Multiple sequence alignment - TraesCS2D01G490400

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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 TraesCS2D01G490400 chr2D 100.000 3326 0 0 1 3326 589281300 589284625 0.000000e+00 6143
1 TraesCS2D01G490400 chr2D 86.950 1341 161 9 993 2326 589522761 589524094 0.000000e+00 1495
2 TraesCS2D01G490400 chr2D 86.869 1348 162 9 986 2326 589684853 589683514 0.000000e+00 1495
3 TraesCS2D01G490400 chr2B 91.738 1743 83 16 638 2347 712889358 712891072 0.000000e+00 2364
4 TraesCS2D01G490400 chr2B 86.622 1338 171 6 993 2326 713791108 713792441 0.000000e+00 1472
5 TraesCS2D01G490400 chr2B 86.424 1348 165 12 986 2326 713940344 713939008 0.000000e+00 1459
6 TraesCS2D01G490400 chr2B 91.373 1020 41 13 2349 3326 712891340 712892354 0.000000e+00 1352
7 TraesCS2D01G490400 chr2A 94.888 1467 70 2 876 2340 723625218 723626681 0.000000e+00 2289
8 TraesCS2D01G490400 chr2A 86.567 1340 167 8 990 2326 724018466 724017137 0.000000e+00 1465
9 TraesCS2D01G490400 chr2A 86.125 1355 163 11 993 2326 723867205 723868555 0.000000e+00 1437
10 TraesCS2D01G490400 chr2A 86.460 613 51 9 2380 2986 723626957 723627543 0.000000e+00 643
11 TraesCS2D01G490400 chr2A 87.281 228 12 4 638 848 723624997 723625224 9.220000e-61 244
12 TraesCS2D01G490400 chr6B 79.904 1249 223 19 1072 2311 686363867 686365096 0.000000e+00 891
13 TraesCS2D01G490400 chr7B 78.441 1257 232 26 1072 2315 679359754 679360984 0.000000e+00 784
14 TraesCS2D01G490400 chr7B 80.182 550 84 14 1 529 708412691 708413236 4.020000e-104 388
15 TraesCS2D01G490400 chrUn 76.089 1263 243 42 1077 2314 15345647 15346875 3.670000e-169 604
16 TraesCS2D01G490400 chr1D 81.064 639 76 25 1 620 225408539 225409151 5.020000e-128 468
17 TraesCS2D01G490400 chr1D 79.121 637 100 24 1 614 486131628 486131002 3.090000e-110 409
18 TraesCS2D01G490400 chr1D 85.000 360 49 3 1 355 2890928 2891287 8.770000e-96 361
19 TraesCS2D01G490400 chr3B 82.643 507 77 7 5 509 581131628 581131131 3.940000e-119 438
20 TraesCS2D01G490400 chr4D 79.321 648 95 26 1 620 8141393 8142029 5.130000e-113 418
21 TraesCS2D01G490400 chr6D 80.545 550 80 15 1 528 210729429 210728885 6.690000e-107 398
22 TraesCS2D01G490400 chr6D 83.708 356 54 4 1 354 98280930 98281283 1.910000e-87 333
23 TraesCS2D01G490400 chr5D 78.922 631 87 24 1 608 23761000 23761607 1.450000e-103 387
24 TraesCS2D01G490400 chr3D 78.537 629 92 22 1 608 552418583 552419189 1.130000e-99 374
25 TraesCS2D01G490400 chr6A 83.196 363 57 4 4 362 68605628 68605266 2.470000e-86 329
26 TraesCS2D01G490400 chr7D 82.709 347 31 2 178 504 372961760 372961423 7.030000e-72 281


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 TraesCS2D01G490400 chr2D 589281300 589284625 3325 False 6143.000000 6143 100.0000 1 3326 1 chr2D.!!$F1 3325
1 TraesCS2D01G490400 chr2D 589522761 589524094 1333 False 1495.000000 1495 86.9500 993 2326 1 chr2D.!!$F2 1333
2 TraesCS2D01G490400 chr2D 589683514 589684853 1339 True 1495.000000 1495 86.8690 986 2326 1 chr2D.!!$R1 1340
3 TraesCS2D01G490400 chr2B 712889358 712892354 2996 False 1858.000000 2364 91.5555 638 3326 2 chr2B.!!$F2 2688
4 TraesCS2D01G490400 chr2B 713791108 713792441 1333 False 1472.000000 1472 86.6220 993 2326 1 chr2B.!!$F1 1333
5 TraesCS2D01G490400 chr2B 713939008 713940344 1336 True 1459.000000 1459 86.4240 986 2326 1 chr2B.!!$R1 1340
6 TraesCS2D01G490400 chr2A 724017137 724018466 1329 True 1465.000000 1465 86.5670 990 2326 1 chr2A.!!$R1 1336
7 TraesCS2D01G490400 chr2A 723867205 723868555 1350 False 1437.000000 1437 86.1250 993 2326 1 chr2A.!!$F1 1333
8 TraesCS2D01G490400 chr2A 723624997 723627543 2546 False 1058.666667 2289 89.5430 638 2986 3 chr2A.!!$F2 2348
9 TraesCS2D01G490400 chr6B 686363867 686365096 1229 False 891.000000 891 79.9040 1072 2311 1 chr6B.!!$F1 1239
10 TraesCS2D01G490400 chr7B 679359754 679360984 1230 False 784.000000 784 78.4410 1072 2315 1 chr7B.!!$F1 1243
11 TraesCS2D01G490400 chr7B 708412691 708413236 545 False 388.000000 388 80.1820 1 529 1 chr7B.!!$F2 528
12 TraesCS2D01G490400 chrUn 15345647 15346875 1228 False 604.000000 604 76.0890 1077 2314 1 chrUn.!!$F1 1237
13 TraesCS2D01G490400 chr1D 225408539 225409151 612 False 468.000000 468 81.0640 1 620 1 chr1D.!!$F2 619
14 TraesCS2D01G490400 chr1D 486131002 486131628 626 True 409.000000 409 79.1210 1 614 1 chr1D.!!$R1 613
15 TraesCS2D01G490400 chr4D 8141393 8142029 636 False 418.000000 418 79.3210 1 620 1 chr4D.!!$F1 619
16 TraesCS2D01G490400 chr6D 210728885 210729429 544 True 398.000000 398 80.5450 1 528 1 chr6D.!!$R1 527
17 TraesCS2D01G490400 chr5D 23761000 23761607 607 False 387.000000 387 78.9220 1 608 1 chr5D.!!$F1 607
18 TraesCS2D01G490400 chr3D 552418583 552419189 606 False 374.000000 374 78.5370 1 608 1 chr3D.!!$F1 607

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
300 315 0.032815 TCAACGGAGATGCACGACAA 59.967 50.0 1.06 0.0 0.00 3.18 F
634 689 0.400670 GGAGGCCTAAGGGAGATGGT 60.401 60.0 4.42 0.0 33.58 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 1411 0.392706 ATCGGCATGACGCTATCCAA 59.607 50.0 18.42 0.0 41.91 3.53 R
2616 3047 0.470766 ACCCTACACACCTCGCAAAA 59.529 50.0 0.00 0.0 0.00 2.44 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
61 62 5.163992 GCGATGTCTTCAACAAGATAACGAA 60.164 40.000 12.93 0.00 43.99 3.85
125 126 1.533129 GGTTTTCACCGGCAATATCGC 60.533 52.381 0.00 0.00 31.60 4.58
148 151 3.130160 ACTCGACGCCGGGACTAC 61.130 66.667 0.00 0.00 38.95 2.73
158 161 0.319040 CCGGGACTACATGCGAGATG 60.319 60.000 0.00 0.00 0.00 2.90
162 165 1.495878 GACTACATGCGAGATGCCAG 58.504 55.000 2.34 0.00 45.60 4.85
171 174 1.817099 GAGATGCCAGAACCAGCCG 60.817 63.158 0.00 0.00 0.00 5.52
253 268 2.358737 CCTCGTGTTGCAGGTCCC 60.359 66.667 0.00 0.00 0.00 4.46
275 290 1.664649 CAGAAGCCGCTTGACGTCA 60.665 57.895 15.76 15.76 41.42 4.35
300 315 0.032815 TCAACGGAGATGCACGACAA 59.967 50.000 1.06 0.00 0.00 3.18
302 317 1.282248 AACGGAGATGCACGACAACG 61.282 55.000 1.06 0.00 45.75 4.10
418 454 4.794648 CCGCCCTTGATTCGGCCA 62.795 66.667 2.24 0.00 42.53 5.36
427 463 3.181461 CCTTGATTCGGCCAGAGTAGAAT 60.181 47.826 2.24 1.74 36.19 2.40
452 488 2.367202 ACCCAGATCCAATCGCGGT 61.367 57.895 6.13 0.00 32.79 5.68
475 511 2.124151 GAGGATTGCCACCGCCAT 60.124 61.111 0.00 0.00 36.29 4.40
504 540 2.787915 GCAAGCTTAGCCTGCGAC 59.212 61.111 12.21 0.00 36.27 5.19
542 597 4.394712 GAGGTGGGGTCGCTGGTG 62.395 72.222 0.00 0.00 0.00 4.17
543 598 4.954118 AGGTGGGGTCGCTGGTGA 62.954 66.667 0.00 0.00 0.00 4.02
544 599 3.717294 GGTGGGGTCGCTGGTGAT 61.717 66.667 0.00 0.00 0.00 3.06
545 600 2.436646 GTGGGGTCGCTGGTGATG 60.437 66.667 0.00 0.00 0.00 3.07
546 601 2.606213 TGGGGTCGCTGGTGATGA 60.606 61.111 0.00 0.00 0.00 2.92
549 604 1.327690 GGGGTCGCTGGTGATGACTA 61.328 60.000 0.00 0.00 33.21 2.59
618 673 4.862823 GAGGAGGGGTCGGGGGAG 62.863 77.778 0.00 0.00 0.00 4.30
624 679 4.810184 GGGTCGGGGGAGGCCTAA 62.810 72.222 4.42 0.00 35.87 2.69
625 680 3.162154 GGTCGGGGGAGGCCTAAG 61.162 72.222 4.42 0.00 32.02 2.18
626 681 3.162154 GTCGGGGGAGGCCTAAGG 61.162 72.222 4.42 0.00 0.00 2.69
627 682 4.492303 TCGGGGGAGGCCTAAGGG 62.492 72.222 4.42 0.00 0.00 3.95
628 683 4.492303 CGGGGGAGGCCTAAGGGA 62.492 72.222 4.42 0.00 33.58 4.20
629 684 2.448736 GGGGGAGGCCTAAGGGAG 60.449 72.222 4.42 0.00 33.58 4.30
630 685 2.703430 GGGGAGGCCTAAGGGAGA 59.297 66.667 4.42 0.00 33.58 3.71
631 686 1.240428 GGGGAGGCCTAAGGGAGAT 59.760 63.158 4.42 0.00 33.58 2.75
632 687 1.130678 GGGGAGGCCTAAGGGAGATG 61.131 65.000 4.42 0.00 33.58 2.90
633 688 1.130678 GGGAGGCCTAAGGGAGATGG 61.131 65.000 4.42 0.00 33.58 3.51
634 689 0.400670 GGAGGCCTAAGGGAGATGGT 60.401 60.000 4.42 0.00 33.58 3.55
635 690 1.132817 GGAGGCCTAAGGGAGATGGTA 60.133 57.143 4.42 0.00 33.58 3.25
636 691 1.972075 GAGGCCTAAGGGAGATGGTAC 59.028 57.143 4.42 0.00 33.58 3.34
642 697 0.537188 AAGGGAGATGGTACGCAGTG 59.463 55.000 0.00 0.00 45.73 3.66
660 715 4.503910 CAGTGCAATAGCTAGTGTACCAA 58.496 43.478 30.22 8.24 37.55 3.67
681 740 2.443416 ACATGTGCATGCATGAAGAGT 58.557 42.857 30.64 15.03 46.65 3.24
804 892 3.179265 CAGCCGTAGCGTTCACCG 61.179 66.667 0.00 0.00 46.67 4.94
845 933 2.677836 TCGTGCATTAACAATCTCTGGC 59.322 45.455 0.00 0.00 0.00 4.85
846 934 2.679837 CGTGCATTAACAATCTCTGGCT 59.320 45.455 0.00 0.00 0.00 4.75
847 935 3.871006 CGTGCATTAACAATCTCTGGCTA 59.129 43.478 0.00 0.00 0.00 3.93
848 936 4.025396 CGTGCATTAACAATCTCTGGCTAG 60.025 45.833 0.00 0.00 0.00 3.42
849 937 3.879295 TGCATTAACAATCTCTGGCTAGC 59.121 43.478 6.04 6.04 0.00 3.42
850 938 4.133078 GCATTAACAATCTCTGGCTAGCT 58.867 43.478 15.72 0.00 0.00 3.32
851 939 4.213059 GCATTAACAATCTCTGGCTAGCTC 59.787 45.833 15.72 5.44 0.00 4.09
852 940 5.363101 CATTAACAATCTCTGGCTAGCTCA 58.637 41.667 15.72 10.05 0.00 4.26
853 941 2.977772 ACAATCTCTGGCTAGCTCAC 57.022 50.000 15.72 0.00 0.00 3.51
854 942 1.484240 ACAATCTCTGGCTAGCTCACC 59.516 52.381 15.72 0.00 0.00 4.02
855 943 0.749649 AATCTCTGGCTAGCTCACCG 59.250 55.000 15.72 0.84 0.00 4.94
856 944 1.743321 ATCTCTGGCTAGCTCACCGC 61.743 60.000 15.72 0.00 39.57 5.68
857 945 3.438017 CTCTGGCTAGCTCACCGCC 62.438 68.421 15.72 8.76 44.02 6.13
858 946 3.465403 CTGGCTAGCTCACCGCCT 61.465 66.667 15.72 0.00 44.09 5.52
859 947 3.438017 CTGGCTAGCTCACCGCCTC 62.438 68.421 15.72 0.00 44.09 4.70
860 948 3.461773 GGCTAGCTCACCGCCTCA 61.462 66.667 15.72 0.00 40.62 3.86
861 949 2.202810 GCTAGCTCACCGCCTCAC 60.203 66.667 7.70 0.00 40.39 3.51
862 950 2.496817 CTAGCTCACCGCCTCACC 59.503 66.667 0.00 0.00 40.39 4.02
863 951 3.075005 TAGCTCACCGCCTCACCC 61.075 66.667 0.00 0.00 40.39 4.61
864 952 3.602075 TAGCTCACCGCCTCACCCT 62.602 63.158 0.00 0.00 40.39 4.34
865 953 4.459089 GCTCACCGCCTCACCCTC 62.459 72.222 0.00 0.00 0.00 4.30
866 954 4.135153 CTCACCGCCTCACCCTCG 62.135 72.222 0.00 0.00 0.00 4.63
871 959 3.827898 CGCCTCACCCTCGGTCTC 61.828 72.222 0.00 0.00 31.02 3.36
872 960 2.363147 GCCTCACCCTCGGTCTCT 60.363 66.667 0.00 0.00 31.02 3.10
873 961 1.076923 GCCTCACCCTCGGTCTCTA 60.077 63.158 0.00 0.00 31.02 2.43
874 962 1.104577 GCCTCACCCTCGGTCTCTAG 61.105 65.000 0.00 0.00 31.02 2.43
890 980 9.316594 TCGGTCTCTAGCTAGCTATCTATATAT 57.683 37.037 24.36 0.00 0.00 0.86
1006 1096 1.236616 TGCACTTGTCGCCATGAAGG 61.237 55.000 0.00 0.00 41.84 3.46
1179 1269 2.281208 CCCAACGCCGTCCTTGAA 60.281 61.111 0.00 0.00 0.00 2.69
1845 1980 3.645975 CGCGTTTCCACCAGCGTT 61.646 61.111 0.00 0.00 46.48 4.84
2077 2215 2.604686 AGAAGGAGCGGCTGGTGA 60.605 61.111 7.50 0.00 0.00 4.02
2202 2354 3.774766 TCTTCTTCATGCCAAGCTACCTA 59.225 43.478 0.00 0.00 0.00 3.08
2347 2499 7.985184 AGTAGATTTGCATCGTTGGAGTTAATA 59.015 33.333 0.00 0.00 34.17 0.98
2637 3068 1.116536 TTGCGAGGTGTGTAGGGTGA 61.117 55.000 0.00 0.00 0.00 4.02
2703 3154 5.995282 TGTTCGTTGTGTTCTTCATTATCCT 59.005 36.000 0.00 0.00 0.00 3.24
2740 3191 6.657836 TCGAATTTTCTCGGGATTAAGTTC 57.342 37.500 0.00 0.00 39.35 3.01
2836 3287 6.691754 TTAATATGGATGACACGCAATGTT 57.308 33.333 0.00 0.00 43.56 2.71
2900 3351 1.872952 TCAATGCACCAAGACAAGTCG 59.127 47.619 0.00 0.00 34.09 4.18
2935 3386 4.038642 TGTTTGTGCTTATTTGGACCCTTC 59.961 41.667 0.00 0.00 0.00 3.46
2949 3401 1.004758 CCTTCCCCTCCTCCCATGA 59.995 63.158 0.00 0.00 0.00 3.07
2971 3423 2.703536 GTTCCCAGGTGAAAACCCAATT 59.296 45.455 0.00 0.00 0.00 2.32
2978 3430 4.037222 AGGTGAAAACCCAATTGTTTCCT 58.963 39.130 14.15 6.18 37.46 3.36
3015 3467 1.172812 GCTCTTGCGTTGTCCCCTTT 61.173 55.000 0.00 0.00 0.00 3.11
3018 3470 1.407258 TCTTGCGTTGTCCCCTTTTTG 59.593 47.619 0.00 0.00 0.00 2.44
3025 3477 1.289066 GTCCCCTTTTTGGAAGCGC 59.711 57.895 0.00 0.00 38.35 5.92
3077 3529 1.076332 GCGGCGAATATATGGTGGTC 58.924 55.000 12.98 0.00 0.00 4.02
3078 3530 1.606994 GCGGCGAATATATGGTGGTCA 60.607 52.381 12.98 0.00 0.00 4.02
3084 3536 4.065088 CGAATATATGGTGGTCACTTGGG 58.935 47.826 0.93 0.00 0.00 4.12
3095 3547 2.565841 GTCACTTGGGGCTATGCTTAG 58.434 52.381 2.28 2.28 0.00 2.18
3139 3591 1.006571 TCGTTCGGAAGTGCCACTC 60.007 57.895 0.00 0.00 35.94 3.51
3201 3653 2.165437 TGGTGTTTTGTTCTTGGACAGC 59.835 45.455 0.00 0.00 38.72 4.40
3215 3667 0.875059 GACAGCTGTTGGTTGCTACC 59.125 55.000 22.65 10.70 45.26 3.18
3251 3725 2.030701 GTGAGCGACTCTACCGAACTAG 59.969 54.545 8.07 0.00 0.00 2.57
3284 3758 3.053896 GGCCCTTTTCGTCGGTGG 61.054 66.667 0.00 0.00 0.00 4.61
3310 3784 5.671493 ACGGGATTAATTTTGACTCGATCT 58.329 37.500 0.83 0.00 0.00 2.75
3316 3790 6.721571 TTAATTTTGACTCGATCTGACCAC 57.278 37.500 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.448365 CATCGCCACTGCAGCTACA 60.448 57.895 15.27 0.00 37.32 2.74
92 93 2.415512 GTGAAAACCGTGCTATGACTCC 59.584 50.000 0.00 0.00 0.00 3.85
148 151 0.745486 TGGTTCTGGCATCTCGCATG 60.745 55.000 0.00 0.00 45.17 4.06
171 174 4.162690 CGCTAGAGGTGGGTGGCC 62.163 72.222 0.00 0.00 0.00 5.36
175 190 0.684805 CTCCTTCGCTAGAGGTGGGT 60.685 60.000 0.00 0.00 0.00 4.51
176 191 0.395862 TCTCCTTCGCTAGAGGTGGG 60.396 60.000 0.00 0.00 0.00 4.61
184 199 1.686325 GGTGGCCATCTCCTTCGCTA 61.686 60.000 9.72 0.00 0.00 4.26
185 200 2.586792 GTGGCCATCTCCTTCGCT 59.413 61.111 9.72 0.00 0.00 4.93
302 317 3.443045 CAATGGGCCGCTCCACAC 61.443 66.667 0.00 0.00 39.97 3.82
418 454 1.522569 GGTGGCGGCATTCTACTCT 59.477 57.895 17.19 0.00 0.00 3.24
490 526 4.821589 GGCGTCGCAGGCTAAGCT 62.822 66.667 20.50 0.00 0.00 3.74
531 586 0.103208 CTAGTCATCACCAGCGACCC 59.897 60.000 0.00 0.00 0.00 4.46
534 589 1.393603 CCTCTAGTCATCACCAGCGA 58.606 55.000 0.00 0.00 0.00 4.93
535 590 0.249238 GCCTCTAGTCATCACCAGCG 60.249 60.000 0.00 0.00 0.00 5.18
537 592 0.387202 CCGCCTCTAGTCATCACCAG 59.613 60.000 0.00 0.00 0.00 4.00
538 593 1.676678 GCCGCCTCTAGTCATCACCA 61.677 60.000 0.00 0.00 0.00 4.17
539 594 1.068250 GCCGCCTCTAGTCATCACC 59.932 63.158 0.00 0.00 0.00 4.02
540 595 1.068250 GGCCGCCTCTAGTCATCAC 59.932 63.158 0.71 0.00 0.00 3.06
541 596 2.490148 CGGCCGCCTCTAGTCATCA 61.490 63.158 14.67 0.00 0.00 3.07
542 597 2.336809 CGGCCGCCTCTAGTCATC 59.663 66.667 14.67 0.00 0.00 2.92
543 598 3.227276 CCGGCCGCCTCTAGTCAT 61.227 66.667 22.85 0.00 0.00 3.06
611 666 4.492303 TCCCTTAGGCCTCCCCCG 62.492 72.222 9.68 0.00 0.00 5.73
615 670 0.400670 ACCATCTCCCTTAGGCCTCC 60.401 60.000 9.68 0.00 0.00 4.30
617 672 1.758123 CGTACCATCTCCCTTAGGCCT 60.758 57.143 11.78 11.78 0.00 5.19
618 673 0.680061 CGTACCATCTCCCTTAGGCC 59.320 60.000 0.00 0.00 0.00 5.19
619 674 0.033642 GCGTACCATCTCCCTTAGGC 59.966 60.000 0.00 0.00 0.00 3.93
620 675 1.341531 CTGCGTACCATCTCCCTTAGG 59.658 57.143 0.00 0.00 0.00 2.69
621 676 2.032620 ACTGCGTACCATCTCCCTTAG 58.967 52.381 0.00 0.00 0.00 2.18
622 677 1.754803 CACTGCGTACCATCTCCCTTA 59.245 52.381 0.00 0.00 0.00 2.69
623 678 0.537188 CACTGCGTACCATCTCCCTT 59.463 55.000 0.00 0.00 0.00 3.95
624 679 1.961180 GCACTGCGTACCATCTCCCT 61.961 60.000 0.00 0.00 0.00 4.20
625 680 1.521681 GCACTGCGTACCATCTCCC 60.522 63.158 0.00 0.00 0.00 4.30
626 681 0.391130 TTGCACTGCGTACCATCTCC 60.391 55.000 0.00 0.00 0.00 3.71
627 682 1.656652 ATTGCACTGCGTACCATCTC 58.343 50.000 0.00 0.00 0.00 2.75
628 683 2.826428 CTATTGCACTGCGTACCATCT 58.174 47.619 0.00 0.00 0.00 2.90
629 684 1.261619 GCTATTGCACTGCGTACCATC 59.738 52.381 0.00 0.00 39.41 3.51
630 685 1.134401 AGCTATTGCACTGCGTACCAT 60.134 47.619 1.12 0.00 42.74 3.55
631 686 0.249120 AGCTATTGCACTGCGTACCA 59.751 50.000 1.12 0.00 42.74 3.25
632 687 2.128035 CTAGCTATTGCACTGCGTACC 58.872 52.381 1.12 0.00 42.74 3.34
633 688 2.535984 CACTAGCTATTGCACTGCGTAC 59.464 50.000 1.12 0.00 42.74 3.67
634 689 2.165641 ACACTAGCTATTGCACTGCGTA 59.834 45.455 10.78 0.00 42.74 4.42
635 690 1.066858 ACACTAGCTATTGCACTGCGT 60.067 47.619 10.78 0.00 42.74 5.24
636 691 1.645034 ACACTAGCTATTGCACTGCG 58.355 50.000 10.78 0.00 42.74 5.18
642 697 5.354234 ACATGTTTGGTACACTAGCTATTGC 59.646 40.000 10.78 0.00 40.19 3.56
660 715 2.823747 ACTCTTCATGCATGCACATGTT 59.176 40.909 25.37 3.10 46.15 2.71
681 740 0.249031 CACGAGCACCATATCTGCGA 60.249 55.000 0.00 0.00 39.79 5.10
738 797 5.250543 TCTGGGTGAAGGTTATGATTTCTCA 59.749 40.000 0.00 0.00 35.41 3.27
804 892 3.732471 CGAGAAGAGATCAAACGAGGGTC 60.732 52.174 0.00 0.00 0.00 4.46
849 937 4.135153 CGAGGGTGAGGCGGTGAG 62.135 72.222 0.00 0.00 0.00 3.51
854 942 2.888464 TAGAGACCGAGGGTGAGGCG 62.888 65.000 0.00 0.00 35.25 5.52
855 943 1.076923 TAGAGACCGAGGGTGAGGC 60.077 63.158 0.00 0.00 35.25 4.70
856 944 1.104577 GCTAGAGACCGAGGGTGAGG 61.105 65.000 0.00 0.00 35.25 3.86
857 945 0.106918 AGCTAGAGACCGAGGGTGAG 60.107 60.000 0.00 0.00 35.25 3.51
858 946 1.141254 CTAGCTAGAGACCGAGGGTGA 59.859 57.143 16.15 0.00 35.25 4.02
859 947 1.600023 CTAGCTAGAGACCGAGGGTG 58.400 60.000 16.15 0.00 35.25 4.61
860 948 0.179012 GCTAGCTAGAGACCGAGGGT 60.179 60.000 25.15 0.00 39.44 4.34
861 949 0.109723 AGCTAGCTAGAGACCGAGGG 59.890 60.000 25.15 0.00 0.00 4.30
862 950 2.843401 TAGCTAGCTAGAGACCGAGG 57.157 55.000 25.15 0.00 0.00 4.63
863 951 4.202245 AGATAGCTAGCTAGAGACCGAG 57.798 50.000 27.42 0.00 31.45 4.63
864 952 5.943349 ATAGATAGCTAGCTAGAGACCGA 57.057 43.478 27.42 6.32 31.45 4.69
890 980 8.264347 TGTTAGCTAAAATCATCCAGTGATGTA 58.736 33.333 7.99 0.00 46.80 2.29
938 1028 7.101652 ACCTTGTAGTATCACTGTATGTCTG 57.898 40.000 0.00 0.00 0.00 3.51
1006 1096 2.219325 CTGGAGGAGAGCACGGTGAC 62.219 65.000 13.29 5.01 0.00 3.67
1191 1281 2.117156 GTAGTCGACCAGCGCCCTA 61.117 63.158 13.01 0.00 40.61 3.53
1315 1411 0.392706 ATCGGCATGACGCTATCCAA 59.607 50.000 18.42 0.00 41.91 3.53
1320 1416 1.286501 GTTTCATCGGCATGACGCTA 58.713 50.000 18.42 0.00 38.86 4.26
1587 1698 1.664965 GCGGTGCTCGAACTCAACT 60.665 57.895 4.33 0.00 42.43 3.16
2347 2499 6.959639 ACAACCATACTTTGACAAGACAAT 57.040 33.333 0.00 0.00 33.72 2.71
2385 2810 3.740832 CACATATGTATACGTGGCACTGG 59.259 47.826 16.72 3.31 0.00 4.00
2616 3047 0.470766 ACCCTACACACCTCGCAAAA 59.529 50.000 0.00 0.00 0.00 2.44
2637 3068 4.828939 TCAGCATCCTCACAAAACTGAAAT 59.171 37.500 0.00 0.00 30.24 2.17
2703 3154 7.202016 AGAAAATTCGAGCTATTGAACACAA 57.798 32.000 0.00 0.00 31.46 3.33
2740 3191 5.690409 ACTTCATGTGTGTAGTAACAAGTCG 59.310 40.000 0.00 0.00 37.36 4.18
2836 3287 7.201644 GCATCTTCTCATTTTGACCGAAGATTA 60.202 37.037 14.48 0.00 41.56 1.75
2894 3345 5.858049 ACAAACATCATAAACATGCGACTTG 59.142 36.000 0.00 0.00 0.00 3.16
2900 3351 7.760131 ATAAGCACAAACATCATAAACATGC 57.240 32.000 0.00 0.00 0.00 4.06
2935 3386 1.348775 GGAACTCATGGGAGGAGGGG 61.349 65.000 0.00 0.00 45.81 4.79
2949 3401 0.930726 TGGGTTTTCACCTGGGAACT 59.069 50.000 0.00 0.00 43.65 3.01
2971 3423 0.958091 CGCCACCAAATCAGGAAACA 59.042 50.000 0.00 0.00 0.00 2.83
2978 3430 1.945522 CGTTGTCGCCACCAAATCA 59.054 52.632 0.00 0.00 0.00 2.57
3015 3467 0.038709 CCCATTTTCGCGCTTCCAAA 60.039 50.000 5.56 0.00 0.00 3.28
3018 3470 2.489751 CCCCATTTTCGCGCTTCC 59.510 61.111 5.56 0.00 0.00 3.46
3025 3477 0.254747 TACTCCCAGCCCCATTTTCG 59.745 55.000 0.00 0.00 0.00 3.46
3095 3547 1.294780 CATAGGAGAGGGATGCCGC 59.705 63.158 0.00 0.00 0.00 6.53
3097 3549 0.767375 TTGCATAGGAGAGGGATGCC 59.233 55.000 0.00 0.00 44.34 4.40
3104 3556 0.596083 CGAGCGGTTGCATAGGAGAG 60.596 60.000 0.00 0.00 46.23 3.20
3105 3557 1.320344 ACGAGCGGTTGCATAGGAGA 61.320 55.000 0.64 0.00 46.23 3.71
3139 3591 2.927429 CGAGCTCGTCATAGGATCAAG 58.073 52.381 27.79 0.00 34.11 3.02
3215 3667 0.671781 CTCACCCCTGAGCTTGAACG 60.672 60.000 0.00 0.00 37.72 3.95
3236 3688 0.662085 CGCCCTAGTTCGGTAGAGTC 59.338 60.000 0.00 0.00 0.00 3.36
3238 3690 0.945813 CTCGCCCTAGTTCGGTAGAG 59.054 60.000 1.81 0.73 0.00 2.43
3266 3740 3.053896 CACCGACGAAAAGGGCCC 61.054 66.667 16.46 16.46 0.00 5.80
3267 3741 3.053896 CCACCGACGAAAAGGGCC 61.054 66.667 0.00 0.00 0.00 5.80
3284 3758 5.107133 TCGAGTCAAAATTAATCCCGTCTC 58.893 41.667 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.