Multiple sequence alignment - TraesCS1B01G420700

Loading Multiple Alignment...

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 TraesCS1B01G420700 chr1B 100.000 3528 0 0 1 3528 643909299 643905772 0.000000e+00 6516.0
1 TraesCS1B01G420700 chr1B 87.345 1209 76 35 984 2153 644527400 644526230 0.000000e+00 1314.0
2 TraesCS1B01G420700 chr1B 95.498 622 25 2 2143 2761 653673512 653674133 0.000000e+00 990.0
3 TraesCS1B01G420700 chr1B 88.542 768 79 3 977 1735 644799050 644798283 0.000000e+00 922.0
4 TraesCS1B01G420700 chr1B 86.594 731 66 11 1017 1734 644310574 644311285 0.000000e+00 778.0
5 TraesCS1B01G420700 chr1B 95.745 423 18 0 984 1406 644341713 644342135 0.000000e+00 682.0
6 TraesCS1B01G420700 chr1B 89.239 381 33 7 977 1350 645092888 645093267 1.480000e-128 470.0
7 TraesCS1B01G420700 chr1B 88.076 369 28 7 1377 1735 645095715 645096077 1.170000e-114 424.0
8 TraesCS1B01G420700 chr1B 80.132 604 84 22 2926 3528 514350551 514349983 5.450000e-113 418.0
9 TraesCS1B01G420700 chr1B 97.561 164 4 0 594 757 644341119 644341282 7.460000e-72 281.0
10 TraesCS1B01G420700 chr1B 97.561 164 4 0 594 757 644527994 644527831 7.460000e-72 281.0
11 TraesCS1B01G420700 chr1B 91.964 112 6 2 2045 2153 644311448 644311559 1.700000e-33 154.0
12 TraesCS1B01G420700 chr1B 93.407 91 5 1 2063 2153 644798027 644797938 2.210000e-27 134.0
13 TraesCS1B01G420700 chr1B 96.104 77 2 1 755 830 644341555 644341631 1.330000e-24 124.0
14 TraesCS1B01G420700 chr1B 96.104 77 2 1 755 830 644527558 644527482 1.330000e-24 124.0
15 TraesCS1B01G420700 chr1A 88.909 1632 106 27 568 2153 559046002 559044400 0.000000e+00 1941.0
16 TraesCS1B01G420700 chr1A 82.827 1217 149 35 545 1735 559348886 559350068 0.000000e+00 1035.0
17 TraesCS1B01G420700 chr1A 82.329 498 58 23 3 482 137811168 137810683 4.240000e-109 405.0
18 TraesCS1B01G420700 chr1A 90.756 119 8 2 2038 2153 559232431 559232313 4.720000e-34 156.0
19 TraesCS1B01G420700 chr1A 93.407 91 5 1 2063 2153 559350369 559350458 2.210000e-27 134.0
20 TraesCS1B01G420700 chr1D 92.058 1234 62 15 951 2153 467108583 467107355 0.000000e+00 1703.0
21 TraesCS1B01G420700 chr1D 82.855 1219 139 39 545 1735 467298950 467300126 0.000000e+00 1029.0
22 TraesCS1B01G420700 chr1D 93.407 91 5 1 2063 2153 467300399 467300488 2.210000e-27 134.0
23 TraesCS1B01G420700 chr3B 96.411 613 20 2 2150 2761 829474233 829473622 0.000000e+00 1009.0
24 TraesCS1B01G420700 chr3B 96.667 600 19 1 2163 2761 48018291 48018890 0.000000e+00 996.0
25 TraesCS1B01G420700 chr3B 95.928 614 23 1 2150 2761 47674915 47675528 0.000000e+00 994.0
26 TraesCS1B01G420700 chr3B 95.902 610 24 1 2150 2759 577493076 577492468 0.000000e+00 987.0
27 TraesCS1B01G420700 chr3B 95.364 604 26 1 2163 2766 803090110 803089509 0.000000e+00 959.0
28 TraesCS1B01G420700 chr3B 95.175 601 27 1 2163 2761 783294888 783294288 0.000000e+00 948.0
29 TraesCS1B01G420700 chr3B 94.719 606 29 3 2163 2767 14988606 14988003 0.000000e+00 939.0
30 TraesCS1B01G420700 chr3B 87.186 757 68 13 2770 3519 734503548 734504282 0.000000e+00 833.0
31 TraesCS1B01G420700 chr3B 87.349 498 43 12 1 480 778389379 778389874 1.430000e-153 553.0
32 TraesCS1B01G420700 chr3B 82.258 496 60 22 3 476 61675920 61676409 1.530000e-108 403.0
33 TraesCS1B01G420700 chr2B 95.861 604 21 3 2163 2765 93076268 93075668 0.000000e+00 974.0
34 TraesCS1B01G420700 chr2B 85.986 735 82 8 2794 3528 775133000 775132287 0.000000e+00 767.0
35 TraesCS1B01G420700 chr2B 85.380 513 38 19 1 479 666080508 666079999 6.800000e-137 497.0
36 TraesCS1B01G420700 chr2B 84.648 469 37 21 1 435 785519803 785520270 5.410000e-118 435.0
37 TraesCS1B01G420700 chr2B 84.501 471 30 23 48 478 765729779 765729312 3.260000e-115 425.0
38 TraesCS1B01G420700 chr7B 87.270 762 77 7 2770 3528 666409919 666409175 0.000000e+00 852.0
39 TraesCS1B01G420700 chr7B 85.887 496 48 15 1 476 603247035 603247528 3.140000e-140 508.0
40 TraesCS1B01G420700 chr7B 85.000 520 36 23 1 478 548117972 548118491 1.140000e-134 490.0
41 TraesCS1B01G420700 chr7B 80.237 506 62 24 1 479 2236214 2236708 2.610000e-91 346.0
42 TraesCS1B01G420700 chr7B 81.548 168 19 8 2907 3073 631052066 631051910 1.030000e-25 128.0
43 TraesCS1B01G420700 chr4B 87.417 755 78 6 2774 3528 622322863 622322126 0.000000e+00 852.0
44 TraesCS1B01G420700 chr4B 83.669 496 57 19 3 484 667408130 667407645 2.500000e-121 446.0
45 TraesCS1B01G420700 chr6B 86.034 759 77 9 2770 3526 177719727 177718996 0.000000e+00 787.0
46 TraesCS1B01G420700 chr6B 85.271 516 32 23 1 476 521032267 521032778 3.160000e-135 492.0
47 TraesCS1B01G420700 chr6B 84.889 450 29 20 65 478 612865648 612865202 5.450000e-113 418.0
48 TraesCS1B01G420700 chr6B 84.615 325 30 16 168 479 136936219 136935902 4.420000e-79 305.0
49 TraesCS1B01G420700 chr5B 85.098 765 78 12 2770 3528 592070138 592069404 0.000000e+00 749.0
50 TraesCS1B01G420700 chr5B 84.797 763 89 7 2770 3528 445552053 445551314 0.000000e+00 741.0
51 TraesCS1B01G420700 chr5B 83.399 765 87 9 2770 3528 319881766 319882496 0.000000e+00 673.0
52 TraesCS1B01G420700 chr5B 86.372 521 29 16 1 479 378910495 378909975 6.710000e-147 531.0
53 TraesCS1B01G420700 chr5B 84.940 498 42 20 1 479 536888975 536889458 1.150000e-129 473.0
54 TraesCS1B01G420700 chr7D 83.978 543 71 9 2990 3526 430936047 430935515 1.130000e-139 507.0
55 TraesCS1B01G420700 chr7D 81.653 496 64 21 3 476 575586447 575586937 1.540000e-103 387.0
56 TraesCS1B01G420700 chrUn 85.772 499 45 19 1 480 286005476 286005967 4.060000e-139 505.0
57 TraesCS1B01G420700 chrUn 78.474 511 71 26 3030 3528 250194659 250195142 7.400000e-77 298.0
58 TraesCS1B01G420700 chr6A 79.014 629 100 23 2907 3528 200242410 200243013 5.490000e-108 401.0
59 TraesCS1B01G420700 chr5A 78.520 554 91 20 2918 3459 514777249 514777786 4.360000e-89 339.0
60 TraesCS1B01G420700 chr4D 85.886 333 29 14 157 478 336250220 336249895 4.360000e-89 339.0
61 TraesCS1B01G420700 chr7A 82.011 189 22 7 301 479 92408296 92408482 2.190000e-32 150.0
62 TraesCS1B01G420700 chr6D 86.022 93 7 6 2990 3079 408696758 408696847 1.040000e-15 95.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G420700 chr1B 643905772 643909299 3527 True 6516.000000 6516 100.0000 1 3528 1 chr1B.!!$R2 3527
1 TraesCS1B01G420700 chr1B 653673512 653674133 621 False 990.000000 990 95.4980 2143 2761 1 chr1B.!!$F1 618
2 TraesCS1B01G420700 chr1B 644526230 644527994 1764 True 573.000000 1314 93.6700 594 2153 3 chr1B.!!$R3 1559
3 TraesCS1B01G420700 chr1B 644797938 644799050 1112 True 528.000000 922 90.9745 977 2153 2 chr1B.!!$R4 1176
4 TraesCS1B01G420700 chr1B 644310574 644311559 985 False 466.000000 778 89.2790 1017 2153 2 chr1B.!!$F2 1136
5 TraesCS1B01G420700 chr1B 645092888 645096077 3189 False 447.000000 470 88.6575 977 1735 2 chr1B.!!$F4 758
6 TraesCS1B01G420700 chr1B 514349983 514350551 568 True 418.000000 418 80.1320 2926 3528 1 chr1B.!!$R1 602
7 TraesCS1B01G420700 chr1B 644341119 644342135 1016 False 362.333333 682 96.4700 594 1406 3 chr1B.!!$F3 812
8 TraesCS1B01G420700 chr1A 559044400 559046002 1602 True 1941.000000 1941 88.9090 568 2153 1 chr1A.!!$R2 1585
9 TraesCS1B01G420700 chr1A 559348886 559350458 1572 False 584.500000 1035 88.1170 545 2153 2 chr1A.!!$F1 1608
10 TraesCS1B01G420700 chr1D 467107355 467108583 1228 True 1703.000000 1703 92.0580 951 2153 1 chr1D.!!$R1 1202
11 TraesCS1B01G420700 chr1D 467298950 467300488 1538 False 581.500000 1029 88.1310 545 2153 2 chr1D.!!$F1 1608
12 TraesCS1B01G420700 chr3B 829473622 829474233 611 True 1009.000000 1009 96.4110 2150 2761 1 chr3B.!!$R5 611
13 TraesCS1B01G420700 chr3B 48018291 48018890 599 False 996.000000 996 96.6670 2163 2761 1 chr3B.!!$F2 598
14 TraesCS1B01G420700 chr3B 47674915 47675528 613 False 994.000000 994 95.9280 2150 2761 1 chr3B.!!$F1 611
15 TraesCS1B01G420700 chr3B 577492468 577493076 608 True 987.000000 987 95.9020 2150 2759 1 chr3B.!!$R2 609
16 TraesCS1B01G420700 chr3B 803089509 803090110 601 True 959.000000 959 95.3640 2163 2766 1 chr3B.!!$R4 603
17 TraesCS1B01G420700 chr3B 783294288 783294888 600 True 948.000000 948 95.1750 2163 2761 1 chr3B.!!$R3 598
18 TraesCS1B01G420700 chr3B 14988003 14988606 603 True 939.000000 939 94.7190 2163 2767 1 chr3B.!!$R1 604
19 TraesCS1B01G420700 chr3B 734503548 734504282 734 False 833.000000 833 87.1860 2770 3519 1 chr3B.!!$F4 749
20 TraesCS1B01G420700 chr2B 93075668 93076268 600 True 974.000000 974 95.8610 2163 2765 1 chr2B.!!$R1 602
21 TraesCS1B01G420700 chr2B 775132287 775133000 713 True 767.000000 767 85.9860 2794 3528 1 chr2B.!!$R4 734
22 TraesCS1B01G420700 chr2B 666079999 666080508 509 True 497.000000 497 85.3800 1 479 1 chr2B.!!$R2 478
23 TraesCS1B01G420700 chr7B 666409175 666409919 744 True 852.000000 852 87.2700 2770 3528 1 chr7B.!!$R2 758
24 TraesCS1B01G420700 chr7B 548117972 548118491 519 False 490.000000 490 85.0000 1 478 1 chr7B.!!$F2 477
25 TraesCS1B01G420700 chr4B 622322126 622322863 737 True 852.000000 852 87.4170 2774 3528 1 chr4B.!!$R1 754
26 TraesCS1B01G420700 chr6B 177718996 177719727 731 True 787.000000 787 86.0340 2770 3526 1 chr6B.!!$R2 756
27 TraesCS1B01G420700 chr6B 521032267 521032778 511 False 492.000000 492 85.2710 1 476 1 chr6B.!!$F1 475
28 TraesCS1B01G420700 chr5B 592069404 592070138 734 True 749.000000 749 85.0980 2770 3528 1 chr5B.!!$R3 758
29 TraesCS1B01G420700 chr5B 445551314 445552053 739 True 741.000000 741 84.7970 2770 3528 1 chr5B.!!$R2 758
30 TraesCS1B01G420700 chr5B 319881766 319882496 730 False 673.000000 673 83.3990 2770 3528 1 chr5B.!!$F1 758
31 TraesCS1B01G420700 chr5B 378909975 378910495 520 True 531.000000 531 86.3720 1 479 1 chr5B.!!$R1 478
32 TraesCS1B01G420700 chr7D 430935515 430936047 532 True 507.000000 507 83.9780 2990 3526 1 chr7D.!!$R1 536
33 TraesCS1B01G420700 chr6A 200242410 200243013 603 False 401.000000 401 79.0140 2907 3528 1 chr6A.!!$F1 621
34 TraesCS1B01G420700 chr5A 514777249 514777786 537 False 339.000000 339 78.5200 2918 3459 1 chr5A.!!$F1 541

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
504 547 0.254462 TCTGCATATTCACGCCCCAA 59.746 50.0 0.0 0.0 0.0 4.12 F
1712 4564 0.179108 CCCGATTCCCTCTTCGTCAC 60.179 60.0 0.0 0.0 33.6 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 4587 1.031235 TGAGTGTGTGGTGGCAATTG 58.969 50.0 0.00 0.00 0.0 2.32 R
3284 6350 1.364626 CTACGTCCGCGAGTAGGTGT 61.365 60.0 20.73 8.28 42.0 4.16 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
18 19 3.362262 CCGACGAGGTGGTCAAGA 58.638 61.111 0.00 0.00 36.73 3.02
60 61 1.615384 GCCTCATCCTGAACCAGCTTT 60.615 52.381 0.00 0.00 0.00 3.51
74 75 2.567049 CTTTCCTCGACGACGCCT 59.433 61.111 1.48 0.00 39.58 5.52
147 148 4.916293 GCCCGAGCGATGATGCCA 62.916 66.667 0.00 0.00 34.65 4.92
150 151 2.202919 CGAGCGATGATGCCACCA 60.203 61.111 0.00 0.00 34.65 4.17
180 211 1.837051 ACAGAGACCCCGTCAAGCA 60.837 57.895 0.00 0.00 34.60 3.91
280 311 2.268298 CCGAACTTTTCATCCGATCGT 58.732 47.619 15.09 0.00 0.00 3.73
304 335 2.437180 CTGCTGGCCGCTTGATCA 60.437 61.111 18.14 0.00 40.11 2.92
326 357 3.199677 CCGGATTGTGGCGTCTATTTTA 58.800 45.455 0.00 0.00 0.00 1.52
335 366 0.511221 CGTCTATTTTATGCGCGGGG 59.489 55.000 8.83 0.00 0.00 5.73
339 370 2.037902 TCTATTTTATGCGCGGGGATGA 59.962 45.455 16.80 5.46 0.00 2.92
340 371 1.686355 ATTTTATGCGCGGGGATGAA 58.314 45.000 16.80 11.79 0.00 2.57
441 483 4.050934 GGCTCGCCCCCGTTTTTG 62.051 66.667 0.00 0.00 35.54 2.44
479 522 1.035923 CGGCTGGAGATGCTCTAAGA 58.964 55.000 0.00 0.00 0.00 2.10
480 523 1.000385 CGGCTGGAGATGCTCTAAGAG 60.000 57.143 0.00 0.00 0.00 2.85
481 524 2.315176 GGCTGGAGATGCTCTAAGAGA 58.685 52.381 0.00 0.00 0.00 3.10
482 525 2.297033 GGCTGGAGATGCTCTAAGAGAG 59.703 54.545 4.34 4.34 45.04 3.20
483 526 2.958355 GCTGGAGATGCTCTAAGAGAGT 59.042 50.000 7.47 0.00 44.12 3.24
484 527 4.141287 GCTGGAGATGCTCTAAGAGAGTA 58.859 47.826 7.47 3.15 44.12 2.59
501 544 2.996621 GAGTATCTGCATATTCACGCCC 59.003 50.000 0.00 0.00 0.00 6.13
502 545 2.076863 GTATCTGCATATTCACGCCCC 58.923 52.381 0.00 0.00 0.00 5.80
503 546 0.473755 ATCTGCATATTCACGCCCCA 59.526 50.000 0.00 0.00 0.00 4.96
504 547 0.254462 TCTGCATATTCACGCCCCAA 59.746 50.000 0.00 0.00 0.00 4.12
505 548 0.664761 CTGCATATTCACGCCCCAAG 59.335 55.000 0.00 0.00 0.00 3.61
506 549 0.254462 TGCATATTCACGCCCCAAGA 59.746 50.000 0.00 0.00 0.00 3.02
507 550 1.133823 TGCATATTCACGCCCCAAGAT 60.134 47.619 0.00 0.00 0.00 2.40
508 551 2.105649 TGCATATTCACGCCCCAAGATA 59.894 45.455 0.00 0.00 0.00 1.98
509 552 3.244875 TGCATATTCACGCCCCAAGATAT 60.245 43.478 0.00 0.00 0.00 1.63
510 553 3.758554 GCATATTCACGCCCCAAGATATT 59.241 43.478 0.00 0.00 0.00 1.28
511 554 4.941263 GCATATTCACGCCCCAAGATATTA 59.059 41.667 0.00 0.00 0.00 0.98
512 555 5.163754 GCATATTCACGCCCCAAGATATTAC 60.164 44.000 0.00 0.00 0.00 1.89
513 556 2.519377 TCACGCCCCAAGATATTACG 57.481 50.000 0.00 0.00 0.00 3.18
514 557 1.758280 TCACGCCCCAAGATATTACGT 59.242 47.619 0.00 0.00 0.00 3.57
515 558 1.864711 CACGCCCCAAGATATTACGTG 59.135 52.381 0.00 0.00 42.59 4.49
516 559 1.758280 ACGCCCCAAGATATTACGTGA 59.242 47.619 0.00 0.00 0.00 4.35
517 560 2.168936 ACGCCCCAAGATATTACGTGAA 59.831 45.455 0.00 0.00 0.00 3.18
518 561 3.199677 CGCCCCAAGATATTACGTGAAA 58.800 45.455 0.00 0.00 0.00 2.69
519 562 3.247648 CGCCCCAAGATATTACGTGAAAG 59.752 47.826 0.00 0.00 0.00 2.62
520 563 4.448210 GCCCCAAGATATTACGTGAAAGA 58.552 43.478 0.00 0.00 0.00 2.52
521 564 4.879545 GCCCCAAGATATTACGTGAAAGAA 59.120 41.667 0.00 0.00 0.00 2.52
522 565 5.007724 GCCCCAAGATATTACGTGAAAGAAG 59.992 44.000 0.00 0.00 0.00 2.85
523 566 6.346096 CCCCAAGATATTACGTGAAAGAAGA 58.654 40.000 0.00 0.00 0.00 2.87
524 567 6.821665 CCCCAAGATATTACGTGAAAGAAGAA 59.178 38.462 0.00 0.00 0.00 2.52
525 568 7.335924 CCCCAAGATATTACGTGAAAGAAGAAA 59.664 37.037 0.00 0.00 0.00 2.52
526 569 8.391106 CCCAAGATATTACGTGAAAGAAGAAAG 58.609 37.037 0.00 0.00 0.00 2.62
527 570 9.151471 CCAAGATATTACGTGAAAGAAGAAAGA 57.849 33.333 0.00 0.00 0.00 2.52
533 576 8.888579 ATTACGTGAAAGAAGAAAGAAGAGAA 57.111 30.769 0.00 0.00 0.00 2.87
534 577 8.712285 TTACGTGAAAGAAGAAAGAAGAGAAA 57.288 30.769 0.00 0.00 0.00 2.52
535 578 7.006187 ACGTGAAAGAAGAAAGAAGAGAAAC 57.994 36.000 0.00 0.00 0.00 2.78
536 579 6.819146 ACGTGAAAGAAGAAAGAAGAGAAACT 59.181 34.615 0.00 0.00 0.00 2.66
537 580 7.980099 ACGTGAAAGAAGAAAGAAGAGAAACTA 59.020 33.333 0.00 0.00 0.00 2.24
538 581 8.818057 CGTGAAAGAAGAAAGAAGAGAAACTAA 58.182 33.333 0.00 0.00 0.00 2.24
548 591 9.657121 GAAAGAAGAGAAACTAAATCTGTGTTG 57.343 33.333 0.00 0.00 0.00 3.33
552 595 8.506168 AAGAGAAACTAAATCTGTGTTGAACA 57.494 30.769 0.00 0.00 37.22 3.18
585 628 3.654414 TCGAGAGCAAGGAAAAGTCTTC 58.346 45.455 0.00 0.00 0.00 2.87
601 644 3.133362 AGTCTTCTGTTTCCGTTACACCA 59.867 43.478 0.00 0.00 0.00 4.17
832 1210 4.893524 TCATGTCGCCTATATATACCAGGG 59.106 45.833 12.18 0.00 0.00 4.45
836 1214 3.454371 GCCTATATATACCAGGGCGTG 57.546 52.381 12.18 0.00 0.00 5.34
839 1217 4.021229 CCTATATATACCAGGGCGTGACA 58.979 47.826 9.09 0.00 0.00 3.58
892 1272 4.019174 CAGCTCCTCTCTTCTCTTCTCTT 58.981 47.826 0.00 0.00 0.00 2.85
899 1279 4.016444 TCTCTTCTCTTCTCTTCTGCTCC 58.984 47.826 0.00 0.00 0.00 4.70
900 1280 3.763360 CTCTTCTCTTCTCTTCTGCTCCA 59.237 47.826 0.00 0.00 0.00 3.86
903 1283 4.308526 TCTCTTCTCTTCTGCTCCACTA 57.691 45.455 0.00 0.00 0.00 2.74
906 1299 4.348486 TCTTCTCTTCTGCTCCACTACAT 58.652 43.478 0.00 0.00 0.00 2.29
914 1307 2.501723 CTGCTCCACTACATACCAGGTT 59.498 50.000 0.00 0.00 0.00 3.50
916 1309 2.766828 GCTCCACTACATACCAGGTTCT 59.233 50.000 0.00 0.00 0.00 3.01
919 1312 4.023980 TCCACTACATACCAGGTTCTCTG 58.976 47.826 0.00 0.00 43.00 3.35
923 1316 5.869888 CACTACATACCAGGTTCTCTGTTTC 59.130 44.000 0.00 0.00 41.83 2.78
927 1320 1.151668 CCAGGTTCTCTGTTTCGCTG 58.848 55.000 0.00 0.00 41.83 5.18
929 1322 0.759346 AGGTTCTCTGTTTCGCTGGT 59.241 50.000 0.00 0.00 0.00 4.00
935 1328 4.371855 TCTCTGTTTCGCTGGTACATAG 57.628 45.455 0.00 0.00 38.20 2.23
937 1330 2.496070 TCTGTTTCGCTGGTACATAGCT 59.504 45.455 16.29 0.00 38.20 3.32
938 1331 3.697542 TCTGTTTCGCTGGTACATAGCTA 59.302 43.478 16.29 0.00 38.20 3.32
939 1332 4.341235 TCTGTTTCGCTGGTACATAGCTAT 59.659 41.667 16.29 0.00 38.20 2.97
940 1333 5.533528 TCTGTTTCGCTGGTACATAGCTATA 59.466 40.000 5.77 0.00 38.20 1.31
941 1334 6.208797 TCTGTTTCGCTGGTACATAGCTATAT 59.791 38.462 5.77 0.00 38.20 0.86
942 1335 7.392393 TCTGTTTCGCTGGTACATAGCTATATA 59.608 37.037 5.77 0.00 38.20 0.86
943 1336 7.310664 TGTTTCGCTGGTACATAGCTATATAC 58.689 38.462 12.87 12.87 38.20 1.47
944 1337 7.040271 TGTTTCGCTGGTACATAGCTATATACA 60.040 37.037 20.81 10.68 38.20 2.29
945 1338 7.457024 TTCGCTGGTACATAGCTATATACAA 57.543 36.000 20.81 11.11 38.20 2.41
949 1342 7.484975 GCTGGTACATAGCTATATACAAGGAG 58.515 42.308 22.53 13.65 38.20 3.69
963 1356 1.597989 AGGAGCTGCTCTGCTTCAG 59.402 57.895 27.09 0.00 40.95 3.02
1191 1600 3.626924 GCCACCCTCACGGACACT 61.627 66.667 0.00 0.00 34.64 3.55
1712 4564 0.179108 CCCGATTCCCTCTTCGTCAC 60.179 60.000 0.00 0.00 33.60 3.67
1735 4587 4.377263 GGGACTCCCTCCAGGTAC 57.623 66.667 6.90 0.00 41.63 3.34
1736 4588 1.390926 GGGACTCCCTCCAGGTACA 59.609 63.158 6.90 0.00 41.63 2.90
1797 4717 3.710209 CCATTCATCTACCTGGGATCC 57.290 52.381 1.92 1.92 0.00 3.36
1798 4718 2.981784 CCATTCATCTACCTGGGATCCA 59.018 50.000 15.23 0.00 0.00 3.41
1799 4719 3.590630 CCATTCATCTACCTGGGATCCAT 59.409 47.826 15.23 0.00 30.82 3.41
1800 4720 4.567116 CCATTCATCTACCTGGGATCCATG 60.567 50.000 15.23 6.86 30.82 3.66
1866 4811 2.222007 TTGGCATGGCGCATTATTTC 57.778 45.000 15.27 0.00 45.17 2.17
2310 5331 0.972983 CGGGAGAAGGAGAAGGAGCA 60.973 60.000 0.00 0.00 0.00 4.26
2317 5338 0.472734 AGGAGAAGGAGCACCAGTGT 60.473 55.000 2.07 0.00 38.94 3.55
2557 5579 6.520790 GGTTAACGTAATGTTTGGACGAATTC 59.479 38.462 0.00 0.00 42.09 2.17
2767 5794 0.178068 GGCTGGAGATGCCGTTAGAA 59.822 55.000 0.00 0.00 41.03 2.10
2768 5795 1.202698 GGCTGGAGATGCCGTTAGAAT 60.203 52.381 0.00 0.00 41.03 2.40
2769 5796 2.037251 GGCTGGAGATGCCGTTAGAATA 59.963 50.000 0.00 0.00 41.03 1.75
2770 5797 3.307059 GGCTGGAGATGCCGTTAGAATAT 60.307 47.826 0.00 0.00 41.03 1.28
2771 5798 3.929610 GCTGGAGATGCCGTTAGAATATC 59.070 47.826 0.00 0.00 40.66 1.63
2772 5799 4.322349 GCTGGAGATGCCGTTAGAATATCT 60.322 45.833 0.00 0.00 40.66 1.98
2846 5877 1.476845 TAGTTTGGCGTCTGGAGGCA 61.477 55.000 15.47 0.50 43.38 4.75
2898 5929 1.337447 CCCTGAGTTCGGCGAAAACTA 60.337 52.381 25.48 10.13 37.10 2.24
2899 5930 1.725164 CCTGAGTTCGGCGAAAACTAC 59.275 52.381 25.48 12.47 37.10 2.73
2900 5931 1.725164 CTGAGTTCGGCGAAAACTACC 59.275 52.381 25.48 10.77 37.10 3.18
3008 6054 0.822532 ACTACGCCGCTAGCCACTAT 60.823 55.000 9.66 0.00 38.78 2.12
3010 6056 1.848932 TACGCCGCTAGCCACTATCG 61.849 60.000 9.66 6.29 38.78 2.92
3056 6107 1.616374 GCCGAGAAGCCTATAGAAGCT 59.384 52.381 0.00 0.00 42.40 3.74
3207 6273 0.889306 CCTCTTCCTCCTCGTCGTTT 59.111 55.000 0.00 0.00 0.00 3.60
3233 6299 2.892425 GATGACGCCGCCCTCTTG 60.892 66.667 0.00 0.00 0.00 3.02
3380 6446 3.458163 CGGCTTCACGGGGAGCTA 61.458 66.667 19.58 0.00 0.00 3.32
3410 6476 4.452733 CTTCGACCGGACCAGGCC 62.453 72.222 9.46 0.00 33.69 5.19
3460 6529 3.247056 TTGATGACGAGGGCGCCAA 62.247 57.895 30.85 7.45 42.48 4.52
3493 6562 3.001514 GCTGGGGCATCTCCTTCA 58.998 61.111 0.00 0.00 38.54 3.02
3499 6568 0.106521 GGGCATCTCCTTCAGCTCTC 59.893 60.000 0.00 0.00 34.39 3.20
3504 6573 2.130272 TCTCCTTCAGCTCTCGCTTA 57.870 50.000 0.00 0.00 46.47 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.069513 CCAAGTACCACGTCTTGACCA 59.930 52.381 14.41 0.00 42.22 4.02
18 19 2.032634 CATGCGCCAAGTACCACGT 61.033 57.895 4.18 0.00 0.00 4.49
147 148 3.832237 CTGTGCGGGCAGTCTTGGT 62.832 63.158 0.00 0.00 0.00 3.67
150 151 2.210013 TCTCTGTGCGGGCAGTCTT 61.210 57.895 0.00 0.00 37.70 3.01
304 335 0.539986 AATAGACGCCACAATCCGGT 59.460 50.000 0.00 0.00 0.00 5.28
326 357 1.667830 CGTATTCATCCCCGCGCAT 60.668 57.895 8.75 0.00 0.00 4.73
335 366 5.003402 CACGGCAAATTCAAACGTATTCATC 59.997 40.000 0.00 0.00 35.85 2.92
339 370 3.570559 CCACGGCAAATTCAAACGTATT 58.429 40.909 0.00 0.00 35.85 1.89
340 371 2.669950 GCCACGGCAAATTCAAACGTAT 60.670 45.455 2.36 0.00 41.49 3.06
479 522 3.306364 GGGCGTGAATATGCAGATACTCT 60.306 47.826 0.00 0.00 40.68 3.24
480 523 2.996621 GGGCGTGAATATGCAGATACTC 59.003 50.000 0.00 0.00 40.68 2.59
481 524 2.289694 GGGGCGTGAATATGCAGATACT 60.290 50.000 0.00 0.00 40.68 2.12
482 525 2.076863 GGGGCGTGAATATGCAGATAC 58.923 52.381 0.00 0.00 40.68 2.24
483 526 1.696884 TGGGGCGTGAATATGCAGATA 59.303 47.619 0.00 0.00 40.68 1.98
484 527 0.473755 TGGGGCGTGAATATGCAGAT 59.526 50.000 0.00 0.00 40.68 2.90
485 528 0.254462 TTGGGGCGTGAATATGCAGA 59.746 50.000 0.00 0.00 40.68 4.26
486 529 0.664761 CTTGGGGCGTGAATATGCAG 59.335 55.000 0.00 0.00 40.68 4.41
487 530 0.254462 TCTTGGGGCGTGAATATGCA 59.746 50.000 0.00 0.00 40.68 3.96
488 531 1.609208 ATCTTGGGGCGTGAATATGC 58.391 50.000 0.00 0.00 38.12 3.14
489 532 5.063438 CGTAATATCTTGGGGCGTGAATATG 59.937 44.000 0.00 0.00 0.00 1.78
490 533 5.175859 CGTAATATCTTGGGGCGTGAATAT 58.824 41.667 0.00 0.00 0.00 1.28
491 534 4.039488 ACGTAATATCTTGGGGCGTGAATA 59.961 41.667 0.00 0.00 0.00 1.75
492 535 3.181458 ACGTAATATCTTGGGGCGTGAAT 60.181 43.478 0.00 0.00 0.00 2.57
493 536 2.168936 ACGTAATATCTTGGGGCGTGAA 59.831 45.455 0.00 0.00 0.00 3.18
494 537 1.758280 ACGTAATATCTTGGGGCGTGA 59.242 47.619 0.00 0.00 0.00 4.35
495 538 1.864711 CACGTAATATCTTGGGGCGTG 59.135 52.381 0.00 0.00 41.26 5.34
496 539 1.758280 TCACGTAATATCTTGGGGCGT 59.242 47.619 0.00 0.00 0.00 5.68
497 540 2.519377 TCACGTAATATCTTGGGGCG 57.481 50.000 0.00 0.00 0.00 6.13
498 541 4.448210 TCTTTCACGTAATATCTTGGGGC 58.552 43.478 0.00 0.00 0.00 5.80
499 542 6.346096 TCTTCTTTCACGTAATATCTTGGGG 58.654 40.000 0.00 0.00 0.00 4.96
500 543 7.843490 TTCTTCTTTCACGTAATATCTTGGG 57.157 36.000 0.00 0.00 0.00 4.12
501 544 9.151471 TCTTTCTTCTTTCACGTAATATCTTGG 57.849 33.333 0.00 0.00 0.00 3.61
507 550 9.976511 TTCTCTTCTTTCTTCTTTCACGTAATA 57.023 29.630 0.00 0.00 0.00 0.98
508 551 8.888579 TTCTCTTCTTTCTTCTTTCACGTAAT 57.111 30.769 0.00 0.00 0.00 1.89
509 552 8.601476 GTTTCTCTTCTTTCTTCTTTCACGTAA 58.399 33.333 0.00 0.00 0.00 3.18
510 553 7.980099 AGTTTCTCTTCTTTCTTCTTTCACGTA 59.020 33.333 0.00 0.00 0.00 3.57
511 554 6.819146 AGTTTCTCTTCTTTCTTCTTTCACGT 59.181 34.615 0.00 0.00 0.00 4.49
512 555 7.240414 AGTTTCTCTTCTTTCTTCTTTCACG 57.760 36.000 0.00 0.00 0.00 4.35
520 563 9.620259 ACACAGATTTAGTTTCTCTTCTTTCTT 57.380 29.630 0.00 0.00 0.00 2.52
521 564 9.620259 AACACAGATTTAGTTTCTCTTCTTTCT 57.380 29.630 0.00 0.00 0.00 2.52
522 565 9.657121 CAACACAGATTTAGTTTCTCTTCTTTC 57.343 33.333 0.00 0.00 0.00 2.62
523 566 9.396022 TCAACACAGATTTAGTTTCTCTTCTTT 57.604 29.630 0.00 0.00 0.00 2.52
524 567 8.964476 TCAACACAGATTTAGTTTCTCTTCTT 57.036 30.769 0.00 0.00 0.00 2.52
525 568 8.831550 GTTCAACACAGATTTAGTTTCTCTTCT 58.168 33.333 0.00 0.00 0.00 2.85
526 569 8.612619 TGTTCAACACAGATTTAGTTTCTCTTC 58.387 33.333 0.00 0.00 0.00 2.87
527 570 8.506168 TGTTCAACACAGATTTAGTTTCTCTT 57.494 30.769 0.00 0.00 0.00 2.85
564 607 3.322254 AGAAGACTTTTCCTTGCTCTCGA 59.678 43.478 0.00 0.00 0.00 4.04
585 628 5.172411 CGAATTTTTGGTGTAACGGAAACAG 59.828 40.000 0.00 0.00 38.12 3.16
601 644 1.516169 GCATCCGCGCCGAATTTTT 60.516 52.632 0.00 0.00 0.00 1.94
693 765 1.476488 TCAGAGCAAGCTACGTGCATA 59.524 47.619 11.29 0.00 44.74 3.14
832 1210 1.080772 TCATCTGACGGTGTCACGC 60.081 57.895 0.00 0.00 37.67 5.34
836 1214 0.317160 TGTGGTCATCTGACGGTGTC 59.683 55.000 4.36 0.00 45.65 3.67
839 1217 1.048601 AGTTGTGGTCATCTGACGGT 58.951 50.000 4.36 0.00 45.65 4.83
892 1272 2.292257 ACCTGGTATGTAGTGGAGCAGA 60.292 50.000 0.00 0.00 40.36 4.26
899 1279 5.794894 AAACAGAGAACCTGGTATGTAGTG 58.205 41.667 0.00 0.00 43.32 2.74
900 1280 5.336531 CGAAACAGAGAACCTGGTATGTAGT 60.337 44.000 0.00 0.00 43.32 2.73
903 1283 3.864921 GCGAAACAGAGAACCTGGTATGT 60.865 47.826 0.00 0.24 43.32 2.29
906 1299 1.968493 AGCGAAACAGAGAACCTGGTA 59.032 47.619 0.00 0.00 43.32 3.25
914 1307 3.428999 GCTATGTACCAGCGAAACAGAGA 60.429 47.826 9.37 0.00 35.07 3.10
916 1309 2.496070 AGCTATGTACCAGCGAAACAGA 59.504 45.455 10.05 0.00 43.97 3.41
919 1312 7.310664 TGTATATAGCTATGTACCAGCGAAAC 58.689 38.462 27.89 11.12 43.97 2.78
923 1316 6.095021 TCCTTGTATATAGCTATGTACCAGCG 59.905 42.308 27.89 21.04 43.97 5.18
927 1320 7.484975 CAGCTCCTTGTATATAGCTATGTACC 58.515 42.308 27.89 16.42 43.26 3.34
929 1322 6.892456 AGCAGCTCCTTGTATATAGCTATGTA 59.108 38.462 16.77 11.24 43.26 2.29
935 1328 4.493547 CAGAGCAGCTCCTTGTATATAGC 58.506 47.826 19.40 0.00 35.16 2.97
937 1330 4.155709 AGCAGAGCAGCTCCTTGTATATA 58.844 43.478 19.40 0.00 42.18 0.86
938 1331 2.971330 AGCAGAGCAGCTCCTTGTATAT 59.029 45.455 19.40 0.00 42.18 0.86
939 1332 2.392662 AGCAGAGCAGCTCCTTGTATA 58.607 47.619 19.40 0.00 42.18 1.47
940 1333 1.202330 AGCAGAGCAGCTCCTTGTAT 58.798 50.000 19.40 2.66 42.18 2.29
941 1334 0.979665 AAGCAGAGCAGCTCCTTGTA 59.020 50.000 19.40 0.00 45.89 2.41
942 1335 0.321475 GAAGCAGAGCAGCTCCTTGT 60.321 55.000 19.40 2.25 45.89 3.16
943 1336 0.321387 TGAAGCAGAGCAGCTCCTTG 60.321 55.000 19.40 12.73 45.89 3.61
944 1337 0.036199 CTGAAGCAGAGCAGCTCCTT 60.036 55.000 19.40 15.44 45.89 3.36
945 1338 1.193462 ACTGAAGCAGAGCAGCTCCT 61.193 55.000 19.40 7.09 45.89 3.69
949 1342 2.021355 ATGTACTGAAGCAGAGCAGC 57.979 50.000 0.82 0.00 35.57 5.25
963 1356 0.935366 GCAGAGCGCCTCGTATGTAC 60.935 60.000 2.29 0.00 35.36 2.90
1735 4587 1.031235 TGAGTGTGTGGTGGCAATTG 58.969 50.000 0.00 0.00 0.00 2.32
1736 4588 1.032014 GTGAGTGTGTGGTGGCAATT 58.968 50.000 0.00 0.00 0.00 2.32
1797 4717 2.819154 TGCGCGTCCATGGACATG 60.819 61.111 37.42 29.84 44.77 3.21
1798 4718 2.819595 GTGCGCGTCCATGGACAT 60.820 61.111 37.42 0.00 44.77 3.06
1822 4742 4.400251 CCAGACCAAAACATACATCTGCAT 59.600 41.667 0.00 0.00 33.71 3.96
1823 4743 3.758023 CCAGACCAAAACATACATCTGCA 59.242 43.478 0.00 0.00 33.71 4.41
1824 4744 3.758554 ACCAGACCAAAACATACATCTGC 59.241 43.478 0.00 0.00 33.71 4.26
1825 4745 5.964958 AACCAGACCAAAACATACATCTG 57.035 39.130 0.00 0.00 34.62 2.90
1826 4746 5.243730 CCAAACCAGACCAAAACATACATCT 59.756 40.000 0.00 0.00 0.00 2.90
1827 4747 5.469479 CCAAACCAGACCAAAACATACATC 58.531 41.667 0.00 0.00 0.00 3.06
1828 4748 4.262420 GCCAAACCAGACCAAAACATACAT 60.262 41.667 0.00 0.00 0.00 2.29
1829 4749 3.068873 GCCAAACCAGACCAAAACATACA 59.931 43.478 0.00 0.00 0.00 2.29
1830 4750 3.068873 TGCCAAACCAGACCAAAACATAC 59.931 43.478 0.00 0.00 0.00 2.39
1831 4751 3.300388 TGCCAAACCAGACCAAAACATA 58.700 40.909 0.00 0.00 0.00 2.29
2060 5078 4.508861 CAGCACCTGAAATTCACCAAAAAG 59.491 41.667 0.00 0.00 32.44 2.27
2154 5175 2.915659 ACTCCGTCTTCACCGGCA 60.916 61.111 0.00 0.00 45.09 5.69
2310 5331 4.016706 GTAGGGCGGCACACTGGT 62.017 66.667 12.47 0.00 0.00 4.00
2557 5579 2.179018 CATGGCAAGTTTCGGCGG 59.821 61.111 7.21 0.00 0.00 6.13
2761 5788 3.982058 CCGAACGGCTGAGATATTCTAAC 59.018 47.826 0.00 0.00 0.00 2.34
2899 5930 5.006358 CCGATTTTAAACCAGATCTACGTGG 59.994 44.000 0.00 0.00 39.98 4.94
2900 5931 5.501897 GCCGATTTTAAACCAGATCTACGTG 60.502 44.000 0.00 0.00 0.00 4.49
2988 6034 1.442526 TAGTGGCTAGCGGCGTAGTC 61.443 60.000 9.37 11.14 42.94 2.59
3284 6350 1.364626 CTACGTCCGCGAGTAGGTGT 61.365 60.000 20.73 8.28 42.00 4.16
3410 6476 4.521062 CCTCCTCGCGCTCCCTTG 62.521 72.222 5.56 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.