Multiple sequence alignment - TraesCS3B01G451600

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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 TraesCS3B01G451600 chr3B 100.000 3376 0 0 1 3376 692113430 692116805 0.000000e+00 6235.0
1 TraesCS3B01G451600 chr3B 81.442 749 103 21 1865 2582 433749775 433749032 6.280000e-162 580.0
2 TraesCS3B01G451600 chr3D 92.382 1549 81 10 1862 3376 524760094 524761639 0.000000e+00 2172.0
3 TraesCS3B01G451600 chr3D 90.571 1209 74 11 2 1178 524758107 524759307 0.000000e+00 1565.0
4 TraesCS3B01G451600 chr3D 91.768 826 51 12 1041 1864 524759230 524760040 0.000000e+00 1133.0
5 TraesCS3B01G451600 chr3D 80.000 750 98 25 1862 2582 335196261 335195535 1.080000e-139 507.0
6 TraesCS3B01G451600 chr3D 76.042 288 62 6 602 885 562585762 562585478 3.510000e-30 143.0
7 TraesCS3B01G451600 chr3A 89.537 1424 108 12 1971 3370 659026199 659027605 0.000000e+00 1766.0
8 TraesCS3B01G451600 chr3A 91.150 1130 76 12 2 1118 659024184 659025302 0.000000e+00 1511.0
9 TraesCS3B01G451600 chr3A 90.495 768 61 8 1103 1864 659025227 659025988 0.000000e+00 1003.0
10 TraesCS3B01G451600 chr3A 80.160 751 116 14 1862 2582 453297718 453296971 6.410000e-147 531.0
11 TraesCS3B01G451600 chr3A 82.883 333 49 7 602 931 453298295 453297968 3.290000e-75 292.0
12 TraesCS3B01G451600 chr3A 75.424 472 89 16 602 1068 730095896 730095447 1.590000e-48 204.0
13 TraesCS3B01G451600 chr3A 75.316 474 86 19 602 1068 730008138 730008587 7.390000e-47 198.0
14 TraesCS3B01G451600 chr3A 75.105 474 87 19 602 1068 730522792 730522343 3.440000e-45 193.0
15 TraesCS3B01G451600 chr3A 89.677 155 8 2 1718 1864 730594135 730593981 1.240000e-44 191.0
16 TraesCS3B01G451600 chr3A 89.032 155 9 2 1718 1864 730009114 730009268 5.750000e-43 185.0
17 TraesCS3B01G451600 chr3A 89.032 155 9 2 1718 1864 730466121 730465967 5.750000e-43 185.0
18 TraesCS3B01G451600 chr3A 89.032 155 9 2 1718 1864 730521816 730521662 5.750000e-43 185.0
19 TraesCS3B01G451600 chr3A 94.118 119 7 0 1862 1980 659026042 659026160 7.440000e-42 182.0
20 TraesCS3B01G451600 chr3A 73.234 269 61 10 602 864 697689568 697689305 1.670000e-13 87.9
21 TraesCS3B01G451600 chr2B 84.915 590 83 4 1139 1724 689859819 689859232 2.900000e-165 592.0
22 TraesCS3B01G451600 chr2B 81.419 592 94 7 1139 1724 396399897 396399316 1.420000e-128 470.0
23 TraesCS3B01G451600 chr6D 84.757 597 76 12 1132 1720 447900159 447899570 4.850000e-163 584.0
24 TraesCS3B01G451600 chr6D 83.305 581 87 8 1139 1712 358088667 358089244 8.300000e-146 527.0
25 TraesCS3B01G451600 chr6D 87.464 343 43 0 2232 2574 447898249 447897907 2.440000e-106 396.0
26 TraesCS3B01G451600 chr6D 81.311 305 56 1 2079 2382 36656121 36656425 2.600000e-61 246.0
27 TraesCS3B01G451600 chr6D 88.961 154 13 4 1718 1868 447899531 447899379 1.600000e-43 187.0
28 TraesCS3B01G451600 chr6D 92.437 119 9 0 1862 1980 447899301 447899183 1.610000e-38 171.0
29 TraesCS3B01G451600 chr5D 84.524 588 82 7 1136 1716 215248171 215248756 1.050000e-159 573.0
30 TraesCS3B01G451600 chr5D 78.193 642 93 29 1972 2582 214864972 214865597 1.910000e-97 366.0
31 TraesCS3B01G451600 chr5D 80.000 125 22 1 1863 1984 82297305 82297429 4.640000e-14 89.8
32 TraesCS3B01G451600 chr1D 79.745 627 97 15 1892 2490 478802911 478803535 8.660000e-116 427.0
33 TraesCS3B01G451600 chr1D 80.978 368 65 4 2100 2466 237917643 237917280 1.530000e-73 287.0
34 TraesCS3B01G451600 chr1D 88.321 137 14 2 2581 2717 473108735 473108601 2.700000e-36 163.0
35 TraesCS3B01G451600 chr1D 88.636 132 13 2 2587 2718 473050471 473050342 3.490000e-35 159.0
36 TraesCS3B01G451600 chr1D 87.597 129 14 2 2585 2713 473081783 473081657 7.550000e-32 148.0
37 TraesCS3B01G451600 chr1D 84.672 137 19 2 2581 2717 473086397 473086263 5.880000e-28 135.0
38 TraesCS3B01G451600 chr1D 84.672 137 19 2 2581 2717 473093166 473093032 5.880000e-28 135.0
39 TraesCS3B01G451600 chr1D 84.733 131 19 1 599 728 362593235 362593105 2.730000e-26 130.0
40 TraesCS3B01G451600 chr1D 79.412 170 32 3 601 768 268460342 268460174 2.130000e-22 117.0
41 TraesCS3B01G451600 chr4D 84.870 423 61 3 2079 2499 22045218 22045639 1.120000e-114 424.0
42 TraesCS3B01G451600 chr4A 80.276 507 95 5 2079 2582 518856551 518857055 8.840000e-101 377.0
43 TraesCS3B01G451600 chr4A 79.093 507 102 4 2079 2582 416227617 416227112 2.490000e-91 346.0
44 TraesCS3B01G451600 chr4A 83.462 260 30 5 54 304 465344416 465344671 2.620000e-56 230.0
45 TraesCS3B01G451600 chr4A 75.338 296 62 11 602 891 63445464 63445754 7.600000e-27 132.0
46 TraesCS3B01G451600 chr5B 81.457 453 73 9 1156 1601 230661203 230661651 8.910000e-96 361.0
47 TraesCS3B01G451600 chr5B 79.424 486 94 4 2020 2500 648856545 648856061 4.170000e-89 339.0
48 TraesCS3B01G451600 chr5B 79.679 187 33 4 1540 1722 693207485 693207670 2.730000e-26 130.0
49 TraesCS3B01G451600 chr5B 86.139 101 11 3 1885 1984 544664824 544664726 4.610000e-19 106.0
50 TraesCS3B01G451600 chr7B 77.778 549 107 13 1175 1713 595299211 595298668 1.170000e-84 324.0
51 TraesCS3B01G451600 chr1A 77.800 491 90 12 602 1088 254988396 254987921 5.510000e-73 285.0
52 TraesCS3B01G451600 chr4B 78.475 446 66 23 601 1029 168575933 168575501 7.180000e-67 265.0
53 TraesCS3B01G451600 chr4B 74.225 516 100 28 2079 2582 593380373 593380867 5.750000e-43 185.0
54 TraesCS3B01G451600 chr4B 82.203 118 18 1 1868 1982 392696345 392696228 7.710000e-17 99.0
55 TraesCS3B01G451600 chrUn 75.316 474 86 19 602 1068 359215111 359214662 7.390000e-47 198.0
56 TraesCS3B01G451600 chrUn 89.677 155 8 2 1718 1864 324058930 324058776 1.240000e-44 191.0
57 TraesCS3B01G451600 chrUn 89.032 155 9 2 1718 1864 359214135 359213981 5.750000e-43 185.0
58 TraesCS3B01G451600 chr2A 76.842 380 61 12 706 1081 221283963 221283607 4.450000e-44 189.0
59 TraesCS3B01G451600 chr1B 88.550 131 13 2 2587 2717 657694062 657693934 1.250000e-34 158.0
60 TraesCS3B01G451600 chr1B 85.714 133 17 2 2585 2717 657649723 657649593 4.540000e-29 139.0
61 TraesCS3B01G451600 chr7D 81.006 179 31 3 1540 1717 539699865 539699689 4.540000e-29 139.0


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 TraesCS3B01G451600 chr3B 692113430 692116805 3375 False 6235.000000 6235 100.000000 1 3376 1 chr3B.!!$F1 3375
1 TraesCS3B01G451600 chr3B 433749032 433749775 743 True 580.000000 580 81.442000 1865 2582 1 chr3B.!!$R1 717
2 TraesCS3B01G451600 chr3D 524758107 524761639 3532 False 1623.333333 2172 91.573667 2 3376 3 chr3D.!!$F1 3374
3 TraesCS3B01G451600 chr3D 335195535 335196261 726 True 507.000000 507 80.000000 1862 2582 1 chr3D.!!$R1 720
4 TraesCS3B01G451600 chr3A 659024184 659027605 3421 False 1115.500000 1766 91.325000 2 3370 4 chr3A.!!$F1 3368
5 TraesCS3B01G451600 chr3A 453296971 453298295 1324 True 411.500000 531 81.521500 602 2582 2 chr3A.!!$R5 1980
6 TraesCS3B01G451600 chr2B 689859232 689859819 587 True 592.000000 592 84.915000 1139 1724 1 chr2B.!!$R2 585
7 TraesCS3B01G451600 chr2B 396399316 396399897 581 True 470.000000 470 81.419000 1139 1724 1 chr2B.!!$R1 585
8 TraesCS3B01G451600 chr6D 358088667 358089244 577 False 527.000000 527 83.305000 1139 1712 1 chr6D.!!$F2 573
9 TraesCS3B01G451600 chr6D 447897907 447900159 2252 True 334.500000 584 88.404750 1132 2574 4 chr6D.!!$R1 1442
10 TraesCS3B01G451600 chr5D 215248171 215248756 585 False 573.000000 573 84.524000 1136 1716 1 chr5D.!!$F3 580
11 TraesCS3B01G451600 chr5D 214864972 214865597 625 False 366.000000 366 78.193000 1972 2582 1 chr5D.!!$F2 610
12 TraesCS3B01G451600 chr1D 478802911 478803535 624 False 427.000000 427 79.745000 1892 2490 1 chr1D.!!$F1 598
13 TraesCS3B01G451600 chr4A 518856551 518857055 504 False 377.000000 377 80.276000 2079 2582 1 chr4A.!!$F3 503
14 TraesCS3B01G451600 chr4A 416227112 416227617 505 True 346.000000 346 79.093000 2079 2582 1 chr4A.!!$R1 503
15 TraesCS3B01G451600 chr7B 595298668 595299211 543 True 324.000000 324 77.778000 1175 1713 1 chr7B.!!$R1 538

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
42 43 0.113190 CAGGAAAGGAGGGCAGGTTT 59.887 55.0 0.00 0.0 0.00 3.27 F
1003 1046 0.249447 CCATAGCACTTCGGCGATGA 60.249 55.0 26.72 5.4 45.96 2.92 F
1103 1146 0.102481 GCTCAGATTCGGTCCGCTTA 59.898 55.0 6.34 0.0 0.00 3.09 F
1113 1156 0.106149 GGTCCGCTTAATCCATCCGT 59.894 55.0 0.00 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1084 1127 0.102481 TAAGCGGACCGAATCTGAGC 59.898 55.0 20.50 0.00 35.44 4.26 R
1923 2269 0.889186 TCCTTGCCCTTGTTCTTCGC 60.889 55.0 0.00 0.00 0.00 4.70 R
2173 3281 0.955428 GCCGTTCATCAGCTGGACAA 60.955 55.0 15.13 0.74 32.23 3.18 R
2848 3992 1.112916 TGGCTCCAACTCGACAGTCA 61.113 55.0 0.41 0.00 29.93 3.41 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
42 43 0.113190 CAGGAAAGGAGGGCAGGTTT 59.887 55.000 0.00 0.00 0.00 3.27
109 110 7.431249 TGTGTAGTTTATTTCAGAGAAGTCGT 58.569 34.615 0.00 0.00 0.00 4.34
157 158 8.150945 TCTATTTGCAGAGAAGTTAGTCAAAGT 58.849 33.333 0.00 0.00 0.00 2.66
356 357 2.503331 TCATGCATGTGTTCGGAAACT 58.497 42.857 25.43 0.00 36.30 2.66
379 380 9.467258 AACTAAGTTCAAAATCATGATGTGTTG 57.533 29.630 9.46 13.59 0.00 3.33
454 456 4.488126 TGCTTGATTTTCGTCTTCCTTG 57.512 40.909 0.00 0.00 0.00 3.61
467 469 1.452145 TTCCTTGCGCCTTTGGTCAC 61.452 55.000 4.18 0.00 0.00 3.67
470 472 2.406452 CTTGCGCCTTTGGTCACCAC 62.406 60.000 4.18 0.00 30.78 4.16
507 509 3.444742 TGTCTCAATTCATGGGCATTCAC 59.555 43.478 0.00 0.00 0.00 3.18
547 549 8.579850 AATTCTTCACTTATTGGTAGATGCAA 57.420 30.769 0.00 0.00 0.00 4.08
581 583 4.447724 GTGTTGACTCATTTTGCTCGTAGA 59.552 41.667 0.00 0.00 0.00 2.59
589 591 4.215185 TCATTTTGCTCGTAGAAATGCACA 59.785 37.500 0.00 0.00 39.44 4.57
590 592 4.560136 TTTTGCTCGTAGAAATGCACAA 57.440 36.364 0.00 0.00 34.99 3.33
691 702 2.719531 TGTGTTCACTGTTTGGCCTA 57.280 45.000 3.32 0.00 0.00 3.93
699 710 1.340017 ACTGTTTGGCCTACATCGCAT 60.340 47.619 3.32 0.00 0.00 4.73
741 753 2.666098 GGCCCGCTAGGAACCTCAA 61.666 63.158 0.00 0.00 41.02 3.02
757 769 5.357742 ACCTCAAAATTGGCAGTTTTTCT 57.642 34.783 16.82 0.00 0.00 2.52
789 801 2.516930 GGGATGCACATGGTCGGG 60.517 66.667 0.00 0.00 0.00 5.14
790 802 3.211963 GGATGCACATGGTCGGGC 61.212 66.667 0.00 0.00 0.00 6.13
792 804 4.408821 ATGCACATGGTCGGGCGT 62.409 61.111 0.00 0.00 0.00 5.68
825 858 0.811915 GAGCCACGCTAGAGACTTCA 59.188 55.000 0.00 0.00 39.88 3.02
860 893 4.476628 ACCGTCGACAATAATTACCCTT 57.523 40.909 17.16 0.00 0.00 3.95
875 918 0.908180 CCCTTACCTTCCCTCACCGT 60.908 60.000 0.00 0.00 0.00 4.83
882 925 1.551452 CTTCCCTCACCGTTCTCTCT 58.449 55.000 0.00 0.00 0.00 3.10
885 928 1.324005 CCCTCACCGTTCTCTCTCCC 61.324 65.000 0.00 0.00 0.00 4.30
895 938 3.688702 CGTTCTCTCTCCCCTCTCCATTA 60.689 52.174 0.00 0.00 0.00 1.90
940 983 0.606096 TTCAGCGGATCGGAGAACAA 59.394 50.000 4.16 0.00 43.58 2.83
999 1042 2.173669 CACCCATAGCACTTCGGCG 61.174 63.158 0.00 0.00 39.27 6.46
1003 1046 0.249447 CCATAGCACTTCGGCGATGA 60.249 55.000 26.72 5.40 45.96 2.92
1004 1047 1.606480 CCATAGCACTTCGGCGATGAT 60.606 52.381 26.72 17.06 45.96 2.45
1035 1078 4.412199 CCTATTTTCACCTCCTCCCATACA 59.588 45.833 0.00 0.00 0.00 2.29
1063 1106 1.556564 TTCGATCCGCGTTCAGATTC 58.443 50.000 4.92 0.00 41.80 2.52
1064 1107 0.454196 TCGATCCGCGTTCAGATTCA 59.546 50.000 4.92 0.00 41.80 2.57
1065 1108 0.848942 CGATCCGCGTTCAGATTCAG 59.151 55.000 4.92 0.00 34.64 3.02
1066 1109 1.799181 CGATCCGCGTTCAGATTCAGT 60.799 52.381 4.92 0.00 34.64 3.41
1067 1110 1.855360 GATCCGCGTTCAGATTCAGTC 59.145 52.381 4.92 0.00 0.00 3.51
1068 1111 0.888619 TCCGCGTTCAGATTCAGTCT 59.111 50.000 4.92 0.00 37.80 3.24
1077 1120 1.661341 AGATTCAGTCTGCGCAATCC 58.339 50.000 13.05 1.46 35.31 3.01
1078 1121 1.065926 AGATTCAGTCTGCGCAATCCA 60.066 47.619 13.05 0.00 35.31 3.41
1079 1122 1.945394 GATTCAGTCTGCGCAATCCAT 59.055 47.619 13.05 0.00 0.00 3.41
1080 1123 1.372582 TTCAGTCTGCGCAATCCATC 58.627 50.000 13.05 0.00 0.00 3.51
1081 1124 0.462581 TCAGTCTGCGCAATCCATCC 60.463 55.000 13.05 0.00 0.00 3.51
1082 1125 1.522355 AGTCTGCGCAATCCATCCG 60.522 57.895 13.05 0.00 0.00 4.18
1087 1130 4.005472 CGCAATCCATCCGCGCTC 62.005 66.667 5.56 0.00 42.79 5.03
1088 1131 2.896854 GCAATCCATCCGCGCTCA 60.897 61.111 5.56 0.00 0.00 4.26
1089 1132 2.890109 GCAATCCATCCGCGCTCAG 61.890 63.158 5.56 0.00 0.00 3.35
1090 1133 1.227350 CAATCCATCCGCGCTCAGA 60.227 57.895 5.56 0.00 0.00 3.27
1091 1134 0.602106 CAATCCATCCGCGCTCAGAT 60.602 55.000 5.56 1.79 0.00 2.90
1092 1135 0.107456 AATCCATCCGCGCTCAGATT 59.893 50.000 5.56 3.61 0.00 2.40
1093 1136 0.320247 ATCCATCCGCGCTCAGATTC 60.320 55.000 5.56 0.00 0.00 2.52
1094 1137 2.305853 CCATCCGCGCTCAGATTCG 61.306 63.158 5.56 0.00 0.00 3.34
1095 1138 2.028190 ATCCGCGCTCAGATTCGG 59.972 61.111 5.56 0.00 42.96 4.30
1096 1139 2.786495 ATCCGCGCTCAGATTCGGT 61.786 57.895 5.56 0.00 42.28 4.69
1097 1140 2.685387 ATCCGCGCTCAGATTCGGTC 62.685 60.000 5.56 0.00 42.28 4.79
1098 1141 2.956964 CGCGCTCAGATTCGGTCC 60.957 66.667 5.56 0.00 0.00 4.46
1099 1142 2.956964 GCGCTCAGATTCGGTCCG 60.957 66.667 4.39 4.39 0.00 4.79
1100 1143 2.956964 CGCTCAGATTCGGTCCGC 60.957 66.667 6.34 0.00 0.00 5.54
1101 1144 2.496817 GCTCAGATTCGGTCCGCT 59.503 61.111 6.34 0.00 0.00 5.52
1102 1145 1.153549 GCTCAGATTCGGTCCGCTT 60.154 57.895 6.34 0.00 0.00 4.68
1103 1146 0.102481 GCTCAGATTCGGTCCGCTTA 59.898 55.000 6.34 0.00 0.00 3.09
1104 1147 1.470979 GCTCAGATTCGGTCCGCTTAA 60.471 52.381 6.34 0.00 0.00 1.85
1105 1148 2.803492 GCTCAGATTCGGTCCGCTTAAT 60.803 50.000 6.34 0.81 0.00 1.40
1106 1149 3.053455 CTCAGATTCGGTCCGCTTAATC 58.947 50.000 6.34 10.97 0.00 1.75
1107 1150 2.135933 CAGATTCGGTCCGCTTAATCC 58.864 52.381 16.53 4.11 0.00 3.01
1108 1151 1.760613 AGATTCGGTCCGCTTAATCCA 59.239 47.619 16.53 0.00 0.00 3.41
1109 1152 2.368875 AGATTCGGTCCGCTTAATCCAT 59.631 45.455 16.53 1.85 0.00 3.41
1110 1153 2.234300 TTCGGTCCGCTTAATCCATC 57.766 50.000 6.34 0.00 0.00 3.51
1111 1154 0.391597 TCGGTCCGCTTAATCCATCC 59.608 55.000 6.34 0.00 0.00 3.51
1112 1155 0.944311 CGGTCCGCTTAATCCATCCG 60.944 60.000 0.00 0.00 0.00 4.18
1113 1156 0.106149 GGTCCGCTTAATCCATCCGT 59.894 55.000 0.00 0.00 0.00 4.69
1114 1157 1.217882 GTCCGCTTAATCCATCCGTG 58.782 55.000 0.00 0.00 0.00 4.94
1115 1158 0.828022 TCCGCTTAATCCATCCGTGT 59.172 50.000 0.00 0.00 0.00 4.49
1116 1159 1.208535 TCCGCTTAATCCATCCGTGTT 59.791 47.619 0.00 0.00 0.00 3.32
1117 1160 1.597663 CCGCTTAATCCATCCGTGTTC 59.402 52.381 0.00 0.00 0.00 3.18
1118 1161 2.276201 CGCTTAATCCATCCGTGTTCA 58.724 47.619 0.00 0.00 0.00 3.18
1119 1162 2.285220 CGCTTAATCCATCCGTGTTCAG 59.715 50.000 0.00 0.00 0.00 3.02
1120 1163 3.531538 GCTTAATCCATCCGTGTTCAGA 58.468 45.455 0.00 0.00 0.00 3.27
1121 1164 4.130118 GCTTAATCCATCCGTGTTCAGAT 58.870 43.478 0.00 0.00 0.00 2.90
1122 1165 4.576463 GCTTAATCCATCCGTGTTCAGATT 59.424 41.667 0.00 0.00 0.00 2.40
1128 1171 0.963225 TCCGTGTTCAGATTCGGTCA 59.037 50.000 0.00 0.00 42.95 4.02
1150 1193 1.217882 GTAATCCATCCGCGTTCAGG 58.782 55.000 4.92 1.07 0.00 3.86
1158 1201 1.597027 CCGCGTTCAGGTTTGGTCT 60.597 57.895 4.92 0.00 0.00 3.85
1289 1469 3.263425 TCTGGATTGAGTACAAGGGGAAC 59.737 47.826 0.00 0.00 39.46 3.62
1312 1493 4.132336 GGGATTCGGGGTTAATCTTACAC 58.868 47.826 0.00 0.00 34.43 2.90
1338 1519 1.949465 CTTTAAATCCTAGCCGCGGT 58.051 50.000 28.70 16.08 0.00 5.68
1494 1678 0.606401 CTTGACCACCATCGCCACTT 60.606 55.000 0.00 0.00 0.00 3.16
1596 1798 2.952116 GGAGCTCTGTACTCCCTGTAT 58.048 52.381 14.64 0.00 46.81 2.29
1602 1804 2.167693 TCTGTACTCCCTGTATTTGGCG 59.832 50.000 0.00 0.00 33.23 5.69
1628 1830 2.435410 CCTCTGTGCAGCATCGCA 60.435 61.111 0.00 0.00 40.32 5.10
1631 1833 4.175489 CTGTGCAGCATCGCAGGC 62.175 66.667 0.00 0.00 44.05 4.85
1694 1896 1.889530 GCGCCCTTCACTAGGTCAGT 61.890 60.000 0.00 0.00 43.07 3.41
1779 2022 1.594293 CGAACTTGGTGCGGTCACT 60.594 57.895 3.32 0.00 42.72 3.41
1853 2116 0.533755 GGAGTTCATGGCGATGGAGG 60.534 60.000 8.98 0.00 0.00 4.30
1854 2117 0.179000 GAGTTCATGGCGATGGAGGT 59.821 55.000 8.98 0.00 0.00 3.85
1856 2119 1.097547 GTTCATGGCGATGGAGGTGG 61.098 60.000 8.98 0.00 0.00 4.61
1857 2120 1.561769 TTCATGGCGATGGAGGTGGT 61.562 55.000 8.98 0.00 0.00 4.16
1858 2121 0.689412 TCATGGCGATGGAGGTGGTA 60.689 55.000 8.98 0.00 0.00 3.25
1859 2122 0.250038 CATGGCGATGGAGGTGGTAG 60.250 60.000 0.00 0.00 0.00 3.18
1919 2265 7.436118 ACTTTGTGTTGTTCATAATGCAGATT 58.564 30.769 0.00 0.00 0.00 2.40
1923 2269 6.032094 GTGTTGTTCATAATGCAGATTGAGG 58.968 40.000 0.00 0.00 0.00 3.86
2069 2532 1.434513 ATGAGGGTGGGCCAACTCAA 61.435 55.000 32.84 21.70 42.55 3.02
2078 2541 1.344114 GGGCCAACTCAATTCTGCAAA 59.656 47.619 4.39 0.00 0.00 3.68
2082 2545 3.054878 CCAACTCAATTCTGCAAAGTGC 58.945 45.455 0.00 0.00 45.29 4.40
2158 2647 0.868406 CTGAAGACAAACACCGGCTC 59.132 55.000 0.00 0.00 0.00 4.70
2160 2649 1.228154 AAGACAAACACCGGCTCCC 60.228 57.895 0.00 0.00 0.00 4.30
2204 3314 1.301479 GAACGGCCGAGTCAACCTT 60.301 57.895 35.90 13.40 0.00 3.50
2281 3401 2.170397 TGACCTTCAAGTTGCTGACTCA 59.830 45.455 0.00 0.00 37.72 3.41
2349 3469 2.515398 CCAAGTGTGGGAGGCACA 59.485 61.111 0.00 0.00 41.77 4.57
2551 3694 1.580845 CTGCCTGCCTAGTGTGTTGC 61.581 60.000 0.00 0.00 0.00 4.17
2561 3705 4.562963 GCCTAGTGTGTTGCTAACCTTACT 60.563 45.833 0.00 0.00 0.00 2.24
2635 3779 1.644786 ATCGCCTGGCTACGCAAAAC 61.645 55.000 17.92 0.00 0.00 2.43
2789 3933 8.999220 AAAACACCAAAATTTACTAACCGAAA 57.001 26.923 0.00 0.00 0.00 3.46
2848 3992 3.645975 CCCAACAAGAACGCGCGT 61.646 61.111 32.73 32.73 0.00 6.01
2891 4035 0.753867 GGAGGAGAAAGGGGATCGAC 59.246 60.000 0.00 0.00 0.00 4.20
2894 4038 1.196012 GGAGAAAGGGGATCGACTGT 58.804 55.000 0.00 0.00 0.00 3.55
2947 4091 2.126372 CCCCAAGACCCACCCCTA 59.874 66.667 0.00 0.00 0.00 3.53
2949 4093 1.229853 CCCAAGACCCACCCCTAGT 60.230 63.158 0.00 0.00 0.00 2.57
3054 4198 3.612717 CGGCATGCTAGTAGTAGTGGATG 60.613 52.174 18.92 7.47 0.00 3.51
3080 4224 8.616076 GTTAGGATAGATCTCACCATTGTTTTG 58.384 37.037 16.87 0.00 0.00 2.44
3097 4241 1.344065 TTGAAGTCGTCCCTAAGGCA 58.656 50.000 0.00 0.00 0.00 4.75
3100 4244 1.480954 GAAGTCGTCCCTAAGGCATCA 59.519 52.381 0.00 0.00 0.00 3.07
3143 4287 1.098050 CCTTGCCTTAGACACATGCC 58.902 55.000 0.00 0.00 0.00 4.40
3147 4291 3.712016 TGCCTTAGACACATGCCTAAA 57.288 42.857 0.00 0.00 0.00 1.85
3180 4324 2.738521 CACAGGGCGTCCAAGTCG 60.739 66.667 9.71 0.00 34.83 4.18
3203 4347 1.613836 GCCTAGGCAAATCTGGATGG 58.386 55.000 29.33 0.00 41.49 3.51
3207 4351 3.196040 GGCAAATCTGGATGGCTCA 57.804 52.632 7.20 0.00 38.91 4.26
3246 4390 0.034896 GGCGGGAAACAGAGTCTTGA 59.965 55.000 0.00 0.00 0.00 3.02
3250 4394 1.000955 GGGAAACAGAGTCTTGAGCGA 59.999 52.381 0.00 0.00 0.00 4.93
3267 4424 2.573920 GAGAACCAGAGGCTCTCGT 58.426 57.895 15.60 12.15 35.60 4.18
3277 4434 3.972227 GCTCTCGTGTGCCAACAT 58.028 55.556 0.21 0.00 38.92 2.71
3304 4461 2.090606 AGCAGGGGAATCAGAGAGATCT 60.091 50.000 0.00 0.00 35.39 2.75
3322 4479 5.098663 AGATCTAACTAGTTTTCCCCCACA 58.901 41.667 14.49 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.269381 TGCCCTCCTTTCCTGAAATACAT 59.731 43.478 0.00 0.00 0.00 2.29
18 19 2.242196 CCTGCCCTCCTTTCCTGAAATA 59.758 50.000 0.00 0.00 0.00 1.40
42 43 2.224917 CCTTGCTTGTTAACCCCCTACA 60.225 50.000 2.48 0.00 0.00 2.74
94 95 7.607250 AGAAATCAGTACGACTTCTCTGAAAT 58.393 34.615 5.87 0.00 35.27 2.17
356 357 7.802720 CGACAACACATCATGATTTTGAACTTA 59.197 33.333 20.69 0.00 0.00 2.24
379 380 9.166126 CACAACTTAGAAATTAAAGAAACCGAC 57.834 33.333 3.00 0.00 0.00 4.79
454 456 2.904866 TGTGGTGACCAAAGGCGC 60.905 61.111 5.57 0.00 34.18 6.53
589 591 0.392998 CACGCCCTAGGACAATGCTT 60.393 55.000 11.48 0.00 0.00 3.91
590 592 1.221840 CACGCCCTAGGACAATGCT 59.778 57.895 11.48 0.00 0.00 3.79
644 646 5.617252 ACCAAACAGACTATTTTCTTCCGA 58.383 37.500 0.00 0.00 0.00 4.55
645 647 5.941948 ACCAAACAGACTATTTTCTTCCG 57.058 39.130 0.00 0.00 0.00 4.30
699 710 2.819608 GCTGGAGGTGCTTTAAACATCA 59.180 45.455 4.57 0.00 30.08 3.07
825 858 1.292992 GACGGTTCTGGAAACAACGT 58.707 50.000 0.00 0.00 42.06 3.99
860 893 1.076677 AGAGAACGGTGAGGGAAGGTA 59.923 52.381 0.00 0.00 0.00 3.08
875 918 4.449968 GGATAATGGAGAGGGGAGAGAGAA 60.450 50.000 0.00 0.00 0.00 2.87
882 925 1.585592 AGTGGGATAATGGAGAGGGGA 59.414 52.381 0.00 0.00 0.00 4.81
885 928 3.041211 TGACAGTGGGATAATGGAGAGG 58.959 50.000 0.00 0.00 0.00 3.69
895 938 2.592993 CCCGGTGTGACAGTGGGAT 61.593 63.158 15.17 0.00 42.77 3.85
940 983 2.676471 GGCCGATGGTTGCCTTGT 60.676 61.111 0.00 0.00 44.46 3.16
999 1042 5.241728 GGTGAAAATAGGGCTTACCATCATC 59.758 44.000 0.00 0.00 43.89 2.92
1003 1046 4.386424 GGAGGTGAAAATAGGGCTTACCAT 60.386 45.833 0.00 0.00 43.89 3.55
1004 1047 3.053917 GGAGGTGAAAATAGGGCTTACCA 60.054 47.826 0.00 0.00 43.89 3.25
1063 1106 1.769098 CGGATGGATTGCGCAGACTG 61.769 60.000 11.31 0.00 30.45 3.51
1064 1107 1.522355 CGGATGGATTGCGCAGACT 60.522 57.895 11.31 0.00 30.45 3.24
1065 1108 3.017323 CGGATGGATTGCGCAGAC 58.983 61.111 11.31 8.85 30.45 3.51
1071 1114 2.890109 CTGAGCGCGGATGGATTGC 61.890 63.158 8.83 0.00 0.00 3.56
1072 1115 0.602106 ATCTGAGCGCGGATGGATTG 60.602 55.000 11.32 0.00 38.69 2.67
1073 1116 0.107456 AATCTGAGCGCGGATGGATT 59.893 50.000 12.88 6.54 40.02 3.01
1074 1117 0.320247 GAATCTGAGCGCGGATGGAT 60.320 55.000 12.88 0.00 40.02 3.41
1075 1118 1.068083 GAATCTGAGCGCGGATGGA 59.932 57.895 12.88 0.00 40.02 3.41
1076 1119 2.305853 CGAATCTGAGCGCGGATGG 61.306 63.158 12.88 4.50 40.02 3.51
1077 1120 2.305853 CCGAATCTGAGCGCGGATG 61.306 63.158 12.88 1.17 46.29 3.51
1078 1121 2.028190 CCGAATCTGAGCGCGGAT 59.972 61.111 8.83 5.87 46.29 4.18
1079 1122 3.411418 GACCGAATCTGAGCGCGGA 62.411 63.158 18.36 0.00 46.29 5.54
1081 1124 2.956964 GGACCGAATCTGAGCGCG 60.957 66.667 0.00 0.00 0.00 6.86
1082 1125 2.956964 CGGACCGAATCTGAGCGC 60.957 66.667 8.64 0.00 35.44 5.92
1083 1126 2.890847 AAGCGGACCGAATCTGAGCG 62.891 60.000 20.50 0.00 35.44 5.03
1084 1127 0.102481 TAAGCGGACCGAATCTGAGC 59.898 55.000 20.50 0.00 35.44 4.26
1085 1128 2.579207 TTAAGCGGACCGAATCTGAG 57.421 50.000 20.50 0.00 35.44 3.35
1086 1129 2.223971 GGATTAAGCGGACCGAATCTGA 60.224 50.000 20.50 0.00 35.44 3.27
1087 1130 2.135933 GGATTAAGCGGACCGAATCTG 58.864 52.381 20.50 0.00 36.68 2.90
1088 1131 1.760613 TGGATTAAGCGGACCGAATCT 59.239 47.619 20.50 1.67 0.00 2.40
1089 1132 2.234300 TGGATTAAGCGGACCGAATC 57.766 50.000 20.50 17.16 0.00 2.52
1090 1133 2.550208 GGATGGATTAAGCGGACCGAAT 60.550 50.000 20.50 8.68 0.00 3.34
1091 1134 1.202604 GGATGGATTAAGCGGACCGAA 60.203 52.381 20.50 3.03 0.00 4.30
1092 1135 0.391597 GGATGGATTAAGCGGACCGA 59.608 55.000 20.50 0.00 0.00 4.69
1093 1136 0.944311 CGGATGGATTAAGCGGACCG 60.944 60.000 10.29 10.29 0.00 4.79
1094 1137 0.106149 ACGGATGGATTAAGCGGACC 59.894 55.000 0.00 0.00 0.00 4.46
1095 1138 1.217882 CACGGATGGATTAAGCGGAC 58.782 55.000 0.00 0.00 0.00 4.79
1096 1139 0.828022 ACACGGATGGATTAAGCGGA 59.172 50.000 0.00 0.00 0.00 5.54
1097 1140 1.597663 GAACACGGATGGATTAAGCGG 59.402 52.381 0.00 0.00 0.00 5.52
1098 1141 2.276201 TGAACACGGATGGATTAAGCG 58.724 47.619 0.00 0.00 0.00 4.68
1099 1142 3.531538 TCTGAACACGGATGGATTAAGC 58.468 45.455 0.00 0.00 0.00 3.09
1100 1143 5.050769 CGAATCTGAACACGGATGGATTAAG 60.051 44.000 0.00 0.00 31.05 1.85
1101 1144 4.808895 CGAATCTGAACACGGATGGATTAA 59.191 41.667 0.00 0.00 31.05 1.40
1102 1145 4.368315 CGAATCTGAACACGGATGGATTA 58.632 43.478 0.00 0.00 31.05 1.75
1103 1146 3.198068 CGAATCTGAACACGGATGGATT 58.802 45.455 0.00 0.00 31.05 3.01
1104 1147 2.483714 CCGAATCTGAACACGGATGGAT 60.484 50.000 12.68 0.00 46.94 3.41
1105 1148 1.134818 CCGAATCTGAACACGGATGGA 60.135 52.381 12.68 0.00 46.94 3.41
1106 1149 1.290203 CCGAATCTGAACACGGATGG 58.710 55.000 12.68 0.00 46.94 3.51
1107 1150 1.927174 GACCGAATCTGAACACGGATG 59.073 52.381 20.79 2.74 46.94 3.51
1108 1151 1.548719 TGACCGAATCTGAACACGGAT 59.451 47.619 20.79 9.79 46.94 4.18
1109 1152 0.963225 TGACCGAATCTGAACACGGA 59.037 50.000 20.79 3.75 46.94 4.69
1111 1154 1.721389 CACTGACCGAATCTGAACACG 59.279 52.381 0.00 0.00 0.00 4.49
1112 1155 2.755650 ACACTGACCGAATCTGAACAC 58.244 47.619 0.00 0.00 0.00 3.32
1113 1156 4.594123 TTACACTGACCGAATCTGAACA 57.406 40.909 0.00 0.00 0.00 3.18
1114 1157 4.567159 GGATTACACTGACCGAATCTGAAC 59.433 45.833 0.00 0.00 0.00 3.18
1115 1158 4.221924 TGGATTACACTGACCGAATCTGAA 59.778 41.667 0.00 0.00 0.00 3.02
1116 1159 3.767131 TGGATTACACTGACCGAATCTGA 59.233 43.478 0.00 0.00 0.00 3.27
1117 1160 4.123497 TGGATTACACTGACCGAATCTG 57.877 45.455 0.00 0.00 0.00 2.90
1118 1161 4.202264 GGATGGATTACACTGACCGAATCT 60.202 45.833 0.00 0.00 0.00 2.40
1119 1162 4.058817 GGATGGATTACACTGACCGAATC 58.941 47.826 0.00 0.00 0.00 2.52
1120 1163 3.492656 CGGATGGATTACACTGACCGAAT 60.493 47.826 0.00 0.00 37.18 3.34
1121 1164 2.159156 CGGATGGATTACACTGACCGAA 60.159 50.000 0.00 0.00 37.18 4.30
1122 1165 1.407618 CGGATGGATTACACTGACCGA 59.592 52.381 0.00 0.00 37.18 4.69
1128 1171 1.206132 TGAACGCGGATGGATTACACT 59.794 47.619 12.47 0.00 0.00 3.55
1150 1193 3.063997 CAGATGGATTACGCAGACCAAAC 59.936 47.826 0.00 0.00 36.00 2.93
1158 1201 1.134818 AGAACGCAGATGGATTACGCA 60.135 47.619 0.00 0.00 0.00 5.24
1289 1469 2.632987 AAGATTAACCCCGAATCCCG 57.367 50.000 0.00 0.00 34.42 5.14
1312 1493 4.058817 CGGCTAGGATTTAAAGCTACTGG 58.941 47.826 3.10 0.00 36.48 4.00
1338 1519 4.020617 CAAGCGCCTCCAGGGTCA 62.021 66.667 2.29 0.00 37.43 4.02
1476 1660 0.888736 CAAGTGGCGATGGTGGTCAA 60.889 55.000 0.00 0.00 0.00 3.18
1602 1804 1.654954 CTGCACAGAGGGCAAGATGC 61.655 60.000 0.00 0.00 41.39 3.91
1631 1833 1.954528 GCCATGAATCAGGCCGATG 59.045 57.895 10.25 0.00 45.18 3.84
1632 1834 4.488790 GCCATGAATCAGGCCGAT 57.511 55.556 11.11 0.00 45.18 4.18
1694 1896 3.119101 GGAGGAGTTGAAGACGCTGATTA 60.119 47.826 0.00 0.00 0.00 1.75
1853 2116 6.645790 TTAAATCCTATCGTCCTCTACCAC 57.354 41.667 0.00 0.00 0.00 4.16
1854 2117 6.295123 GCATTAAATCCTATCGTCCTCTACCA 60.295 42.308 0.00 0.00 0.00 3.25
1856 2119 6.100668 GGCATTAAATCCTATCGTCCTCTAC 58.899 44.000 0.00 0.00 0.00 2.59
1857 2120 5.105877 CGGCATTAAATCCTATCGTCCTCTA 60.106 44.000 0.00 0.00 0.00 2.43
1858 2121 4.322049 CGGCATTAAATCCTATCGTCCTCT 60.322 45.833 0.00 0.00 0.00 3.69
1859 2122 3.927142 CGGCATTAAATCCTATCGTCCTC 59.073 47.826 0.00 0.00 0.00 3.71
1919 2265 1.302511 GCCCTTGTTCTTCGCCTCA 60.303 57.895 0.00 0.00 0.00 3.86
1923 2269 0.889186 TCCTTGCCCTTGTTCTTCGC 60.889 55.000 0.00 0.00 0.00 4.70
1993 2453 2.923035 CCTCCACCACCACGTCCT 60.923 66.667 0.00 0.00 0.00 3.85
2082 2545 1.356124 AGTCTAGGGGCATAGGCATG 58.644 55.000 0.15 0.00 43.71 4.06
2083 2546 1.981495 GAAGTCTAGGGGCATAGGCAT 59.019 52.381 0.15 0.00 43.71 4.40
2084 2547 1.343985 TGAAGTCTAGGGGCATAGGCA 60.344 52.381 0.15 0.00 43.71 4.75
2085 2548 1.070914 GTGAAGTCTAGGGGCATAGGC 59.929 57.143 0.00 0.00 40.13 3.93
2173 3281 0.955428 GCCGTTCATCAGCTGGACAA 60.955 55.000 15.13 0.74 32.23 3.18
2221 3331 2.029964 GGTGGACGACGGCAAAGA 59.970 61.111 1.63 0.00 0.00 2.52
2363 3483 2.026636 AGAGCTCTCCTAGACGTTCACT 60.027 50.000 11.45 0.00 0.00 3.41
2551 3694 5.793030 CCTCATGGAGGTAGTAAGGTTAG 57.207 47.826 4.08 0.00 44.25 2.34
2645 3789 4.814234 CACGTCCTATTAAATAGCCAAGCA 59.186 41.667 0.00 0.00 0.00 3.91
2678 3822 1.577242 AGGATTTGGATGCCCTTCCAT 59.423 47.619 4.02 0.00 45.08 3.41
2848 3992 1.112916 TGGCTCCAACTCGACAGTCA 61.113 55.000 0.41 0.00 29.93 3.41
2891 4035 2.180017 GCCGCAATGCTTGGACAG 59.820 61.111 2.94 0.00 0.00 3.51
2894 4038 2.033911 TGAGCCGCAATGCTTGGA 59.966 55.556 2.94 0.00 42.95 3.53
2915 4059 2.006991 GGGGCTTACCAGGGGTCAT 61.007 63.158 0.00 0.00 42.91 3.06
2975 4119 4.585216 AACCCTCCCCACCGTCCA 62.585 66.667 0.00 0.00 0.00 4.02
3054 4198 8.616076 CAAAACAATGGTGAGATCTATCCTAAC 58.384 37.037 14.27 0.25 0.00 2.34
3080 4224 1.480954 TGATGCCTTAGGGACGACTTC 59.519 52.381 0.00 0.00 33.58 3.01
3097 4241 1.935973 TAGGCGTCCCCTAGGTGAT 59.064 57.895 8.29 0.00 44.08 3.06
3147 4291 1.003718 GTGACCTAAGGCAACCGCT 60.004 57.895 0.00 0.00 38.60 5.52
3151 4295 0.960861 GCCCTGTGACCTAAGGCAAC 60.961 60.000 0.00 0.00 43.32 4.17
3152 4296 1.378762 GCCCTGTGACCTAAGGCAA 59.621 57.895 0.00 0.00 43.32 4.52
3180 4324 0.815615 CCAGATTTGCCTAGGCGGAC 60.816 60.000 28.28 18.38 45.51 4.79
3246 4390 1.304879 AGAGCCTCTGGTTCTCGCT 60.305 57.895 0.00 0.00 38.96 4.93
3250 4394 0.540830 ACACGAGAGCCTCTGGTTCT 60.541 55.000 6.65 2.64 45.73 3.01
3267 4424 1.535028 CTGCTCGTAAATGTTGGCACA 59.465 47.619 0.00 0.00 37.31 4.57
3277 4434 2.168521 CTCTGATTCCCCTGCTCGTAAA 59.831 50.000 0.00 0.00 0.00 2.01
3304 4461 5.318630 GTTCATGTGGGGGAAAACTAGTTA 58.681 41.667 8.92 0.00 0.00 2.24
3322 4479 2.275380 GCCGCCACCAAAGGTTCAT 61.275 57.895 0.00 0.00 31.02 2.57


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

AutoCloner maintained by Alex Coulton.