Multiple sequence alignment - TraesCS2D01G115700

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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 TraesCS2D01G115700 chr2D 100.000 3286 0 0 1 3286 64156313 64159598 0.000000e+00 6069.0
1 TraesCS2D01G115700 chr2B 89.814 3328 155 79 69 3286 100324839 100328092 0.000000e+00 4098.0
2 TraesCS2D01G115700 chr2A 89.231 3343 183 86 59 3286 65651849 65655129 0.000000e+00 4015.0
3 TraesCS2D01G115700 chr5D 92.593 81 3 3 2021 2100 40183814 40183892 2.680000e-21 113.0
4 TraesCS2D01G115700 chr5A 93.421 76 5 0 2012 2087 28228879 28228954 2.680000e-21 113.0
5 TraesCS2D01G115700 chr5B 92.500 80 3 3 2021 2099 33556623 33556546 9.640000e-21 111.0
6 TraesCS2D01G115700 chr4D 93.056 72 5 0 2016 2087 291587224 291587295 4.480000e-19 106.0
7 TraesCS2D01G115700 chr1D 93.220 59 4 0 1192 1250 87776235 87776293 1.620000e-13 87.9
8 TraesCS2D01G115700 chr1A 91.525 59 5 0 1192 1250 84022813 84022871 7.560000e-12 82.4


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 TraesCS2D01G115700 chr2D 64156313 64159598 3285 False 6069 6069 100.000 1 3286 1 chr2D.!!$F1 3285
1 TraesCS2D01G115700 chr2B 100324839 100328092 3253 False 4098 4098 89.814 69 3286 1 chr2B.!!$F1 3217
2 TraesCS2D01G115700 chr2A 65651849 65655129 3280 False 4015 4015 89.231 59 3286 1 chr2A.!!$F1 3227

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
358 368 0.026803 GCTGTGCGTCCATTTCGATC 59.973 55.0 0.0 0.0 0.0 3.69 F
1141 1215 0.503961 GCTGACATTGTGTTTTGCGC 59.496 50.0 0.0 0.0 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1700 1819 0.115152 TCTCAGGAACCTCTGCCTCA 59.885 55.0 0.0 0.0 34.91 3.86 R
3116 3294 0.888736 TGATTTGACCACTGCCACCG 60.889 55.0 0.0 0.0 0.00 4.94 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
25 26 7.485810 ACCCGTTTGATATAATTTGGTTTAGC 58.514 34.615 0.00 0.00 0.00 3.09
26 27 6.921307 CCCGTTTGATATAATTTGGTTTAGCC 59.079 38.462 0.00 0.00 37.90 3.93
36 37 2.877097 TGGTTTAGCCAGCAATCTCA 57.123 45.000 0.00 0.00 43.61 3.27
37 38 3.153369 TGGTTTAGCCAGCAATCTCAA 57.847 42.857 0.00 0.00 43.61 3.02
38 39 3.495331 TGGTTTAGCCAGCAATCTCAAA 58.505 40.909 0.00 0.00 43.61 2.69
39 40 3.507233 TGGTTTAGCCAGCAATCTCAAAG 59.493 43.478 0.00 0.00 43.61 2.77
40 41 3.507622 GGTTTAGCCAGCAATCTCAAAGT 59.492 43.478 0.00 0.00 37.17 2.66
41 42 4.021981 GGTTTAGCCAGCAATCTCAAAGTT 60.022 41.667 0.00 0.00 37.17 2.66
42 43 5.183140 GGTTTAGCCAGCAATCTCAAAGTTA 59.817 40.000 0.00 0.00 37.17 2.24
43 44 5.880054 TTAGCCAGCAATCTCAAAGTTAC 57.120 39.130 0.00 0.00 0.00 2.50
44 45 4.026356 AGCCAGCAATCTCAAAGTTACT 57.974 40.909 0.00 0.00 0.00 2.24
45 46 4.006319 AGCCAGCAATCTCAAAGTTACTC 58.994 43.478 0.00 0.00 0.00 2.59
46 47 4.006319 GCCAGCAATCTCAAAGTTACTCT 58.994 43.478 0.00 0.00 0.00 3.24
47 48 4.457257 GCCAGCAATCTCAAAGTTACTCTT 59.543 41.667 0.00 0.00 38.10 2.85
48 49 5.618640 GCCAGCAATCTCAAAGTTACTCTTG 60.619 44.000 0.00 0.00 36.40 3.02
49 50 5.106396 CCAGCAATCTCAAAGTTACTCTTGG 60.106 44.000 7.18 0.00 36.40 3.61
50 51 5.702670 CAGCAATCTCAAAGTTACTCTTGGA 59.297 40.000 7.18 0.00 36.40 3.53
51 52 5.703130 AGCAATCTCAAAGTTACTCTTGGAC 59.297 40.000 7.18 0.00 36.40 4.02
52 53 5.389935 GCAATCTCAAAGTTACTCTTGGACG 60.390 44.000 7.18 0.00 36.40 4.79
53 54 5.723672 ATCTCAAAGTTACTCTTGGACGA 57.276 39.130 0.00 4.01 36.40 4.20
54 55 5.122512 TCTCAAAGTTACTCTTGGACGAG 57.877 43.478 0.00 0.00 36.40 4.18
55 56 4.583489 TCTCAAAGTTACTCTTGGACGAGT 59.417 41.667 0.00 0.00 45.62 4.18
56 57 5.766670 TCTCAAAGTTACTCTTGGACGAGTA 59.233 40.000 0.00 0.00 42.19 2.59
57 58 6.010294 TCAAAGTTACTCTTGGACGAGTAG 57.990 41.667 0.00 0.00 44.65 2.57
58 59 5.766670 TCAAAGTTACTCTTGGACGAGTAGA 59.233 40.000 0.00 0.00 44.65 2.59
59 60 5.625921 AAGTTACTCTTGGACGAGTAGAC 57.374 43.478 0.00 0.00 44.65 2.59
60 61 4.649692 AGTTACTCTTGGACGAGTAGACA 58.350 43.478 0.00 0.00 44.65 3.41
61 62 5.068636 AGTTACTCTTGGACGAGTAGACAA 58.931 41.667 0.00 0.00 44.65 3.18
62 63 3.919223 ACTCTTGGACGAGTAGACAAC 57.081 47.619 0.00 0.00 42.19 3.32
63 64 3.488363 ACTCTTGGACGAGTAGACAACT 58.512 45.455 0.00 0.00 42.19 3.16
64 65 3.253677 ACTCTTGGACGAGTAGACAACTG 59.746 47.826 0.00 0.00 42.19 3.16
65 66 3.483421 TCTTGGACGAGTAGACAACTGA 58.517 45.455 0.00 0.00 39.07 3.41
66 67 4.079970 TCTTGGACGAGTAGACAACTGAT 58.920 43.478 0.00 0.00 39.07 2.90
74 75 6.404708 ACGAGTAGACAACTGATCTGTAGTA 58.595 40.000 5.59 0.00 39.07 1.82
171 175 1.142097 GACAACGAGAGCTAGCCCC 59.858 63.158 12.13 3.61 0.00 5.80
206 210 3.311596 CGCACCTAATTAACCCTACTTGC 59.688 47.826 0.00 0.00 0.00 4.01
233 238 1.353103 CATTGATGGAACGCCTCGC 59.647 57.895 0.00 0.00 34.31 5.03
259 264 1.901464 GGTTTCCGAAAGCCAGCCA 60.901 57.895 11.30 0.00 35.90 4.75
260 265 1.581447 GTTTCCGAAAGCCAGCCAG 59.419 57.895 0.00 0.00 0.00 4.85
261 266 2.268076 TTTCCGAAAGCCAGCCAGC 61.268 57.895 0.00 0.00 0.00 4.85
262 267 4.722700 TCCGAAAGCCAGCCAGCC 62.723 66.667 0.00 0.00 0.00 4.85
276 284 0.321919 CCAGCCAGCAAGCTTACTCA 60.322 55.000 0.00 0.00 42.61 3.41
279 287 2.611292 CAGCCAGCAAGCTTACTCATAC 59.389 50.000 0.00 0.00 42.61 2.39
280 288 2.503356 AGCCAGCAAGCTTACTCATACT 59.497 45.455 0.00 0.00 41.41 2.12
281 289 2.869192 GCCAGCAAGCTTACTCATACTC 59.131 50.000 0.00 0.00 0.00 2.59
344 354 5.599999 ACCCTAGTTATTACTCAGCTGTG 57.400 43.478 14.67 14.35 35.78 3.66
352 362 0.608130 TACTCAGCTGTGCGTCCATT 59.392 50.000 14.67 0.00 0.00 3.16
353 363 0.250467 ACTCAGCTGTGCGTCCATTT 60.250 50.000 14.67 0.00 0.00 2.32
354 364 0.445436 CTCAGCTGTGCGTCCATTTC 59.555 55.000 14.67 0.00 0.00 2.17
356 366 1.005037 AGCTGTGCGTCCATTTCGA 60.005 52.632 0.00 0.00 0.00 3.71
358 368 0.026803 GCTGTGCGTCCATTTCGATC 59.973 55.000 0.00 0.00 0.00 3.69
438 453 2.270986 CCTCACCAAACCCTGCAGC 61.271 63.158 8.66 0.00 0.00 5.25
492 528 5.003804 TCTGTATTCTTCTGAAGGCAAACC 58.996 41.667 16.83 2.54 35.44 3.27
573 609 3.181475 ACACGCGATCCTCACAAGATATT 60.181 43.478 15.93 0.00 0.00 1.28
581 617 5.779241 TCCTCACAAGATATTTTGGAGGT 57.221 39.130 25.75 3.44 41.39 3.85
720 765 2.109593 GTGGTGGTTCGGTTCGGT 59.890 61.111 0.00 0.00 0.00 4.69
740 786 4.446413 GGCGTGTCACCGGTAGGG 62.446 72.222 6.87 0.00 43.47 3.53
742 788 4.789075 CGTGTCACCGGTAGGGCG 62.789 72.222 6.87 6.59 43.47 6.13
858 906 0.867478 AAAGGCCCCTTCTTTCCCTT 59.133 50.000 0.00 0.00 37.50 3.95
924 974 2.202730 GCCACTGAGAGCGAGCTC 60.203 66.667 16.63 16.63 43.03 4.09
929 979 4.645809 TGAGAGCGAGCTCAGCTA 57.354 55.556 25.72 12.99 46.13 3.32
930 980 2.102554 TGAGAGCGAGCTCAGCTAC 58.897 57.895 25.72 22.10 46.13 3.58
931 981 1.358759 GAGAGCGAGCTCAGCTACC 59.641 63.158 25.72 18.34 46.13 3.18
933 983 3.145422 GAGCGAGCTCAGCTACCCC 62.145 68.421 25.72 14.08 46.13 4.95
935 985 2.811101 CGAGCTCAGCTACCCCAG 59.189 66.667 15.40 0.00 39.88 4.45
1048 1104 0.743345 GTACACGGTGAGCCATTCCC 60.743 60.000 16.29 0.00 34.09 3.97
1071 1145 2.243810 AGAGCTTCACCGTCTTCTTCT 58.756 47.619 0.00 0.00 0.00 2.85
1102 1176 9.757227 CTTCTTCTTCTTCTTCTTCTTCTTGTA 57.243 33.333 0.00 0.00 0.00 2.41
1106 1180 7.140048 TCTTCTTCTTCTTCTTCTTGTACGTC 58.860 38.462 0.00 0.00 0.00 4.34
1139 1213 4.093261 AGTTTTGCTGACATTGTGTTTTGC 59.907 37.500 0.00 0.00 0.00 3.68
1140 1214 1.837648 TGCTGACATTGTGTTTTGCG 58.162 45.000 0.00 0.00 0.00 4.85
1141 1215 0.503961 GCTGACATTGTGTTTTGCGC 59.496 50.000 0.00 0.00 0.00 6.09
1142 1216 1.865248 GCTGACATTGTGTTTTGCGCT 60.865 47.619 9.73 0.00 0.00 5.92
1143 1217 2.462889 CTGACATTGTGTTTTGCGCTT 58.537 42.857 9.73 0.00 0.00 4.68
1144 1218 2.859538 CTGACATTGTGTTTTGCGCTTT 59.140 40.909 9.73 0.00 0.00 3.51
1155 1232 3.408851 GCGCTTTGCTTTGCTGCC 61.409 61.111 0.00 0.00 41.73 4.85
1176 1253 2.282040 GCTGGCTTGCAGACCACT 60.282 61.111 5.71 0.00 0.00 4.00
1283 1360 1.202177 CCGCTTCGGTTGATTGATTGG 60.202 52.381 0.00 0.00 42.73 3.16
1305 1399 3.390135 AGTTCATTCTTCTTGCGACGAA 58.610 40.909 0.00 0.00 32.79 3.85
1307 1401 4.452455 AGTTCATTCTTCTTGCGACGAAAT 59.548 37.500 0.00 0.00 32.13 2.17
1308 1402 4.326413 TCATTCTTCTTGCGACGAAATG 57.674 40.909 0.00 0.00 32.13 2.32
1310 1404 4.213270 TCATTCTTCTTGCGACGAAATGTT 59.787 37.500 0.00 0.00 32.13 2.71
1311 1405 4.545823 TTCTTCTTGCGACGAAATGTTT 57.454 36.364 0.00 0.00 0.00 2.83
1312 1406 3.872354 TCTTCTTGCGACGAAATGTTTG 58.128 40.909 0.00 0.00 0.00 2.93
1325 1444 5.692204 ACGAAATGTTTGTGTTTGTTTGTGA 59.308 32.000 0.00 0.00 0.00 3.58
1334 1453 9.687717 GTTTGTGTTTGTTTGTGATTTAGATTG 57.312 29.630 0.00 0.00 0.00 2.67
1337 1456 9.814899 TGTGTTTGTTTGTGATTTAGATTGATT 57.185 25.926 0.00 0.00 0.00 2.57
1351 1470 8.956533 TTTAGATTGATTGAATATGTGGACGA 57.043 30.769 0.00 0.00 0.00 4.20
1352 1471 9.559732 TTTAGATTGATTGAATATGTGGACGAT 57.440 29.630 0.00 0.00 0.00 3.73
1353 1472 9.559732 TTAGATTGATTGAATATGTGGACGATT 57.440 29.630 0.00 0.00 0.00 3.34
1354 1473 7.868775 AGATTGATTGAATATGTGGACGATTG 58.131 34.615 0.00 0.00 0.00 2.67
1355 1474 7.500227 AGATTGATTGAATATGTGGACGATTGT 59.500 33.333 0.00 0.00 0.00 2.71
1356 1475 7.389803 TTGATTGAATATGTGGACGATTGTT 57.610 32.000 0.00 0.00 0.00 2.83
1357 1476 7.389803 TGATTGAATATGTGGACGATTGTTT 57.610 32.000 0.00 0.00 0.00 2.83
1358 1477 8.499403 TGATTGAATATGTGGACGATTGTTTA 57.501 30.769 0.00 0.00 0.00 2.01
1359 1478 9.119418 TGATTGAATATGTGGACGATTGTTTAT 57.881 29.630 0.00 0.00 0.00 1.40
1360 1479 9.950680 GATTGAATATGTGGACGATTGTTTATT 57.049 29.630 0.00 0.00 0.00 1.40
1597 1716 4.680237 GCCCAAAAAGGTGGCCGC 62.680 66.667 8.12 8.12 39.30 6.53
1658 1777 2.731976 CGAAGGTTCAGAGAAGAAACCG 59.268 50.000 0.00 0.00 35.83 4.44
1667 1786 2.077627 GAGAAGAAACCGGAGAAAGCC 58.922 52.381 9.46 0.00 0.00 4.35
1700 1819 1.604378 CAAGGACGAGGCCAAGGAT 59.396 57.895 5.01 0.00 0.00 3.24
2198 2323 1.066918 GCCGGAGTACATGTACGGG 59.933 63.158 26.17 26.25 44.39 5.28
2433 2573 4.072131 TCAAAGCTCTTATTGACCACACC 58.928 43.478 0.00 0.00 30.94 4.16
2471 2614 3.132629 TCGACTTGATTAGCTCGTCAC 57.867 47.619 0.00 0.00 32.70 3.67
2581 2739 6.318144 AGAAGATAGCTCACATGAATTTGGTG 59.682 38.462 0.00 0.00 0.00 4.17
2584 2742 2.490903 AGCTCACATGAATTTGGTGCTC 59.509 45.455 0.00 0.00 32.69 4.26
2599 2757 4.264253 TGGTGCTCAATTGATTCGAATCT 58.736 39.130 32.08 15.46 36.39 2.40
2604 2762 5.163723 TGCTCAATTGATTCGAATCTTGTCC 60.164 40.000 32.08 22.64 36.39 4.02
2609 2767 6.910536 ATTGATTCGAATCTTGTCCTACAC 57.089 37.500 32.08 8.57 36.39 2.90
2620 2778 6.428083 TCTTGTCCTACACAAATAACCTCA 57.572 37.500 0.00 0.00 44.71 3.86
2639 2809 4.452825 CTCAGATGCAGAGAATCCACAAT 58.547 43.478 0.00 0.00 35.09 2.71
2678 2849 6.660521 TCATTTGAACTCATGCCTACAAGATT 59.339 34.615 0.00 0.00 0.00 2.40
2681 2852 5.428253 TGAACTCATGCCTACAAGATTACC 58.572 41.667 0.00 0.00 0.00 2.85
2686 2857 6.114187 TCATGCCTACAAGATTACCTATGG 57.886 41.667 0.00 0.00 0.00 2.74
2687 2858 5.606749 TCATGCCTACAAGATTACCTATGGT 59.393 40.000 0.00 0.00 40.16 3.55
2688 2859 5.290493 TGCCTACAAGATTACCTATGGTG 57.710 43.478 0.00 0.00 36.19 4.17
2689 2860 4.065789 GCCTACAAGATTACCTATGGTGC 58.934 47.826 0.00 0.00 36.19 5.01
2695 2866 5.951747 ACAAGATTACCTATGGTGCACAAAT 59.048 36.000 20.43 13.94 36.19 2.32
2698 2869 2.897271 ACCTATGGTGCACAAATCCA 57.103 45.000 20.43 7.39 32.98 3.41
2699 2870 3.386932 ACCTATGGTGCACAAATCCAT 57.613 42.857 20.43 14.73 43.30 3.41
2701 2872 4.865905 ACCTATGGTGCACAAATCCATAA 58.134 39.130 20.43 1.55 41.64 1.90
2702 2873 4.889409 ACCTATGGTGCACAAATCCATAAG 59.111 41.667 20.43 12.45 41.64 1.73
2704 2875 4.989279 ATGGTGCACAAATCCATAAGAC 57.011 40.909 20.43 0.00 39.76 3.01
2706 2877 4.148079 TGGTGCACAAATCCATAAGACAA 58.852 39.130 20.43 0.00 0.00 3.18
2720 2891 6.202570 TCCATAAGACAAAGCAACAAATTTGC 59.797 34.615 18.12 5.24 45.22 3.68
2740 2912 4.732784 TGCGTCCAAATTAAGCATTTCTC 58.267 39.130 0.00 0.00 32.24 2.87
2743 2915 5.095490 CGTCCAAATTAAGCATTTCTCCAC 58.905 41.667 0.00 0.00 32.24 4.02
2744 2916 5.410924 GTCCAAATTAAGCATTTCTCCACC 58.589 41.667 0.00 0.00 32.24 4.61
2887 3065 6.545666 TCACTTAATCACTTTGGCAAAGAAGA 59.454 34.615 38.62 32.62 41.02 2.87
3116 3294 1.792949 CCGTAATGATGGAACGCTAGC 59.207 52.381 4.06 4.06 35.36 3.42
3148 3326 3.084786 GTCAAATCAGGAGGGACAAAGG 58.915 50.000 0.00 0.00 0.00 3.11
3153 3331 2.361737 GGAGGGACAAAGGGCTGC 60.362 66.667 0.00 0.00 0.00 5.25
3162 3340 4.142160 GGGACAAAGGGCTGCTTAAATTAG 60.142 45.833 0.00 0.00 0.00 1.73
3164 3342 5.391312 ACAAAGGGCTGCTTAAATTAGTG 57.609 39.130 0.00 0.00 0.00 2.74
3165 3343 4.176271 CAAAGGGCTGCTTAAATTAGTGC 58.824 43.478 0.00 0.00 0.00 4.40
3179 3367 2.820728 TAGTGCTACTGCCAGTCCTA 57.179 50.000 0.00 0.00 38.71 2.94
3187 3375 1.207791 CTGCCAGTCCTACCAATCCT 58.792 55.000 0.00 0.00 0.00 3.24
3201 3389 6.935208 CCTACCAATCCTATTGTTAAGTAGGC 59.065 42.308 14.43 0.00 38.29 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.924103 GGCTAAACCAAATTATATCAAACGG 57.076 36.000 0.00 0.00 38.86 4.44
18 19 3.507622 ACTTTGAGATTGCTGGCTAAACC 59.492 43.478 0.00 0.00 39.84 3.27
19 20 4.773323 ACTTTGAGATTGCTGGCTAAAC 57.227 40.909 0.00 0.00 0.00 2.01
20 21 6.003950 AGTAACTTTGAGATTGCTGGCTAAA 58.996 36.000 0.00 0.00 0.00 1.85
21 22 5.560724 AGTAACTTTGAGATTGCTGGCTAA 58.439 37.500 0.00 0.00 0.00 3.09
22 23 5.046304 AGAGTAACTTTGAGATTGCTGGCTA 60.046 40.000 0.00 0.00 0.00 3.93
23 24 4.006319 GAGTAACTTTGAGATTGCTGGCT 58.994 43.478 0.00 0.00 0.00 4.75
24 25 4.006319 AGAGTAACTTTGAGATTGCTGGC 58.994 43.478 0.00 0.00 0.00 4.85
25 26 5.106396 CCAAGAGTAACTTTGAGATTGCTGG 60.106 44.000 0.00 0.00 36.61 4.85
26 27 5.702670 TCCAAGAGTAACTTTGAGATTGCTG 59.297 40.000 0.00 0.00 36.61 4.41
27 28 5.703130 GTCCAAGAGTAACTTTGAGATTGCT 59.297 40.000 0.00 0.00 36.61 3.91
28 29 5.389935 CGTCCAAGAGTAACTTTGAGATTGC 60.390 44.000 0.00 0.00 36.61 3.56
29 30 5.926542 TCGTCCAAGAGTAACTTTGAGATTG 59.073 40.000 0.00 0.00 36.61 2.67
30 31 6.097915 TCGTCCAAGAGTAACTTTGAGATT 57.902 37.500 0.00 0.00 36.61 2.40
31 32 5.715070 CTCGTCCAAGAGTAACTTTGAGAT 58.285 41.667 0.00 0.00 36.61 2.75
32 33 5.122512 CTCGTCCAAGAGTAACTTTGAGA 57.877 43.478 0.00 0.00 36.61 3.27
43 44 3.502595 TCAGTTGTCTACTCGTCCAAGAG 59.497 47.826 0.00 0.00 43.56 2.85
44 45 3.483421 TCAGTTGTCTACTCGTCCAAGA 58.517 45.455 0.00 0.00 33.85 3.02
45 46 3.917329 TCAGTTGTCTACTCGTCCAAG 57.083 47.619 0.00 0.00 33.85 3.61
46 47 4.079970 AGATCAGTTGTCTACTCGTCCAA 58.920 43.478 0.00 0.00 33.85 3.53
47 48 3.440522 CAGATCAGTTGTCTACTCGTCCA 59.559 47.826 0.00 0.00 33.85 4.02
48 49 3.440872 ACAGATCAGTTGTCTACTCGTCC 59.559 47.826 0.00 0.00 33.85 4.79
49 50 4.688511 ACAGATCAGTTGTCTACTCGTC 57.311 45.455 0.00 0.00 33.85 4.20
50 51 5.247084 ACTACAGATCAGTTGTCTACTCGT 58.753 41.667 0.00 0.00 33.85 4.18
51 52 5.804692 ACTACAGATCAGTTGTCTACTCG 57.195 43.478 0.00 0.00 33.85 4.18
52 53 7.852971 AGTACTACAGATCAGTTGTCTACTC 57.147 40.000 8.49 0.00 33.85 2.59
53 54 9.908747 AATAGTACTACAGATCAGTTGTCTACT 57.091 33.333 4.31 10.02 37.68 2.57
56 57 9.244292 TCAAATAGTACTACAGATCAGTTGTCT 57.756 33.333 4.31 8.59 0.00 3.41
61 62 8.356657 GCAGATCAAATAGTACTACAGATCAGT 58.643 37.037 26.49 14.52 34.40 3.41
62 63 7.536964 CGCAGATCAAATAGTACTACAGATCAG 59.463 40.741 26.49 22.68 34.40 2.90
63 64 7.363431 CGCAGATCAAATAGTACTACAGATCA 58.637 38.462 26.49 3.56 34.40 2.92
64 65 6.804295 CCGCAGATCAAATAGTACTACAGATC 59.196 42.308 21.82 21.82 0.00 2.75
65 66 6.490381 TCCGCAGATCAAATAGTACTACAGAT 59.510 38.462 4.31 8.77 0.00 2.90
66 67 5.826208 TCCGCAGATCAAATAGTACTACAGA 59.174 40.000 4.31 4.10 0.00 3.41
74 75 6.582636 TGTTCTTATCCGCAGATCAAATAGT 58.417 36.000 0.00 0.00 33.67 2.12
149 152 1.351153 GCTAGCTCTCGTTGTCCAAC 58.649 55.000 7.70 0.00 37.92 3.77
171 175 3.470567 GTGCGCCTTCTCGACGTG 61.471 66.667 4.18 0.00 0.00 4.49
206 210 2.159476 CGTTCCATCAATGTGCCTTCTG 60.159 50.000 0.00 0.00 0.00 3.02
233 238 1.740025 GCTTTCGGAAACCTGATCTGG 59.260 52.381 16.56 16.56 0.00 3.86
259 264 2.503356 AGTATGAGTAAGCTTGCTGGCT 59.497 45.455 22.52 10.66 45.30 4.75
260 265 2.869192 GAGTATGAGTAAGCTTGCTGGC 59.131 50.000 22.52 8.97 0.00 4.85
261 266 3.133721 AGGAGTATGAGTAAGCTTGCTGG 59.866 47.826 22.52 0.00 0.00 4.85
262 267 4.367450 GAGGAGTATGAGTAAGCTTGCTG 58.633 47.826 22.52 0.00 0.00 4.41
276 284 4.746089 GCTGCTTGATTCATGGAGGAGTAT 60.746 45.833 18.45 0.00 30.17 2.12
279 287 1.948145 GCTGCTTGATTCATGGAGGAG 59.052 52.381 18.45 10.78 30.17 3.69
280 288 1.282738 TGCTGCTTGATTCATGGAGGA 59.717 47.619 18.45 14.63 30.17 3.71
281 289 1.676529 CTGCTGCTTGATTCATGGAGG 59.323 52.381 18.45 3.96 30.17 4.30
344 354 3.309682 TCAAATCAGATCGAAATGGACGC 59.690 43.478 0.00 0.00 0.00 5.19
352 362 3.065786 GGCAGCATTCAAATCAGATCGAA 59.934 43.478 0.00 0.00 0.00 3.71
353 363 2.615447 GGCAGCATTCAAATCAGATCGA 59.385 45.455 0.00 0.00 0.00 3.59
354 364 2.601504 CGGCAGCATTCAAATCAGATCG 60.602 50.000 0.00 0.00 0.00 3.69
356 366 1.066605 GCGGCAGCATTCAAATCAGAT 59.933 47.619 3.18 0.00 44.35 2.90
358 368 2.953669 GCGGCAGCATTCAAATCAG 58.046 52.632 3.18 0.00 44.35 2.90
412 427 0.325272 GGTTTGGTGAGGAGGAGGTC 59.675 60.000 0.00 0.00 0.00 3.85
573 609 0.543410 TCACTCGGGCTACCTCCAAA 60.543 55.000 0.00 0.00 33.28 3.28
581 617 4.214986 TGATGAATTTTCACTCGGGCTA 57.785 40.909 0.00 0.00 40.49 3.93
907 957 2.202730 GAGCTCGCTCTCAGTGGC 60.203 66.667 11.49 0.00 39.80 5.01
908 958 3.282271 TGAGCTCGCTCTCAGTGG 58.718 61.111 18.63 0.00 43.12 4.00
918 968 2.811101 CTGGGGTAGCTGAGCTCG 59.189 66.667 11.68 5.21 40.44 5.03
929 979 1.305718 GAGAGTGGAGAGCTGGGGT 60.306 63.158 0.00 0.00 0.00 4.95
930 980 2.422231 CGAGAGTGGAGAGCTGGGG 61.422 68.421 0.00 0.00 0.00 4.96
931 981 0.967887 TTCGAGAGTGGAGAGCTGGG 60.968 60.000 0.00 0.00 0.00 4.45
933 983 0.179140 GCTTCGAGAGTGGAGAGCTG 60.179 60.000 0.00 0.00 0.00 4.24
935 985 1.064952 GTAGCTTCGAGAGTGGAGAGC 59.935 57.143 0.00 0.00 0.00 4.09
937 987 1.682394 GGGTAGCTTCGAGAGTGGAGA 60.682 57.143 0.00 0.00 0.00 3.71
1048 1104 2.760374 AGAAGACGGTGAAGCTCTTTG 58.240 47.619 0.00 0.00 0.00 2.77
1071 1145 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1102 1176 2.660258 AAAACTGCCTCGCCAGACGT 62.660 55.000 0.00 0.00 44.19 4.34
1106 1180 2.256461 GCAAAACTGCCTCGCCAG 59.744 61.111 0.00 0.00 38.78 4.85
1137 1211 2.659244 GCAGCAAAGCAAAGCGCA 60.659 55.556 11.47 0.00 46.13 6.09
1139 1213 3.101428 CGGCAGCAAAGCAAAGCG 61.101 61.111 0.00 0.00 35.83 4.68
1140 1214 2.735857 CCGGCAGCAAAGCAAAGC 60.736 61.111 0.00 0.00 35.83 3.51
1141 1215 1.662446 CACCGGCAGCAAAGCAAAG 60.662 57.895 0.00 0.00 35.83 2.77
1142 1216 2.416678 CACCGGCAGCAAAGCAAA 59.583 55.556 0.00 0.00 35.83 3.68
1143 1217 4.283403 GCACCGGCAGCAAAGCAA 62.283 61.111 14.06 0.00 40.72 3.91
1155 1232 3.730761 GTCTGCAAGCCAGCACCG 61.731 66.667 0.00 0.00 41.50 4.94
1176 1253 3.899981 GATGGACACCCGCAGCACA 62.900 63.158 0.00 0.00 34.29 4.57
1274 1351 6.750963 GCAAGAAGAATGAACTCCAATCAATC 59.249 38.462 0.00 0.00 0.00 2.67
1305 1399 9.429359 TCTAAATCACAAACAAACACAAACATT 57.571 25.926 0.00 0.00 0.00 2.71
1307 1401 8.994429 ATCTAAATCACAAACAAACACAAACA 57.006 26.923 0.00 0.00 0.00 2.83
1308 1402 9.687717 CAATCTAAATCACAAACAAACACAAAC 57.312 29.630 0.00 0.00 0.00 2.93
1310 1404 9.814899 ATCAATCTAAATCACAAACAAACACAA 57.185 25.926 0.00 0.00 0.00 3.33
1311 1405 9.814899 AATCAATCTAAATCACAAACAAACACA 57.185 25.926 0.00 0.00 0.00 3.72
1325 1444 9.559732 TCGTCCACATATTCAATCAATCTAAAT 57.440 29.630 0.00 0.00 0.00 1.40
1329 1448 7.500227 ACAATCGTCCACATATTCAATCAATCT 59.500 33.333 0.00 0.00 0.00 2.40
1334 1453 9.950680 AATAAACAATCGTCCACATATTCAATC 57.049 29.630 0.00 0.00 0.00 2.67
1337 1456 9.051679 CCTAATAAACAATCGTCCACATATTCA 57.948 33.333 0.00 0.00 0.00 2.57
1342 1461 6.093495 CACACCTAATAAACAATCGTCCACAT 59.907 38.462 0.00 0.00 0.00 3.21
1346 1465 6.591062 TGTACACACCTAATAAACAATCGTCC 59.409 38.462 0.00 0.00 0.00 4.79
1347 1466 7.585286 TGTACACACCTAATAAACAATCGTC 57.415 36.000 0.00 0.00 0.00 4.20
1348 1467 7.118680 CCTTGTACACACCTAATAAACAATCGT 59.881 37.037 0.00 0.00 0.00 3.73
1349 1468 7.118680 ACCTTGTACACACCTAATAAACAATCG 59.881 37.037 0.00 0.00 0.00 3.34
1351 1470 7.940137 TCACCTTGTACACACCTAATAAACAAT 59.060 33.333 0.00 0.00 0.00 2.71
1352 1471 7.227116 GTCACCTTGTACACACCTAATAAACAA 59.773 37.037 0.00 0.00 0.00 2.83
1353 1472 6.707161 GTCACCTTGTACACACCTAATAAACA 59.293 38.462 0.00 0.00 0.00 2.83
1354 1473 6.128742 CGTCACCTTGTACACACCTAATAAAC 60.129 42.308 0.00 0.00 0.00 2.01
1355 1474 5.927689 CGTCACCTTGTACACACCTAATAAA 59.072 40.000 0.00 0.00 0.00 1.40
1356 1475 5.243507 TCGTCACCTTGTACACACCTAATAA 59.756 40.000 0.00 0.00 0.00 1.40
1357 1476 4.766373 TCGTCACCTTGTACACACCTAATA 59.234 41.667 0.00 0.00 0.00 0.98
1358 1477 3.575256 TCGTCACCTTGTACACACCTAAT 59.425 43.478 0.00 0.00 0.00 1.73
1359 1478 2.957680 TCGTCACCTTGTACACACCTAA 59.042 45.455 0.00 0.00 0.00 2.69
1360 1479 2.585330 TCGTCACCTTGTACACACCTA 58.415 47.619 0.00 0.00 0.00 3.08
1559 1678 4.070552 GCGTCCACCTTCTCCGCT 62.071 66.667 0.00 0.00 41.06 5.52
1597 1716 1.894756 CTCTCCGGCTCTACCTCGG 60.895 68.421 0.00 0.00 44.59 4.63
1669 1788 0.251653 GTCCTTGGGTTTCTTCCCCC 60.252 60.000 0.00 0.00 46.48 5.40
1672 1791 1.610886 CCTCGTCCTTGGGTTTCTTCC 60.611 57.143 0.00 0.00 0.00 3.46
1700 1819 0.115152 TCTCAGGAACCTCTGCCTCA 59.885 55.000 0.00 0.00 34.91 3.86
1705 1824 3.169099 TCCTTCTTCTCAGGAACCTCTG 58.831 50.000 0.00 0.00 37.51 3.35
1817 1936 4.641989 TGCTGCTTGTTCTTCTTCTTCTTT 59.358 37.500 0.00 0.00 0.00 2.52
2096 2221 2.044650 ATTGGCTGCATGGACGCT 60.045 55.556 0.50 0.00 0.00 5.07
2310 2439 7.062371 CCACTTTTAACTACAGAAGACTCGATG 59.938 40.741 0.00 0.00 0.00 3.84
2317 2446 5.237236 CCCCCACTTTTAACTACAGAAGA 57.763 43.478 0.00 0.00 0.00 2.87
2433 2573 9.289303 TCAAGTCGAAAATTTGAAGAGAAAAAG 57.711 29.630 0.00 0.00 0.00 2.27
2471 2614 9.901724 GTGAAATAAAATACTCATGTCACTACG 57.098 33.333 0.00 0.00 32.16 3.51
2548 2692 5.682234 TGTGAGCTATCTTCTCAAATGGA 57.318 39.130 0.00 0.00 41.66 3.41
2581 2739 5.065731 AGGACAAGATTCGAATCAATTGAGC 59.934 40.000 31.15 24.13 37.89 4.26
2584 2742 7.148423 TGTGTAGGACAAGATTCGAATCAATTG 60.148 37.037 33.42 29.48 37.89 2.32
2599 2757 6.428083 TCTGAGGTTATTTGTGTAGGACAA 57.572 37.500 0.00 0.00 43.11 3.18
2604 2762 6.108687 TCTGCATCTGAGGTTATTTGTGTAG 58.891 40.000 0.00 0.00 0.00 2.74
2609 2767 6.017275 GGATTCTCTGCATCTGAGGTTATTTG 60.017 42.308 1.97 0.00 31.73 2.32
2620 2778 5.479375 ACAAAATTGTGGATTCTCTGCATCT 59.521 36.000 0.00 0.00 40.49 2.90
2678 2849 4.518278 ATGGATTTGTGCACCATAGGTA 57.482 40.909 15.69 0.00 41.77 3.08
2681 2852 5.589855 TGTCTTATGGATTTGTGCACCATAG 59.410 40.000 15.69 8.45 44.11 2.23
2686 2857 4.622740 GCTTTGTCTTATGGATTTGTGCAC 59.377 41.667 10.75 10.75 0.00 4.57
2687 2858 4.280425 TGCTTTGTCTTATGGATTTGTGCA 59.720 37.500 0.00 0.00 0.00 4.57
2688 2859 4.808558 TGCTTTGTCTTATGGATTTGTGC 58.191 39.130 0.00 0.00 0.00 4.57
2689 2860 6.215121 TGTTGCTTTGTCTTATGGATTTGTG 58.785 36.000 0.00 0.00 0.00 3.33
2695 2866 6.202570 GCAAATTTGTTGCTTTGTCTTATGGA 59.797 34.615 19.03 0.00 41.87 3.41
2698 2869 5.752955 ACGCAAATTTGTTGCTTTGTCTTAT 59.247 32.000 19.03 0.00 42.87 1.73
2699 2870 5.105752 ACGCAAATTTGTTGCTTTGTCTTA 58.894 33.333 19.03 0.00 42.87 2.10
2701 2872 3.520569 ACGCAAATTTGTTGCTTTGTCT 58.479 36.364 19.03 0.00 42.87 3.41
2702 2873 3.302415 GGACGCAAATTTGTTGCTTTGTC 60.302 43.478 19.03 13.82 42.87 3.18
2704 2875 2.606725 TGGACGCAAATTTGTTGCTTTG 59.393 40.909 19.03 4.25 42.87 2.77
2706 2877 2.593346 TGGACGCAAATTTGTTGCTT 57.407 40.000 19.03 0.00 42.87 3.91
2720 2891 5.095490 GTGGAGAAATGCTTAATTTGGACG 58.905 41.667 0.00 0.00 38.64 4.79
2724 2895 6.755141 CAGATGGTGGAGAAATGCTTAATTTG 59.245 38.462 0.00 0.00 38.64 2.32
2730 2901 3.726557 TCAGATGGTGGAGAAATGCTT 57.273 42.857 0.00 0.00 0.00 3.91
2731 2902 3.726557 TTCAGATGGTGGAGAAATGCT 57.273 42.857 0.00 0.00 0.00 3.79
2743 2915 1.826720 CACCCCACCAAATTCAGATGG 59.173 52.381 0.00 0.00 42.60 3.51
2744 2916 1.205417 GCACCCCACCAAATTCAGATG 59.795 52.381 0.00 0.00 0.00 2.90
3116 3294 0.888736 TGATTTGACCACTGCCACCG 60.889 55.000 0.00 0.00 0.00 4.94
3148 3326 4.496507 GCAGTAGCACTAATTTAAGCAGCC 60.497 45.833 0.00 0.00 41.58 4.85
3153 3331 5.294552 GGACTGGCAGTAGCACTAATTTAAG 59.705 44.000 22.11 0.00 44.61 1.85
3162 3340 0.175989 GGTAGGACTGGCAGTAGCAC 59.824 60.000 22.11 16.91 44.61 4.40
3164 3342 0.902531 TTGGTAGGACTGGCAGTAGC 59.097 55.000 22.11 15.32 41.10 3.58
3165 3343 2.103263 GGATTGGTAGGACTGGCAGTAG 59.897 54.545 22.11 0.00 0.00 2.57
3179 3367 6.576778 AGCCTACTTAACAATAGGATTGGT 57.423 37.500 1.41 0.00 40.53 3.67
3187 3375 7.107542 CCAGTGGTTTAGCCTACTTAACAATA 58.892 38.462 0.00 0.00 37.20 1.90
3201 3389 3.632145 ACAAGTTGAAGCCAGTGGTTTAG 59.368 43.478 11.70 1.04 30.94 1.85


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

AutoCloner maintained by Alex Coulton.