Multiple sequence alignment - TraesCS3D01G122900

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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 TraesCS3D01G122900 chr3D 100.000 3422 0 0 1 3422 80631469 80628048 0.000000e+00 6320.0
1 TraesCS3D01G122900 chr3D 90.954 1636 100 17 835 2431 80917679 80916053 0.000000e+00 2158.0
2 TraesCS3D01G122900 chr3D 89.969 1605 93 27 843 2405 80601528 80599950 0.000000e+00 2010.0
3 TraesCS3D01G122900 chr3D 83.473 1434 183 19 984 2402 81122197 81120803 0.000000e+00 1286.0
4 TraesCS3D01G122900 chr3D 85.432 405 36 13 443 834 80632020 80632414 1.910000e-107 399.0
5 TraesCS3D01G122900 chr3D 82.679 433 55 10 996 1422 81057715 81057297 1.940000e-97 366.0
6 TraesCS3D01G122900 chr3D 82.759 406 40 13 449 835 610887616 610888010 5.470000e-88 335.0
7 TraesCS3D01G122900 chr3D 88.415 164 16 3 2740 2902 80915831 80915670 9.690000e-46 195.0
8 TraesCS3D01G122900 chr3D 82.667 75 5 5 1309 1379 396434481 396434551 3.690000e-05 60.2
9 TraesCS3D01G122900 chr3B 91.457 2622 146 27 836 3422 126459195 126456617 0.000000e+00 3530.0
10 TraesCS3D01G122900 chr3B 91.539 1631 92 18 836 2431 126400979 126399360 0.000000e+00 2206.0
11 TraesCS3D01G122900 chr3B 83.646 1437 181 23 984 2402 126733609 126732209 0.000000e+00 1303.0
12 TraesCS3D01G122900 chr3B 82.863 1418 187 22 996 2394 126664589 126663209 0.000000e+00 1221.0
13 TraesCS3D01G122900 chr3B 83.538 407 58 5 984 1381 126715069 126714663 4.170000e-99 372.0
14 TraesCS3D01G122900 chr3B 89.524 105 9 2 672 774 687631140 687631036 7.710000e-27 132.0
15 TraesCS3D01G122900 chr3B 91.781 73 6 0 2597 2669 126399021 126398949 6.040000e-18 102.0
16 TraesCS3D01G122900 chr3A 92.976 1808 89 20 1216 2996 94384152 94382356 0.000000e+00 2601.0
17 TraesCS3D01G122900 chr3A 87.998 1908 127 47 843 2663 94255483 94253591 0.000000e+00 2161.0
18 TraesCS3D01G122900 chr3A 91.060 1622 107 18 836 2431 94859324 94857715 0.000000e+00 2158.0
19 TraesCS3D01G122900 chr3A 84.225 1420 177 17 996 2402 95359679 95358294 0.000000e+00 1338.0
20 TraesCS3D01G122900 chr3A 90.705 667 49 7 1 667 93330540 93331193 0.000000e+00 876.0
21 TraesCS3D01G122900 chr3A 98.228 395 7 0 835 1229 94385092 94384698 0.000000e+00 691.0
22 TraesCS3D01G122900 chr3A 88.249 434 47 3 2989 3422 94348784 94348355 1.820000e-142 516.0
23 TraesCS3D01G122900 chr3A 88.018 434 48 3 2989 3422 94377103 94376674 8.470000e-141 510.0
24 TraesCS3D01G122900 chr3A 78.947 456 46 22 2252 2663 94203076 94202627 7.280000e-67 265.0
25 TraesCS3D01G122900 chr2D 93.939 759 29 7 1 755 628603914 628604659 0.000000e+00 1131.0
26 TraesCS3D01G122900 chr2D 96.033 605 11 4 1 605 634656384 634655793 0.000000e+00 972.0
27 TraesCS3D01G122900 chr2D 93.361 241 7 4 603 834 634655675 634655435 7.030000e-92 348.0
28 TraesCS3D01G122900 chr2D 83.333 402 41 13 445 834 634656945 634657332 7.030000e-92 348.0
29 TraesCS3D01G122900 chr2D 80.597 335 47 17 443 770 628603351 628603028 3.410000e-60 243.0
30 TraesCS3D01G122900 chr2D 81.290 155 26 3 2992 3145 580399301 580399149 4.640000e-24 122.0
31 TraesCS3D01G122900 chr2D 94.444 36 1 1 806 841 584251922 584251888 2.000000e-03 54.7
32 TraesCS3D01G122900 chr7A 79.327 1427 213 50 997 2400 53295177 53293810 0.000000e+00 926.0
33 TraesCS3D01G122900 chr7A 80.631 888 144 20 1216 2094 53521081 53520213 0.000000e+00 662.0
34 TraesCS3D01G122900 chr7D 79.044 1422 214 48 997 2400 50428917 50427562 0.000000e+00 898.0
35 TraesCS3D01G122900 chr7D 78.829 1417 220 51 999 2402 50641748 50640399 0.000000e+00 881.0
36 TraesCS3D01G122900 chr7D 90.196 102 6 4 672 770 185806264 185806164 2.770000e-26 130.0
37 TraesCS3D01G122900 chr7D 80.240 167 30 2 1229 1395 613522267 613522430 4.640000e-24 122.0
38 TraesCS3D01G122900 chr4A 79.018 1406 216 44 1008 2402 665438853 665440190 0.000000e+00 889.0
39 TraesCS3D01G122900 chr4A 78.801 1434 218 53 984 2398 665318868 665317502 0.000000e+00 885.0
40 TraesCS3D01G122900 chr4A 83.976 337 44 3 317 652 707213257 707213584 7.130000e-82 315.0
41 TraesCS3D01G122900 chr6D 94.058 589 17 10 1 588 45664731 45664160 0.000000e+00 878.0
42 TraesCS3D01G122900 chr6D 83.916 286 29 12 496 774 45665338 45665613 1.220000e-64 257.0
43 TraesCS3D01G122900 chrUn 90.719 668 44 9 1 667 292816666 292816016 0.000000e+00 874.0
44 TraesCS3D01G122900 chrUn 90.419 668 47 9 1 667 201617705 201618356 0.000000e+00 863.0
45 TraesCS3D01G122900 chrUn 89.820 668 51 9 1 667 201628056 201628707 0.000000e+00 841.0
46 TraesCS3D01G122900 chrUn 80.000 115 12 5 730 834 465064287 465064400 1.320000e-09 75.0
47 TraesCS3D01G122900 chr4B 87.113 582 47 13 1 578 574695429 574694872 4.820000e-178 634.0
48 TraesCS3D01G122900 chr5D 96.199 342 8 2 1 342 489168784 489168448 3.860000e-154 555.0
49 TraesCS3D01G122900 chr5D 90.520 327 25 1 341 667 489168288 489167968 8.780000e-116 427.0
50 TraesCS3D01G122900 chr5D 80.870 115 11 5 730 834 399165499 399165386 2.830000e-11 80.5
51 TraesCS3D01G122900 chr5D 94.286 35 0 2 806 840 255473118 255473086 6.000000e-03 52.8
52 TraesCS3D01G122900 chr6B 90.093 323 29 3 235 555 128194658 128194979 1.900000e-112 416.0
53 TraesCS3D01G122900 chr4D 90.566 106 5 5 672 774 504072028 504071925 5.960000e-28 135.0
54 TraesCS3D01G122900 chr7B 82.639 144 22 3 1244 1386 703995801 703995942 1.290000e-24 124.0
55 TraesCS3D01G122900 chr7B 76.879 173 28 6 673 834 312348958 312348787 1.690000e-13 87.9
56 TraesCS3D01G122900 chr7B 81.897 116 9 6 730 834 485615187 485615073 1.690000e-13 87.9
57 TraesCS3D01G122900 chr7B 76.074 163 26 7 683 834 115205201 115205361 4.740000e-09 73.1
58 TraesCS3D01G122900 chr2B 77.576 165 24 7 681 834 25232772 25232610 1.690000e-13 87.9


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 TraesCS3D01G122900 chr3D 80628048 80631469 3421 True 6320.0 6320 100.0000 1 3422 1 chr3D.!!$R2 3421
1 TraesCS3D01G122900 chr3D 80599950 80601528 1578 True 2010.0 2010 89.9690 843 2405 1 chr3D.!!$R1 1562
2 TraesCS3D01G122900 chr3D 81120803 81122197 1394 True 1286.0 1286 83.4730 984 2402 1 chr3D.!!$R4 1418
3 TraesCS3D01G122900 chr3D 80915670 80917679 2009 True 1176.5 2158 89.6845 835 2902 2 chr3D.!!$R5 2067
4 TraesCS3D01G122900 chr3B 126456617 126459195 2578 True 3530.0 3530 91.4570 836 3422 1 chr3B.!!$R1 2586
5 TraesCS3D01G122900 chr3B 126732209 126733609 1400 True 1303.0 1303 83.6460 984 2402 1 chr3B.!!$R4 1418
6 TraesCS3D01G122900 chr3B 126663209 126664589 1380 True 1221.0 1221 82.8630 996 2394 1 chr3B.!!$R2 1398
7 TraesCS3D01G122900 chr3B 126398949 126400979 2030 True 1154.0 2206 91.6600 836 2669 2 chr3B.!!$R6 1833
8 TraesCS3D01G122900 chr3A 94253591 94255483 1892 True 2161.0 2161 87.9980 843 2663 1 chr3A.!!$R2 1820
9 TraesCS3D01G122900 chr3A 94857715 94859324 1609 True 2158.0 2158 91.0600 836 2431 1 chr3A.!!$R5 1595
10 TraesCS3D01G122900 chr3A 94382356 94385092 2736 True 1646.0 2601 95.6020 835 2996 2 chr3A.!!$R7 2161
11 TraesCS3D01G122900 chr3A 95358294 95359679 1385 True 1338.0 1338 84.2250 996 2402 1 chr3A.!!$R6 1406
12 TraesCS3D01G122900 chr3A 93330540 93331193 653 False 876.0 876 90.7050 1 667 1 chr3A.!!$F1 666
13 TraesCS3D01G122900 chr2D 628603914 628604659 745 False 1131.0 1131 93.9390 1 755 1 chr2D.!!$F1 754
14 TraesCS3D01G122900 chr2D 634655435 634656384 949 True 660.0 972 94.6970 1 834 2 chr2D.!!$R4 833
15 TraesCS3D01G122900 chr7A 53293810 53295177 1367 True 926.0 926 79.3270 997 2400 1 chr7A.!!$R1 1403
16 TraesCS3D01G122900 chr7A 53520213 53521081 868 True 662.0 662 80.6310 1216 2094 1 chr7A.!!$R2 878
17 TraesCS3D01G122900 chr7D 50427562 50428917 1355 True 898.0 898 79.0440 997 2400 1 chr7D.!!$R1 1403
18 TraesCS3D01G122900 chr7D 50640399 50641748 1349 True 881.0 881 78.8290 999 2402 1 chr7D.!!$R2 1403
19 TraesCS3D01G122900 chr4A 665438853 665440190 1337 False 889.0 889 79.0180 1008 2402 1 chr4A.!!$F1 1394
20 TraesCS3D01G122900 chr4A 665317502 665318868 1366 True 885.0 885 78.8010 984 2398 1 chr4A.!!$R1 1414
21 TraesCS3D01G122900 chr6D 45664160 45664731 571 True 878.0 878 94.0580 1 588 1 chr6D.!!$R1 587
22 TraesCS3D01G122900 chrUn 292816016 292816666 650 True 874.0 874 90.7190 1 667 1 chrUn.!!$R1 666
23 TraesCS3D01G122900 chrUn 201617705 201618356 651 False 863.0 863 90.4190 1 667 1 chrUn.!!$F1 666
24 TraesCS3D01G122900 chrUn 201628056 201628707 651 False 841.0 841 89.8200 1 667 1 chrUn.!!$F2 666
25 TraesCS3D01G122900 chr4B 574694872 574695429 557 True 634.0 634 87.1130 1 578 1 chr4B.!!$R1 577
26 TraesCS3D01G122900 chr5D 489167968 489168784 816 True 491.0 555 93.3595 1 667 2 chr5D.!!$R3 666

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
597 889 0.457035 ATCGCCTGCGCATCATTTTT 59.543 45.0 12.24 0.0 39.59 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2468 3478 1.070108 CAGATGCATTCGATCGCAAGG 60.07 52.381 11.09 8.74 42.37 3.61 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
357 523 6.744082 CAGACATATATAAAACATGCATGCCG 59.256 38.462 26.53 9.08 0.00 5.69
492 658 6.263617 TGTTTAAAGGCGAAAGAATACAAGGT 59.736 34.615 0.00 0.00 0.00 3.50
544 710 2.269241 GTGTAGTGGCTGGGAGGC 59.731 66.667 0.00 0.00 41.77 4.70
578 870 0.596600 GCAGGTCGCCGATTCGAATA 60.597 55.000 11.38 0.00 40.43 1.75
589 881 0.599991 ATTCGAATATCGCCTGCGCA 60.600 50.000 10.98 10.98 40.21 6.09
590 882 0.599991 TTCGAATATCGCCTGCGCAT 60.600 50.000 12.24 0.00 40.21 4.73
596 888 1.308047 TATCGCCTGCGCATCATTTT 58.692 45.000 12.24 0.00 39.59 1.82
597 889 0.457035 ATCGCCTGCGCATCATTTTT 59.543 45.000 12.24 0.00 39.59 1.94
760 1057 7.820044 TTTTGTCACGAAATTAGCAAAAAGT 57.180 28.000 0.00 0.00 34.33 2.66
761 1058 6.804534 TTGTCACGAAATTAGCAAAAAGTG 57.195 33.333 0.00 0.00 0.00 3.16
762 1059 5.277825 TGTCACGAAATTAGCAAAAAGTGG 58.722 37.500 0.00 0.00 0.00 4.00
763 1060 5.066634 TGTCACGAAATTAGCAAAAAGTGGA 59.933 36.000 0.00 0.00 0.00 4.02
764 1061 5.974751 GTCACGAAATTAGCAAAAAGTGGAA 59.025 36.000 0.00 0.00 0.00 3.53
765 1062 6.142320 GTCACGAAATTAGCAAAAAGTGGAAG 59.858 38.462 0.00 0.00 0.00 3.46
766 1063 5.977129 CACGAAATTAGCAAAAAGTGGAAGT 59.023 36.000 0.00 0.00 0.00 3.01
767 1064 6.475402 CACGAAATTAGCAAAAAGTGGAAGTT 59.525 34.615 0.00 0.00 0.00 2.66
768 1065 7.010091 CACGAAATTAGCAAAAAGTGGAAGTTT 59.990 33.333 0.00 0.00 42.32 2.66
777 1074 5.900865 AAAAGTGGAAGTTTTCGGTACAA 57.099 34.783 0.00 0.00 45.87 2.41
778 1075 5.900865 AAAGTGGAAGTTTTCGGTACAAA 57.099 34.783 0.00 0.00 35.56 2.83
779 1076 5.900865 AAGTGGAAGTTTTCGGTACAAAA 57.099 34.783 0.00 0.00 0.00 2.44
780 1077 6.459670 AAGTGGAAGTTTTCGGTACAAAAT 57.540 33.333 0.00 0.00 0.00 1.82
781 1078 6.068473 AGTGGAAGTTTTCGGTACAAAATC 57.932 37.500 0.00 0.00 0.00 2.17
782 1079 4.907582 GTGGAAGTTTTCGGTACAAAATCG 59.092 41.667 0.00 0.00 0.00 3.34
783 1080 4.575645 TGGAAGTTTTCGGTACAAAATCGT 59.424 37.500 0.00 0.00 0.00 3.73
784 1081 5.757320 TGGAAGTTTTCGGTACAAAATCGTA 59.243 36.000 0.00 0.00 0.00 3.43
785 1082 6.259608 TGGAAGTTTTCGGTACAAAATCGTAA 59.740 34.615 0.00 0.00 0.00 3.18
786 1083 7.131565 GGAAGTTTTCGGTACAAAATCGTAAA 58.868 34.615 0.00 0.00 0.00 2.01
787 1084 7.321984 GGAAGTTTTCGGTACAAAATCGTAAAG 59.678 37.037 0.00 0.00 0.00 1.85
788 1085 7.250445 AGTTTTCGGTACAAAATCGTAAAGT 57.750 32.000 0.00 0.00 0.00 2.66
789 1086 7.127686 AGTTTTCGGTACAAAATCGTAAAGTG 58.872 34.615 0.00 0.00 0.00 3.16
790 1087 5.594724 TTCGGTACAAAATCGTAAAGTGG 57.405 39.130 0.00 0.00 0.00 4.00
791 1088 4.630111 TCGGTACAAAATCGTAAAGTGGT 58.370 39.130 0.00 0.00 0.00 4.16
792 1089 5.777802 TCGGTACAAAATCGTAAAGTGGTA 58.222 37.500 0.00 0.00 0.00 3.25
793 1090 5.863397 TCGGTACAAAATCGTAAAGTGGTAG 59.137 40.000 0.00 0.00 0.00 3.18
794 1091 5.634859 CGGTACAAAATCGTAAAGTGGTAGT 59.365 40.000 0.00 0.00 0.00 2.73
795 1092 6.146021 CGGTACAAAATCGTAAAGTGGTAGTT 59.854 38.462 0.00 0.00 0.00 2.24
796 1093 7.293018 GGTACAAAATCGTAAAGTGGTAGTTG 58.707 38.462 0.00 0.00 0.00 3.16
797 1094 6.930667 ACAAAATCGTAAAGTGGTAGTTGT 57.069 33.333 0.00 0.00 0.00 3.32
798 1095 7.324354 ACAAAATCGTAAAGTGGTAGTTGTT 57.676 32.000 0.00 0.00 0.00 2.83
799 1096 7.764331 ACAAAATCGTAAAGTGGTAGTTGTTT 58.236 30.769 0.00 0.00 0.00 2.83
800 1097 8.245491 ACAAAATCGTAAAGTGGTAGTTGTTTT 58.755 29.630 0.00 0.00 0.00 2.43
801 1098 8.739461 CAAAATCGTAAAGTGGTAGTTGTTTTC 58.261 33.333 0.00 0.00 0.00 2.29
802 1099 5.989551 TCGTAAAGTGGTAGTTGTTTTCC 57.010 39.130 0.00 0.00 0.00 3.13
803 1100 4.507388 TCGTAAAGTGGTAGTTGTTTTCCG 59.493 41.667 0.00 0.00 0.00 4.30
804 1101 4.270808 CGTAAAGTGGTAGTTGTTTTCCGT 59.729 41.667 0.00 0.00 0.00 4.69
805 1102 4.625972 AAAGTGGTAGTTGTTTTCCGTG 57.374 40.909 0.00 0.00 0.00 4.94
806 1103 3.547054 AGTGGTAGTTGTTTTCCGTGA 57.453 42.857 0.00 0.00 0.00 4.35
807 1104 3.876341 AGTGGTAGTTGTTTTCCGTGAA 58.124 40.909 0.00 0.00 0.00 3.18
808 1105 4.457466 AGTGGTAGTTGTTTTCCGTGAAT 58.543 39.130 0.00 0.00 0.00 2.57
809 1106 4.885325 AGTGGTAGTTGTTTTCCGTGAATT 59.115 37.500 0.00 0.00 0.00 2.17
810 1107 4.973663 GTGGTAGTTGTTTTCCGTGAATTG 59.026 41.667 0.00 0.00 0.00 2.32
811 1108 4.641094 TGGTAGTTGTTTTCCGTGAATTGT 59.359 37.500 0.00 0.00 0.00 2.71
812 1109 4.973663 GGTAGTTGTTTTCCGTGAATTGTG 59.026 41.667 0.00 0.00 0.00 3.33
813 1110 4.040445 AGTTGTTTTCCGTGAATTGTGG 57.960 40.909 0.00 0.00 0.00 4.17
814 1111 3.445805 AGTTGTTTTCCGTGAATTGTGGT 59.554 39.130 0.00 0.00 0.00 4.16
815 1112 4.641094 AGTTGTTTTCCGTGAATTGTGGTA 59.359 37.500 0.00 0.00 0.00 3.25
816 1113 5.125739 AGTTGTTTTCCGTGAATTGTGGTAA 59.874 36.000 0.00 0.00 0.00 2.85
817 1114 5.776173 TGTTTTCCGTGAATTGTGGTAAT 57.224 34.783 0.00 0.00 0.00 1.89
818 1115 6.150396 TGTTTTCCGTGAATTGTGGTAATT 57.850 33.333 0.00 0.00 0.00 1.40
819 1116 6.574350 TGTTTTCCGTGAATTGTGGTAATTT 58.426 32.000 0.00 0.00 0.00 1.82
820 1117 7.042335 TGTTTTCCGTGAATTGTGGTAATTTT 58.958 30.769 0.00 0.00 0.00 1.82
821 1118 7.549488 TGTTTTCCGTGAATTGTGGTAATTTTT 59.451 29.630 0.00 0.00 0.00 1.94
822 1119 7.470289 TTTCCGTGAATTGTGGTAATTTTTG 57.530 32.000 0.00 0.00 0.00 2.44
823 1120 5.533482 TCCGTGAATTGTGGTAATTTTTGG 58.467 37.500 0.00 0.00 0.00 3.28
824 1121 5.069251 TCCGTGAATTGTGGTAATTTTTGGT 59.931 36.000 0.00 0.00 0.00 3.67
825 1122 5.755861 CCGTGAATTGTGGTAATTTTTGGTT 59.244 36.000 0.00 0.00 0.00 3.67
826 1123 6.924060 CCGTGAATTGTGGTAATTTTTGGTTA 59.076 34.615 0.00 0.00 0.00 2.85
827 1124 7.438459 CCGTGAATTGTGGTAATTTTTGGTTAA 59.562 33.333 0.00 0.00 0.00 2.01
828 1125 8.818057 CGTGAATTGTGGTAATTTTTGGTTAAA 58.182 29.630 0.00 0.00 0.00 1.52
893 1194 6.836527 AGTTCATAGCCTATACTGACTTGTCT 59.163 38.462 2.35 0.00 0.00 3.41
2010 2984 1.035932 AGGAGTACCCCGTCATCGTG 61.036 60.000 0.00 0.00 36.73 4.35
2185 3162 1.592669 GCGATGATCCCTGACGTGG 60.593 63.158 0.00 0.00 0.00 4.94
2196 3173 3.414700 GACGTGGCGCTGGAACTG 61.415 66.667 7.64 1.10 0.00 3.16
2197 3174 4.988598 ACGTGGCGCTGGAACTGG 62.989 66.667 7.64 0.00 0.00 4.00
2247 3224 0.040603 AGTCGGAGAACACGTTCGTC 60.041 55.000 4.35 3.33 43.97 4.20
2468 3478 9.602568 CTTTTTAGACTAGGGGAGACTTATTTC 57.397 37.037 0.00 0.00 32.16 2.17
2509 3521 5.462729 TCTGCAAGATACAAAACGTTACGAA 59.537 36.000 13.03 0.00 38.67 3.85
2531 3543 8.288208 ACGAAAAATGAGATTCTATCATGCATC 58.712 33.333 0.00 0.00 37.46 3.91
2541 3553 2.369983 ATCATGCATCCACGGGAATT 57.630 45.000 0.00 0.00 34.34 2.17
2565 3581 4.710324 ACCGTTGATGGTTACTTTGAGAA 58.290 39.130 0.00 0.00 39.99 2.87
2704 3933 4.173256 CACAGCAGAACATACATCGTGTA 58.827 43.478 1.30 1.30 37.24 2.90
2710 3939 6.763135 AGCAGAACATACATCGTGTATCATTT 59.237 34.615 7.43 3.35 41.28 2.32
2849 4095 6.032956 AGCATGAATCTCAAAAGCAATCAA 57.967 33.333 0.00 0.00 0.00 2.57
2852 4098 5.395682 TGAATCTCAAAAGCAATCAAGGG 57.604 39.130 0.00 0.00 0.00 3.95
2915 4161 8.631480 AAACATTATTCTCTTCCTAAAACGGT 57.369 30.769 0.00 0.00 0.00 4.83
2943 4189 3.670105 TGGAAGATCCAACAAGCCC 57.330 52.632 0.00 0.00 45.00 5.19
2947 4193 2.026262 GGAAGATCCAACAAGCCCAGTA 60.026 50.000 0.00 0.00 36.28 2.74
2967 4213 4.946157 AGTAAAAGCTTGCTCACTATGCAT 59.054 37.500 3.79 3.79 40.34 3.96
2982 4228 1.838112 TGCATAAAGAAGGTGGCTGG 58.162 50.000 0.00 0.00 0.00 4.85
2984 4230 1.767759 CATAAAGAAGGTGGCTGGGG 58.232 55.000 0.00 0.00 0.00 4.96
3005 4251 2.814336 GGCTCTCTTAAGGGTGTGTTTG 59.186 50.000 1.39 0.00 0.00 2.93
3015 4261 4.506937 AGGGTGTGTTTGGTAGTTGTTA 57.493 40.909 0.00 0.00 0.00 2.41
3018 4264 4.083696 GGGTGTGTTTGGTAGTTGTTATCG 60.084 45.833 0.00 0.00 0.00 2.92
3035 4281 6.270815 TGTTATCGTCCTAGCATAGTTGTTC 58.729 40.000 0.00 0.00 36.82 3.18
3050 4296 7.362920 GCATAGTTGTTCCCTTTTGATACATGT 60.363 37.037 2.69 2.69 0.00 3.21
3081 4327 3.879932 CATGCTGAGTACATGCATCTG 57.120 47.619 14.43 0.00 44.39 2.90
3082 4328 1.660167 TGCTGAGTACATGCATCTGC 58.340 50.000 0.00 13.78 42.50 4.26
3098 4344 5.258622 GCATCTGCAGTTGTTTAATAGTCG 58.741 41.667 22.50 0.00 41.59 4.18
3104 4350 7.056002 TGCAGTTGTTTAATAGTCGTGTATG 57.944 36.000 0.00 0.00 0.00 2.39
3107 4353 6.953743 CAGTTGTTTAATAGTCGTGTATGTGC 59.046 38.462 0.00 0.00 0.00 4.57
3122 4368 0.607217 TGTGCTGAGACATGCTTGGG 60.607 55.000 4.44 0.00 0.00 4.12
3128 4374 1.911357 TGAGACATGCTTGGGTGAGAT 59.089 47.619 4.44 0.00 0.00 2.75
3129 4375 2.306805 TGAGACATGCTTGGGTGAGATT 59.693 45.455 4.44 0.00 0.00 2.40
3185 4431 2.035193 TGCTAAATTTCAGCGGCACAAA 59.965 40.909 1.45 0.37 42.13 2.83
3190 4436 1.850377 TTTCAGCGGCACAAATGTTG 58.150 45.000 1.45 0.00 0.00 3.33
3269 4515 8.641541 ACTTAGAACAAAAATCAACATCCATGT 58.358 29.630 0.00 0.00 44.20 3.21
3270 4516 8.815141 TTAGAACAAAAATCAACATCCATGTG 57.185 30.769 0.00 0.00 41.61 3.21
3285 4531 5.648178 TCCATGTGGAAAATGTTCATCAG 57.352 39.130 0.00 0.00 42.18 2.90
3300 4546 8.902540 ATGTTCATCAGTTAACAAGAACACTA 57.097 30.769 24.28 11.86 45.28 2.74
3305 4551 8.201464 TCATCAGTTAACAAGAACACTAGACAA 58.799 33.333 8.61 0.00 0.00 3.18
3341 4587 7.156876 TCCATTTACATTGGAAGACATCAAC 57.843 36.000 0.00 0.00 40.29 3.18
3361 4607 5.105269 TCAACGCTATTGGGACTATAACACA 60.105 40.000 0.00 0.00 0.00 3.72
3362 4608 4.945246 ACGCTATTGGGACTATAACACAG 58.055 43.478 0.00 0.00 0.00 3.66
3363 4609 4.202223 ACGCTATTGGGACTATAACACAGG 60.202 45.833 0.00 0.00 0.00 4.00
3373 4619 2.851263 ATAACACAGGCGACCTTGAA 57.149 45.000 0.00 0.00 0.00 2.69
3374 4620 2.851263 TAACACAGGCGACCTTGAAT 57.149 45.000 0.00 0.00 0.00 2.57
3383 4629 1.148310 CGACCTTGAATGCGAACTGT 58.852 50.000 0.00 0.00 0.00 3.55
3385 4631 2.345641 CGACCTTGAATGCGAACTGTAG 59.654 50.000 0.00 0.00 0.00 2.74
3390 4636 0.107654 GAATGCGAACTGTAGGGGCT 60.108 55.000 0.00 0.00 0.00 5.19
3401 4647 1.536418 TAGGGGCTATCTGCGGCAT 60.536 57.895 1.75 0.00 44.05 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
224 228 3.274067 GCCACCGGCTCGAAATTT 58.726 55.556 0.00 0.00 46.69 1.82
357 523 4.998672 ACAGAGATACTCGCATCTAGGTAC 59.001 45.833 0.00 0.00 35.37 3.34
578 870 0.457035 AAAAATGATGCGCAGGCGAT 59.543 45.000 18.32 8.01 44.10 4.58
755 1052 5.900865 TTGTACCGAAAACTTCCACTTTT 57.099 34.783 0.00 0.00 0.00 2.27
756 1053 5.900865 TTTGTACCGAAAACTTCCACTTT 57.099 34.783 0.00 0.00 0.00 2.66
757 1054 5.900865 TTTTGTACCGAAAACTTCCACTT 57.099 34.783 0.00 0.00 0.00 3.16
758 1055 5.277634 CGATTTTGTACCGAAAACTTCCACT 60.278 40.000 0.00 0.00 0.00 4.00
759 1056 4.907582 CGATTTTGTACCGAAAACTTCCAC 59.092 41.667 0.00 0.00 0.00 4.02
760 1057 4.575645 ACGATTTTGTACCGAAAACTTCCA 59.424 37.500 0.00 0.00 0.00 3.53
761 1058 5.099484 ACGATTTTGTACCGAAAACTTCC 57.901 39.130 0.00 0.00 0.00 3.46
762 1059 7.852454 ACTTTACGATTTTGTACCGAAAACTTC 59.148 33.333 0.00 0.00 0.00 3.01
763 1060 7.641020 CACTTTACGATTTTGTACCGAAAACTT 59.359 33.333 0.00 0.00 0.00 2.66
764 1061 7.127686 CACTTTACGATTTTGTACCGAAAACT 58.872 34.615 0.00 0.00 0.00 2.66
765 1062 6.357766 CCACTTTACGATTTTGTACCGAAAAC 59.642 38.462 0.00 0.00 0.00 2.43
766 1063 6.038050 ACCACTTTACGATTTTGTACCGAAAA 59.962 34.615 0.00 0.00 0.00 2.29
767 1064 5.526846 ACCACTTTACGATTTTGTACCGAAA 59.473 36.000 0.00 0.00 0.00 3.46
768 1065 5.055812 ACCACTTTACGATTTTGTACCGAA 58.944 37.500 0.00 0.00 0.00 4.30
769 1066 4.630111 ACCACTTTACGATTTTGTACCGA 58.370 39.130 0.00 0.00 0.00 4.69
770 1067 4.996062 ACCACTTTACGATTTTGTACCG 57.004 40.909 0.00 0.00 0.00 4.02
771 1068 7.041848 ACAACTACCACTTTACGATTTTGTACC 60.042 37.037 0.00 0.00 0.00 3.34
772 1069 7.854534 ACAACTACCACTTTACGATTTTGTAC 58.145 34.615 0.00 0.00 0.00 2.90
773 1070 8.436046 AACAACTACCACTTTACGATTTTGTA 57.564 30.769 0.00 0.00 0.00 2.41
774 1071 6.930667 ACAACTACCACTTTACGATTTTGT 57.069 33.333 0.00 0.00 0.00 2.83
775 1072 8.623310 AAAACAACTACCACTTTACGATTTTG 57.377 30.769 0.00 0.00 0.00 2.44
776 1073 7.916977 GGAAAACAACTACCACTTTACGATTTT 59.083 33.333 0.00 0.00 0.00 1.82
777 1074 7.420002 GGAAAACAACTACCACTTTACGATTT 58.580 34.615 0.00 0.00 0.00 2.17
778 1075 6.293027 CGGAAAACAACTACCACTTTACGATT 60.293 38.462 0.00 0.00 35.77 3.34
779 1076 5.178067 CGGAAAACAACTACCACTTTACGAT 59.822 40.000 0.00 0.00 35.77 3.73
780 1077 4.507388 CGGAAAACAACTACCACTTTACGA 59.493 41.667 0.00 0.00 35.77 3.43
781 1078 4.270808 ACGGAAAACAACTACCACTTTACG 59.729 41.667 0.00 0.00 38.86 3.18
782 1079 5.294060 TCACGGAAAACAACTACCACTTTAC 59.706 40.000 0.00 0.00 0.00 2.01
783 1080 5.426504 TCACGGAAAACAACTACCACTTTA 58.573 37.500 0.00 0.00 0.00 1.85
784 1081 4.263435 TCACGGAAAACAACTACCACTTT 58.737 39.130 0.00 0.00 0.00 2.66
785 1082 3.876341 TCACGGAAAACAACTACCACTT 58.124 40.909 0.00 0.00 0.00 3.16
786 1083 3.547054 TCACGGAAAACAACTACCACT 57.453 42.857 0.00 0.00 0.00 4.00
787 1084 4.823790 ATTCACGGAAAACAACTACCAC 57.176 40.909 0.00 0.00 0.00 4.16
788 1085 4.641094 ACAATTCACGGAAAACAACTACCA 59.359 37.500 0.00 0.00 0.00 3.25
789 1086 4.973663 CACAATTCACGGAAAACAACTACC 59.026 41.667 0.00 0.00 0.00 3.18
790 1087 4.973663 CCACAATTCACGGAAAACAACTAC 59.026 41.667 0.00 0.00 0.00 2.73
791 1088 4.641094 ACCACAATTCACGGAAAACAACTA 59.359 37.500 0.00 0.00 0.00 2.24
792 1089 3.445805 ACCACAATTCACGGAAAACAACT 59.554 39.130 0.00 0.00 0.00 3.16
793 1090 3.776340 ACCACAATTCACGGAAAACAAC 58.224 40.909 0.00 0.00 0.00 3.32
794 1091 5.578005 TTACCACAATTCACGGAAAACAA 57.422 34.783 0.00 0.00 0.00 2.83
795 1092 5.776173 ATTACCACAATTCACGGAAAACA 57.224 34.783 0.00 0.00 0.00 2.83
796 1093 7.471657 AAAATTACCACAATTCACGGAAAAC 57.528 32.000 0.00 0.00 0.00 2.43
797 1094 7.011482 CCAAAAATTACCACAATTCACGGAAAA 59.989 33.333 0.00 0.00 0.00 2.29
798 1095 6.480320 CCAAAAATTACCACAATTCACGGAAA 59.520 34.615 0.00 0.00 0.00 3.13
799 1096 5.986135 CCAAAAATTACCACAATTCACGGAA 59.014 36.000 0.00 0.00 0.00 4.30
800 1097 5.069251 ACCAAAAATTACCACAATTCACGGA 59.931 36.000 0.00 0.00 0.00 4.69
801 1098 5.293560 ACCAAAAATTACCACAATTCACGG 58.706 37.500 0.00 0.00 0.00 4.94
802 1099 6.836577 AACCAAAAATTACCACAATTCACG 57.163 33.333 0.00 0.00 0.00 4.35
810 1107 9.135843 GCAGAGTATTTAACCAAAAATTACCAC 57.864 33.333 0.00 0.00 31.63 4.16
811 1108 8.861086 TGCAGAGTATTTAACCAAAAATTACCA 58.139 29.630 0.00 0.00 31.63 3.25
812 1109 9.869757 ATGCAGAGTATTTAACCAAAAATTACC 57.130 29.630 0.00 0.00 31.63 2.85
817 1114 9.364989 GCATTATGCAGAGTATTTAACCAAAAA 57.635 29.630 12.80 0.00 44.26 1.94
818 1115 8.925161 GCATTATGCAGAGTATTTAACCAAAA 57.075 30.769 12.80 0.00 44.26 2.44
1260 2183 0.469892 TGGAGGTGAGCTCAGACACA 60.470 55.000 18.89 11.66 38.57 3.72
1691 2665 4.742201 TCGTGGAGCAGCCGAAGC 62.742 66.667 0.00 0.00 40.66 3.86
2166 3143 1.946156 CACGTCAGGGATCATCGCG 60.946 63.158 0.00 0.00 34.19 5.87
2256 3233 3.322466 AAGCACAGGGTCCCCTCG 61.322 66.667 3.51 1.25 46.28 4.63
2452 3459 3.134081 CGCAAGGAAATAAGTCTCCCCTA 59.866 47.826 0.00 0.00 31.50 3.53
2468 3478 1.070108 CAGATGCATTCGATCGCAAGG 60.070 52.381 11.09 8.74 42.37 3.61
2509 3521 7.308408 CGTGGATGCATGATAGAATCTCATTTT 60.308 37.037 2.46 0.00 31.00 1.82
2541 3553 5.856156 TCTCAAAGTAACCATCAACGGTAA 58.144 37.500 0.00 0.00 38.76 2.85
2629 3858 8.729756 ACGATGAAACATTATGATTCACTTTGA 58.270 29.630 17.78 0.00 40.97 2.69
2683 3912 3.319137 ACACGATGTATGTTCTGCTGT 57.681 42.857 0.00 0.00 0.00 4.40
2813 4057 9.539825 TTGAGATTCATGCTATTTCTCTACTTC 57.460 33.333 0.00 0.00 35.09 3.01
2819 4063 7.478322 TGCTTTTGAGATTCATGCTATTTCTC 58.522 34.615 0.00 0.00 34.70 2.87
2849 4095 0.398522 TCCTGTGTATGGATCGCCCT 60.399 55.000 0.00 0.00 35.38 5.19
2852 4098 4.727507 ATATCTCCTGTGTATGGATCGC 57.272 45.455 0.00 0.00 32.56 4.58
2925 4171 0.776810 TGGGCTTGTTGGATCTTCCA 59.223 50.000 0.00 0.00 46.61 3.53
2926 4172 1.272147 ACTGGGCTTGTTGGATCTTCC 60.272 52.381 0.00 0.00 36.96 3.46
2927 4173 2.206576 ACTGGGCTTGTTGGATCTTC 57.793 50.000 0.00 0.00 0.00 2.87
2943 4189 4.154737 TGCATAGTGAGCAAGCTTTTACTG 59.845 41.667 0.00 0.00 39.39 2.74
2947 4193 5.902613 TTATGCATAGTGAGCAAGCTTTT 57.097 34.783 6.50 0.00 46.27 2.27
2967 4213 2.083715 CCCCCAGCCACCTTCTTTA 58.916 57.895 0.00 0.00 0.00 1.85
2982 4228 0.253327 CACACCCTTAAGAGAGCCCC 59.747 60.000 3.36 0.00 0.00 5.80
2984 4230 2.814336 CAAACACACCCTTAAGAGAGCC 59.186 50.000 3.36 0.00 0.00 4.70
2989 4235 5.127491 CAACTACCAAACACACCCTTAAGA 58.873 41.667 3.36 0.00 0.00 2.10
3005 4251 4.644103 TGCTAGGACGATAACAACTACC 57.356 45.455 0.00 0.00 0.00 3.18
3015 4261 3.069729 GGGAACAACTATGCTAGGACGAT 59.930 47.826 0.00 0.00 0.00 3.73
3018 4264 4.489306 AAGGGAACAACTATGCTAGGAC 57.511 45.455 0.00 0.00 0.00 3.85
3035 4281 8.665685 GTCTACACTAAACATGTATCAAAAGGG 58.334 37.037 0.00 0.00 32.24 3.95
3050 4296 6.584185 TGTACTCAGCATGTCTACACTAAA 57.416 37.500 0.00 0.00 37.40 1.85
3081 4327 6.953743 CACATACACGACTATTAAACAACTGC 59.046 38.462 0.00 0.00 0.00 4.40
3082 4328 6.953743 GCACATACACGACTATTAAACAACTG 59.046 38.462 0.00 0.00 0.00 3.16
3087 4333 6.750501 TCTCAGCACATACACGACTATTAAAC 59.249 38.462 0.00 0.00 0.00 2.01
3091 4337 4.157840 TGTCTCAGCACATACACGACTATT 59.842 41.667 0.00 0.00 0.00 1.73
3092 4338 3.694566 TGTCTCAGCACATACACGACTAT 59.305 43.478 0.00 0.00 0.00 2.12
3094 4340 1.886542 TGTCTCAGCACATACACGACT 59.113 47.619 0.00 0.00 0.00 4.18
3098 4344 2.625737 AGCATGTCTCAGCACATACAC 58.374 47.619 0.00 0.00 35.10 2.90
3104 4350 0.607489 ACCCAAGCATGTCTCAGCAC 60.607 55.000 0.00 0.00 0.00 4.40
3107 4353 1.277273 TCTCACCCAAGCATGTCTCAG 59.723 52.381 0.00 0.00 0.00 3.35
3122 4368 4.216257 ACATGCTACCAAACACAATCTCAC 59.784 41.667 0.00 0.00 0.00 3.51
3128 4374 3.020274 ACACACATGCTACCAAACACAA 58.980 40.909 0.00 0.00 0.00 3.33
3129 4375 2.357323 CACACACATGCTACCAAACACA 59.643 45.455 0.00 0.00 0.00 3.72
3170 4416 2.406130 CAACATTTGTGCCGCTGAAAT 58.594 42.857 0.00 0.00 0.00 2.17
3248 4494 6.222389 TCCACATGGATGTTGATTTTTGTTC 58.778 36.000 0.00 0.00 39.78 3.18
3249 4495 6.172136 TCCACATGGATGTTGATTTTTGTT 57.828 33.333 0.00 0.00 39.78 2.83
3269 4515 8.231692 TCTTGTTAACTGATGAACATTTTCCA 57.768 30.769 7.22 0.00 35.57 3.53
3270 4516 8.968242 GTTCTTGTTAACTGATGAACATTTTCC 58.032 33.333 18.82 2.03 35.57 3.13
3285 4531 8.149973 TGGAATTGTCTAGTGTTCTTGTTAAC 57.850 34.615 0.00 0.00 0.00 2.01
3319 4565 5.512788 GCGTTGATGTCTTCCAATGTAAATG 59.487 40.000 0.00 0.00 33.20 2.32
3333 4579 2.906354 AGTCCCAATAGCGTTGATGTC 58.094 47.619 6.47 0.00 0.00 3.06
3337 4583 5.105269 TGTGTTATAGTCCCAATAGCGTTGA 60.105 40.000 6.47 0.00 0.00 3.18
3338 4584 5.113383 TGTGTTATAGTCCCAATAGCGTTG 58.887 41.667 0.00 0.00 0.00 4.10
3341 4587 4.307432 CCTGTGTTATAGTCCCAATAGCG 58.693 47.826 0.00 0.00 0.00 4.26
3361 4607 1.003839 TTCGCATTCAAGGTCGCCT 60.004 52.632 0.00 0.00 33.87 5.52
3362 4608 1.134694 GTTCGCATTCAAGGTCGCC 59.865 57.895 0.00 0.00 0.00 5.54
3363 4609 0.179215 CAGTTCGCATTCAAGGTCGC 60.179 55.000 0.00 0.00 0.00 5.19
3373 4619 1.344763 GATAGCCCCTACAGTTCGCAT 59.655 52.381 0.00 0.00 0.00 4.73
3374 4620 0.750850 GATAGCCCCTACAGTTCGCA 59.249 55.000 0.00 0.00 0.00 5.10
3383 4629 1.536418 ATGCCGCAGATAGCCCCTA 60.536 57.895 0.00 0.00 41.38 3.53
3385 4631 2.670934 CATGCCGCAGATAGCCCC 60.671 66.667 0.00 0.00 41.38 5.80
3390 4636 0.964700 CCTCTCTCATGCCGCAGATA 59.035 55.000 0.00 0.00 0.00 1.98
3401 4647 3.088789 GTTAGTCCTCCACCTCTCTCA 57.911 52.381 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.