Multiple sequence alignment - TraesCS4A01G071700

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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 TraesCS4A01G071700 chr4A 100.000 3615 0 0 1 3615 69312926 69316540 0.000000e+00 6676
1 TraesCS4A01G071700 chr4A 89.535 258 25 2 2977 3233 6192404 6192660 3.480000e-85 326
2 TraesCS4A01G071700 chr4D 92.696 2355 104 28 228 2564 388116290 388118594 0.000000e+00 3334
3 TraesCS4A01G071700 chr4D 94.484 562 22 5 3049 3610 388120192 388120744 0.000000e+00 857
4 TraesCS4A01G071700 chr4D 89.508 305 9 4 2774 3057 388118747 388119049 7.380000e-97 364
5 TraesCS4A01G071700 chr4D 86.294 197 21 3 15 206 388115857 388116052 3.660000e-50 209
6 TraesCS4A01G071700 chr4B 86.268 2374 148 70 264 2564 476264346 476266614 0.000000e+00 2414
7 TraesCS4A01G071700 chr4B 88.837 215 18 5 15 226 476263971 476264182 3.580000e-65 259
8 TraesCS4A01G071700 chr6B 89.883 257 23 3 2977 3232 604594661 604594915 9.680000e-86 327
9 TraesCS4A01G071700 chr2B 89.494 257 25 2 2977 3232 368375868 368376123 1.250000e-84 324
10 TraesCS4A01G071700 chr1A 89.764 254 25 1 2979 3232 572223372 572223120 1.250000e-84 324
11 TraesCS4A01G071700 chr7B 89.453 256 25 2 2977 3231 62453468 62453214 4.500000e-84 322
12 TraesCS4A01G071700 chr5B 89.105 257 26 2 2977 3232 84973356 84973101 5.820000e-83 318
13 TraesCS4A01G071700 chr1B 89.105 257 26 2 2977 3232 348417833 348417578 5.820000e-83 318
14 TraesCS4A01G071700 chr3B 86.552 290 35 4 2956 3242 77666226 77665938 2.090000e-82 316


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 TraesCS4A01G071700 chr4A 69312926 69316540 3614 False 6676.0 6676 100.0000 1 3615 1 chr4A.!!$F2 3614
1 TraesCS4A01G071700 chr4D 388115857 388120744 4887 False 1191.0 3334 90.7455 15 3610 4 chr4D.!!$F1 3595
2 TraesCS4A01G071700 chr4B 476263971 476266614 2643 False 1336.5 2414 87.5525 15 2564 2 chr4B.!!$F1 2549

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
997 1321 0.183014 AGCCCATCTCATCAGCCTTG 59.817 55.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2623 3009 0.583438 CCAATATCTCGCCAAGCACG 59.417 55.0 0.0 0.0 0.0 5.34 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
69 70 2.510064 TTAGTTACCGGCCGGCACTG 62.510 60.000 40.75 24.03 39.32 3.66
89 92 2.771372 TGCATAGTGAGTGGCAGGATAA 59.229 45.455 0.00 0.00 0.00 1.75
99 102 4.281657 AGTGGCAGGATAAATTTTCTCCC 58.718 43.478 13.22 3.42 0.00 4.30
133 139 7.774224 TGACGTTTTCAAATAATTGTGATCG 57.226 32.000 0.00 0.00 37.79 3.69
142 148 8.153479 TCAAATAATTGTGATCGGTTGGATAG 57.847 34.615 0.00 0.00 37.79 2.08
143 149 7.990314 TCAAATAATTGTGATCGGTTGGATAGA 59.010 33.333 0.00 0.00 37.79 1.98
144 150 8.620416 CAAATAATTGTGATCGGTTGGATAGAA 58.380 33.333 0.00 0.00 34.82 2.10
145 151 8.746052 AATAATTGTGATCGGTTGGATAGAAA 57.254 30.769 0.00 0.00 34.82 2.52
173 179 1.451651 GTCAAGCGGCAAAATGAAACG 59.548 47.619 1.45 0.00 0.00 3.60
191 197 0.529992 CGGTTAGGGCTCATTCGGTC 60.530 60.000 0.00 0.00 0.00 4.79
205 393 6.183360 GCTCATTCGGTCTACATCATTTCAAA 60.183 38.462 0.00 0.00 0.00 2.69
209 397 6.662414 TCGGTCTACATCATTTCAAATCAC 57.338 37.500 0.00 0.00 0.00 3.06
221 409 4.933505 TTCAAATCACAGAAATGGTGCA 57.066 36.364 0.00 0.00 36.22 4.57
222 410 4.933505 TCAAATCACAGAAATGGTGCAA 57.066 36.364 0.00 0.00 36.22 4.08
223 411 4.873817 TCAAATCACAGAAATGGTGCAAG 58.126 39.130 0.00 0.00 36.22 4.01
225 413 5.534278 TCAAATCACAGAAATGGTGCAAGTA 59.466 36.000 0.00 0.00 36.22 2.24
232 463 5.048713 ACAGAAATGGTGCAAGTAGCTTAAC 60.049 40.000 0.00 0.00 45.94 2.01
252 537 5.358298 AACGCTAAGAATCCTGTCAAAAC 57.642 39.130 0.00 0.00 0.00 2.43
259 544 4.074970 AGAATCCTGTCAAAACGAATGCT 58.925 39.130 0.00 0.00 0.00 3.79
260 545 5.245531 AGAATCCTGTCAAAACGAATGCTA 58.754 37.500 0.00 0.00 0.00 3.49
261 546 5.352569 AGAATCCTGTCAAAACGAATGCTAG 59.647 40.000 0.00 0.00 0.00 3.42
282 581 6.183360 GCTAGTAAACATGGATGAAAATGCCT 60.183 38.462 0.00 0.00 0.00 4.75
289 588 3.290710 TGGATGAAAATGCCTTAGGAGC 58.709 45.455 0.69 0.00 0.00 4.70
290 589 3.290710 GGATGAAAATGCCTTAGGAGCA 58.709 45.455 0.69 0.00 45.94 4.26
308 607 4.162888 GGAGCATTCCAAAAATCCTCCAAT 59.837 41.667 3.39 0.00 43.45 3.16
309 608 5.093849 AGCATTCCAAAAATCCTCCAATG 57.906 39.130 0.00 0.00 0.00 2.82
325 624 5.221185 CCTCCAATGTGAATGAGCCATTAAG 60.221 44.000 1.06 0.00 33.90 1.85
329 628 4.970662 TGTGAATGAGCCATTAAGAAGC 57.029 40.909 1.06 0.00 33.90 3.86
333 632 1.755179 TGAGCCATTAAGAAGCAGCC 58.245 50.000 0.00 0.00 0.00 4.85
335 634 1.674962 GAGCCATTAAGAAGCAGCCAG 59.325 52.381 0.00 0.00 0.00 4.85
366 665 9.841295 ATAGCATAATTGAAAGGCATGATTTTT 57.159 25.926 0.00 0.00 0.00 1.94
398 698 8.846211 CCATATAACCGAAAGACATAATTTGGT 58.154 33.333 0.00 0.00 0.00 3.67
430 730 7.379797 CGTAGTCGAAATCTAATGTCATGATGT 59.620 37.037 0.00 0.00 39.71 3.06
431 731 9.678941 GTAGTCGAAATCTAATGTCATGATGTA 57.321 33.333 0.00 0.00 0.00 2.29
492 793 4.335315 TCATGATCGCATTTTTACCCTCAC 59.665 41.667 0.00 0.00 30.68 3.51
543 844 5.784578 AACATCTTAAAACCCCAAGACAC 57.215 39.130 0.00 0.00 33.78 3.67
556 857 5.487488 ACCCCAAGACACAGATAAATGAGTA 59.513 40.000 0.00 0.00 0.00 2.59
580 881 6.122277 ACAATGTGCATGTACTATAAGGCTT 58.878 36.000 15.25 4.58 0.00 4.35
585 886 4.163268 TGCATGTACTATAAGGCTTGGTCA 59.837 41.667 10.69 7.08 0.00 4.02
608 909 3.798889 GCGGATTGCACTATGCTGTACTA 60.799 47.826 2.02 0.00 45.31 1.82
615 916 7.680442 TTGCACTATGCTGTACTAATTTCAA 57.320 32.000 2.02 0.00 45.31 2.69
663 969 3.844211 TGCTAGAATAGTTGGAACCACCT 59.156 43.478 0.00 0.00 41.93 4.00
666 972 2.576648 AGAATAGTTGGAACCACCTCCC 59.423 50.000 0.00 0.00 39.86 4.30
760 1068 5.048713 ACGAGGTTCTTTTGCCAAGAATAAG 60.049 40.000 10.49 6.57 38.39 1.73
779 1087 7.828223 AGAATAAGACATCTATCCATGAATGCC 59.172 37.037 0.00 0.00 0.00 4.40
799 1107 2.738846 CCATTCTCCGAATAATGCTCCG 59.261 50.000 0.00 0.00 32.79 4.63
864 1172 2.962421 CAGCAAAAGTTTCTAACCCCCA 59.038 45.455 0.00 0.00 0.00 4.96
866 1174 3.578282 AGCAAAAGTTTCTAACCCCCATG 59.422 43.478 0.00 0.00 0.00 3.66
868 1176 2.231716 AAGTTTCTAACCCCCATGCC 57.768 50.000 0.00 0.00 0.00 4.40
874 1182 3.354233 TCTAACCCCCATGCCATAGTA 57.646 47.619 0.00 0.00 0.00 1.82
875 1183 3.671079 TCTAACCCCCATGCCATAGTAA 58.329 45.455 0.00 0.00 0.00 2.24
917 1240 6.312399 TGCCATTAGTAACACACAAGAAAG 57.688 37.500 0.00 0.00 0.00 2.62
977 1301 2.616842 CACAGTACTCAACCAACCAACC 59.383 50.000 0.00 0.00 0.00 3.77
979 1303 2.878406 CAGTACTCAACCAACCAACCAG 59.122 50.000 0.00 0.00 0.00 4.00
992 1316 1.676746 CAACCAGCCCATCTCATCAG 58.323 55.000 0.00 0.00 0.00 2.90
997 1321 0.183014 AGCCCATCTCATCAGCCTTG 59.817 55.000 0.00 0.00 0.00 3.61
1089 1413 2.506957 GGCTAGCTGCTCCCTCCTC 61.507 68.421 15.72 0.00 42.39 3.71
1090 1414 1.457455 GCTAGCTGCTCCCTCCTCT 60.457 63.158 4.91 0.00 38.95 3.69
1091 1415 1.463553 GCTAGCTGCTCCCTCCTCTC 61.464 65.000 4.91 0.00 38.95 3.20
1092 1416 0.827507 CTAGCTGCTCCCTCCTCTCC 60.828 65.000 4.91 0.00 0.00 3.71
1093 1417 2.305314 TAGCTGCTCCCTCCTCTCCC 62.305 65.000 4.91 0.00 0.00 4.30
1129 1453 3.362797 TAGATAGAGCGCCGGCCG 61.363 66.667 23.46 21.04 41.24 6.13
1147 1471 1.235724 CGGCCTTTTCTTCGGTTCTT 58.764 50.000 0.00 0.00 0.00 2.52
1148 1472 1.197036 CGGCCTTTTCTTCGGTTCTTC 59.803 52.381 0.00 0.00 0.00 2.87
1149 1473 2.227194 GGCCTTTTCTTCGGTTCTTCA 58.773 47.619 0.00 0.00 0.00 3.02
1182 1506 9.732130 ATATAGATAGCTTCCATCTTTTTGGTC 57.268 33.333 2.87 0.00 38.01 4.02
1190 1514 2.562738 CCATCTTTTTGGTCCACTTCCC 59.437 50.000 0.00 0.00 31.74 3.97
1211 1535 3.129988 CCCTTCTTGCATGTTCTTGATCC 59.870 47.826 0.00 0.00 0.00 3.36
1229 1553 4.101119 TGATCCCTTCTCGATCTAAAACCC 59.899 45.833 0.00 0.00 37.59 4.11
1236 1560 1.779569 CGATCTAAAACCCCCGATCG 58.220 55.000 8.51 8.51 45.87 3.69
1238 1562 3.679824 GATCTAAAACCCCCGATCGAT 57.320 47.619 18.66 0.00 0.00 3.59
1239 1563 3.586892 GATCTAAAACCCCCGATCGATC 58.413 50.000 18.66 15.68 0.00 3.69
1287 1611 6.264518 TGTTGTTTTTCTTCCCAAGGATCTAC 59.735 38.462 0.00 0.00 0.00 2.59
1288 1612 5.001232 TGTTTTTCTTCCCAAGGATCTACG 58.999 41.667 0.00 0.00 0.00 3.51
1289 1613 5.221762 TGTTTTTCTTCCCAAGGATCTACGA 60.222 40.000 0.00 0.00 0.00 3.43
1290 1614 4.737855 TTTCTTCCCAAGGATCTACGAG 57.262 45.455 0.00 0.00 0.00 4.18
1291 1615 3.383698 TCTTCCCAAGGATCTACGAGT 57.616 47.619 0.00 0.00 0.00 4.18
1292 1616 4.515028 TCTTCCCAAGGATCTACGAGTA 57.485 45.455 0.00 0.00 0.00 2.59
1293 1617 4.462133 TCTTCCCAAGGATCTACGAGTAG 58.538 47.826 3.98 3.98 34.56 2.57
1294 1618 2.584236 TCCCAAGGATCTACGAGTAGC 58.416 52.381 5.44 0.00 33.32 3.58
1295 1619 2.175069 TCCCAAGGATCTACGAGTAGCT 59.825 50.000 5.44 0.00 33.32 3.32
1296 1620 3.393609 TCCCAAGGATCTACGAGTAGCTA 59.606 47.826 5.44 0.00 33.32 3.32
1297 1621 3.754323 CCCAAGGATCTACGAGTAGCTAG 59.246 52.174 5.44 0.00 33.32 3.42
1298 1622 3.189702 CCAAGGATCTACGAGTAGCTAGC 59.810 52.174 6.62 6.62 33.32 3.42
1299 1623 4.069304 CAAGGATCTACGAGTAGCTAGCT 58.931 47.826 23.12 23.12 33.32 3.32
1300 1624 4.360951 AGGATCTACGAGTAGCTAGCTT 57.639 45.455 24.88 5.38 33.32 3.74
1301 1625 4.320870 AGGATCTACGAGTAGCTAGCTTC 58.679 47.826 24.88 18.51 33.32 3.86
1408 1766 6.852908 TCTTCTCCTCCTACTCCTATCTAGTT 59.147 42.308 0.00 0.00 0.00 2.24
1409 1767 7.351454 TCTTCTCCTCCTACTCCTATCTAGTTT 59.649 40.741 0.00 0.00 0.00 2.66
1553 1911 4.154918 CAGTACCATCACTTCCAGAAAAGC 59.845 45.833 0.00 0.00 0.00 3.51
2154 2512 3.556513 CGCCTCTAGTATCGTGACAATC 58.443 50.000 0.00 0.00 0.00 2.67
2159 2517 2.981859 AGTATCGTGACAATCACCCC 57.018 50.000 3.45 0.00 44.20 4.95
2195 2553 2.581409 GTACGTGATCCCGGCGTG 60.581 66.667 13.38 0.00 39.31 5.34
2258 2616 2.285977 CTGGCTGGGAAAATACGTACC 58.714 52.381 0.00 0.00 0.00 3.34
2274 2635 7.928307 ATACGTACCACTACTAGAAGACAAA 57.072 36.000 0.00 0.00 0.00 2.83
2276 2637 5.182760 ACGTACCACTACTAGAAGACAAAGG 59.817 44.000 0.00 0.00 0.00 3.11
2339 2708 1.148157 CGTGATGTGGCCGTCAGATC 61.148 60.000 3.20 3.20 43.93 2.75
2340 2709 1.141665 TGATGTGGCCGTCAGATCG 59.858 57.895 5.72 0.00 45.86 3.69
2341 2710 1.319614 TGATGTGGCCGTCAGATCGA 61.320 55.000 5.72 0.00 45.86 3.59
2342 2711 0.032678 GATGTGGCCGTCAGATCGAT 59.967 55.000 0.00 0.00 36.60 3.59
2499 2879 3.542875 CGCGTATGCTCTTGTTCTTGATG 60.543 47.826 5.20 0.00 39.65 3.07
2607 2993 7.701539 ATGTATGTGGTGATGTTTATGTGTT 57.298 32.000 0.00 0.00 0.00 3.32
2653 3039 1.521423 GAGATATTGGCGCGTGTACAC 59.479 52.381 16.32 16.32 0.00 2.90
2664 3050 3.613563 CGCGTGTACACATTGTTTTTCT 58.386 40.909 24.98 0.00 0.00 2.52
2677 3063 8.111836 CACATTGTTTTTCTTGTGATCTTTGTG 58.888 33.333 0.00 0.00 41.50 3.33
2693 3079 4.570369 TCTTTGTGTGCATGTATGTATCCG 59.430 41.667 0.00 0.00 0.00 4.18
2704 3090 4.476297 TGTATGTATCCGGTGGACACTAT 58.524 43.478 0.00 0.00 32.98 2.12
2718 3104 6.442952 GTGGACACTATTAGCTAGACATCAG 58.557 44.000 0.00 0.00 0.00 2.90
2735 3121 7.170965 AGACATCAGTTATGAATGGACAGTTT 58.829 34.615 0.00 0.00 39.39 2.66
2737 3123 8.862325 ACATCAGTTATGAATGGACAGTTTTA 57.138 30.769 0.00 0.00 39.39 1.52
2739 3125 9.941664 CATCAGTTATGAATGGACAGTTTTATC 57.058 33.333 0.00 0.00 39.39 1.75
2742 3128 9.388506 CAGTTATGAATGGACAGTTTTATCTCT 57.611 33.333 0.00 0.00 0.00 3.10
2743 3129 9.965902 AGTTATGAATGGACAGTTTTATCTCTT 57.034 29.630 0.00 0.00 0.00 2.85
2767 3153 4.691326 TTTTTGCGGGGTTAAAAGGATT 57.309 36.364 0.00 0.00 0.00 3.01
2768 3154 4.691326 TTTTGCGGGGTTAAAAGGATTT 57.309 36.364 0.00 0.00 42.41 2.17
2769 3155 3.945981 TTGCGGGGTTAAAAGGATTTC 57.054 42.857 0.00 0.00 37.28 2.17
2770 3156 2.877866 TGCGGGGTTAAAAGGATTTCA 58.122 42.857 0.00 0.00 37.28 2.69
2771 3157 3.436243 TGCGGGGTTAAAAGGATTTCAT 58.564 40.909 0.00 0.00 37.28 2.57
2772 3158 3.835395 TGCGGGGTTAAAAGGATTTCATT 59.165 39.130 0.00 0.00 37.28 2.57
2799 3185 1.923148 CCAAGTCCCTTTACCCCATCT 59.077 52.381 0.00 0.00 0.00 2.90
2800 3186 2.092375 CCAAGTCCCTTTACCCCATCTC 60.092 54.545 0.00 0.00 0.00 2.75
2830 3216 9.170584 GTTTTAATTCTGAAGACAAACAGTAGC 57.829 33.333 12.58 0.00 35.84 3.58
2846 3232 8.819974 CAAACAGTAGCATTTGAACTGAAATTT 58.180 29.630 15.95 0.00 42.59 1.82
2877 3263 7.442364 GTGGAAACTATATAGATGCACACATGT 59.558 37.037 25.01 0.00 36.35 3.21
2930 3316 2.378547 AGAAATGCCCCTTGTTCCACTA 59.621 45.455 0.00 0.00 0.00 2.74
2975 3361 7.064490 GGACATTTTTCTTTTCTTGAACAAGCA 59.936 33.333 9.38 0.00 38.28 3.91
2997 3403 5.123344 GCATCCGTTTCTAAATGTAAGGTGT 59.877 40.000 0.00 0.00 0.00 4.16
3225 4783 9.780186 AATACACCTTATATTTAGGAACAGAGC 57.220 33.333 9.82 0.00 36.58 4.09
3236 4794 7.812690 TTTAGGAACAGAGCGAGTATATACA 57.187 36.000 15.18 0.00 0.00 2.29
3244 4802 4.917998 AGAGCGAGTATATACAAACATGCG 59.082 41.667 15.18 7.58 0.00 4.73
3368 4926 9.434420 TTGCCTTGTGGATATAATTTTCTTTTG 57.566 29.630 0.00 0.00 34.57 2.44
3606 5164 1.192146 AGCACGGGCCTTCTCAGTTA 61.192 55.000 5.73 0.00 42.56 2.24
3610 5168 1.275573 ACGGGCCTTCTCAGTTAAGAC 59.724 52.381 0.84 0.00 0.00 3.01
3611 5169 1.275291 CGGGCCTTCTCAGTTAAGACA 59.725 52.381 0.84 0.00 0.00 3.41
3612 5170 2.093447 CGGGCCTTCTCAGTTAAGACAT 60.093 50.000 0.84 0.00 0.00 3.06
3613 5171 3.619979 CGGGCCTTCTCAGTTAAGACATT 60.620 47.826 0.84 0.00 0.00 2.71
3614 5172 3.942115 GGGCCTTCTCAGTTAAGACATTC 59.058 47.826 0.84 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.598685 GTTTTGGCCGAGGACCGAA 60.599 57.895 0.00 0.00 41.76 4.30
1 2 2.031465 GTTTTGGCCGAGGACCGA 59.969 61.111 0.00 0.00 41.76 4.69
2 3 1.448922 TTTGTTTTGGCCGAGGACCG 61.449 55.000 0.00 0.00 38.18 4.79
3 4 0.966179 ATTTGTTTTGGCCGAGGACC 59.034 50.000 0.00 0.00 0.00 4.46
4 5 1.401018 CGATTTGTTTTGGCCGAGGAC 60.401 52.381 0.00 0.00 0.00 3.85
5 6 0.878416 CGATTTGTTTTGGCCGAGGA 59.122 50.000 0.00 0.00 0.00 3.71
6 7 0.878416 TCGATTTGTTTTGGCCGAGG 59.122 50.000 0.00 0.00 0.00 4.63
7 8 2.287308 TGTTCGATTTGTTTTGGCCGAG 60.287 45.455 0.00 0.00 0.00 4.63
8 9 1.676529 TGTTCGATTTGTTTTGGCCGA 59.323 42.857 0.00 0.00 0.00 5.54
9 10 2.126914 TGTTCGATTTGTTTTGGCCG 57.873 45.000 0.00 0.00 0.00 6.13
10 11 2.799978 CCTTGTTCGATTTGTTTTGGCC 59.200 45.455 0.00 0.00 0.00 5.36
11 12 3.453424 ACCTTGTTCGATTTGTTTTGGC 58.547 40.909 0.00 0.00 0.00 4.52
12 13 6.291374 CGTTTACCTTGTTCGATTTGTTTTGG 60.291 38.462 0.00 0.00 0.00 3.28
13 14 6.623633 CGTTTACCTTGTTCGATTTGTTTTG 58.376 36.000 0.00 0.00 0.00 2.44
69 70 3.475566 TTATCCTGCCACTCACTATGC 57.524 47.619 0.00 0.00 0.00 3.14
89 92 7.967908 ACGTCATAGATAGATGGGAGAAAATT 58.032 34.615 0.00 0.00 0.00 1.82
144 150 6.426328 TCATTTTGCCGCTTGACATAATTTTT 59.574 30.769 0.00 0.00 0.00 1.94
145 151 5.931146 TCATTTTGCCGCTTGACATAATTTT 59.069 32.000 0.00 0.00 0.00 1.82
149 155 4.511617 TTCATTTTGCCGCTTGACATAA 57.488 36.364 0.00 0.00 0.00 1.90
159 165 2.591133 CCTAACCGTTTCATTTTGCCG 58.409 47.619 0.00 0.00 0.00 5.69
162 168 3.254657 TGAGCCCTAACCGTTTCATTTTG 59.745 43.478 0.00 0.00 0.00 2.44
173 179 0.831307 AGACCGAATGAGCCCTAACC 59.169 55.000 0.00 0.00 0.00 2.85
205 393 3.441572 GCTACTTGCACCATTTCTGTGAT 59.558 43.478 0.00 0.00 42.31 3.06
209 397 5.393962 GTTAAGCTACTTGCACCATTTCTG 58.606 41.667 0.00 0.00 45.94 3.02
232 463 3.678072 TCGTTTTGACAGGATTCTTAGCG 59.322 43.478 0.00 0.00 0.00 4.26
252 537 6.603237 TTCATCCATGTTTACTAGCATTCG 57.397 37.500 0.00 0.00 0.00 3.34
259 544 7.716799 AAGGCATTTTCATCCATGTTTACTA 57.283 32.000 0.00 0.00 0.00 1.82
260 545 6.610075 AAGGCATTTTCATCCATGTTTACT 57.390 33.333 0.00 0.00 0.00 2.24
261 546 6.980397 CCTAAGGCATTTTCATCCATGTTTAC 59.020 38.462 0.00 0.00 0.00 2.01
289 588 6.040209 TCACATTGGAGGATTTTTGGAATG 57.960 37.500 0.00 0.00 0.00 2.67
290 589 6.684897 TTCACATTGGAGGATTTTTGGAAT 57.315 33.333 0.00 0.00 0.00 3.01
308 607 4.334552 TGCTTCTTAATGGCTCATTCACA 58.665 39.130 4.01 0.00 35.54 3.58
309 608 4.732938 GCTGCTTCTTAATGGCTCATTCAC 60.733 45.833 4.01 0.00 35.54 3.18
325 624 1.012841 GCTATGTCACTGGCTGCTTC 58.987 55.000 0.00 0.00 0.00 3.86
329 628 4.818005 TCAATTATGCTATGTCACTGGCTG 59.182 41.667 0.00 0.00 0.00 4.85
333 632 6.183360 TGCCTTTCAATTATGCTATGTCACTG 60.183 38.462 0.00 0.00 0.00 3.66
335 634 6.135290 TGCCTTTCAATTATGCTATGTCAC 57.865 37.500 0.00 0.00 0.00 3.67
366 665 5.991861 TGTCTTTCGGTTATATGGCCTAAA 58.008 37.500 3.32 0.00 0.00 1.85
369 668 4.706842 ATGTCTTTCGGTTATATGGCCT 57.293 40.909 3.32 0.00 0.00 5.19
370 669 7.448748 AATTATGTCTTTCGGTTATATGGCC 57.551 36.000 0.00 0.00 0.00 5.36
492 793 0.111253 AGACTTGTCCCTTGGCCAAG 59.889 55.000 34.60 34.60 41.02 3.61
543 844 7.700505 ACATGCACATTGTACTCATTTATCTG 58.299 34.615 0.00 0.00 0.00 2.90
556 857 5.684704 AGCCTTATAGTACATGCACATTGT 58.315 37.500 0.00 0.00 0.00 2.71
580 881 0.541392 ATAGTGCAATCCGCTGACCA 59.459 50.000 0.00 0.00 43.06 4.02
663 969 1.078988 GGTTGCGTTCGGTATGGGA 60.079 57.895 0.00 0.00 0.00 4.37
666 972 2.222953 GCTTTAGGTTGCGTTCGGTATG 60.223 50.000 0.00 0.00 0.00 2.39
733 1040 2.341846 TGGCAAAAGAACCTCGTCTT 57.658 45.000 0.00 0.00 39.60 3.01
734 1041 2.158813 TCTTGGCAAAAGAACCTCGTCT 60.159 45.455 0.00 0.00 0.00 4.18
760 1068 5.944599 AGAATGGCATTCATGGATAGATGTC 59.055 40.000 34.54 9.98 41.71 3.06
779 1087 2.738846 CCGGAGCATTATTCGGAGAATG 59.261 50.000 6.69 6.69 45.90 2.67
799 1107 0.915364 ACTGATTCCTTGCCTCTCCC 59.085 55.000 0.00 0.00 0.00 4.30
864 1172 6.127869 TGCACGTGTTAATTTTACTATGGCAT 60.128 34.615 18.38 4.88 0.00 4.40
866 1174 5.632959 TGCACGTGTTAATTTTACTATGGC 58.367 37.500 18.38 0.00 0.00 4.40
868 1176 7.806014 AGGTTTGCACGTGTTAATTTTACTATG 59.194 33.333 18.38 0.00 0.00 2.23
917 1240 6.697892 CCTCACATAAACTATCTTCCTCGAAC 59.302 42.308 0.00 0.00 0.00 3.95
958 1282 2.878406 CTGGTTGGTTGGTTGAGTACTG 59.122 50.000 0.00 0.00 0.00 2.74
977 1301 0.183014 AAGGCTGATGAGATGGGCTG 59.817 55.000 0.00 0.00 34.86 4.85
979 1303 1.453762 GCAAGGCTGATGAGATGGGC 61.454 60.000 0.00 0.00 0.00 5.36
1089 1413 1.292941 TGGAGAGGAGAGGAGGGGAG 61.293 65.000 0.00 0.00 0.00 4.30
1090 1414 1.230650 TGGAGAGGAGAGGAGGGGA 60.231 63.158 0.00 0.00 0.00 4.81
1091 1415 1.075600 GTGGAGAGGAGAGGAGGGG 60.076 68.421 0.00 0.00 0.00 4.79
1092 1416 1.075600 GGTGGAGAGGAGAGGAGGG 60.076 68.421 0.00 0.00 0.00 4.30
1093 1417 1.454847 CGGTGGAGAGGAGAGGAGG 60.455 68.421 0.00 0.00 0.00 4.30
1129 1453 2.227194 TGAAGAACCGAAGAAAAGGCC 58.773 47.619 0.00 0.00 0.00 5.19
1130 1454 3.502211 TGATGAAGAACCGAAGAAAAGGC 59.498 43.478 0.00 0.00 0.00 4.35
1131 1455 4.757149 AGTGATGAAGAACCGAAGAAAAGG 59.243 41.667 0.00 0.00 0.00 3.11
1132 1456 5.466728 TCAGTGATGAAGAACCGAAGAAAAG 59.533 40.000 0.00 0.00 0.00 2.27
1147 1471 8.835550 ATGGAAGCTATCTATATCAGTGATGA 57.164 34.615 16.15 5.02 0.00 2.92
1148 1472 8.916062 AGATGGAAGCTATCTATATCAGTGATG 58.084 37.037 16.15 0.00 33.30 3.07
1149 1473 9.491406 AAGATGGAAGCTATCTATATCAGTGAT 57.509 33.333 11.12 11.12 33.92 3.06
1182 1506 1.180029 CATGCAAGAAGGGGAAGTGG 58.820 55.000 0.00 0.00 0.00 4.00
1190 1514 3.129988 GGGATCAAGAACATGCAAGAAGG 59.870 47.826 0.00 0.00 0.00 3.46
1211 1535 2.483188 CGGGGGTTTTAGATCGAGAAGG 60.483 54.545 0.00 0.00 0.00 3.46
1237 1561 2.992593 TGCTAGCTAGGATCGATCGAT 58.007 47.619 29.76 29.76 37.59 3.59
1238 1562 2.474410 TGCTAGCTAGGATCGATCGA 57.526 50.000 21.86 21.86 0.00 3.59
1239 1563 3.332761 GATGCTAGCTAGGATCGATCG 57.667 52.381 31.56 9.36 40.48 3.69
1287 1611 3.112580 GCAAGAAGAAGCTAGCTACTCG 58.887 50.000 19.70 6.23 0.00 4.18
1288 1612 4.111916 CTGCAAGAAGAAGCTAGCTACTC 58.888 47.826 19.70 13.18 34.07 2.59
1289 1613 3.766591 TCTGCAAGAAGAAGCTAGCTACT 59.233 43.478 19.70 12.19 42.31 2.57
1290 1614 4.116747 TCTGCAAGAAGAAGCTAGCTAC 57.883 45.455 19.70 10.07 42.31 3.58
1408 1766 2.143122 GCAGAACGTTCTCCATGTCAA 58.857 47.619 27.54 0.00 34.74 3.18
1409 1767 1.344438 AGCAGAACGTTCTCCATGTCA 59.656 47.619 27.54 0.00 34.74 3.58
1577 1935 4.301027 GCATACGGGAGAGCGGGG 62.301 72.222 0.00 0.00 0.00 5.73
1787 2145 4.383861 TGGCTCAGCTGGCGTGAG 62.384 66.667 15.13 4.58 43.77 3.51
2171 2529 1.429021 GGGATCACGTACGTGCGTA 59.571 57.895 37.13 24.13 43.83 4.42
2172 2530 2.180017 GGGATCACGTACGTGCGT 59.820 61.111 37.13 28.58 46.88 5.24
2195 2553 5.969435 GGAAATAATTAACAGTAGCAACGGC 59.031 40.000 0.00 0.00 41.61 5.68
2258 2616 7.887381 TCTTCTTCCTTTGTCTTCTAGTAGTG 58.113 38.462 0.00 0.00 0.00 2.74
2274 2635 3.072184 AGCATCACACAACTCTTCTTCCT 59.928 43.478 0.00 0.00 0.00 3.36
2276 2637 3.188048 CCAGCATCACACAACTCTTCTTC 59.812 47.826 0.00 0.00 0.00 2.87
2354 2727 3.083997 ACGGCTGGACCCCATCTC 61.084 66.667 0.00 0.00 30.82 2.75
2450 2830 2.245096 CAGGCACGTAACGTACAGTAC 58.755 52.381 0.00 0.00 38.32 2.73
2572 2958 9.905713 ACATCACCACATACATTATACTCTTTT 57.094 29.630 0.00 0.00 0.00 2.27
2573 2959 9.905713 AACATCACCACATACATTATACTCTTT 57.094 29.630 0.00 0.00 0.00 2.52
2574 2960 9.905713 AAACATCACCACATACATTATACTCTT 57.094 29.630 0.00 0.00 0.00 2.85
2602 2988 8.995220 AGCACGAGATTTAATTTAAGTAACACA 58.005 29.630 0.00 0.00 0.00 3.72
2607 2993 7.469260 GCCAAGCACGAGATTTAATTTAAGTA 58.531 34.615 0.00 0.00 0.00 2.24
2623 3009 0.583438 CCAATATCTCGCCAAGCACG 59.417 55.000 0.00 0.00 0.00 5.34
2635 3021 1.282817 TGTGTACACGCGCCAATATC 58.717 50.000 20.61 0.00 0.00 1.63
2653 3039 8.111836 CACACAAAGATCACAAGAAAAACAATG 58.888 33.333 0.00 0.00 0.00 2.82
2664 3050 5.241285 ACATACATGCACACAAAGATCACAA 59.759 36.000 0.00 0.00 0.00 3.33
2677 3063 2.143122 CCACCGGATACATACATGCAC 58.857 52.381 9.46 0.00 0.00 4.57
2693 3079 5.302059 TGATGTCTAGCTAATAGTGTCCACC 59.698 44.000 0.00 0.00 32.85 4.61
2704 3090 8.144478 GTCCATTCATAACTGATGTCTAGCTAA 58.856 37.037 0.00 0.00 36.84 3.09
2746 3132 4.691326 AATCCTTTTAACCCCGCAAAAA 57.309 36.364 0.00 0.00 0.00 1.94
2747 3133 4.101119 TGAAATCCTTTTAACCCCGCAAAA 59.899 37.500 0.00 0.00 0.00 2.44
2748 3134 3.641906 TGAAATCCTTTTAACCCCGCAAA 59.358 39.130 0.00 0.00 0.00 3.68
2749 3135 3.231818 TGAAATCCTTTTAACCCCGCAA 58.768 40.909 0.00 0.00 0.00 4.85
2750 3136 2.877866 TGAAATCCTTTTAACCCCGCA 58.122 42.857 0.00 0.00 0.00 5.69
2751 3137 4.465632 AATGAAATCCTTTTAACCCCGC 57.534 40.909 0.00 0.00 0.00 6.13
2752 3138 7.158697 AGAAAAATGAAATCCTTTTAACCCCG 58.841 34.615 0.00 0.00 0.00 5.73
2753 3139 8.918202 AAGAAAAATGAAATCCTTTTAACCCC 57.082 30.769 0.00 0.00 0.00 4.95
2754 3140 8.999431 GGAAGAAAAATGAAATCCTTTTAACCC 58.001 33.333 0.00 0.00 0.00 4.11
2755 3141 9.554395 TGGAAGAAAAATGAAATCCTTTTAACC 57.446 29.630 0.00 0.00 0.00 2.85
2759 3145 9.330063 GACTTGGAAGAAAAATGAAATCCTTTT 57.670 29.630 0.00 0.00 0.00 2.27
2760 3146 7.933577 GGACTTGGAAGAAAAATGAAATCCTTT 59.066 33.333 0.00 0.00 0.00 3.11
2761 3147 7.445121 GGACTTGGAAGAAAAATGAAATCCTT 58.555 34.615 0.00 0.00 0.00 3.36
2762 3148 6.014242 GGGACTTGGAAGAAAAATGAAATCCT 60.014 38.462 0.00 0.00 0.00 3.24
2763 3149 6.014242 AGGGACTTGGAAGAAAAATGAAATCC 60.014 38.462 0.00 0.00 27.25 3.01
2764 3150 6.997655 AGGGACTTGGAAGAAAAATGAAATC 58.002 36.000 0.00 0.00 27.25 2.17
2799 3185 8.616942 TGTTTGTCTTCAGAATTAAAACATCGA 58.383 29.630 10.92 0.00 0.00 3.59
2800 3186 8.781067 TGTTTGTCTTCAGAATTAAAACATCG 57.219 30.769 10.92 0.00 0.00 3.84
2830 3216 7.432869 TCCACTACCAAATTTCAGTTCAAATG 58.567 34.615 0.00 0.00 0.00 2.32
2846 3232 7.289084 TGTGCATCTATATAGTTTCCACTACCA 59.711 37.037 9.58 0.00 38.38 3.25
2915 3301 3.737702 TGTTAGTGGAACAAGGGGC 57.262 52.632 0.00 0.00 45.23 5.80
2930 3316 4.583871 GTCCTGGAGACATTGATCTTGTT 58.416 43.478 0.00 0.00 45.55 2.83
3224 4782 3.183574 TGCGCATGTTTGTATATACTCGC 59.816 43.478 5.66 14.73 39.33 5.03
3225 4783 4.679654 TCTGCGCATGTTTGTATATACTCG 59.320 41.667 12.24 7.08 0.00 4.18


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

AutoCloner maintained by Alex Coulton.