Multiple sequence alignment - TraesCS7A01G274900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G274900 chr7A 100.000 3301 0 0 1 3301 287665685 287662385 0.000000e+00 6096.0
1 TraesCS7A01G274900 chr7A 89.624 983 85 10 2081 3051 116466026 116465049 0.000000e+00 1234.0
2 TraesCS7A01G274900 chr7A 91.153 633 52 4 2419 3048 494866450 494867081 0.000000e+00 856.0
3 TraesCS7A01G274900 chr5A 95.937 3052 94 11 1 3047 450326627 450323601 0.000000e+00 4922.0
4 TraesCS7A01G274900 chr5A 95.109 184 4 5 3121 3301 627257230 627257411 5.390000e-73 285.0
5 TraesCS7A01G274900 chr5A 93.194 191 6 7 3117 3301 330006592 330006781 1.170000e-69 274.0
6 TraesCS7A01G274900 chr5A 93.814 97 6 0 3047 3143 122793767 122793671 2.650000e-31 147.0
7 TraesCS7A01G274900 chr5A 92.708 96 7 0 3047 3142 122801770 122801675 4.440000e-29 139.0
8 TraesCS7A01G274900 chr3B 94.582 3064 149 14 1 3050 785215293 785212233 0.000000e+00 4723.0
9 TraesCS7A01G274900 chr4B 94.303 3054 153 13 1 3047 215239658 215236619 0.000000e+00 4656.0
10 TraesCS7A01G274900 chr4B 87.241 1254 115 16 1615 2849 333386184 333387411 0.000000e+00 1387.0
11 TraesCS7A01G274900 chr4B 92.877 365 25 1 1 365 203234855 203235218 2.260000e-146 529.0
12 TraesCS7A01G274900 chr4B 81.513 119 12 5 2148 2258 367624580 367624696 4.540000e-14 89.8
13 TraesCS7A01G274900 chr4B 84.270 89 10 4 2137 2222 203235568 203235655 2.110000e-12 84.2
14 TraesCS7A01G274900 chr4B 79.832 119 14 5 2148 2258 639307563 639307679 9.820000e-11 78.7
15 TraesCS7A01G274900 chr6B 93.787 3058 170 16 1 3047 1183430 1186478 0.000000e+00 4577.0
16 TraesCS7A01G274900 chr6B 89.808 1305 111 14 856 2148 686923486 686924780 0.000000e+00 1653.0
17 TraesCS7A01G274900 chr5B 96.052 1925 74 2 1 1924 517431733 517429810 0.000000e+00 3133.0
18 TraesCS7A01G274900 chr5B 94.908 491 22 1 1920 2407 517425692 517425202 0.000000e+00 765.0
19 TraesCS7A01G274900 chr3D 90.721 1304 99 13 856 2148 231219332 231220624 0.000000e+00 1718.0
20 TraesCS7A01G274900 chr3D 91.753 97 7 1 3047 3143 501338087 501337992 2.070000e-27 134.0
21 TraesCS7A01G274900 chr3D 90.722 97 9 0 3047 3143 203098295 203098391 2.670000e-26 130.0
22 TraesCS7A01G274900 chr4D 90.473 1312 101 16 856 2154 73858781 73857481 0.000000e+00 1709.0
23 TraesCS7A01G274900 chr4D 89.137 985 88 10 2078 3047 168891117 168892097 0.000000e+00 1208.0
24 TraesCS7A01G274900 chr4D 81.893 845 98 35 2228 3050 73857238 73856427 0.000000e+00 662.0
25 TraesCS7A01G274900 chr4D 92.784 194 8 5 3113 3301 427996647 427996839 3.240000e-70 276.0
26 TraesCS7A01G274900 chr4D 90.431 209 10 8 3099 3301 77132746 77132950 1.950000e-67 267.0
27 TraesCS7A01G274900 chr4D 92.784 97 7 0 3047 3143 407074567 407074471 1.230000e-29 141.0
28 TraesCS7A01G274900 chr4D 91.753 97 8 0 3047 3143 153116129 153116033 5.750000e-28 135.0
29 TraesCS7A01G274900 chr4D 91.753 97 8 0 3047 3143 153145227 153145131 5.750000e-28 135.0
30 TraesCS7A01G274900 chr4D 91.753 97 8 0 3047 3143 316762468 316762564 5.750000e-28 135.0
31 TraesCS7A01G274900 chr1D 89.292 1158 76 18 1134 2271 479643956 479645085 0.000000e+00 1408.0
32 TraesCS7A01G274900 chr1D 91.534 626 50 3 2425 3048 494241458 494240834 0.000000e+00 859.0
33 TraesCS7A01G274900 chr1D 91.500 200 11 5 3104 3301 4655689 4655884 1.510000e-68 270.0
34 TraesCS7A01G274900 chr2B 88.943 1031 96 12 1134 2154 380573033 380572011 0.000000e+00 1256.0
35 TraesCS7A01G274900 chr2B 87.724 391 32 5 2081 2457 724447226 724446838 3.020000e-120 442.0
36 TraesCS7A01G274900 chr7D 91.040 625 53 3 2425 3047 599755056 599754433 0.000000e+00 841.0
37 TraesCS7A01G274900 chr7D 86.667 105 12 2 3039 3143 278134692 278134794 7.490000e-22 115.0
38 TraesCS7A01G274900 chr7D 80.909 110 13 3 2157 2258 262858991 262858882 2.730000e-11 80.5
39 TraesCS7A01G274900 chr5D 90.895 626 53 4 2425 3048 406000813 406001436 0.000000e+00 837.0
40 TraesCS7A01G274900 chr7B 82.524 927 122 9 2154 3047 716661032 716661951 0.000000e+00 778.0
41 TraesCS7A01G274900 chr6A 83.462 647 56 31 1669 2271 589429316 589429955 3.720000e-154 555.0
42 TraesCS7A01G274900 chr6A 91.500 200 12 4 3107 3301 15555917 15556116 1.510000e-68 270.0
43 TraesCS7A01G274900 chr6A 89.855 69 6 1 2155 2222 34645138 34645070 1.630000e-13 87.9
44 TraesCS7A01G274900 chr1B 79.022 777 73 37 67 815 10000988 10001702 1.810000e-122 449.0
45 TraesCS7A01G274900 chr1B 83.851 322 29 9 550 854 519301690 519302005 5.390000e-73 285.0
46 TraesCS7A01G274900 chr1B 89.552 67 6 1 2157 2222 250523082 250523016 2.110000e-12 84.2
47 TraesCS7A01G274900 chr2D 93.264 193 8 5 3111 3301 195538635 195538824 2.510000e-71 279.0
48 TraesCS7A01G274900 chr6D 90.431 209 11 6 3101 3301 422573973 422573766 1.950000e-67 267.0
49 TraesCS7A01G274900 chr6D 89.904 208 14 7 3100 3301 44957080 44956874 9.090000e-66 261.0
50 TraesCS7A01G274900 chr3A 80.303 132 16 4 2137 2258 549235031 549234900 1.260000e-14 91.6
51 TraesCS7A01G274900 chrUn 78.992 119 15 5 2148 2258 77138559 77138675 4.570000e-09 73.1


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 TraesCS7A01G274900 chr7A 287662385 287665685 3300 True 6096.0 6096 100.0000 1 3301 1 chr7A.!!$R2 3300
1 TraesCS7A01G274900 chr7A 116465049 116466026 977 True 1234.0 1234 89.6240 2081 3051 1 chr7A.!!$R1 970
2 TraesCS7A01G274900 chr7A 494866450 494867081 631 False 856.0 856 91.1530 2419 3048 1 chr7A.!!$F1 629
3 TraesCS7A01G274900 chr5A 450323601 450326627 3026 True 4922.0 4922 95.9370 1 3047 1 chr5A.!!$R3 3046
4 TraesCS7A01G274900 chr3B 785212233 785215293 3060 True 4723.0 4723 94.5820 1 3050 1 chr3B.!!$R1 3049
5 TraesCS7A01G274900 chr4B 215236619 215239658 3039 True 4656.0 4656 94.3030 1 3047 1 chr4B.!!$R1 3046
6 TraesCS7A01G274900 chr4B 333386184 333387411 1227 False 1387.0 1387 87.2410 1615 2849 1 chr4B.!!$F1 1234
7 TraesCS7A01G274900 chr4B 203234855 203235655 800 False 306.6 529 88.5735 1 2222 2 chr4B.!!$F4 2221
8 TraesCS7A01G274900 chr6B 1183430 1186478 3048 False 4577.0 4577 93.7870 1 3047 1 chr6B.!!$F1 3046
9 TraesCS7A01G274900 chr6B 686923486 686924780 1294 False 1653.0 1653 89.8080 856 2148 1 chr6B.!!$F2 1292
10 TraesCS7A01G274900 chr5B 517429810 517431733 1923 True 3133.0 3133 96.0520 1 1924 1 chr5B.!!$R2 1923
11 TraesCS7A01G274900 chr3D 231219332 231220624 1292 False 1718.0 1718 90.7210 856 2148 1 chr3D.!!$F2 1292
12 TraesCS7A01G274900 chr4D 168891117 168892097 980 False 1208.0 1208 89.1370 2078 3047 1 chr4D.!!$F2 969
13 TraesCS7A01G274900 chr4D 73856427 73858781 2354 True 1185.5 1709 86.1830 856 3050 2 chr4D.!!$R4 2194
14 TraesCS7A01G274900 chr1D 479643956 479645085 1129 False 1408.0 1408 89.2920 1134 2271 1 chr1D.!!$F2 1137
15 TraesCS7A01G274900 chr1D 494240834 494241458 624 True 859.0 859 91.5340 2425 3048 1 chr1D.!!$R1 623
16 TraesCS7A01G274900 chr2B 380572011 380573033 1022 True 1256.0 1256 88.9430 1134 2154 1 chr2B.!!$R1 1020
17 TraesCS7A01G274900 chr7D 599754433 599755056 623 True 841.0 841 91.0400 2425 3047 1 chr7D.!!$R2 622
18 TraesCS7A01G274900 chr5D 406000813 406001436 623 False 837.0 837 90.8950 2425 3048 1 chr5D.!!$F1 623
19 TraesCS7A01G274900 chr7B 716661032 716661951 919 False 778.0 778 82.5240 2154 3047 1 chr7B.!!$F1 893
20 TraesCS7A01G274900 chr6A 589429316 589429955 639 False 555.0 555 83.4620 1669 2271 1 chr6A.!!$F2 602
21 TraesCS7A01G274900 chr1B 10000988 10001702 714 False 449.0 449 79.0220 67 815 1 chr1B.!!$F1 748

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
25 26 1.438651 TTCTTGCTGACGTACCATGC 58.561 50.000 0.0 0.0 0.0 4.06 F
837 883 2.165437 GTCCCTCTGCTTGTGTCTCTAG 59.835 54.545 0.0 0.0 0.0 2.43 F
1821 1876 2.096819 GCGATGAAATTTTGGCGGACTA 59.903 45.455 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1340 1393 1.901591 TTCTTGGCCTTGCTCTTCTG 58.098 50.0 3.32 0.0 0.0 3.02 R
2132 2247 0.109781 GCAAATGGTAGTGTGGTGCG 60.110 55.0 0.00 0.0 0.0 5.34 R
3137 3474 0.668535 GCATATTTCCTTCACCGGCC 59.331 55.0 0.00 0.0 0.0 6.13 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
25 26 1.438651 TTCTTGCTGACGTACCATGC 58.561 50.000 0.00 0.00 0.00 4.06
90 91 5.166407 TCATTTGGGTAAAATCCCCCTTTT 58.834 37.500 0.00 0.00 46.48 2.27
280 281 6.413269 GTTGTTTCAATTCATGTTCAGTTGC 58.587 36.000 0.00 0.00 0.00 4.17
325 326 5.920840 GCAACTATTTTTCTGGGTTTCACTC 59.079 40.000 0.00 0.00 0.00 3.51
383 388 7.441836 TGTAAATCTACTGCTCAAGAGTTTCA 58.558 34.615 0.00 1.31 32.73 2.69
415 440 7.150783 AGTTCCTGATGTAAATTCTTGCTTC 57.849 36.000 0.00 0.00 0.00 3.86
487 512 7.939784 TTGTTGATAGCTAGTCTCTTCACTA 57.060 36.000 0.00 0.00 0.00 2.74
571 613 3.412386 GCCAAAGGCTCTCTGAAAACTA 58.588 45.455 0.00 0.00 46.69 2.24
712 758 2.988010 TCTGCAATCTACATCGCCTT 57.012 45.000 0.00 0.00 0.00 4.35
742 788 9.799106 ATTAATAGTACATCTCATTTTGGAGGG 57.201 33.333 0.00 0.00 35.58 4.30
837 883 2.165437 GTCCCTCTGCTTGTGTCTCTAG 59.835 54.545 0.00 0.00 0.00 2.43
840 886 2.451490 CTCTGCTTGTGTCTCTAGGGA 58.549 52.381 0.00 0.00 0.00 4.20
1216 1266 9.429359 CAGTCTTTCTTACTCAGTGTTATCATT 57.571 33.333 0.00 0.00 0.00 2.57
1279 1329 3.826157 CTGCTTGGGTTTTCCTGATGTTA 59.174 43.478 0.00 0.00 40.46 2.41
1340 1393 2.327343 TGGCGATGCAGACTTGTGC 61.327 57.895 0.00 0.00 44.27 4.57
1821 1876 2.096819 GCGATGAAATTTTGGCGGACTA 59.903 45.455 0.00 0.00 0.00 2.59
1979 2052 3.502191 TGGTGTCTTGTGTTCAAAAGC 57.498 42.857 0.00 0.00 32.87 3.51
2006 2089 5.693769 AGCCTTGTAGCCTTGTTAGAATA 57.306 39.130 0.00 0.00 0.00 1.75
2144 2259 2.558554 ATCGCCTCGCACCACACTAC 62.559 60.000 0.00 0.00 0.00 2.73
2259 2550 1.710341 CAAGGGGAGGGGGTCTCTA 59.290 63.158 0.00 0.00 42.10 2.43
2266 2557 2.581246 GGGAGGGGGTCTCTAAAATGTT 59.419 50.000 0.00 0.00 42.10 2.71
2271 2562 2.617021 GGGGTCTCTAAAATGTTGCCGA 60.617 50.000 0.00 0.00 0.00 5.54
2278 2569 0.109319 AAAATGTTGCCGATGTCGCC 60.109 50.000 0.00 0.00 38.18 5.54
2358 2649 2.526432 ACCTCCTTGTCTTTCTAGCGA 58.474 47.619 0.00 0.00 0.00 4.93
2434 2728 3.634568 TTGCCCTTTGTTGAATGTACG 57.365 42.857 0.00 0.00 0.00 3.67
3050 3387 8.480643 AGTTGACATATTTCTTGTAGTGCTAC 57.519 34.615 2.60 2.60 36.63 3.58
3051 3388 7.275779 AGTTGACATATTTCTTGTAGTGCTACG 59.724 37.037 5.08 0.00 38.85 3.51
3052 3389 6.040247 TGACATATTTCTTGTAGTGCTACGG 58.960 40.000 5.08 1.59 38.85 4.02
3053 3390 6.127563 TGACATATTTCTTGTAGTGCTACGGA 60.128 38.462 5.08 3.62 38.85 4.69
3054 3391 6.636705 ACATATTTCTTGTAGTGCTACGGAA 58.363 36.000 5.08 8.49 38.85 4.30
3055 3392 6.534079 ACATATTTCTTGTAGTGCTACGGAAC 59.466 38.462 13.11 0.00 38.85 3.62
3082 3419 4.899239 GAGGCGCATCCGGTGGAG 62.899 72.222 11.78 0.00 40.77 3.86
3087 3424 4.760047 GCATCCGGTGGAGCACGT 62.760 66.667 0.00 0.00 34.05 4.49
3088 3425 2.815211 CATCCGGTGGAGCACGTG 60.815 66.667 12.28 12.28 34.05 4.49
3089 3426 4.082523 ATCCGGTGGAGCACGTGG 62.083 66.667 18.88 0.00 34.05 4.94
3091 3428 4.742201 CCGGTGGAGCACGTGGAG 62.742 72.222 18.88 0.00 34.08 3.86
3092 3429 3.680786 CGGTGGAGCACGTGGAGA 61.681 66.667 18.88 0.00 34.83 3.71
3093 3430 2.262915 GGTGGAGCACGTGGAGAG 59.737 66.667 18.88 0.00 34.83 3.20
3094 3431 2.276116 GGTGGAGCACGTGGAGAGA 61.276 63.158 18.88 0.00 34.83 3.10
3095 3432 1.214062 GTGGAGCACGTGGAGAGAG 59.786 63.158 18.88 0.00 0.00 3.20
3096 3433 2.183046 GGAGCACGTGGAGAGAGC 59.817 66.667 18.88 0.00 0.00 4.09
3097 3434 2.347322 GGAGCACGTGGAGAGAGCT 61.347 63.158 18.88 5.75 38.43 4.09
3098 3435 1.153862 GAGCACGTGGAGAGAGCTG 60.154 63.158 18.88 0.00 35.36 4.24
3099 3436 2.125753 GCACGTGGAGAGAGCTGG 60.126 66.667 18.88 0.00 0.00 4.85
3100 3437 2.575993 CACGTGGAGAGAGCTGGG 59.424 66.667 7.95 0.00 0.00 4.45
3101 3438 2.681778 ACGTGGAGAGAGCTGGGG 60.682 66.667 0.00 0.00 0.00 4.96
3102 3439 2.681778 CGTGGAGAGAGCTGGGGT 60.682 66.667 0.00 0.00 0.00 4.95
3103 3440 2.985456 GTGGAGAGAGCTGGGGTG 59.015 66.667 0.00 0.00 0.00 4.61
3104 3441 2.284921 TGGAGAGAGCTGGGGTGG 60.285 66.667 0.00 0.00 0.00 4.61
3105 3442 3.791586 GGAGAGAGCTGGGGTGGC 61.792 72.222 0.00 0.00 0.00 5.01
3106 3443 3.791586 GAGAGAGCTGGGGTGGCC 61.792 72.222 0.00 0.00 0.00 5.36
3152 3489 2.750237 GCGGCCGGTGAAGGAAAT 60.750 61.111 29.38 0.00 0.00 2.17
3153 3490 1.450669 GCGGCCGGTGAAGGAAATA 60.451 57.895 29.38 0.00 0.00 1.40
3154 3491 0.818040 GCGGCCGGTGAAGGAAATAT 60.818 55.000 29.38 0.00 0.00 1.28
3155 3492 0.944386 CGGCCGGTGAAGGAAATATG 59.056 55.000 20.10 0.00 0.00 1.78
3156 3493 0.668535 GGCCGGTGAAGGAAATATGC 59.331 55.000 1.90 0.00 0.00 3.14
3157 3494 0.668535 GCCGGTGAAGGAAATATGCC 59.331 55.000 1.90 0.00 0.00 4.40
3158 3495 1.750682 GCCGGTGAAGGAAATATGCCT 60.751 52.381 1.90 0.00 37.35 4.75
3159 3496 2.486548 GCCGGTGAAGGAAATATGCCTA 60.487 50.000 1.90 0.00 33.76 3.93
3160 3497 3.403038 CCGGTGAAGGAAATATGCCTAG 58.597 50.000 0.00 0.00 33.76 3.02
3161 3498 3.071023 CCGGTGAAGGAAATATGCCTAGA 59.929 47.826 0.00 0.00 33.76 2.43
3162 3499 4.310769 CGGTGAAGGAAATATGCCTAGAG 58.689 47.826 0.00 0.00 33.76 2.43
3163 3500 4.646572 GGTGAAGGAAATATGCCTAGAGG 58.353 47.826 0.00 0.00 33.76 3.69
3238 3575 8.902540 ATTCATGCTAGAATTGTATTAACCGA 57.097 30.769 0.00 0.00 34.70 4.69
3239 3576 8.725405 TTCATGCTAGAATTGTATTAACCGAA 57.275 30.769 0.00 0.00 0.00 4.30
3240 3577 8.725405 TCATGCTAGAATTGTATTAACCGAAA 57.275 30.769 0.00 0.00 0.00 3.46
3241 3578 8.609176 TCATGCTAGAATTGTATTAACCGAAAC 58.391 33.333 0.00 0.00 0.00 2.78
3242 3579 8.612619 CATGCTAGAATTGTATTAACCGAAACT 58.387 33.333 0.00 0.00 0.00 2.66
3243 3580 8.556213 TGCTAGAATTGTATTAACCGAAACTT 57.444 30.769 0.00 0.00 0.00 2.66
3244 3581 9.656040 TGCTAGAATTGTATTAACCGAAACTTA 57.344 29.630 0.00 0.00 0.00 2.24
3252 3589 9.709495 TTGTATTAACCGAAACTTAGTACATGT 57.291 29.630 2.69 2.69 30.70 3.21
3253 3590 9.142515 TGTATTAACCGAAACTTAGTACATGTG 57.857 33.333 9.11 0.00 27.39 3.21
3254 3591 9.143631 GTATTAACCGAAACTTAGTACATGTGT 57.856 33.333 9.11 0.00 0.00 3.72
3255 3592 5.917541 AACCGAAACTTAGTACATGTGTG 57.082 39.130 9.11 0.00 0.00 3.82
3256 3593 5.204409 ACCGAAACTTAGTACATGTGTGA 57.796 39.130 9.11 0.00 0.00 3.58
3257 3594 5.603596 ACCGAAACTTAGTACATGTGTGAA 58.396 37.500 9.11 0.00 0.00 3.18
3258 3595 6.228258 ACCGAAACTTAGTACATGTGTGAAT 58.772 36.000 9.11 0.00 0.00 2.57
3259 3596 7.380536 ACCGAAACTTAGTACATGTGTGAATA 58.619 34.615 9.11 0.00 0.00 1.75
3260 3597 7.330208 ACCGAAACTTAGTACATGTGTGAATAC 59.670 37.037 9.11 0.00 0.00 1.89
3261 3598 7.329962 CCGAAACTTAGTACATGTGTGAATACA 59.670 37.037 9.11 0.00 34.63 2.29
3262 3599 8.869897 CGAAACTTAGTACATGTGTGAATACAT 58.130 33.333 9.11 0.00 41.77 2.29
3270 3607 9.151471 AGTACATGTGTGAATACATAGACAAAC 57.849 33.333 9.11 0.00 39.17 2.93
3271 3608 7.977789 ACATGTGTGAATACATAGACAAACA 57.022 32.000 0.00 0.00 39.17 2.83
3272 3609 8.032952 ACATGTGTGAATACATAGACAAACAG 57.967 34.615 0.00 0.00 39.17 3.16
3273 3610 7.877612 ACATGTGTGAATACATAGACAAACAGA 59.122 33.333 0.00 0.00 39.17 3.41
3274 3611 7.889589 TGTGTGAATACATAGACAAACAGAG 57.110 36.000 0.00 0.00 39.39 3.35
3275 3612 7.441836 TGTGTGAATACATAGACAAACAGAGT 58.558 34.615 0.00 0.00 39.39 3.24
3276 3613 7.384932 TGTGTGAATACATAGACAAACAGAGTG 59.615 37.037 0.00 0.00 39.39 3.51
3277 3614 7.385205 GTGTGAATACATAGACAAACAGAGTGT 59.615 37.037 0.00 0.00 39.39 3.55
3278 3615 7.598869 TGTGAATACATAGACAAACAGAGTGTC 59.401 37.037 0.00 0.00 44.75 3.67
3279 3616 7.598869 GTGAATACATAGACAAACAGAGTGTCA 59.401 37.037 7.26 0.00 46.44 3.58
3280 3617 7.598869 TGAATACATAGACAAACAGAGTGTCAC 59.401 37.037 7.26 0.00 46.44 3.67
3281 3618 5.537300 ACATAGACAAACAGAGTGTCACT 57.463 39.130 4.81 4.81 46.44 3.41
3282 3619 6.650427 ACATAGACAAACAGAGTGTCACTA 57.350 37.500 5.21 0.00 46.44 2.74
3283 3620 6.682746 ACATAGACAAACAGAGTGTCACTAG 58.317 40.000 5.21 4.44 46.44 2.57
3284 3621 6.265649 ACATAGACAAACAGAGTGTCACTAGT 59.734 38.462 5.21 5.11 46.44 2.57
3285 3622 7.447545 ACATAGACAAACAGAGTGTCACTAGTA 59.552 37.037 5.21 0.00 46.44 1.82
3286 3623 6.902771 AGACAAACAGAGTGTCACTAGTAT 57.097 37.500 5.21 0.00 46.44 2.12
3287 3624 6.682746 AGACAAACAGAGTGTCACTAGTATG 58.317 40.000 5.21 5.56 46.44 2.39
3288 3625 5.230942 ACAAACAGAGTGTCACTAGTATGC 58.769 41.667 5.21 0.00 0.00 3.14
3289 3626 4.457834 AACAGAGTGTCACTAGTATGCC 57.542 45.455 5.21 0.00 0.00 4.40
3290 3627 3.702792 ACAGAGTGTCACTAGTATGCCT 58.297 45.455 5.21 0.00 0.00 4.75
3291 3628 3.697045 ACAGAGTGTCACTAGTATGCCTC 59.303 47.826 5.21 0.00 0.00 4.70
3292 3629 3.951037 CAGAGTGTCACTAGTATGCCTCT 59.049 47.826 5.21 1.89 0.00 3.69
3293 3630 5.126779 CAGAGTGTCACTAGTATGCCTCTA 58.873 45.833 5.21 0.00 0.00 2.43
3294 3631 5.008217 CAGAGTGTCACTAGTATGCCTCTAC 59.992 48.000 5.21 0.00 0.00 2.59
3295 3632 5.104277 AGAGTGTCACTAGTATGCCTCTACT 60.104 44.000 5.21 0.00 36.04 2.57
3296 3633 5.511363 AGTGTCACTAGTATGCCTCTACTT 58.489 41.667 2.87 0.00 33.96 2.24
3297 3634 5.358442 AGTGTCACTAGTATGCCTCTACTTG 59.642 44.000 2.87 0.00 33.96 3.16
3298 3635 5.357314 GTGTCACTAGTATGCCTCTACTTGA 59.643 44.000 0.00 0.18 33.96 3.02
3299 3636 5.357314 TGTCACTAGTATGCCTCTACTTGAC 59.643 44.000 0.00 11.98 38.64 3.18
3300 3637 5.591067 GTCACTAGTATGCCTCTACTTGACT 59.409 44.000 0.00 0.00 36.95 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 2.136298 TTGGCCCAATTAAGATGCGA 57.864 45.000 0.00 0.00 0.00 5.10
228 229 9.338622 ACAACTTAGCACTGTAAACTCTTAATT 57.661 29.630 0.00 0.00 0.00 1.40
280 281 3.484649 GCATGCAGCACAGAAAATATTCG 59.515 43.478 14.21 0.00 44.79 3.34
325 326 1.004044 ACCCTCCAGCTCTGAACAATG 59.996 52.381 0.00 0.00 0.00 2.82
383 388 2.664402 ACATCAGGAACTTGGCAGTT 57.336 45.000 2.63 2.63 46.64 3.16
487 512 7.504238 CAGTAGAGGAGGAGAAACATGTATAGT 59.496 40.741 0.00 0.00 0.00 2.12
676 722 8.587608 AGATTGCAGATCAAAAAGGAAATACAA 58.412 29.630 10.26 0.00 38.34 2.41
742 788 1.860326 GCAAAGCAACCACACACAATC 59.140 47.619 0.00 0.00 0.00 2.67
837 883 3.928375 TCAGTTATCTTAAAACGCGTCCC 59.072 43.478 14.44 0.00 32.00 4.46
840 886 7.858879 ACAAAAATCAGTTATCTTAAAACGCGT 59.141 29.630 5.58 5.58 32.00 6.01
933 979 2.486982 CAGACCAGGAATCAGCACAAAG 59.513 50.000 0.00 0.00 0.00 2.77
1216 1266 3.003897 GTCCATCACGTAAAACCAAGCAA 59.996 43.478 0.00 0.00 0.00 3.91
1279 1329 2.231235 GGATCAGAACCCAACGCAAAAT 59.769 45.455 0.00 0.00 0.00 1.82
1340 1393 1.901591 TTCTTGGCCTTGCTCTTCTG 58.098 50.000 3.32 0.00 0.00 3.02
1396 1449 2.102252 GAGGCTCACATGAGGACTAAGG 59.898 54.545 10.25 0.00 42.29 2.69
1821 1876 5.363580 AGAAACATGGAAGAAACCAACACAT 59.636 36.000 0.00 0.00 43.47 3.21
1913 1968 7.568349 AGGAAGTAGATCAACAATTGCATAGA 58.432 34.615 5.05 0.00 0.00 1.98
2006 2089 7.503549 TGAATCAATGAGCACAGACTATACAT 58.496 34.615 0.00 0.00 0.00 2.29
2115 2230 2.917971 GTGCGAGGCGATAGATTACATC 59.082 50.000 0.00 0.00 39.76 3.06
2132 2247 0.109781 GCAAATGGTAGTGTGGTGCG 60.110 55.000 0.00 0.00 0.00 5.34
2144 2259 2.364324 CAGGGAATCATGGAGCAAATGG 59.636 50.000 0.00 0.00 0.00 3.16
2259 2550 3.399879 GCGACATCGGCAACATTTT 57.600 47.368 3.08 0.00 40.23 1.82
2278 2569 4.631131 TCAATCGGTGATACTAGCAATGG 58.369 43.478 0.00 0.00 0.00 3.16
2358 2649 2.205022 TTTCTACCAGCAGCAGCAAT 57.795 45.000 3.17 0.00 45.49 3.56
2434 2728 0.319405 AGCCACGGGTACAACAGTAC 59.681 55.000 0.00 0.00 37.88 2.73
2829 3165 6.783708 TCTATTTTGGTTGTTGGTTGTCTT 57.216 33.333 0.00 0.00 0.00 3.01
3065 3402 4.899239 CTCCACCGGATGCGCCTC 62.899 72.222 9.46 3.99 0.00 4.70
3070 3407 4.760047 ACGTGCTCCACCGGATGC 62.760 66.667 9.46 7.14 0.00 3.91
3071 3408 2.815211 CACGTGCTCCACCGGATG 60.815 66.667 9.46 2.15 0.00 3.51
3072 3409 4.082523 CCACGTGCTCCACCGGAT 62.083 66.667 9.46 0.00 0.00 4.18
3074 3411 4.742201 CTCCACGTGCTCCACCGG 62.742 72.222 10.91 0.00 0.00 5.28
3075 3412 3.633094 CTCTCCACGTGCTCCACCG 62.633 68.421 10.91 0.00 0.00 4.94
3076 3413 2.219325 CTCTCTCCACGTGCTCCACC 62.219 65.000 10.91 0.00 0.00 4.61
3077 3414 1.214062 CTCTCTCCACGTGCTCCAC 59.786 63.158 10.91 0.00 0.00 4.02
3078 3415 2.640302 GCTCTCTCCACGTGCTCCA 61.640 63.158 10.91 0.00 0.00 3.86
3079 3416 2.183046 GCTCTCTCCACGTGCTCC 59.817 66.667 10.91 0.00 0.00 4.70
3080 3417 1.153862 CAGCTCTCTCCACGTGCTC 60.154 63.158 10.91 0.00 0.00 4.26
3081 3418 2.644212 CCAGCTCTCTCCACGTGCT 61.644 63.158 10.91 0.00 0.00 4.40
3082 3419 2.125753 CCAGCTCTCTCCACGTGC 60.126 66.667 10.91 0.00 0.00 5.34
3083 3420 2.575993 CCCAGCTCTCTCCACGTG 59.424 66.667 9.08 9.08 0.00 4.49
3084 3421 2.681778 CCCCAGCTCTCTCCACGT 60.682 66.667 0.00 0.00 0.00 4.49
3085 3422 2.681778 ACCCCAGCTCTCTCCACG 60.682 66.667 0.00 0.00 0.00 4.94
3086 3423 2.664081 CCACCCCAGCTCTCTCCAC 61.664 68.421 0.00 0.00 0.00 4.02
3087 3424 2.284921 CCACCCCAGCTCTCTCCA 60.285 66.667 0.00 0.00 0.00 3.86
3088 3425 3.791586 GCCACCCCAGCTCTCTCC 61.792 72.222 0.00 0.00 0.00 3.71
3089 3426 3.791586 GGCCACCCCAGCTCTCTC 61.792 72.222 0.00 0.00 0.00 3.20
3134 3471 2.879813 TATTTCCTTCACCGGCCGCC 62.880 60.000 22.85 0.00 0.00 6.13
3135 3472 0.818040 ATATTTCCTTCACCGGCCGC 60.818 55.000 22.85 0.00 0.00 6.53
3136 3473 0.944386 CATATTTCCTTCACCGGCCG 59.056 55.000 21.04 21.04 0.00 6.13
3137 3474 0.668535 GCATATTTCCTTCACCGGCC 59.331 55.000 0.00 0.00 0.00 6.13
3138 3475 0.668535 GGCATATTTCCTTCACCGGC 59.331 55.000 0.00 0.00 0.00 6.13
3139 3476 2.348411 AGGCATATTTCCTTCACCGG 57.652 50.000 0.00 0.00 0.00 5.28
3140 3477 4.310769 CTCTAGGCATATTTCCTTCACCG 58.689 47.826 0.00 0.00 35.21 4.94
3141 3478 4.646572 CCTCTAGGCATATTTCCTTCACC 58.353 47.826 0.00 0.00 35.21 4.02
3212 3549 9.990360 TCGGTTAATACAATTCTAGCATGAATA 57.010 29.630 0.00 0.00 35.82 1.75
3213 3550 8.902540 TCGGTTAATACAATTCTAGCATGAAT 57.097 30.769 0.00 0.00 38.19 2.57
3214 3551 8.725405 TTCGGTTAATACAATTCTAGCATGAA 57.275 30.769 0.00 0.00 0.00 2.57
3215 3552 8.609176 GTTTCGGTTAATACAATTCTAGCATGA 58.391 33.333 0.00 0.00 0.00 3.07
3216 3553 8.612619 AGTTTCGGTTAATACAATTCTAGCATG 58.387 33.333 0.00 0.00 0.00 4.06
3217 3554 8.732746 AGTTTCGGTTAATACAATTCTAGCAT 57.267 30.769 0.00 0.00 0.00 3.79
3218 3555 8.556213 AAGTTTCGGTTAATACAATTCTAGCA 57.444 30.769 0.00 0.00 0.00 3.49
3226 3563 9.709495 ACATGTACTAAGTTTCGGTTAATACAA 57.291 29.630 0.00 0.00 28.92 2.41
3227 3564 9.142515 CACATGTACTAAGTTTCGGTTAATACA 57.857 33.333 0.00 0.00 29.47 2.29
3228 3565 9.143631 ACACATGTACTAAGTTTCGGTTAATAC 57.856 33.333 0.00 0.00 0.00 1.89
3229 3566 9.142515 CACACATGTACTAAGTTTCGGTTAATA 57.857 33.333 0.00 0.00 0.00 0.98
3230 3567 7.874016 TCACACATGTACTAAGTTTCGGTTAAT 59.126 33.333 0.00 0.00 0.00 1.40
3231 3568 7.208777 TCACACATGTACTAAGTTTCGGTTAA 58.791 34.615 0.00 0.00 0.00 2.01
3232 3569 6.747125 TCACACATGTACTAAGTTTCGGTTA 58.253 36.000 0.00 0.00 0.00 2.85
3233 3570 5.603596 TCACACATGTACTAAGTTTCGGTT 58.396 37.500 0.00 0.00 0.00 4.44
3234 3571 5.204409 TCACACATGTACTAAGTTTCGGT 57.796 39.130 0.00 0.00 0.00 4.69
3235 3572 6.721571 ATTCACACATGTACTAAGTTTCGG 57.278 37.500 0.00 0.00 0.00 4.30
3236 3573 8.234887 TGTATTCACACATGTACTAAGTTTCG 57.765 34.615 0.00 0.00 0.00 3.46
3244 3581 9.151471 GTTTGTCTATGTATTCACACATGTACT 57.849 33.333 0.00 0.00 39.46 2.73
3245 3582 8.931775 TGTTTGTCTATGTATTCACACATGTAC 58.068 33.333 0.00 0.00 39.46 2.90
3246 3583 9.150348 CTGTTTGTCTATGTATTCACACATGTA 57.850 33.333 0.00 0.00 39.46 2.29
3247 3584 7.877612 TCTGTTTGTCTATGTATTCACACATGT 59.122 33.333 0.00 0.00 39.46 3.21
3248 3585 8.255394 TCTGTTTGTCTATGTATTCACACATG 57.745 34.615 0.00 0.00 39.46 3.21
3249 3586 8.097038 ACTCTGTTTGTCTATGTATTCACACAT 58.903 33.333 0.00 0.00 41.88 3.21
3250 3587 7.384932 CACTCTGTTTGTCTATGTATTCACACA 59.615 37.037 0.00 0.00 37.54 3.72
3251 3588 7.385205 ACACTCTGTTTGTCTATGTATTCACAC 59.615 37.037 0.00 0.00 37.54 3.82
3252 3589 7.441836 ACACTCTGTTTGTCTATGTATTCACA 58.558 34.615 0.00 0.00 39.52 3.58
3253 3590 7.598869 TGACACTCTGTTTGTCTATGTATTCAC 59.401 37.037 11.01 0.00 43.30 3.18
3254 3591 7.598869 GTGACACTCTGTTTGTCTATGTATTCA 59.401 37.037 0.00 0.00 43.30 2.57
3255 3592 7.815068 AGTGACACTCTGTTTGTCTATGTATTC 59.185 37.037 1.07 0.00 43.30 1.75
3256 3593 7.671302 AGTGACACTCTGTTTGTCTATGTATT 58.329 34.615 1.07 0.00 43.30 1.89
3257 3594 7.233389 AGTGACACTCTGTTTGTCTATGTAT 57.767 36.000 1.07 0.00 43.30 2.29
3258 3595 6.650427 AGTGACACTCTGTTTGTCTATGTA 57.350 37.500 1.07 0.00 43.30 2.29
3259 3596 5.537300 AGTGACACTCTGTTTGTCTATGT 57.463 39.130 1.07 0.00 43.30 2.29
3260 3597 6.682746 ACTAGTGACACTCTGTTTGTCTATG 58.317 40.000 12.39 0.00 43.30 2.23
3261 3598 6.902771 ACTAGTGACACTCTGTTTGTCTAT 57.097 37.500 12.39 0.00 43.30 1.98
3262 3599 7.575155 GCATACTAGTGACACTCTGTTTGTCTA 60.575 40.741 12.39 0.00 43.30 2.59
3263 3600 6.682746 CATACTAGTGACACTCTGTTTGTCT 58.317 40.000 12.39 0.00 43.30 3.41
3264 3601 5.346281 GCATACTAGTGACACTCTGTTTGTC 59.654 44.000 12.39 9.81 43.22 3.18
3265 3602 5.230942 GCATACTAGTGACACTCTGTTTGT 58.769 41.667 12.39 5.61 0.00 2.83
3266 3603 4.627467 GGCATACTAGTGACACTCTGTTTG 59.373 45.833 12.39 16.63 0.00 2.93
3267 3604 4.528596 AGGCATACTAGTGACACTCTGTTT 59.471 41.667 12.39 5.23 0.00 2.83
3268 3605 4.090090 AGGCATACTAGTGACACTCTGTT 58.910 43.478 12.39 0.00 0.00 3.16
3269 3606 3.697045 GAGGCATACTAGTGACACTCTGT 59.303 47.826 12.39 14.35 0.00 3.41
3270 3607 3.951037 AGAGGCATACTAGTGACACTCTG 59.049 47.826 12.39 9.04 33.23 3.35
3271 3608 4.243793 AGAGGCATACTAGTGACACTCT 57.756 45.455 12.39 10.40 0.00 3.24
3272 3609 5.127491 AGTAGAGGCATACTAGTGACACTC 58.873 45.833 12.39 8.31 34.21 3.51
3273 3610 5.118729 AGTAGAGGCATACTAGTGACACT 57.881 43.478 13.68 13.68 34.21 3.55
3274 3611 5.357314 TCAAGTAGAGGCATACTAGTGACAC 59.643 44.000 5.39 0.00 34.90 3.67
3275 3612 5.357314 GTCAAGTAGAGGCATACTAGTGACA 59.643 44.000 19.41 0.00 40.28 3.58
3276 3613 5.591067 AGTCAAGTAGAGGCATACTAGTGAC 59.409 44.000 17.97 17.97 40.57 3.67
3277 3614 5.756918 AGTCAAGTAGAGGCATACTAGTGA 58.243 41.667 5.39 2.59 34.90 3.41


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

AutoCloner maintained by Alex Coulton.