Multiple sequence alignment - TraesCS3B01G165100

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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 TraesCS3B01G165100 chr3B 100.000 2540 0 0 1 2540 163152605 163155144 0.000000e+00 4691.0
1 TraesCS3B01G165100 chr3B 81.720 93 15 2 2335 2426 96959932 96960023 2.710000e-10 76.8
2 TraesCS3B01G165100 chr3D 87.491 1383 83 47 252 1591 112332222 112333557 0.000000e+00 1513.0
3 TraesCS3B01G165100 chr3D 90.772 596 25 16 1587 2161 112333599 112334185 0.000000e+00 769.0
4 TraesCS3B01G165100 chr3D 84.615 338 44 8 2196 2527 112349289 112349624 1.880000e-86 329.0
5 TraesCS3B01G165100 chr3D 79.464 224 44 2 2203 2426 152169021 152169242 9.410000e-35 158.0
6 TraesCS3B01G165100 chr3D 78.733 221 38 8 2192 2409 110218735 110218521 3.410000e-29 139.0
7 TraesCS3B01G165100 chr3A 83.387 1252 97 49 380 1572 107974626 107975825 0.000000e+00 1057.0
8 TraesCS3B01G165100 chr3A 81.414 764 71 43 1836 2540 107976123 107976874 2.210000e-155 558.0
9 TraesCS3B01G165100 chr3A 89.744 117 6 3 1587 1698 107975878 107975993 7.320000e-31 145.0
10 TraesCS3B01G165100 chr3A 79.747 158 24 7 2247 2400 639150944 639150791 9.610000e-20 108.0
11 TraesCS3B01G165100 chr5B 99.603 252 1 0 1 252 286879414 286879665 6.400000e-126 460.0
12 TraesCS3B01G165100 chr1B 96.838 253 7 1 1 252 666990247 666990499 3.020000e-114 422.0
13 TraesCS3B01G165100 chr1B 96.443 253 8 1 1 252 666989827 666990079 1.410000e-112 416.0
14 TraesCS3B01G165100 chr1B 90.446 157 14 1 105 260 596046676 596046520 3.310000e-49 206.0
15 TraesCS3B01G165100 chr5A 92.188 256 18 2 1 255 234922198 234921944 6.680000e-96 361.0
16 TraesCS3B01G165100 chr2B 91.946 149 11 1 105 252 422238691 422238839 9.210000e-50 207.0
17 TraesCS3B01G165100 chr2D 90.323 155 14 1 105 258 393203349 393203195 4.280000e-48 202.0
18 TraesCS3B01G165100 chr7D 83.028 218 29 6 2213 2426 22652427 22652640 9.270000e-45 191.0
19 TraesCS3B01G165100 chr1D 78.075 187 31 8 2216 2400 482528169 482527991 2.670000e-20 110.0
20 TraesCS3B01G165100 chr7A 79.054 148 29 2 2280 2426 109433680 109433826 1.610000e-17 100.0
21 TraesCS3B01G165100 chr5D 75.385 260 37 13 1 257 498379548 498379783 1.610000e-17 100.0
22 TraesCS3B01G165100 chr5D 81.203 133 18 4 2234 2365 519795780 519795906 1.610000e-17 100.0
23 TraesCS3B01G165100 chr1A 77.358 159 23 7 103 259 387224661 387224514 5.820000e-12 82.4


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 TraesCS3B01G165100 chr3B 163152605 163155144 2539 False 4691.000000 4691 100.000000 1 2540 1 chr3B.!!$F2 2539
1 TraesCS3B01G165100 chr3D 112332222 112334185 1963 False 1141.000000 1513 89.131500 252 2161 2 chr3D.!!$F3 1909
2 TraesCS3B01G165100 chr3A 107974626 107976874 2248 False 586.666667 1057 84.848333 380 2540 3 chr3A.!!$F1 2160
3 TraesCS3B01G165100 chr1B 666989827 666990499 672 False 419.000000 422 96.640500 1 252 2 chr1B.!!$F1 251

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
704 1166 0.03601 CCGTCAGGCTCCAGAAACAT 60.036 55.0 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2565 0.24691 GGAAGGAACTCTCGGTGGAC 59.753 60.0 0.0 0.0 38.49 4.02 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
225 647 2.267192 GGGATTAGACCCCTGGGATAC 58.733 57.143 16.20 4.97 43.81 2.24
252 674 3.829601 CCATTACAACCAAACAAGGCCTA 59.170 43.478 5.16 0.00 0.00 3.93
253 675 4.282195 CCATTACAACCAAACAAGGCCTAA 59.718 41.667 5.16 0.00 0.00 2.69
254 676 5.469479 CATTACAACCAAACAAGGCCTAAG 58.531 41.667 5.16 4.24 0.00 2.18
255 677 3.306472 ACAACCAAACAAGGCCTAAGA 57.694 42.857 5.16 0.00 0.00 2.10
256 678 3.222603 ACAACCAAACAAGGCCTAAGAG 58.777 45.455 5.16 0.00 0.00 2.85
274 696 3.462678 GTCGGGTCCCTCCTGCTC 61.463 72.222 6.29 0.00 42.13 4.26
300 722 6.846325 GCAAAGGAGCGAAATAATACTAGT 57.154 37.500 0.00 0.00 0.00 2.57
301 723 7.941795 GCAAAGGAGCGAAATAATACTAGTA 57.058 36.000 4.77 4.77 0.00 1.82
302 724 7.785144 GCAAAGGAGCGAAATAATACTAGTAC 58.215 38.462 4.31 0.00 0.00 2.73
303 725 7.437267 GCAAAGGAGCGAAATAATACTAGTACA 59.563 37.037 4.31 0.00 0.00 2.90
308 730 8.562892 GGAGCGAAATAATACTAGTACAGTACA 58.437 37.037 13.37 0.00 42.56 2.90
317 739 5.209818 ACTAGTACAGTACAAGCAAGCAA 57.790 39.130 13.37 0.00 34.98 3.91
326 748 1.289276 CAAGCAAGCAAAGCCGTTTT 58.711 45.000 0.00 0.00 0.00 2.43
358 780 1.754234 GGCCGTGGGAGCAATTGAT 60.754 57.895 10.34 1.34 0.00 2.57
359 781 1.322538 GGCCGTGGGAGCAATTGATT 61.323 55.000 10.34 0.00 0.00 2.57
360 782 0.532115 GCCGTGGGAGCAATTGATTT 59.468 50.000 10.34 0.00 0.00 2.17
361 783 1.736696 GCCGTGGGAGCAATTGATTTG 60.737 52.381 10.34 0.00 38.43 2.32
362 784 1.818060 CCGTGGGAGCAATTGATTTGA 59.182 47.619 10.34 0.00 37.53 2.69
363 785 2.415893 CCGTGGGAGCAATTGATTTGAC 60.416 50.000 10.34 0.00 37.53 3.18
365 787 1.818060 TGGGAGCAATTGATTTGACGG 59.182 47.619 10.34 0.00 37.53 4.79
367 789 2.159379 GGGAGCAATTGATTTGACGGAC 60.159 50.000 10.34 0.00 37.53 4.79
368 790 2.487762 GGAGCAATTGATTTGACGGACA 59.512 45.455 10.34 0.00 37.53 4.02
369 791 3.426695 GGAGCAATTGATTTGACGGACAG 60.427 47.826 10.34 0.00 37.53 3.51
371 793 2.351641 GCAATTGATTTGACGGACAGCA 60.352 45.455 10.34 0.00 37.53 4.41
444 870 6.686630 AGAAGAGTCGAGCATAAATATCCAG 58.313 40.000 0.00 0.00 0.00 3.86
490 918 4.394712 GGTCGGGGGAGCACAGTG 62.395 72.222 0.00 0.00 0.00 3.66
549 987 2.273179 TGTGTCCCTTCCTCCGTCG 61.273 63.158 0.00 0.00 0.00 5.12
569 1015 0.389426 ATCGTCGACCCTTTTCACCG 60.389 55.000 10.58 0.00 0.00 4.94
574 1020 4.653888 ACCCTTTTCACCGCGGGG 62.654 66.667 31.76 28.69 41.11 5.73
575 1021 4.338710 CCCTTTTCACCGCGGGGA 62.339 66.667 30.05 30.05 39.42 4.81
609 1066 1.080093 TCGTGCGGACAGATGGAAC 60.080 57.895 8.11 0.00 0.00 3.62
611 1068 1.745489 GTGCGGACAGATGGAACCC 60.745 63.158 0.63 0.00 0.00 4.11
612 1069 2.220586 TGCGGACAGATGGAACCCA 61.221 57.895 0.00 0.00 38.19 4.51
613 1070 1.002624 GCGGACAGATGGAACCCAA 60.003 57.895 0.00 0.00 36.95 4.12
614 1071 0.394352 GCGGACAGATGGAACCCAAT 60.394 55.000 0.00 0.00 36.95 3.16
615 1072 1.668419 CGGACAGATGGAACCCAATC 58.332 55.000 0.00 0.00 36.95 2.67
616 1073 1.668419 GGACAGATGGAACCCAATCG 58.332 55.000 0.00 0.00 36.95 3.34
617 1074 1.017387 GACAGATGGAACCCAATCGC 58.983 55.000 0.00 0.00 36.95 4.58
618 1075 0.620556 ACAGATGGAACCCAATCGCT 59.379 50.000 0.00 0.00 36.95 4.93
619 1076 1.303309 CAGATGGAACCCAATCGCTC 58.697 55.000 0.00 0.00 36.95 5.03
620 1077 0.179073 AGATGGAACCCAATCGCTCG 60.179 55.000 0.00 0.00 36.95 5.03
621 1078 1.776034 GATGGAACCCAATCGCTCGC 61.776 60.000 0.00 0.00 36.95 5.03
622 1079 3.564027 GGAACCCAATCGCTCGCG 61.564 66.667 0.00 0.00 41.35 5.87
669 1126 2.891936 TCACTCATCATGCGCGGC 60.892 61.111 8.83 0.00 0.00 6.53
670 1127 4.289379 CACTCATCATGCGCGGCG 62.289 66.667 19.62 19.62 0.00 6.46
704 1166 0.036010 CCGTCAGGCTCCAGAAACAT 60.036 55.000 0.00 0.00 0.00 2.71
707 1169 2.284190 GTCAGGCTCCAGAAACATAGC 58.716 52.381 0.00 0.00 0.00 2.97
758 1220 0.108424 GCGAGCTCACTGATCACCTT 60.108 55.000 15.40 0.00 0.00 3.50
759 1221 1.919918 CGAGCTCACTGATCACCTTC 58.080 55.000 15.40 0.00 0.00 3.46
785 1256 3.793144 GTTGCGCCGAAGCCTCAG 61.793 66.667 4.18 0.00 36.02 3.35
786 1257 4.002506 TTGCGCCGAAGCCTCAGA 62.003 61.111 4.18 0.00 36.02 3.27
787 1258 4.742201 TGCGCCGAAGCCTCAGAC 62.742 66.667 4.18 0.00 36.02 3.51
846 1322 3.749064 GGCAGAGACGCGACCTCA 61.749 66.667 25.85 0.00 33.25 3.86
858 1334 2.350772 CGCGACCTCAGCAAAAAGAAAT 60.351 45.455 0.00 0.00 34.19 2.17
859 1335 3.237628 GCGACCTCAGCAAAAAGAAATC 58.762 45.455 0.00 0.00 34.19 2.17
860 1336 3.304659 GCGACCTCAGCAAAAAGAAATCA 60.305 43.478 0.00 0.00 34.19 2.57
861 1337 4.792704 GCGACCTCAGCAAAAAGAAATCAA 60.793 41.667 0.00 0.00 34.19 2.57
862 1338 5.280945 CGACCTCAGCAAAAAGAAATCAAA 58.719 37.500 0.00 0.00 0.00 2.69
864 1340 5.976458 ACCTCAGCAAAAAGAAATCAAACA 58.024 33.333 0.00 0.00 0.00 2.83
866 1342 5.234972 CCTCAGCAAAAAGAAATCAAACACC 59.765 40.000 0.00 0.00 0.00 4.16
867 1343 5.976458 TCAGCAAAAAGAAATCAAACACCT 58.024 33.333 0.00 0.00 0.00 4.00
869 1345 5.043248 AGCAAAAAGAAATCAAACACCTCG 58.957 37.500 0.00 0.00 0.00 4.63
870 1346 4.318050 GCAAAAAGAAATCAAACACCTCGC 60.318 41.667 0.00 0.00 0.00 5.03
871 1347 4.918810 AAAAGAAATCAAACACCTCGCT 57.081 36.364 0.00 0.00 0.00 4.93
872 1348 4.489679 AAAGAAATCAAACACCTCGCTC 57.510 40.909 0.00 0.00 0.00 5.03
873 1349 2.069273 AGAAATCAAACACCTCGCTCG 58.931 47.619 0.00 0.00 0.00 5.03
874 1350 1.128692 GAAATCAAACACCTCGCTCGG 59.871 52.381 0.00 0.00 0.00 4.63
875 1351 1.298859 AATCAAACACCTCGCTCGGC 61.299 55.000 0.00 0.00 0.00 5.54
876 1352 2.172483 ATCAAACACCTCGCTCGGCT 62.172 55.000 0.00 0.00 0.00 5.52
877 1353 2.357517 AAACACCTCGCTCGGCTG 60.358 61.111 0.00 0.00 0.00 4.85
894 1370 2.126580 GCTTGCTTGCTTGCTCCG 60.127 61.111 3.47 0.00 0.00 4.63
1013 1514 2.331893 CCAAGATGAACGCGCCCAA 61.332 57.895 5.73 0.00 0.00 4.12
1264 1771 1.069378 CCCGACGTTCTTGTACGAGC 61.069 60.000 5.12 0.00 43.99 5.03
1664 2240 4.652175 TCGTAGTACGTGTACAGAAGTG 57.348 45.455 21.38 0.00 43.14 3.16
1688 2264 7.430211 GTGTCTGTGACGTCGATTGTATTATTA 59.570 37.037 11.62 0.00 34.95 0.98
1726 2318 6.037172 TCACTTCTATTCTAGGCGATTTTTGC 59.963 38.462 0.00 0.00 0.00 3.68
1739 2331 5.287035 GGCGATTTTTGCTTGAGTAAATGAG 59.713 40.000 0.00 0.00 30.13 2.90
1768 2360 1.428219 GCTCGTAGCACGCACTCTA 59.572 57.895 4.15 0.00 42.21 2.43
1791 2383 1.925946 GCAACACATCTTGTCGTTGGC 60.926 52.381 16.89 10.25 37.51 4.52
1912 2526 2.968697 GGTGCGTTCCGTTCCGTT 60.969 61.111 0.00 0.00 0.00 4.44
1913 2527 2.547798 GTGCGTTCCGTTCCGTTC 59.452 61.111 0.00 0.00 0.00 3.95
1914 2528 2.662527 TGCGTTCCGTTCCGTTCC 60.663 61.111 0.00 0.00 0.00 3.62
1915 2529 3.770424 GCGTTCCGTTCCGTTCCG 61.770 66.667 0.00 0.00 0.00 4.30
1993 2616 0.534203 TTCGCTGCGTTTTCCTTCCT 60.534 50.000 22.48 0.00 0.00 3.36
2044 2672 1.002746 TAGCCGTGCAAGCATCCAA 60.003 52.632 12.15 0.00 0.00 3.53
2104 2735 3.406361 GGTGCGCACTCGTCTGTG 61.406 66.667 36.84 0.00 40.62 3.66
2107 2738 1.227118 TGCGCACTCGTCTGTGAAA 60.227 52.632 5.66 0.00 40.12 2.69
2157 2816 1.045407 TATGACCCCGACAGCCATAC 58.955 55.000 0.00 0.00 0.00 2.39
2173 2832 4.220821 AGCCATACTAACTGTCGATATGGG 59.779 45.833 16.75 3.80 41.71 4.00
2194 2853 4.502016 GGTACTCCCTCGGTTTCTTTAAG 58.498 47.826 0.00 0.00 0.00 1.85
2199 2866 6.228995 ACTCCCTCGGTTTCTTTAAGTAAAG 58.771 40.000 4.70 4.70 43.01 1.85
2212 2879 8.839947 TCTTTAAGTAAAGTTTGTTTAACGCC 57.160 30.769 9.95 0.00 42.43 5.68
2214 2881 8.617761 TTTAAGTAAAGTTTGTTTAACGCCAG 57.382 30.769 0.00 0.00 41.78 4.85
2224 2891 6.715344 TTGTTTAACGCCAGACTACATAAG 57.285 37.500 0.00 0.00 0.00 1.73
2229 2896 3.858247 ACGCCAGACTACATAAGGTTTC 58.142 45.455 0.00 0.00 0.00 2.78
2231 2898 3.617263 CGCCAGACTACATAAGGTTTCAC 59.383 47.826 0.00 0.00 0.00 3.18
2238 2905 8.576442 CAGACTACATAAGGTTTCACCAAATTT 58.424 33.333 0.00 0.00 41.95 1.82
2322 2989 9.196552 TCATGACACAACTAATGATATCGATTC 57.803 33.333 1.71 1.87 0.00 2.52
2323 2990 8.981647 CATGACACAACTAATGATATCGATTCA 58.018 33.333 1.71 7.95 0.00 2.57
2324 2991 9.716531 ATGACACAACTAATGATATCGATTCAT 57.283 29.630 1.71 9.95 35.35 2.57
2462 3130 2.804647 CATTCTGGCACATACGTCGTA 58.195 47.619 7.69 7.69 38.20 3.43
2479 3147 2.094700 TCGTATGCATTCGGATAGGAGC 60.095 50.000 23.04 0.00 36.00 4.70
2502 3170 5.931724 GCATATGGCCAAAAACTACAACTTT 59.068 36.000 10.96 0.00 36.11 2.66
2517 3185 4.313282 ACAACTTTAGCGACTAGGGTTTC 58.687 43.478 0.00 0.00 0.00 2.78
2521 3189 3.323751 TTAGCGACTAGGGTTTCCAAC 57.676 47.619 0.00 0.00 34.83 3.77
2532 3200 2.152016 GGTTTCCAACACTACTGCTCC 58.848 52.381 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 532 1.893786 CAGAGGGGAGGAGTTCACG 59.106 63.158 0.00 0.00 0.00 4.35
178 600 2.590821 GGGGATTTCCATGGTCATCTG 58.409 52.381 12.58 0.00 37.91 2.90
225 647 4.262420 CCTTGTTTGGTTGTAATGGGGAAG 60.262 45.833 0.00 0.00 0.00 3.46
296 718 5.389935 GCTTTGCTTGCTTGTACTGTACTAG 60.390 44.000 20.32 20.32 35.16 2.57
297 719 4.451096 GCTTTGCTTGCTTGTACTGTACTA 59.549 41.667 17.98 10.30 0.00 1.82
298 720 3.251004 GCTTTGCTTGCTTGTACTGTACT 59.749 43.478 17.98 0.00 0.00 2.73
299 721 3.555518 GCTTTGCTTGCTTGTACTGTAC 58.444 45.455 10.98 10.98 0.00 2.90
300 722 2.552315 GGCTTTGCTTGCTTGTACTGTA 59.448 45.455 0.00 0.00 0.00 2.74
301 723 1.338020 GGCTTTGCTTGCTTGTACTGT 59.662 47.619 0.00 0.00 0.00 3.55
302 724 1.664016 CGGCTTTGCTTGCTTGTACTG 60.664 52.381 0.00 0.00 0.00 2.74
303 725 0.593128 CGGCTTTGCTTGCTTGTACT 59.407 50.000 0.00 0.00 0.00 2.73
308 730 1.289276 CAAAACGGCTTTGCTTGCTT 58.711 45.000 0.05 0.00 38.17 3.91
326 748 4.329545 GGCCTCACCTTCACCGCA 62.330 66.667 0.00 0.00 34.51 5.69
352 774 3.317711 TGTTGCTGTCCGTCAAATCAATT 59.682 39.130 0.00 0.00 0.00 2.32
358 780 1.433053 CCGTGTTGCTGTCCGTCAAA 61.433 55.000 0.00 0.00 0.00 2.69
359 781 1.885388 CCGTGTTGCTGTCCGTCAA 60.885 57.895 0.00 0.00 0.00 3.18
360 782 2.094757 ATCCGTGTTGCTGTCCGTCA 62.095 55.000 0.00 0.00 0.00 4.35
361 783 1.374252 ATCCGTGTTGCTGTCCGTC 60.374 57.895 0.00 0.00 0.00 4.79
362 784 1.667830 CATCCGTGTTGCTGTCCGT 60.668 57.895 0.00 0.00 0.00 4.69
363 785 2.390599 CCATCCGTGTTGCTGTCCG 61.391 63.158 0.00 0.00 0.00 4.79
365 787 1.803334 TTACCATCCGTGTTGCTGTC 58.197 50.000 0.00 0.00 0.00 3.51
367 789 3.634568 TTTTTACCATCCGTGTTGCTG 57.365 42.857 0.00 0.00 0.00 4.41
401 825 2.435693 CCAGGCCGACTAGGAAGGG 61.436 68.421 0.00 0.00 45.00 3.95
406 832 0.395862 TCTTCTCCAGGCCGACTAGG 60.396 60.000 0.00 0.00 44.97 3.02
490 918 0.811616 GACCACCAGATCCATGCGTC 60.812 60.000 0.00 0.00 0.00 5.19
533 971 1.000019 ATCGACGGAGGAAGGGACA 60.000 57.895 0.00 0.00 0.00 4.02
549 987 1.356938 GGTGAAAAGGGTCGACGATC 58.643 55.000 9.92 0.00 0.00 3.69
557 995 4.653888 CCCCGCGGTGAAAAGGGT 62.654 66.667 26.12 0.00 42.26 4.34
589 1046 2.812542 TTCCATCTGTCCGCACGACG 62.813 60.000 0.00 0.00 45.23 5.12
591 1048 1.080093 GTTCCATCTGTCCGCACGA 60.080 57.895 0.00 0.00 0.00 4.35
592 1049 2.100631 GGTTCCATCTGTCCGCACG 61.101 63.158 0.00 0.00 0.00 5.34
621 1078 0.043053 CAGATATTTGTGCGACCGCG 60.043 55.000 9.91 0.00 45.51 6.46
622 1079 0.304705 CCAGATATTTGTGCGACCGC 59.695 55.000 7.53 7.53 42.35 5.68
692 1154 0.744414 TGGCGCTATGTTTCTGGAGC 60.744 55.000 7.64 0.00 0.00 4.70
737 1199 0.527385 GGTGATCAGTGAGCTCGCTC 60.527 60.000 26.70 16.37 43.01 5.03
738 1200 0.969917 AGGTGATCAGTGAGCTCGCT 60.970 55.000 24.06 24.06 37.13 4.93
739 1201 0.108424 AAGGTGATCAGTGAGCTCGC 60.108 55.000 19.76 19.76 0.00 5.03
740 1202 1.796982 CGAAGGTGATCAGTGAGCTCG 60.797 57.143 10.19 6.65 0.00 5.03
741 1203 1.919918 CGAAGGTGATCAGTGAGCTC 58.080 55.000 10.19 6.82 0.00 4.09
742 1204 0.108424 GCGAAGGTGATCAGTGAGCT 60.108 55.000 10.19 0.00 0.00 4.09
743 1205 1.416813 CGCGAAGGTGATCAGTGAGC 61.417 60.000 0.00 0.17 0.00 4.26
744 1206 0.109086 ACGCGAAGGTGATCAGTGAG 60.109 55.000 15.93 0.00 0.00 3.51
745 1207 0.317160 AACGCGAAGGTGATCAGTGA 59.683 50.000 15.93 0.00 0.00 3.41
772 1243 4.116328 TCGTCTGAGGCTTCGGCG 62.116 66.667 0.00 0.00 42.91 6.46
775 1246 2.182030 GGGTCGTCTGAGGCTTCG 59.818 66.667 0.00 0.00 0.00 3.79
785 1256 0.393402 ATTTAAAGGGGCGGGTCGTC 60.393 55.000 0.00 0.00 0.00 4.20
786 1257 0.911053 TATTTAAAGGGGCGGGTCGT 59.089 50.000 0.00 0.00 0.00 4.34
787 1258 1.302366 GTATTTAAAGGGGCGGGTCG 58.698 55.000 0.00 0.00 0.00 4.79
788 1259 1.302366 CGTATTTAAAGGGGCGGGTC 58.698 55.000 0.00 0.00 0.00 4.46
846 1322 5.043248 CGAGGTGTTTGATTTCTTTTTGCT 58.957 37.500 0.00 0.00 0.00 3.91
858 1334 2.357034 GCCGAGCGAGGTGTTTGA 60.357 61.111 2.58 0.00 0.00 2.69
859 1335 2.357517 AGCCGAGCGAGGTGTTTG 60.358 61.111 2.58 0.00 0.00 2.93
860 1336 2.357517 CAGCCGAGCGAGGTGTTT 60.358 61.111 2.58 0.00 0.00 2.83
864 1340 4.749310 CAAGCAGCCGAGCGAGGT 62.749 66.667 2.58 0.00 40.15 3.85
874 1350 1.733399 GAGCAAGCAAGCAAGCAGC 60.733 57.895 10.52 6.48 46.19 5.25
875 1351 1.080705 GGAGCAAGCAAGCAAGCAG 60.081 57.895 10.52 0.00 36.85 4.24
876 1352 2.911484 CGGAGCAAGCAAGCAAGCA 61.911 57.895 10.52 0.00 36.85 3.91
877 1353 2.126580 CGGAGCAAGCAAGCAAGC 60.127 61.111 3.19 0.00 36.85 4.01
878 1354 2.564975 CCGGAGCAAGCAAGCAAG 59.435 61.111 0.00 0.00 36.85 4.01
900 1376 3.412879 GACGCGAGCTCTGGGGTAC 62.413 68.421 15.93 6.58 34.88 3.34
901 1377 3.138798 GACGCGAGCTCTGGGGTA 61.139 66.667 15.93 0.00 34.88 3.69
987 1488 2.609459 CGCGTTCATCTTGGAAATAGCT 59.391 45.455 0.00 0.00 0.00 3.32
990 1491 1.668751 GGCGCGTTCATCTTGGAAATA 59.331 47.619 8.43 0.00 0.00 1.40
1062 1563 1.144936 GGAGAGGCCCATGAAGACG 59.855 63.158 0.00 0.00 0.00 4.18
1577 2099 1.206849 AGCTAGCTCAGTTCAGCCTTC 59.793 52.381 12.68 0.00 40.65 3.46
1664 2240 6.807708 AATAATACAATCGACGTCACAGAC 57.192 37.500 17.16 0.00 0.00 3.51
1726 2318 7.763528 AGCACTAGATTCACTCATTTACTCAAG 59.236 37.037 0.00 0.00 0.00 3.02
1768 2360 1.953559 ACGACAAGATGTGTTGCAGT 58.046 45.000 0.00 0.00 44.58 4.40
1791 2383 2.494870 CAAGAGAAAATGGGGAGGCTTG 59.505 50.000 0.00 0.00 0.00 4.01
1838 2431 4.724697 CAGCTGAACCGCGCAACG 62.725 66.667 8.42 0.00 43.15 4.10
1951 2565 0.246910 GGAAGGAACTCTCGGTGGAC 59.753 60.000 0.00 0.00 38.49 4.02
2044 2672 1.135083 CAGGAGTAGGCACGAAACGAT 60.135 52.381 0.00 0.00 0.00 3.73
2095 2726 2.057316 CAGCACTCTTTCACAGACGAG 58.943 52.381 0.00 0.00 0.00 4.18
2157 2816 5.373981 GGAGTACCCATATCGACAGTTAG 57.626 47.826 0.00 0.00 34.14 2.34
2173 2832 5.144692 ACTTAAAGAAACCGAGGGAGTAC 57.855 43.478 0.00 0.00 0.00 2.73
2188 2847 8.617761 TGGCGTTAAACAAACTTTACTTAAAG 57.382 30.769 7.12 7.12 46.12 1.85
2192 2851 6.094464 AGTCTGGCGTTAAACAAACTTTACTT 59.906 34.615 0.00 0.00 35.81 2.24
2194 2853 5.813717 AGTCTGGCGTTAAACAAACTTTAC 58.186 37.500 0.00 0.00 35.81 2.01
2199 2866 4.799419 TGTAGTCTGGCGTTAAACAAAC 57.201 40.909 0.00 0.00 34.52 2.93
2209 2876 3.617263 GTGAAACCTTATGTAGTCTGGCG 59.383 47.826 0.00 0.00 0.00 5.69
2298 2965 9.716531 ATGAATCGATATCATTAGTTGTGTCAT 57.283 29.630 13.79 5.74 33.84 3.06
2311 2978 9.546428 AACAAGTCACATTATGAATCGATATCA 57.454 29.630 0.00 5.56 39.72 2.15
2395 3063 7.420680 CCCTCCATTTCTCTTTGGTCTACATAT 60.421 40.741 0.00 0.00 34.48 1.78
2400 3068 4.435137 TCCCTCCATTTCTCTTTGGTCTA 58.565 43.478 0.00 0.00 34.48 2.59
2404 3072 3.728385 ACTCCCTCCATTTCTCTTTGG 57.272 47.619 0.00 0.00 0.00 3.28
2405 3073 7.613411 AGAAATTACTCCCTCCATTTCTCTTTG 59.387 37.037 0.00 0.00 40.42 2.77
2409 3077 7.946381 AAAGAAATTACTCCCTCCATTTCTC 57.054 36.000 6.48 0.00 42.53 2.87
2418 3086 8.201242 TGCCATTTTAAAAGAAATTACTCCCT 57.799 30.769 6.79 0.00 0.00 4.20
2419 3087 9.448438 AATGCCATTTTAAAAGAAATTACTCCC 57.552 29.630 6.79 0.00 0.00 4.30
2454 3122 3.120095 CCTATCCGAATGCATACGACGTA 60.120 47.826 10.62 10.62 0.00 3.57
2462 3130 4.449131 CATATGCTCCTATCCGAATGCAT 58.551 43.478 0.00 0.00 42.64 3.96
2479 3147 7.275560 GCTAAAGTTGTAGTTTTTGGCCATATG 59.724 37.037 6.09 0.00 33.75 1.78
2517 3185 0.537188 ATCGGGAGCAGTAGTGTTGG 59.463 55.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.