Multiple sequence alignment - TraesCS1B01G068600

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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 TraesCS1B01G068600 chr1B 100.000 3098 0 0 1 3098 53251441 53248344 0 5722
1 TraesCS1B01G068600 chr1A 87.056 1437 98 36 132 1523 33375835 33374442 0 1543
2 TraesCS1B01G068600 chr1A 94.347 513 28 1 1760 2271 33373974 33373462 0 785
3 TraesCS1B01G068600 chr1A 93.053 475 24 4 2625 3096 33373203 33372735 0 686
4 TraesCS1B01G068600 chr1D 88.968 979 52 32 805 1755 34946406 34945456 0 1158
5 TraesCS1B01G068600 chr1D 90.806 707 32 21 1 693 34947489 34946802 0 915
6 TraesCS1B01G068600 chr1D 95.306 490 19 2 1760 2248 34945384 34944898 0 774
7 TraesCS1B01G068600 chr1D 92.395 526 18 7 2575 3098 34944531 34944026 0 730


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 TraesCS1B01G068600 chr1B 53248344 53251441 3097 True 5722.000000 5722 100.000000 1 3098 1 chr1B.!!$R1 3097
1 TraesCS1B01G068600 chr1A 33372735 33375835 3100 True 1004.666667 1543 91.485333 132 3096 3 chr1A.!!$R1 2964
2 TraesCS1B01G068600 chr1D 34944026 34947489 3463 True 894.250000 1158 91.868750 1 3098 4 chr1D.!!$R1 3097

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
987 1360 0.251742 AGCTCACTCAGGTCAGCTCT 60.252 55.0 0.0 0.0 46.81 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2316 2956 0.032678 CTTAGGAGTGGCGCGATCAT 59.967 55.0 12.1 1.42 0.0 2.45 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
31 32 7.390440 CACTTTGGTTTGATGATCTACCTACAA 59.610 37.037 15.03 7.43 0.00 2.41
55 56 1.936547 GATGGAATTCGCTGGACAGTC 59.063 52.381 0.00 0.00 0.00 3.51
56 57 0.976641 TGGAATTCGCTGGACAGTCT 59.023 50.000 0.00 0.00 0.00 3.24
57 58 1.347707 TGGAATTCGCTGGACAGTCTT 59.652 47.619 0.00 0.00 0.00 3.01
58 59 2.003301 GGAATTCGCTGGACAGTCTTC 58.997 52.381 0.00 0.00 0.00 2.87
59 60 2.612972 GGAATTCGCTGGACAGTCTTCA 60.613 50.000 0.00 0.00 0.00 3.02
60 61 3.265791 GAATTCGCTGGACAGTCTTCAT 58.734 45.455 0.00 0.00 0.00 2.57
61 62 4.433615 GAATTCGCTGGACAGTCTTCATA 58.566 43.478 0.00 0.00 0.00 2.15
62 63 4.679373 ATTCGCTGGACAGTCTTCATAT 57.321 40.909 0.00 0.00 0.00 1.78
63 64 3.443099 TCGCTGGACAGTCTTCATATG 57.557 47.619 0.00 0.00 0.00 1.78
64 65 2.760650 TCGCTGGACAGTCTTCATATGT 59.239 45.455 1.90 0.00 0.00 2.29
137 138 6.478344 CAGTGCTTTGACAGTATATCCTCTTC 59.522 42.308 0.00 0.00 0.00 2.87
150 151 3.121738 TCCTCTTCCGTTCCTGTTTTC 57.878 47.619 0.00 0.00 0.00 2.29
173 174 2.093447 AGACTAGCTCCAATGGGTTTCG 60.093 50.000 0.00 0.00 34.93 3.46
363 364 4.506255 CCGCTCCCCCACCCAATC 62.506 72.222 0.00 0.00 0.00 2.67
459 467 3.777106 TTTGAGCAATGACTCTGTCCT 57.223 42.857 6.33 0.00 37.58 3.85
466 474 1.757682 ATGACTCTGTCCTCTCCGTC 58.242 55.000 0.00 0.00 0.00 4.79
591 622 5.163602 ACGTTTTTGTTTGACTTGCATCCTA 60.164 36.000 0.00 0.00 0.00 2.94
594 625 7.042791 CGTTTTTGTTTGACTTGCATCCTAATT 60.043 33.333 0.00 0.00 0.00 1.40
600 631 8.028354 TGTTTGACTTGCATCCTAATTATTGTG 58.972 33.333 0.00 0.00 0.00 3.33
640 671 7.494298 AGTTTATGCCAAGGTTGTTAAGTTTTG 59.506 33.333 0.00 0.00 0.00 2.44
642 673 5.916661 TGCCAAGGTTGTTAAGTTTTGTA 57.083 34.783 0.00 0.00 0.00 2.41
644 675 5.185249 TGCCAAGGTTGTTAAGTTTTGTACA 59.815 36.000 0.00 0.00 0.00 2.90
646 677 6.759356 GCCAAGGTTGTTAAGTTTTGTACAAT 59.241 34.615 9.56 0.00 33.57 2.71
647 678 7.254286 GCCAAGGTTGTTAAGTTTTGTACAATG 60.254 37.037 9.56 0.00 33.57 2.82
649 680 6.277605 AGGTTGTTAAGTTTTGTACAATGGC 58.722 36.000 9.56 2.99 33.57 4.40
663 856 2.242043 CAATGGCTTTCTTGTGAGGGT 58.758 47.619 0.00 0.00 0.00 4.34
670 863 1.131638 TTCTTGTGAGGGTGTCAGCT 58.868 50.000 1.41 0.00 35.13 4.24
680 873 2.769095 AGGGTGTCAGCTTAGATTCTCC 59.231 50.000 1.41 0.00 0.00 3.71
686 879 2.435805 TCAGCTTAGATTCTCCCGCAAT 59.564 45.455 0.00 0.00 0.00 3.56
692 885 0.817013 GATTCTCCCGCAATTTGCCA 59.183 50.000 15.45 0.00 41.12 4.92
693 886 1.410153 GATTCTCCCGCAATTTGCCAT 59.590 47.619 15.45 0.00 41.12 4.40
694 887 0.531657 TTCTCCCGCAATTTGCCATG 59.468 50.000 15.45 4.69 41.12 3.66
695 888 0.323269 TCTCCCGCAATTTGCCATGA 60.323 50.000 15.45 8.51 41.12 3.07
718 968 0.463620 TGTTGGGACTTTTTGCTGCC 59.536 50.000 0.00 0.00 0.00 4.85
727 977 3.186909 ACTTTTTGCTGCCGAGTTTTTC 58.813 40.909 0.00 0.00 0.00 2.29
787 1141 2.666190 CACTCACTGTGCGGTGGG 60.666 66.667 18.86 9.31 42.85 4.61
788 1142 3.161450 ACTCACTGTGCGGTGGGT 61.161 61.111 10.63 10.63 44.98 4.51
842 1204 2.741092 CACCACGTAGCACCCACT 59.259 61.111 0.00 0.00 0.00 4.00
874 1236 2.394563 GCAAAGCAGAGCGAGACCC 61.395 63.158 0.00 0.00 0.00 4.46
905 1271 0.951040 CGCCTTTCTCGCTTGTTCCT 60.951 55.000 0.00 0.00 0.00 3.36
906 1272 0.799393 GCCTTTCTCGCTTGTTCCTC 59.201 55.000 0.00 0.00 0.00 3.71
929 1296 2.856000 ACTTGCCCACCCAGCTCT 60.856 61.111 0.00 0.00 0.00 4.09
930 1297 2.045536 CTTGCCCACCCAGCTCTC 60.046 66.667 0.00 0.00 0.00 3.20
931 1298 2.853542 TTGCCCACCCAGCTCTCA 60.854 61.111 0.00 0.00 0.00 3.27
932 1299 2.416107 CTTGCCCACCCAGCTCTCAA 62.416 60.000 0.00 0.00 0.00 3.02
933 1300 2.360475 GCCCACCCAGCTCTCAAC 60.360 66.667 0.00 0.00 0.00 3.18
934 1301 2.900106 GCCCACCCAGCTCTCAACT 61.900 63.158 0.00 0.00 0.00 3.16
935 1302 1.298014 CCCACCCAGCTCTCAACTC 59.702 63.158 0.00 0.00 0.00 3.01
936 1303 1.298014 CCACCCAGCTCTCAACTCC 59.702 63.158 0.00 0.00 0.00 3.85
937 1304 1.483595 CCACCCAGCTCTCAACTCCA 61.484 60.000 0.00 0.00 0.00 3.86
938 1305 0.397941 CACCCAGCTCTCAACTCCAA 59.602 55.000 0.00 0.00 0.00 3.53
939 1306 0.689623 ACCCAGCTCTCAACTCCAAG 59.310 55.000 0.00 0.00 0.00 3.61
987 1360 0.251742 AGCTCACTCAGGTCAGCTCT 60.252 55.000 0.00 0.00 46.81 4.09
989 1362 1.838112 CTCACTCAGGTCAGCTCTCT 58.162 55.000 0.00 0.00 0.00 3.10
990 1363 2.170166 CTCACTCAGGTCAGCTCTCTT 58.830 52.381 0.00 0.00 0.00 2.85
992 1387 3.085533 TCACTCAGGTCAGCTCTCTTAC 58.914 50.000 0.00 0.00 0.00 2.34
1015 1410 3.541831 CGATGGCGTCGTTCCACG 61.542 66.667 20.53 0.00 45.19 4.94
1194 1589 1.521616 CTCCTTCCTGCAGCTCTCC 59.478 63.158 8.66 0.00 0.00 3.71
1237 1632 0.747283 CATCTTCACCCAGAGCAGCC 60.747 60.000 0.00 0.00 0.00 4.85
1428 1823 1.300931 CCGCTACATCATCCCCGTG 60.301 63.158 0.00 0.00 0.00 4.94
1528 1981 2.478200 CGGAGCCTCGTAAGTCTTCTTC 60.478 54.545 0.00 0.00 35.36 2.87
1538 1991 7.364522 TCGTAAGTCTTCTTCCATGAAAATG 57.635 36.000 0.00 0.00 35.36 2.32
1567 2020 1.742831 TGTATGCCGATTCACTTTGCC 59.257 47.619 0.00 0.00 0.00 4.52
1596 2155 1.791555 CGCCGTCATCTTGCATTGTTC 60.792 52.381 0.00 0.00 0.00 3.18
1600 2159 4.787563 GCCGTCATCTTGCATTGTTCATAG 60.788 45.833 0.00 0.00 0.00 2.23
1617 2176 8.232913 TGTTCATAGCTTTGTTAGAAAAGGTT 57.767 30.769 6.68 0.00 43.46 3.50
1618 2177 9.344772 TGTTCATAGCTTTGTTAGAAAAGGTTA 57.655 29.630 6.68 0.00 43.46 2.85
1661 2220 2.100846 TGCCATTCTGCATTCGCTC 58.899 52.632 0.00 0.00 39.64 5.03
1672 2231 1.229428 CATTCGCTCAAGGTGTGTGT 58.771 50.000 0.00 0.00 0.00 3.72
1673 2232 2.412870 CATTCGCTCAAGGTGTGTGTA 58.587 47.619 0.00 0.00 0.00 2.90
1674 2233 2.605837 TTCGCTCAAGGTGTGTGTAA 57.394 45.000 0.00 0.00 0.00 2.41
1675 2234 2.831685 TCGCTCAAGGTGTGTGTAAT 57.168 45.000 0.00 0.00 0.00 1.89
1679 2238 5.968254 TCGCTCAAGGTGTGTGTAATATTA 58.032 37.500 0.00 0.00 0.00 0.98
1781 2419 9.480053 ACATTTCATTTTTCTGATCATTTCGTT 57.520 25.926 0.00 0.00 0.00 3.85
2004 2642 2.440796 AACATGCTCATGGGGGCG 60.441 61.111 13.69 0.00 42.91 6.13
2098 2736 0.107312 CTCCGTCTTCCCCGACTAGA 60.107 60.000 0.00 0.00 0.00 2.43
2119 2758 2.594592 GGCCAGACAAGCAACCGT 60.595 61.111 0.00 0.00 0.00 4.83
2136 2775 2.676342 ACCGTTCTGTTTTCTGTGTGAC 59.324 45.455 0.00 0.00 0.00 3.67
2137 2776 2.675844 CCGTTCTGTTTTCTGTGTGACA 59.324 45.455 0.00 0.00 0.00 3.58
2237 2877 0.690192 TCCGTCAATTCTGGGCTTGA 59.310 50.000 0.00 0.00 0.00 3.02
2266 2906 5.883503 TTTTAACCTCGGCGACATTTATT 57.116 34.783 4.99 0.00 0.00 1.40
2271 2911 4.255301 ACCTCGGCGACATTTATTAAACA 58.745 39.130 4.99 0.00 0.00 2.83
2272 2912 4.331717 ACCTCGGCGACATTTATTAAACAG 59.668 41.667 4.99 0.00 0.00 3.16
2273 2913 4.331717 CCTCGGCGACATTTATTAAACAGT 59.668 41.667 4.99 0.00 0.00 3.55
2274 2914 5.521010 CCTCGGCGACATTTATTAAACAGTA 59.479 40.000 4.99 0.00 0.00 2.74
2275 2915 6.202188 CCTCGGCGACATTTATTAAACAGTAT 59.798 38.462 4.99 0.00 0.00 2.12
2276 2916 7.169035 TCGGCGACATTTATTAAACAGTATC 57.831 36.000 4.99 0.00 0.00 2.24
2278 2918 7.278203 TCGGCGACATTTATTAAACAGTATCAA 59.722 33.333 4.99 0.00 0.00 2.57
2279 2919 8.067784 CGGCGACATTTATTAAACAGTATCAAT 58.932 33.333 0.00 0.00 0.00 2.57
2308 2948 6.503944 TCTACAAGAGAGGGGATTAAGAAGT 58.496 40.000 0.00 0.00 0.00 3.01
2309 2949 5.685520 ACAAGAGAGGGGATTAAGAAGTC 57.314 43.478 0.00 0.00 0.00 3.01
2310 2950 5.094387 ACAAGAGAGGGGATTAAGAAGTCA 58.906 41.667 0.00 0.00 0.00 3.41
2312 2952 4.294347 AGAGAGGGGATTAAGAAGTCAGG 58.706 47.826 0.00 0.00 0.00 3.86
2314 2954 4.294347 AGAGGGGATTAAGAAGTCAGGAG 58.706 47.826 0.00 0.00 0.00 3.69
2316 2956 3.014110 AGGGGATTAAGAAGTCAGGAGGA 59.986 47.826 0.00 0.00 0.00 3.71
2318 2958 4.202409 GGGGATTAAGAAGTCAGGAGGATG 60.202 50.000 0.00 0.00 0.00 3.51
2319 2959 4.656112 GGGATTAAGAAGTCAGGAGGATGA 59.344 45.833 0.00 0.00 0.00 2.92
2320 2960 5.309282 GGGATTAAGAAGTCAGGAGGATGAT 59.691 44.000 0.00 0.00 0.00 2.45
2321 2961 6.463360 GGATTAAGAAGTCAGGAGGATGATC 58.537 44.000 0.00 0.00 0.00 2.92
2322 2962 5.521906 TTAAGAAGTCAGGAGGATGATCG 57.478 43.478 0.00 0.00 0.00 3.69
2323 2963 1.686052 AGAAGTCAGGAGGATGATCGC 59.314 52.381 0.00 0.00 0.00 4.58
2324 2964 0.387202 AAGTCAGGAGGATGATCGCG 59.613 55.000 0.00 0.00 0.00 5.87
2326 2966 2.356793 CAGGAGGATGATCGCGCC 60.357 66.667 0.00 0.00 0.00 6.53
2328 2968 2.663188 GGAGGATGATCGCGCCAC 60.663 66.667 0.00 0.00 0.00 5.01
2330 2970 1.663074 GAGGATGATCGCGCCACTC 60.663 63.158 0.00 2.40 0.00 3.51
2336 3022 1.035385 TGATCGCGCCACTCCTAAGA 61.035 55.000 0.00 0.00 0.00 2.10
2340 3026 1.153353 CGCGCCACTCCTAAGAAAAA 58.847 50.000 0.00 0.00 0.00 1.94
2362 3057 4.983671 ACACAGTGCGTCTAGATATCAA 57.016 40.909 5.32 0.00 0.00 2.57
2364 3059 5.284864 ACACAGTGCGTCTAGATATCAATG 58.715 41.667 5.32 13.79 0.00 2.82
2386 3081 3.424962 GCTGCTCTGAAACCGATTGTAAC 60.425 47.826 0.00 0.00 0.00 2.50
2389 3084 3.120304 GCTCTGAAACCGATTGTAACACC 60.120 47.826 0.00 0.00 0.00 4.16
2393 3088 1.153353 AACCGATTGTAACACCGCTG 58.847 50.000 0.00 0.00 0.00 5.18
2404 3099 1.156736 ACACCGCTGTGCAAGATTAC 58.843 50.000 8.32 0.00 46.86 1.89
2407 3102 1.060937 CGCTGTGCAAGATTACCGC 59.939 57.895 0.00 0.00 0.00 5.68
2411 3106 1.929836 CTGTGCAAGATTACCGCTCTC 59.070 52.381 0.00 0.00 0.00 3.20
2423 3128 1.603802 ACCGCTCTCAAACACAATGTG 59.396 47.619 12.40 12.40 39.75 3.21
2435 3140 1.536766 CACAATGTGGCATCGAACAGT 59.463 47.619 5.29 0.00 0.00 3.55
2437 3142 2.226437 ACAATGTGGCATCGAACAGTTC 59.774 45.455 2.85 2.85 0.00 3.01
2439 3144 1.960417 TGTGGCATCGAACAGTTCAA 58.040 45.000 13.82 0.00 0.00 2.69
2441 3146 3.669536 TGTGGCATCGAACAGTTCAATA 58.330 40.909 13.82 0.00 0.00 1.90
2459 3164 9.739276 AGTTCAATATGTTCTTTACAGGATCAA 57.261 29.630 0.00 0.00 40.83 2.57
2476 3181 7.122055 ACAGGATCAAAACAAGTTTGTAACAGA 59.878 33.333 0.00 0.00 45.83 3.41
2477 3182 7.645340 CAGGATCAAAACAAGTTTGTAACAGAG 59.355 37.037 0.00 0.00 45.83 3.35
2478 3183 6.417930 GGATCAAAACAAGTTTGTAACAGAGC 59.582 38.462 0.00 0.00 45.83 4.09
2485 3190 4.252971 AGTTTGTAACAGAGCGCTCTAA 57.747 40.909 37.74 25.27 37.98 2.10
2488 3193 5.701290 AGTTTGTAACAGAGCGCTCTAAAAT 59.299 36.000 37.74 28.02 37.98 1.82
2493 3198 2.744202 ACAGAGCGCTCTAAAATGTTGG 59.256 45.455 37.74 23.95 37.98 3.77
2495 3200 2.744202 AGAGCGCTCTAAAATGTTGGTG 59.256 45.455 37.61 0.00 38.35 4.17
2500 3205 3.502211 CGCTCTAAAATGTTGGTGAGGTT 59.498 43.478 0.00 0.00 0.00 3.50
2511 3254 1.398958 GGTGAGGTTTTGCTTGCCCA 61.399 55.000 0.00 0.00 0.00 5.36
2513 3256 0.685785 TGAGGTTTTGCTTGCCCACA 60.686 50.000 0.00 0.00 0.00 4.17
2532 3291 4.158764 CCACACTTTTGGGTTTAGTCACAA 59.841 41.667 0.00 0.00 30.69 3.33
2538 3297 6.647481 ACTTTTGGGTTTAGTCACAACAAAAC 59.353 34.615 0.00 0.00 34.29 2.43
2541 3300 4.767928 TGGGTTTAGTCACAACAAAACTGT 59.232 37.500 0.00 0.00 33.40 3.55
2551 3310 6.145371 GTCACAACAAAACTGTCACATGTTTT 59.855 34.615 10.53 10.53 44.18 2.43
2552 3311 6.703607 TCACAACAAAACTGTCACATGTTTTT 59.296 30.769 12.62 0.00 42.29 1.94
2562 3321 3.004734 GTCACATGTTTTTGGTCAGGAGG 59.995 47.826 0.00 0.00 0.00 4.30
2564 3323 3.254166 CACATGTTTTTGGTCAGGAGGAG 59.746 47.826 0.00 0.00 0.00 3.69
2572 3333 0.322816 GGTCAGGAGGAGCAATTGCA 60.323 55.000 30.89 5.95 45.16 4.08
2596 3357 1.660104 GCAAAGCAAACACAACACCAG 59.340 47.619 0.00 0.00 0.00 4.00
2604 3365 3.627395 AACACAACACCAGTTCAGAGA 57.373 42.857 0.00 0.00 35.28 3.10
2605 3366 3.627395 ACACAACACCAGTTCAGAGAA 57.373 42.857 0.00 0.00 35.28 2.87
2606 3367 3.270877 ACACAACACCAGTTCAGAGAAC 58.729 45.455 1.77 1.77 35.28 3.01
2615 3376 3.558746 CCAGTTCAGAGAACAAGATGCCT 60.559 47.826 11.92 0.00 0.00 4.75
2622 3383 4.758674 CAGAGAACAAGATGCCTCAGAAAA 59.241 41.667 0.00 0.00 0.00 2.29
2644 3405 4.404507 AACAACGACATATGAACAGCAC 57.595 40.909 10.38 0.00 0.00 4.40
2648 3409 1.328680 CGACATATGAACAGCACCAGC 59.671 52.381 10.38 0.00 42.56 4.85
2692 3453 8.696374 CCAGACAGAATTCAGGTACTTATTAGA 58.304 37.037 8.44 0.00 34.60 2.10
2693 3454 9.743057 CAGACAGAATTCAGGTACTTATTAGAG 57.257 37.037 8.44 0.00 34.60 2.43
2719 3480 3.926527 GTCATATCTTGTCACAGACGCAA 59.073 43.478 0.00 0.00 34.95 4.85
2744 3505 6.696411 ACTAGAGTGCCAAATCATATAGAGC 58.304 40.000 0.00 0.00 0.00 4.09
2749 3510 6.125029 AGTGCCAAATCATATAGAGCAAAGT 58.875 36.000 0.00 0.00 0.00 2.66
2751 3512 7.775093 AGTGCCAAATCATATAGAGCAAAGTAA 59.225 33.333 0.00 0.00 0.00 2.24
2835 3597 1.133606 TCCCTGACCAAACCAAGTTCC 60.134 52.381 0.00 0.00 0.00 3.62
2864 3626 6.856135 CCTACACGAAGAGTTTAGGTTTTT 57.144 37.500 0.00 0.00 44.43 1.94
2899 3661 0.253044 TCAGCCATGGTGAAGCTACC 59.747 55.000 14.67 0.00 37.11 3.18
3076 3841 1.637035 CCCATCATGCCTCCCATCATA 59.363 52.381 0.00 0.00 29.71 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.141620 ACTGTCCAGCGAATTCCATCTATT 60.142 41.667 0.00 0.00 0.00 1.73
55 56 9.162793 GCAAATTCGTCTATGAAACATATGAAG 57.837 33.333 10.38 0.00 0.00 3.02
56 57 8.672815 TGCAAATTCGTCTATGAAACATATGAA 58.327 29.630 10.38 0.00 0.00 2.57
57 58 8.207521 TGCAAATTCGTCTATGAAACATATGA 57.792 30.769 10.38 0.00 0.00 2.15
150 151 1.207791 ACCCATTGGAGCTAGTCTGG 58.792 55.000 3.62 0.00 34.81 3.86
173 174 1.446966 GCGAGAAGGTGCTCTGGAC 60.447 63.158 0.00 0.00 32.71 4.02
466 474 2.821437 TCCCCAGGACAGAGTCTTAAG 58.179 52.381 0.00 0.00 32.47 1.85
526 535 5.909621 ACAGGTCTTTCATCCATTCATTG 57.090 39.130 0.00 0.00 0.00 2.82
530 539 6.314896 CAGTCTAACAGGTCTTTCATCCATTC 59.685 42.308 0.00 0.00 0.00 2.67
541 551 1.617322 TCACGCAGTCTAACAGGTCT 58.383 50.000 0.00 0.00 41.61 3.85
640 671 3.191371 CCCTCACAAGAAAGCCATTGTAC 59.809 47.826 0.00 0.00 37.54 2.90
642 673 2.242043 CCCTCACAAGAAAGCCATTGT 58.758 47.619 0.00 0.00 40.18 2.71
644 675 2.242043 CACCCTCACAAGAAAGCCATT 58.758 47.619 0.00 0.00 0.00 3.16
646 677 0.550914 ACACCCTCACAAGAAAGCCA 59.449 50.000 0.00 0.00 0.00 4.75
647 678 1.239347 GACACCCTCACAAGAAAGCC 58.761 55.000 0.00 0.00 0.00 4.35
649 680 1.876156 GCTGACACCCTCACAAGAAAG 59.124 52.381 0.00 0.00 0.00 2.62
663 856 1.137086 GCGGGAGAATCTAAGCTGACA 59.863 52.381 0.00 0.00 33.73 3.58
670 863 2.687935 GGCAAATTGCGGGAGAATCTAA 59.312 45.455 12.15 0.00 46.21 2.10
680 873 3.392769 CAATTTCATGGCAAATTGCGG 57.607 42.857 12.15 4.33 46.21 5.69
686 879 3.390639 AGTCCCAACAATTTCATGGCAAA 59.609 39.130 0.00 0.00 32.71 3.68
692 885 5.528320 CAGCAAAAAGTCCCAACAATTTCAT 59.472 36.000 0.00 0.00 0.00 2.57
693 886 4.874966 CAGCAAAAAGTCCCAACAATTTCA 59.125 37.500 0.00 0.00 0.00 2.69
694 887 4.260743 GCAGCAAAAAGTCCCAACAATTTC 60.261 41.667 0.00 0.00 0.00 2.17
695 888 3.627123 GCAGCAAAAAGTCCCAACAATTT 59.373 39.130 0.00 0.00 0.00 1.82
700 950 0.597377 CGGCAGCAAAAAGTCCCAAC 60.597 55.000 0.00 0.00 0.00 3.77
704 954 0.668535 AACTCGGCAGCAAAAAGTCC 59.331 50.000 0.00 0.00 0.00 3.85
718 968 8.989160 ACGAAAGAATCTAAAAGAAAAACTCG 57.011 30.769 0.00 0.00 0.00 4.18
727 977 6.363473 ACGCAAAGACGAAAGAATCTAAAAG 58.637 36.000 0.00 0.00 36.70 2.27
868 1230 1.529309 GCTGAATGGGAGGGGTCTC 59.471 63.158 0.00 0.00 39.25 3.36
869 1231 2.370445 CGCTGAATGGGAGGGGTCT 61.370 63.158 0.00 0.00 0.00 3.85
874 1236 1.379044 AAAGGCGCTGAATGGGAGG 60.379 57.895 7.64 0.00 0.00 4.30
923 1290 1.001746 TGAGCTTGGAGTTGAGAGCTG 59.998 52.381 0.92 0.00 44.88 4.24
979 1352 0.523757 GTCGCCGTAAGAGAGCTGAC 60.524 60.000 0.00 0.00 43.02 3.51
987 1360 2.103538 GCCATCGTCGCCGTAAGA 59.896 61.111 0.00 0.00 43.02 2.10
1009 1404 4.680237 CTCCTGCGCCACGTGGAA 62.680 66.667 38.30 20.49 37.39 3.53
1237 1632 2.420890 GAGCAGGATCCAGAGCGG 59.579 66.667 15.82 0.00 0.00 5.52
1359 1754 2.047274 AGGAACATGGTGACGGCG 60.047 61.111 4.80 4.80 0.00 6.46
1528 1981 8.339714 GGCATACAATTTGATTCATTTTCATGG 58.660 33.333 2.79 0.00 0.00 3.66
1538 1991 6.498304 AGTGAATCGGCATACAATTTGATTC 58.502 36.000 2.79 5.95 41.12 2.52
1577 2030 1.199789 TGAACAATGCAAGATGACGGC 59.800 47.619 0.00 0.00 0.00 5.68
1596 2155 9.959749 TTGTTAACCTTTTCTAACAAAGCTATG 57.040 29.630 2.48 0.00 42.25 2.23
1600 2159 9.961265 ATACTTGTTAACCTTTTCTAACAAAGC 57.039 29.630 2.48 0.00 43.69 3.51
1619 2178 8.504005 GCATGGCGTAAAAGATATTATACTTGT 58.496 33.333 0.00 0.00 0.00 3.16
1657 2216 6.844696 ATAATATTACACACACCTTGAGCG 57.155 37.500 0.00 0.00 0.00 5.03
1726 2290 9.153952 GAATTTGTTTTAAATGTCGAAAAAGGC 57.846 29.630 0.00 0.00 0.00 4.35
1755 2322 9.480053 AACGAAATGATCAGAAAAATGAAATGT 57.520 25.926 0.09 0.00 31.76 2.71
1756 2323 9.735646 CAACGAAATGATCAGAAAAATGAAATG 57.264 29.630 0.09 0.00 31.76 2.32
1758 2325 7.437565 TGCAACGAAATGATCAGAAAAATGAAA 59.562 29.630 0.09 0.00 31.76 2.69
1779 2417 3.050275 GCCGTCTCCACCTGCAAC 61.050 66.667 0.00 0.00 0.00 4.17
2004 2642 2.046892 ATGCTGCTGACGGTGGAC 60.047 61.111 0.00 0.00 0.00 4.02
2089 2727 1.043116 TCTGGCCATGTCTAGTCGGG 61.043 60.000 5.51 0.00 0.00 5.14
2098 2736 1.181098 GGTTGCTTGTCTGGCCATGT 61.181 55.000 5.51 0.00 0.00 3.21
2119 2758 5.414144 TGTCATTGTCACACAGAAAACAGAA 59.586 36.000 0.00 0.00 0.00 3.02
2168 2808 2.875933 CAGCCCAAACGACTTTGAAGTA 59.124 45.455 0.00 0.00 39.43 2.24
2171 2811 1.946768 CTCAGCCCAAACGACTTTGAA 59.053 47.619 0.36 0.00 39.43 2.69
2195 2835 4.022068 ACGGAATTCTGCATGAAAACATGT 60.022 37.500 14.40 0.00 38.29 3.21
2209 2849 3.262420 CAGAATTGACGGACGGAATTCT 58.738 45.455 19.53 19.53 43.86 2.40
2215 2855 2.106683 GCCCAGAATTGACGGACGG 61.107 63.158 0.00 0.00 0.00 4.79
2251 2891 5.464965 ACTGTTTAATAAATGTCGCCGAG 57.535 39.130 0.00 0.00 0.00 4.63
2285 2925 6.381420 TGACTTCTTAATCCCCTCTCTTGTAG 59.619 42.308 0.00 0.00 0.00 2.74
2287 2927 5.094387 TGACTTCTTAATCCCCTCTCTTGT 58.906 41.667 0.00 0.00 0.00 3.16
2289 2929 4.719273 CCTGACTTCTTAATCCCCTCTCTT 59.281 45.833 0.00 0.00 0.00 2.85
2290 2930 4.016105 TCCTGACTTCTTAATCCCCTCTCT 60.016 45.833 0.00 0.00 0.00 3.10
2305 2945 0.387202 CGCGATCATCCTCCTGACTT 59.613 55.000 0.00 0.00 0.00 3.01
2307 2947 1.663074 GCGCGATCATCCTCCTGAC 60.663 63.158 12.10 0.00 0.00 3.51
2308 2948 2.730733 GCGCGATCATCCTCCTGA 59.269 61.111 12.10 0.00 0.00 3.86
2309 2949 2.356793 GGCGCGATCATCCTCCTG 60.357 66.667 12.10 0.00 0.00 3.86
2310 2950 2.839632 TGGCGCGATCATCCTCCT 60.840 61.111 12.10 0.00 0.00 3.69
2312 2952 1.663074 GAGTGGCGCGATCATCCTC 60.663 63.158 12.10 7.47 0.00 3.71
2314 2954 1.806461 TAGGAGTGGCGCGATCATCC 61.806 60.000 12.10 11.71 0.00 3.51
2316 2956 0.032678 CTTAGGAGTGGCGCGATCAT 59.967 55.000 12.10 1.42 0.00 2.45
2318 2958 0.102481 TTCTTAGGAGTGGCGCGATC 59.898 55.000 12.10 0.51 0.00 3.69
2319 2959 0.535335 TTTCTTAGGAGTGGCGCGAT 59.465 50.000 12.10 0.00 0.00 4.58
2320 2960 0.319083 TTTTCTTAGGAGTGGCGCGA 59.681 50.000 12.10 0.00 0.00 5.87
2321 2961 1.153353 TTTTTCTTAGGAGTGGCGCG 58.847 50.000 0.00 0.00 0.00 6.86
2340 3026 4.983671 TGATATCTAGACGCACTGTGTT 57.016 40.909 9.86 0.00 0.00 3.32
2342 3028 4.149571 GCATTGATATCTAGACGCACTGTG 59.850 45.833 2.76 2.76 0.00 3.66
2357 3052 2.938451 CGGTTTCAGAGCAGCATTGATA 59.062 45.455 0.00 0.00 0.00 2.15
2362 3057 1.741706 CAATCGGTTTCAGAGCAGCAT 59.258 47.619 0.00 0.00 0.00 3.79
2364 3059 1.160137 ACAATCGGTTTCAGAGCAGC 58.840 50.000 0.00 0.00 0.00 5.25
2389 3084 1.060937 GCGGTAATCTTGCACAGCG 59.939 57.895 0.00 0.00 35.17 5.18
2393 3088 2.010145 TGAGAGCGGTAATCTTGCAC 57.990 50.000 0.00 0.00 0.00 4.57
2404 3099 1.069022 CCACATTGTGTTTGAGAGCGG 60.069 52.381 15.34 0.00 0.00 5.52
2407 3102 3.668757 CGATGCCACATTGTGTTTGAGAG 60.669 47.826 15.34 0.00 0.00 3.20
2411 3106 2.702898 TCGATGCCACATTGTGTTTG 57.297 45.000 15.34 1.96 0.00 2.93
2423 3128 4.882671 ACATATTGAACTGTTCGATGCC 57.117 40.909 26.31 1.24 35.44 4.40
2441 3146 8.237811 ACTTGTTTTGATCCTGTAAAGAACAT 57.762 30.769 0.00 0.00 37.50 2.71
2459 3164 3.377172 AGCGCTCTGTTACAAACTTGTTT 59.623 39.130 2.64 0.00 42.35 2.83
2461 3166 2.544267 GAGCGCTCTGTTACAAACTTGT 59.456 45.455 29.88 0.07 44.86 3.16
2462 3167 2.802816 AGAGCGCTCTGTTACAAACTTG 59.197 45.455 37.86 0.00 38.75 3.16
2476 3181 2.744202 CTCACCAACATTTTAGAGCGCT 59.256 45.455 11.27 11.27 0.00 5.92
2477 3182 2.159517 CCTCACCAACATTTTAGAGCGC 60.160 50.000 0.00 0.00 0.00 5.92
2478 3183 3.074412 ACCTCACCAACATTTTAGAGCG 58.926 45.455 0.00 0.00 0.00 5.03
2485 3190 4.190772 CAAGCAAAACCTCACCAACATTT 58.809 39.130 0.00 0.00 0.00 2.32
2488 3193 1.134848 GCAAGCAAAACCTCACCAACA 60.135 47.619 0.00 0.00 0.00 3.33
2493 3198 0.249447 GTGGGCAAGCAAAACCTCAC 60.249 55.000 0.00 0.00 0.00 3.51
2495 3200 0.249447 GTGTGGGCAAGCAAAACCTC 60.249 55.000 0.00 0.00 0.00 3.85
2500 3205 1.406614 CCAAAAGTGTGGGCAAGCAAA 60.407 47.619 0.00 0.00 34.77 3.68
2511 3254 4.767928 TGTTGTGACTAAACCCAAAAGTGT 59.232 37.500 0.00 0.00 0.00 3.55
2513 3256 5.986501 TTGTTGTGACTAAACCCAAAAGT 57.013 34.783 0.00 0.00 0.00 2.66
2521 3264 6.375377 TGTGACAGTTTTGTTGTGACTAAAC 58.625 36.000 8.01 8.01 45.58 2.01
2522 3265 6.561737 TGTGACAGTTTTGTTGTGACTAAA 57.438 33.333 0.00 0.00 37.76 1.85
2523 3266 6.150307 ACATGTGACAGTTTTGTTGTGACTAA 59.850 34.615 0.00 0.00 37.76 2.24
2524 3267 5.645929 ACATGTGACAGTTTTGTTGTGACTA 59.354 36.000 0.00 0.00 37.76 2.59
2525 3268 4.458989 ACATGTGACAGTTTTGTTGTGACT 59.541 37.500 0.00 0.00 37.76 3.41
2526 3269 4.732784 ACATGTGACAGTTTTGTTGTGAC 58.267 39.130 0.00 0.00 37.76 3.67
2527 3270 5.384063 AACATGTGACAGTTTTGTTGTGA 57.616 34.783 0.00 0.00 37.76 3.58
2528 3271 6.464895 AAAACATGTGACAGTTTTGTTGTG 57.535 33.333 18.27 1.49 43.88 3.33
2529 3272 6.073331 CCAAAAACATGTGACAGTTTTGTTGT 60.073 34.615 22.09 8.27 44.54 3.32
2532 3291 5.546526 ACCAAAAACATGTGACAGTTTTGT 58.453 33.333 22.09 14.69 44.54 2.83
2538 3297 3.631686 TCCTGACCAAAAACATGTGACAG 59.368 43.478 0.00 2.39 0.00 3.51
2541 3300 3.117701 TCCTCCTGACCAAAAACATGTGA 60.118 43.478 0.00 0.00 0.00 3.58
2551 3310 1.887956 GCAATTGCTCCTCCTGACCAA 60.888 52.381 23.21 0.00 38.21 3.67
2552 3311 0.322816 GCAATTGCTCCTCCTGACCA 60.323 55.000 23.21 0.00 38.21 4.02
2572 3333 1.274728 TGTTGTGTTTGCTTTGCTGGT 59.725 42.857 0.00 0.00 0.00 4.00
2596 3357 3.668447 TGAGGCATCTTGTTCTCTGAAC 58.332 45.455 0.00 3.74 0.00 3.18
2622 3383 4.320202 GGTGCTGTTCATATGTCGTTGTTT 60.320 41.667 1.90 0.00 0.00 2.83
2644 3405 1.959042 CTATGCTTACCCTGTGCTGG 58.041 55.000 0.00 0.00 0.00 4.85
2648 3409 1.065491 TGGTGCTATGCTTACCCTGTG 60.065 52.381 0.00 0.00 33.51 3.66
2719 3480 7.158021 GCTCTATATGATTTGGCACTCTAGTT 58.842 38.462 0.00 0.00 0.00 2.24
2744 3505 2.996621 CTCGTGGAGCTTCCTTACTTTG 59.003 50.000 0.00 0.00 37.46 2.77
2749 3510 1.676529 CGATCTCGTGGAGCTTCCTTA 59.323 52.381 0.00 0.00 37.46 2.69
2751 3512 0.394488 TCGATCTCGTGGAGCTTCCT 60.394 55.000 0.00 0.00 40.80 3.36
2835 3597 0.526662 ACTCTTCGTGTAGGCTTCCG 59.473 55.000 0.00 0.00 0.00 4.30
2899 3661 2.611292 GTGGAAGTAATGCTGCTAGCTG 59.389 50.000 17.23 16.92 42.97 4.24
2907 3669 5.625150 AGTTCAAGAAGTGGAAGTAATGCT 58.375 37.500 0.00 0.00 0.00 3.79
3076 3841 3.068881 CACGGTGGAGGTGGACAT 58.931 61.111 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.