Multiple sequence alignment - TraesCS3A01G041200

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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 TraesCS3A01G041200 chr3A 100.000 3053 0 0 1 3053 21786343 21789395 0.000000e+00 5638.0
1 TraesCS3A01G041200 chr3D 90.142 3033 191 53 2 3004 14556868 14553914 0.000000e+00 3845.0
2 TraesCS3A01G041200 chr3D 100.000 33 0 0 2760 2792 14545616 14545584 9.140000e-06 62.1
3 TraesCS3A01G041200 chr3B 89.402 2123 140 46 1 2084 21772116 21770040 0.000000e+00 2595.0
4 TraesCS3A01G041200 chr3B 90.839 775 40 17 2086 2836 21769747 21768980 0.000000e+00 1009.0
5 TraesCS3A01G041200 chr7A 92.982 456 21 8 2000 2455 532123299 532122855 0.000000e+00 654.0
6 TraesCS3A01G041200 chr1A 93.961 414 21 3 1997 2409 44861242 44861652 9.300000e-175 623.0
7 TraesCS3A01G041200 chr2D 98.182 55 0 1 400 453 6095182 6095128 9.010000e-16 95.3


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 TraesCS3A01G041200 chr3A 21786343 21789395 3052 False 5638 5638 100.0000 1 3053 1 chr3A.!!$F1 3052
1 TraesCS3A01G041200 chr3D 14553914 14556868 2954 True 3845 3845 90.1420 2 3004 1 chr3D.!!$R2 3002
2 TraesCS3A01G041200 chr3B 21768980 21772116 3136 True 1802 2595 90.1205 1 2836 2 chr3B.!!$R1 2835

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
115 116 0.039798 TCACGTTCGCTACACTGACC 60.040 55.0 0.00 0.0 0.00 4.02 F
474 484 0.173708 CCGTCGGGGAAGAAGAAGAG 59.826 60.0 2.34 0.0 38.47 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 1769 0.606401 GTGTGGACACCATCACAGGG 60.606 60.0 13.93 0.0 43.45 4.45 R
2200 2542 0.395862 TGCTCGGGAGACTAGGGAAG 60.396 60.0 0.00 0.0 33.60 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
86 87 1.002142 TCTGCGATACGATGGGTTACG 60.002 52.381 0.00 0.00 0.00 3.18
87 88 0.595567 TGCGATACGATGGGTTACGC 60.596 55.000 0.00 0.00 45.28 4.42
115 116 0.039798 TCACGTTCGCTACACTGACC 60.040 55.000 0.00 0.00 0.00 4.02
156 157 4.742201 CCCGCGTGTCAGTCTGGG 62.742 72.222 4.92 0.00 0.00 4.45
165 166 1.606601 TCAGTCTGGGACGTGGAGG 60.607 63.158 0.00 0.00 37.67 4.30
200 201 1.151777 ACAGCGCCCGAATATCAACG 61.152 55.000 2.29 0.00 0.00 4.10
204 205 1.647084 GCCCGAATATCAACGGTGC 59.353 57.895 0.00 0.00 46.53 5.01
224 225 2.747446 GCCACTTTCCATTTCTTCGCTA 59.253 45.455 0.00 0.00 0.00 4.26
225 226 3.378427 GCCACTTTCCATTTCTTCGCTAT 59.622 43.478 0.00 0.00 0.00 2.97
226 227 4.731773 GCCACTTTCCATTTCTTCGCTATG 60.732 45.833 0.00 0.00 0.00 2.23
254 255 4.557605 GCAATGACATGCGGGCCG 62.558 66.667 24.35 24.35 36.45 6.13
375 376 2.595750 ATATCGGAGGAGGAGACCAG 57.404 55.000 0.00 0.00 0.00 4.00
382 383 2.266055 GAGGAGACCAGCCCAACG 59.734 66.667 0.00 0.00 0.00 4.10
474 484 0.173708 CCGTCGGGGAAGAAGAAGAG 59.826 60.000 2.34 0.00 38.47 2.85
478 488 0.537653 CGGGGAAGAAGAAGAGGACC 59.462 60.000 0.00 0.00 0.00 4.46
479 489 1.657804 GGGGAAGAAGAAGAGGACCA 58.342 55.000 0.00 0.00 0.00 4.02
481 491 1.978580 GGGAAGAAGAAGAGGACCACA 59.021 52.381 0.00 0.00 0.00 4.17
528 542 2.411535 CGCCGATCTGGTGGTAGTA 58.588 57.895 8.67 0.00 44.97 1.82
576 593 3.371063 GTCGTCCTCCTCCACGCA 61.371 66.667 0.00 0.00 35.93 5.24
651 668 1.517257 GTCGATGCTCAGGTCCGTG 60.517 63.158 0.00 0.00 0.00 4.94
678 697 2.536897 CCCCCTCCCTTTTCCCCA 60.537 66.667 0.00 0.00 0.00 4.96
721 740 3.431725 GCCCTTTTCGGCTCCGTG 61.432 66.667 8.28 0.00 46.10 4.94
722 741 2.345991 CCCTTTTCGGCTCCGTGA 59.654 61.111 8.28 0.00 40.74 4.35
723 742 1.741770 CCCTTTTCGGCTCCGTGAG 60.742 63.158 8.28 5.08 40.74 3.51
769 803 3.428045 GGGTTTTGATGGATTCTTGCTCG 60.428 47.826 0.00 0.00 0.00 5.03
771 805 4.321230 GGTTTTGATGGATTCTTGCTCGTT 60.321 41.667 0.00 0.00 0.00 3.85
772 806 5.222631 GTTTTGATGGATTCTTGCTCGTTT 58.777 37.500 0.00 0.00 0.00 3.60
773 807 4.685169 TTGATGGATTCTTGCTCGTTTC 57.315 40.909 0.00 0.00 0.00 2.78
774 808 3.942829 TGATGGATTCTTGCTCGTTTCT 58.057 40.909 0.00 0.00 0.00 2.52
862 899 1.587043 TTGCGAGGAGACTGACGGAG 61.587 60.000 0.00 0.00 44.43 4.63
954 992 5.023452 AGAGTTTTTCCCCTTCAGTTTTGT 58.977 37.500 0.00 0.00 0.00 2.83
958 996 6.439375 AGTTTTTCCCCTTCAGTTTTGTTAGT 59.561 34.615 0.00 0.00 0.00 2.24
959 997 6.459670 TTTTCCCCTTCAGTTTTGTTAGTC 57.540 37.500 0.00 0.00 0.00 2.59
987 1025 6.551601 AGTCAGTGTTAGAGGAAGAAGAAGAA 59.448 38.462 0.00 0.00 0.00 2.52
992 1030 5.046950 TGTTAGAGGAAGAAGAAGAAGAGGC 60.047 44.000 0.00 0.00 0.00 4.70
997 1035 3.369366 GGAAGAAGAAGAAGAGGCAGGAG 60.369 52.174 0.00 0.00 0.00 3.69
1052 1090 2.347490 GGACGCTCTGGCCAAGAA 59.653 61.111 7.01 0.00 33.37 2.52
1054 1092 1.293498 GACGCTCTGGCCAAGAAGA 59.707 57.895 7.01 0.00 33.37 2.87
1080 1118 2.040544 CAAGATGCTCGCCGGGTTT 61.041 57.895 2.18 0.00 0.00 3.27
1647 1694 4.838152 TCGGCTGCTCCATTCGCC 62.838 66.667 0.00 0.00 39.14 5.54
1677 1724 1.254284 CGTCCTCTGTCCTGGAAGCT 61.254 60.000 0.00 0.00 33.72 3.74
1722 1769 2.888863 CCTGAGCCGACTCCAGTC 59.111 66.667 0.00 0.00 42.74 3.51
1725 1772 2.363147 GAGCCGACTCCAGTCCCT 60.363 66.667 1.01 0.00 41.86 4.20
1728 1775 2.973899 CCGACTCCAGTCCCTGTG 59.026 66.667 1.01 0.00 41.86 3.66
1730 1777 0.972983 CCGACTCCAGTCCCTGTGAT 60.973 60.000 1.01 0.00 41.86 3.06
1731 1778 0.174389 CGACTCCAGTCCCTGTGATG 59.826 60.000 1.01 0.00 41.86 3.07
1732 1779 0.539051 GACTCCAGTCCCTGTGATGG 59.461 60.000 0.00 0.00 39.07 3.51
1733 1780 0.178891 ACTCCAGTCCCTGTGATGGT 60.179 55.000 0.00 0.00 34.32 3.55
1734 1781 0.251354 CTCCAGTCCCTGTGATGGTG 59.749 60.000 0.00 0.00 34.32 4.17
1735 1782 0.473694 TCCAGTCCCTGTGATGGTGT 60.474 55.000 0.00 0.00 34.32 4.16
1736 1783 0.036010 CCAGTCCCTGTGATGGTGTC 60.036 60.000 0.00 0.00 0.00 3.67
1737 1784 0.036010 CAGTCCCTGTGATGGTGTCC 60.036 60.000 0.00 0.00 0.00 4.02
1738 1785 0.473694 AGTCCCTGTGATGGTGTCCA 60.474 55.000 0.00 0.00 38.19 4.02
1739 1786 0.321653 GTCCCTGTGATGGTGTCCAC 60.322 60.000 0.00 0.00 35.80 4.02
1740 1787 0.766288 TCCCTGTGATGGTGTCCACA 60.766 55.000 0.00 0.00 40.56 4.17
1741 1788 0.606401 CCCTGTGATGGTGTCCACAC 60.606 60.000 0.85 0.85 45.72 3.82
1806 1853 2.541466 CCAGAGTTCTACCAGGACCTT 58.459 52.381 0.00 0.00 0.00 3.50
1833 1880 0.674895 GTCTTCAGCTGCCGGACATT 60.675 55.000 20.48 0.00 0.00 2.71
1839 1886 2.350895 CTGCCGGACATTGACCCA 59.649 61.111 5.05 0.00 0.00 4.51
1986 2033 2.202453 GGCGACGACTTCCTCGAC 60.202 66.667 0.00 0.00 46.14 4.20
2072 2119 7.172703 CGTGTGAATTAAGAGAGGTTTAAGGTT 59.827 37.037 0.00 0.00 0.00 3.50
2200 2542 0.036732 TGCCCAAGATGGTGTCTGTC 59.963 55.000 0.00 0.00 37.23 3.51
2260 2604 6.404293 GGTGAGAGTGAGTGAGAGAGTATTTC 60.404 46.154 0.00 0.00 0.00 2.17
2497 2848 6.237901 TGTCTTACCTGCTCATTTGTATGTT 58.762 36.000 0.00 0.00 33.34 2.71
2499 2850 7.094805 TGTCTTACCTGCTCATTTGTATGTTTC 60.095 37.037 0.00 0.00 33.34 2.78
2507 2861 6.035650 TGCTCATTTGTATGTTTCGTACTAGC 59.964 38.462 0.00 0.00 33.34 3.42
2593 2948 5.971763 TGGATGTTGTTTAGCTTGTTTTGT 58.028 33.333 0.00 0.00 0.00 2.83
2594 2949 7.101652 TGGATGTTGTTTAGCTTGTTTTGTA 57.898 32.000 0.00 0.00 0.00 2.41
2595 2950 6.975772 TGGATGTTGTTTAGCTTGTTTTGTAC 59.024 34.615 0.00 0.00 0.00 2.90
2596 2951 6.141685 GGATGTTGTTTAGCTTGTTTTGTACG 59.858 38.462 0.00 0.00 0.00 3.67
2597 2952 5.333513 TGTTGTTTAGCTTGTTTTGTACGG 58.666 37.500 0.00 0.00 0.00 4.02
2598 2953 5.123502 TGTTGTTTAGCTTGTTTTGTACGGA 59.876 36.000 0.00 0.00 0.00 4.69
2599 2954 5.412526 TGTTTAGCTTGTTTTGTACGGAG 57.587 39.130 0.00 0.00 0.00 4.63
2620 2978 9.850576 ACGGAGTATGTACCCTAGTACTATGCC 62.851 48.148 2.33 0.00 44.71 4.40
2637 2995 5.940470 ACTATGCCGAAAAAGAAAGATGAGT 59.060 36.000 0.00 0.00 0.00 3.41
2639 2997 6.817765 ATGCCGAAAAAGAAAGATGAGTTA 57.182 33.333 0.00 0.00 0.00 2.24
2676 3034 3.251972 CCACTTCCTGCTCTTTTTGAGAC 59.748 47.826 0.00 0.00 45.39 3.36
2707 3065 3.339253 ACTGTGCTCATCTGTATGCAA 57.661 42.857 0.00 0.00 37.17 4.08
2750 3111 4.641541 TGGATGCTCATTTGTATCTTGTGG 59.358 41.667 0.00 0.00 31.28 4.17
2800 3161 1.623811 ACCAGTGGTGTTAGGCACTAG 59.376 52.381 15.86 0.00 46.86 2.57
2820 3182 1.136305 GTGCTATGGTCGTGGAGCTAA 59.864 52.381 0.00 0.00 35.89 3.09
2839 3209 6.404712 GCTAATCTAGTAGCAACGTTTGTT 57.595 37.500 0.00 0.00 44.94 2.83
2841 3211 7.295930 GCTAATCTAGTAGCAACGTTTGTTTT 58.704 34.615 0.00 0.00 44.94 2.43
2846 3216 8.597662 TCTAGTAGCAACGTTTGTTTTTATCT 57.402 30.769 0.00 0.00 35.72 1.98
2848 3218 9.659830 CTAGTAGCAACGTTTGTTTTTATCTTT 57.340 29.630 0.00 0.00 35.72 2.52
2854 3224 8.539674 GCAACGTTTGTTTTTATCTTTCATTCT 58.460 29.630 0.00 0.00 35.72 2.40
2872 3242 9.912634 TTTCATTCTATTGGATGTTTTCAACTC 57.087 29.630 0.00 0.00 0.00 3.01
2875 3245 7.504924 TTCTATTGGATGTTTTCAACTCGTT 57.495 32.000 0.00 0.00 0.00 3.85
2899 3269 7.034685 TGAATGCATTATGTGAGAATCCTTG 57.965 36.000 12.97 0.00 0.00 3.61
2900 3270 6.040054 TGAATGCATTATGTGAGAATCCTTGG 59.960 38.462 12.97 0.00 0.00 3.61
2916 3286 2.619849 CCTTGGAGGATTGATGCTGTGT 60.620 50.000 0.00 0.00 37.67 3.72
2934 3304 7.251704 GCTGTGTAGCTCATTTTGTATGTAT 57.748 36.000 0.00 0.00 46.57 2.29
2939 3309 8.491152 GTGTAGCTCATTTTGTATGTATGCTAG 58.509 37.037 0.00 0.00 32.28 3.42
2952 3325 8.793592 TGTATGTATGCTAGTACTATGGTGAAG 58.206 37.037 2.33 0.00 0.00 3.02
2965 3338 6.525629 ACTATGGTGAAGTGCTATTCATACC 58.474 40.000 7.31 6.01 41.05 2.73
2970 3343 6.491745 TGGTGAAGTGCTATTCATACCAAAAA 59.508 34.615 7.31 0.00 41.05 1.94
2996 3371 0.038166 TCCTGGGTGGAATGCAACTC 59.962 55.000 0.00 0.00 42.94 3.01
3004 3379 3.521560 GTGGAATGCAACTCGTGAGATA 58.478 45.455 3.44 0.00 40.84 1.98
3005 3380 3.932710 GTGGAATGCAACTCGTGAGATAA 59.067 43.478 3.44 0.00 40.84 1.75
3006 3381 4.391830 GTGGAATGCAACTCGTGAGATAAA 59.608 41.667 3.44 0.00 40.84 1.40
3007 3382 4.391830 TGGAATGCAACTCGTGAGATAAAC 59.608 41.667 3.44 0.00 40.84 2.01
3008 3383 4.391830 GGAATGCAACTCGTGAGATAAACA 59.608 41.667 3.44 0.00 40.84 2.83
3009 3384 5.065218 GGAATGCAACTCGTGAGATAAACAT 59.935 40.000 3.44 0.00 40.84 2.71
3010 3385 6.403636 GGAATGCAACTCGTGAGATAAACATT 60.404 38.462 3.44 6.10 40.84 2.71
3011 3386 5.281693 TGCAACTCGTGAGATAAACATTG 57.718 39.130 3.44 0.00 40.84 2.82
3012 3387 4.994217 TGCAACTCGTGAGATAAACATTGA 59.006 37.500 3.44 0.00 40.84 2.57
3013 3388 5.643348 TGCAACTCGTGAGATAAACATTGAT 59.357 36.000 3.44 0.00 40.84 2.57
3014 3389 6.149308 TGCAACTCGTGAGATAAACATTGATT 59.851 34.615 3.44 0.00 40.84 2.57
3015 3390 6.467047 GCAACTCGTGAGATAAACATTGATTG 59.533 38.462 3.44 0.00 40.84 2.67
3016 3391 7.624134 GCAACTCGTGAGATAAACATTGATTGA 60.624 37.037 3.44 0.00 40.84 2.57
3017 3392 7.531280 ACTCGTGAGATAAACATTGATTGAG 57.469 36.000 3.44 0.00 40.84 3.02
3018 3393 6.536582 ACTCGTGAGATAAACATTGATTGAGG 59.463 38.462 3.44 0.00 40.84 3.86
3019 3394 6.639563 TCGTGAGATAAACATTGATTGAGGA 58.360 36.000 0.00 0.00 33.31 3.71
3020 3395 7.275183 TCGTGAGATAAACATTGATTGAGGAT 58.725 34.615 0.00 0.00 33.31 3.24
3021 3396 7.225341 TCGTGAGATAAACATTGATTGAGGATG 59.775 37.037 0.00 0.00 33.31 3.51
3022 3397 7.137426 GTGAGATAAACATTGATTGAGGATGC 58.863 38.462 0.00 0.00 0.00 3.91
3023 3398 6.017687 TGAGATAAACATTGATTGAGGATGCG 60.018 38.462 0.00 0.00 0.00 4.73
3024 3399 3.788333 AAACATTGATTGAGGATGCGG 57.212 42.857 0.00 0.00 0.00 5.69
3025 3400 2.425143 ACATTGATTGAGGATGCGGT 57.575 45.000 0.00 0.00 0.00 5.68
3026 3401 2.019249 ACATTGATTGAGGATGCGGTG 58.981 47.619 0.00 0.00 0.00 4.94
3027 3402 1.027357 ATTGATTGAGGATGCGGTGC 58.973 50.000 0.00 0.00 0.00 5.01
3028 3403 0.322366 TTGATTGAGGATGCGGTGCA 60.322 50.000 0.00 0.00 44.86 4.57
3029 3404 0.745486 TGATTGAGGATGCGGTGCAG 60.745 55.000 0.00 0.00 43.65 4.41
3030 3405 2.056481 GATTGAGGATGCGGTGCAGC 62.056 60.000 5.64 5.64 43.65 5.25
3031 3406 2.547640 ATTGAGGATGCGGTGCAGCT 62.548 55.000 14.92 0.00 44.90 4.24
3032 3407 1.898330 TTGAGGATGCGGTGCAGCTA 61.898 55.000 14.92 3.11 44.90 3.32
3033 3408 1.153369 GAGGATGCGGTGCAGCTAA 60.153 57.895 14.92 1.80 44.90 3.09
3034 3409 0.744414 GAGGATGCGGTGCAGCTAAA 60.744 55.000 14.92 0.00 44.90 1.85
3035 3410 0.107017 AGGATGCGGTGCAGCTAAAT 60.107 50.000 14.92 4.47 44.90 1.40
3036 3411 0.740737 GGATGCGGTGCAGCTAAATT 59.259 50.000 14.92 0.00 44.90 1.82
3037 3412 1.134946 GGATGCGGTGCAGCTAAATTT 59.865 47.619 14.92 0.00 44.90 1.82
3038 3413 2.187707 GATGCGGTGCAGCTAAATTTG 58.812 47.619 14.92 0.00 43.65 2.32
3039 3414 0.958091 TGCGGTGCAGCTAAATTTGT 59.042 45.000 14.92 0.00 38.13 2.83
3040 3415 1.339610 TGCGGTGCAGCTAAATTTGTT 59.660 42.857 14.92 0.00 38.13 2.83
3041 3416 2.554462 TGCGGTGCAGCTAAATTTGTTA 59.446 40.909 14.92 0.00 38.13 2.41
3042 3417 2.914838 GCGGTGCAGCTAAATTTGTTAC 59.085 45.455 14.92 0.00 0.00 2.50
3043 3418 3.498082 CGGTGCAGCTAAATTTGTTACC 58.502 45.455 14.92 0.65 0.00 2.85
3044 3419 3.190535 CGGTGCAGCTAAATTTGTTACCT 59.809 43.478 14.92 0.00 0.00 3.08
3045 3420 4.485163 GGTGCAGCTAAATTTGTTACCTG 58.515 43.478 9.07 1.68 0.00 4.00
3046 3421 3.920412 GTGCAGCTAAATTTGTTACCTGC 59.080 43.478 16.50 16.50 43.17 4.85
3047 3422 4.173036 GCAGCTAAATTTGTTACCTGCA 57.827 40.909 17.57 0.00 42.60 4.41
3048 3423 3.920412 GCAGCTAAATTTGTTACCTGCAC 59.080 43.478 17.57 0.00 42.60 4.57
3049 3424 4.558496 GCAGCTAAATTTGTTACCTGCACA 60.558 41.667 17.57 0.00 42.60 4.57
3050 3425 5.527951 CAGCTAAATTTGTTACCTGCACAA 58.472 37.500 0.00 0.00 32.16 3.33
3051 3426 6.158598 CAGCTAAATTTGTTACCTGCACAAT 58.841 36.000 0.00 0.00 34.13 2.71
3052 3427 6.646240 CAGCTAAATTTGTTACCTGCACAATT 59.354 34.615 0.00 0.00 34.13 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.729862 CGCGCGCCCATCTACTAC 60.730 66.667 27.72 0.00 0.00 2.73
14 15 3.214123 ACGCGCGCCCATCTACTA 61.214 61.111 32.58 0.00 0.00 1.82
15 16 4.873129 CACGCGCGCCCATCTACT 62.873 66.667 32.58 3.21 0.00 2.57
65 66 2.662700 GTAACCCATCGTATCGCAGAG 58.337 52.381 0.00 0.00 43.63 3.35
95 96 1.402456 GGTCAGTGTAGCGAACGTGAT 60.402 52.381 0.00 0.00 0.00 3.06
96 97 0.039798 GGTCAGTGTAGCGAACGTGA 60.040 55.000 0.00 0.00 0.00 4.35
144 145 1.006102 CCACGTCCCAGACTGACAC 60.006 63.158 3.32 0.00 32.91 3.67
149 150 2.997897 GCCTCCACGTCCCAGACT 60.998 66.667 0.00 0.00 0.00 3.24
156 157 2.685387 CTAGCCATCGCCTCCACGTC 62.685 65.000 0.00 0.00 34.57 4.34
180 181 0.304705 GTTGATATTCGGGCGCTGTG 59.695 55.000 7.64 0.00 0.00 3.66
200 201 2.351738 CGAAGAAATGGAAAGTGGCACC 60.352 50.000 15.27 0.00 0.00 5.01
204 205 4.731773 GCATAGCGAAGAAATGGAAAGTGG 60.732 45.833 0.00 0.00 0.00 4.00
382 383 2.402572 GGCGAGAGGAGCAAAAGGC 61.403 63.158 0.00 0.00 45.30 4.35
474 484 0.452987 TATACGAGCGTGTGTGGTCC 59.547 55.000 5.69 0.00 32.83 4.46
478 488 3.066369 AGACATATACGAGCGTGTGTG 57.934 47.619 13.15 13.15 35.27 3.82
479 489 3.377485 AGAAGACATATACGAGCGTGTGT 59.623 43.478 5.69 7.83 0.00 3.72
481 491 4.352039 CAAGAAGACATATACGAGCGTGT 58.648 43.478 5.69 1.25 0.00 4.49
668 687 1.627864 AATTGACGGTGGGGAAAAGG 58.372 50.000 0.00 0.00 0.00 3.11
669 688 2.890945 AGAAATTGACGGTGGGGAAAAG 59.109 45.455 0.00 0.00 0.00 2.27
670 689 2.888414 GAGAAATTGACGGTGGGGAAAA 59.112 45.455 0.00 0.00 0.00 2.29
671 690 2.158593 TGAGAAATTGACGGTGGGGAAA 60.159 45.455 0.00 0.00 0.00 3.13
672 691 1.422024 TGAGAAATTGACGGTGGGGAA 59.578 47.619 0.00 0.00 0.00 3.97
678 697 5.689819 CGAAAAAGATGAGAAATTGACGGT 58.310 37.500 0.00 0.00 0.00 4.83
715 734 1.440893 CAGATCTGGGCTCACGGAG 59.559 63.158 15.38 0.00 0.00 4.63
716 735 2.060383 CCAGATCTGGGCTCACGGA 61.060 63.158 31.14 0.00 46.81 4.69
717 736 2.503061 CCAGATCTGGGCTCACGG 59.497 66.667 31.14 5.46 46.81 4.94
769 803 1.000938 CCCTGCAGCAACAAGAGAAAC 60.001 52.381 8.66 0.00 0.00 2.78
771 805 0.473755 TCCCTGCAGCAACAAGAGAA 59.526 50.000 8.66 0.00 0.00 2.87
772 806 0.250467 GTCCCTGCAGCAACAAGAGA 60.250 55.000 8.66 0.00 0.00 3.10
773 807 1.572085 CGTCCCTGCAGCAACAAGAG 61.572 60.000 8.66 0.00 0.00 2.85
774 808 1.597854 CGTCCCTGCAGCAACAAGA 60.598 57.895 8.66 0.00 0.00 3.02
954 992 5.877491 TCCTCTAACACTGACTGAGACTAA 58.123 41.667 0.00 0.00 0.00 2.24
958 996 4.986783 TCTTCCTCTAACACTGACTGAGA 58.013 43.478 0.00 0.00 0.00 3.27
959 997 5.475220 TCTTCTTCCTCTAACACTGACTGAG 59.525 44.000 0.00 0.00 0.00 3.35
1052 1090 1.066573 CGAGCATCTTGGTCTTGGTCT 60.067 52.381 5.31 0.00 42.30 3.85
1054 1092 0.674895 GCGAGCATCTTGGTCTTGGT 60.675 55.000 5.31 0.00 42.30 3.67
1095 1133 4.847444 GGCTTGGAGAGAGCGGCC 62.847 72.222 0.00 0.00 41.03 6.13
1283 1327 2.811101 CAAACAACTTGGCCGGCA 59.189 55.556 30.85 12.04 0.00 5.69
1294 1338 1.754621 TGACCGGCTTGGCAAACAA 60.755 52.632 0.00 0.00 43.94 2.83
1565 1609 2.108157 TTGTTGACGCAGCCGACT 59.892 55.556 0.00 0.00 38.29 4.18
1722 1769 0.606401 GTGTGGACACCATCACAGGG 60.606 60.000 13.93 0.00 43.45 4.45
1755 1802 4.299547 TGCGCAGTCTCAGCCGTT 62.300 61.111 5.66 0.00 0.00 4.44
1806 1853 1.005748 CAGCTGAAGACCACGCAGA 60.006 57.895 8.42 0.00 0.00 4.26
1833 1880 1.002624 GCGGAAGTCCATTGGGTCA 60.003 57.895 2.09 0.00 35.14 4.02
1944 1991 1.607801 CGAGGTCCATGTCCAGCTCA 61.608 60.000 13.25 0.00 37.04 4.26
1986 2033 2.338015 AAAGTCGCAGCCAGGCATG 61.338 57.895 15.80 10.29 0.00 4.06
2072 2119 8.856153 TCACACCAGCATTACTTAAAGATAAA 57.144 30.769 0.00 0.00 0.00 1.40
2200 2542 0.395862 TGCTCGGGAGACTAGGGAAG 60.396 60.000 0.00 0.00 33.60 3.46
2442 2793 3.638160 TCAAAGAAAGATGGCAAGCAAGT 59.362 39.130 0.00 0.00 0.00 3.16
2497 2848 2.671351 GCACTTCAGCAGCTAGTACGAA 60.671 50.000 0.00 0.00 0.00 3.85
2499 2850 1.135257 AGCACTTCAGCAGCTAGTACG 60.135 52.381 0.00 0.00 36.73 3.67
2507 2861 1.671328 CATCCATCAGCACTTCAGCAG 59.329 52.381 0.00 0.00 36.85 4.24
2571 2926 6.141685 CGTACAAAACAAGCTAAACAACATCC 59.858 38.462 0.00 0.00 0.00 3.51
2586 2941 4.527816 AGGGTACATACTCCGTACAAAACA 59.472 41.667 0.00 0.00 40.84 2.83
2620 2978 8.506140 TGCATTTAACTCATCTTTCTTTTTCG 57.494 30.769 0.00 0.00 0.00 3.46
2676 3034 1.889170 TGAGCACAGTACAGAGACCAG 59.111 52.381 0.00 0.00 0.00 4.00
2707 3065 3.131396 CAAGACGGTTCAGCAAGTAAGT 58.869 45.455 0.00 0.00 0.00 2.24
2750 3111 3.923017 ACAAAATTAGCTCCAGCACAC 57.077 42.857 0.48 0.00 45.16 3.82
2800 3161 0.744874 TAGCTCCACGACCATAGCAC 59.255 55.000 0.00 0.00 37.44 4.40
2807 3168 3.058085 GCTACTAGATTAGCTCCACGACC 60.058 52.174 0.00 0.00 41.24 4.79
2820 3182 9.216117 AGATAAAAACAAACGTTGCTACTAGAT 57.784 29.630 0.00 0.00 0.00 1.98
2872 3242 5.911280 GGATTCTCACATAATGCATTCAACG 59.089 40.000 16.86 5.53 0.00 4.10
2875 3245 6.040054 CCAAGGATTCTCACATAATGCATTCA 59.960 38.462 16.86 3.12 0.00 2.57
2879 3249 5.114764 TCCAAGGATTCTCACATAATGCA 57.885 39.130 0.00 0.00 0.00 3.96
2916 3286 9.692749 GTACTAGCATACATACAAAATGAGCTA 57.307 33.333 0.00 0.00 31.79 3.32
2934 3304 4.023980 AGCACTTCACCATAGTACTAGCA 58.976 43.478 8.85 0.00 0.00 3.49
2939 3309 7.599245 GGTATGAATAGCACTTCACCATAGTAC 59.401 40.741 3.41 2.41 37.93 2.73
2979 3352 0.606401 ACGAGTTGCATTCCACCCAG 60.606 55.000 0.00 0.00 0.00 4.45
2980 3353 0.888736 CACGAGTTGCATTCCACCCA 60.889 55.000 0.00 0.00 0.00 4.51
2981 3354 0.605319 TCACGAGTTGCATTCCACCC 60.605 55.000 0.00 0.00 0.00 4.61
2982 3355 0.798776 CTCACGAGTTGCATTCCACC 59.201 55.000 0.00 0.00 0.00 4.61
2984 3357 2.768253 ATCTCACGAGTTGCATTCCA 57.232 45.000 0.00 0.00 0.00 3.53
2985 3358 4.391830 TGTTTATCTCACGAGTTGCATTCC 59.608 41.667 0.00 0.00 0.00 3.01
2996 3371 6.908870 TCCTCAATCAATGTTTATCTCACG 57.091 37.500 0.00 0.00 0.00 4.35
3004 3379 3.091545 ACCGCATCCTCAATCAATGTTT 58.908 40.909 0.00 0.00 0.00 2.83
3005 3380 2.424601 CACCGCATCCTCAATCAATGTT 59.575 45.455 0.00 0.00 0.00 2.71
3006 3381 2.019249 CACCGCATCCTCAATCAATGT 58.981 47.619 0.00 0.00 0.00 2.71
3007 3382 1.268896 GCACCGCATCCTCAATCAATG 60.269 52.381 0.00 0.00 0.00 2.82
3008 3383 1.027357 GCACCGCATCCTCAATCAAT 58.973 50.000 0.00 0.00 0.00 2.57
3009 3384 0.322366 TGCACCGCATCCTCAATCAA 60.322 50.000 0.00 0.00 31.71 2.57
3010 3385 0.745486 CTGCACCGCATCCTCAATCA 60.745 55.000 0.00 0.00 38.13 2.57
3011 3386 2.020131 CTGCACCGCATCCTCAATC 58.980 57.895 0.00 0.00 38.13 2.67
3012 3387 2.117156 GCTGCACCGCATCCTCAAT 61.117 57.895 0.00 0.00 38.13 2.57
3013 3388 1.898330 TAGCTGCACCGCATCCTCAA 61.898 55.000 1.02 0.00 38.13 3.02
3014 3389 1.898330 TTAGCTGCACCGCATCCTCA 61.898 55.000 1.02 0.00 38.13 3.86
3015 3390 0.744414 TTTAGCTGCACCGCATCCTC 60.744 55.000 1.02 0.00 38.13 3.71
3016 3391 0.107017 ATTTAGCTGCACCGCATCCT 60.107 50.000 1.02 0.00 38.13 3.24
3017 3392 0.740737 AATTTAGCTGCACCGCATCC 59.259 50.000 1.02 0.00 38.13 3.51
3018 3393 2.187707 CAAATTTAGCTGCACCGCATC 58.812 47.619 1.02 0.00 38.13 3.91
3019 3394 1.545582 ACAAATTTAGCTGCACCGCAT 59.454 42.857 1.02 0.00 38.13 4.73
3020 3395 0.958091 ACAAATTTAGCTGCACCGCA 59.042 45.000 1.02 0.00 36.92 5.69
3021 3396 2.064573 AACAAATTTAGCTGCACCGC 57.935 45.000 1.02 0.00 0.00 5.68
3022 3397 3.190535 AGGTAACAAATTTAGCTGCACCG 59.809 43.478 1.02 0.00 41.41 4.94
3023 3398 4.485163 CAGGTAACAAATTTAGCTGCACC 58.515 43.478 1.02 0.00 41.58 5.01
3028 3403 5.782893 TTGTGCAGGTAACAAATTTAGCT 57.217 34.783 0.00 0.00 34.68 3.32


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

AutoCloner maintained by Alex Coulton.