Multiple sequence alignment - TraesCS3D01G122700

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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 TraesCS3D01G122700 chr3D 100.000 2770 0 0 1 2770 80578626 80575857 0.000000e+00 5116.0
1 TraesCS3D01G122700 chr3D 92.069 870 44 8 739 1604 80220507 80221355 0.000000e+00 1201.0
2 TraesCS3D01G122700 chr3D 92.043 842 67 0 1601 2442 80226745 80227586 0.000000e+00 1184.0
3 TraesCS3D01G122700 chr3D 100.000 317 0 0 3115 3431 80575512 80575196 1.370000e-163 586.0
4 TraesCS3D01G122700 chr3D 76.386 1046 190 36 1047 2077 80417933 80416930 8.490000e-141 510.0
5 TraesCS3D01G122700 chr3D 93.385 257 17 0 2509 2765 486147832 486147576 6.950000e-102 381.0
6 TraesCS3D01G122700 chr3D 93.103 261 14 1 2510 2770 39167979 39168235 2.500000e-101 379.0
7 TraesCS3D01G122700 chr3D 74.370 952 204 26 1434 2374 80917026 80916104 1.500000e-98 370.0
8 TraesCS3D01G122700 chr3D 74.160 952 206 23 1434 2374 80600897 80599975 3.260000e-95 359.0
9 TraesCS3D01G122700 chr3D 74.086 957 201 35 1434 2374 80630015 80629090 1.960000e-92 350.0
10 TraesCS3D01G122700 chr3D 89.773 176 16 2 3197 3372 9440671 9440844 1.240000e-54 224.0
11 TraesCS3D01G122700 chr3D 86.861 137 6 4 3115 3239 9440545 9440681 3.570000e-30 143.0
12 TraesCS3D01G122700 chr3D 97.101 69 1 1 3363 3430 397773185 397773117 7.780000e-22 115.0
13 TraesCS3D01G122700 chr3A 92.179 1675 115 11 739 2406 94192751 94191086 0.000000e+00 2353.0
14 TraesCS3D01G122700 chr3A 94.200 500 23 2 140 639 24705879 24705386 0.000000e+00 758.0
15 TraesCS3D01G122700 chr3A 74.947 950 202 24 1434 2374 94254828 94253906 1.480000e-108 403.0
16 TraesCS3D01G122700 chr3A 74.664 967 203 28 1434 2388 94858688 94857752 1.150000e-104 390.0
17 TraesCS3D01G122700 chr3A 90.909 165 13 2 140 303 628892848 628892685 1.600000e-53 220.0
18 TraesCS3D01G122700 chr3A 89.697 165 15 2 140 303 696184914 696184751 3.470000e-50 209.0
19 TraesCS3D01G122700 chr3A 91.045 67 3 1 3115 3178 11942584 11942650 1.700000e-13 87.9
20 TraesCS3D01G122700 chr3B 91.998 1687 90 18 803 2449 126375588 126373907 0.000000e+00 2326.0
21 TraesCS3D01G122700 chr3B 76.611 1086 197 34 1022 2095 126299512 126298472 2.330000e-151 545.0
22 TraesCS3D01G122700 chr3B 74.372 956 197 28 1434 2374 126400333 126399411 7.000000e-97 364.0
23 TraesCS3D01G122700 chr3B 88.991 109 2 8 610 709 310871166 310871273 3.590000e-25 126.0
24 TraesCS3D01G122700 chr3B 95.556 45 2 0 3117 3161 612296607 612296651 4.750000e-09 73.1
25 TraesCS3D01G122700 chr3B 87.500 56 4 2 2455 2507 746021673 746021618 1.030000e-05 62.1
26 TraesCS3D01G122700 chr5D 97.884 709 6 7 1 705 323560145 323560848 0.000000e+00 1218.0
27 TraesCS3D01G122700 chr4D 96.672 661 16 2 1 655 481215152 481215812 0.000000e+00 1094.0
28 TraesCS3D01G122700 chr4D 93.750 144 8 1 3229 3372 503479520 503479662 7.460000e-52 215.0
29 TraesCS3D01G122700 chr4D 88.068 176 12 8 3192 3365 439786241 439786409 2.090000e-47 200.0
30 TraesCS3D01G122700 chr4D 89.362 141 10 5 3233 3372 94417651 94417515 4.550000e-39 172.0
31 TraesCS3D01G122700 chr4D 95.714 70 2 1 3363 3431 84236931 84237000 1.010000e-20 111.0
32 TraesCS3D01G122700 chr4D 95.714 70 2 1 3363 3431 439786445 439786514 1.010000e-20 111.0
33 TraesCS3D01G122700 chr4D 94.286 70 3 1 3363 3431 503479691 503479760 4.680000e-19 106.0
34 TraesCS3D01G122700 chr7B 95.248 505 19 1 140 639 568667922 568667418 0.000000e+00 795.0
35 TraesCS3D01G122700 chr7D 94.357 443 16 4 228 663 611284656 611285096 0.000000e+00 671.0
36 TraesCS3D01G122700 chr7D 95.785 261 11 0 2510 2770 105202506 105202246 4.090000e-114 422.0
37 TraesCS3D01G122700 chr7D 92.029 276 4 9 447 705 116793676 116793402 4.180000e-99 372.0
38 TraesCS3D01G122700 chr7D 92.366 262 16 1 2509 2770 147589864 147589607 1.500000e-98 370.0
39 TraesCS3D01G122700 chr7D 92.692 260 14 2 2509 2768 604331167 604331421 1.500000e-98 370.0
40 TraesCS3D01G122700 chr7D 79.570 372 21 20 3115 3431 105202221 105201850 7.460000e-52 215.0
41 TraesCS3D01G122700 chr7D 95.789 95 3 1 6 100 255123655 255123748 5.930000e-33 152.0
42 TraesCS3D01G122700 chr7D 100.000 29 0 0 2457 2485 599718095 599718123 2.000000e-03 54.7
43 TraesCS3D01G122700 chr1B 87.856 527 31 8 140 663 642925151 642924655 3.810000e-164 588.0
44 TraesCS3D01G122700 chr1B 95.714 140 6 0 3233 3372 688759688 688759549 3.450000e-55 226.0
45 TraesCS3D01G122700 chr1B 97.980 99 2 0 2 100 159867430 159867528 4.550000e-39 172.0
46 TraesCS3D01G122700 chr1B 95.000 100 5 0 1 100 205886279 205886378 1.270000e-34 158.0
47 TraesCS3D01G122700 chr1A 91.791 402 24 6 140 537 561060007 561060403 5.000000e-153 551.0
48 TraesCS3D01G122700 chr1A 93.333 45 2 1 2454 2498 61718723 61718766 7.950000e-07 65.8
49 TraesCS3D01G122700 chr5A 93.333 345 20 1 188 532 705300836 705301177 1.100000e-139 507.0
50 TraesCS3D01G122700 chr5A 84.112 107 14 2 1091 1197 21418869 21418972 2.180000e-17 100.0
51 TraesCS3D01G122700 chr6B 93.651 315 15 5 315 625 33959561 33959874 1.860000e-127 466.0
52 TraesCS3D01G122700 chr6B 96.350 137 5 0 3234 3370 687042570 687042434 3.450000e-55 226.0
53 TraesCS3D01G122700 chr6B 85.714 105 12 2 1093 1197 683371744 683371845 1.300000e-19 108.0
54 TraesCS3D01G122700 chr6B 84.762 105 13 2 1093 1197 683317132 683317233 6.060000e-18 102.0
55 TraesCS3D01G122700 chr2D 96.970 264 3 4 447 706 476869736 476869474 4.070000e-119 438.0
56 TraesCS3D01G122700 chr2D 94.841 252 11 2 2512 2762 480758748 480758498 3.210000e-105 392.0
57 TraesCS3D01G122700 chr2D 93.130 262 18 0 2509 2770 625193053 625192792 5.370000e-103 385.0
58 TraesCS3D01G122700 chr2D 87.727 220 11 5 3169 3372 44610289 44610508 3.420000e-60 243.0
59 TraesCS3D01G122700 chr2D 96.479 142 5 0 3231 3372 35521437 35521296 5.720000e-58 235.0
60 TraesCS3D01G122700 chr2D 94.681 94 2 1 3115 3205 139720923 139721016 3.570000e-30 143.0
61 TraesCS3D01G122700 chr2D 100.000 66 0 0 3366 3431 625192177 625192112 4.650000e-24 122.0
62 TraesCS3D01G122700 chr2D 97.561 41 1 0 3115 3155 625192767 625192727 1.710000e-08 71.3
63 TraesCS3D01G122700 chr2D 93.182 44 3 0 2445 2488 640283354 640283397 7.950000e-07 65.8
64 TraesCS3D01G122700 chr6A 92.748 262 19 0 2509 2770 59806615 59806876 2.500000e-101 379.0
65 TraesCS3D01G122700 chr6A 94.483 145 8 0 3228 3372 59807493 59807637 1.240000e-54 224.0
66 TraesCS3D01G122700 chr6A 92.079 101 3 5 617 714 570990179 570990277 1.660000e-28 137.0
67 TraesCS3D01G122700 chr6A 97.143 70 1 1 3363 3431 59807666 59807735 2.160000e-22 117.0
68 TraesCS3D01G122700 chr6A 92.157 51 1 1 2455 2502 533992033 533991983 6.140000e-08 69.4
69 TraesCS3D01G122700 chr6D 90.036 281 22 4 2486 2764 417530055 417529779 3.260000e-95 359.0
70 TraesCS3D01G122700 chr6D 97.241 145 4 0 3228 3372 397361244 397361388 2.640000e-61 246.0
71 TraesCS3D01G122700 chr6D 95.105 143 7 0 3228 3370 131699468 131699610 3.450000e-55 226.0
72 TraesCS3D01G122700 chr6D 95.070 142 7 0 3231 3372 131698827 131698686 1.240000e-54 224.0
73 TraesCS3D01G122700 chr6D 98.571 70 0 1 3363 3431 131698657 131698588 4.650000e-24 122.0
74 TraesCS3D01G122700 chr6D 98.571 70 0 1 3363 3431 131699641 131699710 4.650000e-24 122.0
75 TraesCS3D01G122700 chr6D 97.143 70 1 1 3363 3431 397361417 397361486 2.160000e-22 117.0
76 TraesCS3D01G122700 chr6D 97.959 49 1 0 3115 3163 397360827 397360875 6.100000e-13 86.1
77 TraesCS3D01G122700 chr1D 92.965 199 11 2 3233 3431 260981485 260981680 1.560000e-73 287.0
78 TraesCS3D01G122700 chr1D 95.862 145 6 0 3228 3372 119302071 119302215 5.720000e-58 235.0
79 TraesCS3D01G122700 chr1D 95.172 145 7 0 3228 3372 16967539 16967683 2.660000e-56 230.0
80 TraesCS3D01G122700 chr1D 87.500 176 20 2 3197 3372 113904076 113904249 5.810000e-48 202.0
81 TraesCS3D01G122700 chr1D 93.617 94 3 1 3115 3205 16966810 16966903 1.660000e-28 137.0
82 TraesCS3D01G122700 chr1D 98.571 70 0 1 3363 3431 119302244 119302313 4.650000e-24 122.0
83 TraesCS3D01G122700 chr1D 95.714 70 2 1 3363 3431 113904278 113904347 1.010000e-20 111.0
84 TraesCS3D01G122700 chr1D 96.970 66 2 0 3366 3431 374481592 374481527 1.010000e-20 111.0
85 TraesCS3D01G122700 chr1D 95.714 70 2 1 3363 3431 458886315 458886246 1.010000e-20 111.0
86 TraesCS3D01G122700 chr1D 95.714 70 2 1 3363 3431 493699329 493699398 1.010000e-20 111.0
87 TraesCS3D01G122700 chr1D 81.818 88 13 1 3159 3243 51046369 51046282 1.710000e-08 71.3
88 TraesCS3D01G122700 chr4A 88.298 188 17 4 3185 3372 512017382 512017200 1.600000e-53 220.0
89 TraesCS3D01G122700 chr4A 97.143 70 1 1 3363 3431 512017171 512017102 2.160000e-22 117.0
90 TraesCS3D01G122700 chr7A 94.000 100 5 1 1 100 613723770 613723672 2.130000e-32 150.0
91 TraesCS3D01G122700 chr7A 87.387 111 9 4 600 709 689683968 689683862 4.650000e-24 122.0
92 TraesCS3D01G122700 chr7A 88.462 52 5 1 2451 2501 145474009 145474060 1.030000e-05 62.1
93 TraesCS3D01G122700 chr2A 90.722 97 7 2 611 705 606805850 606805946 9.990000e-26 128.0
94 TraesCS3D01G122700 chr2A 96.053 76 1 2 634 707 17725300 17725225 4.650000e-24 122.0
95 TraesCS3D01G122700 chr2A 89.333 75 5 3 634 705 739240717 739240643 1.310000e-14 91.6
96 TraesCS3D01G122700 chr2A 97.500 40 1 0 2452 2491 115703944 115703983 6.140000e-08 69.4
97 TraesCS3D01G122700 chr2A 100.000 36 0 0 670 705 667954166 667954131 2.210000e-07 67.6
98 TraesCS3D01G122700 chr5B 97.143 70 1 1 3363 3431 582884189 582884120 2.160000e-22 117.0
99 TraesCS3D01G122700 chr5B 87.037 54 4 3 2432 2483 13379100 13379152 1.330000e-04 58.4
100 TraesCS3D01G122700 chr2B 95.455 44 2 0 3115 3158 573188104 573188147 1.710000e-08 71.3
101 TraesCS3D01G122700 chr4B 91.111 45 2 1 2441 2485 426774325 426774367 3.700000e-05 60.2


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 TraesCS3D01G122700 chr3D 80575196 80578626 3430 True 2851.0 5116 100.000000 1 3431 2 chr3D.!!$R7 3430
1 TraesCS3D01G122700 chr3D 80220507 80221355 848 False 1201.0 1201 92.069000 739 1604 1 chr3D.!!$F2 865
2 TraesCS3D01G122700 chr3D 80226745 80227586 841 False 1184.0 1184 92.043000 1601 2442 1 chr3D.!!$F3 841
3 TraesCS3D01G122700 chr3D 80416930 80417933 1003 True 510.0 510 76.386000 1047 2077 1 chr3D.!!$R1 1030
4 TraesCS3D01G122700 chr3D 80916104 80917026 922 True 370.0 370 74.370000 1434 2374 1 chr3D.!!$R4 940
5 TraesCS3D01G122700 chr3D 80599975 80600897 922 True 359.0 359 74.160000 1434 2374 1 chr3D.!!$R2 940
6 TraesCS3D01G122700 chr3D 80629090 80630015 925 True 350.0 350 74.086000 1434 2374 1 chr3D.!!$R3 940
7 TraesCS3D01G122700 chr3A 94191086 94192751 1665 True 2353.0 2353 92.179000 739 2406 1 chr3A.!!$R2 1667
8 TraesCS3D01G122700 chr3A 94253906 94254828 922 True 403.0 403 74.947000 1434 2374 1 chr3A.!!$R3 940
9 TraesCS3D01G122700 chr3A 94857752 94858688 936 True 390.0 390 74.664000 1434 2388 1 chr3A.!!$R4 954
10 TraesCS3D01G122700 chr3B 126373907 126375588 1681 True 2326.0 2326 91.998000 803 2449 1 chr3B.!!$R2 1646
11 TraesCS3D01G122700 chr3B 126298472 126299512 1040 True 545.0 545 76.611000 1022 2095 1 chr3B.!!$R1 1073
12 TraesCS3D01G122700 chr3B 126399411 126400333 922 True 364.0 364 74.372000 1434 2374 1 chr3B.!!$R3 940
13 TraesCS3D01G122700 chr5D 323560145 323560848 703 False 1218.0 1218 97.884000 1 705 1 chr5D.!!$F1 704
14 TraesCS3D01G122700 chr4D 481215152 481215812 660 False 1094.0 1094 96.672000 1 655 1 chr4D.!!$F2 654
15 TraesCS3D01G122700 chr7B 568667418 568667922 504 True 795.0 795 95.248000 140 639 1 chr7B.!!$R1 499
16 TraesCS3D01G122700 chr7D 105201850 105202506 656 True 318.5 422 87.677500 2510 3431 2 chr7D.!!$R3 921
17 TraesCS3D01G122700 chr6A 59806615 59807735 1120 False 240.0 379 94.791333 2509 3431 3 chr6A.!!$F2 922

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
947 986 0.880441 TAGTACGTACGCAGCACCAA 59.120 50.0 19.49 0.0 0.0 3.67 F
1035 1090 0.390866 CTCATGCTGTCCTGCTCGTT 60.391 55.0 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2416 2495 0.033991 AGAAGCTACAGAGAGGCCGA 60.034 55.0 0.0 0.0 0.0 5.54 R
2455 2534 0.639943 TCCCCACTATGACCAGCCTA 59.360 55.0 0.0 0.0 0.0 3.93 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
248 249 2.418628 CGAGAAAAATACGCACCCATGT 59.581 45.455 0.00 0.00 0.00 3.21
605 606 3.141488 TTTTTGGGGTGCGTGCGT 61.141 55.556 0.00 0.00 0.00 5.24
606 607 3.417275 TTTTTGGGGTGCGTGCGTG 62.417 57.895 0.00 0.00 0.00 5.34
707 722 7.931578 CTCGTCCATTAGGAGTAGAGATTAT 57.068 40.000 0.00 0.00 46.92 1.28
709 724 9.621629 CTCGTCCATTAGGAGTAGAGATTATAT 57.378 37.037 0.00 0.00 46.92 0.86
710 725 9.976776 TCGTCCATTAGGAGTAGAGATTATATT 57.023 33.333 0.00 0.00 46.92 1.28
732 747 9.811995 ATATTCAAACTACATTACGCTTCTACA 57.188 29.630 0.00 0.00 0.00 2.74
733 748 7.949903 TTCAAACTACATTACGCTTCTACAA 57.050 32.000 0.00 0.00 0.00 2.41
734 749 7.949903 TCAAACTACATTACGCTTCTACAAA 57.050 32.000 0.00 0.00 0.00 2.83
735 750 8.367943 TCAAACTACATTACGCTTCTACAAAA 57.632 30.769 0.00 0.00 0.00 2.44
736 751 8.277713 TCAAACTACATTACGCTTCTACAAAAC 58.722 33.333 0.00 0.00 0.00 2.43
737 752 7.958053 AACTACATTACGCTTCTACAAAACT 57.042 32.000 0.00 0.00 0.00 2.66
796 812 7.857734 TTAATGTACGATCACCATTCATTGT 57.142 32.000 5.14 0.00 31.63 2.71
797 813 6.757897 AATGTACGATCACCATTCATTGTT 57.242 33.333 0.00 0.00 0.00 2.83
928 961 7.441836 TCTATGCTACACCATCATCGTTTATT 58.558 34.615 0.00 0.00 0.00 1.40
947 986 0.880441 TAGTACGTACGCAGCACCAA 59.120 50.000 19.49 0.00 0.00 3.67
1035 1090 0.390866 CTCATGCTGTCCTGCTCGTT 60.391 55.000 0.00 0.00 0.00 3.85
1236 1297 4.778415 CTGGCACGCTCGTACGCT 62.778 66.667 11.24 0.00 36.19 5.07
1725 1792 2.110213 ACGAAAGGCGCCTTCACA 59.890 55.556 40.13 0.00 46.04 3.58
1845 1912 1.374252 CTCCTTCGTGAACACCCCG 60.374 63.158 0.00 0.00 0.00 5.73
1848 1915 1.068417 CTTCGTGAACACCCCGTCA 59.932 57.895 0.00 0.00 0.00 4.35
2079 2149 2.363147 GAGGAGCTGACCCGGAGT 60.363 66.667 0.73 0.00 0.00 3.85
2268 2344 2.124570 GGGACGATGTGCATGGCT 60.125 61.111 0.00 0.00 0.00 4.75
2407 2486 0.570727 TACCTCCTATCCATGGCCCA 59.429 55.000 6.96 0.00 0.00 5.36
2433 2512 1.658686 CGTCGGCCTCTCTGTAGCTT 61.659 60.000 0.00 0.00 0.00 3.74
2451 2530 4.608073 GCTTCTGCTTCTAGTTTTAGCC 57.392 45.455 0.00 0.00 34.03 3.93
2452 2531 4.257731 GCTTCTGCTTCTAGTTTTAGCCT 58.742 43.478 0.00 0.00 34.03 4.58
2453 2532 4.697828 GCTTCTGCTTCTAGTTTTAGCCTT 59.302 41.667 0.00 0.00 34.03 4.35
2454 2533 5.182190 GCTTCTGCTTCTAGTTTTAGCCTTT 59.818 40.000 0.00 0.00 34.03 3.11
2455 2534 6.294231 GCTTCTGCTTCTAGTTTTAGCCTTTT 60.294 38.462 0.00 0.00 34.03 2.27
2456 2535 7.094762 GCTTCTGCTTCTAGTTTTAGCCTTTTA 60.095 37.037 0.00 0.00 34.03 1.52
2457 2536 7.907214 TCTGCTTCTAGTTTTAGCCTTTTAG 57.093 36.000 0.00 0.00 34.03 1.85
2458 2537 6.879458 TCTGCTTCTAGTTTTAGCCTTTTAGG 59.121 38.462 0.00 0.00 38.80 2.69
2471 2550 3.545703 CCTTTTAGGCTGGTCATAGTGG 58.454 50.000 0.00 0.00 0.00 4.00
2472 2551 3.545703 CTTTTAGGCTGGTCATAGTGGG 58.454 50.000 0.00 0.00 0.00 4.61
2473 2552 1.507140 TTAGGCTGGTCATAGTGGGG 58.493 55.000 0.00 0.00 0.00 4.96
2474 2553 0.639943 TAGGCTGGTCATAGTGGGGA 59.360 55.000 0.00 0.00 0.00 4.81
2475 2554 0.692419 AGGCTGGTCATAGTGGGGAG 60.692 60.000 0.00 0.00 0.00 4.30
2476 2555 0.983378 GGCTGGTCATAGTGGGGAGT 60.983 60.000 0.00 0.00 0.00 3.85
2477 2556 1.691482 GGCTGGTCATAGTGGGGAGTA 60.691 57.143 0.00 0.00 0.00 2.59
2478 2557 2.116238 GCTGGTCATAGTGGGGAGTAA 58.884 52.381 0.00 0.00 0.00 2.24
2479 2558 2.158943 GCTGGTCATAGTGGGGAGTAAC 60.159 54.545 0.00 0.00 0.00 2.50
2480 2559 3.375699 CTGGTCATAGTGGGGAGTAACT 58.624 50.000 0.00 0.00 0.00 2.24
2481 2560 3.775316 CTGGTCATAGTGGGGAGTAACTT 59.225 47.826 0.00 0.00 0.00 2.66
2482 2561 4.950361 TGGTCATAGTGGGGAGTAACTTA 58.050 43.478 0.00 0.00 0.00 2.24
2483 2562 5.535029 TGGTCATAGTGGGGAGTAACTTAT 58.465 41.667 0.00 0.00 0.00 1.73
2484 2563 6.685541 TGGTCATAGTGGGGAGTAACTTATA 58.314 40.000 0.00 0.00 0.00 0.98
2485 2564 7.310634 TGGTCATAGTGGGGAGTAACTTATAT 58.689 38.462 0.00 0.00 0.00 0.86
2486 2565 7.792736 TGGTCATAGTGGGGAGTAACTTATATT 59.207 37.037 0.00 0.00 0.00 1.28
2487 2566 9.317827 GGTCATAGTGGGGAGTAACTTATATTA 57.682 37.037 0.00 0.00 0.00 0.98
2507 2586 6.927294 ATTACTACCTTCATAGTGCAAAGC 57.073 37.500 0.00 0.00 36.09 3.51
2567 2646 2.721425 AACTTTTGAACCGTCTGGGA 57.279 45.000 0.00 0.00 40.75 4.37
2627 2706 2.764637 ATTTGGACCGCGGCCTTCTT 62.765 55.000 30.01 11.47 0.00 2.52
2735 2814 1.472480 CCGCCATTTCATTTCCGTTCT 59.528 47.619 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 249 2.347490 GCGCTGGAGGAGGAACAA 59.653 61.111 0.00 0.00 0.00 2.83
663 677 2.041216 AGTTGGTTGAATAGTCCCCCAC 59.959 50.000 0.00 0.00 0.00 4.61
706 721 9.811995 TGTAGAAGCGTAATGTAGTTTGAATAT 57.188 29.630 0.00 0.00 0.00 1.28
707 722 9.642327 TTGTAGAAGCGTAATGTAGTTTGAATA 57.358 29.630 0.00 0.00 0.00 1.75
708 723 8.542497 TTGTAGAAGCGTAATGTAGTTTGAAT 57.458 30.769 0.00 0.00 0.00 2.57
709 724 7.949903 TTGTAGAAGCGTAATGTAGTTTGAA 57.050 32.000 0.00 0.00 0.00 2.69
710 725 7.949903 TTTGTAGAAGCGTAATGTAGTTTGA 57.050 32.000 0.00 0.00 0.00 2.69
711 726 8.280497 AGTTTTGTAGAAGCGTAATGTAGTTTG 58.720 33.333 0.00 0.00 0.00 2.93
712 727 8.374327 AGTTTTGTAGAAGCGTAATGTAGTTT 57.626 30.769 0.00 0.00 0.00 2.66
713 728 7.958053 AGTTTTGTAGAAGCGTAATGTAGTT 57.042 32.000 0.00 0.00 0.00 2.24
714 729 9.649167 ATTAGTTTTGTAGAAGCGTAATGTAGT 57.351 29.630 0.00 0.00 0.00 2.73
726 741 9.656040 TGCGGTTTCTATATTAGTTTTGTAGAA 57.344 29.630 0.00 0.00 31.56 2.10
727 742 9.826574 ATGCGGTTTCTATATTAGTTTTGTAGA 57.173 29.630 0.00 0.00 0.00 2.59
728 743 9.864034 CATGCGGTTTCTATATTAGTTTTGTAG 57.136 33.333 0.00 0.00 0.00 2.74
729 744 9.602568 TCATGCGGTTTCTATATTAGTTTTGTA 57.397 29.630 0.00 0.00 0.00 2.41
730 745 8.500753 TCATGCGGTTTCTATATTAGTTTTGT 57.499 30.769 0.00 0.00 0.00 2.83
731 746 9.599322 GATCATGCGGTTTCTATATTAGTTTTG 57.401 33.333 0.00 0.00 0.00 2.44
732 747 8.784043 GGATCATGCGGTTTCTATATTAGTTTT 58.216 33.333 0.00 0.00 0.00 2.43
733 748 7.390718 GGGATCATGCGGTTTCTATATTAGTTT 59.609 37.037 0.00 0.00 0.00 2.66
734 749 6.879458 GGGATCATGCGGTTTCTATATTAGTT 59.121 38.462 0.00 0.00 0.00 2.24
735 750 6.213600 AGGGATCATGCGGTTTCTATATTAGT 59.786 38.462 0.00 0.00 0.00 2.24
736 751 6.644347 AGGGATCATGCGGTTTCTATATTAG 58.356 40.000 0.00 0.00 0.00 1.73
737 752 6.440647 AGAGGGATCATGCGGTTTCTATATTA 59.559 38.462 0.00 0.00 0.00 0.98
823 839 9.791820 TGAATTGTGATTGACTGCAAAATATAG 57.208 29.630 0.00 0.00 37.59 1.31
928 961 0.880441 TTGGTGCTGCGTACGTACTA 59.120 50.000 22.55 11.08 0.00 1.82
1035 1090 4.357947 GTCAGGAGCACGACGCCA 62.358 66.667 0.00 0.00 44.04 5.69
1272 1333 1.126488 GGATGGAGATGACCTCAGCA 58.874 55.000 0.00 0.00 43.76 4.41
1405 1466 1.078426 CGGCTTTGGGAAGATCGGT 60.078 57.895 0.00 0.00 34.71 4.69
1725 1792 1.995626 CCCAACGAGTCCATCCCCT 60.996 63.158 0.00 0.00 0.00 4.79
1758 1825 1.604378 CTGGTTGGCGAGGGAGAAT 59.396 57.895 0.00 0.00 0.00 2.40
1845 1912 0.721718 CGCCGAAGTTGAGGATTGAC 59.278 55.000 0.00 0.00 0.00 3.18
1848 1915 1.745489 GGCGCCGAAGTTGAGGATT 60.745 57.895 12.58 0.00 0.00 3.01
2079 2149 2.762459 ACCCGCCGGAGCTTGATA 60.762 61.111 5.05 0.00 36.60 2.15
2268 2344 0.251742 CCTTGTGGGCCTCCATCAAA 60.252 55.000 4.53 0.00 46.09 2.69
2416 2495 0.033991 AGAAGCTACAGAGAGGCCGA 60.034 55.000 0.00 0.00 0.00 5.54
2433 2512 6.879458 CCTAAAAGGCTAAAACTAGAAGCAGA 59.121 38.462 0.00 0.00 38.01 4.26
2450 2529 3.545703 CCACTATGACCAGCCTAAAAGG 58.454 50.000 0.00 0.00 38.80 3.11
2451 2530 3.545703 CCCACTATGACCAGCCTAAAAG 58.454 50.000 0.00 0.00 0.00 2.27
2452 2531 2.241176 CCCCACTATGACCAGCCTAAAA 59.759 50.000 0.00 0.00 0.00 1.52
2453 2532 1.843851 CCCCACTATGACCAGCCTAAA 59.156 52.381 0.00 0.00 0.00 1.85
2454 2533 1.009060 TCCCCACTATGACCAGCCTAA 59.991 52.381 0.00 0.00 0.00 2.69
2455 2534 0.639943 TCCCCACTATGACCAGCCTA 59.360 55.000 0.00 0.00 0.00 3.93
2456 2535 0.692419 CTCCCCACTATGACCAGCCT 60.692 60.000 0.00 0.00 0.00 4.58
2457 2536 0.983378 ACTCCCCACTATGACCAGCC 60.983 60.000 0.00 0.00 0.00 4.85
2458 2537 1.789523 TACTCCCCACTATGACCAGC 58.210 55.000 0.00 0.00 0.00 4.85
2459 2538 3.375699 AGTTACTCCCCACTATGACCAG 58.624 50.000 0.00 0.00 0.00 4.00
2460 2539 3.484953 AGTTACTCCCCACTATGACCA 57.515 47.619 0.00 0.00 0.00 4.02
2461 2540 7.793948 ATATAAGTTACTCCCCACTATGACC 57.206 40.000 0.00 0.00 0.00 4.02
2466 2545 9.813826 GGTAGTAATATAAGTTACTCCCCACTA 57.186 37.037 2.67 0.00 42.35 2.74
2467 2546 8.517896 AGGTAGTAATATAAGTTACTCCCCACT 58.482 37.037 2.67 0.00 39.94 4.00
2468 2547 8.718158 AGGTAGTAATATAAGTTACTCCCCAC 57.282 38.462 2.67 0.00 39.94 4.61
2469 2548 9.372189 GAAGGTAGTAATATAAGTTACTCCCCA 57.628 37.037 2.67 0.00 39.94 4.96
2470 2549 9.372189 TGAAGGTAGTAATATAAGTTACTCCCC 57.628 37.037 2.67 5.04 39.94 4.81
2481 2560 9.706691 GCTTTGCACTATGAAGGTAGTAATATA 57.293 33.333 0.00 0.00 33.29 0.86
2482 2561 8.210946 TGCTTTGCACTATGAAGGTAGTAATAT 58.789 33.333 0.00 0.00 33.29 1.28
2483 2562 7.561251 TGCTTTGCACTATGAAGGTAGTAATA 58.439 34.615 0.00 0.00 33.29 0.98
2484 2563 6.414732 TGCTTTGCACTATGAAGGTAGTAAT 58.585 36.000 0.00 0.00 33.29 1.89
2485 2564 5.800296 TGCTTTGCACTATGAAGGTAGTAA 58.200 37.500 0.00 0.00 33.29 2.24
2486 2565 5.414789 TGCTTTGCACTATGAAGGTAGTA 57.585 39.130 0.00 0.00 33.29 1.82
2487 2566 4.286297 TGCTTTGCACTATGAAGGTAGT 57.714 40.909 0.00 0.00 35.34 2.73
2488 2567 4.937620 TCTTGCTTTGCACTATGAAGGTAG 59.062 41.667 0.00 0.00 38.71 3.18
2489 2568 4.905429 TCTTGCTTTGCACTATGAAGGTA 58.095 39.130 0.00 0.00 38.71 3.08
2490 2569 3.754965 TCTTGCTTTGCACTATGAAGGT 58.245 40.909 0.00 0.00 38.71 3.50
2491 2570 3.427233 GCTCTTGCTTTGCACTATGAAGG 60.427 47.826 0.00 0.00 38.71 3.46
2492 2571 3.189910 TGCTCTTGCTTTGCACTATGAAG 59.810 43.478 0.00 0.00 38.71 3.02
2493 2572 3.148412 TGCTCTTGCTTTGCACTATGAA 58.852 40.909 0.00 0.00 38.71 2.57
2494 2573 2.781923 TGCTCTTGCTTTGCACTATGA 58.218 42.857 0.00 0.00 38.71 2.15
2495 2574 3.377485 AGATGCTCTTGCTTTGCACTATG 59.623 43.478 0.00 0.00 38.71 2.23
2496 2575 3.618351 AGATGCTCTTGCTTTGCACTAT 58.382 40.909 0.00 0.00 38.71 2.12
2497 2576 3.063510 AGATGCTCTTGCTTTGCACTA 57.936 42.857 0.00 0.00 38.71 2.74
2498 2577 1.906990 AGATGCTCTTGCTTTGCACT 58.093 45.000 0.00 0.00 38.71 4.40
2499 2578 2.030540 TGAAGATGCTCTTGCTTTGCAC 60.031 45.455 3.55 0.00 38.71 4.57
2500 2579 2.232399 TGAAGATGCTCTTGCTTTGCA 58.768 42.857 3.55 0.00 36.73 4.08
2501 2580 3.293311 TTGAAGATGCTCTTGCTTTGC 57.707 42.857 3.55 0.00 36.73 3.68
2502 2581 6.256686 GTCTATTGAAGATGCTCTTGCTTTG 58.743 40.000 3.55 0.00 36.73 2.77
2503 2582 5.064452 CGTCTATTGAAGATGCTCTTGCTTT 59.936 40.000 3.55 0.00 36.73 3.51
2504 2583 4.569966 CGTCTATTGAAGATGCTCTTGCTT 59.430 41.667 3.55 0.00 36.73 3.91
2505 2584 4.118410 CGTCTATTGAAGATGCTCTTGCT 58.882 43.478 3.55 0.00 36.73 3.91
2506 2585 3.247173 CCGTCTATTGAAGATGCTCTTGC 59.753 47.826 3.55 0.00 39.56 4.01
2507 2586 4.437239 ACCGTCTATTGAAGATGCTCTTG 58.563 43.478 3.55 0.00 39.56 3.02
2627 2706 4.320129 CGAGGTGTTGCATTTTACATCACA 60.320 41.667 2.54 0.00 38.77 3.58
3332 3901 3.919973 TTCACCGGCCGCGTAGAAC 62.920 63.158 22.85 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.