Multiple sequence alignment - TraesCS4D01G343700

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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 TraesCS4D01G343700 chr4D 100.000 2435 0 0 1 2435 499478319 499480753 0.000000e+00 4497.0
1 TraesCS4D01G343700 chr4D 80.749 187 32 4 287 471 442881384 442881568 2.520000e-30 143.0
2 TraesCS4D01G343700 chr4B 86.793 1999 175 46 472 2429 642434561 642436511 0.000000e+00 2146.0
3 TraesCS4D01G343700 chr5A 87.206 1571 125 34 2 1528 680324679 680326217 0.000000e+00 1718.0
4 TraesCS4D01G343700 chr5A 90.342 994 68 15 472 1454 680280609 680281585 0.000000e+00 1279.0
5 TraesCS4D01G343700 chr5A 84.888 1297 111 38 471 1709 680273126 680274395 0.000000e+00 1230.0
6 TraesCS4D01G343700 chr5A 85.287 870 91 25 1336 2185 680464938 680465790 0.000000e+00 863.0
7 TraesCS4D01G343700 chr5A 84.416 539 49 22 594 1106 680446976 680447505 4.680000e-137 497.0
8 TraesCS4D01G343700 chr5A 77.463 741 115 35 1578 2312 680465822 680466516 1.750000e-106 396.0
9 TraesCS4D01G343700 chr5A 95.885 243 10 0 1099 1341 680458590 680458832 6.310000e-106 394.0
10 TraesCS4D01G343700 chr5A 79.118 431 56 16 16 426 573057081 573057497 1.440000e-67 267.0
11 TraesCS4D01G343700 chr5A 83.333 108 7 2 1457 1557 680281708 680281811 3.330000e-14 89.8
12 TraesCS4D01G343700 chr5D 80.000 445 70 15 41 480 397207034 397206604 6.540000e-81 311.0
13 TraesCS4D01G343700 chr5D 76.786 224 47 5 251 471 502887982 502888203 1.180000e-23 121.0
14 TraesCS4D01G343700 chr5D 77.315 216 36 12 263 471 498552891 498552682 5.500000e-22 115.0
15 TraesCS4D01G343700 chr2B 87.786 131 16 0 41 171 775139129 775139259 1.170000e-33 154.0
16 TraesCS4D01G343700 chr2B 78.319 226 42 7 250 471 36918641 36918419 3.260000e-29 139.0
17 TraesCS4D01G343700 chr6B 79.204 226 40 7 250 471 592450488 592450710 1.510000e-32 150.0
18 TraesCS4D01G343700 chr1D 79.018 224 44 3 250 471 118883388 118883166 1.510000e-32 150.0
19 TraesCS4D01G343700 chr2A 80.412 194 32 6 287 477 105409148 105408958 2.520000e-30 143.0
20 TraesCS4D01G343700 chr2D 81.046 153 21 6 319 471 586900471 586900615 5.500000e-22 115.0
21 TraesCS4D01G343700 chr2D 100.000 30 0 0 2209 2238 294662658 294662687 3.380000e-04 56.5


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 TraesCS4D01G343700 chr4D 499478319 499480753 2434 False 4497.0 4497 100.0000 1 2435 1 chr4D.!!$F2 2434
1 TraesCS4D01G343700 chr4B 642434561 642436511 1950 False 2146.0 2146 86.7930 472 2429 1 chr4B.!!$F1 1957
2 TraesCS4D01G343700 chr5A 680324679 680326217 1538 False 1718.0 1718 87.2060 2 1528 1 chr5A.!!$F3 1526
3 TraesCS4D01G343700 chr5A 680273126 680274395 1269 False 1230.0 1230 84.8880 471 1709 1 chr5A.!!$F2 1238
4 TraesCS4D01G343700 chr5A 680280609 680281811 1202 False 684.4 1279 86.8375 472 1557 2 chr5A.!!$F6 1085
5 TraesCS4D01G343700 chr5A 680464938 680466516 1578 False 629.5 863 81.3750 1336 2312 2 chr5A.!!$F7 976
6 TraesCS4D01G343700 chr5A 680446976 680447505 529 False 497.0 497 84.4160 594 1106 1 chr5A.!!$F4 512

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
976 1029 0.241749 AGATCGTCAACACCGCGTTA 59.758 50.0 4.92 0.0 35.52 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 3247 0.179056 CACGGTGACACCTTTGGTCT 60.179 55.0 22.14 0.0 35.66 3.85 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 5.867716 AGAGCGATACGTGAAAAGTGTTTAT 59.132 36.000 0.00 0.00 0.00 1.40
70 71 7.734726 GCGATACGTGAAAAGTGTTTATATAGC 59.265 37.037 0.00 0.00 0.00 2.97
108 109 1.938625 ACGCAATGCATATTTTGGCC 58.061 45.000 5.91 0.00 0.00 5.36
129 131 1.476891 GAGTGGACAGATCAAGCCGTA 59.523 52.381 0.00 0.00 0.00 4.02
160 162 2.496070 GAGGTGCCAGGTTTTAAATCCC 59.504 50.000 11.03 4.33 0.00 3.85
161 163 2.158234 AGGTGCCAGGTTTTAAATCCCA 60.158 45.455 11.03 1.19 0.00 4.37
265 269 3.621892 AACTCACGCGCGGAGTACC 62.622 63.158 36.55 0.00 44.50 3.34
275 279 1.019805 GCGGAGTACCCAGCACTTTC 61.020 60.000 0.00 0.00 35.50 2.62
278 282 0.391263 GAGTACCCAGCACTTTCCCG 60.391 60.000 0.00 0.00 0.00 5.14
285 289 0.603707 CAGCACTTTCCCGCTCTCAA 60.604 55.000 0.00 0.00 35.96 3.02
295 299 1.673033 CCCGCTCTCAACCACTTACAG 60.673 57.143 0.00 0.00 0.00 2.74
318 322 4.735132 TCACCGCCACGCTAGCAC 62.735 66.667 16.45 0.00 0.00 4.40
340 344 3.261951 CGCGGGCTGGACGTTATG 61.262 66.667 0.00 0.00 0.00 1.90
362 366 1.446366 GGATACGGAAGGAGGCACC 59.554 63.158 0.00 0.00 39.35 5.01
375 379 1.949525 GAGGCACCGTATTTGCATGAT 59.050 47.619 0.00 0.00 42.12 2.45
377 381 1.949525 GGCACCGTATTTGCATGATCT 59.050 47.619 0.00 0.00 42.12 2.75
378 382 3.138304 GGCACCGTATTTGCATGATCTA 58.862 45.455 0.00 0.00 42.12 1.98
387 391 7.413988 CCGTATTTGCATGATCTAACAAGTTCA 60.414 37.037 0.00 0.00 0.00 3.18
392 396 5.416639 TGCATGATCTAACAAGTTCAAGCAT 59.583 36.000 10.59 0.00 37.33 3.79
395 399 7.532571 CATGATCTAACAAGTTCAAGCATCAA 58.467 34.615 0.00 0.00 0.00 2.57
435 440 2.910688 AGACATCAAACTGACCGTGT 57.089 45.000 0.00 0.00 0.00 4.49
443 448 3.070446 TCAAACTGACCGTGTAGGACAAT 59.930 43.478 0.00 0.00 43.65 2.71
445 450 3.314541 ACTGACCGTGTAGGACAATTC 57.685 47.619 0.00 0.00 43.65 2.17
448 453 2.094906 TGACCGTGTAGGACAATTCGAG 60.095 50.000 0.00 0.00 45.00 4.04
452 457 2.915463 CGTGTAGGACAATTCGAGACAC 59.085 50.000 0.00 0.00 33.92 3.67
453 458 3.251571 GTGTAGGACAATTCGAGACACC 58.748 50.000 0.00 0.00 31.65 4.16
454 459 3.056749 GTGTAGGACAATTCGAGACACCT 60.057 47.826 0.00 0.00 31.65 4.00
455 460 3.192844 TGTAGGACAATTCGAGACACCTC 59.807 47.826 0.00 0.00 36.08 3.85
456 461 1.550976 AGGACAATTCGAGACACCTCC 59.449 52.381 0.00 0.00 36.04 4.30
457 462 1.405661 GGACAATTCGAGACACCTCCC 60.406 57.143 0.00 0.00 36.04 4.30
458 463 0.246635 ACAATTCGAGACACCTCCCG 59.753 55.000 0.00 0.00 36.04 5.14
459 464 0.246635 CAATTCGAGACACCTCCCGT 59.753 55.000 0.00 0.00 36.04 5.28
502 508 4.658071 AGTAAAAAGACATAATTGCGCCG 58.342 39.130 4.18 0.00 0.00 6.46
586 597 6.807720 CAGCATACATTTTCAATTGTGCTACA 59.192 34.615 13.54 0.00 0.00 2.74
587 598 7.490079 CAGCATACATTTTCAATTGTGCTACAT 59.510 33.333 13.54 0.00 0.00 2.29
588 599 8.036575 AGCATACATTTTCAATTGTGCTACATT 58.963 29.630 12.61 0.00 0.00 2.71
589 600 8.111836 GCATACATTTTCAATTGTGCTACATTG 58.888 33.333 5.13 0.00 0.00 2.82
590 601 6.470557 ACATTTTCAATTGTGCTACATTGC 57.529 33.333 5.13 0.00 0.00 3.56
591 602 5.990386 ACATTTTCAATTGTGCTACATTGCA 59.010 32.000 5.13 0.00 41.05 4.08
592 603 6.651643 ACATTTTCAATTGTGCTACATTGCAT 59.348 30.769 5.13 0.00 45.23 3.96
713 726 5.228945 TCTTCCTTCTTCACCACTTAAGG 57.771 43.478 7.53 0.00 38.44 2.69
720 734 2.561478 TCACCACTTAAGGGCTCAAC 57.439 50.000 7.53 0.00 0.00 3.18
788 803 6.476243 ACGTAGTTCCAAACATATTGACAC 57.524 37.500 0.00 0.00 37.78 3.67
793 808 9.088512 GTAGTTCCAAACATATTGACACTCTAG 57.911 37.037 0.00 0.00 0.00 2.43
794 809 7.907389 AGTTCCAAACATATTGACACTCTAGA 58.093 34.615 0.00 0.00 0.00 2.43
807 826 7.009179 TGACACTCTAGAAGAAATCACCAAT 57.991 36.000 0.00 0.00 0.00 3.16
881 925 5.533154 AGCTTTCTCGCATCTACTACTACAT 59.467 40.000 0.00 0.00 0.00 2.29
882 926 5.627367 GCTTTCTCGCATCTACTACTACATG 59.373 44.000 0.00 0.00 0.00 3.21
916 969 0.396435 TACCTTGGCCTGGCATATCG 59.604 55.000 22.05 5.76 0.00 2.92
927 980 2.153645 TGGCATATCGCATTCCATCAC 58.846 47.619 0.00 0.00 45.17 3.06
938 991 0.824109 TTCCATCACTCACGGCTAGG 59.176 55.000 0.00 0.00 0.00 3.02
976 1029 0.241749 AGATCGTCAACACCGCGTTA 59.758 50.000 4.92 0.00 35.52 3.18
988 1041 5.961395 ACACCGCGTTACAGAAAATATAG 57.039 39.130 4.92 0.00 0.00 1.31
989 1042 4.269363 ACACCGCGTTACAGAAAATATAGC 59.731 41.667 4.92 0.00 0.00 2.97
990 1043 4.269123 CACCGCGTTACAGAAAATATAGCA 59.731 41.667 4.92 0.00 0.00 3.49
1032 1087 2.430921 GTCGAGAGCCACCGTGTG 60.431 66.667 0.00 0.00 0.00 3.82
1227 1282 2.154854 TCAAGAAGGTGAAGCAGACG 57.845 50.000 0.00 0.00 0.00 4.18
1271 1326 2.125512 CTTCGTGGAGCCGGGAAG 60.126 66.667 2.18 2.15 0.00 3.46
1386 1450 1.966451 CACCTTCAAGACCGGCACC 60.966 63.158 0.00 0.00 0.00 5.01
1407 1471 3.439895 GGTCTCTCCGATACCTTTGAC 57.560 52.381 0.00 0.00 0.00 3.18
1559 1760 0.109342 AAGTGTCCAGTTCCTGCCTG 59.891 55.000 0.00 0.00 0.00 4.85
1560 1761 1.968540 GTGTCCAGTTCCTGCCTGC 60.969 63.158 0.00 0.00 0.00 4.85
1561 1762 2.360475 GTCCAGTTCCTGCCTGCC 60.360 66.667 0.00 0.00 0.00 4.85
1562 1763 2.530151 TCCAGTTCCTGCCTGCCT 60.530 61.111 0.00 0.00 0.00 4.75
1565 1766 2.204059 AGTTCCTGCCTGCCTCCT 60.204 61.111 0.00 0.00 0.00 3.69
1625 1858 2.628696 CCCGAGCAAATGCACAGCA 61.629 57.895 8.28 0.00 45.16 4.41
1638 1871 0.108709 CACAGCACTGAGGAGCTCTC 60.109 60.000 14.64 9.73 42.74 3.20
1709 1943 8.642935 TTTCTTTTTCCCATTTTGGTTTTCTT 57.357 26.923 0.00 0.00 35.17 2.52
1712 1946 6.993786 TTTTCCCATTTTGGTTTTCTTCAC 57.006 33.333 0.00 0.00 35.17 3.18
1714 1948 5.683876 TCCCATTTTGGTTTTCTTCACAA 57.316 34.783 0.00 0.00 35.17 3.33
1828 2077 8.810990 TTATGTTCGGTATGTTCCCTTTTATT 57.189 30.769 0.00 0.00 0.00 1.40
1863 2113 9.620660 ATTCATGACCTTTTTAAAATACACGAC 57.379 29.630 0.55 0.00 0.00 4.34
1898 2150 6.639632 ACAGTATGAGCTGAACATTTTTGT 57.360 33.333 0.00 0.00 39.69 2.83
1902 2154 8.453320 CAGTATGAGCTGAACATTTTTGTGATA 58.547 33.333 0.00 0.00 39.69 2.15
1927 2179 5.179368 CAGGACGAACATGTTTCAATACACT 59.821 40.000 13.36 1.23 0.00 3.55
1934 2186 6.662414 ACATGTTTCAATACACTATCCACG 57.338 37.500 0.00 0.00 0.00 4.94
1952 2204 3.744426 CCACGTTTTCCAAATACTCGACT 59.256 43.478 0.00 0.00 0.00 4.18
2168 2425 6.687604 TCTGACGAATATTTTCTCACTCACA 58.312 36.000 0.00 0.00 0.00 3.58
2180 2437 4.640364 TCTCACTCACAAACATGCACATA 58.360 39.130 0.00 0.00 0.00 2.29
2189 2446 8.604640 TCACAAACATGCACATATTTTCATTT 57.395 26.923 0.00 0.00 0.00 2.32
2191 2448 8.714179 CACAAACATGCACATATTTTCATTTCT 58.286 29.630 0.00 0.00 0.00 2.52
2192 2449 8.928733 ACAAACATGCACATATTTTCATTTCTC 58.071 29.630 0.00 0.00 0.00 2.87
2196 2453 7.699391 ACATGCACATATTTTCATTTCTCGAAG 59.301 33.333 0.00 0.00 0.00 3.79
2198 2455 6.127925 TGCACATATTTTCATTTCTCGAAGCT 60.128 34.615 0.00 0.00 0.00 3.74
2199 2456 6.195983 GCACATATTTTCATTTCTCGAAGCTG 59.804 38.462 0.00 0.00 0.00 4.24
2201 2458 7.964559 CACATATTTTCATTTCTCGAAGCTGAA 59.035 33.333 0.00 0.00 0.00 3.02
2205 2462 6.558771 TTTCATTTCTCGAAGCTGAATTCA 57.441 33.333 8.12 8.12 0.00 2.57
2206 2463 6.558771 TTCATTTCTCGAAGCTGAATTCAA 57.441 33.333 9.88 0.00 0.00 2.69
2207 2464 6.558771 TCATTTCTCGAAGCTGAATTCAAA 57.441 33.333 9.88 0.00 0.00 2.69
2319 3181 2.609610 TATCCCCCGCCCCTATGC 60.610 66.667 0.00 0.00 0.00 3.14
2332 3194 0.247736 CCTATGCGGGGACTATGAGC 59.752 60.000 0.00 0.00 0.00 4.26
2333 3195 1.261480 CTATGCGGGGACTATGAGCT 58.739 55.000 0.00 0.00 0.00 4.09
2337 3199 2.045280 CGGGGACTATGAGCTCTGG 58.955 63.158 16.19 7.39 0.00 3.86
2338 3200 0.468214 CGGGGACTATGAGCTCTGGA 60.468 60.000 16.19 0.00 0.00 3.86
2339 3201 1.337118 GGGGACTATGAGCTCTGGAG 58.663 60.000 16.19 11.43 0.00 3.86
2340 3202 1.133325 GGGGACTATGAGCTCTGGAGA 60.133 57.143 16.19 0.00 0.00 3.71
2348 3210 0.678366 GAGCTCTGGAGACGAGACCA 60.678 60.000 6.43 0.00 34.36 4.02
2357 3219 1.891150 GAGACGAGACCAAAGGTACCA 59.109 52.381 15.94 0.00 35.25 3.25
2367 3229 0.763035 AAAGGTACCACCGTGCTCTT 59.237 50.000 15.94 0.00 44.90 2.85
2373 3235 1.157870 ACCACCGTGCTCTTGTTTCG 61.158 55.000 0.00 0.00 0.00 3.46
2406 3268 2.631428 CAAAGGTGTCACCGTGCG 59.369 61.111 16.44 4.92 44.90 5.34
2418 3280 0.393808 ACCGTGCGATAAATTGGGCT 60.394 50.000 0.00 0.00 0.00 5.19
2429 3291 5.119279 CGATAAATTGGGCTCTAGTTGATCG 59.881 44.000 0.00 0.00 0.00 3.69
2430 3292 2.246719 ATTGGGCTCTAGTTGATCGC 57.753 50.000 0.00 0.00 0.00 4.58
2431 3293 0.179111 TTGGGCTCTAGTTGATCGCG 60.179 55.000 0.00 0.00 0.00 5.87
2432 3294 1.035385 TGGGCTCTAGTTGATCGCGA 61.035 55.000 13.09 13.09 0.00 5.87
2433 3295 0.102481 GGGCTCTAGTTGATCGCGAA 59.898 55.000 15.24 0.00 0.00 4.70
2434 3296 1.201343 GGCTCTAGTTGATCGCGAAC 58.799 55.000 15.24 12.18 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.798982 GCTCTGTAATTTTCCTAATGCGTTATC 59.201 37.037 0.00 0.00 0.00 1.75
40 41 2.987149 ACACTTTTCACGTATCGCTCTG 59.013 45.455 0.00 0.00 0.00 3.35
70 71 3.860536 GCGTTCACCTCTTAGCTAGAAAG 59.139 47.826 0.00 0.00 30.91 2.62
108 109 0.803768 CGGCTTGATCTGTCCACTCG 60.804 60.000 0.00 0.00 0.00 4.18
129 131 0.616111 CTGGCACCTCCTGGTCTACT 60.616 60.000 0.00 0.00 46.60 2.57
256 260 1.003718 AAAGTGCTGGGTACTCCGC 60.004 57.895 1.57 1.57 38.76 5.54
258 262 0.035343 GGGAAAGTGCTGGGTACTCC 60.035 60.000 0.00 0.00 0.00 3.85
265 269 1.743252 GAGAGCGGGAAAGTGCTGG 60.743 63.158 0.00 0.00 42.60 4.85
275 279 0.320374 TGTAAGTGGTTGAGAGCGGG 59.680 55.000 0.00 0.00 0.00 6.13
278 282 2.417719 CACCTGTAAGTGGTTGAGAGC 58.582 52.381 0.00 0.00 35.28 4.09
336 340 3.319972 CCTCCTTCCGTATCCGAACATAA 59.680 47.826 0.00 0.00 35.63 1.90
340 344 0.249363 GCCTCCTTCCGTATCCGAAC 60.249 60.000 0.00 0.00 35.63 3.95
355 359 1.378531 TCATGCAAATACGGTGCCTC 58.621 50.000 0.00 0.00 41.49 4.70
356 360 1.949525 GATCATGCAAATACGGTGCCT 59.050 47.619 0.00 0.00 41.49 4.75
358 362 4.035091 TGTTAGATCATGCAAATACGGTGC 59.965 41.667 0.00 0.00 42.55 5.01
359 363 5.733226 TGTTAGATCATGCAAATACGGTG 57.267 39.130 0.00 0.00 0.00 4.94
360 364 5.880332 ACTTGTTAGATCATGCAAATACGGT 59.120 36.000 0.00 0.00 0.00 4.83
361 365 6.363577 ACTTGTTAGATCATGCAAATACGG 57.636 37.500 0.00 0.00 0.00 4.02
362 366 7.463544 TGAACTTGTTAGATCATGCAAATACG 58.536 34.615 0.00 0.00 29.26 3.06
377 381 9.979578 ACATAAAATTGATGCTTGAACTTGTTA 57.020 25.926 0.00 0.00 0.00 2.41
378 382 8.891671 ACATAAAATTGATGCTTGAACTTGTT 57.108 26.923 0.00 0.00 0.00 2.83
409 414 6.422701 CACGGTCAGTTTGATGTCTAAAACTA 59.577 38.462 0.84 0.00 43.09 2.24
411 416 5.007332 ACACGGTCAGTTTGATGTCTAAAAC 59.993 40.000 0.00 0.00 36.69 2.43
412 417 5.120399 ACACGGTCAGTTTGATGTCTAAAA 58.880 37.500 0.00 0.00 0.00 1.52
421 426 2.033372 TGTCCTACACGGTCAGTTTGA 58.967 47.619 0.00 0.00 0.00 2.69
429 434 2.094854 GTCTCGAATTGTCCTACACGGT 60.095 50.000 0.00 0.00 0.00 4.83
435 440 2.758979 GGAGGTGTCTCGAATTGTCCTA 59.241 50.000 0.00 0.00 40.85 2.94
452 457 6.563222 TTTTTGAGTTAAATACACGGGAGG 57.437 37.500 0.00 0.00 0.00 4.30
502 508 6.645790 ATCTCTATTTGGAACATCATTGCC 57.354 37.500 0.00 0.00 39.30 4.52
589 600 6.457355 TGAATTGAATGGGTATGCAATATGC 58.543 36.000 0.00 0.00 40.90 3.14
590 601 6.588756 GCTGAATTGAATGGGTATGCAATATG 59.411 38.462 0.00 0.00 40.90 1.78
591 602 6.570957 CGCTGAATTGAATGGGTATGCAATAT 60.571 38.462 0.00 0.00 40.90 1.28
592 603 5.278414 CGCTGAATTGAATGGGTATGCAATA 60.278 40.000 0.00 0.00 40.90 1.90
713 726 3.441572 ACATATGTGAGCTTTGTTGAGCC 59.558 43.478 7.78 0.00 43.74 4.70
720 734 4.926860 TCGTCAACATATGTGAGCTTTG 57.073 40.909 9.63 2.78 0.00 2.77
760 775 8.378421 GTCAATATGTTTGGAACTACGTACTTC 58.622 37.037 6.45 6.45 0.00 3.01
771 786 8.593679 TCTTCTAGAGTGTCAATATGTTTGGAA 58.406 33.333 0.00 0.00 0.00 3.53
788 803 7.437862 GCTACAGATTGGTGATTTCTTCTAGAG 59.562 40.741 0.00 0.00 0.00 2.43
793 808 6.112058 AGAGCTACAGATTGGTGATTTCTTC 58.888 40.000 0.00 0.00 0.00 2.87
794 809 6.059787 AGAGCTACAGATTGGTGATTTCTT 57.940 37.500 0.00 0.00 0.00 2.52
807 826 7.671302 AGTATTTTCTGTTTGAGAGCTACAGA 58.329 34.615 11.42 11.42 44.66 3.41
881 925 6.550108 GGCCAAGGTATATATAGCTAGCTACA 59.450 42.308 26.41 16.56 39.95 2.74
882 926 6.778559 AGGCCAAGGTATATATAGCTAGCTAC 59.221 42.308 26.41 15.01 39.95 3.58
916 969 0.745845 AGCCGTGAGTGATGGAATGC 60.746 55.000 0.00 0.00 31.27 3.56
938 991 0.523072 TTGCGAAATGGAAGAGCTGC 59.477 50.000 0.00 0.00 0.00 5.25
946 999 2.378445 TGACGATCTTGCGAAATGGA 57.622 45.000 0.00 0.00 34.83 3.41
976 1029 6.653020 TGTCAGGTGATGCTATATTTTCTGT 58.347 36.000 0.00 0.00 0.00 3.41
988 1041 0.666913 GATGCCATGTCAGGTGATGC 59.333 55.000 0.00 0.00 0.00 3.91
989 1042 1.315690 GGATGCCATGTCAGGTGATG 58.684 55.000 0.00 0.00 0.00 3.07
990 1043 0.184451 GGGATGCCATGTCAGGTGAT 59.816 55.000 0.00 0.00 0.00 3.06
1271 1326 2.279784 CGGCGATCTTCCTCAGCC 60.280 66.667 0.00 0.00 44.00 4.85
1422 1486 5.552870 ACACAACTACTCATTCTCCAAGT 57.447 39.130 0.00 0.00 0.00 3.16
1559 1760 1.336125 GTGCTGAATTGCATAGGAGGC 59.664 52.381 0.00 0.00 45.23 4.70
1560 1761 2.617308 CAGTGCTGAATTGCATAGGAGG 59.383 50.000 0.00 0.00 45.23 4.30
1561 1762 2.033049 GCAGTGCTGAATTGCATAGGAG 59.967 50.000 8.18 0.00 45.23 3.69
1562 1763 2.019249 GCAGTGCTGAATTGCATAGGA 58.981 47.619 8.18 0.00 45.23 2.94
1565 1766 1.667212 CTCGCAGTGCTGAATTGCATA 59.333 47.619 14.33 0.00 45.23 3.14
1625 1858 1.257055 GGCACAGAGAGCTCCTCAGT 61.257 60.000 10.93 7.66 44.40 3.41
1650 1883 2.158561 AAAATCGGCAGCCCAACAGC 62.159 55.000 5.63 0.00 0.00 4.40
1723 1957 5.570844 CGGGAAGAAAAAGACAGGAAGGATA 60.571 44.000 0.00 0.00 0.00 2.59
1800 2049 7.527568 AAAGGGAACATACCGAACATAAAAA 57.472 32.000 0.00 0.00 0.00 1.94
1898 2150 4.888917 TGAAACATGTTCGTCCTGTATCA 58.111 39.130 12.39 5.65 0.00 2.15
1902 2154 5.049680 GTGTATTGAAACATGTTCGTCCTGT 60.050 40.000 12.39 0.00 0.00 4.00
1927 2179 5.577945 GTCGAGTATTTGGAAAACGTGGATA 59.422 40.000 0.00 0.00 0.00 2.59
1934 2186 9.673454 AAAATGTTAGTCGAGTATTTGGAAAAC 57.327 29.630 0.00 0.00 0.00 2.43
2145 2402 6.951256 TGTGAGTGAGAAAATATTCGTCAG 57.049 37.500 0.00 0.00 40.63 3.51
2168 2425 8.028354 TCGAGAAATGAAAATATGTGCATGTTT 58.972 29.630 0.00 1.85 34.29 2.83
2180 2437 7.596494 TGAATTCAGCTTCGAGAAATGAAAAT 58.404 30.769 3.38 8.41 33.00 1.82
2236 3096 5.150683 TGTCACGTGTTGAGAAAAAGTTTG 58.849 37.500 16.51 0.00 33.71 2.93
2319 3181 0.468214 TCCAGAGCTCATAGTCCCCG 60.468 60.000 17.77 0.00 0.00 5.73
2325 3187 2.548057 GTCTCGTCTCCAGAGCTCATAG 59.452 54.545 17.77 9.92 35.79 2.23
2329 3191 0.678366 TGGTCTCGTCTCCAGAGCTC 60.678 60.000 5.27 5.27 38.87 4.09
2330 3192 0.251386 TTGGTCTCGTCTCCAGAGCT 60.251 55.000 0.00 0.00 38.87 4.09
2332 3194 1.203523 CCTTTGGTCTCGTCTCCAGAG 59.796 57.143 0.00 0.00 36.22 3.35
2333 3195 1.257743 CCTTTGGTCTCGTCTCCAGA 58.742 55.000 0.00 0.00 35.05 3.86
2337 3199 1.891150 TGGTACCTTTGGTCTCGTCTC 59.109 52.381 14.36 0.00 37.09 3.36
2338 3200 1.617357 GTGGTACCTTTGGTCTCGTCT 59.383 52.381 14.36 0.00 37.09 4.18
2339 3201 1.337541 GGTGGTACCTTTGGTCTCGTC 60.338 57.143 14.36 0.00 37.09 4.20
2340 3202 0.683412 GGTGGTACCTTTGGTCTCGT 59.317 55.000 14.36 0.00 37.09 4.18
2348 3210 0.763035 AAGAGCACGGTGGTACCTTT 59.237 50.000 13.47 3.28 35.66 3.11
2357 3219 1.092921 TTGCGAAACAAGAGCACGGT 61.093 50.000 0.00 0.00 40.92 4.83
2385 3247 0.179056 CACGGTGACACCTTTGGTCT 60.179 55.000 22.14 0.00 35.66 3.85
2386 3248 1.782028 GCACGGTGACACCTTTGGTC 61.782 60.000 22.14 4.42 35.66 4.02
2387 3249 1.822186 GCACGGTGACACCTTTGGT 60.822 57.895 22.14 9.87 35.66 3.67
2388 3250 2.892334 CGCACGGTGACACCTTTGG 61.892 63.158 22.14 9.21 35.66 3.28
2389 3251 1.227999 ATCGCACGGTGACACCTTTG 61.228 55.000 22.14 18.46 35.66 2.77
2396 3258 1.063469 CCCAATTTATCGCACGGTGAC 59.937 52.381 13.29 2.36 0.00 3.67
2397 3259 1.374560 CCCAATTTATCGCACGGTGA 58.625 50.000 13.29 0.00 0.00 4.02
2399 3261 0.393808 AGCCCAATTTATCGCACGGT 60.394 50.000 0.00 0.00 0.00 4.83
2406 3268 5.106908 GCGATCAACTAGAGCCCAATTTATC 60.107 44.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.