Multiple sequence alignment - TraesCS3A01G192300

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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 TraesCS3A01G192300 chr3A 100.000 2588 0 0 1 2588 249745082 249747669 0.000000e+00 4780.0
1 TraesCS3A01G192300 chr3A 87.037 162 21 0 1483 1644 290754020 290753859 1.580000e-42 183.0
2 TraesCS3A01G192300 chr3A 92.000 50 3 1 1073 1122 365184118 365184166 4.620000e-08 69.4
3 TraesCS3A01G192300 chr3A 92.000 50 3 1 1073 1122 583826717 583826765 4.620000e-08 69.4
4 TraesCS3A01G192300 chr3A 86.885 61 6 2 1462 1522 278943919 278943977 1.660000e-07 67.6
5 TraesCS3A01G192300 chr6D 82.930 2601 337 73 53 2588 162719371 162721929 0.000000e+00 2244.0
6 TraesCS3A01G192300 chr6D 81.563 499 75 13 53 540 103943122 103943614 1.870000e-106 396.0
7 TraesCS3A01G192300 chr4A 83.160 2494 335 55 129 2588 401230123 401232565 0.000000e+00 2200.0
8 TraesCS3A01G192300 chr4A 78.815 675 102 31 61 708 321287066 321286406 1.430000e-112 416.0
9 TraesCS3A01G192300 chr4A 78.797 665 97 34 74 710 321325708 321325060 8.620000e-110 407.0
10 TraesCS3A01G192300 chr4A 90.566 53 5 0 1 53 704326550 704326498 1.280000e-08 71.3
11 TraesCS3A01G192300 chr2A 84.885 827 106 16 1771 2588 465926638 465927454 0.000000e+00 817.0
12 TraesCS3A01G192300 chr2A 83.790 876 116 21 1726 2588 731074660 731073798 0.000000e+00 808.0
13 TraesCS3A01G192300 chr2A 82.592 517 66 20 53 560 351149185 351148684 3.960000e-118 435.0
14 TraesCS3A01G192300 chr2A 81.274 518 77 19 53 563 351066679 351066175 4.010000e-108 401.0
15 TraesCS3A01G192300 chr2A 90.000 60 6 0 1076 1135 427038300 427038241 7.680000e-11 78.7
16 TraesCS3A01G192300 chr4B 84.468 837 106 20 1726 2550 117676785 117675961 0.000000e+00 804.0
17 TraesCS3A01G192300 chr4B 91.837 49 4 0 2 50 562874121 562874169 4.620000e-08 69.4
18 TraesCS3A01G192300 chr4D 85.176 796 101 15 1801 2588 275920496 275919710 0.000000e+00 800.0
19 TraesCS3A01G192300 chr4D 79.359 562 89 24 61 608 89654229 89653681 1.130000e-98 370.0
20 TraesCS3A01G192300 chr4D 87.931 58 5 2 2 57 378699438 378699495 1.660000e-07 67.6
21 TraesCS3A01G192300 chr2D 83.390 879 120 20 1726 2588 347230580 347229712 0.000000e+00 791.0
22 TraesCS3A01G192300 chr2D 83.238 877 125 17 1726 2588 347238121 347237253 0.000000e+00 785.0
23 TraesCS3A01G192300 chr2D 87.931 58 5 2 2 57 398809609 398809666 1.660000e-07 67.6
24 TraesCS3A01G192300 chr3B 82.770 888 120 29 1681 2550 616749617 616750489 0.000000e+00 761.0
25 TraesCS3A01G192300 chr3B 81.285 903 135 26 1665 2550 182112321 182113206 0.000000e+00 701.0
26 TraesCS3A01G192300 chr7A 82.834 868 123 21 1731 2588 555431016 555431867 0.000000e+00 754.0
27 TraesCS3A01G192300 chr7A 90.000 60 6 0 1073 1132 89489297 89489356 7.680000e-11 78.7
28 TraesCS3A01G192300 chr6A 82.804 535 73 14 53 574 329862029 329861501 6.530000e-126 460.0
29 TraesCS3A01G192300 chr6A 82.822 163 18 5 1097 1249 249551743 249551581 1.250000e-28 137.0
30 TraesCS3A01G192300 chr6A 88.333 60 7 0 1076 1135 388247323 388247264 3.570000e-09 73.1
31 TraesCS3A01G192300 chr1D 81.404 527 78 16 61 575 54136481 54135963 1.850000e-111 412.0
32 TraesCS3A01G192300 chr1D 79.887 532 88 16 53 573 156756044 156756567 3.150000e-99 372.0
33 TraesCS3A01G192300 chr5A 79.754 568 88 24 61 613 412162919 412162364 1.120000e-103 387.0
34 TraesCS3A01G192300 chr6B 80.150 534 87 12 49 573 122587586 122588109 5.230000e-102 381.0
35 TraesCS3A01G192300 chr5D 96.000 50 2 0 1073 1122 510183004 510183053 5.940000e-12 82.4
36 TraesCS3A01G192300 chr5D 94.231 52 3 0 2 53 479552301 479552250 2.130000e-11 80.5
37 TraesCS3A01G192300 chr2B 80.508 118 11 7 1081 1187 310005568 310005684 2.130000e-11 80.5
38 TraesCS3A01G192300 chr7B 92.308 52 4 0 2 53 523806373 523806424 9.930000e-10 75.0
39 TraesCS3A01G192300 chr7B 97.143 35 1 0 1266 1300 533322490 533322456 2.780000e-05 60.2
40 TraesCS3A01G192300 chr1B 92.308 52 4 0 2 53 320224617 320224566 9.930000e-10 75.0
41 TraesCS3A01G192300 chr1B 97.143 35 1 0 1266 1300 671021395 671021429 2.780000e-05 60.2
42 TraesCS3A01G192300 chr5B 92.000 50 2 2 2 50 295306831 295306879 4.620000e-08 69.4
43 TraesCS3A01G192300 chr5B 90.385 52 5 0 2 53 383082867 383082918 4.620000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G192300 chr3A 249745082 249747669 2587 False 4780 4780 100.000 1 2588 1 chr3A.!!$F1 2587
1 TraesCS3A01G192300 chr6D 162719371 162721929 2558 False 2244 2244 82.930 53 2588 1 chr6D.!!$F2 2535
2 TraesCS3A01G192300 chr4A 401230123 401232565 2442 False 2200 2200 83.160 129 2588 1 chr4A.!!$F1 2459
3 TraesCS3A01G192300 chr4A 321286406 321287066 660 True 416 416 78.815 61 708 1 chr4A.!!$R1 647
4 TraesCS3A01G192300 chr4A 321325060 321325708 648 True 407 407 78.797 74 710 1 chr4A.!!$R2 636
5 TraesCS3A01G192300 chr2A 465926638 465927454 816 False 817 817 84.885 1771 2588 1 chr2A.!!$F1 817
6 TraesCS3A01G192300 chr2A 731073798 731074660 862 True 808 808 83.790 1726 2588 1 chr2A.!!$R4 862
7 TraesCS3A01G192300 chr2A 351148684 351149185 501 True 435 435 82.592 53 560 1 chr2A.!!$R2 507
8 TraesCS3A01G192300 chr2A 351066175 351066679 504 True 401 401 81.274 53 563 1 chr2A.!!$R1 510
9 TraesCS3A01G192300 chr4B 117675961 117676785 824 True 804 804 84.468 1726 2550 1 chr4B.!!$R1 824
10 TraesCS3A01G192300 chr4D 275919710 275920496 786 True 800 800 85.176 1801 2588 1 chr4D.!!$R2 787
11 TraesCS3A01G192300 chr4D 89653681 89654229 548 True 370 370 79.359 61 608 1 chr4D.!!$R1 547
12 TraesCS3A01G192300 chr2D 347229712 347230580 868 True 791 791 83.390 1726 2588 1 chr2D.!!$R1 862
13 TraesCS3A01G192300 chr2D 347237253 347238121 868 True 785 785 83.238 1726 2588 1 chr2D.!!$R2 862
14 TraesCS3A01G192300 chr3B 616749617 616750489 872 False 761 761 82.770 1681 2550 1 chr3B.!!$F2 869
15 TraesCS3A01G192300 chr3B 182112321 182113206 885 False 701 701 81.285 1665 2550 1 chr3B.!!$F1 885
16 TraesCS3A01G192300 chr7A 555431016 555431867 851 False 754 754 82.834 1731 2588 1 chr7A.!!$F2 857
17 TraesCS3A01G192300 chr6A 329861501 329862029 528 True 460 460 82.804 53 574 1 chr6A.!!$R2 521
18 TraesCS3A01G192300 chr1D 54135963 54136481 518 True 412 412 81.404 61 575 1 chr1D.!!$R1 514
19 TraesCS3A01G192300 chr1D 156756044 156756567 523 False 372 372 79.887 53 573 1 chr1D.!!$F1 520
20 TraesCS3A01G192300 chr5A 412162364 412162919 555 True 387 387 79.754 61 613 1 chr5A.!!$R1 552
21 TraesCS3A01G192300 chr6B 122587586 122588109 523 False 381 381 80.150 49 573 1 chr6B.!!$F1 524

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
645 700 0.118144 AGGAGGGTCCTTCTCTTGCT 59.882 55.0 0.36 0.0 46.91 3.91 F
1208 1310 0.456221 GACCTCGTCGTCATCCATGT 59.544 55.0 0.00 0.0 32.74 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 1557 0.690762 GACTAGGGCCTTGGTCAACA 59.309 55.000 24.04 1.93 0.00 3.33 R
2447 2589 1.547372 GAGGCATGGCATGACAAAGTT 59.453 47.619 33.41 14.03 42.15 2.66 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
25 26 7.887996 TTAGTTCCATTCAAATCATGCAAAC 57.112 32.000 0.00 0.00 0.00 2.93
26 27 6.105397 AGTTCCATTCAAATCATGCAAACT 57.895 33.333 0.00 0.00 0.00 2.66
27 28 7.230849 AGTTCCATTCAAATCATGCAAACTA 57.769 32.000 0.00 0.00 30.42 2.24
28 29 7.318141 AGTTCCATTCAAATCATGCAAACTAG 58.682 34.615 0.00 0.00 30.42 2.57
29 30 7.177216 AGTTCCATTCAAATCATGCAAACTAGA 59.823 33.333 0.00 0.00 30.42 2.43
30 31 7.465353 TCCATTCAAATCATGCAAACTAGAA 57.535 32.000 0.00 0.00 0.00 2.10
31 32 8.070034 TCCATTCAAATCATGCAAACTAGAAT 57.930 30.769 0.00 0.00 0.00 2.40
32 33 8.192774 TCCATTCAAATCATGCAAACTAGAATC 58.807 33.333 0.00 0.00 0.00 2.52
33 34 7.437267 CCATTCAAATCATGCAAACTAGAATCC 59.563 37.037 0.00 0.00 0.00 3.01
34 35 7.465353 TTCAAATCATGCAAACTAGAATCCA 57.535 32.000 0.00 0.00 0.00 3.41
35 36 7.465353 TCAAATCATGCAAACTAGAATCCAA 57.535 32.000 0.00 0.00 0.00 3.53
36 37 7.894708 TCAAATCATGCAAACTAGAATCCAAA 58.105 30.769 0.00 0.00 0.00 3.28
37 38 8.366401 TCAAATCATGCAAACTAGAATCCAAAA 58.634 29.630 0.00 0.00 0.00 2.44
38 39 8.437742 CAAATCATGCAAACTAGAATCCAAAAC 58.562 33.333 0.00 0.00 0.00 2.43
39 40 5.698832 TCATGCAAACTAGAATCCAAAACG 58.301 37.500 0.00 0.00 0.00 3.60
40 41 5.471797 TCATGCAAACTAGAATCCAAAACGA 59.528 36.000 0.00 0.00 0.00 3.85
41 42 5.103290 TGCAAACTAGAATCCAAAACGAC 57.897 39.130 0.00 0.00 0.00 4.34
42 43 4.576873 TGCAAACTAGAATCCAAAACGACA 59.423 37.500 0.00 0.00 0.00 4.35
43 44 5.147162 GCAAACTAGAATCCAAAACGACAG 58.853 41.667 0.00 0.00 0.00 3.51
44 45 5.049680 GCAAACTAGAATCCAAAACGACAGA 60.050 40.000 0.00 0.00 0.00 3.41
45 46 6.512741 GCAAACTAGAATCCAAAACGACAGAA 60.513 38.462 0.00 0.00 0.00 3.02
46 47 7.414436 CAAACTAGAATCCAAAACGACAGAAA 58.586 34.615 0.00 0.00 0.00 2.52
47 48 7.562454 AACTAGAATCCAAAACGACAGAAAA 57.438 32.000 0.00 0.00 0.00 2.29
48 49 7.562454 ACTAGAATCCAAAACGACAGAAAAA 57.438 32.000 0.00 0.00 0.00 1.94
49 50 7.639945 ACTAGAATCCAAAACGACAGAAAAAG 58.360 34.615 0.00 0.00 0.00 2.27
50 51 6.451064 AGAATCCAAAACGACAGAAAAAGT 57.549 33.333 0.00 0.00 0.00 2.66
107 110 4.019858 TCCATTTATTTCCATTGTCGCCA 58.980 39.130 0.00 0.00 0.00 5.69
266 294 9.847224 TTTCTCTTTATAACATATCCTCCCAAC 57.153 33.333 0.00 0.00 0.00 3.77
341 372 5.599732 GCACATGCAATTTAATCCCATGTA 58.400 37.500 17.05 0.00 43.13 2.29
419 456 1.826385 AGCTCCACCAAAAATCCGAG 58.174 50.000 0.00 0.00 0.00 4.63
496 538 7.653767 TTCGAAGGAGTTTGAATTTAGTCTC 57.346 36.000 0.00 0.00 32.00 3.36
517 560 4.978099 TCTCAATCATGCCCCTTCTATTC 58.022 43.478 0.00 0.00 0.00 1.75
520 563 5.380043 TCAATCATGCCCCTTCTATTCTTC 58.620 41.667 0.00 0.00 0.00 2.87
523 566 4.566837 TCATGCCCCTTCTATTCTTCCTA 58.433 43.478 0.00 0.00 0.00 2.94
525 568 4.280789 TGCCCCTTCTATTCTTCCTAGA 57.719 45.455 0.00 0.00 0.00 2.43
528 571 4.841246 GCCCCTTCTATTCTTCCTAGATCA 59.159 45.833 0.00 0.00 0.00 2.92
530 573 6.742926 GCCCCTTCTATTCTTCCTAGATCAAC 60.743 46.154 0.00 0.00 0.00 3.18
531 574 6.239743 CCCCTTCTATTCTTCCTAGATCAACC 60.240 46.154 0.00 0.00 0.00 3.77
532 575 6.556874 CCCTTCTATTCTTCCTAGATCAACCT 59.443 42.308 0.00 0.00 0.00 3.50
534 577 9.148879 CCTTCTATTCTTCCTAGATCAACCTTA 57.851 37.037 0.00 0.00 0.00 2.69
592 636 2.387757 AGCATCTCTCTTCACCTCTCC 58.612 52.381 0.00 0.00 0.00 3.71
595 639 2.411628 TCTCTCTTCACCTCTCCTCG 57.588 55.000 0.00 0.00 0.00 4.63
619 672 5.668558 TTCCTTTCTTCGTTCTGCTTTAC 57.331 39.130 0.00 0.00 0.00 2.01
620 673 4.062991 TCCTTTCTTCGTTCTGCTTTACC 58.937 43.478 0.00 0.00 0.00 2.85
645 700 0.118144 AGGAGGGTCCTTCTCTTGCT 59.882 55.000 0.36 0.00 46.91 3.91
652 742 1.349357 GTCCTTCTCTTGCTTCCAGGT 59.651 52.381 0.00 0.00 0.00 4.00
672 762 2.913501 CTGCAGCCAGCCCTCATA 59.086 61.111 0.00 0.00 44.83 2.15
741 831 3.406498 AGTGATCCCTATAACCCTAGCCT 59.594 47.826 0.00 0.00 0.00 4.58
744 834 3.255634 TCCCTATAACCCTAGCCTGAC 57.744 52.381 0.00 0.00 0.00 3.51
745 835 2.795960 TCCCTATAACCCTAGCCTGACT 59.204 50.000 0.00 0.00 0.00 3.41
746 836 3.992311 TCCCTATAACCCTAGCCTGACTA 59.008 47.826 0.00 0.00 0.00 2.59
750 840 6.017192 CCTATAACCCTAGCCTGACTAATCA 58.983 44.000 0.00 0.00 0.00 2.57
869 959 2.756283 CGCCTTCCTCCTCCGTCT 60.756 66.667 0.00 0.00 0.00 4.18
870 960 1.453379 CGCCTTCCTCCTCCGTCTA 60.453 63.158 0.00 0.00 0.00 2.59
878 968 2.124236 CCTCCGTCTACTCCGCCT 60.124 66.667 0.00 0.00 0.00 5.52
898 989 4.187056 CGGTTCTTCTTCCTCCGC 57.813 61.111 0.00 0.00 35.01 5.54
964 1055 2.204291 ATCCCCTCAACCCCTGCA 60.204 61.111 0.00 0.00 0.00 4.41
968 1059 2.845345 CCCTCAACCCCTGCACCTT 61.845 63.158 0.00 0.00 0.00 3.50
1032 1124 1.419374 CGTGCTTCTGCTACTTCGTT 58.581 50.000 0.00 0.00 40.48 3.85
1135 1227 1.559682 GGAACCCACTATCTTCTGCCA 59.440 52.381 0.00 0.00 0.00 4.92
1136 1228 2.026262 GGAACCCACTATCTTCTGCCAA 60.026 50.000 0.00 0.00 0.00 4.52
1163 1265 4.699522 GCTCCGCCCGTCCTTTGT 62.700 66.667 0.00 0.00 0.00 2.83
1174 1276 2.359975 CCTTTGTCCCGCCTCCAC 60.360 66.667 0.00 0.00 0.00 4.02
1177 1279 3.190738 TTTGTCCCGCCTCCACCAG 62.191 63.158 0.00 0.00 0.00 4.00
1208 1310 0.456221 GACCTCGTCGTCATCCATGT 59.544 55.000 0.00 0.00 32.74 3.21
1249 1351 4.020617 CCTTCCACTGCCTCGCCA 62.021 66.667 0.00 0.00 0.00 5.69
1263 1365 2.997897 GCCAGTGACCTCCTCCGT 60.998 66.667 0.00 0.00 0.00 4.69
1300 1402 3.995809 GACCCATCCCCGACCTCCA 62.996 68.421 0.00 0.00 0.00 3.86
1323 1425 2.833582 GACTCCTCGCCGGATCCA 60.834 66.667 13.41 0.00 42.12 3.41
1432 1534 3.744719 AGCAGCACAAGCCGCATG 61.745 61.111 0.00 0.00 46.59 4.06
1440 1542 4.349503 AAGCCGCATGGAGCCACA 62.350 61.111 0.00 0.00 41.38 4.17
1441 1543 3.866379 AAGCCGCATGGAGCCACAA 62.866 57.895 0.00 0.00 41.38 3.33
1455 1557 0.829990 CCACAACCAAAACCTGCCTT 59.170 50.000 0.00 0.00 0.00 4.35
1472 1574 1.826385 CTTGTTGACCAAGGCCCTAG 58.174 55.000 0.00 0.00 45.70 3.02
1482 1584 2.187163 GGCCCTAGTCAAGCCGTC 59.813 66.667 0.00 0.00 36.84 4.79
1483 1585 2.656069 GGCCCTAGTCAAGCCGTCA 61.656 63.158 0.00 0.00 36.84 4.35
1484 1586 1.295423 GCCCTAGTCAAGCCGTCAA 59.705 57.895 0.00 0.00 0.00 3.18
1485 1587 0.741221 GCCCTAGTCAAGCCGTCAAG 60.741 60.000 0.00 0.00 0.00 3.02
1486 1588 0.895530 CCCTAGTCAAGCCGTCAAGA 59.104 55.000 0.00 0.00 0.00 3.02
1487 1589 1.404315 CCCTAGTCAAGCCGTCAAGAC 60.404 57.143 0.00 0.00 0.00 3.01
1488 1590 1.404315 CCTAGTCAAGCCGTCAAGACC 60.404 57.143 0.00 0.00 0.00 3.85
1527 1629 6.042781 ACATGAAACTTCCAAGTACCTCTACA 59.957 38.462 0.00 0.00 38.57 2.74
1531 1633 4.220724 ACTTCCAAGTACCTCTACACACA 58.779 43.478 0.00 0.00 37.52 3.72
1532 1634 4.652421 ACTTCCAAGTACCTCTACACACAA 59.348 41.667 0.00 0.00 37.52 3.33
1540 1642 1.390123 CCTCTACACACAAATGCGTCG 59.610 52.381 0.00 0.00 0.00 5.12
1573 1675 3.131577 GGATATCGACAAGTACACCACCA 59.868 47.826 0.00 0.00 0.00 4.17
1594 1696 1.003118 GCAAGACCACATAGACACCCA 59.997 52.381 0.00 0.00 0.00 4.51
1610 1712 0.322098 CCCAAATGACTACCGCACCA 60.322 55.000 0.00 0.00 0.00 4.17
1626 1728 0.673437 ACCAAAATGCCAAGACCGTG 59.327 50.000 0.00 0.00 0.00 4.94
1631 1733 1.238439 AATGCCAAGACCGTGAAGTG 58.762 50.000 0.00 0.00 0.00 3.16
1640 1742 1.287815 CCGTGAAGTGCGACTACCA 59.712 57.895 0.00 0.00 0.00 3.25
1643 1745 1.402325 CGTGAAGTGCGACTACCATCA 60.402 52.381 0.00 0.00 0.00 3.07
1649 1751 1.479323 GTGCGACTACCATCAACCCTA 59.521 52.381 0.00 0.00 0.00 3.53
1695 1797 3.753272 CCTCTTTGAACCATGTACCACTG 59.247 47.826 0.00 0.00 0.00 3.66
1697 1799 2.949177 TTGAACCATGTACCACTGCT 57.051 45.000 0.00 0.00 0.00 4.24
1708 1810 2.338015 CCACTGCTGTCACCATGGC 61.338 63.158 13.04 0.00 0.00 4.40
1809 1927 4.404394 TGAATCATCCTGATTGCATGCTTT 59.596 37.500 20.33 5.90 46.20 3.51
1863 1984 5.163632 TGGATGAATGCATGTGTGTTGTATC 60.164 40.000 0.00 0.00 34.11 2.24
1895 2017 1.305219 TTGCACTATGCCCGAGTTGC 61.305 55.000 0.00 0.00 44.23 4.17
1912 2035 1.302511 GCCTTTGCTCGTTCCTCCA 60.303 57.895 0.00 0.00 33.53 3.86
1920 2044 2.224523 TGCTCGTTCCTCCATGTTTTCT 60.225 45.455 0.00 0.00 0.00 2.52
1965 2089 1.852157 GCAACCAGGATCACTCCCCA 61.852 60.000 0.00 0.00 43.21 4.96
2003 2133 2.034558 CGCACATCCACACTTCCTTTTT 59.965 45.455 0.00 0.00 0.00 1.94
2122 2255 6.127563 ACAAAATGCTTCATCACATGCTCATA 60.128 34.615 0.00 0.00 0.00 2.15
2124 2257 6.650427 AATGCTTCATCACATGCTCATATT 57.350 33.333 0.00 0.00 0.00 1.28
2174 2312 5.622770 TGAATATGTCATCTGCATCATGC 57.377 39.130 1.35 1.35 45.29 4.06
2266 2406 9.015367 TCCAGAATTGTTGTTTATTATTTCCGA 57.985 29.630 0.00 0.00 0.00 4.55
2273 2413 9.451002 TTGTTGTTTATTATTTCCGACCTCATA 57.549 29.630 0.00 0.00 0.00 2.15
2341 2481 8.918116 TGCCATGCTAACCAACATTTAATATTA 58.082 29.630 0.00 0.00 0.00 0.98
2484 2626 3.181488 TGCCTCATTAAAATGGACATGCG 60.181 43.478 3.00 0.00 37.03 4.73
2528 2671 3.184986 GCCATGATTGTGCTTGTTTGTTC 59.815 43.478 0.00 0.00 0.00 3.18
2550 2693 9.066892 TGTTCACTATATTGTTTGCTTCTTTCT 57.933 29.630 0.00 0.00 0.00 2.52
2561 2704 2.224079 TGCTTCTTTCTAGTTGCGCTTG 59.776 45.455 9.73 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.669427 AGTTTGCATGATTTGAATGGAACTAA 58.331 30.769 0.00 0.00 35.43 2.24
3 4 6.105397 AGTTTGCATGATTTGAATGGAACT 57.895 33.333 0.00 0.00 35.43 3.01
5 6 7.465353 TCTAGTTTGCATGATTTGAATGGAA 57.535 32.000 0.00 0.00 34.09 3.53
6 7 7.465353 TTCTAGTTTGCATGATTTGAATGGA 57.535 32.000 0.00 0.00 0.00 3.41
7 8 7.437267 GGATTCTAGTTTGCATGATTTGAATGG 59.563 37.037 0.00 0.00 0.00 3.16
8 9 7.977293 TGGATTCTAGTTTGCATGATTTGAATG 59.023 33.333 0.00 0.00 0.00 2.67
9 10 8.070034 TGGATTCTAGTTTGCATGATTTGAAT 57.930 30.769 0.00 0.00 0.00 2.57
10 11 7.465353 TGGATTCTAGTTTGCATGATTTGAA 57.535 32.000 0.00 0.00 0.00 2.69
11 12 7.465353 TTGGATTCTAGTTTGCATGATTTGA 57.535 32.000 0.00 0.00 0.00 2.69
12 13 8.437742 GTTTTGGATTCTAGTTTGCATGATTTG 58.562 33.333 0.00 0.00 0.00 2.32
13 14 7.329226 CGTTTTGGATTCTAGTTTGCATGATTT 59.671 33.333 0.00 0.00 0.00 2.17
14 15 6.808212 CGTTTTGGATTCTAGTTTGCATGATT 59.192 34.615 0.00 0.00 0.00 2.57
15 16 6.150976 TCGTTTTGGATTCTAGTTTGCATGAT 59.849 34.615 0.00 0.00 0.00 2.45
16 17 5.471797 TCGTTTTGGATTCTAGTTTGCATGA 59.528 36.000 0.00 0.00 0.00 3.07
17 18 5.569059 GTCGTTTTGGATTCTAGTTTGCATG 59.431 40.000 0.00 0.00 0.00 4.06
18 19 5.240623 TGTCGTTTTGGATTCTAGTTTGCAT 59.759 36.000 0.00 0.00 0.00 3.96
19 20 4.576873 TGTCGTTTTGGATTCTAGTTTGCA 59.423 37.500 0.00 0.00 0.00 4.08
20 21 5.049680 TCTGTCGTTTTGGATTCTAGTTTGC 60.050 40.000 0.00 0.00 0.00 3.68
21 22 6.539649 TCTGTCGTTTTGGATTCTAGTTTG 57.460 37.500 0.00 0.00 0.00 2.93
22 23 7.562454 TTTCTGTCGTTTTGGATTCTAGTTT 57.438 32.000 0.00 0.00 0.00 2.66
23 24 7.562454 TTTTCTGTCGTTTTGGATTCTAGTT 57.438 32.000 0.00 0.00 0.00 2.24
24 25 7.282450 ACTTTTTCTGTCGTTTTGGATTCTAGT 59.718 33.333 0.00 0.00 0.00 2.57
25 26 7.587757 CACTTTTTCTGTCGTTTTGGATTCTAG 59.412 37.037 0.00 0.00 0.00 2.43
26 27 7.066525 ACACTTTTTCTGTCGTTTTGGATTCTA 59.933 33.333 0.00 0.00 0.00 2.10
27 28 6.127730 ACACTTTTTCTGTCGTTTTGGATTCT 60.128 34.615 0.00 0.00 0.00 2.40
28 29 6.020678 CACACTTTTTCTGTCGTTTTGGATTC 60.021 38.462 0.00 0.00 0.00 2.52
29 30 5.804979 CACACTTTTTCTGTCGTTTTGGATT 59.195 36.000 0.00 0.00 0.00 3.01
30 31 5.105917 ACACACTTTTTCTGTCGTTTTGGAT 60.106 36.000 0.00 0.00 0.00 3.41
31 32 4.216687 ACACACTTTTTCTGTCGTTTTGGA 59.783 37.500 0.00 0.00 0.00 3.53
32 33 4.481463 ACACACTTTTTCTGTCGTTTTGG 58.519 39.130 0.00 0.00 0.00 3.28
33 34 6.236838 CGTTACACACTTTTTCTGTCGTTTTG 60.237 38.462 0.00 0.00 0.00 2.44
34 35 5.791480 CGTTACACACTTTTTCTGTCGTTTT 59.209 36.000 0.00 0.00 0.00 2.43
35 36 5.120519 TCGTTACACACTTTTTCTGTCGTTT 59.879 36.000 0.00 0.00 0.00 3.60
36 37 4.626604 TCGTTACACACTTTTTCTGTCGTT 59.373 37.500 0.00 0.00 0.00 3.85
37 38 4.032104 GTCGTTACACACTTTTTCTGTCGT 59.968 41.667 0.00 0.00 0.00 4.34
38 39 4.502558 GTCGTTACACACTTTTTCTGTCG 58.497 43.478 0.00 0.00 0.00 4.35
39 40 4.260497 GGGTCGTTACACACTTTTTCTGTC 60.260 45.833 0.00 0.00 0.00 3.51
40 41 3.624410 GGGTCGTTACACACTTTTTCTGT 59.376 43.478 0.00 0.00 0.00 3.41
41 42 3.623960 TGGGTCGTTACACACTTTTTCTG 59.376 43.478 0.00 0.00 32.77 3.02
42 43 3.876341 TGGGTCGTTACACACTTTTTCT 58.124 40.909 0.00 0.00 32.77 2.52
43 44 4.333372 TCTTGGGTCGTTACACACTTTTTC 59.667 41.667 0.00 0.00 39.26 2.29
44 45 4.095334 GTCTTGGGTCGTTACACACTTTTT 59.905 41.667 0.00 0.00 39.26 1.94
45 46 3.624410 GTCTTGGGTCGTTACACACTTTT 59.376 43.478 0.00 0.00 39.26 2.27
46 47 3.200483 GTCTTGGGTCGTTACACACTTT 58.800 45.455 0.00 0.00 39.26 2.66
47 48 2.484241 GGTCTTGGGTCGTTACACACTT 60.484 50.000 0.00 0.00 39.26 3.16
48 49 1.069668 GGTCTTGGGTCGTTACACACT 59.930 52.381 0.00 0.00 39.26 3.55
49 50 1.505425 GGTCTTGGGTCGTTACACAC 58.495 55.000 0.00 0.00 39.26 3.82
50 51 0.032403 CGGTCTTGGGTCGTTACACA 59.968 55.000 0.00 0.00 37.19 3.72
107 110 8.671921 TGAATGCAACAAACAAATAAAACACAT 58.328 25.926 0.00 0.00 0.00 3.21
419 456 4.039852 TGGTAAAGGAAGGTCCAAAAATGC 59.960 41.667 0.00 0.00 39.61 3.56
475 516 8.608844 TTGAGAGACTAAATTCAAACTCCTTC 57.391 34.615 0.00 0.00 0.00 3.46
478 519 8.553459 TGATTGAGAGACTAAATTCAAACTCC 57.447 34.615 0.00 0.00 33.71 3.85
492 533 2.172293 AGAAGGGGCATGATTGAGAGAC 59.828 50.000 0.00 0.00 0.00 3.36
496 538 4.983053 AGAATAGAAGGGGCATGATTGAG 58.017 43.478 0.00 0.00 0.00 3.02
592 636 3.363084 GCAGAACGAAGAAAGGAAACGAG 60.363 47.826 0.00 0.00 0.00 4.18
595 639 4.553756 AAGCAGAACGAAGAAAGGAAAC 57.446 40.909 0.00 0.00 0.00 2.78
645 700 4.704833 GGCTGCAGCGACCTGGAA 62.705 66.667 31.19 0.00 39.04 3.53
741 831 4.527944 AGGTCGAGAGATGTGATTAGTCA 58.472 43.478 0.00 0.00 45.19 3.41
744 834 4.215399 GGAGAGGTCGAGAGATGTGATTAG 59.785 50.000 0.00 0.00 45.19 1.73
745 835 4.138290 GGAGAGGTCGAGAGATGTGATTA 58.862 47.826 0.00 0.00 45.19 1.75
746 836 2.955660 GGAGAGGTCGAGAGATGTGATT 59.044 50.000 0.00 0.00 45.19 2.57
750 840 1.283613 AGTGGAGAGGTCGAGAGATGT 59.716 52.381 0.00 0.00 45.19 3.06
878 968 1.590147 GGAGGAAGAAGAACCGCGA 59.410 57.895 8.23 0.00 0.00 5.87
898 989 3.846430 GTAGGGGAAGGGGTCGCG 61.846 72.222 0.00 0.00 40.09 5.87
945 1036 2.308722 GCAGGGGTTGAGGGGATCA 61.309 63.158 0.00 0.00 35.62 2.92
964 1055 2.639327 GCTTGGGCGATGCAAAGGT 61.639 57.895 2.51 0.00 0.00 3.50
968 1059 2.751436 GAGGCTTGGGCGATGCAA 60.751 61.111 9.44 0.00 39.81 4.08
972 1063 3.077556 AGACGAGGCTTGGGCGAT 61.078 61.111 6.71 0.00 39.81 4.58
1015 1107 1.148310 GCAACGAAGTAGCAGAAGCA 58.852 50.000 0.00 0.00 45.00 3.91
1118 1210 2.619074 GCTTTGGCAGAAGATAGTGGGT 60.619 50.000 11.81 0.00 38.54 4.51
1121 1213 2.941720 GGAGCTTTGGCAGAAGATAGTG 59.058 50.000 11.81 0.00 41.70 2.74
1160 1262 3.636231 CTGGTGGAGGCGGGACAA 61.636 66.667 0.00 0.00 0.00 3.18
1193 1295 3.713936 GTCACATGGATGACGACGA 57.286 52.632 0.00 0.00 39.69 4.20
1240 1342 3.695606 GAGGTCACTGGCGAGGCA 61.696 66.667 0.00 0.00 0.00 4.75
1249 1351 0.323542 CCAGTACGGAGGAGGTCACT 60.324 60.000 0.00 0.00 36.56 3.41
1263 1365 0.824109 CGTTGAGGCTGGATCCAGTA 59.176 55.000 36.32 20.80 45.24 2.74
1279 1381 3.396570 GGTCGGGGATGGGTCGTT 61.397 66.667 0.00 0.00 0.00 3.85
1323 1425 3.063084 GGCACGACGAGGACCTCT 61.063 66.667 19.39 6.55 0.00 3.69
1407 1509 2.666190 TTGTGCTGCTGGTCGCTC 60.666 61.111 0.00 0.00 40.11 5.03
1408 1510 2.667536 CTTGTGCTGCTGGTCGCT 60.668 61.111 0.00 0.00 40.11 4.93
1409 1511 4.395583 GCTTGTGCTGCTGGTCGC 62.396 66.667 0.00 0.00 39.77 5.19
1432 1534 0.389025 CAGGTTTTGGTTGTGGCTCC 59.611 55.000 0.00 0.00 0.00 4.70
1440 1542 2.093711 GTCAACAAGGCAGGTTTTGGTT 60.094 45.455 0.00 0.00 0.00 3.67
1441 1543 1.480545 GTCAACAAGGCAGGTTTTGGT 59.519 47.619 0.00 0.00 0.00 3.67
1455 1557 0.690762 GACTAGGGCCTTGGTCAACA 59.309 55.000 24.04 1.93 0.00 3.33
1471 1573 1.006102 CGGTCTTGACGGCTTGACT 60.006 57.895 12.51 0.00 0.00 3.41
1472 1574 2.027625 CCGGTCTTGACGGCTTGAC 61.028 63.158 5.80 5.80 45.34 3.18
1480 1582 3.967715 GGTCTTGCCGGTCTTGAC 58.032 61.111 1.90 6.89 0.00 3.18
1527 1629 1.282248 CGGTCTCGACGCATTTGTGT 61.282 55.000 0.00 0.00 42.13 3.72
1559 1661 1.488812 TCTTGCTGGTGGTGTACTTGT 59.511 47.619 0.00 0.00 0.00 3.16
1573 1675 1.279271 GGGTGTCTATGTGGTCTTGCT 59.721 52.381 0.00 0.00 0.00 3.91
1594 1696 3.613910 GCATTTTGGTGCGGTAGTCATTT 60.614 43.478 0.00 0.00 35.10 2.32
1610 1712 2.034558 CACTTCACGGTCTTGGCATTTT 59.965 45.455 0.00 0.00 0.00 1.82
1626 1728 2.000447 GGTTGATGGTAGTCGCACTTC 59.000 52.381 0.00 0.00 0.00 3.01
1631 1733 1.068741 CCTAGGGTTGATGGTAGTCGC 59.931 57.143 0.00 0.00 0.00 5.19
1640 1742 4.233287 ACTCTTAGACCTCCTAGGGTTGAT 59.767 45.833 9.46 0.00 40.58 2.57
1643 1745 3.371810 CGACTCTTAGACCTCCTAGGGTT 60.372 52.174 9.46 0.00 40.58 4.11
1649 1751 3.244981 ACTTGACGACTCTTAGACCTCCT 60.245 47.826 0.00 0.00 0.00 3.69
1708 1810 1.642037 TACTCGCGGTCTTGTCGGAG 61.642 60.000 6.13 0.00 33.98 4.63
1809 1927 1.406539 GTCTCGGCGGTTATACCTTCA 59.593 52.381 7.21 0.00 35.66 3.02
1863 1984 3.373020 GTGCAAACACGAGCATCTG 57.627 52.632 0.00 0.00 43.44 2.90
1895 2017 1.089920 CATGGAGGAACGAGCAAAGG 58.910 55.000 0.00 0.00 0.00 3.11
1912 2035 3.518590 GGGTCGACGACATAGAAAACAT 58.481 45.455 27.77 0.00 33.68 2.71
1920 2044 3.879682 CCGCGGGTCGACGACATA 61.880 66.667 27.77 0.00 41.67 2.29
1943 2067 1.685224 GAGTGATCCTGGTTGCCCA 59.315 57.895 0.00 0.00 38.87 5.36
1952 2076 1.293458 AGAGTGATGGGGAGTGATCCT 59.707 52.381 0.00 0.00 0.00 3.24
1965 2089 2.095567 GTGCGAAACATGCAAGAGTGAT 60.096 45.455 0.00 0.00 45.23 3.06
2003 2133 2.454336 ACTCATGGAGATACCGGTGA 57.546 50.000 19.93 1.59 42.61 4.02
2099 2232 4.794278 TGAGCATGTGATGAAGCATTTT 57.206 36.364 0.00 0.00 0.00 1.82
2341 2481 8.275040 AGTTCACTCCCATTTATGCTACTTATT 58.725 33.333 0.00 0.00 0.00 1.40
2344 2484 6.067217 AGTTCACTCCCATTTATGCTACTT 57.933 37.500 0.00 0.00 0.00 2.24
2377 2518 4.097714 GCATATTGACGAAACACCACATG 58.902 43.478 0.00 0.00 0.00 3.21
2447 2589 1.547372 GAGGCATGGCATGACAAAGTT 59.453 47.619 33.41 14.03 42.15 2.66
2454 2596 4.202274 CCATTTTAATGAGGCATGGCATGA 60.202 41.667 30.69 10.42 38.70 3.07
2515 2657 8.479280 CAAACAATATAGTGAACAAACAAGCAC 58.521 33.333 7.27 0.00 0.00 4.40
2550 2693 2.472695 ATGAAGGACAAGCGCAACTA 57.527 45.000 11.47 0.00 0.00 2.24
2561 2704 5.019785 ACATAACCGGAACTATGAAGGAC 57.980 43.478 21.63 0.00 31.28 3.85


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

AutoCloner maintained by Alex Coulton.