Multiple sequence alignment - TraesCS3A01G394700

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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 TraesCS3A01G394700 chr3A 100.000 3462 0 0 1 3462 642157665 642161126 0.000000e+00 6394
1 TraesCS3A01G394700 chr3A 93.407 91 6 0 2993 3083 427762740 427762650 6.030000e-28 135
2 TraesCS3A01G394700 chr3B 90.107 1587 71 30 1904 3462 665258615 665260143 0.000000e+00 1982
3 TraesCS3A01G394700 chr3B 80.000 1150 97 61 1 1098 665256516 665257584 0.000000e+00 726
4 TraesCS3A01G394700 chr3B 81.323 771 80 33 1178 1909 665257837 665258582 5.010000e-158 568
5 TraesCS3A01G394700 chr3B 94.318 88 5 0 2995 3082 372246297 372246384 6.030000e-28 135
6 TraesCS3A01G394700 chr3D 83.510 1977 165 88 1 1909 503855751 503857634 0.000000e+00 1696
7 TraesCS3A01G394700 chr3D 94.112 1087 46 12 1920 2993 503857690 503858771 0.000000e+00 1637
8 TraesCS3A01G394700 chr3D 86.375 389 23 4 3078 3460 503858781 503859145 6.960000e-107 398
9 TraesCS3A01G394700 chr5B 96.703 91 3 0 2993 3083 162772863 162772773 5.980000e-33 152
10 TraesCS3A01G394700 chr5B 90.654 107 8 2 2982 3088 51965508 51965404 1.300000e-29 141
11 TraesCS3A01G394700 chr6B 95.455 88 4 0 2993 3080 713960524 713960611 1.300000e-29 141
12 TraesCS3A01G394700 chr2D 95.402 87 4 0 2995 3081 643235908 643235822 4.660000e-29 139
13 TraesCS3A01G394700 chr2B 90.476 105 8 2 2995 3099 167084528 167084630 1.680000e-28 137
14 TraesCS3A01G394700 chr4A 88.496 113 11 2 2978 3089 214314521 214314410 6.030000e-28 135


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 TraesCS3A01G394700 chr3A 642157665 642161126 3461 False 6394.000000 6394 100.000 1 3462 1 chr3A.!!$F1 3461
1 TraesCS3A01G394700 chr3B 665256516 665260143 3627 False 1092.000000 1982 83.810 1 3462 3 chr3B.!!$F2 3461
2 TraesCS3A01G394700 chr3D 503855751 503859145 3394 False 1243.666667 1696 87.999 1 3460 3 chr3D.!!$F1 3459

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
867 941 0.107703 TAGCAACATTCCTGCCTCCG 60.108 55.0 0.0 0.0 40.86 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2525 2977 0.035317 AGTTGCAGCAGATGTCGGAA 59.965 50.0 2.55 0.0 0.0 4.3 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
102 103 1.599542 GCCTTGTTACGAGATGATGCC 59.400 52.381 0.31 0.00 0.00 4.40
104 105 3.126831 CCTTGTTACGAGATGATGCCTC 58.873 50.000 0.31 0.00 0.00 4.70
108 109 3.701542 TGTTACGAGATGATGCCTCTCTT 59.298 43.478 0.00 0.00 37.57 2.85
109 110 4.202060 TGTTACGAGATGATGCCTCTCTTC 60.202 45.833 0.00 0.00 37.57 2.87
110 111 1.686052 ACGAGATGATGCCTCTCTTCC 59.314 52.381 0.00 0.00 37.57 3.46
111 112 1.000731 CGAGATGATGCCTCTCTTCCC 59.999 57.143 0.00 0.00 37.57 3.97
112 113 2.328319 GAGATGATGCCTCTCTTCCCT 58.672 52.381 0.00 0.00 36.91 4.20
113 114 2.705127 GAGATGATGCCTCTCTTCCCTT 59.295 50.000 0.00 0.00 36.91 3.95
152 153 4.729595 ACCGTTTGTTCTCTTTTGTCAAC 58.270 39.130 0.00 0.00 0.00 3.18
226 237 1.153745 CGTTCTTCAGGGAGGCTCG 60.154 63.158 8.69 0.00 0.00 5.03
262 273 5.817816 AGGAGATTTATTTACTTGCTCACGG 59.182 40.000 0.00 0.00 0.00 4.94
290 301 1.001764 TGCTTGCTCATCCAGGTGG 60.002 57.895 0.00 0.00 0.00 4.61
335 346 1.463831 CTGATTATCATCGGCTGCTGC 59.536 52.381 7.10 7.10 38.76 5.25
351 362 2.435059 GCCTCTGCGTGGAAGGAC 60.435 66.667 0.00 0.00 0.00 3.85
352 363 2.125912 CCTCTGCGTGGAAGGACG 60.126 66.667 0.00 0.00 42.42 4.79
416 438 4.499188 CCAACATGAATGGATGCATGAGAC 60.499 45.833 13.65 0.00 43.43 3.36
417 439 4.166246 ACATGAATGGATGCATGAGACT 57.834 40.909 13.65 0.00 43.43 3.24
419 441 3.639672 TGAATGGATGCATGAGACTGT 57.360 42.857 2.46 0.00 0.00 3.55
420 442 3.275999 TGAATGGATGCATGAGACTGTG 58.724 45.455 2.46 0.00 0.00 3.66
422 444 2.685850 TGGATGCATGAGACTGTGAG 57.314 50.000 2.46 0.00 0.00 3.51
423 445 2.181975 TGGATGCATGAGACTGTGAGA 58.818 47.619 2.46 0.00 0.00 3.27
424 446 2.167900 TGGATGCATGAGACTGTGAGAG 59.832 50.000 2.46 0.00 0.00 3.20
425 447 2.483363 GGATGCATGAGACTGTGAGAGG 60.483 54.545 2.46 0.00 0.00 3.69
426 448 0.900421 TGCATGAGACTGTGAGAGGG 59.100 55.000 0.00 0.00 0.00 4.30
436 458 2.106684 ACTGTGAGAGGGAAAAAGGACC 59.893 50.000 0.00 0.00 0.00 4.46
474 496 2.266055 GACAGCACGGAGGAAGGG 59.734 66.667 0.00 0.00 0.00 3.95
475 497 3.959991 GACAGCACGGAGGAAGGGC 62.960 68.421 0.00 0.00 0.00 5.19
510 532 2.022129 CACGTGCTGTCCCGTTCTC 61.022 63.158 0.82 0.00 34.59 2.87
526 548 2.513666 TCCGCACGGGATGATTGC 60.514 61.111 9.58 0.00 40.94 3.56
535 572 4.619140 GATGATTGCGCGGCAGGC 62.619 66.667 8.83 3.27 40.61 4.85
548 585 2.875711 CAGGCGCGCGAATTTTGG 60.876 61.111 37.18 10.84 0.00 3.28
559 596 2.719798 CGAATTTTGGCATCATCCGTC 58.280 47.619 0.00 0.00 0.00 4.79
561 598 1.024271 ATTTTGGCATCATCCGTCGG 58.976 50.000 4.39 4.39 0.00 4.79
564 601 2.189521 GGCATCATCCGTCGGGTT 59.810 61.111 12.29 0.00 33.83 4.11
568 606 1.006832 CATCATCCGTCGGGTTTCAC 58.993 55.000 12.29 0.00 33.83 3.18
569 607 0.107848 ATCATCCGTCGGGTTTCACC 60.108 55.000 12.29 0.00 37.60 4.02
574 612 1.666872 CGTCGGGTTTCACCTCACC 60.667 63.158 0.00 0.00 38.64 4.02
586 624 4.803426 CTCACCTGGTCGAGCGGC 62.803 72.222 18.04 0.00 0.00 6.53
678 724 0.450184 CGGTTATTTGTGGCGGGAAG 59.550 55.000 0.00 0.00 0.00 3.46
714 760 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
715 761 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
716 762 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
717 763 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
718 764 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
719 765 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
720 766 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
721 767 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
722 768 4.179599 GAGGGAGGGAGGGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
867 941 0.107703 TAGCAACATTCCTGCCTCCG 60.108 55.000 0.00 0.00 40.86 4.63
879 957 3.213402 CCTCCGTCTCGCTCTCCC 61.213 72.222 0.00 0.00 0.00 4.30
882 960 1.720694 CTCCGTCTCGCTCTCCCTTC 61.721 65.000 0.00 0.00 0.00 3.46
894 972 0.886563 CTCCCTTCCTGCTTTGCTTG 59.113 55.000 0.00 0.00 0.00 4.01
906 984 3.057596 TGCTTTGCTTGTTATTCCTTCCG 60.058 43.478 0.00 0.00 0.00 4.30
942 1026 2.125350 CTGCCGTGGAAGAGGAGC 60.125 66.667 0.00 0.00 0.00 4.70
948 1032 1.301293 GTGGAAGAGGAGCAAGGGG 59.699 63.158 0.00 0.00 0.00 4.79
1059 1143 1.202087 CGTACGTCCTCTGCTTCTCTG 60.202 57.143 7.22 0.00 0.00 3.35
1060 1144 0.811915 TACGTCCTCTGCTTCTCTGC 59.188 55.000 0.00 0.00 0.00 4.26
1061 1145 0.897863 ACGTCCTCTGCTTCTCTGCT 60.898 55.000 0.00 0.00 0.00 4.24
1062 1146 0.246086 CGTCCTCTGCTTCTCTGCTT 59.754 55.000 0.00 0.00 0.00 3.91
1063 1147 1.735369 CGTCCTCTGCTTCTCTGCTTC 60.735 57.143 0.00 0.00 0.00 3.86
1064 1148 1.550072 GTCCTCTGCTTCTCTGCTTCT 59.450 52.381 0.00 0.00 0.00 2.85
1065 1149 1.824230 TCCTCTGCTTCTCTGCTTCTC 59.176 52.381 0.00 0.00 0.00 2.87
1066 1150 1.826720 CCTCTGCTTCTCTGCTTCTCT 59.173 52.381 0.00 0.00 0.00 3.10
1067 1151 2.417651 CCTCTGCTTCTCTGCTTCTCTG 60.418 54.545 0.00 0.00 0.00 3.35
1089 1173 1.230635 TTGCTTGCTGCGTCTTCCTC 61.231 55.000 0.00 0.00 46.63 3.71
1098 1182 1.009389 GCGTCTTCCTCGTCTTGGTG 61.009 60.000 0.00 0.00 0.00 4.17
1099 1183 1.009389 CGTCTTCCTCGTCTTGGTGC 61.009 60.000 0.00 0.00 0.00 5.01
1111 1195 0.609662 CTTGGTGCATGAAAAGGGGG 59.390 55.000 0.00 0.00 0.00 5.40
1119 1203 3.007831 TGCATGAAAAGGGGGATTGTTTC 59.992 43.478 0.00 0.00 0.00 2.78
1136 1220 5.978934 TGTTTCGATGATGATCATGACAG 57.021 39.130 14.30 2.57 37.20 3.51
1140 1224 6.594284 TTCGATGATGATCATGACAGAAAC 57.406 37.500 14.30 0.00 37.20 2.78
1148 1232 7.446319 TGATGATCATGACAGAAACAGAGTTTT 59.554 33.333 14.30 0.00 0.00 2.43
1176 1429 5.465532 TTGCTTCTTGTTGCCATGATTTA 57.534 34.783 0.00 0.00 0.00 1.40
1209 1470 2.457598 ACGATCTTGAGCCTGGTCTAA 58.542 47.619 0.00 0.00 0.00 2.10
1233 1499 1.003233 GGAGGAAAGAGCGGGAGAAAA 59.997 52.381 0.00 0.00 0.00 2.29
1244 1510 2.097629 GCGGGAGAAAACAGATTTAGGC 59.902 50.000 0.00 0.00 0.00 3.93
1259 1525 3.398954 TTAGGCGTTGATTTGAATCGC 57.601 42.857 0.00 0.00 44.95 4.58
1300 1566 0.622665 AAGATGCCTCCCTGGTCTTG 59.377 55.000 0.00 0.00 38.35 3.02
1320 1586 2.165437 TGTTCGCCTTCCATATTTTGCC 59.835 45.455 0.00 0.00 0.00 4.52
1321 1587 1.021202 TCGCCTTCCATATTTTGCCG 58.979 50.000 0.00 0.00 0.00 5.69
1326 1592 2.618709 CCTTCCATATTTTGCCGTCTCC 59.381 50.000 0.00 0.00 0.00 3.71
1327 1593 3.278574 CTTCCATATTTTGCCGTCTCCA 58.721 45.455 0.00 0.00 0.00 3.86
1329 1595 3.213506 TCCATATTTTGCCGTCTCCATG 58.786 45.455 0.00 0.00 0.00 3.66
1344 1610 4.098654 GTCTCCATGCACTGTATGACTAGT 59.901 45.833 8.57 0.00 0.00 2.57
1345 1611 4.711846 TCTCCATGCACTGTATGACTAGTT 59.288 41.667 8.57 0.00 0.00 2.24
1346 1612 5.187772 TCTCCATGCACTGTATGACTAGTTT 59.812 40.000 8.57 0.00 0.00 2.66
1347 1613 6.379988 TCTCCATGCACTGTATGACTAGTTTA 59.620 38.462 8.57 0.00 0.00 2.01
1348 1614 6.941857 TCCATGCACTGTATGACTAGTTTAA 58.058 36.000 8.57 0.00 0.00 1.52
1349 1615 7.390823 TCCATGCACTGTATGACTAGTTTAAA 58.609 34.615 8.57 0.00 0.00 1.52
1350 1616 7.333423 TCCATGCACTGTATGACTAGTTTAAAC 59.667 37.037 10.47 10.47 0.00 2.01
1364 1630 7.139392 ACTAGTTTAAACTTTAAAGCAGCAGC 58.861 34.615 25.07 0.00 40.37 5.25
1388 1654 6.745474 GCCTTTGCATAACTGGGTATCTATCT 60.745 42.308 0.00 0.00 37.47 1.98
1389 1655 7.527196 GCCTTTGCATAACTGGGTATCTATCTA 60.527 40.741 0.00 0.00 37.47 1.98
1390 1656 8.543774 CCTTTGCATAACTGGGTATCTATCTAT 58.456 37.037 0.00 0.00 0.00 1.98
1391 1657 9.593134 CTTTGCATAACTGGGTATCTATCTATC 57.407 37.037 0.00 0.00 0.00 2.08
1392 1658 8.901472 TTGCATAACTGGGTATCTATCTATCT 57.099 34.615 0.00 0.00 0.00 1.98
1393 1659 9.990868 TTGCATAACTGGGTATCTATCTATCTA 57.009 33.333 0.00 0.00 0.00 1.98
1500 1834 1.075482 CCACCTGGGATGTGTGCTT 59.925 57.895 0.00 0.00 40.01 3.91
1501 1835 0.540365 CCACCTGGGATGTGTGCTTT 60.540 55.000 0.00 0.00 40.01 3.51
1506 1840 1.464608 CTGGGATGTGTGCTTTGTACG 59.535 52.381 0.00 0.00 0.00 3.67
1553 1889 2.550180 GTTCCTGTGAAACTCTCCAAGC 59.450 50.000 0.00 0.00 38.04 4.01
1625 1990 5.462530 TCTGAACATTGGAAACTCGACTA 57.537 39.130 0.00 0.00 0.00 2.59
1677 2064 2.440796 TTCCGGTCCGTCGCCTAT 60.441 61.111 11.06 0.00 0.00 2.57
1758 2145 0.601558 ACGAGCTTCGAGCAAAGGTA 59.398 50.000 11.64 0.00 45.56 3.08
1761 2148 1.732809 GAGCTTCGAGCAAAGGTAACC 59.267 52.381 9.09 0.00 45.56 2.85
1764 2151 2.767505 CTTCGAGCAAAGGTAACCACT 58.232 47.619 0.00 0.00 37.17 4.00
1776 2163 2.140717 GTAACCACTCAACCGGTTCAG 58.859 52.381 17.61 17.61 44.40 3.02
1801 2188 1.553248 TGATGATTCCGTTCCGTTCCT 59.447 47.619 0.00 0.00 0.00 3.36
1838 2225 0.326264 AGATTGCTGACCCACCTGTC 59.674 55.000 0.00 0.00 35.77 3.51
1961 2396 7.447594 ACATGATCTTTTCTTTCCTGCAAAAT 58.552 30.769 0.00 0.00 0.00 1.82
2118 2562 3.653836 TCTTGGGTAGGCACCTTTCTTTA 59.346 43.478 0.00 0.00 45.04 1.85
2119 2563 3.428413 TGGGTAGGCACCTTTCTTTAC 57.572 47.619 0.00 0.00 45.04 2.01
2120 2564 2.712087 TGGGTAGGCACCTTTCTTTACA 59.288 45.455 0.00 0.00 45.04 2.41
2121 2565 3.332485 TGGGTAGGCACCTTTCTTTACAT 59.668 43.478 0.00 0.00 45.04 2.29
2122 2566 3.694566 GGGTAGGCACCTTTCTTTACATG 59.305 47.826 0.00 0.00 45.04 3.21
2225 2670 0.251121 CCACATGTACACCAAGGGCA 60.251 55.000 0.00 0.00 0.00 5.36
2439 2885 2.437413 GAACCAATGTTCCCTCCTGTC 58.563 52.381 0.00 0.00 44.20 3.51
2476 2922 2.135664 CGTAGCTAACCGGAGAATGG 57.864 55.000 9.46 0.00 0.00 3.16
2477 2923 1.407979 CGTAGCTAACCGGAGAATGGT 59.592 52.381 9.46 1.37 42.98 3.55
2514 2966 5.712084 TCTTCTACTACTTCTCTAGGGCA 57.288 43.478 0.00 0.00 0.00 5.36
2525 2977 0.764890 TCTAGGGCAGCCGCATAAAT 59.235 50.000 5.00 0.00 41.24 1.40
2569 3021 0.601057 TCGTTCGAGTTGGCAGATCA 59.399 50.000 0.00 0.00 0.00 2.92
2588 3040 4.783764 TCACGGTATAGCACATATGGAG 57.216 45.455 7.80 0.17 0.00 3.86
2612 3064 3.458163 CCCGGGTTCGCTGCTCTA 61.458 66.667 14.18 0.00 34.56 2.43
2648 3100 9.429359 CTTCTTCGAGGCTGATGTATAAATAAT 57.571 33.333 0.00 0.00 0.00 1.28
2768 3220 9.520515 TCTGGAATATTTTACTCTGAAAGCTTT 57.479 29.630 12.53 12.53 0.00 3.51
2784 3236 3.220110 AGCTTTGCTGATGGACATATGG 58.780 45.455 7.80 0.00 37.57 2.74
2844 3296 4.963953 CGGCGAATGTGAATACAATCTTTC 59.036 41.667 0.00 0.00 40.84 2.62
2967 3420 4.994217 GGCTCTCCTTAGACTGATATTTGC 59.006 45.833 0.00 0.00 0.00 3.68
2993 3447 4.937201 TTGACACATGCCTATCGAGTAT 57.063 40.909 0.00 0.00 0.00 2.12
3002 3456 4.333690 TGCCTATCGAGTATTACTCCCTC 58.666 47.826 16.36 3.33 42.12 4.30
3013 3467 7.980099 CGAGTATTACTCCCTCTGTAAACAAAT 59.020 37.037 16.36 0.00 42.12 2.32
3075 3529 5.932883 GCTCTTATATTTCTTTACGGAGGGG 59.067 44.000 0.00 0.00 0.00 4.79
3123 3583 0.613777 AAAGACTAGCCCGGAACCAG 59.386 55.000 0.73 0.00 0.00 4.00
3130 3590 3.003173 CCCGGAACCAGCAGAGGA 61.003 66.667 0.73 0.00 0.00 3.71
3164 3624 0.693622 TATGGGGCACGTTCAAAGGA 59.306 50.000 0.00 0.00 0.00 3.36
3204 3688 5.902431 AGATAGAAGATGCTTGGAAGTACCT 59.098 40.000 0.00 0.00 39.86 3.08
3206 3690 3.054802 AGAAGATGCTTGGAAGTACCTGG 60.055 47.826 0.00 0.00 39.86 4.45
3207 3691 2.551270 AGATGCTTGGAAGTACCTGGA 58.449 47.619 0.00 0.00 39.86 3.86
3208 3692 3.118531 AGATGCTTGGAAGTACCTGGAT 58.881 45.455 0.00 0.00 39.86 3.41
3209 3693 3.525199 AGATGCTTGGAAGTACCTGGATT 59.475 43.478 0.00 0.00 39.86 3.01
3210 3694 4.721776 AGATGCTTGGAAGTACCTGGATTA 59.278 41.667 0.00 0.00 39.86 1.75
3211 3695 4.487714 TGCTTGGAAGTACCTGGATTAG 57.512 45.455 0.00 0.00 39.86 1.73
3212 3696 4.101114 TGCTTGGAAGTACCTGGATTAGA 58.899 43.478 0.00 0.00 39.86 2.10
3213 3697 4.534500 TGCTTGGAAGTACCTGGATTAGAA 59.466 41.667 0.00 0.00 39.86 2.10
3214 3698 5.119694 GCTTGGAAGTACCTGGATTAGAAG 58.880 45.833 0.00 0.14 39.86 2.85
3215 3699 5.104900 GCTTGGAAGTACCTGGATTAGAAGA 60.105 44.000 0.00 0.00 39.86 2.87
3216 3700 6.408662 GCTTGGAAGTACCTGGATTAGAAGAT 60.409 42.308 0.00 0.00 39.86 2.40
3217 3701 7.510675 TTGGAAGTACCTGGATTAGAAGATT 57.489 36.000 0.00 0.00 39.86 2.40
3218 3702 6.889198 TGGAAGTACCTGGATTAGAAGATTG 58.111 40.000 0.00 0.00 39.86 2.67
3219 3703 6.126768 TGGAAGTACCTGGATTAGAAGATTGG 60.127 42.308 0.00 0.00 39.86 3.16
3220 3704 6.099845 GGAAGTACCTGGATTAGAAGATTGGA 59.900 42.308 0.00 0.00 35.41 3.53
3221 3705 6.739331 AGTACCTGGATTAGAAGATTGGAG 57.261 41.667 0.00 0.00 0.00 3.86
3222 3706 6.444704 AGTACCTGGATTAGAAGATTGGAGA 58.555 40.000 0.00 0.00 0.00 3.71
3223 3707 7.079048 AGTACCTGGATTAGAAGATTGGAGAT 58.921 38.462 0.00 0.00 0.00 2.75
3224 3708 8.235230 AGTACCTGGATTAGAAGATTGGAGATA 58.765 37.037 0.00 0.00 0.00 1.98
3225 3709 7.309770 ACCTGGATTAGAAGATTGGAGATAC 57.690 40.000 0.00 0.00 0.00 2.24
3226 3710 6.271159 ACCTGGATTAGAAGATTGGAGATACC 59.729 42.308 0.00 0.00 39.54 2.73
3251 3735 5.248380 ACAGAAAGGTGGCTCTTTTCTAT 57.752 39.130 21.27 11.60 46.07 1.98
3434 3919 1.334689 CGAAAGTGCCGGGAAAAAGTC 60.335 52.381 2.18 0.00 0.00 3.01
3441 3926 0.447801 CCGGGAAAAAGTCATGCTCG 59.552 55.000 0.00 0.00 0.00 5.03
3442 3927 0.447801 CGGGAAAAAGTCATGCTCGG 59.552 55.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 4.040952 TGACTGAAAAGGAAGGGAAGAGAG 59.959 45.833 0.00 0.00 0.00 3.20
104 105 4.357918 TGACTGAAAAGGAAGGGAAGAG 57.642 45.455 0.00 0.00 0.00 2.85
108 109 2.174639 TGCTTGACTGAAAAGGAAGGGA 59.825 45.455 0.00 0.00 0.00 4.20
109 110 2.586425 TGCTTGACTGAAAAGGAAGGG 58.414 47.619 0.00 0.00 0.00 3.95
110 111 3.243535 GGTTGCTTGACTGAAAAGGAAGG 60.244 47.826 2.50 0.00 35.91 3.46
111 112 3.548818 CGGTTGCTTGACTGAAAAGGAAG 60.549 47.826 2.50 0.00 35.91 3.46
112 113 2.357637 CGGTTGCTTGACTGAAAAGGAA 59.642 45.455 0.00 0.00 33.25 3.36
113 114 1.946768 CGGTTGCTTGACTGAAAAGGA 59.053 47.619 0.00 0.00 0.00 3.36
152 153 2.179517 GAGCAGAGGACCGTCGTG 59.820 66.667 0.00 0.00 0.00 4.35
159 160 1.274728 ACATGTCAGTGAGCAGAGGAC 59.725 52.381 0.00 0.00 0.00 3.85
290 301 1.045407 GGACAAAAAGGAACCCACCC 58.955 55.000 0.00 0.00 0.00 4.61
335 346 2.125912 CGTCCTTCCACGCAGAGG 60.126 66.667 0.00 0.00 40.53 3.69
345 356 2.185608 GAGGCCTCTGCGTCCTTC 59.814 66.667 26.25 0.00 44.61 3.46
395 417 4.338400 CAGTCTCATGCATCCATTCATGTT 59.662 41.667 0.00 0.00 40.54 2.71
416 438 2.784347 GGTCCTTTTTCCCTCTCACAG 58.216 52.381 0.00 0.00 0.00 3.66
417 439 1.071699 CGGTCCTTTTTCCCTCTCACA 59.928 52.381 0.00 0.00 0.00 3.58
419 441 0.690762 CCGGTCCTTTTTCCCTCTCA 59.309 55.000 0.00 0.00 0.00 3.27
420 442 0.677098 GCCGGTCCTTTTTCCCTCTC 60.677 60.000 1.90 0.00 0.00 3.20
422 444 1.677966 GGCCGGTCCTTTTTCCCTC 60.678 63.158 1.90 0.00 0.00 4.30
423 445 2.439245 GGCCGGTCCTTTTTCCCT 59.561 61.111 1.90 0.00 0.00 4.20
424 446 2.116556 TGGCCGGTCCTTTTTCCC 59.883 61.111 2.12 0.00 35.26 3.97
425 447 2.273179 GGTGGCCGGTCCTTTTTCC 61.273 63.158 2.12 0.00 35.26 3.13
426 448 1.529713 TGGTGGCCGGTCCTTTTTC 60.530 57.895 2.12 0.00 35.26 2.29
456 478 2.125912 CCTTCCTCCGTGCTGTCG 60.126 66.667 0.00 0.00 0.00 4.35
474 496 2.411547 CGTGAGTGAAAATGAACCTCGC 60.412 50.000 0.00 0.00 0.00 5.03
475 497 2.800544 ACGTGAGTGAAAATGAACCTCG 59.199 45.455 0.00 0.00 46.97 4.63
535 572 0.866906 ATGATGCCAAAATTCGCGCG 60.867 50.000 26.76 26.76 0.00 6.86
536 573 0.848305 GATGATGCCAAAATTCGCGC 59.152 50.000 0.00 0.00 0.00 6.86
538 575 1.202290 ACGGATGATGCCAAAATTCGC 60.202 47.619 0.00 0.00 0.00 4.70
539 576 2.719798 GACGGATGATGCCAAAATTCG 58.280 47.619 0.00 0.00 0.00 3.34
540 577 2.541588 CCGACGGATGATGCCAAAATTC 60.542 50.000 8.64 0.00 0.00 2.17
543 580 1.029408 CCCGACGGATGATGCCAAAA 61.029 55.000 17.49 0.00 0.00 2.44
548 585 0.742990 TGAAACCCGACGGATGATGC 60.743 55.000 17.49 0.00 0.00 3.91
564 601 1.816863 GCTCGACCAGGTGAGGTGAA 61.817 60.000 16.43 0.00 43.38 3.18
568 606 4.135153 CCGCTCGACCAGGTGAGG 62.135 72.222 16.43 3.17 32.78 3.86
569 607 4.803426 GCCGCTCGACCAGGTGAG 62.803 72.222 0.00 5.74 35.30 3.51
586 624 3.947841 CGCTCCGCTCCTCGAGAG 61.948 72.222 15.71 10.58 46.29 3.20
631 669 6.176896 GCTCCTAATTAAATCAGATCCCCTC 58.823 44.000 0.00 0.00 0.00 4.30
636 674 5.257262 GGGGGCTCCTAATTAAATCAGATC 58.743 45.833 0.52 0.00 0.00 2.75
637 675 4.263506 CGGGGGCTCCTAATTAAATCAGAT 60.264 45.833 0.52 0.00 0.00 2.90
638 676 3.072476 CGGGGGCTCCTAATTAAATCAGA 59.928 47.826 0.52 0.00 0.00 3.27
639 677 3.412386 CGGGGGCTCCTAATTAAATCAG 58.588 50.000 0.52 0.00 0.00 2.90
640 678 2.107552 CCGGGGGCTCCTAATTAAATCA 59.892 50.000 0.52 0.00 0.00 2.57
702 748 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
703 749 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
802 876 2.244651 GGGCGTGGAATCGGATTCG 61.245 63.158 21.03 13.52 40.17 3.34
867 941 1.813192 CAGGAAGGGAGAGCGAGAC 59.187 63.158 0.00 0.00 0.00 3.36
879 957 4.219288 AGGAATAACAAGCAAAGCAGGAAG 59.781 41.667 0.00 0.00 0.00 3.46
882 960 4.488879 GAAGGAATAACAAGCAAAGCAGG 58.511 43.478 0.00 0.00 0.00 4.85
894 972 0.746923 AAGCGGGCGGAAGGAATAAC 60.747 55.000 0.00 0.00 0.00 1.89
923 1001 3.003173 TCCTCTTCCACGGCAGGG 61.003 66.667 0.00 0.00 0.00 4.45
930 1014 1.201429 TCCCCTTGCTCCTCTTCCAC 61.201 60.000 0.00 0.00 0.00 4.02
942 1026 2.684499 GGCCCTCTTCCTCCCCTTG 61.684 68.421 0.00 0.00 0.00 3.61
1059 1143 1.197264 CAGCAAGCAAGACAGAGAAGC 59.803 52.381 0.00 0.00 0.00 3.86
1060 1144 1.197264 GCAGCAAGCAAGACAGAGAAG 59.803 52.381 0.00 0.00 44.79 2.85
1061 1145 1.233019 GCAGCAAGCAAGACAGAGAA 58.767 50.000 0.00 0.00 44.79 2.87
1062 1146 0.947660 CGCAGCAAGCAAGACAGAGA 60.948 55.000 0.00 0.00 46.13 3.10
1063 1147 1.226686 ACGCAGCAAGCAAGACAGAG 61.227 55.000 0.00 0.00 46.13 3.35
1064 1148 1.224069 GACGCAGCAAGCAAGACAGA 61.224 55.000 0.00 0.00 46.13 3.41
1065 1149 1.206072 GACGCAGCAAGCAAGACAG 59.794 57.895 0.00 0.00 46.13 3.51
1066 1150 0.815213 AAGACGCAGCAAGCAAGACA 60.815 50.000 0.00 0.00 46.13 3.41
1067 1151 0.110464 GAAGACGCAGCAAGCAAGAC 60.110 55.000 0.00 0.00 46.13 3.01
1089 1173 1.068333 CCCTTTTCATGCACCAAGACG 60.068 52.381 0.00 0.00 0.00 4.18
1098 1182 3.599343 GAAACAATCCCCCTTTTCATGC 58.401 45.455 0.00 0.00 0.00 4.06
1099 1183 3.509575 TCGAAACAATCCCCCTTTTCATG 59.490 43.478 0.00 0.00 0.00 3.07
1111 1195 6.951643 TGTCATGATCATCATCGAAACAATC 58.048 36.000 4.86 0.00 34.28 2.67
1119 1203 5.751990 TCTGTTTCTGTCATGATCATCATCG 59.248 40.000 4.86 0.00 34.28 3.84
1163 1255 6.039047 ACTGATCACAGATAAATCATGGCAAC 59.961 38.462 0.00 0.00 46.03 4.17
1196 1457 0.118346 TCCCCTTTAGACCAGGCTCA 59.882 55.000 0.00 0.00 0.00 4.26
1209 1470 2.301738 CCCGCTCTTTCCTCCCCTT 61.302 63.158 0.00 0.00 0.00 3.95
1233 1499 5.957842 TTCAAATCAACGCCTAAATCTGT 57.042 34.783 0.00 0.00 0.00 3.41
1244 1510 9.697250 TTAGTTTAATAGCGATTCAAATCAACG 57.303 29.630 0.00 0.00 35.11 4.10
1300 1566 2.809446 GGCAAAATATGGAAGGCGAAC 58.191 47.619 0.00 0.00 0.00 3.95
1320 1586 2.159184 AGTCATACAGTGCATGGAGACG 60.159 50.000 3.47 0.00 34.91 4.18
1321 1587 3.533606 AGTCATACAGTGCATGGAGAC 57.466 47.619 3.47 0.00 0.00 3.36
1326 1592 8.256611 AGTTTAAACTAGTCATACAGTGCATG 57.743 34.615 19.26 0.00 37.52 4.06
1327 1593 8.848474 AAGTTTAAACTAGTCATACAGTGCAT 57.152 30.769 20.83 0.00 38.57 3.96
1344 1610 5.529581 AGGCTGCTGCTTTAAAGTTTAAA 57.470 34.783 17.62 17.62 39.59 1.52
1345 1611 5.529581 AAGGCTGCTGCTTTAAAGTTTAA 57.470 34.783 16.38 3.88 36.71 1.52
1346 1612 5.288804 CAAAGGCTGCTGCTTTAAAGTTTA 58.711 37.500 16.38 3.42 37.52 2.01
1347 1613 4.122046 CAAAGGCTGCTGCTTTAAAGTTT 58.878 39.130 16.38 4.09 37.52 2.66
1348 1614 3.721035 CAAAGGCTGCTGCTTTAAAGTT 58.279 40.909 16.38 0.00 37.52 2.66
1349 1615 3.375782 CAAAGGCTGCTGCTTTAAAGT 57.624 42.857 16.38 0.00 37.52 2.66
1364 1630 6.773638 AGATAGATACCCAGTTATGCAAAGG 58.226 40.000 0.00 0.00 0.00 3.11
1412 1678 9.350357 CTTGTTGAATTTATGTCAAAGGAGATG 57.650 33.333 0.00 0.00 36.77 2.90
1418 1684 9.918630 ATCTTCCTTGTTGAATTTATGTCAAAG 57.081 29.630 0.00 0.00 36.77 2.77
1553 1889 5.941733 TGAAAATCACATCAGAATCAACCG 58.058 37.500 0.00 0.00 0.00 4.44
1625 1990 4.705023 CGTCCCCTGTAATTCCTGAAAAAT 59.295 41.667 0.00 0.00 0.00 1.82
1677 2064 2.190313 CTCCTTATGCAGGCGCCA 59.810 61.111 31.54 8.70 43.55 5.69
1721 2108 2.125512 CGGCGAGTTCCTTCTGGG 60.126 66.667 0.00 0.00 0.00 4.45
1761 2148 0.532862 AGTGCTGAACCGGTTGAGTG 60.533 55.000 30.49 16.01 0.00 3.51
1764 2151 0.179234 TCAAGTGCTGAACCGGTTGA 59.821 50.000 27.87 17.00 0.00 3.18
1776 2163 2.832672 GGAACGGAATCATCAAGTGC 57.167 50.000 0.00 0.00 0.00 4.40
1801 2188 6.890558 GCAATCTCTTTTGCTAAAATTGCAA 58.109 32.000 24.07 0.00 46.66 4.08
1875 2262 1.954382 TCACCATTCGGTATCTCCTCG 59.046 52.381 0.00 0.00 46.94 4.63
1936 2368 6.409524 TTTGCAGGAAAGAAAAGATCATGT 57.590 33.333 0.00 0.00 0.00 3.21
1945 2377 8.878769 GTTACTTTTGATTTTGCAGGAAAGAAA 58.121 29.630 0.00 0.00 0.00 2.52
1948 2380 7.769272 TGTTACTTTTGATTTTGCAGGAAAG 57.231 32.000 0.00 0.00 0.00 2.62
1961 2396 9.558648 CATCGAAAATGATCATGTTACTTTTGA 57.441 29.630 11.22 14.56 0.00 2.69
1983 2418 6.292389 GAACCTATCCAAAGATTCACATCG 57.708 41.667 0.00 0.00 34.17 3.84
2225 2670 2.118403 ATGATCCTGGGGTTATCGGT 57.882 50.000 0.00 0.00 0.00 4.69
2378 2823 3.388308 CCAAATGTTGTCGGATTTTGCA 58.612 40.909 0.00 0.00 0.00 4.08
2426 2872 2.238521 GCAAATTGACAGGAGGGAACA 58.761 47.619 0.00 0.00 0.00 3.18
2439 2885 0.731417 CGCTCCTCTCCTGCAAATTG 59.269 55.000 0.00 0.00 0.00 2.32
2525 2977 0.035317 AGTTGCAGCAGATGTCGGAA 59.965 50.000 2.55 0.00 0.00 4.30
2569 3021 3.507411 ACCTCCATATGTGCTATACCGT 58.493 45.455 1.24 0.00 0.00 4.83
2768 3220 2.837498 CGAACCATATGTCCATCAGCA 58.163 47.619 1.24 0.00 0.00 4.41
2784 3236 0.789383 CGAAGCAATTGTCGGCGAAC 60.789 55.000 12.92 6.86 33.62 3.95
2967 3420 2.291465 CGATAGGCATGTGTCAATTGGG 59.709 50.000 5.42 0.00 0.00 4.12
3069 3523 3.387012 TGTATTGGTTAGTACCCCCTCC 58.613 50.000 0.00 0.00 44.35 4.30
3075 3529 9.477484 CTAATCATCACTGTATTGGTTAGTACC 57.523 37.037 11.30 0.00 45.26 3.34
3106 3560 2.359967 GCTGGTTCCGGGCTAGTCT 61.360 63.158 0.00 0.00 0.00 3.24
3164 3624 6.603997 TCTTCTATCTTCGTAGAAAAGAGCCT 59.396 38.462 0.00 0.00 45.90 4.58
3217 3701 4.506625 CCACCTTTCTGTTTGGTATCTCCA 60.507 45.833 0.00 0.00 45.60 3.86
3218 3702 4.010349 CCACCTTTCTGTTTGGTATCTCC 58.990 47.826 0.00 0.00 32.13 3.71
3219 3703 3.440522 GCCACCTTTCTGTTTGGTATCTC 59.559 47.826 0.00 0.00 32.13 2.75
3220 3704 3.074538 AGCCACCTTTCTGTTTGGTATCT 59.925 43.478 0.00 0.00 32.13 1.98
3221 3705 3.421844 AGCCACCTTTCTGTTTGGTATC 58.578 45.455 0.00 0.00 32.13 2.24
3222 3706 3.074538 AGAGCCACCTTTCTGTTTGGTAT 59.925 43.478 0.00 0.00 32.13 2.73
3223 3707 2.441750 AGAGCCACCTTTCTGTTTGGTA 59.558 45.455 0.00 0.00 32.13 3.25
3224 3708 1.215423 AGAGCCACCTTTCTGTTTGGT 59.785 47.619 0.00 0.00 33.87 3.67
3225 3709 1.986882 AGAGCCACCTTTCTGTTTGG 58.013 50.000 0.00 0.00 0.00 3.28
3226 3710 4.098501 AGAAAAGAGCCACCTTTCTGTTTG 59.901 41.667 4.88 0.00 35.50 2.93
3227 3711 4.281657 AGAAAAGAGCCACCTTTCTGTTT 58.718 39.130 4.88 0.00 35.50 2.83
3228 3712 3.903467 AGAAAAGAGCCACCTTTCTGTT 58.097 40.909 4.88 0.00 35.50 3.16
3232 3716 5.940470 TCTTCATAGAAAAGAGCCACCTTTC 59.060 40.000 0.00 0.00 35.50 2.62
3251 3735 6.305272 ACTTCCAAGCATCTTCTATCTTCA 57.695 37.500 0.00 0.00 0.00 3.02
3425 3910 2.749621 ACATCCGAGCATGACTTTTTCC 59.250 45.455 0.00 0.00 0.00 3.13
3434 3919 2.145958 CTCTGGTACATCCGAGCATG 57.854 55.000 0.00 0.00 38.20 4.06


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

AutoCloner maintained by Alex Coulton.