Multiple sequence alignment - TraesCS2D01G499700

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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 TraesCS2D01G499700 chr2D 100.000 5510 0 0 1 5510 594552079 594546570 0.000000e+00 10176
1 TraesCS2D01G499700 chr2D 83.946 299 34 8 4240 4535 301752598 301752885 1.960000e-69 274
2 TraesCS2D01G499700 chr2D 94.690 113 6 0 1119 1231 499027106 499026994 5.670000e-40 176
3 TraesCS2D01G499700 chr2D 83.516 182 22 7 1426 1604 499026991 499026815 4.420000e-36 163
4 TraesCS2D01G499700 chr2A 92.848 2223 103 25 3290 5510 729171152 729168984 0.000000e+00 3173
5 TraesCS2D01G499700 chr2A 86.235 1206 72 39 709 1858 729174816 729173649 0.000000e+00 1221
6 TraesCS2D01G499700 chr2A 95.113 573 24 4 2361 2930 729172875 729172304 0.000000e+00 900
7 TraesCS2D01G499700 chr2A 91.737 472 24 7 1904 2361 729173506 729173036 4.650000e-180 641
8 TraesCS2D01G499700 chr2A 85.759 646 34 11 1 636 729175431 729174834 1.010000e-176 630
9 TraesCS2D01G499700 chr2A 87.530 417 34 5 2846 3248 729171576 729171164 3.010000e-127 466
10 TraesCS2D01G499700 chr2A 80.376 372 42 11 2587 2934 729171941 729171577 2.550000e-63 254
11 TraesCS2D01G499700 chr2A 90.811 185 3 3 2913 3083 729172121 729171937 9.230000e-58 235
12 TraesCS2D01G499700 chr2A 95.575 113 5 0 1119 1231 622751738 622751850 1.220000e-41 182
13 TraesCS2D01G499700 chr2B 92.986 1326 60 13 3459 4783 722090693 722089400 0.000000e+00 1903
14 TraesCS2D01G499700 chr2B 88.394 1258 80 25 672 1895 722094875 722093650 0.000000e+00 1454
15 TraesCS2D01G499700 chr2B 91.456 831 44 14 1923 2730 722093531 722092705 0.000000e+00 1116
16 TraesCS2D01G499700 chr2B 93.469 689 23 4 4840 5509 722089384 722088699 0.000000e+00 1003
17 TraesCS2D01G499700 chr2B 85.751 779 63 20 2727 3476 722092676 722091917 0.000000e+00 780
18 TraesCS2D01G499700 chr2B 90.339 590 28 10 1 576 722095493 722094919 0.000000e+00 747
19 TraesCS2D01G499700 chr2B 88.818 313 19 6 669 981 102553492 102553788 2.420000e-98 370
20 TraesCS2D01G499700 chr3B 90.096 313 16 5 669 981 604554675 604554378 5.170000e-105 392
21 TraesCS2D01G499700 chr3B 89.776 313 21 5 669 981 738229324 738229023 1.860000e-104 390
22 TraesCS2D01G499700 chrUn 89.776 313 17 5 669 981 249824328 249824031 2.410000e-103 387
23 TraesCS2D01G499700 chrUn 89.776 313 17 5 669 981 316039625 316039328 2.410000e-103 387
24 TraesCS2D01G499700 chr1B 89.776 313 17 5 669 981 45043151 45043448 2.410000e-103 387
25 TraesCS2D01G499700 chr1B 89.776 313 17 5 669 981 45050656 45050953 2.410000e-103 387
26 TraesCS2D01G499700 chr4B 89.137 313 19 5 669 981 610015379 610015676 5.210000e-100 375
27 TraesCS2D01G499700 chr6D 86.264 182 17 6 1426 1604 419597963 419597787 2.030000e-44 191
28 TraesCS2D01G499700 chr6D 85.714 182 18 6 1426 1604 427935863 427935687 9.430000e-43 185
29 TraesCS2D01G499700 chr6D 94.690 113 6 0 1119 1231 419598078 419597966 5.670000e-40 176
30 TraesCS2D01G499700 chr6D 97.000 100 3 0 1132 1231 427935965 427935866 9.490000e-38 169
31 TraesCS2D01G499700 chr6D 87.500 128 13 3 1480 1604 427611454 427611327 1.600000e-30 145
32 TraesCS2D01G499700 chr1A 85.714 182 18 6 1426 1604 144559183 144559007 9.430000e-43 185
33 TraesCS2D01G499700 chr3A 90.780 141 7 3 5375 5510 750496290 750496151 3.390000e-42 183
34 TraesCS2D01G499700 chr7A 95.349 86 4 0 1146 1231 126704804 126704719 2.680000e-28 137
35 TraesCS2D01G499700 chr7B 89.720 107 7 2 533 635 673853183 673853077 3.460000e-27 134
36 TraesCS2D01G499700 chr1D 98.667 75 1 0 1157 1231 350880614 350880688 3.460000e-27 134


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 TraesCS2D01G499700 chr2D 594546570 594552079 5509 True 10176.000000 10176 100.000000 1 5510 1 chr2D.!!$R1 5509
1 TraesCS2D01G499700 chr2A 729168984 729175431 6447 True 940.000000 3173 88.801125 1 5510 8 chr2A.!!$R1 5509
2 TraesCS2D01G499700 chr2B 722088699 722095493 6794 True 1167.166667 1903 90.399167 1 5509 6 chr2B.!!$R1 5508

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
209 210 0.179187 AGAGCAAGATCGTCGTCGTG 60.179 55.000 1.33 0.00 38.33 4.35 F
843 891 0.607489 CCCTCTTGTCTTGTGGCCAG 60.607 60.000 5.11 0.00 0.00 4.85 F
1617 1722 0.035881 TTGCTGAAGTGAGGCCTCTG 59.964 55.000 32.28 15.91 0.00 3.35 F
1864 1975 1.035139 CTTCATGGTATGGCCTTGGC 58.965 55.000 3.32 2.49 41.33 4.52 F
3303 4587 1.822186 CGCCGGGGTTGATTTAGGG 60.822 63.158 11.01 0.00 0.00 3.53 F
3814 6346 0.896940 AAGTTGCAGGGCACAGGATG 60.897 55.000 0.00 0.00 38.71 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1287 1347 0.113580 AAAATGGGGCTTACACGGGT 59.886 50.000 0.0 0.0 0.00 5.28 R
2274 2522 0.898320 CCTCCCAGTATATCCCTGCG 59.102 60.000 0.0 0.0 0.00 5.18 R
3451 4737 0.955428 ATTGCACGCAGATGACCGTT 60.955 50.000 0.0 0.0 35.17 4.44 R
3710 6241 0.105913 TCCCCGCCCCCAATTTAATC 60.106 55.000 0.0 0.0 0.00 1.75 R
4367 6900 3.369261 GCTTCTTCCAATGCTCTCTCTCA 60.369 47.826 0.0 0.0 0.00 3.27 R
4783 7316 3.475566 TGTGCTATACCTTGCATCTCC 57.524 47.619 0.0 0.0 41.45 3.71 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
74 75 1.964448 ACGCCTGTTCGTCATCTCA 59.036 52.632 0.00 0.00 38.44 3.27
209 210 0.179187 AGAGCAAGATCGTCGTCGTG 60.179 55.000 1.33 0.00 38.33 4.35
254 255 1.202222 GGCCATGTCAAGAAGCAATCG 60.202 52.381 0.00 0.00 0.00 3.34
256 257 1.202222 CCATGTCAAGAAGCAATCGGC 60.202 52.381 0.00 0.00 45.30 5.54
380 391 3.084786 ACATGCTTAAAACTCTGCCTCC 58.915 45.455 0.00 0.00 0.00 4.30
386 397 4.142513 GCTTAAAACTCTGCCTCCAGAATG 60.143 45.833 0.00 0.00 46.84 2.67
396 411 2.548875 CCTCCAGAATGAAAGCTCTCG 58.451 52.381 0.00 0.00 39.69 4.04
408 430 3.386768 AAGCTCTCGTAGTCTGCAAAA 57.613 42.857 0.00 0.00 0.00 2.44
409 431 3.386768 AGCTCTCGTAGTCTGCAAAAA 57.613 42.857 0.00 0.00 0.00 1.94
436 458 6.468956 GCCTTGTTTCATATTCGTGTATGTTG 59.531 38.462 8.78 0.00 34.44 3.33
476 498 7.129457 TCTTTCCTGCTGTCATCTTGTATAT 57.871 36.000 0.00 0.00 0.00 0.86
477 499 8.250143 TCTTTCCTGCTGTCATCTTGTATATA 57.750 34.615 0.00 0.00 0.00 0.86
478 500 8.874156 TCTTTCCTGCTGTCATCTTGTATATAT 58.126 33.333 0.00 0.00 0.00 0.86
513 539 7.838771 TGATGATGTATCAGTGAAGAAACAG 57.161 36.000 0.00 0.00 40.82 3.16
534 560 5.511234 AGTTCGAAACTGTACTGTACTGT 57.489 39.130 20.48 20.48 41.01 3.55
577 603 6.655930 TGTTTCTGGGTACTGAACTAAACTT 58.344 36.000 0.00 0.00 34.78 2.66
605 631 8.507249 ACTGTTGCATTTCACTTCTTATCTTAC 58.493 33.333 0.00 0.00 0.00 2.34
618 644 6.378710 TCTTATCTTACACTGATCCGACTG 57.621 41.667 0.00 0.00 0.00 3.51
620 646 1.476891 TCTTACACTGATCCGACTGGC 59.523 52.381 0.00 0.00 34.14 4.85
632 658 1.159285 CGACTGGCTGCTGAATTTCA 58.841 50.000 0.00 0.00 0.00 2.69
636 662 2.694628 ACTGGCTGCTGAATTTCAAACA 59.305 40.909 0.00 1.63 0.00 2.83
637 663 3.243636 ACTGGCTGCTGAATTTCAAACAG 60.244 43.478 18.28 18.28 35.14 3.16
638 664 2.957680 TGGCTGCTGAATTTCAAACAGA 59.042 40.909 23.43 8.77 34.39 3.41
641 667 3.924686 GCTGCTGAATTTCAAACAGATGG 59.075 43.478 23.43 7.19 34.39 3.51
642 668 4.321452 GCTGCTGAATTTCAAACAGATGGA 60.321 41.667 23.43 4.21 34.39 3.41
643 669 5.623824 GCTGCTGAATTTCAAACAGATGGAT 60.624 40.000 23.43 0.00 34.39 3.41
644 670 6.405065 GCTGCTGAATTTCAAACAGATGGATA 60.405 38.462 23.43 0.00 34.39 2.59
645 671 6.855836 TGCTGAATTTCAAACAGATGGATAC 58.144 36.000 0.01 0.00 34.07 2.24
646 672 6.660521 TGCTGAATTTCAAACAGATGGATACT 59.339 34.615 0.01 0.00 34.07 2.12
647 673 7.828717 TGCTGAATTTCAAACAGATGGATACTA 59.171 33.333 0.01 0.00 34.07 1.82
648 674 8.125448 GCTGAATTTCAAACAGATGGATACTAC 58.875 37.037 0.01 0.00 34.07 2.73
649 675 9.388506 CTGAATTTCAAACAGATGGATACTACT 57.611 33.333 0.01 0.00 34.07 2.57
650 676 9.739276 TGAATTTCAAACAGATGGATACTACTT 57.261 29.630 0.00 0.00 37.61 2.24
682 708 8.654230 ATGAGTGCTACTACATTTGTATTCTG 57.346 34.615 0.00 0.00 0.00 3.02
700 726 0.827368 TGGCCTTGGTCAAACAAACC 59.173 50.000 3.32 0.00 37.31 3.27
702 728 1.202521 GGCCTTGGTCAAACAAACCTG 60.203 52.381 0.00 0.00 37.69 4.00
742 773 3.763360 TGCCAGATGATTGGACGAAAAAT 59.237 39.130 0.00 0.00 40.87 1.82
743 774 4.946772 TGCCAGATGATTGGACGAAAAATA 59.053 37.500 0.00 0.00 40.87 1.40
810 858 2.017049 AGTCCACAACAGCACAAGAAC 58.983 47.619 0.00 0.00 0.00 3.01
843 891 0.607489 CCCTCTTGTCTTGTGGCCAG 60.607 60.000 5.11 0.00 0.00 4.85
878 929 5.519927 CCAACTGAAACCTGACATTGAAAAC 59.480 40.000 0.00 0.00 0.00 2.43
955 1011 8.531146 TGATAAATCCTGAATTTTTCCCTTGTC 58.469 33.333 0.00 0.00 38.53 3.18
960 1016 6.951971 TCCTGAATTTTTCCCTTGTCAAAAA 58.048 32.000 0.00 0.00 36.25 1.94
961 1017 6.821160 TCCTGAATTTTTCCCTTGTCAAAAAC 59.179 34.615 0.00 0.00 35.00 2.43
1113 1173 4.052229 CGTTCCGCTCGAGGTGGT 62.052 66.667 15.58 0.00 45.32 4.16
1115 1175 3.691342 TTCCGCTCGAGGTGGTGG 61.691 66.667 15.58 5.01 45.32 4.61
1287 1347 4.458829 ATCGCCTCCACCTCCGGA 62.459 66.667 2.93 2.93 0.00 5.14
1306 1391 0.113580 ACCCGTGTAAGCCCCATTTT 59.886 50.000 0.00 0.00 0.00 1.82
1395 1497 7.205992 TGCTTGTTGTCTGCAAAACATATTTA 58.794 30.769 9.36 0.00 36.26 1.40
1465 1567 3.379372 CCTCATTATTTGCACTGAGGTGG 59.621 47.826 15.33 1.33 46.35 4.61
1473 1575 2.066340 CACTGAGGTGGGCCAGTTA 58.934 57.895 6.40 0.00 41.26 2.24
1536 1641 2.075979 GGTACGAACAGAACCCACTC 57.924 55.000 0.00 0.00 0.00 3.51
1582 1687 1.725931 CGGCGCAAGAACAAGATGAAC 60.726 52.381 10.83 0.00 43.02 3.18
1615 1720 1.093159 CATTGCTGAAGTGAGGCCTC 58.907 55.000 26.78 26.78 0.00 4.70
1617 1722 0.035881 TTGCTGAAGTGAGGCCTCTG 59.964 55.000 32.28 15.91 0.00 3.35
1658 1763 5.471556 TCCACGTTGATTGGTTTCTACTA 57.528 39.130 0.00 0.00 35.42 1.82
1659 1764 5.232463 TCCACGTTGATTGGTTTCTACTAC 58.768 41.667 0.00 0.00 35.42 2.73
1660 1765 5.011329 TCCACGTTGATTGGTTTCTACTACT 59.989 40.000 0.00 0.00 35.42 2.57
1661 1766 5.347907 CCACGTTGATTGGTTTCTACTACTC 59.652 44.000 0.00 0.00 0.00 2.59
1662 1767 5.347907 CACGTTGATTGGTTTCTACTACTCC 59.652 44.000 0.00 0.00 0.00 3.85
1666 1771 7.576287 CGTTGATTGGTTTCTACTACTCCAGTA 60.576 40.741 0.00 0.00 38.80 2.74
1864 1975 1.035139 CTTCATGGTATGGCCTTGGC 58.965 55.000 3.32 2.49 41.33 4.52
1963 2188 3.548745 TCTGATGGCTCACACCTAATG 57.451 47.619 0.00 0.00 0.00 1.90
1966 2191 2.092968 TGATGGCTCACACCTAATGGTC 60.093 50.000 0.00 0.00 46.60 4.02
1996 2233 8.100791 ACTATGCAAATTGTCTACTTGGTCTAA 58.899 33.333 0.00 0.00 0.00 2.10
2003 2240 8.480643 AATTGTCTACTTGGTCTAATTTCTCG 57.519 34.615 0.00 0.00 0.00 4.04
2052 2300 5.763204 CCACCACCATTAGTCCATTACATAC 59.237 44.000 0.00 0.00 0.00 2.39
2145 2393 3.541632 CCCAGGCAATAATCTGTACGTT 58.458 45.455 0.00 0.00 0.00 3.99
2274 2522 1.952296 CTGATGCCTCATAAGGTTGCC 59.048 52.381 0.00 0.00 45.34 4.52
2479 2888 3.798794 TGGTTGACCAACTGGACTG 57.201 52.632 12.02 0.00 44.35 3.51
2698 3110 7.095102 TGACAGCTTTAACCCGTTTAGTTATTC 60.095 37.037 0.00 0.00 30.17 1.75
3142 4426 3.242518 GCTGCTTTTCATTCCCGTTAAC 58.757 45.455 0.00 0.00 0.00 2.01
3144 4428 4.475944 CTGCTTTTCATTCCCGTTAACTG 58.524 43.478 3.71 0.00 0.00 3.16
3176 4460 7.543359 AAGTACACAAGGTTAGTACATGGTA 57.457 36.000 0.00 0.00 40.32 3.25
3249 4533 1.916181 AGAGGTGGGGAAACTATGGTG 59.084 52.381 0.00 0.00 0.00 4.17
3301 4585 2.478033 GGCGCCGGGGTTGATTTAG 61.478 63.158 20.83 0.00 0.00 1.85
3303 4587 1.822186 CGCCGGGGTTGATTTAGGG 60.822 63.158 11.01 0.00 0.00 3.53
3323 4607 3.442625 GGGGAGAAAACCGAAACATTAGG 59.557 47.826 0.00 0.00 0.00 2.69
3370 4654 3.390967 TCAGACCAGACACTTTCCATTCA 59.609 43.478 0.00 0.00 0.00 2.57
3378 4662 7.052873 CCAGACACTTTCCATTCATCTATCTT 58.947 38.462 0.00 0.00 0.00 2.40
3451 4737 6.357579 AGACCATGTTGGCATTATTTTTCA 57.642 33.333 0.00 0.00 42.67 2.69
3452 4738 6.767456 AGACCATGTTGGCATTATTTTTCAA 58.233 32.000 0.00 0.00 42.67 2.69
3504 6035 3.056821 TGTCCTTTACGACAGGATGAGTG 60.057 47.826 5.49 0.00 42.63 3.51
3536 6067 2.987821 CACAAAATTGACATGATGCGCA 59.012 40.909 14.96 14.96 0.00 6.09
3539 6070 2.267188 AATTGACATGATGCGCACAC 57.733 45.000 14.90 11.26 0.00 3.82
3559 6090 6.324819 CACACTTCAAACACAGAATTCAGTT 58.675 36.000 8.44 6.67 0.00 3.16
3566 6097 7.864686 TCAAACACAGAATTCAGTTACATGAG 58.135 34.615 8.44 0.00 0.00 2.90
3654 6185 3.370840 AGCTGATGTTGGGAATTGCTA 57.629 42.857 0.00 0.00 0.00 3.49
3655 6186 3.907221 AGCTGATGTTGGGAATTGCTAT 58.093 40.909 0.00 0.00 0.00 2.97
3705 6236 6.533730 TCCTGACTGTGTTATCAGTTTCATT 58.466 36.000 0.98 0.00 46.81 2.57
3710 6241 5.106948 ACTGTGTTATCAGTTTCATTGCGAG 60.107 40.000 0.00 0.00 44.92 5.03
3758 6289 6.646653 CCTTAATTTGAAAAGGAGGTTGAAGC 59.353 38.462 0.00 0.00 44.27 3.86
3768 6300 2.365293 GGAGGTTGAAGCAAACATGGTT 59.635 45.455 0.00 0.00 32.84 3.67
3780 6312 8.907222 AAGCAAACATGGTTTTTCATATCTTT 57.093 26.923 0.00 0.00 0.00 2.52
3781 6313 8.907222 AGCAAACATGGTTTTTCATATCTTTT 57.093 26.923 0.00 0.00 0.00 2.27
3814 6346 0.896940 AAGTTGCAGGGCACAGGATG 60.897 55.000 0.00 0.00 38.71 3.51
3854 6386 8.709308 AGCTAGAACTATGATCAAATAACTGGT 58.291 33.333 0.00 0.00 0.00 4.00
3873 6405 7.193377 ACTGGTAGTTGTAAATTTGTAACGG 57.807 36.000 0.00 0.00 0.00 4.44
3885 6417 5.656213 ATTTGTAACGGCTGTACTACTCT 57.344 39.130 0.00 0.00 0.00 3.24
3937 6469 2.040278 TGCACCCTTGAAGAGTATGCTT 59.960 45.455 0.00 0.00 36.06 3.91
3975 6507 9.585099 GAGCATCATAAATCTAGATAGTTCTGG 57.415 37.037 5.46 0.00 31.47 3.86
4024 6557 8.462016 GCTTGTTTCATATCCTGAACTAACATT 58.538 33.333 0.00 0.00 43.54 2.71
4053 6586 3.523606 TGTTTCACAGTGCATTTTGCT 57.476 38.095 0.00 0.00 45.31 3.91
4056 6589 1.855513 TCACAGTGCATTTTGCTTGC 58.144 45.000 0.00 0.00 45.31 4.01
4125 6658 8.461249 AATTGTCTATTCAGCATAGCTTTGAT 57.539 30.769 8.49 0.00 36.40 2.57
4127 6660 7.870509 TGTCTATTCAGCATAGCTTTGATTT 57.129 32.000 8.49 0.00 36.40 2.17
4367 6900 2.434428 CAGCTTCCTGCATCAGAAACT 58.566 47.619 0.00 0.00 45.94 2.66
4401 6934 1.785041 GAAGAAGCGGCACAGCAACA 61.785 55.000 1.45 0.00 40.15 3.33
4405 6938 3.595758 GCGGCACAGCAACAACCT 61.596 61.111 0.00 0.00 37.05 3.50
4535 7068 3.593442 ACACCAACAGGGAGAAATCAA 57.407 42.857 0.00 0.00 41.15 2.57
4598 7131 8.997323 AGCTATGTATGATTGAATCAAAGCTAC 58.003 33.333 20.54 15.31 43.50 3.58
4599 7132 8.997323 GCTATGTATGATTGAATCAAAGCTACT 58.003 33.333 12.36 0.00 43.50 2.57
4601 7134 7.792374 TGTATGATTGAATCAAAGCTACTCC 57.208 36.000 12.36 0.00 43.50 3.85
4602 7135 5.998454 ATGATTGAATCAAAGCTACTCCG 57.002 39.130 12.36 0.00 43.50 4.63
4603 7136 4.832248 TGATTGAATCAAAGCTACTCCGT 58.168 39.130 5.21 0.00 36.11 4.69
4604 7137 5.972935 TGATTGAATCAAAGCTACTCCGTA 58.027 37.500 5.21 0.00 36.11 4.02
4646 7179 6.111382 TCTGAGATCAATGGAAAGACACATC 58.889 40.000 0.00 0.00 0.00 3.06
4647 7180 6.058553 TGAGATCAATGGAAAGACACATCT 57.941 37.500 0.00 0.00 36.42 2.90
4649 7182 7.623630 TGAGATCAATGGAAAGACACATCTTA 58.376 34.615 0.00 0.00 44.82 2.10
4651 7184 8.674263 AGATCAATGGAAAGACACATCTTATC 57.326 34.615 0.00 0.00 44.82 1.75
4653 7186 9.118300 GATCAATGGAAAGACACATCTTATCTT 57.882 33.333 0.00 0.00 44.82 2.40
4655 7188 9.300681 TCAATGGAAAGACACATCTTATCTTTT 57.699 29.630 0.41 0.00 44.82 2.27
4743 7276 3.181451 TGTTGTGTGATCTTTGCTCTCCT 60.181 43.478 0.00 0.00 0.00 3.69
4747 7280 2.027745 TGTGATCTTTGCTCTCCTCCAC 60.028 50.000 0.00 0.00 0.00 4.02
4765 7298 5.411361 CCTCCACATGACAAATTTACTCGAA 59.589 40.000 0.00 0.00 0.00 3.71
4783 7316 6.835914 ACTCGAAAGCAAGTTCAAAGATATG 58.164 36.000 0.00 0.00 0.00 1.78
4841 7374 7.006509 AGGGATTGCTTGCACAAACTATATAT 58.993 34.615 0.00 0.00 32.27 0.86
4893 7426 5.511386 ACAAGACCTTTCTCCAGATCATT 57.489 39.130 0.00 0.00 0.00 2.57
5001 7536 1.848388 TGCCTGATTCAGATCCACCAT 59.152 47.619 15.36 0.00 32.44 3.55
5002 7537 2.158711 TGCCTGATTCAGATCCACCATC 60.159 50.000 15.36 0.00 32.44 3.51
5003 7538 2.763933 CCTGATTCAGATCCACCATCG 58.236 52.381 15.36 0.00 36.50 3.84
5041 7576 1.305219 GGCCGTGCTGCTATTTGACA 61.305 55.000 0.00 0.00 0.00 3.58
5044 7579 2.286418 GCCGTGCTGCTATTTGACATAC 60.286 50.000 0.00 0.00 0.00 2.39
5372 7925 4.398044 AGCAAGAAGTTTCGAAGAAACCAA 59.602 37.500 18.51 0.00 45.90 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 3.054287 TCACCTTCATCCTCTCGTACTCT 60.054 47.826 0.00 0.00 0.00 3.24
152 153 0.105593 GAGGCTTCATGATCCGCTCA 59.894 55.000 0.00 0.00 38.53 4.26
218 219 1.524621 GCCGATCACCACATGGAGG 60.525 63.158 4.53 0.62 38.94 4.30
344 351 5.557891 AAGCATGTAAAATCTGACTGCTC 57.442 39.130 0.00 0.00 37.49 4.26
380 391 4.797868 CAGACTACGAGAGCTTTCATTCTG 59.202 45.833 4.97 6.14 0.00 3.02
386 397 2.638556 TGCAGACTACGAGAGCTTTC 57.361 50.000 0.00 0.00 0.00 2.62
408 430 5.705609 ACACGAATATGAAACAAGGCTTT 57.294 34.783 0.00 0.00 0.00 3.51
409 431 6.374333 ACATACACGAATATGAAACAAGGCTT 59.626 34.615 14.74 0.00 36.27 4.35
410 432 5.880332 ACATACACGAATATGAAACAAGGCT 59.120 36.000 14.74 0.00 36.27 4.58
414 436 9.814507 GTAACAACATACACGAATATGAAACAA 57.185 29.630 14.74 0.00 36.27 2.83
423 445 9.309516 CCACTAATAGTAACAACATACACGAAT 57.690 33.333 0.00 0.00 0.00 3.34
426 448 7.972277 AGTCCACTAATAGTAACAACATACACG 59.028 37.037 0.00 0.00 0.00 4.49
477 499 9.516546 ACTGATACATCATCATTTGCAGATTAT 57.483 29.630 0.00 0.00 42.82 1.28
478 500 8.780249 CACTGATACATCATCATTTGCAGATTA 58.220 33.333 0.00 0.00 42.82 1.75
479 501 7.501225 TCACTGATACATCATCATTTGCAGATT 59.499 33.333 0.00 0.00 42.82 2.40
513 539 5.517770 ACAACAGTACAGTACAGTTTCGAAC 59.482 40.000 16.65 0.00 36.44 3.95
577 603 8.621532 AGATAAGAAGTGAAATGCAACAGTTA 57.378 30.769 10.44 0.04 31.11 2.24
605 631 1.812922 GCAGCCAGTCGGATCAGTG 60.813 63.158 0.00 0.00 0.00 3.66
618 644 3.648339 TCTGTTTGAAATTCAGCAGCC 57.352 42.857 18.26 0.74 33.94 4.85
620 646 5.381174 TCCATCTGTTTGAAATTCAGCAG 57.619 39.130 17.47 17.47 34.66 4.24
656 682 9.750125 CAGAATACAAATGTAGTAGCACTCATA 57.250 33.333 0.00 0.00 33.52 2.15
657 683 7.712639 CCAGAATACAAATGTAGTAGCACTCAT 59.287 37.037 0.00 0.00 33.52 2.90
658 684 7.041721 CCAGAATACAAATGTAGTAGCACTCA 58.958 38.462 0.00 0.00 33.52 3.41
659 685 6.018669 GCCAGAATACAAATGTAGTAGCACTC 60.019 42.308 0.00 0.00 33.52 3.51
660 686 5.817816 GCCAGAATACAAATGTAGTAGCACT 59.182 40.000 0.00 0.00 33.52 4.40
661 687 5.007724 GGCCAGAATACAAATGTAGTAGCAC 59.992 44.000 0.00 0.00 33.52 4.40
662 688 5.104527 AGGCCAGAATACAAATGTAGTAGCA 60.105 40.000 5.01 0.00 33.52 3.49
663 689 5.368989 AGGCCAGAATACAAATGTAGTAGC 58.631 41.667 5.01 1.59 33.52 3.58
664 690 6.260936 CCAAGGCCAGAATACAAATGTAGTAG 59.739 42.308 5.01 0.00 33.52 2.57
665 691 6.119536 CCAAGGCCAGAATACAAATGTAGTA 58.880 40.000 5.01 0.00 33.52 1.82
666 692 4.949856 CCAAGGCCAGAATACAAATGTAGT 59.050 41.667 5.01 0.00 33.52 2.73
667 693 4.949856 ACCAAGGCCAGAATACAAATGTAG 59.050 41.667 5.01 0.00 33.52 2.74
670 696 3.763360 TGACCAAGGCCAGAATACAAATG 59.237 43.478 5.01 0.00 0.00 2.32
682 708 1.119684 AGGTTTGTTTGACCAAGGCC 58.880 50.000 0.00 0.00 39.71 5.19
700 726 6.319446 TGGCACAAATGGAGACTGAATACAG 61.319 44.000 0.00 0.00 42.66 2.74
702 728 4.009675 TGGCACAAATGGAGACTGAATAC 58.990 43.478 0.00 0.00 31.92 1.89
742 773 6.317312 ACACGTAGGTAGATGGGGATTTATA 58.683 40.000 0.00 0.00 0.00 0.98
743 774 5.152934 ACACGTAGGTAGATGGGGATTTAT 58.847 41.667 0.00 0.00 0.00 1.40
810 858 0.545071 AGAGGGCATTTTGGGTTGGG 60.545 55.000 0.00 0.00 0.00 4.12
843 891 3.578688 GTTTCAGTTGGTGGATTGATGC 58.421 45.455 0.00 0.00 0.00 3.91
878 929 3.731652 TGAAATTGGTTCAGTTGCCTG 57.268 42.857 0.00 0.00 41.47 4.85
955 1011 2.973224 CGATCTCCGCAACTTGTTTTTG 59.027 45.455 0.00 0.00 0.00 2.44
960 1016 1.714794 CTTCGATCTCCGCAACTTGT 58.285 50.000 0.00 0.00 38.37 3.16
961 1017 0.371645 GCTTCGATCTCCGCAACTTG 59.628 55.000 0.00 0.00 38.37 3.16
1267 1327 4.899239 GGAGGTGGAGGCGATGCG 62.899 72.222 0.00 0.00 0.00 4.73
1281 1341 2.183555 GCTTACACGGGTCCGGAG 59.816 66.667 3.06 8.28 44.69 4.63
1287 1347 0.113580 AAAATGGGGCTTACACGGGT 59.886 50.000 0.00 0.00 0.00 5.28
1306 1391 3.202906 CGAAACTTGTCAGGGAGTTGAA 58.797 45.455 0.00 0.00 36.31 2.69
1395 1497 7.879160 ACACACAAAAGAAATCCATTGCAATAT 59.121 29.630 12.53 0.00 0.00 1.28
1414 1516 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
1415 1517 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1465 1567 5.170748 CCTTCATCAAACAAATAACTGGCC 58.829 41.667 0.00 0.00 0.00 5.36
1473 1575 3.191371 GGAGACGCCTTCATCAAACAAAT 59.809 43.478 0.00 0.00 0.00 2.32
1536 1641 3.605002 CGTCATAGCAGTAGTAGACGCTG 60.605 52.174 0.00 3.84 41.59 5.18
1582 1687 1.816835 AGCAATGCACATCTTGAGGTG 59.183 47.619 8.35 10.57 38.05 4.00
1615 1720 1.002868 CCAACACAGAGGAGGGCAG 60.003 63.158 0.00 0.00 0.00 4.85
1617 1722 0.329596 AATCCAACACAGAGGAGGGC 59.670 55.000 0.00 0.00 37.34 5.19
1619 1724 1.630369 TGGAATCCAACACAGAGGAGG 59.370 52.381 0.00 0.00 37.34 4.30
1711 1822 5.385198 ACAGTCAACAATGTAATGACCCTT 58.615 37.500 12.93 0.00 43.46 3.95
1895 2006 2.485814 GCAACAGGATCAGAACACTTCC 59.514 50.000 0.00 0.00 0.00 3.46
1896 2007 3.141398 TGCAACAGGATCAGAACACTTC 58.859 45.455 0.00 0.00 0.00 3.01
1898 2009 2.936919 TGCAACAGGATCAGAACACT 57.063 45.000 0.00 0.00 0.00 3.55
1900 2011 3.261580 CGTATGCAACAGGATCAGAACA 58.738 45.455 0.00 0.00 0.00 3.18
1901 2012 2.609459 CCGTATGCAACAGGATCAGAAC 59.391 50.000 0.00 0.00 0.00 3.01
1902 2013 2.236146 ACCGTATGCAACAGGATCAGAA 59.764 45.455 11.01 0.00 0.00 3.02
1903 2014 1.831106 ACCGTATGCAACAGGATCAGA 59.169 47.619 11.01 0.00 0.00 3.27
1904 2015 1.935873 CACCGTATGCAACAGGATCAG 59.064 52.381 11.01 0.00 0.00 2.90
1905 2016 2.022764 CACCGTATGCAACAGGATCA 57.977 50.000 11.01 0.00 0.00 2.92
1963 2188 8.494016 AGTAGACAATTTGCATAGTAAAGACC 57.506 34.615 0.00 0.00 0.00 3.85
1966 2191 8.730680 ACCAAGTAGACAATTTGCATAGTAAAG 58.269 33.333 0.00 0.00 0.00 1.85
2002 2239 7.703298 TCGGATATAACAAGTCCAAATTACG 57.297 36.000 0.00 0.00 32.23 3.18
2003 2240 8.718734 GGATCGGATATAACAAGTCCAAATTAC 58.281 37.037 0.00 0.00 32.23 1.89
2052 2300 5.774498 ACAAAAAGGAAAGCCACTAAGAG 57.226 39.130 0.00 0.00 36.29 2.85
2139 2387 1.727880 TGAACCGCAATAGCAACGTAC 59.272 47.619 0.00 0.00 42.27 3.67
2145 2393 4.711892 TGCTGAACCGCAATAGCA 57.288 50.000 0.00 0.00 43.26 3.49
2166 2414 6.535540 TGCAGTAAAATAGTTCCCAAGTGTA 58.464 36.000 0.00 0.00 0.00 2.90
2214 2462 3.364964 GCTTAACCGAGTCATTTGTGTGG 60.365 47.826 0.00 0.00 0.00 4.17
2217 2465 4.201724 GCTAGCTTAACCGAGTCATTTGTG 60.202 45.833 7.70 0.00 0.00 3.33
2220 2468 4.202245 TGCTAGCTTAACCGAGTCATTT 57.798 40.909 17.23 0.00 0.00 2.32
2274 2522 0.898320 CCTCCCAGTATATCCCTGCG 59.102 60.000 0.00 0.00 0.00 5.18
2366 2775 6.857848 TCTGAAGGACTGTCTATGAGGATAT 58.142 40.000 7.85 0.00 0.00 1.63
2397 2806 6.547510 AGAAAAGTAACCAGCAAGTTGATCTT 59.452 34.615 7.16 0.00 36.75 2.40
2698 3110 2.159254 CCCACCTTGTCAAGTTTGTGTG 60.159 50.000 11.61 10.89 0.00 3.82
2978 3625 4.806640 ATCTTGCCACAATTTACCCTTG 57.193 40.909 0.00 0.00 0.00 3.61
3012 3660 5.239525 CCCCTTGAGTTGTGAAGTCTTTTAG 59.760 44.000 0.00 0.00 0.00 1.85
3120 4404 1.327303 AACGGGAATGAAAAGCAGCA 58.673 45.000 0.00 0.00 0.00 4.41
3134 4418 2.224695 ACTTTTCCCCTCAGTTAACGGG 60.225 50.000 9.42 9.42 37.73 5.28
3142 4426 3.181443 ACCTTGTGTACTTTTCCCCTCAG 60.181 47.826 0.00 0.00 0.00 3.35
3144 4428 3.503800 ACCTTGTGTACTTTTCCCCTC 57.496 47.619 0.00 0.00 0.00 4.30
3230 4514 1.064685 CCACCATAGTTTCCCCACCTC 60.065 57.143 0.00 0.00 0.00 3.85
3249 4533 3.982576 AAGACGTGTTTTGATGGAACC 57.017 42.857 0.00 0.00 0.00 3.62
3288 4572 1.209621 TCTCCCCTAAATCAACCCCG 58.790 55.000 0.00 0.00 0.00 5.73
3292 4576 4.329392 TCGGTTTTCTCCCCTAAATCAAC 58.671 43.478 0.00 0.00 0.00 3.18
3301 4585 3.442625 CCTAATGTTTCGGTTTTCTCCCC 59.557 47.826 0.00 0.00 0.00 4.81
3303 4587 3.119602 GCCCTAATGTTTCGGTTTTCTCC 60.120 47.826 0.00 0.00 0.00 3.71
3352 4636 4.647564 AGATGAATGGAAAGTGTCTGGT 57.352 40.909 0.00 0.00 0.00 4.00
3370 4654 5.893255 ACAGCTTCTCTCTGACAAGATAGAT 59.107 40.000 0.00 0.00 36.03 1.98
3378 4662 2.295629 CTGTCACAGCTTCTCTCTGACA 59.704 50.000 0.00 3.68 44.74 3.58
3451 4737 0.955428 ATTGCACGCAGATGACCGTT 60.955 50.000 0.00 0.00 35.17 4.44
3452 4738 1.361668 GATTGCACGCAGATGACCGT 61.362 55.000 0.00 0.00 38.35 4.83
3536 6067 6.515272 AACTGAATTCTGTGTTTGAAGTGT 57.485 33.333 17.51 0.00 0.00 3.55
3539 6070 8.344831 TCATGTAACTGAATTCTGTGTTTGAAG 58.655 33.333 17.51 0.87 0.00 3.02
3559 6090 7.931407 TCTTCTGAACTTTTAACAGCTCATGTA 59.069 33.333 0.00 0.00 43.00 2.29
3566 6097 8.184848 AGAAAAGTCTTCTGAACTTTTAACAGC 58.815 33.333 16.20 7.35 41.83 4.40
3673 6204 6.170506 TGATAACACAGTCAGGATGTTTACC 58.829 40.000 0.00 0.00 37.68 2.85
3705 6236 1.398692 GCCCCCAATTTAATCTCGCA 58.601 50.000 0.00 0.00 0.00 5.10
3710 6241 0.105913 TCCCCGCCCCCAATTTAATC 60.106 55.000 0.00 0.00 0.00 1.75
3780 6312 5.221106 CCTGCAACTTCAAAATCTGAGACAA 60.221 40.000 0.00 0.00 34.81 3.18
3781 6313 4.276678 CCTGCAACTTCAAAATCTGAGACA 59.723 41.667 0.00 0.00 34.81 3.41
3847 6379 8.772705 CCGTTACAAATTTACAACTACCAGTTA 58.227 33.333 10.61 0.00 36.03 2.24
3854 6386 6.864360 ACAGCCGTTACAAATTTACAACTA 57.136 33.333 10.61 0.00 0.00 2.24
3868 6400 3.941483 GGTGTAGAGTAGTACAGCCGTTA 59.059 47.826 2.52 0.00 42.90 3.18
3873 6405 5.450688 CCATCTTGGTGTAGAGTAGTACAGC 60.451 48.000 2.52 6.32 46.88 4.40
3885 6417 6.966490 CAAGTTACTTGGACCATCTTGGTGTA 60.966 42.308 16.62 0.00 42.34 2.90
3907 6439 0.609957 TCAAGGGTGCATCTGCCAAG 60.610 55.000 0.00 0.00 41.18 3.61
3975 6507 7.213678 AGCTATCTCCTAATTTTAGTGACAGC 58.786 38.462 10.34 10.34 34.78 4.40
4056 6589 1.758280 AGGGCCACAAATGCATGTATG 59.242 47.619 6.18 2.69 30.84 2.39
4145 6678 4.763279 TGTCCAGTAACAATCGACTGACTA 59.237 41.667 0.00 0.00 44.88 2.59
4367 6900 3.369261 GCTTCTTCCAATGCTCTCTCTCA 60.369 47.826 0.00 0.00 0.00 3.27
4401 6934 5.827797 TGAGTTTTCTGCTGTTTCATAGGTT 59.172 36.000 0.00 0.00 0.00 3.50
4405 6938 6.096141 TGGTTTGAGTTTTCTGCTGTTTCATA 59.904 34.615 0.00 0.00 0.00 2.15
4557 7090 5.726980 ACATAGCTTGGAGCATTTCAAAA 57.273 34.783 0.00 0.00 45.56 2.44
4598 7131 3.824443 ACCCCAGAAAACAAAATACGGAG 59.176 43.478 0.00 0.00 0.00 4.63
4599 7132 3.834938 ACCCCAGAAAACAAAATACGGA 58.165 40.909 0.00 0.00 0.00 4.69
4600 7133 5.650703 AGATACCCCAGAAAACAAAATACGG 59.349 40.000 0.00 0.00 0.00 4.02
4601 7134 6.373216 TCAGATACCCCAGAAAACAAAATACG 59.627 38.462 0.00 0.00 0.00 3.06
4602 7135 7.610305 TCTCAGATACCCCAGAAAACAAAATAC 59.390 37.037 0.00 0.00 0.00 1.89
4603 7136 7.695055 TCTCAGATACCCCAGAAAACAAAATA 58.305 34.615 0.00 0.00 0.00 1.40
4604 7137 6.552008 TCTCAGATACCCCAGAAAACAAAAT 58.448 36.000 0.00 0.00 0.00 1.82
4661 7194 9.483916 CCTGACACATAAATATGTACGGAAATA 57.516 33.333 5.78 0.00 44.57 1.40
4662 7195 8.208224 TCCTGACACATAAATATGTACGGAAAT 58.792 33.333 5.78 0.00 44.57 2.17
4663 7196 7.557724 TCCTGACACATAAATATGTACGGAAA 58.442 34.615 5.78 0.34 44.57 3.13
4664 7197 7.114866 TCCTGACACATAAATATGTACGGAA 57.885 36.000 5.78 0.00 44.57 4.30
4665 7198 6.718522 TCCTGACACATAAATATGTACGGA 57.281 37.500 5.78 10.47 44.57 4.69
4666 7199 7.962964 AATCCTGACACATAAATATGTACGG 57.037 36.000 5.78 8.19 44.57 4.02
4680 7213 5.886960 ATCACTGCTAAAAATCCTGACAC 57.113 39.130 0.00 0.00 0.00 3.67
4696 7229 5.126061 CCAAAATGTAGGGAGGAAATCACTG 59.874 44.000 0.00 0.00 43.44 3.66
4743 7276 6.567701 GCTTTCGAGTAAATTTGTCATGTGGA 60.568 38.462 0.00 0.00 0.00 4.02
4747 7280 6.857964 ACTTGCTTTCGAGTAAATTTGTCATG 59.142 34.615 0.00 0.00 35.20 3.07
4765 7298 6.183360 GCATCTCCATATCTTTGAACTTGCTT 60.183 38.462 0.00 0.00 0.00 3.91
4783 7316 3.475566 TGTGCTATACCTTGCATCTCC 57.524 47.619 0.00 0.00 41.45 3.71
5212 7747 6.259550 AGGATGCAAGATTACAACACTTTC 57.740 37.500 0.00 0.00 0.00 2.62
5372 7925 3.944015 GCATTTCCTGTTACTGAGCTGAT 59.056 43.478 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.