Multiple sequence alignment - TraesCS5B01G321100

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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 TraesCS5B01G321100 chr5B 100.000 2192 0 0 1 2192 506657437 506655246 0.000000e+00 4048.0
1 TraesCS5B01G321100 chr5B 90.141 639 43 11 1 623 590701739 590702373 0.000000e+00 813.0
2 TraesCS5B01G321100 chr5B 89.952 627 38 4 1 623 541660266 541659661 0.000000e+00 785.0
3 TraesCS5B01G321100 chr5B 90.582 584 22 20 628 1208 506714500 506713947 0.000000e+00 743.0
4 TraesCS5B01G321100 chr5B 90.582 584 22 20 628 1208 506747707 506747154 0.000000e+00 743.0
5 TraesCS5B01G321100 chr5B 80.507 513 53 22 710 1195 506531541 506531049 1.250000e-92 350.0
6 TraesCS5B01G321100 chr4D 91.680 625 33 6 1 622 324406406 324405798 0.000000e+00 848.0
7 TraesCS5B01G321100 chr4D 90.016 631 42 10 3 617 445042599 445041974 0.000000e+00 797.0
8 TraesCS5B01G321100 chr4D 82.000 100 14 3 1211 1307 450013515 450013417 5.020000e-12 82.4
9 TraesCS5B01G321100 chr4D 92.500 40 1 2 1222 1260 359359989 359359951 3.040000e-04 56.5
10 TraesCS5B01G321100 chr1D 91.250 640 28 8 1 617 69304699 69305333 0.000000e+00 846.0
11 TraesCS5B01G321100 chr1D 86.538 104 13 1 1209 1311 3654373 3654270 1.780000e-21 113.0
12 TraesCS5B01G321100 chr1D 87.000 100 13 0 1208 1307 20563759 20563660 1.780000e-21 113.0
13 TraesCS5B01G321100 chr1D 86.598 97 13 0 1211 1307 246043100 246043004 8.280000e-20 108.0
14 TraesCS5B01G321100 chr1D 85.567 97 14 0 1211 1307 447257723 447257627 3.850000e-18 102.0
15 TraesCS5B01G321100 chr1D 88.462 52 5 1 1210 1260 490940873 490940822 6.530000e-06 62.1
16 TraesCS5B01G321100 chr7D 91.069 627 36 9 5 615 203345068 203344446 0.000000e+00 830.0
17 TraesCS5B01G321100 chr7D 89.319 646 42 7 1 623 271299727 271299086 0.000000e+00 785.0
18 TraesCS5B01G321100 chr7D 84.536 97 15 0 1211 1307 614436476 614436572 1.790000e-16 97.1
19 TraesCS5B01G321100 chr7D 83.168 101 16 1 1208 1307 182833558 182833458 8.330000e-15 91.6
20 TraesCS5B01G321100 chr3B 91.667 600 28 9 39 617 704370950 704371548 0.000000e+00 811.0
21 TraesCS5B01G321100 chr1B 89.875 642 44 7 1 623 654712042 654712681 0.000000e+00 806.0
22 TraesCS5B01G321100 chr1B 88.924 641 50 6 1 623 242295215 242295852 0.000000e+00 771.0
23 TraesCS5B01G321100 chr1B 95.228 482 22 1 1622 2102 161379113 161379594 0.000000e+00 761.0
24 TraesCS5B01G321100 chr1B 87.480 631 36 15 1 623 410156384 410155789 0.000000e+00 688.0
25 TraesCS5B01G321100 chr1B 91.519 283 20 3 337 617 167710279 167710559 9.490000e-104 387.0
26 TraesCS5B01G321100 chr1B 91.007 278 22 2 342 617 167703225 167703501 2.660000e-99 372.0
27 TraesCS5B01G321100 chr1B 95.192 104 5 0 2089 2192 161385221 161385324 4.840000e-37 165.0
28 TraesCS5B01G321100 chr1B 86.726 113 10 5 1618 1725 637635962 637635850 1.060000e-23 121.0
29 TraesCS5B01G321100 chr2B 89.984 639 41 8 1 623 731580724 731580093 0.000000e+00 804.0
30 TraesCS5B01G321100 chr2B 86.598 97 12 1 1212 1307 166407182 166407086 2.980000e-19 106.0
31 TraesCS5B01G321100 chr7B 89.335 647 41 13 1 623 11830601 11831243 0.000000e+00 787.0
32 TraesCS5B01G321100 chr1A 91.364 579 41 4 1623 2192 6172054 6172632 0.000000e+00 784.0
33 TraesCS5B01G321100 chr4B 90.328 579 46 5 1624 2192 614068703 614069281 0.000000e+00 750.0
34 TraesCS5B01G321100 chr4B 83.838 99 16 0 1210 1308 17108611 17108709 6.440000e-16 95.3
35 TraesCS5B01G321100 chr3A 89.015 619 39 11 10 622 138200984 138200389 0.000000e+00 739.0
36 TraesCS5B01G321100 chr3A 84.536 97 15 0 1211 1307 699566755 699566851 1.790000e-16 97.1
37 TraesCS5B01G321100 chr7A 88.997 618 39 7 13 622 481323284 481323880 0.000000e+00 737.0
38 TraesCS5B01G321100 chr5A 93.578 327 20 1 643 968 533988218 533987892 9.100000e-134 486.0
39 TraesCS5B01G321100 chr5A 93.396 212 11 1 1000 1208 533987891 533987680 5.880000e-81 311.0
40 TraesCS5B01G321100 chr5A 85.357 280 21 7 1623 1889 395061436 395061708 2.770000e-69 272.0
41 TraesCS5B01G321100 chr5A 85.000 100 14 1 1209 1308 425004730 425004828 1.380000e-17 100.0
42 TraesCS5B01G321100 chr5D 91.667 348 21 6 628 968 420596075 420595729 1.970000e-130 475.0
43 TraesCS5B01G321100 chr5D 95.000 220 5 3 1363 1582 420595250 420595037 7.490000e-90 340.0
44 TraesCS5B01G321100 chr5D 93.088 217 8 3 1000 1210 420595728 420595513 5.880000e-81 311.0
45 TraesCS5B01G321100 chr5D 77.821 514 61 27 710 1195 420452894 420452406 3.590000e-68 268.0
46 TraesCS5B01G321100 chr5D 86.458 96 11 2 1211 1305 380846927 380847021 1.070000e-18 104.0
47 TraesCS5B01G321100 chr5D 88.158 76 9 0 1207 1282 549314940 549314865 8.330000e-15 91.6
48 TraesCS5B01G321100 chr4A 89.170 277 18 5 1623 1889 18072400 18072674 3.490000e-88 335.0
49 TraesCS5B01G321100 chr4A 94.030 134 5 3 1758 1889 18110640 18110772 1.330000e-47 200.0
50 TraesCS5B01G321100 chr2D 82.967 182 13 9 1619 1789 12292681 12292855 4.880000e-32 148.0
51 TraesCS5B01G321100 chr2D 81.633 98 18 0 1211 1308 46469955 46469858 5.020000e-12 82.4
52 TraesCS5B01G321100 chr3D 91.358 81 6 1 1619 1699 90774416 90774495 2.300000e-20 110.0
53 TraesCS5B01G321100 chr3D 86.885 61 6 2 1211 1270 86237863 86237922 1.400000e-07 67.6
54 TraesCS5B01G321100 chrUn 97.222 36 1 0 1762 1797 12470595 12470560 6.530000e-06 62.1


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 TraesCS5B01G321100 chr5B 506655246 506657437 2191 True 4048.000000 4048 100.000000 1 2192 1 chr5B.!!$R2 2191
1 TraesCS5B01G321100 chr5B 590701739 590702373 634 False 813.000000 813 90.141000 1 623 1 chr5B.!!$F1 622
2 TraesCS5B01G321100 chr5B 541659661 541660266 605 True 785.000000 785 89.952000 1 623 1 chr5B.!!$R5 622
3 TraesCS5B01G321100 chr5B 506713947 506714500 553 True 743.000000 743 90.582000 628 1208 1 chr5B.!!$R3 580
4 TraesCS5B01G321100 chr5B 506747154 506747707 553 True 743.000000 743 90.582000 628 1208 1 chr5B.!!$R4 580
5 TraesCS5B01G321100 chr4D 324405798 324406406 608 True 848.000000 848 91.680000 1 622 1 chr4D.!!$R1 621
6 TraesCS5B01G321100 chr4D 445041974 445042599 625 True 797.000000 797 90.016000 3 617 1 chr4D.!!$R3 614
7 TraesCS5B01G321100 chr1D 69304699 69305333 634 False 846.000000 846 91.250000 1 617 1 chr1D.!!$F1 616
8 TraesCS5B01G321100 chr7D 203344446 203345068 622 True 830.000000 830 91.069000 5 615 1 chr7D.!!$R2 610
9 TraesCS5B01G321100 chr7D 271299086 271299727 641 True 785.000000 785 89.319000 1 623 1 chr7D.!!$R3 622
10 TraesCS5B01G321100 chr3B 704370950 704371548 598 False 811.000000 811 91.667000 39 617 1 chr3B.!!$F1 578
11 TraesCS5B01G321100 chr1B 654712042 654712681 639 False 806.000000 806 89.875000 1 623 1 chr1B.!!$F6 622
12 TraesCS5B01G321100 chr1B 242295215 242295852 637 False 771.000000 771 88.924000 1 623 1 chr1B.!!$F5 622
13 TraesCS5B01G321100 chr1B 410155789 410156384 595 True 688.000000 688 87.480000 1 623 1 chr1B.!!$R1 622
14 TraesCS5B01G321100 chr2B 731580093 731580724 631 True 804.000000 804 89.984000 1 623 1 chr2B.!!$R2 622
15 TraesCS5B01G321100 chr7B 11830601 11831243 642 False 787.000000 787 89.335000 1 623 1 chr7B.!!$F1 622
16 TraesCS5B01G321100 chr1A 6172054 6172632 578 False 784.000000 784 91.364000 1623 2192 1 chr1A.!!$F1 569
17 TraesCS5B01G321100 chr4B 614068703 614069281 578 False 750.000000 750 90.328000 1624 2192 1 chr4B.!!$F2 568
18 TraesCS5B01G321100 chr3A 138200389 138200984 595 True 739.000000 739 89.015000 10 622 1 chr3A.!!$R1 612
19 TraesCS5B01G321100 chr7A 481323284 481323880 596 False 737.000000 737 88.997000 13 622 1 chr7A.!!$F1 609
20 TraesCS5B01G321100 chr5A 533987680 533988218 538 True 398.500000 486 93.487000 643 1208 2 chr5A.!!$R1 565
21 TraesCS5B01G321100 chr5D 420595037 420596075 1038 True 375.333333 475 93.251667 628 1582 3 chr5D.!!$R3 954

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
968 1090 0.100861 GGTTAGAGAGGCTCGGTTCG 59.899 60.0 9.22 0.0 35.36 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2424 0.399454 ATGATCTCCCCCGCAATGAG 59.601 55.0 0.0 0.0 0.0 2.9 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
33 42 9.010029 TCTTCTTCTTCTAGTCTTCTTCTTCTC 57.990 37.037 0.00 0.00 0.00 2.87
324 351 4.499865 GGATACATCATACGTCTGCTGTGT 60.500 45.833 17.53 12.39 29.11 3.72
420 490 2.836981 AGCCTCTTTGTCATCTGCTAGT 59.163 45.455 0.00 0.00 0.00 2.57
629 742 3.005341 GCTCTTTGCTGTCCTTTGAAC 57.995 47.619 0.00 0.00 38.95 3.18
630 743 2.287849 GCTCTTTGCTGTCCTTTGAACC 60.288 50.000 0.00 0.00 38.95 3.62
631 744 1.946768 TCTTTGCTGTCCTTTGAACCG 59.053 47.619 0.00 0.00 0.00 4.44
859 976 2.391724 ATTCACCGTGGTCGCCAAGT 62.392 55.000 9.92 4.67 34.18 3.16
902 1021 3.123620 GGCAGCAGCAACTCCTCG 61.124 66.667 2.65 0.00 44.61 4.63
924 1043 1.082690 GGCACAAGAGAACAGCTAGC 58.917 55.000 6.62 6.62 0.00 3.42
968 1090 0.100861 GGTTAGAGAGGCTCGGTTCG 59.899 60.000 9.22 0.00 35.36 3.95
969 1091 0.100861 GTTAGAGAGGCTCGGTTCGG 59.899 60.000 9.22 0.00 35.36 4.30
970 1092 0.323178 TTAGAGAGGCTCGGTTCGGT 60.323 55.000 9.22 0.00 35.36 4.69
971 1093 0.323178 TAGAGAGGCTCGGTTCGGTT 60.323 55.000 9.22 0.00 35.36 4.44
972 1094 1.153804 GAGAGGCTCGGTTCGGTTC 60.154 63.158 9.22 0.00 0.00 3.62
973 1095 2.125633 GAGGCTCGGTTCGGTTCC 60.126 66.667 0.00 0.00 0.00 3.62
974 1096 2.920912 AGGCTCGGTTCGGTTCCA 60.921 61.111 0.00 0.00 0.00 3.53
975 1097 2.240162 GAGGCTCGGTTCGGTTCCAT 62.240 60.000 0.00 0.00 0.00 3.41
976 1098 1.376812 GGCTCGGTTCGGTTCCATT 60.377 57.895 0.00 0.00 0.00 3.16
977 1099 0.108041 GGCTCGGTTCGGTTCCATTA 60.108 55.000 0.00 0.00 0.00 1.90
978 1100 1.287425 GCTCGGTTCGGTTCCATTAG 58.713 55.000 0.00 0.00 0.00 1.73
979 1101 1.405121 GCTCGGTTCGGTTCCATTAGT 60.405 52.381 0.00 0.00 0.00 2.24
980 1102 2.159198 GCTCGGTTCGGTTCCATTAGTA 60.159 50.000 0.00 0.00 0.00 1.82
981 1103 3.703420 CTCGGTTCGGTTCCATTAGTAG 58.297 50.000 0.00 0.00 0.00 2.57
982 1104 2.159198 TCGGTTCGGTTCCATTAGTAGC 60.159 50.000 0.00 0.00 0.00 3.58
983 1105 2.159142 CGGTTCGGTTCCATTAGTAGCT 60.159 50.000 0.00 0.00 0.00 3.32
984 1106 3.067180 CGGTTCGGTTCCATTAGTAGCTA 59.933 47.826 0.00 0.00 0.00 3.32
985 1107 4.618965 GGTTCGGTTCCATTAGTAGCTAG 58.381 47.826 0.00 0.00 0.00 3.42
986 1108 4.049869 GTTCGGTTCCATTAGTAGCTAGC 58.950 47.826 6.62 6.62 0.00 3.42
987 1109 2.626743 TCGGTTCCATTAGTAGCTAGCC 59.373 50.000 12.13 0.00 0.00 3.93
988 1110 2.288886 CGGTTCCATTAGTAGCTAGCCC 60.289 54.545 12.13 2.00 0.00 5.19
989 1111 2.288886 GGTTCCATTAGTAGCTAGCCCG 60.289 54.545 12.13 0.00 0.00 6.13
990 1112 0.966920 TCCATTAGTAGCTAGCCCGC 59.033 55.000 12.13 1.57 0.00 6.13
991 1113 0.969894 CCATTAGTAGCTAGCCCGCT 59.030 55.000 12.13 9.69 43.83 5.52
992 1114 1.337260 CCATTAGTAGCTAGCCCGCTG 60.337 57.143 12.13 1.97 41.12 5.18
993 1115 0.318762 ATTAGTAGCTAGCCCGCTGC 59.681 55.000 12.13 6.25 41.12 5.25
994 1116 1.745320 TTAGTAGCTAGCCCGCTGCC 61.745 60.000 12.13 0.00 42.63 4.85
995 1117 4.951963 GTAGCTAGCCCGCTGCCG 62.952 72.222 12.13 0.00 42.71 5.69
1056 1178 2.258726 GGTGGTGGCGTCTTGGTTC 61.259 63.158 0.00 0.00 0.00 3.62
1073 1198 4.741781 CGCTTGCTTTCGCCCACG 62.742 66.667 0.00 0.00 42.01 4.94
1208 1336 3.635373 GGATGATTCATGCCATGTCTGTT 59.365 43.478 3.32 0.00 0.00 3.16
1211 1339 4.587891 TGATTCATGCCATGTCTGTTGTA 58.412 39.130 4.31 0.00 0.00 2.41
1213 1341 3.701205 TCATGCCATGTCTGTTGTACT 57.299 42.857 4.31 0.00 0.00 2.73
1214 1342 3.599343 TCATGCCATGTCTGTTGTACTC 58.401 45.455 4.31 0.00 0.00 2.59
1215 1343 2.472695 TGCCATGTCTGTTGTACTCC 57.527 50.000 0.00 0.00 0.00 3.85
1216 1344 1.003118 TGCCATGTCTGTTGTACTCCC 59.997 52.381 0.00 0.00 0.00 4.30
1217 1345 1.279271 GCCATGTCTGTTGTACTCCCT 59.721 52.381 0.00 0.00 0.00 4.20
1218 1346 2.678190 GCCATGTCTGTTGTACTCCCTC 60.678 54.545 0.00 0.00 0.00 4.30
1220 1348 3.368843 CCATGTCTGTTGTACTCCCTCTG 60.369 52.174 0.00 0.00 0.00 3.35
1221 1349 2.958818 TGTCTGTTGTACTCCCTCTGT 58.041 47.619 0.00 0.00 0.00 3.41
1222 1350 3.305720 TGTCTGTTGTACTCCCTCTGTT 58.694 45.455 0.00 0.00 0.00 3.16
1223 1351 3.709653 TGTCTGTTGTACTCCCTCTGTTT 59.290 43.478 0.00 0.00 0.00 2.83
1225 1353 5.364446 TGTCTGTTGTACTCCCTCTGTTTTA 59.636 40.000 0.00 0.00 0.00 1.52
1228 1546 8.092687 GTCTGTTGTACTCCCTCTGTTTTAATA 58.907 37.037 0.00 0.00 0.00 0.98
1312 1630 8.680903 CATTTTAGAATGGATGGAGTATATGGC 58.319 37.037 0.00 0.00 39.17 4.40
1313 1631 6.950860 TTAGAATGGATGGAGTATATGGCA 57.049 37.500 0.00 0.00 0.00 4.92
1314 1632 7.515004 TTAGAATGGATGGAGTATATGGCAT 57.485 36.000 4.88 4.88 0.00 4.40
1315 1633 5.999044 AGAATGGATGGAGTATATGGCATC 58.001 41.667 1.65 0.00 0.00 3.91
1316 1634 5.489997 AGAATGGATGGAGTATATGGCATCA 59.510 40.000 1.65 0.00 0.00 3.07
1317 1635 5.988865 ATGGATGGAGTATATGGCATCAT 57.011 39.130 1.65 0.00 37.40 2.45
1318 1636 5.784398 TGGATGGAGTATATGGCATCATT 57.216 39.130 1.65 0.00 34.96 2.57
1319 1637 5.503002 TGGATGGAGTATATGGCATCATTG 58.497 41.667 1.65 0.00 34.96 2.82
1329 1647 1.990674 GCATCATTGCGTTTTCGGC 59.009 52.632 0.00 0.00 44.29 5.54
1330 1648 0.732196 GCATCATTGCGTTTTCGGCA 60.732 50.000 0.00 0.00 44.29 5.69
1331 1649 1.912001 CATCATTGCGTTTTCGGCAT 58.088 45.000 0.00 0.00 44.29 4.40
1332 1650 1.584761 CATCATTGCGTTTTCGGCATG 59.415 47.619 0.00 0.00 44.29 4.06
1333 1651 0.595588 TCATTGCGTTTTCGGCATGT 59.404 45.000 0.00 0.00 44.29 3.21
1334 1652 0.709467 CATTGCGTTTTCGGCATGTG 59.291 50.000 0.00 0.00 44.29 3.21
1335 1653 0.313672 ATTGCGTTTTCGGCATGTGT 59.686 45.000 0.00 0.00 44.29 3.72
1336 1654 0.593518 TTGCGTTTTCGGCATGTGTG 60.594 50.000 0.00 0.00 44.29 3.82
1348 1666 0.654160 CATGTGTGCACTATGGCTCG 59.346 55.000 19.41 0.00 34.04 5.03
1349 1667 0.250234 ATGTGTGCACTATGGCTCGT 59.750 50.000 19.41 0.00 34.04 4.18
1350 1668 0.892063 TGTGTGCACTATGGCTCGTA 59.108 50.000 19.41 0.00 34.04 3.43
1351 1669 1.480545 TGTGTGCACTATGGCTCGTAT 59.519 47.619 19.41 0.00 34.04 3.06
1352 1670 2.691011 TGTGTGCACTATGGCTCGTATA 59.309 45.455 19.41 0.00 34.04 1.47
1353 1671 3.243401 TGTGTGCACTATGGCTCGTATAG 60.243 47.826 19.41 0.00 34.92 1.31
1354 1672 3.004419 GTGTGCACTATGGCTCGTATAGA 59.996 47.826 19.41 0.00 33.40 1.98
1355 1673 3.634910 TGTGCACTATGGCTCGTATAGAA 59.365 43.478 19.41 0.00 33.40 2.10
1356 1674 3.982058 GTGCACTATGGCTCGTATAGAAC 59.018 47.826 10.32 0.00 33.40 3.01
1357 1675 3.634910 TGCACTATGGCTCGTATAGAACA 59.365 43.478 0.00 0.00 33.40 3.18
1358 1676 4.280929 TGCACTATGGCTCGTATAGAACAT 59.719 41.667 0.00 0.00 33.40 2.71
1359 1677 5.475564 TGCACTATGGCTCGTATAGAACATA 59.524 40.000 0.00 0.00 33.40 2.29
1360 1678 6.015772 TGCACTATGGCTCGTATAGAACATAA 60.016 38.462 0.00 0.00 32.19 1.90
1361 1679 6.866770 GCACTATGGCTCGTATAGAACATAAA 59.133 38.462 0.00 0.00 32.19 1.40
1370 1688 9.810231 GCTCGTATAGAACATAAACTAGTACTC 57.190 37.037 0.00 0.00 0.00 2.59
1459 1777 2.177531 CCGTCGACGTGTACCTGG 59.822 66.667 33.49 14.06 37.74 4.45
1481 1799 0.250901 ACACAATGGCTCCACTCCAC 60.251 55.000 0.00 0.00 36.26 4.02
1584 1902 8.420374 AGAATCAAACATAACTATGTACCACG 57.580 34.615 2.85 0.00 45.55 4.94
1585 1903 7.494625 AGAATCAAACATAACTATGTACCACGG 59.505 37.037 2.85 0.00 45.55 4.94
1586 1904 6.283544 TCAAACATAACTATGTACCACGGA 57.716 37.500 2.85 0.00 45.55 4.69
1587 1905 6.699366 TCAAACATAACTATGTACCACGGAA 58.301 36.000 2.85 0.00 45.55 4.30
1588 1906 7.332557 TCAAACATAACTATGTACCACGGAAT 58.667 34.615 2.85 0.00 45.55 3.01
1589 1907 7.493320 TCAAACATAACTATGTACCACGGAATC 59.507 37.037 2.85 0.00 45.55 2.52
1590 1908 6.474140 ACATAACTATGTACCACGGAATCA 57.526 37.500 0.39 0.00 44.54 2.57
1591 1909 6.278363 ACATAACTATGTACCACGGAATCAC 58.722 40.000 0.39 0.00 44.54 3.06
1592 1910 3.814005 ACTATGTACCACGGAATCACC 57.186 47.619 0.00 0.00 0.00 4.02
1593 1911 3.371965 ACTATGTACCACGGAATCACCT 58.628 45.455 0.00 0.00 36.31 4.00
1594 1912 3.773119 ACTATGTACCACGGAATCACCTT 59.227 43.478 0.00 0.00 36.31 3.50
1595 1913 2.465860 TGTACCACGGAATCACCTTG 57.534 50.000 0.00 0.00 37.61 3.61
1596 1914 1.084289 GTACCACGGAATCACCTTGC 58.916 55.000 0.00 0.00 36.71 4.01
1597 1915 0.687920 TACCACGGAATCACCTTGCA 59.312 50.000 0.00 0.00 36.71 4.08
1598 1916 0.889186 ACCACGGAATCACCTTGCAC 60.889 55.000 0.00 0.00 36.71 4.57
1599 1917 1.586154 CCACGGAATCACCTTGCACC 61.586 60.000 0.00 0.00 36.71 5.01
1600 1918 0.888736 CACGGAATCACCTTGCACCA 60.889 55.000 0.00 0.00 36.31 4.17
1601 1919 0.889186 ACGGAATCACCTTGCACCAC 60.889 55.000 0.00 0.00 36.31 4.16
1602 1920 0.606401 CGGAATCACCTTGCACCACT 60.606 55.000 0.00 0.00 36.31 4.00
1603 1921 1.168714 GGAATCACCTTGCACCACTC 58.831 55.000 0.00 0.00 35.41 3.51
1604 1922 0.798776 GAATCACCTTGCACCACTCG 59.201 55.000 0.00 0.00 0.00 4.18
1605 1923 0.108585 AATCACCTTGCACCACTCGT 59.891 50.000 0.00 0.00 0.00 4.18
1606 1924 0.320771 ATCACCTTGCACCACTCGTC 60.321 55.000 0.00 0.00 0.00 4.20
1607 1925 2.029073 ACCTTGCACCACTCGTCG 59.971 61.111 0.00 0.00 0.00 5.12
1608 1926 2.029073 CCTTGCACCACTCGTCGT 59.971 61.111 0.00 0.00 0.00 4.34
1609 1927 1.594293 CCTTGCACCACTCGTCGTT 60.594 57.895 0.00 0.00 0.00 3.85
1610 1928 1.557443 CCTTGCACCACTCGTCGTTC 61.557 60.000 0.00 0.00 0.00 3.95
1611 1929 0.597637 CTTGCACCACTCGTCGTTCT 60.598 55.000 0.00 0.00 0.00 3.01
1612 1930 0.596600 TTGCACCACTCGTCGTTCTC 60.597 55.000 0.00 0.00 0.00 2.87
1613 1931 2.081212 GCACCACTCGTCGTTCTCG 61.081 63.158 0.00 0.00 38.55 4.04
1614 1932 2.081212 CACCACTCGTCGTTCTCGC 61.081 63.158 0.00 0.00 36.96 5.03
1615 1933 2.870161 CCACTCGTCGTTCTCGCG 60.870 66.667 0.00 0.00 37.70 5.87
1616 1934 2.870161 CACTCGTCGTTCTCGCGG 60.870 66.667 6.13 0.00 37.27 6.46
1617 1935 3.046087 ACTCGTCGTTCTCGCGGA 61.046 61.111 6.13 0.00 37.27 5.54
1618 1936 2.396955 ACTCGTCGTTCTCGCGGAT 61.397 57.895 6.13 0.00 37.27 4.18
1619 1937 1.651730 CTCGTCGTTCTCGCGGATC 60.652 63.158 6.13 0.85 37.27 3.36
1620 1938 2.037913 CTCGTCGTTCTCGCGGATCT 62.038 60.000 6.13 0.00 37.27 2.75
1621 1939 1.651730 CGTCGTTCTCGCGGATCTC 60.652 63.158 6.13 0.00 36.96 2.75
1658 1977 2.422479 GCATGAGAACTGCATGTGACAT 59.578 45.455 0.00 0.00 43.79 3.06
1663 1982 7.308408 GCATGAGAACTGCATGTGACATTATAT 60.308 37.037 0.00 0.00 43.79 0.86
1722 2042 2.563702 CCAACAGCAACAAAAAGGCAT 58.436 42.857 0.00 0.00 0.00 4.40
1726 2046 3.993920 ACAGCAACAAAAAGGCATAAGG 58.006 40.909 0.00 0.00 0.00 2.69
1727 2047 3.640967 ACAGCAACAAAAAGGCATAAGGA 59.359 39.130 0.00 0.00 0.00 3.36
1731 2051 4.083855 GCAACAAAAAGGCATAAGGAAAGC 60.084 41.667 0.00 0.00 0.00 3.51
1732 2052 5.299949 CAACAAAAAGGCATAAGGAAAGCT 58.700 37.500 0.00 0.00 0.00 3.74
1756 2084 2.761208 CCTAGGAGAACAACGACCTCAT 59.239 50.000 1.05 0.00 33.90 2.90
1811 2139 3.308530 GTCGCCTTTGATTTTGTCCAAG 58.691 45.455 0.00 0.00 31.17 3.61
1824 2152 6.435430 TTTTGTCCAAGATACGATCAATGG 57.565 37.500 0.00 1.79 38.89 3.16
1879 2207 3.057315 CGCTCATTCCAAATTGTCCAAGT 60.057 43.478 0.00 0.00 0.00 3.16
1883 2211 5.139727 TCATTCCAAATTGTCCAAGTCACT 58.860 37.500 0.00 0.00 0.00 3.41
1932 2260 3.401033 TCTCGCTTGAAGGAACATTCA 57.599 42.857 0.00 0.00 37.41 2.57
1955 2283 0.250124 TAGCCGTTGTCCACCAGTTG 60.250 55.000 0.00 0.00 0.00 3.16
1965 2293 3.214328 GTCCACCAGTTGACAAATGAGT 58.786 45.455 16.82 9.97 0.00 3.41
1968 2296 5.049405 GTCCACCAGTTGACAAATGAGTTAG 60.049 44.000 16.82 2.60 0.00 2.34
1982 2310 2.300152 TGAGTTAGCCACAACTGGAGAG 59.700 50.000 1.04 0.00 40.55 3.20
1988 2316 4.851639 AGCCACAACTGGAGAGATATTT 57.148 40.909 0.00 0.00 40.55 1.40
2047 2375 0.925558 TTGGATATGGAGCAGCCCAA 59.074 50.000 6.69 0.27 40.04 4.12
2083 2411 1.299165 CCTCCTCATCGGCGTTACG 60.299 63.158 6.85 0.00 0.00 3.18
2096 2424 1.278238 CGTTACGGAGGATGCAACTC 58.722 55.000 12.06 12.06 0.00 3.01
2151 2480 1.081840 GCAGTCCAAAGTCGCTTGC 60.082 57.895 0.00 0.00 0.00 4.01
2156 2485 2.250939 CCAAAGTCGCTTGCGGACA 61.251 57.895 15.10 0.00 36.87 4.02
2157 2486 1.646540 CAAAGTCGCTTGCGGACAA 59.353 52.632 15.10 0.00 36.87 3.18
2159 2488 1.782028 AAAGTCGCTTGCGGACAACC 61.782 55.000 15.10 0.00 36.87 3.77
2181 2510 2.028203 AGCCACACAAAAACTTTGCAGT 60.028 40.909 0.00 0.00 33.11 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 42 7.676004 AGAAAACTAGAAGAAGAAGAAGGAGG 58.324 38.462 0.00 0.00 0.00 4.30
115 139 1.317431 GCACTCCATCCATGCAAGCA 61.317 55.000 0.00 0.00 39.23 3.91
313 340 1.570813 TTTCACAGACACAGCAGACG 58.429 50.000 0.00 0.00 0.00 4.18
339 379 8.806429 TTCACTGGAATTCACACACATATATT 57.194 30.769 7.93 0.00 0.00 1.28
420 490 2.330254 CAAAGCTCTTTGCCGTCCA 58.670 52.632 9.14 0.00 42.66 4.02
641 754 2.596904 AACGTCAGTGTAGTTGCAGT 57.403 45.000 0.00 0.00 0.00 4.40
859 976 5.569630 GCCTAGCCTCTTATAGCATTGCTTA 60.570 44.000 17.71 6.48 40.44 3.09
902 1021 0.601311 AGCTGTTCTCTTGTGCCGAC 60.601 55.000 0.00 0.00 0.00 4.79
924 1043 4.501559 TCACGTTTGTTCGTCTCTTTAGTG 59.498 41.667 0.00 0.00 42.27 2.74
968 1090 2.288886 CGGGCTAGCTACTAATGGAACC 60.289 54.545 15.72 1.30 0.00 3.62
969 1091 2.866855 GCGGGCTAGCTACTAATGGAAC 60.867 54.545 15.72 0.00 0.00 3.62
970 1092 1.343465 GCGGGCTAGCTACTAATGGAA 59.657 52.381 15.72 0.00 0.00 3.53
971 1093 0.966920 GCGGGCTAGCTACTAATGGA 59.033 55.000 15.72 0.00 0.00 3.41
972 1094 3.516578 GCGGGCTAGCTACTAATGG 57.483 57.895 15.72 0.00 0.00 3.16
990 1112 3.473647 TCTCCCATGAGCCGGCAG 61.474 66.667 31.54 15.68 38.58 4.85
991 1113 3.785859 GTCTCCCATGAGCCGGCA 61.786 66.667 31.54 9.64 38.58 5.69
992 1114 4.899239 CGTCTCCCATGAGCCGGC 62.899 72.222 21.89 21.89 36.39 6.13
994 1116 1.672854 TTACCGTCTCCCATGAGCCG 61.673 60.000 0.00 0.00 39.58 5.52
995 1117 0.105039 CTTACCGTCTCCCATGAGCC 59.895 60.000 0.00 0.00 38.58 4.70
996 1118 1.112113 TCTTACCGTCTCCCATGAGC 58.888 55.000 0.00 0.00 38.58 4.26
997 1119 3.887621 TTTCTTACCGTCTCCCATGAG 57.112 47.619 0.00 0.00 40.17 2.90
998 1120 3.134081 GGATTTCTTACCGTCTCCCATGA 59.866 47.826 0.00 0.00 0.00 3.07
1073 1198 1.810030 CTCGCCGCCTTGACCTTAC 60.810 63.158 0.00 0.00 0.00 2.34
1286 1604 8.680903 GCCATATACTCCATCCATTCTAAAATG 58.319 37.037 0.00 0.00 41.69 2.32
1287 1605 8.393259 TGCCATATACTCCATCCATTCTAAAAT 58.607 33.333 0.00 0.00 0.00 1.82
1288 1606 7.754624 TGCCATATACTCCATCCATTCTAAAA 58.245 34.615 0.00 0.00 0.00 1.52
1289 1607 7.328404 TGCCATATACTCCATCCATTCTAAA 57.672 36.000 0.00 0.00 0.00 1.85
1290 1608 6.950860 TGCCATATACTCCATCCATTCTAA 57.049 37.500 0.00 0.00 0.00 2.10
1291 1609 6.673537 TGATGCCATATACTCCATCCATTCTA 59.326 38.462 0.00 0.00 34.61 2.10
1292 1610 5.489997 TGATGCCATATACTCCATCCATTCT 59.510 40.000 0.00 0.00 34.61 2.40
1293 1611 5.748402 TGATGCCATATACTCCATCCATTC 58.252 41.667 0.00 0.00 34.61 2.67
1294 1612 5.784398 TGATGCCATATACTCCATCCATT 57.216 39.130 0.00 0.00 34.61 3.16
1295 1613 5.988865 ATGATGCCATATACTCCATCCAT 57.011 39.130 0.00 0.00 34.61 3.41
1296 1614 5.503002 CAATGATGCCATATACTCCATCCA 58.497 41.667 0.00 0.00 34.61 3.41
1312 1630 1.584761 CATGCCGAAAACGCAATGATG 59.415 47.619 0.00 0.00 40.22 3.07
1313 1631 1.202114 ACATGCCGAAAACGCAATGAT 59.798 42.857 0.00 0.00 40.22 2.45
1314 1632 0.595588 ACATGCCGAAAACGCAATGA 59.404 45.000 0.00 0.00 40.22 2.57
1315 1633 0.709467 CACATGCCGAAAACGCAATG 59.291 50.000 0.00 0.00 40.22 2.82
1316 1634 0.313672 ACACATGCCGAAAACGCAAT 59.686 45.000 0.00 0.00 40.22 3.56
1317 1635 0.593518 CACACATGCCGAAAACGCAA 60.594 50.000 0.00 0.00 40.22 4.85
1318 1636 1.009108 CACACATGCCGAAAACGCA 60.009 52.632 0.00 0.00 41.28 5.24
1319 1637 2.364311 GCACACATGCCGAAAACGC 61.364 57.895 0.00 0.00 46.97 4.84
1320 1638 3.827524 GCACACATGCCGAAAACG 58.172 55.556 0.00 0.00 46.97 3.60
1329 1647 0.654160 CGAGCCATAGTGCACACATG 59.346 55.000 21.04 20.01 0.00 3.21
1330 1648 0.250234 ACGAGCCATAGTGCACACAT 59.750 50.000 21.04 8.95 0.00 3.21
1331 1649 0.892063 TACGAGCCATAGTGCACACA 59.108 50.000 21.04 6.62 0.00 3.72
1332 1650 2.225068 ATACGAGCCATAGTGCACAC 57.775 50.000 21.04 2.62 0.00 3.82
1333 1651 3.219281 TCTATACGAGCCATAGTGCACA 58.781 45.455 21.04 5.47 0.00 4.57
1334 1652 3.917329 TCTATACGAGCCATAGTGCAC 57.083 47.619 9.40 9.40 0.00 4.57
1335 1653 3.634910 TGTTCTATACGAGCCATAGTGCA 59.365 43.478 0.00 0.00 0.00 4.57
1336 1654 4.238761 TGTTCTATACGAGCCATAGTGC 57.761 45.455 0.00 0.00 0.00 4.40
1337 1655 8.082852 AGTTTATGTTCTATACGAGCCATAGTG 58.917 37.037 0.00 0.00 0.00 2.74
1338 1656 8.179509 AGTTTATGTTCTATACGAGCCATAGT 57.820 34.615 0.00 0.00 0.00 2.12
1339 1657 9.776158 CTAGTTTATGTTCTATACGAGCCATAG 57.224 37.037 0.00 0.00 0.00 2.23
1340 1658 9.293404 ACTAGTTTATGTTCTATACGAGCCATA 57.707 33.333 0.00 0.00 0.00 2.74
1341 1659 8.179509 ACTAGTTTATGTTCTATACGAGCCAT 57.820 34.615 0.00 0.00 0.00 4.40
1342 1660 7.578310 ACTAGTTTATGTTCTATACGAGCCA 57.422 36.000 0.00 0.00 0.00 4.75
1343 1661 8.782144 AGTACTAGTTTATGTTCTATACGAGCC 58.218 37.037 0.00 0.00 0.00 4.70
1344 1662 9.810231 GAGTACTAGTTTATGTTCTATACGAGC 57.190 37.037 0.00 0.00 0.00 5.03
1352 1670 9.425577 GCTTGAAAGAGTACTAGTTTATGTTCT 57.574 33.333 0.00 0.00 0.00 3.01
1353 1671 8.657729 GGCTTGAAAGAGTACTAGTTTATGTTC 58.342 37.037 0.00 1.23 0.00 3.18
1354 1672 8.376270 AGGCTTGAAAGAGTACTAGTTTATGTT 58.624 33.333 0.00 0.00 0.00 2.71
1355 1673 7.908453 AGGCTTGAAAGAGTACTAGTTTATGT 58.092 34.615 0.00 0.00 0.00 2.29
1356 1674 8.035394 TGAGGCTTGAAAGAGTACTAGTTTATG 58.965 37.037 0.00 0.00 0.00 1.90
1357 1675 8.035984 GTGAGGCTTGAAAGAGTACTAGTTTAT 58.964 37.037 0.00 0.00 0.00 1.40
1358 1676 7.014905 TGTGAGGCTTGAAAGAGTACTAGTTTA 59.985 37.037 0.00 0.00 0.00 2.01
1359 1677 6.183360 TGTGAGGCTTGAAAGAGTACTAGTTT 60.183 38.462 0.00 0.00 0.00 2.66
1360 1678 5.304614 TGTGAGGCTTGAAAGAGTACTAGTT 59.695 40.000 0.00 0.00 0.00 2.24
1361 1679 4.833380 TGTGAGGCTTGAAAGAGTACTAGT 59.167 41.667 0.00 0.00 0.00 2.57
1370 1688 6.428159 ACATAGTTAACTGTGAGGCTTGAAAG 59.572 38.462 31.62 7.63 38.30 2.62
1417 1735 0.730265 CGGCGGCAGCTAATACAAAA 59.270 50.000 10.53 0.00 44.37 2.44
1418 1736 0.108089 TCGGCGGCAGCTAATACAAA 60.108 50.000 10.53 0.00 44.37 2.83
1459 1777 1.160137 GAGTGGAGCCATTGTGTGAC 58.840 55.000 0.00 0.00 0.00 3.67
1565 1883 7.279313 GTGATTCCGTGGTACATAGTTATGTTT 59.721 37.037 9.82 0.00 43.99 2.83
1578 1896 0.687920 TGCAAGGTGATTCCGTGGTA 59.312 50.000 0.00 0.00 44.02 3.25
1579 1897 0.889186 GTGCAAGGTGATTCCGTGGT 60.889 55.000 0.00 0.00 44.02 4.16
1581 1899 0.888736 TGGTGCAAGGTGATTCCGTG 60.889 55.000 0.00 0.00 46.03 4.94
1582 1900 0.889186 GTGGTGCAAGGTGATTCCGT 60.889 55.000 0.00 0.00 41.99 4.69
1583 1901 0.606401 AGTGGTGCAAGGTGATTCCG 60.606 55.000 0.00 0.00 41.99 4.30
1584 1902 1.168714 GAGTGGTGCAAGGTGATTCC 58.831 55.000 0.00 0.00 0.00 3.01
1585 1903 0.798776 CGAGTGGTGCAAGGTGATTC 59.201 55.000 0.00 0.00 0.00 2.52
1586 1904 0.108585 ACGAGTGGTGCAAGGTGATT 59.891 50.000 0.00 0.00 0.00 2.57
1587 1905 0.320771 GACGAGTGGTGCAAGGTGAT 60.321 55.000 0.00 0.00 0.00 3.06
1588 1906 1.069090 GACGAGTGGTGCAAGGTGA 59.931 57.895 0.00 0.00 0.00 4.02
1589 1907 2.310233 CGACGAGTGGTGCAAGGTG 61.310 63.158 0.00 0.00 0.00 4.00
1590 1908 2.029073 CGACGAGTGGTGCAAGGT 59.971 61.111 0.00 0.00 0.00 3.50
1591 1909 1.557443 GAACGACGAGTGGTGCAAGG 61.557 60.000 0.00 0.00 0.00 3.61
1592 1910 0.597637 AGAACGACGAGTGGTGCAAG 60.598 55.000 0.00 0.00 0.00 4.01
1593 1911 0.596600 GAGAACGACGAGTGGTGCAA 60.597 55.000 0.00 0.00 0.00 4.08
1594 1912 1.007734 GAGAACGACGAGTGGTGCA 60.008 57.895 0.00 0.00 0.00 4.57
1595 1913 2.081212 CGAGAACGACGAGTGGTGC 61.081 63.158 0.00 0.00 42.66 5.01
1596 1914 2.081212 GCGAGAACGACGAGTGGTG 61.081 63.158 0.00 0.00 42.66 4.17
1597 1915 2.254651 GCGAGAACGACGAGTGGT 59.745 61.111 0.00 0.00 42.66 4.16
1598 1916 2.870161 CGCGAGAACGACGAGTGG 60.870 66.667 0.00 0.00 42.66 4.00
1599 1917 2.579241 ATCCGCGAGAACGACGAGTG 62.579 60.000 8.23 0.00 42.66 3.51
1600 1918 2.307137 GATCCGCGAGAACGACGAGT 62.307 60.000 8.23 0.00 42.66 4.18
1601 1919 1.651730 GATCCGCGAGAACGACGAG 60.652 63.158 8.23 0.00 42.66 4.18
1602 1920 2.033328 GAGATCCGCGAGAACGACGA 62.033 60.000 8.23 0.00 42.66 4.20
1603 1921 1.651730 GAGATCCGCGAGAACGACG 60.652 63.158 8.23 0.00 42.66 5.12
1604 1922 0.099082 AAGAGATCCGCGAGAACGAC 59.901 55.000 8.23 2.79 42.66 4.34
1605 1923 0.809385 AAAGAGATCCGCGAGAACGA 59.191 50.000 8.23 0.00 42.66 3.85
1606 1924 1.630148 AAAAGAGATCCGCGAGAACG 58.370 50.000 8.23 0.00 42.93 3.95
1640 1959 9.264719 CTTATATAATGTCACATGCAGTTCTCA 57.735 33.333 0.00 0.00 0.00 3.27
1722 2042 6.441222 TGTTCTCCTAGGATAGCTTTCCTTA 58.559 40.000 27.82 14.45 43.88 2.69
1726 2046 5.044558 CGTTGTTCTCCTAGGATAGCTTTC 58.955 45.833 13.12 0.00 37.37 2.62
1727 2047 4.710375 TCGTTGTTCTCCTAGGATAGCTTT 59.290 41.667 13.12 0.00 37.37 3.51
1731 2051 4.208746 AGGTCGTTGTTCTCCTAGGATAG 58.791 47.826 13.12 1.15 38.80 2.08
1732 2052 4.205587 GAGGTCGTTGTTCTCCTAGGATA 58.794 47.826 13.12 1.39 0.00 2.59
1811 2139 4.448537 AGCTAGCTCCATTGATCGTATC 57.551 45.455 12.68 0.00 0.00 2.24
1824 2152 8.655651 AGAGTATTTGATAACAAAGCTAGCTC 57.344 34.615 19.65 4.17 46.84 4.09
1879 2207 9.121658 AGTTGAATAGTATGATCGTCTTAGTGA 57.878 33.333 0.00 0.00 0.00 3.41
1891 2219 9.464714 GCGAGATTAAGAAGTTGAATAGTATGA 57.535 33.333 0.00 0.00 0.00 2.15
1892 2220 9.469807 AGCGAGATTAAGAAGTTGAATAGTATG 57.530 33.333 0.00 0.00 0.00 2.39
1932 2260 0.907704 TGGTGGACAACGGCTAGGAT 60.908 55.000 0.00 0.00 0.00 3.24
1955 2283 4.320494 CCAGTTGTGGCTAACTCATTTGTC 60.320 45.833 5.02 0.00 38.78 3.18
1965 2293 5.957771 AATATCTCTCCAGTTGTGGCTAA 57.042 39.130 0.00 0.00 44.60 3.09
1968 2296 3.629398 CCAAATATCTCTCCAGTTGTGGC 59.371 47.826 0.00 0.00 44.60 5.01
1982 2310 4.962155 ACTGGATCGGTCTTCCAAATATC 58.038 43.478 0.00 0.00 42.56 1.63
1988 2316 1.639722 TGAACTGGATCGGTCTTCCA 58.360 50.000 0.00 0.00 40.96 3.53
2070 2398 1.105167 ATCCTCCGTAACGCCGATGA 61.105 55.000 0.00 0.00 0.00 2.92
2096 2424 0.399454 ATGATCTCCCCCGCAATGAG 59.601 55.000 0.00 0.00 0.00 2.90
2103 2431 2.429058 CAGGCATGATCTCCCCCG 59.571 66.667 0.00 0.00 0.00 5.73
2151 2480 1.380403 TTTGTGTGGCTGGTTGTCCG 61.380 55.000 0.00 0.00 36.30 4.79
2156 2485 3.333804 CAAAGTTTTTGTGTGGCTGGTT 58.666 40.909 0.00 0.00 0.00 3.67
2157 2486 2.934801 GCAAAGTTTTTGTGTGGCTGGT 60.935 45.455 3.77 0.00 0.00 4.00
2159 2488 2.344950 TGCAAAGTTTTTGTGTGGCTG 58.655 42.857 3.77 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.