Multiple sequence alignment - TraesCS7B01G188100

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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 TraesCS7B01G188100 chr7B 100.000 2551 0 0 1 2551 318370906 318368356 0.000000e+00 4711.0
1 TraesCS7B01G188100 chr7B 90.393 1093 96 4 617 1701 648212423 648213514 0.000000e+00 1428.0
2 TraesCS7B01G188100 chr5B 91.247 1965 138 15 619 2551 636962477 636964439 0.000000e+00 2645.0
3 TraesCS7B01G188100 chr5B 79.545 616 87 19 4 618 229063589 229063012 1.100000e-108 403.0
4 TraesCS7B01G188100 chr4A 90.396 1968 146 17 618 2551 664111687 664109729 0.000000e+00 2547.0
5 TraesCS7B01G188100 chr4A 90.291 1823 140 17 759 2551 702863849 702865664 0.000000e+00 2351.0
6 TraesCS7B01G188100 chr4A 80.937 619 94 8 4 618 219446776 219446178 3.840000e-128 468.0
7 TraesCS7B01G188100 chr1B 91.977 1558 108 15 1001 2551 628772877 628771330 0.000000e+00 2169.0
8 TraesCS7B01G188100 chr1B 81.250 576 58 22 5 576 239813237 239813766 1.090000e-113 420.0
9 TraesCS7B01G188100 chr1B 79.736 607 99 14 4 596 457513728 457514324 3.930000e-113 418.0
10 TraesCS7B01G188100 chr3B 93.515 1064 58 11 1495 2551 821332239 821333298 0.000000e+00 1572.0
11 TraesCS7B01G188100 chr3B 93.146 1065 59 14 1495 2551 821268713 821269771 0.000000e+00 1550.0
12 TraesCS7B01G188100 chr6D 91.598 1095 80 5 619 1701 329896761 329895667 0.000000e+00 1502.0
13 TraesCS7B01G188100 chr6D 93.918 855 46 6 1702 2551 323167733 323168586 0.000000e+00 1286.0
14 TraesCS7B01G188100 chr6D 85.714 616 70 4 4 618 111481231 111480633 3.580000e-178 634.0
15 TraesCS7B01G188100 chr6D 83.973 599 73 11 1 596 311328120 311328698 1.030000e-153 553.0
16 TraesCS7B01G188100 chr6D 82.942 639 69 15 1 618 307125862 307126481 8.030000e-150 540.0
17 TraesCS7B01G188100 chr6D 82.609 621 71 20 4 618 200255249 200254660 4.870000e-142 514.0
18 TraesCS7B01G188100 chr6D 82.334 617 71 12 4 618 328031820 328031240 3.790000e-138 501.0
19 TraesCS7B01G188100 chr6D 85.657 495 47 10 1 492 193647830 193648303 1.360000e-137 499.0
20 TraesCS7B01G188100 chr6D 81.659 627 82 16 4 618 272255117 272254512 8.200000e-135 490.0
21 TraesCS7B01G188100 chr6D 81.221 639 80 13 1 618 288423202 288423821 1.780000e-131 479.0
22 TraesCS7B01G188100 chr6D 81.426 533 69 9 1 520 458809154 458809669 2.360000e-110 409.0
23 TraesCS7B01G188100 chr6D 85.052 194 28 1 425 618 324306776 324306584 2.000000e-46 196.0
24 TraesCS7B01G188100 chrUn 90.759 1093 92 4 617 1701 355013875 355014966 0.000000e+00 1450.0
25 TraesCS7B01G188100 chr2D 90.668 1093 82 12 618 1701 16065485 16066566 0.000000e+00 1435.0
26 TraesCS7B01G188100 chr2D 84.084 622 75 11 4 618 151912839 151912235 1.700000e-161 579.0
27 TraesCS7B01G188100 chr2D 82.137 627 86 14 4 618 500345348 500344736 4.870000e-142 514.0
28 TraesCS7B01G188100 chr2D 82.609 621 60 13 4 618 366699867 366699289 2.930000e-139 505.0
29 TraesCS7B01G188100 chr2D 88.312 154 17 1 465 618 114092480 114092328 1.560000e-42 183.0
30 TraesCS7B01G188100 chr5A 90.009 1091 93 10 622 1701 553455274 553454189 0.000000e+00 1397.0
31 TraesCS7B01G188100 chr5A 81.220 623 76 23 4 618 306803386 306802797 4.970000e-127 464.0
32 TraesCS7B01G188100 chr5A 79.012 648 86 19 4 618 355206813 355206183 5.110000e-107 398.0
33 TraesCS7B01G188100 chr5A 77.383 619 71 30 1 615 80022987 80023540 1.150000e-78 303.0
34 TraesCS7B01G188100 chr3D 94.179 859 39 9 1702 2551 4247297 4248153 0.000000e+00 1299.0
35 TraesCS7B01G188100 chr3D 81.511 622 71 17 1 618 146737255 146737836 2.970000e-129 472.0
36 TraesCS7B01G188100 chr3D 83.333 498 63 9 4 495 293664077 293663594 2.330000e-120 442.0
37 TraesCS7B01G188100 chr3D 90.323 155 7 1 4 158 113307068 113306922 2.000000e-46 196.0
38 TraesCS7B01G188100 chr3D 81.624 234 41 2 385 618 222081680 222081449 2.590000e-45 193.0
39 TraesCS7B01G188100 chr3D 85.955 178 24 1 441 618 246280029 246280205 3.350000e-44 189.0
40 TraesCS7B01G188100 chr1D 93.590 858 42 10 1702 2551 481624733 481623881 0.000000e+00 1267.0
41 TraesCS7B01G188100 chr1D 82.512 629 85 13 1 618 326259464 326260078 1.740000e-146 529.0
42 TraesCS7B01G188100 chr1D 82.459 610 65 20 4 609 108919475 108918904 1.760000e-136 496.0
43 TraesCS7B01G188100 chr1D 81.906 619 65 17 4 618 223336541 223335966 1.780000e-131 479.0
44 TraesCS7B01G188100 chr1D 81.111 630 86 19 1 618 335708372 335708980 8.260000e-130 473.0
45 TraesCS7B01G188100 chr1D 80.775 645 78 20 1 618 61334846 61335471 1.790000e-126 462.0
46 TraesCS7B01G188100 chr1D 81.331 616 72 13 4 617 364020178 364019604 6.430000e-126 460.0
47 TraesCS7B01G188100 chr1D 83.297 455 57 4 4 456 278637865 278637428 3.950000e-108 401.0
48 TraesCS7B01G188100 chr1D 83.716 436 49 11 4 433 194805386 194804967 2.380000e-105 392.0
49 TraesCS7B01G188100 chr1D 83.527 431 53 4 4 433 194582312 194581899 1.110000e-103 387.0
50 TraesCS7B01G188100 chr1D 83.654 416 50 7 1 412 277685056 277685457 2.400000e-100 375.0
51 TraesCS7B01G188100 chr1D 85.143 350 42 2 1 348 279618671 279619012 1.450000e-92 350.0
52 TraesCS7B01G188100 chr1D 81.735 438 58 5 4 435 3030730 3031151 1.880000e-91 346.0
53 TraesCS7B01G188100 chr1D 85.231 325 38 2 1 323 124645138 124645454 2.450000e-85 326.0
54 TraesCS7B01G188100 chr1D 85.139 323 38 2 4 324 245904924 245904610 3.170000e-84 322.0
55 TraesCS7B01G188100 chr1D 85.806 310 34 2 29 336 137288071 137288372 1.140000e-83 320.0
56 TraesCS7B01G188100 chr1D 84.179 335 43 2 4 336 102696874 102696548 1.470000e-82 316.0
57 TraesCS7B01G188100 chr1D 87.160 257 31 1 117 371 149111004 149110748 8.930000e-75 291.0
58 TraesCS7B01G188100 chr1D 82.840 338 43 10 133 462 370169196 370168866 3.210000e-74 289.0
59 TraesCS7B01G188100 chr1D 84.444 180 21 4 445 618 140377089 140377267 1.210000e-38 171.0
60 TraesCS7B01G188100 chr4D 84.000 625 76 10 1 618 133112326 133112933 1.700000e-161 579.0
61 TraesCS7B01G188100 chr4D 82.935 627 76 14 4 618 240658525 240657918 1.040000e-148 536.0
62 TraesCS7B01G188100 chr4D 82.692 624 84 13 6 618 277673249 277672639 1.340000e-147 532.0
63 TraesCS7B01G188100 chr4D 80.952 504 60 17 117 618 71145150 71145619 1.440000e-97 366.0
64 TraesCS7B01G188100 chr4D 93.939 99 6 0 1 99 71096619 71096717 1.580000e-32 150.0
65 TraesCS7B01G188100 chr7A 83.439 628 90 5 1 618 502767493 502768116 2.850000e-159 571.0
66 TraesCS7B01G188100 chr7D 83.736 621 77 9 1 618 457720778 457721377 1.320000e-157 566.0
67 TraesCS7B01G188100 chr7D 82.658 617 66 13 4 618 372326011 372325434 2.260000e-140 508.0
68 TraesCS7B01G188100 chr7D 81.848 617 69 13 4 618 215352552 215351977 1.780000e-131 479.0
69 TraesCS7B01G188100 chr7D 82.809 477 67 7 1 473 225506727 225507192 1.830000e-111 412.0
70 TraesCS7B01G188100 chr7D 79.109 651 85 19 1 618 370990210 370990842 3.950000e-108 401.0
71 TraesCS7B01G188100 chr7D 87.143 70 9 0 364 433 401122652 401122583 2.100000e-11 80.5
72 TraesCS7B01G188100 chr6A 83.226 620 90 5 1 618 589037702 589038309 7.970000e-155 556.0
73 TraesCS7B01G188100 chr6A 80.837 621 82 14 1 618 65905690 65906276 1.080000e-123 453.0
74 TraesCS7B01G188100 chr6A 88.312 154 17 1 465 618 550520973 550520821 1.560000e-42 183.0
75 TraesCS7B01G188100 chr5D 81.935 620 71 13 1 618 199818839 199819419 1.060000e-133 486.0
76 TraesCS7B01G188100 chr5D 85.343 423 40 7 1 422 92469241 92469642 3.930000e-113 418.0
77 TraesCS7B01G188100 chr5D 85.523 373 44 3 1 371 286870388 286870752 5.150000e-102 381.0
78 TraesCS7B01G188100 chr5D 86.620 142 17 2 478 618 469591605 469591745 3.400000e-34 156.0
79 TraesCS7B01G188100 chr5D 84.768 151 22 1 468 618 94932627 94932478 1.580000e-32 150.0
80 TraesCS7B01G188100 chr4B 83.438 477 60 7 4 479 143746888 143746430 2.350000e-115 425.0
81 TraesCS7B01G188100 chr4B 82.061 262 29 10 357 618 349548670 349548913 9.250000e-50 207.0
82 TraesCS7B01G188100 chr2A 82.510 486 78 3 113 596 108576659 108577139 1.090000e-113 420.0
83 TraesCS7B01G188100 chr2A 84.615 234 34 2 385 618 750863811 750864042 5.490000e-57 231.0
84 TraesCS7B01G188100 chr3A 83.404 235 36 3 385 618 96206816 96207048 5.530000e-52 215.0
85 TraesCS7B01G188100 chr3A 85.882 170 22 2 449 618 234327452 234327619 2.020000e-41 180.0


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 TraesCS7B01G188100 chr7B 318368356 318370906 2550 True 4711 4711 100.000 1 2551 1 chr7B.!!$R1 2550
1 TraesCS7B01G188100 chr7B 648212423 648213514 1091 False 1428 1428 90.393 617 1701 1 chr7B.!!$F1 1084
2 TraesCS7B01G188100 chr5B 636962477 636964439 1962 False 2645 2645 91.247 619 2551 1 chr5B.!!$F1 1932
3 TraesCS7B01G188100 chr5B 229063012 229063589 577 True 403 403 79.545 4 618 1 chr5B.!!$R1 614
4 TraesCS7B01G188100 chr4A 664109729 664111687 1958 True 2547 2547 90.396 618 2551 1 chr4A.!!$R2 1933
5 TraesCS7B01G188100 chr4A 702863849 702865664 1815 False 2351 2351 90.291 759 2551 1 chr4A.!!$F1 1792
6 TraesCS7B01G188100 chr4A 219446178 219446776 598 True 468 468 80.937 4 618 1 chr4A.!!$R1 614
7 TraesCS7B01G188100 chr1B 628771330 628772877 1547 True 2169 2169 91.977 1001 2551 1 chr1B.!!$R1 1550
8 TraesCS7B01G188100 chr1B 239813237 239813766 529 False 420 420 81.250 5 576 1 chr1B.!!$F1 571
9 TraesCS7B01G188100 chr1B 457513728 457514324 596 False 418 418 79.736 4 596 1 chr1B.!!$F2 592
10 TraesCS7B01G188100 chr3B 821332239 821333298 1059 False 1572 1572 93.515 1495 2551 1 chr3B.!!$F2 1056
11 TraesCS7B01G188100 chr3B 821268713 821269771 1058 False 1550 1550 93.146 1495 2551 1 chr3B.!!$F1 1056
12 TraesCS7B01G188100 chr6D 329895667 329896761 1094 True 1502 1502 91.598 619 1701 1 chr6D.!!$R6 1082
13 TraesCS7B01G188100 chr6D 323167733 323168586 853 False 1286 1286 93.918 1702 2551 1 chr6D.!!$F5 849
14 TraesCS7B01G188100 chr6D 111480633 111481231 598 True 634 634 85.714 4 618 1 chr6D.!!$R1 614
15 TraesCS7B01G188100 chr6D 311328120 311328698 578 False 553 553 83.973 1 596 1 chr6D.!!$F4 595
16 TraesCS7B01G188100 chr6D 307125862 307126481 619 False 540 540 82.942 1 618 1 chr6D.!!$F3 617
17 TraesCS7B01G188100 chr6D 200254660 200255249 589 True 514 514 82.609 4 618 1 chr6D.!!$R2 614
18 TraesCS7B01G188100 chr6D 328031240 328031820 580 True 501 501 82.334 4 618 1 chr6D.!!$R5 614
19 TraesCS7B01G188100 chr6D 272254512 272255117 605 True 490 490 81.659 4 618 1 chr6D.!!$R3 614
20 TraesCS7B01G188100 chr6D 288423202 288423821 619 False 479 479 81.221 1 618 1 chr6D.!!$F2 617
21 TraesCS7B01G188100 chr6D 458809154 458809669 515 False 409 409 81.426 1 520 1 chr6D.!!$F6 519
22 TraesCS7B01G188100 chrUn 355013875 355014966 1091 False 1450 1450 90.759 617 1701 1 chrUn.!!$F1 1084
23 TraesCS7B01G188100 chr2D 16065485 16066566 1081 False 1435 1435 90.668 618 1701 1 chr2D.!!$F1 1083
24 TraesCS7B01G188100 chr2D 151912235 151912839 604 True 579 579 84.084 4 618 1 chr2D.!!$R2 614
25 TraesCS7B01G188100 chr2D 500344736 500345348 612 True 514 514 82.137 4 618 1 chr2D.!!$R4 614
26 TraesCS7B01G188100 chr2D 366699289 366699867 578 True 505 505 82.609 4 618 1 chr2D.!!$R3 614
27 TraesCS7B01G188100 chr5A 553454189 553455274 1085 True 1397 1397 90.009 622 1701 1 chr5A.!!$R3 1079
28 TraesCS7B01G188100 chr5A 306802797 306803386 589 True 464 464 81.220 4 618 1 chr5A.!!$R1 614
29 TraesCS7B01G188100 chr5A 355206183 355206813 630 True 398 398 79.012 4 618 1 chr5A.!!$R2 614
30 TraesCS7B01G188100 chr5A 80022987 80023540 553 False 303 303 77.383 1 615 1 chr5A.!!$F1 614
31 TraesCS7B01G188100 chr3D 4247297 4248153 856 False 1299 1299 94.179 1702 2551 1 chr3D.!!$F1 849
32 TraesCS7B01G188100 chr3D 146737255 146737836 581 False 472 472 81.511 1 618 1 chr3D.!!$F2 617
33 TraesCS7B01G188100 chr1D 481623881 481624733 852 True 1267 1267 93.590 1702 2551 1 chr1D.!!$R11 849
34 TraesCS7B01G188100 chr1D 326259464 326260078 614 False 529 529 82.512 1 618 1 chr1D.!!$F8 617
35 TraesCS7B01G188100 chr1D 108918904 108919475 571 True 496 496 82.459 4 609 1 chr1D.!!$R2 605
36 TraesCS7B01G188100 chr1D 223335966 223336541 575 True 479 479 81.906 4 618 1 chr1D.!!$R6 614
37 TraesCS7B01G188100 chr1D 335708372 335708980 608 False 473 473 81.111 1 618 1 chr1D.!!$F9 617
38 TraesCS7B01G188100 chr1D 61334846 61335471 625 False 462 462 80.775 1 618 1 chr1D.!!$F2 617
39 TraesCS7B01G188100 chr1D 364019604 364020178 574 True 460 460 81.331 4 617 1 chr1D.!!$R9 613
40 TraesCS7B01G188100 chr4D 133112326 133112933 607 False 579 579 84.000 1 618 1 chr4D.!!$F3 617
41 TraesCS7B01G188100 chr4D 240657918 240658525 607 True 536 536 82.935 4 618 1 chr4D.!!$R1 614
42 TraesCS7B01G188100 chr4D 277672639 277673249 610 True 532 532 82.692 6 618 1 chr4D.!!$R2 612
43 TraesCS7B01G188100 chr7A 502767493 502768116 623 False 571 571 83.439 1 618 1 chr7A.!!$F1 617
44 TraesCS7B01G188100 chr7D 457720778 457721377 599 False 566 566 83.736 1 618 1 chr7D.!!$F3 617
45 TraesCS7B01G188100 chr7D 372325434 372326011 577 True 508 508 82.658 4 618 1 chr7D.!!$R2 614
46 TraesCS7B01G188100 chr7D 215351977 215352552 575 True 479 479 81.848 4 618 1 chr7D.!!$R1 614
47 TraesCS7B01G188100 chr7D 370990210 370990842 632 False 401 401 79.109 1 618 1 chr7D.!!$F2 617
48 TraesCS7B01G188100 chr6A 589037702 589038309 607 False 556 556 83.226 1 618 1 chr6A.!!$F2 617
49 TraesCS7B01G188100 chr6A 65905690 65906276 586 False 453 453 80.837 1 618 1 chr6A.!!$F1 617
50 TraesCS7B01G188100 chr5D 199818839 199819419 580 False 486 486 81.935 1 618 1 chr5D.!!$F2 617

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
787 1087 0.104882 TTACAGGTGGGACCAGGTGA 60.105 55.0 0.0 0.0 41.95 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1855 2198 0.397957 TGGCCCATTAGTCTAGCCGA 60.398 55.0 0.0 0.0 46.92 5.54 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
88 102 4.616143 CGAGATCGAAAGGTTGAAGAGACA 60.616 45.833 0.00 0.00 43.02 3.41
94 108 4.335594 CGAAAGGTTGAAGAGACAAAGGTT 59.664 41.667 0.00 0.00 0.00 3.50
99 113 8.990163 AAGGTTGAAGAGACAAAGGTTATAAA 57.010 30.769 0.00 0.00 0.00 1.40
100 114 8.392372 AGGTTGAAGAGACAAAGGTTATAAAC 57.608 34.615 0.00 0.00 0.00 2.01
115 129 5.409214 GGTTATAAACTTATAATGGCCGCGA 59.591 40.000 8.23 0.00 37.77 5.87
179 198 3.181497 CCGGATGGCAGTTCTAATTTGTG 60.181 47.826 0.00 0.00 0.00 3.33
433 633 1.185618 TGGAGGTACGCAAGCAGAGT 61.186 55.000 0.00 0.00 45.62 3.24
447 673 2.194212 AGAGTGTGCTGACGGACGT 61.194 57.895 0.00 0.00 33.68 4.34
459 686 4.724602 GGACGTGAGCAGAGCGCA 62.725 66.667 11.47 0.00 46.13 6.09
583 880 7.390996 GGAGACATCAAGCATGAATCAGATTAT 59.609 37.037 0.00 0.00 39.49 1.28
599 896 3.679980 AGATTATGAGTTGCGTGTGTGAC 59.320 43.478 0.00 0.00 0.00 3.67
642 939 5.163447 GGGTTAATTATCCTTTTGCCCTCAC 60.163 44.000 11.51 0.00 0.00 3.51
650 947 0.817634 TTTTGCCCTCACTGGTGTCG 60.818 55.000 0.53 0.00 0.00 4.35
653 950 1.153549 GCCCTCACTGGTGTCGATC 60.154 63.158 0.00 0.00 0.00 3.69
672 969 1.133823 TCTGCTCAGTTTTGCCCTCAA 60.134 47.619 0.00 0.00 0.00 3.02
680 977 1.792367 GTTTTGCCCTCAAATGCGAAC 59.208 47.619 0.00 0.00 41.37 3.95
708 1005 1.774856 AGTTTTGCCCCTAGTCTGTGT 59.225 47.619 0.00 0.00 0.00 3.72
755 1055 0.244178 GTCTCCGTCAGGTCAACCTC 59.756 60.000 0.00 0.00 46.65 3.85
787 1087 0.104882 TTACAGGTGGGACCAGGTGA 60.105 55.000 0.00 0.00 41.95 4.02
822 1123 2.740714 GATCAGACCGTTGCACGCC 61.741 63.158 0.00 0.00 40.91 5.68
824 1125 1.884075 ATCAGACCGTTGCACGCCTA 61.884 55.000 0.00 0.00 40.91 3.93
904 1224 2.026445 CGGTGACCACGACGACAA 59.974 61.111 0.00 0.00 0.00 3.18
910 1230 1.606350 GACCACGACGACAAAGAGCG 61.606 60.000 0.00 0.00 0.00 5.03
915 1235 1.954146 GACGACAAAGAGCGTGGCA 60.954 57.895 0.00 0.00 41.34 4.92
937 1265 3.443925 CCACCGCGAGAGAGAGCA 61.444 66.667 8.23 0.00 0.00 4.26
940 1268 3.819920 CCGCGAGAGAGAGCAGCA 61.820 66.667 8.23 0.00 0.00 4.41
995 1323 1.045911 AGATCCCCTTCGGCTCTGAC 61.046 60.000 0.00 0.00 0.00 3.51
1075 1403 2.138320 ACATGCTTGTCTTCGTCTGTG 58.862 47.619 0.00 0.00 0.00 3.66
1109 1437 0.108041 GGCGTTGATCGGAGGGTTTA 60.108 55.000 0.00 0.00 40.26 2.01
1133 1461 1.001974 CACACCGAGGAACCAGAATCA 59.998 52.381 0.00 0.00 0.00 2.57
1178 1506 0.750546 GGGGTAAGAATCGGGGCAAC 60.751 60.000 0.00 0.00 0.00 4.17
1195 1523 1.598601 CAACTGCACCATTTTTGTGGC 59.401 47.619 0.00 0.00 43.27 5.01
1239 1567 1.246649 TCTGTTTGGCGTTCATGCAT 58.753 45.000 0.00 0.00 36.28 3.96
1261 1589 4.206375 TGTGACATGCTTCTTTCTTTGGA 58.794 39.130 0.00 0.00 0.00 3.53
1322 1654 2.799017 AGAGCATGAAGAATGGTTGCA 58.201 42.857 0.00 0.00 46.95 4.08
1328 1660 1.273048 TGAAGAATGGTTGCACATGCC 59.727 47.619 0.49 0.00 41.18 4.40
1368 1700 2.551270 GCACGAGCTCCACAAACG 59.449 61.111 8.47 0.00 37.91 3.60
1370 1702 2.665185 ACGAGCTCCACAAACGGC 60.665 61.111 8.47 0.00 0.00 5.68
1407 1740 2.020720 GCACTGACAGAGAGCTAGCTA 58.979 52.381 19.38 0.00 35.53 3.32
1492 1825 4.349342 ACCCATTTGCAATTACTTTTGGGA 59.651 37.500 21.16 0.00 44.36 4.37
1507 1841 5.186992 ACTTTTGGGAATTTGTAGGTATGGC 59.813 40.000 0.00 0.00 0.00 4.40
1515 1849 2.928801 TGTAGGTATGGCAATCGCAT 57.071 45.000 0.00 0.00 41.24 4.73
1840 2183 3.117888 TCCTCTATGGGCCAAATTCAGAC 60.118 47.826 11.89 0.00 36.20 3.51
1855 2198 2.598565 TCAGACTGTAGAGCCAAGTGT 58.401 47.619 1.59 0.00 0.00 3.55
1882 2227 2.173569 AGACTAATGGGCCAACTGATCC 59.826 50.000 11.89 0.00 0.00 3.36
1897 2242 3.052642 ACTGATCCATTAGGCCCATTTGT 60.053 43.478 0.00 0.00 33.74 2.83
1911 2256 0.105246 ATTTGTGGGGTTCCCTTGCA 60.105 50.000 7.87 2.29 45.70 4.08
1971 2316 8.801913 GCAGTAAATCATAATGCTGAAACTTTC 58.198 33.333 1.10 0.00 35.86 2.62
2019 2364 7.669722 TCCAGAGCCAAACAATTAAGTTTAGAT 59.330 33.333 0.00 0.00 39.55 1.98
2318 2668 1.227674 CCGCTAGGGCAGATGGAAC 60.228 63.158 0.19 0.00 38.60 3.62
2386 2736 6.506200 CGTTTGTTTGTACTGAATGTTTGCAG 60.506 38.462 0.00 0.00 38.10 4.41
2418 2768 4.252878 AGTGGTTTTCCTTTGTTTTGCAG 58.747 39.130 0.00 0.00 41.38 4.41
2421 2771 5.290885 GTGGTTTTCCTTTGTTTTGCAGTAG 59.709 40.000 0.00 0.00 41.38 2.57
2491 2843 3.073274 AGATGGCACTTGGTTTAGGAC 57.927 47.619 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 102 7.520937 CGCGGCCATTATAAGTTTATAACCTTT 60.521 37.037 2.24 0.00 38.14 3.11
94 108 6.028146 TCTCGCGGCCATTATAAGTTTATA 57.972 37.500 6.13 0.00 0.00 0.98
99 113 2.902705 TTCTCGCGGCCATTATAAGT 57.097 45.000 6.13 0.00 0.00 2.24
100 114 5.856126 TTAATTCTCGCGGCCATTATAAG 57.144 39.130 6.13 0.00 0.00 1.73
115 129 1.850345 TCCGGCTTCCCCATTAATTCT 59.150 47.619 0.00 0.00 0.00 2.40
179 198 1.933853 GACACGATGGAGTTACATGCC 59.066 52.381 0.00 0.00 0.00 4.40
433 633 2.335011 CTCACGTCCGTCAGCACA 59.665 61.111 0.00 0.00 0.00 4.57
447 673 4.426112 CTCGGTGCGCTCTGCTCA 62.426 66.667 13.38 0.00 46.63 4.26
459 686 3.081409 ACCATTAGGCGCCTCGGT 61.081 61.111 36.73 32.51 39.06 4.69
463 736 2.190578 GCTCACCATTAGGCGCCT 59.809 61.111 34.85 34.85 39.06 5.52
516 812 6.730960 TTGTCTTATTTTCCACGTATCACC 57.269 37.500 0.00 0.00 0.00 4.02
583 880 0.936600 CATGTCACACACGCAACTCA 59.063 50.000 0.00 0.00 0.00 3.41
599 896 6.395426 AACCCATCAACTATATGCAACATG 57.605 37.500 0.00 0.00 0.00 3.21
642 939 0.529833 ACTGAGCAGATCGACACCAG 59.470 55.000 4.21 0.00 0.00 4.00
650 947 1.742268 GAGGGCAAAACTGAGCAGATC 59.258 52.381 4.21 0.00 0.00 2.75
653 950 1.321474 TTGAGGGCAAAACTGAGCAG 58.679 50.000 0.00 0.00 0.00 4.24
672 969 1.538047 AACTGAGCATGGTTCGCATT 58.462 45.000 0.00 0.00 0.00 3.56
680 977 0.901580 AGGGGCAAAACTGAGCATGG 60.902 55.000 0.00 0.00 0.00 3.66
787 1087 3.833650 CTGATCATCTAGGGCATCTCTGT 59.166 47.826 0.00 0.00 0.00 3.41
822 1123 1.078143 GCTGGGTCCCACAAGCTAG 60.078 63.158 6.47 0.00 0.00 3.42
824 1125 3.177884 TGCTGGGTCCCACAAGCT 61.178 61.111 18.72 0.00 0.00 3.74
904 1224 2.031163 GGTCACTGCCACGCTCTT 59.969 61.111 0.00 0.00 0.00 2.85
915 1235 2.282251 TCTCTCGCGGTGGTCACT 60.282 61.111 6.13 0.00 0.00 3.41
924 1244 2.278077 CTGCTGCTCTCTCTCGCG 60.278 66.667 0.00 0.00 0.00 5.87
937 1265 1.197430 ACAGCTAGCTTCCCACTGCT 61.197 55.000 16.46 0.00 42.67 4.24
940 1268 0.545309 TCCACAGCTAGCTTCCCACT 60.545 55.000 16.46 0.00 0.00 4.00
969 1297 1.517832 CGAAGGGGATCTGAACGCT 59.482 57.895 2.25 0.00 0.00 5.07
995 1323 1.558756 AGCTTGAGGAAGACATGGAGG 59.441 52.381 0.00 0.00 0.00 4.30
1109 1437 0.321671 CTGGTTCCTCGGTGTGTGAT 59.678 55.000 0.00 0.00 0.00 3.06
1178 1506 0.945265 CGGCCACAAAAATGGTGCAG 60.945 55.000 2.24 0.00 42.28 4.41
1195 1523 1.027357 CCATTGCTCAAAGATCCCGG 58.973 55.000 0.00 0.00 0.00 5.73
1239 1567 4.206375 TCCAAAGAAAGAAGCATGTCACA 58.794 39.130 0.00 0.00 0.00 3.58
1261 1589 0.179062 GTCTTGGCCAGAGCATCGAT 60.179 55.000 5.11 0.00 42.67 3.59
1363 1695 3.814268 CGCCCTCCATGCCGTTTG 61.814 66.667 0.00 0.00 0.00 2.93
1366 1698 4.473520 CTTCGCCCTCCATGCCGT 62.474 66.667 0.00 0.00 0.00 5.68
1368 1700 3.125376 ATCCTTCGCCCTCCATGCC 62.125 63.158 0.00 0.00 0.00 4.40
1370 1702 1.895707 GCATCCTTCGCCCTCCATG 60.896 63.158 0.00 0.00 0.00 3.66
1384 1717 2.799207 GCTAGCTCTCTGTCAGTGCATC 60.799 54.545 7.70 0.00 43.07 3.91
1407 1740 6.715280 TCTTCTTCAACATCCTAAGCTCAAT 58.285 36.000 0.00 0.00 0.00 2.57
1460 1793 6.665680 AGTAATTGCAAATGGGTATTGGTACA 59.334 34.615 1.71 0.00 32.25 2.90
1461 1794 7.107639 AGTAATTGCAAATGGGTATTGGTAC 57.892 36.000 1.71 0.00 0.00 3.34
1492 1825 3.951037 TGCGATTGCCATACCTACAAATT 59.049 39.130 1.50 0.00 41.78 1.82
1507 1841 3.781079 ACATTACACCCAATGCGATTG 57.219 42.857 0.00 0.00 39.13 2.67
1515 1849 7.233553 TCCATACAATTTCAACATTACACCCAA 59.766 33.333 0.00 0.00 0.00 4.12
1573 1907 8.739972 ACTAGGTGAATTTGTCATACAATTTCC 58.260 33.333 17.82 12.11 42.87 3.13
1586 1920 9.191995 GACCAACATTTAAACTAGGTGAATTTG 57.808 33.333 7.84 0.00 0.00 2.32
1840 2183 3.425578 CCGACACTTGGCTCTACAG 57.574 57.895 0.00 0.00 0.00 2.74
1855 2198 0.397957 TGGCCCATTAGTCTAGCCGA 60.398 55.000 0.00 0.00 46.92 5.54
1973 2318 9.075678 CTCTGGAATAATTCAATTAGCTTCCAT 57.924 33.333 19.18 0.00 40.42 3.41
2068 2415 8.788806 TCTTTCATTTAAATCACGGTGTATTGT 58.211 29.630 8.17 2.17 0.00 2.71
2069 2416 9.061610 GTCTTTCATTTAAATCACGGTGTATTG 57.938 33.333 8.17 0.00 0.00 1.90
2089 2436 7.442062 ACATTTTCCATGACATTTTGGTCTTTC 59.558 33.333 0.00 0.00 38.61 2.62
2141 2489 7.814264 AAATGTTCATTAATTTTGGCACCAA 57.186 28.000 0.00 0.00 0.00 3.67
2240 2589 1.684734 GGGTTCGAGTCCCCAGCTA 60.685 63.158 14.49 0.00 40.88 3.32
2318 2668 1.553248 TCCCTACCCATGTCAAAGTCG 59.447 52.381 0.00 0.00 0.00 4.18
2386 2736 1.464997 GGAAAACCACTCTCACGCATC 59.535 52.381 0.00 0.00 0.00 3.91
2418 2768 4.864704 TTGCAACCCTCCAAAATTCTAC 57.135 40.909 0.00 0.00 0.00 2.59
2421 2771 2.799978 CGTTTGCAACCCTCCAAAATTC 59.200 45.455 0.00 0.00 33.25 2.17


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

AutoCloner maintained by Alex Coulton.