Multiple sequence alignment - TraesCS7B01G381700

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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 TraesCS7B01G381700 chr7B 100.000 4115 0 0 1 4115 647012918 647008804 0.000000e+00 7600.0
1 TraesCS7B01G381700 chr7B 86.239 952 88 20 2210 3138 715812093 715811162 0.000000e+00 992.0
2 TraesCS7B01G381700 chr7B 86.761 355 27 13 3324 3667 715810856 715810511 1.080000e-100 377.0
3 TraesCS7B01G381700 chr7B 85.542 166 11 3 1386 1549 640714925 640715079 1.180000e-35 161.0
4 TraesCS7B01G381700 chr5A 99.025 3896 21 3 1 3895 226796842 226792963 0.000000e+00 6968.0
5 TraesCS7B01G381700 chr5A 86.127 901 93 13 2210 3083 63623871 63624766 0.000000e+00 942.0
6 TraesCS7B01G381700 chr5A 79.769 173 28 1 33 198 63557166 63557338 7.230000e-23 119.0
7 TraesCS7B01G381700 chr1D 91.720 3297 163 37 490 3743 206078544 206081773 0.000000e+00 4475.0
8 TraesCS7B01G381700 chr1D 84.703 438 26 5 9 411 206076554 206076985 2.300000e-107 399.0
9 TraesCS7B01G381700 chr1D 83.575 414 25 3 32 411 206077004 206077408 8.470000e-92 348.0
10 TraesCS7B01G381700 chr1D 93.878 196 6 2 216 411 206077440 206077629 1.450000e-74 291.0
11 TraesCS7B01G381700 chr1D 92.821 195 6 3 217 411 206078331 206078517 4.050000e-70 276.0
12 TraesCS7B01G381700 chr6A 89.252 1777 119 25 1981 3749 189431773 189430061 0.000000e+00 2158.0
13 TraesCS7B01G381700 chr3D 84.729 2174 246 47 33 2152 513938367 513940508 0.000000e+00 2097.0
14 TraesCS7B01G381700 chr3D 90.242 1117 90 13 2210 3312 513940880 513941991 0.000000e+00 1441.0
15 TraesCS7B01G381700 chr3D 87.829 304 23 7 3326 3621 513942038 513942335 1.100000e-90 344.0
16 TraesCS7B01G381700 chr3D 84.091 352 40 8 3403 3743 534119477 534119131 3.970000e-85 326.0
17 TraesCS7B01G381700 chr3D 77.971 345 42 13 33 346 73377828 73378169 7.020000e-43 185.0
18 TraesCS7B01G381700 chr2A 91.992 1461 103 9 2003 3450 753528611 753530070 0.000000e+00 2037.0
19 TraesCS7B01G381700 chr2A 83.689 515 53 11 1728 2211 751647804 751647290 1.350000e-124 457.0
20 TraesCS7B01G381700 chr2A 86.555 238 23 3 3520 3749 753530064 753530300 1.900000e-63 254.0
21 TraesCS7B01G381700 chr7A 88.948 1122 99 11 2210 3312 612738910 612740025 0.000000e+00 1362.0
22 TraesCS7B01G381700 chr7A 82.867 1214 159 28 33 1212 612702183 612703381 0.000000e+00 1044.0
23 TraesCS7B01G381700 chr7A 83.057 1027 107 26 2347 3315 690406183 690405166 0.000000e+00 870.0
24 TraesCS7B01G381700 chr7A 83.969 786 90 18 2557 3312 492422481 492423260 0.000000e+00 721.0
25 TraesCS7B01G381700 chr7A 87.715 407 44 5 1749 2152 612738135 612738538 1.730000e-128 470.0
26 TraesCS7B01G381700 chr7A 89.275 345 30 7 1262 1604 612711153 612711492 3.800000e-115 425.0
27 TraesCS7B01G381700 chr7A 82.186 247 25 12 1317 1555 669514713 669514948 1.170000e-45 195.0
28 TraesCS7B01G381700 chr1A 85.617 1328 121 41 728 2019 563755092 563756385 0.000000e+00 1330.0
29 TraesCS7B01G381700 chr1A 92.478 226 12 3 3892 4112 578474858 578474633 6.640000e-83 318.0
30 TraesCS7B01G381700 chr1A 86.232 138 7 4 3892 4028 578904648 578904774 5.550000e-29 139.0
31 TraesCS7B01G381700 chr6B 85.305 1327 125 45 728 2019 502721400 502722691 0.000000e+00 1306.0
32 TraesCS7B01G381700 chr6B 85.174 1322 126 39 734 2019 705836956 705835669 0.000000e+00 1291.0
33 TraesCS7B01G381700 chr6B 93.750 224 11 2 3892 4112 17494001 17493778 2.370000e-87 333.0
34 TraesCS7B01G381700 chr5B 86.196 949 87 21 2210 3135 669635107 669636034 0.000000e+00 987.0
35 TraesCS7B01G381700 chr5B 86.479 355 29 11 3324 3667 669636343 669636689 5.020000e-99 372.0
36 TraesCS7B01G381700 chr1B 81.296 1080 124 40 181 1220 473220526 473221567 0.000000e+00 804.0
37 TraesCS7B01G381700 chr1B 83.333 516 54 12 1728 2211 473221600 473222115 8.110000e-122 448.0
38 TraesCS7B01G381700 chr1B 82.448 433 63 9 3325 3749 103401068 103401495 2.340000e-97 366.0
39 TraesCS7B01G381700 chr1B 97.297 37 1 0 3860 3896 103424783 103424819 3.430000e-06 63.9
40 TraesCS7B01G381700 chr4B 81.268 1057 127 33 2748 3744 453511205 453510160 0.000000e+00 789.0
41 TraesCS7B01G381700 chr4B 83.433 833 101 12 2519 3320 55324845 55325671 0.000000e+00 739.0
42 TraesCS7B01G381700 chr2D 84.311 835 98 21 2509 3316 29523301 29522473 0.000000e+00 785.0
43 TraesCS7B01G381700 chr2B 83.553 833 99 12 2519 3320 72977864 72977039 0.000000e+00 745.0
44 TraesCS7B01G381700 chr2B 89.161 572 42 8 2536 3091 245168699 245169266 0.000000e+00 695.0
45 TraesCS7B01G381700 chr2B 84.937 239 25 3 3521 3749 245169678 245169915 8.900000e-57 231.0
46 TraesCS7B01G381700 chrUn 81.897 917 113 33 319 1220 13902405 13903283 0.000000e+00 725.0
47 TraesCS7B01G381700 chrUn 83.883 515 52 11 1728 2211 13903316 13903830 2.900000e-126 462.0
48 TraesCS7B01G381700 chr5D 95.089 224 8 2 3892 4112 41708700 41708477 2.350000e-92 350.0
49 TraesCS7B01G381700 chr3B 91.964 224 14 3 3893 4112 341453951 341453728 1.110000e-80 311.0
50 TraesCS7B01G381700 chr3B 82.778 180 16 10 181 348 118709084 118709260 3.310000e-31 147.0
51 TraesCS7B01G381700 chr7D 82.196 337 43 11 931 1266 577261595 577261915 1.460000e-69 274.0
52 TraesCS7B01G381700 chr3A 75.275 364 39 18 33 346 86337650 86338012 4.320000e-25 126.0
53 TraesCS7B01G381700 chr6D 79.096 177 28 5 655 829 169715209 169715378 3.360000e-21 113.0


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 TraesCS7B01G381700 chr7B 647008804 647012918 4114 True 7600.0 7600 100.0000 1 4115 1 chr7B.!!$R1 4114
1 TraesCS7B01G381700 chr7B 715810511 715812093 1582 True 684.5 992 86.5000 2210 3667 2 chr7B.!!$R2 1457
2 TraesCS7B01G381700 chr5A 226792963 226796842 3879 True 6968.0 6968 99.0250 1 3895 1 chr5A.!!$R1 3894
3 TraesCS7B01G381700 chr5A 63623871 63624766 895 False 942.0 942 86.1270 2210 3083 1 chr5A.!!$F2 873
4 TraesCS7B01G381700 chr1D 206076554 206081773 5219 False 1157.8 4475 89.3394 9 3743 5 chr1D.!!$F1 3734
5 TraesCS7B01G381700 chr6A 189430061 189431773 1712 True 2158.0 2158 89.2520 1981 3749 1 chr6A.!!$R1 1768
6 TraesCS7B01G381700 chr3D 513938367 513942335 3968 False 1294.0 2097 87.6000 33 3621 3 chr3D.!!$F2 3588
7 TraesCS7B01G381700 chr2A 753528611 753530300 1689 False 1145.5 2037 89.2735 2003 3749 2 chr2A.!!$F1 1746
8 TraesCS7B01G381700 chr2A 751647290 751647804 514 True 457.0 457 83.6890 1728 2211 1 chr2A.!!$R1 483
9 TraesCS7B01G381700 chr7A 612702183 612703381 1198 False 1044.0 1044 82.8670 33 1212 1 chr7A.!!$F2 1179
10 TraesCS7B01G381700 chr7A 612738135 612740025 1890 False 916.0 1362 88.3315 1749 3312 2 chr7A.!!$F5 1563
11 TraesCS7B01G381700 chr7A 690405166 690406183 1017 True 870.0 870 83.0570 2347 3315 1 chr7A.!!$R1 968
12 TraesCS7B01G381700 chr7A 492422481 492423260 779 False 721.0 721 83.9690 2557 3312 1 chr7A.!!$F1 755
13 TraesCS7B01G381700 chr1A 563755092 563756385 1293 False 1330.0 1330 85.6170 728 2019 1 chr1A.!!$F1 1291
14 TraesCS7B01G381700 chr6B 502721400 502722691 1291 False 1306.0 1306 85.3050 728 2019 1 chr6B.!!$F1 1291
15 TraesCS7B01G381700 chr6B 705835669 705836956 1287 True 1291.0 1291 85.1740 734 2019 1 chr6B.!!$R2 1285
16 TraesCS7B01G381700 chr5B 669635107 669636689 1582 False 679.5 987 86.3375 2210 3667 2 chr5B.!!$F1 1457
17 TraesCS7B01G381700 chr1B 473220526 473222115 1589 False 626.0 804 82.3145 181 2211 2 chr1B.!!$F3 2030
18 TraesCS7B01G381700 chr4B 453510160 453511205 1045 True 789.0 789 81.2680 2748 3744 1 chr4B.!!$R1 996
19 TraesCS7B01G381700 chr4B 55324845 55325671 826 False 739.0 739 83.4330 2519 3320 1 chr4B.!!$F1 801
20 TraesCS7B01G381700 chr2D 29522473 29523301 828 True 785.0 785 84.3110 2509 3316 1 chr2D.!!$R1 807
21 TraesCS7B01G381700 chr2B 72977039 72977864 825 True 745.0 745 83.5530 2519 3320 1 chr2B.!!$R1 801
22 TraesCS7B01G381700 chr2B 245168699 245169915 1216 False 463.0 695 87.0490 2536 3749 2 chr2B.!!$F1 1213
23 TraesCS7B01G381700 chrUn 13902405 13903830 1425 False 593.5 725 82.8900 319 2211 2 chrUn.!!$F1 1892

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
433 915 1.002134 CACCAGGGTCCATCACACC 60.002 63.158 0.00 0.0 0.00 4.16 F
1177 2758 1.543642 TTCCTCATGGGGAAGGCCA 60.544 57.895 23.76 0.0 40.08 5.36 F
2248 4253 4.805719 TCGCATAGATGTTGATCACAGTTC 59.194 41.667 0.00 0.0 39.40 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2248 4253 8.876275 TGGATTCTCTTTTCATTTTGAAGTTG 57.124 30.769 0.0 0.0 37.7 3.16 R
2911 5007 7.739498 ACCGACATTACACTAAAAATTGTCT 57.261 32.000 0.0 0.0 0.0 3.41 R
4064 6601 1.073603 TCTCCACATGCATTGACACCA 59.926 47.619 0.0 0.0 0.0 4.17 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
93 95 3.124921 GATGGTGTTCGTGGCCGG 61.125 66.667 0.00 0.00 33.95 6.13
432 914 1.675641 GCACCAGGGTCCATCACAC 60.676 63.158 0.00 0.00 0.00 3.82
433 915 1.002134 CACCAGGGTCCATCACACC 60.002 63.158 0.00 0.00 0.00 4.16
1177 2758 1.543642 TTCCTCATGGGGAAGGCCA 60.544 57.895 23.76 0.00 40.08 5.36
1501 3124 5.278907 CCAGTCCATGTGAATTGCTTTTGTA 60.279 40.000 0.00 0.00 0.00 2.41
1502 3125 6.392354 CAGTCCATGTGAATTGCTTTTGTAT 58.608 36.000 0.00 0.00 0.00 2.29
1503 3126 7.362834 CCAGTCCATGTGAATTGCTTTTGTATA 60.363 37.037 0.00 0.00 0.00 1.47
1504 3127 8.192774 CAGTCCATGTGAATTGCTTTTGTATAT 58.807 33.333 0.00 0.00 0.00 0.86
1505 3128 8.752187 AGTCCATGTGAATTGCTTTTGTATATT 58.248 29.630 0.00 0.00 0.00 1.28
1506 3129 9.023967 GTCCATGTGAATTGCTTTTGTATATTC 57.976 33.333 0.00 0.00 0.00 1.75
1507 3130 7.914871 TCCATGTGAATTGCTTTTGTATATTCG 59.085 33.333 0.00 0.00 0.00 3.34
1508 3131 7.914871 CCATGTGAATTGCTTTTGTATATTCGA 59.085 33.333 0.00 0.00 0.00 3.71
1509 3132 9.454585 CATGTGAATTGCTTTTGTATATTCGAT 57.545 29.630 0.00 0.00 0.00 3.59
2248 4253 4.805719 TCGCATAGATGTTGATCACAGTTC 59.194 41.667 0.00 0.00 39.40 3.01
2911 5007 8.947055 ATTTTGAGCAAGCTTTCTTTTTCTTA 57.053 26.923 0.00 0.00 0.00 2.10
3145 5332 4.347876 TGTGGACTATGGATTCATACCAGG 59.652 45.833 3.99 0.00 40.89 4.45
3795 6332 4.036518 ACTACATGCCAGAATCCTCTCTT 58.963 43.478 0.00 0.00 0.00 2.85
3844 6381 6.822170 TCCGCATACTATGTATAGACGAGATT 59.178 38.462 5.93 0.00 34.50 2.40
3846 6383 7.640630 CCGCATACTATGTATAGACGAGATTTC 59.359 40.741 5.93 0.00 34.50 2.17
3895 6432 6.236017 GCACATGCACACTTACTAGTTTTA 57.764 37.500 0.00 0.00 41.59 1.52
3896 6433 6.842163 GCACATGCACACTTACTAGTTTTAT 58.158 36.000 0.00 0.00 41.59 1.40
3897 6434 7.305474 GCACATGCACACTTACTAGTTTTATT 58.695 34.615 0.00 0.00 41.59 1.40
3898 6435 8.447833 GCACATGCACACTTACTAGTTTTATTA 58.552 33.333 0.00 0.00 41.59 0.98
3924 6461 9.801873 AAAATACCAAACATGAGTATAATGCAC 57.198 29.630 0.00 0.00 0.00 4.57
3925 6462 5.835113 ACCAAACATGAGTATAATGCACC 57.165 39.130 0.00 0.00 0.00 5.01
3926 6463 5.260424 ACCAAACATGAGTATAATGCACCA 58.740 37.500 0.00 0.00 0.00 4.17
3927 6464 5.714333 ACCAAACATGAGTATAATGCACCAA 59.286 36.000 0.00 0.00 0.00 3.67
3928 6465 6.380846 ACCAAACATGAGTATAATGCACCAAT 59.619 34.615 0.00 0.00 0.00 3.16
3929 6466 7.093377 ACCAAACATGAGTATAATGCACCAATT 60.093 33.333 0.00 0.00 0.00 2.32
3930 6467 7.223193 CCAAACATGAGTATAATGCACCAATTG 59.777 37.037 0.00 0.00 0.00 2.32
3931 6468 6.395426 ACATGAGTATAATGCACCAATTGG 57.605 37.500 23.31 23.31 42.17 3.16
3932 6469 4.916983 TGAGTATAATGCACCAATTGGC 57.083 40.909 24.79 11.93 39.32 4.52
3933 6470 4.276642 TGAGTATAATGCACCAATTGGCA 58.723 39.130 24.79 17.37 45.23 4.92
3934 6471 4.708909 TGAGTATAATGCACCAATTGGCAA 59.291 37.500 24.79 10.50 44.20 4.52
3935 6472 5.363292 TGAGTATAATGCACCAATTGGCAAT 59.637 36.000 24.79 12.76 44.20 3.56
3936 6473 6.548993 TGAGTATAATGCACCAATTGGCAATA 59.451 34.615 24.79 14.47 44.20 1.90
3937 6474 7.069208 TGAGTATAATGCACCAATTGGCAATAA 59.931 33.333 24.79 6.40 44.20 1.40
3938 6475 7.436118 AGTATAATGCACCAATTGGCAATAAG 58.564 34.615 24.79 10.29 44.20 1.73
3939 6476 4.556592 AATGCACCAATTGGCAATAAGT 57.443 36.364 24.79 10.95 44.20 2.24
3940 6477 4.556592 ATGCACCAATTGGCAATAAGTT 57.443 36.364 24.79 0.00 44.20 2.66
3941 6478 5.674052 ATGCACCAATTGGCAATAAGTTA 57.326 34.783 24.79 6.04 44.20 2.24
3942 6479 5.474578 TGCACCAATTGGCAATAAGTTAA 57.525 34.783 24.79 2.10 37.03 2.01
3943 6480 5.233988 TGCACCAATTGGCAATAAGTTAAC 58.766 37.500 24.79 0.00 37.03 2.01
3944 6481 5.011533 TGCACCAATTGGCAATAAGTTAACT 59.988 36.000 24.79 1.12 37.03 2.24
3945 6482 5.348451 GCACCAATTGGCAATAAGTTAACTG 59.652 40.000 24.79 11.02 39.32 3.16
3946 6483 6.686630 CACCAATTGGCAATAAGTTAACTGA 58.313 36.000 24.79 0.93 39.32 3.41
3947 6484 7.151308 CACCAATTGGCAATAAGTTAACTGAA 58.849 34.615 24.79 0.80 39.32 3.02
3948 6485 7.818930 CACCAATTGGCAATAAGTTAACTGAAT 59.181 33.333 24.79 3.39 39.32 2.57
3949 6486 8.034804 ACCAATTGGCAATAAGTTAACTGAATC 58.965 33.333 24.79 0.00 39.32 2.52
3950 6487 8.253113 CCAATTGGCAATAAGTTAACTGAATCT 58.747 33.333 14.05 0.00 0.00 2.40
3953 6490 8.506168 TTGGCAATAAGTTAACTGAATCTAGG 57.494 34.615 9.34 0.00 0.00 3.02
3954 6491 7.630082 TGGCAATAAGTTAACTGAATCTAGGT 58.370 34.615 9.34 0.00 0.00 3.08
3955 6492 8.107095 TGGCAATAAGTTAACTGAATCTAGGTT 58.893 33.333 9.34 0.00 0.00 3.50
3956 6493 8.613482 GGCAATAAGTTAACTGAATCTAGGTTC 58.387 37.037 9.34 8.91 0.00 3.62
3957 6494 9.162764 GCAATAAGTTAACTGAATCTAGGTTCA 57.837 33.333 17.41 17.41 36.70 3.18
4003 6540 9.905713 AAGTTTGAGCATGTTAGATTATAAGGA 57.094 29.630 0.00 0.00 0.00 3.36
4004 6541 9.905713 AGTTTGAGCATGTTAGATTATAAGGAA 57.094 29.630 0.00 0.00 0.00 3.36
4036 6573 8.000780 AGAATTAATTTGTCTTCTGGTATGCC 57.999 34.615 1.43 0.00 0.00 4.40
4037 6574 7.836183 AGAATTAATTTGTCTTCTGGTATGCCT 59.164 33.333 1.43 0.00 35.27 4.75
4038 6575 7.961326 ATTAATTTGTCTTCTGGTATGCCTT 57.039 32.000 0.16 0.00 35.27 4.35
4039 6576 7.775053 TTAATTTGTCTTCTGGTATGCCTTT 57.225 32.000 0.16 0.00 35.27 3.11
4040 6577 5.649782 ATTTGTCTTCTGGTATGCCTTTG 57.350 39.130 0.16 0.00 35.27 2.77
4041 6578 4.365514 TTGTCTTCTGGTATGCCTTTGA 57.634 40.909 0.16 0.00 35.27 2.69
4042 6579 4.574674 TGTCTTCTGGTATGCCTTTGAT 57.425 40.909 0.16 0.00 35.27 2.57
4043 6580 4.922206 TGTCTTCTGGTATGCCTTTGATT 58.078 39.130 0.16 0.00 35.27 2.57
4044 6581 5.324409 TGTCTTCTGGTATGCCTTTGATTT 58.676 37.500 0.16 0.00 35.27 2.17
4045 6582 6.480763 TGTCTTCTGGTATGCCTTTGATTTA 58.519 36.000 0.16 0.00 35.27 1.40
4046 6583 6.945435 TGTCTTCTGGTATGCCTTTGATTTAA 59.055 34.615 0.16 0.00 35.27 1.52
4047 6584 7.615365 TGTCTTCTGGTATGCCTTTGATTTAAT 59.385 33.333 0.16 0.00 35.27 1.40
4048 6585 7.917505 GTCTTCTGGTATGCCTTTGATTTAATG 59.082 37.037 0.16 0.00 35.27 1.90
4049 6586 7.615365 TCTTCTGGTATGCCTTTGATTTAATGT 59.385 33.333 0.16 0.00 35.27 2.71
4050 6587 7.333528 TCTGGTATGCCTTTGATTTAATGTC 57.666 36.000 0.16 0.00 35.27 3.06
4051 6588 6.889177 TCTGGTATGCCTTTGATTTAATGTCA 59.111 34.615 0.16 0.00 35.27 3.58
4052 6589 7.395772 TCTGGTATGCCTTTGATTTAATGTCAA 59.604 33.333 0.16 0.98 34.01 3.18
4053 6590 7.319646 TGGTATGCCTTTGATTTAATGTCAAC 58.680 34.615 0.16 0.00 35.47 3.18
4054 6591 7.178274 TGGTATGCCTTTGATTTAATGTCAACT 59.822 33.333 0.16 0.00 35.47 3.16
4055 6592 8.682710 GGTATGCCTTTGATTTAATGTCAACTA 58.317 33.333 0.00 0.00 35.47 2.24
4059 6596 9.421806 TGCCTTTGATTTAATGTCAACTATTTG 57.578 29.630 3.95 0.00 35.47 2.32
4060 6597 9.638239 GCCTTTGATTTAATGTCAACTATTTGA 57.362 29.630 3.95 0.00 39.55 2.69
4082 6619 1.992538 TTGGTGTCAATGCATGTGGA 58.007 45.000 0.00 0.00 0.00 4.02
4083 6620 1.536940 TGGTGTCAATGCATGTGGAG 58.463 50.000 0.00 0.00 0.00 3.86
4084 6621 1.073603 TGGTGTCAATGCATGTGGAGA 59.926 47.619 0.00 0.00 0.00 3.71
4085 6622 2.291089 TGGTGTCAATGCATGTGGAGAT 60.291 45.455 0.00 0.00 0.00 2.75
4086 6623 3.054508 TGGTGTCAATGCATGTGGAGATA 60.055 43.478 0.00 0.00 0.00 1.98
4087 6624 4.139786 GGTGTCAATGCATGTGGAGATAT 58.860 43.478 0.00 0.00 0.00 1.63
4088 6625 4.581824 GGTGTCAATGCATGTGGAGATATT 59.418 41.667 0.00 0.00 0.00 1.28
4089 6626 5.068198 GGTGTCAATGCATGTGGAGATATTT 59.932 40.000 0.00 0.00 0.00 1.40
4090 6627 5.975344 GTGTCAATGCATGTGGAGATATTTG 59.025 40.000 0.00 0.00 0.00 2.32
4091 6628 5.653330 TGTCAATGCATGTGGAGATATTTGT 59.347 36.000 0.00 0.00 0.00 2.83
4092 6629 5.975344 GTCAATGCATGTGGAGATATTTGTG 59.025 40.000 0.00 0.00 0.00 3.33
4093 6630 5.653330 TCAATGCATGTGGAGATATTTGTGT 59.347 36.000 0.00 0.00 0.00 3.72
4094 6631 6.153170 TCAATGCATGTGGAGATATTTGTGTT 59.847 34.615 0.00 0.00 0.00 3.32
4095 6632 5.313520 TGCATGTGGAGATATTTGTGTTG 57.686 39.130 0.00 0.00 0.00 3.33
4096 6633 4.107622 GCATGTGGAGATATTTGTGTTGC 58.892 43.478 0.00 0.00 0.00 4.17
4097 6634 4.380761 GCATGTGGAGATATTTGTGTTGCA 60.381 41.667 0.00 0.00 0.00 4.08
4098 6635 5.712004 CATGTGGAGATATTTGTGTTGCAA 58.288 37.500 0.00 0.00 34.87 4.08
4110 6647 6.884096 TTTGTGTTGCAAAATCTACAACTG 57.116 33.333 0.00 0.00 43.39 3.16
4111 6648 5.574891 TGTGTTGCAAAATCTACAACTGT 57.425 34.783 0.00 0.00 43.19 3.55
4112 6649 5.960113 TGTGTTGCAAAATCTACAACTGTT 58.040 33.333 0.00 0.00 43.19 3.16
4113 6650 6.393990 TGTGTTGCAAAATCTACAACTGTTT 58.606 32.000 0.00 0.00 43.19 2.83
4114 6651 6.870965 TGTGTTGCAAAATCTACAACTGTTTT 59.129 30.769 0.00 0.00 43.19 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
432 914 2.146061 GGGAGGATGCTGGAGGAGG 61.146 68.421 0.00 0.00 0.00 4.30
433 915 2.146061 GGGGAGGATGCTGGAGGAG 61.146 68.421 0.00 0.00 0.00 3.69
1177 2758 1.282157 GTTGGCTAGGATGACCTTGGT 59.718 52.381 0.00 0.00 45.36 3.67
2248 4253 8.876275 TGGATTCTCTTTTCATTTTGAAGTTG 57.124 30.769 0.00 0.00 37.70 3.16
2911 5007 7.739498 ACCGACATTACACTAAAAATTGTCT 57.261 32.000 0.00 0.00 0.00 3.41
3795 6332 7.390718 GGATTCTGCAAAGAGGAAGTTAAGTAA 59.609 37.037 0.00 0.00 0.00 2.24
3898 6435 9.801873 GTGCATTATACTCATGTTTGGTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
3899 6436 8.413229 GGTGCATTATACTCATGTTTGGTATTT 58.587 33.333 0.00 0.00 0.00 1.40
3900 6437 7.559533 TGGTGCATTATACTCATGTTTGGTATT 59.440 33.333 0.00 0.00 0.00 1.89
3901 6438 7.059788 TGGTGCATTATACTCATGTTTGGTAT 58.940 34.615 0.00 1.35 0.00 2.73
3902 6439 6.418946 TGGTGCATTATACTCATGTTTGGTA 58.581 36.000 0.00 0.00 0.00 3.25
3903 6440 5.260424 TGGTGCATTATACTCATGTTTGGT 58.740 37.500 0.00 0.00 0.00 3.67
3904 6441 5.833406 TGGTGCATTATACTCATGTTTGG 57.167 39.130 0.00 0.00 0.00 3.28
3905 6442 7.223193 CCAATTGGTGCATTATACTCATGTTTG 59.777 37.037 16.90 0.00 0.00 2.93
3906 6443 7.267128 CCAATTGGTGCATTATACTCATGTTT 58.733 34.615 16.90 0.00 0.00 2.83
3907 6444 6.683610 GCCAATTGGTGCATTATACTCATGTT 60.684 38.462 25.19 0.00 37.57 2.71
3908 6445 5.221303 GCCAATTGGTGCATTATACTCATGT 60.221 40.000 25.19 0.00 37.57 3.21
3909 6446 5.221283 TGCCAATTGGTGCATTATACTCATG 60.221 40.000 25.19 0.00 37.57 3.07
3910 6447 4.894705 TGCCAATTGGTGCATTATACTCAT 59.105 37.500 25.19 0.00 37.57 2.90
3911 6448 4.276642 TGCCAATTGGTGCATTATACTCA 58.723 39.130 25.19 7.55 37.57 3.41
3912 6449 4.916983 TGCCAATTGGTGCATTATACTC 57.083 40.909 25.19 4.97 37.57 2.59
3913 6450 5.874897 ATTGCCAATTGGTGCATTATACT 57.125 34.783 25.19 0.00 37.33 2.12
3914 6451 7.209475 ACTTATTGCCAATTGGTGCATTATAC 58.791 34.615 25.19 6.20 37.33 1.47
3915 6452 7.358770 ACTTATTGCCAATTGGTGCATTATA 57.641 32.000 25.19 10.67 37.33 0.98
3916 6453 6.237887 ACTTATTGCCAATTGGTGCATTAT 57.762 33.333 25.19 11.55 37.33 1.28
3917 6454 5.674052 ACTTATTGCCAATTGGTGCATTA 57.326 34.783 25.19 14.63 37.33 1.90
3918 6455 4.556592 ACTTATTGCCAATTGGTGCATT 57.443 36.364 25.19 15.53 37.33 3.56
3919 6456 4.556592 AACTTATTGCCAATTGGTGCAT 57.443 36.364 25.19 16.20 37.33 3.96
3920 6457 5.011533 AGTTAACTTATTGCCAATTGGTGCA 59.988 36.000 25.19 15.14 37.57 4.57
3921 6458 5.348451 CAGTTAACTTATTGCCAATTGGTGC 59.652 40.000 25.19 12.64 37.57 5.01
3922 6459 6.686630 TCAGTTAACTTATTGCCAATTGGTG 58.313 36.000 25.19 10.90 37.57 4.17
3923 6460 6.909550 TCAGTTAACTTATTGCCAATTGGT 57.090 33.333 25.19 8.79 37.57 3.67
3924 6461 8.253113 AGATTCAGTTAACTTATTGCCAATTGG 58.747 33.333 20.81 20.81 38.53 3.16
3927 6464 9.125026 CCTAGATTCAGTTAACTTATTGCCAAT 57.875 33.333 5.07 0.00 0.00 3.16
3928 6465 8.107095 ACCTAGATTCAGTTAACTTATTGCCAA 58.893 33.333 5.07 0.00 0.00 4.52
3929 6466 7.630082 ACCTAGATTCAGTTAACTTATTGCCA 58.370 34.615 5.07 0.00 0.00 4.92
3930 6467 8.507524 AACCTAGATTCAGTTAACTTATTGCC 57.492 34.615 5.07 0.00 0.00 4.52
3931 6468 9.162764 TGAACCTAGATTCAGTTAACTTATTGC 57.837 33.333 5.07 0.00 33.62 3.56
3977 6514 9.905713 TCCTTATAATCTAACATGCTCAAACTT 57.094 29.630 0.00 0.00 0.00 2.66
3978 6515 9.905713 TTCCTTATAATCTAACATGCTCAAACT 57.094 29.630 0.00 0.00 0.00 2.66
4010 6547 9.120538 GGCATACCAGAAGACAAATTAATTCTA 57.879 33.333 0.10 0.00 35.26 2.10
4011 6548 7.836183 AGGCATACCAGAAGACAAATTAATTCT 59.164 33.333 0.10 0.00 39.06 2.40
4012 6549 8.000780 AGGCATACCAGAAGACAAATTAATTC 57.999 34.615 0.10 0.00 39.06 2.17
4013 6550 7.961326 AGGCATACCAGAAGACAAATTAATT 57.039 32.000 0.00 0.00 39.06 1.40
4014 6551 7.961326 AAGGCATACCAGAAGACAAATTAAT 57.039 32.000 0.00 0.00 39.06 1.40
4015 6552 7.450014 TCAAAGGCATACCAGAAGACAAATTAA 59.550 33.333 0.00 0.00 39.06 1.40
4016 6553 6.945435 TCAAAGGCATACCAGAAGACAAATTA 59.055 34.615 0.00 0.00 39.06 1.40
4017 6554 5.774690 TCAAAGGCATACCAGAAGACAAATT 59.225 36.000 0.00 0.00 39.06 1.82
4018 6555 5.324409 TCAAAGGCATACCAGAAGACAAAT 58.676 37.500 0.00 0.00 39.06 2.32
4019 6556 4.724399 TCAAAGGCATACCAGAAGACAAA 58.276 39.130 0.00 0.00 39.06 2.83
4020 6557 4.365514 TCAAAGGCATACCAGAAGACAA 57.634 40.909 0.00 0.00 39.06 3.18
4021 6558 4.574674 ATCAAAGGCATACCAGAAGACA 57.425 40.909 0.00 0.00 39.06 3.41
4022 6559 5.904362 AAATCAAAGGCATACCAGAAGAC 57.096 39.130 0.00 0.00 39.06 3.01
4023 6560 7.615365 ACATTAAATCAAAGGCATACCAGAAGA 59.385 33.333 0.00 0.00 39.06 2.87
4024 6561 7.775120 ACATTAAATCAAAGGCATACCAGAAG 58.225 34.615 0.00 0.00 39.06 2.85
4025 6562 7.395772 TGACATTAAATCAAAGGCATACCAGAA 59.604 33.333 0.00 0.00 39.06 3.02
4026 6563 6.889177 TGACATTAAATCAAAGGCATACCAGA 59.111 34.615 0.00 0.00 39.06 3.86
4027 6564 7.099266 TGACATTAAATCAAAGGCATACCAG 57.901 36.000 0.00 0.00 39.06 4.00
4028 6565 7.178274 AGTTGACATTAAATCAAAGGCATACCA 59.822 33.333 7.01 0.00 37.80 3.25
4029 6566 7.547227 AGTTGACATTAAATCAAAGGCATACC 58.453 34.615 7.01 0.00 37.80 2.73
4033 6570 9.421806 CAAATAGTTGACATTAAATCAAAGGCA 57.578 29.630 0.00 0.00 37.80 4.75
4034 6571 9.638239 TCAAATAGTTGACATTAAATCAAAGGC 57.362 29.630 0.56 0.00 38.88 4.35
4062 6599 2.494471 CTCCACATGCATTGACACCAAT 59.506 45.455 0.00 0.00 43.37 3.16
4063 6600 1.887854 CTCCACATGCATTGACACCAA 59.112 47.619 0.00 0.00 36.61 3.67
4064 6601 1.073603 TCTCCACATGCATTGACACCA 59.926 47.619 0.00 0.00 0.00 4.17
4065 6602 1.825090 TCTCCACATGCATTGACACC 58.175 50.000 0.00 0.00 0.00 4.16
4066 6603 5.762825 AATATCTCCACATGCATTGACAC 57.237 39.130 0.00 0.00 0.00 3.67
4067 6604 5.653330 ACAAATATCTCCACATGCATTGACA 59.347 36.000 0.00 0.00 0.00 3.58
4068 6605 5.975344 CACAAATATCTCCACATGCATTGAC 59.025 40.000 0.00 0.00 0.00 3.18
4069 6606 5.653330 ACACAAATATCTCCACATGCATTGA 59.347 36.000 0.00 0.00 0.00 2.57
4070 6607 5.898174 ACACAAATATCTCCACATGCATTG 58.102 37.500 0.00 0.00 0.00 2.82
4071 6608 6.334989 CAACACAAATATCTCCACATGCATT 58.665 36.000 0.00 0.00 0.00 3.56
4072 6609 5.680408 GCAACACAAATATCTCCACATGCAT 60.680 40.000 0.00 0.00 0.00 3.96
4073 6610 4.380761 GCAACACAAATATCTCCACATGCA 60.381 41.667 0.00 0.00 0.00 3.96
4074 6611 4.107622 GCAACACAAATATCTCCACATGC 58.892 43.478 0.00 0.00 0.00 4.06
4075 6612 5.313520 TGCAACACAAATATCTCCACATG 57.686 39.130 0.00 0.00 0.00 3.21
4076 6613 5.981088 TTGCAACACAAATATCTCCACAT 57.019 34.783 0.00 0.00 34.56 3.21
4077 6614 5.781210 TTTGCAACACAAATATCTCCACA 57.219 34.783 0.00 0.00 43.35 4.17


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

AutoCloner maintained by Alex Coulton.