Multiple sequence alignment - TraesCS5A01G145300

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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 TraesCS5A01G145300 chr5A 100.000 2777 0 0 1 2777 321325253 321328029 0 5129
1 TraesCS5A01G145300 chr5B 89.370 2841 166 56 1 2765 271668667 271665887 0 3448
2 TraesCS5A01G145300 chr5D 89.617 2090 135 37 724 2777 233410731 233412774 0 2582
3 TraesCS5A01G145300 chr5D 90.767 704 47 10 1 699 233410045 233410735 0 924


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 TraesCS5A01G145300 chr5A 321325253 321328029 2776 False 5129 5129 100.000 1 2777 1 chr5A.!!$F1 2776
1 TraesCS5A01G145300 chr5B 271665887 271668667 2780 True 3448 3448 89.370 1 2765 1 chr5B.!!$R1 2764
2 TraesCS5A01G145300 chr5D 233410045 233412774 2729 False 1753 2582 90.192 1 2777 2 chr5D.!!$F1 2776

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
332 336 0.456653 TTAGGCGTTCGCGAGGTAAC 60.457 55.0 9.59 3.35 44.71 2.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2282 2339 0.03563 ACAGGAAGAGCAGCCATCAC 60.036 55.0 0.0 0.0 0.0 3.06 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
220 224 1.523032 GGTATCGTGCCCTTTCCCG 60.523 63.158 0.00 0.00 0.00 5.14
241 245 2.109126 GCAGATCTGGTTCCGGTGC 61.109 63.158 23.89 3.42 0.00 5.01
313 317 6.656632 TCTCTCCGATTGATAAGTTGCTAT 57.343 37.500 0.00 0.00 0.00 2.97
332 336 0.456653 TTAGGCGTTCGCGAGGTAAC 60.457 55.000 9.59 3.35 44.71 2.50
351 355 2.076863 ACTGCTAGGCGTTGATTTGTC 58.923 47.619 0.00 0.00 0.00 3.18
355 359 2.281762 GCTAGGCGTTGATTTGTCGTAG 59.718 50.000 0.00 0.00 0.00 3.51
358 362 1.396996 GGCGTTGATTTGTCGTAGCAT 59.603 47.619 0.00 0.00 0.00 3.79
429 433 7.274686 CGTGTTTCTGAAATACTTTTGGTTTGT 59.725 33.333 22.11 0.00 31.22 2.83
447 452 5.878669 GGTTTGTCGAATTACTAATCTGGGT 59.121 40.000 0.00 0.00 0.00 4.51
451 456 6.267817 TGTCGAATTACTAATCTGGGTTACG 58.732 40.000 0.00 0.00 0.00 3.18
460 465 4.579647 AATCTGGGTTACGGTGGTTATT 57.420 40.909 0.00 0.00 0.00 1.40
463 468 3.118665 TCTGGGTTACGGTGGTTATTAGC 60.119 47.826 0.00 0.00 0.00 3.09
501 510 2.764314 GGCTCCCGTCTACGCGTAA 61.764 63.158 20.97 8.63 38.18 3.18
564 576 8.922058 CATAGTTGCAGATCAGCTTAATTTTT 57.078 30.769 11.68 0.00 37.44 1.94
601 617 6.839124 TTGCAGGATGATGTAATTTTGTCT 57.161 33.333 0.00 0.00 39.69 3.41
646 662 7.896383 TTTTAATCTAAAGCACATATGGCCT 57.104 32.000 3.32 0.00 0.00 5.19
648 664 3.213206 TCTAAAGCACATATGGCCTGG 57.787 47.619 3.32 0.00 0.00 4.45
664 680 0.877071 CTGGAGCACGTCTTTGCATT 59.123 50.000 0.00 0.00 45.62 3.56
669 685 4.697828 TGGAGCACGTCTTTGCATTAATAA 59.302 37.500 0.00 0.00 45.62 1.40
693 709 7.757097 AGATGACGTAATGTTGTAATCTGAC 57.243 36.000 0.00 0.00 0.00 3.51
706 722 4.923871 TGTAATCTGACTTCTGAAAGCGTC 59.076 41.667 2.34 2.34 35.81 5.19
716 732 2.154462 CTGAAAGCGTCCTGTTCCAAT 58.846 47.619 0.00 0.00 0.00 3.16
735 751 1.167851 TTGTATGTTCTGCTGCTGCC 58.832 50.000 13.47 0.00 38.71 4.85
912 932 7.093322 TCTACCGTTATACTGACCTTTTCTC 57.907 40.000 0.00 0.00 0.00 2.87
937 957 5.008613 TGTTGCAGGTTTTGATACTGAAGTC 59.991 40.000 0.00 0.00 34.21 3.01
938 958 4.973168 TGCAGGTTTTGATACTGAAGTCT 58.027 39.130 0.00 0.00 34.21 3.24
942 962 4.010349 GGTTTTGATACTGAAGTCTGGGG 58.990 47.826 0.00 0.00 0.00 4.96
947 967 3.271225 TGATACTGAAGTCTGGGGGAGTA 59.729 47.826 0.00 0.00 0.00 2.59
1026 1046 1.523938 GGCTGAATCCGCACTACCC 60.524 63.158 0.00 0.00 0.00 3.69
1029 1049 2.185867 GAATCCGCACTACCCGCA 59.814 61.111 0.00 0.00 0.00 5.69
1032 1052 2.180159 AATCCGCACTACCCGCAGTT 62.180 55.000 0.00 0.00 0.00 3.16
1113 1133 2.802816 CACAGTTGTAGAAGTGCTGGAC 59.197 50.000 7.33 0.00 36.13 4.02
1123 1143 2.031012 TGCTGGACAAGAGTGCCG 59.969 61.111 0.00 0.00 34.84 5.69
1126 1146 1.669115 CTGGACAAGAGTGCCGGTG 60.669 63.158 1.90 0.00 34.84 4.94
1132 1152 1.151668 CAAGAGTGCCGGTGAAGAAG 58.848 55.000 1.90 0.00 0.00 2.85
1135 1155 1.149148 GAGTGCCGGTGAAGAAGTTC 58.851 55.000 1.90 0.00 0.00 3.01
1138 1158 0.599204 TGCCGGTGAAGAAGTTCGTC 60.599 55.000 11.40 11.40 35.17 4.20
1144 1164 2.808543 GGTGAAGAAGTTCGTCTGCAAT 59.191 45.455 17.86 0.00 34.83 3.56
1158 1178 3.261643 GTCTGCAATTTCCCTTGGGAAAT 59.738 43.478 30.68 30.68 46.53 2.17
1167 1187 5.813965 TTCCCTTGGGAAATAAGGAAGAT 57.186 39.130 17.99 0.00 46.08 2.40
1168 1188 5.129368 TCCCTTGGGAAATAAGGAAGATG 57.871 43.478 5.82 0.00 46.08 2.90
1422 1442 0.176680 TCTCCCGCAGAAAGCTCATC 59.823 55.000 0.00 0.00 42.61 2.92
1476 1496 7.231317 AGGTTAAGCTTTGAGTTTGATGATTCA 59.769 33.333 3.20 0.00 0.00 2.57
1563 1583 2.266055 CTGGAGGCAACCGGAGAC 59.734 66.667 9.46 1.29 38.49 3.36
1623 1643 2.551270 AGCTACAAGACCCCTGAATCA 58.449 47.619 0.00 0.00 0.00 2.57
1704 1724 0.106335 AGATGATCAAGCTCAGCCCG 59.894 55.000 0.00 0.00 31.94 6.13
1783 1803 3.118811 AGACAATAAGAGCTGAGCCTGTC 60.119 47.826 0.00 5.17 0.00 3.51
1793 1813 1.225704 GAGCCTGTCCCCATCCTTG 59.774 63.158 0.00 0.00 0.00 3.61
1842 1873 2.359107 AGGCATGTCAGCGTGGTG 60.359 61.111 0.00 0.00 34.64 4.17
2002 2033 4.212716 TCATTGATGTAGTAGTACCGGCT 58.787 43.478 0.00 0.00 0.00 5.52
2054 2085 8.699749 AGCGTTTTGTAAATCTTGAAAAATAGC 58.300 29.630 0.00 0.00 31.95 2.97
2120 2151 5.393896 GCAGATTCATCCTTGCTTAGCTTTT 60.394 40.000 5.60 0.00 0.00 2.27
2121 2152 6.628185 CAGATTCATCCTTGCTTAGCTTTTT 58.372 36.000 5.60 0.00 0.00 1.94
2132 2163 5.469479 TGCTTAGCTTTTTATCTTTGCACC 58.531 37.500 5.60 0.00 0.00 5.01
2160 2209 1.135717 CGAAATGATGCAGTGGCGAAA 60.136 47.619 0.00 0.00 45.35 3.46
2174 2228 1.538276 GCGAAATCGAACATGGCTTG 58.462 50.000 7.06 0.00 43.02 4.01
2175 2229 1.795162 GCGAAATCGAACATGGCTTGG 60.795 52.381 7.06 0.00 43.02 3.61
2176 2230 1.795162 CGAAATCGAACATGGCTTGGC 60.795 52.381 5.31 0.00 43.02 4.52
2177 2231 1.474077 GAAATCGAACATGGCTTGGCT 59.526 47.619 5.31 0.00 0.00 4.75
2178 2232 1.549203 AATCGAACATGGCTTGGCTT 58.451 45.000 5.31 0.00 0.00 4.35
2206 2260 1.533469 GCGACTGGTGTAGGGTGAGT 61.533 60.000 0.00 0.00 0.00 3.41
2219 2276 1.291877 GGTGAGTTGCTGGCGTACTG 61.292 60.000 5.20 0.00 0.00 2.74
2268 2325 5.887598 TCATCTGCCTTATTAATTGTGCTGT 59.112 36.000 0.00 0.00 0.00 4.40
2269 2326 5.818136 TCTGCCTTATTAATTGTGCTGTC 57.182 39.130 0.00 0.00 0.00 3.51
2280 2337 0.392706 TGTGCTGTCCTGTCACGATT 59.607 50.000 0.00 0.00 33.69 3.34
2282 2339 2.263077 GTGCTGTCCTGTCACGATTAG 58.737 52.381 0.00 0.00 0.00 1.73
2328 2385 1.769026 AGCCGTCAGATAGAGCTTCA 58.231 50.000 0.00 0.00 0.00 3.02
2335 2392 4.218200 CGTCAGATAGAGCTTCAGATGGAT 59.782 45.833 0.00 0.00 0.00 3.41
2359 2416 1.218316 GACGGCCTCGATTTGTCCT 59.782 57.895 0.00 0.00 40.11 3.85
2362 2419 1.803289 GGCCTCGATTTGTCCTTGC 59.197 57.895 0.00 0.00 0.00 4.01
2371 2428 4.394920 TCGATTTGTCCTTGCCTTTGATAC 59.605 41.667 0.00 0.00 0.00 2.24
2382 2439 3.892588 TGCCTTTGATACCCTTTTTCGTT 59.107 39.130 0.00 0.00 0.00 3.85
2388 2445 4.329392 TGATACCCTTTTTCGTTCCCTTC 58.671 43.478 0.00 0.00 0.00 3.46
2390 2447 0.240145 CCCTTTTTCGTTCCCTTCGC 59.760 55.000 0.00 0.00 0.00 4.70
2425 2482 5.416952 GGAGCTTTCATTGATCAGAGGAAAA 59.583 40.000 15.07 5.73 0.00 2.29
2433 2490 7.106239 TCATTGATCAGAGGAAAAAGGACTAC 58.894 38.462 0.00 0.00 0.00 2.73
2435 2492 5.794894 TGATCAGAGGAAAAAGGACTACAC 58.205 41.667 0.00 0.00 0.00 2.90
2470 2529 4.829064 TTCACTGCTTGTATGTTTGACC 57.171 40.909 0.00 0.00 0.00 4.02
2545 2604 5.592282 TGAAAATTACTTTCAGCACAGGTGA 59.408 36.000 3.10 0.00 46.80 4.02
2547 2606 3.552132 TTACTTTCAGCACAGGTGACA 57.448 42.857 3.10 0.00 39.84 3.58
2548 2607 1.959042 ACTTTCAGCACAGGTGACAG 58.041 50.000 3.10 9.93 41.66 3.51
2549 2608 1.233019 CTTTCAGCACAGGTGACAGG 58.767 55.000 3.10 0.00 39.84 4.00
2564 2648 1.541588 GACAGGTGGCTTGGCTTTAAG 59.458 52.381 0.00 0.00 0.00 1.85
2566 2650 0.777446 AGGTGGCTTGGCTTTAAGGA 59.223 50.000 0.00 0.00 0.00 3.36
2567 2651 1.359130 AGGTGGCTTGGCTTTAAGGAT 59.641 47.619 0.00 0.00 0.00 3.24
2569 2653 3.011257 AGGTGGCTTGGCTTTAAGGATTA 59.989 43.478 0.00 0.00 0.00 1.75
2570 2654 3.960755 GGTGGCTTGGCTTTAAGGATTAT 59.039 43.478 0.00 0.00 0.00 1.28
2571 2655 5.103686 AGGTGGCTTGGCTTTAAGGATTATA 60.104 40.000 0.00 0.00 0.00 0.98
2572 2656 5.775195 GGTGGCTTGGCTTTAAGGATTATAT 59.225 40.000 0.00 0.00 0.00 0.86
2573 2657 6.946009 GGTGGCTTGGCTTTAAGGATTATATA 59.054 38.462 0.00 0.00 0.00 0.86
2574 2658 7.615757 GGTGGCTTGGCTTTAAGGATTATATAT 59.384 37.037 0.00 0.00 0.00 0.86
2575 2659 9.681062 GTGGCTTGGCTTTAAGGATTATATATA 57.319 33.333 0.00 0.00 0.00 0.86
2576 2660 9.905713 TGGCTTGGCTTTAAGGATTATATATAG 57.094 33.333 0.00 0.00 0.00 1.31
2598 2682 6.713762 AGAGAGTAATCAGAGGATCAAGTG 57.286 41.667 0.00 0.00 37.82 3.16
2610 2694 2.543067 ATCAAGTGCTCGGGGAAGGC 62.543 60.000 0.00 0.00 0.00 4.35
2683 2779 1.084370 GTGCTTAGGATTCGTGCGCT 61.084 55.000 9.73 0.00 0.00 5.92
2706 2802 6.675002 GCTCAAAGCAAGAATCTAGACACATG 60.675 42.308 0.00 0.00 41.89 3.21
2707 2803 6.466812 TCAAAGCAAGAATCTAGACACATGA 58.533 36.000 0.00 0.00 0.00 3.07
2708 2804 7.108194 TCAAAGCAAGAATCTAGACACATGAT 58.892 34.615 0.00 0.00 0.00 2.45
2709 2805 6.922247 AAGCAAGAATCTAGACACATGATG 57.078 37.500 0.00 0.00 0.00 3.07
2744 2840 6.880529 TGATGTGATGAACAATAAGAGCAAGA 59.119 34.615 0.00 0.00 43.61 3.02
2766 2862 9.908152 CAAGACATATCCGTGTATACTAATCAA 57.092 33.333 4.17 0.00 31.16 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
220 224 1.519455 CCGGAACCAGATCTGCGAC 60.519 63.158 17.76 9.53 0.00 5.19
241 245 1.470098 CGGAACAGGCAAAATGAGGAG 59.530 52.381 0.00 0.00 0.00 3.69
313 317 0.456653 GTTACCTCGCGAACGCCTAA 60.457 55.000 11.33 0.00 39.84 2.69
332 336 1.061131 CGACAAATCAACGCCTAGCAG 59.939 52.381 0.00 0.00 0.00 4.24
341 345 3.125146 TGCAGATGCTACGACAAATCAAC 59.875 43.478 6.35 0.00 42.66 3.18
351 355 2.224217 CGGTCGTGCAGATGCTACG 61.224 63.158 17.69 17.69 42.46 3.51
429 433 5.360714 ACCGTAACCCAGATTAGTAATTCGA 59.639 40.000 0.00 0.00 0.00 3.71
447 452 3.207778 GGCATGCTAATAACCACCGTAA 58.792 45.455 18.92 0.00 0.00 3.18
451 456 0.310854 GCGGCATGCTAATAACCACC 59.689 55.000 18.92 0.00 41.73 4.61
460 465 2.007113 CAGCAATTGGCGGCATGCTA 62.007 55.000 31.71 11.48 46.75 3.49
497 506 9.958234 AGAATCGATGAAGATATATGGATTACG 57.042 33.333 0.00 0.00 33.67 3.18
627 643 3.395607 TCCAGGCCATATGTGCTTTAGAT 59.604 43.478 5.01 0.00 0.00 1.98
628 644 2.777114 TCCAGGCCATATGTGCTTTAGA 59.223 45.455 5.01 5.43 0.00 2.10
629 645 3.144506 CTCCAGGCCATATGTGCTTTAG 58.855 50.000 5.01 5.22 0.00 1.85
630 646 2.749466 GCTCCAGGCCATATGTGCTTTA 60.749 50.000 5.01 0.45 34.27 1.85
633 649 1.150081 GCTCCAGGCCATATGTGCT 59.850 57.895 5.01 1.22 34.27 4.40
634 650 1.152902 TGCTCCAGGCCATATGTGC 60.153 57.895 5.01 4.88 40.92 4.57
635 651 1.162181 CGTGCTCCAGGCCATATGTG 61.162 60.000 5.01 0.00 40.92 3.21
636 652 1.146930 CGTGCTCCAGGCCATATGT 59.853 57.895 5.01 0.00 40.92 2.29
637 653 0.882042 GACGTGCTCCAGGCCATATG 60.882 60.000 5.01 0.00 40.92 1.78
638 654 1.050988 AGACGTGCTCCAGGCCATAT 61.051 55.000 5.01 0.00 40.92 1.78
639 655 1.264749 AAGACGTGCTCCAGGCCATA 61.265 55.000 5.01 0.00 40.92 2.74
640 656 2.129555 AAAGACGTGCTCCAGGCCAT 62.130 55.000 5.01 0.00 40.92 4.40
641 657 2.818169 AAAGACGTGCTCCAGGCCA 61.818 57.895 5.01 0.00 40.92 5.36
642 658 2.032681 AAAGACGTGCTCCAGGCC 59.967 61.111 0.00 0.00 40.92 5.19
643 659 2.970974 GCAAAGACGTGCTCCAGGC 61.971 63.158 0.00 0.00 41.51 4.85
646 662 2.177394 TAATGCAAAGACGTGCTCCA 57.823 45.000 0.00 0.00 45.17 3.86
648 664 6.106877 TCTTATTAATGCAAAGACGTGCTC 57.893 37.500 0.00 0.00 45.17 4.26
669 685 7.548097 AGTCAGATTACAACATTACGTCATCT 58.452 34.615 0.00 0.00 0.00 2.90
693 709 1.801178 GGAACAGGACGCTTTCAGAAG 59.199 52.381 0.00 0.00 35.92 2.85
706 722 4.460382 AGCAGAACATACAATTGGAACAGG 59.540 41.667 10.83 0.00 42.39 4.00
716 732 1.167851 GGCAGCAGCAGAACATACAA 58.832 50.000 2.65 0.00 44.61 2.41
757 773 3.825908 TTTCAGAATAAACAGGGGCCT 57.174 42.857 0.84 0.00 0.00 5.19
758 774 4.222810 ACAATTTCAGAATAAACAGGGGCC 59.777 41.667 0.00 0.00 0.00 5.80
882 902 9.632638 AAAGGTCAGTATAACGGTAGATACTAA 57.367 33.333 12.67 0.41 36.87 2.24
912 932 5.009010 ACTTCAGTATCAAAACCTGCAACAG 59.991 40.000 0.00 0.00 0.00 3.16
968 988 9.203421 GAAGTGGTTTATTCCAAAACTAAATGG 57.797 33.333 0.00 0.00 39.34 3.16
975 995 6.183360 TGTGGAGAAGTGGTTTATTCCAAAAC 60.183 38.462 0.00 0.00 39.34 2.43
979 999 4.715534 TGTGGAGAAGTGGTTTATTCCA 57.284 40.909 0.00 0.00 32.89 3.53
980 1000 4.399303 CCATGTGGAGAAGTGGTTTATTCC 59.601 45.833 0.00 0.00 37.39 3.01
984 1004 2.790433 GCCATGTGGAGAAGTGGTTTA 58.210 47.619 2.55 0.00 37.39 2.01
1021 1041 1.935873 CACATGATCAACTGCGGGTAG 59.064 52.381 0.00 0.00 0.00 3.18
1026 1046 1.159285 ACACCACATGATCAACTGCG 58.841 50.000 0.00 0.00 0.00 5.18
1029 1049 3.507162 TCCAACACCACATGATCAACT 57.493 42.857 0.00 0.00 0.00 3.16
1032 1052 4.916183 TGTTATCCAACACCACATGATCA 58.084 39.130 0.00 0.00 39.75 2.92
1113 1133 1.151668 CTTCTTCACCGGCACTCTTG 58.848 55.000 0.00 0.00 0.00 3.02
1123 1143 1.865865 TGCAGACGAACTTCTTCACC 58.134 50.000 0.00 0.00 0.00 4.02
1126 1146 4.467735 GGAAATTGCAGACGAACTTCTTC 58.532 43.478 0.00 0.00 0.00 2.87
1132 1152 2.351738 CCAAGGGAAATTGCAGACGAAC 60.352 50.000 0.00 0.00 0.00 3.95
1135 1155 0.527565 CCCAAGGGAAATTGCAGACG 59.472 55.000 0.00 0.00 37.50 4.18
1158 1178 5.163195 GCCAAGGGATTCTACATCTTCCTTA 60.163 44.000 0.00 0.00 32.56 2.69
1167 1187 1.985159 ACTGTGCCAAGGGATTCTACA 59.015 47.619 0.00 0.00 0.00 2.74
1168 1188 2.789409 ACTGTGCCAAGGGATTCTAC 57.211 50.000 0.00 0.00 0.00 2.59
1206 1226 1.340017 GCCTCAGCAACATTACCCTCA 60.340 52.381 0.00 0.00 39.53 3.86
1422 1442 5.251764 ACTGGGAAGTCATCAGATTCAAAG 58.748 41.667 7.58 0.00 33.19 2.77
1476 1496 4.418526 TGGAGATACAGATCTTCCTCCTCT 59.581 45.833 20.89 8.15 42.80 3.69
1563 1583 0.596083 CTATCAGAACAGCCTCGCCG 60.596 60.000 0.00 0.00 0.00 6.46
1793 1813 1.250840 GCACCAAGACCATGTTCCCC 61.251 60.000 0.00 0.00 0.00 4.81
1834 1863 1.202651 AGTTAGCAAAGTCACCACGCT 60.203 47.619 0.00 0.00 36.72 5.07
1842 1873 4.061596 ACAGCTTCAGAGTTAGCAAAGTC 58.938 43.478 0.00 0.00 39.85 3.01
1876 1907 2.027192 TGCTTCCTACTCAACCATCACC 60.027 50.000 0.00 0.00 0.00 4.02
1944 1975 3.351794 AGACTGGGCTTAGCTAAAACC 57.648 47.619 15.75 15.75 0.00 3.27
1945 1976 5.351740 CAGTAAGACTGGGCTTAGCTAAAAC 59.648 44.000 7.74 2.71 42.35 2.43
2054 2085 2.032204 GCAAGCACAGAGAGACAACAAG 60.032 50.000 0.00 0.00 0.00 3.16
2120 2151 2.811431 CGGTGTCAAGGTGCAAAGATAA 59.189 45.455 0.00 0.00 0.00 1.75
2121 2152 2.037902 TCGGTGTCAAGGTGCAAAGATA 59.962 45.455 0.00 0.00 0.00 1.98
2132 2163 2.485426 ACTGCATCATTTCGGTGTCAAG 59.515 45.455 0.00 0.00 0.00 3.02
2160 2209 0.813184 CAAGCCAAGCCATGTTCGAT 59.187 50.000 0.00 0.00 0.00 3.59
2174 2228 0.109597 CAGTCGCATCAAACCAAGCC 60.110 55.000 0.00 0.00 0.00 4.35
2175 2229 0.109597 CCAGTCGCATCAAACCAAGC 60.110 55.000 0.00 0.00 0.00 4.01
2176 2230 1.069022 CACCAGTCGCATCAAACCAAG 60.069 52.381 0.00 0.00 0.00 3.61
2177 2231 0.950836 CACCAGTCGCATCAAACCAA 59.049 50.000 0.00 0.00 0.00 3.67
2178 2232 0.179032 ACACCAGTCGCATCAAACCA 60.179 50.000 0.00 0.00 0.00 3.67
2206 2260 0.393448 TAACACCAGTACGCCAGCAA 59.607 50.000 0.00 0.00 0.00 3.91
2219 2276 2.554032 ACAGCTCAGCACAATTAACACC 59.446 45.455 0.00 0.00 0.00 4.16
2280 2337 1.483827 CAGGAAGAGCAGCCATCACTA 59.516 52.381 0.00 0.00 0.00 2.74
2282 2339 0.035630 ACAGGAAGAGCAGCCATCAC 60.036 55.000 0.00 0.00 0.00 3.06
2328 2385 1.153086 GCCGTCAGCCAATCCATCT 60.153 57.895 0.00 0.00 34.35 2.90
2359 2416 3.892588 ACGAAAAAGGGTATCAAAGGCAA 59.107 39.130 0.00 0.00 0.00 4.52
2362 2419 4.082408 GGGAACGAAAAAGGGTATCAAAGG 60.082 45.833 0.00 0.00 0.00 3.11
2371 2428 0.240145 GCGAAGGGAACGAAAAAGGG 59.760 55.000 0.00 0.00 0.00 3.95
2388 2445 2.804828 AAGCTCCCCTTTTCCTCGCG 62.805 60.000 0.00 0.00 0.00 5.87
2390 2447 1.271379 TGAAAGCTCCCCTTTTCCTCG 60.271 52.381 0.00 0.00 43.64 4.63
2425 2482 5.578157 AATAAACCCTGTGTGTAGTCCTT 57.422 39.130 0.00 0.00 0.00 3.36
2433 2490 4.744631 GCAGTGAAAAATAAACCCTGTGTG 59.255 41.667 0.00 0.00 0.00 3.82
2435 2492 5.200368 AGCAGTGAAAAATAAACCCTGTG 57.800 39.130 0.00 0.00 0.00 3.66
2470 2529 5.273170 CACCAAATATGTCGGCAAATACAG 58.727 41.667 0.00 0.00 0.00 2.74
2545 2604 1.620822 CTTAAAGCCAAGCCACCTGT 58.379 50.000 0.00 0.00 0.00 4.00
2547 2606 0.777446 TCCTTAAAGCCAAGCCACCT 59.223 50.000 0.00 0.00 0.00 4.00
2548 2607 1.852633 ATCCTTAAAGCCAAGCCACC 58.147 50.000 0.00 0.00 0.00 4.61
2549 2608 6.901081 ATATAATCCTTAAAGCCAAGCCAC 57.099 37.500 0.00 0.00 0.00 5.01
2572 2656 9.513906 CACTTGATCCTCTGATTACTCTCTATA 57.486 37.037 0.00 0.00 0.00 1.31
2573 2657 7.039784 GCACTTGATCCTCTGATTACTCTCTAT 60.040 40.741 0.00 0.00 0.00 1.98
2574 2658 6.264292 GCACTTGATCCTCTGATTACTCTCTA 59.736 42.308 0.00 0.00 0.00 2.43
2575 2659 5.068987 GCACTTGATCCTCTGATTACTCTCT 59.931 44.000 0.00 0.00 0.00 3.10
2576 2660 5.068987 AGCACTTGATCCTCTGATTACTCTC 59.931 44.000 0.00 0.00 0.00 3.20
2589 2673 0.462759 CTTCCCCGAGCACTTGATCC 60.463 60.000 0.00 0.00 0.00 3.36
2590 2674 0.462759 CCTTCCCCGAGCACTTGATC 60.463 60.000 0.00 0.00 0.00 2.92
2603 2687 3.771160 TCGCTTCGAGGCCTTCCC 61.771 66.667 14.49 0.00 0.00 3.97
2610 2694 2.703798 TTACGGGGTCGCTTCGAGG 61.704 63.158 0.00 0.00 40.63 4.63
2614 2698 2.098831 GCTGTTACGGGGTCGCTTC 61.099 63.158 0.00 0.00 40.63 3.86
2615 2699 2.047560 GCTGTTACGGGGTCGCTT 60.048 61.111 0.00 0.00 40.63 4.68
2654 2740 1.112113 TCCTAAGCACGACCTCATCC 58.888 55.000 0.00 0.00 0.00 3.51
2662 2758 0.800683 CGCACGAATCCTAAGCACGA 60.801 55.000 0.00 0.00 0.00 4.35
2683 2779 6.466812 TCATGTGTCTAGATTCTTGCTTTGA 58.533 36.000 0.00 0.00 0.00 2.69
2706 2802 7.041372 TGTTCATCACATCATCATCATCACATC 60.041 37.037 0.00 0.00 0.00 3.06
2707 2803 6.770785 TGTTCATCACATCATCATCATCACAT 59.229 34.615 0.00 0.00 0.00 3.21
2708 2804 6.116806 TGTTCATCACATCATCATCATCACA 58.883 36.000 0.00 0.00 0.00 3.58
2709 2805 6.613755 TGTTCATCACATCATCATCATCAC 57.386 37.500 0.00 0.00 0.00 3.06
2710 2806 7.817418 ATTGTTCATCACATCATCATCATCA 57.183 32.000 0.00 0.00 34.43 3.07
2711 2807 9.827411 CTTATTGTTCATCACATCATCATCATC 57.173 33.333 0.00 0.00 34.43 2.92
2712 2808 9.569122 TCTTATTGTTCATCACATCATCATCAT 57.431 29.630 0.00 0.00 34.43 2.45
2713 2809 8.967664 TCTTATTGTTCATCACATCATCATCA 57.032 30.769 0.00 0.00 34.43 3.07
2744 2840 9.031537 TGGATTGATTAGTATACACGGATATGT 57.968 33.333 5.50 0.00 36.56 2.29


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

AutoCloner maintained by Alex Coulton.