Multiple sequence alignment - TraesCS1D01G273500

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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 TraesCS1D01G273500 chr1D 100.000 3315 0 0 1 3315 367846757 367850071 0.000000e+00 6122.0
1 TraesCS1D01G273500 chr1D 78.626 131 28 0 1856 1986 433253062 433253192 1.640000e-13 87.9
2 TraesCS1D01G273500 chr1B 92.833 2093 90 30 384 2442 492305699 492307765 0.000000e+00 2979.0
3 TraesCS1D01G273500 chr1B 93.758 801 41 4 2523 3315 492307763 492308562 0.000000e+00 1194.0
4 TraesCS1D01G273500 chr1B 87.119 295 19 7 1 287 492305385 492305668 1.920000e-82 316.0
5 TraesCS1D01G273500 chr1B 78.626 131 28 0 1856 1986 585166359 585166489 1.640000e-13 87.9
6 TraesCS1D01G273500 chr1B 95.833 48 2 0 2076 2123 13592270 13592317 9.860000e-11 78.7
7 TraesCS1D01G273500 chr1A 91.041 1105 67 15 1363 2442 467184977 467186074 0.000000e+00 1463.0
8 TraesCS1D01G273500 chr1A 89.531 831 44 18 2523 3315 467186072 467186897 0.000000e+00 1013.0
9 TraesCS1D01G273500 chr1A 85.758 990 49 37 397 1359 467184007 467184931 0.000000e+00 963.0
10 TraesCS1D01G273500 chr1A 84.722 216 27 4 2678 2888 467186108 467186322 9.320000e-51 211.0
11 TraesCS1D01G273500 chr1A 97.015 67 2 0 1 67 467183612 467183678 2.700000e-21 113.0
12 TraesCS1D01G273500 chr1A 78.626 131 28 0 1856 1986 531643420 531643550 1.640000e-13 87.9
13 TraesCS1D01G273500 chr1A 83.516 91 13 2 2078 2167 21024736 21024647 2.120000e-12 84.2
14 TraesCS1D01G273500 chr7D 98.901 91 1 0 2439 2529 26757914 26757824 2.650000e-36 163.0
15 TraesCS1D01G273500 chr2D 95.050 101 1 4 2441 2539 419467268 419467170 4.430000e-34 156.0
16 TraesCS1D01G273500 chr5D 95.833 96 0 4 2433 2526 385037231 385037324 5.730000e-33 152.0
17 TraesCS1D01G273500 chr5D 97.674 86 0 2 2441 2525 543829310 543829394 2.660000e-31 147.0
18 TraesCS1D01G273500 chr4B 94.898 98 3 2 2433 2529 403270786 403270690 5.730000e-33 152.0
19 TraesCS1D01G273500 chr4D 93.069 101 7 0 2428 2528 39220525 39220625 7.410000e-32 148.0
20 TraesCS1D01G273500 chr4A 93.137 102 4 3 2425 2525 674937180 674937279 2.660000e-31 147.0
21 TraesCS1D01G273500 chrUn 92.308 104 5 3 2424 2525 67407010 67407112 9.580000e-31 145.0
22 TraesCS1D01G273500 chrUn 77.778 126 28 0 1859 1984 480633121 480633246 9.860000e-11 78.7
23 TraesCS1D01G273500 chr7A 92.233 103 6 1 2440 2542 167905100 167905200 9.580000e-31 145.0
24 TraesCS1D01G273500 chr3A 87.368 95 12 0 1043 1137 746351509 746351603 3.500000e-20 110.0
25 TraesCS1D01G273500 chr3A 87.368 95 12 0 1043 1137 746363950 746363856 3.500000e-20 110.0
26 TraesCS1D01G273500 chr3A 86.316 95 13 0 1043 1137 746313267 746313361 1.630000e-18 104.0
27 TraesCS1D01G273500 chr3A 80.315 127 25 0 1859 1985 746351869 746351995 2.720000e-16 97.1
28 TraesCS1D01G273500 chr3A 82.143 112 20 0 1874 1985 746363575 746363464 2.720000e-16 97.1
29 TraesCS1D01G273500 chr3A 83.838 99 14 2 1259 1356 746351602 746351699 3.520000e-15 93.5
30 TraesCS1D01G273500 chr3A 88.462 78 7 2 1280 1356 746363836 746363760 3.520000e-15 93.5
31 TraesCS1D01G273500 chr3A 77.344 128 27 2 1859 1985 746313627 746313753 1.280000e-09 75.0
32 TraesCS1D01G273500 chr3D 90.667 75 7 0 1063 1137 611568453 611568379 2.100000e-17 100.0
33 TraesCS1D01G273500 chr3D 80.469 128 23 2 1859 1985 611559000 611559126 2.720000e-16 97.1
34 TraesCS1D01G273500 chr3D 89.855 69 7 0 1288 1356 611558762 611558830 4.560000e-14 89.8
35 TraesCS1D01G273500 chr3D 89.855 69 7 0 1288 1356 611568264 611568196 4.560000e-14 89.8
36 TraesCS1D01G273500 chr3B 88.462 78 7 2 1280 1356 829288982 829288906 3.520000e-15 93.5
37 TraesCS1D01G273500 chr3B 77.778 126 28 0 1859 1984 829273922 829274047 9.860000e-11 78.7
38 TraesCS1D01G273500 chr3B 79.279 111 23 0 1874 1984 829288721 829288611 9.860000e-11 78.7
39 TraesCS1D01G273500 chr3B 97.368 38 0 1 2076 2112 48886425 48886388 2.760000e-06 63.9
40 TraesCS1D01G273500 chr6D 86.885 61 8 0 2078 2138 356598478 356598418 5.930000e-08 69.4


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 TraesCS1D01G273500 chr1D 367846757 367850071 3314 False 6122.000000 6122 100.000000 1 3315 1 chr1D.!!$F1 3314
1 TraesCS1D01G273500 chr1B 492305385 492308562 3177 False 1496.333333 2979 91.236667 1 3315 3 chr1B.!!$F3 3314
2 TraesCS1D01G273500 chr1A 467183612 467186897 3285 False 752.600000 1463 89.613400 1 3315 5 chr1A.!!$F2 3314

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
240 336 0.322008 CCACAGTGGAGGGAAGCTTC 60.322 60.0 18.54 18.54 40.96 3.86 F
1175 1321 0.170561 CGTTTCAGATCCGTCCGTCT 59.829 55.0 0.00 0.00 0.00 4.18 F
1765 1972 0.679960 GGCACGCTAAACCAATCCCT 60.680 55.0 0.00 0.00 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1439 1640 0.169009 GGTACACCACGGACGAGTAC 59.831 60.000 0.00 5.97 35.51 2.73 R
2207 2422 1.826487 GGAGCCTCGAGGACTCTCC 60.826 68.421 34.51 32.27 37.98 3.71 R
3003 3242 2.159282 CGTTAGCATTGGTACGACTCCT 60.159 50.000 10.34 0.00 0.00 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
36 37 2.363975 AATGGGCATTGGCAGCAGG 61.364 57.895 12.70 0.00 43.71 4.85
51 52 1.476007 GCAGGGCTATCCGGATGACT 61.476 60.000 27.55 15.47 41.52 3.41
69 70 5.996669 TGACTTGCATCAGCTTATACATG 57.003 39.130 0.00 0.00 42.74 3.21
84 169 6.349115 GCTTATACATGATTCCTGGAGCATTG 60.349 42.308 0.00 9.13 0.00 2.82
86 171 2.307768 CATGATTCCTGGAGCATTGCT 58.692 47.619 11.79 11.79 43.88 3.91
155 247 7.032580 CCTGATACAAAGAACAAACAAACACA 58.967 34.615 0.00 0.00 0.00 3.72
181 273 5.892568 ACTCGACTTGTGTTATGTAGATCC 58.107 41.667 0.00 0.00 0.00 3.36
212 304 1.066430 GGCACCTGTTCGTCCATTAGA 60.066 52.381 0.00 0.00 0.00 2.10
213 305 2.000447 GCACCTGTTCGTCCATTAGAC 59.000 52.381 0.00 0.00 42.54 2.59
214 306 2.618053 CACCTGTTCGTCCATTAGACC 58.382 52.381 0.00 0.00 43.08 3.85
216 308 2.838202 ACCTGTTCGTCCATTAGACCAT 59.162 45.455 0.00 0.00 43.08 3.55
217 309 4.028131 ACCTGTTCGTCCATTAGACCATA 58.972 43.478 0.00 0.00 43.08 2.74
218 310 4.654262 ACCTGTTCGTCCATTAGACCATAT 59.346 41.667 0.00 0.00 43.08 1.78
224 320 4.038763 TCGTCCATTAGACCATATCACCAC 59.961 45.833 0.00 0.00 43.08 4.16
240 336 0.322008 CCACAGTGGAGGGAAGCTTC 60.322 60.000 18.54 18.54 40.96 3.86
266 367 2.044793 TCATCCTCTCCCAACACCTT 57.955 50.000 0.00 0.00 0.00 3.50
267 368 2.348472 TCATCCTCTCCCAACACCTTT 58.652 47.619 0.00 0.00 0.00 3.11
275 376 1.566703 TCCCAACACCTTTTGACTGGA 59.433 47.619 0.00 0.00 35.10 3.86
279 380 3.005791 CCAACACCTTTTGACTGGAATCC 59.994 47.826 0.00 0.00 35.10 3.01
300 401 0.378610 GTACAGTACGTACTCCGGGC 59.621 60.000 25.10 10.24 46.01 6.13
301 402 0.748005 TACAGTACGTACTCCGGGCC 60.748 60.000 25.10 0.00 42.24 5.80
302 403 2.048023 CAGTACGTACTCCGGGCCA 61.048 63.158 25.10 0.00 42.24 5.36
303 404 2.048603 AGTACGTACTCCGGGCCAC 61.049 63.158 22.45 0.00 42.24 5.01
304 405 3.133464 TACGTACTCCGGGCCACG 61.133 66.667 17.28 17.28 42.24 4.94
331 432 2.599578 GGGCGAGCGGGGAGTATA 60.600 66.667 0.00 0.00 0.00 1.47
350 451 0.660488 AAACATTCACTGCGCGTTCA 59.340 45.000 8.43 0.00 0.00 3.18
361 462 1.591594 CGCGTTCACAGTCCACAGT 60.592 57.895 0.00 0.00 0.00 3.55
363 464 0.529773 GCGTTCACAGTCCACAGTCA 60.530 55.000 0.00 0.00 0.00 3.41
364 465 1.491670 CGTTCACAGTCCACAGTCAG 58.508 55.000 0.00 0.00 0.00 3.51
365 466 1.067060 CGTTCACAGTCCACAGTCAGA 59.933 52.381 0.00 0.00 0.00 3.27
366 467 2.288457 CGTTCACAGTCCACAGTCAGAT 60.288 50.000 0.00 0.00 0.00 2.90
367 468 3.733337 GTTCACAGTCCACAGTCAGATT 58.267 45.455 0.00 0.00 0.00 2.40
368 469 4.130118 GTTCACAGTCCACAGTCAGATTT 58.870 43.478 0.00 0.00 0.00 2.17
369 470 4.422073 TCACAGTCCACAGTCAGATTTT 57.578 40.909 0.00 0.00 0.00 1.82
370 471 4.780815 TCACAGTCCACAGTCAGATTTTT 58.219 39.130 0.00 0.00 0.00 1.94
442 545 8.461222 TGCTTCGATGTGAAATGAAATAAATCT 58.539 29.630 0.00 0.00 35.79 2.40
462 567 3.871775 TTCGTCGCGAAACTAACCT 57.128 47.368 12.06 0.00 43.00 3.50
621 729 3.764885 CCAGTGGCAGCTTTTATGTAC 57.235 47.619 0.00 0.00 0.00 2.90
626 734 6.095440 CCAGTGGCAGCTTTTATGTACTTTAT 59.905 38.462 0.00 0.00 0.00 1.40
628 736 8.028938 CAGTGGCAGCTTTTATGTACTTTATTT 58.971 33.333 0.00 0.00 0.00 1.40
629 737 9.238368 AGTGGCAGCTTTTATGTACTTTATTTA 57.762 29.630 0.00 0.00 0.00 1.40
630 738 9.849166 GTGGCAGCTTTTATGTACTTTATTTAA 57.151 29.630 0.00 0.00 0.00 1.52
632 740 9.516314 GGCAGCTTTTATGTACTTTATTTAAGG 57.484 33.333 0.00 0.00 38.23 2.69
648 777 1.895020 AAGGTATGAACGAGGGCGCA 61.895 55.000 10.83 0.00 42.48 6.09
677 806 1.462283 CGTGAGTGACTGGATGCTTTG 59.538 52.381 0.00 0.00 0.00 2.77
678 807 2.771089 GTGAGTGACTGGATGCTTTGA 58.229 47.619 0.00 0.00 0.00 2.69
679 808 3.341823 GTGAGTGACTGGATGCTTTGAT 58.658 45.455 0.00 0.00 0.00 2.57
680 809 3.373439 GTGAGTGACTGGATGCTTTGATC 59.627 47.826 0.00 0.00 0.00 2.92
746 876 5.529800 AGTTGCCGAGTTTGTTTATACTGTT 59.470 36.000 0.00 0.00 0.00 3.16
747 877 6.707161 AGTTGCCGAGTTTGTTTATACTGTTA 59.293 34.615 0.00 0.00 0.00 2.41
885 1030 3.655211 CCCCCTGCCAACTGCTCT 61.655 66.667 0.00 0.00 42.00 4.09
1147 1293 1.908483 GAGATCGGTGAGCCCCTTT 59.092 57.895 0.00 0.00 0.00 3.11
1149 1295 0.618968 AGATCGGTGAGCCCCTTTCT 60.619 55.000 0.00 0.00 0.00 2.52
1159 1305 1.075536 AGCCCCTTTCTCCATTTCGTT 59.924 47.619 0.00 0.00 0.00 3.85
1169 1315 3.056107 TCTCCATTTCGTTTCAGATCCGT 60.056 43.478 0.00 0.00 0.00 4.69
1175 1321 0.170561 CGTTTCAGATCCGTCCGTCT 59.829 55.000 0.00 0.00 0.00 4.18
1228 1374 0.804364 GGAACGCATGTGCTGATTGA 59.196 50.000 6.08 0.00 39.32 2.57
1249 1395 1.298638 GATCCCTTGCGCGAATTGC 60.299 57.895 12.10 0.00 41.47 3.56
1367 1554 6.385033 GGATGATCAAGGTCTGAAACTTTTG 58.615 40.000 0.00 0.00 37.67 2.44
1411 1601 3.619929 CGCATGAATGTGTTCTGAGATCA 59.380 43.478 0.00 0.00 35.33 2.92
1412 1602 4.272748 CGCATGAATGTGTTCTGAGATCAT 59.727 41.667 0.00 0.00 35.33 2.45
1414 1604 5.296035 GCATGAATGTGTTCTGAGATCATCA 59.704 40.000 0.00 0.00 35.33 3.07
1415 1605 6.017026 GCATGAATGTGTTCTGAGATCATCAT 60.017 38.462 0.00 0.31 37.28 2.45
1416 1606 7.577107 CATGAATGTGTTCTGAGATCATCATC 58.423 38.462 5.54 2.20 37.28 2.92
1417 1607 6.885922 TGAATGTGTTCTGAGATCATCATCT 58.114 36.000 0.00 0.00 37.37 2.90
1439 1640 1.221840 CCAGGTTGACCGGATCCTG 59.778 63.158 22.05 22.05 44.74 3.86
1641 1843 2.290641 CCCACCGTTCTTTTTCTGACAG 59.709 50.000 0.00 0.00 0.00 3.51
1686 1893 4.681074 TTTCATTTCAAACCAGGAACCC 57.319 40.909 0.00 0.00 0.00 4.11
1765 1972 0.679960 GGCACGCTAAACCAATCCCT 60.680 55.000 0.00 0.00 0.00 4.20
1784 1991 3.244700 CCCTTCATCTCTGTCCAAGTGTT 60.245 47.826 0.00 0.00 0.00 3.32
1863 2074 7.231467 TCTCTGCTATTTTTCTTAAACAGGGT 58.769 34.615 0.00 0.00 0.00 4.34
1998 2209 3.808728 AGATTGTACGCATACCATTGCT 58.191 40.909 0.00 0.00 40.54 3.91
2024 2239 1.463674 ATCTCGCATTTCCACAACCC 58.536 50.000 0.00 0.00 0.00 4.11
2051 2266 2.157738 GCATCTTCAGGCTTCAAGTGT 58.842 47.619 3.48 0.00 0.00 3.55
2052 2267 2.095364 GCATCTTCAGGCTTCAAGTGTG 60.095 50.000 3.48 5.35 0.00 3.82
2182 2397 5.221185 CCATGTAAGCTCTCATCATTTTGGG 60.221 44.000 0.00 0.00 0.00 4.12
2351 2566 5.899278 ACTATTTTTCCTTTGCCCTTCCTA 58.101 37.500 0.00 0.00 0.00 2.94
2412 2627 2.424956 GGATCTGATGAACAACCAAGCC 59.575 50.000 0.00 0.00 0.00 4.35
2419 2634 0.312102 GAACAACCAAGCCAGTCTGC 59.688 55.000 0.00 0.00 0.00 4.26
2442 2657 7.028962 TGCATTTCTACATTCTTGCATTGTAC 58.971 34.615 0.00 0.00 35.36 2.90
2443 2658 7.094248 TGCATTTCTACATTCTTGCATTGTACT 60.094 33.333 0.00 0.00 35.36 2.73
2444 2659 7.430502 GCATTTCTACATTCTTGCATTGTACTC 59.569 37.037 0.00 0.00 0.00 2.59
2445 2660 6.985188 TTCTACATTCTTGCATTGTACTCC 57.015 37.500 0.00 0.00 0.00 3.85
2446 2661 5.428253 TCTACATTCTTGCATTGTACTCCC 58.572 41.667 0.00 0.00 0.00 4.30
2447 2662 4.307032 ACATTCTTGCATTGTACTCCCT 57.693 40.909 0.00 0.00 0.00 4.20
2448 2663 4.265073 ACATTCTTGCATTGTACTCCCTC 58.735 43.478 0.00 0.00 0.00 4.30
2449 2664 4.018960 ACATTCTTGCATTGTACTCCCTCT 60.019 41.667 0.00 0.00 0.00 3.69
2450 2665 3.616956 TCTTGCATTGTACTCCCTCTG 57.383 47.619 0.00 0.00 0.00 3.35
2451 2666 2.906389 TCTTGCATTGTACTCCCTCTGT 59.094 45.455 0.00 0.00 0.00 3.41
2452 2667 4.093743 TCTTGCATTGTACTCCCTCTGTA 58.906 43.478 0.00 0.00 0.00 2.74
2453 2668 4.530553 TCTTGCATTGTACTCCCTCTGTAA 59.469 41.667 0.00 0.00 0.00 2.41
2454 2669 4.901197 TGCATTGTACTCCCTCTGTAAA 57.099 40.909 0.00 0.00 0.00 2.01
2455 2670 4.575885 TGCATTGTACTCCCTCTGTAAAC 58.424 43.478 0.00 0.00 0.00 2.01
2456 2671 4.286032 TGCATTGTACTCCCTCTGTAAACT 59.714 41.667 0.00 0.00 0.00 2.66
2457 2672 5.482526 TGCATTGTACTCCCTCTGTAAACTA 59.517 40.000 0.00 0.00 0.00 2.24
2458 2673 6.014070 TGCATTGTACTCCCTCTGTAAACTAA 60.014 38.462 0.00 0.00 0.00 2.24
2459 2674 7.048512 GCATTGTACTCCCTCTGTAAACTAAT 58.951 38.462 0.00 0.00 0.00 1.73
2460 2675 8.202137 GCATTGTACTCCCTCTGTAAACTAATA 58.798 37.037 0.00 0.00 0.00 0.98
2467 2682 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
2469 2684 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
2487 2702 8.989653 AAGAGTGTTTAGATCACTACTTTAGC 57.010 34.615 0.00 0.00 44.68 3.09
2488 2703 8.356000 AGAGTGTTTAGATCACTACTTTAGCT 57.644 34.615 0.00 0.00 44.68 3.32
2489 2704 9.463902 AGAGTGTTTAGATCACTACTTTAGCTA 57.536 33.333 0.00 0.00 44.68 3.32
2498 2713 8.077386 AGATCACTACTTTAGCTATCTAAACGC 58.923 37.037 0.00 0.00 39.23 4.84
2499 2714 7.330900 TCACTACTTTAGCTATCTAAACGCT 57.669 36.000 0.00 0.00 39.23 5.07
2500 2715 7.416022 TCACTACTTTAGCTATCTAAACGCTC 58.584 38.462 0.00 0.00 39.23 5.03
2501 2716 7.282675 TCACTACTTTAGCTATCTAAACGCTCT 59.717 37.037 0.00 0.00 39.23 4.09
2502 2717 7.916450 CACTACTTTAGCTATCTAAACGCTCTT 59.084 37.037 0.00 0.00 39.23 2.85
2503 2718 9.118300 ACTACTTTAGCTATCTAAACGCTCTTA 57.882 33.333 0.00 0.00 39.23 2.10
2516 2731 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2517 2732 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2518 2733 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2519 2734 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2520 2735 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2521 2736 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
2522 2737 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
2523 2738 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
2524 2739 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
2566 2781 7.334844 TCACTGTGGTACTATGTATCTCAAG 57.665 40.000 8.11 0.00 0.00 3.02
2720 2936 1.263217 CTTGTGGTTTGGCTCGTGTAC 59.737 52.381 0.00 0.00 0.00 2.90
2724 2940 0.872388 GGTTTGGCTCGTGTACCTTG 59.128 55.000 0.00 0.00 0.00 3.61
2795 3022 6.289834 TCTGAGATACTGCAGTACTACCTAC 58.710 44.000 28.28 14.98 32.72 3.18
2798 3025 6.015991 AGATACTGCAGTACTACCTACCTT 57.984 41.667 28.28 8.83 32.72 3.50
2844 3071 0.468226 TGGCCCGTGTATCATCTTCC 59.532 55.000 0.00 0.00 0.00 3.46
2856 3083 7.165483 CGTGTATCATCTTCCGTTCTTACTAAC 59.835 40.741 0.00 0.00 0.00 2.34
2933 3165 6.603201 TCACCCCTTGTCAGATTGATTATTTC 59.397 38.462 0.00 0.00 0.00 2.17
2990 3229 5.776173 TTTAATTCCGGACATTGTGTGTT 57.224 34.783 1.83 0.00 42.36 3.32
3003 3242 6.009589 ACATTGTGTGTTCCTCATTCCATTA 58.990 36.000 0.00 0.00 38.01 1.90
3029 3276 1.369625 GTACCAATGCTAACGCTGCT 58.630 50.000 0.00 0.00 36.97 4.24
3120 3371 9.691362 GGATGCTAAACAAATTCAGAAGTTTAA 57.309 29.630 0.00 0.00 36.39 1.52
3216 3468 3.743521 CCCTGTCATCTCACAAACTCAA 58.256 45.455 0.00 0.00 0.00 3.02
3217 3469 3.499918 CCCTGTCATCTCACAAACTCAAC 59.500 47.826 0.00 0.00 0.00 3.18
3220 3472 4.512484 TGTCATCTCACAAACTCAACACA 58.488 39.130 0.00 0.00 0.00 3.72
3223 3475 3.904800 TCTCACAAACTCAACACAGGA 57.095 42.857 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.106708 TGCAAGTCATCCGGATAGCC 59.893 55.000 18.63 7.85 0.00 3.93
51 52 6.206048 CAGGAATCATGTATAAGCTGATGCAA 59.794 38.462 5.88 0.00 42.74 4.08
69 70 1.030457 CCAGCAATGCTCCAGGAATC 58.970 55.000 4.03 0.00 36.40 2.52
104 189 5.186198 ACATGGGTGATTAACTCAAGCTAC 58.814 41.667 0.00 0.00 44.40 3.58
155 247 6.570672 TCTACATAACACAAGTCGAGTTCT 57.429 37.500 1.51 0.00 30.49 3.01
181 273 0.107508 ACAGGTGCCGGATTCAGATG 60.108 55.000 5.05 0.00 0.00 2.90
212 304 1.839994 CCTCCACTGTGGTGATATGGT 59.160 52.381 25.97 0.00 45.61 3.55
213 305 1.141657 CCCTCCACTGTGGTGATATGG 59.858 57.143 25.97 16.17 45.61 2.74
214 306 2.118679 TCCCTCCACTGTGGTGATATG 58.881 52.381 25.97 11.82 45.61 1.78
216 308 2.187958 CTTCCCTCCACTGTGGTGATA 58.812 52.381 25.97 13.02 45.61 2.15
217 309 0.987294 CTTCCCTCCACTGTGGTGAT 59.013 55.000 25.97 0.00 45.61 3.06
218 310 1.768684 GCTTCCCTCCACTGTGGTGA 61.769 60.000 25.97 17.93 45.61 4.02
224 320 0.689623 ACTGAAGCTTCCCTCCACTG 59.310 55.000 23.42 4.38 0.00 3.66
240 336 4.878397 GTGTTGGGAGAGGATGATTAACTG 59.122 45.833 0.00 0.00 0.00 3.16
287 388 3.133464 CGTGGCCCGGAGTACGTA 61.133 66.667 0.73 0.00 42.24 3.57
314 415 1.751349 TTTATACTCCCCGCTCGCCC 61.751 60.000 0.00 0.00 0.00 6.13
315 416 0.599466 GTTTATACTCCCCGCTCGCC 60.599 60.000 0.00 0.00 0.00 5.54
316 417 0.103572 TGTTTATACTCCCCGCTCGC 59.896 55.000 0.00 0.00 0.00 5.03
317 418 2.814280 ATGTTTATACTCCCCGCTCG 57.186 50.000 0.00 0.00 0.00 5.03
318 419 3.808174 GTGAATGTTTATACTCCCCGCTC 59.192 47.826 0.00 0.00 0.00 5.03
319 420 3.454812 AGTGAATGTTTATACTCCCCGCT 59.545 43.478 0.00 0.00 0.00 5.52
320 421 3.560068 CAGTGAATGTTTATACTCCCCGC 59.440 47.826 0.00 0.00 0.00 6.13
331 432 0.660488 TGAACGCGCAGTGAATGTTT 59.340 45.000 5.73 0.00 43.07 2.83
371 472 4.340617 ACTGTGGACTGTTTCCTCAAAAA 58.659 39.130 0.00 0.00 45.34 1.94
372 473 3.945285 GACTGTGGACTGTTTCCTCAAAA 59.055 43.478 0.00 0.00 45.34 2.44
373 474 3.054728 TGACTGTGGACTGTTTCCTCAAA 60.055 43.478 0.00 0.00 45.34 2.69
374 475 2.503765 TGACTGTGGACTGTTTCCTCAA 59.496 45.455 0.00 0.00 45.34 3.02
375 476 2.103094 CTGACTGTGGACTGTTTCCTCA 59.897 50.000 0.00 0.00 46.10 3.86
376 477 2.103263 ACTGACTGTGGACTGTTTCCTC 59.897 50.000 0.00 0.00 46.10 3.71
377 478 2.119495 ACTGACTGTGGACTGTTTCCT 58.881 47.619 0.00 0.00 46.10 3.36
378 479 2.622064 ACTGACTGTGGACTGTTTCC 57.378 50.000 0.00 0.00 46.13 3.13
379 480 3.309954 GTGAACTGACTGTGGACTGTTTC 59.690 47.826 0.00 0.00 32.19 2.78
380 481 3.270877 GTGAACTGACTGTGGACTGTTT 58.729 45.455 0.00 0.00 32.19 2.83
381 482 2.738643 CGTGAACTGACTGTGGACTGTT 60.739 50.000 0.00 0.00 33.85 3.16
382 483 1.202417 CGTGAACTGACTGTGGACTGT 60.202 52.381 0.00 0.00 0.00 3.55
383 484 1.491670 CGTGAACTGACTGTGGACTG 58.508 55.000 0.00 0.00 0.00 3.51
384 485 0.389391 CCGTGAACTGACTGTGGACT 59.611 55.000 0.00 0.00 0.00 3.85
385 486 1.222115 GCCGTGAACTGACTGTGGAC 61.222 60.000 0.00 0.00 0.00 4.02
386 487 1.069090 GCCGTGAACTGACTGTGGA 59.931 57.895 0.00 0.00 0.00 4.02
387 488 2.310233 CGCCGTGAACTGACTGTGG 61.310 63.158 0.00 0.00 0.00 4.17
388 489 1.278172 CTCGCCGTGAACTGACTGTG 61.278 60.000 0.00 0.00 0.00 3.66
389 490 1.007271 CTCGCCGTGAACTGACTGT 60.007 57.895 0.00 0.00 0.00 3.55
390 491 2.375766 GCTCGCCGTGAACTGACTG 61.376 63.158 0.00 0.00 0.00 3.51
391 492 2.049063 GCTCGCCGTGAACTGACT 60.049 61.111 0.00 0.00 0.00 3.41
392 493 2.049063 AGCTCGCCGTGAACTGAC 60.049 61.111 0.00 0.00 0.00 3.51
393 494 2.049156 CAGCTCGCCGTGAACTGA 60.049 61.111 6.51 0.00 42.28 3.41
394 495 1.016130 AATCAGCTCGCCGTGAACTG 61.016 55.000 6.08 6.08 41.28 3.16
395 496 0.320771 AAATCAGCTCGCCGTGAACT 60.321 50.000 0.00 0.00 0.00 3.01
442 545 3.173599 CAGGTTAGTTTCGCGACGAATA 58.826 45.455 9.15 0.81 45.28 1.75
444 547 1.269206 ACAGGTTAGTTTCGCGACGAA 60.269 47.619 9.15 9.97 44.28 3.85
446 549 0.433492 CACAGGTTAGTTTCGCGACG 59.567 55.000 9.15 0.00 0.00 5.12
447 550 0.788391 CCACAGGTTAGTTTCGCGAC 59.212 55.000 9.15 0.00 0.00 5.19
457 562 1.710996 CCACCCACCACCACAGGTTA 61.711 60.000 0.00 0.00 40.77 2.85
462 567 3.494254 GACCCACCCACCACCACA 61.494 66.667 0.00 0.00 0.00 4.17
499 605 1.099689 CGTGTCAACTTTGTGGGGTT 58.900 50.000 0.00 0.00 0.00 4.11
505 611 3.184379 CGTGATCATCGTGTCAACTTTGT 59.816 43.478 0.00 0.00 0.00 2.83
618 726 9.038803 CCCTCGTTCATACCTTAAATAAAGTAC 57.961 37.037 0.00 0.00 32.89 2.73
619 727 7.712205 GCCCTCGTTCATACCTTAAATAAAGTA 59.288 37.037 0.00 0.00 32.89 2.24
621 729 6.292703 CGCCCTCGTTCATACCTTAAATAAAG 60.293 42.308 0.00 0.00 34.73 1.85
626 734 2.896168 CGCCCTCGTTCATACCTTAAA 58.104 47.619 0.00 0.00 0.00 1.52
628 736 0.103572 GCGCCCTCGTTCATACCTTA 59.896 55.000 0.00 0.00 38.14 2.69
629 737 1.153429 GCGCCCTCGTTCATACCTT 60.153 57.895 0.00 0.00 38.14 3.50
630 738 1.686325 ATGCGCCCTCGTTCATACCT 61.686 55.000 4.18 0.00 38.14 3.08
631 739 0.032952 TATGCGCCCTCGTTCATACC 59.967 55.000 4.18 0.00 38.14 2.73
632 740 1.269621 ACTATGCGCCCTCGTTCATAC 60.270 52.381 4.18 0.00 38.14 2.39
648 777 1.135660 CAGTCACTCACGACGCACTAT 60.136 52.381 0.00 0.00 40.98 2.12
657 786 1.462283 CAAAGCATCCAGTCACTCACG 59.538 52.381 0.00 0.00 0.00 4.35
677 806 0.041839 GCAACGTGCATGGATCGATC 60.042 55.000 17.36 17.36 44.26 3.69
678 807 1.765161 CGCAACGTGCATGGATCGAT 61.765 55.000 11.36 0.00 45.36 3.59
679 808 2.451990 CGCAACGTGCATGGATCGA 61.452 57.895 11.36 0.00 45.36 3.59
680 809 2.021793 CGCAACGTGCATGGATCG 59.978 61.111 11.36 6.24 45.36 3.69
769 899 0.878523 ACCGATCACACCAACACGTG 60.879 55.000 15.48 15.48 39.75 4.49
770 900 0.599204 GACCGATCACACCAACACGT 60.599 55.000 0.00 0.00 0.00 4.49
771 901 0.319555 AGACCGATCACACCAACACG 60.320 55.000 0.00 0.00 0.00 4.49
772 902 1.148310 CAGACCGATCACACCAACAC 58.852 55.000 0.00 0.00 0.00 3.32
773 903 0.034756 CCAGACCGATCACACCAACA 59.965 55.000 0.00 0.00 0.00 3.33
774 904 0.320374 TCCAGACCGATCACACCAAC 59.680 55.000 0.00 0.00 0.00 3.77
831 961 4.806481 CGCGTCGTCGTCGGATGT 62.806 66.667 13.43 0.00 39.49 3.06
874 1019 0.392327 GGGAGAGAAGAGCAGTTGGC 60.392 60.000 0.00 0.00 45.30 4.52
875 1020 0.251634 GGGGAGAGAAGAGCAGTTGG 59.748 60.000 0.00 0.00 0.00 3.77
876 1021 1.274712 AGGGGAGAGAAGAGCAGTTG 58.725 55.000 0.00 0.00 0.00 3.16
877 1022 2.930109 TAGGGGAGAGAAGAGCAGTT 57.070 50.000 0.00 0.00 0.00 3.16
878 1023 4.757997 ATATAGGGGAGAGAAGAGCAGT 57.242 45.455 0.00 0.00 0.00 4.40
880 1025 4.959210 GCATATATAGGGGAGAGAAGAGCA 59.041 45.833 0.00 0.00 0.00 4.26
881 1026 4.959210 TGCATATATAGGGGAGAGAAGAGC 59.041 45.833 0.00 0.00 0.00 4.09
883 1028 4.950475 CGTGCATATATAGGGGAGAGAAGA 59.050 45.833 0.00 0.00 0.00 2.87
884 1029 4.440802 GCGTGCATATATAGGGGAGAGAAG 60.441 50.000 0.00 0.00 0.00 2.85
885 1030 3.447586 GCGTGCATATATAGGGGAGAGAA 59.552 47.826 0.00 0.00 0.00 2.87
979 1125 2.001361 TTCGATCGAAGGAGGTCGCC 62.001 60.000 25.96 0.00 40.88 5.54
1147 1293 3.056107 ACGGATCTGAAACGAAATGGAGA 60.056 43.478 9.00 0.00 0.00 3.71
1149 1295 3.259064 GACGGATCTGAAACGAAATGGA 58.741 45.455 9.00 0.00 0.00 3.41
1159 1305 1.945354 GCCAGACGGACGGATCTGAA 61.945 60.000 9.00 0.00 44.32 3.02
1175 1321 3.884774 AACCAACAGCTCCGGCCA 61.885 61.111 2.24 0.00 39.73 5.36
1216 1362 4.180377 AGGGATCAATCAATCAGCACAT 57.820 40.909 0.00 0.00 0.00 3.21
1217 1363 3.657398 AGGGATCAATCAATCAGCACA 57.343 42.857 0.00 0.00 0.00 4.57
1367 1554 1.802508 GCCGATGCAAATTAACAGGGC 60.803 52.381 0.00 8.70 37.47 5.19
1389 1576 3.619929 TGATCTCAGAACACATTCATGCG 59.380 43.478 0.00 0.00 37.29 4.73
1411 1601 1.211457 GGTCAACCTGGCAGAGATGAT 59.789 52.381 17.94 0.00 0.00 2.45
1412 1602 0.615331 GGTCAACCTGGCAGAGATGA 59.385 55.000 17.94 13.80 0.00 2.92
1414 1604 1.599047 CGGTCAACCTGGCAGAGAT 59.401 57.895 17.94 0.00 0.00 2.75
1415 1605 2.583441 CCGGTCAACCTGGCAGAGA 61.583 63.158 17.94 8.13 0.00 3.10
1416 1606 1.903877 ATCCGGTCAACCTGGCAGAG 61.904 60.000 17.94 8.80 32.31 3.35
1417 1607 1.899437 GATCCGGTCAACCTGGCAGA 61.899 60.000 17.94 0.00 32.31 4.26
1439 1640 0.169009 GGTACACCACGGACGAGTAC 59.831 60.000 0.00 5.97 35.51 2.73
1641 1843 7.617533 ATGAAATAATTAATTAACACGCGGC 57.382 32.000 12.47 0.00 0.00 6.53
1765 1972 4.687901 TGAACACTTGGACAGAGATGAA 57.312 40.909 0.00 0.00 0.00 2.57
1784 1991 2.297701 GTGGCTGGAAAGTTGACTTGA 58.702 47.619 0.00 0.00 36.12 3.02
1844 2051 8.515414 CCTTCTCACCCTGTTTAAGAAAAATAG 58.485 37.037 0.00 0.00 0.00 1.73
1846 2053 7.066781 TCCTTCTCACCCTGTTTAAGAAAAAT 58.933 34.615 0.00 0.00 0.00 1.82
1863 2074 5.221601 GGCTATGATCTTGTCATCCTTCTCA 60.222 44.000 0.00 0.00 44.23 3.27
1998 2209 2.682856 GTGGAAATGCGAGATAAGGCAA 59.317 45.455 0.00 0.00 43.26 4.52
2024 2239 3.442625 TGAAGCCTGAAGATGCATGAAAG 59.557 43.478 2.46 0.00 0.00 2.62
2051 2266 5.258841 AGATTTGATCAGCCAAGAATCACA 58.741 37.500 14.78 0.00 0.00 3.58
2052 2267 5.831702 AGATTTGATCAGCCAAGAATCAC 57.168 39.130 14.78 0.00 0.00 3.06
2195 2410 5.065731 TCGAGGACTCTCCGTCTTTAATTAC 59.934 44.000 0.00 0.00 42.75 1.89
2207 2422 1.826487 GGAGCCTCGAGGACTCTCC 60.826 68.421 34.51 32.27 37.98 3.71
2351 2566 5.441718 TCTTCTTTGCTTCCCATCATAGT 57.558 39.130 0.00 0.00 0.00 2.12
2412 2627 5.106436 TGCAAGAATGTAGAAATGCAGACTG 60.106 40.000 0.00 0.00 38.73 3.51
2419 2634 7.912250 GGAGTACAATGCAAGAATGTAGAAATG 59.088 37.037 0.00 0.00 30.70 2.32
2443 2658 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
2462 2677 8.808092 AGCTAAAGTAGTGATCTAAACACTCTT 58.192 33.333 0.00 0.00 45.58 2.85
2463 2678 8.356000 AGCTAAAGTAGTGATCTAAACACTCT 57.644 34.615 0.00 0.00 45.58 3.24
2472 2687 8.077386 GCGTTTAGATAGCTAAAGTAGTGATCT 58.923 37.037 13.29 0.00 44.78 2.75
2473 2688 8.077386 AGCGTTTAGATAGCTAAAGTAGTGATC 58.923 37.037 13.29 0.00 44.78 2.92
2474 2689 7.942990 AGCGTTTAGATAGCTAAAGTAGTGAT 58.057 34.615 13.29 0.00 44.78 3.06
2475 2690 7.282675 AGAGCGTTTAGATAGCTAAAGTAGTGA 59.717 37.037 13.29 0.00 44.78 3.41
2476 2691 7.419204 AGAGCGTTTAGATAGCTAAAGTAGTG 58.581 38.462 13.29 3.53 44.78 2.74
2477 2692 7.571080 AGAGCGTTTAGATAGCTAAAGTAGT 57.429 36.000 13.29 0.00 44.78 2.73
2490 2705 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2491 2706 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2492 2707 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2493 2708 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2494 2709 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2495 2710 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2496 2711 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2497 2712 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2498 2713 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2503 2718 8.747471 GCTAATACTCCCTCCGTAAACTAATAT 58.253 37.037 0.00 0.00 0.00 1.28
2504 2719 7.177392 GGCTAATACTCCCTCCGTAAACTAATA 59.823 40.741 0.00 0.00 0.00 0.98
2505 2720 6.014755 GGCTAATACTCCCTCCGTAAACTAAT 60.015 42.308 0.00 0.00 0.00 1.73
2506 2721 5.302823 GGCTAATACTCCCTCCGTAAACTAA 59.697 44.000 0.00 0.00 0.00 2.24
2507 2722 4.829492 GGCTAATACTCCCTCCGTAAACTA 59.171 45.833 0.00 0.00 0.00 2.24
2508 2723 3.640498 GGCTAATACTCCCTCCGTAAACT 59.360 47.826 0.00 0.00 0.00 2.66
2509 2724 3.385755 TGGCTAATACTCCCTCCGTAAAC 59.614 47.826 0.00 0.00 0.00 2.01
2510 2725 3.645434 TGGCTAATACTCCCTCCGTAAA 58.355 45.455 0.00 0.00 0.00 2.01
2511 2726 3.317455 TGGCTAATACTCCCTCCGTAA 57.683 47.619 0.00 0.00 0.00 3.18
2512 2727 3.537795 ATGGCTAATACTCCCTCCGTA 57.462 47.619 0.00 0.00 0.00 4.02
2513 2728 2.400467 ATGGCTAATACTCCCTCCGT 57.600 50.000 0.00 0.00 0.00 4.69
2514 2729 5.422214 AAATATGGCTAATACTCCCTCCG 57.578 43.478 0.00 0.00 0.00 4.63
2515 2730 6.181190 GGAAAATATGGCTAATACTCCCTCC 58.819 44.000 0.00 0.00 0.00 4.30
2516 2731 6.181190 GGGAAAATATGGCTAATACTCCCTC 58.819 44.000 0.00 0.00 35.94 4.30
2517 2732 5.615261 TGGGAAAATATGGCTAATACTCCCT 59.385 40.000 16.22 0.00 37.87 4.20
2518 2733 5.887754 TGGGAAAATATGGCTAATACTCCC 58.112 41.667 0.00 0.00 37.69 4.30
2519 2734 7.121315 GTGATGGGAAAATATGGCTAATACTCC 59.879 40.741 0.00 0.00 0.00 3.85
2520 2735 7.885399 AGTGATGGGAAAATATGGCTAATACTC 59.115 37.037 0.00 0.00 0.00 2.59
2521 2736 7.667219 CAGTGATGGGAAAATATGGCTAATACT 59.333 37.037 0.00 0.00 0.00 2.12
2522 2737 7.448469 ACAGTGATGGGAAAATATGGCTAATAC 59.552 37.037 0.00 0.00 0.00 1.89
2523 2738 7.448161 CACAGTGATGGGAAAATATGGCTAATA 59.552 37.037 0.00 0.00 0.00 0.98
2524 2739 6.266103 CACAGTGATGGGAAAATATGGCTAAT 59.734 38.462 0.00 0.00 0.00 1.73
2566 2781 4.663636 CCACAAGGTCTCGAATACAAAC 57.336 45.455 0.00 0.00 0.00 2.93
2795 3022 9.410556 CACAAGGTCTTCAATACAAATTTAAGG 57.589 33.333 0.00 0.00 30.46 2.69
2990 3229 3.643237 ACGACTCCTAATGGAATGAGGA 58.357 45.455 0.00 0.00 42.66 3.71
3003 3242 2.159282 CGTTAGCATTGGTACGACTCCT 60.159 50.000 10.34 0.00 0.00 3.69
3120 3371 7.280356 ACTCACACTCAGTAAACAAATAGGTT 58.720 34.615 0.00 0.00 0.00 3.50
3158 3410 9.151471 TGCTAAGTCTATTCATTGACACTTTAC 57.849 33.333 4.54 0.00 35.46 2.01
3168 3420 7.168219 TCACCACTTTGCTAAGTCTATTCATT 58.832 34.615 10.73 0.00 42.67 2.57


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

AutoCloner maintained by Alex Coulton.