Multiple sequence alignment - TraesCS4A01G192200

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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 TraesCS4A01G192200 chr4A 100.000 4412 0 0 1 4412 472647853 472652264 0.000000e+00 8148.0
1 TraesCS4A01G192200 chr4A 73.523 457 101 16 1758 2209 694667021 694667462 5.910000e-34 156.0
2 TraesCS4A01G192200 chr4A 86.429 140 14 4 4239 4376 96478752 96478888 9.890000e-32 148.0
3 TraesCS4A01G192200 chr4A 83.146 89 14 1 2419 2506 694667631 694667719 3.660000e-11 80.5
4 TraesCS4A01G192200 chr4D 92.537 3484 155 34 5 3460 102391117 102387711 0.000000e+00 4896.0
5 TraesCS4A01G192200 chr4D 93.945 578 24 5 3477 4051 102387653 102387084 0.000000e+00 863.0
6 TraesCS4A01G192200 chr4D 92.120 368 21 2 4048 4412 102387004 102386642 3.040000e-141 512.0
7 TraesCS4A01G192200 chr4D 77.305 282 33 20 3780 4053 462548414 462548156 2.140000e-28 137.0
8 TraesCS4A01G192200 chr4B 93.922 2879 137 15 600 3460 146559732 146556874 0.000000e+00 4313.0
9 TraesCS4A01G192200 chr4B 92.073 492 32 4 3923 4412 146533792 146533306 0.000000e+00 686.0
10 TraesCS4A01G192200 chr4B 92.162 370 15 4 3543 3911 146534262 146533906 1.090000e-140 510.0
11 TraesCS4A01G192200 chr4B 78.355 231 22 18 3779 3997 578350942 578351156 1.670000e-24 124.0
12 TraesCS4A01G192200 chr4B 94.366 71 3 1 3476 3545 146536429 146536359 1.680000e-19 108.0
13 TraesCS4A01G192200 chr7A 75.115 868 180 26 1647 2503 32300762 32299920 1.500000e-99 374.0
14 TraesCS4A01G192200 chr7A 77.901 362 47 19 3647 3997 541897585 541897246 1.250000e-45 195.0
15 TraesCS4A01G192200 chr7A 77.812 329 60 7 1005 1322 32301849 32301523 1.620000e-44 191.0
16 TraesCS4A01G192200 chr7A 94.444 36 1 1 416 451 261886603 261886569 2.000000e-03 54.7
17 TraesCS4A01G192200 chr7D 74.512 871 186 24 1647 2506 31996480 31995635 3.270000e-91 346.0
18 TraesCS4A01G192200 chr7D 79.118 340 50 13 4050 4376 309501858 309502189 9.610000e-52 215.0
19 TraesCS4A01G192200 chr7D 77.477 333 57 10 1005 1322 31997774 31997445 2.710000e-42 183.0
20 TraesCS4A01G192200 chr7D 76.440 191 35 9 215 400 612934553 612934368 1.310000e-15 95.3
21 TraesCS4A01G192200 chrUn 74.087 876 187 27 1644 2506 366954297 366953449 1.530000e-84 324.0
22 TraesCS4A01G192200 chrUn 74.087 876 187 27 1644 2506 366956268 366955420 1.530000e-84 324.0
23 TraesCS4A01G192200 chrUn 75.610 574 119 12 1644 2212 444589950 444590507 9.410000e-67 265.0
24 TraesCS4A01G192200 chrUn 73.259 359 61 22 1184 1525 366954732 366954392 1.010000e-16 99.0
25 TraesCS4A01G192200 chrUn 73.259 359 61 22 1184 1525 366956703 366956363 1.010000e-16 99.0
26 TraesCS4A01G192200 chrUn 73.259 359 61 22 1184 1525 444589515 444589855 1.010000e-16 99.0
27 TraesCS4A01G192200 chr3B 84.000 350 42 12 3658 3997 383722515 383722860 1.530000e-84 324.0
28 TraesCS4A01G192200 chr3B 80.000 355 49 14 3658 3997 759107207 759107554 4.410000e-60 243.0
29 TraesCS4A01G192200 chr3B 85.350 157 20 3 4243 4398 809343340 809343494 4.570000e-35 159.0
30 TraesCS4A01G192200 chr3B 77.320 194 33 9 216 403 30653760 30653572 2.170000e-18 104.0
31 TraesCS4A01G192200 chr3D 83.429 350 44 12 3658 3997 290874957 290875302 3.310000e-81 313.0
32 TraesCS4A01G192200 chr3D 83.969 262 31 10 3744 3997 4400689 4400947 1.590000e-59 241.0
33 TraesCS4A01G192200 chr5D 82.967 364 35 23 3649 4003 437445310 437444965 1.990000e-78 303.0
34 TraesCS4A01G192200 chr5D 100.000 29 0 0 415 443 303386385 303386413 2.000000e-03 54.7
35 TraesCS4A01G192200 chr3A 82.510 263 35 9 3744 3997 10208389 10208649 2.070000e-53 220.0
36 TraesCS4A01G192200 chr3A 85.821 134 17 2 3864 3997 57016452 57016321 1.650000e-29 141.0
37 TraesCS4A01G192200 chr3A 85.156 128 15 4 3872 3997 383710067 383710192 1.290000e-25 128.0
38 TraesCS4A01G192200 chr3A 84.375 128 17 3 3658 3785 57016797 57016673 5.990000e-24 122.0
39 TraesCS4A01G192200 chr3A 90.805 87 5 3 317 401 546680525 546680440 3.610000e-21 113.0
40 TraesCS4A01G192200 chr7B 79.056 339 50 15 4050 4376 304987316 304986987 3.460000e-51 213.0
41 TraesCS4A01G192200 chr7B 82.857 140 17 7 3668 3807 663743228 663743360 7.750000e-23 119.0
42 TraesCS4A01G192200 chr5B 77.841 352 48 14 3649 3995 545190729 545190403 1.620000e-44 191.0
43 TraesCS4A01G192200 chr5B 79.688 192 31 8 213 400 8011717 8011530 9.960000e-27 132.0
44 TraesCS4A01G192200 chr5B 80.531 113 18 4 4243 4353 263477245 263477355 2.830000e-12 84.2
45 TraesCS4A01G192200 chr2B 83.537 164 25 2 4236 4398 30126471 30126633 7.640000e-33 152.0
46 TraesCS4A01G192200 chr2B 80.531 113 18 4 4243 4353 205852776 205852886 2.830000e-12 84.2
47 TraesCS4A01G192200 chr2D 84.516 155 21 3 4243 4396 350354131 350354283 2.750000e-32 150.0
48 TraesCS4A01G192200 chr2D 83.333 108 16 2 296 402 647089207 647089313 1.010000e-16 99.0
49 TraesCS4A01G192200 chr2D 86.885 61 8 0 1834 1894 64184858 64184798 7.920000e-08 69.4
50 TraesCS4A01G192200 chr1D 83.230 161 22 5 4238 4396 257348915 257349072 4.600000e-30 143.0
51 TraesCS4A01G192200 chr1D 78.313 166 28 8 238 397 479923350 479923513 2.810000e-17 100.0
52 TraesCS4A01G192200 chr6D 81.699 153 22 6 252 399 458718231 458718080 5.990000e-24 122.0
53 TraesCS4A01G192200 chr5A 78.146 151 29 4 253 400 399304411 399304560 4.700000e-15 93.5
54 TraesCS4A01G192200 chr2A 87.500 56 6 1 413 467 565077490 565077545 3.680000e-06 63.9


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 TraesCS4A01G192200 chr4A 472647853 472652264 4411 False 8148.000000 8148 100.000000 1 4412 1 chr4A.!!$F2 4411
1 TraesCS4A01G192200 chr4D 102386642 102391117 4475 True 2090.333333 4896 92.867333 5 4412 3 chr4D.!!$R2 4407
2 TraesCS4A01G192200 chr4B 146556874 146559732 2858 True 4313.000000 4313 93.922000 600 3460 1 chr4B.!!$R1 2860
3 TraesCS4A01G192200 chr4B 146533306 146536429 3123 True 434.666667 686 92.867000 3476 4412 3 chr4B.!!$R2 936
4 TraesCS4A01G192200 chr7A 32299920 32301849 1929 True 282.500000 374 76.463500 1005 2503 2 chr7A.!!$R3 1498
5 TraesCS4A01G192200 chr7D 31995635 31997774 2139 True 264.500000 346 75.994500 1005 2506 2 chr7D.!!$R2 1501
6 TraesCS4A01G192200 chrUn 366953449 366956703 3254 True 211.500000 324 73.673000 1184 2506 4 chrUn.!!$R1 1322

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
527 535 0.811616 GCTTAGCCCAGTCGGTGATG 60.812 60.0 0.00 0.00 0.00 3.07 F
1237 3233 0.386100 CTCCGCGTATGAGGACATCG 60.386 60.0 4.92 0.00 39.36 3.84 F
1912 4635 0.456312 GTGGAGTCGTCGACCATGTC 60.456 60.0 21.40 12.17 36.09 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1400 3923 1.133025 GCTGCATTAGACGTGGCAAAT 59.867 47.619 0.00 0.0 35.59 2.32 R
2479 5205 1.331214 CCTGCAAAGGTGGTGACAAT 58.669 50.000 0.00 0.0 46.06 2.71 R
3460 6188 0.548510 GCCTAGGCACCATTTCCTCT 59.451 55.000 29.33 0.0 41.49 3.69 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
35 36 7.781693 AGGCACATATTTAATTCCATGAGAAGT 59.218 33.333 0.00 0.00 38.07 3.01
53 54 4.672587 AAGTACAGTTGTGCTTCTCTGA 57.327 40.909 9.39 0.00 45.60 3.27
104 105 2.479566 TTCTTCTCATGGAGGCACAC 57.520 50.000 0.00 0.00 0.00 3.82
113 114 5.045942 TCTCATGGAGGCACACATTTACTTA 60.046 40.000 0.00 0.00 0.00 2.24
116 117 3.694072 TGGAGGCACACATTTACTTATGC 59.306 43.478 0.00 0.00 0.00 3.14
117 118 3.694072 GGAGGCACACATTTACTTATGCA 59.306 43.478 0.00 0.00 34.73 3.96
127 128 7.601130 ACACATTTACTTATGCAAGAAGTACGA 59.399 33.333 19.06 13.31 38.73 3.43
129 130 7.817962 ACATTTACTTATGCAAGAAGTACGACT 59.182 33.333 19.06 6.52 38.73 4.18
140 141 3.728076 AAGTACGACTGTGCTTCTTGA 57.272 42.857 0.00 0.00 46.38 3.02
144 145 4.873827 AGTACGACTGTGCTTCTTGAAAAA 59.126 37.500 0.00 0.00 37.86 1.94
149 151 5.650543 GACTGTGCTTCTTGAAAAAGGAAA 58.349 37.500 0.00 0.00 0.00 3.13
191 193 3.619233 AACATATATTTGGTTCCGCGC 57.381 42.857 0.00 0.00 0.00 6.86
287 290 7.671495 AAAATTGTTGAAACCTATTGGCATC 57.329 32.000 0.00 0.00 36.63 3.91
307 310 4.932268 TCGTATGTGGTTTCGAAAATCC 57.068 40.909 13.10 11.26 0.00 3.01
309 312 3.484557 CGTATGTGGTTTCGAAAATCCCG 60.485 47.826 13.10 5.59 0.00 5.14
327 330 1.508632 CGACGCGGGAAATCCAATAT 58.491 50.000 12.47 0.00 37.91 1.28
334 337 5.163457 ACGCGGGAAATCCAATATTGAAAAT 60.163 36.000 17.23 4.79 37.91 1.82
359 362 5.227152 GTTTAGAATTTGGACGCATGGTTT 58.773 37.500 0.00 0.00 0.00 3.27
424 428 4.321718 ACACATGTCAACATCTGAGAAGG 58.678 43.478 0.00 0.00 33.60 3.46
427 431 3.407424 TGTCAACATCTGAGAAGGTGG 57.593 47.619 2.64 0.00 33.60 4.61
439 443 3.008375 TGAGAAGGTGGGAGTGATCTTTG 59.992 47.826 0.00 0.00 0.00 2.77
440 444 2.982488 AGAAGGTGGGAGTGATCTTTGT 59.018 45.455 0.00 0.00 0.00 2.83
526 534 0.978146 AGCTTAGCCCAGTCGGTGAT 60.978 55.000 0.00 0.00 0.00 3.06
527 535 0.811616 GCTTAGCCCAGTCGGTGATG 60.812 60.000 0.00 0.00 0.00 3.07
528 536 0.824109 CTTAGCCCAGTCGGTGATGA 59.176 55.000 0.00 0.00 0.00 2.92
529 537 0.824109 TTAGCCCAGTCGGTGATGAG 59.176 55.000 0.00 0.00 0.00 2.90
530 538 1.043116 TAGCCCAGTCGGTGATGAGG 61.043 60.000 0.00 0.00 0.00 3.86
531 539 2.187946 CCCAGTCGGTGATGAGGC 59.812 66.667 0.00 0.00 0.00 4.70
532 540 2.659063 CCCAGTCGGTGATGAGGCA 61.659 63.158 0.00 0.00 0.00 4.75
533 541 1.153489 CCAGTCGGTGATGAGGCAG 60.153 63.158 0.00 0.00 0.00 4.85
534 542 1.153489 CAGTCGGTGATGAGGCAGG 60.153 63.158 0.00 0.00 0.00 4.85
535 543 2.512515 GTCGGTGATGAGGCAGGC 60.513 66.667 0.00 0.00 0.00 4.85
536 544 3.785859 TCGGTGATGAGGCAGGCC 61.786 66.667 0.97 0.97 0.00 5.19
537 545 4.100084 CGGTGATGAGGCAGGCCA 62.100 66.667 13.63 0.55 38.92 5.36
538 546 2.439156 GGTGATGAGGCAGGCCAC 60.439 66.667 13.63 6.96 38.92 5.01
539 547 2.439156 GTGATGAGGCAGGCCACC 60.439 66.667 13.63 6.01 38.92 4.61
540 548 2.611800 TGATGAGGCAGGCCACCT 60.612 61.111 16.82 16.82 41.41 4.00
627 635 4.077184 TTACGGAGCTGGGCCACG 62.077 66.667 0.00 7.55 35.07 4.94
769 780 3.053291 GTGGTTGGCCGCAATCGA 61.053 61.111 0.00 0.00 44.43 3.59
773 784 1.579429 GTTGGCCGCAATCGAAGTT 59.421 52.632 0.00 0.00 38.10 2.66
775 786 1.169661 TTGGCCGCAATCGAAGTTGT 61.170 50.000 0.00 0.00 38.10 3.32
895 909 3.755378 GCTTGCATGCCATAGCTAATAGT 59.245 43.478 22.11 0.00 40.80 2.12
896 910 4.937620 GCTTGCATGCCATAGCTAATAGTA 59.062 41.667 22.11 0.00 40.80 1.82
897 911 5.064452 GCTTGCATGCCATAGCTAATAGTAG 59.936 44.000 22.11 0.00 40.80 2.57
927 941 9.676861 TGTAAGTATAAATCGGATAGCTAGCTA 57.323 33.333 26.09 26.09 0.00 3.32
946 967 3.428316 GCTAGCTCGGATAGGTGCTAATC 60.428 52.174 7.70 0.00 37.53 1.75
947 968 2.598565 AGCTCGGATAGGTGCTAATCA 58.401 47.619 0.00 0.00 33.68 2.57
948 969 2.297597 AGCTCGGATAGGTGCTAATCAC 59.702 50.000 0.00 0.00 44.90 3.06
961 982 6.753897 GTGCTAATCACCAGAAAACAAAAG 57.246 37.500 0.00 0.00 39.79 2.27
967 992 1.208259 CCAGAAAACAAAAGGTGCGC 58.792 50.000 0.00 0.00 0.00 6.09
1162 1187 2.590007 GCTTCCTGGATCGCGCAT 60.590 61.111 8.75 0.00 0.00 4.73
1237 3233 0.386100 CTCCGCGTATGAGGACATCG 60.386 60.000 4.92 0.00 39.36 3.84
1368 3891 2.793232 GTGTGAGAAGGTCGTGTTGTAC 59.207 50.000 0.00 0.00 0.00 2.90
1384 3907 4.390603 TGTTGTACATACGTTTCTCATGGC 59.609 41.667 0.00 0.00 0.00 4.40
1385 3908 3.527533 TGTACATACGTTTCTCATGGCC 58.472 45.455 0.00 0.00 0.00 5.36
1462 4167 2.005451 CTGAAGCTCTTTCCATCCACG 58.995 52.381 0.00 0.00 34.77 4.94
1534 4239 3.266772 TGAGGAAGATGTAAGCATTGGGT 59.733 43.478 0.00 0.00 35.07 4.51
1566 4271 7.151999 TCGAATTTATTTGGCCGCATAATAT 57.848 32.000 0.00 0.00 0.00 1.28
1726 4449 1.920325 CCCTGGAAGCCTGACCTCA 60.920 63.158 0.00 0.00 0.00 3.86
1804 4527 2.914908 GCACGACATTGGCGGGTTT 61.915 57.895 16.83 0.00 34.00 3.27
1910 4633 1.514228 CGTGGAGTCGTCGACCATG 60.514 63.158 21.40 14.62 36.09 3.66
1911 4634 1.585006 GTGGAGTCGTCGACCATGT 59.415 57.895 21.40 2.96 36.09 3.21
1912 4635 0.456312 GTGGAGTCGTCGACCATGTC 60.456 60.000 21.40 12.17 36.09 3.06
2103 4826 2.125512 GCACTGGCCGACGAGATT 60.126 61.111 0.00 0.00 0.00 2.40
2175 4898 2.662866 CCAGGAGTTCGGTACATCCTA 58.337 52.381 0.00 0.00 40.23 2.94
2201 4924 4.498520 CACCGGCTCGATGTCGCT 62.499 66.667 0.00 0.00 43.31 4.93
2253 4979 2.360350 CTGCCATTGGTGTCGCCT 60.360 61.111 4.26 0.00 38.35 5.52
2265 4991 1.593006 GTGTCGCCTATGTATGTGTGC 59.407 52.381 0.00 0.00 0.00 4.57
2305 5031 6.179906 GGATCAATCTGAACCCTCTTGATA 57.820 41.667 0.00 0.00 36.85 2.15
2367 5093 2.622064 ACTTCGAGTTTGCAGAGGTT 57.378 45.000 0.00 0.00 0.00 3.50
2430 5156 4.580868 TGTATGACAATTTGGGCGAGTTA 58.419 39.130 0.78 0.00 0.00 2.24
2479 5205 4.175489 GTCGGCGCTACGAGCTGA 62.175 66.667 7.64 0.00 46.55 4.26
2641 5367 3.555966 AGTTATCTGCCCTGCCAATTAC 58.444 45.455 0.00 0.00 0.00 1.89
2650 5376 3.081804 CCCTGCCAATTACGAAGAAACT 58.918 45.455 0.00 0.00 0.00 2.66
2690 5416 5.500234 TCACTGCAGTAAGGCAATTAATCT 58.500 37.500 21.20 0.00 44.40 2.40
2774 5502 3.249799 TCAACAATACAACAACCGCTGAG 59.750 43.478 0.00 0.00 0.00 3.35
2920 5648 0.468226 ACTGTTCCGCTTCACTGGAA 59.532 50.000 0.00 0.00 41.83 3.53
2932 5660 0.880278 CACTGGAAGGTGTGGTGTCG 60.880 60.000 0.00 0.00 39.30 4.35
2948 5676 6.987992 TGTGGTGTCGTCTTAAAAATAGACTT 59.012 34.615 0.00 0.00 39.86 3.01
2994 5722 0.968405 TGAAGGCCATTTCACAAGCC 59.032 50.000 5.01 0.00 46.13 4.35
3172 5900 2.281484 GCTGTTTGGCCGTGGAGA 60.281 61.111 0.00 0.00 0.00 3.71
3174 5902 1.244019 GCTGTTTGGCCGTGGAGAAT 61.244 55.000 0.00 0.00 0.00 2.40
3196 5924 2.279741 GCTTTGATCAGATGTACCGCA 58.720 47.619 0.00 0.00 0.00 5.69
3341 6069 3.119101 ACGGCTATTCGATCAGAACAAGT 60.119 43.478 0.00 0.00 42.39 3.16
3460 6188 1.542915 GTTAGTAGGTGTGCAGGACGA 59.457 52.381 0.00 0.00 0.00 4.20
3461 6189 1.460504 TAGTAGGTGTGCAGGACGAG 58.539 55.000 0.00 0.00 0.00 4.18
3462 6190 0.251209 AGTAGGTGTGCAGGACGAGA 60.251 55.000 0.00 0.00 0.00 4.04
3463 6191 0.171455 GTAGGTGTGCAGGACGAGAG 59.829 60.000 0.00 0.00 0.00 3.20
3464 6192 0.965866 TAGGTGTGCAGGACGAGAGG 60.966 60.000 0.00 0.00 0.00 3.69
3466 6194 1.666011 GTGTGCAGGACGAGAGGAA 59.334 57.895 0.00 0.00 0.00 3.36
3467 6195 0.033504 GTGTGCAGGACGAGAGGAAA 59.966 55.000 0.00 0.00 0.00 3.13
3468 6196 0.976641 TGTGCAGGACGAGAGGAAAT 59.023 50.000 0.00 0.00 0.00 2.17
3469 6197 1.338105 TGTGCAGGACGAGAGGAAATG 60.338 52.381 0.00 0.00 0.00 2.32
3470 6198 0.250234 TGCAGGACGAGAGGAAATGG 59.750 55.000 0.00 0.00 0.00 3.16
3472 6200 2.009042 GCAGGACGAGAGGAAATGGTG 61.009 57.143 0.00 0.00 0.00 4.17
3474 6202 0.744771 GGACGAGAGGAAATGGTGCC 60.745 60.000 0.00 0.00 0.00 5.01
3612 8481 2.226330 TCCACTTTAGCATGCGTGTTT 58.774 42.857 13.01 0.00 0.00 2.83
3620 8489 7.377397 CACTTTAGCATGCGTGTTTTTAGTTTA 59.623 33.333 13.01 0.00 0.00 2.01
3840 8709 2.807967 CACATGTCACGTCATCAAAGGT 59.192 45.455 0.00 0.00 0.00 3.50
3981 8956 2.621055 TCCAAATGTTTGCGTACAAGCT 59.379 40.909 0.00 0.00 37.82 3.74
4034 9009 0.393808 ATATTCCCGCCACAACGCTT 60.394 50.000 0.00 0.00 0.00 4.68
4119 9182 2.728690 TGCAAGCATGTCATTTCACC 57.271 45.000 0.00 0.00 0.00 4.02
4120 9183 1.962100 TGCAAGCATGTCATTTCACCA 59.038 42.857 0.00 0.00 0.00 4.17
4121 9184 2.563620 TGCAAGCATGTCATTTCACCAT 59.436 40.909 0.00 0.00 0.00 3.55
4122 9185 3.762823 TGCAAGCATGTCATTTCACCATA 59.237 39.130 0.00 0.00 0.00 2.74
4123 9186 4.107622 GCAAGCATGTCATTTCACCATAC 58.892 43.478 0.00 0.00 0.00 2.39
4145 9208 7.474793 CATACAACTATGAATAGGGTGACCCAT 60.475 40.741 24.93 11.50 41.27 4.00
4179 9242 3.950397 TCATGTATGTGAAAGACCCACC 58.050 45.455 0.00 0.00 33.80 4.61
4187 9250 0.240945 GAAAGACCCACCGCAACATG 59.759 55.000 0.00 0.00 0.00 3.21
4191 9254 1.876497 GACCCACCGCAACATGCAAT 61.876 55.000 2.99 0.00 45.36 3.56
4376 9443 1.339610 TCAACCAATTCCCGCAACAAG 59.660 47.619 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 8.110612 CAGTCGTACTTCTTGCATAAGTAAATG 58.889 37.037 18.60 12.35 40.22 2.32
113 114 2.069273 GCACAGTCGTACTTCTTGCAT 58.931 47.619 0.00 0.00 0.00 3.96
127 128 5.659440 TTTCCTTTTTCAAGAAGCACAGT 57.341 34.783 0.00 0.00 30.57 3.55
175 177 1.937278 TTCGCGCGGAACCAAATATA 58.063 45.000 31.69 1.90 0.00 0.86
183 185 1.681825 ATTTTCTTTTCGCGCGGAAC 58.318 45.000 31.69 0.00 33.42 3.62
266 268 4.462483 ACGATGCCAATAGGTTTCAACAAT 59.538 37.500 0.00 0.00 37.19 2.71
267 269 3.823873 ACGATGCCAATAGGTTTCAACAA 59.176 39.130 0.00 0.00 37.19 2.83
271 274 4.574421 CACATACGATGCCAATAGGTTTCA 59.426 41.667 0.00 0.00 37.19 2.69
283 286 3.733024 TTTCGAAACCACATACGATGC 57.267 42.857 6.47 0.00 34.85 3.91
287 290 3.484557 CGGGATTTTCGAAACCACATACG 60.485 47.826 10.79 6.33 0.00 3.06
309 312 2.875933 TCAATATTGGATTTCCCGCGTC 59.124 45.455 15.36 0.00 37.93 5.19
327 330 6.422400 GCGTCCAAATTCTAAACCATTTTCAA 59.578 34.615 0.00 0.00 0.00 2.69
334 337 3.192422 CCATGCGTCCAAATTCTAAACCA 59.808 43.478 0.00 0.00 0.00 3.67
341 344 5.054390 TCTTAAACCATGCGTCCAAATTC 57.946 39.130 0.00 0.00 0.00 2.17
342 345 5.659440 ATCTTAAACCATGCGTCCAAATT 57.341 34.783 0.00 0.00 0.00 1.82
400 403 4.879197 TCTCAGATGTTGACATGTGTCT 57.121 40.909 17.45 1.10 44.88 3.41
401 404 4.391216 CCTTCTCAGATGTTGACATGTGTC 59.609 45.833 17.45 6.21 44.88 3.67
412 416 1.905215 CACTCCCACCTTCTCAGATGT 59.095 52.381 0.00 0.00 0.00 3.06
415 419 2.043664 AGATCACTCCCACCTTCTCAGA 59.956 50.000 0.00 0.00 0.00 3.27
424 428 3.263425 TCCCTTACAAAGATCACTCCCAC 59.737 47.826 0.00 0.00 0.00 4.61
427 431 6.539103 GTGTTATCCCTTACAAAGATCACTCC 59.461 42.308 0.00 0.00 0.00 3.85
507 515 0.978146 ATCACCGACTGGGCTAAGCT 60.978 55.000 0.00 0.00 40.62 3.74
553 561 2.883267 CTAGCCCAGGCCAGCACTTC 62.883 65.000 5.01 0.00 43.17 3.01
601 609 4.203618 GCTCCGTAAGCCTCCAAC 57.796 61.111 0.00 0.00 45.92 3.77
788 799 4.899239 GCCGCACCAGATCCGGAG 62.899 72.222 11.34 0.00 44.55 4.63
855 866 1.003349 AGCCATGCTATCATCCTCTGC 59.997 52.381 0.00 0.00 36.99 4.26
895 909 9.582431 GCTATCCGATTTATACTTACATTGCTA 57.418 33.333 0.00 0.00 0.00 3.49
896 910 8.314751 AGCTATCCGATTTATACTTACATTGCT 58.685 33.333 0.00 0.00 0.00 3.91
897 911 8.480643 AGCTATCCGATTTATACTTACATTGC 57.519 34.615 0.00 0.00 0.00 3.56
927 941 2.297597 GTGATTAGCACCTATCCGAGCT 59.702 50.000 0.00 0.00 41.78 4.09
947 968 1.470805 GCGCACCTTTTGTTTTCTGGT 60.471 47.619 0.30 0.00 0.00 4.00
948 969 1.208259 GCGCACCTTTTGTTTTCTGG 58.792 50.000 0.30 0.00 0.00 3.86
949 970 0.845768 CGCGCACCTTTTGTTTTCTG 59.154 50.000 8.75 0.00 0.00 3.02
950 971 0.454196 ACGCGCACCTTTTGTTTTCT 59.546 45.000 5.73 0.00 0.00 2.52
951 972 1.254313 GAACGCGCACCTTTTGTTTTC 59.746 47.619 5.73 0.00 0.00 2.29
953 974 0.454196 AGAACGCGCACCTTTTGTTT 59.546 45.000 5.73 0.00 0.00 2.83
954 975 0.248458 CAGAACGCGCACCTTTTGTT 60.248 50.000 5.73 0.33 0.00 2.83
955 976 1.355210 CAGAACGCGCACCTTTTGT 59.645 52.632 5.73 0.00 0.00 2.83
956 977 1.370414 CCAGAACGCGCACCTTTTG 60.370 57.895 5.73 0.00 0.00 2.44
957 978 1.782028 GACCAGAACGCGCACCTTTT 61.782 55.000 5.73 0.00 0.00 2.27
958 979 2.203153 ACCAGAACGCGCACCTTT 60.203 55.556 5.73 0.00 0.00 3.11
959 980 2.665185 GACCAGAACGCGCACCTT 60.665 61.111 5.73 0.00 0.00 3.50
960 981 4.681978 GGACCAGAACGCGCACCT 62.682 66.667 5.73 0.00 0.00 4.00
967 992 3.530910 AAGCACCGGGACCAGAACG 62.531 63.158 6.32 0.00 0.00 3.95
1102 1127 1.735376 TTCCGCCTGAGTATCTCCGC 61.735 60.000 0.00 0.00 34.92 5.54
1223 1248 0.386100 CGGCTCGATGTCCTCATACG 60.386 60.000 0.00 0.00 34.06 3.06
1335 3577 1.134075 CTCACACGACCGAGTACCG 59.866 63.158 0.00 0.00 38.18 4.02
1368 3891 1.327460 CACGGCCATGAGAAACGTATG 59.673 52.381 2.24 0.00 35.85 2.39
1385 3908 3.646023 AAATGCCAATGCCGCCACG 62.646 57.895 0.00 0.00 36.33 4.94
1400 3923 1.133025 GCTGCATTAGACGTGGCAAAT 59.867 47.619 0.00 0.00 35.59 2.32
1462 4167 3.708220 CTGGTCGAGCTTCTCCGCC 62.708 68.421 16.64 0.00 0.00 6.13
1534 4239 4.162812 GCCAAATAAATTCGAACAAGCGA 58.837 39.130 0.00 0.00 38.72 4.93
1566 4271 3.726607 GGTCCAATGCATGTTGACAAAA 58.273 40.909 19.25 0.00 0.00 2.44
1726 4449 1.681666 CATGATAGGCAGGCCGGAT 59.318 57.895 5.05 2.51 41.95 4.18
1894 4617 1.880894 GACATGGTCGACGACTCCA 59.119 57.895 25.87 17.66 35.64 3.86
2061 4784 3.681835 GGTCCTCGCAGGTGACGT 61.682 66.667 0.00 0.00 36.53 4.34
2103 4826 2.046988 CTGGCACACTCGGATGCA 60.047 61.111 4.64 0.00 43.93 3.96
2162 4885 2.769663 ACAATGGCTAGGATGTACCGAA 59.230 45.455 0.00 0.00 44.74 4.30
2163 4886 2.364324 GACAATGGCTAGGATGTACCGA 59.636 50.000 0.00 0.00 44.74 4.69
2201 4924 3.576982 ACTCTCAAGAACCGGAATGTACA 59.423 43.478 9.46 0.00 0.00 2.90
2305 5031 2.159421 CGTACGACACAGCAGAAGGTAT 60.159 50.000 10.44 0.00 0.00 2.73
2367 5093 2.371910 TTTCATCGTCACCATGCGTA 57.628 45.000 0.00 0.00 0.00 4.42
2430 5156 3.228188 TCCACAAGATCCACAAGCTTT 57.772 42.857 0.00 0.00 28.98 3.51
2479 5205 1.331214 CCTGCAAAGGTGGTGACAAT 58.669 50.000 0.00 0.00 46.06 2.71
2500 5226 9.585099 CAGATTGGAGATAATAATGAGTAGCTC 57.415 37.037 0.00 0.00 37.81 4.09
2630 5356 3.751175 TCAGTTTCTTCGTAATTGGCAGG 59.249 43.478 0.00 0.00 0.00 4.85
2641 5367 6.073548 AGTGCTAGTTCAATTCAGTTTCTTCG 60.074 38.462 0.00 0.00 0.00 3.79
2650 5376 4.214119 GCAGTGAAGTGCTAGTTCAATTCA 59.786 41.667 8.54 8.54 45.16 2.57
2732 5460 7.721402 TGTTGATTTTATAACACCACAAAGCT 58.279 30.769 0.00 0.00 32.30 3.74
2760 5488 2.038387 ACTTTCTCAGCGGTTGTTGT 57.962 45.000 0.00 0.00 0.00 3.32
2774 5502 9.525409 TCTTACACAAGTTAGACTACAACTTTC 57.475 33.333 1.33 0.00 42.18 2.62
2920 5648 3.547054 TTTTAAGACGACACCACACCT 57.453 42.857 0.00 0.00 0.00 4.00
2948 5676 2.367894 TCCTCCTCGCTTATACTCTCGA 59.632 50.000 0.00 0.00 0.00 4.04
2994 5722 1.604185 GGCCTAAGATGCAGCTCGTAG 60.604 57.143 4.22 4.13 0.00 3.51
3172 5900 4.201950 GCGGTACATCTGATCAAAGCAATT 60.202 41.667 0.00 0.00 0.00 2.32
3174 5902 2.677836 GCGGTACATCTGATCAAAGCAA 59.322 45.455 0.00 0.00 0.00 3.91
3341 6069 2.113774 CCTCCAACACCAGCAGCA 59.886 61.111 0.00 0.00 0.00 4.41
3460 6188 0.548510 GCCTAGGCACCATTTCCTCT 59.451 55.000 29.33 0.00 41.49 3.69
3461 6189 3.102090 GCCTAGGCACCATTTCCTC 57.898 57.895 29.33 0.00 41.49 3.71
3702 8571 5.163632 TGTGATAATGTGGCATTTGTGCTAG 60.164 40.000 0.00 0.00 34.73 3.42
3703 8572 4.704057 TGTGATAATGTGGCATTTGTGCTA 59.296 37.500 0.00 0.00 34.73 3.49
3704 8573 3.510753 TGTGATAATGTGGCATTTGTGCT 59.489 39.130 0.00 0.00 34.73 4.40
3710 8579 2.034124 GGCCTGTGATAATGTGGCATT 58.966 47.619 0.00 0.00 44.85 3.56
3840 8709 5.999205 AAAATCTATGCATGTTTGGTGGA 57.001 34.783 10.16 0.00 0.00 4.02
3999 8974 9.095065 GGCGGGAATATGTTGTAGTAATATAAG 57.905 37.037 0.00 0.00 0.00 1.73
4000 8975 8.595421 TGGCGGGAATATGTTGTAGTAATATAA 58.405 33.333 0.00 0.00 0.00 0.98
4003 8978 6.183360 TGTGGCGGGAATATGTTGTAGTAATA 60.183 38.462 0.00 0.00 0.00 0.98
4004 8979 5.061179 GTGGCGGGAATATGTTGTAGTAAT 58.939 41.667 0.00 0.00 0.00 1.89
4005 8980 4.081031 TGTGGCGGGAATATGTTGTAGTAA 60.081 41.667 0.00 0.00 0.00 2.24
4008 8983 2.912771 TGTGGCGGGAATATGTTGTAG 58.087 47.619 0.00 0.00 0.00 2.74
4119 9182 6.183361 TGGGTCACCCTATTCATAGTTGTATG 60.183 42.308 16.04 0.00 45.70 2.39
4120 9183 5.908831 TGGGTCACCCTATTCATAGTTGTAT 59.091 40.000 16.04 0.00 45.70 2.29
4121 9184 5.282129 TGGGTCACCCTATTCATAGTTGTA 58.718 41.667 16.04 0.00 45.70 2.41
4122 9185 4.108570 TGGGTCACCCTATTCATAGTTGT 58.891 43.478 16.04 0.00 45.70 3.32
4123 9186 4.771114 TGGGTCACCCTATTCATAGTTG 57.229 45.455 16.04 0.00 45.70 3.16
4187 9250 6.864165 AAAAACAATTTTCCATGCATGATTGC 59.136 30.769 28.31 0.00 40.79 3.56
4350 9417 5.175127 GTTGCGGGAATTGGTTGATTAAAT 58.825 37.500 0.00 0.00 0.00 1.40
4376 9443 5.009811 AGTTAACTAGATGATACGAGGCACC 59.990 44.000 6.26 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.