Multiple sequence alignment - TraesCS6A01G409900

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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 TraesCS6A01G409900 chr6A 100.000 3464 0 0 1 3464 613492946 613496409 0.000000e+00 6397.0
1 TraesCS6A01G409900 chr6A 86.667 75 7 2 2 75 64168010 64167938 2.870000e-11 80.5
2 TraesCS6A01G409900 chr1B 90.014 2854 156 43 678 3442 46830360 46827547 0.000000e+00 3572.0
3 TraesCS6A01G409900 chr1B 88.681 2721 219 41 705 3358 4597570 4594872 0.000000e+00 3236.0
4 TraesCS6A01G409900 chr1B 88.155 2769 239 38 399 3118 4954764 4952036 0.000000e+00 3214.0
5 TraesCS6A01G409900 chr1B 90.276 2427 177 27 589 2988 4110093 4112487 0.000000e+00 3120.0
6 TraesCS6A01G409900 chr1B 88.091 2368 217 27 591 2936 4519082 4516758 0.000000e+00 2750.0
7 TraesCS6A01G409900 chr1B 89.347 2037 166 20 685 2683 70232782 70234805 0.000000e+00 2512.0
8 TraesCS6A01G409900 chr1B 88.889 1971 169 25 589 2535 4144643 4146587 0.000000e+00 2381.0
9 TraesCS6A01G409900 chr1B 89.895 1148 86 13 399 1528 4542271 4541136 0.000000e+00 1450.0
10 TraesCS6A01G409900 chr1B 80.307 782 78 37 2482 3225 46693720 46694463 3.960000e-144 521.0
11 TraesCS6A01G409900 chr1B 88.652 282 15 8 3199 3464 4797620 4797340 9.270000e-86 327.0
12 TraesCS6A01G409900 chr1B 87.986 283 16 9 3197 3464 4112639 4112918 5.580000e-83 318.0
13 TraesCS6A01G409900 chr1B 92.899 169 8 2 3 171 4542755 4542591 3.450000e-60 243.0
14 TraesCS6A01G409900 chr1B 84.181 177 14 7 3291 3459 4951733 4951563 3.580000e-35 159.0
15 TraesCS6A01G409900 chr1B 90.566 106 5 1 3291 3396 4538996 4538896 6.030000e-28 135.0
16 TraesCS6A01G409900 chr1B 90.722 97 2 4 50 144 4597991 4597900 4.690000e-24 122.0
17 TraesCS6A01G409900 chr1B 77.778 162 19 12 3039 3197 4516594 4516447 2.220000e-12 84.2
18 TraesCS6A01G409900 chr3D 88.475 2629 229 34 589 3183 560024970 560022382 0.000000e+00 3109.0
19 TraesCS6A01G409900 chr3D 83.125 160 10 9 3242 3384 560022381 560022222 2.810000e-26 130.0
20 TraesCS6A01G409900 chr5B 88.423 2626 226 45 589 3164 60826081 60823484 0.000000e+00 3094.0
21 TraesCS6A01G409900 chr5D 89.003 2337 188 32 589 2885 57819443 57821750 0.000000e+00 2828.0
22 TraesCS6A01G409900 chr1A 87.872 2251 208 26 734 2938 2943269 2945500 0.000000e+00 2584.0
23 TraesCS6A01G409900 chr1A 90.935 1765 151 7 989 2751 3013330 3015087 0.000000e+00 2364.0
24 TraesCS6A01G409900 chr1A 84.720 517 57 12 2697 3197 3015084 3015594 6.680000e-137 497.0
25 TraesCS6A01G409900 chr1A 91.813 171 7 3 1 171 2942604 2942767 7.480000e-57 231.0
26 TraesCS6A01G409900 chr1A 90.341 176 13 1 167 342 2942805 2942976 9.670000e-56 228.0
27 TraesCS6A01G409900 chr1A 87.273 165 17 3 3293 3457 32548116 32548276 5.900000e-43 185.0
28 TraesCS6A01G409900 chr1A 80.447 179 11 14 3302 3457 3015776 3015953 7.860000e-22 115.0
29 TraesCS6A01G409900 chr1A 97.297 37 1 0 55 91 2942823 2942859 2.890000e-06 63.9
30 TraesCS6A01G409900 chr6B 88.659 2081 186 25 589 2654 120595510 120593465 0.000000e+00 2490.0
31 TraesCS6A01G409900 chr6B 86.424 2335 230 38 619 2934 120355155 120352889 0.000000e+00 2475.0
32 TraesCS6A01G409900 chr6B 86.486 74 4 2 2 75 120355238 120355171 3.710000e-10 76.8
33 TraesCS6A01G409900 chr6B 89.286 56 6 0 3138 3193 120592849 120592794 1.720000e-08 71.3
34 TraesCS6A01G409900 chr7B 88.471 2047 168 38 589 2621 591461543 591463535 0.000000e+00 2410.0
35 TraesCS6A01G409900 chr7B 87.912 91 7 2 405 492 591461428 591461517 1.700000e-18 104.0
36 TraesCS6A01G409900 chr7D 88.232 2048 174 39 589 2621 548230992 548232987 0.000000e+00 2385.0
37 TraesCS6A01G409900 chr7A 88.207 2052 167 43 589 2621 631984334 631986329 0.000000e+00 2379.0
38 TraesCS6A01G409900 chr1D 85.230 1002 62 29 2511 3456 387236 388207 0.000000e+00 952.0
39 TraesCS6A01G409900 chrUn 91.813 171 7 3 1 171 361631009 361631172 7.480000e-57 231.0
40 TraesCS6A01G409900 chrUn 90.341 176 13 1 167 342 361631210 361631381 9.670000e-56 228.0
41 TraesCS6A01G409900 chrUn 97.297 37 1 0 55 91 361631228 361631264 2.890000e-06 63.9
42 TraesCS6A01G409900 chr2A 86.842 76 7 3 416 491 774906584 774906512 7.970000e-12 82.4
43 TraesCS6A01G409900 chr6D 87.500 72 3 2 4 75 53176160 53176095 1.030000e-10 78.7
44 TraesCS6A01G409900 chr6D 90.385 52 5 0 3139 3190 51076577 51076628 6.200000e-08 69.4
45 TraesCS6A01G409900 chr6D 90.385 52 5 0 3139 3190 51351392 51351443 6.200000e-08 69.4


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 TraesCS6A01G409900 chr6A 613492946 613496409 3463 False 6397.000000 6397 100.000000 1 3464 1 chr6A.!!$F1 3463
1 TraesCS6A01G409900 chr1B 46827547 46830360 2813 True 3572.000000 3572 90.014000 678 3442 1 chr1B.!!$R2 2764
2 TraesCS6A01G409900 chr1B 70232782 70234805 2023 False 2512.000000 2512 89.347000 685 2683 1 chr1B.!!$F3 1998
3 TraesCS6A01G409900 chr1B 4144643 4146587 1944 False 2381.000000 2381 88.889000 589 2535 1 chr1B.!!$F1 1946
4 TraesCS6A01G409900 chr1B 4110093 4112918 2825 False 1719.000000 3120 89.131000 589 3464 2 chr1B.!!$F4 2875
5 TraesCS6A01G409900 chr1B 4951563 4954764 3201 True 1686.500000 3214 86.168000 399 3459 2 chr1B.!!$R6 3060
6 TraesCS6A01G409900 chr1B 4594872 4597991 3119 True 1679.000000 3236 89.701500 50 3358 2 chr1B.!!$R5 3308
7 TraesCS6A01G409900 chr1B 4516447 4519082 2635 True 1417.100000 2750 82.934500 591 3197 2 chr1B.!!$R3 2606
8 TraesCS6A01G409900 chr1B 4538896 4542755 3859 True 609.333333 1450 91.120000 3 3396 3 chr1B.!!$R4 3393
9 TraesCS6A01G409900 chr1B 46693720 46694463 743 False 521.000000 521 80.307000 2482 3225 1 chr1B.!!$F2 743
10 TraesCS6A01G409900 chr3D 560022222 560024970 2748 True 1619.500000 3109 85.800000 589 3384 2 chr3D.!!$R1 2795
11 TraesCS6A01G409900 chr5B 60823484 60826081 2597 True 3094.000000 3094 88.423000 589 3164 1 chr5B.!!$R1 2575
12 TraesCS6A01G409900 chr5D 57819443 57821750 2307 False 2828.000000 2828 89.003000 589 2885 1 chr5D.!!$F1 2296
13 TraesCS6A01G409900 chr1A 3013330 3015953 2623 False 992.000000 2364 85.367333 989 3457 3 chr1A.!!$F3 2468
14 TraesCS6A01G409900 chr1A 2942604 2945500 2896 False 776.725000 2584 91.830750 1 2938 4 chr1A.!!$F2 2937
15 TraesCS6A01G409900 chr6B 120592794 120595510 2716 True 1280.650000 2490 88.972500 589 3193 2 chr6B.!!$R2 2604
16 TraesCS6A01G409900 chr6B 120352889 120355238 2349 True 1275.900000 2475 86.455000 2 2934 2 chr6B.!!$R1 2932
17 TraesCS6A01G409900 chr7B 591461428 591463535 2107 False 1257.000000 2410 88.191500 405 2621 2 chr7B.!!$F1 2216
18 TraesCS6A01G409900 chr7D 548230992 548232987 1995 False 2385.000000 2385 88.232000 589 2621 1 chr7D.!!$F1 2032
19 TraesCS6A01G409900 chr7A 631984334 631986329 1995 False 2379.000000 2379 88.207000 589 2621 1 chr7A.!!$F1 2032
20 TraesCS6A01G409900 chr1D 387236 388207 971 False 952.000000 952 85.230000 2511 3456 1 chr1D.!!$F1 945

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
510 632 0.693049 AGTTGGTTCGGATTCAGCCT 59.307 50.0 0.0 0.0 0.0 4.58 F
524 649 0.817654 CAGCCTGACGTGACTGGATA 59.182 55.0 0.0 0.0 0.0 2.59 F
1156 1713 1.165907 TTCCGGTCTTTGCACTGCTG 61.166 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2162 3082 0.397675 ATGAGGTGAGGATGCGAGGA 60.398 55.000 0.00 0.0 0.00 3.71 R
2412 3333 1.707427 AGGGCATCTGAACAGTCCTTT 59.293 47.619 1.73 0.0 0.00 3.11 R
2641 3583 0.249955 TCATTCAGCAGATGCCGTCA 59.750 50.000 0.14 0.0 43.38 4.35 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
198 241 1.425066 TGCCTGGTTGGTTCAGATTCT 59.575 47.619 0.00 0.00 38.35 2.40
199 242 2.158475 TGCCTGGTTGGTTCAGATTCTT 60.158 45.455 0.00 0.00 38.35 2.52
200 243 2.893489 GCCTGGTTGGTTCAGATTCTTT 59.107 45.455 0.00 0.00 38.35 2.52
203 246 5.070001 CCTGGTTGGTTCAGATTCTTTACA 58.930 41.667 0.00 0.00 34.36 2.41
207 250 8.698973 TGGTTGGTTCAGATTCTTTACATTTA 57.301 30.769 0.00 0.00 0.00 1.40
208 251 8.573035 TGGTTGGTTCAGATTCTTTACATTTAC 58.427 33.333 0.00 0.00 0.00 2.01
270 320 6.842163 AGTTAATGTTGTAAAGCCATTCTCG 58.158 36.000 0.00 0.00 31.63 4.04
328 381 3.253188 TGGTTGCAGCAAATACTGAGTTC 59.747 43.478 10.11 0.00 40.25 3.01
361 444 3.676172 TGAACTCGTTAATAACTGCACCG 59.324 43.478 1.42 0.00 0.00 4.94
397 480 1.617850 TCGGCTGTGGCAAAATGATTT 59.382 42.857 0.00 0.00 40.87 2.17
403 508 4.800249 GCTGTGGCAAAATGATTTCCAAGA 60.800 41.667 0.48 0.00 38.54 3.02
414 519 3.569701 TGATTTCCAAGAAAGAGCCACAC 59.430 43.478 0.00 0.00 0.00 3.82
435 543 8.273557 CCACACGTACTAACTAATTTGCATATC 58.726 37.037 0.00 0.00 0.00 1.63
486 601 5.335976 GGTGCCTCCAAATAAGTTCTCAAAG 60.336 44.000 0.00 0.00 35.97 2.77
510 632 0.693049 AGTTGGTTCGGATTCAGCCT 59.307 50.000 0.00 0.00 0.00 4.58
524 649 0.817654 CAGCCTGACGTGACTGGATA 59.182 55.000 0.00 0.00 0.00 2.59
541 666 5.104360 ACTGGATAGCATACACATGGTTCTT 60.104 40.000 0.00 0.00 42.71 2.52
637 765 6.147164 TGCGTCAATTCTATCTCGTTTCTTTT 59.853 34.615 0.00 0.00 0.00 2.27
683 818 5.814188 CAGTATTCAGAATCTGCTTGCTACA 59.186 40.000 5.18 0.00 0.00 2.74
821 1300 6.040278 TCCATGCTTATGAACAAAACACAAGA 59.960 34.615 0.00 0.00 0.00 3.02
877 1370 9.964253 CATCAATATATTCTTCGTAATGAGTGC 57.036 33.333 0.00 0.00 0.00 4.40
892 1395 2.591429 TGCTTGTCGCCAGTGTGG 60.591 61.111 0.00 0.00 41.55 4.17
993 1550 6.127535 CCTGATTGGTACAGCTGAATTGAATT 60.128 38.462 23.35 0.00 42.39 2.17
1050 1607 4.776837 ACAGAGATTCTCAACAGGATCACT 59.223 41.667 15.83 0.00 37.12 3.41
1088 1645 4.078639 ACTCTCTTTCCCTTGTGTCAAG 57.921 45.455 2.90 2.90 0.00 3.02
1156 1713 1.165907 TTCCGGTCTTTGCACTGCTG 61.166 55.000 0.00 0.00 0.00 4.41
1320 1877 2.972713 TGACCTCACCTTAAGCTTCTGT 59.027 45.455 0.00 0.00 0.00 3.41
1534 2442 1.486726 GGGATGGATCGTTGGAAGAGT 59.513 52.381 0.00 0.00 0.00 3.24
1657 2575 9.522804 GAGGAAAATATGATAGTCTTATAGCCG 57.477 37.037 0.00 0.00 0.00 5.52
1658 2576 9.036980 AGGAAAATATGATAGTCTTATAGCCGT 57.963 33.333 0.00 0.00 0.00 5.68
1684 2602 2.293955 GGTAAGGTCTATGACTCCTCGC 59.706 54.545 0.00 0.00 32.47 5.03
1965 2885 3.810941 GTGAAACCAGGACGTCATTTACA 59.189 43.478 18.91 5.54 0.00 2.41
2149 3069 2.571212 ACGCCAACTTCTTTGATGACA 58.429 42.857 0.00 0.00 37.39 3.58
2162 3082 2.278245 TGATGACAAGGGGATGAAGGT 58.722 47.619 0.00 0.00 0.00 3.50
2300 3220 5.276868 GGATGTGTCATAACGTTACTGATGC 60.277 44.000 10.81 11.73 0.00 3.91
2405 3326 1.278637 GTGTTGCCAAGTCGGTTCG 59.721 57.895 0.00 0.00 36.97 3.95
2412 3333 0.242825 CCAAGTCGGTTCGCTACTCA 59.757 55.000 0.00 0.00 0.00 3.41
2454 3378 6.040842 CCCTTATGAATACAATTGGTCTTGGG 59.959 42.308 10.83 9.85 0.00 4.12
2537 3465 3.423749 TGTTCAGTGTGCATCATTGGAT 58.576 40.909 10.32 0.00 35.03 3.41
2621 3563 6.632909 TCACTGCAATGATTTTCCTTTATGG 58.367 36.000 0.00 0.00 37.10 2.74
2629 3571 7.814264 ATGATTTTCCTTTATGGCAGTCTAG 57.186 36.000 0.00 0.00 35.26 2.43
2641 3583 5.426689 TGGCAGTCTAGTGATGATCTTTT 57.573 39.130 0.00 0.00 0.00 2.27
2653 3595 1.739466 TGATCTTTTGACGGCATCTGC 59.261 47.619 0.00 0.00 41.14 4.26
2723 3741 5.220340 CCGTACGTAATTCTGGTTGCTTAAG 60.220 44.000 15.21 0.00 0.00 1.85
2733 3751 6.420913 TCTGGTTGCTTAAGTTCTACTCTT 57.579 37.500 4.02 0.00 0.00 2.85
2793 3812 1.064017 TCCCTGTTTTTGCTGTGGAGT 60.064 47.619 0.00 0.00 0.00 3.85
2903 3945 3.160557 CTGCCTGCTATGTTCGCGC 62.161 63.158 0.00 0.00 0.00 6.86
2993 4037 2.256174 CGGCATGCTTGTTTTGATGAG 58.744 47.619 18.92 0.00 0.00 2.90
3121 4370 7.239438 ACTACTGAAGGCCTATAACATAGCTA 58.761 38.462 5.16 0.00 0.00 3.32
3143 4609 8.827177 GCTATGTGCTAATTACATGTAGGTAA 57.173 34.615 5.56 0.00 39.03 2.85
3190 4662 3.485394 TCCAGCACTCAACAGCATTTTA 58.515 40.909 0.00 0.00 0.00 1.52
3197 4669 7.484007 CAGCACTCAACAGCATTTTATTCTTAG 59.516 37.037 0.00 0.00 0.00 2.18
3202 4682 5.206905 ACAGCATTTTATTCTTAGGGGGT 57.793 39.130 0.00 0.00 0.00 4.95
3233 4792 9.739276 ATCTCTTTTTACCTATCATGTGTTTGA 57.261 29.630 0.00 0.00 0.00 2.69
3287 4848 7.445121 GGGTTCTGATTTTCTGAATCCTTTTT 58.555 34.615 15.34 0.00 46.13 1.94
3288 4849 8.585018 GGGTTCTGATTTTCTGAATCCTTTTTA 58.415 33.333 15.34 0.00 46.13 1.52
3289 4850 9.411801 GGTTCTGATTTTCTGAATCCTTTTTAC 57.588 33.333 0.00 0.00 36.85 2.01
3296 4875 6.959639 TTCTGAATCCTTTTTACACAGCTT 57.040 33.333 0.00 0.00 0.00 3.74
3365 4946 3.442977 AGCTCATCAAGATGCCAACTTTC 59.557 43.478 5.19 0.00 38.65 2.62
3366 4947 3.428589 GCTCATCAAGATGCCAACTTTCC 60.429 47.826 5.19 0.00 38.65 3.13
3367 4948 4.015084 CTCATCAAGATGCCAACTTTCCT 58.985 43.478 5.19 0.00 38.65 3.36
3368 4949 4.410099 TCATCAAGATGCCAACTTTCCTT 58.590 39.130 5.19 0.00 38.65 3.36
3369 4950 4.834496 TCATCAAGATGCCAACTTTCCTTT 59.166 37.500 5.19 0.00 38.65 3.11
3386 4992 6.603940 TTCCTTTGCTGGCTATGTAATTTT 57.396 33.333 0.00 0.00 0.00 1.82
3428 5042 3.061161 GCTAAAATGAAACATGCGCCTTG 59.939 43.478 4.18 5.26 0.00 3.61
3442 5056 2.403259 CGCCTTGCCCTTGTTAAAAAG 58.597 47.619 0.00 0.00 0.00 2.27
3460 5074 9.787435 GTTAAAAAGGGGGTGAATATTTTTCTT 57.213 29.630 0.00 0.00 35.39 2.52
3463 5077 9.787435 AAAAAGGGGGTGAATATTTTTCTTTAC 57.213 29.630 0.00 0.00 29.54 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 0.462759 GTAGCAAGCAGAGCCGGAAT 60.463 55.000 5.05 0.00 0.00 3.01
110 111 1.079127 GTAGCAAGCAGAGCCGGAA 60.079 57.895 5.05 0.00 0.00 4.30
111 112 1.544825 AAGTAGCAAGCAGAGCCGGA 61.545 55.000 5.05 0.00 0.00 5.14
112 113 0.674895 AAAGTAGCAAGCAGAGCCGG 60.675 55.000 0.00 0.00 0.00 6.13
113 114 2.010145 TAAAGTAGCAAGCAGAGCCG 57.990 50.000 0.00 0.00 0.00 5.52
154 155 4.333649 CGCATGGAGATTGCTAGAAAGAAA 59.666 41.667 0.00 0.00 37.96 2.52
164 165 2.117156 AGGCACGCATGGAGATTGC 61.117 57.895 0.00 0.00 36.74 3.56
207 250 9.819267 GGACTAACTAAGATAATGCAAAGTAGT 57.181 33.333 0.00 0.00 0.00 2.73
208 251 9.817809 TGGACTAACTAAGATAATGCAAAGTAG 57.182 33.333 0.00 0.00 0.00 2.57
259 309 4.534797 AGTACTACCTACGAGAATGGCTT 58.465 43.478 0.00 0.00 0.00 4.35
270 320 9.830975 AGCTTACTTTCTACTAGTACTACCTAC 57.169 37.037 0.00 0.00 0.00 3.18
342 395 2.991190 CACGGTGCAGTTATTAACGAGT 59.009 45.455 0.00 0.00 36.23 4.18
343 396 2.991190 ACACGGTGCAGTTATTAACGAG 59.009 45.455 8.30 0.28 36.23 4.18
344 397 2.732500 CACACGGTGCAGTTATTAACGA 59.267 45.455 8.30 0.00 36.23 3.85
345 398 2.732500 TCACACGGTGCAGTTATTAACG 59.267 45.455 8.30 0.00 32.98 3.18
346 399 4.735662 TTCACACGGTGCAGTTATTAAC 57.264 40.909 8.30 0.00 32.98 2.01
347 400 5.470437 TGAATTCACACGGTGCAGTTATTAA 59.530 36.000 8.30 0.00 32.98 1.40
348 401 4.998033 TGAATTCACACGGTGCAGTTATTA 59.002 37.500 8.30 0.00 32.98 0.98
361 444 2.744202 AGCCGATGAGTTGAATTCACAC 59.256 45.455 7.89 9.77 0.00 3.82
397 480 0.468226 ACGTGTGGCTCTTTCTTGGA 59.532 50.000 0.00 0.00 0.00 3.53
403 508 5.458041 TTAGTTAGTACGTGTGGCTCTTT 57.542 39.130 0.00 0.00 0.00 2.52
414 519 8.299262 AGCAGATATGCAAATTAGTTAGTACG 57.701 34.615 15.82 0.00 37.25 3.67
486 601 3.981416 GCTGAATCCGAACCAACTTTTTC 59.019 43.478 0.00 0.00 0.00 2.29
510 632 3.020984 TGTATGCTATCCAGTCACGTCA 58.979 45.455 0.00 0.00 0.00 4.35
524 649 3.719268 TGGAAGAACCATGTGTATGCT 57.281 42.857 0.00 0.00 44.64 3.79
563 688 6.095021 GGTCGGGCTTACTTTAATTCTGAATT 59.905 38.462 18.64 18.64 34.90 2.17
661 796 6.857777 ATGTAGCAAGCAGATTCTGAATAC 57.142 37.500 17.87 11.10 32.44 1.89
669 804 7.941238 AGACCATAATTATGTAGCAAGCAGATT 59.059 33.333 21.20 0.00 31.82 2.40
670 805 7.456725 AGACCATAATTATGTAGCAAGCAGAT 58.543 34.615 21.20 0.00 31.82 2.90
877 1370 0.946221 GAGACCACACTGGCGACAAG 60.946 60.000 0.00 0.00 42.67 3.16
892 1395 6.485984 AGAATAATGCATGTGAAGATGGAGAC 59.514 38.462 0.00 0.00 0.00 3.36
1014 1571 4.527426 TCTGTCAGCAGAGCCTCA 57.473 55.556 0.00 0.00 45.94 3.86
1050 1607 5.575157 AGAGAGTTGAGATCACTTGTCCTA 58.425 41.667 0.00 0.00 0.00 2.94
1088 1645 2.298729 CCCTCTATCTTGTAGAGCTGCC 59.701 54.545 0.00 0.00 39.66 4.85
1156 1713 3.427528 CACAATGATGTCAGTGCTTTTGC 59.572 43.478 10.06 0.00 44.85 3.68
1320 1877 3.284617 CCCAGAGTCATCAATGCATGAA 58.715 45.455 0.00 0.00 42.54 2.57
1367 2275 1.552337 TCAGCCTGAGAGACACCAATC 59.448 52.381 0.00 0.00 0.00 2.67
1534 2442 9.248291 GATTCTTTTGCAATTCTTCACTACAAA 57.752 29.630 0.00 0.00 0.00 2.83
1655 2573 3.317430 GTCATAGACCTTACCACCTACGG 59.683 52.174 0.00 0.00 0.00 4.02
1656 2574 4.205587 AGTCATAGACCTTACCACCTACG 58.794 47.826 0.00 0.00 32.18 3.51
1657 2575 4.583907 GGAGTCATAGACCTTACCACCTAC 59.416 50.000 0.00 0.00 32.18 3.18
1658 2576 4.481280 AGGAGTCATAGACCTTACCACCTA 59.519 45.833 0.00 0.00 32.18 3.08
1659 2577 3.272551 AGGAGTCATAGACCTTACCACCT 59.727 47.826 0.00 0.00 32.18 4.00
1660 2578 3.637694 GAGGAGTCATAGACCTTACCACC 59.362 52.174 0.00 0.00 33.89 4.61
1965 2885 4.500035 GCTAGAGCGTAAAGGCTGTTATCT 60.500 45.833 1.26 0.00 44.93 1.98
2149 3069 1.627297 GCGAGGACCTTCATCCCCTT 61.627 60.000 0.00 0.00 39.91 3.95
2162 3082 0.397675 ATGAGGTGAGGATGCGAGGA 60.398 55.000 0.00 0.00 0.00 3.71
2300 3220 2.046892 CCAGTTCAGCCACTCCGG 60.047 66.667 0.00 0.00 38.11 5.14
2405 3326 4.258702 TCTGAACAGTCCTTTGAGTAGC 57.741 45.455 1.73 0.00 0.00 3.58
2412 3333 1.707427 AGGGCATCTGAACAGTCCTTT 59.293 47.619 1.73 0.00 0.00 3.11
2537 3465 2.627945 GTCGGATGATGCACAACCTTA 58.372 47.619 11.68 1.12 38.97 2.69
2621 3563 5.005203 CGTCAAAAGATCATCACTAGACTGC 59.995 44.000 0.00 0.00 0.00 4.40
2629 3571 3.624861 AGATGCCGTCAAAAGATCATCAC 59.375 43.478 0.00 0.00 34.42 3.06
2641 3583 0.249955 TCATTCAGCAGATGCCGTCA 59.750 50.000 0.14 0.00 43.38 4.35
2653 3595 8.398665 GGTGCCTACTATTAAAGTTTCATTCAG 58.601 37.037 0.00 0.00 39.80 3.02
2696 3655 3.187022 GCAACCAGAATTACGTACGGTTT 59.813 43.478 21.06 9.66 34.57 3.27
2700 3659 5.346822 ACTTAAGCAACCAGAATTACGTACG 59.653 40.000 15.01 15.01 0.00 3.67
2733 3751 1.334243 CCGGTTTCAAAACGGCTACAA 59.666 47.619 15.04 0.00 39.77 2.41
2766 3784 3.960102 ACAGCAAAAACAGGGAATCTTGA 59.040 39.130 0.00 0.00 0.00 3.02
2793 3812 4.811969 ACACCAAACGGTCATATAGTGA 57.188 40.909 0.00 0.00 33.11 3.41
2854 3891 5.108517 TGTCTTCAAAATCACTTTGGCAAC 58.891 37.500 0.00 0.00 44.00 4.17
2903 3945 2.357637 ACGATCCATACCAAAATTGCCG 59.642 45.455 0.00 0.00 0.00 5.69
2993 4037 2.763448 ACATCCTCCAGTAGAGTTGAGC 59.237 50.000 0.00 0.00 41.47 4.26
3051 4190 9.331466 TCAGGCCATCTTAGAATCTAAATCTAT 57.669 33.333 5.01 0.00 29.93 1.98
3068 4209 2.087646 GTTCCTCAACTTCAGGCCATC 58.912 52.381 5.01 0.00 0.00 3.51
3121 4370 9.273016 GTGATTACCTACATGTAATTAGCACAT 57.727 33.333 7.06 0.00 40.57 3.21
3143 4609 3.945921 CCAGAGCAAAGACATGATGTGAT 59.054 43.478 1.23 0.00 32.28 3.06
3190 4662 2.104963 GAGATGCGAACCCCCTAAGAAT 59.895 50.000 0.00 0.00 0.00 2.40
3197 4669 1.545841 AAAAAGAGATGCGAACCCCC 58.454 50.000 0.00 0.00 0.00 5.40
3202 4682 7.011389 CACATGATAGGTAAAAAGAGATGCGAA 59.989 37.037 0.00 0.00 0.00 4.70
3287 4848 2.849942 ACTGATGCAACAAGCTGTGTA 58.150 42.857 0.00 0.00 45.94 2.90
3288 4849 1.683943 ACTGATGCAACAAGCTGTGT 58.316 45.000 0.00 0.00 45.94 3.72
3289 4850 2.033675 TGAACTGATGCAACAAGCTGTG 59.966 45.455 0.00 0.00 45.94 3.66
3296 4875 1.150827 CGAGCTGAACTGATGCAACA 58.849 50.000 0.00 0.00 0.00 3.33
3365 4946 6.165577 ACAAAAATTACATAGCCAGCAAAGG 58.834 36.000 0.00 0.00 0.00 3.11
3366 4947 7.171337 ACAACAAAAATTACATAGCCAGCAAAG 59.829 33.333 0.00 0.00 0.00 2.77
3367 4948 6.989169 ACAACAAAAATTACATAGCCAGCAAA 59.011 30.769 0.00 0.00 0.00 3.68
3368 4949 6.520272 ACAACAAAAATTACATAGCCAGCAA 58.480 32.000 0.00 0.00 0.00 3.91
3369 4950 6.095432 ACAACAAAAATTACATAGCCAGCA 57.905 33.333 0.00 0.00 0.00 4.41
3403 5016 3.428045 GGCGCATGTTTCATTTTAGCTCT 60.428 43.478 10.83 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.