Multiple sequence alignment - TraesCS2A01G022900

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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 TraesCS2A01G022900 chr2A 100.000 3315 0 0 1 3315 11045643 11042329 0.000000e+00 6122
1 TraesCS2A01G022900 chr2A 90.059 3048 237 29 283 3315 11310073 11307077 0.000000e+00 3890
2 TraesCS2A01G022900 chr2A 89.722 360 34 2 2958 3315 11237972 11237614 1.080000e-124 457
3 TraesCS2A01G022900 chr2B 92.606 3327 182 24 1 3315 15639138 15635864 0.000000e+00 4723
4 TraesCS2A01G022900 chr2B 90.691 2879 217 22 448 3315 15119809 15116971 0.000000e+00 3784
5 TraesCS2A01G022900 chr2B 91.806 2746 173 22 43 2783 15818992 15816294 0.000000e+00 3777
6 TraesCS2A01G022900 chr2B 91.770 2746 174 22 43 2783 15917963 15915265 0.000000e+00 3771
7 TraesCS2A01G022900 chr2B 91.588 2746 178 23 43 2783 15695685 15692988 0.000000e+00 3742
8 TraesCS2A01G022900 chr2B 87.481 3299 303 48 10 3265 15382941 15379710 0.000000e+00 3703
9 TraesCS2A01G022900 chr2B 88.438 2958 273 38 54 2977 15883478 15880556 0.000000e+00 3504
10 TraesCS2A01G022900 chr2B 88.438 2958 267 43 54 2977 15962873 15959957 0.000000e+00 3498
11 TraesCS2A01G022900 chr2B 88.291 2955 277 43 54 2977 15727655 15724739 0.000000e+00 3476
12 TraesCS2A01G022900 chr2B 88.807 2859 258 39 143 2977 15790625 15787805 0.000000e+00 3450
13 TraesCS2A01G022900 chr2B 90.561 1070 66 11 43 1108 15757806 15756768 0.000000e+00 1384
14 TraesCS2A01G022900 chr2B 81.992 994 121 29 54 1021 15983732 15982771 0.000000e+00 791
15 TraesCS2A01G022900 chr2B 88.321 548 58 5 2771 3315 15692700 15692156 0.000000e+00 652
16 TraesCS2A01G022900 chr2B 88.139 548 59 5 2771 3315 15914977 15914433 0.000000e+00 647
17 TraesCS2A01G022900 chr2B 87.956 548 60 5 2771 3315 15816006 15815462 2.790000e-180 641
18 TraesCS2A01G022900 chr2B 86.765 340 33 7 1 329 15120237 15119899 5.220000e-98 368
19 TraesCS2A01G022900 chr2D 92.259 2196 136 16 283 2467 10800703 10798531 0.000000e+00 3083
20 TraesCS2A01G022900 chr2D 89.818 825 57 5 2498 3315 10798534 10797730 0.000000e+00 1033
21 TraesCS2A01G022900 chr2D 92.238 554 35 4 2498 3046 10250980 10251530 0.000000e+00 778
22 TraesCS2A01G022900 chrUn 88.831 2489 223 32 143 2612 339546387 339548839 0.000000e+00 3005
23 TraesCS2A01G022900 chrUn 88.710 2489 226 32 143 2612 339561656 339559204 0.000000e+00 2988
24 TraesCS2A01G022900 chrUn 88.283 2219 204 27 54 2247 349087642 349085455 0.000000e+00 2606
25 TraesCS2A01G022900 chrUn 88.148 2219 207 27 54 2247 349092415 349094602 0.000000e+00 2590
26 TraesCS2A01G022900 chrUn 76.989 352 57 14 54 385 328699613 328699960 2.630000e-41 180


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 TraesCS2A01G022900 chr2A 11042329 11045643 3314 True 6122 6122 100.0000 1 3315 1 chr2A.!!$R1 3314
1 TraesCS2A01G022900 chr2A 11307077 11310073 2996 True 3890 3890 90.0590 283 3315 1 chr2A.!!$R3 3032
2 TraesCS2A01G022900 chr2B 15635864 15639138 3274 True 4723 4723 92.6060 1 3315 1 chr2B.!!$R2 3314
3 TraesCS2A01G022900 chr2B 15379710 15382941 3231 True 3703 3703 87.4810 10 3265 1 chr2B.!!$R1 3255
4 TraesCS2A01G022900 chr2B 15880556 15883478 2922 True 3504 3504 88.4380 54 2977 1 chr2B.!!$R6 2923
5 TraesCS2A01G022900 chr2B 15959957 15962873 2916 True 3498 3498 88.4380 54 2977 1 chr2B.!!$R7 2923
6 TraesCS2A01G022900 chr2B 15724739 15727655 2916 True 3476 3476 88.2910 54 2977 1 chr2B.!!$R3 2923
7 TraesCS2A01G022900 chr2B 15787805 15790625 2820 True 3450 3450 88.8070 143 2977 1 chr2B.!!$R5 2834
8 TraesCS2A01G022900 chr2B 15815462 15818992 3530 True 2209 3777 89.8810 43 3315 2 chr2B.!!$R11 3272
9 TraesCS2A01G022900 chr2B 15914433 15917963 3530 True 2209 3771 89.9545 43 3315 2 chr2B.!!$R12 3272
10 TraesCS2A01G022900 chr2B 15692156 15695685 3529 True 2197 3742 89.9545 43 3315 2 chr2B.!!$R10 3272
11 TraesCS2A01G022900 chr2B 15116971 15120237 3266 True 2076 3784 88.7280 1 3315 2 chr2B.!!$R9 3314
12 TraesCS2A01G022900 chr2B 15756768 15757806 1038 True 1384 1384 90.5610 43 1108 1 chr2B.!!$R4 1065
13 TraesCS2A01G022900 chr2B 15982771 15983732 961 True 791 791 81.9920 54 1021 1 chr2B.!!$R8 967
14 TraesCS2A01G022900 chr2D 10797730 10800703 2973 True 2058 3083 91.0385 283 3315 2 chr2D.!!$R1 3032
15 TraesCS2A01G022900 chr2D 10250980 10251530 550 False 778 778 92.2380 2498 3046 1 chr2D.!!$F1 548
16 TraesCS2A01G022900 chrUn 339546387 339548839 2452 False 3005 3005 88.8310 143 2612 1 chrUn.!!$F2 2469
17 TraesCS2A01G022900 chrUn 339559204 339561656 2452 True 2988 2988 88.7100 143 2612 1 chrUn.!!$R1 2469
18 TraesCS2A01G022900 chrUn 349085455 349087642 2187 True 2606 2606 88.2830 54 2247 1 chrUn.!!$R2 2193
19 TraesCS2A01G022900 chrUn 349092415 349094602 2187 False 2590 2590 88.1480 54 2247 1 chrUn.!!$F3 2193

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
29 30 0.171007 GGTTGTGTGCATCAATCGGG 59.829 55.0 9.76 0.0 0.00 5.14 F
1353 1478 0.112606 CCCTCATAGGCCTCGACCTA 59.887 60.0 9.68 4.4 46.25 3.08 F
1448 1573 0.469917 ATCCGCGAAAGGTCATCCAT 59.530 50.0 8.23 0.0 35.89 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 1643 0.251341 ACAGCAATGGTTGTCCCTCC 60.251 55.0 0.00 0.0 32.53 4.30 R
2275 2401 0.534203 CCAACCGTGGTGTAGCTTGT 60.534 55.0 0.00 0.0 40.42 3.16 R
2612 2748 1.247567 GGGCACACAATTGTACAGCT 58.752 50.0 21.08 0.0 33.30 4.24 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
29 30 0.171007 GGTTGTGTGCATCAATCGGG 59.829 55.000 9.76 0.00 0.00 5.14
34 36 2.170397 TGTGTGCATCAATCGGGTAGAT 59.830 45.455 0.00 0.00 42.43 1.98
38 40 2.549064 CATCAATCGGGTAGATGCCA 57.451 50.000 0.00 0.00 40.02 4.92
82 85 2.609459 CCCGTGACACTATGAAATGAGC 59.391 50.000 3.68 0.00 0.00 4.26
121 131 5.104067 ACTTTTAAGGTTCCTTCTCACCTGT 60.104 40.000 7.41 0.00 43.05 4.00
179 190 1.632409 TCAGCAAAGGCCTTCTCTGAT 59.368 47.619 30.51 19.22 42.56 2.90
258 272 5.070313 AGTGGCCAACATTCACTTAATTTGT 59.930 36.000 7.24 0.00 38.44 2.83
417 490 4.665833 TTCTGTACATCAAGGATACCCG 57.334 45.455 0.00 0.00 37.58 5.28
418 491 2.364324 TCTGTACATCAAGGATACCCGC 59.636 50.000 0.00 0.00 37.58 6.13
419 492 2.102420 CTGTACATCAAGGATACCCGCA 59.898 50.000 0.00 0.00 37.58 5.69
420 493 2.502130 TGTACATCAAGGATACCCGCAA 59.498 45.455 0.00 0.00 37.58 4.85
421 494 2.799126 ACATCAAGGATACCCGCAAA 57.201 45.000 0.00 0.00 37.58 3.68
422 495 3.080300 ACATCAAGGATACCCGCAAAA 57.920 42.857 0.00 0.00 37.58 2.44
423 496 2.752903 ACATCAAGGATACCCGCAAAAC 59.247 45.455 0.00 0.00 37.58 2.43
424 497 2.871096 TCAAGGATACCCGCAAAACT 57.129 45.000 0.00 0.00 37.58 2.66
425 498 3.985019 TCAAGGATACCCGCAAAACTA 57.015 42.857 0.00 0.00 37.58 2.24
426 499 4.289238 TCAAGGATACCCGCAAAACTAA 57.711 40.909 0.00 0.00 37.58 2.24
427 500 4.004982 TCAAGGATACCCGCAAAACTAAC 58.995 43.478 0.00 0.00 37.58 2.34
428 501 2.995283 AGGATACCCGCAAAACTAACC 58.005 47.619 0.00 0.00 37.58 2.85
429 502 2.306512 AGGATACCCGCAAAACTAACCA 59.693 45.455 0.00 0.00 37.58 3.67
430 503 2.681344 GGATACCCGCAAAACTAACCAG 59.319 50.000 0.00 0.00 0.00 4.00
431 504 1.525941 TACCCGCAAAACTAACCAGC 58.474 50.000 0.00 0.00 0.00 4.85
432 505 0.466555 ACCCGCAAAACTAACCAGCA 60.467 50.000 0.00 0.00 0.00 4.41
433 506 0.671251 CCCGCAAAACTAACCAGCAA 59.329 50.000 0.00 0.00 0.00 3.91
434 507 1.067821 CCCGCAAAACTAACCAGCAAA 59.932 47.619 0.00 0.00 0.00 3.68
435 508 2.393764 CCGCAAAACTAACCAGCAAAG 58.606 47.619 0.00 0.00 0.00 2.77
436 509 2.034053 CCGCAAAACTAACCAGCAAAGA 59.966 45.455 0.00 0.00 0.00 2.52
437 510 3.305335 CCGCAAAACTAACCAGCAAAGAT 60.305 43.478 0.00 0.00 0.00 2.40
438 511 3.670055 CGCAAAACTAACCAGCAAAGATG 59.330 43.478 0.00 0.00 0.00 2.90
527 648 7.483375 TCTTCAAACACAACTGTTAAAACATCG 59.517 33.333 0.00 0.00 39.88 3.84
558 679 2.811431 CGACTAGTTCCACAAATTGCCA 59.189 45.455 0.00 0.00 0.00 4.92
816 938 3.607741 CTGCTCAAGGAGATGAACACAT 58.392 45.455 0.00 0.00 35.31 3.21
951 1075 1.972872 CCTCGGGCATATTCAGCTTT 58.027 50.000 0.00 0.00 0.00 3.51
952 1076 2.301346 CCTCGGGCATATTCAGCTTTT 58.699 47.619 0.00 0.00 0.00 2.27
1146 1271 2.596346 TGTCCAGGCAACATTGTCAAT 58.404 42.857 0.00 0.00 34.61 2.57
1161 1286 4.265904 TGTCAATGTCCGTCATGTAACT 57.734 40.909 0.00 0.00 36.81 2.24
1209 1334 2.227194 AGGCTTGTGTTCGGTAAAAGG 58.773 47.619 0.00 0.00 0.00 3.11
1228 1353 3.853207 AGGTACTTCAGTGACCTACCAA 58.147 45.455 20.49 0.00 41.91 3.67
1244 1369 4.466370 CCTACCAACTTCATCCACTAGTGA 59.534 45.833 24.68 10.67 0.00 3.41
1353 1478 0.112606 CCCTCATAGGCCTCGACCTA 59.887 60.000 9.68 4.40 46.25 3.08
1404 1529 2.039818 TGCAAACACTCAACCGGTTA 57.960 45.000 21.79 7.88 0.00 2.85
1448 1573 0.469917 ATCCGCGAAAGGTCATCCAT 59.530 50.000 8.23 0.00 35.89 3.41
1603 1729 7.322938 CGCATTATGCTCAATAGAAAGTTCATG 59.677 37.037 15.54 0.00 42.25 3.07
1762 1888 2.950309 GGCACTTGCTGAGATGATGAAT 59.050 45.455 0.38 0.00 41.70 2.57
1927 2053 2.502130 TCTTAATGTACCCCATGTCGCA 59.498 45.455 0.00 0.00 32.82 5.10
2155 2281 5.130477 TGGGATTTCACTTGGTACCTCTATC 59.870 44.000 14.36 6.36 0.00 2.08
2177 2303 1.987770 CAATGATGTTGTTCGCAAGGC 59.012 47.619 0.00 0.00 37.85 4.35
2243 2369 5.663106 AGTATCAGTCTCCAAGAAGGCAATA 59.337 40.000 0.00 0.00 37.29 1.90
2466 2597 5.186996 ACAAACAAAGAAGCAATCGATGT 57.813 34.783 0.00 0.00 34.51 3.06
2467 2598 6.312399 ACAAACAAAGAAGCAATCGATGTA 57.688 33.333 0.00 0.00 33.28 2.29
2468 2599 6.734137 ACAAACAAAGAAGCAATCGATGTAA 58.266 32.000 0.00 0.00 33.28 2.41
2469 2600 7.370383 ACAAACAAAGAAGCAATCGATGTAAT 58.630 30.769 0.00 0.00 33.28 1.89
2470 2601 8.511321 ACAAACAAAGAAGCAATCGATGTAATA 58.489 29.630 0.00 0.00 33.28 0.98
2472 2603 9.906660 AAACAAAGAAGCAATCGATGTAATAAA 57.093 25.926 0.00 0.00 33.28 1.40
2579 2711 5.991861 TGCAAATAATCCTTGGAATTGCAT 58.008 33.333 20.75 0.00 44.53 3.96
2702 2838 4.930963 TGTATTGCCAACTTGTTGTTCTG 58.069 39.130 11.82 0.00 36.63 3.02
2717 2856 9.834628 CTTGTTGTTCTGTGAACTAAGTTTTTA 57.165 29.630 11.06 0.00 0.00 1.52
2757 2896 6.204108 GGGTTTCTTTTGTCGTGAGAAATCTA 59.796 38.462 7.88 0.00 45.01 1.98
2797 3836 6.528537 AAGCTGTATCACCATGCATTTTAA 57.471 33.333 0.00 0.00 0.00 1.52
2837 3880 2.878406 CAATGATTAACGAGCCGGGAAT 59.122 45.455 2.18 0.00 0.00 3.01
2897 3945 3.118371 CGTCCTAATTAGGTTCAAGGCCT 60.118 47.826 27.14 0.00 44.02 5.19
2904 3952 0.779997 AGGTTCAAGGCCTGGTTCAT 59.220 50.000 5.69 0.00 34.56 2.57
2945 3995 3.771577 AATTCTGAAGAACTGGACCGT 57.228 42.857 0.00 0.00 36.80 4.83
2953 4003 0.535335 GAACTGGACCGTGGCAGATA 59.465 55.000 0.00 0.00 0.00 1.98
2954 4004 0.981183 AACTGGACCGTGGCAGATAA 59.019 50.000 0.00 0.00 0.00 1.75
2990 4040 2.354821 GTGAAACAGGTTGTCCACAGAC 59.645 50.000 8.72 0.00 39.36 3.51
3016 4066 0.313672 TGGTGCTTGAAAACGATGCC 59.686 50.000 0.00 0.00 0.00 4.40
3111 4162 5.748670 TGTCAGGCTAGTGGTTATTGTTA 57.251 39.130 0.00 0.00 0.00 2.41
3170 4224 6.708949 TGTACTCTCAGCTTTTCCGTTTATTT 59.291 34.615 0.00 0.00 0.00 1.40
3228 4282 2.823196 TCAGTGCAACAACAAAGACG 57.177 45.000 0.00 0.00 41.43 4.18
3233 4287 3.130340 AGTGCAACAACAAAGACGGAAAT 59.870 39.130 0.00 0.00 41.43 2.17
3234 4288 3.862845 GTGCAACAACAAAGACGGAAATT 59.137 39.130 0.00 0.00 36.32 1.82
3235 4289 3.862267 TGCAACAACAAAGACGGAAATTG 59.138 39.130 0.00 0.00 0.00 2.32
3239 4293 6.465978 CAACAACAAAGACGGAAATTGAAAC 58.534 36.000 0.00 0.00 0.00 2.78
3261 4317 4.157289 ACTTATTGCTGAATCACAGGCAAG 59.843 41.667 12.66 3.90 45.82 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.094739 CGATTGATGCACACAACCATCTAA 59.905 41.667 9.77 0.00 38.84 2.10
29 30 9.860898 AAAGATTTACAATTTTCTGGCATCTAC 57.139 29.630 0.00 0.00 0.00 2.59
38 40 9.965824 CGGGCATATAAAGATTTACAATTTTCT 57.034 29.630 0.00 0.00 0.00 2.52
82 85 9.996554 AACCTTAAAAGTTTTATGGAAATCCTG 57.003 29.630 31.86 13.78 36.82 3.86
121 131 7.162082 GGAGTCTTTCCTTCATTCAGACTTTA 58.838 38.462 1.84 0.00 43.42 1.85
179 190 3.966979 TGAGCTCTTCCAATTGGCATAA 58.033 40.909 20.33 8.22 34.44 1.90
278 299 2.158310 TGGAGAGTCCACCTTCTTCTGA 60.158 50.000 5.72 0.00 42.67 3.27
281 302 2.530701 TCTGGAGAGTCCACCTTCTTC 58.469 52.381 5.72 0.00 42.67 2.87
322 343 1.306148 CATTCATGTCGCCTCATGCT 58.694 50.000 9.91 0.12 43.18 3.79
323 344 0.309922 CCATTCATGTCGCCTCATGC 59.690 55.000 9.91 0.00 43.18 4.06
398 471 2.102420 TGCGGGTATCCTTGATGTACAG 59.898 50.000 0.33 0.00 0.00 2.74
404 477 3.366052 AGTTTTGCGGGTATCCTTGAT 57.634 42.857 0.00 0.00 0.00 2.57
413 486 0.466555 TGCTGGTTAGTTTTGCGGGT 60.467 50.000 0.00 0.00 0.00 5.28
414 487 0.671251 TTGCTGGTTAGTTTTGCGGG 59.329 50.000 0.00 0.00 0.00 6.13
415 488 2.034053 TCTTTGCTGGTTAGTTTTGCGG 59.966 45.455 0.00 0.00 0.00 5.69
416 489 3.347958 TCTTTGCTGGTTAGTTTTGCG 57.652 42.857 0.00 0.00 0.00 4.85
417 490 3.429881 GCATCTTTGCTGGTTAGTTTTGC 59.570 43.478 0.00 0.00 45.77 3.68
431 504 0.036010 ACAGACGGGGAGCATCTTTG 60.036 55.000 0.00 0.00 33.73 2.77
432 505 0.250513 GACAGACGGGGAGCATCTTT 59.749 55.000 0.00 0.00 33.73 2.52
433 506 1.617947 GGACAGACGGGGAGCATCTT 61.618 60.000 0.00 0.00 33.73 2.40
434 507 2.060980 GGACAGACGGGGAGCATCT 61.061 63.158 0.00 0.00 33.73 2.90
435 508 0.755698 TAGGACAGACGGGGAGCATC 60.756 60.000 0.00 0.00 0.00 3.91
436 509 0.105453 ATAGGACAGACGGGGAGCAT 60.105 55.000 0.00 0.00 0.00 3.79
437 510 0.554305 TATAGGACAGACGGGGAGCA 59.446 55.000 0.00 0.00 0.00 4.26
438 511 1.700955 TTATAGGACAGACGGGGAGC 58.299 55.000 0.00 0.00 0.00 4.70
439 512 4.220163 GGTATTTATAGGACAGACGGGGAG 59.780 50.000 0.00 0.00 0.00 4.30
440 513 4.154942 GGTATTTATAGGACAGACGGGGA 58.845 47.826 0.00 0.00 0.00 4.81
444 517 3.005050 TGCGGGTATTTATAGGACAGACG 59.995 47.826 0.00 0.00 0.00 4.18
527 648 2.762327 TGGAACTAGTCGGTAATGGACC 59.238 50.000 0.00 0.00 45.91 4.46
558 679 9.261035 CAGGGTGTTATATGAAGTAGGATAGAT 57.739 37.037 0.00 0.00 0.00 1.98
816 938 1.409064 GAGACGGAGGCACATGATGTA 59.591 52.381 0.00 0.00 0.00 2.29
951 1075 1.668826 AGATGGAGCCCTTGTACCAA 58.331 50.000 0.00 0.00 36.00 3.67
952 1076 1.559682 GAAGATGGAGCCCTTGTACCA 59.440 52.381 0.00 0.00 36.83 3.25
1146 1271 3.069016 AGTGTTGAGTTACATGACGGACA 59.931 43.478 0.00 0.00 0.00 4.02
1209 1334 4.868314 AGTTGGTAGGTCACTGAAGTAC 57.132 45.455 0.00 0.00 0.00 2.73
1228 1353 2.499289 CAGGCTCACTAGTGGATGAAGT 59.501 50.000 22.48 0.00 0.00 3.01
1244 1369 0.545171 CACCTCATCATGTCCAGGCT 59.455 55.000 6.52 0.00 0.00 4.58
1353 1478 2.833943 GGAAACCTTTTCATGGCCATCT 59.166 45.455 17.61 0.00 0.00 2.90
1404 1529 4.161189 CGCTCCTCTATAATGGGATCATGT 59.839 45.833 0.00 0.00 33.18 3.21
1448 1573 7.403312 TTCTTTTCACCACATTTCTCAAGAA 57.597 32.000 0.00 0.00 0.00 2.52
1518 1643 0.251341 ACAGCAATGGTTGTCCCTCC 60.251 55.000 0.00 0.00 32.53 4.30
1580 1705 8.229253 TGCATGAACTTTCTATTGAGCATAAT 57.771 30.769 0.00 0.00 0.00 1.28
1584 1709 6.071784 ACAATGCATGAACTTTCTATTGAGCA 60.072 34.615 0.00 0.00 0.00 4.26
1603 1729 8.352201 TGTATAATATGGCTCAAAGAACAATGC 58.648 33.333 0.00 0.00 0.00 3.56
1762 1888 2.203470 TTTGCATGATCTCTGGCACA 57.797 45.000 0.00 0.00 35.74 4.57
1784 1910 2.163815 CGGTATCGAGTTCCTCAGTTGT 59.836 50.000 0.00 0.00 39.00 3.32
1927 2053 0.667993 CAACAGTTGTGTCCGCCATT 59.332 50.000 4.99 0.00 35.08 3.16
2125 2251 2.224867 ACCAAGTGAAATCCCAGGACAG 60.225 50.000 0.00 0.00 0.00 3.51
2155 2281 2.981805 CCTTGCGAACAACATCATTGTG 59.018 45.455 0.00 0.00 35.83 3.33
2177 2303 1.542915 CCAAGTGAATCCCTGCAACAG 59.457 52.381 0.00 0.00 0.00 3.16
2243 2369 0.613853 TCAGCTAGTACAAGGCCCGT 60.614 55.000 0.00 0.00 0.00 5.28
2275 2401 0.534203 CCAACCGTGGTGTAGCTTGT 60.534 55.000 0.00 0.00 40.42 3.16
2366 2494 7.563888 TGTAACACGCACTAGTTCTAGATAT 57.436 36.000 12.97 0.00 0.00 1.63
2372 2500 4.252971 ACATGTAACACGCACTAGTTCT 57.747 40.909 0.00 0.00 0.00 3.01
2382 2510 2.548057 AGTGCCAGAAACATGTAACACG 59.452 45.455 0.00 0.00 32.22 4.49
2612 2748 1.247567 GGGCACACAATTGTACAGCT 58.752 50.000 21.08 0.00 33.30 4.24
2679 2815 5.105554 ACAGAACAACAAGTTGGCAATACAA 60.106 36.000 16.45 0.00 44.45 2.41
2837 3880 1.476110 CCTTTTCGGTGACAGGGAACA 60.476 52.381 0.00 0.00 0.00 3.18
2876 3924 4.200092 CAGGCCTTGAACCTAATTAGGAC 58.800 47.826 33.60 25.21 46.63 3.85
2884 3932 1.440618 TGAACCAGGCCTTGAACCTA 58.559 50.000 11.55 0.00 35.10 3.08
2897 3945 5.683876 TGTTTCAAAGGGAAAATGAACCA 57.316 34.783 0.00 0.00 46.53 3.67
2904 3952 7.667635 AGAATTTTGGTTGTTTCAAAGGGAAAA 59.332 29.630 0.00 0.00 46.53 2.29
2953 4003 8.806146 ACCTGTTTCACTTGATTATTAAGCATT 58.194 29.630 0.00 0.00 0.00 3.56
2954 4004 8.353423 ACCTGTTTCACTTGATTATTAAGCAT 57.647 30.769 0.00 0.00 0.00 3.79
3064 4115 8.588789 CAATACACTGTCATGCAAAATACAATG 58.411 33.333 0.00 0.00 0.00 2.82
3131 4182 5.945155 TGAGAGTACAAACCAAACAACAAC 58.055 37.500 0.00 0.00 0.00 3.32
3170 4224 7.707624 ATTATTGAAATGAAGAACCTGCAGA 57.292 32.000 17.39 0.00 0.00 4.26
3228 4282 8.650714 GTGATTCAGCAATAAGTTTCAATTTCC 58.349 33.333 0.00 0.00 0.00 3.13
3233 4287 6.680810 CCTGTGATTCAGCAATAAGTTTCAA 58.319 36.000 0.00 0.00 42.38 2.69
3234 4288 5.335897 GCCTGTGATTCAGCAATAAGTTTCA 60.336 40.000 0.00 0.00 42.38 2.69
3235 4289 5.098211 GCCTGTGATTCAGCAATAAGTTTC 58.902 41.667 0.00 0.00 42.38 2.78
3239 4293 4.439700 CCTTGCCTGTGATTCAGCAATAAG 60.440 45.833 10.98 2.34 42.38 1.73


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

AutoCloner maintained by Alex Coulton.