Multiple sequence alignment - TraesCS4B01G122200

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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 TraesCS4B01G122200 chr4B 100.000 3104 0 0 1 3104 145370199 145373302 0.000000e+00 5733.0
1 TraesCS4B01G122200 chr4A 93.722 1975 110 5 750 2717 473946896 473944929 0.000000e+00 2948.0
2 TraesCS4B01G122200 chr4A 85.734 743 75 15 1 718 473947717 473946981 0.000000e+00 756.0
3 TraesCS4B01G122200 chr4A 79.319 382 31 25 2761 3102 473944927 473944554 1.120000e-54 224.0
4 TraesCS4B01G122200 chr4D 96.284 1507 52 4 733 2236 101436037 101437542 0.000000e+00 2470.0
5 TraesCS4B01G122200 chr4D 88.507 757 58 9 1 728 101435236 101435992 0.000000e+00 889.0
6 TraesCS4B01G122200 chr4D 87.829 608 47 13 2240 2846 101437654 101438235 0.000000e+00 688.0
7 TraesCS4B01G122200 chr4D 77.206 544 98 13 1 528 14647992 14648525 8.420000e-76 294.0
8 TraesCS4B01G122200 chr4D 77.206 544 98 13 1 528 266955184 266955717 8.420000e-76 294.0
9 TraesCS4B01G122200 chr1A 76.054 735 119 30 2 691 399194897 399194175 2.310000e-86 329.0
10 TraesCS4B01G122200 chr6A 82.514 366 62 2 1716 2080 502366909 502367273 1.390000e-83 320.0
11 TraesCS4B01G122200 chrUn 75.600 750 126 30 1 704 30409544 30408806 5.000000e-83 318.0
12 TraesCS4B01G122200 chr6D 82.240 366 63 2 1716 2080 361380423 361380787 6.460000e-82 315.0
13 TraesCS4B01G122200 chr6B 77.912 498 104 5 1586 2080 542585795 542586289 3.890000e-79 305.0
14 TraesCS4B01G122200 chr7D 78.044 501 84 13 1 485 384444372 384443882 3.030000e-75 292.0
15 TraesCS4B01G122200 chr1D 77.022 544 97 14 1 528 12324122 12324653 1.410000e-73 287.0
16 TraesCS4B01G122200 chr3A 73.361 244 37 17 2884 3102 620465343 620465583 7.180000e-07 65.8
17 TraesCS4B01G122200 chr2A 94.737 38 2 0 3054 3091 550888372 550888409 3.340000e-05 60.2


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 TraesCS4B01G122200 chr4B 145370199 145373302 3103 False 5733.000000 5733 100.000000 1 3104 1 chr4B.!!$F1 3103
1 TraesCS4B01G122200 chr4A 473944554 473947717 3163 True 1309.333333 2948 86.258333 1 3102 3 chr4A.!!$R1 3101
2 TraesCS4B01G122200 chr4D 101435236 101438235 2999 False 1349.000000 2470 90.873333 1 2846 3 chr4D.!!$F3 2845
3 TraesCS4B01G122200 chr4D 14647992 14648525 533 False 294.000000 294 77.206000 1 528 1 chr4D.!!$F1 527
4 TraesCS4B01G122200 chr4D 266955184 266955717 533 False 294.000000 294 77.206000 1 528 1 chr4D.!!$F2 527
5 TraesCS4B01G122200 chr1A 399194175 399194897 722 True 329.000000 329 76.054000 2 691 1 chr1A.!!$R1 689
6 TraesCS4B01G122200 chrUn 30408806 30409544 738 True 318.000000 318 75.600000 1 704 1 chrUn.!!$R1 703
7 TraesCS4B01G122200 chr1D 12324122 12324653 531 False 287.000000 287 77.022000 1 528 1 chr1D.!!$F1 527

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
500 527 0.521735 GAACCGGAAGCCACATTCAC 59.478 55.0 9.46 0.00 0.0 3.18 F
961 1077 0.861837 GTCCTCGACAAAGCTGTGTG 59.138 55.0 16.08 7.19 35.3 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 1731 0.814457 TTGTGTGCGGCAAAAGTCTT 59.186 45.0 3.23 0.0 0.0 3.01 R
2865 3107 0.598562 CGAGCTATAGATGCACCCGT 59.401 55.0 3.21 0.0 0.0 5.28 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
79 81 2.752807 AACGGCCTCCACCAACACT 61.753 57.895 0.00 0.00 0.00 3.55
81 83 1.198759 ACGGCCTCCACCAACACTAT 61.199 55.000 0.00 0.00 0.00 2.12
172 177 4.999950 CAGGAGCATCAAAGACTTTAGTGT 59.000 41.667 0.00 0.00 36.25 3.55
184 189 2.951642 ACTTTAGTGTGTGTGCTTGCAT 59.048 40.909 0.00 0.00 0.00 3.96
203 208 1.563924 TGTGGTGGGTAGTTAGCGAT 58.436 50.000 0.00 0.00 0.00 4.58
210 215 3.131755 GTGGGTAGTTAGCGATGTACCTT 59.868 47.826 8.15 0.00 36.06 3.50
233 238 2.609459 ACAGCGACAAAGTCAACTTCAG 59.391 45.455 0.00 0.00 34.61 3.02
319 327 6.428159 GGTGATTTCCATATTAGCACGAGATT 59.572 38.462 0.00 0.00 0.00 2.40
328 336 8.773645 CCATATTAGCACGAGATTTGTTATCAA 58.226 33.333 0.00 0.00 0.00 2.57
416 425 2.471815 ATCAGTCTCACCCCGGATAA 57.528 50.000 0.73 0.00 0.00 1.75
427 454 0.768622 CCCGGATAAGGTAATGGCCA 59.231 55.000 8.56 8.56 0.00 5.36
439 466 6.204852 AGGTAATGGCCATGAAATATGAGA 57.795 37.500 21.63 0.00 0.00 3.27
450 477 6.347240 CCATGAAATATGAGAAACTAGCGAGC 60.347 42.308 0.00 0.00 0.00 5.03
455 482 1.893137 TGAGAAACTAGCGAGCAGGAA 59.107 47.619 0.00 0.00 0.00 3.36
485 512 1.021968 ACCGCAGACAACAAAGAACC 58.978 50.000 0.00 0.00 0.00 3.62
500 527 0.521735 GAACCGGAAGCCACATTCAC 59.478 55.000 9.46 0.00 0.00 3.18
508 535 3.376546 GGAAGCCACATTCACAGATCTTC 59.623 47.826 0.00 0.00 0.00 2.87
536 569 7.969536 TCAAAGAAGAGGAAGAATACTTGTG 57.030 36.000 0.00 0.00 36.39 3.33
547 580 7.554118 AGGAAGAATACTTGTGGTCATTGTATG 59.446 37.037 0.00 0.00 36.39 2.39
642 698 2.359848 GGTTTTAACGAGGCAACCACTT 59.640 45.455 0.00 0.00 38.89 3.16
666 722 2.393271 AGCTCAAGATTTCTCCCACG 57.607 50.000 0.00 0.00 0.00 4.94
675 734 2.234300 TTTCTCCCACGTGACACTTC 57.766 50.000 19.30 0.00 0.00 3.01
681 740 1.372997 CACGTGACACTTCCCCTCG 60.373 63.158 10.90 0.00 0.00 4.63
749 835 2.730066 AAAACATGCTTTGGCGGGCC 62.730 55.000 1.86 1.86 42.25 5.80
799 915 1.031571 GTCCCATTGCCTTCGCATCA 61.032 55.000 0.00 0.00 46.67 3.07
825 941 1.028905 CAGATCTCACCTCTCCCGTC 58.971 60.000 0.00 0.00 0.00 4.79
854 970 3.114390 CTCAGACCTCCCCTCCCT 58.886 66.667 0.00 0.00 0.00 4.20
884 1000 2.443016 CCCCTCACCTCCTCCTCG 60.443 72.222 0.00 0.00 0.00 4.63
913 1029 3.314693 ACTTTCCAAGGTACTCCACTCA 58.685 45.455 0.00 0.00 38.49 3.41
961 1077 0.861837 GTCCTCGACAAAGCTGTGTG 59.138 55.000 16.08 7.19 35.30 3.82
1038 1154 2.569059 CTGATGGCACTCGAATCCAAT 58.431 47.619 0.00 0.00 33.04 3.16
1047 1163 2.496070 ACTCGAATCCAATTCCTCGTCA 59.504 45.455 0.00 0.00 35.89 4.35
1093 1209 2.621338 GAACGCATGTCTTGGAGATCA 58.379 47.619 0.00 0.00 0.00 2.92
1127 1243 0.914417 AAGAAGGGCCTGGGAATCGA 60.914 55.000 6.92 0.00 0.00 3.59
1488 1610 6.202762 GTGTACTCACAGTCATCAAACAATCA 59.797 38.462 0.00 0.00 43.37 2.57
1536 1658 3.334691 TGAAATCAAGGTGTCATCGTCC 58.665 45.455 0.00 0.00 0.00 4.79
1545 1667 2.858344 GGTGTCATCGTCCAACTTATCG 59.142 50.000 0.00 0.00 0.00 2.92
1554 1676 5.424757 TCGTCCAACTTATCGGATCATTTT 58.575 37.500 0.00 0.00 32.83 1.82
1609 1731 1.496857 TGACATTCAGTGTTGGGGGAA 59.503 47.619 0.00 0.00 42.36 3.97
1652 1774 2.028567 TCATACTTGTGGCACGATCACA 60.029 45.455 13.77 0.00 42.57 3.58
1691 1813 4.455606 CTGTATGGAGGGATGAAGGAAAC 58.544 47.826 0.00 0.00 0.00 2.78
1746 1868 0.038526 CTGCTGCTTTCAAGGCCTTG 60.039 55.000 35.52 35.52 41.71 3.61
1767 1889 4.816392 TGCTGCATTTCGTATATACCGAT 58.184 39.130 7.30 0.00 33.81 4.18
1890 2012 2.799126 TATGCCAAAACATCCTCGGT 57.201 45.000 0.00 0.00 0.00 4.69
1967 2089 2.706190 ACTGTGACAGGCTTAAGGAAGT 59.294 45.455 17.92 0.00 35.51 3.01
2007 2129 3.055240 CCTCTAAGGATGAGATGGATGCC 60.055 52.174 0.00 0.00 37.67 4.40
2048 2170 9.628500 AGGTTACAGTAATCTCAAAAGAACTTT 57.372 29.630 0.00 0.00 34.49 2.66
2124 2246 1.939255 GTGAGCAGCTCATTCTAAGCC 59.061 52.381 27.86 8.91 42.73 4.35
2125 2247 1.556451 TGAGCAGCTCATTCTAAGCCA 59.444 47.619 21.85 0.00 40.75 4.75
2127 2249 3.212685 GAGCAGCTCATTCTAAGCCAAT 58.787 45.455 18.17 0.00 40.75 3.16
2130 2252 3.631227 GCAGCTCATTCTAAGCCAATTCT 59.369 43.478 0.00 0.00 40.75 2.40
2196 2318 5.394773 GCTAGTTAGTTTCCTAGAGCAGCTT 60.395 44.000 0.00 0.00 33.93 3.74
2236 2358 5.878669 GGTGGGTGGTAAGTCTAGTTTATTG 59.121 44.000 0.00 0.00 0.00 1.90
2299 2529 2.494059 CTGAACGTCAGGGTGTTGAAT 58.506 47.619 7.01 0.00 40.71 2.57
2316 2546 4.842531 TGAATTGTTCTGGCCTCATCTA 57.157 40.909 3.32 0.00 0.00 1.98
2317 2547 5.378230 TGAATTGTTCTGGCCTCATCTAT 57.622 39.130 3.32 0.00 0.00 1.98
2318 2548 5.759059 TGAATTGTTCTGGCCTCATCTATT 58.241 37.500 3.32 1.38 0.00 1.73
2319 2549 5.591472 TGAATTGTTCTGGCCTCATCTATTG 59.409 40.000 3.32 0.00 0.00 1.90
2320 2550 4.574674 TTGTTCTGGCCTCATCTATTGT 57.425 40.909 3.32 0.00 0.00 2.71
2321 2551 5.692115 TTGTTCTGGCCTCATCTATTGTA 57.308 39.130 3.32 0.00 0.00 2.41
2345 2581 9.964253 GTAATGAATGAATATCAGATAACAGCG 57.036 33.333 0.00 0.00 0.00 5.18
2415 2652 2.430332 CAAAACTGAAAACTGGGGCAGA 59.570 45.455 0.00 0.00 35.18 4.26
2417 2654 2.452600 ACTGAAAACTGGGGCAGAAA 57.547 45.000 0.00 0.00 35.18 2.52
2427 2664 1.344114 TGGGGCAGAAAATGAGCAAAC 59.656 47.619 0.00 0.00 0.00 2.93
2442 2679 1.835121 CAAACATCATCTGGCGCATG 58.165 50.000 10.83 4.54 0.00 4.06
2490 2727 6.914215 GTCTGTTAAACTTTTACCTTTTCGGG 59.086 38.462 0.00 0.00 36.97 5.14
2498 2735 7.019656 ACTTTTACCTTTTCGGGTTCCTATA 57.980 36.000 0.00 0.00 40.48 1.31
2547 2784 3.380142 ACAACAATTTGGTGAACGCATC 58.620 40.909 20.90 0.00 37.20 3.91
2575 2812 2.026915 TGTATCATGCACTGAAGCCTGT 60.027 45.455 0.00 0.00 37.44 4.00
2712 2953 5.715279 TGAACTTCATGCACTAGTACCTAGT 59.285 40.000 0.00 0.00 46.75 2.57
2740 2981 8.431910 TTTTTCAGATTCACTAGTACCTAGGT 57.568 34.615 20.57 20.57 38.30 3.08
2741 2982 8.431910 TTTTCAGATTCACTAGTACCTAGGTT 57.568 34.615 22.11 5.38 38.30 3.50
2742 2983 8.431910 TTTCAGATTCACTAGTACCTAGGTTT 57.568 34.615 22.11 11.71 38.30 3.27
2743 2984 8.431910 TTCAGATTCACTAGTACCTAGGTTTT 57.568 34.615 22.11 11.33 38.30 2.43
2859 3101 7.313951 ACAAAGAGTAATTCAGAATAGCAGC 57.686 36.000 0.00 0.00 0.00 5.25
2860 3102 7.108847 ACAAAGAGTAATTCAGAATAGCAGCT 58.891 34.615 0.00 0.00 0.00 4.24
2861 3103 8.260818 ACAAAGAGTAATTCAGAATAGCAGCTA 58.739 33.333 4.10 4.10 0.00 3.32
2863 3105 8.830201 AAGAGTAATTCAGAATAGCAGCTATG 57.170 34.615 16.00 5.45 0.00 2.23
2864 3106 8.187913 AGAGTAATTCAGAATAGCAGCTATGA 57.812 34.615 16.00 7.86 0.00 2.15
2865 3107 8.646004 AGAGTAATTCAGAATAGCAGCTATGAA 58.354 33.333 16.00 16.00 0.00 2.57
2866 3108 8.600449 AGTAATTCAGAATAGCAGCTATGAAC 57.400 34.615 16.00 10.33 0.00 3.18
2867 3109 6.536731 AATTCAGAATAGCAGCTATGAACG 57.463 37.500 16.00 5.52 0.00 3.95
2868 3110 3.982475 TCAGAATAGCAGCTATGAACGG 58.018 45.455 16.00 10.87 0.00 4.44
2870 3112 2.700897 AGAATAGCAGCTATGAACGGGT 59.299 45.455 16.00 0.00 0.00 5.28
2872 3114 3.102097 GCAGCTATGAACGGGTGC 58.898 61.111 0.00 0.00 46.73 5.01
2873 3115 4.615901 CAGCTATGAACGGGTGCA 57.384 55.556 0.00 0.00 0.00 4.57
2874 3116 3.085208 CAGCTATGAACGGGTGCAT 57.915 52.632 0.00 0.00 0.00 3.96
2875 3117 0.940126 CAGCTATGAACGGGTGCATC 59.060 55.000 0.00 0.00 0.00 3.91
2876 3118 0.833287 AGCTATGAACGGGTGCATCT 59.167 50.000 0.00 0.00 0.00 2.90
2877 3119 2.039418 AGCTATGAACGGGTGCATCTA 58.961 47.619 0.00 0.00 0.00 1.98
2881 3146 2.526304 TGAACGGGTGCATCTATAGC 57.474 50.000 0.00 0.00 0.00 2.97
2885 3150 0.598562 CGGGTGCATCTATAGCTCGT 59.401 55.000 0.00 0.00 0.00 4.18
2894 3159 2.505405 TCTATAGCTCGTGATCGCCTT 58.495 47.619 0.00 0.00 36.96 4.35
2897 3162 3.728076 ATAGCTCGTGATCGCCTTAAA 57.272 42.857 0.00 0.00 36.96 1.52
2898 3163 2.380084 AGCTCGTGATCGCCTTAAAA 57.620 45.000 0.00 0.00 36.96 1.52
2905 3170 3.797256 CGTGATCGCCTTAAAAGACCTAG 59.203 47.826 0.00 0.00 0.00 3.02
2917 3182 3.387225 GACCTAGAAGTGGGCCGGC 62.387 68.421 21.18 21.18 0.00 6.13
2931 3196 1.025113 GCCGGCCCAGTTAGTTCTTC 61.025 60.000 18.11 0.00 0.00 2.87
2934 3199 1.723220 GGCCCAGTTAGTTCTTCGTC 58.277 55.000 0.00 0.00 0.00 4.20
2935 3200 1.275573 GGCCCAGTTAGTTCTTCGTCT 59.724 52.381 0.00 0.00 0.00 4.18
2940 3205 5.623824 GCCCAGTTAGTTCTTCGTCTCATTA 60.624 44.000 0.00 0.00 0.00 1.90
2941 3206 6.037098 CCCAGTTAGTTCTTCGTCTCATTAG 58.963 44.000 0.00 0.00 0.00 1.73
2945 3210 7.007546 CAGTTAGTTCTTCGTCTCATTAGTTCG 59.992 40.741 0.00 0.00 0.00 3.95
3053 3318 8.169268 ACTTAAAAGATCGAGAATTTAACAGCG 58.831 33.333 0.00 0.00 0.00 5.18
3054 3319 6.481954 AAAAGATCGAGAATTTAACAGCGT 57.518 33.333 0.00 0.00 0.00 5.07
3055 3320 7.591006 AAAAGATCGAGAATTTAACAGCGTA 57.409 32.000 0.00 0.00 0.00 4.42
3056 3321 6.570690 AAGATCGAGAATTTAACAGCGTAC 57.429 37.500 0.00 0.00 0.00 3.67
3057 3322 5.892568 AGATCGAGAATTTAACAGCGTACT 58.107 37.500 0.00 0.00 0.00 2.73
3060 3336 6.385537 TCGAGAATTTAACAGCGTACTTTC 57.614 37.500 0.00 0.00 0.00 2.62
3069 3345 7.775397 TTAACAGCGTACTTTCTTTGTTAGT 57.225 32.000 0.00 0.00 33.94 2.24
3070 3346 5.652744 ACAGCGTACTTTCTTTGTTAGTG 57.347 39.130 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 58 4.643387 GGTGGAGGCCGTTGCACT 62.643 66.667 14.89 0.00 39.14 4.40
103 108 5.648092 AGGAAGAACCAAATATCTTGTTCCG 59.352 40.000 0.00 0.00 40.57 4.30
172 177 1.734748 CACCACATGCAAGCACACA 59.265 52.632 0.00 0.00 0.00 3.72
184 189 1.206132 CATCGCTAACTACCCACCACA 59.794 52.381 0.00 0.00 0.00 4.17
203 208 4.053295 GACTTTGTCGCTGTTAAGGTACA 58.947 43.478 0.00 0.00 0.00 2.90
210 215 4.185394 TGAAGTTGACTTTGTCGCTGTTA 58.815 39.130 0.00 0.00 36.11 2.41
233 238 3.577649 TGAAGTCCTCGTCATCTTCAC 57.422 47.619 0.00 0.00 40.46 3.18
319 327 6.143919 GTCGATGAGATGCGTATTGATAACAA 59.856 38.462 0.00 0.00 40.42 2.83
328 336 2.226674 ACGATGTCGATGAGATGCGTAT 59.773 45.455 9.67 0.00 43.02 3.06
416 425 6.204852 TCTCATATTTCATGGCCATTACCT 57.795 37.500 17.92 4.09 0.00 3.08
427 454 6.283694 TGCTCGCTAGTTTCTCATATTTCAT 58.716 36.000 0.00 0.00 0.00 2.57
439 466 1.270839 TGCTTTCCTGCTCGCTAGTTT 60.271 47.619 0.00 0.00 0.00 2.66
450 477 1.135689 GCGGTGTATTGTGCTTTCCTG 60.136 52.381 0.00 0.00 0.00 3.86
455 482 1.156736 GTCTGCGGTGTATTGTGCTT 58.843 50.000 0.00 0.00 0.00 3.91
485 512 1.667724 GATCTGTGAATGTGGCTTCCG 59.332 52.381 0.00 0.00 0.00 4.30
500 527 6.413052 TCCTCTTCTTTGATTGGAAGATCTG 58.587 40.000 0.00 0.41 44.30 2.90
508 535 8.457261 CAAGTATTCTTCCTCTTCTTTGATTGG 58.543 37.037 0.00 0.00 0.00 3.16
615 671 2.223745 TGCCTCGTTAAAACCTTCCAC 58.776 47.619 0.00 0.00 0.00 4.02
642 698 6.049149 CGTGGGAGAAATCTTGAGCTTTATA 58.951 40.000 0.00 0.00 0.00 0.98
666 722 1.963172 AAAACGAGGGGAAGTGTCAC 58.037 50.000 0.00 0.00 0.00 3.67
675 734 6.769134 ATACAGGAAAATAAAAACGAGGGG 57.231 37.500 0.00 0.00 0.00 4.79
749 835 3.118454 CTACAAGGGCCGTGCGTG 61.118 66.667 19.78 6.00 0.00 5.34
799 915 2.760092 GAGAGGTGAGATCTGAGCAACT 59.240 50.000 13.91 11.58 31.05 3.16
810 926 1.303615 GGAGACGGGAGAGGTGAGA 59.696 63.158 0.00 0.00 0.00 3.27
825 941 0.179078 GGTCTGAGCAGCTGATGGAG 60.179 60.000 20.43 9.67 0.00 3.86
884 1000 0.250338 ACCTTGGAAAGTCGGCAGAC 60.250 55.000 9.15 9.15 44.25 3.51
913 1029 0.473117 TGGGGAAGAAACGAGAGGGT 60.473 55.000 0.00 0.00 0.00 4.34
961 1077 2.355132 TCTGAGAATACGAGAGGAACGC 59.645 50.000 0.00 0.00 0.00 4.84
1001 1117 2.598394 GCCCTGCAACCAAGAGCA 60.598 61.111 0.00 0.00 39.25 4.26
1093 1209 1.482593 CTTCTTGAGGCTGTACCCGAT 59.517 52.381 0.00 0.00 40.58 4.18
1127 1243 1.300697 GCCGACTGGACGAACTTGT 60.301 57.895 0.00 0.00 37.49 3.16
1488 1610 2.495669 CCCTGTTGTTTTTGTCACCTGT 59.504 45.455 0.00 0.00 0.00 4.00
1536 1658 5.247507 TGCCAAAATGATCCGATAAGTTG 57.752 39.130 0.00 0.00 0.00 3.16
1545 1667 2.997986 CAACAGCTTGCCAAAATGATCC 59.002 45.455 0.00 0.00 0.00 3.36
1554 1676 1.545428 CCCTCTAACAACAGCTTGCCA 60.545 52.381 0.00 0.00 0.00 4.92
1609 1731 0.814457 TTGTGTGCGGCAAAAGTCTT 59.186 45.000 3.23 0.00 0.00 3.01
1640 1762 1.805943 CAAAGACATGTGATCGTGCCA 59.194 47.619 1.15 0.00 34.22 4.92
1652 1774 1.350351 ACAGCTCTGCCTCAAAGACAT 59.650 47.619 0.00 0.00 0.00 3.06
1691 1813 3.679389 ACTGTAATGGACTCTGCCTTTG 58.321 45.455 0.00 0.00 0.00 2.77
1746 1868 5.347635 TGAATCGGTATATACGAAATGCAGC 59.652 40.000 6.79 0.00 44.20 5.25
1767 1889 0.888736 CACCCACGTCAGGCAATGAA 60.889 55.000 0.91 0.00 40.43 2.57
1890 2012 4.079253 GAGTCTCCATGGCAAGGTTTTTA 58.921 43.478 6.96 0.00 0.00 1.52
1967 2089 5.664294 AGAGGCAATAAATTCAATGCACA 57.336 34.783 10.32 0.00 40.51 4.57
2007 2129 1.341080 AACCTTGGGTTGCCATCAAG 58.659 50.000 0.77 0.00 45.07 3.02
2093 2215 1.004044 AGCTGCTCACCTATGCTTTGT 59.996 47.619 0.00 0.00 0.00 2.83
2169 2291 6.546428 TGCTCTAGGAAACTAACTAGCAAT 57.454 37.500 0.00 0.00 44.05 3.56
2196 2318 2.425592 CCGGTTCAGGTCAGCACA 59.574 61.111 0.00 0.00 0.00 4.57
2202 2324 2.032071 CACCCACCGGTTCAGGTC 59.968 66.667 16.13 0.00 43.89 3.85
2255 2485 2.969821 TTGGGCATCCAGTAGTTTGT 57.030 45.000 0.00 0.00 45.04 2.83
2299 2529 4.574674 ACAATAGATGAGGCCAGAACAA 57.425 40.909 5.01 0.00 0.00 2.83
2319 2549 9.964253 CGCTGTTATCTGATATTCATTCATTAC 57.036 33.333 0.00 0.00 0.00 1.89
2320 2550 9.710900 ACGCTGTTATCTGATATTCATTCATTA 57.289 29.630 0.00 0.00 0.00 1.90
2321 2551 8.613060 ACGCTGTTATCTGATATTCATTCATT 57.387 30.769 0.00 0.00 0.00 2.57
2406 2642 1.259609 TTGCTCATTTTCTGCCCCAG 58.740 50.000 0.00 0.00 0.00 4.45
2415 2652 4.501071 GCCAGATGATGTTTGCTCATTTT 58.499 39.130 0.00 0.00 33.56 1.82
2417 2654 2.098607 CGCCAGATGATGTTTGCTCATT 59.901 45.455 0.00 0.00 33.56 2.57
2427 2664 1.596603 TAACCATGCGCCAGATGATG 58.403 50.000 4.18 0.00 0.00 3.07
2442 2679 1.076332 GCATATGTCCCGCGATAACC 58.924 55.000 8.23 0.00 0.00 2.85
2450 2687 1.269778 ACAGACGATGCATATGTCCCG 60.270 52.381 21.69 17.10 33.09 5.14
2547 2784 5.742453 GCTTCAGTGCATGATACATCAAAAG 59.258 40.000 0.00 0.00 40.69 2.27
2595 2833 3.096092 GGCACAACAAATAGGAATCCCA 58.904 45.455 0.00 0.00 33.88 4.37
2644 2882 7.809806 ACTGAAATTAAGCTGTTTATCAAGCAC 59.190 33.333 0.00 0.00 0.00 4.40
2730 2971 8.893560 TGTTAAGGGAAATAAAACCTAGGTACT 58.106 33.333 16.67 7.91 46.37 2.73
2731 2972 9.519191 TTGTTAAGGGAAATAAAACCTAGGTAC 57.481 33.333 16.67 4.77 33.37 3.34
2732 2973 9.743581 CTTGTTAAGGGAAATAAAACCTAGGTA 57.256 33.333 16.67 0.00 33.37 3.08
2733 2974 7.672660 CCTTGTTAAGGGAAATAAAACCTAGGT 59.327 37.037 9.21 9.21 45.27 3.08
2734 2975 8.063200 CCTTGTTAAGGGAAATAAAACCTAGG 57.937 38.462 7.41 7.41 45.27 3.02
2759 3000 7.186128 TGCAACATGAAAATATGTCGACATAC 58.814 34.615 34.29 23.46 41.15 2.39
2857 3099 0.833287 AGATGCACCCGTTCATAGCT 59.167 50.000 0.00 0.00 0.00 3.32
2858 3100 2.526304 TAGATGCACCCGTTCATAGC 57.474 50.000 0.00 0.00 0.00 2.97
2859 3101 4.081972 AGCTATAGATGCACCCGTTCATAG 60.082 45.833 3.21 0.00 0.00 2.23
2860 3102 3.832490 AGCTATAGATGCACCCGTTCATA 59.168 43.478 3.21 0.00 0.00 2.15
2861 3103 2.634940 AGCTATAGATGCACCCGTTCAT 59.365 45.455 3.21 0.00 0.00 2.57
2863 3105 2.678324 GAGCTATAGATGCACCCGTTC 58.322 52.381 3.21 0.00 0.00 3.95
2864 3106 1.000163 CGAGCTATAGATGCACCCGTT 60.000 52.381 3.21 0.00 0.00 4.44
2865 3107 0.598562 CGAGCTATAGATGCACCCGT 59.401 55.000 3.21 0.00 0.00 5.28
2866 3108 0.598562 ACGAGCTATAGATGCACCCG 59.401 55.000 3.21 0.00 0.00 5.28
2867 3109 1.613925 TCACGAGCTATAGATGCACCC 59.386 52.381 3.21 0.00 0.00 4.61
2868 3110 3.506810 GATCACGAGCTATAGATGCACC 58.493 50.000 3.21 0.00 0.00 5.01
2870 3112 2.414691 GCGATCACGAGCTATAGATGCA 60.415 50.000 3.21 0.00 42.66 3.96
2872 3114 2.421775 AGGCGATCACGAGCTATAGATG 59.578 50.000 3.21 0.00 42.66 2.90
2873 3115 2.717390 AGGCGATCACGAGCTATAGAT 58.283 47.619 3.21 0.00 42.66 1.98
2874 3116 2.186532 AGGCGATCACGAGCTATAGA 57.813 50.000 3.21 0.00 42.66 1.98
2875 3117 2.999507 AAGGCGATCACGAGCTATAG 57.000 50.000 0.00 0.00 42.66 1.31
2876 3118 4.841443 TTTAAGGCGATCACGAGCTATA 57.159 40.909 0.00 0.00 42.66 1.31
2877 3119 3.728076 TTTAAGGCGATCACGAGCTAT 57.272 42.857 0.00 0.00 42.66 2.97
2881 3146 2.603560 GGTCTTTTAAGGCGATCACGAG 59.396 50.000 0.00 0.00 42.66 4.18
2885 3150 5.187186 ACTTCTAGGTCTTTTAAGGCGATCA 59.813 40.000 0.00 0.00 0.00 2.92
2894 3159 2.235402 CGGCCCACTTCTAGGTCTTTTA 59.765 50.000 0.00 0.00 0.00 1.52
2897 3162 1.265454 CCGGCCCACTTCTAGGTCTT 61.265 60.000 0.00 0.00 0.00 3.01
2898 3163 1.686110 CCGGCCCACTTCTAGGTCT 60.686 63.158 0.00 0.00 0.00 3.85
2917 3182 3.936372 TGAGACGAAGAACTAACTGGG 57.064 47.619 0.00 0.00 0.00 4.45
2925 3190 5.628193 TGAACGAACTAATGAGACGAAGAAC 59.372 40.000 8.03 0.00 33.15 3.01
2931 3196 5.911615 GTAGTGAACGAACTAATGAGACG 57.088 43.478 0.00 0.00 34.50 4.18
3035 3300 6.570690 AAGTACGCTGTTAAATTCTCGATC 57.429 37.500 0.00 0.00 0.00 3.69
3042 3307 9.659830 CTAACAAAGAAAGTACGCTGTTAAATT 57.340 29.630 0.00 0.00 31.05 1.82
3047 3312 5.583457 ACACTAACAAAGAAAGTACGCTGTT 59.417 36.000 0.00 0.00 0.00 3.16
3048 3313 5.114081 ACACTAACAAAGAAAGTACGCTGT 58.886 37.500 0.00 0.00 0.00 4.40
3049 3314 5.652744 ACACTAACAAAGAAAGTACGCTG 57.347 39.130 0.00 0.00 0.00 5.18
3051 3316 7.170240 AGTTACACTAACAAAGAAAGTACGC 57.830 36.000 0.00 0.00 41.07 4.42


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

AutoCloner maintained by Alex Coulton.