Multiple sequence alignment - TraesCS5A01G373600

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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 TraesCS5A01G373600 chr5A 100.000 5834 0 0 1 5834 571678963 571684796 0.000000e+00 10774.0
1 TraesCS5A01G373600 chr5A 79.716 774 133 19 3451 4214 26133718 26134477 6.650000e-149 538.0
2 TraesCS5A01G373600 chr5B 94.835 2633 76 17 2245 4847 553178961 553181563 0.000000e+00 4054.0
3 TraesCS5A01G373600 chr5B 93.286 1266 66 12 779 2028 553177246 553178508 0.000000e+00 1849.0
4 TraesCS5A01G373600 chr5B 77.131 962 177 32 3273 4214 27805634 27806572 8.670000e-143 518.0
5 TraesCS5A01G373600 chr5B 94.444 288 11 3 5461 5743 553184696 553184983 6.940000e-119 438.0
6 TraesCS5A01G373600 chr5B 92.308 247 18 1 2017 2263 553178533 553178778 3.350000e-92 350.0
7 TraesCS5A01G373600 chr5B 92.632 190 13 1 5225 5414 553184517 553184705 7.450000e-69 272.0
8 TraesCS5A01G373600 chr5B 81.877 309 27 17 77 381 553176528 553176811 3.520000e-57 233.0
9 TraesCS5A01G373600 chr5B 95.890 73 3 0 5060 5132 553181957 553182029 1.030000e-22 119.0
10 TraesCS5A01G373600 chr5B 97.015 67 2 0 5768 5834 553184983 553185049 4.780000e-21 113.0
11 TraesCS5A01G373600 chr5B 86.792 53 5 2 4962 5013 17726158 17726209 2.270000e-04 58.4
12 TraesCS5A01G373600 chr5D 95.020 1767 59 11 3194 4933 452678381 452680145 0.000000e+00 2748.0
13 TraesCS5A01G373600 chr5D 92.609 1353 72 18 706 2036 452675668 452677014 0.000000e+00 1919.0
14 TraesCS5A01G373600 chr5D 94.269 1169 45 5 2017 3180 452677032 452678183 0.000000e+00 1768.0
15 TraesCS5A01G373600 chr5D 84.022 726 82 23 3 710 452674827 452675536 0.000000e+00 667.0
16 TraesCS5A01G373600 chr5D 96.306 379 10 4 5459 5834 452680758 452681135 2.310000e-173 619.0
17 TraesCS5A01G373600 chr5D 77.534 957 179 28 3273 4214 37136574 37137509 1.430000e-150 544.0
18 TraesCS5A01G373600 chr5D 84.950 505 25 11 4948 5414 452680278 452680769 1.150000e-126 464.0
19 TraesCS5A01G373600 chr5D 91.667 48 3 1 4954 5001 238778045 238778091 1.360000e-06 65.8
20 TraesCS5A01G373600 chr1B 90.431 209 18 1 5153 5359 440500634 440500426 2.070000e-69 274.0
21 TraesCS5A01G373600 chr1B 92.553 94 4 1 5744 5834 98393016 98392923 1.320000e-26 132.0
22 TraesCS5A01G373600 chr1B 92.553 94 4 1 5744 5834 98440368 98440275 1.320000e-26 132.0
23 TraesCS5A01G373600 chr7A 78.423 241 38 13 495 729 33296857 33296625 1.690000e-30 145.0
24 TraesCS5A01G373600 chr4A 76.727 275 52 11 458 725 548314853 548315122 6.090000e-30 143.0
25 TraesCS5A01G373600 chr4A 77.439 164 32 5 496 657 648414545 648414385 6.220000e-15 93.5
26 TraesCS5A01G373600 chr2B 76.307 287 54 14 451 728 767412314 767412033 2.190000e-29 141.0
27 TraesCS5A01G373600 chr6B 73.944 284 56 15 439 712 506719580 506719305 1.340000e-16 99.0
28 TraesCS5A01G373600 chr6B 87.879 66 5 2 4949 5013 616309920 616309857 2.250000e-09 75.0
29 TraesCS5A01G373600 chr3B 93.182 44 3 0 4967 5010 716712577 716712534 1.360000e-06 65.8
30 TraesCS5A01G373600 chr2D 91.667 48 2 2 4964 5009 198462274 198462321 1.360000e-06 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G373600 chr5A 571678963 571684796 5833 False 10774.000000 10774 100.000000 1 5834 1 chr5A.!!$F2 5833
1 TraesCS5A01G373600 chr5A 26133718 26134477 759 False 538.000000 538 79.716000 3451 4214 1 chr5A.!!$F1 763
2 TraesCS5A01G373600 chr5B 553176528 553185049 8521 False 928.500000 4054 92.785875 77 5834 8 chr5B.!!$F3 5757
3 TraesCS5A01G373600 chr5B 27805634 27806572 938 False 518.000000 518 77.131000 3273 4214 1 chr5B.!!$F2 941
4 TraesCS5A01G373600 chr5D 452674827 452681135 6308 False 1364.166667 2748 91.196000 3 5834 6 chr5D.!!$F3 5831
5 TraesCS5A01G373600 chr5D 37136574 37137509 935 False 544.000000 544 77.534000 3273 4214 1 chr5D.!!$F1 941

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
359 371 0.108585 TGTGTGCTTCTCCCCAAGAC 59.891 55.000 0.0 0.0 32.27 3.01 F
384 452 1.067295 AAGACAGATGTGCTTCCCCA 58.933 50.000 0.0 0.0 0.00 4.96 F
972 1195 1.276421 TCTCTTTCCCTTCTGCCTTCG 59.724 52.381 0.0 0.0 0.00 3.79 F
1544 1784 0.527565 GTGCATGGCTGAACGGAATT 59.472 50.000 0.0 0.0 0.00 2.17 F
2555 3076 1.243902 GTCGTTTTCCTGGGCATGAA 58.756 50.000 0.0 0.0 0.00 2.57 F
3704 4416 0.401356 TCTGAATCTGCCTTGGTGCA 59.599 50.000 0.0 0.0 39.37 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 1536 0.313987 CGGGCTTCAAAACAGAACCC 59.686 55.000 0.00 0.0 36.41 4.11 R
1544 1784 0.544120 GGGGGCCTGAAAACATTCCA 60.544 55.000 0.84 0.0 0.00 3.53 R
1931 2175 1.068125 GGGTTTTACATTGACGCACCC 60.068 52.381 0.00 0.0 35.84 4.61 R
2828 3350 1.141254 TCAGGGCAACGGTAGAACAAA 59.859 47.619 0.00 0.0 37.60 2.83 R
4074 4789 0.534877 ACGCCATCAACAACTCAGCA 60.535 50.000 0.00 0.0 0.00 4.41 R
4862 5608 0.110823 CGTCACTTTACCTTGCACGC 60.111 55.000 0.00 0.0 0.00 5.34 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.472909 GCATGCCAAGGGTAGACGC 61.473 63.158 6.36 0.00 0.00 5.19
28 29 1.736645 CAAGGGTAGACGCGTGGTG 60.737 63.158 20.70 0.00 35.38 4.17
53 54 2.281414 CCACCACCATGTGTCGCA 60.281 61.111 0.00 0.00 34.35 5.10
69 70 3.931130 CACGTTGTTCGCACCGCA 61.931 61.111 0.00 0.00 44.19 5.69
70 71 3.196394 ACGTTGTTCGCACCGCAA 61.196 55.556 0.00 0.00 44.19 4.85
71 72 2.251075 CGTTGTTCGCACCGCAAT 59.749 55.556 0.00 0.00 0.00 3.56
72 73 1.222766 ACGTTGTTCGCACCGCAATA 61.223 50.000 0.00 0.00 44.19 1.90
75 76 1.069500 GTTGTTCGCACCGCAATAACT 60.069 47.619 0.00 0.00 0.00 2.24
119 120 8.766000 TTTTTCTTGGTGTTTCCTAGTTTTTC 57.234 30.769 0.00 0.00 39.47 2.29
121 122 6.937436 TCTTGGTGTTTCCTAGTTTTTCTC 57.063 37.500 0.00 0.00 39.47 2.87
122 123 5.526111 TCTTGGTGTTTCCTAGTTTTTCTCG 59.474 40.000 0.00 0.00 39.47 4.04
285 295 2.352388 CGGAAAAGTGAAAGGCGGATA 58.648 47.619 0.00 0.00 0.00 2.59
318 328 3.430098 TGTGAAACACATTTGTGCTTCCC 60.430 43.478 18.93 11.52 45.67 3.97
359 371 0.108585 TGTGTGCTTCTCCCCAAGAC 59.891 55.000 0.00 0.00 32.27 3.01
367 379 3.254411 GCTTCTCCCCAAGACTGAAAAAG 59.746 47.826 0.00 0.00 32.27 2.27
370 383 3.458118 TCTCCCCAAGACTGAAAAAGACA 59.542 43.478 0.00 0.00 0.00 3.41
384 452 1.067295 AAGACAGATGTGCTTCCCCA 58.933 50.000 0.00 0.00 0.00 4.96
396 464 4.080638 TGTGCTTCCCCAAAAAGTGAAAAT 60.081 37.500 0.00 0.00 0.00 1.82
399 467 5.163216 TGCTTCCCCAAAAAGTGAAAATCAT 60.163 36.000 0.00 0.00 0.00 2.45
411 479 9.744468 AAAAGTGAAAATCATAGTTACGCTTTT 57.256 25.926 0.00 0.00 39.77 2.27
423 491 8.995906 CATAGTTACGCTTTTAGTTTATTGTGC 58.004 33.333 0.00 0.00 0.00 4.57
434 502 3.323691 AGTTTATTGTGCTTTGGGGGTTC 59.676 43.478 0.00 0.00 0.00 3.62
544 625 3.793797 TCGAGGCGAGAAACATAATGA 57.206 42.857 0.00 0.00 0.00 2.57
563 644 8.961092 CATAATGATGAAAACGGTTCATGATTC 58.039 33.333 22.55 11.38 40.27 2.52
564 645 6.764308 ATGATGAAAACGGTTCATGATTCT 57.236 33.333 18.11 0.00 39.08 2.40
589 670 5.296813 ACGCATGGTTCAAGAGATAAAAC 57.703 39.130 0.00 0.00 0.00 2.43
597 678 7.936584 TGGTTCAAGAGATAAAACGTTTTGAT 58.063 30.769 31.26 20.88 0.00 2.57
631 712 6.713450 TGTATGAAAGAAGTACAAAACTCCCC 59.287 38.462 0.00 0.00 37.50 4.81
642 723 2.406002 AAACTCCCCGGTTGCGACAT 62.406 55.000 6.39 0.00 0.00 3.06
659 740 3.882025 TGCGTCGCACATGCAATA 58.118 50.000 17.58 0.00 44.51 1.90
683 764 2.933906 TCACTTGTCACCACGAGAAAAC 59.066 45.455 0.00 0.00 37.46 2.43
728 946 6.786967 GGTACCCTCTAGTTACTGATTTCA 57.213 41.667 0.00 0.00 0.00 2.69
838 1059 3.247411 GCCATTTCCGTTTCCAAACAAAG 59.753 43.478 3.21 0.00 38.81 2.77
839 1060 4.688021 CCATTTCCGTTTCCAAACAAAGA 58.312 39.130 3.21 0.00 38.81 2.52
843 1064 6.713792 TTTCCGTTTCCAAACAAAGAAAAG 57.286 33.333 3.21 0.00 38.81 2.27
844 1065 5.394224 TCCGTTTCCAAACAAAGAAAAGT 57.606 34.783 3.21 0.00 38.81 2.66
845 1066 6.512342 TCCGTTTCCAAACAAAGAAAAGTA 57.488 33.333 3.21 0.00 38.81 2.24
919 1140 1.677637 CTAGGCTCGACTCCAACCCC 61.678 65.000 0.00 0.00 0.00 4.95
960 1182 3.027974 ACAGCAACGTACTCTCTTTCC 57.972 47.619 0.00 0.00 0.00 3.13
972 1195 1.276421 TCTCTTTCCCTTCTGCCTTCG 59.724 52.381 0.00 0.00 0.00 3.79
1278 1508 2.202892 GGTTCCGGCCTCATCGAC 60.203 66.667 0.00 0.00 0.00 4.20
1291 1524 3.090219 ATCGACCTGTAAGCGCCCC 62.090 63.158 2.29 0.00 0.00 5.80
1293 1526 4.078516 GACCTGTAAGCGCCCCGT 62.079 66.667 2.29 0.00 0.00 5.28
1298 1532 3.459063 GTAAGCGCCCCGTCCTCT 61.459 66.667 2.29 0.00 0.00 3.69
1347 1581 1.390463 GTTCGACGAATTGCCTCTGAC 59.610 52.381 14.27 0.00 0.00 3.51
1490 1728 3.343421 GCTCGGCACCGTCGTTTT 61.343 61.111 9.23 0.00 40.74 2.43
1491 1729 2.851104 CTCGGCACCGTCGTTTTC 59.149 61.111 9.23 0.00 40.74 2.29
1519 1759 2.825861 TTGGTCGTCTTTAGTGGGAC 57.174 50.000 0.00 0.00 0.00 4.46
1520 1760 1.707106 TGGTCGTCTTTAGTGGGACA 58.293 50.000 0.00 0.00 33.19 4.02
1544 1784 0.527565 GTGCATGGCTGAACGGAATT 59.472 50.000 0.00 0.00 0.00 2.17
1547 1787 1.462616 CATGGCTGAACGGAATTGGA 58.537 50.000 0.00 0.00 0.00 3.53
1582 1822 4.231140 TGGACTGCCCAGATGACA 57.769 55.556 1.69 0.00 40.82 3.58
1674 1914 4.752101 GCACTTCTCTGCTTTGTTTCTAGA 59.248 41.667 0.00 0.00 34.06 2.43
1700 1940 7.203910 AGTGCCGTTGTTCAAAAATTACATTA 58.796 30.769 0.00 0.00 0.00 1.90
1764 2005 8.491152 CGAGTATATTTCATGAAACATCAGGTC 58.509 37.037 22.71 12.25 32.51 3.85
1782 2023 2.483188 GGTCTATGGCCTTAGTTGTCGG 60.483 54.545 21.63 0.00 0.00 4.79
1812 2053 9.573166 TCTCCGGATTTGTATTCATATCATTTT 57.427 29.630 3.57 0.00 35.00 1.82
1824 2065 8.608185 ATTCATATCATTTTGGTAAACCCACT 57.392 30.769 0.00 0.00 45.19 4.00
1838 2079 1.904537 ACCCACTTAAGTAACTCCCCG 59.095 52.381 8.04 0.00 0.00 5.73
1925 2169 5.066968 ACGGTGTTGTTTGTTTCTCAAAT 57.933 34.783 0.00 0.00 45.88 2.32
1931 2175 8.327429 GGTGTTGTTTGTTTCTCAAATTATGTG 58.673 33.333 0.00 0.00 45.88 3.21
1954 2198 3.498082 GTGCGTCAATGTAAAACCCATC 58.502 45.455 0.00 0.00 0.00 3.51
1962 2206 4.989279 ATGTAAAACCCATCTCATGTGC 57.011 40.909 0.00 0.00 0.00 4.57
2088 2404 5.512753 TGAAAAGATGCAAAGTGCTACAA 57.487 34.783 0.00 0.00 45.31 2.41
2089 2405 5.522456 TGAAAAGATGCAAAGTGCTACAAG 58.478 37.500 0.00 0.00 45.31 3.16
2090 2406 5.067674 TGAAAAGATGCAAAGTGCTACAAGT 59.932 36.000 0.00 0.00 45.31 3.16
2091 2407 6.262049 TGAAAAGATGCAAAGTGCTACAAGTA 59.738 34.615 0.00 0.00 45.31 2.24
2092 2408 6.633500 AAAGATGCAAAGTGCTACAAGTAA 57.367 33.333 0.00 0.00 45.31 2.24
2215 2536 4.739195 ACTCTTTAGAACGTCTGAGCATC 58.261 43.478 0.00 0.00 0.00 3.91
2235 2556 7.441017 AGCATCTAGTCCATCTAAGTGAATTC 58.559 38.462 0.00 0.00 0.00 2.17
2280 2800 9.953697 GTTTGTTGTACACAAGTCCATTATAAA 57.046 29.630 0.00 0.00 46.37 1.40
2480 3001 8.366401 TCATTTGCCATTTATCTCACTTTTCAA 58.634 29.630 0.00 0.00 0.00 2.69
2555 3076 1.243902 GTCGTTTTCCTGGGCATGAA 58.756 50.000 0.00 0.00 0.00 2.57
2699 3220 7.924541 ACCTTATTGTCTTGGTAGTATTGGAA 58.075 34.615 0.00 0.00 0.00 3.53
2875 3397 8.675504 TCTTGAGGTACTTAGAATTTAGACTCG 58.324 37.037 0.00 0.00 41.55 4.18
2912 3439 8.788806 TCCTATTGTGTTTAACTTACATGGTTG 58.211 33.333 0.00 0.00 0.00 3.77
2918 3445 9.999660 TGTGTTTAACTTACATGGTTGTCTATA 57.000 29.630 0.00 0.00 37.28 1.31
2971 3498 2.536761 TGACCGGTACCTTGAGTTTG 57.463 50.000 7.34 0.00 0.00 2.93
3012 3539 6.040278 TGGTTGTTGCATTATTTGTTCTCTGA 59.960 34.615 0.00 0.00 0.00 3.27
3068 3595 7.438160 CCTGAAATGTTGGTTCTTCTTTAAACC 59.562 37.037 0.00 0.00 44.29 3.27
3096 3623 5.316167 ACTGCAGTTTTAGGATTCACATCA 58.684 37.500 15.25 0.00 0.00 3.07
3147 3674 7.361542 CCTTCTGATATGTGAGGTGTTTGAAAG 60.362 40.741 0.00 0.00 0.00 2.62
3150 3677 6.774673 TGATATGTGAGGTGTTTGAAAGGTA 58.225 36.000 0.00 0.00 0.00 3.08
3389 4100 2.827921 GGAGGTGCATTTGATTTCCAGT 59.172 45.455 0.00 0.00 0.00 4.00
3650 4362 4.036852 GGAGTATATTGTGAGCCAAAAGGC 59.963 45.833 0.00 0.00 36.44 4.35
3704 4416 0.401356 TCTGAATCTGCCTTGGTGCA 59.599 50.000 0.00 0.00 39.37 4.57
3807 4522 5.312120 AGAAGACTGGTGTAACATCTACG 57.688 43.478 0.00 0.00 39.98 3.51
4074 4789 2.283529 ATCTCGACCACCAACCGCT 61.284 57.895 0.00 0.00 0.00 5.52
4556 5271 3.006940 CCGTTAATCTTGCTGCCAGTAA 58.993 45.455 0.00 0.00 0.00 2.24
4742 5458 1.202290 ACTTGCGTTTGCCACTTTCTG 60.202 47.619 0.00 0.00 41.78 3.02
4765 5484 4.393062 GTGTTGCAGTAATATGCTCTGTGT 59.607 41.667 0.00 0.00 46.63 3.72
4769 5488 3.384668 CAGTAATATGCTCTGTGTCGGG 58.615 50.000 0.00 0.00 0.00 5.14
4774 5493 1.981256 ATGCTCTGTGTCGGGTTTTT 58.019 45.000 0.00 0.00 0.00 1.94
4796 5515 2.187958 AGCAGTTCACTGGCTGGTATA 58.812 47.619 9.01 0.00 43.94 1.47
4912 5669 0.944311 ACTGCGTCCAACATGTCGAC 60.944 55.000 9.11 9.11 0.00 4.20
4933 5734 3.253677 ACGAACAAAACAGGTCACAACAA 59.746 39.130 0.00 0.00 0.00 2.83
4936 5737 5.391097 CGAACAAAACAGGTCACAACAAGTA 60.391 40.000 0.00 0.00 0.00 2.24
4937 5738 5.968528 ACAAAACAGGTCACAACAAGTAA 57.031 34.783 0.00 0.00 0.00 2.24
4938 5739 5.949735 ACAAAACAGGTCACAACAAGTAAG 58.050 37.500 0.00 0.00 0.00 2.34
4939 5740 4.632538 AAACAGGTCACAACAAGTAAGC 57.367 40.909 0.00 0.00 0.00 3.09
4940 5741 3.275617 ACAGGTCACAACAAGTAAGCA 57.724 42.857 0.00 0.00 0.00 3.91
4942 5743 3.118408 ACAGGTCACAACAAGTAAGCAGA 60.118 43.478 0.00 0.00 0.00 4.26
4943 5744 3.876914 CAGGTCACAACAAGTAAGCAGAA 59.123 43.478 0.00 0.00 0.00 3.02
4945 5746 3.877508 GGTCACAACAAGTAAGCAGAACT 59.122 43.478 0.00 0.00 0.00 3.01
4952 5871 3.244457 ACAAGTAAGCAGAACTGGTACCC 60.244 47.826 10.07 0.00 40.87 3.69
5036 5971 7.016153 TCCACTACTGAATGAACCTTACAAT 57.984 36.000 0.00 0.00 0.00 2.71
5040 5975 7.604164 CACTACTGAATGAACCTTACAATCTGT 59.396 37.037 0.00 0.00 35.06 3.41
5058 5993 5.779241 TCTGTCCCCAAGAATACAGAAAT 57.221 39.130 0.00 0.00 43.90 2.17
5098 6033 8.417106 TCAATTCAAATGTACTTTAAACAGGCA 58.583 29.630 0.00 0.00 0.00 4.75
5145 6080 5.528043 TTTGCAAAAGTAGCCAAAGATGA 57.472 34.783 10.02 0.00 0.00 2.92
5146 6081 5.528043 TTGCAAAAGTAGCCAAAGATGAA 57.472 34.783 0.00 0.00 0.00 2.57
5147 6082 5.528043 TGCAAAAGTAGCCAAAGATGAAA 57.472 34.783 0.00 0.00 0.00 2.69
5148 6083 6.100404 TGCAAAAGTAGCCAAAGATGAAAT 57.900 33.333 0.00 0.00 0.00 2.17
5149 6084 7.225784 TGCAAAAGTAGCCAAAGATGAAATA 57.774 32.000 0.00 0.00 0.00 1.40
5187 8572 4.805719 CAGCAGTGTAGATGAAATAGCGAA 59.194 41.667 0.00 0.00 0.00 4.70
5188 8573 5.464722 CAGCAGTGTAGATGAAATAGCGAAT 59.535 40.000 0.00 0.00 0.00 3.34
5210 8595 9.520204 CGAATTATAACCAAGCAAATCATTCTT 57.480 29.630 0.00 0.00 0.00 2.52
5282 8667 2.142292 AAATGAGGCCGGCTGGAACT 62.142 55.000 28.56 14.88 37.49 3.01
5343 8728 3.935203 CACCGCTGATTCAGACACTAAAT 59.065 43.478 17.87 0.00 32.44 1.40
5359 8744 6.068670 ACACTAAATGGCAACCCCTATAATC 58.931 40.000 0.00 0.00 0.00 1.75
5360 8745 6.126185 ACACTAAATGGCAACCCCTATAATCT 60.126 38.462 0.00 0.00 0.00 2.40
5397 8782 5.574443 GCTCAAAATTAGCTGACAAATGTCC 59.426 40.000 10.83 0.00 44.15 4.02
5400 8785 7.495901 TCAAAATTAGCTGACAAATGTCCAAA 58.504 30.769 10.83 1.34 44.15 3.28
5402 8787 7.713764 AAATTAGCTGACAAATGTCCAAAAC 57.286 32.000 10.83 0.00 44.15 2.43
5403 8788 3.733443 AGCTGACAAATGTCCAAAACC 57.267 42.857 10.83 0.00 44.15 3.27
5404 8789 3.030291 AGCTGACAAATGTCCAAAACCA 58.970 40.909 10.83 0.00 44.15 3.67
5405 8790 3.068590 AGCTGACAAATGTCCAAAACCAG 59.931 43.478 10.83 2.12 44.15 4.00
5406 8791 3.383761 CTGACAAATGTCCAAAACCAGC 58.616 45.455 10.83 0.00 44.15 4.85
5407 8792 2.102252 TGACAAATGTCCAAAACCAGCC 59.898 45.455 10.83 0.00 44.15 4.85
5408 8793 2.102252 GACAAATGTCCAAAACCAGCCA 59.898 45.455 2.04 0.00 39.07 4.75
5409 8794 2.503356 ACAAATGTCCAAAACCAGCCAA 59.497 40.909 0.00 0.00 0.00 4.52
5410 8795 3.054802 ACAAATGTCCAAAACCAGCCAAA 60.055 39.130 0.00 0.00 0.00 3.28
5411 8796 4.136051 CAAATGTCCAAAACCAGCCAAAT 58.864 39.130 0.00 0.00 0.00 2.32
5412 8797 5.163258 ACAAATGTCCAAAACCAGCCAAATA 60.163 36.000 0.00 0.00 0.00 1.40
5413 8798 5.559148 AATGTCCAAAACCAGCCAAATAA 57.441 34.783 0.00 0.00 0.00 1.40
5414 8799 4.329462 TGTCCAAAACCAGCCAAATAAC 57.671 40.909 0.00 0.00 0.00 1.89
5415 8800 3.243569 TGTCCAAAACCAGCCAAATAACG 60.244 43.478 0.00 0.00 0.00 3.18
5416 8801 2.297597 TCCAAAACCAGCCAAATAACGG 59.702 45.455 0.00 0.00 0.00 4.44
5417 8802 2.611722 CCAAAACCAGCCAAATAACGGG 60.612 50.000 0.00 0.00 0.00 5.28
5418 8803 2.003937 AAACCAGCCAAATAACGGGT 57.996 45.000 0.00 0.00 35.77 5.28
5419 8804 1.541379 AACCAGCCAAATAACGGGTC 58.459 50.000 0.00 0.00 32.90 4.46
5420 8805 0.402504 ACCAGCCAAATAACGGGTCA 59.597 50.000 0.00 0.00 27.07 4.02
5421 8806 1.202952 ACCAGCCAAATAACGGGTCAA 60.203 47.619 0.00 0.00 27.07 3.18
5422 8807 1.889829 CCAGCCAAATAACGGGTCAAA 59.110 47.619 0.00 0.00 29.87 2.69
5423 8808 2.297597 CCAGCCAAATAACGGGTCAAAA 59.702 45.455 0.00 0.00 29.87 2.44
5424 8809 3.243907 CCAGCCAAATAACGGGTCAAAAA 60.244 43.478 0.00 0.00 29.87 1.94
5445 8830 3.394674 AAAAACCAGCCAAATAACGGG 57.605 42.857 0.00 0.00 0.00 5.28
5446 8831 2.003937 AAACCAGCCAAATAACGGGT 57.996 45.000 0.00 0.00 35.77 5.28
5447 8832 1.541379 AACCAGCCAAATAACGGGTC 58.459 50.000 0.00 0.00 32.90 4.46
5448 8833 0.402504 ACCAGCCAAATAACGGGTCA 59.597 50.000 0.00 0.00 27.07 4.02
5449 8834 1.202952 ACCAGCCAAATAACGGGTCAA 60.203 47.619 0.00 0.00 27.07 3.18
5450 8835 1.889829 CCAGCCAAATAACGGGTCAAA 59.110 47.619 0.00 0.00 29.87 2.69
5451 8836 2.297597 CCAGCCAAATAACGGGTCAAAA 59.702 45.455 0.00 0.00 29.87 2.44
5452 8837 3.243907 CCAGCCAAATAACGGGTCAAAAA 60.244 43.478 0.00 0.00 29.87 1.94
5548 8936 4.281941 AGTGCTCACTCAGTTACTGATTGA 59.718 41.667 26.17 26.17 44.10 2.57
5550 8938 4.039124 TGCTCACTCAGTTACTGATTGACA 59.961 41.667 24.86 22.81 42.41 3.58
5572 8960 5.465724 ACAAACTGATTACTGGACGAACTTC 59.534 40.000 0.00 0.00 0.00 3.01
5585 8974 4.319549 GGACGAACTTCCTGTCAATTGTTC 60.320 45.833 5.13 1.16 34.32 3.18
5718 9108 6.428465 TCTCCATATTAGTTCACGAGCTAGAG 59.572 42.308 0.00 0.00 0.00 2.43
5757 9148 7.660030 ATAATTCCCACCAAAAGAATCGAAT 57.340 32.000 0.00 0.00 30.06 3.34
5800 9191 0.745486 CCCATCTTGCAGATCACGCA 60.745 55.000 5.78 5.78 31.32 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.749454 GTCTACCCTTGGCATGCCTG 60.749 60.000 35.53 26.44 36.94 4.85
7 8 3.307906 ACGCGTCTACCCTTGGCA 61.308 61.111 5.58 0.00 0.00 4.92
10 11 1.736645 CACCACGCGTCTACCCTTG 60.737 63.158 9.86 0.00 0.00 3.61
12 13 4.065281 GCACCACGCGTCTACCCT 62.065 66.667 9.86 0.00 0.00 4.34
38 39 2.664851 CGTGCGACACATGGTGGT 60.665 61.111 9.95 0.00 37.94 4.16
141 142 6.345298 TGATATGCTTCACACGAGGAAAATA 58.655 36.000 0.00 0.00 0.00 1.40
142 143 5.185454 TGATATGCTTCACACGAGGAAAAT 58.815 37.500 0.00 0.00 0.00 1.82
211 221 0.313987 GTGCTTTTCACTTTCGGGGG 59.686 55.000 0.00 0.00 42.38 5.40
232 242 2.020720 TGCTTCACCGTGAAACACAAT 58.979 42.857 14.74 0.00 35.73 2.71
241 251 2.518949 GCATAATTGTGCTTCACCGTG 58.481 47.619 18.85 0.00 41.82 4.94
359 371 4.320788 GGGAAGCACATCTGTCTTTTTCAG 60.321 45.833 0.00 0.00 0.00 3.02
367 379 1.909700 TTTGGGGAAGCACATCTGTC 58.090 50.000 0.00 0.00 0.00 3.51
370 383 2.629617 CACTTTTTGGGGAAGCACATCT 59.370 45.455 0.00 0.00 0.00 2.90
384 452 9.744468 AAAGCGTAACTATGATTTTCACTTTTT 57.256 25.926 0.00 0.00 27.32 1.94
399 467 8.314143 AGCACAATAAACTAAAAGCGTAACTA 57.686 30.769 0.00 0.00 0.00 2.24
411 479 4.120946 ACCCCCAAAGCACAATAAACTA 57.879 40.909 0.00 0.00 0.00 2.24
412 480 2.970987 ACCCCCAAAGCACAATAAACT 58.029 42.857 0.00 0.00 0.00 2.66
484 562 9.087424 GAATTCATGTTAATAGGCTTGGAAAAC 57.913 33.333 0.00 0.00 0.00 2.43
485 563 9.034800 AGAATTCATGTTAATAGGCTTGGAAAA 57.965 29.630 8.44 0.00 0.00 2.29
523 604 4.322080 TCATTATGTTTCTCGCCTCGAT 57.678 40.909 0.00 0.00 34.61 3.59
544 625 5.009631 TCCAGAATCATGAACCGTTTTCAT 58.990 37.500 0.00 4.13 39.53 2.57
563 644 1.081892 CTCTTGAACCATGCGTCCAG 58.918 55.000 0.00 0.00 0.00 3.86
564 645 0.684535 TCTCTTGAACCATGCGTCCA 59.315 50.000 0.00 0.00 0.00 4.02
589 670 9.265938 CTTTCATACACTCATTGTATCAAAACG 57.734 33.333 0.00 0.00 46.84 3.60
597 678 9.990360 TTGTACTTCTTTCATACACTCATTGTA 57.010 29.630 0.00 0.00 45.03 2.41
602 683 8.958119 AGTTTTGTACTTCTTTCATACACTCA 57.042 30.769 0.00 0.00 31.29 3.41
619 700 0.885596 CGCAACCGGGGAGTTTTGTA 60.886 55.000 6.32 0.00 0.00 2.41
642 723 1.423450 GTATTGCATGTGCGACGCA 59.577 52.632 20.50 20.50 45.83 5.24
644 725 0.314259 GACGTATTGCATGTGCGACG 60.314 55.000 18.84 18.84 45.83 5.12
659 740 0.248907 CTCGTGGTGACAAGTGACGT 60.249 55.000 0.00 0.00 46.06 4.34
774 995 5.859648 CCGCTCCAATATTTTTAAACACGTT 59.140 36.000 0.00 0.00 0.00 3.99
838 1059 4.307432 GGCCCAGCTTCTTTTTACTTTTC 58.693 43.478 0.00 0.00 0.00 2.29
839 1060 3.243737 CGGCCCAGCTTCTTTTTACTTTT 60.244 43.478 0.00 0.00 0.00 2.27
843 1064 1.244816 ACGGCCCAGCTTCTTTTTAC 58.755 50.000 0.00 0.00 0.00 2.01
844 1065 1.989706 AACGGCCCAGCTTCTTTTTA 58.010 45.000 0.00 0.00 0.00 1.52
845 1066 1.119684 AAACGGCCCAGCTTCTTTTT 58.880 45.000 0.00 0.00 0.00 1.94
960 1182 1.134175 GAGAGAGACGAAGGCAGAAGG 59.866 57.143 0.00 0.00 0.00 3.46
1278 1508 4.832608 GGACGGGGCGCTTACAGG 62.833 72.222 7.64 0.00 0.00 4.00
1302 1536 0.313987 CGGGCTTCAAAACAGAACCC 59.686 55.000 0.00 0.00 36.41 4.11
1315 1549 3.936203 TCGAACACCTGCGGGCTT 61.936 61.111 12.89 2.58 35.63 4.35
1316 1550 4.681978 GTCGAACACCTGCGGGCT 62.682 66.667 12.89 0.00 35.63 5.19
1347 1581 1.591504 AAATAAACGCAGGCCCCGTG 61.592 55.000 18.38 10.53 39.13 4.94
1356 1590 3.046390 CCTGAAACGCAAAATAAACGCA 58.954 40.909 0.00 0.00 0.00 5.24
1510 1750 1.302192 GCACGGCTTGTCCCACTAA 60.302 57.895 0.00 0.00 0.00 2.24
1511 1751 1.836999 ATGCACGGCTTGTCCCACTA 61.837 55.000 0.00 0.00 0.00 2.74
1533 1773 5.527951 TGAAAACATTCCAATTCCGTTCAG 58.472 37.500 0.00 0.00 0.00 3.02
1544 1784 0.544120 GGGGGCCTGAAAACATTCCA 60.544 55.000 0.84 0.00 0.00 3.53
1547 1787 1.155155 ACGGGGGCCTGAAAACATT 59.845 52.632 0.84 0.00 0.00 2.71
1674 1914 5.411781 TGTAATTTTTGAACAACGGCACTT 58.588 33.333 0.00 0.00 0.00 3.16
1700 1940 2.639327 GCCCAGCGTGCAAAGGAAT 61.639 57.895 0.00 0.00 0.00 3.01
1764 2005 3.536956 TTCCGACAACTAAGGCCATAG 57.463 47.619 13.47 13.47 0.00 2.23
1824 2065 1.279846 CCAAGGCGGGGAGTTACTTAA 59.720 52.381 0.00 0.00 0.00 1.85
1838 2079 2.531522 AATTGTCAAAGTGCCAAGGC 57.468 45.000 3.61 3.61 42.35 4.35
1925 2169 2.192664 ACATTGACGCACCCACATAA 57.807 45.000 0.00 0.00 0.00 1.90
1931 2175 1.068125 GGGTTTTACATTGACGCACCC 60.068 52.381 0.00 0.00 35.84 4.61
1962 2206 4.222124 ACCTGAGGGTTTATTGCTACAG 57.778 45.455 2.38 0.00 44.73 2.74
2200 2521 2.685897 GGACTAGATGCTCAGACGTTCT 59.314 50.000 0.00 0.00 0.00 3.01
2280 2800 2.157738 GCAATCTGCAGAACACCTCTT 58.842 47.619 22.50 5.50 44.26 2.85
2480 3001 4.783227 ACCTACTGGTAATGTCCAACTGAT 59.217 41.667 0.00 0.00 46.43 2.90
2686 3207 5.072600 AGTCACAAAGGTTCCAATACTACCA 59.927 40.000 0.00 0.00 34.32 3.25
2699 3220 2.498167 GCTGATCACAGTCACAAAGGT 58.502 47.619 0.00 0.00 45.04 3.50
2828 3350 1.141254 TCAGGGCAACGGTAGAACAAA 59.859 47.619 0.00 0.00 37.60 2.83
2887 3409 8.573035 ACAACCATGTAAGTTAAACACAATAGG 58.427 33.333 0.00 0.00 38.24 2.57
2929 3456 8.352942 GTCATCTAACACCAATGGGAATTTATC 58.647 37.037 3.55 0.00 38.05 1.75
2944 3471 3.194116 TCAAGGTACCGGTCATCTAACAC 59.806 47.826 12.40 0.00 0.00 3.32
2971 3498 1.884235 ACCAGCAGTAGCAACAAGTC 58.116 50.000 0.00 0.00 45.49 3.01
3012 3539 4.701651 TGGATTTCAATGCTTCGACAAGAT 59.298 37.500 0.00 0.00 0.00 2.40
3096 3623 8.139989 GGCAGTAAAGAATGAAGCATTGATTAT 58.860 33.333 0.00 0.00 30.17 1.28
3147 3674 4.820894 AGTCTCAAATACCACACCTACC 57.179 45.455 0.00 0.00 0.00 3.18
3150 3677 4.081420 CAGCTAGTCTCAAATACCACACCT 60.081 45.833 0.00 0.00 0.00 4.00
3389 4100 4.350368 TCACAGCAGACACCAAAGATAA 57.650 40.909 0.00 0.00 0.00 1.75
3704 4416 0.968393 AACAACCACACGCTTGGGTT 60.968 50.000 9.37 9.37 45.42 4.11
4074 4789 0.534877 ACGCCATCAACAACTCAGCA 60.535 50.000 0.00 0.00 0.00 4.41
4556 5271 2.417933 CACTAACCTACGACGCTAGTGT 59.582 50.000 9.11 9.11 36.36 3.55
4606 5321 1.128809 TACAGAAAGGGGTTCGGGCA 61.129 55.000 0.00 0.00 41.52 5.36
4742 5458 4.393062 ACACAGAGCATATTACTGCAACAC 59.607 41.667 0.00 0.00 44.77 3.32
4774 5493 0.764890 ACCAGCCAGTGAACTGCTAA 59.235 50.000 4.87 0.00 42.47 3.09
4861 5607 0.941542 GTCACTTTACCTTGCACGCA 59.058 50.000 0.00 0.00 0.00 5.24
4862 5608 0.110823 CGTCACTTTACCTTGCACGC 60.111 55.000 0.00 0.00 0.00 5.34
4872 5618 1.337074 CCCGTTACAGCCGTCACTTTA 60.337 52.381 0.00 0.00 0.00 1.85
4876 5622 1.735559 GTCCCGTTACAGCCGTCAC 60.736 63.158 0.00 0.00 0.00 3.67
4912 5669 3.479505 TGTTGTGACCTGTTTTGTTCG 57.520 42.857 0.00 0.00 0.00 3.95
5001 5921 8.948631 TCATTCAGTAGTGGAATAAAGATGTC 57.051 34.615 0.00 0.00 33.40 3.06
5036 5971 5.500234 CATTTCTGTATTCTTGGGGACAGA 58.500 41.667 0.00 0.00 44.95 3.41
5040 5975 4.272489 CTGCATTTCTGTATTCTTGGGGA 58.728 43.478 0.00 0.00 0.00 4.81
5058 5993 4.652421 TGAATTGAAAGTTTCTGCTGCA 57.348 36.364 16.33 0.88 0.00 4.41
5098 6033 9.768662 AATTTACAGTTGAATTTGAGAATTGCT 57.231 25.926 0.00 0.00 35.65 3.91
5145 6080 3.686016 CTGGTGTTACCCTGTGCTATTT 58.314 45.455 0.00 0.00 37.50 1.40
5146 6081 2.618045 GCTGGTGTTACCCTGTGCTATT 60.618 50.000 0.00 0.00 37.50 1.73
5147 6082 1.065418 GCTGGTGTTACCCTGTGCTAT 60.065 52.381 0.00 0.00 37.50 2.97
5148 6083 0.323629 GCTGGTGTTACCCTGTGCTA 59.676 55.000 0.00 0.00 37.50 3.49
5149 6084 1.073199 GCTGGTGTTACCCTGTGCT 59.927 57.895 0.00 0.00 37.50 4.40
5173 8540 8.507249 GCTTGGTTATAATTCGCTATTTCATCT 58.493 33.333 0.00 0.00 0.00 2.90
5182 8549 6.449635 TGATTTGCTTGGTTATAATTCGCT 57.550 33.333 0.00 0.00 0.00 4.93
5188 8573 9.859427 CTCAAAGAATGATTTGCTTGGTTATAA 57.141 29.630 0.00 0.00 39.51 0.98
5233 8618 4.560108 GCAACAGCAAGAATTTCCTGACAT 60.560 41.667 7.79 0.00 31.44 3.06
5282 8667 5.342433 CCGTGTTCTGTTCGGTATATGTTA 58.658 41.667 0.00 0.00 39.51 2.41
5343 8728 5.718801 TGTAAAGATTATAGGGGTTGCCA 57.281 39.130 0.00 0.00 0.00 4.92
5383 8768 3.030291 TGGTTTTGGACATTTGTCAGCT 58.970 40.909 12.43 0.00 46.47 4.24
5397 8782 2.036604 ACCCGTTATTTGGCTGGTTTTG 59.963 45.455 0.00 0.00 0.00 2.44
5400 8785 1.202952 TGACCCGTTATTTGGCTGGTT 60.203 47.619 0.00 0.00 0.00 3.67
5402 8787 1.540267 TTGACCCGTTATTTGGCTGG 58.460 50.000 0.00 0.00 0.00 4.85
5403 8788 3.651803 TTTTGACCCGTTATTTGGCTG 57.348 42.857 0.00 0.00 0.00 4.85
5425 8810 2.701423 ACCCGTTATTTGGCTGGTTTTT 59.299 40.909 0.00 0.00 0.00 1.94
5426 8811 2.297880 GACCCGTTATTTGGCTGGTTTT 59.702 45.455 0.00 0.00 0.00 2.43
5427 8812 1.890489 GACCCGTTATTTGGCTGGTTT 59.110 47.619 0.00 0.00 0.00 3.27
5428 8813 1.202952 TGACCCGTTATTTGGCTGGTT 60.203 47.619 0.00 0.00 0.00 3.67
5429 8814 0.402504 TGACCCGTTATTTGGCTGGT 59.597 50.000 0.00 0.00 0.00 4.00
5430 8815 1.540267 TTGACCCGTTATTTGGCTGG 58.460 50.000 0.00 0.00 0.00 4.85
5431 8816 3.651803 TTTTGACCCGTTATTTGGCTG 57.348 42.857 0.00 0.00 0.00 4.85
5452 8837 4.040339 CCACTCTTATTTGGCTGGGTTTTT 59.960 41.667 0.00 0.00 0.00 1.94
5453 8838 3.578282 CCACTCTTATTTGGCTGGGTTTT 59.422 43.478 0.00 0.00 0.00 2.43
5454 8839 3.165071 CCACTCTTATTTGGCTGGGTTT 58.835 45.455 0.00 0.00 0.00 3.27
5455 8840 2.807676 CCACTCTTATTTGGCTGGGTT 58.192 47.619 0.00 0.00 0.00 4.11
5456 8841 2.514458 CCACTCTTATTTGGCTGGGT 57.486 50.000 0.00 0.00 0.00 4.51
5548 8936 4.957296 AGTTCGTCCAGTAATCAGTTTGT 58.043 39.130 0.00 0.00 0.00 2.83
5550 8938 4.995487 GGAAGTTCGTCCAGTAATCAGTTT 59.005 41.667 0.00 0.00 37.65 2.66
5572 8960 2.787723 CGTAGCGAACAATTGACAGG 57.212 50.000 13.59 0.00 0.00 4.00
5718 9108 4.270325 GGGAATTATACACTGTTCACGAGC 59.730 45.833 0.00 0.00 0.00 5.03
5800 9191 9.705290 GATGTGAATTATTTTGTTTTACCTGGT 57.295 29.630 4.05 4.05 0.00 4.00


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

AutoCloner maintained by Alex Coulton.