Multiple sequence alignment - TraesCS2D01G246200

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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 TraesCS2D01G246200 chr2D 100.000 1592 0 0 1 1592 286753296 286751705 0.000000e+00 2940
1 TraesCS2D01G246200 chr2D 100.000 584 0 0 1909 2492 286751388 286750805 0.000000e+00 1079
2 TraesCS2D01G246200 chr2D 89.455 569 60 0 956 1524 182498839 182498271 0.000000e+00 719
3 TraesCS2D01G246200 chr2A 95.315 1302 60 1 1 1301 329588067 329589368 0.000000e+00 2065
4 TraesCS2D01G246200 chr2A 71.854 302 72 11 138 433 629985186 629984892 9.560000e-10 75
5 TraesCS2D01G246200 chr1D 89.843 1526 130 4 1 1524 313881172 313882674 0.000000e+00 1936
6 TraesCS2D01G246200 chrUn 90.099 1313 108 6 1 1312 95934402 95933111 0.000000e+00 1685
7 TraesCS2D01G246200 chr7D 91.297 586 46 5 1909 2492 418664888 418665470 0.000000e+00 795
8 TraesCS2D01G246200 chr7D 90.986 588 48 4 1909 2492 417944852 417945438 0.000000e+00 787
9 TraesCS2D01G246200 chr7D 90.614 586 50 5 1909 2492 418082068 418082650 0.000000e+00 773
10 TraesCS2D01G246200 chr7D 89.761 586 57 3 1909 2492 129513781 129514365 0.000000e+00 747
11 TraesCS2D01G246200 chr6D 90.846 579 48 5 1917 2492 326311448 326310872 0.000000e+00 771
12 TraesCS2D01G246200 chr5D 90.085 585 53 5 1909 2492 291255090 291255670 0.000000e+00 754
13 TraesCS2D01G246200 chr5D 90.172 580 54 3 1915 2492 180481099 180480521 0.000000e+00 752
14 TraesCS2D01G246200 chr5B 90.034 582 52 6 1915 2492 240847483 240846904 0.000000e+00 749
15 TraesCS2D01G246200 chr1A 89.608 587 56 5 1909 2492 174044502 174045086 0.000000e+00 741
16 TraesCS2D01G246200 chr4B 86.973 261 20 5 1265 1524 646377018 646376771 5.250000e-72 281
17 TraesCS2D01G246200 chr4B 89.552 201 20 1 1325 1524 672133818 672133618 1.140000e-63 254


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 TraesCS2D01G246200 chr2D 286750805 286753296 2491 True 2009.5 2940 100.000 1 2492 2 chr2D.!!$R2 2491
1 TraesCS2D01G246200 chr2D 182498271 182498839 568 True 719.0 719 89.455 956 1524 1 chr2D.!!$R1 568
2 TraesCS2D01G246200 chr2A 329588067 329589368 1301 False 2065.0 2065 95.315 1 1301 1 chr2A.!!$F1 1300
3 TraesCS2D01G246200 chr1D 313881172 313882674 1502 False 1936.0 1936 89.843 1 1524 1 chr1D.!!$F1 1523
4 TraesCS2D01G246200 chrUn 95933111 95934402 1291 True 1685.0 1685 90.099 1 1312 1 chrUn.!!$R1 1311
5 TraesCS2D01G246200 chr7D 418664888 418665470 582 False 795.0 795 91.297 1909 2492 1 chr7D.!!$F4 583
6 TraesCS2D01G246200 chr7D 417944852 417945438 586 False 787.0 787 90.986 1909 2492 1 chr7D.!!$F2 583
7 TraesCS2D01G246200 chr7D 418082068 418082650 582 False 773.0 773 90.614 1909 2492 1 chr7D.!!$F3 583
8 TraesCS2D01G246200 chr7D 129513781 129514365 584 False 747.0 747 89.761 1909 2492 1 chr7D.!!$F1 583
9 TraesCS2D01G246200 chr6D 326310872 326311448 576 True 771.0 771 90.846 1917 2492 1 chr6D.!!$R1 575
10 TraesCS2D01G246200 chr5D 291255090 291255670 580 False 754.0 754 90.085 1909 2492 1 chr5D.!!$F1 583
11 TraesCS2D01G246200 chr5D 180480521 180481099 578 True 752.0 752 90.172 1915 2492 1 chr5D.!!$R1 577
12 TraesCS2D01G246200 chr5B 240846904 240847483 579 True 749.0 749 90.034 1915 2492 1 chr5B.!!$R1 577
13 TraesCS2D01G246200 chr1A 174044502 174045086 584 False 741.0 741 89.608 1909 2492 1 chr1A.!!$F1 583

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
853 855 1.383799 CTCTGGATTTGGTGGGCCA 59.616 57.895 0.0 0.0 44.38 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2064 2.482336 GCCAAAAATTTAACTTGGGCCG 59.518 45.455 17.73 0.0 40.05 6.13 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
55 57 6.433404 GGTCCTATCATCGAAGTACTATCCAA 59.567 42.308 0.00 0.00 0.00 3.53
138 140 8.396272 TCTTGAAAGGAATTAGTCTTTTGGAG 57.604 34.615 0.00 0.00 35.78 3.86
159 161 7.544650 TGGAGAAGGGAATAATATGGAGAGTA 58.455 38.462 0.00 0.00 0.00 2.59
169 171 8.940012 AATAATATGGAGAGTAGGGAATGGAT 57.060 34.615 0.00 0.00 0.00 3.41
316 318 4.441913 GGGATGTGCAATTATTGAACCAGG 60.442 45.833 13.03 0.00 38.50 4.45
323 325 3.884037 ATTATTGAACCAGGCCCTAGG 57.116 47.619 0.06 0.06 0.00 3.02
399 401 2.752075 TCCCTGCATGGCATTATGAA 57.248 45.000 2.62 0.00 38.13 2.57
530 532 6.112734 ACAAAGGTTTTCAATGGAAGAAACC 58.887 36.000 8.00 8.00 41.29 3.27
531 533 5.948742 AAGGTTTTCAATGGAAGAAACCA 57.051 34.783 15.79 0.00 42.51 3.67
612 614 2.158971 TCTGCCTATGCGCATGAAACTA 60.159 45.455 32.48 10.74 41.78 2.24
695 697 8.717717 AGATGGAGGTCATGTCTTTATCAAATA 58.282 33.333 0.00 0.00 35.97 1.40
853 855 1.383799 CTCTGGATTTGGTGGGCCA 59.616 57.895 0.00 0.00 44.38 5.36
862 864 3.567902 TGGTGGGCCAAAAGGAATT 57.432 47.368 8.40 0.00 42.83 2.17
864 866 3.197927 TGGTGGGCCAAAAGGAATTAT 57.802 42.857 8.40 0.00 42.83 1.28
874 876 5.732633 CCAAAAGGAATTATGCCAATGTCA 58.267 37.500 0.00 0.00 0.00 3.58
902 904 9.218525 TGATAGAATAAGATCTTCAAAGGAGGT 57.781 33.333 12.24 0.00 0.00 3.85
1010 1012 3.934457 GGTGTTTCCCATGGTTAACTG 57.066 47.619 20.55 3.05 0.00 3.16
1017 1019 6.039941 TGTTTCCCATGGTTAACTGTGTTAAG 59.960 38.462 20.55 0.00 0.00 1.85
1038 1040 5.818678 AGATTAATACTGATGGGGCGTTA 57.181 39.130 0.00 0.00 0.00 3.18
1144 1146 1.981495 AGGGAGTAAGCTCTGCACTTT 59.019 47.619 0.00 0.00 41.38 2.66
1368 1371 6.025749 TGTATGAGGTCTTGTAACTCTGTG 57.974 41.667 0.00 0.00 32.58 3.66
1370 1373 3.305720 TGAGGTCTTGTAACTCTGTGGT 58.694 45.455 0.00 0.00 32.58 4.16
1371 1374 3.069586 TGAGGTCTTGTAACTCTGTGGTG 59.930 47.826 0.00 0.00 32.58 4.17
1386 1389 2.502510 GTGCATGAACTTGCCGCG 60.503 61.111 0.00 0.00 42.06 6.46
1414 1417 1.304713 CTGCAAGGGGATGGCAACT 60.305 57.895 0.00 0.00 37.06 3.16
1415 1418 1.601419 CTGCAAGGGGATGGCAACTG 61.601 60.000 0.00 0.00 37.06 3.16
1443 1446 0.681243 GGGTTGGCCATCTTCCTCAC 60.681 60.000 6.09 0.00 36.17 3.51
1466 1469 3.535280 TGTACTGAACTTGTGTGCTGA 57.465 42.857 0.00 0.00 0.00 4.26
1473 1476 2.812358 ACTTGTGTGCTGACGATGTA 57.188 45.000 0.00 0.00 0.00 2.29
1484 1487 1.409064 TGACGATGTATCCAGTGCCTC 59.591 52.381 0.00 0.00 0.00 4.70
1485 1488 0.385751 ACGATGTATCCAGTGCCTCG 59.614 55.000 0.00 0.00 36.82 4.63
1524 1527 6.311200 CCTTCAACAGTGTTCCTTTCAAAAAG 59.689 38.462 5.27 0.00 0.00 2.27
1525 1528 5.719173 TCAACAGTGTTCCTTTCAAAAAGG 58.281 37.500 5.27 11.46 38.78 3.11
1526 1529 4.736126 ACAGTGTTCCTTTCAAAAAGGG 57.264 40.909 16.36 4.24 37.99 3.95
1527 1530 4.349365 ACAGTGTTCCTTTCAAAAAGGGA 58.651 39.130 16.36 6.96 38.77 4.20
1528 1531 4.962362 ACAGTGTTCCTTTCAAAAAGGGAT 59.038 37.500 16.36 0.00 40.09 3.85
1529 1532 5.163416 ACAGTGTTCCTTTCAAAAAGGGATG 60.163 40.000 16.36 7.67 40.09 3.51
1530 1533 4.344968 AGTGTTCCTTTCAAAAAGGGATGG 59.655 41.667 16.36 0.00 40.09 3.51
1531 1534 3.645687 TGTTCCTTTCAAAAAGGGATGGG 59.354 43.478 16.36 0.00 40.09 4.00
1532 1535 2.901291 TCCTTTCAAAAAGGGATGGGG 58.099 47.619 16.36 0.00 35.83 4.96
1533 1536 1.908619 CCTTTCAAAAAGGGATGGGGG 59.091 52.381 10.09 0.00 33.49 5.40
1534 1537 2.619931 CTTTCAAAAAGGGATGGGGGT 58.380 47.619 0.00 0.00 0.00 4.95
1535 1538 3.503227 CCTTTCAAAAAGGGATGGGGGTA 60.503 47.826 10.09 0.00 33.49 3.69
1536 1539 3.466395 TTCAAAAAGGGATGGGGGTAG 57.534 47.619 0.00 0.00 0.00 3.18
1537 1540 1.006639 TCAAAAAGGGATGGGGGTAGC 59.993 52.381 0.00 0.00 0.00 3.58
1538 1541 0.033503 AAAAAGGGATGGGGGTAGCG 60.034 55.000 0.00 0.00 0.00 4.26
1539 1542 0.917333 AAAAGGGATGGGGGTAGCGA 60.917 55.000 0.00 0.00 0.00 4.93
1540 1543 0.917333 AAAGGGATGGGGGTAGCGAA 60.917 55.000 0.00 0.00 0.00 4.70
1541 1544 1.345715 AAGGGATGGGGGTAGCGAAG 61.346 60.000 0.00 0.00 0.00 3.79
1542 1545 2.819284 GGGATGGGGGTAGCGAAGG 61.819 68.421 0.00 0.00 0.00 3.46
1543 1546 1.764854 GGATGGGGGTAGCGAAGGA 60.765 63.158 0.00 0.00 0.00 3.36
1544 1547 1.749033 GATGGGGGTAGCGAAGGAG 59.251 63.158 0.00 0.00 0.00 3.69
1545 1548 0.759436 GATGGGGGTAGCGAAGGAGA 60.759 60.000 0.00 0.00 0.00 3.71
1546 1549 0.326238 ATGGGGGTAGCGAAGGAGAA 60.326 55.000 0.00 0.00 0.00 2.87
1547 1550 0.545787 TGGGGGTAGCGAAGGAGAAA 60.546 55.000 0.00 0.00 0.00 2.52
1548 1551 0.107800 GGGGGTAGCGAAGGAGAAAC 60.108 60.000 0.00 0.00 0.00 2.78
1549 1552 0.459759 GGGGTAGCGAAGGAGAAACG 60.460 60.000 0.00 0.00 0.00 3.60
1550 1553 0.459759 GGGTAGCGAAGGAGAAACGG 60.460 60.000 0.00 0.00 0.00 4.44
1551 1554 0.245813 GGTAGCGAAGGAGAAACGGT 59.754 55.000 0.00 0.00 40.60 4.83
1552 1555 1.347320 GTAGCGAAGGAGAAACGGTG 58.653 55.000 0.00 0.00 38.59 4.94
1553 1556 0.963962 TAGCGAAGGAGAAACGGTGT 59.036 50.000 0.00 0.00 38.59 4.16
1554 1557 0.600255 AGCGAAGGAGAAACGGTGTG 60.600 55.000 0.00 0.00 36.45 3.82
1555 1558 0.878961 GCGAAGGAGAAACGGTGTGT 60.879 55.000 0.00 0.00 0.00 3.72
1556 1559 1.603678 GCGAAGGAGAAACGGTGTGTA 60.604 52.381 0.00 0.00 0.00 2.90
1557 1560 2.325761 CGAAGGAGAAACGGTGTGTAG 58.674 52.381 0.00 0.00 0.00 2.74
1558 1561 2.030540 CGAAGGAGAAACGGTGTGTAGA 60.031 50.000 0.00 0.00 0.00 2.59
1559 1562 3.367087 CGAAGGAGAAACGGTGTGTAGAT 60.367 47.826 0.00 0.00 0.00 1.98
1560 1563 3.594603 AGGAGAAACGGTGTGTAGATG 57.405 47.619 0.00 0.00 0.00 2.90
1561 1564 2.233922 AGGAGAAACGGTGTGTAGATGG 59.766 50.000 0.00 0.00 0.00 3.51
1562 1565 2.028385 GGAGAAACGGTGTGTAGATGGT 60.028 50.000 0.00 0.00 0.00 3.55
1563 1566 2.993899 GAGAAACGGTGTGTAGATGGTG 59.006 50.000 0.00 0.00 0.00 4.17
1564 1567 2.631062 AGAAACGGTGTGTAGATGGTGA 59.369 45.455 0.00 0.00 0.00 4.02
1565 1568 2.743636 AACGGTGTGTAGATGGTGAG 57.256 50.000 0.00 0.00 0.00 3.51
1566 1569 1.919240 ACGGTGTGTAGATGGTGAGA 58.081 50.000 0.00 0.00 0.00 3.27
1567 1570 1.819288 ACGGTGTGTAGATGGTGAGAG 59.181 52.381 0.00 0.00 0.00 3.20
1568 1571 2.092323 CGGTGTGTAGATGGTGAGAGA 58.908 52.381 0.00 0.00 0.00 3.10
1569 1572 2.098280 CGGTGTGTAGATGGTGAGAGAG 59.902 54.545 0.00 0.00 0.00 3.20
1570 1573 3.357203 GGTGTGTAGATGGTGAGAGAGA 58.643 50.000 0.00 0.00 0.00 3.10
1571 1574 3.764434 GGTGTGTAGATGGTGAGAGAGAA 59.236 47.826 0.00 0.00 0.00 2.87
1572 1575 4.381079 GGTGTGTAGATGGTGAGAGAGAAC 60.381 50.000 0.00 0.00 0.00 3.01
1573 1576 4.218635 GTGTGTAGATGGTGAGAGAGAACA 59.781 45.833 0.00 0.00 0.00 3.18
1574 1577 5.019470 TGTGTAGATGGTGAGAGAGAACAT 58.981 41.667 0.00 0.00 0.00 2.71
1575 1578 5.126222 TGTGTAGATGGTGAGAGAGAACATC 59.874 44.000 0.00 0.00 38.50 3.06
1576 1579 5.126222 GTGTAGATGGTGAGAGAGAACATCA 59.874 44.000 0.00 0.00 40.17 3.07
1577 1580 5.359292 TGTAGATGGTGAGAGAGAACATCAG 59.641 44.000 0.00 0.00 40.17 2.90
1578 1581 4.608269 AGATGGTGAGAGAGAACATCAGA 58.392 43.478 0.00 0.00 40.17 3.27
1579 1582 4.646040 AGATGGTGAGAGAGAACATCAGAG 59.354 45.833 0.00 0.00 40.17 3.35
1580 1583 3.095332 TGGTGAGAGAGAACATCAGAGG 58.905 50.000 0.00 0.00 0.00 3.69
1581 1584 3.245407 TGGTGAGAGAGAACATCAGAGGA 60.245 47.826 0.00 0.00 0.00 3.71
1582 1585 3.766591 GGTGAGAGAGAACATCAGAGGAA 59.233 47.826 0.00 0.00 0.00 3.36
1583 1586 4.221703 GGTGAGAGAGAACATCAGAGGAAA 59.778 45.833 0.00 0.00 0.00 3.13
1584 1587 5.167845 GTGAGAGAGAACATCAGAGGAAAC 58.832 45.833 0.00 0.00 0.00 2.78
1585 1588 4.221703 TGAGAGAGAACATCAGAGGAAACC 59.778 45.833 0.00 0.00 0.00 3.27
1586 1589 4.163427 AGAGAGAACATCAGAGGAAACCA 58.837 43.478 0.00 0.00 0.00 3.67
1587 1590 4.594920 AGAGAGAACATCAGAGGAAACCAA 59.405 41.667 0.00 0.00 0.00 3.67
1588 1591 4.904241 AGAGAACATCAGAGGAAACCAAG 58.096 43.478 0.00 0.00 0.00 3.61
1589 1592 4.349342 AGAGAACATCAGAGGAAACCAAGT 59.651 41.667 0.00 0.00 0.00 3.16
1590 1593 5.053978 AGAACATCAGAGGAAACCAAGTT 57.946 39.130 0.00 0.00 0.00 2.66
1591 1594 6.043243 AGAGAACATCAGAGGAAACCAAGTTA 59.957 38.462 0.00 0.00 0.00 2.24
1950 1954 2.959516 TCTGATCACAACTAACCTGCG 58.040 47.619 0.00 0.00 0.00 5.18
2018 2024 0.827507 AACATTGCTCAAACGGGGCT 60.828 50.000 0.00 0.00 0.00 5.19
2034 2040 2.548493 GGGGCTTTGCGATATACCGTTA 60.548 50.000 0.00 0.00 0.00 3.18
2052 2058 4.360563 CGTTAGAAAGCTATGGACACGAT 58.639 43.478 0.00 0.00 31.04 3.73
2058 2064 5.986135 AGAAAGCTATGGACACGATTATCAC 59.014 40.000 0.00 0.00 0.00 3.06
2060 2066 2.987149 GCTATGGACACGATTATCACGG 59.013 50.000 0.00 0.00 34.93 4.94
2082 2088 4.261405 GGCCCAAGTTAAATTTTTGGCAAC 60.261 41.667 17.36 4.14 39.98 4.17
2093 2099 3.273048 TGGCAACATGTAAGCGGC 58.727 55.556 14.70 9.69 46.17 6.53
2176 2184 5.473796 TCGCATTTCTAAACCGTTTATCC 57.526 39.130 4.19 0.00 0.00 2.59
2198 2206 4.380867 CCGAATGAGGCAAATAATATGGCC 60.381 45.833 0.00 0.00 46.77 5.36
2241 2250 3.313526 CGCTCCTTCCATATGTTGAAAGG 59.686 47.826 13.34 13.34 0.00 3.11
2327 2336 5.462068 CAGCCGAGTTCATATTTTCGATGTA 59.538 40.000 0.00 0.00 35.19 2.29
2360 2369 4.278170 CGGCTAATCCAATTGAGGCAAATA 59.722 41.667 7.12 0.00 34.30 1.40
2409 2418 6.927933 ATGCGCTACTTTTTCATGTTAAAC 57.072 33.333 9.73 0.00 0.00 2.01
2480 2491 5.432885 AGTTCCACCGAGTTTGTATTTTG 57.567 39.130 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.419574 GGCGCAAAGGGTACTCAGATTA 60.420 50.000 10.83 0.00 0.00 1.75
12 13 1.003839 CTGGCGCAAAGGGTACTCA 60.004 57.895 10.83 0.00 0.00 3.41
55 57 2.513753 TGCGTCCAGAATTTGACCATT 58.486 42.857 0.00 0.00 0.00 3.16
138 140 6.960542 TCCCTACTCTCCATATTATTCCCTTC 59.039 42.308 0.00 0.00 0.00 3.46
169 171 9.566331 AGGGTCATTCCAGATATTGATATTCTA 57.434 33.333 0.00 0.00 38.11 2.10
316 318 1.141858 CACATCTTCTTCCCCTAGGGC 59.858 57.143 23.84 0.00 43.94 5.19
323 325 0.813821 GGCTTGCACATCTTCTTCCC 59.186 55.000 0.00 0.00 0.00 3.97
370 372 1.579698 CATGCAGGGAAGTCATCGAG 58.420 55.000 0.00 0.00 0.00 4.04
399 401 3.199946 TGACTGAGAACACACCCTTCTTT 59.800 43.478 0.00 0.00 0.00 2.52
530 532 3.920231 TTGGGAGAGAGATTGACCATG 57.080 47.619 0.00 0.00 0.00 3.66
531 533 6.581388 TTATTTGGGAGAGAGATTGACCAT 57.419 37.500 0.00 0.00 0.00 3.55
612 614 2.311841 CACCTCCATACCCCTTTTCCTT 59.688 50.000 0.00 0.00 0.00 3.36
695 697 6.887545 TCTCCGGATTGGTTTAACACATTTAT 59.112 34.615 3.57 0.00 39.52 1.40
853 855 6.211184 TCACTGACATTGGCATAATTCCTTTT 59.789 34.615 0.00 0.00 0.00 2.27
855 857 5.263599 TCACTGACATTGGCATAATTCCTT 58.736 37.500 0.00 0.00 0.00 3.36
862 864 8.650490 TCTTATTCTATCACTGACATTGGCATA 58.350 33.333 0.00 0.00 0.00 3.14
864 866 6.888105 TCTTATTCTATCACTGACATTGGCA 58.112 36.000 0.00 0.00 0.00 4.92
895 897 5.188751 CAGAAATAGAAGAGACCACCTCCTT 59.811 44.000 0.00 0.00 42.97 3.36
902 904 4.890158 TGTGCAGAAATAGAAGAGACCA 57.110 40.909 0.00 0.00 0.00 4.02
993 995 4.929819 AACACAGTTAACCATGGGAAAC 57.070 40.909 18.09 18.56 0.00 2.78
1010 1012 6.073222 CGCCCCATCAGTATTAATCTTAACAC 60.073 42.308 0.00 0.00 0.00 3.32
1017 1019 5.938125 ACATAACGCCCCATCAGTATTAATC 59.062 40.000 0.00 0.00 0.00 1.75
1112 1114 1.204146 TACTCCCTGGAGATGGTTGC 58.796 55.000 19.85 0.00 44.53 4.17
1144 1146 1.533625 AGCGCCAAAGCTTCAACATA 58.466 45.000 2.29 0.00 46.80 2.29
1306 1308 6.262049 ACACTATCATAAGCAACACACAACAA 59.738 34.615 0.00 0.00 0.00 2.83
1340 1343 8.417106 CAGAGTTACAAGACCTCATACATACAT 58.583 37.037 0.00 0.00 0.00 2.29
1400 1403 0.188342 AACACAGTTGCCATCCCCTT 59.812 50.000 0.00 0.00 0.00 3.95
1414 1417 2.055042 GGCCAACCCACACAACACA 61.055 57.895 0.00 0.00 0.00 3.72
1415 1418 2.055042 TGGCCAACCCACACAACAC 61.055 57.895 0.61 0.00 39.18 3.32
1443 1446 4.332543 TCAGCACACAAGTTCAGTACAAAG 59.667 41.667 0.00 0.00 0.00 2.77
1473 1476 2.643551 CATTAAACCGAGGCACTGGAT 58.356 47.619 0.00 0.00 41.55 3.41
1484 1487 4.173256 GTTGAAGGCATTCCATTAAACCG 58.827 43.478 8.88 0.00 34.28 4.44
1485 1488 5.146010 TGTTGAAGGCATTCCATTAAACC 57.854 39.130 8.88 0.00 34.28 3.27
1524 1527 2.819284 CCTTCGCTACCCCCATCCC 61.819 68.421 0.00 0.00 0.00 3.85
1525 1528 1.759459 CTCCTTCGCTACCCCCATCC 61.759 65.000 0.00 0.00 0.00 3.51
1526 1529 0.759436 TCTCCTTCGCTACCCCCATC 60.759 60.000 0.00 0.00 0.00 3.51
1527 1530 0.326238 TTCTCCTTCGCTACCCCCAT 60.326 55.000 0.00 0.00 0.00 4.00
1528 1531 0.545787 TTTCTCCTTCGCTACCCCCA 60.546 55.000 0.00 0.00 0.00 4.96
1529 1532 0.107800 GTTTCTCCTTCGCTACCCCC 60.108 60.000 0.00 0.00 0.00 5.40
1530 1533 0.459759 CGTTTCTCCTTCGCTACCCC 60.460 60.000 0.00 0.00 0.00 4.95
1531 1534 0.459759 CCGTTTCTCCTTCGCTACCC 60.460 60.000 0.00 0.00 0.00 3.69
1532 1535 0.245813 ACCGTTTCTCCTTCGCTACC 59.754 55.000 0.00 0.00 0.00 3.18
1533 1536 1.336609 ACACCGTTTCTCCTTCGCTAC 60.337 52.381 0.00 0.00 0.00 3.58
1534 1537 0.963962 ACACCGTTTCTCCTTCGCTA 59.036 50.000 0.00 0.00 0.00 4.26
1535 1538 0.600255 CACACCGTTTCTCCTTCGCT 60.600 55.000 0.00 0.00 0.00 4.93
1536 1539 0.878961 ACACACCGTTTCTCCTTCGC 60.879 55.000 0.00 0.00 0.00 4.70
1537 1540 2.030540 TCTACACACCGTTTCTCCTTCG 60.031 50.000 0.00 0.00 0.00 3.79
1538 1541 3.655276 TCTACACACCGTTTCTCCTTC 57.345 47.619 0.00 0.00 0.00 3.46
1539 1542 3.306780 CCATCTACACACCGTTTCTCCTT 60.307 47.826 0.00 0.00 0.00 3.36
1540 1543 2.233922 CCATCTACACACCGTTTCTCCT 59.766 50.000 0.00 0.00 0.00 3.69
1541 1544 2.028385 ACCATCTACACACCGTTTCTCC 60.028 50.000 0.00 0.00 0.00 3.71
1542 1545 2.993899 CACCATCTACACACCGTTTCTC 59.006 50.000 0.00 0.00 0.00 2.87
1543 1546 2.631062 TCACCATCTACACACCGTTTCT 59.369 45.455 0.00 0.00 0.00 2.52
1544 1547 2.993899 CTCACCATCTACACACCGTTTC 59.006 50.000 0.00 0.00 0.00 2.78
1545 1548 2.631062 TCTCACCATCTACACACCGTTT 59.369 45.455 0.00 0.00 0.00 3.60
1546 1549 2.231478 CTCTCACCATCTACACACCGTT 59.769 50.000 0.00 0.00 0.00 4.44
1547 1550 1.819288 CTCTCACCATCTACACACCGT 59.181 52.381 0.00 0.00 0.00 4.83
1548 1551 2.092323 TCTCTCACCATCTACACACCG 58.908 52.381 0.00 0.00 0.00 4.94
1549 1552 3.357203 TCTCTCTCACCATCTACACACC 58.643 50.000 0.00 0.00 0.00 4.16
1550 1553 4.218635 TGTTCTCTCTCACCATCTACACAC 59.781 45.833 0.00 0.00 0.00 3.82
1551 1554 4.407365 TGTTCTCTCTCACCATCTACACA 58.593 43.478 0.00 0.00 0.00 3.72
1552 1555 5.126222 TGATGTTCTCTCTCACCATCTACAC 59.874 44.000 0.00 0.00 34.44 2.90
1553 1556 5.264395 TGATGTTCTCTCTCACCATCTACA 58.736 41.667 0.00 0.00 34.44 2.74
1554 1557 5.592282 TCTGATGTTCTCTCTCACCATCTAC 59.408 44.000 0.00 0.00 34.44 2.59
1555 1558 5.760131 TCTGATGTTCTCTCTCACCATCTA 58.240 41.667 0.00 0.00 34.44 1.98
1556 1559 4.608269 TCTGATGTTCTCTCTCACCATCT 58.392 43.478 0.00 0.00 34.44 2.90
1557 1560 4.202141 CCTCTGATGTTCTCTCTCACCATC 60.202 50.000 0.00 0.00 34.03 3.51
1558 1561 3.705579 CCTCTGATGTTCTCTCTCACCAT 59.294 47.826 0.00 0.00 0.00 3.55
1559 1562 3.095332 CCTCTGATGTTCTCTCTCACCA 58.905 50.000 0.00 0.00 0.00 4.17
1560 1563 3.360867 TCCTCTGATGTTCTCTCTCACC 58.639 50.000 0.00 0.00 0.00 4.02
1561 1564 5.167845 GTTTCCTCTGATGTTCTCTCTCAC 58.832 45.833 0.00 0.00 0.00 3.51
1562 1565 4.221703 GGTTTCCTCTGATGTTCTCTCTCA 59.778 45.833 0.00 0.00 0.00 3.27
1563 1566 4.221703 TGGTTTCCTCTGATGTTCTCTCTC 59.778 45.833 0.00 0.00 0.00 3.20
1564 1567 4.163427 TGGTTTCCTCTGATGTTCTCTCT 58.837 43.478 0.00 0.00 0.00 3.10
1565 1568 4.543590 TGGTTTCCTCTGATGTTCTCTC 57.456 45.455 0.00 0.00 0.00 3.20
1566 1569 4.349342 ACTTGGTTTCCTCTGATGTTCTCT 59.651 41.667 0.00 0.00 0.00 3.10
1567 1570 4.646572 ACTTGGTTTCCTCTGATGTTCTC 58.353 43.478 0.00 0.00 0.00 2.87
1568 1571 4.713792 ACTTGGTTTCCTCTGATGTTCT 57.286 40.909 0.00 0.00 0.00 3.01
1950 1954 4.870991 GGAAGTTCAACATACTACTGCCTC 59.129 45.833 5.01 0.00 34.10 4.70
2018 2024 5.353938 AGCTTTCTAACGGTATATCGCAAA 58.646 37.500 5.03 0.00 0.00 3.68
2034 2040 5.986135 GTGATAATCGTGTCCATAGCTTTCT 59.014 40.000 0.00 0.00 0.00 2.52
2052 2058 5.986501 AAATTTAACTTGGGCCGTGATAA 57.013 34.783 0.00 0.00 0.00 1.75
2058 2064 2.482336 GCCAAAAATTTAACTTGGGCCG 59.518 45.455 17.73 0.00 40.05 6.13
2060 2066 4.336713 TGTTGCCAAAAATTTAACTTGGGC 59.663 37.500 17.73 9.84 40.05 5.36
2093 2099 5.578776 ACGGTTTTCAAAACTGCTCTTAAG 58.421 37.500 19.93 0.00 0.00 1.85
2176 2184 4.737054 GGCCATATTATTTGCCTCATTCG 58.263 43.478 0.00 0.00 40.77 3.34
2198 2206 3.126073 GGTTTTGAAGCAGCTTTCCAAG 58.874 45.455 9.62 0.00 0.00 3.61
2254 2263 9.859427 TTTTCGAAATTACTCTTTATCCGTAGA 57.141 29.630 12.12 0.00 0.00 2.59
2327 2336 8.062065 TCAATTGGATTAGCCGTTTAGAAATT 57.938 30.769 5.42 0.00 40.66 1.82
2360 2369 4.887071 TCATAAGCTTTCCAACGCCATATT 59.113 37.500 3.20 0.00 0.00 1.28
2451 2462 4.202326 ACAAACTCGGTGGAACTTGTATCT 60.202 41.667 0.00 0.00 36.74 1.98


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

AutoCloner maintained by Alex Coulton.