Multiple sequence alignment - TraesCS2A01G334900

Loading Multiple Alignment...

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 TraesCS2A01G334900 chr2A 100.000 1902 0 0 610 2511 568577684 568579585 0.000000e+00 3513.0
1 TraesCS2A01G334900 chr2A 100.000 335 0 0 1 335 568577075 568577409 9.870000e-174 619.0
2 TraesCS2A01G334900 chr2D 93.823 1279 54 13 1243 2511 422324471 422325734 0.000000e+00 1901.0
3 TraesCS2A01G334900 chr2D 89.492 295 17 7 830 1110 422324092 422324386 6.600000e-96 361.0
4 TraesCS2A01G334900 chr2D 87.500 128 5 1 712 828 422323926 422324053 1.210000e-28 137.0
5 TraesCS2A01G334900 chr2D 80.952 168 20 8 15 179 473174192 473174350 3.390000e-24 122.0
6 TraesCS2A01G334900 chr2D 89.091 55 3 3 664 716 585381051 585380998 5.800000e-07 65.8
7 TraesCS2A01G334900 chr2B 83.990 787 65 34 1243 2000 494877343 494878097 0.000000e+00 699.0
8 TraesCS2A01G334900 chr2B 92.754 483 23 7 2036 2511 494878279 494878756 0.000000e+00 688.0
9 TraesCS2A01G334900 chr2B 78.711 1024 121 47 833 1841 494860035 494860976 5.980000e-166 593.0
10 TraesCS2A01G334900 chr2B 86.622 299 22 8 830 1110 494876964 494877262 5.210000e-82 315.0
11 TraesCS2A01G334900 chr2B 100.000 45 0 0 725 769 494876623 494876667 1.600000e-12 84.2
12 TraesCS2A01G334900 chr6A 84.916 179 17 6 1 179 283929758 283929926 3.320000e-39 172.0
13 TraesCS2A01G334900 chr6A 100.000 32 0 0 1651 1682 158316628 158316597 2.700000e-05 60.2
14 TraesCS2A01G334900 chr6A 96.970 33 0 1 689 721 19940849 19940880 1.000000e-03 54.7
15 TraesCS2A01G334900 chr5D 93.878 98 6 0 10 107 59941961 59942058 5.600000e-32 148.0
16 TraesCS2A01G334900 chr5D 85.047 107 14 2 610 715 328392254 328392149 9.500000e-20 108.0
17 TraesCS2A01G334900 chr5D 86.458 96 4 1 93 179 59941961 59942056 2.060000e-16 97.1
18 TraesCS2A01G334900 chr5D 91.111 45 2 1 1653 1697 31209683 31209725 2.700000e-05 60.2
19 TraesCS2A01G334900 chr3A 89.394 66 4 3 654 718 720852096 720852033 2.070000e-11 80.5
20 TraesCS2A01G334900 chr1A 81.522 92 14 2 625 715 391943308 391943219 3.460000e-09 73.1
21 TraesCS2A01G334900 chr1A 100.000 33 0 0 1650 1682 508125224 508125256 7.500000e-06 62.1
22 TraesCS2A01G334900 chr3D 92.157 51 3 1 667 716 14127257 14127207 1.250000e-08 71.3
23 TraesCS2A01G334900 chr7B 100.000 31 0 0 1650 1680 595448377 595448407 9.700000e-05 58.4
24 TraesCS2A01G334900 chr6B 100.000 31 0 0 1652 1682 129485616 129485586 9.700000e-05 58.4
25 TraesCS2A01G334900 chr6B 100.000 31 0 0 1653 1683 561249092 561249062 9.700000e-05 58.4
26 TraesCS2A01G334900 chr4A 100.000 31 0 0 1652 1682 713832886 713832916 9.700000e-05 58.4
27 TraesCS2A01G334900 chr1B 100.000 31 0 0 1652 1682 3122653 3122623 9.700000e-05 58.4
28 TraesCS2A01G334900 chr5A 90.909 44 1 3 1641 1682 474327723 474327681 3.490000e-04 56.5


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 TraesCS2A01G334900 chr2A 568577075 568579585 2510 False 2066.000000 3513 100.000000 1 2511 2 chr2A.!!$F1 2510
1 TraesCS2A01G334900 chr2D 422323926 422325734 1808 False 799.666667 1901 90.271667 712 2511 3 chr2D.!!$F2 1799
2 TraesCS2A01G334900 chr2B 494860035 494860976 941 False 593.000000 593 78.711000 833 1841 1 chr2B.!!$F1 1008
3 TraesCS2A01G334900 chr2B 494876623 494878756 2133 False 446.550000 699 90.841500 725 2511 4 chr2B.!!$F2 1786

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
779 979 0.478072 TGGGTTGATCAGGCACAAGT 59.522 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 2251 0.109532 TTCAGTTTGCCATGACCCGA 59.89 50.0 0.0 0.0 0.0 5.14 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
34 35 4.077184 CGCTTGGTCGTGCCCCTA 62.077 66.667 0.00 0.00 36.04 3.53
35 36 2.436115 GCTTGGTCGTGCCCCTAC 60.436 66.667 0.00 0.00 36.04 3.18
36 37 2.125673 CTTGGTCGTGCCCCTACG 60.126 66.667 0.00 0.00 44.98 3.51
44 45 2.662596 TGCCCCTACGAGCACTTG 59.337 61.111 0.00 0.00 33.08 3.16
45 46 2.820037 GCCCCTACGAGCACTTGC 60.820 66.667 0.00 0.00 42.49 4.01
55 56 4.755614 GCACTTGCGAGCTGCTGC 62.756 66.667 7.01 11.90 46.63 5.25
65 66 4.719106 GCTGCTGCTGCCTCCTGT 62.719 66.667 19.30 0.00 38.71 4.00
66 67 2.746671 CTGCTGCTGCCTCCTGTG 60.747 66.667 13.47 0.00 38.71 3.66
138 139 2.960170 GCACTTTGCTGCCTCCTG 59.040 61.111 0.00 0.00 40.96 3.86
139 140 2.960170 CACTTTGCTGCCTCCTGC 59.040 61.111 0.00 0.00 41.77 4.85
140 141 2.670934 ACTTTGCTGCCTCCTGCG 60.671 61.111 0.00 0.00 45.60 5.18
141 142 4.112341 CTTTGCTGCCTCCTGCGC 62.112 66.667 0.00 0.00 45.60 6.09
212 213 4.755614 GCACTTGCGAGCTGCTGC 62.756 66.667 7.01 11.90 46.63 5.25
222 223 4.117661 GCTGCTGCTGCTTCCTGC 62.118 66.667 22.10 9.17 40.48 4.85
223 224 3.800863 CTGCTGCTGCTTCCTGCG 61.801 66.667 17.00 0.00 46.63 5.18
268 269 4.099170 CTGCCTGCTGCTTGCGTC 62.099 66.667 0.00 0.00 46.63 5.19
272 273 4.440987 CTGCTGCTTGCGTCGCTG 62.441 66.667 19.50 12.19 46.63 5.18
275 276 4.440987 CTGCTTGCGTCGCTGCTG 62.441 66.667 26.51 23.42 35.36 4.41
278 279 4.440987 CTTGCGTCGCTGCTGCTG 62.441 66.667 19.50 0.77 36.97 4.41
300 301 4.154347 CTCGCCCTGCCTCACCTC 62.154 72.222 0.00 0.00 0.00 3.85
301 302 4.704103 TCGCCCTGCCTCACCTCT 62.704 66.667 0.00 0.00 0.00 3.69
302 303 4.463879 CGCCCTGCCTCACCTCTG 62.464 72.222 0.00 0.00 0.00 3.35
303 304 4.106925 GCCCTGCCTCACCTCTGG 62.107 72.222 0.00 0.00 0.00 3.86
632 633 4.969484 ACGAGTGGATAATATTTCACCCC 58.031 43.478 0.00 0.00 0.00 4.95
633 634 4.202430 ACGAGTGGATAATATTTCACCCCC 60.202 45.833 0.00 0.00 0.00 5.40
634 635 4.202419 CGAGTGGATAATATTTCACCCCCA 60.202 45.833 0.00 0.00 0.00 4.96
635 636 5.316987 GAGTGGATAATATTTCACCCCCAG 58.683 45.833 0.00 0.00 0.00 4.45
636 637 4.981647 AGTGGATAATATTTCACCCCCAGA 59.018 41.667 0.00 0.00 0.00 3.86
637 638 5.073691 AGTGGATAATATTTCACCCCCAGAG 59.926 44.000 0.00 0.00 0.00 3.35
638 639 4.981647 TGGATAATATTTCACCCCCAGAGT 59.018 41.667 0.00 0.00 0.00 3.24
639 640 6.043938 GTGGATAATATTTCACCCCCAGAGTA 59.956 42.308 0.00 0.00 0.00 2.59
640 641 6.621931 TGGATAATATTTCACCCCCAGAGTAA 59.378 38.462 0.00 0.00 0.00 2.24
641 642 7.129660 TGGATAATATTTCACCCCCAGAGTAAA 59.870 37.037 0.00 0.00 0.00 2.01
642 643 8.170730 GGATAATATTTCACCCCCAGAGTAAAT 58.829 37.037 0.00 0.00 0.00 1.40
643 644 8.940397 ATAATATTTCACCCCCAGAGTAAATG 57.060 34.615 0.00 0.00 0.00 2.32
644 645 4.675063 ATTTCACCCCCAGAGTAAATGT 57.325 40.909 0.00 0.00 0.00 2.71
645 646 4.463050 TTTCACCCCCAGAGTAAATGTT 57.537 40.909 0.00 0.00 0.00 2.71
646 647 4.463050 TTCACCCCCAGAGTAAATGTTT 57.537 40.909 0.00 0.00 0.00 2.83
647 648 4.028993 TCACCCCCAGAGTAAATGTTTC 57.971 45.455 0.00 0.00 0.00 2.78
648 649 2.747446 CACCCCCAGAGTAAATGTTTCG 59.253 50.000 0.00 0.00 0.00 3.46
649 650 1.743394 CCCCCAGAGTAAATGTTTCGC 59.257 52.381 0.00 0.00 0.00 4.70
650 651 1.743394 CCCCAGAGTAAATGTTTCGCC 59.257 52.381 0.00 0.00 0.00 5.54
651 652 2.432444 CCCAGAGTAAATGTTTCGCCA 58.568 47.619 0.00 0.00 0.00 5.69
652 653 2.420022 CCCAGAGTAAATGTTTCGCCAG 59.580 50.000 0.00 0.00 0.00 4.85
653 654 3.334691 CCAGAGTAAATGTTTCGCCAGA 58.665 45.455 0.00 0.00 0.00 3.86
654 655 3.751175 CCAGAGTAAATGTTTCGCCAGAA 59.249 43.478 0.00 0.00 33.98 3.02
655 656 4.378459 CCAGAGTAAATGTTTCGCCAGAAC 60.378 45.833 0.00 0.00 35.86 3.01
656 657 3.751698 AGAGTAAATGTTTCGCCAGAACC 59.248 43.478 0.00 0.00 35.86 3.62
657 658 2.817844 AGTAAATGTTTCGCCAGAACCC 59.182 45.455 0.00 0.00 35.86 4.11
658 659 0.966179 AAATGTTTCGCCAGAACCCC 59.034 50.000 0.00 0.00 35.86 4.95
659 660 0.898326 AATGTTTCGCCAGAACCCCC 60.898 55.000 0.00 0.00 35.86 5.40
697 698 2.846371 CCTCTTGAAGGCTCAACGG 58.154 57.895 0.00 0.00 38.67 4.44
698 699 1.301677 CCTCTTGAAGGCTCAACGGC 61.302 60.000 0.00 0.00 38.67 5.68
705 706 2.586792 GGCTCAACGGCTGGAGAT 59.413 61.111 0.00 0.00 32.87 2.75
706 707 1.817099 GGCTCAACGGCTGGAGATG 60.817 63.158 0.00 0.00 32.87 2.90
707 708 2.467826 GCTCAACGGCTGGAGATGC 61.468 63.158 0.00 0.00 32.87 3.91
708 709 1.220206 CTCAACGGCTGGAGATGCT 59.780 57.895 0.00 0.00 32.87 3.79
709 710 0.809241 CTCAACGGCTGGAGATGCTC 60.809 60.000 0.00 0.00 32.87 4.26
710 711 1.220206 CAACGGCTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
722 723 3.244044 GGAGATGCTCTAAGGACCATCAC 60.244 52.174 0.00 0.00 37.14 3.06
778 978 1.619654 TTGGGTTGATCAGGCACAAG 58.380 50.000 11.48 0.00 0.00 3.16
779 979 0.478072 TGGGTTGATCAGGCACAAGT 59.522 50.000 0.00 0.00 0.00 3.16
828 1028 4.338012 CCTGGGGGTTCGTTAAGTAAAAT 58.662 43.478 0.00 0.00 0.00 1.82
831 1031 6.433716 CCTGGGGGTTCGTTAAGTAAAATTAA 59.566 38.462 0.00 0.00 0.00 1.40
882 1128 1.068434 CTAGACTCTAGCAAGCCAGCC 59.932 57.143 0.00 0.00 34.23 4.85
929 1179 9.148879 TGATTTCCCTATAAAACCTCAACAAAA 57.851 29.630 0.00 0.00 0.00 2.44
969 1220 4.556233 TCTTCAACTCCTATTGACACACG 58.444 43.478 0.00 0.00 38.31 4.49
976 1227 3.386486 TCCTATTGACACACGAACACAC 58.614 45.455 0.00 0.00 0.00 3.82
978 1229 3.745975 CCTATTGACACACGAACACACAT 59.254 43.478 0.00 0.00 0.00 3.21
992 1246 5.580691 CGAACACACATAGCAGGAAAAGATA 59.419 40.000 0.00 0.00 0.00 1.98
1011 1265 0.607489 AGAACACCATGAGCTGCACC 60.607 55.000 1.02 0.00 0.00 5.01
1012 1266 1.589716 GAACACCATGAGCTGCACCC 61.590 60.000 1.02 0.00 0.00 4.61
1023 1277 4.408821 TGCACCCGGATCAGTGGC 62.409 66.667 0.73 0.00 34.48 5.01
1054 1308 0.823356 TTTTGCCTTGCTCTTCGCCT 60.823 50.000 0.00 0.00 38.05 5.52
1089 1343 1.192146 TCTACCTTCCCGCTGCTTGT 61.192 55.000 0.00 0.00 0.00 3.16
1109 1363 1.599047 CTCGCCATGGTGAGTTCCT 59.401 57.895 36.95 0.00 44.90 3.36
1111 1365 1.207089 CTCGCCATGGTGAGTTCCTTA 59.793 52.381 36.95 12.21 44.90 2.69
1112 1366 1.066430 TCGCCATGGTGAGTTCCTTAC 60.066 52.381 24.20 0.00 0.00 2.34
1113 1367 1.066143 CGCCATGGTGAGTTCCTTACT 60.066 52.381 21.19 0.00 40.71 2.24
1114 1368 2.359900 GCCATGGTGAGTTCCTTACTG 58.640 52.381 14.67 0.00 37.17 2.74
1116 1370 3.600388 CCATGGTGAGTTCCTTACTGTC 58.400 50.000 2.57 0.00 37.17 3.51
1117 1371 3.261897 CCATGGTGAGTTCCTTACTGTCT 59.738 47.826 2.57 0.00 37.17 3.41
1118 1372 4.263068 CCATGGTGAGTTCCTTACTGTCTT 60.263 45.833 2.57 0.00 37.17 3.01
1119 1373 4.602340 TGGTGAGTTCCTTACTGTCTTC 57.398 45.455 0.00 0.00 37.17 2.87
1123 1377 5.011227 GGTGAGTTCCTTACTGTCTTCTCTT 59.989 44.000 0.00 0.00 37.17 2.85
1128 1382 3.833070 TCCTTACTGTCTTCTCTTCACCC 59.167 47.826 0.00 0.00 0.00 4.61
1136 1390 3.099905 TCTTCTCTTCACCCATCGACAT 58.900 45.455 0.00 0.00 0.00 3.06
1141 1395 5.631119 TCTCTTCACCCATCGACATATCTA 58.369 41.667 0.00 0.00 0.00 1.98
1179 1441 3.634910 TCCTCCTTTGTTACTTTGTTGGC 59.365 43.478 0.00 0.00 0.00 4.52
1184 1446 5.046950 TCCTTTGTTACTTTGTTGGCTTTGT 60.047 36.000 0.00 0.00 0.00 2.83
1185 1447 5.641636 CCTTTGTTACTTTGTTGGCTTTGTT 59.358 36.000 0.00 0.00 0.00 2.83
1186 1448 6.402011 CCTTTGTTACTTTGTTGGCTTTGTTG 60.402 38.462 0.00 0.00 0.00 3.33
1187 1449 5.392767 TGTTACTTTGTTGGCTTTGTTGA 57.607 34.783 0.00 0.00 0.00 3.18
1188 1450 5.406649 TGTTACTTTGTTGGCTTTGTTGAG 58.593 37.500 0.00 0.00 0.00 3.02
1189 1451 5.184096 TGTTACTTTGTTGGCTTTGTTGAGA 59.816 36.000 0.00 0.00 0.00 3.27
1190 1452 6.127479 TGTTACTTTGTTGGCTTTGTTGAGAT 60.127 34.615 0.00 0.00 0.00 2.75
1191 1453 4.685924 ACTTTGTTGGCTTTGTTGAGATG 58.314 39.130 0.00 0.00 0.00 2.90
1192 1454 3.731652 TTGTTGGCTTTGTTGAGATGG 57.268 42.857 0.00 0.00 0.00 3.51
1193 1455 2.665165 TGTTGGCTTTGTTGAGATGGT 58.335 42.857 0.00 0.00 0.00 3.55
1194 1456 3.826524 TGTTGGCTTTGTTGAGATGGTA 58.173 40.909 0.00 0.00 0.00 3.25
1208 1489 7.557358 TGTTGAGATGGTAAGATTTGCATACAT 59.443 33.333 0.00 0.00 0.00 2.29
1227 1508 1.444836 TCCCTTGTTAAATCGTGGCG 58.555 50.000 0.00 0.00 0.00 5.69
1229 1510 0.802494 CCTTGTTAAATCGTGGCGCT 59.198 50.000 7.64 0.00 0.00 5.92
1230 1511 2.004017 CCTTGTTAAATCGTGGCGCTA 58.996 47.619 7.64 0.00 0.00 4.26
1231 1512 2.222953 CCTTGTTAAATCGTGGCGCTAC 60.223 50.000 14.71 14.71 0.00 3.58
1232 1513 2.373540 TGTTAAATCGTGGCGCTACT 57.626 45.000 22.04 5.45 0.00 2.57
1233 1514 1.996898 TGTTAAATCGTGGCGCTACTG 59.003 47.619 22.04 14.85 0.00 2.74
1234 1515 1.997606 GTTAAATCGTGGCGCTACTGT 59.002 47.619 22.04 7.20 0.00 3.55
1235 1516 3.181397 GTTAAATCGTGGCGCTACTGTA 58.819 45.455 22.04 7.59 0.00 2.74
1236 1517 2.596904 AAATCGTGGCGCTACTGTAT 57.403 45.000 22.04 9.60 0.00 2.29
1237 1518 2.596904 AATCGTGGCGCTACTGTATT 57.403 45.000 22.04 14.69 0.00 1.89
1268 1549 3.402681 TGGTGCTGCTAGAGGCCC 61.403 66.667 0.00 1.45 40.92 5.80
1330 1614 1.377202 TGATGACGCAGGAAAGGCC 60.377 57.895 0.00 0.00 0.00 5.19
1619 1907 9.248291 CTACTACTGCTACTACTACAACTAGTC 57.752 40.741 0.00 0.00 34.79 2.59
1654 1942 2.623416 GGCTTGCAGGATACCCAAATAC 59.377 50.000 0.00 0.00 33.88 1.89
1655 1943 3.555966 GCTTGCAGGATACCCAAATACT 58.444 45.455 0.00 0.00 33.88 2.12
1656 1944 3.565902 GCTTGCAGGATACCCAAATACTC 59.434 47.826 0.00 0.00 33.88 2.59
1658 1946 2.441750 TGCAGGATACCCAAATACTCCC 59.558 50.000 0.00 0.00 33.88 4.30
1660 1948 3.138468 GCAGGATACCCAAATACTCCCTT 59.862 47.826 0.00 0.00 33.88 3.95
1661 1949 4.386424 GCAGGATACCCAAATACTCCCTTT 60.386 45.833 0.00 0.00 33.88 3.11
1664 1952 5.104067 AGGATACCCAAATACTCCCTTTGTC 60.104 44.000 0.00 0.00 32.83 3.18
1667 1955 2.042433 CCCAAATACTCCCTTTGTCCCA 59.958 50.000 0.00 0.00 32.83 4.37
1668 1956 3.309848 CCCAAATACTCCCTTTGTCCCAT 60.310 47.826 0.00 0.00 32.83 4.00
1677 1965 7.947782 ACTCCCTTTGTCCCATAATATAAGA 57.052 36.000 0.00 0.00 0.00 2.10
1678 1966 8.344939 ACTCCCTTTGTCCCATAATATAAGAA 57.655 34.615 0.00 0.00 0.00 2.52
1679 1967 8.218488 ACTCCCTTTGTCCCATAATATAAGAAC 58.782 37.037 0.00 0.00 0.00 3.01
1680 1968 7.221450 TCCCTTTGTCCCATAATATAAGAACG 58.779 38.462 0.00 0.00 0.00 3.95
1682 1970 7.172703 CCCTTTGTCCCATAATATAAGAACGTC 59.827 40.741 0.00 0.00 0.00 4.34
1684 1972 9.104965 CTTTGTCCCATAATATAAGAACGTCAA 57.895 33.333 0.00 0.00 0.00 3.18
1686 1974 7.788026 TGTCCCATAATATAAGAACGTCAAGT 58.212 34.615 0.00 0.00 0.00 3.16
1689 1977 7.713507 TCCCATAATATAAGAACGTCAAGTTGG 59.286 37.037 2.34 0.00 44.35 3.77
1690 1978 7.497909 CCCATAATATAAGAACGTCAAGTTGGT 59.502 37.037 2.34 0.00 44.35 3.67
1691 1979 9.537192 CCATAATATAAGAACGTCAAGTTGGTA 57.463 33.333 2.34 0.00 44.35 3.25
1699 2002 3.973657 ACGTCAAGTTGGTACTACAGTG 58.026 45.455 2.34 0.00 33.17 3.66
1778 2082 2.185004 TTTCTGCAAGGACTACTGGC 57.815 50.000 0.00 0.00 46.97 4.85
1909 2216 4.747108 AGAATATCAGCGTTCTATGTGTGC 59.253 41.667 0.00 0.00 33.15 4.57
1937 2251 8.491331 AACTTATTTTGTTGCTTGTTCACATT 57.509 26.923 0.00 0.00 0.00 2.71
1950 2264 0.037447 TCACATTCGGGTCATGGCAA 59.963 50.000 0.00 0.00 0.00 4.52
2058 2519 1.471119 CAATCAGGAATGCTGGCAGT 58.529 50.000 17.16 0.00 0.00 4.40
2096 2560 7.430760 AAGCTATACCTCTTCATTTCTCACT 57.569 36.000 0.00 0.00 0.00 3.41
2124 2588 3.503363 TCTCTGCAAATTACAAGCCACTG 59.497 43.478 0.00 0.00 0.00 3.66
2186 2650 8.496707 AAATAAAAATAAAAGAGCAGGGCATG 57.503 30.769 0.00 0.00 0.00 4.06
2306 2773 4.981806 GAGCTAGACTCATCAGACAGTT 57.018 45.455 0.00 0.00 45.49 3.16
2421 2890 2.331132 GGCTGCTGTTCCACTCTGC 61.331 63.158 0.00 0.00 0.00 4.26
2437 2906 0.179062 CTGCCTGTAGCCTGTGGATC 60.179 60.000 0.00 0.00 42.71 3.36
2457 2926 8.677300 GTGGATCAACACATATGAGTTTATGTT 58.323 33.333 14.87 8.27 40.07 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.077184 TAGGGGCACGACCAAGCG 62.077 66.667 0.00 0.00 42.05 4.68
18 19 2.436115 GTAGGGGCACGACCAAGC 60.436 66.667 0.00 0.00 42.05 4.01
19 20 2.125673 CGTAGGGGCACGACCAAG 60.126 66.667 0.00 0.00 44.69 3.61
20 21 2.601067 TCGTAGGGGCACGACCAA 60.601 61.111 0.00 0.00 45.45 3.67
21 22 3.066190 CTCGTAGGGGCACGACCA 61.066 66.667 0.00 0.00 45.45 4.02
22 23 4.509737 GCTCGTAGGGGCACGACC 62.510 72.222 1.51 0.00 45.45 4.79
23 24 3.755628 TGCTCGTAGGGGCACGAC 61.756 66.667 5.72 0.00 45.45 4.34
27 28 2.662596 CAAGTGCTCGTAGGGGCA 59.337 61.111 5.72 5.72 34.89 5.36
28 29 2.820037 GCAAGTGCTCGTAGGGGC 60.820 66.667 0.00 0.00 38.21 5.80
29 30 2.509336 CGCAAGTGCTCGTAGGGG 60.509 66.667 1.21 0.00 39.32 4.79
30 31 1.517257 CTCGCAAGTGCTCGTAGGG 60.517 63.158 1.21 0.00 39.32 3.53
31 32 4.079090 CTCGCAAGTGCTCGTAGG 57.921 61.111 1.21 0.00 39.32 3.18
48 49 4.719106 ACAGGAGGCAGCAGCAGC 62.719 66.667 2.65 0.00 44.61 5.25
49 50 2.746671 CACAGGAGGCAGCAGCAG 60.747 66.667 2.65 0.00 44.61 4.24
121 122 2.960170 CAGGAGGCAGCAAAGTGC 59.040 61.111 0.00 0.00 45.46 4.40
122 123 2.960170 GCAGGAGGCAGCAAAGTG 59.040 61.111 0.00 0.00 43.97 3.16
123 124 2.670934 CGCAGGAGGCAGCAAAGT 60.671 61.111 0.00 0.00 45.17 2.66
124 125 4.112341 GCGCAGGAGGCAGCAAAG 62.112 66.667 0.30 0.00 45.17 2.77
205 206 4.117661 GCAGGAAGCAGCAGCAGC 62.118 66.667 3.17 0.46 45.49 5.25
206 207 3.800863 CGCAGGAAGCAGCAGCAG 61.801 66.667 3.17 0.00 46.13 4.24
255 256 4.440987 CAGCGACGCAAGCAGCAG 62.441 66.667 23.70 0.00 46.13 4.24
258 259 4.440987 CAGCAGCGACGCAAGCAG 62.441 66.667 29.98 22.13 45.62 4.24
283 284 4.154347 GAGGTGAGGCAGGGCGAG 62.154 72.222 0.00 0.00 0.00 5.03
284 285 4.704103 AGAGGTGAGGCAGGGCGA 62.704 66.667 0.00 0.00 0.00 5.54
285 286 4.463879 CAGAGGTGAGGCAGGGCG 62.464 72.222 0.00 0.00 0.00 6.13
286 287 4.106925 CCAGAGGTGAGGCAGGGC 62.107 72.222 0.00 0.00 0.00 5.19
609 610 5.374071 GGGGTGAAATATTATCCACTCGTT 58.626 41.667 12.37 0.00 31.10 3.85
610 611 4.202430 GGGGGTGAAATATTATCCACTCGT 60.202 45.833 12.37 0.00 31.10 4.18
611 612 4.202419 TGGGGGTGAAATATTATCCACTCG 60.202 45.833 12.37 0.00 31.10 4.18
612 613 5.073144 TCTGGGGGTGAAATATTATCCACTC 59.927 44.000 12.37 9.72 0.00 3.51
613 614 4.981647 TCTGGGGGTGAAATATTATCCACT 59.018 41.667 12.37 0.00 0.00 4.00
614 615 5.163088 ACTCTGGGGGTGAAATATTATCCAC 60.163 44.000 6.89 6.89 0.00 4.02
615 616 4.981647 ACTCTGGGGGTGAAATATTATCCA 59.018 41.667 0.00 0.00 0.00 3.41
616 617 5.584551 ACTCTGGGGGTGAAATATTATCC 57.415 43.478 0.00 0.00 0.00 2.59
617 618 9.014297 CATTTACTCTGGGGGTGAAATATTATC 57.986 37.037 0.00 0.00 0.00 1.75
618 619 8.511126 ACATTTACTCTGGGGGTGAAATATTAT 58.489 33.333 0.00 0.00 0.00 1.28
619 620 7.878495 ACATTTACTCTGGGGGTGAAATATTA 58.122 34.615 0.00 0.00 0.00 0.98
620 621 6.741724 ACATTTACTCTGGGGGTGAAATATT 58.258 36.000 0.00 0.00 0.00 1.28
621 622 6.341408 ACATTTACTCTGGGGGTGAAATAT 57.659 37.500 0.00 0.00 0.00 1.28
622 623 5.789574 ACATTTACTCTGGGGGTGAAATA 57.210 39.130 0.00 0.00 0.00 1.40
623 624 4.675063 ACATTTACTCTGGGGGTGAAAT 57.325 40.909 0.00 0.00 0.00 2.17
624 625 4.463050 AACATTTACTCTGGGGGTGAAA 57.537 40.909 0.00 0.00 0.00 2.69
625 626 4.403734 GAAACATTTACTCTGGGGGTGAA 58.596 43.478 0.00 0.00 0.00 3.18
626 627 3.558321 CGAAACATTTACTCTGGGGGTGA 60.558 47.826 0.00 0.00 0.00 4.02
627 628 2.747446 CGAAACATTTACTCTGGGGGTG 59.253 50.000 0.00 0.00 0.00 4.61
628 629 2.878526 GCGAAACATTTACTCTGGGGGT 60.879 50.000 0.00 0.00 0.00 4.95
629 630 1.743394 GCGAAACATTTACTCTGGGGG 59.257 52.381 0.00 0.00 0.00 5.40
630 631 1.743394 GGCGAAACATTTACTCTGGGG 59.257 52.381 0.00 0.00 0.00 4.96
631 632 2.420022 CTGGCGAAACATTTACTCTGGG 59.580 50.000 0.00 0.00 0.00 4.45
632 633 3.334691 TCTGGCGAAACATTTACTCTGG 58.665 45.455 0.00 0.00 0.00 3.86
633 634 4.378459 GGTTCTGGCGAAACATTTACTCTG 60.378 45.833 4.51 0.00 36.83 3.35
634 635 3.751698 GGTTCTGGCGAAACATTTACTCT 59.248 43.478 4.51 0.00 36.83 3.24
635 636 3.119955 GGGTTCTGGCGAAACATTTACTC 60.120 47.826 8.84 0.00 38.63 2.59
636 637 2.817844 GGGTTCTGGCGAAACATTTACT 59.182 45.455 8.84 0.00 38.63 2.24
637 638 2.094906 GGGGTTCTGGCGAAACATTTAC 60.095 50.000 8.84 0.00 38.63 2.01
638 639 2.164338 GGGGTTCTGGCGAAACATTTA 58.836 47.619 8.84 0.00 38.63 1.40
639 640 0.966179 GGGGTTCTGGCGAAACATTT 59.034 50.000 8.84 0.00 38.63 2.32
640 641 0.898326 GGGGGTTCTGGCGAAACATT 60.898 55.000 8.84 0.00 38.63 2.71
641 642 1.304134 GGGGGTTCTGGCGAAACAT 60.304 57.895 8.84 0.00 38.63 2.71
642 643 2.114411 GGGGGTTCTGGCGAAACA 59.886 61.111 8.84 0.00 38.63 2.83
680 681 0.321122 AGCCGTTGAGCCTTCAAGAG 60.321 55.000 0.00 0.00 43.66 2.85
681 682 0.603707 CAGCCGTTGAGCCTTCAAGA 60.604 55.000 0.00 0.00 43.66 3.02
682 683 1.580845 CCAGCCGTTGAGCCTTCAAG 61.581 60.000 0.00 0.00 43.66 3.02
683 684 1.600636 CCAGCCGTTGAGCCTTCAA 60.601 57.895 0.00 0.00 40.92 2.69
684 685 2.032528 CCAGCCGTTGAGCCTTCA 59.967 61.111 0.00 0.00 0.00 3.02
685 686 1.743252 CTCCAGCCGTTGAGCCTTC 60.743 63.158 0.00 0.00 0.00 3.46
686 687 1.557269 ATCTCCAGCCGTTGAGCCTT 61.557 55.000 0.00 0.00 0.00 4.35
687 688 1.992277 ATCTCCAGCCGTTGAGCCT 60.992 57.895 0.00 0.00 0.00 4.58
688 689 1.817099 CATCTCCAGCCGTTGAGCC 60.817 63.158 0.00 0.00 0.00 4.70
689 690 2.467826 GCATCTCCAGCCGTTGAGC 61.468 63.158 0.00 0.00 0.00 4.26
690 691 0.809241 GAGCATCTCCAGCCGTTGAG 60.809 60.000 0.00 0.00 0.00 3.02
691 692 1.219124 GAGCATCTCCAGCCGTTGA 59.781 57.895 0.00 0.00 0.00 3.18
692 693 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
705 706 6.103415 TCAGTATGTGATGGTCCTTAGAGCA 61.103 44.000 0.00 0.00 45.99 4.26
706 707 4.342378 TCAGTATGTGATGGTCCTTAGAGC 59.658 45.833 0.00 0.00 38.05 4.09
707 708 5.596361 ACTCAGTATGTGATGGTCCTTAGAG 59.404 44.000 0.00 0.00 37.40 2.43
708 709 5.360999 CACTCAGTATGTGATGGTCCTTAGA 59.639 44.000 0.00 0.00 37.60 2.10
709 710 5.360999 TCACTCAGTATGTGATGGTCCTTAG 59.639 44.000 0.00 0.00 39.23 2.18
710 711 5.269189 TCACTCAGTATGTGATGGTCCTTA 58.731 41.667 0.00 0.00 39.23 2.69
778 978 4.938226 ACTTGTTTAATGCTCTGCTCCTAC 59.062 41.667 0.00 0.00 0.00 3.18
779 979 5.165961 ACTTGTTTAATGCTCTGCTCCTA 57.834 39.130 0.00 0.00 0.00 2.94
828 1028 4.569943 CAGTCAAAGCTAGCTGAGGTTAA 58.430 43.478 20.16 0.00 45.23 2.01
831 1031 1.338579 GCAGTCAAAGCTAGCTGAGGT 60.339 52.381 20.16 0.00 37.55 3.85
868 1105 2.270205 GCTGGCTGGCTTGCTAGA 59.730 61.111 17.08 0.00 42.97 2.43
882 1128 1.000274 GTGGCCAGTGTTTTTAGGCTG 60.000 52.381 5.11 0.00 46.23 4.85
929 1179 1.132495 AGAGAAGGTACAGGGTTGGGT 60.132 52.381 0.00 0.00 0.00 4.51
969 1220 5.886960 ATCTTTTCCTGCTATGTGTGTTC 57.113 39.130 0.00 0.00 0.00 3.18
976 1227 6.115446 TGGTGTTCTATCTTTTCCTGCTATG 58.885 40.000 0.00 0.00 0.00 2.23
978 1229 5.755409 TGGTGTTCTATCTTTTCCTGCTA 57.245 39.130 0.00 0.00 0.00 3.49
992 1246 0.607489 GGTGCAGCTCATGGTGTTCT 60.607 55.000 9.07 0.00 43.05 3.01
1011 1265 4.457496 ACTGCGCCACTGATCCGG 62.457 66.667 4.18 0.00 0.00 5.14
1012 1266 2.887568 GACTGCGCCACTGATCCG 60.888 66.667 4.18 0.00 0.00 4.18
1023 1277 1.082104 GGCAAAAACGAGGACTGCG 60.082 57.895 0.00 0.00 33.76 5.18
1089 1343 1.375908 GAACTCACCATGGCGAGCA 60.376 57.895 26.36 0.00 32.21 4.26
1109 1363 4.082190 CGATGGGTGAAGAGAAGACAGTAA 60.082 45.833 0.00 0.00 0.00 2.24
1111 1365 2.232452 CGATGGGTGAAGAGAAGACAGT 59.768 50.000 0.00 0.00 0.00 3.55
1112 1366 2.493675 TCGATGGGTGAAGAGAAGACAG 59.506 50.000 0.00 0.00 0.00 3.51
1113 1367 2.231478 GTCGATGGGTGAAGAGAAGACA 59.769 50.000 0.00 0.00 0.00 3.41
1114 1368 2.231478 TGTCGATGGGTGAAGAGAAGAC 59.769 50.000 0.00 0.00 0.00 3.01
1116 1370 3.533606 ATGTCGATGGGTGAAGAGAAG 57.466 47.619 0.00 0.00 0.00 2.85
1117 1371 4.895889 AGATATGTCGATGGGTGAAGAGAA 59.104 41.667 0.00 0.00 0.00 2.87
1118 1372 4.474394 AGATATGTCGATGGGTGAAGAGA 58.526 43.478 0.00 0.00 0.00 3.10
1119 1373 4.862902 AGATATGTCGATGGGTGAAGAG 57.137 45.455 0.00 0.00 0.00 2.85
1123 1377 7.119387 ACAGATATAGATATGTCGATGGGTGA 58.881 38.462 0.00 0.00 31.81 4.02
1157 1419 3.634910 GCCAACAAAGTAACAAAGGAGGA 59.365 43.478 0.00 0.00 0.00 3.71
1160 1422 5.046950 ACAAAGCCAACAAAGTAACAAAGGA 60.047 36.000 0.00 0.00 0.00 3.36
1161 1423 5.175127 ACAAAGCCAACAAAGTAACAAAGG 58.825 37.500 0.00 0.00 0.00 3.11
1162 1424 6.367422 TCAACAAAGCCAACAAAGTAACAAAG 59.633 34.615 0.00 0.00 0.00 2.77
1163 1425 6.223852 TCAACAAAGCCAACAAAGTAACAAA 58.776 32.000 0.00 0.00 0.00 2.83
1164 1426 5.784177 TCAACAAAGCCAACAAAGTAACAA 58.216 33.333 0.00 0.00 0.00 2.83
1168 1430 5.221224 CCATCTCAACAAAGCCAACAAAGTA 60.221 40.000 0.00 0.00 0.00 2.24
1169 1431 4.441913 CCATCTCAACAAAGCCAACAAAGT 60.442 41.667 0.00 0.00 0.00 2.66
1170 1432 4.053295 CCATCTCAACAAAGCCAACAAAG 58.947 43.478 0.00 0.00 0.00 2.77
1179 1441 6.680810 TGCAAATCTTACCATCTCAACAAAG 58.319 36.000 0.00 0.00 0.00 2.77
1184 1446 7.229306 GGATGTATGCAAATCTTACCATCTCAA 59.771 37.037 0.00 0.00 0.00 3.02
1185 1447 6.712095 GGATGTATGCAAATCTTACCATCTCA 59.288 38.462 0.00 0.00 0.00 3.27
1186 1448 6.150140 GGGATGTATGCAAATCTTACCATCTC 59.850 42.308 0.00 0.00 0.00 2.75
1187 1449 6.006449 GGGATGTATGCAAATCTTACCATCT 58.994 40.000 0.00 0.00 0.00 2.90
1188 1450 6.006449 AGGGATGTATGCAAATCTTACCATC 58.994 40.000 0.00 0.00 0.00 3.51
1189 1451 5.957132 AGGGATGTATGCAAATCTTACCAT 58.043 37.500 0.00 0.00 0.00 3.55
1190 1452 5.387113 AGGGATGTATGCAAATCTTACCA 57.613 39.130 0.00 0.00 0.00 3.25
1191 1453 5.594317 ACAAGGGATGTATGCAAATCTTACC 59.406 40.000 0.00 0.00 41.63 2.85
1192 1454 6.699575 ACAAGGGATGTATGCAAATCTTAC 57.300 37.500 0.00 0.00 41.63 2.34
1193 1455 8.815565 TTAACAAGGGATGTATGCAAATCTTA 57.184 30.769 0.00 0.00 42.99 2.10
1194 1456 7.716799 TTAACAAGGGATGTATGCAAATCTT 57.283 32.000 0.00 0.00 42.99 2.40
1208 1489 1.444836 CGCCACGATTTAACAAGGGA 58.555 50.000 0.00 0.00 0.00 4.20
1227 1508 7.081349 CACTGCAGAGATAGTAATACAGTAGC 58.919 42.308 23.35 0.00 35.49 3.58
1229 1510 7.013369 CACCACTGCAGAGATAGTAATACAGTA 59.987 40.741 23.35 0.00 35.49 2.74
1230 1511 5.894393 ACCACTGCAGAGATAGTAATACAGT 59.106 40.000 23.35 0.00 37.60 3.55
1231 1512 6.212235 CACCACTGCAGAGATAGTAATACAG 58.788 44.000 23.35 0.00 0.00 2.74
1232 1513 5.451937 GCACCACTGCAGAGATAGTAATACA 60.452 44.000 23.35 0.00 43.62 2.29
1233 1514 4.985409 GCACCACTGCAGAGATAGTAATAC 59.015 45.833 23.35 0.00 43.62 1.89
1234 1515 4.895889 AGCACCACTGCAGAGATAGTAATA 59.104 41.667 23.35 0.00 46.97 0.98
1235 1516 3.708631 AGCACCACTGCAGAGATAGTAAT 59.291 43.478 23.35 0.00 46.97 1.89
1236 1517 3.099905 AGCACCACTGCAGAGATAGTAA 58.900 45.455 23.35 0.00 46.97 2.24
1237 1518 2.428530 CAGCACCACTGCAGAGATAGTA 59.571 50.000 23.35 0.00 46.97 1.82
1256 1537 0.108207 CCATCTTGGGCCTCTAGCAG 59.892 60.000 4.53 0.00 46.50 4.24
1268 1549 1.019673 CCGATGTTCAGGCCATCTTG 58.980 55.000 5.01 0.00 37.22 3.02
1477 1761 2.254350 CGAGGCTCGTCGTTGTGA 59.746 61.111 27.92 0.00 34.72 3.58
1502 1786 0.896226 GTCTGACGGACTTAGGGCTT 59.104 55.000 7.20 0.00 41.46 4.35
1591 1879 9.467258 CTAGTTGTAGTAGTAGCAGTAGTAGAG 57.533 40.741 0.00 0.00 0.00 2.43
1593 1881 9.248291 GACTAGTTGTAGTAGTAGCAGTAGTAG 57.752 40.741 0.00 0.00 39.78 2.57
1619 1907 2.846039 CAAGCCTGCAAATCTAGCTG 57.154 50.000 0.00 0.00 33.18 4.24
1664 1952 7.497909 ACCAACTTGACGTTCTTATATTATGGG 59.502 37.037 0.00 0.00 32.27 4.00
1674 1962 5.163478 ACTGTAGTACCAACTTGACGTTCTT 60.163 40.000 0.00 0.00 37.15 2.52
1676 1964 4.443394 CACTGTAGTACCAACTTGACGTTC 59.557 45.833 0.00 0.00 37.15 3.95
1677 1965 4.142093 ACACTGTAGTACCAACTTGACGTT 60.142 41.667 0.00 0.00 37.15 3.99
1678 1966 3.382546 ACACTGTAGTACCAACTTGACGT 59.617 43.478 0.00 0.00 37.15 4.34
1679 1967 3.973657 ACACTGTAGTACCAACTTGACG 58.026 45.455 0.00 0.00 37.15 4.35
1680 1968 6.684686 TGATACACTGTAGTACCAACTTGAC 58.315 40.000 0.00 0.00 37.15 3.18
1682 1970 9.302345 CTAATGATACACTGTAGTACCAACTTG 57.698 37.037 0.00 0.00 37.15 3.16
1684 1972 7.342284 AGCTAATGATACACTGTAGTACCAACT 59.658 37.037 0.00 0.00 39.91 3.16
1686 1974 7.417456 CCAGCTAATGATACACTGTAGTACCAA 60.417 40.741 0.00 0.00 0.00 3.67
1689 1977 7.040473 ACCAGCTAATGATACACTGTAGTAC 57.960 40.000 0.00 0.00 0.00 2.73
1690 1978 6.831868 TGACCAGCTAATGATACACTGTAGTA 59.168 38.462 0.00 0.00 0.00 1.82
1691 1979 5.656859 TGACCAGCTAATGATACACTGTAGT 59.343 40.000 0.00 0.00 0.00 2.73
1692 1980 6.149129 TGACCAGCTAATGATACACTGTAG 57.851 41.667 0.00 0.00 0.00 2.74
1778 2082 0.941542 TTTTTCCGCACGAACTCCTG 59.058 50.000 0.00 0.00 0.00 3.86
1937 2251 0.109532 TTCAGTTTGCCATGACCCGA 59.890 50.000 0.00 0.00 0.00 5.14
1950 2264 2.431057 ACTCACCAGAACGAGTTCAGTT 59.569 45.455 17.00 0.00 39.45 3.16
2015 2343 5.918576 GCTTATACATACATGTAGTGCGACA 59.081 40.000 11.91 0.00 45.46 4.35
2058 2519 9.422681 AGAGGTATAGCTTTCTTTCATGTACTA 57.577 33.333 5.80 0.00 0.00 1.82
2096 2560 5.335897 GGCTTGTAATTTGCAGAGATTGTGA 60.336 40.000 0.00 0.00 0.00 3.58
2124 2588 1.776034 GATGGCTTGTCGGATTCGCC 61.776 60.000 7.25 7.25 41.06 5.54
2244 2711 4.542075 GCTAGTGTTAGCCAGCCC 57.458 61.111 0.00 0.00 45.34 5.19
2421 2890 1.278985 TGTTGATCCACAGGCTACAGG 59.721 52.381 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.