Multiple sequence alignment - TraesCS2D01G402000

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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 TraesCS2D01G402000 chr2D 100.000 3411 0 0 977 4387 516862211 516865621 0.000000e+00 6300.0
1 TraesCS2D01G402000 chr2D 100.000 691 0 0 1 691 516861235 516861925 0.000000e+00 1277.0
2 TraesCS2D01G402000 chr2D 81.734 1188 156 32 1940 3106 516925496 516926643 0.000000e+00 935.0
3 TraesCS2D01G402000 chr2D 86.332 578 59 5 2006 2583 517087283 517087840 2.900000e-171 612.0
4 TraesCS2D01G402000 chr2D 87.731 432 42 4 2006 2430 517038306 517038733 1.100000e-135 494.0
5 TraesCS2D01G402000 chr2D 78.182 825 91 41 1192 1946 517086355 517087160 1.120000e-120 444.0
6 TraesCS2D01G402000 chr2D 81.120 482 67 12 2629 3106 517087915 517088376 8.970000e-97 364.0
7 TraesCS2D01G402000 chr2D 86.447 273 37 0 4115 4387 446931142 446930870 2.560000e-77 300.0
8 TraesCS2D01G402000 chr2D 86.719 256 31 3 2853 3106 517045917 517046171 9.290000e-72 281.0
9 TraesCS2D01G402000 chr2D 85.938 192 24 2 2629 2820 517045664 517045852 7.440000e-48 202.0
10 TraesCS2D01G402000 chr2D 92.248 129 10 0 2455 2583 517045445 517045573 2.690000e-42 183.0
11 TraesCS2D01G402000 chr2D 77.328 247 31 15 419 651 517036940 517037175 5.960000e-24 122.0
12 TraesCS2D01G402000 chr2D 75.622 201 31 12 427 613 517085859 517086055 2.810000e-12 84.2
13 TraesCS2D01G402000 chr2D 94.595 37 1 1 1093 1129 517086249 517086284 6.130000e-04 56.5
14 TraesCS2D01G402000 chr2B 93.301 2881 131 28 988 3847 608539812 608542651 0.000000e+00 4194.0
15 TraesCS2D01G402000 chr2B 92.057 705 37 6 3 691 608538751 608539452 0.000000e+00 974.0
16 TraesCS2D01G402000 chr2B 81.880 1181 155 31 1940 3106 608668035 608669170 0.000000e+00 941.0
17 TraesCS2D01G402000 chr2B 86.395 588 63 9 2006 2583 608802832 608803412 1.040000e-175 627.0
18 TraesCS2D01G402000 chr2B 82.239 518 80 8 3873 4387 765759136 765758628 1.870000e-118 436.0
19 TraesCS2D01G402000 chr2B 78.843 709 76 34 1193 1851 608802001 608802685 1.140000e-110 411.0
20 TraesCS2D01G402000 chr2B 87.919 149 18 0 2629 2777 608803503 608803651 4.510000e-40 176.0
21 TraesCS2D01G402000 chr2B 94.000 50 3 0 526 575 608801499 608801548 4.700000e-10 76.8
22 TraesCS2D01G402000 chr2B 92.105 38 2 1 3683 3719 437938178 437938141 8.000000e-03 52.8
23 TraesCS2D01G402000 chr2A 93.939 2178 93 12 977 3125 661081643 661083810 0.000000e+00 3254.0
24 TraesCS2D01G402000 chr2A 91.773 705 36 13 1 691 661080835 661081531 0.000000e+00 961.0
25 TraesCS2D01G402000 chr2A 81.810 1182 155 35 1940 3106 661152440 661153576 0.000000e+00 937.0
26 TraesCS2D01G402000 chr2A 79.506 1498 166 78 1193 2583 661394543 661396006 0.000000e+00 935.0
27 TraesCS2D01G402000 chr2A 81.737 1117 154 27 2006 3106 661448236 661449318 0.000000e+00 887.0
28 TraesCS2D01G402000 chr2A 90.654 428 31 5 3429 3847 661084109 661084536 1.070000e-155 560.0
29 TraesCS2D01G402000 chr2A 95.638 298 10 3 3144 3440 661083796 661084091 3.970000e-130 475.0
30 TraesCS2D01G402000 chr2A 85.955 178 22 2 2643 2820 661396102 661396276 2.080000e-43 187.0
31 TraesCS2D01G402000 chr2A 75.210 238 38 11 419 638 661394096 661394330 4.670000e-15 93.5
32 TraesCS2D01G402000 chr2A 81.301 123 12 6 526 641 661149033 661149151 6.040000e-14 89.8
33 TraesCS2D01G402000 chr2A 80.672 119 14 5 526 638 661393822 661393937 2.810000e-12 84.2
34 TraesCS2D01G402000 chr2A 81.944 72 11 2 2853 2923 661396341 661396411 4.740000e-05 60.2
35 TraesCS2D01G402000 chr1B 91.118 912 70 7 1053 1961 676246643 676247546 0.000000e+00 1225.0
36 TraesCS2D01G402000 chr1B 90.909 561 46 4 1053 1612 491697443 491697999 0.000000e+00 749.0
37 TraesCS2D01G402000 chr1B 87.645 259 17 4 1603 1850 491699549 491699803 2.000000e-73 287.0
38 TraesCS2D01G402000 chr1B 91.463 82 6 1 1837 1918 491699923 491700003 1.290000e-20 111.0
39 TraesCS2D01G402000 chr5A 90.508 885 73 7 1053 1934 419361107 419361983 0.000000e+00 1158.0
40 TraesCS2D01G402000 chr5A 82.081 519 75 11 3872 4387 438848381 438848884 1.130000e-115 427.0
41 TraesCS2D01G402000 chr5A 85.000 60 4 3 3686 3740 255924649 255924708 6.130000e-04 56.5
42 TraesCS2D01G402000 chr5A 85.000 60 4 3 3686 3740 582549625 582549684 6.130000e-04 56.5
43 TraesCS2D01G402000 chr4A 89.769 909 61 15 1053 1961 541336971 541336095 0.000000e+00 1134.0
44 TraesCS2D01G402000 chr7B 89.733 487 46 2 1478 1961 541490096 541490581 1.730000e-173 619.0
45 TraesCS2D01G402000 chr7B 80.078 512 87 13 3872 4382 748496519 748497016 2.490000e-97 366.0
46 TraesCS2D01G402000 chr7A 83.172 517 80 6 3872 4387 6959213 6958703 2.390000e-127 466.0
47 TraesCS2D01G402000 chr3B 82.342 521 69 12 3877 4387 757479224 757478717 8.720000e-117 431.0
48 TraesCS2D01G402000 chr7D 82.205 517 68 15 3872 4387 10065100 10064607 1.460000e-114 424.0
49 TraesCS2D01G402000 chr1D 80.705 482 76 13 3872 4352 481547873 481548338 4.170000e-95 359.0
50 TraesCS2D01G402000 chr3D 86.813 273 35 1 4116 4387 55159339 55159067 1.980000e-78 303.0
51 TraesCS2D01G402000 chr6A 87.037 54 2 3 3692 3740 390364832 390364779 6.130000e-04 56.5
52 TraesCS2D01G402000 chr3A 100.000 28 0 0 3692 3719 479194867 479194840 8.000000e-03 52.8


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 TraesCS2D01G402000 chr2D 516861235 516865621 4386 False 3788.500000 6300 100.000000 1 4387 2 chr2D.!!$F2 4386
1 TraesCS2D01G402000 chr2D 516925496 516926643 1147 False 935.000000 935 81.734000 1940 3106 1 chr2D.!!$F1 1166
2 TraesCS2D01G402000 chr2D 517085859 517088376 2517 False 312.140000 612 83.170200 427 3106 5 chr2D.!!$F5 2679
3 TraesCS2D01G402000 chr2D 517036940 517038733 1793 False 308.000000 494 82.529500 419 2430 2 chr2D.!!$F3 2011
4 TraesCS2D01G402000 chr2D 517045445 517046171 726 False 222.000000 281 88.301667 2455 3106 3 chr2D.!!$F4 651
5 TraesCS2D01G402000 chr2B 608538751 608542651 3900 False 2584.000000 4194 92.679000 3 3847 2 chr2B.!!$F2 3844
6 TraesCS2D01G402000 chr2B 608668035 608669170 1135 False 941.000000 941 81.880000 1940 3106 1 chr2B.!!$F1 1166
7 TraesCS2D01G402000 chr2B 765758628 765759136 508 True 436.000000 436 82.239000 3873 4387 1 chr2B.!!$R2 514
8 TraesCS2D01G402000 chr2B 608801499 608803651 2152 False 322.700000 627 86.789250 526 2777 4 chr2B.!!$F3 2251
9 TraesCS2D01G402000 chr2A 661080835 661084536 3701 False 1312.500000 3254 93.001000 1 3847 4 chr2A.!!$F2 3846
10 TraesCS2D01G402000 chr2A 661448236 661449318 1082 False 887.000000 887 81.737000 2006 3106 1 chr2A.!!$F1 1100
11 TraesCS2D01G402000 chr2A 661149033 661153576 4543 False 513.400000 937 81.555500 526 3106 2 chr2A.!!$F3 2580
12 TraesCS2D01G402000 chr2A 661393822 661396411 2589 False 271.980000 935 80.657400 419 2923 5 chr2A.!!$F4 2504
13 TraesCS2D01G402000 chr1B 676246643 676247546 903 False 1225.000000 1225 91.118000 1053 1961 1 chr1B.!!$F1 908
14 TraesCS2D01G402000 chr1B 491697443 491700003 2560 False 382.333333 749 90.005667 1053 1918 3 chr1B.!!$F2 865
15 TraesCS2D01G402000 chr5A 419361107 419361983 876 False 1158.000000 1158 90.508000 1053 1934 1 chr5A.!!$F2 881
16 TraesCS2D01G402000 chr5A 438848381 438848884 503 False 427.000000 427 82.081000 3872 4387 1 chr5A.!!$F3 515
17 TraesCS2D01G402000 chr4A 541336095 541336971 876 True 1134.000000 1134 89.769000 1053 1961 1 chr4A.!!$R1 908
18 TraesCS2D01G402000 chr7A 6958703 6959213 510 True 466.000000 466 83.172000 3872 4387 1 chr7A.!!$R1 515
19 TraesCS2D01G402000 chr3B 757478717 757479224 507 True 431.000000 431 82.342000 3877 4387 1 chr3B.!!$R1 510

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
499 519 1.069022 CAGCACCGGTGATTGTTGAAG 60.069 52.381 38.30 14.39 32.22 3.02 F
1145 3429 0.457166 GTACGTGCGTGCTGGTGATA 60.457 55.000 7.55 0.00 0.00 2.15 F
2266 6563 0.323629 ACATCACCGGTTCGACCATT 59.676 50.000 2.97 0.00 38.47 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 5599 1.180456 TCGTGCCCAAGACCTACGAA 61.180 55.0 0.0 0.00 40.33 3.85 R
2626 6997 0.732571 AACAATGTAATCAGCCGGCG 59.267 50.0 23.2 16.49 0.00 6.46 R
3726 8215 0.034896 CTCCGCACTTTGTACACCCT 59.965 55.0 0.0 0.00 0.00 4.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 8.735692 TCATATTTATGAGCAGACAAATCACA 57.264 30.769 0.00 0.00 37.76 3.58
34 38 5.412594 TGAGCAGACAAATCACAAGATAACC 59.587 40.000 0.00 0.00 33.08 2.85
73 77 2.812011 GCCCGTGTGTTCTAGTGATTTT 59.188 45.455 0.00 0.00 0.00 1.82
79 83 8.079809 CCCGTGTGTTCTAGTGATTTTAAAAAT 58.920 33.333 4.44 0.00 0.00 1.82
114 118 3.953612 TGGTGCATTGATTTGGTAGATCC 59.046 43.478 0.00 0.00 0.00 3.36
117 121 5.376625 GTGCATTGATTTGGTAGATCCCTA 58.623 41.667 0.00 0.00 34.77 3.53
271 282 3.914426 ACTCTTGGATACGCCTTCATT 57.086 42.857 0.00 0.00 42.51 2.57
277 288 6.591935 TCTTGGATACGCCTTCATTAATTCT 58.408 36.000 0.00 0.00 42.51 2.40
287 298 5.751680 CCTTCATTAATTCTGTACGCCATG 58.248 41.667 0.00 0.00 0.00 3.66
345 356 3.504863 GCACGTCTACTCACCGAAATTA 58.495 45.455 0.00 0.00 0.00 1.40
370 381 1.584761 CGCATTCAATTTGGCACGATG 59.415 47.619 0.00 0.00 0.00 3.84
399 410 2.655474 GCGATCGAACGTATATGTCACC 59.345 50.000 21.57 0.00 35.59 4.02
477 497 1.286354 GAACACGACGCCGAATCCAA 61.286 55.000 0.00 0.00 39.50 3.53
499 519 1.069022 CAGCACCGGTGATTGTTGAAG 60.069 52.381 38.30 14.39 32.22 3.02
643 2819 5.753438 GTCGGGGTGCACATATATATACATG 59.247 44.000 20.43 0.00 0.00 3.21
1072 3346 6.745116 ACACGCTCTGTATATATTAGTGCAA 58.255 36.000 17.01 0.00 32.22 4.08
1145 3429 0.457166 GTACGTGCGTGCTGGTGATA 60.457 55.000 7.55 0.00 0.00 2.15
1153 3437 1.854743 CGTGCTGGTGATAAGTGATCG 59.145 52.381 0.00 0.00 37.38 3.69
1214 3512 1.715785 TCATGCAGGGTATCATCGGA 58.284 50.000 0.00 0.00 0.00 4.55
1527 3878 1.303799 CGAAGTCCTTCCTCGTCGGA 61.304 60.000 1.61 0.00 41.06 4.55
1646 5593 4.041567 TCATCTGGTCAGGAAAACTTGCTA 59.958 41.667 0.00 0.00 0.00 3.49
1652 5599 5.362430 TGGTCAGGAAAACTTGCTATGTTTT 59.638 36.000 12.31 12.31 46.30 2.43
1991 6259 9.143631 GCACCGACGGTTAGTATATAAATAAAT 57.856 33.333 19.02 0.00 31.02 1.40
2143 6440 3.274586 CCGCAGATGCACATCGGG 61.275 66.667 11.81 11.00 42.48 5.14
2224 6521 3.998672 AACACCGACGGCGTCCAT 61.999 61.111 31.86 18.68 35.23 3.41
2266 6563 0.323629 ACATCACCGGTTCGACCATT 59.676 50.000 2.97 0.00 38.47 3.16
2381 6690 3.288092 CAAAGGGTTACAATAGGGAGGC 58.712 50.000 0.00 0.00 0.00 4.70
2624 6990 6.668323 TGTTACAATTACAAAGAAGCTGAGC 58.332 36.000 0.00 0.00 0.00 4.26
2626 6997 3.507622 ACAATTACAAAGAAGCTGAGCCC 59.492 43.478 0.00 0.00 0.00 5.19
2725 7096 2.032634 CACCAACGTGGACCATCCG 61.033 63.158 10.46 0.00 40.96 4.18
2795 7166 4.514441 CGGTACTCTACTACTATGTGTGGG 59.486 50.000 0.00 0.00 0.00 4.61
2846 7258 2.597578 TGTGTGGTGGAGTAGCTAGA 57.402 50.000 0.00 0.00 0.00 2.43
2870 7286 5.748592 ACTAAAATGTTTGTGCGTCTTCTC 58.251 37.500 0.00 0.00 0.00 2.87
3106 7523 2.108970 GTCTACCCGAAGATCCCTTGT 58.891 52.381 0.00 0.00 31.62 3.16
3119 7536 1.203994 TCCCTTGTGTAGCTAACGCTC 59.796 52.381 0.00 0.00 45.15 5.03
3125 7542 0.384309 TGTAGCTAACGCTCCATCGG 59.616 55.000 0.00 0.00 45.15 4.18
3126 7543 0.940047 GTAGCTAACGCTCCATCGGC 60.940 60.000 0.00 0.00 45.15 5.54
3127 7544 2.083835 TAGCTAACGCTCCATCGGCC 62.084 60.000 0.00 0.00 45.15 6.13
3128 7545 2.658593 CTAACGCTCCATCGGCCG 60.659 66.667 22.12 22.12 0.00 6.13
3129 7546 4.215742 TAACGCTCCATCGGCCGG 62.216 66.667 27.83 10.29 0.00 6.13
3319 7770 5.301805 GCCATGTATATTGCCCAGTTACTTT 59.698 40.000 0.00 0.00 0.00 2.66
3394 7845 9.252962 GATAGAAAATGGAATAATGCTGGTTTG 57.747 33.333 0.00 0.00 0.00 2.93
3433 7884 1.271325 TGGACAATCACGCATGAAGGT 60.271 47.619 0.00 0.00 38.69 3.50
3434 7885 2.027653 TGGACAATCACGCATGAAGGTA 60.028 45.455 0.00 0.00 38.69 3.08
3491 7975 5.171476 GCAGTTACATAGTTTCAGAGAGCA 58.829 41.667 0.00 0.00 0.00 4.26
3608 8095 4.526970 AGGGTAATTGTAGGCTCATGTTG 58.473 43.478 0.00 0.00 0.00 3.33
3620 8109 5.324409 AGGCTCATGTTGTCAAATCCTTTA 58.676 37.500 0.00 0.00 0.00 1.85
3630 8119 8.349245 TGTTGTCAAATCCTTTAATAGTGTGTG 58.651 33.333 0.00 0.00 0.00 3.82
3662 8151 5.220931 GCTGGATGAAACAGATGGATAACAC 60.221 44.000 0.00 0.00 38.20 3.32
3670 8159 3.118261 ACAGATGGATAACACGAGGCAAT 60.118 43.478 0.00 0.00 0.00 3.56
3719 8208 4.240888 CCTACATCCTGCTCGATTGTATG 58.759 47.826 0.00 0.00 0.00 2.39
3720 8209 4.021981 CCTACATCCTGCTCGATTGTATGA 60.022 45.833 0.00 0.00 0.00 2.15
3721 8210 4.613925 ACATCCTGCTCGATTGTATGAT 57.386 40.909 0.00 0.00 0.00 2.45
3722 8211 4.313282 ACATCCTGCTCGATTGTATGATG 58.687 43.478 6.52 6.52 33.54 3.07
3723 8212 4.039609 ACATCCTGCTCGATTGTATGATGA 59.960 41.667 12.28 0.00 32.44 2.92
3724 8213 4.670896 TCCTGCTCGATTGTATGATGAA 57.329 40.909 0.00 0.00 0.00 2.57
3725 8214 5.219343 TCCTGCTCGATTGTATGATGAAT 57.781 39.130 0.00 0.00 0.00 2.57
3726 8215 6.345096 TCCTGCTCGATTGTATGATGAATA 57.655 37.500 0.00 0.00 0.00 1.75
3745 8235 0.034896 AGGGTGTACAAAGTGCGGAG 59.965 55.000 0.00 0.00 0.00 4.63
3754 8244 4.228912 ACAAAGTGCGGAGATGAAAAAG 57.771 40.909 0.00 0.00 0.00 2.27
3772 8262 1.549203 AGTAGCGGTTCCGGTTTCTA 58.451 50.000 20.40 6.73 40.66 2.10
3773 8263 1.203287 AGTAGCGGTTCCGGTTTCTAC 59.797 52.381 20.40 16.78 40.66 2.59
3805 8295 1.227645 GCTCGCCATGTATGCAGGA 60.228 57.895 0.00 0.00 0.00 3.86
3806 8296 0.815213 GCTCGCCATGTATGCAGGAA 60.815 55.000 0.00 0.00 0.00 3.36
3815 8305 5.765176 CCATGTATGCAGGAATACACAATG 58.235 41.667 2.23 0.00 43.83 2.82
3826 8316 6.646653 CAGGAATACACAATGCATACGAGTAT 59.353 38.462 0.00 6.48 0.00 2.12
3832 8322 6.806751 ACACAATGCATACGAGTATTCTACT 58.193 36.000 0.00 0.00 42.86 2.57
3848 8338 9.003658 AGTATTCTACTGAATTCAACTGTTTGG 57.996 33.333 9.88 0.00 42.37 3.28
3849 8339 7.823745 ATTCTACTGAATTCAACTGTTTGGT 57.176 32.000 9.88 3.94 39.68 3.67
3850 8340 6.861065 TCTACTGAATTCAACTGTTTGGTC 57.139 37.500 9.88 0.00 33.06 4.02
3851 8341 4.918810 ACTGAATTCAACTGTTTGGTCC 57.081 40.909 9.88 0.00 33.06 4.46
3852 8342 4.277476 ACTGAATTCAACTGTTTGGTCCA 58.723 39.130 9.88 0.00 33.06 4.02
3853 8343 4.339247 ACTGAATTCAACTGTTTGGTCCAG 59.661 41.667 9.88 0.00 33.06 3.86
3854 8344 4.531854 TGAATTCAACTGTTTGGTCCAGA 58.468 39.130 5.45 0.00 34.04 3.86
3855 8345 4.952957 TGAATTCAACTGTTTGGTCCAGAA 59.047 37.500 5.45 0.00 34.04 3.02
3856 8346 4.918810 ATTCAACTGTTTGGTCCAGAAC 57.081 40.909 8.96 8.96 34.04 3.01
3857 8347 3.358111 TCAACTGTTTGGTCCAGAACA 57.642 42.857 14.81 14.81 34.80 3.18
3858 8348 3.013921 TCAACTGTTTGGTCCAGAACAC 58.986 45.455 12.73 1.99 32.73 3.32
3859 8349 2.052782 ACTGTTTGGTCCAGAACACC 57.947 50.000 12.73 0.00 32.73 4.16
3860 8350 1.318576 CTGTTTGGTCCAGAACACCC 58.681 55.000 12.73 0.00 32.73 4.61
3861 8351 0.106419 TGTTTGGTCCAGAACACCCC 60.106 55.000 12.73 0.00 31.30 4.95
3862 8352 0.826256 GTTTGGTCCAGAACACCCCC 60.826 60.000 10.35 0.00 32.24 5.40
3927 8417 2.862223 CGCCCCGATCTCTCTTCCC 61.862 68.421 0.00 0.00 0.00 3.97
3946 8440 4.748798 CAGCTCCCCCTCACCCCT 62.749 72.222 0.00 0.00 0.00 4.79
3951 8445 4.825679 CCCCCTCACCCCTCCCTC 62.826 77.778 0.00 0.00 0.00 4.30
4045 8539 1.684049 CCCCTCTCGGTTGCTCTCT 60.684 63.158 0.00 0.00 0.00 3.10
4046 8540 1.261238 CCCCTCTCGGTTGCTCTCTT 61.261 60.000 0.00 0.00 0.00 2.85
4079 8573 1.460689 TTCTCCGTGGGGTGTTCCT 60.461 57.895 0.00 0.00 35.33 3.36
4080 8574 1.477685 TTCTCCGTGGGGTGTTCCTC 61.478 60.000 0.00 0.00 35.33 3.71
4133 8628 3.896133 GGCGCGACACGGGAGATA 61.896 66.667 12.10 0.00 42.31 1.98
4138 8633 1.655329 CGACACGGGAGATAGGCTC 59.345 63.158 0.00 0.00 43.17 4.70
4142 8637 1.101635 CACGGGAGATAGGCTCGACA 61.102 60.000 0.00 0.00 44.91 4.35
4267 8770 2.126189 GGTCTACGGCGCGACTTT 60.126 61.111 23.12 0.00 0.00 2.66
4272 8775 2.814183 CTACGGCGCGACTTTCAGGT 62.814 60.000 12.10 0.45 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 38 8.495949 CACACGGGCATTTAAATATTCTAGTAG 58.504 37.037 0.00 0.00 0.00 2.57
73 77 5.771469 CACCAGATTGTGAGTGCATTTTTA 58.229 37.500 0.00 0.00 38.55 1.52
79 83 2.632643 GCACCAGATTGTGAGTGCA 58.367 52.632 16.85 0.00 45.46 4.57
114 118 1.001268 CGGATCATCTGACGTGGTAGG 60.001 57.143 0.00 0.00 0.00 3.18
117 121 1.403814 ATCGGATCATCTGACGTGGT 58.596 50.000 0.00 0.00 34.08 4.16
146 150 0.172578 GTTTGCATTTACGGGGAGCC 59.827 55.000 0.00 0.00 0.00 4.70
271 282 4.647853 AGGTAGACATGGCGTACAGAATTA 59.352 41.667 0.00 0.00 0.00 1.40
277 288 2.139323 AGAGGTAGACATGGCGTACA 57.861 50.000 0.00 0.00 0.00 2.90
287 298 7.272037 AGACTACTACTACGTAGAGGTAGAC 57.728 44.000 35.84 32.28 41.95 2.59
345 356 3.510719 GTGCCAAATTGAATGCGTACAT 58.489 40.909 0.00 0.00 38.49 2.29
370 381 1.196946 CGTTCGATCGCGCAGATTC 59.803 57.895 11.09 5.18 40.26 2.52
399 410 4.788679 ACGTCCTATTTATTTTGAGGGGG 58.211 43.478 0.00 0.00 0.00 5.40
416 435 4.371855 TGATTGAGTGACAGATACGTCC 57.628 45.455 0.00 0.00 34.88 4.79
417 436 6.269315 AGATTGATTGAGTGACAGATACGTC 58.731 40.000 0.00 0.00 36.40 4.34
477 497 1.150536 AACAATCACCGGTGCTGGT 59.849 52.632 30.25 23.55 45.21 4.00
499 519 2.786777 TGCCAGATCATGCATGTATCC 58.213 47.619 25.43 13.01 31.31 2.59
643 2819 4.137615 GGTGGGGGTGGGTATGGC 62.138 72.222 0.00 0.00 0.00 4.40
1225 3523 2.244117 GACGAGGAGCAGGATGGCAA 62.244 60.000 0.00 0.00 35.86 4.52
1286 3587 0.662374 CGTTGAACACGCCGTCTACT 60.662 55.000 0.00 0.00 43.37 2.57
1527 3878 2.056906 GCCCACTGAACCTGGTGAGT 62.057 60.000 0.00 2.74 35.69 3.41
1646 5593 2.817844 GCCCAAGACCTACGAAAAACAT 59.182 45.455 0.00 0.00 0.00 2.71
1652 5599 1.180456 TCGTGCCCAAGACCTACGAA 61.180 55.000 0.00 0.00 40.33 3.85
1991 6259 8.541733 CGATTTGCGAATTAATACTTGCTTTA 57.458 30.769 0.00 0.00 44.57 1.85
2224 6521 2.670592 TCTTCGCTCCGGTCGACA 60.671 61.111 18.91 7.93 35.51 4.35
2381 6690 4.451629 AAATGCAGATGGAAGAAGCAAG 57.548 40.909 0.00 0.00 38.85 4.01
2624 6990 1.525995 AATGTAATCAGCCGGCGGG 60.526 57.895 29.48 20.14 0.00 6.13
2626 6997 0.732571 AACAATGTAATCAGCCGGCG 59.267 50.000 23.20 16.49 0.00 6.46
2725 7096 3.865745 CGTAGAACTGGTTGATGATCACC 59.134 47.826 0.00 0.84 0.00 4.02
2795 7166 7.649973 AGTATATAGATCGTCCAACACTCAAC 58.350 38.462 0.00 0.00 0.00 3.18
2846 7258 6.131544 AGAAGACGCACAAACATTTTAGTT 57.868 33.333 0.00 0.00 0.00 2.24
2870 7286 2.035832 CCTGCAATAAATTTAGCCCCCG 59.964 50.000 3.94 0.00 0.00 5.73
3427 7878 9.598320 AGTAATGCACTCAAATGGGTACCTTCA 62.598 40.741 12.72 2.11 41.87 3.02
3491 7975 1.682684 CGGCACTACCTCACCTCCT 60.683 63.158 0.00 0.00 35.61 3.69
3608 8095 8.094798 TGTCACACACTATTAAAGGATTTGAC 57.905 34.615 0.00 0.00 39.63 3.18
3620 8109 4.283467 TCCAGCTAGTTGTCACACACTATT 59.717 41.667 5.81 0.00 0.00 1.73
3630 8119 4.569943 TCTGTTTCATCCAGCTAGTTGTC 58.430 43.478 5.81 0.00 0.00 3.18
3662 8151 6.016192 TCAGAACCTAGATAACTATTGCCTCG 60.016 42.308 0.00 0.00 0.00 4.63
3719 8208 4.034048 CGCACTTTGTACACCCTATTCATC 59.966 45.833 0.00 0.00 0.00 2.92
3720 8209 3.938963 CGCACTTTGTACACCCTATTCAT 59.061 43.478 0.00 0.00 0.00 2.57
3721 8210 3.331150 CGCACTTTGTACACCCTATTCA 58.669 45.455 0.00 0.00 0.00 2.57
3722 8211 2.676342 CCGCACTTTGTACACCCTATTC 59.324 50.000 0.00 0.00 0.00 1.75
3723 8212 2.303600 TCCGCACTTTGTACACCCTATT 59.696 45.455 0.00 0.00 0.00 1.73
3724 8213 1.903860 TCCGCACTTTGTACACCCTAT 59.096 47.619 0.00 0.00 0.00 2.57
3725 8214 1.274167 CTCCGCACTTTGTACACCCTA 59.726 52.381 0.00 0.00 0.00 3.53
3726 8215 0.034896 CTCCGCACTTTGTACACCCT 59.965 55.000 0.00 0.00 0.00 4.34
3745 8235 2.095372 CCGGAACCGCTACTTTTTCATC 59.905 50.000 7.80 0.00 38.24 2.92
3754 8244 1.633561 GTAGAAACCGGAACCGCTAC 58.366 55.000 9.46 8.59 38.24 3.58
3805 8295 9.193133 GTAGAATACTCGTATGCATTGTGTATT 57.807 33.333 24.17 24.17 38.91 1.89
3806 8296 8.744008 GTAGAATACTCGTATGCATTGTGTAT 57.256 34.615 3.54 11.73 38.91 2.29
3826 8316 6.262273 GGACCAAACAGTTGAATTCAGTAGAA 59.738 38.462 8.41 0.00 36.83 2.10
3832 8322 4.531854 TCTGGACCAAACAGTTGAATTCA 58.468 39.130 3.38 3.38 36.83 2.57
3918 8408 2.069430 GGGAGCTGGGGGAAGAGAG 61.069 68.421 0.00 0.00 0.00 3.20
3919 8409 2.041265 GGGAGCTGGGGGAAGAGA 59.959 66.667 0.00 0.00 0.00 3.10
3923 8413 4.760220 GAGGGGGAGCTGGGGGAA 62.760 72.222 0.00 0.00 0.00 3.97
4057 8551 1.705997 AACACCCCACGGAGAAGCTT 61.706 55.000 0.00 0.00 0.00 3.74
4060 8554 1.003718 GGAACACCCCACGGAGAAG 60.004 63.158 0.00 0.00 0.00 2.85
4061 8555 1.460689 AGGAACACCCCACGGAGAA 60.461 57.895 0.00 0.00 34.66 2.87
4062 8556 1.911766 GAGGAACACCCCACGGAGA 60.912 63.158 0.00 0.00 34.66 3.71
4063 8557 2.663196 GAGGAACACCCCACGGAG 59.337 66.667 0.00 0.00 34.66 4.63
4064 8558 3.307906 CGAGGAACACCCCACGGA 61.308 66.667 0.00 0.00 34.66 4.69
4122 8617 1.102222 GTCGAGCCTATCTCCCGTGT 61.102 60.000 0.00 0.00 38.62 4.49
4124 8619 0.820074 CTGTCGAGCCTATCTCCCGT 60.820 60.000 0.00 0.00 38.62 5.28
4254 8757 2.126228 CCTGAAAGTCGCGCCGTA 60.126 61.111 0.00 0.00 0.00 4.02
4261 8764 2.742372 CCCGCCACCTGAAAGTCG 60.742 66.667 0.00 0.00 0.00 4.18
4263 8766 3.966543 CCCCCGCCACCTGAAAGT 61.967 66.667 0.00 0.00 0.00 2.66
4285 8788 2.345991 CACCCCATCGACCAACGT 59.654 61.111 0.00 0.00 43.13 3.99
4288 8791 2.350895 CAGCACCCCATCGACCAA 59.649 61.111 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.