Multiple sequence alignment - TraesCS1B01G407600

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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 TraesCS1B01G407600 chr1B 100.000 5194 0 0 1 5194 634778042 634783235 0.000000e+00 9592.0
1 TraesCS1B01G407600 chr1B 96.772 1456 39 4 842 2293 634995614 634997065 0.000000e+00 2422.0
2 TraesCS1B01G407600 chr1B 95.742 1456 37 9 842 2293 635102974 635104408 0.000000e+00 2322.0
3 TraesCS1B01G407600 chr1B 87.472 902 58 19 1 849 634994690 634995589 0.000000e+00 989.0
4 TraesCS1B01G407600 chr1B 96.751 554 13 3 2346 2895 635104401 635104953 0.000000e+00 918.0
5 TraesCS1B01G407600 chr1B 96.863 542 13 2 2346 2884 634997058 634997598 0.000000e+00 904.0
6 TraesCS1B01G407600 chr1B 97.234 470 12 1 2960 3429 634997848 634998316 0.000000e+00 795.0
7 TraesCS1B01G407600 chr1B 94.242 521 27 2 3254 3773 635116069 635116587 0.000000e+00 793.0
8 TraesCS1B01G407600 chr1B 97.044 406 12 0 4789 5194 634998315 634998720 0.000000e+00 684.0
9 TraesCS1B01G407600 chr1B 85.060 502 48 21 1 481 635102037 635102532 2.170000e-133 486.0
10 TraesCS1B01G407600 chr1B 98.485 264 4 0 2994 3257 635105208 635105471 2.830000e-127 466.0
11 TraesCS1B01G407600 chr1B 78.771 537 58 28 4543 5035 635119526 635120050 5.050000e-80 309.0
12 TraesCS1B01G407600 chr1B 90.798 163 15 0 5032 5194 635126463 635126625 8.760000e-53 219.0
13 TraesCS1B01G407600 chr1B 91.111 135 11 1 3796 3929 635117888 635118022 1.150000e-41 182.0
14 TraesCS1B01G407600 chr1B 90.991 111 7 2 4427 4534 635119375 635119485 4.190000e-31 147.0
15 TraesCS1B01G407600 chr1D 92.439 1878 82 18 2940 4800 461764250 461766084 0.000000e+00 2627.0
16 TraesCS1B01G407600 chr1D 92.286 700 36 11 1605 2293 461762728 461763420 0.000000e+00 977.0
17 TraesCS1B01G407600 chr1D 90.305 722 58 8 932 1642 461762004 461762724 0.000000e+00 935.0
18 TraesCS1B01G407600 chr1D 91.667 552 37 5 2346 2890 461763413 461763962 0.000000e+00 756.0
19 TraesCS1B01G407600 chr1D 94.949 396 19 1 4799 5194 461785071 461785465 2.050000e-173 619.0
20 TraesCS1B01G407600 chr1D 93.160 307 19 2 173 479 461760982 461761286 2.850000e-122 449.0
21 TraesCS1B01G407600 chr1D 87.536 345 24 9 522 849 461761366 461761708 1.060000e-101 381.0
22 TraesCS1B01G407600 chr1D 95.652 184 7 1 1 184 461759235 461759417 1.410000e-75 294.0
23 TraesCS1B01G407600 chr1D 92.473 93 7 0 842 934 461761733 461761825 3.260000e-27 134.0
24 TraesCS1B01G407600 chr1A 90.706 1474 100 15 843 2293 552978757 552980216 0.000000e+00 1929.0
25 TraesCS1B01G407600 chr1A 89.325 815 73 7 842 1648 553049798 553050606 0.000000e+00 1011.0
26 TraesCS1B01G407600 chr1A 91.463 656 38 8 3281 3929 553052419 553053063 0.000000e+00 885.0
27 TraesCS1B01G407600 chr1A 90.135 517 40 6 3416 3929 552981356 552981864 0.000000e+00 662.0
28 TraesCS1B01G407600 chr1A 88.669 556 45 9 2721 3270 553051778 553052321 0.000000e+00 662.0
29 TraesCS1B01G407600 chr1A 87.395 476 39 8 2433 2899 552980271 552980734 1.280000e-145 527.0
30 TraesCS1B01G407600 chr1A 91.573 356 27 1 2346 2698 553051321 553051676 6.050000e-134 488.0
31 TraesCS1B01G407600 chr1A 88.764 356 31 5 1605 1958 553050604 553050952 1.340000e-115 427.0
32 TraesCS1B01G407600 chr1A 88.095 336 19 10 1960 2293 553051012 553051328 3.800000e-101 379.0
33 TraesCS1B01G407600 chr1A 85.417 336 34 7 3994 4314 553053073 553053408 8.330000e-88 335.0
34 TraesCS1B01G407600 chr1A 87.705 244 19 6 4954 5194 553066383 553066618 1.840000e-69 274.0
35 TraesCS1B01G407600 chr1A 81.657 338 43 15 522 849 552978403 552978731 3.990000e-66 263.0
36 TraesCS1B01G407600 chr1A 87.692 195 14 7 4343 4534 553061027 553061214 8.760000e-53 219.0
37 TraesCS1B01G407600 chr1A 87.629 194 15 6 4344 4534 552982518 552982705 3.150000e-52 217.0
38 TraesCS1B01G407600 chr1A 100.000 61 0 0 2294 2354 583789189 583789129 4.250000e-21 113.0
39 TraesCS1B01G407600 chr1A 93.478 46 2 1 382 427 552976879 552976923 3.360000e-07 67.6
40 TraesCS1B01G407600 chr1A 93.478 46 2 1 382 427 553047901 553047945 3.360000e-07 67.6
41 TraesCS1B01G407600 chr2D 84.721 1682 156 55 2355 3965 430467576 430465925 0.000000e+00 1589.0
42 TraesCS1B01G407600 chr2D 87.252 706 67 14 1594 2293 430468266 430467578 0.000000e+00 784.0
43 TraesCS1B01G407600 chr2D 79.896 771 79 22 844 1584 430469084 430468360 3.610000e-136 496.0
44 TraesCS1B01G407600 chr2D 84.659 352 49 2 4678 5025 430464706 430464356 3.850000e-91 346.0
45 TraesCS1B01G407600 chr2D 81.651 436 53 16 4114 4529 430465834 430465406 2.320000e-88 337.0
46 TraesCS1B01G407600 chr2A 83.700 1681 169 54 2346 3958 555818526 555820169 0.000000e+00 1489.0
47 TraesCS1B01G407600 chr2A 86.932 704 71 14 1594 2293 555817847 555818533 0.000000e+00 771.0
48 TraesCS1B01G407600 chr2A 80.602 665 67 19 947 1584 555817124 555817753 1.700000e-124 457.0
49 TraesCS1B01G407600 chr2A 85.511 352 46 2 4678 5025 555821344 555821694 3.820000e-96 363.0
50 TraesCS1B01G407600 chr2A 81.000 500 54 21 4067 4534 555820205 555820695 4.950000e-95 359.0
51 TraesCS1B01G407600 chr2A 96.970 66 1 1 2294 2359 649490077 649490013 5.500000e-20 110.0
52 TraesCS1B01G407600 chr2A 86.885 61 8 0 3966 4026 304477040 304476980 9.330000e-08 69.4
53 TraesCS1B01G407600 chr2A 86.885 61 8 0 3966 4026 381411640 381411580 9.330000e-08 69.4
54 TraesCS1B01G407600 chr2B 83.932 946 85 30 3069 3965 508366607 508365680 0.000000e+00 843.0
55 TraesCS1B01G407600 chr2B 85.493 710 75 12 1594 2293 508367971 508367280 0.000000e+00 715.0
56 TraesCS1B01G407600 chr2B 83.195 482 56 11 4067 4534 508365649 508365179 8.040000e-113 418.0
57 TraesCS1B01G407600 chr2B 90.411 292 15 7 2474 2756 508367131 508366844 6.350000e-99 372.0
58 TraesCS1B01G407600 chr2B 85.795 352 45 3 4678 5025 508251036 508250686 8.220000e-98 368.0
59 TraesCS1B01G407600 chr2B 79.123 479 46 19 842 1290 508368977 508368523 1.100000e-71 281.0
60 TraesCS1B01G407600 chr2B 93.056 72 4 1 2975 3045 508366841 508366770 2.560000e-18 104.0
61 TraesCS1B01G407600 chr5D 81.759 307 45 10 4089 4387 481667914 481667611 4.020000e-61 246.0
62 TraesCS1B01G407600 chr5B 100.000 63 0 0 2294 2356 660145751 660145813 3.290000e-22 117.0
63 TraesCS1B01G407600 chr5B 98.462 65 0 1 2294 2358 515818783 515818846 4.250000e-21 113.0
64 TraesCS1B01G407600 chr7A 98.438 64 1 0 2294 2357 105168935 105168998 4.250000e-21 113.0
65 TraesCS1B01G407600 chr7A 96.970 66 1 1 2294 2359 84761055 84760991 5.500000e-20 110.0
66 TraesCS1B01G407600 chr7A 80.620 129 18 6 2761 2885 178008968 178008843 5.540000e-15 93.5
67 TraesCS1B01G407600 chr3B 98.462 65 0 1 2294 2357 301337357 301337421 4.250000e-21 113.0
68 TraesCS1B01G407600 chr6B 97.015 67 1 1 2294 2359 93384647 93384713 1.530000e-20 111.0
69 TraesCS1B01G407600 chr6B 89.744 78 8 0 3179 3256 400147803 400147880 3.310000e-17 100.0
70 TraesCS1B01G407600 chr3A 98.413 63 1 0 2294 2356 642038880 642038942 1.530000e-20 111.0
71 TraesCS1B01G407600 chr3A 85.938 64 9 0 3964 4027 698730940 698730877 9.330000e-08 69.4
72 TraesCS1B01G407600 chr7B 89.394 66 7 0 3961 4026 225837280 225837215 3.330000e-12 84.2
73 TraesCS1B01G407600 chr4B 89.552 67 5 2 3961 4026 78119861 78119796 3.330000e-12 84.2
74 TraesCS1B01G407600 chr4B 85.938 64 9 0 3963 4026 413686982 413686919 9.330000e-08 69.4
75 TraesCS1B01G407600 chr7D 87.692 65 7 1 3964 4027 117879248 117879184 2.010000e-09 75.0
76 TraesCS1B01G407600 chr4A 87.692 65 6 2 3963 4026 442979460 442979397 2.010000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G407600 chr1B 634778042 634783235 5193 False 9592.000000 9592 100.000000 1 5194 1 chr1B.!!$F1 5193
1 TraesCS1B01G407600 chr1B 634994690 634998720 4030 False 1158.800000 2422 95.077000 1 5194 5 chr1B.!!$F3 5193
2 TraesCS1B01G407600 chr1B 635102037 635105471 3434 False 1048.000000 2322 94.009500 1 3257 4 chr1B.!!$F4 3256
3 TraesCS1B01G407600 chr1B 635116069 635120050 3981 False 357.750000 793 88.778750 3254 5035 4 chr1B.!!$F5 1781
4 TraesCS1B01G407600 chr1D 461759235 461766084 6849 False 819.125000 2627 91.939750 1 4800 8 chr1D.!!$F2 4799
5 TraesCS1B01G407600 chr1A 552976879 552982705 5826 False 610.933333 1929 88.500000 382 4534 6 chr1A.!!$F3 4152
6 TraesCS1B01G407600 chr1A 553047901 553053408 5507 False 531.825000 1011 89.598000 382 4314 8 chr1A.!!$F4 3932
7 TraesCS1B01G407600 chr2D 430464356 430469084 4728 True 710.400000 1589 83.635800 844 5025 5 chr2D.!!$R1 4181
8 TraesCS1B01G407600 chr2A 555817124 555821694 4570 False 687.800000 1489 83.549000 947 5025 5 chr2A.!!$F1 4078
9 TraesCS1B01G407600 chr2B 508365179 508368977 3798 True 455.500000 843 85.868333 842 4534 6 chr2B.!!$R2 3692

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
614 3644 0.524862 TCTAGTCCCGTTGAACGCTC 59.475 55.0 12.95 4.69 40.91 5.03 F
2306 5967 0.118346 TTGCTAGACCCTTCCCCAGA 59.882 55.0 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 5980 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.0 45.94 4.30 R
4207 10477 1.000896 CAAGGGTCCCGGCTTCAAT 60.001 57.895 0.99 0.0 0.00 2.57 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
279 1865 3.141272 ACCCACATTACCCCAGAGAAAAA 59.859 43.478 0.00 0.00 0.00 1.94
370 1966 4.379243 ACTTGGGCGCTCTCGTGG 62.379 66.667 9.62 0.00 38.14 4.94
380 1976 2.351447 GCGCTCTCGTGGTATTAGCATA 60.351 50.000 0.00 0.00 38.14 3.14
439 2037 2.418471 CCGCCACAAACCAATATGCATT 60.418 45.455 3.54 0.00 0.00 3.56
505 3510 5.473066 TGAGTTAAGCCTTTACCTACGTT 57.527 39.130 0.00 0.00 0.00 3.99
520 3525 1.591594 CGTTGATCCGACCATCCCG 60.592 63.158 0.00 0.00 0.00 5.14
551 3580 6.938030 ACCGATCAACTTAAAATCACCTTACA 59.062 34.615 0.00 0.00 0.00 2.41
604 3634 1.519751 CGCCATCTCCTCTAGTCCCG 61.520 65.000 0.00 0.00 0.00 5.14
614 3644 0.524862 TCTAGTCCCGTTGAACGCTC 59.475 55.000 12.95 4.69 40.91 5.03
645 3675 6.835488 AGTCCTTATAACATCAATGCCATTGT 59.165 34.615 16.55 2.41 41.02 2.71
703 3750 4.038271 ACCCATCATTGAGCTCTTGAAA 57.962 40.909 16.19 0.35 0.00 2.69
755 3810 1.002366 CTCCAATCTCTCGCCGTTTG 58.998 55.000 0.00 0.00 0.00 2.93
767 3822 1.939934 CGCCGTTTGACCATCACATAT 59.060 47.619 0.00 0.00 0.00 1.78
810 3866 4.034048 GTGACACCATTATAAGCACCTTCG 59.966 45.833 0.00 0.00 0.00 3.79
1241 4568 1.093159 CTTAGCTGCTTCAAGCCCTG 58.907 55.000 7.79 0.00 44.68 4.45
1400 4898 2.505819 TCATGTTTCTCCTCTTAGCCCC 59.494 50.000 0.00 0.00 0.00 5.80
1411 4909 3.916438 TTAGCCCCCTCTGTCGCCA 62.916 63.158 0.00 0.00 0.00 5.69
1426 4924 2.060980 GCCACCGACCTCTCCATCT 61.061 63.158 0.00 0.00 0.00 2.90
1431 4929 1.564818 ACCGACCTCTCCATCTACTCA 59.435 52.381 0.00 0.00 0.00 3.41
1607 5189 1.293498 GAGAGCAAGCAACCGAGGA 59.707 57.895 0.00 0.00 0.00 3.71
1741 5329 8.642020 GCTTGATGTGTTTCTGTAAAATTCATC 58.358 33.333 0.00 0.00 33.60 2.92
1755 5343 3.992943 ATTCATCTGTTTGGGTCCGTA 57.007 42.857 0.00 0.00 0.00 4.02
2104 5763 8.158025 TCTTATTCATTAGAGAAACCCCTTGA 57.842 34.615 0.00 0.00 0.00 3.02
2164 5825 7.976175 TGTGAACAATGTAGCATTTGTTTGTTA 59.024 29.630 2.92 0.00 43.95 2.41
2294 5955 7.806409 TGCAGCATTTATAGATTTTGCTAGA 57.194 32.000 0.00 0.00 41.47 2.43
2295 5956 7.642669 TGCAGCATTTATAGATTTTGCTAGAC 58.357 34.615 0.00 0.00 41.47 2.59
2296 5957 7.080724 GCAGCATTTATAGATTTTGCTAGACC 58.919 38.462 0.00 0.00 41.47 3.85
2297 5958 7.588512 CAGCATTTATAGATTTTGCTAGACCC 58.411 38.462 0.00 0.00 41.47 4.46
2298 5959 7.446625 CAGCATTTATAGATTTTGCTAGACCCT 59.553 37.037 0.00 0.00 41.47 4.34
2299 5960 8.001292 AGCATTTATAGATTTTGCTAGACCCTT 58.999 33.333 0.00 0.00 41.58 3.95
2300 5961 8.293157 GCATTTATAGATTTTGCTAGACCCTTC 58.707 37.037 0.00 0.00 0.00 3.46
2301 5962 8.787852 CATTTATAGATTTTGCTAGACCCTTCC 58.212 37.037 0.00 0.00 0.00 3.46
2302 5963 3.653835 AGATTTTGCTAGACCCTTCCC 57.346 47.619 0.00 0.00 0.00 3.97
2303 5964 2.242452 AGATTTTGCTAGACCCTTCCCC 59.758 50.000 0.00 0.00 0.00 4.81
2304 5965 1.451449 TTTTGCTAGACCCTTCCCCA 58.549 50.000 0.00 0.00 0.00 4.96
2305 5966 0.991920 TTTGCTAGACCCTTCCCCAG 59.008 55.000 0.00 0.00 0.00 4.45
2306 5967 0.118346 TTGCTAGACCCTTCCCCAGA 59.882 55.000 0.00 0.00 0.00 3.86
2307 5968 0.617820 TGCTAGACCCTTCCCCAGAC 60.618 60.000 0.00 0.00 0.00 3.51
2308 5969 1.338890 GCTAGACCCTTCCCCAGACC 61.339 65.000 0.00 0.00 0.00 3.85
2309 5970 0.691413 CTAGACCCTTCCCCAGACCC 60.691 65.000 0.00 0.00 0.00 4.46
2310 5971 1.160289 TAGACCCTTCCCCAGACCCT 61.160 60.000 0.00 0.00 0.00 4.34
2311 5972 2.204151 ACCCTTCCCCAGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2312 5973 3.732849 CCCTTCCCCAGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
2313 5974 4.101448 CCTTCCCCAGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2314 5975 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2335 5996 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
2336 5997 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
2337 5998 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
2338 5999 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96
2339 6000 1.821332 GAGCTACATGCACTGGGGC 60.821 63.158 0.00 0.00 45.94 5.80
2340 6001 2.262774 GAGCTACATGCACTGGGGCT 62.263 60.000 13.29 13.29 45.94 5.19
2341 6002 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
2342 6003 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
2343 6004 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
2348 6009 2.203684 CACTGGGGCTGCCCTTTT 60.204 61.111 34.99 17.53 44.66 2.27
2349 6010 1.838396 CACTGGGGCTGCCCTTTTT 60.838 57.895 34.99 15.74 44.66 1.94
2599 6303 6.756542 ACTATCAAAAGTCAAAACAAAGTGGC 59.243 34.615 0.00 0.00 0.00 5.01
2667 6378 8.830580 AGTTACATGTACAAGCTATGCTATTTG 58.169 33.333 4.68 0.00 38.25 2.32
3284 7570 9.814899 AGACATGAACTAGAATGAGACATTTAG 57.185 33.333 0.00 0.00 0.00 1.85
3408 7695 6.096001 ACCATCAGTTTTGCAAGGATTATCTC 59.904 38.462 0.00 0.00 0.00 2.75
3524 7817 1.831580 AATTGCTGGGCTGAAGACTC 58.168 50.000 0.00 0.00 0.00 3.36
3718 8022 5.363101 TGAATGATTCTACAGCATCACCTC 58.637 41.667 6.73 0.00 31.00 3.85
3739 8043 8.610896 CACCTCATCAATTCTTATCTTCTGTTC 58.389 37.037 0.00 0.00 0.00 3.18
3741 8049 7.239166 TCATCAATTCTTATCTTCTGTTCGC 57.761 36.000 0.00 0.00 0.00 4.70
3918 9532 8.991026 GTGGTATAACCGTATAATGCATGTTAA 58.009 33.333 0.00 0.00 42.58 2.01
3964 9578 5.478332 CCCTGAACCTGAATTTTAAGCTCTT 59.522 40.000 0.00 0.00 0.00 2.85
4064 10170 4.389374 TGTCTTCACATTCACTCCCTTTC 58.611 43.478 0.00 0.00 0.00 2.62
4065 10171 4.103153 TGTCTTCACATTCACTCCCTTTCT 59.897 41.667 0.00 0.00 0.00 2.52
4073 10179 5.474876 ACATTCACTCCCTTTCTTAAAGCTG 59.525 40.000 0.00 0.00 37.18 4.24
4075 10181 3.394606 TCACTCCCTTTCTTAAAGCTGGT 59.605 43.478 0.00 0.00 37.18 4.00
4142 10411 9.527157 TGATGGTATGTTTCCATTTCTTAAAGA 57.473 29.630 0.00 0.00 44.52 2.52
4185 10454 3.118038 TCTTGTTTTGCAGGGTGTAGAGT 60.118 43.478 0.00 0.00 0.00 3.24
4186 10455 4.101898 TCTTGTTTTGCAGGGTGTAGAGTA 59.898 41.667 0.00 0.00 0.00 2.59
4265 10535 2.019984 GTGCCTGCCTATTTCTTCCTG 58.980 52.381 0.00 0.00 0.00 3.86
4279 10551 4.380843 TCTTCCTGTTTTTGGCTGGATA 57.619 40.909 0.00 0.00 34.65 2.59
4280 10552 4.934356 TCTTCCTGTTTTTGGCTGGATAT 58.066 39.130 0.00 0.00 34.65 1.63
4356 10635 8.624776 GGTGTTTCTTATATTTTGAGATGGAGG 58.375 37.037 0.00 0.00 0.00 4.30
4487 11083 2.229784 GCAGATTCAAGTCCAGTTTGGG 59.770 50.000 0.00 0.00 38.32 4.12
4492 11088 6.209391 CAGATTCAAGTCCAGTTTGGGTTTAT 59.791 38.462 0.00 0.00 38.32 1.40
4494 11090 4.403734 TCAAGTCCAGTTTGGGTTTATCC 58.596 43.478 0.00 0.00 38.32 2.59
4580 11220 8.937884 CATGATGCTCCTCTTTAATATCAGAAG 58.062 37.037 0.00 0.00 0.00 2.85
4581 11221 8.255111 TGATGCTCCTCTTTAATATCAGAAGA 57.745 34.615 0.00 0.00 0.00 2.87
4609 11731 1.181741 TCTCTGCTTGAGTCGCCTGT 61.182 55.000 7.08 0.00 43.13 4.00
4775 11935 3.542676 ACGCCCCGTCACACTCAA 61.543 61.111 0.00 0.00 33.69 3.02
4780 11940 1.147376 CCCGTCACACTCAACCCAA 59.853 57.895 0.00 0.00 0.00 4.12
4890 12055 4.501714 GACGACATGCCCGCCGTA 62.502 66.667 7.85 0.00 35.22 4.02
5184 12356 4.621068 TGCTTCATTTTTAGGATCTGCG 57.379 40.909 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
251 1837 2.507886 CTGGGGTAATGTGGGTATGTCA 59.492 50.000 0.00 0.00 0.00 3.58
450 3430 4.215109 TGAGGGATCGTCAACATGATCTA 58.785 43.478 0.00 0.00 42.66 1.98
453 3433 3.912496 TTGAGGGATCGTCAACATGAT 57.088 42.857 0.00 0.00 34.10 2.45
481 3461 5.416947 ACGTAGGTAAAGGCTTAACTCATG 58.583 41.667 0.00 0.00 36.44 3.07
483 3463 5.010922 TCAACGTAGGTAAAGGCTTAACTCA 59.989 40.000 0.00 0.00 36.44 3.41
487 3467 5.422145 GGATCAACGTAGGTAAAGGCTTAA 58.578 41.667 0.00 0.00 0.00 1.85
488 3468 4.440525 CGGATCAACGTAGGTAAAGGCTTA 60.441 45.833 0.00 0.00 0.00 3.09
496 3501 2.127271 TGGTCGGATCAACGTAGGTA 57.873 50.000 0.00 0.00 34.94 3.08
520 3525 7.413767 GGTGATTTTAAGTTGATCGGTTAGACC 60.414 40.741 0.00 0.00 34.05 3.85
536 3565 9.933723 GTTACCTACTCTGTAAGGTGATTTTAA 57.066 33.333 4.29 0.00 45.75 1.52
551 3580 3.388350 GCCTGGCTATTGTTACCTACTCT 59.612 47.826 12.43 0.00 0.00 3.24
579 3608 2.967507 TAGAGGAGATGGCGCGCTCT 62.968 60.000 32.29 26.39 0.00 4.09
604 3634 0.714439 GACTTAGGCGAGCGTTCAAC 59.286 55.000 0.00 0.00 0.00 3.18
614 3644 6.347725 GCATTGATGTTATAAGGACTTAGGCG 60.348 42.308 0.00 0.00 0.00 5.52
676 3706 0.743097 GCTCAATGATGGGTTGCTCC 59.257 55.000 0.00 0.00 0.00 4.70
677 3707 1.674962 GAGCTCAATGATGGGTTGCTC 59.325 52.381 9.40 4.55 38.58 4.26
717 3764 3.057946 GGAGAAAGGCATGTTGACTTGTC 60.058 47.826 0.00 0.00 46.95 3.18
719 3766 2.886523 TGGAGAAAGGCATGTTGACTTG 59.113 45.455 0.00 0.00 46.95 3.16
726 3773 3.681034 CGAGAGATTGGAGAAAGGCATGT 60.681 47.826 0.00 0.00 0.00 3.21
755 3810 6.925610 TGTTGCTCTTTATATGTGATGGTC 57.074 37.500 0.00 0.00 0.00 4.02
767 3822 6.039159 TGTCACAATTGTCATGTTGCTCTTTA 59.961 34.615 8.48 0.00 0.00 1.85
810 3866 4.937620 TGGATTCACTCTTGCACTACATTC 59.062 41.667 0.00 0.00 0.00 2.67
1088 4385 1.379443 AGTATCCCGTCGCAGTCCA 60.379 57.895 0.00 0.00 0.00 4.02
1197 4524 4.816984 GAGAGGGCGGAGGGTCGA 62.817 72.222 0.00 0.00 0.00 4.20
1381 4878 1.847088 GGGGGCTAAGAGGAGAAACAT 59.153 52.381 0.00 0.00 0.00 2.71
1400 4898 4.436998 GGTCGGTGGCGACAGAGG 62.437 72.222 1.27 0.00 44.46 3.69
1411 4909 1.564818 TGAGTAGATGGAGAGGTCGGT 59.435 52.381 0.00 0.00 0.00 4.69
1426 4924 2.185867 GCGGTGGGCGAATGAGTA 59.814 61.111 0.00 0.00 0.00 2.59
1607 5189 1.503784 TCCCGGAATACATCTCCTCCT 59.496 52.381 0.73 0.00 0.00 3.69
1741 5329 4.035208 GCATATTTCTACGGACCCAAACAG 59.965 45.833 0.00 0.00 0.00 3.16
1755 5343 4.158394 ACAACCAAAGCGATGCATATTTCT 59.842 37.500 0.00 0.00 0.00 2.52
1839 5428 6.581171 AAATTCCTTGGATTCTGACTCAAC 57.419 37.500 0.00 0.00 0.00 3.18
1928 5522 9.686683 ATATGAAAACTCTACCTTAGCATTTGT 57.313 29.630 0.00 0.00 0.00 2.83
2104 5763 9.515226 TGAGCACTTATAGGTTAACAAGAAAAT 57.485 29.630 8.10 0.00 0.00 1.82
2164 5825 5.217978 TCCAAGCAATGCAATCTCTTTTT 57.782 34.783 8.35 0.00 0.00 1.94
2293 5954 2.125225 AGGGTCTGGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2294 5955 2.204151 CAGGGTCTGGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
2295 5956 3.732849 GCAGGGTCTGGGGAAGGG 61.733 72.222 0.00 0.00 31.21 3.95
2296 5957 4.101448 CGCAGGGTCTGGGGAAGG 62.101 72.222 4.35 0.00 40.11 3.46
2297 5958 4.785453 GCGCAGGGTCTGGGGAAG 62.785 72.222 0.30 0.00 43.28 3.46
2309 5970 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2312 5973 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2313 5974 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2314 5975 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2315 5976 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2317 5978 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
2318 5979 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
2319 5980 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
2320 5981 1.153086 CCCCAGTGCATGTAGCTCC 60.153 63.158 0.00 0.00 45.94 4.70
2321 5982 1.821332 GCCCCAGTGCATGTAGCTC 60.821 63.158 0.00 0.00 45.94 4.09
2322 5983 2.273449 GCCCCAGTGCATGTAGCT 59.727 61.111 0.00 0.00 45.94 3.32
2323 5984 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
2324 5985 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
2325 5986 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
2347 6008 6.096695 GCGCAGATTAAGGGAAACATAAAAA 58.903 36.000 0.30 0.00 0.00 1.94
2348 6009 5.184096 TGCGCAGATTAAGGGAAACATAAAA 59.816 36.000 5.66 0.00 0.00 1.52
2349 6010 4.702612 TGCGCAGATTAAGGGAAACATAAA 59.297 37.500 5.66 0.00 0.00 1.40
2350 6011 4.265893 TGCGCAGATTAAGGGAAACATAA 58.734 39.130 5.66 0.00 0.00 1.90
2351 6012 3.879998 TGCGCAGATTAAGGGAAACATA 58.120 40.909 5.66 0.00 0.00 2.29
2352 6013 2.722094 TGCGCAGATTAAGGGAAACAT 58.278 42.857 5.66 0.00 0.00 2.71
2599 6303 8.115490 ACTAATCATCCAGAAAAAGGAAACTG 57.885 34.615 0.00 0.00 42.68 3.16
2667 6378 6.313164 GCTATAGGTCAACACTTAAACTCACC 59.687 42.308 1.04 0.00 0.00 4.02
2909 6715 7.094549 CCTCGTATTTTGGGTCAATTGACTAAA 60.095 37.037 31.81 27.59 44.20 1.85
3284 7570 8.099364 TGAAGACATGTTAAAACCTGAATCTC 57.901 34.615 0.00 0.00 0.00 2.75
3340 7627 8.680903 AGAGATAGCAACAACAAAATGATAAGG 58.319 33.333 0.00 0.00 0.00 2.69
3408 7695 8.309656 TGGTGCTGATCTCAATAACATATCTAG 58.690 37.037 0.00 0.00 0.00 2.43
3524 7817 3.118956 ACAAGATCTCTGCCCTTACTTCG 60.119 47.826 0.00 0.00 0.00 3.79
3718 8022 7.008440 TGCGAACAGAAGATAAGAATTGATG 57.992 36.000 0.00 0.00 0.00 3.07
3739 8043 3.674281 TGCAAGCAAACAAATAAGATGCG 59.326 39.130 0.00 0.00 41.72 4.73
3741 8049 6.146510 ACACATGCAAGCAAACAAATAAGATG 59.853 34.615 0.00 0.00 0.00 2.90
3853 9463 2.120312 TGGACAGTTAAGACACACCCA 58.880 47.619 0.00 0.00 0.00 4.51
3854 9464 2.104281 AGTGGACAGTTAAGACACACCC 59.896 50.000 0.00 0.00 34.65 4.61
4064 10170 7.382218 CCACTAATGTTCAAAACCAGCTTTAAG 59.618 37.037 0.00 0.00 0.00 1.85
4065 10171 7.147811 ACCACTAATGTTCAAAACCAGCTTTAA 60.148 33.333 0.00 0.00 0.00 1.52
4073 10179 4.261867 GGGTCACCACTAATGTTCAAAACC 60.262 45.833 0.00 0.00 36.50 3.27
4075 10181 3.566322 CGGGTCACCACTAATGTTCAAAA 59.434 43.478 0.00 0.00 36.13 2.44
4142 10411 7.287696 ACAAGATGTAAAGGAAGTCAAAACCAT 59.712 33.333 0.00 0.00 0.00 3.55
4185 10454 9.567776 TCAATTTTTGTGACCTTCTTACAGATA 57.432 29.630 0.00 0.00 0.00 1.98
4186 10455 8.463930 TCAATTTTTGTGACCTTCTTACAGAT 57.536 30.769 0.00 0.00 0.00 2.90
4207 10477 1.000896 CAAGGGTCCCGGCTTCAAT 60.001 57.895 0.99 0.00 0.00 2.57
4265 10535 5.869344 GTCCAGAAAATATCCAGCCAAAAAC 59.131 40.000 0.00 0.00 0.00 2.43
4351 10630 5.244626 GGTTTCACAGTTACTACTACCTCCA 59.755 44.000 0.00 0.00 31.96 3.86
4397 10977 0.673333 TGATGCCACGTCTCGCATTT 60.673 50.000 13.74 0.00 45.52 2.32
4402 10982 0.298707 CGAAATGATGCCACGTCTCG 59.701 55.000 0.00 0.00 0.00 4.04
4758 11918 3.542676 TTGAGTGTGACGGGGCGT 61.543 61.111 0.00 0.00 45.10 5.68
4775 11935 1.259840 GCCAATGCCATCACTTGGGT 61.260 55.000 3.01 0.00 46.55 4.51
4890 12055 3.632080 TTGATGACGGTGGGCGGT 61.632 61.111 0.00 0.00 0.00 5.68
5111 12283 3.370104 ACTTGTGGTTGTCCAAATTGGA 58.630 40.909 11.23 11.23 45.98 3.53


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

AutoCloner maintained by Alex Coulton.