Multiple sequence alignment - TraesCS5D01G128400

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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 TraesCS5D01G128400 chr5D 100.000 3610 0 0 1 3610 200784286 200787895 0.000000e+00 6667.0
1 TraesCS5D01G128400 chr5D 86.025 644 59 9 16 634 200697757 200698394 0.000000e+00 662.0
2 TraesCS5D01G128400 chr5D 89.145 304 20 5 335 635 200697464 200697757 2.050000e-97 366.0
3 TraesCS5D01G128400 chr5D 85.494 324 22 9 2 317 205454595 205454901 7.520000e-82 315.0
4 TraesCS5D01G128400 chr5D 77.381 336 39 26 2 326 200668634 200668943 8.020000e-37 165.0
5 TraesCS5D01G128400 chr5D 83.654 104 13 2 2144 2246 389453036 389453136 1.070000e-15 95.3
6 TraesCS5D01G128400 chr5D 78.571 140 20 9 2124 2258 442858085 442857951 2.310000e-12 84.2
7 TraesCS5D01G128400 chr5D 81.308 107 15 5 2125 2229 28038501 28038604 8.310000e-12 82.4
8 TraesCS5D01G128400 chr5A 93.146 1634 72 16 698 2322 214952770 214954372 0.000000e+00 2361.0
9 TraesCS5D01G128400 chr5A 96.438 730 15 6 2892 3610 214955068 214955797 0.000000e+00 1194.0
10 TraesCS5D01G128400 chr5A 96.510 573 20 0 2321 2893 214954459 214955031 0.000000e+00 948.0
11 TraesCS5D01G128400 chr5A 81.185 675 75 36 2 632 270887510 270886844 2.500000e-136 496.0
12 TraesCS5D01G128400 chr5A 85.714 112 15 1 2126 2237 52281154 52281264 2.280000e-22 117.0
13 TraesCS5D01G128400 chr5A 83.471 121 16 4 2128 2246 631857699 631857817 3.810000e-20 110.0
14 TraesCS5D01G128400 chr5A 82.857 105 13 3 2144 2246 492626890 492626991 4.960000e-14 89.8
15 TraesCS5D01G128400 chr5B 95.164 1158 26 13 703 1835 211733677 211734829 0.000000e+00 1801.0
16 TraesCS5D01G128400 chr5B 96.347 1013 32 4 1834 2845 211737661 211738669 0.000000e+00 1661.0
17 TraesCS5D01G128400 chr5B 96.671 721 18 5 2892 3610 211738736 211739452 0.000000e+00 1194.0
18 TraesCS5D01G128400 chr5B 84.375 96 13 2 2127 2222 698471210 698471117 3.840000e-15 93.5
19 TraesCS5D01G128400 chr5B 84.536 97 8 4 230 324 101867370 101867461 4.960000e-14 89.8
20 TraesCS5D01G128400 chr5B 81.553 103 16 3 2124 2225 27361878 27361978 8.310000e-12 82.4
21 TraesCS5D01G128400 chr7D 84.825 659 69 15 2 634 266443557 266444210 5.080000e-178 634.0
22 TraesCS5D01G128400 chr7D 86.513 304 35 4 336 634 265714426 265714728 2.690000e-86 329.0
23 TraesCS5D01G128400 chr7D 86.275 204 13 9 2 197 312472935 312473131 1.310000e-49 207.0
24 TraesCS5D01G128400 chr7D 82.857 105 16 2 2131 2235 204871003 204870901 3.840000e-15 93.5
25 TraesCS5D01G128400 chr7D 80.952 105 18 2 2124 2228 598483393 598483291 8.310000e-12 82.4
26 TraesCS5D01G128400 chr7D 79.630 108 21 1 2128 2235 436499200 436499094 3.870000e-10 76.8
27 TraesCS5D01G128400 chr7D 87.037 54 5 2 2126 2178 129400684 129400736 3.890000e-05 60.2
28 TraesCS5D01G128400 chr2D 80.375 693 73 18 3 634 485710393 485711083 5.460000e-128 468.0
29 TraesCS5D01G128400 chr2D 81.731 104 16 3 2127 2229 583317024 583317125 2.310000e-12 84.2
30 TraesCS5D01G128400 chr3D 80.152 660 82 30 3 635 126189116 126188479 7.110000e-122 448.0
31 TraesCS5D01G128400 chr3D 86.495 311 35 5 335 639 121084014 121083705 5.780000e-88 335.0
32 TraesCS5D01G128400 chr3D 97.143 35 1 0 2191 2225 603588557 603588523 3.890000e-05 60.2
33 TraesCS5D01G128400 chr4B 79.794 678 80 39 2 634 378773495 378772830 1.190000e-119 440.0
34 TraesCS5D01G128400 chr4B 80.851 141 19 8 2128 2265 561752442 561752307 1.770000e-18 104.0
35 TraesCS5D01G128400 chr2A 92.131 305 21 1 333 634 420984261 420983957 9.260000e-116 427.0
36 TraesCS5D01G128400 chr2A 84.483 116 17 1 2128 2243 384331897 384331783 2.950000e-21 113.0
37 TraesCS5D01G128400 chr6B 78.459 636 93 32 2 621 416904914 416905521 3.400000e-100 375.0
38 TraesCS5D01G128400 chr6B 82.143 308 34 14 2 289 382033941 382033635 1.000000e-60 244.0
39 TraesCS5D01G128400 chr6A 78.922 631 72 38 50 634 502369753 502369138 4.400000e-99 372.0
40 TraesCS5D01G128400 chr6A 83.077 130 20 2 2127 2256 594634370 594634497 2.280000e-22 117.0
41 TraesCS5D01G128400 chr6A 83.962 106 15 2 2125 2229 3014714 3014610 2.290000e-17 100.0
42 TraesCS5D01G128400 chr2B 88.487 304 29 5 335 634 135241603 135241904 2.650000e-96 363.0
43 TraesCS5D01G128400 chr2B 81.818 121 17 5 2128 2246 638994094 638993977 2.970000e-16 97.1
44 TraesCS5D01G128400 chr1D 77.614 679 98 34 2 634 138349022 138349692 2.650000e-96 363.0
45 TraesCS5D01G128400 chr1D 77.074 663 107 28 3 634 289473513 289474161 1.240000e-89 340.0
46 TraesCS5D01G128400 chr1D 88.462 52 6 0 2127 2178 230209315 230209264 3.010000e-06 63.9
47 TraesCS5D01G128400 chr4D 86.513 304 35 4 335 634 261357360 261357059 2.690000e-86 329.0
48 TraesCS5D01G128400 chrUn 95.980 199 2 3 2892 3084 471412642 471412444 5.820000e-83 318.0
49 TraesCS5D01G128400 chr3B 78.426 394 57 13 266 634 332384228 332384618 7.800000e-57 231.0
50 TraesCS5D01G128400 chr3B 80.645 124 20 4 2123 2245 815388407 815388287 3.840000e-15 93.5
51 TraesCS5D01G128400 chr3B 91.667 60 3 2 266 324 332363906 332363964 8.310000e-12 82.4
52 TraesCS5D01G128400 chr6D 86.139 202 13 8 3 197 65772124 65772317 1.700000e-48 204.0
53 TraesCS5D01G128400 chr7A 85.354 198 16 9 7 196 384537989 384538181 3.680000e-45 193.0
54 TraesCS5D01G128400 chr7A 83.654 104 14 3 2127 2229 115238976 115239077 1.070000e-15 95.3
55 TraesCS5D01G128400 chr7A 82.075 106 17 2 2125 2229 486156530 486156634 4.960000e-14 89.8
56 TraesCS5D01G128400 chr7A 79.839 124 22 3 2124 2246 5906678 5906557 1.790000e-13 87.9
57 TraesCS5D01G128400 chr7B 82.143 112 18 2 2124 2235 677474363 677474254 1.070000e-15 95.3
58 TraesCS5D01G128400 chr7B 82.474 97 10 4 230 324 480389849 480389758 1.070000e-10 78.7
59 TraesCS5D01G128400 chr1A 81.081 111 16 5 2127 2235 377423889 377423782 2.310000e-12 84.2
60 TraesCS5D01G128400 chr1A 81.720 93 15 2 2133 2225 357433469 357433559 3.870000e-10 76.8


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 TraesCS5D01G128400 chr5D 200784286 200787895 3609 False 6667 6667 100.000000 1 3610 1 chr5D.!!$F3 3609
1 TraesCS5D01G128400 chr5D 200697464 200698394 930 False 514 662 87.585000 16 635 2 chr5D.!!$F6 619
2 TraesCS5D01G128400 chr5A 214952770 214955797 3027 False 1501 2361 95.364667 698 3610 3 chr5A.!!$F4 2912
3 TraesCS5D01G128400 chr5A 270886844 270887510 666 True 496 496 81.185000 2 632 1 chr5A.!!$R1 630
4 TraesCS5D01G128400 chr5B 211733677 211739452 5775 False 1552 1801 96.060667 703 3610 3 chr5B.!!$F3 2907
5 TraesCS5D01G128400 chr7D 266443557 266444210 653 False 634 634 84.825000 2 634 1 chr7D.!!$F3 632
6 TraesCS5D01G128400 chr2D 485710393 485711083 690 False 468 468 80.375000 3 634 1 chr2D.!!$F1 631
7 TraesCS5D01G128400 chr3D 126188479 126189116 637 True 448 448 80.152000 3 635 1 chr3D.!!$R2 632
8 TraesCS5D01G128400 chr4B 378772830 378773495 665 True 440 440 79.794000 2 634 1 chr4B.!!$R1 632
9 TraesCS5D01G128400 chr6B 416904914 416905521 607 False 375 375 78.459000 2 621 1 chr6B.!!$F1 619
10 TraesCS5D01G128400 chr6A 502369138 502369753 615 True 372 372 78.922000 50 634 1 chr6A.!!$R2 584
11 TraesCS5D01G128400 chr1D 138349022 138349692 670 False 363 363 77.614000 2 634 1 chr1D.!!$F1 632
12 TraesCS5D01G128400 chr1D 289473513 289474161 648 False 340 340 77.074000 3 634 1 chr1D.!!$F2 631

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
684 1135 0.256752 TGTATGGCCATCAGCTTGCT 59.743 50.0 24.80 0.0 43.05 3.91 F
690 1141 0.389426 GCCATCAGCTTGCTTTGGTG 60.389 55.0 17.42 5.9 38.99 4.17 F
691 1142 0.963962 CCATCAGCTTGCTTTGGTGT 59.036 50.0 11.25 0.0 34.86 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2453 5857 0.325296 ACCTGAGATTACCGCCTCCA 60.325 55.000 0.00 0.00 0.00 3.86 R
2586 5990 1.450312 GCAATAGCCGGACAGCTGT 60.450 57.895 21.88 21.88 44.67 4.40 R
2624 6028 4.644103 AACCAGATATTCACAGCAATGC 57.356 40.909 0.00 0.00 0.00 3.56 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
75 365 2.292828 AAAATGGTGGTGGAGGAGTG 57.707 50.000 0.00 0.00 0.00 3.51
107 400 2.372074 GGGGCGAAGGGTACATGGA 61.372 63.158 0.00 0.00 0.00 3.41
112 405 1.742750 GCGAAGGGTACATGGACTTCC 60.743 57.143 8.27 1.17 36.80 3.46
238 598 3.012518 CTGTGAAGAATGCCGGATTTCT 58.987 45.455 5.05 9.80 33.69 2.52
242 602 0.625849 AGAATGCCGGATTTCTGGGT 59.374 50.000 16.02 0.00 42.72 4.51
385 833 2.576832 GGTTCCTTCCGTCGGTCCA 61.577 63.158 11.88 0.00 0.00 4.02
462 910 3.464907 CTCTTGGTACCTGATCATGCAG 58.535 50.000 14.36 0.00 35.66 4.41
487 938 7.563924 AGAACATTGACTTAGGTAGTAGCCATA 59.436 37.037 0.00 0.00 37.17 2.74
519 970 7.734865 AGTGGGTCATATGGAATATCACTAAGA 59.265 37.037 2.13 0.00 38.26 2.10
603 1054 2.045131 GTGAGGCGTCGGTAGGTCT 61.045 63.158 1.39 0.00 0.00 3.85
642 1093 4.785346 ATGCTCCACATCAATTACTCCT 57.215 40.909 0.00 0.00 31.52 3.69
643 1094 4.142609 TGCTCCACATCAATTACTCCTC 57.857 45.455 0.00 0.00 0.00 3.71
644 1095 3.519107 TGCTCCACATCAATTACTCCTCA 59.481 43.478 0.00 0.00 0.00 3.86
645 1096 3.873952 GCTCCACATCAATTACTCCTCAC 59.126 47.826 0.00 0.00 0.00 3.51
646 1097 4.115516 CTCCACATCAATTACTCCTCACG 58.884 47.826 0.00 0.00 0.00 4.35
647 1098 3.767131 TCCACATCAATTACTCCTCACGA 59.233 43.478 0.00 0.00 0.00 4.35
648 1099 4.221924 TCCACATCAATTACTCCTCACGAA 59.778 41.667 0.00 0.00 0.00 3.85
649 1100 4.935205 CCACATCAATTACTCCTCACGAAA 59.065 41.667 0.00 0.00 0.00 3.46
650 1101 5.586243 CCACATCAATTACTCCTCACGAAAT 59.414 40.000 0.00 0.00 0.00 2.17
651 1102 6.094048 CCACATCAATTACTCCTCACGAAATT 59.906 38.462 0.00 0.00 0.00 1.82
652 1103 6.963242 CACATCAATTACTCCTCACGAAATTG 59.037 38.462 0.00 0.00 38.36 2.32
653 1104 6.878923 ACATCAATTACTCCTCACGAAATTGA 59.121 34.615 10.23 10.23 45.45 2.57
654 1105 6.721571 TCAATTACTCCTCACGAAATTGAC 57.278 37.500 5.03 0.00 40.04 3.18
655 1106 5.347635 TCAATTACTCCTCACGAAATTGACG 59.652 40.000 5.03 4.19 40.04 4.35
656 1107 2.814280 ACTCCTCACGAAATTGACGT 57.186 45.000 5.34 5.34 44.83 4.34
657 1108 3.928727 ACTCCTCACGAAATTGACGTA 57.071 42.857 9.89 0.00 42.07 3.57
658 1109 3.834610 ACTCCTCACGAAATTGACGTAG 58.165 45.455 9.89 7.26 42.07 3.51
659 1110 2.599082 CTCCTCACGAAATTGACGTAGC 59.401 50.000 9.89 0.00 42.07 3.58
660 1111 2.029739 TCCTCACGAAATTGACGTAGCA 60.030 45.455 9.89 0.00 42.07 3.49
661 1112 2.930040 CCTCACGAAATTGACGTAGCAT 59.070 45.455 9.89 0.00 42.07 3.79
662 1113 3.242091 CCTCACGAAATTGACGTAGCATG 60.242 47.826 9.89 0.00 42.07 4.06
663 1114 3.322369 TCACGAAATTGACGTAGCATGT 58.678 40.909 9.89 0.00 42.07 3.21
664 1115 3.122780 TCACGAAATTGACGTAGCATGTG 59.877 43.478 9.89 0.00 42.07 3.21
665 1116 3.064207 ACGAAATTGACGTAGCATGTGT 58.936 40.909 8.76 0.00 42.17 3.72
666 1117 3.120683 ACGAAATTGACGTAGCATGTGTG 60.121 43.478 8.76 0.00 42.17 3.82
667 1118 3.120683 CGAAATTGACGTAGCATGTGTGT 60.121 43.478 0.00 0.00 0.00 3.72
668 1119 4.090786 CGAAATTGACGTAGCATGTGTGTA 59.909 41.667 0.00 0.00 0.00 2.90
669 1120 5.220397 CGAAATTGACGTAGCATGTGTGTAT 60.220 40.000 0.00 0.00 0.00 2.29
670 1121 5.469373 AATTGACGTAGCATGTGTGTATG 57.531 39.130 0.00 0.00 0.00 2.39
671 1122 2.887337 TGACGTAGCATGTGTGTATGG 58.113 47.619 0.00 0.00 0.00 2.74
672 1123 1.593006 GACGTAGCATGTGTGTATGGC 59.407 52.381 0.00 0.00 0.00 4.40
673 1124 0.937304 CGTAGCATGTGTGTATGGCC 59.063 55.000 0.00 0.00 0.00 5.36
674 1125 1.742071 CGTAGCATGTGTGTATGGCCA 60.742 52.381 8.56 8.56 0.00 5.36
675 1126 2.575532 GTAGCATGTGTGTATGGCCAT 58.424 47.619 24.45 24.45 0.00 4.40
676 1127 1.683943 AGCATGTGTGTATGGCCATC 58.316 50.000 24.80 14.58 0.00 3.51
677 1128 1.064537 AGCATGTGTGTATGGCCATCA 60.065 47.619 24.80 17.14 0.00 3.07
678 1129 1.335810 GCATGTGTGTATGGCCATCAG 59.664 52.381 24.80 8.90 0.00 2.90
679 1130 1.335810 CATGTGTGTATGGCCATCAGC 59.664 52.381 24.80 14.40 42.60 4.26
680 1131 0.620030 TGTGTGTATGGCCATCAGCT 59.380 50.000 24.80 0.00 43.05 4.24
681 1132 1.004628 TGTGTGTATGGCCATCAGCTT 59.995 47.619 24.80 0.00 43.05 3.74
682 1133 1.402968 GTGTGTATGGCCATCAGCTTG 59.597 52.381 24.80 0.00 43.05 4.01
683 1134 0.383231 GTGTATGGCCATCAGCTTGC 59.617 55.000 24.80 1.43 43.05 4.01
684 1135 0.256752 TGTATGGCCATCAGCTTGCT 59.743 50.000 24.80 0.00 43.05 3.91
685 1136 1.341285 TGTATGGCCATCAGCTTGCTT 60.341 47.619 24.80 0.00 43.05 3.91
686 1137 1.753073 GTATGGCCATCAGCTTGCTTT 59.247 47.619 24.80 0.00 43.05 3.51
687 1138 0.535335 ATGGCCATCAGCTTGCTTTG 59.465 50.000 14.09 0.00 43.05 2.77
688 1139 1.217244 GGCCATCAGCTTGCTTTGG 59.783 57.895 13.89 13.89 43.05 3.28
689 1140 1.538687 GGCCATCAGCTTGCTTTGGT 61.539 55.000 17.42 0.00 43.05 3.67
690 1141 0.389426 GCCATCAGCTTGCTTTGGTG 60.389 55.000 17.42 5.90 38.99 4.17
691 1142 0.963962 CCATCAGCTTGCTTTGGTGT 59.036 50.000 11.25 0.00 34.86 4.16
692 1143 1.342174 CCATCAGCTTGCTTTGGTGTT 59.658 47.619 11.25 0.00 34.86 3.32
693 1144 2.224113 CCATCAGCTTGCTTTGGTGTTT 60.224 45.455 11.25 0.00 34.86 2.83
694 1145 3.460103 CATCAGCTTGCTTTGGTGTTTT 58.540 40.909 0.00 0.00 34.86 2.43
695 1146 3.608316 TCAGCTTGCTTTGGTGTTTTT 57.392 38.095 0.00 0.00 34.86 1.94
779 1230 4.776322 CCGGCTTCCGCATGTGGA 62.776 66.667 24.20 24.20 46.86 4.02
1052 1522 2.488820 GACCACCTCGCCGTCTAC 59.511 66.667 0.00 0.00 0.00 2.59
1053 1523 3.061260 GACCACCTCGCCGTCTACC 62.061 68.421 0.00 0.00 0.00 3.18
1054 1524 2.754658 CCACCTCGCCGTCTACCT 60.755 66.667 0.00 0.00 0.00 3.08
1111 1587 3.935828 GTCTCTTCTTGCTTATCCGCTTT 59.064 43.478 0.00 0.00 0.00 3.51
1155 1631 1.476110 CGTTTCAAGGTTGGGGTCTCA 60.476 52.381 0.00 0.00 0.00 3.27
1156 1632 1.954382 GTTTCAAGGTTGGGGTCTCAC 59.046 52.381 0.00 0.00 0.00 3.51
1252 1728 1.118965 TGAGACTTCCGTCCTTGCCA 61.119 55.000 0.00 0.00 41.16 4.92
1292 1768 6.017026 TGACAGTTCGATATGCTAGTCCTTAG 60.017 42.308 0.00 0.00 0.00 2.18
1451 1927 4.802051 ATGGCAGACGGCGGCAAT 62.802 61.111 18.30 6.58 46.16 3.56
1481 1957 2.288213 GCATGAGATCGACGGGAATGTA 60.288 50.000 0.00 0.00 0.00 2.29
1709 2186 7.487484 TCAAAATTCTAATTGTGCAGACAACA 58.513 30.769 1.38 0.00 44.90 3.33
1762 2239 4.439563 CGGGTATTTGTCAAGCATTAACCC 60.440 45.833 0.00 0.00 38.24 4.11
1767 2244 7.284489 GGTATTTGTCAAGCATTAACCCATCTA 59.716 37.037 0.00 0.00 0.00 1.98
1944 5258 2.238646 TCACATACCATTCTGGGGTGTC 59.761 50.000 11.84 0.00 43.37 3.67
1949 5263 1.635817 CCATTCTGGGGTGTCGGGAT 61.636 60.000 0.00 0.00 32.67 3.85
1991 5305 1.190643 TCGTGCCATGGACAGTATCA 58.809 50.000 18.40 0.00 0.00 2.15
2144 5459 3.326880 ACATGTACTCCCTCCGTTTCTTT 59.673 43.478 0.00 0.00 0.00 2.52
2284 5600 6.716934 AGACATTATACATCGTCTCCTTGT 57.283 37.500 0.00 0.00 33.49 3.16
2285 5601 7.113658 AGACATTATACATCGTCTCCTTGTT 57.886 36.000 0.00 0.00 33.49 2.83
2366 5770 0.978151 TGGGCGAAAACCAGTAGCTA 59.022 50.000 0.00 0.00 33.23 3.32
2453 5857 3.849951 CCATACCTCACCGGCGCT 61.850 66.667 7.64 0.00 35.61 5.92
2477 5881 2.039879 AGGCGGTAATCTCAGGTTTGTT 59.960 45.455 0.00 0.00 0.00 2.83
2586 5990 3.902467 CAGAGAGAAGATCCCATCCATCA 59.098 47.826 0.00 0.00 0.00 3.07
2624 6028 2.918131 GCCGTAAGCTTCAACTGCAAAG 60.918 50.000 0.00 0.00 38.99 2.77
2790 6195 5.502079 TGTAACAAGGTTCTTTTGGTCTCA 58.498 37.500 0.00 0.00 0.00 3.27
2863 6268 5.556194 CGTTGCTTTGCCTGAAAAATTACAC 60.556 40.000 0.00 0.00 0.00 2.90
3270 6719 0.759436 TAGATGGCGGAAGGGAGGAC 60.759 60.000 0.00 0.00 0.00 3.85
3516 6965 2.679287 GGGAGACGACGGGGAAGT 60.679 66.667 0.00 0.00 0.00 3.01
3517 6966 2.572284 GGAGACGACGGGGAAGTG 59.428 66.667 0.00 0.00 0.00 3.16
3526 6980 1.602377 GACGGGGAAGTGTTTGTCTTG 59.398 52.381 0.00 0.00 0.00 3.02
3573 7027 1.205064 CAAGAAGACGCAACGCAGG 59.795 57.895 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.590821 AGCTTTGCTCATCCACTTGTT 58.409 42.857 0.00 0.00 30.62 2.83
92 384 1.653151 GAAGTCCATGTACCCTTCGC 58.347 55.000 0.00 0.00 0.00 4.70
93 385 1.470979 CGGAAGTCCATGTACCCTTCG 60.471 57.143 0.00 0.00 35.31 3.79
96 388 1.623542 GGCGGAAGTCCATGTACCCT 61.624 60.000 0.00 0.00 35.14 4.34
107 400 0.535102 CACAGTGAAAGGGCGGAAGT 60.535 55.000 0.00 0.00 0.00 3.01
198 544 1.228552 AATGCAACCGAAGCCACCT 60.229 52.632 0.00 0.00 0.00 4.00
407 855 4.820897 AGATGCACGTGAAGATAGACAAA 58.179 39.130 22.23 0.00 0.00 2.83
462 910 5.974108 TGGCTACTACCTAAGTCAATGTTC 58.026 41.667 0.00 0.00 39.80 3.18
487 938 5.919348 ATTCCATATGACCCACTTGAGAT 57.081 39.130 3.65 0.00 0.00 2.75
519 970 4.019858 TCGAGATCAAGGTGACATCTCTT 58.980 43.478 8.43 0.00 32.88 2.85
563 1014 0.606401 AGTGCCAAGTGGACCGATTG 60.606 55.000 0.18 2.23 37.39 2.67
564 1015 0.110486 AAGTGCCAAGTGGACCGATT 59.890 50.000 0.18 0.00 37.39 3.34
603 1054 2.846206 GCATCCTATGGTCATCCCCATA 59.154 50.000 0.00 0.00 43.48 2.74
635 1086 4.247267 ACGTCAATTTCGTGAGGAGTAA 57.753 40.909 4.91 0.00 40.07 2.24
636 1087 3.928727 ACGTCAATTTCGTGAGGAGTA 57.071 42.857 4.91 0.00 40.07 2.59
637 1088 2.814280 ACGTCAATTTCGTGAGGAGT 57.186 45.000 4.91 0.00 40.07 3.85
638 1089 2.599082 GCTACGTCAATTTCGTGAGGAG 59.401 50.000 13.47 6.09 41.62 3.69
639 1090 2.029739 TGCTACGTCAATTTCGTGAGGA 60.030 45.455 13.47 7.27 41.62 3.71
640 1091 2.333926 TGCTACGTCAATTTCGTGAGG 58.666 47.619 13.47 0.47 41.62 3.86
641 1092 3.367932 ACATGCTACGTCAATTTCGTGAG 59.632 43.478 13.47 9.03 41.62 3.51
642 1093 3.122780 CACATGCTACGTCAATTTCGTGA 59.877 43.478 13.47 1.53 41.62 4.35
643 1094 3.120683 ACACATGCTACGTCAATTTCGTG 60.121 43.478 13.47 0.00 41.62 4.35
644 1095 3.064207 ACACATGCTACGTCAATTTCGT 58.936 40.909 0.00 9.75 43.86 3.85
645 1096 3.120683 ACACACATGCTACGTCAATTTCG 60.121 43.478 0.00 0.00 0.00 3.46
646 1097 4.404507 ACACACATGCTACGTCAATTTC 57.595 40.909 0.00 0.00 0.00 2.17
647 1098 5.163764 CCATACACACATGCTACGTCAATTT 60.164 40.000 0.00 0.00 0.00 1.82
648 1099 4.332543 CCATACACACATGCTACGTCAATT 59.667 41.667 0.00 0.00 0.00 2.32
649 1100 3.871006 CCATACACACATGCTACGTCAAT 59.129 43.478 0.00 0.00 0.00 2.57
650 1101 3.258228 CCATACACACATGCTACGTCAA 58.742 45.455 0.00 0.00 0.00 3.18
651 1102 2.887337 CCATACACACATGCTACGTCA 58.113 47.619 0.00 0.00 0.00 4.35
652 1103 1.593006 GCCATACACACATGCTACGTC 59.407 52.381 0.00 0.00 0.00 4.34
653 1104 1.651987 GCCATACACACATGCTACGT 58.348 50.000 0.00 0.00 0.00 3.57
654 1105 0.937304 GGCCATACACACATGCTACG 59.063 55.000 0.00 0.00 0.00 3.51
655 1106 2.036958 TGGCCATACACACATGCTAC 57.963 50.000 0.00 0.00 0.00 3.58
656 1107 2.172293 TGATGGCCATACACACATGCTA 59.828 45.455 20.84 0.00 0.00 3.49
657 1108 1.064537 TGATGGCCATACACACATGCT 60.065 47.619 20.84 0.00 0.00 3.79
658 1109 1.335810 CTGATGGCCATACACACATGC 59.664 52.381 20.84 2.96 0.00 4.06
659 1110 1.335810 GCTGATGGCCATACACACATG 59.664 52.381 20.84 7.48 34.27 3.21
660 1111 1.213678 AGCTGATGGCCATACACACAT 59.786 47.619 20.84 0.00 43.05 3.21
661 1112 0.620030 AGCTGATGGCCATACACACA 59.380 50.000 20.84 11.20 43.05 3.72
662 1113 1.402968 CAAGCTGATGGCCATACACAC 59.597 52.381 20.84 6.29 43.05 3.82
663 1114 1.753930 CAAGCTGATGGCCATACACA 58.246 50.000 20.84 12.01 43.05 3.72
664 1115 0.383231 GCAAGCTGATGGCCATACAC 59.617 55.000 20.84 10.81 43.05 2.90
665 1116 0.256752 AGCAAGCTGATGGCCATACA 59.743 50.000 20.84 16.91 43.05 2.29
666 1117 1.396653 AAGCAAGCTGATGGCCATAC 58.603 50.000 20.84 11.61 43.05 2.39
667 1118 1.752498 CAAAGCAAGCTGATGGCCATA 59.248 47.619 20.84 6.47 43.05 2.74
668 1119 0.535335 CAAAGCAAGCTGATGGCCAT 59.465 50.000 20.96 20.96 43.05 4.40
669 1120 1.537814 CCAAAGCAAGCTGATGGCCA 61.538 55.000 8.56 8.56 43.05 5.36
670 1121 1.217244 CCAAAGCAAGCTGATGGCC 59.783 57.895 12.44 0.00 43.05 5.36
671 1122 0.389426 CACCAAAGCAAGCTGATGGC 60.389 55.000 20.71 0.00 37.36 4.40
672 1123 0.963962 ACACCAAAGCAAGCTGATGG 59.036 50.000 19.71 19.71 38.82 3.51
673 1124 2.806608 AACACCAAAGCAAGCTGATG 57.193 45.000 0.00 0.00 0.00 3.07
674 1125 3.825143 AAAACACCAAAGCAAGCTGAT 57.175 38.095 0.00 0.00 0.00 2.90
675 1126 3.608316 AAAAACACCAAAGCAAGCTGA 57.392 38.095 0.00 0.00 0.00 4.26
745 1196 1.748403 GGCCATCCATCGCTGTCTA 59.252 57.895 0.00 0.00 0.00 2.59
1026 1496 3.771160 GAGGTGGTCGGCGTCCAT 61.771 66.667 27.25 13.76 37.30 3.41
1052 1522 2.552093 TACCTTGAAGGAGGAGGAGG 57.448 55.000 19.83 0.00 37.67 4.30
1111 1587 3.762288 ACAGCTCCTCGTTAGACAACATA 59.238 43.478 0.00 0.00 34.05 2.29
1252 1728 5.335740 CGAACTGTCACTATAGTTGGTCTGT 60.336 44.000 1.56 0.00 37.20 3.41
1292 1768 9.660180 AGATGAAACTTTGAAATCTACCTCTAC 57.340 33.333 0.00 0.00 0.00 2.59
1451 1927 1.089112 CGATCTCATGCAAGGCAACA 58.911 50.000 0.00 0.00 43.62 3.33
1481 1957 0.605860 CTTGCAGCTTGAGCCTCACT 60.606 55.000 0.00 0.00 43.38 3.41
1709 2186 4.700268 TTTGCACTGCATCGAATTGTAT 57.300 36.364 4.10 0.00 38.76 2.29
1908 5222 9.912634 AATGGTATGTGAAATTAAAGACAACAG 57.087 29.630 0.00 0.00 0.00 3.16
1944 5258 4.020573 TGTTGCTCCAGGTATATAATCCCG 60.021 45.833 0.00 0.00 0.00 5.14
1949 5263 5.968676 AGGTTGTTGCTCCAGGTATATAA 57.031 39.130 0.00 0.00 0.00 0.98
1991 5305 6.049955 TCTTATCAAAAGAAGATGGACGGT 57.950 37.500 0.00 0.00 27.93 4.83
2023 5337 5.817816 TGCCACAAAATTTAACGGACAAATT 59.182 32.000 0.00 0.00 37.22 1.82
2144 5459 7.166691 AGAGAAACCTAATACGCAGAGTAAA 57.833 36.000 0.00 0.00 39.04 2.01
2259 5575 7.877003 ACAAGGAGACGATGTATAATGTCTAG 58.123 38.462 0.00 0.00 41.50 2.43
2274 5590 3.044986 CAATGTGCAAAACAAGGAGACG 58.955 45.455 0.00 0.00 43.61 4.18
2284 5600 3.561143 AGGTGTAGGACAATGTGCAAAA 58.439 40.909 7.79 0.00 0.00 2.44
2285 5601 3.222173 AGGTGTAGGACAATGTGCAAA 57.778 42.857 7.79 0.00 0.00 3.68
2366 5770 9.515226 TTTCAAATATGTACCTTTAGTTGCTCT 57.485 29.630 0.00 0.00 0.00 4.09
2453 5857 0.325296 ACCTGAGATTACCGCCTCCA 60.325 55.000 0.00 0.00 0.00 3.86
2477 5881 3.496507 TCACGAAGAATTTGTTGATCGCA 59.503 39.130 0.00 0.00 40.60 5.10
2556 5960 3.706086 GGGATCTTCTCTCTGAGCTTCTT 59.294 47.826 0.00 0.00 0.00 2.52
2586 5990 1.450312 GCAATAGCCGGACAGCTGT 60.450 57.895 21.88 21.88 44.67 4.40
2624 6028 4.644103 AACCAGATATTCACAGCAATGC 57.356 40.909 0.00 0.00 0.00 3.56
2790 6195 3.201363 TCCATTTCCTTCCCAAGAGGAT 58.799 45.455 0.00 0.00 46.94 3.24
2863 6268 2.989166 GCCTTGGCTTCTTTCAAAATCG 59.011 45.455 4.11 0.00 0.00 3.34
2885 6290 1.742268 GCTCAGGTGAATCTGCTTTCC 59.258 52.381 0.00 0.00 34.91 3.13
2999 6447 2.364970 TGTTCCTTTGTTCATGGCTTGG 59.635 45.455 0.09 0.00 0.00 3.61
3270 6719 1.077930 TACCTCGTCGTCTCCCAGG 60.078 63.158 0.00 0.00 0.00 4.45
3445 6894 1.139734 GAAGAGGTCATCTGCGCGA 59.860 57.895 12.10 3.27 38.67 5.87
3516 6965 7.156000 TCTTGTCGTTATATCCAAGACAAACA 58.844 34.615 13.63 5.18 46.71 2.83
3517 6966 7.544566 TCTCTTGTCGTTATATCCAAGACAAAC 59.455 37.037 13.63 0.00 46.71 2.93
3526 6980 3.734735 GCCGTTCTCTTGTCGTTATATCC 59.265 47.826 0.00 0.00 0.00 2.59
3573 7027 2.756207 ACGCCTCTCCTTCTTTAGTCTC 59.244 50.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.