Multiple sequence alignment - TraesCS5A01G063900

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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 TraesCS5A01G063900 chr5A 100.000 3356 0 0 1 3356 69139695 69143050 0.000000e+00 6198
1 TraesCS5A01G063900 chr5A 86.184 304 22 9 856 1142 69222864 69222564 9.040000e-81 311
2 TraesCS5A01G063900 chr5D 90.548 2666 127 50 4 2618 74144075 74146666 0.000000e+00 3411
3 TraesCS5A01G063900 chr5D 90.632 427 31 5 2930 3356 74146981 74147398 2.920000e-155 558
4 TraesCS5A01G063900 chr5D 86.207 319 18 10 2610 2913 74146691 74146998 4.180000e-84 322
5 TraesCS5A01G063900 chr5B 90.220 2679 129 55 2 2618 78222236 78219629 0.000000e+00 3373
6 TraesCS5A01G063900 chr5B 88.941 425 31 8 2934 3356 78219238 78218828 8.310000e-141 510
7 TraesCS5A01G063900 chr5B 88.068 176 12 2 2671 2845 78219481 78219314 2.040000e-47 200
8 TraesCS5A01G063900 chr4A 79.055 1122 189 39 1153 2257 552832916 552831824 0.000000e+00 728
9 TraesCS5A01G063900 chr4A 78.495 1116 201 30 1153 2256 552817054 552818142 0.000000e+00 695
10 TraesCS5A01G063900 chr4D 78.501 1121 195 36 1153 2256 46187188 46186097 0.000000e+00 693
11 TraesCS5A01G063900 chr4B 78.214 1120 202 35 1153 2257 67095230 67096322 0.000000e+00 678
12 TraesCS5A01G063900 chr4B 78.027 1115 208 31 1153 2256 67543626 67542538 0.000000e+00 667
13 TraesCS5A01G063900 chr4B 77.040 1115 219 30 1153 2256 67354025 67352937 1.030000e-169 606
14 TraesCS5A01G063900 chr4B 76.692 1034 206 30 1234 2254 67484854 67483843 2.950000e-150 542
15 TraesCS5A01G063900 chr7B 92.308 208 16 0 2135 2342 449873714 449873507 2.530000e-76 296


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 TraesCS5A01G063900 chr5A 69139695 69143050 3355 False 6198.000000 6198 100.000000 1 3356 1 chr5A.!!$F1 3355
1 TraesCS5A01G063900 chr5D 74144075 74147398 3323 False 1430.333333 3411 89.129000 4 3356 3 chr5D.!!$F1 3352
2 TraesCS5A01G063900 chr5B 78218828 78222236 3408 True 1361.000000 3373 89.076333 2 3356 3 chr5B.!!$R1 3354
3 TraesCS5A01G063900 chr4A 552831824 552832916 1092 True 728.000000 728 79.055000 1153 2257 1 chr4A.!!$R1 1104
4 TraesCS5A01G063900 chr4A 552817054 552818142 1088 False 695.000000 695 78.495000 1153 2256 1 chr4A.!!$F1 1103
5 TraesCS5A01G063900 chr4D 46186097 46187188 1091 True 693.000000 693 78.501000 1153 2256 1 chr4D.!!$R1 1103
6 TraesCS5A01G063900 chr4B 67095230 67096322 1092 False 678.000000 678 78.214000 1153 2257 1 chr4B.!!$F1 1104
7 TraesCS5A01G063900 chr4B 67542538 67543626 1088 True 667.000000 667 78.027000 1153 2256 1 chr4B.!!$R3 1103
8 TraesCS5A01G063900 chr4B 67352937 67354025 1088 True 606.000000 606 77.040000 1153 2256 1 chr4B.!!$R1 1103
9 TraesCS5A01G063900 chr4B 67483843 67484854 1011 True 542.000000 542 76.692000 1234 2254 1 chr4B.!!$R2 1020

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
619 660 0.107831 TACTGCACCACTCACCCAAC 59.892 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2487 2588 0.318107 GCGCCACACCGTATACGTAT 60.318 55.0 22.87 13.54 37.74 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
85 87 1.908483 GGCTGGGAAGGATCGAGTT 59.092 57.895 0.00 0.00 0.00 3.01
86 88 1.120530 GGCTGGGAAGGATCGAGTTA 58.879 55.000 0.00 0.00 0.00 2.24
105 108 1.276622 ATAACACGTCCCAAGGAGCT 58.723 50.000 0.00 0.00 29.39 4.09
108 111 1.079543 CACGTCCCAAGGAGCTGAG 60.080 63.158 0.00 0.00 29.39 3.35
116 119 2.553904 CCCAAGGAGCTGAGTCAACATT 60.554 50.000 0.00 0.00 0.00 2.71
117 120 3.307691 CCCAAGGAGCTGAGTCAACATTA 60.308 47.826 0.00 0.00 0.00 1.90
118 121 3.937706 CCAAGGAGCTGAGTCAACATTAG 59.062 47.826 0.00 0.00 0.00 1.73
119 122 3.902881 AGGAGCTGAGTCAACATTAGG 57.097 47.619 0.00 0.00 0.00 2.69
124 147 2.924290 GCTGAGTCAACATTAGGACGTC 59.076 50.000 7.13 7.13 39.01 4.34
159 184 3.493129 CGTGATCCGAGACTTTGTCAAAA 59.507 43.478 0.00 0.00 39.56 2.44
162 187 3.553828 TCCGAGACTTTGTCAAAAGGT 57.446 42.857 0.00 0.00 46.01 3.50
185 214 6.700520 GGTAAAGTGCTGCGTCTATAATTAGT 59.299 38.462 0.00 0.00 0.00 2.24
187 216 4.051922 AGTGCTGCGTCTATAATTAGTGC 58.948 43.478 0.00 0.00 0.00 4.40
188 217 3.802139 GTGCTGCGTCTATAATTAGTGCA 59.198 43.478 0.00 0.00 36.85 4.57
213 242 4.713321 GGGATTAGTATATTAGACCCGGCA 59.287 45.833 0.00 0.00 0.00 5.69
230 259 1.597854 CATGTCGTGTGGCTGTGGT 60.598 57.895 0.00 0.00 0.00 4.16
231 260 1.148273 ATGTCGTGTGGCTGTGGTT 59.852 52.632 0.00 0.00 0.00 3.67
232 261 1.165907 ATGTCGTGTGGCTGTGGTTG 61.166 55.000 0.00 0.00 0.00 3.77
233 262 2.899838 TCGTGTGGCTGTGGTTGC 60.900 61.111 0.00 0.00 0.00 4.17
234 263 3.208383 CGTGTGGCTGTGGTTGCA 61.208 61.111 0.00 0.00 0.00 4.08
235 264 2.723746 GTGTGGCTGTGGTTGCAG 59.276 61.111 0.00 0.00 39.37 4.41
257 286 2.669364 CTTGCAGGTCAAGTCAAATGC 58.331 47.619 0.00 0.00 45.48 3.56
278 307 2.380410 GCGGCGTACTTGTCACCTG 61.380 63.158 9.37 0.00 0.00 4.00
335 370 2.154462 CTTGCAACCTGGAGATTTCGT 58.846 47.619 0.00 0.00 0.00 3.85
348 383 2.161609 AGATTTCGTTGCCAAATCGTCC 59.838 45.455 0.00 0.00 42.68 4.79
361 396 5.104374 CCAAATCGTCCATCTTTTTCCATG 58.896 41.667 0.00 0.00 0.00 3.66
364 399 6.683974 AATCGTCCATCTTTTTCCATGTAG 57.316 37.500 0.00 0.00 0.00 2.74
365 400 5.160607 TCGTCCATCTTTTTCCATGTAGT 57.839 39.130 0.00 0.00 0.00 2.73
366 401 6.288941 TCGTCCATCTTTTTCCATGTAGTA 57.711 37.500 0.00 0.00 0.00 1.82
372 407 8.258007 TCCATCTTTTTCCATGTAGTAGTACTG 58.742 37.037 13.29 5.10 0.00 2.74
373 408 8.041323 CCATCTTTTTCCATGTAGTAGTACTGT 58.959 37.037 13.29 0.00 0.00 3.55
376 411 9.081204 TCTTTTTCCATGTAGTAGTACTGTACA 57.919 33.333 19.27 17.54 0.00 2.90
377 412 9.355215 CTTTTTCCATGTAGTAGTACTGTACAG 57.645 37.037 21.44 21.44 0.00 2.74
437 472 3.819564 ACGTATCCACACACTATGCAT 57.180 42.857 3.79 3.79 0.00 3.96
442 477 5.507315 CGTATCCACACACTATGCATCAGTA 60.507 44.000 0.19 0.00 0.00 2.74
443 478 4.391405 TCCACACACTATGCATCAGTAG 57.609 45.455 0.19 0.00 0.00 2.57
444 479 2.868583 CCACACACTATGCATCAGTAGC 59.131 50.000 0.19 0.00 0.00 3.58
445 480 2.868583 CACACACTATGCATCAGTAGCC 59.131 50.000 0.19 0.00 0.00 3.93
446 481 2.158900 ACACACTATGCATCAGTAGCCC 60.159 50.000 0.19 0.00 0.00 5.19
447 482 2.118679 ACACTATGCATCAGTAGCCCA 58.881 47.619 0.19 0.00 0.00 5.36
489 524 2.226330 AGCGTGACATGCCAACTTTTA 58.774 42.857 16.06 0.00 0.00 1.52
490 525 2.226437 AGCGTGACATGCCAACTTTTAG 59.774 45.455 16.06 0.00 0.00 1.85
600 641 4.415150 CCGCCACCAGCACCAGAT 62.415 66.667 0.00 0.00 44.04 2.90
618 659 1.003118 GATACTGCACCACTCACCCAA 59.997 52.381 0.00 0.00 0.00 4.12
619 660 0.107831 TACTGCACCACTCACCCAAC 59.892 55.000 0.00 0.00 0.00 3.77
620 661 1.898574 CTGCACCACTCACCCAACC 60.899 63.158 0.00 0.00 0.00 3.77
621 662 2.597510 GCACCACTCACCCAACCC 60.598 66.667 0.00 0.00 0.00 4.11
622 663 2.923035 CACCACTCACCCAACCCA 59.077 61.111 0.00 0.00 0.00 4.51
659 700 0.746563 AATCATTGTACCGCACCCCG 60.747 55.000 0.00 0.00 0.00 5.73
728 769 2.510551 GCAAAGGCCCAAGCAACCT 61.511 57.895 0.00 0.00 42.56 3.50
732 773 2.361737 GGCCCAAGCAACCTCTCC 60.362 66.667 0.00 0.00 42.56 3.71
801 860 1.603293 CGCTATATATATCCCGCGCG 58.397 55.000 25.67 25.67 34.05 6.86
840 899 2.902065 AAATCTTTCTTCTTCGCCGC 57.098 45.000 0.00 0.00 0.00 6.53
841 900 1.087501 AATCTTTCTTCTTCGCCGCC 58.912 50.000 0.00 0.00 0.00 6.13
842 901 1.084370 ATCTTTCTTCTTCGCCGCCG 61.084 55.000 0.00 0.00 0.00 6.46
948 1010 1.447838 GATCGCTCCAAGGTCGCAA 60.448 57.895 4.60 0.00 0.00 4.85
970 1032 6.943981 CAAAGACTCGATACTTTGTTGAACA 58.056 36.000 23.90 0.00 44.20 3.18
1020 1104 4.219288 GCCATGAGGAATCACAAGAAGTTT 59.781 41.667 0.00 0.00 36.89 2.66
1041 1125 4.473520 CAGTTCCTGCGGCCGGAT 62.474 66.667 29.38 5.35 0.00 4.18
1230 1314 2.182030 GACGAGACCGGGCTCTTG 59.818 66.667 34.05 22.22 40.78 3.02
1551 1635 2.568912 GCACTACATCGAGACGCGC 61.569 63.158 5.73 0.00 40.61 6.86
1914 2007 2.047560 GTGGTGTACGTGGCCTCC 60.048 66.667 3.32 0.00 0.00 4.30
2413 2514 2.280933 TAAACCGTGTGGCCGTGG 60.281 61.111 0.00 0.00 39.70 4.94
2414 2515 3.828694 TAAACCGTGTGGCCGTGGG 62.829 63.158 0.00 0.00 39.70 4.61
2468 2569 8.181487 GTGCAACGTAGTAAAAGAGAATCATA 57.819 34.615 0.00 0.00 45.00 2.15
2470 2571 7.008901 TGCAACGTAGTAAAAGAGAATCATACG 59.991 37.037 0.00 0.00 45.00 3.06
2471 2572 7.328112 CAACGTAGTAAAAGAGAATCATACGC 58.672 38.462 0.00 0.00 45.00 4.42
2502 2603 6.974932 ATCTAGGTATACGTATACGGTGTG 57.025 41.667 29.91 20.35 44.95 3.82
2506 2607 0.318107 ATACGTATACGGTGTGGCGC 60.318 55.000 27.62 0.00 44.95 6.53
2573 2678 2.409870 CCCTGAAATGGACGGCTGC 61.410 63.158 0.00 0.00 0.00 5.25
2579 2684 1.647545 AAATGGACGGCTGCGATGTG 61.648 55.000 0.00 0.00 0.00 3.21
2583 2688 3.649277 GACGGCTGCGATGTGGACT 62.649 63.158 0.00 0.00 0.00 3.85
2584 2689 2.887568 CGGCTGCGATGTGGACTC 60.888 66.667 0.00 0.00 0.00 3.36
2641 2778 4.523173 AGACTGAGAGGTCGATTTGTACAA 59.477 41.667 3.59 3.59 40.76 2.41
2652 2789 6.696148 GGTCGATTTGTACAATCTCGACTAAT 59.304 38.462 38.70 20.91 45.21 1.73
2653 2790 7.859377 GGTCGATTTGTACAATCTCGACTAATA 59.141 37.037 38.70 21.88 45.21 0.98
2655 2792 9.447040 TCGATTTGTACAATCTCGACTAATAAG 57.553 33.333 26.87 8.66 33.16 1.73
2656 2793 8.208560 CGATTTGTACAATCTCGACTAATAAGC 58.791 37.037 25.32 4.75 31.59 3.09
2658 2795 8.766000 TTTGTACAATCTCGACTAATAAGCAA 57.234 30.769 9.56 0.00 0.00 3.91
2660 2797 8.407457 TGTACAATCTCGACTAATAAGCAAAG 57.593 34.615 0.00 0.00 0.00 2.77
2661 2798 6.910536 ACAATCTCGACTAATAAGCAAAGG 57.089 37.500 0.00 0.00 0.00 3.11
2662 2799 6.640518 ACAATCTCGACTAATAAGCAAAGGA 58.359 36.000 0.00 0.00 0.00 3.36
2663 2800 7.103641 ACAATCTCGACTAATAAGCAAAGGAA 58.896 34.615 0.00 0.00 0.00 3.36
2664 2801 7.770897 ACAATCTCGACTAATAAGCAAAGGAAT 59.229 33.333 0.00 0.00 0.00 3.01
2665 2802 8.616076 CAATCTCGACTAATAAGCAAAGGAATT 58.384 33.333 0.00 0.00 0.00 2.17
2666 2803 7.539712 TCTCGACTAATAAGCAAAGGAATTG 57.460 36.000 0.00 0.00 42.21 2.32
2752 2952 3.418684 AGCTGTTCAAATTAGGTCCGT 57.581 42.857 0.00 0.00 0.00 4.69
2753 2953 3.751518 AGCTGTTCAAATTAGGTCCGTT 58.248 40.909 0.00 0.00 0.00 4.44
2754 2954 4.142038 AGCTGTTCAAATTAGGTCCGTTT 58.858 39.130 0.00 0.00 0.00 3.60
2755 2955 5.310451 AGCTGTTCAAATTAGGTCCGTTTA 58.690 37.500 0.00 0.00 0.00 2.01
2756 2956 5.944007 AGCTGTTCAAATTAGGTCCGTTTAT 59.056 36.000 0.00 0.00 0.00 1.40
2757 2957 6.433093 AGCTGTTCAAATTAGGTCCGTTTATT 59.567 34.615 0.00 0.00 0.00 1.40
2758 2958 7.039993 AGCTGTTCAAATTAGGTCCGTTTATTT 60.040 33.333 0.00 0.00 0.00 1.40
2759 2959 8.238631 GCTGTTCAAATTAGGTCCGTTTATTTA 58.761 33.333 0.00 0.00 0.00 1.40
2801 3005 6.403746 GCGAGAAGGGAAAATTAAAGAAGGAG 60.404 42.308 0.00 0.00 0.00 3.69
2803 3007 6.256819 AGAAGGGAAAATTAAAGAAGGAGGG 58.743 40.000 0.00 0.00 0.00 4.30
2819 3024 1.527380 GGGTGTGGGTTCGCTTTGA 60.527 57.895 0.00 0.00 0.00 2.69
2823 3028 0.871722 TGTGGGTTCGCTTTGAATCG 59.128 50.000 0.00 0.00 38.68 3.34
2838 3043 2.796245 AATCGTTTCTTTGCCGCGGC 62.796 55.000 42.35 42.35 42.35 6.53
2881 3109 1.798813 GTAGAAAACGGTGCCTGTGAG 59.201 52.381 0.00 0.00 0.00 3.51
2882 3110 0.468226 AGAAAACGGTGCCTGTGAGA 59.532 50.000 0.00 0.00 0.00 3.27
2883 3111 0.586802 GAAAACGGTGCCTGTGAGAC 59.413 55.000 0.00 0.00 0.00 3.36
2890 3121 1.517242 GTGCCTGTGAGACCTTTCAG 58.483 55.000 0.00 0.00 0.00 3.02
2903 3134 4.346418 AGACCTTTCAGATGTCAAGACAGT 59.654 41.667 8.99 0.00 45.48 3.55
2908 3139 4.879197 TCAGATGTCAAGACAGTGATGT 57.121 40.909 8.99 0.00 45.48 3.06
2916 3147 1.280457 AGACAGTGATGTCTTCCCCC 58.720 55.000 5.09 0.00 45.94 5.40
2917 3148 0.108138 GACAGTGATGTCTTCCCCCG 60.108 60.000 0.00 0.00 36.01 5.73
2918 3149 1.450312 CAGTGATGTCTTCCCCCGC 60.450 63.158 0.00 0.00 0.00 6.13
2919 3150 1.918293 AGTGATGTCTTCCCCCGCA 60.918 57.895 0.00 0.00 0.00 5.69
2920 3151 1.002624 GTGATGTCTTCCCCCGCAA 60.003 57.895 0.00 0.00 0.00 4.85
2921 3152 0.608035 GTGATGTCTTCCCCCGCAAA 60.608 55.000 0.00 0.00 0.00 3.68
2922 3153 0.111446 TGATGTCTTCCCCCGCAAAA 59.889 50.000 0.00 0.00 0.00 2.44
2923 3154 1.253100 GATGTCTTCCCCCGCAAAAA 58.747 50.000 0.00 0.00 0.00 1.94
2949 3180 4.336889 AAAAGGACAGTGATGTCTTCGA 57.663 40.909 8.18 0.00 38.74 3.71
2950 3181 4.543590 AAAGGACAGTGATGTCTTCGAT 57.456 40.909 8.18 0.00 38.74 3.59
2951 3182 4.543590 AAGGACAGTGATGTCTTCGATT 57.456 40.909 8.18 0.00 38.74 3.34
2952 3183 4.116747 AGGACAGTGATGTCTTCGATTC 57.883 45.455 8.18 0.00 38.74 2.52
2953 3184 3.511540 AGGACAGTGATGTCTTCGATTCA 59.488 43.478 8.18 0.00 38.74 2.57
2954 3185 3.862267 GGACAGTGATGTCTTCGATTCAG 59.138 47.826 8.18 0.00 38.74 3.02
2955 3186 4.380973 GGACAGTGATGTCTTCGATTCAGA 60.381 45.833 8.18 0.00 38.74 3.27
2956 3187 5.336150 ACAGTGATGTCTTCGATTCAGAT 57.664 39.130 0.00 0.00 0.00 2.90
2957 3188 5.107824 ACAGTGATGTCTTCGATTCAGATG 58.892 41.667 0.00 0.00 0.00 2.90
2958 3189 5.105595 ACAGTGATGTCTTCGATTCAGATGA 60.106 40.000 0.00 0.00 0.00 2.92
2963 3198 6.700520 TGATGTCTTCGATTCAGATGAATGAG 59.299 38.462 12.62 6.97 44.14 2.90
3014 3249 3.070018 CGGGGAAGATATCTGTCATTGC 58.930 50.000 5.86 0.00 0.00 3.56
3017 3252 4.070716 GGGAAGATATCTGTCATTGCAGG 58.929 47.826 5.86 0.00 37.12 4.85
3020 3255 6.291377 GGAAGATATCTGTCATTGCAGGTAA 58.709 40.000 5.86 0.00 35.90 2.85
3021 3256 6.426328 GGAAGATATCTGTCATTGCAGGTAAG 59.574 42.308 5.86 0.00 35.90 2.34
3022 3257 5.303971 AGATATCTGTCATTGCAGGTAAGC 58.696 41.667 3.89 0.00 35.90 3.09
3023 3258 2.857186 TCTGTCATTGCAGGTAAGCA 57.143 45.000 7.82 0.00 43.99 3.91
3057 3292 2.036571 GTACTTTTCGTGGCCCGGG 61.037 63.158 19.09 19.09 37.11 5.73
3081 3316 3.362304 CGTAAAAAGGAAGGTCGTGTTCG 60.362 47.826 0.00 0.00 38.55 3.95
3108 3343 1.154413 CCGTGACATGCAACGAAGC 60.154 57.895 19.20 0.00 0.00 3.86
3110 3345 1.859398 GTGACATGCAACGAAGCGA 59.141 52.632 0.00 0.00 37.31 4.93
3111 3346 0.234625 GTGACATGCAACGAAGCGAA 59.765 50.000 0.00 0.00 37.31 4.70
3131 3366 2.826488 AGCCACAAGGAGTAGATGAGT 58.174 47.619 0.00 0.00 36.89 3.41
3181 3416 1.523938 GCTATCGTTGGTGCCTCCC 60.524 63.158 0.00 0.00 34.77 4.30
3207 3442 3.561241 GGAAGAGGGGGCCGATCC 61.561 72.222 0.00 0.00 0.00 3.36
3286 3521 2.106683 GTGCGCCGGCTAAGTGATT 61.107 57.895 26.68 0.00 40.82 2.57
3288 3523 2.534903 GCGCCGGCTAAGTGATTCC 61.535 63.158 26.68 0.00 35.83 3.01
3305 3540 0.037590 TCCCGCAGCCTTACACATTT 59.962 50.000 0.00 0.00 0.00 2.32
3311 3546 2.327568 CAGCCTTACACATTTTTGCCG 58.672 47.619 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 87 2.167693 CAGCTCCTTGGGACGTGTTATA 59.832 50.000 0.00 0.00 0.00 0.98
86 88 1.066143 CAGCTCCTTGGGACGTGTTAT 60.066 52.381 0.00 0.00 0.00 1.89
105 108 2.555325 ACGACGTCCTAATGTTGACTCA 59.445 45.455 10.58 0.00 31.22 3.41
108 111 4.674211 GCTATACGACGTCCTAATGTTGAC 59.326 45.833 10.58 0.00 31.22 3.18
116 119 3.001634 CGTGAAAGCTATACGACGTCCTA 59.998 47.826 10.58 3.05 40.01 2.94
117 120 2.223203 CGTGAAAGCTATACGACGTCCT 60.223 50.000 10.58 0.34 40.01 3.85
118 121 2.107178 CGTGAAAGCTATACGACGTCC 58.893 52.381 10.58 0.00 40.01 4.79
119 122 2.525096 CACGTGAAAGCTATACGACGTC 59.475 50.000 10.90 5.18 37.92 4.34
124 147 2.719556 CGGATCACGTGAAAGCTATACG 59.280 50.000 24.13 13.67 42.98 3.06
159 184 4.730949 TTATAGACGCAGCACTTTACCT 57.269 40.909 0.00 0.00 0.00 3.08
162 187 6.200286 GCACTAATTATAGACGCAGCACTTTA 59.800 38.462 0.00 0.00 33.86 1.85
185 214 6.127168 CGGGTCTAATATACTAATCCCATGCA 60.127 42.308 0.00 0.00 33.92 3.96
187 216 6.685620 GCCGGGTCTAATATACTAATCCCATG 60.686 46.154 2.18 0.00 33.92 3.66
188 217 5.365895 GCCGGGTCTAATATACTAATCCCAT 59.634 44.000 2.18 0.00 33.92 4.00
213 242 1.148273 AACCACAGCCACACGACAT 59.852 52.632 0.00 0.00 0.00 3.06
301 336 1.295792 TGCAAGGAAATCGTATCGGC 58.704 50.000 0.00 0.00 0.00 5.54
335 370 4.555262 GAAAAAGATGGACGATTTGGCAA 58.445 39.130 0.00 0.00 0.00 4.52
361 396 5.466393 GCTAGGAGCTGTACAGTACTACTAC 59.534 48.000 23.44 12.39 38.45 2.73
364 399 3.248125 CGCTAGGAGCTGTACAGTACTAC 59.752 52.174 23.44 13.78 39.60 2.73
365 400 3.133542 TCGCTAGGAGCTGTACAGTACTA 59.866 47.826 23.44 19.44 39.60 1.82
366 401 2.093075 TCGCTAGGAGCTGTACAGTACT 60.093 50.000 23.44 19.37 39.60 2.73
372 407 2.474816 CCAAATCGCTAGGAGCTGTAC 58.525 52.381 0.00 0.00 39.60 2.90
373 408 1.412710 CCCAAATCGCTAGGAGCTGTA 59.587 52.381 0.00 0.00 39.60 2.74
374 409 0.179000 CCCAAATCGCTAGGAGCTGT 59.821 55.000 0.00 0.00 39.60 4.40
375 410 0.179000 ACCCAAATCGCTAGGAGCTG 59.821 55.000 0.00 0.00 39.60 4.24
376 411 0.912486 AACCCAAATCGCTAGGAGCT 59.088 50.000 0.00 0.00 39.60 4.09
377 412 1.401905 CAAACCCAAATCGCTAGGAGC 59.598 52.381 0.00 0.00 38.02 4.70
443 478 7.510549 TTCTACATCATAATTAAGCTTGGGC 57.489 36.000 9.86 0.00 39.06 5.36
446 481 9.964253 CGCTATTCTACATCATAATTAAGCTTG 57.036 33.333 9.86 0.00 0.00 4.01
447 482 9.712305 ACGCTATTCTACATCATAATTAAGCTT 57.288 29.630 3.48 3.48 0.00 3.74
456 491 5.863935 GCATGTCACGCTATTCTACATCATA 59.136 40.000 0.00 0.00 0.00 2.15
457 492 4.687948 GCATGTCACGCTATTCTACATCAT 59.312 41.667 0.00 0.00 0.00 2.45
458 493 4.051237 GCATGTCACGCTATTCTACATCA 58.949 43.478 0.00 0.00 0.00 3.07
459 494 3.430218 GGCATGTCACGCTATTCTACATC 59.570 47.826 0.00 0.00 0.00 3.06
460 495 3.181466 TGGCATGTCACGCTATTCTACAT 60.181 43.478 0.00 0.00 0.00 2.29
461 496 2.167487 TGGCATGTCACGCTATTCTACA 59.833 45.455 0.00 0.00 0.00 2.74
462 497 2.821546 TGGCATGTCACGCTATTCTAC 58.178 47.619 0.00 0.00 0.00 2.59
463 498 3.118775 AGTTGGCATGTCACGCTATTCTA 60.119 43.478 0.00 0.00 0.00 2.10
464 499 2.009774 GTTGGCATGTCACGCTATTCT 58.990 47.619 0.00 0.00 0.00 2.40
465 500 2.009774 AGTTGGCATGTCACGCTATTC 58.990 47.619 0.00 0.00 0.00 1.75
489 524 1.927487 TTGAATGCAGTTCCCATGCT 58.073 45.000 0.00 0.00 44.17 3.79
490 525 2.747396 TTTGAATGCAGTTCCCATGC 57.253 45.000 0.00 0.00 44.11 4.06
585 626 0.745845 CAGTATCTGGTGCTGGTGGC 60.746 60.000 0.00 0.00 36.95 5.01
586 627 0.745845 GCAGTATCTGGTGCTGGTGG 60.746 60.000 8.12 0.00 40.49 4.61
592 633 0.036010 AGTGGTGCAGTATCTGGTGC 60.036 55.000 0.00 0.00 40.29 5.01
594 635 1.276421 GTGAGTGGTGCAGTATCTGGT 59.724 52.381 0.00 0.00 31.21 4.00
595 636 1.406069 GGTGAGTGGTGCAGTATCTGG 60.406 57.143 0.00 0.00 31.21 3.86
596 637 1.406069 GGGTGAGTGGTGCAGTATCTG 60.406 57.143 0.00 0.00 34.12 2.90
597 638 0.905357 GGGTGAGTGGTGCAGTATCT 59.095 55.000 0.00 0.00 0.00 1.98
598 639 0.613260 TGGGTGAGTGGTGCAGTATC 59.387 55.000 0.00 0.00 0.00 2.24
599 640 1.064003 TTGGGTGAGTGGTGCAGTAT 58.936 50.000 0.00 0.00 0.00 2.12
600 641 0.107831 GTTGGGTGAGTGGTGCAGTA 59.892 55.000 0.00 0.00 0.00 2.74
619 660 4.856801 ATAGCGGCGCAGGTTGGG 62.857 66.667 35.02 0.00 0.00 4.12
620 661 3.576356 CATAGCGGCGCAGGTTGG 61.576 66.667 35.02 12.86 0.00 3.77
621 662 4.241999 GCATAGCGGCGCAGGTTG 62.242 66.667 35.02 23.79 0.00 3.77
622 663 4.776322 TGCATAGCGGCGCAGGTT 62.776 61.111 35.02 16.12 36.28 3.50
728 769 1.258445 GCCGAGGTTTGGAGAGGAGA 61.258 60.000 0.00 0.00 0.00 3.71
732 773 2.125512 CGGCCGAGGTTTGGAGAG 60.126 66.667 24.07 0.00 0.00 3.20
818 877 3.408150 CGGCGAAGAAGAAAGATTTTCG 58.592 45.455 0.00 1.00 42.39 3.46
911 973 1.007387 GAACCGGCTGCCAAAACTG 60.007 57.895 20.29 0.28 0.00 3.16
913 975 1.862602 ATCGAACCGGCTGCCAAAAC 61.863 55.000 20.29 6.20 0.00 2.43
948 1010 6.281405 ACTGTTCAACAAAGTATCGAGTCTT 58.719 36.000 0.00 0.00 0.00 3.01
970 1032 2.111043 CAACACCAGCCACCGACT 59.889 61.111 0.00 0.00 0.00 4.18
1221 1305 3.952628 GAACGACCCCAAGAGCCCG 62.953 68.421 0.00 0.00 0.00 6.13
1228 1312 1.070105 CCTTGACGAACGACCCCAA 59.930 57.895 0.14 0.00 0.00 4.12
1230 1314 1.080025 CTCCTTGACGAACGACCCC 60.080 63.158 0.14 0.00 0.00 4.95
1281 1365 2.352032 GCCGGTGTAGAGCAGGTCT 61.352 63.158 7.43 7.43 39.59 3.85
1338 1422 3.952628 CTGGAACCCCGCGAACTCC 62.953 68.421 8.23 8.66 34.29 3.85
1347 1431 4.410400 CTCCCGCACTGGAACCCC 62.410 72.222 0.00 0.00 42.00 4.95
1407 1491 2.527123 TCCTGGTGGCCGGTGTAA 60.527 61.111 1.90 0.00 0.00 2.41
1506 1590 1.273606 CTGACGGAGCTCCTGAGAAAA 59.726 52.381 29.73 7.91 0.00 2.29
2448 2549 6.471519 GTGCGTATGATTCTCTTTTACTACGT 59.528 38.462 0.00 0.00 34.72 3.57
2454 2555 4.565166 CGGTGTGCGTATGATTCTCTTTTA 59.435 41.667 0.00 0.00 0.00 1.52
2455 2556 3.370978 CGGTGTGCGTATGATTCTCTTTT 59.629 43.478 0.00 0.00 0.00 2.27
2456 2557 2.930040 CGGTGTGCGTATGATTCTCTTT 59.070 45.455 0.00 0.00 0.00 2.52
2457 2558 2.094182 ACGGTGTGCGTATGATTCTCTT 60.094 45.455 0.00 0.00 0.00 2.85
2458 2559 1.476891 ACGGTGTGCGTATGATTCTCT 59.523 47.619 0.00 0.00 0.00 3.10
2459 2560 1.922570 ACGGTGTGCGTATGATTCTC 58.077 50.000 0.00 0.00 0.00 2.87
2460 2561 3.318275 AGATACGGTGTGCGTATGATTCT 59.682 43.478 0.00 0.00 33.35 2.40
2461 2562 3.639538 AGATACGGTGTGCGTATGATTC 58.360 45.455 0.00 0.00 33.35 2.52
2468 2569 2.042686 TACCTAGATACGGTGTGCGT 57.957 50.000 0.00 0.00 35.98 5.24
2481 2582 4.142816 GCCACACCGTATACGTATACCTAG 60.143 50.000 30.55 23.44 36.13 3.02
2487 2588 0.318107 GCGCCACACCGTATACGTAT 60.318 55.000 22.87 13.54 37.74 3.06
2488 2589 1.063972 GCGCCACACCGTATACGTA 59.936 57.895 22.87 0.00 37.74 3.57
2502 2603 2.497107 ATAACAAATCAGCATGCGCC 57.503 45.000 13.01 0.00 39.83 6.53
2535 2640 2.544903 GGGACACCAAAATGGACAAACG 60.545 50.000 2.85 0.00 40.96 3.60
2573 2678 1.284657 GCACTCATGAGTCCACATCG 58.715 55.000 25.58 13.40 40.20 3.84
2579 2684 1.016130 CACACGGCACTCATGAGTCC 61.016 60.000 25.58 24.44 40.20 3.85
2583 2688 1.301637 CACCACACGGCACTCATGA 60.302 57.895 0.00 0.00 34.57 3.07
2584 2689 2.327343 CCACCACACGGCACTCATG 61.327 63.158 0.00 0.00 34.57 3.07
2593 2698 0.591170 GACCAAATCACCACCACACG 59.409 55.000 0.00 0.00 0.00 4.49
2641 2778 8.147642 CAATTCCTTTGCTTATTAGTCGAGAT 57.852 34.615 0.00 0.00 0.00 2.75
2656 2793 3.983344 CCAAAAGTCGAGCAATTCCTTTG 59.017 43.478 0.00 0.00 38.43 2.77
2658 2795 3.486383 TCCAAAAGTCGAGCAATTCCTT 58.514 40.909 0.00 0.00 0.00 3.36
2660 2797 3.074412 TCTCCAAAAGTCGAGCAATTCC 58.926 45.455 0.00 0.00 0.00 3.01
2661 2798 4.154918 ACATCTCCAAAAGTCGAGCAATTC 59.845 41.667 0.00 0.00 0.00 2.17
2662 2799 4.074970 ACATCTCCAAAAGTCGAGCAATT 58.925 39.130 0.00 0.00 0.00 2.32
2663 2800 3.438087 CACATCTCCAAAAGTCGAGCAAT 59.562 43.478 0.00 0.00 0.00 3.56
2664 2801 2.807967 CACATCTCCAAAAGTCGAGCAA 59.192 45.455 0.00 0.00 0.00 3.91
2665 2802 2.037121 TCACATCTCCAAAAGTCGAGCA 59.963 45.455 0.00 0.00 0.00 4.26
2666 2803 2.688507 TCACATCTCCAAAAGTCGAGC 58.311 47.619 0.00 0.00 0.00 5.03
2667 2804 3.121944 CGTTCACATCTCCAAAAGTCGAG 59.878 47.826 0.00 0.00 0.00 4.04
2668 2805 3.057019 CGTTCACATCTCCAAAAGTCGA 58.943 45.455 0.00 0.00 0.00 4.20
2669 2806 2.157668 CCGTTCACATCTCCAAAAGTCG 59.842 50.000 0.00 0.00 0.00 4.18
2752 2952 7.329717 CGCACAAGCAAACCCTTTATAAATAAA 59.670 33.333 0.00 0.00 42.27 1.40
2753 2953 6.809196 CGCACAAGCAAACCCTTTATAAATAA 59.191 34.615 0.00 0.00 42.27 1.40
2754 2954 6.151312 TCGCACAAGCAAACCCTTTATAAATA 59.849 34.615 0.00 0.00 42.27 1.40
2755 2955 5.047660 TCGCACAAGCAAACCCTTTATAAAT 60.048 36.000 0.00 0.00 42.27 1.40
2756 2956 4.278669 TCGCACAAGCAAACCCTTTATAAA 59.721 37.500 0.00 0.00 42.27 1.40
2757 2957 3.821600 TCGCACAAGCAAACCCTTTATAA 59.178 39.130 0.00 0.00 42.27 0.98
2758 2958 3.413327 TCGCACAAGCAAACCCTTTATA 58.587 40.909 0.00 0.00 42.27 0.98
2759 2959 2.228822 CTCGCACAAGCAAACCCTTTAT 59.771 45.455 0.00 0.00 42.27 1.40
2766 2970 0.040067 CCCTTCTCGCACAAGCAAAC 60.040 55.000 0.00 0.00 42.27 2.93
2801 3005 1.104577 TTCAAAGCGAACCCACACCC 61.105 55.000 0.00 0.00 0.00 4.61
2803 3007 1.399727 CGATTCAAAGCGAACCCACAC 60.400 52.381 0.00 0.00 40.84 3.82
2819 3024 1.209127 CCGCGGCAAAGAAACGATT 59.791 52.632 14.67 0.00 0.00 3.34
2881 3109 4.450419 CACTGTCTTGACATCTGAAAGGTC 59.550 45.833 3.79 0.00 0.00 3.85
2882 3110 4.101585 TCACTGTCTTGACATCTGAAAGGT 59.898 41.667 3.79 0.00 0.00 3.50
2883 3111 4.635223 TCACTGTCTTGACATCTGAAAGG 58.365 43.478 3.79 0.00 0.00 3.11
2903 3134 0.111446 TTTTGCGGGGGAAGACATCA 59.889 50.000 0.00 0.00 0.00 3.07
2934 3165 4.790765 TCTGAATCGAAGACATCACTGT 57.209 40.909 0.00 0.00 42.51 3.55
2935 3166 5.346522 TCATCTGAATCGAAGACATCACTG 58.653 41.667 0.00 0.00 42.51 3.66
2936 3167 5.588958 TCATCTGAATCGAAGACATCACT 57.411 39.130 0.00 0.00 42.51 3.41
2937 3168 6.478016 TCATTCATCTGAATCGAAGACATCAC 59.522 38.462 2.45 0.00 42.41 3.06
2938 3169 6.576185 TCATTCATCTGAATCGAAGACATCA 58.424 36.000 2.45 0.00 42.41 3.07
2939 3170 6.700960 ACTCATTCATCTGAATCGAAGACATC 59.299 38.462 2.45 0.00 42.41 3.06
2940 3171 6.580788 ACTCATTCATCTGAATCGAAGACAT 58.419 36.000 2.45 0.00 42.41 3.06
2941 3172 5.970592 ACTCATTCATCTGAATCGAAGACA 58.029 37.500 2.45 0.00 42.41 3.41
2942 3173 6.900568 AACTCATTCATCTGAATCGAAGAC 57.099 37.500 2.45 0.00 42.41 3.01
2943 3174 9.605275 AATTAACTCATTCATCTGAATCGAAGA 57.395 29.630 2.45 0.00 42.41 2.87
2944 3175 9.861138 GAATTAACTCATTCATCTGAATCGAAG 57.139 33.333 2.45 4.34 42.41 3.79
2945 3176 8.830580 GGAATTAACTCATTCATCTGAATCGAA 58.169 33.333 2.45 0.00 42.41 3.71
2946 3177 7.442364 GGGAATTAACTCATTCATCTGAATCGA 59.558 37.037 2.45 0.00 42.41 3.59
2947 3178 7.570140 CGGGAATTAACTCATTCATCTGAATCG 60.570 40.741 2.45 0.93 42.41 3.34
2948 3179 7.308229 CCGGGAATTAACTCATTCATCTGAATC 60.308 40.741 2.45 0.00 42.41 2.52
2949 3180 6.488006 CCGGGAATTAACTCATTCATCTGAAT 59.512 38.462 0.00 0.00 44.93 2.57
2950 3181 5.822519 CCGGGAATTAACTCATTCATCTGAA 59.177 40.000 0.00 0.00 35.18 3.02
2951 3182 5.104527 ACCGGGAATTAACTCATTCATCTGA 60.105 40.000 6.32 0.00 35.18 3.27
2952 3183 5.126067 ACCGGGAATTAACTCATTCATCTG 58.874 41.667 6.32 0.00 35.18 2.90
2953 3184 5.373812 ACCGGGAATTAACTCATTCATCT 57.626 39.130 6.32 0.00 35.18 2.90
2954 3185 5.733373 GCAACCGGGAATTAACTCATTCATC 60.733 44.000 6.32 0.00 35.18 2.92
2955 3186 4.097892 GCAACCGGGAATTAACTCATTCAT 59.902 41.667 6.32 0.00 35.18 2.57
2956 3187 3.442273 GCAACCGGGAATTAACTCATTCA 59.558 43.478 6.32 0.00 35.18 2.57
2957 3188 3.694566 AGCAACCGGGAATTAACTCATTC 59.305 43.478 6.32 0.00 33.04 2.67
2958 3189 3.697166 AGCAACCGGGAATTAACTCATT 58.303 40.909 6.32 0.00 0.00 2.57
2963 3198 3.428862 CCATGAAGCAACCGGGAATTAAC 60.429 47.826 6.32 0.00 0.00 2.01
2994 3229 4.070716 CTGCAATGACAGATATCTTCCCC 58.929 47.826 1.33 0.00 40.25 4.81
2995 3230 4.070716 CCTGCAATGACAGATATCTTCCC 58.929 47.826 1.33 0.00 40.25 3.97
3057 3292 3.126073 ACACGACCTTCCTTTTTACGAC 58.874 45.455 0.00 0.00 0.00 4.34
3108 3343 2.166459 TCATCTACTCCTTGTGGCTTCG 59.834 50.000 0.00 0.00 0.00 3.79
3110 3345 3.055530 CACTCATCTACTCCTTGTGGCTT 60.056 47.826 0.00 0.00 0.00 4.35
3111 3346 2.499289 CACTCATCTACTCCTTGTGGCT 59.501 50.000 0.00 0.00 0.00 4.75
3117 3352 3.191581 CGTCACACACTCATCTACTCCTT 59.808 47.826 0.00 0.00 0.00 3.36
3118 3353 2.750166 CGTCACACACTCATCTACTCCT 59.250 50.000 0.00 0.00 0.00 3.69
3119 3354 2.732597 GCGTCACACACTCATCTACTCC 60.733 54.545 0.00 0.00 0.00 3.85
3120 3355 2.520979 GCGTCACACACTCATCTACTC 58.479 52.381 0.00 0.00 0.00 2.59
3131 3366 1.142097 TCAGTTTCGGCGTCACACA 59.858 52.632 6.85 0.00 0.00 3.72
3181 3416 2.261671 CCCTCTTCCACCACGACG 59.738 66.667 0.00 0.00 0.00 5.12
3207 3442 1.319374 CGCACGTACGGTACTCATTTG 59.681 52.381 21.06 6.29 0.00 2.32
3286 3521 0.037590 AAATGTGTAAGGCTGCGGGA 59.962 50.000 0.00 0.00 0.00 5.14
3288 3523 2.327568 CAAAAATGTGTAAGGCTGCGG 58.672 47.619 0.00 0.00 0.00 5.69
3305 3540 6.399639 AAAGAAAAGGTAGAATTCGGCAAA 57.600 33.333 0.00 0.00 0.00 3.68
3311 3546 8.127327 GCCGGTATAAAAGAAAAGGTAGAATTC 58.873 37.037 1.90 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.