Multiple sequence alignment - TraesCS7D01G115000

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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 TraesCS7D01G115000 chr7D 100.000 3152 0 0 1 3152 70737660 70734509 0.000000e+00 5821.0
1 TraesCS7D01G115000 chr7D 93.459 1269 46 10 868 2105 70154006 70152744 0.000000e+00 1849.0
2 TraesCS7D01G115000 chr7D 93.144 1269 50 10 868 2105 70048300 70049562 0.000000e+00 1827.0
3 TraesCS7D01G115000 chr7D 91.732 1270 62 13 869 2105 69954183 69955442 0.000000e+00 1724.0
4 TraesCS7D01G115000 chr7D 92.776 969 38 14 2100 3068 70049591 70050527 0.000000e+00 1373.0
5 TraesCS7D01G115000 chr7D 92.570 969 40 14 2100 3068 70152715 70151779 0.000000e+00 1362.0
6 TraesCS7D01G115000 chr7D 88.753 489 36 8 2100 2573 69955471 69955955 5.860000e-162 580.0
7 TraesCS7D01G115000 chr7D 87.892 446 42 3 53 495 69952213 69952649 6.030000e-142 514.0
8 TraesCS7D01G115000 chr7D 84.242 495 66 3 62 553 70047370 70047855 3.680000e-129 472.0
9 TraesCS7D01G115000 chr7D 84.040 495 67 4 62 553 70154947 70154462 1.710000e-127 466.0
10 TraesCS7D01G115000 chr7D 95.882 170 7 0 1831 2000 70362283 70362114 3.100000e-70 276.0
11 TraesCS7D01G115000 chr7D 86.555 238 16 11 614 839 70154316 70154083 6.750000e-62 248.0
12 TraesCS7D01G115000 chr7D 90.576 191 8 4 869 1053 70361896 70362082 8.730000e-61 244.0
13 TraesCS7D01G115000 chr7D 84.746 236 13 13 614 839 70048001 70048223 6.850000e-52 215.0
14 TraesCS7D01G115000 chr7D 77.895 190 16 14 660 834 69953926 69954104 9.310000e-16 95.3
15 TraesCS7D01G115000 chr7D 85.556 90 4 5 754 834 70361728 70361817 5.600000e-13 86.1
16 TraesCS7D01G115000 chr7D 96.970 33 0 1 1 33 70179449 70179418 2.000000e-03 54.7
17 TraesCS7D01G115000 chr7B 89.618 1570 67 30 614 2105 12719693 12718142 0.000000e+00 1908.0
18 TraesCS7D01G115000 chr7B 91.779 1265 58 20 869 2099 12951932 12953184 0.000000e+00 1718.0
19 TraesCS7D01G115000 chr7B 88.608 474 39 6 2100 2573 12718113 12717655 2.120000e-156 562.0
20 TraesCS7D01G115000 chr7B 88.139 489 37 10 2100 2573 12953219 12953701 2.120000e-156 562.0
21 TraesCS7D01G115000 chr7B 89.242 409 18 3 839 1225 12716379 12716783 3.650000e-134 488.0
22 TraesCS7D01G115000 chr7B 83.902 410 41 14 1 406 12715541 12715929 4.970000e-98 368.0
23 TraesCS7D01G115000 chr7B 88.462 104 11 1 613 715 12716090 12716193 1.190000e-24 124.0
24 TraesCS7D01G115000 chr7B 86.916 107 12 2 595 700 130268807 130268702 5.520000e-23 119.0
25 TraesCS7D01G115000 chr7B 100.000 55 0 0 2572 2626 1252644 1252590 5.560000e-18 102.0
26 TraesCS7D01G115000 chr7B 85.057 87 4 7 757 834 12951767 12951853 2.610000e-11 80.5
27 TraesCS7D01G115000 chr7B 92.857 42 1 2 1 42 12744264 12744225 3.400000e-05 60.2
28 TraesCS7D01G115000 chr7A 89.351 986 53 18 2102 3068 76550227 76551179 0.000000e+00 1192.0
29 TraesCS7D01G115000 chr7A 83.571 560 76 11 1 553 76818354 76818904 7.800000e-141 510.0
30 TraesCS7D01G115000 chr7A 87.037 108 10 4 595 700 343648983 343649088 5.520000e-23 119.0
31 TraesCS7D01G115000 chr7A 92.105 76 5 1 735 810 76819183 76819257 4.300000e-19 106.0
32 TraesCS7D01G115000 chr2B 86.667 180 23 1 392 570 201236675 201236854 6.900000e-47 198.0
33 TraesCS7D01G115000 chr2B 100.000 56 0 0 2572 2627 653585399 653585344 1.550000e-18 104.0
34 TraesCS7D01G115000 chr6B 86.034 179 25 0 392 570 51740753 51740575 3.210000e-45 193.0
35 TraesCS7D01G115000 chr6B 100.000 55 0 0 2572 2626 116281157 116281103 5.560000e-18 102.0
36 TraesCS7D01G115000 chr2D 86.111 180 24 1 392 570 632465501 632465680 3.210000e-45 193.0
37 TraesCS7D01G115000 chr2D 97.619 84 2 0 3069 3152 23344111 23344028 9.110000e-31 145.0
38 TraesCS7D01G115000 chr4A 85.246 183 27 0 388 570 426438040 426438222 4.150000e-44 189.0
39 TraesCS7D01G115000 chr4A 98.276 58 0 1 2572 2629 741030517 741030573 2.000000e-17 100.0
40 TraesCS7D01G115000 chr5B 86.047 172 24 0 392 563 672112433 672112262 5.370000e-43 185.0
41 TraesCS7D01G115000 chr4B 85.000 180 26 1 392 570 529837134 529837313 6.940000e-42 182.0
42 TraesCS7D01G115000 chr1A 84.916 179 27 0 392 570 472948868 472948690 6.940000e-42 182.0
43 TraesCS7D01G115000 chr3D 98.810 84 1 0 3069 3152 607913541 607913458 1.960000e-32 150.0
44 TraesCS7D01G115000 chr3D 96.774 62 2 0 2566 2627 526278391 526278452 1.550000e-18 104.0
45 TraesCS7D01G115000 chr3D 100.000 56 0 0 2572 2627 535746908 535746853 1.550000e-18 104.0
46 TraesCS7D01G115000 chr6D 97.590 83 2 0 3070 3152 464099193 464099275 3.280000e-30 143.0
47 TraesCS7D01G115000 chr6D 100.000 37 0 0 3070 3106 6329222 6329258 5.640000e-08 69.4
48 TraesCS7D01G115000 chr5A 97.561 82 2 0 3071 3152 677178202 677178283 1.180000e-29 141.0
49 TraesCS7D01G115000 chr3B 89.720 107 9 2 595 700 751844142 751844037 5.480000e-28 135.0
50 TraesCS7D01G115000 chr3B 87.963 108 11 2 595 701 404354780 404354886 3.300000e-25 126.0
51 TraesCS7D01G115000 chr5D 87.037 108 12 2 595 701 486260554 486260448 1.540000e-23 121.0
52 TraesCS7D01G115000 chr1B 90.110 91 6 3 3065 3152 548202736 548202826 7.140000e-22 115.0
53 TraesCS7D01G115000 chr2A 85.981 107 13 2 595 700 8186343 8186238 2.570000e-21 113.0
54 TraesCS7D01G115000 chr2A 96.667 60 2 0 2572 2631 630090959 630090900 2.000000e-17 100.0
55 TraesCS7D01G115000 chr6A 100.000 57 0 0 2572 2628 20747058 20747002 4.300000e-19 106.0
56 TraesCS7D01G115000 chr3A 100.000 55 0 0 2572 2626 86793001 86792947 5.560000e-18 102.0


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 TraesCS7D01G115000 chr7D 70734509 70737660 3151 True 5821.000000 5821 100.000 1 3152 1 chr7D.!!$R3 3151
1 TraesCS7D01G115000 chr7D 70151779 70154947 3168 True 981.250000 1849 89.156 62 3068 4 chr7D.!!$R4 3006
2 TraesCS7D01G115000 chr7D 70047370 70050527 3157 False 971.750000 1827 88.727 62 3068 4 chr7D.!!$F2 3006
3 TraesCS7D01G115000 chr7D 69952213 69955955 3742 False 728.325000 1724 86.568 53 2573 4 chr7D.!!$F1 2520
4 TraesCS7D01G115000 chr7B 12717655 12719693 2038 True 1235.000000 1908 89.113 614 2573 2 chr7B.!!$R4 1959
5 TraesCS7D01G115000 chr7B 12951767 12953701 1934 False 786.833333 1718 88.325 757 2573 3 chr7B.!!$F2 1816
6 TraesCS7D01G115000 chr7B 12715541 12716783 1242 False 326.666667 488 87.202 1 1225 3 chr7B.!!$F1 1224
7 TraesCS7D01G115000 chr7A 76550227 76551179 952 False 1192.000000 1192 89.351 2102 3068 1 chr7A.!!$F1 966
8 TraesCS7D01G115000 chr7A 76818354 76819257 903 False 308.000000 510 87.838 1 810 2 chr7A.!!$F3 809

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
518 531 0.251209 ACGTCTAGGGCTGTGACTGA 60.251 55.0 0.0 0.0 0.00 3.41 F
521 534 0.251787 TCTAGGGCTGTGACTGAGCA 60.252 55.0 0.0 0.0 38.27 4.26 F
528 541 0.612229 CTGTGACTGAGCATGGAGGT 59.388 55.0 0.0 0.0 0.00 3.85 F
986 2359 0.743688 GAGATCTGAGCAAGCCGAGA 59.256 55.0 0.0 0.0 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 3137 1.415659 GGGTACAGCTGCATGATCTCT 59.584 52.381 15.27 0.0 0.00 3.10 R
1747 3138 1.871408 CGGGTACAGCTGCATGATCTC 60.871 57.143 15.27 0.0 0.00 2.75 R
1813 3204 2.700897 AGTAGTTGCATAGGCTCGGATT 59.299 45.455 0.00 0.0 41.91 3.01 R
2616 4086 1.269998 CGACGGATCCAATCTACTCCC 59.730 57.143 13.41 0.0 0.00 4.30 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
83 88 9.490083 ACCTTCTAAGATAGTGTAGGTTGTATT 57.510 33.333 0.00 0.00 33.04 1.89
179 187 7.894376 ATTTTAGCATGTTTGGATTGTTGAG 57.106 32.000 0.00 0.00 0.00 3.02
185 193 1.336755 GTTTGGATTGTTGAGCCGTGT 59.663 47.619 0.00 0.00 36.27 4.49
188 196 2.028130 TGGATTGTTGAGCCGTGTTTT 58.972 42.857 0.00 0.00 36.27 2.43
275 285 8.253113 ACATGAATGACATAAATTTGAGGGTTC 58.747 33.333 0.00 0.00 37.46 3.62
301 311 1.289160 AAGGAGTATGGCTGCCTCAA 58.711 50.000 21.03 0.00 36.05 3.02
302 312 1.289160 AGGAGTATGGCTGCCTCAAA 58.711 50.000 21.03 0.00 36.05 2.69
313 323 2.345991 CCTCAAAGGCCGTCCGAA 59.654 61.111 0.00 0.00 37.47 4.30
319 329 3.883744 AAGGCCGTCCGAAGCTGTG 62.884 63.158 0.00 0.00 37.47 3.66
327 337 1.227527 CCGAAGCTGTGTGTGGACA 60.228 57.895 0.00 0.00 0.00 4.02
366 379 0.321564 TGGGCGGATTTGAGTGAGTG 60.322 55.000 0.00 0.00 0.00 3.51
428 441 2.198426 CCAACCAGGCCAACCAGT 59.802 61.111 5.01 0.00 39.06 4.00
518 531 0.251209 ACGTCTAGGGCTGTGACTGA 60.251 55.000 0.00 0.00 0.00 3.41
521 534 0.251787 TCTAGGGCTGTGACTGAGCA 60.252 55.000 0.00 0.00 38.27 4.26
528 541 0.612229 CTGTGACTGAGCATGGAGGT 59.388 55.000 0.00 0.00 0.00 3.85
533 546 1.136329 ACTGAGCATGGAGGTTGGGT 61.136 55.000 0.00 0.00 0.00 4.51
565 578 3.967734 CGGCACAGTCCGTTTATTG 57.032 52.632 3.91 0.00 44.18 1.90
571 631 3.662186 GCACAGTCCGTTTATTGTTTTCG 59.338 43.478 0.00 0.00 0.00 3.46
587 647 6.591313 TGTTTTCGGAATTTAAAAACCAGC 57.409 33.333 15.49 0.00 40.48 4.85
588 648 5.524281 TGTTTTCGGAATTTAAAAACCAGCC 59.476 36.000 15.49 0.00 40.48 4.85
589 649 3.945981 TCGGAATTTAAAAACCAGCCC 57.054 42.857 12.35 0.00 0.00 5.19
590 650 2.229302 TCGGAATTTAAAAACCAGCCCG 59.771 45.455 12.35 0.00 36.14 6.13
591 651 2.029739 CGGAATTTAAAAACCAGCCCGT 60.030 45.455 12.35 0.00 0.00 5.28
592 652 3.553302 CGGAATTTAAAAACCAGCCCGTT 60.553 43.478 12.35 0.00 0.00 4.44
593 653 4.382291 GGAATTTAAAAACCAGCCCGTTT 58.618 39.130 8.52 0.00 37.56 3.60
594 654 4.212425 GGAATTTAAAAACCAGCCCGTTTG 59.788 41.667 8.52 0.00 36.12 2.93
595 655 2.226602 TTAAAAACCAGCCCGTTTGC 57.773 45.000 0.00 0.00 36.12 3.68
609 717 3.613737 CCCGTTTGCTGAAAAATATGCAG 59.386 43.478 0.00 0.00 36.75 4.41
657 768 1.755380 CGGCCTGTTTAGTAGCTAGGT 59.245 52.381 0.00 0.00 0.00 3.08
715 1987 2.919856 ACACCAGCTCTGCTCCGT 60.920 61.111 0.00 0.00 36.40 4.69
716 1988 2.345244 CACCAGCTCTGCTCCGTT 59.655 61.111 0.00 0.00 36.40 4.44
733 2005 6.027749 GCTCCGTTGTGTGGATTAAATAAAG 58.972 40.000 0.00 0.00 34.32 1.85
793 2097 2.041922 CTCCATCCCCTCCGGTCA 60.042 66.667 0.00 0.00 0.00 4.02
834 2151 3.518303 GCCCTAAGTTTCTTCCTCACCTA 59.482 47.826 0.00 0.00 0.00 3.08
835 2152 4.623409 GCCCTAAGTTTCTTCCTCACCTAC 60.623 50.000 0.00 0.00 0.00 3.18
836 2153 4.081031 CCCTAAGTTTCTTCCTCACCTACC 60.081 50.000 0.00 0.00 0.00 3.18
837 2154 4.778427 CCTAAGTTTCTTCCTCACCTACCT 59.222 45.833 0.00 0.00 0.00 3.08
986 2359 0.743688 GAGATCTGAGCAAGCCGAGA 59.256 55.000 0.00 0.00 0.00 4.04
1074 2465 4.722535 TCCTTGGCCCCGCTCTCT 62.723 66.667 0.00 0.00 0.00 3.10
1413 2804 1.079405 GATCGTCGGCTTCACCCAA 60.079 57.895 0.00 0.00 33.26 4.12
1614 3005 4.678743 GTGGTGGCCTGGTTCCCC 62.679 72.222 3.32 0.00 0.00 4.81
1747 3138 4.651867 CCATGGGTGGCTCAAGAG 57.348 61.111 2.85 0.00 39.01 2.85
1842 3233 3.067742 GCCTATGCAACTACTTCCTCGTA 59.932 47.826 0.00 0.00 37.47 3.43
2029 3447 1.447489 CTCCCTTCTGTGAGCAGCG 60.447 63.158 0.00 0.00 42.29 5.18
2138 3590 2.573340 CGCCCTTTCACCATTGCC 59.427 61.111 0.00 0.00 0.00 4.52
2185 3637 4.593206 TCCTCATGAGTGGTAAGTCTGTTT 59.407 41.667 21.11 0.00 0.00 2.83
2227 3679 5.643379 TGCATCTATCATGTGCGATACTA 57.357 39.130 0.00 0.00 41.61 1.82
2320 3773 4.333926 CCTGAATCTTTCGAGGAATTGACC 59.666 45.833 0.00 0.00 32.90 4.02
2414 3867 1.650912 GCCACAGCACTTCACACTG 59.349 57.895 0.00 0.00 39.53 3.66
2490 3958 1.383523 GGATCTTTGTGTGGCTAGGC 58.616 55.000 9.85 9.85 0.00 3.93
2599 4069 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
2601 4071 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
2602 4072 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
2603 4073 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
2604 4074 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
2605 4075 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
2606 4076 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
2607 4077 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
2608 4078 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
2609 4079 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
2610 4080 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
2611 4081 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
2612 4082 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
2613 4083 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
2614 4084 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
2615 4085 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
2616 4086 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
2617 4087 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2618 4088 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2619 4089 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2620 4090 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2751 4221 8.915871 ATTGCATATGATGTTTGTACTTGAAC 57.084 30.769 6.97 0.00 0.00 3.18
2752 4222 7.446001 TGCATATGATGTTTGTACTTGAACA 57.554 32.000 6.97 10.80 39.78 3.18
2782 4252 7.108841 ACTTGCGATTAACAGAATCCTACTA 57.891 36.000 0.00 0.00 0.00 1.82
2783 4253 7.553334 ACTTGCGATTAACAGAATCCTACTAA 58.447 34.615 0.00 0.00 0.00 2.24
2784 4254 8.204836 ACTTGCGATTAACAGAATCCTACTAAT 58.795 33.333 0.00 0.00 0.00 1.73
2785 4255 7.946655 TGCGATTAACAGAATCCTACTAATG 57.053 36.000 0.00 0.00 0.00 1.90
2786 4256 7.497595 TGCGATTAACAGAATCCTACTAATGT 58.502 34.615 0.00 0.00 0.00 2.71
2787 4257 8.635328 TGCGATTAACAGAATCCTACTAATGTA 58.365 33.333 0.00 0.00 0.00 2.29
2788 4258 9.130312 GCGATTAACAGAATCCTACTAATGTAG 57.870 37.037 0.00 0.00 44.23 2.74
2890 4364 8.755696 TTTTTCTGTATGTGAATAACAATGCC 57.244 30.769 0.00 0.00 43.61 4.40
2891 4365 5.733226 TCTGTATGTGAATAACAATGCCG 57.267 39.130 0.00 0.00 43.61 5.69
2900 4374 2.552599 TAACAATGCCGAGTTGTGGA 57.447 45.000 1.74 0.00 39.57 4.02
3032 4506 6.824305 AAATCCAACCTCAACACAATCTAG 57.176 37.500 0.00 0.00 0.00 2.43
3068 4542 9.736023 GTTCTCATGAAGAGTTGTTGTATTTTT 57.264 29.630 0.00 0.00 44.98 1.94
3103 4577 9.974750 GCGGATAGAATAATTTCATTACTTAGC 57.025 33.333 0.00 0.00 34.08 3.09
3111 4585 9.905713 AATAATTTCATTACTTAGCCAGAGTCA 57.094 29.630 0.00 0.00 0.00 3.41
3113 4587 8.814038 AATTTCATTACTTAGCCAGAGTCATT 57.186 30.769 0.00 0.00 0.00 2.57
3114 4588 9.905713 AATTTCATTACTTAGCCAGAGTCATTA 57.094 29.630 0.00 0.00 0.00 1.90
3115 4589 8.718102 TTTCATTACTTAGCCAGAGTCATTAC 57.282 34.615 0.00 0.00 0.00 1.89
3116 4590 7.418337 TCATTACTTAGCCAGAGTCATTACA 57.582 36.000 0.00 0.00 0.00 2.41
3117 4591 8.023021 TCATTACTTAGCCAGAGTCATTACAT 57.977 34.615 0.00 0.00 0.00 2.29
3118 4592 8.486210 TCATTACTTAGCCAGAGTCATTACATT 58.514 33.333 0.00 0.00 0.00 2.71
3119 4593 8.768955 CATTACTTAGCCAGAGTCATTACATTC 58.231 37.037 0.00 0.00 0.00 2.67
3120 4594 6.299805 ACTTAGCCAGAGTCATTACATTCA 57.700 37.500 0.00 0.00 0.00 2.57
3121 4595 6.344500 ACTTAGCCAGAGTCATTACATTCAG 58.656 40.000 0.00 0.00 0.00 3.02
3122 4596 6.155221 ACTTAGCCAGAGTCATTACATTCAGA 59.845 38.462 0.00 0.00 0.00 3.27
3123 4597 5.627182 AGCCAGAGTCATTACATTCAGAT 57.373 39.130 0.00 0.00 0.00 2.90
3124 4598 5.999044 AGCCAGAGTCATTACATTCAGATT 58.001 37.500 0.00 0.00 0.00 2.40
3125 4599 5.821470 AGCCAGAGTCATTACATTCAGATTG 59.179 40.000 0.00 0.00 0.00 2.67
3126 4600 5.819379 GCCAGAGTCATTACATTCAGATTGA 59.181 40.000 0.00 0.00 0.00 2.57
3127 4601 6.238320 GCCAGAGTCATTACATTCAGATTGAC 60.238 42.308 0.00 0.00 34.99 3.18
3128 4602 6.019237 CCAGAGTCATTACATTCAGATTGACG 60.019 42.308 0.00 0.00 38.72 4.35
3129 4603 6.533012 CAGAGTCATTACATTCAGATTGACGT 59.467 38.462 0.00 0.00 38.72 4.34
3130 4604 7.702348 CAGAGTCATTACATTCAGATTGACGTA 59.298 37.037 0.00 0.00 38.72 3.57
3131 4605 7.918033 AGAGTCATTACATTCAGATTGACGTAG 59.082 37.037 0.00 0.00 38.72 3.51
3132 4606 7.772166 AGTCATTACATTCAGATTGACGTAGA 58.228 34.615 0.00 0.00 38.72 2.59
3133 4607 7.918033 AGTCATTACATTCAGATTGACGTAGAG 59.082 37.037 0.00 0.00 38.72 2.43
3134 4608 6.697455 TCATTACATTCAGATTGACGTAGAGC 59.303 38.462 0.00 0.00 0.00 4.09
3135 4609 4.456280 ACATTCAGATTGACGTAGAGCA 57.544 40.909 0.00 0.00 0.00 4.26
3136 4610 4.820897 ACATTCAGATTGACGTAGAGCAA 58.179 39.130 0.00 0.00 0.00 3.91
3137 4611 4.867047 ACATTCAGATTGACGTAGAGCAAG 59.133 41.667 0.00 0.00 0.00 4.01
3138 4612 4.783764 TTCAGATTGACGTAGAGCAAGA 57.216 40.909 0.00 0.00 0.00 3.02
3139 4613 4.783764 TCAGATTGACGTAGAGCAAGAA 57.216 40.909 0.00 0.00 0.00 2.52
3140 4614 5.330455 TCAGATTGACGTAGAGCAAGAAT 57.670 39.130 0.00 0.00 0.00 2.40
3141 4615 5.344066 TCAGATTGACGTAGAGCAAGAATC 58.656 41.667 0.00 0.00 0.00 2.52
3142 4616 5.126222 TCAGATTGACGTAGAGCAAGAATCT 59.874 40.000 0.00 0.00 0.00 2.40
3143 4617 5.458452 CAGATTGACGTAGAGCAAGAATCTC 59.542 44.000 0.00 0.00 0.00 2.75
3144 4618 3.406728 TGACGTAGAGCAAGAATCTCG 57.593 47.619 0.00 0.00 35.79 4.04
3145 4619 2.747989 TGACGTAGAGCAAGAATCTCGT 59.252 45.455 0.00 0.00 35.09 4.18
3146 4620 3.181509 TGACGTAGAGCAAGAATCTCGTC 60.182 47.826 10.24 10.24 41.86 4.20
3147 4621 2.097791 ACGTAGAGCAAGAATCTCGTCC 59.902 50.000 0.00 0.00 35.79 4.79
3148 4622 2.722071 GTAGAGCAAGAATCTCGTCCG 58.278 52.381 0.00 0.00 35.79 4.79
3149 4623 0.457851 AGAGCAAGAATCTCGTCCGG 59.542 55.000 0.00 0.00 35.79 5.14
3150 4624 1.148759 GAGCAAGAATCTCGTCCGGC 61.149 60.000 0.00 0.00 0.00 6.13
3151 4625 2.517450 GCAAGAATCTCGTCCGGCG 61.517 63.158 11.37 11.37 43.01 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 8.651389 AGGTAAGTTACATCATACATGCATAGT 58.349 33.333 14.81 2.80 0.00 2.12
35 36 9.494271 AAGGTAAGTTACATCATACATGCATAG 57.506 33.333 14.81 0.00 0.00 2.23
36 37 9.489084 GAAGGTAAGTTACATCATACATGCATA 57.511 33.333 14.81 0.00 0.00 3.14
37 38 8.213679 AGAAGGTAAGTTACATCATACATGCAT 58.786 33.333 14.81 0.00 0.00 3.96
38 39 7.564793 AGAAGGTAAGTTACATCATACATGCA 58.435 34.615 14.81 0.00 0.00 3.96
39 40 9.542462 TTAGAAGGTAAGTTACATCATACATGC 57.458 33.333 14.81 0.00 0.00 4.06
54 55 8.968969 ACAACCTACACTATCTTAGAAGGTAAG 58.031 37.037 1.94 1.84 36.60 2.34
83 88 4.748102 GGACGTCATTTGTTGTCTTGACTA 59.252 41.667 18.91 0.00 37.04 2.59
249 259 7.722949 ACCCTCAAATTTATGTCATTCATGT 57.277 32.000 0.00 0.00 37.91 3.21
275 285 4.646492 AGGCAGCCATACTCCTTAAATTTG 59.354 41.667 15.80 0.00 0.00 2.32
301 311 3.626924 ACAGCTTCGGACGGCCTT 61.627 61.111 5.33 0.00 0.00 4.35
302 312 4.379243 CACAGCTTCGGACGGCCT 62.379 66.667 5.33 0.00 0.00 5.19
341 351 4.114997 CAAATCCGCCCACCGCAC 62.115 66.667 0.00 0.00 37.30 5.34
423 436 4.664677 GCCGACGTGCTCACTGGT 62.665 66.667 0.00 0.00 0.00 4.00
426 439 2.433145 CATGCCGACGTGCTCACT 60.433 61.111 0.00 0.00 0.00 3.41
450 463 3.006133 TGTCGTGCCTGGCCCATA 61.006 61.111 17.53 0.00 0.00 2.74
510 523 1.059098 AACCTCCATGCTCAGTCACA 58.941 50.000 0.00 0.00 0.00 3.58
514 527 1.136329 ACCCAACCTCCATGCTCAGT 61.136 55.000 0.00 0.00 0.00 3.41
518 531 1.602237 CGTACCCAACCTCCATGCT 59.398 57.895 0.00 0.00 0.00 3.79
521 534 2.582436 CGCGTACCCAACCTCCAT 59.418 61.111 0.00 0.00 0.00 3.41
565 578 5.049954 GGGCTGGTTTTTAAATTCCGAAAAC 60.050 40.000 12.16 12.16 40.65 2.43
571 631 3.671008 ACGGGCTGGTTTTTAAATTCC 57.329 42.857 0.00 0.00 0.00 3.01
577 637 1.404843 AGCAAACGGGCTGGTTTTTA 58.595 45.000 0.00 0.00 43.89 1.52
578 638 2.207580 AGCAAACGGGCTGGTTTTT 58.792 47.368 0.00 0.00 43.89 1.94
586 646 2.348362 GCATATTTTTCAGCAAACGGGC 59.652 45.455 0.00 0.00 0.00 6.13
587 647 3.583806 TGCATATTTTTCAGCAAACGGG 58.416 40.909 0.00 0.00 33.48 5.28
588 648 4.828291 CTGCATATTTTTCAGCAAACGG 57.172 40.909 0.00 0.00 36.44 4.44
595 655 5.093457 CACACTCAGCTGCATATTTTTCAG 58.907 41.667 9.47 0.00 0.00 3.02
609 717 1.912371 GCCCGTTTAGCACACTCAGC 61.912 60.000 0.00 0.00 0.00 4.26
611 719 1.302192 GGCCCGTTTAGCACACTCA 60.302 57.895 0.00 0.00 0.00 3.41
700 1972 2.345244 CAACGGAGCAGAGCTGGT 59.655 61.111 1.26 1.26 39.88 4.00
811 2115 2.347731 GTGAGGAAGAAACTTAGGGCG 58.652 52.381 0.00 0.00 0.00 6.13
815 2128 5.393243 CGAGGTAGGTGAGGAAGAAACTTAG 60.393 48.000 0.00 0.00 0.00 2.18
851 2193 2.184579 GGAGGAAGAAGCCGTCGG 59.815 66.667 6.99 6.99 0.00 4.79
855 2197 2.496817 CGAGGGAGGAAGAAGCCG 59.503 66.667 0.00 0.00 0.00 5.52
1249 2640 2.429930 CCAGAGGTCCGGTTTGCA 59.570 61.111 0.00 0.00 0.00 4.08
1413 2804 5.752036 TGTTCAGAAGAATGATCAGTCCT 57.248 39.130 18.99 6.77 35.92 3.85
1533 2924 4.672024 GCATTCATGTCAAGCAGAGAGTTG 60.672 45.833 0.00 0.00 0.00 3.16
1581 2972 4.778143 ACGGCAATGGAGGTCGCC 62.778 66.667 0.00 0.00 41.30 5.54
1746 3137 1.415659 GGGTACAGCTGCATGATCTCT 59.584 52.381 15.27 0.00 0.00 3.10
1747 3138 1.871408 CGGGTACAGCTGCATGATCTC 60.871 57.143 15.27 0.00 0.00 2.75
1813 3204 2.700897 AGTAGTTGCATAGGCTCGGATT 59.299 45.455 0.00 0.00 41.91 3.01
1842 3233 4.680537 ACTCGCCCACCGGACTCT 62.681 66.667 9.46 0.00 37.59 3.24
2029 3447 4.436183 GCGCAAAGAGAAGTAAATGGAGTC 60.436 45.833 0.30 0.00 0.00 3.36
2138 3590 3.491104 GGCAGTAGGTTAGAAGATGGTCG 60.491 52.174 0.00 0.00 0.00 4.79
2210 3662 9.573133 TCATAATGTTAGTATCGCACATGATAG 57.427 33.333 0.00 0.00 31.72 2.08
2227 3679 6.830838 GGGGAAGAGAAGACAATCATAATGTT 59.169 38.462 0.00 0.00 0.00 2.71
2414 3867 4.022849 GTCTATTGGCATTATTCACTGGCC 60.023 45.833 0.00 0.00 44.82 5.36
2575 4045 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
2576 4046 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
2577 4047 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
2578 4048 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
2579 4049 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
2582 4052 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
2583 4053 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
2584 4054 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
2586 4056 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
2587 4057 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
2588 4058 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
2589 4059 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
2591 4061 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
2592 4062 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
2593 4063 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
2594 4064 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
2595 4065 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2597 4067 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2599 4069 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2601 4071 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2602 4072 4.355549 TCTACTCCCTCCGTTCCAAATTA 58.644 43.478 0.00 0.00 0.00 1.40
2603 4073 3.178865 TCTACTCCCTCCGTTCCAAATT 58.821 45.455 0.00 0.00 0.00 1.82
2604 4074 2.829023 TCTACTCCCTCCGTTCCAAAT 58.171 47.619 0.00 0.00 0.00 2.32
2605 4075 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
2606 4076 2.500098 CAATCTACTCCCTCCGTTCCAA 59.500 50.000 0.00 0.00 0.00 3.53
2607 4077 2.108168 CAATCTACTCCCTCCGTTCCA 58.892 52.381 0.00 0.00 0.00 3.53
2608 4078 1.413077 CCAATCTACTCCCTCCGTTCC 59.587 57.143 0.00 0.00 0.00 3.62
2609 4079 2.385803 TCCAATCTACTCCCTCCGTTC 58.614 52.381 0.00 0.00 0.00 3.95
2610 4080 2.544844 TCCAATCTACTCCCTCCGTT 57.455 50.000 0.00 0.00 0.00 4.44
2611 4081 2.599677 GATCCAATCTACTCCCTCCGT 58.400 52.381 0.00 0.00 0.00 4.69
2612 4082 1.896465 GGATCCAATCTACTCCCTCCG 59.104 57.143 6.95 0.00 0.00 4.63
2613 4083 1.896465 CGGATCCAATCTACTCCCTCC 59.104 57.143 13.41 0.00 0.00 4.30
2614 4084 2.559231 GACGGATCCAATCTACTCCCTC 59.441 54.545 13.41 0.00 0.00 4.30
2615 4085 2.599677 GACGGATCCAATCTACTCCCT 58.400 52.381 13.41 0.00 0.00 4.20
2616 4086 1.269998 CGACGGATCCAATCTACTCCC 59.730 57.143 13.41 0.00 0.00 4.30
2617 4087 2.228059 TCGACGGATCCAATCTACTCC 58.772 52.381 13.41 0.00 0.00 3.85
2618 4088 3.066342 TGTTCGACGGATCCAATCTACTC 59.934 47.826 13.41 1.11 0.00 2.59
2619 4089 3.021695 TGTTCGACGGATCCAATCTACT 58.978 45.455 13.41 0.00 0.00 2.57
2620 4090 3.431922 TGTTCGACGGATCCAATCTAC 57.568 47.619 13.41 9.66 0.00 2.59
2752 4222 3.146066 TCTGTTAATCGCAAGTTGCCTT 58.854 40.909 21.84 16.88 41.12 4.35
2782 4252 8.321353 TGATAACAGAGACATTGTTCCTACATT 58.679 33.333 0.00 0.00 39.36 2.71
2783 4253 7.851228 TGATAACAGAGACATTGTTCCTACAT 58.149 34.615 0.00 0.00 39.36 2.29
2784 4254 7.239763 TGATAACAGAGACATTGTTCCTACA 57.760 36.000 0.00 0.00 39.36 2.74
2785 4255 6.256757 GCTGATAACAGAGACATTGTTCCTAC 59.743 42.308 3.85 0.00 46.03 3.18
2786 4256 6.070824 TGCTGATAACAGAGACATTGTTCCTA 60.071 38.462 3.85 0.00 46.03 2.94
2787 4257 5.181748 GCTGATAACAGAGACATTGTTCCT 58.818 41.667 3.85 0.00 46.03 3.36
2788 4258 4.937620 TGCTGATAACAGAGACATTGTTCC 59.062 41.667 3.85 0.00 46.03 3.62
2789 4259 6.674694 ATGCTGATAACAGAGACATTGTTC 57.325 37.500 3.85 0.00 46.03 3.18
2790 4260 7.458409 AAATGCTGATAACAGAGACATTGTT 57.542 32.000 3.85 0.00 46.03 2.83
2791 4261 8.618677 CATAAATGCTGATAACAGAGACATTGT 58.381 33.333 3.85 0.00 46.03 2.71
2792 4262 8.074370 CCATAAATGCTGATAACAGAGACATTG 58.926 37.037 3.85 0.00 46.03 2.82
2890 4364 3.684305 TCTGCATATGTTTCCACAACTCG 59.316 43.478 4.29 0.00 36.16 4.18
2891 4365 5.392380 CCTTCTGCATATGTTTCCACAACTC 60.392 44.000 4.29 0.00 36.16 3.01
2900 4374 2.418368 TCGCCCTTCTGCATATGTTT 57.582 45.000 4.29 0.00 0.00 2.83
3032 4506 2.462456 TCATGAGAACAGCACACCTC 57.538 50.000 0.00 0.00 0.00 3.85
3077 4551 9.974750 GCTAAGTAATGAAATTATTCTATCCGC 57.025 33.333 0.00 0.00 41.51 5.54
3085 4559 9.905713 TGACTCTGGCTAAGTAATGAAATTATT 57.094 29.630 0.00 0.00 41.51 1.40
3087 4561 9.905713 AATGACTCTGGCTAAGTAATGAAATTA 57.094 29.630 0.00 0.00 37.87 1.40
3088 4562 8.814038 AATGACTCTGGCTAAGTAATGAAATT 57.186 30.769 0.00 0.00 41.28 1.82
3089 4563 9.331282 GTAATGACTCTGGCTAAGTAATGAAAT 57.669 33.333 0.00 0.00 0.00 2.17
3090 4564 8.318412 TGTAATGACTCTGGCTAAGTAATGAAA 58.682 33.333 0.00 0.00 0.00 2.69
3091 4565 7.847096 TGTAATGACTCTGGCTAAGTAATGAA 58.153 34.615 0.00 0.00 0.00 2.57
3092 4566 7.418337 TGTAATGACTCTGGCTAAGTAATGA 57.582 36.000 0.00 0.00 0.00 2.57
3093 4567 8.668510 AATGTAATGACTCTGGCTAAGTAATG 57.331 34.615 0.00 0.00 0.00 1.90
3094 4568 8.486210 TGAATGTAATGACTCTGGCTAAGTAAT 58.514 33.333 0.00 0.00 0.00 1.89
3095 4569 7.847096 TGAATGTAATGACTCTGGCTAAGTAA 58.153 34.615 0.00 0.00 0.00 2.24
3096 4570 7.342026 TCTGAATGTAATGACTCTGGCTAAGTA 59.658 37.037 0.00 0.00 0.00 2.24
3097 4571 6.155221 TCTGAATGTAATGACTCTGGCTAAGT 59.845 38.462 0.00 0.00 0.00 2.24
3098 4572 6.577103 TCTGAATGTAATGACTCTGGCTAAG 58.423 40.000 0.00 0.00 0.00 2.18
3099 4573 6.544928 TCTGAATGTAATGACTCTGGCTAA 57.455 37.500 0.00 0.00 0.00 3.09
3100 4574 6.737720 ATCTGAATGTAATGACTCTGGCTA 57.262 37.500 0.00 0.00 0.00 3.93
3101 4575 5.627182 ATCTGAATGTAATGACTCTGGCT 57.373 39.130 0.00 0.00 0.00 4.75
3102 4576 5.819379 TCAATCTGAATGTAATGACTCTGGC 59.181 40.000 0.00 0.00 0.00 4.85
3103 4577 6.019237 CGTCAATCTGAATGTAATGACTCTGG 60.019 42.308 0.00 0.00 36.05 3.86
3104 4578 6.533012 ACGTCAATCTGAATGTAATGACTCTG 59.467 38.462 0.00 0.00 36.05 3.35
3105 4579 6.634805 ACGTCAATCTGAATGTAATGACTCT 58.365 36.000 0.00 0.00 36.05 3.24
3106 4580 6.893958 ACGTCAATCTGAATGTAATGACTC 57.106 37.500 0.00 0.00 36.05 3.36
3107 4581 7.772166 TCTACGTCAATCTGAATGTAATGACT 58.228 34.615 0.00 0.00 36.05 3.41
3108 4582 7.306283 GCTCTACGTCAATCTGAATGTAATGAC 60.306 40.741 0.00 0.00 35.13 3.06
3109 4583 6.697455 GCTCTACGTCAATCTGAATGTAATGA 59.303 38.462 0.00 0.00 0.00 2.57
3110 4584 6.476706 TGCTCTACGTCAATCTGAATGTAATG 59.523 38.462 0.00 0.00 0.00 1.90
3111 4585 6.573434 TGCTCTACGTCAATCTGAATGTAAT 58.427 36.000 0.00 0.00 0.00 1.89
3112 4586 5.961272 TGCTCTACGTCAATCTGAATGTAA 58.039 37.500 0.00 0.00 0.00 2.41
3113 4587 5.576447 TGCTCTACGTCAATCTGAATGTA 57.424 39.130 0.00 0.00 0.00 2.29
3114 4588 4.456280 TGCTCTACGTCAATCTGAATGT 57.544 40.909 0.00 0.00 0.00 2.71
3115 4589 5.105063 TCTTGCTCTACGTCAATCTGAATG 58.895 41.667 0.00 0.00 0.00 2.67
3116 4590 5.330455 TCTTGCTCTACGTCAATCTGAAT 57.670 39.130 0.00 0.00 0.00 2.57
3117 4591 4.783764 TCTTGCTCTACGTCAATCTGAA 57.216 40.909 0.00 0.00 0.00 3.02
3118 4592 4.783764 TTCTTGCTCTACGTCAATCTGA 57.216 40.909 0.00 0.00 0.00 3.27
3119 4593 5.347342 AGATTCTTGCTCTACGTCAATCTG 58.653 41.667 0.00 0.00 29.87 2.90
3120 4594 5.587289 GAGATTCTTGCTCTACGTCAATCT 58.413 41.667 0.00 0.00 32.94 2.40
3121 4595 4.439449 CGAGATTCTTGCTCTACGTCAATC 59.561 45.833 0.00 0.00 0.00 2.67
3122 4596 4.142359 ACGAGATTCTTGCTCTACGTCAAT 60.142 41.667 0.00 0.00 0.00 2.57
3123 4597 3.190744 ACGAGATTCTTGCTCTACGTCAA 59.809 43.478 0.00 0.00 0.00 3.18
3124 4598 2.747989 ACGAGATTCTTGCTCTACGTCA 59.252 45.455 0.00 0.00 0.00 4.35
3125 4599 3.356145 GACGAGATTCTTGCTCTACGTC 58.644 50.000 0.00 0.00 36.79 4.34
3126 4600 2.097791 GGACGAGATTCTTGCTCTACGT 59.902 50.000 0.49 0.00 32.86 3.57
3127 4601 2.722071 GGACGAGATTCTTGCTCTACG 58.278 52.381 0.49 0.00 0.00 3.51
3128 4602 2.541999 CCGGACGAGATTCTTGCTCTAC 60.542 54.545 0.00 0.00 0.00 2.59
3129 4603 1.676529 CCGGACGAGATTCTTGCTCTA 59.323 52.381 0.00 0.00 0.00 2.43
3130 4604 0.457851 CCGGACGAGATTCTTGCTCT 59.542 55.000 0.00 0.00 0.00 4.09
3131 4605 1.148759 GCCGGACGAGATTCTTGCTC 61.149 60.000 5.05 0.00 0.00 4.26
3132 4606 1.153549 GCCGGACGAGATTCTTGCT 60.154 57.895 5.05 0.00 0.00 3.91
3133 4607 3.400007 GCCGGACGAGATTCTTGC 58.600 61.111 5.05 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.