Multiple sequence alignment - TraesCS3B01G016900

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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 TraesCS3B01G016900 chr3B 100.000 3509 0 0 1 3509 6964273 6960765 0.000000e+00 6481.0
1 TraesCS3B01G016900 chr3B 94.118 119 7 0 3243 3361 101923993 101923875 7.740000e-42 182.0
2 TraesCS3B01G016900 chr3B 97.059 34 1 0 815 848 6963272 6963305 1.360000e-04 58.4
3 TraesCS3B01G016900 chr3B 97.059 34 1 0 966 999 6963423 6963456 1.360000e-04 58.4
4 TraesCS3B01G016900 chr3D 94.400 2750 129 11 778 3509 6429170 6431912 0.000000e+00 4202.0
5 TraesCS3B01G016900 chr3D 87.865 890 104 4 1027 1914 3614143 3613256 0.000000e+00 1042.0
6 TraesCS3B01G016900 chr3D 87.954 606 67 4 1920 2519 3608294 3607689 0.000000e+00 710.0
7 TraesCS3B01G016900 chr3D 90.779 488 31 8 1 481 6428423 6428903 1.060000e-179 640.0
8 TraesCS3B01G016900 chr3D 95.652 115 5 0 614 728 6429040 6429154 5.980000e-43 185.0
9 TraesCS3B01G016900 chr3D 87.662 154 11 1 3364 3509 292060029 292060182 4.660000e-39 172.0
10 TraesCS3B01G016900 chr3D 97.059 34 1 0 818 851 6429391 6429358 1.360000e-04 58.4
11 TraesCS3B01G016900 chr3D 96.875 32 0 1 578 609 6428991 6429021 6.000000e-03 52.8
12 TraesCS3B01G016900 chr3A 93.567 855 55 0 1746 2600 13849613 13848759 0.000000e+00 1275.0
13 TraesCS3B01G016900 chr3A 86.326 724 31 17 2 661 13850337 13849618 0.000000e+00 726.0
14 TraesCS3B01G016900 chr3A 94.118 119 7 0 3243 3361 105557843 105557961 7.740000e-42 182.0
15 TraesCS3B01G016900 chr3A 83.007 153 20 3 3358 3506 197192554 197192404 2.200000e-27 134.0
16 TraesCS3B01G016900 chr1B 78.647 1419 280 14 1091 2487 50950668 50952085 0.000000e+00 920.0
17 TraesCS3B01G016900 chr1B 78.365 1419 284 14 1091 2487 50900769 50902186 0.000000e+00 898.0
18 TraesCS3B01G016900 chr1D 78.169 1420 285 15 1091 2487 33595840 33597257 0.000000e+00 881.0
19 TraesCS3B01G016900 chr1D 93.966 232 14 0 2813 3044 254419468 254419237 5.570000e-93 351.0
20 TraesCS3B01G016900 chr1D 87.000 200 22 4 3045 3242 254465401 254465598 4.560000e-54 222.0
21 TraesCS3B01G016900 chr1D 81.034 174 30 3 46 217 107360393 107360221 6.110000e-28 135.0
22 TraesCS3B01G016900 chr1D 77.778 153 26 6 1 146 370624499 370624348 1.740000e-13 87.9
23 TraesCS3B01G016900 chr7D 78.068 1418 290 12 1091 2487 497320625 497319208 0.000000e+00 876.0
24 TraesCS3B01G016900 chr7D 78.385 1189 227 19 1289 2454 497359237 497358056 0.000000e+00 745.0
25 TraesCS3B01G016900 chr7D 93.277 119 8 0 3243 3361 530709382 530709264 3.600000e-40 176.0
26 TraesCS3B01G016900 chr7A 77.989 1422 284 19 1091 2487 563246722 563245305 0.000000e+00 865.0
27 TraesCS3B01G016900 chr7A 94.118 119 7 0 3243 3361 706286061 706286179 7.740000e-42 182.0
28 TraesCS3B01G016900 chr4B 77.686 1452 285 29 1057 2478 664677742 664679184 0.000000e+00 850.0
29 TraesCS3B01G016900 chr2D 77.481 1421 293 13 1091 2487 608559285 608557868 0.000000e+00 826.0
30 TraesCS3B01G016900 chr2D 93.966 232 14 0 2813 3044 33936549 33936318 5.570000e-93 351.0
31 TraesCS3B01G016900 chr2D 93.133 233 15 1 2813 3044 630273024 630272792 1.210000e-89 340.0
32 TraesCS3B01G016900 chr2D 80.714 140 20 3 1 139 544190827 544190960 6.200000e-18 102.0
33 TraesCS3B01G016900 chr2D 77.419 155 28 7 1 152 638352818 638352968 6.240000e-13 86.1
34 TraesCS3B01G016900 chr2A 77.394 1420 296 16 1091 2487 740142944 740141527 0.000000e+00 821.0
35 TraesCS3B01G016900 chr2A 77.183 1420 299 16 1091 2487 740078912 740077495 0.000000e+00 804.0
36 TraesCS3B01G016900 chr2A 93.966 232 14 0 2813 3044 14162744 14162975 5.570000e-93 351.0
37 TraesCS3B01G016900 chr2A 90.769 65 6 0 3364 3428 531199502 531199566 1.740000e-13 87.9
38 TraesCS3B01G016900 chr7B 77.356 1422 297 15 1089 2487 525598402 525596983 0.000000e+00 819.0
39 TraesCS3B01G016900 chr7B 88.000 200 20 4 3045 3242 662749076 662748879 2.110000e-57 233.0
40 TraesCS3B01G016900 chr7B 92.913 127 6 3 3238 3361 592608943 592608817 7.740000e-42 182.0
41 TraesCS3B01G016900 chrUn 93.966 232 14 0 2813 3044 452651248 452651017 5.570000e-93 351.0
42 TraesCS3B01G016900 chrUn 93.534 232 15 0 2813 3044 114878673 114878904 2.590000e-91 346.0
43 TraesCS3B01G016900 chrUn 78.877 374 79 0 1184 1557 478925988 478925615 1.620000e-63 254.0
44 TraesCS3B01G016900 chrUn 87.500 200 21 4 3045 3242 422744455 422744652 9.800000e-56 228.0
45 TraesCS3B01G016900 chrUn 87.500 200 21 4 3045 3242 424637939 424637742 9.800000e-56 228.0
46 TraesCS3B01G016900 chr5B 93.966 232 14 0 2813 3044 429039349 429039118 5.570000e-93 351.0
47 TraesCS3B01G016900 chr5B 94.118 119 7 0 3243 3361 57516009 57516127 7.740000e-42 182.0
48 TraesCS3B01G016900 chr5A 93.966 232 14 0 2813 3044 482026670 482026901 5.570000e-93 351.0
49 TraesCS3B01G016900 chr5D 88.000 200 20 4 3045 3242 6247281 6247084 2.110000e-57 233.0
50 TraesCS3B01G016900 chr5D 87.500 200 21 4 3045 3242 503319491 503319688 9.800000e-56 228.0
51 TraesCS3B01G016900 chr5D 87.500 200 21 4 3045 3242 503345427 503345624 9.800000e-56 228.0
52 TraesCS3B01G016900 chr5D 92.063 126 8 1 3238 3361 6254159 6254284 3.600000e-40 176.0
53 TraesCS3B01G016900 chr5D 93.277 119 8 0 3243 3361 503338557 503338439 3.600000e-40 176.0
54 TraesCS3B01G016900 chr1A 87.500 200 21 4 3045 3242 554488022 554488219 9.800000e-56 228.0
55 TraesCS3B01G016900 chr2B 92.000 50 2 2 91 139 365951487 365951439 6.290000e-08 69.4


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 TraesCS3B01G016900 chr3B 6960765 6964273 3508 True 6481.00 6481 100.0000 1 3509 1 chr3B.!!$R1 3508
1 TraesCS3B01G016900 chr3D 6428423 6431912 3489 False 1269.95 4202 94.4265 1 3509 4 chr3D.!!$F2 3508
2 TraesCS3B01G016900 chr3D 3613256 3614143 887 True 1042.00 1042 87.8650 1027 1914 1 chr3D.!!$R2 887
3 TraesCS3B01G016900 chr3D 3607689 3608294 605 True 710.00 710 87.9540 1920 2519 1 chr3D.!!$R1 599
4 TraesCS3B01G016900 chr3A 13848759 13850337 1578 True 1000.50 1275 89.9465 2 2600 2 chr3A.!!$R2 2598
5 TraesCS3B01G016900 chr1B 50950668 50952085 1417 False 920.00 920 78.6470 1091 2487 1 chr1B.!!$F2 1396
6 TraesCS3B01G016900 chr1B 50900769 50902186 1417 False 898.00 898 78.3650 1091 2487 1 chr1B.!!$F1 1396
7 TraesCS3B01G016900 chr1D 33595840 33597257 1417 False 881.00 881 78.1690 1091 2487 1 chr1D.!!$F1 1396
8 TraesCS3B01G016900 chr7D 497319208 497320625 1417 True 876.00 876 78.0680 1091 2487 1 chr7D.!!$R1 1396
9 TraesCS3B01G016900 chr7D 497358056 497359237 1181 True 745.00 745 78.3850 1289 2454 1 chr7D.!!$R2 1165
10 TraesCS3B01G016900 chr7A 563245305 563246722 1417 True 865.00 865 77.9890 1091 2487 1 chr7A.!!$R1 1396
11 TraesCS3B01G016900 chr4B 664677742 664679184 1442 False 850.00 850 77.6860 1057 2478 1 chr4B.!!$F1 1421
12 TraesCS3B01G016900 chr2D 608557868 608559285 1417 True 826.00 826 77.4810 1091 2487 1 chr2D.!!$R2 1396
13 TraesCS3B01G016900 chr2A 740141527 740142944 1417 True 821.00 821 77.3940 1091 2487 1 chr2A.!!$R2 1396
14 TraesCS3B01G016900 chr2A 740077495 740078912 1417 True 804.00 804 77.1830 1091 2487 1 chr2A.!!$R1 1396
15 TraesCS3B01G016900 chr7B 525596983 525598402 1419 True 819.00 819 77.3560 1089 2487 1 chr7B.!!$R1 1398

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
522 555 0.025513 GCTAGCTGCGTCGAACATTG 59.974 55.0 7.70 0.00 0.00 2.82 F
571 624 0.032952 TTCGTCAAGGAAGGGACACG 59.967 55.0 0.00 0.00 33.66 4.49 F
580 633 0.036306 GAAGGGACACGGTGTTGGAT 59.964 55.0 15.94 2.87 0.00 3.41 F
650 730 0.615827 GGGGCTTGGCTTTTGGAGAT 60.616 55.0 0.00 0.00 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2133 0.408700 AGGTACTCGGGGTCAGTCTT 59.591 55.000 0.00 0.00 0.0 3.01 R
2209 2301 0.482446 TCAAACATCTTGGCCAGGGT 59.518 50.000 15.86 4.44 0.0 4.34 R
2212 2304 1.815003 GTCCTCAAACATCTTGGCCAG 59.185 52.381 5.11 0.00 0.0 4.85 R
2613 2726 1.081376 CCCTCACGTCACGAGTCAC 60.081 63.158 2.91 0.00 0.0 3.67 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
105 114 3.818210 TCCAACGAACACAGTATGCAAAT 59.182 39.130 0.00 0.00 42.53 2.32
187 196 2.505364 AAAGGCATGAGAGGTGGGGC 62.505 60.000 0.00 0.00 0.00 5.80
234 243 0.174845 CTGGCATGCATTGAACCCAG 59.825 55.000 21.36 10.81 34.54 4.45
252 261 1.131126 CAGTGCAACGATTAAGGGCTG 59.869 52.381 0.00 0.00 45.86 4.85
272 281 6.183360 GGGCTGATGAAATAAACTAGTGCATT 60.183 38.462 0.00 0.00 0.00 3.56
344 355 6.074409 TGCGAATTTTCAAACATTGTAAGCAG 60.074 34.615 0.00 0.00 0.00 4.24
511 544 2.142319 GCTTTGGATCTAGCTAGCTGC 58.858 52.381 27.68 14.38 43.29 5.25
521 554 2.373938 GCTAGCTGCGTCGAACATT 58.626 52.632 7.70 0.00 0.00 2.71
522 555 0.025513 GCTAGCTGCGTCGAACATTG 59.974 55.000 7.70 0.00 0.00 2.82
568 621 0.321996 AGCTTCGTCAAGGAAGGGAC 59.678 55.000 12.80 0.00 42.88 4.46
569 622 0.034896 GCTTCGTCAAGGAAGGGACA 59.965 55.000 12.80 0.00 42.88 4.02
570 623 1.797025 CTTCGTCAAGGAAGGGACAC 58.203 55.000 4.86 0.00 39.76 3.67
571 624 0.032952 TTCGTCAAGGAAGGGACACG 59.967 55.000 0.00 0.00 33.66 4.49
572 625 1.374252 CGTCAAGGAAGGGACACGG 60.374 63.158 0.00 0.00 33.66 4.94
573 626 1.752833 GTCAAGGAAGGGACACGGT 59.247 57.895 0.00 0.00 34.22 4.83
574 627 0.602905 GTCAAGGAAGGGACACGGTG 60.603 60.000 6.58 6.58 34.22 4.94
575 628 1.052124 TCAAGGAAGGGACACGGTGT 61.052 55.000 14.66 14.66 0.00 4.16
576 629 0.179029 CAAGGAAGGGACACGGTGTT 60.179 55.000 15.94 0.00 0.00 3.32
577 630 0.179029 AAGGAAGGGACACGGTGTTG 60.179 55.000 15.94 0.00 0.00 3.33
578 631 1.599797 GGAAGGGACACGGTGTTGG 60.600 63.158 15.94 0.00 0.00 3.77
579 632 1.448497 GAAGGGACACGGTGTTGGA 59.552 57.895 15.94 0.00 0.00 3.53
580 633 0.036306 GAAGGGACACGGTGTTGGAT 59.964 55.000 15.94 2.87 0.00 3.41
650 730 0.615827 GGGGCTTGGCTTTTGGAGAT 60.616 55.000 0.00 0.00 0.00 2.75
700 780 6.978343 TTCGGAGATGTTAGGTTAATTGTG 57.022 37.500 0.00 0.00 35.04 3.33
714 794 0.963962 ATTGTGTTTGCTGGCTCTGG 59.036 50.000 0.00 0.00 0.00 3.86
719 799 0.964358 GTTTGCTGGCTCTGGCTCAT 60.964 55.000 0.00 0.00 38.73 2.90
728 808 1.681166 GCTCTGGCTCATGGTTCATGT 60.681 52.381 7.63 0.00 41.98 3.21
729 809 2.719739 CTCTGGCTCATGGTTCATGTT 58.280 47.619 7.63 0.00 41.98 2.71
733 813 1.678101 GGCTCATGGTTCATGTTAGCC 59.322 52.381 18.42 18.42 46.69 3.93
737 817 4.769688 CTCATGGTTCATGTTAGCCTGTA 58.230 43.478 7.63 0.00 41.98 2.74
738 818 4.513442 TCATGGTTCATGTTAGCCTGTAC 58.487 43.478 7.63 0.00 41.98 2.90
739 819 4.019771 TCATGGTTCATGTTAGCCTGTACA 60.020 41.667 7.63 0.00 41.98 2.90
741 821 4.720046 TGGTTCATGTTAGCCTGTACAAA 58.280 39.130 0.00 0.00 0.00 2.83
742 822 5.133941 TGGTTCATGTTAGCCTGTACAAAA 58.866 37.500 0.00 0.00 0.00 2.44
743 823 5.772672 TGGTTCATGTTAGCCTGTACAAAAT 59.227 36.000 0.00 0.00 0.00 1.82
744 824 6.266558 TGGTTCATGTTAGCCTGTACAAAATT 59.733 34.615 0.00 0.00 0.00 1.82
745 825 7.151976 GGTTCATGTTAGCCTGTACAAAATTT 58.848 34.615 0.00 0.00 0.00 1.82
746 826 8.301002 GGTTCATGTTAGCCTGTACAAAATTTA 58.699 33.333 0.00 0.00 0.00 1.40
747 827 9.685828 GTTCATGTTAGCCTGTACAAAATTTAA 57.314 29.630 0.00 0.00 0.00 1.52
763 843 9.278978 ACAAAATTTAAATTTGTGGATGGTACC 57.721 29.630 23.34 4.43 46.26 3.34
764 844 9.277783 CAAAATTTAAATTTGTGGATGGTACCA 57.722 29.630 23.34 18.99 38.53 3.25
765 845 9.853177 AAAATTTAAATTTGTGGATGGTACCAA 57.147 25.926 23.34 0.00 38.36 3.67
767 847 9.447157 AATTTAAATTTGTGGATGGTACCAATG 57.553 29.630 20.76 0.00 41.87 2.82
768 848 5.419239 AAATTTGTGGATGGTACCAATGG 57.581 39.130 20.76 0.00 41.87 3.16
769 849 2.523325 TTGTGGATGGTACCAATGGG 57.477 50.000 20.76 0.00 41.87 4.00
770 850 1.675007 TGTGGATGGTACCAATGGGA 58.325 50.000 20.76 0.00 41.87 4.37
771 851 2.213310 TGTGGATGGTACCAATGGGAT 58.787 47.619 20.76 0.00 41.87 3.85
772 852 2.091939 TGTGGATGGTACCAATGGGATG 60.092 50.000 20.76 0.00 41.87 3.51
773 853 2.174639 GTGGATGGTACCAATGGGATGA 59.825 50.000 20.76 0.00 41.87 2.92
774 854 2.855599 TGGATGGTACCAATGGGATGAA 59.144 45.455 20.76 0.00 36.96 2.57
775 855 3.222603 GGATGGTACCAATGGGATGAAC 58.777 50.000 20.76 0.82 38.05 3.18
776 856 3.372566 GGATGGTACCAATGGGATGAACA 60.373 47.826 20.76 0.00 38.05 3.18
816 896 8.875168 ACCTGGGACATGAACAAAATTTAAATA 58.125 29.630 0.00 0.00 38.20 1.40
862 942 1.197036 GCCTTGTTTACAGTTCCGCTC 59.803 52.381 0.00 0.00 0.00 5.03
909 989 3.711704 ACAGGGTATGTATGGAGTCCTTG 59.288 47.826 11.33 0.00 41.60 3.61
916 996 4.069312 TGTATGGAGTCCTTGGTCCTTA 57.931 45.455 11.33 0.00 33.57 2.69
957 1037 1.700955 AGAGAGGTACGTGTTGGTGT 58.299 50.000 0.00 0.00 0.00 4.16
1043 1123 2.342279 CCTCGTCACCGCCTTTGA 59.658 61.111 0.00 0.00 0.00 2.69
1062 1142 2.360475 GAGCTGCCACCCTTCCAC 60.360 66.667 0.00 0.00 0.00 4.02
1228 1308 2.852075 ACCCAGCCCCTTTCGACA 60.852 61.111 0.00 0.00 0.00 4.35
1254 1334 1.283347 TGAAAGAGCTCAGGGCATCT 58.717 50.000 17.77 0.00 44.79 2.90
1296 1376 1.603739 GGCCAGCCCGAACTTCTTT 60.604 57.895 0.00 0.00 0.00 2.52
1539 1619 2.265739 GAGGCCATGCTCGTCACA 59.734 61.111 5.01 0.00 0.00 3.58
1614 1706 2.491022 GGCCGTCTACGCCTCTGAT 61.491 63.158 0.00 0.00 38.18 2.90
1791 1883 2.588314 TACGTTTGCGCCACGGTT 60.588 55.556 26.91 13.70 42.14 4.44
1911 2003 4.049640 GCGTGCATTTGCCCGGAA 62.050 61.111 0.73 0.00 42.05 4.30
2124 2216 1.296392 CATGCAGGTTGGAGTCGGA 59.704 57.895 0.00 0.00 0.00 4.55
2209 2301 1.212751 CACATCCGCAGAGACGTCA 59.787 57.895 19.50 0.00 0.00 4.35
2212 2304 2.711922 ATCCGCAGAGACGTCACCC 61.712 63.158 19.50 6.42 0.00 4.61
2284 2376 0.307760 CGTGCCGAGAAACTTTGCTT 59.692 50.000 0.00 0.00 0.00 3.91
2305 2397 2.259917 TGGTCTGCTTCAGGATCAAGA 58.740 47.619 0.00 0.00 31.51 3.02
2478 2579 2.673523 AGCGCTTGGGAGCTCATT 59.326 55.556 17.19 0.00 45.01 2.57
2489 2590 2.035321 GGGAGCTCATTAGGAAGACGAG 59.965 54.545 17.19 0.00 0.00 4.18
2505 2609 2.857152 GACGAGCAGTGAGATGATGAAC 59.143 50.000 0.00 0.00 0.00 3.18
2526 2630 5.660629 ACTGAGTTCACTATCGACTATCG 57.339 43.478 0.00 0.00 42.10 2.92
2541 2653 2.286831 ACTATCGAGCCGTGACATTACG 60.287 50.000 0.00 0.00 43.35 3.18
2620 2733 4.271590 TGTGAACATTTGTTGTGACTCG 57.728 40.909 0.00 0.00 38.99 4.18
2621 2734 3.687212 TGTGAACATTTGTTGTGACTCGT 59.313 39.130 0.00 0.00 38.99 4.18
2622 2735 4.028383 GTGAACATTTGTTGTGACTCGTG 58.972 43.478 0.00 0.00 38.99 4.35
2623 2736 3.935828 TGAACATTTGTTGTGACTCGTGA 59.064 39.130 0.00 0.00 38.99 4.35
2686 2799 5.685511 CCAATTGGTTGTAAAAGAGTGTTCG 59.314 40.000 16.90 0.00 33.36 3.95
2719 2832 3.323751 ACACGGTAATACTTGGTGTCC 57.676 47.619 8.70 0.00 37.25 4.02
2728 2841 1.878953 ACTTGGTGTCCGATGTTCAC 58.121 50.000 0.00 0.00 0.00 3.18
2763 2876 7.315247 TGTTGTTATTGCATACACTCATACC 57.685 36.000 0.00 0.00 0.00 2.73
2804 2917 8.215050 TCTGTCACTAGGTCTTTTATTTTCCAA 58.785 33.333 0.00 0.00 0.00 3.53
2853 2966 4.387598 GCAGGCAGATTCACATCTCTTAT 58.612 43.478 0.00 0.00 37.71 1.73
2857 2970 6.426328 CAGGCAGATTCACATCTCTTATAACC 59.574 42.308 0.00 0.00 37.71 2.85
2880 2993 2.093973 ACACAATCTTCGATTCTCGGCT 60.094 45.455 0.00 0.00 40.88 5.52
2936 3049 9.268282 TCCTAGGGTATCATTTCTAATACATCC 57.732 37.037 9.46 0.00 31.33 3.51
2937 3050 9.046846 CCTAGGGTATCATTTCTAATACATCCA 57.953 37.037 0.00 0.00 31.33 3.41
3076 3189 4.518970 GTCATGTCCAAGCCAAAGAACTTA 59.481 41.667 0.00 0.00 0.00 2.24
3079 3192 3.117663 TGTCCAAGCCAAAGAACTTACCT 60.118 43.478 0.00 0.00 0.00 3.08
3117 3230 2.771372 TGATGATTGGGACGAGATTCCA 59.229 45.455 0.00 0.00 37.40 3.53
3154 3267 3.490439 AAAGCTTGGTTTCCATTTGGG 57.510 42.857 0.00 0.00 31.53 4.12
3166 3279 6.209788 GGTTTCCATTTGGGTTGTAGATGTAA 59.790 38.462 0.00 0.00 38.11 2.41
3167 3280 7.093509 GGTTTCCATTTGGGTTGTAGATGTAAT 60.094 37.037 0.00 0.00 38.11 1.89
3198 3311 8.454106 CCACTATTGAAGGACAATGTAGAAAAG 58.546 37.037 0.00 0.00 46.93 2.27
3206 3319 9.823647 GAAGGACAATGTAGAAAAGATGATAGA 57.176 33.333 0.00 0.00 0.00 1.98
3247 3360 6.780706 AAAGATCTTCATTGCTGCAAAAAG 57.219 33.333 20.06 22.50 0.00 2.27
3361 3476 6.877611 ATACCGCTTGTAAATAATCCAAGG 57.122 37.500 0.00 0.00 36.84 3.61
3400 3515 3.953775 CCCCACTCCAGCCGTTGT 61.954 66.667 0.00 0.00 0.00 3.32
3447 3569 1.135575 CCTTCAGCCACGCAAATTCTC 60.136 52.381 0.00 0.00 0.00 2.87
3462 3584 6.032460 CGCAAATTCTCGATGTTCCTTTTTAC 59.968 38.462 0.00 0.00 0.00 2.01
3483 3605 4.012374 ACTTCTCATCAAACGAATGGCAT 58.988 39.130 0.00 0.00 0.00 4.40
3499 3621 6.649973 CGAATGGCATCTTCATCTAGAAATCT 59.350 38.462 0.00 0.00 35.40 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 196 2.360350 AGTTGCATGAGCCACCCG 60.360 61.111 0.00 0.00 37.11 5.28
234 243 1.448985 TCAGCCCTTAATCGTTGCAC 58.551 50.000 0.00 0.00 0.00 4.57
344 355 5.053145 TGTTTGGTGCCAAATTATTGACAC 58.947 37.500 18.00 4.99 45.80 3.67
423 434 1.459348 AAGGGGTTGCTTGGTTGGG 60.459 57.895 0.00 0.00 0.00 4.12
425 436 1.341080 ATGAAGGGGTTGCTTGGTTG 58.659 50.000 0.00 0.00 0.00 3.77
503 536 0.025513 CAATGTTCGACGCAGCTAGC 59.974 55.000 6.62 6.62 40.87 3.42
549 582 0.321996 GTCCCTTCCTTGACGAAGCT 59.678 55.000 0.00 0.00 38.35 3.74
568 621 0.677731 AGCCATGATCCAACACCGTG 60.678 55.000 0.00 0.00 0.00 4.94
569 622 0.038166 AAGCCATGATCCAACACCGT 59.962 50.000 0.00 0.00 0.00 4.83
570 623 1.176527 AAAGCCATGATCCAACACCG 58.823 50.000 0.00 0.00 0.00 4.94
571 624 2.354003 CCAAAAGCCATGATCCAACACC 60.354 50.000 0.00 0.00 0.00 4.16
572 625 2.354003 CCCAAAAGCCATGATCCAACAC 60.354 50.000 0.00 0.00 0.00 3.32
573 626 1.901159 CCCAAAAGCCATGATCCAACA 59.099 47.619 0.00 0.00 0.00 3.33
574 627 1.901833 ACCCAAAAGCCATGATCCAAC 59.098 47.619 0.00 0.00 0.00 3.77
575 628 2.178580 GACCCAAAAGCCATGATCCAA 58.821 47.619 0.00 0.00 0.00 3.53
576 629 1.358787 AGACCCAAAAGCCATGATCCA 59.641 47.619 0.00 0.00 0.00 3.41
577 630 2.027385 GAGACCCAAAAGCCATGATCC 58.973 52.381 0.00 0.00 0.00 3.36
578 631 2.027385 GGAGACCCAAAAGCCATGATC 58.973 52.381 0.00 0.00 0.00 2.92
579 632 1.683011 CGGAGACCCAAAAGCCATGAT 60.683 52.381 0.00 0.00 0.00 2.45
580 633 0.322456 CGGAGACCCAAAAGCCATGA 60.322 55.000 0.00 0.00 0.00 3.07
650 730 6.652205 ATCTTCCTAATTTTGGACCCACTA 57.348 37.500 0.00 0.00 32.65 2.74
696 776 1.737355 GCCAGAGCCAGCAAACACAA 61.737 55.000 0.00 0.00 0.00 3.33
700 780 0.964358 ATGAGCCAGAGCCAGCAAAC 60.964 55.000 0.00 0.00 41.25 2.93
714 794 2.357009 CAGGCTAACATGAACCATGAGC 59.643 50.000 13.22 11.62 43.81 4.26
719 799 4.359434 TTGTACAGGCTAACATGAACCA 57.641 40.909 0.00 0.00 0.00 3.67
729 809 9.482627 CCACAAATTTAAATTTTGTACAGGCTA 57.517 29.630 20.92 0.00 36.52 3.93
737 817 9.278978 GGTACCATCCACAAATTTAAATTTTGT 57.721 29.630 20.92 18.26 36.52 2.83
738 818 9.277783 TGGTACCATCCACAAATTTAAATTTTG 57.722 29.630 20.92 19.60 33.06 2.44
739 819 9.853177 TTGGTACCATCCACAAATTTAAATTTT 57.147 25.926 20.92 11.43 34.77 1.82
741 821 9.447157 CATTGGTACCATCCACAAATTTAAATT 57.553 29.630 17.17 7.64 37.20 1.82
742 822 8.046107 CCATTGGTACCATCCACAAATTTAAAT 58.954 33.333 17.17 0.00 37.20 1.40
743 823 7.390027 CCATTGGTACCATCCACAAATTTAAA 58.610 34.615 17.17 0.00 37.20 1.52
744 824 6.070538 CCCATTGGTACCATCCACAAATTTAA 60.071 38.462 17.17 0.00 37.20 1.52
745 825 5.423610 CCCATTGGTACCATCCACAAATTTA 59.576 40.000 17.17 0.00 37.20 1.40
746 826 4.224818 CCCATTGGTACCATCCACAAATTT 59.775 41.667 17.17 0.00 37.20 1.82
747 827 3.774216 CCCATTGGTACCATCCACAAATT 59.226 43.478 17.17 0.00 37.20 1.82
748 828 3.012274 TCCCATTGGTACCATCCACAAAT 59.988 43.478 17.17 0.65 37.20 2.32
749 829 2.380249 TCCCATTGGTACCATCCACAAA 59.620 45.455 17.17 0.00 37.20 2.83
750 830 1.996291 TCCCATTGGTACCATCCACAA 59.004 47.619 17.17 0.00 37.20 3.33
751 831 1.675007 TCCCATTGGTACCATCCACA 58.325 50.000 17.17 0.00 37.20 4.17
752 832 2.174639 TCATCCCATTGGTACCATCCAC 59.825 50.000 17.17 0.00 37.20 4.02
753 833 2.497368 TCATCCCATTGGTACCATCCA 58.503 47.619 17.17 0.22 35.49 3.41
754 834 3.222603 GTTCATCCCATTGGTACCATCC 58.777 50.000 17.17 0.00 0.00 3.51
755 835 3.897239 TGTTCATCCCATTGGTACCATC 58.103 45.455 17.17 0.00 0.00 3.51
756 836 4.329638 TTGTTCATCCCATTGGTACCAT 57.670 40.909 17.17 3.05 0.00 3.55
757 837 3.816398 TTGTTCATCCCATTGGTACCA 57.184 42.857 11.60 11.60 0.00 3.25
758 838 5.675684 ATTTTGTTCATCCCATTGGTACC 57.324 39.130 4.43 4.43 0.00 3.34
759 839 7.093509 ACCTAATTTTGTTCATCCCATTGGTAC 60.094 37.037 1.20 0.00 0.00 3.34
760 840 6.957020 ACCTAATTTTGTTCATCCCATTGGTA 59.043 34.615 1.20 0.00 0.00 3.25
761 841 5.784906 ACCTAATTTTGTTCATCCCATTGGT 59.215 36.000 1.20 0.00 0.00 3.67
762 842 6.108015 CACCTAATTTTGTTCATCCCATTGG 58.892 40.000 0.00 0.00 0.00 3.16
763 843 5.581874 GCACCTAATTTTGTTCATCCCATTG 59.418 40.000 0.00 0.00 0.00 2.82
764 844 5.338300 GGCACCTAATTTTGTTCATCCCATT 60.338 40.000 0.00 0.00 0.00 3.16
765 845 4.162131 GGCACCTAATTTTGTTCATCCCAT 59.838 41.667 0.00 0.00 0.00 4.00
766 846 3.513515 GGCACCTAATTTTGTTCATCCCA 59.486 43.478 0.00 0.00 0.00 4.37
767 847 3.513515 TGGCACCTAATTTTGTTCATCCC 59.486 43.478 0.00 0.00 0.00 3.85
768 848 4.799564 TGGCACCTAATTTTGTTCATCC 57.200 40.909 0.00 0.00 0.00 3.51
769 849 4.929211 GGTTGGCACCTAATTTTGTTCATC 59.071 41.667 0.00 0.00 40.44 2.92
770 850 4.893608 GGTTGGCACCTAATTTTGTTCAT 58.106 39.130 0.00 0.00 40.44 2.57
771 851 4.329462 GGTTGGCACCTAATTTTGTTCA 57.671 40.909 0.00 0.00 40.44 3.18
816 896 4.446745 CCATCTCATTGGTACCATCCACAT 60.447 45.833 17.17 2.33 37.20 3.21
824 904 1.680338 GCACCCATCTCATTGGTACC 58.320 55.000 4.43 4.43 34.77 3.34
862 942 2.792674 CTCACAGCAAAAGCAACACATG 59.207 45.455 0.00 0.00 0.00 3.21
890 970 3.046374 ACCAAGGACTCCATACATACCC 58.954 50.000 0.00 0.00 0.00 3.69
957 1037 2.645297 TGGGTGCCTTGATTGGTACTAA 59.355 45.455 0.00 0.00 41.50 2.24
1043 1123 2.233566 TGGAAGGGTGGCAGCTCAT 61.234 57.895 17.16 2.86 0.00 2.90
1062 1142 1.071019 CGTCATCGTCGTTGAGTGGG 61.071 60.000 6.25 0.00 0.00 4.61
1228 1308 1.474677 CCTGAGCTCTTTCATGGCGAT 60.475 52.381 16.19 0.00 0.00 4.58
1539 1619 4.299547 TCACGAGCAGCGGCAAGT 62.300 61.111 12.44 7.52 46.49 3.16
1614 1706 2.581216 AGAACGTAGAGTGGGTCTGA 57.419 50.000 0.00 0.00 36.64 3.27
1770 1862 2.554272 GTGGCGCAAACGTAGGTG 59.446 61.111 10.83 0.00 42.83 4.00
1791 1883 2.525124 ATTGGAGGACGTGGTGCCA 61.525 57.895 0.00 0.00 0.00 4.92
1889 1981 4.705519 GGCAAATGCACGCGCTGT 62.706 61.111 5.73 1.79 44.36 4.40
1911 2003 1.234615 CGTTGAGGTGGTGCCGAAAT 61.235 55.000 0.00 0.00 43.70 2.17
2041 2133 0.408700 AGGTACTCGGGGTCAGTCTT 59.591 55.000 0.00 0.00 0.00 3.01
2209 2301 0.482446 TCAAACATCTTGGCCAGGGT 59.518 50.000 15.86 4.44 0.00 4.34
2212 2304 1.815003 GTCCTCAAACATCTTGGCCAG 59.185 52.381 5.11 0.00 0.00 4.85
2284 2376 2.639347 TCTTGATCCTGAAGCAGACCAA 59.361 45.455 0.00 0.00 32.44 3.67
2305 2397 2.348888 CGGCCCTAACTCCAGTCGT 61.349 63.158 0.00 0.00 0.00 4.34
2478 2579 2.491675 TCTCACTGCTCGTCTTCCTA 57.508 50.000 0.00 0.00 0.00 2.94
2489 2590 3.859443 ACTCAGTTCATCATCTCACTGC 58.141 45.455 0.00 0.00 37.22 4.40
2505 2609 5.908916 TCGATAGTCGATAGTGAACTCAG 57.091 43.478 0.00 0.00 44.82 3.35
2526 2630 3.351020 AGATACGTAATGTCACGGCTC 57.649 47.619 0.00 0.00 46.12 4.70
2600 2713 4.028383 CACGAGTCACAACAAATGTTCAC 58.972 43.478 0.00 0.00 41.46 3.18
2613 2726 1.081376 CCCTCACGTCACGAGTCAC 60.081 63.158 2.91 0.00 0.00 3.67
2619 2732 3.690139 AGCTATATATCCCTCACGTCACG 59.310 47.826 0.00 0.00 0.00 4.35
2620 2733 5.220892 GCTAGCTATATATCCCTCACGTCAC 60.221 48.000 7.70 0.00 0.00 3.67
2621 2734 4.882427 GCTAGCTATATATCCCTCACGTCA 59.118 45.833 7.70 0.00 0.00 4.35
2622 2735 5.008217 CAGCTAGCTATATATCCCTCACGTC 59.992 48.000 18.86 0.00 0.00 4.34
2623 2736 4.884744 CAGCTAGCTATATATCCCTCACGT 59.115 45.833 18.86 0.00 0.00 4.49
2686 2799 9.987272 AAGTATTACCGTGTACTAAATATTCCC 57.013 33.333 0.00 0.00 31.25 3.97
2719 2832 3.928992 ACATAACAGCTCAGTGAACATCG 59.071 43.478 0.00 0.00 0.00 3.84
2728 2841 5.941733 TGCAATAACAACATAACAGCTCAG 58.058 37.500 0.00 0.00 0.00 3.35
2763 2876 7.385205 CCTAGTGACAGATTAATACAATTCCCG 59.615 40.741 0.00 0.00 0.00 5.14
2853 2966 5.160607 AGAATCGAAGATTGTGTGGGTTA 57.839 39.130 0.00 0.00 45.12 2.85
2897 3010 3.190439 ACCCTAGGATGGTTGTAAAGCT 58.810 45.455 11.48 0.00 46.34 3.74
2906 3019 9.047947 GTATTAGAAATGATACCCTAGGATGGT 57.952 37.037 11.48 1.88 39.97 3.55
2907 3020 9.046846 TGTATTAGAAATGATACCCTAGGATGG 57.953 37.037 11.48 0.00 0.00 3.51
2936 3049 3.503827 TGTGTACGAGCTAGTCCAATG 57.496 47.619 1.52 0.00 0.00 2.82
2937 3050 4.159693 TCAATGTGTACGAGCTAGTCCAAT 59.840 41.667 1.52 0.00 0.00 3.16
2939 3052 3.086282 TCAATGTGTACGAGCTAGTCCA 58.914 45.455 1.52 0.00 0.00 4.02
3049 3162 3.507233 TCTTTGGCTTGGACATGACATTC 59.493 43.478 0.00 0.00 0.00 2.67
3076 3189 8.010733 TCATCATTTTTCAGAACTTTTCAGGT 57.989 30.769 0.00 0.00 0.00 4.00
3079 3192 9.263538 CCAATCATCATTTTTCAGAACTTTTCA 57.736 29.630 0.00 0.00 0.00 2.69
3117 3230 6.018832 CCAAGCTTTTCGTGATTCAAAAACAT 60.019 34.615 0.00 0.00 0.00 2.71
3154 3267 8.612619 CAATAGTGGGTTGATTACATCTACAAC 58.387 37.037 0.00 0.00 40.90 3.32
3166 3279 4.927267 TGTCCTTCAATAGTGGGTTGAT 57.073 40.909 0.00 0.00 35.68 2.57
3167 3280 4.715534 TTGTCCTTCAATAGTGGGTTGA 57.284 40.909 0.00 0.00 34.01 3.18
3180 3293 9.823647 TCTATCATCTTTTCTACATTGTCCTTC 57.176 33.333 0.00 0.00 0.00 3.46
3222 3335 8.092687 ACTTTTTGCAGCAATGAAGATCTTTAT 58.907 29.630 26.53 8.26 0.00 1.40
3276 3391 1.281867 GTGAATCCATGGAGGGTCACA 59.718 52.381 31.80 19.03 45.08 3.58
3277 3392 1.408822 GGTGAATCCATGGAGGGTCAC 60.409 57.143 30.36 30.36 45.04 3.67
3306 3421 2.515926 TTTTGCAACATTAGCCGCAA 57.484 40.000 0.00 0.00 42.29 4.85
3313 3428 6.673106 TCACGCTCTTATTTTTGCAACATTA 58.327 32.000 0.00 0.00 0.00 1.90
3361 3476 4.311606 GGAGTCAGAGTCAAAAAGAGGTC 58.688 47.826 7.59 0.00 0.00 3.85
3400 3515 2.823984 TCGCGGTAACAGAAAGAAACA 58.176 42.857 6.13 0.00 0.00 2.83
3447 3569 7.364522 TGATGAGAAGTAAAAAGGAACATCG 57.635 36.000 0.00 0.00 35.76 3.84
3462 3584 4.334759 AGATGCCATTCGTTTGATGAGAAG 59.665 41.667 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.