Multiple sequence alignment - TraesCS7D01G394500

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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 TraesCS7D01G394500 chr7D 100.000 3053 0 0 1 3053 509620314 509617262 0.000000e+00 5638.0
1 TraesCS7D01G394500 chr7D 90.805 435 38 2 1 434 227560703 227560270 5.670000e-162 580.0
2 TraesCS7D01G394500 chr7D 87.075 294 29 5 447 731 227560214 227559921 1.060000e-84 324.0
3 TraesCS7D01G394500 chr7A 95.174 2238 73 11 847 3053 580514305 580512072 0.000000e+00 3502.0
4 TraesCS7D01G394500 chr7A 92.760 663 39 1 1828 2481 267260924 267260262 0.000000e+00 950.0
5 TraesCS7D01G394500 chr7A 82.069 290 34 7 447 727 50630588 50630868 6.580000e-57 231.0
6 TraesCS7D01G394500 chr7B 94.528 1663 58 13 894 2524 537838117 537836456 0.000000e+00 2536.0
7 TraesCS7D01G394500 chr7B 97.368 494 13 0 2560 3053 537836250 537835757 0.000000e+00 841.0
8 TraesCS7D01G394500 chr7B 100.000 30 0 0 855 884 537838144 537838115 4.250000e-04 56.5
9 TraesCS7D01G394500 chr1A 86.839 737 75 13 1 719 337017657 337018389 0.000000e+00 804.0
10 TraesCS7D01G394500 chr3D 91.204 432 36 2 1 431 240516504 240516074 1.220000e-163 586.0
11 TraesCS7D01G394500 chr3D 84.536 291 27 7 447 728 240516019 240515738 3.880000e-69 272.0
12 TraesCS7D01G394500 chr3A 90.022 451 39 4 1 446 9829541 9829092 2.040000e-161 579.0
13 TraesCS7D01G394500 chr3A 88.964 444 45 4 4 446 47062396 47061956 2.070000e-151 545.0
14 TraesCS7D01G394500 chr3A 85.333 300 32 8 447 735 47061917 47061619 1.780000e-77 300.0
15 TraesCS7D01G394500 chr3A 88.947 190 16 4 551 735 9828652 9828463 2.370000e-56 230.0
16 TraesCS7D01G394500 chr3A 83.462 260 27 5 447 699 450008613 450008863 8.520000e-56 228.0
17 TraesCS7D01G394500 chr1D 90.509 432 39 2 1 431 373416346 373416776 1.230000e-158 569.0
18 TraesCS7D01G394500 chr1D 86.207 290 31 5 447 727 373416830 373417119 3.820000e-79 305.0
19 TraesCS7D01G394500 chr1B 91.912 408 31 2 2 408 319250998 319251404 1.230000e-158 569.0
20 TraesCS7D01G394500 chr1B 86.561 253 25 6 484 727 319251741 319251993 1.400000e-68 270.0
21 TraesCS7D01G394500 chr6B 90.046 432 41 2 1 431 426817920 426818350 2.660000e-155 558.0
22 TraesCS7D01G394500 chr2B 88.814 447 48 2 1 446 20030713 20031158 5.760000e-152 547.0
23 TraesCS7D01G394500 chr2B 85.567 291 34 5 445 727 20031194 20031484 6.400000e-77 298.0
24 TraesCS7D01G394500 chr2D 82.741 197 24 6 445 633 25747373 25747567 1.880000e-37 167.0


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 TraesCS7D01G394500 chr7D 509617262 509620314 3052 True 5638.0 5638 100.000000 1 3053 1 chr7D.!!$R1 3052
1 TraesCS7D01G394500 chr7D 227559921 227560703 782 True 452.0 580 88.940000 1 731 2 chr7D.!!$R2 730
2 TraesCS7D01G394500 chr7A 580512072 580514305 2233 True 3502.0 3502 95.174000 847 3053 1 chr7A.!!$R2 2206
3 TraesCS7D01G394500 chr7A 267260262 267260924 662 True 950.0 950 92.760000 1828 2481 1 chr7A.!!$R1 653
4 TraesCS7D01G394500 chr7B 537835757 537838144 2387 True 1144.5 2536 97.298667 855 3053 3 chr7B.!!$R1 2198
5 TraesCS7D01G394500 chr1A 337017657 337018389 732 False 804.0 804 86.839000 1 719 1 chr1A.!!$F1 718
6 TraesCS7D01G394500 chr3D 240515738 240516504 766 True 429.0 586 87.870000 1 728 2 chr3D.!!$R1 727
7 TraesCS7D01G394500 chr3A 47061619 47062396 777 True 422.5 545 87.148500 4 735 2 chr3A.!!$R2 731
8 TraesCS7D01G394500 chr3A 9828463 9829541 1078 True 404.5 579 89.484500 1 735 2 chr3A.!!$R1 734
9 TraesCS7D01G394500 chr1D 373416346 373417119 773 False 437.0 569 88.358000 1 727 2 chr1D.!!$F1 726
10 TraesCS7D01G394500 chr1B 319250998 319251993 995 False 419.5 569 89.236500 2 727 2 chr1B.!!$F1 725
11 TraesCS7D01G394500 chr2B 20030713 20031484 771 False 422.5 547 87.190500 1 727 2 chr2B.!!$F1 726

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
534 810 0.323360 CGCCCTCCCAAATCCAGAAA 60.323 55.000 0.00 0.0 0.00 2.52 F
578 1133 0.527565 GAGGCCAATTGCACGAATGT 59.472 50.000 5.01 0.0 43.89 2.71 F
920 1482 1.002274 GCTCCTCCTCCTCCTTCCA 59.998 63.158 0.00 0.0 0.00 3.53 F
1680 2276 1.282875 GGCGCACCTGTTTGTTCTC 59.717 57.895 10.83 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 2108 0.611618 TGCCAAGGATCGCAAATGGT 60.612 50.000 0.0 0.0 33.63 3.55 R
1680 2276 0.933097 CCAAGAACAGCCGATCATCG 59.067 55.000 0.0 0.0 40.07 3.84 R
2018 2614 2.328099 CGTTGTCCCAGCAAGAGGC 61.328 63.158 0.0 0.0 45.30 4.70 R
2609 3384 3.065786 CAGTAATTATGCTGTGCCACCTG 59.934 47.826 0.0 0.0 34.87 4.00 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
85 86 3.340337 AGAGCTTTGTTGCGAAACTTC 57.660 42.857 8.00 0.00 38.13 3.01
86 87 2.945668 AGAGCTTTGTTGCGAAACTTCT 59.054 40.909 8.00 0.00 38.13 2.85
131 132 1.067060 AGCTTTGTTGCGAAAACTCCC 59.933 47.619 0.00 0.00 38.13 4.30
137 139 3.020984 TGTTGCGAAAACTCCCTTTCTT 58.979 40.909 0.00 0.00 33.86 2.52
147 149 9.181805 CGAAAACTCCCTTTCTTTAATTTTCTC 57.818 33.333 0.00 0.00 34.28 2.87
178 181 6.775629 AGTCCCTGTTGCAAAAACTCTTATTA 59.224 34.615 0.00 0.00 0.00 0.98
287 290 6.538021 TGCTACAAAAATTGCAACAACATCTT 59.462 30.769 0.00 0.00 32.12 2.40
290 293 4.713854 AAAATTGCAACAACATCTTCGC 57.286 36.364 0.00 0.00 0.00 4.70
434 441 2.751436 TCGCCCAGAAATGCAGGC 60.751 61.111 2.38 2.38 42.18 4.85
435 442 3.063704 CGCCCAGAAATGCAGGCA 61.064 61.111 12.34 0.00 46.08 4.75
439 446 0.529378 CCCAGAAATGCAGGCAGAAC 59.471 55.000 0.00 0.00 0.00 3.01
480 747 2.125952 CAGTCGCCATCACGCTGA 60.126 61.111 0.00 0.00 38.56 4.26
482 749 1.738099 AGTCGCCATCACGCTGAAC 60.738 57.895 0.00 0.00 0.00 3.18
534 810 0.323360 CGCCCTCCCAAATCCAGAAA 60.323 55.000 0.00 0.00 0.00 2.52
536 812 1.549950 GCCCTCCCAAATCCAGAAACA 60.550 52.381 0.00 0.00 0.00 2.83
538 815 3.444029 CCCTCCCAAATCCAGAAACATT 58.556 45.455 0.00 0.00 0.00 2.71
578 1133 0.527565 GAGGCCAATTGCACGAATGT 59.472 50.000 5.01 0.00 43.89 2.71
658 1215 2.478031 CGTTCTCGTCCGTCTGATCAAT 60.478 50.000 0.00 0.00 0.00 2.57
731 1292 5.185056 GCTGAAGGTAAGCTTTTCCCATTTA 59.815 40.000 3.20 0.00 37.69 1.40
732 1293 6.625960 GCTGAAGGTAAGCTTTTCCCATTTAG 60.626 42.308 3.20 6.95 37.69 1.85
733 1294 6.548321 TGAAGGTAAGCTTTTCCCATTTAGA 58.452 36.000 3.20 0.00 0.00 2.10
735 1296 7.673926 TGAAGGTAAGCTTTTCCCATTTAGAAT 59.326 33.333 3.20 0.00 0.00 2.40
736 1297 8.435931 AAGGTAAGCTTTTCCCATTTAGAATT 57.564 30.769 3.20 0.00 0.00 2.17
737 1298 8.067751 AGGTAAGCTTTTCCCATTTAGAATTC 57.932 34.615 3.20 0.00 0.00 2.17
738 1299 7.673926 AGGTAAGCTTTTCCCATTTAGAATTCA 59.326 33.333 3.20 0.00 0.00 2.57
739 1300 7.759886 GGTAAGCTTTTCCCATTTAGAATTCAC 59.240 37.037 3.20 0.00 0.00 3.18
740 1301 6.286240 AGCTTTTCCCATTTAGAATTCACC 57.714 37.500 8.44 0.00 0.00 4.02
741 1302 5.187772 AGCTTTTCCCATTTAGAATTCACCC 59.812 40.000 8.44 0.00 0.00 4.61
742 1303 5.187772 GCTTTTCCCATTTAGAATTCACCCT 59.812 40.000 8.44 0.00 0.00 4.34
743 1304 6.379988 GCTTTTCCCATTTAGAATTCACCCTA 59.620 38.462 8.44 0.00 0.00 3.53
744 1305 7.069950 GCTTTTCCCATTTAGAATTCACCCTAT 59.930 37.037 8.44 0.00 0.00 2.57
745 1306 8.909423 TTTTCCCATTTAGAATTCACCCTATT 57.091 30.769 8.44 0.00 0.00 1.73
746 1307 8.533569 TTTCCCATTTAGAATTCACCCTATTC 57.466 34.615 8.44 0.00 33.23 1.75
747 1308 7.465900 TCCCATTTAGAATTCACCCTATTCT 57.534 36.000 8.44 0.00 43.06 2.40
748 1309 7.882755 TCCCATTTAGAATTCACCCTATTCTT 58.117 34.615 8.44 0.00 41.36 2.52
749 1310 8.343787 TCCCATTTAGAATTCACCCTATTCTTT 58.656 33.333 8.44 0.00 41.36 2.52
750 1311 8.416329 CCCATTTAGAATTCACCCTATTCTTTG 58.584 37.037 8.44 0.00 41.36 2.77
751 1312 9.189156 CCATTTAGAATTCACCCTATTCTTTGA 57.811 33.333 8.44 0.00 41.36 2.69
757 1318 9.927081 AGAATTCACCCTATTCTTTGATAATGT 57.073 29.630 8.44 0.00 38.81 2.71
758 1319 9.956720 GAATTCACCCTATTCTTTGATAATGTG 57.043 33.333 0.00 0.00 0.00 3.21
759 1320 9.699410 AATTCACCCTATTCTTTGATAATGTGA 57.301 29.630 0.00 0.00 0.00 3.58
760 1321 9.699410 ATTCACCCTATTCTTTGATAATGTGAA 57.301 29.630 0.00 0.00 36.98 3.18
761 1322 9.699410 TTCACCCTATTCTTTGATAATGTGAAT 57.301 29.630 0.00 0.00 32.70 2.57
762 1323 9.342308 TCACCCTATTCTTTGATAATGTGAATC 57.658 33.333 0.00 0.00 0.00 2.52
763 1324 9.123902 CACCCTATTCTTTGATAATGTGAATCA 57.876 33.333 0.00 0.00 0.00 2.57
764 1325 9.125026 ACCCTATTCTTTGATAATGTGAATCAC 57.875 33.333 6.41 6.41 33.18 3.06
765 1326 8.285394 CCCTATTCTTTGATAATGTGAATCACG 58.715 37.037 9.00 0.00 37.14 4.35
766 1327 9.045223 CCTATTCTTTGATAATGTGAATCACGA 57.955 33.333 9.00 0.00 37.14 4.35
769 1330 9.941664 ATTCTTTGATAATGTGAATCACGAATC 57.058 29.630 9.00 11.16 37.14 2.52
770 1331 7.621102 TCTTTGATAATGTGAATCACGAATCG 58.379 34.615 9.00 0.00 37.14 3.34
771 1332 5.328886 TGATAATGTGAATCACGAATCGC 57.671 39.130 9.00 0.00 37.14 4.58
772 1333 4.808364 TGATAATGTGAATCACGAATCGCA 59.192 37.500 9.00 1.13 40.05 5.10
773 1334 5.293079 TGATAATGTGAATCACGAATCGCAA 59.707 36.000 9.00 0.00 39.29 4.85
774 1335 4.621068 AATGTGAATCACGAATCGCAAT 57.379 36.364 9.00 0.00 39.29 3.56
775 1336 4.621068 ATGTGAATCACGAATCGCAATT 57.379 36.364 9.00 2.45 39.29 2.32
776 1337 4.002267 TGTGAATCACGAATCGCAATTC 57.998 40.909 17.95 17.95 37.14 2.17
777 1338 3.434984 TGTGAATCACGAATCGCAATTCA 59.565 39.130 21.42 21.42 41.22 2.57
778 1339 4.094739 TGTGAATCACGAATCGCAATTCAT 59.905 37.500 25.28 0.85 40.43 2.57
779 1340 5.293079 TGTGAATCACGAATCGCAATTCATA 59.707 36.000 25.28 21.92 40.43 2.15
780 1341 6.183360 TGTGAATCACGAATCGCAATTCATAA 60.183 34.615 25.28 17.98 40.43 1.90
781 1342 6.355405 GTGAATCACGAATCGCAATTCATAAG 59.645 38.462 25.28 0.00 40.43 1.73
782 1343 5.991328 ATCACGAATCGCAATTCATAAGT 57.009 34.783 1.15 0.00 41.22 2.24
783 1344 5.142635 TCACGAATCGCAATTCATAAGTG 57.857 39.130 1.15 0.00 41.22 3.16
784 1345 4.033932 TCACGAATCGCAATTCATAAGTGG 59.966 41.667 1.15 0.00 41.22 4.00
785 1346 3.938963 ACGAATCGCAATTCATAAGTGGT 59.061 39.130 1.15 0.00 41.22 4.16
786 1347 4.034048 ACGAATCGCAATTCATAAGTGGTC 59.966 41.667 1.15 0.00 41.22 4.02
787 1348 4.518217 GAATCGCAATTCATAAGTGGTCG 58.482 43.478 0.00 0.00 40.90 4.79
788 1349 2.967362 TCGCAATTCATAAGTGGTCGT 58.033 42.857 0.00 0.00 0.00 4.34
789 1350 2.670905 TCGCAATTCATAAGTGGTCGTG 59.329 45.455 0.00 0.00 0.00 4.35
790 1351 2.223021 CGCAATTCATAAGTGGTCGTGG 60.223 50.000 0.00 0.00 0.00 4.94
791 1352 3.006940 GCAATTCATAAGTGGTCGTGGA 58.993 45.455 0.00 0.00 0.00 4.02
792 1353 3.438781 GCAATTCATAAGTGGTCGTGGAA 59.561 43.478 0.00 0.00 0.00 3.53
793 1354 4.096382 GCAATTCATAAGTGGTCGTGGAAT 59.904 41.667 0.00 0.00 0.00 3.01
794 1355 5.393027 GCAATTCATAAGTGGTCGTGGAATT 60.393 40.000 0.00 0.00 34.77 2.17
795 1356 6.620678 CAATTCATAAGTGGTCGTGGAATTT 58.379 36.000 0.00 0.00 32.83 1.82
796 1357 5.873179 TTCATAAGTGGTCGTGGAATTTC 57.127 39.130 0.00 0.00 0.00 2.17
797 1358 5.160607 TCATAAGTGGTCGTGGAATTTCT 57.839 39.130 0.00 0.00 0.00 2.52
798 1359 5.175859 TCATAAGTGGTCGTGGAATTTCTC 58.824 41.667 0.00 0.00 0.00 2.87
799 1360 3.771577 AAGTGGTCGTGGAATTTCTCT 57.228 42.857 0.00 0.00 0.00 3.10
800 1361 3.320673 AGTGGTCGTGGAATTTCTCTC 57.679 47.619 0.00 0.00 0.00 3.20
801 1362 2.900546 AGTGGTCGTGGAATTTCTCTCT 59.099 45.455 0.00 0.00 0.00 3.10
802 1363 3.325135 AGTGGTCGTGGAATTTCTCTCTT 59.675 43.478 0.00 0.00 0.00 2.85
803 1364 4.065789 GTGGTCGTGGAATTTCTCTCTTT 58.934 43.478 0.00 0.00 0.00 2.52
804 1365 4.515567 GTGGTCGTGGAATTTCTCTCTTTT 59.484 41.667 0.00 0.00 0.00 2.27
805 1366 4.755123 TGGTCGTGGAATTTCTCTCTTTTC 59.245 41.667 0.00 0.00 0.00 2.29
806 1367 4.998033 GGTCGTGGAATTTCTCTCTTTTCT 59.002 41.667 0.00 0.00 0.00 2.52
807 1368 5.120986 GGTCGTGGAATTTCTCTCTTTTCTC 59.879 44.000 0.00 0.00 0.00 2.87
808 1369 5.929415 GTCGTGGAATTTCTCTCTTTTCTCT 59.071 40.000 0.00 0.00 0.00 3.10
809 1370 6.425417 GTCGTGGAATTTCTCTCTTTTCTCTT 59.575 38.462 0.00 0.00 0.00 2.85
810 1371 6.992715 TCGTGGAATTTCTCTCTTTTCTCTTT 59.007 34.615 0.00 0.00 0.00 2.52
811 1372 7.499232 TCGTGGAATTTCTCTCTTTTCTCTTTT 59.501 33.333 0.00 0.00 0.00 2.27
812 1373 8.131731 CGTGGAATTTCTCTCTTTTCTCTTTTT 58.868 33.333 0.00 0.00 0.00 1.94
891 1453 3.751246 CCCACATGCCAGCCAACG 61.751 66.667 0.00 0.00 0.00 4.10
894 1456 3.058160 ACATGCCAGCCAACGAGC 61.058 61.111 0.00 0.00 0.00 5.03
917 1479 1.076339 CTCGCTCCTCCTCCTCCTT 60.076 63.158 0.00 0.00 0.00 3.36
920 1482 1.002274 GCTCCTCCTCCTCCTTCCA 59.998 63.158 0.00 0.00 0.00 3.53
973 1566 4.386951 CACCGTGATCCGCCACCA 62.387 66.667 0.00 0.00 33.67 4.17
974 1567 4.082523 ACCGTGATCCGCCACCAG 62.083 66.667 0.00 0.00 33.67 4.00
1368 1961 2.196925 CCGCTCCTACCTCATCGCT 61.197 63.158 0.00 0.00 0.00 4.93
1680 2276 1.282875 GGCGCACCTGTTTGTTCTC 59.717 57.895 10.83 0.00 0.00 2.87
1789 2385 2.808206 GGATGGGTGGAGGTAGCCG 61.808 68.421 0.00 0.00 41.09 5.52
2152 2748 8.212312 TGGTTGTTTGTAAGTAGGAATAACTGA 58.788 33.333 0.00 0.00 0.00 3.41
2203 2799 2.884639 GCAACCTTGTCCTTGTATGTGT 59.115 45.455 0.00 0.00 0.00 3.72
2386 2991 4.662145 CCATACGCTTGAATGAAACCTTC 58.338 43.478 0.00 0.00 0.00 3.46
2499 3104 1.068748 CATGTGAGTCAAGGCTGTTGC 60.069 52.381 0.00 0.00 38.76 4.17
2519 3124 6.587226 TGTTGCATCACATAAGCTCAAAATTC 59.413 34.615 0.00 0.00 0.00 2.17
2525 3130 5.047377 TCACATAAGCTCAAAATTCCCCAAC 60.047 40.000 0.00 0.00 0.00 3.77
2544 3149 6.039159 CCCCAACAATTTTATGTGCAGTTTTT 59.961 34.615 0.00 0.00 32.81 1.94
2581 3356 5.843673 TGATTTTGCCTACTGTTTGTCAA 57.156 34.783 0.00 0.00 0.00 3.18
2609 3384 1.909700 TGTCAAAGCCCCTCAACATC 58.090 50.000 0.00 0.00 0.00 3.06
2665 3440 6.208599 TCTGTCACTGTCATTCATACTGTGTA 59.791 38.462 11.36 4.15 43.37 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.124277 TCGCAACTAGACTAGCTCCA 57.876 50.000 9.52 0.00 0.00 3.86
85 86 6.748333 TGTTGCAGGAAATTAGAGATGAAG 57.252 37.500 0.00 0.00 0.00 3.02
86 87 6.942005 TCTTGTTGCAGGAAATTAGAGATGAA 59.058 34.615 0.00 0.00 0.00 2.57
131 132 9.249457 GGACTTGTTGGAGAAAATTAAAGAAAG 57.751 33.333 0.00 0.00 0.00 2.62
137 139 6.133356 ACAGGGACTTGTTGGAGAAAATTAA 58.867 36.000 0.00 0.00 34.60 1.40
147 149 1.110442 TTGCAACAGGGACTTGTTGG 58.890 50.000 23.02 9.68 42.92 3.77
178 181 6.012745 AGGGTCTTGTTGCAGAAAATTAGAT 58.987 36.000 0.00 0.00 0.00 1.98
241 244 5.010012 AGCAAGGGTCTTGTTACAGAAAATG 59.990 40.000 9.07 0.00 0.00 2.32
372 378 3.753272 GCTAGACACAACCACATCACAAT 59.247 43.478 0.00 0.00 0.00 2.71
464 521 1.738099 GTTCAGCGTGATGGCGACT 60.738 57.895 0.00 0.00 38.18 4.18
510 786 4.060667 ATTTGGGAGGGCGGTGGG 62.061 66.667 0.00 0.00 0.00 4.61
511 787 2.440247 GATTTGGGAGGGCGGTGG 60.440 66.667 0.00 0.00 0.00 4.61
512 788 2.440247 GGATTTGGGAGGGCGGTG 60.440 66.667 0.00 0.00 0.00 4.94
513 789 2.938798 TGGATTTGGGAGGGCGGT 60.939 61.111 0.00 0.00 0.00 5.68
534 810 1.771255 GACTCTATGGGAGGGCAATGT 59.229 52.381 0.00 0.00 45.83 2.71
536 812 2.173569 GTTGACTCTATGGGAGGGCAAT 59.826 50.000 0.00 0.00 45.83 3.56
538 815 1.204146 GTTGACTCTATGGGAGGGCA 58.796 55.000 0.00 0.00 45.83 5.36
578 1133 8.635765 AAACAGAGCTATTGTTTCAGGATAAA 57.364 30.769 18.28 0.00 43.26 1.40
658 1215 0.390603 CGTGTCCGTTGGATTGCCTA 60.391 55.000 0.00 0.00 32.73 3.93
731 1292 9.927081 ACATTATCAAAGAATAGGGTGAATTCT 57.073 29.630 7.05 0.00 43.80 2.40
732 1293 9.956720 CACATTATCAAAGAATAGGGTGAATTC 57.043 33.333 0.00 0.00 34.23 2.17
733 1294 9.699410 TCACATTATCAAAGAATAGGGTGAATT 57.301 29.630 0.00 0.00 30.07 2.17
735 1296 9.699410 ATTCACATTATCAAAGAATAGGGTGAA 57.301 29.630 0.00 0.00 38.67 3.18
736 1297 9.342308 GATTCACATTATCAAAGAATAGGGTGA 57.658 33.333 0.00 0.00 30.60 4.02
737 1298 9.123902 TGATTCACATTATCAAAGAATAGGGTG 57.876 33.333 0.00 0.00 0.00 4.61
738 1299 9.125026 GTGATTCACATTATCAAAGAATAGGGT 57.875 33.333 11.93 0.00 34.06 4.34
739 1300 8.285394 CGTGATTCACATTATCAAAGAATAGGG 58.715 37.037 16.61 0.00 34.06 3.53
740 1301 9.045223 TCGTGATTCACATTATCAAAGAATAGG 57.955 33.333 16.61 0.00 34.06 2.57
743 1304 9.941664 GATTCGTGATTCACATTATCAAAGAAT 57.058 29.630 16.61 12.34 40.43 2.40
744 1305 8.116136 CGATTCGTGATTCACATTATCAAAGAA 58.884 33.333 16.61 8.57 36.39 2.52
745 1306 7.621102 CGATTCGTGATTCACATTATCAAAGA 58.379 34.615 16.61 0.07 34.06 2.52
746 1307 6.355405 GCGATTCGTGATTCACATTATCAAAG 59.645 38.462 16.61 5.24 34.06 2.77
747 1308 6.183360 TGCGATTCGTGATTCACATTATCAAA 60.183 34.615 16.61 4.66 34.06 2.69
748 1309 5.293079 TGCGATTCGTGATTCACATTATCAA 59.707 36.000 16.61 4.94 34.06 2.57
749 1310 4.808364 TGCGATTCGTGATTCACATTATCA 59.192 37.500 16.61 4.51 33.40 2.15
750 1311 5.328886 TGCGATTCGTGATTCACATTATC 57.671 39.130 16.61 12.99 33.40 1.75
751 1312 5.733226 TTGCGATTCGTGATTCACATTAT 57.267 34.783 16.61 6.35 33.40 1.28
752 1313 5.733226 ATTGCGATTCGTGATTCACATTA 57.267 34.783 16.61 1.79 33.40 1.90
753 1314 4.621068 ATTGCGATTCGTGATTCACATT 57.379 36.364 16.61 0.64 33.40 2.71
754 1315 4.094739 TGAATTGCGATTCGTGATTCACAT 59.905 37.500 23.09 3.65 43.75 3.21
755 1316 3.434984 TGAATTGCGATTCGTGATTCACA 59.565 39.130 23.09 11.39 43.75 3.58
756 1317 4.002267 TGAATTGCGATTCGTGATTCAC 57.998 40.909 23.09 6.73 43.75 3.18
757 1318 4.880886 ATGAATTGCGATTCGTGATTCA 57.119 36.364 26.16 26.16 43.75 2.57
758 1319 6.355405 CACTTATGAATTGCGATTCGTGATTC 59.645 38.462 25.64 20.07 43.75 2.52
759 1320 6.194463 CACTTATGAATTGCGATTCGTGATT 58.806 36.000 25.64 12.93 43.75 2.57
760 1321 5.277490 CCACTTATGAATTGCGATTCGTGAT 60.277 40.000 25.64 14.82 43.75 3.06
761 1322 4.033932 CCACTTATGAATTGCGATTCGTGA 59.966 41.667 25.64 18.74 43.75 4.35
762 1323 4.201812 ACCACTTATGAATTGCGATTCGTG 60.202 41.667 25.64 21.70 43.75 4.35
763 1324 3.938963 ACCACTTATGAATTGCGATTCGT 59.061 39.130 22.18 22.18 43.75 3.85
764 1325 4.518217 GACCACTTATGAATTGCGATTCG 58.482 43.478 19.55 9.36 43.75 3.34
765 1326 4.034048 ACGACCACTTATGAATTGCGATTC 59.966 41.667 18.36 18.36 41.67 2.52
766 1327 3.938963 ACGACCACTTATGAATTGCGATT 59.061 39.130 0.00 0.00 0.00 3.34
767 1328 3.309682 CACGACCACTTATGAATTGCGAT 59.690 43.478 0.00 0.00 0.00 4.58
768 1329 2.670905 CACGACCACTTATGAATTGCGA 59.329 45.455 0.00 0.00 0.00 5.10
769 1330 2.223021 CCACGACCACTTATGAATTGCG 60.223 50.000 0.00 0.00 0.00 4.85
770 1331 3.006940 TCCACGACCACTTATGAATTGC 58.993 45.455 0.00 0.00 0.00 3.56
771 1332 5.818136 ATTCCACGACCACTTATGAATTG 57.182 39.130 0.00 0.00 0.00 2.32
772 1333 6.659242 AGAAATTCCACGACCACTTATGAATT 59.341 34.615 0.00 0.00 33.67 2.17
773 1334 6.180472 AGAAATTCCACGACCACTTATGAAT 58.820 36.000 0.00 0.00 0.00 2.57
774 1335 5.556915 AGAAATTCCACGACCACTTATGAA 58.443 37.500 0.00 0.00 0.00 2.57
775 1336 5.046591 AGAGAAATTCCACGACCACTTATGA 60.047 40.000 0.00 0.00 0.00 2.15
776 1337 5.178797 AGAGAAATTCCACGACCACTTATG 58.821 41.667 0.00 0.00 0.00 1.90
777 1338 5.187967 AGAGAGAAATTCCACGACCACTTAT 59.812 40.000 0.00 0.00 0.00 1.73
778 1339 4.527038 AGAGAGAAATTCCACGACCACTTA 59.473 41.667 0.00 0.00 0.00 2.24
779 1340 3.325135 AGAGAGAAATTCCACGACCACTT 59.675 43.478 0.00 0.00 0.00 3.16
780 1341 2.900546 AGAGAGAAATTCCACGACCACT 59.099 45.455 0.00 0.00 0.00 4.00
781 1342 3.320673 AGAGAGAAATTCCACGACCAC 57.679 47.619 0.00 0.00 0.00 4.16
782 1343 4.351874 AAAGAGAGAAATTCCACGACCA 57.648 40.909 0.00 0.00 0.00 4.02
783 1344 4.998033 AGAAAAGAGAGAAATTCCACGACC 59.002 41.667 0.00 0.00 0.00 4.79
784 1345 5.929415 AGAGAAAAGAGAGAAATTCCACGAC 59.071 40.000 0.00 0.00 0.00 4.34
785 1346 6.102897 AGAGAAAAGAGAGAAATTCCACGA 57.897 37.500 0.00 0.00 0.00 4.35
786 1347 6.793492 AAGAGAAAAGAGAGAAATTCCACG 57.207 37.500 0.00 0.00 0.00 4.94
839 1400 9.929180 GGCTCGATGGCATTTATATAGATATAA 57.071 33.333 0.00 0.00 41.37 0.98
840 1401 9.314133 AGGCTCGATGGCATTTATATAGATATA 57.686 33.333 0.00 0.00 44.55 0.86
841 1402 8.200024 AGGCTCGATGGCATTTATATAGATAT 57.800 34.615 0.00 0.00 44.55 1.63
842 1403 7.603180 AGGCTCGATGGCATTTATATAGATA 57.397 36.000 0.00 0.00 44.55 1.98
843 1404 6.491714 AGGCTCGATGGCATTTATATAGAT 57.508 37.500 0.00 0.00 44.55 1.98
844 1405 5.939764 AGGCTCGATGGCATTTATATAGA 57.060 39.130 0.00 0.00 44.55 1.98
845 1406 5.525378 GGAAGGCTCGATGGCATTTATATAG 59.475 44.000 0.00 0.00 44.55 1.31
853 1414 2.512896 GGGAAGGCTCGATGGCAT 59.487 61.111 0.00 0.00 44.55 4.40
894 1456 2.131067 GGAGGAGGAGCGAGAAGGG 61.131 68.421 0.00 0.00 0.00 3.95
917 1479 1.622607 ATGGGGACGCGAGAAATGGA 61.623 55.000 15.93 0.00 0.00 3.41
920 1482 1.379527 GAAATGGGGACGCGAGAAAT 58.620 50.000 15.93 0.00 0.00 2.17
1368 1961 2.987547 GAGGGTGGGACGACGACA 60.988 66.667 0.00 0.00 0.00 4.35
1512 2108 0.611618 TGCCAAGGATCGCAAATGGT 60.612 50.000 0.00 0.00 33.63 3.55
1555 2151 2.734673 CGAGCACAAAGAGCCGAGC 61.735 63.158 0.00 0.00 0.00 5.03
1590 2186 1.895798 TCGAGATCAAGCACCAGAAGT 59.104 47.619 0.00 0.00 0.00 3.01
1659 2255 2.331019 GAACAAACAGGTGCGCCGTT 62.331 55.000 17.10 17.10 40.50 4.44
1680 2276 0.933097 CCAAGAACAGCCGATCATCG 59.067 55.000 0.00 0.00 40.07 3.84
2018 2614 2.328099 CGTTGTCCCAGCAAGAGGC 61.328 63.158 0.00 0.00 45.30 4.70
2386 2991 6.877611 AACACTGAGGTACATGTAAAAAGG 57.122 37.500 7.25 1.39 0.00 3.11
2499 3104 5.127519 TGGGGAATTTTGAGCTTATGTGATG 59.872 40.000 0.00 0.00 0.00 3.07
2519 3124 4.270245 ACTGCACATAAAATTGTTGGGG 57.730 40.909 0.00 0.00 0.00 4.96
2556 3179 5.359576 TGACAAACAGTAGGCAAAATCAACT 59.640 36.000 0.00 0.00 0.00 3.16
2558 3333 5.843673 TGACAAACAGTAGGCAAAATCAA 57.156 34.783 0.00 0.00 0.00 2.57
2566 3341 5.567138 ATGCTAATTGACAAACAGTAGGC 57.433 39.130 0.00 0.00 0.00 3.93
2567 3342 7.370383 ACAAATGCTAATTGACAAACAGTAGG 58.630 34.615 0.00 0.00 0.00 3.18
2581 3356 3.444029 AGGGGCTTTGACAAATGCTAAT 58.556 40.909 16.59 5.68 36.82 1.73
2609 3384 3.065786 CAGTAATTATGCTGTGCCACCTG 59.934 47.826 0.00 0.00 34.87 4.00
2665 3440 6.767524 TGACATGGTTGAGTTACTTGTTTT 57.232 33.333 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.