Multiple sequence alignment - TraesCS3D01G233300

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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 TraesCS3D01G233300 chr3D 100.000 4200 0 0 1 4200 321876661 321872462 0.000000e+00 7757.0
1 TraesCS3D01G233300 chr3D 89.583 144 15 0 2943 3086 508465700 508465557 2.580000e-42 183.0
2 TraesCS3D01G233300 chr3D 83.240 179 15 7 2780 2945 508466646 508466470 2.620000e-32 150.0
3 TraesCS3D01G233300 chr3D 85.567 97 4 2 3148 3244 606777910 606777996 4.470000e-15 93.5
4 TraesCS3D01G233300 chr2D 92.471 2351 89 44 971 3287 634651744 634649448 0.000000e+00 3280.0
5 TraesCS3D01G233300 chr2D 84.272 604 56 15 3620 4200 634647636 634647049 1.710000e-153 553.0
6 TraesCS3D01G233300 chr2D 96.117 309 11 1 3275 3583 634648048 634647741 1.740000e-138 503.0
7 TraesCS3D01G233300 chr2D 80.786 229 32 7 262 489 11844092 11843875 7.220000e-38 169.0
8 TraesCS3D01G233300 chr2D 94.792 96 4 1 483 577 263240491 263240586 9.410000e-32 148.0
9 TraesCS3D01G233300 chr2D 88.596 114 11 2 479 592 592207426 592207315 2.040000e-28 137.0
10 TraesCS3D01G233300 chr3A 94.914 2045 57 21 2193 4200 402133640 402135674 0.000000e+00 3157.0
11 TraesCS3D01G233300 chr3A 91.529 1629 68 36 589 2194 402131384 402132965 0.000000e+00 2180.0
12 TraesCS3D01G233300 chr3A 90.606 330 11 5 1 320 402130970 402131289 1.810000e-113 420.0
13 TraesCS3D01G233300 chr1B 92.960 1605 57 20 1997 3583 637911338 637912904 0.000000e+00 2287.0
14 TraesCS3D01G233300 chr1B 93.000 100 5 2 478 577 352884943 352885040 1.220000e-30 145.0
15 TraesCS3D01G233300 chr1B 89.474 114 8 4 480 591 74411505 74411616 1.570000e-29 141.0
16 TraesCS3D01G233300 chr3B 92.669 1596 70 22 2015 3583 397675913 397677488 0.000000e+00 2255.0
17 TraesCS3D01G233300 chr3B 88.522 1394 64 53 620 1987 397674595 397675918 0.000000e+00 1600.0
18 TraesCS3D01G233300 chr3B 85.075 603 57 11 3623 4200 397677597 397678191 6.050000e-163 584.0
19 TraesCS3D01G233300 chr3B 93.906 361 14 4 1 358 397674101 397674456 4.780000e-149 538.0
20 TraesCS3D01G233300 chr3B 97.753 89 2 0 489 577 421670498 421670586 2.020000e-33 154.0
21 TraesCS3D01G233300 chr3B 97.727 88 2 0 486 573 489058797 489058884 7.270000e-33 152.0
22 TraesCS3D01G233300 chr1D 93.653 835 40 8 2559 3386 462946843 462947671 0.000000e+00 1236.0
23 TraesCS3D01G233300 chr1D 83.748 603 59 15 3620 4200 462965613 462966198 6.180000e-148 534.0
24 TraesCS3D01G233300 chr1D 97.115 208 6 0 3376 3583 462965301 462965508 6.680000e-93 351.0
25 TraesCS3D01G233300 chr6A 84.760 479 50 9 2645 3109 508249581 508249112 3.830000e-125 459.0
26 TraesCS3D01G233300 chr6D 84.548 343 30 11 2597 2924 367749855 367749521 6.780000e-83 318.0
27 TraesCS3D01G233300 chr6D 79.654 231 31 8 260 489 462206846 462207061 7.270000e-33 152.0
28 TraesCS3D01G233300 chr7D 85.227 264 27 4 2780 3032 41303535 41303797 1.160000e-65 261.0
29 TraesCS3D01G233300 chr7D 87.442 215 16 3 3030 3244 41306157 41306360 1.950000e-58 237.0
30 TraesCS3D01G233300 chr5A 79.762 252 37 9 242 489 404557294 404557053 2.010000e-38 171.0
31 TraesCS3D01G233300 chr6B 87.324 142 13 4 260 400 501774170 501774033 1.560000e-34 158.0
32 TraesCS3D01G233300 chr6B 93.000 100 7 0 481 580 411556659 411556560 3.380000e-31 147.0
33 TraesCS3D01G233300 chr6B 79.556 225 24 11 260 480 73172312 73172518 1.570000e-29 141.0
34 TraesCS3D01G233300 chrUn 97.753 89 1 1 485 573 37006357 37006444 7.270000e-33 152.0
35 TraesCS3D01G233300 chr2B 92.523 107 4 3 468 573 136179716 136179819 2.620000e-32 150.0
36 TraesCS3D01G233300 chr2A 75.893 224 42 10 260 481 621133544 621133757 2.070000e-18 104.0
37 TraesCS3D01G233300 chr7A 89.583 48 4 1 257 303 55008941 55008988 4.530000e-05 60.2
38 TraesCS3D01G233300 chr7A 89.583 48 4 1 257 303 55017800 55017847 4.530000e-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 TraesCS3D01G233300 chr3D 321872462 321876661 4199 True 7757.000000 7757 100.000000 1 4200 1 chr3D.!!$R1 4199
1 TraesCS3D01G233300 chr2D 634647049 634651744 4695 True 1445.333333 3280 90.953333 971 4200 3 chr2D.!!$R3 3229
2 TraesCS3D01G233300 chr3A 402130970 402135674 4704 False 1919.000000 3157 92.349667 1 4200 3 chr3A.!!$F1 4199
3 TraesCS3D01G233300 chr1B 637911338 637912904 1566 False 2287.000000 2287 92.960000 1997 3583 1 chr1B.!!$F3 1586
4 TraesCS3D01G233300 chr3B 397674101 397678191 4090 False 1244.250000 2255 90.043000 1 4200 4 chr3B.!!$F3 4199
5 TraesCS3D01G233300 chr1D 462946843 462947671 828 False 1236.000000 1236 93.653000 2559 3386 1 chr1D.!!$F1 827
6 TraesCS3D01G233300 chr1D 462965301 462966198 897 False 442.500000 534 90.431500 3376 4200 2 chr1D.!!$F2 824
7 TraesCS3D01G233300 chr7D 41303535 41306360 2825 False 249.000000 261 86.334500 2780 3244 2 chr7D.!!$F1 464

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
948 1002 0.179116 CAGACCAGCTCACCTGATCG 60.179 60.0 0.72 0.00 44.64 3.69 F
1510 1596 0.041926 TAGACACACGACACGACACG 60.042 55.0 0.00 0.00 0.00 4.49 F
2227 3014 0.249573 TTGGCTGCAGCTTTGCTTTC 60.250 50.0 35.82 18.32 36.40 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2489 3305 0.107312 CCCAAGCCTCACTGGAGATG 60.107 60.0 0.0 0.00 44.26 2.90 R
2740 3565 0.620556 TCAATCTTGGTCCTCAGGGC 59.379 55.0 0.0 0.00 0.00 5.19 R
3683 8387 0.809385 CTTGGCAGCCAGATCAACAG 59.191 55.0 15.5 3.15 33.81 3.16 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
161 166 2.376518 TCTCCACTGCCAAGAAAAGGAT 59.623 45.455 0.00 0.00 0.00 3.24
178 183 6.570672 AAAGGATGCATATATTCTGCTGTG 57.429 37.500 0.00 0.00 40.34 3.66
222 227 1.431496 ACGTACGCCCATGTTTGTAC 58.569 50.000 16.72 7.98 35.11 2.90
270 275 1.265454 ACCGGAAGTTAGGGCTCCTG 61.265 60.000 9.46 0.00 34.61 3.86
313 324 9.844257 CATAGGAACTTTTGAGGATTAGAATCT 57.156 33.333 2.44 0.00 41.75 2.40
412 424 8.669055 TTTTGGTACTACTACTTCCCATAAGA 57.331 34.615 0.00 0.00 0.00 2.10
413 425 8.849543 TTTGGTACTACTACTTCCCATAAGAT 57.150 34.615 0.00 0.00 0.00 2.40
414 426 8.849543 TTGGTACTACTACTTCCCATAAGATT 57.150 34.615 0.00 0.00 0.00 2.40
415 427 8.849543 TGGTACTACTACTTCCCATAAGATTT 57.150 34.615 0.00 0.00 0.00 2.17
416 428 8.921205 TGGTACTACTACTTCCCATAAGATTTC 58.079 37.037 0.00 0.00 0.00 2.17
425 437 7.051000 ACTTCCCATAAGATTTCTTCTAGCAC 58.949 38.462 0.00 0.00 37.40 4.40
426 438 6.814954 TCCCATAAGATTTCTTCTAGCACT 57.185 37.500 0.00 0.00 37.40 4.40
442 454 3.471680 AGCACTCACTCAAACCTCTTTC 58.528 45.455 0.00 0.00 0.00 2.62
451 464 6.828273 TCACTCAAACCTCTTTCAAAGAATCA 59.172 34.615 0.48 0.00 37.02 2.57
494 507 9.107177 TGCAATCAAACAATCAAAAATTGTACT 57.893 25.926 4.01 0.00 40.94 2.73
497 510 8.831715 ATCAAACAATCAAAAATTGTACTCCC 57.168 30.769 4.01 0.00 40.94 4.30
499 512 8.141268 TCAAACAATCAAAAATTGTACTCCCTC 58.859 33.333 4.01 0.00 40.94 4.30
500 513 7.839680 AACAATCAAAAATTGTACTCCCTCT 57.160 32.000 4.01 0.00 40.94 3.69
502 515 6.777580 ACAATCAAAAATTGTACTCCCTCTGT 59.222 34.615 1.72 0.00 40.12 3.41
503 516 7.040409 ACAATCAAAAATTGTACTCCCTCTGTC 60.040 37.037 1.72 0.00 40.12 3.51
504 517 5.313712 TCAAAAATTGTACTCCCTCTGTCC 58.686 41.667 0.00 0.00 0.00 4.02
505 518 4.302559 AAAATTGTACTCCCTCTGTCCC 57.697 45.455 0.00 0.00 0.00 4.46
510 523 3.256704 TGTACTCCCTCTGTCCCAAAAT 58.743 45.455 0.00 0.00 0.00 1.82
511 524 4.431378 TGTACTCCCTCTGTCCCAAAATA 58.569 43.478 0.00 0.00 0.00 1.40
512 525 5.036916 TGTACTCCCTCTGTCCCAAAATAT 58.963 41.667 0.00 0.00 0.00 1.28
515 528 6.253946 ACTCCCTCTGTCCCAAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
516 529 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
517 530 6.447084 ACTCCCTCTGTCCCAAAATATAAGAA 59.553 38.462 0.00 0.00 0.00 2.52
518 531 6.659824 TCCCTCTGTCCCAAAATATAAGAAC 58.340 40.000 0.00 0.00 0.00 3.01
521 534 6.598064 CCTCTGTCCCAAAATATAAGAACGTT 59.402 38.462 0.00 0.00 0.00 3.99
522 535 7.120726 CCTCTGTCCCAAAATATAAGAACGTTT 59.879 37.037 0.46 0.00 0.00 3.60
523 536 8.398878 TCTGTCCCAAAATATAAGAACGTTTT 57.601 30.769 0.46 0.00 0.00 2.43
524 537 8.852135 TCTGTCCCAAAATATAAGAACGTTTTT 58.148 29.630 9.22 9.22 0.00 1.94
534 547 9.745323 AATATAAGAACGTTTTTAACACTACGC 57.255 29.630 14.41 0.00 37.51 4.42
535 548 5.723492 AAGAACGTTTTTAACACTACGCT 57.277 34.783 0.46 0.00 37.51 5.07
536 549 6.826893 AAGAACGTTTTTAACACTACGCTA 57.173 33.333 0.46 0.00 37.51 4.26
537 550 6.443876 AGAACGTTTTTAACACTACGCTAG 57.556 37.500 0.46 0.00 37.51 3.42
538 551 5.979517 AGAACGTTTTTAACACTACGCTAGT 59.020 36.000 0.46 0.00 40.28 2.57
549 562 3.709987 ACTACGCTAGTGTCAAAAACGT 58.290 40.909 13.25 1.74 37.69 3.99
550 563 4.114794 ACTACGCTAGTGTCAAAAACGTT 58.885 39.130 13.25 0.00 37.69 3.99
551 564 3.580794 ACGCTAGTGTCAAAAACGTTC 57.419 42.857 2.24 0.00 0.00 3.95
552 565 3.192466 ACGCTAGTGTCAAAAACGTTCT 58.808 40.909 2.24 0.00 0.00 3.01
553 566 3.619929 ACGCTAGTGTCAAAAACGTTCTT 59.380 39.130 2.24 0.00 0.00 2.52
554 567 4.805192 ACGCTAGTGTCAAAAACGTTCTTA 59.195 37.500 2.24 0.00 0.00 2.10
555 568 5.464389 ACGCTAGTGTCAAAAACGTTCTTAT 59.536 36.000 2.24 0.00 0.00 1.73
556 569 6.642131 ACGCTAGTGTCAAAAACGTTCTTATA 59.358 34.615 2.24 0.00 0.00 0.98
557 570 7.330208 ACGCTAGTGTCAAAAACGTTCTTATAT 59.670 33.333 2.24 0.00 0.00 0.86
558 571 8.166706 CGCTAGTGTCAAAAACGTTCTTATATT 58.833 33.333 0.00 0.00 0.00 1.28
563 576 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
564 577 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
565 578 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
566 579 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
567 580 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
568 581 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
569 582 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
573 586 5.657446 TCTTATATTATGGGACGGAGGGAA 58.343 41.667 0.00 0.00 0.00 3.97
576 589 7.563924 TCTTATATTATGGGACGGAGGGAATAG 59.436 40.741 0.00 0.00 0.00 1.73
583 596 2.300437 GGACGGAGGGAATAGGATGAAG 59.700 54.545 0.00 0.00 0.00 3.02
647 660 1.996292 TTCAGAATCCTGCGAACGAG 58.004 50.000 0.00 0.00 40.20 4.18
859 884 0.747283 CCTCTGCATGCCTCCTTCAC 60.747 60.000 16.68 0.00 0.00 3.18
911 937 3.624707 GCTCTCTCTCTTCTTCTCTCCCA 60.625 52.174 0.00 0.00 0.00 4.37
912 938 4.202441 CTCTCTCTCTTCTTCTCTCCCAG 58.798 52.174 0.00 0.00 0.00 4.45
919 945 0.336737 TCTTCTCTCCCAGTCCCTCC 59.663 60.000 0.00 0.00 0.00 4.30
940 994 2.745698 CACCAGCAGACCAGCTCA 59.254 61.111 0.00 0.00 44.54 4.26
941 995 1.670406 CACCAGCAGACCAGCTCAC 60.670 63.158 0.00 0.00 44.54 3.51
942 996 2.046507 CCAGCAGACCAGCTCACC 60.047 66.667 0.00 0.00 44.54 4.02
943 997 2.591072 CCAGCAGACCAGCTCACCT 61.591 63.158 0.00 0.00 44.54 4.00
944 998 1.375652 CAGCAGACCAGCTCACCTG 60.376 63.158 0.00 0.00 44.54 4.00
945 999 1.534959 AGCAGACCAGCTCACCTGA 60.535 57.895 9.27 0.00 42.18 3.86
946 1000 0.908656 AGCAGACCAGCTCACCTGAT 60.909 55.000 9.27 1.22 42.18 2.90
947 1001 0.461693 GCAGACCAGCTCACCTGATC 60.462 60.000 9.27 0.00 44.64 2.92
948 1002 0.179116 CAGACCAGCTCACCTGATCG 60.179 60.000 0.72 0.00 44.64 3.69
949 1003 0.323816 AGACCAGCTCACCTGATCGA 60.324 55.000 0.00 0.00 44.64 3.59
950 1004 0.749649 GACCAGCTCACCTGATCGAT 59.250 55.000 0.00 0.00 44.64 3.59
951 1005 0.749649 ACCAGCTCACCTGATCGATC 59.250 55.000 18.72 18.72 44.64 3.69
952 1006 0.318529 CCAGCTCACCTGATCGATCG 60.319 60.000 20.03 9.36 44.64 3.69
953 1007 0.318529 CAGCTCACCTGATCGATCGG 60.319 60.000 24.71 24.71 44.64 4.18
954 1008 0.753479 AGCTCACCTGATCGATCGGT 60.753 55.000 28.08 26.97 35.26 4.69
955 1009 0.318275 GCTCACCTGATCGATCGGTC 60.318 60.000 27.77 21.50 33.58 4.79
966 1020 3.498676 GATCGGTCGATCCATCACC 57.501 57.895 19.21 0.00 43.71 4.02
967 1021 0.387367 GATCGGTCGATCCATCACCG 60.387 60.000 19.21 17.51 44.83 4.94
968 1022 1.107538 ATCGGTCGATCCATCACCGT 61.108 55.000 20.41 11.49 44.34 4.83
969 1023 1.588932 CGGTCGATCCATCACCGTG 60.589 63.158 16.27 0.00 41.80 4.94
1079 1133 3.933332 GACTCGGTTTTCAGTAAGATGGG 59.067 47.826 0.00 0.00 0.00 4.00
1080 1134 3.326880 ACTCGGTTTTCAGTAAGATGGGT 59.673 43.478 0.00 0.00 0.00 4.51
1081 1135 3.670625 TCGGTTTTCAGTAAGATGGGTG 58.329 45.455 0.00 0.00 0.00 4.61
1082 1136 2.161609 CGGTTTTCAGTAAGATGGGTGC 59.838 50.000 0.00 0.00 0.00 5.01
1083 1137 3.421844 GGTTTTCAGTAAGATGGGTGCT 58.578 45.455 0.00 0.00 0.00 4.40
1084 1138 3.191371 GGTTTTCAGTAAGATGGGTGCTG 59.809 47.826 0.00 0.00 0.00 4.41
1089 1155 0.453390 GTAAGATGGGTGCTGCTTGC 59.547 55.000 0.00 0.00 43.25 4.01
1271 1343 0.240145 CTCCATGTTGCACTGCACTG 59.760 55.000 2.26 2.06 38.71 3.66
1416 1495 9.332502 CAGTAGGAACATATACTCGCTAGATAT 57.667 37.037 0.00 0.00 29.77 1.63
1424 1503 9.247126 ACATATACTCGCTAGATATGTAGTACG 57.753 37.037 15.36 4.99 42.31 3.67
1505 1591 2.095869 AGCTAGTTAGACACACGACACG 60.096 50.000 0.00 0.00 0.00 4.49
1506 1592 2.096069 GCTAGTTAGACACACGACACGA 60.096 50.000 0.00 0.00 0.00 4.35
1507 1593 2.396160 AGTTAGACACACGACACGAC 57.604 50.000 0.00 0.00 0.00 4.34
1508 1594 1.672363 AGTTAGACACACGACACGACA 59.328 47.619 0.00 0.00 0.00 4.35
1509 1595 1.777461 GTTAGACACACGACACGACAC 59.223 52.381 0.00 0.00 0.00 3.67
1510 1596 0.041926 TAGACACACGACACGACACG 60.042 55.000 0.00 0.00 0.00 4.49
1511 1597 1.297819 GACACACGACACGACACGA 60.298 57.895 0.00 0.00 0.00 4.35
1512 1598 1.526617 GACACACGACACGACACGAC 61.527 60.000 0.00 0.00 0.00 4.34
1513 1599 1.584225 CACACGACACGACACGACA 60.584 57.895 0.00 0.00 0.00 4.35
1514 1600 1.584483 ACACGACACGACACGACAC 60.584 57.895 0.00 0.00 0.00 3.67
1515 1601 2.025156 ACGACACGACACGACACC 59.975 61.111 0.00 0.00 0.00 4.16
1593 1679 1.181098 ATGCCACAACCAGAACCAGC 61.181 55.000 0.00 0.00 0.00 4.85
1599 1685 1.321474 CAACCAGAACCAGCACACAT 58.679 50.000 0.00 0.00 0.00 3.21
1600 1686 1.267806 CAACCAGAACCAGCACACATC 59.732 52.381 0.00 0.00 0.00 3.06
1708 1802 7.272037 TCAGTCAGTCGAATATATGCAAGTA 57.728 36.000 0.00 0.00 0.00 2.24
1733 1827 3.181501 TGTTTTGCAAGAGGAACGTGAAG 60.182 43.478 0.00 0.00 0.00 3.02
1739 1833 4.819630 TGCAAGAGGAACGTGAAGTAAAAT 59.180 37.500 0.00 0.00 0.00 1.82
1746 1843 9.939802 AGAGGAACGTGAAGTAAAATTTATAGT 57.060 29.630 0.00 0.00 0.00 2.12
1842 1941 4.279922 CCTAATTTGTTCCTTTTCCACGGT 59.720 41.667 0.00 0.00 0.00 4.83
2227 3014 0.249573 TTGGCTGCAGCTTTGCTTTC 60.250 50.000 35.82 18.32 36.40 2.62
2229 3017 1.364901 GCTGCAGCTTTGCTTTCCA 59.635 52.632 31.33 0.00 36.40 3.53
2244 3032 4.219725 TGCTTTCCACCCAGTTTTTATAGC 59.780 41.667 0.00 0.00 0.00 2.97
2246 3034 2.993937 TCCACCCAGTTTTTATAGCCG 58.006 47.619 0.00 0.00 0.00 5.52
2489 3305 4.304110 TGTACTAATGCTAATAGCGCACC 58.696 43.478 11.47 0.00 46.26 5.01
2616 3435 2.567615 CCCTATTACCCTCAGCGCTATT 59.432 50.000 10.99 0.00 0.00 1.73
2837 3663 5.509498 TGGAAGAGGTTAGCATTGCTATTT 58.491 37.500 18.62 7.81 41.01 1.40
2838 3664 5.951747 TGGAAGAGGTTAGCATTGCTATTTT 59.048 36.000 18.62 6.27 41.01 1.82
2950 3797 0.024238 CGACGAGGTAGTCACGTACG 59.976 60.000 15.01 15.01 40.98 3.67
3077 6289 9.731819 CCACATGATCATTATTTTTCTTCTGAG 57.268 33.333 5.16 0.00 0.00 3.35
3434 8066 5.815740 ACCACACCAGTAATTTATGACGATC 59.184 40.000 0.00 0.00 0.00 3.69
3683 8387 4.253685 TCAAGATCAACTTCCACCGAATC 58.746 43.478 0.00 0.00 36.61 2.52
3776 8483 0.935898 GTCATTGCTCAGCGATCCAG 59.064 55.000 0.00 0.00 28.96 3.86
3823 8530 2.632028 TGTTTGGGGATCAACATTGTGG 59.368 45.455 0.00 0.00 34.67 4.17
3846 8553 6.205464 TGGTGAAAGTCTGAATGATTGAAGAC 59.795 38.462 8.74 8.74 39.47 3.01
3892 8599 5.477984 ACTGCACAAAGGAACACATGATTAT 59.522 36.000 0.00 0.00 0.00 1.28
3927 8636 6.042781 ACATCCCATATACCGTAAACTGTCAT 59.957 38.462 0.00 0.00 0.00 3.06
3941 8650 3.225104 ACTGTCATTTGCATGTTGGTCT 58.775 40.909 0.00 0.00 0.00 3.85
4007 8716 7.805071 CACAAAGAAGACTTATCACATCAAACC 59.195 37.037 0.00 0.00 35.05 3.27
4071 8801 5.451798 GGATCATAATTTGGCAACGATTGGT 60.452 40.000 0.00 0.00 42.51 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 33 1.110442 CACTGGTTTGGCCTCACAAA 58.890 50.000 3.32 0.00 37.96 2.83
37 40 1.544246 GTAATGTCCACTGGTTTGGCC 59.456 52.381 0.00 0.00 36.48 5.36
161 166 4.383173 CAGGTCACAGCAGAATATATGCA 58.617 43.478 13.59 0.00 46.31 3.96
178 183 0.694444 TAATCCCTCTGGCCCAGGTC 60.694 60.000 11.68 0.00 31.51 3.85
246 251 0.679960 GCCCTAACTTCCGGTTGCAT 60.680 55.000 0.00 0.00 38.75 3.96
253 258 0.108138 CACAGGAGCCCTAACTTCCG 60.108 60.000 0.00 0.00 29.64 4.30
270 275 8.743714 AGTTCCTATGAAAATCCTTTGAATCAC 58.256 33.333 0.00 0.00 30.79 3.06
386 398 9.103582 TCTTATGGGAAGTAGTAGTACCAAAAA 57.896 33.333 4.02 3.84 0.00 1.94
387 399 8.669055 TCTTATGGGAAGTAGTAGTACCAAAA 57.331 34.615 4.02 0.00 0.00 2.44
388 400 8.849543 ATCTTATGGGAAGTAGTAGTACCAAA 57.150 34.615 4.02 2.75 0.00 3.28
389 401 8.849543 AATCTTATGGGAAGTAGTAGTACCAA 57.150 34.615 4.02 0.00 0.00 3.67
390 402 8.849543 AAATCTTATGGGAAGTAGTAGTACCA 57.150 34.615 4.02 4.34 0.00 3.25
391 403 9.145442 AGAAATCTTATGGGAAGTAGTAGTACC 57.855 37.037 4.02 0.00 0.00 3.34
394 406 9.495382 AGAAGAAATCTTATGGGAAGTAGTAGT 57.505 33.333 0.00 0.00 33.39 2.73
397 409 8.425703 GCTAGAAGAAATCTTATGGGAAGTAGT 58.574 37.037 0.00 0.00 39.71 2.73
398 410 8.424918 TGCTAGAAGAAATCTTATGGGAAGTAG 58.575 37.037 0.00 0.00 39.71 2.57
399 411 8.204836 GTGCTAGAAGAAATCTTATGGGAAGTA 58.795 37.037 0.00 0.00 39.71 2.24
400 412 7.051000 GTGCTAGAAGAAATCTTATGGGAAGT 58.949 38.462 0.00 0.00 39.71 3.01
401 413 7.278875 AGTGCTAGAAGAAATCTTATGGGAAG 58.721 38.462 0.00 0.00 39.71 3.46
402 414 7.092891 TGAGTGCTAGAAGAAATCTTATGGGAA 60.093 37.037 0.00 0.00 39.71 3.97
403 415 6.384015 TGAGTGCTAGAAGAAATCTTATGGGA 59.616 38.462 0.00 0.00 39.71 4.37
404 416 6.481644 GTGAGTGCTAGAAGAAATCTTATGGG 59.518 42.308 0.00 0.00 39.71 4.00
405 417 7.271511 AGTGAGTGCTAGAAGAAATCTTATGG 58.728 38.462 0.00 0.00 39.71 2.74
406 418 7.978414 TGAGTGAGTGCTAGAAGAAATCTTATG 59.022 37.037 0.00 0.00 39.71 1.90
407 419 8.072321 TGAGTGAGTGCTAGAAGAAATCTTAT 57.928 34.615 0.00 0.00 39.71 1.73
408 420 7.468141 TGAGTGAGTGCTAGAAGAAATCTTA 57.532 36.000 0.00 0.00 39.71 2.10
409 421 6.352016 TGAGTGAGTGCTAGAAGAAATCTT 57.648 37.500 0.00 0.00 39.71 2.40
410 422 5.991933 TGAGTGAGTGCTAGAAGAAATCT 57.008 39.130 0.00 0.00 42.48 2.40
411 423 6.128418 GGTTTGAGTGAGTGCTAGAAGAAATC 60.128 42.308 0.00 0.00 0.00 2.17
412 424 5.703130 GGTTTGAGTGAGTGCTAGAAGAAAT 59.297 40.000 0.00 0.00 0.00 2.17
413 425 5.057149 GGTTTGAGTGAGTGCTAGAAGAAA 58.943 41.667 0.00 0.00 0.00 2.52
414 426 4.345257 AGGTTTGAGTGAGTGCTAGAAGAA 59.655 41.667 0.00 0.00 0.00 2.52
415 427 3.898123 AGGTTTGAGTGAGTGCTAGAAGA 59.102 43.478 0.00 0.00 0.00 2.87
416 428 4.021544 AGAGGTTTGAGTGAGTGCTAGAAG 60.022 45.833 0.00 0.00 0.00 2.85
425 437 6.683974 TTCTTTGAAAGAGGTTTGAGTGAG 57.316 37.500 7.76 0.00 39.03 3.51
426 438 6.828273 TGATTCTTTGAAAGAGGTTTGAGTGA 59.172 34.615 7.76 0.00 39.03 3.41
460 473 8.920509 TTTGATTGTTTGATTGCATCATAGAG 57.079 30.769 0.00 0.00 39.39 2.43
461 474 9.708092 TTTTTGATTGTTTGATTGCATCATAGA 57.292 25.926 0.00 0.00 39.39 1.98
480 493 5.946377 GGACAGAGGGAGTACAATTTTTGAT 59.054 40.000 0.00 0.00 0.00 2.57
481 494 5.313712 GGACAGAGGGAGTACAATTTTTGA 58.686 41.667 0.00 0.00 0.00 2.69
485 498 3.256704 TGGGACAGAGGGAGTACAATTT 58.743 45.455 0.00 0.00 0.00 1.82
486 499 2.915869 TGGGACAGAGGGAGTACAATT 58.084 47.619 0.00 0.00 0.00 2.32
488 501 2.409064 TTGGGACAGAGGGAGTACAA 57.591 50.000 0.00 0.00 42.39 2.41
490 503 5.632034 ATATTTTGGGACAGAGGGAGTAC 57.368 43.478 0.00 0.00 42.39 2.73
492 505 5.970640 TCTTATATTTTGGGACAGAGGGAGT 59.029 40.000 0.00 0.00 42.39 3.85
494 507 6.631766 CGTTCTTATATTTTGGGACAGAGGGA 60.632 42.308 0.00 0.00 42.39 4.20
496 509 6.113411 ACGTTCTTATATTTTGGGACAGAGG 58.887 40.000 0.00 0.00 42.39 3.69
497 510 7.611213 AACGTTCTTATATTTTGGGACAGAG 57.389 36.000 0.00 0.00 42.39 3.35
510 523 8.519492 AGCGTAGTGTTAAAAACGTTCTTATA 57.481 30.769 0.00 0.00 37.64 0.98
511 524 7.412137 AGCGTAGTGTTAAAAACGTTCTTAT 57.588 32.000 0.00 0.00 37.64 1.73
512 525 6.826893 AGCGTAGTGTTAAAAACGTTCTTA 57.173 33.333 0.00 0.00 37.64 2.10
515 528 6.202815 ACTAGCGTAGTGTTAAAAACGTTC 57.797 37.500 0.00 0.00 37.69 3.95
528 541 3.709987 ACGTTTTTGACACTAGCGTAGT 58.290 40.909 0.00 0.00 40.28 2.73
529 542 4.443394 AGAACGTTTTTGACACTAGCGTAG 59.557 41.667 0.46 0.00 0.00 3.51
530 543 4.362279 AGAACGTTTTTGACACTAGCGTA 58.638 39.130 0.46 0.00 0.00 4.42
531 544 3.192466 AGAACGTTTTTGACACTAGCGT 58.808 40.909 0.46 0.00 0.00 5.07
532 545 3.854286 AGAACGTTTTTGACACTAGCG 57.146 42.857 0.46 0.00 0.00 4.26
537 550 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
538 551 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
539 552 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
540 553 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
541 554 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
542 555 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
543 556 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
544 557 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
545 558 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
546 559 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
547 560 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
548 561 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
549 562 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
550 563 5.279562 TCCCTCCGTCCCATAATATAAGA 57.720 43.478 0.00 0.00 0.00 2.10
551 564 6.561519 ATTCCCTCCGTCCCATAATATAAG 57.438 41.667 0.00 0.00 0.00 1.73
552 565 6.614087 CCTATTCCCTCCGTCCCATAATATAA 59.386 42.308 0.00 0.00 0.00 0.98
553 566 6.068081 TCCTATTCCCTCCGTCCCATAATATA 60.068 42.308 0.00 0.00 0.00 0.86
554 567 4.969359 CCTATTCCCTCCGTCCCATAATAT 59.031 45.833 0.00 0.00 0.00 1.28
555 568 4.046231 TCCTATTCCCTCCGTCCCATAATA 59.954 45.833 0.00 0.00 0.00 0.98
556 569 3.181399 TCCTATTCCCTCCGTCCCATAAT 60.181 47.826 0.00 0.00 0.00 1.28
557 570 2.180529 TCCTATTCCCTCCGTCCCATAA 59.819 50.000 0.00 0.00 0.00 1.90
558 571 1.790779 TCCTATTCCCTCCGTCCCATA 59.209 52.381 0.00 0.00 0.00 2.74
559 572 0.566176 TCCTATTCCCTCCGTCCCAT 59.434 55.000 0.00 0.00 0.00 4.00
560 573 0.566176 ATCCTATTCCCTCCGTCCCA 59.434 55.000 0.00 0.00 0.00 4.37
561 574 0.977395 CATCCTATTCCCTCCGTCCC 59.023 60.000 0.00 0.00 0.00 4.46
562 575 2.011122 TCATCCTATTCCCTCCGTCC 57.989 55.000 0.00 0.00 0.00 4.79
563 576 3.231818 TCTTCATCCTATTCCCTCCGTC 58.768 50.000 0.00 0.00 0.00 4.79
564 577 3.330126 TCTTCATCCTATTCCCTCCGT 57.670 47.619 0.00 0.00 0.00 4.69
565 578 3.834813 TCATCTTCATCCTATTCCCTCCG 59.165 47.826 0.00 0.00 0.00 4.63
566 579 5.090139 TCTCATCTTCATCCTATTCCCTCC 58.910 45.833 0.00 0.00 0.00 4.30
567 580 6.872585 ATCTCATCTTCATCCTATTCCCTC 57.127 41.667 0.00 0.00 0.00 4.30
568 581 6.215227 GGAATCTCATCTTCATCCTATTCCCT 59.785 42.308 0.00 0.00 36.63 4.20
569 582 6.413892 GGAATCTCATCTTCATCCTATTCCC 58.586 44.000 0.00 0.00 36.63 3.97
573 586 6.098124 GGATCGGAATCTCATCTTCATCCTAT 59.902 42.308 0.00 0.00 29.18 2.57
576 589 4.222588 AGGATCGGAATCTCATCTTCATCC 59.777 45.833 0.00 0.00 30.67 3.51
583 596 7.736447 AAAAACATAGGATCGGAATCTCATC 57.264 36.000 0.00 0.00 32.12 2.92
610 623 1.600485 GAAAACGCGGGAACAGAAGAA 59.400 47.619 12.47 0.00 0.00 2.52
612 625 0.941542 TGAAAACGCGGGAACAGAAG 59.058 50.000 12.47 0.00 0.00 2.85
617 630 1.135774 GGATTCTGAAAACGCGGGAAC 60.136 52.381 12.47 0.00 0.00 3.62
647 660 2.098117 CACCCAAATGAAATCGCCTCTC 59.902 50.000 0.00 0.00 0.00 3.20
859 884 1.972872 ATTCTTGCCCGGATGCTAAG 58.027 50.000 0.73 5.84 0.00 2.18
893 918 3.308832 GGACTGGGAGAGAAGAAGAGAGA 60.309 52.174 0.00 0.00 0.00 3.10
912 938 4.035102 GCTGGTGGTGGGAGGGAC 62.035 72.222 0.00 0.00 0.00 4.46
919 945 2.033141 CTGGTCTGCTGGTGGTGG 59.967 66.667 0.00 0.00 0.00 4.61
948 1002 0.387367 CGGTGATGGATCGACCGATC 60.387 60.000 20.51 20.51 45.55 3.69
949 1003 1.107538 ACGGTGATGGATCGACCGAT 61.108 55.000 24.70 3.96 45.55 4.18
950 1004 1.751544 ACGGTGATGGATCGACCGA 60.752 57.895 24.70 0.00 45.55 4.69
951 1005 1.588932 CACGGTGATGGATCGACCG 60.589 63.158 19.98 19.98 46.74 4.79
952 1006 1.883084 GCACGGTGATGGATCGACC 60.883 63.158 13.29 0.00 39.54 4.79
953 1007 2.230940 CGCACGGTGATGGATCGAC 61.231 63.158 13.29 0.00 0.00 4.20
954 1008 2.104132 CGCACGGTGATGGATCGA 59.896 61.111 13.29 0.00 0.00 3.59
955 1009 2.202743 ACGCACGGTGATGGATCG 60.203 61.111 13.29 7.16 0.00 3.69
1081 1135 1.012486 GCAAACCATCAGCAAGCAGC 61.012 55.000 0.00 0.00 46.19 5.25
1082 1136 0.315886 TGCAAACCATCAGCAAGCAG 59.684 50.000 0.00 0.00 34.97 4.24
1083 1137 0.315886 CTGCAAACCATCAGCAAGCA 59.684 50.000 0.00 0.00 37.89 3.91
1084 1138 0.389426 CCTGCAAACCATCAGCAAGC 60.389 55.000 0.00 0.00 37.89 4.01
1089 1155 2.180017 GCGCCTGCAAACCATCAG 59.820 61.111 0.00 0.00 42.15 2.90
1271 1343 3.427161 ACAAACAAAACAGAGCAGAGC 57.573 42.857 0.00 0.00 0.00 4.09
1331 1403 4.572909 CTTGGAAGATCACATGTCACTCA 58.427 43.478 0.00 0.00 0.00 3.41
1404 1483 6.686630 AGTACGTACTACATATCTAGCGAGT 58.313 40.000 26.36 0.00 34.13 4.18
1407 1486 8.180920 TCTCTAGTACGTACTACATATCTAGCG 58.819 40.741 27.51 14.40 37.73 4.26
1416 1495 7.223582 GTGCTTGTATCTCTAGTACGTACTACA 59.776 40.741 27.51 22.55 37.73 2.74
1424 1503 4.612943 GCCTGTGCTTGTATCTCTAGTAC 58.387 47.826 0.00 0.00 35.83 2.73
1454 1533 2.527100 GCATGCATTCAGACAAGAAGC 58.473 47.619 14.21 0.00 0.00 3.86
1455 1534 2.417586 TCGCATGCATTCAGACAAGAAG 59.582 45.455 19.57 0.00 0.00 2.85
1456 1535 2.160219 GTCGCATGCATTCAGACAAGAA 59.840 45.455 19.57 0.00 32.57 2.52
1457 1536 1.733912 GTCGCATGCATTCAGACAAGA 59.266 47.619 19.57 0.00 32.57 3.02
1505 1591 2.235016 CGTGGTGTGGTGTCGTGTC 61.235 63.158 0.00 0.00 0.00 3.67
1506 1592 2.202824 CGTGGTGTGGTGTCGTGT 60.203 61.111 0.00 0.00 0.00 4.49
1507 1593 2.909614 TTCCGTGGTGTGGTGTCGTG 62.910 60.000 0.00 0.00 0.00 4.35
1508 1594 2.638330 CTTCCGTGGTGTGGTGTCGT 62.638 60.000 0.00 0.00 0.00 4.34
1509 1595 1.954146 CTTCCGTGGTGTGGTGTCG 60.954 63.158 0.00 0.00 0.00 4.35
1510 1596 1.145377 ACTTCCGTGGTGTGGTGTC 59.855 57.895 0.00 0.00 0.00 3.67
1511 1597 1.153249 CACTTCCGTGGTGTGGTGT 60.153 57.895 6.82 0.00 37.50 4.16
1512 1598 1.153249 ACACTTCCGTGGTGTGGTG 60.153 57.895 15.16 9.34 44.82 4.17
1513 1599 3.316029 ACACTTCCGTGGTGTGGT 58.684 55.556 15.16 3.56 44.82 4.16
1593 1679 5.235186 GTGAGGAAGGAATAATCGATGTGTG 59.765 44.000 0.00 0.00 0.00 3.82
1599 1685 5.656859 TGAGAAGTGAGGAAGGAATAATCGA 59.343 40.000 0.00 0.00 0.00 3.59
1600 1686 5.751028 GTGAGAAGTGAGGAAGGAATAATCG 59.249 44.000 0.00 0.00 0.00 3.34
1708 1802 2.687935 ACGTTCCTCTTGCAAAACATGT 59.312 40.909 11.24 0.00 0.00 3.21
1745 1842 7.095857 GCTAGTCATCAACTTGTGCAGATATAC 60.096 40.741 0.00 0.00 39.55 1.47
1746 1843 6.925718 GCTAGTCATCAACTTGTGCAGATATA 59.074 38.462 0.00 0.00 39.55 0.86
1747 1844 5.757320 GCTAGTCATCAACTTGTGCAGATAT 59.243 40.000 0.00 0.00 39.55 1.63
1753 1850 2.159599 GCAGCTAGTCATCAACTTGTGC 60.160 50.000 0.00 0.00 39.55 4.57
1815 1914 6.428771 CGTGGAAAAGGAACAAATTAGGTCTA 59.571 38.462 0.00 0.00 0.00 2.59
1842 1941 0.662619 CCAGCTGCACAAGACGAAAA 59.337 50.000 8.66 0.00 0.00 2.29
2024 2127 5.019470 TGAAGAGGATAACTGAGCTTGAGA 58.981 41.667 0.00 0.00 0.00 3.27
2074 2180 4.148825 ACGGAGATGCACGAGGCC 62.149 66.667 0.00 0.00 43.89 5.19
2227 3014 2.021457 CCGGCTATAAAAACTGGGTGG 58.979 52.381 0.00 0.00 0.00 4.61
2229 3017 3.444792 AACCGGCTATAAAAACTGGGT 57.555 42.857 0.00 0.00 33.89 4.51
2489 3305 0.107312 CCCAAGCCTCACTGGAGATG 60.107 60.000 0.00 0.00 44.26 2.90
2616 3435 1.077787 CCAGCCGCTCAACCCAATA 60.078 57.895 0.00 0.00 0.00 1.90
2740 3565 0.620556 TCAATCTTGGTCCTCAGGGC 59.379 55.000 0.00 0.00 0.00 5.19
2838 3664 2.030371 TCAGCACATGGACTGCAAAAA 58.970 42.857 11.32 0.00 37.08 1.94
2950 3797 4.493747 CGACCTCTCGCCGTTCCC 62.494 72.222 0.00 0.00 31.91 3.97
3140 6352 1.673033 CCACTTGGAGACATCGTCCAC 60.673 57.143 0.00 0.00 44.06 4.02
3233 6449 9.950496 ATAGTGTCAATACTTTTCTCTCATGTT 57.050 29.630 0.00 0.00 32.19 2.71
3434 8066 9.370126 GTAGAACACAAGCATATATTAAAAGCG 57.630 33.333 0.00 0.00 0.00 4.68
3466 8101 5.406780 GTGAAAAGTCTACACTGGACTGATG 59.593 44.000 0.00 0.00 42.39 3.07
3574 8209 9.646522 ATCTTCCAAATAGCCACAAATTAGTAT 57.353 29.630 0.00 0.00 0.00 2.12
3683 8387 0.809385 CTTGGCAGCCAGATCAACAG 59.191 55.000 15.50 3.15 33.81 3.16
3823 8530 6.146184 TCGTCTTCAATCATTCAGACTTTCAC 59.854 38.462 5.16 0.00 34.62 3.18
3863 8570 1.295792 GTTCCTTTGTGCAGTGACGA 58.704 50.000 0.00 0.00 0.00 4.20
3892 8599 6.014070 ACGGTATATGGGATGTGTTAGCATTA 60.014 38.462 0.00 0.00 0.00 1.90
3927 8636 4.933505 TTTCATCAGACCAACATGCAAA 57.066 36.364 0.00 0.00 0.00 3.68
3941 8650 3.192422 CCACGGCTTGGTTTATTTCATCA 59.808 43.478 1.04 0.00 41.10 3.07
4007 8716 3.360956 CGCAGCAAACTTTTTCATGAACG 60.361 43.478 7.89 2.40 0.00 3.95
4149 8880 9.677567 CGGAGTGAAATTTCAAAAGATAAGAAA 57.322 29.630 22.07 0.00 39.21 2.52
4150 8881 8.846211 ACGGAGTGAAATTTCAAAAGATAAGAA 58.154 29.630 22.07 0.00 42.51 2.52
4151 8882 8.391075 ACGGAGTGAAATTTCAAAAGATAAGA 57.609 30.769 22.07 0.00 42.51 2.10
4152 8883 9.118236 GAACGGAGTGAAATTTCAAAAGATAAG 57.882 33.333 22.07 10.68 45.00 1.73
4155 8886 6.142817 CGAACGGAGTGAAATTTCAAAAGAT 58.857 36.000 22.07 9.06 45.00 2.40


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

AutoCloner maintained by Alex Coulton.