Multiple sequence alignment - TraesCS3D01G416400

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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 TraesCS3D01G416400 chr3D 100.000 3250 0 0 1 3250 527676709 527673460 0.000000e+00 6002.0
1 TraesCS3D01G416400 chr3A 87.341 2275 158 65 313 2513 662414422 662412204 0.000000e+00 2486.0
2 TraesCS3D01G416400 chr3A 86.607 560 37 15 2606 3157 662411081 662410552 4.670000e-163 584.0
3 TraesCS3D01G416400 chr3A 82.692 208 21 9 13 215 662414660 662414463 1.550000e-38 171.0
4 TraesCS3D01G416400 chr3A 97.561 41 1 0 2905 2945 662410525 662410485 1.620000e-08 71.3
5 TraesCS3D01G416400 chr3B 94.204 1225 42 12 799 2019 697911397 697910198 0.000000e+00 1842.0
6 TraesCS3D01G416400 chr3B 89.067 686 37 18 2572 3242 697909452 697908790 0.000000e+00 817.0
7 TraesCS3D01G416400 chr3B 82.647 801 74 34 7 773 697912243 697911474 0.000000e+00 649.0
8 TraesCS3D01G416400 chr3B 82.770 592 51 26 2041 2594 697910135 697909557 6.310000e-132 481.0


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 TraesCS3D01G416400 chr3D 527673460 527676709 3249 True 6002.000 6002 100.00000 1 3250 1 chr3D.!!$R1 3249
1 TraesCS3D01G416400 chr3A 662410485 662414660 4175 True 828.075 2486 88.55025 13 3157 4 chr3A.!!$R1 3144
2 TraesCS3D01G416400 chr3B 697908790 697912243 3453 True 947.250 1842 87.17200 7 3242 4 chr3B.!!$R1 3235

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
613 654 0.249699 AGACGTCGTGTTCATTGGCA 60.25 50.0 10.46 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2523 2726 0.310854 GGCCAGTGTTTTCGTGAAGG 59.689 55.0 0.0 0.0 0.0 3.46 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
126 127 1.304381 GCTGACCTGGCCCAATGAA 60.304 57.895 0.00 0.00 0.00 2.57
132 133 3.340953 CTGGCCCAATGAAACGCGG 62.341 63.158 12.47 0.00 0.00 6.46
303 326 2.125310 TGCTACGTTGATGCCCCG 60.125 61.111 0.00 0.00 0.00 5.73
322 345 1.202348 CGCCCCAACTCCAATTCTTTC 59.798 52.381 0.00 0.00 0.00 2.62
333 356 0.739813 AATTCTTTCGAGGACGGGCG 60.740 55.000 0.00 0.00 40.21 6.13
366 398 2.540973 GGCACTCGTGAAAGTTTCAACC 60.541 50.000 19.63 7.89 42.15 3.77
369 401 3.621268 CACTCGTGAAAGTTTCAACCAGA 59.379 43.478 19.63 14.58 42.15 3.86
389 421 1.382522 AGACGTTCCGCCTAATCGTA 58.617 50.000 0.00 0.00 34.93 3.43
390 422 1.745087 AGACGTTCCGCCTAATCGTAA 59.255 47.619 0.00 0.00 34.93 3.18
391 423 2.360165 AGACGTTCCGCCTAATCGTAAT 59.640 45.455 0.00 0.00 34.93 1.89
409 449 4.986034 CGTAATCGAATATGCTGGTACCAA 59.014 41.667 17.11 1.69 39.71 3.67
425 465 3.239253 AACCCGTGAACCCGCTCT 61.239 61.111 0.00 0.00 0.00 4.09
426 466 2.814835 AACCCGTGAACCCGCTCTT 61.815 57.895 0.00 0.00 0.00 2.85
509 550 5.179368 ACTGATAATCCGATGCAAATTACCG 59.821 40.000 0.00 0.00 0.00 4.02
524 565 2.011741 TACCGCCACTGCTATCACGG 62.012 60.000 0.00 0.00 45.86 4.94
548 589 2.098607 AGCGTTTCCTCGATCGTTATCA 59.901 45.455 15.94 0.00 31.93 2.15
549 590 3.050619 GCGTTTCCTCGATCGTTATCAT 58.949 45.455 15.94 0.00 31.93 2.45
550 591 3.119792 GCGTTTCCTCGATCGTTATCATC 59.880 47.826 15.94 1.45 31.93 2.92
551 592 4.537965 CGTTTCCTCGATCGTTATCATCT 58.462 43.478 15.94 0.00 31.93 2.90
552 593 4.976731 CGTTTCCTCGATCGTTATCATCTT 59.023 41.667 15.94 0.00 31.93 2.40
553 594 5.459107 CGTTTCCTCGATCGTTATCATCTTT 59.541 40.000 15.94 0.00 31.93 2.52
557 598 6.669278 TCCTCGATCGTTATCATCTTTGTAG 58.331 40.000 15.94 0.00 31.93 2.74
558 599 6.262496 TCCTCGATCGTTATCATCTTTGTAGT 59.738 38.462 15.94 0.00 31.93 2.73
560 601 7.534578 CCTCGATCGTTATCATCTTTGTAGTAC 59.465 40.741 15.94 0.00 31.93 2.73
561 602 7.358066 TCGATCGTTATCATCTTTGTAGTACC 58.642 38.462 15.94 0.00 31.93 3.34
562 603 7.012610 TCGATCGTTATCATCTTTGTAGTACCA 59.987 37.037 15.94 0.00 31.93 3.25
563 604 7.808381 CGATCGTTATCATCTTTGTAGTACCAT 59.192 37.037 7.03 0.00 31.93 3.55
564 605 9.477484 GATCGTTATCATCTTTGTAGTACCATT 57.523 33.333 0.00 0.00 31.93 3.16
565 606 8.867112 TCGTTATCATCTTTGTAGTACCATTC 57.133 34.615 0.00 0.00 0.00 2.67
575 616 6.548441 TTGTAGTACCATTCTTTTCAACGG 57.452 37.500 0.00 0.00 0.00 4.44
613 654 0.249699 AGACGTCGTGTTCATTGGCA 60.250 50.000 10.46 0.00 0.00 4.92
615 656 1.206578 CGTCGTGTTCATTGGCACC 59.793 57.895 0.00 0.00 32.40 5.01
645 696 3.884774 TGTTCAGGGCCACGGCTT 61.885 61.111 6.18 0.00 41.60 4.35
648 699 3.126703 TTCAGGGCCACGGCTTTGA 62.127 57.895 6.18 9.20 41.60 2.69
652 703 1.377987 GGGCCACGGCTTTGACATA 60.378 57.895 4.39 0.00 41.60 2.29
654 705 0.676782 GGCCACGGCTTTGACATACT 60.677 55.000 8.20 0.00 41.60 2.12
655 706 0.447801 GCCACGGCTTTGACATACTG 59.552 55.000 0.00 0.00 38.26 2.74
656 707 1.808411 CCACGGCTTTGACATACTGT 58.192 50.000 0.00 0.00 0.00 3.55
658 709 1.464608 CACGGCTTTGACATACTGTGG 59.535 52.381 0.00 0.00 36.08 4.17
659 710 0.447801 CGGCTTTGACATACTGTGGC 59.552 55.000 0.00 0.00 35.91 5.01
660 711 0.447801 GGCTTTGACATACTGTGGCG 59.552 55.000 0.00 0.00 39.40 5.69
661 712 0.447801 GCTTTGACATACTGTGGCGG 59.552 55.000 0.00 0.00 39.40 6.13
662 713 0.447801 CTTTGACATACTGTGGCGGC 59.552 55.000 0.00 0.00 39.40 6.53
663 714 1.295357 TTTGACATACTGTGGCGGCG 61.295 55.000 0.51 0.51 39.40 6.46
664 715 2.890474 GACATACTGTGGCGGCGG 60.890 66.667 9.78 0.00 0.00 6.13
665 716 4.467084 ACATACTGTGGCGGCGGG 62.467 66.667 9.78 0.00 0.00 6.13
681 732 2.617274 GGGCAAGCTGTCGAACCAC 61.617 63.158 0.00 0.00 0.00 4.16
698 749 2.597217 CGGTTGGGGCTGCAAGAA 60.597 61.111 0.50 0.00 34.07 2.52
727 778 4.615452 CGAGCTACCAGTAAACGTTTCTCT 60.615 45.833 18.42 14.07 0.00 3.10
729 780 5.228665 AGCTACCAGTAAACGTTTCTCTTC 58.771 41.667 18.42 4.61 0.00 2.87
753 804 3.442625 ACATTGTCAGCCATCAGTCAATG 59.557 43.478 12.16 12.16 43.99 2.82
776 861 0.602638 TCACAATCAGACGTGGCACC 60.603 55.000 12.86 0.00 33.83 5.01
783 868 2.147958 TCAGACGTGGCACCATTAAAC 58.852 47.619 12.86 0.00 0.00 2.01
961 1069 1.693083 CCTACTAACGCAAGCACGCC 61.693 60.000 0.00 0.00 45.62 5.68
965 1073 1.565156 CTAACGCAAGCACGCCAAGA 61.565 55.000 0.00 0.00 45.62 3.02
989 1097 0.460635 TCCGCCGAATAAACCCTTCG 60.461 55.000 0.00 0.00 43.82 3.79
1011 1119 0.463116 CAACCGCCCTATAAAGCCGT 60.463 55.000 0.00 0.00 0.00 5.68
1069 1177 1.228154 ACCGCAACCTCCAAGTTCC 60.228 57.895 0.00 0.00 0.00 3.62
1079 1187 2.654863 CTCCAAGTTCCAACCACAACT 58.345 47.619 0.00 0.00 34.16 3.16
1083 1191 0.818040 AGTTCCAACCACAACTCGCC 60.818 55.000 0.00 0.00 0.00 5.54
1084 1192 1.890041 TTCCAACCACAACTCGCCG 60.890 57.895 0.00 0.00 0.00 6.46
1905 2020 4.112341 CCGTCGTCCACCTCGTCC 62.112 72.222 0.00 0.00 0.00 4.79
1906 2021 3.359523 CGTCGTCCACCTCGTCCA 61.360 66.667 0.00 0.00 0.00 4.02
1965 2080 1.374252 GGACGTCATCAAGTGCCGT 60.374 57.895 18.91 0.00 0.00 5.68
2022 2140 0.596083 CGGCGAGGATCAAGTAGCTG 60.596 60.000 0.00 0.00 33.17 4.24
2184 2353 0.312102 GTCAACCTTGAAGCAGCCAC 59.688 55.000 0.00 0.00 39.21 5.01
2201 2372 1.191647 CCACGGCGCGATTAAACTATC 59.808 52.381 12.10 0.00 0.00 2.08
2234 2405 1.539388 CTGGAAACATAAAGGCGTGCA 59.461 47.619 0.00 0.00 41.51 4.57
2358 2541 7.072030 GTCGAATGATGGCATTACTTTATCAC 58.928 38.462 0.00 0.00 44.47 3.06
2402 2591 6.756189 CGAGATCGTACTAATATACAACGC 57.244 41.667 0.00 0.00 33.75 4.84
2403 2592 5.444075 CGAGATCGTACTAATATACAACGCG 59.556 44.000 3.53 3.53 33.75 6.01
2404 2593 6.471976 AGATCGTACTAATATACAACGCGA 57.528 37.500 15.93 0.00 33.75 5.87
2405 2594 7.069852 AGATCGTACTAATATACAACGCGAT 57.930 36.000 15.93 0.00 38.90 4.58
2406 2595 7.178741 AGATCGTACTAATATACAACGCGATC 58.821 38.462 15.93 13.09 46.87 3.69
2407 2596 5.308147 TCGTACTAATATACAACGCGATCG 58.692 41.667 15.93 11.69 42.43 3.69
2442 2645 6.407202 AGTGTTATCCTAAACGAATCAAGCT 58.593 36.000 0.00 0.00 31.76 3.74
2443 2646 6.313905 AGTGTTATCCTAAACGAATCAAGCTG 59.686 38.462 0.00 0.00 31.76 4.24
2445 2648 3.973206 TCCTAAACGAATCAAGCTGGA 57.027 42.857 0.00 0.00 0.00 3.86
2471 2674 0.389817 TCTGGGCGTGATCTTTCGTG 60.390 55.000 0.00 0.00 0.00 4.35
2521 2724 3.362581 GCACATGGCGTTCTAGCTA 57.637 52.632 0.00 0.00 37.29 3.32
2522 2725 1.212616 GCACATGGCGTTCTAGCTAG 58.787 55.000 15.01 15.01 37.29 3.42
2523 2726 1.212616 CACATGGCGTTCTAGCTAGC 58.787 55.000 16.35 6.62 37.29 3.42
2527 2730 3.276021 GGCGTTCTAGCTAGCCTTC 57.724 57.895 16.35 5.28 45.67 3.46
2528 2731 0.460311 GGCGTTCTAGCTAGCCTTCA 59.540 55.000 16.35 0.00 45.67 3.02
2530 2733 1.828832 CGTTCTAGCTAGCCTTCACG 58.171 55.000 16.35 11.64 0.00 4.35
2531 2734 1.400846 CGTTCTAGCTAGCCTTCACGA 59.599 52.381 16.35 0.00 0.00 4.35
2540 2743 1.308998 AGCCTTCACGAAAACACTGG 58.691 50.000 0.00 0.00 0.00 4.00
2545 2748 1.008538 CACGAAAACACTGGCCTGC 60.009 57.895 9.95 0.00 0.00 4.85
2546 2749 2.252260 CGAAAACACTGGCCTGCG 59.748 61.111 9.95 2.31 0.00 5.18
2548 2751 2.519302 AAAACACTGGCCTGCGCT 60.519 55.556 9.73 0.00 34.44 5.92
2549 2752 2.737932 GAAAACACTGGCCTGCGCTG 62.738 60.000 9.73 8.47 34.44 5.18
2550 2753 4.569180 AACACTGGCCTGCGCTGT 62.569 61.111 9.73 4.01 34.44 4.40
2594 3201 4.820173 ACTGTAGGAGCACCAAAAAGTAAC 59.180 41.667 2.07 0.00 38.94 2.50
2596 3203 2.227194 AGGAGCACCAAAAAGTAACCG 58.773 47.619 2.07 0.00 38.94 4.44
2597 3204 1.335597 GGAGCACCAAAAAGTAACCGC 60.336 52.381 0.00 0.00 35.97 5.68
2599 3206 1.960689 AGCACCAAAAAGTAACCGCAT 59.039 42.857 0.00 0.00 0.00 4.73
2600 3207 2.058057 GCACCAAAAAGTAACCGCATG 58.942 47.619 0.00 0.00 0.00 4.06
2601 3208 2.058057 CACCAAAAAGTAACCGCATGC 58.942 47.619 7.91 7.91 0.00 4.06
2602 3209 1.000394 ACCAAAAAGTAACCGCATGCC 60.000 47.619 13.15 0.00 0.00 4.40
2603 3210 1.671556 CCAAAAAGTAACCGCATGCCC 60.672 52.381 13.15 0.00 0.00 5.36
2619 3852 2.510906 CCCCCGTAGCATCAAGGG 59.489 66.667 0.00 0.00 43.41 3.95
2650 3883 4.083110 GGATTGCCATTTCGGTAGATGATG 60.083 45.833 0.00 0.00 36.97 3.07
2665 3898 7.275920 GGTAGATGATGAAACAGTAGTTGGAT 58.724 38.462 0.00 0.00 38.17 3.41
2667 3900 7.621428 AGATGATGAAACAGTAGTTGGATTG 57.379 36.000 0.00 0.00 38.17 2.67
2668 3901 6.600822 AGATGATGAAACAGTAGTTGGATTGG 59.399 38.462 0.00 0.00 38.17 3.16
2669 3902 5.875224 TGATGAAACAGTAGTTGGATTGGA 58.125 37.500 0.00 0.00 38.17 3.53
2670 3903 5.939883 TGATGAAACAGTAGTTGGATTGGAG 59.060 40.000 0.00 0.00 38.17 3.86
2671 3904 5.560722 TGAAACAGTAGTTGGATTGGAGA 57.439 39.130 0.00 0.00 38.17 3.71
2672 3905 5.935945 TGAAACAGTAGTTGGATTGGAGAA 58.064 37.500 0.00 0.00 38.17 2.87
2673 3906 6.542821 TGAAACAGTAGTTGGATTGGAGAAT 58.457 36.000 0.00 0.00 38.17 2.40
2707 3940 0.409484 AAAGGTGATGGAGTTGGGGG 59.591 55.000 0.00 0.00 0.00 5.40
2708 3941 0.477597 AAGGTGATGGAGTTGGGGGA 60.478 55.000 0.00 0.00 0.00 4.81
2756 3991 4.296912 TGGTTAGATGGATAACGGGGTAA 58.703 43.478 0.00 0.00 36.66 2.85
2760 3995 2.642807 AGATGGATAACGGGGTAATGGG 59.357 50.000 0.00 0.00 0.00 4.00
2761 3996 1.142060 TGGATAACGGGGTAATGGGG 58.858 55.000 0.00 0.00 0.00 4.96
2762 3997 0.251033 GGATAACGGGGTAATGGGGC 60.251 60.000 0.00 0.00 0.00 5.80
2763 3998 0.251033 GATAACGGGGTAATGGGGCC 60.251 60.000 0.00 0.00 0.00 5.80
2861 4103 1.395954 CTGATTCCGTCGTACGTCTCA 59.604 52.381 16.05 8.38 40.58 3.27
2873 4116 3.605002 CGTACGTCTCAGATCGATCAAGG 60.605 52.174 26.47 15.34 0.00 3.61
3137 4382 1.336755 CTTCTCGGTTGGTGGTTTTGG 59.663 52.381 0.00 0.00 0.00 3.28
3147 4393 5.247084 GTTGGTGGTTTTGGTTTTTACCTT 58.753 37.500 0.00 0.00 0.00 3.50
3153 4399 7.201661 GGTGGTTTTGGTTTTTACCTTCATTTC 60.202 37.037 0.00 0.00 0.00 2.17
3157 4403 9.031360 GTTTTGGTTTTTACCTTCATTTCTCTC 57.969 33.333 0.00 0.00 0.00 3.20
3158 4404 7.889873 TTGGTTTTTACCTTCATTTCTCTCA 57.110 32.000 0.00 0.00 0.00 3.27
3159 4405 7.510549 TGGTTTTTACCTTCATTTCTCTCAG 57.489 36.000 0.00 0.00 0.00 3.35
3160 4406 6.490040 TGGTTTTTACCTTCATTTCTCTCAGG 59.510 38.462 0.00 0.00 0.00 3.86
3161 4407 6.490381 GGTTTTTACCTTCATTTCTCTCAGGT 59.510 38.462 0.00 0.00 41.00 4.00
3162 4408 7.014326 GGTTTTTACCTTCATTTCTCTCAGGTT 59.986 37.037 0.00 0.00 38.80 3.50
3163 4409 9.063615 GTTTTTACCTTCATTTCTCTCAGGTTA 57.936 33.333 0.00 0.00 38.80 2.85
3164 4410 8.617290 TTTTACCTTCATTTCTCTCAGGTTAC 57.383 34.615 0.00 0.00 38.80 2.50
3165 4411 5.167303 ACCTTCATTTCTCTCAGGTTACC 57.833 43.478 0.00 0.00 33.89 2.85
3166 4412 4.597507 ACCTTCATTTCTCTCAGGTTACCA 59.402 41.667 3.51 0.00 33.89 3.25
3167 4413 5.251700 ACCTTCATTTCTCTCAGGTTACCAT 59.748 40.000 3.51 0.00 33.89 3.55
3170 4416 5.032846 TCATTTCTCTCAGGTTACCATCCT 58.967 41.667 3.51 0.00 35.45 3.24
3171 4417 5.129485 TCATTTCTCTCAGGTTACCATCCTC 59.871 44.000 3.51 0.00 32.37 3.71
3172 4418 3.757947 TCTCTCAGGTTACCATCCTCA 57.242 47.619 3.51 0.00 32.37 3.86
3180 4430 2.158957 GGTTACCATCCTCATTGCTCGA 60.159 50.000 0.00 0.00 0.00 4.04
3181 4431 3.531538 GTTACCATCCTCATTGCTCGAA 58.468 45.455 0.00 0.00 0.00 3.71
3199 4449 3.345714 CGAAGATTTCGCTCGAATTTGG 58.654 45.455 5.50 0.30 46.97 3.28
3210 4460 3.593771 GAATTTGGGTGGGCGGGGA 62.594 63.158 0.00 0.00 0.00 4.81
3242 4492 1.227556 CACCACCGGCCTAGTATGC 60.228 63.158 0.00 0.00 0.00 3.14
3243 4493 2.029073 CCACCGGCCTAGTATGCG 59.971 66.667 0.00 0.00 0.00 4.73
3244 4494 2.661866 CACCGGCCTAGTATGCGC 60.662 66.667 0.00 0.00 0.00 6.09
3245 4495 3.925090 ACCGGCCTAGTATGCGCC 61.925 66.667 4.18 0.00 39.41 6.53
3248 4498 2.657237 GGCCTAGTATGCGCCGAT 59.343 61.111 4.18 0.00 31.92 4.18
3249 4499 1.446272 GGCCTAGTATGCGCCGATC 60.446 63.158 4.18 0.00 31.92 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
183 189 2.192861 CCGCGGCATCTCTCTCTCT 61.193 63.158 14.67 0.00 0.00 3.10
303 326 1.202348 CGAAAGAATTGGAGTTGGGGC 59.798 52.381 0.00 0.00 0.00 5.80
339 362 1.227823 TTTCACGAGTGCCCTGTGG 60.228 57.895 0.00 0.00 34.43 4.17
389 421 4.134563 GGTTGGTACCAGCATATTCGATT 58.865 43.478 27.48 0.00 44.36 3.34
390 422 3.496160 GGGTTGGTACCAGCATATTCGAT 60.496 47.826 27.48 0.00 46.96 3.59
391 423 2.158871 GGGTTGGTACCAGCATATTCGA 60.159 50.000 27.48 1.95 46.96 3.71
402 435 1.302752 GGGTTCACGGGTTGGTACC 60.303 63.158 4.43 4.43 44.22 3.34
409 449 3.239253 AAGAGCGGGTTCACGGGT 61.239 61.111 0.00 0.00 0.00 5.28
425 465 0.401395 AGGTGACCCTCCTTGACCAA 60.401 55.000 0.00 0.00 35.62 3.67
426 466 0.490017 TAGGTGACCCTCCTTGACCA 59.510 55.000 0.00 0.00 41.45 4.02
454 494 6.346758 CGCGTCTCTTCTAGAAGAACGTATAT 60.347 42.308 36.60 0.00 45.75 0.86
457 498 3.061831 CGCGTCTCTTCTAGAAGAACGTA 59.938 47.826 36.60 23.77 45.75 3.57
461 502 2.434428 ACCGCGTCTCTTCTAGAAGAA 58.566 47.619 30.08 19.99 45.75 2.52
509 550 2.897350 GGCCGTGATAGCAGTGGC 60.897 66.667 14.27 14.27 42.92 5.01
524 565 2.517450 CGATCGAGGAAACGCTGGC 61.517 63.158 10.26 0.00 0.00 4.85
548 589 8.504005 CGTTGAAAAGAATGGTACTACAAAGAT 58.496 33.333 0.00 0.00 0.00 2.40
549 590 7.041644 CCGTTGAAAAGAATGGTACTACAAAGA 60.042 37.037 0.00 0.00 0.00 2.52
550 591 7.075741 CCGTTGAAAAGAATGGTACTACAAAG 58.924 38.462 0.00 0.00 0.00 2.77
551 592 6.543100 ACCGTTGAAAAGAATGGTACTACAAA 59.457 34.615 0.00 0.00 42.41 2.83
552 593 6.017770 CACCGTTGAAAAGAATGGTACTACAA 60.018 38.462 0.00 0.00 42.35 2.41
553 594 5.467399 CACCGTTGAAAAGAATGGTACTACA 59.533 40.000 0.00 0.00 42.35 2.74
557 598 5.008316 ACTTCACCGTTGAAAAGAATGGTAC 59.992 40.000 0.00 0.00 42.35 3.34
558 599 5.127491 ACTTCACCGTTGAAAAGAATGGTA 58.873 37.500 0.00 0.00 42.35 3.25
560 601 4.568152 ACTTCACCGTTGAAAAGAATGG 57.432 40.909 0.00 0.00 41.34 3.16
561 602 6.140108 CGTTTACTTCACCGTTGAAAAGAATG 59.860 38.462 0.00 0.00 41.34 2.67
562 603 6.037391 TCGTTTACTTCACCGTTGAAAAGAAT 59.963 34.615 0.00 0.00 41.34 2.40
563 604 5.350914 TCGTTTACTTCACCGTTGAAAAGAA 59.649 36.000 0.00 0.00 41.34 2.52
564 605 4.869297 TCGTTTACTTCACCGTTGAAAAGA 59.131 37.500 0.00 0.00 41.34 2.52
565 606 5.146482 TCGTTTACTTCACCGTTGAAAAG 57.854 39.130 0.00 0.00 41.34 2.27
613 654 0.108329 GAACACGTGGATCCGATGGT 60.108 55.000 21.57 3.38 0.00 3.55
615 656 1.280982 CTGAACACGTGGATCCGATG 58.719 55.000 21.57 7.68 0.00 3.84
661 712 4.090057 GTTCGACAGCTTGCCCGC 62.090 66.667 0.00 0.00 0.00 6.13
662 713 3.423154 GGTTCGACAGCTTGCCCG 61.423 66.667 0.00 0.00 0.00 6.13
663 714 2.281484 TGGTTCGACAGCTTGCCC 60.281 61.111 0.00 0.00 0.00 5.36
664 715 2.946762 GTGGTTCGACAGCTTGCC 59.053 61.111 0.00 0.00 0.00 4.52
665 716 2.551270 CGTGGTTCGACAGCTTGC 59.449 61.111 0.00 0.00 42.86 4.01
666 717 1.157870 AACCGTGGTTCGACAGCTTG 61.158 55.000 0.00 0.00 42.86 4.01
667 718 1.145377 AACCGTGGTTCGACAGCTT 59.855 52.632 0.00 0.00 42.86 3.74
668 719 1.594293 CAACCGTGGTTCGACAGCT 60.594 57.895 0.16 0.00 42.86 4.24
669 720 2.604174 CCAACCGTGGTTCGACAGC 61.604 63.158 0.16 0.00 40.42 4.40
670 721 1.959226 CCCAACCGTGGTTCGACAG 60.959 63.158 0.16 0.00 44.30 3.51
681 732 1.743321 TTTTCTTGCAGCCCCAACCG 61.743 55.000 0.00 0.00 0.00 4.44
703 754 3.005155 AGAAACGTTTACTGGTAGCTCGT 59.995 43.478 14.65 0.00 0.00 4.18
704 755 3.572584 AGAAACGTTTACTGGTAGCTCG 58.427 45.455 14.65 0.00 0.00 5.03
727 778 3.489355 ACTGATGGCTGACAATGTTGAA 58.511 40.909 0.00 0.00 0.00 2.69
729 780 2.815503 TGACTGATGGCTGACAATGTTG 59.184 45.455 0.00 0.00 0.00 3.33
753 804 1.714794 CCACGTCTGATTGTGAGTCC 58.285 55.000 12.74 0.00 38.36 3.85
754 805 1.071605 GCCACGTCTGATTGTGAGTC 58.928 55.000 12.74 0.00 38.36 3.36
757 808 0.602638 GGTGCCACGTCTGATTGTGA 60.603 55.000 12.74 0.00 38.36 3.58
763 815 2.147958 GTTTAATGGTGCCACGTCTGA 58.852 47.619 0.00 0.00 0.00 3.27
766 818 2.095372 GCTAGTTTAATGGTGCCACGTC 59.905 50.000 0.00 0.00 0.00 4.34
776 861 6.092259 ACGTCCAAAGCTAAGCTAGTTTAATG 59.908 38.462 0.48 0.00 38.25 1.90
783 868 2.924290 GTCACGTCCAAAGCTAAGCTAG 59.076 50.000 0.00 0.00 38.25 3.42
860 963 0.322975 CCTGGAATATGCTCCTCCGG 59.677 60.000 0.00 0.00 36.35 5.14
863 966 1.003003 GAGCCCTGGAATATGCTCCTC 59.997 57.143 9.86 0.00 43.40 3.71
864 967 1.063183 GAGCCCTGGAATATGCTCCT 58.937 55.000 9.86 0.00 43.40 3.69
961 1069 5.449304 GGTTTATTCGGCGGATTAATCTTG 58.551 41.667 5.75 9.20 0.00 3.02
965 1073 4.094830 AGGGTTTATTCGGCGGATTAAT 57.905 40.909 5.75 0.75 0.00 1.40
997 1105 1.897137 GGCCACGGCTTTATAGGGC 60.897 63.158 8.20 0.00 41.60 5.19
1011 1119 4.980805 GTTGACACTCGCGGGCCA 62.981 66.667 5.51 0.00 0.00 5.36
1069 1177 4.368808 CGCGGCGAGTTGTGGTTG 62.369 66.667 19.16 0.00 0.00 3.77
1084 1192 3.862063 CTCGGCTTTGTGTGTGCGC 62.862 63.158 0.00 0.00 0.00 6.09
1698 1813 2.670934 ACGACCACCGCGTACTCT 60.671 61.111 4.92 0.00 43.32 3.24
1893 2008 4.736896 GCCGTGGACGAGGTGGAC 62.737 72.222 0.00 0.00 43.02 4.02
2022 2140 4.511617 TCTATGACATCGATCTTCCAGC 57.488 45.455 0.00 0.00 0.00 4.85
2117 2274 6.928492 GGACCAACAATTTGCTCTTTTTCATA 59.072 34.615 0.00 0.00 0.00 2.15
2184 2353 1.401530 TCGATAGTTTAATCGCGCCG 58.598 50.000 0.00 0.00 46.51 6.46
2188 2359 5.690409 TGACCAAGATCGATAGTTTAATCGC 59.310 40.000 0.00 0.00 46.51 4.58
2201 2372 1.734465 GTTTCCAGCTGACCAAGATCG 59.266 52.381 17.39 0.00 0.00 3.69
2255 2433 8.368962 TCCTTTTCACCCTTCTCTTTTTAAAA 57.631 30.769 0.00 0.00 0.00 1.52
2262 2440 2.224892 GGCTCCTTTTCACCCTTCTCTT 60.225 50.000 0.00 0.00 0.00 2.85
2268 2446 1.075601 TCATGGCTCCTTTTCACCCT 58.924 50.000 0.00 0.00 0.00 4.34
2269 2447 1.923356 TTCATGGCTCCTTTTCACCC 58.077 50.000 0.00 0.00 0.00 4.61
2270 2448 3.368739 CCATTTCATGGCTCCTTTTCACC 60.369 47.826 0.00 0.00 44.70 4.02
2271 2449 3.853475 CCATTTCATGGCTCCTTTTCAC 58.147 45.455 0.00 0.00 44.70 3.18
2358 2541 2.738521 CCGACAACCACCGCAGAG 60.739 66.667 0.00 0.00 0.00 3.35
2392 2581 5.637809 ACATATGTCGATCGCGTTGTATAT 58.362 37.500 11.09 5.25 38.98 0.86
2395 2584 3.343380 ACATATGTCGATCGCGTTGTA 57.657 42.857 11.09 0.00 38.98 2.41
2396 2585 2.203800 ACATATGTCGATCGCGTTGT 57.796 45.000 11.09 6.70 38.98 3.32
2397 2586 3.569304 AAACATATGTCGATCGCGTTG 57.431 42.857 11.09 6.07 38.98 4.10
2401 2590 5.637104 AACACTAAACATATGTCGATCGC 57.363 39.130 11.09 6.41 0.00 4.58
2402 2591 7.808381 AGGATAACACTAAACATATGTCGATCG 59.192 37.037 9.23 9.36 0.00 3.69
2439 2642 1.604378 CCCAGAATTCCGTCCAGCT 59.396 57.895 0.65 0.00 0.00 4.24
2442 2645 2.267642 CGCCCAGAATTCCGTCCA 59.732 61.111 0.65 0.00 0.00 4.02
2443 2646 2.106683 CACGCCCAGAATTCCGTCC 61.107 63.158 0.65 0.00 0.00 4.79
2445 2648 0.462047 GATCACGCCCAGAATTCCGT 60.462 55.000 0.65 1.54 0.00 4.69
2471 2674 2.223572 CCTTGCCCAGACAAAATATCGC 60.224 50.000 0.00 0.00 0.00 4.58
2513 2716 4.243270 GTTTTCGTGAAGGCTAGCTAGAA 58.757 43.478 25.15 4.35 0.00 2.10
2514 2717 3.257375 TGTTTTCGTGAAGGCTAGCTAGA 59.743 43.478 25.15 0.00 0.00 2.43
2517 2720 2.143925 GTGTTTTCGTGAAGGCTAGCT 58.856 47.619 15.72 0.00 0.00 3.32
2518 2721 2.096218 CAGTGTTTTCGTGAAGGCTAGC 60.096 50.000 6.04 6.04 0.00 3.42
2521 2724 1.308998 CCAGTGTTTTCGTGAAGGCT 58.691 50.000 0.00 0.00 0.00 4.58
2522 2725 0.317854 GCCAGTGTTTTCGTGAAGGC 60.318 55.000 0.00 0.00 0.00 4.35
2523 2726 0.310854 GGCCAGTGTTTTCGTGAAGG 59.689 55.000 0.00 0.00 0.00 3.46
2525 2728 1.021202 CAGGCCAGTGTTTTCGTGAA 58.979 50.000 5.01 0.00 0.00 3.18
2527 2730 1.008538 GCAGGCCAGTGTTTTCGTG 60.009 57.895 5.01 0.00 0.00 4.35
2528 2731 2.542907 CGCAGGCCAGTGTTTTCGT 61.543 57.895 5.01 0.00 0.00 3.85
2530 2733 2.050077 GCGCAGGCCAGTGTTTTC 60.050 61.111 5.01 0.00 0.00 2.29
2531 2734 2.519302 AGCGCAGGCCAGTGTTTT 60.519 55.556 11.47 0.00 41.24 2.43
2545 2748 0.804364 TAAGCCTGAAATGCACAGCG 59.196 50.000 0.00 0.00 34.47 5.18
2546 2749 2.989166 GTTTAAGCCTGAAATGCACAGC 59.011 45.455 0.00 0.00 34.47 4.40
2548 2751 4.340666 TCTTGTTTAAGCCTGAAATGCACA 59.659 37.500 0.00 0.00 33.82 4.57
2549 2752 4.681483 GTCTTGTTTAAGCCTGAAATGCAC 59.319 41.667 0.00 0.00 33.82 4.57
2550 2753 4.584325 AGTCTTGTTTAAGCCTGAAATGCA 59.416 37.500 0.00 0.00 33.82 3.96
2552 2755 6.076981 ACAGTCTTGTTTAAGCCTGAAATG 57.923 37.500 5.24 0.00 41.26 2.32
2602 3209 1.632018 TTCCCTTGATGCTACGGGGG 61.632 60.000 0.00 0.00 37.30 5.40
2603 3210 0.463833 GTTCCCTTGATGCTACGGGG 60.464 60.000 0.00 0.00 37.30 5.73
2619 3852 2.606108 GAAATGGCAATCCCGTTGTTC 58.394 47.619 0.00 0.00 42.07 3.18
2650 3883 6.127897 CCATTCTCCAATCCAACTACTGTTTC 60.128 42.308 0.00 0.00 33.52 2.78
2665 3898 4.895836 TCCTTATCCTCTCCATTCTCCAA 58.104 43.478 0.00 0.00 0.00 3.53
2667 3900 5.896073 TTTCCTTATCCTCTCCATTCTCC 57.104 43.478 0.00 0.00 0.00 3.71
2668 3901 6.126623 ACCTTTTCCTTATCCTCTCCATTCTC 60.127 42.308 0.00 0.00 0.00 2.87
2669 3902 5.733647 ACCTTTTCCTTATCCTCTCCATTCT 59.266 40.000 0.00 0.00 0.00 2.40
2670 3903 5.825151 CACCTTTTCCTTATCCTCTCCATTC 59.175 44.000 0.00 0.00 0.00 2.67
2671 3904 5.492524 TCACCTTTTCCTTATCCTCTCCATT 59.507 40.000 0.00 0.00 0.00 3.16
2672 3905 5.039645 TCACCTTTTCCTTATCCTCTCCAT 58.960 41.667 0.00 0.00 0.00 3.41
2673 3906 4.435137 TCACCTTTTCCTTATCCTCTCCA 58.565 43.478 0.00 0.00 0.00 3.86
2707 3940 2.099098 CACACCCGGCATTATTTTCCTC 59.901 50.000 0.00 0.00 0.00 3.71
2708 3941 2.099405 CACACCCGGCATTATTTTCCT 58.901 47.619 0.00 0.00 0.00 3.36
2763 3998 4.379243 AGGTCTTGTCGCTGGCCG 62.379 66.667 0.00 0.00 38.61 6.13
2774 4009 1.867919 CGCTCGAGTGGACAGGTCTT 61.868 60.000 18.36 0.00 0.00 3.01
2802 4037 1.596477 GCATGGGCGAGGAAGCTAG 60.596 63.158 0.00 0.00 37.29 3.42
2861 4103 1.742768 GTCGGGCCTTGATCGATCT 59.257 57.895 25.02 0.00 35.35 2.75
3085 4330 1.014044 TCGAGACGATTGCAGTTGCC 61.014 55.000 1.06 0.00 41.18 4.52
3088 4333 1.542030 AGAGTCGAGACGATTGCAGTT 59.458 47.619 0.00 0.00 38.42 3.16
3089 4334 1.169577 AGAGTCGAGACGATTGCAGT 58.830 50.000 0.00 0.00 38.42 4.40
3090 4335 2.353269 AGTAGAGTCGAGACGATTGCAG 59.647 50.000 0.00 0.00 38.42 4.41
3091 4336 2.352034 GAGTAGAGTCGAGACGATTGCA 59.648 50.000 0.00 0.00 38.42 4.08
3092 4337 2.597971 CGAGTAGAGTCGAGACGATTGC 60.598 54.545 0.28 0.00 42.85 3.56
3093 4338 2.604011 ACGAGTAGAGTCGAGACGATTG 59.396 50.000 13.47 0.00 42.85 2.67
3137 4382 7.511959 ACCTGAGAGAAATGAAGGTAAAAAC 57.488 36.000 0.00 0.00 39.48 2.43
3147 4393 5.032846 AGGATGGTAACCTGAGAGAAATGA 58.967 41.667 0.00 0.00 36.30 2.57
3153 4399 4.701765 CAATGAGGATGGTAACCTGAGAG 58.298 47.826 0.00 0.00 37.93 3.20
3157 4403 3.209410 GAGCAATGAGGATGGTAACCTG 58.791 50.000 0.00 0.00 37.93 4.00
3158 4404 2.158900 CGAGCAATGAGGATGGTAACCT 60.159 50.000 0.00 0.00 40.80 3.50
3159 4405 2.158957 TCGAGCAATGAGGATGGTAACC 60.159 50.000 0.00 0.00 0.00 2.85
3160 4406 3.179443 TCGAGCAATGAGGATGGTAAC 57.821 47.619 0.00 0.00 0.00 2.50
3161 4407 3.450817 TCTTCGAGCAATGAGGATGGTAA 59.549 43.478 0.00 0.00 0.00 2.85
3162 4408 3.031013 TCTTCGAGCAATGAGGATGGTA 58.969 45.455 0.00 0.00 0.00 3.25
3163 4409 1.833630 TCTTCGAGCAATGAGGATGGT 59.166 47.619 0.00 0.00 0.00 3.55
3164 4410 2.609427 TCTTCGAGCAATGAGGATGG 57.391 50.000 0.00 0.00 0.00 3.51
3165 4411 5.093169 GAAATCTTCGAGCAATGAGGATG 57.907 43.478 0.00 0.00 33.09 3.51
3180 4430 3.081804 ACCCAAATTCGAGCGAAATCTT 58.918 40.909 9.52 1.46 37.69 2.40
3181 4431 2.420022 CACCCAAATTCGAGCGAAATCT 59.580 45.455 9.52 0.00 37.69 2.40
3192 4442 3.074369 CCCCGCCCACCCAAATTC 61.074 66.667 0.00 0.00 0.00 2.17
3224 4474 1.227556 GCATACTAGGCCGGTGGTG 60.228 63.158 13.41 12.36 0.00 4.17


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

AutoCloner maintained by Alex Coulton.