Multiple sequence alignment - TraesCS5A01G176700

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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 TraesCS5A01G176700 chr5A 100.000 4089 0 0 1 4089 372159229 372155141 0.000000e+00 7552
1 TraesCS5A01G176700 chr5A 94.186 86 5 0 566 651 463357477 463357562 9.220000e-27 132
2 TraesCS5A01G176700 chr5A 85.833 120 12 2 3820 3934 372155527 372155408 5.550000e-24 122
3 TraesCS5A01G176700 chr5A 86.667 105 10 4 567 671 694880977 694880877 3.340000e-21 113
4 TraesCS5A01G176700 chr5D 94.402 3287 96 33 839 4089 280390342 280393576 0.000000e+00 4970
5 TraesCS5A01G176700 chr5D 86.621 583 54 10 1 568 280389096 280389669 1.250000e-174 623
6 TraesCS5A01G176700 chr5D 87.117 163 9 3 674 835 280389716 280389867 1.510000e-39 174
7 TraesCS5A01G176700 chr5B 94.466 1771 69 19 822 2573 318279846 318281606 0.000000e+00 2700
8 TraesCS5A01G176700 chr5B 95.074 1218 45 6 2887 4089 318283642 318284859 0.000000e+00 1903
9 TraesCS5A01G176700 chr5B 96.923 260 7 1 2573 2832 318283380 318283638 6.280000e-118 435
10 TraesCS5A01G176700 chr5B 92.941 85 6 0 567 651 436618375 436618459 1.540000e-24 124
11 TraesCS5A01G176700 chr7D 89.619 289 24 4 3512 3796 551607824 551608110 3.000000e-96 363
12 TraesCS5A01G176700 chr7D 89.310 290 23 6 3512 3796 551503896 551504182 1.400000e-94 357
13 TraesCS5A01G176700 chr7D 86.182 275 23 7 3821 4089 551608019 551608284 2.410000e-72 283
14 TraesCS5A01G176700 chr7D 85.766 274 24 7 3820 4087 551504090 551504354 4.030000e-70 276
15 TraesCS5A01G176700 chr1D 90.071 282 22 4 3478 3755 50915724 50915445 1.080000e-95 361
16 TraesCS5A01G176700 chr7A 86.997 323 32 7 3480 3796 637078317 637078635 5.030000e-94 355
17 TraesCS5A01G176700 chr6D 86.000 350 24 10 3479 3818 358210184 358209850 6.500000e-93 351
18 TraesCS5A01G176700 chr6D 90.551 127 7 2 3820 3941 430447125 430446999 3.270000e-36 163
19 TraesCS5A01G176700 chr6D 90.217 92 9 0 560 651 410110907 410110816 2.000000e-23 121
20 TraesCS5A01G176700 chr2A 90.040 251 18 4 3538 3783 780721073 780721321 6.600000e-83 318
21 TraesCS5A01G176700 chr2D 83.165 297 38 9 3478 3765 4600374 4600081 1.130000e-65 261
22 TraesCS5A01G176700 chr7B 83.755 277 30 4 3820 4089 596539764 596540032 8.780000e-62 248
23 TraesCS5A01G176700 chr1A 92.708 96 7 0 556 651 52458336 52458241 5.510000e-29 139
24 TraesCS5A01G176700 chr3B 94.382 89 5 0 567 655 246109067 246108979 1.980000e-28 137
25 TraesCS5A01G176700 chr3B 83.929 112 18 0 539 650 542551127 542551238 1.550000e-19 108
26 TraesCS5A01G176700 chr4A 94.318 88 5 0 567 654 713832887 713832974 7.130000e-28 135
27 TraesCS5A01G176700 chr2B 94.118 85 5 0 567 651 435504871 435504955 3.320000e-26 130


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 TraesCS5A01G176700 chr5A 372155141 372159229 4088 True 3837.000000 7552 92.916500 1 4089 2 chr5A.!!$R2 4088
1 TraesCS5A01G176700 chr5D 280389096 280393576 4480 False 1922.333333 4970 89.380000 1 4089 3 chr5D.!!$F1 4088
2 TraesCS5A01G176700 chr5B 318279846 318284859 5013 False 1679.333333 2700 95.487667 822 4089 3 chr5B.!!$F2 3267

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
395 407 0.107945 GAGCCGATCCAAGCTTGAGT 60.108 55.000 28.05 15.16 40.11 3.41 F
657 673 0.535335 GACGGAGGGAGTATGTTGCA 59.465 55.000 0.00 0.00 0.00 4.08 F
741 782 0.737367 TCAGATTTGACTGCTCGCGG 60.737 55.000 6.13 0.00 37.75 6.46 F
2132 2669 0.250338 ACCGAGGCAGGTTTCAAGTC 60.250 55.000 0.00 0.00 43.00 3.01 F
2811 5127 2.301870 ACTCGCCCAACATCAGTTTCTA 59.698 45.455 0.00 0.00 35.28 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1541 2067 0.184211 ACAAAACCCGTAGCCCAACT 59.816 50.000 0.0 0.0 0.00 3.16 R
1551 2077 0.885196 CCCACCATACACAAAACCCG 59.115 55.000 0.0 0.0 0.00 5.28 R
2321 2859 1.467734 CCTGAAGCTCAACATCACTGC 59.532 52.381 0.0 0.0 0.00 4.40 R
2936 5252 0.036388 CTGCCGCCTTTTCTGGTAGA 60.036 55.000 0.0 0.0 37.66 2.59 R
3833 6162 0.681175 GCAGCCCAACAACCAGAAAT 59.319 50.000 0.0 0.0 0.00 2.17 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
20 21 1.416401 TCAACCGGCTCAAAAGAGACT 59.584 47.619 0.00 0.00 0.00 3.24
22 23 1.343069 ACCGGCTCAAAAGAGACTCT 58.657 50.000 0.00 0.00 0.00 3.24
26 27 1.337260 GGCTCAAAAGAGACTCTGCGA 60.337 52.381 5.55 2.38 0.00 5.10
29 30 1.964223 TCAAAAGAGACTCTGCGACCT 59.036 47.619 5.55 0.00 0.00 3.85
30 31 2.365617 TCAAAAGAGACTCTGCGACCTT 59.634 45.455 5.55 0.00 0.00 3.50
32 33 1.621992 AAGAGACTCTGCGACCTTCA 58.378 50.000 5.55 0.00 0.00 3.02
40 41 0.742281 CTGCGACCTTCATGTCCCTG 60.742 60.000 0.00 0.00 31.35 4.45
61 62 1.374252 GACCCACGCACGTCTTCAT 60.374 57.895 0.00 0.00 0.00 2.57
77 78 3.519510 TCTTCATCTTTCCTGATTCCCGT 59.480 43.478 0.00 0.00 0.00 5.28
86 87 1.730064 CCTGATTCCCGTAACAACACG 59.270 52.381 0.00 0.00 41.59 4.49
92 93 1.280444 CCGTAACAACACGCCAACC 59.720 57.895 0.00 0.00 40.59 3.77
111 112 2.081462 CCGTAACATTGTCCCCTTGAC 58.919 52.381 0.00 0.00 44.72 3.18
115 116 3.425162 AACATTGTCCCCTTGACTCTC 57.575 47.619 0.00 0.00 44.75 3.20
135 136 1.473610 CCTCTTCCTCTCGCGTCTCTA 60.474 57.143 5.77 0.00 0.00 2.43
137 138 0.658897 CTTCCTCTCGCGTCTCTACC 59.341 60.000 5.77 0.00 0.00 3.18
144 156 1.598601 CTCGCGTCTCTACCCTTAGAC 59.401 57.143 5.77 0.00 39.00 2.59
154 166 4.570663 CCTTAGACGAGGCGCCGG 62.571 72.222 23.20 19.93 0.00 6.13
182 194 4.386951 CCCCGCCACACACATCGA 62.387 66.667 0.00 0.00 0.00 3.59
191 203 1.532437 CACACACATCGATGTTGCACT 59.468 47.619 28.04 11.16 39.39 4.40
226 238 1.032657 ATCTAGATCGGGATCGCCGG 61.033 60.000 18.67 0.00 42.48 6.13
256 268 1.440353 GGTTGTGCACGACATTCGC 60.440 57.895 32.88 15.46 45.12 4.70
263 275 4.673298 ACGACATTCGCGTGGCCA 62.673 61.111 0.00 0.00 45.12 5.36
274 286 2.184579 GTGGCCAGGTCGTAGCTC 59.815 66.667 5.11 0.00 0.00 4.09
275 287 2.037367 TGGCCAGGTCGTAGCTCT 59.963 61.111 0.00 0.00 0.00 4.09
313 325 3.053291 TTGGCATTGTCGACGCCC 61.053 61.111 24.42 15.72 45.63 6.13
315 327 2.824041 GGCATTGTCGACGCCCAT 60.824 61.111 18.93 3.06 40.07 4.00
324 336 4.554036 GACGCCCATGGAGCCCTC 62.554 72.222 15.22 7.44 0.00 4.30
341 353 1.620524 CCTCCCCACTGATTTGGCAAT 60.621 52.381 0.00 0.00 35.00 3.56
345 357 1.134907 CCCACTGATTTGGCAATCTGC 60.135 52.381 0.00 0.00 40.40 4.26
357 369 2.969806 AATCTGCGTGCAAGCACCG 61.970 57.895 23.72 14.89 42.92 4.94
377 389 1.078214 CCGCTGATGGCAAGAAGGA 60.078 57.895 0.00 0.00 41.91 3.36
395 407 0.107945 GAGCCGATCCAAGCTTGAGT 60.108 55.000 28.05 15.16 40.11 3.41
488 500 1.503818 AACAGCGGTGTTGCTAACGG 61.504 55.000 30.41 0.00 45.58 4.44
576 592 8.887264 ATCTACAATAAGACCTACTCCCTATG 57.113 38.462 0.00 0.00 0.00 2.23
577 593 7.823635 TCTACAATAAGACCTACTCCCTATGT 58.176 38.462 0.00 0.00 0.00 2.29
578 594 6.980416 ACAATAAGACCTACTCCCTATGTC 57.020 41.667 0.00 0.00 0.00 3.06
579 595 5.839606 ACAATAAGACCTACTCCCTATGTCC 59.160 44.000 0.00 0.00 0.00 4.02
580 596 3.331718 AAGACCTACTCCCTATGTCCC 57.668 52.381 0.00 0.00 0.00 4.46
581 597 2.224077 AGACCTACTCCCTATGTCCCA 58.776 52.381 0.00 0.00 0.00 4.37
582 598 2.798368 AGACCTACTCCCTATGTCCCAT 59.202 50.000 0.00 0.00 0.00 4.00
583 599 3.995077 AGACCTACTCCCTATGTCCCATA 59.005 47.826 0.00 0.00 0.00 2.74
584 600 4.422592 AGACCTACTCCCTATGTCCCATAA 59.577 45.833 0.00 0.00 0.00 1.90
585 601 5.078006 AGACCTACTCCCTATGTCCCATAAT 59.922 44.000 0.00 0.00 0.00 1.28
586 602 6.279682 AGACCTACTCCCTATGTCCCATAATA 59.720 42.308 0.00 0.00 0.00 0.98
587 603 7.035022 AGACCTACTCCCTATGTCCCATAATAT 60.035 40.741 0.00 0.00 0.00 1.28
588 604 8.195933 ACCTACTCCCTATGTCCCATAATATA 57.804 38.462 0.00 0.00 0.00 0.86
589 605 8.639200 ACCTACTCCCTATGTCCCATAATATAA 58.361 37.037 0.00 0.00 0.00 0.98
590 606 9.676129 CCTACTCCCTATGTCCCATAATATAAT 57.324 37.037 0.00 0.00 0.00 1.28
594 610 9.982651 CTCCCTATGTCCCATAATATAATAACG 57.017 37.037 0.00 0.00 0.00 3.18
595 611 9.496710 TCCCTATGTCCCATAATATAATAACGT 57.503 33.333 0.00 0.00 0.00 3.99
612 628 9.784680 ATAATAACGTTTCTGACACTAGTGTAG 57.215 33.333 27.98 22.31 45.05 2.74
613 629 5.511234 AACGTTTCTGACACTAGTGTAGT 57.489 39.130 27.98 15.35 45.05 2.73
614 630 6.624352 AACGTTTCTGACACTAGTGTAGTA 57.376 37.500 27.98 15.99 45.05 1.82
615 631 6.814506 ACGTTTCTGACACTAGTGTAGTAT 57.185 37.500 27.98 5.50 45.05 2.12
616 632 6.840075 ACGTTTCTGACACTAGTGTAGTATC 58.160 40.000 27.98 15.61 45.05 2.24
617 633 6.429078 ACGTTTCTGACACTAGTGTAGTATCA 59.571 38.462 27.98 19.12 45.05 2.15
618 634 7.040892 ACGTTTCTGACACTAGTGTAGTATCAA 60.041 37.037 27.98 13.26 41.25 2.57
619 635 7.806487 CGTTTCTGACACTAGTGTAGTATCAAA 59.194 37.037 27.98 16.65 41.25 2.69
620 636 9.472361 GTTTCTGACACTAGTGTAGTATCAAAA 57.528 33.333 27.98 17.92 41.25 2.44
622 638 9.472361 TTCTGACACTAGTGTAGTATCAAAAAC 57.528 33.333 27.98 11.61 41.25 2.43
623 639 7.806487 TCTGACACTAGTGTAGTATCAAAAACG 59.194 37.037 27.98 9.40 41.25 3.60
624 640 7.428020 TGACACTAGTGTAGTATCAAAAACGT 58.572 34.615 27.98 0.00 39.11 3.99
625 641 7.922278 TGACACTAGTGTAGTATCAAAAACGTT 59.078 33.333 27.98 0.00 39.11 3.99
626 642 8.290663 ACACTAGTGTAGTATCAAAAACGTTC 57.709 34.615 26.91 0.00 42.90 3.95
627 643 8.139989 ACACTAGTGTAGTATCAAAAACGTTCT 58.860 33.333 26.91 0.00 42.90 3.01
628 644 8.975439 CACTAGTGTAGTATCAAAAACGTTCTT 58.025 33.333 15.06 0.00 37.23 2.52
642 658 9.632969 CAAAAACGTTCTTATATTATGAGACGG 57.367 33.333 0.00 8.31 0.00 4.79
643 659 9.590451 AAAAACGTTCTTATATTATGAGACGGA 57.410 29.630 0.00 0.00 0.00 4.69
644 660 8.798748 AAACGTTCTTATATTATGAGACGGAG 57.201 34.615 0.00 6.40 0.00 4.63
645 661 6.910995 ACGTTCTTATATTATGAGACGGAGG 58.089 40.000 16.71 6.29 0.00 4.30
646 662 6.072064 ACGTTCTTATATTATGAGACGGAGGG 60.072 42.308 16.71 2.79 0.00 4.30
647 663 6.150641 CGTTCTTATATTATGAGACGGAGGGA 59.849 42.308 0.00 0.00 0.00 4.20
648 664 7.540299 GTTCTTATATTATGAGACGGAGGGAG 58.460 42.308 0.00 0.00 0.00 4.30
649 665 6.791371 TCTTATATTATGAGACGGAGGGAGT 58.209 40.000 0.00 0.00 0.00 3.85
650 666 7.925622 TCTTATATTATGAGACGGAGGGAGTA 58.074 38.462 0.00 0.00 0.00 2.59
651 667 8.558312 TCTTATATTATGAGACGGAGGGAGTAT 58.442 37.037 0.00 0.00 0.00 2.12
652 668 8.521170 TTATATTATGAGACGGAGGGAGTATG 57.479 38.462 0.00 0.00 0.00 2.39
653 669 2.757894 ATGAGACGGAGGGAGTATGT 57.242 50.000 0.00 0.00 0.00 2.29
654 670 2.526888 TGAGACGGAGGGAGTATGTT 57.473 50.000 0.00 0.00 0.00 2.71
655 671 2.100197 TGAGACGGAGGGAGTATGTTG 58.900 52.381 0.00 0.00 0.00 3.33
656 672 0.824759 AGACGGAGGGAGTATGTTGC 59.175 55.000 0.00 0.00 0.00 4.17
657 673 0.535335 GACGGAGGGAGTATGTTGCA 59.465 55.000 0.00 0.00 0.00 4.08
658 674 0.981183 ACGGAGGGAGTATGTTGCAA 59.019 50.000 0.00 0.00 0.00 4.08
659 675 1.066143 ACGGAGGGAGTATGTTGCAAG 60.066 52.381 0.00 0.00 0.00 4.01
663 679 3.691609 GGAGGGAGTATGTTGCAAGAAAG 59.308 47.826 0.00 0.00 0.00 2.62
669 685 7.015584 AGGGAGTATGTTGCAAGAAAGAAAATT 59.984 33.333 0.00 0.00 0.00 1.82
709 750 1.645034 AATGATGAAGACGTGCTCGG 58.355 50.000 13.32 0.00 41.85 4.63
730 771 2.730090 GCCGCTTGATGTGTCAGATTTG 60.730 50.000 0.00 0.00 35.39 2.32
731 772 2.743664 CCGCTTGATGTGTCAGATTTGA 59.256 45.455 0.00 0.00 35.39 2.69
740 781 2.741930 TCAGATTTGACTGCTCGCG 58.258 52.632 0.00 0.00 37.75 5.87
741 782 0.737367 TCAGATTTGACTGCTCGCGG 60.737 55.000 6.13 0.00 37.75 6.46
742 783 2.103042 AGATTTGACTGCTCGCGGC 61.103 57.895 6.13 9.69 42.22 6.53
743 784 3.100862 GATTTGACTGCTCGCGGCC 62.101 63.158 6.13 0.00 40.92 6.13
744 785 3.612247 ATTTGACTGCTCGCGGCCT 62.612 57.895 6.13 0.00 40.92 5.19
754 795 3.592814 CGCGGCCTGGTCGATCTA 61.593 66.667 26.96 0.00 29.41 1.98
784 825 1.881252 CACCCGGCGAATTCGTAGG 60.881 63.158 27.24 26.61 42.22 3.18
790 831 1.207377 GGCGAATTCGTAGGACGCTC 61.207 60.000 27.24 8.53 46.71 5.03
801 843 4.148696 TCGTAGGACGCTCGTTTTTAAAAG 59.851 41.667 0.14 0.00 42.21 2.27
836 878 3.241067 TGCCCTAAACTAGCGTTGTAG 57.759 47.619 0.00 0.00 32.65 2.74
878 1393 5.818336 GGAGGAAACAAAATACTAGCCTCTC 59.182 44.000 0.00 0.00 40.31 3.20
883 1398 7.362142 GGAAACAAAATACTAGCCTCTCCAAAG 60.362 40.741 0.00 0.00 0.00 2.77
885 1400 6.174049 ACAAAATACTAGCCTCTCCAAAGTC 58.826 40.000 0.00 0.00 0.00 3.01
887 1402 2.327325 ACTAGCCTCTCCAAAGTCCA 57.673 50.000 0.00 0.00 0.00 4.02
1282 1808 1.805254 CGATACGTTCCGGTGAGGT 59.195 57.895 0.00 6.26 41.99 3.85
1541 2067 1.977854 TGGCCTTCTACTTCAGCTTGA 59.022 47.619 3.32 0.00 0.00 3.02
1546 2072 3.999663 CCTTCTACTTCAGCTTGAGTTGG 59.000 47.826 4.22 0.07 0.00 3.77
1551 2077 2.079925 CTTCAGCTTGAGTTGGGCTAC 58.920 52.381 0.00 0.00 34.71 3.58
1554 2080 1.745489 GCTTGAGTTGGGCTACGGG 60.745 63.158 0.00 0.00 0.00 5.28
1558 2084 0.475044 TGAGTTGGGCTACGGGTTTT 59.525 50.000 0.00 0.00 0.00 2.43
1581 2118 4.202514 TGTGTATGGTGGGAATTTCAGACA 60.203 41.667 0.00 0.00 0.00 3.41
1618 2155 1.182667 AGGCTATTTCCGGGCAAAAC 58.817 50.000 0.00 0.00 0.00 2.43
1955 2492 5.540911 ACTATTGTGCTTGGTTTGATTTGG 58.459 37.500 0.00 0.00 0.00 3.28
2091 2628 3.551846 ACAATTTTCGTGAAGACCCTGT 58.448 40.909 0.00 0.00 0.00 4.00
2120 2657 1.339727 ACCACTATCCAAAACCGAGGC 60.340 52.381 0.00 0.00 0.00 4.70
2132 2669 0.250338 ACCGAGGCAGGTTTCAAGTC 60.250 55.000 0.00 0.00 43.00 3.01
2260 2797 8.523658 TGTGTACATATATGATAGCCTCTTGTC 58.476 37.037 19.63 0.00 0.00 3.18
2261 2798 8.744652 GTGTACATATATGATAGCCTCTTGTCT 58.255 37.037 19.63 0.00 0.00 3.41
2262 2799 9.314133 TGTACATATATGATAGCCTCTTGTCTT 57.686 33.333 19.63 0.00 0.00 3.01
2263 2800 9.579768 GTACATATATGATAGCCTCTTGTCTTG 57.420 37.037 19.63 0.00 0.00 3.02
2264 2801 8.200024 ACATATATGATAGCCTCTTGTCTTGT 57.800 34.615 19.63 0.00 0.00 3.16
2321 2859 5.987347 TCTTTTACTTTGTTCCTACAGTCGG 59.013 40.000 0.00 0.00 35.28 4.79
2420 2958 3.674753 GTGTGCACTGAAAATATTGCCAC 59.325 43.478 19.41 0.00 33.86 5.01
2485 3023 5.578005 TGTAACTTCCAGTTCGAGGATAG 57.422 43.478 0.00 0.00 39.51 2.08
2503 3041 7.364232 CGAGGATAGGGCTAATGATACAGATTT 60.364 40.741 0.00 0.00 0.00 2.17
2583 4899 6.560253 ATGGACAAGTTCAGTTTCATGTAC 57.440 37.500 0.00 0.00 0.00 2.90
2584 4900 4.509970 TGGACAAGTTCAGTTTCATGTACG 59.490 41.667 0.00 0.00 0.00 3.67
2585 4901 4.510340 GGACAAGTTCAGTTTCATGTACGT 59.490 41.667 0.00 0.00 0.00 3.57
2586 4902 5.693104 GGACAAGTTCAGTTTCATGTACGTA 59.307 40.000 0.00 0.00 0.00 3.57
2707 5023 6.795098 TGTAAAGTTCAGCGATATGTTTGT 57.205 33.333 0.00 0.00 0.00 2.83
2811 5127 2.301870 ACTCGCCCAACATCAGTTTCTA 59.698 45.455 0.00 0.00 35.28 2.10
2855 5171 6.998968 ACATTTTCTTTGCCAGAGAGATAG 57.001 37.500 0.00 0.00 31.12 2.08
2897 5213 8.306038 ACCACAGTGATAAAACTTATACGTGTA 58.694 33.333 0.62 0.00 0.00 2.90
2936 5252 1.978455 TTCGGGTGTGCCACAGAACT 61.978 55.000 0.00 0.00 35.86 3.01
3094 5410 4.773013 AGAGGAAAGTGTTTTAACCGTCA 58.227 39.130 0.00 0.00 0.00 4.35
3164 5481 1.200948 GAGTTCTGCACCATCTTTGCC 59.799 52.381 0.00 0.00 39.39 4.52
3327 5644 3.127425 ACTTGTGAGGAAACTGGTAGC 57.873 47.619 0.00 0.00 44.43 3.58
3349 5666 0.531974 ACTGTGTACCAGCACGTTGG 60.532 55.000 4.68 4.68 45.68 3.77
3467 5785 8.860088 TCCTTTTTCCTTTCTCTTTTATTGAGG 58.140 33.333 0.00 0.00 32.78 3.86
3627 5954 0.592637 TGTGAGCCACTTCATTTGCG 59.407 50.000 6.83 0.00 35.11 4.85
3658 5987 5.065346 CGACACTGTATATGAGACACTCACT 59.935 44.000 3.54 0.00 43.63 3.41
3679 6008 6.013206 TCACTAAGTCCAGCCCTAAATGTTTA 60.013 38.462 0.00 0.00 0.00 2.01
3715 6044 2.092267 TGCAACATCTGAGCCCACATAT 60.092 45.455 0.00 0.00 0.00 1.78
3722 6051 5.130975 ACATCTGAGCCCACATATGTTTCTA 59.869 40.000 5.37 0.00 35.23 2.10
3727 6056 3.947834 AGCCCACATATGTTTCTAGTTGC 59.052 43.478 5.37 0.34 0.00 4.17
3760 6089 3.507233 CCACCACAAAGCTACAATGTGAT 59.493 43.478 18.16 3.84 45.61 3.06
3833 6162 0.104855 GATCGCTGAGCCCACATACA 59.895 55.000 0.00 0.00 0.00 2.29
3847 6176 4.321899 CCCACATACATTTCTGGTTGTTGG 60.322 45.833 0.00 0.00 0.00 3.77
3978 6313 3.132289 GGTCACCTGAGGAACGAATCATA 59.868 47.826 4.99 0.00 0.00 2.15
3982 6317 5.104941 TCACCTGAGGAACGAATCATATTGT 60.105 40.000 4.99 0.00 0.00 2.71
4011 6346 5.198965 CAATGAAGTTCCCTCTTCCATCAT 58.801 41.667 0.00 0.00 41.96 2.45
4077 6412 4.927425 GCAGCATCAACATTGATTTTGACT 59.073 37.500 14.72 3.58 45.13 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.596934 GGGACATGAAGGTCGCAGA 59.403 57.895 0.00 0.00 46.51 4.26
26 27 3.180449 TCCACAGGGACATGAAGGT 57.820 52.632 0.00 0.00 38.64 3.50
40 41 3.802418 AAGACGTGCGTGGGTCCAC 62.802 63.158 9.96 9.96 43.01 4.02
47 48 1.126846 GGAAAGATGAAGACGTGCGTG 59.873 52.381 0.67 0.00 0.00 5.34
50 51 2.688507 TCAGGAAAGATGAAGACGTGC 58.311 47.619 0.00 0.00 0.00 5.34
61 62 4.202377 TGTTGTTACGGGAATCAGGAAAGA 60.202 41.667 0.00 0.00 0.00 2.52
77 78 1.596727 GTTACGGTTGGCGTGTTGTTA 59.403 47.619 0.00 0.00 0.00 2.41
86 87 0.524414 GGGACAATGTTACGGTTGGC 59.476 55.000 5.54 2.27 32.51 4.52
111 112 0.746563 ACGCGAGAGGAAGAGGAGAG 60.747 60.000 15.93 0.00 0.00 3.20
115 116 0.746563 AGAGACGCGAGAGGAAGAGG 60.747 60.000 15.93 0.00 0.00 3.69
135 136 3.459063 GGCGCCTCGTCTAAGGGT 61.459 66.667 22.15 0.00 36.88 4.34
137 138 4.570663 CCGGCGCCTCGTCTAAGG 62.571 72.222 26.68 11.93 39.62 2.69
180 192 2.614057 GGGAAATAGGAGTGCAACATCG 59.386 50.000 0.00 0.00 41.43 3.84
182 194 2.582636 AGGGGAAATAGGAGTGCAACAT 59.417 45.455 0.00 0.00 41.43 2.71
191 203 4.566837 TCTAGATGCAAGGGGAAATAGGA 58.433 43.478 0.00 0.00 0.00 2.94
228 240 3.103911 GCACAACCTCCGACGTCG 61.104 66.667 30.33 30.33 39.44 5.12
237 249 1.841663 GCGAATGTCGTGCACAACCT 61.842 55.000 18.64 0.00 42.81 3.50
256 268 3.701604 GAGCTACGACCTGGCCACG 62.702 68.421 12.30 12.30 0.00 4.94
263 275 1.096386 CGCCACTAGAGCTACGACCT 61.096 60.000 0.00 0.00 0.00 3.85
274 286 0.944311 AAGACGTTGTGCGCCACTAG 60.944 55.000 4.18 0.00 46.11 2.57
275 287 0.531090 AAAGACGTTGTGCGCCACTA 60.531 50.000 4.18 0.00 46.11 2.74
324 336 1.479323 CAGATTGCCAAATCAGTGGGG 59.521 52.381 1.64 0.00 44.05 4.96
327 339 1.200716 ACGCAGATTGCCAAATCAGTG 59.799 47.619 1.64 2.76 44.05 3.66
328 340 1.200716 CACGCAGATTGCCAAATCAGT 59.799 47.619 1.64 0.00 44.05 3.41
361 373 2.105124 GCTCCTTCTTGCCATCAGC 58.895 57.895 0.00 0.00 44.14 4.26
377 389 0.326264 AACTCAAGCTTGGATCGGCT 59.674 50.000 25.73 1.89 40.85 5.52
382 394 3.228188 TGGACAAACTCAAGCTTGGAT 57.772 42.857 25.73 11.78 0.00 3.41
383 395 2.727123 TGGACAAACTCAAGCTTGGA 57.273 45.000 25.73 11.84 0.00 3.53
412 424 5.830912 TGCAAATAAATTATCCTTCGGCTG 58.169 37.500 0.00 0.00 0.00 4.85
416 428 7.222611 CCCTTGTTGCAAATAAATTATCCTTCG 59.777 37.037 0.00 0.00 0.00 3.79
418 430 7.823799 CACCCTTGTTGCAAATAAATTATCCTT 59.176 33.333 0.00 0.00 0.00 3.36
469 481 1.503818 CCGTTAGCAACACCGCTGTT 61.504 55.000 0.00 0.00 43.68 3.16
470 482 1.959226 CCGTTAGCAACACCGCTGT 60.959 57.895 0.00 0.00 43.68 4.40
471 483 2.860293 CCGTTAGCAACACCGCTG 59.140 61.111 0.00 0.00 43.68 5.18
472 484 3.047877 GCCGTTAGCAACACCGCT 61.048 61.111 0.00 0.00 46.26 5.52
473 485 4.439472 CGCCGTTAGCAACACCGC 62.439 66.667 0.00 0.00 44.04 5.68
474 486 3.784412 CCGCCGTTAGCAACACCG 61.784 66.667 0.00 0.00 44.04 4.94
486 498 4.444024 CGTCATTGTGCACCGCCG 62.444 66.667 15.69 5.76 0.00 6.46
488 500 0.301687 CTATCGTCATTGTGCACCGC 59.698 55.000 15.69 0.00 0.00 5.68
550 566 9.315363 CATAGGGAGTAGGTCTTATTGTAGATT 57.685 37.037 0.00 0.00 0.00 2.40
551 567 8.457757 ACATAGGGAGTAGGTCTTATTGTAGAT 58.542 37.037 0.00 0.00 0.00 1.98
552 568 7.823635 ACATAGGGAGTAGGTCTTATTGTAGA 58.176 38.462 0.00 0.00 0.00 2.59
555 571 5.839606 GGACATAGGGAGTAGGTCTTATTGT 59.160 44.000 0.00 0.00 41.37 2.71
586 602 9.784680 CTACACTAGTGTCAGAAACGTTATTAT 57.215 33.333 31.11 3.94 43.74 1.28
587 603 8.786898 ACTACACTAGTGTCAGAAACGTTATTA 58.213 33.333 31.11 8.36 43.74 0.98
588 604 7.655490 ACTACACTAGTGTCAGAAACGTTATT 58.345 34.615 31.11 4.99 43.74 1.40
589 605 7.211966 ACTACACTAGTGTCAGAAACGTTAT 57.788 36.000 31.11 5.44 43.74 1.89
590 606 6.624352 ACTACACTAGTGTCAGAAACGTTA 57.376 37.500 31.11 9.52 43.74 3.18
591 607 5.511234 ACTACACTAGTGTCAGAAACGTT 57.489 39.130 31.11 6.17 43.74 3.99
592 608 6.814506 ATACTACACTAGTGTCAGAAACGT 57.185 37.500 31.11 18.06 43.74 3.99
600 616 7.864307 ACGTTTTTGATACTACACTAGTGTC 57.136 36.000 31.11 17.07 44.30 3.67
601 617 8.139989 AGAACGTTTTTGATACTACACTAGTGT 58.860 33.333 30.13 30.13 46.87 3.55
602 618 8.516811 AGAACGTTTTTGATACTACACTAGTG 57.483 34.615 21.44 21.44 39.81 2.74
616 632 9.632969 CCGTCTCATAATATAAGAACGTTTTTG 57.367 33.333 13.87 0.00 0.00 2.44
617 633 9.590451 TCCGTCTCATAATATAAGAACGTTTTT 57.410 29.630 9.22 9.22 0.00 1.94
618 634 9.245962 CTCCGTCTCATAATATAAGAACGTTTT 57.754 33.333 0.46 0.00 0.00 2.43
619 635 7.866393 CCTCCGTCTCATAATATAAGAACGTTT 59.134 37.037 0.46 0.00 0.00 3.60
620 636 7.368833 CCTCCGTCTCATAATATAAGAACGTT 58.631 38.462 0.00 0.00 0.00 3.99
621 637 6.072064 CCCTCCGTCTCATAATATAAGAACGT 60.072 42.308 0.00 0.00 0.00 3.99
622 638 6.150641 TCCCTCCGTCTCATAATATAAGAACG 59.849 42.308 0.00 0.00 0.00 3.95
623 639 7.177041 ACTCCCTCCGTCTCATAATATAAGAAC 59.823 40.741 0.00 0.00 0.00 3.01
624 640 7.239438 ACTCCCTCCGTCTCATAATATAAGAA 58.761 38.462 0.00 0.00 0.00 2.52
625 641 6.791371 ACTCCCTCCGTCTCATAATATAAGA 58.209 40.000 0.00 0.00 0.00 2.10
626 642 8.625651 CATACTCCCTCCGTCTCATAATATAAG 58.374 40.741 0.00 0.00 0.00 1.73
627 643 8.114102 ACATACTCCCTCCGTCTCATAATATAA 58.886 37.037 0.00 0.00 0.00 0.98
628 644 7.640313 ACATACTCCCTCCGTCTCATAATATA 58.360 38.462 0.00 0.00 0.00 0.86
629 645 6.494952 ACATACTCCCTCCGTCTCATAATAT 58.505 40.000 0.00 0.00 0.00 1.28
630 646 5.888901 ACATACTCCCTCCGTCTCATAATA 58.111 41.667 0.00 0.00 0.00 0.98
631 647 4.742012 ACATACTCCCTCCGTCTCATAAT 58.258 43.478 0.00 0.00 0.00 1.28
632 648 4.180377 ACATACTCCCTCCGTCTCATAA 57.820 45.455 0.00 0.00 0.00 1.90
633 649 3.878237 ACATACTCCCTCCGTCTCATA 57.122 47.619 0.00 0.00 0.00 2.15
634 650 2.695666 CAACATACTCCCTCCGTCTCAT 59.304 50.000 0.00 0.00 0.00 2.90
635 651 2.100197 CAACATACTCCCTCCGTCTCA 58.900 52.381 0.00 0.00 0.00 3.27
636 652 1.202428 GCAACATACTCCCTCCGTCTC 60.202 57.143 0.00 0.00 0.00 3.36
637 653 0.824759 GCAACATACTCCCTCCGTCT 59.175 55.000 0.00 0.00 0.00 4.18
638 654 0.535335 TGCAACATACTCCCTCCGTC 59.465 55.000 0.00 0.00 0.00 4.79
639 655 0.981183 TTGCAACATACTCCCTCCGT 59.019 50.000 0.00 0.00 0.00 4.69
640 656 1.207089 TCTTGCAACATACTCCCTCCG 59.793 52.381 0.00 0.00 0.00 4.63
641 657 3.350219 TTCTTGCAACATACTCCCTCC 57.650 47.619 0.00 0.00 0.00 4.30
642 658 4.579869 TCTTTCTTGCAACATACTCCCTC 58.420 43.478 0.00 0.00 0.00 4.30
643 659 4.640771 TCTTTCTTGCAACATACTCCCT 57.359 40.909 0.00 0.00 0.00 4.20
644 660 5.705609 TTTCTTTCTTGCAACATACTCCC 57.294 39.130 0.00 0.00 0.00 4.30
645 661 8.593492 AAATTTTCTTTCTTGCAACATACTCC 57.407 30.769 0.00 0.00 0.00 3.85
650 666 9.160496 TGTTGTAAATTTTCTTTCTTGCAACAT 57.840 25.926 11.54 0.00 44.18 2.71
651 667 8.539770 TGTTGTAAATTTTCTTTCTTGCAACA 57.460 26.923 11.54 11.54 45.67 3.33
652 668 9.476761 CTTGTTGTAAATTTTCTTTCTTGCAAC 57.523 29.630 0.00 7.41 41.71 4.17
653 669 9.429359 TCTTGTTGTAAATTTTCTTTCTTGCAA 57.571 25.926 0.00 0.00 0.00 4.08
654 670 8.994429 TCTTGTTGTAAATTTTCTTTCTTGCA 57.006 26.923 0.00 0.00 0.00 4.08
688 704 2.535984 CCGAGCACGTCTTCATCATTAC 59.464 50.000 2.18 0.00 37.88 1.89
690 706 1.645034 CCGAGCACGTCTTCATCATT 58.355 50.000 2.18 0.00 37.88 2.57
709 750 1.089920 AATCTGACACATCAAGCGGC 58.910 50.000 0.00 0.00 33.30 6.53
735 776 4.933064 GATCGACCAGGCCGCGAG 62.933 72.222 8.23 0.00 37.48 5.03
737 778 2.421877 AATAGATCGACCAGGCCGCG 62.422 60.000 0.00 0.00 0.00 6.46
738 779 0.249911 AAATAGATCGACCAGGCCGC 60.250 55.000 0.00 0.00 0.00 6.53
739 780 3.380479 TTAAATAGATCGACCAGGCCG 57.620 47.619 0.00 0.00 0.00 6.13
740 781 5.820947 TCTTTTTAAATAGATCGACCAGGCC 59.179 40.000 4.45 0.00 0.00 5.19
741 782 6.238402 GGTCTTTTTAAATAGATCGACCAGGC 60.238 42.308 10.92 0.00 39.47 4.85
742 783 6.821665 TGGTCTTTTTAAATAGATCGACCAGG 59.178 38.462 10.92 0.00 43.21 4.45
743 784 7.843490 TGGTCTTTTTAAATAGATCGACCAG 57.157 36.000 10.92 0.00 43.21 4.00
744 785 6.596497 GGTGGTCTTTTTAAATAGATCGACCA 59.404 38.462 21.51 16.98 45.13 4.02
745 786 6.037940 GGGTGGTCTTTTTAAATAGATCGACC 59.962 42.308 19.95 19.95 39.96 4.79
754 795 1.542472 CGCCGGGTGGTCTTTTTAAAT 59.458 47.619 2.18 0.00 37.67 1.40
768 809 1.590792 GTCCTACGAATTCGCCGGG 60.591 63.158 27.03 23.40 44.43 5.73
784 825 6.543187 TTTGTTCTTTTAAAAACGAGCGTC 57.457 33.333 1.66 0.00 0.00 5.19
801 843 8.000780 AGTTTAGGGCATCTTATGATTTGTTC 57.999 34.615 0.00 0.00 0.00 3.18
878 1393 2.297033 CCTTTGTGGATGTGGACTTTGG 59.703 50.000 0.00 0.00 38.35 3.28
936 1462 2.722201 GCGAGGTGGGTAGGGAGTG 61.722 68.421 0.00 0.00 0.00 3.51
1080 1606 4.760047 CGCCACTTCCTGACGGGG 62.760 72.222 0.00 0.00 35.33 5.73
1170 1696 0.608308 GCACCACCTTGTTACCCCTC 60.608 60.000 0.00 0.00 0.00 4.30
1282 1808 6.306987 AGACCTAATCTTTGAAGCCAAGAAA 58.693 36.000 0.00 0.00 31.62 2.52
1400 1926 4.394920 ACATTGTGCCTAAAACTATGACCG 59.605 41.667 5.27 0.00 35.29 4.79
1487 2013 2.589157 ATTTCCGGCGTCCAGACCA 61.589 57.895 6.01 0.00 0.00 4.02
1541 2067 0.184211 ACAAAACCCGTAGCCCAACT 59.816 50.000 0.00 0.00 0.00 3.16
1546 2072 1.741145 CCATACACAAAACCCGTAGCC 59.259 52.381 0.00 0.00 0.00 3.93
1551 2077 0.885196 CCCACCATACACAAAACCCG 59.115 55.000 0.00 0.00 0.00 5.28
1554 2080 5.848406 TGAAATTCCCACCATACACAAAAC 58.152 37.500 0.00 0.00 0.00 2.43
1558 2084 4.202514 TGTCTGAAATTCCCACCATACACA 60.203 41.667 0.00 0.00 0.00 3.72
1581 2118 2.766828 GCCTACTACCCTCATCAACTGT 59.233 50.000 0.00 0.00 0.00 3.55
2078 2615 1.732259 GTGCATTACAGGGTCTTCACG 59.268 52.381 0.00 0.00 0.00 4.35
2091 2628 5.047660 GGTTTTGGATAGTGGTTGTGCATTA 60.048 40.000 0.00 0.00 0.00 1.90
2120 2657 7.038154 TCTAAAACCATTGACTTGAAACCTG 57.962 36.000 0.00 0.00 0.00 4.00
2132 2669 6.405278 ACCCTGAACTTTCTAAAACCATTG 57.595 37.500 0.00 0.00 0.00 2.82
2321 2859 1.467734 CCTGAAGCTCAACATCACTGC 59.532 52.381 0.00 0.00 0.00 4.40
2485 3023 6.939163 AGATGACAAATCTGTATCATTAGCCC 59.061 38.462 0.00 0.00 35.30 5.19
2503 3041 6.009589 ACCATTTGTTTACCATCAGATGACA 58.990 36.000 12.41 5.32 30.90 3.58
2583 4899 2.166254 AGCCCAGCAAATCCAAAATACG 59.834 45.455 0.00 0.00 0.00 3.06
2584 4900 3.893326 AGCCCAGCAAATCCAAAATAC 57.107 42.857 0.00 0.00 0.00 1.89
2585 4901 4.285517 TGAAAGCCCAGCAAATCCAAAATA 59.714 37.500 0.00 0.00 0.00 1.40
2586 4902 3.072768 TGAAAGCCCAGCAAATCCAAAAT 59.927 39.130 0.00 0.00 0.00 1.82
2723 5039 6.131961 AGGGAAAATGAGCTTAGCACAATAT 58.868 36.000 8.57 0.00 32.39 1.28
2840 5156 2.679059 GCTGTGCTATCTCTCTGGCAAA 60.679 50.000 0.00 0.00 36.43 3.68
2872 5188 7.591006 ACACGTATAAGTTTTATCACTGTGG 57.409 36.000 8.11 0.00 0.00 4.17
2897 5213 4.322801 CGAAACCTGAAAGAGGGTACAGAT 60.323 45.833 0.00 0.00 43.30 2.90
2936 5252 0.036388 CTGCCGCCTTTTCTGGTAGA 60.036 55.000 0.00 0.00 37.66 2.59
3094 5410 4.583907 GCTTAGGTTCTAGTATCCGAGGTT 59.416 45.833 0.00 0.00 0.00 3.50
3164 5481 1.043116 TACTCCAGGGACCTCGCATG 61.043 60.000 0.00 0.00 0.00 4.06
3349 5666 5.292101 CACGACTGAAAAGGATTCCATAGAC 59.708 44.000 5.29 0.00 0.00 2.59
3658 5987 6.129414 TGTAAACATTTAGGGCTGGACTTA 57.871 37.500 0.00 0.00 0.00 2.24
3679 6008 5.477984 AGATGTTGCAATGGTACTTGAATGT 59.522 36.000 0.59 0.00 0.00 2.71
3715 6044 1.603802 GCAGTGCAGCAACTAGAAACA 59.396 47.619 11.09 0.00 0.00 2.83
3722 6051 1.152902 TGGAAGCAGTGCAGCAACT 60.153 52.632 19.20 0.00 36.85 3.16
3760 6089 8.620116 TCAGATGTAACAAAGTGATCATTGAA 57.380 30.769 14.50 1.65 0.00 2.69
3833 6162 0.681175 GCAGCCCAACAACCAGAAAT 59.319 50.000 0.00 0.00 0.00 2.17
3847 6176 3.367395 GGATTGTAGTTTTGGAAGCAGCC 60.367 47.826 0.00 0.00 0.00 4.85
3982 6317 4.982241 AGAGGGAACTTCATTGTTGAGA 57.018 40.909 0.00 0.00 44.43 3.27


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

AutoCloner maintained by Alex Coulton.