Multiple sequence alignment - TraesCS1A01G226200

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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 TraesCS1A01G226200 chr1A 100.000 2960 0 0 1 2960 396424566 396427525 0.000000e+00 5467.0
1 TraesCS1A01G226200 chr1B 89.036 1286 87 22 1 1250 428065916 428067183 0.000000e+00 1544.0
2 TraesCS1A01G226200 chr1B 91.022 724 33 16 1478 2191 428067268 428067969 0.000000e+00 948.0
3 TraesCS1A01G226200 chr1B 94.643 224 11 1 2737 2960 428068434 428068656 2.180000e-91 346.0
4 TraesCS1A01G226200 chr1D 83.180 1522 124 67 753 2191 315976049 315977521 0.000000e+00 1271.0
5 TraesCS1A01G226200 chr1D 87.037 756 54 16 1 739 315975144 315975872 0.000000e+00 813.0
6 TraesCS1A01G226200 chr1D 96.175 366 14 0 2595 2960 315978130 315978495 1.520000e-167 599.0
7 TraesCS1A01G226200 chr1D 84.987 393 32 11 2207 2578 315977699 315978085 1.000000e-99 374.0
8 TraesCS1A01G226200 chr1D 81.890 127 15 6 1278 1396 405101302 405101176 1.880000e-17 100.0
9 TraesCS1A01G226200 chr1D 94.286 35 1 1 2186 2219 315977629 315977663 5.000000e-03 52.8
10 TraesCS1A01G226200 chr5A 93.421 76 5 0 1278 1353 374665645 374665720 2.410000e-21 113.0
11 TraesCS1A01G226200 chr5A 79.104 134 18 7 1273 1396 579217037 579217170 1.890000e-12 84.2
12 TraesCS1A01G226200 chr4B 91.358 81 6 1 1274 1353 520933538 520933618 3.120000e-20 110.0
13 TraesCS1A01G226200 chr4A 85.047 107 14 2 1279 1383 486498062 486497956 1.120000e-19 108.0
14 TraesCS1A01G226200 chr3B 87.640 89 9 2 1265 1353 107640585 107640671 5.220000e-18 102.0
15 TraesCS1A01G226200 chr6D 82.400 125 13 6 1278 1394 264177665 264177788 1.880000e-17 100.0
16 TraesCS1A01G226200 chr6D 89.610 77 8 0 1277 1353 84091496 84091572 6.750000e-17 99.0


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 TraesCS1A01G226200 chr1A 396424566 396427525 2959 False 5467.00 5467 100.000 1 2960 1 chr1A.!!$F1 2959
1 TraesCS1A01G226200 chr1B 428065916 428068656 2740 False 946.00 1544 91.567 1 2960 3 chr1B.!!$F1 2959
2 TraesCS1A01G226200 chr1D 315975144 315978495 3351 False 621.96 1271 89.133 1 2960 5 chr1D.!!$F1 2959

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
65 66 0.553612 AGGGATTTTCCTCAGGGGCT 60.554 55.000 0.0 0.0 36.57 5.19 F
446 463 1.064803 CGGCAAAAGTTACACAGCACA 59.935 47.619 0.0 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1069 1284 0.251354 CTAGAGAAGCAGCCTGGCAA 59.749 55.0 22.65 0.0 35.83 4.52 R
2071 2359 0.459899 TGAGAGAATACCACGCGCAT 59.540 50.0 5.73 0.0 0.00 4.73 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
65 66 0.553612 AGGGATTTTCCTCAGGGGCT 60.554 55.000 0.00 0.00 36.57 5.19
94 95 4.998033 TCGAAAAATGTACATGGTGTAGCA 59.002 37.500 9.63 0.00 32.84 3.49
164 177 9.213819 CTGTGTTTATAATGTGTGATCATTTCG 57.786 33.333 0.00 0.00 38.68 3.46
262 275 6.830912 CCTGTTAGAGGGTCATTGATTATGA 58.169 40.000 0.00 0.00 38.35 2.15
263 276 7.456725 CCTGTTAGAGGGTCATTGATTATGAT 58.543 38.462 0.00 0.00 38.03 2.45
264 277 7.941238 CCTGTTAGAGGGTCATTGATTATGATT 59.059 37.037 0.00 0.00 38.03 2.57
377 394 6.853872 GTCACATGAAAAGCATACGTTTTACA 59.146 34.615 0.00 0.00 34.82 2.41
396 413 3.604582 ACAAGATGAGCAAGTAGGCTTC 58.395 45.455 0.00 0.00 45.99 3.86
446 463 1.064803 CGGCAAAAGTTACACAGCACA 59.935 47.619 0.00 0.00 0.00 4.57
477 494 4.217754 TGGCGTAACAAGTGACAAAATC 57.782 40.909 0.00 0.00 0.00 2.17
666 689 5.064558 TGAAACTTTAGTGCCGGTGAAATA 58.935 37.500 1.90 0.00 0.00 1.40
697 723 9.847224 ACTAATATAATAGAAACTGTTGGTGGG 57.153 33.333 1.72 0.00 0.00 4.61
722 748 3.188048 CACACCTTGAGAAAGTGCATCTC 59.812 47.826 8.58 8.58 42.94 2.75
730 756 3.357203 AGAAAGTGCATCTCGAGGAGTA 58.643 45.455 13.56 1.99 0.00 2.59
731 757 3.129638 AGAAAGTGCATCTCGAGGAGTAC 59.870 47.826 13.56 14.34 0.00 2.73
739 765 6.480320 GTGCATCTCGAGGAGTACAAATATTT 59.520 38.462 13.56 0.00 0.00 1.40
776 965 1.448985 TCCTTTTCAAATCTCCGCCG 58.551 50.000 0.00 0.00 0.00 6.46
789 978 1.849829 CTCCGCCGAAAACAAAAACAC 59.150 47.619 0.00 0.00 0.00 3.32
803 992 3.525268 AAAACACTGCAGAAAGTTGGG 57.475 42.857 23.35 0.00 0.00 4.12
806 995 1.108727 CACTGCAGAAAGTTGGGCCA 61.109 55.000 23.35 0.00 0.00 5.36
853 1042 2.294233 GCAAAGAGTGAGCAATTGACCA 59.706 45.455 10.34 2.72 0.00 4.02
909 1124 7.226128 GCAGGAAATTAACCCCGTATATATAGC 59.774 40.741 0.00 0.00 0.00 2.97
927 1142 1.154921 CCAATCAACCCACACCCCA 59.845 57.895 0.00 0.00 0.00 4.96
970 1185 2.096819 CGGCACTGGCGTAAAACATATT 59.903 45.455 16.48 0.00 46.33 1.28
994 1209 3.426568 GCTCAGCACACCTTCCGC 61.427 66.667 0.00 0.00 0.00 5.54
1020 1235 2.679716 GCAATGCCTCCTCACCCT 59.320 61.111 0.00 0.00 0.00 4.34
1022 1237 1.318158 GCAATGCCTCCTCACCCTTG 61.318 60.000 0.00 0.00 0.00 3.61
1026 1241 2.266055 CCTCCTCACCCTTGTCGC 59.734 66.667 0.00 0.00 0.00 5.19
1027 1242 2.125912 CTCCTCACCCTTGTCGCG 60.126 66.667 0.00 0.00 0.00 5.87
1086 1301 1.303155 GTTGCCAGGCTGCTTCTCT 60.303 57.895 14.15 0.00 0.00 3.10
1094 1309 1.824230 AGGCTGCTTCTCTAGTGAGTG 59.176 52.381 0.00 0.00 40.98 3.51
1104 1319 9.443323 TGCTTCTCTAGTGAGTGTATATCTATC 57.557 37.037 0.00 0.00 40.98 2.08
1158 1379 5.485209 AAATCAGTCTCGGGAAAACTAGT 57.515 39.130 0.00 0.00 0.00 2.57
1163 1384 4.448060 CAGTCTCGGGAAAACTAGTTCAAC 59.552 45.833 8.95 3.57 0.00 3.18
1164 1385 4.344390 AGTCTCGGGAAAACTAGTTCAACT 59.656 41.667 8.95 0.00 0.00 3.16
1166 1387 5.526479 GTCTCGGGAAAACTAGTTCAACTTT 59.474 40.000 8.95 0.00 0.00 2.66
1167 1388 6.037940 GTCTCGGGAAAACTAGTTCAACTTTT 59.962 38.462 8.95 0.00 0.00 2.27
1169 1390 6.117488 TCGGGAAAACTAGTTCAACTTTTCT 58.883 36.000 8.95 0.00 28.51 2.52
1170 1391 6.037830 TCGGGAAAACTAGTTCAACTTTTCTG 59.962 38.462 8.95 3.31 28.51 3.02
1194 1434 0.680618 CTCCATGGTTGCAGGCAAAA 59.319 50.000 12.58 0.70 37.70 2.44
1254 1494 3.060761 CGACGACCACAATGTAAGTCATG 59.939 47.826 13.75 0.00 36.81 3.07
1263 1503 2.717580 TGTAAGTCATGTCGAAGCGT 57.282 45.000 0.00 0.00 0.00 5.07
1323 1563 5.784177 ACTTAATGAAGTCACAGTCGATGT 58.216 37.500 0.00 0.00 42.50 3.06
1337 1577 6.858478 CACAGTCGATGTTATATTCGTGAGAT 59.142 38.462 0.00 0.00 41.41 2.75
1353 1593 3.632604 GTGAGATCTTACGTGGAGATCCA 59.367 47.826 26.80 22.66 46.88 3.41
1355 1595 9.785971 TCGTGAGATCTTACGTGGAGATCCATA 62.786 44.444 31.40 11.53 46.88 2.74
1391 1654 7.459795 TTTATATGTTGTGCCATTTGACTGA 57.540 32.000 0.00 0.00 0.00 3.41
1394 1670 2.618241 TGTTGTGCCATTTGACTGAGAC 59.382 45.455 0.00 0.00 0.00 3.36
1403 1679 5.110598 CCATTTGACTGAGACTGAGATCTG 58.889 45.833 0.00 0.00 0.00 2.90
1407 1683 0.752054 CTGAGACTGAGATCTGGCCC 59.248 60.000 0.00 0.00 0.00 5.80
1412 1688 2.692368 TGAGATCTGGCCCCACCC 60.692 66.667 0.00 0.00 37.83 4.61
1415 1691 0.694444 GAGATCTGGCCCCACCCTAA 60.694 60.000 0.00 0.00 37.83 2.69
1421 1697 0.626916 TGGCCCCACCCTAAACATAC 59.373 55.000 0.00 0.00 37.83 2.39
1422 1698 0.626916 GGCCCCACCCTAAACATACA 59.373 55.000 0.00 0.00 0.00 2.29
1442 1718 3.687212 ACATGTTTGTGAAAGTGACGACA 59.313 39.130 0.00 0.00 33.85 4.35
1469 1749 6.095440 ACATATATGGTGTTTGAAACTGCCTC 59.905 38.462 16.96 3.17 0.00 4.70
1713 1993 4.735132 TGCAGCTACACGCCCGAC 62.735 66.667 0.00 0.00 40.39 4.79
1734 2014 1.134560 AGAGGAACCTTCGACATACGC 59.865 52.381 0.00 0.00 42.26 4.42
1780 2060 3.455469 GGTACGGCTACCACGGCT 61.455 66.667 7.89 0.00 42.16 5.52
1781 2061 2.120909 GGTACGGCTACCACGGCTA 61.121 63.158 7.89 0.00 42.16 3.93
1782 2062 1.064783 GTACGGCTACCACGGCTAC 59.935 63.158 0.00 0.00 35.23 3.58
1784 2064 4.564116 CGGCTACCACGGCTACGG 62.564 72.222 0.00 0.00 46.48 4.02
1785 2065 4.886121 GGCTACCACGGCTACGGC 62.886 72.222 0.00 0.00 46.48 5.68
1975 2255 5.564768 CCGTATGAGCGATAGTGATCTTAG 58.435 45.833 0.00 0.00 39.35 2.18
1982 2270 6.149640 TGAGCGATAGTGATCTTAGGATGTAC 59.850 42.308 0.00 0.00 39.35 2.90
1991 2279 7.928706 AGTGATCTTAGGATGTACTTGTAATGC 59.071 37.037 0.00 0.00 31.46 3.56
2014 2302 5.920840 GCTTTTGGTTTCAGGTTGAGTTATC 59.079 40.000 0.00 0.00 0.00 1.75
2095 2383 2.933495 CGTGGTATTCTCTCACGGAA 57.067 50.000 7.13 0.00 46.96 4.30
2213 2631 3.191078 AGAGCTACATGTGGAATGCTC 57.809 47.619 14.15 18.68 44.85 4.26
2217 2683 3.693085 AGCTACATGTGGAATGCTCAAAG 59.307 43.478 14.15 0.00 0.00 2.77
2222 2688 3.490439 TGTGGAATGCTCAAAGAGACA 57.510 42.857 0.00 0.00 0.00 3.41
2231 2697 0.874390 TCAAAGAGACATGCCGCAAC 59.126 50.000 0.00 0.00 0.00 4.17
2339 2806 3.063510 ACACTGTCAATCTGTCATGGG 57.936 47.619 0.00 0.00 0.00 4.00
2415 2906 6.601217 AGCAAATGGAAGAGAAAATCCTCTAC 59.399 38.462 0.00 0.00 42.31 2.59
2419 2910 9.844257 AAATGGAAGAGAAAATCCTCTACATAG 57.156 33.333 0.00 0.00 42.31 2.23
2444 2935 4.372656 AGATAGTTTTCGCATCCTACAGC 58.627 43.478 0.00 0.00 0.00 4.40
2470 2961 9.736023 CTACCTTTAAAGCAAATCATACAATCC 57.264 33.333 9.86 0.00 0.00 3.01
2478 2969 4.562394 GCAAATCATACAATCCAAACACCG 59.438 41.667 0.00 0.00 0.00 4.94
2482 2973 7.639113 AATCATACAATCCAAACACCGTTAT 57.361 32.000 0.00 0.00 0.00 1.89
2490 2981 2.422127 CCAAACACCGTTATGTCCATCC 59.578 50.000 0.00 0.00 30.55 3.51
2496 2987 2.687935 ACCGTTATGTCCATCCAATTGC 59.312 45.455 0.00 0.00 0.00 3.56
2534 3025 2.083774 CATTTTCCTACTGGAGCGCAA 58.916 47.619 11.47 0.00 44.24 4.85
2538 3029 2.489938 TCCTACTGGAGCGCAAAAAT 57.510 45.000 11.47 0.00 37.46 1.82
2542 3033 3.251004 CCTACTGGAGCGCAAAAATATCC 59.749 47.826 11.47 6.39 34.57 2.59
2548 3039 3.374745 GAGCGCAAAAATATCCACCATG 58.625 45.455 11.47 0.00 0.00 3.66
2553 3044 3.675775 GCAAAAATATCCACCATGTGCGT 60.676 43.478 0.00 0.00 31.34 5.24
2578 3069 4.589908 ACCAACTCAAACAGGGCTAATAG 58.410 43.478 0.00 0.00 0.00 1.73
2579 3070 3.378427 CCAACTCAAACAGGGCTAATAGC 59.622 47.826 3.17 3.17 41.46 2.97
2580 3071 4.265073 CAACTCAAACAGGGCTAATAGCT 58.735 43.478 12.41 0.00 41.99 3.32
2581 3072 5.428253 CAACTCAAACAGGGCTAATAGCTA 58.572 41.667 12.41 0.00 41.99 3.32
2582 3073 5.024785 ACTCAAACAGGGCTAATAGCTAC 57.975 43.478 12.41 5.87 41.99 3.58
2583 3074 4.051922 CTCAAACAGGGCTAATAGCTACG 58.948 47.826 12.41 3.33 41.99 3.51
2584 3075 3.131396 CAAACAGGGCTAATAGCTACGG 58.869 50.000 12.41 8.78 41.99 4.02
2586 3077 0.037232 CAGGGCTAATAGCTACGGCC 60.037 60.000 19.26 19.26 41.99 6.13
2588 3079 2.363297 GGCTAATAGCTACGGCCCT 58.637 57.895 12.41 0.00 41.99 5.19
2589 3080 1.553706 GGCTAATAGCTACGGCCCTA 58.446 55.000 12.41 0.00 41.99 3.53
2592 3083 3.318557 GGCTAATAGCTACGGCCCTATAG 59.681 52.174 12.41 0.00 41.99 1.31
2614 3133 5.491982 AGAAATTGGACCTCTACACATGAC 58.508 41.667 0.00 0.00 0.00 3.06
2671 3190 8.893563 AAAAAGATGATACAAAGTATTCCCCA 57.106 30.769 0.00 0.00 0.00 4.96
2672 3191 7.881775 AAAGATGATACAAAGTATTCCCCAC 57.118 36.000 0.00 0.00 0.00 4.61
2679 3198 4.798882 ACAAAGTATTCCCCACAGAAACA 58.201 39.130 0.00 0.00 0.00 2.83
2727 3246 9.923143 GCTACCAAATTCTTATAGGTTGTTTTT 57.077 29.630 0.00 0.00 33.91 1.94
2786 3305 4.574599 AAGATGCACCAAACACTTTCTC 57.425 40.909 0.00 0.00 0.00 2.87
2856 3375 4.156008 CAGGTAAGGTGCACTTAAATGGTC 59.844 45.833 17.98 0.00 42.99 4.02
2863 3382 1.466360 GCACTTAAATGGTCAGCAGCG 60.466 52.381 0.00 0.00 0.00 5.18
2933 3452 9.545105 AGATTTTCAAAACAATTAACAGATGCA 57.455 25.926 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.741221 GAAGCAACTCGGGCGAGAAT 60.741 55.000 0.00 0.00 44.53 2.40
65 66 6.038825 ACACCATGTACATTTTTCGAAACTCA 59.961 34.615 10.79 4.49 0.00 3.41
94 95 4.870636 TGGCAATCATAGGACCTTTTGAT 58.129 39.130 0.00 6.56 0.00 2.57
164 177 6.769512 TGTAATTCTGGGAAGGCATAGATAC 58.230 40.000 0.00 0.00 0.00 2.24
263 276 9.701098 ACCGATTTATTTAGTTGATCGCTATAA 57.299 29.630 0.00 0.00 38.52 0.98
265 278 9.701098 TTACCGATTTATTTAGTTGATCGCTAT 57.299 29.630 0.00 0.00 38.52 2.97
338 352 7.815840 TTTCATGTGACCAACTTAATCTTCA 57.184 32.000 0.00 0.00 0.00 3.02
377 394 3.370315 CCAGAAGCCTACTTGCTCATCTT 60.370 47.826 0.00 0.00 41.80 2.40
396 413 2.026641 CCAACCACTGCCAATATCCAG 58.973 52.381 0.00 0.00 35.26 3.86
446 463 3.195825 ACTTGTTACGCCAGCTTCTCTAT 59.804 43.478 0.00 0.00 0.00 1.98
544 562 1.066286 CCTCCTCTCTTTGCAGGACTG 60.066 57.143 0.00 0.00 34.87 3.51
697 723 2.763249 CACTTTCTCAAGGTGTGCAC 57.237 50.000 10.75 10.75 33.82 4.57
758 947 1.448985 TCGGCGGAGATTTGAAAAGG 58.551 50.000 7.21 0.00 0.00 3.11
771 960 1.586123 CAGTGTTTTTGTTTTCGGCGG 59.414 47.619 7.21 0.00 0.00 6.13
776 965 6.466308 ACTTTCTGCAGTGTTTTTGTTTTC 57.534 33.333 14.67 0.00 0.00 2.29
789 978 0.245539 CATGGCCCAACTTTCTGCAG 59.754 55.000 7.63 7.63 0.00 4.41
803 992 1.134907 CCCACAAGAAATGCTCATGGC 60.135 52.381 0.00 0.00 42.22 4.40
806 995 1.927487 TGCCCACAAGAAATGCTCAT 58.073 45.000 0.00 0.00 0.00 2.90
853 1042 5.399497 CCTTCCATTACTCCATCCAAAGGAT 60.399 44.000 0.00 0.00 44.21 3.24
909 1124 0.899717 CTGGGGTGTGGGTTGATTGG 60.900 60.000 0.00 0.00 0.00 3.16
927 1142 4.494362 CGTCGTCTCTGATCGTTTACATCT 60.494 45.833 0.00 0.00 0.00 2.90
984 1199 4.344865 ATTGCCCGCGGAAGGTGT 62.345 61.111 30.73 4.08 0.00 4.16
1009 1224 2.266055 GCGACAAGGGTGAGGAGG 59.734 66.667 0.00 0.00 0.00 4.30
1069 1284 0.251354 CTAGAGAAGCAGCCTGGCAA 59.749 55.000 22.65 0.00 35.83 4.52
1071 1286 0.461693 CACTAGAGAAGCAGCCTGGC 60.462 60.000 11.65 11.65 0.00 4.85
1153 1374 7.610305 TGGAGAAAACAGAAAAGTTGAACTAGT 59.390 33.333 0.00 0.00 0.00 2.57
1154 1375 7.985476 TGGAGAAAACAGAAAAGTTGAACTAG 58.015 34.615 0.00 0.00 0.00 2.57
1158 1379 6.154363 ACCATGGAGAAAACAGAAAAGTTGAA 59.846 34.615 21.47 0.00 0.00 2.69
1163 1384 4.746611 GCAACCATGGAGAAAACAGAAAAG 59.253 41.667 21.47 0.00 0.00 2.27
1164 1385 4.161189 TGCAACCATGGAGAAAACAGAAAA 59.839 37.500 21.47 0.00 0.00 2.29
1166 1387 3.295093 TGCAACCATGGAGAAAACAGAA 58.705 40.909 21.47 0.00 0.00 3.02
1167 1388 2.942804 TGCAACCATGGAGAAAACAGA 58.057 42.857 21.47 0.00 0.00 3.41
1194 1434 1.415659 CTCGAAGATCTCCAGGGCAAT 59.584 52.381 0.00 0.00 33.89 3.56
1254 1494 1.585214 CCGGTATGTTTACGCTTCGAC 59.415 52.381 0.00 0.00 0.00 4.20
1263 1503 3.996921 TTAGCAACCCCGGTATGTTTA 57.003 42.857 0.00 0.00 0.00 2.01
1308 1548 6.472486 CACGAATATAACATCGACTGTGACTT 59.528 38.462 11.44 0.00 41.43 3.01
1323 1563 7.443272 TCTCCACGTAAGATCTCACGAATATAA 59.557 37.037 25.04 3.09 40.56 0.98
1380 1643 5.110598 CAGATCTCAGTCTCAGTCAAATGG 58.889 45.833 0.00 0.00 0.00 3.16
1391 1654 0.980231 GTGGGGCCAGATCTCAGTCT 60.980 60.000 4.39 0.00 0.00 3.24
1394 1670 2.750657 GGGTGGGGCCAGATCTCAG 61.751 68.421 4.39 0.00 39.65 3.35
1403 1679 0.626916 TGTATGTTTAGGGTGGGGCC 59.373 55.000 0.00 0.00 0.00 5.80
1421 1697 4.271590 TGTCGTCACTTTCACAAACATG 57.728 40.909 0.00 0.00 0.00 3.21
1422 1698 5.525745 TGTATGTCGTCACTTTCACAAACAT 59.474 36.000 0.00 0.00 0.00 2.71
1442 1718 7.779798 AGGCAGTTTCAAACACCATATATGTAT 59.220 33.333 11.73 0.00 33.65 2.29
1469 1749 1.000274 CCTTCAAAGTTTTCGGCCCAG 60.000 52.381 0.00 0.00 0.00 4.45
1710 1990 0.596577 TGTCGAAGGTTCCTCTGTCG 59.403 55.000 5.41 5.41 0.00 4.35
1713 1993 2.798680 CGTATGTCGAAGGTTCCTCTG 58.201 52.381 0.00 0.00 42.86 3.35
1757 2037 3.120105 GGTAGCCGTACCCGTACC 58.880 66.667 0.00 0.00 42.91 3.34
1780 2060 4.801624 CTGCTGCTGCTCGCCGTA 62.802 66.667 17.00 0.00 40.48 4.02
1975 2255 6.267496 ACCAAAAGCATTACAAGTACATCC 57.733 37.500 0.00 0.00 0.00 3.51
1982 2270 5.600696 ACCTGAAACCAAAAGCATTACAAG 58.399 37.500 0.00 0.00 0.00 3.16
1991 2279 7.277174 AGATAACTCAACCTGAAACCAAAAG 57.723 36.000 0.00 0.00 0.00 2.27
2071 2359 0.459899 TGAGAGAATACCACGCGCAT 59.540 50.000 5.73 0.00 0.00 4.73
2077 2365 3.587797 TGTTCCGTGAGAGAATACCAC 57.412 47.619 0.00 0.00 0.00 4.16
2092 2380 7.067129 ACTCTTGTTTTAGTTCTTCCTTGTTCC 59.933 37.037 0.00 0.00 0.00 3.62
2094 2382 7.939784 ACTCTTGTTTTAGTTCTTCCTTGTT 57.060 32.000 0.00 0.00 0.00 2.83
2095 2383 7.498239 GGTACTCTTGTTTTAGTTCTTCCTTGT 59.502 37.037 0.00 0.00 0.00 3.16
2167 2459 8.962884 AGCATTTTTAGAGGATTTTTGTTTGT 57.037 26.923 0.00 0.00 0.00 2.83
2213 2631 0.592637 TGTTGCGGCATGTCTCTTTG 59.407 50.000 2.28 0.00 0.00 2.77
2217 2683 1.987770 CAAATTGTTGCGGCATGTCTC 59.012 47.619 2.28 0.00 0.00 3.36
2231 2697 7.915397 AGTCTAAACACACTTTACTGCAAATTG 59.085 33.333 0.00 0.00 34.01 2.32
2241 2707 6.770785 AGCATCCAAAGTCTAAACACACTTTA 59.229 34.615 0.00 0.00 32.01 1.85
2318 2785 3.619733 GCCCATGACAGATTGACAGTGTA 60.620 47.826 0.00 0.00 0.00 2.90
2368 2859 6.151691 GCTTCTCAATAACAAGCATGTGAAA 58.848 36.000 0.00 0.00 41.87 2.69
2370 2861 4.761227 TGCTTCTCAATAACAAGCATGTGA 59.239 37.500 0.00 0.00 45.91 3.58
2371 2862 5.050644 TGCTTCTCAATAACAAGCATGTG 57.949 39.130 0.00 0.00 45.91 3.21
2384 2875 6.713762 TTTTCTCTTCCATTTGCTTCTCAA 57.286 33.333 0.00 0.00 0.00 3.02
2415 2906 6.226787 AGGATGCGAAAACTATCTTCCTATG 58.773 40.000 0.00 0.00 30.74 2.23
2419 2910 5.357257 TGTAGGATGCGAAAACTATCTTCC 58.643 41.667 0.00 0.00 0.00 3.46
2444 2935 9.736023 GGATTGTATGATTTGCTTTAAAGGTAG 57.264 33.333 16.78 0.00 0.00 3.18
2470 2961 3.078097 TGGATGGACATAACGGTGTTTG 58.922 45.455 0.00 0.00 31.16 2.93
2478 2969 8.770438 TTTAAAAGCAATTGGATGGACATAAC 57.230 30.769 7.72 0.00 0.00 1.89
2482 2973 7.050377 TGTTTTTAAAAGCAATTGGATGGACA 58.950 30.769 14.23 2.67 0.00 4.02
2513 3004 1.017387 GCGCTCCAGTAGGAAAATGG 58.983 55.000 0.00 0.00 45.19 3.16
2534 3025 3.781079 CACGCACATGGTGGATATTTT 57.219 42.857 0.00 0.00 33.64 1.82
2542 3033 1.896183 TTGGTCCACGCACATGGTG 60.896 57.895 0.00 0.00 40.95 4.17
2548 3039 0.028902 GTTTGAGTTGGTCCACGCAC 59.971 55.000 0.00 0.00 0.00 5.34
2553 3044 0.467290 GCCCTGTTTGAGTTGGTCCA 60.467 55.000 0.00 0.00 0.00 4.02
2578 3069 3.007614 TCCAATTTCTATAGGGCCGTAGC 59.992 47.826 11.42 0.00 38.76 3.58
2579 3070 4.562963 GGTCCAATTTCTATAGGGCCGTAG 60.563 50.000 11.42 11.41 35.98 3.51
2580 3071 3.325716 GGTCCAATTTCTATAGGGCCGTA 59.674 47.826 7.78 7.78 35.98 4.02
2581 3072 2.105993 GGTCCAATTTCTATAGGGCCGT 59.894 50.000 2.24 2.24 35.98 5.68
2582 3073 2.779506 GGTCCAATTTCTATAGGGCCG 58.220 52.381 0.00 0.00 35.98 6.13
2583 3074 3.653352 AGAGGTCCAATTTCTATAGGGCC 59.347 47.826 0.00 0.00 46.35 5.80
2584 3075 4.984146 AGAGGTCCAATTTCTATAGGGC 57.016 45.455 0.00 0.00 0.00 5.19
2586 3077 7.361457 TGTGTAGAGGTCCAATTTCTATAGG 57.639 40.000 0.00 0.00 0.00 2.57
2588 3079 8.421784 GTCATGTGTAGAGGTCCAATTTCTATA 58.578 37.037 0.00 0.00 0.00 1.31
2589 3080 7.275920 GTCATGTGTAGAGGTCCAATTTCTAT 58.724 38.462 0.00 0.00 0.00 1.98
2592 3083 4.636206 GGTCATGTGTAGAGGTCCAATTTC 59.364 45.833 0.00 0.00 0.00 2.17
2614 3133 0.603569 CTATAGGGCCGTAGCTGTGG 59.396 60.000 11.42 0.00 39.73 4.17
2660 3179 6.994421 AAATTGTTTCTGTGGGGAATACTT 57.006 33.333 0.00 0.00 0.00 2.24
2667 3186 6.588719 TGATCTAAAATTGTTTCTGTGGGG 57.411 37.500 0.00 0.00 0.00 4.96
2679 3198 9.717942 GTAGCACCATCTCTATGATCTAAAATT 57.282 33.333 0.00 0.00 34.84 1.82
2741 3260 9.985318 CTTTATCTGAATTTTGCTGTTCTAGAG 57.015 33.333 0.00 0.00 0.00 2.43
2786 3305 3.981071 TCTGTTCTGGTGGTGGAATAG 57.019 47.619 0.00 0.00 33.82 1.73
2856 3375 4.623167 GGTACATCTTCATATACGCTGCTG 59.377 45.833 0.00 0.00 0.00 4.41
2933 3452 4.802248 GCGGAGATTTAGATCATCTTGCCT 60.802 45.833 0.00 0.00 34.60 4.75


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

AutoCloner maintained by Alex Coulton.