6.337356 TGTTCTGACCCAATTTGTCTTTTTC 58.663 36.000 6.47 0.00 33.83 2.29
4080 10223 2.138320 TGTCTTTTTCGCTGAGAGCTG 58.862 47.619 0.00 0.00 39.60 4.24
4097 10240 1.997606 GCTGCTCAAATGTCCAAATGC 59.002 47.619 0.00 0.00 0.00 3.56
4122 10265 1.577328 AATTTGGAGCGCACCTCACG 61.577 55.000 24.52 0.00 42.62 4.35
4219 10362 3.141398 GGCTCAGAATTGGATATTCGCA 58.859 45.455 0.00 0.00 33.51 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.108847 AGCTCTGCTCAGTTTTACTTAATCAT 58.891 34.615 0.00 0.00 30.62 2.45
47 48 6.761714 TCCGAAGAATAATAAAACCAGAGCTC 59.238 38.462 5.27 5.27 0.00 4.09
52 53 8.673711 TGAACATCCGAAGAATAATAAAACCAG 58.326 33.333 0.00 0.00 0.00 4.00
80 81 3.314331 CACCCAGAGTCGCCACCT 61.314 66.667 0.00 0.00 0.00 4.00
118 119 3.561528 CCCCTCCCAAAGAAAAGAGGTAC 60.562 52.174 4.34 0.00 43.73 3.34
133 134 3.903530 ACCAATTGATAATCCCCTCCC 57.096 47.619 7.12 0.00 0.00 4.30
147 148 9.737844 AAAAATGGCAGTGATATTTTACCAATT 57.262 25.926 14.33 0.00 34.07 2.32
201 202 1.554160 ACACTCAGAGCAGGAAGATGG 59.446 52.381 0.00 0.00 0.00 3.51
209 210 0.249676 ATCAGCCACACTCAGAGCAG 59.750 55.000 0.00 0.00 0.00 4.24
262 263 3.865164 CCAAAGAAGAGCACAAAAACCAC 59.135 43.478 0.00 0.00 0.00 4.16
278 279 0.107410 AGCACGAACACCACCAAAGA 60.107 50.000 0.00 0.00 0.00 2.52
282 283 2.279851 CGAGCACGAACACCACCA 60.280 61.111 0.00 0.00 42.66 4.17
283 284 3.041940 CCGAGCACGAACACCACC 61.042 66.667 4.70 0.00 42.66 4.61
399 400 3.159141 CCACCTATGTCGGGGGTAT 57.841 57.895 0.00 0.00 43.03 2.73
445 446 1.514873 GCAATCAAAAGGCGCCTCG 60.515 57.895 32.93 21.38 0.00 4.63
457 458 3.109547 GCACCGTCGACGCAATCA 61.110 61.111 31.73 0.00 38.18 2.57
518 519 2.486042 GAGACCGAGACGCCACTC 59.514 66.667 0.00 0.00 0.00 3.51
558 559 1.092921 GCGACACCACCTTTGTCACA 61.093 55.000 3.58 0.00 43.09 3.58
602 603 4.494199 CCATCGACGTAATTGAAAGGCTTC 60.494 45.833 0.00 0.00 0.00 3.86
620 621 3.792047 CACGGCACTGCACCATCG 61.792 66.667 2.82 0.00 0.00 3.84
623 624 4.497984 AACCACGGCACTGCACCA 62.498 61.111 2.82 0.00 0.00 4.17
679 680 2.675844 GGGAAACACAACAAAAAGCACC 59.324 45.455 0.00 0.00 0.00 5.01
685 686 3.759618 ACGAAGAGGGAAACACAACAAAA 59.240 39.130 0.00 0.00 0.00 2.44
705 706 2.754946 TACACCTAGCAGGGAAAACG 57.245 50.000 7.06 0.00 40.58 3.60
709 710 2.167693 CGACAATACACCTAGCAGGGAA 59.832 50.000 7.06 0.00 40.58 3.97
889 893 5.163258 ACATCAGTTGCTAGATAAAGGGAGG 60.163 44.000 0.00 0.00 0.00 4.30
964 981 2.894126 ACTGTGGACTCGAATCAGAAGT 59.106 45.455 0.00 0.00 0.00 3.01
965 982 3.506810 GACTGTGGACTCGAATCAGAAG 58.493 50.000 0.00 0.00 0.00 2.85
966 983 2.231478 GGACTGTGGACTCGAATCAGAA 59.769 50.000 0.00 0.00 0.00 3.02
967 984 1.819288 GGACTGTGGACTCGAATCAGA 59.181 52.381 0.00 0.00 0.00 3.27
969 986 1.272490 GTGGACTGTGGACTCGAATCA 59.728 52.381 0.00 0.00 0.00 2.57
970 987 1.272490 TGTGGACTGTGGACTCGAATC 59.728 52.381 0.00 0.00 0.00 2.52
971 988 1.000955 GTGTGGACTGTGGACTCGAAT 59.999 52.381 0.00 0.00 0.00 3.34
1010 1030 7.883311 AGGATATTTTGTTTTCTCTCCGAAAGA 59.117 33.333 0.00 0.00 42.22 2.52
1011 1031 8.045176 AGGATATTTTGTTTTCTCTCCGAAAG 57.955 34.615 0.00 0.00 42.22 2.62
1012 1032 7.120726 GGAGGATATTTTGTTTTCTCTCCGAAA 59.879 37.037 0.00 0.00 39.76 3.46
1014 1034 6.113411 GGAGGATATTTTGTTTTCTCTCCGA 58.887 40.000 0.00 0.00 0.00 4.55
1015 1035 5.297029 GGGAGGATATTTTGTTTTCTCTCCG 59.703 44.000 0.00 0.00 39.15 4.63
1018 1038 4.640647 GCGGGAGGATATTTTGTTTTCTCT 59.359 41.667 0.00 0.00 0.00 3.10
1026 1046 1.949525 CTGGTGCGGGAGGATATTTTG 59.050 52.381 0.00 0.00 0.00 2.44
1032 1052 2.284625 TCACTGGTGCGGGAGGAT 60.285 61.111 0.00 0.00 0.00 3.24
1939 5778 6.240549 AGTTATCCTCTTCCATAACTGTGG 57.759 41.667 3.99 0.00 41.98 4.17
2097 5957 0.899720 TGAAGAGGCCGATAACCGTT 59.100 50.000 0.00 0.00 36.31 4.44
2147 6007 1.154197 GGTCGTAGTGTTGGAAAGCC 58.846 55.000 0.00 0.00 0.00 4.35
2322 6218 8.792831 AAGCAGCGAAAGAAATAAATGATATG 57.207 30.769 0.00 0.00 0.00 1.78
2323 6219 8.623903 TGAAGCAGCGAAAGAAATAAATGATAT 58.376 29.630 0.00 0.00 0.00 1.63
2454 6610 8.871125 ACATAACAAACACTAGCTATAGCCTAT 58.129 33.333 21.17 5.65 43.38 2.57
2455 6611 8.246430 ACATAACAAACACTAGCTATAGCCTA 57.754 34.615 21.17 11.50 43.38 3.93
2456 6612 7.125792 ACATAACAAACACTAGCTATAGCCT 57.874 36.000 21.17 10.97 43.38 4.58
2457 6613 7.787725 AACATAACAAACACTAGCTATAGCC 57.212 36.000 21.17 3.64 43.38 3.93
2743 6948 7.063074 CGCAGCAGTTATACACTAAAAGTAAGT 59.937 37.037 0.00 0.00 32.76 2.24
2998 8630 1.412710 TCCACTCGCAACAGACTCTTT 59.587 47.619 0.00 0.00 0.00 2.52
3455 9543 4.966965 AAAGATTCAAGATGCAGCTCAG 57.033 40.909 4.22 0.73 0.00 3.35
3500 9588 2.238144 TGCTGAGGAAGGATGAGGAAAG 59.762 50.000 0.00 0.00 0.00 2.62
3501 9589 2.238144 CTGCTGAGGAAGGATGAGGAAA 59.762 50.000 0.00 0.00 0.00 3.13
3502 9590 1.836166 CTGCTGAGGAAGGATGAGGAA 59.164 52.381 0.00 0.00 0.00 3.36
3503 9591 1.273495 ACTGCTGAGGAAGGATGAGGA 60.273 52.381 0.00 0.00 0.00 3.71
3504 9592 1.202330 ACTGCTGAGGAAGGATGAGG 58.798 55.000 0.00 0.00 0.00 3.86
3505 9593 3.347077 AAACTGCTGAGGAAGGATGAG 57.653 47.619 0.00 0.00 0.00 2.90
3506 9594 3.560025 GGAAAACTGCTGAGGAAGGATGA 60.560 47.826 0.00 0.00 0.00 2.92
3507 9595 2.751806 GGAAAACTGCTGAGGAAGGATG 59.248 50.000 0.00 0.00 0.00 3.51
3508 9596 2.616510 CGGAAAACTGCTGAGGAAGGAT 60.617 50.000 0.00 0.00 0.00 3.24
3509 9597 1.270839 CGGAAAACTGCTGAGGAAGGA 60.271 52.381 0.00 0.00 0.00 3.36
3510 9598 1.160137 CGGAAAACTGCTGAGGAAGG 58.840 55.000 0.00 0.00 0.00 3.46
3548 9636 4.284550 CAGGTGGGTGGGTGGGTG 62.285 72.222 0.00 0.00 0.00 4.61
3552 9640 3.868200 GAAGGCAGGTGGGTGGGTG 62.868 68.421 0.00 0.00 0.00 4.61
3553 9641 3.580319 GAAGGCAGGTGGGTGGGT 61.580 66.667 0.00 0.00 0.00 4.51
3554 9642 3.574074 CTGAAGGCAGGTGGGTGGG 62.574 68.421 0.00 0.00 38.51 4.61
3555 9643 2.034687 CTGAAGGCAGGTGGGTGG 59.965 66.667 0.00 0.00 38.51 4.61
3556 9644 0.468029 AAACTGAAGGCAGGTGGGTG 60.468 55.000 0.00 0.00 42.49 4.61
3557 9645 0.261696 AAAACTGAAGGCAGGTGGGT 59.738 50.000 0.00 0.00 42.49 4.51
3558 9646 2.286365 TAAAACTGAAGGCAGGTGGG 57.714 50.000 0.00 0.00 42.49 4.61
3559 9647 4.871933 AAATAAAACTGAAGGCAGGTGG 57.128 40.909 0.00 0.00 42.49 4.61
3612 9708 2.210116 GTGTGGAAGCGAGTGAAAGAA 58.790 47.619 0.00 0.00 0.00 2.52
3625 9721 2.933287 AGCCGGATGGGTGTGGAA 60.933 61.111 5.05 0.00 46.48 3.53
3835 9977 0.776810 TGATCCTGGGAGGCAAAACA 59.223 50.000 0.00 0.00 34.61 2.83
3842 9984 0.108207 GTGCAGATGATCCTGGGAGG 59.892 60.000 0.00 0.00 36.46 4.30
3978 10121 0.318614 GCCGAGAGCTACTCAGATGC 60.319 60.000 11.93 6.28 45.14 3.91
4080 10223 3.192001 TCAGAGCATTTGGACATTTGAGC 59.808 43.478 0.00 0.00 0.00 4.26
4097 10240 1.135575 GGTGCGCTCCAAATTTCAGAG 60.136 52.381 23.09 9.49 0.00 3.35
4122 10265 4.157656 TGTGCAAGGTAGATAATTTGGTGC 59.842 41.667 0.00 0.00 0.00 5.01
4163 10306 4.441356 GCACCCACTCAAGAAACAATTCAA 60.441 41.667 0.00 0.00 38.06 2.69


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

AutoCloner maintained by Alex Coulton.