Multiple sequence alignment - TraesCS2B01G554600

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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 TraesCS2B01G554600 chr2B 100.000 2311 0 0 1 2311 749688366 749686056 0.000000e+00 4268.0
1 TraesCS2B01G554600 chr2B 90.943 530 31 5 56 569 599220309 599220837 0.000000e+00 697.0
2 TraesCS2B01G554600 chr2B 100.000 324 0 0 2842 3165 749685525 749685202 1.620000e-167 599.0
3 TraesCS2B01G554600 chr2B 93.769 337 4 4 56 378 639233126 639232793 1.020000e-134 490.0
4 TraesCS2B01G554600 chr2A 93.416 1291 77 6 962 2249 745299854 745298569 0.000000e+00 1906.0
5 TraesCS2B01G554600 chr2A 93.269 312 20 1 584 894 745300134 745299823 2.880000e-125 459.0
6 TraesCS2B01G554600 chr2A 83.410 217 17 8 2845 3061 745298246 745298049 1.940000e-42 183.0
7 TraesCS2B01G554600 chr2A 86.585 82 11 0 2077 2158 147540517 147540598 1.210000e-14 91.6
8 TraesCS2B01G554600 chr2D 94.020 1020 49 3 962 1981 615150511 615149504 0.000000e+00 1535.0
9 TraesCS2B01G554600 chr2D 94.953 317 14 2 580 894 615150796 615150480 2.190000e-136 496.0
10 TraesCS2B01G554600 chr2D 82.020 495 52 21 61 529 66163909 66163426 1.380000e-103 387.0
11 TraesCS2B01G554600 chr2D 87.241 290 20 7 2845 3118 615148869 615148581 6.590000e-82 315.0
12 TraesCS2B01G554600 chr3B 91.887 530 26 5 56 569 758729191 758729719 0.000000e+00 725.0
13 TraesCS2B01G554600 chr3B 91.778 523 28 2 56 563 783983719 783984241 0.000000e+00 713.0
14 TraesCS2B01G554600 chr1B 91.887 530 25 6 56 569 346413247 346412720 0.000000e+00 725.0
15 TraesCS2B01G554600 chr1B 91.321 530 29 4 56 569 689675524 689676052 0.000000e+00 708.0
16 TraesCS2B01G554600 chr1B 89.894 376 22 9 204 563 595615967 595616342 1.330000e-128 470.0
17 TraesCS2B01G554600 chr1B 94.314 299 16 1 272 569 510806632 510806930 1.030000e-124 457.0
18 TraesCS2B01G554600 chrUn 91.509 530 27 5 56 569 283528414 283527887 0.000000e+00 713.0
19 TraesCS2B01G554600 chrUn 91.509 530 27 5 56 569 302274148 302274675 0.000000e+00 713.0
20 TraesCS2B01G554600 chrUn 87.947 531 35 11 56 563 377705717 377706241 1.620000e-167 599.0
21 TraesCS2B01G554600 chr4D 90.421 522 33 4 56 563 508233863 508233345 0.000000e+00 671.0
22 TraesCS2B01G554600 chr4D 87.709 537 37 11 56 569 500541852 500541322 1.620000e-167 599.0
23 TraesCS2B01G554600 chr1D 83.613 537 56 15 56 563 175788120 175787587 2.860000e-130 475.0
24 TraesCS2B01G554600 chr6D 83.051 472 57 15 61 520 278650418 278649958 1.060000e-109 407.0
25 TraesCS2B01G554600 chr5D 82.180 477 54 14 60 510 507841713 507841242 6.410000e-102 381.0
26 TraesCS2B01G554600 chr5D 84.848 165 23 2 1392 1555 562018001 562017838 7.020000e-37 165.0
27 TraesCS2B01G554600 chr7B 85.890 163 21 2 1394 1555 801474 801635 4.200000e-39 172.0
28 TraesCS2B01G554600 chr5B 86.250 160 20 2 1397 1555 712391694 712391536 4.200000e-39 172.0
29 TraesCS2B01G554600 chr3D 97.368 38 1 0 2916 2953 7412111 7412148 7.330000e-07 65.8


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 TraesCS2B01G554600 chr2B 749685202 749688366 3164 True 2433.500000 4268 100.000000 1 3165 2 chr2B.!!$R2 3164
1 TraesCS2B01G554600 chr2B 599220309 599220837 528 False 697.000000 697 90.943000 56 569 1 chr2B.!!$F1 513
2 TraesCS2B01G554600 chr2A 745298049 745300134 2085 True 849.333333 1906 90.031667 584 3061 3 chr2A.!!$R1 2477
3 TraesCS2B01G554600 chr2D 615148581 615150796 2215 True 782.000000 1535 92.071333 580 3118 3 chr2D.!!$R2 2538
4 TraesCS2B01G554600 chr3B 758729191 758729719 528 False 725.000000 725 91.887000 56 569 1 chr3B.!!$F1 513
5 TraesCS2B01G554600 chr3B 783983719 783984241 522 False 713.000000 713 91.778000 56 563 1 chr3B.!!$F2 507
6 TraesCS2B01G554600 chr1B 346412720 346413247 527 True 725.000000 725 91.887000 56 569 1 chr1B.!!$R1 513
7 TraesCS2B01G554600 chr1B 689675524 689676052 528 False 708.000000 708 91.321000 56 569 1 chr1B.!!$F3 513
8 TraesCS2B01G554600 chrUn 283527887 283528414 527 True 713.000000 713 91.509000 56 569 1 chrUn.!!$R1 513
9 TraesCS2B01G554600 chrUn 302274148 302274675 527 False 713.000000 713 91.509000 56 569 1 chrUn.!!$F1 513
10 TraesCS2B01G554600 chrUn 377705717 377706241 524 False 599.000000 599 87.947000 56 563 1 chrUn.!!$F2 507
11 TraesCS2B01G554600 chr4D 508233345 508233863 518 True 671.000000 671 90.421000 56 563 1 chr4D.!!$R2 507
12 TraesCS2B01G554600 chr4D 500541322 500541852 530 True 599.000000 599 87.709000 56 569 1 chr4D.!!$R1 513
13 TraesCS2B01G554600 chr1D 175787587 175788120 533 True 475.000000 475 83.613000 56 563 1 chr1D.!!$R1 507

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
588 631 0.387202 CACGAAAATTGGCCACCACA 59.613 50.0 3.88 0.0 30.78 4.17 F
1567 1611 0.039437 GACCGAGAAGAAGCACGTGA 60.039 55.0 22.23 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1855 1902 1.025113 TACAGCGACTCCGAGTCCTG 61.025 60.0 28.00 28.0 42.12 3.86 R
3140 3526 0.030807 TGATGGCCTGAGAGGGATGA 60.031 55.0 3.32 0.0 35.37 2.92 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
34 35 8.116624 AGAACTAATTAAGAACTAATGCGACG 57.883 34.615 0.00 0.00 30.24 5.12
35 36 7.972277 AGAACTAATTAAGAACTAATGCGACGA 59.028 33.333 0.00 0.00 30.24 4.20
36 37 8.470040 AACTAATTAAGAACTAATGCGACGAA 57.530 30.769 0.00 0.00 30.24 3.85
37 38 8.644318 ACTAATTAAGAACTAATGCGACGAAT 57.356 30.769 0.00 0.00 30.24 3.34
38 39 8.753175 ACTAATTAAGAACTAATGCGACGAATC 58.247 33.333 0.00 0.00 30.24 2.52
39 40 7.534085 AATTAAGAACTAATGCGACGAATCA 57.466 32.000 0.00 0.00 30.24 2.57
40 41 6.954616 TTAAGAACTAATGCGACGAATCAA 57.045 33.333 0.00 0.00 0.00 2.57
41 42 5.856126 AAGAACTAATGCGACGAATCAAA 57.144 34.783 0.00 0.00 0.00 2.69
42 43 6.422776 AAGAACTAATGCGACGAATCAAAT 57.577 33.333 0.00 0.00 0.00 2.32
43 44 7.534085 AAGAACTAATGCGACGAATCAAATA 57.466 32.000 0.00 0.00 0.00 1.40
44 45 7.534085 AGAACTAATGCGACGAATCAAATAA 57.466 32.000 0.00 0.00 0.00 1.40
45 46 8.142994 AGAACTAATGCGACGAATCAAATAAT 57.857 30.769 0.00 0.00 0.00 1.28
46 47 8.064222 AGAACTAATGCGACGAATCAAATAATG 58.936 33.333 0.00 0.00 0.00 1.90
47 48 6.658831 ACTAATGCGACGAATCAAATAATGG 58.341 36.000 0.00 0.00 0.00 3.16
48 49 5.499139 AATGCGACGAATCAAATAATGGT 57.501 34.783 0.00 0.00 0.00 3.55
49 50 4.271590 TGCGACGAATCAAATAATGGTG 57.728 40.909 0.00 0.00 0.00 4.17
50 51 3.935828 TGCGACGAATCAAATAATGGTGA 59.064 39.130 0.00 0.00 0.00 4.02
51 52 4.574421 TGCGACGAATCAAATAATGGTGAT 59.426 37.500 0.00 0.00 36.00 3.06
52 53 5.065859 TGCGACGAATCAAATAATGGTGATT 59.934 36.000 0.00 0.00 45.03 2.57
53 54 5.971202 GCGACGAATCAAATAATGGTGATTT 59.029 36.000 0.00 0.00 42.98 2.17
54 55 6.075415 GCGACGAATCAAATAATGGTGATTTG 60.075 38.462 0.00 10.65 45.40 2.32
151 153 5.693769 AAACTAATTGGAGGGATCGAAGA 57.306 39.130 0.00 0.00 45.75 2.87
261 267 1.962321 GAGGGGCGAGAGGAAGAACC 61.962 65.000 0.00 0.00 39.35 3.62
322 349 0.884704 CGGCTTATAACTGCCCGCAT 60.885 55.000 9.51 0.00 45.90 4.73
365 392 0.554305 TAGGATCGGACAGGCTACCA 59.446 55.000 9.89 0.00 0.00 3.25
427 465 2.484264 GCTGCTGACGTGGATAAGTTTT 59.516 45.455 0.00 0.00 0.00 2.43
446 484 3.636313 CTACCGCCGCAGTTTCCGA 62.636 63.158 0.00 0.00 0.00 4.55
447 485 2.901051 CTACCGCCGCAGTTTCCGAT 62.901 60.000 0.00 0.00 0.00 4.18
462 500 3.317455 TCCGATGGTAGCCTAGGTAAA 57.683 47.619 11.31 0.00 0.00 2.01
571 614 7.172654 ACAAAAGTGTCAAAACTCAAAACAC 57.827 32.000 0.00 0.00 40.33 3.32
572 615 6.074569 ACAAAAGTGTCAAAACTCAAAACACG 60.075 34.615 0.00 0.00 43.76 4.49
573 616 5.365403 AAGTGTCAAAACTCAAAACACGA 57.635 34.783 0.00 0.00 43.76 4.35
574 617 5.365403 AGTGTCAAAACTCAAAACACGAA 57.635 34.783 0.00 0.00 43.76 3.85
575 618 5.764131 AGTGTCAAAACTCAAAACACGAAA 58.236 33.333 0.00 0.00 43.76 3.46
576 619 6.210078 AGTGTCAAAACTCAAAACACGAAAA 58.790 32.000 0.00 0.00 43.76 2.29
577 620 6.866248 AGTGTCAAAACTCAAAACACGAAAAT 59.134 30.769 0.00 0.00 43.76 1.82
578 621 7.383843 AGTGTCAAAACTCAAAACACGAAAATT 59.616 29.630 0.00 0.00 43.76 1.82
579 622 7.474025 GTGTCAAAACTCAAAACACGAAAATTG 59.526 33.333 0.00 0.00 31.90 2.32
580 623 6.953189 GTCAAAACTCAAAACACGAAAATTGG 59.047 34.615 0.00 0.00 0.00 3.16
581 624 5.463499 AAACTCAAAACACGAAAATTGGC 57.537 34.783 0.00 0.00 0.00 4.52
582 625 3.453424 ACTCAAAACACGAAAATTGGCC 58.547 40.909 0.00 0.00 0.00 5.36
583 626 3.118956 ACTCAAAACACGAAAATTGGCCA 60.119 39.130 0.00 0.00 0.00 5.36
584 627 3.190874 TCAAAACACGAAAATTGGCCAC 58.809 40.909 3.88 0.00 0.00 5.01
585 628 2.232756 AAACACGAAAATTGGCCACC 57.767 45.000 3.88 0.00 0.00 4.61
586 629 1.115467 AACACGAAAATTGGCCACCA 58.885 45.000 3.88 0.00 0.00 4.17
587 630 0.387565 ACACGAAAATTGGCCACCAC 59.612 50.000 3.88 0.00 30.78 4.16
588 631 0.387202 CACGAAAATTGGCCACCACA 59.613 50.000 3.88 0.00 30.78 4.17
634 677 5.008613 GCGTAATCAAAAGCCCAGAATATCA 59.991 40.000 0.00 0.00 0.00 2.15
890 934 4.821589 CCGGTTGCTCTCGCCTCC 62.822 72.222 0.00 0.00 34.43 4.30
891 935 4.821589 CGGTTGCTCTCGCCTCCC 62.822 72.222 0.00 0.00 34.43 4.30
892 936 4.821589 GGTTGCTCTCGCCTCCCG 62.822 72.222 0.00 0.00 38.61 5.14
917 961 4.874977 GCACCGCCGGTAGCTCTC 62.875 72.222 9.25 0.00 40.39 3.20
918 962 4.554363 CACCGCCGGTAGCTCTCG 62.554 72.222 9.25 0.00 40.39 4.04
922 966 4.273257 GCCGGTAGCTCTCGCCTC 62.273 72.222 1.90 0.00 38.99 4.70
923 967 3.597728 CCGGTAGCTCTCGCCTCC 61.598 72.222 0.00 0.00 36.60 4.30
924 968 3.597728 CGGTAGCTCTCGCCTCCC 61.598 72.222 0.00 0.00 36.60 4.30
925 969 3.597728 GGTAGCTCTCGCCTCCCG 61.598 72.222 0.00 0.00 36.60 5.14
926 970 4.273257 GTAGCTCTCGCCTCCCGC 62.273 72.222 0.00 0.00 36.60 6.13
927 971 4.507916 TAGCTCTCGCCTCCCGCT 62.508 66.667 0.00 0.00 36.60 5.52
950 994 4.874977 GCACCGCCGGTAGCTCTC 62.875 72.222 9.25 0.00 40.39 3.20
951 995 4.554363 CACCGCCGGTAGCTCTCG 62.554 72.222 9.25 0.00 40.39 4.04
955 999 4.273257 GCCGGTAGCTCTCGCCTC 62.273 72.222 1.90 0.00 38.99 4.70
956 1000 2.829003 CCGGTAGCTCTCGCCTCA 60.829 66.667 0.00 0.00 36.60 3.86
957 1001 2.409651 CGGTAGCTCTCGCCTCAC 59.590 66.667 0.00 0.00 36.60 3.51
958 1002 2.409651 GGTAGCTCTCGCCTCACG 59.590 66.667 0.00 0.00 45.62 4.35
959 1003 2.408241 GGTAGCTCTCGCCTCACGT 61.408 63.158 0.00 0.00 44.19 4.49
960 1004 1.062845 GTAGCTCTCGCCTCACGTC 59.937 63.158 0.00 0.00 44.19 4.34
993 1037 4.507916 TAGCTCTCGCCTCCCGCT 62.508 66.667 0.00 0.00 36.60 5.52
999 1043 2.441348 TCGCCTCCCGCTGATACA 60.441 61.111 0.00 0.00 36.73 2.29
1036 1080 4.265056 ACCCCGAGCGCAAAAGGT 62.265 61.111 11.47 8.43 0.00 3.50
1083 1127 1.005394 GTCGTCCGTGGACACCATT 60.005 57.895 18.54 0.00 44.77 3.16
1269 1313 2.514824 GGGATTCTGACGCCAGCC 60.515 66.667 0.00 0.00 40.20 4.85
1345 1389 2.465097 GATCATCTCGCCCTCGACCG 62.465 65.000 0.00 0.00 40.21 4.79
1401 1445 2.669229 CGGCACATGACTGGCACA 60.669 61.111 0.00 0.00 36.51 4.57
1567 1611 0.039437 GACCGAGAAGAAGCACGTGA 60.039 55.000 22.23 0.00 0.00 4.35
1635 1682 3.157523 CAGCACGACGACGACGAC 61.158 66.667 25.15 16.04 42.66 4.34
1665 1712 0.397675 TCCATGAGCCGATCTGGACT 60.398 55.000 7.64 4.59 42.00 3.85
1677 1724 4.375272 CGATCTGGACTATGTTCTGCAAT 58.625 43.478 0.00 0.00 0.00 3.56
1855 1902 0.319900 CGATCACATCATCGGGTCCC 60.320 60.000 0.00 0.00 41.71 4.46
1890 1937 4.830765 TACATGCTCGGGCCGCAC 62.831 66.667 23.83 16.26 40.65 5.34
1992 2039 4.963199 CGAACACTTCGTGTACGTATAC 57.037 45.455 12.05 12.05 46.79 1.47
1993 2040 3.471444 CGAACACTTCGTGTACGTATACG 59.529 47.826 31.33 31.33 46.79 3.06
1994 2041 4.394795 GAACACTTCGTGTACGTATACGT 58.605 43.478 33.81 31.42 46.79 3.57
2104 2206 7.148918 CGATTTTCATTAAAGAAACTGCCACAG 60.149 37.037 5.40 0.00 37.24 3.66
2158 2260 3.829601 GGAAGTCTCACGGATATGAGGAT 59.170 47.826 3.10 0.00 45.30 3.24
2164 2266 6.323996 AGTCTCACGGATATGAGGATTACAAA 59.676 38.462 3.10 0.00 45.30 2.83
2165 2267 6.984474 GTCTCACGGATATGAGGATTACAAAA 59.016 38.462 3.10 0.00 45.30 2.44
2166 2268 7.657761 GTCTCACGGATATGAGGATTACAAAAT 59.342 37.037 3.10 0.00 45.30 1.82
2171 2273 9.621629 ACGGATATGAGGATTACAAAATAAACA 57.378 29.630 0.00 0.00 0.00 2.83
2190 2292 4.589216 ACATGGTGAAAGTGGACAAATG 57.411 40.909 0.00 0.00 0.00 2.32
2206 2308 6.525121 GACAAATGTGGCCTTTTCTAAAAC 57.475 37.500 3.32 0.00 0.00 2.43
2207 2309 6.233905 ACAAATGTGGCCTTTTCTAAAACT 57.766 33.333 3.32 0.00 0.00 2.66
2210 2312 8.261522 ACAAATGTGGCCTTTTCTAAAACTTTA 58.738 29.630 3.32 0.00 0.00 1.85
2211 2313 8.547894 CAAATGTGGCCTTTTCTAAAACTTTAC 58.452 33.333 3.32 0.00 0.00 2.01
2232 2335 7.811117 TTACCATAAAATAAACCCGATCCAG 57.189 36.000 0.00 0.00 0.00 3.86
2250 2354 6.570186 CGATCCAGAACAATTCCACAAAATGA 60.570 38.462 0.00 0.00 0.00 2.57
2251 2355 6.669125 TCCAGAACAATTCCACAAAATGAT 57.331 33.333 0.00 0.00 0.00 2.45
2252 2356 6.457355 TCCAGAACAATTCCACAAAATGATG 58.543 36.000 0.00 0.00 0.00 3.07
2255 2359 8.252417 CCAGAACAATTCCACAAAATGATGATA 58.748 33.333 0.00 0.00 0.00 2.15
2281 2651 2.346766 TGAAGCAAGGCAGAAACTCA 57.653 45.000 0.00 0.00 0.00 3.41
2282 2652 2.224606 TGAAGCAAGGCAGAAACTCAG 58.775 47.619 0.00 0.00 0.00 3.35
2283 2653 2.158769 TGAAGCAAGGCAGAAACTCAGA 60.159 45.455 0.00 0.00 0.00 3.27
2284 2654 2.645838 AGCAAGGCAGAAACTCAGAA 57.354 45.000 0.00 0.00 0.00 3.02
2286 2656 3.290710 AGCAAGGCAGAAACTCAGAAAA 58.709 40.909 0.00 0.00 0.00 2.29
2290 2660 5.566230 GCAAGGCAGAAACTCAGAAAATGAT 60.566 40.000 0.00 0.00 37.28 2.45
2291 2661 5.640189 AGGCAGAAACTCAGAAAATGATG 57.360 39.130 0.00 0.00 37.28 3.07
2293 2663 5.950549 AGGCAGAAACTCAGAAAATGATGAT 59.049 36.000 0.00 0.00 37.28 2.45
2294 2664 6.034591 GGCAGAAACTCAGAAAATGATGATG 58.965 40.000 0.00 0.00 37.28 3.07
2295 2665 6.034591 GCAGAAACTCAGAAAATGATGATGG 58.965 40.000 0.00 0.00 37.28 3.51
2296 2666 6.127814 GCAGAAACTCAGAAAATGATGATGGA 60.128 38.462 0.00 0.00 37.28 3.41
2297 2667 7.473366 CAGAAACTCAGAAAATGATGATGGAG 58.527 38.462 0.00 0.00 37.28 3.86
2298 2668 7.336176 CAGAAACTCAGAAAATGATGATGGAGA 59.664 37.037 0.00 0.00 37.28 3.71
2299 2669 8.053963 AGAAACTCAGAAAATGATGATGGAGAT 58.946 33.333 0.00 0.00 37.28 2.75
2300 2670 7.804843 AACTCAGAAAATGATGATGGAGATC 57.195 36.000 0.00 0.00 37.28 2.75
2301 2671 6.896883 ACTCAGAAAATGATGATGGAGATCA 58.103 36.000 0.00 0.00 42.92 2.92
2302 2672 7.344134 ACTCAGAAAATGATGATGGAGATCAA 58.656 34.615 0.00 0.00 42.02 2.57
2303 2673 7.499563 ACTCAGAAAATGATGATGGAGATCAAG 59.500 37.037 0.00 0.00 42.02 3.02
2304 2674 6.771267 TCAGAAAATGATGATGGAGATCAAGG 59.229 38.462 0.00 0.00 42.02 3.61
2305 2675 6.771267 CAGAAAATGATGATGGAGATCAAGGA 59.229 38.462 0.00 0.00 42.02 3.36
2306 2676 6.999272 AGAAAATGATGATGGAGATCAAGGAG 59.001 38.462 0.00 0.00 42.02 3.69
2307 2677 4.912317 ATGATGATGGAGATCAAGGAGG 57.088 45.455 0.00 0.00 42.02 4.30
2308 2678 3.662078 TGATGATGGAGATCAAGGAGGT 58.338 45.455 0.00 0.00 42.02 3.85
2309 2679 3.645212 TGATGATGGAGATCAAGGAGGTC 59.355 47.826 0.00 0.00 42.02 3.85
2310 2680 3.411454 TGATGGAGATCAAGGAGGTCT 57.589 47.619 0.00 0.00 35.55 3.85
2900 3270 5.046304 CCTCACAAAAGACCTCCTTCATCTA 60.046 44.000 0.00 0.00 33.02 1.98
3061 3447 3.833650 TCAGGTAGTCCGGTAAATTGTCA 59.166 43.478 0.00 0.00 39.05 3.58
3120 3506 4.142780 GCCCCGGCATTTAGAGAC 57.857 61.111 0.00 0.00 41.49 3.36
3121 3507 1.223487 GCCCCGGCATTTAGAGACA 59.777 57.895 0.00 0.00 41.49 3.41
3122 3508 0.179018 GCCCCGGCATTTAGAGACAT 60.179 55.000 0.00 0.00 41.49 3.06
3123 3509 1.750682 GCCCCGGCATTTAGAGACATT 60.751 52.381 0.00 0.00 41.49 2.71
3124 3510 2.486548 GCCCCGGCATTTAGAGACATTA 60.487 50.000 0.00 0.00 41.49 1.90
3125 3511 3.815809 CCCCGGCATTTAGAGACATTAA 58.184 45.455 0.00 0.00 0.00 1.40
3126 3512 4.398319 CCCCGGCATTTAGAGACATTAAT 58.602 43.478 0.00 0.00 0.00 1.40
3127 3513 5.556915 CCCCGGCATTTAGAGACATTAATA 58.443 41.667 0.00 0.00 0.00 0.98
3128 3514 5.411669 CCCCGGCATTTAGAGACATTAATAC 59.588 44.000 0.00 0.00 0.00 1.89
3129 3515 6.231211 CCCGGCATTTAGAGACATTAATACT 58.769 40.000 0.00 0.00 0.00 2.12
3130 3516 6.147821 CCCGGCATTTAGAGACATTAATACTG 59.852 42.308 0.00 0.00 0.00 2.74
3131 3517 6.706270 CCGGCATTTAGAGACATTAATACTGT 59.294 38.462 0.00 0.00 0.00 3.55
3132 3518 7.307396 CCGGCATTTAGAGACATTAATACTGTG 60.307 40.741 0.00 0.00 0.00 3.66
3133 3519 7.355778 GGCATTTAGAGACATTAATACTGTGC 58.644 38.462 0.00 0.00 0.00 4.57
3134 3520 7.012327 GGCATTTAGAGACATTAATACTGTGCA 59.988 37.037 0.00 0.00 0.00 4.57
3135 3521 8.562892 GCATTTAGAGACATTAATACTGTGCAT 58.437 33.333 0.00 0.00 0.00 3.96
3138 3524 9.890629 TTTAGAGACATTAATACTGTGCATCTT 57.109 29.630 0.00 0.00 0.00 2.40
3139 3525 9.890629 TTAGAGACATTAATACTGTGCATCTTT 57.109 29.630 0.00 0.00 0.00 2.52
3140 3526 8.798859 AGAGACATTAATACTGTGCATCTTTT 57.201 30.769 0.00 0.00 0.00 2.27
3141 3527 8.887717 AGAGACATTAATACTGTGCATCTTTTC 58.112 33.333 0.00 0.00 0.00 2.29
3142 3528 8.565896 AGACATTAATACTGTGCATCTTTTCA 57.434 30.769 0.00 0.00 0.00 2.69
3143 3529 9.182214 AGACATTAATACTGTGCATCTTTTCAT 57.818 29.630 0.00 0.00 0.00 2.57
3144 3530 9.443283 GACATTAATACTGTGCATCTTTTCATC 57.557 33.333 0.00 0.00 0.00 2.92
3145 3531 8.408601 ACATTAATACTGTGCATCTTTTCATCC 58.591 33.333 0.00 0.00 0.00 3.51
3146 3532 5.841957 AATACTGTGCATCTTTTCATCCC 57.158 39.130 0.00 0.00 0.00 3.85
3147 3533 3.446442 ACTGTGCATCTTTTCATCCCT 57.554 42.857 0.00 0.00 0.00 4.20
3148 3534 3.350833 ACTGTGCATCTTTTCATCCCTC 58.649 45.455 0.00 0.00 0.00 4.30
3149 3535 3.009916 ACTGTGCATCTTTTCATCCCTCT 59.990 43.478 0.00 0.00 0.00 3.69
3150 3536 3.614092 TGTGCATCTTTTCATCCCTCTC 58.386 45.455 0.00 0.00 0.00 3.20
3151 3537 3.009363 TGTGCATCTTTTCATCCCTCTCA 59.991 43.478 0.00 0.00 0.00 3.27
3152 3538 3.626670 GTGCATCTTTTCATCCCTCTCAG 59.373 47.826 0.00 0.00 0.00 3.35
3153 3539 3.212685 GCATCTTTTCATCCCTCTCAGG 58.787 50.000 0.00 0.00 34.30 3.86
3154 3540 3.212685 CATCTTTTCATCCCTCTCAGGC 58.787 50.000 0.00 0.00 32.73 4.85
3155 3541 1.561542 TCTTTTCATCCCTCTCAGGCC 59.438 52.381 0.00 0.00 32.73 5.19
3156 3542 1.283029 CTTTTCATCCCTCTCAGGCCA 59.717 52.381 5.01 0.00 32.73 5.36
3157 3543 1.600058 TTTCATCCCTCTCAGGCCAT 58.400 50.000 5.01 0.00 32.73 4.40
3158 3544 1.135094 TTCATCCCTCTCAGGCCATC 58.865 55.000 5.01 0.00 32.73 3.51
3159 3545 0.030807 TCATCCCTCTCAGGCCATCA 60.031 55.000 5.01 0.00 32.73 3.07
3160 3546 0.397187 CATCCCTCTCAGGCCATCAG 59.603 60.000 5.01 0.00 32.73 2.90
3161 3547 1.417288 ATCCCTCTCAGGCCATCAGC 61.417 60.000 5.01 0.00 42.60 4.26
3162 3548 2.372890 CCCTCTCAGGCCATCAGCA 61.373 63.158 5.01 0.00 46.50 4.41
3163 3549 1.706995 CCCTCTCAGGCCATCAGCAT 61.707 60.000 5.01 0.00 46.50 3.79
3164 3550 0.183014 CCTCTCAGGCCATCAGCATT 59.817 55.000 5.01 0.00 46.50 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.972277 TCGTCGCATTAGTTCTTAATTAGTTCT 59.028 33.333 0.00 0.00 29.37 3.01
11 12 8.470040 TTCGTCGCATTAGTTCTTAATTAGTT 57.530 30.769 0.00 0.00 29.37 2.24
12 13 8.644318 ATTCGTCGCATTAGTTCTTAATTAGT 57.356 30.769 0.00 0.00 29.37 2.24
13 14 8.752254 TGATTCGTCGCATTAGTTCTTAATTAG 58.248 33.333 0.00 0.00 29.37 1.73
14 15 8.637281 TGATTCGTCGCATTAGTTCTTAATTA 57.363 30.769 0.00 0.00 29.37 1.40
15 16 7.534085 TGATTCGTCGCATTAGTTCTTAATT 57.466 32.000 0.00 0.00 29.37 1.40
16 17 7.534085 TTGATTCGTCGCATTAGTTCTTAAT 57.466 32.000 0.00 0.00 32.08 1.40
17 18 6.954616 TTGATTCGTCGCATTAGTTCTTAA 57.045 33.333 0.00 0.00 0.00 1.85
18 19 6.954616 TTTGATTCGTCGCATTAGTTCTTA 57.045 33.333 0.00 0.00 0.00 2.10
19 20 5.856126 TTTGATTCGTCGCATTAGTTCTT 57.144 34.783 0.00 0.00 0.00 2.52
20 21 7.534085 TTATTTGATTCGTCGCATTAGTTCT 57.466 32.000 0.00 0.00 0.00 3.01
21 22 7.321271 CCATTATTTGATTCGTCGCATTAGTTC 59.679 37.037 0.00 0.00 0.00 3.01
22 23 7.132213 CCATTATTTGATTCGTCGCATTAGTT 58.868 34.615 0.00 0.00 0.00 2.24
23 24 6.260050 ACCATTATTTGATTCGTCGCATTAGT 59.740 34.615 0.00 0.00 0.00 2.24
24 25 6.574832 CACCATTATTTGATTCGTCGCATTAG 59.425 38.462 0.00 0.00 0.00 1.73
25 26 6.258947 TCACCATTATTTGATTCGTCGCATTA 59.741 34.615 0.00 0.00 0.00 1.90
26 27 5.065859 TCACCATTATTTGATTCGTCGCATT 59.934 36.000 0.00 0.00 0.00 3.56
27 28 4.574421 TCACCATTATTTGATTCGTCGCAT 59.426 37.500 0.00 0.00 0.00 4.73
28 29 3.935828 TCACCATTATTTGATTCGTCGCA 59.064 39.130 0.00 0.00 0.00 5.10
29 30 4.530094 TCACCATTATTTGATTCGTCGC 57.470 40.909 0.00 0.00 0.00 5.19
30 31 7.186128 TCAAATCACCATTATTTGATTCGTCG 58.814 34.615 7.05 0.00 44.39 5.12
31 32 8.909708 TTCAAATCACCATTATTTGATTCGTC 57.090 30.769 10.94 0.00 46.93 4.20
84 86 6.686679 TCGTCGCATTATTTGATTCAAATCAC 59.313 34.615 24.14 13.11 44.54 3.06
151 153 4.519350 CCCCGAAGAAAGAAAAGTAAGCTT 59.481 41.667 3.48 3.48 36.30 3.74
261 267 0.547712 TCTCCCCCAAGAACAGAGGG 60.548 60.000 0.00 0.00 42.44 4.30
427 465 2.263540 GGAAACTGCGGCGGTAGA 59.736 61.111 15.95 0.00 0.00 2.59
525 568 5.521906 TCAAACAAAATCGGGATTTGACA 57.478 34.783 7.37 0.00 40.57 3.58
554 597 7.359598 CCAATTTTCGTGTTTTGAGTTTTGACA 60.360 33.333 0.00 0.00 0.00 3.58
563 606 3.190874 GTGGCCAATTTTCGTGTTTTGA 58.809 40.909 7.24 0.00 0.00 2.69
565 608 2.093447 TGGTGGCCAATTTTCGTGTTTT 60.093 40.909 7.24 0.00 0.00 2.43
569 612 0.387202 TGTGGTGGCCAATTTTCGTG 59.613 50.000 7.24 0.00 34.18 4.35
570 613 0.387565 GTGTGGTGGCCAATTTTCGT 59.612 50.000 7.24 0.00 34.18 3.85
571 614 0.662970 CGTGTGGTGGCCAATTTTCG 60.663 55.000 7.24 6.76 34.18 3.46
572 615 0.319469 CCGTGTGGTGGCCAATTTTC 60.319 55.000 7.24 0.00 34.18 2.29
573 616 1.745264 CCGTGTGGTGGCCAATTTT 59.255 52.632 7.24 0.00 34.18 1.82
574 617 3.453988 CCGTGTGGTGGCCAATTT 58.546 55.556 7.24 0.00 34.18 1.82
634 677 1.152756 GCGGTGGAATGGCCCTTAT 60.153 57.895 0.00 0.00 34.97 1.73
643 686 0.327924 TGGTGATTCTGCGGTGGAAT 59.672 50.000 0.00 0.00 36.29 3.01
713 756 0.179258 GATTCGGTGTGTTCGTTCGC 60.179 55.000 0.00 0.00 0.00 4.70
743 786 3.567797 GTTCGAGCTGCCGGATGC 61.568 66.667 5.05 8.59 41.77 3.91
757 800 2.284417 GTCTTTGATACCATCGCCGTTC 59.716 50.000 0.00 0.00 0.00 3.95
769 812 1.820581 CGGGGCGAGGTCTTTGATA 59.179 57.895 0.00 0.00 0.00 2.15
790 833 2.908015 GCGGTGCCCATAAGAGGA 59.092 61.111 0.00 0.00 0.00 3.71
1036 1080 4.688419 GGACGACGTCAACCGCGA 62.688 66.667 27.77 0.00 41.42 5.87
1083 1127 4.816984 GAGGGCGGGAGACGGAGA 62.817 72.222 0.00 0.00 44.51 3.71
1434 1478 4.704833 GGGTTCTCCTGCAGCGCA 62.705 66.667 11.47 3.35 36.92 6.09
1677 1724 2.204074 TAGCCCACCCTCTTGCCA 60.204 61.111 0.00 0.00 0.00 4.92
1855 1902 1.025113 TACAGCGACTCCGAGTCCTG 61.025 60.000 28.00 28.00 42.12 3.86
1990 2037 6.418523 CGTGCCATTTTGTATCTATGTACGTA 59.581 38.462 0.00 0.00 0.00 3.57
1991 2038 5.233476 CGTGCCATTTTGTATCTATGTACGT 59.767 40.000 0.00 0.00 0.00 3.57
1992 2039 5.666203 CGTGCCATTTTGTATCTATGTACG 58.334 41.667 0.00 0.00 0.00 3.67
1993 2040 5.440685 GCGTGCCATTTTGTATCTATGTAC 58.559 41.667 0.00 0.00 0.00 2.90
1994 2041 4.210328 CGCGTGCCATTTTGTATCTATGTA 59.790 41.667 0.00 0.00 0.00 2.29
2009 2110 2.977456 AAGCATTCACGCGTGCCA 60.977 55.556 33.63 22.52 42.20 4.92
2068 2170 9.899661 TTCTTTAATGAAAATCGATAAGGAGGA 57.100 29.630 0.00 0.00 0.00 3.71
2081 2183 6.872920 ACTGTGGCAGTTTCTTTAATGAAAA 58.127 32.000 15.76 0.87 42.59 2.29
2104 2206 8.552865 AGTTTTTGTTGTTCTTGGTTTGTAAAC 58.447 29.630 0.00 0.00 38.17 2.01
2158 2260 8.696374 TCCACTTTCACCATGTTTATTTTGTAA 58.304 29.630 0.00 0.00 0.00 2.41
2164 2266 6.723298 TTGTCCACTTTCACCATGTTTATT 57.277 33.333 0.00 0.00 0.00 1.40
2165 2267 6.723298 TTTGTCCACTTTCACCATGTTTAT 57.277 33.333 0.00 0.00 0.00 1.40
2166 2268 6.097554 ACATTTGTCCACTTTCACCATGTTTA 59.902 34.615 0.00 0.00 0.00 2.01
2171 2273 3.321682 CCACATTTGTCCACTTTCACCAT 59.678 43.478 0.00 0.00 0.00 3.55
2190 2292 6.151663 TGGTAAAGTTTTAGAAAAGGCCAC 57.848 37.500 5.01 0.00 0.00 5.01
2206 2308 8.228035 TGGATCGGGTTTATTTTATGGTAAAG 57.772 34.615 0.00 0.00 0.00 1.85
2207 2309 8.053963 TCTGGATCGGGTTTATTTTATGGTAAA 58.946 33.333 0.00 0.00 0.00 2.01
2210 2312 6.008696 TCTGGATCGGGTTTATTTTATGGT 57.991 37.500 0.00 0.00 0.00 3.55
2211 2313 6.320164 TGTTCTGGATCGGGTTTATTTTATGG 59.680 38.462 0.00 0.00 0.00 2.74
2220 2323 3.089284 GGAATTGTTCTGGATCGGGTTT 58.911 45.455 0.00 0.00 0.00 3.27
2250 2354 7.229308 TCTGCCTTGCTTCATCTAAATATCAT 58.771 34.615 0.00 0.00 0.00 2.45
2251 2355 6.594744 TCTGCCTTGCTTCATCTAAATATCA 58.405 36.000 0.00 0.00 0.00 2.15
2252 2356 7.502120 TTCTGCCTTGCTTCATCTAAATATC 57.498 36.000 0.00 0.00 0.00 1.63
2255 2359 5.713861 AGTTTCTGCCTTGCTTCATCTAAAT 59.286 36.000 0.00 0.00 0.00 1.40
2281 2651 6.907961 TCCTTGATCTCCATCATCATTTTCT 58.092 36.000 0.00 0.00 38.89 2.52
2282 2652 6.207025 CCTCCTTGATCTCCATCATCATTTTC 59.793 42.308 0.00 0.00 38.89 2.29
2283 2653 6.069331 CCTCCTTGATCTCCATCATCATTTT 58.931 40.000 0.00 0.00 38.89 1.82
2284 2654 5.133999 ACCTCCTTGATCTCCATCATCATTT 59.866 40.000 0.00 0.00 38.89 2.32
2286 2656 4.241151 ACCTCCTTGATCTCCATCATCAT 58.759 43.478 0.00 0.00 38.89 2.45
2290 2660 3.411454 AGACCTCCTTGATCTCCATCA 57.589 47.619 0.00 0.00 37.24 3.07
2853 3223 0.681887 TTGCCAGAGTGCATGGATGG 60.682 55.000 9.06 7.34 41.70 3.51
2883 3253 5.284582 AGGATGTAGATGAAGGAGGTCTTT 58.715 41.667 0.00 0.00 35.50 2.52
2900 3270 4.837860 AGACAGAAGAGAAACTGAGGATGT 59.162 41.667 0.00 0.00 37.54 3.06
2973 3359 9.669353 CCAATGATCGGATCACTTTTATTTTAG 57.331 33.333 22.09 0.99 43.01 1.85
2979 3365 7.880160 AAATCCAATGATCGGATCACTTTTA 57.120 32.000 22.09 8.28 42.62 1.52
3023 3409 8.537858 GGACTACCTGAAAGACTAAAAATAGGA 58.462 37.037 0.00 0.00 34.07 2.94
3039 3425 3.833650 TGACAATTTACCGGACTACCTGA 59.166 43.478 9.46 0.00 0.00 3.86
3104 3490 2.348411 AATGTCTCTAAATGCCGGGG 57.652 50.000 2.18 0.00 0.00 5.73
3107 3493 7.567571 CACAGTATTAATGTCTCTAAATGCCG 58.432 38.462 0.00 0.00 0.00 5.69
3118 3504 9.443283 GATGAAAAGATGCACAGTATTAATGTC 57.557 33.333 0.00 0.00 0.00 3.06
3119 3505 8.408601 GGATGAAAAGATGCACAGTATTAATGT 58.591 33.333 0.00 0.00 0.00 2.71
3120 3506 7.864379 GGGATGAAAAGATGCACAGTATTAATG 59.136 37.037 0.00 0.00 0.00 1.90
3121 3507 7.781693 AGGGATGAAAAGATGCACAGTATTAAT 59.218 33.333 0.00 0.00 0.00 1.40
3122 3508 7.118723 AGGGATGAAAAGATGCACAGTATTAA 58.881 34.615 0.00 0.00 0.00 1.40
3123 3509 6.662755 AGGGATGAAAAGATGCACAGTATTA 58.337 36.000 0.00 0.00 0.00 0.98
3124 3510 5.513233 AGGGATGAAAAGATGCACAGTATT 58.487 37.500 0.00 0.00 0.00 1.89
3125 3511 5.104193 AGAGGGATGAAAAGATGCACAGTAT 60.104 40.000 0.00 0.00 0.00 2.12
3126 3512 4.225942 AGAGGGATGAAAAGATGCACAGTA 59.774 41.667 0.00 0.00 0.00 2.74
3127 3513 3.009916 AGAGGGATGAAAAGATGCACAGT 59.990 43.478 0.00 0.00 0.00 3.55
3128 3514 3.618351 AGAGGGATGAAAAGATGCACAG 58.382 45.455 0.00 0.00 0.00 3.66
3129 3515 3.009363 TGAGAGGGATGAAAAGATGCACA 59.991 43.478 0.00 0.00 0.00 4.57
3130 3516 3.614092 TGAGAGGGATGAAAAGATGCAC 58.386 45.455 0.00 0.00 0.00 4.57
3131 3517 3.371273 CCTGAGAGGGATGAAAAGATGCA 60.371 47.826 0.00 0.00 0.00 3.96
3132 3518 3.212685 CCTGAGAGGGATGAAAAGATGC 58.787 50.000 0.00 0.00 0.00 3.91
3133 3519 3.212685 GCCTGAGAGGGATGAAAAGATG 58.787 50.000 0.00 0.00 35.37 2.90
3134 3520 2.174424 GGCCTGAGAGGGATGAAAAGAT 59.826 50.000 0.00 0.00 35.37 2.40
3135 3521 1.561542 GGCCTGAGAGGGATGAAAAGA 59.438 52.381 0.00 0.00 35.37 2.52
3136 3522 1.283029 TGGCCTGAGAGGGATGAAAAG 59.717 52.381 3.32 0.00 35.37 2.27
3137 3523 1.371467 TGGCCTGAGAGGGATGAAAA 58.629 50.000 3.32 0.00 35.37 2.29
3138 3524 1.492176 GATGGCCTGAGAGGGATGAAA 59.508 52.381 3.32 0.00 35.37 2.69
3139 3525 1.135094 GATGGCCTGAGAGGGATGAA 58.865 55.000 3.32 0.00 35.37 2.57
3140 3526 0.030807 TGATGGCCTGAGAGGGATGA 60.031 55.000 3.32 0.00 35.37 2.92
3141 3527 0.397187 CTGATGGCCTGAGAGGGATG 59.603 60.000 3.32 0.00 35.37 3.51
3142 3528 1.417288 GCTGATGGCCTGAGAGGGAT 61.417 60.000 3.32 0.00 35.37 3.85
3143 3529 2.068821 GCTGATGGCCTGAGAGGGA 61.069 63.158 3.32 0.00 35.37 4.20
3144 3530 1.706995 ATGCTGATGGCCTGAGAGGG 61.707 60.000 3.32 0.00 40.92 4.30
3145 3531 0.183014 AATGCTGATGGCCTGAGAGG 59.817 55.000 3.32 0.00 40.92 3.69
3146 3532 3.802862 AATGCTGATGGCCTGAGAG 57.197 52.632 3.32 0.00 40.92 3.20


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

AutoCloner maintained by Alex Coulton.