Multiple sequence alignment - TraesCS1D01G306400

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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 TraesCS1D01G306400 chr1D 100.000 2951 0 0 1 2951 403530385 403527435 0.000000e+00 5450.0
1 TraesCS1D01G306400 chr1D 90.767 639 41 13 1 623 230711477 230710841 0.000000e+00 837.0
2 TraesCS1D01G306400 chr1D 82.792 616 78 12 1349 1957 403518035 403517441 2.610000e-145 525.0
3 TraesCS1D01G306400 chr1D 82.160 611 76 17 1349 1941 403377570 403376975 7.350000e-136 494.0
4 TraesCS1D01G306400 chr1D 96.571 175 6 0 448 622 403545305 403545131 1.030000e-74 291.0
5 TraesCS1D01G306400 chr1D 91.979 187 12 3 281 465 18582716 18582531 2.920000e-65 259.0
6 TraesCS1D01G306400 chr1D 86.404 228 25 1 1349 1576 403554272 403554051 8.170000e-61 244.0
7 TraesCS1D01G306400 chr1D 85.780 218 19 4 1349 1566 403339214 403339009 1.380000e-53 220.0
8 TraesCS1D01G306400 chr1D 84.375 224 28 2 1731 1954 403550452 403550236 2.300000e-51 213.0
9 TraesCS1D01G306400 chr1D 83.857 223 24 4 1348 1570 403349760 403349550 4.990000e-48 202.0
10 TraesCS1D01G306400 chr1D 85.263 190 18 3 2762 2951 403517226 403517047 1.400000e-43 187.0
11 TraesCS1D01G306400 chr1D 84.737 190 19 3 2762 2951 403338371 403338192 6.500000e-42 182.0
12 TraesCS1D01G306400 chr1D 86.777 121 16 0 2645 2765 403376934 403376814 5.130000e-28 135.0
13 TraesCS1D01G306400 chr1D 81.879 149 24 2 2617 2765 403550233 403550088 3.990000e-24 122.0
14 TraesCS1D01G306400 chr1B 94.439 1007 43 2 953 1959 542726816 542725823 0.000000e+00 1537.0
15 TraesCS1D01G306400 chr1B 90.491 631 49 7 1 622 276267325 276266697 0.000000e+00 822.0
16 TraesCS1D01G306400 chr1B 82.581 620 76 11 1343 1945 542628517 542627913 4.360000e-143 518.0
17 TraesCS1D01G306400 chr1B 81.095 603 89 9 1349 1945 542768086 542767503 2.680000e-125 459.0
18 TraesCS1D01G306400 chr1B 80.645 620 92 15 1348 1954 542762840 542762236 3.470000e-124 455.0
19 TraesCS1D01G306400 chr1B 79.967 609 94 12 1349 1957 542715807 542715227 9.780000e-115 424.0
20 TraesCS1D01G306400 chr1B 95.333 150 7 0 2616 2765 542725826 542725677 3.800000e-59 239.0
21 TraesCS1D01G306400 chr1B 89.231 195 9 6 2758 2951 542725614 542725431 1.770000e-57 233.0
22 TraesCS1D01G306400 chr1B 80.602 299 22 6 675 969 542727097 542726831 6.450000e-47 198.0
23 TraesCS1D01G306400 chr1B 87.421 159 16 2 2793 2951 542714976 542714822 2.340000e-41 180.0
24 TraesCS1D01G306400 chr1B 84.211 190 20 3 2762 2951 542582207 542582028 3.020000e-40 176.0
25 TraesCS1D01G306400 chr1B 83.221 149 22 2 2617 2765 542762233 542762088 1.850000e-27 134.0
26 TraesCS1D01G306400 chr1B 80.531 113 22 0 2653 2765 542715188 542715076 1.460000e-13 87.9
27 TraesCS1D01G306400 chr1B 83.146 89 12 1 2616 2704 542767492 542767407 8.770000e-11 78.7
28 TraesCS1D01G306400 chrUn 98.618 651 8 1 1967 2616 9745729 9745079 0.000000e+00 1151.0
29 TraesCS1D01G306400 chrUn 95.859 652 20 3 1967 2616 62137119 62136473 0.000000e+00 1048.0
30 TraesCS1D01G306400 chrUn 85.465 344 15 9 1967 2280 46108650 46108312 2.840000e-85 326.0
31 TraesCS1D01G306400 chr7A 96.615 650 17 1 1967 2616 315706299 315705655 0.000000e+00 1074.0
32 TraesCS1D01G306400 chr3B 95.619 662 21 3 1958 2618 745175644 745176298 0.000000e+00 1055.0
33 TraesCS1D01G306400 chr5A 96.000 650 20 2 1967 2616 33314036 33313393 0.000000e+00 1051.0
34 TraesCS1D01G306400 chr1A 95.692 650 23 1 1967 2616 46482918 46482274 0.000000e+00 1040.0
35 TraesCS1D01G306400 chr1A 89.984 639 33 10 1 622 462752049 462751425 0.000000e+00 797.0
36 TraesCS1D01G306400 chr1A 81.072 597 94 9 1349 1945 498797216 498796639 2.680000e-125 459.0
37 TraesCS1D01G306400 chr1A 80.820 610 90 12 1349 1957 498668483 498667900 1.250000e-123 453.0
38 TraesCS1D01G306400 chr1A 89.143 175 15 2 450 622 462770966 462770794 6.410000e-52 215.0
39 TraesCS1D01G306400 chr1A 84.737 190 19 6 2762 2951 498667676 498667497 6.500000e-42 182.0
40 TraesCS1D01G306400 chr1A 86.164 159 16 2 2793 2951 498796389 498796237 1.820000e-37 167.0
41 TraesCS1D01G306400 chr1A 83.158 190 22 3 2762 2951 498600028 498599849 6.540000e-37 165.0
42 TraesCS1D01G306400 chr1A 79.832 119 16 6 2648 2762 498796599 498796485 2.440000e-11 80.5
43 TraesCS1D01G306400 chr4D 88.462 676 46 14 1967 2616 410094962 410095631 0.000000e+00 787.0
44 TraesCS1D01G306400 chr4D 87.073 673 64 12 1967 2625 391052712 391053375 0.000000e+00 739.0
45 TraesCS1D01G306400 chr4D 94.118 51 2 1 105 154 282827039 282826989 3.150000e-10 76.8
46 TraesCS1D01G306400 chr3A 88.419 639 41 13 1 624 729361202 729360582 0.000000e+00 739.0
47 TraesCS1D01G306400 chr3A 90.960 177 14 1 446 622 729385618 729385444 1.370000e-58 237.0
48 TraesCS1D01G306400 chr3A 84.358 179 20 4 450 622 11797114 11797290 5.060000e-38 169.0
49 TraesCS1D01G306400 chr2A 88.730 630 38 6 2019 2622 764145320 764144698 0.000000e+00 739.0
50 TraesCS1D01G306400 chr7D 85.103 678 68 8 1967 2616 364634244 364634916 0.000000e+00 662.0
51 TraesCS1D01G306400 chr4A 92.906 437 15 6 1 423 548002640 548002206 3.230000e-174 621.0
52 TraesCS1D01G306400 chr4A 93.561 264 14 3 272 534 548001966 548001705 9.920000e-105 390.0
53 TraesCS1D01G306400 chr4A 90.751 173 14 2 450 622 548053054 548052884 2.290000e-56 230.0
54 TraesCS1D01G306400 chr6B 85.263 190 19 4 2762 2951 117494215 117494035 1.400000e-43 187.0


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 TraesCS1D01G306400 chr1D 403527435 403530385 2950 True 5450.000000 5450 100.000000 1 2951 1 chr1D.!!$R4 2950
1 TraesCS1D01G306400 chr1D 230710841 230711477 636 True 837.000000 837 90.767000 1 623 1 chr1D.!!$R2 622
2 TraesCS1D01G306400 chr1D 403517047 403518035 988 True 356.000000 525 84.027500 1349 2951 2 chr1D.!!$R8 1602
3 TraesCS1D01G306400 chr1D 403376814 403377570 756 True 314.500000 494 84.468500 1349 2765 2 chr1D.!!$R7 1416
4 TraesCS1D01G306400 chr1D 403338192 403339214 1022 True 201.000000 220 85.258500 1349 2951 2 chr1D.!!$R6 1602
5 TraesCS1D01G306400 chr1B 276266697 276267325 628 True 822.000000 822 90.491000 1 622 1 chr1B.!!$R1 621
6 TraesCS1D01G306400 chr1B 542725431 542727097 1666 True 551.750000 1537 89.901250 675 2951 4 chr1B.!!$R5 2276
7 TraesCS1D01G306400 chr1B 542627913 542628517 604 True 518.000000 518 82.581000 1343 1945 1 chr1B.!!$R3 602
8 TraesCS1D01G306400 chr1B 542762088 542762840 752 True 294.500000 455 81.933000 1348 2765 2 chr1B.!!$R6 1417
9 TraesCS1D01G306400 chr1B 542767407 542768086 679 True 268.850000 459 82.120500 1349 2704 2 chr1B.!!$R7 1355
10 TraesCS1D01G306400 chr1B 542714822 542715807 985 True 230.633333 424 82.639667 1349 2951 3 chr1B.!!$R4 1602
11 TraesCS1D01G306400 chrUn 9745079 9745729 650 True 1151.000000 1151 98.618000 1967 2616 1 chrUn.!!$R1 649
12 TraesCS1D01G306400 chrUn 62136473 62137119 646 True 1048.000000 1048 95.859000 1967 2616 1 chrUn.!!$R3 649
13 TraesCS1D01G306400 chr7A 315705655 315706299 644 True 1074.000000 1074 96.615000 1967 2616 1 chr7A.!!$R1 649
14 TraesCS1D01G306400 chr3B 745175644 745176298 654 False 1055.000000 1055 95.619000 1958 2618 1 chr3B.!!$F1 660
15 TraesCS1D01G306400 chr5A 33313393 33314036 643 True 1051.000000 1051 96.000000 1967 2616 1 chr5A.!!$R1 649
16 TraesCS1D01G306400 chr1A 46482274 46482918 644 True 1040.000000 1040 95.692000 1967 2616 1 chr1A.!!$R1 649
17 TraesCS1D01G306400 chr1A 462751425 462752049 624 True 797.000000 797 89.984000 1 622 1 chr1A.!!$R2 621
18 TraesCS1D01G306400 chr1A 498667497 498668483 986 True 317.500000 453 82.778500 1349 2951 2 chr1A.!!$R5 1602
19 TraesCS1D01G306400 chr1A 498796237 498797216 979 True 235.500000 459 82.356000 1349 2951 3 chr1A.!!$R6 1602
20 TraesCS1D01G306400 chr4D 410094962 410095631 669 False 787.000000 787 88.462000 1967 2616 1 chr4D.!!$F2 649
21 TraesCS1D01G306400 chr4D 391052712 391053375 663 False 739.000000 739 87.073000 1967 2625 1 chr4D.!!$F1 658
22 TraesCS1D01G306400 chr3A 729360582 729361202 620 True 739.000000 739 88.419000 1 624 1 chr3A.!!$R1 623
23 TraesCS1D01G306400 chr2A 764144698 764145320 622 True 739.000000 739 88.730000 2019 2622 1 chr2A.!!$R1 603
24 TraesCS1D01G306400 chr7D 364634244 364634916 672 False 662.000000 662 85.103000 1967 2616 1 chr7D.!!$F1 649
25 TraesCS1D01G306400 chr4A 548001705 548002640 935 True 505.500000 621 93.233500 1 534 2 chr4A.!!$R2 533

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
885 1305 0.040425 AAAGCCAAACACGACGATGC 60.04 50.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 2498 0.179076 GCTGCCAAACTTGCCAAACT 60.179 50.0 0.0 0.0 0.0 2.66 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
279 293 2.045926 ACCAAGGGCATCGCTGTC 60.046 61.111 0.00 0.00 0.00 3.51
373 780 2.246993 CTGCTCTTCGAGACGTCGCT 62.247 60.000 17.32 0.00 46.39 4.93
470 887 6.034044 CGTATTGAAAAGAAACGAGAGAGAGG 59.966 42.308 0.00 0.00 33.83 3.69
477 894 2.818751 AACGAGAGAGAGGGAGACAT 57.181 50.000 0.00 0.00 0.00 3.06
497 914 9.424319 GAGACATACAGAAGTAAAAGTGAATCA 57.576 33.333 0.00 0.00 33.13 2.57
558 978 1.005394 GAAAGGGTGCGTCCGAAGA 60.005 57.895 0.00 0.00 37.00 2.87
571 991 1.535896 TCCGAAGAGACACGAGACAAG 59.464 52.381 0.00 0.00 0.00 3.16
572 992 1.267261 CCGAAGAGACACGAGACAAGT 59.733 52.381 0.00 0.00 0.00 3.16
658 1078 4.884458 GCAAATGCTAAAGGTAGGAGTC 57.116 45.455 0.00 0.00 38.21 3.36
659 1079 4.261801 GCAAATGCTAAAGGTAGGAGTCA 58.738 43.478 0.00 0.00 38.21 3.41
660 1080 4.700213 GCAAATGCTAAAGGTAGGAGTCAA 59.300 41.667 0.00 0.00 38.21 3.18
661 1081 5.183140 GCAAATGCTAAAGGTAGGAGTCAAA 59.817 40.000 0.00 0.00 38.21 2.69
662 1082 6.612306 CAAATGCTAAAGGTAGGAGTCAAAC 58.388 40.000 0.00 0.00 30.32 2.93
663 1083 4.967084 TGCTAAAGGTAGGAGTCAAACA 57.033 40.909 0.00 0.00 0.00 2.83
664 1084 5.499004 TGCTAAAGGTAGGAGTCAAACAT 57.501 39.130 0.00 0.00 0.00 2.71
665 1085 5.876357 TGCTAAAGGTAGGAGTCAAACATT 58.124 37.500 0.00 0.00 0.00 2.71
666 1086 5.705441 TGCTAAAGGTAGGAGTCAAACATTG 59.295 40.000 0.00 0.00 0.00 2.82
667 1087 5.938125 GCTAAAGGTAGGAGTCAAACATTGA 59.062 40.000 0.00 0.00 37.33 2.57
668 1088 6.430000 GCTAAAGGTAGGAGTCAAACATTGAA 59.570 38.462 0.00 0.00 42.15 2.69
669 1089 6.635030 AAAGGTAGGAGTCAAACATTGAAC 57.365 37.500 0.00 0.00 42.15 3.18
670 1090 5.568620 AGGTAGGAGTCAAACATTGAACT 57.431 39.130 0.00 0.00 42.15 3.01
671 1091 5.941788 AGGTAGGAGTCAAACATTGAACTT 58.058 37.500 0.00 0.00 42.15 2.66
672 1092 5.998363 AGGTAGGAGTCAAACATTGAACTTC 59.002 40.000 0.00 0.00 42.15 3.01
673 1093 5.181433 GGTAGGAGTCAAACATTGAACTTCC 59.819 44.000 9.67 9.67 42.15 3.46
698 1118 9.827411 CCTTAAATGTAAACTTCTTCTAAGTGC 57.173 33.333 0.00 0.00 0.00 4.40
728 1148 2.184167 TTTATTAGCTGCGCCCGCC 61.184 57.895 14.20 0.00 41.09 6.13
729 1149 4.961511 TATTAGCTGCGCCCGCCG 62.962 66.667 14.20 4.90 41.09 6.46
740 1160 3.202706 CCCGCCGCCTAGAAAAGC 61.203 66.667 0.00 0.00 0.00 3.51
788 1208 2.353605 GCCCGCAAAATCTTCCATTTCA 60.354 45.455 0.00 0.00 0.00 2.69
804 1224 8.426569 TTCCATTTCATTTCTTTTCCTCTCAT 57.573 30.769 0.00 0.00 0.00 2.90
805 1225 8.059798 TCCATTTCATTTCTTTTCCTCTCATC 57.940 34.615 0.00 0.00 0.00 2.92
813 1233 9.610705 CATTTCTTTTCCTCTCATCAGATAGAA 57.389 33.333 0.00 0.00 0.00 2.10
847 1267 2.796557 TGATTTAATTGGACGGTGGCA 58.203 42.857 0.00 0.00 0.00 4.92
848 1268 2.752354 TGATTTAATTGGACGGTGGCAG 59.248 45.455 0.00 0.00 0.00 4.85
849 1269 2.570415 TTTAATTGGACGGTGGCAGA 57.430 45.000 0.00 0.00 0.00 4.26
850 1270 2.799126 TTAATTGGACGGTGGCAGAT 57.201 45.000 0.00 0.00 0.00 2.90
851 1271 2.036958 TAATTGGACGGTGGCAGATG 57.963 50.000 0.00 0.00 0.00 2.90
852 1272 0.680921 AATTGGACGGTGGCAGATGG 60.681 55.000 0.00 0.00 0.00 3.51
853 1273 1.561769 ATTGGACGGTGGCAGATGGA 61.562 55.000 0.00 0.00 0.00 3.41
854 1274 1.561769 TTGGACGGTGGCAGATGGAT 61.562 55.000 0.00 0.00 0.00 3.41
855 1275 1.224592 GGACGGTGGCAGATGGATT 59.775 57.895 0.00 0.00 0.00 3.01
856 1276 0.468226 GGACGGTGGCAGATGGATTA 59.532 55.000 0.00 0.00 0.00 1.75
857 1277 1.134220 GGACGGTGGCAGATGGATTAA 60.134 52.381 0.00 0.00 0.00 1.40
858 1278 2.487265 GGACGGTGGCAGATGGATTAAT 60.487 50.000 0.00 0.00 0.00 1.40
859 1279 2.808543 GACGGTGGCAGATGGATTAATC 59.191 50.000 6.93 6.93 0.00 1.75
860 1280 2.172505 ACGGTGGCAGATGGATTAATCA 59.827 45.455 17.07 4.18 0.00 2.57
861 1281 3.181440 ACGGTGGCAGATGGATTAATCAT 60.181 43.478 17.07 8.60 0.00 2.45
862 1282 3.822735 CGGTGGCAGATGGATTAATCATT 59.177 43.478 17.07 3.59 0.00 2.57
863 1283 4.320714 CGGTGGCAGATGGATTAATCATTG 60.321 45.833 17.07 9.76 0.00 2.82
864 1284 4.553323 GTGGCAGATGGATTAATCATTGC 58.447 43.478 17.07 17.23 32.86 3.56
865 1285 3.575256 TGGCAGATGGATTAATCATTGCC 59.425 43.478 27.42 27.42 42.35 4.52
866 1286 3.575256 GGCAGATGGATTAATCATTGCCA 59.425 43.478 28.28 16.53 42.03 4.92
867 1287 4.039488 GGCAGATGGATTAATCATTGCCAA 59.961 41.667 28.28 7.44 42.03 4.52
868 1288 5.453621 GGCAGATGGATTAATCATTGCCAAA 60.454 40.000 28.28 6.43 42.03 3.28
869 1289 5.694910 GCAGATGGATTAATCATTGCCAAAG 59.305 40.000 17.07 2.65 31.53 2.77
870 1290 5.694910 CAGATGGATTAATCATTGCCAAAGC 59.305 40.000 17.07 1.57 40.48 3.51
885 1305 0.040425 AAAGCCAAACACGACGATGC 60.040 50.000 0.00 0.00 0.00 3.91
922 1346 1.603739 GTTCCCACTTCCCAGCACC 60.604 63.158 0.00 0.00 0.00 5.01
924 1348 4.722700 CCCACTTCCCAGCACCCG 62.723 72.222 0.00 0.00 0.00 5.28
943 1367 0.618981 GAGTCGTTCCCAATTCCCCT 59.381 55.000 0.00 0.00 0.00 4.79
946 1370 0.913924 TCGTTCCCAATTCCCCTACC 59.086 55.000 0.00 0.00 0.00 3.18
962 1386 2.170607 CCTACCACACCAACATCCCTAG 59.829 54.545 0.00 0.00 0.00 3.02
986 1441 1.376609 ATCATTCCAAAGCGTCCGGC 61.377 55.000 0.00 0.00 44.05 6.13
1234 1689 4.314440 TGAAGGCTTCGGCTGCGT 62.314 61.111 21.42 0.00 36.44 5.24
1307 1762 2.464459 CGGTGGCGATTCAGGCTTC 61.464 63.158 0.00 0.00 37.59 3.86
1317 1772 0.606401 TTCAGGCTTCCAAGAAGCGG 60.606 55.000 19.86 15.29 43.89 5.52
1338 1793 2.510768 AGTTCCATCTTATCGACGGC 57.489 50.000 0.00 0.00 0.00 5.68
1463 1918 4.863925 GCGTCCGCTCTGGCTCTC 62.864 72.222 4.10 0.00 37.80 3.20
1464 1919 4.200283 CGTCCGCTCTGGCTCTCC 62.200 72.222 0.00 0.00 37.80 3.71
1465 1920 4.200283 GTCCGCTCTGGCTCTCCG 62.200 72.222 0.00 0.00 37.80 4.63
1514 1984 2.232452 ACTCTGAACTCAAGACCATCGG 59.768 50.000 0.00 0.00 0.00 4.18
1614 2129 1.227497 CAGGATCGAAGGCTGGCTC 60.227 63.158 3.48 0.00 0.00 4.70
1662 2177 3.854669 CTCGAGCTCGCCCCCAAT 61.855 66.667 30.97 0.00 39.60 3.16
1798 2338 0.955919 GCTGTCCCTCAAGTTTCCGG 60.956 60.000 0.00 0.00 0.00 5.14
1846 2387 2.060980 ACCATCTCAGAGGACGCCC 61.061 63.158 0.00 0.00 0.00 6.13
1957 2498 3.309296 CTCCCAGACCATTAGGAGCTTA 58.691 50.000 0.00 0.00 39.54 3.09
1958 2499 3.309296 TCCCAGACCATTAGGAGCTTAG 58.691 50.000 0.00 0.00 38.69 2.18
1959 2500 3.041946 CCCAGACCATTAGGAGCTTAGT 58.958 50.000 0.00 0.00 38.69 2.24
1960 2501 3.456277 CCCAGACCATTAGGAGCTTAGTT 59.544 47.826 0.00 0.00 38.69 2.24
1961 2502 4.080299 CCCAGACCATTAGGAGCTTAGTTT 60.080 45.833 0.00 0.00 38.69 2.66
1962 2503 4.878397 CCAGACCATTAGGAGCTTAGTTTG 59.122 45.833 0.00 0.00 38.69 2.93
1963 2504 4.878397 CAGACCATTAGGAGCTTAGTTTGG 59.122 45.833 0.00 0.00 38.69 3.28
1964 2505 3.621558 ACCATTAGGAGCTTAGTTTGGC 58.378 45.455 0.00 0.00 38.69 4.52
1965 2506 3.010138 ACCATTAGGAGCTTAGTTTGGCA 59.990 43.478 0.00 0.00 38.69 4.92
2091 2634 4.804108 TGTTTTGCGGAAACCATCTATTG 58.196 39.130 0.00 0.00 45.66 1.90
2705 3299 1.818642 GTGCCTTGAGAGATTGCTGT 58.181 50.000 0.00 0.00 0.00 4.40
2720 3314 0.737715 GCTGTCGCTCGATCCAAAGT 60.738 55.000 0.00 0.00 0.00 2.66
2784 3464 1.159285 CCTTCAGCAGTTGCATTCGA 58.841 50.000 6.90 0.00 45.16 3.71
2785 3465 1.536766 CCTTCAGCAGTTGCATTCGAA 59.463 47.619 0.00 0.00 45.16 3.71
2786 3466 2.578495 CTTCAGCAGTTGCATTCGAAC 58.422 47.619 0.00 0.00 45.16 3.95
2787 3467 1.882912 TCAGCAGTTGCATTCGAACT 58.117 45.000 0.00 0.00 45.16 3.01
2788 3468 1.800586 TCAGCAGTTGCATTCGAACTC 59.199 47.619 0.00 0.00 45.16 3.01
2791 3471 1.400242 GCAGTTGCATTCGAACTCACC 60.400 52.381 0.00 0.00 41.59 4.02
2818 3498 9.494271 TTCTTATGTGCAGGCTATTATTCTTAG 57.506 33.333 0.00 0.00 0.00 2.18
2819 3499 8.870116 TCTTATGTGCAGGCTATTATTCTTAGA 58.130 33.333 0.00 0.00 0.00 2.10
2820 3500 9.149225 CTTATGTGCAGGCTATTATTCTTAGAG 57.851 37.037 0.00 0.00 0.00 2.43
2821 3501 6.731292 TGTGCAGGCTATTATTCTTAGAGA 57.269 37.500 0.00 0.00 0.00 3.10
2822 3502 7.124573 TGTGCAGGCTATTATTCTTAGAGAA 57.875 36.000 0.00 0.00 38.78 2.87
2826 3507 9.881649 TGCAGGCTATTATTCTTAGAGAATATG 57.118 33.333 10.28 6.74 44.13 1.78
2854 3535 4.998671 TTGTTCTGCAGAAAATGGTTGA 57.001 36.364 29.99 6.53 35.58 3.18
2864 3545 5.754890 GCAGAAAATGGTTGATGTCAGTTTT 59.245 36.000 0.00 0.00 32.45 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.321653 AATCGGAGTCAAGCACCACC 60.322 55.000 0.00 0.00 0.00 4.61
250 256 2.348888 CCTTGGTCCCGTCGCTACT 61.349 63.158 0.00 0.00 0.00 2.57
439 846 7.660059 TCTCGTTTCTTTTCAATACGTTATCG 58.340 34.615 0.00 0.00 43.34 2.92
470 887 8.779354 ATTCACTTTTACTTCTGTATGTCTCC 57.221 34.615 0.00 0.00 0.00 3.71
558 978 2.431023 AGGCACTTGTCTCGTGTCT 58.569 52.632 0.00 0.00 42.08 3.41
571 991 5.418840 TCCATTCTTTTCCTAATCAAGGCAC 59.581 40.000 0.00 0.00 46.10 5.01
572 992 5.579047 TCCATTCTTTTCCTAATCAAGGCA 58.421 37.500 0.00 0.00 46.10 4.75
637 1057 4.261801 TGACTCCTACCTTTAGCATTTGC 58.738 43.478 0.00 0.00 42.49 3.68
638 1058 6.206634 TGTTTGACTCCTACCTTTAGCATTTG 59.793 38.462 0.00 0.00 0.00 2.32
639 1059 6.303839 TGTTTGACTCCTACCTTTAGCATTT 58.696 36.000 0.00 0.00 0.00 2.32
640 1060 5.876357 TGTTTGACTCCTACCTTTAGCATT 58.124 37.500 0.00 0.00 0.00 3.56
641 1061 5.499004 TGTTTGACTCCTACCTTTAGCAT 57.501 39.130 0.00 0.00 0.00 3.79
642 1062 4.967084 TGTTTGACTCCTACCTTTAGCA 57.033 40.909 0.00 0.00 0.00 3.49
643 1063 5.938125 TCAATGTTTGACTCCTACCTTTAGC 59.062 40.000 0.00 0.00 34.08 3.09
644 1064 7.661847 AGTTCAATGTTTGACTCCTACCTTTAG 59.338 37.037 0.00 0.00 39.87 1.85
645 1065 7.514721 AGTTCAATGTTTGACTCCTACCTTTA 58.485 34.615 0.00 0.00 39.87 1.85
646 1066 6.365520 AGTTCAATGTTTGACTCCTACCTTT 58.634 36.000 0.00 0.00 39.87 3.11
647 1067 5.941788 AGTTCAATGTTTGACTCCTACCTT 58.058 37.500 0.00 0.00 39.87 3.50
648 1068 5.568620 AGTTCAATGTTTGACTCCTACCT 57.431 39.130 0.00 0.00 39.87 3.08
649 1069 5.181433 GGAAGTTCAATGTTTGACTCCTACC 59.819 44.000 5.01 0.00 39.87 3.18
650 1070 5.998363 AGGAAGTTCAATGTTTGACTCCTAC 59.002 40.000 5.01 0.00 39.87 3.18
651 1071 6.187727 AGGAAGTTCAATGTTTGACTCCTA 57.812 37.500 5.01 0.00 39.87 2.94
652 1072 5.053978 AGGAAGTTCAATGTTTGACTCCT 57.946 39.130 5.01 8.09 39.87 3.69
653 1073 5.774498 AAGGAAGTTCAATGTTTGACTCC 57.226 39.130 5.01 0.00 39.87 3.85
654 1074 9.185192 CATTTAAGGAAGTTCAATGTTTGACTC 57.815 33.333 5.01 0.00 39.87 3.36
655 1075 8.695456 ACATTTAAGGAAGTTCAATGTTTGACT 58.305 29.630 11.55 0.00 39.08 3.41
656 1076 8.871686 ACATTTAAGGAAGTTCAATGTTTGAC 57.128 30.769 11.55 0.00 39.08 3.18
672 1092 9.827411 GCACTTAGAAGAAGTTTACATTTAAGG 57.173 33.333 0.00 0.00 0.00 2.69
728 1148 1.401539 GCCAACTTGCTTTTCTAGGCG 60.402 52.381 0.00 0.00 0.00 5.52
729 1149 1.401539 CGCCAACTTGCTTTTCTAGGC 60.402 52.381 0.00 0.00 37.54 3.93
730 1150 1.401539 GCGCCAACTTGCTTTTCTAGG 60.402 52.381 0.00 0.00 0.00 3.02
731 1151 1.725931 CGCGCCAACTTGCTTTTCTAG 60.726 52.381 0.00 0.00 0.00 2.43
735 1155 0.179124 TTTCGCGCCAACTTGCTTTT 60.179 45.000 0.00 0.00 0.00 2.27
737 1157 0.869880 GTTTTCGCGCCAACTTGCTT 60.870 50.000 0.00 0.00 0.00 3.91
740 1160 3.509995 CGTTTTCGCGCCAACTTG 58.490 55.556 15.44 0.00 36.22 3.16
769 1189 5.870978 AGAAATGAAATGGAAGATTTTGCGG 59.129 36.000 0.00 0.00 0.00 5.69
804 1224 6.712998 TCAACGGTTTGGATTTTTCTATCTGA 59.287 34.615 0.00 0.00 33.06 3.27
805 1225 6.908825 TCAACGGTTTGGATTTTTCTATCTG 58.091 36.000 0.00 0.00 33.06 2.90
813 1233 7.934120 TCCAATTAAATCAACGGTTTGGATTTT 59.066 29.630 18.47 5.34 36.98 1.82
814 1234 7.386573 GTCCAATTAAATCAACGGTTTGGATTT 59.613 33.333 17.76 17.76 42.06 2.17
816 1236 6.394809 GTCCAATTAAATCAACGGTTTGGAT 58.605 36.000 3.97 0.00 42.06 3.41
847 1267 5.221581 GGCTTTGGCAATGATTAATCCATCT 60.222 40.000 16.43 0.00 40.87 2.90
848 1268 4.992951 GGCTTTGGCAATGATTAATCCATC 59.007 41.667 16.43 0.14 40.87 3.51
849 1269 4.409574 TGGCTTTGGCAATGATTAATCCAT 59.590 37.500 16.43 4.13 40.87 3.41
850 1270 3.773667 TGGCTTTGGCAATGATTAATCCA 59.226 39.130 16.43 9.84 40.87 3.41
851 1271 4.405116 TGGCTTTGGCAATGATTAATCC 57.595 40.909 16.43 7.57 40.87 3.01
852 1272 5.642919 TGTTTGGCTTTGGCAATGATTAATC 59.357 36.000 16.43 8.60 46.84 1.75
853 1273 5.412286 GTGTTTGGCTTTGGCAATGATTAAT 59.588 36.000 16.43 0.00 46.84 1.40
854 1274 4.754114 GTGTTTGGCTTTGGCAATGATTAA 59.246 37.500 16.43 5.44 46.84 1.40
855 1275 4.314121 GTGTTTGGCTTTGGCAATGATTA 58.686 39.130 16.43 0.00 46.84 1.75
856 1276 3.140623 GTGTTTGGCTTTGGCAATGATT 58.859 40.909 16.43 0.00 46.84 2.57
857 1277 2.769893 GTGTTTGGCTTTGGCAATGAT 58.230 42.857 16.43 0.00 46.84 2.45
858 1278 1.537776 CGTGTTTGGCTTTGGCAATGA 60.538 47.619 16.43 0.00 46.84 2.57
859 1279 0.860533 CGTGTTTGGCTTTGGCAATG 59.139 50.000 0.00 4.50 46.84 2.82
860 1280 0.749649 TCGTGTTTGGCTTTGGCAAT 59.250 45.000 0.00 0.00 46.84 3.56
861 1281 0.179124 GTCGTGTTTGGCTTTGGCAA 60.179 50.000 0.00 0.00 46.03 4.52
862 1282 1.435515 GTCGTGTTTGGCTTTGGCA 59.564 52.632 0.00 0.00 40.87 4.92
863 1283 1.657181 CGTCGTGTTTGGCTTTGGC 60.657 57.895 0.00 0.00 37.82 4.52
864 1284 0.591170 ATCGTCGTGTTTGGCTTTGG 59.409 50.000 0.00 0.00 0.00 3.28
865 1285 1.673760 CATCGTCGTGTTTGGCTTTG 58.326 50.000 0.00 0.00 0.00 2.77
866 1286 0.040425 GCATCGTCGTGTTTGGCTTT 60.040 50.000 0.00 0.00 0.00 3.51
867 1287 0.884704 AGCATCGTCGTGTTTGGCTT 60.885 50.000 0.00 0.00 0.00 4.35
868 1288 1.301716 AGCATCGTCGTGTTTGGCT 60.302 52.632 0.00 0.00 0.00 4.75
869 1289 1.154413 CAGCATCGTCGTGTTTGGC 60.154 57.895 0.00 0.00 0.00 4.52
870 1290 1.078709 ATCAGCATCGTCGTGTTTGG 58.921 50.000 0.00 0.00 0.00 3.28
885 1305 3.629142 ACCGAGGAGGGTTTTTATCAG 57.371 47.619 0.00 0.00 46.96 2.90
922 1346 0.743345 GGGAATTGGGAACGACTCGG 60.743 60.000 2.98 0.00 0.00 4.63
924 1348 0.618981 AGGGGAATTGGGAACGACTC 59.381 55.000 0.00 0.00 0.00 3.36
943 1367 3.193395 TCTAGGGATGTTGGTGTGGTA 57.807 47.619 0.00 0.00 0.00 3.25
946 1370 5.476599 TGATTTTTCTAGGGATGTTGGTGTG 59.523 40.000 0.00 0.00 0.00 3.82
962 1386 3.608073 CGGACGCTTTGGAATGATTTTTC 59.392 43.478 0.00 0.00 0.00 2.29
1098 1553 3.288308 CTCCACCGCAGTCGAAGCT 62.288 63.158 9.14 0.00 38.10 3.74
1307 1762 1.740025 GATGGAACTTCCGCTTCTTGG 59.260 52.381 3.28 0.00 40.17 3.61
1614 2129 1.741770 GTACAGCGCCTGGGAACTG 60.742 63.158 2.29 0.00 35.51 3.16
1711 2235 2.805353 CGTGGACGAGAAGCGGTG 60.805 66.667 0.00 0.00 46.49 4.94
1798 2338 4.828925 GGTCAGCTGCTCGAGGCC 62.829 72.222 15.58 0.00 40.92 5.19
1846 2387 0.179078 GCATGCTCTGGAGTCTGGAG 60.179 60.000 11.37 8.02 0.00 3.86
1847 2388 0.616964 AGCATGCTCTGGAGTCTGGA 60.617 55.000 16.30 0.00 0.00 3.86
1848 2389 0.179078 GAGCATGCTCTGGAGTCTGG 60.179 60.000 35.26 0.00 39.80 3.86
1849 2390 3.365976 GAGCATGCTCTGGAGTCTG 57.634 57.895 35.26 0.00 39.80 3.51
1954 2495 3.383761 CTGCCAAACTTGCCAAACTAAG 58.616 45.455 0.00 0.00 0.00 2.18
1957 2498 0.179076 GCTGCCAAACTTGCCAAACT 60.179 50.000 0.00 0.00 0.00 2.66
1958 2499 0.461693 TGCTGCCAAACTTGCCAAAC 60.462 50.000 0.00 0.00 0.00 2.93
1959 2500 0.461693 GTGCTGCCAAACTTGCCAAA 60.462 50.000 0.00 0.00 0.00 3.28
1960 2501 1.143620 GTGCTGCCAAACTTGCCAA 59.856 52.632 0.00 0.00 0.00 4.52
1961 2502 1.757731 AGTGCTGCCAAACTTGCCA 60.758 52.632 0.00 0.00 0.00 4.92
1962 2503 1.300388 CAGTGCTGCCAAACTTGCC 60.300 57.895 0.00 0.00 0.00 4.52
1963 2504 0.595825 GACAGTGCTGCCAAACTTGC 60.596 55.000 0.00 0.00 0.00 4.01
1964 2505 1.027357 AGACAGTGCTGCCAAACTTG 58.973 50.000 0.00 0.00 0.00 3.16
1965 2506 1.767759 AAGACAGTGCTGCCAAACTT 58.232 45.000 0.00 0.00 0.00 2.66
2091 2634 5.106357 ACAAGAAAACAACATTTGCCAAACC 60.106 36.000 0.00 0.00 0.00 3.27
2388 2971 2.266055 CGTGCCTCCAACTCCTCC 59.734 66.667 0.00 0.00 0.00 4.30
2705 3299 3.122150 CACACTTTGGATCGAGCGA 57.878 52.632 0.00 0.00 0.00 4.93
2720 3314 1.355005 CGTATGATCGTTGTGCCACA 58.645 50.000 0.00 0.00 0.00 4.17
2774 3454 2.808543 AGAAGGTGAGTTCGAATGCAAC 59.191 45.455 0.00 5.61 0.00 4.17
2784 3464 3.679389 CCTGCACATAAGAAGGTGAGTT 58.321 45.455 0.00 0.00 39.79 3.01
2785 3465 2.616510 GCCTGCACATAAGAAGGTGAGT 60.617 50.000 0.00 0.00 39.79 3.41
2786 3466 2.012673 GCCTGCACATAAGAAGGTGAG 58.987 52.381 0.00 0.00 39.79 3.51
2787 3467 1.630369 AGCCTGCACATAAGAAGGTGA 59.370 47.619 0.00 0.00 39.79 4.02
2788 3468 2.119801 AGCCTGCACATAAGAAGGTG 57.880 50.000 0.00 0.00 40.37 4.00
2791 3471 7.976135 AGAATAATAGCCTGCACATAAGAAG 57.024 36.000 0.00 0.00 0.00 2.85
2818 3498 5.091431 GCAGAACAAAGTGCACATATTCTC 58.909 41.667 21.04 8.08 39.62 2.87
2819 3499 4.520111 TGCAGAACAAAGTGCACATATTCT 59.480 37.500 21.04 17.76 44.70 2.40
2820 3500 4.797471 TGCAGAACAAAGTGCACATATTC 58.203 39.130 21.04 15.88 44.70 1.75
2821 3501 4.520111 TCTGCAGAACAAAGTGCACATATT 59.480 37.500 21.04 8.18 44.70 1.28
2822 3502 4.074259 TCTGCAGAACAAAGTGCACATAT 58.926 39.130 21.04 1.26 44.70 1.78
2826 3507 2.849880 TTCTGCAGAACAAAGTGCAC 57.150 45.000 25.16 9.40 44.70 4.57
2854 3535 6.257630 GTGCATTTTGGTTGTAAAACTGACAT 59.742 34.615 0.00 0.00 32.01 3.06
2864 3545 3.638627 TCATGGTGTGCATTTTGGTTGTA 59.361 39.130 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.