Multiple sequence alignment - TraesCS4B01G060500

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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 TraesCS4B01G060500 chr4B 100.000 3434 0 0 1 3434 52396493 52399926 0.000000e+00 6342.0
1 TraesCS4B01G060500 chr4B 93.603 891 56 1 1544 2433 52412402 52413292 0.000000e+00 1328.0
2 TraesCS4B01G060500 chr4B 91.459 761 43 10 1793 2542 53044715 53043966 0.000000e+00 1026.0
3 TraesCS4B01G060500 chr4B 89.954 647 49 9 1950 2596 52817855 52818485 0.000000e+00 821.0
4 TraesCS4B01G060500 chr4B 88.126 699 62 8 1907 2596 52828427 52829113 0.000000e+00 811.0
5 TraesCS4B01G060500 chr4B 89.512 410 40 1 1531 1937 52829687 52830096 1.830000e-142 516.0
6 TraesCS4B01G060500 chr4B 94.044 319 17 1 1793 2109 52895473 52895791 1.850000e-132 483.0
7 TraesCS4B01G060500 chr4B 89.688 320 33 0 1592 1911 52819838 52820157 3.190000e-110 409.0
8 TraesCS4B01G060500 chr4B 92.647 272 20 0 2144 2415 52895790 52896061 3.210000e-105 392.0
9 TraesCS4B01G060500 chr4B 80.278 360 59 7 174 531 60081178 60080829 9.450000e-66 261.0
10 TraesCS4B01G060500 chr4B 81.105 344 42 15 2663 2998 53043961 53043633 1.580000e-63 254.0
11 TraesCS4B01G060500 chr4B 81.346 327 20 17 3149 3434 52929695 52930021 9.590000e-56 228.0
12 TraesCS4B01G060500 chr4B 81.346 327 20 17 3149 3434 53043551 53043225 9.590000e-56 228.0
13 TraesCS4B01G060500 chr4B 97.368 76 2 0 2482 2557 52928091 52928166 2.780000e-26 130.0
14 TraesCS4B01G060500 chr4B 78.836 189 29 8 2616 2795 652390988 652391174 2.170000e-22 117.0
15 TraesCS4B01G060500 chr4A 89.265 1919 100 54 692 2528 566289642 566291536 0.000000e+00 2305.0
16 TraesCS4B01G060500 chr4A 88.034 1989 137 50 1447 3370 565842611 565840659 0.000000e+00 2261.0
17 TraesCS4B01G060500 chr4A 85.899 695 49 32 793 1448 565843559 565842875 0.000000e+00 695.0
18 TraesCS4B01G060500 chr4A 80.882 408 67 5 127 531 626550333 626550732 9.250000e-81 311.0
19 TraesCS4B01G060500 chr4A 81.215 362 57 7 173 531 571644123 571643770 7.260000e-72 281.0
20 TraesCS4B01G060500 chr4A 82.955 88 11 3 2608 2694 596772301 596772385 3.670000e-10 76.8
21 TraesCS4B01G060500 chr4D 88.211 1476 117 13 1 1428 36418305 36419771 0.000000e+00 1709.0
22 TraesCS4B01G060500 chr4D 94.527 1078 50 6 1467 2538 36420078 36421152 0.000000e+00 1655.0
23 TraesCS4B01G060500 chr4D 85.845 219 13 6 2523 2741 36421170 36421370 2.080000e-52 217.0
24 TraesCS4B01G060500 chr6B 82.368 380 58 4 155 531 279006363 279005990 4.280000e-84 322.0
25 TraesCS4B01G060500 chr3B 80.808 396 59 9 140 531 4651829 4651447 9.320000e-76 294.0
26 TraesCS4B01G060500 chr6A 79.259 405 71 6 134 532 54372385 54372782 1.570000e-68 270.0
27 TraesCS4B01G060500 chr6A 78.856 402 75 5 132 531 397224680 397225073 2.630000e-66 263.0
28 TraesCS4B01G060500 chr7D 78.398 412 76 9 127 531 521902171 521902576 4.400000e-64 255.0
29 TraesCS4B01G060500 chr7D 95.000 40 1 1 2756 2795 106629441 106629479 1.030000e-05 62.1
30 TraesCS4B01G060500 chr2B 80.526 190 25 11 2612 2795 18130622 18130439 5.980000e-28 135.0
31 TraesCS4B01G060500 chr5B 78.333 180 26 10 2624 2794 14895959 14895784 1.690000e-18 104.0
32 TraesCS4B01G060500 chr5B 95.000 40 1 1 2756 2795 545814847 545814885 1.030000e-05 62.1
33 TraesCS4B01G060500 chr1D 76.684 193 33 10 2612 2795 239554767 239554578 2.820000e-16 97.1
34 TraesCS4B01G060500 chr1D 91.489 47 4 0 2634 2680 386168187 386168233 7.950000e-07 65.8
35 TraesCS4B01G060500 chr1D 79.545 88 11 7 1561 1645 63429216 63429133 4.790000e-04 56.5
36 TraesCS4B01G060500 chr1B 70.998 431 91 29 1561 1974 101527952 101527539 4.750000e-09 73.1
37 TraesCS4B01G060500 chr1B 79.545 88 11 7 1561 1645 101271281 101271198 4.790000e-04 56.5
38 TraesCS4B01G060500 chr5D 93.182 44 3 0 2637 2680 99258071 99258114 7.950000e-07 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 TraesCS4B01G060500 chr4B 52396493 52399926 3433 False 6342.000000 6342 100.000000 1 3434 1 chr4B.!!$F1 3433
1 TraesCS4B01G060500 chr4B 52412402 52413292 890 False 1328.000000 1328 93.603000 1544 2433 1 chr4B.!!$F2 889
2 TraesCS4B01G060500 chr4B 52828427 52830096 1669 False 663.500000 811 88.819000 1531 2596 2 chr4B.!!$F5 1065
3 TraesCS4B01G060500 chr4B 52817855 52820157 2302 False 615.000000 821 89.821000 1592 2596 2 chr4B.!!$F4 1004
4 TraesCS4B01G060500 chr4B 53043225 53044715 1490 True 502.666667 1026 84.636667 1793 3434 3 chr4B.!!$R2 1641
5 TraesCS4B01G060500 chr4B 52895473 52896061 588 False 437.500000 483 93.345500 1793 2415 2 chr4B.!!$F6 622
6 TraesCS4B01G060500 chr4A 566289642 566291536 1894 False 2305.000000 2305 89.265000 692 2528 1 chr4A.!!$F1 1836
7 TraesCS4B01G060500 chr4A 565840659 565843559 2900 True 1478.000000 2261 86.966500 793 3370 2 chr4A.!!$R2 2577
8 TraesCS4B01G060500 chr4D 36418305 36421370 3065 False 1193.666667 1709 89.527667 1 2741 3 chr4D.!!$F1 2740

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
262 264 0.088530 CGTCGTTTGTCTACGTTCGC 59.911 55.0 0.00 0.0 42.01 4.70 F
440 444 0.161024 CGTCTTCGGCTCGTTTCAAC 59.839 55.0 0.00 0.0 0.00 3.18 F
455 459 0.856641 TCAACGCTTGTAGTTGTCGC 59.143 50.0 8.62 0.0 46.42 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 2128 0.249073 CTAGGAACTGCAGCGCGTAT 60.249 55.000 15.27 0.0 41.52 3.06 R
1903 2282 3.518998 CTCGTCGCGGATGAGGGT 61.519 66.667 6.13 0.0 40.76 4.34 R
2480 2886 4.410228 TCAAATCCCAACAACATTTTCCCA 59.590 37.500 0.00 0.0 0.00 4.37 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 2.109425 AAGTGTTGAATAGGCGGGAC 57.891 50.000 0.00 0.00 0.00 4.46
34 35 1.717032 ATAGGCGGGACTTCATGCTA 58.283 50.000 0.00 0.00 0.00 3.49
41 42 2.093973 CGGGACTTCATGCTAGTCTTGT 60.094 50.000 20.28 0.00 41.37 3.16
55 56 2.084546 GTCTTGTTGGGTCTGTATGGC 58.915 52.381 0.00 0.00 0.00 4.40
56 57 1.086696 CTTGTTGGGTCTGTATGGCG 58.913 55.000 0.00 0.00 0.00 5.69
57 58 0.958382 TTGTTGGGTCTGTATGGCGC 60.958 55.000 0.00 0.00 0.00 6.53
58 59 1.376683 GTTGGGTCTGTATGGCGCA 60.377 57.895 10.83 0.00 41.54 6.09
78 80 1.176527 TTTGGTTGCCTGCATCTAGC 58.823 50.000 0.00 0.00 45.96 3.42
87 89 2.787994 CCTGCATCTAGCCCAAATAGG 58.212 52.381 0.00 0.00 44.83 2.57
114 116 3.156293 TGGATGCAAGAAAAGCTGCTTA 58.844 40.909 16.31 0.00 0.00 3.09
148 150 6.831353 CACAAGATTCTCTCCTTCTAGTCCTA 59.169 42.308 0.00 0.00 0.00 2.94
153 155 5.327737 TCTCTCCTTCTAGTCCTAATCCC 57.672 47.826 0.00 0.00 0.00 3.85
171 173 0.458669 CCGGTGGTGCGTCTAGTATT 59.541 55.000 0.00 0.00 0.00 1.89
173 175 1.135199 CGGTGGTGCGTCTAGTATTGT 60.135 52.381 0.00 0.00 0.00 2.71
176 178 2.086094 TGGTGCGTCTAGTATTGTCGA 58.914 47.619 0.00 0.00 0.00 4.20
190 192 2.994995 TCGATGGGCGTGTGGAGT 60.995 61.111 0.00 0.00 41.80 3.85
191 193 2.047274 CGATGGGCGTGTGGAGTT 60.047 61.111 0.00 0.00 34.64 3.01
206 208 0.608640 GAGTTGTGTCTCCGGTGGAT 59.391 55.000 0.00 0.00 0.00 3.41
222 224 3.503748 GGTGGATCTGTCTTTGTCTTTGG 59.496 47.826 0.00 0.00 0.00 3.28
224 226 4.023707 GTGGATCTGTCTTTGTCTTTGGTG 60.024 45.833 0.00 0.00 0.00 4.17
228 230 4.792068 TCTGTCTTTGTCTTTGGTGGATT 58.208 39.130 0.00 0.00 0.00 3.01
231 233 4.051237 GTCTTTGTCTTTGGTGGATTTGC 58.949 43.478 0.00 0.00 0.00 3.68
234 236 2.942804 TGTCTTTGGTGGATTTGCTCA 58.057 42.857 0.00 0.00 0.00 4.26
240 242 4.842531 TTGGTGGATTTGCTCAGATCTA 57.157 40.909 0.00 0.00 0.00 1.98
250 252 4.371855 TGCTCAGATCTAATCGTCGTTT 57.628 40.909 0.00 0.00 0.00 3.60
251 253 4.105486 TGCTCAGATCTAATCGTCGTTTG 58.895 43.478 0.00 0.00 0.00 2.93
255 257 6.673154 TCAGATCTAATCGTCGTTTGTCTA 57.327 37.500 0.00 0.00 0.00 2.59
262 264 0.088530 CGTCGTTTGTCTACGTTCGC 59.911 55.000 0.00 0.00 42.01 4.70
267 269 1.005294 TTTGTCTACGTTCGCGAGCC 61.005 55.000 17.61 7.57 44.71 4.70
269 271 1.154073 GTCTACGTTCGCGAGCCTT 60.154 57.895 17.61 7.15 44.71 4.35
284 286 1.713078 AGCCTTCAGGTTGGATCCTTT 59.287 47.619 14.23 0.00 35.37 3.11
289 291 5.509498 CCTTCAGGTTGGATCCTTTTGATA 58.491 41.667 14.23 3.13 35.37 2.15
290 292 6.131961 CCTTCAGGTTGGATCCTTTTGATAT 58.868 40.000 14.23 0.00 35.37 1.63
291 293 6.040166 CCTTCAGGTTGGATCCTTTTGATATG 59.960 42.308 14.23 1.61 35.37 1.78
292 294 6.078456 TCAGGTTGGATCCTTTTGATATGT 57.922 37.500 14.23 0.00 35.37 2.29
299 301 9.125026 GTTGGATCCTTTTGATATGTGATACTT 57.875 33.333 14.23 0.00 32.41 2.24
312 316 1.287425 GATACTTTTCAGACGGCGGG 58.713 55.000 13.24 0.00 0.00 6.13
315 319 2.966309 CTTTTCAGACGGCGGGTGC 61.966 63.158 13.24 0.00 41.71 5.01
325 329 2.345991 GCGGGTGCTGTTCTGGTA 59.654 61.111 0.00 0.00 38.39 3.25
330 334 0.245539 GGTGCTGTTCTGGTACGCTA 59.754 55.000 0.00 0.00 0.00 4.26
333 337 1.616865 TGCTGTTCTGGTACGCTAGTT 59.383 47.619 0.00 0.00 0.00 2.24
337 341 4.326548 GCTGTTCTGGTACGCTAGTTTTAG 59.673 45.833 0.00 0.00 0.00 1.85
349 353 3.433314 GCTAGTTTTAGGGGGTCTTAGCC 60.433 52.174 0.00 0.00 34.31 3.93
395 399 0.465460 ACAAGTTTTGCTGGCTCCGA 60.465 50.000 0.00 0.00 0.00 4.55
415 419 4.458829 AGGGAGGGGCGATGACGA 62.459 66.667 0.00 0.00 42.66 4.20
439 443 1.554042 GCGTCTTCGGCTCGTTTCAA 61.554 55.000 0.00 0.00 37.56 2.69
440 444 0.161024 CGTCTTCGGCTCGTTTCAAC 59.839 55.000 0.00 0.00 0.00 3.18
455 459 0.856641 TCAACGCTTGTAGTTGTCGC 59.143 50.000 8.62 0.00 46.42 5.19
458 462 2.427232 ACGCTTGTAGTTGTCGCTAA 57.573 45.000 0.00 0.00 0.00 3.09
459 463 2.955614 ACGCTTGTAGTTGTCGCTAAT 58.044 42.857 0.00 0.00 0.00 1.73
474 478 5.985530 TGTCGCTAATTGGTCTATGAATCTG 59.014 40.000 0.00 0.00 0.00 2.90
478 482 7.386025 TCGCTAATTGGTCTATGAATCTGAATG 59.614 37.037 0.00 0.00 0.00 2.67
520 524 4.539152 GTTGCACTGCCACGATTG 57.461 55.556 0.00 0.00 0.00 2.67
531 535 6.348786 GCACTGCCACGATTGAATATGAATAT 60.349 38.462 0.00 0.00 0.00 1.28
539 543 9.195411 CACGATTGAATATGAATATTTTTGGGG 57.805 33.333 0.00 0.00 33.37 4.96
545 549 7.178274 TGAATATGAATATTTTTGGGGCGCTAT 59.822 33.333 7.64 0.00 33.37 2.97
571 575 6.405278 TTTTCCAGAAAAGCTTAGAAAGGG 57.595 37.500 0.00 0.00 35.57 3.95
597 601 4.972751 AGCTCTGAAGAAAGGAAGAAGT 57.027 40.909 0.00 0.00 0.00 3.01
599 603 5.689835 AGCTCTGAAGAAAGGAAGAAGTTT 58.310 37.500 0.00 0.00 0.00 2.66
624 628 1.109920 TGCGAGGGGTAGAGATGCTC 61.110 60.000 0.00 0.00 0.00 4.26
680 684 2.280708 CACGGCGCATAGTAACAAGTAC 59.719 50.000 10.83 0.00 0.00 2.73
681 685 2.165030 ACGGCGCATAGTAACAAGTACT 59.835 45.455 10.83 0.00 45.42 2.73
682 686 3.378112 ACGGCGCATAGTAACAAGTACTA 59.622 43.478 10.83 0.00 46.89 1.82
688 692 5.052567 CGCATAGTAACAAGTACTAGCAACG 60.053 44.000 0.00 0.00 46.22 4.10
689 693 6.032094 GCATAGTAACAAGTACTAGCAACGA 58.968 40.000 0.00 0.00 46.22 3.85
690 694 6.696148 GCATAGTAACAAGTACTAGCAACGAT 59.304 38.462 0.00 0.00 46.22 3.73
726 730 1.074850 TGACTGGTCACTGTCCCCA 60.075 57.895 0.00 0.00 42.80 4.96
727 731 1.371558 GACTGGTCACTGTCCCCAC 59.628 63.158 0.00 0.00 39.01 4.61
728 732 1.074471 ACTGGTCACTGTCCCCACT 60.074 57.895 0.00 0.00 0.00 4.00
730 734 1.348064 CTGGTCACTGTCCCCACTTA 58.652 55.000 0.00 0.00 0.00 2.24
833 837 2.434884 AGATTCACAGCGCACCCG 60.435 61.111 11.47 0.00 37.57 5.28
906 916 1.615919 GCCCTGCCTTTTTAGCCACTA 60.616 52.381 0.00 0.00 0.00 2.74
908 918 2.290960 CCCTGCCTTTTTAGCCACTACT 60.291 50.000 0.00 0.00 0.00 2.57
943 987 1.946768 CCCAAGAGACAAAACAGCGAA 59.053 47.619 0.00 0.00 0.00 4.70
981 1040 6.435430 ACAAGCAAGAAAACCAAAAATTCC 57.565 33.333 0.00 0.00 0.00 3.01
986 1045 6.260714 AGCAAGAAAACCAAAAATTCCATCAC 59.739 34.615 0.00 0.00 0.00 3.06
995 1054 2.723124 AATTCCATCACACAAACGCC 57.277 45.000 0.00 0.00 0.00 5.68
1009 1068 1.135094 AACGCCCATCATGGAGAGAT 58.865 50.000 4.75 0.00 40.96 2.75
1035 1094 2.478370 GCTACGTATGGTCGTGCTGTTA 60.478 50.000 0.00 0.00 43.93 2.41
1356 1436 2.650116 CCACACCAGGGTCTCCGAG 61.650 68.421 0.00 0.00 38.33 4.63
1392 1472 2.124236 CTCCGCTACCTCGACCCT 60.124 66.667 0.00 0.00 0.00 4.34
1407 1487 2.364647 CGACCCTACCCTCAAGTAATCC 59.635 54.545 0.00 0.00 0.00 3.01
1413 1493 3.821421 ACCCTCAAGTAATCCATCGAC 57.179 47.619 0.00 0.00 0.00 4.20
1429 1509 4.642885 CCATCGACCTCTTCTTCTTCTACT 59.357 45.833 0.00 0.00 0.00 2.57
1430 1510 5.823570 CCATCGACCTCTTCTTCTTCTACTA 59.176 44.000 0.00 0.00 0.00 1.82
1431 1511 6.238538 CCATCGACCTCTTCTTCTTCTACTAC 60.239 46.154 0.00 0.00 0.00 2.73
1432 1512 6.052405 TCGACCTCTTCTTCTTCTACTACT 57.948 41.667 0.00 0.00 0.00 2.57
1435 1515 8.266473 TCGACCTCTTCTTCTTCTACTACTATT 58.734 37.037 0.00 0.00 0.00 1.73
1456 1827 6.769134 ATTTCTTCATGTCAATGATGCAGA 57.231 33.333 0.00 0.00 42.41 4.26
1695 2074 3.991051 CTGGTGGAGTCCGCGTGT 61.991 66.667 16.46 0.00 34.37 4.49
2181 2562 1.371558 GGTGGAGAGCCTCGTGTTT 59.628 57.895 0.00 0.00 34.31 2.83
2193 2574 2.671963 GTGTTTGGGGACGAGGGC 60.672 66.667 0.00 0.00 0.00 5.19
2433 2830 4.219944 AGCACCACGACTTATCAGTCTTAA 59.780 41.667 5.54 0.00 46.67 1.85
2439 2836 7.496591 ACCACGACTTATCAGTCTTAAAACAAA 59.503 33.333 5.54 0.00 46.67 2.83
2440 2837 8.504005 CCACGACTTATCAGTCTTAAAACAAAT 58.496 33.333 5.54 0.00 46.67 2.32
2496 2902 3.444703 TCGTTGGGAAAATGTTGTTGG 57.555 42.857 0.00 0.00 0.00 3.77
2503 2909 4.410228 TGGGAAAATGTTGTTGGGATTTGA 59.590 37.500 0.00 0.00 0.00 2.69
2545 2987 5.146010 GATGGGAGTAGAGATCAACCATC 57.854 47.826 0.00 0.00 43.97 3.51
2567 3009 7.391554 CCATCTTCTTATTGACTTCAACAAGGA 59.608 37.037 9.54 1.14 39.94 3.36
2580 3022 6.603201 ACTTCAACAAGGATTCAACAAAGAGA 59.397 34.615 0.00 0.00 33.37 3.10
2603 3045 6.547880 AGACATCTAGTGTTGAGTCGGAATAT 59.452 38.462 0.00 0.00 42.36 1.28
2606 3048 3.543680 AGTGTTGAGTCGGAATATGGG 57.456 47.619 0.00 0.00 0.00 4.00
2607 3049 1.940613 GTGTTGAGTCGGAATATGGGC 59.059 52.381 0.00 0.00 0.00 5.36
2608 3050 1.557371 TGTTGAGTCGGAATATGGGCA 59.443 47.619 0.00 0.00 0.00 5.36
2610 3052 3.389656 TGTTGAGTCGGAATATGGGCATA 59.610 43.478 0.00 0.00 0.00 3.14
2611 3053 4.041567 TGTTGAGTCGGAATATGGGCATAT 59.958 41.667 0.00 0.00 35.63 1.78
2645 3094 6.386050 AGAAAAGAAGAATTATCCCCGTCCTA 59.614 38.462 0.00 0.00 0.00 2.94
2672 3121 6.370442 GCATTATAATGATGCATGCAACCATT 59.630 34.615 33.94 33.94 46.96 3.16
2690 3141 8.487176 GCAACCATTTTATTAAGCAAATATCCG 58.513 33.333 0.00 0.00 30.11 4.18
2779 3235 4.192317 GGCAAAAATAGGACGAGATGACT 58.808 43.478 0.00 0.00 0.00 3.41
2785 3241 8.883731 CAAAAATAGGACGAGATGACTAAACAT 58.116 33.333 0.00 0.00 0.00 2.71
2797 3253 7.826918 GATGACTAAACATCTAGACCTAGGT 57.173 40.000 16.26 16.26 42.09 3.08
2798 3254 7.826918 ATGACTAAACATCTAGACCTAGGTC 57.173 40.000 31.29 31.29 44.86 3.85
2799 3255 6.127793 TGACTAAACATCTAGACCTAGGTCC 58.872 44.000 33.81 18.53 45.59 4.46
2800 3256 6.088541 ACTAAACATCTAGACCTAGGTCCA 57.911 41.667 33.81 22.66 45.59 4.02
2801 3257 6.684538 ACTAAACATCTAGACCTAGGTCCAT 58.315 40.000 33.81 21.85 45.59 3.41
2802 3258 5.878406 AAACATCTAGACCTAGGTCCATG 57.122 43.478 33.81 30.74 45.59 3.66
2803 3259 4.544564 ACATCTAGACCTAGGTCCATGT 57.455 45.455 33.81 31.28 45.59 3.21
2869 3328 8.785329 AAAATGAGTTAAAGTTTGAAAAGGCA 57.215 26.923 0.00 0.00 0.00 4.75
2910 3369 4.775253 AGTTAGAGATGCCCCTAAGATAGC 59.225 45.833 0.00 0.00 0.00 2.97
2917 3376 2.179204 TGCCCCTAAGATAGCTACTCCA 59.821 50.000 0.00 0.00 0.00 3.86
2921 3380 3.697045 CCCTAAGATAGCTACTCCATCCG 59.303 52.174 0.00 0.00 0.00 4.18
2922 3381 4.567958 CCCTAAGATAGCTACTCCATCCGA 60.568 50.000 0.00 0.00 0.00 4.55
2926 3385 1.880271 TAGCTACTCCATCCGACTCG 58.120 55.000 0.00 0.00 0.00 4.18
2927 3386 0.180642 AGCTACTCCATCCGACTCGA 59.819 55.000 0.00 0.00 0.00 4.04
2935 3394 6.401047 ACTCCATCCGACTCGAAATATAAA 57.599 37.500 0.00 0.00 0.00 1.40
2988 3447 3.670625 TGGTCTTACATTTTGAGACGGG 58.329 45.455 0.00 0.00 40.47 5.28
3000 3459 1.891150 TGAGACGGGTGGAGTACTTTC 59.109 52.381 0.00 0.00 0.00 2.62
3012 3489 4.587684 TGGAGTACTTTCTCGTTCTTTCCT 59.412 41.667 0.00 0.00 35.52 3.36
3017 3494 5.037383 ACTTTCTCGTTCTTTCCTTTCCT 57.963 39.130 0.00 0.00 0.00 3.36
3028 3505 2.656947 TCCTTTCCTTGTTCCCTGTG 57.343 50.000 0.00 0.00 0.00 3.66
3054 3531 5.867330 TGGACAAAATCTTGCATTTCCATT 58.133 33.333 0.00 0.00 32.07 3.16
3065 3542 7.761409 TCTTGCATTTCCATTATGTGACTAAC 58.239 34.615 0.00 0.00 0.00 2.34
3066 3543 7.392953 TCTTGCATTTCCATTATGTGACTAACA 59.607 33.333 0.00 0.00 44.79 2.41
3074 3551 6.071616 TCCATTATGTGACTAACAAAAAGGGC 60.072 38.462 0.00 0.00 43.61 5.19
3076 3553 6.909550 TTATGTGACTAACAAAAAGGGCAT 57.090 33.333 0.00 0.00 43.61 4.40
3078 3555 5.195001 TGTGACTAACAAAAAGGGCATTC 57.805 39.130 0.00 0.00 35.24 2.67
3079 3556 4.226761 GTGACTAACAAAAAGGGCATTCG 58.773 43.478 0.00 0.00 0.00 3.34
3083 3573 6.039493 TGACTAACAAAAAGGGCATTCGTAAA 59.961 34.615 0.00 0.00 0.00 2.01
3127 3617 3.875727 CACAGTGAGCTTGAATATCCTGG 59.124 47.826 0.00 0.00 0.00 4.45
3134 3624 2.614057 GCTTGAATATCCTGGTTCACCG 59.386 50.000 0.00 0.00 39.43 4.94
3141 3631 0.395312 TCCTGGTTCACCGTTTCTCC 59.605 55.000 0.00 0.00 39.43 3.71
3144 3634 0.531090 TGGTTCACCGTTTCTCCGTG 60.531 55.000 0.00 0.00 39.43 4.94
3194 3696 7.478322 TCTACTTGTTACATATTCTGGTCGAC 58.522 38.462 7.13 7.13 0.00 4.20
3227 3729 3.367087 CCTGTCGACGGAAATTAGTGAGT 60.367 47.826 26.01 0.00 0.00 3.41
3247 3749 0.955919 AGGCGAGCTTTCCTTTTCGG 60.956 55.000 2.19 0.00 33.89 4.30
3269 3774 0.606401 AGAAGGTGACATGCCAACCG 60.606 55.000 0.00 0.00 0.00 4.44
3366 3909 4.899502 CCTAGAGGCACAAAGAAAGAGAA 58.100 43.478 0.00 0.00 0.00 2.87
3377 3920 7.358830 CACAAAGAAAGAGAAAGAATGTCCTC 58.641 38.462 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.040646 CTAGCATGAAGTCCCGCCTA 58.959 55.000 0.00 0.00 0.00 3.93
25 26 3.679389 ACCCAACAAGACTAGCATGAAG 58.321 45.455 0.00 0.00 0.00 3.02
34 35 2.290323 GCCATACAGACCCAACAAGACT 60.290 50.000 0.00 0.00 0.00 3.24
41 42 0.034574 AATGCGCCATACAGACCCAA 60.035 50.000 4.18 0.00 0.00 4.12
56 57 0.248289 AGATGCAGGCAACCAAATGC 59.752 50.000 0.00 0.00 45.67 3.56
57 58 2.480759 GCTAGATGCAGGCAACCAAATG 60.481 50.000 0.00 0.00 42.31 2.32
58 59 1.753073 GCTAGATGCAGGCAACCAAAT 59.247 47.619 0.00 0.00 42.31 2.32
78 80 0.106217 ATCCAACGGGCCTATTTGGG 60.106 55.000 22.61 10.37 40.31 4.12
87 89 0.316841 TTTTCTTGCATCCAACGGGC 59.683 50.000 0.00 0.00 0.00 6.13
129 131 6.319715 GGGATTAGGACTAGAAGGAGAGAAT 58.680 44.000 0.00 0.00 0.00 2.40
136 138 2.628657 CACCGGGATTAGGACTAGAAGG 59.371 54.545 6.32 0.00 0.00 3.46
137 139 2.628657 CCACCGGGATTAGGACTAGAAG 59.371 54.545 6.32 0.00 35.59 2.85
148 150 1.956629 CTAGACGCACCACCGGGATT 61.957 60.000 6.32 0.00 38.05 3.01
153 155 1.135199 ACAATACTAGACGCACCACCG 60.135 52.381 0.00 0.00 0.00 4.94
171 173 3.295304 CTCCACACGCCCATCGACA 62.295 63.158 0.00 0.00 41.67 4.35
173 175 2.579657 AACTCCACACGCCCATCGA 61.580 57.895 0.00 0.00 41.67 3.59
176 178 1.600636 CACAACTCCACACGCCCAT 60.601 57.895 0.00 0.00 0.00 4.00
190 192 0.608130 CAGATCCACCGGAGACACAA 59.392 55.000 9.46 0.00 34.05 3.33
191 193 0.541998 ACAGATCCACCGGAGACACA 60.542 55.000 9.46 0.00 34.05 3.72
199 201 2.751166 AGACAAAGACAGATCCACCG 57.249 50.000 0.00 0.00 0.00 4.94
206 208 3.924114 TCCACCAAAGACAAAGACAGA 57.076 42.857 0.00 0.00 0.00 3.41
222 224 5.053145 ACGATTAGATCTGAGCAAATCCAC 58.947 41.667 5.18 0.00 0.00 4.02
224 226 4.384247 CGACGATTAGATCTGAGCAAATCC 59.616 45.833 5.18 0.00 0.00 3.01
228 230 4.371855 AACGACGATTAGATCTGAGCAA 57.628 40.909 5.18 0.00 0.00 3.91
231 233 5.574082 AGACAAACGACGATTAGATCTGAG 58.426 41.667 5.18 0.00 0.00 3.35
250 252 1.859427 AAGGCTCGCGAACGTAGACA 61.859 55.000 11.33 0.00 41.18 3.41
251 253 1.132780 GAAGGCTCGCGAACGTAGAC 61.133 60.000 11.33 0.00 41.18 2.59
255 257 2.430921 CTGAAGGCTCGCGAACGT 60.431 61.111 11.33 4.14 41.18 3.99
262 264 0.462759 GGATCCAACCTGAAGGCTCG 60.463 60.000 6.95 0.00 39.32 5.03
267 269 6.604795 ACATATCAAAAGGATCCAACCTGAAG 59.395 38.462 15.82 7.92 40.49 3.02
269 271 5.887598 CACATATCAAAAGGATCCAACCTGA 59.112 40.000 15.82 11.07 40.49 3.86
284 286 6.257849 GCCGTCTGAAAAGTATCACATATCAA 59.742 38.462 0.00 0.00 0.00 2.57
289 291 2.930040 CGCCGTCTGAAAAGTATCACAT 59.070 45.455 0.00 0.00 0.00 3.21
290 292 2.333926 CGCCGTCTGAAAAGTATCACA 58.666 47.619 0.00 0.00 0.00 3.58
291 293 1.659098 CCGCCGTCTGAAAAGTATCAC 59.341 52.381 0.00 0.00 0.00 3.06
292 294 1.404986 CCCGCCGTCTGAAAAGTATCA 60.405 52.381 0.00 0.00 0.00 2.15
299 301 3.936203 AGCACCCGCCGTCTGAAA 61.936 61.111 0.00 0.00 39.83 2.69
312 316 1.067776 ACTAGCGTACCAGAACAGCAC 60.068 52.381 0.00 0.00 0.00 4.40
315 319 4.863131 CCTAAAACTAGCGTACCAGAACAG 59.137 45.833 0.00 0.00 0.00 3.16
317 321 4.179298 CCCTAAAACTAGCGTACCAGAAC 58.821 47.826 0.00 0.00 0.00 3.01
323 327 2.762887 AGACCCCCTAAAACTAGCGTAC 59.237 50.000 0.00 0.00 0.00 3.67
325 329 1.948391 AGACCCCCTAAAACTAGCGT 58.052 50.000 0.00 0.00 0.00 5.07
330 334 2.576648 CTGGCTAAGACCCCCTAAAACT 59.423 50.000 0.00 0.00 0.00 2.66
333 337 2.653543 TCTGGCTAAGACCCCCTAAA 57.346 50.000 0.00 0.00 0.00 1.85
395 399 2.143419 GTCATCGCCCCTCCCTCAT 61.143 63.158 0.00 0.00 0.00 2.90
439 443 2.427232 TTAGCGACAACTACAAGCGT 57.573 45.000 0.00 0.00 0.00 5.07
440 444 3.483574 CCAATTAGCGACAACTACAAGCG 60.484 47.826 0.00 0.00 0.00 4.68
442 446 4.929808 AGACCAATTAGCGACAACTACAAG 59.070 41.667 0.00 0.00 0.00 3.16
493 497 1.227527 CAGTGCAACGGACACCAGA 60.228 57.895 0.00 0.00 45.86 3.86
520 524 5.783111 AGCGCCCCAAAAATATTCATATTC 58.217 37.500 2.29 0.00 32.08 1.75
552 556 3.767711 ACCCCTTTCTAAGCTTTTCTGG 58.232 45.455 3.20 1.23 0.00 3.86
554 558 5.477291 GCTTAACCCCTTTCTAAGCTTTTCT 59.523 40.000 3.20 0.00 42.69 2.52
571 575 5.552178 TCTTCCTTTCTTCAGAGCTTAACC 58.448 41.667 0.00 0.00 0.00 2.85
599 603 2.811410 TCTCTACCCCTCGCACTAAAA 58.189 47.619 0.00 0.00 0.00 1.52
624 628 0.800683 TTCATACGCACCGAGCTTCG 60.801 55.000 0.00 0.00 42.61 3.79
661 665 2.805845 AGTACTTGTTACTATGCGCCG 58.194 47.619 4.18 0.00 39.45 6.46
665 669 6.032094 TCGTTGCTAGTACTTGTTACTATGC 58.968 40.000 0.00 0.00 41.58 3.14
669 673 4.863131 GCATCGTTGCTAGTACTTGTTACT 59.137 41.667 11.21 0.00 45.77 2.24
726 730 3.181468 GGTAGCCTACCTGCGATTTAAGT 60.181 47.826 13.87 0.00 45.52 2.24
727 731 3.391049 GGTAGCCTACCTGCGATTTAAG 58.609 50.000 13.87 0.00 45.52 1.85
728 732 3.464111 GGTAGCCTACCTGCGATTTAA 57.536 47.619 13.87 0.00 45.52 1.52
833 837 0.324091 TTGGAGGGGTCGGTAGTCTC 60.324 60.000 0.00 0.00 0.00 3.36
906 916 0.759346 GGGATCGGATGGCTTGTAGT 59.241 55.000 0.00 0.00 0.00 2.73
908 918 1.140852 CTTGGGATCGGATGGCTTGTA 59.859 52.381 0.00 0.00 0.00 2.41
943 987 2.503356 TGCTTGTTTTGGGATTTGGTGT 59.497 40.909 0.00 0.00 0.00 4.16
981 1040 0.880441 TGATGGGCGTTTGTGTGATG 59.120 50.000 0.00 0.00 0.00 3.07
986 1045 0.452987 CTCCATGATGGGCGTTTGTG 59.547 55.000 12.26 0.00 38.32 3.33
995 1054 2.765135 AGCGGATATCTCTCCATGATGG 59.235 50.000 4.74 4.74 39.43 3.51
1009 1068 1.532437 CACGACCATACGTAGCGGATA 59.468 52.381 18.16 0.00 44.76 2.59
1356 1436 2.047179 GTGGAGGTGGAGCCGAAC 60.047 66.667 0.00 0.00 43.70 3.95
1392 1472 3.640029 GGTCGATGGATTACTTGAGGGTA 59.360 47.826 0.00 0.00 0.00 3.69
1407 1487 5.828299 AGTAGAAGAAGAAGAGGTCGATG 57.172 43.478 0.00 0.00 0.00 3.84
1429 1509 8.735692 TGCATCATTGACATGAAGAAATAGTA 57.264 30.769 0.00 0.00 42.93 1.82
1430 1510 7.555195 TCTGCATCATTGACATGAAGAAATAGT 59.445 33.333 0.00 0.00 42.93 2.12
1431 1511 7.927048 TCTGCATCATTGACATGAAGAAATAG 58.073 34.615 0.00 0.00 42.93 1.73
1432 1512 7.868906 TCTGCATCATTGACATGAAGAAATA 57.131 32.000 0.00 0.00 42.93 1.40
1435 1515 5.650703 ACATCTGCATCATTGACATGAAGAA 59.349 36.000 0.00 0.00 42.93 2.52
1437 1517 5.500645 ACATCTGCATCATTGACATGAAG 57.499 39.130 0.00 0.00 42.93 3.02
1440 1520 3.848554 GCGACATCTGCATCATTGACATG 60.849 47.826 0.00 0.00 0.00 3.21
1456 1827 0.742505 CCCATTGCTGATTGCGACAT 59.257 50.000 0.00 0.00 46.63 3.06
1485 1861 3.058293 TCAATTTTGGCATGTCGTCTCAC 60.058 43.478 0.00 0.00 0.00 3.51
1491 1867 1.978097 CACGTCAATTTTGGCATGTCG 59.022 47.619 4.39 4.39 31.86 4.35
1749 2128 0.249073 CTAGGAACTGCAGCGCGTAT 60.249 55.000 15.27 0.00 41.52 3.06
1903 2282 3.518998 CTCGTCGCGGATGAGGGT 61.519 66.667 6.13 0.00 40.76 4.34
2480 2886 4.410228 TCAAATCCCAACAACATTTTCCCA 59.590 37.500 0.00 0.00 0.00 4.37
2496 2902 4.078639 AGTGCCACTAGCTATCAAATCC 57.921 45.455 0.00 0.00 44.23 3.01
2567 3009 7.933577 TCAACACTAGATGTCTCTTTGTTGAAT 59.066 33.333 20.41 0.00 46.84 2.57
2580 3022 6.461648 CCATATTCCGACTCAACACTAGATGT 60.462 42.308 0.00 0.00 46.42 3.06
2630 3079 4.657814 AATGCATAGGACGGGGATAATT 57.342 40.909 0.00 0.00 0.00 1.40
2690 3141 5.560953 GCTTGTACCACATCACAGACTTTTC 60.561 44.000 0.00 0.00 0.00 2.29
2779 3235 6.441222 ACATGGACCTAGGTCTAGATGTTTA 58.559 40.000 35.12 14.53 44.04 2.01
2910 3369 3.992260 ATTTCGAGTCGGATGGAGTAG 57.008 47.619 13.54 0.00 0.00 2.57
2956 3415 9.349713 TCAAAATGTAAGACCATCTTTTACACT 57.650 29.630 0.00 0.00 39.34 3.55
2957 3416 9.612620 CTCAAAATGTAAGACCATCTTTTACAC 57.387 33.333 0.00 0.00 39.34 2.90
2965 3424 4.332819 CCCGTCTCAAAATGTAAGACCATC 59.667 45.833 0.00 0.00 36.84 3.51
2981 3440 2.164017 GAGAAAGTACTCCACCCGTCTC 59.836 54.545 0.00 0.00 0.00 3.36
2988 3447 4.685165 GGAAAGAACGAGAAAGTACTCCAC 59.315 45.833 0.00 0.00 33.83 4.02
3000 3459 4.023963 GGAACAAGGAAAGGAAAGAACGAG 60.024 45.833 0.00 0.00 0.00 4.18
3012 3489 2.031120 CAAGCACAGGGAACAAGGAAA 58.969 47.619 0.00 0.00 0.00 3.13
3017 3494 0.257328 TGTCCAAGCACAGGGAACAA 59.743 50.000 0.00 0.00 34.34 2.83
3028 3505 4.152938 GGAAATGCAAGATTTTGTCCAAGC 59.847 41.667 0.00 0.00 36.65 4.01
3054 3531 6.348950 CGAATGCCCTTTTTGTTAGTCACATA 60.349 38.462 0.00 0.00 34.43 2.29
3083 3573 7.555087 TGTGGACAAAATCAGAATTCAGTTTT 58.445 30.769 8.44 8.59 0.00 2.43
3086 3576 5.829924 ACTGTGGACAAAATCAGAATTCAGT 59.170 36.000 8.44 0.00 0.00 3.41
3100 3590 2.708216 TTCAAGCTCACTGTGGACAA 57.292 45.000 8.11 0.00 0.00 3.18
3134 3624 5.798934 CAGTATATATACGCCACGGAGAAAC 59.201 44.000 15.57 0.00 38.28 2.78
3141 3631 6.421501 TGAAAAACCAGTATATATACGCCACG 59.578 38.462 15.57 6.68 38.28 4.94
3144 3634 8.773404 AGATGAAAAACCAGTATATATACGCC 57.227 34.615 15.57 0.00 38.28 5.68
3194 3696 2.157668 CCGTCGACAGGAGAATGTTTTG 59.842 50.000 17.16 0.00 32.25 2.44
3227 3729 1.674817 CCGAAAAGGAAAGCTCGCCTA 60.675 52.381 7.67 0.00 45.00 3.93
3247 3749 2.029918 GGTTGGCATGTCACCTTCTTTC 60.030 50.000 0.00 0.00 0.00 2.62
3269 3774 3.187842 GGAAGGTATTGTCACGTGGAAAC 59.812 47.826 17.00 7.35 0.00 2.78
3366 3909 3.368948 GGAGAAGCTTCGAGGACATTCTT 60.369 47.826 20.43 0.00 0.00 2.52
3377 3920 3.191539 GCAGCCGGAGAAGCTTCG 61.192 66.667 20.43 9.83 38.95 3.79


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

AutoCloner maintained by Alex Coulton.