Multiple sequence alignment - TraesCS2A01G356800

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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 TraesCS2A01G356800 chr2A 100.000 1625 0 0 721 2345 601481385 601483009 0.000000e+00 3001.0
1 TraesCS2A01G356800 chr2A 100.000 411 0 0 1 411 601480665 601481075 0.000000e+00 760.0
2 TraesCS2A01G356800 chr2A 86.147 231 24 6 1 228 734069 733844 2.330000e-60 243.0
3 TraesCS2A01G356800 chr2D 94.695 886 24 11 746 1628 457889084 457889949 0.000000e+00 1354.0
4 TraesCS2A01G356800 chr2D 89.143 350 17 11 1 336 457888750 457889092 1.300000e-112 416.0
5 TraesCS2A01G356800 chr2D 98.701 77 1 0 335 411 449513514 449513438 1.130000e-28 137.0
6 TraesCS2A01G356800 chr2B 95.882 680 25 1 861 1537 539089700 539090379 0.000000e+00 1098.0
7 TraesCS2A01G356800 chr2B 90.997 722 58 6 1630 2345 55166872 55166152 0.000000e+00 966.0
8 TraesCS2A01G356800 chr2B 81.194 335 53 8 1017 1346 685502910 685503239 6.430000e-66 261.0
9 TraesCS2A01G356800 chr2B 80.896 335 54 8 1017 1346 685518192 685518521 2.990000e-64 255.0
10 TraesCS2A01G356800 chr2B 80.186 323 60 3 1015 1335 686041098 686041418 3.010000e-59 239.0
11 TraesCS2A01G356800 chr2B 87.640 178 7 7 769 933 539089453 539089628 2.380000e-45 193.0
12 TraesCS2A01G356800 chr2B 98.718 78 1 0 334 411 526838998 526839075 3.140000e-29 139.0
13 TraesCS2A01G356800 chr2B 98.630 73 1 0 861 933 539089628 539089700 1.890000e-26 130.0
14 TraesCS2A01G356800 chr4A 88.611 720 74 5 1630 2345 359448490 359449205 0.000000e+00 869.0
15 TraesCS2A01G356800 chr4A 85.417 336 27 14 1 321 726695350 726695022 1.740000e-86 329.0
16 TraesCS2A01G356800 chr4A 96.970 33 0 1 34 66 620280596 620280627 1.000000e-03 54.7
17 TraesCS2A01G356800 chr6B 87.795 721 84 3 1629 2345 694103432 694102712 0.000000e+00 841.0
18 TraesCS2A01G356800 chr3D 86.130 721 96 3 1629 2345 48303131 48302411 0.000000e+00 774.0
19 TraesCS2A01G356800 chr3D 100.000 75 0 0 337 411 481706722 481706648 3.140000e-29 139.0
20 TraesCS2A01G356800 chr4D 85.853 721 98 3 1629 2345 11503027 11502307 0.000000e+00 763.0
21 TraesCS2A01G356800 chr5A 84.094 723 100 9 1629 2345 381753170 381752457 0.000000e+00 684.0
22 TraesCS2A01G356800 chr5A 86.514 393 49 3 1629 2018 365610468 365610859 1.670000e-116 429.0
23 TraesCS2A01G356800 chr5A 100.000 29 0 0 721 749 224206626 224206654 1.000000e-03 54.7
24 TraesCS2A01G356800 chr1B 84.241 698 106 3 1650 2343 26642156 26642853 0.000000e+00 676.0
25 TraesCS2A01G356800 chr1B 98.750 80 0 1 333 411 683570223 683570302 8.740000e-30 141.0
26 TraesCS2A01G356800 chr1B 96.341 82 2 1 330 411 10761816 10761736 1.460000e-27 134.0
27 TraesCS2A01G356800 chr3B 83.197 732 117 5 1618 2345 4806659 4805930 0.000000e+00 665.0
28 TraesCS2A01G356800 chr3B 92.308 91 5 2 322 411 519400211 519400122 6.800000e-26 128.0
29 TraesCS2A01G356800 chr3A 87.059 340 30 7 1 336 517660532 517660861 2.850000e-99 372.0
30 TraesCS2A01G356800 chr4B 100.000 76 0 0 336 411 429347387 429347462 8.740000e-30 141.0
31 TraesCS2A01G356800 chr7D 100.000 75 0 0 337 411 29555515 29555589 3.140000e-29 139.0
32 TraesCS2A01G356800 chr7D 100.000 75 0 0 337 411 78321458 78321384 3.140000e-29 139.0
33 TraesCS2A01G356800 chr5B 94.118 51 2 1 286 336 670783779 670783828 2.500000e-10 76.8
34 TraesCS2A01G356800 chr6A 100.000 29 0 0 721 749 162536772 162536744 1.000000e-03 54.7


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 TraesCS2A01G356800 chr2A 601480665 601483009 2344 False 1880.500000 3001 100.000000 1 2345 2 chr2A.!!$F1 2344
1 TraesCS2A01G356800 chr2D 457888750 457889949 1199 False 885.000000 1354 91.919000 1 1628 2 chr2D.!!$F1 1627
2 TraesCS2A01G356800 chr2B 55166152 55166872 720 True 966.000000 966 90.997000 1630 2345 1 chr2B.!!$R1 715
3 TraesCS2A01G356800 chr2B 539089453 539090379 926 False 473.666667 1098 94.050667 769 1537 3 chr2B.!!$F5 768
4 TraesCS2A01G356800 chr4A 359448490 359449205 715 False 869.000000 869 88.611000 1630 2345 1 chr4A.!!$F1 715
5 TraesCS2A01G356800 chr6B 694102712 694103432 720 True 841.000000 841 87.795000 1629 2345 1 chr6B.!!$R1 716
6 TraesCS2A01G356800 chr3D 48302411 48303131 720 True 774.000000 774 86.130000 1629 2345 1 chr3D.!!$R1 716
7 TraesCS2A01G356800 chr4D 11502307 11503027 720 True 763.000000 763 85.853000 1629 2345 1 chr4D.!!$R1 716
8 TraesCS2A01G356800 chr5A 381752457 381753170 713 True 684.000000 684 84.094000 1629 2345 1 chr5A.!!$R1 716
9 TraesCS2A01G356800 chr1B 26642156 26642853 697 False 676.000000 676 84.241000 1650 2343 1 chr1B.!!$F1 693
10 TraesCS2A01G356800 chr3B 4805930 4806659 729 True 665.000000 665 83.197000 1618 2345 1 chr3B.!!$R1 727

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
410 425 0.036022 TGGATGACACGTGGCATTCA 59.964 50.0 36.64 36.64 46.54 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 1629 0.240411 AACGTAGACCTCGTGCTCAC 59.76 55.0 0.0 0.0 41.38 3.51 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
110 114 9.636879 CAAATTTCAAGGTTTCCAAAAATGTTT 57.363 25.926 0.00 0.00 0.00 2.83
118 122 7.257003 AGGTTTCCAAAAATGTTTGCAAATTC 58.743 30.769 16.21 3.86 42.44 2.17
138 142 4.086199 TCGAAGAACTGTTTGCGTTTTT 57.914 36.364 0.00 0.00 0.00 1.94
183 187 2.383442 AGAGTGTGGTACAGTGGACT 57.617 50.000 5.24 0.00 41.80 3.85
265 269 4.451096 TCGCTACAGGCTTTCTTTTAGTTG 59.549 41.667 0.00 0.00 39.13 3.16
268 272 5.240844 GCTACAGGCTTTCTTTTAGTTGGAA 59.759 40.000 0.00 0.00 38.06 3.53
269 273 5.774498 ACAGGCTTTCTTTTAGTTGGAAG 57.226 39.130 0.00 0.00 0.00 3.46
270 274 5.201243 ACAGGCTTTCTTTTAGTTGGAAGT 58.799 37.500 0.00 0.00 0.00 3.01
271 275 5.067805 ACAGGCTTTCTTTTAGTTGGAAGTG 59.932 40.000 0.00 0.00 0.00 3.16
272 276 5.299279 CAGGCTTTCTTTTAGTTGGAAGTGA 59.701 40.000 0.00 0.00 0.00 3.41
273 277 5.532779 AGGCTTTCTTTTAGTTGGAAGTGAG 59.467 40.000 0.00 0.00 0.00 3.51
279 294 2.961526 TAGTTGGAAGTGAGCGATCC 57.038 50.000 0.00 0.00 0.00 3.36
339 354 4.344865 GGAGGCTGGCAACCGGAA 62.345 66.667 9.46 0.00 29.82 4.30
340 355 2.282180 GAGGCTGGCAACCGGAAA 60.282 61.111 9.46 0.00 29.82 3.13
341 356 1.901464 GAGGCTGGCAACCGGAAAA 60.901 57.895 9.46 0.00 29.82 2.29
369 384 4.621269 AGACCAGGTCTCACGGTT 57.379 55.556 17.31 0.00 38.71 4.44
370 385 3.759865 AGACCAGGTCTCACGGTTA 57.240 52.632 17.31 0.00 38.71 2.85
371 386 1.546961 AGACCAGGTCTCACGGTTAG 58.453 55.000 17.31 0.00 38.71 2.34
372 387 0.108756 GACCAGGTCTCACGGTTAGC 60.109 60.000 12.94 0.00 31.63 3.09
373 388 0.830444 ACCAGGTCTCACGGTTAGCA 60.830 55.000 0.00 0.00 0.00 3.49
374 389 0.108615 CCAGGTCTCACGGTTAGCAG 60.109 60.000 0.00 0.00 0.00 4.24
375 390 0.108615 CAGGTCTCACGGTTAGCAGG 60.109 60.000 0.00 0.00 0.00 4.85
376 391 0.542232 AGGTCTCACGGTTAGCAGGT 60.542 55.000 0.00 0.00 0.00 4.00
377 392 0.389948 GGTCTCACGGTTAGCAGGTG 60.390 60.000 0.00 0.00 0.00 4.00
378 393 0.601558 GTCTCACGGTTAGCAGGTGA 59.398 55.000 3.41 3.41 38.29 4.02
380 395 3.045518 TCACGGTTAGCAGGTGAGA 57.954 52.632 0.00 0.00 35.89 3.27
381 396 0.601558 TCACGGTTAGCAGGTGAGAC 59.398 55.000 0.00 0.00 35.89 3.36
382 397 0.389948 CACGGTTAGCAGGTGAGACC 60.390 60.000 0.00 0.00 38.99 3.85
383 398 1.218316 CGGTTAGCAGGTGAGACCC 59.782 63.158 0.00 0.00 39.75 4.46
384 399 1.218316 GGTTAGCAGGTGAGACCCG 59.782 63.158 0.00 0.00 39.75 5.28
385 400 1.448013 GTTAGCAGGTGAGACCCGC 60.448 63.158 0.00 0.00 41.94 6.13
386 401 2.656069 TTAGCAGGTGAGACCCGCC 61.656 63.158 0.00 0.00 42.60 6.13
389 404 4.087892 CAGGTGAGACCCGCCCTG 62.088 72.222 0.00 0.00 46.65 4.45
390 405 4.316823 AGGTGAGACCCGCCCTGA 62.317 66.667 0.00 0.00 46.65 3.86
391 406 3.083997 GGTGAGACCCGCCCTGAT 61.084 66.667 0.00 0.00 39.55 2.90
392 407 2.187946 GTGAGACCCGCCCTGATG 59.812 66.667 0.00 0.00 0.00 3.07
393 408 3.083349 TGAGACCCGCCCTGATGG 61.083 66.667 0.00 0.00 37.09 3.51
394 409 2.764128 GAGACCCGCCCTGATGGA 60.764 66.667 0.00 0.00 35.39 3.41
395 410 2.040464 AGACCCGCCCTGATGGAT 60.040 61.111 0.00 0.00 35.39 3.41
396 411 2.111878 GACCCGCCCTGATGGATG 59.888 66.667 0.00 0.00 35.39 3.51
397 412 2.366837 ACCCGCCCTGATGGATGA 60.367 61.111 0.00 0.00 35.39 2.92
398 413 2.111878 CCCGCCCTGATGGATGAC 59.888 66.667 0.00 0.00 35.39 3.06
399 414 2.745308 CCCGCCCTGATGGATGACA 61.745 63.158 0.00 0.00 35.39 3.58
400 415 1.524621 CCGCCCTGATGGATGACAC 60.525 63.158 0.00 0.00 35.39 3.67
401 416 1.884464 CGCCCTGATGGATGACACG 60.884 63.158 0.00 0.00 35.39 4.49
402 417 1.221840 GCCCTGATGGATGACACGT 59.778 57.895 0.00 0.00 35.39 4.49
403 418 1.091771 GCCCTGATGGATGACACGTG 61.092 60.000 15.48 15.48 35.39 4.49
404 419 0.462581 CCCTGATGGATGACACGTGG 60.463 60.000 21.57 1.66 35.39 4.94
405 420 1.091771 CCTGATGGATGACACGTGGC 61.092 60.000 21.57 19.24 34.57 5.01
406 421 0.391528 CTGATGGATGACACGTGGCA 60.392 55.000 29.28 29.28 37.54 4.92
408 423 1.339920 TGATGGATGACACGTGGCATT 60.340 47.619 36.07 22.11 45.42 3.56
409 424 1.331756 GATGGATGACACGTGGCATTC 59.668 52.381 36.07 34.16 45.42 2.67
410 425 0.036022 TGGATGACACGTGGCATTCA 59.964 50.000 36.64 36.64 46.54 2.57
738 753 2.699073 CATCAGGATGGGTCTTGCG 58.301 57.895 1.25 0.00 36.16 4.85
739 754 0.107508 CATCAGGATGGGTCTTGCGT 60.108 55.000 1.25 0.00 36.16 5.24
740 755 0.107508 ATCAGGATGGGTCTTGCGTG 60.108 55.000 0.00 0.00 36.16 5.34
741 756 1.191489 TCAGGATGGGTCTTGCGTGA 61.191 55.000 0.00 0.00 36.16 4.35
742 757 0.742281 CAGGATGGGTCTTGCGTGAG 60.742 60.000 0.00 0.00 0.00 3.51
743 758 0.904865 AGGATGGGTCTTGCGTGAGA 60.905 55.000 0.00 0.00 0.00 3.27
744 759 0.741221 GGATGGGTCTTGCGTGAGAC 60.741 60.000 10.63 10.63 44.20 3.36
748 763 4.268687 GTCTTGCGTGAGACCTGG 57.731 61.111 8.56 0.00 40.10 4.45
749 764 2.029844 GTCTTGCGTGAGACCTGGC 61.030 63.158 8.56 0.00 40.10 4.85
750 765 2.031012 CTTGCGTGAGACCTGGCA 59.969 61.111 0.00 0.00 0.00 4.92
751 766 1.597854 CTTGCGTGAGACCTGGCAA 60.598 57.895 0.00 0.00 42.54 4.52
752 767 1.845809 CTTGCGTGAGACCTGGCAAC 61.846 60.000 0.00 0.00 40.17 4.17
753 768 3.050275 GCGTGAGACCTGGCAACC 61.050 66.667 0.00 0.00 0.00 3.77
754 769 2.743718 CGTGAGACCTGGCAACCT 59.256 61.111 0.00 0.00 0.00 3.50
755 770 1.669115 CGTGAGACCTGGCAACCTG 60.669 63.158 0.00 0.00 0.00 4.00
756 771 1.754745 GTGAGACCTGGCAACCTGA 59.245 57.895 0.00 0.00 0.00 3.86
757 772 0.603975 GTGAGACCTGGCAACCTGAC 60.604 60.000 0.00 0.00 0.00 3.51
758 773 1.374758 GAGACCTGGCAACCTGACG 60.375 63.158 0.00 0.00 0.00 4.35
759 774 3.050275 GACCTGGCAACCTGACGC 61.050 66.667 0.00 0.00 0.00 5.19
760 775 4.988598 ACCTGGCAACCTGACGCG 62.989 66.667 3.53 3.53 0.00 6.01
805 822 8.854237 AAAAGAAAAAGGCAAGGGGTATATAT 57.146 30.769 0.00 0.00 0.00 0.86
856 884 3.310307 GGCCGCCACCCACATTTT 61.310 61.111 3.91 0.00 0.00 1.82
860 888 1.667510 CGCCACCCACATTTTTGCC 60.668 57.895 0.00 0.00 0.00 4.52
945 1117 1.734477 CGAGACCACAAGCCGAGTG 60.734 63.158 0.00 0.00 36.76 3.51
1032 1204 0.447801 GCTTGATTTCCGACGCATGT 59.552 50.000 0.00 0.00 0.00 3.21
1128 1300 3.160269 CATTTTCAAAGCTCCAGGAGGT 58.840 45.455 16.01 16.01 42.52 3.85
1269 1441 4.379243 CGTGCTGCCGGGAAGACT 62.379 66.667 6.09 0.00 0.00 3.24
1413 1588 9.458374 ACTGTATTTAAATTGTTGTTGTACAGC 57.542 29.630 16.39 2.25 39.82 4.40
1428 1623 6.589907 TGTTGTACAGCACAGTATATGAGTTG 59.410 38.462 8.48 0.00 38.72 3.16
1429 1624 5.660460 TGTACAGCACAGTATATGAGTTGG 58.340 41.667 0.00 0.00 35.52 3.77
1430 1625 3.535561 ACAGCACAGTATATGAGTTGGC 58.464 45.455 0.00 0.00 35.52 4.52
1431 1626 3.198635 ACAGCACAGTATATGAGTTGGCT 59.801 43.478 0.00 0.00 35.52 4.75
1432 1627 3.558829 CAGCACAGTATATGAGTTGGCTG 59.441 47.826 0.00 0.00 40.00 4.85
1433 1628 2.289002 GCACAGTATATGAGTTGGCTGC 59.711 50.000 0.00 0.00 0.00 5.25
1434 1629 2.541346 CACAGTATATGAGTTGGCTGCG 59.459 50.000 0.00 0.00 0.00 5.18
1435 1630 2.168521 ACAGTATATGAGTTGGCTGCGT 59.831 45.455 0.00 0.00 0.00 5.24
1436 1631 2.541346 CAGTATATGAGTTGGCTGCGTG 59.459 50.000 0.00 0.00 0.00 5.34
1437 1632 2.430694 AGTATATGAGTTGGCTGCGTGA 59.569 45.455 0.00 0.00 0.00 4.35
1438 1633 1.945387 ATATGAGTTGGCTGCGTGAG 58.055 50.000 0.00 0.00 0.00 3.51
1482 1677 5.794894 AGTTTCCACTTGTACACTCATAGG 58.205 41.667 0.00 0.00 0.00 2.57
1522 1717 7.439157 TGCTAGTATTATTCATGCAATGGAC 57.561 36.000 0.00 0.00 46.73 4.02
1609 1804 3.386078 TCAGAGAGGCATCAGTTGTATCC 59.614 47.826 0.00 0.00 0.00 2.59
1688 1883 6.466308 AAAGTTACGGTCCGTATTACAAAC 57.534 37.500 24.26 18.97 41.97 2.93
1708 1903 8.450578 ACAAACATCAATAACTTCTGTCAAGA 57.549 30.769 0.00 0.00 0.00 3.02
1790 1985 6.948309 TCACTAGCAGTATTCTGGCTATGATA 59.052 38.462 1.21 0.00 41.57 2.15
1943 2141 1.819903 AGGTAGCTCCGTTCTCTGAAC 59.180 52.381 0.00 0.77 41.99 3.18
1952 2151 2.095567 CCGTTCTCTGAACTGCAATTGG 60.096 50.000 7.72 0.00 0.00 3.16
2011 2210 3.558109 GGCATTCCTACAGGAGAATAGCC 60.558 52.174 10.61 10.61 46.36 3.93
2036 2235 7.180946 CCCCCTACATGATGTAAAGATGATCTA 59.819 40.741 6.75 0.00 31.67 1.98
2041 2240 6.043590 ACATGATGTAAAGATGATCTAGCCCA 59.956 38.462 0.00 0.00 0.00 5.36
2089 2288 4.082523 CACCACCATCGGCCGTCT 62.083 66.667 27.15 11.42 0.00 4.18
2124 2324 1.907240 TTATTTAGCCCAGCCCTCCT 58.093 50.000 0.00 0.00 0.00 3.69
2152 2352 0.106708 GTCCATGGAGCATTAGCCGA 59.893 55.000 16.81 0.00 43.56 5.54
2177 2377 0.534412 CCACTCTCTCACGAGGCAAT 59.466 55.000 0.00 0.00 37.86 3.56
2179 2379 2.223688 CCACTCTCTCACGAGGCAATAG 60.224 54.545 0.00 0.00 37.86 1.73
2218 2418 2.378208 TCACATGTTTCCCCTTCATCCA 59.622 45.455 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 91 6.207417 TGCAAACATTTTTGGAAACCTTGAAA 59.793 30.769 6.47 0.00 39.83 2.69
91 94 5.557891 TGCAAACATTTTTGGAAACCTTG 57.442 34.783 6.47 0.00 39.83 3.61
99 102 6.713520 TCTTCGAATTTGCAAACATTTTTGG 58.286 32.000 15.41 6.10 42.22 3.28
110 114 3.796178 GCAAACAGTTCTTCGAATTTGCA 59.204 39.130 27.27 0.00 46.95 4.08
118 122 5.918387 TTAAAAACGCAAACAGTTCTTCG 57.082 34.783 0.00 0.00 0.00 3.79
166 170 1.964223 CTCAGTCCACTGTACCACACT 59.036 52.381 6.61 0.00 44.12 3.55
167 171 1.961394 TCTCAGTCCACTGTACCACAC 59.039 52.381 6.61 0.00 44.12 3.82
168 172 2.239400 CTCTCAGTCCACTGTACCACA 58.761 52.381 6.61 0.00 44.12 4.17
183 187 2.095750 CGGTACTGTAGCGCTCTCA 58.904 57.895 23.85 14.30 42.95 3.27
217 221 1.376812 GGGCACTGTAGAAACCCGG 60.377 63.158 0.00 0.00 0.00 5.73
265 269 1.086634 GCACAGGATCGCTCACTTCC 61.087 60.000 0.00 0.00 0.00 3.46
268 272 2.182791 CGCACAGGATCGCTCACT 59.817 61.111 0.00 0.00 0.00 3.41
269 273 3.558411 GCGCACAGGATCGCTCAC 61.558 66.667 0.30 0.00 46.92 3.51
352 367 1.546961 CTAACCGTGAGACCTGGTCT 58.453 55.000 28.70 28.70 46.42 3.85
353 368 0.108756 GCTAACCGTGAGACCTGGTC 60.109 60.000 19.20 19.20 34.11 4.02
354 369 0.830444 TGCTAACCGTGAGACCTGGT 60.830 55.000 0.00 0.00 37.68 4.00
355 370 0.108615 CTGCTAACCGTGAGACCTGG 60.109 60.000 0.00 0.00 0.00 4.45
356 371 0.108615 CCTGCTAACCGTGAGACCTG 60.109 60.000 0.00 0.00 0.00 4.00
357 372 0.542232 ACCTGCTAACCGTGAGACCT 60.542 55.000 0.00 0.00 0.00 3.85
358 373 0.389948 CACCTGCTAACCGTGAGACC 60.390 60.000 0.00 0.00 0.00 3.85
359 374 0.601558 TCACCTGCTAACCGTGAGAC 59.398 55.000 0.00 0.00 32.85 3.36
360 375 3.045518 TCACCTGCTAACCGTGAGA 57.954 52.632 0.00 0.00 32.85 3.27
361 376 3.425578 CTCACCTGCTAACCGTGAG 57.574 57.895 2.35 2.35 45.33 3.51
362 377 0.601558 GTCTCACCTGCTAACCGTGA 59.398 55.000 0.00 0.00 35.34 4.35
363 378 0.389948 GGTCTCACCTGCTAACCGTG 60.390 60.000 0.00 0.00 34.73 4.94
364 379 1.542187 GGGTCTCACCTGCTAACCGT 61.542 60.000 0.00 0.00 38.64 4.83
365 380 1.218316 GGGTCTCACCTGCTAACCG 59.782 63.158 0.00 0.00 38.64 4.44
366 381 1.218316 CGGGTCTCACCTGCTAACC 59.782 63.158 0.00 0.00 37.90 2.85
367 382 4.913126 CGGGTCTCACCTGCTAAC 57.087 61.111 0.00 0.00 37.90 2.34
373 388 3.625632 ATCAGGGCGGGTCTCACCT 62.626 63.158 0.00 0.00 38.64 4.00
374 389 3.083997 ATCAGGGCGGGTCTCACC 61.084 66.667 0.00 0.00 37.60 4.02
375 390 2.187946 CATCAGGGCGGGTCTCAC 59.812 66.667 0.00 0.00 0.00 3.51
376 391 2.896677 ATCCATCAGGGCGGGTCTCA 62.897 60.000 0.00 0.00 36.21 3.27
377 392 2.143419 ATCCATCAGGGCGGGTCTC 61.143 63.158 0.00 0.00 36.21 3.36
378 393 2.040464 ATCCATCAGGGCGGGTCT 60.040 61.111 0.00 0.00 36.21 3.85
379 394 2.111878 CATCCATCAGGGCGGGTC 59.888 66.667 0.00 0.00 36.21 4.46
380 395 2.366837 TCATCCATCAGGGCGGGT 60.367 61.111 0.00 0.00 36.21 5.28
381 396 2.111878 GTCATCCATCAGGGCGGG 59.888 66.667 0.00 0.00 36.21 6.13
382 397 1.524621 GTGTCATCCATCAGGGCGG 60.525 63.158 0.00 0.00 36.21 6.13
383 398 1.884464 CGTGTCATCCATCAGGGCG 60.884 63.158 0.00 0.00 36.21 6.13
384 399 1.091771 CACGTGTCATCCATCAGGGC 61.092 60.000 7.58 0.00 36.21 5.19
385 400 0.462581 CCACGTGTCATCCATCAGGG 60.463 60.000 15.65 0.00 34.83 4.45
386 401 1.091771 GCCACGTGTCATCCATCAGG 61.092 60.000 15.65 0.00 0.00 3.86
387 402 0.391528 TGCCACGTGTCATCCATCAG 60.392 55.000 15.65 0.00 0.00 2.90
388 403 0.252761 ATGCCACGTGTCATCCATCA 59.747 50.000 15.65 0.00 0.00 3.07
389 404 1.331756 GAATGCCACGTGTCATCCATC 59.668 52.381 13.12 3.25 0.00 3.51
390 405 1.339920 TGAATGCCACGTGTCATCCAT 60.340 47.619 13.12 0.00 0.00 3.41
391 406 0.036022 TGAATGCCACGTGTCATCCA 59.964 50.000 13.12 2.86 0.00 3.41
392 407 2.853159 TGAATGCCACGTGTCATCC 58.147 52.632 13.12 0.00 0.00 3.51
720 735 0.107508 ACGCAAGACCCATCCTGATG 60.108 55.000 0.00 0.00 43.62 3.07
721 736 0.107508 CACGCAAGACCCATCCTGAT 60.108 55.000 0.00 0.00 43.62 2.90
722 737 1.191489 TCACGCAAGACCCATCCTGA 61.191 55.000 0.00 0.00 43.62 3.86
723 738 0.742281 CTCACGCAAGACCCATCCTG 60.742 60.000 0.00 0.00 43.62 3.86
724 739 0.904865 TCTCACGCAAGACCCATCCT 60.905 55.000 0.00 0.00 43.62 3.24
725 740 0.741221 GTCTCACGCAAGACCCATCC 60.741 60.000 6.53 0.00 39.85 3.51
726 741 2.755929 GTCTCACGCAAGACCCATC 58.244 57.895 6.53 0.00 39.85 3.51
731 746 2.029844 GCCAGGTCTCACGCAAGAC 61.030 63.158 8.83 8.83 44.08 3.01
732 747 2.038814 TTGCCAGGTCTCACGCAAGA 62.039 55.000 0.00 0.00 36.36 3.02
733 748 1.597854 TTGCCAGGTCTCACGCAAG 60.598 57.895 0.00 0.00 36.36 4.01
734 749 1.891919 GTTGCCAGGTCTCACGCAA 60.892 57.895 0.00 0.00 38.82 4.85
735 750 2.280797 GTTGCCAGGTCTCACGCA 60.281 61.111 0.00 0.00 0.00 5.24
736 751 3.050275 GGTTGCCAGGTCTCACGC 61.050 66.667 0.00 0.00 0.00 5.34
737 752 1.669115 CAGGTTGCCAGGTCTCACG 60.669 63.158 0.00 0.00 0.00 4.35
738 753 0.603975 GTCAGGTTGCCAGGTCTCAC 60.604 60.000 0.00 0.00 0.00 3.51
739 754 1.754745 GTCAGGTTGCCAGGTCTCA 59.245 57.895 0.00 0.00 0.00 3.27
740 755 1.374758 CGTCAGGTTGCCAGGTCTC 60.375 63.158 0.00 0.00 0.00 3.36
741 756 2.743718 CGTCAGGTTGCCAGGTCT 59.256 61.111 0.00 0.00 0.00 3.85
742 757 3.050275 GCGTCAGGTTGCCAGGTC 61.050 66.667 0.00 0.00 0.00 3.85
743 758 4.988598 CGCGTCAGGTTGCCAGGT 62.989 66.667 0.00 0.00 0.00 4.00
745 760 4.988598 ACCGCGTCAGGTTGCCAG 62.989 66.667 4.92 0.00 43.00 4.85
758 773 1.004927 GAGACAAATATGACGCACCGC 60.005 52.381 0.00 0.00 0.00 5.68
759 774 2.267426 TGAGACAAATATGACGCACCG 58.733 47.619 0.00 0.00 0.00 4.94
760 775 4.678509 TTTGAGACAAATATGACGCACC 57.321 40.909 0.00 0.00 31.83 5.01
761 776 6.370593 TCTTTTTGAGACAAATATGACGCAC 58.629 36.000 0.00 0.00 31.83 5.34
805 822 1.265635 GCGCAGTGTGAAAATGTACCA 59.734 47.619 8.15 0.00 0.00 3.25
819 836 2.740055 CAGGAAGCTTCGCGCAGT 60.740 61.111 19.91 0.00 42.61 4.40
839 867 2.878089 AAAAATGTGGGTGGCGGCC 61.878 57.895 13.32 13.32 0.00 6.13
860 888 2.450050 TACGAAAACGTTGACGCGCG 62.450 55.000 30.96 30.96 44.43 6.86
945 1117 2.035442 GTGGTGAGCCGGAGAAAGC 61.035 63.158 5.05 0.00 37.67 3.51
947 1119 2.144078 TGGTGGTGAGCCGGAGAAA 61.144 57.895 5.05 0.00 37.67 2.52
953 1125 2.210116 GTAATATGTGGTGGTGAGCCG 58.790 52.381 0.00 0.00 37.67 5.52
1032 1204 1.080501 CAGCTTCTCCGCGTTGAGA 60.081 57.895 10.52 10.52 39.58 3.27
1128 1300 4.728772 CCTTGCCATGGTGGAGAAATATA 58.271 43.478 14.67 0.00 40.96 0.86
1269 1441 3.221771 CAGGATGGACACAAACAGGAAA 58.778 45.455 0.00 0.00 0.00 3.13
1413 1588 2.541346 CGCAGCCAACTCATATACTGTG 59.459 50.000 0.00 0.00 0.00 3.66
1434 1629 0.240411 AACGTAGACCTCGTGCTCAC 59.760 55.000 0.00 0.00 41.38 3.51
1435 1630 0.956633 AAACGTAGACCTCGTGCTCA 59.043 50.000 0.00 0.00 41.38 4.26
1436 1631 1.068748 TGAAACGTAGACCTCGTGCTC 60.069 52.381 0.00 0.00 41.38 4.26
1437 1632 0.956633 TGAAACGTAGACCTCGTGCT 59.043 50.000 0.00 0.00 41.38 4.40
1438 1633 1.992170 ATGAAACGTAGACCTCGTGC 58.008 50.000 0.00 0.00 41.38 5.34
1439 1634 4.730657 ACTAATGAAACGTAGACCTCGTG 58.269 43.478 0.00 0.00 41.38 4.35
1440 1635 5.382618 AACTAATGAAACGTAGACCTCGT 57.617 39.130 0.00 0.00 43.45 4.18
1441 1636 5.287992 GGAAACTAATGAAACGTAGACCTCG 59.712 44.000 0.00 0.00 0.00 4.63
1442 1637 6.090493 GTGGAAACTAATGAAACGTAGACCTC 59.910 42.308 0.00 0.00 0.00 3.85
1443 1638 5.930569 GTGGAAACTAATGAAACGTAGACCT 59.069 40.000 0.00 0.00 0.00 3.85
1444 1639 5.930569 AGTGGAAACTAATGAAACGTAGACC 59.069 40.000 0.00 0.00 0.00 3.85
1445 1640 7.042254 ACAAGTGGAAACTAATGAAACGTAGAC 60.042 37.037 0.00 0.00 0.00 2.59
1446 1641 6.987992 ACAAGTGGAAACTAATGAAACGTAGA 59.012 34.615 0.00 0.00 0.00 2.59
1447 1642 7.186021 ACAAGTGGAAACTAATGAAACGTAG 57.814 36.000 0.00 0.00 0.00 3.51
1482 1677 7.710766 ATACTAGCAGCTTAATAACCGAAAC 57.289 36.000 0.00 0.00 0.00 2.78
1522 1717 2.941333 CACAGCACAAGCCAGACG 59.059 61.111 0.00 0.00 43.56 4.18
1609 1804 0.939577 ACAACAGTACTCGTGCGCTG 60.940 55.000 9.73 0.40 35.31 5.18
1670 1865 5.321959 TGATGTTTGTAATACGGACCGTA 57.678 39.130 27.90 27.90 46.28 4.02
1688 1883 7.601886 ACTCTGTCTTGACAGAAGTTATTGATG 59.398 37.037 26.86 16.63 44.98 3.07
1703 1898 3.388024 AGTGTGGCTTAACTCTGTCTTGA 59.612 43.478 0.00 0.00 0.00 3.02
1708 1903 2.029290 CCGTAGTGTGGCTTAACTCTGT 60.029 50.000 0.00 0.00 0.00 3.41
1771 1966 9.605275 TCATATTTATCATAGCCAGAATACTGC 57.395 33.333 0.00 0.00 42.25 4.40
1803 1998 6.999272 AGCATCTTCGTACTCTCCTAGAATTA 59.001 38.462 0.00 0.00 0.00 1.40
1805 2000 5.381757 AGCATCTTCGTACTCTCCTAGAAT 58.618 41.667 0.00 0.00 0.00 2.40
1806 2001 4.783055 AGCATCTTCGTACTCTCCTAGAA 58.217 43.478 0.00 0.00 0.00 2.10
1807 2002 4.425180 AGCATCTTCGTACTCTCCTAGA 57.575 45.455 0.00 0.00 0.00 2.43
1808 2003 4.576873 TCAAGCATCTTCGTACTCTCCTAG 59.423 45.833 0.00 0.00 0.00 3.02
1810 2005 3.357203 TCAAGCATCTTCGTACTCTCCT 58.643 45.455 0.00 0.00 0.00 3.69
1943 2141 3.017048 TGGAGGGATTACCAATTGCAG 57.983 47.619 0.00 0.00 43.89 4.41
1952 2151 4.067896 CAGTGCATGTATGGAGGGATTAC 58.932 47.826 0.00 0.00 0.00 1.89
2011 2210 7.013823 AGATCATCTTTACATCATGTAGGGG 57.986 40.000 0.00 0.00 33.92 4.79
2041 2240 3.172339 GGATGGTCCTCTGAGATAGCAT 58.828 50.000 18.34 18.34 32.53 3.79
2051 2250 1.997874 GGTGCTGGGATGGTCCTCT 60.998 63.158 0.00 0.00 36.57 3.69
2089 2288 6.055588 GCTAAATAAACACTGATGGAGCCTA 58.944 40.000 0.00 0.00 0.00 3.93
2124 2324 1.143838 CTCCATGGACGATGCCGAA 59.856 57.895 11.44 0.00 39.50 4.30
2177 2377 7.601705 TGTGATCTCATATGACCATGTTCTA 57.398 36.000 0.00 0.00 0.00 2.10
2179 2379 6.709397 ACATGTGATCTCATATGACCATGTTC 59.291 38.462 19.74 8.20 44.87 3.18
2218 2418 5.723887 ACACTTAATCACTCTGAGGAGGAAT 59.276 40.000 9.85 0.01 43.46 3.01


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

AutoCloner maintained by Alex Coulton.