Multiple sequence alignment - TraesCS1D01G056500

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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 TraesCS1D01G056500 chr1D 100.000 3870 0 0 1 3870 37439771 37435902 0.000000e+00 7147.0
1 TraesCS1D01G056500 chr1A 93.676 2372 102 22 987 3327 36621349 36618995 0.000000e+00 3506.0
2 TraesCS1D01G056500 chr1A 90.210 2380 109 49 913 3243 31894791 31897095 0.000000e+00 2990.0
3 TraesCS1D01G056500 chr1A 94.828 580 16 9 3292 3870 36618995 36618429 0.000000e+00 893.0
4 TraesCS1D01G056500 chr1A 82.274 897 108 35 6 865 36622236 36621354 0.000000e+00 728.0
5 TraesCS1D01G056500 chr1A 83.733 793 95 18 6 778 31893346 31894124 0.000000e+00 719.0
6 TraesCS1D01G056500 chr1A 86.316 190 20 3 3319 3507 31897085 31897269 6.560000e-48 202.0
7 TraesCS1D01G056500 chr1A 86.335 161 17 5 3711 3870 31899948 31900104 1.850000e-38 171.0
8 TraesCS1D01G056500 chr1B 93.089 1939 80 24 970 2889 57024482 57022579 0.000000e+00 2789.0
9 TraesCS1D01G056500 chr1B 93.213 1164 55 6 1291 2433 57070847 57069687 0.000000e+00 1690.0
10 TraesCS1D01G056500 chr1B 92.835 963 53 4 1484 2433 57045406 57044447 0.000000e+00 1382.0
11 TraesCS1D01G056500 chr1B 96.532 519 18 0 970 1488 57051152 57050634 0.000000e+00 859.0
12 TraesCS1D01G056500 chr1B 81.122 588 61 21 89 652 57145841 57145280 3.570000e-115 425.0
13 TraesCS1D01G056500 chr1B 79.260 622 83 26 269 865 57071694 57071094 3.620000e-105 392.0
14 TraesCS1D01G056500 chr1B 90.749 227 21 0 924 1150 57071070 57070844 1.750000e-78 303.0
15 TraesCS1D01G056500 chr1B 88.889 252 9 4 2431 2678 57043045 57042809 3.780000e-75 292.0
16 TraesCS1D01G056500 chr1B 88.845 251 11 2 2431 2678 57068284 57068048 3.780000e-75 292.0
17 TraesCS1D01G056500 chr1B 87.347 245 18 2 2676 2908 57067909 57067666 6.370000e-68 268.0
18 TraesCS1D01G056500 chr1B 86.939 245 19 2 2676 2908 57042670 57042427 2.970000e-66 263.0
19 TraesCS1D01G056500 chr1B 81.844 347 28 20 3506 3844 57022004 57021685 3.840000e-65 259.0
20 TraesCS1D01G056500 chr1B 86.364 88 10 2 3238 3323 56061717 56061804 1.140000e-15 95.3
21 TraesCS1D01G056500 chr1B 83.333 84 12 2 3241 3323 487174426 487174508 4.150000e-10 76.8
22 TraesCS1D01G056500 chr7A 90.052 191 14 3 2223 2413 465753347 465753162 3.860000e-60 243.0
23 TraesCS1D01G056500 chr7A 85.401 137 15 2 2449 2581 679957153 679957018 1.880000e-28 137.0
24 TraesCS1D01G056500 chr7B 88.172 186 18 1 3322 3507 154565947 154566128 6.510000e-53 219.0
25 TraesCS1D01G056500 chr7B 86.822 129 11 3 2453 2575 59069230 59069358 5.210000e-29 139.0
26 TraesCS1D01G056500 chr4B 88.172 186 18 1 3322 3507 665338864 665338683 6.510000e-53 219.0
27 TraesCS1D01G056500 chr4B 86.905 84 6 4 3240 3323 415114513 415114591 5.330000e-14 89.8
28 TraesCS1D01G056500 chr4D 78.431 357 50 17 2585 2921 12320962 12320613 1.410000e-49 207.0
29 TraesCS1D01G056500 chr6A 76.771 353 56 17 2585 2918 502509971 502509626 1.430000e-39 174.0
30 TraesCS1D01G056500 chr6A 80.383 209 27 9 2115 2322 142076355 142076550 3.120000e-31 147.0
31 TraesCS1D01G056500 chr7D 85.401 137 15 2 2449 2581 588081912 588081777 1.880000e-28 137.0
32 TraesCS1D01G056500 chr2B 85.714 133 14 2 2453 2581 251374832 251374963 6.740000e-28 135.0
33 TraesCS1D01G056500 chr2B 86.957 92 7 3 3237 3323 39970997 39971088 8.850000e-17 99.0
34 TraesCS1D01G056500 chr3A 70.628 732 178 27 1307 2030 623777070 623777772 4.060000e-25 126.0
35 TraesCS1D01G056500 chr3A 84.507 71 9 2 3241 3309 114570308 114570378 6.940000e-08 69.4
36 TraesCS1D01G056500 chr3D 76.000 250 54 5 1784 2030 480969936 480970182 1.460000e-24 124.0
37 TraesCS1D01G056500 chr3D 100.000 31 0 0 1790 1820 578259650 578259620 1.500000e-04 58.4
38 TraesCS1D01G056500 chr3B 75.200 250 56 5 1784 2030 641805193 641805439 3.160000e-21 113.0
39 TraesCS1D01G056500 chr3B 86.047 86 10 2 3240 3323 778392732 778392817 1.480000e-14 91.6
40 TraesCS1D01G056500 chr3B 100.000 31 0 0 1790 1820 771558308 771558278 1.500000e-04 58.4
41 TraesCS1D01G056500 chr3B 87.500 48 4 2 1771 1818 773569338 773569383 2.000000e-03 54.7
42 TraesCS1D01G056500 chr2D 73.209 321 68 16 325 637 522266218 522265908 2.460000e-17 100.0
43 TraesCS1D01G056500 chr2A 90.000 70 5 2 3241 3309 639054346 639054414 5.330000e-14 89.8
44 TraesCS1D01G056500 chr4A 100.000 32 0 0 3242 3273 524268774 524268743 4.180000e-05 60.2


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 TraesCS1D01G056500 chr1D 37435902 37439771 3869 True 7147.000000 7147 100.000000 1 3870 1 chr1D.!!$R1 3869
1 TraesCS1D01G056500 chr1A 36618429 36622236 3807 True 1709.000000 3506 90.259333 6 3870 3 chr1A.!!$R1 3864
2 TraesCS1D01G056500 chr1A 31893346 31900104 6758 False 1020.500000 2990 86.648500 6 3870 4 chr1A.!!$F1 3864
3 TraesCS1D01G056500 chr1B 57021685 57024482 2797 True 1524.000000 2789 87.466500 970 3844 2 chr1B.!!$R3 2874
4 TraesCS1D01G056500 chr1B 57050634 57051152 518 True 859.000000 859 96.532000 970 1488 1 chr1B.!!$R1 518
5 TraesCS1D01G056500 chr1B 57042427 57045406 2979 True 645.666667 1382 89.554333 1484 2908 3 chr1B.!!$R4 1424
6 TraesCS1D01G056500 chr1B 57067666 57071694 4028 True 589.000000 1690 87.882800 269 2908 5 chr1B.!!$R5 2639
7 TraesCS1D01G056500 chr1B 57145280 57145841 561 True 425.000000 425 81.122000 89 652 1 chr1B.!!$R2 563

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
776 833 0.031449 GATCAGACGGCTGGCTAGAC 59.969 60.0 20.5 0.0 42.53 2.59 F
916 1536 0.036577 AGCAGTCACTCATCACAGCC 60.037 55.0 0.0 0.0 0.00 4.85 F
917 1537 0.321034 GCAGTCACTCATCACAGCCA 60.321 55.0 0.0 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2681 5210 2.103263 GGTCACTTGACACTGTTCTCCT 59.897 50.000 11.40 0.0 46.47 3.69 R
2764 5293 2.559668 CACATCAGCAGGTGACCAAAAT 59.440 45.455 3.92 0.0 38.28 1.82 R
2922 5487 0.980423 GACACCAGAGGCTTCCTTCT 59.020 55.000 0.00 0.0 31.76 2.85 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
26 27 2.024176 ATCAGCATTACGGACACCAC 57.976 50.000 0.00 0.00 0.00 4.16
29 30 0.321298 AGCATTACGGACACCACCAC 60.321 55.000 0.00 0.00 0.00 4.16
81 82 5.700832 TGATCACACAACAAGTTATCACCTC 59.299 40.000 0.00 0.00 0.00 3.85
113 114 0.874390 CGGGATCCCACATATTTGCG 59.126 55.000 30.42 8.42 35.37 4.85
145 146 2.510768 ATAGCCCGACGAGATTTGAC 57.489 50.000 0.00 0.00 0.00 3.18
165 166 0.745845 CACTCCAAATGCCCTCTCCG 60.746 60.000 0.00 0.00 0.00 4.63
180 181 0.755686 CTCCGCAGCCTTCCTAGAAT 59.244 55.000 0.00 0.00 0.00 2.40
188 189 4.625083 GCAGCCTTCCTAGAATCTTCTTGT 60.625 45.833 0.00 0.00 38.70 3.16
206 207 8.647796 TCTTCTTGTATTTGGACAAAGAGACTA 58.352 33.333 3.71 0.00 38.80 2.59
209 210 9.793259 TCTTGTATTTGGACAAAGAGACTATTT 57.207 29.630 3.71 0.00 38.80 1.40
240 246 1.393603 TGGCTCGGAGATAGTCAGTG 58.606 55.000 9.69 0.00 33.89 3.66
262 268 1.688735 TCGGCCAATGAGGATAGACAG 59.311 52.381 2.24 0.00 41.22 3.51
285 310 3.034721 TCGGTAGTTGTGTCCATTGAC 57.965 47.619 0.00 0.00 42.12 3.18
336 361 7.799447 CACATGACAAAGTTTTGCAAATAATGG 59.201 33.333 13.65 5.96 41.79 3.16
343 368 5.894807 AGTTTTGCAAATAATGGAGATCGG 58.105 37.500 13.65 0.00 0.00 4.18
354 379 0.454600 GGAGATCGGTGAAGCACGTA 59.545 55.000 0.00 0.00 34.83 3.57
376 401 4.443978 AATATCATTGTGAGACCCTGGG 57.556 45.455 12.28 12.28 0.00 4.45
377 402 1.971149 ATCATTGTGAGACCCTGGGA 58.029 50.000 22.23 0.00 0.00 4.37
401 426 5.596836 TGCCAAAGAAAGAGTGTCAAATT 57.403 34.783 0.00 0.00 0.00 1.82
404 429 6.183360 TGCCAAAGAAAGAGTGTCAAATTCAT 60.183 34.615 0.00 0.00 0.00 2.57
410 435 7.453393 AGAAAGAGTGTCAAATTCATAGGTCA 58.547 34.615 0.00 0.00 0.00 4.02
449 474 1.284198 AGCATGATTGTTGGCTCTCCT 59.716 47.619 0.00 0.00 28.71 3.69
490 529 3.132111 CCTTGCAAACCTACCAACAGTTT 59.868 43.478 0.00 0.00 34.13 2.66
519 558 1.534163 CTAGTGCATGCAATCGATGGG 59.466 52.381 25.74 5.45 0.00 4.00
523 562 1.241165 GCATGCAATCGATGGGATCA 58.759 50.000 14.21 0.00 33.02 2.92
537 576 5.121925 CGATGGGATCAAGCATATTGAGAAG 59.878 44.000 0.00 0.00 0.00 2.85
558 599 3.008485 AGCCCTCTTACTTCTTCAAGTGG 59.992 47.826 0.00 0.00 43.17 4.00
572 614 3.027412 TCAAGTGGCAAAAGCTTGGTTA 58.973 40.909 13.58 0.00 39.80 2.85
575 617 2.068519 GTGGCAAAAGCTTGGTTATGC 58.931 47.619 0.00 6.32 32.76 3.14
587 629 2.088423 TGGTTATGCCCACGACATTTC 58.912 47.619 0.00 0.00 36.04 2.17
600 642 2.343843 CGACATTTCGCTCTCTCAAGTG 59.656 50.000 0.00 0.00 38.71 3.16
608 651 2.765122 GCTCTCTCAAGTGCTCTTTGT 58.235 47.619 0.00 0.00 38.64 2.83
653 696 9.726034 GAGTGACAAATTAAAAATATTGTTGCG 57.274 29.630 0.78 0.00 36.22 4.85
654 697 9.255304 AGTGACAAATTAAAAATATTGTTGCGT 57.745 25.926 0.78 0.00 36.22 5.24
666 718 3.725459 TTGCGTGCAGATGCCACG 61.725 61.111 18.77 18.77 43.26 4.94
668 720 3.197790 GCGTGCAGATGCCACGAT 61.198 61.111 23.93 0.00 43.15 3.73
683 735 2.608016 CCACGATGTAGATGGTCGATGG 60.608 54.545 0.69 2.01 38.63 3.51
706 758 1.002134 CGTGGTGGATGAAAGGCCT 60.002 57.895 0.00 0.00 0.00 5.19
710 762 0.620556 GGTGGATGAAAGGCCTGAGA 59.379 55.000 5.69 0.00 0.00 3.27
742 799 3.173599 CAACAATTTGCTGCGATCGAAT 58.826 40.909 21.57 6.21 0.00 3.34
761 818 4.783621 GCCACCAGCGCCAGATCA 62.784 66.667 2.29 0.00 0.00 2.92
772 829 2.729479 CCAGATCAGACGGCTGGCT 61.729 63.158 20.50 13.69 42.30 4.75
773 830 1.395045 CCAGATCAGACGGCTGGCTA 61.395 60.000 20.50 0.00 42.30 3.93
774 831 0.031857 CAGATCAGACGGCTGGCTAG 59.968 60.000 20.50 2.63 42.53 3.42
775 832 0.106469 AGATCAGACGGCTGGCTAGA 60.106 55.000 20.50 1.10 42.53 2.43
776 833 0.031449 GATCAGACGGCTGGCTAGAC 59.969 60.000 20.50 0.00 42.53 2.59
777 834 0.684479 ATCAGACGGCTGGCTAGACA 60.684 55.000 20.50 0.00 42.53 3.41
778 835 1.153745 CAGACGGCTGGCTAGACAC 60.154 63.158 11.57 0.00 38.51 3.67
780 837 2.675423 ACGGCTGGCTAGACACGA 60.675 61.111 14.94 0.00 0.00 4.35
793 866 1.825474 AGACACGAGAAATCATCCGGT 59.175 47.619 0.00 0.00 0.00 5.28
865 1482 2.436109 GAGCCCACTCCAAGCCAA 59.564 61.111 0.00 0.00 36.90 4.52
866 1483 1.676967 GAGCCCACTCCAAGCCAAG 60.677 63.158 0.00 0.00 36.90 3.61
868 1485 1.676967 GCCCACTCCAAGCCAAGAG 60.677 63.158 0.00 0.00 36.16 2.85
871 1488 1.202927 CCCACTCCAAGCCAAGAGAAA 60.203 52.381 1.80 0.00 34.13 2.52
872 1489 2.586425 CCACTCCAAGCCAAGAGAAAA 58.414 47.619 1.80 0.00 34.13 2.29
874 1491 2.294512 CACTCCAAGCCAAGAGAAAACC 59.705 50.000 1.80 0.00 34.13 3.27
875 1492 1.889170 CTCCAAGCCAAGAGAAAACCC 59.111 52.381 0.00 0.00 31.43 4.11
876 1493 0.969149 CCAAGCCAAGAGAAAACCCC 59.031 55.000 0.00 0.00 0.00 4.95
877 1494 1.481242 CCAAGCCAAGAGAAAACCCCT 60.481 52.381 0.00 0.00 0.00 4.79
878 1495 1.615392 CAAGCCAAGAGAAAACCCCTG 59.385 52.381 0.00 0.00 0.00 4.45
879 1496 1.149101 AGCCAAGAGAAAACCCCTGA 58.851 50.000 0.00 0.00 0.00 3.86
895 1515 1.943116 CTGACTCCAGCTCACTCCGG 61.943 65.000 0.00 0.00 33.07 5.14
896 1516 1.979693 GACTCCAGCTCACTCCGGT 60.980 63.158 0.00 0.00 0.00 5.28
897 1517 0.680280 GACTCCAGCTCACTCCGGTA 60.680 60.000 0.00 0.00 0.00 4.02
898 1518 0.681564 ACTCCAGCTCACTCCGGTAG 60.682 60.000 0.00 0.00 0.00 3.18
899 1519 2.010582 CTCCAGCTCACTCCGGTAGC 62.011 65.000 0.00 7.05 36.48 3.58
900 1520 2.351244 CCAGCTCACTCCGGTAGCA 61.351 63.158 18.24 0.00 38.75 3.49
901 1521 1.140589 CAGCTCACTCCGGTAGCAG 59.859 63.158 18.24 9.95 38.75 4.24
902 1522 1.304547 AGCTCACTCCGGTAGCAGT 60.305 57.895 18.24 5.79 38.75 4.40
903 1523 1.139947 GCTCACTCCGGTAGCAGTC 59.860 63.158 0.00 0.00 36.26 3.51
904 1524 1.595993 GCTCACTCCGGTAGCAGTCA 61.596 60.000 0.00 0.00 36.26 3.41
905 1525 0.171455 CTCACTCCGGTAGCAGTCAC 59.829 60.000 0.00 0.00 0.00 3.67
906 1526 0.251209 TCACTCCGGTAGCAGTCACT 60.251 55.000 0.00 0.00 0.00 3.41
907 1527 0.171455 CACTCCGGTAGCAGTCACTC 59.829 60.000 0.00 0.00 0.00 3.51
908 1528 0.251209 ACTCCGGTAGCAGTCACTCA 60.251 55.000 0.00 0.00 0.00 3.41
909 1529 1.107114 CTCCGGTAGCAGTCACTCAT 58.893 55.000 0.00 0.00 0.00 2.90
910 1530 1.066303 CTCCGGTAGCAGTCACTCATC 59.934 57.143 0.00 0.00 0.00 2.92
911 1531 0.817654 CCGGTAGCAGTCACTCATCA 59.182 55.000 0.00 0.00 0.00 3.07
912 1532 1.469940 CCGGTAGCAGTCACTCATCAC 60.470 57.143 0.00 0.00 0.00 3.06
913 1533 1.202348 CGGTAGCAGTCACTCATCACA 59.798 52.381 0.00 0.00 0.00 3.58
914 1534 2.733542 CGGTAGCAGTCACTCATCACAG 60.734 54.545 0.00 0.00 0.00 3.66
915 1535 2.266554 GTAGCAGTCACTCATCACAGC 58.733 52.381 0.00 0.00 0.00 4.40
916 1536 0.036577 AGCAGTCACTCATCACAGCC 60.037 55.000 0.00 0.00 0.00 4.85
917 1537 0.321034 GCAGTCACTCATCACAGCCA 60.321 55.000 0.00 0.00 0.00 4.75
918 1538 1.436600 CAGTCACTCATCACAGCCAC 58.563 55.000 0.00 0.00 0.00 5.01
919 1539 1.001746 CAGTCACTCATCACAGCCACT 59.998 52.381 0.00 0.00 0.00 4.00
920 1540 1.001746 AGTCACTCATCACAGCCACTG 59.998 52.381 0.00 0.00 37.52 3.66
921 1541 0.321034 TCACTCATCACAGCCACTGC 60.321 55.000 0.00 0.00 34.37 4.40
922 1542 0.604511 CACTCATCACAGCCACTGCA 60.605 55.000 0.00 0.00 41.13 4.41
1025 1645 4.527583 CCTGCTCCTCCTGCTCGC 62.528 72.222 0.00 0.00 0.00 5.03
1552 2460 2.364186 TGCTCTGCCCGATCCTCA 60.364 61.111 0.00 0.00 0.00 3.86
1841 2770 2.504244 CAACGAGACCGGAGCGAC 60.504 66.667 9.46 0.00 40.78 5.19
1842 2771 4.099170 AACGAGACCGGAGCGACG 62.099 66.667 9.46 13.29 40.78 5.12
1979 2908 4.447342 CATGAAGCCCGGCCCCTT 62.447 66.667 5.55 0.00 0.00 3.95
2230 3188 1.514678 TTTGTCCGCGCTTTGCATCT 61.515 50.000 5.56 0.00 46.97 2.90
2263 3221 6.096705 TCTGAACTGAAAAAGCTCCATTTTGA 59.903 34.615 0.00 0.00 32.81 2.69
2268 3226 7.203218 ACTGAAAAAGCTCCATTTTGAACTAC 58.797 34.615 0.00 0.00 32.81 2.73
2409 3374 6.707440 TTGCTTGATCCAAAACTCTGTTTA 57.293 33.333 0.00 0.00 0.00 2.01
2413 3378 6.583806 GCTTGATCCAAAACTCTGTTTATGTG 59.416 38.462 0.00 0.00 0.00 3.21
2419 3384 8.322906 TCCAAAACTCTGTTTATGTGATGTAG 57.677 34.615 0.00 0.00 0.00 2.74
2420 3385 7.936847 TCCAAAACTCTGTTTATGTGATGTAGT 59.063 33.333 0.00 0.00 0.00 2.73
2424 3389 9.998106 AAACTCTGTTTATGTGATGTAGTAAGT 57.002 29.630 0.00 0.00 0.00 2.24
2533 4918 7.375834 TCACTCATTTCAGTTCGTATGTAGTT 58.624 34.615 0.00 0.00 0.00 2.24
2536 4921 7.328737 ACTCATTTCAGTTCGTATGTAGTTCAC 59.671 37.037 0.00 0.00 0.00 3.18
2674 5062 7.431084 GCCATACAATACAAAACTATGAAACCG 59.569 37.037 0.00 0.00 0.00 4.44
2681 5210 8.851541 ATACAAAACTATGAAACCGTAAAGGA 57.148 30.769 0.00 0.00 45.00 3.36
2687 5216 4.903045 ATGAAACCGTAAAGGAGGAGAA 57.097 40.909 0.00 0.00 45.00 2.87
2693 5222 2.299297 CCGTAAAGGAGGAGAACAGTGT 59.701 50.000 0.00 0.00 45.00 3.55
2717 5246 6.588756 GTCAAGTGACCTGTAATCATAAACGA 59.411 38.462 0.00 0.00 39.07 3.85
2757 5286 2.158623 TGACCTGTCTTCATGTTGGCTT 60.159 45.455 0.00 0.00 0.00 4.35
2761 5290 2.030371 TGTCTTCATGTTGGCTTTGCA 58.970 42.857 0.00 0.00 0.00 4.08
2764 5293 1.068895 CTTCATGTTGGCTTTGCACCA 59.931 47.619 0.00 0.00 34.65 4.17
2922 5487 4.229353 TGGAAGGATATGTGTGGATGGAAA 59.771 41.667 0.00 0.00 0.00 3.13
2983 5549 0.600057 CCTGGTTTCTTGAAGCCTGC 59.400 55.000 15.35 0.00 34.86 4.85
3013 5579 9.070179 GGAAAAACTATTTTGTCCTTAGGTGTA 57.930 33.333 7.38 0.00 38.83 2.90
3046 5613 1.811965 TCCAATCTGCCATGTTGTTCG 59.188 47.619 0.00 0.00 0.00 3.95
3073 5640 3.218453 TGTGGTCTTGTAATTGGTGGTG 58.782 45.455 0.00 0.00 0.00 4.17
3119 5700 7.435192 GTCATTAAACCAGACACTTCTTTTTGG 59.565 37.037 0.00 0.00 32.68 3.28
3193 5834 0.461548 TCGCTGGCTCCAATACAGAG 59.538 55.000 0.00 0.00 34.21 3.35
3257 5898 7.427989 AGTAAAATACTCCCTCCGTATCAAA 57.572 36.000 0.00 0.00 32.47 2.69
3289 5930 6.519382 ACGTTTTTGTAGTCTAGTTTAGCCT 58.481 36.000 0.00 0.00 0.00 4.58
3290 5931 7.661040 ACGTTTTTGTAGTCTAGTTTAGCCTA 58.339 34.615 0.00 0.00 0.00 3.93
3341 6021 8.475639 AGGTAGTACATATGTTCGTTGAAAGAT 58.524 33.333 14.77 0.00 0.00 2.40
3357 6037 8.843733 CGTTGAAAGATCTGTTTTGACAATATG 58.156 33.333 0.00 0.00 0.00 1.78
3633 8024 7.691993 AGGTGGTCTTATATATTCCACACTT 57.308 36.000 21.79 11.42 46.96 3.16
3636 8027 6.645415 GTGGTCTTATATATTCCACACTTCCG 59.355 42.308 18.38 0.00 45.22 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.075682 TGTCCGTAATGCTGATTTGGAAA 58.924 39.130 0.00 0.00 30.69 3.13
2 3 3.006940 GTGTCCGTAATGCTGATTTGGA 58.993 45.455 0.00 0.00 0.00 3.53
3 4 2.097466 GGTGTCCGTAATGCTGATTTGG 59.903 50.000 0.00 0.00 0.00 3.28
4 5 2.746904 TGGTGTCCGTAATGCTGATTTG 59.253 45.455 0.00 0.00 0.00 2.32
11 12 1.303091 GGTGGTGGTGTCCGTAATGC 61.303 60.000 0.00 0.00 0.00 3.56
26 27 2.814805 ATTGTGAAGGATGAGGGTGG 57.185 50.000 0.00 0.00 0.00 4.61
29 30 9.971922 GAAAAATATAATTGTGAAGGATGAGGG 57.028 33.333 0.00 0.00 0.00 4.30
81 82 2.504367 GGATCCCGATACATTTGTGGG 58.496 52.381 0.00 0.00 41.43 4.61
113 114 0.746923 GGGCTATTGTTCGTGGACCC 60.747 60.000 0.00 0.00 0.00 4.46
145 146 0.394899 GGAGAGGGCATTTGGAGTGG 60.395 60.000 0.00 0.00 0.00 4.00
165 166 3.836365 AGAAGATTCTAGGAAGGCTGC 57.164 47.619 0.00 0.00 35.34 5.25
180 181 7.509546 AGTCTCTTTGTCCAAATACAAGAAGA 58.490 34.615 0.00 0.00 40.29 2.87
206 207 5.258051 TCCGAGCCAAAAGGTAACATAAAT 58.742 37.500 0.00 0.00 41.41 1.40
209 210 3.516300 TCTCCGAGCCAAAAGGTAACATA 59.484 43.478 0.00 0.00 41.41 2.29
240 246 2.300152 TGTCTATCCTCATTGGCCGATC 59.700 50.000 1.06 0.00 35.26 3.69
262 268 4.565564 GTCAATGGACACAACTACCGATAC 59.434 45.833 0.00 0.00 43.73 2.24
336 361 2.273370 TTACGTGCTTCACCGATCTC 57.727 50.000 0.00 0.00 0.00 2.75
343 368 6.771076 TCACAATGATATTTACGTGCTTCAC 58.229 36.000 0.00 0.00 0.00 3.18
354 379 4.478317 TCCCAGGGTCTCACAATGATATTT 59.522 41.667 5.01 0.00 0.00 1.40
376 401 4.836125 TGACACTCTTTCTTTGGCATTC 57.164 40.909 0.00 0.00 0.00 2.67
377 402 5.596836 TTTGACACTCTTTCTTTGGCATT 57.403 34.783 0.00 0.00 0.00 3.56
401 426 2.773661 AGTGCCATCACATGACCTATGA 59.226 45.455 0.00 0.00 45.49 2.15
404 429 1.407299 GCAGTGCCATCACATGACCTA 60.407 52.381 2.85 0.00 45.49 3.08
410 435 2.915349 CTAGAAGCAGTGCCATCACAT 58.085 47.619 12.58 0.00 45.49 3.21
440 465 4.809193 ACTAAGATCATACAGGAGAGCCA 58.191 43.478 0.00 0.00 36.29 4.75
449 474 5.997746 GCAAGGGCAATACTAAGATCATACA 59.002 40.000 0.00 0.00 40.72 2.29
519 558 4.396522 AGGGCTTCTCAATATGCTTGATC 58.603 43.478 0.00 0.00 0.00 2.92
523 562 4.516652 AAGAGGGCTTCTCAATATGCTT 57.483 40.909 0.00 0.00 44.81 3.91
537 576 3.339141 CCACTTGAAGAAGTAAGAGGGC 58.661 50.000 0.00 0.00 40.68 5.19
558 599 1.001860 TGGGCATAACCAAGCTTTTGC 59.998 47.619 0.00 1.38 43.54 3.68
587 629 1.725706 CAAAGAGCACTTGAGAGAGCG 59.274 52.381 0.00 0.00 43.25 5.03
600 642 1.668751 TCCACGTGTTTGACAAAGAGC 59.331 47.619 15.65 0.00 0.00 4.09
608 651 0.462937 CCAGTGGTCCACGTGTTTGA 60.463 55.000 16.44 1.38 39.64 2.69
639 682 4.091800 GCATCTGCACGCAACAATATTTTT 59.908 37.500 0.00 0.00 41.59 1.94
640 683 3.613737 GCATCTGCACGCAACAATATTTT 59.386 39.130 0.00 0.00 41.59 1.82
644 687 0.451383 GGCATCTGCACGCAACAATA 59.549 50.000 4.33 0.00 44.36 1.90
645 688 1.213537 GGCATCTGCACGCAACAAT 59.786 52.632 4.33 0.00 44.36 2.71
647 690 2.594013 TGGCATCTGCACGCAACA 60.594 55.556 4.33 0.00 44.36 3.33
648 691 2.126734 GTGGCATCTGCACGCAAC 60.127 61.111 4.33 0.00 44.36 4.17
651 694 3.197790 ATCGTGGCATCTGCACGC 61.198 61.111 16.74 7.74 44.36 5.34
652 695 0.805711 TACATCGTGGCATCTGCACG 60.806 55.000 15.93 15.93 44.36 5.34
653 696 0.933097 CTACATCGTGGCATCTGCAC 59.067 55.000 4.33 0.29 44.36 4.57
654 697 0.823460 TCTACATCGTGGCATCTGCA 59.177 50.000 4.33 0.00 44.36 4.41
666 718 2.408050 GCACCATCGACCATCTACATC 58.592 52.381 0.00 0.00 0.00 3.06
668 720 0.102300 CGCACCATCGACCATCTACA 59.898 55.000 0.00 0.00 0.00 2.74
683 735 2.513065 CTTTCATCCACCACGCGCAC 62.513 60.000 5.73 0.00 0.00 5.34
717 769 3.181521 CGATCGCAGCAAATTGTTGTCTA 60.182 43.478 11.28 0.00 37.06 2.59
719 771 1.906966 CGATCGCAGCAAATTGTTGTC 59.093 47.619 11.28 3.51 37.06 3.18
721 773 2.245795 TCGATCGCAGCAAATTGTTG 57.754 45.000 11.09 5.43 37.83 3.33
723 775 2.478370 CCATTCGATCGCAGCAAATTGT 60.478 45.455 11.09 0.00 0.00 2.71
724 776 2.114056 CCATTCGATCGCAGCAAATTG 58.886 47.619 11.09 0.00 0.00 2.32
725 777 1.534595 GCCATTCGATCGCAGCAAATT 60.535 47.619 11.09 0.00 0.00 1.82
761 818 2.701780 CGTGTCTAGCCAGCCGTCT 61.702 63.158 0.00 0.00 0.00 4.18
772 829 3.021695 ACCGGATGATTTCTCGTGTCTA 58.978 45.455 9.46 0.00 0.00 2.59
773 830 1.825474 ACCGGATGATTTCTCGTGTCT 59.175 47.619 9.46 0.00 0.00 3.41
774 831 2.295253 ACCGGATGATTTCTCGTGTC 57.705 50.000 9.46 0.00 0.00 3.67
775 832 2.742053 CAAACCGGATGATTTCTCGTGT 59.258 45.455 9.46 0.00 0.00 4.49
776 833 3.000041 TCAAACCGGATGATTTCTCGTG 59.000 45.455 9.46 0.00 0.00 4.35
777 834 3.328382 TCAAACCGGATGATTTCTCGT 57.672 42.857 9.46 0.00 0.00 4.18
778 835 4.882671 AATCAAACCGGATGATTTCTCG 57.117 40.909 24.75 1.09 43.19 4.04
793 866 1.094785 GGCGGCTGCTAGAAATCAAA 58.905 50.000 18.85 0.00 42.25 2.69
800 873 0.108329 GTACAAAGGCGGCTGCTAGA 60.108 55.000 18.85 0.00 42.25 2.43
827 900 0.668706 CCTGGTGAGTGCTCTGTTCG 60.669 60.000 0.00 0.00 0.00 3.95
831 904 2.433838 CGCCTGGTGAGTGCTCTG 60.434 66.667 0.00 0.00 0.00 3.35
832 905 2.601666 TCGCCTGGTGAGTGCTCT 60.602 61.111 5.70 0.00 0.00 4.09
833 906 2.125753 CTCGCCTGGTGAGTGCTC 60.126 66.667 25.58 0.00 35.69 4.26
834 907 4.385405 GCTCGCCTGGTGAGTGCT 62.385 66.667 31.54 0.00 41.62 4.40
838 911 4.767255 GTGGGCTCGCCTGGTGAG 62.767 72.222 28.64 28.64 42.38 3.51
840 913 4.767255 GAGTGGGCTCGCCTGGTG 62.767 72.222 8.00 0.00 36.10 4.17
865 1482 1.981495 CTGGAGTCAGGGGTTTTCTCT 59.019 52.381 0.00 0.00 37.36 3.10
866 1483 1.611936 GCTGGAGTCAGGGGTTTTCTC 60.612 57.143 0.00 0.00 41.19 2.87
868 1485 0.402121 AGCTGGAGTCAGGGGTTTTC 59.598 55.000 0.00 0.00 41.19 2.29
871 1488 1.152030 TGAGCTGGAGTCAGGGGTT 60.152 57.895 0.00 0.00 41.19 4.11
872 1489 1.915769 GTGAGCTGGAGTCAGGGGT 60.916 63.158 0.00 0.00 41.19 4.95
874 1491 1.612395 GGAGTGAGCTGGAGTCAGGG 61.612 65.000 0.00 0.00 41.19 4.45
875 1492 1.896694 GGAGTGAGCTGGAGTCAGG 59.103 63.158 0.00 0.00 41.19 3.86
876 1493 1.510383 CGGAGTGAGCTGGAGTCAG 59.490 63.158 0.00 0.00 43.64 3.51
877 1494 1.979155 CCGGAGTGAGCTGGAGTCA 60.979 63.158 0.00 0.00 36.35 3.41
878 1495 0.680280 TACCGGAGTGAGCTGGAGTC 60.680 60.000 9.46 0.00 37.74 3.36
879 1496 0.681564 CTACCGGAGTGAGCTGGAGT 60.682 60.000 9.46 0.00 37.74 3.85
895 1515 2.266554 GCTGTGATGAGTGACTGCTAC 58.733 52.381 0.00 0.00 34.49 3.58
896 1516 1.205655 GGCTGTGATGAGTGACTGCTA 59.794 52.381 0.00 0.00 36.80 3.49
897 1517 0.036577 GGCTGTGATGAGTGACTGCT 60.037 55.000 0.00 0.00 36.80 4.24
898 1518 0.321034 TGGCTGTGATGAGTGACTGC 60.321 55.000 0.00 0.00 36.08 4.40
899 1519 1.001746 AGTGGCTGTGATGAGTGACTG 59.998 52.381 0.00 0.00 0.00 3.51
900 1520 1.001746 CAGTGGCTGTGATGAGTGACT 59.998 52.381 0.00 0.00 0.00 3.41
901 1521 1.436600 CAGTGGCTGTGATGAGTGAC 58.563 55.000 0.00 0.00 0.00 3.67
902 1522 0.321034 GCAGTGGCTGTGATGAGTGA 60.321 55.000 0.00 0.00 36.96 3.41
903 1523 0.604511 TGCAGTGGCTGTGATGAGTG 60.605 55.000 0.00 0.00 41.91 3.51
904 1524 0.604780 GTGCAGTGGCTGTGATGAGT 60.605 55.000 0.00 0.00 41.91 3.41
905 1525 0.604511 TGTGCAGTGGCTGTGATGAG 60.605 55.000 0.00 0.00 41.91 2.90
906 1526 0.886043 GTGTGCAGTGGCTGTGATGA 60.886 55.000 0.00 0.00 41.91 2.92
907 1527 1.167781 TGTGTGCAGTGGCTGTGATG 61.168 55.000 0.00 0.00 41.91 3.07
908 1528 0.466007 TTGTGTGCAGTGGCTGTGAT 60.466 50.000 0.00 0.00 41.91 3.06
909 1529 0.466007 ATTGTGTGCAGTGGCTGTGA 60.466 50.000 0.00 0.00 41.91 3.58
910 1530 0.039798 GATTGTGTGCAGTGGCTGTG 60.040 55.000 0.00 0.00 41.91 3.66
911 1531 0.179009 AGATTGTGTGCAGTGGCTGT 60.179 50.000 0.00 0.00 41.91 4.40
912 1532 0.520404 GAGATTGTGTGCAGTGGCTG 59.480 55.000 0.00 0.00 41.91 4.85
913 1533 0.109153 TGAGATTGTGTGCAGTGGCT 59.891 50.000 0.00 0.00 41.91 4.75
914 1534 0.239347 GTGAGATTGTGTGCAGTGGC 59.761 55.000 0.00 0.00 41.68 5.01
915 1535 1.802960 GAGTGAGATTGTGTGCAGTGG 59.197 52.381 0.00 0.00 0.00 4.00
916 1536 2.222678 GTGAGTGAGATTGTGTGCAGTG 59.777 50.000 0.00 0.00 0.00 3.66
917 1537 2.103771 AGTGAGTGAGATTGTGTGCAGT 59.896 45.455 0.00 0.00 0.00 4.40
918 1538 2.735663 GAGTGAGTGAGATTGTGTGCAG 59.264 50.000 0.00 0.00 0.00 4.41
919 1539 2.548707 GGAGTGAGTGAGATTGTGTGCA 60.549 50.000 0.00 0.00 0.00 4.57
920 1540 2.072298 GGAGTGAGTGAGATTGTGTGC 58.928 52.381 0.00 0.00 0.00 4.57
921 1541 3.324117 CTGGAGTGAGTGAGATTGTGTG 58.676 50.000 0.00 0.00 0.00 3.82
922 1542 2.289320 GCTGGAGTGAGTGAGATTGTGT 60.289 50.000 0.00 0.00 0.00 3.72
1071 1691 2.125310 CGGCCGTAGTTGATGCCA 60.125 61.111 19.50 0.00 44.22 4.92
1629 2537 2.697761 GGCGTACTCGAGCTCCACA 61.698 63.158 13.61 0.00 39.71 4.17
1847 2776 3.919973 TTGTACCTCGCGGCGTTCC 62.920 63.158 22.90 7.68 0.00 3.62
1848 2777 2.431260 TTGTACCTCGCGGCGTTC 60.431 61.111 22.90 9.64 0.00 3.95
1849 2778 2.735857 GTTGTACCTCGCGGCGTT 60.736 61.111 22.90 10.43 0.00 4.84
1979 2908 2.126618 CGTAGTTGCGCTCCGACA 60.127 61.111 9.73 0.00 0.00 4.35
2088 3026 3.830192 CTGCCGGCAATGCTTCCC 61.830 66.667 32.09 0.00 0.00 3.97
2230 3188 7.040409 GGAGCTTTTTCAGTTCAGAAAGGAATA 60.040 37.037 0.00 0.00 38.60 1.75
2268 3226 7.904461 CACTTTTACCATGAAAACTTTGCAAAG 59.096 33.333 32.53 32.53 41.73 2.77
2413 3378 8.150945 ACCATGGTTATGATGACTTACTACATC 58.849 37.037 13.00 0.00 41.94 3.06
2419 3384 9.950680 CAAATTACCATGGTTATGATGACTTAC 57.049 33.333 25.38 0.00 36.36 2.34
2420 3385 9.913310 TCAAATTACCATGGTTATGATGACTTA 57.087 29.630 25.38 4.18 36.36 2.24
2422 3387 8.821686 TTCAAATTACCATGGTTATGATGACT 57.178 30.769 25.38 0.00 36.36 3.41
2423 3388 9.520204 CTTTCAAATTACCATGGTTATGATGAC 57.480 33.333 25.38 0.00 36.36 3.06
2424 3389 9.253832 ACTTTCAAATTACCATGGTTATGATGA 57.746 29.630 25.38 22.12 36.36 2.92
2674 5062 4.602340 TGACACTGTTCTCCTCCTTTAC 57.398 45.455 0.00 0.00 0.00 2.01
2681 5210 2.103263 GGTCACTTGACACTGTTCTCCT 59.897 50.000 11.40 0.00 46.47 3.69
2693 5222 6.693466 TCGTTTATGATTACAGGTCACTTGA 58.307 36.000 0.00 0.00 0.00 3.02
2717 5246 6.360618 AGGTCACTGAGAATTTGTTCTTCTT 58.639 36.000 0.00 0.00 33.18 2.52
2764 5293 2.559668 CACATCAGCAGGTGACCAAAAT 59.440 45.455 3.92 0.00 38.28 1.82
2922 5487 0.980423 GACACCAGAGGCTTCCTTCT 59.020 55.000 0.00 0.00 31.76 2.85
2983 5549 8.088365 CCTAAGGACAAAATAGTTTTTCCAAGG 58.912 37.037 19.76 19.51 34.82 3.61
3013 5579 4.102367 GGCAGATTGGAGAGAAAGGAGTAT 59.898 45.833 0.00 0.00 0.00 2.12
3046 5613 4.522789 ACCAATTACAAGACCACATCAACC 59.477 41.667 0.00 0.00 0.00 3.77
3073 5640 4.081642 TGACACTGACTAACCCATTAGCTC 60.082 45.833 0.00 0.00 41.48 4.09
3119 5700 5.756195 TGCATTGCATGATTACTAGGAAC 57.244 39.130 7.38 0.00 31.71 3.62
3193 5834 7.880059 ATTGCTTCTAAAATTTGAAGTGCTC 57.120 32.000 15.74 4.43 40.53 4.26
3257 5898 9.538508 AACTAGACTACAAAAACGTCTTGTATT 57.461 29.630 18.34 14.65 40.83 1.89
3314 5955 8.308931 TCTTTCAACGAACATATGTACTACCTT 58.691 33.333 9.21 0.00 0.00 3.50
3341 6021 6.899393 AAAGGAGCATATTGTCAAAACAGA 57.101 33.333 0.00 0.00 36.57 3.41
3357 6037 3.956744 ACATAGAACTGGGAAAAGGAGC 58.043 45.455 0.00 0.00 0.00 4.70
3624 8015 1.686355 ATTGTTGCGGAAGTGTGGAA 58.314 45.000 0.00 0.00 0.00 3.53
3633 8024 1.807981 CGCGGAGTATTGTTGCGGA 60.808 57.895 0.00 0.00 44.65 5.54
3636 8027 2.222953 CCTTAACGCGGAGTATTGTTGC 60.223 50.000 12.47 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.