Multiple sequence alignment - TraesCS6D01G221900

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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 TraesCS6D01G221900 chr6D 100.000 3685 0 0 1 3685 312803783 312807467 0.000000e+00 6806.0
1 TraesCS6D01G221900 chr6D 83.390 584 94 3 3103 3684 328336830 328336248 4.190000e-149 538.0
2 TraesCS6D01G221900 chr6D 81.667 540 97 2 2126 2664 14241493 14242031 7.260000e-122 448.0
3 TraesCS6D01G221900 chr6B 91.579 2862 152 40 25 2816 513891078 513888236 0.000000e+00 3868.0
4 TraesCS6D01G221900 chr6B 80.370 540 104 2 2126 2664 26004843 26005381 3.430000e-110 409.0
5 TraesCS6D01G221900 chr6B 79.444 540 102 6 2126 2664 26120787 26120256 1.250000e-99 374.0
6 TraesCS6D01G221900 chr6B 75.649 501 94 20 1093 1582 25976018 25975535 1.330000e-54 224.0
7 TraesCS6D01G221900 chr6A 96.566 2184 50 6 654 2816 449667132 449669311 0.000000e+00 3594.0
8 TraesCS6D01G221900 chr6A 82.994 541 88 4 2126 2664 15542665 15543203 1.540000e-133 486.0
9 TraesCS6D01G221900 chr6A 75.681 514 97 21 1093 1595 15461569 15461073 7.960000e-57 231.0
10 TraesCS6D01G221900 chr7B 85.747 863 104 16 2833 3684 640000263 640001117 0.000000e+00 894.0
11 TraesCS6D01G221900 chr7B 73.921 533 108 22 1067 1586 507141133 507140619 6.280000e-43 185.0
12 TraesCS6D01G221900 chr7B 73.932 468 114 7 2189 2651 507139298 507138834 8.130000e-42 182.0
13 TraesCS6D01G221900 chr5D 85.284 863 102 18 2834 3683 88525600 88526450 0.000000e+00 867.0
14 TraesCS6D01G221900 chr1A 83.546 863 105 23 2835 3684 515123561 515122723 0.000000e+00 773.0
15 TraesCS6D01G221900 chr1A 83.430 863 107 22 2835 3684 514867317 514866478 0.000000e+00 769.0
16 TraesCS6D01G221900 chr1A 80.475 589 112 3 3097 3683 592557788 592557201 7.260000e-122 448.0
17 TraesCS6D01G221900 chr3A 86.228 639 80 6 3051 3684 32887433 32888068 0.000000e+00 686.0
18 TraesCS6D01G221900 chr3A 88.000 175 15 5 2834 3005 32884333 32884504 6.240000e-48 202.0
19 TraesCS6D01G221900 chr3A 75.128 390 71 20 179 557 10527995 10528369 3.810000e-35 159.0
20 TraesCS6D01G221900 chr2D 81.555 862 127 24 2833 3683 633441477 633442317 0.000000e+00 682.0
21 TraesCS6D01G221900 chr2D 83.866 595 93 2 3091 3684 31899919 31900511 6.910000e-157 564.0
22 TraesCS6D01G221900 chr2D 75.798 376 67 10 217 575 605473740 605473372 6.330000e-38 169.0
23 TraesCS6D01G221900 chr2D 87.838 74 9 0 1370 1443 637445258 637445185 1.820000e-13 87.9
24 TraesCS6D01G221900 chr5A 81.607 859 115 29 2834 3681 545640172 545640998 0.000000e+00 671.0
25 TraesCS6D01G221900 chr7D 83.220 590 96 3 3097 3684 3723425 3722837 4.190000e-149 538.0
26 TraesCS6D01G221900 chr7D 73.596 534 108 21 1067 1586 481697519 481697005 1.360000e-39 174.0
27 TraesCS6D01G221900 chr3D 77.857 420 63 16 148 547 322769068 322768659 2.210000e-57 233.0
28 TraesCS6D01G221900 chr3D 74.532 534 107 22 1067 1585 536327450 536327969 4.820000e-49 206.0
29 TraesCS6D01G221900 chr3D 77.953 254 44 10 200 448 305660497 305660251 8.250000e-32 148.0
30 TraesCS6D01G221900 chr3B 75.514 535 100 22 1067 1585 708520793 708520274 2.210000e-57 233.0
31 TraesCS6D01G221900 chr4A 75.829 422 80 13 172 575 717453825 717454242 1.040000e-45 195.0
32 TraesCS6D01G221900 chr4D 80.335 239 38 7 125 358 506691196 506691430 4.890000e-39 172.0
33 TraesCS6D01G221900 chr4D 83.696 92 11 3 401 491 136182323 136182235 2.360000e-12 84.2
34 TraesCS6D01G221900 chr7A 73.843 497 98 20 1103 1586 548585806 548585329 6.330000e-38 169.0
35 TraesCS6D01G221900 chr2B 74.151 383 81 13 202 575 736102673 736102300 3.840000e-30 143.0
36 TraesCS6D01G221900 chr1B 79.592 196 38 2 200 394 411826112 411825918 4.960000e-29 139.0
37 TraesCS6D01G221900 chr2A 87.838 74 9 0 1370 1443 762568427 762568500 1.820000e-13 87.9


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 TraesCS6D01G221900 chr6D 312803783 312807467 3684 False 6806 6806 100.000 1 3685 1 chr6D.!!$F2 3684
1 TraesCS6D01G221900 chr6D 328336248 328336830 582 True 538 538 83.390 3103 3684 1 chr6D.!!$R1 581
2 TraesCS6D01G221900 chr6D 14241493 14242031 538 False 448 448 81.667 2126 2664 1 chr6D.!!$F1 538
3 TraesCS6D01G221900 chr6B 513888236 513891078 2842 True 3868 3868 91.579 25 2816 1 chr6B.!!$R3 2791
4 TraesCS6D01G221900 chr6B 26004843 26005381 538 False 409 409 80.370 2126 2664 1 chr6B.!!$F1 538
5 TraesCS6D01G221900 chr6B 26120256 26120787 531 True 374 374 79.444 2126 2664 1 chr6B.!!$R2 538
6 TraesCS6D01G221900 chr6A 449667132 449669311 2179 False 3594 3594 96.566 654 2816 1 chr6A.!!$F2 2162
7 TraesCS6D01G221900 chr6A 15542665 15543203 538 False 486 486 82.994 2126 2664 1 chr6A.!!$F1 538
8 TraesCS6D01G221900 chr7B 640000263 640001117 854 False 894 894 85.747 2833 3684 1 chr7B.!!$F1 851
9 TraesCS6D01G221900 chr5D 88525600 88526450 850 False 867 867 85.284 2834 3683 1 chr5D.!!$F1 849
10 TraesCS6D01G221900 chr1A 515122723 515123561 838 True 773 773 83.546 2835 3684 1 chr1A.!!$R2 849
11 TraesCS6D01G221900 chr1A 514866478 514867317 839 True 769 769 83.430 2835 3684 1 chr1A.!!$R1 849
12 TraesCS6D01G221900 chr1A 592557201 592557788 587 True 448 448 80.475 3097 3683 1 chr1A.!!$R3 586
13 TraesCS6D01G221900 chr3A 32884333 32888068 3735 False 444 686 87.114 2834 3684 2 chr3A.!!$F2 850
14 TraesCS6D01G221900 chr2D 633441477 633442317 840 False 682 682 81.555 2833 3683 1 chr2D.!!$F2 850
15 TraesCS6D01G221900 chr2D 31899919 31900511 592 False 564 564 83.866 3091 3684 1 chr2D.!!$F1 593
16 TraesCS6D01G221900 chr5A 545640172 545640998 826 False 671 671 81.607 2834 3681 1 chr5A.!!$F1 847
17 TraesCS6D01G221900 chr7D 3722837 3723425 588 True 538 538 83.220 3097 3684 1 chr7D.!!$R1 587
18 TraesCS6D01G221900 chr3D 536327450 536327969 519 False 206 206 74.532 1067 1585 1 chr3D.!!$F1 518
19 TraesCS6D01G221900 chr3B 708520274 708520793 519 True 233 233 75.514 1067 1585 1 chr3B.!!$R1 518

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
143 144 0.172578 CAGTTGTCCATCCTACGCGA 59.827 55.0 15.93 0.0 0.00 5.87 F
358 359 0.250553 TGCACCTTTACTTCACGGGG 60.251 55.0 0.00 0.0 0.00 5.73 F
614 659 0.321210 TTCACGGATGAATGCGGTGT 60.321 50.0 9.05 0.0 46.28 4.16 F
2218 2307 0.325933 CTGGACATCAGCTTCCACCA 59.674 55.0 0.46 0.0 36.96 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1376 1442 0.257616 CTCGAGGAACCTCTCCCTCT 59.742 60.000 17.18 0.00 46.81 3.69 R
2249 2338 1.154338 GTACTCCGTGGTGTCGTCG 60.154 63.158 0.00 0.00 0.00 5.12 R
2384 2473 4.457496 ACGATCCGCCTGCAGGTG 62.457 66.667 34.93 34.93 45.02 4.00 R
3085 6096 0.321671 CTCCGAAGAGCTGGGTTTCA 59.678 55.000 0.00 0.00 32.13 2.69 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
17 18 4.708386 TCGCGCCGAACCCCAATT 62.708 61.111 0.00 0.00 31.06 2.32
18 19 3.743636 CGCGCCGAACCCCAATTT 61.744 61.111 0.00 0.00 0.00 1.82
19 20 2.654289 GCGCCGAACCCCAATTTT 59.346 55.556 0.00 0.00 0.00 1.82
20 21 1.736282 GCGCCGAACCCCAATTTTG 60.736 57.895 0.00 0.00 0.00 2.44
21 22 1.663173 CGCCGAACCCCAATTTTGT 59.337 52.632 0.00 0.00 0.00 2.83
22 23 0.388006 CGCCGAACCCCAATTTTGTC 60.388 55.000 0.00 0.00 0.00 3.18
23 24 0.388006 GCCGAACCCCAATTTTGTCG 60.388 55.000 0.00 0.00 0.00 4.35
29 30 1.241315 CCCCAATTTTGTCGCCGAGT 61.241 55.000 0.00 0.00 0.00 4.18
42 43 1.649815 CCGAGTAGTAGGCGCTCTG 59.350 63.158 7.64 0.00 0.00 3.35
91 92 1.016627 GCAATGTGAAGGCGATGCTA 58.983 50.000 0.00 0.00 0.00 3.49
116 117 1.800586 CACAGTTGATTGTGGACGAGG 59.199 52.381 0.00 0.00 43.65 4.63
133 134 4.980805 GACGGCGCCAGTTGTCCA 62.981 66.667 28.98 0.00 0.00 4.02
143 144 0.172578 CAGTTGTCCATCCTACGCGA 59.827 55.000 15.93 0.00 0.00 5.87
174 175 2.961893 TTTGGCCGCGTCATAGGGT 61.962 57.895 4.92 0.00 0.00 4.34
205 206 1.153289 CAGCCCCTTCACTCCATCG 60.153 63.158 0.00 0.00 0.00 3.84
208 209 1.221840 CCCCTTCACTCCATCGTGG 59.778 63.158 0.00 0.00 39.43 4.94
215 216 0.826715 CACTCCATCGTGGACCTCAT 59.173 55.000 3.02 0.00 42.67 2.90
217 218 0.826715 CTCCATCGTGGACCTCATGT 59.173 55.000 3.02 0.00 42.67 3.21
236 237 1.344763 GTCCACTAGCAACAGACAGGT 59.655 52.381 0.00 0.00 0.00 4.00
253 254 2.047560 TCGCTGACTCCGACGAGA 60.048 61.111 0.00 0.00 38.52 4.04
272 273 2.441001 AGAATGAGTAGGGCATGGAAGG 59.559 50.000 0.00 0.00 0.00 3.46
307 308 4.733542 CCAAATGGGCCGGTCCGT 62.734 66.667 22.68 19.54 34.94 4.69
329 330 4.468153 GTCTCCCATGTTCTACTCTTCCTT 59.532 45.833 0.00 0.00 0.00 3.36
338 339 0.606604 TACTCTTCCTTGCCGGTGAC 59.393 55.000 1.90 0.00 0.00 3.67
358 359 0.250553 TGCACCTTTACTTCACGGGG 60.251 55.000 0.00 0.00 0.00 5.73
365 366 3.943381 CCTTTACTTCACGGGGTTTATCC 59.057 47.826 0.00 0.00 0.00 2.59
377 378 1.066430 GGTTTATCCCTGTCGCTCACA 60.066 52.381 0.00 0.00 0.00 3.58
387 388 3.114616 CGCTCACAAGGACGGCAG 61.115 66.667 0.00 0.00 0.00 4.85
391 392 0.742281 CTCACAAGGACGGCAGATGG 60.742 60.000 0.00 0.00 0.00 3.51
394 395 0.904865 ACAAGGACGGCAGATGGAGA 60.905 55.000 0.00 0.00 0.00 3.71
399 400 0.460987 GACGGCAGATGGAGAAGGTG 60.461 60.000 0.00 0.00 0.00 4.00
409 426 4.288105 AGATGGAGAAGGTGAACAATGACT 59.712 41.667 0.00 0.00 0.00 3.41
415 432 3.576078 AGGTGAACAATGACTTGGACA 57.424 42.857 0.00 0.00 36.64 4.02
423 440 0.773644 ATGACTTGGACAAGGGCACT 59.226 50.000 15.72 0.00 42.53 4.40
452 469 0.325577 TAGGTTTAGGTCCGGTCCCC 60.326 60.000 14.60 8.31 0.00 4.81
454 471 1.614525 GTTTAGGTCCGGTCCCCCT 60.615 63.158 14.60 11.41 0.00 4.79
475 492 9.214957 CCCCCTTTTTATTTAATGAAAACTGTC 57.785 33.333 3.94 0.00 0.00 3.51
529 546 3.909776 ATATCATTCGGCTTGCATGTG 57.090 42.857 1.14 0.00 0.00 3.21
533 550 2.097954 TCATTCGGCTTGCATGTGATTC 59.902 45.455 1.14 0.00 0.00 2.52
534 551 1.532523 TTCGGCTTGCATGTGATTCA 58.467 45.000 1.14 0.00 0.00 2.57
553 570 7.742089 GTGATTCATTTGACTAGTTGAAACTCG 59.258 37.037 10.85 0.00 40.37 4.18
554 571 6.539649 TTCATTTGACTAGTTGAAACTCGG 57.460 37.500 5.44 0.00 40.37 4.63
557 574 3.299340 TGACTAGTTGAAACTCGGCTC 57.701 47.619 0.00 0.00 40.37 4.70
563 580 2.480419 AGTTGAAACTCGGCTCGAAATG 59.520 45.455 0.00 0.00 34.74 2.32
590 635 4.584325 GCAAATAGCACCAATTCCCTCATA 59.416 41.667 0.00 0.00 44.79 2.15
598 643 4.949238 CACCAATTCCCTCATATGTGTTCA 59.051 41.667 1.90 0.00 0.00 3.18
605 650 3.181466 CCCTCATATGTGTTCACGGATGA 60.181 47.826 1.90 14.39 0.00 2.92
614 659 0.321210 TTCACGGATGAATGCGGTGT 60.321 50.000 9.05 0.00 46.28 4.16
688 734 5.581126 TCCCGCGTCTTTAGTTTATTCTA 57.419 39.130 4.92 0.00 0.00 2.10
787 833 1.542915 ACACAATCTGCAAGCATCACC 59.457 47.619 0.00 0.00 0.00 4.02
892 942 1.598183 CGATTCGACGGTCTGGATCTG 60.598 57.143 6.57 3.62 0.00 2.90
936 999 4.962995 ACACAGTGGTAAGCATATCTAGGT 59.037 41.667 5.31 0.00 0.00 3.08
968 1031 0.874175 CATGGCGCTGCAATTCATGG 60.874 55.000 7.64 0.00 33.60 3.66
1254 1320 2.948720 GCTCCTCCACTTGCTCCGT 61.949 63.158 0.00 0.00 0.00 4.69
1376 1442 2.757508 CAGCTGCGAGGAGGAGGA 60.758 66.667 0.00 0.00 38.88 3.71
1493 1565 2.125912 CGACCCCGTCTTCAGCAG 60.126 66.667 0.00 0.00 0.00 4.24
1829 1901 5.243207 TGCTACCTTTTAGCTTCTTACCAC 58.757 41.667 0.00 0.00 40.95 4.16
1967 2056 1.016653 GGCAGCAGAACGAGGACTTC 61.017 60.000 0.00 0.00 0.00 3.01
2218 2307 0.325933 CTGGACATCAGCTTCCACCA 59.674 55.000 0.46 0.00 36.96 4.17
2688 2784 1.303643 GCCACCACCAGCTAGCTTT 60.304 57.895 16.46 1.42 0.00 3.51
2762 2865 2.838736 AGTGAAGCGTGTTTGATCACT 58.161 42.857 0.00 1.13 44.26 3.41
2816 2919 5.066117 GCATCAATTCATGACTGTGATGACT 59.934 40.000 29.44 1.87 45.44 3.41
2817 2920 6.487103 CATCAATTCATGACTGTGATGACTG 58.513 40.000 24.96 10.05 45.44 3.51
2818 2921 5.554070 TCAATTCATGACTGTGATGACTGT 58.446 37.500 9.50 0.00 36.99 3.55
2819 2922 5.410439 TCAATTCATGACTGTGATGACTGTG 59.590 40.000 9.50 8.18 34.62 3.66
2820 2923 4.605640 TTCATGACTGTGATGACTGTGA 57.394 40.909 9.50 0.00 34.62 3.58
2821 2924 4.813750 TCATGACTGTGATGACTGTGAT 57.186 40.909 5.82 0.00 34.62 3.06
2822 2925 4.501071 TCATGACTGTGATGACTGTGATG 58.499 43.478 13.46 13.46 42.85 3.07
2823 2926 4.221262 TCATGACTGTGATGACTGTGATGA 59.779 41.667 16.95 16.95 45.59 2.92
2824 2927 3.917988 TGACTGTGATGACTGTGATGAC 58.082 45.455 0.00 0.00 34.62 3.06
2825 2928 3.321682 TGACTGTGATGACTGTGATGACA 59.678 43.478 0.00 0.00 34.62 3.58
2826 2929 4.020839 TGACTGTGATGACTGTGATGACAT 60.021 41.667 0.00 0.00 34.62 3.06
2827 2930 4.903054 ACTGTGATGACTGTGATGACATT 58.097 39.130 0.00 0.00 33.33 2.71
2828 2931 6.041423 ACTGTGATGACTGTGATGACATTA 57.959 37.500 0.00 0.00 33.33 1.90
2829 2932 5.871524 ACTGTGATGACTGTGATGACATTAC 59.128 40.000 0.00 3.46 33.33 1.89
2830 2933 6.041423 TGTGATGACTGTGATGACATTACT 57.959 37.500 11.24 0.00 32.93 2.24
2831 2934 6.101997 TGTGATGACTGTGATGACATTACTC 58.898 40.000 11.24 2.97 32.93 2.59
2895 3003 2.290464 ACGAAACCACCGAACATTTGA 58.710 42.857 0.00 0.00 0.00 2.69
2896 3004 2.289547 ACGAAACCACCGAACATTTGAG 59.710 45.455 0.00 0.00 0.00 3.02
2928 3041 0.963355 AGGCGCGCAGGGAAAAATAA 60.963 50.000 34.42 0.00 46.37 1.40
2998 3114 3.554934 TGAAGGAGCAAGAGAGCAAAAA 58.445 40.909 0.00 0.00 36.85 1.94
3000 3116 1.885233 AGGAGCAAGAGAGCAAAAAGC 59.115 47.619 0.00 0.00 46.19 3.51
3040 6043 8.504005 ACAAGTACTACAAACATCAACATTAGC 58.496 33.333 0.00 0.00 0.00 3.09
3041 6044 8.721478 CAAGTACTACAAACATCAACATTAGCT 58.279 33.333 0.00 0.00 0.00 3.32
3085 6096 2.566952 GCAACAGGCGCATCTTTTAT 57.433 45.000 10.83 0.00 0.00 1.40
3086 6097 2.187707 GCAACAGGCGCATCTTTTATG 58.812 47.619 10.83 0.00 0.00 1.90
3087 6098 2.159393 GCAACAGGCGCATCTTTTATGA 60.159 45.455 10.83 0.00 0.00 2.15
3095 6106 3.438360 CGCATCTTTTATGAAACCCAGC 58.562 45.455 0.00 0.00 0.00 4.85
3101 6112 4.695455 TCTTTTATGAAACCCAGCTCTTCG 59.305 41.667 0.00 0.00 0.00 3.79
3130 6144 1.907739 CCATCCCTGAAGCGAGGAA 59.092 57.895 1.34 0.00 34.69 3.36
3182 6196 1.186267 GGTCCGGACACAGGAGAAGT 61.186 60.000 34.40 0.00 38.65 3.01
3207 6221 2.145905 GCTCGCGCCAAATGTTTCG 61.146 57.895 0.00 0.00 0.00 3.46
3214 6228 2.350964 GCGCCAAATGTTTCGGTCTTTA 60.351 45.455 0.00 0.00 0.00 1.85
3264 6278 0.689080 ATCCGCACACCTGATCTCCT 60.689 55.000 0.00 0.00 0.00 3.69
3266 6280 1.043816 CCGCACACCTGATCTCCTAT 58.956 55.000 0.00 0.00 0.00 2.57
3369 6384 6.376864 CGATATCTCCAGAGAGTCCATAATGT 59.623 42.308 3.41 0.00 41.33 2.71
3397 6412 5.629097 GCATGAAGCATAATATCTGCAGTC 58.371 41.667 14.67 0.00 44.79 3.51
3437 6452 1.831286 CATTCCAGGAGCCCATGCC 60.831 63.158 0.00 0.00 38.69 4.40
3452 6467 1.003116 CATGCCAGTTAAGCTCGATGC 60.003 52.381 0.00 0.00 43.29 3.91
3499 6515 3.756434 CTCTCCAGAGTTCTCTCGAAACT 59.244 47.826 0.63 0.63 44.65 2.66
3507 6525 4.557205 AGTTCTCTCGAAACTACGCAATT 58.443 39.130 0.00 0.00 0.00 2.32
3520 6539 8.687824 AAACTACGCAATTGAAAAATAGATGG 57.312 30.769 10.34 0.00 0.00 3.51
3564 6583 6.054860 ACAATAAAGACAGGTAGCATCAGT 57.945 37.500 0.00 0.00 0.00 3.41
3568 6587 3.784701 AGACAGGTAGCATCAGTTACG 57.215 47.619 0.00 0.00 32.80 3.18
3625 6644 8.186163 AGTAACTTGTTTTTAACTAGCAACCAC 58.814 33.333 0.00 0.00 37.70 4.16
3636 6655 5.499004 ACTAGCAACCACAGGAAAATCTA 57.501 39.130 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.275832 AAAATTGGGGTTCGGCGCG 62.276 57.895 0.00 0.00 0.00 6.86
2 3 1.736282 CAAAATTGGGGTTCGGCGC 60.736 57.895 0.00 0.00 0.00 6.53
5 6 0.388006 GCGACAAAATTGGGGTTCGG 60.388 55.000 0.00 0.00 0.00 4.30
6 7 0.388006 GGCGACAAAATTGGGGTTCG 60.388 55.000 0.00 0.00 0.00 3.95
7 8 0.388006 CGGCGACAAAATTGGGGTTC 60.388 55.000 0.00 0.00 0.00 3.62
8 9 0.824182 TCGGCGACAAAATTGGGGTT 60.824 50.000 4.99 0.00 0.00 4.11
9 10 1.228306 TCGGCGACAAAATTGGGGT 60.228 52.632 4.99 0.00 0.00 4.95
10 11 1.241315 ACTCGGCGACAAAATTGGGG 61.241 55.000 4.99 0.00 0.00 4.96
11 12 1.396996 CTACTCGGCGACAAAATTGGG 59.603 52.381 4.99 0.00 0.00 4.12
12 13 2.073816 ACTACTCGGCGACAAAATTGG 58.926 47.619 4.99 0.00 0.00 3.16
13 14 3.306166 CCTACTACTCGGCGACAAAATTG 59.694 47.826 4.99 0.00 0.00 2.32
14 15 3.518590 CCTACTACTCGGCGACAAAATT 58.481 45.455 4.99 0.00 0.00 1.82
15 16 2.737679 GCCTACTACTCGGCGACAAAAT 60.738 50.000 4.99 0.00 36.45 1.82
16 17 1.403249 GCCTACTACTCGGCGACAAAA 60.403 52.381 4.99 0.00 36.45 2.44
17 18 0.171903 GCCTACTACTCGGCGACAAA 59.828 55.000 4.99 0.00 36.45 2.83
18 19 1.805254 GCCTACTACTCGGCGACAA 59.195 57.895 4.99 0.00 36.45 3.18
19 20 3.506108 GCCTACTACTCGGCGACA 58.494 61.111 4.99 0.00 36.45 4.35
23 24 2.188161 AGAGCGCCTACTACTCGGC 61.188 63.158 2.29 0.00 42.86 5.54
45 46 4.749310 CTTGAGCGCAGGCGACCT 62.749 66.667 18.96 5.63 46.35 3.85
66 67 2.787249 CCTTCACATTGCGAGCCG 59.213 61.111 0.00 0.00 0.00 5.52
67 68 2.486966 GCCTTCACATTGCGAGCC 59.513 61.111 0.00 0.00 0.00 4.70
91 92 0.956633 CCACAATCAACTGTGCAGCT 59.043 50.000 0.00 0.00 44.47 4.24
101 102 0.037697 CCGTCCTCGTCCACAATCAA 60.038 55.000 0.00 0.00 35.01 2.57
116 117 4.980805 TGGACAACTGGCGCCGTC 62.981 66.667 23.90 21.71 0.00 4.79
123 124 0.806102 CGCGTAGGATGGACAACTGG 60.806 60.000 0.00 0.00 0.00 4.00
133 134 1.808390 GTTTGGCGTCGCGTAGGAT 60.808 57.895 11.75 0.00 0.00 3.24
153 154 1.705337 CCTATGACGCGGCCAAACAG 61.705 60.000 10.82 6.47 0.00 3.16
161 162 2.025727 GTCGACCCTATGACGCGG 59.974 66.667 12.47 0.00 0.00 6.46
208 209 2.028112 TGTTGCTAGTGGACATGAGGTC 60.028 50.000 0.00 0.00 46.20 3.85
215 216 1.344438 CCTGTCTGTTGCTAGTGGACA 59.656 52.381 0.00 0.00 35.90 4.02
217 218 1.618837 GACCTGTCTGTTGCTAGTGGA 59.381 52.381 0.00 0.00 0.00 4.02
236 237 1.025113 ATTCTCGTCGGAGTCAGCGA 61.025 55.000 8.78 8.78 41.26 4.93
253 254 1.133668 GCCTTCCATGCCCTACTCATT 60.134 52.381 0.00 0.00 0.00 2.57
277 278 2.680370 ATTTGGGACTCGAGCCCCC 61.680 63.158 31.41 29.36 45.40 5.40
298 299 4.530857 CATGGGAGACGGACCGGC 62.531 72.222 20.00 17.01 33.59 6.13
299 300 2.573609 GAACATGGGAGACGGACCGG 62.574 65.000 20.00 0.00 0.00 5.28
304 305 2.379972 AGAGTAGAACATGGGAGACGG 58.620 52.381 0.00 0.00 0.00 4.79
305 306 3.181485 GGAAGAGTAGAACATGGGAGACG 60.181 52.174 0.00 0.00 0.00 4.18
307 308 4.338795 AGGAAGAGTAGAACATGGGAGA 57.661 45.455 0.00 0.00 0.00 3.71
311 312 3.274288 GGCAAGGAAGAGTAGAACATGG 58.726 50.000 0.00 0.00 0.00 3.66
338 339 1.156736 CCCGTGAAGTAAAGGTGCAG 58.843 55.000 0.00 0.00 0.00 4.41
358 359 2.380084 TGTGAGCGACAGGGATAAAC 57.620 50.000 0.00 0.00 0.00 2.01
365 366 1.734477 CGTCCTTGTGAGCGACAGG 60.734 63.158 0.00 0.00 35.44 4.00
367 368 2.338620 CCGTCCTTGTGAGCGACA 59.661 61.111 0.00 0.00 0.00 4.35
369 370 3.573772 CTGCCGTCCTTGTGAGCGA 62.574 63.158 0.00 0.00 0.00 4.93
377 378 0.539051 CTTCTCCATCTGCCGTCCTT 59.461 55.000 0.00 0.00 0.00 3.36
387 388 4.583871 AGTCATTGTTCACCTTCTCCATC 58.416 43.478 0.00 0.00 0.00 3.51
391 392 4.214332 GTCCAAGTCATTGTTCACCTTCTC 59.786 45.833 0.00 0.00 34.39 2.87
394 395 3.897239 TGTCCAAGTCATTGTTCACCTT 58.103 40.909 0.00 0.00 34.39 3.50
399 400 2.029918 GCCCTTGTCCAAGTCATTGTTC 60.030 50.000 6.31 0.00 36.72 3.18
409 426 2.203480 GGCAGTGCCCTTGTCCAA 60.203 61.111 24.53 0.00 44.06 3.53
452 469 9.685828 TCGGACAGTTTTCATTAAATAAAAAGG 57.314 29.630 1.23 0.69 0.00 3.11
510 527 2.916640 TCACATGCAAGCCGAATGATA 58.083 42.857 0.00 0.00 0.00 2.15
516 533 1.753930 ATGAATCACATGCAAGCCGA 58.246 45.000 0.00 0.00 37.87 5.54
517 534 2.572191 AATGAATCACATGCAAGCCG 57.428 45.000 0.00 0.00 39.39 5.52
519 536 4.491676 AGTCAAATGAATCACATGCAAGC 58.508 39.130 0.00 0.00 39.39 4.01
520 537 6.849502 ACTAGTCAAATGAATCACATGCAAG 58.150 36.000 0.00 0.00 39.39 4.01
529 546 7.237173 CCGAGTTTCAACTAGTCAAATGAATC 58.763 38.462 8.22 7.85 39.88 2.52
533 550 4.452455 AGCCGAGTTTCAACTAGTCAAATG 59.548 41.667 0.00 0.00 39.88 2.32
534 551 4.642429 AGCCGAGTTTCAACTAGTCAAAT 58.358 39.130 0.00 0.00 39.88 2.32
553 570 4.222114 GCTATTTGCATACATTTCGAGCC 58.778 43.478 0.00 0.00 42.31 4.70
579 624 4.080582 TCCGTGAACACATATGAGGGAATT 60.081 41.667 10.38 0.00 0.00 2.17
581 626 2.835156 TCCGTGAACACATATGAGGGAA 59.165 45.455 10.38 0.00 0.00 3.97
590 635 1.398041 CGCATTCATCCGTGAACACAT 59.602 47.619 5.80 0.00 46.43 3.21
598 643 2.398554 GCACACCGCATTCATCCGT 61.399 57.895 0.00 0.00 41.79 4.69
605 650 4.634703 TGACCCGCACACCGCATT 62.635 61.111 0.00 0.00 42.60 3.56
662 707 3.665745 AAACTAAAGACGCGGGAACTA 57.334 42.857 12.47 0.00 0.00 2.24
688 734 5.221461 ACACACGGATCTGAGTAAAAGAAGT 60.221 40.000 9.00 0.00 0.00 3.01
787 833 2.035632 GACAGAGACTAGGTGGGATGG 58.964 57.143 0.00 0.00 0.00 3.51
892 942 4.041723 GTGTTGCACACTTTGGAATGTAC 58.958 43.478 10.87 0.00 45.27 2.90
936 999 2.334946 GCCATGCAACAGGAGCGAA 61.335 57.895 7.33 0.00 33.85 4.70
984 1047 2.548875 GCCATCTGAGTCACTTGCTAG 58.451 52.381 0.00 0.00 0.00 3.42
986 1049 0.390866 CGCCATCTGAGTCACTTGCT 60.391 55.000 0.00 0.00 0.00 3.91
1376 1442 0.257616 CTCGAGGAACCTCTCCCTCT 59.742 60.000 17.18 0.00 46.81 3.69
1493 1565 3.605749 TTGTAGAGCAGGCCGTGGC 62.606 63.158 1.16 1.16 41.06 5.01
1967 2056 1.996786 GCTGCACCATCCGGTTGATG 61.997 60.000 14.27 8.40 46.31 3.07
2249 2338 1.154338 GTACTCCGTGGTGTCGTCG 60.154 63.158 0.00 0.00 0.00 5.12
2384 2473 4.457496 ACGATCCGCCTGCAGGTG 62.457 66.667 34.93 34.93 45.02 4.00
2762 2865 6.751514 AACATTATCGATAAAAGCCACACA 57.248 33.333 21.05 0.00 0.00 3.72
2798 2901 5.156608 TCACAGTCATCACAGTCATGAAT 57.843 39.130 0.00 0.00 31.98 2.57
2816 2919 9.166173 CCTCTAAAAATGAGTAATGTCATCACA 57.834 33.333 0.00 0.00 36.07 3.58
2817 2920 9.383519 TCCTCTAAAAATGAGTAATGTCATCAC 57.616 33.333 0.00 0.00 36.07 3.06
2818 2921 9.958180 TTCCTCTAAAAATGAGTAATGTCATCA 57.042 29.630 0.00 0.00 36.07 3.07
2823 2926 9.025041 CCCTTTTCCTCTAAAAATGAGTAATGT 57.975 33.333 0.00 0.00 36.64 2.71
2824 2927 7.976175 GCCCTTTTCCTCTAAAAATGAGTAATG 59.024 37.037 0.00 0.00 36.64 1.90
2825 2928 7.895962 AGCCCTTTTCCTCTAAAAATGAGTAAT 59.104 33.333 0.00 0.00 36.64 1.89
2826 2929 7.238710 AGCCCTTTTCCTCTAAAAATGAGTAA 58.761 34.615 0.00 0.00 36.64 2.24
2827 2930 6.790319 AGCCCTTTTCCTCTAAAAATGAGTA 58.210 36.000 0.00 0.00 36.64 2.59
2828 2931 5.645201 AGCCCTTTTCCTCTAAAAATGAGT 58.355 37.500 0.00 0.00 36.64 3.41
2829 2932 5.711976 TGAGCCCTTTTCCTCTAAAAATGAG 59.288 40.000 0.00 0.00 36.64 2.90
2830 2933 5.476945 GTGAGCCCTTTTCCTCTAAAAATGA 59.523 40.000 0.00 0.00 36.64 2.57
2831 2934 5.243730 TGTGAGCCCTTTTCCTCTAAAAATG 59.756 40.000 0.00 0.00 36.64 2.32
2895 3003 0.955919 GCGCCTTGTAGCTCCAAACT 60.956 55.000 0.00 0.00 0.00 2.66
2896 3004 1.502190 GCGCCTTGTAGCTCCAAAC 59.498 57.895 0.00 0.00 0.00 2.93
2951 3064 3.181518 GCGTAGACTGTCTAGAGTGTGTC 60.182 52.174 17.43 3.20 28.01 3.67
2955 3071 2.610374 GGAGCGTAGACTGTCTAGAGTG 59.390 54.545 17.43 9.25 28.01 3.51
2998 3114 7.958053 AGTACTTGTTACTGTTATTTTCGCT 57.042 32.000 0.00 0.00 39.78 4.93
3009 6012 8.822855 TGTTGATGTTTGTAGTACTTGTTACTG 58.177 33.333 0.00 0.00 41.48 2.74
3014 6017 8.504005 GCTAATGTTGATGTTTGTAGTACTTGT 58.496 33.333 0.00 0.00 0.00 3.16
3037 6040 2.954989 CCTGATGTCTGTAGCTGAGCTA 59.045 50.000 10.65 10.65 40.44 3.32
3040 6043 4.462508 TTTCCTGATGTCTGTAGCTGAG 57.537 45.455 0.00 0.00 0.00 3.35
3041 6044 5.426689 AATTTCCTGATGTCTGTAGCTGA 57.573 39.130 0.00 0.00 0.00 4.26
3085 6096 0.321671 CTCCGAAGAGCTGGGTTTCA 59.678 55.000 0.00 0.00 32.13 2.69
3086 6097 3.145228 CTCCGAAGAGCTGGGTTTC 57.855 57.895 0.00 0.00 32.13 2.78
3107 6118 2.176273 CGCTTCAGGGATGGCTTCG 61.176 63.158 0.00 0.00 0.00 3.79
3115 6126 0.392998 GCAATTCCTCGCTTCAGGGA 60.393 55.000 0.00 0.00 33.81 4.20
3170 6184 2.140792 ACCGCCACTTCTCCTGTGT 61.141 57.895 0.00 0.00 33.92 3.72
3207 6221 3.243636 TGTCGTCTCTTGGTGTAAAGACC 60.244 47.826 0.00 0.00 35.76 3.85
3264 6278 5.944007 GGACAGCTTCCTTTTTAACCTCATA 59.056 40.000 7.46 0.00 41.95 2.15
3266 6280 4.142038 GGACAGCTTCCTTTTTAACCTCA 58.858 43.478 7.46 0.00 41.95 3.86
3397 6412 3.578688 GTGGGCTAGAAATTGCAACAAG 58.421 45.455 0.00 0.00 0.00 3.16
3469 6485 8.754461 TCGAGAGAACTCTGGAGAGAGATTTTC 61.754 44.444 10.71 3.71 42.59 2.29
3499 6515 9.562583 GTAAACCATCTATTTTTCAATTGCGTA 57.437 29.630 0.00 0.00 0.00 4.42
3564 6583 4.193090 TCTTCAGAAAAGGCAACACGTAA 58.807 39.130 0.00 0.00 41.41 3.18
3568 6587 4.936891 ACAATCTTCAGAAAAGGCAACAC 58.063 39.130 0.00 0.00 41.41 3.32
3625 6644 8.672815 GTTCCTCAGAGAATTTAGATTTTCCTG 58.327 37.037 0.00 0.00 29.05 3.86
3636 6655 7.121907 GGAAAGCTAATGTTCCTCAGAGAATTT 59.878 37.037 7.53 0.00 40.24 1.82


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

AutoCloner maintained by Alex Coulton.