Multiple sequence alignment - TraesCS7D01G168200

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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 TraesCS7D01G168200 chr7D 100.000 3344 0 0 1 3344 118395102 118391759 0.000000e+00 6176.0
1 TraesCS7D01G168200 chr7D 96.233 292 9 2 604 895 118377276 118376987 8.390000e-131 477.0
2 TraesCS7D01G168200 chr7D 92.462 199 11 3 126 324 118818766 118818572 7.060000e-72 281.0
3 TraesCS7D01G168200 chr7D 85.981 214 18 3 395 603 118601953 118601747 5.620000e-53 219.0
4 TraesCS7D01G168200 chr7D 91.129 124 6 4 1 123 118818918 118818799 2.670000e-36 163.0
5 TraesCS7D01G168200 chr7D 75.141 354 80 7 2995 3344 18798597 18798248 3.450000e-35 159.0
6 TraesCS7D01G168200 chr7D 84.946 93 5 4 320 406 118818289 118818200 5.940000e-13 86.1
7 TraesCS7D01G168200 chr7D 91.837 49 4 0 2672 2720 602804319 602804271 5.990000e-08 69.4
8 TraesCS7D01G168200 chr1B 82.381 2713 438 35 647 3344 28298283 28300970 0.000000e+00 2326.0
9 TraesCS7D01G168200 chr1B 79.793 193 26 12 709 895 473006806 473006991 9.740000e-26 128.0
10 TraesCS7D01G168200 chr5B 82.227 2712 451 29 647 3344 470619784 470617090 0.000000e+00 2309.0
11 TraesCS7D01G168200 chr3D 78.992 2618 485 48 752 3344 109738074 109735497 0.000000e+00 1727.0
12 TraesCS7D01G168200 chr1D 78.490 2622 495 58 755 3341 233324038 233321451 0.000000e+00 1653.0
13 TraesCS7D01G168200 chr3B 77.695 2672 508 67 716 3342 566993826 566991198 0.000000e+00 1552.0
14 TraesCS7D01G168200 chr5A 76.271 2714 558 63 661 3341 680725802 680723142 0.000000e+00 1365.0
15 TraesCS7D01G168200 chr6A 74.670 2045 460 46 1324 3341 9252295 9254308 0.000000e+00 854.0
16 TraesCS7D01G168200 chr7B 86.856 563 39 14 1 549 79380746 79380205 6.180000e-167 597.0
17 TraesCS7D01G168200 chr7A 83.793 617 50 18 1 603 122743902 122743322 1.060000e-149 540.0
18 TraesCS7D01G168200 chr7A 75.500 1000 218 24 1502 2487 269104162 269105148 6.530000e-127 464.0
19 TraesCS7D01G168200 chr4A 77.154 499 87 17 868 1363 740891028 740890554 7.110000e-67 265.0
20 TraesCS7D01G168200 chr5D 78.014 282 56 4 3063 3341 458174187 458174465 4.440000e-39 172.0
21 TraesCS7D01G168200 chr5D 91.837 49 4 0 2672 2720 54835310 54835262 5.990000e-08 69.4
22 TraesCS7D01G168200 chr4D 76.325 283 65 2 3063 3344 499529763 499529482 2.080000e-32 150.0


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 TraesCS7D01G168200 chr7D 118391759 118395102 3343 True 6176 6176 100.000 1 3344 1 chr7D.!!$R3 3343
1 TraesCS7D01G168200 chr1B 28298283 28300970 2687 False 2326 2326 82.381 647 3344 1 chr1B.!!$F1 2697
2 TraesCS7D01G168200 chr5B 470617090 470619784 2694 True 2309 2309 82.227 647 3344 1 chr5B.!!$R1 2697
3 TraesCS7D01G168200 chr3D 109735497 109738074 2577 True 1727 1727 78.992 752 3344 1 chr3D.!!$R1 2592
4 TraesCS7D01G168200 chr1D 233321451 233324038 2587 True 1653 1653 78.490 755 3341 1 chr1D.!!$R1 2586
5 TraesCS7D01G168200 chr3B 566991198 566993826 2628 True 1552 1552 77.695 716 3342 1 chr3B.!!$R1 2626
6 TraesCS7D01G168200 chr5A 680723142 680725802 2660 True 1365 1365 76.271 661 3341 1 chr5A.!!$R1 2680
7 TraesCS7D01G168200 chr6A 9252295 9254308 2013 False 854 854 74.670 1324 3341 1 chr6A.!!$F1 2017
8 TraesCS7D01G168200 chr7B 79380205 79380746 541 True 597 597 86.856 1 549 1 chr7B.!!$R1 548
9 TraesCS7D01G168200 chr7A 122743322 122743902 580 True 540 540 83.793 1 603 1 chr7A.!!$R1 602
10 TraesCS7D01G168200 chr7A 269104162 269105148 986 False 464 464 75.500 1502 2487 1 chr7A.!!$F1 985

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
814 831 0.034059 CTCCCTCGATCCCCATTTCG 59.966 60.0 0.0 0.0 36.72 3.46 F
1482 1508 0.121197 TCATGGGAGAGAGGGGGTTT 59.879 55.0 0.0 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1694 0.037326 CTTGGTAAGCGAGGTGAGCA 60.037 55.0 0.0 0.0 37.01 4.26 R
3240 3276 0.107017 CGATGACTGGCAAGGGGAAT 60.107 55.0 0.0 0.0 0.00 3.01 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
24 25 2.121948 ACTGCTTGCCTATCTCCATGA 58.878 47.619 0.00 0.00 0.00 3.07
42 43 7.449395 TCTCCATGACAAATGGAAATATGGATC 59.551 37.037 8.34 0.00 46.50 3.36
43 44 7.068061 TCCATGACAAATGGAAATATGGATCA 58.932 34.615 4.58 0.00 44.54 2.92
44 45 7.731235 TCCATGACAAATGGAAATATGGATCAT 59.269 33.333 4.58 0.00 44.54 2.45
45 46 7.817478 CCATGACAAATGGAAATATGGATCATG 59.183 37.037 0.00 0.00 41.64 3.07
46 47 6.751157 TGACAAATGGAAATATGGATCATGC 58.249 36.000 0.00 0.00 0.00 4.06
47 48 6.551975 TGACAAATGGAAATATGGATCATGCT 59.448 34.615 0.00 0.00 0.00 3.79
48 49 6.755206 ACAAATGGAAATATGGATCATGCTG 58.245 36.000 0.00 0.00 0.00 4.41
49 50 5.401531 AATGGAAATATGGATCATGCTGC 57.598 39.130 0.00 0.00 0.00 5.25
137 140 2.689553 TAATGCATGTGCCTCGAGAA 57.310 45.000 15.71 0.00 41.18 2.87
157 160 4.279671 AGAAGCGGATCTAGTGGAACATAG 59.720 45.833 0.00 0.00 44.52 2.23
177 180 9.486497 AACATAGTTATCAAGCAGTATCATCAG 57.514 33.333 0.00 0.00 0.00 2.90
179 182 8.923683 CATAGTTATCAAGCAGTATCATCAGTG 58.076 37.037 0.00 0.00 0.00 3.66
182 185 7.826252 AGTTATCAAGCAGTATCATCAGTGTTT 59.174 33.333 0.00 0.00 0.00 2.83
189 192 7.208777 AGCAGTATCATCAGTGTTTCTCATAG 58.791 38.462 0.00 0.00 0.00 2.23
190 193 6.983307 GCAGTATCATCAGTGTTTCTCATAGT 59.017 38.462 0.00 0.00 0.00 2.12
231 234 5.977129 CGCAACAAACCTAGAACATTCTTTT 59.023 36.000 0.00 0.00 38.70 2.27
238 241 7.602517 AACCTAGAACATTCTTTTCAGATCG 57.397 36.000 0.00 0.00 38.70 3.69
286 289 2.968574 GCCATCCTCTTCCTAGTGATCA 59.031 50.000 0.00 0.00 0.00 2.92
308 311 2.819154 CCCATGCATGTCGCGTCA 60.819 61.111 24.58 8.78 46.97 4.35
351 354 0.915872 TGAGGAGGACCCATGCATGT 60.916 55.000 24.58 7.78 37.41 3.21
352 355 1.131638 GAGGAGGACCCATGCATGTA 58.868 55.000 24.58 0.00 37.41 2.29
353 356 0.839946 AGGAGGACCCATGCATGTAC 59.160 55.000 24.58 14.58 37.41 2.90
354 357 0.532862 GGAGGACCCATGCATGTACG 60.533 60.000 24.58 13.90 34.14 3.67
355 358 0.178068 GAGGACCCATGCATGTACGT 59.822 55.000 24.58 16.87 0.00 3.57
356 359 1.411246 GAGGACCCATGCATGTACGTA 59.589 52.381 24.58 0.00 0.00 3.57
357 360 1.138266 AGGACCCATGCATGTACGTAC 59.862 52.381 24.58 18.90 0.00 3.67
376 379 6.509656 ACGTACTATCACAAAGACTGTTCAA 58.490 36.000 0.00 0.00 35.47 2.69
377 380 6.982141 ACGTACTATCACAAAGACTGTTCAAA 59.018 34.615 0.00 0.00 35.47 2.69
408 416 2.147387 AGCGTGTGGGGTTCCTTCT 61.147 57.895 0.00 0.00 0.00 2.85
414 422 0.609406 GTGGGGTTCCTTCTCCAAGC 60.609 60.000 0.00 0.00 0.00 4.01
448 456 2.751259 TCCAAGTACGTGTCGCTCTTAT 59.249 45.455 8.02 0.00 0.00 1.73
450 458 3.924686 CCAAGTACGTGTCGCTCTTATTT 59.075 43.478 8.02 0.00 0.00 1.40
451 459 4.201589 CCAAGTACGTGTCGCTCTTATTTG 60.202 45.833 8.02 0.00 0.00 2.32
453 461 4.164294 AGTACGTGTCGCTCTTATTTGTC 58.836 43.478 0.00 0.00 0.00 3.18
484 499 8.682710 TGCCCAATAATTCACTTTGTCTTATAC 58.317 33.333 0.00 0.00 0.00 1.47
485 500 7.855904 GCCCAATAATTCACTTTGTCTTATACG 59.144 37.037 0.00 0.00 0.00 3.06
486 501 8.342634 CCCAATAATTCACTTTGTCTTATACGG 58.657 37.037 0.00 0.00 0.00 4.02
487 502 9.104965 CCAATAATTCACTTTGTCTTATACGGA 57.895 33.333 0.00 0.00 0.00 4.69
519 534 3.589988 AGCTACTTGATTCACCGTTGAG 58.410 45.455 0.00 0.00 31.71 3.02
549 564 6.512297 TCACTTCAAAATTTAACCCTTCTGC 58.488 36.000 0.00 0.00 0.00 4.26
554 569 5.129485 TCAAAATTTAACCCTTCTGCCAACA 59.871 36.000 0.00 0.00 0.00 3.33
555 570 4.600692 AATTTAACCCTTCTGCCAACAC 57.399 40.909 0.00 0.00 0.00 3.32
556 571 3.306472 TTTAACCCTTCTGCCAACACT 57.694 42.857 0.00 0.00 0.00 3.55
568 584 1.024271 CCAACACTTGGCCGATATGG 58.976 55.000 0.00 0.00 45.17 2.74
600 616 0.818296 AGCAGAAGCCGTCGAGTATT 59.182 50.000 0.00 0.00 43.56 1.89
603 619 2.799917 GCAGAAGCCGTCGAGTATTCAT 60.800 50.000 0.00 0.00 33.58 2.57
604 620 2.791560 CAGAAGCCGTCGAGTATTCATG 59.208 50.000 0.00 0.00 0.00 3.07
605 621 2.427453 AGAAGCCGTCGAGTATTCATGT 59.573 45.455 0.00 0.00 0.00 3.21
606 622 2.961526 AGCCGTCGAGTATTCATGTT 57.038 45.000 0.00 0.00 0.00 2.71
607 623 4.097437 AGAAGCCGTCGAGTATTCATGTTA 59.903 41.667 0.00 0.00 0.00 2.41
608 624 3.703420 AGCCGTCGAGTATTCATGTTAC 58.297 45.455 0.00 0.00 0.00 2.50
609 625 2.466571 GCCGTCGAGTATTCATGTTACG 59.533 50.000 0.00 0.00 0.00 3.18
610 626 3.040795 CCGTCGAGTATTCATGTTACGG 58.959 50.000 0.00 0.00 42.12 4.02
611 627 2.466571 CGTCGAGTATTCATGTTACGGC 59.533 50.000 0.00 0.00 0.00 5.68
612 628 2.793232 GTCGAGTATTCATGTTACGGCC 59.207 50.000 0.00 0.00 0.00 6.13
613 629 2.132762 CGAGTATTCATGTTACGGCCC 58.867 52.381 0.00 0.00 0.00 5.80
614 630 2.490991 GAGTATTCATGTTACGGCCCC 58.509 52.381 0.00 0.00 0.00 5.80
615 631 2.104281 GAGTATTCATGTTACGGCCCCT 59.896 50.000 0.00 0.00 0.00 4.79
616 632 2.158813 AGTATTCATGTTACGGCCCCTG 60.159 50.000 0.00 0.00 0.00 4.45
617 633 0.751643 ATTCATGTTACGGCCCCTGC 60.752 55.000 0.00 0.00 0.00 4.85
628 644 2.688666 CCCCTGCCAGCACCTCTA 60.689 66.667 0.00 0.00 0.00 2.43
629 645 2.586792 CCCTGCCAGCACCTCTAC 59.413 66.667 0.00 0.00 0.00 2.59
630 646 2.586792 CCTGCCAGCACCTCTACC 59.413 66.667 0.00 0.00 0.00 3.18
631 647 2.586792 CTGCCAGCACCTCTACCC 59.413 66.667 0.00 0.00 0.00 3.69
632 648 3.376935 CTGCCAGCACCTCTACCCG 62.377 68.421 0.00 0.00 0.00 5.28
633 649 4.840005 GCCAGCACCTCTACCCGC 62.840 72.222 0.00 0.00 0.00 6.13
634 650 4.514577 CCAGCACCTCTACCCGCG 62.515 72.222 0.00 0.00 0.00 6.46
635 651 4.514577 CAGCACCTCTACCCGCGG 62.515 72.222 21.04 21.04 0.00 6.46
642 658 4.853142 TCTACCCGCGGCCCTCAT 62.853 66.667 22.85 2.35 0.00 2.90
643 659 4.609018 CTACCCGCGGCCCTCATG 62.609 72.222 22.85 6.71 0.00 3.07
658 674 0.329261 TCATGAAGGAACAGCCCAGG 59.671 55.000 0.00 0.00 37.37 4.45
665 681 3.185203 AACAGCCCAGGAGCCCAA 61.185 61.111 0.00 0.00 0.00 4.12
672 688 3.741476 CAGGAGCCCAACAAGCGC 61.741 66.667 0.00 0.00 34.64 5.92
678 694 3.591835 CCCAACAAGCGCAACCGT 61.592 61.111 11.47 0.00 36.67 4.83
680 696 1.649815 CCAACAAGCGCAACCGTAA 59.350 52.632 11.47 0.00 36.67 3.18
688 704 2.359975 GCAACCGTAAGCCCAGCT 60.360 61.111 0.00 0.00 42.56 4.24
690 706 1.296715 CAACCGTAAGCCCAGCTCT 59.703 57.895 0.00 0.00 38.25 4.09
734 750 4.381292 GGAAACCTAGCGAGTACTTAAGCA 60.381 45.833 17.23 0.00 0.00 3.91
743 760 3.368236 CGAGTACTTAAGCAAGAAGGCAC 59.632 47.826 1.29 0.00 35.60 5.01
745 762 2.543777 ACTTAAGCAAGAAGGCACGA 57.456 45.000 1.29 0.00 35.60 4.35
746 763 2.846193 ACTTAAGCAAGAAGGCACGAA 58.154 42.857 1.29 0.00 35.60 3.85
748 765 3.251004 ACTTAAGCAAGAAGGCACGAAAG 59.749 43.478 1.29 0.00 35.60 2.62
750 767 0.108585 AGCAAGAAGGCACGAAAGGA 59.891 50.000 0.00 0.00 35.83 3.36
766 783 3.979101 AAGGAGAAGGCAAGAAGAGAG 57.021 47.619 0.00 0.00 0.00 3.20
800 817 3.234730 CGGCGGCTATTCCTCCCT 61.235 66.667 7.61 0.00 36.31 4.20
809 826 0.864659 TATTCCTCCCTCGATCCCCA 59.135 55.000 0.00 0.00 0.00 4.96
814 831 0.034059 CTCCCTCGATCCCCATTTCG 59.966 60.000 0.00 0.00 36.72 3.46
817 834 0.249911 CCTCGATCCCCATTTCGTCC 60.250 60.000 0.00 0.00 36.74 4.79
819 836 1.961394 CTCGATCCCCATTTCGTCCTA 59.039 52.381 0.00 0.00 36.74 2.94
821 838 1.605712 CGATCCCCATTTCGTCCTAGC 60.606 57.143 0.00 0.00 0.00 3.42
854 880 5.797051 AGCTACCTACCAAATTCGTGTAAA 58.203 37.500 0.00 0.00 0.00 2.01
855 881 6.412214 AGCTACCTACCAAATTCGTGTAAAT 58.588 36.000 0.00 0.00 0.00 1.40
860 886 6.594159 ACCTACCAAATTCGTGTAAATCAGAG 59.406 38.462 0.00 0.00 0.00 3.35
863 889 6.231211 ACCAAATTCGTGTAAATCAGAGACT 58.769 36.000 0.00 0.00 0.00 3.24
865 891 7.095187 ACCAAATTCGTGTAAATCAGAGACTTC 60.095 37.037 0.00 0.00 0.00 3.01
886 912 4.851843 TCCTGTACTAGATCGAACCAAGA 58.148 43.478 0.00 0.00 0.00 3.02
924 950 1.140312 AGAGCCTTTTCCTCACCACA 58.860 50.000 0.00 0.00 0.00 4.17
926 952 2.087646 GAGCCTTTTCCTCACCACATC 58.912 52.381 0.00 0.00 0.00 3.06
929 955 2.350522 CCTTTTCCTCACCACATCTCG 58.649 52.381 0.00 0.00 0.00 4.04
936 962 1.135139 CTCACCACATCTCGTCCGATT 59.865 52.381 0.00 0.00 0.00 3.34
978 1004 4.681942 CGATTTCTGTCGATTATCCAGACC 59.318 45.833 2.42 0.00 44.06 3.85
1008 1034 2.435938 GCAACCGCGATGGAGGAA 60.436 61.111 8.23 0.00 42.00 3.36
1021 1047 1.492993 GGAGGAACAGACCAAGGCCT 61.493 60.000 0.00 0.00 0.00 5.19
1171 1197 4.704833 ATCTGCGCGGGCTGTTGT 62.705 61.111 25.62 12.30 40.82 3.32
1172 1198 4.927782 TCTGCGCGGGCTGTTGTT 62.928 61.111 25.62 0.00 40.82 2.83
1233 1259 4.910585 CTACCGCCGCCACCATCC 62.911 72.222 0.00 0.00 0.00 3.51
1243 1269 2.361104 CACCATCCCAACCACCGG 60.361 66.667 0.00 0.00 0.00 5.28
1278 1304 3.125376 GCCGCCCCTGATTCCTCAT 62.125 63.158 0.00 0.00 0.00 2.90
1288 1314 2.650813 GATTCCTCATGCGGCGGAGT 62.651 60.000 9.78 5.29 0.00 3.85
1301 1327 4.742201 GGAGTCGAGCTTGGCGCA 62.742 66.667 10.83 0.00 42.61 6.09
1365 1391 4.740822 ATTGGCCACGGCAGGACC 62.741 66.667 3.88 0.00 44.11 4.46
1450 1476 1.750206 TCGATTCCCGTCATCCGTTTA 59.250 47.619 0.00 0.00 39.75 2.01
1457 1483 2.623889 CCCGTCATCCGTTTAGAGAGAT 59.376 50.000 0.00 0.00 33.66 2.75
1482 1508 0.121197 TCATGGGAGAGAGGGGGTTT 59.879 55.000 0.00 0.00 0.00 3.27
1584 1610 2.029365 GTGCGAGGCTTATTTTCGAGTC 59.971 50.000 0.00 0.00 36.49 3.36
1644 1670 0.537653 TGTATTTCATCGACGGGGCA 59.462 50.000 0.00 0.00 0.00 5.36
1668 1694 7.445402 GCACTATCATGGTTACAATCTACCAAT 59.555 37.037 0.00 0.00 46.74 3.16
1679 1705 0.175760 TCTACCAATGCTCACCTCGC 59.824 55.000 0.00 0.00 0.00 5.03
1691 1717 1.968493 TCACCTCGCTTACCAAGAGTT 59.032 47.619 0.00 0.00 0.00 3.01
1715 1741 1.062148 GGAATTTGCTAACGCGGTCTC 59.938 52.381 12.47 0.00 39.65 3.36
1720 1746 1.226717 GCTAACGCGGTCTCTGAGG 60.227 63.158 12.47 0.00 0.00 3.86
1772 1798 2.594303 CCAGTTCAACCGGCTGCA 60.594 61.111 0.00 0.00 0.00 4.41
1900 1926 1.205655 TCGATGGACTGCAGAAGGAAG 59.794 52.381 23.35 7.63 0.00 3.46
1918 1944 0.105964 AGTTCGTGCAGCTGTGGTAA 59.894 50.000 16.64 2.63 0.00 2.85
1951 1977 3.660501 AAACACTCGATACTGCTGTCA 57.339 42.857 0.00 0.00 0.00 3.58
2025 2054 3.207354 GAGGATCGCCGGTTCAGA 58.793 61.111 1.90 0.00 39.96 3.27
2079 2111 1.445716 CGCTACCTCTACCACCTCCG 61.446 65.000 0.00 0.00 0.00 4.63
2113 2145 1.228306 CCCAAACCGGTAGCACCAA 60.228 57.895 8.00 0.00 38.47 3.67
2160 2192 3.695606 ATCGAGGCGGCACACACT 61.696 61.111 13.08 0.00 0.00 3.55
2196 2231 2.969238 GCAGCGCTCCGTGCATAT 60.969 61.111 7.13 0.00 42.00 1.78
2227 2262 1.228245 GGCCTCTGTTTCACCTGCA 60.228 57.895 0.00 0.00 0.00 4.41
2271 2306 4.822628 TGTGGGCCAACCGTGCAA 62.823 61.111 8.40 0.00 44.64 4.08
2322 2357 3.125658 TGATGAACAACGAGATGCACATG 59.874 43.478 0.00 0.00 0.00 3.21
2323 2358 1.197492 TGAACAACGAGATGCACATGC 59.803 47.619 0.00 0.00 42.50 4.06
2328 2363 0.461516 ACGAGATGCACATGCCAGAG 60.462 55.000 0.49 0.00 41.18 3.35
2336 2371 2.005266 ACATGCCAGAGGAGCCCAT 61.005 57.895 0.00 0.00 0.00 4.00
2397 2432 2.060383 TGTCATCTCCCAGGAGGCG 61.060 63.158 13.73 5.53 42.20 5.52
2406 2441 2.127869 CCAGGAGGCGATCGAAGGA 61.128 63.158 21.57 0.00 0.00 3.36
2418 2453 2.344203 CGAAGGAGCCGAGTCACCT 61.344 63.158 0.00 0.00 0.00 4.00
2421 2456 0.971447 AAGGAGCCGAGTCACCTACC 60.971 60.000 0.00 0.00 32.06 3.18
2423 2458 1.043673 GGAGCCGAGTCACCTACCAT 61.044 60.000 0.00 0.00 0.00 3.55
2433 2468 0.464373 CACCTACCATCATGCGCCTT 60.464 55.000 4.18 0.00 0.00 4.35
2469 2504 1.610522 GACCACAAAGTGCTGATGCTT 59.389 47.619 0.00 0.00 40.48 3.91
2489 2524 1.979155 TGGACTCTGGCTCCTCACG 60.979 63.158 0.00 0.00 0.00 4.35
2529 2565 0.397941 TAGCTGAGCACTTGCAAGGT 59.602 50.000 29.18 14.12 45.16 3.50
2560 2596 1.541147 GCAAAAGCACTATGGCTGTCA 59.459 47.619 0.00 0.00 45.07 3.58
2577 2613 1.675310 CAGAGTGGCAAATGGCGGA 60.675 57.895 2.36 0.00 46.16 5.54
2584 2620 1.031571 GGCAAATGGCGGAGTGATGA 61.032 55.000 0.00 0.00 46.16 2.92
2613 2649 4.021925 GAGTTGCCGGCCTGTCCT 62.022 66.667 26.77 12.13 0.00 3.85
2680 2716 2.214181 CTTGGGCTGCTACGACGTCT 62.214 60.000 14.70 3.37 0.00 4.18
2683 2719 0.669625 GGGCTGCTACGACGTCTTTT 60.670 55.000 14.70 0.00 0.00 2.27
2720 2756 2.050350 CCCAGCACAGCCCAATGAG 61.050 63.158 0.00 0.00 0.00 2.90
2755 2791 3.753797 GGAGAAGACCATGAAGTTTGACC 59.246 47.826 0.00 0.00 0.00 4.02
2841 2877 3.553922 CCGGAGATGATCTAAACCAGCTC 60.554 52.174 0.00 0.00 43.00 4.09
2844 2880 4.881920 GAGATGATCTAAACCAGCTCCTC 58.118 47.826 0.00 0.00 39.23 3.71
2877 2913 2.380410 GGCGCGTGTCGTTCATCTT 61.380 57.895 8.43 0.00 41.07 2.40
2891 2927 1.139989 CATCTTTGTGCGACGACTGT 58.860 50.000 0.00 0.00 0.00 3.55
2895 2931 0.874175 TTTGTGCGACGACTGTGGAG 60.874 55.000 0.00 0.00 0.00 3.86
2906 2942 1.694696 GACTGTGGAGGGAGTCAAAGT 59.305 52.381 0.00 0.00 38.80 2.66
2922 2958 2.175878 AAGTTACAGAGCTGCCAGTG 57.824 50.000 0.00 0.00 0.00 3.66
2952 2988 4.500116 GCCGACCTGCTCCGAGAC 62.500 72.222 0.00 0.00 0.00 3.36
2962 2998 0.889306 GCTCCGAGACTACCAACACT 59.111 55.000 0.00 0.00 0.00 3.55
3181 3217 2.038295 CTGCTGGTTCAGAAGAAGGACT 59.962 50.000 0.00 0.00 39.42 3.85
3240 3276 0.109458 CGGTGACCGTGAAGAATCGA 60.109 55.000 17.28 0.00 42.73 3.59
3286 3322 3.104602 CTTGATGAGCTTGCGGGCG 62.105 63.158 0.00 0.00 37.29 6.13
3310 3346 0.318762 GTTCTTCACCAGCCTCGACT 59.681 55.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.740401 GCAGCATGATCCATATTTCCATTTGT 60.740 38.462 0.00 0.00 39.69 2.83
45 46 1.535437 GCTTAGTCAATGCATGGCAGC 60.535 52.381 0.00 0.00 43.65 5.25
46 47 1.746787 TGCTTAGTCAATGCATGGCAG 59.253 47.619 0.00 0.00 43.65 4.85
47 48 1.836802 TGCTTAGTCAATGCATGGCA 58.163 45.000 0.00 0.00 44.86 4.92
48 49 2.945447 TTGCTTAGTCAATGCATGGC 57.055 45.000 0.00 0.00 36.55 4.40
49 50 4.707030 TCTTTGCTTAGTCAATGCATGG 57.293 40.909 0.00 0.00 36.55 3.66
123 126 2.169789 CCGCTTCTCGAGGCACATG 61.170 63.158 13.56 0.00 41.67 3.21
137 140 3.567397 ACTATGTTCCACTAGATCCGCT 58.433 45.455 0.00 0.00 0.00 5.52
157 160 7.545362 AACACTGATGATACTGCTTGATAAC 57.455 36.000 0.00 0.00 0.00 1.89
182 185 9.626045 CGCTTGATTATATTGTACACTATGAGA 57.374 33.333 14.26 3.16 0.00 3.27
189 192 6.482835 TGTTGCGCTTGATTATATTGTACAC 58.517 36.000 9.73 0.00 0.00 2.90
190 193 6.670077 TGTTGCGCTTGATTATATTGTACA 57.330 33.333 9.73 0.00 0.00 2.90
203 206 2.032799 TGTTCTAGGTTTGTTGCGCTTG 59.967 45.455 9.73 0.00 0.00 4.01
231 234 2.190313 GGGGTGCATGCGATCTGA 59.810 61.111 14.09 0.00 0.00 3.27
238 241 0.244721 GAGAGTTTTGGGGTGCATGC 59.755 55.000 11.82 11.82 0.00 4.06
271 274 2.103941 GGCCCTTGATCACTAGGAAGAG 59.896 54.545 14.09 0.00 40.51 2.85
286 289 2.440796 CGACATGCATGGGCCCTT 60.441 61.111 29.41 15.22 40.13 3.95
308 311 1.580059 TCGTTTAGGAGGGGAAGCAT 58.420 50.000 0.00 0.00 0.00 3.79
351 354 7.205737 TGAACAGTCTTTGTGATAGTACGTA 57.794 36.000 0.00 0.00 40.74 3.57
352 355 6.080648 TGAACAGTCTTTGTGATAGTACGT 57.919 37.500 0.00 0.00 40.74 3.57
353 356 7.402811 TTTGAACAGTCTTTGTGATAGTACG 57.597 36.000 0.00 0.00 40.74 3.67
355 358 9.135843 CGTATTTGAACAGTCTTTGTGATAGTA 57.864 33.333 0.00 0.00 40.74 1.82
356 359 7.656137 ACGTATTTGAACAGTCTTTGTGATAGT 59.344 33.333 0.00 0.00 40.74 2.12
357 360 7.952101 CACGTATTTGAACAGTCTTTGTGATAG 59.048 37.037 0.00 0.00 40.74 2.08
376 379 3.487202 CGCTGCCACGCACGTATT 61.487 61.111 0.00 0.00 33.79 1.89
377 380 4.735132 ACGCTGCCACGCACGTAT 62.735 61.111 10.86 0.00 41.44 3.06
408 416 1.687146 AGCTGGATCGGAGCTTGGA 60.687 57.895 11.20 0.00 44.65 3.53
414 422 0.539051 ACTTGGAAGCTGGATCGGAG 59.461 55.000 0.00 0.00 0.00 4.63
448 456 7.118723 AGTGAATTATTGGGCATCTAGACAAA 58.881 34.615 0.00 0.00 0.00 2.83
450 458 6.252599 AGTGAATTATTGGGCATCTAGACA 57.747 37.500 0.00 0.00 0.00 3.41
451 459 7.067494 ACAAAGTGAATTATTGGGCATCTAGAC 59.933 37.037 0.00 0.00 0.00 2.59
453 461 7.284034 AGACAAAGTGAATTATTGGGCATCTAG 59.716 37.037 0.00 0.00 0.00 2.43
488 503 6.294843 GGTGAATCAAGTAGCTAGGGAGATAC 60.295 46.154 0.00 0.00 43.59 2.24
489 504 5.775701 GGTGAATCAAGTAGCTAGGGAGATA 59.224 44.000 0.00 0.00 0.00 1.98
490 505 4.591072 GGTGAATCAAGTAGCTAGGGAGAT 59.409 45.833 0.00 0.00 0.00 2.75
564 580 0.175760 GCTTGGAGTGCTCGACCATA 59.824 55.000 8.13 1.53 33.56 2.74
568 584 0.319900 TTCTGCTTGGAGTGCTCGAC 60.320 55.000 0.00 0.00 0.00 4.20
571 587 1.304509 GGCTTCTGCTTGGAGTGCTC 61.305 60.000 8.74 0.00 39.59 4.26
576 592 2.097038 CGACGGCTTCTGCTTGGAG 61.097 63.158 0.00 0.00 39.59 3.86
600 616 2.270850 GCAGGGGCCGTAACATGA 59.729 61.111 0.00 0.00 0.00 3.07
611 627 2.688666 TAGAGGTGCTGGCAGGGG 60.689 66.667 17.64 0.00 0.00 4.79
612 628 2.586792 GTAGAGGTGCTGGCAGGG 59.413 66.667 17.64 0.00 0.00 4.45
613 629 2.586792 GGTAGAGGTGCTGGCAGG 59.413 66.667 17.64 0.00 0.00 4.85
614 630 2.586792 GGGTAGAGGTGCTGGCAG 59.413 66.667 10.94 10.94 0.00 4.85
615 631 3.390521 CGGGTAGAGGTGCTGGCA 61.391 66.667 0.00 0.00 0.00 4.92
616 632 4.840005 GCGGGTAGAGGTGCTGGC 62.840 72.222 0.00 0.00 0.00 4.85
617 633 4.514577 CGCGGGTAGAGGTGCTGG 62.515 72.222 0.00 0.00 0.00 4.85
618 634 4.514577 CCGCGGGTAGAGGTGCTG 62.515 72.222 20.10 0.00 34.87 4.41
625 641 4.853142 ATGAGGGCCGCGGGTAGA 62.853 66.667 29.38 0.00 0.00 2.59
626 642 4.609018 CATGAGGGCCGCGGGTAG 62.609 72.222 29.38 0.38 0.00 3.18
631 647 3.680620 TTCCTTCATGAGGGCCGCG 62.681 63.158 18.84 0.00 46.31 6.46
632 648 2.115291 GTTCCTTCATGAGGGCCGC 61.115 63.158 18.84 0.00 46.31 6.53
633 649 0.745845 CTGTTCCTTCATGAGGGCCG 60.746 60.000 18.84 3.47 46.31 6.13
634 650 1.034292 GCTGTTCCTTCATGAGGGCC 61.034 60.000 18.84 11.89 46.31 5.80
635 651 1.034292 GGCTGTTCCTTCATGAGGGC 61.034 60.000 18.84 6.76 46.31 5.19
636 652 0.394899 GGGCTGTTCCTTCATGAGGG 60.395 60.000 17.63 17.63 46.31 4.30
638 654 1.681166 CCTGGGCTGTTCCTTCATGAG 60.681 57.143 0.00 0.00 34.39 2.90
639 655 0.329261 CCTGGGCTGTTCCTTCATGA 59.671 55.000 0.00 0.00 34.39 3.07
640 656 0.329261 TCCTGGGCTGTTCCTTCATG 59.671 55.000 0.00 0.00 34.39 3.07
641 657 0.622665 CTCCTGGGCTGTTCCTTCAT 59.377 55.000 0.00 0.00 34.39 2.57
642 658 2.069776 CTCCTGGGCTGTTCCTTCA 58.930 57.895 0.00 0.00 34.39 3.02
643 659 1.377856 GCTCCTGGGCTGTTCCTTC 60.378 63.158 0.00 0.00 34.39 3.46
644 660 2.759795 GCTCCTGGGCTGTTCCTT 59.240 61.111 0.00 0.00 34.39 3.36
645 661 3.334054 GGCTCCTGGGCTGTTCCT 61.334 66.667 7.03 0.00 37.53 3.36
651 667 3.185203 TTGTTGGGCTCCTGGGCT 61.185 61.111 7.03 0.00 40.65 5.19
665 681 2.613506 GGCTTACGGTTGCGCTTGT 61.614 57.895 9.73 4.21 0.00 3.16
672 688 0.741221 GAGAGCTGGGCTTACGGTTG 60.741 60.000 0.00 0.00 39.88 3.77
678 694 1.614241 GGAACCGAGAGCTGGGCTTA 61.614 60.000 0.00 0.00 39.88 3.09
680 696 3.394836 GGAACCGAGAGCTGGGCT 61.395 66.667 0.00 0.00 43.88 5.19
734 750 2.551071 CCTTCTCCTTTCGTGCCTTCTT 60.551 50.000 0.00 0.00 0.00 2.52
743 760 2.999355 CTCTTCTTGCCTTCTCCTTTCG 59.001 50.000 0.00 0.00 0.00 3.46
745 762 3.906846 TCTCTCTTCTTGCCTTCTCCTTT 59.093 43.478 0.00 0.00 0.00 3.11
746 763 3.515562 TCTCTCTTCTTGCCTTCTCCTT 58.484 45.455 0.00 0.00 0.00 3.36
748 765 3.513515 TCTTCTCTCTTCTTGCCTTCTCC 59.486 47.826 0.00 0.00 0.00 3.71
750 767 3.056891 CGTCTTCTCTCTTCTTGCCTTCT 60.057 47.826 0.00 0.00 0.00 2.85
766 783 2.507324 GCCGCCAGAGTCGTCTTC 60.507 66.667 0.00 0.00 0.00 2.87
800 817 1.961394 CTAGGACGAAATGGGGATCGA 59.039 52.381 1.84 0.00 0.00 3.59
809 826 2.572104 AGGGTTCAAGCTAGGACGAAAT 59.428 45.455 0.00 0.00 0.00 2.17
814 831 2.605837 GCTAGGGTTCAAGCTAGGAC 57.394 55.000 0.00 0.00 35.80 3.85
821 838 3.371965 TGGTAGGTAGCTAGGGTTCAAG 58.628 50.000 0.86 0.00 0.00 3.02
854 880 5.995282 CGATCTAGTACAGGAAGTCTCTGAT 59.005 44.000 0.00 0.00 36.22 2.90
855 881 5.128991 TCGATCTAGTACAGGAAGTCTCTGA 59.871 44.000 0.00 0.00 36.22 3.27
860 886 4.639310 TGGTTCGATCTAGTACAGGAAGTC 59.361 45.833 0.00 0.00 0.00 3.01
863 889 5.258841 TCTTGGTTCGATCTAGTACAGGAA 58.741 41.667 0.00 0.00 0.00 3.36
865 891 4.498345 GCTCTTGGTTCGATCTAGTACAGG 60.498 50.000 0.00 0.00 0.00 4.00
886 912 4.495422 CTCTGATTACCAACTGTTACGCT 58.505 43.478 0.00 0.00 0.00 5.07
924 950 1.883084 GCGCCAAATCGGACGAGAT 60.883 57.895 0.00 0.00 36.70 2.75
926 952 2.296692 CTTGCGCCAAATCGGACGAG 62.297 60.000 4.18 0.00 36.70 4.18
929 955 2.202479 GCTTGCGCCAAATCGGAC 60.202 61.111 4.18 0.00 36.56 4.79
962 988 1.412710 GCCTGGTCTGGATAATCGACA 59.587 52.381 0.00 0.00 0.00 4.35
978 1004 4.347453 GTTGCCTTGCCGTGCCTG 62.347 66.667 0.00 0.00 0.00 4.85
993 1019 1.079127 CTGTTCCTCCATCGCGGTT 60.079 57.895 6.13 0.00 35.57 4.44
1008 1034 0.326264 CTGCTAAGGCCTTGGTCTGT 59.674 55.000 28.77 1.45 37.74 3.41
1021 1047 2.571757 CGCCGTCAGGTCTGCTAA 59.428 61.111 0.00 0.00 40.50 3.09
1050 1076 0.842613 CGTCGATCTTCGCTGACATG 59.157 55.000 0.00 0.00 40.21 3.21
1056 1082 2.716244 ATCGCGTCGATCTTCGCT 59.284 55.556 21.98 8.03 43.45 4.93
1161 1187 1.654220 CTTGTCCAACAACAGCCCG 59.346 57.895 0.00 0.00 33.96 6.13
1171 1197 1.600636 CGCTCTTGCCCTTGTCCAA 60.601 57.895 0.00 0.00 35.36 3.53
1172 1198 2.032528 CGCTCTTGCCCTTGTCCA 59.967 61.111 0.00 0.00 35.36 4.02
1223 1249 3.061848 GTGGTTGGGATGGTGGCG 61.062 66.667 0.00 0.00 0.00 5.69
1230 1256 3.712907 CGGACCGGTGGTTGGGAT 61.713 66.667 14.63 0.00 35.25 3.85
1243 1269 2.202987 CAGATCCAGCAGCCGGAC 60.203 66.667 5.05 0.00 34.69 4.79
1365 1391 1.050988 ACATCCCCCGGTGATCTGAG 61.051 60.000 0.00 0.00 0.00 3.35
1366 1392 1.002921 ACATCCCCCGGTGATCTGA 59.997 57.895 0.00 0.00 0.00 3.27
1450 1476 5.904169 TCTCTCCCATGAATGAAATCTCTCT 59.096 40.000 0.00 0.00 0.00 3.10
1457 1483 2.511218 CCCCTCTCTCCCATGAATGAAA 59.489 50.000 0.00 0.00 0.00 2.69
1482 1508 1.064979 GGGGGATAGCGAGAAAAACCA 60.065 52.381 0.00 0.00 0.00 3.67
1555 1581 0.966179 TAAGCCTCGCACTTCAGACA 59.034 50.000 0.00 0.00 0.00 3.41
1584 1610 3.811083 AGTATCCGGACTCAGAGTACAG 58.189 50.000 6.12 1.19 0.00 2.74
1644 1670 7.445402 GCATTGGTAGATTGTAACCATGATAGT 59.555 37.037 0.00 0.00 44.98 2.12
1668 1694 0.037326 CTTGGTAAGCGAGGTGAGCA 60.037 55.000 0.00 0.00 37.01 4.26
1691 1717 1.083489 CGCGTTAGCAAATTCCTCCA 58.917 50.000 0.00 0.00 45.49 3.86
1698 1724 1.067142 TCAGAGACCGCGTTAGCAAAT 60.067 47.619 4.92 0.00 45.49 2.32
1715 1741 2.045926 CCCGCCCAAACTCCTCAG 60.046 66.667 0.00 0.00 0.00 3.35
1720 1746 2.125766 AACTCCTCCCGCCCAAACTC 62.126 60.000 0.00 0.00 0.00 3.01
1772 1798 3.303135 TCACCGTTCCGCTCTGCT 61.303 61.111 0.00 0.00 0.00 4.24
1791 1817 8.045176 ACTGAGTAAATTTTTCTGCATACTCC 57.955 34.615 14.23 1.92 38.83 3.85
1900 1926 1.135972 CATTACCACAGCTGCACGAAC 60.136 52.381 15.27 0.00 0.00 3.95
1918 1944 2.095768 CGAGTGTTTTTGGACGATGCAT 60.096 45.455 0.00 0.00 0.00 3.96
1951 1977 0.183492 TCCTGCAGACAAGCAAGGTT 59.817 50.000 17.39 0.00 45.13 3.50
2064 2096 2.363925 GGCGGAGGTGGTAGAGGT 60.364 66.667 0.00 0.00 0.00 3.85
2067 2099 4.371417 ACCGGCGGAGGTGGTAGA 62.371 66.667 35.78 0.00 44.07 2.59
2100 2132 1.833787 ATTCCGTTGGTGCTACCGGT 61.834 55.000 13.98 13.98 42.58 5.28
2160 2192 0.609406 CGACTCTGTCCTCAGGTGGA 60.609 60.000 0.00 0.00 41.59 4.02
2256 2291 4.514585 AGTTGCACGGTTGGCCCA 62.515 61.111 0.00 0.00 0.00 5.36
2322 2357 3.883549 GGGATGGGCTCCTCTGGC 61.884 72.222 0.00 0.00 44.28 4.85
2323 2358 0.474466 TATGGGATGGGCTCCTCTGG 60.474 60.000 0.00 0.00 44.28 3.86
2328 2363 2.158475 TGATTGTTATGGGATGGGCTCC 60.158 50.000 0.00 0.00 44.11 4.70
2336 2371 3.605634 CTCGGTGTTGATTGTTATGGGA 58.394 45.455 0.00 0.00 0.00 4.37
2341 2376 2.442212 TCGCTCGGTGTTGATTGTTA 57.558 45.000 0.00 0.00 0.00 2.41
2397 2432 0.248702 GTGACTCGGCTCCTTCGATC 60.249 60.000 0.00 0.00 36.01 3.69
2406 2441 0.324368 TGATGGTAGGTGACTCGGCT 60.324 55.000 0.00 0.00 43.67 5.52
2418 2453 1.596603 CATGAAGGCGCATGATGGTA 58.403 50.000 10.83 0.00 46.64 3.25
2421 2456 1.105167 ACCCATGAAGGCGCATGATG 61.105 55.000 20.15 8.59 46.64 3.07
2423 2458 1.750018 CACCCATGAAGGCGCATGA 60.750 57.895 20.15 0.00 46.64 3.07
2433 2468 1.497309 GGTCCTGAACCCACCCATGA 61.497 60.000 0.00 0.00 42.85 3.07
2453 2488 1.338973 CCACAAGCATCAGCACTTTGT 59.661 47.619 0.00 0.00 45.49 2.83
2455 2490 1.610522 GTCCACAAGCATCAGCACTTT 59.389 47.619 0.00 0.00 45.49 2.66
2469 2504 1.156095 TGAGGAGCCAGAGTCCACA 59.844 57.895 0.00 0.00 36.43 4.17
2529 2565 2.844451 GCTTTTGCACGCCTCCACA 61.844 57.895 0.00 0.00 46.58 4.17
2560 2596 1.377725 CTCCGCCATTTGCCACTCT 60.378 57.895 0.00 0.00 36.24 3.24
2577 2613 1.421268 TCCCTGTTGCACTTCATCACT 59.579 47.619 0.00 0.00 0.00 3.41
2680 2716 0.539438 AGCCAGTCGATGCCCAAAAA 60.539 50.000 0.00 0.00 0.00 1.94
2683 2719 2.268920 GAGCCAGTCGATGCCCAA 59.731 61.111 0.00 0.00 0.00 4.12
2720 2756 1.070758 TCTTCTCCTTCCAGTGCACAC 59.929 52.381 21.04 0.00 0.00 3.82
2755 2791 2.562912 GACTTGTGTGCCGCCATG 59.437 61.111 0.00 0.00 0.00 3.66
2759 2795 2.186826 AGTTGGACTTGTGTGCCGC 61.187 57.895 0.00 0.00 33.32 6.53
2802 2838 1.382522 CGGATAGTTGCTGGCATTGT 58.617 50.000 0.00 0.00 0.00 2.71
2865 2901 1.525197 GTCGCACAAAGATGAACGACA 59.475 47.619 16.98 0.00 47.00 4.35
2877 2913 1.299850 CTCCACAGTCGTCGCACAA 60.300 57.895 0.00 0.00 0.00 3.33
2891 2927 3.578716 CTCTGTAACTTTGACTCCCTCCA 59.421 47.826 0.00 0.00 0.00 3.86
2895 2931 3.330267 CAGCTCTGTAACTTTGACTCCC 58.670 50.000 0.00 0.00 0.00 4.30
2906 2942 1.003355 GGCACTGGCAGCTCTGTAA 60.003 57.895 15.89 0.00 43.71 2.41
2952 2988 3.251004 GCTCCTCAAACAAGTGTTGGTAG 59.749 47.826 0.00 0.00 38.44 3.18
2962 2998 2.250939 CGCGTGGCTCCTCAAACAA 61.251 57.895 0.00 0.00 0.00 2.83
3181 3217 0.814457 ACACAAAAGCGCCAAGTCAA 59.186 45.000 2.29 0.00 0.00 3.18
3228 3264 2.604046 AGGGGAATCGATTCTTCACG 57.396 50.000 31.32 0.00 37.00 4.35
3240 3276 0.107017 CGATGACTGGCAAGGGGAAT 60.107 55.000 0.00 0.00 0.00 3.01
3286 3322 0.538287 AGGCTGGTGAAGAACTTGGC 60.538 55.000 0.00 0.00 0.00 4.52
3310 3346 4.382320 GTGGTACCCCGAGCGCAA 62.382 66.667 11.47 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.