Multiple sequence alignment - TraesCS6A01G407900

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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 TraesCS6A01G407900 chr6A 100.000 4008 0 0 1 4008 613078302 613082309 0.000000e+00 7402.0
1 TraesCS6A01G407900 chr6A 91.084 886 73 4 2220 3099 612568152 612567267 0.000000e+00 1194.0
2 TraesCS6A01G407900 chr6A 82.226 1339 189 32 1204 2508 573636267 573637590 0.000000e+00 1109.0
3 TraesCS6A01G407900 chr6A 93.516 694 33 7 2701 3384 613038420 613039111 0.000000e+00 1022.0
4 TraesCS6A01G407900 chr6A 88.778 499 33 13 468 948 612110072 612109579 1.240000e-164 590.0
5 TraesCS6A01G407900 chr6A 89.751 361 21 2 536 881 125259255 125259614 7.900000e-122 448.0
6 TraesCS6A01G407900 chr6A 87.955 357 24 4 570 909 611901233 611901587 1.730000e-108 403.0
7 TraesCS6A01G407900 chr6A 85.600 375 29 13 473 846 612299299 612299649 1.760000e-98 370.0
8 TraesCS6A01G407900 chr6A 91.593 226 9 2 3789 4008 613039618 613039839 1.810000e-78 303.0
9 TraesCS6A01G407900 chr6A 97.452 157 4 0 3476 3632 613039312 613039468 6.600000e-68 268.0
10 TraesCS6A01G407900 chr6A 88.718 195 18 2 464 657 612578605 612578414 6.700000e-58 235.0
11 TraesCS6A01G407900 chr6A 76.235 425 85 13 2590 3006 554833215 554832799 1.130000e-50 211.0
12 TraesCS6A01G407900 chr6A 87.097 186 20 2 473 657 612290562 612290744 1.460000e-49 207.0
13 TraesCS6A01G407900 chr6A 94.167 120 5 2 3635 3752 613039500 613039619 8.850000e-42 182.0
14 TraesCS6A01G407900 chr6A 97.059 34 0 1 3008 3041 54179440 54179472 5.600000e-04 56.5
15 TraesCS6A01G407900 chr6A 96.970 33 1 0 3428 3460 613039281 613039313 5.600000e-04 56.5
16 TraesCS6A01G407900 chr6A 96.970 33 0 1 3008 3040 25690534 25690565 2.000000e-03 54.7
17 TraesCS6A01G407900 chr1B 94.767 2656 73 30 802 3419 92327153 92324526 0.000000e+00 4074.0
18 TraesCS6A01G407900 chr1B 92.803 264 15 4 3747 4008 92322096 92321835 2.920000e-101 379.0
19 TraesCS6A01G407900 chr1B 85.321 327 27 7 115 422 92327788 92327464 6.460000e-83 318.0
20 TraesCS6A01G407900 chr1B 95.833 120 5 0 3428 3547 92324474 92324355 1.140000e-45 195.0
21 TraesCS6A01G407900 chr1B 93.701 127 3 2 3635 3760 92324250 92324128 6.840000e-43 185.0
22 TraesCS6A01G407900 chr1B 91.919 99 8 0 313 411 92353372 92353274 5.400000e-29 139.0
23 TraesCS6A01G407900 chr1B 97.561 41 1 0 3580 3620 92324343 92324303 2.000000e-08 71.3
24 TraesCS6A01G407900 chr6B 95.598 2476 79 20 969 3419 711723787 711726257 0.000000e+00 3941.0
25 TraesCS6A01G407900 chr6B 92.839 1201 81 5 1362 2559 711655471 711654273 0.000000e+00 1736.0
26 TraesCS6A01G407900 chr6B 82.385 1811 276 30 1214 3008 710318981 710317198 0.000000e+00 1537.0
27 TraesCS6A01G407900 chr6B 81.233 1460 211 41 1094 2508 645653324 645654765 0.000000e+00 1120.0
28 TraesCS6A01G407900 chr6B 81.662 1336 199 28 1213 2514 646010227 646008904 0.000000e+00 1068.0
29 TraesCS6A01G407900 chr6B 81.391 1193 185 22 1348 2508 710222850 710224037 0.000000e+00 939.0
30 TraesCS6A01G407900 chr6B 91.773 547 43 1 2555 3099 711636617 711636071 0.000000e+00 760.0
31 TraesCS6A01G407900 chr6B 90.596 436 32 8 460 891 710643463 710643033 1.620000e-158 569.0
32 TraesCS6A01G407900 chr6B 87.173 421 36 11 1 408 711876471 711876886 2.820000e-126 462.0
33 TraesCS6A01G407900 chr6B 84.760 479 36 20 458 925 711709290 711709742 2.840000e-121 446.0
34 TraesCS6A01G407900 chr6B 87.563 394 24 11 3464 3849 711726380 711726756 2.210000e-117 433.0
35 TraesCS6A01G407900 chr6B 81.590 478 44 15 468 939 710152198 710151759 4.930000e-94 355.0
36 TraesCS6A01G407900 chr6B 83.841 328 34 12 1 320 711714715 711715031 1.090000e-75 294.0
37 TraesCS6A01G407900 chr6B 90.351 228 17 4 701 926 711876955 711877179 1.090000e-75 294.0
38 TraesCS6A01G407900 chr6B 78.571 532 51 29 460 946 711238019 711237506 3.920000e-75 292.0
39 TraesCS6A01G407900 chr6B 77.368 380 73 11 2633 3006 615085612 615085240 3.140000e-51 213.0
40 TraesCS6A01G407900 chr6B 76.602 359 73 8 2626 2980 711738124 711737773 1.900000e-43 187.0
41 TraesCS6A01G407900 chr6B 98.551 69 1 0 3428 3496 711726309 711726377 5.440000e-24 122.0
42 TraesCS6A01G407900 chr6B 85.859 99 11 2 926 1023 710319321 710319225 7.090000e-18 102.0
43 TraesCS6A01G407900 chr6D 81.361 2028 300 48 1027 3008 465348093 465346098 0.000000e+00 1580.0
44 TraesCS6A01G407900 chr6D 81.664 1358 196 36 1186 2508 428960208 428961547 0.000000e+00 1079.0
45 TraesCS6A01G407900 chr6D 89.104 413 29 2 497 894 465745607 465745196 2.150000e-137 499.0
46 TraesCS6A01G407900 chr6D 87.042 355 40 4 1 355 466621147 466621495 2.900000e-106 396.0
47 TraesCS6A01G407900 chr6D 82.405 449 61 9 468 916 462838862 462839292 3.780000e-100 375.0
48 TraesCS6A01G407900 chr6D 84.673 398 33 13 494 890 465348596 465348226 4.890000e-99 372.0
49 TraesCS6A01G407900 chr6D 90.351 228 16 5 701 926 466621602 466621825 1.090000e-75 294.0
50 TraesCS6A01G407900 chr6D 85.878 262 11 6 460 721 465967576 465967341 5.140000e-64 255.0
51 TraesCS6A01G407900 chr6D 77.114 402 77 13 2590 2980 466525200 466525597 6.740000e-53 219.0
52 TraesCS6A01G407900 chr6D 86.735 98 12 1 926 1023 465348222 465348126 1.520000e-19 108.0
53 TraesCS6A01G407900 chr3B 81.241 1386 196 40 1204 2562 197791970 197790622 0.000000e+00 1061.0
54 TraesCS6A01G407900 chr3B 82.828 198 19 10 3805 4001 153527986 153527803 3.210000e-36 163.0
55 TraesCS6A01G407900 chr3D 79.474 1140 168 42 1808 2919 464051502 464052603 0.000000e+00 749.0
56 TraesCS6A01G407900 chr3D 75.610 205 39 8 45 243 123319342 123319541 1.530000e-14 91.6
57 TraesCS6A01G407900 chr5D 83.920 199 24 6 3805 4001 331068893 331069085 2.460000e-42 183.0
58 TraesCS6A01G407900 chr5D 74.561 228 44 10 23 243 264927831 264928051 1.980000e-13 87.9
59 TraesCS6A01G407900 chr5D 77.564 156 22 9 67 215 402990702 402990851 9.230000e-12 82.4
60 TraesCS6A01G407900 chr1D 83.168 202 25 7 3802 4001 58620014 58619820 4.120000e-40 176.0
61 TraesCS6A01G407900 chr1D 88.679 53 3 3 3143 3192 101291190 101291242 1.200000e-05 62.1
62 TraesCS6A01G407900 chr7D 78.698 169 26 8 17 179 92720238 92720074 1.970000e-18 104.0
63 TraesCS6A01G407900 chr5A 74.900 251 50 9 1 243 333439432 333439677 7.090000e-18 102.0
64 TraesCS6A01G407900 chr1A 89.041 73 7 1 3803 3875 577565360 577565289 5.520000e-14 89.8
65 TraesCS6A01G407900 chr1A 92.000 50 1 3 3146 3192 104210628 104210579 2.590000e-07 67.6
66 TraesCS6A01G407900 chr1A 91.667 48 1 3 3148 3192 104210589 104210542 3.340000e-06 63.9
67 TraesCS6A01G407900 chr5B 92.188 64 2 3 3801 3863 338950824 338950885 1.980000e-13 87.9
68 TraesCS6A01G407900 chr5B 75.132 189 38 7 3807 3993 681735528 681735347 3.320000e-11 80.5
69 TraesCS6A01G407900 chr4B 73.705 251 54 9 1 244 466730896 466731141 1.980000e-13 87.9
70 TraesCS6A01G407900 chr2A 93.333 45 3 0 3143 3187 587741634 587741678 2.590000e-07 67.6
71 TraesCS6A01G407900 chrUn 89.796 49 5 0 3144 3192 42338373 42338325 3.340000e-06 63.9
72 TraesCS6A01G407900 chrUn 100.000 31 0 0 2648 2678 33026942 33026912 1.560000e-04 58.4
73 TraesCS6A01G407900 chrUn 97.059 34 1 0 3144 3177 474064229 474064262 1.560000e-04 58.4
74 TraesCS6A01G407900 chr7A 89.583 48 2 2 3132 3176 547766603 547766556 1.560000e-04 58.4
75 TraesCS6A01G407900 chr4D 100.000 31 0 0 3011 3041 58265951 58265921 1.560000e-04 58.4
76 TraesCS6A01G407900 chr4D 100.000 30 0 0 3015 3044 503868606 503868577 5.600000e-04 56.5


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 TraesCS6A01G407900 chr6A 613078302 613082309 4007 False 7402.000000 7402 100.000000 1 4008 1 chr6A.!!$F8 4007
1 TraesCS6A01G407900 chr6A 612567267 612568152 885 True 1194.000000 1194 91.084000 2220 3099 1 chr6A.!!$R3 879
2 TraesCS6A01G407900 chr6A 573636267 573637590 1323 False 1109.000000 1109 82.226000 1204 2508 1 chr6A.!!$F4 1304
3 TraesCS6A01G407900 chr6A 613038420 613039839 1419 False 366.300000 1022 94.739600 2701 4008 5 chr6A.!!$F9 1307
4 TraesCS6A01G407900 chr1B 92321835 92327788 5953 True 870.383333 4074 93.331000 115 4008 6 chr1B.!!$R2 3893
5 TraesCS6A01G407900 chr6B 711654273 711655471 1198 True 1736.000000 1736 92.839000 1362 2559 1 chr6B.!!$R7 1197
6 TraesCS6A01G407900 chr6B 711723787 711726756 2969 False 1498.666667 3941 93.904000 969 3849 3 chr6B.!!$F5 2880
7 TraesCS6A01G407900 chr6B 645653324 645654765 1441 False 1120.000000 1120 81.233000 1094 2508 1 chr6B.!!$F1 1414
8 TraesCS6A01G407900 chr6B 646008904 646010227 1323 True 1068.000000 1068 81.662000 1213 2514 1 chr6B.!!$R2 1301
9 TraesCS6A01G407900 chr6B 710222850 710224037 1187 False 939.000000 939 81.391000 1348 2508 1 chr6B.!!$F2 1160
10 TraesCS6A01G407900 chr6B 710317198 710319321 2123 True 819.500000 1537 84.122000 926 3008 2 chr6B.!!$R9 2082
11 TraesCS6A01G407900 chr6B 711636071 711636617 546 True 760.000000 760 91.773000 2555 3099 1 chr6B.!!$R6 544
12 TraesCS6A01G407900 chr6B 711876471 711877179 708 False 378.000000 462 88.762000 1 926 2 chr6B.!!$F6 925
13 TraesCS6A01G407900 chr6B 711237506 711238019 513 True 292.000000 292 78.571000 460 946 1 chr6B.!!$R5 486
14 TraesCS6A01G407900 chr6D 428960208 428961547 1339 False 1079.000000 1079 81.664000 1186 2508 1 chr6D.!!$F1 1322
15 TraesCS6A01G407900 chr6D 465346098 465348596 2498 True 686.666667 1580 84.256333 494 3008 3 chr6D.!!$R3 2514
16 TraesCS6A01G407900 chr6D 466621147 466621825 678 False 345.000000 396 88.696500 1 926 2 chr6D.!!$F4 925
17 TraesCS6A01G407900 chr3B 197790622 197791970 1348 True 1061.000000 1061 81.241000 1204 2562 1 chr3B.!!$R2 1358
18 TraesCS6A01G407900 chr3D 464051502 464052603 1101 False 749.000000 749 79.474000 1808 2919 1 chr3D.!!$F2 1111

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
92 94 0.112995 ATTCAAGCTCAAGGGTGCCA 59.887 50.0 0.0 0.0 34.1 4.92 F
770 861 0.179111 CGCAATCGAAGTAGCTCCCA 60.179 55.0 0.0 0.0 38.1 4.37 F
2020 2323 0.180406 ACCTGCAACTCCGTGAACTT 59.820 50.0 0.0 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2323 4.081697 TCAAGACTGCTATCCGAAATCACA 60.082 41.667 0.00 0.00 0.0 3.58 R
2975 3339 1.467374 GCGAATCCCAACATTTGACGG 60.467 52.381 0.00 0.00 0.0 4.79 R
3744 4341 0.460987 CGGAAGAGAGACCATGGTGC 60.461 60.000 25.52 14.34 0.0 5.01 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
74 76 1.539827 GGCAAGTAACAAGCGTTGGAT 59.460 47.619 3.42 0.00 36.52 3.41
86 88 1.135575 GCGTTGGATTCAAGCTCAAGG 60.136 52.381 0.00 0.00 32.92 3.61
90 92 0.813821 GGATTCAAGCTCAAGGGTGC 59.186 55.000 0.00 0.00 0.00 5.01
92 94 0.112995 ATTCAAGCTCAAGGGTGCCA 59.887 50.000 0.00 0.00 34.10 4.92
137 141 1.002468 CTTGACGGTCCTTTGTGCAAG 60.002 52.381 5.55 0.00 0.00 4.01
180 184 6.833342 TTTTACTAGTTTTGTCAGGTCGAC 57.167 37.500 7.13 7.13 45.61 4.20
199 203 5.702622 CGACATCTTCGTGTGATTTGTAT 57.297 39.130 0.00 0.00 43.24 2.29
301 310 7.422399 CAGAGAGTAGAGAAATACTACAAGCC 58.578 42.308 0.00 0.00 41.56 4.35
305 314 8.254508 AGAGTAGAGAAATACTACAAGCCTTTG 58.745 37.037 0.00 0.00 41.56 2.77
345 373 1.034838 CCTGGACCTCGAGGACTGAG 61.035 65.000 37.69 26.40 43.58 3.35
354 382 1.081892 CGAGGACTGAGCAACAATGG 58.918 55.000 0.00 0.00 0.00 3.16
379 407 3.672808 CAATTGCACATTGGGCCTTTAA 58.327 40.909 8.73 0.00 0.00 1.52
414 442 1.639635 ATTCCTCCATCGCAGGCCTT 61.640 55.000 0.00 0.00 0.00 4.35
422 450 2.079158 CATCGCAGGCCTTGGTATATG 58.921 52.381 0.00 0.00 0.00 1.78
424 452 1.977854 TCGCAGGCCTTGGTATATGAT 59.022 47.619 0.00 0.00 0.00 2.45
425 453 2.079158 CGCAGGCCTTGGTATATGATG 58.921 52.381 0.00 0.00 0.00 3.07
426 454 2.440409 GCAGGCCTTGGTATATGATGG 58.560 52.381 0.00 0.00 0.00 3.51
428 456 3.415212 CAGGCCTTGGTATATGATGGTG 58.585 50.000 0.00 0.00 0.00 4.17
429 457 3.072915 CAGGCCTTGGTATATGATGGTGA 59.927 47.826 0.00 0.00 0.00 4.02
430 458 3.918912 AGGCCTTGGTATATGATGGTGAT 59.081 43.478 0.00 0.00 0.00 3.06
431 459 4.012374 GGCCTTGGTATATGATGGTGATG 58.988 47.826 0.00 0.00 0.00 3.07
432 460 4.507335 GGCCTTGGTATATGATGGTGATGT 60.507 45.833 0.00 0.00 0.00 3.06
433 461 5.072741 GCCTTGGTATATGATGGTGATGTT 58.927 41.667 0.00 0.00 0.00 2.71
434 462 5.536161 GCCTTGGTATATGATGGTGATGTTT 59.464 40.000 0.00 0.00 0.00 2.83
435 463 6.294176 GCCTTGGTATATGATGGTGATGTTTC 60.294 42.308 0.00 0.00 0.00 2.78
436 464 7.000472 CCTTGGTATATGATGGTGATGTTTCT 59.000 38.462 0.00 0.00 0.00 2.52
437 465 7.173907 CCTTGGTATATGATGGTGATGTTTCTC 59.826 40.741 0.00 0.00 0.00 2.87
438 466 7.135591 TGGTATATGATGGTGATGTTTCTCA 57.864 36.000 0.00 0.00 0.00 3.27
439 467 7.572814 TGGTATATGATGGTGATGTTTCTCAA 58.427 34.615 0.00 0.00 0.00 3.02
440 468 8.052141 TGGTATATGATGGTGATGTTTCTCAAA 58.948 33.333 0.00 0.00 0.00 2.69
441 469 8.902806 GGTATATGATGGTGATGTTTCTCAAAA 58.097 33.333 0.00 0.00 0.00 2.44
466 494 0.396556 AAAAACAGTTCGCCCACCCT 60.397 50.000 0.00 0.00 0.00 4.34
485 519 1.834263 CTTAGGGTTCCACCAGAGAGG 59.166 57.143 0.00 0.00 41.02 3.69
499 534 0.691413 GAGAGGAAAGGGGATCGGGT 60.691 60.000 0.00 0.00 0.00 5.28
560 604 2.509336 CCTCTCGCCGTCGCAATT 60.509 61.111 0.00 0.00 35.26 2.32
603 647 0.679002 ATCCACTGCTGCTTGCGAAT 60.679 50.000 0.00 0.00 46.63 3.34
662 721 2.838202 ACTCCCCAATCGAAGCTCTTTA 59.162 45.455 0.00 0.00 0.00 1.85
762 853 2.094659 CGCAGTCCGCAATCGAAGT 61.095 57.895 0.00 0.00 42.60 3.01
763 854 0.800683 CGCAGTCCGCAATCGAAGTA 60.801 55.000 0.00 0.00 42.60 2.24
770 861 0.179111 CGCAATCGAAGTAGCTCCCA 60.179 55.000 0.00 0.00 38.10 4.37
782 873 2.907458 AGCTCCCATTTTTAGTGGCT 57.093 45.000 0.00 0.00 35.35 4.75
783 874 4.473559 AGTAGCTCCCATTTTTAGTGGCTA 59.526 41.667 0.00 0.00 35.35 3.93
784 875 4.316025 AGCTCCCATTTTTAGTGGCTAA 57.684 40.909 0.00 0.00 35.35 3.09
785 876 4.871822 AGCTCCCATTTTTAGTGGCTAAT 58.128 39.130 0.00 0.00 35.35 1.73
786 877 4.889995 AGCTCCCATTTTTAGTGGCTAATC 59.110 41.667 0.00 0.00 35.35 1.75
787 878 4.038042 GCTCCCATTTTTAGTGGCTAATCC 59.962 45.833 0.00 0.00 35.35 3.01
798 889 3.199946 AGTGGCTAATCCGGAATCAAAGA 59.800 43.478 9.01 0.00 37.80 2.52
935 1081 1.847328 ACCCGCCAATTTTAAGAGGG 58.153 50.000 0.00 0.00 42.82 4.30
1101 1283 9.975218 AAAAAGTACTGTAGGAACCATAATCAT 57.025 29.630 0.00 0.00 0.00 2.45
1242 1480 4.787551 TGTGTGTTTCTGTGGGAAAGTAT 58.212 39.130 0.00 0.00 43.59 2.12
1243 1481 4.578516 TGTGTGTTTCTGTGGGAAAGTATG 59.421 41.667 0.00 0.00 43.59 2.39
1244 1482 4.819630 GTGTGTTTCTGTGGGAAAGTATGA 59.180 41.667 0.00 0.00 43.59 2.15
1245 1483 5.298276 GTGTGTTTCTGTGGGAAAGTATGAA 59.702 40.000 0.00 0.00 43.59 2.57
1246 1484 5.888724 TGTGTTTCTGTGGGAAAGTATGAAA 59.111 36.000 0.00 0.00 43.59 2.69
1247 1485 6.549364 TGTGTTTCTGTGGGAAAGTATGAAAT 59.451 34.615 0.00 0.00 43.59 2.17
1248 1486 7.069331 TGTGTTTCTGTGGGAAAGTATGAAATT 59.931 33.333 0.00 0.00 43.59 1.82
1249 1487 7.926018 GTGTTTCTGTGGGAAAGTATGAAATTT 59.074 33.333 0.00 0.00 43.59 1.82
1250 1488 8.141268 TGTTTCTGTGGGAAAGTATGAAATTTC 58.859 33.333 11.41 11.41 43.59 2.17
1251 1489 8.360390 GTTTCTGTGGGAAAGTATGAAATTTCT 58.640 33.333 18.64 7.42 43.59 2.52
1252 1490 9.581289 TTTCTGTGGGAAAGTATGAAATTTCTA 57.419 29.630 18.64 6.30 38.81 2.10
1253 1491 8.561738 TCTGTGGGAAAGTATGAAATTTCTAC 57.438 34.615 18.64 16.32 36.03 2.59
1254 1492 8.160765 TCTGTGGGAAAGTATGAAATTTCTACA 58.839 33.333 18.64 0.07 36.03 2.74
1344 1637 4.526650 TGCACCTGTCTCAGTAAGTAATCA 59.473 41.667 0.00 0.00 0.00 2.57
1555 1855 4.760047 GAGCCCAAGCGCGGAAGA 62.760 66.667 8.83 0.00 46.67 2.87
1559 1859 4.082523 CCAAGCGCGGAAGAGGGA 62.083 66.667 8.83 0.00 0.00 4.20
1560 1860 2.815647 CAAGCGCGGAAGAGGGAC 60.816 66.667 8.83 0.00 0.00 4.46
2020 2323 0.180406 ACCTGCAACTCCGTGAACTT 59.820 50.000 0.00 0.00 0.00 2.66
2121 2427 5.776173 TTATCTCGAGATGACCCTTTCTC 57.224 43.478 33.22 0.00 36.05 2.87
2975 3339 3.445096 AGACAAAATCAGCAAGGGTATGC 59.555 43.478 0.00 0.00 46.78 3.14
3160 3524 4.273235 TGCTGTCAGCGACAATTAATATGG 59.727 41.667 19.68 0.64 46.26 2.74
3265 3631 4.235079 TGTTGGGTTAGCTGCTTCATAT 57.765 40.909 7.79 0.00 0.00 1.78
3266 3632 5.366482 TGTTGGGTTAGCTGCTTCATATA 57.634 39.130 7.79 0.00 0.00 0.86
3269 3635 6.486657 TGTTGGGTTAGCTGCTTCATATAATC 59.513 38.462 7.79 0.00 0.00 1.75
3270 3636 6.439636 TGGGTTAGCTGCTTCATATAATCT 57.560 37.500 7.79 0.00 0.00 2.40
3271 3637 6.841601 TGGGTTAGCTGCTTCATATAATCTT 58.158 36.000 7.79 0.00 0.00 2.40
3342 3716 3.010420 GAGAGCTTGTATTGGTTGACCC 58.990 50.000 0.00 0.00 34.29 4.46
3508 4065 2.483876 CGTTGTGGACTCAACAGTGAT 58.516 47.619 15.00 0.00 45.28 3.06
3663 4260 1.807755 CGGTCGATGATCATGGTTGCT 60.808 52.381 14.30 0.00 0.00 3.91
3728 4325 6.128282 GGTTCTATCTCTTCAAAATGTGCGAA 60.128 38.462 0.00 0.00 0.00 4.70
3736 4333 1.169661 AAAATGTGCGAACGCCCAGA 61.170 50.000 16.27 0.00 41.09 3.86
3740 4337 1.169661 TGTGCGAACGCCCAGAAAAT 61.170 50.000 16.27 0.00 41.09 1.82
3741 4338 0.729140 GTGCGAACGCCCAGAAAATG 60.729 55.000 16.27 0.00 41.09 2.32
3742 4339 0.886938 TGCGAACGCCCAGAAAATGA 60.887 50.000 16.27 0.00 41.09 2.57
3744 4341 1.729149 GCGAACGCCCAGAAAATGAAG 60.729 52.381 8.03 0.00 34.56 3.02
3745 4342 1.729149 CGAACGCCCAGAAAATGAAGC 60.729 52.381 0.00 0.00 0.00 3.86
3786 6429 1.076332 GTCAGGGACGTCGGAAAATG 58.924 55.000 9.92 2.03 0.00 2.32
3801 6444 3.243839 GGAAAATGGTGTCAGCATGTGTT 60.244 43.478 17.87 12.20 36.31 3.32
3803 6446 4.405116 AAATGGTGTCAGCATGTGTTTT 57.595 36.364 17.87 6.52 36.31 2.43
3899 6549 0.397535 CCCCAGGCAGCCAAATATGT 60.398 55.000 15.80 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 29 2.186160 CACCGCAGCAAACACCAGA 61.186 57.895 0.00 0.00 0.00 3.86
64 66 1.896220 TGAGCTTGAATCCAACGCTT 58.104 45.000 0.00 0.00 37.10 4.68
74 76 0.112995 ATGGCACCCTTGAGCTTGAA 59.887 50.000 0.00 0.00 0.00 2.69
86 88 0.734889 CAATCAAGACCGATGGCACC 59.265 55.000 0.00 0.00 0.00 5.01
90 92 7.088589 AGAAAATTACAATCAAGACCGATGG 57.911 36.000 0.00 0.00 0.00 3.51
92 94 9.014297 AGAAAGAAAATTACAATCAAGACCGAT 57.986 29.630 0.00 0.00 0.00 4.18
137 141 5.966742 AAAAGACATCTGAAAACTAGCCC 57.033 39.130 0.00 0.00 0.00 5.19
180 184 8.900511 ATCAAAATACAAATCACACGAAGATG 57.099 30.769 0.00 0.00 0.00 2.90
181 185 8.729756 TGATCAAAATACAAATCACACGAAGAT 58.270 29.630 0.00 0.00 0.00 2.40
264 273 2.875094 ACTCTCTGCTGCTTCCAATT 57.125 45.000 0.00 0.00 0.00 2.32
265 274 3.102972 TCTACTCTCTGCTGCTTCCAAT 58.897 45.455 0.00 0.00 0.00 3.16
273 282 7.561021 TGTAGTATTTCTCTACTCTCTGCTG 57.439 40.000 0.00 0.00 38.67 4.41
326 354 1.000771 TCAGTCCTCGAGGTCCAGG 60.001 63.158 30.17 16.83 36.34 4.45
414 442 7.135591 TGAGAAACATCACCATCATATACCA 57.864 36.000 0.00 0.00 0.00 3.25
447 475 0.396556 AGGGTGGGCGAACTGTTTTT 60.397 50.000 0.00 0.00 0.00 1.94
448 476 0.396556 AAGGGTGGGCGAACTGTTTT 60.397 50.000 0.00 0.00 0.00 2.43
449 477 0.475044 TAAGGGTGGGCGAACTGTTT 59.525 50.000 0.00 0.00 0.00 2.83
450 478 0.036306 CTAAGGGTGGGCGAACTGTT 59.964 55.000 0.00 0.00 0.00 3.16
451 479 1.677552 CTAAGGGTGGGCGAACTGT 59.322 57.895 0.00 0.00 0.00 3.55
485 519 0.107654 CTGACACCCGATCCCCTTTC 60.108 60.000 0.00 0.00 0.00 2.62
499 534 2.817834 GGCGGCGCATAACTGACA 60.818 61.111 34.36 0.00 0.00 3.58
603 647 1.209504 AGCTGCTTATTTGGTCGCCTA 59.790 47.619 0.00 0.00 0.00 3.93
642 686 2.409948 AAAGAGCTTCGATTGGGGAG 57.590 50.000 0.00 0.00 0.00 4.30
716 807 0.895100 TGGAGCCGCTTGATTGCTTT 60.895 50.000 0.00 0.00 34.99 3.51
762 853 5.444744 TTAGCCACTAAAAATGGGAGCTA 57.555 39.130 0.00 0.00 37.73 3.32
763 854 2.907458 AGCCACTAAAAATGGGAGCT 57.093 45.000 0.00 0.00 37.73 4.09
770 861 6.126409 TGATTCCGGATTAGCCACTAAAAAT 58.874 36.000 4.15 0.00 35.94 1.82
782 873 5.693769 AGGACTTCTTTGATTCCGGATTA 57.306 39.130 4.15 0.00 32.97 1.75
783 874 4.576330 AGGACTTCTTTGATTCCGGATT 57.424 40.909 4.15 0.01 32.97 3.01
784 875 4.576330 AAGGACTTCTTTGATTCCGGAT 57.424 40.909 4.15 0.00 32.97 4.18
785 876 4.324267 GAAAGGACTTCTTTGATTCCGGA 58.676 43.478 0.00 0.00 45.00 5.14
786 877 3.440522 GGAAAGGACTTCTTTGATTCCGG 59.559 47.826 0.00 0.00 45.00 5.14
787 878 3.125316 CGGAAAGGACTTCTTTGATTCCG 59.875 47.826 9.30 9.30 45.00 4.30
884 1020 2.029290 CCGCCCGGCCAGATATATATAC 60.029 54.545 2.24 0.00 0.00 1.47
900 1039 4.747529 GTACCGTGGTGTCCGCCC 62.748 72.222 0.72 0.00 0.00 6.13
1200 1402 8.774586 ACACACAATTTTGATAGTACAGTTCTC 58.225 33.333 0.00 0.00 0.00 2.87
1248 1486 9.734620 CAGAAAGACACAAATTTGATTGTAGAA 57.265 29.630 24.64 0.00 41.44 2.10
1249 1487 8.902806 ACAGAAAGACACAAATTTGATTGTAGA 58.097 29.630 24.64 0.00 41.44 2.59
1250 1488 8.961092 CACAGAAAGACACAAATTTGATTGTAG 58.039 33.333 24.64 9.00 41.44 2.74
1251 1489 8.681806 TCACAGAAAGACACAAATTTGATTGTA 58.318 29.630 24.64 0.00 41.44 2.41
1252 1490 7.546358 TCACAGAAAGACACAAATTTGATTGT 58.454 30.769 24.64 18.18 44.08 2.71
1253 1491 7.916977 TCTCACAGAAAGACACAAATTTGATTG 59.083 33.333 24.64 15.14 36.37 2.67
1254 1492 7.999679 TCTCACAGAAAGACACAAATTTGATT 58.000 30.769 24.64 10.32 0.00 2.57
1555 1855 5.640147 TCATGTGAGGTTAATTTTGTCCCT 58.360 37.500 0.00 0.00 0.00 4.20
1558 1858 9.884465 GCTATATCATGTGAGGTTAATTTTGTC 57.116 33.333 0.00 0.00 0.00 3.18
1559 1859 9.632638 AGCTATATCATGTGAGGTTAATTTTGT 57.367 29.630 0.00 0.00 0.00 2.83
2020 2323 4.081697 TCAAGACTGCTATCCGAAATCACA 60.082 41.667 0.00 0.00 0.00 3.58
2975 3339 1.467374 GCGAATCCCAACATTTGACGG 60.467 52.381 0.00 0.00 0.00 4.79
3106 3470 3.244345 TCTTAGACAAAACAACGCACTCG 59.756 43.478 0.00 0.00 42.43 4.18
3135 3499 4.764679 ATTAATTGTCGCTGACAGCAAA 57.235 36.364 26.32 17.01 43.69 3.68
3160 3524 3.952967 ACAACTTAGTACTCCCTCCGATC 59.047 47.826 0.00 0.00 0.00 3.69
3228 3592 2.762327 CCAACAAGGAATGGAGAATGGG 59.238 50.000 0.00 0.00 41.22 4.00
3229 3593 2.762327 CCCAACAAGGAATGGAGAATGG 59.238 50.000 0.00 0.00 41.22 3.16
3236 3602 2.493278 CAGCTAACCCAACAAGGAATGG 59.507 50.000 0.00 0.00 41.22 3.16
3284 3652 6.094048 CGTGGATCCTGTTTCAGTTTTGATAT 59.906 38.462 14.23 0.00 32.27 1.63
3342 3716 9.746711 GCAACTCATTATTAAGCTTATATGTCG 57.253 33.333 7.08 9.45 0.00 4.35
3425 3904 9.817809 GGTAGAGAAATGTAGATTTGTGATACA 57.182 33.333 2.01 0.00 31.58 2.29
3489 4046 2.549754 CCATCACTGTTGAGTCCACAAC 59.450 50.000 0.00 0.00 46.83 3.32
3508 4065 0.762418 TCGAAAGGGAGAAAGCACCA 59.238 50.000 0.00 0.00 0.00 4.17
3716 4313 1.003262 CTGGGCGTTCGCACATTTTG 61.003 55.000 21.86 7.26 44.08 2.44
3728 4325 0.598065 GTGCTTCATTTTCTGGGCGT 59.402 50.000 0.00 0.00 0.00 5.68
3736 4333 3.760684 GAGAGACCATGGTGCTTCATTTT 59.239 43.478 25.52 1.12 0.00 1.82
3740 4337 1.649321 AGAGAGACCATGGTGCTTCA 58.351 50.000 25.52 0.00 0.00 3.02
3741 4338 2.626840 GAAGAGAGACCATGGTGCTTC 58.373 52.381 25.52 22.54 0.00 3.86
3742 4339 1.280421 GGAAGAGAGACCATGGTGCTT 59.720 52.381 25.52 18.87 0.00 3.91
3744 4341 0.460987 CGGAAGAGAGACCATGGTGC 60.461 60.000 25.52 14.34 0.00 5.01
3745 4342 0.898320 ACGGAAGAGAGACCATGGTG 59.102 55.000 25.52 6.84 0.00 4.17
3783 6426 4.405116 AAAAACACATGCTGACACCATT 57.595 36.364 0.00 0.00 0.00 3.16
3856 6500 4.946646 ACCCCATGATCAAAACCTTGTAT 58.053 39.130 0.00 0.00 33.94 2.29
3931 6581 9.443323 TGTTTAATTTCGAACCTCATAATCTCA 57.557 29.630 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.