Multiple sequence alignment - TraesCS7A01G143000

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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 TraesCS7A01G143000 chr7A 100.000 4032 0 0 1 4032 94393040 94397071 0.000000e+00 7446.0
1 TraesCS7A01G143000 chr7A 81.106 1085 158 30 2960 4005 93141753 93140677 0.000000e+00 824.0
2 TraesCS7A01G143000 chr7A 92.473 558 15 7 1 555 251802139 251801606 0.000000e+00 773.0
3 TraesCS7A01G143000 chr7A 92.000 550 23 8 8 555 474199899 474199369 0.000000e+00 752.0
4 TraesCS7A01G143000 chr7A 91.871 529 17 5 34 555 579317190 579317699 0.000000e+00 715.0
5 TraesCS7A01G143000 chr7A 90.070 574 19 7 1 555 154373337 154373891 0.000000e+00 710.0
6 TraesCS7A01G143000 chr7A 89.161 572 26 9 1 555 657148100 657147548 0.000000e+00 680.0
7 TraesCS7A01G143000 chr7A 89.408 557 25 16 1 555 111940695 111941219 0.000000e+00 671.0
8 TraesCS7A01G143000 chr7A 78.134 686 111 22 2957 3639 94376672 94377321 2.260000e-107 399.0
9 TraesCS7A01G143000 chr7A 85.333 300 37 3 2485 2780 94376328 94376624 1.820000e-78 303.0
10 TraesCS7A01G143000 chr7A 84.211 152 22 2 3636 3786 94382589 94382739 3.250000e-31 147.0
11 TraesCS7A01G143000 chr7B 93.629 1083 43 7 2066 3127 44268603 44269680 0.000000e+00 1594.0
12 TraesCS7A01G143000 chr7B 84.693 1091 134 9 979 2039 44265718 44266805 0.000000e+00 1059.0
13 TraesCS7A01G143000 chr7B 84.947 950 135 6 1027 1975 577306014 577305072 0.000000e+00 955.0
14 TraesCS7A01G143000 chr7B 94.943 435 20 1 3600 4032 44270289 44270723 0.000000e+00 680.0
15 TraesCS7A01G143000 chr7B 80.367 871 122 32 2855 3705 43268532 43269373 2.060000e-172 616.0
16 TraesCS7A01G143000 chr7B 78.643 899 136 32 2897 3786 44256216 44257067 2.740000e-151 545.0
17 TraesCS7A01G143000 chr7B 95.172 290 14 0 3125 3414 44270005 44270294 3.670000e-125 459.0
18 TraesCS7A01G143000 chr7B 80.330 666 76 24 2161 2780 44255539 44256195 1.710000e-123 453.0
19 TraesCS7A01G143000 chr7B 88.127 379 35 8 561 938 44265260 44265629 3.700000e-120 442.0
20 TraesCS7A01G143000 chr7B 85.464 399 54 4 1642 2039 607933118 607932723 2.900000e-111 412.0
21 TraesCS7A01G143000 chr7B 78.814 236 39 7 3554 3782 43547832 43548063 9.030000e-32 148.0
22 TraesCS7A01G143000 chr7B 89.286 112 10 2 557 668 508821717 508821826 5.430000e-29 139.0
23 TraesCS7A01G143000 chr3D 86.876 1021 98 9 983 1971 308983452 308984468 0.000000e+00 1110.0
24 TraesCS7A01G143000 chr3D 86.836 433 53 4 1547 1977 587300077 587300507 7.840000e-132 481.0
25 TraesCS7A01G143000 chr3D 82.824 262 39 6 721 979 354265075 354265333 3.130000e-56 230.0
26 TraesCS7A01G143000 chr3D 77.586 232 45 7 723 951 120721734 120721507 2.530000e-27 134.0
27 TraesCS7A01G143000 chr3D 78.286 175 23 9 792 965 347448872 347448712 9.220000e-17 99.0
28 TraesCS7A01G143000 chr7D 84.757 1030 143 6 998 2016 560226396 560225370 0.000000e+00 1020.0
29 TraesCS7A01G143000 chr7D 80.463 1080 165 32 2960 4002 91664677 91663607 0.000000e+00 784.0
30 TraesCS7A01G143000 chr7D 80.229 698 95 22 2145 2808 92226646 92227334 6.060000e-133 484.0
31 TraesCS7A01G143000 chr7D 74.561 456 73 24 2957 3403 92227357 92227778 4.170000e-35 159.0
32 TraesCS7A01G143000 chr1A 85.050 1010 132 10 982 1976 588201038 588200033 0.000000e+00 1011.0
33 TraesCS7A01G143000 chr1A 84.851 1010 134 10 982 1976 588164907 588163902 0.000000e+00 1000.0
34 TraesCS7A01G143000 chr1A 84.851 1010 134 10 982 1976 588217362 588216357 0.000000e+00 1000.0
35 TraesCS7A01G143000 chr1A 92.101 557 23 8 1 555 145898812 145898275 0.000000e+00 765.0
36 TraesCS7A01G143000 chr1A 88.112 429 14 4 1 412 477703273 477703681 3.650000e-130 475.0
37 TraesCS7A01G143000 chr3B 82.369 1089 149 16 974 2039 677288631 677287563 0.000000e+00 907.0
38 TraesCS7A01G143000 chr3B 84.832 745 112 1 982 1725 2261057 2260313 0.000000e+00 749.0
39 TraesCS7A01G143000 chr5B 81.509 1087 164 14 982 2039 470644131 470643053 0.000000e+00 859.0
40 TraesCS7A01G143000 chr5B 81.467 259 41 7 725 979 428133887 428134142 5.280000e-49 206.0
41 TraesCS7A01G143000 chr5B 92.381 105 8 0 557 661 586860070 586860174 2.510000e-32 150.0
42 TraesCS7A01G143000 chr5B 96.667 60 2 0 2460 2519 466985211 466985152 2.560000e-17 100.0
43 TraesCS7A01G143000 chr2B 81.444 1094 159 19 974 2039 40817804 40818881 0.000000e+00 856.0
44 TraesCS7A01G143000 chr2B 87.149 249 32 0 722 970 57782905 57783153 2.370000e-72 283.0
45 TraesCS7A01G143000 chr2B 82.320 181 30 2 725 904 245826116 245826295 5.400000e-34 156.0
46 TraesCS7A01G143000 chr2B 91.667 108 9 0 557 664 65070069 65069962 2.510000e-32 150.0
47 TraesCS7A01G143000 chr5D 81.545 1100 142 21 974 2039 510473271 510472199 0.000000e+00 850.0
48 TraesCS7A01G143000 chr5D 84.115 768 92 8 982 1719 452362920 452363687 0.000000e+00 715.0
49 TraesCS7A01G143000 chr5D 82.904 427 64 9 2358 2780 388337981 388337560 3.800000e-100 375.0
50 TraesCS7A01G143000 chr5D 89.091 110 12 0 557 666 517672557 517672448 1.950000e-28 137.0
51 TraesCS7A01G143000 chr5D 89.720 107 9 1 557 661 495464902 495464796 7.030000e-28 135.0
52 TraesCS7A01G143000 chr2D 81.543 1089 142 16 982 2039 591700442 591699382 0.000000e+00 843.0
53 TraesCS7A01G143000 chr2D 82.143 616 73 18 1456 2039 73208690 73208080 1.010000e-135 494.0
54 TraesCS7A01G143000 chr2D 91.667 108 9 0 557 664 608522616 608522509 2.510000e-32 150.0
55 TraesCS7A01G143000 chr2A 82.998 894 129 12 1033 1925 498589457 498588586 0.000000e+00 787.0
56 TraesCS7A01G143000 chr2A 92.557 524 18 4 34 555 668911970 668912474 0.000000e+00 732.0
57 TraesCS7A01G143000 chr4A 80.857 1050 154 24 1016 2039 601131923 601132951 0.000000e+00 782.0
58 TraesCS7A01G143000 chr4A 91.297 563 22 6 1 555 54409600 54410143 0.000000e+00 743.0
59 TraesCS7A01G143000 chr4A 91.697 542 22 10 16 553 6440371 6439849 0.000000e+00 730.0
60 TraesCS7A01G143000 chr4A 76.842 190 43 1 722 910 619407003 619406814 5.510000e-19 106.0
61 TraesCS7A01G143000 chr3A 92.115 558 23 12 1 556 749256477 749255939 0.000000e+00 767.0
62 TraesCS7A01G143000 chr3A 84.231 520 67 10 1531 2039 30541971 30542486 3.620000e-135 492.0
63 TraesCS7A01G143000 chr6A 91.993 562 18 12 2 555 549437656 549438198 0.000000e+00 763.0
64 TraesCS7A01G143000 chr6A 87.826 575 31 14 1 555 52690983 52691538 4.390000e-179 638.0
65 TraesCS7A01G143000 chr6A 86.667 105 14 0 557 661 480628434 480628538 2.550000e-22 117.0
66 TraesCS7A01G143000 chr5A 91.906 556 16 7 1 556 457428920 457429446 0.000000e+00 750.0
67 TraesCS7A01G143000 chr5A 90.861 569 16 12 4 555 73750965 73750416 0.000000e+00 730.0
68 TraesCS7A01G143000 chr5A 93.202 456 22 4 109 555 315471662 315472117 0.000000e+00 662.0
69 TraesCS7A01G143000 chr5A 82.824 425 68 5 2358 2780 491375760 491375339 3.800000e-100 375.0
70 TraesCS7A01G143000 chr5A 82.182 275 40 5 718 990 693133711 693133444 1.130000e-55 228.0
71 TraesCS7A01G143000 chr5A 80.546 293 53 3 3418 3708 491374103 491373813 5.250000e-54 222.0
72 TraesCS7A01G143000 chr6B 84.718 746 103 3 982 1718 695478591 695477848 0.000000e+00 736.0
73 TraesCS7A01G143000 chr6B 78.947 209 41 2 721 929 488887150 488886945 5.430000e-29 139.0
74 TraesCS7A01G143000 chr1B 82.692 260 33 6 723 982 662247698 662247451 1.890000e-53 220.0
75 TraesCS7A01G143000 chr1B 90.741 108 9 1 557 664 684111659 684111553 4.200000e-30 143.0
76 TraesCS7A01G143000 chr4B 90.566 106 8 2 557 661 99042250 99042354 5.430000e-29 139.0
77 TraesCS7A01G143000 chr4B 89.623 106 9 2 557 661 99050413 99050517 2.530000e-27 134.0
78 TraesCS7A01G143000 chr4B 88.991 109 10 2 557 664 574057515 574057622 2.530000e-27 134.0
79 TraesCS7A01G143000 chr1D 75.490 204 47 3 721 923 341808444 341808645 3.320000e-16 97.1
80 TraesCS7A01G143000 chrUn 80.583 103 17 3 792 894 317325574 317325475 4.320000e-10 76.8
81 TraesCS7A01G143000 chrUn 80.583 103 17 3 792 894 393157479 393157380 4.320000e-10 76.8
82 TraesCS7A01G143000 chr4D 87.500 64 8 0 557 620 108225011 108225074 1.550000e-09 75.0


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 TraesCS7A01G143000 chr7A 94393040 94397071 4031 False 7446.0 7446 100.0000 1 4032 1 chr7A.!!$F2 4031
1 TraesCS7A01G143000 chr7A 93140677 93141753 1076 True 824.0 824 81.1060 2960 4005 1 chr7A.!!$R1 1045
2 TraesCS7A01G143000 chr7A 251801606 251802139 533 True 773.0 773 92.4730 1 555 1 chr7A.!!$R2 554
3 TraesCS7A01G143000 chr7A 474199369 474199899 530 True 752.0 752 92.0000 8 555 1 chr7A.!!$R3 547
4 TraesCS7A01G143000 chr7A 579317190 579317699 509 False 715.0 715 91.8710 34 555 1 chr7A.!!$F5 521
5 TraesCS7A01G143000 chr7A 154373337 154373891 554 False 710.0 710 90.0700 1 555 1 chr7A.!!$F4 554
6 TraesCS7A01G143000 chr7A 657147548 657148100 552 True 680.0 680 89.1610 1 555 1 chr7A.!!$R4 554
7 TraesCS7A01G143000 chr7A 111940695 111941219 524 False 671.0 671 89.4080 1 555 1 chr7A.!!$F3 554
8 TraesCS7A01G143000 chr7A 94376328 94377321 993 False 351.0 399 81.7335 2485 3639 2 chr7A.!!$F6 1154
9 TraesCS7A01G143000 chr7B 577305072 577306014 942 True 955.0 955 84.9470 1027 1975 1 chr7B.!!$R1 948
10 TraesCS7A01G143000 chr7B 44265260 44270723 5463 False 846.8 1594 91.3128 561 4032 5 chr7B.!!$F5 3471
11 TraesCS7A01G143000 chr7B 43268532 43269373 841 False 616.0 616 80.3670 2855 3705 1 chr7B.!!$F1 850
12 TraesCS7A01G143000 chr7B 44255539 44257067 1528 False 499.0 545 79.4865 2161 3786 2 chr7B.!!$F4 1625
13 TraesCS7A01G143000 chr3D 308983452 308984468 1016 False 1110.0 1110 86.8760 983 1971 1 chr3D.!!$F1 988
14 TraesCS7A01G143000 chr7D 560225370 560226396 1026 True 1020.0 1020 84.7570 998 2016 1 chr7D.!!$R2 1018
15 TraesCS7A01G143000 chr7D 91663607 91664677 1070 True 784.0 784 80.4630 2960 4002 1 chr7D.!!$R1 1042
16 TraesCS7A01G143000 chr7D 92226646 92227778 1132 False 321.5 484 77.3950 2145 3403 2 chr7D.!!$F1 1258
17 TraesCS7A01G143000 chr1A 588200033 588201038 1005 True 1011.0 1011 85.0500 982 1976 1 chr1A.!!$R3 994
18 TraesCS7A01G143000 chr1A 588163902 588164907 1005 True 1000.0 1000 84.8510 982 1976 1 chr1A.!!$R2 994
19 TraesCS7A01G143000 chr1A 588216357 588217362 1005 True 1000.0 1000 84.8510 982 1976 1 chr1A.!!$R4 994
20 TraesCS7A01G143000 chr1A 145898275 145898812 537 True 765.0 765 92.1010 1 555 1 chr1A.!!$R1 554
21 TraesCS7A01G143000 chr3B 677287563 677288631 1068 True 907.0 907 82.3690 974 2039 1 chr3B.!!$R2 1065
22 TraesCS7A01G143000 chr3B 2260313 2261057 744 True 749.0 749 84.8320 982 1725 1 chr3B.!!$R1 743
23 TraesCS7A01G143000 chr5B 470643053 470644131 1078 True 859.0 859 81.5090 982 2039 1 chr5B.!!$R2 1057
24 TraesCS7A01G143000 chr2B 40817804 40818881 1077 False 856.0 856 81.4440 974 2039 1 chr2B.!!$F1 1065
25 TraesCS7A01G143000 chr5D 510472199 510473271 1072 True 850.0 850 81.5450 974 2039 1 chr5D.!!$R3 1065
26 TraesCS7A01G143000 chr5D 452362920 452363687 767 False 715.0 715 84.1150 982 1719 1 chr5D.!!$F1 737
27 TraesCS7A01G143000 chr2D 591699382 591700442 1060 True 843.0 843 81.5430 982 2039 1 chr2D.!!$R2 1057
28 TraesCS7A01G143000 chr2D 73208080 73208690 610 True 494.0 494 82.1430 1456 2039 1 chr2D.!!$R1 583
29 TraesCS7A01G143000 chr2A 498588586 498589457 871 True 787.0 787 82.9980 1033 1925 1 chr2A.!!$R1 892
30 TraesCS7A01G143000 chr2A 668911970 668912474 504 False 732.0 732 92.5570 34 555 1 chr2A.!!$F1 521
31 TraesCS7A01G143000 chr4A 601131923 601132951 1028 False 782.0 782 80.8570 1016 2039 1 chr4A.!!$F2 1023
32 TraesCS7A01G143000 chr4A 54409600 54410143 543 False 743.0 743 91.2970 1 555 1 chr4A.!!$F1 554
33 TraesCS7A01G143000 chr4A 6439849 6440371 522 True 730.0 730 91.6970 16 553 1 chr4A.!!$R1 537
34 TraesCS7A01G143000 chr3A 749255939 749256477 538 True 767.0 767 92.1150 1 556 1 chr3A.!!$R1 555
35 TraesCS7A01G143000 chr3A 30541971 30542486 515 False 492.0 492 84.2310 1531 2039 1 chr3A.!!$F1 508
36 TraesCS7A01G143000 chr6A 549437656 549438198 542 False 763.0 763 91.9930 2 555 1 chr6A.!!$F3 553
37 TraesCS7A01G143000 chr6A 52690983 52691538 555 False 638.0 638 87.8260 1 555 1 chr6A.!!$F1 554
38 TraesCS7A01G143000 chr5A 457428920 457429446 526 False 750.0 750 91.9060 1 556 1 chr5A.!!$F2 555
39 TraesCS7A01G143000 chr5A 73750416 73750965 549 True 730.0 730 90.8610 4 555 1 chr5A.!!$R1 551
40 TraesCS7A01G143000 chr5A 491373813 491375760 1947 True 298.5 375 81.6850 2358 3708 2 chr5A.!!$R3 1350
41 TraesCS7A01G143000 chr6B 695477848 695478591 743 True 736.0 736 84.7180 982 1718 1 chr6B.!!$R2 736

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
897 953 0.470833 AGAGCGGATATGAGGTGGCT 60.471 55.0 0.00 0.0 0.00 4.75 F
1977 2185 0.378257 GGTCAGTATCCGCGAACGTA 59.622 55.0 8.23 0.0 37.70 3.57 F
2048 2258 0.029035 GCAGATGCTCGGAAATGCAG 59.971 55.0 0.00 0.0 42.74 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 2210 0.610785 TTTGACAAATCCGGCTCCCC 60.611 55.0 0.00 0.0 0.00 4.81 R
3020 5088 0.595567 CGTTGACGTCAGGGTCGAAA 60.596 55.0 19.11 0.0 39.83 3.46 R
3916 7131 0.725686 CTGATCTTGCTTCAGCCACG 59.274 55.0 0.00 0.0 41.18 4.94 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
134 135 0.959553 AAACGAAGAGACAGAGGCGA 59.040 50.000 0.00 0.00 0.00 5.54
135 136 0.959553 AACGAAGAGACAGAGGCGAA 59.040 50.000 0.00 0.00 0.00 4.70
136 137 0.959553 ACGAAGAGACAGAGGCGAAA 59.040 50.000 0.00 0.00 0.00 3.46
137 138 1.336056 ACGAAGAGACAGAGGCGAAAC 60.336 52.381 0.00 0.00 0.00 2.78
138 139 1.341606 GAAGAGACAGAGGCGAAACG 58.658 55.000 0.00 0.00 0.00 3.60
139 140 0.959553 AAGAGACAGAGGCGAAACGA 59.040 50.000 0.00 0.00 0.00 3.85
140 141 0.959553 AGAGACAGAGGCGAAACGAA 59.040 50.000 0.00 0.00 0.00 3.85
141 142 1.068194 AGAGACAGAGGCGAAACGAAG 60.068 52.381 0.00 0.00 0.00 3.79
142 143 0.959553 AGACAGAGGCGAAACGAAGA 59.040 50.000 0.00 0.00 0.00 2.87
143 144 1.068194 AGACAGAGGCGAAACGAAGAG 60.068 52.381 0.00 0.00 0.00 2.85
144 145 0.959553 ACAGAGGCGAAACGAAGAGA 59.040 50.000 0.00 0.00 0.00 3.10
145 146 1.336056 ACAGAGGCGAAACGAAGAGAC 60.336 52.381 0.00 0.00 0.00 3.36
146 147 0.959553 AGAGGCGAAACGAAGAGACA 59.040 50.000 0.00 0.00 0.00 3.41
147 148 1.068194 AGAGGCGAAACGAAGAGACAG 60.068 52.381 0.00 0.00 0.00 3.51
148 149 0.959553 AGGCGAAACGAAGAGACAGA 59.040 50.000 0.00 0.00 0.00 3.41
149 150 1.068194 AGGCGAAACGAAGAGACAGAG 60.068 52.381 0.00 0.00 0.00 3.35
150 151 1.068472 GGCGAAACGAAGAGACAGAGA 60.068 52.381 0.00 0.00 0.00 3.10
151 152 1.980156 GCGAAACGAAGAGACAGAGAC 59.020 52.381 0.00 0.00 0.00 3.36
152 153 2.350964 GCGAAACGAAGAGACAGAGACT 60.351 50.000 0.00 0.00 0.00 3.24
176 177 3.182590 AACAGCCAGCAGCCGAAGA 62.183 57.895 0.00 0.00 45.47 2.87
221 224 6.106003 ACTCCACTTTCGCAAAAATCTTTTT 58.894 32.000 0.00 0.00 40.75 1.94
259 262 0.657312 CGTATACCCGTAGTGCGTGA 59.343 55.000 0.00 0.00 39.32 4.35
363 415 1.080434 GCGCGTGGATATCCCTCTC 60.080 63.158 19.34 6.62 35.38 3.20
463 515 8.766476 GGGACTAAACTTTAGTAGTATCCCTTT 58.234 37.037 19.41 0.00 39.52 3.11
556 611 6.152661 CCCAAAATAGACTAAATTCCAGCACA 59.847 38.462 0.00 0.00 0.00 4.57
557 612 7.309744 CCCAAAATAGACTAAATTCCAGCACAA 60.310 37.037 0.00 0.00 0.00 3.33
558 613 7.542130 CCAAAATAGACTAAATTCCAGCACAAC 59.458 37.037 0.00 0.00 0.00 3.32
559 614 7.759489 AAATAGACTAAATTCCAGCACAACA 57.241 32.000 0.00 0.00 0.00 3.33
584 639 4.048470 GGTTGGGCTCTGGTCCCC 62.048 72.222 0.00 0.00 43.24 4.81
585 640 2.936032 GTTGGGCTCTGGTCCCCT 60.936 66.667 0.00 0.00 43.24 4.79
586 641 2.610859 TTGGGCTCTGGTCCCCTC 60.611 66.667 0.00 0.00 43.24 4.30
600 655 1.293498 CCCTCGAGGTTGTGGACTG 59.707 63.158 29.25 7.44 0.00 3.51
606 661 1.069513 CGAGGTTGTGGACTGGTGTAA 59.930 52.381 0.00 0.00 0.00 2.41
610 665 2.038033 GGTTGTGGACTGGTGTAAGCTA 59.962 50.000 0.00 0.00 33.76 3.32
621 676 8.202137 GGACTGGTGTAAGCTAGATTGTAATTA 58.798 37.037 2.82 0.00 33.76 1.40
647 702 7.127955 ACCTGGATCCTTGATTAATACAAGTCT 59.872 37.037 14.23 10.27 41.88 3.24
744 800 2.962253 GCATCTACAGCCGGACGC 60.962 66.667 5.05 0.00 37.98 5.19
752 808 1.119574 ACAGCCGGACGCCCTATATT 61.120 55.000 5.05 0.00 38.78 1.28
830 886 2.391389 CCGAAGCTCTCAAACGGGC 61.391 63.158 0.00 0.00 39.92 6.13
832 888 1.302511 GAAGCTCTCAAACGGGCCA 60.303 57.895 4.39 0.00 0.00 5.36
838 894 1.008995 CTCAAACGGGCCACAAACG 60.009 57.895 4.39 0.00 0.00 3.60
860 916 3.637273 GACTGACCGGCACCCCTT 61.637 66.667 0.00 0.00 0.00 3.95
872 928 1.065418 GCACCCCTTATATCCATCCCG 60.065 57.143 0.00 0.00 0.00 5.14
880 936 5.661312 CCCTTATATCCATCCCGAATGTAGA 59.339 44.000 0.00 0.00 33.13 2.59
882 938 4.744795 ATATCCATCCCGAATGTAGAGC 57.255 45.455 0.00 0.00 33.13 4.09
897 953 0.470833 AGAGCGGATATGAGGTGGCT 60.471 55.000 0.00 0.00 0.00 4.75
931 987 3.321648 TGTCCGCCATGTCAGCCT 61.322 61.111 0.00 0.00 0.00 4.58
933 989 4.100084 TCCGCCATGTCAGCCTGG 62.100 66.667 0.00 0.00 34.11 4.45
937 993 4.051167 CCATGTCAGCCTGGCCCA 62.051 66.667 16.57 10.43 0.00 5.36
938 994 2.753043 CATGTCAGCCTGGCCCAC 60.753 66.667 16.57 12.78 0.00 4.61
939 995 4.052518 ATGTCAGCCTGGCCCACC 62.053 66.667 16.57 1.48 0.00 4.61
1075 1191 1.140407 GCTTCGTATTGCGCTCGAGT 61.140 55.000 15.13 0.00 41.07 4.18
1126 1243 2.360350 CCAGTGCGATGCCACCTT 60.360 61.111 0.00 0.00 36.38 3.50
1184 1301 1.069765 CCTATCCTGCGCGTGGATT 59.930 57.895 30.54 18.73 41.13 3.01
1371 1507 2.692368 ATGGCGGGTGGGTCTGAT 60.692 61.111 0.00 0.00 0.00 2.90
1440 1576 1.901948 TCTCTTCGAGTGGGCGTGT 60.902 57.895 0.00 0.00 0.00 4.49
1497 1634 2.262915 CTTCGGAGGCTCAACGCT 59.737 61.111 17.69 0.00 39.13 5.07
1516 1653 2.867333 TAAGCAGCTTCGACTCGGCG 62.867 60.000 12.07 0.00 0.00 6.46
1596 1759 2.357034 GTCCGACGCTTGCAAGGA 60.357 61.111 27.10 14.07 0.00 3.36
1635 1831 1.677966 CTCCTCCTTCGACGGGTCA 60.678 63.158 8.26 0.00 0.00 4.02
1760 1966 9.516314 AAGTTTTTAGATGTAGTTTGAACTTGC 57.484 29.630 1.20 0.00 40.37 4.01
1828 2034 4.462483 GCCCTGGTTGTGATCTTTTGATAA 59.538 41.667 0.00 0.00 39.67 1.75
1869 2075 3.146847 TGTCCGCTCATGATCTACGTAT 58.853 45.455 0.00 0.00 0.00 3.06
1977 2185 0.378257 GGTCAGTATCCGCGAACGTA 59.622 55.000 8.23 0.00 37.70 3.57
2028 2237 0.526211 GGATTTGTCAAAGTCCGGCC 59.474 55.000 0.00 0.00 33.05 6.13
2030 2240 1.862602 ATTTGTCAAAGTCCGGCCGC 61.863 55.000 22.85 7.25 0.00 6.53
2047 2257 1.708193 CGCAGATGCTCGGAAATGCA 61.708 55.000 2.95 0.00 43.67 3.96
2048 2258 0.029035 GCAGATGCTCGGAAATGCAG 59.971 55.000 0.00 0.00 42.74 4.41
2049 2259 1.376543 CAGATGCTCGGAAATGCAGT 58.623 50.000 0.00 0.00 42.74 4.40
2050 2260 1.741706 CAGATGCTCGGAAATGCAGTT 59.258 47.619 0.00 0.00 42.74 3.16
2052 2262 3.374988 CAGATGCTCGGAAATGCAGTTTA 59.625 43.478 0.00 0.00 42.74 2.01
2095 4082 1.893137 CCTGCCACCCCTAAAGAAAAC 59.107 52.381 0.00 0.00 0.00 2.43
2097 4084 2.962421 CTGCCACCCCTAAAGAAAACAA 59.038 45.455 0.00 0.00 0.00 2.83
2099 4086 3.970640 TGCCACCCCTAAAGAAAACAAAT 59.029 39.130 0.00 0.00 0.00 2.32
2109 4096 2.791655 AGAAAACAAATCCCTCGTCCC 58.208 47.619 0.00 0.00 0.00 4.46
2143 4130 2.037687 TTCGCCCTCGTCCCCTTA 59.962 61.111 0.00 0.00 36.96 2.69
2165 4152 1.542108 CCTCCATCTCAATCCCTTCGC 60.542 57.143 0.00 0.00 0.00 4.70
2353 4377 4.093291 CTCTTGCTCCAGCGGGCT 62.093 66.667 0.00 0.00 45.83 5.19
2446 4471 5.107133 CCAATCTTAAATCTTTGCCTGCAG 58.893 41.667 6.78 6.78 0.00 4.41
2682 4717 2.032071 GTGGGAGGACAACGTGGG 59.968 66.667 0.00 0.00 0.00 4.61
2939 4998 2.695666 GACGAAGATGAAGATGAGGGGA 59.304 50.000 0.00 0.00 0.00 4.81
2998 5066 1.740296 CGTGTCGGGAAAGCCGAAT 60.740 57.895 0.00 0.00 41.39 3.34
3000 5068 1.078708 TGTCGGGAAAGCCGAATCC 60.079 57.895 0.00 0.00 41.39 3.01
3128 5523 3.546271 GGCCATTTTTCGTCGCTTTAATC 59.454 43.478 0.00 0.00 0.00 1.75
3145 5540 2.298158 ATCGGCCTTGACAGCTACCG 62.298 60.000 0.00 0.00 41.92 4.02
3174 5595 2.515926 TGACGATGATAAGAGGCTGC 57.484 50.000 0.00 0.00 0.00 5.25
3191 5621 0.308684 TGCGGGCGTTAGTATACTCG 59.691 55.000 9.12 9.10 0.00 4.18
3434 6613 2.283809 CCCCCTCCTCATCTCGGT 59.716 66.667 0.00 0.00 0.00 4.69
3528 6707 0.885879 TTGATGGAGTAGCGTCGTGT 59.114 50.000 0.00 0.00 0.00 4.49
3539 6718 1.271379 AGCGTCGTGTATCCAACTCAA 59.729 47.619 0.00 0.00 0.00 3.02
3556 6735 4.401925 ACTCAAAGAAATGGACCTCAAGG 58.598 43.478 0.00 0.00 42.17 3.61
3574 6753 2.361610 CGCTTGTCCCCATTGGCT 60.362 61.111 0.00 0.00 0.00 4.75
3591 6770 1.001860 GGCTATCCCATGAGCTCAGAC 59.998 57.143 22.96 4.64 38.79 3.51
3741 6920 7.815641 TCACATTCAAGCGAGATTCATTTAAA 58.184 30.769 0.00 0.00 0.00 1.52
3774 6953 1.148310 ACACGAGCTTCAACAATCCG 58.852 50.000 0.00 0.00 0.00 4.18
4005 7221 2.666619 CGTTGAAGCATGGAAGTTGAGC 60.667 50.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 4.614078 CGCTTAGTCTCTGTCTCTTCGTTT 60.614 45.833 0.00 0.00 0.00 3.60
135 136 3.120130 CGCTTAGTCTCTGTCTCTTCGTT 60.120 47.826 0.00 0.00 0.00 3.85
136 137 2.417239 CGCTTAGTCTCTGTCTCTTCGT 59.583 50.000 0.00 0.00 0.00 3.85
137 138 2.673862 TCGCTTAGTCTCTGTCTCTTCG 59.326 50.000 0.00 0.00 0.00 3.79
138 139 4.083217 TGTTCGCTTAGTCTCTGTCTCTTC 60.083 45.833 0.00 0.00 0.00 2.87
139 140 3.821600 TGTTCGCTTAGTCTCTGTCTCTT 59.178 43.478 0.00 0.00 0.00 2.85
140 141 3.413327 TGTTCGCTTAGTCTCTGTCTCT 58.587 45.455 0.00 0.00 0.00 3.10
141 142 3.753842 CTGTTCGCTTAGTCTCTGTCTC 58.246 50.000 0.00 0.00 0.00 3.36
142 143 2.094957 GCTGTTCGCTTAGTCTCTGTCT 60.095 50.000 0.00 0.00 35.14 3.41
143 144 2.255316 GCTGTTCGCTTAGTCTCTGTC 58.745 52.381 0.00 0.00 35.14 3.51
144 145 1.067495 GGCTGTTCGCTTAGTCTCTGT 60.067 52.381 0.00 0.00 39.13 3.41
145 146 1.067565 TGGCTGTTCGCTTAGTCTCTG 60.068 52.381 0.00 0.00 39.13 3.35
146 147 1.203523 CTGGCTGTTCGCTTAGTCTCT 59.796 52.381 0.00 0.00 39.13 3.10
147 148 1.634702 CTGGCTGTTCGCTTAGTCTC 58.365 55.000 0.00 0.00 39.13 3.36
148 149 0.390472 GCTGGCTGTTCGCTTAGTCT 60.390 55.000 0.00 0.00 39.13 3.24
149 150 0.670546 TGCTGGCTGTTCGCTTAGTC 60.671 55.000 0.00 0.00 39.13 2.59
150 151 0.671781 CTGCTGGCTGTTCGCTTAGT 60.672 55.000 0.00 0.00 39.13 2.24
151 152 1.975363 GCTGCTGGCTGTTCGCTTAG 61.975 60.000 0.00 0.00 39.13 2.18
152 153 2.034879 GCTGCTGGCTGTTCGCTTA 61.035 57.895 0.00 0.00 39.13 3.09
176 177 2.669569 AATGCGAACGGTGCAGCT 60.670 55.556 14.92 0.00 46.98 4.24
221 224 1.336517 CGAAAGGTCACACGGAAGCTA 60.337 52.381 0.00 0.00 0.00 3.32
259 262 5.277828 GCCGAGCCGATATCTAAATTTTTGT 60.278 40.000 0.00 0.00 0.00 2.83
363 415 2.342651 CACTTGTACGAGCATGAGAACG 59.657 50.000 10.23 0.00 0.00 3.95
419 471 4.286032 AGTCCCACATTGCTAGTTTAGTGA 59.714 41.667 8.45 0.00 0.00 3.41
463 515 2.170166 CTTAGCCCATTTGTGCAAGGA 58.830 47.619 0.00 0.00 0.00 3.36
556 611 2.174854 AGAGCCCAACCAAACTACTGTT 59.825 45.455 0.00 0.00 38.16 3.16
557 612 1.774856 AGAGCCCAACCAAACTACTGT 59.225 47.619 0.00 0.00 0.00 3.55
558 613 2.154462 CAGAGCCCAACCAAACTACTG 58.846 52.381 0.00 0.00 0.00 2.74
559 614 1.073923 CCAGAGCCCAACCAAACTACT 59.926 52.381 0.00 0.00 0.00 2.57
584 639 0.319900 CACCAGTCCACAACCTCGAG 60.320 60.000 5.13 5.13 0.00 4.04
585 640 1.046472 ACACCAGTCCACAACCTCGA 61.046 55.000 0.00 0.00 0.00 4.04
586 641 0.677288 TACACCAGTCCACAACCTCG 59.323 55.000 0.00 0.00 0.00 4.63
600 655 7.441458 CCAGGTAATTACAATCTAGCTTACACC 59.559 40.741 17.16 0.00 0.00 4.16
606 661 6.789959 AGGATCCAGGTAATTACAATCTAGCT 59.210 38.462 15.82 0.00 0.00 3.32
610 665 7.451731 TCAAGGATCCAGGTAATTACAATCT 57.548 36.000 15.82 2.75 0.00 2.40
621 676 7.127955 AGACTTGTATTAATCAAGGATCCAGGT 59.872 37.037 15.82 0.00 44.29 4.00
741 797 4.698583 GTATGAGACGAATATAGGGCGT 57.301 45.455 0.00 0.00 41.45 5.68
811 867 2.391389 CCCGTTTGAGAGCTTCGGC 61.391 63.158 0.00 0.00 39.87 5.54
830 886 3.353836 CAGTCCGGGCGTTTGTGG 61.354 66.667 0.00 0.00 0.00 4.17
832 888 2.280592 GTCAGTCCGGGCGTTTGT 60.281 61.111 0.00 0.00 0.00 2.83
860 916 4.338400 CGCTCTACATTCGGGATGGATATA 59.662 45.833 0.55 0.00 40.21 0.86
872 928 4.489810 CACCTCATATCCGCTCTACATTC 58.510 47.826 0.00 0.00 0.00 2.67
880 936 1.810606 CGAGCCACCTCATATCCGCT 61.811 60.000 0.00 0.00 38.00 5.52
882 938 1.290324 CCGAGCCACCTCATATCCG 59.710 63.158 0.00 0.00 38.00 4.18
914 970 3.321648 AGGCTGACATGGCGGACA 61.322 61.111 17.85 0.00 37.59 4.02
915 971 2.821366 CAGGCTGACATGGCGGAC 60.821 66.667 13.00 8.97 37.59 4.79
920 976 4.051167 TGGGCCAGGCTGACATGG 62.051 66.667 17.94 0.00 39.73 3.66
936 992 4.473520 CAGGGTGGGCTAGCGGTG 62.474 72.222 9.00 0.00 0.00 4.94
966 1022 1.566298 GGGATCTGCCAGACAAGGGT 61.566 60.000 0.00 0.00 38.95 4.34
970 1026 0.833287 GCTAGGGATCTGCCAGACAA 59.167 55.000 0.00 0.00 38.95 3.18
971 1027 1.395045 CGCTAGGGATCTGCCAGACA 61.395 60.000 0.00 0.00 38.95 3.41
972 1028 1.365633 CGCTAGGGATCTGCCAGAC 59.634 63.158 0.00 0.00 38.95 3.51
977 1092 2.336809 CCGACGCTAGGGATCTGC 59.663 66.667 14.59 0.00 0.00 4.26
980 1095 3.256716 CTCGCCGACGCTAGGGATC 62.257 68.421 14.59 6.56 39.84 3.36
1029 1145 1.751162 CTCCTCGTCTCCGGAGCTT 60.751 63.158 27.39 0.00 40.27 3.74
1075 1191 1.396607 CCCATATCGACCCGTGACCA 61.397 60.000 0.00 0.00 0.00 4.02
1184 1301 3.687321 GATCAGGCAGGCCTCGCAA 62.687 63.158 23.05 11.89 46.28 4.85
1401 1537 2.362503 TCCTCATCGTCGGGCACT 60.363 61.111 0.00 0.00 0.00 4.40
1440 1576 1.657751 CCTCAGTCAGTGATCGGCGA 61.658 60.000 13.87 13.87 33.51 5.54
1497 1634 1.153823 GCCGAGTCGAAGCTGCTTA 60.154 57.895 15.95 0.00 0.00 3.09
1516 1653 2.464459 CCCGCTCGGATTGCTCAAC 61.464 63.158 10.28 0.00 37.50 3.18
1596 1759 5.184864 GGAGGAATCAGAGATGACGATGTAT 59.815 44.000 0.00 0.00 0.00 2.29
1760 1966 5.062934 CACATAATACACATAATACGGCGGG 59.937 44.000 13.24 0.00 0.00 6.13
1802 2008 2.610438 AAGATCACAACCAGGGCATT 57.390 45.000 0.00 0.00 0.00 3.56
1828 2034 6.035843 GGACATACAAATGCACAATCGATTT 58.964 36.000 8.21 0.00 36.50 2.17
1936 2144 4.274950 CCGGGCATTCTTTATATTCACGTT 59.725 41.667 0.00 0.00 0.00 3.99
2001 2210 0.610785 TTTGACAAATCCGGCTCCCC 60.611 55.000 0.00 0.00 0.00 4.81
2030 2240 1.376543 ACTGCATTTCCGAGCATCTG 58.623 50.000 0.00 0.00 40.42 2.90
2085 4066 5.106277 GGGACGAGGGATTTGTTTTCTTTAG 60.106 44.000 0.00 0.00 0.00 1.85
2086 4067 4.763279 GGGACGAGGGATTTGTTTTCTTTA 59.237 41.667 0.00 0.00 0.00 1.85
2095 4082 1.452108 GGCAGGGACGAGGGATTTG 60.452 63.158 0.00 0.00 0.00 2.32
2097 4084 2.285368 TGGCAGGGACGAGGGATT 60.285 61.111 0.00 0.00 0.00 3.01
2099 4086 4.316823 AGTGGCAGGGACGAGGGA 62.317 66.667 0.00 0.00 0.00 4.20
2109 4096 0.673022 GAAGAGGTGCAGAGTGGCAG 60.673 60.000 0.00 0.00 45.96 4.85
2143 4130 2.131023 GAAGGGATTGAGATGGAGGGT 58.869 52.381 0.00 0.00 0.00 4.34
2165 4152 1.202651 GGGACGAGAGGAGAGAGAGAG 60.203 61.905 0.00 0.00 0.00 3.20
2688 4723 1.152839 AACTTTGTGGTGGGGACGG 60.153 57.895 0.00 0.00 0.00 4.79
2822 4872 6.780031 TCCTCGATATCATCTTCTTCCTCTTT 59.220 38.462 3.12 0.00 0.00 2.52
2939 4998 1.827969 CGAGACCCTGTCATCTTCCTT 59.172 52.381 0.00 0.00 34.60 3.36
2991 5059 3.127533 GCGCAACTGGATTCGGCT 61.128 61.111 0.30 0.00 0.00 5.52
3020 5088 0.595567 CGTTGACGTCAGGGTCGAAA 60.596 55.000 19.11 0.00 39.83 3.46
3128 5523 2.509336 CGGTAGCTGTCAAGGCCG 60.509 66.667 0.00 0.00 0.00 6.13
3145 5540 2.370281 ATCATCGTCATCATACGGCC 57.630 50.000 0.00 0.00 43.05 6.13
3174 5595 1.599071 TGACGAGTATACTAACGCCCG 59.401 52.381 5.09 6.62 0.00 6.13
3191 5621 0.976073 TCCATTCCCGGGTCTCTGAC 60.976 60.000 22.86 0.00 0.00 3.51
3434 6613 2.605607 CCCAGCCCACTGTCATCCA 61.606 63.158 0.00 0.00 42.81 3.41
3528 6707 6.139679 AGGTCCATTTCTTTGAGTTGGATA 57.860 37.500 0.00 0.00 38.64 2.59
3539 6718 1.826385 CGCCTTGAGGTCCATTTCTT 58.174 50.000 0.00 0.00 37.57 2.52
3574 6753 3.139957 AGAGAGTCTGAGCTCATGGGATA 59.860 47.826 18.63 0.00 37.94 2.59
3591 6770 3.077359 CCAGCCAACCAACTTTAGAGAG 58.923 50.000 0.00 0.00 0.00 3.20
3829 7040 8.734030 GTGAATTTCTTTGTTTAACTTGACGAG 58.266 33.333 0.00 0.00 0.00 4.18
3916 7131 0.725686 CTGATCTTGCTTCAGCCACG 59.274 55.000 0.00 0.00 41.18 4.94
4005 7221 5.067674 TGAGAACCACCACAAAAAGATCAAG 59.932 40.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.