Multiple sequence alignment - TraesCS3A01G071000

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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 TraesCS3A01G071000 chr3A 100.000 4426 0 0 1 4426 43120758 43125183 0.000000e+00 8174.0
1 TraesCS3A01G071000 chr2B 93.681 2801 156 16 1637 4426 2138909 2141699 0.000000e+00 4172.0
2 TraesCS3A01G071000 chr2B 93.538 2801 157 17 1637 4426 2158673 2161460 0.000000e+00 4148.0
3 TraesCS3A01G071000 chr2B 92.308 2457 166 17 1982 4426 2178242 2180687 0.000000e+00 3469.0
4 TraesCS3A01G071000 chr2B 91.982 1983 118 24 1 1955 2176276 2178245 0.000000e+00 2743.0
5 TraesCS3A01G071000 chr2B 91.318 1578 95 12 1 1552 2137347 2138908 0.000000e+00 2117.0
6 TraesCS3A01G071000 chr2B 91.307 1576 95 15 1 1552 2157115 2158672 0.000000e+00 2113.0
7 TraesCS3A01G071000 chr6A 82.710 989 158 11 3443 4426 74035414 74034434 0.000000e+00 867.0
8 TraesCS3A01G071000 chr5A 79.518 664 136 0 1281 1944 658865104 658865767 1.440000e-129 473.0
9 TraesCS3A01G071000 chr2A 79.710 207 40 2 3691 3896 718353419 718353624 9.920000e-32 148.0
10 TraesCS3A01G071000 chr4D 86.517 89 10 2 3810 3897 390850864 390850951 3.640000e-16 97.1
11 TraesCS3A01G071000 chr4D 86.517 89 10 2 3810 3897 448520229 448520142 3.640000e-16 97.1


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 TraesCS3A01G071000 chr3A 43120758 43125183 4425 False 8174.0 8174 100.0000 1 4426 1 chr3A.!!$F1 4425
1 TraesCS3A01G071000 chr2B 2137347 2141699 4352 False 3144.5 4172 92.4995 1 4426 2 chr2B.!!$F1 4425
2 TraesCS3A01G071000 chr2B 2157115 2161460 4345 False 3130.5 4148 92.4225 1 4426 2 chr2B.!!$F2 4425
3 TraesCS3A01G071000 chr2B 2176276 2180687 4411 False 3106.0 3469 92.1450 1 4426 2 chr2B.!!$F3 4425
4 TraesCS3A01G071000 chr6A 74034434 74035414 980 True 867.0 867 82.7100 3443 4426 1 chr6A.!!$R1 983
5 TraesCS3A01G071000 chr5A 658865104 658865767 663 False 473.0 473 79.5180 1281 1944 1 chr5A.!!$F1 663

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
545 573 0.313672 TGTTTTTCATCCACTGCGGC 59.686 50.0 0.00 0.00 33.14 6.53 F
1992 2106 0.109132 GCAAATGCTGTAGGTGCACC 60.109 55.0 29.22 29.22 43.59 5.01 F
2712 2833 0.322648 CGATGGCCCTCATGCATCTA 59.677 55.0 8.86 0.00 35.97 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2124 0.106149 GTCCGATGCCCGAATAAGGT 59.894 55.0 0.00 0.00 41.76 3.50 R
3042 3163 0.179067 TGTCGTCCCACCTTCACAAC 60.179 55.0 0.00 0.00 0.00 3.32 R
4175 4301 0.099436 GGTCTGCATGCCGCTAAAAG 59.901 55.0 16.68 3.71 43.06 2.27 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
25 26 2.114670 AGCCGGTCATGGATTTGCG 61.115 57.895 1.90 0.00 0.00 4.85
291 319 8.980143 GCAATGTACTTTGCTTAAGGAAATTA 57.020 30.769 29.44 16.67 46.66 1.40
340 368 4.481072 AGAGTGTGTAGTTTAGTCAGGGT 58.519 43.478 0.00 0.00 0.00 4.34
341 369 4.523558 AGAGTGTGTAGTTTAGTCAGGGTC 59.476 45.833 0.00 0.00 0.00 4.46
342 370 4.220724 AGTGTGTAGTTTAGTCAGGGTCA 58.779 43.478 0.00 0.00 0.00 4.02
400 428 1.986882 CCTGTTTCCCCCTATCATGC 58.013 55.000 0.00 0.00 0.00 4.06
403 431 0.537371 GTTTCCCCCTATCATGCCGG 60.537 60.000 0.00 0.00 0.00 6.13
457 485 5.197451 GGTGATCCCCATGTAATGTGTTAA 58.803 41.667 0.00 0.00 44.81 2.01
469 497 7.354025 TGTAATGTGTTAACAGACGTTATGG 57.646 36.000 8.98 0.00 40.39 2.74
482 510 7.103641 ACAGACGTTATGGAGATTGTAATGTT 58.896 34.615 6.66 0.00 30.13 2.71
523 551 3.711704 CCTGTTCTATTCAAGCCCCTCTA 59.288 47.826 0.00 0.00 0.00 2.43
533 561 5.722021 TCAAGCCCCTCTAAATGTTTTTC 57.278 39.130 0.00 0.00 0.00 2.29
534 562 5.144100 TCAAGCCCCTCTAAATGTTTTTCA 58.856 37.500 0.00 0.00 0.00 2.69
545 573 0.313672 TGTTTTTCATCCACTGCGGC 59.686 50.000 0.00 0.00 33.14 6.53
586 614 1.450312 GCCCTCAATCACTGGACGG 60.450 63.158 0.00 0.00 0.00 4.79
661 690 0.896923 TACGGCCGTCTTTACACCAT 59.103 50.000 38.01 8.07 0.00 3.55
663 692 0.672401 CGGCCGTCTTTACACCATGT 60.672 55.000 19.50 0.00 0.00 3.21
679 708 2.029892 ATGTCCCCCAACCCAGCAAA 62.030 55.000 0.00 0.00 0.00 3.68
717 746 6.920569 ACTTTGTTTCACTTATCAACGACT 57.079 33.333 0.00 0.00 0.00 4.18
730 759 0.702902 AACGACTCTAGAGGGGGACA 59.297 55.000 23.50 0.00 0.00 4.02
738 767 1.122632 TAGAGGGGGACACGTTTGCA 61.123 55.000 0.00 0.00 0.00 4.08
741 770 2.686816 GGGGGACACGTTTGCATCG 61.687 63.158 9.66 9.66 0.00 3.84
747 776 1.527736 GACACGTTTGCATCGTACCAA 59.472 47.619 15.09 0.00 39.55 3.67
748 777 1.529438 ACACGTTTGCATCGTACCAAG 59.471 47.619 15.09 7.21 39.55 3.61
749 778 1.795872 CACGTTTGCATCGTACCAAGA 59.204 47.619 15.09 0.00 39.55 3.02
750 779 1.796459 ACGTTTGCATCGTACCAAGAC 59.204 47.619 14.17 0.00 39.78 3.01
751 780 1.201769 CGTTTGCATCGTACCAAGACG 60.202 52.381 0.00 0.00 44.29 4.18
764 793 1.208052 CCAAGACGATCTGGGTCACAT 59.792 52.381 0.00 0.00 32.70 3.21
766 795 1.561643 AGACGATCTGGGTCACATGT 58.438 50.000 0.00 0.00 36.87 3.21
767 796 2.735151 AGACGATCTGGGTCACATGTA 58.265 47.619 0.00 0.00 36.87 2.29
878 907 1.687840 CCCACCGGGTCATGTAGGA 60.688 63.158 6.32 0.00 38.25 2.94
965 994 4.736896 GCCGCCGGTCTTTCTCGT 62.737 66.667 4.45 0.00 0.00 4.18
966 995 2.506438 CCGCCGGTCTTTCTCGTC 60.506 66.667 1.90 0.00 0.00 4.20
967 996 2.567049 CGCCGGTCTTTCTCGTCT 59.433 61.111 1.90 0.00 0.00 4.18
983 1012 0.898789 GTCTCCAGGTCTCCCGTTCA 60.899 60.000 0.00 0.00 35.12 3.18
1007 1036 1.947642 GCCGCCGTAGAATGGTACG 60.948 63.158 1.05 1.05 44.42 3.67
1022 1052 1.602416 GGTACGCTTTCTCCTATCGCC 60.602 57.143 0.00 0.00 0.00 5.54
1039 1069 6.710744 CCTATCGCCCTTTGTTCAGTATTTAT 59.289 38.462 0.00 0.00 0.00 1.40
1044 1074 5.652452 GCCCTTTGTTCAGTATTTATCTGGT 59.348 40.000 0.00 0.00 34.15 4.00
1061 1091 2.039084 CTGGTACCCTTATCATCTGCCC 59.961 54.545 10.07 0.00 0.00 5.36
1062 1092 1.351350 GGTACCCTTATCATCTGCCCC 59.649 57.143 0.00 0.00 0.00 5.80
1065 1095 1.418908 CCCTTATCATCTGCCCCCGT 61.419 60.000 0.00 0.00 0.00 5.28
1066 1096 0.474184 CCTTATCATCTGCCCCCGTT 59.526 55.000 0.00 0.00 0.00 4.44
1134 1164 2.593346 TTTGTTTTGTGCATCCGCTT 57.407 40.000 0.00 0.00 39.64 4.68
1159 1189 2.813042 GAGCACAGCTCGCAGTCC 60.813 66.667 2.96 0.00 45.85 3.85
1180 1210 3.640407 AGCTGTGGCGACCATGGT 61.640 61.111 19.89 19.89 44.37 3.55
1237 1267 1.740718 GCTGGGTCTGATTCCGACTTC 60.741 57.143 7.96 2.86 0.00 3.01
1266 1296 2.684843 CCTCAAGCGCTGTTCCTGC 61.685 63.158 12.58 0.00 0.00 4.85
1315 1345 1.509644 CCGTGAAGCATGCAGTGTGT 61.510 55.000 21.98 0.00 0.00 3.72
1488 1518 2.711009 TGAGGGACAACAAGGTTCTGAT 59.289 45.455 0.00 0.00 0.00 2.90
1489 1519 3.138283 TGAGGGACAACAAGGTTCTGATT 59.862 43.478 0.00 0.00 0.00 2.57
1577 1691 3.255149 GGATGCAAGCATAAATCCTGAGG 59.745 47.826 7.64 0.00 36.46 3.86
1618 1732 3.971245 ACTCTCCAGATGAACAGAACC 57.029 47.619 0.00 0.00 0.00 3.62
1623 1737 1.270839 CCAGATGAACAGAACCGGTGT 60.271 52.381 8.52 0.00 0.00 4.16
1685 1799 6.585695 ACATCAATGAGAATTCAAGCAAGT 57.414 33.333 8.44 0.00 36.78 3.16
1855 1969 2.549332 GCTTCAGCACCTCCTTGAC 58.451 57.895 0.00 0.00 41.59 3.18
1883 1997 7.763528 CAGTCACTAAGCTGAAGAAAGATATGT 59.236 37.037 3.45 0.00 34.87 2.29
1955 2069 4.766891 AGGCAAGTTAACAGCAACATGTAT 59.233 37.500 20.15 0.00 31.45 2.29
1972 2086 8.604035 CAACATGTATTGATGTACACTAGAACC 58.396 37.037 0.00 0.00 37.40 3.62
1987 2101 1.165270 GAACCGCAAATGCTGTAGGT 58.835 50.000 2.86 0.21 37.51 3.08
1992 2106 0.109132 GCAAATGCTGTAGGTGCACC 60.109 55.000 29.22 29.22 43.59 5.01
2010 2124 3.861508 GCACCACAATGCACATTCATCAA 60.862 43.478 0.00 0.00 45.39 2.57
2015 2129 5.336610 CCACAATGCACATTCATCAACCTTA 60.337 40.000 0.00 0.00 0.00 2.69
2020 2134 4.096231 TGCACATTCATCAACCTTATTCGG 59.904 41.667 0.00 0.00 0.00 4.30
2026 2140 1.948104 TCAACCTTATTCGGGCATCG 58.052 50.000 0.00 0.00 40.90 3.84
2033 2147 2.736144 TATTCGGGCATCGGACATAC 57.264 50.000 0.00 0.00 39.77 2.39
2114 2228 2.605818 TGTCTGTAACAAGTCGCACAAC 59.394 45.455 0.00 0.00 34.03 3.32
2176 2290 1.028330 CGAATGCTCACCATGGCTGT 61.028 55.000 13.04 0.00 33.49 4.40
2229 2343 4.207635 CGCATGCCAATGTAACATTGATTC 59.792 41.667 13.15 0.00 36.08 2.52
2233 2347 3.705604 CCAATGTAACATTGATTCCCGC 58.294 45.455 1.50 0.00 0.00 6.13
2236 2350 5.505654 CCAATGTAACATTGATTCCCGCTAC 60.506 44.000 1.50 0.00 0.00 3.58
2243 2357 0.539986 TGATTCCCGCTACCACCTTC 59.460 55.000 0.00 0.00 0.00 3.46
2259 2373 2.105993 ACCTTCTGGTTGTTGGTACCTC 59.894 50.000 14.36 7.07 46.05 3.85
2261 2375 3.181443 CCTTCTGGTTGTTGGTACCTCTT 60.181 47.826 14.36 0.00 36.60 2.85
2292 2406 8.527810 CCATGGTTTGGTTTTATACTAACACAT 58.472 33.333 2.57 0.00 40.99 3.21
2308 2422 6.670027 ACTAACACATCACTTTCTATCCTCCT 59.330 38.462 0.00 0.00 0.00 3.69
2350 2464 4.796830 GCATCGTCAGTTTGTTATACGAGA 59.203 41.667 0.00 0.00 44.69 4.04
2363 2477 2.342910 TACGAGACAGAAGTTTCCGC 57.657 50.000 0.00 0.00 0.00 5.54
2377 2491 1.888436 TTCCGCATTCAGCTCCGTCT 61.888 55.000 0.00 0.00 42.61 4.18
2379 2493 1.021390 CCGCATTCAGCTCCGTCTTT 61.021 55.000 0.00 0.00 42.61 2.52
2380 2494 0.371645 CGCATTCAGCTCCGTCTTTC 59.628 55.000 0.00 0.00 42.61 2.62
2391 2505 1.569493 CGTCTTTCGCAACCACCAG 59.431 57.895 0.00 0.00 0.00 4.00
2443 2557 1.531840 AGGACACACGAGGAGCACT 60.532 57.895 0.00 0.00 0.00 4.40
2457 2571 0.620556 AGCACTCCACCCCTATTGTG 59.379 55.000 0.00 0.00 0.00 3.33
2542 2656 5.330295 GCACTTGACTTTGCAAGATATCTG 58.670 41.667 5.86 2.06 46.31 2.90
2569 2683 6.069331 GGAGAAGTATCCACACCTAGTATGA 58.931 44.000 0.00 0.00 39.34 2.15
2596 2710 4.548451 TCTCTCATTTCTGTCATGCACT 57.452 40.909 0.00 0.00 0.00 4.40
2619 2733 7.601508 CACTATTTTCCCTTTCGTTGTAGTACT 59.398 37.037 0.00 0.00 0.00 2.73
2623 2737 2.993899 CCCTTTCGTTGTAGTACTGCAG 59.006 50.000 13.48 13.48 0.00 4.41
2624 2738 2.412089 CCTTTCGTTGTAGTACTGCAGC 59.588 50.000 15.27 16.08 0.00 5.25
2626 2747 1.254026 TCGTTGTAGTACTGCAGCCT 58.746 50.000 19.23 12.69 0.00 4.58
2638 2759 0.535780 TGCAGCCTTTCTCACCACAG 60.536 55.000 0.00 0.00 0.00 3.66
2667 2788 2.148916 TGCAGGTACAAGACGAGTTG 57.851 50.000 0.00 0.00 0.00 3.16
2675 2796 5.652891 AGGTACAAGACGAGTTGACTATGAT 59.347 40.000 8.22 0.00 0.00 2.45
2712 2833 0.322648 CGATGGCCCTCATGCATCTA 59.677 55.000 8.86 0.00 35.97 1.98
2714 2835 2.811504 CGATGGCCCTCATGCATCTAAA 60.812 50.000 8.86 0.00 35.97 1.85
2743 2864 1.542492 CAACTCAATCCAGCAGGCTT 58.458 50.000 0.00 0.00 33.74 4.35
2863 2984 1.997669 CTTTACTGAGTGTCCGGAGC 58.002 55.000 3.06 0.00 0.00 4.70
2885 3006 3.251004 CCAGGTCAGCAAAACTACACTTC 59.749 47.826 0.00 0.00 0.00 3.01
2892 3013 3.997021 AGCAAAACTACACTTCTGATCCG 59.003 43.478 0.00 0.00 0.00 4.18
2906 3027 2.093537 GATCCGCCGGCTCAATCTCT 62.094 60.000 26.68 0.00 0.00 3.10
2912 3033 2.221981 CGCCGGCTCAATCTCTTTATTC 59.778 50.000 26.68 0.00 0.00 1.75
2965 3086 0.605319 TTTTTCACGGATCAGCGGCT 60.605 50.000 0.00 0.00 0.00 5.52
3054 3175 2.991250 CCTATCTGGTTGTGAAGGTGG 58.009 52.381 0.00 0.00 0.00 4.61
3075 3196 4.552166 GGACGACATTTCCCATTACATG 57.448 45.455 0.00 0.00 0.00 3.21
3121 3243 3.131577 TCATCCATGGAGATGCAAAAAGC 59.868 43.478 21.33 0.00 42.84 3.51
3141 3263 2.489437 GCACACCCTTTTTACACCCCTA 60.489 50.000 0.00 0.00 0.00 3.53
3185 3309 2.695127 TTTATGTTATGGGCGGTCGT 57.305 45.000 0.00 0.00 0.00 4.34
3279 3403 3.585862 TCTACCAGCAAGAAATCGACAC 58.414 45.455 0.00 0.00 0.00 3.67
3292 3416 0.251608 TCGACACCAGGGTCATCTCA 60.252 55.000 0.27 0.00 37.66 3.27
3359 3483 1.147153 GTATGCAGACCTCCCAGCC 59.853 63.158 0.00 0.00 0.00 4.85
3423 3547 6.948886 TCTAGAGAGGCGGAAATACATATTCT 59.051 38.462 0.00 0.00 0.00 2.40
3491 3615 2.985282 CCACATGCGCCAACCACT 60.985 61.111 4.18 0.00 0.00 4.00
3528 3652 2.721971 CTTCTCACAGCTGCCACCGT 62.722 60.000 15.27 0.00 0.00 4.83
3571 3695 2.418197 CGAATCTCTTTCCGCTTACCCA 60.418 50.000 0.00 0.00 0.00 4.51
3577 3701 1.472480 CTTTCCGCTTACCCACAATGG 59.528 52.381 0.00 0.00 37.25 3.16
3599 3723 5.189736 TGGCTTATCCATGTACTCTCAGTTT 59.810 40.000 0.00 0.00 40.72 2.66
3659 3785 2.604914 CACTGATGATCGTGCTAACCAC 59.395 50.000 0.00 0.00 41.15 4.16
3667 3793 1.154035 GTGCTAACCACGCCATTGC 60.154 57.895 0.00 0.00 34.22 3.56
3686 3812 2.614983 TGCTTTTGGACGTACCTTGTTC 59.385 45.455 0.00 0.00 39.86 3.18
3694 3820 0.928229 CGTACCTTGTTCCGCTATGC 59.072 55.000 0.00 0.00 0.00 3.14
3714 3840 3.134442 TGCAGGCACTACATCATACATGA 59.866 43.478 0.00 0.00 38.03 3.07
3771 3897 1.290203 CGTGAACAGCTAATCGGCAT 58.710 50.000 0.00 0.00 34.17 4.40
3794 3920 1.893062 CATCTCCACCACGAGCTCA 59.107 57.895 15.40 0.00 0.00 4.26
3799 3925 1.807165 CCACCACGAGCTCATGTCG 60.807 63.158 15.40 2.20 43.25 4.35
3800 3926 2.125912 ACCACGAGCTCATGTCGC 60.126 61.111 15.40 3.22 41.26 5.19
3985 4111 3.499918 CGATTCAGTTGTCTCAAAGGCTT 59.500 43.478 0.00 0.00 0.00 4.35
4083 4209 2.416747 TCGATTCAGAAACAGCTGGTG 58.583 47.619 19.93 9.80 36.55 4.17
4163 4289 5.327737 TCCACACCTTTTTAATGGGTAGT 57.672 39.130 0.00 0.00 0.00 2.73
4183 4309 9.242477 GGGTAGTACTAATAAAGACTTTTAGCG 57.758 37.037 5.61 0.00 32.58 4.26
4185 4311 7.767745 AGTACTAATAAAGACTTTTAGCGGC 57.232 36.000 5.61 0.00 32.58 6.53
4186 4312 7.325694 AGTACTAATAAAGACTTTTAGCGGCA 58.674 34.615 5.61 0.00 32.58 5.69
4212 4341 4.396166 CAGACCTGTGTTTTTCTTGACACT 59.604 41.667 7.95 0.00 44.87 3.55
4213 4342 5.010282 AGACCTGTGTTTTTCTTGACACTT 58.990 37.500 7.95 0.00 44.87 3.16
4226 4355 9.567848 TTTTCTTGACACTTGTTCATTTTAGAC 57.432 29.630 0.00 0.00 0.00 2.59
4388 4520 0.040067 GCCCAAGCGACACAAAGAAG 60.040 55.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
285 313 5.106317 TGCTTGAAACGATGTCCCTAATTTC 60.106 40.000 0.00 0.00 0.00 2.17
291 319 1.347707 TCTGCTTGAAACGATGTCCCT 59.652 47.619 0.00 0.00 0.00 4.20
322 350 4.220724 ACTGACCCTGACTAAACTACACA 58.779 43.478 0.00 0.00 0.00 3.72
340 368 4.009675 CACCCTTGCTAGCAATTAACTGA 58.990 43.478 29.40 5.94 35.20 3.41
341 369 3.129287 CCACCCTTGCTAGCAATTAACTG 59.871 47.826 29.40 16.58 35.20 3.16
342 370 3.356290 CCACCCTTGCTAGCAATTAACT 58.644 45.455 29.40 8.74 35.20 2.24
370 398 2.093075 GGGGAAACAGGCTTAGAGGTAC 60.093 54.545 0.00 0.00 0.00 3.34
400 428 0.038618 GGTGCTTAGTTTTTGGCCGG 60.039 55.000 0.00 0.00 0.00 6.13
403 431 0.038618 CGGGGTGCTTAGTTTTTGGC 60.039 55.000 0.00 0.00 0.00 4.52
435 463 5.650266 TGTTAACACATTACATGGGGATCAC 59.350 40.000 3.59 0.00 38.23 3.06
436 464 5.821097 TGTTAACACATTACATGGGGATCA 58.179 37.500 3.59 0.00 38.23 2.92
437 465 6.038271 GTCTGTTAACACATTACATGGGGATC 59.962 42.308 3.59 0.00 38.23 3.36
438 466 5.885912 GTCTGTTAACACATTACATGGGGAT 59.114 40.000 3.59 0.00 38.23 3.85
439 467 5.250200 GTCTGTTAACACATTACATGGGGA 58.750 41.667 3.59 0.00 38.23 4.81
441 469 4.693566 ACGTCTGTTAACACATTACATGGG 59.306 41.667 3.59 0.00 40.30 4.00
442 470 5.856126 ACGTCTGTTAACACATTACATGG 57.144 39.130 3.59 0.00 30.39 3.66
457 485 6.640518 ACATTACAATCTCCATAACGTCTGT 58.359 36.000 0.00 0.00 0.00 3.41
482 510 9.096823 AGAACAGGTCACCCGATATATAATTAA 57.903 33.333 0.00 0.00 35.12 1.40
495 523 3.010420 GCTTGAATAGAACAGGTCACCC 58.990 50.000 0.00 0.00 0.00 4.61
500 528 2.239907 GAGGGGCTTGAATAGAACAGGT 59.760 50.000 0.00 0.00 0.00 4.00
507 535 7.410120 AAAACATTTAGAGGGGCTTGAATAG 57.590 36.000 0.00 0.00 0.00 1.73
510 538 5.600484 TGAAAAACATTTAGAGGGGCTTGAA 59.400 36.000 0.00 0.00 0.00 2.69
515 543 4.466015 TGGATGAAAAACATTTAGAGGGGC 59.534 41.667 0.00 0.00 39.56 5.80
523 551 3.652274 CCGCAGTGGATGAAAAACATTT 58.348 40.909 0.00 0.00 42.00 2.32
533 561 1.139989 CTAATACGCCGCAGTGGATG 58.860 55.000 3.39 0.00 42.00 3.51
534 562 0.750850 ACTAATACGCCGCAGTGGAT 59.249 50.000 3.39 0.00 42.00 3.41
545 573 6.127403 GCCTTGCGAATTAAGAACTAATACG 58.873 40.000 0.00 0.00 29.59 3.06
586 614 2.476185 GCACGACATTGCATTACTGGTC 60.476 50.000 0.00 0.00 42.49 4.02
661 690 2.029892 ATTTGCTGGGTTGGGGGACA 62.030 55.000 0.00 0.00 0.00 4.02
663 692 1.014804 ATATTTGCTGGGTTGGGGGA 58.985 50.000 0.00 0.00 0.00 4.81
695 724 7.178712 AGAGTCGTTGATAAGTGAAACAAAG 57.821 36.000 0.00 0.00 41.43 2.77
703 732 4.036971 CCCCTCTAGAGTCGTTGATAAGTG 59.963 50.000 18.42 0.00 0.00 3.16
717 746 1.263356 CAAACGTGTCCCCCTCTAGA 58.737 55.000 0.00 0.00 0.00 2.43
741 770 1.822990 TGACCCAGATCGTCTTGGTAC 59.177 52.381 9.64 0.00 41.98 3.34
747 776 1.561643 ACATGTGACCCAGATCGTCT 58.438 50.000 0.00 0.00 0.00 4.18
748 777 2.799917 GCTACATGTGACCCAGATCGTC 60.800 54.545 9.11 0.00 0.00 4.20
749 778 1.137086 GCTACATGTGACCCAGATCGT 59.863 52.381 9.11 0.00 0.00 3.73
750 779 1.858091 GCTACATGTGACCCAGATCG 58.142 55.000 9.11 0.00 0.00 3.69
751 780 1.858091 CGCTACATGTGACCCAGATC 58.142 55.000 9.11 0.00 0.00 2.75
752 781 0.179073 GCGCTACATGTGACCCAGAT 60.179 55.000 9.11 0.00 0.00 2.90
753 782 1.218047 GCGCTACATGTGACCCAGA 59.782 57.895 9.11 0.00 0.00 3.86
868 897 3.043586 CGTTATGAGCGTCCTACATGAC 58.956 50.000 0.00 0.00 0.00 3.06
1007 1036 1.943340 CAAAGGGCGATAGGAGAAAGC 59.057 52.381 0.00 0.00 0.00 3.51
1022 1052 8.209917 GGTACCAGATAAATACTGAACAAAGG 57.790 38.462 7.15 0.00 37.54 3.11
1044 1074 1.742308 GGGGGCAGATGATAAGGGTA 58.258 55.000 0.00 0.00 0.00 3.69
1104 1134 3.127895 GCACAAAACAAAAAGGGGGTTTC 59.872 43.478 0.00 0.00 33.91 2.78
1107 1137 1.630878 TGCACAAAACAAAAAGGGGGT 59.369 42.857 0.00 0.00 0.00 4.95
1113 1143 2.898705 AGCGGATGCACAAAACAAAAA 58.101 38.095 0.00 0.00 46.23 1.94
1114 1144 2.593346 AGCGGATGCACAAAACAAAA 57.407 40.000 0.00 0.00 46.23 2.44
1115 1145 2.200067 CAAGCGGATGCACAAAACAAA 58.800 42.857 0.00 0.00 46.23 2.83
1134 1164 3.075186 AGCTGTGCTCATCCTGCA 58.925 55.556 0.00 0.00 30.62 4.41
1213 1243 2.586792 GAATCAGACCCAGCGGCT 59.413 61.111 0.00 0.00 0.00 5.52
1257 1287 0.393537 GGGTGGATCTGCAGGAACAG 60.394 60.000 15.13 0.00 39.12 3.16
1266 1296 0.112218 TGTTGGGTTGGGTGGATCTG 59.888 55.000 0.00 0.00 0.00 2.90
1315 1345 1.341852 TCGTCAAACTTCCGGATCACA 59.658 47.619 4.15 0.00 0.00 3.58
1494 1524 2.371841 ACCTTGTGTACATCCTCAGCAA 59.628 45.455 0.00 0.00 0.00 3.91
1577 1691 5.464168 AGTTGTCTTTATGAATTGCACAGC 58.536 37.500 0.00 0.00 0.00 4.40
1618 1732 2.811431 TGCCTTCAAACTATGAACACCG 59.189 45.455 0.00 0.00 43.08 4.94
1623 1737 4.019792 TCAGCTGCCTTCAAACTATGAA 57.980 40.909 9.47 0.00 45.71 2.57
1627 1741 3.769739 TCTTCAGCTGCCTTCAAACTA 57.230 42.857 9.47 0.00 0.00 2.24
1685 1799 7.094205 GGCAATCTGGAAACAATCTTTCTCTAA 60.094 37.037 0.00 0.00 42.06 2.10
1855 1969 2.354109 TCTTCAGCTTAGTGACTGCG 57.646 50.000 0.00 0.00 33.80 5.18
1864 1978 5.590259 GGCCAACATATCTTTCTTCAGCTTA 59.410 40.000 0.00 0.00 0.00 3.09
1883 1997 2.500509 GTCGACAAATTGTTGGCCAA 57.499 45.000 16.05 16.05 39.94 4.52
1955 2069 3.945981 TGCGGTTCTAGTGTACATCAA 57.054 42.857 0.00 0.00 0.00 2.57
1965 2079 2.609459 CCTACAGCATTTGCGGTTCTAG 59.391 50.000 13.31 5.56 46.84 2.43
1992 2106 4.182693 AGGTTGATGAATGTGCATTGTG 57.817 40.909 1.77 0.00 0.00 3.33
2010 2124 0.106149 GTCCGATGCCCGAATAAGGT 59.894 55.000 0.00 0.00 41.76 3.50
2015 2129 0.319555 CGTATGTCCGATGCCCGAAT 60.320 55.000 0.00 0.00 41.76 3.34
2020 2134 1.419374 GATGTCGTATGTCCGATGCC 58.581 55.000 0.00 0.00 39.34 4.40
2026 2140 4.876107 ACAAATTCAGGATGTCGTATGTCC 59.124 41.667 0.00 0.00 37.40 4.02
2033 2147 6.255453 ACAAAACAAACAAATTCAGGATGTCG 59.745 34.615 0.00 0.00 37.40 4.35
2114 2228 1.377725 AGCAATTCTGGGGAGCACG 60.378 57.895 0.00 0.00 0.00 5.34
2176 2290 1.002624 GTGCCCTTGATCGGGTCAA 60.003 57.895 3.30 3.30 46.47 3.18
2195 2309 0.812549 TGGCATGCGAGTACGAAGTA 59.187 50.000 12.44 0.00 45.11 2.24
2229 2343 2.584608 CCAGAAGGTGGTAGCGGG 59.415 66.667 0.00 0.00 42.17 6.13
2243 2357 1.880027 GCAAGAGGTACCAACAACCAG 59.120 52.381 15.94 0.00 39.64 4.00
2292 2406 6.642733 ATGGAAAAGGAGGATAGAAAGTGA 57.357 37.500 0.00 0.00 0.00 3.41
2299 2413 5.541868 TCTCAGCTATGGAAAAGGAGGATAG 59.458 44.000 0.00 0.00 0.00 2.08
2301 2415 4.302067 TCTCAGCTATGGAAAAGGAGGAT 58.698 43.478 0.00 0.00 0.00 3.24
2305 2419 4.444022 GCATCTCTCAGCTATGGAAAAGGA 60.444 45.833 0.00 0.00 0.00 3.36
2308 2422 4.492494 TGCATCTCTCAGCTATGGAAAA 57.508 40.909 0.00 0.00 0.00 2.29
2350 2464 1.537202 GCTGAATGCGGAAACTTCTGT 59.463 47.619 0.47 0.00 35.96 3.41
2363 2477 0.371645 GCGAAAGACGGAGCTGAATG 59.628 55.000 0.00 0.00 42.83 2.67
2377 2491 0.887387 GCCTACTGGTGGTTGCGAAA 60.887 55.000 0.00 0.00 35.27 3.46
2379 2493 1.764571 AAGCCTACTGGTGGTTGCGA 61.765 55.000 0.00 0.00 35.27 5.10
2380 2494 0.889186 AAAGCCTACTGGTGGTTGCG 60.889 55.000 0.00 0.00 35.27 4.85
2391 2505 2.750888 CGCCGCCTTGAAAGCCTAC 61.751 63.158 0.00 0.00 0.00 3.18
2421 2535 3.633094 CTCCTCGTGTGTCCTGCCG 62.633 68.421 0.00 0.00 0.00 5.69
2492 2606 3.708734 GCCGTCGGTTGGTGTTCG 61.709 66.667 13.94 0.00 0.00 3.95
2519 2633 5.330295 CAGATATCTTGCAAAGTCAAGTGC 58.670 41.667 1.33 0.00 46.34 4.40
2542 2656 0.179081 GGTGTGGATACTTCTCCCGC 60.179 60.000 0.00 0.00 34.12 6.13
2569 2683 5.642919 GCATGACAGAAATGAGAGAAAGACT 59.357 40.000 0.00 0.00 0.00 3.24
2596 2710 6.369615 GCAGTACTACAACGAAAGGGAAAATA 59.630 38.462 0.00 0.00 0.00 1.40
2619 2733 0.535780 CTGTGGTGAGAAAGGCTGCA 60.536 55.000 0.50 0.00 0.00 4.41
2623 2737 3.059352 ACATACTGTGGTGAGAAAGGC 57.941 47.619 0.00 0.00 0.00 4.35
2624 2738 6.391227 AAAAACATACTGTGGTGAGAAAGG 57.609 37.500 0.00 0.00 0.00 3.11
2658 2779 9.268268 TGTTTTAAAATCATAGTCAACTCGTCT 57.732 29.630 3.52 0.00 0.00 4.18
2667 2788 7.409343 GCGTTGTGCTGTTTTAAAATCATAGTC 60.409 37.037 3.52 0.00 41.73 2.59
2675 2796 3.132629 TCGCGTTGTGCTGTTTTAAAA 57.867 38.095 5.77 0.00 43.27 1.52
2712 2833 4.039488 TGGATTGAGTTGCTTGCTTGATTT 59.961 37.500 0.00 0.00 0.00 2.17
2714 2835 3.159472 TGGATTGAGTTGCTTGCTTGAT 58.841 40.909 0.00 0.00 0.00 2.57
2743 2864 2.295885 CCCATTTTTGGCTTGCAACAA 58.704 42.857 0.00 0.00 0.00 2.83
2764 2885 8.349245 TGAAAACTTGTACATGTCCATTTGTAG 58.651 33.333 14.17 0.00 0.00 2.74
2863 2984 2.851195 AGTGTAGTTTTGCTGACCTGG 58.149 47.619 0.00 0.00 0.00 4.45
2892 3013 3.471680 AGAATAAAGAGATTGAGCCGGC 58.528 45.455 21.89 21.89 0.00 6.13
2906 3027 7.012799 TGGCGTGTGCATATATGAAAGAATAAA 59.987 33.333 17.10 0.00 45.35 1.40
2912 3033 4.754372 ATGGCGTGTGCATATATGAAAG 57.246 40.909 17.10 2.64 45.35 2.62
2949 3070 2.184322 GAGCCGCTGATCCGTGAA 59.816 61.111 0.00 0.00 0.00 3.18
2950 3071 3.838271 GGAGCCGCTGATCCGTGA 61.838 66.667 0.00 0.00 37.30 4.35
2962 3083 1.468914 GACTTGGAATTCGTTGGAGCC 59.531 52.381 0.00 0.00 0.00 4.70
2965 3086 1.071071 ACCGACTTGGAATTCGTTGGA 59.929 47.619 19.54 0.00 42.00 3.53
3042 3163 0.179067 TGTCGTCCCACCTTCACAAC 60.179 55.000 0.00 0.00 0.00 3.32
3054 3175 4.552166 CATGTAATGGGAAATGTCGTCC 57.448 45.455 0.00 0.00 41.79 4.79
3075 3196 4.202295 TGGAGATCATATGAAGCAGTGGAC 60.202 45.833 9.99 0.00 0.00 4.02
3116 3238 3.118555 GGGTGTAAAAAGGGTGTGCTTTT 60.119 43.478 0.00 0.00 34.66 2.27
3121 3243 2.375014 AGGGGTGTAAAAAGGGTGTG 57.625 50.000 0.00 0.00 0.00 3.82
3168 3292 2.678836 CAAAACGACCGCCCATAACATA 59.321 45.455 0.00 0.00 0.00 2.29
3235 3359 4.220821 AGTTAGAATCCTCTGCGTTGAAGA 59.779 41.667 0.00 0.00 32.70 2.87
3279 3403 2.238144 ACAGATTGTGAGATGACCCTGG 59.762 50.000 0.00 0.00 0.00 4.45
3292 3416 8.450578 TGACTTGAAGTAATTGAACAGATTGT 57.549 30.769 0.00 0.00 0.00 2.71
3423 3547 1.541147 GTCAGTTGCAAAGCCATGCTA 59.459 47.619 0.00 2.47 46.54 3.49
3463 3587 2.815211 CATGTGGTGGACGAGGCG 60.815 66.667 0.00 0.00 0.00 5.52
3491 3615 3.584406 AGAAGTGGGTGACAATGAGATCA 59.416 43.478 0.00 0.00 0.00 2.92
3528 3652 0.468226 AAACACCTCTGCAAGTCCGA 59.532 50.000 0.00 0.00 33.76 4.55
3577 3701 7.617041 AAAAACTGAGAGTACATGGATAAGC 57.383 36.000 0.00 0.00 0.00 3.09
3626 3751 5.064452 ACGATCATCAGTGAAGATCTTTTGC 59.936 40.000 27.10 8.85 35.46 3.68
3659 3785 4.876269 GGTACGTCCAAAAGCAATGGCG 62.876 54.545 0.00 13.39 40.69 5.69
3664 3790 2.645802 ACAAGGTACGTCCAAAAGCAA 58.354 42.857 0.00 0.00 39.02 3.91
3667 3793 2.222445 CGGAACAAGGTACGTCCAAAAG 59.778 50.000 0.00 0.00 39.02 2.27
3686 3812 0.250038 ATGTAGTGCCTGCATAGCGG 60.250 55.000 0.00 0.00 35.20 5.52
3694 3820 7.279536 GGATTATCATGTATGATGTAGTGCCTG 59.720 40.741 15.72 0.00 46.34 4.85
3714 3840 1.268899 CGCGGACGAACCTAGGATTAT 59.731 52.381 17.98 0.00 43.93 1.28
3794 3920 8.530311 AGAATATCTTCTCATGATTAGCGACAT 58.470 33.333 0.00 0.00 37.09 3.06
3829 3955 2.030451 GCTTTCTGAGTTGGCTTCTTGG 60.030 50.000 0.00 0.00 0.00 3.61
3937 4063 7.149973 GGGCGTGTACTCACATAATATAAGAA 58.850 38.462 0.00 0.00 44.02 2.52
3942 4068 3.305813 CGGGGCGTGTACTCACATAATAT 60.306 47.826 0.00 0.00 44.02 1.28
3950 4076 1.252215 TGAATCGGGGCGTGTACTCA 61.252 55.000 0.00 0.00 0.00 3.41
3953 4079 0.390735 AACTGAATCGGGGCGTGTAC 60.391 55.000 0.00 0.00 0.00 2.90
3956 4082 1.635663 GACAACTGAATCGGGGCGTG 61.636 60.000 0.00 0.00 0.00 5.34
3957 4083 1.375523 GACAACTGAATCGGGGCGT 60.376 57.895 0.00 0.00 0.00 5.68
3996 4122 0.952280 ACGGATGCATACGAGACGAT 59.048 50.000 36.90 11.42 37.61 3.73
3998 4124 1.121240 GAACGGATGCATACGAGACG 58.879 55.000 36.90 17.85 37.61 4.18
4139 4265 5.773176 ACTACCCATTAAAAAGGTGTGGAAG 59.227 40.000 5.03 0.00 35.02 3.46
4163 4289 7.254658 GCATGCCGCTAAAAGTCTTTATTAGTA 60.255 37.037 6.36 0.00 37.77 1.82
4175 4301 0.099436 GGTCTGCATGCCGCTAAAAG 59.901 55.000 16.68 3.71 43.06 2.27
4180 4306 4.025858 ACAGGTCTGCATGCCGCT 62.026 61.111 16.68 0.00 43.06 5.52
4181 4307 3.807538 CACAGGTCTGCATGCCGC 61.808 66.667 16.68 4.92 42.89 6.53
4182 4308 1.518056 AAACACAGGTCTGCATGCCG 61.518 55.000 16.68 9.39 0.00 5.69
4183 4309 0.675633 AAAACACAGGTCTGCATGCC 59.324 50.000 16.68 0.00 0.00 4.40
4185 4311 3.996150 AGAAAAACACAGGTCTGCATG 57.004 42.857 0.00 0.00 0.00 4.06
4186 4312 3.953612 TCAAGAAAAACACAGGTCTGCAT 59.046 39.130 0.00 0.00 0.00 3.96
4265 4394 1.072331 GGGACTGGCAAGAAGAACTGA 59.928 52.381 0.00 0.00 0.00 3.41
4388 4520 3.893813 AGGCAATCAATTCAAGGCTATCC 59.106 43.478 0.00 0.00 32.99 2.59


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

AutoCloner maintained by Alex Coulton.