Multiple sequence alignment - TraesCS3B01G307200

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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 TraesCS3B01G307200 chr3B 100.000 3765 0 0 1 3765 493570120 493573884 0.000000e+00 6953.0
1 TraesCS3B01G307200 chr3B 93.506 77 4 1 3687 3763 276882586 276882661 3.070000e-21 113.0
2 TraesCS3B01G307200 chr3B 93.506 77 4 1 3687 3763 276909202 276909277 3.070000e-21 113.0
3 TraesCS3B01G307200 chr3B 100.000 33 0 0 2889 2921 390236645 390236677 1.130000e-05 62.1
4 TraesCS3B01G307200 chr7B 87.967 2435 225 42 592 3010 648440269 648442651 0.000000e+00 2811.0
5 TraesCS3B01G307200 chr7B 88.050 1364 143 15 1423 2770 286566253 286564894 0.000000e+00 1598.0
6 TraesCS3B01G307200 chr7B 80.556 540 73 21 74 590 209397980 209398510 1.640000e-103 387.0
7 TraesCS3B01G307200 chr7B 89.744 312 19 7 3163 3465 715226670 715226363 1.640000e-103 387.0
8 TraesCS3B01G307200 chr7B 94.444 72 3 1 3694 3765 715225830 715225760 3.980000e-20 110.0
9 TraesCS3B01G307200 chr7B 97.143 35 1 0 2889 2923 648442587 648442621 4.060000e-05 60.2
10 TraesCS3B01G307200 chr7D 87.911 2432 208 43 592 3010 580776658 580779016 0.000000e+00 2784.0
11 TraesCS3B01G307200 chr7D 93.770 305 19 0 1 305 477931122 477930818 3.430000e-125 459.0
12 TraesCS3B01G307200 chr7D 87.137 241 24 4 3391 3626 403269837 403269599 2.230000e-67 267.0
13 TraesCS3B01G307200 chr7D 94.937 79 3 1 3687 3765 580780007 580780084 5.110000e-24 122.0
14 TraesCS3B01G307200 chr2D 88.677 2199 218 24 592 2775 548895233 548897415 0.000000e+00 2652.0
15 TraesCS3B01G307200 chr2D 88.374 1316 134 11 1474 2770 110057575 110056260 0.000000e+00 1565.0
16 TraesCS3B01G307200 chr2D 93.169 366 23 1 3163 3526 316642584 316642219 1.540000e-148 536.0
17 TraesCS3B01G307200 chr2D 87.375 301 34 2 294 590 548894503 548894803 3.600000e-90 342.0
18 TraesCS3B01G307200 chr1B 88.448 1385 140 14 1436 2803 439538880 439537499 0.000000e+00 1653.0
19 TraesCS3B01G307200 chr1B 85.660 265 26 5 3391 3649 427879 428137 6.200000e-68 268.0
20 TraesCS3B01G307200 chr1B 85.660 265 26 5 3391 3649 435004 435262 6.200000e-68 268.0
21 TraesCS3B01G307200 chr4A 87.611 1348 148 15 1474 2803 90328553 90329899 0.000000e+00 1546.0
22 TraesCS3B01G307200 chr4A 90.100 798 78 1 592 1388 90327415 90328212 0.000000e+00 1035.0
23 TraesCS3B01G307200 chr4A 90.388 593 54 1 1 590 95389910 95389318 0.000000e+00 776.0
24 TraesCS3B01G307200 chr4A 90.219 593 52 2 1 590 90326398 90326987 0.000000e+00 769.0
25 TraesCS3B01G307200 chr3D 87.023 1364 151 18 1424 2770 189780289 189781643 0.000000e+00 1515.0
26 TraesCS3B01G307200 chr3D 90.213 797 78 0 592 1388 189779334 189780130 0.000000e+00 1040.0
27 TraesCS3B01G307200 chr3D 92.683 164 10 2 2854 3017 184668760 184668921 6.290000e-58 235.0
28 TraesCS3B01G307200 chr3D 90.909 77 6 1 3687 3763 184669891 184669966 6.650000e-18 102.0
29 TraesCS3B01G307200 chr3D 100.000 32 0 0 2889 2920 184668851 184668882 4.060000e-05 60.2
30 TraesCS3B01G307200 chr6B 86.784 1362 132 20 1474 2788 172268715 172267355 0.000000e+00 1474.0
31 TraesCS3B01G307200 chr6B 90.375 800 73 3 592 1388 172269854 172269056 0.000000e+00 1048.0
32 TraesCS3B01G307200 chr6B 81.447 539 68 23 74 590 489797515 489798043 2.710000e-111 412.0
33 TraesCS3B01G307200 chr7A 93.468 842 50 5 2928 3765 441111072 441110232 0.000000e+00 1245.0
34 TraesCS3B01G307200 chr7A 86.588 1096 122 16 1709 2788 674268882 674267796 0.000000e+00 1186.0
35 TraesCS3B01G307200 chr7A 100.000 33 0 0 2889 2921 441111055 441111023 1.130000e-05 62.1
36 TraesCS3B01G307200 chr5A 90.226 798 77 1 592 1388 582939901 582940698 0.000000e+00 1040.0
37 TraesCS3B01G307200 chr5A 89.975 798 77 3 592 1388 616788747 616789542 0.000000e+00 1027.0
38 TraesCS3B01G307200 chr5A 89.237 799 82 3 592 1388 129148100 129148896 0.000000e+00 996.0
39 TraesCS3B01G307200 chr5A 89.039 593 60 3 1 590 616787726 616788316 0.000000e+00 730.0
40 TraesCS3B01G307200 chr5A 91.126 293 22 4 1 292 582920064 582920353 9.800000e-106 394.0
41 TraesCS3B01G307200 chr5A 87.842 329 37 1 265 590 582939142 582939470 2.120000e-102 383.0
42 TraesCS3B01G307200 chr5A 97.143 70 1 1 1424 1492 129149326 129149395 2.380000e-22 117.0
43 TraesCS3B01G307200 chr1D 89.041 803 78 5 592 1388 442118317 442117519 0.000000e+00 987.0
44 TraesCS3B01G307200 chr2B 89.899 594 49 3 1 590 572102978 572102392 0.000000e+00 754.0
45 TraesCS3B01G307200 chr2B 89.207 593 58 2 1 590 177890321 177890910 0.000000e+00 736.0
46 TraesCS3B01G307200 chr2B 94.118 85 4 1 3083 3167 471443472 471443389 1.100000e-25 128.0
47 TraesCS3B01G307200 chr2B 95.556 45 1 1 3334 3378 113282241 113282198 1.880000e-08 71.3
48 TraesCS3B01G307200 chr2A 90.951 431 36 1 1 428 138532201 138531771 9.070000e-161 577.0
49 TraesCS3B01G307200 chr2A 95.556 45 1 1 3334 3378 73548443 73548400 1.880000e-08 71.3
50 TraesCS3B01G307200 chr4B 92.412 369 23 3 3163 3526 40740374 40740006 4.310000e-144 521.0
51 TraesCS3B01G307200 chr1A 91.954 348 28 0 1 348 137797279 137796932 4.370000e-134 488.0
52 TraesCS3B01G307200 chr6D 93.831 308 15 2 3223 3526 110865529 110865222 9.530000e-126 460.0
53 TraesCS3B01G307200 chr3A 90.145 345 34 0 4 348 146885914 146885570 2.060000e-122 449.0
54 TraesCS3B01G307200 chr3A 93.160 307 18 2 3223 3526 303562968 303562662 7.420000e-122 448.0
55 TraesCS3B01G307200 chr3A 88.764 89 10 0 2778 2866 303563653 303563565 3.980000e-20 110.0
56 TraesCS3B01G307200 chr3A 90.909 77 6 1 3571 3646 741050391 741050467 6.650000e-18 102.0
57 TraesCS3B01G307200 chr6A 87.097 217 19 7 3437 3649 360521896 360522107 1.750000e-58 237.0
58 TraesCS3B01G307200 chr6A 94.737 133 5 1 3001 3133 73018134 73018264 4.930000e-49 206.0
59 TraesCS3B01G307200 chr6A 91.538 130 9 1 3004 3133 72999097 72999224 1.070000e-40 178.0
60 TraesCS3B01G307200 chr6A 91.667 96 8 0 2735 2830 73018042 73018137 2.360000e-27 134.0


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 TraesCS3B01G307200 chr3B 493570120 493573884 3764 False 6953.000000 6953 100.0000 1 3765 1 chr3B.!!$F4 3764
1 TraesCS3B01G307200 chr7B 286564894 286566253 1359 True 1598.000000 1598 88.0500 1423 2770 1 chr7B.!!$R1 1347
2 TraesCS3B01G307200 chr7B 648440269 648442651 2382 False 1435.600000 2811 92.5550 592 3010 2 chr7B.!!$F2 2418
3 TraesCS3B01G307200 chr7B 209397980 209398510 530 False 387.000000 387 80.5560 74 590 1 chr7B.!!$F1 516
4 TraesCS3B01G307200 chr7B 715225760 715226670 910 True 248.500000 387 92.0940 3163 3765 2 chr7B.!!$R2 602
5 TraesCS3B01G307200 chr7D 580776658 580780084 3426 False 1453.000000 2784 91.4240 592 3765 2 chr7D.!!$F1 3173
6 TraesCS3B01G307200 chr2D 110056260 110057575 1315 True 1565.000000 1565 88.3740 1474 2770 1 chr2D.!!$R1 1296
7 TraesCS3B01G307200 chr2D 548894503 548897415 2912 False 1497.000000 2652 88.0260 294 2775 2 chr2D.!!$F1 2481
8 TraesCS3B01G307200 chr1B 439537499 439538880 1381 True 1653.000000 1653 88.4480 1436 2803 1 chr1B.!!$R1 1367
9 TraesCS3B01G307200 chr4A 90326398 90329899 3501 False 1116.666667 1546 89.3100 1 2803 3 chr4A.!!$F1 2802
10 TraesCS3B01G307200 chr4A 95389318 95389910 592 True 776.000000 776 90.3880 1 590 1 chr4A.!!$R1 589
11 TraesCS3B01G307200 chr3D 189779334 189781643 2309 False 1277.500000 1515 88.6180 592 2770 2 chr3D.!!$F2 2178
12 TraesCS3B01G307200 chr6B 172267355 172269854 2499 True 1261.000000 1474 88.5795 592 2788 2 chr6B.!!$R1 2196
13 TraesCS3B01G307200 chr6B 489797515 489798043 528 False 412.000000 412 81.4470 74 590 1 chr6B.!!$F1 516
14 TraesCS3B01G307200 chr7A 674267796 674268882 1086 True 1186.000000 1186 86.5880 1709 2788 1 chr7A.!!$R1 1079
15 TraesCS3B01G307200 chr7A 441110232 441111072 840 True 653.550000 1245 96.7340 2889 3765 2 chr7A.!!$R2 876
16 TraesCS3B01G307200 chr5A 616787726 616789542 1816 False 878.500000 1027 89.5070 1 1388 2 chr5A.!!$F4 1387
17 TraesCS3B01G307200 chr5A 582939142 582940698 1556 False 711.500000 1040 89.0340 265 1388 2 chr5A.!!$F3 1123
18 TraesCS3B01G307200 chr5A 129148100 129149395 1295 False 556.500000 996 93.1900 592 1492 2 chr5A.!!$F2 900
19 TraesCS3B01G307200 chr1D 442117519 442118317 798 True 987.000000 987 89.0410 592 1388 1 chr1D.!!$R1 796
20 TraesCS3B01G307200 chr2B 572102392 572102978 586 True 754.000000 754 89.8990 1 590 1 chr2B.!!$R3 589
21 TraesCS3B01G307200 chr2B 177890321 177890910 589 False 736.000000 736 89.2070 1 590 1 chr2B.!!$F1 589
22 TraesCS3B01G307200 chr3A 303562662 303563653 991 True 279.000000 448 90.9620 2778 3526 2 chr3A.!!$R2 748

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
206 228 0.667993 TGAGCTTGTTTCTTTGCCGG 59.332 50.000 0.00 0.0 0.00 6.13 F
822 1314 0.762418 TTTGTCATGGACACCCTCGT 59.238 50.000 0.00 0.0 42.60 4.18 F
1185 1678 1.134946 GAATAGCCAACATGGTGGTGC 59.865 52.381 30.13 17.2 40.46 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 1835 0.400213 TTGGGTGATGGCTTCTTCGT 59.600 50.0 1.86 0.0 0.00 3.85 R
2627 3807 0.901827 TAGGCATCGGCTCTTTCACA 59.098 50.0 0.00 0.0 39.70 3.58 R
2952 4137 2.026262 TCATGAGGCCACCCTAGTTTTC 60.026 50.0 5.01 0.0 43.12 2.29 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
139 143 0.776810 TTGCCTCCATCTTGGGAACA 59.223 50.000 0.00 0.00 38.32 3.18
162 166 1.670083 GCCACGCCTAACTTCGGTT 60.670 57.895 0.00 0.00 41.52 4.44
206 228 0.667993 TGAGCTTGTTTCTTTGCCGG 59.332 50.000 0.00 0.00 0.00 6.13
381 439 3.380637 TCGAACGAAATAGGAGGAGAAGG 59.619 47.826 0.00 0.00 0.00 3.46
389 447 1.022903 AGGAGGAGAAGGGAGGATGT 58.977 55.000 0.00 0.00 0.00 3.06
396 454 3.369997 GGAGAAGGGAGGATGTTGAAGAC 60.370 52.174 0.00 0.00 0.00 3.01
413 471 4.142838 TGAAGACATGCTGCACTTTATTCG 60.143 41.667 3.57 0.00 0.00 3.34
522 580 3.006967 ACGATATCCTTACAGGGCATGTC 59.993 47.826 8.59 0.00 42.70 3.06
569 627 1.771255 GGAGCCACATATCTTCCAGGT 59.229 52.381 0.00 0.00 0.00 4.00
573 631 4.273318 AGCCACATATCTTCCAGGTTTTC 58.727 43.478 0.00 0.00 0.00 2.29
590 648 7.402640 CAGGTTTTCGCATCTTATCTTAGAAC 58.597 38.462 0.00 0.00 0.00 3.01
619 1106 2.820330 TGATTGCATGCGACTTCGATA 58.180 42.857 10.57 0.00 43.02 2.92
656 1143 1.077265 CATGTGGCTGGGAGGGTTT 59.923 57.895 0.00 0.00 0.00 3.27
672 1159 2.100916 GGGTTTAGCTACAGATGCGAGA 59.899 50.000 0.00 0.00 35.28 4.04
720 1207 4.966805 TGATTTAGAGTACCCGAGGGAAAT 59.033 41.667 16.26 8.88 38.96 2.17
741 1228 6.801718 AATTTTTACCTAGTTAATGGGGGC 57.198 37.500 0.00 0.00 32.60 5.80
746 1233 3.676750 ACCTAGTTAATGGGGGCTATGT 58.323 45.455 0.00 0.00 32.60 2.29
755 1242 1.208535 TGGGGGCTATGTAAACACTCG 59.791 52.381 0.00 0.00 0.00 4.18
805 1292 6.435904 TGTCCGGTATCATTTGAAGGAATTTT 59.564 34.615 0.00 0.00 0.00 1.82
822 1314 0.762418 TTTGTCATGGACACCCTCGT 59.238 50.000 0.00 0.00 42.60 4.18
831 1323 1.892209 GACACCCTCGTCCACAAAAT 58.108 50.000 0.00 0.00 0.00 1.82
951 1444 4.572389 GGCACACTACATTCAATCGAGAAT 59.428 41.667 0.00 0.00 38.72 2.40
952 1445 5.065218 GGCACACTACATTCAATCGAGAATT 59.935 40.000 0.00 0.00 36.13 2.17
953 1446 5.961843 GCACACTACATTCAATCGAGAATTG 59.038 40.000 0.00 0.00 45.22 2.32
973 1466 3.226884 GTGAAACTTCCCGCAGCTA 57.773 52.632 0.00 0.00 0.00 3.32
1029 1522 2.306805 TGGTGATGAGACTTGGCTTGAT 59.693 45.455 0.00 0.00 0.00 2.57
1037 1530 2.307098 AGACTTGGCTTGATAACCAGCT 59.693 45.455 0.00 0.00 37.24 4.24
1056 1549 3.871594 AGCTCGATAACATAGTGCCAAAC 59.128 43.478 0.00 0.00 0.00 2.93
1058 1551 4.109766 CTCGATAACATAGTGCCAAACGA 58.890 43.478 0.00 0.00 0.00 3.85
1074 1567 4.022416 CCAAACGATTTTGTTGATCTCCCA 60.022 41.667 0.00 0.00 40.61 4.37
1079 1572 5.476599 ACGATTTTGTTGATCTCCCAAATGA 59.523 36.000 0.00 0.00 0.00 2.57
1092 1585 6.283694 TCTCCCAAATGATGACGAGAATAAG 58.716 40.000 0.00 0.00 33.75 1.73
1094 1587 5.817296 TCCCAAATGATGACGAGAATAAGTG 59.183 40.000 0.00 0.00 0.00 3.16
1134 1627 5.254032 AGGGAACACTCTAAGGGATGAAATT 59.746 40.000 0.00 0.00 0.00 1.82
1162 1655 3.243636 GCAAATCTGGGAAGCATACCATG 60.244 47.826 0.00 0.00 35.93 3.66
1185 1678 1.134946 GAATAGCCAACATGGTGGTGC 59.865 52.381 30.13 17.20 40.46 5.01
1248 1744 8.031864 ACTTATGCCGTCTTCATCATCTAATAG 58.968 37.037 0.00 0.00 0.00 1.73
1254 1750 7.308649 GCCGTCTTCATCATCTAATAGTGTAGA 60.309 40.741 0.00 0.00 34.65 2.59
1268 1764 9.639601 CTAATAGTGTAGAGTGTGTTGAAATGA 57.360 33.333 0.00 0.00 0.00 2.57
1316 1812 8.034215 CCCAAAGTACAATATCATGAAAGCAAA 58.966 33.333 0.00 0.00 0.00 3.68
1371 1867 6.043127 AGCCATCACCCAAAATTAAAAAGACT 59.957 34.615 0.00 0.00 0.00 3.24
1415 1912 5.945191 TGCTTCATCTCCACATGTAATTTCA 59.055 36.000 0.00 0.00 0.00 2.69
1599 2667 4.006319 GAGCTCAATGTAAGTTGGCTCTT 58.994 43.478 9.40 0.00 42.54 2.85
1632 2702 2.237392 GGTGGAGTTACTTCAGGAGCAT 59.763 50.000 0.00 0.00 0.00 3.79
1633 2703 3.265791 GTGGAGTTACTTCAGGAGCATG 58.734 50.000 0.00 0.00 0.00 4.06
1643 2713 1.344438 TCAGGAGCATGACACTTCGTT 59.656 47.619 0.00 0.00 0.00 3.85
1652 2723 1.553248 TGACACTTCGTTCCATAGGGG 59.447 52.381 0.00 0.00 38.37 4.79
1693 2764 2.941480 AGCTTGGAATAGGATGGCAAG 58.059 47.619 0.00 0.00 0.00 4.01
1741 2812 8.385111 CCATGCAAATTTTACAAAGCAATAGAG 58.615 33.333 3.13 0.00 35.45 2.43
1756 2827 4.094146 GCAATAGAGTCAGGAAAAGCAGAC 59.906 45.833 0.00 0.00 0.00 3.51
1832 2904 4.711846 TCAGCTGGAACTATCATACACACT 59.288 41.667 15.13 0.00 0.00 3.55
1878 2950 2.554893 GGCAAAACCTGATGACCGTAAA 59.445 45.455 0.00 0.00 34.51 2.01
1929 3008 8.324163 ACAACTTCTAACTTGTATTCCATGAC 57.676 34.615 0.00 0.00 0.00 3.06
1943 3023 9.330063 TGTATTCCATGACTTTGTAATCATCTC 57.670 33.333 0.00 0.00 33.18 2.75
2016 3098 5.475564 GTGGCCAGAAATAACTAAGTTCCAA 59.524 40.000 5.11 0.00 0.00 3.53
2051 3137 3.244700 CCCCTCTATGATAAGCTTGGTGG 60.245 52.174 9.86 0.00 0.00 4.61
2075 3161 6.266558 GGTCTCTATGATGGTGAGTTACTGAT 59.733 42.308 0.00 0.00 0.00 2.90
2222 3316 7.051623 TCACATCAACTAAGGTTACACAAGTT 58.948 34.615 0.00 0.00 33.88 2.66
2271 3365 3.145286 GAGCAGACTGCCTTCTCTTTTT 58.855 45.455 23.74 0.67 46.52 1.94
2286 3380 9.231297 CCTTCTCTTTTTACCTGAATCAATACA 57.769 33.333 0.00 0.00 0.00 2.29
2314 3408 4.518211 TGATGTGCACATGTACAACAATCA 59.482 37.500 35.92 20.90 43.49 2.57
2327 3421 5.779529 ACAACAATCAAAGAGATGTTGCT 57.220 34.783 19.62 10.35 42.72 3.91
2329 3423 5.300034 ACAACAATCAAAGAGATGTTGCTCA 59.700 36.000 19.62 0.00 42.72 4.26
2330 3424 6.183360 ACAACAATCAAAGAGATGTTGCTCAA 60.183 34.615 19.62 0.00 42.72 3.02
2331 3425 6.395426 ACAATCAAAGAGATGTTGCTCAAA 57.605 33.333 0.00 0.00 36.96 2.69
2332 3426 6.444633 ACAATCAAAGAGATGTTGCTCAAAG 58.555 36.000 0.00 0.00 36.96 2.77
2333 3427 6.040166 ACAATCAAAGAGATGTTGCTCAAAGT 59.960 34.615 0.00 0.00 36.96 2.66
2334 3428 7.229306 ACAATCAAAGAGATGTTGCTCAAAGTA 59.771 33.333 0.00 0.00 36.96 2.24
2335 3429 7.750229 ATCAAAGAGATGTTGCTCAAAGTAA 57.250 32.000 0.00 0.00 37.37 2.24
2336 3430 7.750229 TCAAAGAGATGTTGCTCAAAGTAAT 57.250 32.000 0.00 0.00 37.37 1.89
2337 3431 7.587629 TCAAAGAGATGTTGCTCAAAGTAATG 58.412 34.615 0.00 0.00 37.37 1.90
2338 3432 7.445096 TCAAAGAGATGTTGCTCAAAGTAATGA 59.555 33.333 0.00 0.00 37.37 2.57
2349 3443 6.360844 CTCAAAGTAATGAGCCAAGAGATG 57.639 41.667 0.00 0.00 40.31 2.90
2350 3444 4.637534 TCAAAGTAATGAGCCAAGAGATGC 59.362 41.667 0.00 0.00 0.00 3.91
2351 3445 4.500499 AAGTAATGAGCCAAGAGATGCT 57.500 40.909 0.00 0.00 41.42 3.79
2352 3446 5.620738 AAGTAATGAGCCAAGAGATGCTA 57.379 39.130 0.00 0.00 38.11 3.49
2353 3447 4.954875 AGTAATGAGCCAAGAGATGCTAC 58.045 43.478 0.00 0.00 38.11 3.58
2354 3448 3.920231 AATGAGCCAAGAGATGCTACA 57.080 42.857 0.00 0.00 38.11 2.74
2378 3500 4.647564 AGTGATGGTCCAAGAGATGTTT 57.352 40.909 0.00 0.00 0.00 2.83
2418 3594 3.834813 AGAGATGCTACACAAAGAGGTGA 59.165 43.478 0.00 0.00 41.32 4.02
2451 3631 8.125978 TCAAATAAGAAGCATGTGAAGGAATT 57.874 30.769 0.00 0.00 0.00 2.17
2461 3641 5.418840 GCATGTGAAGGAATTAAAGAAGGGA 59.581 40.000 0.00 0.00 0.00 4.20
2575 3755 3.576550 GGTCCAAAAATGCCCAAGAGTTA 59.423 43.478 0.00 0.00 0.00 2.24
2581 3761 6.408869 CAAAAATGCCCAAGAGTTATCCATT 58.591 36.000 0.00 0.00 0.00 3.16
2618 3798 2.555757 GTTCTGCACAAGATGGAAAGCT 59.444 45.455 0.00 0.00 33.93 3.74
2640 3820 1.581934 CAACACTGTGAAAGAGCCGA 58.418 50.000 15.86 0.00 0.00 5.54
2699 3879 2.350522 TCTTTCTCAATTCTGCCGCTC 58.649 47.619 0.00 0.00 0.00 5.03
2733 3914 2.349275 GTGTTGTCGTGTTTCTTCGGAA 59.651 45.455 0.00 0.00 0.00 4.30
2742 3923 4.678622 GTGTTTCTTCGGAACAAAATGGT 58.321 39.130 0.00 0.00 33.18 3.55
2821 4005 7.947782 TTTGGTATTCCCTACTCCTCATATT 57.052 36.000 0.00 0.00 0.00 1.28
2822 4006 7.947782 TTGGTATTCCCTACTCCTCATATTT 57.052 36.000 0.00 0.00 0.00 1.40
2833 4017 9.342308 CCTACTCCTCATATTTTGCTTCAATTA 57.658 33.333 0.00 0.00 0.00 1.40
2952 4137 6.907212 GCTTTGTATATTCTGGTCATCAAACG 59.093 38.462 0.00 0.00 0.00 3.60
2969 4154 0.323957 ACGAAAACTAGGGTGGCCTC 59.676 55.000 3.32 0.00 0.00 4.70
3075 4465 7.722728 TCAAGTGACTTAGTTTCAGTAGGACTA 59.277 37.037 0.00 0.00 0.00 2.59
3085 4475 7.104290 AGTTTCAGTAGGACTATTGCCTAAAC 58.896 38.462 0.00 0.00 39.58 2.01
3131 4521 3.878778 ACAGTAATCTTGGGCATGTCTC 58.121 45.455 0.00 0.00 0.00 3.36
3154 4544 4.853924 TGGAGATTTGCACCTTTTCTTC 57.146 40.909 0.00 0.00 0.00 2.87
3167 4557 7.084486 GCACCTTTTCTTCGATTCAATTACTT 58.916 34.615 0.00 0.00 0.00 2.24
3168 4558 7.061094 GCACCTTTTCTTCGATTCAATTACTTG 59.939 37.037 0.00 0.00 0.00 3.16
3340 4805 7.342799 AGACATTGAATTATGTGTATTTGGGCT 59.657 33.333 0.00 0.00 38.80 5.19
3433 4947 2.574450 TGTGTGTGCTGATGATGTTGT 58.426 42.857 0.00 0.00 0.00 3.32
3442 4956 7.381948 GTGTGCTGATGATGTTGTTATTTTTGA 59.618 33.333 0.00 0.00 0.00 2.69
3489 5360 9.846248 ATCAATGTTTTCTTGCAGAGTTATTAC 57.154 29.630 0.00 0.00 0.00 1.89
3535 5406 4.141846 TGGAGTTAGATGCTAGCAAAGGAG 60.142 45.833 23.54 0.00 0.00 3.69
3549 5420 4.897025 CAAAGGAGAGATCTCAATTGCC 57.103 45.455 24.39 15.71 44.60 4.52
3554 5425 3.525537 GAGAGATCTCAATTGCCAACGA 58.474 45.455 24.39 0.00 42.42 3.85
3575 5446 4.612259 CGACAATATGAAATGCAGCTAGCC 60.612 45.833 12.13 0.00 44.83 3.93
3585 5456 5.603170 AATGCAGCTAGCCAAATACAAAT 57.397 34.783 12.13 0.00 44.83 2.32
3619 5659 6.264518 CACCCTCTGTTAAACTTGGTTGTAAT 59.735 38.462 0.00 0.00 0.00 1.89
3632 5672 8.904099 ACTTGGTTGTAATAGAATACTATGCC 57.096 34.615 0.00 0.00 39.04 4.40
3633 5673 8.714906 ACTTGGTTGTAATAGAATACTATGCCT 58.285 33.333 0.00 0.00 39.04 4.75
3689 5793 6.715718 GCTAGTATCAGTATTGTGAGGACCTA 59.284 42.308 0.00 0.00 0.00 3.08
3692 5796 8.554490 AGTATCAGTATTGTGAGGACCTATTT 57.446 34.615 0.00 0.00 0.00 1.40
3749 5854 4.274459 GCATATTCTGGGAGCAAGTACAAG 59.726 45.833 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 5.651172 TGTGAAAATAAGAGTCACACACG 57.349 39.130 1.74 0.00 45.02 4.49
168 172 1.959282 CAAGAGGCCAAGAAGCTTGTT 59.041 47.619 2.10 2.27 33.22 2.83
235 257 2.094390 GTGTGCCAAGATGTGCAATGAT 60.094 45.455 0.00 0.00 39.57 2.45
312 367 7.499895 ACACTAAAACTAGAATCGGGAAACAAA 59.500 33.333 0.00 0.00 0.00 2.83
316 371 5.865552 CGACACTAAAACTAGAATCGGGAAA 59.134 40.000 0.00 0.00 0.00 3.13
368 423 2.800788 ACATCCTCCCTTCTCCTCCTAT 59.199 50.000 0.00 0.00 0.00 2.57
381 439 2.681848 CAGCATGTCTTCAACATCCTCC 59.318 50.000 0.00 0.00 45.78 4.30
389 447 5.617529 CGAATAAAGTGCAGCATGTCTTCAA 60.618 40.000 0.00 0.00 39.31 2.69
396 454 1.534595 GGCCGAATAAAGTGCAGCATG 60.535 52.381 0.00 0.00 40.87 4.06
400 458 1.024579 ACGGGCCGAATAAAGTGCAG 61.025 55.000 35.78 0.00 0.00 4.41
403 461 2.286772 GCAATACGGGCCGAATAAAGTG 60.287 50.000 35.78 20.32 0.00 3.16
404 462 1.944709 GCAATACGGGCCGAATAAAGT 59.055 47.619 35.78 11.04 0.00 2.66
413 471 0.238289 CATTCGATGCAATACGGGCC 59.762 55.000 0.00 0.00 0.00 5.80
522 580 7.671302 TCCTATAAGCTACTAGGCAATTCTTG 58.329 38.462 14.12 0.00 35.46 3.02
590 648 7.633664 CGAAGTCGCATGCAATCATAATATTAG 59.366 37.037 19.57 0.00 0.00 1.73
601 1088 5.230182 TCTTATATCGAAGTCGCATGCAAT 58.770 37.500 19.57 1.07 39.60 3.56
619 1106 8.790718 GCCACATGATATGAAAGTGAATCTTAT 58.209 33.333 0.00 0.00 35.02 1.73
656 1143 3.546724 AGAACTCTCGCATCTGTAGCTA 58.453 45.455 0.00 0.00 0.00 3.32
697 1184 3.675348 TCCCTCGGGTACTCTAAATCA 57.325 47.619 1.18 0.00 36.47 2.57
720 1207 5.539669 AGCCCCCATTAACTAGGTAAAAA 57.460 39.130 3.92 0.00 0.00 1.94
733 1220 3.684413 CGAGTGTTTACATAGCCCCCATT 60.684 47.826 0.00 0.00 0.00 3.16
741 1228 6.020599 CGAGAAATGACCGAGTGTTTACATAG 60.021 42.308 0.00 0.00 0.00 2.23
746 1233 2.991190 GCGAGAAATGACCGAGTGTTTA 59.009 45.455 0.00 0.00 0.00 2.01
755 1242 3.531538 TGATAAGGTGCGAGAAATGACC 58.468 45.455 0.00 0.00 0.00 4.02
805 1292 1.972198 GACGAGGGTGTCCATGACA 59.028 57.895 0.00 0.00 40.50 3.58
822 1314 4.222336 ACAATTCCCTGTGATTTTGTGGA 58.778 39.130 0.00 0.00 31.88 4.02
831 1323 5.047164 CCAATGATTGAACAATTCCCTGTGA 60.047 40.000 6.76 0.00 0.00 3.58
878 1370 8.726870 TTTAAGAATTCCTAGGGACATTAACG 57.273 34.615 9.46 0.00 0.00 3.18
884 1376 6.433093 GCACTTTTTAAGAATTCCTAGGGACA 59.567 38.462 9.46 0.00 0.00 4.02
951 1444 1.593196 CTGCGGGAAGTTTCACTCAA 58.407 50.000 0.00 0.00 0.00 3.02
952 1445 0.884704 GCTGCGGGAAGTTTCACTCA 60.885 55.000 0.00 0.00 0.00 3.41
953 1446 0.603975 AGCTGCGGGAAGTTTCACTC 60.604 55.000 0.00 0.00 0.00 3.51
973 1466 3.937814 TGATATTGTGAAGAACTGCGGT 58.062 40.909 0.00 0.00 0.00 5.68
1029 1522 4.500887 GGCACTATGTTATCGAGCTGGTTA 60.501 45.833 0.00 0.00 0.00 2.85
1037 1530 4.112716 TCGTTTGGCACTATGTTATCGA 57.887 40.909 0.00 0.00 0.00 3.59
1056 1549 5.953183 TCATTTGGGAGATCAACAAAATCG 58.047 37.500 11.68 6.03 37.60 3.34
1058 1551 7.325694 GTCATCATTTGGGAGATCAACAAAAT 58.674 34.615 11.68 5.27 37.60 1.82
1074 1567 5.586243 CCCACACTTATTCTCGTCATCATTT 59.414 40.000 0.00 0.00 0.00 2.32
1079 1572 4.020573 TGTTCCCACACTTATTCTCGTCAT 60.021 41.667 0.00 0.00 0.00 3.06
1092 1585 2.140717 CCTAAGTCGTTGTTCCCACAC 58.859 52.381 0.00 0.00 30.32 3.82
1094 1587 1.345415 TCCCTAAGTCGTTGTTCCCAC 59.655 52.381 0.00 0.00 0.00 4.61
1134 1627 1.066716 GCTTCCCAGATTTGCATTGCA 60.067 47.619 7.38 7.38 36.47 4.08
1146 1639 3.003394 TCAACATGGTATGCTTCCCAG 57.997 47.619 0.00 0.00 33.39 4.45
1162 1655 2.825532 ACCACCATGTTGGCTATTCAAC 59.174 45.455 9.58 0.00 42.67 3.18
1226 1722 6.162079 CACTATTAGATGATGAAGACGGCAT 58.838 40.000 0.00 0.00 0.00 4.40
1229 1725 8.100508 TCTACACTATTAGATGATGAAGACGG 57.899 38.462 0.00 0.00 0.00 4.79
1248 1744 6.844696 TCTTCATTTCAACACACTCTACAC 57.155 37.500 0.00 0.00 0.00 2.90
1254 1750 9.113838 GGATACATATCTTCATTTCAACACACT 57.886 33.333 0.00 0.00 33.28 3.55
1339 1835 0.400213 TTGGGTGATGGCTTCTTCGT 59.600 50.000 1.86 0.00 0.00 3.85
1388 1884 7.414222 AATTACATGTGGAGATGAAGCATTT 57.586 32.000 9.11 0.00 0.00 2.32
1504 2571 6.478344 GCTCAACATGATAAGAGGAGTTACTG 59.522 42.308 0.00 0.00 0.00 2.74
1587 2655 4.178956 ACCCTTTTCAAGAGCCAACTTA 57.821 40.909 0.00 0.00 0.00 2.24
1590 2658 3.457234 CAAACCCTTTTCAAGAGCCAAC 58.543 45.455 0.00 0.00 0.00 3.77
1591 2659 2.433970 CCAAACCCTTTTCAAGAGCCAA 59.566 45.455 0.00 0.00 0.00 4.52
1592 2660 2.038659 CCAAACCCTTTTCAAGAGCCA 58.961 47.619 0.00 0.00 0.00 4.75
1599 2667 2.838637 ACTCCACCAAACCCTTTTCA 57.161 45.000 0.00 0.00 0.00 2.69
1632 2702 1.553248 CCCCTATGGAACGAAGTGTCA 59.447 52.381 0.00 0.00 45.00 3.58
1633 2703 1.742750 GCCCCTATGGAACGAAGTGTC 60.743 57.143 0.00 0.00 35.60 3.67
1643 2713 2.465813 CAACCATTTTGCCCCTATGGA 58.534 47.619 7.30 0.00 41.05 3.41
1652 2723 3.451141 TCAGTTGACCAACCATTTTGC 57.549 42.857 9.07 0.00 42.06 3.68
1713 2784 4.132336 TGCTTTGTAAAATTTGCATGGCA 58.868 34.783 15.35 15.35 36.47 4.92
1719 2790 8.519492 TGACTCTATTGCTTTGTAAAATTTGC 57.481 30.769 0.00 0.00 0.00 3.68
1741 2812 4.516698 TCAAATCTGTCTGCTTTTCCTGAC 59.483 41.667 0.00 0.00 35.16 3.51
1756 2827 5.125097 AGCCTGTATTGAGCTTTCAAATCTG 59.875 40.000 0.00 0.00 31.27 2.90
2016 3098 6.341408 TCATAGAGGGGAAAAGGCTTATTT 57.659 37.500 0.00 0.00 0.00 1.40
2051 3137 6.701145 TCAGTAACTCACCATCATAGAGAC 57.299 41.667 0.00 0.00 33.69 3.36
2208 3302 5.763204 CACCATCACTAACTTGTGTAACCTT 59.237 40.000 0.00 0.00 38.90 3.50
2222 3316 2.747177 ACTTCGGGATCACCATCACTA 58.253 47.619 0.00 0.00 40.22 2.74
2271 3365 9.059260 CACATCATCATTGTATTGATTCAGGTA 57.941 33.333 0.00 0.00 34.09 3.08
2286 3380 5.183522 TGTTGTACATGTGCACATCATCATT 59.816 36.000 29.23 5.05 33.61 2.57
2314 3408 7.750229 TCATTACTTTGAGCAACATCTCTTT 57.250 32.000 0.00 0.00 34.29 2.52
2327 3421 4.637534 GCATCTCTTGGCTCATTACTTTGA 59.362 41.667 0.00 0.00 0.00 2.69
2329 3423 4.853007 AGCATCTCTTGGCTCATTACTTT 58.147 39.130 0.00 0.00 34.76 2.66
2330 3424 4.500499 AGCATCTCTTGGCTCATTACTT 57.500 40.909 0.00 0.00 34.76 2.24
2331 3425 4.406972 TGTAGCATCTCTTGGCTCATTACT 59.593 41.667 0.00 0.00 41.41 2.24
2332 3426 4.509600 GTGTAGCATCTCTTGGCTCATTAC 59.490 45.833 0.00 0.00 41.41 1.89
2333 3427 4.162131 TGTGTAGCATCTCTTGGCTCATTA 59.838 41.667 0.00 0.00 41.41 1.90
2334 3428 3.054875 TGTGTAGCATCTCTTGGCTCATT 60.055 43.478 0.00 0.00 41.41 2.57
2335 3429 2.502947 TGTGTAGCATCTCTTGGCTCAT 59.497 45.455 0.00 0.00 41.41 2.90
2336 3430 1.901833 TGTGTAGCATCTCTTGGCTCA 59.098 47.619 0.00 0.00 41.41 4.26
2337 3431 2.680312 TGTGTAGCATCTCTTGGCTC 57.320 50.000 0.00 0.00 41.41 4.70
2338 3432 2.304180 ACTTGTGTAGCATCTCTTGGCT 59.696 45.455 0.00 0.00 43.94 4.75
2339 3433 2.417933 CACTTGTGTAGCATCTCTTGGC 59.582 50.000 0.00 0.00 0.00 4.52
2340 3434 3.930336 TCACTTGTGTAGCATCTCTTGG 58.070 45.455 0.46 0.00 0.00 3.61
2341 3435 4.331992 CCATCACTTGTGTAGCATCTCTTG 59.668 45.833 0.46 0.00 0.00 3.02
2342 3436 4.019860 ACCATCACTTGTGTAGCATCTCTT 60.020 41.667 0.46 0.00 0.00 2.85
2343 3437 3.517100 ACCATCACTTGTGTAGCATCTCT 59.483 43.478 0.46 0.00 0.00 3.10
2344 3438 3.866651 ACCATCACTTGTGTAGCATCTC 58.133 45.455 0.46 0.00 0.00 2.75
2345 3439 3.369892 GGACCATCACTTGTGTAGCATCT 60.370 47.826 0.46 0.00 0.00 2.90
2346 3440 2.939103 GGACCATCACTTGTGTAGCATC 59.061 50.000 0.46 0.00 0.00 3.91
2347 3441 2.305635 TGGACCATCACTTGTGTAGCAT 59.694 45.455 0.00 0.00 0.00 3.79
2348 3442 1.696884 TGGACCATCACTTGTGTAGCA 59.303 47.619 0.00 0.00 0.00 3.49
2349 3443 2.472695 TGGACCATCACTTGTGTAGC 57.527 50.000 0.00 0.00 0.00 3.58
2350 3444 4.021104 TCTCTTGGACCATCACTTGTGTAG 60.021 45.833 0.00 0.00 0.00 2.74
2351 3445 3.901222 TCTCTTGGACCATCACTTGTGTA 59.099 43.478 0.00 0.00 0.00 2.90
2352 3446 2.705658 TCTCTTGGACCATCACTTGTGT 59.294 45.455 0.00 0.00 0.00 3.72
2353 3447 3.407424 TCTCTTGGACCATCACTTGTG 57.593 47.619 0.00 0.00 0.00 3.33
2354 3448 3.328931 ACATCTCTTGGACCATCACTTGT 59.671 43.478 0.00 0.00 0.00 3.16
2378 3500 4.717877 TCTCTTGGCTCATCACTTTGAAA 58.282 39.130 0.00 0.00 0.00 2.69
2451 3631 4.345859 TCACGCTTCTTTCCCTTCTTTA 57.654 40.909 0.00 0.00 0.00 1.85
2461 3641 3.379372 CCATTGGATCATCACGCTTCTTT 59.621 43.478 0.00 0.00 0.00 2.52
2516 3696 1.349026 CTCCTCCTTCACTTGCTTCCA 59.651 52.381 0.00 0.00 0.00 3.53
2575 3755 4.221262 ACAACAATGCACTTGCTAATGGAT 59.779 37.500 2.33 0.00 42.66 3.41
2581 3761 3.550639 GCAGAACAACAATGCACTTGCTA 60.551 43.478 2.33 0.00 42.66 3.49
2618 3798 2.297701 GGCTCTTTCACAGTGTTGGAA 58.702 47.619 0.00 0.00 0.00 3.53
2627 3807 0.901827 TAGGCATCGGCTCTTTCACA 59.098 50.000 0.00 0.00 39.70 3.58
2640 3820 5.466393 GCATTTTTGAACACTTTGTAGGCAT 59.534 36.000 0.00 0.00 0.00 4.40
2699 3879 4.149571 CACGACAACACTCTCTTCATCTTG 59.850 45.833 0.00 0.00 0.00 3.02
2789 3970 9.684702 AGGAGTAGGGAATACCAAAATAAGATA 57.315 33.333 0.00 0.00 43.89 1.98
2821 4005 4.343231 TCCCATCAGCTAATTGAAGCAAA 58.657 39.130 3.15 0.00 45.30 3.68
2822 4006 3.966979 TCCCATCAGCTAATTGAAGCAA 58.033 40.909 3.15 0.00 45.30 3.91
2833 4017 8.628905 ACTCTATGAGACTGATCCCATCAGCT 62.629 46.154 12.53 10.57 45.11 4.24
2922 4106 9.679661 TGATGACCAGAATATACAAAGCTAAAA 57.320 29.630 0.00 0.00 0.00 1.52
2925 4109 9.109393 GTTTGATGACCAGAATATACAAAGCTA 57.891 33.333 0.00 0.00 0.00 3.32
2952 4137 2.026262 TCATGAGGCCACCCTAGTTTTC 60.026 50.000 5.01 0.00 43.12 2.29
3027 4417 6.121590 TGAGCATCAACCACACACATTATAT 58.878 36.000 0.00 0.00 45.97 0.86
3075 4465 8.288689 ACGACCATTTAAATAGTTTAGGCAAT 57.711 30.769 0.00 0.00 0.00 3.56
3131 4521 4.796038 AGAAAAGGTGCAAATCTCCATG 57.204 40.909 0.00 0.00 0.00 3.66
3154 4544 8.926710 AGTAAGTCACTTCAAGTAATTGAATCG 58.073 33.333 17.81 12.13 39.85 3.34
3167 4557 4.127171 GGTGCTTTCAGTAAGTCACTTCA 58.873 43.478 0.00 0.00 39.13 3.02
3168 4558 4.381411 AGGTGCTTTCAGTAAGTCACTTC 58.619 43.478 0.00 0.00 39.13 3.01
3181 4571 4.695455 TCAGCATAGTAACAAGGTGCTTTC 59.305 41.667 0.00 0.00 43.03 2.62
3489 5360 3.670627 GCCTGGAAAGCAACAAATACTCG 60.671 47.826 0.00 0.00 0.00 4.18
3535 5406 3.002791 TGTCGTTGGCAATTGAGATCTC 58.997 45.455 16.21 16.21 0.00 2.75
3549 5420 4.665212 AGCTGCATTTCATATTGTCGTTG 58.335 39.130 1.02 0.00 0.00 4.10
3554 5425 4.209538 TGGCTAGCTGCATTTCATATTGT 58.790 39.130 15.72 0.00 45.15 2.71
3619 5659 7.067421 ACAACAGTCCTAGGCATAGTATTCTA 58.933 38.462 2.96 0.00 0.00 2.10
3626 5666 4.396166 CCAAAACAACAGTCCTAGGCATAG 59.604 45.833 2.96 0.00 0.00 2.23
3628 5668 3.157087 CCAAAACAACAGTCCTAGGCAT 58.843 45.455 2.96 0.00 0.00 4.40
3632 5672 2.582052 TGGCCAAAACAACAGTCCTAG 58.418 47.619 0.61 0.00 0.00 3.02
3633 5673 2.738587 TGGCCAAAACAACAGTCCTA 57.261 45.000 0.61 0.00 0.00 2.94
3666 5707 9.656323 AAATAGGTCCTCACAATACTGATACTA 57.344 33.333 0.00 0.00 0.00 1.82
3692 5796 4.993028 ACTAAGGGCATCACCTACAAAAA 58.007 39.130 0.00 0.00 40.87 1.94
3705 5809 3.005367 GCAAAGTAGCAAAACTAAGGGCA 59.995 43.478 0.00 0.00 30.90 5.36


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

AutoCloner maintained by Alex Coulton.