Multiple sequence alignment - TraesCS1D01G144900

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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 TraesCS1D01G144900 chr1D 100.000 4052 0 0 1 4052 200096326 200092275 0.000000e+00 7483.0
1 TraesCS1D01G144900 chr1B 94.690 2354 85 12 788 3118 287840719 287843055 0.000000e+00 3618.0
2 TraesCS1D01G144900 chr1B 91.919 792 55 7 3264 4052 288022474 288023259 0.000000e+00 1099.0
3 TraesCS1D01G144900 chr1B 76.056 994 196 35 1636 2619 671225467 671226428 2.830000e-131 479.0
4 TraesCS1D01G144900 chr1B 79.430 491 88 11 221 703 421369561 421369076 6.490000e-88 335.0
5 TraesCS1D01G144900 chr1B 87.500 208 25 1 4 211 396119969 396119763 5.230000e-59 239.0
6 TraesCS1D01G144900 chr1A 95.245 2103 93 1 1000 3095 253037163 253035061 0.000000e+00 3323.0
7 TraesCS1D01G144900 chr1A 90.850 612 39 13 3127 3728 253035063 253034459 0.000000e+00 804.0
8 TraesCS1D01G144900 chr1A 83.588 786 109 16 1 769 253047966 253047184 0.000000e+00 719.0
9 TraesCS1D01G144900 chr1A 93.694 333 20 1 3721 4052 253017140 253016808 7.820000e-137 497.0
10 TraesCS1D01G144900 chr1A 96.951 164 5 0 782 945 253037337 253037174 3.990000e-70 276.0
11 TraesCS1D01G144900 chr4B 75.378 1389 275 54 1507 2851 637724108 637722743 3.460000e-170 608.0
12 TraesCS1D01G144900 chr4B 74.352 694 150 15 1636 2323 637729762 637729091 1.860000e-68 270.0
13 TraesCS1D01G144900 chr4B 87.019 208 27 0 7 214 614718673 614718466 6.770000e-58 235.0
14 TraesCS1D01G144900 chr4D 74.549 1387 290 52 1507 2851 497152452 497151087 7.660000e-152 547.0
15 TraesCS1D01G144900 chr4D 73.527 1069 227 41 1637 2681 497158282 497157246 4.980000e-94 355.0
16 TraesCS1D01G144900 chr4D 85.782 211 30 0 1 211 435662344 435662554 1.470000e-54 224.0
17 TraesCS1D01G144900 chr5A 74.496 1388 289 48 1507 2851 676951017 676949652 3.560000e-150 542.0
18 TraesCS1D01G144900 chr5A 76.389 720 138 19 1636 2334 676943810 676943102 3.850000e-95 359.0
19 TraesCS1D01G144900 chr7B 73.749 1379 287 58 1508 2855 575388039 575386705 4.740000e-129 472.0
20 TraesCS1D01G144900 chr7B 81.224 490 68 17 222 704 433526851 433526379 1.380000e-99 374.0
21 TraesCS1D01G144900 chr7B 73.904 912 175 33 1517 2416 577142844 577141984 1.410000e-79 307.0
22 TraesCS1D01G144900 chr7A 73.489 1373 296 50 1508 2855 615376101 615374772 1.330000e-124 457.0
23 TraesCS1D01G144900 chr7D 83.893 447 59 12 265 703 417792308 417791867 8.100000e-112 414.0
24 TraesCS1D01G144900 chr2A 81.875 480 65 14 221 689 10740487 10740019 6.350000e-103 385.0
25 TraesCS1D01G144900 chr2A 79.959 484 79 12 221 693 667966635 667966159 1.390000e-89 340.0
26 TraesCS1D01G144900 chr2A 84.466 103 16 0 586 688 765240010 765239908 7.170000e-18 102.0
27 TraesCS1D01G144900 chr3A 85.143 350 45 6 351 695 1598289 1598636 6.440000e-93 351.0
28 TraesCS1D01G144900 chr3D 83.721 344 47 8 224 560 450261309 450261650 2.350000e-82 316.0
29 TraesCS1D01G144900 chr6B 78.419 468 89 11 218 677 677604999 677605462 1.100000e-75 294.0
30 TraesCS1D01G144900 chr2B 73.762 808 173 28 1626 2409 709992115 709992907 8.570000e-72 281.0
31 TraesCS1D01G144900 chr2B 74.396 207 51 2 517 723 88851807 88851603 2.010000e-13 87.9
32 TraesCS1D01G144900 chr2D 87.324 213 27 0 1 213 503312111 503312323 1.130000e-60 244.0
33 TraesCS1D01G144900 chr2D 86.256 211 29 0 1 211 615457952 615458162 3.150000e-56 230.0
34 TraesCS1D01G144900 chr2D 85.308 211 31 0 4 214 622388916 622388706 6.820000e-53 219.0
35 TraesCS1D01G144900 chr2D 72.646 786 158 43 1653 2409 587357188 587357945 1.480000e-49 207.0
36 TraesCS1D01G144900 chr3B 86.730 211 27 1 1 211 159307772 159307981 2.440000e-57 233.0
37 TraesCS1D01G144900 chr4A 85.922 206 29 0 1 206 71170876 71171081 1.900000e-53 220.0


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 TraesCS1D01G144900 chr1D 200092275 200096326 4051 True 7483.000000 7483 100.000000 1 4052 1 chr1D.!!$R1 4051
1 TraesCS1D01G144900 chr1B 287840719 287843055 2336 False 3618.000000 3618 94.690000 788 3118 1 chr1B.!!$F1 2330
2 TraesCS1D01G144900 chr1B 288022474 288023259 785 False 1099.000000 1099 91.919000 3264 4052 1 chr1B.!!$F2 788
3 TraesCS1D01G144900 chr1B 671225467 671226428 961 False 479.000000 479 76.056000 1636 2619 1 chr1B.!!$F3 983
4 TraesCS1D01G144900 chr1A 253034459 253037337 2878 True 1467.666667 3323 94.348667 782 3728 3 chr1A.!!$R3 2946
5 TraesCS1D01G144900 chr1A 253047184 253047966 782 True 719.000000 719 83.588000 1 769 1 chr1A.!!$R2 768
6 TraesCS1D01G144900 chr4B 637722743 637724108 1365 True 608.000000 608 75.378000 1507 2851 1 chr4B.!!$R2 1344
7 TraesCS1D01G144900 chr4B 637729091 637729762 671 True 270.000000 270 74.352000 1636 2323 1 chr4B.!!$R3 687
8 TraesCS1D01G144900 chr4D 497151087 497152452 1365 True 547.000000 547 74.549000 1507 2851 1 chr4D.!!$R1 1344
9 TraesCS1D01G144900 chr4D 497157246 497158282 1036 True 355.000000 355 73.527000 1637 2681 1 chr4D.!!$R2 1044
10 TraesCS1D01G144900 chr5A 676949652 676951017 1365 True 542.000000 542 74.496000 1507 2851 1 chr5A.!!$R2 1344
11 TraesCS1D01G144900 chr5A 676943102 676943810 708 True 359.000000 359 76.389000 1636 2334 1 chr5A.!!$R1 698
12 TraesCS1D01G144900 chr7B 575386705 575388039 1334 True 472.000000 472 73.749000 1508 2855 1 chr7B.!!$R2 1347
13 TraesCS1D01G144900 chr7B 577141984 577142844 860 True 307.000000 307 73.904000 1517 2416 1 chr7B.!!$R3 899
14 TraesCS1D01G144900 chr7A 615374772 615376101 1329 True 457.000000 457 73.489000 1508 2855 1 chr7A.!!$R1 1347
15 TraesCS1D01G144900 chr2B 709992115 709992907 792 False 281.000000 281 73.762000 1626 2409 1 chr2B.!!$F1 783
16 TraesCS1D01G144900 chr2D 587357188 587357945 757 False 207.000000 207 72.646000 1653 2409 1 chr2D.!!$F2 756

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
175 176 0.033503 TAGACCCATGCGAGGAGACA 60.034 55.0 0.0 0.0 0.00 3.41 F
569 572 0.033796 AACAGATGTGGGGCTGATGG 60.034 55.0 0.0 0.0 36.07 3.51 F
755 772 0.322277 TGAGACGGGTACGAGAAGCT 60.322 55.0 0.0 0.0 44.60 3.74 F
2325 2449 0.108585 ACAGGAGCCACATCAACGTT 59.891 50.0 0.0 0.0 0.00 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1090 1130 1.138247 CGCAGGCAGAGGAAATTGC 59.862 57.895 0.00 0.00 39.56 3.56 R
1581 1621 4.746309 GGAGCCCTGGCATGCACA 62.746 66.667 21.36 13.92 44.88 4.57 R
2700 2830 1.305802 TACGCACATGGAGTCCCCT 60.306 57.895 6.74 0.00 35.38 4.79 R
3295 3427 0.235665 AACAACGCTCAAGCATCACG 59.764 50.000 2.50 0.00 42.21 4.35 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.373116 GCTCCCGCGTCAACCTGA 62.373 66.667 4.92 0.00 0.00 3.86
25 26 2.579201 CTCCCGCGTCAACCTGAT 59.421 61.111 4.92 0.00 0.00 2.90
56 57 3.708220 CTCCGTCGCTGCCTCCTTC 62.708 68.421 0.00 0.00 0.00 3.46
92 93 2.315246 CTCAATAGCAAGCCGGAGC 58.685 57.895 5.05 5.59 40.32 4.70
93 94 0.462581 CTCAATAGCAAGCCGGAGCA 60.463 55.000 5.05 0.00 43.56 4.26
94 95 0.035534 TCAATAGCAAGCCGGAGCAA 60.036 50.000 5.05 0.00 43.56 3.91
111 112 1.065551 GCAACTTGGCGTTCTTCTGTT 59.934 47.619 0.00 0.00 32.27 3.16
175 176 0.033503 TAGACCCATGCGAGGAGACA 60.034 55.000 0.00 0.00 0.00 3.41
176 177 0.689080 AGACCCATGCGAGGAGACAT 60.689 55.000 0.00 0.00 0.00 3.06
177 178 0.531532 GACCCATGCGAGGAGACATG 60.532 60.000 0.00 0.00 42.67 3.21
233 234 2.362120 TCGTCGGGGGAAGGAGAC 60.362 66.667 0.00 0.00 0.00 3.36
267 268 4.828925 GGACTGCGCTCTCCTGGC 62.829 72.222 9.73 0.00 0.00 4.85
306 307 2.427753 GGATCCAGTCCGGCATCC 59.572 66.667 6.95 0.00 37.23 3.51
349 350 2.252346 GGCGACGCTCTAGATCCGA 61.252 63.158 20.77 0.00 0.00 4.55
357 358 0.039617 CTCTAGATCCGAAGCTGCCG 60.040 60.000 0.00 0.00 0.00 5.69
366 368 4.749310 AAGCTGCCGCAGTCTCCG 62.749 66.667 21.29 0.00 39.10 4.63
376 378 3.382832 AGTCTCCGCCTTGGACCG 61.383 66.667 0.00 0.00 43.74 4.79
379 381 4.821589 CTCCGCCTTGGACCGCTC 62.822 72.222 0.00 0.00 43.74 5.03
407 410 2.206536 CGAGGGCCATCTCCTCCTC 61.207 68.421 16.60 3.53 46.01 3.71
424 427 2.172372 TCGTAGTCGAGCTCGGAGC 61.172 63.158 33.98 22.13 41.35 4.70
431 434 3.894947 GAGCTCGGAGCCGGAGTC 61.895 72.222 25.49 12.85 43.77 3.36
457 460 1.781786 GGAGCTGGACATCCTAGTGA 58.218 55.000 0.00 0.00 36.82 3.41
466 469 3.306364 GGACATCCTAGTGAATGGGATCG 60.306 52.174 0.00 0.00 45.80 3.69
467 470 3.574396 GACATCCTAGTGAATGGGATCGA 59.426 47.826 0.00 0.00 45.80 3.59
473 476 7.700044 ATCCTAGTGAATGGGATCGAAATCGA 61.700 42.308 8.09 8.09 45.80 3.59
492 495 0.257616 AAGAGGGAGAGGAGAGGACG 59.742 60.000 0.00 0.00 0.00 4.79
498 501 2.124653 GAGGAGAGGACGGAGCGA 60.125 66.667 0.00 0.00 0.00 4.93
500 503 2.124653 GGAGAGGACGGAGCGAGA 60.125 66.667 0.00 0.00 0.00 4.04
517 520 1.673920 GAGAGAGTGAGCTAGGGTTCG 59.326 57.143 0.00 0.00 0.00 3.95
526 529 3.140225 CTAGGGTTCGGAGCGAGGC 62.140 68.421 0.00 0.00 37.14 4.70
562 565 0.893270 TTTGCGGAACAGATGTGGGG 60.893 55.000 0.00 0.00 0.00 4.96
563 566 3.134127 GCGGAACAGATGTGGGGC 61.134 66.667 0.00 0.00 0.00 5.80
564 567 2.671070 CGGAACAGATGTGGGGCT 59.329 61.111 0.00 0.00 0.00 5.19
566 569 1.685224 GGAACAGATGTGGGGCTGA 59.315 57.895 0.00 0.00 36.07 4.26
567 570 0.257039 GGAACAGATGTGGGGCTGAT 59.743 55.000 0.00 0.00 36.07 2.90
569 572 0.033796 AACAGATGTGGGGCTGATGG 60.034 55.000 0.00 0.00 36.07 3.51
570 573 1.210204 ACAGATGTGGGGCTGATGGT 61.210 55.000 0.00 0.00 36.07 3.55
573 576 2.916527 GATGTGGGGCTGATGGTGGG 62.917 65.000 0.00 0.00 0.00 4.61
620 623 2.109181 GTGCCCGAGCTATCCCAC 59.891 66.667 0.00 0.00 40.80 4.61
621 624 2.364973 TGCCCGAGCTATCCCACA 60.365 61.111 0.00 0.00 40.80 4.17
624 627 1.674057 CCCGAGCTATCCCACATCC 59.326 63.158 0.00 0.00 0.00 3.51
626 629 1.464376 CCGAGCTATCCCACATCCGT 61.464 60.000 0.00 0.00 0.00 4.69
628 631 1.040646 GAGCTATCCCACATCCGTCA 58.959 55.000 0.00 0.00 0.00 4.35
635 638 6.156949 AGCTATCCCACATCCGTCATATATTT 59.843 38.462 0.00 0.00 0.00 1.40
638 641 4.009675 CCCACATCCGTCATATATTTGGG 58.990 47.826 0.00 0.00 35.47 4.12
646 649 4.876107 CCGTCATATATTTGGGCTGGATAC 59.124 45.833 0.00 0.00 0.00 2.24
651 654 0.474184 ATTTGGGCTGGATACGAGGG 59.526 55.000 0.00 0.00 42.51 4.30
654 659 2.808206 GGGCTGGATACGAGGGGTG 61.808 68.421 0.00 0.00 42.51 4.61
657 662 3.151710 TGGATACGAGGGGTGCCG 61.152 66.667 0.00 0.00 42.51 5.69
660 665 3.148031 GATACGAGGGGTGCCGGTC 62.148 68.421 1.90 0.00 0.00 4.79
661 666 3.968837 ATACGAGGGGTGCCGGTCA 62.969 63.158 1.90 0.00 0.00 4.02
685 690 1.496934 GGGCGTTTGTTCATGGTTTG 58.503 50.000 0.00 0.00 0.00 2.93
689 694 3.490078 GGCGTTTGTTCATGGTTTGAGAA 60.490 43.478 0.00 0.00 35.27 2.87
690 695 3.730715 GCGTTTGTTCATGGTTTGAGAAG 59.269 43.478 0.00 0.00 35.27 2.85
691 696 4.733523 GCGTTTGTTCATGGTTTGAGAAGT 60.734 41.667 0.00 0.00 35.27 3.01
692 697 5.339990 CGTTTGTTCATGGTTTGAGAAGTT 58.660 37.500 0.00 0.00 35.27 2.66
695 700 4.447290 TGTTCATGGTTTGAGAAGTTCGA 58.553 39.130 0.00 0.00 35.27 3.71
698 703 6.708502 TGTTCATGGTTTGAGAAGTTCGATTA 59.291 34.615 0.00 0.00 35.27 1.75
702 707 5.235516 TGGTTTGAGAAGTTCGATTAGGTC 58.764 41.667 0.00 0.00 0.00 3.85
705 710 6.204108 GGTTTGAGAAGTTCGATTAGGTCAAA 59.796 38.462 9.07 9.07 31.89 2.69
706 711 7.255001 GGTTTGAGAAGTTCGATTAGGTCAAAA 60.255 37.037 12.91 0.60 35.18 2.44
709 714 7.806690 TGAGAAGTTCGATTAGGTCAAAATTG 58.193 34.615 0.00 0.00 0.00 2.32
752 769 2.712057 GTTTGAGACGGGTACGAGAA 57.288 50.000 0.00 0.00 44.60 2.87
755 772 0.322277 TGAGACGGGTACGAGAAGCT 60.322 55.000 0.00 0.00 44.60 3.74
769 786 1.202627 AGAAGCTCGATTGGAGATGCC 60.203 52.381 0.00 0.00 46.23 4.40
770 787 0.543277 AAGCTCGATTGGAGATGCCA 59.457 50.000 0.00 0.00 46.23 4.92
781 798 3.808728 TGGAGATGCCACTAATTACAGC 58.191 45.455 0.00 0.00 43.33 4.40
782 799 3.455910 TGGAGATGCCACTAATTACAGCT 59.544 43.478 0.00 0.00 43.33 4.24
783 800 4.080356 TGGAGATGCCACTAATTACAGCTT 60.080 41.667 0.00 0.00 43.33 3.74
784 801 4.884164 GGAGATGCCACTAATTACAGCTTT 59.116 41.667 0.00 0.00 36.34 3.51
785 802 5.220931 GGAGATGCCACTAATTACAGCTTTG 60.221 44.000 0.00 0.00 36.34 2.77
786 803 4.641989 AGATGCCACTAATTACAGCTTTGG 59.358 41.667 0.00 0.00 0.00 3.28
921 945 1.464608 CCACGTCAACGAAATCAGCAT 59.535 47.619 9.88 0.00 43.02 3.79
947 971 2.234300 TCTTATTCGGCGGTGGATTC 57.766 50.000 7.21 0.00 0.00 2.52
958 982 4.704965 GGCGGTGGATTCTTCTAAACTAT 58.295 43.478 0.00 0.00 0.00 2.12
959 983 5.508489 CGGCGGTGGATTCTTCTAAACTATA 60.508 44.000 0.00 0.00 0.00 1.31
960 984 5.695363 GGCGGTGGATTCTTCTAAACTATAC 59.305 44.000 0.00 0.00 0.00 1.47
961 985 6.462628 GGCGGTGGATTCTTCTAAACTATACT 60.463 42.308 0.00 0.00 0.00 2.12
962 986 7.255730 GGCGGTGGATTCTTCTAAACTATACTA 60.256 40.741 0.00 0.00 0.00 1.82
963 987 7.594386 GCGGTGGATTCTTCTAAACTATACTAC 59.406 40.741 0.00 0.00 0.00 2.73
964 988 8.627403 CGGTGGATTCTTCTAAACTATACTACA 58.373 37.037 0.00 0.00 0.00 2.74
965 989 9.968870 GGTGGATTCTTCTAAACTATACTACAG 57.031 37.037 0.00 0.00 0.00 2.74
988 1012 4.882671 AGTAATTTATCTGCAGCAACCG 57.117 40.909 9.47 0.00 0.00 4.44
991 1015 3.976793 ATTTATCTGCAGCAACCGATG 57.023 42.857 9.47 0.00 0.00 3.84
1090 1130 2.526304 TTGTCAAACCTCTCTCACCG 57.474 50.000 0.00 0.00 0.00 4.94
1248 1288 1.477685 CCCACCAGTTCCACTACCGT 61.478 60.000 0.00 0.00 0.00 4.83
1398 1438 4.090057 GCACAGCCGTTCTTCCGC 62.090 66.667 0.00 0.00 0.00 5.54
1581 1621 2.022129 CGAGAACTTCGCCGTGCTT 61.022 57.895 0.00 0.00 43.22 3.91
1662 1711 3.195698 GCGCCAATCGACCTGGTC 61.196 66.667 16.99 16.99 41.67 4.02
2325 2449 0.108585 ACAGGAGCCACATCAACGTT 59.891 50.000 0.00 0.00 0.00 3.99
2757 2887 2.782222 GGAGATGAGCACCCGCGTA 61.782 63.158 4.92 0.00 45.49 4.42
2853 2983 4.050934 ACGTCGCGGCAGATGTCA 62.051 61.111 12.89 0.00 35.65 3.58
3061 3191 1.275291 CACACTACTGAACCCACCGAT 59.725 52.381 0.00 0.00 0.00 4.18
3155 3285 4.127171 TCTCTACAGTCCACAAACTTTGC 58.873 43.478 1.14 0.00 0.00 3.68
3169 3299 4.595762 AACTTTGCTTGCATGTGATTCT 57.404 36.364 1.14 0.00 0.00 2.40
3288 3420 2.359900 GCGATCTTTGATGGTTGGACT 58.640 47.619 0.00 0.00 0.00 3.85
3295 3427 2.787473 TGATGGTTGGACTGATGACC 57.213 50.000 0.00 0.00 0.00 4.02
3311 3443 1.291877 GACCGTGATGCTTGAGCGTT 61.292 55.000 0.00 0.00 45.83 4.84
3357 3491 3.876320 GCCAAGAATCTCTCTCATTGTCC 59.124 47.826 0.00 0.00 31.02 4.02
3429 3563 5.616866 CGTCAACCGCTGTATTGATTTCTTT 60.617 40.000 0.00 0.00 37.19 2.52
3435 3569 4.201950 CGCTGTATTGATTTCTTTGGAGGG 60.202 45.833 0.00 0.00 0.00 4.30
3460 3595 2.543777 TTTCGTGTAGGCAGAGCTTT 57.456 45.000 0.00 0.00 0.00 3.51
3471 3606 5.620738 AGGCAGAGCTTTGATCTTGTATA 57.379 39.130 8.73 0.00 0.00 1.47
3485 3620 9.944376 TTGATCTTGTATAGTTTGCTCTTTAGT 57.056 29.630 0.00 0.00 0.00 2.24
3513 3653 2.284263 TTGTGTGTGCGCATTTTTGA 57.716 40.000 15.91 0.00 34.80 2.69
3520 3660 1.460359 GTGCGCATTTTTGATGGTTGG 59.540 47.619 15.91 0.00 0.00 3.77
3551 3691 6.363330 CTTCGTCATGCAGAAGTTGGATACA 61.363 44.000 16.78 0.00 40.94 2.29
3678 3821 3.756783 CCCGTCTCCCTCCTCCCT 61.757 72.222 0.00 0.00 0.00 4.20
3731 3874 2.040359 TCACACCACCACTCCCCA 60.040 61.111 0.00 0.00 0.00 4.96
3764 3907 4.083271 CGAAAACCAAGGATTTCTCTCCAC 60.083 45.833 16.53 0.00 37.81 4.02
3766 3909 2.257207 ACCAAGGATTTCTCTCCACGA 58.743 47.619 0.00 0.00 37.81 4.35
3783 3926 1.079405 GACCAGCGGACCGATTCAA 60.079 57.895 20.50 0.00 0.00 2.69
3785 3928 1.079127 CCAGCGGACCGATTCAACT 60.079 57.895 20.50 0.00 0.00 3.16
3793 3936 0.039618 ACCGATTCAACTGGCCCAAT 59.960 50.000 0.00 0.00 0.00 3.16
3835 3978 0.603707 ACACGGTGCTTGTGATGGAG 60.604 55.000 8.30 0.00 39.73 3.86
3871 4014 1.631071 TTGGAGATATGGCGGTGGCA 61.631 55.000 0.00 0.00 43.52 4.92
3967 4110 1.296715 GGCACTGTTGGAGGACGAT 59.703 57.895 0.00 0.00 0.00 3.73
3971 4114 1.273606 CACTGTTGGAGGACGATGAGT 59.726 52.381 0.00 0.00 0.00 3.41
4005 4148 3.941188 CCCTGCGCCGGTATCCAT 61.941 66.667 17.16 0.00 0.00 3.41
4006 4149 2.666190 CCTGCGCCGGTATCCATG 60.666 66.667 10.08 0.00 0.00 3.66
4015 4158 2.972505 GTATCCATGCGGGCGGTG 60.973 66.667 0.00 0.00 36.21 4.94
4041 4184 2.182030 CGGGAGTCGGAGCTCAAC 59.818 66.667 17.19 12.97 37.24 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.811266 CATCAGGTTGACGCGGGAG 60.811 63.158 12.47 0.00 0.00 4.30
15 16 0.741221 GCTCGGGTCATCAGGTTGAC 60.741 60.000 2.58 2.58 44.27 3.18
24 25 2.427245 CGGAGAAGGCTCGGGTCAT 61.427 63.158 0.00 0.00 42.25 3.06
25 26 3.068691 CGGAGAAGGCTCGGGTCA 61.069 66.667 0.00 0.00 42.25 4.02
88 89 0.238553 GAAGAACGCCAAGTTGCTCC 59.761 55.000 0.00 0.00 44.35 4.70
92 93 2.541588 CCAACAGAAGAACGCCAAGTTG 60.542 50.000 0.00 0.00 44.35 3.16
94 95 1.134220 TCCAACAGAAGAACGCCAAGT 60.134 47.619 0.00 0.00 0.00 3.16
148 149 4.910585 CATGGGTCTACCGCCGGC 62.911 72.222 19.07 19.07 44.64 6.13
175 176 3.319198 ACCCCAACGAGGACGCAT 61.319 61.111 0.00 0.00 43.96 4.73
176 177 4.308458 CACCCCAACGAGGACGCA 62.308 66.667 0.00 0.00 43.96 5.24
210 211 3.649277 CTTCCCCCGACGACAGCAG 62.649 68.421 0.00 0.00 0.00 4.24
211 212 3.691342 CTTCCCCCGACGACAGCA 61.691 66.667 0.00 0.00 0.00 4.41
213 214 2.678934 TCCTTCCCCCGACGACAG 60.679 66.667 0.00 0.00 0.00 3.51
214 215 2.678934 CTCCTTCCCCCGACGACA 60.679 66.667 0.00 0.00 0.00 4.35
216 217 2.362120 GTCTCCTTCCCCCGACGA 60.362 66.667 0.00 0.00 0.00 4.20
217 218 3.823330 CGTCTCCTTCCCCCGACG 61.823 72.222 0.00 0.00 42.39 5.12
250 251 4.828925 GCCAGGAGAGCGCAGTCC 62.829 72.222 17.98 17.98 0.00 3.85
279 280 4.888325 CTGGATCCTCCCGGCCCT 62.888 72.222 14.23 0.00 35.03 5.19
285 286 3.551407 GCCGGACTGGATCCTCCC 61.551 72.222 14.23 10.13 46.69 4.30
341 342 2.355445 CTGCGGCAGCTTCGGATCTA 62.355 60.000 18.16 0.00 45.42 1.98
349 350 4.749310 CGGAGACTGCGGCAGCTT 62.749 66.667 28.80 17.43 45.42 3.74
383 385 2.517875 AGATGGCCCTCGCATTGC 60.518 61.111 0.00 0.00 36.38 3.56
407 410 2.325166 GCTCCGAGCTCGACTACG 59.675 66.667 36.59 19.55 43.02 3.51
436 439 0.757188 ACTAGGATGTCCAGCTCCGG 60.757 60.000 0.00 0.00 38.89 5.14
447 450 4.607293 TTCGATCCCATTCACTAGGATG 57.393 45.455 0.00 0.00 40.54 3.51
466 469 3.292460 TCTCCTCTCCCTCTTCGATTTC 58.708 50.000 0.00 0.00 0.00 2.17
467 470 3.295973 CTCTCCTCTCCCTCTTCGATTT 58.704 50.000 0.00 0.00 0.00 2.17
473 476 0.257616 CGTCCTCTCCTCTCCCTCTT 59.742 60.000 0.00 0.00 0.00 2.85
481 484 2.124653 TCGCTCCGTCCTCTCCTC 60.125 66.667 0.00 0.00 0.00 3.71
492 495 0.944386 CTAGCTCACTCTCTCGCTCC 59.056 60.000 0.00 0.00 34.14 4.70
498 501 1.683629 CCGAACCCTAGCTCACTCTCT 60.684 57.143 0.00 0.00 0.00 3.10
500 503 0.331954 TCCGAACCCTAGCTCACTCT 59.668 55.000 0.00 0.00 0.00 3.24
547 550 1.746615 CAGCCCCACATCTGTTCCG 60.747 63.158 0.00 0.00 0.00 4.30
553 556 1.611419 CACCATCAGCCCCACATCT 59.389 57.895 0.00 0.00 0.00 2.90
554 557 1.454479 CCACCATCAGCCCCACATC 60.454 63.158 0.00 0.00 0.00 3.06
613 616 6.352651 CCCAAATATATGACGGATGTGGGATA 60.353 42.308 5.05 0.00 45.05 2.59
614 617 5.500234 CCAAATATATGACGGATGTGGGAT 58.500 41.667 0.00 0.00 0.00 3.85
620 623 3.691118 CCAGCCCAAATATATGACGGATG 59.309 47.826 4.32 4.32 0.00 3.51
621 624 3.587061 TCCAGCCCAAATATATGACGGAT 59.413 43.478 0.00 0.00 0.00 4.18
624 627 4.566759 CGTATCCAGCCCAAATATATGACG 59.433 45.833 0.00 0.00 0.00 4.35
626 629 5.104941 CCTCGTATCCAGCCCAAATATATGA 60.105 44.000 0.00 0.00 0.00 2.15
628 631 4.164221 CCCTCGTATCCAGCCCAAATATAT 59.836 45.833 0.00 0.00 0.00 0.86
635 638 2.445845 CCCCTCGTATCCAGCCCA 60.446 66.667 0.00 0.00 0.00 5.36
638 641 2.109181 GCACCCCTCGTATCCAGC 59.891 66.667 0.00 0.00 0.00 4.85
660 665 4.038080 GAACAAACGCCCGGGCTG 62.038 66.667 41.01 33.54 39.32 4.85
661 666 3.860930 ATGAACAAACGCCCGGGCT 62.861 57.895 41.01 26.06 39.32 5.19
666 671 1.067821 TCAAACCATGAACAAACGCCC 59.932 47.619 0.00 0.00 34.30 6.13
685 690 7.807680 ACAATTTTGACCTAATCGAACTTCTC 58.192 34.615 0.00 0.00 29.73 2.87
689 694 7.936584 TCAAACAATTTTGACCTAATCGAACT 58.063 30.769 0.00 0.00 45.08 3.01
702 707 3.553917 GGTTGTCCGGTCAAACAATTTTG 59.446 43.478 22.29 0.00 43.17 2.44
705 710 2.360801 CAGGTTGTCCGGTCAAACAATT 59.639 45.455 27.42 7.93 37.67 2.32
706 711 1.953686 CAGGTTGTCCGGTCAAACAAT 59.046 47.619 27.42 8.62 37.67 2.71
709 714 3.089788 ACAGGTTGTCCGGTCAAAC 57.910 52.632 20.12 20.12 37.59 2.93
733 749 2.593257 CTTCTCGTACCCGTCTCAAAC 58.407 52.381 0.00 0.00 35.01 2.93
752 769 2.215191 TGGCATCTCCAATCGAGCT 58.785 52.632 0.00 0.00 43.21 4.09
769 786 5.705609 AACCACCAAAGCTGTAATTAGTG 57.294 39.130 0.00 0.00 0.00 2.74
770 787 5.010617 CCAAACCACCAAAGCTGTAATTAGT 59.989 40.000 0.00 0.00 0.00 2.24
771 788 5.010617 ACCAAACCACCAAAGCTGTAATTAG 59.989 40.000 0.00 0.00 0.00 1.73
772 789 4.896482 ACCAAACCACCAAAGCTGTAATTA 59.104 37.500 0.00 0.00 0.00 1.40
773 790 3.709141 ACCAAACCACCAAAGCTGTAATT 59.291 39.130 0.00 0.00 0.00 1.40
774 791 3.304829 ACCAAACCACCAAAGCTGTAAT 58.695 40.909 0.00 0.00 0.00 1.89
775 792 2.691011 GACCAAACCACCAAAGCTGTAA 59.309 45.455 0.00 0.00 0.00 2.41
776 793 2.092103 AGACCAAACCACCAAAGCTGTA 60.092 45.455 0.00 0.00 0.00 2.74
777 794 1.111277 GACCAAACCACCAAAGCTGT 58.889 50.000 0.00 0.00 0.00 4.40
778 795 1.402787 AGACCAAACCACCAAAGCTG 58.597 50.000 0.00 0.00 0.00 4.24
779 796 2.031870 GAAGACCAAACCACCAAAGCT 58.968 47.619 0.00 0.00 0.00 3.74
780 797 2.031870 AGAAGACCAAACCACCAAAGC 58.968 47.619 0.00 0.00 0.00 3.51
781 798 3.023832 ACAGAAGACCAAACCACCAAAG 58.976 45.455 0.00 0.00 0.00 2.77
782 799 3.094484 ACAGAAGACCAAACCACCAAA 57.906 42.857 0.00 0.00 0.00 3.28
783 800 2.818751 ACAGAAGACCAAACCACCAA 57.181 45.000 0.00 0.00 0.00 3.67
784 801 2.818751 AACAGAAGACCAAACCACCA 57.181 45.000 0.00 0.00 0.00 4.17
785 802 3.816994 ACTAACAGAAGACCAAACCACC 58.183 45.455 0.00 0.00 0.00 4.61
786 803 5.608449 AGTACTAACAGAAGACCAAACCAC 58.392 41.667 0.00 0.00 0.00 4.16
921 945 2.680841 CACCGCCGAATAAGAATTCCAA 59.319 45.455 0.65 0.00 38.66 3.53
958 982 8.909923 TGCTGCAGATAAATTACTACTGTAGTA 58.090 33.333 20.43 20.74 41.08 1.82
959 983 7.782049 TGCTGCAGATAAATTACTACTGTAGT 58.218 34.615 22.72 22.72 41.08 2.73
960 984 8.543774 GTTGCTGCAGATAAATTACTACTGTAG 58.456 37.037 20.43 13.13 41.60 2.74
961 985 7.494625 GGTTGCTGCAGATAAATTACTACTGTA 59.505 37.037 20.43 0.00 0.00 2.74
962 986 6.316390 GGTTGCTGCAGATAAATTACTACTGT 59.684 38.462 20.43 0.00 0.00 3.55
963 987 6.510157 CGGTTGCTGCAGATAAATTACTACTG 60.510 42.308 20.43 5.38 0.00 2.74
964 988 5.523916 CGGTTGCTGCAGATAAATTACTACT 59.476 40.000 20.43 0.00 0.00 2.57
965 989 5.522460 TCGGTTGCTGCAGATAAATTACTAC 59.478 40.000 20.43 3.87 0.00 2.73
966 990 5.666462 TCGGTTGCTGCAGATAAATTACTA 58.334 37.500 20.43 0.00 0.00 1.82
967 991 4.513442 TCGGTTGCTGCAGATAAATTACT 58.487 39.130 20.43 0.00 0.00 2.24
972 996 2.677836 GTCATCGGTTGCTGCAGATAAA 59.322 45.455 20.43 5.28 0.00 1.40
974 998 1.482182 AGTCATCGGTTGCTGCAGATA 59.518 47.619 20.43 1.74 0.00 1.98
1090 1130 1.138247 CGCAGGCAGAGGAAATTGC 59.862 57.895 0.00 0.00 39.56 3.56
1581 1621 4.746309 GGAGCCCTGGCATGCACA 62.746 66.667 21.36 13.92 44.88 4.57
2700 2830 1.305802 TACGCACATGGAGTCCCCT 60.306 57.895 6.74 0.00 35.38 4.79
3061 3191 4.271807 AGGTCAATCCTGATCCTCTACA 57.728 45.455 0.00 0.00 46.19 2.74
3118 3248 5.167303 TGTAGAGAGAAGCTCAGTACAGA 57.833 43.478 0.00 0.00 46.45 3.41
3119 3249 4.941263 ACTGTAGAGAGAAGCTCAGTACAG 59.059 45.833 21.93 21.93 46.45 2.74
3120 3250 4.912586 ACTGTAGAGAGAAGCTCAGTACA 58.087 43.478 0.00 0.00 46.45 2.90
3121 3251 4.334481 GGACTGTAGAGAGAAGCTCAGTAC 59.666 50.000 0.00 0.00 46.45 2.73
3122 3252 4.019231 TGGACTGTAGAGAGAAGCTCAGTA 60.019 45.833 0.00 0.00 46.45 2.74
3123 3253 3.245087 TGGACTGTAGAGAGAAGCTCAGT 60.245 47.826 0.47 0.47 46.45 3.41
3124 3254 3.128589 GTGGACTGTAGAGAGAAGCTCAG 59.871 52.174 0.00 0.00 46.45 3.35
3125 3255 3.085533 GTGGACTGTAGAGAGAAGCTCA 58.914 50.000 0.00 0.00 46.45 4.26
3126 3256 3.085533 TGTGGACTGTAGAGAGAAGCTC 58.914 50.000 0.00 0.00 44.29 4.09
3127 3257 3.162147 TGTGGACTGTAGAGAGAAGCT 57.838 47.619 0.00 0.00 0.00 3.74
3128 3258 3.944055 TTGTGGACTGTAGAGAGAAGC 57.056 47.619 0.00 0.00 0.00 3.86
3155 3285 4.161333 GGACGAAAAGAATCACATGCAAG 58.839 43.478 0.00 0.00 0.00 4.01
3231 3363 0.238289 GTGCATATTTCGCCCCATCG 59.762 55.000 0.00 0.00 0.00 3.84
3288 3420 2.008543 GCTCAAGCATCACGGTCATCA 61.009 52.381 0.00 0.00 41.59 3.07
3295 3427 0.235665 AACAACGCTCAAGCATCACG 59.764 50.000 2.50 0.00 42.21 4.35
3442 3576 1.343142 TCAAAGCTCTGCCTACACGAA 59.657 47.619 0.00 0.00 0.00 3.85
3444 3578 1.929836 GATCAAAGCTCTGCCTACACG 59.070 52.381 0.00 0.00 0.00 4.49
3460 3595 9.944376 AACTAAAGAGCAAACTATACAAGATCA 57.056 29.630 0.00 0.00 0.00 2.92
3513 3653 2.780595 CGAAGATTCGCCCAACCAT 58.219 52.632 1.55 0.00 44.26 3.55
3678 3821 4.079253 GTGAAAGTAGGGGAGAAATGCAA 58.921 43.478 0.00 0.00 0.00 4.08
3731 3874 4.895961 TCCTTGGTTTTCGTTTGGTTTTT 58.104 34.783 0.00 0.00 0.00 1.94
3764 3907 2.582498 GAATCGGTCCGCTGGTCG 60.582 66.667 6.34 1.92 38.08 4.79
3766 3909 1.375523 GTTGAATCGGTCCGCTGGT 60.376 57.895 6.34 0.00 0.00 4.00
3783 3926 4.096003 CGTCGGGATTGGGCCAGT 62.096 66.667 6.23 2.72 0.00 4.00
3785 3928 3.781307 CTCGTCGGGATTGGGCCA 61.781 66.667 0.00 0.00 0.00 5.36
3793 3936 1.077285 TGCATAGGTCTCGTCGGGA 60.077 57.895 0.00 0.00 0.00 5.14
3835 3978 1.197721 CCAACAAGAACAGATCACGGC 59.802 52.381 0.00 0.00 0.00 5.68
4000 4143 4.856801 GACACCGCCCGCATGGAT 62.857 66.667 0.00 0.00 37.49 3.41
4015 4158 3.507009 CGACTCCCGGACCTCGAC 61.507 72.222 0.73 0.00 42.43 4.20


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

AutoCloner maintained by Alex Coulton.