Multiple sequence alignment - TraesCS1A01G073600

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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 TraesCS1A01G073600 chr1A 100.000 3254 0 0 1 3254 57400723 57397470 0.000000e+00 6010.0
1 TraesCS1A01G073600 chr1A 93.201 1765 102 14 593 2354 57185017 57186766 0.000000e+00 2579.0
2 TraesCS1A01G073600 chr1A 79.357 1027 201 11 664 1687 49346792 49347810 0.000000e+00 712.0
3 TraesCS1A01G073600 chr1A 94.005 417 16 4 2353 2769 57187538 57187945 9.910000e-175 623.0
4 TraesCS1A01G073600 chr1A 87.785 483 48 7 2770 3252 57187976 57188447 3.670000e-154 555.0
5 TraesCS1A01G073600 chr1A 81.934 548 96 3 1690 2236 36606715 36607260 8.230000e-126 460.0
6 TraesCS1A01G073600 chr1A 84.815 270 31 2 2805 3065 293745868 293746136 2.490000e-66 263.0
7 TraesCS1A01G073600 chr1A 78.041 296 42 18 198 485 38586613 38586333 7.220000e-37 165.0
8 TraesCS1A01G073600 chr1A 81.757 148 24 1 46 193 577396777 577396633 1.590000e-23 121.0
9 TraesCS1A01G073600 chr1D 91.682 2729 162 24 570 3254 58444163 58446870 0.000000e+00 3722.0
10 TraesCS1A01G073600 chr1D 90.137 2636 186 36 12 2614 58623615 58621021 0.000000e+00 3360.0
11 TraesCS1A01G073600 chr1D 79.787 1034 191 17 662 1687 50059255 50060278 0.000000e+00 736.0
12 TraesCS1A01G073600 chr1D 78.864 1074 203 20 628 1687 49426354 49425291 0.000000e+00 704.0
13 TraesCS1A01G073600 chr1D 78.802 1052 202 20 644 1687 49956282 49957320 0.000000e+00 688.0
14 TraesCS1A01G073600 chr1D 78.773 1027 194 21 674 1687 49617061 49618076 0.000000e+00 667.0
15 TraesCS1A01G073600 chr1D 79.911 901 148 28 630 1512 58628690 58627805 5.920000e-177 630.0
16 TraesCS1A01G073600 chr1D 77.565 1043 198 26 662 1687 49234963 49233940 6.010000e-167 597.0
17 TraesCS1A01G073600 chr1D 78.016 887 172 18 630 1509 58764192 58763322 1.330000e-148 536.0
18 TraesCS1A01G073600 chr1D 82.940 551 92 2 1687 2236 49975123 49975672 2.260000e-136 496.0
19 TraesCS1A01G073600 chr1D 79.903 617 106 17 1708 2316 36616306 36615700 1.390000e-118 436.0
20 TraesCS1A01G073600 chr1D 77.888 303 59 8 785 1084 49576961 49576664 7.170000e-42 182.0
21 TraesCS1A01G073600 chr1D 81.448 221 22 9 280 498 360426132 360426335 2.600000e-36 163.0
22 TraesCS1A01G073600 chr1B 91.095 831 58 11 1948 2772 94211311 94210491 0.000000e+00 1110.0
23 TraesCS1A01G073600 chr1B 79.537 1036 194 14 662 1687 56501801 56500774 0.000000e+00 723.0
24 TraesCS1A01G073600 chr1B 77.961 1030 206 17 662 1680 70333810 70334829 2.760000e-175 625.0
25 TraesCS1A01G073600 chr1B 95.122 328 15 1 1627 1953 94224180 94223853 1.730000e-142 516.0
26 TraesCS1A01G073600 chr1B 83.032 554 90 4 1687 2237 70497887 70498439 1.740000e-137 499.0
27 TraesCS1A01G073600 chr1B 78.969 718 134 13 977 1687 70185808 70186515 1.060000e-129 473.0
28 TraesCS1A01G073600 chr1B 81.934 548 95 3 1690 2236 56499930 56499386 8.230000e-126 460.0
29 TraesCS1A01G073600 chr1B 77.840 537 79 21 1 517 543078560 543078044 2.450000e-76 296.0
30 TraesCS1A01G073600 chr6B 80.256 547 65 20 1 514 498671443 498670907 3.970000e-99 372.0
31 TraesCS1A01G073600 chr6B 97.778 45 0 1 527 570 498670872 498670828 3.480000e-10 76.8
32 TraesCS1A01G073600 chr3B 80.747 509 62 20 7 503 65346239 65345755 6.630000e-97 364.0
33 TraesCS1A01G073600 chr3B 81.624 468 45 18 40 486 611141516 611141963 1.860000e-92 350.0
34 TraesCS1A01G073600 chr3B 80.290 482 63 21 40 501 672004985 672004516 5.200000e-88 335.0
35 TraesCS1A01G073600 chr3B 84.783 138 16 3 2927 3064 50963928 50964060 2.040000e-27 134.0
36 TraesCS1A01G073600 chr7B 80.189 530 60 31 1 503 68830236 68830747 3.990000e-94 355.0
37 TraesCS1A01G073600 chr7B 79.960 499 50 18 33 503 424570068 424569592 4.050000e-84 322.0
38 TraesCS1A01G073600 chr5A 78.275 603 82 25 1 570 480178023 480178609 3.110000e-90 342.0
39 TraesCS1A01G073600 chr5A 94.444 54 3 0 3002 3055 11884544 11884491 2.080000e-12 84.2
40 TraesCS1A01G073600 chr2D 79.511 532 64 17 1 502 59169821 59169305 1.450000e-88 337.0
41 TraesCS1A01G073600 chr2D 82.824 262 42 2 2805 3065 155470678 155470937 7.020000e-57 231.0
42 TraesCS1A01G073600 chr2D 73.739 476 80 26 37 485 559121678 559121221 9.410000e-31 145.0
43 TraesCS1A01G073600 chr3D 79.017 529 56 28 1 486 531687916 531688432 8.770000e-81 311.0
44 TraesCS1A01G073600 chr3D 78.024 496 64 19 1 477 370531398 370530929 1.490000e-68 270.0
45 TraesCS1A01G073600 chr7A 77.090 598 78 28 1 570 461924223 461923657 1.140000e-74 291.0
46 TraesCS1A01G073600 chr7A 80.374 214 33 7 2826 3034 49426840 49426631 1.560000e-33 154.0
47 TraesCS1A01G073600 chr7A 81.967 122 21 1 449 569 12456351 12456472 5.740000e-18 102.0
48 TraesCS1A01G073600 chr5B 76.835 613 83 40 1 570 295662054 295661458 1.140000e-74 291.0
49 TraesCS1A01G073600 chr4B 78.210 514 62 24 1 498 284640023 284640502 1.910000e-72 283.0
50 TraesCS1A01G073600 chr4B 84.568 162 16 3 33 194 412379459 412379307 5.620000e-33 152.0
51 TraesCS1A01G073600 chrUn 77.298 533 79 24 1 505 361607287 361607805 3.200000e-70 276.0
52 TraesCS1A01G073600 chr2B 77.032 566 67 26 38 570 423824129 423823594 1.920000e-67 267.0
53 TraesCS1A01G073600 chr2B 77.419 527 53 36 1 502 38628436 38628921 1.500000e-63 254.0
54 TraesCS1A01G073600 chr2B 83.206 262 41 2 2805 3065 212770031 212770290 1.510000e-58 237.0
55 TraesCS1A01G073600 chr6A 77.393 491 64 31 40 495 27567529 27568007 6.970000e-62 248.0
56 TraesCS1A01G073600 chr6A 71.534 541 132 18 1025 1557 66423812 66424338 3.410000e-25 126.0
57 TraesCS1A01G073600 chr3A 85.106 141 16 3 2924 3064 40561715 40561850 4.380000e-29 139.0


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 TraesCS1A01G073600 chr1A 57397470 57400723 3253 True 6010.000000 6010 100.000000 1 3254 1 chr1A.!!$R2 3253
1 TraesCS1A01G073600 chr1A 57185017 57188447 3430 False 1252.333333 2579 91.663667 593 3252 3 chr1A.!!$F4 2659
2 TraesCS1A01G073600 chr1A 49346792 49347810 1018 False 712.000000 712 79.357000 664 1687 1 chr1A.!!$F2 1023
3 TraesCS1A01G073600 chr1A 36606715 36607260 545 False 460.000000 460 81.934000 1690 2236 1 chr1A.!!$F1 546
4 TraesCS1A01G073600 chr1D 58444163 58446870 2707 False 3722.000000 3722 91.682000 570 3254 1 chr1D.!!$F5 2684
5 TraesCS1A01G073600 chr1D 58621021 58623615 2594 True 3360.000000 3360 90.137000 12 2614 1 chr1D.!!$R5 2602
6 TraesCS1A01G073600 chr1D 50059255 50060278 1023 False 736.000000 736 79.787000 662 1687 1 chr1D.!!$F4 1025
7 TraesCS1A01G073600 chr1D 49425291 49426354 1063 True 704.000000 704 78.864000 628 1687 1 chr1D.!!$R3 1059
8 TraesCS1A01G073600 chr1D 49956282 49957320 1038 False 688.000000 688 78.802000 644 1687 1 chr1D.!!$F2 1043
9 TraesCS1A01G073600 chr1D 49617061 49618076 1015 False 667.000000 667 78.773000 674 1687 1 chr1D.!!$F1 1013
10 TraesCS1A01G073600 chr1D 58627805 58628690 885 True 630.000000 630 79.911000 630 1512 1 chr1D.!!$R6 882
11 TraesCS1A01G073600 chr1D 49233940 49234963 1023 True 597.000000 597 77.565000 662 1687 1 chr1D.!!$R2 1025
12 TraesCS1A01G073600 chr1D 58763322 58764192 870 True 536.000000 536 78.016000 630 1509 1 chr1D.!!$R7 879
13 TraesCS1A01G073600 chr1D 49975123 49975672 549 False 496.000000 496 82.940000 1687 2236 1 chr1D.!!$F3 549
14 TraesCS1A01G073600 chr1D 36615700 36616306 606 True 436.000000 436 79.903000 1708 2316 1 chr1D.!!$R1 608
15 TraesCS1A01G073600 chr1B 94210491 94211311 820 True 1110.000000 1110 91.095000 1948 2772 1 chr1B.!!$R1 824
16 TraesCS1A01G073600 chr1B 70333810 70334829 1019 False 625.000000 625 77.961000 662 1680 1 chr1B.!!$F2 1018
17 TraesCS1A01G073600 chr1B 56499386 56501801 2415 True 591.500000 723 80.735500 662 2236 2 chr1B.!!$R4 1574
18 TraesCS1A01G073600 chr1B 70497887 70498439 552 False 499.000000 499 83.032000 1687 2237 1 chr1B.!!$F3 550
19 TraesCS1A01G073600 chr1B 70185808 70186515 707 False 473.000000 473 78.969000 977 1687 1 chr1B.!!$F1 710
20 TraesCS1A01G073600 chr1B 543078044 543078560 516 True 296.000000 296 77.840000 1 517 1 chr1B.!!$R3 516
21 TraesCS1A01G073600 chr6B 498670828 498671443 615 True 224.400000 372 89.017000 1 570 2 chr6B.!!$R1 569
22 TraesCS1A01G073600 chr7B 68830236 68830747 511 False 355.000000 355 80.189000 1 503 1 chr7B.!!$F1 502
23 TraesCS1A01G073600 chr5A 480178023 480178609 586 False 342.000000 342 78.275000 1 570 1 chr5A.!!$F1 569
24 TraesCS1A01G073600 chr2D 59169305 59169821 516 True 337.000000 337 79.511000 1 502 1 chr2D.!!$R1 501
25 TraesCS1A01G073600 chr3D 531687916 531688432 516 False 311.000000 311 79.017000 1 486 1 chr3D.!!$F1 485
26 TraesCS1A01G073600 chr7A 461923657 461924223 566 True 291.000000 291 77.090000 1 570 1 chr7A.!!$R2 569
27 TraesCS1A01G073600 chr5B 295661458 295662054 596 True 291.000000 291 76.835000 1 570 1 chr5B.!!$R1 569
28 TraesCS1A01G073600 chrUn 361607287 361607805 518 False 276.000000 276 77.298000 1 505 1 chrUn.!!$F1 504
29 TraesCS1A01G073600 chr2B 423823594 423824129 535 True 267.000000 267 77.032000 38 570 1 chr2B.!!$R1 532

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
86 113 0.119155 ATGGAGGTGGAGGACAAGGA 59.881 55.0 0.00 0.00 0.00 3.36 F
89 116 0.252284 GAGGTGGAGGACAAGGAGGA 60.252 60.0 0.00 0.00 0.00 3.71 F
95 122 0.252284 GAGGACAAGGAGGAGGTGGA 60.252 60.0 0.00 0.00 0.00 4.02 F
96 123 0.252467 AGGACAAGGAGGAGGTGGAG 60.252 60.0 0.00 0.00 0.00 3.86 F
1642 1826 0.308684 TACTCGCAACTCGTTCGTGT 59.691 50.0 11.13 11.13 39.67 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1424 1605 0.169672 GCACAGCGCATCAATCACTT 59.830 50.00 11.47 0.0 41.79 3.16 R
1642 1826 0.251742 CCATGGTTGCAAAGGGAGGA 60.252 55.00 0.00 0.0 0.00 3.71 R
1698 2723 5.754890 GCTCACTGTTGTTCCATTTTCAATT 59.245 36.00 0.00 0.0 0.00 2.32 R
2231 3265 4.780815 TCAACTGTGTCTGACTCCAAAAT 58.219 39.13 9.51 0.0 0.00 1.82 R
2797 4648 0.320858 TCGCCGGCAGTGTATTCAAA 60.321 50.00 28.98 0.0 0.00 2.69 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
81 108 0.976073 TTCCGATGGAGGTGGAGGAC 60.976 60.000 0.00 0.00 31.21 3.85
82 109 1.685765 CCGATGGAGGTGGAGGACA 60.686 63.158 0.00 0.00 0.00 4.02
83 110 1.264749 CCGATGGAGGTGGAGGACAA 61.265 60.000 0.00 0.00 0.00 3.18
84 111 0.176680 CGATGGAGGTGGAGGACAAG 59.823 60.000 0.00 0.00 0.00 3.16
85 112 0.543749 GATGGAGGTGGAGGACAAGG 59.456 60.000 0.00 0.00 0.00 3.61
86 113 0.119155 ATGGAGGTGGAGGACAAGGA 59.881 55.000 0.00 0.00 0.00 3.36
87 114 0.545309 TGGAGGTGGAGGACAAGGAG 60.545 60.000 0.00 0.00 0.00 3.69
88 115 1.268283 GGAGGTGGAGGACAAGGAGG 61.268 65.000 0.00 0.00 0.00 4.30
89 116 0.252284 GAGGTGGAGGACAAGGAGGA 60.252 60.000 0.00 0.00 0.00 3.71
90 117 0.252467 AGGTGGAGGACAAGGAGGAG 60.252 60.000 0.00 0.00 0.00 3.69
91 118 1.268283 GGTGGAGGACAAGGAGGAGG 61.268 65.000 0.00 0.00 0.00 4.30
92 119 0.545548 GTGGAGGACAAGGAGGAGGT 60.546 60.000 0.00 0.00 0.00 3.85
93 120 0.545309 TGGAGGACAAGGAGGAGGTG 60.545 60.000 0.00 0.00 0.00 4.00
94 121 1.268283 GGAGGACAAGGAGGAGGTGG 61.268 65.000 0.00 0.00 0.00 4.61
95 122 0.252284 GAGGACAAGGAGGAGGTGGA 60.252 60.000 0.00 0.00 0.00 4.02
96 123 0.252467 AGGACAAGGAGGAGGTGGAG 60.252 60.000 0.00 0.00 0.00 3.86
103 148 3.663815 GAGGAGGTGGAGGAGCCGA 62.664 68.421 0.00 0.00 40.66 5.54
175 256 1.158484 CGCCTAGTCCGACGAGATGA 61.158 60.000 10.00 0.00 0.00 2.92
262 355 4.965858 CGGAGATCGACGCGCTCC 62.966 72.222 19.69 19.69 43.73 4.70
333 459 4.172512 AGGCGGAGATGCAGCTGG 62.173 66.667 10.40 1.48 37.85 4.85
377 503 4.279671 GGTATGGAGATCGTTGACATCTCT 59.720 45.833 9.99 0.00 44.06 3.10
384 510 1.251355 CGTTGACATCTCTGACGACG 58.749 55.000 0.00 0.00 44.33 5.12
385 511 2.613730 GTTGACATCTCTGACGACGA 57.386 50.000 0.00 0.00 0.00 4.20
386 512 2.510874 GTTGACATCTCTGACGACGAG 58.489 52.381 0.00 0.00 0.00 4.18
387 513 1.809684 TGACATCTCTGACGACGAGT 58.190 50.000 0.00 0.00 0.00 4.18
388 514 2.968675 TGACATCTCTGACGACGAGTA 58.031 47.619 0.00 0.00 0.00 2.59
389 515 2.671888 TGACATCTCTGACGACGAGTAC 59.328 50.000 0.00 0.00 0.00 2.73
390 516 2.931325 GACATCTCTGACGACGAGTACT 59.069 50.000 0.00 0.00 0.00 2.73
391 517 2.931325 ACATCTCTGACGACGAGTACTC 59.069 50.000 13.18 13.18 0.00 2.59
442 569 8.354426 ACGTAGGTTTATTTTAGTTTGCATGTT 58.646 29.630 0.00 0.00 0.00 2.71
486 613 2.945080 ATGAGATGTCCGGATGCAAT 57.055 45.000 7.81 0.00 0.00 3.56
498 625 6.375736 TGTCCGGATGCAATAAGTGAAATTTA 59.624 34.615 7.81 0.00 0.00 1.40
517 644 8.408043 AAATTTAAGGCATATCCGATCATTGA 57.592 30.769 0.00 0.00 40.77 2.57
528 655 1.821216 GATCATTGACCGTGGGTGTT 58.179 50.000 0.00 0.00 35.25 3.32
530 657 1.313772 TCATTGACCGTGGGTGTTTG 58.686 50.000 0.00 0.00 35.25 2.93
531 658 1.134068 TCATTGACCGTGGGTGTTTGA 60.134 47.619 0.00 0.00 35.25 2.69
577 727 6.599638 GGTTGTAGATGCTCTAAGTCCAAAAT 59.400 38.462 0.00 0.00 29.58 1.82
589 739 2.697431 TCCAAAATGGAAAACGCTCG 57.303 45.000 0.00 0.00 45.00 5.03
658 809 3.941188 CACTCCACCACGCCCACT 61.941 66.667 0.00 0.00 0.00 4.00
692 857 3.151022 GCCTCTCCTCCACCTCCG 61.151 72.222 0.00 0.00 0.00 4.63
946 1114 4.379243 AACCGCCTGTGCCGAGAG 62.379 66.667 0.00 0.00 0.00 3.20
959 1130 2.124403 GAGAGCCAGCCCACATGG 60.124 66.667 0.00 0.00 41.04 3.66
1185 1362 2.967397 CCTGAACTCGGCCGTGTA 59.033 61.111 30.97 16.86 0.00 2.90
1194 1371 2.584608 GGCCGTGTACCTGATGCT 59.415 61.111 0.00 0.00 0.00 3.79
1281 1460 3.204526 GCTCCAGATGATGTGGAAAGAG 58.795 50.000 12.70 2.24 43.68 2.85
1311 1492 2.828549 GCCCCTAATGTGGTGGCG 60.829 66.667 0.00 0.00 35.09 5.69
1564 1748 2.036256 CCTCTTTGGGCTGGTGGG 59.964 66.667 0.00 0.00 0.00 4.61
1642 1826 0.308684 TACTCGCAACTCGTTCGTGT 59.691 50.000 11.13 11.13 39.67 4.49
1698 2723 1.002430 GCGGAGATTGCCCATCAGATA 59.998 52.381 0.00 0.00 33.75 1.98
2004 3038 7.228108 TCAATGGAAGAAGCTGATCATATGTTC 59.772 37.037 1.90 4.70 0.00 3.18
2436 4254 0.835543 TTTGGGCATGGAAAGGTGGG 60.836 55.000 0.00 0.00 0.00 4.61
2464 4282 2.304180 AGTCTAGCAGAACTGGTTGCAT 59.696 45.455 11.61 0.45 42.67 3.96
2465 4283 3.077359 GTCTAGCAGAACTGGTTGCATT 58.923 45.455 11.61 0.00 42.67 3.56
2505 4325 5.036916 TCTGGTTGAACAGGGAAGGTATAT 58.963 41.667 0.00 0.00 38.98 0.86
2683 4504 7.681939 TGCAAGGGTAGATTTACTTTAAGTG 57.318 36.000 8.00 0.00 0.00 3.16
2710 4531 6.467194 GGGGAATTTGTGATATATGTCAGGGA 60.467 42.308 1.89 0.00 0.00 4.20
2772 4593 9.223099 TGATGCTATGTTCATTTAGTGGATATG 57.777 33.333 0.00 0.00 0.00 1.78
2773 4594 9.440773 GATGCTATGTTCATTTAGTGGATATGA 57.559 33.333 0.00 0.00 0.00 2.15
2821 4672 1.676678 ATACACTGCCGGCGATGAGT 61.677 55.000 30.33 21.71 0.00 3.41
2823 4674 3.381983 ACTGCCGGCGATGAGTGA 61.382 61.111 23.90 0.00 0.00 3.41
2831 4682 2.481276 CCGGCGATGAGTGATGTCTTTA 60.481 50.000 9.30 0.00 0.00 1.85
2833 4684 3.489229 CGGCGATGAGTGATGTCTTTAGA 60.489 47.826 0.00 0.00 0.00 2.10
2849 4700 2.299993 TAGAAGATTGCAGGCTGACG 57.700 50.000 20.86 0.00 0.00 4.35
2874 4725 2.461695 CTCTCTTCCTTGACTGCCCTA 58.538 52.381 0.00 0.00 0.00 3.53
2899 4750 3.253432 CCTTGGAGCTTAGTTGTTTGGTC 59.747 47.826 0.00 0.00 0.00 4.02
2913 4764 2.281539 TTGGTCGTAGTCCTGTCTGA 57.718 50.000 0.00 0.00 36.46 3.27
2971 4822 1.156736 AGAACAATAGTGTGGCGTGC 58.843 50.000 0.00 0.00 38.27 5.34
2989 4840 3.290098 CGTAGCGTGTTTGAATGGC 57.710 52.632 0.00 0.00 0.00 4.40
3055 4906 6.594744 TGATACACATATCTCCTGCATGTTT 58.405 36.000 0.00 0.00 38.47 2.83
3058 4909 4.880120 ACACATATCTCCTGCATGTTTGAG 59.120 41.667 0.00 0.00 30.59 3.02
3059 4910 5.121105 CACATATCTCCTGCATGTTTGAGA 58.879 41.667 11.02 11.02 38.17 3.27
3144 4995 5.766670 TGAGAGCACACTTCATTGAAGATTT 59.233 36.000 28.60 11.97 41.71 2.17
3148 4999 7.229306 AGAGCACACTTCATTGAAGATTTAACA 59.771 33.333 28.60 0.00 41.71 2.41
3150 5001 8.196771 AGCACACTTCATTGAAGATTTAACAAA 58.803 29.630 28.60 0.00 41.71 2.83
3178 5029 3.709653 TGCTCCTCGTAATGTAGGGAAAT 59.290 43.478 0.00 0.00 33.40 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 108 1.621672 GCTCCTCCACCTCCTCCTTG 61.622 65.000 0.00 0.00 0.00 3.61
82 109 1.306568 GCTCCTCCACCTCCTCCTT 60.307 63.158 0.00 0.00 0.00 3.36
83 110 2.366570 GCTCCTCCACCTCCTCCT 59.633 66.667 0.00 0.00 0.00 3.69
84 111 2.766229 GGCTCCTCCACCTCCTCC 60.766 72.222 0.00 0.00 34.01 4.30
85 112 3.151022 CGGCTCCTCCACCTCCTC 61.151 72.222 0.00 0.00 34.01 3.71
86 113 3.239627 TTCGGCTCCTCCACCTCCT 62.240 63.158 0.00 0.00 34.01 3.69
87 114 2.683933 TTCGGCTCCTCCACCTCC 60.684 66.667 0.00 0.00 34.01 4.30
88 115 2.579738 GTTCGGCTCCTCCACCTC 59.420 66.667 0.00 0.00 34.01 3.85
89 116 3.003763 GGTTCGGCTCCTCCACCT 61.004 66.667 0.00 0.00 30.27 4.00
90 117 3.316573 CTGGTTCGGCTCCTCCACC 62.317 68.421 0.00 0.00 32.82 4.61
91 118 2.266055 CTGGTTCGGCTCCTCCAC 59.734 66.667 0.00 0.00 34.01 4.02
92 119 3.706373 GCTGGTTCGGCTCCTCCA 61.706 66.667 0.00 0.00 32.24 3.86
93 120 3.672295 CTGCTGGTTCGGCTCCTCC 62.672 68.421 0.30 0.00 36.58 4.30
94 121 2.125350 CTGCTGGTTCGGCTCCTC 60.125 66.667 0.30 0.00 36.58 3.71
95 122 3.710722 CCTGCTGGTTCGGCTCCT 61.711 66.667 0.51 0.00 36.58 3.69
96 123 4.021925 ACCTGCTGGTTCGGCTCC 62.022 66.667 9.88 0.00 46.05 4.70
103 148 4.643387 GGCCGACACCTGCTGGTT 62.643 66.667 13.36 4.90 46.05 3.67
175 256 2.056223 GGATGGCATGCTGCTTGGT 61.056 57.895 18.92 0.00 44.28 3.67
194 275 3.902881 CCTCCACATAGGCCTCATATC 57.097 52.381 9.68 0.00 37.29 1.63
311 416 3.157252 TGCATCTCCGCCTCCTCC 61.157 66.667 0.00 0.00 0.00 4.30
312 417 2.420890 CTGCATCTCCGCCTCCTC 59.579 66.667 0.00 0.00 0.00 3.71
313 418 3.859414 GCTGCATCTCCGCCTCCT 61.859 66.667 0.00 0.00 0.00 3.69
314 419 3.859414 AGCTGCATCTCCGCCTCC 61.859 66.667 1.02 0.00 0.00 4.30
315 420 2.588314 CAGCTGCATCTCCGCCTC 60.588 66.667 0.00 0.00 0.00 4.70
316 421 4.172512 CCAGCTGCATCTCCGCCT 62.173 66.667 8.66 0.00 0.00 5.52
356 482 5.009110 GTCAGAGATGTCAACGATCTCCATA 59.991 44.000 7.28 0.00 44.82 2.74
384 510 5.107760 CGATCAACTAGCTACTCGAGTACTC 60.108 48.000 21.25 13.18 30.15 2.59
385 511 4.746115 CGATCAACTAGCTACTCGAGTACT 59.254 45.833 21.25 22.05 30.15 2.73
386 512 4.744137 TCGATCAACTAGCTACTCGAGTAC 59.256 45.833 21.25 16.87 32.08 2.73
387 513 4.744137 GTCGATCAACTAGCTACTCGAGTA 59.256 45.833 23.34 23.34 36.00 2.59
388 514 3.556775 GTCGATCAACTAGCTACTCGAGT 59.443 47.826 23.66 23.66 36.00 4.18
389 515 3.362207 CGTCGATCAACTAGCTACTCGAG 60.362 52.174 11.84 11.84 36.00 4.04
390 516 2.538861 CGTCGATCAACTAGCTACTCGA 59.461 50.000 0.00 4.53 33.23 4.04
391 517 2.284684 ACGTCGATCAACTAGCTACTCG 59.715 50.000 0.00 0.00 0.00 4.18
486 613 8.918202 ATCGGATATGCCTTAAATTTCACTTA 57.082 30.769 0.00 0.00 0.00 2.24
498 625 3.679389 GGTCAATGATCGGATATGCCTT 58.321 45.455 0.00 0.00 0.00 4.35
517 644 2.333701 GACCCTCAAACACCCACGGT 62.334 60.000 0.00 0.00 35.62 4.83
528 655 5.815222 CACATATGACAAATACGACCCTCAA 59.185 40.000 10.38 0.00 0.00 3.02
530 657 4.750098 CCACATATGACAAATACGACCCTC 59.250 45.833 10.38 0.00 0.00 4.30
531 658 4.163458 ACCACATATGACAAATACGACCCT 59.837 41.667 10.38 0.00 0.00 4.34
577 727 2.975799 GTGGCCGAGCGTTTTCCA 60.976 61.111 0.00 0.00 0.00 3.53
946 1114 2.043652 ATGTCCATGTGGGCTGGC 60.044 61.111 5.12 0.00 41.34 4.85
954 1122 2.819595 GGCGACGCATGTCCATGT 60.820 61.111 23.09 0.00 42.37 3.21
959 1130 0.457853 TGTAAGAGGCGACGCATGTC 60.458 55.000 23.09 14.47 41.91 3.06
1154 1326 0.255890 TTCAGGCAACCTATGGAGCC 59.744 55.000 13.78 13.78 43.63 4.70
1180 1357 6.216569 AGTATGATAAAGCATCAGGTACACG 58.783 40.000 0.00 0.00 46.76 4.49
1185 1362 4.345257 ACGGAGTATGATAAAGCATCAGGT 59.655 41.667 0.00 0.00 46.76 4.00
1194 1371 6.816640 CCTTCAGAACAACGGAGTATGATAAA 59.183 38.462 0.00 0.00 45.00 1.40
1311 1492 2.743938 CCGTGGATGACAGTGCTATAC 58.256 52.381 0.00 0.00 0.00 1.47
1320 1501 1.375908 GCAGAAGCCGTGGATGACA 60.376 57.895 0.00 0.00 33.58 3.58
1368 1549 2.991190 CTGCACCATTTCATTGAACAGC 59.009 45.455 0.00 0.48 0.00 4.40
1423 1604 1.891178 CACAGCGCATCAATCACTTG 58.109 50.000 11.47 0.00 0.00 3.16
1424 1605 0.169672 GCACAGCGCATCAATCACTT 59.830 50.000 11.47 0.00 41.79 3.16
1564 1748 8.723942 TCTCTGAATATTTTTACTGCCTCTTC 57.276 34.615 0.00 0.00 0.00 2.87
1642 1826 0.251742 CCATGGTTGCAAAGGGAGGA 60.252 55.000 0.00 0.00 0.00 3.71
1698 2723 5.754890 GCTCACTGTTGTTCCATTTTCAATT 59.245 36.000 0.00 0.00 0.00 2.32
2231 3265 4.780815 TCAACTGTGTCTGACTCCAAAAT 58.219 39.130 9.51 0.00 0.00 1.82
2436 4254 3.452474 CAGTTCTGCTAGACTATGTGGC 58.548 50.000 0.00 0.00 0.00 5.01
2464 4282 5.837829 ACCAGAAGCCATTATCCCTAAAAA 58.162 37.500 0.00 0.00 0.00 1.94
2465 4283 5.466127 ACCAGAAGCCATTATCCCTAAAA 57.534 39.130 0.00 0.00 0.00 1.52
2505 4325 6.099701 TGCTTCTTATGGAAAGAGCACCTATA 59.900 38.462 0.00 0.00 33.07 1.31
2570 4391 8.732854 AGATATTATAAAATCCTGGGTGGTTGA 58.267 33.333 0.00 0.00 37.07 3.18
2679 4500 7.125391 ACATATATCACAAATTCCCCACACTT 58.875 34.615 0.00 0.00 0.00 3.16
2683 4504 6.207417 CCTGACATATATCACAAATTCCCCAC 59.793 42.308 0.00 0.00 0.00 4.61
2710 4531 3.081710 CCTTCATTAGGGACCCGTTTT 57.918 47.619 4.40 0.00 40.67 2.43
2797 4648 0.320858 TCGCCGGCAGTGTATTCAAA 60.321 50.000 28.98 0.00 0.00 2.69
2821 4672 4.637534 GCCTGCAATCTTCTAAAGACATCA 59.362 41.667 0.00 0.00 41.01 3.07
2823 4674 4.639310 CAGCCTGCAATCTTCTAAAGACAT 59.361 41.667 0.00 0.00 41.01 3.06
2831 4682 0.392193 CCGTCAGCCTGCAATCTTCT 60.392 55.000 0.00 0.00 0.00 2.85
2833 4684 1.377725 CCCGTCAGCCTGCAATCTT 60.378 57.895 0.00 0.00 0.00 2.40
2849 4700 0.912006 AGTCAAGGAAGAGAGGCCCC 60.912 60.000 0.00 0.00 0.00 5.80
2874 4725 1.068121 ACAACTAAGCTCCAAGGGCT 58.932 50.000 0.00 0.00 42.31 5.19
2899 4750 3.489180 AAACGATCAGACAGGACTACG 57.511 47.619 0.00 0.00 0.00 3.51
2939 4790 9.639601 CACACTATTGTTCTTAGACTACATTCA 57.360 33.333 0.00 0.00 31.66 2.57
2971 4822 0.796312 AGCCATTCAAACACGCTACG 59.204 50.000 0.00 0.00 0.00 3.51
2981 4832 1.005805 ACCCATACAGCAGCCATTCAA 59.994 47.619 0.00 0.00 0.00 2.69
2985 4836 0.921896 AGAACCCATACAGCAGCCAT 59.078 50.000 0.00 0.00 0.00 4.40
2989 4840 2.359900 GGACAAGAACCCATACAGCAG 58.640 52.381 0.00 0.00 0.00 4.24
3027 4878 8.546322 ACATGCAGGAGATATGTGTATCATTAT 58.454 33.333 4.84 0.00 39.36 1.28
3037 4888 5.363562 TCTCAAACATGCAGGAGATATGT 57.636 39.130 4.84 0.00 36.66 2.29
3084 4935 9.799106 AGATAGCATACTGGCAATACTTTTATT 57.201 29.630 0.00 0.00 35.83 1.40
3105 4956 7.763528 AGTGTGCTCTCAATAACAGAAAGATAG 59.236 37.037 0.00 0.00 0.00 2.08
3144 4995 4.015872 ACGAGGAGCAGGAAATTTGTTA 57.984 40.909 0.00 0.00 0.00 2.41
3148 4999 4.589908 ACATTACGAGGAGCAGGAAATTT 58.410 39.130 0.00 0.00 0.00 1.82
3150 5001 3.914426 ACATTACGAGGAGCAGGAAAT 57.086 42.857 0.00 0.00 0.00 2.17
3178 5029 3.199071 ACCGGTGAATTCTTGGCTATACA 59.801 43.478 6.12 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.