Multiple sequence alignment - TraesCS6A01G411600

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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 TraesCS6A01G411600 chr6A 100.000 2518 0 0 1 2518 613948083 613950600 0.000000e+00 4650.0
1 TraesCS6A01G411600 chr6A 87.030 1596 161 23 940 2518 613896765 613895199 0.000000e+00 1759.0
2 TraesCS6A01G411600 chr6A 95.884 413 16 1 1 413 556917534 556917123 0.000000e+00 667.0
3 TraesCS6A01G411600 chr6A 96.951 328 10 0 86 413 328109155 328108828 3.660000e-153 551.0
4 TraesCS6A01G411600 chr6A 96.479 284 8 1 454 735 556917120 556916837 3.790000e-128 468.0
5 TraesCS6A01G411600 chr6A 96.237 186 7 0 554 739 328108620 328108435 3.150000e-79 305.0
6 TraesCS6A01G411600 chr6A 96.190 105 2 1 454 556 328108825 328108721 1.200000e-38 171.0
7 TraesCS6A01G411600 chr6B 86.216 1596 156 36 935 2512 713145390 713146939 0.000000e+00 1670.0
8 TraesCS6A01G411600 chr6B 83.605 1104 146 20 1425 2518 713719880 713720958 0.000000e+00 1003.0
9 TraesCS6A01G411600 chr6B 85.423 343 43 5 983 1325 713719479 713719814 1.430000e-92 350.0
10 TraesCS6A01G411600 chr6B 85.443 158 6 3 730 882 713145252 713145397 5.610000e-32 148.0
11 TraesCS6A01G411600 chr6D 83.288 1107 150 27 1425 2518 467802179 467801095 0.000000e+00 987.0
12 TraesCS6A01G411600 chr6D 81.946 1141 143 37 1387 2518 467787886 467786800 0.000000e+00 907.0
13 TraesCS6A01G411600 chr6D 81.719 1105 164 23 1425 2518 467828756 467829833 0.000000e+00 887.0
14 TraesCS6A01G411600 chr6D 87.535 353 37 5 972 1324 467802820 467802475 3.900000e-108 401.0
15 TraesCS6A01G411600 chr5A 83.909 926 132 11 1595 2518 482354558 482355468 0.000000e+00 869.0
16 TraesCS6A01G411600 chr5A 85.286 734 92 9 1789 2518 482368832 482369553 0.000000e+00 743.0
17 TraesCS6A01G411600 chr5A 98.063 413 8 0 1 413 590574659 590575071 0.000000e+00 719.0
18 TraesCS6A01G411600 chr5A 98.163 381 7 0 33 413 223051051 223050671 0.000000e+00 665.0
19 TraesCS6A01G411600 chr5A 93.197 294 8 2 454 735 590575074 590575367 2.990000e-114 422.0
20 TraesCS6A01G411600 chr5A 92.593 297 10 2 454 738 223050668 223050372 1.390000e-112 416.0
21 TraesCS6A01G411600 chr5A 79.355 620 91 28 984 1583 482351192 482351794 3.900000e-108 401.0
22 TraesCS6A01G411600 chr5A 100.000 35 0 0 1 35 223051166 223051132 5.810000e-07 65.8
23 TraesCS6A01G411600 chr2A 96.852 413 13 0 1 413 62110169 62110581 0.000000e+00 691.0
24 TraesCS6A01G411600 chr2A 88.920 352 22 4 25 376 673512270 673512604 3.870000e-113 418.0
25 TraesCS6A01G411600 chr2A 93.085 188 13 0 554 741 62110790 62110977 2.470000e-70 276.0
26 TraesCS6A01G411600 chr2A 97.895 95 2 0 454 548 62110584 62110678 5.570000e-37 165.0
27 TraesCS6A01G411600 chr1A 91.768 413 15 11 1 413 394569053 394568660 7.870000e-155 556.0
28 TraesCS6A01G411600 chr1A 94.468 235 12 1 178 412 394484185 394483952 6.620000e-96 361.0
29 TraesCS6A01G411600 chr1A 93.011 186 6 5 554 736 394483742 394483561 5.340000e-67 265.0
30 TraesCS6A01G411600 chr1A 93.805 113 4 2 446 556 394483955 394483844 1.550000e-37 167.0
31 TraesCS6A01G411600 chr1A 95.789 95 4 0 454 548 394568657 394568563 1.210000e-33 154.0
32 TraesCS6A01G411600 chr2B 90.000 350 18 4 25 374 628206881 628207213 1.070000e-118 436.0
33 TraesCS6A01G411600 chr4A 94.643 280 15 0 134 413 63532079 63531800 3.850000e-118 435.0
34 TraesCS6A01G411600 chr4A 89.902 307 6 5 454 735 63531797 63531491 3.060000e-99 372.0
35 TraesCS6A01G411600 chr4A 95.567 203 9 0 1 203 63532287 63532085 2.420000e-85 326.0
36 TraesCS6A01G411600 chr7B 88.172 372 24 7 25 396 368059824 368059473 2.320000e-115 425.0
37 TraesCS6A01G411600 chr7B 89.617 183 17 2 567 747 368059346 368059164 5.420000e-57 231.0
38 TraesCS6A01G411600 chr7D 78.003 591 120 6 1894 2482 631273515 631274097 1.840000e-96 363.0


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 TraesCS6A01G411600 chr6A 613948083 613950600 2517 False 4650.000000 4650 100.000000 1 2518 1 chr6A.!!$F1 2517
1 TraesCS6A01G411600 chr6A 613895199 613896765 1566 True 1759.000000 1759 87.030000 940 2518 1 chr6A.!!$R1 1578
2 TraesCS6A01G411600 chr6A 556916837 556917534 697 True 567.500000 667 96.181500 1 735 2 chr6A.!!$R3 734
3 TraesCS6A01G411600 chr6A 328108435 328109155 720 True 342.333333 551 96.459333 86 739 3 chr6A.!!$R2 653
4 TraesCS6A01G411600 chr6B 713145252 713146939 1687 False 909.000000 1670 85.829500 730 2512 2 chr6B.!!$F1 1782
5 TraesCS6A01G411600 chr6B 713719479 713720958 1479 False 676.500000 1003 84.514000 983 2518 2 chr6B.!!$F2 1535
6 TraesCS6A01G411600 chr6D 467786800 467787886 1086 True 907.000000 907 81.946000 1387 2518 1 chr6D.!!$R1 1131
7 TraesCS6A01G411600 chr6D 467828756 467829833 1077 False 887.000000 887 81.719000 1425 2518 1 chr6D.!!$F1 1093
8 TraesCS6A01G411600 chr6D 467801095 467802820 1725 True 694.000000 987 85.411500 972 2518 2 chr6D.!!$R2 1546
9 TraesCS6A01G411600 chr5A 482368832 482369553 721 False 743.000000 743 85.286000 1789 2518 1 chr5A.!!$F1 729
10 TraesCS6A01G411600 chr5A 482351192 482355468 4276 False 635.000000 869 81.632000 984 2518 2 chr5A.!!$F2 1534
11 TraesCS6A01G411600 chr5A 590574659 590575367 708 False 570.500000 719 95.630000 1 735 2 chr5A.!!$F3 734
12 TraesCS6A01G411600 chr5A 223050372 223051166 794 True 382.266667 665 96.918667 1 738 3 chr5A.!!$R1 737
13 TraesCS6A01G411600 chr2A 62110169 62110977 808 False 377.333333 691 95.944000 1 741 3 chr2A.!!$F2 740
14 TraesCS6A01G411600 chr1A 394483561 394484185 624 True 264.333333 361 93.761333 178 736 3 chr1A.!!$R1 558
15 TraesCS6A01G411600 chr4A 63531491 63532287 796 True 377.666667 435 93.370667 1 735 3 chr4A.!!$R1 734
16 TraesCS6A01G411600 chr7B 368059164 368059824 660 True 328.000000 425 88.894500 25 747 2 chr7B.!!$R1 722
17 TraesCS6A01G411600 chr7D 631273515 631274097 582 False 363.000000 363 78.003000 1894 2482 1 chr7D.!!$F1 588

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
839 1146 0.030638 CAAAAGGTGAACGGGCAGTG 59.969 55.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2383 5745 0.881118 GGCCATCATGTGTTTCGTGT 59.119 50.0 0.0 0.0 34.87 4.49 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
141 225 0.616111 ACCGAAGATGAGGCCAGTCT 60.616 55.000 5.01 1.49 0.00 3.24
209 368 1.140252 AGCTTGGTGTACAAAGGTCGT 59.860 47.619 0.00 0.00 38.91 4.34
216 375 1.614903 TGTACAAAGGTCGTCCGACAT 59.385 47.619 20.10 11.52 46.20 3.06
363 522 8.530311 TGCATATTCCTTTTTGTTCACATACAT 58.470 29.630 0.00 0.00 0.00 2.29
421 580 2.361483 TGCCGCTGCATGTTCCAT 60.361 55.556 0.00 0.00 44.23 3.41
423 582 0.679321 TGCCGCTGCATGTTCCATTA 60.679 50.000 0.00 0.00 44.23 1.90
424 583 0.455410 GCCGCTGCATGTTCCATTAA 59.545 50.000 0.00 0.00 37.47 1.40
425 584 1.798813 GCCGCTGCATGTTCCATTAAC 60.799 52.381 0.00 0.00 36.63 2.01
436 595 5.984233 TGTTCCATTAACAGCGATATCAC 57.016 39.130 3.12 0.00 43.22 3.06
437 596 5.423886 TGTTCCATTAACAGCGATATCACA 58.576 37.500 3.12 0.00 43.22 3.58
438 597 6.054941 TGTTCCATTAACAGCGATATCACAT 58.945 36.000 3.12 0.00 43.22 3.21
439 598 7.213678 TGTTCCATTAACAGCGATATCACATA 58.786 34.615 3.12 0.00 43.22 2.29
440 599 7.170828 TGTTCCATTAACAGCGATATCACATAC 59.829 37.037 3.12 0.00 43.22 2.39
441 600 6.754193 TCCATTAACAGCGATATCACATACA 58.246 36.000 3.12 0.00 0.00 2.29
442 601 7.386059 TCCATTAACAGCGATATCACATACAT 58.614 34.615 3.12 0.00 0.00 2.29
443 602 7.331687 TCCATTAACAGCGATATCACATACATG 59.668 37.037 3.12 0.00 0.00 3.21
444 603 7.331687 CCATTAACAGCGATATCACATACATGA 59.668 37.037 0.00 0.00 0.00 3.07
445 604 7.873739 TTAACAGCGATATCACATACATGAG 57.126 36.000 0.00 0.00 30.46 2.90
446 605 5.712152 ACAGCGATATCACATACATGAGA 57.288 39.130 0.00 0.00 30.46 3.27
447 606 6.278172 ACAGCGATATCACATACATGAGAT 57.722 37.500 0.00 7.21 40.41 2.75
448 607 7.396540 ACAGCGATATCACATACATGAGATA 57.603 36.000 0.00 10.48 41.96 1.98
449 608 8.005192 ACAGCGATATCACATACATGAGATAT 57.995 34.615 16.97 16.97 46.50 1.63
450 609 8.473219 ACAGCGATATCACATACATGAGATATT 58.527 33.333 17.63 5.56 45.03 1.28
451 610 9.310716 CAGCGATATCACATACATGAGATATTT 57.689 33.333 17.63 8.69 45.03 1.40
452 611 9.526713 AGCGATATCACATACATGAGATATTTC 57.473 33.333 17.63 13.68 45.03 2.17
537 706 4.573607 AGTAGCGATCGTTATGTCAGTGTA 59.426 41.667 17.81 0.00 0.00 2.90
623 898 0.827368 TATGCGGCAGTATGTGGACA 59.173 50.000 9.25 0.00 39.31 4.02
772 1079 2.685897 CAACAAAGAAAGGTGAACGGGA 59.314 45.455 0.00 0.00 0.00 5.14
795 1102 1.067916 GGCAGTGGTGGTGCTTTTG 59.932 57.895 0.00 0.00 40.97 2.44
801 1108 1.480545 GTGGTGGTGCTTTTGGACTTT 59.519 47.619 0.00 0.00 40.82 2.66
802 1109 1.754226 TGGTGGTGCTTTTGGACTTTC 59.246 47.619 0.00 0.00 40.82 2.62
803 1110 1.068588 GGTGGTGCTTTTGGACTTTCC 59.931 52.381 0.00 0.00 40.82 3.13
831 1138 4.091365 GCACAACAAAGACAAAAGGTGAAC 59.909 41.667 0.00 0.00 0.00 3.18
832 1139 4.323336 CACAACAAAGACAAAAGGTGAACG 59.677 41.667 0.00 0.00 0.00 3.95
833 1140 3.775661 ACAAAGACAAAAGGTGAACGG 57.224 42.857 0.00 0.00 0.00 4.44
834 1141 2.425668 ACAAAGACAAAAGGTGAACGGG 59.574 45.455 0.00 0.00 0.00 5.28
835 1142 1.029681 AAGACAAAAGGTGAACGGGC 58.970 50.000 0.00 0.00 0.00 6.13
836 1143 0.106918 AGACAAAAGGTGAACGGGCA 60.107 50.000 0.00 0.00 0.00 5.36
837 1144 0.310854 GACAAAAGGTGAACGGGCAG 59.689 55.000 0.00 0.00 0.00 4.85
838 1145 0.395173 ACAAAAGGTGAACGGGCAGT 60.395 50.000 0.00 0.00 0.00 4.40
839 1146 0.030638 CAAAAGGTGAACGGGCAGTG 59.969 55.000 0.00 0.00 0.00 3.66
840 1147 0.106918 AAAAGGTGAACGGGCAGTGA 60.107 50.000 0.00 0.00 0.00 3.41
841 1148 0.106918 AAAGGTGAACGGGCAGTGAA 60.107 50.000 0.00 0.00 0.00 3.18
882 1189 1.961394 TGCGACTACTGTTCTCAACCT 59.039 47.619 0.00 0.00 0.00 3.50
883 1190 2.364324 TGCGACTACTGTTCTCAACCTT 59.636 45.455 0.00 0.00 0.00 3.50
884 1191 3.181469 TGCGACTACTGTTCTCAACCTTT 60.181 43.478 0.00 0.00 0.00 3.11
885 1192 3.429207 GCGACTACTGTTCTCAACCTTTC 59.571 47.826 0.00 0.00 0.00 2.62
886 1193 3.988517 CGACTACTGTTCTCAACCTTTCC 59.011 47.826 0.00 0.00 0.00 3.13
887 1194 4.262079 CGACTACTGTTCTCAACCTTTCCT 60.262 45.833 0.00 0.00 0.00 3.36
888 1195 5.216614 ACTACTGTTCTCAACCTTTCCTC 57.783 43.478 0.00 0.00 0.00 3.71
889 1196 4.902448 ACTACTGTTCTCAACCTTTCCTCT 59.098 41.667 0.00 0.00 0.00 3.69
890 1197 4.779993 ACTGTTCTCAACCTTTCCTCTT 57.220 40.909 0.00 0.00 0.00 2.85
891 1198 4.709250 ACTGTTCTCAACCTTTCCTCTTC 58.291 43.478 0.00 0.00 0.00 2.87
892 1199 4.068599 CTGTTCTCAACCTTTCCTCTTCC 58.931 47.826 0.00 0.00 0.00 3.46
893 1200 3.716872 TGTTCTCAACCTTTCCTCTTCCT 59.283 43.478 0.00 0.00 0.00 3.36
894 1201 4.202367 TGTTCTCAACCTTTCCTCTTCCTC 60.202 45.833 0.00 0.00 0.00 3.71
895 1202 3.863086 TCTCAACCTTTCCTCTTCCTCT 58.137 45.455 0.00 0.00 0.00 3.69
896 1203 3.580458 TCTCAACCTTTCCTCTTCCTCTG 59.420 47.826 0.00 0.00 0.00 3.35
897 1204 3.318313 TCAACCTTTCCTCTTCCTCTGT 58.682 45.455 0.00 0.00 0.00 3.41
898 1205 3.325135 TCAACCTTTCCTCTTCCTCTGTC 59.675 47.826 0.00 0.00 0.00 3.51
899 1206 3.268034 ACCTTTCCTCTTCCTCTGTCT 57.732 47.619 0.00 0.00 0.00 3.41
900 1207 3.169908 ACCTTTCCTCTTCCTCTGTCTC 58.830 50.000 0.00 0.00 0.00 3.36
901 1208 3.181412 ACCTTTCCTCTTCCTCTGTCTCT 60.181 47.826 0.00 0.00 0.00 3.10
902 1209 3.195396 CCTTTCCTCTTCCTCTGTCTCTG 59.805 52.174 0.00 0.00 0.00 3.35
903 1210 3.816398 TTCCTCTTCCTCTGTCTCTGA 57.184 47.619 0.00 0.00 0.00 3.27
904 1211 3.816398 TCCTCTTCCTCTGTCTCTGAA 57.184 47.619 0.00 0.00 0.00 3.02
905 1212 3.426615 TCCTCTTCCTCTGTCTCTGAAC 58.573 50.000 0.00 0.00 0.00 3.18
906 1213 2.495669 CCTCTTCCTCTGTCTCTGAACC 59.504 54.545 0.00 0.00 0.00 3.62
907 1214 2.495669 CTCTTCCTCTGTCTCTGAACCC 59.504 54.545 0.00 0.00 0.00 4.11
908 1215 2.158310 TCTTCCTCTGTCTCTGAACCCA 60.158 50.000 0.00 0.00 0.00 4.51
909 1216 1.633774 TCCTCTGTCTCTGAACCCAC 58.366 55.000 0.00 0.00 0.00 4.61
910 1217 1.148027 TCCTCTGTCTCTGAACCCACT 59.852 52.381 0.00 0.00 0.00 4.00
911 1218 1.548269 CCTCTGTCTCTGAACCCACTC 59.452 57.143 0.00 0.00 0.00 3.51
912 1219 2.524306 CTCTGTCTCTGAACCCACTCT 58.476 52.381 0.00 0.00 0.00 3.24
913 1220 2.491693 CTCTGTCTCTGAACCCACTCTC 59.508 54.545 0.00 0.00 0.00 3.20
914 1221 2.158460 TCTGTCTCTGAACCCACTCTCA 60.158 50.000 0.00 0.00 0.00 3.27
915 1222 1.964223 TGTCTCTGAACCCACTCTCAC 59.036 52.381 0.00 0.00 0.00 3.51
916 1223 2.243810 GTCTCTGAACCCACTCTCACT 58.756 52.381 0.00 0.00 0.00 3.41
917 1224 2.230266 GTCTCTGAACCCACTCTCACTC 59.770 54.545 0.00 0.00 0.00 3.51
918 1225 2.158460 TCTCTGAACCCACTCTCACTCA 60.158 50.000 0.00 0.00 0.00 3.41
919 1226 1.964223 TCTGAACCCACTCTCACTCAC 59.036 52.381 0.00 0.00 0.00 3.51
920 1227 1.967066 CTGAACCCACTCTCACTCACT 59.033 52.381 0.00 0.00 0.00 3.41
921 1228 1.964223 TGAACCCACTCTCACTCACTC 59.036 52.381 0.00 0.00 0.00 3.51
922 1229 1.964223 GAACCCACTCTCACTCACTCA 59.036 52.381 0.00 0.00 0.00 3.41
923 1230 1.333177 ACCCACTCTCACTCACTCAC 58.667 55.000 0.00 0.00 0.00 3.51
924 1231 1.133325 ACCCACTCTCACTCACTCACT 60.133 52.381 0.00 0.00 0.00 3.41
925 1232 1.271934 CCCACTCTCACTCACTCACTG 59.728 57.143 0.00 0.00 0.00 3.66
926 1233 1.336702 CCACTCTCACTCACTCACTGC 60.337 57.143 0.00 0.00 0.00 4.40
927 1234 1.612950 CACTCTCACTCACTCACTGCT 59.387 52.381 0.00 0.00 0.00 4.24
928 1235 1.612950 ACTCTCACTCACTCACTGCTG 59.387 52.381 0.00 0.00 0.00 4.41
929 1236 0.316522 TCTCACTCACTCACTGCTGC 59.683 55.000 0.00 0.00 0.00 5.25
930 1237 0.317799 CTCACTCACTCACTGCTGCT 59.682 55.000 0.00 0.00 0.00 4.24
931 1238 0.033090 TCACTCACTCACTGCTGCTG 59.967 55.000 4.89 4.89 0.00 4.41
932 1239 1.301558 ACTCACTCACTGCTGCTGC 60.302 57.895 8.89 8.89 40.20 5.25
1104 1415 2.746142 CGGCAAGCTGGATTCTTGGATA 60.746 50.000 0.00 0.00 40.79 2.59
1171 1482 2.284625 AGGCGGTGGAGATGGTGA 60.285 61.111 0.00 0.00 0.00 4.02
1172 1483 2.187946 GGCGGTGGAGATGGTGAG 59.812 66.667 0.00 0.00 0.00 3.51
1251 1562 1.407258 GTCAAGGAGCTGCTCTACGAT 59.593 52.381 27.09 8.22 0.00 3.73
1262 1573 0.999228 CTCTACGATGCCGACGATGC 60.999 60.000 0.00 0.00 39.50 3.91
1263 1574 2.016704 CTACGATGCCGACGATGCC 61.017 63.158 0.00 0.00 39.50 4.40
1281 1592 2.955402 GTCGACGAGCTGGACTGT 59.045 61.111 1.44 0.00 0.00 3.55
1357 1921 2.450476 CTTGCTAATTGGCAGTTCCCT 58.550 47.619 16.44 0.00 43.39 4.20
1361 1925 3.006752 TGCTAATTGGCAGTTCCCTTTTG 59.993 43.478 13.03 0.00 37.29 2.44
1459 2024 3.975246 TCCAAACGGATGGAACGC 58.025 55.556 8.80 0.00 46.36 4.84
1507 2084 7.633789 AGAAAATACTGATGATGTACAGGGTT 58.366 34.615 0.33 0.00 38.30 4.11
1558 2141 7.566138 AGGTATGGGATCAATTTGAAATCACAT 59.434 33.333 17.49 17.49 43.90 3.21
1560 2143 7.670605 ATGGGATCAATTTGAAATCACATCT 57.329 32.000 10.59 0.00 38.82 2.90
1574 2157 9.086336 TGAAATCACATCTTTTCTTGAACAAAC 57.914 29.630 0.00 0.00 33.87 2.93
1634 4969 1.131126 CCAAACAGAGCTTATGTGCGG 59.869 52.381 6.31 6.47 38.13 5.69
1665 5000 1.269517 GGGACATCAGTTTTGCGCAAA 60.270 47.619 30.63 30.63 0.00 3.68
1673 5008 3.004629 TCAGTTTTGCGCAAACATCTCAT 59.995 39.130 33.73 12.47 46.55 2.90
1674 5009 3.362831 CAGTTTTGCGCAAACATCTCATC 59.637 43.478 33.73 15.87 46.55 2.92
1830 5184 3.133542 TCTCACTGCTAATCCATGGTCTG 59.866 47.826 12.58 2.17 0.00 3.51
1862 5216 3.036026 CACTGCTGGTGCTACTACG 57.964 57.895 0.00 0.00 39.22 3.51
1873 5227 2.032550 GTGCTACTACGATTCCTACGCA 59.967 50.000 0.00 0.00 0.00 5.24
1881 5235 1.004610 CGATTCCTACGCATGTTGCAG 60.005 52.381 0.00 0.00 45.36 4.41
1891 5245 2.671914 CGCATGTTGCAGCTGGTAATTT 60.672 45.455 17.12 0.00 45.36 1.82
1895 5249 3.221771 TGTTGCAGCTGGTAATTTGTCT 58.778 40.909 17.12 0.00 0.00 3.41
2063 5417 2.237143 CAAGATACTTGGGCCAGACTCA 59.763 50.000 6.23 0.00 0.00 3.41
2068 5428 1.770110 TTGGGCCAGACTCAGGTGT 60.770 57.895 6.23 0.00 0.00 4.16
2080 5440 4.127171 GACTCAGGTGTTGCAAGTTCTAA 58.873 43.478 0.00 0.00 0.00 2.10
2081 5441 4.718961 ACTCAGGTGTTGCAAGTTCTAAT 58.281 39.130 0.00 0.00 0.00 1.73
2082 5442 4.757149 ACTCAGGTGTTGCAAGTTCTAATC 59.243 41.667 0.00 0.00 0.00 1.75
2109 5469 9.708092 ATCACTGTCATATTACAATCTCAGATG 57.292 33.333 0.00 0.00 0.00 2.90
2128 5488 1.421485 CACGCCGAAGAACATCAGC 59.579 57.895 0.00 0.00 0.00 4.26
2334 5696 6.484643 CACAAGATATGGATTTGGGTGTCTAG 59.515 42.308 0.00 0.00 0.00 2.43
2482 5844 9.976511 CGGGTTCTACTTATTTTAGATGATGTA 57.023 33.333 0.00 0.00 0.00 2.29
2512 5874 1.153249 GGATGACGGCCGATGGAAA 60.153 57.895 35.90 10.43 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 203 0.179089 CTGGCCTCATCTTCGGTCAG 60.179 60.000 3.32 0.00 45.48 3.51
120 204 0.904865 ACTGGCCTCATCTTCGGTCA 60.905 55.000 3.32 0.00 33.17 4.02
141 225 1.912731 TCGGAATCAGAATGGTCCCAA 59.087 47.619 0.00 0.00 37.39 4.12
209 368 3.509967 TCTTCTGTCAGCTTTATGTCGGA 59.490 43.478 0.00 0.00 0.00 4.55
216 375 6.114187 TCTTCCATTCTTCTGTCAGCTTTA 57.886 37.500 0.00 0.00 0.00 1.85
363 522 7.173907 GCCTATCAAAGCAGCAGAAATATCTTA 59.826 37.037 0.00 0.00 32.03 2.10
413 572 6.054941 TGTGATATCGCTGTTAATGGAACAT 58.945 36.000 16.85 0.00 46.95 2.71
415 574 5.984233 TGTGATATCGCTGTTAATGGAAC 57.016 39.130 16.85 0.00 38.65 3.62
418 577 7.331687 TCATGTATGTGATATCGCTGTTAATGG 59.668 37.037 16.85 1.54 0.00 3.16
420 579 8.306761 TCTCATGTATGTGATATCGCTGTTAAT 58.693 33.333 16.85 4.80 0.00 1.40
421 580 7.657336 TCTCATGTATGTGATATCGCTGTTAA 58.343 34.615 16.85 0.00 0.00 2.01
423 582 6.089249 TCTCATGTATGTGATATCGCTGTT 57.911 37.500 16.85 5.26 0.00 3.16
424 583 5.712152 TCTCATGTATGTGATATCGCTGT 57.288 39.130 16.85 8.54 0.00 4.40
425 584 8.868635 AATATCTCATGTATGTGATATCGCTG 57.131 34.615 20.78 6.93 45.66 5.18
426 585 9.526713 GAAATATCTCATGTATGTGATATCGCT 57.473 33.333 20.78 13.13 45.66 4.93
427 586 9.526713 AGAAATATCTCATGTATGTGATATCGC 57.473 33.333 20.78 9.41 45.66 4.58
431 590 9.933723 CCACAGAAATATCTCATGTATGTGATA 57.066 33.333 15.10 15.10 43.30 2.15
432 591 8.654094 TCCACAGAAATATCTCATGTATGTGAT 58.346 33.333 12.40 12.40 41.96 3.06
433 592 8.021898 TCCACAGAAATATCTCATGTATGTGA 57.978 34.615 6.57 0.00 32.03 3.58
434 593 8.843885 ATCCACAGAAATATCTCATGTATGTG 57.156 34.615 0.00 0.00 32.03 3.21
435 594 9.857656 AAATCCACAGAAATATCTCATGTATGT 57.142 29.630 0.00 0.00 32.03 2.29
438 597 9.685276 ACAAAATCCACAGAAATATCTCATGTA 57.315 29.630 0.00 0.00 32.03 2.29
439 598 8.585471 ACAAAATCCACAGAAATATCTCATGT 57.415 30.769 0.00 0.00 32.03 3.21
449 608 9.231297 CCTCTAGAATAACAAAATCCACAGAAA 57.769 33.333 0.00 0.00 0.00 2.52
450 609 7.336931 GCCTCTAGAATAACAAAATCCACAGAA 59.663 37.037 0.00 0.00 0.00 3.02
451 610 6.823689 GCCTCTAGAATAACAAAATCCACAGA 59.176 38.462 0.00 0.00 0.00 3.41
452 611 6.238211 CGCCTCTAGAATAACAAAATCCACAG 60.238 42.308 0.00 0.00 0.00 3.66
772 1079 2.203394 CACCACCACTGCCTGCTT 60.203 61.111 0.00 0.00 0.00 3.91
795 1102 1.527380 TTGTGCCGTGGGAAAGTCC 60.527 57.895 0.00 0.00 35.23 3.85
801 1108 1.098712 GTCTTTGTTGTGCCGTGGGA 61.099 55.000 0.00 0.00 0.00 4.37
802 1109 1.358759 GTCTTTGTTGTGCCGTGGG 59.641 57.895 0.00 0.00 0.00 4.61
803 1110 0.453793 TTGTCTTTGTTGTGCCGTGG 59.546 50.000 0.00 0.00 0.00 4.94
831 1138 2.256461 GCTGCTTTTCACTGCCCG 59.744 61.111 0.00 0.00 0.00 6.13
832 1139 2.256461 CGCTGCTTTTCACTGCCC 59.744 61.111 0.00 0.00 0.00 5.36
833 1140 2.256461 CCGCTGCTTTTCACTGCC 59.744 61.111 0.00 0.00 0.00 4.85
834 1141 2.429739 GCCGCTGCTTTTCACTGC 60.430 61.111 0.00 0.00 33.53 4.40
835 1142 2.256461 GGCCGCTGCTTTTCACTG 59.744 61.111 0.00 0.00 37.74 3.66
836 1143 3.357079 CGGCCGCTGCTTTTCACT 61.357 61.111 14.67 0.00 37.74 3.41
837 1144 4.404654 CCGGCCGCTGCTTTTCAC 62.405 66.667 22.85 0.00 37.74 3.18
840 1147 3.853698 TAACCCGGCCGCTGCTTTT 62.854 57.895 22.85 7.94 37.74 2.27
841 1148 4.338710 TAACCCGGCCGCTGCTTT 62.339 61.111 22.85 9.80 37.74 3.51
882 1189 4.119556 TCAGAGACAGAGGAAGAGGAAA 57.880 45.455 0.00 0.00 0.00 3.13
883 1190 3.816398 TCAGAGACAGAGGAAGAGGAA 57.184 47.619 0.00 0.00 0.00 3.36
884 1191 3.426615 GTTCAGAGACAGAGGAAGAGGA 58.573 50.000 0.00 0.00 0.00 3.71
885 1192 2.495669 GGTTCAGAGACAGAGGAAGAGG 59.504 54.545 0.00 0.00 0.00 3.69
886 1193 2.495669 GGGTTCAGAGACAGAGGAAGAG 59.504 54.545 0.00 0.00 0.00 2.85
887 1194 2.158310 TGGGTTCAGAGACAGAGGAAGA 60.158 50.000 0.00 0.00 0.00 2.87
888 1195 2.028567 GTGGGTTCAGAGACAGAGGAAG 60.029 54.545 0.00 0.00 0.00 3.46
889 1196 1.971357 GTGGGTTCAGAGACAGAGGAA 59.029 52.381 0.00 0.00 0.00 3.36
890 1197 1.148027 AGTGGGTTCAGAGACAGAGGA 59.852 52.381 0.00 0.00 0.00 3.71
891 1198 1.548269 GAGTGGGTTCAGAGACAGAGG 59.452 57.143 0.00 0.00 0.00 3.69
892 1199 2.491693 GAGAGTGGGTTCAGAGACAGAG 59.508 54.545 0.00 0.00 0.00 3.35
893 1200 2.158460 TGAGAGTGGGTTCAGAGACAGA 60.158 50.000 0.00 0.00 0.00 3.41
894 1201 2.029470 GTGAGAGTGGGTTCAGAGACAG 60.029 54.545 0.00 0.00 0.00 3.51
895 1202 1.964223 GTGAGAGTGGGTTCAGAGACA 59.036 52.381 0.00 0.00 0.00 3.41
896 1203 2.230266 GAGTGAGAGTGGGTTCAGAGAC 59.770 54.545 0.00 0.00 0.00 3.36
897 1204 2.158460 TGAGTGAGAGTGGGTTCAGAGA 60.158 50.000 0.00 0.00 0.00 3.10
898 1205 2.029470 GTGAGTGAGAGTGGGTTCAGAG 60.029 54.545 0.00 0.00 0.00 3.35
899 1206 1.964223 GTGAGTGAGAGTGGGTTCAGA 59.036 52.381 0.00 0.00 0.00 3.27
900 1207 1.967066 AGTGAGTGAGAGTGGGTTCAG 59.033 52.381 0.00 0.00 0.00 3.02
901 1208 1.964223 GAGTGAGTGAGAGTGGGTTCA 59.036 52.381 0.00 0.00 0.00 3.18
902 1209 1.964223 TGAGTGAGTGAGAGTGGGTTC 59.036 52.381 0.00 0.00 0.00 3.62
903 1210 1.689273 GTGAGTGAGTGAGAGTGGGTT 59.311 52.381 0.00 0.00 0.00 4.11
904 1211 1.133325 AGTGAGTGAGTGAGAGTGGGT 60.133 52.381 0.00 0.00 0.00 4.51
905 1212 1.271934 CAGTGAGTGAGTGAGAGTGGG 59.728 57.143 0.00 0.00 0.00 4.61
906 1213 1.336702 GCAGTGAGTGAGTGAGAGTGG 60.337 57.143 0.00 0.00 0.00 4.00
907 1214 1.612950 AGCAGTGAGTGAGTGAGAGTG 59.387 52.381 0.00 0.00 0.00 3.51
908 1215 1.612950 CAGCAGTGAGTGAGTGAGAGT 59.387 52.381 0.00 0.00 0.00 3.24
909 1216 1.669502 GCAGCAGTGAGTGAGTGAGAG 60.670 57.143 0.00 0.00 0.00 3.20
910 1217 0.316522 GCAGCAGTGAGTGAGTGAGA 59.683 55.000 0.00 0.00 0.00 3.27
911 1218 0.317799 AGCAGCAGTGAGTGAGTGAG 59.682 55.000 0.00 0.00 0.00 3.51
912 1219 0.033090 CAGCAGCAGTGAGTGAGTGA 59.967 55.000 0.00 0.00 0.00 3.41
913 1220 1.566882 GCAGCAGCAGTGAGTGAGTG 61.567 60.000 0.00 0.00 41.58 3.51
914 1221 1.301558 GCAGCAGCAGTGAGTGAGT 60.302 57.895 0.00 0.00 41.58 3.41
915 1222 3.563842 GCAGCAGCAGTGAGTGAG 58.436 61.111 0.00 0.00 41.58 3.51
925 1232 1.801332 CTGGTTCAGATGCAGCAGC 59.199 57.895 4.07 1.15 35.80 5.25
926 1233 0.677098 AGCTGGTTCAGATGCAGCAG 60.677 55.000 4.07 7.22 40.96 4.24
927 1234 0.958876 CAGCTGGTTCAGATGCAGCA 60.959 55.000 5.57 0.00 40.91 4.41
928 1235 1.801332 CAGCTGGTTCAGATGCAGC 59.199 57.895 5.57 0.00 40.91 5.25
933 1240 1.378250 GGCAGCAGCTGGTTCAGAT 60.378 57.895 24.13 0.00 41.70 2.90
934 1241 2.033141 GGCAGCAGCTGGTTCAGA 59.967 61.111 24.13 0.00 41.70 3.27
935 1242 3.060615 GGGCAGCAGCTGGTTCAG 61.061 66.667 24.13 6.52 41.70 3.02
936 1243 3.557903 GAGGGCAGCAGCTGGTTCA 62.558 63.158 24.13 0.00 41.70 3.18
937 1244 2.749441 GAGGGCAGCAGCTGGTTC 60.749 66.667 24.13 11.97 41.70 3.62
938 1245 3.255397 AGAGGGCAGCAGCTGGTT 61.255 61.111 24.13 0.56 41.70 3.67
1098 1409 1.748879 GCCAGCTTGCCGTATCCAA 60.749 57.895 0.00 0.00 0.00 3.53
1262 1573 3.432588 AGTCCAGCTCGTCGACGG 61.433 66.667 35.05 25.93 40.29 4.79
1263 1574 2.202362 CAGTCCAGCTCGTCGACG 60.202 66.667 31.30 31.30 41.45 5.12
1300 1611 2.134789 AAATTACCTGGCTGGAGCTG 57.865 50.000 18.12 0.00 41.70 4.24
1361 1925 8.114905 GTGCCTGACGTAAATAATAGAAAGAAC 58.885 37.037 0.00 0.00 0.00 3.01
1489 2063 2.677902 CGCAACCCTGTACATCATCAGT 60.678 50.000 0.00 0.00 0.00 3.41
1507 2084 1.080298 CGTAACCTGTTATTGCCGCA 58.920 50.000 0.00 0.00 0.00 5.69
1558 2141 3.630312 CCTCCGGTTTGTTCAAGAAAAGA 59.370 43.478 0.00 0.00 0.00 2.52
1560 2143 2.691011 CCCTCCGGTTTGTTCAAGAAAA 59.309 45.455 0.00 0.00 0.00 2.29
1593 4928 1.062206 GCGCTTGCATCTTGCTCTC 59.938 57.895 0.00 0.00 45.31 3.20
1614 4949 1.131126 CCGCACATAAGCTCTGTTTGG 59.869 52.381 0.00 1.82 0.00 3.28
1634 4969 3.690460 ACTGATGTCCCATTCTTGGTTC 58.310 45.455 0.00 0.00 41.91 3.62
1665 5000 4.104383 ACAACCTTTGGTGATGAGATGT 57.896 40.909 0.00 0.00 35.34 3.06
1673 5008 3.006112 TGTTGCTACAACCTTTGGTGA 57.994 42.857 7.91 0.00 35.34 4.02
1674 5009 3.791973 TTGTTGCTACAACCTTTGGTG 57.208 42.857 9.74 0.00 39.29 4.17
1725 5063 8.903820 GGTGCAATGTAGAAAAATAATCTAGGT 58.096 33.333 0.00 0.00 30.33 3.08
1852 5206 2.032550 TGCGTAGGAATCGTAGTAGCAC 59.967 50.000 4.44 0.00 0.00 4.40
1873 5227 3.828451 AGACAAATTACCAGCTGCAACAT 59.172 39.130 8.66 0.00 0.00 2.71
1881 5235 5.880054 TTTCTGCTAGACAAATTACCAGC 57.120 39.130 0.00 0.00 0.00 4.85
1891 5245 5.745312 TCTCATCCTTTTTCTGCTAGACA 57.255 39.130 0.00 0.00 0.00 3.41
1895 5249 5.977635 TCGATTCTCATCCTTTTTCTGCTA 58.022 37.500 0.00 0.00 0.00 3.49
1963 5317 4.522789 TCCTTTCAGAAAATGCACCCTTAC 59.477 41.667 0.00 0.00 0.00 2.34
1964 5318 4.735369 TCCTTTCAGAAAATGCACCCTTA 58.265 39.130 0.00 0.00 0.00 2.69
1969 5323 6.803807 GTCTTGTATCCTTTCAGAAAATGCAC 59.196 38.462 0.00 0.00 0.00 4.57
2063 5417 5.182001 GTGATGATTAGAACTTGCAACACCT 59.818 40.000 0.00 0.00 0.00 4.00
2068 5428 5.997129 TGACAGTGATGATTAGAACTTGCAA 59.003 36.000 0.00 0.00 0.00 4.08
2080 5440 9.708092 CTGAGATTGTAATATGACAGTGATGAT 57.292 33.333 0.00 0.00 0.00 2.45
2081 5441 8.917088 TCTGAGATTGTAATATGACAGTGATGA 58.083 33.333 0.00 0.00 0.00 2.92
2082 5442 9.708092 ATCTGAGATTGTAATATGACAGTGATG 57.292 33.333 0.00 0.00 0.00 3.07
2109 5469 1.421485 CTGATGTTCTTCGGCGTGC 59.579 57.895 6.85 0.00 0.00 5.34
2128 5488 5.182001 CCATACACTTTCCCTTGAACAAGAG 59.818 44.000 14.99 3.13 40.79 2.85
2199 5561 5.992217 AGAACAGTTACACCTTCAGTTGATC 59.008 40.000 0.00 0.00 0.00 2.92
2334 5696 5.855395 GTGAGTCTCATTTCATCAAAGTTGC 59.145 40.000 5.68 0.00 0.00 4.17
2383 5745 0.881118 GGCCATCATGTGTTTCGTGT 59.119 50.000 0.00 0.00 34.87 4.49
2386 5748 2.287188 GCATAGGCCATCATGTGTTTCG 60.287 50.000 5.01 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.