Multiple sequence alignment - TraesCS1D01G152300

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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 TraesCS1D01G152300 chr1D 100.000 9679 0 0 1 9679 211949773 211959451 0.000000e+00 17874.0
1 TraesCS1D01G152300 chr1D 97.897 523 8 3 1 521 291780763 291780242 0.000000e+00 902.0
2 TraesCS1D01G152300 chr1A 96.713 2708 54 12 5118 7806 267798939 267801630 0.000000e+00 4475.0
3 TraesCS1D01G152300 chr1A 96.478 2243 47 7 2864 5084 267796706 267798938 0.000000e+00 3675.0
4 TraesCS1D01G152300 chr1A 96.883 1893 38 4 7800 9679 267801700 267803584 0.000000e+00 3149.0
5 TraesCS1D01G152300 chr1A 95.310 1386 22 7 862 2246 267794536 267795879 0.000000e+00 2159.0
6 TraesCS1D01G152300 chr1A 96.166 626 20 2 2240 2865 267795961 267796582 0.000000e+00 1020.0
7 TraesCS1D01G152300 chr1A 97.484 159 4 0 520 678 267793954 267794112 1.240000e-68 272.0
8 TraesCS1D01G152300 chr1A 84.694 98 9 2 6526 6619 267800477 267800572 1.040000e-14 93.5
9 TraesCS1D01G152300 chr1B 97.021 2249 51 10 5571 7806 304514996 304512751 0.000000e+00 3768.0
10 TraesCS1D01G152300 chr1B 95.402 1892 28 13 7800 9679 304512681 304510837 0.000000e+00 2957.0
11 TraesCS1D01G152300 chr1B 97.489 1633 33 3 3922 5549 304516740 304515111 0.000000e+00 2782.0
12 TraesCS1D01G152300 chr1B 98.163 1143 18 2 772 1913 304519754 304518614 0.000000e+00 1991.0
13 TraesCS1D01G152300 chr1B 94.888 626 25 5 2240 2865 304517819 304517201 0.000000e+00 972.0
14 TraesCS1D01G152300 chr1B 97.159 352 10 0 1896 2247 304518251 304517900 6.470000e-166 595.0
15 TraesCS1D01G152300 chr1B 95.879 364 11 2 2864 3223 304517097 304516734 3.890000e-163 586.0
16 TraesCS1D01G152300 chr1B 98.333 180 3 0 520 699 304520303 304520124 5.640000e-82 316.0
17 TraesCS1D01G152300 chr1B 93.617 94 5 1 3216 3308 154165053 154165146 1.310000e-28 139.0
18 TraesCS1D01G152300 chr1B 90.722 97 7 2 3228 3322 406341844 406341748 2.840000e-25 128.0
19 TraesCS1D01G152300 chr1B 85.106 94 8 2 6530 6619 304513904 304513813 3.720000e-14 91.6
20 TraesCS1D01G152300 chr3D 97.719 526 8 1 2 523 20238533 20238008 0.000000e+00 902.0
21 TraesCS1D01G152300 chr5B 90.234 512 46 3 7 517 491813787 491813279 0.000000e+00 665.0
22 TraesCS1D01G152300 chr5B 95.798 119 4 1 9561 9679 20974083 20974200 3.570000e-44 191.0
23 TraesCS1D01G152300 chr5B 95.556 90 3 1 3225 3313 269975155 269975244 1.010000e-29 143.0
24 TraesCS1D01G152300 chr2B 90.632 459 39 2 61 517 98393777 98393321 2.990000e-169 606.0
25 TraesCS1D01G152300 chr6A 94.737 95 4 1 3215 3308 407093164 407093070 7.830000e-31 147.0
26 TraesCS1D01G152300 chr2A 96.591 88 0 3 3228 3312 729165679 729165592 1.010000e-29 143.0
27 TraesCS1D01G152300 chr2A 92.208 77 6 0 445 521 744821310 744821386 1.030000e-19 110.0
28 TraesCS1D01G152300 chr5D 96.512 86 1 2 3228 3311 526559647 526559562 3.640000e-29 141.0
29 TraesCS1D01G152300 chr5D 91.919 99 7 1 3215 3312 452219492 452219394 4.710000e-28 137.0
30 TraesCS1D01G152300 chr5D 89.333 75 8 0 447 521 88341757 88341683 2.880000e-15 95.3
31 TraesCS1D01G152300 chr4D 93.548 93 5 1 3228 3319 252173786 252173694 4.710000e-28 137.0
32 TraesCS1D01G152300 chr2D 94.118 68 4 0 454 521 88592879 88592812 4.780000e-18 104.0
33 TraesCS1D01G152300 chr2D 92.647 68 5 0 454 521 88661222 88661155 2.220000e-16 99.0
34 TraesCS1D01G152300 chr6D 86.905 84 11 0 434 517 97161956 97162039 2.880000e-15 95.3


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 TraesCS1D01G152300 chr1D 211949773 211959451 9678 False 17874.000000 17874 100.000000 1 9679 1 chr1D.!!$F1 9678
1 TraesCS1D01G152300 chr1D 291780242 291780763 521 True 902.000000 902 97.897000 1 521 1 chr1D.!!$R1 520
2 TraesCS1D01G152300 chr1A 267793954 267803584 9630 False 2120.500000 4475 94.818286 520 9679 7 chr1A.!!$F1 9159
3 TraesCS1D01G152300 chr1B 304510837 304520303 9466 True 1562.066667 3768 95.493333 520 9679 9 chr1B.!!$R2 9159
4 TraesCS1D01G152300 chr3D 20238008 20238533 525 True 902.000000 902 97.719000 2 523 1 chr3D.!!$R1 521
5 TraesCS1D01G152300 chr5B 491813279 491813787 508 True 665.000000 665 90.234000 7 517 1 chr5B.!!$R1 510

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
709 714 0.179073 CCTAGCACCACCATCTTCCG 60.179 60.000 0.00 0.00 0.00 4.30 F
757 762 0.254178 CCCATCTCCTCCACCTGTTG 59.746 60.000 0.00 0.00 0.00 3.33 F
760 765 0.898320 ATCTCCTCCACCTGTTGTCG 59.102 55.000 0.00 0.00 0.00 4.35 F
761 766 1.374758 CTCCTCCACCTGTTGTCGC 60.375 63.158 0.00 0.00 0.00 5.19 F
770 775 1.488957 CTGTTGTCGCTCGCTTGTC 59.511 57.895 0.00 0.00 0.00 3.18 F
2299 3072 1.628846 ACGGTCTCAAGGCTTTACCAT 59.371 47.619 18.31 5.30 43.14 3.55 F
2834 3608 0.988678 GACCAAGTGGCTAGGGGGAT 60.989 60.000 0.00 0.00 39.32 3.85 F
3476 4379 4.180817 GTTTGTTGTTTCTTGGGTCCTTG 58.819 43.478 0.00 0.00 0.00 3.61 F
3785 4693 5.938125 TCTTGGCTTTGGTTACTCTGTTATC 59.062 40.000 0.00 0.00 0.00 1.75 F
5104 6033 6.064846 TGTTTCAAGTGCTGAGAAATCTTC 57.935 37.500 0.00 0.00 34.81 2.87 F
5614 6637 1.667724 GTTCAGGAATGCCATGTCTCG 59.332 52.381 0.00 0.00 36.29 4.04 F
6318 7345 1.869767 GCGTATGCCAAAGAGATGGAG 59.130 52.381 0.00 0.00 43.54 3.86 F
7612 8644 1.946768 GTTGCTTACTGTGCACTTCCA 59.053 47.619 19.41 3.93 40.40 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 1995 1.676529 GCACTAGATCTCGGTACAGCA 59.323 52.381 0.00 0.0 0.00 4.41 R
2306 3079 2.098770 GCATCATTTGGGAGAGCAAGAC 59.901 50.000 0.00 0.0 0.00 3.01 R
2612 3386 3.494045 GCTAAGAAAGCCCAATGTGAC 57.506 47.619 0.00 0.0 46.25 3.67 R
2829 3603 6.295292 GGCAAAAATGGAGAATACATATCCCC 60.295 42.308 0.00 0.0 31.73 4.81 R
2834 3608 7.716799 ACAAGGCAAAAATGGAGAATACATA 57.283 32.000 0.00 0.0 0.00 2.29 R
3476 4379 0.972883 TGGCAAGTACAAAATGGCCC 59.027 50.000 0.00 0.0 40.64 5.80 R
3983 4904 1.194098 CAGAAGAGCAGTCAAACAGCG 59.806 52.381 0.00 0.0 35.63 5.18 R
5195 6124 0.107361 GGATTTACCCTCCCACCACG 60.107 60.000 0.00 0.0 0.00 4.94 R
5278 6207 0.593128 GCAGGGTACTGTGCTTGTTG 59.407 55.000 11.38 0.0 46.62 3.33 R
6553 7581 1.299648 CGGAGAGTTCCCAATGCCA 59.700 57.895 0.00 0.0 40.67 4.92 R
7257 8289 3.098774 TGGCCATCACAACCACATAAT 57.901 42.857 0.00 0.0 0.00 1.28 R
7812 8925 1.202245 GCTTTGTTCACTCGTTTGCCA 60.202 47.619 0.00 0.0 0.00 4.92 R
9070 10185 3.275999 ACCCACACTGGCGATATTAAAC 58.724 45.455 0.00 0.0 35.79 2.01 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
39 40 3.170362 CTTGGGGGAGAGGCAACA 58.830 61.111 0.00 0.00 41.41 3.33
523 528 9.998106 TCTAGGAGGCTTTATATGTTCAATTAC 57.002 33.333 0.00 0.00 0.00 1.89
524 529 9.778741 CTAGGAGGCTTTATATGTTCAATTACA 57.221 33.333 0.00 0.00 0.00 2.41
605 610 3.491208 AGCCACATCAGCTCCATTC 57.509 52.632 0.00 0.00 34.91 2.67
684 689 2.660258 ATCGACGCCCACCATTAGCC 62.660 60.000 0.00 0.00 0.00 3.93
699 704 4.415150 GCCAGCAGCCTAGCACCA 62.415 66.667 0.00 0.00 36.85 4.17
700 705 2.437359 CCAGCAGCCTAGCACCAC 60.437 66.667 0.00 0.00 36.85 4.16
701 706 2.437359 CAGCAGCCTAGCACCACC 60.437 66.667 0.00 0.00 36.85 4.61
702 707 2.930019 AGCAGCCTAGCACCACCA 60.930 61.111 0.00 0.00 36.85 4.17
703 708 2.273449 GCAGCCTAGCACCACCAT 59.727 61.111 0.00 0.00 0.00 3.55
704 709 1.821332 GCAGCCTAGCACCACCATC 60.821 63.158 0.00 0.00 0.00 3.51
705 710 1.910722 CAGCCTAGCACCACCATCT 59.089 57.895 0.00 0.00 0.00 2.90
706 711 0.254178 CAGCCTAGCACCACCATCTT 59.746 55.000 0.00 0.00 0.00 2.40
707 712 0.543749 AGCCTAGCACCACCATCTTC 59.456 55.000 0.00 0.00 0.00 2.87
708 713 0.464554 GCCTAGCACCACCATCTTCC 60.465 60.000 0.00 0.00 0.00 3.46
709 714 0.179073 CCTAGCACCACCATCTTCCG 60.179 60.000 0.00 0.00 0.00 4.30
710 715 0.811616 CTAGCACCACCATCTTCCGC 60.812 60.000 0.00 0.00 0.00 5.54
711 716 1.264749 TAGCACCACCATCTTCCGCT 61.265 55.000 0.00 0.00 0.00 5.52
712 717 2.109126 GCACCACCATCTTCCGCTC 61.109 63.158 0.00 0.00 0.00 5.03
713 718 1.599047 CACCACCATCTTCCGCTCT 59.401 57.895 0.00 0.00 0.00 4.09
714 719 0.460987 CACCACCATCTTCCGCTCTC 60.461 60.000 0.00 0.00 0.00 3.20
715 720 1.144936 CCACCATCTTCCGCTCTCC 59.855 63.158 0.00 0.00 0.00 3.71
716 721 1.144936 CACCATCTTCCGCTCTCCC 59.855 63.158 0.00 0.00 0.00 4.30
717 722 2.066999 ACCATCTTCCGCTCTCCCC 61.067 63.158 0.00 0.00 0.00 4.81
718 723 1.764054 CCATCTTCCGCTCTCCCCT 60.764 63.158 0.00 0.00 0.00 4.79
719 724 1.745264 CATCTTCCGCTCTCCCCTC 59.255 63.158 0.00 0.00 0.00 4.30
720 725 1.458588 ATCTTCCGCTCTCCCCTCC 60.459 63.158 0.00 0.00 0.00 4.30
721 726 2.956077 ATCTTCCGCTCTCCCCTCCC 62.956 65.000 0.00 0.00 0.00 4.30
722 727 4.798682 TTCCGCTCTCCCCTCCCC 62.799 72.222 0.00 0.00 0.00 4.81
753 758 2.374342 CCCCCATCTCCTCCACCT 59.626 66.667 0.00 0.00 0.00 4.00
754 759 2.074948 CCCCCATCTCCTCCACCTG 61.075 68.421 0.00 0.00 0.00 4.00
755 760 1.307343 CCCCATCTCCTCCACCTGT 60.307 63.158 0.00 0.00 0.00 4.00
756 761 0.916358 CCCCATCTCCTCCACCTGTT 60.916 60.000 0.00 0.00 0.00 3.16
757 762 0.254178 CCCATCTCCTCCACCTGTTG 59.746 60.000 0.00 0.00 0.00 3.33
758 763 0.987294 CCATCTCCTCCACCTGTTGT 59.013 55.000 0.00 0.00 0.00 3.32
759 764 1.065854 CCATCTCCTCCACCTGTTGTC 60.066 57.143 0.00 0.00 0.00 3.18
760 765 0.898320 ATCTCCTCCACCTGTTGTCG 59.102 55.000 0.00 0.00 0.00 4.35
761 766 1.374758 CTCCTCCACCTGTTGTCGC 60.375 63.158 0.00 0.00 0.00 5.19
762 767 1.821061 CTCCTCCACCTGTTGTCGCT 61.821 60.000 0.00 0.00 0.00 4.93
763 768 1.374758 CCTCCACCTGTTGTCGCTC 60.375 63.158 0.00 0.00 0.00 5.03
764 769 1.734477 CTCCACCTGTTGTCGCTCG 60.734 63.158 0.00 0.00 0.00 5.03
765 770 3.414700 CCACCTGTTGTCGCTCGC 61.415 66.667 0.00 0.00 0.00 5.03
766 771 2.356313 CACCTGTTGTCGCTCGCT 60.356 61.111 0.00 0.00 0.00 4.93
767 772 1.956170 CACCTGTTGTCGCTCGCTT 60.956 57.895 0.00 0.00 0.00 4.68
768 773 1.956170 ACCTGTTGTCGCTCGCTTG 60.956 57.895 0.00 0.00 0.00 4.01
769 774 1.956170 CCTGTTGTCGCTCGCTTGT 60.956 57.895 0.00 0.00 0.00 3.16
770 775 1.488957 CTGTTGTCGCTCGCTTGTC 59.511 57.895 0.00 0.00 0.00 3.18
789 1091 3.782443 CGGCCTAGGGTTTCGCCT 61.782 66.667 11.72 0.00 39.34 5.52
1203 1505 1.888512 GTGCTCCTTTGGATTTGCTCA 59.111 47.619 0.00 0.00 0.00 4.26
1283 1586 8.926715 AACTCTTGGAAAAATGTTGTTAGAAC 57.073 30.769 0.00 0.00 0.00 3.01
1317 1620 4.353437 GCCTTGTGCTGCAGTGCC 62.353 66.667 16.64 4.02 36.87 5.01
1318 1621 2.596631 CCTTGTGCTGCAGTGCCT 60.597 61.111 16.64 0.00 0.00 4.75
1687 1992 3.454082 GGATTTCAGGAGATGTGGACTCT 59.546 47.826 0.00 0.00 35.10 3.24
1690 1995 3.395054 TCAGGAGATGTGGACTCTGAT 57.605 47.619 0.00 0.00 35.10 2.90
1721 2026 6.266558 ACCGAGATCTAGTGCTATCAAAGATT 59.733 38.462 0.00 0.00 31.23 2.40
1803 2108 6.360618 AGTTCACTCTTCTGAGGACATTTTT 58.639 36.000 0.00 0.00 44.29 1.94
1936 2621 9.762381 TTACTATGTAAATTTTTGATGGAGGGT 57.238 29.630 0.00 0.00 0.00 4.34
2024 2709 8.493547 GTTCTTGATAGTAAAACGTGCTAACTT 58.506 33.333 0.00 0.00 0.00 2.66
2299 3072 1.628846 ACGGTCTCAAGGCTTTACCAT 59.371 47.619 18.31 5.30 43.14 3.55
2306 3079 5.122396 GTCTCAAGGCTTTACCATTAGTGTG 59.878 44.000 0.00 0.00 43.14 3.82
2371 3144 7.860373 GTCTGCTTTGTTATGTTGAATGTTGTA 59.140 33.333 0.00 0.00 0.00 2.41
2375 3148 8.434661 GCTTTGTTATGTTGAATGTTGTATTGG 58.565 33.333 0.00 0.00 0.00 3.16
2407 3180 2.092646 GTGTTATGGGGTGGACATAGCA 60.093 50.000 0.00 0.00 38.92 3.49
2434 3208 5.806654 AGTCAATGGCATGTTACCTTTTT 57.193 34.783 0.00 0.00 0.00 1.94
2435 3209 5.783111 AGTCAATGGCATGTTACCTTTTTC 58.217 37.500 0.00 0.00 0.00 2.29
2436 3210 5.539955 AGTCAATGGCATGTTACCTTTTTCT 59.460 36.000 0.00 0.00 0.00 2.52
2437 3211 5.634859 GTCAATGGCATGTTACCTTTTTCTG 59.365 40.000 0.00 0.00 0.00 3.02
2438 3212 5.304101 TCAATGGCATGTTACCTTTTTCTGT 59.696 36.000 0.00 0.00 0.00 3.41
2612 3386 4.614673 GCTTTGCGAACACACCTG 57.385 55.556 0.00 0.00 0.00 4.00
2829 3603 1.886542 GTTTTGGACCAAGTGGCTAGG 59.113 52.381 7.07 0.00 39.32 3.02
2834 3608 0.988678 GACCAAGTGGCTAGGGGGAT 60.989 60.000 0.00 0.00 39.32 3.85
2965 3864 4.792189 GTCGTGATAACTGTGTAGTGCTAC 59.208 45.833 2.60 2.60 37.19 3.58
3106 4007 7.943079 TTCATGTGTGATTATTTGACTGGAT 57.057 32.000 0.00 0.00 33.56 3.41
3226 4129 6.998673 GGTTTAACCTCTCTGCATATATGGTT 59.001 38.462 14.51 10.05 39.32 3.67
3322 4225 5.757320 CAGAGGGAGTGTATGCTTGAAATAG 59.243 44.000 0.00 0.00 0.00 1.73
3382 4285 8.044908 GGTTTGTTCTATACTTCATTAGTGGGA 58.955 37.037 0.00 0.00 37.73 4.37
3391 4294 8.980481 ATACTTCATTAGTGGGACCTTAAATG 57.020 34.615 0.00 0.00 37.73 2.32
3398 4301 5.319043 AGTGGGACCTTAAATGAAGTTGA 57.681 39.130 0.00 0.00 32.74 3.18
3453 4356 5.100751 CAGCTACACTGTTTTTCTCTTGG 57.899 43.478 0.00 0.00 41.86 3.61
3476 4379 4.180817 GTTTGTTGTTTCTTGGGTCCTTG 58.819 43.478 0.00 0.00 0.00 3.61
3746 4654 6.370718 TCCGAGGCACTAGAACTTTTAATTTC 59.629 38.462 0.00 0.00 41.55 2.17
3785 4693 5.938125 TCTTGGCTTTGGTTACTCTGTTATC 59.062 40.000 0.00 0.00 0.00 1.75
3791 4699 7.553044 GGCTTTGGTTACTCTGTTATCTTACAT 59.447 37.037 0.00 0.00 0.00 2.29
3792 4700 9.595823 GCTTTGGTTACTCTGTTATCTTACATA 57.404 33.333 0.00 0.00 0.00 2.29
4067 4988 7.495279 TGATGTTTTATGCACTTTGCTTTCTTT 59.505 29.630 0.00 0.00 45.31 2.52
4101 5022 6.264067 AGCCTTTCTATAATTGATTCTGTGGC 59.736 38.462 0.00 0.00 0.00 5.01
5058 5987 8.453238 TGTAGCCAAAATTTAGTAGAACACAA 57.547 30.769 0.00 0.00 0.00 3.33
5104 6033 6.064846 TGTTTCAAGTGCTGAGAAATCTTC 57.935 37.500 0.00 0.00 34.81 2.87
5116 6045 7.144661 GCTGAGAAATCTTCGAGATATTCAGA 58.855 38.462 21.04 9.06 38.01 3.27
5149 6078 9.439500 AGTAAAATTAGCATTTGATTGCACAAT 57.561 25.926 0.00 0.00 45.23 2.71
5278 6207 2.802816 CACTACTGTCTGTGCAAGGTTC 59.197 50.000 0.00 0.00 0.00 3.62
5438 6367 4.764823 TGTTTTCTTCTTCAACCAGTGTGT 59.235 37.500 0.00 0.00 0.00 3.72
5614 6637 1.667724 GTTCAGGAATGCCATGTCTCG 59.332 52.381 0.00 0.00 36.29 4.04
5775 6798 6.475504 TGACAATAAGATCACAATGGACACT 58.524 36.000 0.00 0.00 0.00 3.55
5811 6834 5.897377 TTGAAATACTAAGAAAGCCAGGC 57.103 39.130 1.84 1.84 0.00 4.85
6267 7294 3.161866 GCCTTTTTGGTTATGTCCTCCA 58.838 45.455 0.00 0.00 38.35 3.86
6318 7345 1.869767 GCGTATGCCAAAGAGATGGAG 59.130 52.381 0.00 0.00 43.54 3.86
6516 7544 4.640201 TGGTTTTGCTATCTGAAGGTATGC 59.360 41.667 0.00 0.00 0.00 3.14
6553 7581 8.426489 TCTAGTGTGTTCTACAATAAACCTGTT 58.574 33.333 0.00 0.00 41.89 3.16
6616 7644 8.524487 GGTCTTTCTGTCTATCTTAAGAACTCA 58.476 37.037 9.71 6.13 0.00 3.41
6624 7652 9.256228 TGTCTATCTTAAGAACTCATAAGTGGT 57.744 33.333 9.71 0.00 35.36 4.16
6744 7772 7.984617 GGCTGTCTTTCTGTCTATCTTAAGAAT 59.015 37.037 9.71 1.22 0.00 2.40
6809 7837 9.109393 TGTTCAGTAACATAGGAAAATGATAGC 57.891 33.333 0.00 0.00 40.69 2.97
6863 7892 7.661536 AGCTGTTGTTTGTAGAGGATATCTA 57.338 36.000 2.05 0.00 39.64 1.98
7257 8289 4.101585 TCTGTTCTTTCAAGAGCTCCTTCA 59.898 41.667 10.93 0.00 37.20 3.02
7304 8336 5.482878 AGGAATTTCATGGCTTCAGTTGATT 59.517 36.000 0.00 0.00 0.00 2.57
7323 8355 8.997323 AGTTGATTCTACTATATGCTGCAAATC 58.003 33.333 6.36 9.26 0.00 2.17
7339 8371 7.549842 TGCTGCAAATCAAGCATATTTTACATT 59.450 29.630 0.00 0.00 41.82 2.71
7458 8490 8.521170 ACACAGATCATGATTTCTTGATTGAT 57.479 30.769 10.14 0.00 39.77 2.57
7612 8644 1.946768 GTTGCTTACTGTGCACTTCCA 59.053 47.619 19.41 3.93 40.40 3.53
7613 8645 2.554032 GTTGCTTACTGTGCACTTCCAT 59.446 45.455 19.41 1.37 40.40 3.41
7812 8925 8.757982 ACTGTTTTATTATCTGAGGCATTGAT 57.242 30.769 0.00 0.00 0.00 2.57
8492 9607 7.119553 ACTGTTTTGCAATGAAGTGTTTGAATT 59.880 29.630 0.00 0.00 0.00 2.17
8675 9790 2.670414 CGAGTCACTTGAAGCTCCATTC 59.330 50.000 0.00 0.00 0.00 2.67
8724 9839 6.372659 GCTTTCTGGATGAACTTACAGATTCA 59.627 38.462 3.97 0.00 39.46 2.57
8732 9847 9.553064 GGATGAACTTACAGATTCAATACAGAT 57.447 33.333 0.00 0.00 38.29 2.90
8734 9849 8.722480 TGAACTTACAGATTCAATACAGATGG 57.278 34.615 0.00 0.00 31.95 3.51
8735 9850 7.280876 TGAACTTACAGATTCAATACAGATGGC 59.719 37.037 0.00 0.00 31.95 4.40
8736 9851 6.893583 ACTTACAGATTCAATACAGATGGCT 58.106 36.000 0.00 0.00 0.00 4.75
8737 9852 8.023021 ACTTACAGATTCAATACAGATGGCTA 57.977 34.615 0.00 0.00 0.00 3.93
8738 9853 7.928706 ACTTACAGATTCAATACAGATGGCTAC 59.071 37.037 0.00 0.00 0.00 3.58
8739 9854 6.491714 ACAGATTCAATACAGATGGCTACT 57.508 37.500 0.00 0.00 0.00 2.57
9070 10185 7.905493 GCAATTTCTTAAGTTCCGTATCTGAAG 59.095 37.037 1.63 0.00 0.00 3.02
9096 10211 0.038166 ATCGCCAGTGTGGGTTGATT 59.962 50.000 0.00 0.00 38.19 2.57
9272 10397 7.526142 TTATCTCTCGTATAAGCTGGTCATT 57.474 36.000 0.00 0.00 0.00 2.57
9421 10546 5.587388 AACAATTACTCTGGCCATTCATG 57.413 39.130 5.51 2.02 0.00 3.07
9590 10715 4.360563 GGAGTATGTTCTGATGTACCACG 58.639 47.826 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.177669 CTCCTCTCCTCCTCCTCAATCT 59.822 54.545 0.00 0.00 0.00 2.40
278 279 1.070914 TGTGTGCCTGTGTTCCGATAA 59.929 47.619 0.00 0.00 0.00 1.75
523 528 7.918562 TGTTTTTCGGTTCTATTTTCTTTCCTG 59.081 33.333 0.00 0.00 0.00 3.86
524 529 7.919091 GTGTTTTTCGGTTCTATTTTCTTTCCT 59.081 33.333 0.00 0.00 0.00 3.36
605 610 2.664851 TTTCGCTCCGTGTGGCTG 60.665 61.111 0.00 0.00 34.14 4.85
684 689 2.437359 GGTGGTGCTAGGCTGCTG 60.437 66.667 0.00 0.00 0.00 4.41
699 704 2.066999 GGGGAGAGCGGAAGATGGT 61.067 63.158 0.00 0.00 0.00 3.55
700 705 1.753368 GAGGGGAGAGCGGAAGATGG 61.753 65.000 0.00 0.00 0.00 3.51
701 706 1.745264 GAGGGGAGAGCGGAAGATG 59.255 63.158 0.00 0.00 0.00 2.90
702 707 1.458588 GGAGGGGAGAGCGGAAGAT 60.459 63.158 0.00 0.00 0.00 2.40
703 708 2.042843 GGAGGGGAGAGCGGAAGA 60.043 66.667 0.00 0.00 0.00 2.87
704 709 3.157949 GGGAGGGGAGAGCGGAAG 61.158 72.222 0.00 0.00 0.00 3.46
705 710 4.798682 GGGGAGGGGAGAGCGGAA 62.799 72.222 0.00 0.00 0.00 4.30
736 741 2.074948 CAGGTGGAGGAGATGGGGG 61.075 68.421 0.00 0.00 0.00 5.40
737 742 0.916358 AACAGGTGGAGGAGATGGGG 60.916 60.000 0.00 0.00 0.00 4.96
738 743 0.254178 CAACAGGTGGAGGAGATGGG 59.746 60.000 0.00 0.00 0.00 4.00
739 744 0.987294 ACAACAGGTGGAGGAGATGG 59.013 55.000 0.00 0.00 0.00 3.51
740 745 1.404717 CGACAACAGGTGGAGGAGATG 60.405 57.143 0.00 0.00 0.00 2.90
741 746 0.898320 CGACAACAGGTGGAGGAGAT 59.102 55.000 0.00 0.00 0.00 2.75
742 747 1.816863 GCGACAACAGGTGGAGGAGA 61.817 60.000 0.00 0.00 0.00 3.71
743 748 1.374758 GCGACAACAGGTGGAGGAG 60.375 63.158 0.00 0.00 0.00 3.69
744 749 1.816863 GAGCGACAACAGGTGGAGGA 61.817 60.000 0.00 0.00 0.00 3.71
745 750 1.374758 GAGCGACAACAGGTGGAGG 60.375 63.158 0.00 0.00 0.00 4.30
746 751 1.734477 CGAGCGACAACAGGTGGAG 60.734 63.158 0.00 0.00 0.00 3.86
747 752 2.338620 CGAGCGACAACAGGTGGA 59.661 61.111 0.00 0.00 0.00 4.02
748 753 3.414700 GCGAGCGACAACAGGTGG 61.415 66.667 0.00 0.00 0.00 4.61
749 754 1.956170 AAGCGAGCGACAACAGGTG 60.956 57.895 0.00 0.00 0.00 4.00
750 755 1.956170 CAAGCGAGCGACAACAGGT 60.956 57.895 0.00 0.00 0.00 4.00
751 756 1.891060 GACAAGCGAGCGACAACAGG 61.891 60.000 0.00 0.00 0.00 4.00
752 757 1.488957 GACAAGCGAGCGACAACAG 59.511 57.895 0.00 0.00 0.00 3.16
753 758 1.954146 GGACAAGCGAGCGACAACA 60.954 57.895 0.00 0.00 0.00 3.33
754 759 2.668280 GGGACAAGCGAGCGACAAC 61.668 63.158 0.00 0.00 0.00 3.32
755 760 2.357034 GGGACAAGCGAGCGACAA 60.357 61.111 0.00 0.00 0.00 3.18
756 761 4.717629 CGGGACAAGCGAGCGACA 62.718 66.667 0.00 0.00 0.00 4.35
761 766 3.432051 CTAGGCCGGGACAAGCGAG 62.432 68.421 0.92 0.00 0.00 5.03
762 767 3.458163 CTAGGCCGGGACAAGCGA 61.458 66.667 0.92 0.00 0.00 4.93
763 768 4.530857 CCTAGGCCGGGACAAGCG 62.531 72.222 11.67 0.00 0.00 4.68
836 1138 1.676746 CGGACGACTAAGGAGGATCA 58.323 55.000 0.00 0.00 36.25 2.92
1203 1505 1.425412 GACGAACCGCGCCAATATAT 58.575 50.000 0.00 0.00 46.04 0.86
1544 1849 3.896648 AAACCACAAGTAAGCACATCG 57.103 42.857 0.00 0.00 0.00 3.84
1687 1992 3.565902 CACTAGATCTCGGTACAGCATCA 59.434 47.826 0.00 0.00 0.00 3.07
1690 1995 1.676529 GCACTAGATCTCGGTACAGCA 59.323 52.381 0.00 0.00 0.00 4.41
1936 2621 6.174720 AGTCCAAGTAAATGACAGAACAGA 57.825 37.500 0.00 0.00 0.00 3.41
2024 2709 3.582647 TCCATGAGTGCACTAAGGAGAAA 59.417 43.478 21.73 3.21 0.00 2.52
2299 3072 2.325484 TGGGAGAGCAAGACACACTAA 58.675 47.619 0.00 0.00 0.00 2.24
2306 3079 2.098770 GCATCATTTGGGAGAGCAAGAC 59.901 50.000 0.00 0.00 0.00 3.01
2371 3144 6.053005 CCCATAACACTACGTAACATCCAAT 58.947 40.000 0.00 0.00 0.00 3.16
2375 3148 4.807304 CACCCCATAACACTACGTAACATC 59.193 45.833 0.00 0.00 0.00 3.06
2407 3180 6.500589 AGGTAACATGCCATTGACTACTAT 57.499 37.500 0.00 0.00 41.41 2.12
2434 3208 4.716287 TGATAACATCATGTCTCCCACAGA 59.284 41.667 0.00 0.00 38.85 3.41
2435 3209 5.027293 TGATAACATCATGTCTCCCACAG 57.973 43.478 0.00 0.00 38.85 3.66
2436 3210 5.434182 TTGATAACATCATGTCTCCCACA 57.566 39.130 0.00 0.00 39.39 4.17
2437 3211 6.949352 ATTTGATAACATCATGTCTCCCAC 57.051 37.500 0.00 0.00 39.39 4.61
2438 3212 7.147320 ACCTATTTGATAACATCATGTCTCCCA 60.147 37.037 0.00 0.00 39.39 4.37
2612 3386 3.494045 GCTAAGAAAGCCCAATGTGAC 57.506 47.619 0.00 0.00 46.25 3.67
2829 3603 6.295292 GGCAAAAATGGAGAATACATATCCCC 60.295 42.308 0.00 0.00 31.73 4.81
2834 3608 7.716799 ACAAGGCAAAAATGGAGAATACATA 57.283 32.000 0.00 0.00 0.00 2.29
3086 3987 6.375174 CCTGAATCCAGTCAAATAATCACACA 59.625 38.462 0.00 0.00 38.74 3.72
3226 4129 8.598041 GCTCTTATATTTCTTTATGGAGGGAGA 58.402 37.037 0.00 0.00 0.00 3.71
3322 4225 9.717942 ATGTTACATATTCCTAGAAGATTGAGC 57.282 33.333 0.00 0.00 0.00 4.26
3382 4285 4.215613 GCGGACTTCAACTTCATTTAAGGT 59.784 41.667 0.00 0.00 39.73 3.50
3391 4294 4.308265 AGAAACTAGCGGACTTCAACTTC 58.692 43.478 0.00 0.00 0.00 3.01
3398 4301 3.586892 GCTACAAGAAACTAGCGGACTT 58.413 45.455 0.00 0.00 0.00 3.01
3453 4356 2.764010 AGGACCCAAGAAACAACAAACC 59.236 45.455 0.00 0.00 0.00 3.27
3476 4379 0.972883 TGGCAAGTACAAAATGGCCC 59.027 50.000 0.00 0.00 40.64 5.80
3548 4455 2.350772 GCTGATACAAGCACGCAACTTT 60.351 45.455 0.00 0.00 43.01 2.66
3624 4531 8.055181 TGATTGGACTAGCCTCTATTTCAATTT 58.945 33.333 5.06 0.00 37.63 1.82
3625 4532 7.577303 TGATTGGACTAGCCTCTATTTCAATT 58.423 34.615 5.06 0.00 37.63 2.32
3626 4533 7.141758 TGATTGGACTAGCCTCTATTTCAAT 57.858 36.000 5.06 0.00 37.63 2.57
3633 4540 7.709601 TCCTATATTGATTGGACTAGCCTCTA 58.290 38.462 5.06 0.00 32.72 2.43
3746 4654 3.054878 GCCAAGAAAAGAGCACACAATG 58.945 45.455 0.00 0.00 0.00 2.82
3977 4898 1.466167 AGCAGTCAAACAGCGCTATTG 59.534 47.619 22.53 22.53 35.63 1.90
3983 4904 1.194098 CAGAAGAGCAGTCAAACAGCG 59.806 52.381 0.00 0.00 35.63 5.18
4101 5022 2.552315 ACAAAAACAGTAGCATCCCACG 59.448 45.455 0.00 0.00 0.00 4.94
4501 5422 4.682860 CACAGATGCCATTCTCAAACAAAC 59.317 41.667 0.00 0.00 0.00 2.93
4502 5423 4.796946 GCACAGATGCCATTCTCAAACAAA 60.797 41.667 0.00 0.00 46.97 2.83
4503 5424 3.305539 GCACAGATGCCATTCTCAAACAA 60.306 43.478 0.00 0.00 46.97 2.83
5058 5987 8.650143 ACAGGTTAATGTTCCATAATGAACTT 57.350 30.769 5.61 0.00 43.96 2.66
5084 6013 4.631131 TCGAAGATTTCTCAGCACTTGAA 58.369 39.130 0.00 0.00 34.81 2.69
5149 6078 3.884895 ACACACAGATTTCCAACACTGA 58.115 40.909 0.00 0.00 34.88 3.41
5195 6124 0.107361 GGATTTACCCTCCCACCACG 60.107 60.000 0.00 0.00 0.00 4.94
5278 6207 0.593128 GCAGGGTACTGTGCTTGTTG 59.407 55.000 11.38 0.00 46.62 3.33
5438 6367 5.477984 AGCAAGAAAACAATCCAGAAGCATA 59.522 36.000 0.00 0.00 0.00 3.14
5565 6577 9.952030 TTGTTAAATATACATGAGACCACAGAA 57.048 29.630 0.00 0.00 0.00 3.02
5614 6637 4.794981 GCAGCCAAAAAGTAACTACCAACC 60.795 45.833 0.00 0.00 0.00 3.77
5727 6750 8.279800 TCATTAAACCAGTAATCGATAAATGCG 58.720 33.333 0.00 0.00 0.00 4.73
5775 6798 9.778741 CTTAGTATTTCAAATATCTGGGTAGCA 57.221 33.333 0.00 0.00 0.00 3.49
5811 6834 5.449862 GCTGACCTGAGTGAGATAACTGTAG 60.450 48.000 0.00 0.00 26.63 2.74
5990 7017 5.824097 TGTAAAAACTCTAAACCTGGGTGAC 59.176 40.000 0.00 0.00 0.00 3.67
6024 7051 6.867519 TTACCATATCTGTCCTGAAACTCA 57.132 37.500 0.00 0.00 0.00 3.41
6114 7141 4.665212 ACTCAAAATGCACATCTAATGCG 58.335 39.130 0.00 0.00 46.49 4.73
6267 7294 6.380079 AAGGGTATCTGTCTCAAAAGATGT 57.620 37.500 0.00 0.00 34.91 3.06
6332 7359 7.123547 CCTTATTTTATTTCAGTGTTAGCCCCA 59.876 37.037 0.00 0.00 0.00 4.96
6497 7525 8.097038 CCTATAAGCATACCTTCAGATAGCAAA 58.903 37.037 0.00 0.00 34.95 3.68
6553 7581 1.299648 CGGAGAGTTCCCAATGCCA 59.700 57.895 0.00 0.00 40.67 4.92
6616 7644 4.411540 AGCAGAGGATGATGAACCACTTAT 59.588 41.667 0.00 0.00 0.00 1.73
6624 7652 8.212995 TCAACATTTATAGCAGAGGATGATGAA 58.787 33.333 0.00 0.00 0.00 2.57
6809 7837 7.699391 CCTTGCATACAACATTCATGACTAAAG 59.301 37.037 0.00 0.00 0.00 1.85
7257 8289 3.098774 TGGCCATCACAACCACATAAT 57.901 42.857 0.00 0.00 0.00 1.28
7304 8336 6.290605 TGCTTGATTTGCAGCATATAGTAGA 58.709 36.000 0.00 0.00 35.31 2.59
7570 8602 7.112565 GCAACATTAATGCAATCTAACATCTCG 59.887 37.037 15.48 0.00 43.29 4.04
7812 8925 1.202245 GCTTTGTTCACTCGTTTGCCA 60.202 47.619 0.00 0.00 0.00 4.92
8411 9526 7.951565 CGAGTTTCAAATGCCATAAATTTGTTC 59.048 33.333 0.00 0.00 42.83 3.18
8675 9790 5.747675 CACTAGTAGCACTCACATGATTCAG 59.252 44.000 0.00 0.00 0.00 3.02
8724 9839 4.656112 ACTAGCCAAGTAGCCATCTGTATT 59.344 41.667 0.00 0.00 36.36 1.89
8732 9847 5.368145 CATAATTCACTAGCCAAGTAGCCA 58.632 41.667 0.00 0.00 35.76 4.75
8733 9848 4.757149 CCATAATTCACTAGCCAAGTAGCC 59.243 45.833 0.00 0.00 35.76 3.93
8734 9849 5.611374 TCCATAATTCACTAGCCAAGTAGC 58.389 41.667 0.00 0.00 35.76 3.58
8735 9850 7.012421 GGTTTCCATAATTCACTAGCCAAGTAG 59.988 40.741 0.00 0.00 35.76 2.57
8736 9851 6.826741 GGTTTCCATAATTCACTAGCCAAGTA 59.173 38.462 0.00 0.00 35.76 2.24
8737 9852 5.652452 GGTTTCCATAATTCACTAGCCAAGT 59.348 40.000 0.00 0.00 39.81 3.16
8738 9853 5.652014 TGGTTTCCATAATTCACTAGCCAAG 59.348 40.000 0.00 0.00 0.00 3.61
8739 9854 5.417580 GTGGTTTCCATAATTCACTAGCCAA 59.582 40.000 0.00 0.00 35.28 4.52
9070 10185 3.275999 ACCCACACTGGCGATATTAAAC 58.724 45.455 0.00 0.00 35.79 2.01
9096 10211 6.633500 AGCACAATTCAGTTTTTACTGCTA 57.367 33.333 0.50 0.00 37.63 3.49


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

AutoCloner maintained by Alex Coulton.