Multiple sequence alignment - TraesCS3D01G019200

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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 TraesCS3D01G019200 chr3D 100.000 3613 0 0 1 3613 6428393 6432005 0.000000e+00 6673.0
1 TraesCS3D01G019200 chr3D 88.414 889 101 2 1027 1914 3614143 3613256 0.000000e+00 1070.0
2 TraesCS3D01G019200 chr3D 87.459 606 70 4 1920 2519 3608294 3607689 0.000000e+00 693.0
3 TraesCS3D01G019200 chr3D 93.011 186 11 2 3365 3548 292060025 292060210 1.650000e-68 270.0
4 TraesCS3D01G019200 chr3D 95.000 40 2 0 3049 3088 134518900 134518861 3.010000e-06 63.9
5 TraesCS3D01G019200 chr3B 94.372 2843 135 11 778 3613 6963496 6960672 0.000000e+00 4340.0
6 TraesCS3D01G019200 chr3B 91.137 519 31 9 1 511 6964304 6963793 0.000000e+00 689.0
7 TraesCS3D01G019200 chr3B 90.863 197 16 2 3354 3548 92288698 92288502 2.770000e-66 263.0
8 TraesCS3D01G019200 chr3B 95.349 129 5 1 3240 3367 101924001 101923873 1.700000e-48 204.0
9 TraesCS3D01G019200 chr3B 93.548 124 8 0 648 771 6963660 6963537 6.160000e-43 185.0
10 TraesCS3D01G019200 chr3B 97.059 34 1 0 966 999 6963423 6963456 1.400000e-04 58.4
11 TraesCS3D01G019200 chr3B 96.875 32 0 1 599 629 6963696 6963665 7.000000e-03 52.8
12 TraesCS3D01G019200 chr3A 92.130 864 59 5 1748 2611 13849611 13848757 0.000000e+00 1210.0
13 TraesCS3D01G019200 chr3A 90.858 536 29 11 1 522 13850369 13849840 0.000000e+00 701.0
14 TraesCS3D01G019200 chr3A 92.908 141 9 1 2604 2743 13848732 13848592 1.700000e-48 204.0
15 TraesCS3D01G019200 chr3A 88.166 169 5 4 541 695 13849785 13849618 1.710000e-43 187.0
16 TraesCS3D01G019200 chr1D 78.451 1420 281 15 1091 2487 33595840 33597257 0.000000e+00 904.0
17 TraesCS3D01G019200 chr1D 74.305 899 200 23 1603 2480 4623699 4624587 5.740000e-93 351.0
18 TraesCS3D01G019200 chr1D 93.103 232 16 0 2817 3048 254419468 254419237 1.240000e-89 340.0
19 TraesCS3D01G019200 chr2B 78.380 1420 282 14 1091 2487 742172650 742171233 0.000000e+00 898.0
20 TraesCS3D01G019200 chr2D 77.746 1420 291 14 1091 2487 608578315 608576898 0.000000e+00 848.0
21 TraesCS3D01G019200 chr2D 93.966 232 14 0 2817 3048 33936549 33936318 5.740000e-93 351.0
22 TraesCS3D01G019200 chr2D 93.562 233 14 1 2817 3048 630273024 630272792 2.670000e-91 346.0
23 TraesCS3D01G019200 chr2D 85.714 105 11 3 65 166 544190852 544190955 1.370000e-19 108.0
24 TraesCS3D01G019200 chr4B 77.013 1453 293 24 1057 2478 663902041 663903483 0.000000e+00 795.0
25 TraesCS3D01G019200 chr4B 78.165 1264 254 15 1057 2303 664677742 664679000 0.000000e+00 785.0
26 TraesCS3D01G019200 chr6A 76.849 1460 300 24 1058 2488 604505105 604506555 0.000000e+00 789.0
27 TraesCS3D01G019200 chr6A 92.473 186 12 2 3365 3548 84401488 84401303 7.690000e-67 265.0
28 TraesCS3D01G019200 chrUn 93.966 232 14 0 2817 3048 452651248 452651017 5.740000e-93 351.0
29 TraesCS3D01G019200 chrUn 93.534 232 15 0 2817 3048 114878673 114878904 2.670000e-91 346.0
30 TraesCS3D01G019200 chrUn 95.312 128 6 0 3240 3367 423338204 423338331 1.700000e-48 204.0
31 TraesCS3D01G019200 chr5B 93.966 232 14 0 2817 3048 429039349 429039118 5.740000e-93 351.0
32 TraesCS3D01G019200 chr5B 94.615 130 5 1 3240 3367 57516000 57516129 2.200000e-47 200.0
33 TraesCS3D01G019200 chr5A 93.966 232 14 0 2817 3048 482026670 482026901 5.740000e-93 351.0
34 TraesCS3D01G019200 chr5A 93.011 186 11 2 3365 3548 330319734 330319549 1.650000e-68 270.0
35 TraesCS3D01G019200 chr2A 93.966 232 14 0 2817 3048 14162744 14162975 5.740000e-93 351.0
36 TraesCS3D01G019200 chr2A 81.905 105 15 3 70 171 774622100 774622203 6.430000e-13 86.1
37 TraesCS3D01G019200 chr2A 84.127 63 9 1 124 186 428868921 428868860 3.900000e-05 60.2
38 TraesCS3D01G019200 chr7A 93.011 186 11 2 3365 3548 699867646 699867831 1.650000e-68 270.0
39 TraesCS3D01G019200 chr4D 93.011 186 11 2 3365 3548 490364084 490363899 1.650000e-68 270.0
40 TraesCS3D01G019200 chr6D 92.473 186 12 2 3365 3548 168262655 168262470 7.690000e-67 265.0
41 TraesCS3D01G019200 chr5D 92.473 186 12 2 3365 3548 432398869 432399054 7.690000e-67 265.0
42 TraesCS3D01G019200 chr5D 95.312 128 6 0 3240 3367 503338564 503338437 1.700000e-48 204.0
43 TraesCS3D01G019200 chr5D 94.531 128 7 0 3240 3367 6254159 6254286 7.910000e-47 198.0
44 TraesCS3D01G019200 chr7D 95.312 128 6 0 3240 3367 530709389 530709262 1.700000e-48 204.0
45 TraesCS3D01G019200 chr1B 95.312 128 6 0 3240 3367 633716097 633715970 1.700000e-48 204.0
46 TraesCS3D01G019200 chr7B 95.312 128 5 1 3240 3367 662755909 662756035 6.120000e-48 202.0


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 TraesCS3D01G019200 chr3D 6428393 6432005 3612 False 6673.0 6673 100.0000 1 3613 1 chr3D.!!$F1 3612
1 TraesCS3D01G019200 chr3D 3613256 3614143 887 True 1070.0 1070 88.4140 1027 1914 1 chr3D.!!$R2 887
2 TraesCS3D01G019200 chr3D 3607689 3608294 605 True 693.0 693 87.4590 1920 2519 1 chr3D.!!$R1 599
3 TraesCS3D01G019200 chr3B 6960672 6964304 3632 True 1316.7 4340 93.9830 1 3613 4 chr3B.!!$R3 3612
4 TraesCS3D01G019200 chr3A 13848592 13850369 1777 True 575.5 1210 91.0155 1 2743 4 chr3A.!!$R1 2742
5 TraesCS3D01G019200 chr1D 33595840 33597257 1417 False 904.0 904 78.4510 1091 2487 1 chr1D.!!$F2 1396
6 TraesCS3D01G019200 chr1D 4623699 4624587 888 False 351.0 351 74.3050 1603 2480 1 chr1D.!!$F1 877
7 TraesCS3D01G019200 chr2B 742171233 742172650 1417 True 898.0 898 78.3800 1091 2487 1 chr2B.!!$R1 1396
8 TraesCS3D01G019200 chr2D 608576898 608578315 1417 True 848.0 848 77.7460 1091 2487 1 chr2D.!!$R2 1396
9 TraesCS3D01G019200 chr4B 663902041 663903483 1442 False 795.0 795 77.0130 1057 2478 1 chr4B.!!$F1 1421
10 TraesCS3D01G019200 chr4B 664677742 664679000 1258 False 785.0 785 78.1650 1057 2303 1 chr4B.!!$F2 1246
11 TraesCS3D01G019200 chr6A 604505105 604506555 1450 False 789.0 789 76.8490 1058 2488 1 chr6A.!!$F1 1430

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
767 857 0.401356 TCTCAAGGTTCATGCCAGCA 59.599 50.0 0.0 0.0 0.00 4.41 F
1269 1393 0.460284 CGTCAGTGGTGCCTGGTATC 60.460 60.0 0.0 0.0 33.14 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 2077 0.107993 CATGCTGATGGAGTCCACGT 60.108 55.0 15.86 0.00 35.8 4.49 R
2940 3128 1.171308 GTGTACGAGCTAGTCCCACA 58.829 55.0 18.53 9.89 0.0 4.17 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
114 119 9.755064 AAAATTGATATTGTTCGAAAGTACTCG 57.245 29.630 0.00 0.00 40.25 4.18
115 120 8.475331 AATTGATATTGTTCGAAAGTACTCGT 57.525 30.769 0.00 0.00 39.84 4.18
116 121 7.878477 TTGATATTGTTCGAAAGTACTCGTT 57.122 32.000 0.00 0.00 39.84 3.85
283 296 2.602217 CGCAACGATTAAGGGCTAATGC 60.602 50.000 0.00 0.00 38.76 3.56
311 324 2.138596 AGTGCACCAATTTTGAAGCG 57.861 45.000 14.63 0.00 32.79 4.68
318 331 3.674753 CACCAATTTTGAAGCGAATGGAC 59.325 43.478 0.00 0.00 0.00 4.02
319 332 3.320541 ACCAATTTTGAAGCGAATGGACA 59.679 39.130 0.00 0.00 0.00 4.02
322 335 1.896220 TTTGAAGCGAATGGACAGCT 58.104 45.000 0.00 0.00 43.90 4.24
327 340 2.231215 AGCGAATGGACAGCTGTATC 57.769 50.000 21.73 15.61 40.07 2.24
423 436 5.952947 TGGAGTCCAAACCTTTTAAACTTGA 59.047 36.000 10.20 0.00 0.00 3.02
424 437 6.609616 TGGAGTCCAAACCTTTTAAACTTGAT 59.390 34.615 10.20 0.00 0.00 2.57
577 628 2.032681 GTTGCTTCGGTGCCTCCT 59.967 61.111 0.00 0.00 0.00 3.69
629 706 3.502123 TTGGGTCTCCGTCAAAATCTT 57.498 42.857 0.00 0.00 35.24 2.40
633 710 3.596214 GGTCTCCGTCAAAATCTTGCTA 58.404 45.455 0.00 0.00 32.14 3.49
634 711 3.619038 GGTCTCCGTCAAAATCTTGCTAG 59.381 47.826 0.00 0.00 32.14 3.42
635 712 3.062774 GTCTCCGTCAAAATCTTGCTAGC 59.937 47.826 8.10 8.10 32.14 3.42
636 713 3.055819 TCTCCGTCAAAATCTTGCTAGCT 60.056 43.478 17.23 0.00 32.14 3.32
637 714 4.159693 TCTCCGTCAAAATCTTGCTAGCTA 59.840 41.667 17.23 7.59 32.14 3.32
638 715 5.023533 TCCGTCAAAATCTTGCTAGCTAT 57.976 39.130 17.23 4.14 32.14 2.97
639 716 5.050490 TCCGTCAAAATCTTGCTAGCTATC 58.950 41.667 17.23 0.00 32.14 2.08
640 717 5.053145 CCGTCAAAATCTTGCTAGCTATCT 58.947 41.667 17.23 0.00 32.14 1.98
641 718 5.525378 CCGTCAAAATCTTGCTAGCTATCTT 59.475 40.000 17.23 2.08 32.14 2.40
642 719 6.292596 CCGTCAAAATCTTGCTAGCTATCTTC 60.293 42.308 17.23 0.00 32.14 2.87
643 720 6.256539 CGTCAAAATCTTGCTAGCTATCTTCA 59.743 38.462 17.23 0.00 32.14 3.02
644 721 7.042187 CGTCAAAATCTTGCTAGCTATCTTCAT 60.042 37.037 17.23 0.00 32.14 2.57
645 722 8.281893 GTCAAAATCTTGCTAGCTATCTTCATC 58.718 37.037 17.23 0.00 32.14 2.92
646 723 7.443575 TCAAAATCTTGCTAGCTATCTTCATCC 59.556 37.037 17.23 0.00 32.14 3.51
730 820 9.765795 AGATAATTTCGGAGATGTTAGGTTAAG 57.234 33.333 0.00 0.00 35.04 1.85
734 824 5.733620 TCGGAGATGTTAGGTTAAGTGTT 57.266 39.130 0.00 0.00 0.00 3.32
748 838 1.767759 AGTGTTTTTGCTGGCTCTGT 58.232 45.000 0.00 0.00 0.00 3.41
753 843 2.346766 TTTTGCTGGCTCTGTCTCAA 57.653 45.000 0.00 0.00 0.00 3.02
762 852 1.736681 GCTCTGTCTCAAGGTTCATGC 59.263 52.381 0.00 0.00 0.00 4.06
763 853 2.354259 CTCTGTCTCAAGGTTCATGCC 58.646 52.381 0.00 0.00 0.00 4.40
767 857 0.401356 TCTCAAGGTTCATGCCAGCA 59.599 50.000 0.00 0.00 0.00 4.41
816 940 8.217111 ACCTGGGACATGAACAAAATTTAAATT 58.783 29.630 7.64 7.64 38.20 1.82
909 1033 6.041637 GTCACATGGTATGTATGGAGTCCTTA 59.958 42.308 11.33 5.64 42.70 2.69
916 1040 6.015265 GGTATGTATGGAGTCCTTAGTCCTTC 60.015 46.154 11.33 0.00 44.55 3.46
957 1081 0.966920 AGAGAGGTACGTGTTGGTGG 59.033 55.000 0.00 0.00 0.00 4.61
1062 1186 4.115199 GAGCGGCCACCCTTCCAT 62.115 66.667 2.24 0.00 0.00 3.41
1266 1390 4.626081 GCGTCAGTGGTGCCTGGT 62.626 66.667 0.00 0.00 33.14 4.00
1269 1393 0.460284 CGTCAGTGGTGCCTGGTATC 60.460 60.000 0.00 0.00 33.14 2.24
1299 1423 1.172180 CCAGCCCAAACTTCTTCGCA 61.172 55.000 0.00 0.00 0.00 5.10
1422 1546 4.827087 ATGGAGGTGCTCGCGCTG 62.827 66.667 5.56 0.00 36.97 5.18
1588 1724 3.739613 GGAGTGGGGCCGGGATTT 61.740 66.667 2.18 0.00 0.00 2.17
1680 1816 2.706890 GACCCTACAAATTTCCGCTCA 58.293 47.619 0.00 0.00 0.00 4.26
1926 2063 1.071471 AGAGTTTCGGCACCACCTG 59.929 57.895 0.00 0.00 35.61 4.00
1986 2123 1.889105 CAAGTGGCTGCTCACGTGT 60.889 57.895 16.51 8.27 40.49 4.49
1998 2135 1.068083 CACGTGTCTGGACTGCACT 59.932 57.895 7.58 0.00 0.00 4.40
2308 2447 1.078214 TGCTTCAGGATCAAGGCGG 60.078 57.895 0.00 0.00 0.00 6.13
2496 2644 3.129462 TCATCAGGAAGACGATCAGTGAC 59.871 47.826 0.00 0.00 0.00 3.67
2529 2680 3.971150 AGTTCACTATCGACTATGCAGC 58.029 45.455 0.00 0.00 0.00 5.25
2530 2681 3.053455 GTTCACTATCGACTATGCAGCC 58.947 50.000 0.00 0.00 0.00 4.85
2531 2682 1.266989 TCACTATCGACTATGCAGCCG 59.733 52.381 0.00 0.00 0.00 5.52
2532 2683 1.001268 CACTATCGACTATGCAGCCGT 60.001 52.381 0.00 0.00 0.00 5.68
2533 2684 1.001268 ACTATCGACTATGCAGCCGTG 60.001 52.381 0.00 0.00 0.00 4.94
2534 2685 1.266989 CTATCGACTATGCAGCCGTGA 59.733 52.381 0.00 0.00 0.00 4.35
2535 2686 0.031314 ATCGACTATGCAGCCGTGAG 59.969 55.000 0.00 0.00 0.00 3.51
2536 2687 2.233654 CGACTATGCAGCCGTGAGC 61.234 63.158 0.00 0.00 44.25 4.26
2546 2697 2.509336 CCGTGAGCCCGTGACATC 60.509 66.667 0.00 0.00 0.00 3.06
2556 2707 3.005897 AGCCCGTGACATCACATATCTAC 59.994 47.826 12.32 0.00 46.75 2.59
2564 2715 5.109662 ACATCACATATCTACGGTCTTCG 57.890 43.478 0.00 0.00 45.88 3.79
2565 2716 3.620929 TCACATATCTACGGTCTTCGC 57.379 47.619 0.00 0.00 43.89 4.70
2568 2719 4.097437 TCACATATCTACGGTCTTCGCTTT 59.903 41.667 0.00 0.00 43.89 3.51
2732 2920 6.823689 GGTAATACTTGGTGTCTGATGTTCAT 59.176 38.462 0.00 0.00 0.00 2.57
2767 2955 7.913674 TGTTGTTATTGCATACACTCATACA 57.086 32.000 0.00 0.00 0.00 2.29
2825 3013 8.491045 TTTTCCCAGAGAAATCCACTTAAAAT 57.509 30.769 0.00 0.00 43.93 1.82
2857 3045 3.559242 GCAGGCAGATTCACATCTCTTAC 59.441 47.826 0.00 0.00 37.71 2.34
2861 3049 5.046014 AGGCAGATTCACATCTCTTACAACT 60.046 40.000 0.00 0.00 37.71 3.16
2884 3072 1.256376 CACAATCTTCGATTCTCGGCG 59.744 52.381 0.00 0.00 40.88 6.46
3080 3268 3.318839 TCATGTCCAAGCCAAAGAACTTG 59.681 43.478 0.00 0.00 42.35 3.16
3083 3271 0.033920 CCAAGCCAAAGAACTTGCCC 59.966 55.000 0.00 0.00 41.56 5.36
3121 3309 2.224042 TGATGATTGGGACGAGATTCCG 60.224 50.000 0.00 0.00 36.38 4.30
3158 3346 4.702831 GAAAAGCTTGGTTTCCATTTGGA 58.297 39.130 0.00 0.00 43.73 3.53
3170 3358 7.339212 TGGTTTCCATTTGGATTGTAGATGTAG 59.661 37.037 0.00 0.00 44.98 2.74
3171 3359 6.942532 TTCCATTTGGATTGTAGATGTAGC 57.057 37.500 0.00 0.00 44.98 3.58
3192 3381 3.442625 GCCAACCCACTATTAAGGACAAC 59.557 47.826 0.00 0.00 0.00 3.32
3201 3390 7.388500 CCCACTATTAAGGACAACGTAGAAAAA 59.612 37.037 0.00 0.00 0.00 1.94
3248 3438 6.864685 TGTAAAGATCTTCATTGCTGCAAAAG 59.135 34.615 20.06 18.15 0.00 2.27
3249 3439 5.717078 AAGATCTTCATTGCTGCAAAAGA 57.283 34.783 23.94 23.94 28.93 2.52
3250 3440 5.717078 AGATCTTCATTGCTGCAAAAGAA 57.283 34.783 24.94 24.04 28.43 2.52
3251 3441 6.092955 AGATCTTCATTGCTGCAAAAGAAA 57.907 33.333 24.94 18.16 28.43 2.52
3310 3500 5.163258 CCTCCATGGATTCACCTATATAGGC 60.163 48.000 26.01 11.04 42.19 3.93
3365 3555 7.771361 TGAATACCGCTTGTAAATAATCCAAGA 59.229 33.333 0.00 0.00 38.23 3.02
3432 3622 1.542915 TCTGTTACCGCGAAAGTAGCT 59.457 47.619 8.23 0.00 0.00 3.32
3433 3623 1.654105 CTGTTACCGCGAAAGTAGCTG 59.346 52.381 8.23 4.05 0.00 4.24
3434 3624 1.000060 TGTTACCGCGAAAGTAGCTGT 60.000 47.619 8.23 0.00 36.15 4.40
3435 3625 2.064014 GTTACCGCGAAAGTAGCTGTT 58.936 47.619 8.23 0.00 34.13 3.16
3436 3626 1.986698 TACCGCGAAAGTAGCTGTTC 58.013 50.000 8.23 0.00 34.13 3.18
3437 3627 0.032952 ACCGCGAAAGTAGCTGTTCA 59.967 50.000 8.23 0.00 0.00 3.18
3438 3628 0.716108 CCGCGAAAGTAGCTGTTCAG 59.284 55.000 8.23 0.00 0.00 3.02
3458 3648 1.336240 GCTTCAGCCACGCAAATTCTT 60.336 47.619 0.00 0.00 34.31 2.52
3473 3663 7.872483 ACGCAAATTCTTGATGTTCCTTTTTAT 59.128 29.630 0.00 0.00 34.14 1.40
3494 3684 3.829886 TTCTCATCAAACGAATGGCAC 57.170 42.857 0.00 0.00 0.00 5.01
3510 3700 4.156455 TGGCACCTTCATCTAGAAATCC 57.844 45.455 0.00 0.00 35.40 3.01
3533 3723 8.613060 TCCTAGCTATTCTAAGCATGATTTTG 57.387 34.615 0.00 0.00 45.30 2.44
3561 3751 6.998968 ATCTCCTTGCACTAGATTTTCTTG 57.001 37.500 0.00 0.00 0.00 3.02
3577 3767 9.539194 AGATTTTCTTGTCATTATTTCCTTCCT 57.461 29.630 0.00 0.00 0.00 3.36
3579 3769 8.940397 TTTTCTTGTCATTATTTCCTTCCTCT 57.060 30.769 0.00 0.00 0.00 3.69
3582 3772 9.838339 TTCTTGTCATTATTTCCTTCCTCTATC 57.162 33.333 0.00 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.350357 GATAGTCGTGATGTTAAGTTCTACAAA 57.650 33.333 0.00 0.00 0.00 2.83
114 119 7.789341 TGTTTGCATATTATGTTCGTTGAAC 57.211 32.000 5.60 2.80 42.26 3.18
115 120 8.803201 TTTGTTTGCATATTATGTTCGTTGAA 57.197 26.923 5.60 0.00 0.00 2.69
116 121 8.695284 GTTTTGTTTGCATATTATGTTCGTTGA 58.305 29.630 5.60 0.00 0.00 3.18
184 192 8.417273 TCATGCCATTTCATATCATCTCAAAT 57.583 30.769 0.00 0.00 0.00 2.32
202 210 2.204136 ACCCCACCTCTCATGCCA 60.204 61.111 0.00 0.00 0.00 4.92
283 296 8.586570 TTCAAAATTGGTGCACTAGTTTATTG 57.413 30.769 21.01 16.79 0.00 1.90
298 311 3.911868 TGTCCATTCGCTTCAAAATTGG 58.088 40.909 0.00 0.00 0.00 3.16
306 319 2.010145 TACAGCTGTCCATTCGCTTC 57.990 50.000 25.56 0.00 0.00 3.86
327 340 1.573829 GGGCACACACGTACACATGG 61.574 60.000 0.00 0.00 0.00 3.66
441 455 1.138859 GCTTGGTTTGAAGCCACCTTT 59.861 47.619 0.00 0.00 42.23 3.11
538 560 3.005684 CCAAGGAACAGTGCAATAAAGCA 59.994 43.478 0.00 0.00 43.35 3.91
544 595 1.069049 GCAACCAAGGAACAGTGCAAT 59.931 47.619 0.00 0.00 0.00 3.56
629 706 3.384789 ACGTTGGATGAAGATAGCTAGCA 59.615 43.478 18.83 3.19 0.00 3.49
633 710 3.895232 ACACGTTGGATGAAGATAGCT 57.105 42.857 0.00 0.00 0.00 3.32
634 711 5.050091 CCATAACACGTTGGATGAAGATAGC 60.050 44.000 0.00 0.00 34.81 2.97
635 712 5.050091 GCCATAACACGTTGGATGAAGATAG 60.050 44.000 8.20 0.00 34.81 2.08
636 713 4.814234 GCCATAACACGTTGGATGAAGATA 59.186 41.667 8.20 0.00 34.81 1.98
637 714 3.627577 GCCATAACACGTTGGATGAAGAT 59.372 43.478 8.20 0.00 34.81 2.40
638 715 3.006940 GCCATAACACGTTGGATGAAGA 58.993 45.455 8.20 0.00 34.81 2.87
639 716 2.097466 GGCCATAACACGTTGGATGAAG 59.903 50.000 8.20 0.00 34.81 3.02
640 717 2.088423 GGCCATAACACGTTGGATGAA 58.912 47.619 8.20 0.00 34.81 2.57
641 718 1.280710 AGGCCATAACACGTTGGATGA 59.719 47.619 5.01 0.00 34.81 2.92
642 719 1.750193 AGGCCATAACACGTTGGATG 58.250 50.000 5.01 1.15 34.81 3.51
643 720 2.507407 AAGGCCATAACACGTTGGAT 57.493 45.000 5.01 0.00 34.81 3.41
644 721 2.279935 AAAGGCCATAACACGTTGGA 57.720 45.000 5.01 0.00 34.81 3.53
645 722 2.609244 CCAAAAGGCCATAACACGTTGG 60.609 50.000 5.01 0.00 36.03 3.77
646 723 2.609244 CCCAAAAGGCCATAACACGTTG 60.609 50.000 5.01 0.00 0.00 4.10
730 820 1.678101 AGACAGAGCCAGCAAAAACAC 59.322 47.619 0.00 0.00 0.00 3.32
734 824 2.224606 CTTGAGACAGAGCCAGCAAAA 58.775 47.619 0.00 0.00 0.00 2.44
748 838 0.401356 TGCTGGCATGAACCTTGAGA 59.599 50.000 0.00 0.00 0.00 3.27
763 853 3.696051 ACCTAATTTGCTACCACATGCTG 59.304 43.478 0.00 0.00 0.00 4.41
767 857 3.023832 GGCACCTAATTTGCTACCACAT 58.976 45.455 0.92 0.00 40.07 3.21
771 861 2.165641 GGTTGGCACCTAATTTGCTACC 59.834 50.000 0.92 5.47 40.44 3.18
772 862 3.503827 GGTTGGCACCTAATTTGCTAC 57.496 47.619 0.92 0.76 40.44 3.58
816 940 5.163205 CCCATCTCATTGGTACTATCCACAA 60.163 44.000 0.00 0.00 37.20 3.33
824 948 1.212935 GGCACCCATCTCATTGGTACT 59.787 52.381 0.00 0.00 34.77 2.73
862 986 3.047796 CTCACAGCAAAAGCAACACATC 58.952 45.455 0.00 0.00 0.00 3.06
890 1014 5.103215 AGGACTAAGGACTCCATACATACCA 60.103 44.000 0.00 0.00 0.00 3.25
909 1033 6.391479 AGAGTAGTACAACTAGGAAGGACT 57.609 41.667 2.52 0.00 30.12 3.85
957 1081 2.026636 TGGGTGCCTTGATTGGTACTAC 60.027 50.000 0.00 0.00 41.50 2.73
1049 1173 2.043953 GTGGATGGAAGGGTGGCC 60.044 66.667 0.00 0.00 0.00 5.36
1062 1186 0.109919 CGTCATCGTCGTTGAGTGGA 60.110 55.000 6.25 0.00 0.00 4.02
1251 1375 0.613260 TGATACCAGGCACCACTGAC 59.387 55.000 0.00 0.00 40.97 3.51
1266 1390 1.299648 GCTGGCCCAGTGTGTGATA 59.700 57.895 13.35 0.00 33.43 2.15
1588 1724 2.104859 CGTAGACGGCGAGGTCTGA 61.105 63.158 16.62 0.00 46.34 3.27
1666 1802 2.896685 TGGGAATTGAGCGGAAATTTGT 59.103 40.909 0.00 0.00 0.00 2.83
1940 2077 0.107993 CATGCTGATGGAGTCCACGT 60.108 55.000 15.86 0.00 35.80 4.49
1986 2123 1.123861 AGAGGCAAGTGCAGTCCAGA 61.124 55.000 5.52 0.00 44.36 3.86
1998 2135 0.735978 CATCACGCACGTAGAGGCAA 60.736 55.000 0.00 0.00 0.00 4.52
2248 2386 2.259618 CACGACAATCTCGAACCGATT 58.740 47.619 0.00 0.00 46.14 3.34
2308 2447 1.227674 CATCCGCCCTAACTCCAGC 60.228 63.158 0.00 0.00 0.00 4.85
2529 2680 2.509336 GATGTCACGGGCTCACGG 60.509 66.667 0.00 0.00 38.39 4.94
2530 2681 2.094659 GTGATGTCACGGGCTCACG 61.095 63.158 0.00 0.00 37.10 4.35
2531 2682 3.876300 GTGATGTCACGGGCTCAC 58.124 61.111 0.00 0.18 37.10 3.51
2546 2697 3.627732 AGCGAAGACCGTAGATATGTG 57.372 47.619 0.00 0.00 41.15 3.21
2607 2789 7.129622 TCACGAGTCAAAACAAATGTTCATAC 58.870 34.615 0.00 0.00 37.25 2.39
2622 2804 5.571285 AGCTATATATCCCTCACGAGTCAA 58.429 41.667 0.00 0.00 0.00 3.18
2732 2920 6.324561 TGCAATAACAACATAACAGCTCAA 57.675 33.333 0.00 0.00 0.00 3.02
2767 2955 8.432805 CCTAGTGACAGATTAATACAATTCCCT 58.567 37.037 0.00 0.00 0.00 4.20
2800 2988 7.906199 TTTTAAGTGGATTTCTCTGGGAAAA 57.094 32.000 6.82 0.00 45.56 2.29
2804 2992 8.844244 CAGATATTTTAAGTGGATTTCTCTGGG 58.156 37.037 0.00 0.00 0.00 4.45
2808 2996 8.552034 CCGACAGATATTTTAAGTGGATTTCTC 58.448 37.037 0.00 0.00 0.00 2.87
2857 3045 5.852005 GAGAATCGAAGATTGTGTGAGTTG 58.148 41.667 0.00 0.00 45.12 3.16
2901 3089 4.439253 ACCCTAGGATGAATGTAAAGCC 57.561 45.455 11.48 0.00 0.00 4.35
2911 3099 9.837681 TGTATTAGAAATGATACCCTAGGATGA 57.162 33.333 11.48 0.00 0.00 2.92
2940 3128 1.171308 GTGTACGAGCTAGTCCCACA 58.829 55.000 18.53 9.89 0.00 4.17
2941 3129 1.171308 TGTGTACGAGCTAGTCCCAC 58.829 55.000 17.33 17.33 0.00 4.61
2943 3131 2.426024 TCAATGTGTACGAGCTAGTCCC 59.574 50.000 1.52 0.00 0.00 4.46
3053 3241 3.896888 TCTTTGGCTTGGACATGACATTT 59.103 39.130 0.00 0.00 0.00 2.32
3080 3268 4.616953 TCATTTTTCAGAACTTTTCGGGC 58.383 39.130 0.00 0.00 34.02 6.13
3083 3271 8.430063 CCAATCATCATTTTTCAGAACTTTTCG 58.570 33.333 0.00 0.00 34.02 3.46
3121 3309 5.949233 AGCTTTTCGTGATTCAAAAACAC 57.051 34.783 0.00 0.00 0.00 3.32
3158 3346 3.523564 AGTGGGTTGGCTACATCTACAAT 59.476 43.478 0.80 0.00 0.00 2.71
3170 3358 3.359695 TGTCCTTAATAGTGGGTTGGC 57.640 47.619 0.00 0.00 0.00 4.52
3171 3359 3.687698 CGTTGTCCTTAATAGTGGGTTGG 59.312 47.826 0.00 0.00 0.00 3.77
3224 3414 7.086376 TCTTTTGCAGCAATGAAGATCTTTAC 58.914 34.615 15.50 0.00 0.00 2.01
3280 3470 2.487986 GGTGAATCCATGGAGGGTCATC 60.488 54.545 21.33 18.32 35.28 2.92
3281 3471 1.496429 GGTGAATCCATGGAGGGTCAT 59.504 52.381 21.33 0.00 35.28 3.06
3317 3507 5.982516 TCACGCTCTTATTTTTGCAACATTT 59.017 32.000 0.00 0.00 0.00 2.32
3365 3555 4.445019 GGGAGTCAGAGTCAAAAAGAGGTT 60.445 45.833 7.59 0.00 0.00 3.50
3404 3594 1.788308 TCGCGGTAACAGAAAGAAACG 59.212 47.619 6.13 0.00 0.00 3.60
3432 3622 2.253758 GCGTGGCTGAAGCTGAACA 61.254 57.895 1.74 0.00 41.70 3.18
3433 3623 1.785041 TTGCGTGGCTGAAGCTGAAC 61.785 55.000 1.74 0.00 41.70 3.18
3434 3624 1.100463 TTTGCGTGGCTGAAGCTGAA 61.100 50.000 1.74 0.00 41.70 3.02
3435 3625 0.890542 ATTTGCGTGGCTGAAGCTGA 60.891 50.000 1.74 0.00 41.70 4.26
3436 3626 0.038892 AATTTGCGTGGCTGAAGCTG 60.039 50.000 1.74 0.00 41.70 4.24
3437 3627 0.242017 GAATTTGCGTGGCTGAAGCT 59.758 50.000 1.74 0.00 41.70 3.74
3438 3628 0.242017 AGAATTTGCGTGGCTGAAGC 59.758 50.000 0.00 0.00 41.14 3.86
3473 3663 3.057596 GGTGCCATTCGTTTGATGAGAAA 60.058 43.478 0.00 0.00 0.00 2.52
3494 3684 9.034800 AGAATAGCTAGGATTTCTAGATGAAGG 57.965 37.037 2.96 0.00 46.48 3.46
3510 3700 7.094463 CCCCAAAATCATGCTTAGAATAGCTAG 60.094 40.741 0.00 0.00 41.76 3.42
3533 3723 2.119495 TCTAGTGCAAGGAGATTCCCC 58.881 52.381 0.00 0.00 37.19 4.81


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

AutoCloner maintained by Alex Coulton.